Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 109 of 144
Found at i:25363060 original size:49 final size:49
Alignment explanation
Indices: 25362654--25363061 Score: 288
Period size: 49 Copynumber: 8.2 Consensus size: 49
25362644 AAAAATACAA
* * * * *
25362654 AAGGGAAAGGTCTAAGTCGCAACGACAGA-CCATGTACCTCAGAAGACA-C
1 AAGGGAAAGATCTAAGCCGCAACGGCAGATCCA-GTACCAC-GAAGACATG
* * * * * ** *
25362703 AACAGGAAAGCTCTAAGACTGTAACGGCGGATCCAGTACAACAAAAAGACA-A
1 AA-GGGAAAGATCTAAG-CCGCAACGGCAGATCCAGTAC--CACGAAGACATG
* * * * *
25362755 AAGGGAAAGGTCTAAGTCGCAACGGCAGA-CCGTGTACCTCAGAAGACACG
1 AAGGGAAAGATCTAAGCCGCAACGGCAGATCC-AGTACCAC-GAAGACATG
* * * ** **
25362805 ACGGGAAAGATCTAAGATCGCAACAGTGGATCCAGTACCGCAAAAAGACA-G
1 AAGGGAAAGATCTAAG-CCGCAACGGCAGATCCAGTA-C-CACGAAGACATG
** * *
25362856 AAGGGAAAGATCTAAGACAACAACGACAGATCCAGTACCACGAAGACATC
1 AAGGGAAAGATCTAAG-CCGCAACGGCAGATCCAGTACCACGAAGACATG
* * * *
25362906 AAAGGAAAGATTTAAGCTGCAACTGC-GAATCCAGTACCACGAAGACATG
1 AAGGGAAAGATCTAAGCCGCAACGGCAG-ATCCAGTACCACGAAGACATG
* *
25362955 AAGGGAAAGATCTAAGCCGCGACGGCAGATCCAGTAGCACGAAGACATG
1 AAGGGAAAGATCTAAGCCGCAACGGCAGATCCAGTACCACGAAGACATG
* * * * **
25363004 AATGGAAAGATCTAAGCCGCGACGGCGGATCCCGTACCACGAAGATTTG
1 AAGGGAAAGATCTAAGCCGCAACGGCAGATCCAGTACCACGAAGACATG
25363053 AAGGGAAAG
1 AAGGGAAAG
25363062 GTTTAAGTCG
Statistics
Matches: 282, Mismatches: 62, Indels: 30
0.75 0.17 0.08
Matches are distributed among these distances:
48 2 0.01
49 136 0.48
50 55 0.20
51 67 0.24
52 20 0.07
53 2 0.01
ACGTcount: A:0.40, C:0.22, G:0.26, T:0.12
Consensus pattern (49 bp):
AAGGGAAAGATCTAAGCCGCAACGGCAGATCCAGTACCACGAAGACATG
Found at i:25363090 original size:147 final size:149
Alignment explanation
Indices: 25362755--25363090 Score: 326
Period size: 147 Copynumber: 2.2 Consensus size: 149
25362745 AAAAAGACAA
* * * *
25362755 AAGGGAAAGGTCTAAGTCGCAACGGC-AGACCGTGTACCTCAGAAGACACGACGGGAAAGATCTA
1 AAGGGAAAGGTTTAAGTCGCAATGGCGA-ACCG-GTACCACAGAAGACACGAAGGGAAAGATCTA
* **
25362819 AGATCGCAACAGTGGATCCAGTACCGCAAAAAGACAGAAGGGAAAGATCTAAGACAACAACGACA
64 AGACCGCAACAGCAGATCCAGTA-CGCAAAAAGACAGAAGGGAAAGATCTAAGACAACAACGACA
25362884 GATCCAGTACCACGAAGACATC
128 GATCCAGTACCACGAAGACATC
* * * *
25362906 AAAGGAAAGATTTAAG-CTGCAACT-GCGAATCCAGTACCAC-GAAGACATGAAGGGAAAGATCT
1 AAGGGAAAGGTTTAAGTC-GCAA-TGGCGAA-CCGGTACCACAGAAGACACGAAGGGAAAGATCT
* * ** * ** * *
25362968 AAG-CCGCGACGGCAGATCCAGTA-GCACGAAGACATGAATGGAAAGATCTAAG-CCGCGACGGC
63 AAGACCGCAACAGCAGATCCAGTACGCAAAAAGACA-GAAGGGAAAGATCTAAGACAACAACGAC
* * ** *
25363030 GGATCCCGTACCACGAAGATTTG
127 AGATCCAGTACCACGAAGACATC
25363053 AAGGGAAAGGTTTAAGTCGCAATGGCGAACCCGGTACC
1 AAGGGAAAGGTTTAAGTCGCAATGGCGAA-CCGGTACC
25363091 TTAGAAACAT
Statistics
Matches: 149, Mismatches: 29, Indels: 18
0.76 0.15 0.09
Matches are distributed among these distances:
146 1 0.01
147 63 0.42
148 17 0.11
149 15 0.10
150 24 0.16
151 26 0.17
152 3 0.02
ACGTcount: A:0.38, C:0.23, G:0.27, T:0.13
Consensus pattern (149 bp):
AAGGGAAAGGTTTAAGTCGCAATGGCGAACCGGTACCACAGAAGACACGAAGGGAAAGATCTAAG
ACCGCAACAGCAGATCCAGTACGCAAAAAGACAGAAGGGAAAGATCTAAGACAACAACGACAGAT
CCAGTACCACGAAGACATC
Found at i:25363413 original size:78 final size:78
Alignment explanation
Indices: 25363324--25363469 Score: 206
Period size: 78 Copynumber: 1.9 Consensus size: 78
25363314 GAAGATGCTG
* *
25363324 ATCTCTTACCCCGAGCCAGGGGCAGATTG-AAGCCATTTGATCTTTTACCCCGAGCCTGGGGT-A
1 ATCTCTTACCCCGAGCCAGGGGCAGATTGCAA-CCATCTGATATTTTACCCCGAG-CTGGGGTCA
25363387 GATCATCATCAACCA
64 GATCATCATCAACCA
** * *
25363402 ATCTCTTACCCCGAGCTTGGGGTAGATTGCAACCATCTGATATTTTACCCCGAGCTTGGGTCAGA
1 ATCTCTTACCCCGAGCCAGGGGCAGATTGCAACCATCTGATATTTTACCCCGAGCTGGGGTCAGA
25363467 TCA
66 TCA
25363470 CCAGACTCTA
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
77 6 0.10
78 52 0.87
79 2 0.03
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.27
Consensus pattern (78 bp):
ATCTCTTACCCCGAGCCAGGGGCAGATTGCAACCATCTGATATTTTACCCCGAGCTGGGGTCAGA
TCATCATCAACCA
Found at i:25363450 original size:39 final size:39
Alignment explanation
Indices: 25363321--25363461 Score: 126
Period size: 39 Copynumber: 3.6 Consensus size: 39
25363311 AATGAAGATG
* * *
25363321 CTGATCTCTTACCCCGAGCCAGGGGCAGATTG-AAGCCAT
1 CTGATCTTTTACCCCGAGCCTGGGGTAGATTGCAA-CCAT
* * *
25363360 TTGATCTTTTACCCCGAGCCTGGGGTAGA-T-CATCATCAA
1 CTGATCTTTTACCCCGAGCCTGGGGTAGATTGCA--ACCAT
** * *
25363399 CCAATCTCTTACCCCGAGCTTGGGGTAGATTGCAACCAT
1 CTGATCTTTTACCCCGAGCCTGGGGTAGATTGCAACCAT
* *
25363438 CTGATATTTTACCCCGAGCTTGGG
1 CTGATCTTTTACCCCGAGCCTGGG
25363462 TCAGATCACC
Statistics
Matches: 80, Mismatches: 17, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
38 2 0.03
39 74 0.93
40 2 0.03
41 2 0.03
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.27
Consensus pattern (39 bp):
CTGATCTTTTACCCCGAGCCTGGGGTAGATTGCAACCAT
Found at i:25363892 original size:201 final size:200
Alignment explanation
Indices: 25363527--25364044 Score: 757
Period size: 201 Copynumber: 2.5 Consensus size: 200
25363517 CACAAACAGT
* * *
25363527 GAGGCGATCATCTTCCTGATGAGATACAGAGAAGTATGCCAACTCGAGGCTCGAGGCTCGATACG
1 GAGGCGATCATCTTCCTGATGAGATACAGAGAAGTATACCAACTC-A-G-T----GCTCAATGCG
* * *
25363592 AGTAAATCTTCGAACCCAGCTTCCTGATGAGGCACTGAGAAGCAGGTCGAAGCAATAAAATGGTT
59 AGCAAATCTTCGAACCTAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTT
* * * *
25363657 AGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATAAGATACAGAGAAGCGA
124 AGCTTCCTGATGAGACACGGAAAAGTGCACCAAATTCGTCTTCTTGATAAGATACAGAGAAGCGA
25363722 ATTGAAACAAGC
189 ATTGAAACAAGC
* *
25363734 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAGTGCTTAATGCGAGCAAAT
1 GAGGCGATCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAGTGCTCAATGCGAGCAAAT
*
25363799 CTTCGAACCTGAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTG
66 CTTCGAACCT-AGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTC
* *
25363864 TTGATGAGACACGGAAAAGTGCACCAAATTCGTCTTCTTGATGAGATACAGAGAAGCGAATTGAA
130 CTGATGAGACACGGAAAAGTGCACCAAATTCGTCTTCTTGATAAGATACAGAGAAGCGAATTGAA
25363929 ACAAGC
195 ACAAGC
* ** * *
25363935 GAGGCGATCATCTTCTTGATGAGATACAGAGAAGTATACCAACTCAACGCTCAATGTGAGCAAAC
1 GAGGCGATCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAGTGCTCAATGCGAGCAAAT
* * *
25364000 CTTCGAACCTAGCTTCCTAATGAGACACCGAGAAGAAGGTCGAAG
66 CTTCGAACCTAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAG
25364045 TTAACGAAAC
Statistics
Matches: 285, Mismatches: 25, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
200 54 0.19
201 185 0.65
204 1 0.00
205 1 0.00
206 1 0.00
207 43 0.15
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.22
Consensus pattern (200 bp):
GAGGCGATCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAGTGCTCAATGCGAGCAAAT
CTTCGAACCTAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
TGATGAGACACGGAAAAGTGCACCAAATTCGTCTTCTTGATAAGATACAGAGAAGCGAATTGAAA
CAAGC
Found at i:25364424 original size:26 final size:26
Alignment explanation
Indices: 25364395--25364451 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
25364385 AAAATTTTTG
* *
25364395 ATTTTTTAAGTTTGAA-TTGATTTTAA
1 ATTTATTAAGTTTAAATTTG-TTTTAA
25364421 ATTTATTAAGTTTAAATTTGTTTTAA
1 ATTTATTAAGTTTAAATTTGTTTTAA
25364447 ATTTA
1 ATTTA
25364452 AATTTAGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 25 0.89
27 3 0.11
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (26 bp):
ATTTATTAAGTTTAAATTTGTTTTAA
Found at i:25364471 original size:17 final size:16
Alignment explanation
Indices: 25364416--25364469 Score: 67
Period size: 17 Copynumber: 3.4 Consensus size: 16
25364406 TTGAATTGAT
*
25364416 TTTAAATTTA-TTAAG
1 TTTAAATTTAGTTAAA
25364431 TTTAAATTT-GTTTTAAA
1 TTTAAATTTAG--TTAAA
25364448 TTTAAATTTAGTTAAA
1 TTTAAATTTAGTTAAA
25364464 TTTAAA
1 TTTAAA
25364470 ATGGTTTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
15 9 0.26
16 11 0.32
17 13 0.38
18 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.54
Consensus pattern (16 bp):
TTTAAATTTAGTTAAA
Found at i:25364477 original size:33 final size:33
Alignment explanation
Indices: 25364416--25364502 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 33
25364406 TTGAATTGAT
* * *
25364416 TTTAAATTTATTAAGTTTAAATTTG-TTTTAAA
1 TTTAAATTTATTAAATTTAAAATGGTTTTTAAA
25364448 TTTAAATTTAGTTAAATTTAAAATGGTTTTTAAA
1 TTTAAATTTA-TTAAATTTAAAATGGTTTTTAAA
* *
25364482 CTTAAA---ATTAAGTTTAAAATG
1 TTTAAATTTATTAAATTTAAAATG
25364503 TCCAAATACA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
30 13 0.27
31 1 0.02
32 10 0.21
33 12 0.25
34 12 0.25
ACGTcount: A:0.41, C:0.01, G:0.08, T:0.49
Consensus pattern (33 bp):
TTTAAATTTATTAAATTTAAAATGGTTTTTAAA
Found at i:25365154 original size:3 final size:3
Alignment explanation
Indices: 25365141--25365197 Score: 62
Period size: 3 Copynumber: 18.7 Consensus size: 3
25365131 GCATTGAATG
* *
25365141 AAT ATT AAT AAT AAT AAT AAT -AT AGT AATT AAT AAT AAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT -AAT
*
25365187 AAT AAT TAT AA
1 AAT AAT AAT AA
25365198 AAAAAAGAGA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
2 2 0.04
3 37 0.82
4 6 0.13
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:25365176 original size:24 final size:23
Alignment explanation
Indices: 25365144--25365194 Score: 84
Period size: 24 Copynumber: 2.2 Consensus size: 23
25365134 TTGAATGAAT
*
25365144 ATTAATAATAATAATAATATAGTA
1 ATTAATAATAATAATAA-ATAATA
25365168 ATTAATAATAATAATAAATAATA
1 ATTAATAATAATAATAAATAATA
25365191 ATTA
1 ATTA
25365195 TAAAAAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 9 0.35
24 17 0.65
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (23 bp):
ATTAATAATAATAATAAATAATA
Found at i:25365187 original size:13 final size:13
Alignment explanation
Indices: 25365147--25365198 Score: 63
Period size: 13 Copynumber: 4.2 Consensus size: 13
25365137 AATGAATATT
25365147 AATAATAATAAT-
1 AATAATAATAATA
* *
25365159 AAT-ATAGTAATT
1 AATAATAATAATA
25365171 AATAATAATAATA
1 AATAATAATAATA
*
25365184 AATAATAATTATA
1 AATAATAATAATA
25365197 AA
1 AA
25365199 AAAAAGAGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
11 7 0.21
12 6 0.18
13 21 0.62
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (13 bp):
AATAATAATAATA
Found at i:25366383 original size:30 final size:30
Alignment explanation
Indices: 25366331--25366715 Score: 286
Period size: 30 Copynumber: 13.1 Consensus size: 30
25366321 GAAAGTCCTT
** *
25366331 AAACTATCCAAAAATTGTA-TTTTAACCCCC
1 AAACT-TCCAAAAATTACATTTTTAACCCCG
* **
25366361 AAACTTCTCTAAAATTACATTTTTAACCCTA
1 AAACTTC-CAAAAATTACATTTTTAACCCCG
** *
25366392 AAACTTCCAAAAATTACATTTTTGTCCTCG
1 AAACTTCCAAAAATTACATTTTTAACCCCG
* * ****
25366422 -AACTTTCAAAAATTACATTTTTGATATTG
1 AAACTTCCAAAAATTACATTTTTAACCCCG
* ***
25366451 AAACTTCCAAAAATTACATTTTTGACATTG
1 AAACTTCCAAAAATTACATTTTTAACCCCG
* * * *
25366481 AAACTTCAAAAAATTATATTTTT-GCCCCA
1 AAACTTCCAAAAATTACATTTTTAACCCCG
* *
25366510 AAACTTTCAAAAATTACATTTTTAACCTCG
1 AAACTTCCAAAAATTACATTTTTAACCCCG
* * * * *
25366540 AAACTTTCAAAAAATATATTTTT-GCCCCC
1 AAACTTCCAAAAATTACATTTTTAACCCCG
* * *
25366569 AAACTTCCAAAAATTATATTTTTGATCCCG
1 AAACTTCCAAAAATTACATTTTTAACCCCG
*
25366599 AAACTTCCAAAAATTACA-TTTT--CCCCT
1 AAACTTCCAAAAATTACATTTTTAACCCCG
*
25366626 AAACTTCCAAAAATTACATTTTTAA-CCCT
1 AAACTTCCAAAAATTACATTTTTAACCCCG
* * * * * *
25366655 AAAATTCTAAAAATTCCATATTTGAGCCCG
1 AAACTTCCAAAAATTACATTTTTAACCCCG
* *
25366685 ACACTTCC-AAAATTACCA-TTTTACCCCCG
1 AAACTTCCAAAAATTA-CATTTTTAACCCCG
25366714 AA
1 AA
25366716 TGTTTCAAAA
Statistics
Matches: 286, Mismatches: 59, Indels: 21
0.78 0.16 0.06
Matches are distributed among these distances:
27 21 0.07
28 4 0.01
29 113 0.40
30 132 0.46
31 16 0.06
ACGTcount: A:0.38, C:0.23, G:0.04, T:0.35
Consensus pattern (30 bp):
AAACTTCCAAAAATTACATTTTTAACCCCG
Found at i:25366456 original size:59 final size:59
Alignment explanation
Indices: 25366361--25366648 Score: 316
Period size: 59 Copynumber: 4.9 Consensus size: 59
25366351 TTTAACCCCC
* * * *
25366361 AAACTTCTCTAAAATTACATTTTTAACCCTAAAACTTCCAAAAATTACATTTTTGTCCTCG
