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List view: phased small RNA clusters [#Session ID: 1208278272795135]

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Cluster ID Phased small RNA(s) # of hit position
[phased:non-phased]
P-value Matched transcript Transcript description # of cleavage sites guided by input phase-initiator # of complementary regions
#1146 AAAGGTTGTCAACCAGA;
AAGCTTCCGAAGCTGTG;
AAGGTTGTCAACCAGAT;
AGATCTGGTTGACAACC;
AGGTTGTCAACCAGATC;
CAGATCTGGTTGACAAC;
CATCAGCCTCTATTTTC;
CCAAAGTTGTAAATGTG;
GAAAATAGAGGCTGATG;
TTAGTTGAACGGATGGT;
TTCTCCATCTTGTTGAG
8 : 5 3.830e-7 AT1G63080.1 | Symbols: | pentatricopeptide (PPR) repeat-containing protein | chr1:23391296-23394481 REVERSE 1 14
#1183 AAAGGTTGTCAACCAGA;
AAGCTTCCGAAGCTGTG;
AAGGTTGTCAACCAGAT;
AGATCTGGTTGACAACC;
AGGTTGTCAACCAGATC;
CAGATCTGGTTGACAAC;
CATCAGCCTCTATTTTC;
CCAAAGTTGTAAATGTG;
GAAAATAGAGGCTGATG;
TTAGTTGAACGGATGGT;
TTCTCCATCTTGTTGAG
8 : 5 3.830e-7 AT1G63070.1 | Symbols: | pentatricopeptide (PPR) repeat-containing protein | chr1:23388989-23390832 REVERSE 1 13
#1414 AAAATGGGAGATGTCCG;
AACAAGCGAATGAGTCA;
ATGGGAGATGTCCGGAA;
ATTCCGGACATCTCCCA;
CGCTATGTTGGACTTAG;
TCATTCCGGACATCTCC;
TGGGAGATGTCCGGAAT;
TTCTAAGTCCAACATAG;
TTCTAAGTCCAACATAG
6 : 1 1.905e-6 AT1G50055.1 | Symbols: TAS1B | TAS1B; other RNA | chr1:18552872-18553710 REVERSE 1 9
#1129 AAAGGTTGTCAACCAGA;
AAGCTTCCGAAGCTGTG;
AAGGTTGTCAACCAGAT;
AGATCTGGTTGACAACC;
AGGTTGTCAACCAGATC;
CAGATCTGGTTGACAAC;
CATCAGCCTCTATTTTC;
CTTTCTCCATCTTGTTG;
GAAAATAGAGGCTGATG;
TTAGTTGAACGGATGGT;
TTCTCCATCTTGTTGAG
7 : 4 2.582e-6 AT1G63080.1 | Symbols: | pentatricopeptide (PPR) repeat-containing protein | chr1:23391296-23394481 REVERSE 1 14
#1170 AAAGGTTGTCAACCAGA;
AAGCTTCCGAAGCTGTG;
AAGGTTGTCAACCAGAT;
AGATCTGGTTGACAACC;
AGGTTGTCAACCAGATC;
CAGATCTGGTTGACAAC;
CATCAGCCTCTATTTTC;
CTTTCTCCATCTTGTTG;
GAAAATAGAGGCTGATG;
TTAGTTGAACGGATGGT;
TTCTCCATCTTGTTGAG
7 : 5 5.482e-6 AT1G63070.1 | Symbols: | pentatricopeptide (PPR) repeat-containing protein | chr1:23388989-23390832 REVERSE 1 13
#1177 AGATCTGGTTGACAACC;
AGGTTGTCAACCAGATC;
CAGATCTGGTTGACAAC;
CATCAGCCTCTATTTTC;
CTTTCTCCATCTTGTTG;
GAAAATAGAGGCTGATG;
TGGATGATGCATTCGAC;
TTCTCCATCTTGTTGAG
6 : 3 1.653e-5 AT1G63070.1 | Symbols: | pentatricopeptide (PPR) repeat-containing protein | chr1:23388989-23390832 REVERSE 0 13
#1181 AGATCTGGTTGACAACC;
AGGTTGTCAACCAGATC;
CAGATCTGGTTGACAAC;
CATCAGCCTCTATTTTC;
CTTTCTCCATCTTGTTG;
GAAAATAGAGGCTGATG;
TGGATGATGCATTCGAC;
TTCTCCATCTTGTTGAG
6 : 3 1.653e-5 AT1G63070.1 | Symbols: | pentatricopeptide (PPR) repeat-containing protein | chr1:23388989-23390832 REVERSE 0 13
