Reference genes for quantitative Arabidopsis single molecule RNA fluorescence in situ hybridization
Data files
Oct 04, 2022 version files 6.60 GB
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Col_7by8_T30Q570_DAPI_01.tif
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Col_D5_AP2M_01.tif
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Col_D5_AP2M_02.tif
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Col_D5_AP2M_03.tif
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Col_D5_AP2M_04.tif
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Col_D5_AP2M_05.tif
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Col_D5_AP2M_08.tif
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Col_D5_AP2M_09.tif
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Col_D5_AP2M_10.tif
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Col_D5_AP2M_11.tif
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Col_D5_AP2M_12.tif
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Col_D5_AP2M_13.tif
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Col_D5_AP2M_14.tif
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Col_D5_AP2M_15.tif
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Col_D5_AP2M_16.tif
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Col_D5_AP2M_17.tif
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Col_D5_AP2M_18.tif
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Col_D5_AP2M_19.tif
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Col_D5_AP2M_20.tif
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Col_D5_AP2M_21.tif
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Col_D5_AP2M_23.tif
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Col_D5_AP2M_24.tif
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Col_D5_AP2M_25.tif
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Col_D5_AP2M_26.tif
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Col_D5_AP2M_27.tif
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Col_D5_AP2M_29.tif
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Col_D5_AP2M_30.tif
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Col_D5_MON1_01.tif
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Col_D5_MON1_02.tif
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Col_D5_MON1_03.tif
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Col_D5_MON1_07.tif
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Col_D5_MON1_08.tif
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Col_D5_MON1_09.tif
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Col_D5_MON1_10.tif
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Col_D5_MON1_11.tif
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Col_D5_MON1_12.tif
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Col_D5_MON1_13.tif
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Col_D5_MON1_14.tif
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Col_D5_MON1_15.tif
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Col_D5_MON1_16.tif
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Col_D5_MON1_17.tif
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Col_D5_MON1_18.tif
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Col_D5_MON1_19.tif
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Col_D5_MON1_20.tif
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Col_D5_MON1_21.tif
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Col_D5_MON1_22.tif
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Col_D5_MON1_23.tif
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Col_D5_MON1_25.tif
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Col_D5_MON1_26.tif
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Col_D5_MON1_27.tif
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Col_D5_NRPB1_02.tif
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Col_D5_NRPB1_03.tif
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Col_D5_NRPB1_04.tif
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Col_D5_NRPB1_05.tif
