Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013550.1 Corchorus capsularis cultivar CVL-1 contig13571, 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: 19044
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:985 original size:45 final size:45
Alignment explanation
Indices: 917--1004 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 45
907 ATAGAGTAGC
*
917 GGAATTACTAAAAGATCCATACCCCGAATTAGTGATAAGCTGGGT
1 GGAATTACTAAAAGATCCATACCCCGAATTAATGATAAGCTGGGT
* *
962 GGAATTACTAAAAGATCTC-TACCCCGGATTAATGATGAGCTGG
1 GGAATTACTAAAAGATC-CATACCCCGAATTAATGATAAGCTGG
1005 AGAAGTAATC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
45 38 0.97
46 1 0.03
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (45 bp):
GGAATTACTAAAAGATCCATACCCCGAATTAATGATAAGCTGGGT
Found at i:1970 original size:45 final size:45
Alignment explanation
Indices: 1919--2008 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
1909 TAATAGAGTA
*
1919 GTGGAATTACTAAAAGATCCCTACCCTGAATTAATGATGAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATGAGCTGG
* *
1964 GTGGAATTACTAAAAGATCCCTACCCCGGATTAGTGATGAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATGAGCTGG
2009 AGAAGTAATC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (45 bp):
GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATGAGCTGG
Found at i:2400 original size:2 final size:2
Alignment explanation
Indices: 2393--2432 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
2383 TTTTAATTGA
* *
2393 AT AT AT AT AA AT AT AT AT AT AT AT AT A- AT AT AA AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2433 CTACATATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:2736 original size:166 final size:165
Alignment explanation
Indices: 2460--2941 Score: 619
Period size: 166 Copynumber: 2.9 Consensus size: 165
2450 AAACATGTAA
* ** * *
2460 AATTACTAAAAGATCCCCACCCTGGATTAATGAGGAGCGAGAGAACTAATTTTTTTCGTCTTTTT
1 AATTAATAAAAGATCCCCACCAAGGATTAATGATGAGCTAGAGAACTAATTTTTTTCGTC-TTTT
2525 CC-ACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAGACTT
65 CCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTA-AC-T
* *
2589 TTTTG-TCATTTCTCAATTGATTTTAATAGAGTAGTGG
128 TTTTGATCATTTCTCAATTGACTTGAATAGAGTAGTGG
* * * ** ** * * *
2626 AATTACTAAAAGATCCCTACCAAGGCTTGCTTTTGGAGTTAGAGAACT-TTTTTTTTTGTCTTTT
1 AATTAATAAAAGATCCCCACCAAGGATTAATGAT-GAGCTAGAGAACTAATTTTTTTCGTCTTTT
* * * * *
2690 CCTACTTGACATATTACTTAAATGTCCTAACTTTTGATTATTGAGGGAATTAAATAAGTAACCTT
65 CCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAA-CTT
* *
2755 TTTGTTCATTTCTCAATGGACTTGAATAGAGTAGTGG
129 TTTGATCATTTCTCAATTGACTTGAATAGAGTAGTGG
* * *
2792 AATTAATAAAAGATCCCCATCAAGGATTAATGATGAGCTAGAGAACTAATCTTTTTCGTCTTTAC
1 AATTAATAAAAGATCCCCACCAAGGATTAATGATGAGCTAGAGAACTAATTTTTTTCGTCTTTTC
* * *
2857 CTACTTGGTAGATTACTTAAATGTCTTAACTTTTGATTCTTGGGGGGATTAAATAACTAAACTTT
66 CTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACT-AACTTT
2922 TTGATCATTTCTCAATTGAC
130 TTGATCATTTCTCAATTGAC
2942 AAATGACTCA
Statistics
Matches: 266, Mismatches: 44, Indels: 12
0.83 0.14 0.04
Matches are distributed among these distances:
165 25 0.09
166 228 0.86
167 13 0.05
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (165 bp):
AATTAATAAAAGATCCCCACCAAGGATTAATGATGAGCTAGAGAACTAATTTTTTTCGTCTTTTC
CTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAACTTTT
TGATCATTTCTCAATTGACTTGAATAGAGTAGTGG
Found at i:3120 original size:18 final size:17
Alignment explanation
Indices: 3094--3127 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3084 TTTTCCCGTC
3094 GATTATTTTTTGAAAAA
1 GATTATTTTTTGAAAAA
3111 GATTATTTTTTGAAAAA
1 GATTATTTTTTGAAAAA
3128 TCTGTACCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (17 bp):
GATTATTTTTTGAAAAA
Found at i:6010 original size:11 final size:11
Alignment explanation
Indices: 5967--6004 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
5957 TTTCTATATA
*
5967 AAATAAATTAT
1 AAATTAATTAT
5978 CAAA-TAATTAT
1 -AAATTAATTAT
5989 AAATTAATTAT
1 AAATTAATTAT
6000 AAATT
1 AAATT
6005 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:6619 original size:25 final size:24
Alignment explanation
Indices: 6585--6664 Score: 114
Period size: 21 Copynumber: 3.5 Consensus size: 24
6575 TTCAAACCCT
6585 AAACTTCATTTCTAACAACTTCTTC
1 AAACTTCATTTCTAACAA-TTCTTC
6610 AAACTTCATTTCT---AATTCTTC
1 AAACTTCATTTCTAACAATTCTTC
*
6631 AAACTTCATTTCTAACAAATCTTC
1 AAACTTCATTTCTAACAATTCTTC
6655 AAA-TTCATTT
1 AAACTTCATTT
6665 TCCTTCATTT
Statistics
Matches: 51, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
21 19 0.37
22 2 0.04
23 7 0.14
24 10 0.20
25 13 0.25
ACGTcount: A:0.34, C:0.24, G:0.00, T:0.42
Consensus pattern (24 bp):
AAACTTCATTTCTAACAATTCTTC
Found at i:6703 original size:26 final size:26
Alignment explanation
Indices: 6674--6741 Score: 127
Period size: 26 Copynumber: 2.6 Consensus size: 26
6664 TTCCTTCATT
6674 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
6700 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
6726 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
6742 AAACTAAGTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:6741 original size:15 final size:15
Alignment explanation
Indices: 6674--6745 Score: 63
Period size: 11 Copynumber: 5.4 Consensus size: 15
6664 TTCCTTCATT
*
6674 TTAATCATAAACTAA
1 TTAAACATAAACTAA
6689 TT-AA-AT--ACTAA
1 TTAAACATAAACTAA
*
6700 TTAATCATAAACTAA
1 TTAAACATAAACTAA
6715 TT-AA-AT--ACTAA
1 TTAAACATAAACTAA
6726 TTAAACATAAACTAA
1 TTAAACATAAACTAA
6741 -TAAAC
1 TTAAAC
6746 TAAGTAATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 17
0.70 0.05 0.26
Matches are distributed among these distances:
11 14 0.30
12 3 0.07
13 8 0.17
14 7 0.15
15 14 0.30
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (15 bp):
TTAAACATAAACTAA
Found at i:6794 original size:52 final size:49
Alignment explanation
Indices: 6675--6794 Score: 113
Period size: 52 Copynumber: 2.4 Consensus size: 49
6665 TCCTTCATTT
* * *
6675 TAATCATAAACTAATTAA-ATACTAATTAATCATAAACTAATTAAATAC
1 TAATCATAAACTAATTAATAAACTAAGTAATAATAAACTAATTAAATAC
* *
6723 TAAT--TAAACATAAACTAATAAACTAAGTAATTTGAATTAACTAATTTAAA-AC
1 TAATCATAAAC-T-AATTAATAAACTAAGTAA--T-AATAAACTAA-TTAAATAC
6775 TAATCATAAACTAATTAATA
1 TAATCATAAACTAATTAATA
6795 TTAAAAAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
46 5 0.09
47 1 0.02
48 9 0.16
49 9 0.16
51 1 0.02
52 21 0.37
53 6 0.11
54 5 0.09
ACGTcount: A:0.54, C:0.11, G:0.02, T:0.33
Consensus pattern (49 bp):
TAATCATAAACTAATTAATAAACTAAGTAATAATAAACTAATTAAATAC
Found at i:6815 original size:12 final size:11
Alignment explanation
Indices: 6798--6828 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
