Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016064.1 Corchorus capsularis cultivar CVL-1 contig16085, 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: 24561
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:1837 original size:28 final size:27
Alignment explanation
Indices: 1776--1849 Score: 85
Period size: 28 Copynumber: 2.7 Consensus size: 27
1766 ATTAGGGTCG
* *
1776 CCCAAGGGTATTTTGGTCATTTTCGCA
1 CCCAGGGGCATTTTGGTCATTTTCGCA
*
1803 CCCAGGGGCATTTTGGTCATTTTTTGCA
1 CCCAGGGGCATTTTGGTCA-TTTTCGCA
** *
1831 CTTAGGGGCATTTTAGTCA
1 CCCAGGGGCATTTTGGTCA
1850 CCTTCAATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 17 0.43
28 23 0.57
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.38
Consensus pattern (27 bp):
CCCAGGGGCATTTTGGTCATTTTCGCA
Found at i:4364 original size:20 final size:20
Alignment explanation
Indices: 4321--4369 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
4311 GATATTTGGC
* *
4321 TAAAAGATGTAACCTTTAGT
1 TAAAAGATTTAACCTTTAGA
4341 TAAAAGATTTAACCTTT-GAA
1 TAAAAGATTTAACCTTTAG-A
4361 TAAAAGATT
1 TAAAAGATT
4370 GAATATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (20 bp):
TAAAAGATTTAACCTTTAGA
Found at i:4415 original size:50 final size:50
Alignment explanation
Indices: 4352--4710 Score: 384
Period size: 51 Copynumber: 7.2 Consensus size: 50
4342 AAAAGATTTA
* * * *
4352 ACCTTTGAATAAAAGATTGAATATTTAAGTGATTGGTAAAGAAAAATGTC
1 ACCTTTGAGTAAAAGATTGAATTTTTAAGTAATTAGTAAAGAAAAATGTC
* * * * *
4402 ATCTTTGAGTAAAAGATTGAATTTTTAGAGTAATTAGTAAATAAAGATTTA
1 ACCTTTGAGTAAAAGATTGAATTTTTA-AGTAATTAGTAAAGAAAAATGTC
* *
4453 ACCTTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAAGAAAAATGTC
1 ACCTTTGAGTAAAAGATTGAATTTTTAAGTAATTAGTAAAGAAAAATGTC
* * * * ** * *
4503 ATCTTTGAGTAAAAGATTGAATTTTTTAGAATAATTAGTGAATAAAGGTTTA
1 ACCTTTGAGTAAAAGATTGAA-TTTTTA-AGTAATTAGTAAAGAAAAATGTC
* *
4555 ACCTTTGAATAAAAGATTG--TTTTTAAGTAATTGGTAAAGAAAAATGTC
1 ACCTTTGAGTAAAAGATTGAATTTTTAAGTAATTAGTAAAGAAAAATGTC
* * * ** * *
4603 ATCTTTGAGTAAAAGATTGAATCTTTAGAGTAATTAGTAAATAAAGCTTTA
1 ACCTTTGAGTAAAAGATTGAATTTTTA-AGTAATTAGTAAAGAAAAATGTC
4654 ACCTTTGAGTAAAAGATTGAATTTTTAAGTAATTAGT--AGATAAAATGTC
1 ACCTTTGAGTAAAAGATTGAATTTTTAAGTAATTAGTAAAGA-AAAATGTC
*
4703 ACTTTTGA
1 ACCTTTGA
4711 AATAGAAGTG
Statistics
Matches: 249, Mismatches: 53, Indels: 15
0.79 0.17 0.05
Matches are distributed among these distances:
48 34 0.14
49 17 0.07
50 76 0.31
51 90 0.36
52 32 0.13
ACGTcount: A:0.42, C:0.05, G:0.16, T:0.37
Consensus pattern (50 bp):
ACCTTTGAGTAAAAGATTGAATTTTTAAGTAATTAGTAAAGAAAAATGTC
Found at i:4518 original size:101 final size:101
Alignment explanation
Indices: 4343--4707 Score: 596
Period size: 101 Copynumber: 3.6 Consensus size: 101
