Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006943.1 Corchorus capsularis cultivar CVL-1 contig06964, 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: 40898
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:1835 original size:55 final size:55
Alignment explanation
Indices: 1750--1854 Score: 135
Period size: 55 Copynumber: 1.9 Consensus size: 55
1740 ATTTAAGACT
*
1750 CATGCATTTAATTTGGTTAAATAGCACCCTAACA-TATGGGAAAATGCTCATGGTC
1 CATGCATTTAATTTGGTTAAATAGCACCCTAA-ATTATGCGAAAATGCTCATGGTC
* *
1805 CATGC-TTTGAATTTGGTTACATAAG-GCCCTAAATTATGCGAAAATGCTCA
1 CATGCATTT-AATTTGGTTAAAT-AGCACCCTAAATTATGCGAAAATGCTCA
1855 AATAAGGGTA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
54 4 0.09
55 38 0.86
56 2 0.05
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Consensus pattern (55 bp):
CATGCATTTAATTTGGTTAAATAGCACCCTAAATTATGCGAAAATGCTCATGGTC
Found at i:2006 original size:60 final size:60
Alignment explanation
Indices: 1913--2064 Score: 182
Period size: 60 Copynumber: 2.5 Consensus size: 60
1903 GGGCCCTTGT
* * * * * *
1913 TTGAGCATTTTTGCATTCGTTAGGGTCCTATTTAACCAAATTATAAGTATGGGTCCTAAA
1 TTGAGCATTTTTGCATACCTTAGGGTCCTATTTAACCAAATTAAAAGCATGAGCCCTAAA
* *
1973 TTGAGCATTTTTGCATACCTTAGGG-CTTTATTTAACCGAATTAAAAGCATGAGCCCTAAA
1 TTGAGCATTTTTGCATACCTTAGGGTC-CTATTTAACCAAATTAAAAGCATGAGCCCTAAA
* * *
2033 TTGAG-ATTTTTGCATACGTTAAGGACCTATTT
1 TTGAGCATTTTTGCATACCTTAGGGTCCTATTT
2065 GGGCAATAAG
Statistics
Matches: 79, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
59 23 0.29
60 56 0.71
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.38
Consensus pattern (60 bp):
TTGAGCATTTTTGCATACCTTAGGGTCCTATTTAACCAAATTAAAAGCATGAGCCCTAAA
Found at i:6435 original size:21 final size:20
Alignment explanation
Indices: 6398--6436 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6388 TTTAGAAGCA
*
6398 ATTAATTAAAAGCATTAAAC
1 ATTAATTAAAAACATTAAAC
6418 ATTAATTAAAAACAATTAA
1 ATTAATTAAAAAC-ATTAA
6437 GGAAGGGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.31
Consensus pattern (20 bp):
ATTAATTAAAAACATTAAAC
Found at i:6529 original size:74 final size:74
Alignment explanation
Indices: 6448--6599 Score: 259
Period size: 74 Copynumber: 2.1 Consensus size: 74
6438 GAAGGGAAAT
*
6448 GTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATGGGGGAAACTCATAAAAGGGCTTTTTAGTC
1 GTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAAAAGGGCTTTTTAGTC
*
6513 ATCCAAAAA
66 ACCCAAAAA
* *
6522 GTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAGAGGGGCTTTTTAGTC
1 GTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAAAAGGGCTTTTTAGTC
*
6587 ACCCGAAAA
66 ACCCAAAAA
6596 GTGT
1 GTGT
6600 GAAAAGACCA
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.41, C:0.10, G:0.29, T:0.20
Consensus pattern (74 bp):
GTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAAAAGGGCTTTTTAGTC
ACCCAAAAA
Found at i:11987 original size:44 final size:45
Alignment explanation
Indices: 11908--11992 Score: 127
Period size: 44 Copynumber: 1.9 Consensus size: 45
11898 GATTTCTGCA
*
11908 CAAGGAAAGAGCCTCTATGGGTTCAGAATTAAACAAAGAGTTATG
