Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007055.1 Corchorus capsularis cultivar CVL-1 contig07076, 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: 20726
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2445 original size:14 final size:14
Alignment explanation
Indices: 2422--2455 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
2412 TAACTATGAT
*
2422 ACTAATCTAAATGG
1 ACTAAACTAAATGG
2436 ACTAAACTAAATGG
1 ACTAAACTAAATGG
2450 ACTAAA
1 ACTAAA
2456 GTTAATATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.50, C:0.15, G:0.12, T:0.24
Consensus pattern (14 bp):
ACTAAACTAAATGG
Found at i:2810 original size:27 final size:27
Alignment explanation
Indices: 2780--2854 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 27
2770 GAGTTAACTT
*
2780 AAAATGACCAAAATACCCCTAAATGCA
1 AAAATGACCAAAATACCCCTAAACGCA
* * * * **
2807 AAAAAGACTAAAATGCCCCTGAACGTG
1 AAAATGACCAAAATACCCCTAAACGCA
2834 AAAATGACCAAAATACCCCTA
1 AAAATGACCAAAATACCCCTA
2855 TGTGACCCTA
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.49, C:0.25, G:0.11, T:0.15
Consensus pattern (27 bp):
AAAATGACCAAAATACCCCTAAACGCA
Found at i:6001 original size:90 final size:88
Alignment explanation
Indices: 5848--6123 Score: 354
Period size: 90 Copynumber: 3.1 Consensus size: 88
5838 AGGTGATTTT
* * * * * *
5848 CTTAAACAAGAAATTGAGCTTGGAAAGGTAGAGGATGATAAAACAGAACAAACTGCATCTGAAGA
1 CTTAAACAAGAAACTGAGGTTGGAAACGCAGAGG-TGATAAAA-GGAACAAACTGCGTCTGAAGA
*
5913 GTTATTAGATTCTGGCAGTCCAGAG
64 GTTACTAGATTCTGGCAGTCCAGAG
* *
5938 CTTAAACAAGAAAGTGAGGTTGGAAACACAGAGAGTGATACAAAGGAACAAACTGCGTCTGAAGA
1 CTTAAACAAGAAACTGAGGTTGGAAACGCAGAG-GTGATA-AAAGGAACAAACTGCGTCTGAAGA
* *
6003 GTTACTAGATTCTGACATTCCAGAG
64 GTTACTAGATTCTGGCAGTCCAGAG
* * *
6028 CTTAAACAAGAAACCGAGGTTGGAAATGCAGAGGGTGATAAAAAGGAACAAACTGTGTCTGAAGA
1 CTTAAACAAGAAACTGAGGTTGGAAACGCAGA-GGTGAT-AAAAGGAACAAACTGCGTCTGAAGA
* *
6093 GTTACTAGATTCTGGAAGGCCAGAG
64 GTTACTAGATTCTGGCAGTCCAGAG
6118 CTTAAA
1 CTTAAA
6124 GCTGAGCTCT
Statistics
Matches: 163, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
90 157 0.96
91 6 0.04
ACGTcount: A:0.40, C:0.14, G:0.25, T:0.21
Consensus pattern (88 bp):
CTTAAACAAGAAACTGAGGTTGGAAACGCAGAGGTGATAAAAGGAACAAACTGCGTCTGAAGAGT
TACTAGATTCTGGCAGTCCAGAG
Found at i:13750 original size:8 final size:8
Alignment explanation
Indices: 13737--13762 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
13727 GAGTCTAAAG
13737 TTAACCAT
1 TTAACCAT
13745 TTAACCAT
1 TTAACCAT
13753 TTAACCAT
1 TTAACCAT
13761 TT
1 TT
13763 TTGTCATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (8 bp):
TTAACCAT
Found at i:14311 original size:109 final size:109
Alignment explanation
Indices: 14175--14386 Score: 327
Period size: 109 Copynumber: 1.9 Consensus size: 109
14165 GCAAAATACA
*
