Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015392.1 Corchorus olitorius cultivar O-4 contig15425, 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: 128415
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:79 original size:52 final size:52
Alignment explanation
Indices: 1--401 Score: 775
Period size: 52 Copynumber: 7.7 Consensus size: 52
1 ACAGCCCTCATCCGTCTCCCTAATTACTAAATCTTTTTAAATGTTCGGAGGG
1 ACAGCCCTCATCCGTCTCCCTAATTACTAAATCTTTTTAAATGTTCGGAGGG
53 ACAGCCCTCATCCGTCTCCCTAATTACTAAATCTTTTTAAATGTTCGGAGGG
1 ACAGCCCTCATCCGTCTCCCTAATTACTAAATCTTTTTAAATGTTCGGAGGG
*
105 ACAGCCCTCATCCGTCTCCCTAATTACTAAATCTTTTAAAATGTTCGGAGGG
1 ACAGCCCTCATCCGTCTCCCTAATTACTAAATCTTTTTAAATGTTCGGAGGG
*
157 ACAGCCCTCATCCGTCTCCCTAATTACTAAATCTTTTAAAATGTTCGGAGGG
1 ACAGCCCTCATCCGTCTCCCTAATTACTAAATCTTTTTAAATGTTCGGAGGG
209 ACAGCCCTCATCCGTCTCCCTAATTACTAAATCTTTTTAAATGTTCGGAGGG
1 ACAGCCCTCATCCGTCTCCCTAATTACTAAATCTTTTTAAATGTTCGGAGGG
*
261 ACAGCCCTCATCTGTCTCCCTAATTACTAAATCTTTTTAAATGTTCGGAGGG
1 ACAGCCCTCATCCGTCTCCCTAATTACTAAATCTTTTTAAATGTTCGGAGGG
313 ACAGCCCTCATCCGTCTCCCTAATTACTAAATCTTTTTAAATGTTCGGAGGG
1 ACAGCCCTCATCCGTCTCCCTAATTACTAAATCTTTTTAAATGTTCGGAGGG
365 ACAGCCCTCATCCGTCTCCCTAATTACTAAATCTTTT
1 ACAGCCCTCATCCGTCTCCCTAATTACTAAATCTTTT
402 AAACTTTTTA
Statistics
Matches: 345, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 345 1.00
ACGTcount: A:0.25, C:0.27, G:0.14, T:0.33
Consensus pattern (52 bp):
ACAGCCCTCATCCGTCTCCCTAATTACTAAATCTTTTTAAATGTTCGGAGGG
Found at i:1754 original size:23 final size:23
Alignment explanation
Indices: 1728--1773 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1718 TTACGTGGCG
1728 CACTCACCTTGAACCTTACCTCA
1 CACTCACCTTGAACCTTACCTCA
1751 CACTCACCTTGAACCTTACCTCA
1 CACTCACCTTGAACCTTACCTCA
1774 GCGTAACCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.43, G:0.04, T:0.26
Consensus pattern (23 bp):
CACTCACCTTGAACCTTACCTCA
Found at i:2749 original size:2 final size:2
Alignment explanation
Indices: 2744--2776 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2734 ATATATATAG
*
2744 AC AC AC AC AC AC AC AC AC AC AC AC AC AT AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
2777 TATATATAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.45, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:5071 original size:2 final size:2
Alignment explanation
Indices: 5064--5100 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5054 AAAACTGGGA
5064 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
5101 TAAAAAGCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5961 original size:2 final size:2
Alignment explanation
Indices: 5949--5984 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
5939 AGTCACCAAA
*
5949 AT AT A- AT AT AT AT AT AT AT AC 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 AT AT A
5985 AAATAAGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:9163 original size:20 final size:20
Alignment explanation
Indices: 9138--9176 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
9128 TTGCCTACTC
9138 AAGATCGAGCTCAACTCGAA
1 AAGATCGAGCTCAACTCGAA
9158 AAGATCGAGCTCAACTCGA
1 AAGATCGAGCTCAACTCGA
