Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold738
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: 92774
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:684 original size:22 final size:23
Alignment explanation
Indices: 635--684 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
625 ATATTTTTTT
* * *
635 ATTTTTTAAAACAAATAAGATCA
1 ATTTTTTAAAACAAAAAACATAA
*
658 TTTTTTTAAAA-AAAAAACATAA
1 ATTTTTTAAAACAAAAAACATAA
680 ATTTT
1 ATTTT
685 GAAACTTTTC
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (23 bp):
ATTTTTTAAAACAAAAAACATAA
Found at i:832 original size:2 final size:2
Alignment explanation
Indices: 825--855 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
815 GATTTTCAAA
825 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
856 CATGTAAATA
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
Found at i:1241 original size:11 final size:11
Alignment explanation
Indices: 1225--1257 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1215 CCATTTCATA
1225 TTTTTTCTTTT
1 TTTTTTCTTTT
1236 TTTTTTC-TTT
1 TTTTTTCTTTT
*
1246 TTCTTTCTTTT
1 TTTTTTCTTTT
1257 T
1 T
1258 CTTCTTCATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:2558 original size:32 final size:32
Alignment explanation
Indices: 2504--3006 Score: 800
Period size: 32 Copynumber: 15.8 Consensus size: 32
2494 AATATGGTGA
* * **
2504 TTTGAAA-AGGTTGCCACTGACTTGCATGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
2535 TTTTAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
2567 TTTG-AATGAGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
2598 TTTGGAATGAGTTGCCACCGACTTGTGTGGGT
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
2630 TTTGAAAT-GGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
2661 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
2693 TTTGAAAT-GGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
2724 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
2756 TTTGAAATGGGTTGCCACCG-CTTATGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
2787 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
2819 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
2851 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
2883 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
2915 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
2947 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
** * *
2979 TTTGGAAAAAGGTTGCCACGGAGTTGTG
1 TTT-GAAATGGGTTGCCACCGACTTGTG
3007 GACTTAAAAG
Statistics
Matches: 447, Mismatches: 19, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
31 126 0.28
32 302 0.68
33 19 0.04
ACGTcount: A:0.16, C:0.18, G:0.34, T:0.32
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:2612 original size:63 final size:64
Alignment explanation
Indices: 2504--3006 Score: 800
Period size: 63 Copynumber: 7.9 Consensus size: 64
2494 AATATGGTGA
* * ** *
2504 TTTGAAA-AGGTTGCCACTGACTTGCATGGGCTTTTAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * * *
2567 TTTG-AATGAGTTGCCACCGACTTGTGTGGGCTTTGGAATGAGTTGCCACCGACTTGTGTGGGT
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGC
2630 TTTGAAAT-GGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGC
2693 TTTGAAAT-GGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
2756 TTTGAAATGGGTTGCCACCG-CTTATGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
2819 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
2883 TTTGGAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* ** * *
2947 TTTGGAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAAAAAGGTTGCCACGGAGTTGTG
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTT-GAAATGGGTTGCCACCGACTTGTG
3007 GACTTAAAAG
Statistics
Matches: 413, Mismatches: 22, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
62 2 0.00
63 239 0.58
64 153 0.37
65 19 0.05
ACGTcount: A:0.16, C:0.18, G:0.34, T:0.32
Consensus pattern (64 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:2679 original size:95 final size:96
Alignment explanation
Indices: 2512--2985 Score: 803
Period size: 95 Copynumber: 5.0 Consensus size: 96
2502 GATTTGAAAA
* ** * *
2512 GGTTGCCACTGACTTGCATGGGCTTTTAAATGGGTTGCCACCGACTTGTGTGGGCTTTG-AATGA
1 GGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGG
2576 GTTGCCACCGACTTGTGTGGGCTTTGGAATG
66 GTTGCCACCGACTTGTGTGGGCTTTGGAATG
* *
2607 AGTTGCCACCGACTTGTGTGGGTTTTGAAAT-GGTTGCCACCGACTTGTGTGGGCTTTGAAATGG
1 GGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGG
*
2671 GTTGCCACCGACTTGTGTGGGCTTTGAAAT-
66 GTTGCCACCGACTTGTGTGGGCTTTGGAATG
2701 GGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGG
1 GGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGG
* *
2766 GTTGCCACCG-CTTATGTGGGCTTTGAAATG
66 GTTGCCACCGACTTGTGTGGGCTTTGGAATG
*
2796 GGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGG
1 GGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGG
2861 GTTGCCACCGACTTGTGTGGGCTTTGGAATG
66 GTTGCCACCGACTTGTGTGGGCTTTGGAATG
* *
2892 GGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGG
1 GGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGG
2957 GTTGCCACCGACTTGTGTGGGCTTTGGAA
66 GTTGCCACCGACTTGTGTGGGCTTTGGAA
2986 AAAGGTTGCC
Statistics
Matches: 360, Mismatches: 15, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
94 74 0.21
95 175 0.49
96 111 0.31
ACGTcount: A:0.15, C:0.19, G:0.34, T:0.32
Consensus pattern (96 bp):
GGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGG
GTTGCCACCGACTTGTGTGGGCTTTGGAATG
Found at i:3016 original size:27 final size:27
Alignment explanation
Indices: 2985--3617 Score: 971
Period size: 27 Copynumber: 23.2 Consensus size: 27
2975 GGGCTTTGGA
*
2985 AAAAGGTTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
3012 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
3039 AAAAGGGGGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
3066 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
3093 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* *
3120 AAAAGGGTGCTACGGAGTTGTGGTCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
3147 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* *
3174 AAAAGGGATGCCATGGAGTTATGGACTT
1 AAAAGGG-TGCCACGGAGTTGTGGACTT
*
3202 AAAAGAGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
