Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009854.1 Corchorus capsularis cultivar CVL-1 contig09875, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 86926
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2015 original size:975 final size:963
Alignment explanation
Indices: 1--2424 Score: 3693
Period size: 975 Copynumber: 2.5 Consensus size: 963
*
1 TTTTGAATGAATTTTTTGCGCCAAGAGTAATTGAAATATCTATATTCATCTATTCAAATCTCAGG
1 TTTTGAATG-ATTTTTTGCGCCAAGAGTAATTGAAATATCTATATTCATCTATTCAAATCTCAGC
* *
66 CACATAGGATTTAAGGATTTGTTTTTACGAGCATCTGGATCACGTTGCAATTTAATTAGAAATTA
65 CACATAGGATTTAAGGATTTGTTTTTACGAGCATCTGCATCACGTT-CCA---AATT---AATT-
* *
131 ATTCGGAAAAATAAGAAAAATGATATTAGAAGCATGAAAGTCCTTTTTTTTTAATTTTTGGAAAA
122 A---GGAAAAATAAGAAAAA-GATATTAGAAGC-TGAAAATCCATTTTTTTT-A---TT-GAAAA
196 TTAAATAAAAATAAAGAAAGCCCAAAAACAGTCCAAACGGGCCAAAATAACAAAAGCGATAAAAA
177 --AAATAAAAATAAAGAAAGCCCAAAAACAGTCCAAACGGGCCAAAATAACAAAAGCGATAAAAA
* *
261 CTAAAACTCGCGACAGAAAACTGTAACTGGCTTTTTAGGCCCTAAATGAAACGTTGAACCGGAAT
240 CTAAAACTCGCGACAGAAAACTGTAACGGGCTTTTTAGGCCCTAAACGAAACGTTGAA-C----T
** *
326 AGTTGTTCACATTGTTGTAGTAGACTCGAAACCCTTTCAGAAAAGGTATTATAATAGTCAAACCG
300 AACTGTTCACA-TGTTGTAGTAGACTCGAAACCCTTTCCGAAAAGGTATTATAATAGTCAAACCG
* **
391 ACTTACAGTTTGAAAGTTATGCCCTGTTTAAGTTGACCCACCAATAGGAGCTTCAGGCCCAAAAT
364 ACTTACGGTTTGAAAGTTATGCCCTGTTTAAGTTGACCCACCAGCAGGAGCTTCAGGCCCAAAAT
**
456 CCAAAACGTTACACGCCCTTTCGAACGGACTTCTGACGGTCCATACGATTTTATAAATG-T-T--
429 CCAAAACGTTACACGCCCTTTCGAACGGACTTCTGACGGTCCATACGA-TCCATAAATGATATGC
* *
517 ATGCCTATCTCATCCGCATCAATTGTGTCCAAAAATCGATGAAAAAATTTTCAGGTCAGTTTTTG
493 ATGCATATCTCATCCGCATCAATTGTGTCCAAAAATCGAGGAAAAAATTTTCAGGTCAGTTTTTG
582 CCAATTTTTGGACGAGATCGTGTGCTATCCATCACGGTTTTGGGCTGAAAATGCGTTATGGGGAC
558 CCAATTTTTGGACGAGATCGTGTGCTATCCATCACGGTTTTGGGCTGAAAATGCGTTATGGGGAC
**
647 TTGGCTAAGTTTTTAATGAATTTTGGCGCCAAGAGTAATTGAAATATCTATATTCATCTATCCTA
623 CCGGCTAAGTTTTTAATGAATTTTGGCGCCAAGAGTAATTGAAATATCTATATTCATCTATCCTA
*
712 GTCTCAGCCACATTGGATTTATGGATGTCTTTTTATGAGCATCTAGATCACATTTCGATTTAATT
688 GTCTCAGCCACATTGGATTTATGGATGTCTTTTTACGAGCATCTAGATCACATTTCGATTTAATT
* * *
777 AGAAATTAATTCGGAAAAATAAGAAAAACGACATTATAAGCTTGAAAATCTCTTATTTTATTTTT
753 AGAAATTAATTCGGAAAAATAAGAAAAACGACATTAGAAGCTTGAAAATCCCTTATTTTAATTTT
* *
842 GGCGTTGAATTATATATCTTTTATGAGTATTGTGTCCAAAGATTGAAGAAAATTTTTTCGGGTCA
818 GGCGTTGAATTATATATCTTTTATGAGTATTGTGTCCAAAAATTGAAGAAAATTTTTTCGGCTCA
*
907 GTTTTTACCAATTTTTGGACGAAATCGTGTGCTAACCATCACGAATTTTGGCTGAAAATGCGTTC
883 GTTTTTACCAAATTTTGGACGAAATCGTGTGCTAACCATCACGAATTTTGGCTGAAAATGCGTTC
972 CGGGGCCCCGGATCAG
948 CGGGGCCCCGGATCAG
* *
988 TTTTGAATGATTTTTTGCGCCAAGAGTAATTGAAATATATATATTCATCTATTCAAATCCCAGCC
1 TTTTGAATGATTTTTTGCGCCAAGAGTAATTGAAATATCTATATTCATCTATTCAAATCTCAGCC
*