1 AAACTT-TCAAAAATTACATTTTT-GCCCCAAAACTTCCAAAAATTACATTTTTGACCTCG
***** * *
25366422 -AACTTTCAAAAATTACATTTTTGATATTGAAACTTCCAAAAATTACATTTTTGACATTG
1 AAACTTTCAAAAATTACATTTTTG-CCCCAAAACTTCCAAAAATTACATTTTTGACCTCG
* * *
25366481 AAAC-TTCAAAAAATTATATTTTTGCCCCAAAACTTTCAAAAATTACATTTTTAACCTCG
1 AAACTTTC-AAAAATTACATTTTTGCCCCAAAACTTCCAAAAATTACATTTTTGACCTCG
* * * *
25366540 AAACTTTCAAAAAATATATTTTTGCCCCCAAACTTCCAAAAATTATATTTTTGATCC-CG
1 AAACTTTCAAAAATTACATTTTTGCCCCAAAACTTCCAAAAATTACATTTTTGA-CCTCG
* *
25366599 AAACTTCCAAAAATTACA-TTTT-CCCCTAAACTTCCAAAAATTACATTTTT
1 AAACTTTCAAAAATTACATTTTTGCCCCAAAACTTCCAAAAATTACATTTTT
25366649 AACCCTAAAA
Statistics
Matches: 193, Mismatches: 29, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
57 26 0.13
58 4 0.02
59 135 0.70
60 28 0.15
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.37
Consensus pattern (59 bp):
AAACTTTCAAAAATTACATTTTTGCCCCAAAACTTCCAAAAATTACATTTTTGACCTCG
Found at i:25366485 original size:89 final size:88
Alignment explanation
Indices: 25366361--25366669 Score: 322
Period size: 89 Copynumber: 3.5 Consensus size: 88
25366351 TTTAACCCCC
* * *
25366361 AAACTTCTCTAAAATTACATTTTTAACCCTAAAACTTCCAAAAATTACATTTTTGTCCTCGAACT
1 AAACTTC-CAAAAATTACATTTTTGACCCTAAAACTTCCAAAAATTATATTTTTGTCC-CGAACT
* * *
25366426 TTCAAAAATTACATTTTTGATATTG
64 TTCAAAAATTACATTTTTAACATCG
** * * * *
25366451 AAACTTCCAAAAATTACATTTTTGACATTGAAACTTCAAAAAATTATATTTTTGCCCCAAAACTT
1 AAACTTCCAAAAATTACATTTTTGACCCTAAAACTTCCAAAAATTATATTTTTGTCCC-GAACTT
*
25366516 TCAAAAATTACATTTTTAACCTCG
65 TCAAAAATTACATTTTTAACATCG
* * * **
25366540 AAACTTTCAAAAAATATATTTTTG-CCCCCAAACTTCCAAAAATTATATTTTTGATCCCGAAACT
1 AAACTTCCAAAAATTACATTTTTGACCCTAAAACTTCCAAAAATTATATTTTTG-TCCCG-AACT
* ** *
25366604 TCCAAAAATTACA-TTTT--CCCCT
64 TTCAAAAATTACATTTTTAACATCG
* *
25366626 AAACTTCCAAAAATTACATTTTTAACCCTAAAA-TTCTAAAAATT
1 AAACTTCCAAAAATTACATTTTTGACCCTAAAACTTCCAAAAATT
25366670 CCATATTTGA
Statistics
Matches: 182, Mismatches: 33, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
86 33 0.18
87 6 0.03
88 29 0.16
89 107 0.59
90 7 0.04
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.37
Consensus pattern (88 bp):
AAACTTCCAAAAATTACATTTTTGACCCTAAAACTTCCAAAAATTATATTTTTGTCCCGAACTTT
CAAAAATTACATTTTTAACATCG
Found at i:25366830 original size:59 final size:59
Alignment explanation
Indices: 25366689--25366832 Score: 155
Period size: 59 Copynumber: 2.4 Consensus size: 59
25366679 AGCCCGACAC
* * *** * *
25366689 TTCCAAAATTACCATTTTACCCCCGAATGTTTCAAAATCCCATTTTTGATTTTGATTTT
1 TTCCAAAATTACCATTTTACCCTCGAATGTTTCAAAATCCCATTTTTAACCCTAAATTT
* * * **
25366748 TTCAAAAATCATCATTTTACCCTCGAATGTTT-AAAATTTCATTTTTAACCCTAAATTT
1 TTCCAAAATTACCATTTTACCCTCGAATGTTTCAAAATCCCATTTTTAACCCTAAATTT
*
25366806 TTCCAAAATTACCATTTTTGCCCTCGA
1 TTCCAAAATTACCA-TTTTACCCTCGA
25366833 GAGTCTAAAA
Statistics
Matches: 68, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
58 29 0.43
59 39 0.57
ACGTcount: A:0.30, C:0.22, G:0.06, T:0.42
Consensus pattern (59 bp):
TTCCAAAATTACCATTTTACCCTCGAATGTTTCAAAATCCCATTTTTAACCCTAAATTT
Found at i:25366877 original size:28 final size:28
Alignment explanation
Indices: 25366807--25366880 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
25366797 CCTAAATTTT
* *
25366807 TCCAAAATTACCATTTTTGCCCTCGAGAG
1 TCCAAAAGTACCA-TTTTGCCCTCGAGAA
* *
25366836 TCTAAAATTACCATTTTGCCCTCGAGAA
1 TCCAAAAGTACCATTTTGCCCTCGAGAA
* *
25366864 TCCACAAGTCCCATTTT
1 TCCAAAAGTACCATTTT
25366881 CAATCCCGAT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
28 27 0.69
29 12 0.31
ACGTcount: A:0.28, C:0.28, G:0.11, T:0.32
Consensus pattern (28 bp):
TCCAAAAGTACCATTTTGCCCTCGAGAA
Found at i:25369435 original size:28 final size:28
Alignment explanation
Indices: 25369395--25369454 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
25369385 AAATGAGACT
*
25369395 TTTTGGATACTCG-GGTGTAAAATAGTAA
1 TTTTGGATACTCGAGG-GCAAAATAGTAA
*
25369423 TTTTGGACT-CTCGAGGGCAAAATGGTAA
1 TTTTGGA-TACTCGAGGGCAAAATAGTAA
25369451 TTTT
1 TTTT
25369455 AGAAAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 25 0.89
29 3 0.11
ACGTcount: A:0.28, C:0.10, G:0.25, T:0.37
Consensus pattern (28 bp):
TTTTGGATACTCGAGGGCAAAATAGTAA
Found at i:25369562 original size:60 final size:59
Alignment explanation
Indices: 25369495--25369633 Score: 154
Period size: 60 Copynumber: 2.3 Consensus size: 59
25369485 AAATATCTGG
* * *
25369495 GGGTAAAATGATAATTTTATAAAAAAATCGGG-ATCAAAAATAGAATTTTTGGACGTTCGA
1 GGGTAAAATG-TAATTTT-TAAAAAAATCGGGTATCAAAAATAGAATTTTTAGAAGTTCAA
* *** * *
25369555 GGGTAAAATGGTAATTTTTGAAAGTTTCGGGTGTCAAAAATGGAATTTTTAGAAGTTCAA
1 GGGTAAAAT-GTAATTTTTAAAAAAATCGGGTATCAAAAATAGAATTTTTAGAAGTTCAA
25369615 GGGTAAAAATGTAATTTTT
1 GGGT-AAAATGTAATTTTT
25369634 GGAAAGTTTG
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
59 9 0.13
60 52 0.78
61 6 0.09
ACGTcount: A:0.39, C:0.05, G:0.22, T:0.34
Consensus pattern (59 bp):
GGGTAAAATGTAATTTTTAAAAAAATCGGGTATCAAAAATAGAATTTTTAGAAGTTCAA
Found at i:25369570 original size:29 final size:30
Alignment explanation
Indices: 25369530--25369637 Score: 109
Period size: 29 Copynumber: 3.7 Consensus size: 30
25369520 AATCGGGATC
* *
25369530 AAAAATAG-AATTTTTGGACGTTCGAGGGT
1 AAAAATGGTAATTTTTGGAAGTTCGAGGGT
*
25369559 -AAAATGGTAATTTTTGAAAGTTTCG-GGTGT
1 AAAAATGGTAATTTTTGGAAG-TTCGAGG-GT
* *
25369589 CAAAAATGG-AATTTTTAGAAGTTCAAGGGT
1 -AAAAATGGTAATTTTTGGAAGTTCGAGGGT
25369619 AAAAAT-GTAATTTTTGGAA
1 AAAAATGGTAATTTTTGGAA
25369638 AGTTTGGGGG
Statistics
Matches: 65, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
28 7 0.11
29 28 0.43
30 11 0.17
31 12 0.18
32 7 0.11
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.34
Consensus pattern (30 bp):
AAAAATGGTAATTTTTGGAAGTTCGAGGGT
Found at i:25369634 original size:60 final size:61
Alignment explanation
Indices: 25369528--25369642 Score: 171
Period size: 60 Copynumber: 1.9 Consensus size: 61
25369518 AAAATCGGGA
* * *
25369528 TCAAAAATAGAATTTTTGGACGTTCGAGGGTAAAATGGTAATTTTT-GAAAGTTTCGGGTG
1 TCAAAAATAGAATTTTTAGAAGTTCAAGGGTAAAATGGTAATTTTTGGAAAGTTTCGGGTG
*
25369588 TCAAAAATGGAATTTTTAGAAGTTCAAGGGTAAAAAT-GTAATTTTTGGAAAGTTT
1 TCAAAAATAGAATTTTTAGAAGTTCAAGGGT-AAAATGGTAATTTTTGGAAAGTTT
25369643 GGGGGTTAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
60 36 0.73
61 13 0.27
ACGTcount: A:0.36, C:0.05, G:0.23, T:0.36
Consensus pattern (61 bp):
TCAAAAATAGAATTTTTAGAAGTTCAAGGGTAAAATGGTAATTTTTGGAAAGTTTCGGGTG
Found at i:25369678 original size:29 final size:30
Alignment explanation
Indices: 25369615--25369744 Score: 176
Period size: 29 Copynumber: 4.4 Consensus size: 30
25369605 AGAAGTTCAA
* *
25369615 GGGTAAAAATGTAATTTTTGG-AAAGTTTGG
1 GGGTCAAAATATAA-TTTTGGAAAAGTTTGG
*
25369645 GGGTTAAAATATAA-TTTGGAAAAGTTTGG
1 GGGTCAAAATATAATTTTGGAAAAGTTTGG
* * *
25369674 AGGTTAAAATATAATTTTGGAAAAG-TTAG
1 GGGTCAAAATATAATTTTGGAAAAGTTTGG
25369703 GGGTCAAAATATAATTTTGGAAAAGTTTGG
1 GGGTCAAAATATAATTTTGGAAAAGTTTGG
25369733 GGGTCAAAATAT
1 GGGTCAAAATAT
25369745 GGTTTTTGGA
Statistics
Matches: 90, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
28 5 0.06
29 48 0.53
30 37 0.41
ACGTcount: A:0.38, C:0.02, G:0.26, T:0.34
Consensus pattern (30 bp):
GGGTCAAAATATAATTTTGGAAAAGTTTGG
Found at i:25369683 original size:59 final size:59
Alignment explanation
Indices: 25369620--25369744 Score: 173
Period size: 59 Copynumber: 2.1 Consensus size: 59
25369610 TTCAAGGGTA
* * * *
25369620 AAAATGTAATTTTTGG-AAAGTTTGGGGGTTAAAATATAA-TTTGGAAAAGTTTGGAGGTT
1 AAAATATAA-TTTTGGAAAAG-TTAGGGGTCAAAATATAATTTTGGAAAAGTTTGGAGGTC
*
25369679 AAAATATAATTTTGGAAAAGTTAGGGGTCAAAATATAATTTTGGAAAAGTTTGGGGGTC
1 AAAATATAATTTTGGAAAAGTTAGGGGTCAAAATATAATTTTGGAAAAGTTTGGAGGTC
25369738 AAAATAT
1 AAAATAT
25369745 GGTTTTTGGA
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
58 22 0.37
59 37 0.63
ACGTcount: A:0.39, C:0.02, G:0.25, T:0.34
Consensus pattern (59 bp):
AAAATATAATTTTGGAAAAGTTAGGGGTCAAAATATAATTTTGGAAAAGTTTGGAGGTC
Found at i:25370782 original size:12 final size:12
Alignment explanation
Indices: 25370732--25370799 Score: 50
Period size: 12 Copynumber: 5.3 Consensus size: 12
25370722 TTTATTAAAA
25370732 ATTAATATTA--
1 ATTAATATTATT
25370742 ATTAATACTGTCATT
1 ATTAATA-T-T-ATT
25370757 ATTACGATATTTATT
1 ATTA--ATA-TTATT
25370772 ATTAATATTATT
1 ATTAATATTATT
* *
25370784 ACTAACATTATT
1 ATTAATATTATT
25370796 ATTA
1 ATTA
25370800 TTAAAAAGTA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
10 7 0.15
11 1 0.02
12 19 0.40
13 4 0.09
15 11 0.23
16 1 0.02
17 4 0.09
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (12 bp):
ATTAATATTATT
Found at i:25371604 original size:10 final size:11
Alignment explanation
Indices: 25371589--25371638 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
25371579 ATATCAAGTT
25371589 TTTAAATC-AA
1 TTTAAATCAAA
*
25371599 TTTAAATTAAA
1 TTTAAATCAAA
25371610 -TTAAATTCAAA
1 TTTAAA-TCAAA
* *
25371621 ATTAAAGCAAA
1 TTTAAATCAAA
25371632 TTTAAAT
1 TTTAAAT
25371639 TTAAAAGGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
10 12 0.38
11 15 0.47
12 5 0.16
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (11 bp):
TTTAAATCAAA
Found at i:25372281 original size:17 final size:19
Alignment explanation
Indices: 25372261--25372305 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
25372251 AAAAAGAAAA
25372261 AAGAAAAAA-AA-ATGAGT
1 AAGAAAAAAGAACATGAGT
25372278 AAGAACAAAAGAATCATGAGT
1 AAGAA-AAAAGAA-CATGAGT
25372299 AAGAAAA
1 AAGAAAA
25372306 CATGTGAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 5 0.21
18 4 0.17
19 2 0.08
20 2 0.08
21 11 0.46
ACGTcount: A:0.67, C:0.04, G:0.18, T:0.11
Consensus pattern (19 bp):
AAGAAAAAAGAACATGAGT
Found at i:25372747 original size:17 final size:17
Alignment explanation
Indices: 25372725--25372788 Score: 85
Period size: 17 Copynumber: 3.8 Consensus size: 17
25372715 CGGGCCCCTT
25372725 TTAAATTTATTTTAAGA
1 TTAAATTTATTTTAAGA
*
25372742 TTAAATTTGTTTTAA-A
1 TTAAATTTATTTTAAGA
* *
25372758 TTTAAATTTAATTTAAGT
1 -TTAAATTTATTTTAAGA
25372776 TTAAATTTATTTT
1 TTAAATTTATTTT
25372789 TAAATTTAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
16 1 0.03
17 39 0.98
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.58
Consensus pattern (17 bp):
TTAAATTTATTTTAAGA
Found at i:25372761 original size:6 final size:6
Alignment explanation
Indices: 25372752--25372814 Score: 65
Period size: 6 Copynumber: 10.2 Consensus size: 6
25372742 TTAAATTTGT
* **
25372752 TTTAAA TTTAAA TTT-AA TTTAAG TTTAAA TTTATT TTTAAA TTTAAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA
25372800 TTATTAAA TTTAAA T
1 -T-TTAAA TTTAAA T
25372815 AAATAAATAA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
5 5 0.11
6 32 0.68
7 4 0.09
8 4 0.09
9 2 0.04
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:25372767 original size:34 final size:35
Alignment explanation
Indices: 25372724--25372804 Score: 119
Period size: 34 Copynumber: 2.3 Consensus size: 35
25372714 TCGGGCCCCT
25372724 TTTAAATTTATTTTAAGATTAAATTT-GTTTTAAA
1 TTTAAATTTATTTTAAGATTAAATTTAGTTTTAAA
* * *
25372758 TTTAAATTTAATTTAAGTTTAAATTTATTTTTAAA
1 TTTAAATTTATTTTAAGATTAAATTTAGTTTTAAA
*
25372793 TTTAAAATTATT
1 TTTAAATTTATT
25372805 AAATTTAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
34 24 0.59
35 17 0.41
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.57
Consensus pattern (35 bp):
TTTAAATTTATTTTAAGATTAAATTTAGTTTTAAA
Found at i:25372770 original size:11 final size:11
Alignment explanation
Indices: 25372742--25372797 Score: 51
Period size: 12 Copynumber: 4.9 Consensus size: 11
25372732 TATTTTAAGA
**
25372742 TTAAATTTGTT
1 TTAAATTTAAT
25372753 TTAAATTTAAAT
1 TTAAATTT-AAT
25372765 TT-AATTTAAGT
1 TTAAATTTAA-T
*
25372776 TTAAATTTATTT
1 TTAAATTTA-AT
25372788 TTAAATTTAA
1 TTAAATTTAA
25372798 AATTATTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
10 2 0.05
11 16 0.43
12 19 0.51
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:25373525 original size:6 final size:6
Alignment explanation
Indices: 25373514--25373544 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
