Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011776.1 Corchorus capsularis cultivar CVL-1 contig11797, 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: 32603
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:1267 original size:17 final size:18
Alignment explanation
Indices: 1226--1260 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1216 CTTTTCAAAA
*
1226 ATATTTTTTTTTATTTTC
1 ATATTTTTTTTAATTTTC
*
1244 AGATTTTTTTTAATTTT
1 ATATTTTTTTTAATTTT
1261 TTATTTTCCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.74
Consensus pattern (18 bp):
ATATTTTTTTTAATTTTC
Found at i:8641 original size:21 final size:22
Alignment explanation
Indices: 8587--8641 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 22
8577 CTAAAAACAC
*
8587 TATTTTCATTTAAATAAATTCAA
1 TATTTT-ATCTAAATAAATTCAA
8610 TATTTTATTATCTAAA-AAATTCAA
1 TA--TT-TTATCTAAATAAATTCAA
8634 TATTTTAT
1 TATTTTAT
8642 AATTATTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
21 4 0.14
22 2 0.07
23 2 0.07
24 10 0.36
25 8 0.29
26 2 0.07
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (22 bp):
TATTTTATCTAAATAAATTCAA
Found at i:8978 original size:25 final size:27
Alignment explanation
Indices: 8926--8978 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
8916 TTACTCAACT
**
8926 AAAAACTCTATTTTTATTTTTCTGTAA
1 AAAAACTCTATTTTTATTTTAATGTAA
8953 AAAAACTCTATTTTTA-TTTAAT-TAA
1 AAAAACTCTATTTTTATTTTAATGTAA
8978 A
1 A
8979 TCTAATATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 4 0.17
27 16 0.67
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (27 bp):
AAAAACTCTATTTTTATTTTAATGTAA
Found at i:13580 original size:9 final size:9
Alignment explanation
Indices: 13566--13599 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
13556 GAAACTACTA
13566 CTCCTCTTC
1 CTCCTCTTC
13575 CTCCTCTTC
1 CTCCTCTTC
*
13584 CTCTTCTTC
1 CTCCTCTTC
13593 CTCCTCT
1 CTCCTCT
13600 GTGACCTGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (9 bp):
CTCCTCTTC
Found at i:15913 original size:4 final size:4
Alignment explanation
Indices: 15904--15945 Score: 52
Period size: 4 Copynumber: 10.5 Consensus size: 4
15894 TTATATCATT
15904 TTTA TTTA TTTA TTTA TTATA TATTA TTTA --TA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TT-TA T-TTA TTTA TTTA TTTA TTTA TT
15946 ACAAGTAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
2 2 0.06
4 25 0.74
5 6 0.18
6 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:16551 original size:30 final size:30
Alignment explanation
Indices: 16515--16572 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
16505 TTTTTTTGTG
16515 AAAAAAAAAAGATCTTATTAATAGCATCAC
1 AAAAAAAAAAGATCTTATTAATAGCATCAC
16545 AAAAAAAAAAGATCTTATTAATAGCATC
1 AAAAAAAAAAGATCTTATTAATAGCATC
16573 TCATTATTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.57, C:0.12, G:0.07, T:0.24
Consensus pattern (30 bp):
AAAAAAAAAAGATCTTATTAATAGCATCAC
Found at i:19032 original size:18 final size:17
Alignment explanation
Indices: 18999--19033 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
18989 AGTATACACC
*
