Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013639.1 Corchorus olitorius cultivar O-4 contig13672, 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: 58103
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Found at i:3985 original size:41 final size:43
Alignment explanation
Indices: 3913--3993 Score: 130
Period size: 41 Copynumber: 1.9 Consensus size: 43
3903 TTCTTTTACA
* *
3913 AAATCAAACACTTTGTTCCCTCTTTTTCTCTTCCGCCAAAATC
1 AAATCAAACACTCTGTTCACTCTTTTTCTCTTCCGCCAAAATC
3956 AAATCAAAC-CTCTGTTCACT-TTTTTCTCTTCCGCCAAA
1 AAATCAAACACTCTGTTCACTCTTTTTCTCTTCCGCCAAA
3994 GCTTCTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 18 0.50
42 9 0.25
43 9 0.25
ACGTcount: A:0.26, C:0.32, G:0.05, T:0.37
Consensus pattern (43 bp):
AAATCAAACACTCTGTTCACTCTTTTTCTCTTCCGCCAAAATC
Found at i:16049 original size:7 final size:7
Alignment explanation
Indices: 16037--16071 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
16027 TAGAGTGGTA
16037 TGTATTT
1 TGTATTT
16044 TGTATTT
1 TGTATTT
16051 TGTATTT
1 TGTATTT
*
16058 TGTTTTT
1 TGTATTT
16065 TGT-TTT
1 TGTATTT
16071 T
1 T
16072 TCTTTTGCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
6 4 0.15
7 23 0.85
ACGTcount: A:0.09, C:0.00, G:0.14, T:0.77
Consensus pattern (7 bp):
TGTATTT
Found at i:16072 original size:14 final size:14
Alignment explanation
Indices: 16037--16077 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
16027 TAGAGTGGTA
*
16037 TGTATTTTGTATTT
1 TGTATTTTGTTTTT
16051 TGTATTTTGTTTTT
1 TGTATTTTGTTTTT
* *
16065 TGTTTTTTCTTTT
1 TGTATTTTGTTTT
16078 GCTTCTGCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.07, C:0.02, G:0.12, T:0.78
Consensus pattern (14 bp):
TGTATTTTGTTTTT
Found at i:18959 original size:31 final size:31
Alignment explanation
Indices: 18919--18984 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
18909 AACGGTGCGC
* *
18919 ATTGTTCACACGTGAATAGTTAGATTCAATT
1 ATTGCTCACACGTGAATAGTTAGATTCAATG
*
18950 ATTGCTCACATGTGAATAGTTAGATTCAATG
1 ATTGCTCACACGTGAATAGTTAGATTCAATG
18981 ATTG
1 ATTG
18985 TGGCTTGTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (31 bp):
ATTGCTCACACGTGAATAGTTAGATTCAATG
Found at i:28500 original size:2 final size:2
Alignment explanation
Indices: 28493--28518 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28483 CACACCAAAG
28493 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
28519 CATAATTTTT
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:30343 original size:39 final size:39
Alignment explanation
Indices: 30289--30394 Score: 163
Period size: 32 Copynumber: 2.9 Consensus size: 39
30279 AGTTTAGCCA
30289 TGTTGAGTTTGAACAGTCAGTGTTGTAATTATTATGCCC
1 TGTTGAGTTTGAACAGTCAGTGTTGTAATTATTATGCCC
30328 TGTTGAGTTTGAACAGTCA---TTGT-A--ATTA-GCCC
1 TGTTGAGTTTGAACAGTCAGTGTTGTAATTATTATGCCC
30360 TGTTGAGTTTGAACAGTCAGTGTTGTAATTATTAT
1 TGTTGAGTTTGAACAGTCAGTGTTGTAATTATTAT
30395 AATGTAAAAT
Statistics
Matches: 60, Mismatches: 0, Indels: 14
0.81 0.00 0.19
Matches are distributed among these distances:
32 23 0.38
33 4 0.07
35 5 0.08
36 5 0.08
38 4 0.07
39 19 0.32
ACGTcount: A:0.25, C:0.11, G:0.23, T:0.42
Consensus pattern (39 bp):
TGTTGAGTTTGAACAGTCAGTGTTGTAATTATTATGCCC
Found at i:32117 original size:36 final size:36
Alignment explanation
Indices: 32066--32139 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
32056 GTATCCAAAC
32066 TGTAGTTAAAGGGTTTAATTGATATAGAATCCTCAT
1 TGTAGTTAAAGGGTTTAATTGATATAGAATCCTCAT
* *
32102 TGTAGTTAAATGGTTTAATTTATATAGAATCCTCAT
1 TGTAGTTAAAGGGTTTAATTGATATAGAATCCTCAT
32138 TG
1 TG
