Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012707.1 Corchorus capsularis cultivar CVL-1 contig12728, 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: 43109
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:145 original size:20 final size:19
Alignment explanation
Indices: 120--160 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
110 TTATTTAGAA
*
120 ATTTAATTGTTAACCTTTAT
1 ATTTAATTCTTAACC-TTAT
140 ATTTAATTCTTAACCTTAT
1 ATTTAATTCTTAACCTTAT
159 AT
1 AT
161 AAGTTACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.32, C:0.12, G:0.02, T:0.54
Consensus pattern (19 bp):
ATTTAATTCTTAACCTTAT
Found at i:671 original size:21 final size:21
Alignment explanation
Indices: 645--695 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
635 GAATCAATCT
*
645 ACATGATTTGCGGACACGGTA
1 ACATGATTTGCGGACACGGCA
*
666 ACATGATTTGTGGACACGGCA
1 ACATGATTTGCGGACACGGCA
687 ACATGATTT
1 ACATGATTT
696 TCGGCTTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.27
Consensus pattern (21 bp):
ACATGATTTGCGGACACGGCA
Found at i:748 original size:30 final size:30
Alignment explanation
Indices: 712--768 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
702 TCAATCTTGG
* *
712 ATCCTGCTGTAAACAAACTGTTGACTTTGA
1 ATCCTGCTGCAAACAAACAGTTGACTTTGA
* *
742 ATCCTGCTGCAAATACACAGTTGACTT
1 ATCCTGCTGCAAACAAACAGTTGACTT
769 ATTTCATCAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.32
Consensus pattern (30 bp):
ATCCTGCTGCAAACAAACAGTTGACTTTGA
Found at i:5481 original size:21 final size:21
Alignment explanation
Indices: 5455--5505 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
5445 GAATCAATCT
*
5455 ACATGATTTGCGGACACGGTA
1 ACATGATTTGCGGACACGGCA
5476 ACATGATTTGCGGACACGGCA
1 ACATGATTTGCGGACACGGCA
5497 ACATGATTT
1 ACATGATTT
5506 TCGGCTTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (21 bp):
ACATGATTTGCGGACACGGCA
Found at i:10080 original size:9 final size:10
Alignment explanation
Indices: 10048--10079 Score: 50
Period size: 9 Copynumber: 3.4 Consensus size: 10
10038 GGAGGCATGA
10048 AGATGCAAGG
1 AGATGCAAGG
10058 A-ATGCAAGG
1 AGATGCAAGG
10067 AGAT-CAAGG
1 AGATGCAAGG
10076 AGAT
1 AGAT
10080 CTTGAACTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 18 0.86
10 3 0.14
ACGTcount: A:0.44, C:0.09, G:0.34, T:0.12
Consensus pattern (10 bp):
AGATGCAAGG
Found at i:22742 original size:32 final size:32
Alignment explanation
Indices: 22664--22761 Score: 101
Period size: 32 Copynumber: 3.1 Consensus size: 32
22654 AAAGAGTGTT
* * *
22664 TTAGA-TGTTGTTTGCGATGATACTAAACCTAA
1 TTAGAGTGTTGTTTGCGATGAAACTAAATCT-G
* *
22696 TTTGAGTGTTGTTTGCGATGACACTAAATCTG
1 TTAGAGTGTTGTTTGCGATGAAACTAAATCTG
* *
22728 TTA-AGGTGTTGTTTGTGATGAAACAAAATCTG
1 TTAGA-GTGTTGTTTGCGATGAAACTAAATCTG
22760 TT
1 TT
22762 TTGGATGCTA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
31 1 0.02
32 32 0.57
33 23 0.41
ACGTcount: A:0.28, C:0.10, G:0.22, T:0.40
Consensus pattern (32 bp):
TTAGAGTGTTGTTTGCGATGAAACTAAATCTG
Found at i:27581 original size:9 final size:9
Alignment explanation
Indices: 27569--27593 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
27559 CATGAAATTT
27569 TTTTGAAAA
