Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 50 of 240
Found at i:17085990 original size:205 final size:205
Alignment explanation
Indices: 17085638--17086052 Score: 830
Period size: 205 Copynumber: 2.0 Consensus size: 205
17085628 ATCCAAGCCC
17085638 TCACCAACATTTCCAGTCCCAAGCCCGTCCTTCTCAAATGAAAAATTTCCCCTCAGCTCGTTGGT
1 TCACCAACATTTCCAGTCCCAAGCCCGTCCTTCTCAAATGAAAAATTTCCCCTCAGCTCGTTGGT
17085703 CCTCATTACAGGTGATTGGCCCATATTTTTACTATCTTTCATTTCTCCATCCGACGGCCCAATTC
66 CCTCATTACAGGTGATTGGCCCATATTTTTACTATCTTTCATTTCTCCATCCGACGGCCCAATTC
17085768 TCGGCCATTTTCTTTTACCTTTTAAATTTTTTTATAAAAGGTCTTTGCTAGAACTTAGCCCCCAA
131 TCGGCCATTTTCTTTTACCTTTTAAATTTTTTTATAAAAGGTCTTTGCTAGAACTTAGCCCCCAA
17085833 AGTAGCAGAT
196 AGTAGCAGAT
17085843 TCACCAACATTTCCAGTCCCAAGCCCGTCCTTCTCAAATGAAAAATTTCCCCTCAGCTCGTTGGT
1 TCACCAACATTTCCAGTCCCAAGCCCGTCCTTCTCAAATGAAAAATTTCCCCTCAGCTCGTTGGT
17085908 CCTCATTACAGGTGATTGGCCCATATTTTTACTATCTTTCATTTCTCCATCCGACGGCCCAATTC
66 CCTCATTACAGGTGATTGGCCCATATTTTTACTATCTTTCATTTCTCCATCCGACGGCCCAATTC
17085973 TCGGCCATTTTCTTTTACCTTTTAAATTTTTTTATAAAAGGTCTTTGCTAGAACTTAGCCCCCAA
131 TCGGCCATTTTCTTTTACCTTTTAAATTTTTTTATAAAAGGTCTTTGCTAGAACTTAGCCCCCAA
17086038 AGTAGCAGAT
196 AGTAGCAGAT
17086048 TCACC
1 TCACC
17086053 TTCCCCCTTT
Statistics
Matches: 210, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
205 210 1.00
ACGTcount: A:0.24, C:0.29, G:0.13, T:0.35
Consensus pattern (205 bp):
TCACCAACATTTCCAGTCCCAAGCCCGTCCTTCTCAAATGAAAAATTTCCCCTCAGCTCGTTGGT
CCTCATTACAGGTGATTGGCCCATATTTTTACTATCTTTCATTTCTCCATCCGACGGCCCAATTC
TCGGCCATTTTCTTTTACCTTTTAAATTTTTTTATAAAAGGTCTTTGCTAGAACTTAGCCCCCAA
AGTAGCAGAT
Found at i:17090491 original size:21 final size:21
Alignment explanation
Indices: 17090456--17090523 Score: 86
Period size: 22 Copynumber: 3.3 Consensus size: 21
17090446 CAAAAGTGAA
17090456 AATCATGTG--ATTAGCAATC
1 AATCATGTGACATTAGCAATC
17090475 AATCATGTGACATTAGCAATC
1 AATCATGTGACATTAGCAATC
* * *
17090496 AAACATTGTTACATCAGCAATC
1 AATCA-TGTGACATTAGCAATC
17090518 AATCAT
1 AATCAT
17090524 TATTGAAGGG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
19 9 0.21
21 15 0.36
22 18 0.43
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (21 bp):
AATCATGTGACATTAGCAATC
Found at i:17095374 original size:41 final size:40
Alignment explanation
Indices: 17095329--17095428 Score: 103
Period size: 40 Copynumber: 2.5 Consensus size: 40
17095319 TATGAACCCT
* *
17095329 TGTTTATACATCGGTACCCCTGAATCGCACATACGTGCCCC
1 TGTTTGTAC-TCGGTACCCCTGAATCGCACATACATGCCCC
** * *
17095370 TGTTTGTACTTCAATA-CCTTGAATTGCACATACATGCCCC
1 TGTTTGTAC-TCGGTACCCCTGAATCGCACATACATGCCCC
*
17095410 TGATTGTACTACGGTACCC
1 TGTTTGTACT-CGGTACCC
17095429 TTGGATATAC
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
39 1 0.02
40 32 0.68
41 14 0.30
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (40 bp):
TGTTTGTACTCGGTACCCCTGAATCGCACATACATGCCCC
Found at i:17105694 original size:17 final size:18
Alignment explanation
Indices: 17105659--17105701 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
17105649 GGGTCTGATT
17105659 ATTATATAATAAAATATAA
1 ATTATA-AATAAAATATAA
*
17105678 ATTATAAATATAA-ATAA
1 ATTATAAATAAAATATAA
17105695 ATTATAA
1 ATTATAA
17105702 TAATCGTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 11 0.48
18 6 0.26
19 6 0.26
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
ATTATAAATAAAATATAA
Found at i:17108556 original size:19 final size:18
Alignment explanation
Indices: 17108534--17108571 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
17108524 AAAATTACAA
17108534 AAAAATTCAAAATATTTAT
1 AAAAATTCAAAA-ATTTAT
*
17108553 AAAAATTCCAAAATTTAT
1 AAAAATTCAAAAATTTAT
17108571 A
1 A
17108572 TTTTAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAAATTCAAAAATTTAT
Found at i:17109044 original size:18 final size:18
Alignment explanation
Indices: 17109023--17109057 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
17109013 TAAACCGTCT
17109023 GTTCTTTTTCTTTTTTTG
1 GTTCTTTTTCTTTTTTTG
17109041 GTTCTTTTTCTTTTTTT
1 GTTCTTTTTCTTTTTTT
17109058 CTTTTTGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.00, C:0.11, G:0.09, T:0.80
Consensus pattern (18 bp):
GTTCTTTTTCTTTTTTTG
Found at i:17114862 original size:147 final size:142
Alignment explanation
Indices: 17114566--17114870 Score: 326
Period size: 146 Copynumber: 2.1 Consensus size: 142
17114556 ATTACTTAAC
** * * * * *
17114566 CTTAATTATATAATGCTAATTGTATAAATTAAAATTTAGCATAAAGTTAGCACGTTTAGAGTTTA
1 CTTAATTATATAATGCTAACAGTATAAATTAAAATCTACCATAAAGCTAGCACGTTTAAAATTTA
* * * ***
17114631 GGCTTCAATATCATTAATATAAAAATGAACATTATAATATAATAATTTATATAGTGTTACATATC
66 AGCTTCAATATCATTAATATAAAAAAGAACAATATAATATAATAATTTATATAAAATTACATATC
*
17114696 ACTAATAATATA
131 ACTAATAATAGA
** *
17114708 CTCTAATTATATAATGCTAACAGTATATGTTATAATCTACCATAAAGCTAGTTACACGTTTAAAA
1 CT-TAATTATATAATGCTAACAGTATAAATTAAAATCTACCATAAAGCTAG---CACGTTTAAAA
* *
17114773 TTTAAGC-TCACATATCATTAATATAAAAAAGTACAATATAATA-ACATAGTTGTATATAAAATT
62 TTTAAGCTTCA-ATATCATTAATATAAAAAAGAACAATATAATATA-ATAATT-TATATAAAATT
* * *
17114836 GCATATCATTCATAATAGA
124 ACATATCACTAATAATAGA
17114855 TCTTAATTATATAATG
1 -CTTAATTATATAATG
17114871 ATAATTATAT
Statistics
Matches: 133, Mismatches: 22, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
142 2 0.02
143 40 0.30
145 4 0.03
146 49 0.37
147 36 0.27
148 2 0.02
ACGTcount: A:0.44, C:0.10, G:0.09, T:0.37
Consensus pattern (142 bp):
CTTAATTATATAATGCTAACAGTATAAATTAAAATCTACCATAAAGCTAGCACGTTTAAAATTTA
AGCTTCAATATCATTAATATAAAAAAGAACAATATAATATAATAATTTATATAAAATTACATATC
ACTAATAATAGA
Found at i:17114877 original size:14 final size:15
Alignment explanation
Indices: 17114858--17114891 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
17114848 TAATAGATCT
17114858 TAATTATATA-ATGA
1 TAATTATATATATGA
*
17114872 TAATTATATATATTA
1 TAATTATATATATGA
17114887 TAATT
1 TAATT
17114892 TATCATAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
TAATTATATATATGA
Found at i:17114882 original size:147 final size:142
Alignment explanation
Indices: 17114566--17114890 Score: 341
Period size: 147 Copynumber: 2.2 Consensus size: 142
17114556 ATTACTTAAC
* * * * * * * *
17114566 CTTAATTATATAATGCTAATTGTATAAATTAAAATTTAGCATAAAGTTAGCACGTTTAGAGTTTA
1 CTTAATTATATAATGCTAATTATATATATTATAATCTACCATAAAGCTAGCACGTTTAAAATTTA
* * * ***
17114631 GGCTTCAATATCATTAATATAAAAATGAACATTATAATATAATAATTTATATAGTGTTACATATC
66 AGCTTCAATATCATTAATATAAAAAAGAACAATATAATATAATAATTTATATAAAATTACATATC
*
17114696 ACTAATAATATA
131 ACTAATAATAGA
* *
17114708 CTCTAATTATATAATGCTAA-CAGTATATGTTATAATCTACCATAAAGCTAGTTACACGTTTAAA
1 CT-TAATTATATAATGCTAATTA-TATATATTATAATCTACCATAAAGCTAG---CACGTTTAAA
* *
17114772 ATTTAAGC-TCACATATCATTAATATAAAAAAGTACAATATAATA-ACATAGTTGTATATAAAAT
61 ATTTAAGCTTCA-ATATCATTAATATAAAAAAGAACAATATAATATA-ATAATT-TATATAAAAT
* * *
17114835 TGCATATCATTCATAATAGA
123 TACATATCACTAATAATAGA
*
17114855 TCTTAATTATATAATGATAATTATATATATTATAAT
1 -CTTAATTATATAATGCTAATTATATATATTATAAT
17114891 TTATCATAGA
Statistics
Matches: 148, Mismatches: 25, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
142 2 0.01
143 39 0.26
145 4 0.03
146 49 0.33
147 51 0.34
148 3 0.02
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (142 bp):
CTTAATTATATAATGCTAATTATATATATTATAATCTACCATAAAGCTAGCACGTTTAAAATTTA
AGCTTCAATATCATTAATATAAAAAAGAACAATATAATATAATAATTTATATAAAATTACATATC
ACTAATAATAGA
Found at i:17115142 original size:19 final size:19
Alignment explanation
Indices: 17115118--17115161 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
17115108 AATATTTATT
17115118 TTAATTATATA-AATATTAA
1 TTAATTATATATAAT-TTAA
* *
17115137 TTAATTTTTTATAATTTAA
1 TTAATTATATATAATTTAA
17115156 TTAATT
1 TTAATT
17115162 GAGTTGATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 19 0.86
20 3 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTAATTATATATAATTTAA
Found at i:17116357 original size:5 final size:5
Alignment explanation
Indices: 17116347--17116377 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
17116337 AAAAATAAGC
*
17116347 AAATA AAATA AAATA AAATA AAATA GAATA A
1 AAATA AAATA AAATA AAATA AAATA AAATA A
17116378 TAATTAGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:17117844 original size:31 final size:31
Alignment explanation
Indices: 17117777--17117846 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
17117767 CTTAACAGTC
17117777 TAATGACTTAAATAACAACTTTTGAATAACT
1 TAATGACTTAAATAACAACTTTTGAATAACT
* * * * *
17117808 CAATGACTTAAGTGAA-AGCTTTTGAATGATT
1 TAATGACTTAAAT-AACAACTTTTGAATAACT
17117839 TAATGACT
1 TAATGACT
17117847 ATTTTGTAAC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
31 30 0.94
32 2 0.06
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (31 bp):
TAATGACTTAAATAACAACTTTTGAATAACT
Found at i:17141113 original size:25 final size:25
Alignment explanation
Indices: 17141067--17141116 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
17141057 AGTTAAAAAA
* * *
17141067 GATTAAAGCCACATCGGTGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
*
17141092 GATTAAAGCTACAACAGCGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
17141117 ACGCCTCAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (25 bp):
GATTAAAGCCACAACAGCGAATCTT
Found at i:17141488 original size:25 final size:25
Alignment explanation
Indices: 17141442--17141491 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
17141432 CAGTTAAAAA
* * *
17141442 GATTAAAGCCACATCGGTGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
*
17141467 GATTAAAGCTACAACAGCGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
17141492 ACGCCCCAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (25 bp):
GATTAAAGCCACAACAGCGAATCTT
Found at i:17141591 original size:125 final size:125
Alignment explanation
Indices: 17140941--17141579 Score: 1136
Period size: 125 Copynumber: 5.1 Consensus size: 125
17140931 CAATTCAAAT
* *
17140941 GATTAAAGCCACCTCGGTGAATCTTGATTAAAGCTACAACAGTGAATCTTACGCCCCAAGCGATG
