Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D06
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: 62964862
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 132689 characters in sequence are not A, C, G, or T
File 178 of 207
Found at i:54795276 original size:318 final size:318
Alignment explanation
Indices: 54794699--54795333 Score: 1261
Period size: 318 Copynumber: 2.0 Consensus size: 318
54794689 AGGCGGCTGC
54794699 GTGGGTATCATCGGTTGAACTGCTGCGTCGGGTGACTATGTCGGTGCTCTCGTTGGGCCTGGTGA
1 GTGGGTATCATCGGTTGAACTGCTGCGTCGGGTGACTATGTCGGTGCTCTCGTTGGGCCTGGTGA
54794764 TTGCATGACCGCTGATGATGAGCCAGGTGAATGTCTGGGCCTCGTTGAGGGGCTGTCTTTGTCAT
66 TTGCATGACCGCTGATGATGAGCCAGGTGAATGTCTGGGCCTCGTTGAGGGGCTGTCTTTGTCAT
54794829 CTTGTCGTCTTGGATTTAGAGGCCCGCGCCTTTCCCTTTGGACTCATATTTGCCGCTGCCTCTCC
131 CTTGTCGTCTTGGATTTAGAGGCCCGCGCCTTTCCCTTTGGACTCATATTTGCCGCTGCCTCTCC
54794894 TCTGGCGTCAGTAAATACGGCTTGCCATGGATCTTAAACTATGGCATGTATATCGGAACACACGC
196 TCTGGCGTCAGTAAATACGGCTTGCCATGGATCTTAAACTATGGCATGTATATCGGAACACACGC
54794959 TAACTCCGGAACGATGATTGGTTCCCAAGTAGGTATATATTCATACCGATCTTCCCAA
261 TAACTCCGGAACGATGATTGGTTCCCAAGTAGGTATATATTCATACCGATCTTCCCAA
54795017 GTGGGTATCATCGGTTGAACTGCTGCGTCGGGTGACTATGTCGGTGCTCTCGTTGGGCCTGGTGA
1 GTGGGTATCATCGGTTGAACTGCTGCGTCGGGTGACTATGTCGGTGCTCTCGTTGGGCCTGGTGA
54795082 TTGCATGACCGCTGATGATGAGCCAGGTGAATGTCTGGGCCTCGTTGAGGGGCTGTCTTTGTCAT
66 TTGCATGACCGCTGATGATGAGCCAGGTGAATGTCTGGGCCTCGTTGAGGGGCTGTCTTTGTCAT
*
54795147 CTTGTCGTCTTGGATTTAGAGGCCCGCGCTTTTCCCTTTGGACTCATATTTGCCGCTGCCTCTCC
131 CTTGTCGTCTTGGATTTAGAGGCCCGCGCCTTTCCCTTTGGACTCATATTTGCCGCTGCCTCTCC
54795212 TCTGGCGTCAGTAAATACGGCTTGCCATGGATCTTAAACTATGGCATGTATATCGGAACACACGC
196 TCTGGCGTCAGTAAATACGGCTTGCCATGGATCTTAAACTATGGCATGTATATCGGAACACACGC
54795277 TAACTCCGGAACGATGATTGGTTCCCAAGTAGGTATATATTCATACCGATCTTCCCA
261 TAACTCCGGAACGATGATTGGTTCCCAAGTAGGTATATATTCATACCGATCTTCCCA
54795334 CATTTCCATG
Statistics
Matches: 316, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
318 316 1.00
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (318 bp):
GTGGGTATCATCGGTTGAACTGCTGCGTCGGGTGACTATGTCGGTGCTCTCGTTGGGCCTGGTGA
TTGCATGACCGCTGATGATGAGCCAGGTGAATGTCTGGGCCTCGTTGAGGGGCTGTCTTTGTCAT
CTTGTCGTCTTGGATTTAGAGGCCCGCGCCTTTCCCTTTGGACTCATATTTGCCGCTGCCTCTCC
TCTGGCGTCAGTAAATACGGCTTGCCATGGATCTTAAACTATGGCATGTATATCGGAACACACGC
TAACTCCGGAACGATGATTGGTTCCCAAGTAGGTATATATTCATACCGATCTTCCCAA
Found at i:54797780 original size:14 final size:13
Alignment explanation
Indices: 54797756--54797785 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
54797746 GAGGGGGGAG
54797756 AAAGAAAGAAAGA
1 AAAGAAAGAAAGA
54797769 AAAGAGAAGAAAGA
1 AAAGA-AAGAAAGA
54797783 AAA
1 AAA
54797786 AGTATTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAAGA
Found at i:54801541 original size:48 final size:52
Alignment explanation
Indices: 54801481--54801697 Score: 171
Period size: 62 Copynumber: 3.9 Consensus size: 52
54801471 CCAATGTACC
*
54801481 TAATTTATATTAC-AAAGT-TT-G-TTCCAAGTTTTAATGTTGTAATGTATT
1 TAATTTATATTACAAAAATATTAGTTTCCAAGTTTTAATGTTGTAATGTATT
*
54801529 TAATTTATATTACAAAACTAATATTACAAAGTTTGTTTCAAGTTTTAATGTTGTAATGTATT
1 TAATTTATATTAC-AAA--AATATT----AG--T-TTCCAAGTTTTAATGTTGTAATGTATT
54801591 TAATTTATATTACAAAATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATT
1 TAATTTATATTACAAAA---ATATT----AG--T-TTCCAAGTTTTAATGTTGTAATGTATT
*
54801653 TAATTTATATTAC-AAAGT-TT-G-TTCCAAGTTTTAATGTTGTAATGT
1 TAATTTATATTACAAAAATATTAGTTTCCAAGTTTTAATGTTGTAATGT
54801698 TGTAATGTTG
Statistics
Matches: 148, Mismatches: 4, Indels: 34
0.80 0.02 0.18
Matches are distributed among these distances:
48 37 0.25
50 2 0.01
52 3 0.02
53 2 0.01
57 2 0.01
58 2 0.01
59 1 0.01
61 6 0.04
62 93 0.63
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.48
Consensus pattern (52 bp):
TAATTTATATTACAAAAATATTAGTTTCCAAGTTTTAATGTTGTAATGTATT
Found at i:54801563 original size:62 final size:62
Alignment explanation
Indices: 54801487--54801668 Score: 337
Period size: 62 Copynumber: 2.9 Consensus size: 62
54801477 TACCTAATTT
54801487 ATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAATTTATATTACAAAACTA
1 ATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAATTTATATTACAAAACTA
* * *
54801549 ATATTACAAAGTTTGTTTCAAGTTTTAATGTTGTAATGTATTTAATTTATATTACAAAATTT
1 ATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAATTTATATTACAAAACTA
54801611 ATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAATTTATATTACAAA
1 ATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAATTTATATTACAAA
54801669 GTTTGTTCCA
Statistics
Matches: 116, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 116 1.00
ACGTcount: A:0.36, C:0.07, G:0.10, T:0.47
Consensus pattern (62 bp):
ATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAATTTATATTACAAAACTA
Found at i:54801611 original size:14 final size:14
Alignment explanation
Indices: 54801592--54801620 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
54801582 TAATGTATTT
54801592 AATTTATATTACAA
1 AATTTATATTACAA
54801606 AATTTATATTACAA
1 AATTTATATTACAA
54801620 A
1 A
54801621 GTTTGTTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
AATTTATATTACAA
Found at i:54801697 original size:8 final size:8
Alignment explanation
Indices: 54801684--54801719 Score: 72
Period size: 8 Copynumber: 4.5 Consensus size: 8
54801674 TTCCAAGTTT
54801684 TAATGTTG
1 TAATGTTG
54801692 TAATGTTG
1 TAATGTTG
54801700 TAATGTTG
1 TAATGTTG
54801708 TAATGTTG
1 TAATGTTG
54801716 TAAT
1 TAAT
54801720 ATTGCAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.50
Consensus pattern (8 bp):
TAATGTTG
Found at i:54803534 original size:4 final size:4
Alignment explanation
Indices: 54803519--54803551 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
54803509 TAATAGAACT
*
54803519 AGTA AATA AGTA AGTA AGTA AGTA AGTA AGTA A
1 AGTA AGTA AGTA AGTA AGTA AGTA AGTA AGTA A
54803552 TAATAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.21, T:0.24
Consensus pattern (4 bp):
AGTA
Found at i:54807099 original size:12 final size:12
Alignment explanation
Indices: 54807082--54807106 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54807072 TTATAATATT
54807082 TATAAAATAAAA
1 TATAAAATAAAA
54807094 TATAAAATAAAA
1 TATAAAATAAAA
54807106 T
1 T
54807107 TTTAAAACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
TATAAAATAAAA
Found at i:54807208 original size:23 final size:24
Alignment explanation
Indices: 54807182--54807238 Score: 64
Period size: 27 Copynumber: 2.3 Consensus size: 24
54807172 TCTTAATTTA
54807182 TCTCAT-AAATTCCA-ACTCAATGG
1 TCTCATCAAATTCCATA-TCAATGG
54807205 TCTCATTCACAAATTCCATATCAATGG
1 TCTCA-T--CAAATTCCATATCAATGG
54807232 TCTCATC
1 TCTCATC
54807239 TTTTACCTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
23 5 0.17
24 2 0.07
26 1 0.03
27 20 0.69
28 1 0.03
ACGTcount: A:0.32, C:0.28, G:0.07, T:0.33
Consensus pattern (24 bp):
TCTCATCAAATTCCATATCAATGG
Found at i:54808677 original size:40 final size:40
Alignment explanation
Indices: 54808600--54808725 Score: 180
Period size: 40 Copynumber: 3.1 Consensus size: 40
54808590 AGCGGCACTT
* * *
54808600 TTAGCGGTGTTTGGAGCAAAAACGCTGCTAAAGAGTGAGCA
1 TTAGCGGTGTTT-AAGCAAAAGCGCCGCTAAAGAGTGAGCA
*
54808641 TTAGCGGTGTTTAAGTAAAAGCGCCGCTAAAGAGTGAGCA
1 TTAGCGGTGTTTAAGCAAAAGCGCCGCTAAAGAGTGAGCA
* * *
54808681 TTAGTGGCGTTTAAGGAAAAGCGCCGCTAAAGAGTGAGCA
1 TTAGCGGTGTTTAAGCAAAAGCGCCGCTAAAGAGTGAGCA
54808721 TTAGC
1 TTAGC
54808726 AGCGTTTATA
Statistics
Matches: 77, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
40 65 0.84
41 12 0.16
ACGTcount: A:0.32, C:0.15, G:0.31, T:0.22
Consensus pattern (40 bp):
TTAGCGGTGTTTAAGCAAAAGCGCCGCTAAAGAGTGAGCA
Found at i:54809121 original size:113 final size:112
Alignment explanation
Indices: 54808681--54809385 Score: 1110
Period size: 112 Copynumber: 6.3 Consensus size: 112
54808671 AGAGTGAGCA
** * *
54808681 TTAGTGGCGTTTAAGGAAAAGCGCCGCTAAAGAGTGAGCATTAGCAGCGTTTATAAAAAACGCCG
1 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCCG
* *
54808746 CAAATAATACACCCAGACGGTGCCGTTCTGTGGCCTTT-GGGGGGAA
66 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGAC
* *
54808792 ATAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACACCG
1 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCCG
* *
54808857 GAAATAATACACCCAAACGGTGCCGTTTTGTGGCCTTTGGGGGGGAGGAC
66 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTT--GGGGG-GGAC
* * * *
54808907 TTAGTGGCGTTTATTGTAAAGCGCCGTTAAAGACTGAACATTAGCAGCGTTTAT-AAAAATGCCA
1 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCCG
* *
54808971 CAAATAATACACCCAAACGGTGTCGTTTTGTGGCCTTTGGGGGGGGAC
66 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTT-GGGGGGGAC
54809019 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCCG
1 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCCG
* *
54809084 CAAATAATACACCCAGACGGTGCCATTTTGTGGCCTTTGGGGGGGAA
66 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGAC
* *
54809131 TTGGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATGAAAAACGCCG
1 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCCG
* *
54809196 CAAATAATACACCCAGACGGTGCTGTTTTGTGGCCTTTGGAGGGGAC
66 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGAC
54809243 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCC
1 TTAGTGGCGTTTATTGTAAAGCGCCGCT-AAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCC
* *
54809308 ACAAATAATACACCCAGACGGTGCCGTTTTGTGTCCTTTGGGGGGG-C
65 GCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGAC
*
54809355 ATTAGTGGCGTTTTTTGTAAAGCGCCGCTAA
1 -TTAGTGGCGTTTATTGTAAAGCGCCGCTAA
54809386 TCTAGGTGTT
Statistics
Matches: 548, Mismatches: 39, Indels: 13
0.91 0.06 0.02
Matches are distributed among these distances:
111 94 0.17
112 200 0.36
113 153 0.28
114 47 0.09
115 54 0.10
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (112 bp):
TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCCG
CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGAC
Found at i:54809321 original size:225 final size:222
Alignment explanation
Indices: 54808680--54809385 Score: 1117
Period size: 225 Copynumber: 3.1 Consensus size: 222
54808670 AAGAGTGAGC
** * *
54808680 ATTAGTGGCGTTTAAGGAAAAGCGCCGCTAAAGAGTGAGCATTAGCAGCGTTTATAAAAAACGCC
1 ATTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTAT-AAAAACGCC
* * **
54808745 GCAAATAATACACCCAGACGGTGCCGTTCTGTGGCCTTTGGGGGGAAATAGTGGCGTTTATTGTA
65 GCAAATAATACACCCAGACGGTGCTGTTTTGTGGCCTTTGGGGGGACTTAGTGGCGTTTATTGTA
* * *
54808810 AAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACACCGGAAATAATACACCCAAAC
130 AAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCCGCAAATAATACACCCAGAC
54808875 GGTGCCGTTTTGTGGCCTTTGGGGGGGA
195 GGTGCCGTTTTGTGGCCTTTGGGGGGGA
* * *
54808903 GGACTTAGTGGCGTTTATTGTAAAGCGCCGTTAAAGACTGAACATTAGCAGCGTTTATAAAAATG
1 --A-TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAACG
* *
54808968 CCACAAATAATACACCCAAACGGTG-TCGTTTTGTGGCCTTTGGGGGGGGACTTAGTGGCGTTTA
63 CCGCAAATAATACACCCAGACGGTGCT-GTTTTGTGGCCTTT--GGGGGGACTTAGTGGCGTTTA
54809032 TTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCCGCAAATAATACACC
125 TTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCCGCAAATAATACACC
*
54809097 CAGACGGTGCCATTTTGTGGCCTTTGGGGGGGA
190 CAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGA
*
54809130 ATTGGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATGAAAAACGCC
1 ATTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTAT-AAAAACGCC
54809195 GCAAATAATACACCCAGACGGTGCTGTTTTGTGGCCTTTGGAGGGGACTTAGTGGCGTTTATTGT
65 GCAAATAATACACCCAGACGGTGCTGTTTTGTGGCCTTTGG-GGGGACTTAGTGGCGTTTATTGT
*
54809260 AAAGCGCCGCTAAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCCACAAATAATACACCCAG
129 AAAGCGCCGCT-AAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCCGCAAATAATACACCCAG
* *
54809325 ACGGTGCCGTTTTGTGTCCTTTGGGGGGGC
193 ACGGTGCCGTTTTGTGGCCTTTGGGGGGGA
*
54809355 ATTAGTGGCGTTTTTTGTAAAGCGCCGCTAA
1 ATTAGTGGCGTTTATTGTAAAGCGCCGCTAA
54809386 TCTAGGTGTT
Statistics
Matches: 444, Mismatches: 29, Indels: 16
0.91 0.06 0.03
Matches are distributed among these distances:
223 2 0.00
224 85 0.19
225 195 0.44
226 49 0.11
227 113 0.25
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (222 bp):
ATTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAACGCCG
CAAATAATACACCCAGACGGTGCTGTTTTGTGGCCTTTGGGGGGACTTAGTGGCGTTTATTGTAA
AGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCCGCAAATAATACACCCAGACG
GTGCCGTTTTGTGGCCTTTGGGGGGGA
Found at i:54811216 original size:84 final size:84
Alignment explanation
Indices: 54811109--54811305 Score: 322
Period size: 84 Copynumber: 2.3 Consensus size: 84
54811099 TAAACTTTTG
* *
54811109 GTGGCGTTTTTAGGAAAACGCCACAAATAATGTAATTCCAGACCACGAAAACGGTGTCGCTTCTG
1 GTGGCGTTTTTAGGAAAACGCCACAAAAAATGCAATTCCAGACCACGAAAACGGTGTCGCTTCTG
54811174 TTCACAGCTGTAATATTTA
66 TTCACAGCTGTAATATTTA
* * *
54811193 GTGGCATTTTTAGGAAAATGCCACAAAAAATGCAATTCCAGACCACGAAAACGGTGTCGTTTCTG
1 GTGGCGTTTTTAGGAAAACGCCACAAAAAATGCAATTCCAGACCACGAAAACGGTGTCGCTTCTG
54811258 TTCACAGCTGTAATATTTA
66 TTCACAGCTGTAATATTTA
**
54811277 GTGGCGTTTTTACCAAAAACGCCACAAAA
1 GTGGCGTTTTTA-GGAAAACGCCACAAAA
54811306 CAGTGTTAAT
Statistics
Matches: 103, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
84 90 0.87
85 13 0.13
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.27
Consensus pattern (84 bp):
GTGGCGTTTTTAGGAAAACGCCACAAAAAATGCAATTCCAGACCACGAAAACGGTGTCGCTTCTG
TTCACAGCTGTAATATTTA
Found at i:54812948 original size:11 final size:11
Alignment explanation
Indices: 54812928--54812956 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
54812918 GAATATCTCA
54812928 AACT-ATGGGT
1 AACTAATGGGT
54812938 AACTAATGGGT
1 AACTAATGGGT
54812949 AACTAATG
1 AACTAATG
54812957 TATTATCATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.38, C:0.10, G:0.24, T:0.28
Consensus pattern (11 bp):
AACTAATGGGT
Found at i:54813726 original size:17 final size:17
Alignment explanation
Indices: 54813697--54813748 Score: 77
Period size: 17 Copynumber: 3.1 Consensus size: 17
54813687 GATTGAATGT
*
54813697 TAAATTTATTACTAAAA
1 TAAATTAATTACTAAAA
*
54813714 TACATTAATTACTAAAA
1 TAAATTAATTACTAAAA
*
54813731 TAAATTACTTACTAAAA
1 TAAATTAATTACTAAAA
54813748 T
1 T
54813749 TTGTTTAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAATTAATTACTAAAA
Found at i:54813757 original size:23 final size:23
Alignment explanation
Indices: 54813731--54813799 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 23
54813721 ATTACTAAAA
54813731 TAAATTACTTACTAAAATTTGTT
1 TAAATTACTTACTAAAATTTGTT
54813754 TAAATTTA-TTACTAAAA------
1 TAAA-TTACTTACTAAAATTTGTT
*
54813771 TACATTACTTACTAAAATTTGTT
1 TAAATTACTTACTAAAATTTGTT
54813794 TAAATT
1 TAAATT
54813800 TATTACTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 16
0.67 0.04 0.30
Matches are distributed among these distances:
16 3 0.08
17 12 0.33
23 18 0.50
24 3 0.08
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.46
Consensus pattern (23 bp):
TAAATTACTTACTAAAATTTGTT
Found at i:54813821 original size:40 final size:40
Alignment explanation
Indices: 54813721--54813811 Score: 164
Period size: 40 Copynumber: 2.2 Consensus size: 40
54813711 AAATACATTA
*
54813721 ATTACTAAAATAAATTACTTACTAAAATTTGTTTAAATTT
1 ATTACTAAAATACATTACTTACTAAAATTTGTTTAAATTT
54813761 ATTACTAAAATACATTACTTACTAAAATTTGTTTAAATTT
1 ATTACTAAAATACATTACTTACTAAAATTTGTTTAAATTT
54813801 ATTACTTAAAA
1 ATTAC-TAAAA
54813812 ATGTTACTTA
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 44 0.90
41 5 0.10
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (40 bp):
ATTACTAAAATACATTACTTACTAAAATTTGTTTAAATTT
Found at i:54813831 original size:13 final size:13
Alignment explanation
Indices: 54813793--54813837 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
54813783 TAAAATTTGT
54813793 TTAAATTTATTAC
1 TTAAATTTATTAC
** *
54813806 TTAAAAATGTTAC
1 TTAAATTTATTAC
54813819 TTAAATTTATTAC
1 TTAAATTTATTAC
54813832 TTAAAT
1 TTAAAT
54813838 GATTATAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (13 bp):
TTAAATTTATTAC
Found at i:54814069 original size:72 final size:72
Alignment explanation
Indices: 54813988--54814132 Score: 263
Period size: 72 Copynumber: 2.0 Consensus size: 72
54813978 ATAAAATATA
* **
54813988 AAAAAATATGTGGAATATTAATATTGACTATTAAAATAGCATGTTATTTTATTAAATATTATTAA
1 AAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTATTAA
54814053 TAATTAT
66 TAATTAT
54814060 AAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTATTAA
1 AAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTATTAA
54814125 TAATTAT
66 TAATTAT
54814132 A
1 A
54814133 TTAGTAATGT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.42
Consensus pattern (72 bp):
AAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTATTAA
TAATTAT
Found at i:54814211 original size:18 final size:18
Alignment explanation
Indices: 54814188--54814310 Score: 87
Period size: 18 Copynumber: 6.6 Consensus size: 18
54814178 AATAACTTAC
54814188 AACTTACATAATACATTT
1 AACTTACATAATACATTT
*
54814206 AACTTACACAATACATTTAACTT
1 AACTTACATAATACA--T---TT
54814229 ACAACTTACATAATACATTT
1 --AACTTACATAATACATTT
*
54814249 AACTTACA-ACTTACA--T
1 AACTTACATA-ATACATTT
*
54814265 AA--TACATAATA-ACTTAC
1 AACTTACATAATACA-TT-T
54814282 AACTTACATAATACATTT
1 AACTTACATAATACATTT
54814300 AACTTACATAA
1 AACTTACATAA
54814311 CTTACCATTG
Statistics
Matches: 83, Mismatches: 6, Indels: 32
0.69 0.05 0.26
Matches are distributed among these distances:
13 1 0.01
14 6 0.07
15 1 0.01
16 3 0.04
17 3 0.04
18 37 0.45
19 11 0.13
20 4 0.05
23 3 0.04
25 14 0.17
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (18 bp):
AACTTACATAATACATTT
Found at i:54814213 original size:25 final size:25
Alignment explanation
Indices: 54814169--54814307 Score: 193
Period size: 25 Copynumber: 5.8 Consensus size: 25
54814159 ATTTTATTAA
*
54814169 ATAATACATAATAACTTACAACTTAC
1 ATAATACAT-TTAACTTACAACTTAC
54814195 ATAATACATTTAACTT---AC--AC
1 ATAATACATTTAACTTACAACTTAC
54814215 --AATACATTTAACTTACAACTTAC
1 ATAATACATTTAACTTACAACTTAC
54814238 ATAATACATTTAACTTACAACTTAC
1 ATAATACATTTAACTTACAACTTAC
*
54814263 ATAATACATAATAACTTACAACTTAC
1 ATAATACAT-TTAACTTACAACTTAC
54814289 ATAATACATTTAACTTACA
1 ATAATACATTTAACTTACA
54814308 TAACTTACCA
Statistics
Matches: 102, Mismatches: 3, Indels: 17
0.84 0.02 0.14
Matches are distributed among these distances:
18 14 0.14
20 2 0.02
21 2 0.02
22 2 0.02
23 2 0.02
25 47 0.46
26 33 0.32
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.34
Consensus pattern (25 bp):
ATAATACATTTAACTTACAACTTAC
Found at i:54814293 original size:51 final size:50
Alignment explanation
Indices: 54814206--54814307 Score: 177
Period size: 51 Copynumber: 2.0 Consensus size: 50
54814196 TAATACATTT
*
54814206 AACTTACACAATACATTTAACTTACAACTTACATAATACATTTAACTTAC
1 AACTTACACAATACATATAACTTACAACTTACATAATACATTTAACTTAC
*
54814256 AACTTACATAATACATAATAACTTACAACTTACATAATACATTTAACTTAC
1 AACTTACACAATACAT-ATAACTTACAACTTACATAATACATTTAACTTAC
54814307 A
1 A
54814308 TAACTTACCA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
50 15 0.31
51 34 0.69
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (50 bp):
AACTTACACAATACATATAACTTACAACTTACATAATACATTTAACTTAC
Found at i:54819815 original size:21 final size:21
Alignment explanation
Indices: 54819762--54819818 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
54819752 GCTACAACTT
* * *
54819762 AAAGCAGAGGCGGAAGCGAGG
1 AAAGCGGAGGCTGCAGCGAGG
54819783 AAAGCGGAGGCTGCAGCGAGG
1 AAAGCGGAGGCTGCAGCGAGG
*
54819804 GAAGCGGAGGCTGCA
1 AAAGCGGAGGCTGCA
54819819 ATGAGAGAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.32, C:0.18, G:0.47, T:0.04
Consensus pattern (21 bp):
AAAGCGGAGGCTGCAGCGAGG
Found at i:54819828 original size:21 final size:21
Alignment explanation
Indices: 54819784--54819829 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
54819774 GAAGCGAGGA
* *
54819784 AAGCGGAGGCTGCAGCGAGGG
1 AAGCGGAGGCTGCAACGAGAG
*
54819805 AAGCGGAGGCTGCAATGAGAG
1 AAGCGGAGGCTGCAACGAGAG
54819826 AAGC
1 AAGC
54819830 AGAGCAGAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.17, G:0.46, T:0.07
Consensus pattern (21 bp):
AAGCGGAGGCTGCAACGAGAG
Found at i:54820824 original size:20 final size:20
Alignment explanation
Indices: 54820771--54820840 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
54820761 GTATTTTTCA
54820771 AAATAAAAATAAAA-ATAAATT
1 AAAT-AAAATAAAATAT-AATT
* * *
54820792 -AATTAATTAAAATGT-ATT
1 AAATAAAATAAAATATAATT
54820810 ACAATAAAATAAAATATAATT
1 A-AATAAAATAAAATATAATT
54820831 AAATAAAATA
1 AAATAAAATA
54820841 GTTTAAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
18 3 0.08
19 7 0.18
20 25 0.64
21 4 0.10
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (20 bp):
AAATAAAATAAAATATAATT
Found at i:54822770 original size:3 final size:3
Alignment explanation
Indices: 54822762--54822794 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
54822752 TAATTTCATG
54822762 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
54822795 CAACAAGAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:54824005 original size:16 final size:16
Alignment explanation
Indices: 54823965--54824006 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
