Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012557.1 Corchorus olitorius cultivar O-4 contig12590, 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: 53276
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:1858 original size:17 final size:17
Alignment explanation
Indices: 1836--1883 Score: 96
Period size: 17 Copynumber: 2.8 Consensus size: 17
1826 CCCATCATCA
1836 TTGACTTCAACCCACCG
1 TTGACTTCAACCCACCG
1853 TTGACTTCAACCCACCG
1 TTGACTTCAACCCACCG
1870 TTGACTTCAACCCA
1 TTGACTTCAACCCA
1884 TCCTTTTCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.25, C:0.40, G:0.10, T:0.25
Consensus pattern (17 bp):
TTGACTTCAACCCACCG
Found at i:2294 original size:19 final size:19
Alignment explanation
Indices: 2256--2294 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
2246 CGTGTATCTG
**
2256 TAACCGTTTCACCATTGTT
1 TAACCGTTTCACCACCGTT
*
2275 TAACCGTTTCATCACCGTT
1 TAACCGTTTCACCACCGTT
2294 T
1 T
2295 TGGAGCCAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.21, C:0.28, G:0.10, T:0.41
Consensus pattern (19 bp):
TAACCGTTTCACCACCGTT
Found at i:2370 original size:21 final size:19
Alignment explanation
Indices: 2345--2402 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
2335 GCTGCTCTAA
2345 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* *
2366 TAATCTAATCTGTACAGTG
1 TAATCTCATCTGTACAGTC
2385 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
2403 TGCTAAACAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.36
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:8032 original size:2 final size:2
Alignment explanation
Indices: 8025--8107 Score: 139
Period size: 2 Copynumber: 41.5 Consensus size: 2
8015 TGGTAAACAA
* * *
8025 GT GT GT GT GT GT GC GT GT GT GT GT GT GT GT GT GA GT GA GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
8067 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
8108 AGGATTTTTA
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.02, C:0.01, G:0.51, T:0.46
Consensus pattern (2 bp):
GT
Found at i:11795 original size:11 final size:10
Alignment explanation
Indices: 11779--11832 Score: 58
Period size: 11 Copynumber: 5.3 Consensus size: 10
11769 AAAGTTCGTG
11779 ATTGAAGATTT
1 ATTGAAGA-TT
*
11790 ATTGAAGATA
1 ATTGAAGATT
11800 ATTTGAAGA-T
1 A-TTGAAGATT
11810 A-TGAAGATT
1 ATTGAAGATT
11819 ATTGAAGAATT
1 ATTGAAG-ATT
11830 ATT
1 ATT
11833 TTAGAAGCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
8 6 0.16
9 2 0.05
10 8 0.22
11 21 0.57
ACGTcount: A:0.43, C:0.00, G:0.19, T:0.39
Consensus pattern (10 bp):
ATTGAAGATT
Found at i:22810 original size:88 final size:89
Alignment explanation
Indices: 22671--22852 Score: 294
Period size: 88 Copynumber: 2.0 Consensus size: 89
22661 TTGAATATTG
* * *
22671 TATTCCCTAAACAAATATAGTTTTTTTTCCAGCAATTTAATTATGTTAGATTATAATAATTAGAT
1 TATTCCCTAAAAAAATATAG-TTTTTTTCCAGCAATTCAATTATGTTAGATTACAATAATTAGAT
22736 GCTTTGAATCAAAATTAATTTCAAT
65 GCTTTGAATCAAAATTAATTTCAAT
* *
22761 TATTCCCTAAAAAAATATA-TTTTTTTCCAGCAATTCGATTATGTTAGATTACAATAATTGGATG
1 TATTCCCTAAAAAAATATAGTTTTTTTCCAGCAATTCAATTATGTTAGATTACAATAATTAGATG
*
22825 CTTTGAATCATAATTAATTTCAAT
66 CTTTGAATCAAAATTAATTTCAAT
22849 TATT
1 TATT
22853 TTAATAACTT
Statistics
Matches: 86, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
