Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 172 of 208
Found at i:55011837 original size:14 final size:14
Alignment explanation
Indices: 55011804--55011838 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
55011794 TTAAATTTAA
55011804 TTTAAATAATAAAT
1 TTTAAATAATAAAT
**
55011818 AATAAATAATAAAT
1 TTTAAATAATAAAT
55011832 TTTAAAT
1 TTTAAAT
55011839 TTAAATTTAA
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TTTAAATAATAAAT
Found at i:55016940 original size:37 final size:38
Alignment explanation
Indices: 55016874--55016945 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 38
55016864 TCAGCCCAAA
*
55016874 GTTCATAGAAAACAACAGAAAGAAGGAAGATTGTGAAG
1 GTTCATAGAAAACAACAGAAAGAAGGAAGAATGTGAAG
*
55016912 GTTCATAGGAAACAA-AGAAAGATA-GAAGAATGTG
1 GTTCATAGAAAACAACAGAAAGA-AGGAAGAATGTG
55016946 GAAAAAGAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
37 16 0.52
38 15 0.48
ACGTcount: A:0.50, C:0.07, G:0.26, T:0.17
Consensus pattern (38 bp):
GTTCATAGAAAACAACAGAAAGAAGGAAGAATGTGAAG
Found at i:55028629 original size:41 final size:41
Alignment explanation
Indices: 55028583--55028795 Score: 178
Period size: 41 Copynumber: 5.2 Consensus size: 41
55028573 TTTGCCATAC
55028583 GGCCTACCACACGGTCATGTGACCCACACGATCTACCACAT
1 GGCCTACCACACGGTCATGTGACCCACACGATCTACCACAT
* * * * * * * * *
55028624 AGCCTACCACATGTTCGTGTGACACACACGGTCTGCTAAAT
1 GGCCTACCACACGGTCATGTGACCCACACGATCTACCACAT
* * * * * * * *
55028665 GGCTTACTATATGGTCCTGTGACCGACACGTTCTACCACAC
1 GGCCTACCACACGGTCATGTGACCCACACGATCTACCACAT
** * * *
55028706 CACCTACCACACGGTCGTGTGACCCACAC-ATCT-TCGCAT
1 GGCCTACCACACGGTCATGTGACCCACACGATCTACCACAT
* * **
55028745 GGCCTACCACACGGCCATGTGACGCACACGATCTGTCACAT
1 GGCCTACCACACGGTCATGTGACCCACACGATCTACCACAT
55028786 GGCCTACCAC
1 GGCCTACCAC
55028796 TGATCGTGTA
Statistics
Matches: 130, Mismatches: 40, Indels: 4
0.75 0.23 0.02
Matches are distributed among these distances:
39 27 0.21
40 7 0.05
41 96 0.74
ACGTcount: A:0.24, C:0.36, G:0.19, T:0.21
Consensus pattern (41 bp):
GGCCTACCACACGGTCATGTGACCCACACGATCTACCACAT
Found at i:55028753 original size:39 final size:41
Alignment explanation
Indices: 55028583--55028828 Score: 176
Period size: 41 Copynumber: 6.1 Consensus size: 41
55028573 TTTGCCATAC
* **
55028583 GGCCTACCACACGGTCATGTGACCCACACGATCTACCACAT
1 GGCCTACCACACGGTCGTGTGACCCACACGATCTGTCACAT
* * * * * *
55028624 AGCCTACCACATGTTCGTGTGACACACACGGTCTG-CTAAAT
1 GGCCTACCACACGGTCGTGTGACCCACACGATCTGTC-ACAT
* * * * * * * ** *
55028665 GGCTTACTATATGGTCCTGTGACCGACACGTTCTACCACAC
1 GGCCTACCACACGGTCGTGTGACCCACACGATCTGTCACAT
** *
55028706 CACCTACCACACGGTCGTGTGACCCACAC-ATCT-TCGCAT
1 GGCCTACCACACGGTCGTGTGACCCACACGATCTGTCACAT
* * *
55028745 GGCCTACCACACGGCCATGTGACGCACACGATCTGTCACAT
1 GGCCTACCACACGGTCGTGTGACCCACACGATCTGTCACAT
* * * * * *
55028786 GGCCTACCAC-TGATCGTGTAACCCACATGGTCTGCCACAT
1 GGCCTACCACACGGTCGTGTGACCCACACGATCTGTCACAT
55028826 GGC
1 GGC
55028829 TAGTTACACG
Statistics
Matches: 154, Mismatches: 47, Indels: 9
0.73 0.22 0.04
Matches are distributed among these distances:
39 27 0.18
40 32 0.21
41 94 0.61
42 1 0.01
ACGTcount: A:0.24, C:0.35, G:0.20, T:0.21
Consensus pattern (41 bp):
GGCCTACCACACGGTCGTGTGACCCACACGATCTGTCACAT
Found at i:55031601 original size:26 final size:26
Alignment explanation
Indices: 55031570--55031619 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
55031560 AAATGTGAAG
55031570 GGGGTTGCTAAGTGCTGATTCCCCAA
1 GGGGTTGCTAAGTGCTGATTCCCCAA
*
55031596 GGGGTTGCTAAGTGTTGATTCCCC
1 GGGGTTGCTAAGTGCTGATTCCCC
55031620 GATTCATTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.16, C:0.22, G:0.32, T:0.30
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCAA
Found at i:55031635 original size:33 final size:33
Alignment explanation
Indices: 55031598--55031833 Score: 135
Period size: 33 Copynumber: 6.8 Consensus size: 33
55031588 TTCCCCAAGG
*
55031598 GGTTGCTAAGTGTTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
55031631 GGTTGCTAAGTGCTGATTCCACCGTATCTTGAATATAAAGG-
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-T---GGT
55031672 GAGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 G-GTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* * * *
55031706 GGTTGCTAAGTGCTGATCCCACCGTATTTTAAAGGTGAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CA--T--TGGT
*
55031748 GGTTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* * * *
55031775 GGTTTCTAAGTGCTGATTCCCCAAATCACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
55031808 GGTTGCTAAGTGCTGAATCCACCGAT
1 GGTTGCTAAGTGCTGATTCC-CCGAT
55031834 AACGGTTAAT
Statistics
Matches: 161, Mismatches: 15, Indels: 53
0.70 0.07 0.23
Matches are distributed among these distances:
27 21 0.13
28 3 0.02
31 2 0.01
32 2 0.01
33 58 0.36
34 10 0.06
35 2 0.01
36 1 0.01
37 6 0.04
38 5 0.03
39 1 0.01
40 2 0.01
41 6 0.04
42 42 0.26
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
Found at i:55031690 original size:75 final size:74
Alignment explanation
Indices: 55031594--55031769 Score: 271
Period size: 75 Copynumber: 2.4 Consensus size: 74
55031584 CTGATTCCCC
* *
55031594 AAGGGGTTGCTAAGTGTTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATC
* *
55031659 TTGAATATA
66 TTAAAGATA
55031668 AAGGGAGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTAT
1 AAGGG-GTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTAT
* *
55031733 TTTAAAGGTGA
65 CTTAAAGAT-A
*
55031744 AGGGGGTTGCTAAGTGCTGATTCCCC
1 AAGGGGTTGCTAAGTGCTGATTCCCC
55031770 CAAGGGGTTT
Statistics
Matches: 93, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
74 5 0.05
75 83 0.89
76 5 0.05
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (74 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATC
TTAAAGATA
Found at i:55039180 original size:41 final size:41
Alignment explanation
Indices: 55039012--55039184 Score: 152
Period size: 41 Copynumber: 4.3 Consensus size: 41
55039002 TTTGCCATAC
*
55039012 GGCCTACCACATGGTCATGTGACCCACACGATCTACCACA-
1 GGCCTACCACATGGTCGTGTGACCCACACGATCTACCACAT
* * * * * *
55039052 -GCCTACCACATGTTCGTGTGACACACACGGTCTGCTAAAT
1 GGCCTACCACATGGTCGTGTGACCCACACGATCTACCACAT
* * * * * * *
55039092 GGCTTACTATATGGTCCTGTGACCGACACGTTCTACCACAC
1 GGCCTACCACATGGTCGTGTGACCCACACGATCTACCACAT
** * * * *
55039133 CACCTACCATACGGTCGTGTGACCCACACGATCTGCCGCAT
1 GGCCTACCACATGGTCGTGTGACCCACACGATCTACCACAT
55039174 GGCCTACCACA
1 GGCCTACCACA
55039185 CGATCTGTCA
Statistics
Matches: 98, Mismatches: 33, Indels: 3
0.73 0.25 0.02
Matches are distributed among these distances:
39 32 0.33
41 66 0.67
ACGTcount: A:0.24, C:0.35, G:0.19, T:0.21
Consensus pattern (41 bp):
GGCCTACCACATGGTCGTGTGACCCACACGATCTACCACAT
Found at i:55039188 original size:24 final size:24
Alignment explanation
Indices: 55039156--55039213 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
55039146 GTCGTGTGAC
*
55039156 CCACACGATCTGCCGCATGGCCTA
1 CCACACGATCTGCCACATGGCCTA
* *
55039180 CCACACGATCTGTCACATGGCGTA
1 CCACACGATCTGCCACATGGCCTA
*
55039204 CCACATGATC
1 CCACACGATC
55039214 GTGTAACCCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.24, C:0.38, G:0.19, T:0.19
Consensus pattern (24 bp):
CCACACGATCTGCCACATGGCCTA
Found at i:55049600 original size:41 final size:41
Alignment explanation
Indices: 55049555--55049727 Score: 138
Period size: 41 Copynumber: 4.3 Consensus size: 41
55049545 TTGCCATACG
*
55049555 GCCTACCACACGGTCATGTGACCCACACGATCTACCACATA
1 GCCTACCACACGGTCGTGTGACCCACACGATCTACCACATA
* * * * * * * *
55049596 GCCTACCACATGTTCGTGTGACACACACGGTCTGCTAAATG
1 GCCTACCACACGGTCGTGTGACCCACACGATCTACCACATA
* * * * * * * *
55049637 GCTTACTATATGGTCCTGTGACCGACACGTTCTACCACACCA
1 GCCTACCACACGGTCGTGTGACCCACACGATCTACCACA-TA
* *
55049679 -CCTACCACACGGTCGTGTGACCCACAC-ATCT--CGCATG
1 GCCTACCACACGGTCGTGTGACCCACACGATCTACCACATA
55049716 GCCTACCACACG
1 GCCTACCACACG
55049728 ATCTGTCACA
Statistics
Matches: 98, Mismatches: 32, Indels: 7
0.72 0.23 0.05
Matches are distributed among these distances:
38 14 0.14
40 3 0.03
41 81 0.83
ACGTcount: A:0.25, C:0.36, G:0.18, T:0.21
Consensus pattern (41 bp):
GCCTACCACACGGTCGTGTGACCCACACGATCTACCACATA
Found at i:55052563 original size:33 final size:33
Alignment explanation
Indices: 55052499--55052649 Score: 129
Period size: 33 Copynumber: 4.5 Consensus size: 33
55052489 ATGTGAAGGG
*
55052499 GGTTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
55052526 GGTTGCTAAGTGTTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
55052559 GGTTGCTAAGTGCTGATTCCACCGTATCTTGAATATAAAGG-
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-T---GGT
