Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013177.1 Corchorus capsularis cultivar CVL-1 contig13198, 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: 51557
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2249 original size:22 final size:22
Alignment explanation
Indices: 2211--2258 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2201 TCTTTTAAGA
* *
2211 TTTTTTTGTATTTATAATTTT-
1 TTTTTTTCTATTAATAATTTTC
2232 TTTTCTTTCTATTAATAATTTTC
1 TTTT-TTTCTATTAATAATTTTC
2255 TTTT
1 TTTT
2259 AAAAATTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 4 0.17
22 15 0.65
23 4 0.17
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.73
Consensus pattern (22 bp):
TTTTTTTCTATTAATAATTTTC
Found at i:2544 original size:11 final size:10
Alignment explanation
Indices: 2517--2551 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
2507 TTACCTTGAT
2517 AAACGAACAC
1 AAACGAACAC
2527 AAACGAACAC
1 AAACGAACAC
*
2537 TTAACGAACAC
1 -AAACGAACAC
2548 AAAC
1 AAAC
2552 ACGAACCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.57, C:0.29, G:0.09, T:0.06
Consensus pattern (10 bp):
AAACGAACAC
Found at i:8323 original size:1 final size:1
Alignment explanation
Indices: 8319--8354 Score: 72
Period size: 1 Copynumber: 36.0 Consensus size: 1
8309 TAACTAAATT
8319 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
8355 CTAGTATTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:12003 original size:13 final size:13
Alignment explanation
Indices: 11981--12020 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
11971 CAGAGAATAT
11981 TATCAACAGAAGA
1 TATCAACAGAAGA
*
11994 TATCATCAGAAGA
1 TATCAACAGAAGA
* *
12007 TTTCAACTGAAGA
1 TATCAACAGAAGA
12020 T
1 T
12021 TATCTGGAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (13 bp):
TATCAACAGAAGA
Found at i:12460 original size:41 final size:41
Alignment explanation
Indices: 12403--12600 Score: 195
Period size: 41 Copynumber: 4.8 Consensus size: 41
12393 AATAATATTG
* * *
12403 AAAATTACCTTTGACACCAAAAGTTGTCACTTTGGTAAACT
1 AAAATTACCTCTGACACCAGAAGTTGTCACTTTGGTAAATT
* * *
12444 AAAATTA-CTGCTGACACTAGAAGCTGTCACCTTGGTAAATT
1 AAAATTACCT-CTGACACCAGAAGTTGTCACTTTGGTAAATT
12485 AAAATTACCTCTGACACCAGAAGTTGTCACTTTGGTAAATT
1 AAAATTACCTCTGACACCAGAAGTTGTCACTTTGGTAAATT
** * * * *** *
12526 AAAATTATTTTTGACACCATAAG-TGTTACTCCAGTAATTT
1 AAAATTACCTCTGACACCAGAAGTTGTCACTTTGGTAAATT
* *
12566 ATAATTACCGT-TGACACCAGAAATTGTCACATTTG
1 AAAATTACC-TCTGACACCAGAAGTTGTCAC-TTTG
12601 AATTACCACG
Statistics
Matches: 125, Mismatches: 27, Indels: 9
0.78 0.17 0.06
Matches are distributed among these distances:
40 30 0.24
41 92 0.74
42 3 0.02
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (41 bp):
AAAATTACCTCTGACACCAGAAGTTGTCACTTTGGTAAATT
Found at i:21598 original size:15 final size:15
Alignment explanation
Indices: 21578--21607 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
21568 TATAATTCCC
21578 GGGCCTTATAATGTA
1 GGGCCTTATAATGTA
21593 GGGCCTTATAATGTA
1 GGGCCTTATAATGTA
21608 ACACCTTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (15 bp):
GGGCCTTATAATGTA
Found at i:26534 original size:4 final size:4
Alignment explanation
Indices: 26527--26561 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
26517 TTCTTGCTTG
26527 GTTT GTTT GTTT GTTT GTTT GTTT GTTT GTTT GTT
1 GTTT GTTT GTTT GTTT GTTT GTTT GTTT GTTT GTT
26562 CCTTCTTCAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.26, T:0.74
Consensus pattern (4 bp):
GTTT
Found at i:30171 original size:1 final size:1
Alignment explanation
Indices: 30165--30194 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
30155 ATACTTAGAC
*
30165 AAAAAAAAAAAAAAAAAAAAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
