Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold487
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: 167556
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31
Warning! 12863 characters in sequence are not A, C, G, or T
Found at i:651 original size:16 final size:16
Alignment explanation
Indices: 629--668 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
619 CGTTTGGTTC
629 ACTGTAATGGAATAGA
1 ACTGTAATGGAATAGA
* *
645 GCTGTAATGGAATATA
1 ACTGTAATGGAATAGA
661 ACTGTAAT
1 ACTGTAAT
669 AGTAATTCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (16 bp):
ACTGTAATGGAATAGA
Found at i:944 original size:56 final size:56
Alignment explanation
Indices: 829--957 Score: 136
Period size: 56 Copynumber: 2.3 Consensus size: 56
819 AATAAGATTA
* * *
829 TTAATATAAATAATAAATAATTTAATCATATTTTAACATAATTATTATTAAATATAAT
1 TTAATA-AAATAATAAATAATTAAATAAAATTTTAACATAATTATTATT-AATATAAT
* * *
887 TTAATAAAA-AATATATAATTAAATAAAATTCTTAATATAATTATTCTT-ATATGAAT
1 TTAATAAAATAATAAATAATTAAATAAAATT-TTAACATAATTATTATTAATAT-AAT
* *
943 TTACTAAAATCATAA
1 TTAATAAAATAATAA
958 TATATAATAT
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
55 4 0.07
56 28 0.47
57 21 0.36
58 6 0.10
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.43
Consensus pattern (56 bp):
TTAATAAAATAATAAATAATTAAATAAAATTTTAACATAATTATTATTAATATAAT
Found at i:5488 original size:33 final size:33
Alignment explanation
Indices: 5432--5568 Score: 141
Period size: 33 Copynumber: 4.2 Consensus size: 33
5422 ACTTACCCCA
*
5432 TGTTTAATAT-CCAGTGGACTATCTTTGTTCTG
1 TGTTTACTATCCCAGTGGACTATCTTTGTTCTG
* * * * *
5464 TGTTTACTATTCCAGCGGATTATCTCTATTCTG
1 TGTTTACTATCCCAGTGGACTATCTTTGTTCTG
* * * * * *
5497 TGTTTACTGTCCCAGTAGATTGTCTATGTTTTG
1 TGTTTACTATCCCAGTGGACTATCTTTGTTCTG
* *
5530 TGTTTACTGTCCCAGTGAACTATCTTTGTTCTG
1 TGTTTACTATCCCAGTGGACTATCTTTGTTCTG
5563 TGTTTA
1 TGTTTA
5569 TTGTCTTAGC
Statistics
Matches: 85, Mismatches: 19, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
32 9 0.11
33 76 0.89
ACGTcount: A:0.17, C:0.18, G:0.18, T:0.47
Consensus pattern (33 bp):
TGTTTACTATCCCAGTGGACTATCTTTGTTCTG
Found at i:10707 original size:51 final size:51
Alignment explanation
Indices: 10640--10741 Score: 152
Period size: 51 Copynumber: 2.0 Consensus size: 51
10630 CAGATCACAT
*
10640 TTATCACTTCTCACTTGTC-CTTAATCAGATAAGTGTTGCTAAAGCTACCAC
1 TTATCACTTCTCACTTGTCAC-TAATCAGATAAGTGTAGCTAAAGCTACCAC
* * *
10691 TTATCACTTGTTACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTCTCACTTGTCACTAATCAGATAAGTGTAGCTAAAGCTACCAC
10742 CACTACACCA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 45 0.98
52 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (51 bp):
TTATCACTTCTCACTTGTCACTAATCAGATAAGTGTAGCTAAAGCTACCAC
Found at i:10875 original size:42 final size:42
Alignment explanation
Indices: 10827--11039 Score: 207
Period size: 42 Copynumber: 5.0 Consensus size: 42
10817 AAGCGCCGCA
*
10827 AAAAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTAT
1 AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTAT
* * * * *
10869 AAAAACGCTGCTAAAGAAAAAGACCTTTAGCGACGTTTTTAT
1 AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTAT
* *
10911 AAAAATTGCCGCTAAAGAACATGACCTTTAGCGGCGC-TTTACCCA
1 AAAAA-CGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTA---T
* * * * *
10956 AAAAACGTCGCTAAAG-ACATGATCTTTCGCGACGCTTTTTT
1 AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTAT
* * *
10997 CACAAACGCTGCTAAA-AAGCATGACCTTTAGTGGCGCTTTTAT
1 -AAAAACGCCGCTAAAGAA-CATGACCTTTAGCGGCGCTTTTAT
11040 CGCAAACGCC
Statistics
Matches: 137, Mismatches: 26, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
42 60 0.44
43 60 0.44
44 12 0.09
45 5 0.04
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.26
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTAT
Found at i:30670 original size:72 final size:70
Alignment explanation
Indices: 30524--30762 Score: 311
Period size: 72 Copynumber: 3.3 Consensus size: 70
30514 AAAATCATAT
**
30524 ATAAACAACTATTGATAAAACTA-ATTTA-GTATAAATAAGTAGAACATAAATTCAATATCTAAA
1 ATAAACAACTATTGATAAAACTAGA-TTACACATAAATAAGTAGAACATAAATTCAATATC-AAA
30587 GACCAAAC
64 -ACCAAAC
* *
30595 ATAAACAACTATTAATAAAACTAGATTACACATAAATAAGTAGAACATAAAATCAAATATCAAAA
1 ATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACATAAATTC-AATATCAAAA
*
30660 CCCAACC
65 -CCAAAC
* * * *
30667 ATAAACAGCCATTGATAAAACTAGATTACACATAAATAAGTAAAACGTAAATTCAATATCCAAAA
1 ATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAATAT-C-AAA
30732 ACCAAAC
64 ACCAAAC
*
30739 ATAAATAACTATTGATAAAACTAG
1 ATAAACAACTATTGATAAAACTAG
