Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014183.1 Corchorus capsularis cultivar CVL-1 contig14204, 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: 55230
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:1457 original size:2 final size:2
Alignment explanation
Indices: 1450--1477 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1440 AATAATTTTC
1450 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1478 GCTACTTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1731 original size:32 final size:32
Alignment explanation
Indices: 1659--1724 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
1649 TTGGGGTATA
1659 CCCTTATATAGCGGCGTCTGAAGAACAAACCG
1 CCCTTATATAGCGGCGTCTGAAGAACAAACCG
*
1691 CCCTTATATAGCGGCGTCTGAAGAACAAAGCG
1 CCCTTATATAGCGGCGTCTGAAGAACAAACCG
1723 CC
1 CC
1725 GCTATATTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.30, C:0.29, G:0.23, T:0.18
Consensus pattern (32 bp):
CCCTTATATAGCGGCGTCTGAAGAACAAACCG
Found at i:1826 original size:25 final size:24
Alignment explanation
Indices: 1779--1888 Score: 121
Period size: 24 Copynumber: 4.5 Consensus size: 24
1769 GCAGGTAGCA
*
1779 GCGTCTAGACGCCCCCAAATAGTG
1 GCGTCTGGACGCCCCCAAATAGTG
* *
1803 TCTTCTGGACGCCCCCAAAGTAGTG
1 GCGTCTGGACGCCCCCAAA-TAGTG
* *
1828 GCGTCTGGACGCCGCCAAATAGGG
1 GCGTCTGGACGCCCCCAAATAGTG
* ** *
1852 GCGTCTGGACACTGCCAAATAGGG
1 GCGTCTGGACGCCCCCAAATAGTG
*
1876 GCATCTGGACGCC
1 GCGTCTGGACGCC
1889 GCAATATGCT
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
24 52 0.71
25 21 0.29
ACGTcount: A:0.22, C:0.31, G:0.30, T:0.17
Consensus pattern (24 bp):
GCGTCTGGACGCCCCCAAATAGTG
Found at i:1859 original size:49 final size:48
Alignment explanation
Indices: 1779--1890 Score: 125
Period size: 49 Copynumber: 2.3 Consensus size: 48
1769 GCAGGTAGCA
* * * * * * *
1779 GCGTCTAGACGCCCCCAAATAGTGTCTTCTGGACGCCCCCAAAGTAGTG
1 GCGTCTGGACGCCGCCAAATAGGGGCGTCTGGACACCCCCAAA-TAGGG
**
1828 GCGTCTGGACGCCGCCAAATAGGGGCGTCTGGACACTGCCAAATAGGG
1 GCGTCTGGACGCCGCCAAATAGGGGCGTCTGGACACCCCCAAATAGGG
*
1876 GCATCTGGACGCCGC
1 GCGTCTGGACGCCGC
1891 AATATGCTAT
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
48 18 0.34
49 35 0.66
ACGTcount: A:0.21, C:0.31, G:0.30, T:0.17
Consensus pattern (48 bp):
GCGTCTGGACGCCGCCAAATAGGGGCGTCTGGACACCCCCAAATAGGG
Found at i:10029 original size:6 final size:6
Alignment explanation
Indices: 10018--10047 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
10008 GAGGCAACCC
10018 AATTTT AATTTT AATTTT AATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT
10048 CAGTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
AATTTT
Found at i:12966 original size:14 final size:15
Alignment explanation
Indices: 12937--12966 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12927 GTGTGAATTC
12937 AAAATTGATCTTTTG
1 AAAATTGATCTTTTG
12952 AAAATTGAT-TTTTG
1 AAAATTGATCTTTTG
12966 A
1 A
12967 TTAACTTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.37, C:0.03, G:0.13, T:0.47
Consensus pattern (15 bp):
AAAATTGATCTTTTG
Found at i:14084 original size:74 final size:74
Alignment explanation
Indices: 14001--14152 Score: 286
Period size: 74 Copynumber: 2.1 Consensus size: 74
13991 TGCTCACTCA
14001 ATTTATGAGTGAGTAATCCTTTTCTTTTCTCCAATGTAGAATTTAATTGATCTCTTGACTTATAT
1 ATTTATGAGTGAGTAATCCTTTTCTTTTCTCCAATGTAGAATTTAATTGATCTCTTGACTTATAT
14066 CATGATGAG
66 CATGATGAG
*
14075 ATTTATGAGTGATTAATCCTTTTCTTTTCTCCAATGTAGAATTTAATTGATCTCTTGACTTATAT
