Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011800.1 Corchorus capsularis cultivar CVL-1 contig11821, 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: 53684
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:287 original size:154 final size:154
Alignment explanation
Indices: 2--431 Score: 653
Period size: 154 Copynumber: 2.8 Consensus size: 154
1 C
* * * * * *
2 AAATGATTATAGTTAGGCCGTAAACAATTAAAAGAAAAGCTTTTTGGTTTGCCCAATTGAAGACG
1 AAATAATTATAGTTAGGTCGTAAACAATTGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGACG
* * *
67 ATTCAAAACAGCACTAATTGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTAAATGAGCTAAAAA
66 ATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGATAAAAA
**
132 CTTCACAATGGACTAATCTCATCA
131 CTTCACAAAAGACTAATCTCATCA
* *
156 AAATAATTATAGTTAGGTCGTAACCAATTGAAAGAAAAGCTTTGTGGTTTGCTAAATCGAAGACG
1 AAATAATTATAGTTAGGTCGTAAACAATTGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGACG
* *
221 ATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAATAAGTGTTCTGAATGAGATAGAAA
66 ATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGATAAAAA
286 CTTCACAAAAGACTAATCTCATCA
131 CTTCACAAAAGACTAATCTCATCA
* * * * *
310 AAATAATTATACTTAGGTCATAAACTATGGAAAGTAAAGCTTTGTGGTTTGCCAAATCGAAGACG
1 AAATAATTATAGTTAGGTCGTAAACAATTGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGACG
* * *
375 ATTCAAAACACCAGTAATGGGCCACGAAAGGCCCGAAATAACAAGTGTTCTGAATGA
66 ATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGA
432 CTTATAATAG
Statistics
Matches: 250, Mismatches: 26, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
154 250 1.00
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (154 bp):
AAATAATTATAGTTAGGTCGTAAACAATTGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGACG
ATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGATAAAAA
CTTCACAAAAGACTAATCTCATCA
Found at i:678 original size:4 final size:4
Alignment explanation
Indices: 669--701 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
659 TCTAAATATT
669 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
702 AACCTGCAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:1860 original size:2 final size:2
Alignment explanation
Indices: 1853--1881 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1843 AAAATTATGG
1853 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1882 CACACACTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2331 original size:2 final size:2
Alignment explanation
Indices: 2320--2349 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2310 ACAGAGGGAG
2320 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2350 GCACATATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2433 original size:19 final size:19
Alignment explanation
Indices: 2409--2448 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
2399 AACCCTAATT
2409 TTCCTCATAAATCGATTTC
1 TTCCTCATAAATCGATTTC
*
2428 TTCCTCATAAATTGATTTC
1 TTCCTCATAAATCGATTTC
2447 TT
1 TT
2449 TCGGCATCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.25, C:0.23, G:0.05, T:0.47
Consensus pattern (19 bp):
TTCCTCATAAATCGATTTC
Found at i:32670 original size:2 final size:2
Alignment explanation
Indices: 32663--32690 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
32653 AAGAAATTAG
32663 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32691 TCAAAAAATG
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):
AT
Found at i:33495 original size:17 final size:18
Alignment explanation
Indices: 33469--33502 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
33459 GTACTAAAAT
33469 GGGTTATATA-ATGTATA
1 GGGTTATATATATGTATA
*
33486 GGGTTGTATATATGTAT
1 GGGTTATATATATGTAT
33503 GTATATGTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.44
Consensus pattern (18 bp):
GGGTTATATATATGTATA
Found at i:51613 original size:33 final size:33
Alignment explanation
Indices: 51576--51793 Score: 364
Period size: 33 Copynumber: 6.5 Consensus size: 33
51566 TTCCCAATTG
51576 ACATTGAACTTGCCTTAATTCTCACATCCAAAA
1 ACATTGAACTTGCCTTAATTCTCACATCCAAAA
51609 ACATTGAACTTGCCTTAATTCTCACATCCAAAA
1 ACATTGAACTTGCCTTAATTCTCACATCCAAAA
*
51642 ACATTGAACTTGCCTTAATTCTCACATCCAACA
1 ACATTGAACTTGCCTTAATTCTCACATCCAAAA
51675 ACATTGAACTTGCCTTAATTCTCACACACATCCAAAA
1 ACATTGAACTTGCCTTAATTCT----CACATCCAAAA
51712 ACATTGAACTTGCCTTAATTCTCACATCCAAAA
1 ACATTGAACTTGCCTTAATTCTCACATCCAAAA
* * *
51745 ACATTGAACTTGCCTTAATACTCATATCCAACA
1 ACATTGAACTTGCCTTAATTCTCACATCCAAAA
51778 ACATTGAACTTGCCTT
1 ACATTGAACTTGCCTT
51794 CACTCACATT
Statistics
Matches: 176, Mismatches: 5, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
33 144 0.82
37 32 0.18
ACGTcount: A:0.35, C:0.28, G:0.06, T:0.30
Consensus pattern (33 bp):
ACATTGAACTTGCCTTAATTCTCACATCCAAAA
Found at i:51751 original size:103 final size:99
Alignment explanation
Indices: 51576--51793 Score: 382
Period size: 103 Copynumber: 2.2 Consensus size: 99
51566 TTCCCAATTG
51576 ACATTGAACTTGCCTTAATTCTCACATCCAAAAACATTGAACTTGCCTTAATTCTCACATCCAAA
1 ACATTGAACTTGCCTTAATTCTCACATCCAAAAACATTGAACTTGCCTTAATTCTCACATCCAAA
*
51641 AACATTGAACTTGCCTTAATTCTCACATCCAACA
66 AACATTGAACTTGCCTTAATACTCACATCCAACA
51675 ACATTGAACTTGCCTTAATTCTCACACACATCCAAAAACATTGAACTTGCCTTAATTCTCACATC
1 ACATTGAACTTGCCTTAATTCT----CACATCCAAAAACATTGAACTTGCCTTAATTCTCACATC
*
51740 CAAAAACATTGAACTTGCCTTAATACTCATATCCAACA
62 CAAAAACATTGAACTTGCCTTAATACTCACATCCAACA
51778 ACATTGAACTTGCCTT
1 ACATTGAACTTGCCTT
51794 CACTCACATT
Statistics
Matches: 113, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
99 22 0.19
103 91 0.81
ACGTcount: A:0.35, C:0.28, G:0.06, T:0.30
Consensus pattern (99 bp):
ACATTGAACTTGCCTTAATTCTCACATCCAAAAACATTGAACTTGCCTTAATTCTCACATCCAAA
AACATTGAACTTGCCTTAATACTCACATCCAACA
Found at i:52353 original size:45 final size:45
Alignment explanation
Indices: 52302--52387 Score: 118
Period size: 45 Copynumber: 1.9 Consensus size: 45
52292 AAAACGTGAG
** *
52302 GGAGATCACGGAAAGCTTAGGCTCCATGATTGCCAAATGCTTGAA
1 GGAGATCAAAGAAAGCTTAGGCTCCATGATTACCAAATGCTTGAA
* * *
52347 GGAGATCAAAGAGAGCTTTGGCTCCATGATTACCAAGTGCT
1 GGAGATCAAAGAAAGCTTAGGCTCCATGATTACCAAATGCT
52388 CCAAGTTTCG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 35 1.00
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (45 bp):
GGAGATCAAAGAAAGCTTAGGCTCCATGATTACCAAATGCTTGAA
Done.