3229 AAAAGGGTGCCACGGAGTTGTGGATTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
3256 AAAAGGGTGCCACGGAGTTGTGGTA-TT
1 AAAAGGGTGCCACGGAGTTGTGG-ACTT
* *
3283 AAAAGGAATGCCACAGAGTTGTGGACTT
1 AAAAGG-GTGCCACGGAGTTGTGGACTT
3311 AAAAGGGGTGCCACGGAGTTGTGGACTT
1 AAAA-GGGTGCCACGGAGTTGTGGACTT
* **
3339 AAAAGGAATGCCATAGAGTTGTGGACTT
1 AAAAGG-GTGCCACGGAGTTGTGGACTT
3367 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
3394 AAAAAGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
3421 AAAAGGGGGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* *
3448 AAAAGGGTGCCACAGAGTTGTGGACTA
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* *
3475 AAAAGGGTACCACGGAGTTGTGGATTTT
1 AAAAGGGTGCCACGGAGTTGTGGA-CTT
*
3503 AAAAGGGTGCCACAGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
3530 AAAAGGGTACCACGGAGTTGTGGACTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
*
3558 AAAAGGGTGCCACAGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* *
3585 AAAAGGATGCCACAGAGTTGTGGACTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
3613 AAAAG
1 AAAAG
3618 AAAATGCCAC
Statistics
Matches: 555, Mismatches: 42, Indels: 17
0.90 0.07 0.03
Matches are distributed among these distances:
27 405 0.73
28 148 0.27
29 2 0.00
ACGTcount: A:0.29, C:0.14, G:0.35, T:0.23
Consensus pattern (27 bp):
AAAAGGGTGCCACGGAGTTGTGGACTT
Found at i:4685 original size:13 final size:13
Alignment explanation
Indices: 4667--4692 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4657 AGGGTGAAAA
4667 GGTTTTTTTTTTT
1 GGTTTTTTTTTTT
4680 GGTTTTTTTTTTT
1 GGTTTTTTTTTTT
4693 AGGATTAGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (13 bp):
GGTTTTTTTTTTT
Found at i:4971 original size:21 final size:23
Alignment explanation
Indices: 4937--4985 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
4927 GTCCTCGTTT
*
4937 TTTTTTTATTTTTG-TTGTTCCC
1 TTTTTTTATTTTTGCTTGTTCAC
*
4959 TTTTTTTA-TTTTGCTTTTTCAC
1 TTTTTTTATTTTTGCTTGTTCAC
4981 TTTTT
1 TTTTT
4986 CTTTTCATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.06, C:0.12, G:0.06, T:0.76
Consensus pattern (23 bp):
TTTTTTTATTTTTGCTTGTTCAC
Found at i:11463 original size:17 final size:17
Alignment explanation
Indices: 11441--11476 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
11431 CATTTCATAT
* *
11441 TTTTTCTTTTTTTTTTC
1 TTTTTCTTTCTTTCTTC
11458 TTTTTCTTTCTTTCTTC
1 TTTTTCTTTCTTTCTTC
11475 TT
1 TT
11477 CATCTTCCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTCTTTCTTTCTTC
Found at i:13752 original size:23 final size:21
Alignment explanation
Indices: 13707--13772 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 21
13697 ATTATTATTT
* *
13707 TTAATAAA-ATAAAAAA-TAT
1 TTAATAAATTTAAAAAATTAA
*
13726 TTAATTAAATTTAAAAATTTATA
1 TTAA-TAAATTTAAAAAATTA-A
13749 TTAATAAATTTAAAAAATTAA
1 TTAATAAATTTAAAAAATTAA
13770 TTA
1 TTA
13773 TTATGTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
19 4 0.10
20 4 0.10
21 10 0.26
22 17 0.44
23 4 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TTAATAAATTTAAAAAATTAA
Found at i:14543 original size:129 final size:129
Alignment explanation
Indices: 14402--14657 Score: 494
Period size: 129 Copynumber: 2.0 Consensus size: 129
14392 CGTTCGGGTT
14402 TTTTTTTTGAAATTTCGGATATCTAAGATTCAATATAGTAGCCATTATAATGAAAATTCACTTTC
1 TTTTTTTTGAAATTTCGGATATCTAAGATTCAATATAGTAGCCATTATAATGAAAATTCACTTTC
14467 ATCAAATGGACATTCACACATTCGTAATTGAAACGGTGAAGAGAATGACTACACATGTTCGTAA
66 ATCAAATGGACATTCACACATTCGTAATTGAAACGGTGAAGAGAATGACTACACATGTTCGTAA
* *
14531 TTTTTTTTGAAATTTCGGATATCTGAGATTCGATATAGTAGCCATTATAATGAAAATTCACTTTC
1 TTTTTTTTGAAATTTCGGATATCTAAGATTCAATATAGTAGCCATTATAATGAAAATTCACTTTC
14596 ATCAAATGGACATTCACACATTCGTAATTGAAACGGTGAAGAGAATGACTACACATGTTCGT
66 ATCAAATGGACATTCACACATTCGTAATTGAAACGGTGAAGAGAATGACTACACATGTTCGT
14658 GACCGAAAAT
Statistics
Matches: 125, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
129 125 1.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (129 bp):
TTTTTTTTGAAATTTCGGATATCTAAGATTCAATATAGTAGCCATTATAATGAAAATTCACTTTC
ATCAAATGGACATTCACACATTCGTAATTGAAACGGTGAAGAGAATGACTACACATGTTCGTAA
Found at i:14898 original size:14 final size:14
Alignment explanation
Indices: 14879--14950 Score: 74
Period size: 14 Copynumber: 5.1 Consensus size: 14
14869 GCATGCATAT
*
14879 TTTCATGCATTACA
1 TTTCATGCATTTCA
*
14893 TTTCATGCA-TGCA
1 TTTCATGCATTTCA
* * *
14906 TTTTACGTAATGTTCA
1 TTTCATG-CAT-TTCA
14922 TTTCATGCATTTCA
1 TTTCATGCATTTCA
14936 TTTCATGCATTTCA
1 TTTCATGCATTTCA
14950 T
1 T
14951 CAAATTAAGC
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
13 8 0.17
14 29 0.62
15 2 0.04
16 8 0.17
ACGTcount: A:0.24, C:0.19, G:0.10, T:0.47
Consensus pattern (14 bp):
TTTCATGCATTTCA
Found at i:27465 original size:130 final size:130
Alignment explanation
Indices: 27232--27495 Score: 465
Period size: 130 Copynumber: 2.0 Consensus size: 130
27222 CTTCGAGTTT
* *
27232 TGATGGAGACTAAATTAGAAGAAGCCAAGTGGTTACGCGATCGCTATGAACAACTGAACTTCATT
1 TGATGGAGACTAAATTAGAAAAAGCCAAGTGGTTACGAGATCGCTATGAACAACTGAACTTCATT
*
27297 AAAGAAAAAAGGTTGAAAGCTATTCGACATGGGCAAATGTATAAAAAAAGGATGATGAAAGCCCA
66 AAAGAAAAAAGGTTGAAAACTATTCGACATGGGCAAATGTATAAAAAAAGGATGATGAAAGCCCA
27362 TGATGGAGACTAAATTAGAAAAAGCCAAGTGGTTACGAGATCGCTATGAACAACTGAACTTCATT
1 TGATGGAGACTAAATTAGAAAAAGCCAAGTGGTTACGAGATCGCTATGAACAACTGAACTTCATT
* * * *
27427 GAAGAAAAAAGGTTGAAAACTATTCGACATGGGTAAATGTATAAAAAAATGATGATGAAAGCTCA
66 AAAGAAAAAAGGTTGAAAACTATTCGACATGGGCAAATGTATAAAAAAAGGATGATGAAAGCCCA
27492 TGAT
1 TGAT
27496 AAGAAAATGC
Statistics
Matches: 127, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
130 127 1.00
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.22
Consensus pattern (130 bp):
TGATGGAGACTAAATTAGAAAAAGCCAAGTGGTTACGAGATCGCTATGAACAACTGAACTTCATT
AAAGAAAAAAGGTTGAAAACTATTCGACATGGGCAAATGTATAAAAAAAGGATGATGAAAGCCCA
Found at i:29405 original size:42 final size:42
Alignment explanation
Indices: 29359--30046 Score: 191
Period size: 42 Copynumber: 16.4 Consensus size: 42
29349 ATCTAAAGTT
*
29359 TGCCTGTCGGCTTTGACCCCGAAGACTTTTCTACCCTCAGTC
1 TGCCTGTCGGCTTTGACCCCGAAGACTTTCCTACCCTCAGTC
* * * * * * *
29401 TGCCTGTTGGCTTTGACCCTGGAGAC-TGCCTTA-TCTAAAGTT
1 TGCCTGTCGGCTTTGACCCCGAAGACTTTCC-TACCCT-CAGTC
* * *
29443 TGCTTGTCGGTTTTGA-TCCGATAGACTTTCCTACCCTCAGTC
1 TGCCTGTCGGCTTTGACCCCGA-AGACTTTCCTACCCTCAGTC
* * ** * * * *
