Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004852.1 Corchorus capsularis cultivar CVL-1 contig04870, 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: 3560
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:1189 original size:2 final size:2
Alignment explanation
Indices: 1182--1206 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1172 AAATAAGTGA
1182 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
1207 TTTTTTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2289 original size:29 final size:28
Alignment explanation
Indices: 2247--2311 Score: 94
Period size: 29 Copynumber: 2.3 Consensus size: 28
2237 CCAGGACGTC
*
2247 TCCTTCTGGTATATCAGGCGAAAAAATCT
1 TCCTTCTGGTATATCAAGCG-AAAAATCT
*
2276 TCCTTCTGGTATATCAAGCGGAAAATCT
1 TCCTTCTGGTATATCAAGCGAAAAATCT
*
2304 TCCCTCTG
1 TCCTTCTG
2312 ATATGTCACA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 14 0.42
29 19 0.58
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (28 bp):
TCCTTCTGGTATATCAAGCGAAAAATCT
Found at i:2991 original size:155 final size:156
Alignment explanation
Indices: 2589--3309 Score: 1019
Period size: 155 Copynumber: 4.6 Consensus size: 156
2579 TCGAGTCCTG
*
2589 CTTCATGGTGAACTAGGTTTCGCACCCCAAACTGTCCTTAAATGAAAAACGTGCATAAGTTTTTC
1 CTTCATGGTGAACTTGGTTTCGCACCCCAAACTGTCCTTAAATGAAAAACGTGCATAAGTTTTTC
*
2654 ATTATAAGTCTGATTGAGATGAAACTTTTCCAAGGGACTTAGATTATCTCCACAAAACTACGGAA
66 ATTATAAGTCTGATTGAGATGAAACTTTGCCAAGGGACTTAGATTATCTCCACAAAACTACGGAA
*
2719 AAAAGTTC-AAGTAAAATTGAGCTCTC
131 AAAA-TTCTAAGTAAAACTGAGCTCTC
* * * * *
2745 ATTCATGGTGAACTTGGTTTCTCACCCCGAATTGTCCTAAAATGAAAAACGTGCATAAGTTTTTC
1 CTTCATGGTGAACTTGGTTTCGCACCCCAAACTGTCCTTAAATGAAAAACGTGCATAAGTTTTTC
* *
2810 ATTCTAAGTCCT-ATTGAGATGAACCTTTGCCAAGGGACTTAGATTATCTCCACAAAACTACGGA
66 ATTATAAGT-CTGATTGAGATGAAACTTTGCCAAGGGACTTAGATTATCTCCACAAAACTACGGA
* *
2874 AAAAATTCTAAATAAAACAGAGCTCTC
130 AAAAATTCTAAGTAAAACTGAGCTCTC
* * *
2901 CTTCATGGTG-ACTAGGTTCCGCACCCCAAACTGTCCTTAAATGAAAAACGTGCATAAGTTTTTA
1 CTTCATGGTGAACTTGGTTTCGCACCCCAAACTGTCCTTAAATGAAAAACGTGCATAAGTTTTTC
*
2965 ATTATAAGTCTGATTGAGATGAACCTTTGCCAAGGGACTTAGATTATCTCCACAAAACTACGGAA
66 ATTATAAGTCTGATTGAGATGAAACTTTGCCAAGGGACTTAGATTATCTCCACAAAACTACGGAA
3030 AAAATTCTAAGTAAAACTGAGCTCTC
131 AAAATTCTAAGTAAAACTGAGCTCTC
* *
3056 CTTCATGGTGAACTTGGTTTCTCACCCCGAACTGTCCTTAAATGAAAAACGTGCATAAGTTTTTC
1 CTTCATGGTGAACTTGGTTTCGCACCCCAAACTGTCCTTAAATGAAAAACGTGCATAAGTTTTTC
* * * * *
3121 ATTCTGAGTCCT-ATTGAGCTGAAA-TTTGACCAAGGGTCTTAGATTATCTCCACGAAAA-TATG
66 ATTATAAGT-CTGATTGAGATGAAACTTTG-CCAAGGGACTTAGATTATCTCCAC-AAAACTACG
* * *
3183 G-ATAAATTCTAAGTAAAACCGAACTC-C
128 GAAAAAATTCTAAGTAAAACTGAGCTCTC
* * * *
3210 CTTTCATAGTGAAGTTGGTTTCACACCCCAAACTGTCCTTAACTGAAAAACGTGCATAAGTTTTT
1 C-TTCATGGTGAACTTGGTTTCGCACCCCAAACTGTCCTTAAATGAAAAACGTGCATAAGTTTTT
* * *
3275 CATCT-TAAGTCCGTTTGAGATGAAACTTAGCCAAG