30763 TTTAGCATTG
Statistics
Matches: 147, Mismatches: 15, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
71 31 0.21
72 106 0.72
73 10 0.07
ACGTcount: A:0.55, C:0.15, G:0.06, T:0.23
Consensus pattern (70 bp):
ATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAATATCAAAAC
CAAAC
Found at i:34871 original size:16 final size:16
Alignment explanation
Indices: 34852--34886 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
34842 TTACACTGAA
34852 AAATAATAAAATAAAT
1 AAATAATAAAATAAAT
* *
34868 AAATAATATATTAAAT
1 AAATAATAAAATAAAT
34884 AAA
1 AAA
34887 AAAATAACTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATAATAAAATAAAT
Found at i:46217 original size:18 final size:18
Alignment explanation
Indices: 46190--46249 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
46180 TATTATTTTG
46190 AAATTAAAAATATATAAA
1 AAATTAAAAATATATAAA
*
46208 AAATTTAAAATATATAAA
1 AAATTAAAAATATATAAA
**
46226 TTATTAAAAAACTCATATAAA
1 AAATT-AAAAA-T-ATATAAA
46247 AAA
1 AAA
46250 AAACTTAAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
18 20 0.61
19 4 0.12
20 1 0.03
21 8 0.24
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (18 bp):
AAATTAAAAATATATAAA
Found at i:47425 original size:25 final size:25
Alignment explanation
Indices: 47383--47435 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
47373 ATGAAAACAT
*
47383 AAATAAATAAATAAATAAATAGAGA
1 AAATAAATAAATAAATAAAAAGAGA
* ** *
47408 AAATGAATAAATTTATAAAAAGATA
1 AAATAAATAAATAAATAAAAAGAGA
47433 AAA
1 AAA
47436 AGATATATAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.70, C:0.00, G:0.08, T:0.23
Consensus pattern (25 bp):
AAATAAATAAATAAATAAAAAGAGA
Found at i:48669 original size:30 final size:31
Alignment explanation
Indices: 48601--48669 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 31
48591 TAGGTTTAAT
*
48601 TTTGTTGGGTTATATTTGGGTTTTAGGTTGG
1 TTTGTTGGGTTATATTTGGGTTTAAGGTTGG
* *
48632 -TTATTGGG-T-TATTTGGGTTTAAGTTTGGG
1 TTTGTTGGGTTATATTTGGGTTTAAGGTT-GG
48661 TTTGTTGGG
1 TTTGTTGGG
48670 CCCCGAGTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
28 15 0.47
29 3 0.09
30 14 0.44
ACGTcount: A:0.10, C:0.00, G:0.36, T:0.54
Consensus pattern (31 bp):
TTTGTTGGGTTATATTTGGGTTTAAGGTTGG
Found at i:49188 original size:50 final size:50
Alignment explanation
Indices: 49084--49499 Score: 296
Period size: 50 Copynumber: 8.4 Consensus size: 50
49074 CTGTTCACTA
** * ** * ** *
49084 GGGAAGTAAGATTCGTTGTTGTAGCTTCAATCTATTTAAATGCAATG-TT
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCT
* ** * *
49133 GGGGAAGCAAGATTCGCTATTGTAGCTTTAATCTATTCCACTGCACCGCCT
1 -GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCT
* * * *
49184 GGGAAGTAAGATTCGCCG-T-TACGACTTTAATCT-TTGCAATG--TCG---
1 GGGAAGTAAGATTCGCCGTTGTA-G-CTTCAATCTGTTCCACTGCACCGCCT
* *
49228 AGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCG-CT
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCT
* * * * ** * ** *
49277 AGGGAAGTAAGATTCGTCGTTGTGGCTTCAATTTTTTTAATTGCAATGTC-
1 -GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCT
* *
49327 GAGGAAGTAAGATTCACCGTTGTAGCTTCAATTTGTTCCACTGCACCGCCT
1 G-GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCT
* * * ** * ** * *
49378 GGGAAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTTAATTGCAATGTCG
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCT
**
49428 GGGAAGCGAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCT
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCT
* *
49478 GGAAAGTAAGATTCACCGTTGT
1 GGGAAGTAAGATTCGCCGTTGT
49500 GGCCTTAATC
Statistics
Matches: 281, Mismatches: 71, Indels: 28
0.74 0.19 0.07
Matches are distributed among these distances:
44 24 0.09
45 8 0.03
46 2 0.01
47 4 0.01
48 2 0.01
49 9 0.03
50 229 0.81
51 3 0.01
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (50 bp):
GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCT
Found at i:49352 original size:100 final size:100
Alignment explanation
Indices: 49217--49567 Score: 503
Period size: 100 Copynumber: 3.5 Consensus size: 100
49207 ACTTTAATCT
*
49217 TTGCAATGTCGAGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCG-CTAGGG
1 TTGCAATGTCGAGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCT-GGG
*
49281 AAGTAAGATTCGTCGTTGTGGCTTCAATTTTTTTAA
65 AAGTAAGATTCGCCGTTGTGGCTTCAATTTTTTTAA
* *
49317 TTGCAATGTCGAGGAAGTAAGATTCACCGTTGTAGCTTCAATTTGTTCCACTGCACCGCCTGGGA
1 TTGCAATGTCGAGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGGA
* *
49382 AGTAAGATTCGCCGTTGTGGCCTCAATCTTTTTAA
66 AGTAAGATTCGCCGTTGTGGCTTCAATTTTTTTAA
* * * *
