Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013035.1 Corchorus capsularis cultivar CVL-1 contig13056, 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: 30638
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:5311 original size:29 final size:29
Alignment explanation
Indices: 5279--5336 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
5269 ATTGATAAAC
5279 TTTTTTTTAGT-AAAATTCAATAAATTCT
1 TTTTTTTTAGTGAAAATTCAATAAATTCT
*
5307 TTTTTTTTGGTGAAAATTCAATAAATTCT
1 TTTTTTTTAGTGAAAATTCAATAAATTCT
5336 T
1 T
5337 AGCATCTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 10 0.36
29 18 0.64
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (29 bp):
TTTTTTTTAGTGAAAATTCAATAAATTCT
Found at i:9388 original size:2 final size:2
Alignment explanation
Indices: 9381--9410 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
9371 AGTCATGGAA
9381 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
9411 TAAGAGGGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:14466 original size:32 final size:32
Alignment explanation
Indices: 14416--14650 Score: 287
Period size: 32 Copynumber: 7.4 Consensus size: 32
14406 ATCACATTAA
* *
14416 TGGCATTTTCTTCAATATATGCCCCAATTTAG
1 TGGCGTTTTCTTCAATATATGCCACAATTTAG
* *
14448 TGGCGTTTGCTTCAATATATGCCACAAATTAG
1 TGGCGTTTTCTTCAATATATGCCACAATTTAG
* * *
14480 TGGCGTTTT-TTCAATTTTTGCCACAATTCAG
1 TGGCGTTTTCTTCAATATATGCCACAATTTAG
* *
14511 TGGCGTTTTTTTCAATATATGCCACAATTTTG
1 TGGCGTTTTCTTCAATATATGCCACAATTTAG
* ** * *
14543 TGGCCTTTT-TTCAATACGTGCCACATTTTAA
1 TGGCGTTTTCTTCAATATATGCCACAATTTAG
*
14574 TGGCGTTTTCTTCAATATGTGCCACAATTTAG
1 TGGCGTTTTCTTCAATATATGCCACAATTTAG
* * *
14606 TGGCCTTTTCTTCAATATGTGCCACAATTTAA
1 TGGCGTTTTCTTCAATATATGCCACAATTTAG
14638 TGGCGTTTT-TTCA
1 TGGCGTTTTCTTCA
14651 GAGTTTGCCA
Statistics
Matches: 175, Mismatches: 26, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
31 56 0.32
32 119 0.68
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.42
Consensus pattern (32 bp):
TGGCGTTTTCTTCAATATATGCCACAATTTAG
Found at i:14525 original size:63 final size:64
Alignment explanation
Indices: 14411--14650 Score: 297
Period size: 63 Copynumber: 3.8 Consensus size: 64
14401 GAAAGATCAC
* * * * * *
14411 ATTAATGGCATTTTCTTCAATATATGCCCCAATTTAGTGGCGTTTGCTTCAATATATGCCACAA
1 ATTAGTGGCCTTTTCTTCAATATGTGCCACAATTTAATGGCGTTTTCTTCAATATATGCCACAA
* * * * * *
14475 ATTAGTGGCGTTTT-TTCAATTTTTGCCACAATTCAGTGGCGTTTTTTTCAATATATGCCACAA
1 ATTAGTGGCCTTTTCTTCAATATGTGCCACAATTTAATGGCGTTTTCTTCAATATATGCCACAA
* * * * *
14538 TTTTGTGGCCTTTT-TTCAATACGTGCCACATTTTAATGGCGTTTTCTTCAATATGTGCCACAA
1 ATTAGTGGCCTTTTCTTCAATATGTGCCACAATTTAATGGCGTTTTCTTCAATATATGCCACAA
*
14601 TTTAGTGGCCTTTTCTTCAATATGTGCCACAATTTAATGGCGTTTT-TTCA
1 ATTAGTGGCCTTTTCTTCAATATGTGCCACAATTTAATGGCGTTTTCTTCA
14651 GAGTTTGCCA
Statistics
Matches: 153, Mismatches: 22, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
63 112 0.73
64 41 0.27
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.42
Consensus pattern (64 bp):
ATTAGTGGCCTTTTCTTCAATATGTGCCACAATTTAATGGCGTTTTCTTCAATATATGCCACAA
