Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A04
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: 81554553
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2322942 characters in sequence are not A, C, G, or T
File 127 of 253
Found at i:40398526 original size:13 final size:13
Alignment explanation
Indices: 40398508--40398543 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
40398498 TCACAAAAAT
40398508 ATTAGA-GATTACA
1 ATTAGATGA-TACA
40398521 ATTAGATGATACA
1 ATTAGATGATACA
40398534 ATTAGATGAT
1 ATTAGATGAT
40398544 GAATAATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 20 0.91
14 2 0.09
ACGTcount: A:0.44, C:0.06, G:0.17, T:0.33
Consensus pattern (13 bp):
ATTAGATGATACA
Found at i:40403682 original size:24 final size:24
Alignment explanation
Indices: 40403650--40403720 Score: 124
Period size: 24 Copynumber: 3.0 Consensus size: 24
40403640 ATCAGAAGAA
40403650 GATTTAGGAGCTGATAAGGGAGAG
1 GATTTAGGAGCTGATAAGGGAGAG
*
40403674 GATTTAGGAGCTGATGAGGGAGAG
1 GATTTAGGAGCTGATAAGGGAGAG
*
40403698 GATTTAGGAGCTGATTAGGGAGA
1 GATTTAGGAGCTGATAAGGGAGA
40403721 ACGGTGTTGG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.31, C:0.04, G:0.42, T:0.23
Consensus pattern (24 bp):
GATTTAGGAGCTGATAAGGGAGAG
Found at i:40405260 original size:26 final size:26
Alignment explanation
Indices: 40405153--40405263 Score: 141
Period size: 27 Copynumber: 4.2 Consensus size: 26
40405143 AGGAAGCGTC
* *
40405153 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGTT
*
40405180 CTGGTGGCTCTGCCACATATATCTATT
1 CTGGTGGCTCTGCCACAT-TATCTGTT
*
40405207 CTGGTGGCTCTGCCATGATTATCTGTT
1 CTGGTGGCTCTGCCA-CATTATCTGTT
* *
40405234 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGTT
40405260 CTGG
1 CTGG
40405264 CAGCCATGCT
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
26 16 0.22
27 56 0.76
28 2 0.03
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGTT
Found at i:40411572 original size:24 final size:24
Alignment explanation
Indices: 40411540--40411592 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
40411530 AGGCTATCAA
40411540 GAGAAGATTTAGGAGCTGATAAGG
1 GAGAAGATTTAGGAGCTGATAAGG
* *
40411564 GAGAGGATTTAGGAGCTGATTAGG
1 GAGAAGATTTAGGAGCTGATAAGG
40411588 GAGAA
1 GAGAA
40411593 TGGTGTTGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.36, C:0.04, G:0.40, T:0.21
Consensus pattern (24 bp):
GAGAAGATTTAGGAGCTGATAAGG
Found at i:40413063 original size:27 final size:26
Alignment explanation
Indices: 40413023--40413133 Score: 150
Period size: 27 Copynumber: 4.2 Consensus size: 26
40413013 AGGAAGCGTC
* *
40413023 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGTT
40413050 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGTT
40413077 CTGGTGGCTCTGCCACGATTATCTGTT
1 CTGGTGGCTCTGCCAC-ATTATCTGTT
* * *
40413104 CTGGTGACTCTGTCACATAATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGTT
40413130 CTGG
1 CTGG
40413134 CAGCCATGCT
Statistics
Matches: 77, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
26 15 0.19
27 60 0.78
28 2 0.03
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.36
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGTT
Found at i:40413107 original size:54 final size:53
Alignment explanation
Indices: 40413023--40413133 Score: 168
Period size: 54 Copynumber: 2.1 Consensus size: 53
40413013 AGGAAGCGTC
*
40413023 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATA-ATCTGTT
* * * *
40413077 CTGGTGGCTCTGCCACGATTATCTGTTCTGGTGACTCTGTCACATAATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATAATCTGTT
40413130 CTGG
1 CTGG
40413134 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
53 11 0.21
54 41 0.79
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.36
Consensus pattern (53 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATAATCTGTT
Found at i:40422984 original size:14 final size:15
Alignment explanation
Indices: 40422960--40422988 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
40422950 TTTTCTTTCT
40422960 TTTTAGTTTAATTTA
1 TTTTAGTTTAATTTA
40422975 TTTT-GTTTAATTTA
1 TTTTAGTTTAATTTA
40422989 AAATGTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (15 bp):
TTTTAGTTTAATTTA
Found at i:40427497 original size:19 final size:20
Alignment explanation
Indices: 40427468--40427514 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
40427458 AGTTATAAGT
40427468 ATATATATGTGAATAATTTG
1 ATATATATGTGAATAATTTG
* *
40427488 ATAT-TATGTGATTATTTTG
1 ATATATATGTGAATAATTTG
40427507 ATGATATA
1 AT-ATATA
40427515 ACATTTTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 15 0.65
20 6 0.26
21 2 0.09
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (20 bp):
ATATATATGTGAATAATTTG
Found at i:40427981 original size:50 final size:50
Alignment explanation
Indices: 40427868--40428257 Score: 345
Period size: 50 Copynumber: 7.7 Consensus size: 50
40427858 TATGAGAACA
* * * *** * *
40427868 CATGTGTAGTGCTATGTGCTGGCTACTATGTGTTTAAGATAGTTTTAGGTCA
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGAT--TGTTAGGTCG
* * *
40427920 CGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGCCG
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGTTAGGTCG
** * * *
40427970 CATGTGTAGTACTAAGTGCAGGCTACTATACGTACCCGATAGTTTCA-GTCA
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTG-TT-AGGTCG
* * * * * * *
40428021 CGTATGTAGTATTAAGTGCAGGCTACTATGTGTATCAGCTGGTTAGGTCA
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGTTAGGTCG
* * *
40428071 CGTGTGTAGTACTAAGTGCAGGCTACTACGT-TACCAGATTGATAGGTCG
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGTTAGGTCG
* ** * * * * *
40428120 CATATGTAGTACTAAGTGCAGGCTACTATGCATACCCG-TTAACTTTGATCA
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATT--GTTAGGTCG
* * *
40428171 CGTGTGTAGTACTAAGTGCAGGCTACTAAGTGTACCAGATTGATAGGTCG
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGTTAGGTCG
* * *
40428221 CATGTGTAGTACTATGTGCAAGCTACTATGCGTACCA
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCA
40428258 AAGAGCTTTG
Statistics
Matches: 269, Mismatches: 62, Indels: 16
0.78 0.18 0.05
Matches are distributed among these distances:
49 43 0.16
50 118 0.44
51 73 0.27
52 35 0.13
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (50 bp):
CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGTTAGGTCG
Found at i:40428045 original size:101 final size:102
Alignment explanation
Indices: 40427905--40428147 Score: 307
Period size: 101 Copynumber: 2.4 Consensus size: 102
40427895 ATGTGTTTAA
* * * *
40427905 GATAGTTTTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGCCG
1 GATAGTTTCAGGTCACGTATGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGGTTAGGCCA
40427970 CATGTGTAGTACTAAGTGCAGGCTACTATACGTACCC
66 CATGTGTAGTACTAAGTGCAGGCTACTATACGTACCC
* * * * *
40428007 GATAGTTTCA-GTCACGTATGTAGTATTAAGTGCAGGCTACTATGTGTATCAGCTGGTTAGGTCA
1 GATAGTTTCAGGTCACGTATGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGGTTAGGCCA
* *
40428071 CGTGTGTAGTACTAAGTGCAGGCTAC--TACGTTACCA
66 CATGTGTAGTACTAAGTGCAGGCTACTATACG-TACCC
* * * *
40428107 GATTG-AT-AGGTCGCATATGTAGTACTAAGTGCAGGCTACTA
1 GATAGTTTCAGGTCACGTATGTAGTACTAAGTGCAGGCTACTA
40428148 TGCATACCCG
Statistics
Matches: 123, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
98 1 0.01
99 34 0.28
100 8 0.07
101 71 0.58
102 9 0.07
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (102 bp):
GATAGTTTCAGGTCACGTATGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGGTTAGGCCA
CATGTGTAGTACTAAGTGCAGGCTACTATACGTACCC
Found at i:40428147 original size:150 final size:151
Alignment explanation
Indices: 40427912--40428257 Score: 480
Period size: 150 Copynumber: 2.3 Consensus size: 151
40427902 TAAGATAGTT
* *
40427912 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGCCGCATGTGT
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGCCGCATATGT
* * *
40427977 AGTACTAAGTGCAGGCTACTATACGTACCCGAT-AGTTTCAGTCACGTATGTAGTATTAAGTGCA
66 AGTACTAAGTGCAGGCTACTATACATACCCGATAACTTTCA-TCACGTATGTAGTACTAAGTGCA
* * *
40428041 GGCTACTATGTGTATCAGCTGG
130 GGCTACTAAGTGTACCAGATGG
*
40428063 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGT-TACCAGATTGATAGGTCGCATATGT
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGCCGCATATGT
* * * *
40428127 AGTACTAAGTGCAGGCTACTATGCATACCCGTTAACTTTGATCACGTGTGTAGTACTAAGTGCAG
66 AGTACTAAGTGCAGGCTACTATACATACCCGATAACTTTCATCACGTATGTAGTACTAAGTGCAG
*
40428192 GCTACTAAGTGTACCAGATTG
131 GCTACTAAGTGTACCAGATGG
* * * * * * *
40428213 ATAGGTCGCATGTGTAGTACTATGTGCAAGCTACTATGCGTACCA
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCA
40428258 AAGAGCTTTG
Statistics
Matches: 172, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
150 123 0.72
151 49 0.28
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (151 bp):
TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGCCGCATATGT
AGTACTAAGTGCAGGCTACTATACATACCCGATAACTTTCATCACGTATGTAGTACTAAGTGCAG
GCTACTAAGTGTACCAGATGG
Found at i:40428234 original size:101 final size:100
Alignment explanation
Indices: 40428068--40428256 Score: 324
Period size: 101 Copynumber: 1.9 Consensus size: 100
40428058 GCTGGTTAGG
*
40428068 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTTACCAGATTGATAGGTCGCATATGTAGTACT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTAAGTTACCAGATTGATAGGTCGCATATGTAGTACT
*
40428133 AAGTGCAGGCTACTATGCATACCCGTTAACTTTGA
66 AAGTGCAAGCTACTATGCATACCCGTTAACTTTGA
*
40428168 TCACGTGTGTAGTACTAAGTGCAGGCTACTAAGTGTACCAGATTGATAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTAAGT-TACCAGATTGATAGGTCGCATATGTAGTAC
* *
40428233 TATGTGCAAGCTACTATGCGTACC
65 TAAGTGCAAGCTACTATGCATACC
40428257 AAAGAGCTTT
Statistics
Matches: 83, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
100 33 0.40
101 50 0.60
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (100 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTAAGTTACCAGATTGATAGGTCGCATATGTAGTACT
AAGTGCAAGCTACTATGCATACCCGTTAACTTTGA
Found at i:40429075 original size:180 final size:179
Alignment explanation
Indices: 40428819--40429144 Score: 492
Period size: 180 Copynumber: 1.8 Consensus size: 179
40428809 TCTGAGAGCT
*
40428819 GTACCATGAGATAAATAATTTTTAGTGAAGAGAGGTCAAAACTATTAGATAGTGAAACAAGGGTA
1 GTACCATGAAATAAATAATTTTTAGTGAAGAGAGGTCAAAACTATTAGATAGTGAAACAAGGGTA
* * * ** *
40428884 TCTTTAATGAATAAACTGTACTAATTGGCTAAACTAAAAAATCTGAAATTTTTATGGTAATAATA
66 TCTTTAATGAATAAACTATACTAATTGGCCAAACCAAAAAATCT-AAAAATTTATGGTAAGAATA
* *
40428949 TATGTGAGTCTAGTTTCTTGAAAAATTAGTAGTTCTCAATTTGGATTCCC
130 TATATGAATCTAGTTTCTTGAAAAATTAGTAGTTCTCAATTTGGATTCCC
* * * *
40428999 GTACCATGAAATAAATAATTTTTAGTGAAGAGAGGT-AGGAACTATTGGATAGTGAAATAGGGGT
1 GTACCATGAAATAAATAATTTTTAGTGAAGAGAGGTCA-AAACTATTAGATAGTGAAACAAGGGT
* *
40429063 ATCTTTAATGAATAAACTATACTAATTGGCCAGACCAAAAATTCTAAAAATTTATGGTAAGAATA
65 ATCTTTAATGAATAAACTATACTAATTGGCCAAACCAAAAAATCTAAAAATTTATGGTAAGAATA
40429128 TATATGAATCTAGTTTC
130 TATATGAATCTAGTTTC
40429145 ATATAAAATT
Statistics
Matches: 130, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
179 33 0.25
180 97 0.75