1 GATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATG
*
17141006 CAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCTGACATTGCAGTTAAAAAA
66 CAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTT-AAAAA
* **
17141067 GATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCTCAAGTAATG
1 GATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATG
*
17141132 CAGTGGAATAAATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAA
66 CAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAA
* * *
17141192 GATTAAAGCCACATCGGTGAATCTTGACTAAAGCTACAACAGTGAATCTTACGCCCCGAGCGATG
1 GATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATG
*
17141257 CAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAC
66 CAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAA
*
17141317 GATTAAAGCCACCTCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATG
1 GATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATG
17141382 CAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAA
66 CAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAA
17141442 GATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATG
1 GATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATG
*
17141507 CAGTGGAACAGATTAGAA-CCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAA
66 CAGTGGAATAGATTA-AAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAA
17141567 GATTAAAGCCACA
1 GATTAAAGCCACA
17141580 ATGACGAATC
Statistics
Matches: 490, Mismatches: 22, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
125 375 0.77
126 115 0.23
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (125 bp):
GATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATG
CAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAA
Found at i:17144339 original size:109 final size:109
Alignment explanation
Indices: 17144068--17144486 Score: 468
Period size: 109 Copynumber: 3.8 Consensus size: 109
17144058 AAATTGAGGT
** * *
17144068 AATATTTAGTATTTGGAAATTCGAGAAAACATGCTCTAAGGTGCTGGGTGTCGTTTTTTTTCCCT
1 AATATTTAGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCG--ATTTTT--CT
*
17144133 CGTTCAACCCAAATGGCTTAATATCCTTTTTAAAAAATTT-TAAAATAAGGC
62 CGTTCAA-CCAAATGGCTAAATATCC--TTTAAAAAATTTCT-AAATAAGGC
* * * * *
17144184 AATGTTTTGCGTTTGAAAATTCGAGAAAACATGCCCCAAGGAGCTGGGTGTCGATTTTTCTCGTT
1 AATATTTAGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTT
* * * * *
17144249 CAACCAAATAGCTAAATATCCTTTCAAAAATTTCTAATTGAGGT
66 CAACCAAATGGCTAAATATCCTTTAAAAAATTTCTAAATAAGGC
*
17144293 AATATTTAGCCTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTT
1 AATATTTAGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTT
* * * *
17144358 CAACCAAATGGCTTAATATCATTCTTAAAAATTTCAAAATAAGGC
66 CAACCAAATGGCTAAATATCCTT-TAAAAAATTTCTAAATAAGGC
* * * * * *
17144403 AATGTTTTGCGTCTGGAAATTCGAG-GAACGTGCCCTAAGGTGCTGGGTTTCGA--TTTCTCGTT
1 AATATTTAGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTT
* * *
17144465 TAACCAAATTGCCAAATATCCT
66 CAACCAAATGGCTAAATATCCT
17144487 ATTGAATTTA
Statistics
Matches: 260, Mismatches: 41, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
107 26 0.10
109 121 0.47
110 38 0.15
111 16 0.06
112 9 0.03
114 5 0.02
116 45 0.17
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (109 bp):
AATATTTAGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTT
CAACCAAATGGCTAAATATCCTTTAAAAAATTTCTAAATAAGGC
Found at i:17145426 original size:55 final size:56
Alignment explanation
Indices: 17145289--17145426 Score: 190
Period size: 56 Copynumber: 2.5 Consensus size: 56
17145279 TTTTTTTCAC
* * *
17145289 GTGCTGGGACACTGATGGCCGGCATCCTTGTACCAGATTTGAGAAAAAAAATTTTG
1 GTGCTGGGACACTGATGGCTGGCACCCTTGTACCAGATTTGAGAAAAAAAATTTGG
* * *
17145345 GTACTAGGACACTGATGG-TCGACACCCTTGTACCAGATTTGA-AAAAAAAATTTGG
1 GTGCTGGGACACTGATGGCT-GGCACCCTTGTACCAGATTTGAGAAAAAAAATTTGG
*
17145400 GTGCTGGGATACTGATGGCTGGCACCC
1 GTGCTGGGACACTGATGGCTGGCACCC
17145427 ACTTAGTTGG
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
55 33 0.47
56 37 0.53
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (56 bp):
GTGCTGGGACACTGATGGCTGGCACCCTTGTACCAGATTTGAGAAAAAAAATTTGG
Found at i:17146000 original size:21 final size:21
Alignment explanation
Indices: 17145974--17146020 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
17145964 TTTGTTGGTC
*
17145974 AAATTTTATATTTTCGTATAT
1 AAATTTTATATTTTCGTAAAT
17145995 AAATTTTATATTTTCGTAAAT
1 AAATTTTATATTTTCGTAAAT
17146016 AAATT
1 AAATT
17146021 ATTCTAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (21 bp):
AAATTTTATATTTTCGTAAAT
Found at i:17146015 original size:110 final size:110
Alignment explanation
Indices: 17145886--17146132 Score: 431
Period size: 110 Copynumber: 2.2 Consensus size: 110
17145876 TTGTTGGTTG
* * *
17145886 AATTTTATATTTTTGTAAATAAATTATTCTAAAATGTTTGTATTATTTTGGGGTGTTGTAAAAAT
1 AATTTTATATTTTCGTAAATAAATTATTCTAAAATGTTTGAATTATTTTGGGGTGCTGTAAAAAT
*
17145951 ATTTTAATTCATATTTGTTGGTCAAATTTTATATTTTCGTATATA
66 ATTTTAATCCATATTTGTTGGTCAAATTTTATATTTTCGTATATA
17145996 AATTTTATATTTTCGTAAATAAATTATTCTAAAATGTTTGAATTATTTTGGGGTGCTGTAAAAAT
1 AATTTTATATTTTCGTAAATAAATTATTCTAAAATGTTTGAATTATTTTGGGGTGCTGTAAAAAT
*
17146061 ATTTTAATCCATATTTGTTGGTCGAATTTTATATTTTCGTATATA
66 ATTTTAATCCATATTTGTTGGTCAAATTTTATATTTTCGTATATA
* *
17146106 AATTTTATATTTTCGTATATACATTAT
1 AATTTTATATTTTCGTAAATAAATTAT
17146133 ATTTTTTTTG
Statistics
Matches: 130, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
110 130 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (110 bp):
AATTTTATATTTTCGTAAATAAATTATTCTAAAATGTTTGAATTATTTTGGGGTGCTGTAAAAAT
ATTTTAATCCATATTTGTTGGTCAAATTTTATATTTTCGTATATA
Found at i:17146111 original size:21 final size:21
Alignment explanation
Indices: 17146085--17146126 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
17146075 TTGTTGGTCG
17146085 AATTTTATATTTTCGTATATA
1 AATTTTATATTTTCGTATATA
17146106 AATTTTATATTTTCGTATATA
1 AATTTTATATTTTCGTATATA
17146127 CATTATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (21 bp):
AATTTTATATTTTCGTATATA
Found at i:17146132 original size:19 final size:20
Alignment explanation
Indices: 17146088--17146137 Score: 75
Period size: 21 Copynumber: 2.5 Consensus size: 20
17146078 TTGGTCGAAT
17146088 TTTATATTTTCGTATATAAA
1 TTTATATTTTCGTATATAAA
*
17146108 TTTTATATTTTCGTATATACA
1 -TTTATATTTTCGTATATAAA
17146129 -TTATATTTT
1 TTTATATTTT
17146138 TTTTGTAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 9 0.32
21 19 0.68
ACGTcount: A:0.30, C:0.06, G:0.04, T:0.60
Consensus pattern (20 bp):
TTTATATTTTCGTATATAAA
Found at i:17146212 original size:18 final size:17
Alignment explanation
Indices: 17146185--17146218 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
17146175 TTTATTATTA
*
17146185 TTTGAGTTATATTATTTG
1 TTTGAATTATA-TATTTG
17146203 TTTGAATTATATATTT
1 TTTGAATTATATATTT
17146219 TTGACTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.26, C:0.00, G:0.12, T:0.62
Consensus pattern (17 bp):
TTTGAATTATATATTTG
Found at i:17146969 original size:30 final size:27
Alignment explanation
Indices: 17146906--17146970 Score: 76
Period size: 30 Copynumber: 2.3 Consensus size: 27
17146896 TTCTTGATTT
*
17146906 ATATTATAAAAATATTATTTAATTAAA
1 ATATTATAAAAATATTATTAAATTAAA
* *
17146933 ATATTATAAATTATATTAATTAAAGTTAAG
1 ATATTATAAA-AATATT-ATTAAA-TTAAA
17146963 ATATTATA
1 ATATTATA
17146971 TTATAGGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 10 0.31
28 5 0.16
29 5 0.16
30 12 0.38
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (27 bp):
ATATTATAAAAATATTATTAAATTAAA
Found at i:17148498 original size:21 final size:21
Alignment explanation
Indices: 17148443--17148534 Score: 98
Period size: 21 Copynumber: 4.4 Consensus size: 21
17148433 TTATCGGCTT
17148443 TGTCG-ATCAGGCACTTTATG
1 TGTCGTATCAGGCACTTTATG
17148463 TGTCGTATCTCAGGCACTTTATG
1 TGTCGTA--TCAGGCACTTTATG
****
17148486 TGTCGTATCAGGCACCCCGTG
1 TGTCGTATCAGGCACTTTATG
* *
17148507 TGTCGTTTCAGGCA-TATATG
1 TGTCGTATCAGGCACTTTATG
17148527 TGTCGTAT
1 TGTCGTAT
17148535 ACTGATCAGG
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
20 14 0.24
21 24 0.41
23 21 0.36
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.36
Consensus pattern (21 bp):
TGTCGTATCAGGCACTTTATG
Found at i:17148499 original size:44 final size:41
Alignment explanation
Indices: 17148443--17148534 Score: 105
Period size: 44 Copynumber: 2.2 Consensus size: 41
17148433 TTATCGGCTT
*** *
17148443 TGTCG-ATCAGGCACTTTATGTGTCGTATCTCAGGCACTTTATG
1 TGTCGTATCAGGCACCCCATGTGTCGT-T-TCAGGCA-TATATG
*
17148486 TGTCGTATCAGGCACCCCGTGTGTCGTTTCAGGCATATATG
1 TGTCGTATCAGGCACCCCATGTGTCGTTTCAGGCATATATG
17148527 TGTCGTAT
1 TGTCGTAT
17148535 ACTGATCAGG
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
41 13 0.30
42 7 0.16
43 6 0.14
44 17 0.40
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.36
Consensus pattern (41 bp):
TGTCGTATCAGGCACCCCATGTGTCGTTTCAGGCATATATG
Found at i:17149922 original size:8 final size:8
Alignment explanation
Indices: 17149870--17149924 Score: 58
Period size: 8 Copynumber: 6.8 Consensus size: 8
17149860 TTTTTTGAAG
17149870 TATATTAT
1 TATATTAT
*
17149878 TATTTTAT
1 TATATTAT
*
17149886 TATATT-G
1 TATATTAT
*
17149893 TAAATTATAT
1 TATA-T-TAT
17149903 TATATTAT
1 TATATTAT
17149911 TATATTAT
1 TATATTAT
17149919 TATATT
1 TATATT
17149925 TTAAATAAAC
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
7 3 0.08
8 30 0.79
9 2 0.05
10 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (8 bp):
TATATTAT
Found at i:17150156 original size:13 final size:13
Alignment explanation
Indices: 17150125--17150165 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
17150115 GACGAAACAG
*
17150125 AGAAGGAAAG-AA
1 AGAAAGAAAGAAA
*
17150137 GGAAAGAAAGAAA
1 AGAAAGAAAGAAA
17150150 AGAAAGAAAGAAA
1 AGAAAGAAAGAAA
17150163 AGA
1 AGA
17150166 GAAAATTGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
12 8 0.32
13 17 0.68
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (13 bp):
AGAAAGAAAGAAA
