Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012740.1 Corchorus capsularis cultivar CVL-1 contig12761, 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: 39746
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:1099 original size:34 final size:34
Alignment explanation
Indices: 1061--1127 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
1051 CTCTTACAAC
*
1061 CAATGAAGTTATACGGGCCTTCATAACGCCTTTG
1 CAATGAAGTTAAACGGGCCTTCATAACGCCTTTG
*
1095 CAATGAAGTTAAACGGGCCTTCATCACGCCTTT
1 CAATGAAGTTAAACGGGCCTTCATAACGCCTTT
1128 ACAAGTTGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.28
Consensus pattern (34 bp):
CAATGAAGTTAAACGGGCCTTCATAACGCCTTTG
Found at i:7081 original size:167 final size:168
Alignment explanation
Indices: 6804--7137 Score: 607
Period size: 167 Copynumber: 2.0 Consensus size: 168
6794 AGGAGTCTTT
*
6804 AGGTTATTTTTCCACTATAAATACCCACCTTATGTAACCCCAGAAAACAATCTCTCATAATTCTA
1 AGGTTATTTTCCCACTATAAATACCCACCTTATGTAACCCCAGAAAACAATCTCTCATAATTCTA
*
6869 TTCTTCTACCTTTCTTTAGTTTTGTTTTTCTCTAGTTTTAGGTCTAGGGTGCCGCA-CCTCTCTT
66 TTCTTCTACCTTTCTTTAGTTTTGTTTTTCTCTAGTTTAAGGTCTAGGGTGCCGCACCCTCTCTT
* *
6933 TGCATAGAGAGGTGTGGCAACTATAGGGATTGCTAAGG
131 TGCATAGAGAGGTGCGGAAACTATAGGGATTGCTAAGG
6971 AGGTTATTTTCCCACTATAAATACCCACCTTATGTAACCCCAGAAAACAATCTCTCATAATTCTA
1 AGGTTATTTTCCCACTATAAATACCCACCTTATGTAACCCCAGAAAACAATCTCTCATAATTCTA
7036 TTCTTCTACCTTTCTTTAGTTTTGTTTTTCTCTAGTTTAAGGTCTAGGGTGCCGCACCCTCTCTT
66 TTCTTCTACCTTTCTTTAGTTTTGTTTTTCTCTAGTTTAAGGTCTAGGGTGCCGCACCCTCTCTT
* *
7101 TGCTTAGAGAGGTGCGGAAACTCTAGGGATTGCTAAG
131 TGCATAGAGAGGTGCGGAAACTATAGGGATTGCTAAG
7138 AAGGATTCCG
Statistics
Matches: 160, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
167 119 0.74
168 41 0.26
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.37
Consensus pattern (168 bp):
AGGTTATTTTCCCACTATAAATACCCACCTTATGTAACCCCAGAAAACAATCTCTCATAATTCTA
TTCTTCTACCTTTCTTTAGTTTTGTTTTTCTCTAGTTTAAGGTCTAGGGTGCCGCACCCTCTCTT
TGCATAGAGAGGTGCGGAAACTATAGGGATTGCTAAGG
Found at i:15607 original size:6 final size:6
Alignment explanation
Indices: 15596--15634 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
15586 AAAGCAAAGC
15596 AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT AAA
15635 GCAGATTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (6 bp):
AAATCT
Found at i:15646 original size:12 final size:13
Alignment explanation
Indices: 15631--15664 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
15621 AATCTAAATC
*
15631 TAAAGCAGATT-A
1 TAAAGCAAATTAA
15643 TAAAGCAAATTAA
1 TAAAGCAAATTAA
15656 TAAAGCAAA
1 TAAAGCAAA
15665 CAATAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.59, C:0.09, G:0.12, T:0.21
Consensus pattern (13 bp):
TAAAGCAAATTAA
Found at i:16590 original size:10 final size:10
