Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014540.1 Corchorus capsularis cultivar CVL-1 contig14561, 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: 6683
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:241 original size:52 final size:52
Alignment explanation
Indices: 163--498 Score: 600
Period size: 52 Copynumber: 6.4 Consensus size: 52
153 TTTAAAAAGT
163 TTAAAAGATTTAGTAATTAGGGAGACGCATGAGGGCTGCCCCTCCAAACATC
1 TTAAAAGATTTAGTAATTAGGGAGACGCATGAGGGCTGCCCCTCCAAACATC
215 TTAAAAGATTTAGTAATTAGGGAGACGCATGAGGGCTGCCCCTCCAAACATC
1 TTAAAAGATTTAGTAATTAGGGAGACGCATGAGGGCTGCCCCTCCAAACATC
* * *
267 TTAAAAGACTTGGTAATTAGGGAGACGCTTGAGGGCTGCCCCTCCAAACATC
1 TTAAAAGATTTAGTAATTAGGGAGACGCATGAGGGCTGCCCCTCCAAACATC
* *
319 TTAAAGGACTTAGTAATTAGGGAGACGCATGAGGGCTGCCCCTCCAAACATC
1 TTAAAAGATTTAGTAATTAGGGAGACGCATGAGGGCTGCCCCTCCAAACATC
371 TTAAAAGACTTTAGTAATTAGGGAGACGCATGAGGGCTGCCCCTCCAAACATC
1 TTAAAAGA-TTTAGTAATTAGGGAGACGCATGAGGGCTGCCCCTCCAAACATC
*
424 TTAAAAGACTTAGTAATTAGGGAGACGCATGAGGGCCTGCCCCTCCAAACATC
1 TTAAAAGATTTAGTAATTAGGGAGACGCATGAGGG-CTGCCCCTCCAAACATC
477 TTAAAAGATTTAGTAATTAGGG
1 TTAAAAGATTTAGTAATTAGGG
499 TTAAAAGATT
Statistics
Matches: 272, Mismatches: 10, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
52 183 0.67
53 89 0.33
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.23
Consensus pattern (52 bp):
TTAAAAGATTTAGTAATTAGGGAGACGCATGAGGGCTGCCCCTCCAAACATC
Found at i:2878 original size:324 final size:322
Alignment explanation
Indices: 2291--3451 Score: 1494
Period size: 321 Copynumber: 3.6 Consensus size: 322
2281 GACGTTGAAT
* *
2291 GTGAAAACCCCTTCAATCTTTTTGGCGTTGAATTATATACTTTTTATGAGTATTTTGGTAAAAAA
1 GTGAAAACCCCTTCAATCTTTTTGGCGTTGAATTATATA-TTTTTATGAGTATTGTGGCAAAAAA
* * * * * * * * *
2356 TCGAGAAAAAAAATA-TCGGGTCAGTTTTTAGTCGAGATCATGTACTAACTATCACGGTTTTTTG
65 TTGAGAAAAAAAAAATTCGGCTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGG
* * * ** *
2420 CTACAAACGCGTTTCGGGGCCACGGTTCAGTTTTGAATGATTTTTGGCATAAAGTTTGCTTGAAA
130 CTAAAAACGCGTTTCGGGGCCACGGCTCAGTTTTGAATGATTTTTAGCATAAAGACTCCTTGAAA
*
2485 TATCTATATTCATCAAACCAAACCTCAGCCACATTGCATTTAAGGATTTGCCATTACG-GACATC
195 TATCTATATTCATCTAACCAAACCTCAGCCACATTGCATTTAAGGATTTGCCATTACGAG-CATC
2549 TGAATCTTGTTTCAATTTAATTAGAAATAAATTCAAAAAAAAAAAGAAAAACTG-TATTAGAAGC
259 TGAATCTTGTTTCAATTTAATTAGAAATAAATTCAAAAAAAAAAAGAAAAAC-GATATTAGAAGC
* *
2613 GTGAAAACCCCTTCAATCTTTTAGGCGTTGAATTATATACTTTTTATGTGTATTGTGGCAAAAAA
1 GTGAAAACCCCTTCAATCTTTTTGGCGTTGAATTATATA-TTTTTATGAGTATTGTGGCAAAAAA
* * *
2678 TTAAGAAAAAAAAAATTCGGCTCAGTTTTTTGCTGAAAATCGTGTACTAACCATCACAGTTTTTG
