Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013418.1 Corchorus capsularis cultivar CVL-1 contig13439, 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: 66928
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:111 original size:26 final size:26
Alignment explanation
Indices: 82--143 Score: 99
Period size: 26 Copynumber: 2.4 Consensus size: 26
72 TACTTAGTTT
82 ATTAGTTTA-TATTTAATTAGTATCTA
1 ATTAGTTTATTA-TTAATTAGTATCTA
*
108 ATTAGTTTATTATTAATTAGTATTTA
1 ATTAGTTTATTATTAATTAGTATCTA
134 ATTAGTTTAT
1 ATTAGTTTAT
144 GGTTAAAATG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
26 32 0.94
27 2 0.06
ACGTcount: A:0.34, C:0.02, G:0.08, T:0.56
Consensus pattern (26 bp):
ATTAGTTTATTATTAATTAGTATCTA
Found at i:134 original size:11 final size:11
Alignment explanation
Indices: 91--139 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 11
81 TATTAGTTTA
91 TATTTAATTAG
1 TATTTAATTAG
*
102 TATCTAATTAG
1 TATTTAATTAG
113 TTTATTATTAATTAG
1 --TA-T-TTAATTAG
128 TATTTAATTAG
1 TATTTAATTAG
139 T
1 T
140 TTATGGTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
11 19 0.59
12 1 0.03
13 4 0.12
14 1 0.03
15 7 0.22
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.55
Consensus pattern (11 bp):
TATTTAATTAG
Found at i:149 original size:15 final size:13
Alignment explanation
Indices: 52--143 Score: 52
Period size: 11 Copynumber: 7.1 Consensus size: 13
42 TATGATTAGT
*
52 TTTAATTAGTTAA
1 TTTAATTAGTTTA
* *
65 TTAAAATTA-CTTA
1 TT-TAATTAGTTTA
78 GTTT-ATTAGTTTATA
1 -TTTAATTAG-TT-TA
93 TTTAATTAG--TA
1 TTTAATTAGTTTA
*
104 TCTAATTAGTTTA
1 TTTAATTAGTTTA
117 TTATTAATTAG--TA
1 -T-TTAATTAGTTTA
130 TTTAATTAGTTTA
1 TTTAATTAGTTTA
143 T
1 T
144 GGTTAAAATG
Statistics
Matches: 60, Mismatches: 7, Indels: 24
0.66 0.08 0.26
Matches are distributed among these distances:
11 18 0.30
12 5 0.08
13 11 0.18
14 12 0.20
15 14 0.23
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.55
Consensus pattern (13 bp):
TTTAATTAGTTTA
Found at i:197 original size:24 final size:25
Alignment explanation
Indices: 158--217 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
148 AAAATGAAGG
*
158 AAAATGAA-TTTGAAG-ATTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
181 AAAATGAAGTTTGAAGAAGTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
*
206 GAAATGAAGTTT
1 AAAATGAAGTTT
218 AGGGTTTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
23 8 0.24
24 7 0.21
25 18 0.55
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (25 bp):
AAAATGAAGTTTGAAGAAGTTGTTA
Found at i:327 original size:20 final size:21
Alignment explanation
Indices: 287--329 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
277 GCAAAAGTGT
**
287 AAAAAGGGGACGGTATTTAGC
1 AAAAAGGGGACGGTAAATAGC
308 AAAAA-GGGACGGTAAATAGC
1 AAAAAGGGGACGGTAAATAGC
328 AA
1 AA
330 TCCAGTTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.47, C:0.09, G:0.30, T:0.14
Consensus pattern (21 bp):
AAAAAGGGGACGGTAAATAGC
Found at i:4733 original size:20 final size:20
Alignment explanation
Indices: 4708--4747 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
4698 GTCTATAAAT
4708 AAATGTTAAAGCTACCAAAA
1 AAATGTTAAAGCTACCAAAA
**
4728 AAATGTTATTGCTACCAAAA
1 AAATGTTAAAGCTACCAAAA
4748 GAAAAAATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.25
Consensus pattern (20 bp):
AAATGTTAAAGCTACCAAAA
Found at i:7710 original size:61 final size:61
Alignment explanation
Indices: 7600--7792 Score: 307
Period size: 61 Copynumber: 3.1 Consensus size: 61
7590 TTCTTTGACA
* *
7600 AATTAATTATA-TTTGTTTTAAATTTCTTTTCTTTTTGAGGTCTTGTAAATTTATTTTATTTAGC
1 AATTAATTATATTTTGTTTGAAA----TTTT-TTTTT-AGGTCTTTTAAATTTATTTTATTTAGC
7664 TC
60 TC
7666 AATTAATTATATTTTGTTTGAAATTTTTTTTTAGGTCTTTTAAATTTATTTTATTTAGCTC
1 AATTAATTATATTTTGTTTGAAATTTTTTTTTAGGTCTTTTAAATTTATTTTATTTAGCTC
7727 AATTAATTATATTTTGTTTGAAATTTTTTTTTAGGTCTTTTAAATTTATTTTATTTAGCTC
1 AATTAATTATATTTTGTTTGAAATTTTTTTTTAGGTCTTTTAAATTTATTTTATTTAGCTC
7788 AATTA
1 AATTA
7793 GCTTAATGCA
Statistics
Matches: 124, Mismatches: 2, Indels: 7