4333 CCTTTAGTTA
* *
4343 AAAGATTTAACCTTTGAATAAAAGATTGAATATTTAAGTGATTGGTAAAGAAAAATGTCATCTTT
1 AAAGATTTAACCTTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAAGAAAAATGTCATCTTT
4408 GAGTAAAAGATTGAATTTTTAGAGTAATTAGTAAAT
66 GAGTAAAAGATTGAATTTTTAGAGTAATTAGTAAAT
4444 AAAGATTTAACCTTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAAGAAAAATGTCATCTTT
1 AAAGATTTAACCTTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAAGAAAAATGTCATCTTT
* *
4509 GAGTAAAAGATTGAATTTTTTAGAATAATTAGTGAAT
66 GAGTAAAAGATTGAA-TTTTTAGAGTAATTAGTAAAT
*
4546 AAAGGTTTAACCTTTGAATAAAAGATTG--TTTTTAAGTAATTGGTAAAGAAAAATGTCATCTTT
1 AAAGATTTAACCTTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAAGAAAAATGTCATCTTT
*
4609 GAGTAAAAGATTGAATCTTTAGAGTAATTAGTAAAT
66 GAGTAAAAGATTGAATTTTTAGAGTAATTAGTAAAT
* * *
4645 AAAGCTTTAACCTTTGAGTAAAAGATTGAATTTTTAAGTAATTAGT--AGATAAAATGTCA-CTT
1 AAAGATTTAACCTTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAAGA-AAAATGTCATCTT
4707 T
65 T
4708 TGAAATAGAA
Statistics
Matches: 249, Mismatches: 11, Indels: 10
0.92 0.04 0.04
Matches are distributed among these distances:
99 51 0.20
100 59 0.24
101 93 0.37
102 46 0.18
ACGTcount: A:0.42, C:0.05, G:0.16, T:0.37
Consensus pattern (101 bp):
AAAGATTTAACCTTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAAGAAAAATGTCATCTTT
GAGTAAAAGATTGAATTTTTAGAGTAATTAGTAAAT
Found at i:4604 original size:201 final size:200
Alignment explanation
Indices: 4343--4707 Score: 617
Period size: 201 Copynumber: 1.8 Consensus size: 200
4333 CCTTTAGTTA
*
4343 AAAGATTTAACCTTTGAATAAAAGATTGAATATTTAAGTGATTGGTAAAGAAAAATGTCATCTTT
1 AAAGATTTAACCTTTGAATAAAAGATTG-ATATTTAAGTAATTGGTAAAGAAAAATGTCATCTTT
*
4408 GAGTAAAAGATTGAATTTTTAGAGTAATTAGTAAATAAAGATTTAACCTTTGAATAAAAGATTGA
65 GAGTAAAAGATTGAATCTTTAGAGTAATTAGTAAATAAAGATTTAACCTTTGAATAAAAGATTGA
*
4473 ATTTTTAAGTAATTGGTAAAGA-AAAATGTCATCTTTGAGTAAAAGATTGAATTTTTTAGAATAA
130 ATTTTTAAGTAATTAGT--AGATAAAATGTCA-CTTTGAGTAAAAGATTGAATTTTTTAGAATAA
4537 TTAGTGAAT
192 TTAGTGAAT
* *
4546 AAAGGTTTAACCTTTGAATAAAAGATTG-TTTTTAAGTAATTGGTAAAGAAAAATGTCATCTTTG
1 AAAGATTTAACCTTTGAATAAAAGATTGATATTTAAGTAATTGGTAAAGAAAAATGTCATCTTTG
* *
4610 AGTAAAAGATTGAATCTTTAGAGTAATTAGTAAATAAAGCTTTAACCTTTGAGTAAAAGATTGAA
66 AGTAAAAGATTGAATCTTTAGAGTAATTAGTAAATAAAGATTTAACCTTTGAATAAAAGATTGAA
4675 TTTTTAAGTAATTAGTAGATAAAATGTCACTTT
131 TTTTTAAGTAATTAGTAGATAAAATGTCACTTT
4708 TGAAATAGAA
Statistics
Matches: 154, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
199 7 0.05
200 9 0.06
201 111 0.72
203 27 0.18
ACGTcount: A:0.42, C:0.05, G:0.16, T:0.37
Consensus pattern (200 bp):
AAAGATTTAACCTTTGAATAAAAGATTGATATTTAAGTAATTGGTAAAGAAAAATGTCATCTTTG
AGTAAAAGATTGAATCTTTAGAGTAATTAGTAAATAAAGATTTAACCTTTGAATAAAAGATTGAA
