Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008429.1 Corchorus capsularis cultivar CVL-1 contig08450, 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: 29571
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:3867 original size:2 final size:2
Alignment explanation
Indices: 3860--3888 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3850 AATCGGTATC
3860 TA TA 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 T
3889 TTTATTTCAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4722 original size:11 final size:11
Alignment explanation
Indices: 4708--4745 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
4698 ATTCATAACA
4708 AATTTATAATT
1 AATTTATAATT
4719 AATTTATAATT
1 AATTTATAATT
4730 -ATTTGATAATT
1 AATTT-ATAATT
*
4741 TATTT
1 AATTT
4746 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:4921 original size:66 final size:66
Alignment explanation
Indices: 4847--4980 Score: 268
Period size: 66 Copynumber: 2.0 Consensus size: 66
4837 ACTTATCAAA
4847 GAAACCAAATGCGAAGTGGCGCTCAATGAGGGCATTGTACATAAAATTAATAGTAGGTTAAATAA
1 GAAACCAAATGCGAAGTGGCGCTCAATGAGGGCATTGTACATAAAATTAATAGTAGGTTAAATAA
4912 T
66 T
4913 GAAACCAAATGCGAAGTGGCGCTCAATGAGGGCATTGTACATAAAATTAATAGTAGGTTAAATAA
1 GAAACCAAATGCGAAGTGGCGCTCAATGAGGGCATTGTACATAAAATTAATAGTAGGTTAAATAA
4978 T
66 T
4979 GA
1 GA
4981 GTAATAATAC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 68 1.00
ACGTcount: A:0.41, C:0.12, G:0.23, T:0.24
Consensus pattern (66 bp):
GAAACCAAATGCGAAGTGGCGCTCAATGAGGGCATTGTACATAAAATTAATAGTAGGTTAAATAA
T
Found at i:6636 original size:23 final size:23
Alignment explanation
Indices: 6592--6640 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
6582 ATTATTAATT
*
6592 AAACGTTGATTATCTTTCAAAAA
1 AAACGTTGATTAACTTTCAAAAA
*
6615 AAACGTTGATTAAGTTGT-AAAAA
1 AAACGTTGATTAACTT-TCAAAAA
6638 AAA
1 AAA
6641 TTAATCGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 22 0.96
24 1 0.04
ACGTcount: A:0.49, C:0.08, G:0.12, T:0.31
Consensus pattern (23 bp):
AAACGTTGATTAACTTTCAAAAA
Found at i:7662 original size:166 final size:165
Alignment explanation
Indices: 7220--7704 Score: 594
Period size: 166 Copynumber: 2.9 Consensus size: 165
7210 GAATAAACAT
* * * * **
7220 GTGGAATTACTAAAAGATCTCCACCACGGATTAATGAGGAGCGAGAGAACTAATTTTTTTCGTCT
1 GTGGAATTACTAAAAGATCCCCACCAAGGATTGATGATGAGTTAGAGAACTAATTTTTTTCGTCT
* *
7285 TTTCCCACTTGGCAGATTACTTAAATGTCTTAACTTTTAATTCTTGA-GGGATTAAATAACTAGA
66 TTTCCCACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTA-A
* * *
7349 CCTTTTGGTCATTTCTCAATTGACTTTAATAGAGTA
130 ACTTTTGGTCATTTCTCAATGGACTTGAATAGAGTA
* ** * * ** * **
7385 GTGGAATTACTAAAAGGTCCATACCAAGGGTTGCTTTTGGAGTTAGTGAACTTTTTTTTTTTTTC
