Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010527.1 Corchorus capsularis cultivar CVL-1 contig10548, 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: 121223
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:7622 original size:22 final size:22
Alignment explanation
Indices: 7594--7642 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
7584 ATTATATATA
*
7594 AAAATCAAACTATATAAAAAAT
1 AAAATCAAACTACATAAAAAAT
** *
7616 AAAATCATCCTACATAAAATAT
1 AAAATCAAACTACATAAAAAAT
7638 AAAAT
1 AAAAT
7643 ATTACCAAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.63, C:0.12, G:0.00, T:0.24
Consensus pattern (22 bp):
AAAATCAAACTACATAAAAAAT
Found at i:7851 original size:21 final size:21
Alignment explanation
Indices: 7825--7865 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
7815 GACTAATATC
7825 TTGGCCTAATAACAATTAAAT
1 TTGGCCTAATAACAATTAAAT
* *
7846 TTGGCCTGATAATAATTAAA
1 TTGGCCTAATAACAATTAAA
7866 AGTTCATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (21 bp):
TTGGCCTAATAACAATTAAAT
Found at i:7883 original size:2 final size:2
Alignment explanation
Indices: 7871--7903 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
7861 TTAAAAGTTC
7871 AT AT A- 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
7904 TATCCTACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10851 original size:17 final size:19
Alignment explanation
Indices: 10811--10849 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
10801 CACATAAAAG
10811 ATAAAATCATTATATATAT
1 ATAAAATCATTATATATAT
*
10830 ATAAAATCTTTATATATAT
1 ATAAAATCATTATATATAT
10849 A
1 A
10850 AAGAATGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (19 bp):
ATAAAATCATTATATATAT
Found at i:26851 original size:31 final size:31
Alignment explanation
Indices: 26816--26899 Score: 168
Period size: 31 Copynumber: 2.7 Consensus size: 31
26806 GTTGGTACAT
26816 AGACTTGAATTTGCCTATGTTGGCCAAAAAA
1 AGACTTGAATTTGCCTATGTTGGCCAAAAAA
26847 AGACTTGAATTTGCCTATGTTGGCCAAAAAA
1 AGACTTGAATTTGCCTATGTTGGCCAAAAAA
26878 AGACTTGAATTTGCCTATGTTG
1 AGACTTGAATTTGCCTATGTTG
26900 CTAGTCGATA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.32
Consensus pattern (31 bp):
AGACTTGAATTTGCCTATGTTGGCCAAAAAA
Found at i:45694 original size:57 final size:57
Alignment explanation
Indices: 45606--45803 Score: 297
Period size: 57 Copynumber: 3.4 Consensus size: 57
45596 CACATTTGCC
* * *
45606 TTACCCACCCCCTGAAAGCAATTCCCAAGCCCCCTCCACTTATCAACCGCCTGCCCA
1 TTACCCTCCTCCTGAAAGCAATTCCCAAGCCCCTTCCACTTATCAACCGCCTGCCCA
45663 TTACCCTCCTCCTGAAAGCAATTCCCAAGCCCCTTCCACTTATCAACCGCCTGCCCA
1 TTACCCTCCTCCTGAAAGCAATTCCCAAGCCCCTTCCACTTATCAACCGCCTGCCCA
