Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr14
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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 4503000 characters in sequence are not A, C, G, or T
File 138 of 770
Found at i:40613532 original size:40 final size:40
Alignment explanation
Indices: 40613325--40613532 Score: 222
Period size: 40 Copynumber: 5.2 Consensus size: 40
40613315 CGGAATACAA
* *
40613325 CCGGATATAACCAC-ATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACAACTA-GCACAAATGCCTTCGGGTCTTAGC
* * * * *
40613365 CCAGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACAACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
40613405 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACAACTAGCACAAATGCCTTCGGGTCTTAGC
* * * *
40613445 CCGGATGTAGTC-ACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATA-ACAACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
40613485 CCGGATATAATTACTAGCACAAATGTCTTCGGGACTTAGC
1 CCGGATATAACAACTAGCACAAATGCCTTCGGGTCTTAGC
40613525 CCGGATAT
1 CCGGATAT
40613533 CATTCAATTG
Statistics
Matches: 140, Mismatches: 25, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
40 139 0.99
41 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAACAACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:40615833 original size:70 final size:71
Alignment explanation
Indices: 40615683--40615845 Score: 319
Period size: 70 Copynumber: 2.3 Consensus size: 71
40615673 GAGATGTATC
40615683 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
40615748 AGGACA
66 AGGACA
40615754 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCT-GGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
40615818 AGGACA
66 AGGACA
40615824 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
40615846 AGACAAATCG
Statistics
Matches: 92, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
70 52 0.57
71 40 0.43
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:40623351 original size:70 final size:71
Alignment explanation
Indices: 40623200--40623362 Score: 310
Period size: 70 Copynumber: 2.3 Consensus size: 71
40623190 GAGATGTATC
40623200 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
40623265 AGGACA
66 AGGACA
40623271 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCT-GGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
*
40623335 CGGACA
66 AGGACA
40623341 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
40623363 AGACAAATCG
Statistics
Matches: 91, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
70 51 0.56
71 40 0.44
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:40631697 original size:40 final size:39
Alignment explanation
Indices: 40631652--40631858 Score: 218
Period size: 40 Copynumber: 5.2 Consensus size: 39
40631642 CGGAATACAA
*
40631652 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
40631692 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
40631732 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* ** * *
40631772 CCGGATGTAGTCACTAGCACAATTGCCTTC-GGTCTTAAC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
** * *
40631811 CCGGATATAATTACTAGCACAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
40631851 CCGGATAT
1 CCGGATAT
40631859 CATTCAATTG
Statistics
Matches: 141, Mismatches: 24, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
39 34 0.24
40 107 0.76
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC
Found at i:40631792 original size:80 final size:80
Alignment explanation
Indices: 40631652--40631856 Score: 245
Period size: 80 Copynumber: 2.6 Consensus size: 80
40631642 CGGAATACAA
* * *
40631652 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGA-TAGAACGACTTGCACAAAT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTAGAACGACTAGCACAAAT
*
40631716 GCCTTCGGGTATTAGC
66 GCCTTC-GGTATTAAC
* * *
40631732 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAG-TC-ACTAGCACAAT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT-TAGAACGACTAGCACAAA
*
40631795 TGCCTTCGGTCTTAAC
65 TGCCTTCGGTATTAAC
** * * * *
40631811 CCGGATATAATTACTAGCACAAATGTCTTCGGGACTTAGCCCGGAT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT
40631857 ATCATTCAAT
Statistics
Matches: 108, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
79 46 0.43
80 58 0.54
81 1 0.01
82 3 0.03
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (80 bp):
CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTAGAACGACTAGCACAAAT
GCCTTCGGTATTAAC
Found at i:40642136 original size:20 final size:21
Alignment explanation
Indices: 40642107--40642147 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
40642097 TTGACTCATG
40642107 TTTCTCACTTT-TTTCTCTTTT
1 TTTCTCACTTTCTTT-TCTTTT
40642128 TTTCT-ACTTTCTTTTCTTTT
1 TTTCTCACTTTCTTTTCTTTT
40642148 CTTTTTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.05, C:0.22, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTCTCACTTTCTTTTCTTTT
Found at i:40642155 original size:6 final size:6
Alignment explanation
Indices: 40642135--40642188 Score: 51
Period size: 6 Copynumber: 9.3 Consensus size: 6
40642125 TTTTTTCTAC
* * *
40642135 TTTC-T TTTC-T TTTCTT TTTCTT TTTCATT ATT-TT TCTCTT GTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTC-TT TTTCTT TTTCTT TTTCTT
40642181 TTTCTT TT
1 TTTCTT TT
40642189 GATTTTTCTA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
5 12 0.30
6 24 0.60
7 4 0.10
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTCTT
Found at i:40642160 original size:22 final size:22
Alignment explanation
Indices: 40642117--40642188 Score: 67
Period size: 24 Copynumber: 3.2 Consensus size: 22
40642107 TTTCTCACTT
* *
40642117 TTTTCTCTT-TTTTTCTACTTTC
1 TTTTCTTTTCTTTTTCT-TTTTC
40642139 TTTTCTTTTCTTTTTCTTTTTC
1 TTTTCTTTTCTTTTTCTTTTTC
*
40642161 ATTATT-TTTCTCTTGTTCTTTTTC
1 -TT-TTCTTT-TCTTTTTCTTTTTC
40642185 TTTT
1 TTTT
40642189 GATTTTTCTA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
22 14 0.33
23 14 0.33
24 15 0.35
ACGTcount: A:0.04, C:0.18, G:0.01, T:0.76
Consensus pattern (22 bp):
TTTTCTTTTCTTTTTCTTTTTC
Found at i:40645517 original size:26 final size:26
Alignment explanation
Indices: 40645488--40645551 Score: 92
Period size: 26 Copynumber: 2.4 Consensus size: 26
40645478 AATAAACTTA
*
40645488 AGACATATTAAATGGCTGAACTAATT
1 AGACATATTAAATAGCTGAACTAATT
*
40645514 AGACATATTAAATAGCTGAACTGATT
1 AGACATATTAAATAGCTGAACTAATT
*
40645540 AGAACACATTAA
1 AG-ACATATTAA
40645552 TTAACTTAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 26 0.76
27 8 0.24
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.28
Consensus pattern (26 bp):
AGACATATTAAATAGCTGAACTAATT
Found at i:40645564 original size:46 final size:47
Alignment explanation
Indices: 40645514--40645621 Score: 130
Period size: 46 Copynumber: 2.3 Consensus size: 47
40645504 TGAACTAATT
* * **
40645514 AGACATATTAAATAGCTGAA-CTGATTAGAACACATTAATTA-ACTTA
1 AGACATATTAAATA-CCGAATCTAATTAGAACACATTAAACAGACTTA
* *
40645560 AGACATATTAATTACCGAATCTAATTAGAACATATTAAACAGACTTA
1 AGACATATTAAATACCGAATCTAATTAGAACACATTAAACAGACTTA
*
40645607 AGACACATTAAATAC
1 AGACATATTAAATAC
40645622 TTAAACTAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
45 4 0.08
46 30 0.58
47 18 0.35
ACGTcount: A:0.47, C:0.15, G:0.09, T:0.29
Consensus pattern (47 bp):
AGACATATTAAATACCGAATCTAATTAGAACACATTAAACAGACTTA
Found at i:40653179 original size:40 final size:39
Alignment explanation
Indices: 40653102--40653187 Score: 100
Period size: 40 Copynumber: 2.2 Consensus size: 39
40653092 TAACGATTTA
* *
40653102 TCGGCTAAAATGGCACTTAGTGTGCGACTCGAAATAGCT
1 TCGGCTAAAATGGCACTTAGGGTGCAACTCGAAATAGCT
* * * *
40653141 TCGGCTAAAAGTGGCACTTGGGGTGCAATTTGAGATAGCT
1 TCGGCTAAAA-TGGCACTTAGGGTGCAACTCGAAATAGCT
*
40653181 TTGGCTA
1 TCGGCTA
40653188 TATATATATA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
39 10 0.26
40 29 0.74
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (39 bp):
TCGGCTAAAATGGCACTTAGGGTGCAACTCGAAATAGCT
Found at i:40653264 original size:28 final size:28
Alignment explanation
Indices: 40653233--40653297 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
40653223 TATCGAGGAT
*
40653233 GGCACTTAGTGTGCCAAGCATCCAAAAA
1 GGCACTTAGTGTGCCAAACATCCAAAAA
40653261 GGCACTTAGTGTGCCAAACATCCAAAAA
1 GGCACTTAGTGTGCCAAACATCCAAAAA
*
40653289 AGCACTTAG
1 GGCACTTAG
40653298 CGTATGAGGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (28 bp):
GGCACTTAGTGTGCCAAACATCCAAAAA
Found at i:40656035 original size:50 final size:52
Alignment explanation
Indices: 40655960--40656095 Score: 156
Period size: 50 Copynumber: 2.7 Consensus size: 52
40655950 GGCTTGATAT
* * *
40655960 GTGCCAATGTAAGACCATGTCTGGGACATGGCATCG-GCACG-GA-AAGAGGA
1 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACCACGAGATAAGA-AA
* * * *
40656010 GTGCCAGTGTAAGACCATGCCTGGGATATGGCATTCGACCTCGATATAAGAAA
1 GTGCCAGTGTAAGACCATGTCTGGGACATGGCA-TCGACCACGAGATAAGAAA
40656063 GT--CAGTGTAAGACCATGTCTGGGACATGGCATC
1 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATC
40656096 AAATCAATAT
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
50 32 0.44
51 30 0.41
52 3 0.04
53 4 0.05
54 4 0.05
ACGTcount: A:0.29, C:0.21, G:0.30, T:0.21
Consensus pattern (52 bp):
GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACCACGAGATAAGAAA
Found at i:40656195 original size:43 final size:43
Alignment explanation
Indices: 40656102--40656227 Score: 130
Period size: 43 Copynumber: 3.0 Consensus size: 43
40656092 CATCAAATCA
* * *
40656102 ATATGTGATTACATGTAAGGCCATGTCTAGGACATTGGCATTG
1 ATATGTGATTACATGTAAGACCATGTCTAGGACAGTGGCATCG
* * * * *
40656145 -TATTGTGATTTCGTGTAAGACCCTGTGTGGGACAGTGGCATCG
1 ATA-TGTGATTACATGTAAGACCATGTCTAGGACAGTGGCATCG
* * *
40656188 ATATGTGATAACATGTAAGACCATATCTAGGATA-TGGCAT
1 ATATGTGATTACATGTAAGACCATGTCTAGGACAGTGGCAT
40656228 TGTATGAGTT
Statistics
Matches: 65, Mismatches: 16, Indels: 5
0.76 0.19 0.06
Matches are distributed among these distances:
42 8 0.12
43 55 0.85
44 2 0.03
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (43 bp):
ATATGTGATTACATGTAAGACCATGTCTAGGACAGTGGCATCG
Found at i:40658031 original size:40 final size:40
Alignment explanation
Indices: 40657964--40658135 Score: 224
Period size: 40 Copynumber: 4.3 Consensus size: 40
40657954 ACCCAAGTAT
*
40657964 CTTCGGGAT-TTAG-CCGGATATAACAACTCGCACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAGCAACTCGCACAAATGC
40658003 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* * *
40658043 CTTCGGGTCTTAGCCCGGATATGATC-ACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATAT-AGCAACTCGCACAAATGC
* * * *