0.93 0.02 0.05
Matches are distributed among these distances:
61 94 0.76
62 5 0.04
63 4 0.03
66 11 0.09
67 10 0.08
ACGTcount: A:0.26, C:0.06, G:0.08, T:0.60
Consensus pattern (61 bp):
AATTAATTATATTTTGTTTGAAATTTTTTTTTAGGTCTTTTAAATTTATTTTATTTAGCTC
Found at i:16404 original size:23 final size:24
Alignment explanation
Indices: 16360--16406 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
16350 CTATTACCTT
16360 AGAATCCAATTCCAAAGGGGTATA
1 AGAATCCAATTCCAAAGGGGTATA
16384 AGAATCCAATTCC-AAGGGGTATA
1 AGAATCCAATTCCAAAGGGGTATA
16407 TTCAATTGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (24 bp):
AGAATCCAATTCCAAAGGGGTATA
Found at i:26096 original size:17 final size:19
Alignment explanation
Indices: 26074--26109 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
26064 ACTAGACTCG
26074 AAACTGACT-AAAA-AAAC
1 AAACTGACTCAAAACAAAC
26091 AAACTGACTCAAAACAAAC
1 AAACTGACTCAAAACAAAC
26110 TCAAATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.61, C:0.22, G:0.06, T:0.11
Consensus pattern (19 bp):
AAACTGACTCAAAACAAAC
Found at i:32822 original size:39 final size:39
Alignment explanation
Indices: 32740--32837 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
32730 TGGCTGAAGC
* * * *
32740 TCTTCCTCCTCTTCTTCATCCTCATCATCATCTTCTTCT
1 TCTTCCTCCTCTTCCTCATCCTCATCATCATCGTCGTCA
*
32779 TCTTCCTCCTCTTCCTC-TCCATCATCATCGTCGTCGTCA
1 TCTTCCTCCTCTTCCTCATCC-TCATCATCATCGTCGTCA
* * *
32818 TCTTCATCTTCATCCTCATC
1 TCTTCCTCCTCTTCCTCATC
32838 GTCTCCAGTG
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
38 3 0.06
39 44 0.90
40 2 0.04
ACGTcount: A:0.11, C:0.42, G:0.03, T:0.44
Consensus pattern (39 bp):
TCTTCCTCCTCTTCCTCATCCTCATCATCATCGTCGTCA
Found at i:32839 original size:24 final size:24
Alignment explanation
Indices: 32752--32840 Score: 88
Period size: 24 Copynumber: 3.7 Consensus size: 24
32742 TTCCTCCTCT
* *
32752 TCTTCATCCTCATCATCATCTTCT
1 TCTTCATCCTCATCGTCATCTTCA
* * * * *
32776 TCTTCTTCCTCCTCTTCCTCTCCA
1 TCTTCATCCTCATCGTCATCTTCA
* * *
32800 TCATCATCGTCGTCGTCATCTTCA
1 TCTTCATCCTCATCGTCATCTTCA
32824 TCTTCATCCTCATCGTC
1 TCTTCATCCTCATCGTC
32841 TCCAGTGCCG
Statistics
Matches: 49, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.12, C:0.40, G:0.04, T:0.43
Consensus pattern (24 bp):
TCTTCATCCTCATCGTCATCTTCA
Found at i:32915 original size:6 final size:6
Alignment explanation
Indices: 32906--32941 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
32896 TCACCAGATG
* *
32906 CATCTT CATCCT CACCTT CATCTT CATCTT CATCTT
1 CATCTT CATCTT CATCTT CATCTT CATCTT CATCTT
32942 GATCATCTGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.17, C:0.39, G:0.00, T:0.44
Consensus pattern (6 bp):
CATCTT
Found at i:43118 original size:15 final size:15
Alignment explanation
Indices: 43100--43138 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
43090 ACCAAAAAGG
43100 AAGGGAAAGAAA-AAA
1 AAGGGAAA-AAATAAA
*
43115 AAGGGAAAAAATTAA
1 AAGGGAAAAAATAAA
43130 AAGGGAAAA
1 AAGGGAAAA
43139 GCAAATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 3 0.14
15 19 0.86
ACGTcount: A:0.69, C:0.00, G:0.26, T:0.05
Consensus pattern (15 bp):
AAGGGAAAAAATAAA
Found at i:50285 original size:12 final size:12
Alignment explanation
Indices: 50268--50292 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
50258 CTGCAGCTTA
50268 AACGTGCACCCC
1 AACGTGCACCCC
50280 AACGTGCACCCC
1 AACGTGCACCCC
50292 A
1 A
50293 TTGCTATGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.48, G:0.16, T:0.08
Consensus pattern (12 bp):
AACGTGCACCCC
Found at i:54123 original size:33 final size:33
Alignment explanation
Indices: 54055--54123 Score: 77
Period size: 33 Copynumber: 2.1 Consensus size: 33
54045 TATTTTCAAG
* * * * *
54055 TGAGATTAATCTCTCTCATATCCCTTATTGGTT
1 TGAGATTAATCTCTCCCAAATCACTAATTGATT
54088 TGAGATTAATCTCTCCCAAATCAAC-AATTGATT
1 TGAGATTAATCTCTCCCAAATC-ACTAATTGATT
54121 TGA
1 TGA
54124 AATAGTACCT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (33 bp):
TGAGATTAATCTCTCCCAAATCACTAATTGATT
Done.