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.33
Consensus pattern (179 bp):
GTACCATGAAATAAATAATTTTTAGTGAAGAGAGGTCAAAACTATTAGATAGTGAAACAAGGGTA
TCTTTAATGAATAAACTATACTAATTGGCCAAACCAAAAAATCTAAAAATTTATGGTAAGAATAT
ATATGAATCTAGTTTCTTGAAAAATTAGTAGTTCTCAATTTGGATTCCC
Found at i:40440865 original size:27 final size:27
Alignment explanation
Indices: 40440825--40441031 Score: 243
Period size: 27 Copynumber: 7.7 Consensus size: 27
40440815 TGTACCTGAA
* * *
40440825 CCCTTATGTAATAAAATGACGATTTTG
1 CCCTCATGTGATAAAATGATGATTTTG
* *
40440852 CCTTTATGTGATAAAATGATGATTTTG
1 CCCTCATGTGATAAAATGATGATTTTG
**
40440879 CCCTCATGTGATAAAATGGCGATTTTG
1 CCCTCATGTGATAAAATGATGATTTTG
40440906 CCCTCATGTGATAAAATGATGATTTTG
1 CCCTCATGTGATAAAATGATGATTTTG
* * *
40440933 CCCTCATCTGATAGAATGACGATTTTG
1 CCCTCATGTGATAAAATGATGATTTTG
** * * *
40440960 TGCTCATGTGGTAAAATGATAATTTTT
1 CCCTCATGTGATAAAATGATGATTTTG
* * *
40440987 CCCTTAGGTGATAAAATGATGATTTTT
1 CCCTCATGTGATAAAATGATGATTTTG
*
40441014 CCCTGATGTGATAAAATG
1 CCCTCATGTGATAAAATG
40441032 GCGAAATACC
Statistics
Matches: 152, Mismatches: 28, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 152 1.00
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (27 bp):
CCCTCATGTGATAAAATGATGATTTTG
Found at i:40441139 original size:27 final size:27
Alignment explanation
Indices: 40441035--40441123 Score: 135
Period size: 27 Copynumber: 3.3 Consensus size: 27
40441025 TAAAATGGCG
* *
40441035 AAATACCCTAATAGGGTAAAGTGACCA
1 AAATACCCTCATAGGGTAAAATGACCA
40441062 AAATACCCTCATAGGGTAAAATGA-CA
1 AAATACCCTCATAGGGTAAAATGACCA
*
40441088 GAAATACCCTCATAGGGTAGAATGACCA
1 -AAATACCCTCATAGGGTAAAATGACCA
40441116 AAATACCC
1 AAATACCC
40441124 GTGTAGAGTA
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
26 2 0.04
27 53 0.93
28 2 0.04
ACGTcount: A:0.44, C:0.21, G:0.17, T:0.18
Consensus pattern (27 bp):
AAATACCCTCATAGGGTAAAATGACCA
Found at i:40441149 original size:54 final size:54
Alignment explanation
Indices: 40441025--40441139 Score: 155
Period size: 54 Copynumber: 2.1 Consensus size: 54
40441015 CCTGATGTGA
* *
40441025 TAAAATGGC-GAAATACCCTAATAGGGTAAAGTGACCAAAATACCCTCATAGGG
1 TAAAATGACAGAAATACCCTAATAGGGTAAAGTGACCAAAATACCCTCATAGAG
* *
40441078 TAAAATGACAGAAATACCCTCATAGGGTAGAA-TGACCAAAATACCCGT-GTAGAG
1 TAAAATGACAGAAATACCCTAATAGGGTA-AAGTGACCAAAATACCC-TCATAGAG
40441132 TAAAATGA
1 TAAAATGA
40441140 TTGTAATACC
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
53 8 0.15
54 44 0.80
55 3 0.05
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.19
Consensus pattern (54 bp):
TAAAATGACAGAAATACCCTAATAGGGTAAAGTGACCAAAATACCCTCATAGAG
Found at i:40442758 original size:30 final size:30
Alignment explanation
Indices: 40442722--40442785 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
40442712 GATTCAATAA
* *
40442722 CCTATATTTGGGCAAAATGACAATTTTGCC
1 CCTATATTTGGACAAAATGACAATTTTACC
** *
40442752 CCTATATTTTTACAAAATGACCATTTTACC
1 CCTATATTTGGACAAAATGACAATTTTACC
40442782 CCTA
1 CCTA
40442786 GGTCCGAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.31, C:0.23, G:0.09, T:0.36
Consensus pattern (30 bp):
CCTATATTTGGACAAAATGACAATTTTACC
Found at i:40448200 original size:27 final size:26
Alignment explanation
Indices: 40448159--40448246 Score: 122
Period size: 27 Copynumber: 3.3 Consensus size: 26
40448149 CAACATGGCT
* *
40448159 ACCAGAACAGATATTGTGACAGAGTC
1 ACCAGAACAGATATTGTGGCAGAGCC
40448185 ACCAGATACAGATATTGTGGCAGAGCC
1 ACCAGA-ACAGATATTGTGGCAGAGCC
* *
40448212 ACCAGAATAGATATTTGTGGCATAGCC
1 ACCAGAACAGATA-TTGTGGCAGAGCC
40448239 ACCAGAAC
1 ACCAGAAC
40448247 GCTTCCTCCA
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
26 12 0.22
27 43 0.78
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.19
Consensus pattern (26 bp):
ACCAGAACAGATATTGTGGCAGAGCC
Found at i:40449470 original size:37 final size:37
Alignment explanation
Indices: 40449420--40449493 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
40449410 AGCAAAAGAA
40449420 AGAAAAAGAGAAAAACCTAAGGTACCCTACCCTATTT
1 AGAAAAAGAGAAAAACCTAAGGTACCCTACCCTATTT
40449457 AGAAAAAGAGAAAAACCTAAGGTACCCTACCCTATTT
1 AGAAAAAGAGAAAAACCTAAGGTACCCTACCCTATTT
40449494 CGGCAAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.46, C:0.22, G:0.14, T:0.19
Consensus pattern (37 bp):
AGAAAAAGAGAAAAACCTAAGGTACCCTACCCTATTT
Found at i:40452730 original size:22 final size:21
Alignment explanation
Indices: 40452668--40452731 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 21
40452658 CTTGAGCTGA
40452668 TGAACAGTAAGCTCTA--AGC
1 TGAACAGTAAGCTCTATGAGC
*
40452687 TGAACAATAAGCTCTATCGAGC
1 TGAACAGTAAGCTCTAT-GAGC
40452709 TGAACAGTAAGCTCTAATGAGC
1 TGAACAGTAAGCTCT-ATGAGC
40452731 T
1 T
40452732 AAAAATAGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
19 15 0.38
22 22 0.56
23 2 0.05
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.23
Consensus pattern (21 bp):
TGAACAGTAAGCTCTATGAGC
Found at i:40453330 original size:29 final size:27
Alignment explanation
Indices: 40453281--40453348 Score: 66
Period size: 27 Copynumber: 2.4 Consensus size: 27
40453271 AGCCCATATC
*
40453281 TTTTATCATTTTATAATTTTAACCACCATA
1 TTTTA-CATTTTACAATTTTAACC-CC-TA
*
40453311 TTTTACATTTTCACAA-TTTAATCCCTA
1 TTTTACATTTT-ACAATTTTAACCCCTA
*
40453338 TTTTGCATTTT
1 TTTTACATTTT
40453349 TGTCAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 12 0.35
28 2 0.06
29 12 0.35
30 8 0.24
ACGTcount: A:0.28, C:0.18, G:0.01, T:0.53
Consensus pattern (27 bp):
TTTTACATTTTACAATTTTAACCCCTA
Found at i:40454969 original size:25 final size:25
Alignment explanation
Indices: 40454940--40454992 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
40454930 ATTGTAACTC
*
40454940 TATCCCATTTCTACTCAGGAATCAT
1 TATCCCATTTCCACTCAGGAATCAT
40454965 TATCCCATTTCCACTCAGGAATCAT
1 TATCCCATTTCCACTCAGGAATCAT
40454990 TAT
1 TAT
40454993 AGGCTGTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.28, C:0.28, G:0.08, T:0.36
Consensus pattern (25 bp):
TATCCCATTTCCACTCAGGAATCAT
Found at i:40456836 original size:42 final size:43
Alignment explanation
Indices: 40456746--40456843 Score: 121
Period size: 42 Copynumber: 2.3 Consensus size: 43
40456736 CCCATACGTG
* *
40456746 ATCTTACATGTAATCAAATATCGATGCCACTGTCCCAGACAGG
1 ATCTTACACGTAATCAAATATCGATGCCACTGTCCCAGACAGA
* *
40456789 GTCTTACACG-AAGTCAAATA-CGATGCCGA-TGTCCCAGACATA
1 ATCTTACACGTAA-TCAAATATCGATGCC-ACTGTCCCAGACAGA
40456831 ATCTTACACGTAA
1 ATCTTACACGTAA
40456844 ATCTTAAATT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
42 29 0.62
43 18 0.38
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (43 bp):
ATCTTACACGTAATCAAATATCGATGCCACTGTCCCAGACAGA
Found at i:40463210 original size:22 final size:23
Alignment explanation
Indices: 40463182--40463281 Score: 86
Period size: 22 Copynumber: 4.5 Consensus size: 23
40463172 CTTGAGCTGA
*
40463182 TGAACAGTAAGCCT-TATTGAGC
1 TGAACAGTAAGCCTCTATCGAGC
*
40463204 TGAACAGTAAG-CTCTATCGAGT
1 TGAACAGTAAGCCTCTATCGAGC
*
40463226 TGAACAGTAAGCC-C-ATACAAGC
1 TGAACAGTAAGCCTCTAT-CGAGC
* *
40463248 TGAACAATAAG-CTCATAT-GATC
1 TGAACAGTAAGCCTC-TATCGAGC
40463270 TGAAACAGTAAG
1 TG-AACAGTAAG
40463282 ATCCAATGAG
Statistics
Matches: 63, Mismatches: 8, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
21 5 0.08
22 47 0.75
23 9 0.14
24 2 0.03
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.23
Consensus pattern (23 bp):
TGAACAGTAAGCCTCTATCGAGC
Found at i:40467665 original size:27 final size:27
Alignment explanation
Indices: 40467581--40467668 Score: 124
Period size: 27 Copynumber: 3.3 Consensus size: 27
40467571 TAAGTTGTAG
40467581 AATTACCGAAATACCCTTGTAGGGTAGA
1 AATTACCGAAATACCCTTGTAGGGTA-A
* *
40467609 AA-TACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAA
* *
40467635 AATTATCGAGATACCCTTGTAGGGTAA
1 AATTACCGAAATACCCTTGTAGGGTAA
40467662 AATTACC
1 AATTACC
40467669 ATTTTGCCCC
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
26 2 0.04
27 48 0.92
28 2 0.04
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.25
Consensus pattern (27 bp):
AATTACCGAAATACCCTTGTAGGGTAA
Found at i:40467713 original size:27 final size:26
Alignment explanation
Indices: 40467669--40467719 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
40467659 TAAAATTACC
40467669 ATTTTGCCCCTAGGGTGTTAAATGACT
1 ATTTTGCCCCTAGGGTG-TAAATGACT
* *
40467696 ATTTTGCCCCTCGTGTGTAAATGA
1 ATTTTGCCCCTAGGGTGTAAATGA
40467720 GTAACTTGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (26 bp):
ATTTTGCCCCTAGGGTGTAAATGACT
Found at i:40468357 original size:27 final size:26
Alignment explanation
Indices: 40468313--40468364 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
40468303 CTCGCTGCAA
*
40468313 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
40468340 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
40468365 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:40468402 original size:2 final size:2
Alignment explanation
Indices: 40468395--40468428 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
40468385 TGGCTTCACC
40468395 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
40468429 GTTCTGGTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40471134 original size:39 final size:40
Alignment explanation
Indices: 40471057--40471163 Score: 119
Period size: 40 Copynumber: 2.7 Consensus size: 40
40471047 TAGCTCCTCG
* * *
40471057 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATAGTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
* *
40471097 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
**
40471136 CACGAATGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
40471164 ATTAGTATCT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
39 25 0.43
40 33 0.57
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
Found at i:40471152 original size:40 final size:38
Alignment explanation
Indices: 40471099--40471227 Score: 154
Period size: 40 Copynumber: 3.3 Consensus size: 38
40471089 GTAACTCATT
*
40471099 CAATGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCA
1 CAATGCCTTCGGGACTTAACCCGGA-ATTAAAACTCGCA
* *
40471138 CGAATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCA
1 C-AATGCCTTCGGGACTTAACCCGGAATTA-AAACTCGCA
*
40471178 -AAGGCCTTCGGGACTTAACCC-GAATTAATAACTCGCA
1 CAATGCCTTCGGGACTTAACCCGGAATTAA-AACTCGCA
*
40471215 CAAATACCTTCGG
1 C-AATGCCTTCGG
40471228 ATCTTAGTCC
Statistics
Matches: 77, Mismatches: 8, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
37 13 0.17
38 20 0.26
39 13 0.17
40 31 0.40
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (38 bp):
CAATGCCTTCGGGACTTAACCCGGAATTAAAACTCGCA
Found at i:40471162 original size:79 final size:77
Alignment explanation
Indices: 40471063--40471280 Score: 201
Period size: 79 Copynumber: 2.8 Consensus size: 77
40471053 CTCGTTCAAG
* * * *
40471063 TGCCTTCGGGACATAGCCCGGTTATAGTAACTCATTCAATGCCTTCGGGACTTAACCCGGATTTT
1 TGCCTTCGGGACTTAGCCCGG-TATAGTAACTCA-ACAAAGCCTTCGGGACTTAACCCGGA-ATT
*
40471128 AA-AACTCGCACGAA
63 AATAACTCGCACAAA
* * * *
40471142 TGCCTTCGGGACTTAACCCGGAATTAGTATCTC-GCAAAGGCCTTCGGGACTTAACCC-GAATTA