1 GTGGAATTACTAAAAGATCCCCACCAAGGATTGATGAT-GAGTTAGAGAAC---TAATTTTTTTC
* * *
7450 GTATTTTCCCACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTAAGGGGATTAAATAAG
62 GTCTTTTCCCACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAAC
* *
7515 TCATCTTTATGGTCATTTCTCAATGGACTTGAATAGAGTA
127 TAAACTTT-TGGTCATTTCTCAATGGACTTGAATAGAGTA
* * * *
7555 GTGGAATTAATAAAAGATCCCCATCAAGGATTGATGATGAGTTAAAGAACTAATCTTTTTCGTCT
1 GTGGAATTACTAAAAGATCCCCACCAAGGATTGATGATGAGTTAGAGAACTAATTTTTTTCGTCT
* ** *
7620 TTACTTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGTGGATTAAATAACTAAA
66 TTTCCCACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAAA
7685 CTTTTTGGTCATTTCTCAAT
131 C-TTTTGGTCATTTCTCAAT
7705 TGACAAATGA
Statistics
Matches: 265, Mismatches: 48, Indels: 13
0.81 0.15 0.04
Matches are distributed among these distances:
165 27 0.10
166 93 0.35
167 3 0.01
169 71 0.27
170 71 0.27
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (165 bp):
GTGGAATTACTAAAAGATCCCCACCAAGGATTGATGATGAGTTAGAGAACTAATTTTTTTCGTCT
TTTCCCACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAAA
CTTTTGGTCATTTCTCAATGGACTTGAATAGAGTA
Found at i:9792 original size:19 final size:19
Alignment explanation
Indices: 9764--9805 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
9754 TCGGGTTTAG
9764 TCAG-TTTTTTGAGTCAGT
1 TCAGTTTTTTTGAGTCAGT
9782 TCAGTTTTTTTGAGTCAGT
1 TCAGTTTTTTTGAGTCAGT
9801 T-AGTT
1 TCAGTT
9806 CGAGTCTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.17, C:0.10, G:0.21, T:0.52
Consensus pattern (19 bp):
TCAGTTTTTTTGAGTCAGT
Found at i:23380 original size:30 final size:28
Alignment explanation
Indices: 23312--23393 Score: 103
Period size: 27 Copynumber: 2.9 Consensus size: 28
23302 ATTAGAGTCG
*
23312 CCCAGGGGCATTTTGGTCA-TTTTCGCA
1 CCCAGGGGCATTTTGGTCATTTTTTGCA
*
23339 CCCAGGGGCATTTCGGTCATTTTTTGCA
1 CCCAGGGGCATTTTGGTCATTTTTTGCA
* *
23367 CTCAGGAGGGCATTTTAGTCATTTTTT
1 CCCA-G-GGGCATTTTGGTCATTTTTT
23394 TAAGATCACC
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
27 18 0.38
28 10 0.21
29 1 0.02
30 18 0.38
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (28 bp):
CCCAGGGGCATTTTGGTCATTTTTTGCA
Found at i:26212 original size:51 final size:52
Alignment explanation
Indices: 26101--26446 Score: 280
Period size: 51 Copynumber: 6.8 Consensus size: 52
26091 AGGTTTATCA
* * *
26101 TTTGAATAAAAGATTGAATTTTT-ATGTAATTGGTAAAT-AAAAATGTCATC
1 TTTGAATAAAAGATTGAATTTTTAAAGTAATTAGTAAATAAAAAATGTAATC
* * * * * * * *
26151 TTTGAGTAAAACATTGAATTTTTAAAATGATTAGCAAAT-AAAATTTTAAGC
1 TTTGAATAAAAGATTGAATTTTTAAAGTAATTAGTAAATAAAAAATGTAATC
* * *
26202 TTTGAATAAAAGATTGAATTTTT-ATGTAATTGGTAAATAAAAAATGTCATC