55052600 GAGTTGCT-AGTGCTGATTCCCCGATTCATTGGT
1 G-GTTGCTAAGTGCTGATTCCCCGATTCATTGGT
55052633 GGTTGCTAAGTGCTGAT
1 GGTTGCTAAGTGCTGAT
55052650 CCCACCGTAT
Statistics
Matches: 101, Mismatches: 5, Indels: 30
0.74 0.04 0.22
Matches are distributed among these distances:
27 21 0.21
31 2 0.02
32 10 0.10
33 29 0.29
34 3 0.03
35 2 0.02
36 2 0.02
37 4 0.04
38 2 0.02
39 2 0.02
40 3 0.03
41 13 0.13
42 8 0.08
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
Found at i:55052643 original size:74 final size:73
Alignment explanation
Indices: 55052522--55052695 Score: 260
Period size: 74 Copynumber: 2.4 Consensus size: 73
55052512 TGATTCCCCC
* *
55052522 AAGGGGTTGCTAAGTGTTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTAT-
*
55052587 TTGAATATA
65 TTGAAGATA
55052596 AAGGGAGTTGCT-AGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTAT
1 AAGGG-GTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTAT
* *
55052660 TTTAAGGTGA
65 TTGAAGAT-A
*
55052670 AGGGGGTTGCTAAGTGCTGATTCCCC
1 AAGGGGTTGCTAAGTGCTGATTCCCC
55052696 CAAGGGTTTC
Statistics
Matches: 91, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
73 11 0.12
74 74 0.81
75 6 0.07
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.33
Consensus pattern (73 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATT
TGAAGATA
Found at i:55063990 original size:19 final size:19
Alignment explanation
Indices: 55063966--55064003 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
55063956 AATCTGAAGA
55063966 ACAATCCTAAGGTGCTCGT
1 ACAATCCTAAGGTGCTCGT
55063985 ACAATCCTAAGGTGCTCGT
1 ACAATCCTAAGGTGCTCGT
55064004 CATGCTCATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (19 bp):
ACAATCCTAAGGTGCTCGT
Found at i:55069248 original size:15 final size:15
Alignment explanation
Indices: 55069228--55069257 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
55069218 CAAAATTTTG
55069228 AACAAGAGTAAGGCC
1 AACAAGAGTAAGGCC
55069243 AACAAGAGTAAGGCC
1 AACAAGAGTAAGGCC
55069258 TAATTCATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.20, G:0.27, T:0.07
Consensus pattern (15 bp):
AACAAGAGTAAGGCC
Found at i:55075744 original size:15 final size:15
Alignment explanation
Indices: 55075726--55075757 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
55075716 TTCTGCTCTA
55075726 TTCTATTTTGTTCTG
1 TTCTATTTTGTTCTG
*
55075741 TTCTATTTTGTTTTG
1 TTCTATTTTGTTCTG
55075756 TT
1 TT
55075758 TTGTTGAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.09, G:0.12, T:0.72
Consensus pattern (15 bp):
TTCTATTTTGTTCTG
Found at i:55075762 original size:20 final size:20
Alignment explanation
Indices: 55075708--55075762 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
55075698 CATACATTTG
*
55075708 CTATTTTGTTCTGCTCTATT
1 CTATTTTGTTCTGTTCTATT
55075728 CTATTTTGTTCTGTTCTATT
1 CTATTTTGTTCTGTTCTATT
* * *
55075748 TTGTTTTGTTTTGTT
1 CTATTTTGTTCTGTT
55075763 GAACTACCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.07, C:0.13, G:0.13, T:0.67
Consensus pattern (20 bp):
CTATTTTGTTCTGTTCTATT
Found at i:55075969 original size:15 final size:14
Alignment explanation
Indices: 55075942--55076002 Score: 61
Period size: 15 Copynumber: 4.3 Consensus size: 14
55075932 AAACCAAATT
*
55075942 AACCCACTAGCCTA
1 AACCCAATAGCCTA
55075956 AACCCAATTAGCCTA
1 AACCCAA-TAGCCTA
* *
55075971 AGCCCAATA-CCTT
1 AACCCAATAGCCTA
*
55075984 AGCCCAACTAGCCTA
1 AACCCAA-TAGCCTA
55075999 AACC
1 AACC
55076003 AGAAATCAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
13 10 0.26
14 10 0.26
15 19 0.49
ACGTcount: A:0.36, C:0.39, G:0.08, T:0.16
Consensus pattern (14 bp):
AACCCAATAGCCTA
Found at i:55077084 original size:3 final size:3
Alignment explanation
Indices: 55077076--55077125 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
55077066 CTGAACATTT
55077076 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
55077124 TT
1 TT
55077126 TCTGTACTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:55077299 original size:16 final size:15
Alignment explanation
Indices: 55077278--55077307 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
55077268 TGATGTGATA
55077278 TATTATTATTTTAAAT
1 TATTATT-TTTTAAAT
55077294 TATTATTTTTTAAA
1 TATTATTTTTTAAA
55077308 AATTTATCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TATTATTTTTTAAAT
Found at i:55079573 original size:8 final size:8
Alignment explanation
Indices: 55079562--55079588 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
55079552 TAATAAAAAC
55079562 ATTTTTAT
1 ATTTTTAT
55079570 ATTTTTAT
1 ATTTTTAT
55079578 ATTTTTAT
1 ATTTTTAT
55079586 ATT
1 ATT
55079589 AAAATAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
ATTTTTAT
Found at i:55079959 original size:21 final size:20
Alignment explanation
Indices: 55079928--55079966 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
55079918 TTTTTAATAA
55079928 TTTTAAATTTTTAAAATTAT
1 TTTTAAATTTTTAAAATTAT
55079948 TTTTATAATTTTTAAAATT
1 TTTTA-AATTTTTAAAATT
55079967 TTAAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTAAATTTTTAAAATTAT
Found at i:55082900 original size:20 final size:20
Alignment explanation
Indices: 55082819--55082911 Score: 71
Period size: 20 Copynumber: 4.7 Consensus size: 20
55082809 GTATATCAAT
*
55082819 ATTTACCAAGATTTTTAAAG
1 ATTTACCAAAATTTTTAAAG
*
55082839 TTTTACCAAAATTTTT-AAG
1 ATTTACCAAAATTTTTAAAG
** ** *** **
55082858 GCTTACCACGATACCTATGG
1 ATTTACCAAAATTTTTAAAG
55082878 ATTTACCAAAATTTTTAAAG
1 ATTTACCAAAATTTTTAAAG
*
55082898 ATTTATCAAAATTT
1 ATTTACCAAAATTT
55082912 ATAAGATTAT
Statistics
Matches: 51, Mismatches: 21, Indels: 2
0.69 0.28 0.03
Matches are distributed among these distances:
19 12 0.24
20 39 0.76
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.40
Consensus pattern (20 bp):
ATTTACCAAAATTTTTAAAG
Found at i:55082919 original size:19 final size:20
Alignment explanation
Indices: 55082877--55082919 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
55082867 GATACCTATG
*
55082877 GATTTACCAAAATTTTTAAA
1 GATTTACCAAAATTTATAAA
*
55082897 GATTTATCAAAATTTAT-AA
1 GATTTACCAAAATTTATAAA
55082916 GATT
1 GATT
55082920 ATACGATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (20 bp):
GATTTACCAAAATTTATAAA
Found at i:55083006 original size:20 final size:20
Alignment explanation
Indices: 55082983--55083030 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
55082973 CGTTACCAAA
55082983 ATTTCTAAG-G-TTATACTAAT
1 ATTTCTAAGTGTTTATA--AAT
*
55083003 ATTTTTAAGTGTTTATAAAT
1 ATTTCTAAGTGTTTATAAAT
55083023 ATTTCTAA
1 ATTTCTAA
55083031 AGTTTTAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 18 0.75
21 1 0.04
22 5 0.21
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.50
Consensus pattern (20 bp):
ATTTCTAAGTGTTTATAAAT
Found at i:55083037 original size:20 final size:21
Alignment explanation
Indices: 55083000--55083072 Score: 64
Period size: 20 Copynumber: 3.6 Consensus size: 21
55082990 AGGTTATACT
*
55083000 AATATTT-TTAAGTGTTTATA-
1 AATATTTCTAAAGTGTTTA-AC
55083020 AATATTTCTAAAGT-TTTAAC
1 AATATTTCTAAAGTGTTTAAC
* * *
55083040 AATATTCCTAAAG-GTTCACC
1 AATATTTCTAAAGTGTTTAAC
*
55083060 ATTATTTCTAAAG
1 AATATTTCTAAAG
55083073 ATTTTCCTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.02
20 38 0.86
21 5 0.11
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (21 bp):
AATATTTCTAAAGTGTTTAAC
Found at i:55083307 original size:20 final size:20
Alignment explanation
Indices: 55083218--55083312 Score: 54
Period size: 20 Copynumber: 4.8 Consensus size: 20
55083208 GGATATTTAA
* *
55083218 CTTTAAAAATTTGGGTAAAT
1 CTTTAGAAATTTTGGTAAAT
* *
55083238 CCTTATG-CATTTTGGTATAA-
1 CTTTA-GAAATTTTGGTA-AAT
*
55083258 CCTTAGAAAATTTT-GTAAAT
1 CTTTAG-AAATTTTGGTAAAT
* *
55083278 -TCTCGTAAATTTTGGTAAAT
1 CTTTAG-AAATTTTGGTAAAT
*
55083298 CTTTAGAAATATTGG
1 CTTTAGAAATTTTGG
55083313 AAAACCTTGG
Statistics
Matches: 56, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
19 12 0.21
20 34 0.61
21 10 0.18
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.42
Consensus pattern (20 bp):
CTTTAGAAATTTTGGTAAAT
Found at i:55083426 original size:20 final size:20
Alignment explanation
Indices: 55083357--55083499 Score: 92
Period size: 20 Copynumber: 7.0 Consensus size: 20
55083347 TGTCTCAATG
*
55083357 AAATCTTTAGAAATTTTGGT
1 AAATCCTTAGAAATTTTGGT
* * * **
55083377 AAAAACCCTTAGATATATTAAT
1 --AAATCCTTAGAAATTTTGGT
55083399 AAATCCTTAGAAATTTTGGT
1 AAATCCTTAGAAATTTTGGT
* * *
55083419 ATAA-CCTTAAAAATTCTAGT
1 A-AATCCTTAGAAATTTTGGT
* *
55083439 AAATCCTTACATATTTTGGT
1 AAATCCTTAGAAATTTTGGT
* *