#1185 AGCTGCCTCTGTAACTA;
CATCAGCCTCTATTTTC;
CTTTCTCCATCTTGTTG;
GAAAATAGAGGCTGATG;
TGGATGATGCATTCGAC;
TTCCGTAGTTACAGAGG
6 : 3 1.653e-5 AT1G63070.1 | Symbols: | pentatricopeptide (PPR) repeat-containing protein | chr1:23388989-23390832 REVERSE 0 13
#1055 AAAGGTTGTCAACCAGA;
AAGGTTGTCAACCAGAT;
AGAGCTTCAGAAGCAGT;
AGATCTGGTTGACAACC;
AGGTTGTCAACCAGATC;
CACCAGGCTCTATTTTC;
CAGATCTGGTTGACAAC;
CCACTGCTTCTGAAGCT;
GGGAAAATAGAGCCTGG;
TTAGTTGACCGGATGGT
7 : 7 1.896e-5 AT1G63130.1 | Symbols: | pentatricopeptide (PPR) repeat-containing protein | chr1:23416395-23418814 FORWARD 1 21
#1068 AAAGGTTGTCAACCAGA;
AAGGTTGTCAACCAGAT;
AGAGCTTCAGAAGCAGT;
AGATCTGGTTGACAACC;
AGGTTGTCAACCAGATC;
CACCAGGCTCTATTTTC;
CAGATCTGGTTGACAAC;
CCACTGCTTCTGAAGCT;
GGGAAAATAGAGCCTGG;
TTAGTTGACCGGATGGT
7 : 7 1.896e-5 AT1G63130.1 | Symbols: | pentatricopeptide (PPR) repeat-containing protein | chr1:23416395-23418814 FORWARD 1 21
#3057 AAACTGACACATGGCTG;
ATAATTTTCTAAGATCC;
ATTTTCTAAGATCCACC;
CGCTATGTTGGACTTAG;
TATTCCAGGATATGCAA;
TTCTAAGTCCAACATAG
5 : 1 3.481e-5 AT2G39675.1 | Symbols: TAS1C | TAS1C; other RNA | chr2:16544366-16545355 REVERSE 2 10
#3060 ATTTTCTAAGATCCACC;
CGCTATGTTGGACTTAG;
TATTCCAGGATATGCAA;
TTCTAAGTCCAACATAG;
TTTCAAGTCGTCTAAAG
5 : 1 3.481e-5 AT2G39675.1 | Symbols: TAS1C | TAS1C; other RNA | chr2:16544366-16545355 REVERSE 2 10
#1425 AAAATGGGAGATGTCCG;
ATGGGAGATGTCCGGAA;
ATTCCGGACATCTCCCA;
CGCTATGTTGGACTTAG;
TCATTCCGGACATCTCC;
TGGGAGATGTCCGGAAT;
TTCTAAGTCCAACATAG;
TTCTAAGTCCAACATAG
5 : 1 3.481e-5 AT1G50055.1 | Symbols: TAS1B | TAS1B; other RNA | chr1:18552872-18553710 REVERSE 1 9
#1072 ATGCTTCTCGACTACTC;
GAGCCTGGTGTTGTGAT;
GATCACAACACCAGGCT;
TGAACAGATTGAGTGCA;
TGAGTAGTCGAGAAGCA;
TGATGCTTCTCGACTAC
5 : 1 3.481e-5 AT1G63130.1 | Symbols: | pentatricopeptide (PPR) repeat-containing protein | chr1:23416395-23418814 FORWARD 0 21
#1073 ATGCTTCTCGACTACTC;
GAGCCTGGTGTTGTGAT;
GATCACAACACCAGGCT;
TGAACAGATTGAGTGCA;
TGAGTAGTCGAGAAGCA;
TGATGCTTCTCGACTAC
5 : 1 3.481e-5 AT1G63130.1 | Symbols: | pentatricopeptide (PPR) repeat-containing protein | chr1:23416395-23418814 FORWARD 0 21
#1904 ACCAGCGACAGCAACCA;
ATGTTGTCGCTGGTTGC;
ATTGTTCGTTTGTCTGT;
CCAGCGACCAGCGACAG;
CGAACAACTTTTGGTCG;
CGCTGGTTGCTGTCGCT;
CTGTAATTGGTCGCTGA;
GACCAGCGACCAGCGAC;
GCTGAACCAGCGACAGG;
GCTGTCGCTGGTCGCTG;
GTAATTGGTCGCTGAGT;
GTTGTCGCTGGTTGCTG;
TCGCTGGTTGCTGTCGC;
TGCCTGTCGCTGGTTCA;
TGCTGTCGCTGGTCGCT;
TGTTGTCGCTGGTTGCT
10 : 30 6.428e-5 AT2G25370.1 | Symbols: | zinc finger protein-related | chr2:10813779-10816873 FORWARD 0 5
#1882 ATGTTGTCGCTGGTTGC;
ATTGTTCGTTTGTCTGT;
CGAACAACTTTTGGTCG;
CGCTGGTTGCTGTCGCT;
CGTTTGCCTGTCGCTGG;
CTGGCGACTGAAACCAG;
