Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008611.1 Corchorus capsularis cultivar CVL-1 contig08632, 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: 71354
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:10662 original size:66 final size:65
Alignment explanation
Indices: 10519--11083 Score: 521
Period size: 66 Copynumber: 8.5 Consensus size: 65
10509 AAGGCGAAAC
* * * * * *
10519 TGACCCTTCGACCGAAAGGGTA-TTTCTGAAAATACAAAATGCTAAACTTAAATGCGGAAAGACG
1 TGACCCTTTGACCGAAAGGGTATTTTC-GGAAA-AGAAAATACCAAACTTAAATGC-AAAAGAC-
*
10583 AAAC
62 AAAA
* * *
10587 TGACCCTTTGACCGAAAGGGTATTTTCGGAAATGAAAATACTGAAA-TTGAATGCAAAAGACAAA
1 TGACCCTTTGACCGAAAGGGTATTTTCGGAAAAGAAAATAC-CAAACTTAAATGCAAAAGACAAA
10651 A
65 A
* * * * * * *
10652 CTAACCCTTTGACCGAAAGGGTATTTTCGGATATGAAAATACAAAACTTGAATGCAGAAGAAAAA
1 -TGACCCTTTGACCGAAAGGGTATTTTCGGAAAAGAAAATACCAAACTTAAATGCAAAAGACAAA
10717 A
65 A
* * ** * *
10718 CTGACCCTTTGACCAAAAGGGTATTTTCGGAAATGAAAATATTAAACTTGATTGCAAAAGACAAT
1 -TGACCCTTTGACCGAAAGGGTATTTTCGGAAAAGAAAATACCAAACTTAAATGCAAAAGACAA-
*
10783 AT
64 AA
* * * * * *
10785 TGACCCTTTGACTGAAAGGGCATCTTGGGAAAAGAAAATACCATACCTAAATGCAAAAGACGAAA
1 TGACCCTTTGACCGAAAGGGTATTTTCGGAAAAGAAAATACCAAACTTAAATGCAAAAGAC-AAA
10850 A
65 A
** * * * *
10851 TGACCCTTCCACTGAAAGGGTATTTTTGAAAAAGAAAATACCAAACCTAAATGCAAAAGACGAAA
1 TGACCCTTTGACCGAAAGGGTATTTTCGGAAAAGAAAATACCAAACTTAAATGCAAAAGAC-AAA
10916 A
65 A
* * *
10917 TGACCC-TTGCACCGAAAGGGTACTTTT-GAAAAAGAAAATACCAAACCTAAATGCAAAAGATGA
1 TGACCCTTTG-ACCGAAAGGGTA-TTTTCGGAAAAGAAAATACCAAACTTAAATGCAAAAGA-CA
10980 AAA
63 AAA
** **
10983 TGACCCTTCCACCGAAAGGGTAATTTT-GGAAAAAGAAAATATTAAACTTAAATGCGAAAAGACG
1 TGACCCTTTGACCGAAAGGGT-ATTTTCGG-AAAAGAAAATACCAAACTTAAATGC-AAAAGAC-
11047 AAAA
62 AAAA
* *
11051 TAACCCTTTTG-CCGAAAGGGTATTTTTGGAAAA
1 TGACCC-TTTGACCGAAAGGGTATTTTCGGAAAA
11084 ACAAAATAGA
Statistics
Matches: 424, Mismatches: 57, Indels: 33
0.82 0.11 0.06
Matches are distributed among these distances:
65 7 0.02
66 303 0.71
67 53 0.12
68 55 0.13
69 6 0.01
ACGTcount: A:0.43, C:0.16, G:0.18, T:0.22
Consensus pattern (65 bp):
TGACCCTTTGACCGAAAGGGTATTTTCGGAAAAGAAAATACCAAACTTAAATGCAAAAGACAAAA
Found at i:11154 original size:10 final size:10
Alignment explanation
Indices: 11121--11146 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
11111 ATCTTTTCTC
11121 AATTTTTTTG
1 AATTTTTTTG
11131 AATTTTTTTG
1 AATTTTTTTG
11141 AATTTT
1 AATTTT
11147 CTTTAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (10 bp):
AATTTTTTTG
Found at i:12101 original size:21 final size:20
Alignment explanation
Indices: 12077--12119 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
12067 CGTTTCAACC
12077 CTTTATTATTTT-TTCTTCCTT
1 CTTT-TTATTTTCTTCTT-CTT
*
12098 CTTTTTTTTTTCTTCTTCTT
1 CTTTTTATTTTCTTCTTCTT
12118 CT
1 CT
12120 CCTTTCCTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (20 bp):
CTTTTTATTTTCTTCTTCTT
Found at i:20062 original size:17 final size:16
Alignment explanation
Indices: 20040--20099 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 16
20030 GGAGATACTC
20040 TTCAAAAAAGTATGAAG-
1 TTCAAAAAAG-A-GAAGT
20057 TTCAAAGAGAAGAGAAGT
1 TTCAAA-A-AAGAGAAGT
*
20075 TTCAAAAAAGCATAAGT
1 TTCAAAAAAG-AGAAGT
*
20092 TTGAAAAA
1 TTCAAAAA
20100 TAAAGAAGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
16 3 0.08
17 23 0.62
18 8 0.22
19 3 0.08
ACGTcount: A:0.53, C:0.07, G:0.18, T:0.22
Consensus pattern (16 bp):
TTCAAAAAAGAGAAGT
Found at i:24180 original size:30 final size:30
