Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014290.1 Corchorus olitorius cultivar O-4 contig14323, 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: 88812
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:12298 original size:13 final size:12
Alignment explanation
Indices: 12280--12313 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
12270 ACGGGAGGGG
12280 AAAAAAAAGAAA
1 AAAAAAAAGAAA
12292 AAAAAAAAGAAA
1 AAAAAAAAGAAA
12304 AAGAAAAAAG
1 AA-AAAAAAG
12314 GAGTGCCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.67
13 7 0.33
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGAAA
Found at i:21435 original size:26 final size:25
Alignment explanation
Indices: 21381--21436 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
21371 TAATTGAAAC
**
21381 AAAATCTATCACCAATGGTATAAAAA
1 AAAATCTATCACCAA-GAAATAAAAA
21407 AAAATCTATCACCAA-AAATAATAATA
1 AAAATCTATCACCAAGAAATAA-AA-A
21433 AAAA
1 AAAA
21437 AGGGTTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 4 0.15
25 2 0.08
26 20 0.77
ACGTcount: A:0.61, C:0.14, G:0.04, T:0.21
Consensus pattern (25 bp):
AAAATCTATCACCAAGAAATAAAAA
Found at i:38840 original size:51 final size:49
Alignment explanation
Indices: 38774--38874 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 49
38764 CTTCCCTTGT
* *
38774 AAGACTGAACTATCCCACCAACAAGATTCATTCTGTATTTTTCTAATTTGC
1 AAGACTAAACAATCCCACCAACAAGATTCATTCTGTA-TTTT-TAATTTGC
*
38825 AAGACTAAACAATCCCACCAACAAGATTCATTTTGTATTTTTAATTTGC
1 AAGACTAAACAATCCCACCAACAAGATTCATTCTGTATTTTTAATTTGC
38874 A
1 A
38875 TTTTAAATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
49 9 0.19
50 4 0.09
51 34 0.72
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.35
Consensus pattern (49 bp):
AAGACTAAACAATCCCACCAACAAGATTCATTCTGTATTTTTAATTTGC
Found at i:39162 original size:23 final size:23
Alignment explanation
Indices: 39134--39179 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
39124 TAGTTGGATA
39134 ATTGATTTTATGATAAAATTTGG
1 ATTGATTTTATGATAAAATTTGG
*
39157 ATTGATTTTATGTTAAAATTTGG
1 ATTGATTTTATGATAAAATTTGG
39180 GTAAAATTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (23 bp):
ATTGATTTTATGATAAAATTTGG
Found at i:39730 original size:34 final size:37
Alignment explanation
Indices: 39660--39730 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
39650 CTCTCATATG
* * *
39660 AAACAAATACTACCTTAATGAATACTTAATACTTTTA
1 AAACAAATACTACCATAATGAAAACTAAATACTTTTA
39697 AAACAAATACTACCAT-AT-AAAAC-AAATACTTTTA
1 AAACAAATACTACCATAATGAAAACTAAATACTTTTA
39731 CTCGTTGTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
34 10 0.32
35 4 0.13
36 2 0.06
37 15 0.48
ACGTcount: A:0.51, C:0.17, G:0.01, T:0.31
Consensus pattern (37 bp):
AAACAAATACTACCATAATGAAAACTAAATACTTTTA
Found at i:39775 original size:28 final size:28
Alignment explanation
Indices: 39741--39795 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
39731 CTCGTTGTTC
39741 GTATGGAGAGACTACTTTTTTGGTTAAA
1 GTATGGAGAGACTACTTTTTTGGTTAAA
39769 GTATGGAGAGACTACTTTTTTGGTTAA
1 GTATGGAGAGACTACTTTTTTGGTTAA
39796 TACCTTAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.27, C:0.07, G:0.25, T:0.40
Consensus pattern (28 bp):
GTATGGAGAGACTACTTTTTTGGTTAAA
Found at i:51264 original size:28 final size:29
Alignment explanation
Indices: 51205--51275 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 29
51195 AATTTGTAGC
*
51205 TTTTGGATATTTTATCCCATGAACTTCAA
1 TTTTGGACATTTTATCCCATGAACTTCAA
*
51234 TTTTGGACATTTTA-CTCC-TGAATTTCAA
1 TTTTGGACATTTTATC-CCATGAACTTCAA
*
51262 TTTTAGGACGTTTT
1 TTTT-GGACATTTT
51276 GCCCCCTCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 14 0.38
29 23 0.62
ACGTcount: A:0.24, C:0.15, G:0.13, T:0.48
Consensus pattern (29 bp):
TTTTGGACATTTTATCCCATGAACTTCAA
Found at i:51352 original size:33 final size:33
Alignment explanation
Indices: 51310--51393 Score: 132
Period size: 33 Copynumber: 2.5 Consensus size: 33
51300 CAAGCTGCTG
51310 ACGTGGCAATGCCACGTGGGTCGGGTTGATCTA
1 ACGTGGCAATGCCACGTGGGTCGGGTTGATCTA
*
51343 ACGTGGCAATGCCACATGGGTCGGGTTGATCTA
1 ACGTGGCAATGCCACGTGGGTCGGGTTGATCTA
* * *
51376 ACATGGTAATGTCACGTG
1 ACGTGGCAATGCCACGTG
51394 CCATTTTTCT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.21, C:0.20, G:0.33, T:0.25
Consensus pattern (33 bp):
ACGTGGCAATGCCACGTGGGTCGGGTTGATCTA
Found at i:52818 original size:2 final size:2
Alignment explanation
Indices: 52811--52837 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
52801 TATTATACAT
52811 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
