Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009541.1 Corchorus capsularis cultivar CVL-1 contig09562, 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: 3689
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.30
Found at i:1520 original size:333 final size:333
Alignment explanation
Indices: 1--2482 Score: 3442
Period size: 324 Copynumber: 7.5 Consensus size: 333
* * *
1 CCGGAGCACCGGAACGCATTTTCAGCCAAAAACCATGATGGTTAGTTACACGATTTGCGCTAAAA
1 CCGGAGCACCGGAACGCATTTTTAGCCAAAAACCGTGATGGTTAG-TACACGATTTGGGCTAAAA
** * * * *
66 TTTTGCAAAAATTGA-CCAGAAATTTTTTTTCTCCATTTTTTGCCAGAATACTTATAAAAAAATA
65 TTTTGCAAAAATTGACCCA-AAAAATTTTTCCTCAATTTTTGGCCAGAATACTCAT-AAAAAATA
* * *
130 TATAATTCAACGCCAAAAA-ATTGA-GGGATTTTTCACGCTTCTACTATCGATTTTCCTATATTT
128 TATAATTCAACGCCAAAAAGATTGATGGG-CTTATCACGCTTCTAATATCGATTTTCCTATATTT
* * * * *
193 TTCCGAATCAATTTCTTATTAAAACAACAGATGATTCTCATGCTCGTCAAATCAAATCCTTAAAT
192 TTCCGAATTAATTTCTCATTAAATCGACACATGATTCTCATGCTCGTCAAATCAAATCCTTAAAT
* * * * *
258 CCATTGTGGTTG-AGATTTTGTTAGATGAATATAGGTACTTTAATGGGTCTTGGCGCAAAAAATC
257 CCATTGTGGCTGTA-ATTTTGGTAGATGTATATAGGTACTTCAATGAGTCTTGGCGCAAAAAATC
322 ATGCAAAACTGAA
321 ATGCAAAACTGAA
* *
335 CCGGAGCACGGGAACGCATTTTTAGCCAAAAACC------G-T-GTACACGATTTGGGCTAAACT
1 CCGGAGCACCGGAACGCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTGGGCTAAAAT
* * * *
392 TTCGCAAAAATTGACCC-GAAGATTTTTCCTCAATTTTTTGCCAGAATACTCATAAAAAATATAT
66 TTTGCAAAAATTGACCCAAAAAATTTTTCCTCAATTTTTGGCCAGAATACTCATAAAAAATATAT
* ** *
456 AATTCAACGCTAAAAAGATTGATGGGCTTATGGCGCTTCTAATATTGATTTTCCTATATTTTTCC
131 AATTCAACGCCAAAAAGATTGATGGGCTTATCACGCTTCTAATATCGATTTTCCTATATTTTTCC
521 GAATTAATTTCTCATTAAATCGACACATGATTCTCATGCTCGTCAAATCAAATCCTTAAATCCAT
196 GAATTAATTTCTCATTAAATCGACACATGATTCTCATGCTCGTCAAATCAAATCCTTAAATCCAT
** * * * * *
586 TGTGGAAGTGATTTTGGTAGTTGTATATAGGTACTTCAATAATTCTTGGGGC-AAAAATCATGCA
261 TGTGGCTGTAATTTTGGTAGATGTATATAGGTACTTCAATGAGTCTTGGCGCAAAAAATCATGCA
650 AAACTGAA
326 AAACTGAA
* *
658 CCGGAGCACCGGAACGCATTTTTCGCCAAAAACCGTGATGGTTAGTACACGATTTGGGCTAAACT
1 CCGGAGCACCGGAACGCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTGGGCTAAAAT
* * * *
723 TTCGCAAAAATTGACCC-GAAGATTTTTCCTCAATATTTGGCCAGAATACTCATAAAAAATATAT
66 TTTGCAAAAATTGACCCAAAAAATTTTTCCTCAATTTTTGGCCAGAATACTCATAAAAAATATAT
* * * *
787 AATTCAATGCCGAAAAGATTGATGGGCTTTTCGCGCTTCTAATATCGATTTTCCTATA-TTTTCC
131 AATTCAACGCCAAAAAGATTGATGGGCTTATCACGCTTCTAATATCGATTTTCCTATATTTTTCC
* * * *
851 AGAATTAATTTCTCATGAAATCGACACCTGATTCTCATGCTCGTGAAATCAAATCCTTAAATTCA
196 -GAATTAATTTCTCATTAAATCGACACATGATTCTCATGCTCGTCAAATCAAATCCTTAAATCCA
* * ** * *
916 TTGTGGCTG-AGATTTTGTTAGATGAATATAAATATTTCAATGAGTCTTGGCGCAAAAAGTCATG