65 TTGAGAAAAAAAAAATTCGGCTCAGTTTTTAGCCG-AAATCGTGTACTAACCATCACAGTTTTTG
* * * *
2743 GTTAAAAACGTGTTTCGGGGCCTCCGCTCAGTTTTGAATGATTTTTAGCATAAAGACTCCTTGAA
129 GCTAAAAACGCGTTTCGGGGCCACGGCTCAGTTTTGAATGATTTTTAGCATAAAGACTCCTTGAA
* * * * *
2808 ATATCTGTATTCATCTAATCAAACCTCAGTCACATTGCATTTAATGATTTTCCATTACGAGCATC
194 ATATCTATATTCATCTAACCAAACCTCAGCCACATTGCATTTAAGGATTTGCCATTACGAGCATC
* ** * *
2873 TGAATCTTGTTTCGA-TTAATTAGAAATAAATTC-AGGAAAAAAA-TAATACGATATTAGAAGC
259 TGAATCTTGTTTCAATTTAATTAGAAATAAATTCAAAAAAAAAAAGAAAAACGATATTAGAAGC
* * * * * *
2934 GTGAAAACCCATTCAATATTTTTGACGTTGAATTATATATTTTTATGAGTATTTTTGAAAAAAAT
1 GTGAAAACCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTATTGTGGCAAAAAA-
** * * * *
2999 TTGAG-AAAAAAATTTTCCAGATCAGTTTTTAACCGAAATCGTGTACTAACCCATCACGGTTTTT
65 TTGAGAAAAAAAAAATT-CGGCTCAGTTTTTAGCCGAAATCGTGTACTAA-CCATCACAGTTTTT
* * * * * * * * *
3063 TGCTAAAAAAGCATTTCGGGGCCACGGTTCAGTTTTGAATTATTTTTGGCAGAAAGTCTGCTTGA
128 GGCTAAAAACGCGTTTCGGGGCCACGGCTCAGTTTTGAATGATTTTTAGCATAAAGACTCCTTGA
** *
3128 AATATCTATATTCATCTAACCAAATTTCAACCACATTGCATTTAAGGATTTGCCATTACGAGCAT
193 AATATCTATATTCATCTAACCAAACCTCAGCCACATTGCATTTAAGGATTTGCCATTACGAGCAT
3193 CTGAATCTTGTTTCAATTTAATTAGAAATAAATTCAGAAAAAGAAAAAAGAAAAACGATATTAGA
258 CTGAATCTTGTTTCAATTTAATTAGAAATAAATTC--AAAAA-AAAAAAGAAAAACGATATTAGA
3258 AGC
320 AGC
*
3261 GTGAAAA-ACCTTCAATCTTTTTGGCGTTGAATTATATATTTTTAATGAGTATTGTGGCAAAAAA
1 GTGAAAACCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTT-ATGAGTATTGTGGCAAAAAA
* * * * *
3325 TTGAG-AAAAAAAATTTCGACTCATTTTTTTTGCCGAAAATCGTGTAATAACCATCACAGTTTTT
65 TTGAGAAAAAAAAAATTCGGCTCA-GTTTTTAGCCG-AAATCGTGTACTAACCATCACAGTTTTT
* * * *
3389 GGCTAAAAACGCGTTTCAGGGCCTCAGCTCAGTTTTGAATGATATTTAGCATAAAGACTCCTT
128 GGCTAAAAACGCGTTTCGGGGCCACGGCTCAGTTTTGAATGATTTTTAGCATAAAGACTCCTT
3452 TATATATATA
Statistics
Matches: 714, Mismatches: 109, Indels: 28
0.84 0.13 0.03
Matches are distributed among these distances:
320 45 0.06
321 203 0.28
322 99 0.14
323 33 0.05
324 150 0.21
325 7 0.01
326 124 0.17
327 53 0.07
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (322 bp):
GTGAAAACCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTATTGTGGCAAAAAAT
TGAGAAAAAAAAAATTCGGCTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGC
TAAAAACGCGTTTCGGGGCCACGGCTCAGTTTTGAATGATTTTTAGCATAAAGACTCCTTGAAAT
ATCTATATTCATCTAACCAAACCTCAGCCACATTGCATTTAAGGATTTGCCATTACGAGCATCTG
AATCTTGTTTCAATTTAATTAGAAATAAATTCAAAAAAAAAAAGAAAAACGATATTAGAAGC
Found at i:3459 original size:2 final size:2
Alignment explanation
Indices: 3452--3479 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3442 AAGACTCCTT