49417 TTGCAATGTCGGGGAAGCGAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGAA
1 TTGCAATGTCGAGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGGA
* *
49482 AGTAAGATTCACCGTTGTGGCCTT-AA-TCTTTTAA
66 AGTAAGATTCGCCGTTGTGG-CTTCAATTTTTTTAA
* * **
49516 TTGTAATGTC-AGGGAAGCGAGATTCATTGTTGTAGCTTCAATCTGTTCCACT
1 TTGCAATGTCGA-GGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCACT
49568 ACACTACCTG
Statistics
Matches: 227, Mismatches: 21, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
99 52 0.23
100 171 0.75
101 4 0.02
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (100 bp):
TTGCAATGTCGAGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGGA
AGTAAGATTCGCCGTTGTGGCTTCAATTTTTTTAA
Found at i:49736 original size:128 final size:128
Alignment explanation
Indices: 49577--50110 Score: 840
Period size: 128 Copynumber: 4.2 Consensus size: 128
49567 TACACTACCT
* * * * * *
49577 GGGAGATAATATTGGTTGCGATCTACTCTACTGCAAGTTCAGAGAG-ATAAGATCTGTGTTTTTA
1 GGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAG-GTATAAGATCTGTGATTTTA
* *
49641 ATCCGCTCCACTGTAACTTCAAGGAGATAGAATTGATTTCTTCTGTCTGCTCCACTACTGCTTA
65 ATCCGCTCCACTGCAACTTCAAGGAGATAGGATTGATTTCTTCTGTCTGCTCCACTACTGCTTA
*
49705 GGGAGATAAGACTGGATACGATCTGCTCTACTGCAACTTCAGAGAG-ATAAGATCTGTGATTTTA
1 GGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAG-GTATAAGATCTGTGATTTTA
* * * *
49769 ATCCGCTCTACTTCAAATTC-AGGAAGATAGGATTGATTTCTTCTGTCTGCTCTACTACTGCTTA
65 ATCCGCTCCACTGCAACTTCAAGG-AGATAGGATTGATTTCTTCTGTCTGCTCCACTACTGCTTA
*
49833 GGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTTAGAGGTATAAGATCTGTGATTTTAA
1 GGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGGTATAAGATCTGTGATTTTAA
* *
49898 TCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCTTTCTGCTCCACTACTGCTTA
66 TCCGCTCCACTGCAACTTCAAGGAGATAGGATTGATTTCTTCTGTCTGCTCCACTACTGCTTA
* *
49961 AGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTTAGAGGTATAAGATCTGTGATTTTAA
1 GGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGGTATAAGATCTGTGATTTTAA
* *
50026 TCCGCTCCACTGCAACTTCAGGGAGATAGGATTAATTTCTTCTGTCTGCTCCACTACTGCTTA
66 TCCGCTCCACTGCAACTTCAAGGAGATAGGATTGATTTCTTCTGTCTGCTCCACTACTGCTTA
50089 GGGAGATAAGACTGGATGCGAT
1 GGGAGATAAGACTGGATGCGAT
50111 AAATCTGCTT
Statistics
Matches: 378, Mismatches: 25, Indels: 6
0.92 0.06 0.01
Matches are distributed among these distances:
127 4 0.01
128 372 0.98
129 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (128 bp):
GGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGGTATAAGATCTGTGATTTTAA
TCCGCTCCACTGCAACTTCAAGGAGATAGGATTGATTTCTTCTGTCTGCTCCACTACTGCTTA
Found at i:49911 original size:44 final size:44
Alignment explanation
Indices: 49606--50053 Score: 131
Period size: 44 Copynumber: 10.5 Consensus size: 44
49596 GATCTACTCT
* * *
49606 ACTGCAAGTTCAGA-GAGATAAGATCTGTGTTTTTAATCCGCTCC
1 ACTGCAACTTTAGAGGAGATAAGA-CTGTGATTTTAATCCGCTCC
* * * ** *
49650 ACTGTAACTTCA-AGGAGAT-AGAAT-TGATTTCTTCTGTCTGCTCC
1 ACTGCAACTTTAGAGGAGATAAGACTGTGA-TT-TT-AATCCGCTCC
* ** *** * *
49694 ACTACTGC-TTAG-GGAGATAAGACTG-GA-TACGATCTGCTCT
1 ACTGCAACTTTAGAGGAGATAAGACTGTGATTTTAATCCGCTCC
* *
49734 ACTGCAACTTCAGA-GAGATAAGATCTGTGATTTTAATCCGCTCT
1 ACTGCAACTTTAGAGGAGATAAGA-CTGTGATTTTAATCCGCTCC
* * * * * * *
49778 ACTTCAAATTCAG-GAAGATAGGA-T-TGATTTCT--TCTGTCTGC
1 ACTGCAACTTTAGAGGAGATAAGACTGTGATTT-TAATCCG-CTCC
* * * *** * *
49819 TCTACTACTGCTTAG-GGAGATAAGACTG-GA-TGCGATCTGCTCT
1 ACTGCAACT--TTAGAGGAGATAAGACTGTGATTTTAATCCGCTCC
*
49862 ACTGCAACTTTAGAGG-TATAAGATCTGTGATTTTAATCCGCTCC
1 ACTGCAACTTTAGAGGAGATAAGA-CTGTGATTTTAATCCGCTCC
* * ** *
49906 ACTGCAACTTCAG-GGAGATAGGA-T-TGATTTCTTCTTTCTGCTCC
1 ACTGCAACTTTAGAGGAGATAAGACTGTGA-TT-TT-AATCCGCTCC
* ** *** * *
49950 ACTACTGC-TTA-AGGAGATAAGACTG-GA-TGCGATCTGCTCT
1 ACTGCAACTTTAGAGGAGATAAGACTGTGATTTTAATCCGCTCC
*
49990 ACTGCAACTTTAGAGG-TATAAGATCTGTGATTTTAATCCGCTCC
1 ACTGCAACTTTAGAGGAGATAAGA-CTGTGATTTTAATCCGCTCC
*
50034 ACTGCAACTTCAG-GGAGATA
1 ACTGCAACTTTAGAGGAGATA
50054 GGATTAATTT
Statistics
Matches: 286, Mismatches: 80, Indels: 76
0.65 0.18 0.17
Matches are distributed among these distances:
40 27 0.09
41 49 0.17
42 24 0.08
43 57 0.20
44 129 0.45
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (44 bp):
ACTGCAACTTTAGAGGAGATAAGACTGTGATTTTAATCCGCTCC
Found at i:50118 original size:44 final size:44
Alignment explanation
Indices: 50070--50187 Score: 100
Period size: 44 Copynumber: 2.7 Consensus size: 44
50060 ATTTCTTCTG
* *
50070 TCTGCTCCACTACTGCTTAGGGAGATAAGACTGGATG-CGATAAA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTCGACGTC-ATAAA
* * * * **
50114 TCTGCTTCCTACTA-T-C-TCGGGATGATAAGATTCGCCGTCTTCGA
