Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005588.1 Corchorus capsularis cultivar CVL-1 contig05606, 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: 12948
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Found at i:13 original size:2 final size:2
Alignment explanation
Indices: 7--88 Score: 157
Period size: 2 Copynumber: 41.5 Consensus size: 2
1 CTCCTC
7 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
49 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT -T CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
89 GTTTCAGGTT
Statistics
Matches: 79, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 78 0.99
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:6258 original size:15 final size:16
Alignment explanation
Indices: 6231--6261 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
6221 ATTTCCCTAC
6231 AATCCCTTAAAAAAAA
1 AATCCCTTAAAAAAAA
6247 AATCCC-TAAAAAAAA
1 AATCCCTTAAAAAAAA
6262 TATGGGTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.65, C:0.19, G:0.00, T:0.16
Consensus pattern (16 bp):
AATCCCTTAAAAAAAA
Found at i:10395 original size:106 final size:106
Alignment explanation
Indices: 10210--10419 Score: 316
Period size: 106 Copynumber: 2.0 Consensus size: 106
10200 AAGAGCAAGC
* *
10210 GTGTCTTGATGGAAAGCATCAACAATTCCACAGCAGAGAAGGCAAGAGAGAAGACACCTTCTGAT
1 GTGTCTTGATGGAAAGCATCAACAAGTCCACAACAGAGAAGGCAAGAGAGAAGACACCTTCTGAT
* *
10275 CTGTTTGAGGCCAAGCCCGCTAAGAACAAGGCAAGCAGGGA
66 CAGTTTGACGCCAAGCCCGCTAAGAACAAGGCAAGCAGGGA
* *
10316 GTGTCTTGATGGAAAG-AGTCAACAAGTCCGA-AACTGAGAAGGCAAGAGAGAAGACACTTTCTG
1 GTGTCTTGATGGAAAGCA-TCAACAAGTCC-ACAACAGAGAAGGCAAGAGAGAAGACACCTTCTG
**
10379 ATCAGTTTGACGCCAAGCGTGCTAAGAACAAGGCAAGCAGG
64 ATCAGTTTGACGCCAAGCCCGCTAAGAACAAGGCAAGCAGG
10420 CCGGAAGGGA
Statistics
Matches: 94, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
105 1 0.01
106 92 0.98
107 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.28, T:0.17
Consensus pattern (106 bp):
GTGTCTTGATGGAAAGCATCAACAAGTCCACAACAGAGAAGGCAAGAGAGAAGACACCTTCTGAT
CAGTTTGACGCCAAGCCCGCTAAGAACAAGGCAAGCAGGGA
Found at i:12231 original size:332 final size:330
Alignment explanation
Indices: 11489--12505 Score: 1393
Period size: 332 Copynumber: 3.1 Consensus size: 330
11479 ATCGACACAA
* ** * * *
11489 TACACGATTTAGGCTAAAATTTCCCAAGAATTGAC-CCAAAAA--TTTCCTCAA-TTTTGGCCAA