25373504 TATGAATATC
25373514 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT A
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT A
25373545 ACAGTAGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATTAAT
Found at i:25373591 original size:16 final size:16
Alignment explanation
Indices: 25373552--25373592 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
25373542 ATAACAGTAG
*
25373552 TAATAAATATTAATAAT
1 TAAT-AATATTAATAAA
25373569 TAATAATATTAATAAA
1 TAATAATATTAATAAA
*
25373585 TACTAATA
1 TAATAATA
25373593 ACAAAGAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (16 bp):
TAATAATATTAATAAA
Found at i:25374278 original size:69 final size:69
Alignment explanation
Indices: 25374163--25374293 Score: 210
Period size: 69 Copynumber: 1.9 Consensus size: 69
25374153 ATCATTTCCA
* * *
25374163 ATCCGCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTA-AGAGCAA
1 ATCCGCTTGAAATTGAAGTAAAGTGGATAAAAAGTCTTCATCTCTGAAATTGAAGTAGAGAGCAA
25374227 CGTC
66 CGTC
*
25374231 ATCCTCTTGAAATTGAAGTAAAGTTGGATAAAAAGTCTTCATCTCTGAAATTGAAGTAGAGAG
1 ATCCGCTTGAAATTGAAGTAAAG-TGGATAAAAAGTCTTCATCTCTGAAATTGAAGTAGAGAG
25374294 GATAACACGT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
68 21 0.37
69 32 0.56
70 4 0.07
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (69 bp):
ATCCGCTTGAAATTGAAGTAAAGTGGATAAAAAGTCTTCATCTCTGAAATTGAAGTAGAGAGCAA
CGTC
Found at i:25374355 original size:106 final size:105
Alignment explanation
Indices: 25374170--25374606 Score: 387
Period size: 106 Copynumber: 4.1 Consensus size: 105
25374160 CCAATCCGCT
* *
25374170 TGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCATCC
1 TGAAATTGAAGTAGAGAGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACATCATCC
25374235 TCTTGAAATTGAAGTAAAGTTGGATAAAAAGTCTTCATCTC
66 TCTTGAAATTGAAGTAAAG-TGGATAAAAAGTCTTCATCTC
25374276 TGAAATTGAAGTAGAGAGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACATCATCC
1 TGAAATTGAAGTAGAGAGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACATCATCC
* * * *
25374341 TCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTC
66 TCTTGAAATTGAAGTAAAGTGGATAAAAAGTCTTCATCTC
** ** * *
25374381 TGAAATTGAAGTA-AGA-G----CGACGTCACCCCCT-TGAAATTGAAGTAGAGTGGATAACACG
1 TGAAATTGAAGTAGAGAGGATAAC-ACGTCTTCATCTCTGAAATTGAAGTA-AG-AG-CAACA--
* ** ** * * *
25374439 TCTTTATCTCTGAAATTGAAGT-AA---GA-GCAACGTCATCCTCT-
60 TCATCCTCT-TGAAATTGAAGTAAAGTGGATAAAAAGTCTTCATCTC
* * *
25374480 TGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAAGAGTAACATCGTT
1 TGAAATTGAAGTAGAG-AGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACA-----
* ** *
25374545 TCCTATCCTCTTGAAATTGAAGTAAAACTGGATATCAAGTCTTTATCTC
60 T-C-ATCCTCTTGAAATTGAAGT-AAAGTGGATAAAAAGTCTTCATCTC
25374594 TGAAATTGAAGTA
1 TGAAATTGAAGTA
25374607 AAAGCAACGT
Statistics
Matches: 263, Mismatches: 41, Indels: 46
0.75 0.12 0.13
Matches are distributed among these distances:
99 27 0.10
100 21 0.08
101 3 0.01
102 5 0.02
103 6 0.02
104 11 0.04
105 52 0.20
106 96 0.37
107 13 0.05
108 4 0.02
109 2 0.01
112 2 0.01
113 8 0.03
114 13 0.05
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.30
Consensus pattern (105 bp):
TGAAATTGAAGTAGAGAGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACATCATCC
TCTTGAAATTGAAGTAAAGTGGATAAAAAGTCTTCATCTC
Found at i:25374385 original size:68 final size:68
Alignment explanation
Indices: 25374269--25374688 Score: 558
Period size: 68 Copynumber: 6.1 Consensus size: 68
25374259 TAAAAAGTCT
* *
25374269 TCAT-CTC-TGAAATTGAAGTAGAGAGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCA
1 TCATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCA
25374332 ACA
66 ACA
*
25374335 TCATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCG
1 TCATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCA
*
25374400 ACG
66 ACA
* *
25374403 TCACCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCA
1 TCATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCA
*
25374468 ACG
66 ACA
* * *
25374471 TCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAAGAGT
1 TCATCCTCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGC
25374536 AACA
65 AACA
* * * *
25374540 TCGTTTCCTATCCTCTTGAAATTGAAGTAAAACTGGATATCAAGTCTTTATCTCTGAAATTGAAG
1 -----T-C-ATCCTCTTGAAATTGAAGT-AGAGTGGATAACACGTCTTTATCTCTGAAATTGAAG
* *
25374605 TAAAAGCAACG
58 TAAGAGCAACA
*
25374616 TCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAC-TCCTTTATCTCTGAAATTGAAATAAGAG
1 TCATCCTCTTGAAATTGAAGTAGAG-TGGATAACACGT-CTTTATCTCTGAAATTGAAGTAAGAG
*
25374680 CAAGA
64 CAACA
25374685 TCAT
1 TCAT
25374689 TTCCTATCCT
Statistics
Matches: 313, Mismatches: 28, Indels: 23
0.86 0.08 0.06
Matches are distributed among these distances:
66 4 0.01
67 3 0.01
68 146 0.47
69 97 0.31
70 1 0.00
71 1 0.00
74 1 0.00
75 1 0.00
76 57 0.18
77 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.30
Consensus pattern (68 bp):
TCATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCA
ACA
Found at i:25374560 original size:76 final size:75
Alignment explanation
Indices: 25374276--25374739 Score: 439
Period size: 68 Copynumber: 6.5 Consensus size: 75
25374266 TCTTCATCTC
* * * *
25374276 TGAAATTGAAGTAGAG-AGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACA-----
1 TGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAG-AACATCGTT
25374335 T-C-ATCCTCT
65 TCCTATCCTCT
* *
25374344 TGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAG--CGA-CG--
1 TGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGAAC-ATCGTT
* *
25374403 T-C-ACCCCCT
65 TCCTATCCTCT
* * *
25374412 TGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAG--CAACG--T
1 TGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGAACATCGTTT
25374472 -C-ATCCTCT
66 CCTATCCTCT
* *
25374480 TGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAAGAGTAACATCGTT
1 TGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAG-AACATCGTT
25374545 TCCTATCCTCT
65 TCCTATCCTCT
** * * *
25374556 TGAAATTGAAGTAAAACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAA-A-AGCAACG--T
1 TGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGAACATCGTTT
25374617 -C-ATCCTCT
66 CCTATCCTCT
* * * * *
25374625 TGAAATTGAAGTAGAGTTGGATAAC-ACTCCTTTATCTCTGAAATTGAAATAAGAGCAAGATCAT
1 TGAAATTGAAGTAAAGTTGGATAACAAGT-CTTTATCTCTGAAATTGAAGTAAGAG-AACATCGT
25374689 TTCCTATCCTCT
64 TTCCTATCCTCT
* *
25374701 AGAAATTGAAGTAAAGTTGGATAGCAAAGTCTTTATCTC
1 TGAAATTGAAGTAAAGTTGGATAAC-AAGTCTTTATCTC
25374740 CCTGAAGAGC
Statistics
Matches: 344, Mismatches: 30, Indels: 35
0.84 0.07 0.09
Matches are distributed among these distances:
65 1 0.00
66 1 0.00
67 1 0.00
68 141 0.41
69 86 0.25
70 2 0.01
71 1 0.00
72 7 0.02
73 5 0.01
74 2 0.01
75 3 0.01
76 83 0.24
77 9 0.03
78 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (75 bp):
TGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGAACATCGTTT
CCTATCCTCT
Found at i:25374609 original size:38 final size:38
Alignment explanation
Indices: 25374480--25374609 Score: 115
Period size: 38 Copynumber: 3.4 Consensus size: 38
25374470 GTCATCCTCT
* ** * *
25374480 TGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTC
1 TGAAATTGAAGTAAAACTGGATATCAAGTCTTTATCTC
* * * *
25374518 TGAAATTGAAGTAAGAGT-AACATC--GT-TTCCTATCCTC
1 TGAAATTGAAGTAAAACTGGATATCAAGTCTT--TAT-CTC
25374555 TTGAAATTGAAGTAAAACTGGATATCAAGTCTTTATCTC
1 -TGAAATTGAAGTAAAACTGGATATCAAGTCTTTATCTC
25374594 TGAAATTGAAGTAAAA
1 TGAAATTGAAGTAAAA
25374610 GCAACGTCAT
Statistics
Matches: 72, Mismatches: 12, Indels: 16
0.72 0.12 0.16
Matches are distributed among these distances:
34 2 0.03
35 2 0.03
36 2 0.03
37 6 0.08
38 46 0.64
39 7 0.10
40 3 0.04
41 2 0.03
42 2 0.03
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (38 bp):
TGAAATTGAAGTAAAACTGGATATCAAGTCTTTATCTC
Found at i:25374615 original size:145 final size:143
Alignment explanation
Indices: 25374276--25374739 Score: 606
Period size: 145 Copynumber: 3.3 Consensus size: 143
25374266 TCTTCATCTC
* * * *
25374276 TGAAATTGAAGTAGAGA-GGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACATCATC
1 TGAAATTGAAGTA-AAATGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATC
*
25374340 CTCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAG--CGA-
65 CTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGAAC-AT
* *
25374401 CG--T-C-ACCCCCT
129 CGTTTCCTATCCTCT
* * *
25374412 TGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATCC
1 TGAAATTGAAGTAAAATGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATCC
*
25374477 TCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAAGAGTAACATC
66 TCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAG-AACATC
25374542 GTTTCCTATCCTCT
130 GTTTCCTATCCTCT
* *
25374556 TGAAATTGAAGTAAAACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAAAGCAACGTCATC
1 TGAAATTGAAGTAAAA-TGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATC
* * *
25374621 CTCTTGAAATTGAAGTAGAGTTGGATAAC-ACTCCTTTATCTCTGAAATTGAAATAAGAGCAAGA
65 CTCTTGAAATTGAAGTAGAGTTGGATAACAAGT-CTTTATCTCTGAAATTGAAGTAAGAG-AACA
*
25374685 TCATTTCCTATCCTCT
128 TCGTTTCCTATCCTCT
* * *
25374701 AGAAATTGAAGTAAAGTTGGATAGCAAAGTCTTTATCTC
1 TGAAATTGAAGTAAA-ATGGATAAC-AAGTCTTTATCTC
25374740 CCTGAAGAGC
Statistics
Matches: 291, Mismatches: 23, Indels: 18
0.88 0.07 0.05
Matches are distributed among these distances:
136 78 0.27
137 36 0.12
139 1 0.00
140 3 0.01
142 1 0.00
143 1 0.00
144 21 0.07
145 137 0.47
146 13 0.04
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (143 bp):
TGAAATTGAAGTAAAATGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATCC
TCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGAACATCG
TTTCCTATCCTCT
Found at i:25375048 original size:27 final size:27
Alignment explanation
Indices: 25375018--25375072 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
25375008 TTTTCGTTTA
*
25375018 ATTTAGAGTTAAATTGATTTTAAATTT
1 ATTTAAAGTTAAATTGATTTTAAATTT
* *
25375045 ATTTAAATTTAAATTTATTTTAAATTT
1 ATTTAAAGTTAAATTGATTTTAAATTT
25375072 A
1 A
25375073 AATTTAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (27 bp):
ATTTAAAGTTAAATTGATTTTAAATTT
Found at i:25375054 original size:6 final size:6
Alignment explanation
Indices: 25375036--25375135 Score: 82
Period size: 6 Copynumber: 16.8 Consensus size: 6
25375026 TTAAATTGAT
*
25375036 TTTAAA TTT--A TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA TTTAATTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA--A
* * ** * *
25375083 TTTAAA TTT-AC TTTGAA TTTAAA TTTAAA TAAAAA TTAAAA CATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA
25375131 TTTAA
1 TTTAA
25375136 CATTAAAAAA
Statistics
Matches: 76, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
4 4 0.05
5 8 0.11
6 54 0.71
7 4 0.05
8 6 0.08
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:25375054 original size:17 final size:17
Alignment explanation
Indices: 25375036--25375109 Score: 93
Period size: 17 Copynumber: 4.6 Consensus size: 17
25375026 TTAAATTGAT
25375036 TTTAAATTTA-TTTAAA
1 TTTAAATTTACTTTAAA
*
25375052 TTTAAATTTATTTTAAA
1 TTTAAATTTACTTTAAA
*
25375069 TTTAAATTTA-ATT--A
1 TTTAAATTTACTTTAAA
*
25375083 TTTAAATTTACTTTGAA
1 TTTAAATTTACTTTAAA
25375100 TTTAAATTTA
1 TTTAAATTTA
25375110 AATAAAAATT
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
14 11 0.21
15 2 0.04
16 12 0.23
17 27 0.52
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (17 bp):
TTTAAATTTACTTTAAA
Found at i:25375066 original size:11 final size:10
Alignment explanation
Indices: 25375026--25375103 Score: 51
Period size: 11 Copynumber: 7.9 Consensus size: 10
25375016 TAATTTAGAG
*
25375026 TTAAATTGATT
1 TTAAATTTA-T
25375037 TTAAATTTAT
1 TTAAATTTAT
25375047 TT-AA---AT
1 TTAAATTTAT
25375053 TTAAATTTATT
1 TTAAATTTA-T
25375064 TTAAATTTAAAT
1 TTAAATTT--AT
25375076 TT-AA-TTAT
1 TTAAATTTAT
25375084 TTAAATTTACT
1 TTAAATTTA-T
*
25375095 TTGAATTTA
1 TTAAATTTA
25375104 AATTTAAATA
Statistics
Matches: 55, Mismatches: 2, Indels: 20
0.71 0.03 0.26
Matches are distributed among these distances:
6 4 0.07
7 2 0.04
8 4 0.07
9 4 0.07
10 9 0.16