1053 ACATAGGATTTAAGGATTTGTTTTTACGAGCATCTGCATCGCGTTCCAAATTAATTAGGAAAAAT
66 ACATAGGATTTAAGGATTTGTTTTTACGAGCATCTGCATCACGTTCCAAATTAATTAGGAAAAAT
1118 AAGAAAAACGATATTAGAAGCTTGAAAATCCATTTTTTTTCGCATTGAAAAAAATAAAAATAAAG
131 AAGAAAAA-GATATTAGAAGC-TGAAAATCCATTTTTTTT---ATTGAAAAAAATAAAAATAAAG
*
1183 AAAACCCAAAAACAGTCCAAACGGGCCAAAATAACAAAAGCGATAAAAACTAAAACTCGCGACAG
191 AAAGCCCAAAAACAGTCCAAACGGGCCAAAATAACAAAAGCGATAAAAACTAAAACTCGCGACAG
*
1248 AAAACTGTAACGGGCTTTTTAGGCTCTAAACGAAACGTTGAACTACTTTAACTGTTCACCATGTT
256 AAAACTGTAACGGGCTTTTTAGGCCCTAAACGAAACGTTG-A--AC--TAACTGTTCA-CATGTT
1313 GTAGTAGACTCGAAACCCTTTCCGAAAAGGTATTATAATAGTCAAACCGACTTACGGTTTGAAAG
315 GTAGTAGACTCGAAACCCTTTCCGAAAAGGTATTATAATAGTCAAACCGACTTACGGTTTGAAAG
1378 TTATGCCCTGTTTAAGTTGACCCACCAGCAGGAGCTTCAGGCCCAAAATCCAAAACGTTACACGC
380 TTATGCCCTGTTTAAGTTGACCCACCAGCAGGAGCTTCAGGCCCAAAATCCAAAACGTTACACGC
*
1443 CCTTTCGAACGGACTTCTGACGGTCCATATGATCCATAAATGATATGCATAGCATATCTCATCCG
445 CCTTTCGAACGGACTTCTGACGGTCCATACGATCCATAAATGATATGCAT-GCATATCTCATCCG
*
1508 CATCAATTGTGTCCAAAAATTGAGGAAAAAAATTTT-AGGTCAGTTTTTGCCAATTTTTGGACGA
509 CATCAATTGTGTCCAAAAATCGAGG-AAAAAATTTTCAGGTCAGTTTTTGCCAATTTTTGGACGA
* *
1572 GATCGTGTGCTATCCATCACGGTTTTGGGCTGAAAATGCGTTCTGGGGTCCCGGCTCAA-TTTTT
573 GATCGTGTGCTATCCATCACGGTTTTGGGCTGAAAATGCGTTATGGGGACCCGGCT-AAGTTTTT
1636 AATGAATTTTGGCGCCAAGAGTAATTGAAATATCTATATTCATCTATCCTAGTCTCAGCCACATT
637 AATGAATTTTGGCGCCAAGAGTAATTGAAATATCTATATTCATCTATCCTAGTCTCAGCCACATT
* *
1701 GGATTTATGGATTTCTTTTTACGAGCATCTGGATCACATTTCGATTTAATTAGAAATTAATTCGG
702 GGATTTATGGATGTCTTTTTACGAGCATCTAGATCACATTTCGATTTAATTAGAAATTAATTCGG
*
1766 AAAAATAAGAAAAACGACATTAGAAGCTTGAAAATCCCTTTTTTTAATTTTGGCGTTGAATTATA
767 AAAAATAAGAAAAACGACATTAGAAGCTTGAAAATCCCTTATTTTAATTTTGGCGTTGAATTATA
*
1831 TATCTTTTATGAGTATTGTGTCCAAAAATTGAGGAAAATTTTTTCGGCTCAGTTTTTACCAAATT
832 TATCTTTTATGAGTATTGTGTCCAAAAATTGAAGAAAATTTTTTCGGCTCAGTTTTTACCAAATT
* *
1896 TTGGACGAAATCGTGTGCTAACCATCACGGATTTTGGCTGAAAATGCGTTCCGGGGCCCCGGCTC
897 TTGGACGAAATCGTGTGCTAACCATCACGAATTTTGGCTGAAAATGCGTTCCGGGGCCCCGGATC
1961 AG
962 AG
1963 TTTTGAATGATTTTTTGCGCCAAGAGTAATTGAAATATCTATATTCATCTATTCAAATCTCAGCC
1 TTTTGAATGATTTTTTGCGCCAAGAGTAATTGAAATATCTATATTCATCTATTCAAATCTCAGCC
** * * *
2028 ACATAAAATTTAAGGATTTGTTTTTACGAGCATCTGCATCACGTTCCGATTTAATTA--AAAATT
66 ACATAGGATTTAAGGATTTGTTTTTACGAGCATCTGCATCACGTTCCAAATTAATTAGGAAAAAT
* * * *
2091 AATTCG-GAAA-A-A-T--AAG--GAAAA-CGA-------TATT-----AGATAAAAATACAGAA
131 AA---GAAAAAGATATTAGAAGCTGAAAATCCATTTTTTTTATTGAAAAAAATAAAAATAAAGAA
2135 AGCCCAAAAACAGTCCAAACGGGCCAAAATAACAAAAGCGATAAAAACTAAAACTCGCGACAGAA
193 AGCCCAAAAACAGTCCAAACGGGCCAAAATAACAAAAGCGATAAAAACTAAAACTCGCGACAGAA
*
2200 AACTGTAACGGACTTTTTAGGCCCTAAACGAAACGTTG----AAC----CAC--GTTGTAGTAGA
258 AACTGTAACGGGCTTTTTAGGCCCTAAACGAAACGTTGAACTAACTGTTCACATGTTGTAGTAGA
*
