Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012660.1 Corchorus capsularis cultivar CVL-1 contig12681, 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: 11044
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Found at i:508 original size:12 final size:13
Alignment explanation
Indices: 483--516 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
473 ATAATTATTG
483 TTTGCTTTATTAA
1 TTTGCTTTATTAA
496 TTTGCTTTA-TAA
1 TTTGCTTTATTAA
*
508 TCTGCTTTA
1 TTTGCTTTA
517 GATTTAGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.59
Consensus pattern (13 bp):
TTTGCTTTATTAA
Found at i:524 original size:6 final size:6
Alignment explanation
Indices: 513--539 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
503 TATAATCTGC
513 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
540 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:1410 original size:18 final size:18
Alignment explanation
Indices: 1389--1444 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 18
1379 ATAAAAGTAA
1389 ATATATATTTATTATAAT
1 ATATATATTTATTATAAT
1407 ATATATA---ATTATAAT
1 ATATATATTTATTATAAT
1422 -TATA-ATTTA-TATAAT
1 ATATATATTTATTATAAT
*
1437 AAATATAT
1 ATATATAT
1445 ATAAAGTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 11
0.73 0.02 0.25
Matches are distributed among these distances:
13 1 0.03
14 4 0.12
15 14 0.44
16 4 0.12
17 2 0.06
18 7 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATATATTTATTATAAT
Found at i:1419 original size:15 final size:15
Alignment explanation
Indices: 1388--1514 Score: 56
Period size: 15 Copynumber: 8.5 Consensus size: 15
1378 TATAAAAGTA
*
1388 AATATATATTTATTAT
1 AATATATA-TAATTAT
1404 AATATATATAATTAT
1 AATATATATAATTAT
* *
1419 AATTATAATTTATATAAT
1 AA-TAT-ATATA-ATTAT
1437 AAATATATATAA--AGT
1 -AATATATATAATTA-T
1452 AA-ATATATAATTACT
1 AATATATATAATTA-T
*
1467 -TTATATAT-ATT-T
1 AATATATATAATTAT
* *
1479 --TATATTTAAGGTA-
1 AATATATATAA-TTAT
*
1492 AATACATATAATTAT
1 AATATATATAATTAT
1507 AATATATA
1 AATATATA
1515 ATTTATATTT
Statistics
Matches: 85, Mismatches: 12, Indels: 29
0.67 0.10 0.23
Matches are distributed among these distances:
11 6 0.07
12 2 0.02
13 9 0.11
14 8 0.09
15 31 0.36
16 12 0.14
17 8 0.09
18 7 0.08
19 2 0.02
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (15 bp):
AATATATATAATTAT
Found at i:1483 original size:39 final size:38
Alignment explanation
Indices: 1361--1522 Score: 109
Period size: 39 Copynumber: 4.1 Consensus size: 38
1351 TATTTATTTA
* * * *
1361 TATATATAAAATAAAGTTATAAAAGTA-AATATAT-ATT
1 TATATATAAAGTAAA-TAATATAATTATAATATATAATT
* *
1398 TAT-TATAATA-TATATAATTATAATTATAATTTATATAATAAA
1 TATATATAA-AGTAAATAA-TATAATTATAA--TATATAAT--T
* *
1440 TATATATAAAGTAAAT-ATATAATTACTTTATATATATTT
1 TATATATAAAGTAAATAATATAATTA--TAATATATAATT
* *
1479 TATATTTAAGGTAAATACATATAATTATAATATATAATT
1 TATATATAAAGTAAATA-ATATAATTATAATATATAATT
1518 TATAT
1 TATAT
1523 TTATTATTTT
Statistics
Matches: 98, Mismatches: 13, Indels: 26
0.72 0.09 0.19
Matches are distributed among these distances:
35 2 0.02
36 14 0.14
37 6 0.06
39 34 0.35
40 2 0.02
41 24 0.24
42 5 0.05
43 11 0.11
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (38 bp):
TATATATAAAGTAAATAATATAATTATAATATATAATT
Found at i:1522 original size:11 final size:13
Alignment explanation
Indices: 1407--1517 Score: 51
Period size: 13 Copynumber: 8.8 Consensus size: 13
1397 TTATTATAAT
1407 ATATATAATTATA
1 ATATATAATTATA
1420 AT-TATAATT-T-
1 ATATATAATTATA
*
1430 ATATAATAAATAT-
1 ATAT-ATAATTATA
*
1443 ATATA-AAGTA-A
1 ATATATAATTATA
1454 ATATATAATTACT-
1 ATATATAATTA-TA
* *
1467 TTATATATATT-TT
1 ATATATA-ATTATA
* *
1480 ATATTTAAGGTA-A
1 ATATATAA-TTATA
1493 ATACATATAATTATA
1 AT--ATATAATTATA
1508 ATATATAATT
1 ATATATAATT
1518 TATATTTATT
Statistics
Matches: 74, Mismatches: 10, Indels: 28
0.66 0.09 0.25
Matches are distributed among these distances:
10 2 0.03
11 11 0.15
12 19 0.26
13 29 0.39
14 5 0.07
15 8 0.11
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.46
Consensus pattern (13 bp):
ATATATAATTATA
Found at i:4090 original size:17 final size:17
Alignment explanation