29485 TGCTTGTCGGCTTTAACCTTGGAGAC-TGCCT-CATCTAAAGTC
1 TGCCTGTCGGCTTTGACCCCGAAGACTTTCCTAC-CCT-CAGTC
* ** * ** * * *
29527 TGTCTGTCGGCTTTGACCTTGGAGACTTTTTTACCTTTATTC
1 TGCCTGTCGGCTTTGACCCCGAAGACTTTCCTACCCTCAGTC
* * ** * * * *
29569 TACCTATCGGCTTTGACCTTGTAGAC-TACCT-CATCTAAAGTC
1 TGCCTGTCGGCTTTGACCCCGAAGACTTTCCTAC-CCT-CAGTC
* * ** * *
29611 TGCCTATCAGCTTTGACCTTGGAGACTTTCCTACCCTCAGTT
1 TGCCTGTCGGCTTTGACCCCGAAGACTTTCCTACCCTCAGTC
* * ** * ** *
29653 TACCTATCGGCTTTGA-CCTTATAGA-TTGCCT-CATTTAAAGTC
1 TGCCTGTCGGCTTTGACCCCGA-AGACTTTCCTAC-CCT-CAGTC
** * * *
29695 TAACTGTCGGCTTTGA-CCCTAGAGACTTTACTACCCTTAGTC
1 TGCCTGTCGGCTTTGACCCCGA-AGACTTTCCTACCCTCAGTC
* * ** * * *
29737 TGCCTATCGGCTTCGA-CCTTAGAGAC-TGCCT-CATCTAAAGTC
1 TGCCTGTCGGCTTTGACCCCGA-AGACTTTCCTAC-CCT-CAGTC
* ** *
29779 TGCTTGTCGGCTTTGACCTTGGAGACTTTCCTACCCTCAGTC
1 TGCCTGTCGGCTTTGACCCCGAAGACTTTCCTACCCTCAGTC
* * * * ** *
29821 TACTTGTTGACTTTGACCATAGAA-ACTTTCCTACCTTCAGTC
1 TGCCTGTCGGCTTTGACC-CCGAAGACTTTCCTACCCTCAGTC
* * * * *
29863 TGCCTGTCGGCTTTGA-TCCTAGAGAC-TGCCT-CATCTAAAGTC
1 TGCCTGTCGGCTTTGACCCCGA-AGACTTTCCTAC-CCT-CAGTC
* ** *
29905 TGCCTATCGGCTTTGACCTTGAAGACTTTCCTACCCTTAGTC
1 TGCCTGTCGGCTTTGACCCCGAAGACTTTCCTACCCTCAGTC
* * ** *
29947 TACCTGTCGACTTTGACCTTG-AGA-TTACCTTA-CCTCAAGTC
1 TGCCTGTCGGCTTTGACCCCGAAGACTTTCC-TACCCTC-AGTC
* * *
29988 TGCCTGTCGGCTTTGA-CCTGGAGA-TTGCCTTA-CCTCAAGTC
1 TGCCTGTCGGCTTTGACCCCGAAGACTTTCC-TACCCTC-AGTC
*
30029 TGCCTGTTGGCTTTGACC
1 TGCCTGTCGGCTTTGACC
30047 TTGGAGATTT
Statistics
Matches: 482, Mismatches: 128, Indels: 72
0.71 0.19 0.11
Matches are distributed among these distances:
40 16 0.03
41 91 0.19
42 332 0.69
43 38 0.08
44 5 0.01
ACGTcount: A:0.18, C:0.28, G:0.19, T:0.35
Consensus pattern (42 bp):
TGCCTGTCGGCTTTGACCCCGAAGACTTTCCTACCCTCAGTC
Found at i:29451 original size:84 final size:84
Alignment explanation
Indices: 29314--30046 Score: 506
Period size: 84 Copynumber: 8.8 Consensus size: 84
29304 CCTCATCTAA
* * * * *
29314 AGTCTGCCTGTC-GTTTTGACCCTGGAGACTACCTCATCTAAAGTTTGCCTGTCGGCTTTGACCC
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCATCTAAAGTCTGCTTGTCGGCTTTGACCC
*
29378 CGAAGACTTTTCTACCCTC
66 CGAAGACTTTCCTACCCTC
* * * * * *
29397 AGTCTGCCTGTTGGCTTTGACCCTGGAGACTGCCTTATCTAAAGTTTGCTTGTCGGTTTTGA-TC
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCATCTAAAGTCTGCTTGTCGGCTTTGACCC
29461 CGATAGACTTTCCTACCCTC
66 CGA-AGACTTTCCTACCCTC
* *
29481 AGTCTGCTTGTCGGCTTTAACCTTGGAGACTGCCTCATCTAAAGTCTG-TCTGTCGGCTTTGACC
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCATCTAAAGTCTGCT-TGTCGGCTTTGACC
** * ** * *
29545 TTGGAGACTTTTTTACCTTT
65 CCGAAGACTTTCCTACCCTC
* * * * * * * * *
29565 ATTCTACCTATCGGCTTTGACCTTGTAGACTACCTCATCTAAAGTCTGCCTATCAGCTTTGACCT
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCATCTAAAGTCTGCTTGTCGGCTTTGACCC
* *
29630 TGGAGACTTTCCTACCCTC
66 CGAAGACTTTCCTACCCTC
* * * ** * * *
29649 AGTTTACCTATCGGCTTTGACCTTATAGATTGCCTCATTTAAAGTCTAAC-TGTCGGCTTTGA-C
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCATCTAAAGTCT-GCTTGTCGGCTTTGACC
* * *
29712 CCTAGAGACTTTACTACCCTT
65 CCGA-AGACTTTCCTACCCTC
* * * *
29733 AGTCTGCCTATCGGCTTCGACCTTAGAGACTGCCTCATCTAAAGTCTGCTTGTCGGCTTTGACCT
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCATCTAAAGTCTGCTTGTCGGCTTTGACCC
* *
29798 TGGAGACTTTCCTACCCTC
66 CGAAGACTTTCCTACCCTC
* * * * * * * * * ** * *
29817 AGTCTACTTGTTGACTTTGACCATAGAAACTTTCCT-ACCTTCAGTCTGCCTGTCGGCTTTGA-T
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGAC-TGCCTCATCTAAAGTCTGCTTGTCGGCTTTGACC
* * * *
29880 CCTAGAGAC-TGCCT-CATCTAA
65 CCGA-AGACTTTCCTAC-CCT-C
* * * * * * * *
29901 AGTCTGCCTATCGGCTTTGACCTTGAAGACTTTCCT-ACCCT-TAGTCTACCTGTCGACTTTGAC
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGAC-TGCCTCA-TCTAAAGTCTGCTTGTCGGCTTTGAC
** *
29964 CTTG-AGA-TTACCTTA-CCTC
64 CCCGAAGACTTTCC-TACCCTC
* * * * * *
29983 AAGTCTGCCTGTCGGCTTTGACC-TGGAGATTGCCTTACCTCAAGTCTGCCTGTTGGCTTTGACC
1 -AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCATCTAAAGTCTGCTTGTCGGCTTTGACC
30047 TTGGAGATTT
Statistics
Matches: 516, Mismatches: 113, Indels: 43
0.77 0.17 0.06
Matches are distributed among these distances:
81 7 0.01
82 26 0.05
83 53 0.10
84 420 0.81
85 10 0.02
ACGTcount: A:0.18, C:0.28, G:0.19, T:0.35
Consensus pattern (84 bp):
AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCATCTAAAGTCTGCTTGTCGGCTTTGACCC
CGAAGACTTTCCTACCCTC
Found at i:29583 original size:168 final size:167
Alignment explanation
Indices: 29314--30059 Score: 639
Period size: 168 Copynumber: 4.5 Consensus size: 167
29304 CCTCATCTAA
* * * * * *
29314 AGTCTGCCTGTC-GTTTTGACCCTGGAGACTACCTCATCTAAAGTTTGCCTGTCGGCTTTGACCC
1 AGTCTACCTGTCGGCTTTGACCTTGGAGACTGCCTCATCTAAAGTCTGACTGTCGGCTTTGACCC
* * * * * * * *
29378 CGAAGACTTTTCTACCCTCAGTCTGCCTGTTGGCTTTGACCCTGGAGACTGCCTTATCTAAAGTT
66 TGGAGACTTTTCTACCCTTAGTCTGCCTATCGGCTTTGACCTTGGAGACTGCCTCATCTAAAGTC
* *
29443 TGCTTGTCGGTTTTGATCC-GATAGACTTTCCTACCCTC
131 TGCTTGTCGGCTTTGA-CCTG-GAGACTTTCCTACCCTC
* * * * *
29481 AGTCTGCTTGTCGGCTTTAACCTTGGAGACTGCCTCATCTAAAGTCTGTCTGTCGGCTTTGACCT
1 AGTCTACCTGTCGGCTTTGACCTTGGAGACTGCCTCATCTAAAGTCTGACTGTCGGCTTTGACCC
* * * * * *
29546 TGGAGACTTTTTTACCTTTATTCTACCTATCGGCTTTGACCTTGTAGACTACCTCATCTAAAGTC
66 TGGAGACTTTTCTACCCTTAGTCTGCCTATCGGCTTTGACCTTGGAGACTGCCTCATCTAAAGTC
* * *
29611 TGCCTATCAGCTTTGACCTTGGAGACTTTCCTACCCTC
131 TGCTTGTCGGCTTTGACC-TGGAGACTTTCCTACCCTC
* * ** * * *
29649 AGTTTACCTATCGGCTTTGACCTTATAGATTGCCTCATTTAAAGTCTAACTGTCGGCTTTGACCC
1 AGTCTACCTGTCGGCTTTGACCTTGGAGACTGCCTCATCTAAAGTCTGACTGTCGGCTTTGACCC
* * * *
29714 TAGAGACTTTACTACCCTTAGTCTGCCTATCGGCTTCGACCTTAGAGACTGCCTCATCTAAAGTC
66 TGGAGACTTTTCTACCCTTAGTCTGCCTATCGGCTTTGACCTTGGAGACTGCCTCATCTAAAGTC
29779 TGCTTGTCGGCTTTGACCTTGGAGACTTTCCTACCCTC
131 TGCTTGTCGGCTTTGACC-TGGAGACTTTCCTACCCTC
* * * * * * * * ** * *
29817 AGTCTACTTGTTGACTTTGACCATAGAAACTTTCCT-ACCTTCAGTCTGCCTGTCGGCTTTGATC
1 AGTCTACCTGTCGGCTTTGACCTTGGAGAC-TGCCTCATCTAAAGTCTGACTGTCGGCTTTGACC
* ** * * * * *
29881 CTAGAGAC-TGCCT-CATCTAAAGTCTGCCTATCGGCTTTGACCTTGAAGACTTTCCT-ACCCT-
65 CTGGAGACTTTTCTAC-CCT-TAGTCTGCCTATCGGCTTTGACCTTGGAGAC-TGCCTCA-TCTA
* * * * * *
29942 TAGTCTACCTGTCGACTTTGACCTTGAGA-TTACCTTA-CCTC
126 AAGTCTGCTTGTCGGCTTTGACCTGGAGACTTTCC-TACCCTC
* * * * * * *
29983 AAGTCTGCCTGTCGGCTTTGACC-TGGAGATTGCCTTACCTCAAGTCTGCCTGTTGGCTTTGACC
