Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007792.1 Corchorus capsularis cultivar CVL-1 contig07813, 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: 84688
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:824 original size:2 final size:2
Alignment explanation
Indices: 811--841 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
801 GTTAAAAATA
811 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
842 GAAATTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7708 original size:21 final size:21
Alignment explanation
Indices: 7684--7727 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
7674 TGGGCGGCAT
7684 TTATAGAGAAAATAATTATTA
1 TTATAGAGAAAATAATTATTA
***
7705 TTATTTCGAAAATAATTATTA
1 TTATAGAGAAAATAATTATTA
7726 TT
1 TT
7728 TATTAATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (21 bp):
TTATAGAGAAAATAATTATTA
Found at i:8550 original size:2 final size:2
Alignment explanation
Indices: 8543--8569 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
8533 AAAGTTAATA
8543 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 A
8570 CACACACACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11504 original size:99 final size:100
Alignment explanation
Indices: 11265--11558 Score: 285
Period size: 99 Copynumber: 2.9 Consensus size: 100
11255 GTGGGAAAAT
* * * * * * *
11265 AAATAAAATATGGTAAGAAGATTATTTGAAATTTCTAAGAAAATTTTTAATTAATTTAAAGAATG
1 AAATACAATATGGTAAGAAGATCAATTGAAATTTATATGAAAACTTTTAATTAATTTTAAGAATG
* ** *
11330 TAATCAAGTTCATCAATTTACTTTGCACATGTGGGA
66 TAATCAAG-TCATCAATTAAAGTTACACATGTGGGA
* * * *
11366 AAATACAAATATGGTAGGAAGATC-ATT--TATTTCCA-ATGAAAGCTATTAATTAATTTTAA-A
1 AAATAC-AATATGGTAAGAAGATCAATTGAAATTT--ATATGAAAACTTTTAATTAATTTTAAGA
*
11426 ATGTAATTAAGTCATCAATTAAAAGTTACACATGTGGGA
63 ATGTAATCAAGTCATCAATT-AAAGTTACACATGTGGGA
** *
11465 AAATACAATATGGTAAGAA-ATCAATTGAAATTTATATGAAAACTTTTATAATTAAAATAATAAT
1 AAATACAATATGGTAAGAAGATCAATTGAAATTTATATGAAAAC-TTT-TAATT--AATTTTAAG
11529 AATGTAATCAAGTCATCAATTTAAAGTTAC
62 AATGTAATCAAGTCATCAA-TTAAAGTTAC
11559 TACTATAAAA
Statistics
Matches: 156, Mismatches: 23, Indels: 25
0.76 0.11 0.12
Matches are distributed among these distances:
97 3 0.02
98 25 0.16
99 42 0.27
100 25 0.16
101 12 0.08
102 15 0.10
103 6 0.04
104 26 0.17
105 2 0.01
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (100 bp):
AAATACAATATGGTAAGAAGATCAATTGAAATTTATATGAAAACTTTTAATTAATTTTAAGAATG
TAATCAAGTCATCAATTAAAGTTACACATGTGGGA
Found at i:12534 original size:2 final size:2
Alignment explanation
Indices: 12506--12553 Score: 60
Period size: 2 Copynumber: 23.5 Consensus size: 2
12496 CACACAACAC
* * *
12506 AG AG AC AG AC AG AG ACG AG AA AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG A-G AG AG AG AG AG AG AG AG AG AG AG AG AG
12549 AG AG A
1 AG AG A
