Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015739.1 Corchorus capsularis cultivar CVL-1 contig15760, 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: 87330
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:13098 original size:15 final size:15
Alignment explanation
Indices: 13067--13108 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
13057 GCATTTATGG
13067 TTTTATTTATT-AAA
1 TTTTATTTATTAAAA
*
13081 TTTTATTTTTTAAAA
1 TTTTATTTATTAAAA
13096 TTTTATTTATTAA
1 TTTTATTTATTAA
13109 TTTATTAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTATTTATTAAAA
Found at i:14936 original size:7 final size:7
Alignment explanation
Indices: 14926--14950 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
14916 GGGGCACGGC
14926 TACTCAA
1 TACTCAA
14933 TACTCAA
1 TACTCAA
14940 TACTCAA
1 TACTCAA
14947 TACT
1 TACT
14951 AGGAAAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.28, G:0.00, T:0.32
Consensus pattern (7 bp):
TACTCAA
Found at i:21786 original size:25 final size:25
Alignment explanation
Indices: 21758--21886 Score: 127
Period size: 25 Copynumber: 5.2 Consensus size: 25
21748 TGCGCTGGGT
* * *
21758 AAACGCTCATGTTCTTGCGTTTGGC
1 AAACGATCATGTGCTTGCGTTTAGC
* * *
21783 AAACGAGCCTATGCTTGCGTTTAGC
1 AAACGATCATGTGCTTGCGTTTAGC
21808 AAACGAGT-ATGTGCTTGCGTTTAGC
1 AAACGA-TCATGTGCTTGCGTTTAGC
* *
21833 AAACGAGCCA-ATGCTTGCGTTTAGC
1 AAACGA-TCATGTGCTTGCGTTTAGC
* * *
21858 AAACGAGCCTGTGCTTGCGTTTAGA
1 AAACGATCATGTGCTTGCGTTTAGC
21883 AAAC
1 AAAC
21887 ACATAGGCTA
Statistics
Matches: 86, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
24 1 0.01
25 84 0.98
26 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.29
Consensus pattern (25 bp):
AAACGATCATGTGCTTGCGTTTAGC
Found at i:21835 original size:50 final size:50
Alignment explanation
Indices: 21765--21886 Score: 190
Period size: 50 Copynumber: 2.4 Consensus size: 50
21755 GGTAAACGCT
* * *
21765 CATGTTCTTGCGTTTGGCAAACGAGCCTATGCTTGCGTTTAGCAAACGAG
1 CATGTGCTTGCGTTTAGCAAACGAGCCAATGCTTGCGTTTAGCAAACGAG
*
21815 TATGTGCTTGCGTTTAGCAAACGAGCCAATGCTTGCGTTTAGCAAACGAG
1 CATGTGCTTGCGTTTAGCAAACGAGCCAATGCTTGCGTTTAGCAAACGAG
* *
21865 CCTGTGCTTGCGTTTAGAAAAC
1 CATGTGCTTGCGTTTAGCAAAC
21887 ACATAGGCTA
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 65 1.00
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (50 bp):
CATGTGCTTGCGTTTAGCAAACGAGCCAATGCTTGCGTTTAGCAAACGAG
Found at i:24673 original size:18 final size:17
Alignment explanation
Indices: 24644--24678 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
24634 ATTAGGATTG
24644 ATTAATATATATAGTAT
1 ATTAATATATATAGTAT
24661 ATTAATAATATATAGTAT
1 ATTAAT-ATATATAGTAT
24679 TCGAAGTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (17 bp):
ATTAATATATATAGTAT
Found at i:28100 original size:29 final size:28
Alignment explanation
Indices: 28056--28110 Score: 101
Period size: 29 Copynumber: 1.9 Consensus size: 28
28046 CTTGTAAATA
28056 TACCAAAAAAAAATTAACACTAATGATT
1 TACCAAAAAAAAATTAACACTAATGATT
28084 TACCTAAAAAAAAATTAACACTAATGA
1 TACC-AAAAAAAAATTAACACTAATGA
28111 AATGAAAGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 4 0.15