40658083 CTTCGGGACATAGCCCAGATATAGCAACTCGCACGAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
*
40658123 CTTCGGATCTTAG
1 CTTCGGGTCTTAG
40658136 TCCAGTTATC
Statistics
Matches: 115, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
38 1 0.01
39 13 0.11
40 99 0.86
41 2 0.02
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
Found at i:40663174 original size:40 final size:39
Alignment explanation
Indices: 40663097--40663176 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 39
40663087 TAACGACTTA
*
40663097 TCGGCTAAAATGGCACTTAGTGTACGGTTCGAAATAGCT
1 TCGGCTAAAATGGCACTTAGTGTACAGTTCGAAATAGCT
* * * *
40663136 TCGGCTAAAAGTGGCACTTGGTGTGCAGTTTGAGATAGCT
1 TCGGCTAAAA-TGGCACTTAGTGTACAGTTCGAAATAGCT
40663176 T
1 T
40663177 TGGGTATATA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
39 10 0.29
40 25 0.71
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (39 bp):
TCGGCTAAAATGGCACTTAGTGTACAGTTCGAAATAGCT
Found at i:40666438 original size:13 final size:13
Alignment explanation
Indices: 40666420--40666445 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40666410 CCACACTATA
40666420 ATGCTTTGAATTG
1 ATGCTTTGAATTG
40666433 ATGCTTTGAATTG
1 ATGCTTTGAATTG
40666446 TGGTTTAGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (13 bp):
ATGCTTTGAATTG
Found at i:40670623 original size:31 final size:31
Alignment explanation
Indices: 40670588--40670647 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
40670578 CTAAATGAAT
40670588 GTTAATTGTATTGTAAGTCCGATAATGCTCC
1 GTTAATTGTATTGTAAGTCCGATAATGCTCC
*
40670619 GTTAATTGTATTGTAAGTCCGGTAATGCT
1 GTTAATTGTATTGTAAGTCCGATAATGCT
40670648 TCGTAACCCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.40
Consensus pattern (31 bp):
GTTAATTGTATTGTAAGTCCGATAATGCTCC
Found at i:40675608 original size:25 final size:25
Alignment explanation
Indices: 40675565--40675623 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
40675555 GTGGACACAC
* *
40675565 CACAACTCTTATGAGCTTACCAATT
1 CACAGCTCGTATGAGCTTACCAATT
* *
40675590 CTCAGCTCGTATGAGCTTACCGATT
1 CACAGCTCGTATGAGCTTACCAATT
40675615 CACAGCTCG
1 CACAGCTCG
40675624 CGAGAGCATA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.25, C:0.31, G:0.15, T:0.29
Consensus pattern (25 bp):
CACAGCTCGTATGAGCTTACCAATT
Found at i:40675656 original size:25 final size:26
Alignment explanation
Indices: 40675575--40675659 Score: 97
Period size: 25 Copynumber: 3.4 Consensus size: 26
40675565 CACAACTCTT
* * *
40675575 ATGAGCTTACCAATTC-TCAGCTCGT
1 ATGAGCATACCGATTCATCAGCTCGC
*
40675600 ATGAGCTTACCGATTCA-CAGCTCGC
1 ATGAGCATACCGATTCATCAGCTCGC
40675625 GA-GAGCATACCGATTCATC-GCTCGC
1 -ATGAGCATACCGATTCATCAGCTCGC
40675650 ATGAGCATAC
1 ATGAGCATAC
40675660 ATGTACAGGA
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
24 1 0.02
25 50 0.94
26 2 0.04
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (26 bp):
ATGAGCATACCGATTCATCAGCTCGC
Found at i:40677915 original size:30 final size:30
Alignment explanation
Indices: 40677879--40678011 Score: 176
Period size: 30 Copynumber: 4.4 Consensus size: 30
40677869 AAGAAAATTT
40677879 AGGCGTGTGGGCCATACGGGCAAGCCACAC
1 AGGCGTGTGGGCCATACGGGCAAGCCACAC
40677909 AGGCGTGTGGGCCATACGGGCAAGCCACAC
1 AGGCGTGTGGGCCATACGGGCAAGCCACAC
* * *
40677939 AAGCGTGTGGGCCATACGAGCAAGTCACAC
1 AGGCGTGTGGGCCATACGGGCAAGCCACAC
* * * * * *
40677969 GGGCATGTAGGCCATATGGGCGAGCCACAT
1 AGGCGTGTGGGCCATACGGGCAAGCCACAC
*
40677999 AGGCATGTGGGCC
1 AGGCGTGTGGGCC
40678012 CATAATTCTA
Statistics
Matches: 89, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 89 1.00
ACGTcount: A:0.24, C:0.27, G:0.36, T:0.13
Consensus pattern (30 bp):
AGGCGTGTGGGCCATACGGGCAAGCCACAC
Found at i:40683511 original size:51 final size:51
Alignment explanation
Indices: 40683435--40683540 Score: 212
Period size: 51 Copynumber: 2.1 Consensus size: 51
40683425 ATTTATTATT
40683435 TTAGACATAAAGGAAGACAGGGATGTTCAACTGATCCTTGGTAGACTTTTC
1 TTAGACATAAAGGAAGACAGGGATGTTCAACTGATCCTTGGTAGACTTTTC
40683486 TTAGACATAAAGGAAGACAGGGATGTTCAACTGATCCTTGGTAGACTTTTC
1 TTAGACATAAAGGAAGACAGGGATGTTCAACTGATCCTTGGTAGACTTTTC
40683537 TTAG
1 TTAG
40683541 CGACAGTGTG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (51 bp):
TTAGACATAAAGGAAGACAGGGATGTTCAACTGATCCTTGGTAGACTTTTC
Found at i:40683693 original size:51 final size:51
Alignment explanation
Indices: 40683617--40683722 Score: 212
Period size: 51 Copynumber: 2.1 Consensus size: 51
40683607 ATTTATTATT
40683617 TTAGACATAAAGGAAGACAGGGATGTTCAACTGATCCTTGGTAGACTTTTC
1 TTAGACATAAAGGAAGACAGGGATGTTCAACTGATCCTTGGTAGACTTTTC
40683668 TTAGACATAAAGGAAGACAGGGATGTTCAACTGATCCTTGGTAGACTTTTC
1 TTAGACATAAAGGAAGACAGGGATGTTCAACTGATCCTTGGTAGACTTTTC
40683719 TTAG
1 TTAG
40683723 CGACAGTGTG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (51 bp):
TTAGACATAAAGGAAGACAGGGATGTTCAACTGATCCTTGGTAGACTTTTC
Found at i:40683724 original size:182 final size:182
Alignment explanation
Indices: 40683417--40683962 Score: 1092
Period size: 182 Copynumber: 3.0 Consensus size: 182
40683407 ATTCTATTTT
40683417 CCTGCTAAATTTATTATTTTAGACATAAAGGAAGACAGGGATGTTCAACTGATCCTTGGTAGACT
1 CCTGCTAAATTTATTATTTTAGACATAAAGGAAGACAGGGATGTTCAACTGATCCTTGGTAGACT
40683482 TTTCTTAGACATAAAGGAAGACAGGGATGTTCAACTGATCCTTGGTAGACTTTTCTTAGCGACAG
66 TTTCTTAGACATAAAGGAAGACAGGGATGTTCAACTGATCCTTGGTAGACTTTTCTTAGCGACAG
40683547 TGTGAACTTATCAATGTCTAGAAAGGCAAACTCACTATTAGAGTAGAAAATG
131 TGTGAACTTATCAATGTCTAGAAAGGCAAACTCACTATTAGAGTAGAAAATG
40683599 CCTGCTAAATTTATTATTTTAGACATAAAGGAAGACAGGGATGTTCAACTGATCCTTGGTAGACT
1 CCTGCTAAATTTATTATTTTAGACATAAAGGAAGACAGGGATGTTCAACTGATCCTTGGTAGACT
40683664 TTTCTTAGACATAAAGGAAGACAGGGATGTTCAACTGATCCTTGGTAGACTTTTCTTAGCGACAG
66 TTTCTTAGACATAAAGGAAGACAGGGATGTTCAACTGATCCTTGGTAGACTTTTCTTAGCGACAG
40683729 TGTGAACTTATCAATGTCTAGAAAGGCAAACTCACTATTAGAGTAGAAAATG
131 TGTGAACTTATCAATGTCTAGAAAGGCAAACTCACTATTAGAGTAGAAAATG
40683781 CCTGCTAAATTTATTATTTTAGACATAAAGGAAGACAGGGATGTTCAACTGATCCTTGGTAGACT
1 CCTGCTAAATTTATTATTTTAGACATAAAGGAAGACAGGGATGTTCAACTGATCCTTGGTAGACT
40683846 TTTCTTAGACATAAAGGAAGACAGGGATGTTCAACTGATCCTTGGTAGACTTTTCTTAGCGACAG
66 TTTCTTAGACATAAAGGAAGACAGGGATGTTCAACTGATCCTTGGTAGACTTTTCTTAGCGACAG
40683911 TGTGAACTTATCAATGTCTAGAAAGGCAAACTCACTATTAGAGTAGAAAATG
131 TGTGAACTTATCAATGTCTAGAAAGGCAAACTCACTATTAGAGTAGAAAATG
40683963 AATAGGTAAT
Statistics
Matches: 364, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
182 364 1.00
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (182 bp):
CCTGCTAAATTTATTATTTTAGACATAAAGGAAGACAGGGATGTTCAACTGATCCTTGGTAGACT
TTTCTTAGACATAAAGGAAGACAGGGATGTTCAACTGATCCTTGGTAGACTTTTCTTAGCGACAG
TGTGAACTTATCAATGTCTAGAAAGGCAAACTCACTATTAGAGTAGAAAATG
Found at i:40683875 original size:51 final size:51
Alignment explanation
Indices: 40683799--40683904 Score: 212
Period size: 51 Copynumber: 2.1 Consensus size: 51
40683789 ATTTATTATT
40683799 TTAGACATAAAGGAAGACAGGGATGTTCAACTGATCCTTGGTAGACTTTTC
1 TTAGACATAAAGGAAGACAGGGATGTTCAACTGATCCTTGGTAGACTTTTC
40683850 TTAGACATAAAGGAAGACAGGGATGTTCAACTGATCCTTGGTAGACTTTTC
1 TTAGACATAAAGGAAGACAGGGATGTTCAACTGATCCTTGGTAGACTTTTC
40683901 TTAG
1 TTAG
40683905 CGACAGTGTG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (51 bp):
TTAGACATAAAGGAAGACAGGGATGTTCAACTGATCCTTGGTAGACTTTTC
Found at i:40686709 original size:31 final size:31
Alignment explanation
Indices: 40686672--40686732 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
40686662 AACATAATTG
40686672 ATAATGTGCTAAGT-AGTCATAGATTCTGATA
1 ATAATGTGCTAAGTAAG-CATAGATTCTGATA
40686703 ATAATGTGCTAAGTAAGCATAGATTCTGAT
1 ATAATGTGCTAAGTAAGCATAGATTCTGAT
40686733 TTTCCAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 27 0.93
32 2 0.07
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.34
Consensus pattern (31 bp):
ATAATGTGCTAAGTAAGCATAGATTCTGATA
Found at i:40692358 original size:43 final size:43
Alignment explanation
Indices: 40692311--40692418 Score: 121
Period size: 43 Copynumber: 2.5 Consensus size: 43
40692301 TAGCCTAGCT
*
40692311 ATGGTCTTACACGAAATTA-ATTAACGATGCCAATGTCCCAAAC
1 ATGGTCTTACACGAAATCACA-TAACGATGCCAATGTCCCAAAC
* * * * * *
40692354 ATGGTCTTATATGTAATCACATAATGATGCCAATGTCCTATAC
1 ATGGTCTTACACGAAATCACATAACGATGCCAATGTCCCAAAC
40692397 ATGGTCTTACAC-ATAATCACAT
1 ATGGTCTTACACGA-AATCACAT
40692419 CTCGTTAATA
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
43 52 0.98
44 1 0.02
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.31
Consensus pattern (43 bp):
ATGGTCTTACACGAAATCACATAACGATGCCAATGTCCCAAAC
Found at i:40697846 original size:46 final size:46
Alignment explanation
Indices: 40697703--40697846 Score: 122
Period size: 46 Copynumber: 3.1 Consensus size: 46
40697693 CCCGCCCATA
*
40697703 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGC-CTAGTTA-CATCTCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATC-CT
* * * *
40697752 --CGAACTCGGACTCAACTCAACGAGTTCGGACAT-TTGCATCCAT--G
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCT-CAACCATCCT
40697796 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
40697842 AGTGA
1 AGTGA
40697847 CATGTCACTT
Statistics
Matches: 76, Mismatches: 9, Indels: 23
0.70 0.08 0.21
Matches are distributed among these distances:
44 8 0.11
45 1 0.01
46 33 0.43
47 30 0.39
49 3 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (46 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
Found at i:40700261 original size:30 final size:30
Alignment explanation
Indices: 40700217--40700305 Score: 94
Period size: 30 Copynumber: 3.0 Consensus size: 30
40700207 CAAAGATAAC
*
40700217 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAACCCGGAATAAAGAAATCCAAGATA
*
40700246 GAGAAACCCGGAATAAAGAAATCC-AGAATA
1 AAGAAACCCGGAATAAAGAAATCCAAG-ATA
* * *
40700276 AAGAGATCCAGG-ATAAAGAAACCCAAGATA
1 AAGA-AACCCGGAATAAAGAAATCCAAGATA
40700306 CGATACTATG
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
29 9 0.18
30 34 0.68
31 7 0.14
ACGTcount: A:0.56, C:0.16, G:0.18, T:0.10
Consensus pattern (30 bp):
AAGAAACCCGGAATAAAGAAATCCAAGATA
Found at i:40700265 original size:15 final size:14
Alignment explanation
Indices: 40700217--40700299 Score: 58
Period size: 15 Copynumber: 5.6 Consensus size: 14
40700207 CAAAGATAAC
*
40700217 AAGAAAACCGAATA
1 AAGAAACCCGAATA
* *
40700231 AAGAAATCCAAGATA
1 AAGAAACCCGA-ATA
*
40700246 GAGAAACCCGGAATA
1 AAGAAACCC-GAATA
*
40700261 AAGAAATCCAGAATA
1 AAGAAA-CCCGAATA
* * *
40700276 AAGAGATCCAGGATA
1 AAGA-AACCCGAATA
40700291 AAGAAACCC
1 AAGAAACCC
40700300 AAGATACGAT
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
14 12 0.22
15 38 0.70
16 4 0.07
ACGTcount: A:0.55, C:0.17, G:0.18, T:0.10
Consensus pattern (14 bp):