1 TTTTGAAAA
27578 TTTTGAAAA
1 TTTTGAAAA
27587 TTTTGAA
1 TTTTGAA
27594 TTTTTCATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (9 bp):
TTTTGAAAA
Found at i:28865 original size:29 final size:29
Alignment explanation
Indices: 28811--28866 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
28801 TTGAAGATTT
* *
28811 ATTGAAGATAATTTGAAGAATTCAAGACC
1 ATTGAAGATAATTTCAAGAATGCAAGACC
*
28840 ATTGAAGAATTATTTCAAGAA-GCAAGA
1 ATTGAAG-ATAATTTCAAGAATGCAAGA
28867 ATCGAGGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 12 0.52
30 11 0.48
ACGTcount: A:0.46, C:0.09, G:0.18, T:0.27
Consensus pattern (29 bp):
ATTGAAGATAATTTCAAGAATGCAAGACC
Found at i:40660 original size:23 final size:24
Alignment explanation
Indices: 40611--40660 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
40601 ATGAAATCTT
* *
40611 TTTTTTTATAATTTTCAATTTCCA
1 TTTTTTTATAATTTTCAATTGCAA
* *
40635 TTTTTTTATATTTTTGAA-TGCAA
1 TTTTTTTATAATTTTCAATTGCAA
40658 TTT
1 TTT
40661 AAAAAATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.24, C:0.08, G:0.04, T:0.64
Consensus pattern (24 bp):
TTTTTTTATAATTTTCAATTGCAA
Found at i:40752 original size:22 final size:21
Alignment explanation
Indices: 40727--40778 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 21
40717 TGTTATGTTA
40727 TACTAAATGCAAAAAGTGAATT
1 TACTAAATGCAAAAAGTGAA-T
*
40749 TACTAAATGCCAAAAGTGAAT
1 TACTAAATGCAAAAAGTGAAT
*
40770 TACAAAATG
1 TACTAAATG
40779 ACATAAACGA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 9 0.32
22 19 0.68
ACGTcount: A:0.50, C:0.12, G:0.13, T:0.25
Consensus pattern (21 bp):
TACTAAATGCAAAAAGTGAAT
Found at i:41200 original size:47 final size:46
Alignment explanation
Indices: 41064--41218 Score: 202
Period size: 46 Copynumber: 3.3 Consensus size: 46
41054 AGGAAAATAA
* * * *
41064 TTGATTCACCAAATCAAACTTGGAAGAAATATTGCATCGAATTGAC
1 TTGATTCACCAAATCAAACTTTGAAGAAATATTGCACCGCATTAAC
* *
41110 TTGATTCACCGAATCAAACTTTGAAGAAATATTGCACCACATTAAC
1 TTGATTCACCAAATCAAACTTTGAAGAAATATTGCACCGCATTAAC
***
41156 TTGATTCACCAAATCAAACTTTTGAAGAAATAACACACCGCATTAAC
1 TTGATTCACCAAATCAAAC-TTTGAAGAAATATTGCACCGCATTAAC
* *
41203 TTGATCCACCGAATCA
1 TTGATTCACCAAATCA
41219 TCATGAACTG
Statistics
Matches: 95, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
46 58 0.61
47 37 0.39
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (46 bp):
TTGATTCACCAAATCAAACTTTGAAGAAATATTGCACCGCATTAAC
Found at i:41285 original size:90 final size:90
Alignment explanation
Indices: 41177--41691 Score: 742
Period size: 90 Copynumber: 5.7 Consensus size: 90
41167 AATCAAACTT
** * * * * *
41177 TTGAAGAAATAACACACCGCATTAACTTGATCCACCGAATCATCATGAACTGTTTGAAATTATGC
1 TTGAAGAAATAATGCACCGCATCAACTTGATTCACCGAATCATCTTGAACTGTTTGAAAATGTGC
41242 TGCACCGAGCTCACCGAATCCAATC
66 TGCACCGAGCTCACCGAATCCAATC
* * * *
41267 TTGAAGAAATAATGCACCGCATCTACTTGATTCACTGAATCATCCTGAATTGTTTGAAAAATGTG
1 TTGAAGAAATAATGCACCGCATCAACTTGATTCACCGAATCATCTTGAACTGTTTG-AAAATGTG
*
41332 CTGCACCGACCTCACCGAATCCAATC
65 CTGCACCGAGCTCACCGAATCCAATC
** * * *
41358 TTGAAGAAATAATGCACTTCATCAACTTGATTCACCGAATCATCTTGAGCTATTTAAAAATGTGC
1 TTGAAGAAATAATGCACCGCATCAACTTGATTCACCGAATCATCTTGAACTGTTTGAAAATGTGC
