Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 31 of 103
Found at i:11681314 original size:43 final size:43
Alignment explanation
Indices: 11681266--11681348 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
11681256 ATTATGTGAT
*
11681266 AATGATGACCCAGTTATGTGCGAGTAGGGAGTGCACATGAGCC
1 AATGATGACCCAGCTATGTGCGAGTAGGGAGTGCACATGAGCC
* *
11681309 AATGATGACTCGGCTATGTGCGAGTAGGGAGTGCACATGA
1 AATGATGACCCAGCTATGTGCGAGTAGGGAGTGCACATGA
11681349 CGATGAATGA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.28, C:0.17, G:0.34, T:0.22
Consensus pattern (43 bp):
AATGATGACCCAGCTATGTGCGAGTAGGGAGTGCACATGAGCC
Found at i:11692692 original size:55 final size:54
Alignment explanation
Indices: 11692625--11692886 Score: 373
Period size: 55 Copynumber: 4.8 Consensus size: 54
11692615 GATGATGAGC
* * *
11692625 GATTCTAGCTATGTGCAGTGTGGGAGTGCACATGAGCTAATGACTGGTGGATGAC
1 GATTCTAGCTATGTGC-GTGTGGGAGTGCACATGAGCTGATGACCGGTGGATGAT
* * *
11692680 GATTCCAACTATGTGCGATGTGGGAGTGCACATGAGCTGATGACCAGTGGATGAT
1 GATTCTAGCTATGTGCG-TGTGGGAGTGCACATGAGCTGATGACCGGTGGATGAT
* * *
11692735 GATTCCAACTATGTGCGGTGTGGGAATGCACATGAGCTGATGACCGGTGGATGAT
1 GATTCTAGCTATGTGC-GTGTGGGAGTGCACATGAGCTGATGACCGGTGGATGAT
* *
11692790 GATTCTAGCTATGTGTGGTGTGGGAGTGCACATGAGCTGATGATCGGTGGATGAT
1 GATTCTAGCTATGTG-CGTGTGGGAGTGCACATGAGCTGATGACCGGTGGATGAT
11692845 GATTCTAGCTAGTGTG-GTGTGGGAGTGCACATGAGCTGATGA
1 GATTCTAGCTA-TGTGCGTGTGGGAGTGCACATGAGCTGATGA
11692887 GCCGATGGTT
Statistics
Matches: 190, Mismatches: 13, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
54 27 0.14
55 158 0.83
56 5 0.03
ACGTcount: A:0.23, C:0.14, G:0.35, T:0.27
Consensus pattern (54 bp):
GATTCTAGCTATGTGCGTGTGGGAGTGCACATGAGCTGATGACCGGTGGATGAT
Found at i:11696133 original size:25 final size:25
Alignment explanation
Indices: 11696105--11696166 Score: 97
Period size: 25 Copynumber: 2.5 Consensus size: 25
11696095 CCATTTATTT
*
11696105 TTATTTACTATTGGGCCATGCCCAC
1 TTATTTTCTATTGGGCCATGCCCAC
* *
11696130 TTATTTTCTATTGGGTCATGCCCAT
1 TTATTTTCTATTGGGCCATGCCCAC
11696155 TTATTTTCTATT
1 TTATTTTCTATT
11696167 TCTTTTCTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.18, C:0.21, G:0.13, T:0.48
Consensus pattern (25 bp):
TTATTTTCTATTGGGCCATGCCCAC
Found at i:11696366 original size:34 final size:34
Alignment explanation
Indices: 11696323--11696407 Score: 118
Period size: 34 Copynumber: 2.5 Consensus size: 34
11696313 CAACTACCAA
* * * *
11696323 CAAATAGCTCAAATTTTTTTGCACAAATTGGCAG
1 CAAACAGCTCAAATTTTTCTACACAAAATGGCAG
11696357 CAAACAGCTCCAAA-TTTTCTACACAAAATGGCAG
1 CAAACAGCT-CAAATTTTTCTACACAAAATGGCAG
11696391 CAAACAGCTCAAATTTT
1 CAAACAGCTCAAATTTT
11696408 CAGCAGCCAA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
33 4 0.09
34 37 0.82
35 4 0.09
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (34 bp):
CAAACAGCTCAAATTTTTCTACACAAAATGGCAG
Found at i:11702203 original size:124 final size:123
Alignment explanation
Indices: 11701983--11702229 Score: 449
Period size: 124 Copynumber: 2.0 Consensus size: 123
11701973 AAAGTATCGG
*
11701983 TCCCCACATCACATTAAAACTATCTTTTCGTAAAATGTTTATTGCAAATATTTGCATGATATTTT
1 TCCCCACATCACATTAAAACTATCTTTTCGTAAAATGTTCATTGCAAATATTTGCATGATATTTT
11702048 GTATCAAAATAGCATGGTGAATATGTAATAAATTTCATGAATGCACACCACACAAACA
66 GTATCAAAATAGCATGGTGAATATGTAATAAATTTCATGAATGCACACCACACAAACA
* * *
11702106 NTCCCCACATCACGTTAAAACTCTCTTTTCGTAAAATGTTCATTGTAAATATTTGCATGATATTT
1 -TCCCCACATCACATTAAAACTATCTTTTCGTAAAATGTTCATTGCAAATATTTGCATGATATTT
11702171 TGTATCAAAATAGCATGGTGAATATGTAATAAATTTCATGAATGCACACCACACAAACA
65 TGTATCAAAATAGCATGGTGAATATGTAATAAATTTCATGAATGCACACCACACAAACA
11702230 ATAAGGCACA
Statistics
Matches: 119, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
124 119 1.00
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.33
Consensus pattern (123 bp):
TCCCCACATCACATTAAAACTATCTTTTCGTAAAATGTTCATTGCAAATATTTGCATGATATTTT
GTATCAAAATAGCATGGTGAATATGTAATAAATTTCATGAATGCACACCACACAAACA
Found at i:11702309 original size:2 final size:2
Alignment explanation
Indices: 11702302--11702331 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11702292 TTTACGTCTA
11702302 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11702332 TTCAAATGAT
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):
AT
Found at i:11702859 original size:25 final size:25
Alignment explanation
Indices: 11702831--11702885 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
11702821 TTTTTGTTTC
11702831 CTATTGGGCCATGCCCACTTATTTT
1 CTATTGGGCCATGCCCACTTATTTT
* **
11702856 CTATTGGGTCATGCCCTTTTATTTT
1 CTATTGGGCCATGCCCACTTATTTT
11702881 CTATT
1 CTATT
11702886 TCTTTTCTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.15, C:0.24, G:0.15, T:0.47
Consensus pattern (25 bp):
CTATTGGGCCATGCCCACTTATTTT
Found at i:11703065 original size:34 final size:34
Alignment explanation
Indices: 11703014--11703091 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 34
11703004 CACGATGCTG
*
11703014 TCAAATTTTCCTGCACAAACTACCAGCAAACAGC
1 TCAAATTTTCCTACACAAACTACCAGCAAACAGC
* * * ** *
11703048 TCCAATTTTTCTACACAAATTGGCAGCAAACAGG
1 TCAAATTTTCCTACACAAACTACCAGCAAACAGC
11703082 TCAAATTTTC
1 TCAAATTTTC
11703092 AACAGCAAAA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.36, C:0.27, G:0.10, T:0.27
Consensus pattern (34 bp):
TCAAATTTTCCTACACAAACTACCAGCAAACAGC
Found at i:11707672 original size:40 final size:37
Alignment explanation
Indices: 11707613--11707715 Score: 118
Period size: 38 Copynumber: 2.7 Consensus size: 37
11707603 ACCCGGCTCA
* *
11707613 TGTACATCCCCCCATATCGTGCACA-TAGTCGGCACCATTG
1 TGTACATCCCCCCACATCGTGCACATTAGT--G--CCATCG
* *
11707653 TGTGCATCCCCCCACATCGTGCATAATTAGTGCCATCG
1 TGTACATCCCCCCACATCGTGCA-CATTAGTGCCATCG
11707691 TGTACATCCCCCCACATCGTGCACA
1 TGTACATCCCCCCACATCGTGCACA
11707716 CGGGCACTGT
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
37 1 0.02
38 27 0.49
40 22 0.40
41 1 0.02
42 4 0.07
ACGTcount: A:0.22, C:0.37, G:0.17, T:0.24
Consensus pattern (37 bp):
TGTACATCCCCCCACATCGTGCACATTAGTGCCATCG
Found at i:11713409 original size:13 final size:13
Alignment explanation
Indices: 11713391--11713418 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
11713381 ATGAAAATGG
11713391 AAACTCAAGGAAA
1 AAACTCAAGGAAA
11713404 AAACTCAAGGAAA
1 AAACTCAAGGAAA
11713417 AA
1 AA
11713419 TCATTATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.14, G:0.14, T:0.07
Consensus pattern (13 bp):
AAACTCAAGGAAA
Found at i:11721594 original size:16 final size:16
Alignment explanation
Indices: 11721564--11721593 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
11721554 AGAGCATGAT
11721564 TTTTAAGTTTTTTTTG
1 TTTTAAGTTTTTTTTG
11721580 TTTTAA-TTTTTTTT
1 TTTTAAGTTTTTTTT
11721594 TTAAAAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.13, C:0.00, G:0.07, T:0.80
Consensus pattern (16 bp):
TTTTAAGTTTTTTTTG
Found at i:11744479 original size:54 final size:54
Alignment explanation
Indices: 11744420--11744525 Score: 158
Period size: 54 Copynumber: 2.0 Consensus size: 54
11744410 CACATCTCAT
* * *
11744420 CCAGCTTATGTACATCCCCCCAAATCGTGCACATAGTCGGACACCCCATCTTAC
1 CCAGCTCATGTACATCCCCCCAAATCGTCCACATAGCCGGACACCCCATCTTAC
* * *
11744474 CCAGCTCATGTGCATCCCCCCACATCGTCCACATAGCCGGACATCCCATCTT
1 CCAGCTCATGTACATCCCCCCAAATCGTCCACATAGCCGGACACCCCATCTT
11744526 TGTTGCCTCC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.24, C:0.42, G:0.13, T:0.22
Consensus pattern (54 bp):
CCAGCTCATGTACATCCCCCCAAATCGTCCACATAGCCGGACACCCCATCTTAC
Found at i:11749944 original size:36 final size:35
Alignment explanation
Indices: 11749829--11750037 Score: 253
Period size: 35 Copynumber: 6.0 Consensus size: 35
11749819 CTTGATTGAG
* *
11749829 ATTGTTTAATTAAG---TTGTGCCTAATTAATTTA
1 ATTGTTTAATTAAGTTATTGGGCCTAATTAATTAA
* *
11749861 ATTATTTAATTAAATTATTGGGCCTAATTAATTAA
1 ATTGTTTAATTAAGTTATTGGGCCTAATTAATTAA
* *
11749896 ATTGTTTAATTAAGTCATTGGGCCTAATTGATTAA
1 ATTGTTTAATTAAGTTATTGGGCCTAATTAATTAA
* *
11749931 ATTTGTTTAATTAAGTCATTGGGCCTAATTGATTAAA
1 A-TTGTTTAATTAAGTTATTGGGCCTAATTAATT-AA
* * *
11749968 ATTGTTTAATTAAATTGTTGGGCTTAATTAATTAA
1 ATTGTTTAATTAAGTTATTGGGCCTAATTAATTAA
* * *
11750003 ATTATTTACTTAAGTTATTGGGCCTAATCAATTAA
1 ATTGTTTAATTAAGTTATTGGGCCTAATTAATTAA
11750038 GTTAATTGGG
Statistics
Matches: 153, Mismatches: 19, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
32 12 0.08
35 79 0.52
36 59 0.39
37 3 0.02
ACGTcount: A:0.34, C:0.07, G:0.13, T:0.45
Consensus pattern (35 bp):
ATTGTTTAATTAAGTTATTGGGCCTAATTAATTAA
Found at i:11750001 original size:107 final size:103
Alignment explanation
Indices: 11749830--11750030 Score: 285
Period size: 107 Copynumber: 1.9 Consensus size: 103
11749820 TTGATTGAGA
* *
11749830 TTGTTTAATTAAGTTGTGCCTAATTAATTTAATTATTTAATTAAATTATTGGGCCTAATTAATTA
1 TTGTTTAATTAAGTTGGGCCTAATTAATTAAATTATTTAATTAAATTATTGGGCCTAATTAATTA
*
11749895 AATTGTTTAATTAAGTCATTGGGCCTAATTGATTAAAT
66 AATTATTTAATTAAGTCATTGGGCCTAATTGATTAAAT
* * * *
11749933 TTGTTTAATTAAGTCATTGGGCCTAATTGATTAAAATTGTTTAATTAAATTGTTGGGCTTAATTA
1 TTGTTTAATTAAG---TTGGGCCTAATTAATT-AAATTATTTAATTAAATTATTGGGCCTAATTA
* *
11749998 ATTAAATTATTTACTTAAGTTATTGGGCCTAAT
62 ATTAAATTATTTAATTAAGTCATTGGGCCTAAT
11750031 CAATTAAGTT
Statistics
Matches: 85, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
103 13 0.15
106 14 0.16
107 58 0.68
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.46
Consensus pattern (103 bp):
TTGTTTAATTAAGTTGGGCCTAATTAATTAAATTATTTAATTAAATTATTGGGCCTAATTAATTA
AATTATTTAATTAAGTCATTGGGCCTAATTGATTAAAT
Found at i:11759287 original size:16 final size:17
Alignment explanation
Indices: 11759266--11759302 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
11759256 AAGACTCAGT
11759266 GAATAAAATAAGA-AAA
1 GAATAAAATAAGATAAA
*
