Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005647.1 Corchorus capsularis cultivar CVL-1 contig05665, 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: 2807
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Found at i:1021 original size:325 final size:328
Alignment explanation
Indices: 254--1209 Score: 1205
Period size: 325 Copynumber: 2.9 Consensus size: 328
244 ATTGCTTTTT
*
254 TCTA-TTTTTTCC-ACATTAATTTCTAATTAAATCGAAACCGAATTGAGATGCTCGTAAAAACAA
1 TCTATTTTTTTCCGA-ATTAATTTCTAATTAAATCGAAACCGGATTGAGATGCTCGTAAAAACAA
*
317 ATCCTTAAATCCAATGTGACTAAGATTTCGTTAGATAAATATAGATATTTCAATGAGTCTTGGCG
65 ATCCTTAAATCCAATGTGGCTAAGATTTCGTTAGATAAATATAGATATTTCAATGAGTCTTGGCG
* * * * ** * *
382 CAAAAAATCATGTAAAATTGAGCC-GGAGTCCCGGAACGCGTTTTTTAGCCAAAAACCGTGAT-A
130 CCAAAAATCATGCAAAACTGAGCCGGGACT-CCGGAACGCG-TTTTTAGTTAAAAATCGTGATGG
* * *
445 TAACCGTACACGATTTCAGCTAATATTTTGTAAAAATTGACATGAAAGAATTT-TCCTCAATTTT
193 TTA--GTACACGATTTCAGCTAAAATTTTGTAAAAATTGACA-CAAA-AATTTCTCCTCAATTTT
* * * *
509 TGGCCACGATACTCATAAAAAATATATAATTCAACGTCAAAAATATTGAAAGGATTTTCACGCTT
254 CGGCCACAATACTAATAAAAAATATATAATTCAACGTCAAAAAGATTGAAAGGATTTTCACGCTT
*
574 CTAATATCGGTTT
319 CTAATA---GTTG
** *
587 TCCTATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACATGATTTAGATGCTCGTAAAAACAA
1 T-CTATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACCGGATTGAGATGCTCGTAAAAACAA
* * * ** *
652 ATCTTTGAATCCAATGTGGTTAAGATTT-GATTAGATGGATATAGATATTTCAATGAGACTTGGC
65 ATCCTTAAATCCAATGTGGCTAAGATTTCG-TTAGATAAATATAGATATTTCAATGAGTCTTGGC
* * * * *
716 ACCAAAAATCATGCAAAACAGAGCCGGGACTCAGAAACGCGTTTTTAGTTAAAAATTGTGATGGT
129 GCCAAAAATCATGCAAAACTGAGCCGGGACTCCGGAACGCGTTTTTAGTTAAAAATCGTGATGGT
** * * *
781 TAGTACAAAATTTCGGCTAAAATTTTGTAAAAATTGACACAAAACATTTCTCCTTAA-TTTCCGC
194 TAGTACACGATTTCAGCTAAAATTTTGTAAAAATTGACACAAAA-ATTTCTCCTCAATTTTCGGC
* * * * *
845 CACCATACTTATAAAAAATATATAATTCAACGTTAACAAGATT-AAAGAGCTTTTCACGCTTCTA
258 CACAATACTAATAAAAAATATATAATTCAACGTCAAAAAGATTGAAAG-GATTTTCACGCTTCTA
909 ATA-TTG
322 ATAGTTG
915 T-T-TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACCGGATTGAGATGCTCGTAAAAACAAA
1 TCTATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACCGGATTGAGATGCTCGTAAAAACAAA
* * * *
978 TCCTTAAATCCAATCTGGCTGATATTTCGTTAGATAAATATAGATATTTCAATGAGTCTTGGTGC
66 TCCTTAAATCCAATGTGGCTAAGATTTCGTTAGATAAATATAGATATTTCAATGAGTCTTGGCGC
* * * *
1043 CAAAAATCTTGCAAAGCTGAGCCGGGGCTCCGGAACGCGTTTTTAGTTAAAAATCATGATGGTTA
131 CAAAAATCATGCAAAACTGAGCCGGGACTCCGGAACGCGTTTTTAGTTAAAAATCGTGATGGTTA
* * * *
1108 GTACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAGAAATTTCTCCTCAATTTTGGGCCA
196 GTACACGATTTCAGCTAAAATTTTGTAAAAATTGACAC-AAAAATTTCTCCTCAATTTTCGGCCA
*
