Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 294 of 378
Found at i:88861360 original size:27 final size:28
Alignment explanation
Indices: 88861330--88861419 Score: 114
Period size: 27 Copynumber: 3.3 Consensus size: 28
88861320 TTTAGTTTAC
88861330 TAAAATTACCGAAATACCCTTAG-TTTG
1 TAAAATTACCGAAATACCCTTAGATTTG
* *
88861357 TAAAAATACTGAAATACCCTT-GATTTG
1 TAAAATTACCGAAATACCCTTAGATTTG
* * *
88861384 TAAATTTACCGAAATA-CCTTTGACTTG
1 TAAAATTACCGAAATACCCTTAGATTTG
88861411 TAAAATTAC
1 TAAAATTAC
88861420 TAAAGTACCC
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
26 5 0.09
27 49 0.91
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (28 bp):
TAAAATTACCGAAATACCCTTAGATTTG
Found at i:88861585 original size:81 final size:80
Alignment explanation
Indices: 88861437--88861634 Score: 317
Period size: 81 Copynumber: 2.5 Consensus size: 80
88861427 CCCCCGATTC
88861437 ACAGAATTACCGTTTTACCCCTAATTTACATAATTACCGTTTTACCCCTGATTTACATAATTATC
1 ACAGAATTACCGTTTTACCCCTAATTTACATAATTACCGTTTTACCCCTGATTTACATAATTATC
88861502 GTTTTACCCTCGACTT
66 GTTTTA-CCTCGACTT
88861518 ACAGAATTACCGTTTTACCCCTAATTTACATAATTACCGTTTTACCCCTGATTTACATAATTATC
1 ACAGAATTACCGTTTTACCCCTAATTTACATAATTACCGTTTTACCCCTGATTTACATAATTATC
* *
88861583 GTTTTACCTTGATTT
66 GTTTTACCTCGACTT
** * *
88861598 ACAGAATTACTATTTTA-CCCTCGATTTACAAAATTAC
1 ACAGAATTACCGTTTTACCCCT-AATTTACATAATTAC
88861635 TAAAATACCC
Statistics
Matches: 110, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
79 4 0.04
80 35 0.32
81 71 0.65
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.40
Consensus pattern (80 bp):
ACAGAATTACCGTTTTACCCCTAATTTACATAATTACCGTTTTACCCCTGATTTACATAATTATC
GTTTTACCTCGACTT
Found at i:88861636 original size:27 final size:27
Alignment explanation
Indices: 88861425--88861634 Score: 255
Period size: 27 Copynumber: 7.8 Consensus size: 27
88861415 ATTACTAAAG
* * *
88861425 TACCCCCGATTCACAGAATTACCGTTT
1 TACCCCTGATTTACATAATTACCGTTT
*
88861452 TACCCCTAATTTACATAATTACCGTTT
1 TACCCCTGATTTACATAATTACCGTTT
*
88861479 TACCCCTGATTTACATAATTATCGTTT
1 TACCCCTGATTTACATAATTACCGTTT
* *
88861506 TA-CCCTCGACTTACAGAATTACCGTTT
1 TACCCCT-GATTTACATAATTACCGTTT
*
88861533 TACCCCTAATTTACATAATTACCGTTT
1 TACCCCTGATTTACATAATTACCGTTT
*
88861560 TACCCCTGATTTACATAATTATCGTTT
1 TACCCCTGATTTACATAATTACCGTTT
* * **
88861587 TA-CCTTGATTTACAGAATTACTATTT
1 TACCCCTGATTTACATAATTACCGTTT
*
88861613 TA-CCCTCGATTTACAAAATTAC
1 TACCCCT-GATTTACATAATTAC
88861635 TAAAATACCC
Statistics
Matches: 159, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
26 28 0.18
27 127 0.80
28 4 0.03
ACGTcount: A:0.29, C:0.25, G:0.07, T:0.39
Consensus pattern (27 bp):
TACCCCTGATTTACATAATTACCGTTT
Found at i:88861643 original size:27 final size:27
Alignment explanation
Indices: 88861593--88861645 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
88861583 GTTTTACCTT
* ***
88861593 GATTTACAGAATTACTATTTTACCCTC
1 GATTTACAAAATTACTAAAATACCCTC
88861620 GATTTACAAAATTACTAAAATACCCT
1 GATTTACAAAATTACTAAAATACCCT
88861646 TGGTTTGTAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.36
Consensus pattern (27 bp):
GATTTACAAAATTACTAAAATACCCTC
Found at i:88861764 original size:27 final size:27
Alignment explanation
Indices: 88861707--88861769 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
88861697 CCCTAAAAGG
* *
88861707 TAAAAAGACCGTAAAGCCCCTGTAGGG
1 TAAAATGACCGTAAAGCCCCTGTAGGA
* *
88861734 TAAAGTGACCGTAATA-CCCCTGTATGA
1 TAAAATGACCGTAA-AGCCCCTGTAGGA
88861761 TAAAATGAC
1 TAAAATGAC
88861770 GAATATGCCC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 29 0.97
28 1 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (27 bp):
TAAAATGACCGTAAAGCCCCTGTAGGA
Found at i:88862970 original size:24 final size:24
Alignment explanation
Indices: 88862928--88862974 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
88862918 TTATAATATG
* * *
88862928 AAAATGACTATTTTGCCCCTAGGT
1 AAAATGACCATTATACCCCTAGGT
88862952 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
88862975 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (24 bp):
AAAATGACCATTATACCCCTAGGT
Found at i:88863058 original size:11 final size:11
Alignment explanation
Indices: 88863022--88863077 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
88863012 TATGGTATGT
88863022 ATGATATGCAC
1 ATGATATGCAC
* *
88863033 ATGAAATG--T
1 ATGATATGCAC
88863042 ATGATATGCAC
1 ATGATATGCAC
*
88863053 ATGATATG--T
1 ATGATATGCAC
88863062 ATGATATGCAC
1 ATGATATGCAC
88863073 ATGAT
1 ATGAT
88863078 GTAATCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:88863077 original size:20 final size:20
Alignment explanation
Indices: 88863017--88863077 Score: 113
Period size: 20 Copynumber: 3.0 Consensus size: 20
88863007 ATAAATATGG
88863017 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
*
88863037 AATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
88863057 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
88863077 T
1 T
88863078 GTAATCATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.34
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:88863154 original size:24 final size:24
Alignment explanation
Indices: 88863127--88863269 Score: 209
Period size: 24 Copynumber: 6.0 Consensus size: 24
88863117 GAGGAAGTGA
88863127 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
88863151 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
88863175 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
88863198 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
88863222 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
88863246 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
88863270 ATGATAAAGC
Statistics
Matches: 111, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
23 23 0.21
24 77 0.69
25 11 0.10
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:88863220 original size:47 final size:47
Alignment explanation
Indices: 88863127--88863269 Score: 207
Period size: 47 Copynumber: 3.0 Consensus size: 47
88863117 GAGGAAGTGA
88863127 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATC
*
88863175 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
* * *
88863222 GAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTAT
88863270 ATGATAAAGC
Statistics
Matches: 88, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
47 43 0.49
48 34 0.39
49 11 0.12
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
Found at i:88863243 original size:71 final size:72
Alignment explanation
Indices: 88863127--88863270 Score: 220
Period size: 71 Copynumber: 2.0 Consensus size: 72
88863117 GAGGAAGTGA
*
88863127 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAG-GGCTTATGCC-
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGC-TAGGCCT
88863190 CCAGTTAT
65 CCAGTTAT
** * *
88863198 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGCTAGGCCTC
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
88863263 CAGTTAT
66 CAGTTAT
88863270 A
1 A
88863271 TGATAAAGCA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 54 0.82
72 12 0.18
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (72 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
CAGTTAT
Found at i:88863497 original size:31 final size:31
Alignment explanation
Indices: 88863461--88863555 Score: 163
Period size: 31 Copynumber: 3.1 Consensus size: 31
88863451 CATTTACAGT
*
88863461 AAAGGCTTCGGCCTAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
88863492 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
* *
88863523 AAAGGCTTCCGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
88863554 AA
1 AA
88863556 TATGAAAAGG
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 61 1.00
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:88868145 original size:93 final size:93
Alignment explanation
Indices: 88868033--88868204 Score: 247
Period size: 93 Copynumber: 1.8 Consensus size: 93
88868023 GCCCATAAGT
* * *
88868033 GAACTCGGACTCAACTCAACGAGCTT-GGGCGCTCACATCCATAAGTGAACGCAGACTCAACTCA
1 GAACTCGAACTCAACTCAACGAG-TTCGGACACTCACATCCATAAGTGAACGCAGACTCAACTCA
*
88868097 ATGAGCTCGGATGCCTAGTTACATCTCTC
65 ACGAGCTCGGATGCCTAGTTACATCTCTC
* * * *
88868126 GAACTCGAACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGTTCGGACACTCACATCCATAAGTGAACGCAGACTCAACTCAA
*
88868191 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
88868205 CAAATATCCT
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
92 2 0.03
93 67 0.97
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
GAACTCGAACTCAACTCAACGAGTTCGGACACTCACATCCATAAGTGAACGCAGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:88868188 original size:46 final size:45
Alignment explanation
Indices: 88868025--88868200 Score: 151
Period size: 46 Copynumber: 3.8 Consensus size: 45
88868015 TGTAACCCGC
* **
88868025 CCATAAGTGAACTCGGACTCAACTCAACGAGCTT-GGGCGCTCACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAG-TTCGGACATTC-CAT
* * * * *
88868071 CCATAAGTGAACGCAGACTCAACTCAATGAGCTCGG--ATGCCTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCC-A--T
* *** *
88868117 ACATCTCTCGAACTCGAACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGTTCGGACATTC-CAT
88868164 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
88868201 TGCCCAAATA
Statistics
Matches: 100, Mismatches: 22, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
43 1 0.01
44 2 0.02
45 1 0.01
46 63 0.63
47 28 0.28
49 4 0.04
50 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCCAT
Found at i:88870600 original size:30 final size:30
Alignment explanation
Indices: 88870557--88870644 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
88870547 CAAATATAAT
88870557 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
88870586 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * *
88870616 AAGAGATCCAG-ATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
88870645 CGATATATGC
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
29 23 0.46
30 27 0.54
ACGTcount: A:0.58, C:0.16, G:0.16, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:88870605 original size:15 final size:15
