Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021012.1 Corchorus olitorius cultivar O-4 contig21045, 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: 46838
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:1048 original size:35 final size:35
Alignment explanation
Indices: 414--1047 Score: 853
Period size: 35 Copynumber: 17.9 Consensus size: 35
404 CAGTGTGGTC
* *
414 TTTCATAGAAGTTTTCAGA-AATCTA-AGTTAATCTCA
1 TTTCA-AGAAGTTTTC-GATGATC-AGAGTTGATCTCA
* *
450 TTTCAAGAAGTTTTTGATGATCAGAGTTGATCGCA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
* * *
485 TTTCAAGAAGTTTTTGATTATCAGAGTTGATCGCA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
*
520 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCACA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
*
555 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCG
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
*
590 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCC
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
* * *
625 TTTCAAGAAGTTTTCAATGATCAAAGTTGATCTCG
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
* *
660 TTTCAAGAAGTTTTCGATGATTAGAGTTGATCTCG
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
* *
695 TTTCAAGAAGTTTTCGGTGATCAGAGTTGATCTCC
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
*
730 TTTCAAGAAGGTTTCGATGATCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
*
765 TTTCAAGAAGTTTTCAATGATCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
*
800 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCG
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
*
835 TTTCAAGAAGTTTTCAATGATCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
* *
870 TTTCAAGAAGTTTT-TATGATCAGAGTTGATCTCC
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
* *
904 TTTTAAGAAGTTTTTG-TCGATCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCGAT-GATCAGAGTTGATCTCA
** *
939 TTTCAAGAAGTTTTTTTTTAATGGTCAGAGTTGATCTCA
1 TTTCAAGAAG----TTTTCGATGATCAGAGTTGATCTCA
** * *
978 TTTCAAGAAGTTTTTTTTATGATCAAAGTTGATCTTA
1 TTTCAAGAAG--TTTTCGATGATCAGAGTTGATCTCA
*
1015 TTTTAAGAAGTTTTCGATGATCAGAGTTGATCT
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCT
1048 TCACATTGAT
Statistics
Matches: 544, Mismatches: 45, Indels: 19
0.89 0.07 0.03
Matches are distributed among these distances:
34 35 0.06
35 440 0.81
36 5 0.01
37 32 0.06
39 31 0.06
40 1 0.00
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.39
Consensus pattern (35 bp):
TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
Found at i:3770 original size:58 final size:58
Alignment explanation
Indices: 3680--3795 Score: 187
Period size: 58 Copynumber: 2.0 Consensus size: 58
3670 TCGGTGAGAA
* * *
3680 TTCAATACTATTCGACACAAAATTAATCATAATCCAATATGATTATCGGATATTGGAG
1 TTCAACACTATTCGACACAAAATTAATAATAATCCAATATGATTATCGAATATTGGAG
* *
3738 TTCAACACTATTCGACACATAATTAGTAATAATCCAATATGATTATCGAATATTGGAG
1 TTCAACACTATTCGACACAAAATTAATAATAATCCAATATGATTATCGAATATTGGAG