11 28 0.51
12 3 0.05
13 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (10 bp):
TTAAATTTAT
Found at i:25377237 original size:162 final size:161
Alignment explanation
Indices: 25376780--25377259 Score: 825
Period size: 161 Copynumber: 3.0 Consensus size: 161
25376770 AGTTCTCAAT
* * *
25376780 TTAGTACTTTGACTGTTTGATCGCACCAGAGGCTGCCACGTGTCATTTTTGGCTTATTTCTGTAT
1 TTAGTCCTTTGACTGTTTGACCGCACCAGAGGCTGCCACGTGTCATTTTTGGCTTATTTCTGCAT
* *
25376845 TTGGTCCCTGACATTTTTAATTTGTTTTAATTGAATCCCTAAATCAACTTTTATTTAATTACAAA
66 TTGGTCCCTGATATTTTTAATTTGTTTTAATTAAATCCCTAAATCAACTTTTATTTAATTACAAA
* *
25376910 ATTGGCTCGAGAATTTTTCAAGGTCTATAAA
131 ATTGGCCCGAGAATTTTTCAAGGTTTATAAA
*
25376941 TTAGTCCTTTCACTGTTTGACCGCACCAGAGGCTGCCACGTGTCATTTTTGGCTTATTTCTGCAT
1 TTAGTCCTTTGACTGTTTGACCGCACCAGAGGCTGCCACGTGTCATTTTTGGCTTATTTCTGCAT
* *
25377006 TTGGTCCCTGATATTTTTAATTTATTTTAATTAAATCCCTAAACCAACTTTTATTTAATTACAAA
66 TTGGTCCCTGATATTTTTAATTTGTTTTAATTAAATCCCTAAATCAACTTTTATTTAATTACAAA
25377071 ATTGGCCCGAGAATTTTTCAAGGTTTATAAA
131 ATTGGCCCGAGAATTTTTCAAGGTTTATAAA
25377102 TTAGTCCTTTGACTGTTTGACCGCACCAGAGGCTGCCACGTGTCATTTTTTGGCTTATTTCTGCA
1 TTAGTCCTTTGACTGTTTGACCGCACCAGAGGCTGCCACGTGTCA-TTTTTGGCTTATTTCTGCA
* * *
25377167 TTTGATCCCTGATATTTTCAATTTGTTTTAATTTAATCCCTAAATCAACTTTTATTTAATTACAA
65 TTTGGTCCCTGATATTTTTAATTTGTTTTAATTAAATCCCTAAATCAACTTTTATTTAATTACAA
*
25377232 AATTGGCCCAAGAATTTTTCAAGGTTTA
130 AATTGGCCCGAGAATTTTTCAAGGTTTA
25377260 CAATTTAATC
Statistics
Matches: 301, Mismatches: 17, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
161 195 0.65
162 106 0.35
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.42
Consensus pattern (161 bp):
TTAGTCCTTTGACTGTTTGACCGCACCAGAGGCTGCCACGTGTCATTTTTGGCTTATTTCTGCAT
TTGGTCCCTGATATTTTTAATTTGTTTTAATTAAATCCCTAAATCAACTTTTATTTAATTACAAA
ATTGGCCCGAGAATTTTTCAAGGTTTATAAA
Found at i:25377411 original size:29 final size:28
Alignment explanation
Indices: 25377349--25377421 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 28
25377339 CCAAACAGTC
*
25377349 CAAAAATTACATTTTGACCCCAAAATTT
1 CAAAAATTACATTTTGACCCCAAAACTT
* *
25377377 CTAAAAATTACTATTTT-ACCCTCGAACCTT
1 C-AAAAATTAC-ATTTTGACCC-CAAAACTT
*
25377407 CAAAAATTCCATTTT
1 CAAAAATTACATTTT
25377422 TAACCCCGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
28 6 0.16
29 21 0.55
30 11 0.29
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.36
Consensus pattern (28 bp):
CAAAAATTACATTTTGACCCCAAAACTT
Found at i:25377558 original size:117 final size:118
Alignment explanation
Indices: 25377379--25377635 Score: 430
Period size: 117 Copynumber: 2.2 Consensus size: 118
25377369 CAAAATTTCT
*
25377379 AAAAATTACTATTTTACCCTCGAACCTTCAAAAATTCCATTTTTAACCCCGATTTCACCAAAAAT
1 AAAAATTACTATTTTACCCCCGAACCTTCAAAAATTCCATTTTTAACCCCGATTTCACCAAAAAT
* *
25377444 TACCATTTTACCC-CTGAACTTTCCAAAATTCCATTTTTGATCCCGATTTCACC
66 TACCATTTTACCCTC-GAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
* *
25377497 AAAAATTACTATTTTACCCCCGAA-CTTCTAAAATTCCATTTTTAACCCCGATTTCATCAAAAAT
1 AAAAATTACTATTTTACCCCCGAACCTTCAAAAATTCCATTTTTAACCCCGATTTCACCAAAAAT
25377561 TACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
66 TACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
*
25377614 -AAAATTACCATTTTACCCCCGA
1 AAAAATTACTATTTTACCCCCGA
25377636 GTATCCAAAA
Statistics
Matches: 132, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
116 21 0.16
117 87 0.66
118 24 0.18
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (118 bp):
AAAAATTACTATTTTACCCCCGAACCTTCAAAAATTCCATTTTTAACCCCGATTTCACCAAAAAT
TACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
Found at i:25377662 original size:117 final size:117
Alignment explanation
Indices: 25377379--25377671 Score: 394
Period size: 117 Copynumber: 2.5 Consensus size: 117
25377369 CAAAATTTCT
* * * * * *
25377379 AAAAATTACTATTTTACCCTCGAACCTTCAAAAATTCCATTTTTAACCCCGATTTCACCAAAAAT
1 AAAAATTACCATTTTACCCCCGAA-CTTCCAAAATCCCATTTTCAACCCCGATTTCATCAAAAAT
* *
25377444 TACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTGATCCCGATTTCACC
65 TACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
* * * *
25377497 AAAAATTACTATTTTACCCCCGAACTTCTAAAATTCCATTTTTAACCCCGATTTCATCAAAAATT
1 AAAAATTACCATTTTACCCCCGAACTTCCAAAATCCCATTTTCAACCCCGATTTCATCAAAAATT
25377562 ACCATTTTA-CCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
66 ACCATTTTACCCCT-GAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
* * *
25377614 -AAAATTACCATTTTACCCCCG-AGTATCCAAAAGTCCCGTTTTCCACCCCGATTTCATC
1 AAAAATTACCATTTTACCCCCGAACT-TCCAAAA-TCCCATTTTCAACCCCGATTTCATC
25377672 GTTTATCAAT
Statistics
Matches: 160, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
115 2 0.01
116 30 0.19
117 105 0.66
118 23 0.14
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.34
Consensus pattern (117 bp):
AAAAATTACCATTTTACCCCCGAACTTCCAAAATCCCATTTTCAACCCCGATTTCATCAAAAATT
ACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
Found at i:25377669 original size:58 final size:59
Alignment explanation
Indices: 25377379--25377635 Score: 401
Period size: 59 Copynumber: 4.4 Consensus size: 59
25377369 CAAAATTTCT
* * * *
25377379 AAAAATTACTATTTTACCCTCGAACCTTCAAAAATTCCATTTTTAACCCCGATTTCACC
1 AAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
* * *
25377438 AAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTGATCCCGATTTCACC
1 AAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
* * *
25377497 AAAAATTACTATTTTACCCCCGAAC-TTCTAAAATTCCATTTTTAACCCCGATTTCATC
1 AAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
*
25377555 AAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
1 AAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
25377614 -AAAATTACCATTTTACCCCCGA
1 AAAAATTACCATTTTACCCCCGA
25377636 GTATCCAAAA
Statistics
Matches: 179, Mismatches: 18, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
58 73 0.41
59 106 0.59
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (59 bp):
AAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
Found at i:25379494 original size:29 final size:30
Alignment explanation
Indices: 25379448--25379740 Score: 202
Period size: 29 Copynumber: 9.9 Consensus size: 30
25379438 CCCTAAAGGT
*
25379448 CCCT-AAACTATCCAAAAATTACATTTTTA
1 CCCTCAAACTTTCCAAAAATTACATTTTTA
* * *
25379477 CCCTCAATCTTTCC-AAAATTCCATTTTAA
1 CCCTCAAACTTTCCAAAAATTACATTTTTA
* *
25379506 CCCT-AAACTTTCCAAAAATTACATCTTAA
1 CCCTCAAACTTTCCAAAAATTACATTTTTA
*
25379535 CCCTCAAACTTTTCAAAAATTACCA-TTTTA
1 CCCTCAAACTTTCCAAAAATTA-CATTTTTA
* *
25379565 CCCCCCAAAC-TTCCAAAAATTCCATTTTTGA
1 -CCCTCAAACTTTCCAAAAATTACATTTTT-A
* *
25379596 CCC-C-GATTTCTCCAAAAATTACCA-TTTTA
1 CCCTCAAACTT-TCCAAAAATTA-CATTTTTA
*
25379625 CCCTCAAAC-TTCCAAAAATTCCATTTTTGA
1 CCCTCAAACTTTCCAAAAATTACATTTTT-A
** *
25379655 -CCT-TGATTTTCCAAAAATTACCA-TTTTA
1 CCCTCAAACTTTCCAAAAATTA-CATTTTTA
* * * *
25379683 TCCC-CAGA-TGTCTAAAAATTCCATTTTTGA
1 -CCCTCAAACTTTCCAAAAATTACATTTTT-A
* *
25379713 CCCT-GAACTTTCCCAAAATTACCATTTT
1 CCCTCAAACTTTCCAAAAATTA-CATTTT
25379741 ACCATCGAGT
Statistics
Matches: 207, Mismatches: 33, Indels: 46
0.72 0.12 0.16
Matches are distributed among these distances:
28 15 0.07
29 96 0.46
30 76 0.37
31 20 0.10
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.35
Consensus pattern (30 bp):
CCCTCAAACTTTCCAAAAATTACATTTTTA
Found at i:25379700 original size:58 final size:57
Alignment explanation
Indices: 25379452--25379743 Score: 290
Period size: 58 Copynumber: 5.0 Consensus size: 57
25379442 AAAGGTCCCT
* * *
25379452 AAACTATCCAAAAATTACATTTTT-ACCCTCAATCTTTCC-AAAATT-CCATTTTAACCCT
1 AAACT-TCCAAAAATTCCATTTTTGACCCT-GAT-TTTCCAAAAATTACCATTTT-ACCCC
* * * *
25379510 AAACTTTCCAAAAATTACA-TCTTAACCCTCAAACTTTT-CAAAAATTACCATTTTACCCCCC
1 AAAC-TTCCAAAAATTCCATTTTTGACCCT--GA-TTTTCCAAAAATTACCATTTTA--CCCC
*
25379571 AAACTTCCAAAAATTCCATTTTTGACCCCGATTTCTCCAAAAATTACCATTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTTGACCCTGATTT-TCCAAAAATTACCATTTTACCC-C
*
25379630 AAACTTCCAAAAATTCCATTTTTGACCTTGATTTTCCAAAAATTACCATTTTATCCCC
1 AAACTTCCAAAAATTCCATTTTTGACCCTGATTTTCCAAAAATTACCATTTTA-CCCC
* * * *
25379688 AGA-TGTCTAAAAATTCCATTTTTGACCCTGAACTTTCCCAAAATTACCATTTTACC
1 AAACT-TCCAAAAATTCCATTTTTGACCCTG-ATTTTCCAAAAATTACCATTTTACC
25379744 ATCGAGTGAC
Statistics
Matches: 204, Mismatches: 15, Indels: 30
0.82 0.06 0.12
Matches are distributed among these distances:
57 4 0.02
58 76 0.37
59 72 0.35
60 38 0.19
61 14 0.07
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.35
Consensus pattern (57 bp):
AAACTTCCAAAAATTCCATTTTTGACCCTGATTTTCCAAAAATTACCATTTTACCCC
Found at i:25379760 original size:58 final size:55
Alignment explanation
Indices: 25379580--25379769 Score: 168
Period size: 59 Copynumber: 3.3 Consensus size: 55
25379570 CAAACTTCCA
* *
25379580 AAAATTCCATTTTTGACCCCGATTTCTCCAAAAATTACCATTTTACCCTCAAACT-TCC
1 AAAATTCCATTTTTGACCCTGATTTC-CC-AAAATTACCATTTTA-CCTC-AAGTGTCC
* * * *
25379638 AAAAATTCCATTTTTGACCTTGATTTTCCAAAAATTACCATTTTATCC-CCAGATGTCTA
1 -AAAATTCCATTTTTGACCCTGA-TTTCCCAAAATTACCATTTTA-CCTCAAG-TGTC-C
* *
25379697 AAAATTCCATTTTTGACCCTGAACTTTCCCAAAATTACCATTTTACCATCGAGTGACC
1 AAAATTCCATTTTTGACCCTG-A-TTTCCCAAAATTACCATTTTACC-TCAAGTGTCC
*
25379755 GAAATTACCATTTTT
1 AAAATT-CCATTTTT
25379770 CCCTCGAGTA
Statistics
Matches: 109, Mismatches: 14, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
56 1 0.01
57 2 0.02
58 46 0.42
59 53 0.49
60 7 0.06
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36
Consensus pattern (55 bp):
AAAATTCCATTTTTGACCCTGATTTCCCAAAATTACCATTTTACCTCAAGTGTCC
Found at i:25380143 original size:97 final size:99
Alignment explanation
Indices: 25379998--25380197 Score: 282
Period size: 97 Copynumber: 2.0 Consensus size: 99
25379988 TTCATGAAAA
* * *
25379998 CTTTAAAATCGAGGCAATGTTCTTCTATTTTGAGTTTTGAAAATTTGTGCCTTAACTTACTAGGT
1 CTTTAAAATCGAGGCAAGGTTCTTCTATTCTGAGTTCTGAAAATTTGTGCCTTAACTTACTAGGT
*
25380063 GCAATTTTTCCTCAAATCGAAATAATCGAATA-C
66 GCAACTTTTCCTCAAATCGAAATAATCGAATATC
*
25380096 CTTT-AAATCGAGGCAAGGTTTCTT-TATCTCTGA-TTCTGAAAATTTGTGTCTTAACTTACTAG
1 CTTTAAAATCGAGGCAAGG-TTCTTCTAT-TCTGAGTTCTGAAAATTTGTGCCTTAACTTACTAG
* * *
25380158 GTGCGACTTTTCTTCAAATCGAGATAATCGAATATC
64 GTGCAACTTTTCCTCAAATCGAAATAATCGAATATC
25380194 CTTT
1 CTTT
25380198 TCCAAAATTT
Statistics
Matches: 91, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
97 73 0.80
98 18 0.20
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (99 bp):
CTTTAAAATCGAGGCAAGGTTCTTCTATTCTGAGTTCTGAAAATTTGTGCCTTAACTTACTAGGT
GCAACTTTTCCTCAAATCGAAATAATCGAATATC
Found at i:25392744 original size:3 final size:3
Alignment explanation
Indices: 25392736--25392760 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
25392726 TTTTTTGATT
25392736 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
25392761 GTGTGAACTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:25397015 original size:7 final size:8
Alignment explanation
Indices: 25396986--25397014 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
25396976 GATCTCTCAA
25396986 AAAAAATT
1 AAAAAATT
25396994 AAAAAATT
1 AAAAAATT
25397002 AAAAAATT
1 AAAAAATT
25397010 AAAAA
1 AAAAA
25397015 TATTTATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (8 bp):
AAAAAATT
Found at i:25398069 original size:16 final size:16
Alignment explanation
Indices: 25398020--25398072 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
25398010 CAATTATTTT
* *
25398020 ATTTTGTTATTATTAG
1 ATTTTGTTATTATCAA
**
25398036 ATTTTGTTACAATCAA
1 ATTTTGTTATTATCAA
*
25398052 ATTTTGTTATTATGAA
1 ATTTTGTTATTATCAA
25398068 ATTTT
1 ATTTT
25398073 TTCTAGATTA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.30, C:0.04, G:0.09, T:0.57
Consensus pattern (16 bp):
ATTTTGTTATTATCAA
Found at i:25399033 original size:16 final size:16
Alignment explanation
Indices: 25399010--25399081 Score: 117
Period size: 16 Copynumber: 4.5 Consensus size: 16
25399000 CGTTTGGTTC
25399010 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
25399026 GGTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
* *
25399042 ACTGTAATGGAATATA
