Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010900.1 Corchorus capsularis cultivar CVL-1 contig10921, 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: 1715
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.33
Found at i:914 original size:282 final size:279
Alignment explanation
Indices: 129--974 Score: 974
Period size: 277 Copynumber: 3.0 Consensus size: 279
119 AAATTTTTGA
* * * * * * * * * *
129 TTAAATCGAAACATTATTCGGATGCTCGTAAAAATAAATCCTTATGTCTTTTGTGGCT-AAACTT
1 TTAAATCGAAAAATGATTCAGATGCTCGTAAAAACAAATCCATAAGACCTTTG-AGCTGAGA--T
* *
193 TTGTTAGATGAATATAGATATCTCATGGAGTCTTGGTGCCAAAAATCATGCAAAACAGAACTTGG
63 TTGTTAGATGAATATAGATATCTCATGGAGTCTTCGTGCCAAAAATCATACAAAACAGAACTTGG
*
258 GCTCCGGAA-AGCATTTTTAACCAATAACTGTGATGATTAGTACACGATTTCGGCATAAAATTTT
128 GCTCCGGAACA-CATTTTTAACCAAAAACTGTGATGATTAGTACACGATTTCGGC-TAAAATTTT
* * *
322 TCAAAAATTAAATCCGAAATAATTTTACTAAATTTTTTGCCACGATACTCACCGAAAATATATAA
191 GCAAAAATT-AACCCGAAATAATTTTACTAAATTTTTTGCCACAATACTCACCGAAAATATATAA
***
387 TTTAATGTC-AAAT-TTTTGA----
255 TTTAATGTCAAAATATGAAGAGCTT
* * * * * * * *
406 TTAAATCGGAACATTATTCGGATGCTCGTAAAAATAAATCCTTAAGTCCTTTGCAGCTGAGCTTT
1 TTAAATCGAAAAATGATTCAGATGCTCGTAAAAACAAATCCATAAGACCTTTG-AGCTGAG-ATT
* * *
471 TTTTAGATGAATATAGACATCTCATGGAGTCTTCGTGCAAAAAATCATACAAAACAGAACTTGGG
64 TGTTAGATGAATATAGATATCTCATGGAGTCTTCGTGCCAAAAATCATACAAAACAGAACTTGGG
* *
536 CTCCGGAACGCATTTTTAACAAAAAACTGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCA
129 CTCCGGAACACATTTTTAACCAAAAACTGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCA
*
601 AAAATTAACCTGAAATAATTTTACTAAATTTTTTGCCACAATACTCACCGAAAATATATAATTTA
194 AAAATTAACCCGAAATAATTTTACTAAATTTTTTGCCACAATACTCACCGAAAATATATAATTTA
666 ATGTCAAAATGATAGAAGAGCTT
259 ATGTCAAAAT-AT-GAAGAGCTT
*
689 TTAAATCGAAAAATGATTCAGATGCTCGTAAAAACAAATCCATAAGACCATTATG-TCTGAGATT
1 TTAAATCGAAAAATGATTCAGATGCTCGTAAAAACAAATCCATAAGACC-TT-TGAGCTGAGATT
* * * * * * * **
753 TGATTAGATAAACATAGATATCTCATGGAGTTTTCATGCCAATAATCAT-CAAAACTGACCCGGG
64 TG-TTAGATGAATATAGATATCTCATGGAGTCTTCGTGCCAAAAATCATACAAAACAGAACTTGG
* * * * * ** *
817 GCCCCGGAACACGTTTTTAGCCAAAAACTATGATGGTTAGTACACGATTTTTGCTAAAATTTGGC
128 GCTCCGGAACACATTTTTAACCAAAAACTGTGATGATTAGTACACGATTTCGGCTAAAATTTTGC
* * * *
882 AAAAATTAACCCGAAATATTTTTCCTAAATTTTTTGCCACAATAGTCACGGAAAATATATAATTT
193 AAAAATTAACCCGAAATAATTTTACTAAATTTTTTGCCACAATACTCACCGAAAATATATAATTT
**
947 AATACCAAAAATATTGAAGAGCTT
258 AATGTC-AAAATA-TGAAGAGCTT
971 TTAA
1 TTAA
975 CGCTTCTAAT
Statistics
Matches: 493, Mismatches: 60, Indels: 27
0.85 0.10 0.05
Matches are distributed among these distances:
275 61 0.12
276 21 0.04
277 164 0.33
278 2 0.00
279 2 0.00
282 147 0.30
283 92 0.19
284 2 0.00
285 2 0.00
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (279 bp):
TTAAATCGAAAAATGATTCAGATGCTCGTAAAAACAAATCCATAAGACCTTTGAGCTGAGATTTG
TTAGATGAATATAGATATCTCATGGAGTCTTCGTGCCAAAAATCATACAAAACAGAACTTGGGCT
CCGGAACACATTTTTAACCAAAAACTGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAA
AATTAACCCGAAATAATTTTACTAAATTTTTTGCCACAATACTCACCGAAAATATATAATTTAAT
GTCAAAATATGAAGAGCTT
Found at i:1289 original size:328 final size:326
Alignment explanation