260 TTGTGGCTGTA-ATTTTGGTAGATGTATATAGGTACTTCAATGAGTCTTGGCGCAAAAAATCATG
980 CAAAACT---
324 CAAAACTGAA
* *
987 ---GA--ACCGGAACGCATTTTTAGTCAAAAACCGTGATGGTTAGTACACGATTTGCGCTAAAAT
1 CCGGAGCACCGGAACGCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTGGGCTAAAAT
* * *
1047 TTTGTAAAAATTTA-CCAGAAAAA-TTTTCCTCAATTTTTGGCCAGAATACTTATAAAAAATATA
66 TTTGCAAAAATTGACCCA-AAAAATTTTTCCTCAATTTTTGGCCAGAATACTCATAAAAAATATA
* * * *
1110 TAATTCAACGCTAAAAAGATTGATGGGCTTATGACACTTCTAATATTGATTTTCCTATATTTTTC
130 TAATTCAACGCCAAAAAGATTGATGGGCTTATCACGCTTCTAATATCGATTTTCCTATATTTTTC
*
1175 CGAACTAATTTCTCATTAAATCGACACATGATTCTCATGCTCGTCAAATCAAATCCTTAAATCCA
195 CGAATTAATTTCTCATTAAATCGACACATGATTCTCATGCTCGTCAAATCAAATCCTTAAATCCA
* *
1240 TTGTGGCTGTAAATTTGGTAGATGTATATAGGTACTTCAATGAGTCTTGGCGCAAAAAATCATGT
260 TTGTGGCTGTAATTTTGGTAGATGTATATAGGTACTTCAATGAGTCTTGGCGCAAAAAATCATGC
1305 AAAACTGAA
325 AAAACTGAA
** * * * * * *
1314 CCGGAGCACCATAACGAATTTTTAGCCAAAAACTGTGATCGCTAGTACACAATTTGGGCTAAATT
1 CCGGAGCACCGGAACGCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTGGGCTAAAAT
*
1379 TTTGCAAACATTGACCCAAAAAATTTTTCCTCAATTTTTGGCCAGAATACTCATAAAAAATATAT
66 TTTGCAAAAATTGACCCAAAAAATTTTTCCTCAATTTTTGGCCAGAATACTCATAAAAAATATAT
* *
1444 AATTCAAGGCCAAAAAGATTGATGGGCTTTTCACGCTTCTAATATCGATTTTCCTATATTTTTCC
131 AATTCAACGCCAAAAAGATTGATGGGCTTATCACGCTTCTAATATCGATTTTCCTATATTTTTCC
*
1509 GAATCAATTTCTCATTAAATCGACACATGATTCTCATGCTCGTCAAATCAAATCCTTAAATCCAT
196 GAATTAATTTCTCATTAAATCGACACATGATTCTCATGCTCGTCAAATCAAATCCTTAAATCCAT
* * ** * *
1574 TGTGGCTG-AGATTTTGTTAGATGAATATAAATATTTCAATGAGTCTTGGCGCAAAAAGTCATGC
261 TGTGGCTGTA-ATTTTGGTAGATGTATATAGGTACTTCAATGAGTCTTGGCGCAAAAAATCATGC
1638 AAAACTGAA
325 AAAACTGAA
* *
1647 CCGGAGCACCGGAACGCATTTTTAGCCAAAAACCGTGATGGTTAGTAGACGATTTGCGCTAAAAT
1 CCGGAGCACCGGAACGCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTGGGCTAAAAT
** *
1712 TTTGCAAAAATTGACCCGAAAATTTTTTTCCTTAATTTTT-GCCAG-------ATAAAAAATATA
66 TTTGCAAAAATTGACCC-AAAAAATTTTTCCTCAATTTTTGGCCAGAATACTCATAAAAAATATA
* *
1769 TAATTCAACGCCAAAAAGATTGATTGGCTTATCACGCTTCTAATATTGATTTTCCTATATTTTTC
130 TAATTCAACGCCAAAAAGATTGATGGGCTTATCACGCTTCTAATATCGATTTTCCTATATTTTTC
* *
1834 CGAATTAATTTCTCATTAAATCGACACATGATTCTCATACTCGTCAAATCAAATCCTTAAATCTA
195 CGAATTAATTTCTCATTAAATCGACACATGATTCTCATGCTCGTCAAATCAAATCCTTAAATCCA
* *
1899 TTGTGGCTGTGATTTTGGTAGATGTATATAGGTACTTCAATGAGTCTTGGCACAAAAAATCATGC
260 TTGTGGCTGTAATTTTGGTAGATGTATATAGGTACTTCAATGAGTCTTGGCGCAAAAAATCATGC
1964 AAAACTGAA
325 AAAACTGAA
* * * * * *
1973 CCAGAGCACCGGAGCGCATTTTTAGCCAAAAATCGTGATTGTTAATACACGATTTGGCCTAAAAT
1 CCGGAGCACCGGAACGCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTGGGCTAAAAT
* *