52838 GTATGTGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52846 original size:2 final size:2
Alignment explanation
Indices: 52841--52875 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
52831 TATATATGTA
52841 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
52876 AATCTACACG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:58468 original size:17 final size:16
Alignment explanation
Indices: 58437--58472 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
58427 TTTACTAACA
58437 TTTAATTTTTCTTTCT
1 TTTAATTTTTCTTTCT
*
58453 TTTATTTTTCTCTTTCT
1 TTTAATTTT-TCTTTCT
58470 TTT
1 TTT
58473 TTCATATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTAATTTTTCTTTCT
Found at i:74820 original size:27 final size:28
Alignment explanation
Indices: 74782--74838 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 28
74772 TCGATTTCTG
*
74782 GTTAGATTAGGAGTGCAT-CCTCCAGCC
1 GTTAGATTAGGAGTGCATCCCGCCAGCC
*
74809 GTTAGATTAGGAGTGCCTCCCGCCAGCC
1 GTTAGATTAGGAGTGCATCCCGCCAGCC
74837 GT
1 GT
74839 CTTATTTGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 17 0.63
28 10 0.37
ACGTcount: A:0.19, C:0.28, G:0.28, T:0.25
Consensus pattern (28 bp):
GTTAGATTAGGAGTGCATCCCGCCAGCC
Found at i:76178 original size:56 final size:56
Alignment explanation
Indices: 76092--76202 Score: 222
Period size: 56 Copynumber: 2.0 Consensus size: 56
76082 AGCCATCATA
76092 GCCAAACCCACCTCCTCTAGTATCTGTATTTGGATACGTAGAGAATAGTTCACTCG
1 GCCAAACCCACCTCCTCTAGTATCTGTATTTGGATACGTAGAGAATAGTTCACTCG
76148 GCCAAACCCACCTCCTCTAGTATCTGTATTTGGATACGTAGAGAATAGTTCACTC
1 GCCAAACCCACCTCCTCTAGTATCTGTATTTGGATACGTAGAGAATAGTTCACTC
76203 TTAAGATCAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (56 bp):
GCCAAACCCACCTCCTCTAGTATCTGTATTTGGATACGTAGAGAATAGTTCACTCG
Found at i:77927 original size:31 final size:30
Alignment explanation
Indices: 77870--77927 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
77860 TTCGGCTCAT
*
77870 CTGGATTCAGGTCATTCGGTCTCGGGTCTG
1 CTGGATTCAGGTCATGCGGTCTCGGGTCTG
*
77900 CTGGATTTAGGGTCATGCAGGTC-CGGGT
1 CTGGATTCA-GGTCATGC-GGTCTCGGGT
77928 TTTGGCCTCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 8 0.33
31 12 0.50
32 4 0.17
ACGTcount: A:0.12, C:0.21, G:0.36, T:0.31
Consensus pattern (30 bp):
CTGGATTCAGGTCATGCGGTCTCGGGTCTG
Found at i:78648 original size:16 final size:16
Alignment explanation
Indices: 78627--78658 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
78617 AAGTTCTGGG
78627 TGGATAGATGGCTTGA
1 TGGATAGATGGCTTGA
78643 TGGATAGATGGCTTGA
1 TGGATAGATGGCTTGA
78659 AGTACCTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.38, T:0.31
Consensus pattern (16 bp):
TGGATAGATGGCTTGA
Found at i:80131 original size:31 final size:31
Alignment explanation
Indices: 80088--80152 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
80078 ATACTAATTA
* *
80088 ATAATAATAGGTCTCATACTACATATTATGC
1 ATAAGAATAGGTCTCATACTACATATTATAC
80119 ATAAGAATAGGTCTCATACTACATATTATAC
1 ATAAGAATAGGTCTCATACTACATATTATAC
80150 ATA
1 ATA
80153 TCCAATATAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.34
Consensus pattern (31 bp):
ATAAGAATAGGTCTCATACTACATATTATAC
Found at i:81320 original size:14 final size:14
Alignment explanation
Indices: 81301--81327 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
81291 GATAAGCAAA
81301 AGTGAGCCTATAAC
1 AGTGAGCCTATAAC
81315 AGTGAGCCTATAA
1 AGTGAGCCTATAA
81328 TTTTCTGCAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (14 bp):
AGTGAGCCTATAAC
Found at i:81719 original size:14 final size:14
Alignment explanation
Indices: 81700--81726 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
81690 GATAGGCAAA
81700 AGTGAGCCTATAAC
1 AGTGAGCCTATAAC
81714 AGTGAGCCTATAA
1 AGTGAGCCTATAA
81727 TTTTCTGCAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (14 bp):
AGTGAGCCTATAAC
Found at i:82102 original size:46 final size:46
Alignment explanation
Indices: 82030--82148 Score: 193
Period size: 46 Copynumber: 2.6 Consensus size: 46
82020 GCTCTGCATA
* *
82030 AATTCAAAACCATTCATAAAGCACTTAGTTATGTATTGTAAATTCCT
1 AATTCAAAAAC-TTCATAAAGCACTTAGTTATGAATTGTAAATTCCT
*
82077 AATTCAAAAACTTCATAAAGTACTTAGTTATGAATTGTAAATTCCT
1 AATTCAAAAACTTCATAAAGCACTTAGTTATGAATTGTAAATTCCT
*
82123 AATTCAAAAACTTCATAAAACACTTA
1 AATTCAAAAACTTCATAAAGCACTTA
82149 CCATTTCATG
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
46 57 0.85
47 10 0.15
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (46 bp):
AATTCAAAAACTTCATAAAGCACTTAGTTATGAATTGTAAATTCCT
Done.