3796 GTTTGAACCA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.33
Consensus pattern (58 bp):
TTCAACACTATTCGACACAAAATTAATAATAATCCAATATGATTATCGAATATTGGAG
Found at i:12239 original size:15 final size:15
Alignment explanation
Indices: 12213--12254 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
12203 TGACAAAATG
12213 AACCCGACCCGAGAAA
1 AACCCGACCCGA-AAA
12229 AACCC-ACCCG-AAA
1 AACCCGACCCGAAAA
12242 AACCCGAACCCGA
1 AACCCG-ACCCGA
12255 TCTGAACCCG
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 8 0.35
15 10 0.43
16 5 0.22
ACGTcount: A:0.43, C:0.43, G:0.14, T:0.00
Consensus pattern (15 bp):
AACCCGACCCGAAAA
Found at i:12634 original size:32 final size:32
Alignment explanation
Indices: 12590--12692 Score: 152
Period size: 32 Copynumber: 3.2 Consensus size: 32
12580 ACCTAGCCCG
*
12590 AACCCGAACCCGAATTAACCTGACCCAAAATT
1 AACCCGAACCCGAATCAACCTGACCCAAAATT
* * *
12622 GATCCGAACCCGAATCAACCTGACCCAAATTT
1 AACCCGAACCCGAATCAACCTGACCCAAAATT
* *
12654 AACCCAAACCCGAATCAACCTGACCCAAATTT
1 AACCCGAACCCGAATCAACCTGACCCAAAATT
12686 AACCCGA
1 AACCCGA
12693 CCTGACTCAA
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 63 1.00
ACGTcount: A:0.39, C:0.36, G:0.10, T:0.16
Consensus pattern (32 bp):
AACCCGAACCCGAATCAACCTGACCCAAAATT
Found at i:12825 original size:28 final size:29
Alignment explanation
Indices: 12794--12851 Score: 82
Period size: 31 Copynumber: 2.0 Consensus size: 29
12784 TACTATTCCG
*
12794 TTTTTTTTTT-ATCTTTTCCACTAATAAA
1 TTTTTTTTTTAAACTTTTCCACTAATAAA
12822 TTTTTTTTTTAGCAACTTTTCCACTAATAA
1 TTTTTTTTTTA--AACTTTTCCACTAATAA
12852 TCAAGCTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 10 0.38
31 16 0.62
ACGTcount: A:0.26, C:0.16, G:0.02, T:0.57
Consensus pattern (29 bp):
TTTTTTTTTTAAACTTTTCCACTAATAAA
Found at i:17623 original size:36 final size:36
Alignment explanation
Indices: 17583--17789 Score: 187
Period size: 36 Copynumber: 5.7 Consensus size: 36
17573 TTAGCCAGTC
17583 TTCAAATTGGGAAAGTTCCC-TCTAAGTTTTTAAGTT
1 TTCAAATTGGGAAAGTTCCCATC-AAGTTTTTAAGTT
17619 TTCAAATTGGGAAAGTT-CC--CAAGTTTTTAAGTT
1 TTCAAATTGGGAAAGTTCCCATCAAGTTTTTAAGTT
* ** **
17652 TGCAAATTGGGAAAGTTCCCATCCCGTTTTTCAAAAT
1 TTCAAATTGGGAAAGTTCCCATCAAGTTTTT-AAGTT
*
17689 TTCTAAATTGGGAAAGTTCCCATC-AGGTTTT-AGTT
1 TTC-AAATTGGGAAAGTTCCCATCAAGTTTTTAAGTT
* *
17724 TTCAATTTAAGGGAAAGTTCCTGTCATCTTTAG-TTTT-AGTT
1 TTCAAATT--GGGAAAGTTCC---CATC--AAGTTTTTAAGTT
*
17765 TTCAAAGTGGGAAAGTTCCCATCAA
1 TTCAAATTGGGAAAGTTCCCATCAA
17790 AAGCATTTTT
Statistics
Matches: 144, Mismatches: 14, Indels: 28
0.77 0.08 0.15
Matches are distributed among these distances:
33 29 0.20
34 8 0.06
35 7 0.05
36 39 0.27
37 10 0.07
38 20 0.14
39 15 0.10
41 14 0.10
42 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (36 bp):
TTCAAATTGGGAAAGTTCCCATCAAGTTTTTAAGTT
Found at i:19129 original size:20 final size:20
Alignment explanation
Indices: 19101--19144 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
19091 AACTAATTTC
19101 TTTTATTTGT-TTTGCCGCCA
1 TTTTATTTGTCTTTGCCG-CA
* *
19121 TTTTCTTTGTCTTTGTCGCA