29 22 0.85
ACGTcount: A:0.58, C:0.15, G:0.04, T:0.24
Consensus pattern (28 bp):
TACCAAAAAAAAATTAACACTAATGATT
Found at i:29743 original size:31 final size:29
Alignment explanation
Indices: 29686--29756 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 29
29676 TCCCGTTAAA
* *
29686 TTTAGGCCCAATTTGGTTTATCTCAAAAACG
1 TTTAGGCTCAATTTGGTTCATCTC--AAACG
29717 TTTAGGCTCAATTTGGTTCA-CATCAAACG
1 TTTAGGCTCAATTTGGTTCATC-TCAAACG
*
29746 TTTAGACTCAA
1 TTTAGGCTCAA
29757 ATTGAGCAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 15 0.42
30 1 0.03
31 20 0.56
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (29 bp):
TTTAGGCTCAATTTGGTTCATCTCAAACG
Found at i:41282 original size:28 final size:28
Alignment explanation
Indices: 41227--41282 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
41217 TAGATAGATT
** **
41227 ATCTATATCTATAATTTTTTTTGAAATC
1 ATCTATATCTATAATTTAATCGGAAATC
*
41255 ATCTATATCTATAATTTAATCGGTAATC
1 ATCTATATCTATAATTTAATCGGAAATC
41283 GAACTATCTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.34, C:0.12, G:0.05, T:0.48
Consensus pattern (28 bp):
ATCTATATCTATAATTTAATCGGAAATC
Found at i:42605 original size:16 final size:18
Alignment explanation
Indices: 42568--42606 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
42558 GGTTTTCTTT
*
42568 TTATTAATCTTTTAAGAG
1 TTATTAATCTTTCAAGAG
42586 TTATT-ATCTTTCAA-AG
1 TTATTAATCTTTCAAGAG
42602 TTATT
1 TTATT
42607 GTGTGTGCGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 8 0.40
18 5 0.25
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (18 bp):
TTATTAATCTTTCAAGAG
Found at i:46898 original size:5 final size:6
Alignment explanation
Indices: 46868--46895 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
46858 GTTTACTATA
46868 TTTTTC TTTTTC TTTTTC TTTTTC TTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTT
46896 CTTACTGTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTC
Found at i:64760 original size:2 final size:2
Alignment explanation
Indices: 64753--64789 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
64743 AATCTAAAAC
64753 AT 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 AT A
64790 AAGATAACCC
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:68815 original size:73 final size:73
Alignment explanation
Indices: 68695--68871 Score: 264
Period size: 73 Copynumber: 2.4 Consensus size: 73
68685 GGAAAATGGA
* * * *
68695 CCATTTCAGTTGACTAAAACAGAAGTTGAAAGCGCCCAGTCGGTTGTGTCCTTTCTGTATAAACA
1 CCATTTCACTCGACTAAAACAGAAGTTGAAAGCGCCCAGTCGATTGTGTCCTTTCTGTATAAAAA
68760 GTAAAATG
66 GTAAAATG
* *
68768 CCATTTTACTCGACTAAAACAGAAGTTGAAAGCGCCCAGTCTATTGTGTCCTTTCTGTATAAAAA
1 CCATTTCACTCGACTAAAACAGAAGTTGAAAGCGCCCAGTCGATTGTGTCCTTTCTGTATAAAAA
68833 GTAAAATG
66 GTAAAATG
* * * *
68841 CCATTTCAGTCGAATGAAACTGAAGTTGAAA
1 CCATTTCACTCGACTAAAACAGAAGTTGAAA
68872 TGACCTGGGT
Statistics
Matches: 93, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
73 93 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (73 bp):
CCATTTCACTCGACTAAAACAGAAGTTGAAAGCGCCCAGTCGATTGTGTCCTTTCTGTATAAAAA
GTAAAATG
Found at i:73981 original size:73 final size:73
Alignment explanation