Alignment explanation
Indices: 88870557--88870635 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
88870547 CAAATATAAT
*
88870557 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
88870571 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
88870586 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
88870601 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
*
88870616 AAGAGATCCAG-ATA
1 AAGAAATCCAGAATA
88870630 AAGAAA
1 AAGAAA
88870636 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
14 17 0.31
15 37 0.67
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.16, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:88879937 original size:39 final size:39
Alignment explanation
Indices: 88879816--88879993 Score: 225
Period size: 39 Copynumber: 4.5 Consensus size: 39
88879806 GGATATAACG
* *
88879816 ACTCGCTCAAATGCCTTCGGGAC-AAAGCCCGG-TTATAGTA
1 ACTCGCACAAATGCCTTCGGG-CTTAA-CCCGGATT-TAGTA
* * * *
88879856 ACTCGCACGAATGCCTTCGAGACTTAACCCGGGTTTAATA
1 ACTCGCACAAATGCCTTCG-GGCTTAACCCGGATTTAGTA
88879896 ACTCGCACAAATGCCTTCGGGCTTAACCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGCTTAACCCGGATTTAGTA
*
88879935 ACTCGCACAAATGCCTTCGGGCTTAACCCGGATTTATTA
1 ACTCGCACAAATGCCTTCGGGCTTAACCCGGATTTAGTA
* *
88879974 ACTCGCACGAACGCCTTCGG
1 ACTCGCACAAATGCCTTCGG
88879994 ATTTAGTCCG
Statistics
Matches: 123, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
39 73 0.59
40 45 0.37
41 5 0.04
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (39 bp):
ACTCGCACAAATGCCTTCGGGCTTAACCCGGATTTAGTA
Found at i:88880006 original size:39 final size:39
Alignment explanation
Indices: 88879790--88879994 Score: 209
Period size: 39 Copynumber: 5.2 Consensus size: 39
88879780 GAATCACGTA
* * ** *
88879790 CCTTCGGAATTTAA-CCGGATATAACGACTCGCTCAAATG
1 CCTTCGG-ACTTAACCCGGATTTAATAACTCGCACAAATG
* * *
88879829 CCTTCGGGAC-AAAGCCCGG-TTATAGTAACTCGCACGAATG
1 CCTTC-GGACTTAA-CCCGGATT-TAATAACTCGCACAAATG
*
88879869 CCTTCGAGACTTAACCCGGGTTTAATAACTCGCACAAATG
1 CCTTCG-GACTTAACCCGGATTTAATAACTCGCACAAATG
* *
88879909 CCTTCGGGCTTAACCCGGATTTAGTAACTCGCACAAATG
1 CCTTCGGACTTAACCCGGATTTAATAACTCGCACAAATG
* * * *
88879948 CCTTCGGGCTTAACCCGGATTTATTAACTCGCACGAACG
1 CCTTCGGACTTAACCCGGATTTAATAACTCGCACAAATG
88879987 CCTTCGGA
1 CCTTCGGA
88879995 TTTAGTCCGG
Statistics
Matches: 141, Mismatches: 18, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
38 2 0.01
39 81 0.57
40 54 0.38
41 4 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (39 bp):
CCTTCGGACTTAACCCGGATTTAATAACTCGCACAAATG
Found at i:88880029 original size:78 final size:78
Alignment explanation
Indices: 88879816--88880045 Score: 203
Period size: 78 Copynumber: 2.9 Consensus size: 78
88879806 GGATATAACG
* * * * ** * *
88879816 ACTCGCTCAAATGCCTTCGGGAC-AAAGCCCGGTTATAGTAACTCGCACGAATGCCTTCGAGACT
1 ACTCGCACAAACGCCTTC-GGACTTAA-CCCGGATATAGTAACTAACACAAATGCCTTCG-GGCT
*
88879880 TAACCCGGGTTTAATA
63 TAACCCGGATTTAATA
* * * **
88879896 ACTCGCACAAATGCCTTCGGGCTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGGCTTAA
1 ACTCGCACAAACGCCTTCGGACTTAACCCGGATATAGTAACTAACACAAATGCCTTCGGGCTTAA
*
88879961 CCCGGATTTATTA
66 CCCGGATTTAATA
* * ** * *
88879974 ACTCGCACGAACGCCTTCGGATTTAGTCCGGATATGGTCACTTAACACAAA-GCCTTCGGGACTT
1 ACTCGCACAAACGCCTTCGGACTTAACCCGGATATAGTAAC-TAACACAAATGCCTTCGGG-CTT
*
88880038 AGCCCGGA
64 AACCCGGA
88880046 CATCATTCAA
Statistics
Matches: 126, Mismatches: 21, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
78 58 0.46
79 49 0.39
80 19 0.15
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (78 bp):
ACTCGCACAAACGCCTTCGGACTTAACCCGGATATAGTAACTAACACAAATGCCTTCGGGCTTAA
CCCGGATTTAATA
Found at i:88883534 original size:25 final size:25
Alignment explanation
Indices: 88883500--88883549 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
88883490 ACTCAAAGTA
88883500 AACTCCTAATATGCCTAGATATATG
1 AACTCCTAATATGCCTAGATATATG
*
88883525 AACTCCTAATATGCCTAGGTATATG
1 AACTCCTAATATGCCTAGATATATG
88883550 TCTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (25 bp):
AACTCCTAATATGCCTAGATATATG
Found at i:88887238 original size:19 final size:19
Alignment explanation
Indices: 88887184--88887238 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 19
88887174 ATTCAGAAGC
* *
88887184 TAACAAAATTAATAAC--C
1 TAACAAAATTACTAACAAA
* **
88887201 TAACAAAATAACTTTCAAA
1 TAACAAAATTACTAACAAA
88887220 TAACAAAATTACTAACAAA
1 TAACAAAATTACTAACAAA
88887239 ACTATCTATT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
17 12 0.43
19 16 0.57
ACGTcount: A:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (19 bp):
TAACAAAATTACTAACAAA
Found at i:88888022 original size:16 final size:16
Alignment explanation
Indices: 88887990--88888027 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
88887980 ATAATAAGTG
*
88887990 AAAAACAATATATTCA
1 AAAAAAAATATATTCA
88888006 AAAAAAAAT-TATGTCA
1 AAAAAAAATATAT-TCA
88888022 AAAAAA
1 AAAAAA
88888028 TTTATTCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 3 0.15
16 17 0.85
ACGTcount: A:0.68, C:0.08, G:0.03, T:0.21
Consensus pattern (16 bp):
AAAAAAAATATATTCA
Found at i:88896293 original size:48 final size:48
Alignment explanation
Indices: 88896222--88896313 Score: 184
Period size: 48 Copynumber: 1.9 Consensus size: 48
88896212 GTTGGTATTG
88896222 TTTGACAAGTGGGATATGAATAAAAACCTTCTTCTCTAAATTACATTT
1 TTTGACAAGTGGGATATGAATAAAAACCTTCTTCTCTAAATTACATTT
88896270 TTTGACAAGTGGGATATGAATAAAAACCTTCTTCTCTAAATTAC
1 TTTGACAAGTGGGATATGAATAAAAACCTTCTTCTCTAAATTAC
88896314 TTTCTATTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (48 bp):
TTTGACAAGTGGGATATGAATAAAAACCTTCTTCTCTAAATTACATTT
Found at i:88899010 original size:3 final size:3
Alignment explanation
Indices: 88899002--88899059 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
88898992 ATAGCTTCTC
88899002 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
88899050 ATT ATT ATT A
1 ATT ATT ATT A
88899060 CATTTGCAGT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:88905643 original size:16 final size:17
Alignment explanation
Indices: 88905615--88905650 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
88905605 AACAATTTAC
88905615 AGAAAAGAAAAGGAAGA
1 AGAAAAGAAAAGGAAGA
88905632 AGAAAA-AAAAGGAAGA
1 AGAAAAGAAAAGGAAGA
88905648 AGA
1 AGA
88905651 GAGAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (17 bp):
AGAAAAGAAAAGGAAGA
Found at i:88905657 original size:16 final size:16
Alignment explanation
Indices: 88905618--88905658 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
88905608 AATTTACAGA
88905618 AAAGAAAAGGAAGAAG
1 AAAGAAAAGGAAGAAG
*
88905634 AAAAAAAAGGAAGAAG
1 AAAGAAAAGGAAGAAG
*
88905650 AGAGAAAAG
1 AAAGAAAAG
88905659 AAAAGAATCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (16 bp):
AAAGAAAAGGAAGAAG
Found at i:88909467 original size:29 final size:29
Alignment explanation
Indices: 88909381--88909467 Score: 72
Period size: 29 Copynumber: 2.9 Consensus size: 29
88909371 AAATAAACAG
* *
88909381 TCAATAAT-ATGCAATTTCAATCCAAAA-AT
1 TCAATAATCATACAA-TT-AATACAAAATAT
* *
88909410 TCAATTTAATCATTC-ATTAATAGATAAATAT
1 TCAA--TAATCATACAATTAATACA-AAATAT
88909441 TCAATAATCATACAATTAATACAAAAT
1 TCAATAATCATACAATTAATACAAAAT
88909468 GAGACTTAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
29 20 0.43
30 13 0.28
31 11 0.23
32 3 0.06
ACGTcount: A:0.49, C:0.14, G:0.02, T:0.34
Consensus pattern (29 bp):
TCAATAATCATACAATTAATACAAAATAT
Found at i:88911595 original size:40 final size:40
Alignment explanation
Indices: 88911540--88911749 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
88911530 AACATTGGAA
88911540 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
88911580 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
88911620 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
88911660 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
88911699 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
88911740 CTATATCCGG
1 ATATATCCGG
88911750 TTAAATCCCG
Statistics
Matches: 151, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.01
40 149 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:88919731 original size:40 final size:40
Alignment explanation
Indices: 88919676--88919885 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
88919666 AACATTGGAA
88919676 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
88919716 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
88919756 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
88919796 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
88919835 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
88919876 CTATATCCGG
1 ATATATCCGG
88919886 TTAAATCCCG
Statistics
Matches: 151, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.01
40 149 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:88923880 original size:40 final size:40
Alignment explanation
Indices: 88923776--88924005 Score: 192
Period size: 41 Copynumber: 5.9 Consensus size: 40
88923766 CGTTTGTCCG
* * * * **
88923776 AAACGCCACTAAAAGCTAAACTATAGCGGCGTTTTTGCCAA
1 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTATC-A
*
88923817 AAACGCCACTAAAAACTGGTCAATAGCGGCGTTTTTATCA
1 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTATCA
* * *
88923857 AAACGCCACTAAAAGCTGATCAATAGCGGCGTTTTAATCTC
1 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTATC-A
* * *
88923898 AAACGCCACT---AA---AT---T-GCGGTGTTTTTGTCCT
1 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTAT-CA
* * *
88923929 AAACGCCACAAAAAACTGATCAATTGTGGCGTTTTTATCCA
1 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTAT-CA
* *
88923970 AAACGCCACTAAAAACTGATTAATAGCGGTGTTTTT
1 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTT
88924006 GGTCCAAACG
Statistics
Matches: 151, Mismatches: 26, Indels: 24
0.75 0.13 0.12
Matches are distributed among these distances:
31 19 0.13
32 2 0.01
34 2 0.01
35 2 0.01
37 2 0.01
38 1 0.01
40 38 0.25
41 85 0.56
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (40 bp):
AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTATCA
Found at i:88924015 original size:41 final size:41
Alignment explanation
Indices: 88923913--88924024 Score: 136
Period size: 41 Copynumber: 2.7 Consensus size: 41
88923903 CCACTAAATT
* *
88923913 GCGGTGTTTTTGTCCTAAACGCCACAAAAAACTGATCAATT
1 GCGGTGTTTTTGTCCAAAACGCCACAAAAAACTGATCAATA
* * * * *
88923954 GTGGCGTTTTTATCCAAAACGCCACTAAAAACTGATTAATA
1 GCGGTGTTTTTGTCCAAAACGCCACAAAAAACTGATCAATA
*
88923995 GCGGTGTTTTTGGTCC-AAACGCCGCAAAAA
1 GCGGTGTTTTT-GTCCAAAACGCCACAAAAA
88924025 GTTTAGCAGG
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
41 55 0.95
42 3 0.05
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (41 bp):
GCGGTGTTTTTGTCCAAAACGCCACAAAAAACTGATCAATA
Found at i:88924367 original size:28 final size:28
Alignment explanation
Indices: 88924307--88924382 Score: 75
Period size: 28 Copynumber: 2.7 Consensus size: 28
88924297 TGGCTTTCTG
* *
88924307 TAAACCCTTAAATCTTAAACATTAAACCC
1 TAAACCC-TAAATCTTAAACATTAAAACA
*
88924336 TAAACCCTAAATTTTAAATCA-TAAAACA
1 TAAACCCTAAATCTTAAA-CATTAAAACA
*
88924364 TAAACACT-AATCTATAAAC
1 TAAACCCTAAATCT-TAAAC
88924383 TCCAAAACCC
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
27 5 0.12
28 26 0.65
29 9 0.22
ACGTcount: A:0.50, C:0.22, G:0.00, T:0.28
Consensus pattern (28 bp):
TAAACCCTAAATCTTAAACATTAAAACA
Found at i:88926189 original size:39 final size:39
Alignment explanation
Indices: 88926078--88926270 Score: 278
Period size: 39 Copynumber: 4.9 Consensus size: 39
88926068 GTTCAAAACA
* * * * *
88926078 CCTTCGGGACATAGCCCGGTTATGATAACCCGCACAAATG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
* *
88926118 CCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
*
88926158 CCTTCGGGCTTAGCCCGGATATCATAGCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
*
88926197 CCTTCGGGCTTAGCCCGGATATCATAGCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
*
88926236 CCTTCGGGCTTAGCCCGGATATCACAACTCGCACA
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACA
88926271 TTCATACACA
Statistics
Matches: 141, Mismatches: 12, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
39 100 0.71
40 41 0.29
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.23
Consensus pattern (39 bp):
CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
Found at i:88934270 original size:39 final size:39
Alignment explanation
Indices: 88934170--88934390 Score: 325
Period size: 39 Copynumber: 5.6 Consensus size: 39
88934160 CTTCAGGACA
* * * *
88934170 TAGCCCGGTTATGATAACCCGCACAAATGCCTTCGGGACT
1 TAGCCCGGATATCATAACTCGCACAATTGCCTTCGGG-CT
* *
88934210 TAACCCGGATATCACAACTCGCACAATTGCCTTCGGGCT
1 TAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCT
*
88934249 TAGCCCGGATATCATAGCTCGCACAATTGCCTTCGGGCT
1 TAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCT
* * *
88934288 TAGCTCGGATATCATAGCTCGCAAAATTGCCTTCGGGCT
1 TAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCT
*
88934327 TAGCCCGGATATCATAGCTCGCACAATTGCCTTCGGGCT
1 TAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCT
*
88934366 TAGCCCGGATATCACAACTCGCACA
1 TAGCCCGGATATCATAACTCGCACA
88934391 TTCATACACA
Statistics
Matches: 166, Mismatches: 15, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 135 0.81
40 31 0.19
ACGTcount: A:0.24, C:0.31, G:0.21, T:0.24
Consensus pattern (39 bp):
TAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCT
Found at i:88937779 original size:14 final size:15
Alignment explanation
Indices: 88937760--88937789 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
88937750 TGTGTTTATA
88937760 TAAATACAT-AATTC
1 TAAATACATAAATTC
88937774 TAAATACATAAATTC
1 TAAATACATAAATTC
88937789 T
1 T
88937790 GAAGTTTGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAATACATAAATTC
Found at i:88942255 original size:24 final size:24
Alignment explanation
Indices: 88942215--88942281 Score: 93
Period size: 24 Copynumber: 2.8 Consensus size: 24
88942205 ATTATTATTG
*
88942215 AAATATT-CCGTCCGTTTTATCAC
1 AAATATTATCGTCCGTTTTATCAC
*
88942238 AAATATTATTC-TCCGTTTTATTAC
1 AAATATTA-TCGTCCGTTTTATCAC
88942262 AAATATTATCGTCCGTTTTA
1 AAATATTATCGTCCGTTTTA
88942282 CCATTTAAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
23 9 0.23
24 29 0.74
25 1 0.03
ACGTcount: A:0.28, C:0.19, G:0.07, T:0.45
Consensus pattern (24 bp):
AAATATTATCGTCCGTTTTATCAC
Found at i:88942502 original size:15 final size:15
Alignment explanation
Indices: 88942458--88942513 Score: 73
Period size: 15 Copynumber: 3.8 Consensus size: 15
88942448 AACGACATGT
88942458 ATATTATTTAATTAAA
1 ATATTATTTAATT-AA
88942474 ATAATT-TTT-A-TAA
1 AT-ATTATTTAATTAA
88942487 ATATTATTTAATTAA
1 ATATTATTTAATTAA
88942502 ATATTATTTAAT
1 ATATTATTTAAT
88942514 CCCGCTACTT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
12 3 0.08
13 7 0.19
14 2 0.06
15 16 0.44
16 5 0.14
17 3 0.08
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATATTATTTAATTAA
Found at i:88942630 original size:9 final size:9
Alignment explanation
Indices: 88942618--88942834 Score: 125
Period size: 9 Copynumber: 23.6 Consensus size: 9
88942608 TATTTGATAT
*
88942618 CATAATTTA
1 CATAACTTA
88942627 CATAACTTA
1 CATAACTTA
* *
88942636 TATAACATA
1 CATAACTTA
*
88942645 TATAACTTA
1 CATAACTTA
88942654 CATAACTTA
1 CATAACTTA
* *
88942663 TATAACATA
1 CATAACTTA
88942672 CATAACTTA
1 CATAACTTA
*
88942681 TATAACTTA
1 CATAACTTA
*
88942690 TATAACTTA
1 CATAACTTA
* *
88942699 GATAA-ATA
1 CATAACTTA
*
88942707 TATAACTTA
1 CATAACTTA
88942716 CATAACTTA
1 CATAACTTA
88942725 CATAATACTTA
1 CAT-A-ACTTA
* *
88942736 AATATATTTTATA
1 CATA-A--CT-TA
*
88942749 TCATAATTTA
1 -CATAACTTA
88942759 CATAACTTA
1 CATAACTTA
*
88942768 TATAACTTA
1 CATAACTTA
* *
88942777 GATAA-ATA
1 CATAACTTA
* *
88942785 TATAATTTA
1 CATAACTTA
*
88942794 CATAA-ATA
1 CATAACTTA
* * *
88942802 TATATCATA
1 CATAACTTA
*
88942811 TCATAAATTA
1 -CATAACTTA
88942821 CATAACTTA
1 CATAACTTA
88942830 CATAA
1 CATAA
88942835 TACTTAAATA
Statistics
Matches: 165, Mismatches: 33, Indels: 20
0.76 0.15 0.09
Matches are distributed among these distances:
8 17 0.10
9 121 0.73
10 11 0.07
11 9 0.05
12 1 0.01
13 3 0.02
14 3 0.02
ACGTcount: A:0.48, C:0.12, G:0.01, T:0.39
Consensus pattern (9 bp):
CATAACTTA
Found at i:88942640 original size:18 final size:18
Alignment explanation
Indices: 88942619--88942834 Score: 141
Period size: 18 Copynumber: 11.7 Consensus size: 18
88942609 ATTTGATATC
*
88942619 ATAATTTACATAACTTAT
1 ATAACTTACATAACTTAT
* * *
88942637 ATAACATATATAACTTAC
1 ATAACTTACATAACTTAT
* * *
88942655 ATAACTTATATAACATAC
1 ATAACTTACATAACTTAT
*
88942673 ATAACTTATATAACTTAT
1 ATAACTTACATAACTTAT
* *
88942691 ATAACTTAGATAA-ATAT
1 ATAACTTACATAACTTAT
*
88942708 ATAACTTACATAACTTAC
1 ATAACTTACATAACTTAT
* *
88942726 ATAATACTTAAATATATTTTATAT
1 AT-A-ACTTACATA-A--CT-TAT
*
88942750 CATAATTTACATAACTTAT
1 -ATAACTTACATAACTTAT
* *
88942769 ATAACTTAGATAA-ATAT
1 ATAACTTACATAACTTAT
* *
88942786 ATAATTTACATAA-ATAT
1 ATAACTTACATAACTTAT
* * * *
88942803 ATATCATATCATAAATTAC
1 ATAACTTA-CATAACTTAT
88942822 ATAACTTACATAA
1 ATAACTTACATAA
88942835 TACTTAAATA
Statistics
Matches: 157, Mismatches: 31, Indels: 20
0.75 0.15 0.10
Matches are distributed among these distances:
17 38 0.24
18 83 0.53
19 12 0.08
20 9 0.06
21 1 0.01
22 1 0.01
23 8 0.05
24 3 0.02
25 2 0.01
ACGTcount: A:0.48, C:0.12, G:0.01, T:0.39
Consensus pattern (18 bp):
ATAACTTACATAACTTAT
Found at i:88942770 original size:105 final size:105
Alignment explanation
Indices: 88942634--88942858 Score: 294
Period size: 105 Copynumber: 2.2 Consensus size: 105
88942624 TTACATAACT
* * * *
88942634 TATATAACATAT-ATAACTTACATAACTTATATAACATACATAACTTATATAACTTATATAACTT
1 TATATATCATATCATAACTTACATAACTTATATAACATACATAA-ATATATAACTTACATAA-AT
*
88942698 AGATA-AATAT-ATAACTTACATAACTTACATAATACTTAAA
64 AGATATAATATCATAAATTACATAACTTACATAATACTTAAA
* * * * * * *
88942738 TATATTTTATATCATAATTTACATAACTTATATAACTTAGATAAATATATAATTTACATAAATAT
1 TATATATCATATCATAACTTACATAACTTATATAACATACATAAATATATAACTTACATAAATAG
*
88942803 ATATCATATCATAAATTACATAACTTACATAATACTTAAA
66 ATATAATATCATAAATTACATAACTTACATAATACTTAAA
88942843 TATATATCATATCATA
1 TATATATCATATCATA
88942859 CATAACTAGT
Statistics
Matches: 103, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
103 5 0.05
104 27 0.26
105 71 0.69
ACGTcount: A:0.48, C:0.12, G:0.01, T:0.39
Consensus pattern (105 bp):
TATATATCATATCATAACTTACATAACTTATATAACATACATAAATATATAACTTACATAAATAG
ATATAATATCATAAATTACATAACTTACATAATACTTAAA
Found at i:88942798 original size:26 final size:26
Alignment explanation
Indices: 88942760--88942834 Score: 62
Period size: 26 Copynumber: 2.8 Consensus size: 26
88942750 CATAATTTAC
* *
88942760 ATAACTTATATAACTTAGATAAATAT
1 ATAACTTACATAACTTACATAAATAT
* * * *
88942786 ATAATTTACATAA-ATATATATCATAT
1 ATAACTTACATAACTTACATA-AATAT
*
88942812 CATAAATTACATAACTTACATAA
1 -ATAACTTACATAACTTACATAA
88942835 TACTTAAATA
Statistics
Matches: 37, Mismatches: 9, Indels: 5
0.73 0.18 0.10
Matches are distributed among these distances:
25 5 0.14
26 15 0.41
27 12 0.32
28 5 0.14
ACGTcount: A:0.51, C:0.11, G:0.01, T:0.37
Consensus pattern (26 bp):
ATAACTTACATAACTTACATAAATAT
Found at i:88942829 original size:62 final size:61
Alignment explanation
Indices: 88942627--88942826 Score: 208
Period size: 62 Copynumber: 3.2 Consensus size: 61
88942617 TCATAATTTA
* * * *
88942627 CATAACTTATATAACATATATAACTTACATAACTTATATAACATACATAACTTATATAACTTAT
1 CATAACTTACATAACATATATAACTTACATAACTTATAT-A-ATACATAA-ATATATATCATAT
* * * * *
88942691 -ATAACTTAGATAA-ATATATAACTTACATAACTTACATAATACTTAAATATATTTTATAT
1 CATAACTTACATAACATATATAACTTACATAACTTATATAATACATAAATATATATCATAT
* * * *
88942750 CATAATTTACATAACTTATATAACTTAGATAA-ATATATAATTTACATAAATATATATCATAT
1 CATAACTTACATAACATATATAACTTACATAACTTATATAA--TACATAAATATATATCATAT
*
88942812 CATAAATTACATAAC
1 CATAACTTACATAAC
88942827 TTACATAATA
Statistics
Matches: 114, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
59 8 0.07
60 24 0.21
61 16 0.14
62 54 0.47
63 12 0.11
ACGTcount: A:0.48, C:0.12, G:0.01, T:0.39
Consensus pattern (61 bp):
CATAACTTACATAACATATATAACTTACATAACTTATATAATACATAAATATATATCATAT