1 -AGTCTACCTGTCGGCTTTGACCTTGGAGACTGCCTCATCTAAAGTCTGACTGTCGGCTTTGACC
* *
30047 TTGGAGATTTTTC
65 CTGGAGACTTTTC
30060 CACTTTTTAT
Statistics
Matches: 466, Mismatches: 101, Indels: 24
0.79 0.17 0.04
Matches are distributed among these distances:
165 4 0.01
166 42 0.09
167 45 0.10
168 364 0.78
169 11 0.02
ACGTcount: A:0.18, C:0.28, G:0.19, T:0.35
Consensus pattern (167 bp):
AGTCTACCTGTCGGCTTTGACCTTGGAGACTGCCTCATCTAAAGTCTGACTGTCGGCTTTGACCC
TGGAGACTTTTCTACCCTTAGTCTGCCTATCGGCTTTGACCTTGGAGACTGCCTCATCTAAAGTC
TGCTTGTCGGCTTTGACCTGGAGACTTTCCTACCCTC
Found at i:30087 original size:124 final size:125
Alignment explanation
Indices: 29477--30049 Score: 411
Period size: 126 Copynumber: 4.6 Consensus size: 125
29467 ACTTTCCTAC
* * * * * *
29477 CCTC-AGTCTGCTTGTCGGCTTT-AACCTTGGAGACTGCCTCATCTAAAGTCTGTCTGTCGGCTT
1 CCTCAAGTCTGCCTGTCGGCTTTGATCC-TAGAGACTGCCTCACCTAAAGTCTGCCTATCGGCTT
* ** * * ** * * *
29540 TGACCTTGGAGACTTTTTTACCTTTATTCTACCTATCGGCTTTGACCTTGTAGACTACCTCA
65 TGACCTTGAAGACTTTCCTACCCTTAGTCTACCCGTCGACTTTGACCTTG-AGATTACCTTA
* * * * * * * * *
29602 TCTAAAGTCTGCCTATCAGCTTTGA-CCTTGGAGACTTTCCT-ACCCT-CAGTTTACCTATCGGC
1 CCTCAAGTCTGCCTGTCGGCTTTGATCC-TAGAGAC-TGCCTCA-CCTAAAGTCTGCCTATCGGC
* ** * * * *
29664 TTTGACCTT-ATAGA-TTGCCT-CATTTAAAGTCTAACTGTCGGCTTTGACCCTAGAGACTTTA-
63 TTTGACCTTGA-AGACTTTCCTACCCTT--AGTCTACCCGTCGACTTTGA-CCTTGAGA--TTAC
29725 C-TA
122 CTTA
* * * * * *
29728 CC-CTTAGTCTGCCTATCGGCTTCGA-CCTTAGAGACTGCCTCATCTAAAGTCTGCTTGTCGGCT
1 CCTC-AAGTCTGCCTGTCGGCTTTGATCC-TAGAGACTGCCTCACCTAAAGTCTGCCTATCGGCT
* * ** * * * *
29791 TTGACCTTGGAGACTTTCCTACCCTCAGTCTACTTGTTGACTTTGACCATAGAAACTTTCC-TA
64 TTGACCTTGAAGACTTTCCTACCCTTAGTCTACCCGTCGACTTTGACC-TTGAGA-TTACCTTA
*
29854 CCTTC-AGTCTGCCTGTCGGCTTTGATCCTAGAGACTGCCTCATCTAAAGTCTGCCTATCGGCTT
1 CC-TCAAGTCTGCCTGTCGGCTTTGATCCTAGAGACTGCCTCACCTAAAGTCTGCCTATCGGCTT
*
29918 TGACCTTGAAGACTTTCCTACCCTTAGTCTACCTGTCGACTTTGACCTTGAGATTACCTTA
65 TGACCTTGAAGACTTTCCTACCCTTAGTCTACCCGTCGACTTTGACCTTGAGATTACCTTA
* * * * * *
29979 CCTCAAGTCTGCCTGTCGGCTTTGA-CCTGGAGATTGCCTTACCTCAAGTCTGCCTGTTGGCTTT
1 CCTCAAGTCTGCCTGTCGGCTTTGATCCTAGAGACTGCCTCACCTAAAGTCTGCCTATCGGCTTT
30043 GACCTTG
66 GACCTTG
30050 GAGATTTTTC
Statistics
Matches: 359, Mismatches: 66, Indels: 47
0.76 0.14 0.10
Matches are distributed among these distances:
124 49 0.14
125 43 0.12
126 243 0.68
127 19 0.05
128 5 0.01
ACGTcount: A:0.18, C:0.28, G:0.18, T:0.35
Consensus pattern (125 bp):
CCTCAAGTCTGCCTGTCGGCTTTGATCCTAGAGACTGCCTCACCTAAAGTCTGCCTATCGGCTTT
GACCTTGAAGACTTTCCTACCCTTAGTCTACCCGTCGACTTTGACCTTGAGATTACCTTA
Found at i:30585 original size:4 final size:4
Alignment explanation
Indices: 30578--30647 Score: 54
Period size: 4 Copynumber: 17.0 Consensus size: 4
30568 TACATTTATA
* *
30578 AAAT AAAT AAAT AAAT AAAT AAAGT ATATAT AAA- AATT AAAA AAAT -AAT
1 AAAT AAAT AAAT AAAT AAAT AAA-T A-A-AT AAAT AAAT AAAT AAAT AAAT
* *
30627 AAAA AAAGT AAAT AAAG AAAT
1 AAAT AAA-T AAAT AAAT AAAT
30648 CGAATTAGGT
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
3 5 0.10
4 37 0.71
5 6 0.12
6 3 0.06
7 1 0.02
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:30748 original size:29 final size:29
Alignment explanation
Indices: 30707--30772 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
30697 TCATGCATTA
30707 CATTTCATGCATGCATTTCACGTAAT-TT
1 CATTTCATGCATGCATTTCACGTAATGTT
* *
30735 GCATTTCATTCATGCATTTTACGTAATGTT
1 -CATTTCATGCATGCATTTCACGTAATGTT
30765 CATTTCAT
1 CATTTCAT
30773 ATATTTCATT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 32 0.94
30 2 0.06
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.45
Consensus pattern (29 bp):
CATTTCATGCATGCATTTCACGTAATGTT
Found at i:30792 original size:14 final size:14
Alignment explanation
Indices: 30693--30794 Score: 55
Period size: 14 Copynumber: 7.1 Consensus size: 14
30683 TATTTTCATG
*
30693 CATTTCATGCATTA
1 CATTTCATGCATTT
*
30707 CATTTCATGCA-TG
1 CATTTCATGCATTT
* *
30720 CATTTCACGTAATTT
1 CATTTCATG-CATTT
* *
30735 GCATTTCATTCA-TG
1 -CATTTCATGCATTT
* * *
30749 CATTTTACGTAATGTT
1 CATTTCATG-CAT-TT
**
30765 CATTTCATATATTT
1 CATTTCATGCATTT
30779 CATTTCATGCATTT
1 CATTTCATGCATTT
30793 CA
1 CA
30795 CCAAATTAAG
Statistics
Matches: 63, Mismatches: 19, Indels: 12
0.67 0.20 0.13
Matches are distributed among these distances:
13 15 0.24
14 30 0.48
15 4 0.06
16 14 0.22
ACGTcount: A:0.25, C:0.20, G:0.09, T:0.46
Consensus pattern (14 bp):
CATTTCATGCATTT
Found at i:31381 original size:39 final size:40
Alignment explanation
Indices: 31311--31389 Score: 99
Period size: 39 Copynumber: 2.0 Consensus size: 40
31301 TAGCAGCAAC
*
31311 AATCGAAAACCAACAGCAAACTCCAGCAAGCA-GTAAACAG
1 AATCGAAAACCAACAACAAACTCCAGCAAGCACG-AAACAG
* * *
31351 AATCGAAAATCAGCAAC-AACTTCAGCAAGCACGAAACAG
1 AATCGAAAACCAACAACAAACTCCAGCAAGCACGAAACAG
31390 TAGCCACAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
39 19 0.56
40 15 0.44
ACGTcount: A:0.49, C:0.27, G:0.15, T:0.09
Consensus pattern (40 bp):
AATCGAAAACCAACAACAAACTCCAGCAAGCACGAAACAG
Found at i:34053 original size:23 final size:23
Alignment explanation
Indices: 34024--34067 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
34014 TTTAAAATTA
*
34024 TTTTATTT-TAAGGTATAATTTAT
1 TTTTATTTATAAGAT-TAATTTAT
34047 TTTTATTTATAAGATTAATTT
1 TTTTATTTATAAGATTAATTT
34068 GATTAGAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (23 bp):
TTTTATTTATAAGATTAATTTAT
Found at i:34094 original size:27 final size:28
Alignment explanation
Indices: 34064--34126 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 28
34054 TATAAGATTA
*
34064 ATTTGATTAGAG-TTATTATTTA-TTTCT
1 ATTTGATTAAAGTTTA-TATTTATTTTCT
* *
34091 ATTTG-TAAAAGTTTATATTTATTTTTT
1 ATTTGATTAAAGTTTATATTTATTTTCT
34118 ATTTGATTA
1 ATTTGATTA
34127 TATACGTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
26 10 0.34
27 17 0.59
28 2 0.07
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.60
Consensus pattern (28 bp):
ATTTGATTAAAGTTTATATTTATTTTCT
Found at i:35270 original size:21 final size:21
Alignment explanation
Indices: 35226--35280 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
35216 TACACATGAA
35226 AATGTATCGATAC-TTATTGC
1 AATGTATCGATACATTATTGC
35246 AATGTATCGATACATTATGTG-
1 AATGTATCGATACATTAT-TGC
*
35267 AATGTATTGATACA
1 AATGTATCGATACA