Indices: 73861--74037 Score: 300
Period size: 73 Copynumber: 2.4 Consensus size: 73
73851 GGAAAATGGA
* *
73861 CCATTTCAGTCGACTAAAACAGAAGTTGAAAGCGCCTAGTCGGTTGTGTCCTTTCTGTATAAACA
1 CCATTTCAGTCGACTAAAACAGAAGTTGAAAGCGCCCAGTCGATTGTGTCCTTTCTGTATAAACA
73926 GTAAAATG
66 GTAAAATG
*
73934 CCATTTCAGTCGACTAAAACAGAAGTTGAAAGCGCCCAGTCTATTGTGTCCTTTCTGTATAAACA
1 CCATTTCAGTCGACTAAAACAGAAGTTGAAAGCGCCCAGTCGATTGTGTCCTTTCTGTATAAACA
73999 GTAAAATG
66 GTAAAATG
* * *
74007 CCATTTCAGTCGAATGAAACTGAAGTTGAAA
1 CCATTTCAGTCGACTAAAACAGAAGTTGAAA
74038 TGACCCGGGT
Statistics
Matches: 98, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 98 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (73 bp):
CCATTTCAGTCGACTAAAACAGAAGTTGAAAGCGCCCAGTCGATTGTGTCCTTTCTGTATAAACA
GTAAAATG
Found at i:83436 original size:10 final size:10
Alignment explanation
Indices: 83421--83445 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
83411 GTTGCTGGAC
83421 AATTCCAGAA
1 AATTCCAGAA
83431 AATTCCAGAA
1 AATTCCAGAA
83441 AATTC
1 AATTC
83446 TAGAGTCCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (10 bp):
AATTCCAGAA
Found at i:84380 original size:12 final size:12
Alignment explanation
Indices: 84347--84380 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
84337 TGCTTTATAA
*
84347 TTATTGTTTGCT
1 TTATTATTTGCT
84359 TTATTAATTTGCT
1 TTATT-ATTTGCT
84372 TTATTATTT
1 TTATTATTT
84381 AGATTTAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.18, C:0.06, G:0.09, T:0.68
Consensus pattern (12 bp):
TTATTATTTGCT
Found at i:84876 original size:11 final size:11
Alignment explanation
Indices: 84860--84885 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
84850 ACAATGAACA
84860 TGAAAAGAGTT
1 TGAAAAGAGTT
84871 TGAAAAGAGTT
1 TGAAAAGAGTT
84882 TGAA
1 TGAA
84886 TTTTTCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.27, T:0.27
Consensus pattern (11 bp):
TGAAAAGAGTT
Found at i:87034 original size:48 final size:48
Alignment explanation
Indices: 86900--87272 Score: 439
Period size: 49 Copynumber: 7.6 Consensus size: 48
86890 AAAAATTGGC
* * * **
86900 GCCTTCCGTTCGGGAAGGGCATTTTGGGAAGA-AGTAAGTAAAAATAAGC
1 GCCTTCCGTCCGGGAAGGGCATTTTGGGAA-ATAGCAGGT-AAAATAAAT
* * *
86949 GTCTTCCATCCGGGAAGGGCAGTTTTGGAAAATAGCAGGTAAATATAAAT
1 GCCTTCCGTCCGGGAAGGGCA-TTTTGGGAAATAGCAGGTAAA-ATAAAT
86999 GCCTTCCGTCCGGGAAGGGCATTTT-GGAAATAGCAGGTAAATATAAAT
1 GCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGGTAAA-ATAAAT
* * * ** *
87047 GCCTTCCGTCCGGGAAGGGTAGTTTGGGAGATAGTGGGTGAAAA-AGAGT
1 GCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGGT-AAAATA-AAT
* **
87096 GCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCGGGTGAAAAGGAAT
1 GCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGGT-AAAATAAAT
*
87145 GCCTTCCGTCCGTGAAGGGCATTTTGGGAAATAGCAGGTAAAA-AGAAT
1 GCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGGTAAAATA-AAT
* *
87193 GCCTCCCGTCCGGGAAGGGCATTTTGGGTAATAGCAGGTAAATATAAAT
1 GCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGGTAAA-ATAAAT
*
87242 GCCTTCCGTCCGGGAAGGGCAGTTTGGGAAA
1 GCCTTCCGTCCGGGAAGGGCATTTTGGGAAA
87273 AATAAAATTT
Statistics
