Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009653.1 Corchorus capsularis cultivar CVL-1 contig09674, 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: 96978
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:635 original size:332 final size:332
Alignment explanation
Indices: 1--1674 Score: 2216
Period size: 332 Copynumber: 5.1 Consensus size: 332
* ** *
1 TTTGTTGCCAAGAGTCTTTGAAATATCTATATTCATCTAACCAAATCATAACCACATTGGATTTA
1 TTTGTTGCCAAGAGTCCTTGAAATATCTATATTCATCTAACCAAATTTTAGCCACATTGGATTTA
* * * * *
66 AGTA-TAGTTTTTACGAAAATCTGAATC-TATTTTGATTT-ATTA-AAATTAATTCNGAAAAAAT
66 AGGATTTGTTTTTACGAGAATCTGAATCTTATTTCGATTTAATTAGAAATTAATTCAGAAAAAAT
* * * * * * *
127 AAGAGAAATGGTATTTGAAGCCTGGAAAGCCCTCCAATCTTCTTGTGCCTTGAATTATATATTTT
131 AAGAAAAACGATATTAGAAGCCTGAAAAGCCCTCCAATCTTTTTG-GCGTTGAATTATATATTTT
*
192 CTATGATTATTGTGGCGAAAATTTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCC
195 CTATGATTATTGTGGCGAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCC
* * *
257 GAAATCGTGTACTAACCATCACGGGTGTTGGCCGAAAACGCGTTCCTGGGCCCCGGCTCAGTTTT
260 GAAATCGTGTAATAACCATCACGGGTTTTGGCCAAAAACGCGTTCCTGGGCCCCGGCTCAGTTTT
322 GCATGATT
325 GCATGATT
* * **
330 TTGGTTGCTAAGAGTCCTTGAAATATCTATATTCATCTAACCAAATTTTAGCCACAAAGGATTTA
1 TTTGTTGCCAAGAGTCCTTGAAATATCTATATTCATCTAACCAAATTTTAGCCACATTGGATTTA
* *
395 AGGATTTGTTTTTACGAGCATCAGAATCTTATTTCGATTTAATTAGAAATTAATTCAGAAAAAAT
66 AGGATTTGTTTTTACGAGAATCTGAATCTTATTTCGATTTAATTAGAAATTAATTCAGAAAAAAT
**
460 AAGAAAAACGATATTAGAAGCCTGAAAAGCCCTCCAATCTTTTTGGAATTGAATTATATATTTTC
131 AAGAAAAACGATATTAGAAGCCTGAAAAGCCCTCCAATCTTTTTGGCGTTGAATTATATATTTTC
*
525 TATGATTATTGTGGCGAAAAATTGAGGAAAAACCTTTCGGGTCAATTTTTGCAAAATTTTAGCCG
196 TATGATTATTGTGGCGAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCG
* * * * * *
590 AAATCTTGTAATAACCATCCCTGGTCTTGGCCAAAAACTCGTTCCTGGGCCCCGACTCAGTTTTT
261 AAATCGTGTAATAACCATCACGGGTTTTGGCCAAAAACGCGTTCCTGGGCCCCGGCTCAG-TTTT
* *
655 TCAAGATAT
325 GCATGAT-T
* * * * * * * *
664 TTTG-CGCCAAGACTCTTTTAAAAATATATATTCATCTAACCAAATTTCAGCAACATTGGATTTA
1 TTTGTTGCCAAGAGTCCTTGAAATATCTATATTCATCTAACCAAATTTTAGCCACATTGGATTTA
* * * *
728 AGGATTTGTTTTTACGAGTAT-TCAATCTTGTTTCGATTTAATTTGAAATTAATTCAG-AAAAAT
66 AGGATTTGTTTTTACGAGAATCTGAATCTTATTTCGATTTAATTAGAAATTAATTCAGAAAAAAT
* * *
791 AAGAAAAACGATATTAGAAGTCTGAAAAACCCTCCAATCTTTTTGGCGTTGAATTCTATATTTT-
131 AAGAAAAACGATATTAGAAGCCTGAAAAGCCCTCCAATCTTTTTGGCGTTGAATTATATATTTTC
* * * * * *
855 TAAGAGTATTGTGGCTAAAAACTGAGGAAAAATCTTTCGGGTCAATTATTGCAAAATTTTAGCCC
196 TATGATTATTGTGGCGAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCG
* *
920 AAATCGTGT-AT---CAT---GGGTTTTGGCCAAAAACGGGTTCTTGGGCCCCGGCTCAGTTTTG
261 AAATCGTGTAATAACCATCACGGGTTTTGGCCAAAAACGCGTTCCTGGGCCCCGGCTCAGTTTTG
*
978 CCTGATT
326 CATGATT
* *
985 TTTGTTGCCAAGAGTCCTTGAAATATCTATATTTATCTAACCAAATTTTAGCCATATTGGATTTA
1 TTTGTTGCCAAGAGTCCTTGAAATATCTATATTCATCTAACCAAATTTTAGCCACATTGGATTTA
* * * *
1050 AGGATTTGTTTTTACAAGAATCTGAACCTTATTTCGATTTAATTTGAAATTAATTCATAAGAAAA
66 AGGATTTGTTTTTACGAGAATCTGAATCTTATTTCGATTTAATTAGAAATTAATTCAGAA-AAAA
* * * * *
1115 TAAGAAAAATGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGCCGTTGAATTATATATTTC
130 TAAGAAAAACGATATTAGAAGCCTGAAAAGCCCTCCAATCTTTTTGGCGTTGAATTATATATTTT
* * * * *
1180 CTATTATTATTGTGGCTAAAAATTGAGGGAAAATCTTTCGGGTCAATTTTTGTAAAATTATAGCC
195 CTATGATTATTGTGGCGAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCC
* * * * *
1245 GAAATCGTGTACTAAAACCATCACGGGTTTTTTTTGCCAAAAACACGTTCCTGGGCACCGGATCA
260 GAAATCGTGTA--ATAACCATCACGGG---TTTTGGCCAAAAACGCGTTCCTGGGCCCCGGCTCA
*
1310 GTTTTGAATGATT
320 GTTTTGCATGATT
* * * *
1323 TGTT-ATGCGAAGAGTCCTTGAAATAT-TATATTCATCTAACCAAATCTTAGCAACATTGGATTT
1 T-TTGTTGCCAAGAGTCCTTGAAATATCTATATTCATCTAACCAAATTTTAGCCACATTGGATTT
*
1386 AAGGATTTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTCAG-AAAAA
65 AAGGATTTGTTTTTACGAGAATCTGAATCTTATTTCGATTTAATTAGAAATTAATTCAGAAAAAA
* * *
1450 TAAGAAAAACGATATTAGAAGTCTGAAAAGCCCTCCAATTTTTTTAGCGTTGAATTATATATTTT
130 TAAGAAAAACGATATTAGAAGCCTGAAAAGCCCTCCAATCTTTTTGGCGTTGAATTATATATTTT
* *** *
1515 -TAATGAGTATTGTTTTGAAAAATTGATGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGC
195 CT-ATGATTATTGTGGCGAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGC
* * *
1579 CGAAATCGTGTAATAACCATCACGGGTTTTGGCCAAAAATGTGTTCCTGGGCACCGGCTCAGTTT
259 CGAAATCGTGTAATAACCATCACGGGTTTTGGCCAAAAACGCGTTCCTGGGCCCCGGCTCAGTTT
1644 TGCATGATT
324 TGCATGATT
*
1653 TTTGTTGCCAAGAGTCTTTGAA
1 TTTGTTGCCAAGAGTCCTTGAA
1675 CCAAATCTCA
Statistics
Matches: 1164, Mismatches: 155, Indels: 51
0.85 0.11 0.04
Matches are distributed among these distances:
321 5 0.00
322 77 0.07
323 65 0.06
324 1 0.00
325 61 0.05
326 68 0.06
329 65 0.06
330 143 0.12
331 75 0.06
332 172 0.15
333 148 0.13
334 5 0.00
335 128 0.11
336 1 0.00
337 87 0.07
338 61 0.05
339 2 0.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (332 bp):
TTTGTTGCCAAGAGTCCTTGAAATATCTATATTCATCTAACCAAATTTTAGCCACATTGGATTTA
AGGATTTGTTTTTACGAGAATCTGAATCTTATTTCGATTTAATTAGAAATTAATTCAGAAAAAAT
AAGAAAAACGATATTAGAAGCCTGAAAAGCCCTCCAATCTTTTTGGCGTTGAATTATATATTTTC
TATGATTATTGTGGCGAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCG
AAATCGTGTAATAACCATCACGGGTTTTGGCCAAAAACGCGTTCCTGGGCCCCGGCTCAGTTTTG
CATGATT
Found at i:1876 original size:24 final size:24
Alignment explanation
Indices: 1849--1895 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
1839 CTTGGTACAG
1849 ATTTTTTGGGCTTAATTGGTGCCA
1 ATTTTTTGGGCTTAATTGGTGCCA
1873 ATTTTTTGGGCTTAATTGGTGCC
1 ATTTTTTGGGCTTAATTGGTGCC
1896 GGATGCCGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.47
Consensus pattern (24 bp):
ATTTTTTGGGCTTAATTGGTGCCA
Found at i:9042 original size:16 final size:16
Alignment explanation
Indices: 9021--9054 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
9011 ATGATTATTT
9021 GATATTTTTTATAAGC
1 GATATTTTTTATAAGC
9037 GATATTTTTTATAAGC
1 GATATTTTTTATAAGC
9053 GA
1 GA
9055 AAAGTACCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.47
Consensus pattern (16 bp):
GATATTTTTTATAAGC
Found at i:9676 original size:2 final size:2
Alignment explanation
Indices: 9669--9695 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9659 GCTATTTGCA
9669 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
9696 TATGAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:11594 original size:8 final size:8