Alignment explanation
Indices: 24144--24206 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
24134 TCTTCAAGTG
*
24144 GGAGGGAATGATGCGCCCAAG-GCTTATCAT
1 GGAGGGAATGATGCG-CCAAGAACTTATCAT
24174 GGAGGGAATGATGCGCCAAGAACTTATCAT
1 GGAGGGAATGATGCGCCAAGAACTTATCAT
24204 GGA
1 GGA
24207 CTTGAAGACA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 5 0.16
30 26 0.84
ACGTcount: A:0.30, C:0.17, G:0.33, T:0.19
Consensus pattern (30 bp):
GGAGGGAATGATGCGCCAAGAACTTATCAT
Found at i:25359 original size:10 final size:10
Alignment explanation
Indices: 25335--25359 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
25325 GAAAAATATC
25335 AAAAAAATAA
1 AAAAAAATAA
25345 AAAAAAATAA
1 AAAAAAATAA
25355 AAAAA
1 AAAAA
25360 GTTTTCGACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:27570 original size:30 final size:28
Alignment explanation
Indices: 27534--27594 Score: 104
Period size: 30 Copynumber: 2.1 Consensus size: 28
27524 TCTTCAAGTG
27534 GGAGGGAATGATGCGCCCAAGGCTTATCAT
1 GGAGGGAATGATGCG-CCAA-GCTTATCAT
27564 GGAGGGAATGATGCGCCAAGCTTATCAT
1 GGAGGGAATGATGCGCCAAGCTTATCAT
27592 GGA
1 GGA
27595 CTTGAAGACA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 12 0.39
29 4 0.13
30 15 0.48
ACGTcount: A:0.28, C:0.18, G:0.34, T:0.20
Consensus pattern (28 bp):
GGAGGGAATGATGCGCCAAGCTTATCAT
Found at i:32790 original size:24 final size:24
Alignment explanation
Indices: 32763--32832 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
32753 GAAAGCAAAA
* *
32763 GAGCAGCAGAAGAAGAAAAAGAGT
1 GAGCAACAGAAGAAGAAAAAGAAT
* * *
32787 GAGCAATAGCAGAAGAGAAAGAAT
1 GAGCAACAGAAGAAGAAAAAGAAT
*
32811 GAGCAACAGGAAAAAGAAAAAG
1 GAGCAACA-GAAGAAGAAAAAG
32833 CCATTAGTGA
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
24 26 0.72
25 10 0.28
ACGTcount: A:0.57, C:0.09, G:0.30, T:0.04
Consensus pattern (24 bp):
GAGCAACAGAAGAAGAAAAAGAAT
Found at i:35703 original size:18 final size:19
Alignment explanation
Indices: 35669--35706 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
35659 GTCCATCGTT
*
35669 ATCTCCATGGTCTCCATGC
1 ATCTCCATGGCCTCCATGC
35688 ATCTCCAT-GCCTCCATGC
1 ATCTCCATGGCCTCCATGC
35706 A
1 A
35707 ACCCATGCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.18, C:0.39, G:0.13, T:0.29
Consensus pattern (19 bp):
ATCTCCATGGCCTCCATGC
Found at i:37168 original size:2 final size:2
Alignment explanation
Indices: 37157--37192 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
37147 CATTTTGTGT
37157 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
37193 GAGGAGGATC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:38140 original size:17 final size:16
Alignment explanation
Indices: 38100--38142 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
38090 CATGTAATCT
*
38100 TTGATCACCGGTGATC
1 TTGATCACTGGTGATC
38116 TTGCATCACTGGTGATC
1 TTG-ATCACTGGTGATC
38133 TTAGATCACT
1 TT-GATCACT
38143 AGTAATCTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 3 0.12
17 20 0.83
18 1 0.04
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:38150 original size:17 final size:16
Alignment explanation
Indices: 38093--38150 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 16
38083 ATAAACCCAT
*
38093 GTAATCTTTGATCACCG
1 GTAATC-TTGATCACTG
*
38110 GTGATCTTGCATCACTG
1 GTAATCTTG-ATCACTG
* *
38127 GTGATCTTAGATCACTA
1 GTAATCTT-GATCACTG
38144 GTAATCT
1 GTAATCT
38151 GGGGGGTGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
16 3 0.09
17 31 0.89
18 1 0.03