2255 CTCGAAACCCTTTCCGAAAAGGTATTATAGTAGTCAAACCGACTTACGGTTTGAAAGTTATGCCC
323 CTCGAAACCCTTTCCGAAAAGGTATTATAATAGTCAAACCGACTTACGGTTTGAAAGTTATGCCC
*
2320 TGTTTAAGTTGACCCACCAGCAGGAGCTTCAGGCTCAAAATCCAAAACGTTACACGCCCTTTCGA
388 TGTTTAAGTTGACCCACCAGCAGGAGCTTCAGGCCCAAAATCCAAAACGTTACACGCCCTTTCGA
2385 ACGGACTTCTGACGGTCCATACGATCCATAAATGATATGC
453 ACGGACTTCTGACGGTCCATACGATCCATAAATGATATGC
2425 CTAGAGTAAT
Statistics
Matches: 1357, Mismatches: 64, Indels: 85
0.90 0.04 0.06
Matches are distributed among these distances:
934 178 0.13
936 1 0.00
937 2 0.00
941 3 0.00
950 114 0.08
955 3 0.00
958 1 0.00
965 2 0.00
966 5 0.00
969 3 0.00
970 8 0.01
971 286 0.21
972 5 0.00
973 14 0.01
974 5 0.00
975 597 0.44
976 13 0.01
977 1 0.00
978 1 0.00
979 4 0.00
982 4 0.00
985 2 0.00
986 96 0.07
987 9 0.01
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (963 bp):
TTTTGAATGATTTTTTGCGCCAAGAGTAATTGAAATATCTATATTCATCTATTCAAATCTCAGCC
ACATAGGATTTAAGGATTTGTTTTTACGAGCATCTGCATCACGTTCCAAATTAATTAGGAAAAAT
AAGAAAAAGATATTAGAAGCTGAAAATCCATTTTTTTTATTGAAAAAAATAAAAATAAAGAAAGC
CCAAAAACAGTCCAAACGGGCCAAAATAACAAAAGCGATAAAAACTAAAACTCGCGACAGAAAAC
TGTAACGGGCTTTTTAGGCCCTAAACGAAACGTTGAACTAACTGTTCACATGTTGTAGTAGACTC
GAAACCCTTTCCGAAAAGGTATTATAATAGTCAAACCGACTTACGGTTTGAAAGTTATGCCCTGT
TTAAGTTGACCCACCAGCAGGAGCTTCAGGCCCAAAATCCAAAACGTTACACGCCCTTTCGAACG
GACTTCTGACGGTCCATACGATCCATAAATGATATGCATGCATATCTCATCCGCATCAATTGTGT
CCAAAAATCGAGGAAAAAATTTTCAGGTCAGTTTTTGCCAATTTTTGGACGAGATCGTGTGCTAT
CCATCACGGTTTTGGGCTGAAAATGCGTTATGGGGACCCGGCTAAGTTTTTAATGAATTTTGGCG
CCAAGAGTAATTGAAATATCTATATTCATCTATCCTAGTCTCAGCCACATTGGATTTATGGATGT
CTTTTTACGAGCATCTAGATCACATTTCGATTTAATTAGAAATTAATTCGGAAAAATAAGAAAAA
CGACATTAGAAGCTTGAAAATCCCTTATTTTAATTTTGGCGTTGAATTATATATCTTTTATGAGT
ATTGTGTCCAAAAATTGAAGAAAATTTTTTCGGCTCAGTTTTTACCAAATTTTGGACGAAATCGT
GTGCTAACCATCACGAATTTTGGCTGAAAATGCGTTCCGGGGCCCCGGATCAG
Found at i:6573 original size:16 final size:16
Alignment explanation
Indices: 6552--6582 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6542 GCCATGACTC
6552 ATCCGGATCCGACCCT
1 ATCCGGATCCGACCCT
*
6568 ATCCGGATTCGACCC
1 ATCCGGATCCGACCC
6583 AGGCTTTGTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.42, G:0.19, T:0.19
Consensus pattern (16 bp):
ATCCGGATCCGACCCT
Found at i:11492 original size:60 final size:62
Alignment explanation
Indices: 11397--11521 Score: 182
Period size: 60 Copynumber: 2.0 Consensus size: 62
11387 AATTTCCCAT
* *
11397 TTTCATTTGAGCGGCCAGAATTTTCTCCGTAGTTTCTTCCATCT-CCT-TCTTTGCTTCATC
1 TTTCATTTGAGAGGCCAGAATTTTCTCCATAGTTTCTTCCATCTCCCTATCTTTGCTTCATC
* * *
11457 TTTCATTTGAGATGCCAGAATTTTCTTCATCGTTTCTTCCATCTCCCTCATCTTTGCTTCATC
1 TTTCATTTGAGAGGCCAGAATTTTCTCCATAGTTTCTTCCATCTCCCT-ATCTTTGCTTCATC
11520 TT
1 TT
11522 GCCTTTGATA
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
60 39 0.68
61 3 0.05
63 15 0.26