Found at i:88948809 original size:31 final size:31
Alignment explanation
Indices: 88948763--88948829 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
88948753 TGGTTGTATT
* *
88948763 TTTTATGTTAAATTTGCTGTTTTTGGCTGCA
1 TTTTATATTAAATTTGCTGTATTTGGCTGCA
* * * *
88948794 TTTTATATTATATTTGTTGTATTTGGTTGGA
1 TTTTATATTAAATTTGCTGTATTTGGCTGCA
88948825 TTTTA
1 TTTTA
88948830 ATGTAGGAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.18, C:0.04, G:0.18, T:0.60
Consensus pattern (31 bp):
TTTTATATTAAATTTGCTGTATTTGGCTGCA
Found at i:88948957 original size:43 final size:43
Alignment explanation
Indices: 88948907--88949023 Score: 207
Period size: 43 Copynumber: 2.7 Consensus size: 43
88948897 AAAAAGCGCT
* *
88948907 GCTAAAAGCCTTGACGTTTAGCGGTGCTTTTCCCACAAACGCC
1 GCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAACGCC
88948950 GCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAACGCC
1 GCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAACGCC
*
88948993 GCTAAAAGCCTTGACCTTTAGCGGCGTTTTT
1 GCTAAAAGCCTTGACCTTTAGCGGCGCTTTT
88949024 TTTCCAATAA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 71 1.00
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.27
Consensus pattern (43 bp):
GCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAACGCC
Found at i:88950312 original size:27 final size:26
Alignment explanation
Indices: 88950275--88950325 Score: 93
Period size: 27 Copynumber: 1.9 Consensus size: 26
88950265 ATCATTTGTC
88950275 TTTTTATTCAAAATTGGAGAACTTGG
1 TTTTTATTCAAAATTGGAGAACTTGG
88950301 TTTTCTATTCAAAATTGGAGAACTT
1 TTTT-TATTCAAAATTGGAGAACTT
88950326 AGTTATTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (26 bp):
TTTTTATTCAAAATTGGAGAACTTGG
Found at i:88958956 original size:6 final size:6
Alignment explanation
Indices: 88958937--88958967 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
88958927 GTGTGTCAAA
*
88958937 TACTGT TACCGT TACTGT TACTGT TACTGT T
1 TACTGT TACTGT TACTGT TACTGT TACTGT T
88958968 TCGAATTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.48
Consensus pattern (6 bp):
TACTGT
Found at i:88959197 original size:2 final size:2
Alignment explanation
Indices: 88959190--88959219 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
88959180 ATAAGAATGG
88959190 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
88959220 ATTGAATGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:88963113 original size:39 final size:39
Alignment explanation
Indices: 88963048--88963173 Score: 112
Period size: 39 Copynumber: 3.2 Consensus size: 39
88963038 CATATTCACT
* * * *
88963048 TTTAAGCATATATGACATTA-TACATATAAATACACAACA
1 TTTAAACATATATCACAATACT-CATATAAATACATAACA
* * *
88963087 TTTAAACATATATCACAATACTCATATAACTCCATAACG
1 TTTAAACATATATCACAATACTCATATAAATACATAACA
** **
88963126 TTTAAGTATATATCGTAATACTCATAT-AATCACATAACA
1 TTTAAACATATATCACAATACTCATATAAAT-ACATAACA
*
88963165 TTCAAACAT
1 TTTAAACAT
88963174 GGATATTGCA
Statistics
Matches: 68, Mismatches: 17, Indels: 4
0.76 0.19 0.04
Matches are distributed among these distances:
38 2 0.03
39 65 0.96
40 1 0.01
ACGTcount: A:0.45, C:0.18, G:0.04, T:0.33
Consensus pattern (39 bp):
TTTAAACATATATCACAATACTCATATAAATACATAACA
Found at i:88963243 original size:15 final size:15
Alignment explanation
Indices: 88963223--88963265 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
88963213 GCATAATGGT
88963223 CACATATCATATAAA
1 CACATATCATATAAA
* *
88963238 CACATATCACAATACA
1 CACATATCA-TATAAA
88963254 CACATATTCATA
1 CACATA-TCATA
88963266 ATTTAAGATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 9 0.39
16 11 0.48
17 3 0.13
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (15 bp):
CACATATCATATAAA
Found at i:88979119 original size:15 final size:15
Alignment explanation
Indices: 88979084--88979119 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
88979074 TTAAATATAT
88979084 TTTTATTAATTGAAA
1 TTTTATTAATTGAAA
* *
88979099 TATTATTAATTGATA
1 TTTTATTAATTGAAA
88979114 TTTTAT
1 TTTTAT
88979120 GAGTTAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (15 bp):
TTTTATTAATTGAAA
Found at i:88980505 original size:62 final size:62
Alignment explanation
Indices: 88980434--88980557 Score: 230
Period size: 62 Copynumber: 2.0 Consensus size: 62
88980424 ACTTTTCTAC
88980434 ATAACAAAATATTGTTACTATCAACATTATAAACTACAAACAATAACTGGAGACATTGACTT
1 ATAACAAAATATTGTTACTATCAACATTATAAACTACAAACAATAACTGGAGACATTGACTT
* *
88980496 ATAATAAAATATTGTTACTATCAACATTATAAACTACTAACAATAACTGGAGACATTGACTT
1 ATAACAAAATATTGTTACTATCAACATTATAAACTACAAACAATAACTGGAGACATTGACTT
88980558 TCCAGTTTTT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (62 bp):
ATAACAAAATATTGTTACTATCAACATTATAAACTACAAACAATAACTGGAGACATTGACTT
Found at i:88980939 original size:12 final size:12
Alignment explanation
Indices: 88980924--88980948 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
88980914 TGCTTTCAGC
88980924 TATAGTTGGGGG
1 TATAGTTGGGGG
88980936 TATAGTTGGGGG
1 TATAGTTGGGGG
88980948 T
1 T
88980949 CTACGATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.48, T:0.36
Consensus pattern (12 bp):
TATAGTTGGGGG
Found at i:88982226 original size:57 final size:56
Alignment explanation
Indices: 88982134--88982312 Score: 241
Period size: 57 Copynumber: 3.1 Consensus size: 56
88982124 TAATTTTTAT
* * *
88982134 TTTTCATTTTCATTTTGGAGGAAAATCACATTCATTTCCAAATGATTCAATTTCTCCA
1 TTTTCATTTTCATTTTGGA-GAAAATCATAATCATTTCCAAATGATTC-ATTTCTCTA
* *
88982192 TTTTCATTTTCATGTTGGAGAAAATCATAATCATTTCCAAATGATTTCATTTATCTA
1 TTTTCATTTTCATTTTGGAGAAAATCATAATCATTTCCAAATGA-TTCATTTCTCTA
* * *
88982249 TTTTTATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGTTTCCCATTTCTCTA
1 TTTTCATTTTCATTTTGGAGAAAATCATAATCATTTCCAAATGATT--CATTTCTCTA
88982307 TTTTCA
1 TTTTCA
88982313 CCATTTCTAA
Statistics
Matches: 107, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
56 2 0.02
57 70 0.65
58 35 0.33
ACGTcount: A:0.29, C:0.17, G:0.08, T:0.46
Consensus pattern (56 bp):
TTTTCATTTTCATTTTGGAGAAAATCATAATCATTTCCAAATGATTCATTTCTCTA
Found at i:88985469 original size:27 final size:27
Alignment explanation
Indices: 88985372--88985476 Score: 117
Period size: 27 Copynumber: 3.9 Consensus size: 27
88985362 AGGAAGCGTC
*
88985372 CTGGTGACTATGCCACAATTATCTG-AT
1 CTGGTGACTCTGCCACAA-TATCTGTAT
* *
88985399 CTGGTGGCTCTGCCACATATATCTGT-C
1 CTGGTGACTCTGCCACA-ATATCTGTAT
*
88985426 CTGGTGGCTCTGCCACAATATCTGTAT
1 CTGGTGACTCTGCCACAATATCTGTAT
*
88985453 CTGGTGACT-TCGTCACAATATCTG
1 CTGGTGACTCT-GCCACAATATCTG
88985477 GCAGCCTCGC
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
26 9 0.13
27 58 0.85
28 1 0.01
ACGTcount: A:0.20, C:0.26, G:0.21, T:0.33
Consensus pattern (27 bp):
CTGGTGACTCTGCCACAATATCTGTAT
Found at i:88992937 original size:24 final size:21
Alignment explanation
Indices: 88992889--88992937 Score: 53
Period size: 24 Copynumber: 2.2 Consensus size: 21
88992879 CAAAATTCAA
*
88992889 AATAAATAAATAATAAAATCT
1 AATAAATAAATAATAAAATCC
*
88992910 AATAAATACAATATTATCAAATCC
1 AATAAATA-AATA--ATAAAATCC
88992934 AATA
1 AATA
88992938 TGGTTTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 8 0.35
22 4 0.17
24 11 0.48
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (21 bp):
AATAAATAAATAATAAAATCC
Found at i:88993370 original size:2 final size:2
Alignment explanation
Indices: 88993363--88993390 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
88993353 TACACAAATC
88993363 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
88993391 ACTCACGAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:89000014 original size:6 final size:6
Alignment explanation
Indices: 89000003--89000047 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
88999993 GTTTTTAATT
89000003 TGATAC TGATAC TGATAC TGATAC TGATAC TGATAC TGATAC TGA
1 TGATAC TGATAC TGATAC TGATAC TGATAC TGATAC TGATAC TGA
89000048 AGAAATGATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (6 bp):
TGATAC
Found at i:89010066 original size:30 final size:31
Alignment explanation
Indices: 89010030--89010101 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
89010020 ATGTGAAACG
89010030 TAGGTATGGTAT-TTCCATACTCAGCTATGA
1 TAGGTATGGTATCTTCCATACTCAGCTATGA
*
89010060 TAGGTATGGTATCTTCCATACTGAGCTATGA
1 TAGGTATGGTATCTTCCATACTCAGCTATGA
*
89010091 TACGTA-GGTAT
1 TAGGTATGGTAT
89010102 GGTATTTTCC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
30 17 0.44
31 22 0.56
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.36
Consensus pattern (31 bp):
TAGGTATGGTATCTTCCATACTCAGCTATGA
Found at i:89010099 original size:35 final size:35
Alignment explanation
Indices: 89010023--89010183 Score: 206
Period size: 35 Copynumber: 4.7 Consensus size: 35
89010013 TGGAAAAATG
*
89010023 TGAAACGTAGGTATGGTA-TTTCCATACTCAGCTA
1 TGAAACGTAGGTATGGTATTTTCCATACTGAGCTA
*
89010057 TG--A--TAGGTATGGTATCTTCCATACTGAGCTA
1 TGAAACGTAGGTATGGTATTTTCCATACTGAGCTA
* * * *
89010088 TGATACGTAGGTATGGTATTTTCCATACCGAGTTG
1 TGAAACGTAGGTATGGTATTTTCCATACTGAGCTA
* *
89010123 TGAAACGTAGGTATGGTATTTTCCATACTGTGTTA
1 TGAAACGTAGGTATGGTATTTTCCATACTGAGCTA
*
89010158 TGAAACATAGGTATGGTATTTTCCAT
1 TGAAACGTAGGTATGGTATTTTCCAT
89010184 GAGAAAAATC
Statistics
Matches: 111, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
30 11 0.10
31 16 0.14
32 1 0.01
33 1 0.01
34 2 0.02
35 80 0.72
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (35 bp):
TGAAACGTAGGTATGGTATTTTCCATACTGAGCTA
Found at i:89016498 original size:20 final size:20
Alignment explanation
Indices: 89016460--89016497 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
89016450 ATTAAAAGTA
89016460 AAAATGAATGTCAAATTTTG
1 AAAATGAATGTCAAATTTTG
*
89016480 AAAATGTATGTC-AATTTT
1 AAAATGAATGTCAAATTTT
89016498 TATTTTGGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.42, C:0.05, G:0.13, T:0.39
Consensus pattern (20 bp):
AAAATGAATGTCAAATTTTG
Found at i:89018079 original size:86 final size:86
Alignment explanation
Indices: 89017971--89018138 Score: 300
Period size: 86 Copynumber: 2.0 Consensus size: 86
89017961 TTTATTATTA
*
