Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014939.1 Corchorus capsularis cultivar CVL-1 contig14960, 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: 7519
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Found at i:112 original size:22 final size:23
Alignment explanation
Indices: 87--131 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
77 AATAAGATCT
*
87 ACTCATTAAT-CATAAACTAAAA
1 ACTCATAAATCCATAAACTAAAA
109 ACTCATAAATCCATAAACTAAAA
1 ACTCATAAATCCATAAACTAAAA
132 GCCAAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.56, C:0.20, G:0.00, T:0.24
Consensus pattern (23 bp):
ACTCATAAATCCATAAACTAAAA
Found at i:2163 original size:36 final size:36
Alignment explanation
Indices: 2084--2544 Score: 305
Period size: 36 Copynumber: 12.9 Consensus size: 36
2074 TAGAATAAGT
** * * *
2084 AACTGAAGAAAAACCACCCTGGATCATTCC-AAACTG
1 AACTGAAGAACGACCACCCTCGATCATTCCGACA-TA
* * * **
2120 AATTGAAGGACGACCACCCTCTATCATTCCGACGCA
1 AACTGAAGAACGACCACCCTCGATCATTCCGACATA
* * * * * *
2156 AACTGAAGAAAGACCACCCTGGGTCA-ACTGAAATA
1 AACTGAAGAACGACCACCCTCGATCATTCCGACATA
* *
2191 AACTGAAGAATGACCACCCTCGATCATTCCAGAC-TG
1 AACTGAAGAACGACCACCCTCGATCATTCC-GACATA
* * *
2227 AACTAAAGAACAACCACCCTCGATCATTCCGA-TTCA
1 AACTGAAGAACGACCACCCTCGATCATTCCGACAT-A
* * * * * *
2263 AACTGAAGAAAGACCACCCTAGGTCA-ACTGAAATA
1 AACTGAAGAACGACCACCCTCGATCATTCCGACATA
* * *
2298 AACTGAAGAACAACTACCCTCGATCATTCTGGAC-TA
1 AACTGAAGAACGACCACCCTCGATCATTC-CGACATA
** *
2334 AACTGAAGAATAACCACCCTCGATCATTCTGAC-TCA
1 AACTGAAGAACGACCACCCTCGATCATTCCGACAT-A
* * * * * *
2370 AACTGATGAAAGACCACCCTTGATCATTTC-AAACTG
1 AACTGAAGAACGACCACCCTCGATCATTCCGACA-TA
2406 AACTGAAGAACGACCACCCTCGATCATTCCGACATA
1 AACTGAAGAACGACCACCCTCGATCATTCCGACATA
* * **
2442 AACTGAAGATCAACCACCCTCGATCATTCTTAC-TCA
1 AACTGAAGAACGACCACCCTCGATCATTCCGACAT-A
* * * * ** * * *
2478 ACCTAAAGAAAGACCACCCTGGGCCA-ACTGAAATA
1 AACTGAAGAACGACCACCCTCGATCATTCCGACATA
2513 AACTG-AGAAACGACCACCCTCGATCATTCCGA
1 AACTGAAG-AACGACCACCCTCGATCATTCCGA
2545 ACTGAACTTA
Statistics
Matches: 321, Mismatches: 88, Indels: 32
0.73 0.20 0.07
Matches are distributed among these distances:
34 2 0.01
35 82 0.26
36 229 0.71
37 8 0.02
ACGTcount: A:0.38, C:0.30, G:0.14, T:0.19
Consensus pattern (36 bp):
AACTGAAGAACGACCACCCTCGATCATTCCGACATA
Found at i:2217 original size:107 final size:107
Alignment explanation
Indices: 2084--2568 Score: 580
Period size: 107 Copynumber: 4.5 Consensus size: 107
2074 TAGAATAAGT
** * * * * * *
2084 AACTGAAGAAAAACCACCCTGGATCATTCCAAACTGAATTGAAGGACGACCACCCTCTATCATTC
1 AACTGAAGAACGACCACCCTCGATCATTCCAGACTGAACTGAAGAACAACCACCCTCGATCATTC