ACGTcount: A:0.14, C:0.28, G:0.11, T:0.46
Consensus pattern (62 bp):
TTTCATTTGAGAGGCCAGAATTTTCTCCATAGTTTCTTCCATCTCCCTATCTTTGCTTCATC
Found at i:11543 original size:54 final size:54
Alignment explanation
Indices: 11479--11638 Score: 230
Period size: 54 Copynumber: 2.9 Consensus size: 54
11469 TGCCAGAATT
* *
11479 TTCTTCATCGTTTCTTCCATCTCCCTCATCTTTGCTTCATCTTGCCTTTGATAG
1 TTCTTTATCGTTTCTTCAATCTCCCTCATCTTTGCTTCATCTTGCCTTTGATAG
* *
11533 TTCTTTATCGTTTCTTCTATCTCCTTCATCTTTGCTTCATCTTGCCTTTGATAG
1 TTCTTTATCGTTTCTTCAATCTCCCTCATCTTTGCTTCATCTTGCCTTTGATAG
* * *
11587 TTCTTTATCATTCCTTCTATAATTTCCCTCATCTTTGCTTCATCTTGCCTTT
1 TTCTTTATCGTTTCTTC---AATCTCCCTCATCTTTGCTTCATCTTGCCTTT
11639 CATAAATTTC
Statistics
Matches: 95, Mismatches: 8, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
54 66 0.69
57 29 0.31
ACGTcount: A:0.12, C:0.29, G:0.07, T:0.52
Consensus pattern (54 bp):
TTCTTTATCGTTTCTTCAATCTCCCTCATCTTTGCTTCATCTTGCCTTTGATAG
Found at i:12538 original size:17 final size:18
Alignment explanation
Indices: 12499--12540 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
12489 CATAAGATTC
* *
12499 ATATATATTGAATGATCA
1 ATATATAATGAATAATCA
*
12517 CTATATAAT-AATAATCA
1 ATATATAATGAATAATCA
12534 ATATATA
1 ATATATA
12541 TGCATGAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (18 bp):
ATATATAATGAATAATCA
Found at i:14946 original size:24 final size:23
Alignment explanation
Indices: 14925--14968 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
14915 CTTTTTTTAG
* *
14925 GTAAAATAAAATGGATTATTTTC
1 GTAAAAAAAAAAGGATTATTTTC
*
14948 TTAAAAAAAAAAGGATTATTT
1 GTAAAAAAAAAAGGATTATTT
14969 GATTCAAGAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.36
Consensus pattern (23 bp):
GTAAAAAAAAAAGGATTATTTTC
Found at i:18340 original size:22 final size:22
Alignment explanation
Indices: 18231--18340 Score: 125
Period size: 22 Copynumber: 5.0 Consensus size: 22
18221 CTTGTTTCTA
18231 TGTGGTTATCAAAATTTCATAAG
1 TGTGGTTATCAAAATTTCAT-AG
* *
18254 T-TGGTTATTATAATTTCATGAG
1 TGTGGTTATCAAAATTTCAT-AG
* *
18276 -GAGGTTATCAAAATTCCATAG
1 TGTGGTTATCAAAATTTCATAG
*
18297 TGTGGTTACCAAAATTTCATAG
1 TGTGGTTATCAAAATTTCATAG
* *
18319 TGTGGTTACCATAATTTCATAG
1 TGTGGTTATCAAAATTTCATAG
18341 GATCAGGTTA
Statistics
Matches: 74, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
21 2 0.03
22 71 0.96
23 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (22 bp):
TGTGGTTATCAAAATTTCATAG
Found at i:18392 original size:22 final size:22
Alignment explanation
Indices: 18233--18394 Score: 114
Period size: 22 Copynumber: 7.3 Consensus size: 22
18223 TGTTTCTATG
* * *
18233 TGGTTATCAAAATTTCATAAGT
1 TGGTTATTAAAATTTCATAGGA
*
18255 TGGTTATTATAATTTCATGAGGA
1 TGGTTATTAAAATTTCAT-AGGA
* *
18278 -GGTTATCAAAATTCCATAGTG-
1 TGGTTATTAAAATTTCATAG-GA