11759282 GAATAAAATAATATAAA
1 GAATAAAATAAGATAAA
11759299 GAAT
1 GAAT
11759303 GTGTGTATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.70, C:0.00, G:0.11, T:0.19
Consensus pattern (17 bp):
GAATAAAATAAGATAAA
Found at i:11769063 original size:27 final size:27
Alignment explanation
Indices: 11769033--11769086 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
11769023 GAGCCCTAAA
11769033 GCCAATTAGGATTGGTTGAGGCTTGAT
1 GCCAATTAGGATTGGTTGAGGCTTGAT
11769060 GCCAATTAGGATTGGTTGAGGCTTGAT
1 GCCAATTAGGATTGGTTGAGGCTTGAT
11769087 TCCTATCATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.22, C:0.11, G:0.33, T:0.33
Consensus pattern (27 bp):
GCCAATTAGGATTGGTTGAGGCTTGAT
Found at i:11783961 original size:21 final size:22
Alignment explanation
Indices: 11783936--11783976 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
11783926 CTTAGGTGGA
*
11783936 AAAATTCAAGGGAA-AAGTGTG
1 AAAATTCAAGGAAACAAGTGTG
11783957 AAAATTCAAGGAAACAAGTG
1 AAAATTCAAGGAAACAAGTG
11783977 ACAAAAGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.17
Consensus pattern (22 bp):
AAAATTCAAGGAAACAAGTGTG
Found at i:11783982 original size:22 final size:21
Alignment explanation
Indices: 11783936--11783982 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
11783926 CTTAGGTGGA
* **
11783936 AAAATTCAAGGGAAAAGTGTG
1 AAAATTCAAGGAAAAAGTGAC
11783957 AAAATTCAAGGAAACAAGTGAC
1 AAAATTCAAGGAAA-AAGTGAC
11783979 AAAA
1 AAAA
11783983 GGTAAGATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.55, C:0.09, G:0.21, T:0.15
Consensus pattern (21 bp):
AAAATTCAAGGAAAAAGTGAC
Found at i:11786307 original size:11 final size:11
Alignment explanation
Indices: 11786291--11786321 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
11786281 AGATTTTGGG
11786291 TTTAAAATTGT
1 TTTAAAATTGT
*
11786302 TTTAAAGTTGT
1 TTTAAAATTGT
11786313 TTTAAAATT
1 TTTAAAATT
11786322 TATAGTGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (11 bp):
TTTAAAATTGT
Found at i:11793692 original size:72 final size:73
Alignment explanation
Indices: 11793545--11793702 Score: 250
Period size: 72 Copynumber: 2.2 Consensus size: 73
11793535 GTCGTGACAC
* *
11793545 TGGGAGTGCACATGACGGTGATAGTGGTGTGCTGTGTGAGTGCACACACTAATGATATATGCCAG
1 TGGGAGTGCACATGACGGTGATAGTGGTGTGCTGTGTGAGTGCACACACTAATGATATATACCAC
**
11793610 GTGCGGTG
66 GTGCAATG
*
11793618 TGGGAGTGCACATGACGGTGATAGTGGTGT-CTGTGTGAGTGCACACACTGATGATATATACCAC
1 TGGGAGTGCACATGACGGTGATAGTGGTGTGCTGTGTGAGTGCACACACTAATGATATATACCAC
11793682 GTGCAATG
66 GTGCAATG
11793690 TGGGA--GCACATGA
1 TGGGAGTGCACATGA
11793703 TGATATTTCC
Statistics
Matches: 80, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
70 8 0.10
72 42 0.52
73 30 0.38
ACGTcount: A:0.24, C:0.16, G:0.35, T:0.25
Consensus pattern (73 bp):
TGGGAGTGCACATGACGGTGATAGTGGTGTGCTGTGTGAGTGCACACACTAATGATATATACCAC
GTGCAATG
Found at i:11793738 original size:35 final size:36
Alignment explanation
Indices: 11793688--11793773 Score: 99
Period size: 36 Copynumber: 2.5 Consensus size: 36
11793678 CCACGTGCAA
*
11793688 TGTGGGA--GCACATGATGATAT-TTCCT-TGTACAG
1 TGTGGGAGTGCACATGATGAT-TCTACCTATGTACAG
* * *
11793721 TGTGGGAGTGCACATGATGATTCTAGCTATGTGCGG
1 TGTGGGAGTGCACATGATGATTCTACCTATGTACAG
11793757 TGTGGGAGTGCACATGA
1 TGTGGGAGTGCACATGA
11793774 GCTAGTAAGA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
33 7 0.16
34 1 0.02
35 15 0.33
36 22 0.49
ACGTcount: A:0.22, C:0.14, G:0.34, T:0.30
Consensus pattern (36 bp):
TGTGGGAGTGCACATGATGATTCTACCTATGTACAG
Found at i:11797369 original size:35 final size:35
Alignment explanation
Indices: 11797323--11797409 Score: 120
Period size: 35 Copynumber: 2.5 Consensus size: 35
11797313 CTCCCCAGCT
* *
11797323 CATGTGCACTCCCACACCGCACATAGCTAGGTTAA
1 CATGTGCACTCCCACACCGCACATACCTAGGTCAA
* * *
11797358 CATGTGTACTCCCACATCGCACATACCTAGGTCAT
1 CATGTGCACTCCCACACCGCACATACCTAGGTCAA
*
11797393 CATGTGGACTCCCACAC
1 CATGTGCACTCCCACAC
11797410 TACACGTTCC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.26, C:0.36, G:0.16, T:0.22
Consensus pattern (35 bp):
CATGTGCACTCCCACACCGCACATACCTAGGTCAA
Found at i:11798324 original size:3 final size:3
Alignment explanation
Indices: 11798316--11798340 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
11798306 GAAGGGATGG
11798316 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
11798341 TTGATGGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:11799522 original size:18 final size:19
Alignment explanation
Indices: 11799496--11799543 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
11799486 GTAATGGGTG
*
11799496 AAAAGAATATTTTA-TAAT
1 AAAATAATATTTTATTAAT
*
11799514 AAAATAATATTTTATTACT
1 AAAATAATATTTTATTAAT
*
11799533 AAAATATTATT
1 AAAATAATATT
11799544 AAAATATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 13 0.50
19 13 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (19 bp):
AAAATAATATTTTATTAAT
Found at i:11799546 original size:11 final size:11
Alignment explanation
Indices: 11799526--11799585 Score: 66
Period size: 11 Copynumber: 5.5 Consensus size: 11
11799516 AATAATATTT
11799526 TATTACTAAAA
1 TATTACTAAAA
*
11799537 TATTATTAAAA
1 TATTACTAAAA
* ***
11799548 TATTAATATTT
1 TATTACTAAAA
11799559 TATTACTAAAA
1 TATTACTAAAA
*
11799570 TATTATTAAAA
1 TATTACTAAAA
11799581 TATTA
1 TATTA
11799586 ATATTTTATC
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 39 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (11 bp):
TATTACTAAAA
Found at i:11799557 original size:33 final size:33
Alignment explanation
Indices: 11799518--11799594 Score: 154
Period size: 33 Copynumber: 2.3 Consensus size: 33
11799508 TATAATAAAA
11799518 TAATATTTTATTACTAAAATATTATTAAAATAT
1 TAATATTTTATTACTAAAATATTATTAAAATAT
11799551 TAATATTTTATTACTAAAATATTATTAAAATAT
1 TAATATTTTATTACTAAAATATTATTAAAATAT
11799584 TAATATTTTAT
1 TAATATTTTAT
11799595 CTATTGTTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.51
Consensus pattern (33 bp):
TAATATTTTATTACTAAAATATTATTAAAATAT
Found at i:11807847 original size:17 final size:19
Alignment explanation
Indices: 11807806--11807847 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
11807796 ATATATATAT
11807806 ATGAATATATGTTGTGCATTG
1 ATGAATATATGTTGTG-A-TG
11807827 ATGAATA-ATGTTGTG-TG
1 ATGAATATATGTTGTGATG
11807844 ATGA
1 ATGA
11807848 TGTTGAAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 6 0.29
20 8 0.38
21 7 0.33
ACGTcount: A:0.31, C:0.02, G:0.26, T:0.40
Consensus pattern (19 bp):
ATGAATATATGTTGTGATG
Found at i:11807902 original size:37 final size:37
Alignment explanation
Indices: 11807842--11807960 Score: 159
Period size: 37 Copynumber: 3.2 Consensus size: 37
11807832 TAATGTTGTG
* *
11807842 TGATGATGTTGAAGTGTACGAGTAGGGAGTGCACACA
1 TGATGATGTTGAAGTATGCGAGTAGGGAGTGCACACA
* * *
11807879 GGATGATGTT-AGAGTATGTGAGTAGGGAGTGCACAGA
1 TGATGATGTTGA-AGTATGCGAGTAGGGAGTGCACACA
* *
11807916 TGATGATGTTGAAGTGTGCGAGTATGGAGTGCACACA
1 TGATGATGTTGAAGTATGCGAGTAGGGAGTGCACACA
11807953 TGATGATG
1 TGATGATG
11807961 ATATTGCATT
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
36 1 0.01
37 68 0.97
38 1 0.01
ACGTcount: A:0.29, C:0.08, G:0.37, T:0.26
Consensus pattern (37 bp):
TGATGATGTTGAAGTATGCGAGTAGGGAGTGCACACA
Found at i:11808281 original size:22 final size:22
Alignment explanation
Indices: 11808249--11808307 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
11808239 CCAACCCTTT
* *
11808249 TTCTCGTTGCAGTGAAAAAGAA
1 TTCTCGCTGCAGCGAAAAAGAA
* *
11808271 TTCTCGCTGCAGCGAAAATGGA
1 TTCTCGCTGCAGCGAAAAAGAA
*
11808293 TTCTTGCTGCAGCGA
1 TTCTCGCTGCAGCGA
11808308 GAAACTCTCA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (22 bp):
TTCTCGCTGCAGCGAAAAAGAA
Found at i:11811081 original size:37 final size:36
Alignment explanation
Indices: 11811040--11811133 Score: 93
Period size: 36 Copynumber: 2.6 Consensus size: 36
11811030 ACTATCAAAT
*
11811040 TGCCTTTTCAATAAGGTCAGGCGTAACCTTT-ACAGCA
1 TGCCTTTT-AATAAGGTCAGGCGTAA-CTTTCACAACA
* * *
11811077 TGCCTTTGAAT-AGGATAAAGCGTAACTTTCACAACA
1 TGCCTTTTAATAAGG-TCAGGCGTAACTTTCACAACA
* *
11811113 TGCCTTTTACTAAGATCAGGC
1 TGCCTTTTAATAAGGTCAGGC
11811134 ATAATTGTTA
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
35 7 0.16
36 29 0.64
37 9 0.20
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (36 bp):
TGCCTTTTAATAAGGTCAGGCGTAACTTTCACAACA
Found at i:11811458 original size:36 final size:36
Alignment explanation
Indices: 11811417--11811486 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
11811407 TAGGGTCAAC
* * *
11811417 CGTAACTTTTACAACATGTCTTTTAACAAGATCAGG
1 CGTAACCTTCACAACATGCCTTTTAACAAGATCAGG
*
11811453 CGTAACCTTCACAACATGCCTTTTACCAAGATCA
1 CGTAACCTTCACAACATGCCTTTTAACAAGATCA
11811487 CATGTAACTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.33, C:0.26, G:0.11, T:0.30
Consensus pattern (36 bp):
CGTAACCTTCACAACATGCCTTTTAACAAGATCAGG
Found at i:11811494 original size:36 final size:36
Alignment explanation
Indices: 11811417--11811494 Score: 93
Period size: 36 Copynumber: 2.2 Consensus size: 36
11811407 TAGGGTCAAC
* * * **
11811417 CGTAACTTTTACAACATGTCTTTTAACAAGATCAGG
1 CGTAACCTTCACAACATGCCTTTTAACAAGATCACA
*
11811453 CGTAACCTTCACAACATGCCTTTTACCAAGATCACA
1 CGTAACCTTCACAACATGCCTTTTAACAAGATCACA
*
11811489 TGTAAC
1 CGTAAC
11811495 TTCCACCAAC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (36 bp):
CGTAACCTTCACAACATGCCTTTTAACAAGATCACA
Found at i:11814466 original size:42 final size:43
Alignment explanation
Indices: 11814343--11814468 Score: 184
Period size: 43 Copynumber: 2.9 Consensus size: 43
11814333 GCCACACTCC
*
11814343 GCTCATGTGCACTCCCTACTCGCACATAGCTGGGTCATCA-CTA
1 GCTCATGTGCACTCCC-ACACGCACATAGCTGGGTCATCATCTA
11814386 GCTCATGTGCACTCCCACACCGCACATAGCTGGGTCATCATC-A
1 GCTCATGTGCACTCCCACA-CGCACATAGCTGGGTCATCATCTA