1 TTTTATTTGTCTTTGCCGCA
19141 TTTT
1 TTTT
19145 GCATCCATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.07, C:0.18, G:0.14, T:0.61
Consensus pattern (20 bp):
TTTTATTTGTCTTTGCCGCA
Found at i:21908 original size:21 final size:21
Alignment explanation
Indices: 21884--21929 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
21874 GCGCCAAGAT
*
21884 GAAGAGGCGAAA-CACCGTGAA
1 GAAGAGGC-AAAGCACCGAGAA
*
21905 GAAGAGGCAAAGCGCCGAGAA
1 GAAGAGGCAAAGCACCGAGAA
21926 GAAG
1 GAAG
21930 CCACGAATGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.43, C:0.17, G:0.37, T:0.02
Consensus pattern (21 bp):
GAAGAGGCAAAGCACCGAGAA
Found at i:32660 original size:6 final size:6
Alignment explanation
Indices: 32619--32645 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
32609 TCTTTTCATA
32619 TTTAAT TTTAAT TTTAAT TTTAAT TTT
1 TTTAAT TTTAAT TTTAAT TTTAAT TTT
32646 GTTATTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTAAT
Found at i:33524 original size:14 final size:14
Alignment explanation
Indices: 33501--33530 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
33491 CCAATTTAGG
*
33501 TTTAGTTTTAAGTT
1 TTTAGATTTAAGTT
33515 TTTAGATTTAAGTT
1 TTTAGATTTAAGTT
33529 TT
1 TT
33531 ATTTTTATGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.13, T:0.63
Consensus pattern (14 bp):
TTTAGATTTAAGTT
Found at i:33598 original size:30 final size:29
Alignment explanation
Indices: 33554--33610 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 29
33544 TTAGGATTAG
33554 TTATCTATGCTTTAATTTTCAA-TTTCCT
1 TTATCTATGCTTTAATTTTCAAGTTTCCT
33582 TTATCTTATGTCTTTAATTTTCAAGTTTC
1 TTATC-TATG-CTTTAATTTTCAAGTTTC
33611 ATTAATAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 5 0.19
29 4 0.15
30 13 0.50
31 4 0.15
ACGTcount: A:0.21, C:0.16, G:0.05, T:0.58
Consensus pattern (29 bp):
TTATCTATGCTTTAATTTTCAAGTTTCCT
Found at i:38015 original size:39 final size:39
Alignment explanation
Indices: 37972--38498 Score: 813
Period size: 39 Copynumber: 13.5 Consensus size: 39
37962 CATCGACCTC
*
37972 AAACAGGTCATCTTTTTAGCATTTATCAAAGTTGACTGG
1 AAACAGGTCATCTTTTCAGCATTTATCAAAGTTGACTGG
*
38011 AAACAGGTCATCTTTTCAAGCATTTATCAAAATTGACTGG
1 AAACAGGTCATCTTTTC-AGCATTTATCAAAGTTGACTGG
* * *
38051 AAACATGTCATCTTTTTAGCATTTATCAAAGTTGACTAG
1 AAACAGGTCATCTTTTCAGCATTTATCAAAGTTGACTGG
* *
38090 AAACAGGTCATCTTTTTAGCATTTATCAAAGTTGACTAG
1 AAACAGGTCATCTTTTCAGCATTTATCAAAGTTGACTGG
* *
38129 AAACAGGTCATCTTTTCAGGATTTATCAAAGTTGACTAG
1 AAACAGGTCATCTTTTCAGCATTTATCAAAGTTGACTGG
* *
38168 AAACAAGTCATCTTTTCAGCATTTATCAAAGTTGACTAG
1 AAACAGGTCATCTTTTCAGCATTTATCAAAGTTGACTGG
* *
38207 AAACAGGTCATCTTTTTAGCATTTATCAAAGTTGATTGG
1 AAACAGGTCATCTTTTCAGCATTTATCAAAGTTGACTGG
*
38246 AAACAGGTCATCTTTTCAGCATTTATCAAAGTTGACTAG
1 AAACAGGTCATCTTTTCAGCATTTATCAAAGTTGACTGG
* * *
38285 AAACAGGTCATCTTTTCGGCATTCATCAAAGTTGATTGG
1 AAACAGGTCATCTTTTCAGCATTTATCAAAGTTGACTGG
**
38324 AAACAGGTCATCTTTTTGGCATTTATCAAAGTTGACTGG
1 AAACAGGTCATCTTTTCAGCATTTATCAAAGTTGACTGG
* *
38363 AAACATGTCATCTTTTCAGCATTTATGAAAGTTGACTGG
