Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010864.1 Corchorus capsularis cultivar CVL-1 contig10885, 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: 12187
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:1770 original size:328 final size:325
Alignment explanation
Indices: 563--2906 Score: 2454
Period size: 328 Copynumber: 7.2 Consensus size: 325
553 AATAAAAACC
* *
563 TTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAG-CAGGGCTTTTGGAACGCGTTTTTTA
1 TTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGCCGGGGC-TCTGGAACGCG-TTTTTA
* * * *
627 ACCAAAAACTGTGATG--GTTAGTACACGATTTCGGCTAAAAACTGACTCGAAAATATTTTTTCT
64 GCCAAAAACCGTGATGTAGTTAGTACACGATTTCGGCTAAAAACTGACCCG-AAATTTTTTTTCT
* * * * ** *
690 CAATTTTTTGCCACAATAATC--AGAAAATATATAATTTAACACCAAAATTATTGACGAGCTTTT
128 CAATTTTTTGCCACAATACTCAAAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTT
* * *
753 T-ACACTTCTAATATCATTTTTCCATTTTTTTCCGAATTAATTTATAATTAAATCGAAATGTGAT
193 TCACACTTCTAATATCATTTTTCCAATTTTTTCCGAATTAATTTCTAATTAAATCGAAATATGAT
* * * * *
817 TTAGATGCTCGTCAAAATAAATCCTTAATATTCAATGTGGCTGACATTTGGTTCAGTGTATATAG
258 TTAGATGCTCGTAAAAACAAATCCTT-ATATCCAATGTGGCTGGCATTTGGTTCAATGTATATAG
882 ATAT
322 ATAT
*
886 TTCAAGGAGTCTTTGTC-CCAAAAATCATGCAAAATTGA-CTCGGGGCTCCGGAACGCGTTTTTA
1 TTCAAGGAGTCTTTG-CGCCAAAAATCATGCAAAATTGAGC-CGGGGCTCTGGAACGCGTTTTTA
* *
949 GCCAAAAACCGTTATG-A-TTAGTACACGATTTCGGCTAAAAACTAACCCGAAATTTTTTTTCTC
64 GCCAAAAACCGTGATGTAGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAATTTTTTTTCTC
* *
1012 AATTTTTTACCATAATACTCAGAAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGC-TTT
129 AATTTTTTGCCACAATACTCA-AAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTT
* *
1076 TCACACTTCTAATATCATTTTT-CAATTTTTTCCGAATTAATTTCTAATAAAATCAAAATATGAT
193 TCACACTTCTAATATCATTTTTCCAATTTTTTCCGAATTAATTTCTAATTAAATCGAAATATGAT
* * * *
1140 TTAGATGCT-GTAAAAACAAATCCTTATAGCCAACGTGGCTGACAGTTGGTTCAATGTATATAGA
258 TTAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGGCATTTGGTTCAATGTATATAGA
1204 TAT
323 TAT
* * * * *
1207 TTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTC-GGGCTTTCAGAACTCGGTTTTAG
1 TTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGCCGGGGCTCT-GGAACGCGTTTTTAG
* * *
1271 CCAAAAATCGTAATG--GTTAGTACACAATTTCGGCTAAAAACTGACCCAGAAA-TTTTTTTCTT
65 CCAAAAACCGTGATGTAGTTAGTACACGATTTCGGCTAAAAACTGACCC-GAAATTTTTTTTC-T
* *
1333 CAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAATGCCAAAAAGATTGACGGGC-TTT
128 CAATTTTTTGCCACAATACTCAAAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTT
* * * *
1397 TCACGCTTCTGATATCATTTTGTTCCATTTTTTTCCGATTTAATTTCTAATTAAATCGAAATATG