Found at i:14673 original size:95 final size:93
Alignment explanation
Indices: 14416--14677 Score: 301
Period size: 95 Copynumber: 2.8 Consensus size: 93
14406 ATCACATTAA
* *
14416 TGGCATTTTCTTCAATATATGCCCCAATTTAGTGGCGTTTGCTTCAATATATGCCACAAATTAGT
1 TGGCATTTTCTTCAATATATGCCACAATTTAGTGGCGTTT-TTTCAATAT-TGCCACAAATTAGT
* *
14481 GGCGTTTTTTCAATTTTTGCCACAATTCAG
64 GGCGTTTTTTCAATATGTGCCACAATTCAG
* * * * * ** *
14511 TGGCGTTTTTTTCAATATATGCCACAATTTTGTGGCCTTTTTTCAATACGTGCCACATTTTAATG
1 TGGCATTTTCTTCAATATATGCCACAATTTAGTGGCGTTTTTTCAATA-TTGCCACAAATTAGTG
*
14576 GCGTTTTCTTCAATATGTGCCACAATTTAG
65 GCGTTTT-TTCAATATGTGCCACAATTCAG
* * * **
14606 TGGCCTTTTCTTCAATATGTGCCACAATTTAATGGCGTTTTTTCAGAGT-TTGCCACAAAGCAGT
1 TGGCATTTTCTTCAATATATGCCACAATTTAGTGGCGTTTTTTCA-A-TATTGCCACAAATTAGT
14670 GGCGTTTT
64 GGCGTTTT
14678 GTTCTATAAC
Statistics
Matches: 138, Mismatches: 25, Indels: 8
0.81 0.15 0.05
Matches are distributed among these distances:
94 26 0.19
95 110 0.80
96 1 0.01
97 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.41
Consensus pattern (93 bp):
TGGCATTTTCTTCAATATATGCCACAATTTAGTGGCGTTTTTTCAATATTGCCACAAATTAGTGG
CGTTTTTTCAATATGTGCCACAATTCAG
Found at i:16068 original size:69 final size:69
Alignment explanation
Indices: 15957--16095 Score: 224
Period size: 69 Copynumber: 2.0 Consensus size: 69
15947 TACCAGCTGA
* * * *
15957 GAAATTGAATGTCAACAGAGCAGGAAAGTAGCATGAACTGAATTCTGATAAAGTAATGCTAGCAC
1 GAAATTGAATGTAAACAGAGCAGGAAAGTAGAATGAACTGAATTCTGATAAAGTAATGCCACCAC
16022 ACAT
66 ACAT
* *
16026 GAAATTGAATGTAAACAGAGCAGGAAAGTATAATGAACTGAATTCTGATAAATTAATGCCACCAC
1 GAAATTGAATGTAAACAGAGCAGGAAAGTAGAATGAACTGAATTCTGATAAAGTAATGCCACCAC
16091 ACAT
66 ACAT
16095 G
1 G
16096 TTTGGGATCA
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.22
Consensus pattern (69 bp):
GAAATTGAATGTAAACAGAGCAGGAAAGTAGAATGAACTGAATTCTGATAAAGTAATGCCACCAC
ACAT
Found at i:17212 original size:40 final size:40
Alignment explanation
Indices: 17153--17243 Score: 128
Period size: 40 Copynumber: 2.3 Consensus size: 40
17143 AGAAGAATAG
* *
17153 TCATGATTTCAGGACTTGATAATTTCAGAACTTAATAACT
1 TCATAATTTCAGGACTTGATAATTTCAAAACTTAATAACT
* * *
17193 TCATAATTTCAGGAGTTGATAATTTCAAAACTTCATAATT
1 TCATAATTTCAGGACTTGATAATTTCAAAACTTAATAACT
*
17233 TCAGAATTTCA
1 TCATAATTTCA
17244 ACTATAGGTT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.38
Consensus pattern (40 bp):
TCATAATTTCAGGACTTGATAATTTCAAAACTTAATAACT
Found at i:17243 original size:16 final size:16
Alignment explanation
Indices: 17189--17243 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
17179 AGAACTTAAT
17189 AACTTCATAATTTCAG
1 AACTTCATAATTTCAG
* * * *
17205 GAGTTGATAATTTCAA
1 AACTTCATAATTTCAG
17221 AACTTCATAATTTCAG
1 AACTTCATAATTTCAG
*
17237 AATTTCA
1 AACTTCA
17244 ACTATAGGTT
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (16 bp):
AACTTCATAATTTCAG
Found at i:22598 original size:24 final size:25
Alignment explanation
Indices: 22557--22618 Score: 99
Period size: 24 Copynumber: 2.5 Consensus size: 25
22547 CAGAAGGCGT