1 TGCCTTCGGGACTTAGCCCGGTA-TAGTAACTCAACAAA-GCCTTCGGGACTTAACCCGGAATTA
40471205 ATAACTCGCACAAA
64 ATAACTCGCACAAA
* * * * *
40471219 TACCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 TGCCTTCGGGA-CTTAGCCCGG-TATAGTAACTCA--ACAAAGCCTTCGGGACTTAACCCGGA
40471281 CAGCATTCAA
Statistics
Matches: 113, Mismatches: 17, Indels: 17
0.77 0.12 0.12
Matches are distributed among these distances:
76 7 0.06
77 36 0.32
78 20 0.18
79 44 0.39
80 6 0.05
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (77 bp):
TGCCTTCGGGACTTAGCCCGGTATAGTAACTCAACAAAGCCTTCGGGACTTAACCCGGAATTAAT
AACTCGCACAAA
Found at i:40479110 original size:80 final size:80
Alignment explanation
Indices: 40478997--40479176 Score: 210
Period size: 80 Copynumber: 2.3 Consensus size: 80
40478987 CTCATTCAAT
* * *
40478997 GCCTTC-GGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
40479059 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
40479075 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
40479139 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
40479156 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
40479177 CAGCATTCAA
Statistics
Matches: 88, Mismatches: 7, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
79 13 0.15
80 64 0.73
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:40479136 original size:40 final size:40
Alignment explanation
Indices: 40478994--40479176 Score: 187
Period size: 40 Copynumber: 4.6 Consensus size: 40
40478984 TAACTCATTC
* *
40478994 AATGCCTTC-GGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
40479033 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
40479073 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
40479113 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
40479154 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
40479177 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
39 17 0.14
40 93 0.77
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:40482521 original size:27 final size:27
Alignment explanation
Indices: 40482490--40482667 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
40482480 TAAATTGTAC
40482490 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * ** *
40482517 TGCACTAAGTGTGCAAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
40482543 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
40482571 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
40482599 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
40482626 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
40482653 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40482668 GACTCAATAT
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 104 0.82
28 23 0.18
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:40482631 original size:82 final size:81
Alignment explanation
Indices: 40482491--40482646 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
40482481 AAATTGTACA
* *
40482491 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCAAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCAAAATGAATACGATGCACTAAGTGT
40482556 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
* ** *
40482572 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACTAAGT
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCAAAATGAATACGAT-GCACTAAGT
*
40482636 GTGCGAGTTGA
64 GTGCGAATTGA
40482647 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 16 0.24
82 50 0.76
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCAAAATGAATACGATGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:40482658 original size:82 final size:81
Alignment explanation
Indices: 40482487--40482667 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
40482477 GATTAAATTG
* *
40482487 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCAAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCAAAATGAATACGATGCACTAA
40482552 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * * ** *
40482568 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCAAAATGAATACGAT-GCACT
* **
40482632 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
40482650 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
40482668 GACTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 18 0.22
82 65 0.78
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCAAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:40488827 original size:27 final size:26
Alignment explanation
Indices: 40488797--40488884 Score: 97
Period size: 27 Copynumber: 3.3 Consensus size: 26
40488787 TCGATTTTTG
40488797 AAATTACTAAAATACCCTTGACTTGTA
1 AAATTACTAAAATACCCTTGA-TTGTA
**
40488824 AAATTACTAAAATACCCCCGATTTGTA
1 AAATTACTAAAATACCCTTGA-TTGTA
* *
40488851 AAATTA-TCGAAATACCCTTGTAGTGTA
1 AAATTACT-AAAATACCCTTG-ATTGTA
40488878 AAATTAC
1 AAATTAC
40488885 CTAAGTACCC
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
26 1 0.02
27 49 0.96
28 1 0.02
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (26 bp):
AAATTACTAAAATACCCTTGATTGTA
Found at i:40488893 original size:27 final size:27
Alignment explanation
Indices: 40488820--40488908 Score: 81
Period size: 27 Copynumber: 3.3 Consensus size: 27
40488810 ACCCTTGACT
** * *
40488820 TGTAAAATTACTAAAATACCCCCG-ATT
1 TGTAAAATTACCGAAATACCCCTGTA-G
* *
40488847 TGTAAAATTATCGAAATACCCTTGTAG
1 TGTAAAATTACCGAAATACCCCTGTAG
* *
40488874 TGTAAAATTACCTAAGTACCCCTGTAG
1 TGTAAAATTACCGAAATACCCCTGTAG
*
40488901 GGTAAAAT
1 TGTAAAAT
40488909 GACTATTTAG
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
27 49 0.98
28 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.30
Consensus pattern (27 bp):
TGTAAAATTACCGAAATACCCCTGTAG
Found at i:40491876 original size:20 final size:21
Alignment explanation
Indices: 40491833--40491876 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
40491823 CATTTGAATT
**
40491833 TGATTCAAGGTCACATAAGCC
1 TGATTCAAGGTCACATAAAAC
40491854 TGATTCAAGGTC-CATAAAAC
1 TGATTCAAGGTCACATAAAAC
40491874 TGA
1 TGA
40491877 GTGGATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.25
Consensus pattern (21 bp):
TGATTCAAGGTCACATAAAAC
Found at i:40493343 original size:16 final size:17
Alignment explanation
Indices: 40493312--40493345 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
40493302 GTTTAATCGG
*
40493312 TTTAGTTGTTTGTTTAT
1 TTTAGTTGTTTATTTAT
40493329 TTTAG-TGTTTATTTAT
1 TTTAGTTGTTTATTTAT
40493345 T
1 T
40493346 CTAGCTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.71
Consensus pattern (17 bp):
TTTAGTTGTTTATTTAT
Found at i:40503092 original size:40 final size:40
Alignment explanation
Indices: 40503015--40503383 Score: 370
Period size: 40 Copynumber: 9.3 Consensus size: 40
40503005 AATTATTGTA
* * * **
40503015 TGAATGCACATACATGCCCCTGGTTGTATTTTAGTACCCT
1 TGAATGCACATACGTGCCCCTGATTGTACTTCGGTACCCT
* ** * *
40503055 TGAATGCACATACGTGACATTGATTATACTTCGGTACCCC
1 TGAATGCACATACGTGCCCCTGATTGTACTTCGGTACCCT
* * *
40503095 TGAATGCACATACGTGACCTTGATTGTACTTCGGTACCCA
1 TGAATGCACATACGTGCCCCTGATTGTACTTCGGTACCCT
* *
40503135 TGAATGCACATATGTGCCCCTGATTGTACTTCAGTA-CCT
1 TGAATGCACATACGTGCCCCTGATTGTACTTCGGTACCCT
* *
40503174 CTGAATGCACATACGTGCCCCAGATTGTACTTTGGTA-CCT
1 -TGAATGCACATACGTGCCCCTGATTGTACTTCGGTACCCT
* * * *
40503214 CGAATGCACATACGTTCCCCTAATTGTACTTCGGTACCCC
1 TGAATGCACATACGTGCCCCTGATTGTACTTCGGTACCCT
* * * *
40503254 TAAATGCACATACGCGCCCCTGATTGTTCTTTGGTA-CCT
1 TGAATGCACATACGTGCCCCTGATTGTACTTCGGTACCCT
* * ** *
40503293 CTGAATGCACATATGTGCCCCTGATTGTACTTTGACACCCC
1 -TGAATGCACATACGTGCCCCTGATTGTACTTCGGTACCCT
* * * *
40503334 TAAATGCACATGCGTG-CCCTAATTGTACTTCGGCACCCCT
1 TGAATGCACATACGTGCCCCTGATTGTACTTCGGTA-CCCT
40503374 T-AATGCACAT
1 TGAATGCACAT
40503384 GTGTGCCTTT
Statistics
Matches: 274, Mismatches: 50, Indels: 11
0.82 0.15 0.03
Matches are distributed among these distances:
39 60 0.22
40 212 0.77
41 2 0.01
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.31
Consensus pattern (40 bp):
TGAATGCACATACGTGCCCCTGATTGTACTTCGGTACCCT
Found at i:40503159 original size:80 final size:79
Alignment explanation
Indices: 40503015--40503390 Score: 414
Period size: 80 Copynumber: 4.7 Consensus size: 79
40503005 AATTATTGTA
* * * * * * **
40503015 TGAATGCACATACATGCCCCTGGTTGTATTTTAGTACCCTTGAATGCACATACGTGACATTGATT
1 TGAATGCACATACGTGCCCCTGATTGTACTTTGGTACCC-TGAATGCACATATGTGCCCCTGATT
*
40503080 ATACTTCGGTACCCC
65 GTACTTCGGTACCCC
* * *
40503095 TGAATGCACATACGTGACCTTGATTGTACTTCGGTACCCATGAATGCACATATGTGCCCCTGATT
1 TGAATGCACATACGTGCCCCTGATTGTACTTTGGTACCC-TGAATGCACATATGTGCCCCTGATT
* *
40503160 GTACTTCAGTACCTC
65 GTACTTCGGTACCCC
* * * *
40503175 TGAATGCACATACGTGCCCCAGATTGTACTTTGGTA-CCTCGAATGCACATACGTTCCCCTAATT
1 TGAATGCACATACGTGCCCCTGATTGTACTTTGGTACCCT-GAATGCACATATGTGCCCCTGATT
40503239 GTACTTCGGTACCCC
65 GTACTTCGGTACCCC
* * *
40503254 TAAATGCACATACGCGCCCCTGATTGTTCTTTGGTACCTCTGAATGCACATATGTGCCCCTGATT
1 TGAATGCACATACGTGCCCCTGATTGTACTTTGGTACC-CTGAATGCACATATGTGCCCCTGATT
* **
40503319 GTACTTTGACACCCC
65 GTACTTCGGTACCCC
* * * * * * *
40503334 TAAATGCACATGCGTG-CCCTAATTGTACTTCGGCACCCCTTAATGCACATGTGTGCC
1 TGAATGCACATACGTGCCCCTGATTGTACTTTGGTA-CCCTGAATGCACATATGTGCC
40503391 TTTTTTGTAC
Statistics
Matches: 250, Mismatches: 42, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
78 1 0.00
79 100 0.40
80 147 0.59
81 2 0.01
ACGTcount: A:0.23, C:0.28, G:0.18, T:0.31
Consensus pattern (79 bp):
TGAATGCACATACGTGCCCCTGATTGTACTTTGGTACCCTGAATGCACATATGTGCCCCTGATTG
TACTTCGGTACCCC
Found at i:40503273 original size:119 final size:120
Alignment explanation
Indices: 40503017--40503383 Score: 443
Period size: 119 Copynumber: 3.1 Consensus size: 120
40503007 TTATTGTATG
* * * * ** *
40503017 AATGCACATACATGCCCCTGGTTGTATTTTAGTACC-CTTGAATGCACATACGTGACATTGATTA
1 AATGCACATACGTGCCCCTGATTGTACTTTAGTACCTC-TGAATGCACATACGTGCCCCTGATTG
* * * * * *
40503081 TACTTCGGTACCCCTGAATGCACATACGTGACCTTGATTGTACTTCGGTACCCATG
65 TACTTTGGTACCCCTGAATGCACATACGTTACCCTAATTGTACTTCGGTACCCCTA
* * *
40503137 AATGCACATATGTGCCCCTGATTGTACTTCAGTACCTCTGAATGCACATACGTGCCCCAGATTGT
1 AATGCACATACGTGCCCCTGATTGTACTTTAGTACCTCTGAATGCACATACGTGCCCCTGATTGT
* *
40503202 ACTTTGGTACCTC-GAATGCACATACGTTCCCCTAATTGTACTTCGGTACCCCTA
66 ACTTTGGTACCCCTGAATGCACATACGTTACCCTAATTGTACTTCGGTACCCCTA
* * * *
40503256 AATGCACATACGCGCCCCTGATTGTTCTTTGGTACCTCTGAATGCACATATGTGCCCCTGATTGT
1 AATGCACATACGTGCCCCTGATTGTACTTTAGTACCTCTGAATGCACATACGTGCCCCTGATTGT
** * * * * *
40503321 ACTTTGACACCCCTAAATGCACATGCG-TGCCCTAATTGTACTTCGGCACCCCTT
66 ACTTTGGTACCCCTGAATGCACATACGTTACCCTAATTGTACTTCGGTACCCCTA
40503375 AATGCACAT
1 AATGCACAT
40503384 GTGTGCCTTT
Statistics
Matches: 212, Mismatches: 33, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
119 136 0.64
120 75 0.35
121 1 0.00
ACGTcount: A:0.24, C:0.28, G:0.17, T:0.31
Consensus pattern (120 bp):
AATGCACATACGTGCCCCTGATTGTACTTTAGTACCTCTGAATGCACATACGTGCCCCTGATTGT
ACTTTGGTACCCCTGAATGCACATACGTTACCCTAATTGTACTTCGGTACCCCTA
Found at i:40503379 original size:159 final size:159
Alignment explanation
Indices: 40503081--40503383 Score: 414
Period size: 159 Copynumber: 1.9 Consensus size: 159
