Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008227.1 Corchorus capsularis cultivar CVL-1 contig08248, 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: 9126
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.30
Found at i:1036 original size:27 final size:27
Alignment explanation
Indices: 1004--1073 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
994 GGTCGAATTA
* * *
1004 GCATTTTGGTCTTTTTTACATTTAGGG
1 GCATTTTGGTCATTTTTACACTAAGGG
* * *
1031 GTATTTTGGTCATTCTTAGACTAAGGG
1 GCATTTTGGTCATTTTTACACTAAGGG
1058 GCATTTTGGTCATTTT
1 GCATTTTGGTCATTTT
1074 GCACATTCAG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.17, C:0.11, G:0.23, T:0.49
Consensus pattern (27 bp):
GCATTTTGGTCATTTTTACACTAAGGG
Found at i:5093 original size:55 final size:55
Alignment explanation
Indices: 5021--5378 Score: 412
Period size: 55 Copynumber: 6.6 Consensus size: 55
5011 AAAAGGGGGC
*
5021 AATCAGTAATTAAGTAAAAATAGATTAATCAGAATTAAGATAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAATTAAGATAATAGTAATCAGTA
* * * * *
5076 AATCAGTAATTAAGTAAAAAGAAATTAATCGGAGTCAAGGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAATTAAGATAATAGTAATCAGTA
*
5131 AATCAGTAATTAAGT-AAAAGAGATTAATCAGAGTTAA-AGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAATTAAGA-TAATAGTAATCAGTA
* * * * *
5185 AATCAGTAAATAAATAAGAAGAGATTAATCAGAGTTAA-AGTAATAGTAACCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAATTAAGA-TAATAGTAATCAGTA
* *
5240 AATCAGTAATTAAGTAAAAAGAGATTAGTC---A--AAGTTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAATTAAGATAATAGTAATCAGTA
* * * *
5290 AGTCAGTAATTAAAGCAAAAA-AGGATTAATCAGAGA-CAAGGTAATAGTAATCAGTA
1 AATCAGTAATT-AAGTAAAAAGA-GATTAATCAGA-ATTAAGATAATAGTAATCAGTA
* * *
5346 AATCAGTAAATAAGTAAAAAGATAGTAATCAGA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGA
5379 GATCAAGGGT
Statistics
Matches: 262, Mismatches: 30, Indels: 22
0.83 0.10 0.07
Matches are distributed among these distances:
50 27 0.10
51 15 0.06
54 47 0.18
55 145 0.55
56 28 0.11
ACGTcount: A:0.51, C:0.07, G:0.16, T:0.25
Consensus pattern (55 bp):
AATCAGTAATTAAGTAAAAAGAGATTAATCAGAATTAAGATAATAGTAATCAGTA
Found at i:5176 original size:109 final size:109
Alignment explanation
Indices: 5021--5379 Score: 478
Period size: 109 Copynumber: 3.3 Consensus size: 109
5011 AAAAGGGGGC
* *
5021 AATCAGTAATTAAGTAAAAATAGATTAATCAGAATTAAGATAATAGTAATCAGTAAATCAGTAAT
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAG-TAATAGTAATCAGTAAATCAGTAAT
* *
5086 TAAGTAAAAAGAAATTAATCGGAGTCAAGGTAATAGTAATCAGTA
65 TAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
*
5131 AATCAGTAATTAAGT-AAAAGAGATTAATCAGAGTTAAAGTAATAGTAATCAGTAAATCAGTAAA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTT-AAGTAATAGTAATCAGTAAATCAGTAAT
* * * * *
5195 TAAATAAGAAGAGATTAATCAGAGTTAAAGTAATAGTAACCAGTA
65 TAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
* * *
5240 AATCAGTAATTAAGTAAAAAGAGATTAGTCAAAG-T---TAATAGTAATCAGTAAGTCAGTAATT
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGTAATAGTAATCAGTAAATCAGTAATT
* *
5301 AAAGCAAAAA-AGGATTAATCAGAGACAAGGTAATAGTAATCAGTA
66 -AAGTAAAAAGA-GATTAATCAGAGTCAAGGTAATAGTAATCAGTA
* * *
5346 AATCAGTAAATAAGTAAAAAGATAGTAATCAGAG
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAG
5380 ATCAAGGGTC
Statistics
Matches: 219, Mismatches: 26, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
