Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015224.1 Corchorus capsularis cultivar CVL-1 contig15245, 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: 51980
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:1394 original size:17 final size:17
Alignment explanation
Indices: 1369--1403 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1359 TGCATAATGT
1369 TAATATGCCAACAAGAA
1 TAATATGCCAACAAGAA
* *
1386 TAATGTGCCACCAAGAA
1 TAATATGCCAACAAGAA
1403 T
1 T
1404 GCACTTTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.20, G:0.14, T:0.20
Consensus pattern (17 bp):
TAATATGCCAACAAGAA
Found at i:1743 original size:23 final size:23
Alignment explanation
Indices: 1716--1762 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1706 TGGAACACAA
1716 ACACAATTTAGAACTCTATTTGG
1 ACACAATTTAGAACTCTATTTGG
1739 ACACAATTTAGAACTCTATTTGG
1 ACACAATTTAGAACTCTATTTGG
1762 A
1 A
1763 AAGATGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (23 bp):
ACACAATTTAGAACTCTATTTGG
Found at i:2263 original size:27 final size:27
Alignment explanation
Indices: 2233--2403 Score: 270
Period size: 27 Copynumber: 6.3 Consensus size: 27
2223 CCACCATAGG
* *
2233 CGAAGTGGGAGGATCCACTGCTTGGAT
1 CGAAGTGGGAGGATCCACTGCTGGGGT
*
2260 CGAAGTGGGAGGATCCACTGCTGGTGT
1 CGAAGTGGGAGGATCCACTGCTGGGGT
*
2287 CGAAGTAGGAGGATCCACTGCTGGGGT
1 CGAAGTGGGAGGATCCACTGCTGGGGT
2314 CGAAGTGGGAGGATCCACTGCTGGGGT
1 CGAAGTGGGAGGATCCACTGCTGGGGT
* *
2341 CGAAGTGGGAGGATCGAATGCTGGGGT
1 CGAAGTGGGAGGATCCACTGCTGGGGT
* *
2368 CGAAGTGGGAGAATCCACTTCTGGGGT
1 CGAAGTGGGAGGATCCACTGCTGGGGT
2395 CGAAGTGGG
1 CGAAGTGGG
2404 GAGAGAAGAC
Statistics
Matches: 132, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 132 1.00
ACGTcount: A:0.21, C:0.17, G:0.42, T:0.20
Consensus pattern (27 bp):
CGAAGTGGGAGGATCCACTGCTGGGGT
Found at i:4609 original size:6 final size:6
Alignment explanation
Indices: 4591--4648 Score: 55
Period size: 6 Copynumber: 9.8 Consensus size: 6
4581 GAACTCACGG
* * * * *
4591 AAGGAA AAAGAA AAGG-A AATGAA AAGTAA AATGAA AAGTAA AAGGAA
1 AAGGAA AAGGAA AAGGAA AAGGAA AAGGAA AAGGAA AAGGAA AAGGAA
*
4638 AACGAA AAGGA
1 AAGGAA AAGGA
4649 CTTACTGTTG
Statistics
Matches: 39, Mismatches: 12, Indels: 2
0.74 0.23 0.04
Matches are distributed among these distances:
5 4 0.10
6 35 0.90
ACGTcount: A:0.67, C:0.02, G:0.24, T:0.07
Consensus pattern (6 bp):
AAGGAA
Found at i:5411 original size:207 final size:203
Alignment explanation
Indices: 4987--5412 Score: 624
Period size: 203 Copynumber: 2.1 Consensus size: 203
4977 ATTTAAGTTT
* *
4987 CCAAATAGCGGCATCTAGCTTAATGAGACCCCGCCAAATAGTGGCGTTTAAAATGTCAGACGCCG