193 TCACACTTCTAATATCA-TTT-TTCCAATTTTTTCCGAATTAATTTCTAATTAAATCGAAATATG
* *
1462 ATTTAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGGTATTTGGTTCAATGTATATG
256 ATTTAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGGCATTTGGTTCAATGTATATA
1527 GATAT
321 GATAT
* * * * *
1532 TTCAAGGAGTCTTTGTGCCAAAAATTATGGAAAATTGAGCCGGGGCTCTGGGACGCGTTTTTAAC
1 TTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGCCGGGGCTCTGGAACGCGTTTTTAGC
* ** **
1597 AAAAAATTGTGATGGTTAGTTAGTACATTATTTCGGCTAAAAACTGACCCGAAATTTTTTTTCTC
66 CAAAAACCGTGAT-G-TAGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAATTTTTTTTCTC
* * *
1662 AATTTTTGGCCACAATACTCAAAAAAAATTTATAATTCAACGCCAAAAAGATTGGCGGGCTTTTT
129 AATTTTTTGCCACAATACTCAAAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTT
* *
1727 CACGCTTCTAATATCATTTTTCCATATTTTTTCCGAATTAATTTATAATTAAATCGAAATATGAT
194 CACACTTCTAATATCATTTTTCCA-ATTTTTTCCGAATTAATTTCTAATTAAATCGAAATATGAT
* * ** *
1792 TTAGATGCTCGTAAAAACAAATCCTTACATCCAATGTGGCTGACATTTATTTCAATTTATATAGA
258 TTAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGGCATTTGGTTCAATGTATATAGA
1857 TAT
323 TAT
* ** * * * *
1860 TTCATGGAGTCTTTGTACCAAAAATCATGCAAAATTGAGTCGGGGCTCCGGAACGTGTTTTTAGG
1 TTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGCCGGGGCTCTGGAACGCGTTTTTAGC
* *
1925 CAAAAACCGTGATG-A-TTAGTACACGATTTCGGCTAAAAACTTACCCGAAA-TTTTTTTCTCTA
66 CAAAAACCGTGATGTAGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAATTTTTTTTCTCAA
* * * ** *
1987 TTTTTTGCCATAATACTCAGAAAAAATATATAATTCAACCCCAAAAAGATTGACATGC-TTTTCC
131 TTTTTTGCCACAATACTCAAAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTTCA
* * * * * * ** **
2051 CTCTTCGAATATCGTTTTTCC-ATTTTTTCTGAATTAATTTCTAATTAAATTGAAACAAAATTGG
196 CACTTCTAATATCATTTTTCCAATTTTTTCCGAATTAATTTCTAATTAAATCGAAATATGATTTA
** * * ** * * * *
2115 GATAATCGAAAAAAGAAATTATTATATCCAATATGGCTGAG-GTATGGTTCGA--TATATAGATA
261 GATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTG-GCATTTGGTTCAATGTATATAGATA
2177 T
325 T
* * * * * *
2178 TTCAGGGAGTTTTTGCACCAAAAATCATGCAAAATTGAGCTGGGTCTCCGGAACGCGTTTTTAGC
1 TTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGCCGGGGCTCTGGAACGCGTTTTTAGC
* * *
2243 CAAAAACCGTGAT-T-GTTAGTACACGATTACGGCTAAAAACTTACCCGAAAAGTTTTTTTTCTT
66 CAAAAACCGTGATGTAGTTAGTACACGATTTCGGCTAAAAACTGACCCG-AAA-TTTTTTTTCTC
* * **** * * *
2306 AA-TTTTTGTCATAATACTCATGTTAAATATATAATTTAACGCCAGAAAGTTTGACGGG-TTTTT
129 AATTTTTTGCCACAATACTCAAAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTT
* * * * * *
2369 CACGCTTCTAATATTA-TTTTCC-ATTTTTTCTGAATTAATTTTTAATTAAATCGAAACAAGATT
194 CACACTTCTAATATCATTTTTCCAATTTTTTCCGAATTAATTTCTAATTAAATCGAAATATGATT