AAGAAACCCGAATA
Found at i:40700305 original size:15 final size:15
Alignment explanation
Indices: 40700228--40700305 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
40700218 AGAAAACCGA
40700228 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* **
40700243 ATAGAGAAA-CCCGG
1 ATAAAGAAATCCAAG
40700257 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
40700272 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
40700288 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
40700303 ATA
1 ATA
40700306 CGATACTATG
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
14 3 0.06
15 44 0.88
16 3 0.06
ACGTcount: A:0.55, C:0.15, G:0.18, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:40703483 original size:91 final size:93
Alignment explanation
Indices: 40703374--40703542 Score: 261
Period size: 91 Copynumber: 1.8 Consensus size: 93
40703364 GCCCATAAGT
* * * *
40703374 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACT-TGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40703438 CG-GCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* *
40703465 GAACTCGGACTCAACTCAACGAGTTCAGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
40703530 CGAGTTCGGATGC
66 CGAGCTCGGATGC
40703543 TCAACCATCC
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
91 46 0.67
92 14 0.20
93 9 0.13
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:40703536 original size:46 final size:46
Alignment explanation
Indices: 40703366--40703533 Score: 159
Period size: 46 Copynumber: 3.7 Consensus size: 46
40703356 TGTAACCCGC
* * * *
40703366 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGACATTTGCAT
* * * *
40703412 CCATAAGTGAACT-TGACTCAACTCAACG-GCTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC--A-GAC-ATTTGCAT
* *
40703460 CTC-T---CGAACTCGGACTCAACTCAACGAGTTCAGACATTTGCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGCTCAGACATTTGCAT
40703503 CCATAAGTGAACTCGGACTCAACTCAACGAG
1 CCATAAGTGAACTCGGACTCAACTCAACGAG
40703534 TTCGGATGCT
Statistics
Matches: 97, Mismatches: 14, Indels: 22
0.73 0.11 0.17
Matches are distributed among these distances:
42 1 0.01
43 8 0.08
44 6 0.06
45 20 0.21
46 50 0.52
47 5 0.05
48 6 0.06
49 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGACATTTGCAT
Found at i:40706647 original size:43 final size:43
Alignment explanation
Indices: 40706594--40706700 Score: 124
Period size: 43 Copynumber: 2.5 Consensus size: 43
40706584 ATAAACTCGG
* *
40706594 ACCAACTCAACGAGCTCGGATGCCACATATATCACAAACTCAA
1 ACCAACTCAACGAGCTCAGATGCCACATAAATCACAAACTCAA
* ** ** *
40706637 ACCAACTCAACGAGTTCAGATTTCACATAAATCATGAACTCAG
1 ACCAACTCAACGAGCTCAGATGCCACATAAATCACAAACTCAA
* *
40706680 ACCAACTCAATGAGTTCAGAT
1 ACCAACTCAACGAGCTCAGAT
40706701 CATATAATTT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 55 1.00
ACGTcount: A:0.39, C:0.28, G:0.12, T:0.21
Consensus pattern (43 bp):
ACCAACTCAACGAGCTCAGATGCCACATAAATCACAAACTCAA
Found at i:40707070 original size:31 final size:31
Alignment explanation
Indices: 40707032--40707094 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
40707022 CAATTTATGT
40707032 AATAATAGTAAAGAGTTATAATTCAAACATA
1 AATAATAGTAAAGAGTTATAATTCAAACATA
40707063 AATAATAGTAAAGAGTTATAATTCAAACATA
1 AATAATAGTAAAGAGTTATAATTCAAACATA
40707094 A
1 A
40707095 CATTGCATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.56, C:0.06, G:0.10, T:0.29
Consensus pattern (31 bp):
AATAATAGTAAAGAGTTATAATTCAAACATA
Found at i:40710929 original size:39 final size:40
Alignment explanation
Indices: 40710792--40710929 Score: 226
Period size: 40 Copynumber: 3.5 Consensus size: 40
40710782 CGGATGATAA
40710792 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
40710832 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
40710872 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
40710912 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
40710930 TACTTGGTTT
Statistics
Matches: 93, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
39 17 0.18
40 76 0.82
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.23
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:40714341 original size:29 final size:29
Alignment explanation
Indices: 40714302--40714376 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
40714292 GGTTGAGAGA
* *
40714302 ATGGCACTAAGTGTGCGGGCTTGAAA-TGC
1 ATGGCACTAAGTGTGCGAG-TTGAAAGTAC
*
40714331 ATGGCACTAAGTGTGCGAGTTTAAAGTAC
1 ATGGCACTAAGTGTGCGAGTTGAAAGTAC
40714360 ATGGCACTAAGTGTGCG
1 ATGGCACTAAGTGTGCG
40714377 TGGTCGATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
28 5 0.12
29 37 0.88
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (29 bp):
ATGGCACTAAGTGTGCGAGTTGAAAGTAC
Found at i:40718640 original size:93 final size:93
Alignment explanation
Indices: 40718528--40718698 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
40718518 GCCCATAAGT
* *
40718528 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40718593 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
40718621 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40718686 CGAGTTCGGATGC
66 CGAGTTCGGATGC
40718699 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:40718695 original size:46 final size:46
Alignment explanation
Indices: 40718520--40718695 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
40718510 TGTAACCCGC
* * *
40718520 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
40718566 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
40718616 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
40718659 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
40718696 TGCTCAACCA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 64 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:40722924 original size:44 final size:43
Alignment explanation
Indices: 40722874--40722973 Score: 130
Period size: 49 Copynumber: 2.2 Consensus size: 43
40722864 CGAGCTCGGT
40722874 GAAAGTAAA-ATTTTCGGAGTGGATTTGATTAAAGATGCTGAACA
1 GAAAGTAAATATTTTCGGA-TGGATTTGATTAAAGATGCTG-ACA
40722918 GAAAGTAAGTATAATATTTTCGGATGGATTTGATTAAAGATGCTGACA
1 G--A--AAGTA-AATATTTTCGGATGGATTTGATTAAAGATGCTGACA
40722966 GAAAGTAA
1 GAAAGTAA
40722974 GTATAATTCG
Statistics
Matches: 50, Mismatches: 0, Indels: 13
0.79 0.00 0.21
Matches are distributed among these distances:
43 1 0.02
44 6 0.12
46 2 0.04
48 9 0.18
49 23 0.46
50 9 0.18
ACGTcount: A:0.40, C:0.06, G:0.24, T:0.30
Consensus pattern (43 bp):
GAAAGTAAATATTTTCGGATGGATTTGATTAAAGATGCTGACA
Found at i:40722971 original size:48 final size:50
Alignment explanation
Indices: 40722876--40722980 Score: 182
Period size: 48 Copynumber: 2.2 Consensus size: 50
40722866 AGCTCGGTGA
40722876 AAGTA-AA-ATTTTCGGAGTGGATTTGATTAAAGATGCTGAACAGAAAGT
1 AAGTATAATATTTTCGGAGTGGATTTGATTAAAGATGCTGAACAGAAAGT
40722924 AAGTATAATATTTTCGGA-TGGATTTGATTAAAGATGCTG-ACAGAAAGT
1 AAGTATAATATTTTCGGAGTGGATTTGATTAAAGATGCTGAACAGAAAGT
40722972 AAGTATAAT
1 AAGTATAAT
40722981 TCGTGAGAGT
Statistics
Matches: 55, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
48 23 0.42
49 23 0.42
50 9 0.16
ACGTcount: A:0.40, C:0.06, G:0.23, T:0.31
Consensus pattern (50 bp):
AAGTATAATATTTTCGGAGTGGATTTGATTAAAGATGCTGAACAGAAAGT
Found at i:40725050 original size:29 final size:29
Alignment explanation
Indices: 40725011--40725085 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
40725001 GGTTGAGAGA
* *
40725011 ATGGCACTAAGTGTGCGGGCTTGAAA-TGC
1 ATGGCACTAAGTGTGCGAG-TTGAAAGTAC
*
40725040 ATGGCACTAAGTGTGCGAGTTTAAAGTAC
1 ATGGCACTAAGTGTGCGAGTTGAAAGTAC
40725069 ATGGCACTAAGTGTGCG
1 ATGGCACTAAGTGTGCG
40725086 TGGTTGATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
28 5 0.12
29 37 0.88
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (29 bp):
ATGGCACTAAGTGTGCGAGTTGAAAGTAC
Found at i:40728132 original size:27 final size:27
Alignment explanation
Indices: 40728064--40728134 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
40728054 CGACTTGTAA
* *
40728064 AATTACCAAAGTACTCC-CGATTTACAG
1 AATTACCAAAATAC-CCTCAATTTACAG
****
40728091 AATTACCGTTTTACCCTCAATTTACAG
1 AATTACCAAAATACCCTCAATTTACAG
40728118 AATTACCAAAATACCCT
1 AATTACCAAAATACCCT
40728135 TGGTTTATAA
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
26 2 0.06
27 32 0.94
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.30
Consensus pattern (27 bp):
AATTACCAAAATACCCTCAATTTACAG
Found at i:40728141 original size:27 final size:27
Alignment explanation
Indices: 40728118--40728241 Score: 169
Period size: 27 Copynumber: 4.6 Consensus size: 27
40728108 CAATTTACAG
40728118 AATTACCAAAATACCCTTGGTTTATAA
1 AATTACCAAAATACCCTTGGTTTATAA
* * *
40728145 AATCACCAAAATACCCCTGGTTTGTAA
1 AATTACCAAAATACCCTTGGTTTATAA
* *
40728172 AATTACTAAAATACCCTTTGTTTATAA
1 AATTACCAAAATACCCTTGGTTTATAA
*
40728199 AATTACCAAAATACCCATGGTTTGA-AA
1 AATTACCAAAATACCCTTGGTTT-ATAA
*
40728226 AATTACTAAAATACCC
1 AATTACCAAAATACCC
40728242 CTGTAGGGTA
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
27 83 0.99
28 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.31
Consensus pattern (27 bp):
AATTACCAAAATACCCTTGGTTTATAA
Found at i:40728160 original size:54 final size:53
Alignment explanation
Indices: 40728102--40728241 Score: 138
Period size: 54 Copynumber: 2.6 Consensus size: 53
40728092 ATTACCGTTT
40728102 TACCCTCAATT-TACAGAATTACCAAAATACCCTTGGTTTATAAAATCACCAAAA
1 TACCCTCAATTGTA-A-AATTACCAAAATACCCTTGGTTTATAAAATCACCAAAA
*** * * *
40728156 TACCCCTGGTTTGTAAAATTACTAAAATACCCTTTGTTTATAAAATTACCAAAA
1 TA-CCCTCAATTGTAAAATTACCAAAATACCCTTGGTTTATAAAATCACCAAAA
*** * *
40728210 TACCCATGGTTTGAAAAATTACTAAAATACCC
1 TACCC-TCAATTGTAAAATTACCAAAATACCC
40728242 CTGTAGGGTA
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
53 3 0.04
54 64 0.84
55 7 0.09
56 2 0.03
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.31
Consensus pattern (53 bp):
TACCCTCAATTGTAAAATTACCAAAATACCCTTGGTTTATAAAATCACCAAAA
Found at i:40728253 original size:81 final size:81
Alignment explanation
Indices: 40728118--40728270 Score: 220
Period size: 81 Copynumber: 1.9 Consensus size: 81
40728108 CAATTTACAG
* **
40728118 AATTACCAAAATACCCTTGGTTTATAAAATCACCAAAATACCCCTGGTTTGTAAAATTACTAAAA
1 AATTACCAAAATACCCATGGTTTATAAAATCACCAAAATACCCCTGGTGGGTAAAATTACTAAAA
40728183 TACCCTTTGTTTATAA
66 TACCCTTTGTTTATAA
* * *
40728199 AATTACCAAAATACCCATGGTTTGA-AAAATTACTAAAATACCCCT-GTAGGGTAAAATTACTGA
1 AATTACCAAAATACCCATGGTTT-ATAAAATCACCAAAATACCCCTGGT-GGGTAAAATTACTAA
40728262 AATACCCTT
64 AATACCCTT
40728271 GTGGGGTAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
80 2 0.03
81 61 0.95
82 1 0.02