2038 TTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGGCCAGAATACTCATAATATATATAT
66 TTTGCAAAAATTGACCCAAAAAATTTTTCCTCAATTTTTGGCCAGAATACTCATAA-A-AAATAT
* *
2103 ATAATTCAACGCTAAAAAGATTGATGGGCTTATCACGCTTCTAATATTGATTTTCCTATATTTTT
129 ATAATTCAACGCCAAAAAGATTGATGGGCTTATCACGCTTCTAATATCGATTTTCCTATATTTTT
2168 CCGAATTAATTTCTCATTAAATCGACACATGATTCTCATGCTCGTCAAATCAAATCCTTAAATCC
194 CCGAATTAATTTCTCATTAAATCGACACATGATTCTCATGCTCGTCAAATCAAATCCTTAAATCC
* * *
2233 ATTGTGGCTGTGATTTTGGTAGATGTATATAGGTACTTCAATGAGTCAT-GCGTAAAAAATCATG
259 ATTGTGGCTGTAATTTTGGTAGATGTATATAGGTACTTCAATGAGTCTTGGCGCAAAAAATCATG
2297 CAAAACT-AGA
324 CAAAACTGA-A
** * *
2307 CTAGAGCACCGGAACGCATTTTTAGCCAAAAATCGTGATGGTTAGTACACGATTTGAGCTAAAAT
1 CCGGAGCACCGGAACGCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTGGGCTAAAAT
* ** *
2372 TTTGCAAAAATTGACCAAAAAAATTTTT-CTCCTTTTTTTGGCCAGAATACTCATAAAAAAACAT
66 TTTGCAAAAATTGACCCAAAAAATTTTTCCT-CAATTTTTGGCCAGAATACTCAT-AAAAAATAT
* *
2436 ATAATTCAACGCCAAAAAGATT-ATGGGCTTTTCATGCTTCTAATATC
129 ATAATTCAACGCCAAAAAGATTGATGGGCTTATCACGCTTCTAATATC
2483 AAAAAGATTA
Statistics
Matches: 1915, Mismatches: 188, Indels: 92
0.87 0.09 0.04
Matches are distributed among these distances:
323 80 0.04
324 442 0.23
325 62 0.03
326 284 0.15
327 1 0.00
328 1 0.00
329 1 0.00
330 9 0.00
331 235 0.12
332 103 0.05
333 336 0.18
334 180 0.09
335 181 0.09
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (333 bp):
CCGGAGCACCGGAACGCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTGGGCTAAAAT
TTTGCAAAAATTGACCCAAAAAATTTTTCCTCAATTTTTGGCCAGAATACTCATAAAAAATATAT
AATTCAACGCCAAAAAGATTGATGGGCTTATCACGCTTCTAATATCGATTTTCCTATATTTTTCC
GAATTAATTTCTCATTAAATCGACACATGATTCTCATGCTCGTCAAATCAAATCCTTAAATCCAT
TGTGGCTGTAATTTTGGTAGATGTATATAGGTACTTCAATGAGTCTTGGCGCAAAAAATCATGCA
AAACTGAA
Found at i:2491 original size:34 final size:34
Alignment explanation
Indices: 2448--2518 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
2438 AATTCAACGC
2448 CAAAAAGATTATGGGCTTTTCATGCTTCTAATAT
1 CAAAAAGATTATGGGCTTTTCATGCTTCTAATAT
2482 CAAAAAGATTATGGGCTTTTCATGCTTCTAATAT
1 CAAAAAGATTATGGGCTTTTCATGCTTCTAATAT
2516 CAA
1 CAA
2519 TTTTCCTATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (34 bp):
CAAAAAGATTATGGGCTTTTCATGCTTCTAATAT
Found at i:3340 original size:71 final size:69
Alignment explanation
Indices: 3259--3422 Score: 247
Period size: 71 Copynumber: 2.3 Consensus size: 69
3249 CGAGAAGACC
* * *
3259 GGCTCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTATACGAGAAGACACACGAAGACACAAGAA
1 GGCTCTCCGCAGTGAGGCGAGGCCAGAAACGAAGGTACACGAGAAG--ACACGAAGAAACAAGAA
*
3324 AACGGA
64 AACCGA
* *
3330 GGCTCTCCGCAGTGAGGCGAGGCCAGAAACGAAGGTACACGAGAAGACACGAAGAAACGAGAAGA