*
2149 CGACGCAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATA
66 CGACTCAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATA
* *
2191 AACTGAAGAATGACCACCCTCGATCATTCCAGACTGAACTAAAGAACAACCACCCTCGATCATTC
1 AACTGAAGAACGACCACCCTCGATCATTCCAGACTGAACTGAAGAACAACCACCCTCGATCATTC
* *
2256 CGATTCAAACTGAAGAAAGACCACCCTAGGTCAACTGAAATA
66 CGACTCAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATA
* * ** * *
2298 AACTGAAGAACAACTACCCTCGATCATTCTGGACTAAACTGAAGAATAACCACCCTCGATCATTC
1 AACTGAAGAACGACCACCCTCGATCATTCCAGACTGAACTGAAGAACAACCACCCTCGATCATTC
* * * * ** * *
2363 TGACTCAAACTGATGAAAGACCACCCTTGATCATTTCAAACTG
66 CGACTCAAACTGAAGAAAGACCACCCTGGGTCAACTGAAA-TA
* *
2406 AACTGAAGAACGACCACCCTCGATCATTCC-GACATAAACTGAAGATCAACCACCCTCGATCATT
1 AACTGAAGAACGACCACCCTCGATCATTCCAGAC-TGAACTGAAGAACAACCACCCTCGATCATT
** * * *
2470 CTTACTCAACCTAAAGAAAGACCACCCTGGGCCAACTGAAATA
65 CCGACTCAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATA
* * *
2513 AACTG-AGAAACGACCACCCTCGATCATTCC-GAACTGAACTTAAGAGCAAGCACCCT
1 AACTGAAG-AACGACCACCCTCGATCATTCCAG-ACTGAACTGAAGAACAACCACCCT
2569 GGGTCATTGA
Statistics
Matches: 325, Mismatches: 49, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
106 2 0.01
107 234 0.72
108 89 0.27
ACGTcount: A:0.38, C:0.29, G:0.14, T:0.19
Consensus pattern (107 bp):
AACTGAAGAACGACCACCCTCGATCATTCCAGACTGAACTGAAGAACAACCACCCTCGATCATTC
CGACTCAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATA
Found at i:2489 original size:215 final size:214
Alignment explanation
Indices: 2132--2541 Score: 572
Period size: 215 Copynumber: 1.9 Consensus size: 214
2122 TTGAAGGACG
* * *
2132 ACCACCCTCTATCATTCCGACGCAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGA
1 ACCACCCTCGATCATTCCGACGCAAACTGAAGAAAGACCACCCTGGATCAACTCAAATAAACTGA
* * *
2197 AGAATGACCACCCTCGATCATTCCAGACTGAACTAAAGAACAACCACCCTCGATCATTCCGATTC
66 AGAACGACCACCCTCGATCATTCCAGACTAAACTAAAGAACAACCACCCTCGATCATTCCGACTC
* * *
2262 AAACTGAAGAAAGACCACCCTAGGTCAACTGAAATAAACTGA-AGAACAACTACCCTCGATCATT
131 AAACTAAAGAAAGACCACCCTAGGCCAACTGAAATAAACTGAGA-AACAACCACCCTCGATCATT
2326 CTGGACTAAACTGAAGAATA
195 CTGGACTAAACTGAAGAATA
* * * * ** *
2346 ACCACCCTCGATCATTCTGACTCAAACTGATGAAAGACCACCCTTGATCATTTCAAACTGAACTG
1 ACCACCCTCGATCATTCCGACGCAAACTGAAGAAAGACCACCCTGGATCAACTCAAA-TAAACTG
* * **
2411 AAGAACGACCACCCTCGATCATTCC-GACATAAACTGAAGATCAACCACCCTCGATCATTCTTAC
65 AAGAACGACCACCCTCGATCATTCCAGAC-TAAACTAAAGAACAACCACCCTCGATCATTCCGAC
* * *
2475 TCAACCTAAAGAAAGACCACCCTGGGCCAACTGAAATAAACTGAGAAACGACCACCCTCGATCAT
129 TCAAACTAAAGAAAGACCACCCTAGGCCAACTGAAATAAACTGAGAAACAACCACCCTCGATCAT