1 TCTGC-TCC-ACTACTGCTTAGGGA-GATAAGACTCGACGTCATAAA
50158 TCTGCTCCACTACTGCTTAGGGAGATAAGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA
50188 TCTACAATCT
Statistics
Matches: 58, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
42 4 0.07
43 9 0.16
44 31 0.53
45 10 0.17
46 4 0.07
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.29
Consensus pattern (44 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGACTCGACGTCATAAA
Found at i:50613 original size:24 final size:24
Alignment explanation
Indices: 50560--50616 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
50550 GGATTGCCCT
50560 CACTGTAATCTTCAAAGTTCAATC
1 CACTGTAATCTTCAAAGTTCAATC
* * *
50584 CGCTGTAGTCTTCAAGGTT-AAGTC
1 CACTGTAATCTTCAAAGTTCAA-TC
50608 CACTGTAAT
1 CACTGTAAT
50617 TTTGGAACAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 2 0.07
24 25 0.93
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (24 bp):
CACTGTAATCTTCAAAGTTCAATC
Found at i:51480 original size:11 final size:11
Alignment explanation
Indices: 51465--51537 Score: 69
Period size: 11 Copynumber: 6.5 Consensus size: 11
51455 GCCTCTCCTT
51465 TTTTTCTTTT-
1 TTTTTCTTTTA
51475 TCTTTTCTTTTTA
1 T-TTTTC-TTTTA
* *
51488 TTCTTTATTCT-
1 TT-TTTCTTTTA
*
51499 TTATTCTTTTTA
1 TTTTTC-TTTTA
51511 TTTTTCTTTTA
1 TTTTTCTTTTA
51522 TTTTTCTTTTA
1 TTTTTCTTTTA
51533 TTTTT
1 TTTTT
51538 TTTAACATTC
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
10 3 0.06
11 31 0.61
12 13 0.25
13 4 0.08
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTTCTTTTA
Found at i:51491 original size:14 final size:13
Alignment explanation
Indices: 51462--51541 Score: 63
Period size: 14 Copynumber: 5.8 Consensus size: 13
51452 TTGGCCTCTC
*
51462 CTTTTTTTCTTTTT
1 CTTTTTTT-TTATT
51476 CTTTTCTTTTTATT
1 CTTTT-TTTTTATT
*
51490 CTTTATTCTTTATT
1 CTTT-TTTTTTATT
*
51504 CTTTTTATTT-TT
1 CTTTTTTTTTATT
*
51516 CTTTTATTTTTCTT
1 CTTTT-TTTTTATT
*
51530 TTATTTTTTTTA
1 CT-TTTTTTTTA
51542 ACATTCTTTG
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
12 7 0.13
13 9 0.16
14 32 0.58
15 7 0.13
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (13 bp):
CTTTTTTTTTATT
Found at i:51990 original size:16 final size:17
Alignment explanation
Indices: 51969--52007 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
51959 CCCGGTAGAG
51969 TTTTTTGTTTTTT-TATT
1 TTTTTTGTTTTTTGT-TT
51986 TTTTTTGTTTTTTGTTT
1 TTTTTTGTTTTTTGTTT
52003 TTTTT
1 TTTTT
52008 GCCTCCACTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 20 0.95
18 1 0.05
ACGTcount: A:0.03, C:0.00, G:0.08, T:0.90
Consensus pattern (17 bp):
TTTTTTGTTTTTTGTTT
Found at i:52008 original size:16 final size:17
Alignment explanation
Indices: 51969--52008 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
51959 CCCGGTAGAG
51969 TTTTTTGTTTTTTTATT
1 TTTTTTGTTTTTTTATT
*
51986 TTTTTTG-TTTTTTGTT
1 TTTTTTGTTTTTTTATT
52002 TTTTTTG
1 TTTTTTG
52009 CCTCCACTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.03, C:0.00, G:0.10, T:0.88
Consensus pattern (17 bp):
TTTTTTGTTTTTTTATT
Found at i:54772 original size:19 final size:20
Alignment explanation
Indices: 54748--54794 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
54738 TGTGAAAATC
*
54748 TAATGCATATG-ATGCAATG
1 TAATGCAAATGTATGCAATG
*
54767 TAATGCAAATGTATGGAATG
1 TAATGCAAATGTATGCAATG
54787 -AATGCAAA
1 TAATGCAAA
54795 AAGAAAGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.28
Consensus pattern (20 bp):
TAATGCAAATGTATGCAATG
Found at i:57058 original size:37 final size:37
Alignment explanation
Indices: 56986--57058 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
56976 AAAATGAATA
*
56986 AAATTATAAAAATATAAAAAGATATATATGTATATAC
1 AAATTATAAAAATATAAAAAGATATATATGAATATAC
57023 AAATTAT-AAAATATAAAAA-ATATATATAAGAATATA
1 AAATTATAAAAATATAAAAAGATATATAT--GAATATA
57059 TATATACAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
35 8 0.24
36 12 0.36
37 13 0.39
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (37 bp):
AAATTATAAAAATATAAAAAGATATATATGAATATAC
Found at i:58268 original size:30 final size:31
Alignment explanation
Indices: 58200--58268 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 31
58190 TAGGTTTAAT
* *
58200 TTTGTTGGGTTATATTTGGGTTTTAGGTTGG
1 TTTGTTGGGTTATATTTAGGTTTAAGGTTGG
* *
58231 -TTATTGGG-T-TATTTAGGTTTAAGTTTGGG
1 TTTGTTGGGTTATATTTAGGTTTAAGGTT-GG
58260 TTTGTTGGG
1 TTTGTTGGG
58269 CCCCGGGTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
28 14 0.45
29 3 0.10
30 14 0.45
ACGTcount: A:0.12, C:0.00, G:0.35, T:0.54
Consensus pattern (31 bp):
TTTGTTGGGTTATATTTAGGTTTAAGGTTGG
