Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009322.1 Corchorus capsularis cultivar CVL-1 contig09343, 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: 54297
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:7526 original size:14 final size:14
Alignment explanation
Indices: 7507--7539 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
7497 AATAAGAAGA
7507 TTATACAGGAATAT
1 TTATACAGGAATAT
7521 TTATACAGGAATAT
1 TTATACAGGAATAT
7535 TTATA
1 TTATA
7540 AGAAGAAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.39
Consensus pattern (14 bp):
TTATACAGGAATAT
Found at i:9735 original size:33 final size:33
Alignment explanation
Indices: 9698--9767 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
9688 TTCTGTTTTC
* *
9698 AAAAATTTTGGAAACGGAATCAGGGTTTTGGAA
1 AAAAATTTTGGAAACAGAATCAAGGTTTTGGAA
9731 AAAAATTTTGGAAACAGAATCAAGGTTTTGGAA
1 AAAAATTTTGGAAACAGAATCAAGGTTTTGGAA
9764 AAAA
1 AAAA
9768 GTGGAAGTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.46, C:0.06, G:0.23, T:0.26
Consensus pattern (33 bp):
AAAAATTTTGGAAACAGAATCAAGGTTTTGGAA
Found at i:11468 original size:109 final size:109
Alignment explanation
Indices: 11336--11718 Score: 664
Period size: 109 Copynumber: 3.5 Consensus size: 109
11326 AAAAAAATCA
11336 TATAAA-ATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
1 TATAAAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
11399 AAAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
65 AAAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
11444 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
1 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
11509 AAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
66 AAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
11553 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG-
1 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
*
11617 AAAAATTTTAGTATATCCAAATTTTTTGGTAAAAATAAAGTAAT
66 AAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
* *
11661 TATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTAGTAGAATAAAA
1 TATAAAGATATTAGATTTAA-TT-A---AATGAAAATAGAGTTTTTAGTAGAATAAAA
11719 CTATAATAGT
Statistics
Matches: 265, Mismatches: 3, Indels: 9
0.96 0.01 0.03
Matches are distributed among these distances:
108 69 0.26
109 166 0.63
110 2 0.01
113 28 0.11
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (109 bp):
TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
AAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
Found at i:11833 original size:13 final size:13
Alignment explanation
Indices: 11815--11839 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11805 ACTTTTATAT
11815 ATAGTATAGATAG
1 ATAGTATAGATAG
11828 ATAGTATAGATA
1 ATAGTATAGATA
11840 TATATGATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (13 bp):
ATAGTATAGATAG
Found at i:23770 original size:26 final size:26
Alignment explanation
Indices: 23740--23792 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
23730 AAAGTGGAAG
23740 CAAGAATAAAGAGAATGAAAAATAGT
1 CAAGAATAAAGAGAATGAAAAATAGT
23766 CAAGAATAAAGAGAATGAAAAATAGT
1 CAAGAATAAAGAGAATGAAAAATAGT
23792 C
1 C
23793 CAACCAGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.60, C:0.06, G:0.19, T:0.15
Consensus pattern (26 bp):
CAAGAATAAAGAGAATGAAAAATAGT
Found at i:26299 original size:13 final size:13
Alignment explanation
Indices: 26281--26306 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
26271 GTTAACCGAA
26281 GAAGAACTAACAG
1 GAAGAACTAACAG
26294 GAAGAACTAACAG
1 GAAGAACTAACAG
26307 ATAGTAACCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.23, T:0.08
Consensus pattern (13 bp):
GAAGAACTAACAG
Found at i:27510 original size:17 final size:17
Alignment explanation
Indices: 27487--27536 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
27477 TCAAAATATT
27487 TGTTTCAATTAAGTCT-
1 TGTTTCAATTAAGTCTC
*
27503 TGGTTTCAACTTAA-TATC
1 T-GTTTCAA-TTAAGTCTC
27521 TGTTTCAATTAAGTCT
1 TGTTTCAATTAAGTCT
27537 GGATTTTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
16 5 0.18
17 18 0.64
18 5 0.18
ACGTcount: A:0.26, C:0.14, G:0.12, T:0.48
Consensus pattern (17 bp):
TGTTTCAATTAAGTCTC
Found at i:28376 original size:78 final size:78
Alignment explanation
Indices: 28263--28417 Score: 274
Period size: 78 Copynumber: 2.0 Consensus size: 78
28253 ATTTTATTGA
* * *
28263 ATGATTTATAATTTTTTTTCAAAATCCTATGGCGTATAAAAATTTAAGATTTATCCTTTTACAAA
1 ATGATTTATAATTTTTTTTCAAAACCCTATAGCGTATAAAAATTTAAGATTTATCCTTTTAAAAA
28328 ATAAAACAATTTT
66 ATAAAACAATTTT
*
28341 ATGATTTATAATTTTTTTTCAAAACCCTATAGCGTATAAAAATTTTAGATTTATCCTTTTAAAAA
1 ATGATTTATAATTTTTTTTCAAAACCCTATAGCGTATAAAAATTTAAGATTTATCCTTTTAAAAA
28406 ATAAAACAATTT
66 ATAAAACAATTT
28418 AATAATTGAG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 73 1.00
ACGTcount: A:0.41, C:0.10, G:0.06, T:0.43
Consensus pattern (78 bp):