CTGTAATTGGTCGCTGA;
GCTGAACCAGCGACAGG;
GGTTTCAGTCGCCAGCG;
GTAATTGGTCGCTGAGT;
GTTGTCGCTGGTTGCTG;
TCGCTGGTTGCTGTCGC;
TGCCTGTCGCTGGTTCA;
TGTTGTCGCTGGTTGCT
9 : 23 8.085e-5 AT2G25370.1 | Symbols: | zinc finger protein-related | chr2:10813779-10816873 FORWARD 0 5
#704 AACTGCAGTTCGCTCTG;
ATCCTTCTGGATACCGT;
CTTCTGACGGAAGGCAA;
TGCTTCTGACGGAAGGC;
TGTACAGAGCGAACTGC;
TTGCCTTCCGTCAGAAG
5 : 2 0.0001 AT1G07780.3 | Symbols: TRP6, PAI1 | PAI1 (PHOSPHORIBOSYLANTHRANILATE ISOMERASE 1); phosphoribosylanthranilate isomerase | chr1:2410117-2412672 REVERSE 0 5
#710 AACTGCAGTTCGCTCTG;
ATCCTTCTGGATACCGT;
CTTCTGACGGAAGGCAA;
TGCTTCTGACGGAAGGC;
TGTACAGAGCGAACTGC;
TTGCCTTCCGTCAGAAG
5 : 2 0.0001 AT1G07780.3 | Symbols: TRP6, PAI1 | PAI1 (PHOSPHORIBOSYLANTHRANILATE ISOMERASE 1); phosphoribosylanthranilate isomerase | chr1:2410117-2412672 REVERSE 0 5
#6181 AACTGCAGTTCGCTCTG;
ATCCTTCTGGATACCGT;
CTTCTGACGGAAGGCAA;
TGCTTCTGACGGAAGGC;
TGTACAGAGCGAACTGC;
TTGCCTTCCGTCAGAAG
5 : 2 0.0001 AT5G05590.1 | Symbols: PAI2 | PAI2 (PHOSPHORIBOSYLANTHRANILATE ISOMERASE 2); phosphoribosylanthranilate isomerase | chr5:1666472-1668337 REVERSE 0 4
#6188 AACTGCAGTTCGCTCTG;
ATCCTTCTGGATACCGT;
CTTCTGACGGAAGGCAA;
TGCTTCTGACGGAAGGC;
TGTACAGAGCGAACTGC;
TTGCCTTCCGTCAGAAG
5 : 2 0.0001 AT5G05590.1 | Symbols: PAI2 | PAI2 (PHOSPHORIBOSYLANTHRANILATE ISOMERASE 2); phosphoribosylanthranilate isomerase | chr5:1666472-1668337 REVERSE 0 4
#1266 AACTGCAGTTCGCTCTG;
ATCCTTCTGGATACCGT;
CTTCTGACGGAAGGCAA;
TGCTTCTGACGGAAGGC;
TGTACAGAGCGAACTGC;
TTGCCTTCCGTCAGAAG
5 : 2 0.0001 AT1G07780.1 | Symbols: TRP6, PAI1 | PAI1 (PHOSPHORIBOSYLANTHRANILATE ISOMERASE 1); phosphoribosylanthranilate isomerase | chr1:2410117-2412674 REVERSE 0 3
#1272 AACTGCAGTTCGCTCTG;
ATCCTTCTGGATACCGT;
CTTCTGACGGAAGGCAA;
TGCTTCTGACGGAAGGC;
TGTACAGAGCGAACTGC;
TTGCCTTCCGTCAGAAG
5 : 2 0.0001 AT1G07780.1 | Symbols: TRP6, PAI1 | PAI1 (PHOSPHORIBOSYLANTHRANILATE ISOMERASE 1); phosphoribosylanthranilate isomerase | chr1:2410117-2412674 REVERSE 0 3
#1324 AACTGCAGTTCGCTCTG;
ATCCTTCTGGATACCGT;
CTTCTGACGGAAGGCAA;
TGCTTCTGACGGAAGGC;
TGTACAGAGCGAACTGC;
TTGCCTTCCGTCAGAAG
5 : 2 0.0001 AT1G07780.2 | Symbols: TRP6, PAI1 | PAI1 (PHOSPHORIBOSYLANTHRANILATE ISOMERASE 1); phosphoribosylanthranilate isomerase | chr1:2410117-2412670 REVERSE 0 3
#1330 AACTGCAGTTCGCTCTG;
ATCCTTCTGGATACCGT;
CTTCTGACGGAAGGCAA;
TGCTTCTGACGGAAGGC;
TGTACAGAGCGAACTGC;
TTGCCTTCCGTCAGAAG
5 : 2 0.0001 AT1G07780.2 | Symbols: TRP6, PAI1 | PAI1 (PHOSPHORIBOSYLANTHRANILATE ISOMERASE 1); phosphoribosylanthranilate isomerase | chr1:2410117-2412670 REVERSE 0 3
#5905 AACTGCAGTTCGCTCTG;
ATCCTTCTGGATACCGT;