Alignment explanation
Indices: 11581--11605 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
11571 AAAATTCAAT
11581 TAAAATTC
1 TAAAATTC
11589 TAAAATTC
1 TAAAATTC
11597 TAAAATTC
1 TAAAATTC
11605 T
1 T
11606 GTGTGGGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (8 bp):
TAAAATTC
Found at i:17935 original size:61 final size:61
Alignment explanation
Indices: 17865--17986 Score: 235
Period size: 61 Copynumber: 2.0 Consensus size: 61
17855 GAACCGTTTA
17865 GTTAATATATAATTAAATATAAATTTTTATATATAATAATATATATAATTATTAAACGGTT
1 GTTAATATATAATTAAATATAAATTTTTATATATAATAATATATATAATTATTAAACGGTT
*
17926 GTTAATATATAATTAAATATAAATTTTTATATATAATAATATATATAATTATTAAATGGTT
1 GTTAATATATAATTAAATATAAATTTTTATATATAATAATATATATAATTATTAAACGGTT
17987 TAAACTGTCT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.48, C:0.01, G:0.05, T:0.47
Consensus pattern (61 bp):
GTTAATATATAATTAAATATAAATTTTTATATATAATAATATATATAATTATTAAACGGTT
Found at i:50366 original size:3 final size:3
Alignment explanation
Indices: 50358--50388 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
50348 AATTAATTAT
50358 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
50389 AATATTCAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:54432 original size:23 final size:23
Alignment explanation
Indices: 54388--54432 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
54378 GTGAAAGATT
* *
54388 ACAAAAGCAAAATCCTTGTAATA
1 ACAAAAGCAAAATCATTATAATA
54411 ACAAAA-CAAAATCATATATAAT
1 ACAAAAGCAAAATCAT-TATAAT
54433 TAATTGTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.58, C:0.16, G:0.04, T:0.22
Consensus pattern (23 bp):
ACAAAAGCAAAATCATTATAATA
Found at i:61097 original size:32 final size:30
Alignment explanation
Indices: 61025--61097 Score: 71
Period size: 31 Copynumber: 2.4 Consensus size: 30
61015 AAATACATAC
61025 TATT-TTAAT-TTTTAAAAGCTCATTTTTT
1 TATTCTTAATATTTTAAAAGCTCATTTTTT
* *
61053 T-TTGCTACAATATTTTAAAAGTTCATAATTTTT
1 TATT-CT-TAATATTTTAAAAGCTCAT--TTTTT
61086 TATTCTTAATAT
1 TATTCTTAATAT
61098 GATCATAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
27 2 0.06
28 1 0.03
29 1 0.03
30 3 0.09
31 13 0.37
32 5 0.14
33 8 0.23
34 2 0.06
ACGTcount: A:0.32, C:0.08, G:0.04, T:0.56
Consensus pattern (30 bp):
TATTCTTAATATTTTAAAAGCTCATTTTTT
Found at i:62765 original size:90 final size:90
Alignment explanation
Indices: 62605--62769 Score: 210
Period size: 90 Copynumber: 1.8 Consensus size: 90
62595 AGTTGCGACG
***
62605 ACTCATTATGTGGTTACCATACACGGGAAAAAAATGACTTTCTTAACCTCATATAGGATTGGACA
1 ACTCATTATGTGGTTACCATACACGGGAAAAAAATGACTTTCTTAACCTCATATAGGATCCAACA
*
62670 TGACTCAATTTTAAGATTAATTGTA
66 AGACTCAATTTTAAGATTAATTGTA
* * **
62695 ACTCATTTTGTGGTTACCATATACGATTAAAAAAA-GACTTTCTTAACC-C-TATATGGAATCCA
1 ACTCATTATGTGGTTACCATACACG-GGAAAAAAATGACTTTCTTAACCTCATATA-GG-ATCCA
62757 ACAAGACTCAATT
63 ACAAGACTCAATT
62770 CTAAACTAGT
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
88 4 0.06
89 3 0.05
90 50 0.78
91 7 0.11
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (90 bp):
ACTCATTATGTGGTTACCATACACGGGAAAAAAATGACTTTCTTAACCTCATATAGGATCCAACA