55083459 ATAA-CCTTATAAATTTCGGT
1 A-AATCCTTAGAAATTTTGGT
* * *
55083479 AATTTCTTAAAAATTTTGGT
1 AAATCCTTAGAAATTTTGGT
55083499 A
1 A
55083500 TGCCAAAATA
Statistics
Matches: 92, Mismatches: 25, Indels: 10
0.72 0.20 0.08
Matches are distributed among these distances:
19 3 0.03
20 71 0.77
21 4 0.04
22 14 0.15
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (20 bp):
AAATCCTTAGAAATTTTGGT
Found at i:55083442 original size:40 final size:39
Alignment explanation
Indices: 55083357--55083500 Score: 135
Period size: 40 Copynumber: 3.6 Consensus size: 39
55083347 TGTCTCAATG
* * * * *
55083357 AAATCTTTAGAAATTTTGGTAAAAACCCTTAGATATATTAAT
1 AAATCCTTAGAAATTTTGGT-ATAA-CCTTAAAAAT-TTAGT
55083399 AAATCCTTAGAAATTTTGGTATAACCTTAAAAATTCTAGT
1 AAATCCTTAGAAATTTTGGTATAACCTTAAAAATT-TAGT
* * * *
55083439 AAATCCTTACATATTTTGGTATAACCTTATAAATTTCGGT
1 AAATCCTTAGAAATTTTGGTATAACCTTAAAAATTT-AGT
* * *
55083479 AATTTCTTAAAAATTTTGGTAT
1 AAATCCTTAGAAATTTTGGTAT
55083501 GCCAAAATAT
Statistics
Matches: 87, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
39 2 0.02
40 63 0.72
41 3 0.03
42 19 0.22
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (39 bp):
AAATCCTTAGAAATTTTGGTATAACCTTAAAAATTTAGT
Found at i:55083608 original size:20 final size:20
Alignment explanation
Indices: 55083564--55083614 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
55083554 TGGGTAAATT
* *
55083564 CTTAGAAATTTGGGTAAAGC
1 CTTAGAAATTTGGCTAAACC
* *
55083584 TTTAGAAATTTTGCTAAACC
1 CTTAGAAATTTGGCTAAACC
*
55083604 CTTAGATATTT
1 CTTAGAAATTT
55083615 CATTATAAAC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (20 bp):
CTTAGAAATTTGGCTAAACC
Found at i:55086195 original size:32 final size:32
Alignment explanation
Indices: 55086159--55086222 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
55086149 TTGGTAAATG
55086159 ATACCAGTGTTTGCTAATATGAAACTGATTAT
1 ATACCAGTGTTTGCTAATATGAAACTGATTAT
55086191 ATACCAGTGTTTGCTAATATGAAACTGATTAT
1 ATACCAGTGTTTGCTAATATGAAACTGATTAT
55086223 CTTCAGCTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (32 bp):
ATACCAGTGTTTGCTAATATGAAACTGATTAT
Found at i:55092124 original size:23 final size:23
Alignment explanation
Indices: 55092093--55092150 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
55092083 ATAACACTTC
*
55092093 AAAA-ATTTTATTTTCATTTATT
1 AAAATATTTTATTTGCATTTATT
*
55092115 AAAATATTTT-GTTGCATTTATT
1 AAAATATTTTATTTGCATTTATT
*
55092137 AAAACTATATTATT
1 AAAA-TATTTTATT
55092151 ACGTATGGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 18 0.62
23 10 0.34
24 1 0.03
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.53
Consensus pattern (23 bp):
AAAATATTTTATTTGCATTTATT
Found at i:55092775 original size:42 final size:42
Alignment explanation
Indices: 55092708--55092850 Score: 157
Period size: 42 Copynumber: 3.4 Consensus size: 42
55092698 TAAAAATATC
* *
55092708 AAGGAAGCAACATGGAAAAGCAACATCCATG-TCTAGACAAAA
1 AAGGAAGCAACTTGGAAAAGCAACATCCAAGTTC-AGACAAAA
* *
55092750 AATGAAGCAACTTGGGAAAA-TAACATCCAAGTTCAGACAAAA
1 AAGGAAGCAACTT-GGAAAAGCAACATCCAAGTTCAGACAAAA
* ** *
55092792 AAGGAAGCAACTT-AAGAAAGCAACATTTAGGTTCAGACAAAA
1 AAGGAAGCAACTTGGA-AAAGCAACATCCAAGTTCAGACAAAA
*
55092834 AAGGAAGCAACGTGGAA
1 AAGGAAGCAACTTGGAA
55092851 GCAACCATGT
Statistics
Matches: 84, Mismatches: 12, Indels: 10
0.79 0.11 0.09
Matches are distributed among these distances:
40 1 0.01
41 3 0.04
42 71 0.85
43 9 0.11
ACGTcount: A:0.50, C:0.16, G:0.20, T:0.14
Consensus pattern (42 bp):
AAGGAAGCAACTTGGAAAAGCAACATCCAAGTTCAGACAAAA
Found at i:55096887 original size:19 final size:20
Alignment explanation
Indices: 55096865--55096907 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
55096855 TTTTTAATTT
*
55096865 TTAAAAAATTTTAAATAT-A
1 TTAAAAAATGTTAAATATAA
*
55096884 TTAAAAAATGTTAAGTATAA
1 TTAAAAAATGTTAAATATAA
55096904 TTAA
1 TTAA
55096908 TTTTAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (20 bp):
TTAAAAAATGTTAAATATAA
Found at i:55096940 original size:33 final size:31
Alignment explanation
Indices: 55096899--55096988 Score: 123
Period size: 33 Copynumber: 2.9 Consensus size: 31
55096889 AAATGTTAAG
55096899 TATAATTAATTTTAAAATTTTAATATATATAT
1 TATAATTAATTTTAAAATTTTAATATATAT-T
55096931 ATATAATTAATTTTAAAATTTTAATATATATT
1 -TATAATTAATTTTAAAATTTTAATATATATT
55096963 T-TAA-T-ATATTTAAAATTTTTAATATA
1 TATAATTAAT-TTTAAAA-TTTTAATATA
55096989 CTTAATATAT
Statistics
Matches: 55, Mismatches: 0, Indels: 7
0.89 0.00 0.11
Matches are distributed among these distances:
28 2 0.04
29 8 0.15
30 13 0.24
31 1 0.02
32 1 0.02
33 30 0.55
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (31 bp):
TATAATTAATTTTAAAATTTTAATATATATT
Found at i:55096998 original size:29 final size:29
Alignment explanation
Indices: 55096909--55097002 Score: 84
Period size: 33 Copynumber: 3.1 Consensus size: 29
55096899 TATAATTAAT
*
55096909 TTTAAAATTTTAATATATA-TATATATAATTAA
1 TTTAAAATTTTAATATATACT-TAAAT-A-T-A
* *
55096941 TTTTAAAATTTTAATATATATTTTAATATA
1 -TTTAAAATTTTAATATATACTTAAATATA
*
55096971 TTTAAAATTTTTA-ATATACTTAATATATA
1 TTTAAAATTTTAATATATACTTAA-ATATA
55097000 TTT
1 TTT
55097003 TTAAGGGTAA
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
28 8 0.15
29 20 0.37
30 1 0.02
31 1 0.02
32 1 0.02
33 22 0.41
34 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (29 bp):
TTTAAAATTTTAATATATACTTAAATATA
Found at i:55097058 original size:31 final size:29
Alignment explanation
Indices: 55097023--55097092 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
55097013 ACTACCAAAA
* *
55097023 TAGTCACTTTTGTTTGACTCAGGTTACATTT
1 TAGTCACTTATGTTTGA--AAGGTTACATTT
* *
55097054 TAGTCACTTATGTTTGAAATGTTACGTTT
1 TAGTCACTTATGTTTGAAAGGTTACATTT
55097083 TAGTCACTTA
1 TAGTCACTTA
55097093 CGTTATCGTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 19 0.54
31 16 0.46
ACGTcount: A:0.23, C:0.14, G:0.16, T:0.47
Consensus pattern (29 bp):
TAGTCACTTATGTTTGAAAGGTTACATTT
Found at i:55097897 original size:17 final size:17
Alignment explanation
Indices: 55097869--55097974 Score: 108
Period size: 17 Copynumber: 5.9 Consensus size: 17
55097859 ATAACCAATT
55097869 TTAAAA-TTTTAATATA
1 TTAAAATTTTTAATATA
55097885 TTAAAATTTTTAATATA
1 TTAAAATTTTTAATATA
55097902 TTCAATATATTTTTTAAATATA
1 TT-AA-A-A-TTTTT-AATATA
* *
55097924 TTGAAATTTTAAATATA
1 TTAAAATTTTTAATATA
55097941 TTAAAA-TTTTAATATA
1 TTAAAATTTTTAATATA
55097957 TTTAATATATTTTTAATA
1 -TTAA-A-ATTTTTAATA
55097975 GGTAAAGAGA
Statistics
Matches: 76, Mismatches: 4, Indels: 16
0.79 0.04 0.17
Matches are distributed among these distances:
16 15 0.20
17 27 0.36
18 7 0.09
19 3 0.04
20 10 0.13
21 6 0.08
22 8 0.11
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (17 bp):
TTAAAATTTTTAATATA
Found at i:55097960 original size:9 final size:9
Alignment explanation
Indices: 55097876--55097968 Score: 61
Period size: 9 Copynumber: 10.3 Consensus size: 9
55097866 ATTTTAAAAT
55097876 TTTAATATA
1 TTTAATATA
* *
55097885 -TTAAAATT
1 TTTAATATA
55097893 TTTAATATA
1 TTTAATATA
*
55097902 TTCAATATA
1 TTTAATATA
55097911 TTTTTTAAATATA
1 ---TTT-AATATA
*
55097924 TTGAA-AT-
1 TTTAATATA
55097931 TTTAA-ATA
1 TTTAATATA
*
55097939 TATTAAAAT-
1 T-TTAATATA
55097948 TTTAATATA
1 TTTAATATA
55097957 TTTAATATA
1 TTTAATATA
55097966 TTT
1 TTT
55097969 TTAATAGGTA
Statistics
Matches: 66, Mismatches: 9, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
7 6 0.09
8 15 0.23
9 33 0.50
10 4 0.06
12 2 0.03
13 6 0.09
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (9 bp):
TTTAATATA
Found at i:55097971 original size:11 final size:10
Alignment explanation
Indices: 55097866--55097974 Score: 55
Period size: 9 Copynumber: 11.9 Consensus size: 10
55097856 AGTATAACCA
55097866 ATTTTAA-A-
1 ATTTTAATAT
55097874 ATTTTAATAT
1 ATTTTAATAT
*
55097884 A--TTAAAAT
1 ATTTTAATAT
55097892 -TTTTAATAT
1 ATTTTAATAT
*
55097901 A-TTCAATAT
1 ATTTTAATAT
55097910 ATTTTTTAA-AT
1 A--TTTTAATAT
* *
55097921 ATATTGA-A-
1 ATTTTAATAT
55097929 ATTTTAA-AT
1 ATTTTAATAT
*
55097938 ATATTAA-A-
1 ATTTTAATAT
55097946 ATTTTAATAT
1 ATTTTAATAT
55097956 A-TTTAATAT
1 ATTTTAATAT
55097965 ATTTTTAATA
1 A-TTTTAATA
55097975 GGTAAAGAGA
Statistics
Matches: 78, Mismatches: 10, Indels: 23
0.70 0.09 0.21
Matches are distributed among these distances:
8 25 0.32
9 37 0.47
10 2 0.03
11 10 0.13
12 4 0.05
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (10 bp):
ATTTTAATAT
Found at i:55098016 original size:17 final size:16
Alignment explanation
Indices: 55097994--55098056 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 16
55097984 AAAAAATAAT
55097994 TTTTAATATATTTAAAA
