Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011487.1 Corchorus capsularis cultivar CVL-1 contig11508, 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: 77576
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1675 original size:2 final size:2
Alignment explanation
Indices: 1668--1700 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1658 TGTATCAGGC
1668 AT AT AT 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 AT AT AT A
1701 CTACATATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3227 original size:12 final size:11
Alignment explanation
Indices: 3207--3236 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
3197 TGACACGCAT
3207 AAAAAGGAAAA
1 AAAAAGGAAAA
3218 AAAGAAGGAAAA
1 AAA-AAGGAAAA
3230 AAAAAGG
1 AAAAAGG
3237 TTTATTGCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (11 bp):
AAAAAGGAAAA
Found at i:6190 original size:70 final size:68
Alignment explanation
Indices: 6107--6238 Score: 210
Period size: 70 Copynumber: 1.9 Consensus size: 68
6097 ATGGGCGCGT
* *
6107 TAGTAAATATGCGATTGACACTGTTTAAGTACTGTACAAATGAGATTACACTAAACAAATCAAAA
1 TAGTAAAGATGCGATTGACACTGTTTAAGTACTATACAAATGAGATTACACT-AAC-AATCAAAA
6172 CAGTG
64 CAGTG
* *
6177 TAGTAAAGATGCGATTGACACTGTTTAAGTACTATACAGATGAGATTGCACTAACAATCAAA
1 TAGTAAAGATGCGATTGACACTGTTTAAGTACTATACAAATGAGATTACACTAACAATCAAA
6239 GTAGGTACTG
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
68 7 0.12
69 3 0.05
70 48 0.83
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (68 bp):
TAGTAAAGATGCGATTGACACTGTTTAAGTACTATACAAATGAGATTACACTAACAATCAAAACA
GTG
Found at i:11059 original size:8 final size:8
Alignment explanation
Indices: 11044--11075 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
11034 TAATTGTATG
11044 TATTATTA
1 TATTATTA
*
11052 TCTTATTA
1 TATTATTA
11060 TATTATTA
1 TATTATTA
11068 TATTATTA
1 TATTATTA
11076 CTAGTACCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (8 bp):
TATTATTA
Found at i:18281 original size:41 final size:41
Alignment explanation
Indices: 18235--18333 Score: 123
Period size: 41 Copynumber: 2.4 Consensus size: 41
18225 TTTTTCTTAT
* *
18235 TATCTCACCTAGGGTTTA-ATGTATTTTTTGAGGGTTT-CTTC
1 TATCTCACTTAGGGTTTATAT-TATTTGTT-AGGGTTTGCTTC
*
18276 TATCTCACTTAGGGTTTATATTGTTTGTTAGGGTTTGGCTTC
1 TATCTCACTTAGGGTTTATATTATTTGTTAGGGTTT-GCTTC
18318 -ATCTCACTTAGGGTTT
1 TATCTCACTTAGGGTTT
18334 GTCATGTCAT
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
40 7 0.13
41 39 0.75
42 6 0.12
ACGTcount: A:0.16, C:0.14, G:0.21, T:0.48
Consensus pattern (41 bp):
TATCTCACTTAGGGTTTATATTATTTGTTAGGGTTTGCTTC
Found at i:20855 original size:75 final size:75
Alignment explanation
Indices: 20776--20925 Score: 300
Period size: 75 Copynumber: 2.0 Consensus size: 75
20766 TTTGTGTAAT
20776 TCTTTATTTTTGCAGATAGTGATAAGATTCAAGCATGAACATGCCAGGTAGTCCATACATGTTTC
1 TCTTTATTTTTGCAGATAGTGATAAGATTCAAGCATGAACATGCCAGGTAGTCCATACATGTTTC
20841 AATTTATACA
66 AATTTATACA
20851 TCTTTATTTTTGCAGATAGTGATAAGATTCAAGCATGAACATGCCAGGTAGTCCATACATGTTTC
1 TCTTTATTTTTGCAGATAGTGATAAGATTCAAGCATGAACATGCCAGGTAGTCCATACATGTTTC
20916 AATTTATACA
66 AATTTATACA
20926 CTGATTTAAT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (75 bp):
TCTTTATTTTTGCAGATAGTGATAAGATTCAAGCATGAACATGCCAGGTAGTCCATACATGTTTC
AATTTATACA