* * * *
45720 TTACCCTCCTCTTGAAAGCAATTCCCAGGTCCCTTCCACTTATGAACAACAGCCTGCCCA
1 TTACCCTCCTCCTGAAAGCAATTCCCAAGCCCCTTCCACTTAT---CAACCGCCTGCCCA
*
45780 TTACCCTCCTCCTGAAAGTAATTC
1 TTACCCTCCTCCTGAAAGCAATTC
45804 TCAGCTATTA
Statistics
Matches: 129, Mismatches: 9, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
57 94 0.73
60 35 0.27
ACGTcount: A:0.24, C:0.43, G:0.10, T:0.23
Consensus pattern (57 bp):
TTACCCTCCTCCTGAAAGCAATTCCCAAGCCCCTTCCACTTATCAACCGCCTGCCCA
Found at i:53421 original size:18 final size:18
Alignment explanation
Indices: 53398--53433 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
53388 GCATAACGGC
*
53398 TTGCTGCTGTTGTTGTTG
1 TTGCTGCAGTTGTTGTTG
53416 TTGCTGCAGTTGTTGTTG
1 TTGCTGCAGTTGTTGTTG
53434 AGAAGTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.03, C:0.11, G:0.33, T:0.53
Consensus pattern (18 bp):
TTGCTGCAGTTGTTGTTG
Found at i:75106 original size:1 final size:1
Alignment explanation
Indices: 75100--75130 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
75090 AAACTGTATT
75100 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
75131 CTCACATTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:86377 original size:37 final size:37
Alignment explanation
Indices: 86327--86402 Score: 127
Period size: 37 Copynumber: 2.1 Consensus size: 37
86317 CTAGTAATAA
86327 TCCACATTCAAAGATGTAGG-ATATGTTTTTACAAAAT
1 TCCACATTCAAAGATGT-GGTATATGTTTTTACAAAAT
*
86364 TCCACATTCAAAGATGTGGTGTATGTTTTTACAAAAT
1 TCCACATTCAAAGATGTGGTATATGTTTTTACAAAAT
86401 TC
1 TC
86403 TAACTTAGCT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
36 2 0.05
37 35 0.95
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.37
Consensus pattern (37 bp):
TCCACATTCAAAGATGTGGTATATGTTTTTACAAAAT
Found at i:102000 original size:393 final size:395
Alignment explanation
Indices: 101261--102456 Score: 2126
Period size: 393 Copynumber: 3.0 Consensus size: 395
101251 TTTTAATTTG
101261 TAATTTGCTGATTTTGATCTATGTATCGGAGAATAGTACATATATTATGTTCATCTTAATTCTCC
1 TAATTTGCTGATTTTGATCTATGTATCGGAGAATAGTACATATATTATGTTCATCTTAATTCTCC
101326 ATTTTTTTGTCTCTTAATTGCTTAATTAACATTACTGCATCTTGAAATGAATCTGCAAAAATCCA
66 ATTTTTTTGTCTCTTAATTGCTTAATTAACATTACTGCATCTTGAAA-GAATCTGCAAAAATCCA
*
101391 GGGCATTGATTGGGAAAATTTGAAATGTCTATGATTCTGGTGCAATGTGTCTGGTCTCATGGTGA
130 GGGCATTGATTGGGAAAATTTGAAATGTCTATGATTCTTGTGCAATGTGTCTGGTCTCATGGTGA
101456 AATAATAACCTTATTTTACTGCAAAATTTTAAAGACAGTTTGAAAGTACATTCATACACGTGGTA
195 AATAATAACCTTATTTTACTGCAAAA--TT------A-TTTGAAAGTACATTCATACACGTGGTA
101521 TAATTGATTTCCAATTTCATTGCAGTTTACTGCTTAGTGCTTTCTATATATCTAAAATAAAATTC