Found at i:58383 original size:14 final size:14
Alignment explanation
Indices: 58351--58394 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
58341 TCTATATATT
58351 TTTATAATTTTAAA
1 TTTATAATTTTAAA
58365 TTTATCAATTTTAAA
1 TTTAT-AATTTTAAA
58380 -TTAT--TTTTAAA
1 TTTATAATTTTAAA
58391 TTTA
1 TTTA
58395 GGTCTTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 7 0.25
12 3 0.11
14 9 0.32
15 9 0.32
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTATAATTTTAAA
Found at i:59661 original size:25 final size:24
Alignment explanation
Indices: 59603--59653 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
59593 AATTAACTTA
* *
59603 AATAAAGT-TTAATATTATTATAT
1 AATAAATTATTAATATAATTATAT
59626 AATAAATTATTAATATAATTGATAT
1 AATAAATTATTAATATAATT-ATAT
59651 AAT
1 AAT
59654 TTATTATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 7 0.29
24 10 0.42
25 7 0.29
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (24 bp):
AATAAATTATTAATATAATTATAT
Found at i:60395 original size:22 final size:24
Alignment explanation
Indices: 60368--60418 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
60358 AGTTATGATA
60368 AAAAAATTATA-T-TCTAAATCTT
1 AAAAAATTATATTATCTAAATCTT
*
60390 AAAAAATTATATTATTTAAATCTT
1 AAAAAATTATATTATCTAAATCTT
60414 AAAAA
1 AAAAA
60419 GTTTCCAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 11 0.42
23 1 0.04
24 14 0.54
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (24 bp):
AAAAAATTATATTATCTAAATCTT
Found at i:62060 original size:79 final size:78
Alignment explanation
Indices: 61928--62074 Score: 204
Period size: 79 Copynumber: 1.9 Consensus size: 78
61918 TGTAAACATG
* * * * * *
61928 AATCAATTAAATAATTCTGTTTTAGGATTTTATTCCTACCGTTCAATAGAATTTGTTCGATTTTC
1 AATCAATTAAACAATTCTATTTCAGGATTCTATTCCTACCGTTCAATAAAATTTATTCGATTTT-
61993 TGTTTCTCAACAGA
65 TGTTTCTCAACAGA
* **
62007 AATCAATTGAACAATTCTATTTCAGGATTCTATTCCTATTGTTCAATAAAATTTATTCGATTTTT
1 AATCAATTAAACAATTCTATTTCAGGATTCTATTCCTACCGTTCAATAAAATTTATTCGATTTTT
62072 GTT
66 GTT
62075 GTAAACAGTA
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
78 4 0.07
79 55 0.93
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.46
Consensus pattern (78 bp):
AATCAATTAAACAATTCTATTTCAGGATTCTATTCCTACCGTTCAATAAAATTTATTCGATTTTT
GTTTCTCAACAGA
Found at i:74810 original size:21 final size:20
Alignment explanation
Indices: 74777--74815 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
74767 AATTAGAACA
74777 TTTTTTTAAATAAGTATATTG
1 TTTTTTTAAATAA-TATATTG
**
74798 TTTTTTTTTATAATATAT
1 TTTTTTTAAATAATATAT
74816 AGCATGGACA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (20 bp):
TTTTTTTAAATAATATATTG
Found at i:75564 original size:40 final size:39
Alignment explanation
Indices: 75504--75579 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 39
75494 ACAATTTTAA
75504 AATTAAGTGAAAATATTTTTAAC-CAAGTCAAAATGATCTC
1 AATTAAGTGAAAATATTTTTAACAC-A-TCAAAATGATCTC
*
75544 AATTAAGTTAAAATCA-TTTTAACACATCAAAATGAT
1 AATTAAGTGAAAAT-ATTTTTAACACATCAAAATGAT
75580 TTTTAAACAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
39 10 0.30
40 21 0.64
41 2 0.06
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.33
Consensus pattern (39 bp):
AATTAAGTGAAAATATTTTTAACACATCAAAATGATCTC
Found at i:75772 original size:20 final size:20
Alignment explanation
Indices: 75735--75780 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
75725 TGTTTTTGGT
*
75735 ATCGATA-CTTTTTGAAAATA
1 ATCGATACCTTTCTGAAAA-A
75755 ATCGATACCTTTCT-AAAAA
1 ATCGATACCTTTCTGAAAAA
75774 AT-GATAC
1 ATCGATAC
75781 TAGAATTGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 5 0.21
19 3 0.12
20 11 0.46
21 5 0.21
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (20 bp):
ATCGATACCTTTCTGAAAAA
Found at i:75773 original size:21 final size:20
Alignment explanation
Indices: 75735--75773 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
75725 TGTTTTTGGT
* *
75735 ATCGATACTTTTTGAAAATA
1 ATCGATACTTTCTAAAAATA
75755 ATCGATACCTTTCTAAAAA
1 ATCGATA-CTTTCTAAAAA
75774 ATGATACTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (20 bp):
ATCGATACTTTCTAAAAATA
Found at i:76685 original size:3 final size:3
Alignment explanation
Indices: 76677--76712 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
76667 TAAGACCATG
76677 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
76713 ATATGGTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:85190 original size:214 final size:210
Alignment explanation
Indices: 84722--85288 Score: 661
Period size: 214 Copynumber: 2.7 Consensus size: 210
84712 TACCGGCAAG
*