* * *
11814429 GCTCATGTGCACTCCCACAAGCACATAGCCGAGTCATCAT
1 GCTCATGTGCACTCCCACACGCACATAGCTGGGTCATCAT
11814469 TATCACACAA
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
42 20 0.26
43 56 0.73
44 1 0.01
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.22
Consensus pattern (43 bp):
GCTCATGTGCACTCCCACACGCACATAGCTGGGTCATCATCTA
Found at i:11820166 original size:22 final size:23
Alignment explanation
Indices: 11820141--11820184 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
11820131 CAGTGCTTTA
11820141 AGAACTGA-TATCTTC-TCTTTGT
1 AGAACTGATTAT-TTCTTCTTTGT
*
11820163 AGAATTGATTATTTCTTCTTTG
1 AGAACTGATTATTTCTTCTTTG
11820185 CATTTTTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.23, C:0.14, G:0.14, T:0.50
Consensus pattern (23 bp):
AGAACTGATTATTTCTTCTTTGT
Found at i:11827670 original size:16 final size:17
Alignment explanation
Indices: 11827649--11827684 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
11827639 AGACTTAGTC
11827649 AATAAAATAAGA-AAAG
1 AATAAAATAAGATAAAG
*
11827665 AATAAAATAATATAAAG
1 AATAAAATAAGATAAAG
11827682 AAT
1 AAT
11827685 GTGTGTACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.19
Consensus pattern (17 bp):
AATAAAATAAGATAAAG
Found at i:11829787 original size:17 final size:19
Alignment explanation
Indices: 11829746--11829787 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
11829736 GTATATATAT
11829746 ATGAATATATGTTGTGCATTG
1 ATGAATATATGTTGTG-A-TG
11829767 ATGAATA-ATGTTGTG-TG
1 ATGAATATATGTTGTGATG
11829784 ATGA
1 ATGA
11829788 TGTTGAAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 6 0.29
20 8 0.38
21 7 0.33
ACGTcount: A:0.31, C:0.02, G:0.26, T:0.40
Consensus pattern (19 bp):
ATGAATATATGTTGTGATG
Found at i:11829865 original size:40 final size:37
Alignment explanation
Indices: 11829782--11829863 Score: 137
Period size: 37 Copynumber: 2.2 Consensus size: 37
11829772 TAATGTTGTG
* *
11829782 TGATGATGTTGAAGTGTTCGAGTATGGAGTGCACACA
1 TGATGATGTTGAAGTGTACGAGTAAGGAGTGCACACA
11829819 TGATGATGTTGAAGTGTACGAGTAAGGAGTGCACACA
1 TGATGATGTTGAAGTGTACGAGTAAGGAGTGCACACA
*
11829856 TAATGATG
1 TGATGATG
11829864 ATATTGCATT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.30, C:0.10, G:0.32, T:0.28
Consensus pattern (37 bp):
TGATGATGTTGAAGTGTACGAGTAAGGAGTGCACACA
Found at i:11830000 original size:11 final size:11
Alignment explanation
Indices: 11829984--11830012 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
11829974 TGGCATTGTT
11829984 AATTGCTCCCA
1 AATTGCTCCCA
11829995 AATTGCTCCCA
1 AATTGCTCCCA
11830006 AATTGCT
1 AATTGCT
11830013 TTTCATTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.31
Consensus pattern (11 bp):
AATTGCTCCCA
Found at i:11832900 original size:203 final size:202
Alignment explanation
Indices: 11832551--11832955 Score: 801
Period size: 203 Copynumber: 2.0 Consensus size: 202
11832541 TGAATGTTGA
11832551 TATGTCTATGATGTTTAACTGCTGAAAATTGAAGTTTGTTGATATTTTGCTATCTTTGTTGTTTT
1 TATGTCTATGATGTTTAACTGCTGAAAATTGAAGTTTGTTGATATTTTGCTATCTTTGTTGTTTT
11832616 AACTACTGATGACAAAAATCTACTACTGCACTAATATTTGGATTATATGCTGTTGACTGATTTTT
66 AACTACTGATGACAAAAATCTACTACTGCACTAATATTTGGATTATATGCTGTTGACTGATTTTT
11832681 GTTATGACATTGTGGATAAATTGTGATTATAAATAATTATGGATGTTATGTATTGTGTATTGACT
131 GTTATGACATTGTGGATAAATTGTGATTATAAATAATTATGGATGTTATGTATTGTGTATTGACT
11832746 GAATCAT
196 GAATCAT
11832753 NTATGTCTATGATGTTTAACTGCTGAAAATTGAAGTTTGTTGATATTTTGCTATCTTTGTTGTTT
1 -TATGTCTATGATGTTTAACTGCTGAAAATTGAAGTTTGTTGATATTTTGCTATCTTTGTTGTTT
11832818 TAACTACTGATGACAAAAATCTACTACTGCACTAATATTTGGATTATATGCTGTTGACTGATTTT
65 TAACTACTGATGACAAAAATCTACTACTGCACTAATATTTGGATTATATGCTGTTGACTGATTTT
11832883 TGTTATGACATTGTGGATAAATTGTGATTATAAATAATTATGGATGTTATGTATTGTGTATTGAC
130 TGTTATGACATTGTGGATAAATTGTGATTATAAATAATTATGGATGTTATGTATTGTGTATTGAC
11832948 TGAATCAT
195 TGAATCAT
11832956 GAAAGGATTG
Statistics
Matches: 202, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
203 202 1.00
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (202 bp):
TATGTCTATGATGTTTAACTGCTGAAAATTGAAGTTTGTTGATATTTTGCTATCTTTGTTGTTTT
AACTACTGATGACAAAAATCTACTACTGCACTAATATTTGGATTATATGCTGTTGACTGATTTTT
GTTATGACATTGTGGATAAATTGTGATTATAAATAATTATGGATGTTATGTATTGTGTATTGACT
GAATCAT
Found at i:11833186 original size:16 final size:17
Alignment explanation
Indices: 11833153--11833186 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
11833143 GCACACACTA
*
11833153 AGGGGGAGCATATGCTT
1 AGGGGGAGCATATCCTT
11833170 AGGGGGAGCA-ATCCTT
1 AGGGGGAGCATATCCTT
11833186 A
1 A
11833187 TTTTCTGCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.26, C:0.15, G:0.38, T:0.21
Consensus pattern (17 bp):
AGGGGGAGCATATCCTT
Found at i:11836949 original size:20 final size:20
Alignment explanation
Indices: 11836923--11836968 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
11836913 AATCTTACCT
* *
11836923 TTTTTCACTTGTTTCCTTGAA
1 TTTTACACTT-TTCCCTTGAA
11836944 TTTTCACACTTTTCCCTTGAA
1 TTTT-ACACTTTTCCCTTGAA
11836965 TTTT
1 TTTT
11836969 TCCACCTAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.15, C:0.22, G:0.07, T:0.57
Consensus pattern (20 bp):
TTTTACACTTTTCCCTTGAA
Found at i:11836970 original size:22 final size:22
Alignment explanation
Indices: 11836928--11836968 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
11836918 TACCTTTTTT
*
11836928 CACTTGTTTCCTTGAATTTTCA
1 CACTTGTTCCCTTGAATTTTCA
11836950 CACTT-TTCCCTTGAATTTT
1 CACTTGTTCCCTTGAATTTT
11836969 TCCACCTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.17, C:0.24, G:0.07, T:0.51
Consensus pattern (22 bp):
CACTTGTTCCCTTGAATTTTCA
Found at i:11837026 original size:11 final size:11
Alignment explanation
Indices: 11836982--11837020 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
11836972 ACCTAGGGTT
11836982 TTTGTTCTT-C
1 TTTGTTCTTCC
11836992 -TT-TTCTTCC
1 TTTGTTCTTCC
11837001 TTTGTTCTTCC
1 TTTGTTCTTCC
11837012 TTTGTTCTT
1 TTTGTTCTT
11837021 GTTTTGGCCG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 5 0.19
9 3 0.12
10 2 0.08
11 16 0.62
ACGTcount: A:0.00, C:0.23, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTGTTCTTCC
Found at i:11841114 original size:2 final size:2
Alignment explanation
Indices: 11841107--11841144 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
11841097 CTAGACATTT
*
11841107 AG AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
11841145 TACTTTCATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:11841249 original size:2 final size:2
Alignment explanation
Indices: 11841242--11841280 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
11841232 CTAGACATTT
*
11841242 AG AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
11841281 CTTTTCATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:11841287 original size:135 final size:133
Alignment explanation
Indices: 11841041--11841306 Score: 498
Period size: 135 Copynumber: 2.0 Consensus size: 133
11841031 AATGCCCTTT
11841041 CACTTCTACATCTGAAGAACCCTCAAAAGTCTTTCCTCAATACTTTCTCTCACTAGCTAGACATT
1 CACTTCTACATCTGAAGAACCCTCAAAAGTCTTTCCTCAATACTTTCTCTCACTAGCTAGACATT
11841106 TAGAGAGAGAAAGAGAGAGAGAGAGAGAGAGAGAGAGAGTACTTTCATAATAGCTTAGAAAACTC
66 TAGAGAGAGAAAGAGAGAGAGAGAGAGAGAGAGAGAGAGTACTTTCATAATAGCTT-GAAAACTC
11841171 TTAG
130 TTAG
11841175 NCACTTCTACATCTGAAGAACCCTCAAAAGTCTTTCCTCAATACTTTCTCTCACTAGCTAGACAT
1 -CACTTCTACATCTGAAGAACCCTCAAAAGTCTTTCCTCAATACTTTCTCTCACTAGCTAGACAT
11841240 TTAGAGAGAGAAAGAGAGAGAGAGAGAGAGAGAGAGAGAG-ACTTTTCATAATAGCTTGAAAACT
65 TTAGAGAGAGAAAGAGAGAGAGAGAGAGAGAGAGAGAGAGTAC-TTTCATAATAGCTTGAAAACT
11841304 CTT
129 CTT
11841307 GAAAAGGAAT
Statistics
Matches: 130, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
134 12 0.09
135 118 0.91
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (133 bp):
CACTTCTACATCTGAAGAACCCTCAAAAGTCTTTCCTCAATACTTTCTCTCACTAGCTAGACATT
TAGAGAGAGAAAGAGAGAGAGAGAGAGAGAGAGAGAGAGTACTTTCATAATAGCTTGAAAACTCT
TAG
Found at i:11841971 original size:35 final size:35
Alignment explanation
Indices: 11841927--11842042 Score: 98
Period size: 35 Copynumber: 3.4 Consensus size: 35
11841917 TGTGGTGCAA
11841927 GAGTACACATGATGATATTGGAATGTGCGGTATGG
1 GAGTACACATGATGATATTGGAATGTGCGGTATGG
* ** * ** * *
11841962 GAGTGCACATGCCGGTGGT-G-ATGTG-GTGCA--A
1 GAGTACACATGATGATATTGGAATGTGCG-GTATGG
*
11841993 GAGTACACATGATGATATTGGAATGTGCGGTGTGG
1 GAGTACACATGATGATATTGGAATGTGCGGTATGG
*
11842028 GAGTGCACATGATGA
1 GAGTACACATGATGA
11842043 CATATCTTTG
Statistics
Matches: 57, Mismatches: 18, Indels: 12
0.66 0.21 0.14
Matches are distributed among these distances:
31 13 0.23
32 2 0.04
33 13 0.23
34 2 0.04
35 27 0.47
ACGTcount: A:0.26, C:0.11, G:0.37, T:0.26
Consensus pattern (35 bp):
GAGTACACATGATGATATTGGAATGTGCGGTATGG
Found at i:11841990 original size:66 final size:66
Alignment explanation
Indices: 11841884--11842038 Score: 301
Period size: 66 Copynumber: 2.3 Consensus size: 66
11841874 CAACCATGCG
11841884 TGTGCGGTGTGGGAGTGCACATGCCGGTGGTGATGTGGTGCAAGAGTACACATGATGATATTGGA
1 TGTGCGGTGTGGGAGTGCACATGCCGGTGGTGATGTGGTGCAAGAGTACACATGATGATATTGGA
11841949 A
66 A
*
11841950 TGTGCGGTATGGGAGTGCACATGCCGGTGGTGATGTGGTGCAAGAGTACACATGATGATATTGGA
1 TGTGCGGTGTGGGAGTGCACATGCCGGTGGTGATGTGGTGCAAGAGTACACATGATGATATTGGA
11842015 A
66 A
11842016 TGTGCGGTGTGGGAGTGCACATG
1 TGTGCGGTGTGGGAGTGCACATG
11842039 ATGACATATC
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 87 1.00
ACGTcount: A:0.22, C:0.12, G:0.40, T:0.26
Consensus pattern (66 bp):
TGTGCGGTGTGGGAGTGCACATGCCGGTGGTGATGTGGTGCAAGAGTACACATGATGATATTGGA
A
Found at i:11842003 original size:31 final size:31
Alignment explanation
Indices: 11841896--11842003 Score: 83
Period size: 31 Copynumber: 3.4 Consensus size: 31
11841886 TGCGGTGTGG
*
11841896 GAGTGCACATGCCGGTGGTGATGTGGTGCAA