* * * * * * * *
2432 GAGATGCTCGAAAAAAACAAACCCTGATATCCAATATGGCTGAG-ATTTGGTTCGATGAATATAA
259 TAGATGCTCG-TAAAAACAAATCCTTATATCCAATGTGGCTG-GCATTTGGTTCAATGTATATAG
2496 ATAT
322 ATAT
* * * * * * * *
2500 TTCAAGGAGTTTTTACGCCAAAAATCTTGCAAAACTGAGTCGGGGCCCTGAAACGCGTTTTTAGG
1 TTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGCCGGGGCTCTGGAACGCGTTTTTAGC
* * * * * ** * * *
2565 CATAAACAGTTAATGGATGATTTCG-ACTAAAATTT-TG--AAATAACTGACCCGAAAATATTTT
66 CAAAAACCG-TGAT-G-T-AGTTAGTAC-ACGATTTCGGCTAAA-AACTGACCCGAAATTTTTTT
* * * * * ** * *
2626 CCTCAATTTTTTTGCCACAATAGTTACAAAAAATATATAATTCAATGAAAAAAAAACAAATTGAA
125 TCTCAA-TTTTTTGCCACAATACTCAAAAAAAATATATAATTCAACG---CCAAAA-AGATTGAC
* * *
2691 GTG-TTTTTCACACTTCTAATATCATTTTTCC-A-TTTTTCCGAATTTATTTTTAATTAAATC-A
185 GGGCTTTTTCACACTTCTAATATCATTTTTCCAATTTTTTCCGAATTAATTTCTAATTAAATCGA
* * * * * *
2752 AATAAGATTTAGATGCTCATAAAAACAAATCGTTAAATCGAATTTGGCTAGG-ATTTGGTT-AGA
250 AATATGATTTAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCT-GGCATTTGGTTCA-A
*
2815 TGAATATAGATAT
313 TGTATATAGATAT
* * * ** *
2828 TTCAAGGAGACTTT-CTGCCAAAAATCATGCAAAATTGAGCCGGGACCCCAGAACACGTTTTTAG
1 TTCAAGGAGTCTTTGC-GCCAAAAATCATGCAAAATTGAGCCGGGGCTCTGGAACGCGTTTTTAG
*
2892 CCCAAAAACTGTGAT
65 -CCAAAAACCGTGAT
2907 AATACACGAT
Statistics
Matches: 1713, Mismatches: 253, Indels: 105
0.83 0.12 0.05
Matches are distributed among these distances:
318 112 0.07
319 54 0.03
320 175 0.10
321 231 0.13
322 183 0.11
323 161 0.09
324 146 0.09
325 117 0.07
326 46 0.03
327 10 0.01
328 334 0.19
329 85 0.05
330 52 0.03
331 7 0.00
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (325 bp):
TTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGCCGGGGCTCTGGAACGCGTTTTTAGC
CAAAAACCGTGATGTAGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAATTTTTTTTCTCAA
TTTTTTGCCACAATACTCAAAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTTCA
CACTTCTAATATCATTTTTCCAATTTTTTCCGAATTAATTTCTAATTAAATCGAAATATGATTTA
GATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGGCATTTGGTTCAATGTATATAGATAT
Found at i:3400 original size:1 final size:1
Alignment explanation
Indices: 3394--3419 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
3384 CAGTTATAAG
3394 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
3420 GCCTCCACAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:10888 original size:322 final size:321
Alignment explanation
Indices: 10297--11443 Score: 1385
Period size: 323 Copynumber: 3.6 Consensus size: 321
10287 AAAAAAAAAC
* * * * * *
10297 ACTCATAAAAATATGTATAATTCAACGCCAAAAAGGTTG-GAGGACTTTTCACGCTTTTAATATT
1 ACTCAGAAAAA-ATATATAATTCAACGCCAAAAAGATTGACAGG-CTTTTCACGCTTCTAATATC