1 CAAGGAAAGAGCCTCTATGGGTTCAGAATCAAACAAAGAGTTATG
* * *
11953 CAAGGAAATAGCCT-TCTGGGTTCGGAATCAAACAAAGAGT
1 CAAGGAAAGAGCCTCTATGGGTTCAGAATCAAACAAAGAGT
11993 AATCTCAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 23 0.64
45 13 0.36
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.21
Consensus pattern (45 bp):
CAAGGAAAGAGCCTCTATGGGTTCAGAATCAAACAAAGAGTTATG
Found at i:12594 original size:15 final size:15
Alignment explanation
Indices: 12571--12600 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12561 CATTGAAAGA
*
12571 ACACCTACACTAGAG
1 ACACATACACTAGAG
12586 ACACATACACTAGAG
1 ACACATACACTAGAG
12601 GATGAACACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.30, G:0.13, T:0.13
Consensus pattern (15 bp):
ACACATACACTAGAG
Found at i:15568 original size:33 final size:33
Alignment explanation
Indices: 15530--15625 Score: 122
Period size: 33 Copynumber: 2.9 Consensus size: 33
15520 AGTCCAACCT
* *
15530 GAGACCGAACTTGAAAATACCCAAACCCGACCC
1 GAGACCGAACTCGAAAATACCCAAACCCGACCA
*
15563 GAGACCGAACTCGAAAATACCCAAACCC-AACA
1 GAGACCGAACTCGAAAATACCCAAACCCGACCA
* * * *
15595 TAGCCCGAACCCGAACATACCCAAACCCGAC
1 GAGACCGAACTCGAAAATACCCAAACCCGAC
15626 ATAATCCGAA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
32 26 0.48
33 28 0.52
ACGTcount: A:0.41, C:0.39, G:0.14, T:0.07
Consensus pattern (33 bp):
GAGACCGAACTCGAAAATACCCAAACCCGACCA
Found at i:15615 original size:32 final size:32
Alignment explanation
Indices: 15567--15654 Score: 97
Period size: 32 Copynumber: 2.8 Consensus size: 32
15557 CGACCCGAGA
* *
15567 CCGAACTCGAAAATACCCAAACCCAACATAGC
1 CCGAACCCGAAAATACCCAAACCCAACATAAC
* * *
15599 CCGAACCCGAACATACCCAAACCCGACATAAT
1 CCGAACCCGAAAATACCCAAACCCAACATAAC
* *
15631 CCGAACCTGAATAA-ACCCGAACCC
1 CCGAACCCGAA-AATACCCAAACCC
15655 GAGCCCGCTC
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
32 46 0.98
33 1 0.02
ACGTcount: A:0.41, C:0.40, G:0.10, T:0.09
Consensus pattern (32 bp):
CCGAACCCGAAAATACCCAAACCCAACATAAC
Found at i:15621 original size:16 final size:16
Alignment explanation
Indices: 15574--15628 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 16
15564 AGACCGAACT
*
15574 CGAAAATACCCAAACC
1 CGAACATACCCAAACC
*
15590 C-AACATAGCCCGAACC
1 CGAACATA-CCCAAACC
15606 CGAACATACCCAAACC
1 CGAACATACCCAAACC
15622 CG-ACATA
1 CGAACATA
15629 ATCCGAACCT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
15 10 0.29
16 18 0.53
17 6 0.18
ACGTcount: A:0.44, C:0.40, G:0.09, T:0.07
Consensus pattern (16 bp):
CGAACATACCCAAACC
Found at i:15637 original size:16 final size:16
Alignment explanation
Indices: 15581--15656 Score: 66
Period size: 16 Copynumber: 4.8 Consensus size: 16
15571 ACTCGAAAAT
* *
15581 ACCCAAACCCAACATA
1 ACCCGAACCCGACATA
*
15597 GCCCGAACCCGAACAT-
1 ACCCGAACCCG-ACATA
*
15613 ACCCAAACCCGACATA
1 ACCCGAACCCGACATA
* *
15629 ATCCGAACCTGA-ATAA
1 ACCCGAACCCGACAT-A
15645 ACCCGAACCCGA
1 ACCCGAACCCGA
15657 GCCCGCTCAA
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
15 6 0.13
16 37 0.79
17 4 0.09
ACGTcount: A:0.41, C:0.41, G:0.11, T:0.08
Consensus pattern (16 bp):
ACCCGAACCCGACATA