Indices: 4065--4097 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4055 GAAAGTGAAC
4065 CCGAACCCGAACCCGAT
1 CCGAACCCGAACCCGAT
*
4082 CCGAGCCCGAACCCGA
1 CCGAACCCGAACCCGA
4098 AAATACCCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.48, G:0.21, T:0.03
Consensus pattern (17 bp):
CCGAACCCGAACCCGAT
Found at i:4108 original size:16 final size:16
Alignment explanation
Indices: 4087--4161 Score: 143
Period size: 16 Copynumber: 4.8 Consensus size: 16
4077 CCGATCCGAG
4087 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
4103 CCCGAACCCG-AAATA
1 CCCGAACCCGAAAATA
4118 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
4134 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
4150 CCCGAACCCGAA
1 CCCGAACCCGAA
4162 GTATCCGAAC
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
15 15 0.26
16 43 0.74
ACGTcount: A:0.41, C:0.40, G:0.13, T:0.05
Consensus pattern (16 bp):
CCCGAACCCGAAAATA
Found at i:4125 original size:31 final size:32
Alignment explanation
Indices: 4087--4161 Score: 143
Period size: 31 Copynumber: 2.4 Consensus size: 32
4077 CCGATCCGAG
4087 CCCGAACCCGAAAATACCCGAACCCG-AAATA
1 CCCGAACCCGAAAATACCCGAACCCGAAAATA
4118 CCCGAACCCGAAAATACCCGAACCCGAAAATA
1 CCCGAACCCGAAAATACCCGAACCCGAAAATA
4150 CCCGAACCCGAA
1 CCCGAACCCGAA
4162 GTATCCGAAC
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
31 26 0.60
32 17 0.40
ACGTcount: A:0.41, C:0.40, G:0.13, T:0.05
Consensus pattern (32 bp):
CCCGAACCCGAAAATACCCGAACCCGAAAATA
Found at i:4145 original size:6 final size:6
Alignment explanation
Indices: 4061--4098 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
4051 TATCGAAAGT
* *
4061 GAACCC GAACCC GAACCC G-ATCC GAGCCC GAACCC GAA
1 GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC GAA
4099 AATACCCGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.32, C:0.45, G:0.21, T:0.03
Consensus pattern (6 bp):
GAACCC
Found at i:8193 original size:22 final size:22
Alignment explanation
Indices: 8165--8212 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
8155 GTTGTGGCTT
8165 TAAGCAGCTTCTGCTTATAAGC
1 TAAGCAGCTTCTGCTTATAAGC
8187 TAAGCAGCTTCTGCTTATAAGC
1 TAAGCAGCTTCTGCTTATAAGC
8209 TAAG
1 TAAG
8213 TTTAAAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (22 bp):
TAAGCAGCTTCTGCTTATAAGC
Found at i:8742 original size:181 final size:182
Alignment explanation
Indices: 8438--8800 Score: 597
Period size: 181 Copynumber: 2.0 Consensus size: 182
8428 TGAATTCAAT
* * *
8438 TAAACCTACTATTAATTTTATGTATAAGGTCCTTATTGAGTGCCACTTGACATTTGGTTTCTTTG
1 TAAACCTACTATTAATTTTATGTACAAGATCCTCATTGAGTGCCACTTGACATTTGGTTTCTTTG
*
8503 ACAAGTGTCAATATTTAATTTTCTAATTTTTGTTTATTATATTTGTATTCATTTTAGTTTGGAAA
66 ACAAGTGTCAATAATTAATTTTCTAATTTTTGTTTATTATATTTGTATTCATTTTAGTTTGGAAA
*
8568 AATTAAAAGATATTCATCCCCTTTCC-TATATAAAATAAATTATCAAATAAC
131 AATTAAAAGACATTCATCCCCTTTCCATATATAAAATAAATTATCAAATAAC
*
8619 TAAACCTACTATTAATTTTATGTACAATATCCTCATTGAGTGCCACTTG-CAATTTGGTTTCTTT
1 TAAACCTACTATTAATTTTATGTACAAGATCCTCATTGAGTGCCACTTGAC-ATTTGGTTTCTTT
*
8683 TACAAGTGTCAATAATTAATTTTCTAATGTTTTGTTTATTATATTTGTATTCA-TTTAGTTTGGA
65 GACAAGTGTCAATAATTAATTTTCTAAT-TTTTGTTTATTATATTTGTATTCATTTTAGTTTGGA
* *
8747 AACATTAAAAGACATTCATCCCCTTTCCTATATATAAAATAAATTATTAAATAA
129 AAAATTAAAAGACATTCATCCCCTTTCC-ATATATAAAATAAATTATCAAATAA
8801 TTATAAATTA
Statistics
Matches: 169, Mismatches: 9, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
180 1 0.01
181 121 0.72
182 24 0.14
183 23 0.14
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.44
Consensus pattern (182 bp):
TAAACCTACTATTAATTTTATGTACAAGATCCTCATTGAGTGCCACTTGACATTTGGTTTCTTTG
ACAAGTGTCAATAATTAATTTTCTAATTTTTGTTTATTATATTTGTATTCATTTTAGTTTGGAAA
AATTAAAAGACATTCATCCCCTTTCCATATATAAAATAAATTATCAAATAAC
Found at i:8826 original size:11 final size:11
Alignment explanation
Indices: 8783--8820 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
8773 CCTATATATA
*
8783 AAATAAATTATT
1 AAATTAATTA-T
8795 AAA-TAATTAT
1 AAATTAATTAT
8805 AAATTAATTAT
1 AAATTAATTAT
8816 AAATT
1 AAATT
8821 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 4 0.17
11 17 0.71
12 3 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
AAATTAATTAT
Done.