1 GAGTACACATGCCGGTGGTGATGTGGTGCAA
** * ** * *
11841927 GAGTACACATGATGATATTGGAATGTGCG-GTATGG
1 GAGTACACATGCCGGTGGT-G-ATGTG-GTGCA--A
*
11841962 GAGTGCACATGCCGGTGGTGATGTGGTGCAA
1 GAGTACACATGCCGGTGGTGATGTGGTGCAA
11841993 GAGTACACATG
1 GAGTACACATG
11842004 ATGATATTGG
Statistics
Matches: 54, Mismatches: 17, Indels: 12
0.65 0.20 0.14
Matches are distributed among these distances:
31 23 0.43
32 2 0.04
33 14 0.26
34 2 0.04
35 13 0.24
ACGTcount: A:0.24, C:0.14, G:0.38, T:0.24
Consensus pattern (31 bp):
GAGTACACATGCCGGTGGTGATGTGGTGCAA
Found at i:11845783 original size:42 final size:42
Alignment explanation
Indices: 11845732--11845861 Score: 206
Period size: 42 Copynumber: 3.1 Consensus size: 42
11845722 ACATTACCGA
* * * *
11845732 GTCATCACAGCTCATGTGCATTCATACACCGCGCATGGCTGG
1 GTCAGCACAGCTCATGTGCACTCCTACACCGCACATGGCTGG
*
11845774 GTCAGCACAGCTCATGTGCACTCCTACACTGCACATGGCTGG
1 GTCAGCACAGCTCATGTGCACTCCTACACCGCACATGGCTGG
*
11845816 GTCAGCACAGCTCATGTGCAGTCCTACACCGCACATGGCTGG
1 GTCAGCACAGCTCATGTGCACTCCTACACCGCACATGGCTGG
11845858 GTCA
1 GTCA
11845862 TAATTATCAC
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 81 1.00
ACGTcount: A:0.22, C:0.32, G:0.25, T:0.22
Consensus pattern (42 bp):
GTCAGCACAGCTCATGTGCACTCCTACACCGCACATGGCTGG
Found at i:11846486 original size:23 final size:23
Alignment explanation
Indices: 11846440--11846487 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
11846430 TTTCTAAATA
* *
11846440 ATTTCCACCCAAATCCATCTTAT
1 ATTTCCACACAAATCCATCATAT
11846463 ATTTCCACACATAATCCA-CATAT
1 ATTTCCACACA-AATCCATCATAT
11846486 AT
1 AT
11846488 GGCGGCAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.33
Consensus pattern (23 bp):
ATTTCCACACAAATCCATCATAT
Found at i:11848852 original size:8 final size:8
Alignment explanation
Indices: 11848839--11848864 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
11848829 TTATGAATAA
11848839 AAAATATT
1 AAAATATT
11848847 AAAATATT
1 AAAATATT
11848855 AAAATATT
1 AAAATATT
11848863 AA
1 AA
11848865 TATTTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
AAAATATT
Found at i:11849832 original size:14 final size:14
Alignment explanation
Indices: 11849813--11849869 Score: 64
Period size: 14 Copynumber: 4.1 Consensus size: 14
11849803 GCGGTTGGAG
11849813 AAAGAAAGAAAGAA
1 AAAGAAAGAAAGAA
11849827 AAAGAAA-AAGAGAA
1 AAAGAAAGAA-AGAA
* **
11849841 AAAGAGAGAAAGGG
1 AAAGAAAGAAAGAA
11849855 AAAGAAAGAAA-AA
1 AAAGAAAGAAAGAA
11849868 AA
1 AA
11849870 TTGTAAGTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
13 4 0.11
14 29 0.83
15 2 0.06
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (14 bp):
AAAGAAAGAAAGAA
Found at i:11855666 original size:43 final size:43
Alignment explanation
Indices: 11855618--11855749 Score: 158
Period size: 43 Copynumber: 3.1 Consensus size: 43
11855608 CACCATCCCA
* * ** *
11855618 TCATCATCAACTCATGTGCACTCCCTACTCGCACATGGCTGGG
1 TCATCATCAGCTTATGTGCACTCCCTACTCGCACATAACCGGG
*
11855661 TCATCA-CTAGTTTATGTGCACTCCCTACTCGCACATAACCGGG
1 TCATCATC-AGCTTATGTGCACTCCCTACTCGCACATAACCGGG
* * * *
11855704 TCATCATCGGCTTATGCGCACTCCCTACTCGCACATAGCCGAG
1 TCATCATCAGCTTATGTGCACTCCCTACTCGCACATAACCGGG
11855747 TCA
1 TCA
11855750 ATATCATTAC
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
42 1 0.01
43 74 0.97
44 1 0.01
ACGTcount: A:0.22, C:0.35, G:0.17, T:0.26
Consensus pattern (43 bp):
TCATCATCAGCTTATGTGCACTCCCTACTCGCACATAACCGGG
Found at i:11865611 original size:43 final size:43
Alignment explanation
Indices: 11865563--11865694 Score: 183
Period size: 43 Copynumber: 3.1 Consensus size: 43
11865553 CACCATCCCA
* * ** *
11865563 TCATCATCAGCTCATGTGCACTCCCTACTCGCACATGGCTGGG
1 TCATCATCAGCTTATGCGCACTCCCTACTCGCACATAACCGGG
*
11865606 TCATCATCAGTTTATGCGCACTCCCTACTCGCACATAACCGGG
1 TCATCATCAGCTTATGCGCACTCCCTACTCGCACATAACCGGG
* * *
11865649 TCATCATCGGCTTATGCGCACTCCCTACTCGCACATAGCCGAG
1 TCATCATCAGCTTATGCGCACTCCCTACTCGCACATAACCGGG
11865692 TCA
1 TCA
11865695 ATATCATTAC
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 79 1.00
ACGTcount: A:0.21, C:0.36, G:0.18, T:0.25
Consensus pattern (43 bp):
TCATCATCAGCTTATGCGCACTCCCTACTCGCACATAACCGGG
Found at i:11870259 original size:2 final size:2
Alignment explanation
Indices: 11870252--11870288 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
11870242 CTCTGTACAA
11870252 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11870289 NATAGTGATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11870316 original size:105 final size:106
Alignment explanation
Indices: 11870200--11870395 Score: 369
Period size: 105 Copynumber: 1.9 Consensus size: 106
11870190 CGAAGTAGCA
11870200 TCCCGCTATTGTGAGGTGAGTAGGGTGTGTCCATTCTAAAATCTCTGTACAAA-T-ATATATATA
1 TCCCGCTATTGTGAGGTGAGTAGGGTGTGTCCATTCTAAAATCTCTGTACAAATTAATATATATA
11870263 TATATATATATATATATATATATATANATAGTGATGTAGTAC
66 TATATATATATATATATATATATATA-ATAGTGATGTAGTAC
11870305 TCCCGCTATTGTGAGGTGAGTAGGGTGTGTCCATTCTAAAATCTCTGTACAAATTAATATATATA
1 TCCCGCTATTGTGAGGTGAGTAGGGTGTGTCCATTCTAAAATCTCTGTACAAATTAATATATATA
11870370 TATATATATATATATATATATATATA
66 TATATATATATATATATATATATATA
11870396 TATGTGTGTG
Statistics
Matches: 89, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
105 53 0.60
106 1 0.01
107 35 0.39
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (106 bp):
TCCCGCTATTGTGAGGTGAGTAGGGTGTGTCCATTCTAAAATCTCTGTACAAATTAATATATATA
TATATATATATATATATATATATATAATAGTGATGTAGTAC
Found at i:11870368 original size:2 final size:2
Alignment explanation
Indices: 11870361--11870398 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
11870351 GTACAAATTA
11870361 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11870399 GTGTGTGTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11884223 original size:42 final size:43
Alignment explanation
Indices: 11884139--11884384 Score: 268
Period size: 42 Copynumber: 5.8 Consensus size: 43
11884129 TCCTCATCAT
* * * *
11884139 CATCGACTTATGCGTACTCCCTACTCGCACATAGCAGAGTCAG
1 CATCGGCTTATGTGCACTTCCTACTCGCACATAGCAGAGTCAG
** *
11884182 CATCGGCTTATGCACACTTCC-ACTCGCACAAAGCTAG-GTCAG
1 CATCGGCTTATGTGCACTTCCTACTCGCACATAGC-AGAGTCAG
* * * *
11884224 CATCGGCCTATGTGCAC-TCCTACTTGCACATAGCCGAGTCAA
1 CATCGGCTTATGTGCACTTCCTACTCGCACATAGCAGAGTCAG
* * *
11884266 CATCGGCTTATGTACAC-TCCCACTCGCACATAGCAGGGTCAG
1 CATCGGCTTATGTGCACTTCCTACTCGCACATAGCAGAGTCAG
* * *
11884308 CGTCGGCCTATGTGCAC-TCCTACTCGCACATAGCCGAGTCAG
1 CATCGGCTTATGTGCACTTCCTACTCGCACATAGCAGAGTCAG
* * *
11884350 CATCGGCTTATGCGCACTCCCTACTTGCACATAGC
1 CATCGGCTTATGTGCACTTCCTACTCGCACATAGC
11884385 TGGGTCAATA
Statistics
Matches: 169, Mismatches: 30, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
41 4 0.02
42 131 0.78
43 34 0.20
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.23
Consensus pattern (43 bp):
CATCGGCTTATGTGCACTTCCTACTCGCACATAGCAGAGTCAG
Found at i:11884283 original size:84 final size:84
Alignment explanation
Indices: 11884158--11884391 Score: 344
Period size: 84 Copynumber: 2.8 Consensus size: 84
11884148 ATGCGTACTC
* *
11884158 CCTACTCGCACATAGCAGAGTCAGCATCGGCTTATGCACACTTCCACTCGCACAAAGCTA-GGTC
1 CCTACTCGCACATAGCCGAGTCAGCATCGGCTTATGCACACTCCCACTCGCACAAAGC-AGGGTC
11884222 AGCATCGGCCTATGTGCACT
65 AGCATCGGCCTATGTGCACT
* * * *
11884242 CCTACTTGCACATAGCCGAGTCAACATCGGCTTATGTACACTCCCACTCGCACATAGCAGGGTCA
1 CCTACTCGCACATAGCCGAGTCAGCATCGGCTTATGCACACTCCCACTCGCACAAAGCAGGGTCA
*
11884307 GCGTCGGCCTATGTGCACT
66 GCATCGGCCTATGTGCACT
* * * *
11884326 CCTACTCGCACATAGCCGAGTCAGCATCGGCTTATGCGCACTCCCTACTTGCACATAGCTGGGTC
1 CCTACTCGCACATAGCCGAGTCAGCATCGGCTTATGCACACTCCC-ACTCGCACAAAGCAGGGTC
11884391 A
65 A
11884392 ATATCATCAC
Statistics
Matches: 135, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
83 1 0.01
84 116 0.86
85 18 0.13
ACGTcount: A:0.23, C:0.34, G:0.21, T:0.22
Consensus pattern (84 bp):
CCTACTCGCACATAGCCGAGTCAGCATCGGCTTATGCACACTCCCACTCGCACAAAGCAGGGTCA
GCATCGGCCTATGTGCACT
Found at i:11886654 original size:28 final size:28
Alignment explanation
Indices: 11886589--11886758 Score: 142
Period size: 29 Copynumber: 5.8 Consensus size: 28
11886579 CTTTGACATG
*
11886589 TTTGTCTTAATTTAGACAAAAAAACATA
1 TTTGTCTTAATTTAGACAAAAAAATATA
** *
11886617 TGCGATCTTAATTTAGACAAAAAAATATG
1 TTTG-TCTTAATTTAGACAAAAAAATATA
* *
11886646 TTTGCCTTAATTTAAGACAAGAAAAATATTT
1 TTTGTCTTAATTT-AGACAA-AAAAATA-TA
* * * *
11886677 TTTTTCTTAATTTAGTCAAGAAAACATA
1 TTTGTCTTAATTTAGACAAAAAAATATA
* *
11886705 TTTGTCTCAATTTAGACAAGATAAAATATTTT
1 TTTGTCTTAATTTAGACAA-A-AAAATA--TA
*
11886737 TTTGTCTTAATTACAGACAAAA
1 TTTGTCTTAATT-TAGACAAAA
11886759 GTTGTCTTAA
Statistics
Matches: 111, Mismatches: 22, Indels: 15
0.75 0.15 0.10
Matches are distributed among these distances:
28 27 0.24
29 35 0.32
30 17 0.15
31 13 0.12
32 13 0.12
33 6 0.05
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (28 bp):
TTTGTCTTAATTTAGACAAAAAAATATA
Found at i:11886691 original size:59 final size:60
Alignment explanation
Indices: 11886622--11886758 Score: 179
Period size: 59 Copynumber: 2.3 Consensus size: 60
11886612 ACATATGCGA
* * *
11886622 TCTTAATTTAGACAAAAAAATATGTTTGCCTTAATTTAAGACAAGA-AAAATATTTTTTT-
1 TCTTAATTTAGACAAAAAAACATATTTGCCTCAATTT-AGACAAGATAAAATATTTTTTTG
* * *
11886681 TCTTAATTTAGTCAAGAAAACATATTTGTCTCAATTTAGACAAGATAAAATATTTTTTTG
1 TCTTAATTTAGACAAAAAAACATATTTGCCTCAATTTAGACAAGATAAAATATTTTTTTG
*
11886741 TCTTAATTACAGACAAAA
1 TCTTAATT-TAGACAAAA
11886759 GTTGTCTTAA
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
58 8 0.12
59 44 0.67
60 8 0.12
61 6 0.09
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.39
Consensus pattern (60 bp):
TCTTAATTTAGACAAAAAAACATATTTGCCTCAATTTAGACAAGATAAAATATTTTTTTG
Found at i:11886922 original size:17 final size:17
Alignment explanation