2540 TC
194 TC
2542 CGAACTGAAC
Statistics
Matches: 170, Mismatches: 23, Indels: 5
0.86 0.12 0.03
Matches are distributed among these distances:
214 51 0.30
215 118 0.69
216 1 0.01
ACGTcount: A:0.37, C:0.30, G:0.14, T:0.19
Consensus pattern (214 bp):
ACCACCCTCGATCATTCCGACGCAAACTGAAGAAAGACCACCCTGGATCAACTCAAATAAACTGA
AGAACGACCACCCTCGATCATTCCAGACTAAACTAAAGAACAACCACCCTCGATCATTCCGACTC
AAACTAAAGAAAGACCACCCTAGGCCAACTGAAATAAACTGAGAAACAACCACCCTCGATCATTC
TGGACTAAACTGAAGAATA
Found at i:4074 original size:21 final size:23
Alignment explanation
Indices: 4033--4087 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 23
4023 TAGAGCTTTA
*
4033 TCTTTTTTCTTCTTCTGCTCT-T
1 TCTTTTTTCTTTTTCTGCTCTCT
4055 TCTTTTTTCTTTTTCT-CTCTCT
1 TCTTTTTTCTTTTTCTGCTCTCT
4077 T-TTTTTTCTTT
1 TCTTTTTTCTTT
4088 CGTTTCACCA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
21 14 0.45
22 17 0.55
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.75
Consensus pattern (23 bp):
TCTTTTTTCTTTTTCTGCTCTCT
Found at i:4088 original size:19 final size:20
Alignment explanation
Indices: 4033--4088 Score: 71
Period size: 19 Copynumber: 2.8 Consensus size: 20
4023 TAGAGCTTTA
*
4033 TCTTTTTTCTTCTTCTGCTCTT
1 TCTTTTTTCTTCTT-T-CTCTC
4055 TCTTTTTTCTT-TTTCTCTC
1 TCTTTTTTCTTCTTTCTCTC
4074 TCTTTTTT-TTCTTTC
1 TCTTTTTTCTTCTTTC
4089 GTTTCACCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
18 2 0.06
19 16 0.50
20 1 0.03
21 2 0.06
22 11 0.34
ACGTcount: A:0.00, C:0.25, G:0.02, T:0.73
Consensus pattern (20 bp):
TCTTTTTTCTTCTTTCTCTC
Found at i:4824 original size:25 final size:25
Alignment explanation
Indices: 4795--4849 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 25
4785 AAAAACTAAA
* * * *
4795 AAAAACTTTTTGAAAACTCATTTTTG
1 AAAACCTTTTCGAAAA-TAATTCTTG
4821 AAAACCTTTTCGAAAATAATTCTTG
1 AAAACCTTTTCGAAAATAATTCTTG
4846 AAAA
1 AAAA
4850 ATACTTCTCG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 11 0.44
26 14 0.56
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.36
Consensus pattern (25 bp):
AAAACCTTTTCGAAAATAATTCTTG
Found at i:4979 original size:34 final size:32
Alignment explanation
Indices: 4917--4980 Score: 76
Period size: 34 Copynumber: 1.9 Consensus size: 32
4907 ACTTCTTTCT
* *
4917 CTTTTCTCTTTTTCTTCATTTTTTTTTTCATC
1 CTTTTCACTTTTTCTTCATTTTTCTTTTCATC
4949 CTTTTCACTTTTTCTCTTC-TTTTTCCTTTTCA
1 CTTTTCAC-TTTT-TCTTCATTTTT-CTTTTCA
4981 GGAGGGAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 7 0.26
33 9 0.33
34 11 0.41
ACGTcount: A:0.06, C:0.25, G:0.00, T:0.69
Consensus pattern (32 bp):
CTTTTCACTTTTTCTTCATTTTTCTTTTCATC
Done.