12554 AAGGAAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.52, C:0.06, G:0.42, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19643 original size:12 final size:11
Alignment explanation
Indices: 19626--19672 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 11
19616 TTTTTCTCAA
19626 AAAAAAAAAAC
1 AAAAAAAAAAC
19637 GAAAAAAAAAAAC
1 --AAAAAAAAAAC
19650 AAAAACAAAAAC
1 AAAAA-AAAAAC
19662 AAAAAACAAAA
1 AAAAAA-AAAA
19673 AGAGTAATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
11 6 0.19
12 15 0.47
13 11 0.34
ACGTcount: A:0.87, C:0.11, G:0.02, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:19643 original size:13 final size:12
Alignment explanation
Indices: 19625--19673 Score: 71
Period size: 13 Copynumber: 3.9 Consensus size: 12
19615 TTTTTTCTCA
19625 AAAAAAAAAAAC
1 AAAAAAAAAAAC
19637 GAAAAAAAAAAAC
1 -AAAAAAAAAAAC
*
19650 AAAAACAAAAAC
1 AAAAAAAAAAAC
19662 AAAAAACAAAAA
1 AAAAAA-AAAAA
19674 GAGTAATGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
12 16 0.48
13 17 0.52
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAC
Found at i:19648 original size:19 final size:19
Alignment explanation
Indices: 19624--19673 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
19614 CTTTTTTCTC
*
19624 AAAAAAA-AAAAACGAAAA
1 AAAAAAACAAAAACAAAAA
19642 AAAAAAACAAAAACAAAAA
1 AAAAAAACAAAAACAAAAA
*
19661 CAAAAAACAAAAA
1 AAAAAAACAAAAA
19674 GAGTAATGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 7 0.24
19 22 0.76
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (19 bp):
AAAAAAACAAAAACAAAAA
Found at i:20011 original size:6 final size:6
Alignment explanation
Indices: 20000--20033 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
19990 ATAATGCTGG
20000 CTGTGA CTGTGA CTGTGA CTGTGA CTGTGA -TGTG
1 CTGTGA CTGTGA CTGTGA CTGTGA CTGTGA CTGTG
20034 GGAACATTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.14
6 24 0.86
ACGTcount: A:0.15, C:0.15, G:0.35, T:0.35
Consensus pattern (6 bp):
CTGTGA
Found at i:32101 original size:23 final size:23
Alignment explanation
Indices: 32075--32119 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
32065 ACAAGAAACT
32075 TACATT-AGAATTGAAAGATACAA
1 TACATTCA-AATTGAAAGATACAA
32098 TACATTCAAATTGAAAGATACA
1 TACATTCAAATTGAAAGATACA
32120 GTAGGCCACC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 20 0.95
24 1 0.05
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.27
Consensus pattern (23 bp):
TACATTCAAATTGAAAGATACAA
Found at i:43733 original size:15 final size:15
Alignment explanation
Indices: 43715--43744 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
43705 TTTATACCCA
*
43715 TTTCTTTTTTCTTTT
1 TTTCTTTTCTCTTTT
43730 TTTCTTTTCTCTTTT
1 TTTCTTTTCTCTTTT
43745 ATATTTCGAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTCTTTTCTCTTTT
Found at i:60023 original size:20 final size:20