**
18299 TGGTTACCAAAATTTCATAGTG-
1 TGGTTATTAAAATTTCATAG-GA
** *
18321 TGGTTACCATAATTTCATAGGA
1 TGGTTATTAAAATTTCATAGGA
* * *
18343 TCAGGTTATTAAAATCTCTTAGGT
1 T--GGTTATTAAAATTTCATAGGA
* *
18367 TGGTTATTGAAATTTCATAGAA
1 TGGTTATTAAAATTTCATAGGA
18389 TGGTTA
1 TGGTTA
18395 ATTATCACAA
Statistics
Matches: 113, Mismatches: 21, Indels: 12
0.77 0.14 0.08
Matches are distributed among these distances:
21 3 0.03
22 92 0.81
23 2 0.02
24 16 0.14
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.40
Consensus pattern (22 bp):
TGGTTATTAAAATTTCATAGGA
Found at i:18555 original size:22 final size:22
Alignment explanation
Indices: 18494--18559 Score: 55
Period size: 22 Copynumber: 3.0 Consensus size: 22
18484 TTCATTAAAT
* * *
18494 ATTTCATGGGGAGGTTATCAAA
1 ATTTCATAGTGAGATTATCAAA
* * *
18516 ATTTTATAGTGTGGTTATCAAA
1 ATTTCATAGTGAGATTATCAAA
18538 ATTTCATA-TGAAGATTAT-AAA
1 ATTTCATAGTG-AGATTATCAAA
18559 A
1 A
18560 GTCTCAATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
21 6 0.17
22 30 0.83
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (22 bp):
ATTTCATAGTGAGATTATCAAA
Found at i:18623 original size:21 final size:22
Alignment explanation
Indices: 18599--18834 Score: 105
Period size: 22 Copynumber: 10.7 Consensus size: 22
18589 TGATGGAAGG
*
18599 TTATC-AAATCTCATAGAGTGA
1 TTATCAAAATTTCATAGAGTGA
*
18620 TTAT-AGAATTTCATAGAGATCTGA
1 TTATCAAAATTTCATAGAG---TGA
* **
18644 TTATCGAAATTT-ATAGAAAGA
1 TTATCAAAATTTCATAGAGTGA
*
18665 TTATCAAAATTTCATAGTGTTG-
1 TTATCAAAATTTCATAGAG-TGA
* *
18687 TTTTCAAAATTTCAAAGCAAG-G-
1 TTATCAAAATTTCATAG--AGTGA
*
18709 TTATCAAAATTACATA-ATGTGA
1 TTATCAAAATTTCATAGA-GTGA
* *
18731 TTATCATAATTTCATAGAAG-GG
1 TTATCAAAATTTCATAG-AGTGA
* * * * * *
18753 TCAACAAAATTTTATAAAGAGG
1 TTATCAAAATTTCATAGAGTGA
* * *
18775 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGAGTGA
* * *
18797 TTATTAAATTTTCA-AAATGTGA
1 TTATCAAAATTTCATAGA-GTGA
18819 TTA-CAAAATTTTCATA
1 TTATCAAAA-TTTCATA
18835 ATGGTATTTC
Statistics
Matches: 164, Mismatches: 33, Indels: 34
0.71 0.14 0.15
Matches are distributed among these distances:
19 1 0.01
20 1 0.01
21 37 0.23
22 103 0.63
23 3 0.02
24 14 0.09
25 5 0.03
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGAGTGA
Found at i:18798 original size:22 final size:22
Alignment explanation
Indices: 18644--18835 Score: 110
Period size: 22 Copynumber: 8.8 Consensus size: 22
18634 AGAGATCTGA
* *
18644 TTATCGAAATTT-ATAGAA-AGA
1 TTATCAAAATTTCATA-AAGAGG
** **
18665 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAAAGAGG
*
18687 TTTTCAAAATTTC--AAAGCAAGG
1 TTATCAAAATTTCATAAAG--AGG
* * * *
18709 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAAAGAGG
*
18731 TTATCATAATTTCATAGAAG-GG
1 TTATCAAAATTTCATA-AAGAGG
* * *
18753 TCAACAAAATTTTATAAAGAGG
1 TTATCAAAATTTCATAAAGAGG