Found at i:17151443 original size:12 final size:12
Alignment explanation
Indices: 17151426--17151460 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
17151416 GTGTGTCGAA
*
17151426 TACTGTTACTGT
1 TACTGTTACCGT
17151438 TACTGTTACCGT
1 TACTGTTACCGT
*
17151450 TACCGTTACCG
1 TACTGTTACCG
17151461 ATTCGACACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.40
Consensus pattern (12 bp):
TACTGTTACCGT
Found at i:17151479 original size:57 final size:58
Alignment explanation
Indices: 17151391--17151510 Score: 179
Period size: 57 Copynumber: 2.1 Consensus size: 58
17151381 GCCGACTAAT
* * * *
17151391 GTTACTGTTACCGATCCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTG-TTACC
1 GTTACCGTTACCGATCCGACACTTTGTGTGTCGAACACTGTTACCGTTACTGATTACC
* *
17151448 GTTACCGTTACCGATTCGACACTTTGTGTGTCGAACACTGTTACCGTTACTGATTACT
1 GTTACCGTTACCGATCCGACACTTTGTGTGTCGAACACTGTTACCGTTACTGATTACC
17151506 GTTAC
1 GTTAC
17151511 TGGTGTGTTT
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
57 47 0.84
58 9 0.16
ACGTcount: A:0.19, C:0.23, G:0.20, T:0.38
Consensus pattern (58 bp):
GTTACCGTTACCGATCCGACACTTTGTGTGTCGAACACTGTTACCGTTACTGATTACC
Found at i:17156943 original size:21 final size:21
Alignment explanation
Indices: 17156871--17156940 Score: 69
Period size: 19 Copynumber: 3.6 Consensus size: 21
17156861 AGAAATTCAA
17156871 TTAATT-TTTAA-TTTAAACT
1 TTAATTATTTAATTTTAAACT
* *
17156890 ATAATTA-TTAA-GTTAAACT
1 TTAATTATTTAATTTTAAACT
17156909 TTAATTATTTAATTTTAAA-T
1 TTAATTATTTAATTTTAAACT
* *
17156929 TTGATTTTTTAA
1 TTAATTATTTAA
17156941 ATTAAAATTA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
19 22 0.52
20 15 0.36
21 5 0.12
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (21 bp):
TTAATTATTTAATTTTAAACT
Found at i:17156948 original size:20 final size:20
Alignment explanation
Indices: 17156871--17156949 Score: 63
Period size: 20 Copynumber: 4.0 Consensus size: 20
17156861 AGAAATTCAA
* *
17156871 TTAATT-TTTAATTTAAACT
1 TTAATTATTTAAATTAAAAT
* * *
17156890 ATAATTA-TTAAGTTAAACT
1 TTAATTATTTAAATTAAAAT
* *
17156909 TTAATTATTTAATTTTAAAT
1 TTAATTATTTAAATTAAAAT
* *
17156929 TTGATTTTTTAAATTAAAAT
1 TTAATTATTTAAATTAAAAT
17156949 T
1 T
17156950 AAGAATTTCA
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
19 22 0.46
20 26 0.54
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (20 bp):
TTAATTATTTAAATTAAAAT
Found at i:17157173 original size:41 final size:41
Alignment explanation
Indices: 17157105--17157461 Score: 493
Period size: 41 Copynumber: 8.7 Consensus size: 41
17157095 CCATTCGGGG
* * *
17157105 CTTTAGCGGCGTTTTTTAGAAAAGCGCCGCTAATGCTCAGGGT
1 CTTTAGCGGCG-TTTTTGGGAAAGCGCCGCTAATGCTC-TGGT
* *
17157148 -TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTTTGGT
1 CTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCTGGT
* *
17157188 CTTTAGCGGCGTTTTTGGGGAAGCGTCGCTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCTGGT
* * *
17157229 CTTTAGTGGCGTTTTTGGAAAAGCGCCGTTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCTGGT
* * *
17157270 CTTTAGCGGCGTTTTTGGGGAAGCGCCGCTAATACTTTGGT
1 CTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCTGGT
* * *
17157311 CTTTAACGGGGTTTTTGGGGAAGCGCCGCTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCTGGT
*
17157352 CTTTAGCGGCGCTTTTTGGGAAAGCGCCGCTAATACTCTGGT
1 CTTTAGCGGCG-TTTTTGGGAAAGCGCCGCTAATGCTCTGGT
* *
17157394 CTTTAGCGGCGTTTTT-GAAGAAGCGCCGCTAATGCTCTGAT
1 CTTTAGCGGCGTTTTTGGGA-AAGCGCCGCTAATGCTCTGGT
17157435 CTTTAGCGGCGTTTTTGGGAAAGCGCC
1 CTTTAGCGGCGTTTTTGGGAAAGCGCC
17157462 ACAAAAACAT
Statistics
Matches: 280, Mismatches: 30, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
40 5 0.02
41 224 0.80
42 51 0.18
ACGTcount: A:0.17, C:0.20, G:0.31, T:0.33
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCTGGT
Found at i:17157856 original size:22 final size:24
Alignment explanation
Indices: 17157806--17157865 Score: 56
Period size: 22 Copynumber: 2.7 Consensus size: 24
17157796 ATATGATTTA
17157806 GAGTTTAAGGTTTA-GAAGTTACT
1 GAGTTTAAGGTTTATGAAGTTACT
* *
17157829 -ATTTTAAGGTTTATGGA-TTA-T
1 GAGTTTAAGGTTTATGAAGTTACT
* *
17157850 GAGTTTAGGGGTTATG
1 GAGTTTAAGGTTTATG
17157866 TGTTACATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
21 1 0.03
22 27 0.90
23 2 0.07
ACGTcount: A:0.27, C:0.02, G:0.28, T:0.43
Consensus pattern (24 bp):
GAGTTTAAGGTTTATGAAGTTACT
Found at i:17157894 original size:35 final size:36
Alignment explanation
Indices: 17157837--17157921 Score: 109
Period size: 35 Copynumber: 2.4 Consensus size: 36
17157827 CTATTTTAAG
* * * *
17157837 GTTTATGGATTATGAGTTTAGGGGTTATGTGTTACA
1 GTTTATGGTTTAAGAGTTTAGGGGTTAAGGGTTACA
* *
17157873 TTTTATGGTTTAAGA-TTTAGGGTTTAAGGGTTACA
1 GTTTATGGTTTAAGAGTTTAGGGGTTAAGGGTTACA
17157908 GTTTATGGTTTAAG
1 GTTTATGGTTTAAG
17157922 GGTATAGATT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
35 30 0.71
36 12 0.29
ACGTcount: A:0.24, C:0.02, G:0.28, T:0.46
Consensus pattern (36 bp):
GTTTATGGTTTAAGAGTTTAGGGGTTAAGGGTTACA
Found at i:17158345 original size:21 final size:22
Alignment explanation
Indices: 17158321--17158361 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
17158311 ATGGGTTATT
17158321 GTTTAAGGGTT-GGGATTTAAA
1 GTTTAAGGGTTAGGGATTTAAA
* *
17158342 GTTTAGGGGTTAGGGGTTTA
1 GTTTAAGGGTTAGGGATTTA
17158362 GGATTTCAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.22, C:0.00, G:0.39, T:0.39
Consensus pattern (22 bp):
GTTTAAGGGTTAGGGATTTAAA
Found at i:17162466 original size:22 final size:22
Alignment explanation
Indices: 17162439--17162481 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
17162429 CTTATTTTAT
*
17162439 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
17162461 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
17162482 GTTTTGGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.28, G:0.21, T:0.09
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:17162674 original size:9 final size:9
Alignment explanation
Indices: 17162650--17162682 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
17162640 AATAATTGAA
17162650 TAATTTATT
1 TAATTTATT
17162659 T-ATTTATT
1 TAATTTATT
17162667 TAATTTATT
1 TAATTTATT
*
17162676 TACTTTA
1 TAATTTA
17162683 CACTATATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (9 bp):
TAATTTATT
Found at i:17162793 original size:86 final size:86
Alignment explanation
Indices: 17162698--17162876 Score: 315
Period size: 86 Copynumber: 2.1 Consensus size: 86
17162688 TATAATAACT
*
17162698 TAATAATTTATTTATTTAAAACATTTATTTTACACTATATAATAATCAAATAATTTATTTATTTA
1 TAATAATTTATTTATTTAAAACATTTATTTTACACCATATAATAATCAAATAATTTATTTATTTA
17162763 A-TTATTTTACTTTACACTATA
66 ATTTA-TTTACTTTACACTATA
**
17162784 TAATAATTTATTTATTTAAAACATTTATTTTACACCATATAATAATTTAATAATTTATTTATTTA
1 TAATAATTTATTTATTTAAAACATTTATTTTACACCATATAATAATCAAATAATTTATTTATTTA
17162849 ATTTATTTACTTTACACTATA
66 ATTTATTTACTTTACACTATA
17162870 TAATAAT
1 TAATAAT
17162877 GGAATAATTT
Statistics
Matches: 89, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
86 86 0.97
87 3 0.03
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (86 bp):
TAATAATTTATTTATTTAAAACATTTATTTTACACCATATAATAATCAAATAATTTATTTATTTA
ATTTATTTACTTTACACTATA
Found at i:17162824 original size:133 final size:133
Alignment explanation
Indices: 17162656--17162897 Score: 376
Period size: 133 Copynumber: 1.8 Consensus size: 133
17162646 TGAATAATTT
*** *
17162656 ATTTATTTATTTAATTTATTTACTTTACACTATATAATAACTTAATAATTTATTTATTTAAAACA
1 ATTTATTTATTTAAAACATTTACTTTACACCATATAATAACTTAATAATTTATTTATTTAAAACA
*
17162721 TTTATTTTACACTATATAATAATCAAATAATTTATTTATTTAATTATTTTACTTTACACTATATA
66 TTTACTTTACACTATATAATAATCAAATAATTTATTTATTTAATTATTTTACTTTACACTATATA
17162786 ATA
131 ATA
* * ***
17162789 ATTTATTTATTTAAAACATTTATTTTACACCATATAATAATTTAATAATTTATTTATTTAATTTA
1 ATTTATTTATTTAAAACATTTACTTTACACCATATAATAACTTAATAATTTATTTATTTAAAACA
**
17162854 TTTACTTTACACTATATAATAATGGAATAATTTATTTATTTAAT
66 TTTACTTTACACTATATAATAATCAAATAATTTATTTATTTAAT
17162898 AATTGGATAA
Statistics
Matches: 97, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
133 97 1.00
ACGTcount: A:0.40, C:0.07, G:0.01, T:0.52
Consensus pattern (133 bp):
ATTTATTTATTTAAAACATTTACTTTACACCATATAATAACTTAATAATTTATTTATTTAAAACA
TTTACTTTACACTATATAATAATCAAATAATTTATTTATTTAATTATTTTACTTTACACTATATA
ATA
Found at i:17162849 original size:16 final size:16
Alignment explanation
Indices: 17162828--17162926 Score: 55
Period size: 16 Copynumber: 6.2 Consensus size: 16
17162818 CCATATAATA
17162828 ATTTAATAATTTATTT
1 ATTTAATAATTTATTT
17162844 A-TT--TAATTTATTT
1 ATTTAATAATTTATTT
* * *
17162857 ACTTTACACT-ATATAATA
1 A-TTTA-A-TAATTTATTT
**
17162875 ATGGAATAATTTATTT
1 ATTTAATAATTTATTT
* *
17162891 ATTTAATAATTGGA-TA
1 ATTTAATAATT-TATTT
*
17162907 ATTGAATAATTTATTT
1 ATTTAATAATTTATTT
17162923 ATTT
1 ATTT
17162927 CACACTATTT
Statistics
Matches: 58, Mismatches: 16, Indels: 18
0.63 0.17 0.20
Matches are distributed among these distances:
13 11 0.19
15 6 0.10
16 31 0.53
17 3 0.05
18 6 0.10
19 1 0.02
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (16 bp):
ATTTAATAATTTATTT
Found at i:17162852 original size:13 final size:14
Alignment explanation
Indices: 17162834--17162862 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
17162824 AATAATTTAA
17162834 TAATTTATTTA-TT
1 TAATTTATTTACTT
17162847 TAATTTATTTACTT
1 TAATTTATTTACTT
17162861 TA
1 TA
17162863 CACTATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (14 bp):
TAATTTATTTACTT
Found at i:17162897 original size:47 final size:46
Alignment explanation
Indices: 17162656--17162897 Score: 293
Period size: 47 Copynumber: 5.3 Consensus size: 46
17162646 TGAATAATTT
17162656 ATTTATTTATTTAATTTATTTACTTTACACTATATAATAACTTAATA
1 ATTTATTTATTTAATTTATTTACTTTACACTATATAATAA-TTAATA
*** * *
17162703 ATTTATTTATTTAAAACATTTATTTTACACTATATAATAATCAAATA
1 ATTTATTTATTTAATTTATTTACTTTACACTATATAATAAT-TAATA
17162750 ATTTATTTATTTAA-TTATTTTACTTTACACTATATAATAATT--T-
1 ATTTATTTATTTAATTTA-TTTACTTTACACTATATAATAATTAATA