1 CCAAATAGCGGCGTCTAGCTTAATGAGACCCCGCCAAATAGTGGCGTTTAAAATGTCAGACACCG
* ** *
5052 CTATTTGATAAATCAATTTTGAACTAGGGGCCCGGTTGGGGCGAAGTCGGCGCCCAGTCAGGACA
66 CTATTTGAGAAATCAAAGTCGAACTAGGGGCCCGGTTGGGGCGAAGTCGGCGCCCAGTCAGGACA
* * *
5117 GTGACTTCGCCTTGATTTAAGTATCCAACCGGGCTCCCAGGTGAGGGGTAATTGGAGTCCCAAAT
131 GTGACTTCGCCCTGATTTAAGTATCCAACCGGGCTCCCAGCTGAGGGGTAACTGGAGTCCCAAAT
5182 GGACTTCA
196 GGACTTCA
* * * *
5190 CCAAATAACGGCGTCTAGCTTATTGAGACGCCGCTAAATAGTGGCGTTT-AAATCGTCAGACACC
1 CCAAATAGCGGCGTCTAGCTTAATGAGACCCCGCCAAATAGTGGCGTTTAAAAT-GTCAGACACC
* *
5254 GCTATTTGAGAATTACAAAGTCGAACT-GGGGTCCCGGTTGGAGGCGAAGTCGGCGCCCGGTCAG
65 GCTATTTGAGAAAT-CAAAGTCGAACTAGGGG-CCCGGTTGG-GGCGAAGTCGGCGCCCAGTCAG
*
5318 GACAGTGACTTCGCCCTGATTTAATGT-TCCAACCCCGGGCTCCCAGCTGAGGGGTAACTGGGGT
127 GACAGTGACTTCGCCCTGATTTAA-GTATCCAA--CCGGGCTCCCAGCTGAGGGGTAACTGGAGT
5382 CCCAAATGGACTTCA
189 CCCAAATGGACTTCA
5397 CCAAATAGCGGCGTCT
1 CCAAATAGCGGCGTCT
5413 GTTTCAGTGG
Statistics
Matches: 199, Mismatches: 17, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
202 4 0.02
203 69 0.35
204 18 0.09
205 49 0.25
206 2 0.01
207 57 0.29
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.23
Consensus pattern (203 bp):
CCAAATAGCGGCGTCTAGCTTAATGAGACCCCGCCAAATAGTGGCGTTTAAAATGTCAGACACCG
CTATTTGAGAAATCAAAGTCGAACTAGGGGCCCGGTTGGGGCGAAGTCGGCGCCCAGTCAGGACA
GTGACTTCGCCCTGATTTAAGTATCCAACCGGGCTCCCAGCTGAGGGGTAACTGGAGTCCCAAAT
GGACTTCA
Found at i:28636 original size:104 final size:104
Alignment explanation
Indices: 28401--28625 Score: 301
Period size: 105 Copynumber: 2.2 Consensus size: 104
28391 CTGTTAGAAA
* * *
28401 AGTATTAGTCGATGAAAAATTCAGTCTTAATTCCAGTATTAATCGACTAAAACTCCAAGTCTCTT
1 AGTATTAGTCGATG-AAAATTCAGTTTTAATTCCAATATTAATCGACTAAAACTCCAAGTCTCTA
* * *
28466 CTTTCAAAAATGTGGCAGTGTTGACAGCGAACCCGGAGGC
65 CTTTCAAAAATGTGACAATGTTGACAGCGAACCCGGAGCC
* * *
28506 AGTATTAGTTGATGAAAATTCCAGTTTTAATTTCAATATTAATCGACTAAAGCTCCAAGTCT-TC
1 AGTATTAGTCGATGAAAATT-CAGTTTTAATTCCAATATTAATCGACTAAAACTCCAAGTCTCT-
* *
28570 ACTTTGAAAAA-GTGACAATGTTGACAGTGAACCCGGAGCC
64 ACTTTCAAAAATGTGACAATGTTGACAGCGAACCCGGAGCC
*
28610 AGTATTAATCGATGAA
1 AGTATTAGTCGATGAA
28626 TACTTAAGTT
Statistics
Matches: 105, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
104 46 0.44
105 59 0.56
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (104 bp):
AGTATTAGTCGATGAAAATTCAGTTTTAATTCCAATATTAATCGACTAAAACTCCAAGTCTCTAC
TTTCAAAAATGTGACAATGTTGACAGCGAACCCGGAGCC
Found at i:31948 original size:61 final size:61
Alignment explanation
Indices: 31853--31967 Score: 185
Period size: 61 Copynumber: 1.9 Consensus size: 61
31843 AACACATAAC
* * *