CTTCTGACGGAAGGCAA;
TGCTTCTGACGGAAGGC;
TGTACAGAGCGAACTGC;
TTGCCTTCCGTCAGAAG
5 : 2 0.0001 AT5G05590.2 | Symbols: PAI2 | PAI2 (PHOSPHORIBOSYLANTHRANILATE ISOMERASE 2); phosphoribosylanthranilate isomerase | chr5:1666472-1668316 REVERSE 0 3
#5912 AACTGCAGTTCGCTCTG;
ATCCTTCTGGATACCGT;
CTTCTGACGGAAGGCAA;
TGCTTCTGACGGAAGGC;
TGTACAGAGCGAACTGC;
TTGCCTTCCGTCAGAAG
5 : 2 0.0001 AT5G05590.2 | Symbols: PAI2 | PAI2 (PHOSPHORIBOSYLANTHRANILATE ISOMERASE 2); phosphoribosylanthranilate isomerase | chr5:1666472-1668316 REVERSE 0 3
#1166 AAAGGTTGTCAACCAGA;
AAGGTTGTCAACCAGAT;
AGATCTGGTTGACAACC;
AGGTTGTCAACCAGATC;
CAGATCTGGTTGACAAC;
CATCAGCCTCTATTTTC;
GAAAATAGAGGCTGATG;
TTAGTTGAACGGATGGT;
TTCTCCATCTTGTTGAG
6 : 6 0.0001 AT1G63080.1 | Symbols: | pentatricopeptide (PPR) repeat-containing protein | chr1:23391296-23394481 REVERSE 1 14
#1191 AAAGGTTGTCAACCAGA;
AAGGTTGTCAACCAGAT;
AGATCTGGTTGACAACC;
AGGTTGTCAACCAGATC;
CAGATCTGGTTGACAAC;
CATCAGCCTCTATTTTC;
GAAAATAGAGGCTGATG;
TTAGTTGAACGGATGGT;
TTCTCCATCTTGTTGAG
6 : 6 0.0001 AT1G63070.1 | Symbols: | pentatricopeptide (PPR) repeat-containing protein | chr1:23388989-23390832 REVERSE 1 13
#766 AGAGACCACTCGACCCC;
AGGTCGAGTGTCCTCAT;
ATCACCTGACCATCACT;
CATGATCAGGTCCGCTT
4 : 0 0.0002 AT1G40390.1 | Symbols: | similar to unknown protein [Arabidopsis thaliana] (TAIR:AT1G43760.1); similar to putative AP endonuclease/reverse transcriptase [Brassica napus] (GB:AAM82604.1); contains InterPro domain Endonuclease/exonuclease/phosphatase; (InterPro:IPR005135) | chr1:15435017-15437115 REVERSE 0 2
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Session Summary        
Users Input
Number of small RNAs submitted by user 30324,   download original FASTA file
Number of valid small RNAs after pre-processing 30324,   download processed FASTA file and LOG file
transcript/genomic library chosen by user Arabidopsis thaliana TAIR7, cDNA, released 04/25/2007
Number of phase-initiators submitted by user 217,   download original FASTA file
Number of valid phase-initiator sequences after pre-processing 166,   download processed FASTA file and LOG file
Mapping small RNAs onto transcript/genomic sequences
Number of total hits during mapping 6708
Number of small RNAs having hits 3226
Number of transcript/genomic sequences having hits 2212
Clustering phased small RNAs
Number of all phased small RNA clusters (having at least 2 phased small RNAs) 1315
Number of transcript/genomic sequences associated with the phased small RNA clusters 280
Identifying cleavage site
Number of phased small RNA clusters with valid cleavage sites directed by phase-initiators 125