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.31
Consensus pattern (81 bp):
AATTACCAAAATACCCATGGTTTATAAAATCACCAAAATACCCCTGGTGGGTAAAATTACTAAAA
TACCCTTTGTTTATAA
Found at i:40728254 original size:27 final size:27
Alignment explanation
Indices: 40728224--40728285 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
40728214 CATGGTTTGA
40728224 AAAATTACTAAAATACCCCTGTAGGGT
1 AAAATTACTAAAATACCCCTGTAGGGT
* * *
40728251 AAAATTACTGAAATACCCTTGTGGGGT
1 AAAATTACTAAAATACCCCTGTAGGGT
40728278 AAAATTAC
1 AAAATTAC
40728286 CATTTTGCCC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.27
Consensus pattern (27 bp):
AAAATTACTAAAATACCCCTGTAGGGT
Found at i:40728254 original size:54 final size:54
Alignment explanation
Indices: 40728118--40728268 Score: 162
Period size: 54 Copynumber: 2.8 Consensus size: 54
40728108 CAATTTACAG
* ** * * *
40728118 AATTACCAAAATACCCT-TGGTTTATAAAATCACCAAAATACCCCTGGTTTGTAA
1 AATTACTAAAATACCCTCT-GTGGATAAAATTACCAAAATACCCATGGTTTGAAA
* **
40728172 AATTACTAAAATACCCTTTGTTTATAAAATTACCAAAATACCCATGGTTTGAAA
1 AATTACTAAAATACCCTCTGTGGATAAAATTACCAAAATACCCATGGTTTGAAA
* **
40728226 AATTACTAAAATACCC-CTGTAGGGTAAAATTACTGAAATACCC
1 AATTACTAAAATACCCTCTGT-GGATAAAATTACCAAAATACCC
40728269 TTGTGGGGTA
Statistics
Matches: 85, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
53 3 0.04
54 81 0.95
55 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (54 bp):
AATTACTAAAATACCCTCTGTGGATAAAATTACCAAAATACCCATGGTTTGAAA
Found at i:40730472 original size:17 final size:17
Alignment explanation
Indices: 40730450--40730483 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
40730440 CCTTATAAGG
40730450 CTCTATGAGATCTTAAA
1 CTCTATGAGATCTTAAA
40730467 CTCTATGAGATCTTAAA
1 CTCTATGAGATCTTAAA
40730484 ACATACTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (17 bp):
CTCTATGAGATCTTAAA
Found at i:40731866 original size:28 final size:28
Alignment explanation
Indices: 40731820--40731888 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
40731810 TTTAAAACCC
*
40731820 TAGGGGT-ATATCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
40731847 TAGGGGTAATTTCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
40731875 TAGGGGTAATTTCG
1 TAGGGGTAATTTCG
40731889 TGATCTACGC
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 7 0.17
28 33 0.82
ACGTcount: A:0.19, C:0.10, G:0.28, T:0.43
Consensus pattern (28 bp):
TAGGGGTAATTTCGGTAATTTTGCTCTT
Found at i:40733539 original size:20 final size:20
Alignment explanation
Indices: 40733516--40733553 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
40733506 CACATCCAAA
*
40733516 TACAAAATTTTAAAAATCTT
1 TACAAAATATTAAAAATCTT
*
40733536 TACAAAATATTGAAAATC
1 TACAAAATATTAAAAATC
40733554 GCGAATAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (20 bp):
TACAAAATATTAAAAATCTT
Found at i:40739875 original size:28 final size:28
Alignment explanation
Indices: 40739829--40739897 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
40739819 TTTAAAACCC
*
40739829 TAGGGGT-ATATCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
40739856 TAGGGGTAATTTCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
40739884 TAGGGGTAATTTCG
1 TAGGGGTAATTTCG
40739898 TGATCTACGC
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 7 0.17
28 33 0.82
ACGTcount: A:0.19, C:0.10, G:0.28, T:0.43
Consensus pattern (28 bp):
TAGGGGTAATTTCGGTAATTTTGCTCTT
Found at i:40741549 original size:20 final size:20
Alignment explanation
Indices: 40741526--40741563 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
40741516 CACATCCAAA
*
40741526 TACAAAATTTTAAAAATCTT
1 TACAAAATATTAAAAATCTT
*
40741546 TACAAAATATTGAAAATC
1 TACAAAATATTAAAAATC
40741564 GCGAATAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (20 bp):
TACAAAATATTAAAAATCTT
Found at i:40743729 original size:40 final size:40
Alignment explanation
Indices: 40743674--40743764 Score: 155
Period size: 40 Copynumber: 2.3 Consensus size: 40
40743664 TAATTAAGGA
40743674 TTATATCCGGGTTAAGTCCCAAACGCATTTGTGCTGGTTG
1 TTATATCCGGGTTAAGTCCCAAACGCATTTGTGCTGGTTG
* *
40743714 TTATATCCGGGTTAAGTCCCGAAGGCATTTGTGCTGGTTG
1 TTATATCCGGGTTAAGTCCCAAACGCATTTGTGCTGGTTG
*
40743754 TTATATTCGGG
1 TTATATCCGGG
40743765 CTAAATCCTG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.19, C:0.18, G:0.27, T:0.36
Consensus pattern (40 bp):
TTATATCCGGGTTAAGTCCCAAACGCATTTGTGCTGGTTG
Found at i:40743778 original size:40 final size:40
Alignment explanation
Indices: 40743674--40743780 Score: 142
Period size: 40 Copynumber: 2.7 Consensus size: 40
40743664 TAATTAAGGA
* * * *
40743674 TTATATCCGGGTTAAGTCCCAAACGCATTTGTGCTGGTTG
1 TTATATCCGGGCTAAATCCCGAAGGCATTTGTGCTGGTTG
* *
40743714 TTATATCCGGGTTAAGTCCCGAAGGCATTTGTGCTGGTTG
1 TTATATCCGGGCTAAATCCCGAAGGCATTTGTGCTGGTTG
* *
40743754 TTATATTCGGGCTAAATCCTGAAGGCA
1 TTATATCCGGGCTAAATCCCGAAGGCA
40743781 ATTGGATTGG
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 61 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (40 bp):
TTATATCCGGGCTAAATCCCGAAGGCATTTGTGCTGGTTG
Found at i:40749956 original size:40 final size:40
Alignment explanation
Indices: 40749856--40749962 Score: 178
Period size: 40 Copynumber: 2.7 Consensus size: 40
40749846 CAATTGAGGA
* *
40749856 TTATATCCGGGTTAAGTCCCAAACGCATTTGTGCTGGTTG
1 TTATATCCGGGTTAAGTCCCGAAGGCATTTGTGCTGGTTG
40749896 TTATATCCGGGTTAAGTCCCGAAGGCATTTGTGCTGGTTG
1 TTATATCCGGGTTAAGTCCCGAAGGCATTTGTGCTGGTTG
* *
40749936 TTATATCCGGGCTAAATCCCGAAGGCA
1 TTATATCCGGGTTAAGTCCCGAAGGCA
40749963 ATTGGGTTGG
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 63 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (40 bp):
TTATATCCGGGTTAAGTCCCGAAGGCATTTGTGCTGGTTG
Found at i:40761253 original size:23 final size:23
Alignment explanation
Indices: 40761223--40761268 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
40761213 AGCTTGTGAT
40761223 TGATTACCATCCGGGAAGGGCTA
1 TGATTACCATCCGGGAAGGGCTA
40761246 TGATTACCATCCGGGAAGGGCTA
1 TGATTACCATCCGGGAAGGGCTA
40761269 ATGTTGTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.22
Consensus pattern (23 bp):
TGATTACCATCCGGGAAGGGCTA
Found at i:40770018 original size:54 final size:54
Alignment explanation
Indices: 40769955--40770085 Score: 217
Period size: 54 Copynumber: 2.4 Consensus size: 54
40769945 ATTACCAAAG
* *
40769955 TACCTTCGATTTATAGAATTACTGTTTTACCCTTAATTTACAGAATTACTGTTT
1 TACCCTCGATTTATAGAATTACTGTTTTACCCTTAATTTACAGAATTACTATTT
*
40770009 TACCCTCGATTTATAGAATTACTGTTTTACCCTTGATTTACAGAATTACTATTT
1 TACCCTCGATTTATAGAATTACTGTTTTACCCTTAATTTACAGAATTACTATTT
* *
40770063 TACCCTCGATTTACAAAATTACT
1 TACCCTCGATTTATAGAATTACT
40770086 AAAATACCCT
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 72 1.00
ACGTcount: A:0.29, C:0.19, G:0.08, T:0.44
Consensus pattern (54 bp):
TACCCTCGATTTATAGAATTACTGTTTTACCCTTAATTTACAGAATTACTATTT
Found at i:40770086 original size:27 final size:27
Alignment explanation
Indices: 40769955--40770085 Score: 190
Period size: 27 Copynumber: 4.9 Consensus size: 27
40769945 ATTACCAAAG
* *
40769955 TACCTTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
**
40769982 TACCCTTAATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
40770009 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* *
40770036 TACCCTTGATTTACAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
40770063 TACCCTCGATTTACAAAATTACT
1 TACCCTCGATTTACAGAATTACT
40770086 AAAATACCCT
Statistics
Matches: 92, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 92 1.00
ACGTcount: A:0.29, C:0.19, G:0.08, T:0.44
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACTGTTT
Found at i:40770094 original size:54 final size:54
Alignment explanation
Indices: 40769982--40770111 Score: 170
Period size: 54 Copynumber: 2.4 Consensus size: 54
40769972 ATTACTGTTT
* * * * ****
40769982 TACCCTTAATTTACAGAATTACTGTTTTACCCTCGATTTATAGAATTACTGTTT
1 TACCCTTGATTTACAGAATTACTATTTTACCCTCGATTTACAAAATTACTAAAA
40770036 TACCCTTGATTTACAGAATTACTATTTTACCCTCGATTTACAAAATTACTAAAA
1 TACCCTTGATTTACAGAATTACTATTTTACCCTCGATTTACAAAATTACTAAAA
* *
40770090 TACCCTTGGTTTACAAAATTAC
1 TACCCTTGATTTACAGAATTAC
40770112 CAAAATACCC
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 66 1.00
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (54 bp):
TACCCTTGATTTACAGAATTACTATTTTACCCTCGATTTACAAAATTACTAAAA
Found at i:40770110 original size:81 final size:82
Alignment explanation
Indices: 40769957--40770111 Score: 186
Period size: 81 Copynumber: 1.9 Consensus size: 82
40769947 TACCAAAGTA
* * * * ****
40769957 CCTTCGATTTATAGAATTACTGTTTTACCCTTAATTTACAGAATTACTGTTTTACCCTCGATTTA
1 CCTTCGATTTACAGAATTACTATTTTACCCTCAATTTACAAAATTACTAAAATACCCTCGATTTA
* *
40770022 TAGAATTACTGTTTTAC
66 CAAAATTACTGTTTTAC
* * *
40770039 CCTT-GATTTACAGAATTACTATTTTACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTA
1 CCTTCGATTTACAGAATTACTATTTTACCCTCAATTTACAAAATTACTAAAATACCCTCGATTTA
40770103 CAAAATTAC
66 CAAAATTAC
40770112 CAAAATACCC
Statistics
Matches: 60, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
81 56 0.93
82 4 0.07
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.41
Consensus pattern (82 bp):
CCTTCGATTTACAGAATTACTATTTTACCCTCAATTTACAAAATTACTAAAATACCCTCGATTTA
CAAAATTACTGTTTTAC
Found at i:40770121 original size:54 final size:54
Alignment explanation
Indices: 40770009--40770313 Score: 154
Period size: 54 Copynumber: 5.6 Consensus size: 54
40769999 ATTACTGTTT
* ***** * * ***
40770009 TACCCTCGATTTATAGAATTACTGTTTTACCCTTGATTTACAGAATTACTATTT
1 TACCCTCGATTTATAAAATTACCAAAATACCCTTGATTTACAAAATTACCAAAA
* * *
40770063 TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTACAAAATTACCAAAA
1 TACCCTCGATTTATAAAATTACCAAAATACCCTTGATTTACAAAATTACCAAAA
* * * * ** * *
40770117 TACCCTC-AATCAGTAAAATTACCAAAATACCCTAG-TCTGTAAAATTGCTAAAA
1 TACCCTCGATTTA-TAAAATTACCAAAATACCCTTGATTTACAAAATTACCAAAA
* * * ** **
40770170 TACCC-CTGGTTTGTAAAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTC-GATTTATAAAATTACCAAAATACCCTTGATTTACAAAATTACCAAAA
* * ***
40770224 TACCC-CTGATTTACAAAGTTA-CAGAAATACCCTTGACTTT-CTAAAAATTATGGAAA
1 TACCCTC-GATTTATAAAATTACCA-AAATACCCTTGA-TTTAC--AAAATTACCAAAA
* * * **
40770280 TACCATTGGTTTATAAAATTACTGAAATACCCTT
1 TACCCTCGATTTATAAAATTACCAAAATACCCTT
40770314 AGTTTTTAGA
Statistics
Matches: 191, Mismatches: 50, Indels: 18
0.74 0.19 0.07
Matches are distributed among these distances:
52 1 0.01
53 41 0.21
54 111 0.58
55 3 0.02
56 35 0.18
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.33
Consensus pattern (54 bp):
TACCCTCGATTTATAAAATTACCAAAATACCCTTGATTTACAAAATTACCAAAA
Found at i:40770121 original size:81 final size:82
Alignment explanation