31853 CTTGCACTTCACACAAACAAATTCGCCTAAGGTAAGGCAAATGACTTTTTCCCATTTCCCA
1 CTTGCACTTAACACAAACAAATTCACCTAAGGTAAGGCAAATGACCTTTTCCCATTTCCCA
* *
31914 CTTGCACTTAACACAAACACATTCACCTAAGGTAAGGCAAATTACCTTTTCCCA
1 CTTGCACTTAACACAAACAAATTCACCTAAGGTAAGGCAAATGACCTTTTCCCA
31968 CTGTCTTTCC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.33, C:0.30, G:0.10, T:0.27
Consensus pattern (61 bp):
CTTGCACTTAACACAAACAAATTCACCTAAGGTAAGGCAAATGACCTTTTCCCATTTCCCA
Found at i:40485 original size:19 final size:18
Alignment explanation
Indices: 40461--40499 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
40451 TAGAAATTAT
40461 ATTGAAATATAAATTTAAA
1 ATTGAAATATAAA-TTAAA
*
40480 ATTGAAATATACATTAAA
1 ATTGAAATATAAATTAAA
40498 AT
1 AT
40500 ATATAAATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (18 bp):
ATTGAAATATAAATTAAA
Found at i:41760 original size:30 final size:29
Alignment explanation
Indices: 41702--41768 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 29
41692 TTTTGAGGAT
41702 GATTTTGACCGGATGAGAATCCCGAAGAA
1 GATTTTGACCGGATGAGAATCCCGAAGAA
* * * *
41731 GATTTTGACCCGGGTTAGGATCTCGAAGAA
1 GATTTTGA-CCGGATGAGAATCCCGAAGAA
*
41761 GAGTTTGA
1 GATTTTGA
41769 GGAGTCAGAC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 8 0.25
30 24 0.75
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.25
Consensus pattern (29 bp):
GATTTTGACCGGATGAGAATCCCGAAGAA
Found at i:50808 original size:26 final size:27
Alignment explanation
Indices: 50776--50849 Score: 87
Period size: 26 Copynumber: 2.8 Consensus size: 27
50766 TAGGGTCACC
50776 CAGGGGCATTTTGGTCATTTTTACATT
1 CAGGGGCATTTTGGTCATTTTTACATT
* ** *
50803 CA-GGGCATTTTTGTCATTCCTGCATT
1 CAGGGGCATTTTGGTCATTTTTACATT
* *
50829 TAGGGGCATATTGGTCATTTT
1 CAGGGGCATTTTGGTCATTTT
50850 GAGTCCACTT
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
26 21 0.57
27 16 0.43
ACGTcount: A:0.18, C:0.16, G:0.23, T:0.43
Consensus pattern (27 bp):
CAGGGGCATTTTGGTCATTTTTACATT
Found at i:51061 original size:21 final size:21
Alignment explanation
Indices: 51035--51079 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
51025 GATTAAGGGG
*
51035 TTTGCTAAACACCGTCCCCCT
1 TTTGCTAAACACCGCCCCCCT
*
51056 TTTGCTAAATACCGCCCCCCT
1 TTTGCTAAACACCGCCCCCCT
51077 TTT
1 TTT
51080 TATAATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.18, C:0.40, G:0.09, T:0.33
Consensus pattern (21 bp):
TTTGCTAAACACCGCCCCCCT
Found at i:51334 original size:11 final size:12
Alignment explanation
Indices: 51306--51332 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
51296 TTAAAAAAAA
51306 TTTTAAAATTTT
1 TTTTAAAATTTT
51318 TTTTAAAATTTT
1 TTTTAAAATTTT
51330 TTT
1 TTT