Matches: 282, Mismatches: 32, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
48 92 0.33
49 150 0.53
50 40 0.14
ACGTcount: A:0.29, C:0.16, G:0.32, T:0.23
Consensus pattern (48 bp):
GCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGGTAAAATAAAT
Found at i:87115 original size:97 final size:97
Alignment explanation
Indices: 86900--87272 Score: 475
Period size: 97 Copynumber: 3.8 Consensus size: 97
86890 AAAAATTGGC
* * * * ** * *
86900 GCCTTCCGTTCGGGAAGGGCATTTTGGGAAGA-AGTAAGTAAAAATAAGCGTCTTCCATCCGGGA
1 GCCTTCCGTCCGGGAAGGGCATTTTGGGAA-ATAGCAGGTAAATATAAATGCCTTCCGTCCGGGA
*
86964 AGGGCAGTTTTGGAAAATAGCAGGTAAATATA-AAT
65 AGGGCAG-TTTGGGAAATAGCAGGTAAA-A-AGAAT
86999 GCCTTCCGTCCGGGAAGGGCATTTT-GGAAATAGCAGGTAAATATAAATGCCTTCCGTCCGGGAA
1 GCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGGTAAATATAAATGCCTTCCGTCCGGGAA
* * ** *
87063 GGGTAGTTTGGGAGATAGTGGGTGAAAAAGAGT
66 GGGCAGTTTGGGAAATAGCAGGT-AAAAAGAAT
* ** *
87096 GCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCGGGTGAAA-AGGAATGCCTTCCGTCCGTGA
1 GCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGGT-AAATATAAATGCCTTCCGTCCGGGA
*
87160 AGGGCATTTTGGGAAATAGCAGGTAAAAAGAAT
65 AGGGCAGTTTGGGAAATAGCAGGTAAAAAGAAT
* *
87193 GCCTCCCGTCCGGGAAGGGCATTTTGGGTAATAGCAGGTAAATATAAATGCCTTCCGTCCGGGAA
1 GCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGGTAAATATAAATGCCTTCCGTCCGGGAA
87258 GGGCAGTTTGGGAAA
66 GGGCAGTTTGGGAAA
87273 AATAAAATTT
Statistics
Matches: 237, Mismatches: 31, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
96 4 0.02
97 119 0.50
98 87 0.37
99 27 0.11
ACGTcount: A:0.29, C:0.16, G:0.32, T:0.23
Consensus pattern (97 bp):
GCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGGTAAATATAAATGCCTTCCGTCCGGGAA
GGGCAGTTTGGGAAATAGCAGGTAAAAAGAAT
Found at i:87203 original size:146 final size:146
Alignment explanation
Indices: 86951--87272 Score: 422
Period size: 146 Copynumber: 2.2 Consensus size: 146
86941 AAATAAGCGT
* * *
86951 CTTCCATCCGGGAAGGGCAGTTTTGGAAAATAGCAGGTAAATATAAATGCCTTCCGTCCGGGAAG
1 CTTCCGTCCGGGAAGGGCA-TTTTGGGAAATAGCAGGTAAATAGAAATGCCTTCCGTCCGGGAAG
* *
87016 GGCATTTTGGAAATAGCAGGTAAATATAAATGCCTTCCGTCCGGGAAGGGTAGTTTGGG-AGATA
65 GGCATTTTGGAAATAGCAGGTAAATATAAATGCCTCCCGTCCGGGAAGGGCAGTTTGGGTA-ATA
** *
87080 GTGGGTGAAA-A-AGAGTGC
129 GCAGGT-AAATATA-AATGC
* * *
87098 CTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCGGGTGAAA-AGGAATGCCTTCCGTCCGTGAAG
1 CTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGGT-AAATAGAAATGCCTTCCGTCCGGGAAG
*
87162 GGCATTTTGGGAAATAGCAGGTAAA-A-AGAATGCCTCCCGTCCGGGAAGGGCATTTTGGGTAAT
65 GGCATTTT-GGAAATAGCAGGTAAATATA-AATGCCTCCCGTCCGGGAAGGGCAGTTTGGGTAAT
87225 AGCAGGTAAATATAAATGC
128 AGCAGGTAAATATAAATGC
*
87244 CTTCCGTCCGGGAAGGGCAGTTTGGGAAA
1 CTTCCGTCCGGGAAGGGCATTTTGGGAAA
87273 AATAAAATTT
Statistics
Matches: 156, Mismatches: 13, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
145 4 0.03
146 113 0.72
147 39 0.25
ACGTcount: A:0.29, C:0.16, G:0.32, T:0.23
Consensus pattern (146 bp):
CTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGGTAAATAGAAATGCCTTCCGTCCGGGAAGG
GCATTTTGGAAATAGCAGGTAAATATAAATGCCTCCCGTCCGGGAAGGGCAGTTTGGGTAATAGC
AGGTAAATATAAATGC
Done.