Found at i:18315 original size:30 final size:30
Alignment explanation
Indices: 18281--18369 Score: 124
Period size: 31 Copynumber: 2.9 Consensus size: 30
18271 TGTGCACGTG
18281 GCGTGACACGTGTCACTTTTGGTACACATA
1 GCGTGACACGTGTCACTTTTGGTACACATA
* *
18311 GCGTGACAAGTGTCACTTTTTGGTACACATG
1 GCGTGACACGTGTCAC-TTTTGGTACACATA
* *
18342 GCGTGCCACATGTCACTTTTGGGTACAC
1 GCGTGACACGTGTCACTTTT-GGTACAC
18370 GTGGCATGCC
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
30 19 0.37
31 33 0.63
ACGTcount: A:0.21, C:0.24, G:0.25, T:0.30
Consensus pattern (30 bp):
GCGTGACACGTGTCACTTTTGGTACACATA
Found at i:19041 original size:103 final size:105
Alignment explanation
Indices: 18873--19237 Score: 519
Period size: 103 Copynumber: 3.5 Consensus size: 105
18863 AGTTTAGCCT
18873 TAATTTCACCAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
1 TAATTTCACCAAGTTTAGCCCCAAATTAAAA--TTATTTTTATTTTAAGGGTAAATTTCAAAATT
18938 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
64 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
18980 TAATTTCACCAAGTTTAGCCCCAAATTAAAA-T-TTTTTATTTTAAGGGTAAATTTCAAAATTAA
1 TAATTTCACCAAGTTTAGCCCCAAATTAAAATTATTTTTATTTTAAGGGTAAATTTCAAAATTAA
*
19043 TAATTTATTATTATAGGGTTTTAGAAATAAAATACAAAAC
66 TAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
* * * *
19083 TAATTTAACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTCTAAGGGTAAA-TTCTATAAT
1 TAATTTCACCAAGTTTAGCCCCAAATTAAAA--TTATTTTTATTTTAAGGGTAAATTTC-AAAAT
* *
19147 TAATAA--TATTGTTATAGGGTTTTAGAAATAAAATATATAAC
63 TAATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
* * * *
19188 TAA-TTCACTAAGTTCAG-TCCAAATTAAAATTAAAATTTTATTTTAAGGGT
1 TAATTTCACCAAGTTTAGCCCCAAATTAAAATT--ATTTTTATTTTAAGGGT
19238 TAGAAAAATT
Statistics
Matches: 238, Mismatches: 13, Indels: 18
0.88 0.05 0.07
Matches are distributed among these distances:
101 2 0.01
103 125 0.53
104 13 0.05
105 35 0.15
106 4 0.02
107 59 0.25
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.40
Consensus pattern (105 bp):
TAATTTCACCAAGTTTAGCCCCAAATTAAAATTATTTTTATTTTAAGGGTAAATTTCAAAATTAA
TAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
Found at i:21851 original size:2 final size:2
Alignment explanation
Indices: 21844--21874 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
21834 GGTTGATAAC
21844 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21875 CACTCTTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22484 original size:300 final size:300
Alignment explanation
Indices: 21942--22543 Score: 1195
Period size: 300 Copynumber: 2.0 Consensus size: 300
21932 TTAGTGATAT
21942 TCCTGTCTTGAGAATGAGGATGTTAGATGAGGCTCACGTCTTTGGCAATATAAGGTCCTAGCACC
1 TCCTGTCTTGAGAATGAGGATGTTAGATGAGGCTCACGTCTTTGGCAATATAAGGTCCTAGCACC
22007 TAGAGTGCACTTTGCACCCTTGACAATGCTGGGCATATCTAAGGTTGCAGTGGATTTTGAGGAAT
66 TAGAGTGCACTTTGCACCCTTGACAATGCTGGGCATATCTAAGGTTGCAGTGGATTTTGAGGAAT
22072 ATTTACCGTCAGATTCAGTGAGCTGTTTGCTTTAATAAGAATATGGGTCATTTTTATTGGGTGAT
131 ATTTACCGTCAGATTCAGTGAGCTGTTTGCTTTAATAAGAATATGGGTCATTTTTATTGGGTGAT
22137 AGTAAGTATGAGACAAAAGTCTGATATACAAAACCTGGATAGTTGCATTAGGTATGAAAGGAATA