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (16 bp):
GTAATCTTGATCACTG
Found at i:38865 original size:2 final size:2
Alignment explanation
Indices: 38858--38882 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38848 GCTATCTAGT
38858 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
38883 TCTACTTGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41180 original size:2 final size:2
Alignment explanation
Indices: 41173--41199 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
41163 TATGAATTAG
41173 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
41200 CATGTATTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:43281 original size:23 final size:24
Alignment explanation
Indices: 43255--43305 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 24
43245 TATATATATC
*
43255 TTGCTTCAAATTTCAAT-TTCTTT
1 TTGCTTCAAATTTCAATATCCTTT
*
43278 TTGCTTCTAATTTCAATATCCTTT
1 TTGCTTCAAATTTCAATATCCTTT
43302 TTGC
1 TTGC
43306 CATGATAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 16 0.64
24 9 0.36
ACGTcount: A:0.20, C:0.20, G:0.06, T:0.55
Consensus pattern (24 bp):
TTGCTTCAAATTTCAATATCCTTT
Found at i:43802 original size:32 final size:32
Alignment explanation
Indices: 43761--43825 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
43751 TACGGCGACG
43761 TTTTCTTCAGAAGACGCCCCTATATAGCGGCA
1 TTTTCTTCAGAAGACGCCCCTATATAGCGGCA
* *
43793 TTTTCTTCAGAAGACGCTCCTATATCGCGGCA
1 TTTTCTTCAGAAGACGCCCCTATATAGCGGCA
43825 T
1 T
43826 CTTCAAAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.23, C:0.28, G:0.18, T:0.31
Consensus pattern (32 bp):
TTTTCTTCAGAAGACGCCCCTATATAGCGGCA
Found at i:48031 original size:51 final size:50
Alignment explanation
Indices: 47905--48031 Score: 128
Period size: 51 Copynumber: 2.5 Consensus size: 50
47895 TGCCTCTGAG
* * * * * * **
47905 GCTTGCTGCAGCAATCCGAGAAGGAGTTGGAGGACGGGAATTGCTAGAGTG
1 GCTTGCTGCAGTAGT-CGGGAAGGAGATGGAGGACGAGAATTGCCAGAGAA
* * *
47956 GCTTGCTGCATTAGACGGGAAAGGAGATGGAGGACGAGAATTGCCAGGGAA
1 GCTTGCTGCAGTAGTCGGG-AAGGAGATGGAGGACGAGAATTGCCAGAGAA
48007 GCTTGCTGCAGTAGTCGGTGAAGGA
1 GCTTGCTGCAGTAGTCGG-GAAGGA
48032 TCCGTTACCT
Statistics
Matches: 61, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
50 3 0.05
51 57 0.93
52 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.39, T:0.19
Consensus pattern (50 bp):
GCTTGCTGCAGTAGTCGGGAAGGAGATGGAGGACGAGAATTGCCAGAGAA
Found at i:52545 original size:2 final size:2
Alignment explanation
Indices: 52538--52569 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
52528 ATAATTAAAC
52538 AT AT 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 AT AT
52570 GAAGAACAAA
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):
AT
Found at i:54990 original size:2 final size:2
Alignment explanation
Indices: 54978--55017 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
54968 CCTTGTATCT
54978 TA TA GTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
55018 GATTAGATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:65834 original size:15 final size:15
Alignment explanation
Indices: 65814--65855 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
65804 CGATCAAATG
*
65814 TCGGGTCATTTGGGT
1 TCGGGTCATTTGGGC
65829 TCGGGTCAATTATGGGC
1 TCGGGTC-ATT-TGGGC
65846 T-GGGTCATTT
1 TCGGGTCATTT
65856 TCGGGTCATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 1 0.04
15 10 0.42
16 8 0.33
17 5 0.21
ACGTcount: A:0.12, C:0.14, G:0.36, T:0.38
Consensus pattern (15 bp):
TCGGGTCATTTGGGC
Done.