54823955 TGTGTGTTGG
54823965 ATTAAATTAAATATGA
1 ATTAAATTAAATATGA
*
54823981 ATTATATTAAAT-TGA
1 ATTAAATTAAATATGA
*
54823996 GTTAAAATTAA
1 ATT-AAATTAA
54824007 TTCGTATAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.40
Consensus pattern (16 bp):
ATTAAATTAAATATGA
Found at i:54824390 original size:50 final size:50
Alignment explanation
Indices: 54824336--54824430 Score: 120
Period size: 50 Copynumber: 1.9 Consensus size: 50
54824326 TCTATATTTG
* * *
54824336 GCTCATAAGAGCTTCCTGA-TATACAGCTCGTATGAGCTTCCCGTTACTTA
1 GCTCACAAGAGCTTCCT-ATTATACAGCTCGGAAGAGCTTCCCGTTACTTA
* **
54824386 GCTCACATGAGCTTCCTATTATATGGCTCGGAAGAGCTTCCCGTT
1 GCTCACAAGAGCTTCCTATTATACAGCTCGGAAGAGCTTCCCGTT
54824431 TACATGCTTG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
49 1 0.03
50 37 0.97
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (50 bp):
GCTCACAAGAGCTTCCTATTATACAGCTCGGAAGAGCTTCCCGTTACTTA
Found at i:54837353 original size:14 final size:15
Alignment explanation
Indices: 54837335--54837386 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 15
54837325 GACTTCTGGT
54837335 TTAGGCTAGTTGGGC
1 TTAGGCTAGTTGGGC
*
54837350 -TAGGGTA-TTGGGC
1 TTAGGCTAGTTGGGC
*
54837363 TTAGGCTAGTTGGGT
1 TTAGGCTAGTTGGGC
*
54837378 TTAGACTAG
1 TTAGGCTAG
54837387 GTTAGAGTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
13 6 0.19
14 12 0.39
15 13 0.42
ACGTcount: A:0.17, C:0.10, G:0.38, T:0.35
Consensus pattern (15 bp):
TTAGGCTAGTTGGGC
Found at i:54845537 original size:15 final size:15
Alignment explanation
Indices: 54845513--54845550 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
54845503 AAACTCTAGC
54845513 CTAGCCTAAACCCAA
1 CTAGCCTAAACCCAA
*
54845528 CTAGCTTAAACCCAA
1 CTAGCCTAAACCCAA
*
54845543 TTAGCCTA
1 CTAGCCTA
54845551 GCCTCATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.37, C:0.34, G:0.08, T:0.21
Consensus pattern (15 bp):
CTAGCCTAAACCCAA
Found at i:54851079 original size:19 final size:19
Alignment explanation
Indices: 54851055--54851095 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
54851045 TGATTTATTC
*
54851055 TAAGATTTATCTATCTAAA
1 TAAGATTTATCTACCTAAA
54851074 TAAGATTTATCTACCTAAA
1 TAAGATTTATCTACCTAAA
54851093 TAA
1 TAA
54851096 CTTTAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.39
Consensus pattern (19 bp):
TAAGATTTATCTACCTAAA
Found at i:54851796 original size:3 final size:3
Alignment explanation
Indices: 54851788--54851816 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
54851778 AAATAAAAGA
54851788 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
54851817 CAACAACAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:54857209 original size:11 final size:11
Alignment explanation
Indices: 54857111--54857209 Score: 54
Period size: 11 Copynumber: 8.6 Consensus size: 11
54857101 GTTTTCTCAC
*
54857111 TATTTTATTAC
1 TATTTTATTAT
* *
54857122 CATTTCATTAT
1 TATTTTATTAT
* ** *
54857133 TATATTGCTAC
1 TATTTTATTAT
*
54857144 TATTTTATTGT
1 TATTTTATTAT
*
54857155 TATTATTTAGATAT
1 TA-T-TTTA-TTAT
* * *
54857169 TATATAATTGT
1 TATTTTATTAT
54857180 TATTTTATTAT
1 TATTTTATTAT
54857191 TAATTTTATTAT
1 T-ATTTTATTAT
54857203 TATTTTA
1 TATTTTA
54857210 GAGGCATTTG
Statistics
Matches: 61, Mismatches: 23, Indels: 8
0.66 0.25 0.09
Matches are distributed among these distances:
11 38 0.62
12 14 0.23
13 5 0.08
14 4 0.07
ACGTcount: A:0.29, C:0.05, G:0.04, T:0.62
Consensus pattern (11 bp):
TATTTTATTAT
Found at i:54858115 original size:24 final size:22
Alignment explanation
Indices: 54858048--54858115 Score: 54
Period size: 24 Copynumber: 3.1 Consensus size: 22
54858038 TATATCCAAT
54858048 TTTTTAAATTAATAGAAAATGATA
1 TTTTTAAATTAATAG-AAAT-ATA
* *
54858072 TTTTAAAATT-AT---AATCTA
1 TTTTTAAATTAATAGAAATATA
54858090 TTTTTAAATTAATAGAAGATAATA
1 TTTTTAAATTAATAGAA-AT-ATA
54858114 TT
1 TT
54858116 AAACTTATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
18 11 0.32
19 5 0.15
22 1 0.03
23 4 0.12
24 13 0.38
ACGTcount: A:0.47, C:0.01, G:0.06, T:0.46
Consensus pattern (22 bp):
TTTTTAAATTAATAGAAATATA
Found at i:54858133 original size:42 final size:42
Alignment explanation
Indices: 54858048--54858136 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 42
54858038 TATATCCAAT
* *
54858048 TTTTTAAATTAATAGAAAATGATATTTTAAAATTATAATCTA
1 TTTTTAAATTAATAGAAAATGATATATTAAAATTATAAACTA
* *
54858090 TTTTTAAATTAATAGAAGAT-A-ATATTAAACTTATAAAAACTA
1 TTTTTAAATTAATAGAAAATGATATATTAAAATTAT--AAACTA
54858132 TTTTT
1 TTTTT
54858137 TTCACGCTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
40 11 0.27
41 1 0.02
42 29 0.71
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.45
Consensus pattern (42 bp):
TTTTTAAATTAATAGAAAATGATATATTAAAATTATAAACTA
Found at i:54859713 original size:25 final size:25
Alignment explanation
Indices: 54859684--54859763 Score: 99
Period size: 25 Copynumber: 3.2 Consensus size: 25
54859674 AGGTTATCCC
54859684 GAAAATTAGCCACTATA-GCTTTTCA
1 GAAAATTAGCCACTA-AGGCTTTTCA
* * * *
54859709 AAAAATTTGCCATTAAGGTTTTTCA
1 GAAAATTAGCCACTAAGGCTTTTCA
*
54859734 GAAGATTAGCCACTAAGGCTTTTCA
1 GAAAATTAGCCACTAAGGCTTTTCA
54859759 GAAAA
1 GAAAA
54859764 CTTACCGACT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
24 1 0.02
25 43 0.98
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (25 bp):
GAAAATTAGCCACTAAGGCTTTTCA
Found at i:54859717 original size:50 final size:50
Alignment explanation
Indices: 54859662--54859763 Score: 118
Period size: 50 Copynumber: 2.0 Consensus size: 50
54859652 TTTGAGTTCG
*
54859662 AATTTGCCACAT-AGGTTATCCCGAAAATTAGCCACTATA-GCTTTTCAAAA
1 AATTTGCCA-ATAAGGTTATCCAGAAAATTAGCCACTA-AGGCTTTTCAAAA
* * * * *
54859712 AATTTGCCATTAAGGTTTTTCAGAAGATTAGCCACTAAGGCTTTTCAGAA
1 AATTTGCCAATAAGGTTATCCAGAAAATTAGCCACTAAGGCTTTTCAAAA
54859762 AA
1 AA
54859764 CTTACCGACT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
49 2 0.05
50 42 0.95
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (50 bp):
AATTTGCCAATAAGGTTATCCAGAAAATTAGCCACTAAGGCTTTTCAAAA
Found at i:54864946 original size:9 final size:9
Alignment explanation
Indices: 54864932--54864968 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
54864922 TATAGTTTGA
54864932 TATTCGAAT
1 TATTCGAAT
54864941 TATTCGAAT
1 TATTCGAAT
*
54864950 TATTCGAGT
1 TATTCGAAT
54864959 TATTCGAAT
1 TATTCGAAT
54864968 T
1 T
54864969 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:54865044 original size:18 final size:18
Alignment explanation
Indices: 54865021--54865055 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
54865011 ATTCAAGTTG
54865021 ATTCGAATAACTCGATTA
1 ATTCGAATAACTCGATTA
54865039 ATTCGAATAACTCGATT
1 ATTCGAATAACTCGATT
54865056 CGTTTAACTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.34
Consensus pattern (18 bp):
ATTCGAATAACTCGATTA
Found at i:54866497 original size:21 final size:21
Alignment explanation
Indices: 54866471--54866522 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
54866461 ATTGAGGCTT
*
54866471 AAGGATTGAGATAGATGGTTG
1 AAGGATTGAGACAGATGGTTG
*
54866492 AAGGATAGAGACAGATGGTTG
1 AAGGATTGAGACAGATGGTTG
*
54866513 GAGGA-TGAGA
1 AAGGATTGAGA
54866523 AAGAGATCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.37, C:0.02, G:0.40, T:0.21
Consensus pattern (21 bp):
AAGGATTGAGACAGATGGTTG
Found at i:54870465 original size:45 final size:44
Alignment explanation
Indices: 54870397--54870549 Score: 164
Period size: 45 Copynumber: 3.4 Consensus size: 44
54870387 AGCACCACCC
* * * *
54870397 TTATAGTCAATGATACTCGGTGGAATCAACACATAGCAACTACCT
1 TTATAATCAATG-TACCCAGTGGAATCAACACACAGCAACTACCT
* * * *
54870442 TCATAATCAATAGTACCCAGTGGAATCAGCACACAGTAACCACCT
1 TTATAATCAAT-GTACCCAGTGGAATCAACACACAGCAACTACCT
* *
54870487 TTATAATCAATGATACTCGGTGGAATCAACACACAGCAA-TCACCT
1 TTATAATCAATG-TACCCAGTGGAATCAACACACAGCAACT-ACCT
54870532 TTATAATCAATGGTACCC
1 TTATAATCAAT-GTACCC
54870550 GGTACACGTA
Statistics
Matches: 89, Mismatches: 15, Indels: 8
0.79 0.13 0.07
Matches are distributed among these distances:
44 1 0.01
45 86 0.97
46 2 0.02
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.25
Consensus pattern (44 bp):
TTATAATCAATGTACCCAGTGGAATCAACACACAGCAACTACCT
Found at i:54870507 original size:90 final size:88
Alignment explanation
Indices: 54870373--54870549 Score: 257
Period size: 90 Copynumber: 2.0 Consensus size: 88
54870363 CAGATACACG
* * * *
54870373 GTGGATCAGCACATAGCACCACCCTTATAGTCAATGATACTCGGTGGAATCAACACATAGCAA-C
1 GTGGATCAGCACACAGAACCACCCTTATAATCAATGATACTCGGTGGAATCAACACACAGCAATC
54870437 TACCTTCATAATCAATAGTACCCA
66 -ACCTTCATAATCAATAGTACCCA
*
54870461 GTGGAATCAGCACACAGTAACCACCTTTATAATCAATGATACTCGGTGGAATCAACACACAGCAA
1 GTGG-ATCAGCACACAG-AACCACCCTTATAATCAATGATACTCGGTGGAATCAACACACAGCAA
* *
54870526 TCACCTTTATAATCAATGGTACCC
64 TCACCTTCATAATCAATAGTACCC
54870550 GGTACACGTA
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
88 4 0.05
89 11 0.14
90 63 0.80
91 1 0.01
ACGTcount: A:0.36, C:0.27, G:0.15, T:0.23
Consensus pattern (88 bp):
GTGGATCAGCACACAGAACCACCCTTATAATCAATGATACTCGGTGGAATCAACACACAGCAATC
ACCTTCATAATCAATAGTACCCA
Found at i:54876811 original size:9 final size:9
Alignment explanation
Indices: 54876797--54876825 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
54876787 TAAACAATTC
54876797 AATAATATA
1 AATAATATA
54876806 AATAATATA
1 AATAATATA
54876815 AATAATATA
1 AATAATATA
54876824 AA
1 AA
54876826 ACGTGAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
AATAATATA
Found at i:54877139 original size:31 final size:31
Alignment explanation
Indices: 54877080--54877139 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
54877070 GGAGGTGGGA
*
54877080 TGGGAAGGGAATAAAAGTTTTAGGGAAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGAAAAAG
*
54877111 TGGG-AGGGAGTAAAAATTTT-GGGAGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGA-AAAA
54877140 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 4 0.15
30 18 0.69
31 4 0.15
ACGTcount: A:0.43, C:0.00, G:0.37, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGAAAAAG
Found at i:54877336 original size:9 final size:9
Alignment explanation
Indices: 54877322--54877358 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
54877312 TATAGTTTGA
54877322 TATTCGAAT
1 TATTCGAAT
54877331 TATTCGAAT
1 TATTCGAAT
* *
54877340 TATTTGAGT
1 TATTCGAAT
54877349 TATTCGAAT
1 TATTCGAAT
54877358 T
1 T
54877359 TGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:54877429 original size:9 final size:9
Alignment explanation
Indices: 54877412--54877442 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
54877402 TCAAGTTGAT
54877412 TCGAATAAC
1 TCGAATAAC
*
54877421 TCGATTAAC
1 TCGAATAAC
54877430 TCGAATAAC