30195 GCATAATTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:33038 original size:1 final size:1
Alignment explanation
Indices: 33032--33056 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
33022 ATCTTTCTTC
33032 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
33057 CCCTAACAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:37390 original size:2 final size:2
Alignment explanation
Indices: 37380--37418 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
37370 ATTTTTTTTA
37380 AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
37419 CATTTTGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 32 0.91
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:38342 original size:18 final size:18
Alignment explanation
Indices: 38319--38360 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
38309 GATTATGGGA
38319 TCCTGGGAATCCATCAGG
1 TCCTGGGAATCCATCAGG
* *
38337 TCCTGGGAGTCCATGAGG
1 TCCTGGGAATCCATCAGG
38355 TCCTGG
1 TCCTGG
38361 TTGATTTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.26, G:0.33, T:0.24
Consensus pattern (18 bp):
TCCTGGGAATCCATCAGG
Found at i:39540 original size:12 final size:12
Alignment explanation
Indices: 39523--39549 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
39513 CACCCATCGG
39523 ACCCCCAAGGCC
1 ACCCCCAAGGCC
39535 ACCCCCAAGGCC
1 ACCCCCAAGGCC
39547 ACC
1 ACC
39550 GTAACCACCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.59, G:0.15, T:0.00
Consensus pattern (12 bp):
ACCCCCAAGGCC
Found at i:39578 original size:15 final size:15
Alignment explanation
Indices: 39554--39586 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
39544 GCCACCGTAA
*
39554 CCACCCCCATACATT
1 CCACCACCATACATT
39569 CCACCACCATACATT
1 CCACCACCATACATT
39584 CCA
1 CCA
39587 GAATTCCCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.52, G:0.00, T:0.18
Consensus pattern (15 bp):
CCACCACCATACATT
Found at i:40649 original size:6 final size:6
Alignment explanation
Indices: 40638--40670 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
40628 TTAATATTTC
40638 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATT
40671 AAAAGCTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
ATTTTT
Found at i:43588 original size:18 final size:18
Alignment explanation
Indices: 43567--43618 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 18
43557 GAGAGAGGCT
43567 GAGCTTCAGAGGGAGAGA
1 GAGCTTCAGAGGGAGAGA
*
43585 GAGCTT--TA--GAGAGA
1 GAGCTTCAGAGGGAGAGA
43599 G-GC-TCAGAGGGAGAGA
1 GAGCTTCAGAGGGAGAGA
43615 GAGC
1 GAGC
43619 GAGAGAGGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 11
0.68 0.05 0.28
Matches are distributed among these distances:
12 1 0.04
13 2 0.07
14 8 0.30
16 8 0.30
17 2 0.07
18 6 0.22
ACGTcount: A:0.33, C:0.12, G:0.44, T:0.12
Consensus pattern (18 bp):
GAGCTTCAGAGGGAGAGA
Found at i:43622 original size:26 final size:27
Alignment explanation
Indices: 43572--43632 Score: 88
Period size: 30 Copynumber: 2.2 Consensus size: 27
43562 AGGCTGAGCT
43572 TCAGAGGGAGAGAGAGCTTTAGAGAGAGGC
1 TCAGAGGGAGAGAGAGC--T-GAGAGAGGC
43602 TCAGAGGGAGAGAGAGC-GAGAGAGGC
1 TCAGAGGGAGAGAGAGCTGAGAGAGGC
43628 TCAGA
1 TCAGA
43633 TTCTGAGGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
26 14 0.45
30 17 0.55
ACGTcount: A:0.34, C:0.11, G:0.44, T:0.10
Consensus pattern (27 bp):
TCAGAGGGAGAGAGAGCTGAGAGAGGC
Found at i:43905 original size:14 final size:13
Alignment explanation
Indices: 43882--43921 Score: 71
Period size: 13 Copynumber: 3.0 Consensus size: 13
43872 TATTATTAGA
43882 TTAGTAAATTAAT
1 TTAGTAAATTAAT
43895 TTAGTTAAATTAAT
1 TTAG-TAAATTAAT
43909 TTAGTAAATTAAT
1 TTAGTAAATTAAT
43922 CGACATCAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 13 0.50
14 13 0.50
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (13 bp):
TTAGTAAATTAAT