AGACTCAATTTTAAGATTAATTGTA
Found at i:67971 original size:22 final size:22
Alignment explanation
Indices: 67943--67985 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
67933 GAGGCTCCGC
67943 CGTGGTTGAGCCTCCCCAGTGT
1 CGTGGTTGAGCCTCCCCAGTGT
*
67965 CGTGGTTGAGCCTCCCTAGTG
1 CGTGGTTGAGCCTCCCCAGTG
67986 GGGAGGCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.09, C:0.30, G:0.33, T:0.28
Consensus pattern (22 bp):
CGTGGTTGAGCCTCCCCAGTGT
Found at i:83583 original size:31 final size:32
Alignment explanation
Indices: 83510--83607 Score: 112
Period size: 31 Copynumber: 3.2 Consensus size: 32
83500 TTGAAACGTA
*
83510 TGCCACGTGTCATTTTTTGGTACACGT-AGCG
1 TGCCACGTGTCACTTTTTGGTACACGTGAGCG
** *
83541 TGATATGTGTCACTTTTTGGTACACGTGA-CG
1 TGCCACGTGTCACTTTTTGGTACACGTGAGCG
* * *
83572 TGCCACATGTCACTTTTTGGTGCACGTG-GCA
1 TGCCACGTGTCACTTTTTGGTACACGTGAGCG
83603 TGCCA
1 TGCCA
83608 TGTCGGACAC
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
31 54 0.98
32 1 0.02
ACGTcount: A:0.17, C:0.22, G:0.26, T:0.35
Consensus pattern (32 bp):
TGCCACGTGTCACTTTTTGGTACACGTGAGCG
Found at i:84365 original size:2 final size:2
Alignment explanation
Indices: 84360--84387 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
84350 ACACACACAG
84360 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
84388 TTGAATTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:93593 original size:8 final size:9
Alignment explanation
Indices: 93546--93596 Score: 54
Period size: 8 Copynumber: 5.9 Consensus size: 9
93536 TTGCAACATA
93546 TCATGCATG
1 TCATGCATG
*
93555 -CATGGATG
1 TCATGCATG
93563 TCATGCCATG
1 TCATG-CATG
*
93573 TGAT-CATG
1 TCATGCATG
93581 TCATGCATG
1 TCATGCATG
93590 -CATGCAT
1 TCATGCAT
93597 TATACATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
8 21 0.60
9 8 0.23
10 6 0.17
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.31
Consensus pattern (9 bp):
TCATGCATG
Found at i:94957 original size:2 final size:2
Alignment explanation
Indices: 94950--94984 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
94940 TAATAAGGTG
94950 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
94985 CTAGTATTCG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:95746 original size:31 final size:31
Alignment explanation
Indices: 95711--95769 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
95701 TATGTTAGAC
* *
95711 AAATAAGGATATAATTGGCGTTTCAAAAATT
1 AAATAAGGACATAATAGGCGTTTCAAAAATT
* *
95742 AAATAAGGGCATAATAGGTGTTTCAAAA
1 AAATAAGGACATAATAGGCGTTTCAAAA
95770 GTTTTACAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.46, C:0.07, G:0.19, T:0.29
Consensus pattern (31 bp):
AAATAAGGACATAATAGGCGTTTCAAAAATT
Found at i:96389 original size:15 final size:16
Alignment explanation
Indices: 96369--96407 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
96359 CCCTAGCATC
96369 ATATATAC-CAAATAT
1 ATATATACTCAAATAT
*
96384 ATATATTTCTCAAATAT
1 ATATA-TACTCAAATAT
96401 ATATATA
1 ATATATA
96408 TATAGGCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
15 5 0.25
16 3 0.15
17 12 0.60
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATATACTCAAATAT
Done.