1 TCGAATAAC
54877439 TCGA
1 TCGA
54877443 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:54882225 original size:15 final size:16
Alignment explanation
Indices: 54882199--54882228 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
54882189 CTTGAAAGTA
54882199 AGATTAAGATTAGATG
1 AGATTAAGATTAGATG
54882215 AGATT-AGATTAGAT
1 AGATTAAGATTAGAT
54882229 TAATAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.33
Consensus pattern (16 bp):
AGATTAAGATTAGATG
Found at i:54882962 original size:22 final size:22
Alignment explanation
Indices: 54882936--54882992 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
54882926 AAAAAACTAT
* *
54882936 TGTTTTGCTGCTGTTTTTCCAC
1 TGTTTTGCTGCTATTTTCCCAC
*
54882958 TGTTTTACTGCTATTTTCCCAC
1 TGTTTTGCTGCTATTTTCCCAC
*
54882980 TGTTTTGTTGCTA
1 TGTTTTGCTGCTA
54882993 CTATTTTATT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.09, C:0.21, G:0.16, T:0.54
Consensus pattern (22 bp):
TGTTTTGCTGCTATTTTCCCAC
Found at i:54891121 original size:26 final size:26
Alignment explanation
Indices: 54891064--54891114 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
54891054 CTTGATATAT
*
54891064 GGCTCTTCGTGAGCTTCCCGATTAAA
1 GGCTCTTCGTGAGCTTCCCAATTAAA
* *
54891090 GGCTCTTTGTGAGCTTCCTAATTAA
1 GGCTCTTCGTGAGCTTCCCAATTAA
54891115 TTGCTCTCCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.35
Consensus pattern (26 bp):
GGCTCTTCGTGAGCTTCCCAATTAAA
Found at i:54891198 original size:24 final size:24
Alignment explanation
Indices: 54891151--54891216 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
54891141 CTCCCCTAAA
* *
54891151 CTTCCCGATATATGGCTATCCAGAG
1 CTTCCCGTTA-ATGGCTCTCCAGAG
*
54891176 CTTCCCGTTAATGGCTCTTCAGAG
1 CTTCCCGTTAATGGCTCTCCAGAG
* * *
54891200 CTACTCGTTATTGGCTC
1 CTTCCCGTTAATGGCTC
54891217 GCATGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
24 26 0.74
25 9 0.26
ACGTcount: A:0.18, C:0.29, G:0.20, T:0.33
Consensus pattern (24 bp):
CTTCCCGTTAATGGCTCTCCAGAG
Found at i:54891999 original size:18 final size:18
Alignment explanation
Indices: 54891964--54892001 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
54891954 AGAAAAGAAT
*
54891964 AAAAAGAAAAACGGTTCA
1 AAAAAGAAAAACGATTCA
54891982 AAAAAGAGAAAA-GATTCA
1 AAAAAGA-AAAACGATTCA
54892000 AA
1 AA
54892002 GGTTGCTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.66, C:0.08, G:0.16, T:0.11
Consensus pattern (18 bp):
AAAAAGAAAAACGATTCA
Found at i:54892877 original size:7 final size:7
Alignment explanation
Indices: 54892862--54892895 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
54892852 ACTTACATAC
54892862 TTATATT
1 TTATATT
*
54892869 TTATTTT
1 TTATATT
54892876 TTATATT
1 TTATATT
*
54892883 TTATAAT
1 TTATATT
54892890 TTATAT
1 TTATAT
54892896 ATCTATATCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TTATATT
Found at i:54893168 original size:36 final size:36
Alignment explanation
Indices: 54893128--54893196 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
54893118 TTTATGATTT
*
54893128 TTTATCTATTTTCCTTTAT-TGT-TATTTTTATTTTCC
1 TTTATCTA-TTT-ATTTATATGTCTATTTTTATTTTCC
*
54893164 TTTATTTATTTATTTATATGTCTATTTTTATTT
1 TTTATCTATTTATTTATATGTCTATTTTTATTT
54893197 ATTTATTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 5 0.17
35 6 0.21
36 18 0.62
ACGTcount: A:0.17, C:0.09, G:0.03, T:0.71
Consensus pattern (36 bp):
TTTATCTATTTATTTATATGTCTATTTTTATTTTCC
Found at i:54893179 original size:22 final size:21
Alignment explanation
Indices: 54893124--54893180 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 21
54893114 ATATTTTATG
*
54893124 ATTTTTTATCTATTTTCCTTT
1 ATTTTTTATTTATTTTCCTTT
54893145 ATTGTTATT-TTTATTTTCCTTT
1 ATT-TT-TTATTTATTTTCCTTT
54893167 ATTTATTTATTTAT
1 ATTT-TTTATTTAT
54893181 ATGTCTATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
21 6 0.19
22 23 0.74
23 2 0.06
ACGTcount: A:0.18, C:0.09, G:0.02, T:0.72
Consensus pattern (21 bp):
ATTTTTTATTTATTTTCCTTT
Found at i:54893193 original size:22 final size:21
Alignment explanation
Indices: 54893168--54893210 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
54893158 TTTTCCTTTA
54893168 TTTATTTATTTATATGTCTATT
1 TTTATTTATTTATATGT-TATT
*
54893190 TTTATTTATTTATTTGTTATT
1 TTTATTTATTTATATGTTATT
54893211 GTATATACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.72
Consensus pattern (21 bp):
TTTATTTATTTATATGTTATT
Found at i:54893607 original size:110 final size:109
Alignment explanation
Indices: 54893333--54893745 Score: 607
Period size: 109 Copynumber: 3.8 Consensus size: 109
54893323 AAAAGAAATT
* * * *
54893333 TTTTTAAATGAGGCAATGTTTAGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGTTGGGTGT
1 TTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
*
54893398 CGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAA
66 CGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTCAAAAA
* *
54893442 TTTTAAAATAAGACAATGTTTTGCGTTTGGACATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
1 TTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
* * *
54893507 CGATTTTTCTCGTTCAACCAAATGGCTTTATATCATCTTCAGAAA
66 CGATTTTTCTCGTTCAACCAAATGGCTTAATATCCT-TTCAAAAA
* * *
54893552 TTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGATAAAACATACCCTAAGGTGCTGGGTGT
1 TTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
* *
54893617 CGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTCAAAAA
66 CGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTCAAAAA
* * * * *
54893661 TTTCAAAATAAGGCAATGTTTTGCGTTTGAAAATTCGAG-GAACGTGCCCTAAGGTGCTGGGTTT
1 TTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
*
54893725 CGA--TTTCTCGTTTAACCAAAT
66 CGATTTTTCTCGTTCAACCAAAT
54893746 TGCCAAATAT
Statistics
Matches: 274, Mismatches: 29, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
106 17 0.06
108 24 0.09
109 135 0.49
110 98 0.36
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (109 bp):
TTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
CGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTCAAAAA
Found at i:54897451 original size:51 final size:50
Alignment explanation
Indices: 54897262--54897455 Score: 171
Period size: 51 Copynumber: 3.9 Consensus size: 50
54897252 ATGTGAAAGT
*
54897262 GAAAGTGAT-GGTCACGTGTGTAGTGCTATGTGCAGGCTACTACGTGTAC
1 GAAAGTGATAGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTAC
* ** * * * *
54897311 CAAAAAGATAGGTCGCGTGTGTAGTACTGTGTGCAGGCTACTATGCGTACC
1 GAAAGTGATAGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTA-C
* * * * * *
54897362 GGATAGCT--TCGATCACGTGTGTAGTACTATATACAGGCTACTACGTGTATT
1 -GAAAG-TGATAGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTA-C
* *
54897413 GAATAGTGAT-GGTCACATGTGTAGTACTATGTGTAGGCTACTA
1 GAA-AGTGATAGGTCACGTGTGTAGTACTATGTGCAGGCTACTA
54897456 TGTGAACCCG
Statistics
Matches: 110, Mismatches: 28, Indels: 12
0.73 0.19 0.08
Matches are distributed among these distances:
49 6 0.05
50 37 0.34
51 64 0.58
52 3 0.03
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.30
Consensus pattern (50 bp):
GAAAGTGATAGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTAC
Found at i:54897551 original size:42 final size:42
Alignment explanation
Indices: 54897463--54897717 Score: 318
Period size: 42 Copynumber: 6.0 Consensus size: 42
54897453 CTATGTGAAC
* *
54897463 CCGTATCATTGATTATAAGGTGGTTGCTAAATGCTGATTCCA
1 CCGTATCCTTGATTATAAGGTGGTTGCTAAGTGCTGATTCCA
* * * *
54897505 CCGTATCCTTGATTGTGAGAGAGGTTGCTATGTGCTGATTCC-
1 CCGTATCCTTGATTATAAG-GTGGTTGCTAAGTGCTGATTCCA
54897547 CCGTATCCTTGATTATAAGGTGGTTGCTAAGTGCTGATTCCA
1 CCGTATCCTTGATTATAAGGTGGTTGCTAAGTGCTGATTCCA
* *
54897589 CCGTATCCTTGATTGTGAAAGG-GGTTGCTATGTGCTGATTCC-
1 CCGTATCCTTGATTAT--AAGGTGGTTGCTAAGTGCTGATTCCA
* * *
54897631 CCATATCATTGATTATAAGGTGGTTCCTAAGTGCTGATTCCA
1 CCGTATCCTTGATTATAAGGTGGTTGCTAAGTGCTGATTCCA
* * *
54897673 CCGGGATCCTTTGAATATGAGGTGGTTGCTAAGTGCTGATTCCA
1 CC-GTATCC-TTGATTATAAGGTGGTTGCTAAGTGCTGATTCCA
54897717 C
1 C
54897718 TGTGTAATGG
Statistics
Matches: 182, Mismatches: 23, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
40 4 0.02
41 38 0.21
42 63 0.35
43 41 0.23
44 36 0.20
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (42 bp):
CCGTATCCTTGATTATAAGGTGGTTGCTAAGTGCTGATTCCA
Found at i:54897603 original size:84 final size:84
Alignment explanation
Indices: 54897462--54897715 Score: 384
Period size: 84 Copynumber: 3.0 Consensus size: 84
54897452 ACTATGTGAA
*
54897462 CCCGTATCATTGATTATAAGGTGGTTGCTAAATGCTGATTCCACCGTATCCTTGATTGTGAGAGA
1 CCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTGTGAGAGA
54897527 GGTTGCTATGTGCTGATTC
66 GGTTGCTATGTGCTGATTC
* * *
54897546 CCCGTATCCTTGATTATAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTGTGAAAGG
1 CCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTGTGAGAGA
54897611 GGTTGCTATGTGCTGATTC
66 GGTTGCTATGTGCTGATTC
* * * * *
54897630 CCCATATCATTGATTATAAGGTGGTTCCTAAGTGCTGATTCCACCGGGATCCTTTGAATATGAG-
1 CCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCCACC-GTATCC-TTGATTGTGAGA
* *
54897694 GTGGTTGCTAAGTGCTGATTC
64 GAGGTTGCTATGTGCTGATTC
54897715 C
1 C
54897716 ACTGTGTAAT
Statistics
Matches: 155, Mismatches: 13, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
84 122 0.79
85 25 0.16
86 8 0.05
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (84 bp):
CCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTGTGAGAGA
GGTTGCTATGTGCTGATTC
Found at i:54905009 original size:26 final size:26
Alignment explanation
Indices: 54904960--54905010 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
54904950 CCCGATATAT
*
54904960 GGCTCTTCGTGAGCTTCCCGATTAAA
1 GGCTCTTCGTGAGCTTCCCAATTAAA
* *
54904986 GGCTCTTTGTGAGCTTCCTAATTAA
1 GGCTCTTCGTGAGCTTCCCAATTAA
54905011 TGTCTTTCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.35
Consensus pattern (26 bp):
GGCTCTTCGTGAGCTTCCCAATTAAA
Found at i:54905075 original size:25 final size:25
Alignment explanation
Indices: 54905047--54905111 Score: 80
Period size: 24 Copynumber: 2.7 Consensus size: 25
54905037 CTTCCCTGAA
* *
54905047 CTTCCCGGTATATGGCTATTCGGAG
1 CTTCCCGTTATATGGCTATTCAGAG
*
54905072 CTTCCCGTTA-ATGGCTCTTCAGAG
1 CTTCCCGTTATATGGCTATTCAGAG
*
54905096 CTACCCGTTAT-TGGCT
1 CTTCCCGTTATATGGCT
54905112 CGCATGAGCT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
24 26 0.74
25 9 0.26
ACGTcount: A:0.15, C:0.28, G:0.23, T:0.34
Consensus pattern (25 bp):
CTTCCCGTTATATGGCTATTCAGAG
Found at i:54905169 original size:25 final size:25
Alignment explanation
Indices: 54905139--54905205 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 25
54905129 TATGGCTCTT
* *
54905139 ATAAGCTTCCTGTTATGCAGCCCAG