** * *
17162793 ATTTATTTA---AA-ACATTTATTTTACACCATATAATAATTTAATA
1 ATTTATTTATTTAATTTATTTACTTTACACTATATAATAA-TTAATA
*
17162836 ATTTATTTATTTAATTTATTTACTTTACACTATATAATAATGGAATA
1 ATTTATTTATTTAATTTATTTACTTTACACTATATAATAAT-TAATA
17162883 ATTTATTTATTTAAT
1 ATTTATTTATTTAAT
17162898 AATTGGATAA
Statistics
Matches: 166, Mismatches: 18, Indels: 22
0.81 0.09 0.11
Matches are distributed among these distances:
39 20 0.12
40 5 0.03
42 1 0.01
43 18 0.11
44 1 0.01
46 5 0.03
47 116 0.70
ACGTcount: A:0.40, C:0.07, G:0.01, T:0.52
Consensus pattern (46 bp):
ATTTATTTATTTAATTTATTTACTTTACACTATATAATAATTAATA
Found at i:17166558 original size:24 final size:24
Alignment explanation
Indices: 17166531--17166579 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
17166521 TAAAGTGATC
*
17166531 AAGGGTCTCTTTGGATGGACATTT
1 AAGGGTCTCTTTGGATGAACATTT
17166555 AAGGGTCTCTTTGGATGAACATTT
1 AAGGGTCTCTTTGGATGAACATTT
17166579 A
1 A
17166580 TCTTTAGTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.12, G:0.27, T:0.37
Consensus pattern (24 bp):
AAGGGTCTCTTTGGATGAACATTT
Found at i:17170395 original size:16 final size:17
Alignment explanation
Indices: 17170363--17170397 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
17170353 AATTTAGTTG
17170363 AAGTATAAACGATGTAT
1 AAGTATAAACGATGTAT
*
17170380 AAGTATATAC-ATGTAT
1 AAGTATAAACGATGTAT
17170396 AA
1 AA
17170398 ATTATTAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.49, C:0.06, G:0.14, T:0.31
Consensus pattern (17 bp):
AAGTATAAACGATGTAT
Found at i:17171110 original size:41 final size:41
Alignment explanation
Indices: 17171049--17171251 Score: 227
Period size: 41 Copynumber: 5.0 Consensus size: 41
17171039 TGAAAATAAG
* *
17171049 ATGTTTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTG-A
1 ATGTATCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAA
*
17171089 AT-TACTTCAGACTTTATGTCTAGCAGGCTT-AGTGTCGGTGAA
1 ATGTA--TCAGACTTTATGTCTAGCAGGCTTGA-TGCCGGTGAA
* *
17171131 ATGTATCAGACTTTATGTCTAGCAGGCTTTG-TGCTGATGAA
1 ATGTATCAGACTTTATGTCTAGCAGGC-TTGATGCCGGTGAA
*
17171172 ATGTATCAGACTTTATGTCTAGCAGGCTTTG-TGCCGGTGGA
1 ATGTATCAGACTTTATGTCTAGCAGGC-TTGATGCCGGTGAA
* * * * *
17171213 ATGTATCGGGCTTTGTGCCTAGCAGGCTTTATGCCGGTG
1 ATGTATCAGACTTTATGTCTAGCAGGCTTGATGCCGGTG
17171252 TTTTATACAA
Statistics
Matches: 141, Mismatches: 14, Indels: 15
0.83 0.08 0.09
Matches are distributed among these distances:
39 1 0.01
40 5 0.04
41 128 0.91
42 5 0.04
43 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.34
Consensus pattern (41 bp):
ATGTATCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAA
Found at i:17171151 original size:82 final size:82
Alignment explanation
Indices: 17171049--17171251 Score: 250
Period size: 82 Copynumber: 2.5 Consensus size: 82
17171039 TGAAAATAAG
* *
17171049 ATGTTTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTG-AAT-TACTTCAGACTTTATGTCTAG
1 ATGTATCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAAATGTA--TCAGACTTTATGTCTAG
*
17171112 CAGGCTTAGTGTCGGTGAA
64 CAGGCTTAGTGCCGGTGAA
* *
17171131 ATGTATCAGACTTTATGTCTAGCAGGCTTTG-TGCTGATGAAATGTATCAGACTTTATGTCTAGC
1 ATGTATCAGACTTTATGTCTAGCAGGC-TTGATGCCGGTGAAATGTATCAGACTTTATGTCTAGC
* *
17171195 AGGCTTTGTGCCGGTGGA
65 AGGCTTAGTGCCGGTGAA
* * * * *
17171213 ATGTATCGGGCTTTGTGCCTAGCAGGCTTTATGCCGGTG
1 ATGTATCAGACTTTATGTCTAGCAGGCTTGATGCCGGTG
17171252 TTTTATACAA
Statistics
Matches: 103, Mismatches: 14, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
81 2 0.02
82 93 0.90
83 6 0.06
84 2 0.02
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.34
Consensus pattern (82 bp):
ATGTATCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAAATGTATCAGACTTTATGTCTAGCA
GGCTTAGTGCCGGTGAA
Found at i:17181147 original size:15 final size:14
Alignment explanation
Indices: 17181126--17181161 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
17181116 ATAATCCTTA
*
17181126 ATAATTATCTTAAT
1 ATAATTATCCTAAT
17181140 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
17181155 ATAATTA
1 ATAATTA
17181162 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:17185110 original size:14 final size:14
Alignment explanation
Indices: 17185091--17185117 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17185081 CATGATAAAA
17185091 TAAAATACAAGTGG
1 TAAAATACAAGTGG
17185105 TAAAATACAAGTG
1 TAAAATACAAGTG
17185118 TGCAAGAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.19, T:0.22
Consensus pattern (14 bp):
TAAAATACAAGTGG
Found at i:17189954 original size:14 final size:14
Alignment explanation
Indices: 17189935--17189961 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17189925 CATGATAAAA
17189935 TAAAATACAAGTGG
1 TAAAATACAAGTGG
17189949 TAAAATACAAGTG
1 TAAAATACAAGTG
17189962 TGAAAGAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.19, T:0.22
Consensus pattern (14 bp):
TAAAATACAAGTGG
Found at i:17191879 original size:3 final size:3
Alignment explanation
Indices: 17191873--17191907 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
17191863 TATCGATGAT
*
17191873 GAG GAG GTG GAG GAG GAG GAG GAG GAG GAG GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
17191908 CGACAACGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.66, T:0.03
Consensus pattern (3 bp):
GAG
Found at i:17194872 original size:17 final size:17
Alignment explanation
Indices: 17194850--17194882 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
17194840 TGTTTATATA
*
17194850 TTAATTTTTTATGTATT
1 TTAATTTCTTATGTATT
17194867 TTAATTTCTTATGTAT
1 TTAATTTCTTATGTAT
17194883 ATTTGGCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.03, G:0.06, T:0.67
Consensus pattern (17 bp):
TTAATTTCTTATGTATT
Found at i:17196382 original size:53 final size:53
Alignment explanation
Indices: 17196302--17196407 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
17196292 ACAAACACTC
17196302 TTATAGTCCATTATTCCTAACGTAAGCAAGTTGAATTCTCCCAAATACCTTAG
1 TTATAGTCCATTATTCCTAACGTAAGCAAGTTGAATTCTCCCAAATACCTTAG
17196355 TTATAGTCCATTATTCCTAACGTAAGCAAGTTGAATTCTCCCAAATACCTTAG
1 TTATAGTCCATTATTCCTAACGTAAGCAAGTTGAATTCTCCCAAATACCTTAG
17196408 ACCAATATCT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.34
Consensus pattern (53 bp):
TTATAGTCCATTATTCCTAACGTAAGCAAGTTGAATTCTCCCAAATACCTTAG
Found at i:17196919 original size:43 final size:43
Alignment explanation
Indices: 17196882--17196976 Score: 136
Period size: 43 Copynumber: 2.2 Consensus size: 43
17196872 CCGTGTGTCT
17196882 GCCCGTGTGTATATTCGAAATAGGGTCACACGGCCGTGTCGCA
1 GCCCGTGTGTATATTCGAAATAGGGTCACACGGCCGTGTCGCA
* ** * *
17196925 GCCCGTGTGTGTATTCGATGTTGGGTCACACGGCTGTGTCGCA
1 GCCCGTGTGTATATTCGAAATAGGGTCACACGGCCGTGTCGCA
*
17196968 GGCCGTGTG
1 GCCCGTGTG
17196977 CGAGACCGTG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.15, C:0.24, G:0.35, T:0.26
Consensus pattern (43 bp):
GCCCGTGTGTATATTCGAAATAGGGTCACACGGCCGTGTCGCA
Found at i:17198428 original size:43 final size:42
Alignment explanation
Indices: 17198375--17198494 Score: 132
Period size: 43 Copynumber: 2.8 Consensus size: 42
17198365 TTCAAGGTAT
* *
17198375 GATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGATATGA
1 GATTACGTGTAAGACCATGTCTGGGATA-TGGCATCGATATGA
* * *
17198418 GATTACGTGTAAGACCCTGTCTGGGATAGTGGCATTGATATGG
1 GATTACGTGTAAGACCATGTCTGGGATA-TGGCATCGATATGA
* * * * *
17198461 GATAACATGTAGGACTATATCTGGGATATGGCAT
1 GATTACGTGTAAGACCATGTCTGGGATATGGCAT
17198495 TGTATGTGAT
Statistics
Matches: 65, Mismatches: 12, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
42 6 0.09
43 59 0.91
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.30
Consensus pattern (42 bp):
GATTACGTGTAAGACCATGTCTGGGATATGGCATCGATATGA
Found at i:17202080 original size:21 final size:22
Alignment explanation
Indices: 17202054--17202096 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
17202044 AAGTTGAATT
17202054 TAAAGTTATGAAT-TAT-ATATA
1 TAAAGTT-TGAATGTATGATATA
17202075 TAAAGTTTGAATGTATGATATA
1 TAAAGTTTGAATGTATGATATA
17202097 AGTTCTTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 5 0.25
21 10 0.50
22 5 0.25
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (22 bp):
TAAAGTTTGAATGTATGATATA
Found at i:17202095 original size:20 final size:21
Alignment explanation
Indices: 17202054--17202097 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
17202044 AAGTTGAATT
*
17202054 TAAAGTTATGAATTATATATA
1 TAAAGTTATGAATTATAGATA
17202075 TAAAGTT-TGAATGTAT-GATA
1 TAAAGTTATGAAT-TATAGATA
17202095 TAA
1 TAA
17202098 GTTCTTTGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (21 bp):
TAAAGTTATGAATTATAGATA
Found at i:17202252 original size:64 final size:64
Alignment explanation
Indices: 17202166--17202342 Score: 220
Period size: 64 Copynumber: 2.8 Consensus size: 64
17202156 ATATATATTT
* * *
17202166 AAAGTTCTTGAGCTGCATTTAATGTATGAATTATATATACATATGTGGTTCAAATATAGGTTAC
1 AAAGTTTTTGAGCGGAATTTAATGTATGAATTATATATACATATGTGGTTCAAATATAGGTTAC
* * *
17202230 AAAGTTTTTGAGCGGAATTTAATGTATGAATTTTACATACATATGTGGTTCGAATATAGGTTAC
1 AAAGTTTTTGAGCGGAATTTAATGTATGAATTATATATACATATGTGGTTCAAATATAGGTTAC
* *
17202294 AAA-TTCTTTGAGCTGAAATTTAATG-CTGTAA--AT-TATACATATGTGGTTC
1 AAAGTT-TTTGAGC-GGAATTTAATGTATG-AATTATATATACATATGTGGTTC
17202343 GAATGTTTGT
Statistics
Matches: 100, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
62 15 0.15
63 3 0.03
64 70 0.70
65 12 0.12
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (64 bp):
AAAGTTTTTGAGCGGAATTTAATGTATGAATTATATATACATATGTGGTTCAAATATAGGTTAC
Found at i:17202522 original size:41 final size:41
Alignment explanation
Indices: 17202462--17202564 Score: 161
Period size: 41 Copynumber: 2.5 Consensus size: 41
17202452 ATCTGAGATT
* * *
17202462 TTCAGGCTTAATGCCTAGCAGACTTGATGTCGGTGAATTAC
1 TTCAGACTTTATGTCTAGCAGACTTGATGTCGGTGAATTAC
* *
17202503 TTCAGACTTTATGTTTAGCAGACTTGATGTCGGTGAATTTC
1 TTCAGACTTTATGTCTAGCAGACTTGATGTCGGTGAATTAC
17202544 TTCAGACTTTATGTCTAGCAG
1 TTCAGACTTTATGTCTAGCAG
17202565 GCTTTGTGCC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.37