1 ATTTATGAGTGAGTAATCCTTTTCTTTTCTCCAATGTAGAATTTAATTGATCTCTTGACTTATAT
*
14140 CATGGTGAG
66 CATGATGAG
14149 ATTT
1 ATTT
14153 TGTGCTTATA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 76 1.00
ACGTcount: A:0.26, C:0.13, G:0.14, T:0.46
Consensus pattern (74 bp):
ATTTATGAGTGAGTAATCCTTTTCTTTTCTCCAATGTAGAATTTAATTGATCTCTTGACTTATAT
CATGATGAG
Found at i:14119 original size:40 final size:39
Alignment explanation
Indices: 14000--14119 Score: 101
Period size: 40 Copynumber: 3.2 Consensus size: 39
13990 ATGCTCACTC
14000 AATTTATGAGTGAGTAATCCTTTTCTTTTCTCCAATGTAG
1 AATTTATGAGTGA-TAATCCTTTTCTTTTCTCCAATGTAG
* * ** * *
14040 AATTTA--ATTGAT-CT-CTTGACTTATAT-C-ATG-ATG
1 AATTTATGAGTGATAATCCTTTTCTTTTCTCCAATGTA-G
14073 AGATTTATGAGTGATTAATCCTTTTCTTTTCTCCAATGTAG
1 A-ATTTATGAGTGA-TAATCCTTTTCTTTTCTCCAATGTAG
14114 AATTTA
1 AATTTA
14120 ATTGATCTCT
Statistics
Matches: 58, Mismatches: 12, Indels: 20
0.64 0.13 0.22
Matches are distributed among these distances:
32 1 0.02
33 5 0.09
34 6 0.10
35 8 0.14
36 5 0.09
37 2 0.03
38 5 0.09
39 8 0.14
40 12 0.21
41 5 0.09
42 1 0.02
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (39 bp):
AATTTATGAGTGATAATCCTTTTCTTTTCTCCAATGTAG
Found at i:18865 original size:18 final size:18
Alignment explanation
Indices: 18839--18873 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
18829 AAGTCGGTAT
* *
18839 GAGTTAGTTTGTTTTATC
1 GAGTCAGTTTCTTTTATC
18857 GAGTCAGTTTCTTTTAT
1 GAGTCAGTTTCTTTTAT
18874 AGTCTCAGTT
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:0.17, C:0.09, G:0.20, T:0.54
Consensus pattern (18 bp):
GAGTCAGTTTCTTTTATC
Found at i:21235 original size:31 final size:31
Alignment explanation
Indices: 21200--21281 Score: 128
Period size: 31 Copynumber: 2.6 Consensus size: 31
21190 GTTTGCTGTC
* * *
21200 ACGATCAATTTGGGATATAACGTTTTAGAAA
1 ACGATCATTTTAGGATATAACGTTTCAGAAA
21231 ACGATCATTTTAGGATATAACGTTTCAGAAA
1 ACGATCATTTTAGGATATAACGTTTCAGAAA
*
21262 GCGATCATTTTAGGATATAA
1 ACGATCATTTTAGGATATAA
21282 AGAATGATCA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (31 bp):
ACGATCATTTTAGGATATAACGTTTCAGAAA
Found at i:21801 original size:25 final size:25
Alignment explanation
Indices: 21763--21821 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
21753 AAACTCCTTG
* * *
21763 TCTCTACTTCTTTGCGTTCTTCTTC
1 TCTCTTCTTATTTGCCTTCTTCTTC
21788 TCTCTTCTTATTTGCCTTCTTCTTC
1 TCTCTTCTTATTTGCCTTCTTCTTC
*
21813 TCCCTTCTT
1 TCTCTTCTT
21822 TGTTGATTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.03, C:0.34, G:0.05, T:0.58
Consensus pattern (25 bp):
TCTCTTCTTATTTGCCTTCTTCTTC
Found at i:22715 original size:22 final size:22
Alignment explanation
Indices: 22685--22736 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
22675 AGATTTCTGA
* *
22685 TTTGTGGAAGAAGAATCAGGCG
1 TTTGGGGAAGAAGAAACAGGCG
22707 TTTGGGGAAGAAGAAACAGGCG
1 TTTGGGGAAGAAGAAACAGGCG
*
22729 -CTGGGGAA
1 TTTGGGGAA
22737 AAAAGAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 7 0.26
22 20 0.74
ACGTcount: A:0.33, C:0.10, G:0.40, T:0.17
Consensus pattern (22 bp):
TTTGGGGAAGAAGAAACAGGCG
Found at i:22751 original size:11 final size:11
Alignment explanation
Indices: 22735--22774 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
22725 GGCGCTGGGG
22735 AAAAAAGAAGA
1 AAAAAAGAAGA
22746 AAAAAAGAAGAA
1 AAAAAAGAAG-A
*
22758 AAAAAAGAGGA
1 AAAAAAGAAGA
22769 AAAAAA
1 AAAAAA
22775 ATTAAGGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAGA
Found at i:22760 original size:12 final size:12