40503071 ACATTGATTA
* * *
40503081 TACTTCGGTACCCCTGAATGCACATACGTGACCTTGATTGTACTTCGGTACCCATGAATGCACAT
1 TACTTCGGTACCCCTAAATGCACATACGCGACCCTGATTGTACTTCGGTACCCATGAATGCACAT
* * * * *
40503146 ATGTGCCCCTGATTGTACTTCAGTACCTCTGAATGCACATACGTGCCCCAGATTGTACTTTGGTA
66 ATGTGCCCCTGATTGTACTTCAGCACCCCTAAATGCACATACGTGCCCCAGATTGTACTTCGGCA
*
40503211 CCTCGAATGCACATACGTTCCCCTAATTG
131 CCCCGAATGCACATACGTTCCCCTAATTG
* * *
40503240 TACTTCGGTACCCCTAAATGCACATACGCGCCCCTGATTGTTCTTTGGTACCTC-TGAATGCACA
1 TACTTCGGTACCCCTAAATGCACATACGCGACCCTGATTGTACTTCGGTACC-CATGAATGCACA
* * *
40503304 TATGTGCCCCTGATTGTACTT-TGACACCCCTAAATGCACATGCGTGCCCTA-ATTGTACTTCGG
65 TATGTGCCCCTGATTGTACTTCAG-CACCCCTAAATGCACATACGTGCCCCAGATTGTACTTCGG
*
40503367 CACCCCTTAATGCACAT
129 CACCCC-GAATGCACAT
40503384 GTGTGCCTTT
Statistics
Matches: 125, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
158 16 0.13
159 108 0.86
160 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.17, T:0.30
Consensus pattern (159 bp):
TACTTCGGTACCCCTAAATGCACATACGCGACCCTGATTGTACTTCGGTACCCATGAATGCACAT
ATGTGCCCCTGATTGTACTTCAGCACCCCTAAATGCACATACGTGCCCCAGATTGTACTTCGGCA
CCCCGAATGCACATACGTTCCCCTAATTG
Found at i:40510277 original size:24 final size:23
Alignment explanation
Indices: 40510224--40510280 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
40510214 GCTGATGGAC
** *
40510224 AGTAAGCTCTATTGATCTGAAAT
1 AGTAAGCTCTAACGAGCTGAAAT
*
40510247 AGAAAGCTCTAACGAGCTGAGAAT
1 AGTAAGCTCTAACGAGCTGA-AAT
40510271 AGTAAGCTCT
1 AGTAAGCTCT
40510281 TATGAACTGG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 16 0.57
24 12 0.43
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (23 bp):
AGTAAGCTCTAACGAGCTGAAAT
Found at i:40510716 original size:40 final size:40
Alignment explanation
Indices: 40510653--40510914 Score: 348
Period size: 40 Copynumber: 6.6 Consensus size: 40
40510643 ATTCGGATTG
* *
40510653 ATAACCAGGCTAAGTCCTGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * * *
40510693 ATATCCGTGCTAAGTCCGGAAGGCATTTGTGCGAGTTCCT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * *
40510733 ATATCCGAGCTAAGTCCCGAAGGCATTTGTCCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * *
40510773 ATAACCGGGCCAAGTCCTGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
40510813 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
40510853 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CT
* **
40510893 ATATCC-GGCTAAACCCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGG
40510915 TACTTGGTTT
Statistics
Matches: 199, Mismatches: 22, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
39 16 0.08
40 183 0.92
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.24
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:40518830 original size:40 final size:40
Alignment explanation
Indices: 40518770--40519031 Score: 384
Period size: 40 Copynumber: 6.6 Consensus size: 40
40518760 ATTCGGATTG
* *
40518770 ATAATCGGGCTAAGTCCGGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
40518810 ATATCCGGGCTAAGTCCGGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
40518850 ATATCCGGGCTAAGTCCGGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
40518890 ATAACCGGGCCAAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
40518930 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
40518970 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CT
* **
40519010 ATATCC-GGCTAAACCCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGG
40519032 TACTTGGTTT
Statistics
Matches: 209, Mismatches: 12, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
39 16 0.08
40 193 0.92
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.23
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:40522053 original size:45 final size:45
Alignment explanation
Indices: 40522002--40522091 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
40521992 ACCATAAAGG
40522002 AAGCAAGGGGTCCAAGGTTCAAGTCTTGGCTCTTGCAATATATTT
1 AAGCAAGGGGTCCAAGGTTCAAGTCTTGGCTCTTGCAATATATTT
40522047 AAGCAAGGGGTCCAAGGTTCAAGTCTTGGCTCTTGCAATATATTT
1 AAGCAAGGGGTCCAAGGTTCAAGTCTTGGCTCTTGCAATATATTT
40522092 TGGTTTTTCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (45 bp):
AAGCAAGGGGTCCAAGGTTCAAGTCTTGGCTCTTGCAATATATTT
Found at i:40523122 original size:27 final size:26
Alignment explanation
Indices: 40523078--40523129 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
40523068 CTCGCTGCAA
*
40523078 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
40523105 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
40523130 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:40524641 original size:11 final size:11
Alignment explanation
Indices: 40524625--40524651 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
40524615 ACGTGAGAAA
40524625 TGTAATTGAAC
1 TGTAATTGAAC
40524636 TGTAATTGAAC
1 TGTAATTGAAC
40524647 TGTAA
1 TGTAA
40524652 AGTATTACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.37
Consensus pattern (11 bp):
TGTAATTGAAC
Found at i:40525537 original size:19 final size:19
Alignment explanation
Indices: 40525501--40525538 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
40525491 GTTAATATAA
*
40525501 TGATGTGGTTGATTATGGT
1 TGATGTGGTTGATAATGGT
40525520 TGATGTGGTATG-TAATGGT
1 TGATGTGGT-TGATAATGGT
40525539 AAAATAGTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.18, C:0.00, G:0.37, T:0.45
Consensus pattern (19 bp):
TGATGTGGTTGATAATGGT
Found at i:40531130 original size:19 final size:21
Alignment explanation
Indices: 40531096--40531138 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
40531086 AAAGAGCTCG
40531096 ATTGAGCTGAAACGAGCT-GA
1 ATTGAGCTGAAACGAGCTGGA
*
40531116 ATTGAGCT-CAACGAGCTGGA
1 ATTGAGCTGAAACGAGCTGGA
40531136 ATT
1 ATT
40531139 CGAATTACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (21 bp):
ATTGAGCTGAAACGAGCTGGA
Found at i:40535740 original size:27 final size:28
Alignment explanation
Indices: 40535694--40535755 Score: 90
Period size: 27 Copynumber: 2.2 Consensus size: 28
40535684 TACCTAGACC
40535694 CCCTATATATGATAAAATGACTATTTTG
1 CCCTATATATGATAAAATGACTATTTTG
* *
40535722 CCCT-TATATGGTAAGATGACTATTTTG
1 CCCTATATATGATAAAATGACTATTTTG
40535749 CCTCTAT
1 CC-CTAT
40535756 GCGATGCGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 23 0.77
28 6 0.20
29 1 0.03
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (28 bp):
CCCTATATATGATAAAATGACTATTTTG
Found at i:40538630 original size:27 final size:29
Alignment explanation
Indices: 40538600--40538663 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 29
40538590 GTGAGCATGA
40538600 ATATGAATGTGA-CTGGGCC-AACGGGCC
1 ATATGAATGTGATCTGGGCCTAACGGGCC
* * *
40538627 ATATAAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATCTGGGCCTAACGGGCC
40538656 ATATGAAT
1 ATATGAAT
40538664 ATAAATGGGC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 11 0.35
28 6 0.19
29 14 0.45
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.27
Consensus pattern (29 bp):
ATATGAATGTGATCTGGGCCTAACGGGCC
Found at i:40538657 original size:29 final size:27
Alignment explanation
Indices: 40538600--40538659 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
40538590 GTGAGCATGA
*
40538600 ATATGAATGTGACTGGGCCAACGGGCC
1 ATATAAATGTGACTGGGCCAACGGGCC
* *
40538627 ATATAAATGTGATTTGGGCCTAATGGGCC
1 ATATAAATGTGA-CTGGGCC-AACGGGCC
40538656 ATAT
1 ATAT
40538660 GAATATAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 11 0.39
28 6 0.21
29 11 0.39
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.27
Consensus pattern (27 bp):
ATATAAATGTGACTGGGCCAACGGGCC
Found at i:40542353 original size:48 final size:48
Alignment explanation
Indices: 40542282--40542379 Score: 169
Period size: 48 Copynumber: 2.0 Consensus size: 48
40542272 CAAGATAAAT
* *
40542282 ATATATATGTGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGAG
*
40542330 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGAG
40542378 AT
1 AT
40542380 GTGTGTATAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.34, C:0.06, G:0.30, T:0.31
Consensus pattern (48 bp):
ATATATATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGAG
Found at i:40542574 original size:37 final size:37
Alignment explanation
Indices: 40542524--40542659 Score: 245
Period size: 37 Copynumber: 3.7 Consensus size: 37
40542514 ATATATTCCC
40542524 GGTAAGACCCGATGACTACGTGTGGAGATTATGTCCG
1 GGTAAGACCCGATGACTACGTGTGGAGATTATGTCCG
40542561 GGTAAGACCCGATGACTACGTGTGGAGATTATGTCCG
1 GGTAAGACCCGATGACTACGTGTGGAGATTATGTCCG
*
40542598 GGTAAGACCCGATGACTACGTGTGGAGATTTTGTCCG
1 GGTAAGACCCGATGACTACGTGTGGAGATTATGTCCG
* *
40542635 GGTAAGATCCGATAACTACGTGTGG
1 GGTAAGACCCGATGACTACGTGTGG
40542660 GGACTATTCG
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 96 1.00
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.25
Consensus pattern (37 bp):
GGTAAGACCCGATGACTACGTGTGGAGATTATGTCCG
Found at i:40546547 original size:27 final size:27
Alignment explanation
Indices: 40546501--40546572 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
40546491 ATAAACATAC
* *
40546501 ATCACATAGGGGTAAAATAGTTAGCTT
1 ATCACATAAGGGCAAAATAGTTAGCTT
* **
40546528 A-CGATATAAGGGCAAAATAGTTATTTT
1 ATC-ACATAAGGGCAAAATAGTTAGCTT
40546555 ATCACATAAGGGCAAAAT
1 ATCACATAAGGGCAAAAT
40546573 CGTCATTTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
26 1 0.03
27 35 0.95
28 1 0.03
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.28
Consensus pattern (27 bp):
ATCACATAAGGGCAAAATAGTTAGCTT
Found at i:40546649 original size:81 final size:81
Alignment explanation
Indices: 40546533--40546720 Score: 236
Period size: 81 Copynumber: 2.3 Consensus size: 81
40546523 AGCTTACGAT
* * * *
40546533 ATAAGGGCAAAATAGTTATTTTATCACATAAGGGCAAAATC-GTCATTTTACCATA-AAATGGAA
1 ATAAGGGTAAAACAGTCATTTTACCACATAAGGGCAAAA-CAGTCATTTTACCATATAAA-GGAA
*
40546596 AAATAGTCATTTTGCCAC
64 AAACAGTCATTTTGCCAC
* * *
40546614 ATAAGGGTAAAACAGTCATTTTGCCACATAAGGGCAAAACAGTCATTTTGCCATATAAAGGCAAA
1 ATAAGGGTAAAACAGTCATTTTACCACATAAGGGCAAAACAGTCATTTTACCATATAAAGGAAAA
*
40546679 ACAGTCATTTTGCCAT
66 ACAGTCATTTTGCCAC
** *
40546695 ATAAGGGTAAAGTAGTCTTTTTACCA
1 ATAAGGGTAAAACAGTCATTTTACCA
40546721 ATTAGGGTCC
Statistics
Matches: 92, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
80 1 0.01
81 88 0.96
82 3 0.03
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (81 bp):
ATAAGGGTAAAACAGTCATTTTACCACATAAGGGCAAAACAGTCATTTTACCATATAAAGGAAAA
ACAGTCATTTTGCCAC
Found at i:40546711 original size:27 final size:27
Alignment explanation
Indices: 40546531--40546716 Score: 201
Period size: 27 Copynumber: 6.9 Consensus size: 27
40546521 TTAGCTTACG
* **
40546531 ATATAAGGGCAAAATAGTTATTTTATC
1 ATATAAGGGCAAAATAGTCATTTTGCC
* * *
40546558 ACATAAGGGCAAAATCGTCATTTTACC
1 ATATAAGGGCAAAATAGTCATTTTGCC
* * *
40546585 ATAAAATGGAAAAATAGTCATTTTGCC
1 ATATAAGGGCAAAATAGTCATTTTGCC
* * *
40546612 ACATAAGGGTAAAACAGTCATTTTGCC
1 ATATAAGGGCAAAATAGTCATTTTGCC
* *
40546639 ACATAAGGGCAAAACAGTCATTTTGCC
1 ATATAAGGGCAAAATAGTCATTTTGCC
* *
40546666 ATATAAAGGCAAAACAGTCATTTTGCC
1 ATATAAGGGCAAAATAGTCATTTTGCC