84722 GCGTTTGTAGTCCAACGGTTAGGATAATTGCCTTCCAAGCAATAGACCCAGGTTCGACTCCCGGC
1 GCGTTTGTAGTCCAACGGTTAGGATAATTGCCTTCCAAGCAATAGACCCGGGTTCGACTCCCGGC
* * *
84787 AAACGCAATAGCATTATCTTCATTTTCTTTTTTGTTGGGCTTCGGAGTTTGGGCACTCGGGGACT
66 AAACGCAATAGCATTATCTTCATTTTCTATTTTGTTGGGCTTCGGAGTTTGAGCACTCAGGGACT
* ** * * *
84852 TCAACAGGCCCTATGTTTGTAAGTTACATTTTTTTTTTATACATTTTGTGAATATAATTAGCCGG
131 TCAACAGGCCCTATGTTTATAAGTTACATTTTTTTTTTATACATGCTGAGAATATAATTAACCGA
* * ** *
84917 GGTCTATTTAATGAA
196 GATATATCCAACGAA
84932 GCGTTTGTAGTCCAACGGTTAGGATAATTGCCTTCCAAGCAATAGACCCGGGTTCGACTCCCGGC
1 GCGTTTGTAGTCCAACGGTTAGGATAATTGCCTTCCAAGCAATAGACCCGGGTTCGACTCCCGGC
* *
84997 AAACGCAATAGC-TTAAT-TATC-TGTTTCTGATTTTGTTGGG-TTCGTAGTTTTGAGCACTTAG
66 AAACGCAATAGCATT-ATCT-TCAT-TTTCT-ATTTTGTTGGGCTTCGGAG-TTTGAGCACTCAG
* *
85058 GGACTT-AACAGGCCCTAATATAGTTAATATAATTTAC-TTTTTTTTTTA-ATATGCTGAGAAT-
126 GGACTTCAACAGGCCC---TAT-GTT--TATAAGTTACATTTTTTTTTTATACATGCTGAGAATA
* *
85119 T-GTTAACTGAGATATATCGCCAACGAA
185 TAATTAACCGAGATATAT--CCAACGAA
85146 GCGTTTGTAGTCCAACGGTTAGGATAATTGCCTTCCAAGCAATAGACCCGGGTTCGACTCCCGGC
1 GCGTTTGTAGTCCAACGGTTAGGATAATTGCCTTCCAAGCAATAGACCCGGGTTCGACTCCCGGC
* * * * * *
85211 AAACGCAATAGCAATAGT-TTTATTTTCAATTTCCTTTTTGGG-TTTGGAGTTTGAGCACTGAGG
66 AAACGCAATAGCATTA-TCTTCATTTTCTA-TT--TTGTTGGGCTTCGGAGTTTGAGCACTCAGG
85274 GACTTCAACAGGCCC
127 GACTTCAACAGGCCC
85289 CAATATAGTT
Statistics
Matches: 309, Mismatches: 28, Indels: 34
0.83 0.08 0.09
Matches are distributed among these distances:
209 4 0.01
210 100 0.32
211 26 0.08
212 10 0.03
213 5 0.02
214 102 0.33
215 33 0.11
216 29 0.09
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (210 bp):
GCGTTTGTAGTCCAACGGTTAGGATAATTGCCTTCCAAGCAATAGACCCGGGTTCGACTCCCGGC
AAACGCAATAGCATTATCTTCATTTTCTATTTTGTTGGGCTTCGGAGTTTGAGCACTCAGGGACT
TCAACAGGCCCTATGTTTATAAGTTACATTTTTTTTTTATACATGCTGAGAATATAATTAACCGA
GATATATCCAACGAA
Found at i:92139 original size:23 final size:23
Alignment explanation
Indices: 92113--92187 Score: 123
Period size: 23 Copynumber: 3.3 Consensus size: 23
92103 ATAAGTGCAA
*
92113 CACTGATATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
*
92136 CACTGAAATGTAGCCGAAGCTAA
1 CACTGAAATGTAGCCGAAGCTAC
*
92159 CACTGAAACGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
92182 CACTGA
1 CACTGA
92188 TCAATAACAC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.35, C:0.27, G:0.21, T:0.17
Consensus pattern (23 bp):
CACTGAAATGTAGCCGAAGCTAC
Found at i:92426 original size:18 final size:17
Alignment explanation
Indices: 92400--92438 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
92390 ATTTTCCTTC
92400 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
92417 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
92435 CACA
1 CACA
92439 ATTTATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:94798 original size:91 final size:91
Alignment explanation
Indices: 94686--94867 Score: 346
Period size: 91 Copynumber: 2.0 Consensus size: 91
94676 ATCAGAGTCT
94686 CTATTTATAGGCATGAGAAGTATAAAAGAAGTAAAGATCTAATTCTAATAACTACTAGAATTTAA
1 CTATTTATAGGCATGAGAAGTATAAAAGAAGTAAAGATCTAATTCTAATAACTACTAGAATTTAA
*
94751 AGTACATTAAAACTTTATCTTCATCA
66 AGTACATTAAAAATTTATCTTCATCA
*
94777 CTATTTATAGGCATGATAAGTATAAAAGAAGTAAAGATCTAATTCTAATAACTACTAGAATTTAA
1 CTATTTATAGGCATGAGAAGTATAAAAGAAGTAAAGATCTAATTCTAATAACTACTAGAATTTAA
94842 AGTACATTAAAAATTTATCTTCATCA
66 AGTACATTAAAAATTTATCTTCATCA
94868 TGATTGACAT
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 89 1.00
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.34
Consensus pattern (91 bp):
CTATTTATAGGCATGAGAAGTATAAAAGAAGTAAAGATCTAATTCTAATAACTACTAGAATTTAA
AGTACATTAAAAATTTATCTTCATCA
Found at i:98781 original size:16 final size:17
Alignment explanation
Indices: 98756--98788 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
98746 TCTACAAGAT
*
98756 AAATATTAAAT-TAATA
1 AAATACTAAATATAATA
98772 AAATACTAAATATAATA
1 AAATACTAAATATAATA
98789 TAGCAAGACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATACTAAATATAATA
Found at i:98865 original size:103 final size:104
Alignment explanation
Indices: 98674--98882 Score: 377
Period size: 103 Copynumber: 2.0 Consensus size: 104
98664 TATTCATAAC
98674 AAATATAATATTTAGCAAGACAATATTATATTAAATTTAATATGAAATCTTATTAAAATAATTGA
1 AAATATAATA-TTAGCAAGACAATATTATATTAAATTTAATATGAAATCTTATTAAAATAATTGA
*
98739 ACATTTATCTACAAGATAAATATT-AAATTAATAAAATACT
65 ACATTTATCTACAAGATAAATATTAAAAAT-ATAAAATACT
98779 AAATATAATA-TAGCAAGACAATATTATATTAAATTTAATATGAAATCTTATTAAAATAATTGAA
1 AAATATAATATTAGCAAGACAATATTATATTAAATTTAATATGAAATCTTATTAAAATAATTGAA