1 TTTTAA-ATATTTAAAA
*
55098011 TTTTAAAAATTTTAAAAAA
1 TTTTAAATA-TTT--AAAA
*
55098030 TGTTAAATATATTAAAA
1 TTTTAAATAT-TTAAAA
55098047 TTTTAAATAT
1 TTTTAAATAT
55098057 GCTAAAGAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
16 2 0.05
17 22 0.58
18 1 0.03
19 13 0.34
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
TTTTAAATATTTAAAA
Found at i:55098019 original size:9 final size:9
Alignment explanation
Indices: 55098007--55098053 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
55097997 TAATATATTT
55098007 AAAATTTTA
1 AAAATTTTA
55098016 AAAATTTTAA
1 AAAATTTT-A
*
55098026 AAAATGTTA
1 AAAATTTTA
* *
55098035 AATATATT-
1 AAAATTTTA
55098043 AAAATTTTA
1 AAAATTTTA
55098052 AA
1 AA
55098054 TATGCTAAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
8 6 0.19
9 17 0.55
10 8 0.26
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (9 bp):
AAAATTTTA
Found at i:55098035 original size:19 final size:19
Alignment explanation
Indices: 55098007--55098046 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
55097997 TAATATATTT
* *
55098007 AAAATTTTAAAAATTTTAA
1 AAAATGTTAAAAATATTAA
*
55098026 AAAATGTTAAATATATTAA
1 AAAATGTTAAAAATATTAA
55098045 AA
1 AA
55098047 TTTTAAATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
AAAATGTTAAAAATATTAA
Found at i:55098205 original size:80 final size:79
Alignment explanation
Indices: 55098004--55098206 Score: 213
Period size: 81 Copynumber: 2.5 Consensus size: 79
55097994 TTTTAATATA
* *
55098004 TTTAAAATTTTAAAA-AT-TTTAAAAAATGTTAAATATATTAAAATTTTAAATATGCTAAAGAAA
1 TTTAAAATTTTAAAATATATTT--AAAATATTAAA-AAATTAAAATTTTAAATA-GCTAAAGAAA
*
55098067 ATATTGAGTATAACCAAT
62 ATATTAAGTATAACCAAT
* *
55098085 TTTAAAATTTT--AATATACTTAATATATTAAAATATATTAAAATTTTGAAAGTA-CTAAA-AAA
1 TTTAAAATTTTAAAATATATTTAAAATATTAAAA-A-ATTAAAATTTT-AAA-TAGCTAAAGAAA
55098146 AT-TTAAGTATAACCAAT
62 ATATTAAGTATAACCAAT
*
55098163 TTTAAAATATTTAAAATATATTTAAAATTTTAAAAAACTTAAAA
1 TTTAAAAT-TTTAAAATATATTTAAAATATTAAAAAA-TTAAAA
55098207 AAAAAACCTC
Statistics
Matches: 104, Mismatches: 8, Indels: 21
0.78 0.06 0.16
Matches are distributed among these distances:
78 23 0.22
79 20 0.19
80 25 0.24
81 34 0.33
82 2 0.02
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (79 bp):
TTTAAAATTTTAAAATATATTTAAAATATTAAAAAATTAAAATTTTAAATAGCTAAAGAAAATAT
TAAGTATAACCAAT
Found at i:55105724 original size:13 final size:13
Alignment explanation
Indices: 55105706--55105735 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
55105696 AATTAAATCA
55105706 ACAAAATTAAAAT
1 ACAAAATTAAAAT
55105719 ACAAAATTAAAAT
1 ACAAAATTAAAAT
55105732 ACAA
1 ACAA
55105736 CATGTGCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.70, C:0.10, G:0.00, T:0.20
Consensus pattern (13 bp):
ACAAAATTAAAAT
Found at i:55115050 original size:6 final size:6
Alignment explanation
Indices: 55115039--55115066 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
55115029 AATTTAAGGC
55115039 TTTATT TTTATT TTTATT TTTATT TTTA
1 TTTATT TTTATT TTTATT TTTATT TTTA
55115067 ATGATTTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTATT
Found at i:55118824 original size:54 final size:54
Alignment explanation
Indices: 55118731--55118990 Score: 197
Period size: 54 Copynumber: 4.8 Consensus size: 54
55118721 AGTCCACCTC
* * * * * *
55118731 CTAACAACATGGGAGGAATGCCT--TAC-AACAATAGGGGAGGTATGCATGCCAA
1 CTAACAATAGGGGAGGAATGCCTCCTCCTAACAATATGGGAGGAATGC-CGCCAA
* **
55118783 C-AAC-ATGGGGGGAGGAATGCCTCCTCCTAACAATATGGGAGGAATGCCGCCTC
1 CTAACAAT-AGGGGAGGAATGCCTCCTCCTAACAATATGGGAGGAATGCCGCCAA
* * * **
55118836 CTAACAATATGGGAGGAATGCCGCCTCCTAACAGTATGGGAGGAATGCCGCCTC
1 CTAACAATAGGGGAGGAATGCCTCCTCCTAACAATATGGGAGGAATGCCGCCAA
* * * * ** * **
55118890 CTAACAGTATGGGAGGAATGCCACCGCGGAACAACATGGGAGGAGGAATGCCGCCTC
1 CTAACAATAGGGGAGGAATGCCTCCTCCTAACAATAT--G-GGAGGAATGCCGCCAA
* * * *
55118947 CTAACAATATGGGAGGAATGCCGCCTCCTGACAACATGGGAGGA
1 CTAACAATAGGGGAGGAATGCCTCCTCCTAACAATATGGGAGGA
55118991 GGAATGCCGC
Statistics
Matches: 173, Mismatches: 26, Indels: 16
0.80 0.12 0.07
Matches are distributed among these distances:
50 1 0.01
51 16 0.09
52 1 0.01
53 6 0.03
54 98 0.57
55 3 0.02
56 1 0.01
57 47 0.27
ACGTcount: A:0.30, C:0.24, G:0.30, T:0.16
Consensus pattern (54 bp):
CTAACAATAGGGGAGGAATGCCTCCTCCTAACAATATGGGAGGAATGCCGCCAA
Found at i:55118958 original size:57 final size:57
Alignment explanation
Indices: 55118820--55119029 Score: 257
Period size: 57 Copynumber: 3.7 Consensus size: 57
55118810 TAACAATATG
* * * **
55118820 GGAGGAATGCCGCCTCCTAACAATATGGGAGGAATGCCGCCTCCTAACAGTAT--G-
1 GGAGGAATGCCGCCTCCTAACAATATGGGAGGAATGCCACCGCCGAACAACATGGGA
* *
55118874 GGAGGAATGCCGCCTCCTAACAGTATGGGAGGAATGCCACCGCGGAACAACATGGGA
1 GGAGGAATGCCGCCTCCTAACAATATGGGAGGAATGCCACCGCCGAACAACATGGGA
* *
55118931 GGAGGAATGCCGCCTCCTAACAATATGGGAGGAATGCCGCCTCCTG-ACAACATGGGA
1 GGAGGAATGCCGCCTCCTAACAATATGGGAGGAATGCCACCGCC-GAACAACATGGGA
* * * * *
55118988 GGAGGAATGCCGCCGCCGAACAACATGGGTGGGATGCCACCG
1 GGAGGAATGCCGCCTCCTAACAATATGGGAGGAATGCCACCG
55119030 GGACCACCGA
Statistics
Matches: 134, Mismatches: 18, Indels: 5
0.85 0.11 0.03
Matches are distributed among these distances:
54 46 0.34
56 1 0.01
57 86 0.64
58 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.32, T:0.14
Consensus pattern (57 bp):
GGAGGAATGCCGCCTCCTAACAATATGGGAGGAATGCCACCGCCGAACAACATGGGA
Found at i:55119025 original size:27 final size:27
Alignment explanation
Indices: 55118792--55118990 Score: 281
Period size: 27 Copynumber: 7.3 Consensus size: 27
55118782 ACAACATGGG
*
55118792 GGGAGGAATGCCTCCTCCTAACAATAT
1 GGGAGGAATGCCGCCTCCTAACAATAT
55118819 GGGAGGAATGCCGCCTCCTAACAATAT
1 GGGAGGAATGCCGCCTCCTAACAATAT
*
55118846 GGGAGGAATGCCGCCTCCTAACAGTAT
1 GGGAGGAATGCCGCCTCCTAACAATAT
*
55118873 GGGAGGAATGCCGCCTCCTAACAGTAT
1 GGGAGGAATGCCGCCTCCTAACAATAT
* * ** *
55118900 GGGAGGAATGCCACCGCGGAACAACAT
1 GGGAGGAATGCCGCCTCCTAACAATAT
55118927 GGGAGGAGGAATGCCGCCTCCTAACAATAT
1 --G-GGAGGAATGCCGCCTCCTAACAATAT
* *
55118957 GGGAGGAATGCCGCCTCCTGACAACAT
1 GGGAGGAATGCCGCCTCCTAACAATAT
55118984 GGGAGGA
1 GGGAGGA
55118991 GGAATGCCGC
Statistics
Matches: 154, Mismatches: 15, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
27 131 0.85
28 1 0.01
29 1 0.01
30 21 0.14
ACGTcount: A:0.29, C:0.25, G:0.30, T:0.16
Consensus pattern (27 bp):
GGGAGGAATGCCGCCTCCTAACAATAT
Found at i:55119792 original size:21 final size:19
Alignment explanation
Indices: 55119737--55119805 Score: 68
Period size: 21 Copynumber: 3.5 Consensus size: 19
55119727 TTATGTTTGG
55119737 TTAA-TTATGTTTATTTTT
1 TTAATTTATGTTTATTTTT
* *
55119755 TTAAAATTAAGTGTTATTTTT
1 TT-AATTTATGT-TTATTTTT
*
55119776 TTAATTTCATGTATTATTTAT
1 TTAATTT-ATGT-TTATTTTT
55119797 TTAATTTAT
1 TTAATTTAT
55119806 TATTTTTTAC
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
18 2 0.05
19 2 0.05
20 11 0.26
21 27 0.64
ACGTcount: A:0.29, C:0.01, G:0.06, T:0.64
Consensus pattern (19 bp):
TTAATTTATGTTTATTTTT
Found at i:55120561 original size:22 final size:22
Alignment explanation
Indices: 55120536--55120583 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
55120526 TCAATTCCTT
* *
55120536 TCAATTTTCTTCCAAAATTTTC
1 TCAATTTCCTTCCAAAATTCTC
*
55120558 TCAATTTCCTTCTAAAATTCTC
1 TCAATTTCCTTCCAAAATTCTC
55120580 TCAA
1 TCAA
55120584 ATCCATATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.29, C:0.25, G:0.00, T:0.46
Consensus pattern (22 bp):
TCAATTTCCTTCCAAAATTCTC
Found at i:55124411 original size:126 final size:125
Alignment explanation
Indices: 55124101--55124452 Score: 575
Period size: 126 Copynumber: 2.8 Consensus size: 125
55124091 TCCAAACATG
** *
55124101 CTACTGTAGCAAAAGCGCGTCCATAAGGGCGTGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* *
55124166 TAGAATCGATTTTATACTATTTGCTCAGAAACGTC-AAAAAAAATTATTTCTCACATGGC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTCACATGAC
55124225 CTACTGTAGCAAAAGCGCGTCCACGA-GGCAGCGATTTCACAAATTCTTCTCAAATAGCATCCTG
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGC-GCGATTTCACAAATTCTTCTCAAATAGCATCCTG
*
55124289 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTC-CGTGAC
65 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAA-AATTATTTC-TCACATGAC
*
55124351 CTACTGTAGCAAAAGCGCGTTCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
**
55124416 TAGAAGCGATTTTATACTATTTTATCAGAAACGTCAA
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA
55124453 CTCGAAATTA
Statistics
Matches: 214, Mismatches: 9, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
123 3 0.01
124 92 0.43
125 6 0.03
126 108 0.50
127 5 0.02