88 68 0.79
90 18 0.21
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.43
Consensus pattern (89 bp):
TATTCCCTAAAAAAATATAGTTTTTTTCCAGCAATTCAATTATGTTAGATTACAATAATTAGATG
CTTTGAATCAAAATTAATTTCAAT
Found at i:22990 original size:15 final size:15
Alignment explanation
Indices: 22970--22999 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
22960 AGTCTAGAAT
*
22970 AAAATCATGAACAAA
1 AAAATCATAAACAAA
22985 AAAATCATAAACAAA
1 AAAATCATAAACAAA
23000 TATCTTCTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.13, G:0.03, T:0.13
Consensus pattern (15 bp):
AAAATCATAAACAAA
Found at i:26053 original size:32 final size:30
Alignment explanation
Indices: 25965--26053 Score: 72
Period size: 30 Copynumber: 2.9 Consensus size: 30
25955 TTTATTTTAT
* * *
25965 TCTTACAATTGACACCAGAAGTTGTCATGA
1 TCTTGCAATTGACACCATAAGTTGTCATAA
* * *
25995 TCTTGAAATTGACA-CTTGAAGATGTCATAA
1 TCTTGCAATTGACACCAT-AAGTTGTCATAA
* *
26025 TTGTATTCAATTGACACCATAAGTTGTCA
1 -TCT-TGCAATTGACACCATAAGTTGTCA
26054 CATACACTAT
Statistics
Matches: 44, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
29 1 0.02
30 22 0.50
31 2 0.05
32 17 0.39
33 2 0.05
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Consensus pattern (30 bp):
TCTTGCAATTGACACCATAAGTTGTCATAA
Found at i:26655 original size:33 final size:33
Alignment explanation
Indices: 26592--26655 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
26582 ATATTGCTTA
**
26592 ATATTGCCCCTGAAGAGGCACAAATTCATGAGC
1 ATATTGCCCCTGAAGAGGCACAAACCCATGAGC
* *
26625 ATATTGCCCCTGTAGTGGCACAAACCCATGA
1 ATATTGCCCCTGAAGAGGCACAAACCCATGA
26656 AAAGATCACC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (33 bp):
ATATTGCCCCTGAAGAGGCACAAACCCATGAGC
Found at i:40705 original size:20 final size:20
Alignment explanation
Indices: 40667--40704 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
40657 ATTATAGGTA
40667 GTACATATTATATTTTATAT
1 GTACATATTATATTTTATAT
40687 GTACA-ATTATA-TTTATAT
1 GTACATATTATATTTTATAT
40705 AATTAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 6 0.33
20 5 0.28
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (20 bp):
GTACATATTATATTTTATAT
Found at i:52491 original size:21 final size:19
Alignment explanation
Indices: 52447--52505 Score: 82
Period size: 21 Copynumber: 3.0 Consensus size: 19
52437 CTGTTTAACA
*
52447 ACTGTAGAGATGAGATTAT
1 ACTGTACAGATGAGATTAT
*
52466 ACTGTACAGATTAGATTACGT
1 ACTGTACAGATGAGATTA--T
52487 ACTGTACAGATGAGATTAT
1 ACTGTACAGATGAGATTAT
52506 TAGAGCAGCG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 17 0.49
21 18 0.51
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.32
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAT
Found at i:53133 original size:40 final size:39
Alignment explanation
Indices: 53057--53135 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 39
53047 GAGAGATTAC
* * * *
53057 AATTCTAGATAATTAAGGGGGTAGGAGTTATTATAACAT
1 AATTCTAAATAATAAAGGGGATAGGAGTTATCATAACAT
*
53096 AATTCTAAATAATCAAAGGGGATAGGATTTATCATAACAT
1 AATTCTAAATAAT-AAAGGGGATAGGAGTTATCATAACAT
53136 TTATGTGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
39 12 0.35
40 22 0.65
ACGTcount: A:0.42, C:0.08, G:0.19, T:0.32
Consensus pattern (39 bp):
AATTCTAAATAATAAAGGGGATAGGAGTTATCATAACAT
Done.