1 GCTGTAATGGAATAGA
25399058 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
25399074 GCTGTAAT
1 GCTGTAAT
25399082 CAGTAATTCA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.38, C:0.06, G:0.29, T:0.28
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:25399122 original size:46 final size:44
Alignment explanation
Indices: 25399063--25399156 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
25399053 ATATAGCTGT
* *
25399063 AATGGAATAGAGCTGTAATCAGTAATTCAAT-TGTTTGGTTGATTGG
1 AATGGAATAGAGCTGTAAT-AAT-ATTC-ATGTGTTTGGTTGAATGG
*
25399109 AATGGAATAGAGCTGTAATAATATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAGCTGTAATAATATTCATGTGTTTGGTTGAATGG
25399153 AATG
1 AATG
25399157 ATGCTGTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 1 0.02
44 22 0.50
45 2 0.05
46 19 0.43
ACGTcount: A:0.31, C:0.05, G:0.27, T:0.37
Consensus pattern (44 bp):
AATGGAATAGAGCTGTAATAATATTCATGTGTTTGGTTGAATGG
Found at i:25399316 original size:58 final size:55
Alignment explanation
Indices: 25399249--25399394 Score: 168
Period size: 58 Copynumber: 2.5 Consensus size: 55
25399239 AATTTTAATG
*
25399249 ATTATTATTAAATATAATTGAATAAAAATAT-TAATTTATTTAATTATATTTTAACATA
1 ATTATTATTAAATATAATT-AATAAAAATATGTAATTTA-ATAA-TAT-TTTTAACATA
* *
25399307 ATTATTATTAAATACAATTTAATAAAATAATATGTAATTTAATAATATTTTTAATATA
1 ATTATTATTAAATATAA-TTAAT-AAA-AATATGTAATTTAATAATATTTTTAACATA
*
25399365 ATTATTATTAAAATATGAATTAGTAAAAAT
1 ATTATTATT-AAATAT-AATTAATAAAAAT
25399395 TATAATATAT
Statistics
Matches: 77, Mismatches: 5, Indels: 13
0.81 0.05 0.14
Matches are distributed among these distances:
57 3 0.04
58 40 0.52
59 17 0.22
60 10 0.13
61 7 0.09
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (55 bp):
ATTATTATTAAATATAATTAATAAAAATATGTAATTTAATAATATTTTTAACATA
Found at i:25404580 original size:35 final size:37
Alignment explanation
Indices: 25404541--25404616 Score: 111
Period size: 38 Copynumber: 2.1 Consensus size: 37
25404531 TGCAGCATAA
* *
25404541 CAATCCAAAA-TATC-GCTATCATTCATAAGTTTAGC
1 CAATCCAAAACTAACAGCTAACATTCATAAGTTTAGC
25404576 CAATCCAAAAGCTAACAGCTAACATTCATAAGTTTAGC
1 CAATCCAAAA-CTAACAGCTAACATTCATAAGTTTAGC
25404614 CAA
1 CAA
25404617 CCTTTTTTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
35 10 0.28
37 3 0.08
38 23 0.64
ACGTcount: A:0.41, C:0.24, G:0.09, T:0.26
Consensus pattern (37 bp):
CAATCCAAAACTAACAGCTAACATTCATAAGTTTAGC
Found at i:25408779 original size:6 final size:6
Alignment explanation
Indices: 25408758--25408817 Score: 54
Period size: 6 Copynumber: 10.5 Consensus size: 6
25408748 GTTAAAATGG
* * * *
25408758 ATTTAA ATTT-A TTTTAA ATTTAA ATTT-A CTCTAA ATTTAA GTTT-A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
*
25408803 ATTAAA ATTTAA ATT
1 ATTTAA ATTTAA ATT
25408818 GATATTAACC
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
5 10 0.24
6 31 0.76
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (6 bp):
ATTTAA
Found at i:25408780 original size:17 final size:17
Alignment explanation
Indices: 25408758--25408817 Score: 75
Period size: 17 Copynumber: 3.5 Consensus size: 17
25408748 GTTAAAATGG
*
25408758 ATTTAAATTTATTTTAA
1 ATTTAAATTTAATTTAA
* *
25408775 ATTTAAATTTACTCTAA
1 ATTTAAATTTAATTTAA
* *
25408792 ATTTAAGTTTAATTAAA
1 ATTTAAATTTAATTTAA
25408809 ATTTAAATT
1 ATTTAAATT
25408818 GATATTAACC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (17 bp):
ATTTAAATTTAATTTAA
Found at i:25409682 original size:12 final size:12
Alignment explanation
Indices: 25409661--25409691 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
25409651 AATATAATAT
*
25409661 TAATATTTTTAA
1 TAATAATTTTAA
25409673 TAATAATTTTAA
1 TAATAATTTTAA
25409685 TAATAAT
1 TAATAAT
25409692 AAAAAAGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAATAATTTTAA
Found at i:25409688 original size:15 final size:15
Alignment explanation
Indices: 25409635--25409693 Score: 61
Period size: 15 Copynumber: 4.1 Consensus size: 15
25409625 AAGAGTTATA
*
25409635 AATTTTAATAGTAAT
1 AATTTTAATAATAAT
* * *
25409650 AAATATAATATTAAT
1 AATTTTAATAATAAT
25409665 -ATTTT--TAATAAT
1 AATTTTAATAATAAT
25409677 AATTTTAATAATAAT
1 AATTTTAATAATAAT
25409692 AA
1 AA
25409694 AAAAGAGAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
12 6 0.17
13 5 0.14
14 3 0.09
15 21 0.60
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (15 bp):
AATTTTAATAATAAT
Found at i:25410617 original size:29 final size:29
Alignment explanation
Indices: 25410524--25410626 Score: 100
Period size: 30 Copynumber: 3.5 Consensus size: 29
25410514 CTAAATTGTT
* * **
25410524 CAAAAATTATATTTTAACCTCAAAACTTTT
1 CAAAAATTACATTTTAACCCCAAAAC-TAC
** *
25410554 TGAAAATTACATTTTAACCCTAAAACTAC
1 CAAAAATTACATTTTAACCCCAAAACTAC
25410583 CAAAAATTACTATTTTAACCCCAAAACT-C
1 CAAAAATTAC-ATTTTAACCCCAAAACTAC
* *
25410612 CCAAAATTCCATTTT
1 CAAAAATTACATTTT
25410627 TGACCTATAT
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
28 5 0.08
29 18 0.30
30 37 0.62
ACGTcount: A:0.43, C:0.22, G:0.01, T:0.34
Consensus pattern (29 bp):
CAAAAATTACATTTTAACCCCAAAACTAC
Found at i:25410627 original size:29 final size:30
Alignment explanation
Indices: 25410556--25410627 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 30
25410546 AAACTTTTTG
*
25410556 AAAATTACA-TTTTAACCCTAAAACTACCA
1 AAAATTACATTTTTAACCCCAAAACTACCA
*
25410585 AAAATTAC-TATTTTAACCCCAAAACT-CCC
1 AAAATTACAT-TTTTAACCCCAAAACTACCA
*
25410614 AAAATTCCATTTTT
1 AAAATTACATTTTT
25410628 GACCTATATT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
29 21 0.57
30 16 0.43
ACGTcount: A:0.43, C:0.25, G:0.00, T:0.32
Consensus pattern (30 bp):
AAAATTACATTTTTAACCCCAAAACTACCA
Found at i:25410736 original size:58 final size:57
Alignment explanation
Indices: 25410585--25410860 Score: 279
Period size: 58 Copynumber: 4.7 Consensus size: 57
25410575 AAAACTACCA
* * * *
25410585 AAAATTACTATTTTAACCCCAAAAC-TCCCAAAATTCCATTTTTGACCT-ATATTTTACC
1 AAAATTACCATTTT-ACCCC-AAACTTTCCAAAATTCCATTTTTAACCTCA-ATTTCACC
* * * **
25410643 AAAAAATCACCATTTGACCCTCGAACTTTCCAAAATTCCATTTTTAACCTTGATTTCACC
1 --AAAATTACCATTTTACCC-CAAACTTTCCAAAATTCCATTTTTAACCTCAATTTCACC
* * * * *
25410703 AAAATTGCCGTTTTACCCTTAAACTTTCTAAAATCCCATTTTTAACCTCAATTTCACC
1 AAAATTACCATTTTACCC-CAAACTTTCCAAAATTCCATTTTTAACCTCAATTTCACC
* *
25410761 AAAAATTACCATTTTACCCCGAACTTTCCAAAA-TCTCATTTTTAACCTCAATTTTACC
1 -AAAATTACCATTTTACCCCAAACTTTCCAAAATTC-CATTTTTAACCTCAATTTCACC
* *
25410819 AAAATTACCATTTTACCCCCAAACTTTCCACAATTCAATTTT
1 AAAATTACCATTTTA-CCCCAAACTTTCCAAAATTCCATTTT
25410861 GACTTCGATT
Statistics
Matches: 181, Mismatches: 28, Indels: 16
0.80 0.12 0.07
Matches are distributed among these distances:
57 16 0.09
58 100 0.55
59 25 0.14
60 40 0.22
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.36
Consensus pattern (57 bp):
AAAATTACCATTTTACCCCAAACTTTCCAAAATTCCATTTTTAACCTCAATTTCACC
Found at i:25410820 original size:116 final size:116
Alignment explanation
Indices: 25410585--25410897 Score: 346
Period size: 116 Copynumber: 2.7 Consensus size: 116
25410575 AAAACTACCA
* * *
25410585 AAAATTACTATTTTAACCCCAAAAC-TCCCAAAATTCCATTTTTGACCT-ATATTTTACCAAAAA
1 AAAATTACCATTTT-ACCCCCAAACTTTCCAAAA-TCCATTTTTGACCTCA-ATTTTACC-AAAA
* * **
25410648 ATCACCATTTGACCCTCGAACTTTCCAAAATTCCATTTTTAACCTTGATTTCACC
62 ATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCTCAATTTCACC
* * ** * * *
25410703 AAAATTGCCGTTTTACCCTTAAACTTTCTAAAATCCCATTTTTAACCTCAATTTCACCAAAAATT
1 AAAATTACCATTTTACCCCCAAACTTTCCAAAAT-CCATTTTTGACCTCAATTTTACCAAAAATT
*
25410768 ACCATTTTACCC-CGAACTTTCCAAAA-TCTCATTTTTAACCTCAATTTTACC
65 ACCATTTTACCCTCGAACTTTCCAAAATTC-CATTTTTAACCTCAATTTCACC
* * * * * *
25410819 AAAATTACCATTTTACCCCCAAACTTTCCACAATTCAATTTTGACTTCGATTTTATCAAAAATTA
1 AAAATTACCATTTTACCCCCAAACTTTCCAAAATCCATTTTTGACCTCAATTTTACCAAAAATTA
*
25410884 CCATTTTGCCCTCG
66 CCATTTTACCCTCG
25410898 GGCGTCCAAA
Statistics
Matches: 162, Mismatches: 28, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
115 36 0.22
116 63 0.39
117 26 0.16
118 36 0.22
119 1 0.01
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.36
Consensus pattern (116 bp):
AAAATTACCATTTTACCCCCAAACTTTCCAAAATCCATTTTTGACCTCAATTTTACCAAAAATTA
CCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCTCAATTTCACC
Found at i:25410833 original size:29 final size:29
Alignment explanation
Indices: 25410580--25410890 Score: 106
Period size: 29 Copynumber: 10.6 Consensus size: 29
25410570 ACCCTAAAAC
* * ***
25410580 TACCAAAAATTACTATTTTAACCCCAAAAC
1 TACC-AAAATTACCATTTTAACCTCAATTT
* *
25410610 TCCCAAAATT-CCATTTTTGACCT-ATATTT
1 TACCAAAATTACCA-TTTTAACCTCA-ATTT
* * * *
25410639 TACCAAAAAATCACCATTTGACCCTCGAACTT
1 TACC--AAAATTACCATTTTAACCTC-AATTT
**
25410671 T-CCAAAATT-CCATTTTTAACCTTGATTT
1 TACCAAAATTACCA-TTTTAACCTCAATTT
* * * * * *
25410699 CACCAAAATTGCCGTTTTACCCTTAAACTT
1 TACCAAAATTACCATTTTAACC-TCAATTT
* *
25410729 T-CTAAAA-TCCCATTTTTAACCTCAATTT
1 TACCAAAATTACCA-TTTTAACCTCAATTT
* * *
25410757 CACCAAAAATTACCATTTT-ACCCCGAACTT
1 TACC-AAAATTACCATTTTAACCTC-AATTT
25410787 T-CCAAAA-T-CTCATTTTTAACCTCAATTT
1 TACCAAAATTAC-CA-TTTTAACCTCAATTT
* * *
25410815 TACCAAAATTACCATTTTACCCCCAAACTT
1 TACCAAAATTACCATTTTAACCTC-AATTT
* * * * *
25410845 T-CCACAATT-CAATTTTGACTTCGATTT
1 TACCAAAATTACCATTTTAACCTCAATTT
*
25410872 TATCAAAAATTACCATTTT
1 TA-CCAAAATTACCATTTT
25410891 GCCCTCGGGC
Statistics
Matches: 201, Mismatches: 54, Indels: 52
0.65 0.18 0.17
Matches are distributed among these distances:
26 1 0.00
27 7 0.03
28 38 0.19
29 94 0.47
30 35 0.17
31 18 0.09
32 7 0.03
33 1 0.00
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.36
Consensus pattern (29 bp):
TACCAAAATTACCATTTTAACCTCAATTT
Found at i:25410881 original size:58 final size:57
Alignment explanation
Indices: 25410583--25410890 Score: 271
Period size: 58 Copynumber: 5.3 Consensus size: 57
25410573 CTAAAACTAC
* * * *
25410583 CAAAAATTACTATTTTAACCCCAAAAC-TCCCAAAATTCCATTTTTGACCT-ATATTTTA
1 CAAAAATTACCATTTT-ACCCCCAAACTTTCCAAAATT-CATTTTTAACCTCA-ATTTTA
* * * * ** *
25410641 CCAAAAAATCACCATTTGACCCTCGAACTTTCCAAAATTCCATTTTTAACCTTGATTTCA
1 -C-AAAAATTACCATTTTACCCCCAAACTTTCCAAAATT-CATTTTTAACCTCAATTTTA
* * * ** * * *
25410701 CCAAAATTGCCGTTTTACCCTTAAACTTTCTAAAATCCCATTTTTAACCTCAATTTCA
1 CAAAAATTACCATTTTACCCCCAAACTTTCCAAAAT-TCATTTTTAACCTCAATTTTA
*
25410759 CCAAAAATTACCATTTTA-CCCCGAACTTTCCAAAATCTCATTTTTAACCTCAATTTTA
1 -CAAAAATTACCATTTTACCCCCAAACTTTCCAAAAT-TCATTTTTAACCTCAATTTTA
* * * * * *
25410817 CCAAAATTACCATTTTACCCCCAAACTTTCCACAATTCAATTTTGACTTCGATTTTA
1 CAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCATTTTTAACCTCAATTTTA
25410874 TCAAAAATTACCATTTT
1 -CAAAAATTACCATTTT
25410891 GCCCTCGGGC
Statistics
Matches: 204, Mismatches: 38, Indels: 15
0.79 0.15 0.06
Matches are distributed among these distances:
57 33 0.16
58 110 0.54
59 23 0.11
60 38 0.19
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.36
Consensus pattern (57 bp):
CAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCATTTTTAACCTCAATTTTA
Found at i:25423379 original size:200 final size:200
Alignment explanation
Indices: 25423027--25423868 Score: 1274
Period size: 200 Copynumber: 4.2 Consensus size: 200
25423017 AACAAACAGT
* * *
25423027 GAGGCGATAATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCT-AAAAGCGAGCAAA
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACA-CGAGCAAA
* * *
25423091 TCTTCGAACCCAACTTCCTGATGAGACACTGAGAAGCGGGCCGAAACAATAAAATGGTTAGCTTC
65 TCTTCGAACCCAACTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTC
*
25423156 CTGATGAGATACAGAGAAGTGGACCAAATTTGTCTTCCTGAGGAGATCCAGAGAAGCAAATTAAA
130 CTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCAAATTAAA
25423221 ACAACA
195 ACAACA
*
25423227 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCCAAT
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCAAAT
* * *
25423292 CTTCGTACCCAGCTTCCTGATGAGACATTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
66 CTTCGAACCCAACTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
* *
25423357 TGATGAGATACAGAGAAGTGGACCAAATTTGTCTTCTTGAGGAGATCCAGAGAAGCAAATTAAAA