Indices: 40769942--40770122 Score: 177
Period size: 81 Copynumber: 2.2 Consensus size: 82
40769932 CTCAAATTGT
* * * * * *
40769942 AAAATTACCAAAGTA-CCTTCGATTTATAGAATTACTGTTTTACCCTTAATTTACAGAATTACTG
1 AAAATTACCAAAATACCCTTCGATTTACAGAATTACTATTTTACCCTCAATTTACAAAATTACTA
*** *
40770006 TTTTACCCTCGATTTAT
66 AAATACCCTCGATTTAC
* ***** *
40770023 AGAATTACTGTTTTACCCTT-GATTTACAGAATTACTATTTTACCCTCGATTTACAAAATTACTA
1 AAAATTACCAAAATACCCTTCGATTTACAGAATTACTATTTTACCCTCAATTTACAAAATTACTA
* *
40770087 AAATACCCTTGGTTTAC
66 AAATACCCTCGATTTAC
40770104 AAAATTACCAAAATACCCT
1 AAAATTACCAAAATACCCT
40770123 CAATCAGTAA
Statistics
Matches: 75, Mismatches: 24, Indels: 2
0.74 0.24 0.02
Matches are distributed among these distances:
81 71 0.95
82 4 0.05
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.38
Consensus pattern (82 bp):
AAAATTACCAAAATACCCTTCGATTTACAGAATTACTATTTTACCCTCAATTTACAAAATTACTA
AAATACCCTCGATTTAC
Found at i:40770188 original size:80 final size:80
Alignment explanation
Indices: 40770077--40770228 Score: 241
Period size: 80 Copynumber: 1.9 Consensus size: 80
40770067 CTCGATTTAC
*
40770077 AAAATTACTAAAATACCCTTGGTTTACAAAATTACCAAAATACCCTCAATCAGTAAAATTACCAA
1 AAAATTACTAAAATACCCCTGGTTTACAAAATTACCAAAATACCCTCAATCAGTAAAATTACCAA
40770142 AATACCCTAGTCTGT
66 AATACCCTAGTCTGT
* ** * **
40770157 AAAATTGCTAAAATACCCCTGGTTTGTAAAATTACCGAAATACCCTCAATTTGTAAAATTACCAA
1 AAAATTACTAAAATACCCCTGGTTTACAAAATTACCAAAATACCCTCAATCAGTAAAATTACCAA
40770222 AATACCC
66 AATACCC
40770229 CTGATTTACA
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
80 65 1.00
ACGTcount: A:0.43, C:0.22, G:0.07, T:0.28
Consensus pattern (80 bp):
AAAATTACTAAAATACCCCTGGTTTACAAAATTACCAAAATACCCTCAATCAGTAAAATTACCAA
AATACCCTAGTCTGT
Found at i:40770318 original size:27 final size:27
Alignment explanation
Indices: 40770072--40770340 Score: 159
Period size: 27 Copynumber: 9.9 Consensus size: 27
40770062 TTACCCTCGA
* * *
40770072 TTTACAAAATTACTAAAATACCCTTGG
1 TTTATAAAATTACCAAAATACCCTTAG
* *
40770099 TTTACAAAATTACCAAAATACCCTCA-
1 TTTATAAAATTACCAAAATACCCTTAG
* *
40770125 ATCAGTAAAATTACCAAAATACCC-TAG
1 TTTA-TAAAATTACCAAAATACCCTTAG
* * * * * *
40770152 TCTGTAAAATTGCTAAAATACCCCTGG
1 TTTATAAAATTACCAAAATACCCTTAG
* * * *
40770179 TTTGTAAAATTACCGAAATACCCTCAA
1 TTTATAAAATTACCAAAATACCCTTAG
* *
40770206 TTTGTAAAATTACCAAAATACCCCT-G
1 TTTATAAAATTACCAAAATACCCTTAG
* * *
40770232 ATTTACAAAGTTA-CAGAAATACCCTTGAC
1 -TTTATAAAATTACCA-AAATACCCTT-AG
* *** * *
40770261 TTTCTAAAAATTATGGAAATACCATTGG
1 TTTAT-AAAATTACCAAAATACCCTTAG
**
40770289 TTTATAAAATTACTGAAATACCCTTAG
1 TTTATAAAATTACCAAAATACCCTTAG
* * * *
40770316 TTTTTAGATTTACCAAAACACCCTT
1 TTTATAAAATTACCAAAATACCCTT
40770341 GTACGATAAA
Statistics
Matches: 183, Mismatches: 50, Indels: 18
0.73 0.20 0.07
Matches are distributed among these distances:
26 22 0.12
27 139 0.76
28 7 0.04
29 15 0.08
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.31
Consensus pattern (27 bp):
TTTATAAAATTACCAAAATACCCTTAG
Found at i:40770403 original size:27 final size:27
Alignment explanation
Indices: 40770373--40770431 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
40770363 CCCCTATTAT
40770373 GTAAAAAGACCGTAA-AGCCCCTGTAGG
1 GTAAAAAGACCGTAATA-CCCCTGTAGG
** *
40770400 GTAAAGTGACCGTAATACCCCTGTATG
1 GTAAAAAGACCGTAATACCCCTGTAGG
40770427 GTAAA
1 GTAAA
40770432 TGACGAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 27 0.96
28 1 0.04
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.20
Consensus pattern (27 bp):
GTAAAAAGACCGTAATACCCCTGTAGG
Found at i:40771436 original size:52 final size:51
Alignment explanation
Indices: 40771358--40771474 Score: 218
Period size: 52 Copynumber: 2.3 Consensus size: 51
40771348 GAAGTGCAAA
40771358 GCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCGAAAAGG
1 GCTTATGCCCCAGTTTATTGAAAAGGGCTT-TGCCCCAGTTTACCGAAAAGG
40771410 GCTTATGCCCCAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCGAAAAGG
1 GCTTATGCCCCAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCGAAAAGG
40771461 GCTT-TGCCCCAGTT
1 GCTTATGCCCCAGTT
40771475 ATTAAAGAGG
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
50 10 0.15
51 25 0.38
52 30 0.46
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.28
Consensus pattern (51 bp):
GCTTATGCCCCAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCGAAAAGG
Found at i:40771449 original size:25 final size:26
Alignment explanation
Indices: 40771358--40771474 Score: 184
Period size: 26 Copynumber: 4.6 Consensus size: 26
40771348 GAAGTGCAAA
**
40771358 GCTTATGCCCCAGTTTATTGAAAAGG
1 GCTTATGCCCCAGTTTACCGAAAAGG
40771384 GCTTATGCCCCAGTTTACCGAAAAGG
1 GCTTATGCCCCAGTTTACCGAAAAGG
**
40771410 GCTTATGCCCCAGTTTATTGAAAAGG
1 GCTTATGCCCCAGTTTACCGAAAAGG
40771436 GCTT-TGCCCCAGTTTACCGAAAAGG
1 GCTTATGCCCCAGTTTACCGAAAAGG
40771461 GCTT-TGCCCCAGTT
1 GCTTATGCCCCAGTT
40771475 ATTAAAGAGG
Statistics
Matches: 85, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
25 33 0.39
26 52 0.61
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.28
Consensus pattern (26 bp):
GCTTATGCCCCAGTTTACCGAAAAGG
Found at i:40771678 original size:42 final size:42
Alignment explanation
Indices: 40771619--40771710 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
40771609 TAGTCTCCCC
* ** *
40771619 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
40771661 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
40771703 AAATGGGC
1 AAATGGGC
40771711 CTAAGGGCCA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
Found at i:40771811 original size:31 final size:31
Alignment explanation
Indices: 40771734--40771812 Score: 149
Period size: 31 Copynumber: 2.5 Consensus size: 31
40771724 CGTTTACAGT
*
40771734 AAAGGCTTCGGCCCAATGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
40771765 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
40771796 AAAGGCTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
40771813 AACCGTTAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:40774136 original size:54 final size:53
Alignment explanation
Indices: 40774068--40774196 Score: 204
Period size: 54 Copynumber: 2.4 Consensus size: 53
40774058 ATTACCAAAG
* *
40774068 TACCTCGATTTATAGAATTACTGTTTTACCCTTAATTTACAGAATTATTGTTT
1 TACCTCGATTTATAGAATTACTGTTTTACCCTTAATTTACAGAATTACTATTT
*
40774121 TACCCTCGATTTATAGAATTACTGTTTTACCCTTGATTTACAGAATTACTATTT
1 TA-CCTCGATTTATAGAATTACTGTTTTACCCTTAATTTACAGAATTACTATTT
* *
40774175 TACCTCGATTTACAAAATTACT
1 TACCTCGATTTATAGAATTACT
40774197 AAAACCCTTG
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
53 20 0.29
54 50 0.71
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.44
Consensus pattern (53 bp):
TACCTCGATTTATAGAATTACTGTTTTACCCTTAATTTACAGAATTACTATTT
Found at i:40774197 original size:26 final size:27
Alignment explanation
Indices: 40774070--40774196 Score: 175
Period size: 27 Copynumber: 4.7 Consensus size: 27
40774060 TACCAAAGTA
*
40774070 CCTCGATTTATAGAATTACTGTTTTAC
1 CCTCGATTTACAGAATTACTGTTTTAC
** *
40774097 CCTTAATTTACAGAATTATTGTTTTAC
1 CCTCGATTTACAGAATTACTGTTTTAC
*
40774124 CCTCGATTTATAGAATTACTGTTTTAC
1 CCTCGATTTACAGAATTACTGTTTTAC
* *
40774151 CCTTGATTTACAGAATTACTATTTTA-
1 CCTCGATTTACAGAATTACTGTTTTAC
*
40774177 CCTCGATTTACAAAATTACT
1 CCTCGATTTACAGAATTACT
40774197 AAAACCCTTG
Statistics
Matches: 87, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
26 18 0.21
27 69 0.79
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.44
Consensus pattern (27 bp):
CCTCGATTTACAGAATTACTGTTTTAC
Found at i:40774243 original size:26 final size:25
Alignment explanation
Indices: 40774213--40774334 Score: 109
Period size: 26 Copynumber: 4.7 Consensus size: 25
40774203 CTTGGTTTAC
*
40774213 AAATTACCAAAATACCTCGATCAGTA
1 AAATTACCAAAATACC-CGATCTGTA
*
40774239 AAATTACCAAAATACCCTAGTCTGTA
1 AAATTACCAAAATACCCGA-TCTGTA
* * * *
40774265 AAATTGCTAAAATACCCTGGTTTGTA
1 AAATTACCAAAATACCC-GATCTGTA
* * * *
40774291 AAATTATCGAAATACCCTCAATTTGTA
1 AAATTACCAAAATA-CC-CGATCTGTA
40774318 AAATTACCAAAATACCC
1 AAATTACCAAAATACCC
40774335 CTATTTACAA
Statistics
Matches: 77, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
25 3 0.04
26 53 0.69
27 20 0.26
28 1 0.01
ACGTcount: A:0.43, C:0.21, G:0.08, T:0.28
Consensus pattern (25 bp):
AAATTACCAAAATACCCGATCTGTA
Found at i:40774278 original size:52 final size:53
Alignment explanation
Indices: 40774213--40774334 Score: 140
Period size: 52 Copynumber: 2.3 Consensus size: 53
40774203 CTTGGTTTAC
*
40774213 AAATTACCAAAATA-CCTCGATCAGTAAAATTACCAAAATACCCT-AGTCTGTA
1 AAATTACCAAAATACCCT-GATCAGTAAAATTACCAAAATACCCTCAATCTGTA
* * * ** * * *
40774265 AAATTGCTAAAATACCCTGGTTTGTAAAATTATCGAAATACCCTCAATTTGTA
1 AAATTACCAAAATACCCTGATCAGTAAAATTACCAAAATACCCTCAATCTGTA
40774318 AAATTACCAAAATACCC
1 AAATTACCAAAATACCC
40774335 CTATTTACAA
Statistics
Matches: 57, Mismatches: 11, Indels: 3
0.80 0.15 0.04
Matches are distributed among these distances:
52 33 0.58
53 24 0.42
ACGTcount: A:0.43, C:0.21, G:0.08, T:0.28
Consensus pattern (53 bp):
AAATTACCAAAATACCCTGATCAGTAAAATTACCAAAATACCCTCAATCTGTA
Found at i:40774321 original size:27 final size:27
Alignment explanation
Indices: 40774285--40774387 Score: 82
Period size: 27 Copynumber: 3.8 Consensus size: 27
40774275 AATACCCTGG
40774285 TTTGTAAAATTATCGAAATACCCTCAA
1 TTTGTAAAATTATCGAAATACCCTCAA
* * *
40774312 TTTGTAAAATTACCAAAATACCC-CTA
1 TTTGTAAAATTATCGAAATACCCTCAA
** * ** * *
40774338 TTTACAAAGTTAAAGAAATACCCTTAC
1 TTTGTAAAATTATCGAAATACCCTCAA
* *
40774365 TTTCTAAAAATTATGGAAATACC
1 TTTGT-AAAATTATCGAAATACC
40774388 ATTGGTTTAC
Statistics
Matches: 57, Mismatches: 17, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
26 19 0.33
27 24 0.42
28 14 0.25
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (27 bp):
TTTGTAAAATTATCGAAATACCCTCAA
Found at i:40774410 original size:27 final size:27
Alignment explanation
Indices: 40774371--40774422 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
40774361 TTACTTTCTA
40774371 AAAATTATGGAAATACCATTGGTTTAC
1 AAAATTATGGAAATACCATTGGTTTAC
*
40774398 AAAATTACT-GAAATACCCTTGGTTT
1 AAAATTA-TGGAAATACCATTGGTTT
40774423 GTAGATTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.35
Consensus pattern (27 bp):
AAAATTATGGAAATACCATTGGTTTAC
Found at i:40774506 original size:27 final size:27
Alignment explanation
Indices: 40774463--40774528 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
40774453 AAATGACTAA
*
40774463 AATACCCCTATTA-GGTAAAAAGACCGT
1 AATACCCCT-GTAGGGTAAAAAGACCGT
**
40774490 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGTAGGGTAAAAAGACCGT
40774517 AATACCCCTGTA
1 AATACCCCTGTA