105 25 0.11
106 64 0.29
109 96 0.44
110 34 0.16
ACGTcount: A:0.51, C:0.07, G:0.17, T:0.25
Consensus pattern (109 bp):
AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGTAATAGTAATCAGTAAATCAGTAATT
AAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
Found at i:5212 original size:164 final size:161
Alignment explanation
Indices: 5021--5378 Score: 488
Period size: 164 Copynumber: 2.2 Consensus size: 161
5011 AAAAGGGGGC
* * *
5021 AATCAGTAATTAAGTAAAAATAGATTAATCAGAATT-AAGATAATAGTAATCAGTAAATCAGTAA
1 AATCAGTAAATAAGTAAAAAGAGATTAATCAGAATTAAAG-TAATAGTAACCAGTAAATCAGTAA
*
5085 TTAAGTAAAAAGAAATTAATCGGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATT-AAGTAAA
65 TTAAGTAAAAAGAAATTAATC--A---AAGGTAATAGTAATCAGTAAATCAGTAATTAAAGCAAA
* **
5149 AGA-GATTAATCAGAGTTAAAGTAATAGTAATCAGTA
125 AAAGGATTAATCAGAGACAAAGTAATAGTAATCAGTA
* * *
5185 AATCAGTAAATAAATAAGAAGAGATTAATCAGAGTTAAAGTAATAGTAACCAGTAAATCAGTAAT
1 AATCAGTAAATAAGTAAAAAGAGATTAATCAGAATTAAAGTAATAGTAACCAGTAAATCAGTAAT
* * * *
5250 TAAGTAAAAAGAGATTAGTCAAAGTTAATAGTAATCAGTAAGTCAGTAATTAAAGCAAAAAAGGA
66 TAAGTAAAAAGAAATTAATCAAAGGTAATAGTAATCAGTAAATCAGTAATTAAAGCAAAAAAGGA
*
5315 TTAATCAGAGACAAGGTAATAGTAATCAGTA
131 TTAATCAGAGACAAAGTAATAGTAATCAGTA
* *
5346 AATCAGTAAATAAGTAAAAAGATAGTAATCAGA
1 AATCAGTAAATAAGTAAAAAGAGATTAATCAGA
5379 GATCAAGGGT
Statistics
Matches: 172, Mismatches: 19, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
159 28 0.16
160 8 0.05
161 59 0.34
162 1 0.01
164 73 0.42
165 3 0.02
ACGTcount: A:0.51, C:0.07, G:0.16, T:0.25
Consensus pattern (161 bp):
AATCAGTAAATAAGTAAAAAGAGATTAATCAGAATTAAAGTAATAGTAACCAGTAAATCAGTAAT
TAAGTAAAAAGAAATTAATCAAAGGTAATAGTAATCAGTAAATCAGTAATTAAAGCAAAAAAGGA
TTAATCAGAGACAAAGTAATAGTAATCAGTA
Found at i:5504 original size:40 final size:39
Alignment explanation
Indices: 5414--5510 Score: 101
Period size: 40 Copynumber: 2.5 Consensus size: 39
5404 ATCAAGTAAA
* *
5414 AAGATAGTAATCAGTAAATTGATAATTAAGAGTCAAGGT
1 AAGAAAGTAATCAGTAAATAGATAATTAAGAGTCAAGGT
* *
5453 AAGAGATTAATCAGTACAATCAG-TAATTAAAGAGTCAAAGG-
1 AAGAAAGTAATCAGTA-AAT-AGATAATT-AAGAGTC-AAGGT
5494 AA-AAAGTAATCAGTAAA
1 AAGAAAGTAATCAGTAAA
5511 ATGGTAATCA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
39 16 0.33
40 19 0.39
41 10 0.20
42 4 0.08
ACGTcount: A:0.51, C:0.07, G:0.19, T:0.24
Consensus pattern (39 bp):
AAGAAAGTAATCAGTAAATAGATAATTAAGAGTCAAGGT
Found at i:5545 original size:16 final size:15
Alignment explanation
Indices: 5497--5585 Score: 69
Period size: 16 Copynumber: 5.9 Consensus size: 15
5487 TCAAAGGAAA
5497 AAGTAATCAGTAAA-
1 AAGTAATCAGTAAAG
* *
5511 ATGGTAATCA--AGAG
1 A-AGTAATCAGTAAAG
5525 AAGTAATCAGTAAAGG
1 AAGTAATCAGTAAA-G
*
5541 AAGTAATCAGTAAAA
1 AAGTAATCAGTAAAG
* *
5556 AAGGCAA-AAGTAAAAG
1 AA-GTAATCAGT-AAAG
5572 AAGTAATCAGTAAA
1 AAGTAATCAGTAAA
5586 AGTAAAAGAA
Statistics
Matches: 57, Mismatches: 10, Indels: 15
0.70 0.12 0.18
Matches are distributed among these distances:
13 9 0.16
14 2 0.04
15 20 0.35
16 26 0.46
ACGTcount: A:0.55, C:0.07, G:0.20, T:0.18
Consensus pattern (15 bp):
AAGTAATCAGTAAAG
Found at i:5586 original size:16 final size:16
Alignment explanation
Indices: 5523--5620 Score: 85
Period size: 16 Copynumber: 6.1 Consensus size: 16
5513 GGTAATCAAG
5523 AGAAGTAATCAGTAAA
1 AGAAGTAATCAGTAAA
*
5539 GGAAGTAATCAGTAAA