131 TGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCAAATTAAAA
25423422 CAACA
196 CAACA
* *
25423427 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAATGCTCAACACGAGCCAAT
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCAAAT
* *
25423492 CTTCGTACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
66 CTTCGAACCCAACTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
* * * *
25423557 TAATGAGACACAGAGAAATGGACCAAATTCATCTTCCTGAGGAGATCCAGAGAAGCAAATTAAAA
131 TGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCAAATTAAAA
**
25423622 CAAGT
196 CAACA
* ** * ***
25423627 GAGGTGACCATCTTCCTGATGAGACACAGAGAAGAATACCAACTCAACGCTCAATGGGAGCAAAT
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCAAAT
* *
25423692 CTTCGAACCCAACTTCCTGATGAGACATTGAGAAGCAGGTCGAAGCAATAAAAAGGTTAGCTTCC
66 CTTCGAACCCAACTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
* * *
25423757 TGATGAGATACAGAGAAGTGGACCGAATTCGTCTTCCTGAGGAGATTCAGAGAAGCGAATTAAAA
131 TGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCAAATTAAAA
*
25423822 CAGATA
196 CA-ACA
** * * *
25423828 -ATTACGGTCATCTTCCTGATAAGACACAGAGAAGAAGACCA
1 GA-GGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCA
25423869 GGTCAATGAA
Statistics
Matches: 589, Mismatches: 50, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
200 553 0.94
201 36 0.06
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (200 bp):
GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCAAAT
CTTCGAACCCAACTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
TGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCAAATTAAAA
CAACA
Found at i:25424256 original size:17 final size:17
Alignment explanation
Indices: 25424234--25424293 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
25424224 GTTAAAATGG
*
25424234 ATTTAAATTTATTTTAA
1 ATTTAAATTTAATTTAA
** *
25424251 ATTTAAATTTGCTCTAA
1 ATTTAAATTTAATTTAA
* *
25424268 ATTTAAGTTTAATTGAA
1 ATTTAAATTTAATTTAA
25424285 ATTTAAATT
1 ATTTAAATT
25424294 GATATTAACC
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (17 bp):
ATTTAAATTTAATTTAA
Found at i:25425141 original size:15 final size:15
Alignment explanation
Indices: 25425117--25425159 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
25425107 TTATAAGTTT
*
25425117 TAATAGTAATAAATA
1 TAATAATAATAAATA
* * *
25425132 TAATATTAATAATTT
1 TAATAATAATAAATA
25425147 TAATAATAATAAA
1 TAATAATAATAAA
25425160 AAAGAGAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (15 bp):
TAATAATAATAAATA
Found at i:25426188 original size:60 final size:58
Alignment explanation
Indices: 25426093--25426264 Score: 152
Period size: 60 Copynumber: 2.9 Consensus size: 58
25426083 TAAACTGTTC
* * * * *
25426093 AAAAATTA-TATTTTAACCTCAAAACTTTTTGAAAATTACATTTTGACCCTCGAACT-CCTC
1 AAAAAATACTATTTTGACCCCAAAAC-TTCT-AAAATTACATTTTGA-CCTCGAACTACC-A
** * *
25426153 TGAAATTAC-ATTTTTGACCCCAAAACTTCTAAAAATTATATTTTGACCTCGAAACTACCA
1 AAAAAATACTA-TTTTGACCCCAAAACTTCT-AAAATTACATTTTGACCTCG-AACTACCA
* *
25426213 AAAAAATACTATTTTGACCCCAAAACTTCTAAAATTCCATTTTTAACCTCGA
1 AAAAAATACTATTTTGACCCCAAAACTTCTAAAATTACA-TTTTGACCTCGA
25426265 TTTTACCAAA
Statistics
Matches: 92, Mismatches: 14, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
59 13 0.14
60 63 0.68
61 16 0.17
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (58 bp):
AAAAAATACTATTTTGACCCCAAAACTTCTAAAATTACATTTTGACCTCGAACTACCA
Found at i:25426239 original size:31 final size:29
Alignment explanation
Indices: 25426164--25426239 Score: 89
Period size: 31 Copynumber: 2.6 Consensus size: 29
25426154 GAAATTACAT
* * *
25426164 TTTTGACCCCAAAACTTCTAAAAATTATA
1 TTTTGACCCCAAAACTCCAAAAAAATATA
* *
25426193 TTTTGACCTCGAAACTACCAAAAAAATACTA
1 TTTTGACCCCAAAACT-CCAAAAAAATA-TA
25426224 TTTTGACCCCAAAACT
1 TTTTGACCCCAAAACT
25426240 TCTAAAATTC
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 14 0.37
30 8 0.21
31 16 0.42
ACGTcount: A:0.41, C:0.24, G:0.05, T:0.30
Consensus pattern (29 bp):
TTTTGACCCCAAAACTCCAAAAAAATATA
Found at i:25426286 original size:59 final size:59
Alignment explanation
Indices: 25426155--25426515 Score: 297
Period size: 59 Copynumber: 6.2 Consensus size: 59
25426145 AACTCCTCTG
* ***
25426155 AAATTA-CATTTTTGACCCCAAAAC-TTCTAAAAATT--ATATTTTGACCTCGAAACTACCAAA
1 AAATTACCA-TTTT-ACCCCAAAACTTTCT-AAAATTCCAT-TTTTAACCTCGATTTTACC-AA
* *
25426215 AAAATACTATTTTGACCCCAAAAC-TTCTAAAATTCCATTTTTAACCTCGATTTTACCAA
1 AAATTACCATTTT-ACCCCAAAACTTTCTAAAATTCCATTTTTAACCTCGATTTTACCAA
* * *
25426274 AAATTACCATTTTACCCTC-GAACTTTCCAAAA-TCTCGTTTTTAA-CTCAGATTTTACCAA
1 AAATTACCATTTTACCC-CAAAACTTTCTAAAATTC-CATTTTTAACCTC-GATTTTACCAA
* ** *
25426333 AAATTACCGTTTTACCCTTAAACTTTCTAAAA-TCTCATTTTTAACC-CTGATTTCACC-A
1 AAATTACCATTTTACCCCAAAACTTTCTAAAATTC-CATTTTTAACCTC-GATTTTACCAA
* * * *
25426391 AAATTACCATTTTACCCCTAAA----CT-AAATCCCA-TTTTAACCCCGATTTCACCAA
1 AAATTACCATTTTACCCCAAAACTTTCTAAAATTCCATTTTTAACCTCGATTTTACCAA
* * * *
25426444 AAATTACCATTTTACCCCCAAACTTTCCAAAATTCAATTTTTGACCTCGATTTTACCAA
1 AAATTACCATTTTACCCCAAAACTTTCTAAAATTCCATTTTTAACCTCGATTTTACCAA
* *
25426503 AAACTACTATTTT
1 AAATTACCATTTT
25426516 GCCCTCGGGC
Statistics
Matches: 253, Mismatches: 30, Indels: 37
0.79 0.09 0.12
Matches are distributed among these distances:
52 17 0.07
53 28 0.11
54 3 0.01
57 1 0.00
58 39 0.15
59 122 0.48
60 40 0.16
61 3 0.01
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.35
Consensus pattern (59 bp):
AAATTACCATTTTACCCCAAAACTTTCTAAAATTCCATTTTTAACCTCGATTTTACCAA
Found at i:25426287 original size:30 final size:29
Alignment explanation
Indices: 25426243--25426346 Score: 88
Period size: 30 Copynumber: 3.5 Consensus size: 29
25426233 CAAAACTTCT
25426243 AAAATTCCATTTTTAACCTCGATTTTACCA
1 AAAATTCCA-TTTTAACCTCGATTTTACCA
* *
25426273 AAAATTACCATTTTACCCTCGAACTTT-CC-
1 AAAATT-CCATTTTAACCTCG-ATTTTACCA
**
25426302 AAAATCTCGTTTTTAA-CTCAGATTTTACCA
1 AAAAT-TCCATTTTAACCTC-GATTTTACCA
*
25426332 AAAATTACCGTTTTA
1 AAAATT-CCATTTTA
25426347 CCCTTAAACT
Statistics
Matches: 59, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
28 7 0.12
29 15 0.25
30 30 0.51
31 7 0.12
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (29 bp):
AAAATTCCATTTTAACCTCGATTTTACCA
Found at i:25433516 original size:39 final size:38
Alignment explanation
Indices: 25433466--25433540 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 38
25433456 AAAAAATTTA
25433466 TTTTTATTTAACCTACTTATTTTCGGGGTTTTTTTTTTT
1 TTTTTATTTAACCTACTTATTTTC-GGGTTTTTTTTTTT
*
25433505 TTTTTATTTAACCTACTTATTTTCGTGTTTTTTTTT
1 TTTTTATTTAACCTACTTATTTTCGGGTTTTTTTTT
25433541 CCCAAAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 11 0.31
39 24 0.69
ACGTcount: A:0.13, C:0.11, G:0.08, T:0.68
Consensus pattern (38 bp):
TTTTTATTTAACCTACTTATTTTCGGGTTTTTTTTTTT
Found at i:25436443 original size:22 final size:23
Alignment explanation
Indices: 25436417--25436464 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
25436407 CAAAAGAAAT
*
25436417 TTATATTA-TAAATCCTTAAAAA
1 TTATATTATTAAATCCTAAAAAA
25436439 TTATATTATTTAAATCCTAAAAAA
1 TTATATTA-TTAAATCCTAAAAAA
25436463 TT
1 TT
25436465 TCTAAAGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.35
24 15 0.65
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (23 bp):
TTATATTATTAAATCCTAAAAAA
Found at i:25437588 original size:29 final size:29
Alignment explanation
Indices: 25437556--25437726 Score: 139
Period size: 29 Copynumber: 5.8 Consensus size: 29
25437546 GTTTGGGGCC
*
25437556 AAAAATGAAATTTCTGGAAGTTCGAGGGT
1 AAAAATGAAATTTTTGGAAGTTCGAGGGT
* *
25437585 AAAAAT-ATAATTTTTAGAAGTTTC-AAGGT
1 AAAAATGA-AATTTTTGGAAG-TTCGAGGGT
* ** *
25437614 CAAAATCGAGTTTTTTGGAAGTTCGGGGGT
1 AAAAAT-GAAATTTTTGGAAGTTCGAGGGT
* * * * *
25437644 AAAAAAGTAATTTTTGGAAGTTTCAACGTT
1 AAAAATGAAATTTTTGGAAG-TTCGAGGGT
* *
25437674 AAAATTGAGAATTTTTGGAAGTTCGGGGGT
1 AAAAATGA-AATTTTTGGAAGTTCGAGGGT
*
25437704 AAAAATGTAATTTTTGGACAGTT
1 AAAAATGAAATTTTTGGA-AGTT
25437727 TAGGGACCTC
Statistics
Matches: 107, Mismatches: 27, Indels: 15
0.72 0.18 0.10
Matches are distributed among these distances:
28 1 0.01
29 49 0.46
30 44 0.41
31 13 0.12
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.35
Consensus pattern (29 bp):
AAAAATGAAATTTTTGGAAGTTCGAGGGT
Found at i:25437658 original size:30 final size:29
Alignment explanation
Indices: 25437625--25437726 Score: 107
Period size: 30 Copynumber: 3.4 Consensus size: 29
25437615 AAAATCGAGT
25437625 TTTTTGGAAGTTCGGGGGTAAAAAAGTAA
1 TTTTTGGAAGTTCGGGGGTAAAAAAGTAA
*** * *
25437654 TTTTTGGAAGTTTCAACGTTAAAATTGAG-AA
1 TTTTTGGAAG-TTCGGGGGTAAAA--AAGTAA
*
25437685 TTTTTGGAAGTTCGGGGGTAAAAATGTAA
1 TTTTTGGAAGTTCGGGGGTAAAAAAGTAA
25437714 TTTTTGGACAGTT
1 TTTTTGGA-AGTT
25437727 TAGGGACCTC
Statistics
Matches: 57, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
28 1 0.02
29 20 0.35
30 22 0.39
31 12 0.21
32 2 0.04
ACGTcount: A:0.31, C:0.05, G:0.26, T:0.37
Consensus pattern (29 bp):
TTTTTGGAAGTTCGGGGGTAAAAAAGTAA
Found at i:25437698 original size:60 final size:60
Alignment explanation
Indices: 25437555--25437727 Score: 226
Period size: 59 Copynumber: 2.9 Consensus size: 60
25437545 AGTTTGGGGC
* * * * *
25437555 CAAAAATGA-AATTTCTGGAAGTTCGAGGGTAAAAATA-TAATTTTTAGAAGTTTCAAGGT
1 CAAAATTGAGAATTTTTGGAAGTTCGGGGGTAAAAA-AGTAATTTTTGGAAGTTTCAACGT
* *
25437614 CAAAATCGAG-TTTTTTGGAAGTTCGGGGGTAAAAAAGTAATTTTTGGAAGTTTCAACGT
1 CAAAATTGAGAATTTTTGGAAGTTCGGGGGTAAAAAAGTAATTTTTGGAAGTTTCAACGT
* *
25437673 TAAAATTGAGAATTTTTGGAAGTTCGGGGGTAAAAATGTAATTTTTGGACAGTTT
1 CAAAATTGAGAATTTTTGGAAGTTCGGGGGTAAAAAAGTAATTTTTGGA-AGTTT
25437728 AGGGACCTCC
Statistics
Matches: 99, Mismatches: 11, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
58 1 0.01
59 57 0.58
60 36 0.36
61 5 0.05
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (60 bp):
CAAAATTGAGAATTTTTGGAAGTTCGGGGGTAAAAAAGTAATTTTTGGAAGTTTCAACGT
Found at i:25439606 original size:17 final size:17
Alignment explanation
Indices: 25439584--25439650 Score: 71
Period size: 17 Copynumber: 3.8 Consensus size: 17
25439574 TTTTTAATTC
25439584 AATTTAAATTTAAACTT
1 AATTTAAATTTAAACTT
25439601 AATTTAAATTTAAACTTT
1 AATTTAAATTTAAAC-TT
**
25439619 AACTGAAAAGTTTAAACTT
1 AA-TTTAAA-TTTAAACTT
* *
25439638 AAATCAAATTTAA
1 AATTTAAATTTAA
25439651 CCCAAAATGA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
17 20 0.48
18 7 0.17
19 8 0.19
20 7 0.17
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.40
Consensus pattern (17 bp):
AATTTAAATTTAAACTT
Found at i:25440663 original size:39 final size:39
Alignment explanation
Indices: 25440620--25440841 Score: 142
Period size: 39 Copynumber: 5.7 Consensus size: 39
25440610 GTTGATGGTG
* *
25440620 ATCTGCCCCAGGCTTGGGGTAAGAGATCGAATGGTTATA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATCGAATGGTGATA
** ** * ** ** *
25440659 ATCTGCCCTTGGCTCAAGGTAAGAGATTGGTTGACGATG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATCGAATGGTGATA
* * * * * *
25440698 ATCTGCCCCAGACTCGAGGTAAAAGATCAAATGGTTACA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATCGAATGGTGATA
* * ** * *
25440737 ATCTACCCCAGGCTCGGGGTAAGAGATTGGTTGATGATG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATCGAATGGTGATA
* * * *
25440776 ATCTGCCCTAGGCTCGGGGTAAAAGATCAAATGGCTG-CA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATCGAATGG-TGATA
* *
25440815 A-CTTGCCCCAAGCTCGGGGTAATAGAT
1 ATC-TGCCCCAGGCTCGGGGTAAGAGAT
25440842 TGGTTGATGA
Statistics
Matches: 130, Mismatches: 51, Indels: 4
0.70 0.28 0.02
Matches are distributed among these distances:
38 1 0.01
39 127 0.98
40 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (39 bp):
ATCTGCCCCAGGCTCGGGGTAAGAGATCGAATGGTGATA
Found at i:25440708 original size:78 final size:78
Alignment explanation
Indices: 25440597--25440852 Score: 298
Period size: 78 Copynumber: 3.3 Consensus size: 78
25440587 CTGTGATCAG
* * * * *
25440597 GGTAAGGAGATTGGTTGATGGTGATCTGCCCCAGGCTTGGGGTAAGAGATCGAATGGTTATAATC
1 GGTAA-GAGATTGGTTGATGATGATCTGCCCCAGGCTCGGGGTAAAAGATCAAATGGTTACAATC
* **
25440662 TGCCCTTGGCTCAA
65 TACCCCAGGCTCAA
* * *
25440676 GGTAAGAGATTGGTTGACGATGATCTGCCCCAGACTCGAGGTAAAAGATCAAATGGTTACAATCT