* * *
40546693 ATATAAGGGTAAAGTAGTCTTTTT
1 ATATAAGGGCAAAATAGTCATTTT
40546717 ACCAATTAGG
Statistics
Matches: 136, Mismatches: 23, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 136 1.00
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.30
Consensus pattern (27 bp):
ATATAAGGGCAAAATAGTCATTTTGCC
Found at i:40546859 original size:18 final size:17
Alignment explanation
Indices: 40546833--40546866 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40546823 CATATTGCGG
40546833 GCCCATGTGGGCCCACAC
1 GCCCATGT-GGCCCACAC
*
40546851 GCCCGTGTGGCCCACA
1 GCCCATGTGGCCCACA
40546867 TAGCCCAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.15, C:0.44, G:0.29, T:0.12
Consensus pattern (17 bp):
GCCCATGTGGCCCACAC
Found at i:40551359 original size:27 final size:27
Alignment explanation
Indices: 40551329--40551383 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
40551319 TGTATCTGAT
* *
40551329 ACCTGATTCT-GTACTGGGCTCAGGCCC
1 ACCTAATTCTAGTAATGGGCT-AGGCCC
*
40551356 ACCTAATTCTATTAATGGGCTAGGCCC
1 ACCTAATTCTAGTAATGGGCTAGGCCC
40551383 A
1 A
40551384 ACTGTTACTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 16 0.67
28 8 0.33
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (27 bp):
ACCTAATTCTAGTAATGGGCTAGGCCC
Found at i:40557107 original size:47 final size:47
Alignment explanation
Indices: 40557043--40557164 Score: 199
Period size: 47 Copynumber: 2.6 Consensus size: 47
40557033 GCATTGGCAC
*
40557043 TAAGACAAGGATCCCATGTAAGACCATGTTTGGAACATGGCATTTGA
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGA
*
40557090 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGA
* * *
40557137 TAAGATAAGAATATCATGTAAGACCATG
1 TAAGACAAGGATACCATGTAAGACCATG
40557165 CCAGGGCATG
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 70 1.00
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (47 bp):
TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGA
Found at i:40557212 original size:54 final size:54
Alignment explanation
Indices: 40557151--40557339 Score: 204
Period size: 55 Copynumber: 3.5 Consensus size: 54
40557141 ATAAGAATAT
* * * * * *
40557151 CATGTAAGACCATGCCAGGGCATGACATTGATAAGTTCTATAAGGCAAGGAAAT
1 CATGTAAGACCATGCTAAGGCATGGCATTGATGAGTTCTATAAGGCAAGGATAC
* * * *
40557205 CATGTAAGACCATGTTAAGACATGGCATTGATGAGTTACTATATGGCAAAGG-TCC
1 CATGTAAGACCATGCTAAGGCATGGCATTGATGAGTT-CTATAAGGC-AAGGATAC
* *
40557260 CATGTAAGACCATGCTAAGGCAAGGCATTGATGAGTTC-ATAAGACAAGGATAC
1 CATGTAAGACCATGCTAAGGCATGGCATTGATGAGTTCTATAAGGCAAGGATAC
* *
40557313 CACGTAAGACCATG-TCAAGACATGGCA
1 CATGTAAGACCATGCT-AAGGCATGGCA
40557340 ATGGTAAGTT
Statistics
Matches: 112, Mismatches: 19, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
52 5 0.04
53 29 0.26
54 32 0.29
55 42 0.38
56 4 0.04
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (54 bp):
CATGTAAGACCATGCTAAGGCATGGCATTGATGAGTTCTATAAGGCAAGGATAC
Found at i:40557272 original size:55 final size:53
Alignment explanation
Indices: 40557137--40557339 Score: 183
Period size: 54 Copynumber: 3.8 Consensus size: 53
40557127 TGGCATTTGG
* * * ** * * * *
40557137 TAAGATAAGAATATCATGTAAGACCATGCCAGGGCATGACATTGATAAGTTCTA
1 TAAGACAAGGATACCATGTAAGACCATGTTAAGACATGGCATTGATGAGTTC-A
* * *
40557191 TAAGGCAAGGAAATCATGTAAGACCATGTTAAGACATGGCATTGATGAGTTACTA
1 TAAGACAAGGATACCATGTAAGACCATGTTAAGACATGGCATTGATGAGTT-C-A
* * * * * *
40557246 TATGGCAAAGG-TCCCATGTAAGACCATGCTAAGGCAAGGCATTGATGAGTTCA
1 TAAGAC-AAGGATACCATGTAAGACCATGTTAAGACATGGCATTGATGAGTTCA
* *
40557299 TAAGACAAGGATACCACGTAAGACCATGTCAAGACATGGCA
1 TAAGACAAGGATACCATGTAAGACCATGTTAAGACATGGCA
40557340 ATGGTAAGTT
Statistics
Matches: 121, Mismatches: 25, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
52 4 0.03
53 29 0.24
54 42 0.35
55 42 0.35
56 4 0.03
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (53 bp):
TAAGACAAGGATACCATGTAAGACCATGTTAAGACATGGCATTGATGAGTTCA
Found at i:40562336 original size:40 final size:40
Alignment explanation
Indices: 40562259--40562474 Score: 321
Period size: 40 Copynumber: 5.4 Consensus size: 40
40562249 AAACCAAGTA
* *
40562259 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
40562298 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
40562338 CCTTCGGGACCTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
40562378 CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
40562418 CCTTCGGGACATAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
40562458 CCTTCGGGACTTAGCCC
1 CCTTCGGGACTTAGCCC
40562475 AGTTATCATC
Statistics
Matches: 163, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
39 15 0.09
40 148 0.91
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:40564665 original size:29 final size:30
Alignment explanation
Indices: 40564614--40564671 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
40564604 CTTTTGAAAA
* *
40564614 TATTTACAAAAAAAGGAATCTAAGTTTTAT
1 TATTTACAAAAAAAGCAATCTAAATTTTAT
*
40564644 TATTTACAAAAAGAGCAA-CTAAATTTTA
1 TATTTACAAAAAAAGCAATCTAAATTTTA
40564672 AAAATAGTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.34
Consensus pattern (30 bp):
TATTTACAAAAAAAGCAATCTAAATTTTAT
Found at i:40573304 original size:18 final size:18
Alignment explanation
Indices: 40573281--40573318 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
40573271 GGCTAATATG
40573281 TTGAATTTGATTCATGAT
1 TTGAATTTGATTCATGAT
40573299 TTGAATTTGATTCATGAT
1 TTGAATTTGATTCATGAT
40573317 TT
1 TT
40573319 CATACATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.05, G:0.16, T:0.53
Consensus pattern (18 bp):
TTGAATTTGATTCATGAT
Found at i:40573860 original size:40 final size:40
Alignment explanation
Indices: 40573708--40573871 Score: 222
Period size: 40 Copynumber: 4.1 Consensus size: 40
40573698 CGGATGATAA
* * *
40573708 CCGGACTAAGATCCGAAGGCATTCGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
* * * * *
40573748 CCGGGCTATGACCCGAAGGCATTTATGCTAG-CGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATAT
40573788 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
* *
40573828 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTACAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
40573868 CCGG
1 CCGG
40573872 TTAAATCCCG
Statistics
Matches: 107, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
39 1 0.01
40 105 0.98
41 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
Found at i:40576788 original size:25 final size:26
Alignment explanation
Indices: 40576759--40576824 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 26
40576749 TAATAAATTT
*
40576759 GCACACATAGTGCATA-TATT-CATTC
1 GCACACATAGTGC-TACTATTCCATAC
*
40576784 GCACACATAGTGCTAGCTTTTCCATAC
1 GCACACATAGTGCTA-CTATTCCATAC
40576811 GCACACATAGTGCT
1 GCACACATAGTGCT
40576825 GCCCCATTCG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
24 2 0.06
25 13 0.36
26 3 0.08
27 18 0.50
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (26 bp):
GCACACATAGTGCTACTATTCCATAC
Found at i:40579615 original size:25 final size:26
Alignment explanation
Indices: 40579582--40579651 Score: 90
Period size: 27 Copynumber: 2.7 Consensus size: 26
40579572 CGGTTAATAA
40579582 ATTCGCACACATAGTGCATA-TATT-C
1 ATTCGCACACATAGTGC-TACTATTCC
*
40579607 ATTCGCACACATAGTGCTAGCTTTTCC
1 ATTCGCACACATAGTGCTA-CTATTCC
*
40579634 ATACGCACACATAGTGCT
1 ATTCGCACACATAGTGCT
40579652 GCCCCATTCG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
24 2 0.05
25 17 0.43
26 3 0.08
27 18 0.45
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (26 bp):
ATTCGCACACATAGTGCTACTATTCC
Found at i:40589059 original size:95 final size:96
Alignment explanation
Indices: 40588896--40589184 Score: 332
Period size: 102 Copynumber: 3.0 Consensus size: 96
40588886 GACATTTGGG
* * * *
40588896 TGATATGTGTGCTAGTGTAAGACTAAGTCTGAGACATGGCGTCGGCCACGATATGAGAGCCAGTG
1 TGATATGTGCGCTAGTGTAAGACCATGTCTGAGACATGGCATCGGCCACGATATGAGAGCCAGTG
* *
40588961 TAAGACCATG-TTGGTACATAGCATCGGCAA
66 TAAGACCATGTTTGGAACATGGCATCGGCAA
* * *
40588991 TGATATGTGCGCTAGTGTAAGACCATGTTTTAGACATGGCATTGGCCAC-ATTATGAGAGCCAGT
1 TGATATGTGCGCTAGTGTAAGACCATGTCTGAGACATGGCATCGGCCACGA-TATGAGAGCCAGT
* * *
40589055 GTAAGACCTTGTTTGGGACATGGCATCGGCAT
65 GTAAGACCATGTTTGGAACATGGCATCGGCAA
* * * * *
40589087 TGGCAT-TGAGACAAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGACATGTGA
1 T-G-ATATGTG-C----GCTAGTGTAAGACCATGTCTGAGACATGGCATCGGCCACGATATGAGA
40589151 GCCAGTGTAAGACCATGTTTGGAACATGGCATCG
59 GCCAGTGTAAGACCATGTTTGGAACATGGCATCG
40589185 ATAATTCACC
Statistics
Matches: 163, Mismatches: 21, Indels: 13
0.83 0.11 0.07
Matches are distributed among these distances:
94 1 0.01
95 65 0.40
96 18 0.11
97 4 0.02
98 3 0.02
102 71 0.44
103 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (96 bp):
TGATATGTGCGCTAGTGTAAGACCATGTCTGAGACATGGCATCGGCCACGATATGAGAGCCAGTG
TAAGACCATGTTTGGAACATGGCATCGGCAA
Found at i:40589075 original size:48 final size:48
Alignment explanation
Indices: 40588909--40589184 Score: 215
Period size: 48 Copynumber: 5.6 Consensus size: 48
40588899 TATGTGTGCT
* * * * *
40588909 AGTGTAAGACTAAGTCTGAGACATGGCGTCGGCCACGA-TATGAGAGCC
1 AGTGTAAGACCATGTTTGGGACATGGCATCGGCCAC-ATTATGAGAGCC
* * * * *
40588957 AGTGTAAGACCATG-TTGGTACATAGCATCGG-CA-ATGATATGTGCGCT
1 AGTGTAAGACCATGTTTGGGACATGGCATCGGCCACAT--TATGAGAGCC
** *
40589004 AGTGTAAGACCATGTTTTAGACATGGCATTGGCCACATTATGAGAGCC
1 AGTGTAAGACCATGTTTGGGACATGGCATCGGCCACATTATGAGAGCC
* *
40589052 AGTGTAAGACCTTGTTTGGGACATGGCATCGG-CATTGGCATTGA-GACAAGAGCT
1 AGTGTAAGACCATGTTTGGGACATGGCATCGGCCA----CATT-ATG---AGAGCC
* * * *
40589106 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGA-CATGTGAGCC
1 AGTGTAAGACCATGTTTGGGACATGGCATCGGCCAC-ATTATGAGAGCC
*
40589154 AGTGTAAGACCATGTTTGGAACATGGCATCG
1 AGTGTAAGACCATGTTTGGGACATGGCATCG
40589185 ATAATTCACC
Statistics
Matches: 180, Mismatches: 31, Indels: 34
0.73 0.13 0.14
Matches are distributed among these distances:
44 1 0.01
46 2 0.01
47 35 0.19
48 92 0.51
49 2 0.01
50 3 0.02
51 7 0.04
52 2 0.01
54 35 0.19
55 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.24
Consensus pattern (48 bp):
AGTGTAAGACCATGTTTGGGACATGGCATCGGCCACATTATGAGAGCC
Found at i:40592939 original size:30 final size:30
Alignment explanation
Indices: 40592905--40592965 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
40592895 TCCTTAACTA
*
40592905 AAACTTTTGGAAAATTACAATTTTGCCCCT
1 AAACTTTTGCAAAATTACAATTTTGCCCCT
* * *
40592935 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTTGCAAAATTACAATTTTGCCCCT
40592965 A
1 A
40592966 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (30 bp):
AAACTTTTGCAAAATTACAATTTTGCCCCT
Found at i:40594530 original size:18 final size:18
Alignment explanation
Indices: 40594507--40594549 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
40594497 CGTTATATGA
40594507 ACTTACTAAGCATGTAAT
1 ACTTACTAAGCATGTAAT
40594525 ACTTACTAAGCATGTAAT
1 ACTTACTAAGCATGTAAT
*
40594543 GCTTACT
1 ACTTACT
40594550 CCGTTTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.35
Consensus pattern (18 bp):
ACTTACTAAGCATGTAAT
Found at i:40597238 original size:43 final size:43
Alignment explanation