Alignment explanation
Indices: 59998--60049 Score: 77
Period size: 22 Copynumber: 2.5 Consensus size: 20
59988 AAATTAAGGC
59998 ATGACAGCTGATGTACTGGT
1 ATGACAGCTGATGTACTGGT
*
60018 ATGACATACCTGATGTACTGGT
1 ATGAC--AGCTGATGTACTGGT
60040 ATGACAGCTG
1 ATGACAGCTG
60050 TGCAGCTGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 9 0.32
22 19 0.68
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (20 bp):
ATGACAGCTGATGTACTGGT
Found at i:68638 original size:43 final size:43
Alignment explanation
Indices: 68577--68662 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
68567 AGACGTCACA
* *
68577 GCCCTGTGTTCATGATCAATATATTATTGTTTGTGATTTTCTT
1 GCCCTGTGTACATGATCAATATAATATTGTTTGTGATTTTCTT
68620 GCCCTGTGTACATGATCAATATAATATTGTTTGTGATTTTCTT
1 GCCCTGTGTACATGATCAATATAATATTGTTTGTGATTTTCTT
68663 TCTATTTTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.21, C:0.14, G:0.16, T:0.49
Consensus pattern (43 bp):
GCCCTGTGTACATGATCAATATAATATTGTTTGTGATTTTCTT
Found at i:75760 original size:20 final size:20
Alignment explanation
Indices: 75735--75774 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
75725 ATAAATAAAC
75735 AAGTATAATTAATAAAATCA
1 AAGTATAATTAATAAAATCA
75755 AAGTATAATTAATAAAATCA
1 AAGTATAATTAATAAAATCA
75775 TAATAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (20 bp):
AAGTATAATTAATAAAATCA
Found at i:79865 original size:70 final size:69
Alignment explanation
Indices: 79747--79884 Score: 199
Period size: 70 Copynumber: 2.0 Consensus size: 69
79737 GCTTGAAATG
* *
79747 CATTGTCTTTATATCTAATTTTAGCATTTGGATGTAATTAATGGTGTTC-CTACCATTTTTCTCC
1 CATTATCTTTATATCTAATTTTAGCATTTGGATATAATTAATGGTGTTCAC-ACCATTTTT-TCC
79811 TTAGTA
64 TTAGTA
* *
79817 CATTATCTTTATATGTAATTTTAGCA-TTGAGATATAATTAATGGTGTTCACACCATTTTTTTCT
1 CATTATCTTTATATCTAATTTTAGCATTTG-GATATAATTAATGGTGTTCACACCATTTTTTCCT
79881 TAGT
65 TAGT
79885 TGTTAGTTTT
Statistics
Matches: 62, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
69 10 0.16
70 51 0.82
71 1 0.02
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.49
Consensus pattern (69 bp):
CATTATCTTTATATCTAATTTTAGCATTTGGATATAATTAATGGTGTTCACACCATTTTTTCCTT
AGTA
Found at i:81346 original size:23 final size:22
Alignment explanation
Indices: 81313--81388 Score: 71
Period size: 22 Copynumber: 3.3 Consensus size: 22
81303 ATTACACCTT
*
81313 GTAAAAACAAGGGTGATGAAAA
1 GTAAAAACAAGGGTGATCAAAA
* * *
81335 GTAAATGACAAGGTTGATCACAACTT
1 GTAAA-AACAAGGGTGATCA-AA--A
*
81361 GTAAAAACAAGGGTGATTAAAA
1 GTAAAAACAAGGGTGATCAAAA
81383 GTAAAA
1 GTAAAA
81389 GATAGGGTTG
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
22 11 0.26
23 11 0.26
24 4 0.10
25 11 0.26
26 5 0.12
ACGTcount: A:0.50, C:0.08, G:0.22, T:0.20
Consensus pattern (22 bp):
GTAAAAACAAGGGTGATCAAAA
Found at i:83210 original size:33 final size:34
Alignment explanation