1 ATAAGCTTCCTGTTATACAGCCCAC
*
54905164 ATAAGCTT-CTCGTTATACAGCTCAC
1 ATAAGCTTCCT-GTTATACAGCCCAC
*
54905189 ATGAGCTTCCTGTTATA
1 ATAAGCTTCCTGTTATA
54905206 TGGCTCGAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
24 2 0.06
25 32 0.89
26 2 0.06
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.33
Consensus pattern (25 bp):
ATAAGCTTCCTGTTATACAGCCCAC
Found at i:54905211 original size:25 final size:25
Alignment explanation
Indices: 54905069--54905211 Score: 71
Period size: 24 Copynumber: 5.8 Consensus size: 25
54905059 TGGCTATTCG
* *
54905069 GAGCTTCCCGTTA-ATGGCTCTTCA-
1 GAGCTTCCTGTTATATGGCTC-ACAT
* * *
54905093 GAGCTACCCGTTAT-TGGCTCGCAT
1 GAGCTTCCTGTTATATGGCTCACAT
* * **
54905117 GAGCTTCTTG-AATATGGCTCTTAT
1 GAGCTTCCTGTTATATGGCTCACAT
* *** * *
54905141 AAGCTTCCTGTTATGCAGCCCAGAT
1 GAGCTTCCTGTTATATGGCTCACAT
* **
54905166 AAGCTT-CTCGTTATACAGCTCACAT
1 GAGCTTCCT-GTTATATGGCTCACAT
54905191 GAGCTTCCTGTTATATGGCTC
1 GAGCTTCCTGTTATATGGCTC
54905212 GAGAGAGGGC
Statistics
Matches: 90, Mismatches: 23, Indels: 11
0.73 0.19 0.09
Matches are distributed among these distances:
23 4 0.04
24 43 0.48
25 41 0.46
26 2 0.02
ACGTcount: A:0.20, C:0.26, G:0.20, T:0.34
Consensus pattern (25 bp):
GAGCTTCCTGTTATATGGCTCACAT
Found at i:54907472 original size:20 final size:20
Alignment explanation
Indices: 54907447--54907490 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
54907437 TAATATGGTA
54907447 AGAAAAGTGGAGAATTCTCT
1 AGAAAAGTGGAGAATTCTCT
54907467 AGAAAAGTGGAGAATTCTCT
1 AGAAAAGTGGAGAATTCTCT
54907487 AGAA
1 AGAA
54907491 TGTGTTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.43, C:0.09, G:0.25, T:0.23
Consensus pattern (20 bp):
AGAAAAGTGGAGAATTCTCT
Found at i:54910259 original size:30 final size:30
Alignment explanation
Indices: 54910225--54910350 Score: 135
Period size: 30 Copynumber: 4.2 Consensus size: 30
54910215 AACAGTGAGT
* *
54910225 TACACAGCCTGGAAACACGGCCGTGCAACC
1 TACACGGCCTGGAAACACGGCCGTGTAACC
* * *
54910255 TACACGGCTTGGCAACATGGCCGTGTAACC
1 TACACGGCCTGGAAACACGGCCGTGTAACC
* ** *
54910285 TACACGACCTGGCGACACGGTCGTGTAACC
1 TACACGGCCTGGAAACACGGCCGTGTAACC
* * **
54910315 TACACGGCTTGGAGACACGGTTGTGTAACC
1 TACACGGCCTGGAAACACGGCCGTGTAACC
54910345 TACACG
1 TACACG
54910351 AACTAGACAC
Statistics
Matches: 82, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 82 1.00
ACGTcount: A:0.25, C:0.31, G:0.26, T:0.17
Consensus pattern (30 bp):
TACACGGCCTGGAAACACGGCCGTGTAACC
Found at i:54910318 original size:60 final size:60
Alignment explanation
Indices: 54910239--54910351 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
54910229 CAGCCTGGAA
*
54910239 ACACGGCCGTGCAACCTACACGGCTTGGCA-ACATGGCCGTGTAACCTACACGACCTGGCG
1 ACACGGCCGTGCAACCTACACGGCTTGG-AGACACGGCCGTGTAACCTACACGACCTGGCG
* * **
54910299 ACACGGTCGTGTAACCTACACGGCTTGGAGACACGGTTGTGTAACCTACACGA
1 ACACGGCCGTGCAACCTACACGGCTTGGAGACACGGCCGTGTAACCTACACGA
54910352 ACTAGACACA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
59 1 0.02
60 46 0.98
ACGTcount: A:0.25, C:0.31, G:0.27, T:0.18
Consensus pattern (60 bp):
ACACGGCCGTGCAACCTACACGGCTTGGAGACACGGCCGTGTAACCTACACGACCTGGCG
Found at i:54911177 original size:26 final size:26
Alignment explanation
Indices: 54911122--54911216 Score: 72
Period size: 26 Copynumber: 3.5 Consensus size: 26
54911112 TATTTACTTA
*
54911122 TTATTATTTATTTATTA-TCTGTTCATTT
1 TTATT-TTTATTT-TTATTCTGTTTA-TT
54911150 TTATTTTT-TTTCTTATTCTGTTTATT
1 TTATTTTTATTT-TTATTCTGTTTATT
*
54911176 TT-TTTATTATGTTTATTCCTAGTTTTATT
1 TTATTT-TTATTTTTATT-CT-G-TTTATT
54911205 TTA-TTTTATTTT
1 TTATTTTTATTTT
54911217 GTTGTATTAT
Statistics
Matches: 56, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
25 3 0.05
26 17 0.30
27 14 0.25
28 12 0.21
29 10 0.18
ACGTcount: A:0.17, C:0.06, G:0.04, T:0.73
Consensus pattern (26 bp):
TTATTTTTATTTTTATTCTGTTTATT
Found at i:54911182 original size:17 final size:18
Alignment explanation
Indices: 54911156--54911192 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
54911146 ATTTTTATTT
*
54911156 TTTTTCTTATTCTGTTTA
1 TTTTTCTTATTATGTTTA
54911174 TTTTT-TTATTATGTTTA
1 TTTTTCTTATTATGTTTA
54911191 TT
1 TT
54911193 CCTAGTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.14, C:0.05, G:0.05, T:0.76
Consensus pattern (18 bp):
TTTTTCTTATTATGTTTA
Found at i:54911936 original size:13 final size:13
Alignment explanation
Indices: 54911918--54911943 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54911908 ATCGAGCCCA
54911918 CATATATGGAGCT
1 CATATATGGAGCT
54911931 CATATATGGAGCT
1 CATATATGGAGCT
54911944 TACTTTGGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
CATATATGGAGCT
Found at i:54912891 original size:6 final size:6
Alignment explanation
Indices: 54912877--54912914 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
54912867 TTTTGTTTTG
* *
54912877 TTTTA- TTTTAT TTTTAT TTTTAT GTTTAT TGTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT
54912915 CTTAAACTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:54912906 original size:18 final size:17
Alignment explanation
Indices: 54912877--54912914 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
54912867 TTTTGTTTTG
*
54912877 TTTTATTTTATTTTTAT
1 TTTTATTTTATTGTTAT
54912894 TTTTATGTTTATTGTTAT
1 TTTTAT-TTTATTGTTAT
54912912 TTT
1 TTT
54912915 CTTAAACTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.79
Consensus pattern (17 bp):
TTTTATTTTATTGTTAT
Found at i:54917450 original size:30 final size:30
Alignment explanation
Indices: 54917393--54917477 Score: 82
Period size: 30 Copynumber: 2.9 Consensus size: 30
54917383 GGGTAAATAA
* **
54917393 GTTGCTCACACAAGTTGGCATTATATCAGG
1 GTTGCTCACACAAGCTAACATTATATCAGG
* **
54917423 GTTGCTCACACAAGCTAACATTTTATCAAA
1 GTTGCTCACACAAGCTAACATTATATCAGG
** *
54917453 GTTTTTTACACAAGCTAAC-TTATAT
1 GTTGCTCACACAAGCTAACATTATAT
54917478 TAGGTTACCC
Statistics
Matches: 45, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
29 5 0.11
30 40 0.89
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (30 bp):
GTTGCTCACACAAGCTAACATTATATCAGG
Found at i:54920166 original size:18 final size:18
Alignment explanation
Indices: 54920127--54920338 Score: 196
Period size: 18 Copynumber: 11.8 Consensus size: 18
54920117 TTTCGGTGGT
* *
54920127 GGTTCTTTTGG-TTTCTCA
1 GGTTCTTTAGGCTTT-TCG
*
54920145 GGTTCCTTAGGCTTTTCG
1 GGTTCTTTAGGCTTTTCG
*
54920163 GGTTCTTTCGGCTTTTCG
1 GGTTCTTTAGGCTTTTCG
*
54920181 GGTTGTTTAGG-TTTCTCG
1 GGTTCTTTAGGCTTT-TCG
*
54920199 GGTTCTTT-GGGTTTTCCG
1 GGTTCTTTAGGCTTTT-CG
* *
54920217 GGTTCTTTTGGTTTTTCG
1 GGTTCTTTAGGCTTTTCG
*
54920235 GGTGCTTTAGGCTTTTCG
1 GGTTCTTTAGGCTTTTCG
* * *
54920253 GGTTCTTTTGGTTTTTCT
1 GGTTCTTTAGGCTTTTCG
* * *
54920271 GGTACTTTAGGCTTCTCT
1 GGTTCTTTAGGCTTTTCG
* * *
54920289 GGTTCTTTGGGTTTTTCA
1 GGTTCTTTAGGCTTTTCG
* *
54920307 GGTTCTTTGGGCTTTTTG
1 GGTTCTTTAGGCTTTTCG
54920325 GGTTCTTTAGGCTT
1 GGTTCTTTAGGCTT
54920339 CTCAGGCTCA
Statistics
Matches: 160, Mismatches: 29, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
17 6 0.04
18 145 0.91
19 9 0.06
ACGTcount: A:0.04, C:0.16, G:0.28, T:0.52
Consensus pattern (18 bp):
GGTTCTTTAGGCTTTTCG
Found at i:54923406 original size:40 final size:40
Alignment explanation
Indices: 54923337--54923414 Score: 99
Period size: 40 Copynumber: 1.9 Consensus size: 40
54923327 CAAATTTGGG
54923337 CTTGGCTAAATATAGCTTTACTCAATTAAACTA-TTTTTAT
1 CTTGGCTAAATATAGCTTTACTCAATTAAA-TAGTTTTTAT
*
54923377 CTTGGCTAAATATATG-TGTTACT-AGTTAAATAGTTTTT
1 CTTGGCTAAATATA-GCT-TTACTCAATTAAATAGTTTTT
54923415 TTTTCTTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
39 2 0.06
40 26 0.76
41 6 0.18
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.46
Consensus pattern (40 bp):
CTTGGCTAAATATAGCTTTACTCAATTAAATAGTTTTTAT
Found at i:54923853 original size:12 final size:12
Alignment explanation
Indices: 54923811--54923853 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
54923801 AATTTTTATT
54923811 AATTAATAAATA
1 AATTAATAAATA
*
54923823 AATAAATAAATA
1 AATTAATAAATA
* *
54923835 AATTTAATTAATT
1 AA-TTAATAAATA
54923848 AATTAA
1 AATTAA
54923854 CCTTTTCAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 17 0.65
13 9 0.35
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
AATTAATAAATA
Found at i:54924690 original size:28 final size:29
Alignment explanation
Indices: 54924654--54924714 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
54924644 AATAGAATTT
*
54924654 TTTTTAAAATT-TTTATAAATATTTTG-AA
1 TTTTAAAAATTATTT-TAAATATTTTGTAA
* *
54924682 TTTTAAAAATTATTTTGATTATTTTGTAA
1 TTTTAAAAATTATTTTAAATATTTTGTAA
54924711 TTTT
1 TTTT
54924715 TGTTAAGAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 19 0.68
29 9 0.32
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (29 bp):
TTTTAAAAATTATTTTAAATATTTTGTAA
Found at i:54924691 original size:18 final size:19
Alignment explanation
Indices: 54924664--54924699 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
54924654 TTTTTAAAAT
*
54924664 TTTTATAAA-TATTTTGAA
1 TTTTAAAAATTATTTTGAA
54924682 TTTTAAAAATTATTTTGA
1 TTTTAAAAATTATTTTGA
54924700 TTATTTTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (19 bp):
TTTTAAAAATTATTTTGAA
Found at i:54924798 original size:9 final size:9
Alignment explanation
Indices: 54924784--54924831 Score: 78
Period size: 9 Copynumber: 5.3 Consensus size: 9
54924774 ATACTAATCT
54924784 ATTATTCGA
1 ATTATTCGA
54924793 ATTATTCGA
1 ATTATTCGA
*
54924802 GTTATTCGA
1 ATTATTCGA
54924811 ATTATTCGA
1 ATTATTCGA
*
54924820 GTTATTCGA
1 ATTATTCGA
54924829 ATT
1 ATT
54924832 GTAAAAATTC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.29, C:0.10, G:0.15, T:0.46
Consensus pattern (9 bp):
ATTATTCGA
Found at i:54924808 original size:18 final size:18
Alignment explanation
Indices: 54924785--54924831 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
54924775 TACTAATCTA
54924785 TTATTCGAATTATTCGAG
1 TTATTCGAATTATTCGAG
54924803 TTATTCGAATTATTCGAG
1 TTATTCGAATTATTCGAG
54924821 TTATTCGAATT
1 TTATTCGAATT
54924832 GTAAAAATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.47
Consensus pattern (18 bp):
TTATTCGAATTATTCGAG
Found at i:54926876 original size:43 final size:43
Alignment explanation
Indices: 54926815--54926912 Score: 178
Period size: 43 Copynumber: 2.3 Consensus size: 43
54926805 GCCGATCTTT
54926815 AACGCCGCTAAAGAACATGATCTTTAACGGCGCTTTTATCACA
1 AACGCCGCTAAAGAACATGATCTTTAACGGCGCTTTTATCACA
*
54926858 AACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTATCACA
1 AACGCCGCTAAAGAACATGATCTTTAACGGCGCTTTTATCACA
*
54926901 AATGCCGCTAAA
1 AACGCCGCTAAA