14175 TAGTGGGGATGTGGCAAGAAATACAAGTAAATGAGAATTAATTCTAAAAGTACAATTGTTTGGCA
1 TAGTGGGGATGTGGCAAGAAATACAAGTAAATGAGAATTAATTCTAAAAGTACAA-TGGTTGGCA
*
14240 ATT-TTTTTTTAAAATCACAATAGTTTGGTCAAAAACTCAAGATG
65 ATTATTTTTTTAAAAACACAATAGTTTGGTCAAAAACTCAAGATG
* * * * *
14284 TAGTGGGGATGTGGCAAGAAATTCAAGTAAATGGGAATTAATTTTAAAATTACAATGGTTGGGAA
1 TAGTGGGGATGTGGCAAGAAATACAAGTAAATGAGAATTAATTCTAAAAGTACAATGGTTGGCAA
* *
14349 TTATTTTTTTAAAAACACAATGGTTTGGTTAAAAACTC
66 TTATTTTTTTAAAAACACAATAGTTTGGTCAAAAACTC
14387 GATAAAAAAC
Statistics
Matches: 93, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
108 10 0.11
109 83 0.89
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.33
Consensus pattern (109 bp):
TAGTGGGGATGTGGCAAGAAATACAAGTAAATGAGAATTAATTCTAAAAGTACAATGGTTGGCAA
TTATTTTTTTAAAAACACAATAGTTTGGTCAAAAACTCAAGATG
Found at i:15089 original size:133 final size:132
Alignment explanation
Indices: 14846--15236 Score: 500
Period size: 133 Copynumber: 3.0 Consensus size: 132
14836 GTAACTAAAA
* *** *
14846 TAAGATTTCGCAGTGACTTAATTTGTCGTTTCAAAAGTAATGT-TGTTTTTTGTAAAAACTTTAA
1 TAAGATTTCGCAGCGACTTAATTTGTCGTTTCAAAAGTAAT-TATGTTTTTTGTAGCGACTTTCA
** * * *
14910 ATATCGTTGCAAAAATCAATTTGGAAAATATATTAAGCAACGACTAATAGAAGGTCGTTGCGAAA
65 AGGTCGTTGCGAAAATCAATTTGTAAAATATATTAAGCAACGACTAACAGAA-GTCGTTGCGAAA
14975 AGAG
129 AGAG
* * * *
14979 TAAGATTTCGCGGCGACTTAATTTGTCGCTTCAAAGGTAATTATATTTTTTGTAGCGACTTTCAA
1 TAAGATTTCGCAGCGACTTAATTTGTCGTTTCAAAAGTAATTATGTTTTTTGTAGCGACTTTCAA
* * *
15044 GGTCGCTGCGAAAATCAATTTGTAAAATATATTAAGCAACAACTAACAAAAGTCGTTGCGAAAAG
66 GGTCGTTGCGAAAATCAATTTGTAAAATATATTAAGCAACGACTAACAGAAGTCGTTGCGAAAAG
**
15109 TT
131 AG
* * * * *
15111 TAAGATTTCGCAACGACTTAATCTAT--TTTCAAAAGTAATCATGTTTTTTGTAGCGACTCTCAA
1 TAAGATTTCGCAGCGACTTAATTTGTCGTTTCAAAAGTAATTATGTTTTTTGTAGCGACTTTCAA
* * *
15174 GGTCGTTTCGAAAATCAATTTGTAAAATATATTAAACAATGACTAACAGAAGTCGTTGCGAAA
66 GGTCGTTGCGAAAATCAATTTGTAAAATATATTAAGCAACGACTAACAGAAGTCGTTGCGAAA
15237 GACTATGAAT
Statistics
Matches: 223, Mismatches: 34, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
130 89 0.40
132 37 0.17
133 97 0.43
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (132 bp):
TAAGATTTCGCAGCGACTTAATTTGTCGTTTCAAAAGTAATTATGTTTTTTGTAGCGACTTTCAA
GGTCGTTGCGAAAATCAATTTGTAAAATATATTAAGCAACGACTAACAGAAGTCGTTGCGAAAAG
AG
Found at i:15177 original size:130 final size:131
Alignment explanation
Indices: 14921--15257 Score: 435
Period size: 130 Copynumber: 2.6 Consensus size: 131
14911 TATCGTTGCA
* * *
14921 AAAATCAATTTGGAAAATATATTAAGCAACGACTAATAGAAGGTCGTTGCGAAAAGAGTAAGATT
1 AAAATCAATTTGTAAAATATATTAAGCAACGACTAACA-AAAGTCGTTGCGAAAAGAGTAAGATT
** * * * * *
14986 TCGCGGCGACTTAATTTGTCGCTTCAAAGGTAATTATATTTTTTGTAGCGACTTTCAAGGTCGCT
65 TCGCAACGACTTAATCTATC-CTTCAAAAGTAATCATATTTTTTGTAGCGACTCTCAAGGTCGCT
15051 GCG
129 GCG