*
41423 TGCATCGAGCTCACCGAATCCAATC
66 TGCACCGAGCTCACCGAATCCAATC
* *
41448 TTGAAGAAATAATGCACCGCATCAACTTCATTCACCGAATCATCTTGAACTGTTTGAAAATGTGT
1 TTGAAGAAATAATGCACCGCATCAACTTGATTCACCGAATCATCTTGAACTGTTTGAAAATGTGC
* *
41513 TGCACCAAGCTCACCGAATCCATTC
66 TGCACCGAGCTCACCGAATCCAATC
* * *
41538 TTGAAGAAATAATGCACCGCATCAACTTCATTCACCGAATCATCCTTAAACTGTTTTAAAATGTG
1 TTGAAGAAATAATGCACCGCATCAACTTGATTCACCGAATCAT-CTTGAACTGTTTGAAAATGTG
* *
41603 CTGCACTGAGCTCACCAAATCCAATC
65 CTGCACCGAGCTCACCGAATCCAATC
* * *
41629 TTGAAGAAATAATGCACCGTATCAACCTGAATCACCGAATCATCTTGAACTGTTTGAAAATGT
1 TTGAAGAAATAATGCACCGCATCAACTTGATTCACCGAATCATCTTGAACTGTTTGAAAATGT
41692 TTGAAAATGT
Statistics
Matches: 378, Mismatches: 45, Indels: 4
0.89 0.11 0.01
Matches are distributed among these distances:
90 221 0.58
91 157 0.42
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.27
Consensus pattern (90 bp):
TTGAAGAAATAATGCACCGCATCAACTTGATTCACCGAATCATCTTGAACTGTTTGAAAATGTGC
TGCACCGAGCTCACCGAATCCAATC
Found at i:41396 original size:46 final size:44
Alignment explanation
Indices: 41343--41581 Score: 120
Period size: 46 Copynumber: 5.3 Consensus size: 44
41333 TGCACCGACC
*
41343 TCACCGAATCCAATCTTGAAGAAATAATGCACTTCATCAACTTGAT
1 TCACCGAAT-C-ATCTTGAAGAAATAATGCACTGCATCAACTTGAT
* ** * *
41389 TCACCGAATCATCTTG-AGCTATTTAAAAATGTGCTGCATCGA---G-C
1 TCACCGAATCATCTTGAAG--A---AATAATGCACTGCATCAACTTGAT
* *
41433 TCACCGAATCCAATCTTGAAGAAATAATGCACCGCATCAACTTCAT
1 TCACCGAAT-C-ATCTTGAAGAAATAATGCACTGCATCAACTTGAT
* *** * *
41479 TCACCGAATCATCTTGAACTGTTTGAA-AATGTGTTGCACCAA---G-C
1 TCACCGAATCATCTTGAA--G---AAATAATGCACTGCATCAACTTGAT
* *
41523 TCACCGAATCCATTCTTGAAGAAATAATGCACCGCATCAACTTCAT
1 TCACCGAAT-CA-TCTTGAAGAAATAATGCACTGCATCAACTTGAT
41569 TCACCGAATCATC
1 TCACCGAATCATC
41582 CTTAAACTGT
Statistics
Matches: 140, Mismatches: 29, Indels: 50
0.64 0.13 0.23
Matches are distributed among these distances:
41 2 0.01
42 23 0.16
43 2 0.01
44 35 0.25
45 10 0.07
46 41 0.29
47 2 0.01
48 23 0.16
49 2 0.01
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.27
Consensus pattern (44 bp):
TCACCGAATCATCTTGAAGAAATAATGCACTGCATCAACTTGAT
Found at i:41396 original size:181 final size:181
Alignment explanation
Indices: 41177--41735 Score: 751
Period size: 181 Copynumber: 3.0 Consensus size: 181
41167 AATCAAACTT
** * * * * * *
41177 TTGAAGAAATAACACACCGCATTAACTTGATCCACCGAATCATCATGAACTGTTTGAAATTATGC
1 TTGAAGAAATAATGCACCGCATCAACTTGATTCACCGAATCATCTTGAACTGTTTAAAAATGTGC
* *
41242 TGCACCGAGCTCACCGAATCCAATCTTGAAGAAATAATGCACCGCATCTACTTGATTCACTGAAT
66 TGCACCGAGCTCACCGAATCCAATCTTGAAGAAATAATGCACCGCATCAACTTGATTCACCGAAT
* * *
41307 CATCCTGAATTGTTTGAAAAATGTGCTGCACCGACCTCACCGAATCCAATC
131 CATCTTGAACTGTTTGAAAAATGTGCTGCACCGAGCTCACCGAATCCAATC
** * *
41358 TTGAAGAAATAATGCACTTCATCAACTTGATTCACCGAATCATCTTGAGCTATTTAAAAATGTGC
1 TTGAAGAAATAATGCACCGCATCAACTTGATTCACCGAATCATCTTGAACTGTTTAAAAATGTGC
* *
41423 TGCATCGAGCTCACCGAATCCAATCTTGAAGAAATAATGCACCGCATCAACTTCATTCACCGAAT
66 TGCACCGAGCTCACCGAATCCAATCTTGAAGAAATAATGCACCGCATCAACTTGATTCACCGAAT
* * *
41488 CATCTTGAACTGTTTG-AAAATGTGTTGCACCAAGCTCACCGAATCCATTC
131 CATCTTGAACTGTTTGAAAAATGTGCTGCACCGAGCTCACCGAATCCAATC