1 TTTGAATAAAAGATTGAATTTTTAAAGTAATTAGTAAATAAAAAATGTAATC
* * * * * * *
26253 TTTGAGTAAAAGATTGAATCTTTAGAGTAATTAGTAAAT-GAAGATTTAACC
1 TTTGAATAAAAGATTGAATTTTTAAAGTAATTAGTAAATAAAAAATGTAATC
* * * * *
26304 TTTGAATAAAAGATTGAATTTTT-ATGTAATTGGTAAGT-AAAAATGTCATG
1 TTTGAATAAAAGATTGAATTTTTAAAGTAATTAGTAAATAAAAAATGTAATC
** * * * * ** *
26354 TTTGGGTAAAAGATTGAATCTTTAGAGTGATTATTAAAT-AAAGTTTTAA-C
1 TTTGAATAAAAGATTGAATTTTTAAAGTAATTAGTAAATAAAAAATGTAATC
* *
26404 ATTTGAATGAAAGATTGAACTTTT-AAGTAATTAGTAAATAAAA
1 -TTTGAATAAAAGATTGAATTTTTAAAGTAATTAGTAAATAAAA
26447 TGTTACTTTT
Statistics
Matches: 224, Mismatches: 66, Indels: 11
0.74 0.22 0.04
Matches are distributed among these distances:
50 80 0.36
51 132 0.59
52 12 0.05
ACGTcount: A:0.42, C:0.04, G:0.15, T:0.38
Consensus pattern (52 bp):
TTTGAATAAAAGATTGAATTTTTAAAGTAATTAGTAAATAAAAAATGTAATC
Found at i:26403 original size:101 final size:101
Alignment explanation
Indices: 26101--26446 Score: 512
Period size: 101 Copynumber: 3.4 Consensus size: 101
26091 AGGTTTATCA
*
26101 TTTGAATAAAAGATTGAATTTTTATGTAATTGGTAAATAAAAATGTCATCTTTGAGTAAAACATT
1 TTTGAATAAAAGATTGAATTTTTATGTAATTGGTAAATAAAAATGTCATCTTTGAGTAAAAGATT
* * * * * *
26166 GAATTTTTAAAATGATTAGCAAATAAAATTTTAAGC
66 GAATCTTTAGAGTGATTAGTAAATAAAGTTTTAACC
26202 TTTGAATAAAAGATTGAATTTTTATGTAATTGGTAAATAAAAAATGTCATCTTTGAGTAAAAGAT
1 TTTGAATAAAAGATTGAATTTTTATGTAATTGGTAAAT-AAAAATGTCATCTTTGAGTAAAAGAT
* * *
26267 TGAATCTTTAGAGTAATTAGTAAATGAAGATTTAACC
65 TGAATCTTTAGAGTGATTAGTAAATAAAGTTTTAACC
* * *
26304 TTTGAATAAAAGATTGAATTTTTATGTAATTGGTAAGTAAAAATGTCATGTTTGGGTAAAAGATT
1 TTTGAATAAAAGATTGAATTTTTATGTAATTGGTAAATAAAAATGTCATCTTTGAGTAAAAGATT
* *
26369 GAATCTTTAGAGTGATTATTAAATAAAGTTTTAACA
66 GAATCTTTAGAGTGATTAGTAAATAAAGTTTTAACC
* * * *
26405 TTTGAATGAAAGATTGAACTTTTAAGTAATTAGTAAATAAAA
1 TTTGAATAAAAGATTGAATTTTTATGTAATTGGTAAATAAAA
26447 TGTTACTTTT
Statistics
Matches: 221, Mismatches: 23, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
101 131 0.59
102 90 0.41
ACGTcount: A:0.42, C:0.04, G:0.15, T:0.38
Consensus pattern (101 bp):
TTTGAATAAAAGATTGAATTTTTATGTAATTGGTAAATAAAAATGTCATCTTTGAGTAAAAGATT
GAATCTTTAGAGTGATTAGTAAATAAAGTTTTAACC
Found at i:27249 original size:55 final size:56
Alignment explanation
Indices: 27096--27336 Score: 317
Period size: 56 Copynumber: 4.2 Consensus size: 56
27086 GAAAGGGGGC
27096 AATCAGTAAATTAAGTAAAAAAGAAATTAATCATGAGTCAAAGTAGCAGTAATACAGTA
1 AATCAGT-AATTAAGTAAAAAAGAAATTAATCA-GAGTCAAAGTAGCAGTAAT-CAGTA
* *
27155 AATACAGTAATTAAGTAAAAAAGAGATTAATCAGGGTCAAAGTAGCAGTAATCAGTA
1 AAT-CAGTAATTAAGTAAAAAAGAAATTAATCAGAGTCAAAGTAGCAGTAATCAGTA
* * ** *
27212 AATCAGTAATTAAGT-AAAAAGAAATTAATTAGAGTCAAGGTATTAGAAATCAGTA