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.29
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTCACATGAC
Found at i:55125294 original size:16 final size:16
Alignment explanation
Indices: 55125273--55125303 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55125263 TGATTTAATT
*
55125273 TATTTTTATTTTGTTC
1 TATTTTTAATTTGTTC
55125289 TATTTTTAATTTGTT
1 TATTTTTAATTTGTT
55125304 ATCGGATTCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.03, G:0.06, T:0.74
Consensus pattern (16 bp):
TATTTTTAATTTGTTC
Found at i:55125541 original size:8 final size:9
Alignment explanation
Indices: 55125519--55125544 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
55125509 TTAATTTATA
55125519 TAAAAATTT
1 TAAAAATTT
55125528 TAAAAATTT
1 TAAAAATTT
55125537 TAAAAATT
1 TAAAAATT
55125545 CCAAAATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
TAAAAATTT
Found at i:55126393 original size:24 final size:24
Alignment explanation
Indices: 55126348--55126393 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
55126338 CCTTTGTTTT
* *
55126348 AATTTTTTTTTAAAAATGAAATGA
1 AATTGTTTTTTAAAAATAAAATGA
55126372 AATTGTTTTTTAGAAAA-AAAAT
1 AATTGTTTTTTA-AAAATAAAAT
55126394 TGTTTTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (24 bp):
AATTGTTTTTTAAAAATAAAATGA
Found at i:55126826 original size:24 final size:24
Alignment explanation
Indices: 55126797--55126853 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
55126787 AATATTTTTT
*
55126797 TATTATTATCGTCAGTGTTATTA-
1 TATTATTATCATCAGTGTTATTAC
* * *
55126820 TACTTATTCTCATTATTGTTATTAC
1 TA-TTATTATCATCAGTGTTATTAC
55126845 TATTATTAT
1 TATTATTAT
55126854 ATTTAGTGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
23 2 0.07
24 23 0.85
25 2 0.07
ACGTcount: A:0.26, C:0.11, G:0.07, T:0.56
Consensus pattern (24 bp):
TATTATTATCATCAGTGTTATTAC
Found at i:55128104 original size:23 final size:23
Alignment explanation
Indices: 55128078--55128176 Score: 144
Period size: 23 Copynumber: 4.3 Consensus size: 23
55128068 ATAAGTGCAA
55128078 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
55128101 CACTGTTATGTAGCTGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
55128124 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * *
55128147 CACGGAAATGTAGCTGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
55128170 CACTGAT
1 CACTGAT
55128177 CAATAACACT
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 67 1.00
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:55128145 original size:46 final size:46
Alignment explanation
Indices: 55128078--55128175 Score: 160
Period size: 46 Copynumber: 2.1 Consensus size: 46
55128068 ATAAGTGCAA
* * **
55128078 CACTGATATGTAGCCGAAGCTACCACTGTTATGTAGCTGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACGGAAATGTAGCTGAAGCTAC
55128124 CACTGAAATGTAGCCGAAGCTACCACGGAAATGTAGCTGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACGGAAATGTAGCTGAAGCTAC
55128170 CACTGA
1 CACTGA
55128176 TCAATAACAC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.21
Consensus pattern (46 bp):
CACTGAAATGTAGCCGAAGCTACCACGGAAATGTAGCTGAAGCTAC
Found at i:55129671 original size:22 final size:23
Alignment explanation
Indices: 55129641--55129700 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 23
55129631 TTTATTTGTA
*
55129641 TTAATAATTTATTATATTATT-ATT
1 TTAA-AATTTATTATA-CATTAATT
*
55129665 TT-AAATTTATCATACATTAATT
1 TTAAAATTTATTATACATTAATT
*
55129687 TTAAAATTCATTAT
1 TTAAAATTTATTAT
55129701 GTACTGCCAC
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
21 3 0.10
22 15 0.50
23 10 0.33
24 2 0.07
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (23 bp):
TTAAAATTTATTATACATTAATT
Found at i:55133428 original size:16 final size:16
Alignment explanation
Indices: 55133409--55133447 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
55133399 AAAATCAAAT
*
55133409 AAAATTATATTATATA
1 AAAATTACATTATATA
*
55133425 AAAAATACATTATATA
1 AAAATTACATTATATA
55133441 AAAATTA
1 AAAATTA
55133448 AATGAGTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (16 bp):
AAAATTACATTATATA
Found at i:55133949 original size:21 final size:21
Alignment explanation
Indices: 55133897--55133939 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
55133887 TTAAATTTCG
*
55133897 AATATAATATT-AAGTCTTAC
1 AATATAATATTAAAGTCATAC
55133917 AATATAATATTAAAGTCATAC
1 AATATAATATTAAAGTCATAC
55133938 AA
1 AA
55133940 ATTTAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.51, C:0.09, G:0.05, T:0.35
Consensus pattern (21 bp):
AATATAATATTAAAGTCATAC
Found at i:55137118 original size:20 final size:20
Alignment explanation
Indices: 55137093--55137132 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
55137083 AATATTTTCC
*
55137093 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
55137113 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
55137133 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:55137139 original size:34 final size:35
Alignment explanation
Indices: 55137080--55137147 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 35
55137070 TCAAACACCA
*
55137080 TAAAATATTTTCCAGTAAATCATTTTACAGAAAAG
1 TAAAACATTTTCCAGTAAATCATTTTACAGAAAAG
*
55137115 TAAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 TAAAACATTTTCCAGTAAATCATTTTACAGAAAA
55137148 TATTTTACTG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.55
35 14 0.45
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.32
Consensus pattern (35 bp):
TAAAACATTTTCCAGTAAATCATTTTACAGAAAAG
Found at i:55137292 original size:16 final size:16
Alignment explanation
Indices: 55137271--55137304 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
55137261 GTGTTTTTTT
*
55137271 TTAATTTTATGTATTA
1 TTAATTTAATGTATTA
*
55137287 TTAATTTAATTTATTA
1 TTAATTTAATGTATTA
55137303 TT
1 TT
55137305 TTTTACATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (16 bp):
TTAATTTAATGTATTA
Found at i:55143194 original size:24 final size:24
Alignment explanation
Indices: 55143162--55143208 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
55143152 AATATTATAA
*
55143162 TTTTTTTATTTACTAAAAAATATT
1 TTTTTTTATTTACCAAAAAATATT
*
55143186 TTTTTTTATTTACCAAAATATAT
1 TTTTTTTATTTACCAAAAAATAT
55143209 AAAAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTTTTTATTTACCAAAAAATATT
Found at i:55143330 original size:4 final size:4
Alignment explanation
Indices: 55143321--55143464 Score: 88
Period size: 4 Copynumber: 36.0 Consensus size: 4
55143311 AAAGGAGAGG
* * * *
55143321 GAAA GAAA GAAA G-AA -AAA GAAG GAAG GAAG GAGAG GAAA GAAA G-AA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA GAAA
* * *
55143367 -AAA GAAG GAAA GAAAA GGAAA G-GA GAAGA GAAA AAAA GAAA GAAA G-AA
1 GAAA GAAA GAAA G-AAA -GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA
*
55143415 G-AA GAAAA GGAAA GGAGAA GAAA -AAA GAAA GAAA GAAG GAAA GAAA
1 GAAA G-AAA -GAAA -GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
55143461 GAAA
1 GAAA
55143465 AGGAAAGGAG
Statistics
Matches: 116, Mismatches: 10, Indels: 28
0.75 0.06 0.18
Matches are distributed among these distances:
3 19 0.16
4 69 0.59
5 24 0.21
6 4 0.03
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:55143411 original size:24 final size:25
Alignment explanation
Indices: 55143321--55143471 Score: 92
Period size: 26 Copynumber: 6.2 Consensus size: 25
55143311 AAAGGAGAGG
55143321 GAAAG-AAAGAAAGAAA-AAGAAG-
1 GAAAGAAAAGAAAGAAAGAAGAAGA
*
55143343 GAAGGAAGGAGAGGAAAGAAAGAA-AA-A
1 GAAAGAA--A-A-GAAAGAAAGAAGAAGA
* *
55143370 G-AAGGAAAGAAAAGGAAAGGAGAAGA
1 GAAAGAAAAG-AAA-GAAAGAAGAAGA
55143396 GAAA-AAAAGAAAGAAAGAAGAAGA
1 GAAAGAAAAGAAAGAAAGAAGAAGA
* *
55143420 -AAAGGAAAGGAGAAGAAAAAAGAA-A
1 GAAA-GAAAAGA-AAGAAAGAAGAAGA
*
55143445 GAAAG-AAGGAAAGAAAGAA-AAG-
1 GAAAGAAAAGAAAGAAAGAAGAAGA
55143467 GAAAG
1 GAAAG
55143472 GAGAAGAGGA
Statistics
Matches: 103, Mismatches: 9, Indels: 34
0.71 0.06 0.23
Matches are distributed among these distances:
22 12 0.12
23 16 0.16
24 23 0.22
25 13 0.13
26 24 0.23
27 13 0.13
28 2 0.02
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (25 bp):
GAAAGAAAAGAAAGAAAGAAGAAGA
Found at i:55143417 original size:45 final size:42
Alignment explanation
Indices: 55143322--55143499 Score: 172
Period size: 43 Copynumber: 4.2 Consensus size: 42
55143312 AAGGAGAGGG
* * **
55143322 AAAGAAAGAAAGAAAAAG-AAGGAAGGAAGGAGAGGAAAGAAAGAA
1 AAAGAAGGAAAGAAAAGGAAAGG-A-GAA-GAGAAAAAAGAAAG-A
55143367 AAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGAAAG-
1 AAAGAAGGAAAGAAAAGGAAAGGAGAAGAG-AAAAAAGAAAGA
