Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011012.1 Corchorus capsularis cultivar CVL-1 contig11033, 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: 4002
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.31
Found at i:746 original size:314 final size:314
Alignment explanation
Indices: 1--1699 Score: 1681
Period size: 323 Copynumber: 5.4 Consensus size: 314
* * *
1 TGGCGCAAGGACACCTTGAAATATCTATTTTTCATCGAAGCAAATGTCAGCCACATTGGATATAA
1 TGGCGCAAAGACTCCTTGAAATATCTA-TATTCATCGAAGCAAATGTCAGCCACATTGGATATAA
* * * *
66 GAATTT-TTTTTATGTGAATCTAGATCTTGTTTTGATTTAATCAGAAATTAATTAAGAAAAAATT
65 GGATTTGTTTTTACGAGAATCTAGATCTTGTTTCGATTTAATCAGAAATTAATTAAGAAAAAATT
* * *
130 GGAAAAAATGATATTGGAACCGTGAAAAGCCCGCCAATCTTTTTGGCGTTGAATTATATATTTTT
130 GGAAAAAACGATATTAGAACCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTT
* *
195 TATGAGTACTGTGGCAAAAAATTGAGAAAAAACTTTTCTGGTCAATTTTTAGCCGAAATCATGTA
195 TCTGAGTACTGTGGCAAAAAATTGAGAAAAAACTTTTCTGGTCAATTTTTAGCCGAATTCATG--
260 CTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCACGAATTT
258 -------TCACAGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCACGAATTT
324 TGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAAGCAAATGTCAGCCACATTGGATATAAG
1 TGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAAGCAAATGTCAGCCACATTGGATATAAG
*
389 GATTTGTTTTTATGTA-AATCTAGATCTTGTTTCGATTTAATCAGAAATTAATTAAGAAAAAATT
66 GATTTGTTTTTACG-AGAATCTAGATCTTGTTTCGATTTAATCAGAAATTAATTAAGAAAAAATT
* *
453 GGAAAAAATGATATTGGAACCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTT
130 GGAAAAAACGATATTAGAACCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTT
518 TCTGAGTACTGTGGCAAAAAATTGAGAAAAAACTTTTCTGGTCAATTTTTAGCCGAATTCATGTC
195 TCTGAGTACTGTGGCAAAAAATTGAGAAAAAACTTTTCTGGTCAATTTTTAGCCGAATTCATGTC
*
583 ACAGTTTTTGGCTAAAAACGCATTCCGGAGCCCCGGCTCAATTTTGCACGAATTT
260 ACAGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCACGAATTT
* *
638 TGGCGCAAAGACTCCTTGAAATATGTATATTCATCAAAGCAAATGTCAGCCACATTGGATATAAG
1 TGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAAGCAAATGTCAGCCACATTGGATATAAG
* * * *
703 GATTTCTTTTTACGAGAATCTAGATCTTGTTTCAATTTAATCAGACATTAATTCAGAAAAAATTG
66 GATTTGTTTTTACGAGAATCTAGATCTTGTTTCGATTTAATCAGAAATTAATTAAGAAAAAATTG
* * * *
768 GAAAAAACGATATTAGAAGCGTGAATAGCCCATTAATCTTTTTGGCGTTGAATTATATATCTTTT
131 GAAAAAACGATATTAGAACCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATAT-TTTT
* * * * *
833 T-TTAGTATTGTGGCAAAAAATTGAGAAAAAACTCTTCGGGTCAATTTTTAGCCAAAATCGTGTA
195 TCTGAGTACTGTGGCAAAAAATTGAGAAAAAACTTTTCTGGTCAATTTTTAGCC-GAA---T-T-