35281 AGTCATTGAC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 13 0.41
21 17 0.53
22 2 0.06
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (21 bp):
AATGTATCGATACATTATTGC
Found at i:35974 original size:371 final size:370
Alignment explanation
Indices: 35292--36035 Score: 1425
Period size: 371 Copynumber: 2.0 Consensus size: 370
35282 GTCATTGACA
35292 GTAGCTACCCTTCAATTGTATCGATACACATAAATGTATGCATCGATATAAGTCCAAAATGTATT
1 GTAGCTACCCTTCAATTGTATCGATACACATAAATGTATGCATCGATATAAGTCCAAAATGTATT
35357 GATACATCCAATATTGTATCGATACATTTGGCCCAACGGCTATTTTTTTAAAAGCAATGTATCGA
66 GATACATCCAATATTGTATCGATACATTTGGCCCAACGGCTATTTTTTTAAAAGCAATGTATCGA
*
35422 TACATTAAGTAATGTATCAATACAATATCGTGGGAATAAACGAATACATGCATTTATGAGGCCTA
131 TACATTAAGTAATGTATCAATACAATATCATGGGAATAAACGAATACATGCATTTATGAGGCCTA
35487 CAACAGATCTCCAACCACCCAATTAATGTCCAACGACTATAATTTCATTTCAAGCTATAAATTGA
196 CAACAGATCTCCAACCACCCAATTAATGTCCAACGACTATAATTTCATTTCAAGCTATAAATTGA
* *
35552 AGATTCCAACAGCAAGAGAAGCAAGAGAAATAAGAGAAATTCTATCATACAACATCAAAGAGCTG
261 AGATTCCAACAGCAAGAAAAGCAAGAGAAATAAGAGAAATTCTATCATACAACATCAAAGAGCTA
35617 AAAATCAAGTTCTTCATTTGTTATTATTCATTTCTAAGCTTTGTT
326 AAAATCAAGTTCTTCATTTGTTATTATTCATTTCTAAGCTTTGTT
*
35662 GTAGCTACCCTTCAATTGTATCGATACACATAAATGTATGTATCGATATAAGTCCAAAATGTATT
1 GTAGCTACCCTTCAATTGTATCGATACACATAAATGTATGCATCGATATAAGTCCAAAATGTATT
35727 GATACATCCAATATTGTATCGATACATTTGGCCCAACGGCTATTTTTTTTAAAAGCAATGTATCG
66 GATACATCCAATATTGTATCGATACATTTGGCCCAACGGCTA-TTTTTTTAAAAGCAATGTATCG
*
35792 ATACATTAAGTAATGTATCAATATAATATCATGGGAATAAACGAATACATGCATTTATGAGGCCT
130 ATACATTAAGTAATGTATCAATACAATATCATGGGAATAAACGAATACATGCATTTATGAGGCCT
35857 ACAACAGATCTCCAACCACCCAATTAATGTCCAACGACTATAATTTCATTTCAAGCTATAAATTG
195 ACAACAGATCTCCAACCACCCAATTAATGTCCAACGACTATAATTTCATTTCAAGCTATAAATTG
*
35922 AAGGTTCCAACAGCAAGAAAAGCAAGAGAAATAAGAGAAATTCTATCATACAACATCAAAGAGCT
260 AAGATTCCAACAGCAAGAAAAGCAAGAGAAATAAGAGAAATTCTATCATACAACATCAAAGAGCT
35987 AAAAATCAAGTTCTTCATTTGTTATTATTCATTTCTAAGCTTTGTT
325 AAAAATCAAGTTCTTCATTTGTTATTATTCATTTCTAAGCTTTGTT
36033 GTA
1 GTA
36036 TCTTCTTCAT
Statistics
Matches: 367, Mismatches: 6, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
370 106 0.29
371 261 0.71
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.31
Consensus pattern (370 bp):
GTAGCTACCCTTCAATTGTATCGATACACATAAATGTATGCATCGATATAAGTCCAAAATGTATT
GATACATCCAATATTGTATCGATACATTTGGCCCAACGGCTATTTTTTTAAAAGCAATGTATCGA
TACATTAAGTAATGTATCAATACAATATCATGGGAATAAACGAATACATGCATTTATGAGGCCTA
CAACAGATCTCCAACCACCCAATTAATGTCCAACGACTATAATTTCATTTCAAGCTATAAATTGA
AGATTCCAACAGCAAGAAAAGCAAGAGAAATAAGAGAAATTCTATCATACAACATCAAAGAGCTA
AAAATCAAGTTCTTCATTTGTTATTATTCATTTCTAAGCTTTGTT
Found at i:42218 original size:2 final size:2
Alignment explanation
Indices: 42211--42242 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
42201 GACAACCTAA
42211 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
42243 CAACTGTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:44284 original size:20 final size:21
Alignment explanation
Indices: 44259--44309 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
44249 CCCTTATTTT
44259 TATCGATACA-CATGAAAATG
1 TATCGATACATCATGAAAATG
* **
44279 TATCGATACATTATGTGAATG
1 TATCGATACATCATGAAAATG
44300 TATCGATACA
1 TATCGATACA
44310 AATCATTGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (21 bp):
TATCGATACATCATGAAAATG
Found at i:44353 original size:2 final size:2
Alignment explanation
Indices: 44346--44370 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
44336 TTGTATCGAT
44346 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
44371 TATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:48376 original size:115 final size:115
Alignment explanation
Indices: 48264--48476 Score: 324
Period size: 115 Copynumber: 1.9 Consensus size: 115
48254 TTTAAACACT
48264 ATAAGTAATA-TTTAATTTGTTAAATATAAATTTTTTAAACTTAATT-AATATTA-TTTTTATTT
1 ATAAGTAATATTTTAATTT-TTAAATAT-AATTTTTTAAACTTAATTAAATATTATTTTTTATTT
* *
48326 TAATAAAAATTATAATAAAAAACCTTTTTTATTTTTTATTTTATAAAAACATA
64 TAATAAAAATAATAAT-AAAAACCCTTTTTATTTTTTATTTTATAAAAACATA
* * *
48379 ATAATTAATATTTTAATTTTTTAATGTAATTTTTTAAACTTAATTAAATATTATTTTTTATTTTA
1 ATAAGTAATATTTTAATTTTTAAATATAATTTTTTAAACTTAATTAAATATTATTTTTTATTTTA
*
48444 TTAAAAATAATAATAAAAACCCTTTTTATTTTT
66 ATAAAAATAATAATAAAAACCCTTTTTATTTTT
48477 AATTAAATTT
Statistics
Matches: 89, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
114 18 0.20
115 40 0.45
116 31 0.35
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.53
Consensus pattern (115 bp):
ATAAGTAATATTTTAATTTTTAAATATAATTTTTTAAACTTAATTAAATATTATTTTTTATTTTA
ATAAAAATAATAATAAAAACCCTTTTTATTTTTTATTTTATAAAAACATA
Found at i:48503 original size:19 final size:20
Alignment explanation
Indices: 48466--48503 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
48456 ATAAAAACCC
*
48466 TTTTTATTTTTAATTAAATT
1 TTTTTATTTTTAATAAAATT
48486 TTTTTATTTTTAA-AAAAT
1 TTTTTATTTTTAATAAAAT
48504 ATAATAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTTATTTTTAATAAAATT
Found at i:48638 original size:128 final size:126
Alignment explanation
Indices: 48357--48603 Score: 315
Period size: 128 Copynumber: 2.0 Consensus size: 126
48347 ACCTTTTTTA
* *
48357 TTTTTTA-TTTTATAAAAACATAATAATTAATATTTTAATTTTTTAATGTAATTTTTTAAACTTA
1 TTTTTTATTTTTATAAAAACATAATAATTAATATTTTAATTTGTTAATGTAATTTTTAAAACTTA
* *
48421 ATTAAATATTATTTTTTATTTTATTAAAAATAATAATAAAAACCCTTTTTATTTTTAATTAAAT
66 ATTAAATATTA---TTTATTTTATTAAAAATAATAATAAAAACCATTATTATTTTTAATTAAAT
* *
48485 TTTTTTATTTTTA-AAAAATATAATAATTAATATTTTAATTTGTTAATGTAAATTTTTAAAATTT
1 TTTTTTATTTTTATAAAAACATAATAATTAATATTTTAATTTGTTAATGT-AATTTTTAAAACTT
* * * * *
48549 GATTAACTATTA-TT-TTTTATTAAAAATAATAATTAATA-TATTATTATTTATTAAT
65 AATTAAATATTATTTATTTTATTAAAAATAATAATAAAAACCATTATTATTT-TTAAT
48604 ATTTTTAAAT
Statistics
Matches: 105, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
123 8 0.08
124 27 0.26
125 2 0.02
128 41 0.39
129 27 0.26
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (126 bp):
TTTTTTATTTTTATAAAAACATAATAATTAATATTTTAATTTGTTAATGTAATTTTTAAAACTTA
ATTAAATATTATTTATTTTATTAAAAATAATAATAAAAACCATTATTATTTTTAATTAAAT
Found at i:49203 original size:21 final size:24
Alignment explanation
Indices: 49159--49205 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