Consensus pattern (41 bp):
TTCAGACTTTATGTCTAGCAGACTTGATGTCGGTGAATTAC
Found at i:17202578 original size:41 final size:41
Alignment explanation
Indices: 17202462--17202580 Score: 150
Period size: 41 Copynumber: 2.9 Consensus size: 41
17202452 ATCTGAGATT
* * * *
17202462 TTCAGGCTTAATGCCTAGCAGACTTGATGTCGGTGAATTAC
1 TTCAGACTTTATGTCTAGCAGACTTGATGCCGGTGAATTAC
* * *
17202503 TTCAGACTTTATGTTTAGCAGACTTGATGTCGGTGAATTTC
1 TTCAGACTTTATGTCTAGCAGACTTGATGCCGGTGAATTAC
*
17202544 TTCAGACTTTATGTCTAGCAGGCTTTG-TGCCGGTGAA
1 TTCAGACTTTATGTCTAGCAGAC-TTGATGCCGGTGAA
17202581 ATGTATCGGG
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
41 66 0.96
42 3 0.04
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (41 bp):
TTCAGACTTTATGTCTAGCAGACTTGATGCCGGTGAATTAC
Found at i:17205375 original size:25 final size:25
Alignment explanation
Indices: 17205341--17205397 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
17205331 CACATAAACT
*
17205341 GGAAGCTCACATGAGCCATGTAACG
1 GGAAGCTCACATGAACCATGTAACG
17205366 GGAAGCTCACATGAACCATGTAACG
1 GGAAGCTCACATGAACCATGTAACG
*
17205391 AGAAGCT
1 GGAAGCT
17205398 TATTTGGGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.35, C:0.23, G:0.26, T:0.16
Consensus pattern (25 bp):
GGAAGCTCACATGAACCATGTAACG
Found at i:17207947 original size:15 final size:15
Alignment explanation
Indices: 17207927--17207960 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
17207917 TATCATTTTC
17207927 ATGTTAATTATTAAT
1 ATGTTAATTATTAAT
*
17207942 ATGTTAATTATTATT
1 ATGTTAATTATTAAT
17207957 ATGT
1 ATGT
17207961 AGTGGGTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (15 bp):
ATGTTAATTATTAAT
Found at i:17210780 original size:44 final size:44
Alignment explanation
Indices: 17210714--17210875 Score: 216
Period size: 44 Copynumber: 3.5 Consensus size: 44
17210704 TGAGTACTTT
*
17210714 TGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATC
1 TGATCAGTGACAAGTGACAAGTGGTAGCTTTAGCTACACTTATC
17210758 TGATCAGTGACAAGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATC
1 TGATCAGTGACAAGTGACAA--G-T--G-G-TAGCTTTAGCTACACTTATC
* **
17210809 TTATCAGTGACAAGTGATGAGTGGTAGCTTTAGCTACACTTATC
1 TGATCAGTGACAAGTGACAAGTGGTAGCTTTAGCTACACTTATC
*
17210853 TGATCAGGGACAAGTGACAAGTG
1 TGATCAGTGACAAGTGACAAGTG
17210876 ATAAATGTGA
Statistics
Matches: 103, Mismatches: 8, Indels: 14
0.82 0.06 0.11
Matches are distributed among these distances:
44 58 0.56
45 1 0.01
46 2 0.02
47 1 0.01
48 1 0.01
49 2 0.02
50 1 0.01
51 37 0.36
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (44 bp):
TGATCAGTGACAAGTGACAAGTGGTAGCTTTAGCTACACTTATC
Found at i:17210795 original size:51 final size:51
Alignment explanation
Indices: 17210719--17210879 Score: 246
Period size: 51 Copynumber: 3.3 Consensus size: 51
17210709 ACTTTTGATC
17210719 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
*
17210770 AGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCT--T-A-T--C-
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
* *
17210814 AGTGACAAGTGATGAGTGGTAGCTTTAGCTACACTTATCTGATCAGGGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
17210865 AGTGACAAGTGATAA
1 AGTGACAAGTGATAA
17210880 ATGTGATCCG
Statistics
Matches: 98, Mismatches: 5, Indels: 14
0.84 0.04 0.12
Matches are distributed among these distances:
44 38 0.39
45 1 0.01
46 1 0.01
47 2 0.02
48 1 0.01
49 1 0.01
50 1 0.01
51 53 0.54
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
Found at i:17221132 original size:3 final size:3
Alignment explanation
Indices: 17221124--17221166 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
17221114 TCAGTTAAGC
* *
17221124 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAG TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
17221167 TGAATTGGGG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:17226865 original size:34 final size:34
Alignment explanation
Indices: 17226826--17226893 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
17226816 TGGCCGGATC
17226826 ATAATGCGAGAAAACTACTTATATTAGTAGTTAA
1 ATAATGCGAGAAAACTACTTATATTAGTAGTTAA
17226860 ATAATGCGAGAAAACTACTTATATTAGTAGTTAA
1 ATAATGCGAGAAAACTACTTATATTAGTAGTTAA
17226894 TTTAAATAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.32
Consensus pattern (34 bp):
ATAATGCGAGAAAACTACTTATATTAGTAGTTAA
Found at i:17236939 original size:30 final size:32
Alignment explanation
Indices: 17236881--17236973 Score: 86
Period size: 30 Copynumber: 3.0 Consensus size: 32
17236871 TGTGATTTTA
* * * *
17236881 AAATTTT-ATTTTGGTGCAATTGTATAAATAT
1 AAATTTTAATTTTGATTCAACTATATAAATAT
*
17236912 AAA-TTTAATTTTGATTTAA-TATATAAATA-
1 AAATTTTAATTTTGATTCAACTATATAAATAT
* * *
17236941 AAATTTTGATTTTGGTTCAACTATACAAATAT
1 AAATTTTAATTTTGATTCAACTATATAAATAT
17236973 A
1 A
17236974 CCTACAAAGC
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
29 3 0.06
30 25 0.50
31 21 0.42
32 1 0.02
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (32 bp):
AAATTTTAATTTTGATTCAACTATATAAATAT
Found at i:17238145 original size:54 final size:54
Alignment explanation
Indices: 17238063--17238171 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
17238053 CAAACTAGTG
17238063 CCCTTGAGAGATGCTTAGGTTTACCAACCATAGTAGAAAGGAACACAAGAAGAA
1 CCCTTGAGAGATGCTTAGGTTTACCAACCATAGTAGAAAGGAACACAAGAAGAA
17238117 CCCTTGAGAGATGCTTAGGTTTACCAACCATAGTAGAAAGGAACACAAGAAGAA
1 CCCTTGAGAGATGCTTAGGTTTACCAACCATAGTAGAAAGGAACACAAGAAGAA
17238171 C
1 C
17238172 TTTTCATATA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.18
Consensus pattern (54 bp):
CCCTTGAGAGATGCTTAGGTTTACCAACCATAGTAGAAAGGAACACAAGAAGAA
Found at i:17240752 original size:12 final size:12
Alignment explanation
Indices: 17240735--17240777 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
17240725 TTTTAATTAT
17240735 TTTAATTATTTC
1 TTTAATTATTTC
17240747 TTTAATT-TTAAT-
1 TTTAATTATT--TC
17240759 TTTAATTATTTC
1 TTTAATTATTTC
17240771 TTTAATT
1 TTTAATT
17240778 TTAATTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
11 3 0.11
12 21 0.78
13 3 0.11
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTAATTATTTC
Found at i:17240790 original size:33 final size:33
Alignment explanation
Indices: 17240712--17240794 Score: 102
Period size: 33 Copynumber: 2.5 Consensus size: 33
17240702 ATTGCGATGA
17240712 CTAATTAATTTAATTTTAATTATTTTAATTATTT
1 CTAATTAATTTAATTTTAATTATTTT-ATTATTT
17240746 CT--TTAATTTTAATTTTAATTATTTCT-TTAATTT
1 CTAATTAA-TTTAATTTTAATTATTT-TATT-ATTT
17240779 -TAATTAATTTAATTTT
1 CTAATTAATTTAATTTT
17240795 CTTGTTCGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
32 7 0.16
33 30 0.68
34 7 0.16
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.64
Consensus pattern (33 bp):
CTAATTAATTTAATTTTAATTATTTTATTATTT
Found at i:17240793 original size:24 final size:24
Alignment explanation
Indices: 17240720--17240793 Score: 80
Period size: 24 Copynumber: 3.0 Consensus size: 24
17240710 GACTAATTAA
*
17240720 TTTAATTTTAATTATTTTAATTATTTC
1 TTTAATTTTAATTAATTT-A--ATTTC
17240747 TTTAATTTTAATTTTAA-TT-ATTTC
1 TTTAATTTTAA--TTAATTTAATTTC
17240771 TTTAATTTTAATTAATTTAATTT
1 TTTAATTTTAATTAATTTAATTT
17240794 TCTTGTTCGA
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
22 4 0.10
23 2 0.05
24 20 0.48
27 11 0.26
28 2 0.05
29 3 0.07
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (24 bp):
TTTAATTTTAATTAATTTAATTTC
Found at i:17247262 original size:48 final size:48
Alignment explanation
Indices: 17247191--17247423 Score: 331
Period size: 48 Copynumber: 4.9 Consensus size: 48
17247181 CACTGGAGGT
* * * * * * *
17247191 GGCTTCACAACGGGAGGACTTGGGTATACAGGAGGCGTTGGTGTTGGC
1 GGCTTCACAATGGGAGGACTGGGGTAGACGGGAGGCTTTGGAGCTGGC
* * * *
17247239 GGCTTCACAATGGGAGGACTTGGGTATACAGGAGGCTTTGGAACTGGC
1 GGCTTCACAATGGGAGGACTGGGGTAGACGGGAGGCTTTGGAGCTGGC
*
17247287 GGCTTCACAATGGGAGGACTGGGGTAGACGGGAGGCTTTGGAACTGGC
1 GGCTTCACAATGGGAGGACTGGGGTAGACGGGAGGCTTTGGAGCTGGC
*
17247335 GGCTTCACAATGGGAGGACTGGGGTAGACGGGAGGCTTTGGCGCTGGC
1 GGCTTCACAATGGGAGGACTGGGGTAGACGGGAGGCTTTGGAGCTGGC
* *
17247383 GGCTTTACAATAGGAGGACTGGGGTAGACGGGAGGCTTTGG
1 GGCTTCACAATGGGAGGACTGGGGTAGACGGGAGGCTTTGG
17247424 TGGTGGTGAA
Statistics
Matches: 173, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 173 1.00
ACGTcount: A:0.20, C:0.16, G:0.42, T:0.21
Consensus pattern (48 bp):
GGCTTCACAATGGGAGGACTGGGGTAGACGGGAGGCTTTGGAGCTGGC
Found at i:17257875 original size:39 final size:41
Alignment explanation
Indices: 17257761--17257944 Score: 199
Period size: 40 Copynumber: 4.6 Consensus size: 41
17257751 GCTCCTCGTT
* *
17257761 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAATCTCGCA
* *
17257801 CAAATGCCTTCGGGACTTAACCCGGATTTAGT-ATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAATCTCGCA
17257841 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGT-ATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAATCTCGCA
* * *
17257880 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGTAATC-TCGCA
17257921 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
17257945 CATCATTCAA
Statistics
Matches: 129, Mismatches: 7, Indels: 17
0.84 0.05 0.11
Matches are distributed among these distances:
38 2 0.02
39 52 0.40
40 64 0.50
41 11 0.09
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.26
Consensus pattern (41 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAATCTCGCA
Found at i:17257905 original size:79 final size:82
Alignment explanation
Indices: 17257761--17257944 Score: 217
Period size: 79 Copynumber: 2.3 Consensus size: 82
17257751 GCTCCTCGTT
* *
17257761 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCG
*
17257825 GAT-TTAGT-A-TCTCGCA
66 GATATT-GTCACT-TAGCA
**
17257841 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCACAAATGCCTTC-GGATCTTAGTC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAAT-TCGCACAAATGCCTTCGGGA-CTTAACC
17257902 CGGATATTGTCACTTAGCA
64 CGGATATTGTCACTTAGCA
17257921 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
17257945 CATCATTCAA
Statistics