Found at i:44385 original size:9 final size:9
Alignment explanation
Indices: 44372--44406 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
44362 ATATTACTCT
*
44372 TAACATTTT
1 TAACATTTA
44381 TAACATTTA
1 TAACATTTA
*
44390 TAACATGTA
1 TAACATTTA
44399 TAACATTT
1 TAACATTT
44407 GTATTTGTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.40, C:0.11, G:0.03, T:0.46
Consensus pattern (9 bp):
TAACATTTA
Found at i:44466 original size:9 final size:9
Alignment explanation
Indices: 44452--44492 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
44442 GTCAATGGAT
*
44452 ACATTTTTA
1 ACATTTATA
*
44461 ACATTTAGA
1 ACATTTATA
44470 ACATTTATA
1 ACATTTATA
*
44479 ACATGTATA
1 ACATTTATA
44488 ACATT
1 ACATT
44493 ATTGTACGGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.41
Consensus pattern (9 bp):
ACATTTATA
Found at i:48372 original size:25 final size:26
Alignment explanation
Indices: 48348--48395 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
48338 TTAATGTTTA
48348 AAAT-TTATTTT-TGTTAAAAAATTT
1 AAATATTATTTTATGTTAAAAAATTT
* *
48372 AATTATTATTTTATTTTAAAAAAT
1 AAATATTATTTTATGTTAAAAAAT
48396 AAATATGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 3 0.15
25 7 0.35
26 10 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (26 bp):
AAATATTATTTTATGTTAAAAAATTT
Found at i:49811 original size:33 final size:33
Alignment explanation
Indices: 49774--49838 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
49764 AATTATTATG
49774 TTCATAAGTATGCATCAATCACTTAAATTAAAA
1 TTCATAAGTATGCATCAATCACTTAAATTAAAA
49807 TTCATAAGTATGCATCAATCACTTAAATTAAA
1 TTCATAAGTATGCATCAATCACTTAAATTAAA
49839 TGCTTGGGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.45, C:0.15, G:0.06, T:0.34
Consensus pattern (33 bp):
TTCATAAGTATGCATCAATCACTTAAATTAAAA
Found at i:50094 original size:2 final size:2
Alignment explanation
Indices: 50087--50141 Score: 52
Period size: 2 Copynumber: 30.5 Consensus size: 2
50077 AAATGGAAGA
50087 AT AT AT AT AT AT AT AT AT AT -T A- AT -T AT AT A- AT AT ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
50126 -T AT -T AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT A
50142 CTATTATTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 16
0.74 0.00 0.26
Matches are distributed among these distances:
1 7 0.16
2 36 0.80
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:50116 original size:15 final size:14
Alignment explanation
Indices: 50087--50152 Score: 52
Period size: 12 Copynumber: 4.9 Consensus size: 14
50077 AAATGGAAGA
50087 ATATATA-TA-TAT
1 ATATATATTATTAT
50099 ATATATATTAATTAT
1 ATATATATT-ATTAT
*
50114 ATAATATACTATTAT
1 AT-ATATATTATTAT
*
50129 -TATATA-TAATAT
1 ATATATATTATTAT
50141 ACTAT-TATTATT
1 A-TATATATTATT
50153 TGCTAGCTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
12 12 0.27
13 8 0.18
14 8 0.18
15 10 0.23
16 6 0.14
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (14 bp):
ATATATATTATTAT
Found at i:50134 original size:20 final size:20
Alignment explanation
Indices: 50090--50151 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
50080 TGGAAGAATA
*
50090 TATATATATATATA-TATTAA
1 TATATATA-ATATACTATTAT
50110 T-TATATAATATACTATTAT
1 TATATATAATATACTATTAT
50129 TATATATAATATACTATTAT
1 TATATATAATATACTATTAT
50149 TAT
1 TAT
50152 TTGCTAGCTA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
18 5 0.13
19 12 0.31
20 22 0.56
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (20 bp):
TATATATAATATACTATTAT
Found at i:50707 original size:3 final size:3
Alignment explanation
Indices: 50699--50723 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
50689 TACATCTTTA
50699 ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC A
50724 AACCAGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Done.