1 AGAAGTAATCAGTAAA
* *
5555 A-AAGGCAA-AAGTAAA
1 AGAA-GTAATCAGTAAA
5570 AGAAGTAATCAGTAAA
1 AGAAGTAATCAGTAAA
**
5586 AGTAAAAG-AAAAAGTAAA
1 AG---AAGTAATCAGTAAA
*
5604 AGAGGTAATCAGTAAA
1 AGAAGTAATCAGTAAA
5620 A
1 A
5621 TGGTAAGTAA
Statistics
Matches: 64, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
15 14 0.22
16 37 0.58
18 10 0.16
19 3 0.05
ACGTcount: A:0.59, C:0.05, G:0.20, T:0.15
Consensus pattern (16 bp):
AGAAGTAATCAGTAAA
Found at i:5604 original size:34 final size:34
Alignment explanation
Indices: 5533--5659 Score: 125
Period size: 34 Copynumber: 3.6 Consensus size: 34
5523 AGAAGTAATC
* * *
5533 AGTAAAGGAAGTAATCAGT-AAA--AAAGGCAAA
1 AGTAAAAGAAGTAATCAGTAAAAGTAAAAGAAAA
5564 AGTAAAAGAAGTAATCAGTAAAAGTAAAAGAAAA
1 AGTAAAAGAAGTAATCAGTAAAAGTAAAAGAAAA
* *
5598 AGTAAAAGAGGTAATCAGTAAAATGGTAAGTAAGAGTAAG
1 AGTAAAAGAAGTAATCAGTAAAA--GTAA--AAGA--AAA
*
5638 GGTAAAAGAAGTAATCAGTAAA
1 AGTAAAAGAAGTAATCAGTAAA
5660 TCGGTAAAGA
Statistics
Matches: 80, Mismatches: 7, Indels: 9
0.83 0.07 0.09
Matches are distributed among these distances:
31 18 0.22
32 3 0.04
34 29 0.36
36 4 0.05
38 4 0.05
40 22 0.28
ACGTcount: A:0.57, C:0.04, G:0.23, T:0.17
Consensus pattern (34 bp):
AGTAAAAGAAGTAATCAGTAAAAGTAAAAGAAAA
Found at i:5682 original size:40 final size:40
Alignment explanation
Indices: 5599--5720 Score: 107
Period size: 37 Copynumber: 3.1 Consensus size: 40
5589 AAAAGAAAAA
*
5599 GTAAAAGAGGTAATCAGTAAAAT-GGTAAGTAAGAGT-AAG--G
1 GTAAAAGAAGTAATCAGT-AAATCGGT-A--AAGAGTAAAGATG
5639 GTAAAAGAAGTAATCAGTAAATCGGTAAAGAGTAAAGATG
1 GTAAAAGAAGTAATCAGTAAATCGGTAAAGAGTAAAGATG
*** *
5679 GT-AAA-AAGTAGGGAGT-AATCCGTAAAGAGTAAA-ATG
1 GTAAAAGAAGTAATCAGTAAATCGGTAAAGAGTAAAGATG
5715 GTAAAA
1 GTAAAA
5721 TGGTAATTAA
Statistics
Matches: 72, Mismatches: 5, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
36 5 0.07
37 25 0.35
38 11 0.15
39 8 0.11
40 23 0.32
ACGTcount: A:0.49, C:0.04, G:0.27, T:0.20
Consensus pattern (40 bp):
GTAAAAGAAGTAATCAGTAAATCGGTAAAGAGTAAAGATG
Found at i:5740 original size:17 final size:17
Alignment explanation
Indices: 5718--5754 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
5708 TAAAATGGTA
5718 AAATGGTAATTAAATCC
1 AAATGGTAATTAAATCC
* *
5735 AAATGGTGATTAAATTC
1 AAATGGTAATTAAATCC
5752 AAA
1 AAA
5755 GAATTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.08, G:0.14, T:0.30
Consensus pattern (17 bp):
AAATGGTAATTAAATCC
Found at i:5829 original size:14 final size:14
Alignment explanation
Indices: 5791--5836 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
5781 AGGGTAAATT
5791 AGTAATCAGTAAAG
1 AGTAATCAGTAAAG
* **
5805 AGGAAAAAGTAAAG
1 AGTAATCAGTAAAG
5819 AGTAATCAGTAAA-
1 AGTAATCAGTAAAG
5832 AGTAA
1 AGTAA
5837 AGATGGCAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
13 5 0.19
14 21 0.81
ACGTcount: A:0.57, C:0.04, G:0.22, T:0.17
Consensus pattern (14 bp):
AGTAATCAGTAAAG
Found at i:5942 original size:22 final size:21
Alignment explanation
Indices: 5899--5942 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
5889 AATCGGTAAG
*
5899 AGTAAAATAGTAATCAGTAAG
1 AGTAAAATAGTAATCAGCAAG
* *
5920 AGTAAAAATGGTAATTAGCAAG
1 AGT-AAAATAGTAATCAGCAAG
5942 A
1 A
5943 AGTAGTCAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.52, C:0.05, G:0.20, T:0.23
Consensus pattern (21 bp):
AGTAAAATAGTAATCAGCAAG
Done.