* * * * *
10361 GTTTTT-CATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCTGATGCACGTTAA
64 GTTTTTCCATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAA
* * * ** * * **
10425 AACAAATCCTTAAATCCAATGTGGCCT-AGATTTGACTAGACTAATAGAGATATTTCAAGGAGTC
129 AACAAATCCTTATATCCAATGTAG-CTGACATTTGGTTAGACGAATATAGATAAATCAAGGAGTC
* * * ** * * * * * *
10489 TTAGCGCCAAAAACCATTCAAAACAGAGCCATGACCCCGGAAGGCGTTTTTAG-TCAAAATCCGT
193 TTTGCGCCAAAAATCATCCAAAATTGAGACATGGCTCCGAAACGCGTTTTTAGCT-AAAAACCGT
*
10553 GATGAG-TAGTACACAATTTCGGCTAAAAACTTGCCCGAAATTTTTTCTCGATTTTTTGCCACAA
257 GATG-GTTAGTACACGATTTCGGCTAAAAACTTGCCCGAAATTTTTTCTCGATTTTTTGCCACAA
10617 T
321 T
* * * *
10618 ACTCAGAAAAAATATATAATTCAATGTCAAAAACATTAACAGGCTTTTCACGCTTCTAATATCGT
1 ACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACAGGCTTTTCACGCTTCTAATATCGT
*
10683 TTTTTCATTTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
66 TTTTCCA-TTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
* *
10748 ATAAATCCTTATATCCAATGTGGCTGACATTTGGTTAGACGAATATAGATAAATCAAGGAGTCTT
130 ACAAATCCTTATATCCAATGTAGCTGACATTTGGTTAGACGAATATAGATAAATCAAGGAGTCTT
* ** *
10813 TGTGCCAAAAATCATCCAAAATTGAGTTATGGCTCCGAAACGCGTTTTTAGCTAAAAACGGTGAT
195 TGCGCCAAAAATCATCCAAAATTGAGACATGGCTCCGAAACGCGTTTTTAGCTAAAAACCGTGAT
***
10878 GGTTAGTACACGATTTCGGCTAAAAAC-TGACCCGGTTTTTTTTC-CTGAATTTTTTGCCACAAT
260 GGTTAGTACACGATTTCGGCTAAAAACTTG-CCCGAAATTTTTTCTC-G-ATTTTTTGCCACAAT
* * * * *
10941 ACTCAGAAAAAATATATAATTCAACACCAAAAAGATTGA-AGGTATTTTGACGCTTCGAATATCA
1 ACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACAGG-CTTTTCACGCTTCTAATATCG
* * * *
11005 TTTTTCCAATTTTTTTTTCGAATTAATTTATAATTAAATTGAAATAAGATTCAGATGCTCGTAAA
65 TTTTTCC-ATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAA
* * * *
11070 AACAAATCCTTATATCCAATGTAACTGACATTTGGTTCGATGAATATAGATAAACCAAGGAGTCT
129 AACAAATCCTTATATCCAATGTAGCTGACATTTGGTTAGACGAATATAGATAAATCAAGGAGTCT
* * * *
11135 TTGCGCCAAAAATCATGCAAAATTGAGACAGGGCTCCGAAACACGTTTTTAGCCAAAAACCGTGA
194 TTGCGCCAAAAATCATCCAAAATTGAGACATGGCTCCGAAACGCGTTTTTAGCTAAAAACCGTGA
* ** * * *
11200 TGGTTAGTACACGATTTTGGCTAAAAACTAACCCGAAAAGTTTTATCTCAATTTTTGGCCACAAT
259 TGGTTAGTACACGATTTCGGCTAAAAACTTGCCCG-AAA-TTTTTTCTCGATTTTTTGCCACAAT
* *
11265 ACTCAG-AAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTATAATATCGT
1 ACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACAGGCTTTTCACGCTTCTAATATCGT
* * * * *
11329 TTTTCCATTTTTTTCCCGAATTAATTTCTTATTAAATTGAAACAAGATTGAGATGCTCGAAAAAA
66 TTTTCCATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
* * * * *
11394 CAAATCCTTATATCCAATATAGCTGAGATTTGGTTCGATGAAAATAGATA
131 CAAATCCTTATATCCAATGTAGCTGACATTTGGTTAGACGAATATAGATA