Found at i:25723 original size:1 final size:1
Alignment explanation
Indices: 25717--25744 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
25707 TATATGATTT
25717 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
25745 GAGTAGTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:29778 original size:60 final size:59
Alignment explanation
Indices: 29703--29862 Score: 194
Period size: 60 Copynumber: 2.7 Consensus size: 59
29693 GCTAATTACT
* * * ** *
29703 CAAATAAGAGTCTAACGTTTGTCAAAATACTCAAATAAGGGTATGTTCTTTTAATTTGGC
1 CAAATAAGAGCCTAACGTTTG-CAAAATGCTCAAATAAGGGCATCATCTTTGAATTTGGC
* * *
29763 CAAATAAGGGCCTAACGTTTGCAAAAATGTTCAAATAAGGGCCTCATCTTTGAATTTGGC
1 CAAATAAGAGCCTAACGTTTGC-AAAATGCTCAAATAAGGGCATCATCTTTGAATTTGGC
* *
29823 CAAATAAAAACCTAACGTTTGCCAAAATGCTCAAATAAGG
1 CAAATAAGAGCCTAACGTTTG-CAAAATGCTCAAATAAGG
29863 ACTCTCTCAC
Statistics
Matches: 85, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
59 1 0.01
60 83 0.98
61 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.29
Consensus pattern (59 bp):
CAAATAAGAGCCTAACGTTTGCAAAATGCTCAAATAAGGGCATCATCTTTGAATTTGGC
Found at i:29931 original size:31 final size:31
Alignment explanation
Indices: 29888--29967 Score: 106
Period size: 31 Copynumber: 2.6 Consensus size: 31
29878 ATCCAAACTG
* *
29888 ACATCAGGCCCTTATTTGAGCATTTTCAATA
1 ACATTAGGCCCTTATTTGAACATTTTCAATA
** * *
29919 ATGTTAGGCCCTTATTTGAATATTTTCGATA
1 ACATTAGGCCCTTATTTGAACATTTTCAATA
29950 ACATTAGGCCCTTATTTG
1 ACATTAGGCCCTTATTTG
29968 GCCAAATTAA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (31 bp):
ACATTAGGCCCTTATTTGAACATTTTCAATA
Found at i:30760 original size:13 final size:13
Alignment explanation
Indices: 30742--30768 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
30732 AGAATTGATG
30742 AGATTGGTATAAT
1 AGATTGGTATAAT
30755 AGATTGGTATAAT
1 AGATTGGTATAAT
30768 A
1 A
30769 ATTATAAACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (13 bp):
AGATTGGTATAAT
Found at i:44220 original size:37 final size:37
Alignment explanation
Indices: 44170--44244 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
44160 GGTGTAGATG
*
44170 TAAGGACATTGCTTGTTACTTGCACATGCAAAGCGCT
1 TAAGGACATTGCTTGTTACTTGCACATGCAAAACGCT
*
44207 TAAGGCCATTGCTTGTTACTTGCACATGCAAAACGCT
1 TAAGGACATTGCTTGTTACTTGCACATGCAAAACGCT
44244 T
1 T
44245 CCTCCATGCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.31
Consensus pattern (37 bp):
TAAGGACATTGCTTGTTACTTGCACATGCAAAACGCT
Found at i:45324 original size:2 final size:2
Alignment explanation
Indices: 45319--45348 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
45309 GATAAACTTT
*
45319 TG TG TG TG TG TG TG TG TG TG TG TG TT TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
45349 GTTTTGGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.47, T:0.53
Consensus pattern (2 bp):
TG
Found at i:50071 original size:125 final size:127
Alignment explanation
Indices: 49844--50098 Score: 406
Period size: 125 Copynumber: 2.0 Consensus size: 127
49834 ATAAAACTTG
*
49844 CTCTAGATCATTTTTTTTTATAAATGAAGCAAAGAAAAGAAAAGCGGGTGCCAATGTTTCGAGTG
1 CTCTAGATCATTTTTTTTTATAAAT--AG-AAAGAAAAGAAAAGCGGGTGCAAATGTTTCGAGTG
* * *
49909 AAGGAGAAATTGAACATTGATCGAGTGATCATGTTGTAACTATTGAGGCAAATGCTCGGATTTAA
63 AAGGAGAAACTGAACATTGATCAAGTGATCATGTTGTAACTATTGAGCCAAATGCTCGGATTTAA