98843 CATTTATCTACAAGATAAATATTAAAAATATAAAATACT
66 CATTTATCTACAAGATAAATATTAAAAATATAAAATACT
98882 A
1 A
98883 TTAAGATAAA
Statistics
Matches: 102, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
103 88 0.86
104 4 0.04
105 10 0.10
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.36
Consensus pattern (104 bp):
AAATATAATATTAGCAAGACAATATTATATTAAATTTAATATGAAATCTTATTAAAATAATTGAA
CATTTATCTACAAGATAAATATTAAAAATATAAAATACT
Found at i:102222 original size:86 final size:87
Alignment explanation
Indices: 102130--102297 Score: 221
Period size: 87 Copynumber: 1.9 Consensus size: 87
102120 TAAGAGTAGG
* * * * * *
102130 GGCTTAATTGC-GTTTTTGAAAAATTTTGAGGGTATTTTTTATGCATTTTAAAAGTTTAAGTGCT
1 GGCTTAATTGCTGTTTTTGAAAAAGTTTGAGGGCATTTTTGATGCATTTTAAAAGATCAAGTACT
102194 CAATTGAGTGAAAAAAAACAAT
66 CAATTGAGTGAAAAAAAACAAT
* * * **
102216 GGCTTAATTGCTTTTTTTGAAGAAGTTTGAGGGCCTTTTTGATGCATTTTTGAAGATCAAGTACT
1 GGCTTAATTGCTGTTTTTGAAAAAGTTTGAGGGCATTTTTGATGCATTTTAAAAGATCAAGTACT
*
102281 TAATTGAGTGAAAAAAA
66 CAATTGAGTGAAAAAAA
102298 GCTTAATTAC
Statistics
Matches: 69, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
86 11 0.16
87 58 0.84
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (87 bp):
GGCTTAATTGCTGTTTTTGAAAAAGTTTGAGGGCATTTTTGATGCATTTTAAAAGATCAAGTACT
CAATTGAGTGAAAAAAAACAAT
Found at i:104670 original size:16 final size:16
Alignment explanation
Indices: 104649--104699 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
104639 AAGAAAGAGC
104649 AAATACGCTAGTAAAT
1 AAATACGCTAGTAAAT
104665 AAATACGCTAGTAAAT
1 AAATACGCTAGTAAAT
* * *
104681 AAACACTCGAGTAAAT
1 AAATACGCTAGTAAAT
104697 AAA
1 AAA
104700 ATATTAGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.53, C:0.14, G:0.12, T:0.22
Consensus pattern (16 bp):
AAATACGCTAGTAAAT
Found at i:115006 original size:30 final size:30
Alignment explanation
Indices: 114970--115044 Score: 105
Period size: 30 Copynumber: 2.5 Consensus size: 30
114960 CTAACTAGGA
114970 ATCTCCTCTTGGTCTCACTTAAGCATATAG
1 ATCTCCTCTTGGTCTCACTTAAGCATATAG
* *
115000 ATCTCCTATTGGTCTCACTTAGGCATATAG
1 ATCTCCTCTTGGTCTCACTTAAGCATATAG
* * *
115030 GTCTTCTCTCGGTCT
1 ATCTCCTCTTGGTCT
115045 TACTATTCGG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.19, C:0.27, G:0.16, T:0.39
Consensus pattern (30 bp):
ATCTCCTCTTGGTCTCACTTAAGCATATAG
Found at i:122574 original size:16 final size:17
Alignment explanation
Indices: 122547--122581 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
122537 TAAAATTGGG
*
122547 TTGAGAAAATTATTTAA
1 TTGAGAAAATTAATTAA
122564 TTGAG-AAATTAATTAA
1 TTGAGAAAATTAATTAA
122580 TT
1 TT
122582 TAGATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (17 bp):
TTGAGAAAATTAATTAA
Found at i:129974 original size:23 final size:23
Alignment explanation
Indices: 129919--129982 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 23
129909 TAAAGGTTAA
* *
129919 TGAATT-TATATATTTAATCATTC
1 TGAATTATATATATTAAAT-ATAC
129942 T--ATTAT-TATATTAAATATAC
1 TGAATTATATATATTAAATATAC
*
129962 TGAATTATATATATAAAATAT
1 TGAATTATATATATTAAATAT
129983 TAAGTTATCG
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
20 4 0.12
21 12 0.35
22 6 0.18
23 12 0.35
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (23 bp):
TGAATTATATATATTAAATATAC
Found at i:134206 original size:40 final size:39
Alignment explanation
Indices: 134146--134896 Score: 742
Period size: 40 Copynumber: 18.8 Consensus size: 39
134136 TGTATGACTT
**
134146 CACATACGTGCCCCTAATTGTACTTCGGTACCCTTGAATG
1 CACATACGTG-CCCTGTTTGTACTTCGGTACCCTTGAATG
* * * *
134186 TAGATACGTGCCTCTGATTGTACTTTGGTATCCC-TGAATG
1 CACATACGTGCC-CTGTTTGTACTTCGGTA-CCCTTGAATG
* * *
134226 CACATACATGCCCCTGTTTGTACTTCGGTATCCC-TAAATA
1 CACATACGTG-CCCTGTTTGTACTTCGGTA-CCCTTGAATG
* * * *
134266 CACATATGTGCCCCTATTTGTACTTTGGTACCCCTGAATG
1 CACATACGTG-CCCTGTTTGTACTTCGGTACCCTTGAATG
*
134306 CACATATGTGCCCCTGTTTGTACTTCGGTACCCTT-AGATG
1 CACATACGTG-CCCTGTTTGTACTTCGGTACCCTTGA-ATG
* *
134346 CACATACGTGCCTCTGTTTGTACTTCGGTACCCTTGGATA
1 CACATACGTGCC-CTGTTTGTACTTCGGTACCCTTGAATG
** *
134386 CACATATATGCCCCTGTTTGTACTTCGGTATCCTTGAATG
1 CACATACGTG-CCCTGTTTGTACTTCGGTACCCTTGAATG
* * *
134426 CACATACGTGCCCTTATTTGTACTTCGATATCCCTAG-ATG
1 CACATACGTGCCC-TGTTTGTACTTCGGTA-CCCTTGAATG
* *
134466 CACATACGTGTCCCTGTTTGTACTTCAGTACCCCTGAATG
1 CACATACGTG-CCCTGTTTGTACTTCGGTACCCTTGAATG
* *
134506 CACATACGTGCCCTTGATTGTACTTCGGTACCCCTGAATG
1 CACATACGTGCCC-TGTTTGTACTTCGGTACCCTTGAATG
* * * **
134546 TAGATATGTGCCTCTAATTGTACTTCGGTATCCC-TGAATG
1 CACATACGTGCC-CTGTTTGTACTTCGGTA-CCCTTGAATG
* *
134586 CACATACATGCCACTGTTTGTACTTCGGTATCCC-TAAATG