55143409 AAAGAA-G-AAGAAAAGGAAAGGAG-A-AGAAAAAAGAAAGAA
1 AAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAGAAAG-A
*
55143448 AGAAGGAAAGAAAGAAAAGGAAAGGAGAAGAGGAAAAAA-AAAGA
1 A-AA-GAAGGAAAGAAAAGGAAAGGAGAAGA-GAAAAAAGAAAGA
55143492 AGAAGAAG
1 A-AAGAAG
55143500 AGGGAAGGAA
Statistics
Matches: 117, Mismatches: 5, Indels: 24
0.80 0.03 0.16
Matches are distributed among these distances:
37 11 0.09
38 2 0.02
39 2 0.02
40 18 0.15
41 4 0.03
42 7 0.06
43 22 0.19
44 18 0.15
45 22 0.19
46 11 0.09
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (42 bp):
AAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAGAAAGA
Found at i:55143488 original size:49 final size:48
Alignment explanation
Indices: 55143354--55143524 Score: 143
Period size: 49 Copynumber: 3.4 Consensus size: 48
55143344 AAGGAAGGAG
* ** *
55143354 AGGAAAGAAAGAAAA-AGAAGGAAA-GA-AAAGGAAAGGAGAAGAGAAAAA
1 AGGAAAGAAAGAAAAGAAAAGGAAAGGAGAAA--AAAAAAGAA-AGAAAGA
* *
55143402 AAGAAAGAAAGAAGAAGAAAAGGAAAGGAGAAGAAAAAAGAAAGAAAGA
1 AGGAAAGAAAGAA-AAGAAAAGGAAAGGAGAAAAAAAAAGAAAGAAAGA
*
55143451 AGGAAAGAAAGAAAAGGAAAGGAGAA-GAGGAAAAAAAAAGAAGAAGAAGAGGGA
1 AGGAAAGAAAGAAAAGAAAAGGA-AAGGA-GAAAAAAAAAG-A-AAGAA-A--GA
*
55143505 AGGAAAGAAAAAAAAGAAAA
1 AGGAAAGAAAGAAAAGAAAA
55143525 AAAGTAATTT
Statistics
Matches: 101, Mismatches: 11, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
48 23 0.23
49 32 0.32
50 16 0.16
51 7 0.07
52 3 0.03
54 20 0.20
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (48 bp):
AGGAAAGAAAGAAAAGAAAAGGAAAGGAGAAAAAAAAAGAAAGAAAGA
Found at i:55143511 original size:83 final size:81
Alignment explanation
Indices: 55143311--55143500 Score: 245
Period size: 83 Copynumber: 2.4 Consensus size: 81
55143301 GTGGGGGGCA
* * * *
55143311 AAAGGAG-AGGGAAAGAAAGAAAGAAA-AAGAAG-GAAGG-AAGGAG-AG--GAAAGAAAGAAAA
1 AAAGGAGAAGAGAAAAAAAGAAAGAAAGAAGAAGAAAAGGAAAGGAGAAGAAAAAAGAAAGAAAA
*
55143369 AGAAGGAAAGAAAAGG
66 AGAAAGAAAGAAAAGG
55143385 AAAGGAGAAGAGAAAAAAAGAAAGAAAGAAGAAGAAAAGGAAAGGAGAAGAAAAAAGAAAGAAAG
1 AAAGGAGAAGAGAAAAAAAGAAAGAAAGAAGAAGAAAAGGAAAGGAGAAGAAAAAAGAAAGAAA-
55143450 AAGGAAAGAAAGAAAAGG
65 AA-GAAAGAAAGAAAAGG
*
55143468 AAAGGAGAAGAGGAAAAAA-AAAG-AAGAAGAAGA
1 AAAGGAGAAGAGAAAAAAAGAAAGAAAGAAGAAGA
55143501 GGGAAGGAAA
Statistics
Matches: 101, Mismatches: 6, Indels: 11
0.86 0.05 0.09
Matches are distributed among these distances:
74 7 0.07
75 17 0.17
76 6 0.06
77 4 0.04
78 6 0.06
79 2 0.02
81 21 0.21
82 6 0.06
83 32 0.32
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (81 bp):
AAAGGAGAAGAGAAAAAAAGAAAGAAAGAAGAAGAAAAGGAAAGGAGAAGAAAAAAGAAAGAAAA
AGAAAGAAAGAAAAGG
Found at i:55143518 original size:78 final size:81
Alignment explanation
Indices: 55143322--55143528 Score: 241
Period size: 83 Copynumber: 2.6 Consensus size: 81
55143312 AAGGAGAGGG
* * ** *
55143322 AAAGAAAGAAAGAAAAAGAAGG-AAGGA-AGGAGAGGAAAGAAAGAAA-AAGAAGGAAAGAAAAG
1 AAAGAAAGAAAGAAGAAGAAGGAAAGGAGAAGA-AAAAAAGAAAGAAAGAAGAAAGAAAGAAAAG
55143384 GAAAGGAGAAGAGAAAA
65 GAAAGGAGAAGAGAAAA
55143401 AAAGAAAGAAAGAAGAAGAAAAGGAAAGGAGAAG-AAAAAAGAAAGAAAGAAGGAAAGAAAGAAA
1 AAAGAAAGAAAGAAGAAG--AAGGAAAGGAGAAGAAAAAAAGAAAGAAAGAA-GAAAGAAAGAAA
*
55143465 AGGAAAGGAGAAGAGGAAA
63 AGGAAAGGAGAAGAGAAAA
* *
55143484 AAA-AAAG-AAGAAGAAG-AGGGAAGGA-AAGAAAAAAAAGAAAAAAAG
1 AAAGAAAGAAAGAAGAAGAAGGAAAGGAGAAG-AAAAAAAGAAAGAAAG
55143529 TAATTTTTTT
Statistics
Matches: 112, Mismatches: 8, Indels: 16
0.82 0.06 0.12
Matches are distributed among these distances:
77 3 0.03
78 8 0.07
79 31 0.28
81 25 0.22
82 11 0.10
83 34 0.30
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (81 bp):
AAAGAAAGAAAGAAGAAGAAGGAAAGGAGAAGAAAAAAAGAAAGAAAGAAGAAAGAAAGAAAAGG
AAAGGAGAAGAGAAAA
Found at i:55143528 original size:62 final size:60
Alignment explanation
Indices: 55143315--55143528 Score: 164
Period size: 62 Copynumber: 3.5 Consensus size: 60
55143305 GGGGCAAAAG
* * *
55143315 GAGAGGGAAAGAAAGAAAGAAAAAGAAGG-AAGGAAGGAGAGGAAAGAAAGAAA-AAGAAGGAAA
1 GAGAAGGAAAGAAAAAAAGAAAAA-AAGGAAAGG-AGAAGAGGAAA-AAA-AAAGAAGAA-GAAA
* * * * * * ** *
55143378 GAAAAGGAAAGGAGAAGAGAAAAAAA-GAAAGAAAGAAGAAGAAAAGGAAAGGAGAAGAAAA
1 GAGAAGGAAAGAAAAAAAGAAAAAAAGGAAAG-GAGAAGAGGAAAAAAAAAGAAGAAG-AAA
* * **
55143439 AAGAAAGAAAGAAGGAAAGAAAGAAAAGGAAAGGAGAAGAGGAAAAAAAAAGAAGAAGAAGA
1 GAGAAGGAAAGAAAAAAAGAAA-AAAAGGAAAGGAGAAGAGGAAAAAAAAAGAAGAAGAA-A
*
55143501 GGGAAGGAAAGAAAAAAAAGAAAAAAAG
1 GAGAAGGAAAG-AAAAAAAGAAAAAAAG
55143529 TAATTTTTTT
Statistics
Matches: 115, Mismatches: 28, Indels: 17
0.72 0.17 0.11
Matches are distributed among these distances:
60 4 0.03
61 27 0.23
62 52 0.45
63 32 0.28
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (60 bp):
GAGAAGGAAAGAAAAAAAGAAAAAAAGGAAAGGAGAAGAGGAAAAAAAAAGAAGAAGAAA
Found at i:55149137 original size:18 final size:18
Alignment explanation
Indices: 55149114--55149158 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
55149104 ATCCCAATGA
55149114 TCGCCACCACCTTCTTCT
1 TCGCCACCACCTTCTTCT
*
55149132 TCGCCAGCACCTTCTTCT
1 TCGCCACCACCTTCTTCT
*
55149150 TCACCACCA
1 TCGCCACCA
55149159 ACTATATCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.16, C:0.49, G:0.07, T:0.29
Consensus pattern (18 bp):
TCGCCACCACCTTCTTCT
Found at i:55149905 original size:63 final size:63
Alignment explanation
Indices: 55149838--55149958 Score: 165
Period size: 63 Copynumber: 1.9 Consensus size: 63
55149828 AAAATTATTA
*
55149838 ATTTTACTAAA-AATAATAACTAACTAACTATAACAATAATACTAG-TTTTTTACTAACTAGTTT
1 ATTTTACTAAAGAA-AATAA-TAACTAACCATAACAATAATACTAGTTTTTTTACTAACTAGTTT
** *
55149901 ATTTTGGTAAATGAAAATAATAACTAACCATAATAATAATACTAGTTTTTTTACTAAC
1 ATTTTACTAAA-GAAAATAATAACTAACCATAACAATAATACTAGTTTTTTTACTAAC
55149959 AATAATACTA
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
63 32 0.63
64 17 0.33
65 2 0.04
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.39
Consensus pattern (63 bp):
ATTTTACTAAAGAAAATAATAACTAACCATAACAATAATACTAGTTTTTTTACTAACTAGTTT
Found at i:55150016 original size:3 final size:3
Alignment explanation
Indices: 55150008--55150036 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
55149998 TCTTAATACT
55150008 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
55150037 TAATAATACT
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:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:55150411 original size:22 final size:22
Alignment explanation
Indices: 55150381--55150425 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
55150371 TTGTTTTTTT
55150381 ATATATTTTGGTAAATAAAAAA
1 ATATATTTTGGTAAATAAAAAA
*
55150403 ATATTTTTTGGTAAATAAAAAA
1 ATATATTTTGGTAAATAAAAAA
55150425 A
1 A
55150426 GTTATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (22 bp):
ATATATTTTGGTAAATAAAAAA
Found at i:55151221 original size:11 final size:10
Alignment explanation
Indices: 55151188--55151229 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
55151178 TGCACGAAGG
55151188 AGAAGAAAGA
1 AGAAGAAAGA
55151198 A-AAGGAAAGA
1 AGAA-GAAAGA
55151208 AGAAGAAGAGA
1 AGAAGAA-AGA
55151219 AGAAG-AAGA
1 AGAAGAAAGA
55151228 AG
1 AG
55151230 GAGGAGGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
9 7 0.24
10 12 0.41
11 10 0.34
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (10 bp):
AGAAGAAAGA
Found at i:55151221 original size:14 final size:14
Alignment explanation
Indices: 55151187--55151229 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
55151177 CTGCACGAAG
55151187 GAGAAGAAAGAA-AA
1 GAGAAG-AAGAAGAA
55151201 G-GAAAGAAGAAGAA
1 GAG-AAGAAGAAGAA
55151215 GAGAAGAAGAAGAA
1 GAGAAGAAGAAGAA
55151229 G
1 G
55151230 GAGGAGGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 6 0.23
14 19 0.73
15 1 0.04
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (14 bp):
GAGAAGAAGAAGAA
Found at i:55151274 original size:11 final size:11
Alignment explanation
Indices: 55151258--55151330 Score: 51
Period size: 11 Copynumber: 6.5 Consensus size: 11
55151248 GCAATACCGA
55151258 AAAAAGAAAAG
1 AAAAAGAAAAG
*
55151269 AAAAAG-AGAG
1 AAAAAGAAAAG
* *
55151279 AAAGAGAATAG
1 AAAAAGAAAAG
*
55151290 AGAAAGGAGAAAG
1 A-AAAAGA-AAAG
*
55151303 AAAGAGAAAGAG
1 AAAAAGAAA-AG
55151315 AAAAA-AAATAG
1 AAAAAGAAA-AG
55151326 AAAAA
1 AAAAA
55151331 ATAAGGTATT
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
10 8 0.17
11 22 0.46
12 14 0.29
13 4 0.08
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.03
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:55151293 original size:7 final size:6
Alignment explanation
Indices: 55151275--55151317 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
55151265 AAAGAAAAAG