6788 ATTAATATTA
6798 AAAAAAAAGTTT
1 AAAAAAAA-TTT
6810 AAAAAAAATTT
1 AAAAAAAATTT
6821 AAAAAAAA
1 AAAAAAAA
6829 AAACCTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (11 bp):
AAAAAAAATTT
Found at i:6829 original size:12 final size:13
Alignment explanation
Indices: 6795--6829 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
6785 CTAATTAATA
6795 TTAAAAAAAAAGT
1 TTAAAAAAAAAGT
6808 TT-AAAAAAAA-T
1 TTAAAAAAAAAGT
6819 TTAAAAAAAAA
1 TTAAAAAAAAA
6830 AACCTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 3 0.14
12 16 0.76
13 2 0.10
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (13 bp):
TTAAAAAAAAAGT
Found at i:7078 original size:20 final size:20
Alignment explanation
Indices: 7053--7095 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
7043 AAAATTATAA
7053 AAAGGG-GGACGGTATTTAAC
1 AAAGGGAGG-CGGTATTTAAC
*
7073 AAAGGGAGGCGGTGTTTAAC
1 AAAGGGAGGCGGTATTTAAC
7093 AAA
1 AAA
7096 CCCCAAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.37, C:0.09, G:0.35, T:0.19
Consensus pattern (20 bp):
AAAGGGAGGCGGTATTTAAC
Found at i:7315 original size:19 final size:19
Alignment explanation
Indices: 7274--7317 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
7264 TTATCCCTCT
*
7274 TCTCTCTCCTCCCACTAAG
1 TCTCTCTCCTCCCACTAAC
*
7293 TCTCTCTCCTCCCACTTAC
1 TCTCTCTCCTCCCACTAAC
7312 TCTCTC
1 TCTCTC
7318 ATAGTCAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.11, C:0.50, G:0.02, T:0.36
Consensus pattern (19 bp):
TCTCTCTCCTCCCACTAAC
Found at i:7588 original size:16 final size:16
Alignment explanation
Indices: 7567--7599 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
7557 AAATCATAGA
7567 ATTTTATTTTATTAGT
1 ATTTTATTTTATTAGT
7583 ATTTTATTTTATTAGT
1 ATTTTATTTTATTAGT
7599 A
1 A
7600 ATGAGTACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (16 bp):
ATTTTATTTTATTAGT
Found at i:8242 original size:11 final size:11
Alignment explanation
Indices: 8226--8263 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
8216 ATTCATTACA
8226 AATTTATAATT
1 AATTTATAATT
8237 AATTTATAATT
1 AATTTATAATT
8248 -ATTTGATAATT
1 AATTT-ATAATT
*
8259 TATTT
1 AATTT
8264 TATATTGGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:10879 original size:22 final size:23
Alignment explanation
Indices: 10844--10903 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 23
10834 GTAATTAATC
*
10844 ATAAATTAACTAATTAAA-ACTA
1 ATAAATTAAATAATTAAATACTA
*
10866 ATAAACTAAATAATTAAATACTA
1 ATAAATTAAATAATTAAATACTA
*
10889 ATTAATTAAA-AATTA
1 ATAAATTAAATAATTA
10904 TTTAAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 21 0.64
23 12 0.36
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (23 bp):
ATAAATTAAATAATTAAATACTA
Found at i:10978 original size:32 final size:32
Alignment explanation
Indices: 10934--11033 Score: 128
Period size: 32 Copynumber: 3.1 Consensus size: 32
10924 ATTGGCTTTA
* * * *
10934 CCGCCCATTTTGGGAGGCATGCCATGGGCAAG
1 CCGCCCAATTTGGGCGGCCTACCATGGGCAAG
*
10966 CCGCCCAATTTGGGCGGCCTACCATGTGCAAG
1 CCGCCCAATTTGGGCGGCCTACCATGGGCAAG
* * *
10998 CCGCCCAATTTCGGCGGCCTCCCATGGGTAAG
1 CCGCCCAATTTGGGCGGCCTACCATGGGCAAG
11030 CCGC
1 CCGC
11034 AAATCGCATG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 59 1.00
ACGTcount: A:0.17, C:0.35, G:0.30, T:0.18
Consensus pattern (32 bp):
CCGCCCAATTTGGGCGGCCTACCATGGGCAAG
Done.