54926913 AGTACGATTC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 53 1.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (43 bp):
AACGCCGCTAAAGAACATGATCTTTAACGGCGCTTTTATCACA
Found at i:54933848 original size:46 final size:45
Alignment explanation
Indices: 54933764--54934288 Score: 279
Period size: 46 Copynumber: 11.6 Consensus size: 45
54933754 TTTGAGTACT
* * * *
54933764 TCTGATCAAGTGACAAAATGATAAGTGGT-AGCTTTAGCTACACATA
1 TCTGATCAAGTGAC-AAGTGATAAGTGATAAG-TATAGCTACACTTA
*
54933810 TCTGATCAAGTGACAAGTGGA-AAGTGATAAGTAATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAAGT-GATAAGTGATAAGT-ATA------GCTACACTTA
* * *
54933862 TCTGATCAAGTGAAAAAGTGATAAGTGAT-AGCT-TCGGCTATACTTA
1 TCTGATCAAGTG-ACAAGTGATAAGTGATAAG-TAT-AGCTACACTTA
54933908 TCTGATCAAGTGACAAAGTGATAAGTGAT-AGCT-TCAGCTACACTTA
1 TCTGATCAAGTGAC-AAGTGATAAGTGATAAG-TAT-AGCTACACTTA
*
54933954 TCTGATCAAGTGACAAAATGGA-AAGTGATAAGTGATAGCTTCGGTTACACTTA
1 TCTGATCAAGTGAC-AAGT-GATAAGTGATAAGT-ATAG---C---TACACTTA
* *
54934007 TCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAAGTGATAAGTGATAAGT-ATA------GCTACACTTA
* * *
54934059 TATGATCAAGAGACAAAGTGATAAGTGAT-AGCTTTAGCTACACTTA
1 TCTGATCAAGTGAC-AAGTGATAAGTGATAAG-TATAGCTACACTTA
* * * *
54934105 TCTGATCAAGAGAAAAAGTGATAAGTGATAACTTTAGCTACACTTA
1 TCTGATCAAGTG-ACAAGTGATAAGTGATAAGTATAGCTACACTTA
* *
54934151 TCTGATCAAGAGAC-----A-AAGTGATAAG--TGGCTACACTTA
1 TCTGATCAAGTGACAAGTGATAAGTGATAAGTATAGCTACACTTA
* *
54934188 TCTGATCAA--GA-AA--CA-AAGTGATAAG--TGGCTACACTTA
1 TCTGATCAAGTGACAAGTGATAAGTGATAAGTATAGCTACACTTA
* *
54934225 TCTGATCAA--GA-AA--CA-AAGTGATAAG--TGGCTACACTTA
1 TCTGATCAAGTGACAAGTGATAAGTGATAAGTATAGCTACACTTA
*
54934262 TCTGATC-AGGGACAAGTGATAAGTGAT
1 TCTGATCAAGTGACAAGTGATAAGTGAT
54934289 CATACGTAAG
Statistics
Matches: 410, Mismatches: 25, Indels: 92
0.78 0.05 0.17
Matches are distributed among these distances:
35 2 0.00
36 1 0.00
37 87 0.21
38 2 0.00
39 11 0.03
40 1 0.00
41 1 0.00
42 7 0.02
45 12 0.03
46 157 0.38
47 8 0.02
48 1 0.00
50 1 0.00
51 3 0.01
52 65 0.16
53 49 0.12
55 1 0.00
58 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (45 bp):
TCTGATCAAGTGACAAGTGATAAGTGATAAGTATAGCTACACTTA
Found at i:54933934 original size:53 final size:50
Alignment explanation
Indices: 54933764--54934166 Score: 432
Period size: 46 Copynumber: 8.3 Consensus size: 50
54933754 TTTGAGTACT
* ** *
54933764 TCTGATCAAGTGAC-A--AAA-TGATAAGTGGTAGCTTTAGCTACACATA
1 TCTGATCAAGTGACAATGAAAGTGATAAGTGATAGCTTCGGCTACACTTA
* *
54933810 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTAATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAA-T-GAAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
54933862 TCTGATCAAGTG--AA--AAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAATGAAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
54933908 TCTGATCAAGTGAC----AAAGTGATAAGTGATAGCTTCAGCTACACTTA
1 TCTGATCAAGTGACAATGAAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
54933954 TCTGATCAAGTGACAAAATGGAAAGTGATAAGTGATAGCTTCGGTTACACTTA
1 TCTGATCAAGTGAC--AAT-GAAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
54934007 TCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAA-TG-AAAGTGATAAGTGATAGCTTCGGCTACACTTA
* * **
54934059 TATGATCAAGAGAC----AAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAATGAAAGTGATAAGTGATAGCTTCGGCTACACTTA
* * **
54934105 TCTGATCAA--GAGAA--AAAGTGATAAGTGATAACTTTAGCTACACTTA
1 TCTGATCAAGTGACAATGAAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
54934151 TCTGATCAAGAGACAA
1 TCTGATCAAGTGACAA
54934167 AGTGATAAGT
Statistics
Matches: 314, Mismatches: 22, Indels: 40
0.84 0.06 0.11
Matches are distributed among these distances:
44 2 0.01
46 178 0.57
47 1 0.00
48 4 0.01
50 2 0.01
51 6 0.02
52 77 0.25
53 44 0.14
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (50 bp):
TCTGATCAAGTGACAATGAAAGTGATAAGTGATAGCTTCGGCTACACTTA
Found at i:54934092 original size:197 final size:197
Alignment explanation
Indices: 54933782--54934167 Score: 610
Period size: 197 Copynumber: 2.0 Consensus size: 197
54933772 AGTGACAAAA
* * *
54933782 TGATAAGTGGTAGCTTTAGCTACACATATCTGATCAAGTGACAAGTGGAAAGTGATAAGTAATAG
1 TGATAAGTGATAGCTTCAGCTACACATATCTGATCAAGTGACAAGTGAAAAGTGATAAGTAATAG
* * * *
54933847 CTTCGGCTATACTTATCTGATCAAGTGAAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTG
66 CTTCGGCTATACTTATATGATCAAGAGAAAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTG
* * * *
54933912 ATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAAATGGAA
131 ATCAAGAGAAAAAGTGATAAGTGATAACTTCAGCTACACTTATCTGATCAAGAGACAAAATGGAA
54933977 AG
196 AG
* * * *
54933979 TGATAAGTGATAGCTTCGGTTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAG
1 TGATAAGTGATAGCTTCAGCTACACATATCTGATCAAGTGACAAGTGAAAAGTGATAAGTAATAG
* *
54934044 CTTCGGCTATACTTATATGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTG
66 CTTCGGCTATACTTATATGATCAAGAGAAAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTG
*
54934109 ATCAAGAGAAAAAGTGATAAGTGATAACTTTAGCTACACTTATCTGATCAAGAGACAAA
131 ATCAAGAGAAAAAGTGATAAGTGATAACTTCAGCTACACTTATCTGATCAAGAGACAAA
54934168 GTGATAAGTG
Statistics
Matches: 171, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
197 171 1.00
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (197 bp):
TGATAAGTGATAGCTTCAGCTACACATATCTGATCAAGTGACAAGTGAAAAGTGATAAGTAATAG
CTTCGGCTATACTTATATGATCAAGAGAAAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTG
ATCAAGAGAAAAAGTGATAAGTGATAACTTCAGCTACACTTATCTGATCAAGAGACAAAATGGAA
AG
Found at i:54934186 original size:37 final size:37
Alignment explanation
Indices: 54934141--54934286 Score: 251
Period size: 37 Copynumber: 4.0 Consensus size: 37
54934131 GATAACTTTA
*
54934141 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
54934178 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
54934215 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
54934252 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
54934287 ATCATACGTA
Statistics
Matches: 106, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
35 12 0.11
36 4 0.04
37 90 0.85
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:54936916 original size:110 final size:110
Alignment explanation
Indices: 54936723--54937176 Score: 619
Period size: 110 Copynumber: 4.1 Consensus size: 110
54936713 TATGCATACT
* * *
54936723 AATATCCTTTTAAAAAATTTCAAAATAAGGCAATGCTCTGGGTTTGGAAATTCGAGAAAACGTGC
1 AATATCCTTTTAAAAAATTTCAAAATAAGGCAATGTTTTGTGTTTGGAAATTCGAGAAAACGTGC
54936788 CCTAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
66 CCTAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
* *
54936833 AATATCCTTTTAAAAAATTTCAAAATAAGGCAATGTTTTATGTTTGGAAATTCGAGAAATCGTGC
1 AATATCCTTTTAAAAAATTTCAAAATAAGGCAATGTTTTGTGTTTGGAAATTCGAGAAAACGTGC
* * *
54936898 CCTAATGTGCTGGGTTTCGATCTTTCCCGTTCGGCCAAATAGCCA
66 CCTAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
* **** * * *
54936943 AATATCCTCTTCAATTTTTTTTTCAAAATGAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACA
1 AATATCCT-TTTAA--AAAATTTCAAAATAAGGCAATGTTTTGTGTTTGGAAATTCGAGAAAACG
54937008 TGCCCTAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAAT-GACCA
63 TGCCCTAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAG-CCA
* *
54937056 AATATCCTTTT-AAAAACTTCAAAATAAGGCAATGTTTTGTGTTTGAAAATTCGAGAAAACGTGC
1 AATATCCTTTTAAAAAATTTCAAAATAAGGCAATGTTTTGTGTTTGGAAATTCGAGAAAACGTGC
*** * * *
54937120 CCTAATGCATTGGATTTCGA--TTTCTCGTTGGACCAAATAGCCG
66 CCTAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
*
54937163 AATATCCTCTTAAA
1 AATATCCTTTTAAA
54937177 TCTTAATCCA
Statistics
Matches: 300, Mismatches: 38, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
107 29 0.10
108 3 0.01
109 59 0.20
110 110 0.37
111 5 0.02
112 3 0.01
113 91 0.30
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (110 bp):
AATATCCTTTTAAAAAATTTCAAAATAAGGCAATGTTTTGTGTTTGGAAATTCGAGAAAACGTGC
CCTAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
Found at i:54937983 original size:3 final size:3
Alignment explanation
Indices: 54937975--54937999 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
54937965 ACCACATGAT
54937975 CCA CCA CCA CCA CCA CCA CCA CCA C
1 CCA CCA CCA CCA CCA CCA CCA CCA C
54938000 AACCCTTGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:54938966 original size:16 final size:17
Alignment explanation
Indices: 54938945--54939008 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 17
54938935 AAAAAAGCAT
54938945 ATATATATATAT-ACAC
1 ATATATATATATCACAC
54938961 ATATATAT-TATCACAC
1 ATATATATATATCACAC
* *
54938977 TACTATAAATTTATCACAC
1 -A-TATATATATATCACAC
*
54938996 AGATATCATATAT
1 ATATAT-ATATAT
54939009 TTAAATTAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
15 3 0.08
16 12 0.31
17 4 0.10
18 12 0.31
19 8 0.21
ACGTcount: A:0.45, C:0.16, G:0.02, T:0.38
Consensus pattern (17 bp):
ATATATATATATCACAC
Found at i:54940088 original size:18 final size:18
Alignment explanation
Indices: 54940065--54940101 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
54940055 TGAAACAATT
54940065 TGTATAATAAA-ATTAAAA
1 TGTATAA-AAATATTAAAA
54940083 TGTATAAAAATATTAAAA
1 TGTATAAAAATATTAAAA
54940101 T
1 T
54940102 TAAAGCTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (18 bp):
TGTATAAAAATATTAAAA
Found at i:54940659 original size:13 final size:13
Alignment explanation
Indices: 54940641--54940666 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54940631 AAAATGTAGC
54940641 GTTAATGAAGTGA
1 GTTAATGAAGTGA
54940654 GTTAATGAAGTGA
1 GTTAATGAAGTGA
54940667 ACACATAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (13 bp):
GTTAATGAAGTGA
Found at i:54946035 original size:72 final size:72
Alignment explanation
Indices: 54945899--54946035 Score: 161
Period size: 72 Copynumber: 1.9 Consensus size: 72
54945889 GTTTTGAGAC
* * * * **
54945899 ATACCAATATCGAAGCTAAAATTTCTTCAAGGGTGCCCTATCTTGAGACAAAAGCTCATTTGTCT
1 ATACCAATATCAAAGCTAAAATTTCTTCAAGGGTGCCCTAGCTCGAGACAAAAGCCCAAATGTCT
54945964 CAATACA
66 CAATACA
* * *
54945971 ATACCAA-ATCAAAGCTAAATTTCTCTTTAGGGGTG-CCTAGCATCGAGACAAAAGCCCAAATGT
1 ATACCAATATCAAAGCTAAAATT-TCTTCAAGGGTGCCCTAGC-TCGAGACAAAAGCCCAAATGT
54946034 CT
64 CT
54946036 TGAGAAAATC
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
71 18 0.33
72 36 0.67
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (72 bp):
ATACCAATATCAAAGCTAAAATTTCTTCAAGGGTGCCCTAGCTCGAGACAAAAGCCCAAATGTCT
CAATACA
Found at i:54948832 original size:151 final size:148
Alignment explanation
Indices: 54948567--54948883 Score: 415
Period size: 151 Copynumber: 2.1 Consensus size: 148
54948557 AGAAAAGTTC
* * ** * *
54948567 TGATTTTTTTT--AAAAAGAGAAAATTTAGATTTTTAAAAATAAAATTTGTTTTTTAGTCATTTT