9177 TAGTAACTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.26, G:0.21, T:0.15
Consensus pattern (20 bp):
AAGATCGAGCTCAACTCGAA
Found at i:19031 original size:30 final size:31
Alignment explanation
Indices: 18964--19052 Score: 85
Period size: 31 Copynumber: 2.9 Consensus size: 31
18954 TTATAAACTT
* **
18964 CATAAAC-TTCAAA-TCAGGACATTTTGTTC
1 CATAAACTTTCAAATTCAAGACATTTTACTC
*
18993 CATAAACTTTCAAATTCACGACATTTTACTC
1 CATAAACTTTCAAATTCAAGACATTTTACTC
* * *
19024 C-TGAACTTCCCAAATTCAAAACATTTTAC
1 CATAAACTT-TCAAATTCAAGACATTTTAC
19053 CGTATGATGG
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
29 7 0.14
30 12 0.24
31 31 0.62
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.34
Consensus pattern (31 bp):
CATAAACTTTCAAATTCAAGACATTTTACTC
Found at i:27684 original size:9 final size:9
Alignment explanation
Indices: 27672--27706 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
27662 ATCATTTACC
*
27672 CCCCCCCCC
1 CCCCCCCCA
27681 CCCCCCCCAA
1 CCCCCCCC-A
27691 CCCCCCCCA
1 CCCCCCCCA
27700 CCCCCCC
1 CCCCCCC
27707 ACCTAATTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.09, C:0.91, G:0.00, T:0.00
Consensus pattern (9 bp):
CCCCCCCCA
Found at i:27685 original size:10 final size:10
Alignment explanation
Indices: 27669--27706 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
27659 ATGATCATTT
27669 ACCCCCCCCC
1 ACCCCCCCCC
*
27679 CCCCCCCCCC
1 ACCCCCCCCC
*
27689 AACCCCCCCC
1 ACCCCCCCCC
27699 ACCCCCCC
1 ACCCCCCC
27707 ACCTAATTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.11, C:0.89, G:0.00, T:0.00
Consensus pattern (10 bp):
ACCCCCCCCC
Found at i:27696 original size:18 final size:18
Alignment explanation
Indices: 27673--27707 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
27663 TCATTTACCC
*
27673 CCCCCCCCCCCCCCCCAA
1 CCCCCCCCACCCCCCCAA
27691 CCCCCCCCACCCCCCCA
1 CCCCCCCCACCCCCCCA
27708 CCTAATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.89, G:0.00, T:0.00
Consensus pattern (18 bp):
CCCCCCCCACCCCCCCAA
Found at i:29657 original size:3 final size:3
Alignment explanation
Indices: 29651--29676 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
29641 AAAAAAAAGA
29651 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
29677 AGGATCATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:37917 original size:5 final size:5
Alignment explanation
Indices: 37901--37932 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
37891 CTTAACTTTG
37901 TTTTC ATTTTC TTTTC TTTTC TTTTC TTTTC T
1 TTTTC -TTTTC TTTTC TTTTC TTTTC TTTTC T
37933 AATGATCCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:38210 original size:20 final size:21
Alignment explanation
Indices: 38185--38227 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
38175 TGCATAGCTC
*
38185 TTTCTTCTTT-TCTTTTCTTT
1 TTTCTTCTTTCCCTTTTCTTT
38205 TTTCTTCTTTCCCTTTTCTTT
1 TTTCTTCTTTCCCTTTTCTTT
38226 TT
1 TT
38228 AATAATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTCTTCTTTCCCTTTTCTTT
Found at i:44869 original size:16 final size:17
Alignment explanation
Indices: 44850--44883 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
44840 AAAACAGACT
