Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024558.1 Corchorus olitorius cultivar O-4 contig24591, 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: 42698
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:193 original size:27 final size:28
Alignment explanation
Indices: 163--230 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
153 GCACCAGGGC
163 CAGCCTC-CCTCTCCCTA-TACATCCGAG
1 CAGCCTCACC-CTCCCTACTACATCCGAG
*
190 CAGCCTCAGCCTCCCTACTACATCCGAG
1 CAGCCTCACCCTCCCTACTACATCCGAG
*
218 CAGCCTCAACCTC
1 CAGCCTCACCCTC
231 TTTTATCCCG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 14 0.38
28 23 0.62
ACGTcount: A:0.21, C:0.49, G:0.12, T:0.19
Consensus pattern (28 bp):
CAGCCTCACCCTCCCTACTACATCCGAG
Found at i:220 original size:28 final size:27
Alignment explanation
Indices: 173--230 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 27
163 CAGCCTCCCT
*
173 CTCCCTATACATCCGAGCAGCCTCAGC
1 CTCCCTATACATCCGAGCAGCCTCAAC
200 CTCCCTACTACATCCGAGCAGCCTCAAC
1 CTCCCTA-TACATCCGAGCAGCCTCAAC
228 CTC
1 CTC
231 TTTTATCCCG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 7 0.24
28 22 0.76
ACGTcount: A:0.22, C:0.47, G:0.12, T:0.19
Consensus pattern (27 bp):
CTCCCTATACATCCGAGCAGCCTCAAC
Found at i:15824 original size:15 final size:15
Alignment explanation
Indices: 15804--15833 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
15794 ATCAGGCTGC
*
15804 CACGATACACGATAT
1 CACGATACACAATAT
15819 CACGATACACAATAT
1 CACGATACACAATAT
15834 TTCAACCGTA
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:0.43, C:0.27, G:0.10, T:0.20
Consensus pattern (15 bp):
CACGATACACAATAT
Found at i:17438 original size:11 final size:11
Alignment explanation
Indices: 17396--17438 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
17386 TAATTATTAC
17396 TTAACCATAGA
1 TTAACCATAGA
*
17407 CTAACCATAGA
1 TTAACCATAGA
* *
17418 TTAACTATAGC
1 TTAACCATAGA
*
17429 TTGACCATAG
1 TTAACCATAG
17439 GTTAGTAATA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.28
Consensus pattern (11 bp):
TTAACCATAGA
Found at i:22351 original size:11 final size:11
Alignment explanation
Indices: 22309--22351 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
22299 TAACTATTAC
22309 TTAACCATAGA
1 TTAACCATAGA
*
22320 CTAACCATAGA
1 TTAACCATAGA
* *
22331 TTAACTATAGC
1 TTAACCATAGA
*
22342 TTGACCATAG
1 TTAACCATAG
22352 GTTAGTAATA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.28
Consensus pattern (11 bp):
TTAACCATAGA
Found at i:23013 original size:21 final size:21
Alignment explanation
Indices: 22989--23034 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
22979 GGCAAGATTA
22989 GTTTCAAAATTGGGATTTACG
1 GTTTCAAAATTGGGATTTACG
* *
23010 GTTTCAAAATTGGGGTTTATG
1 GTTTCAAAATTGGGATTTACG
23031 GTTT
1 GTTT
23035 GGGATTGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.24, C:0.07, G:0.26, T:0.43
Consensus pattern (21 bp):
GTTTCAAAATTGGGATTTACG
Found at i:23160 original size:46 final size:46
Alignment explanation
Indices: 23092--23210 Score: 215
Period size: 46 Copynumber: 2.6 Consensus size: 46
23082 TGGGATTTAT
*
23092 GGTTTGGGA-TT-GGGTTTCAAAATTGGGGTTTACTTTAAAATCTG
1 GGTTTGGGATTTATGGTTTCAAAATTGGGGTTTACTTTAAAATCTG
23136 GGTTTGGGATTTATGGTTTCAAAATTGGGGTTTACTTTAAAATCTG
1 GGTTTGGGATTTATGGTTTCAAAATTGGGGTTTACTTTAAAATCTG
23182 GGTTTGGGATTTATGGTTTCAAAATTGGG
1 GGTTTGGGATTTATGGTTTCAAAATTGGG
23211 AAGGGATTAT
Statistics
Matches: 72, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
44 9 0.12
45 2 0.03
46 61 0.85
ACGTcount: A:0.23, C:0.06, G:0.29, T:0.42
Consensus pattern (46 bp):
GGTTTGGGATTTATGGTTTCAAAATTGGGGTTTACTTTAAAATCTG
Found at i:23510 original size:1 final size:1
Alignment explanation
Indices: 23506--23535 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
23496 TTTAAAATTC
23506 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
23536 CTGGAAAGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:26403 original size:19 final size:20
Alignment explanation
Indices: 26352--26403 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 20
26342 ATGTGATGAT
26352 TTTAATAA-TAATTATTTAA
1 TTTAATAATTAATTATTTAA
***
26371 GAAAATAATT-ATTATTT-A
1 TTTAATAATTAATTATTTAA
26389 TTTAATAATTAATTA
1 TTTAATAATTAATTA
26404 ATTTCAGCCC
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
18 8 0.32
19 16 0.64
20 1 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
TTTAATAATTAATTATTTAA
Found at i:36425 original size:15 final size:16
Alignment explanation
Indices: 36398--36427 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
36388 AACCATGTAA
36398 AAGCAATTTAAATTAG
1 AAGCAATTTAAATTAG
36414 AAGCAA-TTAAATTA
1 AAGCAATTTAAATTA
36428 TAAAGGGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (16 bp):
AAGCAATTTAAATTAG
Found at i:36671 original size:34 final size:34
Alignment explanation
Indices: 36628--36695 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
36618 TTTTCCTGTT
36628 TCCTACCATTCATGTCTCCTAGATAAATTAGAAG
1 TCCTACCATTCATGTCTCCTAGATAAATTAGAAG
36662 TCCTACCATTCATGTCTCCTAGATAAATTAGAAG
1 TCCTACCATTCATGTCTCCTAGATAAATTAGAAG
36696 CAATTGGGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (34 bp):
TCCTACCATTCATGTCTCCTAGATAAATTAGAAG
Found at i:40075 original size:20 final size:17
Alignment explanation
Indices: 40033--40066 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
40023 TTACTTTTCT
40033 TAATTATTTTTAGATTA
1 TAATTATTTTTAGATTA
*
40050 TAATTATTTTTTGATTA
1 TAATTATTTTTAGATTA
40067 AAATAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (17 bp):
TAATTATTTTTAGATTA
Found at i:40913 original size:17 final size:17
Alignment explanation
Indices: 40891--40926 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
40881 ACATCAATTA
40891 ATATTTACCTATACTAC
1 ATATTTACCTATACTAC
*
40908 ATATTTACGTATACTAC
1 ATATTTACCTATACTAC
40925 AT
1 AT
40927 GCCCAAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.36, C:0.19, G:0.03, T:0.42
Consensus pattern (17 bp):
ATATTTACCTATACTAC
Done.