89017971 TTTTAATATAATGTTTAGTATTATTGATAATTCTTTTTAAATCTTTAAATAGGAAAATAAATCTA
1 TTTTAATATAATGTCTAGTATTATTGATAATTCTTTTTAAATCTTTAAATAGGAAAATAAATCTA
* *
89018036 TTTCAATGCTCTTGAATTAGT
66 TTTCAACGCGCTTGAATTAGT
*
89018057 TTTTAATATAATGTCTAGTATTATTGATAATTCTTTTTAAATCTTTAAATAGGAGAATAAATCTA
1 TTTTAATATAATGTCTAGTATTATTGATAATTCTTTTTAAATCTTTAAATAGGAAAATAAATCTA
89018122 TTTCAACGCGCTTGAAT
66 TTTCAACGCGCTTGAAT
89018139 CTATATCATT
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
86 78 1.00
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (86 bp):
TTTTAATATAATGTCTAGTATTATTGATAATTCTTTTTAAATCTTTAAATAGGAAAATAAATCTA
TTTCAACGCGCTTGAATTAGT
Found at i:89018988 original size:21 final size:20
Alignment explanation
Indices: 89018962--89019011 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
89018952 TTATTTATTT
*
89018962 AAAAATTTTATAAAAAATAAA
1 AAAAATTTT-TAAAAAACAAA
*
89018983 AAAAATATTTTAGAAAACAAA
1 AAAAAT-TTTTAAAAAACAAA
89019004 AGAAAATT
1 A-AAAATT
89019012 GTTTCAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (20 bp):
AAAAATTTTTAAAAAACAAA
Found at i:89023365 original size:11 final size:11
Alignment explanation
Indices: 89023349--89023373 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
89023339 TTCAGCTGAT
89023349 GAAAATGAAGA
1 GAAAATGAAGA
89023360 GAAAATGAAGA
1 GAAAATGAAGA
89023371 GAA
1 GAA
89023374 TTCTAGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.28, T:0.08
Consensus pattern (11 bp):
GAAAATGAAGA
Found at i:89024248 original size:11 final size:10
Alignment explanation
Indices: 89024232--89024293 Score: 65
Period size: 11 Copynumber: 6.0 Consensus size: 10
89024222 AAATTCGGAT
89024232 AGAAAAAAAA
1 AGAAAAAAAA
89024242 CAGAAAAAAAA
1 -AGAAAAAAAA
89024253 CAG--AAAAAA
1 -AGAAAAAAAA
89024262 AGAAACAAAAA
1 AGAAA-AAAAA
*
89024273 AGACTAAAAAA
1 AGA-AAAAAAA
89024284 AGAAAAAAAA
1 AGAAAAAAAA
89024294 CCAATTTGTG
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
8 2 0.04
9 6 0.13
10 7 0.16
11 29 0.64
12 1 0.02
ACGTcount: A:0.82, C:0.06, G:0.10, T:0.02
Consensus pattern (10 bp):
AGAAAAAAAA
Found at i:89024260 original size:22 final size:20
Alignment explanation
Indices: 89024235--89024294 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 20
89024225 TTCGGATAGA
89024235 AAAAAAACAGAAAAAAAACAG
1 AAAAAAA-AGAAAAAAAACAG
89024256 -AAAAAAAGAAACAAAAA-AG
1 AAAAAAAAGAAA-AAAAACAG
89024275 ACTAAAAAAAGAAAAAAAAC
1 A--AAAAAAAGAAAAAAAAC
89024295 CAATTTGTGG
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
19 7 0.21
20 11 0.32
21 5 0.15
22 11 0.32
ACGTcount: A:0.82, C:0.08, G:0.08, T:0.02
Consensus pattern (20 bp):
AAAAAAAAGAAAAAAAACAG
Found at i:89025791 original size:27 final size:26
Alignment explanation
Indices: 89025756--89025806 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 26
89025746 TGAATACTAT
*
89025756 TTAATTTTTTTCATTTATGTAATTTTAG
1 TTAATTTTTTT-ATTT-TATAATTTTAG
89025784 TTAA-TTTTTTATTTTATAATTTT
1 TTAATTTTTTTATTTTATAATTTT
89025807 TTATAATAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 8 0.36
26 4 0.18
27 6 0.27
28 4 0.18
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (26 bp):
TTAATTTTTTTATTTTATAATTTTAG
Found at i:89031119 original size:122 final size:126
Alignment explanation
Indices: 89030796--89031177 Score: 445
Period size: 124 Copynumber: 3.1 Consensus size: 126
89030786 GGCCAAGTAG
* * * * ***
89030796 GAACTACTA-TAGAAAAAGAGCGTCCACGTGAGAGTTTTTTTTCAGTAATTTTACTAATTTTGCA
1 GAACTAC-AGTAGAAAAAGAGCGTCCACATGAGAG-CTTTTTTCAGTAATTTTGCTGACAGTGCA
** * * * * * *
89030860 CCCTGCTCGAAGCGTTTTTGACACTATTTTTTCAAAACCATGTTGTCAAAATTATTTTTTCAG
64 TACTGCTTGAAGCGTTTTTGACATTATTTTTTCAGAACCATCTTCTCAAAATTATTTTTTCAA
* * * * *
89030923 GAACTACTGTAGAAAAAGGGCGTCCACATGGGAGCTTTTTTTAGTAATTTTGCTGACAGTGCATC
1 GAACTACAGTAGAAAAAGAGCGTCCACATGAGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATA
* *
89030988 CTGCTTGAAGCGTTTTTTATATTATTTTTTCAGAA-CAGTCTTCTC-AAATT-TTTTTTCAA
66 CTGCTTGAAGCGTTTTTGACATTATTTTTTCAGAACCA-TCTTCTCAAAATTATTTTTTCAA
* *
89031047 GAATTACAGTAGAAAAAGAGCGTCTACATGAGAGCTTTTTTCAGT-A-TTTGCTGACAGTGCATA
1 GAACTACAGTAGAAAAAGAGCGTCCACATGAGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATA
* *
89031110 CTGCTTGAAGCGTTTTTGACATTATTTTTTTAGAACCATTTTCTCAAAATTATTTTTTC-A
66 CTGCTTGAAGCGTTTTTGACATTATTTTTTCAGAACCATCTTCTCAAAATTATTTTTTCAA
89031170 GAAACTAC
1 G-AACTAC
89031178 TATAAAAAAA
Statistics
Matches: 217, Mismatches: 32, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
122 54 0.25
123 10 0.05
124 59 0.27
125 7 0.03
126 58 0.27
127 29 0.13
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (126 bp):
GAACTACAGTAGAAAAAGAGCGTCCACATGAGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATA
CTGCTTGAAGCGTTTTTGACATTATTTTTTCAGAACCATCTTCTCAAAATTATTTTTTCAA
Found at i:89031185 original size:122 final size:124
Alignment explanation
Indices: 89030801--89031185 Score: 424
Period size: 122 Copynumber: 3.1 Consensus size: 124
89030791 AGTAGGAACT
* * * * *** **
89030801 ACTA-TAGAAAAAGAGCGTCCACGTGAGAGTTTTTTTTCAGTAATTTTACTAATTTTGCACCCTG
1 ACTACTAGAAAAAGAGCGTCCACATGAGAG-CTTTTTTCAGTAATTTTGCTGACAGTGCATACTG
* * * * * *
89030865 CTCGAAGCGTTTTTGACACTATTTTTTCAAAACCATGTTGTCAAAATTATTTTTTCAGGA
65 CTTGAAGCGTTTTTGACATTATTTTTTCAGAACCATCTTCTCAAAATTATTTTTTCAGAA
* * * *
89030925 ACTACTGTAGAAAAAGGGCGTCCACATGGGAGCTTTTTTTAGTAATTTTGCTGACAGTGCATCCT
1 ACTAC--TAGAAAAAGAGCGTCCACATGAGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATACT
* *
89030990 GCTTGAAGCGTTTTTTATATTATTTTTTCAGAA-CAGTCTTCTC-AAATT-TTTTTTCAAGAA
64 GCTTGAAGCGTTTTTGACATTATTTTTTCAGAACCA-TCTTCTCAAAATTATTTTTTC-AGAA
* *
89031050 TTAC-AGTAGAAAAAGAGCGTCTACATGAGAGCTTTTTTCAGT-A-TTTGCTGACAGTGCATACT
1 --ACTACTAGAAAAAGAGCGTCCACATGAGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATACT
* *
89031112 GCTTGAAGCGTTTTTGACATTATTTTTTTAGAACCATTTTCTCAAAATTATTTTTTCAGAA
64 GCTTGAAGCGTTTTTGACATTATTTTTTCAGAACCATCTTCTCAAAATTATTTTTTCAGAA
*
89031173 ACTACTATAAAAA
1 ACTACTAGAAAAA
89031186 AAAAACAAAC
Statistics
Matches: 219, Mismatches: 31, Indels: 24
0.80 0.11 0.09
Matches are distributed among these distances:
121 2 0.01
122 62 0.28
123 12 0.05
124 50 0.23
125 10 0.05
126 59 0.27
127 24 0.11
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (124 bp):
ACTACTAGAAAAAGAGCGTCCACATGAGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATACTGC
TTGAAGCGTTTTTGACATTATTTTTTCAGAACCATCTTCTCAAAATTATTTTTTCAGAA
Found at i:89031338 original size:34 final size:34
Alignment explanation
Indices: 89031300--89031364 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
89031290 CTCTAAGCCC
*
89031300 TAATTTAATTAATTTTCTTAAAAACCATAAACCT
1 TAATTTAATTAATTTACTTAAAAACCATAAACCT
*
89031334 TAATTTAATTAATTTACTTAAAAACCCTAAA
1 TAATTTAATTAATTTACTTAAAAACCATAAA
89031365 ACCCAGGGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (34 bp):
TAATTTAATTAATTTACTTAAAAACCATAAACCT
Found at i:89032164 original size:14 final size:13
Alignment explanation
Indices: 89032115--89032162 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
89032105 TGTGGAAATC
*
89032115 ATAAATATATAAT
1 ATAAATATATATT
*
89032128 ATAAATATATGTTT
1 ATAAATATAT-ATT
*
89032142 AAAAATAATATATT
1 ATAAAT-ATATATT
89032156 ATAAATA
1 ATAAATA
89032163 ATGCCACGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
13 11 0.39
14 13 0.46
15 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (13 bp):
ATAAATATATATT
Found at i:89041904 original size:93 final size:92
Alignment explanation
Indices: 89041746--89041915 Score: 313
Period size: 93 Copynumber: 1.8 Consensus size: 92
89041736 GCCCATAAGT
*
89041746 GAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGCTCGGCGCTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
89041811 GAGTTCGGATGCCTAGTTACATCTCAC
66 GAGTTCGGATGCCTAGTTACATCTCAC
*
89041838 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGG-CGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
89041903 CGAGTTCGGATGC
65 CGAGTTCGGATGC
89041916 TCAACCATCC
Statistics
Matches: 75, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
92 27 0.36
93 48 0.64
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGCTCGGCGCTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCAC
Found at i:89041931 original size:46 final size:46
Alignment explanation
Indices: 89041738--89041917 Score: 233
Period size: 45 Copynumber: 3.9 Consensus size: 46
89041728 TGTAACCCGC
* *
89041738 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG-CGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
89041783 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
89041833 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
*
89041876 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTC
89041918 AACCATCCTA
Statistics
Matches: 116, Mismatches: 11, Indels: 15
0.82 0.08 0.11
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 37 0.32
46 37 0.32
47 32 0.28
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:89044315 original size:30 final size:30
Alignment explanation
Indices: 89044271--89044359 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
89044261 CAAAGATAAC
89044271 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
89044300 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
89044330 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
89044360 CGATACTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 9 0.18
30 39 0.78
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:89044319 original size:15 final size:15
Alignment explanation
Indices: 89044271--89044350 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
89044261 CAAAGATAAC
*
89044271 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
89044285 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
89044300 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
89044315 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
89044330 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
89044345 AAGAAA
1 AAGAAA
89044351 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:89044359 original size:15 final size:15
Alignment explanation