1 AATCAGTAATTAAGTAAAAAAGAAATTAATCAGAGTCAAAGTAGCAGTAATCAGTA
* **
27267 AATACAGTAATTAAGT-AAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
1 AAT-CAGTAATTAAGTAAAAAAGAAATTAATCAGAGTCAAAGTAGCAGTAATCAGTA
27323 AATC-GATAATTAAG
1 AATCAG-TAATTAAG
27337 AGTTAAAATG
Statistics
Matches: 165, Mismatches: 14, Indels: 10
0.87 0.07 0.05
Matches are distributed among these distances:
54 1 0.01
55 45 0.27
56 62 0.38
57 8 0.05
58 18 0.11
59 27 0.16
60 4 0.02
ACGTcount: A:0.51, C:0.07, G:0.17, T:0.25
Consensus pattern (56 bp):
AATCAGTAATTAAGTAAAAAAGAAATTAATCAGAGTCAAAGTAGCAGTAATCAGTA
Found at i:27309 original size:111 final size:115
Alignment explanation
Indices: 27096--27336 Score: 357
Period size: 111 Copynumber: 2.1 Consensus size: 115
27086 GAAAGGGGGC
*
27096 AATCAGTAAATTAAGTAAAAAAGAAATTAATCATGAGTCAAAGTAGCAGTAATACAGTAAATACA
1 AATCAGT-AATTAAGTAAAAAAGAAATTAATCATGAGTCAAAGTAGCAGAAATACAGTAAATACA
* *
27161 GTAATTAAGTAAAAAAGAGATTAATCAGGGTCAAAGTAGCAGTAATCAGTA
65 GTAATTAAGTAAAAAAGAGATTAATCAGAGTCAAAGTAACAGTAATCAGTA
* * **
27212 AATCAGTAATTAAGT-AAAAAGAAATTAATTA-GAGTCAAGGTATTAGAAAT-CAGTAAATACAG
1 AATCAGTAATTAAGTAAAAAAGAAATTAATCATGAGTCAAAGTAGCAGAAATACAGTAAATACAG
*
27274 TAATTAAGT-AAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
66 TAATTAAGTAAAAAAGAGATTAATCAGAGTCAAAGTAACAGTAATCAGTA
27323 AATC-GATAATTAAG
1 AATCAG-TAATTAAG
27337 AGTTAAAATG
Statistics
Matches: 116, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
110 1 0.01
111 49 0.42
112 21 0.18
113 15 0.13
114 15 0.13
115 8 0.07
116 7 0.06
ACGTcount: A:0.51, C:0.07, G:0.17, T:0.25
Consensus pattern (115 bp):
AATCAGTAATTAAGTAAAAAAGAAATTAATCATGAGTCAAAGTAGCAGAAATACAGTAAATACAG
TAATTAAGTAAAAAAGAGATTAATCAGAGTCAAAGTAACAGTAATCAGTA
Found at i:27611 original size:22 final size:22
Alignment explanation
Indices: 27522--27936 Score: 250
Period size: 22 Copynumber: 18.7 Consensus size: 22
27512 AATAGCAGGC
*
27522 AATCAGTAAAAAGTAAAAGGGT
1 AATCAGTAAAAAGTAAAAAGGT
* * **
27544 -ACCTG-AAAGGGTAAAAAGAGT
1 AATCAGTAAAAAGTAAAAAG-GT
*
27565 AATCAGAAAAAGAGTAAAATA-GT
1 AATCAGTAAAA-AGTAAAA-AGGT
*
27588 AATCAGTAAAAAGTAAGAAGGT
1 AATCAGTAAAAAGTAAAAAGGT
*
27610 AATCA--ACAAGAGTAAAATA-GT
1 AATCAGTA-AAAAGTAAAA-AGGT
* *
27631 AGTCAGTAAAAAGTAAATA-GT
1 AATCAGTAAAAAGTAAAAAGGT
* *
27652 AATCAGT-AAGAGTAAAAAAAGT
1 AATCAGTAAAAAGT-AAAAAGGT
* *
27674 AATAAGTAAGAAGTAAAAAGG-
1 AATCAGTAAAAAGTAAAAAGGT
* *
27695 AAACTAGT-AAGAGTAAAAAGGT
1 AATC-AGTAAAAAGTAAAAAGGT
* * *
27717 GATCAGTAAAGAGTAAAAAGCT
1 AATCAGTAAAAAGTAAAAAGGT
* * *
27739 AATCAGCAAGAAGTAAAAAGAT
1 AATCAGTAAAAAGTAAAAAGGT
* *
27761 AATCAGTAAAACGCAAAAAGGT
1 AATCAGTAAAAAGTAAAAAGGT
*
27783 AATCAGTAAAAACT-AAAAGAGT