55151275 AGAGAA AGAGAA TAGAGAA AG-GAGA A-AGAA AGAGAA AGAGAA A
1 AGAGAA AGAGAA -AGAGAA AGAGA-A AGAGAA AGAGAA AGAGAA A
55151318 AAAAATAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
5 4 0.12
6 23 0.70
7 6 0.18
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (6 bp):
AGAGAA
Found at i:55153230 original size:25 final size:26
Alignment explanation
Indices: 55153171--55153231 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
55153161 TAATTAAATT
**
55153171 TATACAAAAAAGTACAAACTTTGTAA
1 TATACAAAAAAGTACAAACTGAGTAA
*
55153197 TATA-AAAAAAATACAAACTAGAGTAA
1 TATACAAAAAAGTACAAACT-GAGTAA
55153223 TAT-CAAAAA
1 TATACAAAAA
55153232 TGCAAGAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 14 0.47
26 16 0.53
ACGTcount: A:0.61, C:0.10, G:0.07, T:0.23
Consensus pattern (26 bp):
TATACAAAAAAGTACAAACTGAGTAA
Found at i:55160078 original size:42 final size:42
Alignment explanation
Indices: 55160031--55160116 Score: 136
Period size: 42 Copynumber: 2.0 Consensus size: 42
55160021 CTAGCTGTCA
* **
55160031 TATTAAGGCTCGCAGGTGAAGAGCTATAGCCTTTAACACAGT
1 TATTAAGGCTCGCAGGTGAAGAGCCATAGCCTCCAACACAGT
*
55160073 TATTAAGGCTCGTAGGTGAAGAGCCATAGCCTCCAACACAGT
1 TATTAAGGCTCGCAGGTGAAGAGCCATAGCCTCCAACACAGT
55160115 TA
1 TA
55160117 GCGAGAACAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.24
Consensus pattern (42 bp):
TATTAAGGCTCGCAGGTGAAGAGCCATAGCCTCCAACACAGT
Found at i:55160159 original size:111 final size:111
Alignment explanation
Indices: 55159977--55160185 Score: 276
Period size: 111 Copynumber: 1.9 Consensus size: 111
55159967 AGGCTTGCAA
* * * * * * *
55159977 GTGAAGAGCCGTAATCTCCAACACCGTTAGCGAGAGCAAAGTCCCTAGCTGTCATATTAAGGCTC
1 GTGAAGAGCCATAACCTCCAACACAGTTAGCGAGAACAAACTCCCTAACTATCATATTAAGGCTC
* **
55160042 GCAGGTGAAGAGCTATAGCCTTTAACACAGTTATTAAGGCTCGTAG
66 GCAGGTGAAGAGCTATAACCTCCAACACAGTTATTAAGGCTCGTAG
*
55160088 GTGAAGAGCCATAGCCTCCAACACAGTTAGCGAGAACAAAACT-CCTAACTATCATATTAAGGCT
1 GTGAAGAGCCATAACCTCCAACACAGTTAGCGAGAAC-AAACTCCCTAACTATCATATTAAGGCT
* * *
55160152 TGCAGGTGATGAGCTGTAACCTCCAACACAGTTA
65 CGCAGGTGAAGAGCTATAACCTCCAACACAGTTA
55160186 GTGAGAGTAA
Statistics
Matches: 83, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
111 79 0.95
112 4 0.05
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.22
Consensus pattern (111 bp):
GTGAAGAGCCATAACCTCCAACACAGTTAGCGAGAACAAACTCCCTAACTATCATATTAAGGCTC
GCAGGTGAAGAGCTATAACCTCCAACACAGTTATTAAGGCTCGTAG
Found at i:55160184 original size:69 final size:69
Alignment explanation
Indices: 55160073--55160393 Score: 302
Period size: 69 Copynumber: 4.7 Consensus size: 69
55160063 TTAACACAGT
* * * *
55160073 TATTAAGGCTCGTAGGTGAAGAGCCATAGCCTCCAACACAGTTAGCGAGAACAAAACTCCTAACT
1 TATTAAGGCTTGCAGGTGAAGAGCCACAGCCTCCAACACAGTTAGCGAGAGCAAAACTCCTAACT
*
55160138 ATCA
66 GTCA
* *** * * * * * *
55160142 TATTAAGGCTTGCAGGTGATGAGCTGTAACCTCCAACACAGTTAGTGAGAGTAAAGCTCCCAGCT
1 TATTAAGGCTTGCAGGTGAAGAGCCACAGCCTCCAACACAGTTAGCGAGAGCAAAACTCCTAACT
55160207 GTCA
66 GTCA
* * * * * * * * * *
55160211 TATTAAGACTAGCAAGTGAAGAGCCGCAGCCTTCAACAAAGTTAGCGTGATC-AAAGTTCTCAAC
1 TATTAAGGCTTGCAGGTGAAGAGCCACAGCCTCCAACACAGTTAGCGAGAGCAAAACTCCT-AAC
55160275 TGTCA
65 TGTCA
* * * *
55160280 TATTAAGGCTTGCAGGTGAAGAGCCACAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCTTAGCA
1 TATTAAGGCTTGCAGGTGAAGAGCCACAGCCTCCAACACAGTTAGCGAGAGCAAAACTCCTAACT
55160345 GTCA
66 GTCA
* * * * * * *
55160349 CATTAAGGCTCGTAGGTGAAGAACCATAGCCTCCAAAATAGTTAG
1 TATTAAGGCTTGCAGGTGAAGAGCCACAGCCTCCAACACAGTTAG
55160394 TACGAGCTTA
Statistics
Matches: 198, Mismatches: 52, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
68 4 0.02
69 190 0.96
70 4 0.02
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.22
Consensus pattern (69 bp):
TATTAAGGCTTGCAGGTGAAGAGCCACAGCCTCCAACACAGTTAGCGAGAGCAAAACTCCTAACT
GTCA
Found at i:55160321 original size:138 final size:138
Alignment explanation
Indices: 55160088--55160393 Score: 346
Period size: 138 Copynumber: 2.2 Consensus size: 138
55160078 AGGCTCGTAG
* *
55160088 GTGAAGAGCCATAGCCTCCAACACAGTTAGCGAGAACAAAACTCCTAACTATCATATTAAGGCTT
1 GTGAAGAGCCACAGCCTCCAACAAAGTTAGCGAGAACAAAACTCCTAACTATCATATTAAGGCTT
* *** * *
55160153 GCAGGTGATGAGCTGTAACCTCCAACACAGTTAGTGAGAGTAAAGCTCCCAGCTGTCATATTAAG
66 GCAGGTGAAGAGCCACAACCTCCAACACAGTTAGCGAGAGCAAAGCTCCCAGCTGTCATATTAAG
55160218 ACTAGCAA
131 ACTAGCAA
* * * * * * *
55160226 GTGAAGAGCCGCAGCCTTCAACAAAGTTAGCGTGATC-AAAGTTCTCAACTGTCATATTAAGGCT
1 GTGAAGAGCCACAGCCTCCAACAAAGTTAGCGAGAACAAAACTCCT-AACTATCATATTAAGGCT
* ** * *
55160290 TGCAGGTGAAGAGCCACAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCTTAGCAGTCACATTAA
65 TGCAGGTGAAGAGCCACAACCTCCAACACAGTTAGCGAGAGCAAAGCTCCCAGCTGTCATATTAA
* * * *
55160355 GGCTCGTAG
130 GACTAGCAA
* *
55160364 GTGAAGAACCATAGCCTCCAA-AATAGTTAG
1 GTGAAGAGCCACAGCCTCCAACAA-AGTTAG
55160394 TACGAGCTTA
Statistics
Matches: 138, Mismatches: 28, Indels: 4
0.81 0.16 0.02
Matches are distributed among these distances:
137 8 0.06
138 130 0.94
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.21
Consensus pattern (138 bp):
GTGAAGAGCCACAGCCTCCAACAAAGTTAGCGAGAACAAAACTCCTAACTATCATATTAAGGCTT
GCAGGTGAAGAGCCACAACCTCCAACACAGTTAGCGAGAGCAAAGCTCCCAGCTGTCATATTAAG
ACTAGCAA
Found at i:55177755 original size:20 final size:20
Alignment explanation
Indices: 55177659--55177756 Score: 106
Period size: 20 Copynumber: 4.9 Consensus size: 20
55177649 TGTTGATGTA
* **
55177659 TGATTGCACTCTAATGCCCC
1 TGATTGCACTTTCGTGCCCC
* *
55177679 TGATTGCACTTTGGTGCCCT
1 TGATTGCACTTTCGTGCCCC
*
55177699 TGATTGCATTTTCGTGCCCC
1 TGATTGCACTTTCGTGCCCC
* * *
55177719 TGATTGCACTCTGGTGCCCT
1 TGATTGCACTTTCGTGCCCC
*
55177739 TGATTGCATTTTCGTGCC
1 TGATTGCACTTTCGTGCC
55177757 TTTATATGTA
Statistics
Matches: 64, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.12, C:0.29, G:0.21, T:0.38
Consensus pattern (20 bp):
TGATTGCACTTTCGTGCCCC
Found at i:55177774 original size:40 final size:40
Alignment explanation
Indices: 55177673--55177756 Score: 159
Period size: 40 Copynumber: 2.1 Consensus size: 40
55177663 TGCACTCTAA
55177673 TGCCCCTGATTGCACTTTGGTGCCCTTGATTGCATTTTCG
1 TGCCCCTGATTGCACTTTGGTGCCCTTGATTGCATTTTCG
*
55177713 TGCCCCTGATTGCACTCTGGTGCCCTTGATTGCATTTTCG
1 TGCCCCTGATTGCACTTTGGTGCCCTTGATTGCATTTTCG
55177753 TGCC
1 TGCC
55177757 TTTATATGTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.10, C:0.30, G:0.23, T:0.38
Consensus pattern (40 bp):
TGCCCCTGATTGCACTTTGGTGCCCTTGATTGCATTTTCG
Found at i:55180469 original size:24 final size:24
Alignment explanation
Indices: 55180425--55180471 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
55180415 CAATGCCAGC
* *
55180425 TGTCATTGTATTGAATGTGTGAAT
1 TGTCAATGTATTGAATATGTGAAT
55180449 TGTCAATGTATT-ACATATGTGAA
1 TGTCAATGTATTGA-ATATGTGAA
55180472 CTATCACTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.30, C:0.06, G:0.21, T:0.43
Consensus pattern (24 bp):
TGTCAATGTATTGAATATGTGAAT
Found at i:55180661 original size:33 final size:33
Alignment explanation
Indices: 55180623--55180839 Score: 163
Period size: 33 Copynumber: 6.5 Consensus size: 33
55180613 TGAGTTTTGT
* *
55180623 TTATATGTGAACTGAG-TTATATGTGAACTGTG
1 TTATATGTGAACTGTGTTTATATGCGAACTGTG
* * * *
55180655 TGTATATGCGAACTGAG-TTATATGCAAATTGTG
1 T-TATATGTGAACTGTGTTTATATGCGAACTGTG
* * *
55180688 TTTATATGTGAATTGTGTTTATATGCAAACTATG
1 -TTATATGTGAACTGTGTTTATATGCGAACTGTG
* * **
55180722 TTTATATGT-AAGTTGTGTTTATATGAGAACTAAG
1 -TTATATGTGAA-CTGTGTTTATATGCGAACTGTG
* * *
55180756 TTATATGCGAACTGTGTTTATATGTGAACTGAG
1 TTATATGTGAACTGTGTTTATATGCGAACTGTG
* * * *
55180789 TTATATG-CAAATAGTGTTTATATGCAAATTGTG
1 TTATATGTGAACT-GTGTTTATATGCGAACTGTG
*
55180822 TTTATATGTGATCTGTGT
1 -TTATATGTGAACTGTGT
55180840 CAATGTGTGG
Statistics
Matches: 152, Mismatches: 25, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
32 4 0.03
33 90 0.59
34 56 0.37
35 2 0.01
ACGTcount: A:0.29, C:0.06, G:0.22, T:0.43
Consensus pattern (33 bp):
TTATATGTGAACTGTGTTTATATGCGAACTGTG
Found at i:55180662 original size:17 final size:17
Alignment explanation
Indices: 55180620--55180839 Score: 173
Period size: 17 Copynumber: 13.2 Consensus size: 17
55180610 GTGTGAGTTT
55180620 TGTTTATATGTGAACTG
1 TGTTTATATGTGAACTG
*
55180637 AG-TTATATGTGAACTG
1 TGTTTATATGTGAACTG
* *
55180653 TGTGTATATGCGAACTG
1 TGTTTATATGTGAACTG
* ** *
55180670 AG-TTATATGCAAATTG
1 TGTTTATATGTGAACTG
*
55180686 TGTTTATATGTGAATTG
1 TGTTTATATGTGAACTG
** *
55180703 TGTTTATATGCAAACTA
1 TGTTTATATGTGAACTG
*
55180720 TGTTTATATGT-AAGTTG
1 TGTTTATATGTGAA-CTG
* *
55180737 TGTTTATATGAGAACTA
1 TGTTTATATGTGAACTG
* *
