Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013792.1 Corchorus capsularis cultivar CVL-1 contig13813, 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: 21502
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.34
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--66 Score: 79
Period size: 2 Copynumber: 35.5 Consensus size: 2
* *
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43 AT A- AT A- AT A- AT AT A- AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
67 ATTGATTAGA
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
1 5 0.09
2 50 0.91
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:3127 original size:3 final size:3
Alignment explanation
Indices: 3119--3149 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
3109 TAACTACATA
3119 TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3150 CATATATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:5567 original size:16 final size:16
Alignment explanation
Indices: 5542--5598 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
5532 TCCCGAACCT
*
5542 GAACCCGAAATTACCC
1 GAACCCGAAAATACCC
*
5558 GAACCTGAAAATACCC
1 GAACCCGAAAATACCC
* *
5574 GAACTCGAGACA-ACCC
1 GAACCCGA-AAATACCC
5590 GAACCCGAA
1 GAACCCGAA
5599 CCCGCCTGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
15 1 0.03
16 31 0.91
17 2 0.06
ACGTcount: A:0.40, C:0.35, G:0.16, T:0.09
Consensus pattern (16 bp):
GAACCCGAAAATACCC
Found at i:5596 original size:6 final size:6
Alignment explanation
Indices: 5585--5630 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
5575 AACTCGAGAC
* *
5585 AACCCG AACCCG AACCCG --CCTG AACCCG AACCCG -ACCCG AGCCCG
1 AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG
5630 A
1 A
5631 GATTAAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
4 3 0.09
5 5 0.15
6 26 0.76
ACGTcount: A:0.28, C:0.50, G:0.20, T:0.02
Consensus pattern (6 bp):
AACCCG
Found at i:5870 original size:31 final size:31
Alignment explanation
Indices: 5799--5870 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 31
5789 GTCCATTAGC
*
5799 TTTTAATTTGTTTAATTTAAGACTTGCATTT
1 TTTTAATTTGTTTAATTTAAGACTTGAATTT
** * * *
5830 TGATGATTTGTTTGATTTAATACTT-AATTT
1 TTTTAATTTGTTTAATTTAAGACTTGAATTT
5860 GTTTTAATTTG
1 -TTTTAATTTG
5871 CTACAATTTA
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.25, C:0.04, G:0.12, T:0.58
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGACTTGAATTT
Found at i:6383 original size:6 final size:6
Alignment explanation
Indices: 6372--6460 Score: 63
Period size: 6 Copynumber: 13.2 Consensus size: 6
6362 TACTCTAAGT
*
6372 GAACCC GAACCC G-ACCC GGACCC GAACCC GAACCC GAAAATACCC GAACCC
1 GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC G---A-ACCC GAACCC
6423 GAAAATACCC GAACCC GAAGTACCC GAACCC GAACCC G
1 G---A-ACCC GAACCC G-A--ACCC GAACCC GAACCC G
6461 CCCGATTGCC
Statistics
Matches: 70, Mismatches: 1, Indels: 24
0.74 0.01 0.25
Matches are distributed among these distances:
5 5 0.07
6 44 0.63
7 3 0.04
8 1 0.01
9 7 0.10
10 10 0.14
ACGTcount: A:0.35, C:0.44, G:0.18, T:0.03
Consensus pattern (6 bp):
GAACCC
Found at i:6396 original size:17 final size:18
Alignment explanation
Indices: 6374--6407 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
6364 CTCTAAGTGA
6374 ACCCGAACCCG-ACCCGG
1 ACCCGAACCCGAACCCGG
6391 ACCCGAACCCGAACCCG
1 ACCCGAACCCGAACCCG
6408 AAAATACCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.26, C:0.53, G:0.21, T:0.00
Consensus pattern (18 bp):
ACCCGAACCCGAACCCGG
Found at i:6448 original size:15 final size:16
Alignment explanation
Indices: 6397--6456 Score: 104
Period size: 16 Copynumber: 3.8 Consensus size: 16
6387 CCGGACCCGA
6397 ACCCGAACCCGAAAAT
1 ACCCGAACCCGAAAAT
6413 ACCCGAACCCGAAAAT
1 ACCCGAACCCGAAAAT
*
6429 ACCCGAACCCG-AAGT