196 AGTAAGTATGAGACAAAAGTCTGATATACAAAACCTGGATAGTTGCATTAGGTATGAAAGGAATA
22202 TCCTATTGTAAGGAAAAAAAATATCTGTGGTCAGGTTCAA
261 TCCTATTGTAAGGAAAAAAAATATCTGTGGTCAGGTTCAA
22242 TCCTGTCTTGAGAATGAGGATGTTAGATGAGGCTCACGTCTTTGGCAATATAAGGTCCTAGCACC
1 TCCTGTCTTGAGAATGAGGATGTTAGATGAGGCTCACGTCTTTGGCAATATAAGGTCCTAGCACC
*
22307 TAGAGTGCACTTTGCGCCCTTGACAATGCTGGGCATATCTAAGGTTGCAGTGGATTTTGAGGAAT
66 TAGAGTGCACTTTGCACCCTTGACAATGCTGGGCATATCTAAGGTTGCAGTGGATTTTGAGGAAT
22372 ATTTACCGTCAGATTCAGTGAGCTGTTTGCTTTAATAAGAATATGGGTCATTTTTATTGGGTGAT
131 ATTTACCGTCAGATTCAGTGAGCTGTTTGCTTTAATAAGAATATGGGTCATTTTTATTGGGTGAT
22437 AGTAAGTATGAGACAAAAGTCTGATATACAAAACCTGGATAGTTGCATTAGGTATGAAAGGAATA
196 AGTAAGTATGAGACAAAAGTCTGATATACAAAACCTGGATAGTTGCATTAGGTATGAAAGGAATA
22502 TCCTATTGTAAGGAAAAAAAATATCTGTGGTCAGGTTCAA
261 TCCTATTGTAAGGAAAAAAAATATCTGTGGTCAGGTTCAA
22542 TC
1 TC
22544 ATACCTCTTT
Statistics
Matches: 301, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
300 301 1.00
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.31
Consensus pattern (300 bp):
TCCTGTCTTGAGAATGAGGATGTTAGATGAGGCTCACGTCTTTGGCAATATAAGGTCCTAGCACC
TAGAGTGCACTTTGCACCCTTGACAATGCTGGGCATATCTAAGGTTGCAGTGGATTTTGAGGAAT
ATTTACCGTCAGATTCAGTGAGCTGTTTGCTTTAATAAGAATATGGGTCATTTTTATTGGGTGAT
AGTAAGTATGAGACAAAAGTCTGATATACAAAACCTGGATAGTTGCATTAGGTATGAAAGGAATA
TCCTATTGTAAGGAAAAAAAATATCTGTGGTCAGGTTCAA
Found at i:34265 original size:2 final size:2
Alignment explanation
Indices: 34258--34291 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
34248 GTAGTATTAG
34258 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34292 CACATAGCTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35250 original size:3 final size:3
Alignment explanation
Indices: 35230--35285 Score: 96
Period size: 3 Copynumber: 18.7 Consensus size: 3
35220 AGAAAAGTTG
35230 TAT TAT ATAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
35275 TAT TAT TAT TA
1 TAT TAT TAT TA
35286 AGTGTTGGTG
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.04
3 46 0.90
4 3 0.06
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:36102 original size:2 final size:2
Alignment explanation
Indices: 36090--36124 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
36080 AATAAATAAA
36090 AT AT CAT 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
36125 CTTACCTACA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:36282 original size:13 final size:14
Alignment explanation
Indices: 36264--36299 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
36254 CACTGTAAAT
36264 TAATTAATCTT-AC
1 TAATTAATCTTGAC
*
36277 TAATTATTCTTGAC
1 TAATTAATCTTGAC
36291 TAATTAATC
1 TAATTAATC
36300 AACGTTCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.36, C:0.14, G:0.03, T:0.47
Consensus pattern (14 bp):
TAATTAATCTTGAC
Found at i:40597 original size:2 final size:2
Alignment explanation
Indices: 40590--40615 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40580 ATCATGTTAG
40590 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
40616 TATTTTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.