Indices: 40597189--40597322 Score: 180
Period size: 43 Copynumber: 3.1 Consensus size: 43
40597179 GATTACCGAG
40597189 ATGTGATTACATATAAGACCATGTCTGGGACATTGGCATTG-T
1 ATGTGATTACATATAAGACCATGTCTGGGACATTGGCATTGTT
* *
40597231 ATTGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTT
1 A-TGTGATTACATATAAGACCATGTCTGGGACATTGGCATTGTT
* * * * * *
40597275 ATATGATTTCCTATAAGACCCTGTCTGGGACAATGGCATTGAT
1 ATGTGATTACATATAAGACCATGTCTGGGACATTGGCATTGTT
40597318 ATGTG
1 ATGTG
40597323 GTAACAAGTA
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
42 1 0.01
43 76 0.96
44 2 0.03
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.34
Consensus pattern (43 bp):
ATGTGATTACATATAAGACCATGTCTGGGACATTGGCATTGTT
Found at i:40599226 original size:33 final size:34
Alignment explanation
Indices: 40599188--40599253 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 34
40599178 TTTCAATTGA
*
40599188 GATTTAGCCTGGACTAGTAATCCTAAT-TGACTG
1 GATTTAGCCTGGACTAGTAATCCAAATATGACTG
*
40599221 GATTTAGCCTGGACTGGTAATCCAAATATGACT
1 GATTTAGCCTGGACTAGTAATCCAAATATGACT
40599254 CTATAGGGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 25 0.83
34 5 0.17
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (34 bp):
GATTTAGCCTGGACTAGTAATCCAAATATGACTG
Found at i:40601513 original size:27 final size:27
Alignment explanation
Indices: 40601482--40601659 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
40601472 TAAATTGTAC
*
40601482 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
40601509 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
40601535 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAATTGACTATGT
* *
40601563 GGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
40601590 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* * * *
40601618 GGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
40601645 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40601660 GACTTAATAT
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 104 0.81
28 24 0.19
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:40601541 original size:54 final size:55
Alignment explanation
Indices: 40601482--40601659 Score: 236
Period size: 54 Copynumber: 3.3 Consensus size: 55
40601472 TAAATTGTAC
* **
40601482 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT
1 AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
* * * *
40601537 -GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTGACTATG-T
1 AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
* *
40601590 AGCACTAAGTGTGCGAGTTTGATTATGTGGCACTAAGTGTGCGAGTTGATTAT-AT
1 AGCACTAAGTGTGCGA-TTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
*
40601645 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40601660 GACTTAATAT
Statistics
Matches: 107, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
53 1 0.01
54 60 0.56
55 46 0.43
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (55 bp):
AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
Found at i:40601595 original size:81 final size:82
Alignment explanation
Indices: 40601483--40601638 Score: 235
Period size: 81 Copynumber: 1.9 Consensus size: 82
40601473 AAATTGTACA
* *
40601483 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGA-AATGAATATGAT-GCACTAAGT
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGAATGAATATG-TGGCACTAAGT
40601546 GTGCGAATTGACCATGCG
65 GTGCGAATTGACCATGCG
** *
40601564 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGTGGCACTAAGTG
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGAATGAATATGTGGCACTAAGTG
*
40601629 TGCGAGTTGA
66 TGCGAATTGA
40601639 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 41 0.61
82 26 0.39
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (82 bp):
GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGAATGAATATGTGGCACTAAGTG
TGCGAATTGACCATGCG
Found at i:40609774 original size:27 final size:27
Alignment explanation
Indices: 40609743--40609920 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
40609733 TAAATTGTAC
*
40609743 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
40609770 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
40609796 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAATTGACTATGT
* *
40609824 GGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
40609851 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* * * *
40609879 GGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
40609906 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40609921 GACTTAATAT
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 104 0.81
28 24 0.19
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:40609804 original size:54 final size:55
Alignment explanation
Indices: 40609743--40609920 Score: 236
Period size: 54 Copynumber: 3.3 Consensus size: 55
40609733 TAAATTGTAC
* **
40609743 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT
1 AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
* * * *
40609798 -GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTGACTATG-T
1 AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
* *
40609851 AGCACTAAGTGTGCGAGTTTGATTATGTGGCACTAAGTGTGCGAGTTGATTAT-AT
1 AGCACTAAGTGTGCGA-TTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
*
40609906 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40609921 GACTTAATAT
Statistics
Matches: 107, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
53 1 0.01
54 60 0.56
55 46 0.43
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (55 bp):
AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
Found at i:40611438 original size:38 final size:39
Alignment explanation
Indices: 40611369--40611453 Score: 97
Period size: 39 Copynumber: 2.2 Consensus size: 39
40611359 CACTAGCAAT
40611369 AAATGCCTTCGGATTAGCCGGATATAGTCGC-TAGC-AC
1 AAATGCCTTCGGATTAGCCGGATATAGTCGCTTAGCGAC
*
40611406 AAATG-CTTCGGATCTTAGTCCGGATGTA-TCGCTTAGCGAC
1 AAATGCCTTCGGA--TTAG-CCGGATATAGTCGCTTAGCGAC
*
40611446 AAAAGCCT
1 AAATGCCT
40611454 CGGGCTACCC
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
36 7 0.17
37 5 0.12
38 8 0.20
39 12 0.30
40 6 0.15
41 2 0.05
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.26
Consensus pattern (39 bp):
AAATGCCTTCGGATTAGCCGGATATAGTCGCTTAGCGAC
Found at i:40614466 original size:40 final size:40
Alignment explanation
Indices: 40614382--40614565 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
40614372 TTGAATGCTG
* * * *
40614382 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
40614421 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
40614462 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
40614502 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
40614542 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
40614566 GAATGAGTTA
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 111 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:40614519 original size:80 final size:81
Alignment explanation
Indices: 40614382--40614562 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
40614372 TTGAATGCTG
* * *
40614382 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
40614446 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
40614462 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
40614523 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
40614542 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
40614563 ATTGAATGAG
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 4 0.04
80 76 0.85
81 9 0.10
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:40614586 original size:39 final size:38
Alignment explanation
Indices: 40614463--40614612 Score: 131
Period size: 40 Copynumber: 3.8 Consensus size: 38
40614453 GTTATTAATT
* ** * *
40614463 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATT
1 CCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTACTAA-A
** *
40614503 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 CCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTACT-AAA
*
40614542 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 -CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTA-AA
* *
40614582 CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 CCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
40614613 GAGCTATATC
Statistics
Matches: 93, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
39 30 0.32
40 63 0.68
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTAAA
Found at i:40614620 original size:40 final size:39
Alignment explanation
Indices: 40614503--40614625 Score: 97
Period size: 40 Copynumber: 3.1 Consensus size: 39
40614493 GATACTAATT
* ** ** *
40614503 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGT-TTTAAAA
1 CCGGGCTAAGTCCCGAAGGCATT-GAACGAGTGACTATAA
* * *
40614542 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTGAACGAGTGACTATAA
* *
40614582 CCGGGCTATGTCCCGAAGGCACTTGAACGAG-GAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCA-TTGAACGAGTGA-CTATAA
40614622 CCGG
1 CCGG
40614626 TTAAATTCCG
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
39 25 0.36
40 44 0.64
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTGAACGAGTGACTATAA
Found at i:40622367 original size:40 final size:40
Alignment explanation
Indices: 40622283--40622466 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
40622273 TTGAATGCTG
* * * *
40622283 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
40622322 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
40622363 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
40622403 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
40622443 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
40622467 GAATGAGTTA
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 111 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:40622420 original size:80 final size:81
Alignment explanation
Indices: 40622283--40622463 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
40622273 TTGAATGCTG
* * *
40622283 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
40622347 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
40622363 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
40622424 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
40622443 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
40622464 ATTGAATGAG
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 4 0.04
80 76 0.85
81 9 0.10
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:40622487 original size:39 final size:38
Alignment explanation
Indices: 40622364--40622513 Score: 131
Period size: 40 Copynumber: 3.8 Consensus size: 38
40622354 GTTATTAATT
* ** * *
40622364 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATT
1 CCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTACTAA-A
** *
40622404 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 CCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTACT-AAA
*
40622443 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 -CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTA-AA