1 AATCAGTAAAAAGTAAAAAG-GT
* *
27805 AATCAGTAAAAAAGGAGCAGAAAATAGT
1 AATCAGT--AAAA--AGTA-AAAA-GGT
*
27833 AATCAGTAAAAGAGTAAAATGGT
1 AATCAGTAAAA-AGTAAAAAGGT
* *
27856 AATCAGTAAAAAGTAAGAAGAT
1 AATCAGTAAAAAGTAAAAAGGT
*
27878 AATCA--ACAAGAGTAAAATA-GT
1 AATCAGTA-AAAAGTAAAA-AGGT
*
27899 AATCAGTACAAAGTAAAGAA--T
1 AATCAGTAAAAAGTAAA-AAGGT
*
27920 AATCAGTGAAATAGTAA
1 AATCAGT-AAAAAGTAA
27937 TGGTAATCAA
Statistics
Matches: 304, Mismatches: 59, Indels: 60
0.72 0.14 0.14
Matches are distributed among these distances:
20 17 0.06
21 76 0.25
22 140 0.46
23 35 0.12
24 13 0.04
25 5 0.02
26 5 0.02
28 13 0.04
ACGTcount: A:0.56, C:0.07, G:0.20, T:0.18
Consensus pattern (22 bp):
AATCAGTAAAAAGTAAAAAGGT
Found at i:27624 original size:43 final size:43
Alignment explanation
Indices: 27554--27915 Score: 275
Period size: 43 Copynumber: 8.1 Consensus size: 43
27544 ACCTGAAAGG
*
27554 GTAAAAAGAGTAATCAGAAAAAGAGTAAAATAGTAATCAGTAAAAA
1 GTAAAAAG-GTAATC--AACAAGAGTAAAATAGTAATCAGTAAAAA
* *
27600 GTAAGAAGGTAATCAACAAGAGTAAAATAGTAGTCAGTAAAAA
1 GTAAAAAGGTAATCAACAAGAGTAAAATAGTAATCAGTAAAAA
* ** * * *
27643 GTAAATA-GTAATCAGTAAGAGTAAAAAAAGTAATAAGTAAGAA
1 GTAAAAAGGTAATCAACAAGAGT-AAAATAGTAATCAGTAAAAA
* ** * *
27686 GTAAAAAGG-AAACTAGTAAGAGTAAAA-AGGTGATCAGTAAAGA
1 GTAAAAAGGTAATC-AACAAGAGTAAAATA-GTAATCAGTAAAAA
* * *
27729 GTAAAAAGCTAATCAGCAAGAAGTAAAA-AGATAATCAGTAAAAC
1 GTAAAAAGGTAATCAACAAG-AGTAAAATAG-TAATCAGTAAAAA
* * * *
27773 GCAAAAAGGTAATCAGTA-AAAACTAAAAGAGTAATCAGTAAAAAAGGA
1 GTAAAAAGGTAATCA--ACAAGAGTAAAATAGTAATCAGT--AAAA--A
* * * *
27821 GCAGAAAATAGTAATCAGTAAAAGAGTAAAATGGTAATCAGTAAAAA
1 GTA-AAAA-GGTAATCA--ACAAGAGTAAAATAGTAATCAGTAAAAA
* * *
27868 GTAAGAAGATAATCAACAAGAGTAAAATAGTAATCAGTACAAA
1 GTAAAAAGGTAATCAACAAGAGTAAAATAGTAATCAGTAAAAA
27911 GTAAA
1 GTAAA
27916 GAATAATCAG
Statistics
Matches: 257, Mismatches: 42, Indels: 37
0.76 0.12 0.11
Matches are distributed among these distances:
42 14 0.05
43 114 0.44
44 58 0.23
45 16 0.06
46 14 0.05
47 3 0.01
48 3 0.01
49 8 0.03
50 10 0.04
51 17 0.07
ACGTcount: A:0.57, C:0.07, G:0.19, T:0.18
Consensus pattern (43 bp):
GTAAAAAGGTAATCAACAAGAGTAAAATAGTAATCAGTAAAAA
Found at i:27814 original size:15 final size:15
Alignment explanation
Indices: 27796--27849 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
27786 CAGTAAAAAC
27796 TAAAAGAGTAATCAG
1 TAAAAGAGTAATCAG
* * *
27811 TAAAAAAG-GAGCAG
1 TAAAAGAGTAATCAG
*
27825 -AAAATAGTAATCAG
1 TAAAAGAGTAATCAG
27839 TAAAAGAGTAA
1 TAAAAGAGTAA
27850 AATGGTAATC
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
13 6 0.20
14 8 0.27
15 16 0.53
ACGTcount: A:0.57, C:0.06, G:0.20, T:0.17
Consensus pattern (15 bp):
TAAAAGAGTAATCAG
Done.