251 TAATTGATTTCCAATTTCATTGCAGTTTACTGCTTAGTGCTTTCTATATATCTAAAATAAAATTC
*
101586 GCATGGTTCCTTTTTATAGTTGAATTTATGGGTAGTTTTTGTAACAGTTGATCACAAAGTAGTTC
316 GCATGGTTTCTTTTTATAGTTGAATTTATGGGTAGTTTTTGTAACAGTTGATCACAAAGTAGTTC
101651 ACCTTTTCTTAATTC
381 ACCTTTTCTTAATTC
*
101666 TAATTTGCTGATTTTGATCTATGTATCGGAGAATAGTACATATATTATGTTCATCTTAAGTCTCC
1 TAATTTGCTGATTTTGATCTATGTATCGGAGAATAGTACATATATTATGTTCATCTTAATTCTCC
*
101731 ATTTTTTTGTCTCTTAATTGCTTAATTAACATTACTGCATCTTGAAAGAATCTGCAAAAATACAG
66 ATTTTTTTGTCTCTTAATTGCTTAATTAACATTACTGCATCTTGAAAGAATCTGCAAAAATCCAG
101796 GGCATTGATTGGGAAAATTTGAAATGTCTATGATTCTTGTGCAATGTGTCTGGTCTCATGGTGAA
131 GGCATTGATTGGGAAAATTTGAAATGTCTATGATTCTTGTGCAATGTGTCTGGTCTCATGGTGAA
* *
101861 ATAATAACCTTATTTTACTGCAAAA-T-TTTGAAAGTACGTTCATACACGTGGTATAATTAATTT
196 ATAATAACCTTATTTTACTGCAAAATTATTTGAAAGTACATTCATACACGTGGTATAATTGATTT
101924 CCAATTTCATTGCAGTTTACTGCTTAGTGCTTTCTATATATCTAAAATAAAATTCGCATGGTTTC
261 CCAATTTCATTGCAGTTTACTGCTTAGTGCTTTCTATATATCTAAAATAAAATTCGCATGGTTTC
* *
101989 TTTTTATAGTTGAATTTATGGGTAGTTTTTGTAACATTTGATCACAAAATAGTTCACCTTTTCTT
326 TTTTTATAGTTGAATTTATGGGTAGTTTTTGTAACAGTTGATCACAAAGTAGTTCACCTTTTCTT
102054 AATTC
391 AATTC
102059 TAATTTGCTGATTTTGATCTATGTATCGGAGAATAGTACATATATTATGTTCATCTTAATTCTCC
1 TAATTTGCTGATTTTGATCTATGTATCGGAGAATAGTACATATATTATGTTCATCTTAATTCTCC
102124 ATTTTTTTGTCTCTTAATTGCTTAATTAACATTACTGCATCTTGAAAGAATCTGCAAAAATCCAG
66 ATTTTTTTGTCTCTTAATTGCTTAATTAACATTACTGCATCTTGAAAGAATCTGCAAAAATCCAG
* *
102189 AGCATTGATTGGGAAAATTTGAAACGTCTATGATTCTTGTGCAATGTGTCTGGTCTCATGGTGAA
131 GGCATTGATTGGGAAAATTTGAAATGTCTATGATTCTTGTGCAATGTGTCTGGTCTCATGGTGAA
102254 ATAATAACCTTATTTTACTGCAAAATTTAAAGACAGTTTGAAAGTACATTCATACACGTGGTATA
196 ATAATAACCTTATTTTACTGCAAAA-TT------A-TTTGAAAGTACATTCATACACGTGGTATA
102319 ATTGATTTCCAATTTCATTGCAGTTTACTGCTTAGTGCTTTCTATATATCTAAAATAAAATTCGC
253 ATTGATTTCCAATTTCATTGCAGTTTACTGCTTAGTGCTTTCTATATATCTAAAATAAAATTCGC
102384 ATGGTTTCTTTTTATAGTTGAATTTATGGGTAGTTTTTGTAACAGTTGATCACAAAGTAGTTCAC
318 ATGGTTTCTTTTTATAGTTGAATTTATGGGTAGTTTTTGTAACAGTTGATCACAAAGTAGTTCAC
102449 CTTTTCTT
383 CTTTTCTT
102457 TTGGTAATGG
Statistics
Matches: 765, Mismatches: 16, Indels: 22
0.95 0.02 0.03
Matches are distributed among these distances:
393 383 0.50
395 1 0.00
401 1 0.00
403 163 0.21
404 106 0.14
405 111 0.15
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.41
Consensus pattern (395 bp):
TAATTTGCTGATTTTGATCTATGTATCGGAGAATAGTACATATATTATGTTCATCTTAATTCTCC
ATTTTTTTGTCTCTTAATTGCTTAATTAACATTACTGCATCTTGAAAGAATCTGCAAAAATCCAG
GGCATTGATTGGGAAAATTTGAAATGTCTATGATTCTTGTGCAATGTGTCTGGTCTCATGGTGAA
ATAATAACCTTATTTTACTGCAAAATTATTTGAAAGTACATTCATACACGTGGTATAATTGATTT