1 AAACAGGTCATCTTTTCAGCATTTATCAAAGTTGACTGG
* *
38402 AAACAGGTAATCTTTTCAGTATTTATCAAAGTTGACTGG
1 AAACAGGTCATCTTTTCAGCATTTATCAAAGTTGACTGG
*
38441 AAACAGGTCATCTGTTCAGCATTTATCAAAGTTGACTGG
1 AAACAGGTCATCTTTTCAGCATTTATCAAAGTTGACTGG
38480 AAACAGGTC-TCTTTCTCAG
1 AAACAGGTCATCTTT-TCAG
38499 TTTCAATTTC
Statistics
Matches: 449, Mismatches: 37, Indels: 4
0.92 0.08 0.01
Matches are distributed among these distances:
38 4 0.01
39 409 0.91
40 36 0.08
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (39 bp):
AAACAGGTCATCTTTTCAGCATTTATCAAAGTTGACTGG
Found at i:38700 original size:141 final size:139
Alignment explanation
Indices: 38443--38707 Score: 336
Period size: 141 Copynumber: 1.9 Consensus size: 139
38433 TTGACTGGAA
* * *
38443 ACAGGTCATCTGTTCAGCATTTATCAAAGTTGACTGGAAACAGGTCTCTTTCTCAGTTTCAATTT
1 ACAGGTCATCTGTTCAGCAGTTACCAAAGTTGACTGGAAACAGGTCTCCTTCTCAGTTTCAATTT
* * *
38508 CGACCTCAAACAGGTCTTTATCTTTCAGTTCCAGATCTTAGACAGGTCTTTCTCAGTTTTAATTT
66 CGACCTCAAACAGGTCTTTATCTTTCAGTTCCAGACCTCAGACAGGCCTTTCTCAGTTTTAATTT
38573 CGACCTCAG
131 CGACCTCAG
* * * * * *
38582 ACAGGTCATCTTTTTAGTAGTTACCAAGGTTGACTGGAAATC-GGTCATCCCTTCTCAGTTTTAT
1 ACAGGTCATCTGTTCAGCAGTTACCAAAGTTGACTGGAAA-CAGGTC-T-CCTTCTCAGTTTCAA
** * *
38646 TTTCGACCTCGGACAGGTCATTT-TCTTTCAGTTTCAGACCTCAGACAGGCCTTTCTTAGTTT
63 TTTCGACCTCAAACAGGTC-TTTATCTTTCAGTTCCAGACCTCAGACAGGCCTTTCTCAGTTT
38708 AAAAGTTATC
Statistics
Matches: 106, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
139 38 0.36
140 2 0.02
141 63 0.59
142 3 0.03
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (139 bp):
ACAGGTCATCTGTTCAGCAGTTACCAAAGTTGACTGGAAACAGGTCTCCTTCTCAGTTTCAATTT
CGACCTCAAACAGGTCTTTATCTTTCAGTTCCAGACCTCAGACAGGCCTTTCTCAGTTTTAATTT
CGACCTCAG
Found at i:42455 original size:52 final size:52
Alignment explanation
Indices: 42315--42462 Score: 178
Period size: 52 Copynumber: 2.9 Consensus size: 52
42305 CAATCAAGAC
* * *
42315 TTCAAAGTATTCAATTTAG-TACTTTTTCAAATCGGGAAAGTT-CCATCAGTT
1 TTCAAAGTATTCAATTTAGCCA-TTTTTCAAATTGGGAAAGTTCCCATCAATT
* * *
42366 TTCAAA-TACTCCATCTAGCTC-TTTTTCAAATTGGGAAAGTTCCCATCAATT
1 TTCAAAGTATTCAATTTAGC-CATTTTTCAAATTGGGAAAGTTCCCATCAATT
* *
42417 TTCAAAGTATTCAATTTAGCCAGTCTTCAAATTGGGAAAGTTCCCA
1 TTCAAAGTATTCAATTTAGCCATTTTTCAAATTGGGAAAGTTCCCA
42463 CTAAGTTTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
50 28 0.35
51 21 0.26
52 32 0.40
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (52 bp):
TTCAAAGTATTCAATTTAGCCATTTTTCAAATTGGGAAAGTTCCCATCAATT
Found at i:42482 original size:36 final size:36
Alignment explanation
Indices: 42442--42647 Score: 206
Period size: 36 Copynumber: 5.6 Consensus size: 36
42432 TTAGCCAGTC
*
42442 TTCAAATTGGGAAAGTTCCCACTAAGTTTTTAAGTT
1 TTCAAATTGGGAAAGTTCCCACTCAGTTTTTAAGTT
*
42478 TTCAAATTGGGAAAGTTCCCACTAAGTTTTTAAGTT
1 TTCAAATTGGGAAAGTTCCCACTCAGTTTTTAAGTT
* * *
42514 TTCAAATTAGGAAAGTTCCCA-TCCCGTTTTTCAAAATT
1 TTCAAATTGGGAAAGTTCCCACT-CAGTTTTT--AAGTT
* *
42552 TCCAAATTGGGAAAGTTCCCA-TCAGGTTTT-AGTT
1 TTCAAATTGGGAAAGTTCCCACTCAGTTTTTAAGTT
*