18999 ATAATAATAATTAGTTA
1 ATAATAATAATAAGTTA
19016 ATAATAACTAATAAGTTA
1 ATAATAA-TAATAAGTTA
19034 CAAAAGATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.37
Consensus pattern (17 bp):
ATAATAATAATAAGTTA
Found at i:19537 original size:23 final size:24
Alignment explanation
Indices: 19511--19563 Score: 63
Period size: 26 Copynumber: 2.2 Consensus size: 24
19501 TTGACCTTCG
19511 ATTGC-ACCATTTAACCGTTGTTA
1 ATTGCAACCATTTAACCGTTGTTA
* *
19534 ATTGAGCAATCGTTTAACCGTTGTTA
1 ATT--GCAACCATTTAACCGTTGTTA
19560 ATTG
1 ATTG
19564 ATTGGTTGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 3 0.12
24 1 0.04
25 2 0.08
26 19 0.76
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (24 bp):
ATTGCAACCATTTAACCGTTGTTA
Found at i:19661 original size:21 final size:21
Alignment explanation
Indices: 19635--19676 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
19625 AGGTTTTTTC
* *
19635 AAAAAGGGTAATTTAGCCTTT
1 AAAAAGAGCAATTTAGCCTTT
*
19656 AAAAAGAGCAATTTAGTCTTT
1 AAAAAGAGCAATTTAGCCTTT
19677 TTGAATAGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (21 bp):
AAAAAGAGCAATTTAGCCTTT
Found at i:22239 original size:21 final size:20
Alignment explanation
Indices: 22215--22254 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
22205 TTACAAAGAA
22215 AACTAACAATTCCGTAAGAGC
1 AACTAAC-ATTCCGTAAGAGC
* *
22236 AACTCACATTCCGTGAGAG
1 AACTAACATTCCGTAAGAG
22255 TAGAACACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
AACTAACATTCCGTAAGAGC
Found at i:23242 original size:12 final size:12
Alignment explanation
Indices: 23221--23254 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
23211 TGAAGGTAGT
*
23221 GGTGGGGGTGGC
1 GGTGGAGGTGGC
23233 GGTGGAGGTGGC
1 GGTGGAGGTGGC
*
23245 GGCGGAGGTG
1 GGTGGAGGTG
23255 ATGGAGGTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.06, C:0.09, G:0.71, T:0.15
Consensus pattern (12 bp):
GGTGGAGGTGGC
Found at i:25891 original size:12 final size:14
Alignment explanation
Indices: 25874--25906 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
25864 GAGTCCACAA
25874 GAACTTT-CC-CCT
1 GAACTTTGCCTCCT
25886 GAACTTTGCCTCCT
1 GAACTTTGCCTCCT
25900 GAACTTT
1 GAACTTT
25907 AATAAATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 2 0.11
14 10 0.53
ACGTcount: A:0.18, C:0.33, G:0.12, T:0.36
Consensus pattern (14 bp):
GAACTTTGCCTCCT
Found at i:32169 original size:112 final size:112
Alignment explanation
Indices: 31972--32202 Score: 462
Period size: 112 Copynumber: 2.1 Consensus size: 112
31962 CTAATACCAC
31972 GAATTTGCCCCTTCAAGGGAGAATAAATGAGTAGTGTACAGCTTCAATTCATTAAAGAAAAGAGG
1 GAATTTGCCCCTTCAAGGGAGAATAAATGAGTAGTGTACAGCTTCAATTCATTAAAGAAAAGAGG
32037 GAGATTTTACTTTTAAATGGGGGAAATGACATGGATGAGGTGACTTG
66 GAGATTTTACTTTTAAATGGGGGAAATGACATGGATGAGGTGACTTG
32084 GAATTTGCCCCTTCAAGGGAGAATAAATGAGTAGTGTACAGCTTCAATTCATTAAAGAAAAGAGG
1 GAATTTGCCCCTTCAAGGGAGAATAAATGAGTAGTGTACAGCTTCAATTCATTAAAGAAAAGAGG
32149 GAGATTTTACTTTTAAATGGGGGAAATGACATGGATGAGGTGACTTG
66 GAGATTTTACTTTTAAATGGGGGAAATGACATGGATGAGGTGACTTG
32196 GAATTTG
1 GAATTTG
32203 GAAGTTATAT