1 TGATTTTTTTTAAAAAAATAGAAAATTTAGATTCTTAAAAATAAAAAATGTTTTTTAGCCATTTC
* * * * *
54948630 AAAGGAAATTTTAAATTTTTAAAATAAAGTTTTGATTTTTTTCAACTATTTCGGAATAAAAGCTT
66 AAAGGAAATTTTAAA-TTTTAAAAAAAAGTTTTAATTTTTTTCAACCATTTCGAAATAAAACCTT
*
54948695 TGATATTTAAGAAAAACAG
130 TCATATTTAAGAAAAACAG
*
54948714 TGATTTTTTTTAAAAAAATAGAAAGTTTAGATTCTTAAAAATAAAAAAAATGTTTTTTAGCCATT
1 TGATTTTTTTTAAAAAAATAGAAAATTTAGATTCTTAAAAAT--AAAAAATGTTTTTTAGCCATT
54948779 TCAAAGGAAATTTTAAA-TTTAAAAAAGAAGTTTTAATTTTTTTTCAACCATTTCGAAATAAAAC
64 TCAAAGGAAATTTTAAATTTTAAAAAA-AAGTTTTAA-TTTTTTTCAACCATTTCGAAATAAAAC
* **
54948843 CTTTCATCTTTAAGAAAAGTAG
127 CTTTCATATTTAAGAAAAACAG
*
54948865 TGATTTTTTTAAAAAAAAT
1 TGATTTTTTTTAAAAAAAT
54948884 CACATATCCG
Statistics
Matches: 147, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
147 11 0.07
149 34 0.23
150 8 0.05
151 94 0.64
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.42
Consensus pattern (148 bp):
TGATTTTTTTTAAAAAAATAGAAAATTTAGATTCTTAAAAATAAAAAATGTTTTTTAGCCATTTC
AAAGGAAATTTTAAATTTTAAAAAAAAGTTTTAATTTTTTTCAACCATTTCGAAATAAAACCTTT
CATATTTAAGAAAAACAG
Found at i:54949197 original size:25 final size:25
Alignment explanation
Indices: 54949128--54949206 Score: 88
Period size: 27 Copynumber: 3.1 Consensus size: 25
54949118 AGATATATGA
* *
54949128 CTCTTCGGAGCTTCCCGATTAAAGG
1 CTCTTCGGAGCTTCTCGATTAATGG
*
54949153 CTCTTTCATGAGCTTCTCGATTAATGG
1 CTC-TTC-GGAGCTTCTCGATTAATGG
* *
54949180 CTCTTCGGAGCTTTTCGA-TATTGG
1 CTCTTCGGAGCTTCTCGATTAATGG
54949204 CTC
1 CTC
54949207 GCTTGAACTT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
24 8 0.17
25 13 0.28
26 6 0.13
27 19 0.41
ACGTcount: A:0.16, C:0.25, G:0.22, T:0.37
Consensus pattern (25 bp):
CTCTTCGGAGCTTCTCGATTAATGG
Found at i:54949288 original size:25 final size:25
Alignment explanation
Indices: 54949235--54949289 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
54949225 TGGCTTGTAT
*
54949235 GAGCTTCCCATTAATGGCTCTTCAA
1 GAGCTTCCCATTAATGGCTCTACAA
* *
54949260 -AGCTTCTCTTTACATGGCTC-ACAA
1 GAGCTTCCCATTA-ATGGCTCTACAA
54949284 GAGCTT
1 GAGCTT
54949290 TCCGTTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
24 13 0.52
25 12 0.48
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (25 bp):
GAGCTTCCCATTAATGGCTCTACAA
Found at i:54956628 original size:24 final size:24
Alignment explanation
Indices: 54956577--54956634 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
54956567 CAGCTCAATA
* * *
54956577 GAGCGTCCCGTTATTAGCTCTCAT
1 GAGCATCCCGTTAATAGCTCTCAG
*
54956601 GAGCTTCCCGTTAATAGCTCTTC-G
1 GAGCATCCCGTTAATAGCTC-TCAG
54956625 GAGCATCCCG
1 GAGCATCCCG
54956635 ATTTGGTTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 27 0.93
25 2 0.07
ACGTcount: A:0.17, C:0.31, G:0.22, T:0.29
Consensus pattern (24 bp):
GAGCATCCCGTTAATAGCTCTCAG
Found at i:54956826 original size:24 final size:25
Alignment explanation
Indices: 54956799--54956891 Score: 75
Period size: 25 Copynumber: 3.7 Consensus size: 25
54956789 TTCAATATTA
54956799 GCTCGTATGAGCTTCCCGTTA-ATG
1 GCTCGTATGAGCTTCCCGTTACATG
* **
54956823 GCTCTTCGGAGCTTCCCGTTACATG
1 GCTCGTATGAGCTTCCCGTTACATG
* * *
54956848 GCTTAG-AAGAGCTTCCCGATTATAT-
1 GC-TCGTATGAGCTTCCCG-TTACATG
*
54956873 GCTCGTATGAACATTCCCG
1 GCTCGTATGAGC-TTCCCG
54956892 AATATGAATT
Statistics
Matches: 53, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
24 20 0.38
25 21 0.40
26 12 0.23
ACGTcount: A:0.19, C:0.27, G:0.23, T:0.31
Consensus pattern (25 bp):
GCTCGTATGAGCTTCCCGTTACATG
Found at i:54957339 original size:11 final size:11
Alignment explanation
Indices: 54957325--54957395 Score: 73
Period size: 11 Copynumber: 6.8 Consensus size: 11
54957315 TTTAAAATAC
54957325 TTTTTTTAAAA
1 TTTTTTTAAAA
54957336 TTTTTTT--AA
1 TTTTTTTAAAA
54957345 ---TTTTAAAA
1 TTTTTTTAAAA
54957353 TTTTTTTAAAA
1 TTTTTTTAAAA
54957364 TTTTTTTAAAA
1 TTTTTTTAAAA
*
54957375 TACTTTTTT-TAA
1 T--TTTTTTAAAA
54957387 TTTTTTTAA
1 TTTTTTTAA
54957396 TTTTAAAATA
Statistics
Matches: 50, Mismatches: 2, Indels: 16
0.74 0.03 0.24
Matches are distributed among these distances:
6 4 0.08
8 2 0.04
9 2 0.04
10 6 0.12
11 27 0.54
12 3 0.06
13 6 0.12
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (11 bp):
TTTTTTTAAAA
Found at i:54957349 original size:51 final size:48
Alignment explanation
Indices: 54957294--54957400 Score: 133
Period size: 51 Copynumber: 2.1 Consensus size: 48
54957284 TAATAAATAT
***
54957294 TTTTATTTTTTTATTTTTTATTTTAAAATACTTTTTTTAAAATTTTTTTAA
1 TTTTATTTTTTTAAAATTT-TTTTAAAATACTTTTTTT--AATTTTTTTAA
54957345 TTTTAAAATTTTTTTAAAATTTTTTTAAAATACTTTTTTTAATTTTTTTAA
1 TTTT---ATTTTTTTAAAATTTTTTTAAAATACTTTTTTTAATTTTTTTAA
54957396 TTTTA
1 TTTTA
54957401 AAATATTTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
48 1 0.02
51 19 0.38
53 18 0.36
54 12 0.24
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (48 bp):
TTTTATTTTTTTAAAATTTTTTTAAAATACTTTTTTTAATTTTTTTAA
Found at i:54957388 original size:23 final size:22
Alignment explanation
Indices: 54957325--54957395 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 22
54957315 TTTAAAATAC
54957325 TTTTTTTAAAATTTTTTT--AA
1 TTTTTTTAAAATTTTTTTAAAA
54957345 ---TTTTAAAATTTTTTTAAAA
1 TTTTTTTAAAATTTTTTTAAAA
*
54957364 TTTTTTTAAAATACTTTTTT-TAA
1 TTTTTTTAAAAT--TTTTTTAAAA
54957387 TTTTTTTAA
1 TTTTTTTAA
54957396 TTTTAAAATA
Statistics
Matches: 43, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
17 15 0.35
19 2 0.05
22 9 0.21
23 11 0.26
24 6 0.14
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTTTTTAAAATTTTTTTAAAA
Found at i:54957403 original size:51 final size:52
Alignment explanation
Indices: 54957314--54957415 Score: 179
Period size: 51 Copynumber: 2.0 Consensus size: 52
54957304 TTATTTTTTA
*
54957314 TTTTAAAATACTTTTTTTAAAATTTTTTTAATTTTAAAATTTTTTTAAAATTT
1 TTTTAAAATACTTTTTTT-AAATTTTTTTAATTTTAAAATATTTTTAAAATTT
54957367 TTTTAAAATACTTTTTTT-AATTTTTTTAATTTTAAAATATTTTTAAAAT
1 TTTTAAAATACTTTTTTTAAATTTTTTTAATTTTAAAATATTTTTAAAAT
54957416 ACTTTTTTTA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
51 30 0.62
53 18 0.38
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (52 bp):
TTTTAAAATACTTTTTTTAAATTTTTTTAATTTTAAAATATTTTTAAAATTT
Found at i:54957456 original size:33 final size:31
Alignment explanation
Indices: 54957388--54957456 Score: 84
Period size: 33 Copynumber: 2.2 Consensus size: 31
54957378 TTTTTTTAAT
**
54957388 TTTTTTAATTTTAAAATATTTTTAAAATACT
1 TTTTTTAATTTTAAAATATTTTTAAAATAAA
**
54957419 TTTTTTAATTTTAATTTTAATTTTTAAAATAAA
1 TTTTTTAATTTTAA-AAT-ATTTTTAAAATAAA
54957452 TTTTT
1 TTTTT
54957457 GGTATTTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 14 0.44
32 1 0.03
33 17 0.53
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (31 bp):
TTTTTTAATTTTAAAATATTTTTAAAATAAA
Found at i:54959164 original size:24 final size:24
Alignment explanation
Indices: 54959119--54959165 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
54959109 TATATATACC
54959119 AATTCAATCAATATAAATTCAATA
1 AATTCAATCAATATAAATTCAATA
54959143 AATTC-ATCACATACTAAA-TCAAT
1 AATTCAATCA-ATA-TAAATTCAAT
54959166 CCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (24 bp):
AATTCAATCAATATAAATTCAATA
Found at i:54959888 original size:15 final size:14
Alignment explanation
Indices: 54959864--54959893 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
54959854 TCTCTGTTTC
54959864 TTTCTCTATTTCTT
1 TTTCTCTATTTCTT
54959878 TTTCTTCTATTTCTT
1 TTTC-TCTATTTCTT
54959893 T
1 T
54959894 GTTTTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTCTCTATTTCTT
Found at i:54965469 original size:41 final size:41
Alignment explanation
Indices: 54965400--54965544 Score: 200
Period size: 41 Copynumber: 3.5 Consensus size: 41
54965390 TTTAACATAT
* *
54965400 TCACCGGCACTTAACCTGCTAAGCTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
* * * *
54965441 TCACTGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAAA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
* * * *
54965482 TCACCAGCACTTAGCCTGGTAGACTTATAGCCTGTTTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
54965523 TCACCGGCACTTAGCCTGCTAG
1 TCACCGGCACTTAGCCTGCTAG
54965545 ACATAAAGTC
Statistics
Matches: 88, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 88 1.00
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
Found at i:54966130 original size:114 final size:112
Alignment explanation
Indices: 54966012--54966366 Score: 584
Period size: 114 Copynumber: 3.1 Consensus size: 112
54966002 CTCAAGATCT
*
54966012 TATACATATTCATATATACATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAACT
1 TATACATA-T-ATATTTACATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAACT
* * * *
54966077 AATTTCAATTTATATACTTTCAATTATAGCTCATCAAGTATACAATAGA
64 AATTTCAATTCATATATTTTTAATTATAGCTCATCAAATATACAATAGA
54966126 TATACATATATATTTACATATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAACT
1 TATACATATATATTTAC--ATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAACT
54966191 AATTTCAATTCATATATTTTTAATTATAGCTCATCAAATATACAATAGA
64 AATTTCAATTCATATATTTTTAATTATAGCTCATCAAATATACAATAGA
* *
54966240 TATACATATATATTTACATTTATTCAAACTTCATTTATGCATATATATAGCATTCATACTTAACT
1 TATACATATATATTTACA--TATTCGAACTTCATTTATGCATATATATAACATTCATACTTAACT
*
54966305 AATTTCAATTCATATATTTTTAATTATAGCTCATAAAATATACAATAGA
64 AATTTCAATTCATATATTTTTAATTATAGCTCATCAAATATACAATAGA
54966354 TATACATATATAT
1 TATACATATATAT
54966367 ATGCTGATTT
Statistics
Matches: 229, Mismatches: 8, Indels: 8
0.93 0.03 0.03
Matches are distributed among these distances:
112 8 0.03
113 1 0.00
114 220 0.96
ACGTcount: A:0.40, C:0.14, G:0.04, T:0.42
Consensus pattern (112 bp):
TATACATATATATTTACATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAACTAA
TTTCAATTCATATATTTTTAATTATAGCTCATCAAATATACAATAGA
Found at i:54967362 original size:13 final size:13
Alignment explanation
Indices: 54967344--54967368 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54967334 CAATCAAATG
54967344 CACACAAAATAAA
1 CACACAAAATAAA
54967357 CACACAAAATAA
1 CACACAAAATAA
54967369 TATTAAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:54968712 original size:21 final size:20
Alignment explanation
Indices: 54968686--54968737 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
54968676 TATACAAATG
*
54968686 AATTTAACATCAATTTAATAC
1 AATTT-ACATCAATTCAATAC
*
54968707 AATTTACATTCAATTCAATCC
1 AATTTACA-TCAATTCAATAC
54968728 AATTTACATC
1 AATTTACATC
54968738 TTAGGTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 5 0.18
21 23 0.82
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.38
Consensus pattern (20 bp):
AATTTACATCAATTCAATAC
Found at i:54971591 original size:24 final size:23