* *
40622483 CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 CCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
40622514 GAGCTATATC
Statistics
Matches: 93, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
39 30 0.32
40 63 0.68
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTAAA
Found at i:40622521 original size:40 final size:39
Alignment explanation
Indices: 40622404--40622526 Score: 97
Period size: 40 Copynumber: 3.1 Consensus size: 39
40622394 GATACTAATT
* ** ** *
40622404 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGT-TTTAAAA
1 CCGGGCTAAGTCCCGAAGGCATT-GAACGAGTGACTATAA
* * *
40622443 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTGAACGAGTGACTATAA
* *
40622483 CCGGGCTATGTCCCGAAGGCACTTGAACGAG-GAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCA-TTGAACGAGTGA-CTATAA
40622523 CCGG
1 CCGG
40622527 TTAAATTCCG
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
39 25 0.36
40 44 0.64
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTGAACGAGTGACTATAA
Found at i:40633773 original size:55 final size:55
Alignment explanation
Indices: 40633639--40633782 Score: 162
Period size: 55 Copynumber: 2.6 Consensus size: 55
40633629 TATAAAGGTC
* ** * * *
40633639 CACACCCGTGTTGTTTTGGCAGGTTCACCCACGGTTGCTTGGCACTGGCGTGTCG
1 CACACCCGTGTTGTTTTGGCAGGTTCGCCCACGGTTGCAAGGCACGGGCATGCCG
* ** * * *
40633694 CACACCCATGTTAATTTGACAGGTTCGGCCACGGTTTCAAGGCACGGGCATGCCG
1 CACACCCGTGTTGTTTTGGCAGGTTCGCCCACGGTTGCAAGGCACGGGCATGCCG
* *
40633749 CACGCCCGTGTTGTTTTGGTAGGTTCGCCCACGG
1 CACACCCGTGTTGTTTTGGCAGGTTCGCCCACGG
40633783 CCATGTTGCA
Statistics
Matches: 70, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
55 70 1.00
ACGTcount: A:0.15, C:0.29, G:0.30, T:0.26
Consensus pattern (55 bp):
CACACCCGTGTTGTTTTGGCAGGTTCGCCCACGGTTGCAAGGCACGGGCATGCCG
Found at i:40641375 original size:15 final size:15
Alignment explanation
Indices: 40641355--40641383 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40641345 TGTTGTTTAA
40641355 AAACAGTTATAAATC
1 AAACAGTTATAAATC
40641370 AAACAGTTATAAAT
1 AAACAGTTATAAAT
40641384 TGAAGTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (15 bp):
AAACAGTTATAAATC
Found at i:40642635 original size:27 final size:26
Alignment explanation
Indices: 40642605--40642688 Score: 87
Period size: 27 Copynumber: 3.1 Consensus size: 26
40642595 ATAAATCGAA
*
40642605 GGTATTTCAGTAATTTTACAAGTCGGG
1 GGTATTTC-GTAATTTTACAAATCGGG
* *
40642632 GGTATTTCGATAATTTTACAAATTGAG
1 GGTATTTCG-TAATTTTACAAATCGGG
* * *
40642659 GGTATTACGGTAATTTCACAAATCAGG
1 GGTATTTC-GTAATTTTACAAATCGGG
40642686 GGT
1 GGT
40642689 TTTAACAACC
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
26 1 0.02
27 45 0.96
28 1 0.02
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.36
Consensus pattern (26 bp):
GGTATTTCGTAATTTTACAAATCGGG
Found at i:40645515 original size:16 final size:18
Alignment explanation
Indices: 40645496--40645530 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
40645486 GCCATATGAA
40645496 TTCCAAAAC-ATA-ATAG
1 TTCCAAAACGATAGATAG
40645512 TTCCAAAACGATAGATAG
1 TTCCAAAACGATAGATAG
40645530 T
1 T
40645531 GTGACGAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 3 0.18
18 5 0.29
ACGTcount: A:0.46, C:0.17, G:0.11, T:0.26
Consensus pattern (18 bp):
TTCCAAAACGATAGATAG
Found at i:40646175 original size:43 final size:43
Alignment explanation
Indices: 40646093--40646212 Score: 161
Period size: 43 Copynumber: 2.8 Consensus size: 43
40646083 TCTGAATTCA
* * *
40646093 TTCACCGGCATT-TCGCCTGCTAGGCTTGAAGCCCGATATTAT
1 TTCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCAATATTAT
* * *
40646135 TTCACCGGCATTATAACCTACTAGGCTCGAGGCCCAATATTAT
1 TTCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCAATATTAT
* *
40646178 TTCACCGGTATTATAGCCTGCTAGGCTTGAAGCCC
1 TTCACCGGCATTATAGCCTGCTAGGCTCGAAGCCC
40646213 GAATTCATCA
Statistics
Matches: 66, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
42 12 0.18
43 54 0.82
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (43 bp):
TTCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCAATATTAT
Found at i:40651847 original size:20 final size:22
Alignment explanation
Indices: 40651820--40651875 Score: 89
Period size: 20 Copynumber: 2.6 Consensus size: 22
40651810 ATAGTCAAGA
40651820 TGGCACAAAGCCATTTTTAGG-
1 TGGCACAAAGCCATTTTTAGGT
40651841 T-GCACAAAGCCATTTTTAGGT
1 TGGCACAAAGCCATTTTTAGGT
*
40651862 TGGCATAAAGCCAT
1 TGGCACAAAGCCAT
40651876 AATCAGATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 19 0.59
21 2 0.06
22 11 0.34
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (22 bp):
TGGCACAAAGCCATTTTTAGGT
Found at i:40652285 original size:27 final size:27
Alignment explanation
Indices: 40652231--40652319 Score: 94
Period size: 27 Copynumber: 3.3 Consensus size: 27
40652221 CAAAACAATC
* *
40652231 ATTTTACCCTACAAGGGTACTT-AGGTA
1 ATTTTACACTACAAGGGTATTTCA-GTA
40652258 ATTTTACACTACAAGGGTATTTCAGTAA
1 ATTTTACACTACAAGGGTATTTCAGT-A
* *
40652286 ATTTATA-AAT-CGAGGGTATTTCAGTA
1 ATTT-TACACTACAAGGGTATTTCAGTA
40652312 ATTTTACA
1 ATTTTACA
40652320 AGTCAGGGGT
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
25 2 0.04
26 6 0.11
27 36 0.67
28 8 0.15
29 2 0.04
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (27 bp):
ATTTTACACTACAAGGGTATTTCAGTA
Found at i:40652329 original size:27 final size:27
Alignment explanation
Indices: 40652255--40652349 Score: 79
Period size: 27 Copynumber: 3.5 Consensus size: 27
40652245 GGGTACTTAG
* *
40652255 GTAATTTTAC-ACTACAAGGGTATTTCA
1 GTAATTTTACAAAT-CAGGGGTATTTCA
* *
40652282 GTAAATTTATAAATC-GAGGGTATTTCA
1 GTAATTTTACAAATCAG-GGGTATTTCA
* *
40652309 GTAATTTTACAAGTCAGGGGTGTTTC-
1 GTAATTTTACAAATCAGGGGTATTTCA
*
40652335 GATAATTTCACAAAT
1 G-TAATTTTACAAAT
40652350 TAAGAGTATT
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
26 1 0.02
27 50 0.93
28 3 0.06
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.37
Consensus pattern (27 bp):
GTAATTTTACAAATCAGGGGTATTTCA
Found at i:40659883 original size:26 final size:26
Alignment explanation
Indices: 40659788--40659890 Score: 82
Period size: 27 Copynumber: 3.9 Consensus size: 26
40659778 TTACCGTATA
* *
40659788 GGGGTATTTTGGTAATTTTACACTACA-
1 GGGGTATTTCGATAATTTTACA--ACAT
* *
40659815 AGGGTATTTCGATAGTTTTACAAACAT
1 GGGGTATTTCGATAATTTTAC-AACAT
* * **
40659842 GTGGTATTTCAATAATTTTACAAGTT
1 GGGGTATTTCGATAATTTTACAACAT
* *
40659868 GGGGTATTTCGGTAATTTCACAA
1 GGGGTATTTCGATAATTTTACAA
40659891 ATTAGAGGTC
Statistics
Matches: 60, Mismatches: 14, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
26 25 0.42
27 34 0.57
28 1 0.02
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (26 bp):
GGGGTATTTCGATAATTTTACAACAT
Found at i:40669741 original size:26 final size:26
Alignment explanation
Indices: 40669705--40669756 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
40669695 CACCACTGAA
* *
40669705 TCGGGGAATCATCACTTAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
40669731 TCGGGGAATCAGCACATAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
40669757 CTTTTCATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.35, G:0.21, T:0.15
Consensus pattern (26 bp):
TCGGGGAATCAGCACATAGCAACCCC
Found at i:40669833 original size:70 final size:71
Alignment explanation
Indices: 40669717--40669867 Score: 241
Period size: 72 Copynumber: 2.1 Consensus size: 71
40669707 GGGGAATCAT
*
40669717 CACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTT-CATTTCAAATATACAATGG
1 CACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTTACATTTCAAAGATACAATGG
40669781 ATATCG
66 ATATCG
* ***
40669787 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
1 CACTTAGCAACCCCTC-GGGGAATCAGCACATAGCAACCCCCTTTTACATTTCAAAGATACAATG
40669852 GATATCG
65 GATATCG
40669859 CACTTAGCA
1 CACTTAGCA
40669868 CCACCAATGA
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
70 16 0.22
71 28 0.38
72 30 0.41
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (71 bp):
CACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTTACATTTCAAAGATACAATGG
ATATCG
Found at i:40670014 original size:26 final size:26
Alignment explanation
Indices: 40669984--40670034 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
40669974 ACCAATGAAC
*
40669984 CGGGGAATCAGCACTTAGCAACCCCT
1 CGGGGAATCAGCACATAGCAACCCCT
40670010 CGGGGAATCAGCACATAGCAACCCC
1 CGGGGAATCAGCACATAGCAACCCC
40670035 CTTTCACATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.35, G:0.24, T:0.12
Consensus pattern (26 bp):
CGGGGAATCAGCACATAGCAACCCCT
Found at i:40670091 original size:103 final size:104
Alignment explanation
Indices: 40669786--40670112 Score: 577
Period size: 104 Copynumber: 3.2 Consensus size: 104
40669776 AATGGATATC
40669786 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
40669851 GGATATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GGATATCGCACTTAGCACCACCAATGAACCGGGGAATCA
40669890 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
40669955 GGATATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GGATATCGCACTTAGCACCACCAATGAACCGGGGAATCA
40669994 GCACTTAGCAACCCCTC-GGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* * * *
40670058 GGATCA-CGCACATAGCACCACCCATAAATCGGGGAATCA
66 GGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCA
**
40670097 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
40670113 TTTATATACA
Statistics
Matches: 216, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
103 94 0.44
104 122 0.56
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.18
Consensus pattern (104 bp):
GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
GGATATCGCACTTAGCACCACCAATGAACCGGGGAATCA
Found at i:40670474 original size:29 final size:29
Alignment explanation
Indices: 40670441--40670504 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
40670431 TAATCCACCA
40670441 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
40670470 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
40670500 CCCAA
1 CCCAA
40670505 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:40670478 original size:30 final size:30
Alignment explanation
Indices: 40670448--40670504 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
40670438 CCACCCAACT
40670448 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
40670477 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
40670505 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:40673882 original size:40 final size:40
Alignment explanation
Indices: 40673845--40674029 Score: 198
Period size: 40 Copynumber: 4.7 Consensus size: 40
40673835 GCTACTCGTT
*
40673845 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* * *
40673885 CAAATGCCTTCGGGATTTAACCCGGATTTAGTAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
40673925 CAAATGCCTTCGGG-CTTAGCCCAGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * * *
40673964 CAAATGCATTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
40674005 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