1 GGCTCTCCGCAGTGAGGCGAGGCCAGAAACGAAGGTACACGAGAAGACACGAAGAAACAAGAAAA
3395 CCGA
66 CCGA
*
3399 GGCTCTCCGCAGTGAGGGGAGGCC
1 GGCTCTCCGCAGTGAGGCGAGGCC
3423 TACACGAGAA
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
69 42 0.49
71 44 0.51
ACGTcount: A:0.34, C:0.24, G:0.34, T:0.07
Consensus pattern (69 bp):
GGCTCTCCGCAGTGAGGCGAGGCCAGAAACGAAGGTACACGAGAAGACACGAAGAAACAAGAAAA
CCGA
Found at i:3421 original size:69 final size:70
Alignment explanation
Indices: 3248--3422 Score: 257
Period size: 69 Copynumber: 2.5 Consensus size: 70
3238 ACATAGGTAC
* *
3248 ACGAGAAGACC--GGCTCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTATACGAGAAGACACAC
1 ACGAGAAGACCGAGGCTCTCCGCAGTGAGGCGAGGCCAGAAACGAAGGTACACGAGAAGA-ACAC
*
3311 GAAGAC
65 GAAGAA
* * *
3317 ACAAGAAAACGGAGGCTCTCCGCAGTGAGGCGAGGCCAGAAACGAAGGTACACGAGAAG-ACACG
1 ACGAGAAGACCGAGGCTCTCCGCAGTGAGGCGAGGCCAGAAACGAAGGTACACGAGAAGAACACG
3381 AAGAA
66 AAGAA
*
3386 ACGAGAAGACCGAGGCTCTCCGCAGTGAGGGGAGGCC
1 ACGAGAAGACCGAGGCTCTCCGCAGTGAGGCGAGGCC
3423 TACACGAGAA
Statistics
Matches: 94, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
69 50 0.53
71 44 0.47
ACGTcount: A:0.35, C:0.25, G:0.34, T:0.07
Consensus pattern (70 bp):
ACGAGAAGACCGAGGCTCTCCGCAGTGAGGCGAGGCCAGAAACGAAGGTACACGAGAAGAACACG
AAGAA
Found at i:3462 original size:40 final size:40
Alignment explanation
Indices: 3386--3462 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
3376 ACACGAAGAA
* **
3386 ACGAGAAGACCGAGGCTCTCCGCAGTGAGGGGAGGCCTAC
1 ACGAGAAGACAGAGGCTCTCCGCAGTGAGGCAAGGCCTAC
3426 ACGAGAAGACAGAGGCTCTCCGCAGTGAGGCAAGGCC
1 ACGAGAAGACAGAGGCTCTCCGCAGTGAGGCAAGGCC
3463 AGACATGAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.27, C:0.27, G:0.36, T:0.09
Consensus pattern (40 bp):
ACGAGAAGACAGAGGCTCTCCGCAGTGAGGCAAGGCCTAC
Found at i:3506 original size:17 final size:17
Alignment explanation
Indices: 3484--3516 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3474 TACACGAGAA
3484 GACACAC-ACGAAGACAC
1 GACACACGA-GAAGACAC
3501 GACACACGAGAAGACA
1 GACACACGAGAAGACA
3517 GAGTGGTGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.93
18 1 0.07
ACGTcount: A:0.48, C:0.30, G:0.21, T:0.00
Consensus pattern (17 bp):
GACACACGAGAAGACAC
Found at i:3607 original size:2 final size:2
Alignment explanation
Indices: 3600--3686 Score: 174
Period size: 2 Copynumber: 43.5 Consensus size: 2
3590 ATATCCTGGG
3600 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3642 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3684 GA G
1 GA G
3687 CAG
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 85 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Done.