Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011917.1 Corchorus capsularis cultivar CVL-1 contig11938, 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: 66837
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:163 original size:86 final size:85
Alignment explanation
Indices: 2--167 Score: 224
Period size: 86 Copynumber: 1.9 Consensus size: 85
1 T
* * * * *
2 CAAAGAAAAATACAGTGAATCAAAGCATTGAATGAAGAAATTAGGCAAAGAAACAGCAGATTTAC
1 CAAACAAAAATACAGTAAATCAAAGCATTGAATAAAGAAATTAGGCAAAGAAACAGCAAATTAAC
*
67 TTGATTCGAACCCAAAAATA
66 TTCATTCGAACCCAAAAATA
* * * * *
87 CAAACAAAAGTACAGTAAATCAAAGCATTGAATCAAAGGATTTGGGCAAATAAACAGCAAATTAA
1 CAAACAAAAATACAGTAAATCAAAGCATTGAAT-AAAGAAATTAGGCAAAGAAACAGCAAATTAA
152 CTTCATTCGAACCCAA
65 CTTCATTCGAACCCAA
168 GAAAATCAAA
Statistics
Matches: 69, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
85 30 0.43
86 39 0.57
ACGTcount: A:0.49, C:0.16, G:0.15, T:0.19
Consensus pattern (85 bp):
CAAACAAAAATACAGTAAATCAAAGCATTGAATAAAGAAATTAGGCAAAGAAACAGCAAATTAAC
TTCATTCGAACCCAAAAATA
Found at i:4811 original size:42 final size:43
Alignment explanation
Indices: 4728--4812 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 43
4718 CTCTATGGGG
*
4728 ATATAGTTGCCCTCATTTGTCCACATCTTGGATTTTTAAAGCA
1 ATATAGTTGCCCTCATTTGTCCAAATCTTGGATTTTTAAAGCA
4771 ATATAGTTGCCCTCATTTG-CCAAATCTTGGATTTTTAAAGCA
1 ATATAGTTGCCCTCATTTGTCCAAATCTTGGATTTTTAAAGCA
4813 CAGAAGACTG
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
42 22 0.54
43 19 0.46
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (43 bp):
ATATAGTTGCCCTCATTTGTCCAAATCTTGGATTTTTAAAGCA
Found at i:8561 original size:102 final size:102
Alignment explanation
Indices: 8385--8984 Score: 611
Period size: 102 Copynumber: 5.9 Consensus size: 102
8375 CTTTCTTGTG
* * ** ** * *
8385 TCACCAGCGGCAGTCTCACTATGCTCTTGAATACCAGGCACTACATTAGTCACTTCAATCTCTTT
1 TCACCAGCAGCATTCTCACTATTTTCTTGAATACCAGATACTACATTACTAACTTCAATCTCTTT
* *
8450 ACTAGAAACCAAATCATGCCCCTCTCTC-TTTTTCAGT
66 AGTAGAAACCACATCATGCCCCTCT-TCATTTTTCAGT
* * *
8487 TCACCAGCAGCAATCTCACTATTATCTTGAATACCAGATACTACATT-CATAACTTCAATCTGTT
1 TCACCAGCAGCATTCTCACTATTTTCTTGAATACCAGATACTACATTAC-TAACTTCAATCTCTT
* *
8551 TAGTAGAAACCACATCATGCCCCTCTTCAATTTCCAGT
65 TAGTAGAAACCACATCATGCCCCTCTTCATTTTTCAGT
* * *
8589 TCACGACCAGCATTCTCACTATTTTCTTGAATACCAGATACCACATTACTAACTTCAATCTCTTT
1 TCACCAGCAGCATTCTCACTATTTTCTTGAATACCAGATACTACATTACTAACTTCAATCTCTTT
* * * * *
8654 GGTAGAGACCACAGCATGCCCCTCTTCATTTGTCTGT
66 AGTAGAAACCACATCATGCCCCTCTTCATTTTTCAGT
* * * *
8691 TCACCAGCAGCATTCTCACTAGTTTCTTGAATACCAGATACTGCATTATTATCTTCAATCTCTTT
1 TCACCAGCAGCATTCTCACTATTTTCTTGAATACCAGATACTACATTACTAACTTCAATCTCTTT
* ** * * *
8756 ATTAGAAACCACAAGATGCCTCTCTTCA-GTTTCAAGC
66 AGTAGAAACCACATCATGCCCCTCTTCATTTTTC-AGT
* * * * * * *
8793 TCACTAGCAG-AGTTCTCTGC-ATTTTCATAAATACCAGATACTATACTACTAACTTCTATCTCT
1 TCACCAGCAGCA-TTCTC-ACTATTTTCTTGAATACCAGATACTACATTACTAACTTCAATCTCT
* * *
8856 TTAGGAGAAACCACATCATGCCACTCTTCAATTTTT-GGT
64 TTAGTAGAAACCACATCATGCCCCTCTTC-ATTTTTCAGT
* * * * * *
8895 TCATCAGCAGCATTATTACTATTTTCTTGAATACCAGATA-TCACGTTACTAGCTTCGATCTCTT
1 TCACCAGCAGCATTCTCACTATTTTCTTGAATACCAGATACT-ACATTACTAACTTCAATCTCTT
* * * *
8959 TAGCAGAAATCGCATCATGCCACTCT
65 TAGTAGAAACCACATCATGCCCCTCT
8985 AATTCAGATG
Statistics
Matches: 410, Mismatches: 77, Indels: 22
0.81 0.15 0.04
Matches are distributed among these distances:
101 8 0.02
102 395 0.96
103 4 0.01
104 3 0.01