65 CAT-TATAAGTCTGATTGAGATGAAACTTTGCCAAG
3310 ATGATCTACA
Statistics
Matches: 507, Mismatches: 47, Indels: 23
0.88 0.08 0.04
Matches are distributed among these distances:
154 5 0.01
155 251 0.50
156 243 0.48
157 8 0.02
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (156 bp):
CTTCATGGTGAACTTGGTTTCGCACCCCAAACTGTCCTTAAATGAAAAACGTGCATAAGTTTTTC
ATTATAAGTCTGATTGAGATGAAACTTTGCCAAGGGACTTAGATTATCTCCACAAAACTACGGAA
AAAATTCTAAGTAAAACTGAGCTCTC
Found at i:3164 original size:311 final size:310
Alignment explanation
Indices: 2589--3309 Score: 1119
Period size: 311 Copynumber: 2.3 Consensus size: 310
2579 TCGAGTCCTG
2589 CTTCATGGTGAACTAGGTTTCGCACCCCAAACTGTCCTTAAATGAAAAACGTGCATAAGTTTTTC
1 CTTCATGGTGAACTAGGTTTCGCACCCCAAACTGTCCTTAAATGAAAAACGTGCATAAGTTTTTC
*
2654 ATTATAAGTCTGATTGAGATGAAACTTTTCCAAGGGACTTAGATTATCTCCACAAAACTACGGAA
66 ATTATAAGTCTGATTGAGATGAAACTTTGCCAAGGGACTTAGATTATCTCCACAAAACTACGGAA
* *
2719 AAAAGTTCAAGTAAAATTGAGCTCTCATTCATGGTGAACTTGGTTTCTCACCCCGAATTGTCCTA
131 AAAAGTTCAAGTAAAACTGAGCTCTCATTCATGGTGAACTTGGTTTCTCACCCCGAACTGTCCTA
*
2784 AAATGAAAAACGTGCATAAGTTTTTCATTCTAAGTCCTATTGAGATGAACCTTTGCCAAGGGACT
196 AAATGAAAAACGTGCATAAGTTTTTCATTCTAAGTCCTATTGAGATGAACATTTGCCAAGGGACT
*
2849 TAGATTATCTCCAC-AAAACTACGGAAAAAATTCTAAATAAAACAGAGCTCTC
261 TAGATTATCTCCACGAAAA-TACGG-AAAAATTCTAAATAAAACAGAACTC-C
* *
2901 CTTCATGGTG-ACTAGGTTCCGCACCCCAAACTGTCCTTAAATGAAAAACGTGCATAAGTTTTTA
1 CTTCATGGTGAACTAGGTTTCGCACCCCAAACTGTCCTTAAATGAAAAACGTGCATAAGTTTTTC
*
2965 ATTATAAGTCTGATTGAGATGAACCTTTGCCAAGGGACTTAGATTATCTCCACAAAACTACGGAA
66 ATTATAAGTCTGATTGAGATGAAACTTTGCCAAGGGACTTAGATTATCTCCACAAAACTACGGAA
*
3030 AAAA-TTCTAAGTAAAACTGAGCTCTCCTTCATGGTGAACTTGGTTTCTCACCCCGAACTGTCCT
131 AAAAGTTC-AAGTAAAACTGAGCTCTCATTCATGGTGAACTTGGTTTCTCACCCCGAACTGTCCT
* * * *
3094 TAAATGAAAAACGTGCATAAGTTTTTCATTCTGAGTCCTATTGAGCTGAA-ATTTGACCAAGGGT
195 AAAATGAAAAACGTGCATAAGTTTTTCATTCTAAGTCCTATTGAGATGAACATTTG-CCAAGGGA
* * * *
3158 CTTAGATTATCTCCACGAAAATATGGATAAATTCTAAGTAAAACCGAACTCC
259 CTTAGATTATCTCCACGAAAATACGGAAAAATTCTAAATAAAACAGAACTCC
* * * * *
3210 CTTTCATAGTGAAGTTGGTTTCACACCCCAAACTGTCCTTAACTGAAAAACGTGCATAAGTTTTT
1 C-TTCATGGTGAACTAGGTTTCGCACCCCAAACTGTCCTTAAATGAAAAACGTGCATAAGTTTTT
* * *
3275 CATCT-TAAGTCCGTTTGAGATGAAACTTAGCCAAG
65 CAT-TATAAGTCTGATTGAGATGAAACTTTGCCAAG
3310 ATGATCTACA
Statistics
Matches: 375, Mismatches: 28, Indels: 13
0.90 0.07 0.03
Matches are distributed among these distances:
309 2 0.01
310 36 0.10
311 322 0.86
312 15 0.04
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (310 bp):
CTTCATGGTGAACTAGGTTTCGCACCCCAAACTGTCCTTAAATGAAAAACGTGCATAAGTTTTTC
ATTATAAGTCTGATTGAGATGAAACTTTGCCAAGGGACTTAGATTATCTCCACAAAACTACGGAA
AAAAGTTCAAGTAAAACTGAGCTCTCATTCATGGTGAACTTGGTTTCTCACCCCGAACTGTCCTA
AAATGAAAAACGTGCATAAGTTTTTCATTCTAAGTCCTATTGAGATGAACATTTGCCAAGGGACT
TAGATTATCTCCACGAAAATACGGAAAAATTCTAAATAAAACAGAACTCC
Done.