51333 AATATTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTTAAAATTTT
Found at i:51407 original size:15 final size:15
Alignment explanation
Indices: 51383--51454 Score: 54
Period size: 11 Copynumber: 5.4 Consensus size: 15
51373 AAATTACTTA
51383 GTTT-ATTAGTTTAT
1 GTTTAATTAGTTTAT
51397 GTTTAATTAG--TA-
1 GTTTAATTAGTTTAT
*
51409 -TCTAATTAGTTTAT
1 GTTTAATTAGTTTAT
*
51423 GATTAATTAG--TA-
1 GTTTAATTAGTTTAT
51435 -TTTAATTAGTTTAT
1 GTTTAATTAGTTTAT
*
51449 GATTAA
1 GTTTAA
51455 AATGAAGGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 17
0.67 0.08 0.26
Matches are distributed among these distances:
11 16 0.36
13 8 0.18
14 4 0.09
15 16 0.36
ACGTcount: A:0.32, C:0.01, G:0.12, T:0.54
Consensus pattern (15 bp):
GTTTAATTAGTTTAT
Found at i:51416 original size:26 final size:26
Alignment explanation
Indices: 51387--51454 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
51377 TACTTAGTTT
*
51387 ATTAGTTTATGTTTAATTAGTATCTA
1 ATTAGTTTATGATTAATTAGTATCTA
*
51413 ATTAGTTTATGATTAATTAGTATTTA
1 ATTAGTTTATGATTAATTAGTATCTA
51439 ATTAGTTTATGATTAA
1 ATTAGTTTATGATTAA
51455 AATGAAGGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.34, C:0.01, G:0.12, T:0.53
Consensus pattern (26 bp):
ATTAGTTTATGATTAATTAGTATCTA
Found at i:51498 original size:24 final size:25
Alignment explanation
Indices: 51464--51522 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
51454 AAATGAAGGA
*
51464 AAATGAA-TTTGAAG-ATTTGTTAG
1 AAATGAAGTTTGAAGAAGTTGTTAG
51487 AAATGAAGTTTGAAGAAGTTGTTAG
1 AAATGAAGTTTGAAGAAGTTGTTAG
51512 AAATGAAGTTT
1 AAATGAAGTTT
51523 AGGGTTTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
23 7 0.21
24 7 0.21
25 19 0.58
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.36
Consensus pattern (25 bp):
AAATGAAGTTTGAAGAAGTTGTTAG
Found at i:51618 original size:20 final size:21
Alignment explanation
Indices: 51593--51632 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
51583 CAAAAGTGTA
51593 AAAAGGGG-GCGGTATTTAGT
1 AAAAGGGGAGCGGTATTTAGT
*
51613 AAAAGGGGAGCGGTGTTTAG
1 AAAAGGGGAGCGGTATTTAG
51633 CAATCCAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.30, C:0.05, G:0.42, T:0.23
Consensus pattern (21 bp):
AAAAGGGGAGCGGTATTTAGT
Found at i:51880 original size:29 final size:29
Alignment explanation
Indices: 51829--51886 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
51819 CATGGCTGCT
* * *
51829 AAATAAAACTTTAGGGGGTAAAATGTCCA
1 AAATAAAACTTTAAGGGGCAAAACGTCCA
* *
51858 AAATAAATCTTTAAGGTGCAAAACGTCCA
1 AAATAAAACTTTAAGGGGCAAAACGTCCA
51887 TGCATAAATG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.24
Consensus pattern (29 bp):
AAATAAAACTTTAAGGGGCAAAACGTCCA
Done.