ACGTcount: A:0.28, C:0.28, G:0.11, T:0.33
Consensus pattern (102 bp):
TCACCAGCAGCATTCTCACTATTTTCTTGAATACCAGATACTACATTACTAACTTCAATCTCTTT
AGTAGAAACCACATCATGCCCCTCTTCATTTTTCAGT
Found at i:29780 original size:2 final size:2
Alignment explanation
Indices: 29773--29809 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
29763 AGTCTCAGTG
29773 TA TA TA 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 TA TA TA T
29810 TGCCACCTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29921 original size:5 final size:5
Alignment explanation
Indices: 29908--29942 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
29898 AAACCGTCCT
*
29908 GAAAA GAAAC GAAAA GAAAA GAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
29943 AGACAGCTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:31288 original size:39 final size:40
Alignment explanation
Indices: 31202--31289 Score: 115
Period size: 44 Copynumber: 2.1 Consensus size: 40
31192 CCCATTTACC
*
31202 TTAGTTTCGGGAAAACAATGTCTTTGAGTTGGGTTGGTTATGTA
1 TTAGTTTCGGGAAAACAATGTCTTTGA----GGTTGGTTATATA
*
31246 TTAGTTTCGGGAAAACGATGTCTTTGA-GTTGGTTATATA
1 TTAGTTTCGGGAAAACAATGTCTTTGAGGTTGGTTATATA
31285 TTAGT
1 TTAGT
31290 CGGCCAATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
39 16 0.38
44 26 0.62
ACGTcount: A:0.24, C:0.07, G:0.27, T:0.42
Consensus pattern (40 bp):
TTAGTTTCGGGAAAACAATGTCTTTGAGGTTGGTTATATA
Found at i:32992 original size:27 final size:27
Alignment explanation
Indices: 32941--32994 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
32931 ATAATTATTA
*
32941 ATGAAAAATAACAAAAAAATTATAATG
1 ATGAAAAATAACAAAAAAATCATAATG
*
32968 ATGAAAAATAATTAAAAAAA-CATAATG
1 ATGAAAAATAA-CAAAAAAATCATAATG
32995 GGGTATAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 17 0.71
28 7 0.29
ACGTcount: A:0.67, C:0.04, G:0.07, T:0.22
Consensus pattern (27 bp):
ATGAAAAATAACAAAAAAATCATAATG
Found at i:35808 original size:13 final size:13
Alignment explanation
Indices: 35790--35817 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
35780 AAAAGGGGTA
35790 AACCAAATCAGGT
1 AACCAAATCAGGT
35803 AACCAAATCAGGT
1 AACCAAATCAGGT
35816 AA
1 AA
35818 AATGAGGAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.21, G:0.14, T:0.14
Consensus pattern (13 bp):
AACCAAATCAGGT
Found at i:36341 original size:14 final size:14
Alignment explanation
Indices: 36322--36348 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
36312 CAATTAACTA
36322 AATTATATATATAT
1 AATTATATATATAT
36336 AATTATATATATA
1 AATTATATATATA
36349 ATTAAAGATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATTATATATATAT
Found at i:36344 original size:12 final size:12
Alignment explanation
Indices: 36327--36352 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
36317 AACTAAATTA
36327 TATATATATAAT
1 TATATATATAAT
36339 TATATATATAAT
1 TATATATATAAT
36351 TA
1 TA
36353 AAGATAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TATATATATAAT
Found at i:36519 original size:20 final size:20
Alignment explanation
Indices: 36494--36533 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
36484 CCGTTAATTA
*
36494 AAACGTGTCACTCGTGTCTT
1 AAACGTGTCAATCGTGTCTT
*
36514 AAACGTGTTAATCGTGTCTT
1 AAACGTGTCAATCGTGTCTT
36534 GACACGATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (20 bp):
AAACGTGTCAATCGTGTCTT
Found at i:36591 original size:42 final size:43
Alignment explanation
Indices: 36521--36603 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 43