Indices: 689--1709 Score: 1338
Period size: 331 Copynumber: 3.1 Consensus size: 326
679 AGAAGAGCTT
* *
689 TTAAATCGAAAAATGATTCAGATGCTCGTAAAAACAAATCCATAAGACCATTATGTCTGAGATTT
1 TTAAATCGAAAAATGATTCAGATGCTCGTAAAAACAAATCCTTAAGTCCATTATGTCTGAGATTT
* * * * *
754 GATTAGATAAACATAGATATCTCATGGAGTTTTCATGCCAATAATC-ATCAAAACTGACCCGGGG
66 GATTAGATAAATATAGATATCTCATGGAGTCTTCATGCCAAAAATCAAGCAAAACTGAACC-GGG
* *
818 CCCCGGAACACGTTTTTAGCCAAAAACTATGATGGTTAGTACACGATTTTTGCTAAAATTTGGCA
130 CCCCGGAACGCGTTTTTAGCCAAAAAC--TG-T-GATAGTACACGATTTTTGCTAAAATTTGGCA
* *
883 AAAATTAACCCGAAATATTTTTCCTAAATTTTTTGCCACAATAGTCACGGAAAATATATAATTTA
191 AAAATTAACCCGAAATATTTTTACTAAATTTTTTGCCACAATAGTCACAGAAAATATATAATTTA
948 ATACCAAAAATATTGAAGAGCTTTTAACGCTTCTAATATTCTTTTTCCAATTTTCTATGAATAAA
256 ATACCAAAAATATTGAAGAGCTTTTAACGCTTCTAATATTC-TTTTCCAATTTTCTATGAATAAA
1013 TTACTGA
320 TTACTGA
* *
1020 TTAAATCGAAAAATGAGTCAGATGCTCGTAAAAACAAATCCTTACGTCCATTATGTCTGAGATTT
1 TTAAATCGAAAAATGATTCAGATGCTCGTAAAAACAAATCCTTAAGTCCATTATGTCTGAGATTT
*
1085 GATTAGATAAATATAGATATCTCATGGAGTCTTCATGCCAAAAATTCAAGCAAAACTGAGCCGGG
66 GATTAGATAAATATAGATATCTCATGGAGTCTTCATGCCAAAAA-TCAAGCAAAACTGAACCGGG
1150 TCCCCGGAACGCGTTTTTAGCCAAAAACTGTGAT-GTACACGATTTTTGCTAAAATTTGGCAAAA
130 -CCCCGGAACGCGTTTTTAGCCAAAAACTGTGATAGTACACGATTTTTGCTAAAATTTGGCAAAA
1214 ATTAACCCGAAATATTTTTACTAAATTTTTTGCCACAATAGTCACAGAAAATATATAATTTAATA
194 ATTAACCCGAAATATTTTTACTAAATTTTTTGCCACAATAGTCACAGAAAATATATAATTTAATA
* * * * *
1279 CCGAAAATATTGAAGAGCTTTTCACGCTTCTAATA-TCGTTTTCCAATTTTATCTGAATAAATTT
259 CCAAAAATATTGAAGAGCTTTTAACGCTTCTAATATTC-TTTTCCAATTTTCTATGAATAAATTA
*
1343 TTGA
323 CTGA
* * * * * ** * *
1347 TTAAATCGAAACATTATTCAAATGCTCGTAAAAATAAATCCTTAAGTCCTTTGCGGCTGAGCTTT
1 TTAAATCGAAAAATGATTCAGATGCTCGTAAAAACAAATCCTTAAGTCCATTATGTCTGAG-ATT
* * ** * * * * *
1412 TG-TTAAATGAATATAGATATCTCATGGAGTCTTGGTACCCAAAATCATGTAAAACAT-AACTTG
65 TGATTAGATAAATATAGATATCTCATGGAGTCTTCATGCCAAAAATCAAGCAAAAC-TGAAC-CG
* * * ** * *
1475 GGCTCC-GAACCGCATTTTTAACCAAAAACTGTGATGGTTAGTACACGATTTCGGATAAAATTTT
128 GGCCCCGGAA-CGCGTTTTTAGCCAAAAACTGTGA----TAGTACACGATTTTTGCTAAAATTTG
** * * * *
1539 GCAAAAATTAAGACGAAATAATTTTACTAAATTTTTTACCACAATACTCACCGAAAATATATAAT
188 GCAAAAATTAACCCGAAATATTTTTACTAAATTTTTTGCCACAATAGTCACAGAAAATATATAAT
** * *
1604 TTAATGTCAAAAAGATTAAAGAG-TTTTAACGCTTCTAATATTCTTTTCCAA-TTTCTATGAATA
253 TTAATACCAAAAATATTGAAGAGCTTTTAACGCTTCTAATATTCTTTTCCAATTTTCTATGAATA
1667 AATTACTGA
318 AATTACTGA
1676 TTAAATCGAAAAATGATTCAGATGCTCGTAAAAA
1 TTAAATCGAAAAATGATTCAGATGCTCGTAAAAA
1710 ATAAAT
Statistics
Matches: 610, Mismatches: 67, Indels: 28
0.87 0.10 0.04
Matches are distributed among these distances:
325 3 0.00
326 36 0.06
327 119 0.20
328 130 0.21
329 50 0.08
330 26 0.04
331 203 0.33
332 5 0.01
333 38 0.06
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (326 bp):
TTAAATCGAAAAATGATTCAGATGCTCGTAAAAACAAATCCTTAAGTCCATTATGTCTGAGATTT
GATTAGATAAATATAGATATCTCATGGAGTCTTCATGCCAAAAATCAAGCAAAACTGAACCGGGC
CCCGGAACGCGTTTTTAGCCAAAAACTGTGATAGTACACGATTTTTGCTAAAATTTGGCAAAAAT
TAACCCGAAATATTTTTACTAAATTTTTTGCCACAATAGTCACAGAAAATATATAATTTAATACC
AAAAATATTGAAGAGCTTTTAACGCTTCTAATATTCTTTTCCAATTTTCTATGAATAAATTACTG
A
Done.