40774529 TGGTTAAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
26 3 0.09
27 29 0.88
28 1 0.03
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (27 bp):
AATACCCCTGTAGGGTAAAAAGACCGT
Found at i:40775428 original size:24 final size:25
Alignment explanation
Indices: 40775339--40775458 Score: 154
Period size: 24 Copynumber: 4.8 Consensus size: 25
40775329 GAGGAAGTGC
*
40775339 AAAAGGGCTTATGCCCTAGTTTATTG
1 AAAAGGGCTT-TGCCCCAGTTTATTG
* **
40775365 AAAAGGGCTTATGCCCCAATTTACCG
1 AAAAGGGCTT-TGCCCCAGTTTATTG
40775391 AAAAGGGCTTTGCCCCAGTTTATTG
1 AAAAGGGCTTTGCCCCAGTTTATTG
**
40775416 AAAA-GGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTATTG
40775440 AAAAGGGC-TTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
40775459 ATTAAAGAGG
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
24 33 0.39
25 19 0.23
26 32 0.38
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.28
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATTG
Found at i:40775662 original size:42 final size:42
Alignment explanation
Indices: 40775603--40775694 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
40775593 TAGTCTCCCC
* * * *
40775603 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGGCATTACATGTGATAATG
40775645 AAATGGGCTTGCATACATCCATTGGCATTACATGTGATAATG
1 AAATGGGCTTGCATACATCCATTGGCATTACATGTGATAATG
40775687 AAATGGGC
1 AAATGGGC
40775695 CTAAGGGCCA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGGCATTACATGTGATAATG
Found at i:40775753 original size:31 final size:31
Alignment explanation
Indices: 40775718--40775787 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
40775708 CGTTTACAGT
40775718 AAAGGCTTCGGCCCAATGATATGATTTATGA
1 AAAGGCTTCGGCCCAATGATATGATTTATGA
*
40775749 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAATGATATGATTTATGA
40775780 AAAGGCTT
1 AAAGGCTT
40775788 TGGCTGTAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAATGATATGATTTATGA
Found at i:40777229 original size:40 final size:41
Alignment explanation
Indices: 40777169--40777295 Score: 156
Period size: 40 Copynumber: 3.2 Consensus size: 41
40777159 CAGAATACAA
40777169 CCGGATA-TAACCACGT-GCACGAATGCCTTCGGGTCTTAGC
1 CCGGATAGTAACCAC-TAGCACGAATGCCTTCGGGTCTTAGC
* *
40777209 CCGGATAG-AACGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATAGTAACCACTAGCACGAATGCCTTCGGGTCTTAGC
* * *
40777249 GCGGAT-GTAGCCACTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATAGTAACCACTAGCACGAA-TGCCTTCGGGTCTTAGC
40777289 CCGGATA
1 CCGGATA
40777296 TAATTTCCAG
Statistics
Matches: 75, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
39 4 0.05
40 71 0.95
ACGTcount: A:0.23, C:0.29, G:0.26, T:0.22
Consensus pattern (41 bp):
CCGGATAGTAACCACTAGCACGAATGCCTTCGGGTCTTAGC
Found at i:40789009 original size:29 final size:29
Alignment explanation
Indices: 40788977--40789111 Score: 155
Period size: 29 Copynumber: 4.7 Consensus size: 29
40788967 ATACCCTCCG
** * *
40788977 AGCTCGCACACCCAGTGCCGTATTTTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
* * * *
40789006 AGCTTGCACACATAGTGTCATATTTTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
*
40789035 AGCAT-GCACACTTAGTGCCTTATATTTCC
1 AGC-TCGCACACTTAGTGCCATATATTTCC
*
40789064 AGCACGCACACTTAGTGCCATATATTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
*
40789093 AGCACGCACACTTAGTGCC
1 AGCTCGCACACTTAGTGCC
40789112 GATCTCGTCA
Statistics
Matches: 93, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
29 92 0.99
30 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.30
Consensus pattern (29 bp):
AGCTCGCACACTTAGTGCCATATATTTCC
Found at i:40789044 original size:58 final size:58
Alignment explanation
Indices: 40788923--40789112 Score: 179
Period size: 58 Copynumber: 3.3 Consensus size: 58
40788913 TACTCGATTT
* * * *** *
40788923 CGCACACTTAGTGCCACGTA-ATTT-AAGCCCGCACACACAGTGCCATA-CCCTCCGAGCT
1 CGCACACTTAGTG-C-CGTATATTTCCAGCACGCACACATAGTGCCATATATTTCC-AGCA
** * ** * *
40788981 CGCACACCCAGTGCCGTATTTTTCCAGCTTGCACACATAGTGTCATATTTTTCCAGCA
1 CGCACACTTAGTGCCGTATATTTCCAGCACGCACACATAGTGCCATATATTTCCAGCA
* * *
40789039 TGCACACTTAGTGCCTTATATTTCCAGCACGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCGTATATTTCCAGCACGCACACATAGTGCCATATATTTCCAGCA
40789097 CGCACACTTAGTGCCG
1 CGCACACTTAGTGCCG
40789113 ATCTCGTCAC
Statistics
Matches: 105, Mismatches: 24, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
56 4 0.04
57 4 0.04
58 94 0.90
59 3 0.03
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.26
Consensus pattern (58 bp):
CGCACACTTAGTGCCGTATATTTCCAGCACGCACACATAGTGCCATATATTTCCAGCA
Found at i:40790908 original size:40 final size:40
Alignment explanation
Indices: 40790850--40791109 Score: 229
Period size: 40 Copynumber: 6.5 Consensus size: 40
40790840 TGATAACCGA
* * *
40790850 GCTAAGTCCC-AAGAGCATTTGAGCTAGTGGCTAATTCCGG
1 GCTAAGTCCCGAAG-GCATTTGTGCAAGTAGCTAATTCCGG
* * *
40790890 GCTAAGTCCTGAAGGCATTCGTGCGAGCTA-CT-ATATCCGG
1 GCTAAGTCCCGAAGGCATTTGTGCAAG-TAGCTAAT-TCCGG
*
40790930 GCTAAGTCCCGAAGGCGTTTGTGC--G-AGCTATTATATCCGG
1 GCTAAGTCCCGAAGGCATTTGTGCAAGTAGCTA--AT-TCCGG
* * *
40790970 GCTAAGTCCCGAAGGCATTTGTGCGAGTTA--TTATACCGG
1 GCTAAGTCCCGAAGGCATTTGTGCAAG-TAGCTAATTCCGG
*
40791009 GCTAAGTCCCGAAGGCATTTGTGCAAGTTACCATAA--CCGG
1 GCTAAGTCCCGAAGGCATTTGTGCAAG-TAGC-TAATTCCGG
*
40791049 GCTAAGTCCCGAAGGCATTTGTGCAAGTTACCATAA--CCGG
1 GCTAAGTCCCGAAGGCATTTGTGCAAG-TAGC-TAATTCCGG
40791089 GCTAAGTCCCGAAGGCATTTG
1 GCTAAGTCCCGAAGGCATTTG
40791110 AGCTAGTGGC
Statistics
Matches: 193, Mismatches: 13, Indels: 28
0.82 0.06 0.12
Matches are distributed among these distances:
36 1 0.01
37 2 0.01
38 1 0.01
39 35 0.18
40 145 0.75
41 4 0.02
42 4 0.02
44 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
GCTAAGTCCCGAAGGCATTTGTGCAAGTAGCTAATTCCGG
Found at i:40791049 original size:79 final size:79
Alignment explanation
Indices: 40790886--40791109 Score: 322
Period size: 79 Copynumber: 2.8 Consensus size: 79
40790876 GTGGCTAATT
* * * *
40790886 CCGGGCTAAGTCCTGAAGGCATTCGTGCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCGTTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-CCGGGCTAAGTCCCGAAGGCATTTG
* ** *
40790951 TGCGAGCTATTATAT
65 TGCAAGCTACCATAA
*
40790966 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTATACCGGGCTAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATACCGGGCTAAGTCCCGAAGGCATTTGT
*
40791031 GCAAGTTACCATAA
66 GCAAGCTACCATAA
* *
40791045 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACCATAACCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT-ACCGGGCTAAGTCCCGAAGGCATTTG
40791110 AGCTAGTGGC
Statistics
Matches: 130, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
79 69 0.53
80 61 0.47
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATACCGGGCTAAGTCCCGAAGGCATTTGT
GCAAGCTACCATAA
Found at i:40791131 original size:119 final size:120
Alignment explanation
Indices: 40790842--40791142 Score: 376
Period size: 119 Copynumber: 2.5 Consensus size: 120
40790832 TGTTCGAATG
* *
40790842 ATAACCGAGCTAAGTCCC-AAGAGCATTTGAGCTAGTGGCTA-ATTCCGGGCTAAGTCCTGAAGG
1 ATAACCGGGCTAAGTCCCGAAG-GCATTTGAGCTAGTGGCTATA-TCCGGGCTAAGTCCCGAAGG
* * * * * **
40790905 CATTCGTGCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCGTTTGTGCGAGCTATT
64 CATTCGTGCAAGCTACCATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGCTACC
* * * ***
40790962 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTATA-CCGGGCTAAGTCCCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCTATATCCGGGCTAAGTCCCGAAGGCA
* * *
40791026 TTTGTGCAAGTTACCATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACC
66 TTCGTGCAAGCTACCATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGCTACC
**
40791081 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCTATATCC-GGCTAAACCCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCTATATCCGGGCTAAGTCCCGAAGG
40791143 TACTTGGTTT
Statistics
Matches: 152, Mismatches: 26, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
119 116 0.76
120 32 0.21
121 4 0.03
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (120 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCTATATCCGGGCTAAGTCCCGAAGGCA
TTCGTGCAAGCTACCATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGCTACC
Found at i:40796094 original size:69 final size:68
Alignment explanation
Indices: 40795987--40796169 Score: 226
Period size: 69 Copynumber: 2.6 Consensus size: 68
40795977 AGACCATAGT
* *
40795987 TGGGGCTATGGCAACATATGAAG-CCCACCGAGACAATAAACATGGGATCATATTATGTAAGACC
1 TGGGGCTATGGCAACATATGAAGTCCCA-AG-GAAAATAAACATGGGATCATATTATGTAAGACC
*
40796051 ACATC
64 ACAAC
* * *
40796056 TGGGGCTATGGCAACATATAAAGTCCGCAAGGATAATAAACATGGGATCTTATTATGTAAGACCA
1 TGGGGCTATGGCAACATATGAAGTCC-CAAGGAAAATAAACATGGGATCATATTATGTAAGACCA
40796121 CAAC
65 CAAC
* * *
40796125 TAGGGCCATGGCAACATTTGAAGTCCACTAA-GAAAATAAACATGG
1 TGGGGCTATGGCAACATATGAAGTCC-C-AAGGAAAATAAACATGG
40796170 CAGCACATAG
Statistics
Matches: 100, Mismatches: 11, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
69 93 0.93
70 5 0.05
71 2 0.02
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.21
Consensus pattern (68 bp):
TGGGGCTATGGCAACATATGAAGTCCCAAGGAAAATAAACATGGGATCATATTATGTAAGACCAC
AAC
Found at i:40797532 original size:25 final size:25
Alignment explanation
Indices: 40797504--40797556 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
40797494 CTATTATACA
*
40797504 GCTCATATAAGCTTCCCGTTACATG
1 GCTCACATAAGCTTCCCGTTACATG
* * * *
40797529 GCTCACATGAGCTTTCTGTTATATG
1 GCTCACATAAGCTTCCCGTTACATG
40797554 GCT
1 GCT
40797557 TGAGAGAGAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (25 bp):
GCTCACATAAGCTTCCCGTTACATG
Found at i:40800986 original size:47 final size:47
Alignment explanation
Indices: 40800932--40801125 Score: 280
Period size: 47 Copynumber: 4.1 Consensus size: 47
40800922 TTAGGATTTT
** * *
40800932 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
40800979 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
40801026 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * * *
40801073 ATGTGGTGAATATGAACATGCATATATGTGGTAAAGCCAAATGGCTA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
40801120 ATGTGA
1 ATGTGA
40801126 AATATGTATG
Statistics
Matches: 132, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 132 1.00
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:40801032 original size:22 final size:22
Alignment explanation
Indices: 40800961--40801032 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
40800951 GTATATATGA
40800961 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCCGAATGGCCAATGT
* * *
40800983 GATGAATG-TGAACAT-GCATATATGT
1 GAT-AAGGCCG-A-ATGGC-CA-ATGT