1173 CAATACTAATAAAAAATATATAACTCAACGTCAAAAA
260 CAATACTAATAAAAAATATATAATTCAACGTCAAAAA
1210 TACTGAAGTG
Statistics
Matches: 535, Mismatches: 76, Indels: 31
0.83 0.12 0.05
Matches are distributed among these distances:
325 211 0.39
326 44 0.08
328 3 0.01
331 5 0.01
332 68 0.13
333 40 0.07
334 21 0.04
335 138 0.26
336 5 0.01
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.32
Consensus pattern (328 bp):
TCTATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACCGGATTGAGATGCTCGTAAAAACAAA
TCCTTAAATCCAATGTGGCTAAGATTTCGTTAGATAAATATAGATATTTCAATGAGTCTTGGCGC
CAAAAATCATGCAAAACTGAGCCGGGACTCCGGAACGCGTTTTTAGTTAAAAATCGTGATGGTTA
GTACACGATTTCAGCTAAAATTTTGTAAAAATTGACACAAAAATTTCTCCTCAATTTTCGGCCAC
AATACTAATAAAAAATATATAATTCAACGTCAAAAAGATTGAAAGGATTTTCACGCTTCTAATAG
TTG
Found at i:1373 original size:27 final size:28
Alignment explanation
Indices: 1314--1380 Score: 84
Period size: 27 Copynumber: 2.4 Consensus size: 28
1304 AAAAAATACA
* *
1314 AAAAATTATATTTTAATAATGGTATAGTT
1 AAAAA-TATATTTTAATAATGGAAAAGTT
*
1343 -AAAATATATTTTAATAAT-GAAAATTT
1 AAAAATATATTTTAATAATGGAAAAGTT
1369 AAAAATATATTT
1 AAAAATATATTT
1381 GAAAAAATAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 5 0.15
27 25 0.74
28 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (28 bp):
AAAAATATATTTTAATAATGGAAAAGTT
Found at i:1483 original size:96 final size:95
Alignment explanation
Indices: 1303--1481 Score: 272
Period size: 94 Copynumber: 1.9 Consensus size: 95
1293 AAATATATTT
* ** *
1303 GAAAAAATACAAAAAATTATATTTTAATAATGGTATAGTTAAAATATATTTTAATAATGAAAATT
1 GAAAAAATACAAAAAATTATATTCTAATAATGACATAATTAAAATATATTTTAATAATGAAAATT
1368 TAAAAATATATTTGAAAAAATAGTACAATC
66 TAAAAATATATTTGAAAAAATAGTACAATC
* *
1398 GAAAAATATACATAAAATTATATTCTAATAATGACATAATT-AAA-ATATTTTAATAATGACAAT
1 GAAAAA-ATACAAAAAATTATATTCTAATAATGACATAATTAAAATATATTTTAATAATGAAAAT
*
1461 TTAGAAATATATTTGAAAAAA
65 TTAAAAATATATTTGAAAAAA
1482 AAGGGTATAA
Statistics
Matches: 76, Mismatches: 7, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
94 38 0.50
95 9 0.12
96 29 0.38
ACGTcount: A:0.55, C:0.04, G:0.07, T:0.35
Consensus pattern (95 bp):
GAAAAAATACAAAAAATTATATTCTAATAATGACATAATTAAAATATATTTTAATAATGAAAATT
TAAAAATATATTTGAAAAAATAGTACAATC
Found at i:2323 original size:45 final size:45
Alignment explanation
Indices: 2272--2357 Score: 163
Period size: 45 Copynumber: 1.9 Consensus size: 45
2262 AGAGTAGTGA
2272 AATTACTAAAAGATCCCTACCCCGAATTAATGATGAGCTGGGTGG
1 AATTACTAAAAGATCCCTACCCCGAATTAATGATGAGCTGGGTGG
*
2317 AATTACTAAAAGATCCCTACCCCGGATTAATGATGAGCTGG
1 AATTACTAAAAGATCCCTACCCCGAATTAATGATGAGCTGG
2358 AGAAATAATC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (45 bp):
AATTACTAAAAGATCCCTACCCCGAATTAATGATGAGCTGGGTGG
Done.