Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016343.1 Corchorus olitorius cultivar O-4 contig16376, 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: 120238
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:712 original size:31 final size:31
Alignment explanation
Indices: 676--752 Score: 154
Period size: 31 Copynumber: 2.5 Consensus size: 31
666 TTTATGAAGC
676 ATAAAATTCAGGATTTACTACCAAAAAGAAA
1 ATAAAATTCAGGATTTACTACCAAAAAGAAA
707 ATAAAATTCAGGATTTACTACCAAAAAGAAA
1 ATAAAATTCAGGATTTACTACCAAAAAGAAA
738 ATAAAATTCAGGATT
1 ATAAAATTCAGGATT
753 AATTATAAGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.53, C:0.12, G:0.10, T:0.25
Consensus pattern (31 bp):
ATAAAATTCAGGATTTACTACCAAAAAGAAA
Found at i:5979 original size:3 final size:3
Alignment explanation
Indices: 5971--5999 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5961 GGTTTAATTA
5971 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
6000 AATTCCCCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:7983 original size:27 final size:26
Alignment explanation
Indices: 7937--7988 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
7927 TTTTTTTACT
*
7937 TTTTTATAAATTAATAATTAGTTATTA
1 TTTTTAAAAATTAATAATTA-TTATTA
* *
7964 TTTTTAAAAATTAGTTATTATTATT
1 TTTTTAAAAATTAATAATTATTATT
7989 TTATATGATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (26 bp):
TTTTTAAAAATTAATAATTATTATTA
Found at i:7999 original size:23 final size:20
Alignment explanation
Indices: 7947--7985 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
7937 TTTTTATAAA
*
7947 TTAATAATTAGTTATTATTT
1 TTAAAAATTAGTTATTATTT
7967 TTAAAAATTAGTTATTATT
1 TTAAAAATTAGTTATTATT
7986 ATTTTATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
TTAAAAATTAGTTATTATTT
Found at i:14006 original size:14 final size:13
Alignment explanation
Indices: 13986--14025 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
13976 ATTATTTTAA
13986 AAATTAAATTATAT
1 AAATT-AATTATAT
*
14000 TAATTAATTATAT
1 AAATTAATTATAT
14013 AAATGTAATTATA
1 AAAT-TAATTATA
14026 AATATAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (13 bp):
AAATTAATTATAT
Found at i:20665 original size:29 final size:29
Alignment explanation
Indices: 20623--20680 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
20613 GCATCTTTTT
20623 TTTTTCTTCCTCTTTTTTTAGTTTCGAAA
1 TTTTTCTTCCTCTTTTTTTAGTTTCGAAA
* *
20652 TTTTTCTTCTTCTTTTTTTGGTTTCGAAA
1 TTTTTCTTCCTCTTTTTTTAGTTTCGAAA
20681 ACTGAGAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.12, C:0.16, G:0.09, T:0.64
Consensus pattern (29 bp):
TTTTTCTTCCTCTTTTTTTAGTTTCGAAA
Found at i:54508 original size:1 final size:1
Alignment explanation
Indices: 54502--54532 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
54492 CACATCACAT
54502 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
54533 CCAATTATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:64362 original size:1 final size:1
Alignment explanation
Indices: 64356--64387 Score: 55
Period size: 1 Copynumber: 32.0 Consensus size: 1
64346 TCATGCTTCC
*
64356 AAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
64388 GCTTGCTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:77301 original size:28 final size:27
Alignment explanation
Indices: 77265--77318 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
77255 TACCATACTA
*
77265 AATTATAATAATTATTAAAAAGGAATAG
1 AATTATAATAATTACTAAAAA-GAATAG
* *
77293 AATTTTAATTATTACTAAAAAGAATA
1 AATTATAATAATTACTAAAAAGAATA
77319 ATAAAATGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.35
Consensus pattern (27 bp):
AATTATAATAATTACTAAAAAGAATAG
Found at i:80172 original size:29 final size:29
Alignment explanation
Indices: 80134--80198 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
80124 AAAGGAAAAA
*
80134 AAAAAAAAAAACTTTGCACAATAAAATCG
1 AAAAAGAAAAACTTTGCACAATAAAATCG
*
80163 AAAAAGAAAAACTTTGCTCAATAAAATCG
1 AAAAAGAAAAACTTTGCACAATAAAATCG
*
80192 AATAAGA
1 AAAAAGA
80199 GCAGTAGCTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.60, C:0.12, G:0.09, T:0.18
Consensus pattern (29 bp):
AAAAAGAAAAACTTTGCACAATAAAATCG
Found at i:85161 original size:1 final size:1
Alignment explanation
Indices: 85157--85182 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
85147 AAGTATCCGG
85157 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
85183 AATTAGTATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:95039 original size:20 final size:21
Alignment explanation
Indices: 95016--95054 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