18775 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAAAGAGG
* * * *
18797 TTATTAAATTTTCA-AAATGTGA
1 TTATCAAAATTTCATAAA-GAGG
18819 TTA-CAAAATTTTCATAA
1 TTATCAAAA-TTTCATAA
18836 TGGTATTTCT
Statistics
Matches: 127, Mismatches: 33, Indels: 20
0.71 0.18 0.11
Matches are distributed among these distances:
20 2 0.02
21 20 0.16
22 98 0.77
23 4 0.03
24 3 0.02
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAAAGAGG
Found at i:18982 original size:22 final size:22
Alignment explanation
Indices: 18954--19034 Score: 92
Period size: 22 Copynumber: 3.7 Consensus size: 22
18944 TCAGGGATGA
18954 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
18976 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
18998 TTTCAAAATTTCAGAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
19020 TATCAAAATTTCATA
1 TATCAAAATTTCATA
19035 GTATGTAGAT
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
22 45 0.96
23 2 0.04
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:19048 original size:44 final size:42
Alignment explanation
Indices: 18916--19051 Score: 129
Period size: 44 Copynumber: 3.2 Consensus size: 42
18906 TTATGGAGCA
* * * *
18916 ATCAAAATTTCAAAGAGGATATCAAAA-TTCA-GGGATG-AT
1 ATCAAAATTTCAAAGAGGTTATCAAAATTTCATAGTATGTAG
*
18955 ATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGT-T-TAG
1 ATCAAAATTTCA-AAG-AGGTTATCAAAATTTCATAGTATGTAG
*
18997 TTTTCAAAATTTCAGAAGAGGGTTATCAAAATTTCATAGTATGTAG
1 --ATCAAAATTTCA-AAGA-GGTTATCAAAATTTCATAGTATGTAG
19043 ATCAAAATT
1 ATCAAAATT
19052 GGGTTATCAC
Statistics
Matches: 78, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
39 12 0.15
40 2 0.03
41 11 0.14
42 6 0.08
43 2 0.03
44 41 0.53
45 1 0.01
46 3 0.04
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.34
Consensus pattern (42 bp):
ATCAAAATTTCAAAGAGGTTATCAAAATTTCATAGTATGTAG
Found at i:19395 original size:21 final size:21
Alignment explanation
Indices: 19371--19415 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
19361 TAAGAGGAAC
**
19371 TAATAAAGCACTGCAAAGTAT
1 TAATAAAGCAAGGCAAAGTAT
*
19392 TAATAAAGTAAGGCAAAGTAT
1 TAATAAAGCAAGGCAAAGTAT
19413 TAA
1 TAA
19416 CCCTAATTGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.51, C:0.09, G:0.16, T:0.24
Consensus pattern (21 bp):
TAATAAAGCAAGGCAAAGTAT
Found at i:38892 original size:30 final size:30
Alignment explanation
Indices: 38857--38933 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 30
38847 TAAAGCCTCT
38857 TTTTACCCCTAAACTTGTTTAAAATT-GATC
1 TTTTACCCCTAAACTTGTTT-AAATTAGATC
*
38887 TTTTACCCCCTAAA--T-TTTAAATTGAGATT
1 TTTTA-CCCCTAAACTTGTTTAAATT-AGATC
38916 TTTTACCCTCTAAACTTG
1 TTTTACCC-CTAAACTTG
38934 CAATATGAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
27 5 0.13
28 6 0.15
29 14 0.36
30 5 0.13
31 9 0.23
ACGTcount: A:0.29, C:0.21, G:0.06, T:0.44