1 ACCCGAACCCGAAAAT
6444 ACCCGAACCCGAA
1 ACCCGAACCCGAA
6457 CCCGCCCGAT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
15 14 0.33
16 28 0.67
ACGTcount: A:0.40, C:0.40, G:0.15, T:0.05
Consensus pattern (16 bp):
ACCCGAACCCGAAAAT
Found at i:6465 original size:31 final size:32
Alignment explanation
Indices: 6380--6465 Score: 86
Period size: 31 Copynumber: 2.7 Consensus size: 32
6370 GTGAACCCGA
*
6380 ACCCG-ACCCGGACCCGAACCCGAACCCGAAAAT
1 ACCCGAACCCGAACCCG--CCCGAACCCGAAAAT
**** *
6413 ACCCGAACCCGAAAATACCCGAACCCG-AAGT
1 ACCCGAACCCGAACCCGCCCGAACCCGAAAAT
6444 ACCCGAACCCGAACCCGCCCGA
1 ACCCGAACCCGAACCCGCCCGA
6466 TTGCCAGTTC
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
31 21 0.50
32 10 0.24
33 5 0.12
34 6 0.14
ACGTcount: A:0.34, C:0.45, G:0.17, T:0.03
Consensus pattern (32 bp):
ACCCGAACCCGAACCCGCCCGAACCCGAAAAT
Found at i:7895 original size:14 final size:13
Alignment explanation
Indices: 7872--7901 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
7862 TTTCTGATTT
7872 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
7885 TTTTTCATTTTTTC
1 TTTTTC-TTTTTTC
7899 TTT
1 TTT
7902 CCTTCTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:12473 original size:6 final size:6
Alignment explanation
Indices: 12462--12497 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
12452 TCATTCTCTT
12462 TTTTTC TTTTTC -TTTT- TTTTTC -TTTTC TTTTTC TTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTT
12498 CACTTTTCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
5 13 0.48
6 14 0.52
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTC
Found at i:12474 original size:16 final size:16
Alignment explanation
Indices: 12455--12487 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
12445 CTTTTCTTCA
12455 TTCTCTTTTTTTCTTT
1 TTCTCTTTTTTTCTTT
*
12471 TTCTTTTTTTTTCTTT
1 TTCTCTTTTTTTCTTT
12487 T
1 T
12488 CTTTTTCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (16 bp):
TTCTCTTTTTTTCTTT
Found at i:12478 original size:14 final size:14
Alignment explanation
Indices: 12444--12493 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
12434 CCCTAGAGCC
* * *
12444 TCTTTTCTTCATTC
1 TCTTTTTTTCTTTT
12458 TCTTTTTTTCTTTT
1 TCTTTTTTTCTTTT
*
12472 TCTTTTTTTTTCTTT
1 TCTTTTTTTCT-TTT
12487 TCTTTTT
1 TCTTTTT
12494 CTTTCACTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 21 0.68
15 10 0.32
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (14 bp):
TCTTTTTTTCTTTT
Found at i:12478 original size:15 final size:16
Alignment explanation
Indices: 12455--12505 Score: 61
Period size: 15 Copynumber: 3.2 Consensus size: 16
12445 CTTTTCTTCA
12455 TTCTCTTTTTTTCT-TT
1 TTCT-TTTTTTTCTCTT
12471 TTCTTTTTTTT-TCTT
1 TTCTTTTTTTTCTCTT
*
12486 TTCTTTTTCTTTCACTT
1 TTCTTTTT-TTTCTCTT
12503 TTC
1 TTC
12506 ACATGCACTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
14 1 0.03
15 17 0.55
16 7 0.23
17 6 0.19
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (16 bp):
TTCTTTTTTTTCTCTT
Found at i:12493 original size:16 final size:16
Alignment explanation
Indices: 12455--12498 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
12445 CTTTTCTTCA
*
12455 TTCTCTTTTTTTCTTT
1 TTCTTTTTTTTTCTTT
12471 TTCTTTTTTTTTC-TT
1 TTCTTTTTTTTTCTTT
*
12486 TTCTTTTTCTTTC
1 TTCTTTTTTTTTC
12499 ACTTTTCACA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 14 0.54
16 12 0.46
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (16 bp):
TTCTTTTTTTTTCTTT
Found at i:12498 original size:10 final size:10
Alignment explanation
Indices: 12455--12498 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
12445 CTTTTCTTCA
12455 TTCTCTTTT-T
1 TTCT-TTTTCT
12465 TTCTTTTTCT
1 TTCTTTTTCT
*
12475 TTTTTTTTCTT
1 TTCTTTTTC-T
12486 TTCTTTTTCT
1 TTCTTTTTCT
12496 TTC
1 TTC