1 CACATACGTGCC-CTGTTTGTACTTCGGTA-CCCTTGAATG
* * * *
134626 CACATATGTGCCCCTATTTGTACTTTGGTACCCCTGAATG
1 CACATACGTG-CCCTGTTTGTACTTCGGTACCCTTGAATG
*
134666 CACATATGTGCCCATGTTTGTACTTCGGTACCCTT-AGATG
1 CACATACGTGCCC-TGTTTGTACTTCGGTACCCTTGA-ATG
* *
134706 CACATACGTGCCTCTGTTTGTACTTCGGTACCCTTGGATA
1 CACATACGTGCC-CTGTTTGTACTTCGGTACCCTTGAATG
** * *
134746 CACATACAAGCCCCTGTTTGTACTTCAGTATCCTTGAATG
1 CACATACGTG-CCCTGTTTGTACTTCGGTACCCTTGAATG
* * * * *
134786 CACATACGTGCCCTTATTTGTACTTTGATACCCCTGGATG
1 CACATACGTGCCC-TGTTTGTACTTCGGTACCCTTGAATG
* * *
134826 CACATACGTGTCCCTGTTTATACTTCAGTACCCCTGAATG
1 CACATACGTG-CCCTGTTTGTACTTCGGTACCCTTGAATG
*
134866 CACATACGTGCCCTTGATTGTACTTCGGTAC
1 CACATACGTGCCC-TGTTTGTACTTCGGTAC
134897 TTATGAAGGC
Statistics
Matches: 598, Mismatches: 88, Indels: 50
0.81 0.12 0.07
Matches are distributed among these distances:
39 31 0.05
40 541 0.90
41 26 0.04
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.34
Consensus pattern (39 bp):
CACATACGTGCCCTGTTTGTACTTCGGTACCCTTGAATG
Found at i:134363 original size:120 final size:119
Alignment explanation
Indices: 134146--134896 Score: 818
Period size: 120 Copynumber: 6.3 Consensus size: 119
134136 TGTATGACTT
* * * * *
134146 CACATACGTGCCCCTAATTGTACTTCGGTACCCTTGAATGTAGATACGTGCCTCTGA-TTGTACT
1 CACATACGTGCCCCTATTTGTACTTCGGTACCCCTGAATGCACATACGTGCCCCT-ATTTGTACT
* * * *
134210 TTGGTATCCCTGA-ATGCACATACATGCCCCTGTTTGTACTTCGGTATCCCTAAATA
65 TCGGTATCCCTTAGATGCACATACGTG-CCCTGTTTGTACTTCGGTA-CCCTGAATA
* * * *
134266 CACATATGTGCCCCTATTTGTACTTTGGTACCCCTGAATGCACATATGTGCCCCTGTTTGTACTT
1 CACATACGTGCCCCTATTTGTACTTCGGTACCCCTGAATGCACATACGTGCCCCTATTTGTACTT
*
134331 CGGTA-CCCTTAGATGCACATACGTGCCTCTGTTTGTACTTCGGTACCCTTGGATA
66 CGGTATCCCTTAGATGCACATACGTGCC-CTGTTTGTACTTCGGTACCC-TGAATA
** * * * *
134386 CACATATATGCCCCTGTTTGTACTTCGGTATCCTTGAATGCACATACGTGCCCTTATTTGTACTT
1 CACATACGTGCCCCTATTTGTACTTCGGTACCCCTGAATGCACATACGTGCCCCTATTTGTACTT
* * *
134451 CGATATCCC-TAGATGCACATACGTGTCCCTGTTTGTACTTCAGTACCCCTGAATG
66 CGGTATCCCTTAGATGCACATACGTG-CCCTGTTTGTACTTCGGTA-CCCTGAATA
* * * * * *
134506 CACATACGTGCCCTTGA-TTGTACTTCGGTACCCCTGAATGTAGATATGTGCCTCTAATTGTACT
1 CACATACGTGCCCCT-ATTTGTACTTCGGTACCCCTGAATGCACATACGTGCCCCTATTTGTACT
* * * *
134570 TCGGTATCCCTGA-ATGCACATACATGCCACTGTTTGTACTTCGGTATCCCTAAATG
65 TCGGTATCCCTTAGATGCACATACGTGCC-CTGTTTGTACTTCGGTA-CCCTGAATA
* * * * *
134626 CACATATGTGCCCCTATTTGTACTTTGGTACCCCTGAATGCACATATGTGCCCATGTTTGTACTT
1 CACATACGTGCCCCTATTTGTACTTCGGTACCCCTGAATGCACATACGTGCCCCTATTTGTACTT
*
134691 CGGTA-CCCTTAGATGCACATACGTGCCTCTGTTTGTACTTCGGTACCCTTGGATA
66 CGGTATCCCTTAGATGCACATACGTGCC-CTGTTTGTACTTCGGTACCC-TGAATA
** * * * * *
134746 CACATACAAGCCCCTGTTTGTACTTCAGTATCCTTGAATGCACATACGTGCCCTTATTTGTACTT
1 CACATACGTGCCCCTATTTGTACTTCGGTACCCCTGAATGCACATACGTGCCCCTATTTGTACTT
* * * * * * *
134811 TGATA-CCCCTGGATGCACATACGTGTCCCTGTTTATACTTCAGTACCCCTGAATG
66 CGGTATCCCTTAGATGCACATACGTG-CCCTGTTTGTACTTCGGTA-CCCTGAATA
*
134866 CACATACGTGCCCTTGA-TTGTACTTCGGTAC
1 CACATACGTGCCCCT-ATTTGTACTTCGGTAC
134897 TTATGAAGGC
Statistics
Matches: 531, Mismatches: 84, Indels: 32
0.82 0.13 0.05
Matches are distributed among these distances:
119 21 0.04
120 496 0.93
121 14 0.03
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.34
Consensus pattern (119 bp):
CACATACGTGCCCCTATTTGTACTTCGGTACCCCTGAATGCACATACGTGCCCCTATTTGTACTT
CGGTATCCCTTAGATGCACATACGTGCCCTGTTTGTACTTCGGTACCCTGAATA
Found at i:137269 original size:15 final size:16
Alignment explanation
Indices: 137251--137284 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
137241 AAATTAAATT
*
137251 AATTAA-CTAGATGCA
1 AATTAACCTAAATGCA
137266 AATTAACCTAAATGCA
1 AATTAACCTAAATGCA
137282 AAT
1 AAT
137285 GAGATGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.50, C:0.15, G:0.09, T:0.26
Consensus pattern (16 bp):
AATTAACCTAAATGCA
Found at i:139819 original size:17 final size:17
Alignment explanation
Indices: 139781--139820 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
139771 GAAGAGTCCA
*
139781 CCAAACCCTAGAGTTCG
1 CCAAATCCTAGAGTTCG
* *
139798 TCAAATCCTAGAGTTTG
1 CCAAATCCTAGAGTTCG
139815 CCAAAT
1 CCAAAT
139821 GGCAAATCCC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.25
Consensus pattern (17 bp):
CCAAATCCTAGAGTTCG
Found at i:140202 original size:10 final size:10
Alignment explanation
Indices: 140187--140211 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
140177 ATCGACAAAA
140187 TAAAATATTT
1 TAAAATATTT
140197 TAAAATATTT
1 TAAAATATTT
140207 TAAAA
1 TAAAA
140212 ATTAAAAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
TAAAATATTT
Done.