11444 TTTTAACCAA
Statistics
Matches: 713, Mismatches: 97, Indels: 31
0.85 0.12 0.04
Matches are distributed among these distances:
320 45 0.06
321 21 0.03
322 291 0.41
323 326 0.46
324 23 0.03
325 6 0.01
326 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.33
Consensus pattern (321 bp):
ACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACAGGCTTTTCACGCTTCTAATATCGT
TTTTCCATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
CAAATCCTTATATCCAATGTAGCTGACATTTGGTTAGACGAATATAGATAAATCAAGGAGTCTTT
GCGCCAAAAATCATCCAAAATTGAGACATGGCTCCGAAACGCGTTTTTAGCTAAAAACCGTGATG
GTTAGTACACGATTTCGGCTAAAAACTTGCCCGAAATTTTTTCTCGATTTTTTGCCACAAT
Found at i:11669 original size:265 final size:263
Alignment explanation
Indices: 11181--11672 Score: 725
Period size: 265 Copynumber: 1.9 Consensus size: 263
11171 CGAAACACGT
* * * * *
11181 TTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAAACTAACCCGAAAAGTTTTAT
1 TTTTAACCAAAAACCGCGATGGTTAGCACACGATTTCGGCTAAAAACTAACCCAAAAAGTTTTAT
*
11246 CTCAATTTTTGGCCACAATACTCAGAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTT
66 CTCAATTTTTGGCCACAATACTCAGAAAAATATATAATTCAACGCCAAAAAGACTGACGGGCTTT
* * * * * *
11311 TCACGCTTATAATATCGTTTTTCCATTTTTTTCCCGAATTAATTTCTTATTAAATTGAAACAAGA
131 TCACACTTATAATACCATTTTTCCATGTTTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGA
*
11376 TTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATAGCTGAGATTTGGTTCGATGAAAATAG
196 TTGAGATGCTCCAAAAAACAAATCCTTATATCCAATATAGCTGAGATTTGGTTCGATGAAAATAG
11441 ATA
261 ATA
* * *
11444 TTTTAACCAACAACCGCGATGGTTAGCACACGATTTCGGCTAAAAACTGATCCCAAAAATTTTTT
1 TTTTAACCAAAAACCGCGATGGTTAGCACACGATTTCGGCTAAAAACT-AACCCAAAAA-GTTTT
* * *
11509 TTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGACTGTCGGGC
64 ATCTCAATTTTTGGCCACAATACTCAG-AAAAATATATAATTCAACGCCAAAAAGACTGACGGGC
* * *
11574 TTTTCACACTTCTAATACCATTTTTCCA-GTTTTTCCTGAATTAATTTCTAATTAAATCGAAATA
128 TTTTCACACTTATAATACCATTTTTCCATGTTTTTCCCGAATTAATTTCTAATTAAATCGAAACA
* * *
11638 TGATTTAGATGCTCCTAAAAACAAATCCTTATATC
193 AGATTGAGATGCTCCAAAAAACAAATCCTTATATC
11673 TAATGAGACT
Statistics
Matches: 201, Mismatches: 25, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
263 43 0.21
264 8 0.04
265 91 0.45
266 59 0.29
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.34
Consensus pattern (263 bp):
TTTTAACCAAAAACCGCGATGGTTAGCACACGATTTCGGCTAAAAACTAACCCAAAAAGTTTTAT
CTCAATTTTTGGCCACAATACTCAGAAAAATATATAATTCAACGCCAAAAAGACTGACGGGCTTT
TCACACTTATAATACCATTTTTCCATGTTTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGA
TTGAGATGCTCCAAAAAACAAATCCTTATATCCAATATAGCTGAGATTTGGTTCGATGAAAATAG
ATA
Done.