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Col_D5_NRPB1_06.tif
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Col_D5_NRPB1_07.tif
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Col_D5_NRPB1_08.tif
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Col_D5_NRPB1_09.tif
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Col_D5_NRPB1_10.tif
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Col_D5_NRPB1_11.tif
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Col_D5_NRPB1_12.tif
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Col_D5_NRPB1_13.tif
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Col_D5_NRPB1_14.tif
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Col_D5_NRPB1_15.tif
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Col_D5_NRPB1_17.tif
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Col_D5_NRPB1_18.tif
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Col_D5_NRPB1_19.tif
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Col_D5_NRPB1_20.tif
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Col_D5_NRPB1_21.tif
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Col_D5_NRPB1_22.tif
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Col_D5_NRPB1_23.tif
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Col_D5_NRPB1_24.tif
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Col_D5_NRPB1_25.tif
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Col_D5_PP2A_01.tif
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Col_D5_PP2A_02.tif
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Col_D5_PP2A_03.tif
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Col_D5_PP2A_04.tif
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Col_D5_PP2A_05.tif
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Col_D5_PP2A_06.tif
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Col_D5_PP2A_07.tif
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Col_D5_PP2A_08.tif
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Col_D5_PP2A_09.tif
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Col_D5_PP2A_10.tif
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Col_D5_PP2A_11.tif
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Col_D5_PP2A_12.tif
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Col_D5_PP2A_13.tif
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Col_D5_PP2A_14.tif
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Col_D5_PP2A_15.tif
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Col_D5_PP2A_16.tif
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Col_D5_PP2A_17.tif
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Col_D5_PP2A_18.tif
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Col_D5_PP2A_19.tif
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Col_D5_PP2A_20.tif
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Col_D5_PP2A_21.tif
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Col_D5_PP2A_22.tif
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Col_D5_TIP41_01.tif
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Col_D5_TIP41_02.tif
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Col_D5_TIP41_03.tif
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Col_D5_TIP41_04.tif
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Col_D5_TIP41_05.tif
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Col_D5_TIP41_06.tif
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Col_D5_TIP41_07.tif
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Col_D5_TIP41_08.tif
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Col_D5_TIP41_09.tif
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Col_D5_TIP41_10.tif
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Col_D5_TIP41_11.tif
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Col_D5_TIP41_12.tif
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Col_D5_TIP41_13.tif
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Col_D5_TIP41_14.tif