Indices: 89044282--89044359 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
89044272 AGAAAACCGA
89044282 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
89044297 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
89044311 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
89044326 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
89044342 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
89044357 ATA
1 ATA
89044360 CGATACTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.08
15 45 0.87
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:89044658 original size:49 final size:49
Alignment explanation
Indices: 89044598--89044720 Score: 219
Period size: 49 Copynumber: 2.5 Consensus size: 49
89044588 ACATATATTT
*
89044598 ACATTGGCCATTAGGCCTCATCACATATACATACACTTTCACATTCACC
1 ACATCGGCCATTAGGCCTCATCACATATACATACACTTTCACATTCACC
*
89044647 ACATCGGCCATTAGGCCTCATCACATATACGTACACTTTCACATTCACC
1 ACATCGGCCATTAGGCCTCATCACATATACATACACTTTCACATTCACC
*
89044696 ACATCGGCCATTAGGCCTTATCACA
1 ACATCGGCCATTAGGCCTCATCACA
89044721 CATATATGTA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 71 1.00
ACGTcount: A:0.29, C:0.33, G:0.11, T:0.27
Consensus pattern (49 bp):
ACATCGGCCATTAGGCCTCATCACATATACATACACTTTCACATTCACC
Found at i:89047835 original size:40 final size:41
Alignment explanation
Indices: 89047791--89047889 Score: 114
Period size: 41 Copynumber: 2.4 Consensus size: 41
89047781 TCGATTGTTC
* * **
89047791 TCGGGACATAGCCCGG-TTATAGTGA-TTTGCACAATTGCCT
1 TCGGGACATAGCCCGGATT-TAGTAACTTAGCACAAACGCCT
89047831 TCGGGA-ATTAGCCCGGATTTAGTAACTTAGCACAAACGCCT
1 TCGGGACA-TAGCCCGGATTTAGTAACTTAGCACAAACGCCT
*
89047872 TCGGGACTTAGCCCGGAT
1 TCGGGACATAGCCCGGAT
89047890 ACCATTCGAA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
39 1 0.02
40 19 0.38
41 30 0.60
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.26
Consensus pattern (41 bp):
TCGGGACATAGCCCGGATTTAGTAACTTAGCACAAACGCCT
Found at i:89048410 original size:29 final size:29
Alignment explanation
Indices: 89048373--89048680 Score: 505
Period size: 29 Copynumber: 10.7 Consensus size: 29
89048363 TGTTGAAAAA
* *
89048373 CTCGTACACACAGTGCCTCAATTACTGAT
1 CTCGCACACACAGTGCCTCGATTACTGAT
*
89048402 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACACAGTGCCTCGATTACTGAT
*
89048431 TTCGCACACACAGTGCCTCGATTACTGAT
1 CTCGCACACACAGTGCCTCGATTACTGAT
89048460 CTCGCACACACAGTGCCTCGATTACTGAT
1 CTCGCACACACAGTGCCTCGATTACTGAT
89048489 CTCGCACACACAGTGCCTCGATTACTGAT
1 CTCGCACACACAGTGCCTCGATTACTGAT
89048518 CTCGCACACACAGTGCCTCGATTACTGAT
1 CTCGCACACACAGTGCCTCGATTACTGAT
89048547 CTCGCACACACAGTGCCTCGATTACTGAT
1 CTCGCACACACAGTGCCTCGATTACTGAT
89048576 CTCGCACACACAGTGCCTCGATTACTGAT
1 CTCGCACACACAGTGCCTCGATTACTGAT
89048605 CTCGCACACACAGTGCCTCGATTACTG-T
1 CTCGCACACACAGTGCCTCGATTACTGAT
* * *
89048633 CTCGCACACATAGTG-CTCGGTTAACGGAAT
1 CTCGCACACACAGTGCCTCGATT-ACTG-AT
*
89048663 -TTGCACACACAGTGCCTC
1 CTCGCACACACAGTGCCTC
89048681 TAATCATTCG
Statistics
Matches: 264, Mismatches: 11, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
27 6 0.02
28 18 0.07
29 236 0.89
30 4 0.02
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.25
Consensus pattern (29 bp):
CTCGCACACACAGTGCCTCGATTACTGAT
Found at i:89050743 original size:36 final size:37
Alignment explanation
Indices: 89050693--89050769 Score: 147
Period size: 36 Copynumber: 2.1 Consensus size: 37
89050683 TATAAAAGAA
89050693 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
89050730 GTCTTA-CCGGTCATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
89050766 GTCT
1 GTCT
89050770 CGCCCGGAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 34 0.85
37 6 0.15
ACGTcount: A:0.21, C:0.31, G:0.19, T:0.29
Consensus pattern (37 bp):
GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
Found at i:89050932 original size:49 final size:49
Alignment explanation
Indices: 89050872--89050994 Score: 219
Period size: 49 Copynumber: 2.5 Consensus size: 49
89050862 CATATATTTT
*
89050872 ACATTGGCCATTAGGCCTCATCACATATACATACACTTTCACATTCACC
1 ACATCGGCCATTAGGCCTCATCACATATACATACACTTTCACATTCACC
*
89050921 ACATCGGCCATTAGGCCTCATCACATATACGTACACTTTCACATTCACC
1 ACATCGGCCATTAGGCCTCATCACATATACATACACTTTCACATTCACC
*
89050970 ACATCGGCCATTAGGCCTTATCACA
1 ACATCGGCCATTAGGCCTCATCACA
89050995 CATATATGTA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 71 1.00
ACGTcount: A:0.29, C:0.33, G:0.11, T:0.27
Consensus pattern (49 bp):
ACATCGGCCATTAGGCCTCATCACATATACATACACTTTCACATTCACC
Found at i:89058188 original size:50 final size:50
Alignment explanation
Indices: 89058130--89058225 Score: 183
Period size: 50 Copynumber: 1.9 Consensus size: 50
89058120 GGGAGTAAGT
89058130 TATAAAGCTTAGTAAGTTTTTATGCAAATAATAAGCATCATAACTAAAGC
1 TATAAAGCTTAGTAAGTTTTTATGCAAATAATAAGCATCATAACTAAAGC
*
89058180 TATAAAGCTTCGTAAGTTTTTATGCAAATAATAAGCATCATAACTA
1 TATAAAGCTTAGTAAGTTTTTATGCAAATAATAAGCATCATAACTA
89058226 CACATTTAAC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.33
Consensus pattern (50 bp):
TATAAAGCTTAGTAAGTTTTTATGCAAATAATAAGCATCATAACTAAAGC
Found at i:89063688 original size:46 final size:45
Alignment explanation
Indices: 89063621--89063795 Score: 181
Period size: 46 Copynumber: 3.8 Consensus size: 45
89063611 TGTAACCCGC
*
89063621 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGC-TTAGCAT
* *
89063667 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--GCTTAGCAT
* *** * ** * *
89063713 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGAACATTTGCGT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGGC-TTAGCAT
*
89063760 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
89063796 ATGCCCAAAT
Statistics
Matches: 106, Mismatches: 18, Indels: 10
0.79 0.13 0.07
Matches are distributed among these distances:
45 1 0.01
46 70 0.66
47 33 0.31
48 2 0.02
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCTTAGCAT
Found at i:89063741 original size:93 final size:93
Alignment explanation
Indices: 89063629--89063800 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
89063619 GCCCATAAGT
** *
89063629 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
89063694 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* * *
89063722 GAACTCGGACTCAACTCAACGAGTTCGAACATTTGCGTCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
89063787 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
89063801 CAAATATCCT
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:89063815 original size:46 final size:46
Alignment explanation
Indices: 89063672--89063815 Score: 111
Period size: 46 Copynumber: 3.1 Consensus size: 46
89063662 CGCATCCATA
* * *
89063672 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA--TATATC-CT
* * * *
89063721 --CGAACTCGGACTCAACTCAACGAGTTC-GA---ACATTTGCGTCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCATAT--ATCC-T
*
89063764 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCATATATCCT
89063811 AGTGA
1 AGTGA
89063816 CATGTCACTT
Statistics
Matches: 73, Mismatches: 12, Indels: 23
0.68 0.11 0.21
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 4 0.05
46 33 0.45
47 28 0.38
48 3 0.04
50 3 0.04
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (46 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCATATATCCT
Found at i:89066858 original size:79 final size:81
Alignment explanation
Indices: 89066757--89066941 Score: 209
Period size: 79 Copynumber: 2.3 Consensus size: 81
89066747 ACGACTCGCG
** * * *
89066757 CAAATGCCTTCGGGACGAAGCCCGG-TTATAGTGACTCACACGAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCACACAAATGCCTTC-GGATCCTAACCC
* *
89066820 GGGTTTAGTAACTT-GCA
64 GGATATAGTAACTTAGCA
* * **
89066837 CAAATGCCTTCGGG-CTTAGCCCGGATTTATTAACTCGCACAAATGCCTTCGGATCCTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAATGCCTTCGGATCCTAACCCGG
*
89066901 ATATAGTCACTTAGCA
66 ATATAGTAACTTAGCA
89066917 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
89066942 CATCATTCGA
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
78 3 0.03
79 52 0.58
80 34 0.38
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAATGCCTTCGGATCCTAACCCGG
ATATAGTAACTTAGCA
Found at i:89066871 original size:39 final size:40
Alignment explanation
Indices: 89066757--89066941 Score: 189
Period size: 40 Copynumber: 4.7 Consensus size: 40
89066747 ACGACTCGCG
** * **
89066757 CAAATGCCTTCGGGACGAAGCCCGG-TTATAGTGACTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTTGCA
* * *
89066797 CGAATGCCTTCGGGACTTAACCCGGGTTTAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTTGCA
* *
89066837 CAAATGCCTTCGGG-CTTAGCCCGGATTTATTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTTGCA
* * * *
89066876 CAAATGCCTTC-GGATCCTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTT-GCA
89066917 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
89066942 CATCATTCGA
Statistics
Matches: 120, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
38 2 0.02
39 32 0.27
40 74 0.62
41 12 0.10
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTTGCA
Found at i:89068943 original size:2 final size:2
Alignment explanation
Indices: 89068936--89068974 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
89068926 TAATAGTAGT
89068936 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
89068975 GTTTTTGTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:89071381 original size:47 final size:47
Alignment explanation
Indices: 89071326--89071456 Score: 158
Period size: 47 Copynumber: 2.8 Consensus size: 47
89071316 CACAATCGAT
* *
89071326 AAGTACCTATGCCATGGCTCGTAGTCAAATCAAGGTAACTTACC-C-CA
1 AAGTACCTATACCATGGCTCGTAGCCAAATCAAGGTAAC-T-CCTCTCA
* * * *
89071373 GAGTACCTATACCATAGCCCGTAGCCAAATCAAGGTAGCTCCTCTCA
1 AAGTACCTATACCATGGCTCGTAGCCAAATCAAGGTAACTCCTCTCA
* *
89071420 AAATACCTATATCATGGCTCGTAGCCAAATCAAGGTA
1 AAGTACCTATACCATGGCTCGTAGCCAAATCAAGGTA
89071457 TTATTCACAC
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
45 2 0.03
46 2 0.03
47 67 0.94
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (47 bp):