Alignment explanation
Indices: 22735--22775 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
22725 GGCGCTGGGG
22735 AAAAAAGAAG-A
1 AAAAAAGAAGAA
22746 AAAAAAGAAGAA
1 AAAAAAGAAGAA
*
22758 AAAAAAGAGGAA
1 AAAAAAGAAGAA
22770 AAAAAA
1 AAAAAA
22776 TTAAGGTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
11 10 0.36
12 18 0.64
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAGAA
Found at i:24381 original size:27 final size:27
Alignment explanation
Indices: 24351--24409 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
24341 ATGGGGAGGT
* * *
24351 GGTGGAGGGTGTACGTGTGGCGGTGGC
1 GGTGGAGGATGTACATGAGGCGGTGGC
* *
24378 GGTGAAGGATGTACATGAGGTGGTGGC
1 GGTGGAGGATGTACATGAGGCGGTGGC
24405 GGTGG
1 GGTGG
24410 CGGCGGTGAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.14, C:0.08, G:0.56, T:0.22
Consensus pattern (27 bp):
GGTGGAGGATGTACATGAGGCGGTGGC
Found at i:37169 original size:58 final size:58
Alignment explanation
Indices: 37103--37221 Score: 229
Period size: 58 Copynumber: 2.1 Consensus size: 58
37093 TATTGCTGAA
*
37103 ATATATAATCATATATCGATCTTTATTTACAATTAAATAAATCTGGTAGGATTAATTT
1 ATATATAATCATATATCGATCTTTATTTACAATTAAATAAATCTGGTAGGAGTAATTT
37161 ATATATAATCATATATCGATCTTTATTTACAATTAAATAAATCTGGTAGGAGTAATTT
1 ATATATAATCATATATCGATCTTTATTTACAATTAAATAAATCTGGTAGGAGTAATTT
37219 ATA
1 ATA
37222 ATGTAGTATT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.42
Consensus pattern (58 bp):
ATATATAATCATATATCGATCTTTATTTACAATTAAATAAATCTGGTAGGAGTAATTT
Found at i:39851 original size:2 final size:2
Alignment explanation
Indices: 39844--39875 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
39834 AAATATCGTT
39844 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39876 GTGCCATTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:46338 original size:32 final size:32
Alignment explanation
Indices: 46297--46363 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
46287 TGCATTTATC
46297 AATCAAAAAATTAATTCTAAGTCAAATAAAAT
1 AATCAAAAAATTAATTCTAAGTCAAATAAAAT
46329 AATCAAAAAATTAATTCTAAGTCAAATAAAAT
1 AATCAAAAAATTAATTCTAAGTCAAATAAAAT
46361 AAT
1 AAT
46364 TCCACGTTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.60, C:0.09, G:0.03, T:0.28
Consensus pattern (32 bp):
AATCAAAAAATTAATTCTAAGTCAAATAAAAT
Found at i:49427 original size:1 final size:1
Alignment explanation
Indices: 49421--49453 Score: 57
Period size: 1 Copynumber: 33.0 Consensus size: 1
49411 TTTAACCCGG
*
49421 AAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
49454 TCTTTCTCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:50045 original size:17 final size:18
Alignment explanation
Indices: 50003--50045 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
49993 TGTGTGTGAA
50003 ATCTCAAGCCTAAAGTTTT
1 ATCT-AAGCCTAAAGTTTT
* *
50022 GTATAAGCC-AAAGTTTT
1 ATCTAAGCCTAAAGTTTT
50039 ATCTAAG
1 ATCTAAG
50046 TGAGGATAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
17 13 0.65
18 5 0.25
19 2 0.10
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (18 bp):
ATCTAAGCCTAAAGTTTT
Found at i:54130 original size:28 final size:28
Alignment explanation
Indices: 54090--54144 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
54080 CAAATAGGTT
54090 GATTTGATGAAAACTAATCTGTTGCTAG
1 GATTTGATGAAAACTAATCTGTTGCTAG
54118 GATTTGATGAAAACTAATCTGTTGCTA
1 GATTTGATGAAAACTAATCTGTTGCTA
54145 TACTATCTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (28 bp):
GATTTGATGAAAACTAATCTGTTGCTAG
Done.