Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012539.1 Corchorus capsularis cultivar CVL-1 contig12560, 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: 30708
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:605 original size:106 final size:106
Alignment explanation
Indices: 394--613 Score: 298
Period size: 106 Copynumber: 2.1 Consensus size: 106
384 AATTATATTT
* * *
394 AAACATGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATACGGTTGAGATTTGGTTAGAT
1 AAAC-TGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATACAGCTAAGATTTGGTTAGAT
* * * *
459 AAATTAAGATATTTCAAGAAGTCTTGGCGCTAATTACATGCG
65 AAATAAAGATATTTCAAGAAGTCTTGGCGCAAAATACATGCA
* *
501 AAACTGATTCAGATACTCGTAAAAACAAATCCTTAAATCCATTGCAGCTAAGATTTGGTTAGATA
1 AAACTGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATACAGCTAAGATTTGGTTAGATA
* * * *
566 AATAAAGATATTTCTAGGAGTTTTGGTGCAAAA-ATCATGCA
66 AATAAAGATATTTCAAGAAGTCTTGGCGCAAAATA-CATGCA
607 AAACTGA
1 AAACTGA
614 GCCGAGGTCC
Statistics
Matches: 99, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
105 1 0.01
106 94 0.95
107 4 0.04
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.30
Consensus pattern (106 bp):
AAACTGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATACAGCTAAGATTTGGTTAGATA
AATAAAGATATTTCAAGAAGTCTTGGCGCAAAATACATGCA
Found at i:895 original size:439 final size:437
Alignment explanation
Indices: 52--923 Score: 1239
Period size: 439 Copynumber: 2.0 Consensus size: 437
42 AATCAATTTC
* * * * * *
52 AATTATATCGAAAATGATTGAGATGCTCGTAAAAACAAATCCTTAAATCAAATACGGTTGAGATT
1 AATTACATCGAAAATGATTCAGATACTCGTAAAAACAAATCCTTAAATCAAATACAGCTAAGATT
*
117 TGGTTAGATAAATTAAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGCAAAACTGAGCCAGG
66 TGGTTAGATAAATAAAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGCAAAACTGAGCCAGG
* * *
182 ACCCAGAGCGCGCATTTTTAGCCAAAATCCATGATGATTAGTACACAATTTCGGCTAAAATTTTT
131 ACCCAGA-CGCGCATTTTTAGCAAAAATCCATGATGATTAGTACACAATTTCAGCTAAAAATTTT
*
247 GAAAAACTGACCTGAAAAAAATTTCCTCAATTTTTGGCCACAATACGAATAAAAAATATATAATT
195 AAAAAACTGACCTGAAAAAAATTTCCTCAATTTTTGGCCACAATACGAATAAAAAATATATAATT
* * * * * * *
312 CAACGCCGAAAGATTGGAGGGCTTTTCATGCTTCTAATTTTATTTTTCAAATTTTTTTCCAAATT
260 CAACGCCAAAAGATCGAAGGACTTCTCACGCTTCTAATTTCATTTTTCAAATTTTTTTCCAAATT
* ***
377 AATTTCTAATTATATTTAAACATGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATACGG
325 AATTTCTAATTAGAACGAAACATGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATACGG
* * *
442 TTGAGATTTGGTTAGATAAATTAAGATATTTCAAGAAGTCTTGGCGCT
390 CTGAAATCTGGTTAGATAAATTAAGATATTTCAAGAAGTCTTGGCGCT
* * * *
490 AATTACATGCGAAACTGATTCAGATACTCGTAAAAACAAATCCTTAAATCCATTGCAGCTAAGAT