** * * *
897 CTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTCCATGATTTT
254 C--A-TGTCACAGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCACGAATTT
* * *
961 TGGCTCAAAGACTCCTTGTAATATCTATATTCATCGAAGC-AATGTCAGCTACATTGGATATAAG
1 TGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAAGCAAATGTCAGCCACATTGGATATAAG
* * * *
1025 GATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATT-
66 GATTTGTTTTTACGAGAATCTAGATCTTGTTTCGATTTAATCAGAAATTAATTAAGAAAAAATTG
* * * * * *
1089 GTAAAAACGATCTTAGAAACGTGAAAAGCCCGTTAATCTTTTAGGCGTTTAATTATATATTTTTT
131 GAAAAAACGATATTAGAACCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTT
* * * *** * * * *
1154 CTGAGCATTGTGGCAAAAAATTCAGGAAAAAA-AAATCGGGTCAGTTTTTAGCCGAAATCGTGTA
196 CTGAGTACTGTGGCAAAAAATTGA-GAAAAAACTTTTCTGGTCAATTTTTAGCCGAATTCATG--
** * * * * ** * **
1218 CTAACCATCACTGTTTTTTACTAAAAAGGCCTTCTGTG-GCCCCGACTCTGTTTTGCATGGTTTT
258 -T---CA-CA--GTTTTTGGCTAAAAACGCGTTCCG-GAGCCCCGGCTCAATTTTGCACGAATTT
* ** * * * * * ** * * *
1282 TGTCGCCGAGACTCCTTGAGATATCTTTTATTAATCTAATCAAAACTCAGTCATATTGGATTTAA
1 TGGCGCAAAGACTCCTTGAAATATC-TATATTCATCGAAGCAAATGTCAGCCACATTGGATATAA
* * * * * * *
1347 GGATTTGTTTTTACGTGCAT-TTGAATCTTTTTTCGATTTAATAAGAAATTAATTCAGAACAAAT
65 GGATTTGTTTTTACGAGAATCTAG-ATCTTGTTTCGATTTAATCAGAAATTAATTAAGAA-AAAA
** ** *
1411 TTAAAAAAAAAACGATATT--AAGTGTGAAAATGTCC-TCCAATCTTTTTGGCGTTGAATTATAT
128 TT--GGAAAAAACGATATTAGAACCGTGAAAA-GCCCGT-CAATCTTTTTGGCGTTGAATTATAT
* * ** * * * * * *
1473 ATATATTTATGAGTGTTTTTGCCAAAAATTGAGGAAAAA-TCTTTCGGGT-TATTTTTA-CC--A
189 AT-TTTTTCTGAGTACTGTGGCAAAAAATTGAGAAAAAACT-TTTCTGGTCAATTTTTAGCCGAA
* * *
1533 -TCATG-----GTTTTTGGCTAAAAACGCGTTCCGG-GCCCCAGCTC---TTTGCATGATTTT
252 TTCATGTCACAGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCACGAATTT
* *** * * * * ** * * *
1586 TGGCACTGTGACTCCTTAAAATATCTATATT-ATCTAATCAAATCTCAGAAATATTGGTTTTAAG
1 TGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAAGCAAATGTCAGCCACATTGGATATAAG
* * * * * *
1650 GATTTATTTTAACAAGTA-CTTAAATCTTGTTTCGATTTAATTAGAAATTA
66 GATTTGTTTTTACGAGAATC-TAGATCTTGTTTCGATTTAATCAGAAATTA
1700 TTTCAAAAAA
Statistics
Matches: 1190, Mismatches: 148, Indels: 97
0.83 0.10 0.07
Matches are distributed among these distances:
302 67 0.06
303 6 0.01
304 31 0.03
307 9 0.01
308 19 0.02
313 1 0.00
314 279 0.23
315 9 0.01
316 1 0.00
318 3 0.00
319 3 0.00
320 8 0.01
321 149 0.13
322 147 0.12
323 364 0.31
324 5 0.00
325 12 0.01
326 39 0.03
327 38 0.03
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.35
Consensus pattern (314 bp):
TGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAAGCAAATGTCAGCCACATTGGATATAAG
GATTTGTTTTTACGAGAATCTAGATCTTGTTTCGATTTAATCAGAAATTAATTAAGAAAAAATTG
GAAAAAACGATATTAGAACCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTT
CTGAGTACTGTGGCAAAAAATTGAGAAAAAACTTTTCTGGTCAATTTTTAGCCGAATTCATGTCA
CAGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCACGAATTT
Found at i:1513 original size:323 final size:319
Alignment explanation
Indices: 1--1512 Score: 1791
Period size: 323 Copynumber: 4.7 Consensus size: 319
* * *
1 TGGCGCAAGGACACCTTGAAATATCTATTTTTCATCGAAGCAAATGTCAGCCACATTGGATATAA
1 TGGCGCAAAGACTCCTTGAAATATCTA-TATTCATCGAAGCAAATGTCAGCCACATTGGATATAA
* * * * *
66 GAATTT-TTTTTATGTGAATCTAGATCTTGTTTTGATTTAATCAGAAATTAATTAAGAAAAAATT
65 GGATTTGTTTTTACGAGAATCTAGATCTTGTTTCGATTTAATCAGAAATTAATTCAGAAAAAATT
* * *
130 GGAAAAAATGATATTGGAACCGTGAAAAGCCCGCCAATCTTTTTGGCGTTGAATTATATATTTTT
130 GGAAAAAACGATATT-GAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTT
* *
195 TATGAGTACTGTGGCAAAAAATTGAGAAAAAACTTTTCTGGTCAATTTTTAGCCGAAATCATGTA
194 TATGAGTATTGTGGCAAAAAATTGAGAAAAAA---TTCGGGTCAATTTTTAGCCGAAATCATGTA
260 CTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCACGAATTT
256 CTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCACGAATTT
324 TGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAAGCAAATGTCAGCCACATTGGATATAAG
1 TGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAAGCAAATGTCAGCCACATTGGATATAAG
* *
389 GATTTGTTTTTATGTA-AATCTAGATCTTGTTTCGATTTAATCAGAAATTAATTAAGAAAAAATT
66 GATTTGTTTTTACG-AGAATCTAGATCTTGTTTCGATTTAATCAGAAATTAATTCAGAAAAAATT
* *
453 GGAAAAAATGATATTGGAACCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTT
130 GGAAAAAACGATATT-GAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTT
* * * *
518 TCTGAGTACTGTGGCAAAAAATTGAGAAAAAACTTTTCTGGTCAATTTTTAGCCGAATTCATG--
194 TATGAGTATTGTGGCAAAAAATTGAGAAAAAA---TTCGGGTCAATTTTTAGCCGAAATCATGTA
*
581 -------TCACAGTTTTTGGCTAAAAACGCATTCCGGAGCCCCGGCTCAATTTTGCACGAATTT
256 CTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCACGAATTT
* *
638 TGGCGCAAAGACTCCTTGAAATATGTATATTCATCAAAGCAAATGTCAGCCACATTGGATATAAG
1 TGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAAGCAAATGTCAGCCACATTGGATATAAG
* * *
703 GATTTCTTTTTACGAGAATCTAGATCTTGTTTCAATTTAATCAGACATTAATTCAGAAAAAATTG
66 GATTTGTTTTTACGAGAATCTAGATCTTGTTTCGATTTAATCAGAAATTAATTCAGAAAAAATTG
* * *
768 GAAAAAACGATATTAGAAGCGTGAATAGCCCATTAATCTTTTTGGCGTTGAATTATATATCTTTT
131 GAAAAAACGATATT-GAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATAT-TTTT
* * *
833 T-TTAGTATTGTGGCAAAAAATTGAGAAAAAACTCTTCGGGTCAATTTTTAGCCAAAATCGTGTA