* * *
41538 TTGAAGAAATAATGCACCGCATCAACTTCATTCACCGAATCATCCTTAAACTGTTTTAAAATGTG
1 TTGAAGAAATAATGCACCGCATCAACTTGATTCACCGAATCAT-CTTGAACTGTTTAAAAATGTG
* * * * *
41603 CTGCACTGAGCTCACCAAATCCAATCTTGAAGAAATAATGCACCGTATCAACCTGAATCACCGAA
65 CTGCACCGAGCTCACCGAATCCAATCTTGAAGAAATAATGCACCGCATCAACTTGATTCACCGAA
41668 TCATCTTGAACTGTTTGAAAATGTTTGAAAATGTGCTGCACCGAGCTCACCGAATCCAATC
130 TCATCTTGAACTGTTTG---A------AAAATGTGCTGCACCGAGCTCACCGAATCCAATC
41729 TTGAAGA
1 TTGAAGA
41736 TACTTGATCG
Statistics
Matches: 328, Mismatches: 39, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
180 70 0.21
181 220 0.67
191 38 0.12
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (181 bp):
TTGAAGAAATAATGCACCGCATCAACTTGATTCACCGAATCATCTTGAACTGTTTAAAAATGTGC
TGCACCGAGCTCACCGAATCCAATCTTGAAGAAATAATGCACCGCATCAACTTGATTCACCGAAT
CATCTTGAACTGTTTGAAAAATGTGCTGCACCGAGCTCACCGAATCCAATC
Found at i:41666 original size:271 final size:271
Alignment explanation
Indices: 41177--41691 Score: 764
Period size: 271 Copynumber: 1.9 Consensus size: 271
41167 AATCAAACTT
* * *
41177 TTGAAGAAATAACACACCGCATTAACTTGATCCACCGAATCATCATGAACTGTTTGAAATTATGC
1 TTGAAGAAATAACACACCGCATCAACTTCATCCACCGAATCATCATGAACTGTTTGAAAATATGC
* * * *
41242 TGCACCGAGCTCACCGAATCCAATCTTGAAGAAATAATGCACCGCATCTACTTGATTCACTGAAT
66 TGCACCAAGCTCACCGAATCCAATCTTGAAGAAATAATGCACCGCATCAACTTCATTCACCGAAT
* * *
41307 CATCCTGAATTGTTTGAAAAATGTGCTGCACCGACCTCACCGAATCCAATCTTGAAGAAATAATG
131 CATCCTAAACTGTTTGAAAAATGTGCTGCACCGACCTCACCAAATCCAATCTTGAAGAAATAATG
* * * *
41372 CACTTCATCAACTTGATTCACCGAATCATCTTGAGCTATTTAAAAATGTGCTGCATCGAGCTCAC
196 CACGTCATCAACCTGAATCACCGAATCATCTTGAACTATTTAAAAATGTGCTGCATCGAGCTCAC
41437 CGAATCCAATC
261 CGAATCCAATC
** * * * *
41448 TTGAAGAAATAATGCACCGCATCAACTTCATTCACCGAATCATCTTGAACTGTTTGAAAATGTGT
1 TTGAAGAAATAACACACCGCATCAACTTCATCCACCGAATCATCATGAACTGTTTGAAAATATGC
*
41513 TGCACCAAGCTCACCGAATCCATTCTTGAAGAAATAATGCACCGCATCAACTTCATTCACCGAAT
66 TGCACCAAGCTCACCGAATCCAATCTTGAAGAAATAATGCACCGCATCAACTTCATTCACCGAAT
* * *
41578 CATCCTTAAACTGTTT-TAAAATGTGCTGCACTGAGCTCACCAAATCCAATCTTGAAGAAATAAT
131 CATCC-TAAACTGTTTGAAAAATGTGCTGCACCGACCTCACCAAATCCAATCTTGAAGAAATAAT
* *
41642 GCACCGT-ATCAACCTGAATCACCGAATCATCTTGAACTGTTTGAAAATGT
195 GCA-CGTCATCAACCTGAATCACCGAATCATCTTGAACTATTTAAAAATGT
41692 TTGAAAATGT
Statistics
Matches: 216, Mismatches: 26, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
271 206 0.95
272 10 0.05
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.27
Consensus pattern (271 bp):
TTGAAGAAATAACACACCGCATCAACTTCATCCACCGAATCATCATGAACTGTTTGAAAATATGC
TGCACCAAGCTCACCGAATCCAATCTTGAAGAAATAATGCACCGCATCAACTTCATTCACCGAAT
CATCCTAAACTGTTTGAAAAATGTGCTGCACCGACCTCACCAAATCCAATCTTGAAGAAATAATG
CACGTCATCAACCTGAATCACCGAATCATCTTGAACTATTTAAAAATGTGCTGCATCGAGCTCAC
CGAATCCAATC
Found at i:42002 original size:19 final size:18
Alignment explanation
Indices: 41978--42013 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
41968 TGAAGATTTC
41978 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
41997 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
42014 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Done.