1 AATTACAT-CGAAAATGATTCAGATACTCGTAAAAACAAATCCTTAAATCAAATACAGCTAAGAT
* * *
555 TTGGTTAGATAAATAAAGATATTTCTAGGAGTTTTGGTGC-AAAAATCATGCAAAACTGAGCCGA
65 TTGGTTAGATAAATAAAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGCAAAACTGAGCC-A
* * * *
619 GGTCCCAGA-GCGCATTTTTAGCAAAAAT-CAGTGGTGATTAGTACACGATTTTAGCTAAAAAAT
129 GGACCCAGACGCGCATTTTTAGCAAAAATCCA-TGATGATTAGTACACAATTTCAGCT-AAAAAT
** * **
682 TTTAAAAAACTGACCTGAAAAATTTTTCTTCAATTTTTGGCCACAATACTCATAAAAAATATATA
192 TTTAAAAAACTGACCTGAAAAAAATTTCCTCAATTTTTGGCCACAATACGAATAAAAAATATATA
* * *
747 ATTCTACGCCAAAAAGATCGAAGGACTTCTCACGTTTCTAATTTCGTTTTTCTAAATTTTTTT-C
257 ATTCAACGCC-AAAAGATCGAAGGACTTCTCACGCTTCTAATTTCATTTTTC-AAATTTTTTTCC
*
811 AAATTAATTTCTAATTAGAACGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAA
320 AAATTAATTTCTAATTAGAACGAAACATGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAA
*
876 TACGGCTGAAATCTGGTTAGATAAATTAAGATATTTCAAGGAGTCTTG
385 TACGGCTGAAATCTGGTTAGATAAATTAAGATATTTCAAGAAGTCTTG
924 CTGCCTAAAC
Statistics
Matches: 382, Mismatches: 46, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
436 2 0.01
437 39 0.10
438 102 0.27
439 229 0.60
440 10 0.03
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.32
Consensus pattern (437 bp):
AATTACATCGAAAATGATTCAGATACTCGTAAAAACAAATCCTTAAATCAAATACAGCTAAGATT
TGGTTAGATAAATAAAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGCAAAACTGAGCCAGG
ACCCAGACGCGCATTTTTAGCAAAAATCCATGATGATTAGTACACAATTTCAGCTAAAAATTTTA
AAAAACTGACCTGAAAAAAATTTCCTCAATTTTTGGCCACAATACGAATAAAAAATATATAATTC
AACGCCAAAAGATCGAAGGACTTCTCACGCTTCTAATTTCATTTTTCAAATTTTTTTCCAAATTA
ATTTCTAATTAGAACGAAACATGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATACGGC
TGAAATCTGGTTAGATAAATTAAGATATTTCAAGAAGTCTTGGCGCT
Found at i:1117 original size:20 final size:21
Alignment explanation
Indices: 1092--1134 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
1082 TAATCGTGTC
*
1092 AAGACACGATTAACACG-TTT
1 AAGACACGAATAACACGCTTT
*
1112 AAGACACGAATGACACGCTTT
1 AAGACACGAATAACACGCTTT
1133 AA
1 AA
1135 TTAACGGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.42, C:0.21, G:0.16, T:0.21
Consensus pattern (21 bp):
AAGACACGAATAACACGCTTT
Found at i:4115 original size:333 final size:332
Alignment explanation
Indices: 1542--4535 Score: 3388
Period size: 333 Copynumber: 9.0 Consensus size: 332
1532 TGCCAGGTCT
* * ** * * *
1542 ATGCAAAACTGAGTCGGGGCCTTGGAGCGCA-TTTTCGCCAAAATCCGTGATG-TAATGTACCCG
1 ATGCAAAACTGAGCCGAGGCCCCGGAGCGCATTTTTAGCCAAAATCCGTGATGATTA-GTACACG
** * *
1605 ATTTTCTACTAAAATTTTTAAAAAACTGACCTGAAAAAGTTTTCCTCAATTTTTGGCCACAATAC
