Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013012.1 Corchorus olitorius cultivar O-4 contig13045, 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: 18467
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:411 original size:43 final size:43
Alignment explanation
Indices: 84--411 Score: 376
Period size: 41 Copynumber: 7.8 Consensus size: 43
74 CAATAACCAA
* *
84 AAAGTCCCCAAACACATATATAACACATG-GACAAT-TCTATTCC
1 AAAGTCCCCAAACACATATATAACACA-GAGGC-ATCTCTATTAC
*
127 AAAAGTCCTCAAACACATATATAACACAGAGGCA-C-CTA-TATC
1 -AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTA-C
* * * *
169 CAAGTCCCCAAACAC--ATATAACACAGGGGCACCTTTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
* * *
210 AAAGTCCTCAAACACATATATAACACAGAGGCACCTATATT-C
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
*
252 -AAGTCCCCAAACACATATATAACACAGGGGCAAT-TCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGC-ATCTCTATTAC
* *
294 AAAGTCCTCAAACACATATATAACACAGATGCAT-T-TA-TATC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTA-C
*
335 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
*
378 AAAGTCCTCAAACACATATATAACACAGAGGCAT
1 AAAGTCCCCAAACACATATATAACACAGAGGCAT
412 TTCTCCTTAT
Statistics
Matches: 246, Mismatches: 23, Indels: 31
0.82 0.08 0.10
Matches are distributed among these distances:
39 15 0.06
40 3 0.01
41 98 0.40
42 13 0.05
43 87 0.35
44 30 0.12
ACGTcount: A:0.42, C:0.27, G:0.10, T:0.21
Consensus pattern (43 bp):
AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
Found at i:413 original size:84 final size:84
Alignment explanation
Indices: 84--410 Score: 511
Period size: 84 Copynumber: 3.9 Consensus size: 84
74 CAATAACCAA
* * *
84 AAAGTCCCCAAACACATATATAACACATGGACAATTCTATTCCAAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTAC-AAAGTCCTCAAACACATATAT
149 AACACAGAGGCACCTATATC
65 AACACAGAGGCACCTATATC
* *
169 CAAGTCCCCAAACAC--ATATAACACAGGGGCACCTT-TATTACAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCA-ATTCTATTACAAAGTCCTCAAACACATATAT
231 AACACAGAGGCACCTATATTC
65 AACACAGAGGCACCTATA-TC
252 -AAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTACAAAGTCCTCAAACACATATATA
* **
316 ACACAGATGCATTTATATC
66 ACACAGAGGCACCTATATC
335 AAAGTCCCCAAACACATATATAACACAGGGGC-ATCTCTATTACAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAAT-TCTATTACAAAGTCCTCAAACACATATAT
399 AACACAGAGGCA
65 AACACAGAGGCA
411 TTTCTCCTTA
Statistics
Matches: 225, Mismatches: 10, Indels: 15
0.90 0.04 0.06
Matches are distributed among these distances:
82 53 0.24
83 27 0.12
84 131 0.58
85 14 0.06
ACGTcount: A:0.42, C:0.27, G:0.10, T:0.21
Consensus pattern (84 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCACCTATATC
Found at i:527 original size:2 final size:2
Alignment explanation
Indices: 520--560 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
510 CACCAAATCC
* *
520 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
561 GTGACAAAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:3016 original size:19 final size:21
Alignment explanation
Indices: 2989--3031 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
2979 TTATTCTTCT
* *
2989 AATATTATT-TTTTATAATTA
1 AATATTATTATTTCATAATAA
3009 AATA-TATTATTTCATAATAA
1 AATATTATTATTTCATAATAA
3029 AAT
1 AAT
3032 TCTGAATAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
AATATTATTATTTCATAATAA
Found at i:3885 original size:19 final size:18
Alignment explanation
Indices: 3857--3898 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
3847 AATTAATTGT
3857 TTTAATATTAAATTTTTA
1 TTTAATATTAAATTTTTA
*
3875 TTTATATATTATATTTTTA
1 TTTA-ATATTAAATTTTTA
*
3894 CTTAA
1 TTTAA
3899 AAATTACTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTAATATTAAATTTTTA
Found at i:11521 original size:18 final size:18
Alignment explanation
Indices: 11498--11540 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
11488 TTCATCACTC
*
11498 TTTTGTTTCGTGTTCTGA
1 TTTTGTTTCATGTTCTGA
11516 TTTTGTTTCATGTTCTGA
1 TTTTGTTTCATGTTCTGA
11534 TTTTGTT
1 TTTTGTT
11541 GTTTGTACTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.07, C:0.09, G:0.19, T:0.65
Consensus pattern (18 bp):
TTTTGTTTCATGTTCTGA
Found at i:13058 original size:12 final size:12
Alignment explanation
Indices: 13041--13072 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
13031 GAAAGGCTGA
13041 TTATGTTGATGC
1 TTATGTTGATGC
13053 TTATGTTGATGC
1 TTATGTTGATGC
13065 TTATGTTG
1 TTATGTTG
13073 GGGTTCAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.16, C:0.06, G:0.25, T:0.53
Consensus pattern (12 bp):
TTATGTTGATGC
Done.