Alignment explanation
Indices: 54971539--54971592 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
54971529 CCTTACTGGT
*
54971539 AGTCACCACCGTCCGACGTCCACC
1 AGTCA-CACCGTCCGACGTACACC
* *
54971563 AGTCACACCGTTCGATGTACACC
1 AGTCACACCGTCCGACGTACACC
54971586 AGGTCAC
1 A-GTCAC
54971593 CATCATTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 16 0.62
24 10 0.38
ACGTcount: A:0.24, C:0.41, G:0.19, T:0.17
Consensus pattern (23 bp):
AGTCACACCGTCCGACGTACACC
Found at i:54973638 original size:25 final size:25
Alignment explanation
Indices: 54973571--54973646 Score: 66
Period size: 25 Copynumber: 3.0 Consensus size: 25
54973561 ATTCATATTG
**
54973571 GGGAATGCTCATACAAGCACATA-AAC
1 GGGAA-GCTCATATGAGC-CATATAAC
* *
54973597 GGAAAGCTC-TTTCGAGCCATATAAC
1 GGGAAGCTCATAT-GAGCCATATAAC
*
54973622 GGGAAGCTCATATGAGCCATGTAAC
1 GGGAAGCTCATATGAGCCATATAAC
54973647 AGAAATTTCA
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
24 5 0.12
25 29 0.73
26 6 0.15
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (25 bp):
GGGAAGCTCATATGAGCCATATAAC
Found at i:54973703 original size:25 final size:24
Alignment explanation
Indices: 54973673--54973778 Score: 76
Period size: 25 Copynumber: 4.3 Consensus size: 24
54973663 CCAATATTGA
54973673 GAAGCTCTGGAGAGCCATTAATCAG
1 GAAGCTCT-GAGAGCCATTAATCAG
* *
54973698 GAAGCTCATAAGAGCCAGTT-ATCGG
1 GAAGCTC-TGAGAGCCA-TTAATCAG
* *
54973723 GAAG-TACATAAGAGCCA-TAAACAG
1 GAAGCT-C-TGAGAGCCATTAATCAG
*
54973747 GAAGCTC-AAGAGCGTCATTAATCAG
1 GAAGCTCTGAGAGC--CATTAATCAG
54973772 GAAGCTC
1 GAAGCTC
54973779 ACGAGAACCA
Statistics
Matches: 68, Mismatches: 5, Indels: 16
0.76 0.06 0.18
Matches are distributed among these distances:
22 6 0.09
23 1 0.01
24 11 0.16
25 47 0.69
26 3 0.04
ACGTcount: A:0.37, C:0.20, G:0.25, T:0.18
Consensus pattern (24 bp):
GAAGCTCTGAGAGCCATTAATCAG
Found at i:54978984 original size:21 final size:21
Alignment explanation
Indices: 54978952--54979128 Score: 115
Period size: 21 Copynumber: 8.4 Consensus size: 21
54978942 GAAGCCCGAA
* *
54978952 AGCTTAACAGAAGCTCATGAG
1 AGCTAAACAGAAGCTCATAAG
*
54978973 AGCTAAATAGAAGCTCATAAG
1 AGCTAAACAGAAGCTCATAAG
* *
54978994 AGCTAAACAGAAACCCATAAG
1 AGCTAAACAGAAGCTCATAAG
* * * ** *
54979015 -GATTGATCAGAAGCTCGCAAA
1 AG-CTAAACAGAAGCTCATAAG
* *
54979036 AGCTTAACAGAAACTCATAAG
1 AGCTAAACAGAAGCTCATAAG
* * *
54979057 AGTTTAACAAAAGCT-AGTAAG
1 AGCTAAACAGAAGCTCA-TAAG
* * * *
54979078 AGCTGAACAGAAACTCGTATG
1 AGCTAAACAGAAGCTCATAAG
* *
54979099 AGTTAAACAGAAGCTCGTAAG
1 AGCTAAACAGAAGCTCATAAG
*
54979120 AGCTGAACA
1 AGCTAAACA
54979129 AAAAGTAAAA
Statistics
Matches: 116, Mismatches: 36, Indels: 8
0.73 0.22 0.05
Matches are distributed among these distances:
20 2 0.02
21 113 0.97
22 1 0.01
ACGTcount: A:0.44, C:0.18, G:0.20, T:0.18
Consensus pattern (21 bp):
AGCTAAACAGAAGCTCATAAG
Found at i:54979027 original size:42 final size:42
Alignment explanation
Indices: 54978981--54979128 Score: 129
Period size: 42 Copynumber: 3.5 Consensus size: 42
54978971 AGAGCTAAAT
*
54978981 AGAAGCTCATAAGAGCTAAACAGAAACCCATAAG-GATTGATC
1 AGAAGCTCATAAGAGCTAAACAGAAACCCATAAGAG-TTGAAC
** * * * *
54979023 AGAAGCTCGCAAAAGCTTAACAGAAACTCATAAGAGTTTAAC
1 AGAAGCTCATAAGAGCTAAACAGAAACCCATAAGAGTTGAAC
* * * * * *
54979065 AAAAGCT-AGTAAGAGCTGAACAGAAACTCGTATGAGTTAAAC
1 AGAAGCTCA-TAAGAGCTAAACAGAAACCCATAAGAGTTGAAC
* *
54979107 AGAAGCTCGTAAGAGCTGAACA
1 AGAAGCTCATAAGAGCTAAACA
54979129 AAAAGTAAAA
Statistics
Matches: 86, Mismatches: 17, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
42 85 0.99
43 1 0.01
ACGTcount: A:0.45, C:0.18, G:0.20, T:0.18
Consensus pattern (42 bp):
AGAAGCTCATAAGAGCTAAACAGAAACCCATAAGAGTTGAAC
Found at i:54979110 original size:84 final size:84
Alignment explanation
Indices: 54978950--54979115 Score: 192
Period size: 84 Copynumber: 2.0 Consensus size: 84
54978940 CAGAAGCCCG
* * * *
54978950 AAAGCTTAACAGAAGCTCATGAGAGCTAAATAGAAGCTCATAAGAGCTAAACAGAAACCCATAAG
1 AAAGCTTAACAGAAACTCATAAGAGCTAAACAAAAGCTCATAAGAGCTAAACAGAAACCCATAAG
* *
54979015 GATTGATCAGAAGCTCGCA
66 GATTAAACAGAAGCTCGCA
* * * * *
54979034 AAAGCTTAACAGAAACTCATAAGAGTTTAACAAAAGCT-AGTAAGAGCTGAACAGAAACTCGT-A
1 AAAGCTTAACAGAAACTCATAAGAGCTAAACAAAAGCTCA-TAAGAGCTAAACAGAAACCCATAA
*
54979097 TGAGTTAAACAGAAGCTCG
65 GGA-TTAAACAGAAGCTCG
54979116 TAAGAGCTGA
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
83 4 0.06
84 64 0.94
ACGTcount: A:0.45, C:0.17, G:0.20, T:0.18
Consensus pattern (84 bp):
AAAGCTTAACAGAAACTCATAAGAGCTAAACAAAAGCTCATAAGAGCTAAACAGAAACCCATAAG
GATTAAACAGAAGCTCGCA
Found at i:54980971 original size:105 final size:105
Alignment explanation
Indices: 54980722--54981094 Score: 642
Period size: 105 Copynumber: 3.6 Consensus size: 105
54980712 TAACCGTTAT
* * ** *
54980722 TGGTGGATCTCGCACTTAGCACCACCGCTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATCACGCACATAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
54980787 AATCAGCACATAGCAACCCCC-TTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
*
54980826 TGGTGGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGG
1 TGGTGGATCA-CGCACATAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGG
54980890 GAATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
65 GAATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
54980931 TGGTGGATCACGCACATAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATCACGCACATAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
54980996 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
* **
54981036 TGGTGGATCACGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGATCACGCACATAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCT
54981095 TTATATACAA
Statistics
Matches: 258, Mismatches: 8, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
104 81 0.31
105 176 0.68
106 1 0.00
ACGTcount: A:0.30, C:0.31, G:0.21, T:0.18
Consensus pattern (105 bp):
TGGTGGATCACGCACATAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
Found at i:54981455 original size:29 final size:29
Alignment explanation
Indices: 54981422--54981485 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
54981412 TAATCCACCA
54981422 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
54981451 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
54981481 CCCAA
1 CCCAA
54981486 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:54981459 original size:30 final size:30
Alignment explanation
Indices: 54981429--54981485 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
54981419 CCACCCAACT
54981429 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
54981458 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
54981486 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:54986698 original size:27 final size:28
Alignment explanation
Indices: 54986662--54986720 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
54986652 ATTTTATATT
*
54986662 TTTAATTTTTAAAAAATATAT-TTTTAA
1 TTTAAATTTTAAAAAATATATATTTTAA
* *
54986689 TTTAAATTTTAATAATTATATATTTTAA
1 TTTAAATTTTAAAAAATATATATTTTAA
54986717 TTTA
1 TTTA
54986721 TTAAATTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 18 0.64
28 10 0.36
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (28 bp):
TTTAAATTTTAAAAAATATATATTTTAA
Found at i:54986704 original size:15 final size:15
Alignment explanation
Indices: 54986686--54986733 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
54986676 AATATATTTT
54986686 TAATTTAAATTTTAA
1 TAATTTAAATTTTAA
*
54986701 TAATTATATATTTTAA
1 TAATT-TAAATTTTAA
*
54986717 T-TTATTAAATTTTAA
1 TAAT-TTAAATTTTAA
54986732 TA
1 TA
54986734 TATAATTAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
15 16 0.59
16 11 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TAATTTAAATTTTAA
Found at i:54986748 original size:31 final size:31
Alignment explanation
Indices: 54986690--54986748 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
54986680 TATTTTTAAT
* **
54986690 TTAAATTTTAATAATTATATATTTTAATTTA
1 TTAAATTTTAATAATAATATAACTTAATTTA
54986721 TTAAATTTTAATATATAAT-TAACTTAAT
1 TTAAATTTTAATA-ATAATATAACTTAAT
54986749 ATTTTTTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 20 0.83
32 4 0.17
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (31 bp):
TTAAATTTTAATAATAATATAACTTAATTTA
Found at i:54990062 original size:73 final size:71
Alignment explanation
Indices: 54989908--54990078 Score: 261
Period size: 73 Copynumber: 2.4 Consensus size: 71
54989898 AAAATAGGCA
54989908 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCGTTTCCCGAGCTTTC
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCGTTTCCCGAGCTTTC
*
54989973 GGGGAT
66 GAGGAT
* * * *
54989979 TTAGCAGCGTTTCTGAGAAAGCGCCGCAAAAAACCATAAGCCCAACGACGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACC-TAAGCCCAACGACG-CGTTTCCCGAGCTT
54990044 TCGAGGAT
64 TCGAGGAT
* *
54990052 TTAGCGGCGTTTTTAAGGAAGCGCCGC
1 TTAGCGGCGTTTTTGAGAAAGCGCCGC
54990079 TAATGCTCAG
Statistics
Matches: 89, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
71 33 0.37
72 14 0.16
73 42 0.47
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.22
Consensus pattern (71 bp):
TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCGTTTCCCGAGCTTTC
GAGGAT
Found at i:54990133 original size:114 final size:114
Alignment explanation
Indices: 54989978--54990345 Score: 594
Period size: 114 Copynumber: 3.2 Consensus size: 114
54989968 CTTTCGGGGA
*
54989978 TTTAGCAGCGTTTCTGAGAAAGCGCCGC-AAAAAACCATAAGCCCAACGACGCCGTTTTCTGAGC
1 TTTAGCGGCGTTTCTGAGAAAGCGCCGCAAAAAAACC-TAAGCCCAACGACGCCGTTTTCTGAGC
* *
54990042 TTTCGAGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGC
65 TTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
*
54990092 TTTAGCGGCGTTTCTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCGGTTTTCTGAGCT
1 TTTAGCGGCGTTTCTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
* *
54990157 TTCGGGGATTTAACGGCGTTTTTAAGAAAGCGTCGCTAATGCTCAGGGC
66 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
* * * * * *
54990206 TTTAGTGGCGTTTTTGGGAAAGTGCCGCAAAAAAACCTAAGCCCAACGATGCCGTTTTCTGAACT
1 TTTAGCGGCGTTTCTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
54990271 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
66 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
* *
54990320 TTTAGCGGCGTTTTTGGGAAAGCGCC
1 TTTAGCGGCGTTTCTGAGAAAGCGCC
54990346 TTTAACAATA
Statistics
Matches: 236, Mismatches: 17, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
114 228 0.97
115 8 0.03
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (114 bp):
TTTAGCGGCGTTTCTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
Done.