32140 ACTAAGTTGC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (36 bp):
TGTAGTTAAAGGGTTTAATTGATATAGAATCCTCAT
Found at i:32365 original size:110 final size:110
Alignment explanation
Indices: 32171--32391 Score: 388
Period size: 110 Copynumber: 2.0 Consensus size: 110
32161 GGTGGGTTGT
*
32171 GTTGGTGATCTTTTGATTGATTACGTTATTTAATTTTGAGATCTTCCTTAAAGCACGTAAAGAAC
1 GTTGGTGATCTTTTGATTGATTACGTTATTTAATCTTGAGATCTTCCTTAAAGCACGTAAAGAAC
* * *
32236 TGGCAAAAAGCACAGTAGGCTCAATCAAATGTATGTCAGTAAATA
66 TGACAAAAAGCACAATAGGCTCAATCAAATCTATGTCAGTAAATA
*
32281 GTTGGTGATCTTTTGATTGATTACGTTATTTAATCTTGAGATCTTCCTTAAAGCATGTAAAGAAC
1 GTTGGTGATCTTTTGATTGATTACGTTATTTAATCTTGAGATCTTCCTTAAAGCACGTAAAGAAC
*
32346 TGACAAAAAGCACAATAGGCTCAATCAAATCTGTGTCAGTAAATA
66 TGACAAAAAGCACAATAGGCTCAATCAAATCTATGTCAGTAAATA
32391 G
1 G
32392 CCATTCCAAA
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
110 105 1.00
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (110 bp):
GTTGGTGATCTTTTGATTGATTACGTTATTTAATCTTGAGATCTTCCTTAAAGCACGTAAAGAAC
TGACAAAAAGCACAATAGGCTCAATCAAATCTATGTCAGTAAATA
Found at i:38159 original size:2 final size:2
Alignment explanation
Indices: 38114--38140 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
38104 ATATTGCTGC
38114 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
38141 TGGTTGAAAC
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:45413 original size:12 final size:12
Alignment explanation
Indices: 45396--45424 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
45386 ATTTTACATT
45396 ATTAGTAATAAA
1 ATTAGTAATAAA
45408 ATTAGTAATAAA
1 ATTAGTAATAAA
45420 ATTAG
1 ATTAG
45425 GAATTATTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.34
Consensus pattern (12 bp):
ATTAGTAATAAA
Found at i:52141 original size:19 final size:19
Alignment explanation
Indices: 52117--52162 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
52107 GTAACCAAGT
52117 GGATCTCGATCTTGGTCAG
1 GGATCTCGATCTTGGTCAG
52136 GGATCTCGATCTTGGTCAG
1 GGATCTCGATCTTGGTCAG
52155 GGATCTCG
1 GGATCTCG
52163 GCAGAAACGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.15, C:0.22, G:0.33, T:0.30
Consensus pattern (19 bp):
GGATCTCGATCTTGGTCAG
Found at i:55721 original size:13 final size:13
Alignment explanation
Indices: 55703--55728 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
55693 CCCTGCAAAA
55703 AATAAAACATTAG
1 AATAAAACATTAG
55716 AATAAAACATTAG
1 AATAAAACATTAG
55729 TTTTATCAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.23
Consensus pattern (13 bp):
AATAAAACATTAG
Found at i:56957 original size:116 final size:116
Alignment explanation
Indices: 56753--56985 Score: 457
Period size: 116 Copynumber: 2.0 Consensus size: 116
56743 ATTTATTTAT
56753 ATATATTCCTGAAAAACTGATTCTAGAAGAGCAGACTATAAAGAAAAATACAATCTTCTAAAGTG
1 ATATATTCCTGAAAAACTGATTCTAGAAGAGCAGACTATAAAGAAAAATACAATCTTCTAAAGTG
*
56818 TAGCTTACTCTGCAGATCAGAACATTTTAAAAGACAGTTGAATTGGATCAG
66 TAGCCTACTCTGCAGATCAGAACATTTTAAAAGACAGTTGAATTGGATCAG
56869 ATATATTCCTGAAAAACTGATTCTAGAAGAGCAGACTATAAAGAAAAATACAATCTTCTAAAGTG
1 ATATATTCCTGAAAAACTGATTCTAGAAGAGCAGACTATAAAGAAAAATACAATCTTCTAAAGTG
56934 TAGCCTACTCTGCAGATCAGAACATTTTAAAAGACAGTTGAATTGGATCAG
66 TAGCCTACTCTGCAGATCAGAACATTTTAAAAGACAGTTGAATTGGATCAG
56985 A
1 A
56986 CACCCAATAG
Statistics
Matches: 116, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
116 116 1.00
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (116 bp):
ATATATTCCTGAAAAACTGATTCTAGAAGAGCAGACTATAAAGAAAAATACAATCTTCTAAAGTG
TAGCCTACTCTGCAGATCAGAACATTTTAAAAGACAGTTGAATTGGATCAG
Done.