*
49974 CTCTAGATCATTTTTTTTTATAAAT-G-AAGTAAAGAAAAGCGGGTGCAAATGTTTCGAGTGAAG
1 CTCTAGATCATTTTTTTTTATAAATAGAAAGAAAAGAAAAGCGGGTGCAAATGTTTCGAGTGAAG
* *
50037 GAGAAACTGAACATTGTTCAAGTGATCATGTTGTAACTATTGAGCCAAATGCTTGGATTTAA
66 GAGAAACTGAACATTGATCAAGTGATCATGTTGTAACTATTGAGCCAAATGCTCGGATTTAA
50099 TAAAGATGGA
Statistics
Matches: 118, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
125 92 0.78
127 1 0.01
130 25 0.21
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.31
Consensus pattern (127 bp):
CTCTAGATCATTTTTTTTTATAAATAGAAAGAAAAGAAAAGCGGGTGCAAATGTTTCGAGTGAAG
GAGAAACTGAACATTGATCAAGTGATCATGTTGTAACTATTGAGCCAAATGCTCGGATTTAA
Found at i:61134 original size:2 final size:2
Alignment explanation
Indices: 61127--61152 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
61117 TTGTTAGAAG
61127 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
61153 GGTGTCCCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:61903 original size:21 final size:21
Alignment explanation
Indices: 61879--61923 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
61869 TAGATACTAT
*
61879 TTAGCAACTGTACAGATTAGA
1 TTAGCAACTGTACAGATGAGA
**
61900 TTAGGTACTGTACAGATGAGA
1 TTAGCAACTGTACAGATGAGA
61921 TTA
1 TTA
61924 TTAGAGCAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (21 bp):
TTAGCAACTGTACAGATGAGA
Found at i:63299 original size:11 final size:11
Alignment explanation
Indices: 63285--63322 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
63275 ATTCATAACA
63285 AATTTATAATT
1 AATTTATAATT
63296 AATTTATAATT
1 AATTTATAATT
63307 -ATTTGATAATT
1 AATTT-ATAATT
*
63318 TATTT
1 AATTT
63323 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:73619 original size:15 final size:15
Alignment explanation
Indices: 73595--73655 Score: 53
Period size: 15 Copynumber: 4.4 Consensus size: 15
73585 AAATTACTTA
73595 GTTT-ATTAGTTTAT
1 GTTTAATTAGTTTAT
73609 GTTTAATTAG--TA-
1 GTTTAATTAGTTTAT
*
73621 -TCTAATTAGTTTAT
1 GTTTAATTAGTTTAT
73635 -TATTAATTAGTTTAT
1 GT-TTAATTAGTTTAT
*
73650 GATTAA
1 GTTTAA
73656 AATGAAGGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
11 8 0.21
13 4 0.11
14 5 0.13
15 21 0.55
ACGTcount: A:0.31, C:0.02, G:0.11, T:0.56
Consensus pattern (15 bp):
GTTTAATTAGTTTAT
Found at i:73654 original size:26 final size:26
Alignment explanation
Indices: 73599--73654 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
73589 TACTTAGTTT
*
73599 ATTAGTTTATGTTTAATTAGTATCTA
1 ATTAGTTTATGTTTAATTAGTATATA
* *
73625 ATTAGTTTAT-TATTAATTAGTTTATG
1 ATTAGTTTATGT-TTAATTAGTATATA
73651 ATTA
1 ATTA
73655 AAATGAAGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 1 0.04
26 25 0.96
ACGTcount: A:0.32, C:0.02, G:0.11, T:0.55
Consensus pattern (26 bp):
ATTAGTTTATGTTTAATTAGTATATA
Found at i:73703 original size:24 final size:25
Alignment explanation
Indices: 73664--73723 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
73654 AAAATGAAGG
*
73664 AAAATGAA-TTTGAAG-ATTTGTTA
1 AAAATGAAGTTTGAAGAAATTGTTA
73687 AAAATGAAGTTTGAAGAAATTGTTA
1 AAAATGAAGTTTGAAGAAATTGTTA
* *
73712 GAAATTAAGTTT
1 AAAATGAAGTTT
73724 AGGGTTTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 8 0.25
24 7 0.22
25 17 0.53
ACGTcount: A:0.45, C:0.00, G:0.18, T:0.37
Consensus pattern (25 bp):
AAAATGAAGTTTGAAGAAATTGTTA
Done.