65 A-TTTCGGCTAAAATTTTTGAAAAACTGACCTGAAAAAATTTTCCTCAATTTTTGGCCACAATAC
* * * * **
1670 GCATTAAAAATATATAATTCAACGCC---GAGATT-AGAGGGCTTTTCGCGCTTCTAAT-TTTTT
129 TCATAAAAAATATATAATTCAACGCCAAAAAGATTGA-AGGGCTTTTCACGCTTCTAATATCATT
* * * *
1730 TTTTCAAATTTTTTCCAAATTAATTTCTAATTAAATCGAAACTTGATTGAGATGCTCATAAAAAC
193 TTTCCAAA-TTTTTCCAAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAAC
* *
1795 AAATCCTTAAATCCATTGCAGCTGAGATTTGGTTAGATAAATTAAGATATATCAAGGAGT-TTAG
257 AAATCCTTAAATCCAATGCAGCTGAGATTTGGTTAGATAAATTAAGATATTTCAAGGAGTCTT-G
1859 GCGCCAAAAATC
321 GCGCCAAAAATC
* ** * * *
1871 ATGCAAAACTGAGCCGAGTCCCTAGACCGCATTTTTAGCCAAAATCCGTCATTATTAGTACACGA
1 ATGCAAAACTGAGCCGAGGCCCCGGAGCGCATTTTTAGCCAAAATCCGTGATGATTAGTACACGA
* *
1936 TTTCGGCTAAAATTTTTGAAAAAAATTGACCTGAAAAAATTTTCCTCAATTTTTGGCCAGAATAC
66 TTTCGGCTAAAATTTTTG--AAAAACTGACCTGAAAAAATTTTCCTCAATTTTTGGCCACAATAC
* * *
2001 TCATTAAAAATATATAATTCAATGCCAAAAAAGATTGATGGGCTTTTCACGCTTCTAATATCATT
129 TCATAAAAAATATATAATTCAACGCC-AAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATT
* * *
2066 TTTCTAAATTTTTCCAAATTAATTTCTAATTAAATCGAAACATGATCCAGATTCTCGTAAAAACA
193 TTTCCAAATTTTTCCAAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACA
* *
2131 AATCCTTTAATCCAATGC-GTCTGAGATTTGGTTAGATAAATTCAGATATTTCAAGGAGTCTTGG
258 AATCCTTAAATCCAATGCAG-CTGAGATTTGGTTAGATAAATTAAGATATTTCAAGGAGTCTTGG
*
2195 CGCC-AAAACC
322 CGCCAAAAATC
* * * *
2205 ATGCAAAACTGAGTCGAGGCTCCGGAGCGCATTATTT-GCCAAATTCCGTGATGATTAGCACACG
1 ATGCAAAACTGAGCCGAGGCCCCGGAGCGCATT-TTTAGCCAAAATCCGTGATGATTAGTACACG
* * * *
2269 GTTTCGGCTAAAATTCTTGAAAAACTGACCTGAAAAAATTTTCCTCAATTTTT-GTCACAATACG
65 ATTTCGGCTAAAATTTTTGAAAAACTGACCTGAAAAAATTTTCCTCAATTTTTGGCCACAATACT
* * * * * * *
2333 CATAAAAAATATATAATTCAATGCCGAAATA-TTTG-AGGACTTTTCACACTTCTAATTTTATTT
130 CATAAAAAATATATAATTCAACGCC-AAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTT
* * * * *
2396 TTCAAAATTTTTTCCAAATGAATTTCTAATTATATCGAAACATGATTCAGATGTTTGTAAAAACA
194 TTCCAAA-TTTTTCCAAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACA
* * * * * *
2461 AATCCTTAAATCCAATGCAGGTGGGATTTGGTTAGATAAATAAAGATATATCAAGGAGTTTTTGC
258 AATCCTTAAATCCAATGCAGCTGAGATTTGGTTAGATAAATTAAGATATTTCAAGGAGTCTTGGC
2526 GCCAAAAATC
323 GCCAAAAATC
* * *
2536 ATGCAAAACTTAGCCGA-ACCCCGGAGCGCATTTTTAGCCAAAATCC--G-T-A--A-TACATGA
1 ATGCAAAACTGAGCCGAGGCCCCGGAGCGCATTTTTAGCCAAAATCCGTGATGATTAGTACACGA
* * * * *
2593 TTTCGACTAAAATTTTTGAAAAAACTAACTTGAAAAATTTTTCCTCAATTTTTGGCCAAAATACT
66 TTTCGGCTAAAATTTTTG-AAAAACTGACCTGAAAAAATTTTCCTCAATTTTTGGCCACAATACT
* * * * *
2658 CATAAAAAATATATAATTCAACG-CAAAAAGATTGATGGGGCTTGTCACGTTTCTAATATCGTTC
130 CATAAAAAATATATAATTCAACGCCAAAAAGATTGA-AGGGCTTTTCACGCTTCTAATATCATTT