Indices: 11886900--11886932 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
11886890 ATAATAATAA
11886900 AATAA-GAGTTATTATTC
1 AATAAGGAGTT-TTATTC
11886917 AATAAGGAGTTTTATT
1 AATAAGGAGTTTTATT
11886933 TTATCAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (17 bp):
AATAAGGAGTTTTATTC
Found at i:11887903 original size:92 final size:93
Alignment explanation
Indices: 11887756--11887969 Score: 326
Period size: 92 Copynumber: 2.3 Consensus size: 93
11887746 TTAGCAGCCT
* * * *
11887756 AAGCTGCTCATTTCACCCTCAAAA-TCGGTAGCCAAAACCTCAAAAATCAGCAGCTAAAGTTGCT
1 AAGCTGCTCATCTCACCCTCAAAACTCGGCAGCCAAAACCTCAAAAATCAGCAGCTAAAGCTACT
11887820 CCTTTCAGCCTTCAAAAATCAACAGCTA
66 CCTTTCAGCCTTCAAAAATCAACAGCTA
* * *
11887848 AAGCTGCTCATCTCACCCTCAAAACT-TGCAGCCTAAACCTCAAAAATCAGTAGCTAAAGCTACT
1 AAGCTGCTCATCTCACCCTCAAAACTCGGCAGCCAAAACCTCAAAAATCAGCAGCTAAAGCTACT
* *
11887912 CCTTTCAGCCTTCAACAATCAATAGCTA
66 CCTTTCAGCCTTCAAAAATCAACAGCTA
11887940 AAGCTGCTCATCTCACCCTCAAAACT-GGCA
1 AAGCTGCTCATCTCACCCTCAAAACTCGGCA
11887970 AAAAAATACC
Statistics
Matches: 111, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
92 110 0.99
93 1 0.01
ACGTcount: A:0.35, C:0.31, G:0.11, T:0.23
Consensus pattern (93 bp):
AAGCTGCTCATCTCACCCTCAAAACTCGGCAGCCAAAACCTCAAAAATCAGCAGCTAAAGCTACT
CCTTTCAGCCTTCAAAAATCAACAGCTA
Found at i:11888073 original size:50 final size:50
Alignment explanation
Indices: 11888010--11888121 Score: 118
Period size: 50 Copynumber: 2.2 Consensus size: 50
11888000 CTCCCTTCCT
* * * *
11888010 TTTCTTTCTTTTCTCTTCCTCACCATTTAACT-TTTCTTTTCTTTTTCTATCC
1 TTTC-TTC-TTTCTCTTCCTCACC-CTCAACTATTTCTCTCCTTTTTCTATCC
* * * *
11888062 TTTCTTCTTTCTCTTTCTCTCCCTCGACTATTTCTCTCCTTTTTCTTTCC
1 TTTCTTCTTTCTCTTCCTCACCCTCAACTATTTCTCTCCTTTTTCTATCC
11888112 TTTCTTCTTT
1 TTTCTTCTTT
11888122 TGCTTTCCTT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
49 4 0.08
50 40 0.78
51 3 0.06
52 4 0.08
ACGTcount: A:0.06, C:0.31, G:0.01, T:0.62
Consensus pattern (50 bp):
TTTCTTCTTTCTCTTCCTCACCCTCAACTATTTCTCTCCTTTTTCTATCC
Found at i:11893891 original size:42 final size:43
Alignment explanation
Indices: 11893810--11893893 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 43
11893800 TCATCATTAT
* *
11893810 CATCGGTTTATGCGTACTCCCTACTCGCACATAGCCGGGTCAG
1 CATCGGCTTATGCGCACTCCCTACTCGCACATAGCCGGGTCAG
* *
11893853 CATCGGCTTATGCGCACT-CCTACTCGCACGTAGTCGGGTCA
1 CATCGGCTTATGCGCACTCCCTACTCGCACATAGCCGGGTCA
11893894 ATATCATCAC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 21 0.57
43 16 0.43
ACGTcount: A:0.18, C:0.33, G:0.24, T:0.25
Consensus pattern (43 bp):
CATCGGCTTATGCGCACTCCCTACTCGCACATAGCCGGGTCAG
Found at i:11895072 original size:19 final size:17
Alignment explanation
Indices: 11895044--11895079 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
11895034 TTCTTTATTA
11895044 TTTATTTATTTTTATTTT
1 TTTATTTATTTTT-TTTT
11895062 TTTACTTTATTTTTTTTT
1 TTTA-TTTATTTTTTTTT
11895080 CACTCATAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTATTTATTTTTTTTT
Found at i:11895312 original size:92 final size:92
Alignment explanation
Indices: 11895176--11895465 Score: 373
Period size: 92 Copynumber: 3.2 Consensus size: 92
11895166 ACCTAAGTTG
* * * * *
11895176 CTCATTTCATCCTCAAAATTGACAACCAAAACCTCAAAAATCAGTAGCTAAAGTTACTCTTTTCA
1 CTCATCTCACCCTCAAAATTGACAGCCAAAACCTCAAAAATCAGTAGCTAAAGCTACTCCTTTCA
*
11895241 GCCTTCAAAAATCAATAGCTAAAGCTA
66 GCCTTCAAAAATCAACAGCTAAAGCTA
* *
11895268 CTCATCTCACCCTCAAAATCGACAGCCAAAACCTCAAAAATCAGTAACTAAAGCTACTCCTTTCA
1 CTCATCTCACCCTCAAAATTGACAGCCAAAACCTCAAAAATCAGTAGCTAAAGCTACTCCTTTCA
* * * *
11895333 GCCTTCAAAAATTAGCAGCTCAAGTTA
66 GCCTTCAAAAATCAACAGCTAAAGCTA
** * *
11895360 CTCATCTCACCCTCAAAATTGGTAGCCAAAACCTCAAAAATTAGCAGCTAAAGCTACTCCTTTCA
1 CTCATCTCACCCTCAAAATTGACAGCCAAAACCTCAAAAATCAGTAGCTAAAGCTACTCCTTTCA
* * * * * * *
11895425 GCCTTTAAAATTTAGCAACTAAAGTTG
66 GCCTTCAAAAATCAACAGCTAAAGCTA
11895452 CTCATCTCACCCTC
1 CTCATCTCACCCTC
11895466 CAAACTAGCA
Statistics
Matches: 175, Mismatches: 23, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
92 175 1.00
ACGTcount: A:0.37, C:0.29, G:0.09, T:0.26
Consensus pattern (92 bp):
CTCATCTCACCCTCAAAATTGACAGCCAAAACCTCAAAAATCAGTAGCTAAAGCTACTCCTTTCA
GCCTTCAAAAATCAACAGCTAAAGCTA
Found at i:11895575 original size:18 final size:18
Alignment explanation
Indices: 11895552--11895638 Score: 67
Period size: 18 Copynumber: 5.1 Consensus size: 18
11895542 TCGACTTTTC
11895552 TCTTCTTTTTCTTTCCTT
1 TCTTCTTTTTCTTTCCTT
* *
11895570 TCTTCTTTCTCTTT-CTC
1 TCTTCTTTTTCTTTCCTT
* * *
11895587 TC-CCTTGGTTGTTT-C--
1 TCTTCTT-TTTCTTTCCTT
*
11895602 TCTTGTTTTTCTTTCCTT
1 TCTTCTTTTTCTTTCCTT
*
11895620 TCTTCTTTTGCTTTCCTT
1 TCTTCTTTTTCTTTCCTT
11895638 T
1 T
11895639 TGCTCTTTCT
Statistics
Matches: 52, Mismatches: 12, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
15 7 0.13
16 6 0.12
17 9 0.17
18 30 0.58
ACGTcount: A:0.00, C:0.28, G:0.06, T:0.67
Consensus pattern (18 bp):
TCTTCTTTTTCTTTCCTT
Found at i:11895575 original size:23 final size:23
Alignment explanation
Indices: 11895549--11895625 Score: 66
Period size: 23 Copynumber: 3.2 Consensus size: 23
11895539 TGTTCGACTT
11895549 TTCTCTTCTTTTTCTTTCCTTTC
1 TTCTCTTCTTTTTCTTTCCTTTC
* * *
11895572 TTCT-TTCTCTTTCTCTCCCTTGGTTGT
1 TTCTCTTCTTTTTCT-TTCC-T--TT-C
*
11895599 TTCTCTTGTTTTTCTTTCCTTTC
1 TTCTCTTCTTTTTCTTTCCTTTC
11895622 TTCT
1 TTCT
11895626 TTTGCTTTCC
Statistics
Matches: 41, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
22 9 0.22
23 11 0.27
24 3 0.07
26 3 0.07
27 7 0.17
28 8 0.20
ACGTcount: A:0.00, C:0.29, G:0.05, T:0.66
Consensus pattern (23 bp):
TTCTCTTCTTTTTCTTTCCTTTC
Found at i:11901781 original size:72 final size:74
Alignment explanation
Indices: 11901702--11901871 Score: 247
Period size: 73 Copynumber: 2.3 Consensus size: 74
11901692 AACCGAGATG
** *
11901702 TGAGTTAGTCGACTAAATGCTCTCTACCAAAATCTAT-ACTTCAAGACAGAACCAACTTAGTCGA
1 TGAGTTAGTCGACTAAATGCTCTCTACCAAAATCTATGACCACAAGACAGAACCAACTTAGTAGA
11901766 CCAAGAA-A
66 CCAAGAAGA
* * *
11901774 TGAGTTAGTCGACTAAATGCTCTCTGCCAAAATCTGTGACCAGAAGACAGAACCAACTTAGTAGA
1 TGAGTTAGTCGACTAAATGCTCTCTACCAAAATCTATGACCACAAGACAGAACCAACTTAGTAGA
11901839 CCAAGAAGA
66 CCAAGAAGA
* *
11901848 -AAGTTAGTCGACTAAAAGCTCTCT
1 TGAGTTAGTCGACTAAATGCTCTCT
11901872 GTTTGCAATT
Statistics
Matches: 88, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
72 35 0.40
73 52 0.59
74 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (74 bp):
TGAGTTAGTCGACTAAATGCTCTCTACCAAAATCTATGACCACAAGACAGAACCAACTTAGTAGA
CCAAGAAGA
Found at i:11904846 original size:37 final size:37
Alignment explanation
Indices: 11904805--11904919 Score: 178
Period size: 37 Copynumber: 3.1 Consensus size: 37
11904795 CATATGCATT
* *
11904805 CATCATCATGTGCGTACTCCCTACTCGCACACTTCAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
11904842 CATCATCATGTGTGCACTCCCTACTCGCACAC-TCTAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTC-AA
* *
11904879 CATCATCATGTGTGCACTCCCTACTCGAACACTTTAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
11904916 CATC
1 CATC
11904920 CTCACACAAC
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
36 2 0.03
37 69 0.96
38 1 0.01
ACGTcount: A:0.25, C:0.37, G:0.10, T:0.28
Consensus pattern (37 bp):
CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
Found at i:11914735 original size:16 final size:16
Alignment explanation
Indices: 11914714--11914747 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
11914704 AGCCAAGGAG
11914714 AAGAAAAAAAAAAGAA
1 AAGAAAAAAAAAAGAA
* *
11914730 AAGAAAAGAAATAGAA
1 AAGAAAAAAAAAAGAA
11914746 AA
1 AA
11914748 TAAATGGGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (16 bp):
AAGAAAAAAAAAAGAA
Found at i:11914767 original size:25 final size:25
Alignment explanation
Indices: 11914739--11914801 Score: 92
Period size: 25 Copynumber: 2.5 Consensus size: 25
11914729 AAAGAAAAGA
11914739 AATAGAAAATAAATGGGCATGACCC
1 AATAGAAAATAAATGGGCATGACCC
* *
11914764 AATAGAAAATAAGTGGGCATGGCCC
1 AATAGAAAATAAATGGGCATGACCC
11914789 AATA-AGAAATAAA
1 AATAGA-AAATAAA
11914802 AATAAATGGG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 1 0.03
25 33 0.97
ACGTcount: A:0.51, C:0.13, G:0.21, T:0.16
Consensus pattern (25 bp):
AATAGAAAATAAATGGGCATGACCC
Found at i:11921075 original size:21 final size:20
Alignment explanation
Indices: 11921050--11921091 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
11921040 AATTAAATAA
11921050 TTTAAATGAATCATATTCAAT
1 TTTAAATGAA-CATATTCAAT
* *
11921071 TTTAAATTAACTTATTCAAT
1 TTTAAATGAACATATTCAAT
11921091 T
1 T
11921092 CCGTAGACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (20 bp):
TTTAAATGAACATATTCAAT
Found at i:11922209 original size:14 final size:15
Alignment explanation
Indices: 11922177--11922210 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
11922167 CCTCCAAATC
*
11922177 TAAAAACATGAAGTT
1 TAAAAACATGAAGTA
11922192 TAAAAACATG-AGTA
1 TAAAAACATGAAGTA
11922206 TAAAA
1 TAAAA
11922211 CTCAGCGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.59, C:0.06, G:0.12, T:0.24
Consensus pattern (15 bp):
TAAAAACATGAAGTA
Found at i:11922908 original size:37 final size:37
Alignment explanation
Indices: 11922867--11922981 Score: 196
Period size: 37 Copynumber: 3.1 Consensus size: 37
11922857 CATATGCATT
* *
11922867 CATCATCATGTGCGCACTCCCTACTCACACACTTCAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
11922904 CATCATCATGTGTGCACTCCCTACTCGCACAC-TCTAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTC-AA
11922941 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
11922978 CATC
1 CATC
11922982 CTCACACAAC
Statistics
Matches: 74, Mismatches: 2, Indels: 4
0.93 0.03 0.05
Matches are distributed among these distances:
36 2 0.03
37 70 0.95
38 2 0.03