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Col_D5_TIP41_15.tif
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Col_D5_TIP41_16.tif
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Col_D5_TIP41_17.tif
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Col_D5_TIP41_18.tif
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Col_D5_TIP41_19.tif
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Col_D5_TIP41_20.tif
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Col_D5_TIP41_21.tif
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Col_D5_TIP41_22.tif
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Col_D5_TIP41_23.tif
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Col_D5_TIP41_24.tif
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Col_D5_TIP41_25.tif
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Col_D5_TIP41_26.tif
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Col_D5_TIP41_27.tif
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Col_D5_TIP41_28.tif
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Col_D5_TIP41_29.tif
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Col_D5_TIP41_30.tif
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README_Duncan_et_al_2022.txt
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Abstract
Single-molecule RNA FISH probes conjugated with Quasar 670 dye were designed to detect MON1 (AT2G28390), TIP41 (AT4G34270), AP2M (AT4G35800), NRPB1 (AT4G35800) and PP2A (AT1G13320) mRNA. These probes were applied to Arabidopsis root meristem cells of 5-day-old Columbia (Col-0) seedlings. Nuclei were also stained with DAPI.
Protocol details can be found here: https://www.protocols.io/view/modified-arabidopsis-root-smrna-fish-protocol-rm7vzyworlx1/v1
Details of the microscope setup used to acquire these raw images:
Microscope model and manufacturer | Zeiss Elyra PS1 inverted wide-field microscope |
Acquisition software | Zen 2.3 (Black) |
Objective | Plan-Apochromat 100x/NA 1.46 DIC |
Immersion | Oil |
Camera | Andor iXon 897 (512x512, QE>90%) |
Voxel Size | x/y 100 nm, z 200 nm |
Frame Averaging | 1 |
Acquisition | Complete z-stacks were acquired for Q670 probes then DAPI, sequentially. |
Q670 probe detection laser | 642 nm laser diode |
Q670 probe emission bandwidth | LP655 nm |
Q670 probe exposure time | 1000 ms |
Q670 probe EM Gain | 24 |
DAPI detection laser | 405 nm laser diode |
DAPI emission bandwidth | 420-480 nm |
DAPI exposure time | 300 ms |
DAPI EM Gain | 25 |
Probe sets used as part of this study are listed below:
AT2G28390 (MON1) | AT4G34270 (TIP41) | AT4G35800 (NRPB1) | AT5G46630 (AP2M) | AT1G13320 (PP2A) |
ggagaagacctcgaatctga | cggactatccaaccaagac | aacggaaacctcgtatccat | tcgacgacggagcaaaggaa | ccgagcgatctatcaatcag |
cgaattcggtgtcggatgat | gatgtcacttgtgtgacca | tccgatcaatcgtaccaaga | tgagatttgaggttcgacga | gacatcctcaccaaaactca |
atcggagctaggatttggat | cactaccttttctcctccg | agccatattagccatacatg | gacgatctggttacaggaga | tcgggtataaaggctcatca |
ttgaacacgctccgaattcg | tctgaatcgccggctaata | gcttagcgagctcaagatag | tcgccacggagattcagaaa | tagctcgtcgataagcacag |
agacttcgctaggttgagat | ctttatcgaccaccgtctc | ctgcttaaacttatgctcct | cggtaggtgcgatttatgag | ccaagagcacgagcaatgat |
gatgcaacctcatcatcatt | ccccggaagacttcagaac | gcctattcttaggattcttg | aaatgcatccaccatgtttc | atcaactcttttcttgtcct |
ccacaccttcacgcaataaa | gacgtccgtcgggaagaag | gctcttttttactggttcat | tcgtctgcattatatgcgta | catcgtcattgttctcacta |
cttaacaaaacctctcctcc | agtcatggatgcgtaaacc | accctcaatagtcagttttg | cacaggacaattccctaact | atagccaaaagcacctcatc |
cttccatcatcagctttata | cgcggagggtttcgatctc | tgacaatccgcgtcactaat | taaacaaaggagcagccacc | atacagaataaaacccccca |
attagcttccctaatctcat | cttcgacagcgagagaagt | aggacgagcaaacttagggt | tgtagacattgctgattcgc | caagtttcctcaacagtgga |
ctcatcaacatggcgttttc | tcttaagctttttttccca | gggtggaggaataggaagga | gcaacattagcattgctact | tcatctgagcaccaattcta |
tccatgacgtagaagcatca | ccatttcaggtaagtgaga | ctgccttttcaagttttcat | agctacagcctcaacaacaa | tagccagaggagtgaaatgc |