22557 TAGGGATTGGGAAAGAAAAAGAAGC
1 TAGGGATTGGGAAAGAAAAAGAAGC
22582 TAGGGATT-GGAAAGAAAAAGAAGC
1 TAGGGATTGGGAAAGAAAAAGAAGC
*
22606 TAGGCATTAGGGA
1 TAGGGATT-GGGA
22619 TTTCAATGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
24 23 0.68
25 8 0.24
26 3 0.09
ACGTcount: A:0.45, C:0.05, G:0.35, T:0.15
Consensus pattern (25 bp):
TAGGGATTGGGAAAGAAAAAGAAGC
Found at i:25929 original size:29 final size:31
Alignment explanation
Indices: 25897--25962 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
25887 AATTTGGTCC
25897 CTCTACCTAATAA-A-TTGTCAATTGAGTCA
1 CTCTACCTAATAACACTTGTCAATTGAGTCA
** * *
25926 CTCTAATTGATAACACTTGTCAATTGAGTCC
1 CTCTACCTAATAACACTTGTCAATTGAGTCA
25957 CTCTAC
1 CTCTAC
25963 TTGTAGGATT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 10 0.33
30 1 0.03
31 19 0.63
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (31 bp):
CTCTACCTAATAACACTTGTCAATTGAGTCA
Found at i:25949 original size:31 final size:30
Alignment explanation
Indices: 25911--25987 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 30
25901 ACCTAATAAA
25911 TTGTCAATTGAGTCACTCTAATTGATAACAC
1 TTGTCAATTGAGTCACTCTAATTG-TAACAC
* * ** *
25942 TTGTCAATTGAGTCCCTCTACTTGTAGGAT
1 TTGTCAATTGAGTCACTCTAATTGTAACAC
25972 TATGTCAATTGAGTCA
1 T-TGTCAATTGAGTCA
25988 ACCACTAACA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 4 0.10
31 35 0.90
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (30 bp):
TTGTCAATTGAGTCACTCTAATTGTAACAC
Found at i:27007 original size:31 final size:30
Alignment explanation
Indices: 26972--27055 Score: 78
Period size: 31 Copynumber: 2.7 Consensus size: 30
26962 ACAATCCTGC
*
26972 AAGTAGAGCGACTCAATTGACAGGTGTTAGT
1 AAGTAGAG-GACTCAATTGACAGGTGCTAGT
* * ** *
27003 AAGTAAAGGGAGTCAATTGTTAGGTGCTATT
1 AAGTAGA-GGACTCAATTGACAGGTGCTAGT
*
27034 AAGTAGATGGACTAAATTGACA
1 AAGTAGA-GGACTCAATTGACA
27056 ATTTTTTTAG
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
31 39 0.98
32 1 0.03
ACGTcount: A:0.36, C:0.10, G:0.27, T:0.27
Consensus pattern (30 bp):
AAGTAGAGGACTCAATTGACAGGTGCTAGT
Found at i:29318 original size:18 final size:18
Alignment explanation
Indices: 29295--29353 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
29285 TTTTATAATA
29295 TATATATATATATTTATT
1 TATATATATATATTTATT
* *
29313 TATATATAAATAATTATT
1 TATATATATATATTTATT
* *
29331 GAT-TAATATATAATTTAAT
1 TATAT-ATATAT-ATTTATT
29350 TATA
1 TATA
29354 AAAATTATTT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
17 1 0.03
18 23 0.74
19 7 0.23
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
TATATATATATATTTATT
Found at i:29320 original size:22 final size:22
Alignment explanation
Indices: 29290--29352 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
29280 TAGGGTTTTA
* *
29290 TAATATATATAT-ATATATTTAT
1 TAATATATAAATAAT-TATTGAT
*
29312 TTATATATAAATAATTATTGAT
1 TAATATATAAATAATTATTGAT
*
29334 TAATATATAATTTAATTAT
1 TAATATATAA-ATAATTAT
29353 AAAAATTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
22 25 0.74
23 9 0.26
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
TAATATATAAATAATTATTGAT
Done.