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
112 119 1.00
ACGTcount: A:0.35, C:0.10, G:0.27, T:0.28
Consensus pattern (112 bp):
GAATTTGCCCCTTCAAGGGAGAATAAATGAGTAGTGTACAGCTTCAATTCATTAAAGAAAAGAGG
GAGATTTTACTTTTAAATGGGGGAAATGACATGGATGAGGTGACTTG
Found at i:32256 original size:21 final size:21
Alignment explanation
Indices: 32230--32272 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
32220 TTAAACTGGA
*
32230 TTGCTAAACATCGCCCCCCTT
1 TTGCTAAACACCGCCCCCCTT
* *
32251 TTGCTAAATACCGTCCCCCTT
1 TTGCTAAACACCGCCCCCCTT
32272 T
1 T
32273 CTACATTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.40, G:0.09, T:0.33
Consensus pattern (21 bp):
TTGCTAAACACCGCCCCCCTT
Found at i:32405 original size:24 final size:25
Alignment explanation
Indices: 32344--32402 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
32334 TTCAAAGCCT
*
32344 AAACTTCATTTCTAACAACTTCTTC
1 AAACTTCATTTCTAACAACATCTTC
32369 AAACTTCATTTCTAACAA-ATCTTC
1 AAACTTCATTTCTAACAACATCTTC
32393 AAA-TTCATTT
1 AAACTTCATTT
32403 TCTTTCATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
23 7 0.21
24 8 0.24
25 18 0.55
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.41
Consensus pattern (25 bp):
AAACTTCATTTCTAACAACATCTTC
Found at i:32441 original size:26 final size:26
Alignment explanation
Indices: 32412--32479 Score: 127
Period size: 26 Copynumber: 2.6 Consensus size: 26
32402 TTCTTTCATT
32412 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
32438 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
32464 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
32480 AAACTAAGTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:32479 original size:15 final size:15
Alignment explanation
Indices: 32412--32483 Score: 63
Period size: 11 Copynumber: 5.4 Consensus size: 15
32402 TTCTTTCATT
*
32412 TTAATCATAAACTAA
1 TTAAACATAAACTAA
32427 TT-AA-AT--ACTAA
1 TTAAACATAAACTAA
*
32438 TTAATCATAAACTAA
1 TTAAACATAAACTAA
32453 TT-AA-AT--ACTAA
1 TTAAACATAAACTAA
32464 TTAAACATAAACTAA
1 TTAAACATAAACTAA
32479 -TAAAC
1 TTAAAC
32484 TAAGTAATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 17
0.70 0.05 0.26
Matches are distributed among these distances:
11 14 0.30
12 3 0.07
13 8 0.17
14 7 0.15
15 14 0.30
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (15 bp):
TTAAACATAAACTAA
Found at i:32532 original size:52 final size:49
Alignment explanation
Indices: 32413--32532 Score: 113
Period size: 52 Copynumber: 2.4 Consensus size: 49
32403 TCTTTCATTT
* * *
32413 TAATCATAAACTAATTAA-ATACTAATTAATCATAAACTAATTAAATAC
1 TAATCATAAACTAATTAATAAACTAAGTAATAATAAACTAATTAAATAC
* *
32461 TAAT--TAAACATAAACTAATAAACTAAGTAATTTGAATTAACTAATTTAAA-AC
1 TAATCATAAAC-T-AATTAATAAACTAAGTAA--T-AATAAACTAA-TTAAATAC
32513 TAATCATAAACTAATTAATA
1 TAATCATAAACTAATTAATA
32533 TTAAAAAATT
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
46 5 0.09
47 1 0.02
48 9 0.16
49 9 0.16
51 1 0.02
52 21 0.37
53 6 0.11
54 5 0.09
ACGTcount: A:0.54, C:0.11, G:0.02, T:0.33
Consensus pattern (49 bp):
TAATCATAAACTAATTAATAAACTAAGTAATAATAAACTAATTAAATAC
Done.