Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018254.1 Corchorus olitorius cultivar O-4 contig18287, 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: 30242
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:14 original size:9 final size:9
Alignment explanation
Indices: 1--194 Score: 388
Period size: 9 Copynumber: 21.6 Consensus size: 9
1 TGGTCGGTC
1 TGGTCGGTC
10 TGGTCGGTC
1 TGGTCGGTC
19 TGGTCGGTC
1 TGGTCGGTC
28 TGGTCGGTC
1 TGGTCGGTC
37 TGGTCGGTC
1 TGGTCGGTC
46 TGGTCGGTC
1 TGGTCGGTC
55 TGGTCGGTC
1 TGGTCGGTC
64 TGGTCGGTC
1 TGGTCGGTC
73 TGGTCGGTC
1 TGGTCGGTC
82 TGGTCGGTC
1 TGGTCGGTC
91 TGGTCGGTC
1 TGGTCGGTC
100 TGGTCGGTC
1 TGGTCGGTC
109 TGGTCGGTC
1 TGGTCGGTC
118 TGGTCGGTC
1 TGGTCGGTC
127 TGGTCGGTC
1 TGGTCGGTC
136 TGGTCGGTC
1 TGGTCGGTC
145 TGGTCGGTC
1 TGGTCGGTC
154 TGGTCGGTC
1 TGGTCGGTC
163 TGGTCGGTC
1 TGGTCGGTC
172 TGGTCGGTC
1 TGGTCGGTC
181 TGGTCGGTC
1 TGGTCGGTC
190 TGGTC
1 TGGTC
195 ATAGGAAAAA
Statistics
Matches: 185, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 185 1.00
ACGTcount: A:0.00, C:0.22, G:0.44, T:0.34
Consensus pattern (9 bp):
TGGTCGGTC
Found at i:282 original size:2 final size:2
Alignment explanation
Indices: 275--372 Score: 54
Period size: 2 Copynumber: 53.5 Consensus size: 2
265 CCGTTTATTA
* *
275 AT AT AT AT A- AT -T AA AT AT AT -T AT AT AT AT A- AT AT CAA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
* * * *
314 AT AT AT TT AT AT AT A- AT AT TT AT TT A- AT -T AT TT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
352 AT -T AT -T AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
373 ATAATTTATA
Statistics
Matches: 71, Mismatches: 14, Indels: 22
0.66 0.13 0.21
Matches are distributed among these distances:
1 10 0.14
2 60 0.85
3 1 0.01
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:359 original size:23 final size:25
Alignment explanation
Indices: 289--377 Score: 89
Period size: 25 Copynumber: 3.7 Consensus size: 25
279 ATATAATTAA
* *
289 ATATATTATATATATAATA-TCAAAT
1 ATATATT-TATATATAATATTTATAT
*
314 ATATATTTATATATAATATTTATTT
1 ATATATTTATATATAATATTTATAT
*
339 A-ATTATTTATAT-TATTA-TTATAT
1 ATA-TATTTATATATAATATTTATAT
362 ATATATTTATA-ATAAT
1 ATATATTTATATATAAT
378 TTATAAAATT
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
23 17 0.31
24 17 0.31
25 20 0.37
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (25 bp):
ATATATTTATATATAATATTTATAT
Found at i:470 original size:13 final size:13
Alignment explanation
Indices: 452--488 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
442 TTATAAAATA
452 CGGTCAAAACCAG
1 CGGTCAAAACCAG
465 CGGTCAAAACCAG
1 CGGTCAAAACCAG
478 CGGTCAAAACC
1 CGGTCAAAACC
489 GCCTAAACCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.38, C:0.32, G:0.22, T:0.08
Consensus pattern (13 bp):
CGGTCAAAACCAG
Found at i:686 original size:58 final size:58
Alignment explanation
Indices: 618--735 Score: 236
Period size: 58 Copynumber: 2.0 Consensus size: 58
608 AACCGAAACC
618 GAACCGACCAATACTCACCCCTATTCCTAGGAGGACTTTCGACAAGTAAAAGAGAATT
1 GAACCGACCAATACTCACCCCTATTCCTAGGAGGACTTTCGACAAGTAAAAGAGAATT
676 GAACCGACCAATACTCACCCCTATTCCTAGGAGGACTTTCGACAAGTAAAAGAGAATT
1 GAACCGACCAATACTCACCCCTATTCCTAGGAGGACTTTCGACAAGTAAAAGAGAATT
734 GA
1 GA
736 CCATCATGAC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.20
Consensus pattern (58 bp):
GAACCGACCAATACTCACCCCTATTCCTAGGAGGACTTTCGACAAGTAAAAGAGAATT
Found at i:1706 original size:33 final size:33
Alignment explanation
Indices: 1664--1729 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
1654 TCCACACATA
1664 TTTAATATTACAAAAAAGGACAGCAGGAAAAGT
1 TTTAATATTACAAAAAAGGACAGCAGGAAAAGT
1697 TTTAATATTACAAAAAAGGACAGCAGGAAAAGT
1 TTTAATATTACAAAAAAGGACAGCAGGAAAAGT
1730 AAGGGAGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.52, C:0.09, G:0.18, T:0.21
Consensus pattern (33 bp):
TTTAATATTACAAAAAAGGACAGCAGGAAAAGT
Found at i:11072 original size:13 final size:13
Alignment explanation
Indices: 11046--11078 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
11036 CAATGGTTTA
11046 TTCTTATTAAATT
1 TTCTTATTAAATT
11059 TTCTT-TTAATATT
1 TTCTTATTAA-ATT
11072 TTCTTAT
1 TTCTTAT
11079 ATTTTATTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.22
13 13 0.72
14 1 0.06
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (13 bp):
TTCTTATTAAATT
Found at i:11139 original size:16 final size:16
Alignment explanation
Indices: 11098--11145 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
11088 CAAATACAAT
*
11098 TCAATTATTAAAAACA
1 TCAATTATTAAAAAAA
** *
11114 T-TTTTTTTAAAAAAA
1 TCAATTATTAAAAAAA
11129 TCAATTATTAAAAAAA
1 TCAATTATTAAAAAAA
11145 T
1 T
11146 TGTGGCAAAT
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (16 bp):
TCAATTATTAAAAAAA
Found at i:21455 original size:33 final size:33
Alignment explanation
Indices: 21418--21495 Score: 138
Period size: 33 Copynumber: 2.4 Consensus size: 33
21408 CTTGTCCTTC
21418 TTCATAAATTTCAGATAATGGAAAATCTATCAA
1 TTCATAAATTTCAGATAATGGAAAATCTATCAA
*
21451 TTCATTAATTTCAGATAATGGAAAATCTATCAA
1 TTCATAAATTTCAGATAATGGAAAATCTATCAA
*
21484 TTCAAAAATTTC
1 TTCATAAATTTC
21496 GGAGCTGAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.36
Consensus pattern (33 bp):
TTCATAAATTTCAGATAATGGAAAATCTATCAA
Done.