194 TATGAGTATTGTGGCAAAAAATTGAGAAAAAA---TTCGGGTCAATTTTTAGCCGAAATCATGTA
* * *
897 CTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTCCATGATTTT
256 CTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCACGAATTT
* * *
961 TGGCTCAAAGACTCCTTGTAATATCTATATTCATCGAAGC-AATGTCAGCTACATTGGATATAAG
1 TGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAAGCAAATGTCAGCCACATTGGATATAAG
* * *
1025 GATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATT-
66 GATTTGTTTTTACGAGAATCTAGATCTTGTTTCGATTTAATCAGAAATTAATTCAGAAAAAATTG
* * * * * *
1089 GTAAAAACGATCTTAGAAACGTGAAAAGCCCGTTAATCTTTTAGGCGTTTAATTATATATTTTTT
131 GAAAAAACGATATT-GAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTT
* * * * * *
1154 CTGAGCATTGTGGCAAAAAATTCAGGAAAAAAAAATCGGGTCAGTTTTTAGCCGAAATCGTGTAC
195 ATGAGTATTGTGGCAAAAAATT---GAGAAAAAATTCGGGTCAATTTTTAGCCGAAATCATGTAC
* ** * * * * ** * **
1219 TAACCATCACTGTTTTTTACTAAAAAGGCCTTCTGTG-GCCCCGACTCTGTTTTGCATGGTTTT
257 TAACCATCACAGTTTTTGGCTAAAAACGCGTTCCG-GAGCCCCGGCTCAATTTTGCACGAATTT
* ** * * * * * ** * * *
1282 TGTCGCCGAGACTCCTTGAGATATCTTTTATTAATCTAATCAAAACTCAGTCATATTGGATTTAA
1 TGGCGCAAAGACTCCTTGAAATATC-TATATTCATCGAAGCAAATGTCAGCCACATTGGATATAA
* * * * * *
1347 GGATTTGTTTTTACGTGCAT-TTGAATCTTTTTTCGATTTAATAAGAAATTAATTCAGAACAAAT
65 GGATTTGTTTTTACGAGAATCTAG-ATCTTGTTTCGATTTAATCAGAAATTAATTCAGAA-AAAA
** * *
1411 TTAAAAAAAAAACGATATT-AAGTGTGAAAATGTCC-TCCAATCTTTTTGGCGTTGAATTATATA
128 TT--GGAAAAAACGATATTGAAGCGTGAAAA-GCCCGT-CAATCTTTTTGGCGTTGAATTATATA
* * * * * *
1474 TATATTTATGAGTGTTTTTGCCAAAAATTGAGGAAAAAT
189 T-TTTTTATGAGTATTGTGGCAAAAAATTGAGAAAAAAT
1513 CTTTCGGGTT
Statistics
Matches: 1051, Mismatches: 110, Indels: 55
0.86 0.09 0.05
Matches are distributed among these distances:
313 1 0.00
314 285 0.27
315 5 0.00
320 5 0.00
321 169 0.16
322 135 0.13
323 363 0.35
324 20 0.02
325 10 0.01
326 27 0.03
327 31 0.03
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (319 bp):
TGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAAGCAAATGTCAGCCACATTGGATATAAG
GATTTGTTTTTACGAGAATCTAGATCTTGTTTCGATTTAATCAGAAATTAATTCAGAAAAAATTG
GAAAAAACGATATTGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTA
TGAGTATTGTGGCAAAAAATTGAGAAAAAATTCGGGTCAATTTTTAGCCGAAATCATGTACTAAC
CATCACAGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCACGAATTT
Found at i:3645 original size:86 final size:86
Alignment explanation
Indices: 3497--3657 Score: 270
Period size: 86 Copynumber: 1.9 Consensus size: 86
3487 GTGGACATGG
* *
3497 AGGTACACGAGAAGGACAGCGGCTCTCAGCATGAGGCTCTCAAAACGGCCGCCAACTGCGAGGCT