TTTTTAAGTAATTAGTAGATAAAATGTCACTTTGAGTAAAAGATTGAATTTTTTAGAATAATTAG
TGAAT
Found at i:5476 original size:47 final size:47
Alignment explanation
Indices: 5422--5627 Score: 342
Period size: 47 Copynumber: 4.4 Consensus size: 47
5412 GTAAAAAGAA
5422 AATCAGTAAATCAGTAAAAAGAGATTAATCGGAGTCAAAGTGATGGT
1 AATCAGTAAATCAGTAAAAAGAGATTAATCGGAGTCAAAGTGATGGT
5469 AATCAGTAAATCAGTAAAAAGAGATTAATCGGAGTCAAAGTGATGGT
1 AATCAGTAAATCAGTAAAAAGAGATTAATCGGAGTCAAAGTGATGGT
5516 AATCAGTAAATCAGTAAAAAGAGATTAATCGGAGTCAAAGTGATGGT
1 AATCAGTAAATCAGTAAAAAGAGATTAATCGGAGTCAAAGTGATGGT
* ** * *
5563 AATCAGTAAATCAGTGAAAAGAGATTAATCAAAAGT-ATAAGTAATAGT
1 AATCAGTAAATCAGTAAAAAGAGATTAATC-GGAGTCA-AAGTGATGGT
5611 AATCAGTAAATCAGTAA
1 AATCAGTAAATCAGTAA
5628 TCAAGTAAAA
Statistics
Matches: 151, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
47 124 0.82
48 27 0.18
ACGTcount: A:0.47, C:0.08, G:0.21, T:0.24
Consensus pattern (47 bp):
AATCAGTAAATCAGTAAAAAGAGATTAATCGGAGTCAAAGTGATGGT
Found at i:5879 original size:35 final size:35
Alignment explanation
Indices: 5836--5981 Score: 161
Period size: 35 Copynumber: 4.2 Consensus size: 35
5826 TTCCAGAGAG
5836 TAATCAGTAAAGGAAAAATGGTAAAGAGTAAAGAA
1 TAATCAGTAAAGGAAAAATGGTAAAGAGTAAAGAA
* * * *
5871 TAATCAGT-AAGGAGTAATTAGTAAA-AGTAAAGAG
1 TAATCAGTAAAGGA-AAAATGGTAAAGAGTAAAGAA
* * * * *
5905 TAATCAGCAAAAGAAGAATGTTAAAAAGTAAAGAA
1 TAATCAGTAAAGGAAAAATGGTAAAGAGTAAAGAA
* **
5940 TAATCAGTAAAGGAAGAATGGTAAAGAGTAAAGGG
1 TAATCAGTAAAGGAAAAATGGTAAAGAGTAAAGAA
5975 TAATCAG
1 TAATCAG
5982 CAAAAAGTAA
Statistics
Matches: 90, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
34 26 0.29
35 64 0.71
ACGTcount: A:0.53, C:0.04, G:0.23, T:0.19
Consensus pattern (35 bp):
TAATCAGTAAAGGAAAAATGGTAAAGAGTAAAGAA
Found at i:5905 original size:69 final size:70
Alignment explanation
Indices: 5832--5986 Score: 208
Period size: 69 Copynumber: 2.2 Consensus size: 70
5822 TAAATTCCAG
* * *
5832 AGAGTAATCAGTAAAGGAAAAATGGTAAAGAGTAAAGAATAATCAGT-AAGG-AGTAATTAGTAA
1 AGAGTAATCAGCAAAAGAAAAATGGTAAAAAGTAAAGAATAATCAGTAAAGGAAG-AA-TAGTAA
5895 A-AGTAA
64 AGAGTAA
* * *
5901 AGAGTAATCAGCAAAAGAAGAATGTTAAAAAGTAAAGAATAATCAGTAAAGGAAGAATGGTAAAG
1 AGAGTAATCAGCAAAAGAAAAATGGTAAAAAGTAAAGAATAATCAGTAAAGGAAGAATAGTAAAG
5966 AGTAA
66 AGTAA
*
5971 AGGGTAATCAGCAAAA
1 AGAGTAATCAGCAAAA
5987 AGTAAAAAGA
Statistics
Matches: 76, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
69 48 0.63
70 26 0.34
71 2 0.03
ACGTcount: A:0.54, C:0.05, G:0.23, T:0.18
Consensus pattern (70 bp):
AGAGTAATCAGCAAAAGAAAAATGGTAAAAAGTAAAGAATAATCAGTAAAGGAAGAATAGTAAAG
AGTAA
Found at i:5916 original size:20 final size:20
Alignment explanation
Indices: 5876--5917 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
5866 AAGAATAATC
* * *
