Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017549.1 Corchorus olitorius cultivar O-4 contig17582, 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: 103669
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:452 original size:2 final size:2
Alignment explanation
Indices: 445--482 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
435 ATTACTAATC
445 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
483 CTCCATGCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5460 original size:12 final size:12
Alignment explanation
Indices: 5443--5467 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5433 CCTGGAGGGG
5443 CGGAGCTAAATC
1 CGGAGCTAAATC
5455 CGGAGCTAAATC
1 CGGAGCTAAATC
5467 C
1 C
5468 TTTCTCGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.28, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGAGCTAAATC
Found at i:6956 original size:1 final size:1
Alignment explanation
Indices: 6950--6976 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
6940 CCAGTTCAGG
6950 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
6977 TGCTCCCTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:11289 original size:2 final size:2
Alignment explanation
Indices: 11284--11308 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11274 AAAAAAGAAA
11284 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
11309 AGAAGAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:14406 original size:36 final size:36
Alignment explanation
Indices: 14358--14429 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
14348 CAATGGCCAA
14358 GCAATAACGAAATGACAGTTTAGTGAATTAATTATC
1 GCAATAACGAAATGACAGTTTAGTGAATTAATTATC
*
14394 GCAATAATGAAATGACAGTTTAGTGAATTAATTATC
1 GCAATAACGAAATGACAGTTTAGTGAATTAATTATC
14430 CTAATCATTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.32
Consensus pattern (36 bp):
GCAATAACGAAATGACAGTTTAGTGAATTAATTATC
Found at i:17400 original size:42 final size:43
Alignment explanation
Indices: 17354--17440 Score: 149
Period size: 42 Copynumber: 2.0 Consensus size: 43
17344 AATAGAACGG
* *
17354 TACAAAATATTACCAACTGCATCAAG-AGCAATAAATTTTTAA
1 TACAAAATATTACCAACCGCATCAAGCAGCAACAAATTTTTAA
17396 TACAAAATATTACCAACCGCATCAAGCAGCAACAAATTTTTAA
1 TACAAAATATTACCAACCGCATCAAGCAGCAACAAATTTTTAA
17439 TA
1 TA
17441 ATATTGGTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
42 25 0.60
43 17 0.40
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.26
Consensus pattern (43 bp):
TACAAAATATTACCAACCGCATCAAGCAGCAACAAATTTTTAA
Found at i:17821 original size:11 final size:11
Alignment explanation
Indices: 17797--17831 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
17787 TTTACAGCGC
17797 AACAAAAACAA
1 AACAAAAACAA
* *
17808 AACGAAAACGA
1 AACAAAAACAA
17819 AACAAAAACAA
1 AACAAAAACAA
17830 AA
1 AA
17832 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:18656 original size:29 final size:30
Alignment explanation
Indices: 18624--18680 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
18614 TTTTCCTAAT
18624 AACT-TCAATTTTGGACATTTTACCCCCCG
1 AACTCTCAATTTTGGACATTTTACCCCCCG
* *
18653 AACTCTCAATTTTGGACGTTTTGCCCCC
1 AACTCTCAATTTTGGACATTTTACCCCC
18681 TTTCAAACGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.21, C:0.32, G:0.12, T:0.35
Consensus pattern (30 bp):
AACTCTCAATTTTGGACATTTTACCCCCCG
Found at i:34291 original size:6 final size:6
Alignment explanation
Indices: 34280--34318 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
34270 TTCGATTGAA
* *
34280 GGGCAG GGGCAG GGGCAG GGGCAG GGCCAG GGCCAG GGG
1 GGGCAG GGGCAG GGGCAG GGGCAG GGGCAG GGGCAG GGG
34319 GATTTTGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.15, C:0.21, G:0.64, T:0.00
Consensus pattern (6 bp):
GGGCAG
Found at i:61146 original size:28 final size:28
Alignment explanation
Indices: 61114--61168 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
61104 GTAATTTATT
*
61114 TATATTATTATAT-ATTAATAATTATAAG
1 TATATTATTATATGAATAATAA-TATAAG
61142 TATATTATTATATGAATAATAATATAA
1 TATATTATTATATGAATAATAATATAA
61169 CATGACATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (28 bp):
TATATTATTATATGAATAATAATATAAG
Found at i:61151 original size:14 final size:15
Alignment explanation
Indices: 61114--61154 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
61104 GTAATTTATT
*
61114 TATATTATTATATAT
1 TATATTATTATATAG
*
61129 TA-ATAATTATA-AG
1 TATATTATTATATAG
61142 TATATTATTATAT
1 TATATTATTATAT
61155 GAATAATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
13 3 0.14
14 16 0.76
15 2 0.10
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATATTATTATATAG
Found at i:61338 original size:21 final size:19
Alignment explanation
Indices: 61291--61349 Score: 82
Period size: 19 Copynumber: 3.0 Consensus size: 19
61281 CTATTTAGCA
61291 ACTGTACAGATGAGATTAT
1 ACTGTACAGATGAGATTAT
*
61310 ACTGTACAGATTAGATTAGGT
1 ACTGTACAGATGAGATTA--T
*
61331 ATTGTACAGATGAGATTAT
1 ACTGTACAGATGAGATTAT
61350 TAGAGCAACG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 18 0.51
21 17 0.49
ACGTcount: A:0.36, C:0.08, G:0.22, T:0.34
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAT
Found at i:67164 original size:12 final size:12
Alignment explanation
Indices: 67147--67171 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
67137 CTTGATATCC
67147 TATGTTCTTAGT
1 TATGTTCTTAGT
67159 TATGTTCTTAGT
1 TATGTTCTTAGT
67171 T
1 T
67172 TGGAAGAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.16, T:0.60
Consensus pattern (12 bp):
TATGTTCTTAGT
Found at i:100770 original size:2 final size:2
Alignment explanation
Indices: 100765--100794 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
100755 AATATATGTG
*
100765 CA CA CA CA CA CA CA TA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
100795 TATATATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.47, G:0.00, T:0.03
Consensus pattern (2 bp):
CA
Found at i:100799 original size:2 final size:2
Alignment explanation
Indices: 100794--100824 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
100784 ACACACACAC
*
100794 AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
100825 AAATTTTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:103643 original size:2 final size:2
Alignment explanation
Indices: 103638--103668 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
103628 ACACACACAC
103638 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
103669 C
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.