1 GGTAAGAGATTGGTTGATGATGATCTGCCCCAGGCTCGGGGTAAAAGATCAAATGGTTACAATCT
**
25440741 ACCCCAGGCTCGG
66 ACCCCAGGCTCAA
* * *
25440754 GGTAAGAGATTGGTTGATGATGATCTGCCCTAGGCTCGGGGTAAAAGATCAAATGGCTGCAA-CT
1 GGTAAGAGATTGGTTGATGATGATCTGCCCCAGGCTCGGGGTAAAAGATCAAATGGTTACAATC-
* * **
25440818 TGCCCCAAGCTCGG
65 TACCCCAGGCTCAA
*
25440832 GGTAATAGATTGGTTGATGAT
1 GGTAAGAGATTGGTTGATGAT
25440853 ATAACTTCAC
Statistics
Matches: 154, Mismatches: 22, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
77 1 0.01
78 148 0.96
79 5 0.03
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.25
Consensus pattern (78 bp):
GGTAAGAGATTGGTTGATGATGATCTGCCCCAGGCTCGGGGTAAAAGATCAAATGGTTACAATCT
ACCCCAGGCTCAA
Found at i:25441257 original size:49 final size:49
Alignment explanation
Indices: 25441200--25441304 Score: 167
Period size: 48 Copynumber: 2.1 Consensus size: 49
25441190 TGACTTAAAC
25441200 CTTTCCCTTCAAATCTTCGTGGTACTGGATCCGCCGTTGCGG-CTTAGAT
1 CTTTCCCTT-AAATCTTCGTGGTACTGGATCCGCCGTTGCGGTCTTAGAT
***
25441249 CTTTCCCTTGTGTCTTCGTGGTACTGGATCCGCCGTTGCGGTCTTAGAT
1 CTTTCCCTTAAATCTTCGTGGTACTGGATCCGCCGTTGCGGTCTTAGAT
25441298 CTTTCCC
1 CTTTCCC
25441305 GTCGTGTTTC
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
48 29 0.56
49 23 0.44
ACGTcount: A:0.10, C:0.30, G:0.23, T:0.37
Consensus pattern (49 bp):
CTTTCCCTTAAATCTTCGTGGTACTGGATCCGCCGTTGCGGTCTTAGAT
Found at i:25442247 original size:20 final size:20
Alignment explanation
Indices: 25442218--25442316 Score: 109
Period size: 20 Copynumber: 5.1 Consensus size: 20
25442208 TCTCCTTTTC
25442218 TTTT-TCTTTTTTTTTTCTT
1 TTTTCTCTTTTTTTTTTCTT
*
25442237 TTTTCTCTTTTTTTATTCTT
1 TTTTCTCTTTTTTTTTTCTT
25442257 TTTTCTCTTTTTTTTTT-TT
1 TTTTCTCTTTTTTTTTTCTT
*
25442276 CTTTT-TCTTTTCCTTTTTC-T
1 -TTTTCTCTTTT-TTTTTTCTT
* *
25442296 TCTTCT-TTTTTCTTTTCTT
1 TTTTCTCTTTTTTTTTTCTT
25442315 TT
1 TT
25442317 ATTCATTGAA
Statistics
Matches: 67, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
18 5 0.07
19 21 0.31
20 41 0.61
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.83
Consensus pattern (20 bp):
TTTTCTCTTTTTTTTTTCTT
Found at i:25442267 original size:46 final size:46
Alignment explanation
Indices: 25442216--25442316 Score: 129
Period size: 46 Copynumber: 2.2 Consensus size: 46
25442206 CCTCTCCTTT
25442216 TCTTTTTCTTTTTTT-TTTCTT-TTTTCTCTTTTT-TTATTCTTTTTTC
1 TCTTTTT-TTTTTTTCTTT-TTCTTTTC-CTTTTTCTTATTCTTTTTTC
*
25442262 TCTTTTTTTTTTTTCTTTTTCTTTTCCTTTTTCTTCTTCTTTTTTC
1 TCTTTTTTTTTTTTCTTTTTCTTTTCCTTTTTCTTATTCTTTTTTC
*
25442308 T-TTTCTTTT
1 TCTTTTTTTT
25442317 ATTCATTGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
45 22 0.44
46 28 0.56
ACGTcount: A:0.01, C:0.17, G:0.00, T:0.82
Consensus pattern (46 bp):
TCTTTTTTTTTTTTCTTTTTCTTTTCCTTTTTCTTATTCTTTTTTC
Found at i:25442312 original size:18 final size:18
Alignment explanation
Indices: 25442213--25442314 Score: 81
Period size: 17 Copynumber: 5.7 Consensus size: 18
25442203 CGACCTCTCC
25442213 TTTTCTTTTTCTT-TT-TT
1 TTTTC-TTTTCTTCTTCTT
* *
25442230 TTTTCTTTTTTCTCTTTTT
1 TTTTCTTTTCT-TCTTCTT
25442249 TTATTCTTTT-TTC-TCTT
1 TT-TTCTTTTCTTCTTCTT
*
25442266 TTTT-TTTT-TTCTTTTT
1 TTTTCTTTTCTTCTTCTT
25442282 CTTTTCCTTTTTCTTCTTCTT
1 -TTTT-C-TTTTCTTCTTCTT
25442303 TTTTCTTTTCTT
1 TTTTCTTTTCTT
25442315 TTATTCATTG
Statistics
Matches: 71, Mismatches: 4, Indels: 19
0.76 0.04 0.20
Matches are distributed among these distances:
15 7 0.10
16 10 0.14
17 15 0.21
18 11 0.15
19 6 0.08
20 15 0.21
21 7 0.10
ACGTcount: A:0.01, C:0.17, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTCTTTTCTTCTTCTT
Found at i:25447363 original size:56 final size:58
Alignment explanation
Indices: 25447296--25447549 Score: 209
Period size: 58 Copynumber: 4.4 Consensus size: 58
25447286 AAAACAAATT
* * *
25447296 TTTTTGGACATCCGAGGGTAAAAGGGTAATTTTGAAAGTTT-GGGGGCAAAAATGGAA
1 TTTTTGGACATCCGAGGGTAAAAGGGTAATTTTGAAAGTTTCAGGGCCAAAAATGAAA
25447353 -TTTTGGACATCC-ATGGGTAAAAGGGTAATTTTGAAAGTTTCAGGGCCAAAAATGAAA
1 TTTTTGGACATCCGA-GGGTAAAAGGGTAATTTTGAAAGTTTCAGGGCCAAAAATGAAA
* *** * * ** *
25447410 TTTTTGGA-AGTTCGAGGGTAAAAATATAATTTTTGGAAGTTTCAAGG-TTAAAATCGAGA
1 TTTTTGGACA-TCCGAGGGTAAAAGGGTAA-TTTTGAAAGTTTCAGGGCCAAAAAT-GAAA
** ** * * * *
25447469 TTTTTGGA-AGTTAG-GGGTAAAAATGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGAA
1 TTTTTGGACA-TCCGAGGGTAAAAGGGTAA-TTTTGAAAGTTTCAGGGCCAAAAATGAAA
25447527 TTTTTGGA-AGTCCGAGGGTAAAA
1 TTTTTGGACA-TCCGAGGGTAAAA
25447550 ATGTGATTTT
Statistics
Matches: 166, Mismatches: 22, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
55 1 0.01
56 38 0.23
57 14 0.08
58 68 0.41
59 45 0.27
ACGTcount: A:0.34, C:0.07, G:0.28, T:0.31
Consensus pattern (58 bp):
TTTTTGGACATCCGAGGGTAAAAGGGTAATTTTGAAAGTTTCAGGGCCAAAAATGAAA
Found at i:25447473 original size:59 final size:56
Alignment explanation
Indices: 25447401--25447628 Score: 226
Period size: 59 Copynumber: 3.9 Consensus size: 56
25447391 TTCAGGGCCA
*
25447401 AAAATGAAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTTGGAAGTTTCAAGGT-T
1 AAAATG-AATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTTC--GGTCT
* *
25447459 AAAATCGAGATTTTTGGAAGTTAG-GGGTAAAAATGTAATTTTTGGAAGTTTCGGGGTCA
1 AAAAT-GA-ATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTTC--GGTCT
* * * * *
25447518 AAAATGGAATTTTTGGAAGTCCGAGGGTAAAAATGTGATTTTTGAAAATTTCGGTGTCA
1 AAAAT-GAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTTC-G-GTCT
** * *
25447577 AAAATAGAATTTTTAAAAGTTTGAGGGTAAACATGTAATTTTTGGATAGTTT
1 AAAAT-GAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGGA-AGTTT
25447629 AGGGACCTCC
Statistics
Matches: 144, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
58 51 0.35
59 89 0.62
60 4 0.03
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (56 bp):
AAAATGAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTTCGGTCT
Found at i:25447632 original size:29 final size:28
Alignment explanation
Indices: 25447367--25447632 Score: 189
Period size: 29 Copynumber: 9.1 Consensus size: 28
25447357 GGACATCCAT
** *
25447367 GGGTAAAAGGGTAA-TTTTGAAAGTTTCA
1 GGGTAAAAATGTAATTTTTGGAAGTTT-A
* * *
25447395 GGGCCAAAAATGAAATTTTTGGAAGTTCGA
1 GGG-TAAAAATGTAATTTTTGGAAGTT-TA
*
25447425 GGGTAAAAATATAATTTTTGGAAGTTTCA
1 GGGTAAAAATGTAATTTTTGGAAGTTT-A
* *
25447454 AGGTTAAAATCG-AGATTTTTGGAAG-TTA
1 GGGTAAAAAT-GTA-ATTTTTGGAAGTTTA
*
25447482 GGGGTAAAAATGTAATTTTTGGAAGTTTCG
1 -GGGTAAAAATGTAATTTTTGGAAGTTT-A
* **
25447512 GGGTCAAAAATGGAATTTTTGGAAGTCCGA
1 GGGT-AAAAATGTAATTTTTGGAAGT-TTA
* * * *
25447542 GGGTAAAAATGTGATTTTTGAAAATTTC
1 GGGTAAAAATGTAATTTTTGGAAGTTTA
**
25447570 GGTGTCAAAAATAG-AATTTTTAAAAGTTTGA
1 GG-GT-AAAAAT-GTAATTTTTGGAAGTTT-A
*
25447601 GGGTAAACATGTAATTTTTGGATAGTTTA
1 GGGTAAAAATGTAATTTTTGGA-AGTTTA
25447630 GGG
1 GGG
25447633 ACCTCCAGAG
Statistics
Matches: 186, Mismatches: 34, Indels: 35
0.73 0.13 0.14
Matches are distributed among these distances:
28 19 0.10
29 90 0.48
30 74 0.40
31 3 0.02
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.34
Consensus pattern (28 bp):
GGGTAAAAATGTAATTTTTGGAAGTTTA
Found at i:25449493 original size:20 final size:20
Alignment explanation
Indices: 25449456--25449492 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
25449446 TAAGATGGAT
25449456 ATTGTAATTTGGCCTTTTAA
1 ATTGTAATTTGGCCTTTTAA
*
25449476 ATTGT-ATTTGGACTTTT
1 ATTGTAATTTGGCCTTTT
25449493 TTTAATTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.22, C:0.08, G:0.16, T:0.54
Consensus pattern (20 bp):
ATTGTAATTTGGCCTTTTAA
Found at i:25449528 original size:17 final size:16
Alignment explanation
Indices: 25449501--25449533 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
25449491 TTTTTAATTC
25449501 AATTTAATTTAAACTT
1 AATTTAATTTAAACTT
25449517 AATTTAAATTTAAACTT
1 AATTT-AATTTAAACTT
25449534 TAACAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (16 bp):
AATTTAATTTAAACTT
Found at i:25449567 original size:17 final size:17
Alignment explanation
Indices: 25449506--25449568 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
25449496 AATTCAATTT
* *
25449506 AATTTAAACTTAATTTA
1 AATTTAAACTTAAATAA
*
25449523 AATTTAAACTTTAACAGAA
1 AATTTAAAC-TTAA-ATAA
*
25449542 AAGTTTAAACTTAAATCA
1 AA-TTTAAACTTAAATAA
25449560 AATTTAAAC
1 AATTTAAAC
25449569 CCAAAATGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
17 16 0.42
18 8 0.21
19 7 0.18
20 7 0.18
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.37
Consensus pattern (17 bp):
AATTTAAACTTAAATAA
Found at i:25458263 original size:72 final size:72
Alignment explanation
Indices: 25458135--25458320 Score: 248
Period size: 72 Copynumber: 2.6 Consensus size: 72
25458125 CACCGCATAA
* * **
25458135 CCCATGACATGGGCTTGAAGTACTTGCCACCCAGGGGATTGTACTGGAGCTGGTGAATACTGCAA
1 CCCATGACATGGGCTTGAAGTGCTTGCCACCCAGGGGATTGTACAGGAGCCAGTGAATACTGCAA
**
25458200 GCCTTGC
66 GCCAGGC
* **
25458207 CCCATGACATGGGCTTGAACTGCTTGCCACCCAGGGGATTGTACAGGCTCCAGTGAATACTGCAA
1 CCCATGACATGGGCTTGAAGTGCTTGCCACCCAGGGGATTGTACAGGAGCCAGTGAATACTGCAA
25458272 GCCAGGC
66 GCCAGGC
* * *
25458279 CCCGTGATATGGGCATGAAGTGCTTGCCACCTC-GGGGATTGT
1 CCCATGACATGGGCTTGAAGTGCTTGCCACC-CAGGGGATTGT
25458321 GCAGTAACTG
Statistics
Matches: 100, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
72 99 0.99
73 1 0.01
ACGTcount: A:0.22, C:0.26, G:0.30, T:0.23
Consensus pattern (72 bp):
CCCATGACATGGGCTTGAAGTGCTTGCCACCCAGGGGATTGTACAGGAGCCAGTGAATACTGCAA
GCCAGGC
Found at i:25460214 original size:159 final size:159
Alignment explanation
Indices: 25459917--25460398 Score: 617
Period size: 159 Copynumber: 3.0 Consensus size: 159
25459907 GAAATTCTCT
* * * * *
25459917 TGCGATCAACATGCTTTTGAGATTCTTTACCATTTCCATTATTTCTTCTTTCCCCATAATTGTTT
1 TGCGATCACCATGTTTTTCAGATTCTTTACCATTTCCAATATTTCTTCTTTCCCCATAACTGTTT
* * * ** *
25459982 CCTGAATCCCTTTCATCACTTGC-TCCACTAAATCCAGATCTCTCAGTGCTGTGTTGTTCATTGG
66 CCTGAATCTCTTTCATCACTT-CTTCCACTAAATCCAGATCTCTCAATGCTGCGTTGTTCAAAGA
* * *
25460046 TATCTGAAGAAAGCATTTTATGAAGGCCAC
130 TTTCTGAAGAAAGCATTCTGTGAAGGCCAC
* * ** **
25460076 TGCGATCACCATGTTTTTTAGATTCTTTACCATTTCCAATATTTCTCCTTTCAACATAACCATTT
1 TGCGATCACCATGTTTTTCAGATTCTTTACCATTTCCAATATTTCTTCTTTCCCCATAACTGTTT
* * **
25460141 CCTGAATCTCTTTCATCACTTCTTTCACTAAATCCAGAGCTCTCAACACTGCGTTGTTCAAAGAT
66 CCTGAATCTCTTTCATCACTTCTTCCACTAAATCCAGATCTCTCAATGCTGCGTTGTTCAAAGAT
*
25460206 TTCAGAAGAAAGCATTCTGTGAAGGCCAC
131 TTCTGAAGAAAGCATTCTGTGAAGGCCAC
* * ** *
25460235 TGTGACCACCATGTTTTTCAGATTCTTTACTGTTTCC-ATAATTTCTTCTTTCCCCGTAACTGTT
1 TGCGATCACCATGTTTTTCAGATTCTTTACCATTTCCAAT-ATTTCTTCTTTCCCCATAACTGTT
** *
25460299 TCCTGAATCTCTTTCATCACTTCTTCCAGAAAATCCAGATCTCTGAATGCTGCGTTGTTCAAAGA
65 TCCTGAATCTCTTTCATCACTTCTTCCACTAAATCCAGATCTCTCAATGCTGCGTTGTTCAAAGA
* *
25460364 TTTCTGAAGAAAGTATTCCGTGAAGGCCAC
130 TTTCTGAAGAAAGCATTCTGTGAAGGCCAC
25460394 TGCGA
1 TGCGA
25460399 GGAGTAAAAG
Statistics
Matches: 275, Mismatches: 46, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
158 3 0.01
159 272 0.99
ACGTcount: A:0.24, C:0.25, G:0.13, T:0.37
Consensus pattern (159 bp):
TGCGATCACCATGTTTTTCAGATTCTTTACCATTTCCAATATTTCTTCTTTCCCCATAACTGTTT
CCTGAATCTCTTTCATCACTTCTTCCACTAAATCCAGATCTCTCAATGCTGCGTTGTTCAAAGAT
TTCTGAAGAAAGCATTCTGTGAAGGCCAC
Found at i:25461501 original size:4 final size:4
Alignment explanation
Indices: 25461492--25461530 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
25461482 TAGTCATTGC
25461492 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
25461531 CACGCACTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (4 bp):
ACAT
Found at i:25464920 original size:31 final size:30
Alignment explanation
Indices: 25464885--25465016 Score: 96
Period size: 31 Copynumber: 4.5 Consensus size: 30
25464875 AAATTATATG
25464885 ATATTTAAATAATTTAATATAATAATAAATT
1 ATATTTAAATAATTTAATATAATAATAAA-T
* * * *
25464916 ATATTTAAATAAATTGATATAATGATAGAT
1 ATATTTAAATAATTTAATATAATAATAAAT
* * ** * *
25464946 GAAATATAAATTAATTTAAT-TTTTAATATAC
1 -ATATTTAAA-TAATTTAATATAATAATAAAT
25464977 AT-TTTAAATAA-TTAATATAAATAA-AAAT
1 ATATTTAAATAATTTAATAT-AATAATAAAT
25465005 AT-TTT-AATAATT