36511 CTTAAACGTG
*
36521 TTAATCGTGTCTTGACACGATTACGACACGAAACACGATAATC
1 TTAATCGTGTCTCGACACGATTACGACACGAAACACGATAATC
*
36564 TTAATCGTGTC-CGACACGATT-CAGACACGAGACACGATAA
1 TTAATCGTGTCTCGACACGATTAC-GACACGAAACACGATAA
36604 GCCAAACACG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 1 0.03
42 25 0.68
43 11 0.30
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (43 bp):
TTAATCGTGTCTCGACACGATTACGACACGAAACACGATAATC
Found at i:37247 original size:3 final size:3
Alignment explanation
Indices: 37239--37297 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
37229 TTCTAGACCA
37239 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
37287 AAG AAG AAG AA
1 AAG AAG AAG AA
37298 ACTGTCTTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:38519 original size:25 final size:25
Alignment explanation
Indices: 38491--38541 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
38481 AGAATAACGT
38491 GAATATTAATAAATGAAAAAAAAAA
1 GAATATTAATAAATGAAAAAAAAAA
* * *
38516 GAATATTACTCAATGAAACAAAAAA
1 GAATATTAATAAATGAAAAAAAAAA
38541 G
1 G
38542 GCGACTTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.65, C:0.06, G:0.10, T:0.20
Consensus pattern (25 bp):
GAATATTAATAAATGAAAAAAAAAA
Found at i:38784 original size:15 final size:15
Alignment explanation
Indices: 38766--38794 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
38756 AAAAAGCAGG
38766 AAGAAAAAAAAAAAA
1 AAGAAAAAAAAAAAA
38781 AAGAAAAAAAAAAA
1 AAGAAAAAAAAAAA
38795 CAGCATCGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (15 bp):
AAGAAAAAAAAAAAA
Found at i:51175 original size:184 final size:185
Alignment explanation
Indices: 50861--51233 Score: 613
Period size: 184 Copynumber: 2.0 Consensus size: 185
50851 CATTTTTTTT
* * * *
50861 AGTCTAAGTGGATTTTAGAGATCTTCTGTTATATATTCTTTTATCTTATACTCGTTTTCTTCTCT
1 AGTCTAAGTGGATCTTACAGATCTTCTGTTATATATCCTCTTATCTTATACTCGTTTTCTTCTCT
* *
50926 AAACTGGCTATAGACCTTTTGGTCAATCCTCGTTCAGTCAACTGAGATGTGTTATTTTTCTTCTT
66 AAACTGGCTATAGACCTTTTGGTCAATCCTCGTCCAGTCAACTGAGATGTGTTATTTTCCTTCTT
*
50991 ATGGGGAGGCAACTTTTATTTTAATTCAGTTAATCTAGAAGGTTTTAAAGCGTTC
131 ATGGGGAGGCAACTTTTAATTTAATTCAGTTAATCTAGAAGGTTTTAAAGCGTTC
* *
51046 AGTCTAAGTGGATCTTACAGATGTTCTGTTATTTATCCTCTTATC-TATACTCGTTTTCTTCTCT
1 AGTCTAAGTGGATCTTACAGATCTTCTGTTATATATCCTCTTATCTTATACTCGTTTTCTTCTCT
* * *
51110 AAACTGGCTATAGAGCTTTTGGTCAATTCTCGTCCAGTCAGCTGAGATGTGTTATTTTCCTTCTT
66 AAACTGGCTATAGACCTTTTGGTCAATCCTCGTCCAGTCAACTGAGATGTGTTATTTTCCTTCTT
* *
51175 ATGGGGAGGCAACTTTTAATTTAATTCAGTTAATCTAGAAGGTTTTTAAGCGTTT
131 ATGGGGAGGCAACTTTTAATTTAATTCAGTTAATCTAGAAGGTTTTAAAGCGTTC
51230 AGTC
1 AGTC
51234 ATCGTCACTG
Statistics
Matches: 174, Mismatches: 14, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
184 135 0.78
185 39 0.22
ACGTcount: A:0.23, C:0.16, G:0.17, T:0.43
Consensus pattern (185 bp):
AGTCTAAGTGGATCTTACAGATCTTCTGTTATATATCCTCTTATCTTATACTCGTTTTCTTCTCT
AAACTGGCTATAGACCTTTTGGTCAATCCTCGTCCAGTCAACTGAGATGTGTTATTTTCCTTCTT
ATGGGGAGGCAACTTTTAATTTAATTCAGTTAATCTAGAAGGTTTTAAAGCGTTC
Found at i:62957 original size:8 final size:8
Alignment explanation
Indices: 62946--62975 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
62936 TTTTTGCTGT
62946 TTTCTTGG
1 TTTCTTGG
62954 TTTCTTGG
1 TTTCTTGG
62962 TTTCTTGG
1 TTTCTTGG
62970 TTTCTT
1 TTTCTT
62976 TGCAACCGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.00, C:0.13, G:0.20, T:0.67
Consensus pattern (8 bp):
TTTCTTGG
Done.