42586 TTCAATTTAAGGGAAAGTTCCTGTCATCTTCAG-TTTT-AGTT
1 TTCAAATT--GGGAAAGTTCC---CA-C-TCAGTTTTTAAGTT
*
42627 TTCAAAGTGGGAAAGTTCCCA
1 TTCAAATTGGGAAAGTTCCCA
42648 TCAAAAGTAT
Statistics
Matches: 146, Mismatches: 13, Indels: 22
0.81 0.07 0.12
Matches are distributed among these distances:
34 9 0.06
35 1 0.01
36 75 0.51
37 6 0.04
38 24 0.16
39 13 0.09
41 14 0.10
42 4 0.03
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (36 bp):
TTCAAATTGGGAAAGTTCCCACTCAGTTTTTAAGTT
Found at i:43355 original size:44 final size:44
Alignment explanation
Indices: 43297--43384 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
43287 ATAATTTCTA
43297 AATTTATGTTCTTTCATTAGATCAGTTAAAATCATACATTAATT
1 AATTTATGTTCTTTCATTAGATCAGTTAAAATCATACATTAATT
*
43341 AATTTATGTTCTTTCATTATATCAGTTAAAATCATACATTAATT
1 AATTTATGTTCTTTCATTAGATCAGTTAAAATCATACATTAATT
43385 GATAATATAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.47
Consensus pattern (44 bp):
AATTTATGTTCTTTCATTAGATCAGTTAAAATCATACATTAATT
Found at i:43380 original size:22 final size:21
Alignment explanation
Indices: 43311--43383 Score: 56
Period size: 22 Copynumber: 3.3 Consensus size: 21
43301 TATGTTCTTT
43311 CATTAGATCAGTTAAAATCATA
1 CATTA-ATCAGTTAAAATCATA
* * *** * *
43333 CATTAATTAATTTATGTTCTTT
1 CATTAA-TCAGTTAAAATCATA
43355 CATTATATCAGTTAAAATCATA
1 CATTA-ATCAGTTAAAATCATA
43377 CATTAAT
1 CATTAAT
43384 TGATAATATA
Statistics
Matches: 35, Mismatches: 14, Indels: 5
0.65 0.26 0.09
Matches are distributed among these distances:
21 3 0.09
22 31 0.89
23 1 0.03
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.42
Consensus pattern (21 bp):
CATTAATCAGTTAAAATCATA
Found at i:44391 original size:25 final size:25
Alignment explanation
Indices: 44341--44392 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
44331 AAATATTTTT
**
44341 AACTAAAATTATCTTTTTCTTTATA
1 AACTAAAATTATCTTTTTCTCAATA
44366 AACTAAAATTATCTTTTAT-TCAATA
1 AACTAAAATTATCTTTT-TCTCAATA
44391 AA
1 AA
44393 ATCTACATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 23 0.96
26 1 0.04
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (25 bp):
AACTAAAATTATCTTTTTCTCAATA
Found at i:44726 original size:102 final size:102
Alignment explanation
Indices: 44618--44814 Score: 349
Period size: 102 Copynumber: 1.9 Consensus size: 102
44608 TTGTTTAAAT
*
44618 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
1 TTTTATAGTTTTAATCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
*
44683 TTTTATTTTTACCATTTTACTATTTTAATTAAAATAC
66 TTTTATTTTTACCATTTTACTAATTTAATTAAAATAC
*
44720 TTTTATAGTTTTAATCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTA
1 TTTTATAGTTTTAATCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
**
44785 TTTTATTTTTATTATTTTACTAATTTAATT
66 TTTTATTTTTACCATTTTACTAATTTAATT
44815 TTAAAACTTA
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 90 1.00
ACGTcount: A:0.35, C:0.12, G:0.01, T:0.53
Consensus pattern (102 bp):
TTTTATAGTTTTAATCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
TTTTATTTTTACCATTTTACTAATTTAATTAAAATAC
Done.