49149 TATTACTTAA
*
49159 ATTTATTATTTAATTGATATAAAT
1 ATTTATTATTTAATTAATATAAAT
49183 ATTTATT-TTTAA-TAATA-AAAT
1 ATTTATTATTTAATTAATATAAAT
49204 AT
1 AT
49206 ATAAATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 6 0.27
22 4 0.18
23 5 0.23
24 7 0.32
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
ATTTATTATTTAATTAATATAAAT
Found at i:49235 original size:19 final size:19
Alignment explanation
Indices: 49175--49250 Score: 59
Period size: 19 Copynumber: 3.9 Consensus size: 19
49165 TATTTAATTG
*
49175 ATATAAATATTTAT-TTTTA
1 ATATAAA-ATTAATATTTTA
* *
49194 ATAATAAAATATATAAATATTA
1 AT-ATAAAAT-TA-ATATTTTA
49216 ATATAAAATTAATATTTTA
1 ATATAAAATTAATATTTTA
*
49235 A-ATAAAAATAA-ATTTT
1 ATATAAAATTAATATTTT
49251 TTAATTCAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
17 5 0.11
18 9 0.19
19 11 0.23
20 8 0.17
21 8 0.17
22 6 0.13
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATATAAAATTAATATTTTA
Found at i:49249 original size:17 final size:17
Alignment explanation
Indices: 49206--49279 Score: 58
Period size: 19 Copynumber: 3.9 Consensus size: 17
49196 AATAAAATAT
*
49206 ATAAATATTAATATAAAA
1 ATAAATTTTAA-ATAAAA
*
49224 TTAATATTTTAAATAAAA
1 ATAA-ATTTTAAATAAAA
*
49242 ATAAATTTTTTAATTCAATAA
1 ATAAA--TTTTAAAT-AA-AA
49263 ATTAAATTTTAAATAAA
1 A-TAAATTTTAAATAAA
49280 TAAATTATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
17 1 0.02
18 13 0.29
19 15 0.33
20 9 0.20
21 3 0.07
22 4 0.09
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAAATTTTAAATAAAA
Found at i:49274 original size:20 final size:20
Alignment explanation
Indices: 49221--49286 Score: 66
Period size: 20 Copynumber: 3.3 Consensus size: 20
49211 TATTAATATA
49221 AAATTAATATTTTAAAT-AA-
1 AAATTAA-ATTTTAAATAAAT
* *
49240 AAA-TAAATTTTTTAATTCAAT
1 AAATTAAA--TTTTAAATAAAT
49261 AAATTAAATTTTAAATAAAT
1 AAATTAAATTTTAAATAAAT
49281 AAATTA
1 AAATTA
49287 TTTTTATATT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
17 1 0.03
18 3 0.08
19 10 0.26
20 18 0.46
21 3 0.08
22 4 0.10
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
AAATTAAATTTTAAATAAAT
Found at i:49661 original size:26 final size:24
Alignment explanation
Indices: 49632--49693 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
49622 AAAATTAAGA
*
49632 TTAATTTTTATATAGATTATAAATAT
1 TTAATTTTTAT-TAAATTAT-AATAT
*
49658 TTAA-TTTTATTAAATTATATTAT
1 TTAATTTTTATTAAATTATAATAT
*
49681 TAAATTTTTATTA
1 TTAATTTTTATTA
49694 TTAATAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 7 0.22
24 15 0.47
25 6 0.19
26 4 0.12
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (24 bp):
TTAATTTTTATTAAATTATAATAT
Found at i:49682 original size:13 final size:14
Alignment explanation
Indices: 49664--49697 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
49654 ATATTTAATT
49664 TTATTAAA-TTATA
1 TTATTAAATTTATA
*
49677 TTATTAAATTTTTA
1 TTATTAAATTTATA
49691 TTATTAA
1 TTATTAA
49698 TAAATTAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTAAATTTATA
Found at i:49702 original size:30 final size:29
Alignment explanation
Indices: 49647--49704 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
49637 TTTTATATAG
*
49647 ATTATAAATATTTAATTTTATTAAATTAT
1 ATTATAAATATTTAATTTTAATAAATTAT
*
49676 ATTATTAAAT-TTTTATTATTAATAAATTA
1 ATTA-TAAATATTTAATT-TTAATAAATTA
49705 AACTATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (29 bp):
ATTATAAATATTTAATTTTAATAAATTAT
Found at i:49728 original size:14 final size:14
Alignment explanation
Indices: 49658--49743 Score: 52
Period size: 13 Copynumber: 6.0 Consensus size: 14
49648 TTATAAATAT
49658 TTAATTTTATTAAA
1 TTAATTTTATTAAA
*
49672 TT-ATATTATTAAA
1 TTAATTTTATTAAA
* *
49685 TTTTTATTATTAATAAA
1 --TTAATT-TTATTAAA
**
49702 TTAA-ACTATTTAAA
1 TTAATTTTA-TTAAA
49716 TTAATTTTATT-AA
1 TTAATTTTATTAAA
*
49729 GTAATTTTAATTAAA
1 TTAATTTT-ATTAAA
49744 AAAGAATTTA
Statistics
Matches: 54, Mismatches: 10, Indels: 15
0.68 0.13 0.19
Matches are distributed among these distances:
13 21 0.39
14 15 0.28
15 9 0.17
16 2 0.04
17 7 0.13
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (14 bp):
TTAATTTTATTAAA
Found at i:58741 original size:2 final size:2
Alignment explanation
Indices: 58734--58766 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
58724 TGGTAAAGTT
58734 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
58767 TTAGTTTGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:62690 original size:16 final size:16
Alignment explanation
Indices: 62603--62691 Score: 88
Period size: 16 Copynumber: 5.6 Consensus size: 16
62593 GTTATTTTCA
*
62603 GGTTCGGATCATTTTG
1 GGTTCGGGTCATTTTG
62619 GGTTCGGGTCATTTTG
1 GGTTCGGGTCATTTTG
* * * *
62635 TGTTCAGGTCACTTTA
1 GGTTCGGGTCATTTTG
* * * *
62651 GATTTGAGTCATTTCG
1 GGTTCGGGTCATTTTG
*
62667 AGTTCGGGTCATTTTG
1 GGTTCGGGTCATTTTG
62683 GGTTCGGGT
1 GGTTCGGGT
62692 TGTTTCGGGT
Statistics
Matches: 54, Mismatches: 19, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 54 1.00
ACGTcount: A:0.12, C:0.13, G:0.31, T:0.43
Consensus pattern (16 bp):
GGTTCGGGTCATTTTG
Found at i:62701 original size:16 final size:16
Alignment explanation
Indices: 62598--62709 Score: 73
Period size: 16 Copynumber: 7.0 Consensus size: 16
62588 TTTGGGTTAT
* *
62598 TTTCAGGTTCGGATCA
1 TTTCGGGTTCGGGTCA
*
62614 TTTTGGGTTCGGGTCA
1 TTTCGGGTTCGGGTCA
* * *
62630 TTTTGTGTTCAGGTCA
1 TTTCGGGTTCGGGTCA
* * * *
62646 CTTT-AGATTTGAGTCA
1 -TTTCGGGTTCGGGTCA
*
62662 TTTCGAGTTCGGGTCA
1 TTTCGGGTTCGGGTCA
* **
62678 TTTTGGGTTCGGGTTG
1 TTTCGGGTTCGGGTCA
*
62694 TTTCGGGTTCAGGTCA
1 TTTCGGGTTCGGGTCA
62710 ATCGGGTTTA
Statistics
Matches: 70, Mismatches: 24, Indels: 4
0.71 0.24 0.04
Matches are distributed among these distances:
15 3 0.04
16 64 0.91
17 3 0.04
ACGTcount: A:0.12, C:0.14, G:0.30, T:0.43
Consensus pattern (16 bp):
TTTCGGGTTCGGGTCA
Found at i:63860 original size:16 final size:16
Alignment explanation
Indices: 63760--63869 Score: 75
Period size: 16 Copynumber: 6.9 Consensus size: 16
63750 TAATTATTCT
* *
63760 GGTCATTTCGAATTTG
1 GGTCATTTCGGATTAG
* *
63776 GGTCATTTCGGGTTTG
1 GGTCATTTCGGATTAG
*
63792 GATCATTTCGGATTCA-
1 GGTCATTTCGGATT-AG
63808 GGTCATTTC-GAGTTCA-
1 GGTCATTTCGGA-TT-AG
* *
63824 GGTTA-TTCTGGATTCG
1 GGTCATTTC-GGATTAG
*
63840 GGTCATTTCGGGTTAG
1 GGTCATTTCGGATTAG
*
63856 GGTCAGTTCGGATT
1 GGTCATTTCGGATT