44850 AAATAAA-AAAAATAAA
1 AAATAAAGAAAAATAAA
44866 AAATAAAGAAAAATAAA
1 AAATAAAGAAAAATAAA
44883 A
1 A
44884 GATTAATGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (17 bp):
AAATAAAGAAAAATAAA
Found at i:50575 original size:14 final size:14
Alignment explanation
Indices: 50555--50597 Score: 77
Period size: 14 Copynumber: 3.0 Consensus size: 14
50545 CTTCCCTTTT
50555 TTTTTTTTTACACCA
1 TTTTTTTTT-CACCA
50570 TTTTTTTTTCACCA
1 TTTTTTTTTCACCA
50584 TTTTTTTTTCACCA
1 TTTTTTTTTCACCA
50598 AAGAAAGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
14 19 0.68
15 9 0.32
ACGTcount: A:0.16, C:0.21, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTTTTTTTCACCA
Found at i:62042 original size:19 final size:20
Alignment explanation
Indices: 61992--62047 Score: 78
Period size: 21 Copynumber: 2.8 Consensus size: 20
61982 GGTATTCTAA
61992 TAATCTCATCTGTACAGTACG
1 TAATCTCATCTGTACAGTA-G
* *
62013 TGATCTAATCTGTACAGT-G
1 TAATCTCATCTGTACAGTAG
62032 TAATCTCATCTGTACA
1 TAATCTCATCTGTACA
62048 ATTACTAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 15 0.48
21 16 0.52
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (20 bp):
TAATCTCATCTGTACAGTAG
Found at i:67881 original size:15 final size:16
Alignment explanation
Indices: 67856--67886 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
67846 AAAGAAAGCT
67856 AAGGTGGAAGAAGAGG
1 AAGGTGGAAGAAGAGG
67872 AAGG-GGAAGAAGAGG
1 AAGGTGGAAGAAGAGG
67887 GGAAAAGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.45, C:0.00, G:0.52, T:0.03
Consensus pattern (16 bp):
AAGGTGGAAGAAGAGG
Found at i:70968 original size:2 final size:2
Alignment explanation
Indices: 70961--70985 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
70951 CAATACCCAA
70961 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
70986 ACCAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:74913 original size:235 final size:235
Alignment explanation
Indices: 74593--75071 Score: 949
Period size: 235 Copynumber: 2.0 Consensus size: 235
74583 ATTTGTCAGG
*
74593 GATTGCTTTGGCTGAACTTTGGTTATGACTACGAGCAATATTGAAACAACATGAAAATGCCCCTT
1 GATTCCTTTGGCTGAACTTTGGTTATGACTACGAGCAATATTGAAACAACATGAAAATGCCCCTT
74658 TAAGCTTTCCAAGCTTCCATTCTGTTATGATGATTTGTACATTTGGTCAATAATATGATATGGCT
66 TAAGCTTTCCAAGCTTCCATTCTGTTATGATGATTTGTACATTTGGTCAATAATATGATATGGCT
74723 TACCCCTGGAAAAATGAAGCATCCACTGGAAATCTGATAGCTATTGACAGAGTTGAAGTTTTTGA
131 TACCCCTGGAAAAATGAAGCATCCACTGGAAATCTGATAGCTATTGACAGAGTTGAAGTTTTTGA
74788 AGCTTCCAGTTTTACAAAGGCACTTATCTTTGCTTGATTT
196 AGCTTCCAGTTTTACAAAGGCACTTATCTTTGCTTGATTT
74828 GATTCCTTTGGCTGAACTTTGGTTATGACTACGAGCAATATTGAAACAACATGAAAATGCCCCTT
1 GATTCCTTTGGCTGAACTTTGGTTATGACTACGAGCAATATTGAAACAACATGAAAATGCCCCTT
74893 TAAGCTTTCCAAGCTTCCATTCTGTTATGATGATTTGTACATTTGGTCAATAATATGATATGGCT
66 TAAGCTTTCCAAGCTTCCATTCTGTTATGATGATTTGTACATTTGGTCAATAATATGATATGGCT
74958 TACCCCTGGAAAAATGAAGCATCCACTGGAAATCTGATAGCTATTGACAGAGTTGAAGTTTTTGA
131 TACCCCTGGAAAAATGAAGCATCCACTGGAAATCTGATAGCTATTGACAGAGTTGAAGTTTTTGA
75023 AGCTTCCAGTTTTACAAAGGCACTTATCTTTGCTTGATTT
196 AGCTTCCAGTTTTACAAAGGCACTTATCTTTGCTTGATTT
75063 GATTCCTTT
1 GATTCCTTT
75072 TCTGAAATAT
Statistics