tgcctgagttactcagtatg | gactaatgcattctcgcca | gtgccgagaaatcaacacgt | gctccaccaaagtatgattt | cattcaccagctgaaagtcg |
gttcatctccatatctggaa | gtgttgctacctaagtgtt | cagagcaatactccacggaa | ttctaatagcgtcttcatca | ggaaaatcccacatgctgat |
gctgaaaatccagcaagctt | accagctagtgcgtcaaac | gtccataatcaacaagctcc | agagattttgtggatagcca | atattgatcttagctccgtc |
accaccattctccacaaaag | caacaggtggaagcccttc | ctggggggagacaatacatt | acaccttcctgagtgatata | attggcatgtcatcttgaca |
ccttgactaagttgacacgg | attgtgctgcagcaggaac | agaggacgaggcttcaagat | gtcttttggcttcgatgaaa | aaattagttgctgcagctct |
aagacaacctggtgatttcc | acggcttgctcctgaattt | gcagagtacctcaacagatt | atgttgcatttggaacaggt | gctgattcaattgtagcagc |
agatatattggccccttaac | aatctagtatcacctgctg | gcaaagagttccggcaagaa | caaccaacagcacctgtaac | ccgaatcttgatcatcttgc |
tgtttcatctgtacagctga | ggcgttgtaaacgtgtaat | tccattagatgtaccaaggg | ttctttttgtaagcaaggcc | caaccctcaacagccaataa |
tatagaagatccaactgccc | actacttcacttccacagt | aacctcttcccaaatgacat | cactttccacaatatccaga | ctccaacaatttcccaagag |
gcaagggtgtcatatcgaac | accgtttctttgtctttct | cgaggaattttctagctgca | ttgcctttagaggacatcag | caaccatataacgcacacgc |
tgagaagacagcatctgtcc | tttggattagcttttgcct | aattgtgtcaccaattccga | cgtcacatcacaccgaagaa | agtagacgagcatatgcagg |
ctgggttccagctaaatgaa | cactgaagagtagcttccc | actgccggataagatctttc | aggcattcccgaaaggaaac | gaacttctgcctcattatca |
ccttaacgcatatggaaggg | atctgatcttcacagttct | tggttaaccctgttctcaaa | cattcaaccccaacttcaaa | cacagggaagaatgtgctgg |
acttcttgcaatatggttcc | ttaagtgagagagcagcca | gcatcatcacgagctttatt | tccttctcaagaccaatttt | tgacgtgctgagaagagtct |
gaataagacaccagacgcgc | gccagttcatcttcataca | caacattttgctgaccgaca | tgggcgagatttcatttctg | cccattataactgatgccaa |
tgtgtctgcacattagtagt | cagtcagaagtgacactcc | tttcaaggaatccagcttct | ctcaatggttttaccactct | tggttcacttggtcaagttt |
gtagaagcaagtcatcggga | cttggcatgactctcactt | cccttcaagtcttcaagatg | caggttcacacactggtgaa | tctacaatggctggcagtaa |
tgagcgttgtatcttggtag | tcgcaagaggaggaaccat | cgagttggaatctgtcagtc | acagtcttctcggagttgaa | cgattatagccagacgtact |
agaagtggacataggcatgc | gcacaccatcaactctcag | caagtgctatcaccatttgt | gatttacaccctctgttatt | gactggccaacaagggaata |
gaacgcatctgaacgtgtgg | ctcgtctctctcaatctca | cagatatgcctcttgatgtt | gtgtacgaccaagttctttg | catcaaagaagcctacacct |
taccctgcaatctttgagat | tcgccaaacctataatgca | tcaacagggtgcatatctga | accttgacatttacttccat | ttgcatgcaaagagcaccaa |
cgcgattgatctttgaacca | cgaagaacagttggtgcct | cacactcaacgcatcatcac | agggcaaacattttagcacc | acggattgagtgaaccttgt |
ggtacatcttcaacacgcat | atgttgcttctctccaaca | attgagcagcaacacaaccg | tggaattttaaccacgaccc | cttcagattgtttgcagcag |
tagtagatgatcgacgcctg | taccctttcgcagatagag | cgtaacgttctttgcactga | cttggaaattggtcttggct | ggaccaaactcttcagcaag |
ggtgagtcttgttcttgatt | ctccagactgctaagtcaa | tgttttgatcctcttagcta | tggattgtatttagcgcgac | ggaactatatgctgcattgc |
atgccaaagtccaaagggac | tgactgatggagctcgggt | ccggagtgagatagactgat | cttagcgtggactctgtttg | gtgggttgttaatcatctct |
gttactgggggtgagaattc | tgcttaatcactggaagcc | acatcttcatctggcatttc | ccattgttgagatcaactca | tgcacgaagaatcgtcatcc |
gacttttctgttgtctgtga | gggatcttcagtttctgtg | aagtagccacggagatatct | cttgtccaagatttcttctc | ttactggagcgagaagcgat |
agtttctggtatgctcgata | aaagctcatcggtacgctc | catctcgcgattcaactcta | tgtgaacattggcacctgaa | gaacatgtgatctcggatcc |
ccaatccttttacatgcatt | agtagtttgtttggctgta | gatgtctggaatacctctga | aacgaactcgcagaccagat | ctctgtctttagatgcagtt |
gtgtagttttcatctcttct | agtcagtggagtaactcct | agcaaagcacgacgaactgc | ttatgtatcgaacccactcg | catcattttggccacgttaa |
tggtgtgacccaacatagaa | gttcatatgaaaccaccac | cgagtgatagccatcagatg | cagcatctgatctcgtaaga | cgtatcatgttctccacaac |
gcaagtggatcaaatgctgc | tcttcagcatctcatcattc | atcaacatctgggtcttcac | ||
cacacctgattgcatatctt | atagctagggagctgaagtt | ttggagagcttgatttgcga | ||
cttcattctccacatctttt | tgacactggtgaacgagcag | acacaattcgttgctgtctt | ||
aaaggactagctccttgcaa | catcatgccttcatggtaag | cgcccaacgaacaaatcaca |
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