63870 CGAGTTGTTG
Statistics
Matches: 75, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
15 5 0.07
16 65 0.87
17 5 0.07
ACGTcount: A:0.15, C:0.15, G:0.30, T:0.40
Consensus pattern (16 bp):
GGTCATTTCGGATTAG
Found at i:63869 original size:32 final size:32
Alignment explanation
Indices: 63760--63871 Score: 120
Period size: 32 Copynumber: 3.5 Consensus size: 32
63750 TAATTATTCT
* * *
63760 GGTCATTTCGAATTTGGGTCATTTCGGGTTTG
1 GGTCATTTCGGATTCGGGTCATTTCGGGTTAG
* * *
63792 GATCATTTCGGATTCAGGTCATTTCGAGTTCA-
1 GGTCATTTCGGATTCGGGTCATTTCGGGTT-AG
*
63824 GGTTA-TTCTGGATTCGGGTCATTTCGGGTTAG
1 GGTCATTTC-GGATTCGGGTCATTTCGGGTTAG
*
63856 GGTCAGTTCGGATTCG
1 GGTCATTTCGGATTCG
63872 AGTTGTTGAC
Statistics
Matches: 65, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
31 4 0.06
32 58 0.89
33 3 0.05
ACGTcount: A:0.15, C:0.15, G:0.30, T:0.39
Consensus pattern (32 bp):
GGTCATTTCGGATTCGGGTCATTTCGGGTTAG
Found at i:66884 original size:4 final size:4
Alignment explanation
Indices: 66856--66926 Score: 65
Period size: 4 Copynumber: 17.8 Consensus size: 4
66846 CAAATCACTT
* * * *
66856 TTTC TTTC TCTT- TTTC TTTTT TTTC TTTC CTTA TTTC -TCC TTTC TTTC
1 TTTC TTTC T-TTC TTTC -TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
*
66904 TTTC TTTC TTTC TTTC TCTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTT
66927 TTTTTTTCCA
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
3 4 0.08
4 44 0.83
5 5 0.09
ACGTcount: A:0.01, C:0.25, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTC
Found at i:66907 original size:27 final size:28
Alignment explanation
Indices: 66860--66934 Score: 91
Period size: 27 Copynumber: 2.7 Consensus size: 28
66850 TCACTTTTTC
*
66860 TTTCTCTTTTTCTTTTTTTTCTTTCCTTA
1 TTTCTCTCTTTC-TTTTTTTCTTTCCTTA
* * *
66889 TTTCTC-CTTTCTTTCTTTCTTTCTTTC
1 TTTCTCTCTTTCTTTTTTTCTTTCCTTA
66916 TTTCTCTCTTT-TTTTTTTC
1 TTTCTCTCTTTCTTTTTTTC
66935 CAAAATCTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
27 26 0.65
28 8 0.20
29 6 0.15
ACGTcount: A:0.01, C:0.24, G:0.00, T:0.75
Consensus pattern (28 bp):
TTTCTCTCTTTCTTTTTTTCTTTCCTTA
Found at i:67517 original size:23 final size:23
Alignment explanation
Indices: 67491--67534 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
67481 TATTTTTTAA
* *
67491 TTAATTAATTAATTAATCAAATT
1 TTAAATAATAAATTAATCAAATT
*
67514 TTAAATAATAAATTACTCAAA
1 TTAAATAATAAATTAATCAAA
67535 AAATTATTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (23 bp):
TTAAATAATAAATTAATCAAATT
Found at i:67947 original size:36 final size:36
Alignment explanation
Indices: 67899--68063 Score: 287
Period size: 36 Copynumber: 4.6 Consensus size: 36
67889 AGGTTGAAGC
*
67899 CTGTTGAATTTGTCTGGAGCCCATTGAAGTCAACGA
1 CTGTTGATTTTGTCTGGAGCCCATTGAAGTCAACGA
67935 CTGTTGATTTTGTCTGGAGCCCATTGAAGTCAACGA
1 CTGTTGATTTTGTCTGGAGCCCATTGAAGTCAACGA
*
67971 CTGTTGATTTTGTCTGGAGCCCATTGAAGTCGACGA
1 CTGTTGATTTTGTCTGGAGCCCATTGAAGTCAACGA
*
68007 CTGTTGATTTTGTCTGGAGCCCATTGAAGT-AGACGC
1 CTGTTGATTTTGTCTGGAGCCCATTGAAGTCA-ACGA
68043 CTGTTGATTTTGTCTGGAGCC
1 CTGTTGATTTTGTCTGGAGCC
68064 GATCTCTGCC
Statistics
Matches: 124, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
36 124 1.00
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (36 bp):
CTGTTGATTTTGTCTGGAGCCCATTGAAGTCAACGA
Found at i:68674 original size:25 final size:25
Alignment explanation
Indices: 68640--68689 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
68630 ATAATATAAC
68640 ATAAATATAAATATCCTATAAATAT
1 ATAAATATAAATATCCTATAAATAT
68665 ATAAATATAAATATCCTATAAATAT
1 ATAAATATAAATATCCTATAAATAT
68690 CCCAATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (25 bp):
ATAAATATAAATATCCTATAAATAT
Found at i:69529 original size:6 final size:6
Alignment explanation
Indices: 69508--69552 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
69498 TACTCTTAAG
*
69508 TTTTC- TTTTC- TTTTCT TTTTCT TTTT-T TTTTTT TTTTGCT TTTTC
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT-CT TTTTC
69553 CTGATAATTG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
5 15 0.42
6 16 0.44
7 5 0.14
ACGTcount: A:0.00, C:0.13, G:0.02, T:0.84
Consensus pattern (6 bp):
TTTTCT
Found at i:71959 original size:16 final size:17
Alignment explanation
Indices: 71938--71970 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
71928 GCACGAGCAA
71938 AATTAATTAATT-TTTT
1 AATTAATTAATTATTTT
71954 AATTAATTAATTATTTT
1 AATTAATTAATTATTTT
71971 TATTTTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
AATTAATTAATTATTTT
Found at i:73148 original size:30 final size:30
Alignment explanation
Indices: 73114--73187 Score: 130
Period size: 30 Copynumber: 2.5 Consensus size: 30
73104 TTTAAAAGAA
* *
73114 GGATTGTTTTTGAAGGTCATGTGTCTTGAT
1 GGATTGTTTTTGAAGGTCATGTGCCTTGAC
73144 GGATTGTTTTTGAAGGTCATGTGCCTTGAC
1 GGATTGTTTTTGAAGGTCATGTGCCTTGAC
73174 GGATTGTTTTTGAA
1 GGATTGTTTTTGAA
73188 CCTAGTCCCC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.18, C:0.08, G:0.30, T:0.45
Consensus pattern (30 bp):
GGATTGTTTTTGAAGGTCATGTGCCTTGAC
Found at i:73257 original size:33 final size:33
Alignment explanation
Indices: 73174--73258 Score: 136
Period size: 33 Copynumber: 2.6 Consensus size: 33
73164 GTGCCTTGAC
*
73174 GGATTGTTT-TTGAACCTAGTCCCCTACCTTGGA
1 GGATT-TTTGTTGAACCTCGTCCCCTACCTTGGA
*
73207 GGATTTTTGTTGAACCTCGTCGCCTACCTTGGA
1 GGATTTTTGTTGAACCTCGTCCCCTACCTTGGA
73240 GGATTTTTGTTGAACCTCG
1 GGATTTTTGTTGAACCTCG
73259 CGTGCTTTGG
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
32 3 0.06
33 46 0.94
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (33 bp):
GGATTTTTGTTGAACCTCGTCCCCTACCTTGGA
Found at i:75824 original size:11 final size:12
Alignment explanation
Indices: 75774--75822 Score: 57
Period size: 13 Copynumber: 4.2 Consensus size: 12
75764 AAAATATCAG
75774 TTTCTCTTCTTAA
1 TTTCTCTTCTT-A
*
75787 TTTTTCTTCTTA
1 TTTCTCTTCTTA
*
75799 -TTCTC-TCCTA
1 TTTCTCTTCTTA
75809 TTTCTCTTCTTA
1 TTTCTCTTCTTA
75821 TT
1 TT
75823 CTTCACAGTC
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
10 4 0.13
11 9 0.30
12 7 0.23
13 10 0.33
ACGTcount: A:0.10, C:0.24, G:0.00, T:0.65
Consensus pattern (12 bp):
TTTCTCTTCTTA
Found at i:76621 original size:22 final size:23
Alignment explanation
Indices: 76568--76622 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
76558 ATTAAACTTG