Consensus pattern (30 bp):
TTTTACCCCTAAACTTGTTTAAATTAGATC
Found at i:42994 original size:81 final size:80
Alignment explanation
Indices: 42889--43129 Score: 365
Period size: 81 Copynumber: 3.0 Consensus size: 80
42879 CTCTTCTTTT
*
42889 GACGAAGTTTCTTCATAGGCAATAACATCTTGGGATAAGCTTTTTGGGGGCGCCTCGAGCAATTT
1 GACGAAGTTTCGTCATAGGCAATAACATCTTGGGATAAGCTTTTTGGGGG-GCCTCGAGCAATTT
*
42954 TTGGTCTTGATTATTC
65 TTGGTCTTGATTATTA
* * ** *
42970 GACGAAGTTTCGTCATGGGCAATAACACCTTGGGATAAGCGGTTTGGAGGGGCCTCAAGCAATTT
1 GACGAAGTTTCGTCATAGGCAATAACATCTTGGGATAAGCTTTTTGG-GGGGCCTCGAGCAATTT
43035 TTGGTCTTGATTATTA
65 TTGGTCTTGATTATTA
* *
43051 GACGAAGTTTCGTCGTAGGCAATAACATCTTGGGATAAGCTCTTTTGGGGGGCCTCGAGCAGTTT
1 GACGAAGTTTCGTCATAGGCAATAACATCTTGGGATAAGCT-TTTTGGGGGGCCTCGAGCAATTT
*
43116 TTGGTCATGATTAT
65 TTGGTCTTGATTAT
43130 GATTAGGCTT
Statistics
Matches: 143, Mismatches: 15, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
81 135 0.94
82 8 0.06
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (80 bp):
GACGAAGTTTCGTCATAGGCAATAACATCTTGGGATAAGCTTTTTGGGGGGCCTCGAGCAATTTT
TGGTCTTGATTATTA
Found at i:50243 original size:40 final size:40
Alignment explanation
Indices: 50188--50264 Score: 154
Period size: 40 Copynumber: 1.9 Consensus size: 40
50178 TTACTTGATT
50188 TTGAGGAAGGTTGCCCTCTGAACCAAAAAGCCAGAAGATA
1 TTGAGGAAGGTTGCCCTCTGAACCAAAAAGCCAGAAGATA
50228 TTGAGGAAGGTTGCCCTCTGAACCAAAAAGCCAGAAG
1 TTGAGGAAGGTTGCCCTCTGAACCAAAAAGCCAGAAG
50265 TTCTGCTCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.36, C:0.21, G:0.26, T:0.17
Consensus pattern (40 bp):
TTGAGGAAGGTTGCCCTCTGAACCAAAAAGCCAGAAGATA
Found at i:67793 original size:2 final size:2
Alignment explanation
Indices: 67786--67823 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
67776 TATTATTGCA
67786 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
67824 TAGATTATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:69969 original size:17 final size:17
Alignment explanation
Indices: 69957--70005 Score: 80
Period size: 17 Copynumber: 2.9 Consensus size: 17
69947 CTAGTGATCT
69957 AAGATCACCAGTGATAC
1 AAGATCACCAGTGATAC
*
69974 AAGATCACCAGTGATGC
1 AAGATCACCAGTGATAC
*
69991 AAGATCACCGGTGAT
1 AAGATCACCAGTGAT
70006 CAAAGAATAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.18
Consensus pattern (17 bp):
AAGATCACCAGTGATAC
Found at i:70011 original size:17 final size:17
Alignment explanation
Indices: 69949--70011 Score: 76
Period size: 17 Copynumber: 3.7 Consensus size: 17
69939 CTAGATTACT
*
69949 AGTGATCTAAGATCACC
1 AGTGATCAAAGATCACC
69966 AGTGAT-ACAAGATCACC
1 AGTGATCA-AAGATCACC
69983 AGTGATGC-AAGATCACC
1 AGTGAT-CAAAGATCACC
*
70000 GGTGATCAAAGA
1 AGTGATCAAAGA
70012 ATACTTGGGT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
16 1 0.03
17 39 0.98