Matches: 243, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
235 243 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (235 bp):
GATTCCTTTGGCTGAACTTTGGTTATGACTACGAGCAATATTGAAACAACATGAAAATGCCCCTT
TAAGCTTTCCAAGCTTCCATTCTGTTATGATGATTTGTACATTTGGTCAATAATATGATATGGCT
TACCCCTGGAAAAATGAAGCATCCACTGGAAATCTGATAGCTATTGACAGAGTTGAAGTTTTTGA
AGCTTCCAGTTTTACAAAGGCACTTATCTTTGCTTGATTT
Found at i:101383 original size:30 final size:30
Alignment explanation
Indices: 101349--101407 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
101339 TAATATGATG
*
101349 TTAAAATTCGAAGGTATAAGAGGATAGTTT
1 TTAAAATTCGAAGGTATAAGAGGAAAGTTT
* *
101379 TTAAAATTTGAGGGTATAAGAGGAAAGTT
1 TTAAAATTCGAAGGTATAAGAGGAAAGTT
101408 AAAATAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.41, C:0.02, G:0.25, T:0.32
Consensus pattern (30 bp):
TTAAAATTCGAAGGTATAAGAGGAAAGTTT
Found at i:101653 original size:15 final size:15
Alignment explanation
Indices: 101633--101662 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
101623 ACGACGATGT
101633 ATTGTTTATATATCC
1 ATTGTTTATATATCC
101648 ATTGTTTATATATCC
1 ATTGTTTATATATCC
101663 GAGATATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.07, T:0.53
Consensus pattern (15 bp):
ATTGTTTATATATCC
Found at i:106213 original size:15 final size:15
Alignment explanation
Indices: 106193--106227 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
106183 TAACATGACA
106193 GAATTGAATGATTCT
1 GAATTGAATGATTCT
106208 GAATTGAATGATTCT
1 GAATTGAATGATTCT
106223 GAATT
1 GAATT
106228 TATGATAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.34, C:0.06, G:0.20, T:0.40
Consensus pattern (15 bp):
GAATTGAATGATTCT
Found at i:107515 original size:13 final size:14
Alignment explanation
Indices: 107488--107518 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
107478 GCCATTTGTC
107488 TTTCCTTTTCTTTT
1 TTTCCTTTTCTTTT
*
107502 TTTCTTTTTCTTTT
1 TTTCCTTTTCTTTT
107516 TTT
1 TTT
107519 AATGTTGTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTCCTTTTCTTTT
Found at i:113039 original size:42 final size:42
Alignment explanation
Indices: 112987--113070 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
112977 GTTGTACGAG
*
112987 TATTCCTGTGCGTTTGTAATCTCAATCTCTTCAAGAAATGAA
1 TATTCATGTGCGTTTGTAATCTCAATCTCTTCAAGAAATGAA
113029 TATTCATGTGCGTTTGTAATCTCAATCTCTTCAAGAAATGAA
1 TATTCATGTGCGTTTGTAATCTCAATCTCTTCAAGAAATGAA
113071 AATGATTCTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (42 bp):
TATTCATGTGCGTTTGTAATCTCAATCTCTTCAAGAAATGAA
Found at i:115635 original size:3 final size:3
Alignment explanation
Indices: 115627--115675 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
115617 ATATATATAC
115627 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
115675 A
1 A
115676 GGAGAAGAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:126200 original size:4 final size:4
Alignment explanation
Indices: 126184--126215 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
126174 AGCTAATTTA
*
126184 CTTC CTTC TTTC CTTC CTTC CTTC CTTC CTTC
1 CTTC CTTC CTTC CTTC CTTC CTTC CTTC CTTC
126216 TTCAACAACC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (4 bp):
CTTC
Done.