ATGATTTATAATTTTTTTTCAAAACCCTATAGCGTATAAAAATTTAAGATTTATCCTTTTAAAAA
ATAAAACAATTTT
Found at i:30822 original size:27 final size:27
Alignment explanation
Indices: 30786--30847 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
30776 CCGGACAAAT
*
30786 AGATGCATTAGTAAT-TAAAGAGATTAG
1 AGATGTATTAGT-ATCTAAAGAGATTAG
* *
30813 AGATGTATTAGTATCTAAGGAGATTGG
1 AGATGTATTAGTATCTAAAGAGATTAG
30840 AGATGTAT
1 AGATGTAT
30848 GGTATCCCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
26 2 0.06
27 29 0.94
ACGTcount: A:0.39, C:0.03, G:0.26, T:0.32
Consensus pattern (27 bp):
AGATGTATTAGTATCTAAAGAGATTAG
Found at i:32053 original size:31 final size:32
Alignment explanation
Indices: 32010--32076 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 32
32000 ACTATTGTCT
*
32010 CTCTGTTTTTTTTTGGTAAAACACGTCAGCTA
1 CTCTGTTTTTTTTTGGTAAAACACGTCAACTA
** *
32042 CTCT-TTTTTTTTTTTTTAAACACGTCAACTA
1 CTCTGTTTTTTTTTGGTAAAACACGTCAACTA
32073 CTCT
1 CTCT
32077 CTACATAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 27 0.87
32 4 0.13
ACGTcount: A:0.21, C:0.21, G:0.09, T:0.49
Consensus pattern (32 bp):
CTCTGTTTTTTTTTGGTAAAACACGTCAACTA
Found at i:33490 original size:23 final size:23
Alignment explanation
Indices: 33460--33504 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
33450 TTCCTCCCAA
33460 TTTTTTTTTT-AATCTAATCTAG
1 TTTTTTTTTTAAATCTAATCTAG
33482 TTTTTTTTTTAAATCTAATCTAG
1 TTTTTTTTTTAAATCTAATCTAG
33505 GGATTTTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.24, C:0.09, G:0.04, T:0.62
Consensus pattern (23 bp):
TTTTTTTTTTAAATCTAATCTAG
Found at i:33511 original size:23 final size:23
Alignment explanation
Indices: 33462--33512 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
33452 CCTCCCAATT
* ***
33462 TTTTTTTTAATCTAATCTAGTTT
1 TTTTTTTAAATCTAATCTAGGGA
33485 TTTTTTTAAATCTAATCTAGGGA
1 TTTTTTTAAATCTAATCTAGGGA
33508 TTTTT
1 TTTTT
33513 GTTTTTAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.61
Consensus pattern (23 bp):
TTTTTTTAAATCTAATCTAGGGA
Found at i:34964 original size:14 final size:14
Alignment explanation
Indices: 34945--34977 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
34935 TTTTTGGGCC
34945 GAATTATATAGTTA
1 GAATTATATAGTTA
34959 GAATTATATAGTTA
1 GAATTATATAGTTA
34973 GAATT
1 GAATT
34978 TAGAAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (14 bp):
GAATTATATAGTTA
Found at i:35019 original size:5 final size:5
Alignment explanation
Indices: 35011--35035 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
35001 TATATATAAT
35011 ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA
35036 TCTAATCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:35046 original size:17 final size:16
Alignment explanation
Indices: 35000--35047 Score: 55
Period size: 15 Copynumber: 3.0 Consensus size: 16
34990 TTACTTGAGG
35000 ATATATATAATATATA
1 ATATATATAATATATA
35016 ATATA-AT-ATAATATA
1 ATATATATAAT-ATATA
*
35031 ATATATCTAATCATATA
1 ATATATATAAT-ATATA
35048 TATTGTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 2 0.07
15 12 0.44
16 6 0.22
17 7 0.26
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATATATAATATATA
Found at i:35269 original size:18 final size:18
Alignment explanation
Indices: 35246--35280 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
35236 CTATCAAGCA
35246 AATCGACGATTTGATCCC
1 AATCGACGATTTGATCCC
35264 AATCGACGATTTGATCC
1 AATCGACGATTTGATCC
35281 AAGAGGTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (18 bp):
AATCGACGATTTGATCCC
Found at i:38671 original size:44 final size:44
Alignment explanation
Indices: 38608--38698 Score: 173
Period size: 44 Copynumber: 2.1 Consensus size: 44
38598 AACAACTCGT
38608 TTGATTATTTCTTCCCCAACCCTTGCCTTTCCAGATTACTAGCG
1 TTGATTATTTCTTCCCCAACCCTTGCCTTTCCAGATTACTAGCG
*
38652 TTGATTATTTCTTCCCCAACCCTTGCCTTTCCAGATTACTAGGG
1 TTGATTATTTCTTCCCCAACCCTTGCCTTTCCAGATTACTAGCG
38696 TTG
1 TTG
38699 CTGCCCGCCC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.18, C:0.30, G:0.13, T:0.40
Consensus pattern (44 bp):
TTGATTATTTCTTCCCCAACCCTTGCCTTTCCAGATTACTAGCG
Found at i:41948 original size:25 final size:25
Alignment explanation
Indices: 41920--41968 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
41910 TCATTTTAGT
41920 CAGGAACCCAATTACACAGGCAAAG
1 CAGGAACCCAATTACACAGGCAAAG
* * *
41945 CAGGAATCTAATTACATAGGCAAA
1 CAGGAACCCAATTACACAGGCAAA
41969 CCAAAACAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.45, C:0.22, G:0.18, T:0.14
Consensus pattern (25 bp):
CAGGAACCCAATTACACAGGCAAAG
Found at i:45274 original size:14 final size:14
Alignment explanation
Indices: 45255--45281 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
45245 GAGATTGGTG
45255 ATGGGGAGATTAGA
1 ATGGGGAGATTAGA
45269 ATGGGGAGATTAG
1 ATGGGGAGATTAG
45282 TTACTGTACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.44, T:0.22
Consensus pattern (14 bp):
ATGGGGAGATTAGA
Done.