Alignment explanation
Indices: 16575--16600 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
16565 GAGGACTCTA
16575 GAATTTTCTG
1 GAATTTTCTG
16585 GAATTTTCTG
1 GAATTTTCTG
16595 GAATTT
1 GAATTT
16601 GGCAGCAACT
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:0.08, G:0.19, T:0.50
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:18472 original size:10 final size:10
Alignment explanation
Indices: 18449--18485 Score: 51
Period size: 9 Copynumber: 3.8 Consensus size: 10
18439 TTCTGGTCGA
18449 ATTTTATTTT-
1 ATTTT-TTTTG
18459 ATTTTTTTTG
1 ATTTTTTTTG
18469 A-TTTTTTTG
1 ATTTTTTTTG
18478 ATTTTTTT
1 ATTTTTTT
18486 CGATATAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 13 0.52
10 12 0.48
ACGTcount: A:0.14, C:0.00, G:0.05, T:0.81
Consensus pattern (10 bp):
ATTTTTTTTG
Found at i:29345 original size:30 final size:30
Alignment explanation
Indices: 29305--29363 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
29295 TGTCTTCAAG
*
29305 TCCATAATAAGTCCTT-GGCGCATCATTCCT
1 TCCATAATAAG-CCTTGGGCACATCATTCCT
*
29335 TCCATGATAAGCCTTGGGCACATCATTCC
1 TCCATAATAAGCCTTGGGCACATCATTCC
29364 CTCCCCCTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.24, C:0.31, G:0.15, T:0.31
Consensus pattern (30 bp):
TCCATAATAAGCCTTGGGCACATCATTCCT
Found at i:29791 original size:33 final size:33
Alignment explanation
Indices: 29754--29860 Score: 187
Period size: 33 Copynumber: 3.2 Consensus size: 33
29744 AAAATAGTCC
29754 TATTTTCAATGCTATGATCAACCAAAACAGAAT
1 TATTTTCAATGCTATGATCAACCAAAACAGAAT
*
29787 TATTTTCAATGCTATGATCAACCAAAACAAAAT
1 TATTTTCAATGCTATGATCAACCAAAACAGAAT
*
29820 TATTTTCAATGCTATGATCAACCAAAACAGATT
1 TATTTTCAATGCTATGATCAACCAAAACAGAAT
*
29853 TGTTTTCA
1 TATTTTCA
29861 TCACAATTAG
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 70 1.00
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.34
Consensus pattern (33 bp):
TATTTTCAATGCTATGATCAACCAAAACAGAAT
Found at i:29878 original size:66 final size:66
Alignment explanation
Indices: 29754--29881 Score: 177
Period size: 66 Copynumber: 1.9 Consensus size: 66
29744 AAAATAGTCC
* * *
29754 TATTTTCAATGCTATGATCAACCAAAACAGAATTATTTTCAATGCTATGATCAACCAAAACAAAA
1 TATTTTCAATGCTATGATCAACCAAAACAGAATTATTTTCAATACAATGAGCAACCAAAACAAAA
29819 T
66 T
* * * *
29820 TATTTTCAATGCTATGATCAACCAAAACAGATTTGTTTTC-ATCACAATTAGCATCCAAAACA
1 TATTTTCAATGCTATGATCAACCAAAACAGAATTATTTTCAAT-ACAATGAGCAACCAAAACA
29882 GATTTAGTGT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
65 2 0.04
66 52 0.96
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (66 bp):
TATTTTCAATGCTATGATCAACCAAAACAGAATTATTTTCAATACAATGAGCAACCAAAACAAAA
T
Found at i:33306 original size:22 final size:22
Alignment explanation
Indices: 33278--33337 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
33268 GAAGTTCGTG