ACGTcount: A:0.25, C:0.39, G:0.10, T:0.26
Consensus pattern (37 bp):
CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
Found at i:11931617 original size:72 final size:73
Alignment explanation
Indices: 11931507--11931667 Score: 243
Period size: 72 Copynumber: 2.2 Consensus size: 73
11931497 AATAGAACTG
** * **
11931507 ACTTAGTCGACCAAGATGTGAGTTAGTCGACTAAATGCTCTCTGCCAAAATCT-AGACTTCAAGA
1 ACTTAGTCGACCAAGAAATGAGTTAGTAGACTAAATGCTCTCTGCCAAAATCTGAGACCACAAGA
11931571 CAGAACCA
66 CAGAACCA
* * *
11931579 ACTTAGTCGACCAAGAAATGAGTTAGTAGACTAAATGCTCTTTGCCAAAATCTGTGACCAGAAGA
1 ACTTAGTCGACCAAGAAATGAGTTAGTAGACTAAATGCTCTCTGCCAAAATCTGAGACCACAAGA
11931644 CAGAACCA
66 CAGAACCA
11931652 ACTTAGTCGACCAAGA
1 ACTTAGTCGACCAAGA
11931668 TGAAAGTTAG
Statistics
Matches: 80, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
72 49 0.61
73 31 0.39
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (73 bp):
ACTTAGTCGACCAAGAAATGAGTTAGTAGACTAAATGCTCTCTGCCAAAATCTGAGACCACAAGA
CAGAACCA
Found at i:11931676 original size:73 final size:72
Alignment explanation
Indices: 11931507--11931695 Score: 233
Period size: 73 Copynumber: 2.6 Consensus size: 72
11931497 AATAGAACTG
** * **
11931507 ACTTAGTCGACCAAGATGTGAGTTAGTCGACTAAATGCTCTCTGCCAAAATCTAGACTTCAAGAC
1 ACTTAGTCGACCAAGATGAAAGTTAGTAGACTAAATGCTCTCTGCCAAAATCTAGACCACAAGAC
11931572 AGAACCA
66 AGAACCA
* * *
11931579 ACTTAGTCGACCAAGA--AATGAGTTAGTAGACTAAATGCTCTTTGCCAAAATCTGTGACCAGAA
1 ACTTAGTCGACCAAGATGAA--AGTTAGTAGACTAAATGCTCTCTGCCAAAATCT-AGACCACAA
11931642 GACAGAACCA
63 GACAGAACCA
11931652 ACTTAGTCGACCAAGATGAAAGTTAGTCA-ACTAAGA-GCTCTCTG
1 ACTTAGTCGACCAAGATGAAAGTTAGT-AGACTAA-ATGCTCTCTG
11931696 TCTGCAATTT
Statistics
Matches: 101, Mismatches: 9, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
72 47 0.47
73 50 0.50
74 2 0.02
75 2 0.02
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (72 bp):
ACTTAGTCGACCAAGATGAAAGTTAGTAGACTAAATGCTCTCTGCCAAAATCTAGACCACAAGAC
AGAACCA
Found at i:11936998 original size:54 final size:54
Alignment explanation
Indices: 11936911--11937070 Score: 248
Period size: 54 Copynumber: 3.0 Consensus size: 54
11936901 AATAATCATT
* *
11936911 CCATCTCACCCAGCTCATGTGCATCCCACCACATTGTGCACATAACCGGACATC
1 CCATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATC
* * * * *
11936965 CCATATCACCCAACTCATGTGCATCCCACCACATCGTGAACAGAGCAGGACATC
1 CCATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATC
*
11937019 CCATCTCACCCAGCTCATGTTCATCCCACCACATCGTGCACATAGCCGGACA
1 CCATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACA
11937071 GTATCACCAT
Statistics
Matches: 93, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 93 1.00
ACGTcount: A:0.28, C:0.40, G:0.14, T:0.19
Consensus pattern (54 bp):
CCATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATC
Found at i:11944965 original size:24 final size:24
Alignment explanation
Indices: 11944938--11945012 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 24
11944928 TCCTTTATAC
11944938 TACATCTATCTAGAGTTAAAGTAG
1 TACATCTATCTAGAGTTAAAGTAG
* * * ** * *
11944962 TACAACT-TCAACA-AAAAANATAC
1 TACATCTATCTAGAGTTAAA-GTAG
11944985 TACATCTATCTAGAGTTAAAGTAG
1 TACATCTATCTAGAGTTAAAGTAG
11945009 TACA
1 TACA
11945013 ACTTCAACAA
Statistics
Matches: 34, Mismatches: 14, Indels: 6
0.63 0.26 0.11
Matches are distributed among these distances:
22 3 0.09
23 12 0.35
24 16 0.47
25 3 0.09
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.28
Consensus pattern (24 bp):
TACATCTATCTAGAGTTAAAGTAG
Found at i:11944988 original size:47 final size:46
Alignment explanation
Indices: 11944934--11945024 Score: 173
Period size: 47 Copynumber: 2.0 Consensus size: 46
11944924 TATTTCCTTT
11944934 ATACTACATCTATCTAGAGTTAAAGTAGTACAACTTCAACAAAAAA
1 ATACTACATCTATCTAGAGTTAAAGTAGTACAACTTCAACAAAAAA
11944980 NATACTACATCTATCTAGAGTTAAAGTAGTACAACTTCAACAAAA
1 -ATACTACATCTATCTAGAGTTAAAGTAGTACAACTTCAACAAAA
11945025 CACTATGTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.46, C:0.18, G:0.09, T:0.26
Consensus pattern (46 bp):
ATACTACATCTATCTAGAGTTAAAGTAGTACAACTTCAACAAAAAA
Found at i:11954145 original size:13 final size:13
Alignment explanation
Indices: 11954127--11954151 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11954117 AGAGAAATTG
11954127 TGATTTTATAAAA
1 TGATTTTATAAAA
11954140 TGATTTTATAAA
1 TGATTTTATAAA
11954152 TTTTCTAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:11958389 original size:32 final size:32
Alignment explanation
Indices: 11958314--11958389 Score: 134
Period size: 32 Copynumber: 2.4 Consensus size: 32
11958304 ACATACTTTC
**
11958314 AGCACTTCACTCCTATCCTTGTAACAAATTTA
1 AGCACTTCACTTATATCCTTGTAACAAATTTA
11958346 AGCACTTCACTTATATCCTTGTAACAAATTTA
1 AGCACTTCACTTATATCCTTGTAACAAATTTA
11958378 AGCACTTCACTT
1 AGCACTTCACTT
11958390 TGTACCGCTC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.32, C:0.26, G:0.07, T:0.36
Consensus pattern (32 bp):
AGCACTTCACTTATATCCTTGTAACAAATTTA
Found at i:11960256 original size:25 final size:25
Alignment explanation
Indices: 11960199--11960258 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
11960189 GTGGTCATAA
* *
11960199 CCATGTGTATCAACTCGTGGCCTAC
1 CCATGTATAACAACTCGTGGCCTAC
* * **
11960224 CCACGTATAACAACTTGTGGCCTTG
1 CCATGTATAACAACTCGTGGCCTAC
11960249 CCATGTATAA
1 CCATGTATAA
11960259 TCATAAACCG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.28
Consensus pattern (25 bp):
CCATGTATAACAACTCGTGGCCTAC
Found at i:11962023 original size:20 final size:20
Alignment explanation
Indices: 11961981--11962024 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
11961971 AAACCTGAGC
*
11961981 CTTCCCCACTTTCTTTCTTT
1 CTTCCCCACTTTCTTTCTCT
*
11962001 CTTCCCCTCTTTTCTTT-TCT
1 CTTCCCCAC-TTTCTTTCTCT
11962021 CTTC
1 CTTC
11962025 GGGTGAAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.02, C:0.41, G:0.00, T:0.57
Consensus pattern (20 bp):
CTTCCCCACTTTCTTTCTCT
Found at i:11962819 original size:31 final size:31
Alignment explanation
Indices: 11962778--11962837 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
11962768 TGTTTCCTTA
* *
11962778 TTTACCATTTGACCCTCCAAACTTTTCATCT
1 TTTACAATTTGACCCTCCAAACATTTCATCT
*
11962809 TTTACAATTTGATCCTCCAAACATTTCAT
1 TTTACAATTTGACCCTCCAAACATTTCAT
11962838 AAATTACAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.27, C:0.28, G:0.03, T:0.42
Consensus pattern (31 bp):
TTTACAATTTGACCCTCCAAACATTTCATCT
Found at i:11962845 original size:31 final size:31
Alignment explanation
Indices: 11962779--11962855 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
11962769 GTTTCCTTAT
* * * ***
11962779 TTACCATTTGACCCTCCAAACTTTTCATCTT
1 TTACAATTTGATCCTCCAAACATTTCATAAA
11962810 TTACAATTTGATCCTCCAAACATTTCATAAA
1 TTACAATTTGATCCTCCAAACATTTCATAAA
*
11962841 TTACAATTTCATCCT
1 TTACAATTTGATCCT
11962856 TCAACTTGTT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.30, C:0.27, G:0.03, T:0.40
Consensus pattern (31 bp):
TTACAATTTGATCCTCCAAACATTTCATAAA
Found at i:11963541 original size:27 final size:27
Alignment explanation
Indices: 11963510--11963716 Score: 177
Period size: 27 Copynumber: 7.5 Consensus size: 27
11963500 TGTTTCACAC
* *
11963510 CATGTTGAAAAGAAAGCTGTTACACGT
1 CATGTTGAAAAAAAAGTTGTTACACGT
* * *
11963537 TATGTTAGAAAAAAAAAAGTTATTACACGC
1 CATGTT-G--AAAAAAAAGTTGTTACACGT
*
11963567 CATGTT-AAAAAACAAGTTGTTACATG-
1 CATGTTGAAAAAA-AAGTTGTTACACGT
* *
11963593 CTATGTTGAAAAAATATTGTTGTTGCACGT
1 C-ATGTTGAAAAAA-A-AGTTGTTACACGT
** * *
11963623 TGTATTG-AAAAAAAGTTGTTACACGA
1 CATGTTGAAAAAAAAGTTGTTACACGT
*
11963649 CATGTTGAAAAAAAAGTTGTTACAAGT
1 CATGTTGAAAAAAAAGTTGTTACACGT
* *
11963676 CATGTTAAAAAAAAAAGTTGTTACATGT
1 CATGTT-GAAAAAAAAGTTGTTACACGT
*
11963704 CATTTTGAAAAAA
1 CATGTTGAAAAAA
11963717 TGTTACAATC
Statistics
Matches: 143, Mismatches: 27, Indels: 20
0.75 0.14 0.11
Matches are distributed among these distances:
26 21 0.15
27 51 0.36
28 37 0.26
29 13 0.09
30 21 0.15
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.31
Consensus pattern (27 bp):
CATGTTGAAAAAAAAGTTGTTACACGT
Found at i:11963689 original size:55 final size:54
Alignment explanation
Indices: 11963547--11963716 Score: 168
Period size: 55 Copynumber: 3.1 Consensus size: 54
11963537 TATGTTAGAA
* * *
11963547 AAAAAAAAGTTATTACACGCCATGTT-AAAAAACAAGTTGTTACATGCTATGTTG
1 AAAAAAAAGTTGTTACACGTCATGTTAAAAAAAAAAGTTGTTACATGC-ATGTTG
* * ** *
11963601 AAAAAATATTGTTGTTGCACGT--TG-TATTGAAAAAAAGTTGTTACACGACATGTTG
1 AAAAAA-A-AGTTGTTACACGTCATGTTA-AAAAAAAAAGTTGTTACATG-CATGTTG
* *
11963656 AAAAAAAAGTTGTTACAAGTCATGTTAAAAAAAAAAGTTGTTACATGTCATTTTG
1 AAAAAAAAGTTGTTACACGTCATGTTAAAAAAAAAAGTTGTTACATG-CATGTTG
11963711 AAAAAA
1 AAAAAA
11963717 TGTTACAATC
Statistics
Matches: 92, Mismatches: 16, Indels: 15
0.75 0.13 0.12
Matches are distributed among these distances:
53 11 0.12
54 9 0.10
55 60 0.65
56 12 0.13
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.31
Consensus pattern (54 bp):
AAAAAAAAGTTGTTACACGTCATGTTAAAAAAAAAAGTTGTTACATGCATGTTG
Found at i:11963716 original size:82 final size:83
Alignment explanation
Indices: 11963547--11963716 Score: 195
Period size: 82 Copynumber: 2.1 Consensus size: 83
11963537 TATGTTAGAA
* * * **
11963547 AAAAAAAAGTTATTACACGCCATGTTAAAAAACAAGTTGTTACATGCTATGTTGAAAAAATATTG
1 AAAAAAAAGTTATTACACGACATGTTAAAAAACAAGTTGTTACAAGCTATGTTGAAAAAAAAAAG
* **
11963612 TTGTTGCACGTTGTATTG
66 TTGTTACACGTCATATTG
*
11963630 -AAAAAAAGTTGTTACACGACATGTTGAAAAAA-AAGTTGTTACAAG-TCATGTT-AAAAAAAAA
1 AAAAAAAAGTTATTACACGACATGTT-AAAAAACAAGTTGTTACAAGCT-ATGTTGAAAAAAAAA
* *
11963691 AGTTGTTACATGTCATTTTG
64 AGTTGTTACACGTCATATTG
11963711 AAAAAA
1 AAAAAA
11963717 TGTTACAATC
Statistics
Matches: 73, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
81 22 0.30
82 45 0.62
83 6 0.08