40674030 CATCATTCAA
Statistics
Matches: 120, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
38 2 0.02
39 30 0.25
40 75 0.62
41 13 0.11
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:40673945 original size:79 final size:81
Alignment explanation
Indices: 40673845--40674029 Score: 211
Period size: 79 Copynumber: 2.3 Consensus size: 81
40673835 GCTACTCGTT
* * *
40673845 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGAT-TTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCATTC-GGATCTTAACCC
* *
40673908 GGATTTAGT-AGC-TCGCA
64 GGATATAGTCA-CTTAGCA
* * **
40673925 CAAATGCCTTCGGG-CTTAGCCCAGAATTAGTATCTCGCACAAATGCATTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCATTCGGATCTTAACCCGG
*
40673989 ATATGGTCACTTAGCA
66 ATATAGTCACTTAGCA
40674005 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
40674030 CATCATTCAA
Statistics
Matches: 89, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
78 4 0.04
79 51 0.57
80 34 0.38
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCATTCGGATCTTAACCCGG
ATATAGTCACTTAGCA
Found at i:40681869 original size:39 final size:39
Alignment explanation
Indices: 40681820--40681924 Score: 124
Period size: 39 Copynumber: 2.7 Consensus size: 39
40681810 AGCCCGGTTA
* * *
40681820 TAGTAAACTCGCACAAATGCCTTCGGAGATTA-ACCGGATT
1 TAGT-AACTCGCACAAATGCCTTCGGAG-CTAGACCAGAAT
*
40681860 TAGTAACTCGCACAAATGCCTTCGG-GCTAGCCCAGAAT
1 TAGTAACTCGCACAAATGCCTTCGGAGCTAGACCAGAAT
*
40681898 TAGTATCATCGCACAAATGCCTTCGGA
1 TAGTAAC-TCGCACAAATGCCTTCGGA
40681925 TCTTAGTCCG
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
37 2 0.04
38 12 0.21
39 39 0.68
40 4 0.07
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (39 bp):
TAGTAACTCGCACAAATGCCTTCGGAGCTAGACCAGAAT
Found at i:40686685 original size:27 final size:27
Alignment explanation
Indices: 40686668--40686844 Score: 176
Period size: 27 Copynumber: 6.6 Consensus size: 27
40686658 ATATTAAGTC
* *
40686668 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAAAT
*
40686695 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTATATAATCAAAT
* * *
40686722 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTATATAATCAAAT
*** ** *
40686749 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTATATAATCAAAT
* **
40686776 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTAT-ATAATCAAAT
* * *
40686803 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTATATAATCAAAT
40686830 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40686845 GTACAATTTA
Statistics
Matches: 129, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
27 128 0.99
28 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAAAT
Found at i:40686750 original size:54 final size:54
Alignment explanation
Indices: 40686668--40686844 Score: 230
Period size: 54 Copynumber: 3.3 Consensus size: 54
40686658 ATATTAAGTC
* * * *
40686668 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
* ** * *
40686722 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
* **
40686776 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
40686830 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40686845 GTACAATTTA
Statistics
Matches: 106, Mismatches: 15, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
53 1 0.01
54 105 0.99
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:40686806 original size:81 final size:81
Alignment explanation
Indices: 40686689--40686843 Score: 240
Period size: 81 Copynumber: 1.9 Consensus size: 81
40686679 TGCTATATAA
* *
40686689 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCTACATAGTCAACTCGCAC
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
40686754 ACTTAGTGCCGCATGG
66 ACTTAGTGCCGCATGG
* * **
40686770 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
40686834 CACTTAGTGC
65 CACTTAGTGC
40686844 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
80 1 0.01
81 66 0.99
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:40694603 original size:27 final size:27
Alignment explanation
Indices: 40694586--40694763 Score: 133
Period size: 27 Copynumber: 6.6 Consensus size: 27
40694576 ATATTAAGTC
40694586 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
* *
40694613 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
* * *
40694641 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTCAGTGCTATATAATCAACT
* *** ** *
40694668 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTCAGTGCTATATAATCAACT
* * **
40694695 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTCAGTGCTAT-ATAATCAACT
* * * * *
40694722 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTCAGTGCTATATAATCAACT
*
40694749 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
40694764 GTACAATTTA
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
27 104 0.79
28 27 0.21
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:40694725 original size:54 final size:54
Alignment explanation
Indices: 40694586--40694762 Score: 214
Period size: 54 Copynumber: 3.3 Consensus size: 54
40694576 ATATTAAGTC
* * *
40694586 CGCACACTCAGTGCTAT-ATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGC-ATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAA-T
* ** * *
40694641 CGCACACTTAGTGC-TACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCAT-CATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
* **
40694695 CGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
40694749 CGCACACTTAGTGC
1 CGCACACTTAGTGC
40694763 TGTACAATTT
Statistics
Matches: 105, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
53 1 0.01
54 60 0.57
55 44 0.42
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:40694752 original size:81 final size:82
Alignment explanation
Indices: 40694607--40694762 Score: 235
Period size: 81 Copynumber: 1.9 Consensus size: 82
40694597 TGCTATATAA
* *
40694607 TCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTACATAGTCAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
40694672 CACTTAGTGCCGCATGG
66 CACTTAGTGCCGCATGG
* * **
40694689 TCAATTCGCACACTTAGTGC-ATCATATTC-ATTTCGCACACTTAGTGCAACATAGTCAAATCGC
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGC
40694752 ACACTTAGTGC
65 ACACTTAGTGC
40694763 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 42 0.63
82 25 0.37
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (82 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
CACTTAGTGCCGCATGG
Found at i:40697043 original size:27 final size:26
Alignment explanation
Indices: 40697011--40697095 Score: 116
Period size: 27 Copynumber: 3.2 Consensus size: 26
40697001 GAAATTAATG
40697011 AATACCATTGGTTTGTAAAATTACCAA
1 AATACC-TTGGTTTGTAAAATTACCAA
* *
40697038 AATACCCCTAGTTTGTAAAATTACCAA
1 AATA-CCTTGGTTTGTAAAATTACCAA
*
40697065 AATAACTCTGGTTTGTAAAATTACCAA
1 AATACCT-TGGTTTGTAAAATTACCAA
40697092 AATA
1 AATA
40697096 TCCCTAATTT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
26 1 0.02
27 48 0.94
28 2 0.04
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.32
Consensus pattern (26 bp):
AATACCTTGGTTTGTAAAATTACCAA
Found at i:40697121 original size:27 final size:26
Alignment explanation
Indices: 40697021--40697276 Score: 138
Period size: 27 Copynumber: 9.5 Consensus size: 26
40697011 AATACCATTG
40697021 GTTTGTAAAATTACCAAAATACCCCTA
1 GTTTGTAAAATTACCAAAATA-CCCTA
* *
40697048 GTTTGTAAAATTACCAAAATAACTCTG
1 GTTTGTAAAATTACCAAAAT-ACCCTA
40697075 GTTTGTAAAATTACCAAAATATCCCTA
1 GTTTGTAAAATTACCAAAATA-CCCTA
* * * * *
40697102 ATTTGTGAAATTATCGAAATACCCTC
1 GTTTGTAAAATTACCAAAATACCCTA
*** ** *
40697128 GACCAGTAAAATTACTGAAATACCTTCA
1 G-TTTGTAAAATTACCAAAATACCCT-A
** * *
40697156 ACTTGTAAAATTACCGAAATACCCTC
1 GTTTGTAAAATTACCAAAATACCCTA
** **
40697182 GACCTGTAAAATTACTGAAATACCCTCCA
1 G-TTTGTAAAATTACCAAAATACCCT--A
* * * *
40697211 -CTTGTAAAATTATCGAAATACCCTC
1 GTTTGTAAAATTACCAAAATACCCTA
* * *
40697236 GATTT-TGAAAATTACCGAGATACCCTT
1 G-TTTGT-AAAATTACCAAAATACCCTA
*
40697263 GATTTGAAAAATTA
1 G-TTTGTAAAATTA
40697277 TAGAAATGCC
Statistics
Matches: 181, Mismatches: 37, Indels: 22
0.75 0.15 0.09
Matches are distributed among these distances:
26 6 0.03
27 174 0.96
28 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.30
Consensus pattern (26 bp):
GTTTGTAAAATTACCAAAATACCCTA
Found at i:40697137 original size:54 final size:54
Alignment explanation
Indices: 40697024--40697237 Score: 218
Period size: 54 Copynumber: 4.0 Consensus size: 54
40697014 ACCATTGGTT
** * * ***
40697024 TGTAAAATTACCAAAATACCC-CTAGTTTGTAAAATTACCAAAATA-ACTCTGGTT
1 TGTAAAATTACCAAAATACCCTC-AACTTGTAAAATTACCGAAATACCCTC-GACC
* * *
40697078 TGTAAAATTACCAAAATATCCCT-AATTTGTGAAATTATCGAAATACCCTCGACC
1 TGTAAAATTACCAAAATA-CCCTCAACTTGTAAAATTACCGAAATACCCTCGACC
* ** *
40697132 AGTAAAATTACTGAAATACCTTCAACTTGTAAAATTACCGAAATACCCTCGACC
1 TGTAAAATTACCAAAATACCCTCAACTTGTAAAATTACCGAAATACCCTCGACC
** * *
40697186 TGTAAAATTACTGAAATACCCTCCACTTGTAAAATTATCGAAATACCCTCGA
1 TGTAAAATTACCAAAATACCCTCAACTTGTAAAATTACCGAAATACCCTCGA
40697238 TTTTGAAAAT
Statistics
Matches: 137, Mismatches: 19, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
53 3 0.02
54 128 0.93
55 6 0.04
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.29
Consensus pattern (54 bp):
TGTAAAATTACCAAAATACCCTCAACTTGTAAAATTACCGAAATACCCTCGACC
Found at i:40697247 original size:81 final size:81
Alignment explanation
Indices: 40697077--40697261 Score: 198
Period size: 81 Copynumber: 2.3 Consensus size: 81
40697067 TAACTCTGGT
* * ** * *
40697077 TTGTAAAATTACCAAAATATCCCT-AATTTGTGAAATTATCGAAATACCCTCGACCAGTAAAATT
1 TTGTAAAATTACCGAAATA-CCCTCGACCTGTAAAATTATCGAAATACCCTCCACCAGTAAAATT
*
40697141 ACTGAAATACCTTCAAC
65 ACTGAAATACCCTCAAC
**
40697158 TTGTAAAATTACCGAAATACCCTCGACCTGTAAAATTA-CTGAAATACCCTCCACTTGTAAAATT
1 TTGTAAAATTACCGAAATACCCTCGACCTGTAAAATTATC-GAAATACCCTCCACCAGTAAAATT
*
40697222 A-TCGAAATACCCTCGA-
65 ACT-GAAATACCCTCAAC
* *
40697238 TTTTGAAAATTACCGAGATACCCT
1 TTGT-AAAATTACCGAAATACCCT
40697262 TGATTTGAAA
Statistics
Matches: 88, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
80 9 0.10
81 79 0.90
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.29
Consensus pattern (81 bp):
TTGTAAAATTACCGAAATACCCTCGACCTGTAAAATTATCGAAATACCCTCCACCAGTAAAATTA
CTGAAATACCCTCAAC
Found at i:40697261 original size:54 final size:54
Alignment explanation
Indices: 40697078--40697237 Score: 232
Period size: 54 Copynumber: 3.0 Consensus size: 54
40697068 AACTCTGGTT
** * *
40697078 TGTAAAATTACCAAAATATCCCT-AATTTGTGAAATTATCGAAATACCCTCGACC
1 TGTAAAATTACTGAAATA-CCCTCAACTTGTAAAATTATCGAAATACCCTCGACC
* * *
40697132 AGTAAAATTACTGAAATACCTTCAACTTGTAAAATTACCGAAATACCCTCGACC
1 TGTAAAATTACTGAAATACCCTCAACTTGTAAAATTATCGAAATACCCTCGACC
*
40697186 TGTAAAATTACTGAAATACCCTCCACTTGTAAAATTATCGAAATACCCTCGA
1 TGTAAAATTACTGAAATACCCTCAACTTGTAAAATTATCGAAATACCCTCGA
40697238 TTTTGAAAAT
Statistics
Matches: 94, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
53 3 0.03
54 91 0.97
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.28
Consensus pattern (54 bp):
TGTAAAATTACTGAAATACCCTCAACTTGTAAAATTATCGAAATACCCTCGACC
Done.