3452 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3480 ATTACCCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4852 original size:23 final size:23
Alignment explanation
Indices: 4821--4873 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
4811 TCGTGAAAAC
4821 TTTTT-ATAGACCTAATGCCCAA
1 TTTTTAATAGACCTAATGCCCAA
*
4843 TTTTTAATAGACCTAGTGCCCAA
1 TTTTTAATAGACCTAATGCCCAA
*
4866 TTTCTAAT
1 TTTTTAAT
4874 TCCTGAACCA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
22 5 0.18
23 23 0.82
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.40
Consensus pattern (23 bp):
TTTTTAATAGACCTAATGCCCAA
Found at i:6520 original size:144 final size:147
Alignment explanation
Indices: 6250--6553 Score: 427
Period size: 144 Copynumber: 2.1 Consensus size: 147
6240 CCAAATACAT
* * *
6250 CAGTGATGCTCCCCGCACGCACAATGGAAGATTATTAGGTTATTATATTATCATCAAGTTAAAAA
1 CAGTGATGCTCCCCGCACACACAACGGAAGATTATTAGGTTACTATATTATCATCAAGTTAAAAA
** * * * * *
6315 GTTGTTATATTTTAAATTGTAATTTTATTACACGGCTCTCGGAAGTGATGCTCCCCGCACACAAC
66 GTTACTATATTTTAAATTATAATTTTATTAAACGGCTCTCGAAAGTGATGCTACCCACACACAAC
** *
6380 GCAGATGCAACTCTCGG
131 GCAGACACAACTCTCAG
*
6397 CAGTGATGCTCCCCGCACACACAACGGAAGATTATTAGGTTACTATA-T-T-ATCAAGTTATAAA
1 CAGTGATGCTCCCCGCACACACAACGGAAGATTATTAGGTTACTATATTATCATCAAGTTAAAAA
*
6459 GTTACTATATTTTAGATTATAATTTTATTAAACGGCTCTC-AACAGTGATGCTACCCACACACAA
66 GTTACTATATTTTAAATTATAATTTTATTAAACGGCTCTCGAA-AGTGATGCTACCCACACACAA
*
6523 CGCAGACACGACTCTCAG
130 CGCAGACACAACTCTCAG
6541 CAGTGATGCTCCC
1 CAGTGATGCTCCC
6554 ACACACATCG
Statistics
Matches: 140, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
143 1 0.01
144 93 0.66
145 1 0.01
146 1 0.01
147 44 0.31
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (147 bp):
CAGTGATGCTCCCCGCACACACAACGGAAGATTATTAGGTTACTATATTATCATCAAGTTAAAAA
GTTACTATATTTTAAATTATAATTTTATTAAACGGCTCTCGAAAGTGATGCTACCCACACACAAC
GCAGACACAACTCTCAG
Found at i:6574 original size:39 final size:40
Alignment explanation
Indices: 6494--6603 Score: 150
Period size: 39 Copynumber: 2.8 Consensus size: 40
6484 TATTAAACGG
* *
6494 CTCTCAACAGTGATGCTACCCACACACAACGCAGACACGA
1 CTCTCAGCAGTGATGCTACCCACACACAACGCAAACACGA
* *
6534 CTCTCAGCAGTGATGCT-CCCACACACATCGCAAACGCGA
1 CTCTCAGCAGTGATGCTACCCACACACAACGCAAACACGA
* * *
6573 CTCTCGGAAGTGATGCTCCCCACACACAACG
1 CTCTCAGCAGTGATGCTACCCACACACAACG
6604 GAAGATTATT
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
39 34 0.55
40 28 0.45
ACGTcount: A:0.30, C:0.38, G:0.17, T:0.15
Consensus pattern (40 bp):
CTCTCAGCAGTGATGCTACCCACACACAACGCAAACACGA
Done.