* *
76568 ATAATATTAAATATAATATAATT
1 ATAATATAAAATACAATATAATT
76591 ATAAT-TAAAATACAATATAA-T
1 ATAATATAAAATACAATATAATT
*
76612 ATGATATAAAA
1 ATAATATAAAA
76623 ATTAATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.18
22 18 0.64
23 5 0.18
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (23 bp):
ATAATATAAAATACAATATAATT
Found at i:76841 original size:44 final size:45
Alignment explanation
Indices: 76786--76894 Score: 166
Period size: 44 Copynumber: 2.4 Consensus size: 45
76776 AAACCCCCCT
* *
76786 TGCTTTGGTGGTTTTCTTTGAGGAGGAAGTTGCTTGA-CCTAACA
1 TGCTTTGGTGGTTTTATTTGAGGAGGAAGTTGCTTGACCCCAACA
* * *
76830 TGCTTTGGTGGTTTTATTTGGGGAGGAATTTGCTTGACCCCAACG
1 TGCTTTGGTGGTTTTATTTGAGGAGGAAGTTGCTTGACCCCAACA
76875 TGCTTTGGTGGTTTTATTTG
1 TGCTTTGGTGGTTTTATTTG
76895 CGGTGGTATT
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
44 34 0.58
45 25 0.42
ACGTcount: A:0.15, C:0.13, G:0.30, T:0.42
Consensus pattern (45 bp):
TGCTTTGGTGGTTTTATTTGAGGAGGAAGTTGCTTGACCCCAACA
Found at i:77112 original size:30 final size:30
Alignment explanation
Indices: 77003--77103 Score: 166
Period size: 30 Copynumber: 3.4 Consensus size: 30
76993 TTGAACATCA
* *
77003 CTTGAAGGATTGTTTTTGAAGGTCATGTGT
1 CTTGATGGATTGCTTTTGAAGGTCATGTGT
77033 CTTGATGGATTGCTTTTGAAGGTCATGTGT
1 CTTGATGGATTGCTTTTGAAGGTCATGTGT
*
77063 CTTGATGGATTGCTTTTGAAGGCCATGTGT
1 CTTGATGGATTGCTTTTGAAGGTCATGTGT
*
77093 CTTGACGGATT
1 CTTGATGGATT
77104 TTTGTTGAAC
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 67 1.00
ACGTcount: A:0.18, C:0.11, G:0.30, T:0.42
Consensus pattern (30 bp):
CTTGATGGATTGCTTTTGAAGGTCATGTGT
Found at i:77136 original size:33 final size:33
Alignment explanation
Indices: 77099--77183 Score: 152
Period size: 33 Copynumber: 2.6 Consensus size: 33
77089 GTGTCTTGAC
77099 GGATTTTTGTTGAACCTCGTCGCCCACCTTGGA
1 GGATTTTTGTTGAACCTCGTCGCCCACCTTGGA
*
77132 GGATTTTTGTTGAACCTCGTCGCCTACCTTGGA
1 GGATTTTTGTTGAACCTCGTCGCCCACCTTGGA
*
77165 GGATTTTTCTTGAACCTCG
1 GGATTTTTGTTGAACCTCG
77184 CGTGCTTTGG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.15, C:0.25, G:0.24, T:0.36
Consensus pattern (33 bp):
GGATTTTTGTTGAACCTCGTCGCCCACCTTGGA
Found at i:80877 original size:30 final size:30
Alignment explanation
Indices: 80843--80918 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
80833 CTTTAAATAA
*
80843 GGAAT-TTGCTTGAACCCCAGGTACACTGAC
1 GGAATGTT-CTTGAACCCCAGCTACACTGAC
* *
80873 GGAATGTTTTTGAACCGCAGCTACACTGAC
1 GGAATGTTCTTGAACCCCAGCTACACTGAC
* *
80903 GGATTGTTTTTGAACC
1 GGAATGTTCTTGAACC
80919 TCACGTTTAC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 39 0.95
31 2 0.05
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (30 bp):
GGAATGTTCTTGAACCCCAGCTACACTGAC
Found at i:80931 original size:30 final size:30
Alignment explanation
Indices: 80867--80971 Score: 113
Period size: 30 Copynumber: 3.5 Consensus size: 30
80857 CCCCAGGTAC
* * **
80867 ACTGACGGAATGTTTTTGAACCGCA-GCTAC
1 ACTGACGGATTGTTTTTGAACCTCACG-TTT
80897 ACTGACGGATTGTTTTTGAACCTCACGTTT
1 ACTGACGGATTGTTTTTGAACCTCACGTTT
* * * *
80927 ACTGACGGATTGTATTTGCAGCTCACTTTT
1 ACTGACGGATTGTTTTTGAACCTCACGTTT
*
80957 ATTGACGGATTGTTT
1 ACTGACGGATTGTTT
80972 CTTAAAATTG
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
30 63 0.98
31 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (30 bp):
ACTGACGGATTGTTTTTGAACCTCACGTTT
Found at i:82432 original size:133 final size:133
Alignment explanation
Indices: 82181--82579 Score: 561
Period size: 133 Copynumber: 3.0 Consensus size: 133
82171 AAAGACAAAA
* * * * * * *
82181 CCATGAGCTTGATGTAAGGATAACAAATTATTTGATTCTATTCTACCTAAACATATATTT-TCTC
1 CCATGAGCTTGATGTAACGATTACAAATGATTTAATTCTATCCTACTTAAACATACATTTCT-TC
* *
82245 GCACTCTT-C-AAATTTTTAAACACTACATATGTTATTATTTTTATACGTGTTTTACGTATACAG
65 GCACT-TTCCAAAATTTTTAAATACTACATATGTTATTATTTTTATGCGTGTTTTACGTATACAG
82308 AGAGC
129 AGAGC
*
82313 CCATGAGCTTAATGTAACGATTACAAATGATTTAATTCTATCCTACTTAAACATACATTTCTTCG
1 CCATGAGCTTGATGTAACGATTACAAATGATTTAATTCTATCCTACTTAAACATACATTTCTTCG
82378 CACTTTCCAAAATTTTTAAATACTACATATGTTATTATTTTTATGCGTGTTTTACGTATACAGAG
66 CACTTTCCAAAATTTTTAAATACTACATATGTTATTATTTTTATGCGTGTTTTACGTATACAGAG
82443 AGC
131 AGC
* * * *
82446 TCATAAACTTGATGTAACGATTACAAATGATTTAATTCTATCCTACTTAAACATACATTTCTTCA
1 CCATGAGCTTGATGTAACGATTACAAATGATTTAATTCTATCCTACTTAAACATACATTTCTTCG
* ** * * * * *
82511 CACTTTCTAAAATTTTTAAATACTATGTATGTTATTGTTTTTATGCGTATTTTACATGTACAAAG
66 CACTTTCCAAAATTTTTAAATACTACATATGTTATTATTTTTATGCGTGTTTTACGTATACAGAG
82576 AGC
131 AGC
82579 C
1 C
82580 TTACATATAA
Statistics
Matches: 240, Mismatches: 24, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
131 2 0.01
132 60 0.25
133 178 0.74
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.41
Consensus pattern (133 bp):
CCATGAGCTTGATGTAACGATTACAAATGATTTAATTCTATCCTACTTAAACATACATTTCTTCG
CACTTTCCAAAATTTTTAAATACTACATATGTTATTATTTTTATGCGTGTTTTACGTATACAGAG
AGC
Found at i:84109 original size:13 final size:13
Alignment explanation
Indices: 84091--84136 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
84081 CCGATTTTCT
84091 ATATTAGAT-TAAA
1 ATATTA-ATATAAA
84104 ATATTAATATAAA
1 ATATTAATATAAA
*
84117 ATTTTAATATAAA
1 ATATTAATATAAA
84130 TATATTA
1 -ATATTA
84137 TTGTTTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 2 0.07
13 22 0.76
14 5 0.17
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (13 bp):
ATATTAATATAAA
Found at i:86755 original size:21 final size:21
Alignment explanation
Indices: 86731--86782 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 21
86721 ATTTACGATA
86731 TTTTATATTAT-TTATATAAAT
1 TTTTATATTATATT-TATAAAT
86752 TTTTA-A-TATATTTATAAAT
1 TTTTATATTATATTTATAAAT
86771 TTTTAT-TTATAT
1 TTTTATATTATAT
86783 AATATTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
19 15 0.54
20 8 0.29
21 5 0.18
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTATATTATATTTATAAAT
Found at i:86779 original size:14 final size:16
Alignment explanation
Indices: 86760--86792 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
86750 ATTTTTAATA
86760 TATTTATA-AAT-TTT
1 TATTTATATAATATTT
86774 TATTTATATAATATTT
1 TATTTATATAATATTT
86790 TAT
1 TAT
86793 ATTAGTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 3 0.18
16 6 0.35
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TATTTATATAATATTT
Done.