1 AGGTACACGAGAAGGACAGCGGCTCTCAGCATGAGGCACTCAAAACGGCCGCCAACTACGAGGCT
3562 CGCCCAACACAACGCACACGA
66 CGCCCAACACAACGCACACGA
*
3583 AGGTACACGAG-AGGACAGCGGCTCTCAGCAGTGAGGCACTCAAAACGTCCGCCAACTACGAGGC
1 AGGTACACGAGAAGGACAGCGGCTCTCAGCA-TGAGGCACTCAAAACGGCCGCCAACTACGAGGC
*
3647 TCGCCCGACAC
65 TCGCCCAACAC
3658 GACACACGAG
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
85 19 0.27
86 51 0.73
ACGTcount: A:0.29, C:0.34, G:0.27, T:0.10
Consensus pattern (86 bp):
AGGTACACGAGAAGGACAGCGGCTCTCAGCATGAGGCACTCAAAACGGCCGCCAACTACGAGGCT
CGCCCAACACAACGCACACGA
Found at i:3863 original size:10 final size:10
Alignment explanation
Indices: 3771--4000 Score: 99
Period size: 10 Copynumber: 22.6 Consensus size: 10
3761 AAAAATAAAC
*
3771 AGAGAGAGAG
1 AGAGAGTGAG
**
3781 AGAGAGCCAG
1 AGAGAGTGAG
**
3791 AGAGAGCCAG
1 AGAGAGTGAG
* * *
3801 AGAGCGAGCG
1 AGAGAGTGAG
*
3811 AGAGAGTGCG
1 AGAGAGTGAG
* *
3821 AGTGAATGAG
1 AGAGAGTGAG
3831 AGAGAGTGAG
1 AGAGAGTGAG
* *
3841 AGTGAATGAG
1 AGAGAGTGAG
3851 AGAGAGTGCGAG
1 AGAGAGT--GAG
*
3863 AGTGCAAGTGAATG
1 AGAG--AGTG-A-G
3877 AGAGAGTGAG
1 AGAGAGTGAG
*
3887 AGAG-GTGTG
1 AGAGAGTGAG
*
3896 CGCA-AGTGAG
1 AG-AGAGTGAG
*
3906 -G-GAGCGAG
1 AGAGAGTGAG
* *
3914 AGAAAGGTGTG
1 AGAGA-GTGAG
* * * *
3925 CGCGCGCGAG
1 AGAGAGTGAG
*
3935 AGAGAGAGAG
1 AGAGAGTGAG
*
3945 AGAGAGAGAG
1 AGAGAGTGAG
*
3955 AGAGAGAGAG
1 AGAGAGTGAG
*
3965 AGAGAGAGAG
1 AGAGAGTGAG
*
3975 AGAGAGAGAG
1 AGAGAGTGAG
*
3985 AGAGAGAGAG
1 AGAGAGTGAG
3995 AGAGAG
1 AGAGAG
4001 AG
Statistics
Matches: 172, Mismatches: 36, Indels: 24
0.74 0.16 0.10
Matches are distributed among these distances:
8 5 0.03
9 7 0.04
10 136 0.79
11 5 0.03
12 11 0.06
13 1 0.01
14 7 0.04
ACGTcount: A:0.39, C:0.07, G:0.47, T:0.07
Consensus pattern (10 bp):
AGAGAGTGAG
Found at i:3937 original size:2 final size:2
Alignment explanation
Indices: 3932--4002 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
3922 GTGCGCGCGC
3932 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
3974 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3943 original size:29 final size:29
Alignment explanation
Indices: 3876--3945 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
3866 GCAAGTGAAT
* * *
3876 GAGAGAGTGAGAGAGGTGTGCGCAAGTGA
1 GAGAGAGAGAGAAAGGTGTGCGCAAGCGA
* * **
3905 GGGAGCGAGAGAAAGGTGTGCGCGCGCGA
1 GAGAGAGAGAGAAAGGTGTGCGCAAGCGA
3934 GAGAGAGAGAGA
1 GAGAGAGAGAGA
3946 GAGAGAGAGA
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.31, C:0.10, G:0.50, T:0.09
Consensus pattern (29 bp):
GAGAGAGAGAGAAAGGTGTGCGCAAGCGA
Done.