Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008711.1 Corchorus capsularis cultivar CVL-1 contig08732, 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: 29419
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:40 original size:10 final size:10
Alignment explanation
Indices: 18--55 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
8 TTTCTTTTTC
18 TTTTTTTAA-
1 TTTTTTTAAT
27 -TTTTTTAAT
1 TTTTTTTAAT
*
36 TTTTTTTAAA
1 TTTTTTTAAT
46 TTTTTTTAAT
1 TTTTTTTAAT
56 ATTAATTAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 8 0.32
10 17 0.68
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTTTTAAT
Found at i:109 original size:39 final size:40
Alignment explanation
Indices: 51--127 Score: 104
Period size: 39 Copynumber: 1.9 Consensus size: 40
41 TTAAATTTTT
*
51 TTAATATTAATTAGTTTATTA-TTA-GTTTTAATTAGTTAA
1 TTAAAATTAATTAGTTTATTAGTTATG-TTTAATTAGTTAA
*
90 TTAAAATTACTTAGTTTATTAGTTTATGTTTAATTAGT
1 TTAAAATTAATTAGTTTATTAG-TTATGTTTAATTAGT
128 ATCTAATTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 19 0.58
41 13 0.39
42 1 0.03
ACGTcount: A:0.34, C:0.01, G:0.09, T:0.56
Consensus pattern (40 bp):
TTAAAATTAATTAGTTTATTAGTTATGTTTAATTAGTTAA
Found at i:127 original size:15 final size:14
Alignment explanation
Indices: 76--168 Score: 58
Period size: 11 Copynumber: 7.1 Consensus size: 14
66 TTATTATTAG
*
76 TTTTAATTAGTTAA
1 TTTTAATTAGTTTA
** *
90 TTAAAATTA-CTTA
1 TTTTAATTAGTTTA
*
103 GTTT-ATTAGTTTA
1 TTTTAATTAGTTTA
116 TGTTTAATTAG--TA
1 T-TTTAATTAGTTTA
*
129 -TCTAATTAGTTTA
1 TTTTAATTAGTTTA
142 TTATTAATTAG--TA
1 TT-TTAATTAGTTTA
155 -TTTAATTAGTTTA
1 TTTTAATTAGTTTA
168 T
1 T
169 GATTAAAATG
Statistics
Matches: 58, Mismatches: 11, Indels: 20
0.65 0.12 0.22
Matches are distributed among these distances:
11 16 0.28
12 5 0.09
13 14 0.24
14 11 0.19
15 12 0.21
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.56
Consensus pattern (14 bp):
TTTTAATTAGTTTA
Found at i:136 original size:26 final size:26
Alignment explanation
Indices: 107--174 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 26
97 TACTTAGTTT
107 ATTAGTTTATGTTTAATTAGTATCTA
1 ATTAGTTTATGTTTAATTAGTATCTA
*
133 ATTAGTTTAT-TATTAATTAGTATTTA
1 ATTAGTTTATGT-TTAATTAGTATCTA
*
159 ATTAGTTTATGATTAA
1 ATTAGTTTATGTTTAA
175 AATGAAGGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 1 0.03
26 37 0.97
ACGTcount: A:0.34, C:0.01, G:0.10, T:0.54
Consensus pattern (26 bp):
ATTAGTTTATGTTTAATTAGTATCTA
Found at i:174 original size:15 final size:13
Alignment explanation
Indices: 57--168 Score: 57
Period size: 11 Copynumber: 9.0 Consensus size: 13
47 TTTTTTAATA
57 TTAATTAGTTTA-
1 TTAATTAGTTTAT
69 TT-ATTAG--T-T
1 TTAATTAGTTTAT
*
78 TTAATTAGTTAAT
1 TTAATTAGTTTAT
* *
91 TAAAATTA-CTTAGT
1 T-TAATTAGTTTA-T
105 TT-ATTAGTTTATGT
1 TTAATTAGTTTA--T
119 TTAATTAG--TAT
1 TTAATTAGTTTAT
*
130 CTAATTAGTTTATT
1 TTAATTAGTTTA-T
144 ATTAATTAG--TAT
1 -TTAATTAGTTTAT
156 TTAATTAGTTTAT
1 TTAATTAGTTTAT
169 GATTAAAATG
Statistics
Matches: 76, Mismatches: 8, Indels: 31
0.66 0.07 0.27
Matches are distributed among these distances:
9 3 0.04
10 5 0.07
11 21 0.28
12 7 0.09
13 16 0.21
14 12 0.16
15 12 0.16
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.56
Consensus pattern (13 bp):
TTAATTAGTTTAT
Found at i:218 original size:24 final size:25
Alignment explanation
Indices: 184--242 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