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.31
Consensus pattern (83 bp):
AAAAAAAAGTTATTACACGACATGTTAAAAAACAAGTTGTTACAAGCTATGTTGAAAAAAAAAAG
TTGTTACACGTCATATTG
Found at i:11964168 original size:16 final size:17
Alignment explanation
Indices: 11964136--11964168 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
11964126 TCTTCTTCTT
*
11964136 TCTTTTTTTCCACTTTC
1 TCTTTTTTTCCAATTTC
11964153 TCTTTTTTT-CAATTTC
1 TCTTTTTTTCCAATTTC
11964169 GCACCAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.09, C:0.24, G:0.00, T:0.67
Consensus pattern (17 bp):
TCTTTTTTTCCAATTTC
Found at i:11967843 original size:39 final size:41
Alignment explanation
Indices: 11967788--11967866 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 41
11967778 TTTGGTTTTT
*
11967788 TTCATCTTAGTTGGGTTTTCAACCAT-GCCAAGATTGGTGA
1 TTCACCTTAGTTGGGTTTTCAACCATCGCCAAGATTGGTGA
* *
11967828 TTCACCTTAG-TGGGTTTTCAACCTTCGCCATGATTGGTG
1 TTCACCTTAGTTGGGTTTTCAACCATCGCCAAGATTGGTG
11967867 TCTTTCACAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
39 14 0.40
40 21 0.60
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (41 bp):
TTCACCTTAGTTGGGTTTTCAACCATCGCCAAGATTGGTGA
Found at i:11989373 original size:21 final size:21
Alignment explanation
Indices: 11989347--11989386 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
11989337 TGACTTGAAG
* *
11989347 TAATGACATTATAACATGAGC
1 TAATGACACTACAACATGAGC
11989368 TAATGACACTACAACATGA
1 TAATGACACTACAACATGA
11989387 ATTGGAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.25
Consensus pattern (21 bp):
TAATGACACTACAACATGAGC
Found at i:11990446 original size:36 final size:36
Alignment explanation
Indices: 11990406--11990506 Score: 148
Period size: 36 Copynumber: 2.8 Consensus size: 36
11990396 ATGGTATTGC
* *
11990406 CTGTGCGCGGTGTGGGGGTGTACACGATGGCATTAG
1 CTGTGCGCGATGTGGGGGTGCACACGATGGCATTAG
* *
11990442 CTGTGCGTGATGTGGGGGTGCACACGATGGTATTAG
1 CTGTGCGCGATGTGGGGGTGCACACGATGGCATTAG
* *
11990478 CTGTACGCGATGTGGGGGTGCAAACGATG
1 CTGTGCGCGATGTGGGGGTGCACACGATG
11990507 ACTTCGGCTA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 58 1.00
ACGTcount: A:0.17, C:0.16, G:0.43, T:0.25
Consensus pattern (36 bp):
CTGTGCGCGATGTGGGGGTGCACACGATGGCATTAG
Found at i:11990576 original size:2 final size:2
Alignment explanation
Indices: 11990569--11990606 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
11990559 GGCATACATG
11990569 TA TA TA TA 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 TA TA TA TA
11990607 GTAGTANNNN
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11990777 original size:2 final size:2
Alignment explanation
Indices: 11990770--11990808 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
11990760 NNNNNNNNNN
11990770 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
11990809 GAGAGGTTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:11995287 original size:28 final size:28
Alignment explanation
Indices: 11995216--11995383 Score: 165
Period size: 29 Copynumber: 5.8 Consensus size: 28
11995206 CTTTAGCATA
* *
11995216 TTTGTCTTAATTTAGACAAGAAAACATT
1 TTTGTCTTAATTTAAACAAGAAAATATT
* *
11995244 TTTGGTCTTAATTTAAACAAGAAAGTATG
1 TTT-GTCTTAATTTAAACAAGAAAATATT
11995273 TTTGTCTTAATTTAAGACAAGAAAAATATTT
1 TTTGTCTTAATTTAA-ACAAG-AAAATA-TT
* * * *
11995304 TTTGTCTTAATCTAGACAAGAAAACATA
1 TTTGTCTTAATTTAAACAAGAAAATATT
* * *
11995332 TTTATCTCAATTTAAAGAAGATAAAATATT
1 TTTGTCTTAATTTAAACAAG--AAAATATT
*
11995362 TTTGTCTTAATTATAGACAAGA
1 TTTGTCTTAATT-TAAACAAGA
11995384 GTTCTCTTAA
Statistics
Matches: 112, Mismatches: 21, Indels: 13
0.77 0.14 0.09
Matches are distributed among these distances:
28 31 0.28
29 35 0.31
30 26 0.23
31 20 0.18
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (28 bp):
TTTGTCTTAATTTAAACAAGAAAATATT
Found at i:11995314 original size:59 final size:59
Alignment explanation
Indices: 11995212--11995383 Score: 208
Period size: 59 Copynumber: 2.9 Consensus size: 59
11995202 GCAGCTTTAG
* * * *
11995212 CATATTTGTCTTAATTT-AGACAAG-AAAACATTTTTGGTCTTAATTTAAACAAGAAAG
1 CATATTTGTCTTAATTTAAGACAAGAAAAATATTTTTTGTCTTAATTTAGACAAGAAAA
* * *
11995269 TATGTTTGTCTTAATTTAAGACAAGAAAAATATTTTTTGTCTTAATCTAGACAAGAAAA
1 CATATTTGTCTTAATTTAAGACAAGAAAAATATTTTTTGTCTTAATTTAGACAAGAAAA
* * *
11995328 CATATTTATCTCAATTTAA-AGAAGATAAAATA-TTTTTGTCTTAATTATAGACAAGA
1 CATATTTGTCTTAATTTAAGACAAGA-AAAATATTTTTTGTCTTAATT-TAGACAAGA
11995384 GTTCTCTTAA
Statistics
Matches: 98, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
57 15 0.15
58 25 0.26
59 58 0.59
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.38
Consensus pattern (59 bp):
CATATTTGTCTTAATTTAAGACAAGAAAAATATTTTTTGTCTTAATTTAGACAAGAAAA
Found at i:11995545 original size:17 final size:17
Alignment explanation
Indices: 11995525--11995557 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
11995515 ATAATAATAA
11995525 AATAA-GAGTTATTATTC
1 AATAAGGAGTT-TTATTC
11995542 AATAAGGAGTTTTATT
1 AATAAGGAGTTTTATT
11995558 TTATCAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (17 bp):
AATAAGGAGTTTTATTC
Found at i:11996754 original size:36 final size:36
Alignment explanation
Indices: 11996714--11996812 Score: 126
Period size: 36 Copynumber: 2.8 Consensus size: 36
11996704 AGCCGGAGTT
*
11996714 ATCGTGTGAACCCCCACATCGCGCACAGCTAATACC
1 ATCGTGTGAACCCCCACATCGCACACAGCTAATACC
* * * *
11996750 ATCGTGTGCACCCCCACATCACACACAGTTAATGCC
1 ATCGTGTGAACCCCCACATCGCACACAGCTAATACC
* * *
11996786 ATCGTGTGTACCCTCACATCGCTCACA
1 ATCGTGTGAACCCCCACATCGCACACA
11996813 AGCAATATCA
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.26, C:0.38, G:0.15, T:0.20
Consensus pattern (36 bp):
ATCGTGTGAACCCCCACATCGCACACAGCTAATACC
Found at i:12011733 original size:19 final size:19
Alignment explanation
Indices: 12011709--12011746 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
12011699 CTGCCAAACC
* *
12011709 CTCAAATTATACTCCAATA
1 CTCAAATCACACTCCAATA
12011728 CTCAAATCACACTCCAATA
1 CTCAAATCACACTCCAATA
12011747 AGTTAAATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (19 bp):
CTCAAATCACACTCCAATA
Found at i:12017570 original size:77 final size:77
Alignment explanation
Indices: 12017434--12017597 Score: 258
Period size: 77 Copynumber: 2.1 Consensus size: 77
12017424 AATGCCATAT
* *
12017434 ATTTTAATTTTGGGTGACTCATAAAAAATAGAAAATTGTTTCCTACTTTAGAAGTAATTCCTAAA
1 ATTTTAATTTTGGGTGACTCATAAAAAATAGAAAATTGTTTCCTACTTTAAAAGAAATTCCTAAA
12017499 ATTAA-AGATAGC
66 ATTAAGA-ATAGC
* * *
12017511 ATTTTAATTTTGGGTGATTCATAAAGAATAGGAAATTGTTTCCTACTTTAAAAGAAATTCCTAAA
1 ATTTTAATTTTGGGTGACTCATAAAAAATAGAAAATTGTTTCCTACTTTAAAAGAAATTCCTAAA
*
12017576 ATTAAGAATAGT
66 ATTAAGAATAGC
12017588 ATTTTAATTT
1 ATTTTAATTT
12017598 AAGAAATTCA
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
77 79 0.99
78 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.39
Consensus pattern (77 bp):
ATTTTAATTTTGGGTGACTCATAAAAAATAGAAAATTGTTTCCTACTTTAAAAGAAATTCCTAAA
ATTAAGAATAGC
Found at i:12028131 original size:5 final size:5
Alignment explanation
Indices: 12028121--12028163 Score: 54
Period size: 5 Copynumber: 8.8 Consensus size: 5
12028111 GTTAGATCTC
*
12028121 ATTTT ATTTT ATTTT TTTTT ATTTT ATTTT CA-TTT A-TTT ATTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT -ATTTT ATTTT ATTT
12028164 ATTGACTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 5 0.15
5 28 0.82
6 1 0.03
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (5 bp):
ATTTT
Found at i:12028721 original size:15 final size:16
Alignment explanation
Indices: 12028701--12028769 Score: 56
Period size: 15 Copynumber: 4.4 Consensus size: 16
12028691 CCCTCTCTCT
12028701 TTCTTTT-TCTTTTCC
1 TTCTTTTCTCTTTTCC
12028716 TTCTTTGTCTCTTTT-C
1 TTCTTT-TCTCTTTTCC
* *
12028732 TT-TTCTTTTCTTTTCTT
1 TTCTT-TTCTCTTTTC-C
*
12028749 TTCTTTTCTCTCTTCC
1 TTCTTTTCTCTTTTCC
12028765 -TCTTT
1 TTCTTT
12028770 CTCCCTCGTC
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
15 20 0.47
16 5 0.12
17 16 0.37
18 2 0.05
ACGTcount: A:0.00, C:0.26, G:0.01, T:0.72
Consensus pattern (16 bp):
TTCTTTTCTCTTTTCC
Found at i:12028733 original size:5 final size:5
Alignment explanation
Indices: 12028725--12028757 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
12028715 CTTCTTTGTC
12028725 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCT
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCT
12028758 CTCTTCCTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (5 bp):
TCTTT
Found at i:12029023 original size:14 final size:13
Alignment explanation
Indices: 12028968--12029020 Score: 54
Period size: 13 Copynumber: 4.1 Consensus size: 13
12028958 CATATCTGAC
12028968 TTTT-TTTCTTTT
1 TTTTATTTCTTTT
*
12028980 TTTTATTGCTTTT
1 TTTTATTTCTTTT
* *
12028993 TTTGATTTTTTTT
1 TTTTATTTCTTTT
*
12029006 TGTTTCTTTCTTTT
1 T-TTTATTTCTTTT
12029020 T
1 T
12029021 GTTGTAATTT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
12 4 0.12
13 18 0.56
14 10 0.31
ACGTcount: A:0.04, C:0.08, G:0.06, T:0.83
Consensus pattern (13 bp):
TTTTATTTCTTTT
Found at i:12029388 original size:12 final size:11
Alignment explanation
Indices: 12029371--12029428 Score: 68
Period size: 11 Copynumber: 5.3 Consensus size: 11
12029361 CGCTCAGTTC
12029371 TTTCTTATTCTT
1 TTTCTTATT-TT
12029383 TTTCTT-TTTT
1 TTTCTTATTTT
12029393 TTCTCTGTATTTT
1 TT-TCT-TATTTT
12029406 TTTCTTA--TT
1 TTTCTTATTTT
12029415 TTTCTTATTTT
1 TTTCTTATTTT
12029426 TTT
1 TTT
12029429 AGTTTTTTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
9 9 0.22
10 4 0.10
11 12 0.29
12 10 0.24
13 6 0.15
ACGTcount: A:0.07, C:0.12, G:0.02, T:0.79
Consensus pattern (11 bp):
TTTCTTATTTT
Found at i:12029423 original size:20 final size:19
Alignment explanation
Indices: 12029371--12029446 Score: 71
Period size: 20 Copynumber: 3.6 Consensus size: 19