Matches: 92, Mismatches: 5, Indels: 15
0.82 0.04 0.13
Matches are distributed among these distances:
78 14 0.15
79 54 0.59
80 23 0.25
81 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.26
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCG
GATATTGTCACTTAGCA
Found at i:17260426 original size:24 final size:24
Alignment explanation
Indices: 17260399--17260446 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
17260389 AAGATTTAGT
17260399 ATTTATTAGTATAATATATTTGAC
1 ATTTATTAGTATAATATATTTGAC
* *
17260423 ATTTATTAGTATAGTTTATTTGAC
1 ATTTATTAGTATAATATATTTGAC
17260447 TTACTAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.33, C:0.04, G:0.10, T:0.52
Consensus pattern (24 bp):
ATTTATTAGTATAATATATTTGAC
Found at i:17262392 original size:24 final size:24
Alignment explanation
Indices: 17262365--17262412 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
17262355 AAGATTTAGT
17262365 ATTTATTAGTATAATATATTTGAC
1 ATTTATTAGTATAATATATTTGAC
* *
17262389 ATTTATTAGTATAGTTTATTTGAC
1 ATTTATTAGTATAATATATTTGAC
17262413 TTACTAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.33, C:0.04, G:0.10, T:0.52
Consensus pattern (24 bp):
ATTTATTAGTATAATATATTTGAC
Found at i:17265262 original size:22 final size:21
Alignment explanation
Indices: 17265237--17265280 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
17265227 AAGCATATGA
*
17265237 AAATGATTTGGTTATATTCAAT
1 AAATGATTTGGTTA-ATACAAT
17265259 AAATGATTTGGTTAATACAAT
1 AAATGATTTGGTTAATACAAT
17265280 A
1 A
17265281 CTTATATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.41
Consensus pattern (21 bp):
AAATGATTTGGTTAATACAAT
Found at i:17265289 original size:22 final size:22
Alignment explanation
Indices: 17265264--17265334 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
17265254 TCAATAAATG
17265264 ATTTGGTTAATACAATACTTAT
1 ATTTGGTTAATACAATACTTAT
* * **
17265286 ATTT-GATAA-GCATATGA-AAAT
1 ATTTGGTTAATACA-AT-ACTTAT
17265307 GATTTGGTTAATACAATACTTAT
1 -ATTTGGTTAATACAATACTTAT
17265330 ATTTG
1 ATTTG
17265335 ATAAGCATAT
Statistics
Matches: 35, Mismatches: 8, Indels: 12
0.64 0.15 0.22
Matches are distributed among these distances:
20 2 0.06
21 8 0.23
22 15 0.43
23 8 0.23
24 2 0.06
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.42
Consensus pattern (22 bp):
ATTTGGTTAATACAATACTTAT
Found at i:17265307 original size:44 final size:44
Alignment explanation
Indices: 17265259--17265352 Score: 188
Period size: 44 Copynumber: 2.1 Consensus size: 44
17265249 TATATTCAAT
17265259 AAATGATTTGGTTAATACAATACTTATATTTGATAAGCATATGA
1 AAATGATTTGGTTAATACAATACTTATATTTGATAAGCATATGA
17265303 AAATGATTTGGTTAATACAATACTTATATTTGATAAGCATATGA
1 AAATGATTTGGTTAATACAATACTTATATTTGATAAGCATATGA
17265347 AAATGA
1 AAATGA
17265353 AAGTCGAGAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 50 1.00
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (44 bp):
AAATGATTTGGTTAATACAATACTTATATTTGATAAGCATATGA
Found at i:17266594 original size:12 final size:12
Alignment explanation
Indices: 17266577--17266617 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
17266567 CTCGTACTCA
17266577 TCTTCTTCGTCT
1 TCTTCTTCGTCT
17266589 TCTTCTTCGTCT
1 TCTTCTTCGTCT
* *
17266601 TCTTCTACATCT
1 TCTTCTTCGTCT
17266613 TCTTC
1 TCTTC
17266618 CTTTGCATCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.05, C:0.34, G:0.05, T:0.56
Consensus pattern (12 bp):
TCTTCTTCGTCT
Found at i:17270806 original size:17 final size:17
Alignment explanation
Indices: 17270786--17270819 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
17270776 TATATTTATT
* *
17270786 TTTTAAATTTTTTTTAA
1 TTTTAAAATATTTTTAA
17270803 TTTTAAAATATTTTTAA
1 TTTTAAAATATTTTTAA
17270820 AATACTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTAAAATATTTTTAA
Found at i:17270806 original size:18 final size:19
Alignment explanation
Indices: 17270780--17270817 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
17270770 AATAAATATA
* *
17270780 TTTATTTTTTAAAT-TTTT
1 TTTAATTTTAAAATATTTT
17270798 TTTAATTTTAAAATATTTT
1 TTTAATTTTAAAATATTTT
17270817 T
1 T
17270818 AAAATACTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTAATTTTAAAATATTTT
Found at i:17270817 original size:11 final size:11
Alignment explanation
Indices: 17270803--17270870 Score: 63
Period size: 11 Copynumber: 6.4 Consensus size: 11
17270793 TTTTTTTTAA
17270803 TTTTAAAATAT
1 TTTTAAAATAT
17270814 TTTTAAAATACT
1 TTTTAAAATA-T
** *
17270826 TTTTTTATTAT
1 TTTTAAAATAT
17270837 TTTT--AA-A-
1 TTTTAAAATAT
17270844 TTTTAAAATAT
1 TTTTAAAATAT
17270855 TTTTAAAATACT
1 TTTTAAAATA-T
17270867 TTTT
1 TTTT
17270871 TAATTTTTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
7 4 0.09
8 1 0.02
9 3 0.06
10 1 0.02
11 25 0.53
12 13 0.28
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:17270829 original size:41 final size:40
Alignment explanation
Indices: 17270784--17270878 Score: 154
Period size: 41 Copynumber: 2.3 Consensus size: 40
17270774 AATATATTTA
*
17270784 TTTTTTAAATTTTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTT-AATTTTTTTAAATTTTAAAATATTTTTAAAATAC
*
17270825 TTTTTTTATTATTTTTAAATTTTAAAATATTTTTAAAATAC
1 TTTTTTAATT-TTTTTAAATTTTAAAATATTTTTAAAATAC
17270866 TTTTTTAATTTTT
1 TTTTTTAATTTTT
17270879 AAAATAAATT
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
40 6 0.12
41 44 0.88
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (40 bp):
TTTTTTAATTTTTTTAAATTTTAAAATATTTTTAAAATAC
Found at i:17270870 original size:30 final size:31
Alignment explanation
Indices: 17270814--17270884 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
17270804 TTTAAAATAT
** *
17270814 TTTTAAAATACTTTTTTTATTA-TTTTTAAA
1 TTTTAAAATACTTTTTAAAATATTTTTTAAA
*
17270844 TTTTAAAATA-TTTTTAAAATACTTTTTTAAT
1 TTTTAAAATACTTTTTAAAATA-TTTTTTAAA
17270875 TTTTAAAATA
1 TTTTAAAATA
17270885 AATTTTTGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 8 0.23
30 10 0.29
31 17 0.49
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (31 bp):
TTTTAAAATACTTTTTAAAATATTTTTTAAA
Found at i:17270890 original size:20 final size:20
Alignment explanation
Indices: 17270853--17270891 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17270843 ATTTTAAAAT
**
17270853 ATTTTTAAAATACTTTTTTA
1 ATTTTTAAAATAAATTTTTA
17270873 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
17270892 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTTTAAAATAAATTTTTA
Found at i:17270898 original size:22 final size:20
Alignment explanation
Indices: 17270852--17270909 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 20
17270842 AATTTTAAAA
*
17270852 TATTTTTAAAAT-ACTTTTT
1 TATTTTTAAAATAAATTTTT
17270871 TAATTTTTAAAATAAATTTTT
1 T-ATTTTTAAAATAAATTTTT
17270892 GGTATTTATTAAAA-AAAT
1 --TATTT-TTAAAATAAAT
17270910 AGGCCGGGCC
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
19 1 0.03
20 11 0.33
21 6 0.18
22 8 0.24
23 7 0.21
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.53
Consensus pattern (20 bp):
TATTTTTAAAATAAATTTTT
Found at i:17271472 original size:15 final size:15
Alignment explanation
Indices: 17271428--17271473 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 15
17271418 ACAATTAGGT
17271428 TAAAATATTTTAAAAA
1 TAAAAT-TTTTAAAAA
* *
17271444 TAAAA--ATTATAAA
1 TAAAATTTTTAAAAA
17271457 TAAAATTTTTAAAAA
1 TAAAATTTTTAAAAA
17271472 TA
1 TA
17271474 TGTATATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
13 11 0.46
15 8 0.33
16 5 0.21
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAAATTTTTAAAAA
Found at i:17278544 original size:18 final size:17
Alignment explanation
Indices: 17278502--17278547 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
17278492 TGAAATAATA
17278502 AATATTT-AA-TTATAT
1 AATATTTAAATTTATAT
17278517 AATAGTTTTAAATTTATAT
1 AATA--TTTAAATTTATAT
17278536 AGATATTTAAAT
1 A-ATATTTAAAT
17278548 ATAAAAAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 4 0.15
17 3 0.12
18 9 0.35
19 7 0.27
20 3 0.12
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (17 bp):
AATATTTAAATTTATAT
Found at i:17280169 original size:42 final size:42
Alignment explanation
Indices: 17280094--17280177 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
17280084 CTTACAATTC
* * ** *
17280094 ATGTTGTGAGTTTGAATTATAGGAATTTTCTACTTGTGATGT
1 ATGTCGTGAATTTGAATTATAGGAATTGCCTACTTATGATGT
* *
17280136 ATGTCGTGAATTTGAGTTGTAGGAATTGCCTACTTATGATGT
1 ATGTCGTGAATTTGAATTATAGGAATTGCCTACTTATGATGT
17280178 GCACATGTGT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.24, C:0.07, G:0.25, T:0.44
Consensus pattern (42 bp):
ATGTCGTGAATTTGAATTATAGGAATTGCCTACTTATGATGT
Found at i:17281936 original size:25 final size:25
Alignment explanation
Indices: 17281908--17281996 Score: 72
Period size: 25 Copynumber: 3.6 Consensus size: 25
17281898 CGAGCATGTA
*
17281908 ATCGGGAAGCTCTTCTGAGCCATAT
1 ATCGGGAAGCTCATCTGAGCCATAT
* * *
17281933 ATCGAGAAGCTCATGTGAGCCATGT
1 ATCGGGAAGCTCATCTGAGCCATAT
* * ****
17281958 AACAGGAAGCTCCGGAGAGCCAT-T
1 ATCGGGAAGCTCATCTGAGCCATAT
17281982 AGTCGGGAAGCTCAT
1 A-TCGGGAAGCTCAT
17281997 ATAAGAGCCT
Statistics
Matches: 49, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
24 2 0.04
25 47 0.96
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.21
Consensus pattern (25 bp):
ATCGGGAAGCTCATCTGAGCCATAT
Found at i:17282067 original size:25 final size:25
Alignment explanation
Indices: 17282032--17282095 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
17282022 ATGCGAGCCA
* * *
17282032 ATATCGAGAAGCTTCGGAGAGCTAGT
1 ATATCGGGAAGCTCCGAAGAGCTA-T
17282058 -TATCGGGAAGCTCCGAAGAGCTAT
1 ATATCGGGAAGCTCCGAAGAGCTAT
*
17282082 ATATCGGGATGCTC
1 ATATCGGGAAGCTC
17282096 ATGAAAGTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
24 1 0.03
25 32 0.97
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (25 bp):
ATATCGGGAAGCTCCGAAGAGCTAT
Found at i:17284471 original size:15 final size:16
Alignment explanation
Indices: 17284439--17284471 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