* ** *
2722 TTCAAAATTTTTTCCAAATTAATTTCTAATTAAATCGAATTATTATTCAGATGCTCGTAAAAACA
194 TTCCAAA-TTTTTCCAAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACA
* * * * * * * * *
2787 AATCCTTAAATCTAATACGGCTGATATTTTGTTAGATAAGTTAATATTTTTCAATGAGTCTTGGC
258 AATCCTTAAATCCAATGCAGCTGAGATTTGGTTAGATAAATTAAGATATTTCAAGGAGTCTTGGC
2852 GCCAAAAATC
323 GCCAAAAATC
* * * * * *
2862 ATGCAAAACAGAGCCGGGGCCCCGGATCGCATTTTTAGCCAAAATCCGTGATGGTTAGTATAGGA
1 ATGCAAAACTGAGCCGAGGCCCCGGAGCGCATTTTTAGCCAAAATCCGTGATGATTAGTACACGA
* * *
2927 TTTCAGCTAAAATTTTTGAAAAACTGGCCTGAAAAAATTTTCCTCAATTTTTGGCCACAATACGC
66 TTTCGGCTAAAATTTTTGAAAAACTGACCTGAAAAAATTTTCCTCAATTTTTGGCCACAATACTC
* * * * * * *
2992 ATAAAAAATATATAATTCAACACC-GAATGATTGGAA-GGCTTTTTACACTTCTAATTTTATTTT
131 ATAAAAAATATATAATTCAACGCCAAAAAGATT-GAAGGGCTTTTCACGCTTCTAATATCATTTT
* * *
3055 T-CAAATTTATTTTCCAAATCAATTTC-AATTATATCGAAA-ATGATTGAGATGCTCGTAAAAAC
195 TCCAAA--T-TTTTCCAAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAAC
* *
3117 AAATCCTTAAATCCAATAC-GACTGAGAGTTGGTTAGATAAATTAAGATATTTCAAGGAGTCTTG
257 AAATCCTTAAATCCAATGCAG-CTGAGATTTGGTTAGATAAATTAAGATATTTCAAGGAGTCTTG
3181 GCGCCAAAAATC
321 GCGCCAAAAATC
* * * * * ** *
3193 ATGTAAAACAGAGCCGGGGCCCCGGAGCACCTTTTTAATCAAAATCCGTGATGATAAAGTACACG
1 ATGCAAAACTGAGCCGAGGCCCCGGAGCGCATTTTTAGCCAAAATCCGTGATGAT-TAGTACACG
* * *
3258 ATTTCGGCT-AAATTTCTTGAAAAACTGACCTGAAAAAATTTTCCTCAATTTTTGACAAGAATAC
65 ATTTCGGCTAAAATTT-TTGAAAAACTGACCTGAAAAAATTTTCCTCAATTTTTGGCCACAATAC
** * * * * *
3322 TCATAAAAAATATATAATT-AATTTCCAAAAAATATTGATGGGCCTTTCACACTTCTAATATCGT
129 TCATAAAAAATATATAATTCAA-CGCC-AAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCAT
* * *
3386 TTTTCTAAATTTTTCCAAATTAATTTCTAATTAAATCGAAAAATGATTCAGATGCTCGAAAAAAC
192 TTTTCCAAATTTTTCCAAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAAC
* * * * * *
3451 AAAT-CTTAAATCAAATACGGCTGAGATTTTGTTAGATAAATTAAGATATTTCGAGGAGTCTTGC
257 AAATCCTTAAATCCAATGCAGCTGAGATTTGGTTAGATAAATTAAGATATTTCAAGGAGTCTTGG
* *
3515 CG-CATAACTC
322 CGCCAAAAATC
*
3525 ATGCAAAACTGAGCCG-GGACCCAGGAGCGCATTTTTAGCCAAAATCCGTGATGATTAGTACACG
1 ATGCAAAACTGAGCCGAGG-CCCCGGAGCGCATTTTTAGCCAAAATCCGTGATGATTAGTACACG
* * * *
3589 ATTTCGGCTAAAATTTTT-AATAACCGACCTGAAAAAAATTTCCTCAATTTTTGGCCATAATACT
65 ATTTCGGCTAAAATTTTTGAAAAACTGACCTGAAAAAATTTTCCTCAATTTTTGGCCACAATACT
* ** * * * *
3653 CATAAAAAATATATAATTCAATG-CTGAAAGATTGGAA-GGCTTTTCGCGCCTCTAGTATTATTT
130 CATAAAAAATATATAATTCAACGCCAAAAAGATT-GAAGGGCTTTTCACGCTTCTAATATCATTT
* * * * *
3716 TTCAAAAAAATTTT-CAAATTAATTTCTAATTATATTGAAACATGATTCAGATGCTCATAAAAAC
194 TTC--CAAATTTTTCCAAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAAC
* * * * * *
3780 AAATTCTTAAATTCATTGCAGCTGAGATTTGGTTAGATAAATAAAGATATTTCAAGGAGTTTTGA
257 AAATCCTTAAATCCAATGCAGCTGAGATTTGGTTAGATAAATTAAGATATTTCAAGGAGTCTTGG
* *
3845 CACGAAAAATC
322 CGCCAAAAATC
* * * * * * *
3856 ATGCAAAACTAAGCCGAAGCCCCGAAGCGCTTTTTTTGCAAAAATCTGTGATGATTAGTACACGA
1 ATGCAAAACTGAGCCGAGGCCCCGGAGCGCATTTTTAGCCAAAATCCGTGATGATTAGTACACGA
* * *
3921 TTTCGGCTAAAATTTTTGAAAAACTGACTTG-AAAAATATTTCCTTACTTTTTGGCCACAATACT
66 TTTCGGCTAAAATTTTTGAAAAACTGACCTGAAAAAAT-TTTCCTCAATTTTTGGCCACAATACT
* *
3985 CATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCATGCTTCTAATATCGTTTT
130 CATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTT
* * * *
4050 TCCTAATTTTTACCAAATTAATTTCTAATTAAATCGAAACCTGATTTAGATGCTTGTAAAAACAA
195 TCCAAATTTTT-CCAAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAA
* * * * * * * * *
4115 ATCTTTAAATTCAATGCGGCTTAGATTTGGTTAGATAAGTAAAGATATTTCAAGTAGTTTTGACG
259 ATCCTTAAATCCAATGCAGCTGAGATTTGGTTAGATAAATTAAGATATTTCAAGGAGTCTTGGCG
**
4180 GTAAAAATC
324 CCAAAAATC
* ** * * * *
4189 ATGCAAAACTGAGCCGAGGCCACAAAGCGCATTTTTAGCCATAAA-CCATGATGGTTAATAAACG
1 ATGCAAAACTGAGCCGAGGCCCCGGAGCGCATTTTTAGCCA-AAATCCGTGATGATTAGTACACG
* * * *
4253 ACTTCGGCTAAAATTTTTGAAAAACTTACCCGAAAAAATTTTCCTCAATTTTTGACCACAATACT
65 ATTTCGGCTAAAATTTTTGAAAAACTGACCTGAAAAAATTTTCCTCAATTTTTGGCCACAATACT
** * * * * * *
4318 CATTGAAAATATATAATTCAACACCGAAAAGATTGAAGGGGTTTTCGCACTTCTAATATCATCTT
130 CATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTT
* * *
4383 TCAAAAATTTTTCCAAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCATGAAAACAA
195 TC-CAAATTTTTCCAAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAA
** * * * **
4448 ATCCTTAAATCCAATGTTTGCTGAGATTTTGTTAGATGAATATAA-ATATTTCAATGAGAGTTGG
259 ATCCTTAAATCCAATG-CAGCTGAGATTTGGTTAGATAAAT-TAAGATATTTCAAGGAGTCTTGG
4512 CGCCAAAAATC
322 CGCCAAAAATC
4523 ATGCAAAACTGAG
1 ATGCAAAACTGAG
4536 TTGGGACCTG
Statistics
Matches: 2250, Mismatches: 350, Indels: 125
0.83 0.13 0.05
Matches are distributed among these distances:
323 24 0.01
324 36 0.02
325 30 0.01
326 152 0.07
327 28 0.01
328 29 0.01
329 125 0.06
330 278 0.12
331 382 0.17
332 276 0.12
333 514 0.23
334 221 0.10
335 143 0.06
336 12 0.01
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.32
Consensus pattern (332 bp):
ATGCAAAACTGAGCCGAGGCCCCGGAGCGCATTTTTAGCCAAAATCCGTGATGATTAGTACACGA
TTTCGGCTAAAATTTTTGAAAAACTGACCTGAAAAAATTTTCCTCAATTTTTGGCCACAATACTC
ATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTT
CCAAATTTTTCCAAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAAT
CCTTAAATCCAATGCAGCTGAGATTTGGTTAGATAAATTAAGATATTTCAAGGAGTCTTGGCGCC
AAAAATC
Done.