AAGTACCTATACCATGGCTCGTAGCCAAATCAAGGTAACTCCTCTCA
Found at i:89076091 original size:18 final size:18
Alignment explanation
Indices: 89076068--89076106 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
89076058 TGGAGGTAGG
*
89076068 CTTCCCTAGCCCCTCCGC
1 CTTCCCTAACCCCTCCGC
89076086 CTTCCCTAACCCCTCCGC
1 CTTCCCTAACCCCTCCGC
89076104 CTT
1 CTT
89076107 GGCCCATACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.08, C:0.59, G:0.08, T:0.26
Consensus pattern (18 bp):
CTTCCCTAACCCCTCCGC
Found at i:89077675 original size:44 final size:46
Alignment explanation
Indices: 89077620--89077828 Score: 162
Period size: 47 Copynumber: 4.5 Consensus size: 46
89077610 TATGCCTGCT
*
89077620 GATGCATGTCCCAAACATGTCTTACACTAGCACAACTCT-T-A-GCC
1 GATGCATGTCCCAGACATGTCTTACACTAGC-CAACTCTGTCAGGCC
* * * *
89077664 GATGCATGTCCCAGACACGTCTTACACTGGCTATCTCTGTCGAGGCC
1 GATGCATGTCCCAGACATGTCTTACACTAGCCAACTCTGTC-AGGCC
* * * *
89077711 GATGCATGTCCCAGACATGTCTTACTCT-GGC-ACTCATAAT-ATGGCT
1 GATGCATGTCCCAGACATGTCTTACACTAGCCAACTC-T-GTCA-GGCC
* ** * * *
89077757 GAAGCATGTCCCAGACATGTCTTACACTAGCCCTCGTCTG-AATGTC
1 GATGCATGTCCCAGACATGTCTTACACTAGCCAAC-TCTGTCAGGCC
89077803 GATGCCATGTCCCAGACATGGTCTTA
1 GATG-CATGTCCCAGACAT-GTCTTA
89077829 TACTGGTGTA
Statistics
Matches: 131, Mismatches: 21, Indels: 22
0.75 0.12 0.13
Matches are distributed among these distances:
43 5 0.04
44 29 0.22
45 4 0.03
46 36 0.27
47 47 0.36
48 8 0.06
49 2 0.02
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.27
Consensus pattern (46 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCCAACTCTGTCAGGCC
Found at i:89078217 original size:30 final size:30
Alignment explanation
Indices: 89078176--89078254 Score: 140
Period size: 30 Copynumber: 2.6 Consensus size: 30
89078166 ATTCAAAACT
*
89078176 TTGGTAAAATGACCATTTTGCCCTTAGGCC
1 TTGGCAAAATGACCATTTTGCCCTTAGGCC
89078206 TTGGCAAAATGACCATTTTGCCCTTAGGCC
1 TTGGCAAAATGACCATTTTGCCCTTAGGCC
*
89078236 TTGGCAAAATGTCCATTTT
1 TTGGCAAAATGACCATTTT
89078255 ACCCCTATGC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (30 bp):
TTGGCAAAATGACCATTTTGCCCTTAGGCC
Found at i:89085043 original size:7 final size:7
Alignment explanation
Indices: 89085024--89085053 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
89085014 TAGCTGAAGC
89085024 TATCTCA
1 TATCTCA
89085031 -ATCTCA
1 TATCTCA
89085037 TATCTCA
1 TATCTCA
89085044 TATCTCA
1 TATCTCA
89085051 TAT
1 TAT
89085054 AATGCTCACT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.43
Consensus pattern (7 bp):
TATCTCA
Found at i:89093009 original size:40 final size:40
Alignment explanation
Indices: 89092943--89093093 Score: 155
Period size: 40 Copynumber: 3.8 Consensus size: 40
89092933 AAATTGAATG
* *
89092943 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGAAATT
* * ****
89092982 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGCGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGAAATT
**
89093022 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GAAATT
* *
89093062 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC
89093094 ACATGCTTAT
Statistics
Matches: 92, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
39 16 0.17
40 74 0.80
41 2 0.02
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGAAATT
Found at i:89093107 original size:40 final size:39
Alignment explanation
Indices: 89092980--89093109 Score: 147
Period size: 40 Copynumber: 3.3 Consensus size: 39
89092970 ATGCTGGAAA
* * *
89092980 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGCGGC
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGC-A-CAGC
* *
89093021 -TATATCCGGGCTAAGACCCGAAGGCATTCGTGC-GAGTC
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCACAG-C
*
89093059 ATTCTATCCGGGCTAAGACCCGAAGGCATTTGTGCACATGC
1 -TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCACA-GC
89093100 TTATATCCGG
1 TTATATCCGG
89093110 TTATATTCCG
Statistics
Matches: 75, Mismatches: 9, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
37 1 0.01
38 1 0.01
40 70 0.93
41 2 0.03
42 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.27, T:0.25
Consensus pattern (39 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCACAGC
Found at i:89101037 original size:40 final size:40
Alignment explanation
Indices: 89100978--89101119 Score: 124
Period size: 40 Copynumber: 3.5 Consensus size: 40
89100968 AAATTGAATG
* * *
89100978 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ***
89101018 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ** *
89101058 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGACAATT-ATGCTAGAAACT
*
89101098 CTATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
89101120 GCATTTGTGC
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
39 3 0.03
40 83 0.97
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:89101143 original size:40 final size:39
Alignment explanation
Indices: 89101016--89101145 Score: 147
Period size: 40 Copynumber: 3.3 Consensus size: 39
89101006 ATGCTGGAAA
* * *
89101016 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGC-AAT-GC
* *
89101057 -TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTC
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCAATG-C
*
89101095 ATTCTATCCGGGCTAAGACCCGAAGGCATTTGTGCACATGC
1 -TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCA-ATGC
89101136 TTATATCCGG
1 TTATATCCGG
89101146 TTATATTCCG
Statistics
Matches: 75, Mismatches: 9, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
37 1 0.01
38 1 0.01
40 70 0.93
41 2 0.03
42 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (39 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCAATGC
Found at i:89104042 original size:22 final size:24
Alignment explanation
Indices: 89104017--89104068 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
89104007 CAAAATATAT
*
89104017 TTTATTTCTA-AA-AGATTTAGTA
1 TTTATTTCTATAATAGATTTAGCA
* *
89104039 TTTATTTGTATAATATATTTAGCA
1 TTTATTTCTATAATAGATTTAGCA
89104063 TTTATT
1 TTTATT
89104069 AATATAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 9 0.36
23 2 0.08
24 14 0.56
ACGTcount: A:0.33, C:0.04, G:0.08, T:0.56
Consensus pattern (24 bp):
TTTATTTCTATAATAGATTTAGCA
Found at i:89104065 original size:24 final size:24
Alignment explanation
Indices: 89104031--89104082 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
89104021 TTTCTAAAAG
* **
89104031 ATTTAGTATTTATTTGTATAATAT
1 ATTTAGCATTTATTAATATAATAT
*
89104055 ATTTAGCATTTATTAATATAATTT
1 ATTTAGCATTTATTAATATAATAT
89104079 ATTT
1 ATTT
89104083 TACCTAGGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.58
Consensus pattern (24 bp):
ATTTAGCATTTATTAATATAATAT
Found at i:89106229 original size:14 final size:14
Alignment explanation
Indices: 89106210--89106237 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
89106200 AATTTACTTT
89106210 TGGTTTAATGATTA
1 TGGTTTAATGATTA
89106224 TGGTTTAATGATTA
1 TGGTTTAATGATTA
89106238 ATAATATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (14 bp):
TGGTTTAATGATTA
Found at i:89108080 original size:1 final size:1
Alignment explanation
Indices: 89108074--89108102 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
89108064 TAGCTGTGTT
89108074 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
89108103 GGAACATTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:89113162 original size:40 final size:41
Alignment explanation
Indices: 89113118--89113196 Score: 151
Period size: 41 Copynumber: 2.0 Consensus size: 41
89113108 TAATAGTAAC
89113118 AATAAACT-AAAGAATTAAACTAAACCTAAATCTACTCCAT
1 AATAAACTAAAAGAATTAAACTAAACCTAAATCTACTCCAT
89113158 AATAAACTAAAAGAATTAAACTAAACCTAAATCTACTCC
1 AATAAACTAAAAGAATTAAACTAAACCTAAATCTACTCC
89113197 TAAGTTCATG
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
40 8 0.21
41 30 0.79
ACGTcount: A:0.53, C:0.20, G:0.03, T:0.24
Consensus pattern (41 bp):
AATAAACTAAAAGAATTAAACTAAACCTAAATCTACTCCAT
Found at i:89117454 original size:29 final size:29
Alignment explanation
Indices: 89117412--89117582 Score: 194
Period size: 29 Copynumber: 6.1 Consensus size: 29
89117402 CACGGCCGTG
* *
89117412 TGTTCCCTCTTTTTTAGATTTTACAATTT
1 TGTTCCCTATTTTTTAGATTTTATAATTT
*
89117441 TGTTCCCTATTTTTTAGATTTTATAGTTT
1 TGTTCCCTATTTTTTAGATTTTATAATTT
89117470 T-TTCCTCTATTTTTTAGATTTTATAATTT
1 TGTTCC-CTATTTTTTAGATTTTATAATTT
* *
89117499 TG-CCCCTA-TTTTTAGATTTTAT-GTTT
1 TGTTCCCTATTTTTTAGATTTTATAATTT
* *
89117525 T-TTCCCTATTTTTCAGATTTTATAGTTT
1 TGTTCCCTATTTTTTAGATTTTATAATTT
* *
89117553 TG--CCTCTATATTTTAGATTTTACAATTT
1 TGTTCC-CTATTTTTTAGATTTTATAATTT
89117581 TG
1 TG
89117583 CCCAAAATTT
Statistics
Matches: 123, Mismatches: 12, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
26 9 0.07
27 29 0.24
28 33 0.27
29 52 0.42
ACGTcount: A:0.19, C:0.13, G:0.08, T:0.60
Consensus pattern (29 bp):
TGTTCCCTATTTTTTAGATTTTATAATTT
Found at i:89118259 original size:85 final size:85
Alignment explanation
Indices: 89118116--89118274 Score: 239
Period size: 85 Copynumber: 1.9 Consensus size: 85
89118106 TACTTTGATT
* * * * *
89118116 ATGAACCATGTGGCAGTTTGTTTAATCAGCAAGTATGTTGTCCACTCACAACAAGTGGCAGTAAT
1 ATGAACCAAGTGGCAATTTGTTTAATCAGCAAATATGTTGTCCACTCACAACAAGTGGCAATAAC
89118181 TGCAAATATGTGGTTCGATC
66 TGCAAATATGTGGTTCGATC
*
89118201 ATGAACCAAGTGGCAATTTGTTTAATCTA-CAAATATGTTGTGCACTCACAACAAGTGGCAATAA
1 ATGAACCAAGTGGCAATTTGTTTAATC-AGCAAATATGTTGTCCACTCACAACAAGTGGCAATAA
*
89118265 CTGTAAATAT
65 CTGCAAATAT
89118275 AACAGCCCAT
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
85 65 0.98
86 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.30
Consensus pattern (85 bp):
ATGAACCAAGTGGCAATTTGTTTAATCAGCAAATATGTTGTCCACTCACAACAAGTGGCAATAAC
TGCAAATATGTGGTTCGATC
Found at i:89118260 original size:45 final size:45
Alignment explanation
Indices: 89118125--89118262 Score: 114
Period size: 45 Copynumber: 3.2 Consensus size: 45
89118115 TATGAACCAT
* *
89118125 GTGGCAGTTTGTTTAATC-AGCAAGTATGTTGTCCACTCACAACAA
1 GTGGCAATTTGTTTAATCTA-CAAATATGTTGTCCACTCACAACAA
* * * *
89118170 GTGGC-A---G--TAAT-TGCAAATATGTGGTTCGA-TCATGAACCAA