CCAATTTCATTGCAGTTTACTGCTTAGTGCTTTCTATATATCTAAAATAAAATTCGCATGGTTTC
TTTTTATAGTTGAATTTATGGGTAGTTTTTGTAACAGTTGATCACAAAGTAGTTCACCTTTTCTT
AATTC
Found at i:115598 original size:32 final size:26
Alignment explanation
Indices: 115533--115595 Score: 126
Period size: 26 Copynumber: 2.4 Consensus size: 26
115523 AATGATTCAA
115533 ATATTTATATTGTTCCAACTTCCAAT
1 ATATTTATATTGTTCCAACTTCCAAT
115559 ATATTTATATTGTTCCAACTTCCAAT
1 ATATTTATATTGTTCCAACTTCCAAT
115585 ATATTTATATT
1 ATATTTATATT
115596 TATTTTGCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.32, C:0.16, G:0.03, T:0.49
Consensus pattern (26 bp):
ATATTTATATTGTTCCAACTTCCAAT
Found at i:116376 original size:21 final size:21
Alignment explanation
Indices: 116352--116392 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
116342 ACATGATTTG
*
116352 ATTAACAAGTTTTGGGGTTTA
1 ATTAACAAGTTTTAGGGTTTA
*
116373 ATTATCAAGTTTTAGGGTTT
1 ATTAACAAGTTTTAGGGTTT
116393 GACCATGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.22, T:0.46
Consensus pattern (21 bp):
ATTAACAAGTTTTAGGGTTTA
Found at i:116571 original size:87 final size:86
Alignment explanation
Indices: 116419--116650 Score: 277
Period size: 87 Copynumber: 2.7 Consensus size: 86
116409 TGAAATATTG
* * ** *** *
116419 TAATGGTCAAACCCCAAATCATGTATGGTGAAATTTAAAGCATGA-GACAAAAACTTATTATTAG
1 TAATGGTCAAACCCCAAATCATGTAT-GTGAACTTTAAAGCATGATTAGGAAAAC-CCCTACTAG
*
116483 TAATGAGATCAAATCCCAAATCA
64 TAATGAGATCAAATCCCAAAGCA
*
116506 TAATGGTCAAACCCCAAATCATGTATAGTGAACTTTAAAGCATGATTAGGTAAACCCCTACTAGT
1 TAATGGTCAAACCCCAAATCATGTAT-GTGAACTTTAAAGCATGATTAGGAAAACCCCTACTAGT
* *
116571 AATGGGATCAAATCCCAAAGCG
65 AATGAGATCAAATCCCAAAGCA
* * *
116593 TAATGGTCAAATCCCAAATCATGTATGATGAAACTGTAAAGCATGATTAGGCAAACCC
1 TAATGGTCAAACCCCAAATCATGTATG-TG-AACTTTAAAGCATGATTAGGAAAACCC
116651 TTAAATAATC
Statistics
Matches: 126, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
86 1 0.01
87 95 0.75
88 30 0.24
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.25
Consensus pattern (86 bp):
TAATGGTCAAACCCCAAATCATGTATGTGAACTTTAAAGCATGATTAGGAAAACCCCTACTAGTA
ATGAGATCAAATCCCAAAGCA
Found at i:116604 original size:21 final size:23
Alignment explanation
Indices: 116569--116610 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
116559 ACCCCTACTA
116569 GTAATGGGATCAAATCCCAAAGC
1 GTAATGGGATCAAATCCCAAAGC
116592 GTAAT-GG-TCAAATCCCAAA
1 GTAATGGGATCAAATCCCAAA
116611 TCATGTATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.63
22 2 0.11
23 5 0.26
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.19
Consensus pattern (23 bp):
GTAATGGGATCAAATCCCAAAGC
Done.