1 TACACGATTTGGGCTAAAATTTTGCAAAAATTGACTCGAAAAATTTTTCCTCAATTTTTGGCCAG
* * * * *
11550 AATACTTATAAAAAATATATAATTCAACGCCAAAAAAATTGATGTGTTTTGACGCTTCTAATAAC
66 AATACTCAT-AGAAATATATAATTCAACGCCAAAAAAATTGATGGGTTTTCACGCTTCTAATATC
* *
11615 GATTGTCCTATATTTTTCC-AACTTAATTTTTCATTAAATCGACACATGATTCTGATGCTCGTCA
130 GATTTTCCTATATTTTTCCGAA-TTAATTTCTCATTAAATCGACACATGATTCTGATGCTCGTCA
* * * *
11679 AATCAAATCCTTAATTCCATTGTGGCTGAGATTTGGTTAGATAAATATAGATATTTCAATGAGTC
194 AATCAAATCCTTAAATCCA-TGTAGCAGAGATTTGGTTAGATGAATATAGATATTTCAATGAGTC
* * * * * *
11744 TTGGGGCAAAAATTCATGCAAAAATGAACCGTAGCACCGGAACGCATTTTTACCCAGAAATCGTG
258 TTGGCGCAAAAAATCATGCAAAACTGAACCGGAGCACCGGAACGCATTTTTAGCCAAAAATCGTG
11809 ATGGTTAG
323 ATGGTTAG
* * *
11817 TACACGATTTGGGCTAAAATTTTGCGAAAATTGAGTCGAAAAATTTGTCCTCAATTTTTGGCCAG
1 TACACGATTTGGGCTAAAATTTTGCAAAAATTGACTCGAAAAATTTTTCCTCAATTTTTGGCCAG
* * *
11882 AATACTCATAAGAAATATATAATTCAGCGCCAAAAATATTGATGGGCATTTCACGCTTCTAATAT
66 AATACTCAT-AGAAATATATAATTCAACGCCAAAAAAATTGATGGG-TTTTCACGCTTCTAATAT
* *
11947 CGATTTTCCCACA-TTTTCCGAATTAATTTCTCATTAAATCGACACATGATTCTGATGCTCGTCA
129 CGATTTTCCTATATTTTTCCGAATTAATTTCTCATTAAATCGACACATGATTCTGATGCTCGTCA
* * *
12011 AATCAAATCCTTAAATCCACTGTAGCAGAGATTTTGTTAGATGAATATAGATATTACAATGATTC
194 AATCAAATCCTTAAATCCA-TGTAGCAGAGATTTGGTTAGATGAATATAGATATTTCAATGAGTC
* *
12076 TTGGCGCAAAAAATCATGCAAAACTGAACCGGAGCACCGGAACACATTTTTAGCCAAAAACCGTG
258 TTGGCGCAAAAAATCATGCAAAACTGAACCGGAGCACCGGAACGCATTTTTAGCCAAAAATCGTG
12141 ATGTGTTAG
323 ATG-GTTAG
* *
12150 TACCCGATTTGGGCTAAAATTTTGCAAAAATTGACTCGAAAAATTTTTTCCTAAATTTTTGGCCA
1 TACACGATTTGGGCTAAAATTTTGCAAAAATTGACTCGAAAAA-TTTTTCCTCAATTTTTGGCCA
* *
12215 GAATACTCAT-GAAATATATATAATTCAACGCCAAAAAGATTGATTGGTTTTTCACGCTTCTAAT
65 GAATACTCATAG-AA-ATATATAATTCAACGCCAAAAAAATTGA-TGGGTTTTCACGCTTCTAAT
* * * *
12279 ATCAATTTTCCTATATTTTTCCGATTTAATTTCTCATTAAATCAACACATGATTCTGTTGCTCGT
127 ATCGATTTTCCTATATTTTTCCGAATTAATTTCTCATTAAATCGACACATGATTCTGATGCTCGT
* * *
12344 AAAATCAAAAT-CTTAAATCCATATAGACAGAGATTTGGTTAAATGAATATAGATATTTCAATGA
192 CAAATC-AAATCCTTAAATCCATGTAG-CAGAGATTTGGTTAGATGAATATAGATATTTCAATGA
* *
12408 GTCATGGCGCAAAAAATCATGCAAAACTGAACCGGGGCACCGGAACGCATTTTTAGCCAAAAATC
255 GTCTTGGCGCAAAAAATCATGCAAAACTGAACCGGAGCACCGGAACGCATTTTTAGCCAAAAATC
*
12473 GTGATAGTTAG
320 GTGATGGTTAG
* *
12484 TACACAATTTGTGCTAAAATTT
1 TACACGATTTGGGCTAAAATTT
12506 GTGTTTTTTA
Statistics