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.19
Consensus pattern (17 bp):
AGTGATCAAAGATCACC
Found at i:85277 original size:33 final size:33
Alignment explanation
Indices: 85228--85410 Score: 154
Period size: 33 Copynumber: 5.8 Consensus size: 33
85218 TGGCCAAGGG
* *
85228 TGCGGTGGATGAGGAGGATGAGGAGGGAATGGA
1 TGCGGCGGGTGAGGAGGATGAGGAGGGAATGGA
* * *
85261 TGCGGCGGGTGTGGAGGATGGGGAGGAAATGG-
1 TGCGGCGGGTGAGGAGGATGAGGAGGGAATGGA
* * * * *
85293 TTCTGGTGGGTAAGGAGGATGAGGAGGAAATGGC
1 TGC-GGCGGGTGAGGAGGATGAGGAGGGAATGGA
*
85327 TGTGGCGGGT---GA-G--GAGGA---AATGG-
1 TGCGGCGGGTGAGGAGGATGAGGAGGGAATGGA
* *
85350 TTCTGGTGGGTGAGGAGGATGAGGAGGGAATGGA
1 TGC-GGCGGGTGAGGAGGATGAGGAGGGAATGGA
85384 TGCGGCGGGTGAGGAGGATGAGGAGGG
1 TGCGGCGGGTGAGGAGGATGAGGAGGG
85411 CGAGGCGGGT
Statistics
Matches: 119, Mismatches: 18, Indels: 26
0.73 0.11 0.16
Matches are distributed among these distances:
23 1 0.01
24 11 0.09
27 7 0.06
28 1 0.01
29 1 0.01
30 7 0.06
32 2 0.02
33 86 0.72
34 3 0.03
ACGTcount: A:0.23, C:0.05, G:0.55, T:0.17
Consensus pattern (33 bp):
TGCGGCGGGTGAGGAGGATGAGGAGGGAATGGA
Found at i:85343 original size:57 final size:57
Alignment explanation
Indices: 85282--85401 Score: 204
Period size: 57 Copynumber: 2.1 Consensus size: 57
85272 TGGAGGATGG
* *
85282 GGAGGAAATGGTTCTGGTGGGTAAGGAGGATGAGGAGGAAATGGCTGTGGCGGGTGA
1 GGAGGAAATGGTTCTGGTGGGTAAGGAGGATGAGGAGGAAATGGATGCGGCGGGTGA
* *
85339 GGAGGAAATGGTTCTGGTGGGTGAGGAGGATGAGGAGGGAATGGATGCGGCGGGTGA
1 GGAGGAAATGGTTCTGGTGGGTAAGGAGGATGAGGAGGAAATGGATGCGGCGGGTGA
85396 GGAGGA
1 GGAGGA
85402 TGAGGAGGGC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.24, C:0.05, G:0.53, T:0.17
Consensus pattern (57 bp):
GGAGGAAATGGTTCTGGTGGGTAAGGAGGATGAGGAGGAAATGGATGCGGCGGGTGA
Found at i:85344 original size:24 final size:24
Alignment explanation
Indices: 85312--85368 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
85302 GTAAGGAGGA
*
85312 TGAGGAGGAAATGGCTGTGGCGGG
1 TGAGGAGGAAATGGCTCTGGCGGG
* *
85336 TGAGGAGGAAATGGTTCTGGTGGG
1 TGAGGAGGAAATGGCTCTGGCGGG
85360 TGAGGAGGA
1 TGAGGAGGA
85369 TGAGGAGGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.23, C:0.05, G:0.53, T:0.19
Consensus pattern (24 bp):
TGAGGAGGAAATGGCTCTGGCGGG
Found at i:85415 original size:18 final size:17
Alignment explanation
Indices: 85361--85427 Score: 50
Period size: 18 Copynumber: 3.9 Consensus size: 17
85351 TCTGGTGGGT
85361 GAGGAGGATGAGGA-GG
1 GAGGAGGATGAGGAGGG
* *
85377 GA--ATGGATGCGGCGGG
1 GAGGA-GGATGAGGAGGG
85393 TGAGGAGGATGAGGAGGG
1 -GAGGAGGATGAGGAGGG
* *
85411 CGAGGCGGGTGAGGAGG
1 -GAGGAGGATGAGGAGG
85428 CCATGGCGGT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
14 1 0.03
15 7 0.18
16 4 0.10
17 2 0.05
18 24 0.62
19 1 0.03
ACGTcount: A:0.24, C:0.06, G:0.61, T:0.09
Consensus pattern (17 bp):
GAGGAGGATGAGGAGGG
Done.