17284429 AAAGTTTTTA
*
17284439 TAAAATAACATAATAT
1 TAAAATAACATAAAAT
17284455 TAAAATAA-ATAAAAT
1 TAAAATAACATAAAAT
17284470 TA
1 TA
17284472 TTCTCCATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (16 bp):
TAAAATAACATAAAAT
Found at i:17300864 original size:15 final size:15
Alignment explanation
Indices: 17300844--17300899 Score: 60
Period size: 15 Copynumber: 3.6 Consensus size: 15
17300834 ATATAATTAT
17300844 TTTTATATTAAAATA
1 TTTTATATTAAAATA
*
17300859 TTTTATTTTAAATTATA
1 TTTTATATTAAA--ATA
*
17300876 TTTTGA-AATAAAATA
1 TTTT-ATATTAAAATA
17300891 TTTTATATT
1 TTTTATATT
17300900 GAGTTAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 1 0.03
15 20 0.61
17 11 0.33
18 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (15 bp):
TTTTATATTAAAATA
Found at i:17301269 original size:42 final size:42
Alignment explanation
Indices: 17301207--17301337 Score: 176
Period size: 41 Copynumber: 3.2 Consensus size: 42
17301197 ACGCTGTAAT
* * *
17301207 AGGTAAAGTAGTAGCAGCGTTTATGAGAAAAACGCCGCAAAA
1 AGGTCAAGCAGTAGCGGCGTTTATGAGAAAAACGCCGCAAAA
* *
17301249 AGGTCAAGCAGTAGTGGCGTTTATGAGAAAAACGCCAC-AAA
1 AGGTCAAGCAGTAGCGGCGTTTATGAGAAAAACGCCGCAAAA
* * *
17301290 AGGTTAAGCAGTAGCGGCGTTTATGAGAAAAACACTGCAAAA
1 AGGTCAAGCAGTAGCGGCGTTTATGAGAAAAACGCCGCAAAA
17301332 A-GTCAA
1 AGGTCAA
17301338 AGAAAAAATC
Statistics
Matches: 77, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
41 40 0.52
42 37 0.48
ACGTcount: A:0.41, C:0.15, G:0.26, T:0.18
Consensus pattern (42 bp):
AGGTCAAGCAGTAGCGGCGTTTATGAGAAAAACGCCGCAAAA
Found at i:17301331 original size:41 final size:41
Alignment explanation
Indices: 17301192--17301331 Score: 172
Period size: 41 Copynumber: 3.4 Consensus size: 41
17301182 GGCGCTAACG
* * * * *
17301192 GAAAAACGCTGTAATAGGTAAAGTAGTAGCAGCGTTTATGA
1 GAAAAACGCCGCAAAAGGTAAAGCAGTAGCGGCGTTTATGA
* *
17301233 GAAAAACGCCGCAAAAAGGTCAAGCAGTAGTGGCGTTTATGA
1 GAAAAACGCCGC-AAAAGGTAAAGCAGTAGCGGCGTTTATGA
* *
17301275 GAAAAACGCCACAAAAGGTTAAGCAGTAGCGGCGTTTATGA
1 GAAAAACGCCGCAAAAGGTAAAGCAGTAGCGGCGTTTATGA
* *
17301316 GAAAAACACTGCAAAA
1 GAAAAACGCCGCAAAA
17301332 AGTCAAAGAA
Statistics
Matches: 85, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
41 50 0.59
42 35 0.41
ACGTcount: A:0.41, C:0.15, G:0.26, T:0.18
Consensus pattern (41 bp):
GAAAAACGCCGCAAAAGGTAAAGCAGTAGCGGCGTTTATGA
Found at i:17302005 original size:18 final size:18
Alignment explanation
Indices: 17301979--17302013 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17301969 TTACATAAAA
*
17301979 AAATTATATAAAAATTTC
1 AAATGATATAAAAATTTC
*
17301997 AAATGATATAATAATTT
1 AAATGATATAAAAATTT
17302014 AATATAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (18 bp):
AAATGATATAAAAATTTC
Found at i:17305298 original size:26 final size:26
Alignment explanation
Indices: 17305264--17305402 Score: 89
Period size: 26 Copynumber: 5.4 Consensus size: 26
17305254 TATATTTTTA
17305264 TTAAATTATATTTAATAATAATTATT
1 TTAAATTATATTTAATAATAATTATT
*
17305290 TTAAATTATATTT--T-AT-AGTATT
1 TTAAATTATATTTAATAATAATTATT
* * *
17305312 ATATATTATGATTT--TAGTAAATTCA-T
1 TTAAATTAT-ATTTAATAAT-AATT-ATT
* * *
17305338 ATAAA-AATATTTAATGTTAAGAATT-TT
1 TTAAATTATATTTAA---TAATAATTATT
17305365 ATTAAATTATATTTAATAATAATTATT
1 -TTAAATTATATTTAATAATAATTATT
17305392 TTAAATTATAT
1 TTAAATTATAT
17305403 CTTATAGTAT
Statistics
Matches: 87, Mismatches: 12, Indels: 28
0.69 0.09 0.22
Matches are distributed among these distances:
22 12 0.14
23 7 0.08
24 6 0.07
25 2 0.02
26 38 0.44
27 4 0.05
28 8 0.09
29 10 0.11
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.52
Consensus pattern (26 bp):
TTAAATTATATTTAATAATAATTATT
Found at i:17305379 original size:102 final size:100
Alignment explanation
Indices: 17305249--17305496 Score: 363
Period size: 102 Copynumber: 2.5 Consensus size: 100
17305239 ATAAGTGGGG
* * *
17305249 AATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTAT
1 AATTATAGAATTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATCTTATAGTATTAT
*
17305314 ATATTATGATTTTAGTAAATTCATATAAAAATATTT
66 ATATTATGATTTTAGTAAATTCATAT-AAAATATTA
17305350 AATGT-TAAGAATTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATCTTATAGTATT
1 AAT-TAT-AGAATTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATCTTATAGTATT
* ***
17305414 ATATATTATGATTTTAGTAAATTTATATATTTTATTA
64 ATATATTATGATTTTAGTAAATTCATATAAAATATTA
* * *
17305451 AATTATATATTTTTATTAAATAATATTTAATAATAATTATTTTAAA
1 AATTATAGAATTTTATTAAATTATATTTAATAATAATTATTTTAAA
17305497 ATATGATTAA
Statistics
Matches: 133, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
100 38 0.29
101 13 0.10
102 82 0.62
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (100 bp):
AATTATAGAATTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATCTTATAGTATTAT
ATATTATGATTTTAGTAAATTCATATAAAATATTA
Found at i:17305447 original size:18 final size:17
Alignment explanation
Indices: 17305424--17305463 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
17305414 ATATATTATG
17305424 ATTTTAGTAAATTTATAT
1 ATTTTAGTAAA-TTATAT
*
17305442 ATTTTATTAAATTATAT
1 ATTTTAGTAAATTATAT
17305459 ATTTT
1 ATTTT
17305464 TATTAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (17 bp):
ATTTTAGTAAATTATAT
Found at i:17305464 original size:18 final size:19
Alignment explanation
Indices: 17305424--17305476 Score: 74
Period size: 18 Copynumber: 2.9 Consensus size: 19
17305414 ATATATTATG
*
17305424 ATTTTAGTAAATT-TATAT
1 ATTTTATTAAATTATATAT
17305442 ATTTTATTAAATTATATAT
1 ATTTTATTAAATTATATAT
*
17305461 -TTTTATTAAATAATAT
1 ATTTTATTAAATTATAT
17305477 TTAATAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
18 27 0.84
19 5 0.16
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
ATTTTATTAAATTATATAT
Found at i:17305732 original size:16 final size:16
Alignment explanation
Indices: 17305711--17305762 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
17305701 AAAATTACCT
*
17305711 ATTACAACTCTATTTC
1 ATTACAACTCTATTCC
17305727 ATTACAGA-TCTATTCC
1 ATTACA-ACTCTATTCC
** *
17305743 ATTACGTCTCTATTGC
1 ATTACAACTCTATTCC
17305759 ATTA
1 ATTA
17305763 GAGTGAACCA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
16 29 0.97
17 1 0.03
ACGTcount: A:0.29, C:0.23, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTACAACTCTATTCC
Found at i:17308904 original size:17 final size:18
Alignment explanation
Indices: 17308873--17308906 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
17308863 AATTTAACTT
17308873 TAATTAAATTATTTAAAA
1 TAATTAAATTATTTAAAA
*
17308891 TAATT-AATTTTTTAAA
1 TAATTAAATTATTTAAA
17308907 TTATAAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATTAAATTATTTAAAA
Found at i:17309152 original size:21 final size:20
Alignment explanation
Indices: 17309118--17309166 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
17309108 GACCCTGAAG
* * *
17309118 TTTAGGGTTTAGGTTTGAGA
1 TTTAGGATTAAGGTTTAAGA
17309138 TTTACGGATTAAGGTTTAAGA
1 TTTA-GGATTAAGGTTTAAGA
17309159 TTTAGGAT
1 TTTAGGAT
17309167 ATAGGATTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.27, C:0.02, G:0.29, T:0.43
Consensus pattern (20 bp):
TTTAGGATTAAGGTTTAAGA
Found at i:17309220 original size:28 final size:28
Alignment explanation
Indices: 17309187--17309246 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
17309177 TAGATTTGGA
* *
17309187 GTTTAGGGTTC-ATGTTTATGGTTCAAGG
1 GTTTAGGGTTCGA-GTTCAAGGTTCAAGG
17309215 GTTTAGGGTTCGAGTTCAAGGTTCAAGG
1 GTTTAGGGTTCGAGTTCAAGGTTCAAGG
17309243 GTTT
1 GTTT
17309247 TGGTTTATGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 28 0.97
29 1 0.03
ACGTcount: A:0.18, C:0.08, G:0.33, T:0.40
Consensus pattern (28 bp):
GTTTAGGGTTCGAGTTCAAGGTTCAAGG
Found at i:17309274 original size:21 final size:21
Alignment explanation
Indices: 17309234--17309279 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
17309224 TCGAGTTCAA
* *
17309234 GGTTCAAGGGTTTTGGTTTATG
1 GGTTCAAGGATTTAGGTTTA-G
17309256 GGTTC-AGGATTTAGGTTTAG
1 GGTTCAAGGATTTAGGTTTAG
17309276 GGTT
1 GGTT
17309280 TTATATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 5 0.23
21 12 0.55
22 5 0.23
ACGTcount: A:0.15, C:0.04, G:0.37, T:0.43
Consensus pattern (21 bp):
GGTTCAAGGATTTAGGTTTAG
Found at i:17310864 original size:31 final size:32
Alignment explanation
Indices: 17310826--17310937 Score: 109
Period size: 31 Copynumber: 3.4 Consensus size: 32
17310816 AATTAAAATA
*
17310826 AAAATTAAAAAATGTATTTTAAAA-ATATTTT
1 AAAATTAAAAAAAGTATTTTAAAATATATTTT
* *
17310857 AAAATTAAAAAAAGTATTTTAAAATTTTTTTT
1 AAAATTAAAAAAAGTATTTTAAAATATATTTT
** * * *
17310889 AAAATTTAAAATTAAAAAAATTAAAAAAAGTATTTT
1 AAAA-TTAAAA--AAAGTATTTTAAAATA-TATTTT
17310925 AAAATTAAAAAAA
1 AAAATTAAAAAAA
17310938 ATAAAAATAT
Statistics
Matches: 66, Mismatches: 10, Indels: 8
0.79 0.12 0.10
Matches are distributed among these distances:
31 23 0.35
32 9 0.14
33 9 0.14
35 16 0.24
36 9 0.14
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (32 bp):
AAAATTAAAAAAAGTATTTTAAAATATATTTT
Found at i:17310944 original size:76 final size:76
Alignment explanation
Indices: 17310801--17310944 Score: 184
Period size: 76 Copynumber: 1.9 Consensus size: 76
17310791 ATAAATACCA
* *** *
17310801 AAAATTTATTTTAAAAATTAAAATAAAAATTAAAAAATGTATTTTAAAAATATTTTAAAATTAAA
1 AAAATTTATTTTAAAAATTAAAATAAAAATTAAAAAAAGTATTTTAAAAATATAAAAAAAATAAA
17310866 AAAAGTATTTT
66 AAAAGTATTTT
* *
17310877 AAAATTTTTTTTAAAATTTAAAATTAAAAAAATTAAAAAAAGTATTTT-AAAAT-TAAAAAAAAT
1 AAAATTTATTTTAAAAATTAAAA-T--AAAAATTAAAAAAAGTATTTTAAAAATATAAAAAAAAT
17310940 AAAAA
63 AAAAA
17310945 TATTTATTAT
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
76 21 0.36
77 12 0.21
78 5 0.09
79 20 0.34
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (76 bp):
AAAATTTATTTTAAAAATTAAAATAAAAATTAAAAAAAGTATTTTAAAAATATAAAAAAAATAAA
AAAAGTATTTT
Found at i:17312164 original size:17 final size:16
Alignment explanation
Indices: 17312124--17312167 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
17312114 TAATAGAATA
17312124 AATTTAGTGTTAATTGT