40801008 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCCGAATGGCCAATGT
40801030 GAT
1 GAT
40801033 GAATGTGAGC
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
22 11 0.30
23 9 0.24
24 9 0.24
25 8 0.22
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (22 bp):
GATAAGGCCGAATGGCCAATGT
Found at i:40801081 original size:25 final size:25
Alignment explanation
Indices: 40801006--40801081 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 25
40800996 ATGCATATAT
40801006 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
* * * *
40801031 ATGA-ATGTG-AGCAT-G-CATATGT-
1 GTGATAAG-GCCGAATGGCCA-ATGTG
40801053 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
40801078 GTGA
1 GTGA
40801082 ATATGAACAT
Statistics
Matches: 36, Mismatches: 8, Indels: 14
0.62 0.14 0.24
Matches are distributed among these distances:
22 6 0.17
23 10 0.28
24 10 0.28
25 10 0.28
ACGTcount: A:0.29, C:0.13, G:0.34, T:0.24
Consensus pattern (25 bp):
GTGATAAGGCCGAATGGCCAATGTG
Found at i:40801253 original size:98 final size:96
Alignment explanation
Indices: 40801096--40801279 Score: 307
Period size: 98 Copynumber: 1.9 Consensus size: 96
40801086 GAACATGCAT
*
40801096 ATATGTGGTAAAGCCAAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGA
1 ATATGTGGTAAAGCCAAATGGCTAATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGA
40801161 ATGGCTAATGTGAAATATGTATGAGATATGC
66 ATGGCTAATGTGAAATATGTATGAGATATGC
*
40801192 ATATGTGGTAAAGCCGAATGG-TCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGC
1 ATATGTGGTAAAGCCAAATGGCT-AATGTG-AA-ATATATATGAGATATGTATATGTGGTAAAGC
*
40801256 CGAATGGCTAGTGTGAAATATGTA
63 CGAATGGCTAATGTGAAATATGTA
40801280 GGCGATGTGC
Statistics
Matches: 82, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
95 1 0.01
96 26 0.32
97 2 0.02
98 53 0.65
ACGTcount: A:0.36, C:0.07, G:0.26, T:0.30
Consensus pattern (96 bp):
ATATGTGGTAAAGCCAAATGGCTAATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGA
ATGGCTAATGTGAAATATGTATGAGATATGC
Found at i:40801295 original size:50 final size:48
Alignment explanation
Indices: 40801095--40801279 Score: 300
Period size: 48 Copynumber: 3.8 Consensus size: 48
40801085 TGAACATGCA
*
40801095 TATATGTGGTAAAGCCAAATGGCTAATGTGAAATATGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
40801143 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
* *
40801191 CATATGTGGTAAAGCCGAATGG-TCAATGTGAAATATATATATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCT-AATGTG-AA-ATATGTATGAGATATG
*
40801241 TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTA
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTA
40801280 GGCGATGTGC
Statistics
Matches: 127, Mismatches: 6, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
47 1 0.01
48 80 0.63
49 4 0.03
50 41 0.32
51 1 0.01
ACGTcount: A:0.36, C:0.07, G:0.26, T:0.31
Consensus pattern (48 bp):
TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
Found at i:40801534 original size:37 final size:37
Alignment explanation
Indices: 40801426--40801534 Score: 182
Period size: 37 Copynumber: 2.9 Consensus size: 37
40801416 GGAAATATAT
*
40801426 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
40801463 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* * *
40801500 TCCGGGTAAGACCCGATAACTTCATGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
40801535 CGTCTGAGCT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:40805386 original size:34 final size:34
Alignment explanation
Indices: 40805341--40805406 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
40805331 CTTAGGCCCC
*
40805341 ACTGATACTGTTACTGAAATAGGCTCAGGCCCAG
1 ACTGATACTGTTACTGAAATAGGCTAAGGCCCAG
* *
40805375 ACTGTTACTGTTACTGAAATTGGCTAAGGCCC
1 ACTGATACTGTTACTGAAATAGGCTAAGGCCC
40805407 TAACTGAGAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (34 bp):
ACTGATACTGTTACTGAAATAGGCTAAGGCCCAG
Found at i:40815805 original size:15 final size:14
Alignment explanation
Indices: 40815767--40815809 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
40815757 TAGCCGTGCG
* *
40815767 TTCTATTTTGCTTT
1 TTCTCTTTTTCTTT
40815781 TTCTCTTTTTCTTT
1 TTCTCTTTTTCTTT
*
40815795 TTCTTTCTTTTCTTT
1 TTCTCT-TTTTCTTT
40815810 GATAAATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 17 0.68
15 8 0.32
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (14 bp):
TTCTCTTTTTCTTT
Found at i:40818079 original size:25 final size:25
Alignment explanation
Indices: 40818050--40818118 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 25
40818040 CTCATGTGAT
* *
40818050 CATACCAATTTATAGCTTGTG-AGAG
1 CATACCAATTTATAGCTCGAGTA-AG
*
40818075 CATACCAATCTATAGCTCGAGTAAG
1 CATACCAATTTATAGCTCGAGTAAG
* *
40818100 CATACCAATTCACAGCTCG
1 CATACCAATTTATAGCTCG
40818119 TATGAGCATA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
25 36 0.97
26 1 0.03
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (25 bp):
CATACCAATTTATAGCTCGAGTAAG
Found at i:40818126 original size:25 final size:25
Alignment explanation
Indices: 40818050--40818129 Score: 76
Period size: 25 Copynumber: 3.2 Consensus size: 25
40818040 CTCATGTGAT
* *
40818050 CATACCAATTTATAGCTTGTGA-GAG
1 CATACCAATTCATAGCTCGT-ATGAG
*
40818075 CATACCAA-TCTATAGCTCG-AGTAAG
1 CATACCAATTC-ATAGCTCGTA-TGAG
*
40818100 CATACCAATTCACAGCTCGTATGAG
1 CATACCAATTCATAGCTCGTATGAG
40818125 CATAC
1 CATAC
40818130 ATGTACATGA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
23 1 0.02
24 1 0.02
25 40 0.89
26 3 0.07
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (25 bp):
CATACCAATTCATAGCTCGTATGAG
Found at i:40823440 original size:19 final size:20
Alignment explanation
Indices: 40823418--40823462 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
40823408 ATAACAGAAT
*
40823418 AATTATTTA-TAAACAGATC
1 AATTATTTATTAAACAGATA
* *
40823437 AATTTTTTATTTAACAGATA
1 AATTATTTATTAAACAGATA
40823457 AATTAT
1 AATTAT
40823463 ATTTTGAAGT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (20 bp):
AATTATTTATTAAACAGATA
Found at i:40824068 original size:17 final size:18
Alignment explanation
Indices: 40824034--40824070 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
40824024 ATTAAATATT
*
40824034 TTATATTTGTTATCATAA
1 TTATATTCGTTATCATAA
40824052 TTATATTCGTT-TCATAA
1 TTATATTCGTTATCATAA
40824069 TT
1 TT
40824071 TTTTAAGCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.30, C:0.08, G:0.05, T:0.57
Consensus pattern (18 bp):
TTATATTCGTTATCATAA
Found at i:40828406 original size:22 final size:25
Alignment explanation
Indices: 40828378--40828433 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
40828368 TTGTTAACAT
40828378 ATTTTATTCA-TTTT-TT-TACACA
1 ATTTTATTCATTTTTATTGTACACA
40828400 ATTTTATTCATTTTTATTGTACACA
1 ATTTTATTCATTTTTATTGTACACA
*
40828425 AATTTATTC
1 ATTTTATTC
40828434 TTCGTCTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 10 0.33
23 4 0.13
24 2 0.07
25 14 0.47
ACGTcount: A:0.29, C:0.12, G:0.02, T:0.57
Consensus pattern (25 bp):
ATTTTATTCATTTTTATTGTACACA
Found at i:40833091 original size:17 final size:17
Alignment explanation
Indices: 40833069--40833102 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40833059 AAAATTATAT
*
40833069 TTTAAAAATGAAAAATA
1 TTTAAAAATCAAAAATA
*
40833086 TTTAAAATTCAAAAATA
1 TTTAAAAATCAAAAATA
40833103 AAGAATAGTT
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:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (17 bp):
TTTAAAAATCAAAAATA
Found at i:40833806 original size:27 final size:23
Alignment explanation
Indices: 40833776--40833836 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 23
40833766 GAATTTTGGA
40833776 ATTTTTTATATTATAAAATTATTTTTT
1 ATTTTTTA-ATT-T-AAATT-TTTTTT
*
40833803 ATTTTTTGAATTTTAATTTTTTTT
1 ATTTTTT-AATTTAAATTTTTTTT
40833827 ATTTTTTAAT
1 ATTTTTTAAT
40833837 AACTTTTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
23 3 0.09
24 13 0.41
25 4 0.12
26 1 0.03
27 10 0.31
28 1 0.03
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (23 bp):
ATTTTTTAATTTAAATTTTTTTT
Found at i:40837217 original size:29 final size:29
Alignment explanation
Indices: 40837185--40837241 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
40837175 TCACATATTT
40837185 AACTTTCACATACTTTTTTTAAATAATAA
1 AACTTTCACATACTTTTTTTAAATAATAA
40837214 AACTTTCACATACTTTTTTTAAATAATA
1 AACTTTCACATACTTTTTTTAAATAATA
40837242 TTTTCACATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.40, C:0.14, G:0.00, T:0.46
Consensus pattern (29 bp):
AACTTTCACATACTTTTTTTAAATAATAA
Found at i:40837238 original size:26 final size:28
Alignment explanation
Indices: 40837185--40837254 Score: 99
Period size: 29 Copynumber: 2.5 Consensus size: 28
40837175 TCACATATTT
40837185 AACTTTCACATACTTTTTTTAAATAATAA
1 AACTTTCACATACTTTTTTT-AATAATAA
40837214 AACTTTCACATACTTTTTTT-A-AATAA
1 AACTTTCACATACTTTTTTTAATAATAA
* *
40837240 TATTTTCACATACTT
1 AACTTTCACATACTT
40837255 ATAATTTATC
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
26 18 0.46
27 1 0.03
29 20 0.51
ACGTcount: A:0.37, C:0.16, G:0.00, T:0.47
Consensus pattern (28 bp):
AACTTTCACATACTTTTTTTAATAATAA
Found at i:40837327 original size:65 final size:65
Alignment explanation
Indices: 40837247--40837375 Score: 240
Period size: 65 Copynumber: 2.0 Consensus size: 65
40837237 TAATATTTTC
40837247 ACATACTTATAATTTATCGATAATTTTTATTGTATGAAATATTTTATTACATAAACTTAGATTCA
1 ACATACTTATAATTTATCGATAATTTTTATTGTATGAAATATTTTATTACATAAACTTAGATTCA
* *
40837312 ACATACTTATAATTTATGGATAATTTTTATTGTATGAAATATTTTATTACATAAATTTAGATTC
1 ACATACTTATAATTTATCGATAATTTTTATTGTATGAAATATTTTATTACATAAACTTAGATTC
40837376 TTAGTTAAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 62 1.00
ACGTcount: A:0.38, C:0.08, G:0.07, T:0.47
Consensus pattern (65 bp):
ACATACTTATAATTTATCGATAATTTTTATTGTATGAAATATTTTATTACATAAACTTAGATTCA
Found at i:40841906 original size:3 final size:3
Alignment explanation
Indices: 40841900--40841931 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
40841890 AGTAATGTTG
40841900 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
40841932 TAAGTTGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:40863283 original size:28 final size:28
Alignment explanation
Indices: 40863218--40863318 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
40863208 ATAGTGAATC
*
40863218 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
40863247 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
40863275 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
40863305 CGCACACTTAGTGC
1 CGCACACTTAGTGC
40863319 CATACCCTTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:40863367 original size:29 final size:29