*
33278 TTTGAAGAATATTTGAAGATAA
1 TTTGAAGAATATTTGAAGACAA
33300 TTTGAAG---ATTTGAAGACAA
1 TTTGAAGAATATTTGAAGACAA
*
33319 -TTGAAGAATTATTTCAAGA
1 TTTGAAGAA-TATTTGAAGA
33338 AGCAAGAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 6 0.19
19 11 0.34
22 15 0.47
ACGTcount: A:0.43, C:0.03, G:0.18, T:0.35
Consensus pattern (22 bp):
TTTGAAGAATATTTGAAGACAA
Found at i:33312 original size:19 final size:18
Alignment explanation
Indices: 33288--33325 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
33278 TTTGAAGAAT
*
33288 ATTTGAAGATAATTTGAAG
1 ATTTGAAGACAA-TTGAAG
33307 ATTTGAAGACAATTGAAG
1 ATTTGAAGACAATTGAAG
33325 A
1 A
33326 ATTATTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.32
Consensus pattern (18 bp):
ATTTGAAGACAATTGAAG
Found at i:34689 original size:6 final size:6
Alignment explanation
Indices: 34674--34722 Score: 73
Period size: 6 Copynumber: 8.3 Consensus size: 6
34664 ATAATTGCTA
* *
34674 TAGATT TAGATA TAGATT TAGATT TAGAAT TAGATT TAGATT TA-ATT
1 TAGATT TAGATT TAGATT TAGATT TAGATT TAGATT TAGATT TAGATT
34721 TA
1 TA
34723 CTTTACTTAG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
5 5 0.13
6 34 0.87
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.47
Consensus pattern (6 bp):
TAGATT
Found at i:35167 original size:110 final size:110
Alignment explanation
Indices: 35041--35256 Score: 389
Period size: 110 Copynumber: 2.0 Consensus size: 110
35031 ATGGGGAGAA
35041 AATTGACAATTGAGAGTTATTAGAGTTATTGAAAATCCTTACTTTTATATAT-TCTGTAGAGTTT
1 AATTGACAATTGAGAGTTATTAGAGTTATTGAAAATCCTTACTTTTATATATGT-TGTAGAGTTT
*
35105 AATGTTTTTATCTAGTGTGTTCAGCATTTGAAAACCAGCATGTGAG
65 AATGTTTTTATCTAGTGTGTTCAACATTTGAAAACCAGCATGTGAG
* *
35151 AATTGAGAATTGAGAGTTATTAGAGTTATTGAAAATCCTTACTTTTATATATGTTGTGGAGTTTA
1 AATTGACAATTGAGAGTTATTAGAGTTATTGAAAATCCTTACTTTTATATATGTTGTAGAGTTTA
35216 ATGTTTTTATCTAGTGTGTTCAACATTTGAAAACCAGCATG
66 ATGTTTTTATCTAGTGTGTTCAACATTTGAAAACCAGCATG
35257 CTTGAAGGAG
Statistics
Matches: 102, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
110 101 0.99
111 1 0.01
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (110 bp):
AATTGACAATTGAGAGTTATTAGAGTTATTGAAAATCCTTACTTTTATATATGTTGTAGAGTTTA
ATGTTTTTATCTAGTGTGTTCAACATTTGAAAACCAGCATGTGAG
Found at i:37059 original size:32 final size:33
Alignment explanation
Indices: 36998--37065 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 33
36988 TTGTCACATT
* *
36998 AGTCCTTTTATTTTAGTATATGAAGTCATTTTAG
1 AGTCCTTTTATTTTAG-ACATGAAATCATTTTAG
*
37032 AGTCTTTTTATTTTAG-CATGAAATCATTTTAG
1 AGTCCTTTTATTTTAGACATGAAATCATTTTAG
37064 AG
1 AG
37066 AAATTGCTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
32 16 0.52
34 15 0.48
ACGTcount: A:0.28, C:0.09, G:0.15, T:0.49
Consensus pattern (33 bp):
AGTCCTTTTATTTTAGACATGAAATCATTTTAG
Done.