95006 CAAAAGGAAG
*
95016 TTGAT-ATTTTTATAAGGTGA
1 TTGATAATTTATATAAGGTGA
95036 TTGATAATTTATATAAGGT
1 TTGATAATTTATATAAGGT
95055 TCTCTTCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.49
Consensus pattern (21 bp):
TTGATAATTTATATAAGGTGA
Found at i:102307 original size:40 final size:40
Alignment explanation
Indices: 102263--102344 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
102253 TGTAGTCTGC
*
102263 TAGATTCCAGTGACGGTGTGTTATATTATATATAAATCCT
1 TAGATTCCAGTGACGGTGTATTATATTATATATAAATCCT
102303 TAGATTCCAGTGACGGTGTATTATATTATATATAAATCCT
1 TAGATTCCAGTGACGGTGTATTATATTATATATAAATCCT
102343 TA
1 TA
102345 ATTAAGATAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (40 bp):
TAGATTCCAGTGACGGTGTATTATATTATATATAAATCCT
Found at i:104208 original size:38 final size:40
Alignment explanation
Indices: 104139--104216 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
104129 TTAAATTGAA
*
104139 TTTTCTACGTGGAGAGTCTATTGAAATATTCT-CCAATTAG
1 TTTTCTACGTGGAGAG-CTATTGAAAAATTCTGCCAATTAG
*
104179 TTTTTTACGTGGAGAG-TATTGAAAAATTCTGCCAATTA
1 TTTTCTACGTGGAGAGCTATTGAAAAATTCTGCCAATTA
104217 AGACTTTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
38 13 0.37
39 7 0.20
40 15 0.43
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (40 bp):
TTTTCTACGTGGAGAGCTATTGAAAAATTCTGCCAATTAG
Found at i:105609 original size:15 final size:16
Alignment explanation
Indices: 105589--105618 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
105579 TTTTGTTTAC
105589 TTCTTTTCC-TTTTCT
1 TTCTTTTCCATTTTCT
105604 TTCTTTTCCATTTTC
1 TTCTTTTCCATTTTC
105619 CCTCTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.03, C:0.27, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCTTTTCCATTTTCT
Found at i:110543 original size:27 final size:27
Alignment explanation
Indices: 110504--110566 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
110494 TATTGTAGAT
*
110504 GATAATCGTGAAAATGATAGATTTAAA
1 GATAATCGCGAAAATGATAGATTTAAA
110531 GATAATCGCGAAAATGATAGATTTAAA
1 GATAATCGCGAAAATGATAGATTTAAA
*
110558 GATATTCGC
1 GATAATCGC
110567 ATTGAGAGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.44, C:0.08, G:0.19, T:0.29
Consensus pattern (27 bp):
GATAATCGCGAAAATGATAGATTTAAA
Found at i:114482 original size:20 final size:20
Alignment explanation
Indices: 114457--114497 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
114447 TAACGTTTTC
114457 TTTTTGGTTAGCAATTTCTT
1 TTTTTGGTTAGCAATTTCTT
114477 TTTTTGGTTAGCAATTTCTT
1 TTTTTGGTTAGCAATTTCTT
114497 T
1 T
114498 GATGTGACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.10, G:0.15, T:0.61
Consensus pattern (20 bp):
TTTTTGGTTAGCAATTTCTT
Found at i:114728 original size:21 final size:19
Alignment explanation
Indices: 114703--114760 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
114693 GCTGCTCTAA
114703 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* *
114724 TAATCTAATCTGTACAGTG
1 TAATCTCATCTGTACAGTC
114743 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
114761 TGCTAAACAA
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:119262 original size:20 final size:22
Alignment explanation
Indices: 119226--119277 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
119216 CTTATTGAAT
*
119226 TATTAT-TATTACTTAT-ATTA
1 TATTATATATTACTTATAATAA
119246 TATTATATATTAC-TATAATAA
1 TATTATATATTACTTATAATAA
119267 TATATATATAT
1 TAT-TATATAT
119278 ATATATGGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 9 0.32
21 12 0.43
22 7 0.25
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (22 bp):
TATTATATATTACTTATAATAA
Found at i:119291 original size:13 final size:14
Alignment explanation
Indices: 119273--119305 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
119263 ATAATATATA
119273 TATATATATATG-G
1 TATATATATATGTG
*
119286 TATATATATGTGTG
1 TATATATATATGTG
119300 TATATA
1 TATATA
119306 AAGTTCTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.48
Consensus pattern (14 bp):
TATATATATATGTG
Found at i:119305 original size:2 final size:2
Alignment explanation
Indices: 119239--119294 Score: 50
Period size: 2 Copynumber: 29.5 Consensus size: 2
119229 TATTATTACT
119239 TA TA T- TA TA T- TA TA TA T- TA CTA TA -A TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
*
119277 TA TA TA TGG TA TA TA TA T
1 TA TA TA T-A TA TA TA TA T
119295 GTGTGTATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
1 5 0.11
2 37 0.82
3 3 0.07
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.50
Consensus pattern (2 bp):
TA
Done.