* **
15054 AAAATCAATTTGTAAAATATATTAAGCAACAACTAACAAAAGTCGTTGCGAAAAGTTTAAGATTT
1 AAAATCAATTTGTAAAATATATTAAGCAACGACTAACAAAAGTCGTTGCGAAAAGAGTAAGATTT
* * * *
15119 CGCAACGACTTAATCTAT-TTTCAAAAGTAATCATGTTTTTTGTAGCGACTCTCAAGGTCGTTTC
66 CGCAACGACTTAATCTATCCTTCAAAAGTAATCATATTTTTTGTAGCGACTCTCAAGGTCGCTGC
15183 G
131 G
* * * * * *
15184 AAAATCAATTTGTAAAATATATTAAACAATGACTAACAGAAGTCGTTGCG-AAAGACTATGAATT
1 AAAATCAATTTGTAAAATATATTAAGCAACGACTAACAAAAGTCGTTGCGAAAAGAGTAAGATTT
15248 CGCAACGACT
66 CGCAACGACT
15258 AATAGAAGTC
Statistics
Matches: 179, Mismatches: 25, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
129 20 0.11
130 86 0.48
132 38 0.21
133 35 0.20
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.31
Consensus pattern (131 bp):
AAAATCAATTTGTAAAATATATTAAGCAACGACTAACAAAAGTCGTTGCGAAAAGAGTAAGATTT
CGCAACGACTTAATCTATCCTTCAAAAGTAATCATATTTTTTGTAGCGACTCTCAAGGTCGCTGC
G
Found at i:16677 original size:23 final size:22
Alignment explanation
Indices: 16651--16700 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
16641 AATGTTGTGA
*
16651 TAAAACCTTTCTATTTTTGTTTT
1 TAAAACCTTT-TATTTTTGCTTT
**
16674 TAAAGTCTTTTATTTTTGCTTT
1 TAAAACCTTTTATTTTTGCTTT
*
16696 GAAAA
1 TAAAA
16701 ATTCCATTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.26, C:0.10, G:0.08, T:0.56
Consensus pattern (22 bp):
TAAAACCTTTTATTTTTGCTTT
Found at i:16817 original size:21 final size:21
Alignment explanation
Indices: 16791--16839 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
16781 TCTCACTAAA
*
16791 TCTGATTTGAAT-TTGAAAATC
1 TCTGATTTAAATCTTGAAAA-C
16812 TCTGA-TTAAATCTTGAAAAC
1 TCTGATTTAAATCTTGAAAAC
16832 TCTTGATT
1 TC-TGATT
16840 ACCCATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 8 0.33
21 15 0.62
22 1 0.04
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (21 bp):
TCTGATTTAAATCTTGAAAAC
Found at i:18274 original size:31 final size:31
Alignment explanation
Indices: 18236--18299 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
18226 ATATATATAT
18236 ATATTAATCATTAAAACCATAAATACTTTAG
1 ATATTAATCATTAAAACCATAAATACTTTAG
18267 ATATTAATCATTAAAACCATAAATACTTTAG
1 ATATTAATCATTAAAACCATAAATACTTTAG
18298 AT
1 AT
18300 CTAGCCATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.48, C:0.12, G:0.03, T:0.36
Consensus pattern (31 bp):
ATATTAATCATTAAAACCATAAATACTTTAG
Found at i:18310 original size:39 final size:39
Alignment explanation
Indices: 18267--18344 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
18257 AATACTTTAG
*
18267 ATATTAATCATTAAAACCATAAATACTTTAGATCTAGCC
1 ATATTAATCATTAAAACCATAAATAATTTAGATCTAGCC
18306 ATATTAATCATTAAAACCATAAATAATTTAGATCTAGCC
1 ATATTAATCATTAAAACCATAAATAATTTAGATCTAGCC
18345 CAATTATTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (39 bp):
ATATTAATCATTAAAACCATAAATAATTTAGATCTAGCC
Done.