Alignment explanation
Indices: 40863306--40863436 Score: 165
Period size: 29 Copynumber: 4.5 Consensus size: 29
40863296 TTTTAAACCC
*** *
40863306 GCACACTTAGTGCCATACCCTTCGAGC-T
1 GCACACTTAGTGCCATATATTTCCAGCAT
** *
40863334 CGCACACCCAGTGCCGTATATTTCCAGCAT
1 -GCACACTTAGTGCCATATATTTCCAGCAT
*
40863364 GCACACTTAGTGCCATATATTTCCAGTAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
*
40863393 GCACACTTAGTGCCATATATTTTCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
40863422 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
40863437 ATCTCGTCAC
Statistics
Matches: 88, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
29 87 0.99
30 1 0.01
ACGTcount: A:0.25, C:0.31, G:0.16, T:0.28
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:40866152 original size:29 final size:29
Alignment explanation
Indices: 40866120--40866179 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
40866110 AATAGTCATG
40866120 TAGATACAATTTATATAATATCAAAGCAT
1 TAGATACAATTTATATAATATCAAAGCAT
40866149 TAGATACAATTTATATAATATCAAAGCAT
1 TAGATACAATTTATATAATATCAAAGCAT
40866178 TA
1 TA
40866180 AAAGAATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.35
Consensus pattern (29 bp):
TAGATACAATTTATATAATATCAAAGCAT
Found at i:40871617 original size:48 final size:50
Alignment explanation
Indices: 40871544--40871651 Score: 175
Period size: 48 Copynumber: 2.2 Consensus size: 50
40871534 TACAAGATAA
* *
40871544 ATATATATATGTGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
40871594 ATATGTATATGT-T-GTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
40871642 ATGTGTATAT
1 ATATGTATAT
40871652 ATTATGGCCG
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
48 43 0.78
49 1 0.02
50 11 0.20
ACGTcount: A:0.34, C:0.06, G:0.26, T:0.34
Consensus pattern (50 bp):
ATATGTATATGTGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
Found at i:40871835 original size:37 final size:37
Alignment explanation
Indices: 40871785--40871856 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
40871775 GAAATATATT
*
40871785 CCGGGTAAGACCCGATGGCTACGTGTGGAGATTATGC
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGC
*
40871822 CCGGGTAAGACCCGATGACTACGTGTGGGGATTAT
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTAT
40871857 TCGAGTTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.22, C:0.21, G:0.35, T:0.22
Consensus pattern (37 bp):
CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGC
Found at i:40873422 original size:42 final size:42
Alignment explanation
Indices: 40873360--40873821 Score: 195
Period size: 48 Copynumber: 10.2 Consensus size: 42
40873350 AACTATTGTT
* *
40873360 TTACAC-AAAGTCTCACATCGATGCCATGTCCCAGACATGGTC
1 TTACACGAAA-TCTCATATCGATGCCATATCCCAGACATGGTC
* * **
40873402 TTATACGAAATCACATATCGATGCCGCATCCCAGACATGGTC
1 TTACACGAAATCTCATATCGATGCCATATCCCAGACATGGTC
* * * * * *
40873444 TTACACGAAATTTCATACCAAAGCCATATCCTAGATATGGTC
1 TTACACGAAATCTCATATCGATGCCATATCCCAGACATGGTC
* *
40873486 TTACACGTAATCTCATATCGATGCCGATGTCATATCCCAGATATGGTC
1 TTACACGAAATCTCATATCGATG-C-----CATATCCCAGACATGGTC
* * *
40873534 TTACAC-AAGATCTCATATTGATGCTGATGCCATATCTCAGATATAGTC
1 TTACACGAA-ATCTC--A-T-AT-C-GATGCCATATCCCAGACATGGTC
* *
40873582 TTACAC-AGGATCTCATATCGATGCTGATGCCATATCCCAGATATGGTC
1 TTACACGA-AATCTC--AT--AT-C-GATGCCATATCCCAGACATGGTC
* * *
40873630 TTACAC-AGGATCTCATATTGATGCCGATATCATATCCCAGATATGGTC
1 TTACACGA-AATCTCATATCGATG-C-----CATATCCCAGACATGGTC
* *
40873678 TTACAC-AAGATCTCATATCGATGCTGATGTCATATCCCAGA-TTGGCC
1 TTACACGAA-ATCTCATATCGATGC------CATATCCCAGACATGGTC
** *
40873725 TTACAC-AAGATCTCATATCGATGCTGATGCCATATCCTGGATATGGTC
1 TTACACGAA-ATCTC--AT--AT-C-GATGCCATATCCCAGACATGGTC
** *
40873773 TTACAC-AGGGTCTCATATCGATGCCATGTCCCA-AGCATGGTC
1 TTACACGA-AATCTCATATCGATGCCATATCCCAGA-CATGGTC
40873815 TTACACG
1 TTACACG
40873822 TATCACGATG
Statistics
Matches: 342, Mismatches: 44, Indels: 67
0.75 0.10 0.15
Matches are distributed among these distances:
41 1 0.00
42 109 0.32
43 6 0.02
44 4 0.01
46 4 0.01
47 30 0.09
48 168 0.49
49 2 0.01
50 1 0.00
51 3 0.01
52 3 0.01
53 7 0.02
54 4 0.01
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (42 bp):
TTACACGAAATCTCATATCGATGCCATATCCCAGACATGGTC
Found at i:40873539 original size:48 final size:47
Alignment explanation
Indices: 40873468--40873796 Score: 399
Period size: 48 Copynumber: 6.9 Consensus size: 47
40873458 ATACCAAAGC
* *
40873468 CATATCCTAGATATGGTCTTACACGTAATCTCATATCGATGCCGATGT
1 CATATCCCAGATATGGTCTTACACG-AATCTCATATCGATGCTGATGT
* * *
40873516 CATATCCCAGATATGGTCTTACACAAGATCTCATATTGATGCTGATGC
1 CATATCCCAGATATGGTCTTACACGA-ATCTCATATCGATGCTGATGT
* * * *
40873564 CATATCTCAGATATAGTCTTACACAGGATCTCATATCGATGCTGATGC
1 CATATCCCAGATATGGTCTTACAC-GAATCTCATATCGATGCTGATGT
* * * *
40873612 CATATCCCAGATATGGTCTTACACAGGATCTCATATTGATGCCGATAT
1 CATATCCCAGATATGGTCTTACAC-GAATCTCATATCGATGCTGATGT
*
40873660 CATATCCCAGATATGGTCTTACACAAGATCTCATATCGATGCTGATGT
1 CATATCCCAGATATGGTCTTACACGA-ATCTCATATCGATGCTGATGT
* * *
40873708 CATATCCCAGAT-TGGCCTTACACAAGATCTCATATCGATGCTGATGC
1 CATATCCCAGATATGGTCTTACACGA-ATCTCATATCGATGCTGATGT
** **
40873755 CATATCCTGGATATGGTCTTACACAGGGTCTCATATCGATGC
1 CATATCCCAGATATGGTCTTACAC-GAATCTCATATCGATGC
40873797 CATGTCCCAA
Statistics
Matches: 247, Mismatches: 29, Indels: 10
0.86 0.10 0.03
Matches are distributed among these distances:
47 44 0.18
48 203 0.82
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (47 bp):
CATATCCCAGATATGGTCTTACACGAATCTCATATCGATGCTGATGT
Found at i:40873597 original size:96 final size:96
Alignment explanation
Indices: 40873466--40873802 Score: 493
Period size: 96 Copynumber: 3.5 Consensus size: 96
40873456 TCATACCAAA
*
40873466 GCCATATCCTAGATATGGTCTTACAC-GTAATCTCATATCGATGCCGATGTCATATCCCAGATAT
1 GCCATATCCTAGATATGGTCTTACACAG-GATCTCATATCGATGCCGATGTCATATCCCAGATAT
40873530 GGTCTTACACAAGATCTCATATTGATGCTGAT
65 GGTCTTACACAAGATCTCATATTGATGCTGAT
* * *
40873562 GCCATAT-CTCAGATATAGTCTTACACAGGATCTCATATCGATGCTGATGCCATATCCCAGATAT
1 GCCATATCCT-AGATATGGTCTTACACAGGATCTCATATCGATGCCGATGTCATATCCCAGATAT
* *
40873626 GGTCTTACACAGGATCTCATATTGATGCCGAT
65 GGTCTTACACAAGATCTCATATTGATGCTGAT
** * * *
40873658 ATCATATCCCAGATATGGTCTTACACAAGATCTCATATCGATGCTGATGTCATATCCCAGAT-TG
1 GCCATATCCTAGATATGGTCTTACACAGGATCTCATATCGATGCCGATGTCATATCCCAGATATG
* *
40873722 GCCTTACACAAGATCTCATATCGATGCTGAT
66 GTCTTACACAAGATCTCATATTGATGCTGAT
* *
40873753 GCCATATCCTGGATATGGTCTTACACAGGGTCTCATATCGATGCC-ATGTC
1 GCCATATCCTAGATATGGTCTTACACAGGATCTCATATCGATGCCGATGTC
40873803 CCAAGCATGG
Statistics
Matches: 215, Mismatches: 23, Indels: 8
0.87 0.09 0.03
Matches are distributed among these distances:
94 5 0.02
95 69 0.32
96 139 0.65
97 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.31
Consensus pattern (96 bp):
GCCATATCCTAGATATGGTCTTACACAGGATCTCATATCGATGCCGATGTCATATCCCAGATATG
GTCTTACACAAGATCTCATATTGATGCTGAT
Found at i:40873701 original size:144 final size:143
Alignment explanation
Indices: 40873466--40873797 Score: 531
Period size: 144 Copynumber: 2.3 Consensus size: 143
40873456 TCATACCAAA
* *
40873466 GCCATATCCTAGATATGGTCTTACAC-GTAATCTCATATCGATGCCGATGTCATATCCCAGATAT
1 GCCATATCCTAGATATGGTCTTACACAG-GATCTCATATCGATGCCGATATCATATCCCAGATAT
* * * *
40873530 GGTCTTACACAAGATCTCATATTGATGCTGATGCCATATCTCAGATATAGTCTTACACAGGATCT
65 GGTCTTACACAAGATCTCATATCGATGCTGATGCCATATCCCAGAT-TAGCCTTACACAAGATCT
40873595 CATATCGATGCTGAT
129 CATATCGATGCTGAT
* *
40873610 GCCATATCCCAGATATGGTCTTACACAGGATCTCATATTGATGCCGATATCATATCCCAGATATG
1 GCCATATCCTAGATATGGTCTTACACAGGATCTCATATCGATGCCGATATCATATCCCAGATATG
* *
40873675 GTCTTACACAAGATCTCATATCGATGCTGATGTCATATCCCAGATTGGCCTTACACAAGATCTCA
66 GTCTTACACAAGATCTCATATCGATGCTGATGCCATATCCCAGATTAGCCTTACACAAGATCTCA
40873740 TATCGATGCTGAT
131 TATCGATGCTGAT
* *
40873753 GCCATATCCTGGATATGGTCTTACACAGGGTCTCATATCGATGCC
1 GCCATATCCTAGATATGGTCTTACACAGGATCTCATATCGATGCC
40873798 ATGTCCCAAG
Statistics
Matches: 173, Mismatches: 14, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
143 71 0.41
144 101 0.58
145 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (143 bp):
GCCATATCCTAGATATGGTCTTACACAGGATCTCATATCGATGCCGATATCATATCCCAGATATG
GTCTTACACAAGATCTCATATCGATGCTGATGCCATATCCCAGATTAGCCTTACACAAGATCTCA
TATCGATGCTGAT
Found at i:40873875 original size:37 final size:36
Alignment explanation
Indices: 40873791--40873966 Score: 223
Period size: 37 Copynumber: 4.8 Consensus size: 36
40873781 GGTCTCATAT
*
40873791 CGATGCCAT-GTCCCAAGC-ATGGTCTTACACGTATCA
1 CGATGCCATAG-CCC-AGCTATGGTCTTACATGTATCA
*
40873827 CGATGCCATAGCCCTGCTATGGTCTTACATGTCATCA
1 CGATGCCATAGCCCAGCTATGGTCTTACATGT-ATCA
* *
40873864 TGATGCCATAGCCTAGCTATGGTCTTACATGTCATCA
1 CGATGCCATAGCCCAGCTATGGTCTTACATGT-ATCA
* *
40873901 CGATGCCATAGCCCAGCTATGGTCTTATACA-CTATTA
1 CGATGCCATAGCCCAGCTATGGTC-T-TACATGTATCA
40873938 CGATGCCATAGCCCAGCTATGGTCTTACA
1 CGATGCCATAGCCCAGCTATGGTCTTACA
40873967 CGTACCACAT
Statistics
Matches: 126, Mismatches: 9, Indels: 11
0.86 0.06 0.08
Matches are distributed among these distances:
35 6 0.05
36 26 0.21
37 88 0.70
38 2 0.02
39 4 0.03
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.28
Consensus pattern (36 bp):
CGATGCCATAGCCCAGCTATGGTCTTACATGTATCA
Found at i:40877293 original size:2 final size:2
Alignment explanation
Indices: 40877286--40877311 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40877276 ACATGCATGC
40877286 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
40877312 GACTAGTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40879329 original size:28 final size:28
Alignment explanation
Indices: 40879285--40879350 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
40879275 CTCGTATACT
40879285 AAGTGCCATACTCAATATATCGCACACC
1 AAGTGCCATACTCAATATATCGCACACC
* * * * *
40879313 AAGTGCCATTCTTAATATTTTGCACACT
1 AAGTGCCATACTCAATATATCGCACACC
40879341 AAGTGCCATA
1 AAGTGCCATA
40879351 TACATATATA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (28 bp):
AAGTGCCATACTCAATATATCGCACACC
Found at i:40881244 original size:24 final size:24
Alignment explanation
Indices: 40881205--40881282 Score: 86
Period size: 24 Copynumber: 3.2 Consensus size: 24
40881195 GCTCCTTTTG
*
40881205 AGCTGATGAACAGTAAGCTCTATCA
1 AGCTGA-GAACAGTAAGCTCTAACA
*
40881230 AGCTG-GAAACAGTAAGCTCTAACG
1 AGCTGAG-AACAGTAAGCTCTAACA
* * *
40881254 AGCTGAGAATAGTAAGCTCTTACG
1 AGCTGAGAACAGTAAGCTCTAACA
40881278 AGCTG
1 AGCTG
40881283 GTAAATCAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
23 1 0.02
24 40 0.85
25 6 0.13
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.22
Consensus pattern (24 bp):
AGCTGAGAACAGTAAGCTCTAACA
Done.