12029361 CGCTCAGTTC
12029371 TTTCTTATTCTTTTTCTTTTTT
1 TTTCTTATT-TTTTTC--TTTT
12029393 TTCTCTGTATTTTTTTCTTATT
1 TT-TCT-TATTTTTTTCTT-TT
*
12029415 TTTCTTATTTTTTTAGTTTT
1 TTTCTTATTTTTTT-CTTTT
*
12029435 TTTATTATTTTT
1 TTTCTTATTTTT
12029447 CATTAATATC
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
20 22 0.46
21 7 0.15
22 6 0.12
23 9 0.19
24 4 0.08
ACGTcount: A:0.09, C:0.09, G:0.03, T:0.79
Consensus pattern (19 bp):
TTTCTTATTTTTTTCTTTT
Found at i:12029445 original size:10 final size:10
Alignment explanation
Indices: 12029403--12029474 Score: 51
Period size: 9 Copynumber: 7.4 Consensus size: 10
12029393 TTCTCTGTAT
*
12029403 TTTTTTCTTA
1 TTTTTTATTA
*
12029413 -TTTTTCTTA
1 TTTTTTATTA
*
12029422 TTTTTTTAGT-
1 -TTTTTTATTA
12029432 TTTTTTATTA
1 TTTTTTATTA
*
12029442 TTTTTCATTA
1 TTTTTTATTA
* * *
12029452 ATATCTATTA
1 TTTTTTATTA
12029462 TTTTTTATT-
1 TTTTTTATTA
12029471 TTTT
1 TTTT
12029475 GAAATAGGTG
Statistics
Matches: 48, Mismatches: 11, Indels: 7
0.73 0.17 0.11
Matches are distributed among these distances:
9 21 0.44
10 21 0.44
11 6 0.12
ACGTcount: A:0.17, C:0.06, G:0.01, T:0.76
Consensus pattern (10 bp):
TTTTTTATTA
Found at i:12029821 original size:59 final size:59
Alignment explanation
Indices: 12029693--12030256 Score: 680
Period size: 59 Copynumber: 9.5 Consensus size: 59
12029683 GATTTAAGTA
* * * ** * * *
12029693 CGACCCATATCAAAATAGGTTCGATTTAAAAAAATAAAAATTTCTAGACTTGGTCTAAGCT
1 CGACCTATCTCAAAACAGGTTCGATTT--AAAAATTGAAATTCCTAGACTTGATCTAGGCT
* * * *
12029754 CGATCTATCTCAAAACAGGTTCGACTTAAATATTGAAATTTCTAGACTTGATCTAGGCT
1 CGACCTATCTCAAAACAGGTTCGATTTAAAAATTGAAATTCCTAGACTTGATCTAGGCT
* * * * *
12029813 AGACCTATCTCACAACAAGTTCGACTTAAAAATTGAAATTTCTAGACTTGATCTAGGCT
1 CGACCTATCTCAAAACAGGTTCGATTTAAAAATTGAAATTCCTAGACTTGATCTAGGCT
* *
12029872 CGAGCTATCTCACAACAGGTTCGATTTAAAAATTGAAATTCCTAGACTTGATCTAGGCT
1 CGACCTATCTCAAAACAGGTTCGATTTAAAAATTGAAATTCCTAGACTTGATCTAGGCT
* * * * *
12029931 CGACCTATCTCAAAACAAGTTCAATTTTAAAAATTGAAATCCCCAAACTTGATCTAGGCT
1 CGACCTATCTCAAAACAGGTTCGA-TTTAAAAATTGAAATTCCTAGACTTGATCTAGGCT
* * * * * *
12029991 CGGCCTATCTCAAAATAGGTTTGA-TTAAAAATTGAAATTCCTAAACTTGATCCAAGCT
1 CGACCTATCTCAAAACAGGTTCGATTTAAAAATTGAAATTCCTAGACTTGATCTAGGCT
* *
12030049 CAACCTATCTCAAAACAGGTTCGATTTTAAAAATTGAAATTCCTAAACTTGATCTAGGCT
1 CGACCTATCTCAAAACAGGTTCGA-TTTAAAAATTGAAATTCCTAGACTTGATCTAGGCT
* * * * *
12030109 CGACCTATCTCAAAACAGGTTTGATTCAAAAAATGAAATTCCTAAACTTGATATAGGCT
1 CGACCTATCTCAAAACAGGTTCGATTTAAAAATTGAAATTCCTAGACTTGATCTAGGCT
* * **
12030168 TGACCTATCTCAAAACAGGTTCGATTAAGAAAATTGAAGCTCCTAGACTTGATCTAGGCT
1 CGACCTATCTCAAAACAGGTTCGATTTA-AAAATTGAAATTCCTAGACTTGATCTAGGCT
* * *
12030228 CGACTTATCTTAAAACAAGTTCGATTTAA
1 CGACCTATCTCAAAACAGGTTCGATTTAA
12030257 TTCACCGATG
Statistics
Matches: 439, Mismatches: 60, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
58 50 0.11
59 213 0.49
60 154 0.35
61 22 0.05
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (59 bp):
CGACCTATCTCAAAACAGGTTCGATTTAAAAATTGAAATTCCTAGACTTGATCTAGGCT
Found at i:12030175 original size:237 final size:237
Alignment explanation
Indices: 12029740--12030256 Score: 664
Period size: 237 Copynumber: 2.2 Consensus size: 237
12029730 AAATTTCTAG
* * * * * *
12029740 ACTTGGTCTAAGCTCGATCTATCTCAAAACAGGTTCGACTTAAATATTGAAATTTCTAGACTTGA
1 ACTTGATCTAGGCTCGACCTATCTCAAAACAGGTTCGACTTAAAAATTGAAATTCCTAAACTTGA
* * * * *
12029805 TCTAGGCTAGACCTATCTCACAACAAGTTCGACTTAAAAATTGAAATTTCTAGACTTGATCTAGG
66 TCCAAGCTAGACCTATCTCAAAACAAGTTCGACTTAAAAATTGAAATTCCTAAACTTGATCTAGG
* * * * * *
12029870 CTCGAGCTATCTCACAACAGGTTCGATTTAAAAATTGAAATTCCTAGACTTGATCTAGGCTCGAC
131 CTCGACCTATCTCAAAACAGGTTCGATTCAAAAAATGAAATTCCTAAACTTGATATAGGCTCGAC
* *
12029935 CTATCTCAAAACAAGTTCAATTTTA-AAAATTGAA-ATCCCCAA
196 CTATCTCAAAACAAGTTCAA-TTAAGAAAATTGAAGCT-CCCAA
* * *
12029977 ACTTGATCTAGGCTCGGCCTATCTCAAAATAGGTTTGA-TTAAAAATTGAAATTCCTAAACTTGA
1 ACTTGATCTAGGCTCGACCTATCTCAAAACAGGTTCGACTTAAAAATTGAAATTCCTAAACTTGA
* *
12030041 TCCAAGCTCA-ACCTATCTCAAAACAGGTTCGATTTTAAAAATTGAAATTCCTAAACTTGATCTA
66 TCCAAGCT-AGACCTATCTCAAAACAAGTTCGA-CTTAAAAATTGAAATTCCTAAACTTGATCTA
* *
12030105 GGCTCGACCTATCTCAAAACAGGTTTGATTCAAAAAATGAAATTCCTAAACTTGATATAGGCTTG
129 GGCTCGACCTATCTCAAAACAGGTTCGATTCAAAAAATGAAATTCCTAAACTTGATATAGGCTCG
* * * *
12030170 ACCTATCTCAAAACAGGTTCGATTAAGAAAATTGAAGCTCCTAG
194 ACCTATCTCAAAACAAGTTCAATTAAGAAAATTGAAGCTCCCAA
* * * *
12030214 ACTTGATCTAGGCTCGACTTATCTTAAAACAAGTTCGATTTAA
1 ACTTGATCTAGGCTCGACCTATCTCAAAACAGGTTCGACTTAA
12030257 TTCACCGATG
Statistics
Matches: 239, Mismatches: 36, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
236 52 0.22
237 182 0.76
238 5 0.02
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (237 bp):
ACTTGATCTAGGCTCGACCTATCTCAAAACAGGTTCGACTTAAAAATTGAAATTCCTAAACTTGA
TCCAAGCTAGACCTATCTCAAAACAAGTTCGACTTAAAAATTGAAATTCCTAAACTTGATCTAGG
CTCGACCTATCTCAAAACAGGTTCGATTCAAAAAATGAAATTCCTAAACTTGATATAGGCTCGAC
CTATCTCAAAACAAGTTCAATTAAGAAAATTGAAGCTCCCAA
Found at i:12039939 original size:28 final size:24
Alignment explanation
Indices: 12039913--12039960 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 24
12039903 CCCTCTTTCT
*
12039913 TTTTCTTTTCCTT-C-TTTCTCTC
1 TTTTCTTTTCTTTCCTTTTCTCTC
12039935 TTTTCTTTTCTTTCCTTTTCTCTC
1 TTTTCTTTTCTTTCCTTTTCTCTC
12039959 TT
1 TT
12039961 CCTCTTTCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 12 0.52
23 1 0.04
24 10 0.43
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (24 bp):
TTTTCTTTTCTTTCCTTTTCTCTC
Found at i:12039960 original size:14 final size:14
Alignment explanation
Indices: 12039910--12039970 Score: 58
Period size: 13 Copynumber: 4.6 Consensus size: 14
12039900 CCTCCCTCTT
* *
12039910 TCTTTTTCTTTTCC
1 TCTTTCTCTCTTCC
*
12039924 TTCTTTCTCTCTT-T
1 -TCTTTCTCTCTTCC
12039938 TCTTT-TCT-TTCC
1 TCTTTCTCTCTTCC
12039950 T-TTTCTCTCTTCC
1 TCTTTCTCTCTTCC
12039963 TCTTTCTC
1 TCTTTCTC
12039971 CCTTGCCAGC
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
11 5 0.13
12 7 0.18
13 10 0.26
14 6 0.16
15 10 0.26
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (14 bp):
TCTTTCTCTCTTCC
Found at i:12040607 original size:4 final size:4
Alignment explanation
Indices: 12040600--12040658 Score: 52
Period size: 4 Copynumber: 14.8 Consensus size: 4
12040590 TTTTTTTTTA
* *
12040600 ATTT ATTT -CTT ATTT TTATT ATTT ATTT ATTT ATTT ATTAT ATTT CA-TT
1 ATTT ATTT ATTT ATTT AT-TT ATTT ATTT ATTT ATTT ATT-T ATTT -ATTT
12040649 A-TT ATTT ATT
1 ATTT ATTT ATT
12040659 ATGTTTTATT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
3 6 0.13
4 32 0.70
5 8 0.17
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.71
Consensus pattern (4 bp):
ATTT
Found at i:12040610 original size:20 final size:20
Alignment explanation
Indices: 12040585--12040660 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
12040575 TCTTATTCTT
*
12040585 TTTCTT-TTTTTTTTAATTTA
1 TTTCTTATTTTTATT-ATTTA
12040605 TTTCTTATTTTTATTATTTA
1 TTTCTTATTTTTATTATTTA
* *
12040625 TTTATT-TATTTATTA--TA
1 TTTCTTATTTTTATTATTTA
12040642 TTTCATTATTATTTATTAT
1 TTTC-TTATT-TTTATTAT
12040661 GTTTTATTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
17 5 0.11
18 2 0.04
19 9 0.20
20 23 0.50
21 7 0.15
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTCTTATTTTTATTATTTA
Found at i:12040612 original size:7 final size:6
Alignment explanation
Indices: 12040583--12040671 Score: 56
Period size: 7 Copynumber: 13.8 Consensus size: 6
12040573 TTTCTTATTC
* *
12040583 TTTTTC TTTTT- TTTTTA -ATTTA TTTCTTA TTTTTA TTATTTA TTTATTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTT-TTA TTTTTA TT-TTTA -TT-TTTA
* *
12040633 TTTATTA TATTTCA TTATTA TTTATTA TGTTTTA TTTTT
1 TTT-TTA T-TTTTA TTTTTA TTT-TTA T-TTTTA TTTTT
12040672 TGAAATAGGT
Statistics
Matches: 68, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
5 9 0.13
6 21 0.31
7 27 0.40
8 11 0.16
ACGTcount: A:0.20, C:0.03, G:0.01, T:0.75
Consensus pattern (6 bp):
TTTTTA
Found at i:12040636 original size:32 final size:32
Alignment explanation
Indices: 12040573--12040638 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
12040563 CACTCAGTCC
* *
12040573 TTTCTTATTCTTTTTCTTTTTTTTTTAATTTA
1 TTTCTTATTCTTTTTATTTTTTATTTAATTTA
12040605 TTTCTTATT-TTTATTATTTATTTATTT-ATTTA
1 TTTCTTATTCTTT-TTATTT-TTTATTTAATTTA
12040637 TT
1 TT
12040639 ATATTTCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 3 0.10
32 21 0.70
33 6 0.20
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (32 bp):
TTTCTTATTCTTTTTATTTTTTATTTAATTTA
Found at i:12040666 original size:10 final size:9
Alignment explanation
Indices: 12040609--12040672 Score: 51
Period size: 10 Copynumber: 6.8 Consensus size: 9
12040599 AATTTATTTC
12040609 TTATTTTTA
1 TTATTTTTA
12040618 TTATTTATTTA
1 TTA-TT-TTTA
*
12040629 TT-TATTTA
1 TTATTTTTA
*
12040637 TTATATTTCA
1 TTAT-TTTTA
12040647 TTATTATTTA
1 TTATT-TTTA
12040657 TTATGTTTTA
1 TTAT-TTTTA
12040667 TT-TTTT
1 TTATTTT
12040673 GAAATAGGTG
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
8 9 0.20
9 7 0.16
10 22 0.49
11 7 0.16
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (9 bp):
TTATTTTTA
Found at i:12040667 original size:17 final size:17
Alignment explanation
Indices: 12040602--12040668 Score: 64
Period size: 20 Copynumber: 3.7 Consensus size: 17
12040592 TTTTTTTAAT
*
12040602 TTATTTCTTATT-TTTA
1 TTATTTTTTATTATTTA
12040618 TTATTTATTTATTTATTTA
1 TTATTT-TTTA-TTATTTA
12040637 TTATATTTCATTATTATTTA
1 TTAT-TTT--TTATTATTTA
*
12040657 TTATGTTTTATT
1 TTATTTTTTATT
12040669 TTTTGAAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
16 6 0.14
17 8 0.19
18 2 0.05
19 11 0.26
20 13 0.30
21 3 0.07
ACGTcount: A:0.24, C:0.03, G:0.01, T:0.72
Consensus pattern (17 bp):
TTATTTTTTATTATTTA
Done.