1 GTGGCAATTTGTTTAATCTACAAATATGTTG-TCCACTCA-CAA-CAA
*
89118210 GTGGCAATTTGTTTAATCTACAAATATGTTGTGCACTCACAACAA
1 GTGGCAATTTGTTTAATCTACAAATATGTTGTCCACTCACAACAA
89118255 GTGGCAAT
1 GTGGCAAT
89118263 AACTGTAAAT
Statistics
Matches: 70, Mismatches: 11, Indels: 24
0.67 0.10 0.23
Matches are distributed among these distances:
38 12 0.17
39 9 0.13
40 8 0.11
41 2 0.03
44 1 0.01
45 16 0.23
46 8 0.11
47 14 0.20
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.30
Consensus pattern (45 bp):
GTGGCAATTTGTTTAATCTACAAATATGTTGTCCACTCACAACAA
Found at i:89119698 original size:43 final size:44
Alignment explanation
Indices: 89119596--89119698 Score: 120
Period size: 43 Copynumber: 2.3 Consensus size: 44
89119586 CCATAGTTGA
89119596 ACCATAGTTGAAAGACGTTATGGCATCATGACGGAAACAAATAAG
1 ACCATAGTTGAAAGACG-TATGGCATCATGACGGAAACAAATAAG
* * * * *
89119641 ACTATAGTTAAAAGAC-TATGGCATCATGACAGG-AGCGAGTAAG
1 ACCATAGTTGAAAGACGTATGGCATCATGAC-GGAAACAAATAAG
*
89119684 ACCATGGTTGAAAGA
1 ACCATAGTTGAAAGA
89119699 TGCAGTGACA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
43 33 0.67
44 2 0.04
45 14 0.29
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (44 bp):
ACCATAGTTGAAAGACGTATGGCATCATGACGGAAACAAATAAG
Found at i:89120012 original size:13 final size:13
Alignment explanation
Indices: 89119994--89120025 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
89119984 AGTTTTGTTA
89119994 AAATGGTTATACG
1 AAATGGTTATACG
*
89120007 AAATGGTTATATG
1 AAATGGTTATACG
89120020 AAATGG
1 AAATGG
89120026 CTACATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.41, C:0.03, G:0.25, T:0.31
Consensus pattern (13 bp):
AAATGGTTATACG
Found at i:89121966 original size:21 final size:21
Alignment explanation
Indices: 89121941--89121995 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
89121931 TGAAGGCTAT
*
89121941 ACTGAAGCACATAAGTGTTAA
1 ACTGAAGCACATAAGAGTTAA
* * *
89121962 ACTGAAACCCATAAGAGTTGA
1 ACTGAAGCACATAAGAGTTAA
* *
89121983 ACAGAAGCTCATA
1 ACTGAAGCACATA
89121996 GGAGCTGAAC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.44, C:0.18, G:0.18, T:0.20
Consensus pattern (21 bp):
ACTGAAGCACATAAGAGTTAA
Found at i:89125863 original size:21 final size:22
Alignment explanation
Indices: 89125820--89125864 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
89125810 ATCATAATAG
89125820 AATCACATACTAACATTGAATTT
1 AATCACATACTAACA-TGAATTT
89125843 AATCA-ATACTATACA-GAATTT
1 AATCACATACTA-ACATGAATTT
89125864 A
1 A
89125865 GTTCATACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 7 0.33
22 6 0.29
23 8 0.38
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33
Consensus pattern (22 bp):
AATCACATACTAACATGAATTT
Found at i:89127778 original size:30 final size:30
Alignment explanation
Indices: 89127744--89127803 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
89127734 ACTTAACAAG
*
89127744 CAAATACCTCTAAAATAATAATAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
* *
89127774 CAAATTCCTTTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
89127804 TAATAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.28
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTAA
Found at i:89132625 original size:85 final size:85
Alignment explanation
Indices: 89132482--89132651 Score: 331
Period size: 85 Copynumber: 2.0 Consensus size: 85
89132472 TGAGATAAGA
*
89132482 TAGAATCATATTGAGAGAATGAATATTACCTCAAAGATATCAAGGATGTCCTATGAGGGTAACAC
1 TAGAATCATATTGAGAGAATGAATATTACCCCAAAGATATCAAGGATGTCCTATGAGGGTAACAC
89132547 ACTAATGACAAGGCCATTGG
66 ACTAATGACAAGGCCATTGG
89132567 TAGAATCATATTGAGAGAATGAATATTACCCCAAAGATATCAAGGATGTCCTATGAGGGTAACAC
1 TAGAATCATATTGAGAGAATGAATATTACCCCAAAGATATCAAGGATGTCCTATGAGGGTAACAC
89132632 ACTAATGACAAGGCCATTGG
66 ACTAATGACAAGGCCATTGG
89132652 ACAAGGTCAT
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 84 1.00
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (85 bp):
TAGAATCATATTGAGAGAATGAATATTACCCCAAAGATATCAAGGATGTCCTATGAGGGTAACAC
ACTAATGACAAGGCCATTGG
Found at i:89140922 original size:30 final size:30
Alignment explanation
Indices: 89140886--89140945 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
89140876 TTCTTCTTAC
89140886 GGTTGAAAATTAAAAGTTTGTAGATTTATT
1 GGTTGAAAATTAAAAGTTTGTAGATTTATT
89140916 GGTTGAAAATTAAAAGTTTGTAGATTTATT
1 GGTTGAAAATTAAAAGTTTGTAGATTTATT
89140946 TTTGTTTATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (30 bp):
GGTTGAAAATTAAAAGTTTGTAGATTTATT
Found at i:89142780 original size:63 final size:63
Alignment explanation
Indices: 89142694--89142878 Score: 235
Period size: 63 Copynumber: 2.9 Consensus size: 63
89142684 TTCCCCTAGA
* * * * * *
89142694 GAATTTGTTGATGTAGGGAATGATTGTGCATGTTGTGGTACTTGTGTAAAATAAACTGGTGCT
1 GAATATGTTGATGTAAGGAATGATTGTGCGTGTTGTGGTGCTTGTGTAAAATAAACTAGAGCT
* * *
89142757 GAATATGTTGATGCATGGAATGATTGTGCGTGTTGTGGTGTTTGTGTAAAATAAACTAGAGCT
1 GAATATGTTGATGTAAGGAATGATTGTGCGTGTTGTGGTGCTTGTGTAAAATAAACTAGAGCT
** * * * *
89142820 GAAGGTGTTGATGTAAGGAATGATTGCGCGTGATGTGATGCTTGTGTCAAATAAACTAG
1 GAATATGTTGATGTAAGGAATGATTGTGCGTGTTGTGGTGCTTGTGTAAAATAAACTAG
89142879 GTAAGAACAA
Statistics
Matches: 105, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 105 1.00
ACGTcount: A:0.27, C:0.07, G:0.31, T:0.35
Consensus pattern (63 bp):
GAATATGTTGATGTAAGGAATGATTGTGCGTGTTGTGGTGCTTGTGTAAAATAAACTAGAGCT
Found at i:89143884 original size:20 final size:21
Alignment explanation
Indices: 89143859--89143902 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
89143849 TGCAATTTAT
89143859 AAATTATAA-AGAATAAAA-TA
1 AAATTA-AAGAGAATAAAATTA
89143879 AAATTAAAGAGAATAAAATTA
1 AAATTAAAGAGAATAAAATTA
89143900 AAA
1 AAA
89143903 AAAAGAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 2 0.09
20 15 0.68
21 5 0.23
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (21 bp):
AAATTAAAGAGAATAAAATTA
Found at i:89143907 original size:20 final size:20
Alignment explanation
Indices: 89143868--89143908 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
89143858 TAAATTATAA
*
89143868 AGAATAAAATAAAATTAAAG
1 AGAATAAAATAAAATAAAAG
89143888 AGAATAAAATTAAAA-AAAAG
1 AGAATAAAA-TAAAATAAAAG
89143908 A
1 A
89143909 ATTAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (20 bp):
AGAATAAAATAAAATAAAAG
Found at i:89143971 original size:21 final size:21
Alignment explanation
Indices: 89143947--89143994 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
89143937 GGAAATTGGA
*
89143947 AATTGAAAATTGAGGATTGAG
1 AATTGAAAATTGAGGATTAAG
* **
89143968 AATTTATGATTGAGGATTAAG
1 AATTGAAAATTGAGGATTAAG
*
89143989 TATTGA
1 AATTGA
89143995 GTATTTGATT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.25, T:0.35
Consensus pattern (21 bp):
AATTGAAAATTGAGGATTAAG
Found at i:89148818 original size:17 final size:17
Alignment explanation
Indices: 89148790--89148833 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
89148780 TTTATTTACT
89148790 TTTTATAATTTTT-TTGAA
1 TTTTA-AATTTTTATT-AA
*
89148808 TTTTAAATTTTTATTAT
1 TTTTAAATTTTTATTAA
89148825 TTTTAAATT
1 TTTTAAATT
89148834 ATTTGTTAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 17 0.71
18 7 0.29
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (17 bp):
TTTTAAATTTTTATTAA
Found at i:89149273 original size:80 final size:79
Alignment explanation
Indices: 89149088--89149280 Score: 222
Period size: 76 Copynumber: 2.5 Consensus size: 79
89149078 CGATTTTTAA
* * *
89149088 TTTTTTATTATTGGATTTTTTTTGACAGAATG------TTTTTTTTAACCTTTGGTATTATTCAG
1 TTTTTTATTATTAGAATTTTTTTGACAGAATGATTTTTTTTTTTTTAACCTTTGGGATTATTCAG
89149147 TAATGTTTCAAAGATTT
66 TAATGTTTCAAAG---T
* *
89149164 TTTTTTATTATTAGAATTTTTTTGACAGAATGAATTTTTTTTTTTTTTACCTTTGGAGATTATTT
1 TTTTTTATTATTAGAATTTTTTTGACAGAATG-ATTTTTTTTTTTTTAACCTTTGG-GATTATTC
89149229 AGTAATGTTTCAAAG-
64 AGTAATGTTTCAAAGT
*
89149244 TTTTTTATTATT-GGATTTTTGTTGACAGAATGATTTT
1 TTTTTTATTATTAGAATTTTT-TTGACAGAATGATTTT
89149281 CTTGTTTGAA
Statistics
Matches: 102, Mismatches: 6, Indels: 15
0.83 0.05 0.12
Matches are distributed among these distances:
76 30 0.29
79 12 0.12
80 23 0.23
83 16 0.16
84 21 0.21
ACGTcount: A:0.24, C:0.05, G:0.13, T:0.57
Consensus pattern (79 bp):
TTTTTTATTATTAGAATTTTTTTGACAGAATGATTTTTTTTTTTTTAACCTTTGGGATTATTCAG
TAATGTTTCAAAGT
Found at i:89149295 original size:84 final size:81
Alignment explanation
Indices: 89149120--89149280 Score: 222
Period size: 84 Copynumber: 2.0 Consensus size: 81
89149110 TGACAGAATG
*
89149120 TTTTTTTTAACCTTTGGTATTATTCAGTAATGTTTCAAAGATTTTTTTTTATTATTAGAATTTTT
1 TTTTTTTTAACCTTTGGGATTATTCAGTAATGTTTCAAAG---TTTTTTTATTATTAGAATTTTT
89149185 TTGACAGAATGAATTTTTT
63 TTGACAGAATGAATTTTTT
* *
89149204 TTTTTTTT-ACCTTTGGAGATTATTTAGTAATGTTTCAAAG-TTTTTTATTATT-GGATTTTTGT
1 TTTTTTTTAACCTTTGG-GATTATTCAGTAATGTTTCAAAGTTTTTTTATTATTAGAATTTTT-T
89149266 TGACAGAATG-ATTTT
64 TGACAGAATGAATTTT
89149281 CTTGTTTGAA
Statistics
Matches: 72, Mismatches: 3, Indels: 9
0.86 0.04 0.11
Matches are distributed among these distances:
79 12 0.17
80 23 0.32
83 8 0.11
84 29 0.40
ACGTcount: A:0.25, C:0.06, G:0.13, T:0.57
Consensus pattern (81 bp):
TTTTTTTTAACCTTTGGGATTATTCAGTAATGTTTCAAAGTTTTTTTATTATTAGAATTTTTTTG
ACAGAATGAATTTTTT
Found at i:89149389 original size:18 final size:19
Alignment explanation
Indices: 89149366--89149401 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
89149356 GAAAATATTT
89149366 TTATA-TTAATATTTTAAG
1 TTATATTTAATATTTTAAG
*
89149384 TTATATTTATTATTTTAA
1 TTATATTTAATATTTTAA
89149402 ATATAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (19 bp):
TTATATTTAATATTTTAAG
Found at i:89152633 original size:28 final size:28
Alignment explanation
Indices: 89152582--89152645 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
89152572 TAAAGTCCAC
* *
89152582 TAGGAAAATAAACACAGATAAAGTTTGT
1 TAGGATAATAAACACAGATAAAGTTCGT
* *
89152610 TGGGATAATAAACACAGGGT-AAGTTCGT
1 TAGGATAATAAACACA-GATAAAGTTCGT
89152638 TAGGATAA
1 TAGGATAA
89152646 GAGAAACTAG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 28 0.93
29 2 0.07
ACGTcount: A:0.44, C:0.08, G:0.23, T:0.25
Consensus pattern (28 bp):
TAGGATAATAAACACAGATAAAGTTCGT
Done.