174 AAATGAAGGA
*
184 AAATGAA-TTTGAAG-ATTTGTTAG
1 AAATGAAGTTTGAAGAAGTTGTTAG
207 AAATGAAGTTTGAAGAAGTTGTTAG
1 AAATGAAGTTTGAAGAAGTTGTTAG
232 AAATGAAGTTT
1 AAATGAAGTTT
243 AGGGTTTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
23 7 0.21
24 7 0.21
25 19 0.58
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.36
Consensus pattern (25 bp):
AAATGAAGTTTGAAGAAGTTGTTAG
Found at i:3509 original size:5 final size:6
Alignment explanation
Indices: 3494--3527 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
3484 AAATATTTAA
3494 AAAAAC AAAAAC AAAAAC GAAAAA- AAAAAC AAAA
1 AAAAAC AAAAAC AAAAAC -AAAAAC AAAAAC AAAA
3528 TTGGACTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 5 0.19
6 16 0.62
7 5 0.19
ACGTcount: A:0.85, C:0.12, G:0.03, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:7693 original size:25 final size:26
Alignment explanation
Indices: 7651--7700 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
7641 AATTGAAGCA
* *
7651 TTTGGACGTTTTGTCCCCTGAATTAC
1 TTTGGACATTTTGCCCCCTGAATTAC
7677 TTTGGACATTTTGCCCCCTGAATT
1 TTTGGACATTTTGCCCCCTGAATT
7701 TTAATTTTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.16, C:0.24, G:0.18, T:0.42
Consensus pattern (26 bp):
TTTGGACATTTTGCCCCCTGAATTAC
Found at i:7966 original size:29 final size:29
Alignment explanation
Indices: 7889--7966 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 29
7879 CGTTAGGCTG
7889 AGGGGGCAAAAC-TTCACAAAATTGAAGTTC
1 AGGGGGCAAAACGTT--CAAAATTGAAGTTC
* * * *
7919 ATGGGACAAAATGTCCAAAATTGAAGTTC
1 AGGGGGCAAAACGTTCAAAATTGAAGTTC
7948 AGGGGGCAAAACGTTCAAA
1 AGGGGGCAAAACGTTCAAA
7967 CACTACAAGT
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
29 29 0.74
30 9 0.23
31 1 0.03
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.19
Consensus pattern (29 bp):
AGGGGGCAAAACGTTCAAAATTGAAGTTC
Found at i:9008 original size:7 final size:7
Alignment explanation
Indices: 8996--9029 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
8986 TCAGTTCAGA
8996 CGGATTT
1 CGGATTT
9003 CGGATTT
1 CGGATTT
9010 CGGATTT
1 CGGATTT
9017 CGGATTT
1 CGGATTT
9024 CGGATT
1 CGGATT
9030 CATTTTGCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.15, C:0.15, G:0.29, T:0.41
Consensus pattern (7 bp):
CGGATTT
Found at i:9117 original size:12 final size:12
Alignment explanation
Indices: 9100--9125 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
9090 TTGGGTACGG
9100 AGTTAGGAAAGT
1 AGTTAGGAAAGT
9112 AGTTAGGAAAGT
1 AGTTAGGAAAGT
9124 AG
1 AG
9126 GTTTCATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.35, T:0.23
Consensus pattern (12 bp):
AGTTAGGAAAGT
Found at i:14862 original size:3 final size:3
Alignment explanation
Indices: 14854--14887 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
14844 TAAACCAGTA
*
14854 TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
14888 TATGAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:15649 original size:21 final size:21
Alignment explanation
Indices: 15636--15676 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
15626 AGAAACTTTC
15636 AAATATAAATAAGAAACCTCT
1 AAATATAAATAAGAAACCTCT
*
15657 AAATATAAATAAGAGACCTC
1 AAATATAAATAAGAAACCTC
15677 CAACATAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.56, C:0.15, G:0.07, T:0.22
Consensus pattern (21 bp):
AAATATAAATAAGAAACCTCT
Done.