12499 ACTTTTCACA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 4 0.13
10 17 0.57
11 9 0.30
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (10 bp):
TTCTTTTTCT
Found at i:13356 original size:44 final size:44
Alignment explanation
Indices: 13218--13404 Score: 220
Period size: 44 Copynumber: 4.2 Consensus size: 44
13208 CACAACTTTG
* * *
13218 GAAAATCC-TTTTATTAAAACCTTTTGAAAACCATGGCTATTTTT
1 GAAAA-CCATTTTATCAAAACCTTTTGAAAACCATGACTCTTTTT
* *
13262 GAAAGAAGCC-TTTTATCAAAA-CTTTTGAAAACTATGAATC-TTTT
1 G-AA-AA-CCATTTTATCAAAACCTTTTGAAAACCATGACTCTTTTT
*
13306 GAAAAACCATTTTATCAAAACCTTTTGAAATCCATGACTCTTTTT
1 G-AAAACCATTTTATCAAAACCTTTTGAAAACCATGACTCTTTTT
* *
13351 GAAAACTATTTTATCAAAACCTTTTGAAATCCATGACTCTTTTT
1 GAAAACCATTTTATCAAAACCTTTTGAAAACCATGACTCTTTTT
13395 CGAAAACCAT
1 -GAAAACCAT
13405 CATTGCTTCT
Statistics
Matches: 126, Mismatches: 11, Indels: 11
0.85 0.07 0.07
Matches are distributed among these distances:
42 2 0.02
43 13 0.10
44 67 0.53
45 30 0.24
46 14 0.11
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.37
Consensus pattern (44 bp):
GAAAACCATTTTATCAAAACCTTTTGAAAACCATGACTCTTTTT
Found at i:13401 original size:89 final size:88
Alignment explanation
Indices: 13213--13404 Score: 221
Period size: 89 Copynumber: 2.2 Consensus size: 88
13203 GAAAACACAA
* * * *
13213 CTTTGGAAAATCC-TTTTATTAAAACCTTTTGAAAACCATGGCTATTTTTGAAAGAAGCCTTTTA
1 CTTTTGAAAA-CCATTTTATCAAAACCTTTTGAAAACCATGACTATTTTTGAAAGAAGCATTTTA
*
13277 TCAAAACTTTTGAAAACTATGAAT
65 TCAAAACTTTTGAAAACCATGAAT
* *
13301 CTTTTGAAAAACCATTTTATCAAAACCTTTTGAAATCCATGACTCTTTTTG-AA-AA-CTATTTT
1 CTTTTG-AAAACCATTTTATCAAAACCTTTTGAAAACCATGACTATTTTTGAAAGAAGC-ATTTT
* *
13363 ATCAAAACCTTTTGAAATCCATGACT
64 ATCAAAA-CTTTTGAAAACCATGAAT
13389 CTTTTTCGAAAACCAT
1 C-TTTT-GAAAACCAT
13405 CATTGCTTCT
Statistics
Matches: 89, Mismatches: 9, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
86 1 0.01
87 13 0.15
88 25 0.28
89 49 0.55
90 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.38
Consensus pattern (88 bp):
CTTTTGAAAACCATTTTATCAAAACCTTTTGAAAACCATGACTATTTTTGAAAGAAGCATTTTAT
CAAAACTTTTGAAAACCATGAAT
Found at i:18927 original size:9 final size:9
Alignment explanation
Indices: 18915--18966 Score: 59
Period size: 9 Copynumber: 5.4 Consensus size: 9
18905 AATTTTCTGA
18915 TTTTTTTCT
1 TTTTTTTCT
*
18924 TTTTTTTCA
1 TTTTTTTCT
18933 TTTTTTTCT
1 TTTTTTTCT
18942 TTTCCTTCTTCT
1 TTT--TT-TTCT
*
18954 TTTTTTGCT
1 TTTTTTTCT
18963 TTTT
1 TTTT
18967 CTTCAAATCT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
9 26 0.70
10 2 0.05
11 2 0.05
12 7 0.19
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.81
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:18928 original size:18 final size:18
Alignment explanation
Indices: 18907--18966 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
18897 CATCTGTTAA
*
18907 TTTTCTGATTTTTTTCTT
1 TTTTCTCATTTTTTTCTT
*
18925 TTTTTTCATTTTTTTCTT
1 TTTTCTCATTTTTTTCTT
18943 TTCCTTCTTC-TTTTTTTGCTT
1 TT--TTC-TCATTTTTTT-CTT
18964 TTT
1 TTT
18967 CTTCAAATCT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
18 18 0.51
19 1 0.03
20 9 0.26
21 7 0.20
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.78
Consensus pattern (18 bp):
TTTTCTCATTTTTTTCTT
Found at i:18968 original size:18 final size:18
Alignment explanation
Indices: 18914--18971 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 18
18904 TAATTTTCTG
*
18914 ATTTTTTTCTTTTTTTTC
1 ATTTTTTTCTTTTTCTTC
18932 ATTTTTTTCTTTTCCTTCTTC
1 ATTTTTTTC-TTT--TTCTTC
18953 -TTTTTTTGCTTTTTCTTC
1 ATTTTTTT-CTTTTTCTTC
18971 A
1 A
18972 AATCTTGATC
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
18 15 0.44
19 3 0.09
20 10 0.29
21 6 0.18
ACGTcount: A:0.05, C:0.17, G:0.02, T:0.76
Consensus pattern (18 bp):
ATTTTTTTCTTTTTCTTC
Done.