Indices: 83158--83228 Score: 117
Period size: 33 Copynumber: 2.1 Consensus size: 34
83148 AATCCGACAA
*
83158 ATAACTTTCTTTTTGCATGTTCTCTATATTATAT
1 ATAACTTTCTTTTTACATGTTCTCTATATTATAT
*
83192 ATAACTTT-TTTTTACATGTTGTCTATATTATAT
1 ATAACTTTCTTTTTACATGTTCTCTATATTATAT
83225 ATAA
1 ATAA
83229 ATTACCGATT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
33 27 0.77
34 8 0.23
ACGTcount: A:0.28, C:0.11, G:0.06, T:0.55
Consensus pattern (34 bp):
ATAACTTTCTTTTTACATGTTCTCTATATTATAT
Found at i:84173 original size:7 final size:7
Alignment explanation
Indices: 84150--84674 Score: 879
Period size: 7 Copynumber: 77.0 Consensus size: 7
84140 GATTTTAGGC
84150 TAGGG-T
1 TAGGGTT
84156 TAGGG-T
1 TAGGGTT
84162 TAGGGTT
1 TAGGGTT
84169 TAGGGTT
1 TAGGGTT
84176 TAGGGTT
1 TAGGGTT
84183 TAGGG-T
1 TAGGGTT
*
84189 TAAGGTT
1 TAGGGTT
84196 TAGGGTT
1 TAGGGTT
84203 TAGGG-T
1 TAGGGTT
84209 TAGGGTT
1 TAGGGTT
84216 TAGGGTT
1 TAGGGTT
84223 TAGGGTT
1 TAGGGTT
84230 TAGGG-T
1 TAGGGTT
84236 TAGGGTT
1 TAGGGTT
84243 TAGGGTT
1 TAGGGTT
84250 TAGGGTT
1 TAGGGTT
84257 TAGGGTT
1 TAGGGTT
84264 TAGGGTT
1 TAGGGTT
84271 TAGGGTT
1 TAGGGTT
84278 TAGGGTT
1 TAGGGTT
84285 TAGGGGTT
1 TA-GGGTT
84293 TAGGGTT
1 TAGGGTT
84300 TAGGG-T
1 TAGGGTT
84306 TAGGGTT
1 TAGGGTT
84313 TAGGG-T
1 TAGGGTT
84319 TAGGGTT
1 TAGGGTT
84326 TAGGG-T
1 TAGGGTT
84332 TAGGG-T
1 TAGGGTT
84338 TAGGGTT
1 TAGGGTT
84345 TAGGGTT
1 TAGGGTT
84352 TAGGGTT
1 TAGGGTT
84359 TAGGGTT
1 TAGGGTT
84366 TAGGGTT
1 TAGGGTT
84373 TAGGGTT
1 TAGGGTT
84380 TAGGGTT
1 TAGGGTT
84387 TAGGGTCGT
1 TAGGGT--T
84396 TAGGGTT
1 TAGGGTT
84403 TAGGGTT
1 TAGGGTT
84410 TAGGG-T
1 TAGGGTT
84416 TAGGG-T
1 TAGGGTT
84422 TAGGGTT
1 TAGGGTT
84429 TAGGGTTT
1 TAGGG-TT
84437 TAGGGTT
1 TAGGGTT
84444 TAGGG-T
1 TAGGGTT
84450 TAGGG-T
1 TAGGGTT
84456 TAGGG-T
1 TAGGGTT
84462 TAGGGTT
1 TAGGGTT
84469 TAGGGTT
1 TAGGGTT
84476 TAGGGTT
1 TAGGGTT
84483 TAGGGTT
1 TAGGGTT
84490 TAGGGTT
1 TAGGGTT
84497 TAGGGTT
1 TAGGGTT
84504 TAGGGTT
1 TAGGGTT
84511 TAGGGTT
1 TAGGGTT
84518 TAGGGTT
1 TAGGGTT
84525 TAGGGTT
1 TAGGGTT
84532 TAGGGTT
1 TAGGGTT
84539 TAGGGTT
1 TAGGGTT
84546 TAGGGTT
1 TAGGGTT
84553 TAGGGTT
1 TAGGGTT
84560 TAGGGTT
1 TAGGGTT
84567 TAGGGTT
1 TAGGGTT
84574 TAGGGTT
1 TAGGGTT
84581 TAGGGTT
1 TAGGGTT
84588 TAGGGTT
1 TAGGGTT
84595 TAGGGTT
1 TAGGGTT
84602 TAGGGTT
1 TAGGGTT
84609 TAGGG-T
1 TAGGGTT
84615 TAGGGTT
1 TAGGGTT
84622 TAGGGTT
1 TAGGGTT
84629 TAGGGTT
1 TAGGGTT
84636 TAGGG-T
1 TAGGGTT
84642 TAGGGTT
1 TAGGGTT
84649 TAGGG-T
1 TAGGGTT
84655 TAGGGTT
1 TAGGGTT
84662 TAGGG-T
1 TAGGGTT
84668 TAGGGTT
1 TAGGGTT
84675 AGGTTAGGTT
Statistics
Matches: 500, Mismatches: 2, Indels: 33
0.93 0.00 0.06
Matches are distributed among these distances:
6 106 0.21
7 373 0.75
8 14 0.03
9 7 0.01
ACGTcount: A:0.15, C:0.00, G:0.44, T:0.41
Consensus pattern (7 bp):
TAGGGTT
Done.