5876 AGTAAGGAGTAATTAGTAAA
1 AGTAAAGAGTAATCAGCAAA
5896 AGTAAAGAGTAATCAGCAAA
1 AGTAAAGAGTAATCAGCAAA
5916 AG
1 AG
5918 AAGAATGTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.52, C:0.05, G:0.24, T:0.19
Consensus pattern (20 bp):
AGTAAAGAGTAATCAGCAAA
Found at i:6288 original size:21 final size:22
Alignment explanation
Indices: 6220--6314 Score: 78
Period size: 21 Copynumber: 4.5 Consensus size: 22
6210 TAGTAAAATG
*
6220 GTAATCAGTAAAAAGT-AAGAA
1 GTAATCAGTACAAAGTAAAGAA
6241 GGTAATCA--ACAAGAGTAAA-ATA
1 -GTAATCAGTACAA-AGTAAAGA-A
6263 GTAATCAGTACAAAGTAAAGAA
1 GTAATCAGTACAAAGTAAAGAA
* *
6285 -TAATCAGTA-AAA-TAATGATG
1 GTAATCAGTACAAAGTAAAGA-A
6305 GTAATCAGTA
1 GTAATCAGTA
6315 ATTCAGTAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 17
0.76 0.04 0.21
Matches are distributed among these distances:
19 5 0.08
20 6 0.10
21 29 0.47
22 17 0.27
23 5 0.08
ACGTcount: A:0.53, C:0.07, G:0.18, T:0.22
Consensus pattern (22 bp):
GTAATCAGTACAAAGTAAAGAA
Found at i:9045 original size:15 final size:16
Alignment explanation
Indices: 9025--9058 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
9015 GATTGATTTC
*
9025 TTAGTTA-ATTTACTT
1 TTAGTTAGATTTAATT
9040 TTAGTTAGATTTAATT
1 TTAGTTAGATTTAATT
9056 TTA
1 TTA
9059 ATTCTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59
Consensus pattern (16 bp):
TTAGTTAGATTTAATT
Found at i:12002 original size:15 final size:17
Alignment explanation
Indices: 11971--12003 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
11961 CATAAGTCTC
11971 ACATAAGATCAAAATAA
1 ACATAAGATCAAAATAA
11988 ACATAAGA-C-AAATAA
1 ACATAAGATCAAAATAA
12003 A
1 A
12004 AATGCATGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 1 0.06
17 8 0.50
ACGTcount: A:0.67, C:0.12, G:0.06, T:0.15
Consensus pattern (17 bp):
ACATAAGATCAAAATAA
Found at i:15032 original size:20 final size:21
Alignment explanation
Indices: 15004--15042 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
14994 TTATAGCTAT
*
15004 TTTTCTATAC-TTTTTACCAC
1 TTTTATATACATTTTTACCAC
15024 TTTTATATACATTTTTACC
1 TTTTATATACATTTTTACC
15043 GTATTTTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.23, C:0.21, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTTATATACATTTTTACCAC
Found at i:24305 original size:27 final size:27
Alignment explanation
Indices: 24275--24350 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
24265 ATTAGAGTCG
* *
24275 CCCAAGGGTATTTTGGTCATTTTTGCA
1 CCCAAGGGCATTTTGGTCATTTTGGCA
*
24302 CCCAGGGGCATTTTGGTCATTTTGGCA
1 CCCAAGGGCATTTTGGTCATTTTGGCA
* *
24329 CTCAAGGGCATTTTAGTCATTT
1 CCCAAGGGCATTTTGGTCATTT
24351 ATTTTTCTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.38
Consensus pattern (27 bp):
CCCAAGGGCATTTTGGTCATTTTGGCA
Done.