1 AATTTAGT-TTAATTGT
* *
17312141 AAATTAGTTTAATTTT
1 AATTTAGTTTAATTGT
17312157 ACATTTAGTTT
1 A-ATTTAGTTT
17312168 GTCAAATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.32, C:0.02, G:0.11, T:0.55
Consensus pattern (16 bp):
AATTTAGTTTAATTGT
Found at i:17313119 original size:26 final size:26
Alignment explanation
Indices: 17313061--17313113 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
17313051 ACAGTAAATA
*
17313061 TATTATTATAAGGATATTTTTTATTT
1 TATTATTATAAGGATATTTATTATTT
* *
17313087 TATTATTATAAGGGTGTTTATTATTT
1 TATTATTATAAGGATATTTATTATTT
17313113 T
1 T
17313114 TATATTGTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.60
Consensus pattern (26 bp):
TATTATTATAAGGATATTTATTATTT
Found at i:17318467 original size:13 final size:13
Alignment explanation
Indices: 17318449--17318512 Score: 67
Period size: 13 Copynumber: 4.9 Consensus size: 13
17318439 AGTTTGGCAA
17318449 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
17318462 TGCTTTAGAAAAG
1 TGCTTTTGAAAAG
* *
17318475 TGCTGTGGACAAA-
1 TGCTTTTGA-AAAG
* *
17318488 TGTTTTTGAGAAG
1 TGCTTTTGAAAAG
17318501 TGCTTTTGAAAA
1 TGCTTTTGAAAA
17318513 ATTTGAGTGT
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
12 2 0.05
13 35 0.88
14 3 0.08
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:17321238 original size:45 final size:45
Alignment explanation
Indices: 17321171--17321270 Score: 159
Period size: 45 Copynumber: 2.2 Consensus size: 45
17321161 CATATGACCT
* *
17321171 CTTATCAC-TTGTCCTTGATCAGATAAGTGTAGCT-AGGCTACCA
1 CTTATCACTTTGCCCTTGATCAGATAAGTGTAGCTGAAGCTACCA
17321214 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGCC-CTTGATCAGATAAGTGTAGCTGAAGCTACCA
17321260 CTTATCACTTT
1 CTTATCACTTT
17321271 ATCACTTTGT
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
43 8 0.15
44 4 0.08
45 21 0.40
46 19 0.37
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (45 bp):
CTTATCACTTTGCCCTTGATCAGATAAGTGTAGCTGAAGCTACCA
Found at i:17321277 original size:46 final size:45
Alignment explanation
Indices: 17321171--17321277 Score: 164
Period size: 46 Copynumber: 2.4 Consensus size: 45
17321161 CATATGACCT
*
17321171 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
17321214 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
*
17321260 CTTATCACTTTATCACTT
1 CTTATCACTTTGTCACTT
17321278 TGTCTCTTGA
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
43 8 0.14
44 4 0.07
45 21 0.37
46 24 0.42
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (45 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:17321316 original size:37 final size:37
Alignment explanation
Indices: 17321269--17321403 Score: 252
Period size: 37 Copynumber: 3.6 Consensus size: 37
17321259 ACTTATCACT
*
17321269 TTATCACTTTGTCTCTTGATCAGATAAGTGTAACCAC
1 TTATCACTTTGTTTCTTGATCAGATAAGTGTAACCAC
17321306 TTATCACTTTGTTTCTTGATCAGATAAGTGTAACCAC
1 TTATCACTTTGTTTCTTGATCAGATAAGTGTAACCAC
*
17321343 TTATCACTTTGTTTCTTGATCAGATAAGTGTAGCCAC
1 TTATCACTTTGTTTCTTGATCAGATAAGTGTAACCAC
17321380 TTATCACTTTGTTTCTTGATCAGA
1 TTATCACTTTGTTTCTTGATCAGA
17321404 AGTACTCAAA
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 96 1.00
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.41
Consensus pattern (37 bp):
TTATCACTTTGTTTCTTGATCAGATAAGTGTAACCAC
Found at i:17325559 original size:24 final size:24
Alignment explanation
Indices: 17325532--17325591 Score: 75
Period size: 25 Copynumber: 2.5 Consensus size: 24
17325522 CTTGAAAGAC
*
17325532 CATCCCGTTATTAGCTCTCATGAG
1 CATCCCGTTATTAGCTCTCACGAG
* *
17325556 CATCCCGATATTTGGCTCTCACGAG
1 CATCCCGTTA-TTAGCTCTCACGAG
*
17325581 CTTCCCGTTAT
1 CATCCCGTTAT
17325592 ATGGTTATTG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 10 0.33
25 20 0.67
ACGTcount: A:0.18, C:0.32, G:0.17, T:0.33
Consensus pattern (24 bp):
CATCCCGTTATTAGCTCTCACGAG
Found at i:17325834 original size:25 final size:25
Alignment explanation
Indices: 17325806--17325854 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
17325796 TACAACTCTT
*
17325806 ATGAGCTTCCCGTTACGTGGCTCAC
1 ATGAGCTTCCCGTTACATGGCTCAC
* *
17325831 ATGAGCTTCCTGTTATATGGCTCA
1 ATGAGCTTCCCGTTACATGGCTCA
17325855 AAAGAGAGCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.18, C:0.27, G:0.22, T:0.33
Consensus pattern (25 bp):
ATGAGCTTCCCGTTACATGGCTCAC
Found at i:17328271 original size:24 final size:24
Alignment explanation
Indices: 17328222--17328274 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
17328212 TTAAACAAAG
**
17328222 ACAAATGTAATGCATAGGTGACGT
1 ACAAATGTAATAAATAGGTGACGT
*
17328246 ACAAATGTAATAAATTATGTGA-GT
1 ACAAATGTAATAAA-TAGGTGACGT
17328270 ACAAA
1 ACAAA
17328275 AGTGTATATG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.26
Consensus pattern (24 bp):
ACAAATGTAATAAATAGGTGACGT
Found at i:17328589 original size:16 final size:16
Alignment explanation
Indices: 17328568--17328600 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
17328558 AAATAAAGTA
*
17328568 AAAGAATAAAAGAAAC
1 AAAGAAGAAAAGAAAC
17328584 AAAGAAGAAAAGAAAC
1 AAAGAAGAAAAGAAAC
17328600 A
1 A
17328601 GAGACCATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.76, C:0.06, G:0.15, T:0.03
Consensus pattern (16 bp):
AAAGAAGAAAAGAAAC
Found at i:17332458 original size:8 final size:8
Alignment explanation
Indices: 17332434--17332558 Score: 53
Period size: 8 Copynumber: 15.1 Consensus size: 8
17332424 ATTATTTTGA
17332434 AAATATAT
1 AAATATAT
17332442 AAA-ATAT
1 AAATATAT
17332449 AAATATAT
1 AAATATAT
*
17332457 AAAATCCTAT
1 -AAAT-ATAT
*
17332467 AACATATGTAAA
1 AA-ATA--T-AT
17332479 AAATATAT
1 AAATATAT
17332487 AAATATAT
1 AAATATAT
17332495 AAA-AGCGTAT
1 AAATA---TAT
* *
17332505 AATTTTAT
1 AAATATAT
17332513 AAATATAT
1 AAATATAT
* *
17332521 -ATTATAA
1 AAATATAT
17332528 AAAT-TAT
1 AAATATAT
17332535 -AATATAT
1 AAATATAT
* *
17332542 AAGTTTAT
1 AAATATAT
*
17332550 AAAAATAT
1 AAATATAT
17332558 A
1 A
17332559 TTAGAAATTT
Statistics
Matches: 86, Mismatches: 17, Indels: 28
0.66 0.13 0.21
Matches are distributed among these distances:
6 3 0.03
7 18 0.21
8 41 0.48
9 7 0.08
10 10 0.12
11 4 0.05
12 3 0.03
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (8 bp):
AAATATAT
Found at i:17332485 original size:18 final size:17
Alignment explanation
Indices: 17332436--17332498 Score: 54
Period size: 19 Copynumber: 3.5 Consensus size: 17
17332426 TATTTTGAAA
*
17332436 ATATATAAAATATAAAT
1 ATATAAAAAATATAAAT
**
17332453 ATATAAAATCCTATAACAT
1 ATATAAAA-AATATAA-AT
*
17332472 ATGTAAAAAATATATAAAT
1 ATAT-AAAAA-ATATAAAT
17332491 ATATAAAA
1 ATATAAAA
17332499 GCGTATAATT
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
17 7 0.20
18 9 0.26
19 10 0.29
20 9 0.26
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.32
Consensus pattern (17 bp):
ATATAAAAAATATAAAT
Found at i:17341893 original size:126 final size:128
Alignment explanation
Indices: 17341666--17342592 Score: 790
Period size: 141 Copynumber: 6.9 Consensus size: 128
17341656 ACATACTATT
*** ** * *
17341666 GGACAAAGCCAACAAATATTTAAGTATTGCCTTAGGCATGTATATACCAACCCTTATACAAAGAG
1 GGACAAAGCCAACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAACCCTTATACAAAGAG
* * * *
17341731 TTGGCCAAAGCATATGTTGACAAGTCTATCCCAACACTTAGGAAAGTGTTGGCATAGTG-TT-
66 TTGGCCAAAGCGTATGTTGGCAAGTCTATCCCAACACTTAGGAAAGTGTTGCCAAAGTGATTA
** * *
17341792 GGACAAAGCTGACTCTTATTGAAACGTTGCCTTAGGCATGCATATCCCAACCCTTATACAAAGAG
1 GGACAAAGCCAACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAACCCTTATACAAAGAG
* * *
17341857 TTGGCCAAAGTGTATGTTGGCAAGTCTATCCTAACACTTAGGAAAGTGTCAGCCCAAAAGTGTAG
66 TTGGCCAAAGCGTATGTTGGCAAGTCTATCCCAACACTTAGGAAAGTGT-TG-CC-AAA--GT--
*
17341922 GCGTAGTGTT
124 --G-A-T-TA
* * * * *
17341932 GGACAAAGTCGACTCTTATTTAAGCGTTGCCTTAAGAATGCATATCCTAACCCTTATACATAA-A
1 GGACAAAGCCAACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAACCCTTATACA-AAGA
* * * **** *
17341996 GTTGACCAAAGCGTATGTCT-GCAAGTCTATCCCAACACTTAGGAAAATGTCGTTTTAG-GACT-
65 GTTGGCCAAAGCGTATGT-TGGCAAGTCTATCCCAACACTTAGGAAAGTGTTGCCAAAGTGATTA
* * *
17342058 GGACAAAGCCAACTCTTATTTAAGCGTTGCCTTAGACATGCGTACCCCAACCCTTATACAAAGAG
1 GGACAAAGCCAACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAACCCTTATACAAAGAG
* * *
17342123 TTGGCCAGAGCGTATGTTGACAAGTCTATCCCAACACTTAGGAAAGTGTAGCCCCAAAAGTTTCG
66 TTGGCCAAAGCGTATGTTGGCAAGTCTATCCCAACACTTAGGAAAGTGTTG--CC-AAAG--T-G
17342188 TATTA
125 -ATTA
* * * * * *
17342193 GGACTACACAAAAACCAACTCTTATTTAAGCGTTGTCTTAGGCATACGTATCTCAACCCTTATGC
1 GG-----AC-AAAGCCAACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAACCCTTATAC
* *
17342258 AAAGAGTTGGCCAAAGCGTATGCTGGCAAGTCTATCCCAACACTTAGGAAAGTGTCTCCCCAAAA
60 AAAGAGTTGGCCAAAGCGTATGTTGGCAAGTCTATCCCAACACTTAGGAAAGTGT-T-GCC--AA
*
17342323 ATGTCATCTTA
121 A-GTGA--TTA
* *
17342334 GGACTACACAAAAGTCAACTCTTATTTAAGCGTTGCCTTAGGCATACATATCCCAACCCTTATAC
1 GG-----AC-AAAGCCAACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAACCCTTATAC
* * *
17342399 AAAGAGTTGACCAAAGCGTATGTTGGCAAGTCTATCCCAACGCTTAGGAAAGTGTCGCCCCAGAA
60 AAAGAGTTGGCCAAAGCGTATGTTGGCAAGTCTATCCCAACACTTAGGAAAGTGTTG--CCA-AA
*
17342464 GTGTCGTCTTA
122 --GT-G-ATTA
*
17342475 GGCCTAGACAAAGCCAACTCTTA-TTAAGTGTTGCCTTAGGCATGCATATCCCAACCCTTATACA
1 -G----GACAAAGCCAACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAACCCTTATACA
* * * * *
17342539 AAGAGTTGGTCAAAGCGTATGTTGATCAA-TTTATCTCAACATTTAGGAAAGTGT
61 AAGAGTTGGCCAAAGCGTATGTTG-GCAAGTCTATCCCAACACTTAGGAAAGTGT
17342593 CACCCCAAAA
Statistics
Matches: 661, Mismatches: 89, Indels: 89
0.79 0.11 0.11
Matches are distributed among these distances:
125 3 0.00
126 197 0.30
127 2 0.00
128 1 0.00
129 5 0.01
130 1 0.00
131 2 0.00
133 1 0.00
134 2 0.00
135 4 0.01
137 1 0.00
138 1 0.00
139 86 0.13
140 118 0.18
141 230 0.35
142 5 0.01
143 1 0.00
146 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (128 bp):
GGACAAAGCCAACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAACCCTTATACAAAGAG
TTGGCCAAAGCGTATGTTGGCAAGTCTATCCCAACACTTAGGAAAGTGTTGCCAAAGTGATTA
Done.