Matches: 609, Mismatches: 66, Indels: 22
0.87 0.09 0.03
Matches are distributed among these distances:
328 29 0.05
329 6 0.01
331 8 0.01
332 215 0.35
333 74 0.12
334 110 0.18
335 163 0.27
336 4 0.01
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (330 bp):
TACACGATTTGGGCTAAAATTTTGCAAAAATTGACTCGAAAAATTTTTCCTCAATTTTTGGCCAG
AATACTCATAGAAATATATAATTCAACGCCAAAAAAATTGATGGGTTTTCACGCTTCTAATATCG
ATTTTCCTATATTTTTCCGAATTAATTTCTCATTAAATCGACACATGATTCTGATGCTCGTCAAA
TCAAATCCTTAAATCCATGTAGCAGAGATTTGGTTAGATGAATATAGATATTTCAATGAGTCTTG
GCGCAAAAAATCATGCAAAACTGAACCGGAGCACCGGAACGCATTTTTAGCCAAAAATCGTGATG
GTTAG
Found at i:12751 original size:246 final size:247
Alignment explanation
Indices: 12261--12732 Score: 720
Period size: 246 Copynumber: 1.9 Consensus size: 247
12251 AGATTGATTG
* * *
12261 GTTTTTCACGCTTCTAATATCAATTTTCCTATATTTTTCCGATTTAATTTCTCATTAAATCAACA
1 GTTTTTCACGCTTCTAATATCAATTTTCCTATATTTTTCCAACTCAATTTCTCATTAAATCAACA
* * *
12326 CATGATTCTGTTGCTCGTAAAATCAAAATCTTAAATCCATATAGACAGAGATTTGGTTAAATGAA
66 CAAGATTCTGATGCTCGTAAAATCAAAATCTTAAATCCATATAGACAGAGATATGGTTAAATGAA
* *
12391 TATAGATATTTCAATGAGTCATGGCGCAAAAAATCATGCAAAACTGAACCGGGGCACCGGAACGC
131 TATAGATATTTCAATGAGTCATGACGCAAAAAATCATGCAAAACTGAACCGGAGCACCGGAACGC
12456 ATTTTTAGCCAAAAATCGTGATAGTTAGTACACAATTTGTGCTAAAATTTGT
196 ATTTTTAGCCAAAAATCGTGATAGTTAGTACACAATTTGTGCTAAAATTTGT
* * *
12508 GTTTTTTACGCTTCTAATATC-GTTTGTCCTATA-TTTTCCAACTCAATTTTTCATTAAATCAAC
1 GTTTTTCACGCTTCTAATATCAATTT-TCCTATATTTTTCCAACTCAATTTCTCATTAAATCAAC
* * * *
12571 CCAAGATTCTGATGCTCGTAAAATC-AAATCCTTAAATCCAT-TGTGGCAGAGATATGGTTAGAT
65 ACAAGATTCTGATGCTCGTAAAATCAAAAT-CTTAAATCCATAT-AGACAGAGATATGGTTAAAT
*
12634 GAATATAGATATTTCAATGAGTCTTGACGCAAAAAATCATGCAAAACTGAACCGGAGCACCGGAA
128 GAATATAGATATTTCAATGAGTCATGACGCAAAAAATCATGCAAAACTGAACCGGAGCACCGGAA
*
12699 CGCATTTTTAGCCAAAAA-CTGTGATGGTTAGTAC
193 CGCATTTTTAGCCAAAAATC-GTGATAGTTAGTAC
12733 TTGATTTAGG
Statistics
Matches: 204, Mismatches: 17, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
245 6 0.03
246 171 0.84
247 27 0.13
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (247 bp):
GTTTTTCACGCTTCTAATATCAATTTTCCTATATTTTTCCAACTCAATTTCTCATTAAATCAACA
CAAGATTCTGATGCTCGTAAAATCAAAATCTTAAATCCATATAGACAGAGATATGGTTAAATGAA
TATAGATATTTCAATGAGTCATGACGCAAAAAATCATGCAAAACTGAACCGGAGCACCGGAACGC
ATTTTTAGCCAAAAATCGTGATAGTTAGTACACAATTTGTGCTAAAATTTGT
Done.