1 ATATTTAAATAATT
25465017 CTTATTTTCA
Statistics
Matches: 77, Mismatches: 19, Indels: 13
0.71 0.17 0.12
Matches are distributed among these distances:
27 10 0.13
28 12 0.16
29 8 0.10
30 2 0.03
31 38 0.49
32 7 0.09
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (30 bp):
ATATTTAAATAATTTAATATAATAATAAAT
Found at i:25469000 original size:20 final size:21
Alignment explanation
Indices: 25468961--25468998 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
25468951 GGTAAAGCTT
25468961 TTTATACTATTAATTCTTTAG
1 TTTATACTATTAATTCTTTAG
25468982 TTTATACT-TTAA-TCTTT
1 TTTATACTATTAATTCTTT
25468999 TAATTTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 4 0.24
21 8 0.47
ACGTcount: A:0.26, C:0.11, G:0.03, T:0.61
Consensus pattern (21 bp):
TTTATACTATTAATTCTTTAG
Found at i:25474919 original size:15 final size:15
Alignment explanation
Indices: 25474895--25474928 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
25474885 GAAACCACTG
* *
25474895 CTTCCGATGGTGTAT
1 CTTCCAATGGTATAT
25474910 CTTCCAATGGTATAT
1 CTTCCAATGGTATAT
25474925 CTTC
1 CTTC
25474929 TACCTGTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.41
Consensus pattern (15 bp):
CTTCCAATGGTATAT
Found at i:25478737 original size:34 final size:34
Alignment explanation
Indices: 25478645--25478746 Score: 115
Period size: 34 Copynumber: 3.1 Consensus size: 34
25478635 TAGCTTGATT
*
25478645 ATTTTTTATAGGATAACATAATTTTTTACTTTTC
1 ATTTTTTATAGGATAACATAATTTTTTACCTTTC
* *
25478679 A-TCTTGAT--GATTAAGTC-T-ATTTTTTACCTTTC
1 ATTTTTTATAGGA-TAA--CATAATTTTTTACCTTTC
25478711 ATTTTTTATAGGATAACATAATTTTTTACCTTTC
1 ATTTTTTATAGGATAACATAATTTTTTACCTTTC
25478745 AT
1 AT
25478747 CTTGACAATT
Statistics
Matches: 55, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
31 2 0.04
32 18 0.33
33 12 0.22
34 21 0.38
35 2 0.04
ACGTcount: A:0.27, C:0.12, G:0.07, T:0.54
Consensus pattern (34 bp):
ATTTTTTATAGGATAACATAATTTTTTACCTTTC
Found at i:25478859 original size:4 final size:4
Alignment explanation
Indices: 25478817--25478841 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
25478807 TACTTGAAAT
25478817 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
25478842 AAATTTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:25482820 original size:31 final size:30
Alignment explanation
Indices: 25482731--25482816 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 30
25482721 ATAATCTCTG
25482731 TATTTTTCATAAA-TTTAAAATTTAATTTTTA
1 TATTTTT--TAAATTTTAAAATTTAATTTTTA
* *
25482762 TACTTTTTT-ATTTTTAGTAAA-TTAATTTTTT
1 TA-TTTTTTAAATTTTA--AAATTTAATTTTTA
25482793 TATTTTTTAAATTTTAAAATTTAA
1 TATTTTTTAAATTTTAAAATTTAA
25482817 ATTTAATTGT
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
29 4 0.09
30 15 0.33
31 19 0.41
32 8 0.17
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (30 bp):
TATTTTTTAAATTTTAAAATTTAATTTTTA
Found at i:25483009 original size:22 final size:21
Alignment explanation
Indices: 25482956--25483014 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
25482946 CGATTAAACT
25482956 TAAATTTTAAAATTTAAATAA
1 TAAATTTTAAAATTTAAATAA
*
25482977 TAAATTCTTAAAATTATAGAA-AG
1 TAAATT-TTAAAATT-TA-AATAA
25483000 TAAATTTT-AAATTTA
1 TAAATTTTAAAATTTA
25483015 CAAAACAATC
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
20 2 0.06
21 11 0.32
22 10 0.29
23 9 0.26
24 2 0.06
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (21 bp):
TAAATTTTAAAATTTAAATAA
Found at i:25483334 original size:30 final size:32
Alignment explanation
Indices: 25483300--25483367 Score: 88
Period size: 30 Copynumber: 2.2 Consensus size: 32
25483290 AGTTAATCTT
25483300 TAAATTTAA-TAATTATTTT-ATATTAAAATC
1 TAAATTTAAGTAATTATTTTCATATTAAAATC
* * *
25483330 TAAA-TTAAGTAATTATTTTCATTTTAAAGTT
1 TAAATTTAAGTAATTATTTTCATATTAAAATC
25483361 TAAATTT
1 TAAATTT
25483368 TTTTTATCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 4 0.12
30 14 0.44
31 12 0.38
32 2 0.06
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (32 bp):
TAAATTTAAGTAATTATTTTCATATTAAAATC
Found at i:25485385 original size:14 final size:15
Alignment explanation
Indices: 25485344--25485390 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
25485334 GTAAAATATT
*
25485344 ATATAAAATTTATAA
1 ATATAAATTTTATAA
25485359 TATATAAATTTTATAA
1 -ATATAAATTTTATAA
*
25485375 ATA-ATATTTTATAA
1 ATATAAATTTTATAA
25485389 AT
1 AT
25485391 TATCCAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 12 0.41
15 3 0.10
16 14 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATAAATTTTATAA
Found at i:25486743 original size:12 final size:12
Alignment explanation
Indices: 25486726--25486757 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
25486716 CCAAAAATTA
25486726 AATGAAAGTTTT
1 AATGAAAGTTTT
25486738 AATGAAAGTTTT
1 AATGAAAGTTTT
25486750 AATGAAAG
1 AATGAAAG
25486758 AGGTTTGTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.34
Consensus pattern (12 bp):
AATGAAAGTTTT
Found at i:25488714 original size:3 final size:3
Alignment explanation
Indices: 25488706--25488730 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
25488696 ATATTTAGGT
25488706 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
25488731 GTATCAACGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:25493754 original size:16 final size:17
Alignment explanation
Indices: 25493726--25493760 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
25493716 ATTGAAATTC
25493726 AAACAATAAAAAGAAGA
1 AAACAATAAAAAGAAGA
25493743 AAACAA-AAAAAGAAGA
1 AAACAATAAAAAGAAGA
25493759 AA
1 AA
25493761 GAAAAAGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.80, C:0.06, G:0.11, T:0.03
Consensus pattern (17 bp):
AAACAATAAAAAGAAGA
Found at i:25498624 original size:18 final size:18
Alignment explanation
Indices: 25498601--25498637 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
25498591 ACAATTCATA
25498601 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
25498619 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
25498637 T
1 T
25498638 TGATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:25503044 original size:14 final size:15
Alignment explanation
Indices: 25503019--25503048 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
25503009 AACTTAACTC
25503019 TAAATGAAATTTTAT
1 TAAATGAAATTTTAT
25503034 TAAAT-AAATTTTAT
1 TAAATGAAATTTTAT
25503048 T
1 T
25503049 TTCTATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
TAAATGAAATTTTAT
Found at i:25507196 original size:23 final size:25
Alignment explanation
Indices: 25507144--25507197 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
25507134 TATATTATAA
* *
25507144 TAAT-ATTATTAAAATATTATATTT
1 TAATAATTATTAAAATAATATACTT
25507168 TAAATAATTATT-AAATAATA-ACTT
1 T-AATAATTATTAAAATAATATACTT
25507192 TAATAA
1 TAATAA
25507198 AAAAAATCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 5 0.19
24 5 0.19
25 10 0.38
26 6 0.23
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TAATAATTATTAAAATAATATACTT
Found at i:25511871 original size:21 final size:23
Alignment explanation
Indices: 25511847--25511888 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
25511837 CATTTATATG
25511847 TTTGAA-CA-AAGTATTTAGTAA
1 TTTGAATCATAAGTATTTAGTAA
*
25511868 TTTGAATTATAAGTATTTAGT
1 TTTGAATCATAAGTATTTAGT
25511889 TTTATAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 1 0.06
23 11 0.61
ACGTcount: A:0.38, C:0.02, G:0.14, T:0.45
Consensus pattern (23 bp):
TTTGAATCATAAGTATTTAGTAA
Found at i:25512433 original size:22 final size:23
Alignment explanation
Indices: 25512386--25512433 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
25512376 AATCAAAAGT
*
25512386 TAAAATTTTAATTTATATTTAAA
1 TAAAATTTTAATTTATATCTAAA
*
25512409 TAAAATTTTAATTTTTA-CTAAA
1 TAAAATTTTAATTTATATCTAAA
25512431 TAA
1 TAA
25512434 TTTGTAAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
TAAAATTTTAATTTATATCTAAA
Found at i:25517835 original size:6 final size:6
Alignment explanation
Indices: 25517801--25517868 Score: 50
Period size: 6 Copynumber: 11.5 Consensus size: 6
25517791 TAATAGGGAT
* * * * *
25517801 TTTCAA TTTACAA -TTC-A TATCAC TTTCAA TTTCAA CTTCAC TTTCAC
1 TTTCAA TTT-CAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA
* *
25517848 TTTCAC TTTCAC TTTCAA TTT
1 TTTCAA TTTCAA TTTCAA TTT
25517869 TGATCACAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
4 1 0.02
5 3 0.06
6 44 0.86
7 3 0.06
ACGTcount: A:0.26, C:0.25, G:0.00, T:0.49
Consensus pattern (6 bp):
TTTCAA
Found at i:25517843 original size:18 final size:18
Alignment explanation
Indices: 25517820--25517868 Score: 73
Period size: 18 Copynumber: 2.7 Consensus size: 18
25517810 ACAATTCATA
25517820 TCACTTTCAATTTCAAC-T
1 TCACTTTCAATTTC-ACTT
*
25517838 TCACTTTCACTTTCACTT
1 TCACTTTCAATTTCACTT
25517856 TCACTTTCAATTT
1 TCACTTTCAATTT
25517869 TGATCACAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 2 0.07
18 26 0.93
ACGTcount: A:0.22, C:0.29, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTTCACTT
Found at i:25517845 original size:12 final size:13
Alignment explanation
Indices: 25517822--25517864 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
25517812 AATTCATATC
*
25517822 ACTTTCAATTTCA
1 ACTTTCACTTTCA
25517835 AC-TTCACTTTC-
1 ACTTTCACTTTCA
25517846 ACTTTCACTTTC-
1 ACTTTCACTTTCA
25517858 ACTTTCA
1 ACTTTCA
25517865 ATTTTGATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 2 0.07
12 24 0.86
13 2 0.07
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (13 bp):
ACTTTCACTTTCA
Found at i:25523321 original size:6 final size:6
Alignment explanation
Indices: 25523287--25523354 Score: 50
Period size: 6 Copynumber: 11.5 Consensus size: 6
25523277 TAATAGGGAT
* * * * *
25523287 TTTCAA TTTACAA -TTC-A TATCAC TTTCAA TTTCAA CTTCAC TTTCAC
1 TTTCAA TTT-CAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA
* *
25523334 TTTCAC TTTCAC TTTCAA TTT
1 TTTCAA TTTCAA TTTCAA TTT
25523355 TGATCACAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
4 1 0.02
5 3 0.06
6 44 0.86
7 3 0.06
ACGTcount: A:0.26, C:0.25, G:0.00, T:0.49
Consensus pattern (6 bp):
TTTCAA
Found at i:25523329 original size:18 final size:18
Alignment explanation
Indices: 25523306--25523354 Score: 73
Period size: 18 Copynumber: 2.7 Consensus size: 18
25523296 ACAATTCATA
25523306 TCACTTTCAATTTCAAC-T
1 TCACTTTCAATTTC-ACTT
*
25523324 TCACTTTCACTTTCACTT
1 TCACTTTCAATTTCACTT
25523342 TCACTTTCAATTT
1 TCACTTTCAATTT
25523355 TGATCACAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 2 0.07
18 26 0.93
ACGTcount: A:0.22, C:0.29, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTTCACTT
Found at i:25523331 original size:12 final size:13
Alignment explanation
Indices: 25523308--25523350 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
25523298 AATTCATATC
*
25523308 ACTTTCAATTTCA
1 ACTTTCACTTTCA
25523321 AC-TTCACTTTC-
1 ACTTTCACTTTCA
25523332 ACTTTCACTTTC-
1 ACTTTCACTTTCA
25523344 ACTTTCA
1 ACTTTCA
25523351 ATTTTGATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 2 0.07
12 24 0.86
13 2 0.07
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (13 bp):
ACTTTCACTTTCA
Found at i:25525783 original size:12 final size:12
Alignment explanation
Indices: 25525766--25525803 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
25525756 GACCGGGCCC
25525766 AAAAAATAATAA
1 AAAAAATAATAA
25525778 AAAAAATAA-AA
1 AAAAAATAATAA
*
25525789 AAAATAAAAATAA
1 AAAA-AATAATAA
25525802 AA
1 AA
25525804 TTCTCAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 6 0.26
12 13 0.57
13 4 0.17
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (12 bp):
AAAAAATAATAA
Found at i:25525785 original size:9 final size:9
Alignment explanation
Indices: 25525766--25525798 Score: 57
Period size: 9 Copynumber: 3.6 Consensus size: 9
25525756 GACCGGGCCC
25525766 AAAAAATAAT
1 AAAAAA-AAT
25525776 AAAAAAAAT
1 AAAAAAAAT
25525785 AAAAAAAAT
1 AAAAAAAAT
25525794 AAAAA
1 AAAAA
25525799 TAAAATTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 17 0.74
10 6 0.26
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAAAAAT
Done.