55180754 AG-TTATATGCGAACTG
1 TGTTTATATGTGAACTG
55180770 TGTTTATATGTGAACTG
1 TGTTTATATGTGAACTG
* * *
55180787 AG-TTATATG-CAAATAG
1 TGTTTATATGTGAACT-G
** *
55180803 TGTTTATATGCAAATTG
1 TGTTTATATGTGAACTG
*
55180820 TGTTTATATGTGATCTG
1 TGTTTATATGTGAACTG
55180837 TGT
1 TGT
55180840 CAATGTGTGG
Statistics
Matches: 159, Mismatches: 36, Indels: 16
0.75 0.17 0.08
Matches are distributed among these distances:
15 3 0.02
16 51 0.32
17 100 0.63
18 5 0.03
ACGTcount: A:0.29, C:0.06, G:0.22, T:0.43
Consensus pattern (17 bp):
TGTTTATATGTGAACTG
Found at i:55180780 original size:50 final size:50
Alignment explanation
Indices: 55180620--55180830 Score: 187
Period size: 50 Copynumber: 4.2 Consensus size: 50
55180610 GTGTGAGTTT
* * *
55180620 TGTTTATATGTGAACTGAG-TTATATGTGAACTGTGTGTATATGCGAACTG
1 TGTTTATATGTAAATTGTGTTTATATGTGAACTGTGT-TATATGCGAACTG
* * * * *
55180670 AG-TTATATGCAAATTGTGTTTATATGTGAATTGTGTTTATATGCAAACTA
1 TGTTTATATGTAAATTGTGTTTATATGTGAACTGTG-TTATATGCGAACTG
* * **
55180720 TGTTTATATGTAAGTTGTGTTTATATGAGAACTAAGTTATATGCGAACTG
1 TGTTTATATGTAAATTGTGTTTATATGTGAACTGTGTTATATGCGAACTG
* * * * * * *
55180770 TGTTTATATGTGAACTGAG-TTATATG-CAAATAGTGTTTATATGCAAATTG
1 TGTTTATATGTAAATTGTGTTTATATGTGAACT-GTG-TTATATGCGAACTG
55180820 TGTTTATATGT
1 TGTTTATATGT
55180831 GATCTGTGTC
Statistics
Matches: 129, Mismatches: 27, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
48 3 0.02
49 20 0.16
50 78 0.60
51 28 0.22
ACGTcount: A:0.29, C:0.06, G:0.21, T:0.43
Consensus pattern (50 bp):
TGTTTATATGTAAATTGTGTTTATATGTGAACTGTGTTATATGCGAACTG
Found at i:55180826 original size:117 final size:117
Alignment explanation
Indices: 55180615--55180829 Score: 349
Period size: 117 Copynumber: 1.8 Consensus size: 117
55180605 ACAATGTGTG
* * * *
55180615 AGTTTTGTTTATATGTGAACTGAGTTATATGTGAACTGTGTGTATATGCGAACTGAGTTATATGC
1 AGTTGTGTTTATATGAGAACTAAGTTATATGCGAACTGTGTGTATATGCGAACTGAGTTATATGC
* **
55180680 AAATTGTGTTTATATGTGAATTGTGTTTATATGCAAACTATGTTTATATGTA
66 AAATAGTGTTTATATGCAAATTGTGTTTATATGCAAACTATGTTTATATGTA
* *
55180732 AGTTGTGTTTATATGAGAACTAAGTTATATGCGAACTGTGTTTATATGTGAACTGAGTTATATGC
1 AGTTGTGTTTATATGAGAACTAAGTTATATGCGAACTGTGTGTATATGCGAACTGAGTTATATGC
55180797 AAATAGTGTTTATATGCAAATTGTGTTTATATG
66 AAATAGTGTTTATATGCAAATTGTGTTTATATG
55180830 TGATCTGTGT
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
117 89 1.00
ACGTcount: A:0.29, C:0.06, G:0.21, T:0.43
Consensus pattern (117 bp):
AGTTGTGTTTATATGAGAACTAAGTTATATGCGAACTGTGTGTATATGCGAACTGAGTTATATGC
AAATAGTGTTTATATGCAAATTGTGTTTATATGCAAACTATGTTTATATGTA
Found at i:55180974 original size:26 final size:26
Alignment explanation
Indices: 55180945--55180999 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
55180935 GTATGTACAT
* *
55180945 GCTCTTTGTAAAGTAATTACGTGCGA
1 GCTCTTTGTAAAGTAACTAAGTGCGA
*
55180971 GCTCTTTGTAAAGTGACTAAGTGCGA
1 GCTCTTTGTAAAGTAACTAAGTGCGA
55180997 GCT
1 GCT
55181000 AGTCTATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.33
Consensus pattern (26 bp):
GCTCTTTGTAAAGTAACTAAGTGCGA
Found at i:55181131 original size:36 final size:36
Alignment explanation
Indices: 55181080--55181152 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
55181070 ATGAGCTGCG
55181080 TCAACTTCTGAGCCGTAGCAAAAGTACAAGCTATAC
1 TCAACTTCTGAGCCGTAGCAAAAGTACAAGCTATAC
* *
55181116 TCAACTTGTGTGCCGTAGCAAAAGTACAAGCTATAC
1 TCAACTTCTGAGCCGTAGCAAAAGTACAAGCTATAC
55181152 T
1 T
55181153 GTGGTAGTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (36 bp):
TCAACTTCTGAGCCGTAGCAAAAGTACAAGCTATAC
Found at i:55191360 original size:3 final size:3
Alignment explanation
Indices: 55191339--55191378 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
55191329 TTGACTTTCA
* * *
55191339 TTG TTA TTG TTG CTG TTG TTG TTG TAG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
55191379 CGTCGTCGTC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.05, C:0.03, G:0.30, T:0.62
Consensus pattern (3 bp):
TTG
Found at i:55196216 original size:7 final size:7
Alignment explanation
Indices: 55196204--55196229 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
55196194 TTTAATTTAA
55196204 AAATAAT
1 AAATAAT
55196211 AAATAAT
1 AAATAAT
55196218 AAATAAT
1 AAATAAT
55196225 AAATA
1 AAATA
55196230 TATTTATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AAATAAT
Found at i:55199852 original size:18 final size:19
Alignment explanation
Indices: 55199818--55199853 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
55199808 TAAATAATAT
55199818 AGTAAAATTTATCAATTTC
1 AGTAAAATTTATCAATTTC
*
55199837 AGTAAATTTTAT-AATTT
1 AGTAAAATTTATCAATTT
55199854 TTTTGAATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.47
Consensus pattern (19 bp):
AGTAAAATTTATCAATTTC
Found at i:55199890 original size:20 final size:20
Alignment explanation
Indices: 55199840--55199896 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
55199830 CAATTTCAGT
*
55199840 AAATTTTATAATTTTTTTGA
1 AAATTTTATAATATTTTTGA
**
55199860 ATGTTTTATAATATTTTTGA
1 AAATTTTATAATATTTTTGA
*
55199880 AAATTTGATAA-ATTTTT
1 AAATTTTATAATATTTTT
55199897 ATTTATAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
19 6 0.19
20 25 0.81
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (20 bp):
AAATTTTATAATATTTTTGA
Found at i:55222899 original size:23 final size:23
Alignment explanation
Indices: 55222864--55222908 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
55222854 TTTTAAATAA
55222864 TTTTGATAATTTTGTAATTTTTC
1 TTTTGATAATTTTGTAATTTTTC
*
55222887 TTTT-ATAATTTTTGTCATTTTT
1 TTTTGATAA-TTTTGTAATTTTT
55222909 GAAGATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.20, C:0.04, G:0.07, T:0.69
Consensus pattern (23 bp):
TTTTGATAATTTTGTAATTTTTC
Found at i:55232573 original size:32 final size:34
Alignment explanation
Indices: 55232536--55232603 Score: 95
Period size: 32 Copynumber: 2.1 Consensus size: 34
55232526 TGTTTAAAAA
**
55232536 TTTTATTAAAAAGTTTTAA-ATTT-TATATAATT
1 TTTTATTAAAAACCTTTAATATTTATATATAATT
*
55232568 TTTTATTAAAAACCTTTAATATTTATATTTAATT
1 TTTTATTAAAAACCTTTAATATTTATATATAATT
55232602 TT
1 TT
55232604 AAAAATAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
32 17 0.55
33 4 0.13
34 10 0.32
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.57
Consensus pattern (34 bp):
TTTTATTAAAAACCTTTAATATTTATATATAATT
Found at i:55236223 original size:43 final size:43
Alignment explanation
Indices: 55236113--55236213 Score: 175
Period size: 43 Copynumber: 2.3 Consensus size: 43
55236103 GATATGTGTT
*
55236113 TTTTTGTGTAAGACCACGTTTGGGACGTTGGCATCGATTTATG
1 TTTTCGTGTAAGACCACGTTTGGGACGTTGGCATCGATTTATG
* *
55236156 TTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGATTTTTG
1 TTTTCGTGTAAGACCACGTTTGGGACGTTGGCATCGATTTATG
55236199 TTTTCGTGTAAGACC
1 TTTTCGTGTAAGACC
55236214 CTATTTGGGA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 55 1.00
ACGTcount: A:0.18, C:0.17, G:0.27, T:0.39
Consensus pattern (43 bp):
TTTTCGTGTAAGACCACGTTTGGGACGTTGGCATCGATTTATG
Found at i:55236231 original size:43 final size:43
Alignment explanation
Indices: 55236113--55236262 Score: 151
Period size: 43 Copynumber: 3.5 Consensus size: 43
55236103 GATATGTGTT
* * * *
55236113 TTTTTGTGTAAGACCACGTTTGGGACGTTGGCATCGATTTATG
1 TTTTCGTGTAAGACCACATCTGGGAAGTTGGCATCGATTTATG
* * *
55236156 TTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGATTTTTG
1 TTTTCGTGTAAGACCACATCTGGGAAGTTGGCATCGATTTATG
* * *
55236199 TTTTCGTGTAAGACC-CTATTTGGGATAG-TGGCATCGATCTGTG
1 TTTTCGTGTAAGACCAC-ATCTGGGA-AGTTGGCATCGATTTATG
* * *
55236242 ATTACATGTAAGACCACATCT
1 TTTTCGTGTAAGACCACATCT
55236263 AGGGCACTGG
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
42 1 0.01
43 89 0.97
44 2 0.02
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.37
Consensus pattern (43 bp):
TTTTCGTGTAAGACCACATCTGGGAAGTTGGCATCGATTTATG
Found at i:55238521 original size:19 final size:21
Alignment explanation
Indices: 55238482--55238521 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
55238472 TCACATGTCC
55238482 CTAGGGTTCGCATATTAATTAT
1 CTAGGGTTCG-ATATTAATTAT
55238504 CTAGGGTTCG-TA-TAATTA
1 CTAGGGTTCGATATTAATTA
55238522 GCATAAGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 2 0.11
22 10 0.56
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (21 bp):
CTAGGGTTCGATATTAATTAT
Found at i:55238608 original size:22 final size:22
Alignment explanation
Indices: 55238581--55238640 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
55238571 TTCATGTAAT
55238581 AAACATATAGGGTTTGCATATA
1 AAACATATAGGGTTTGCATATA
* ** * *
55238603 TAACATCCAGGGTTCGCATGTA
1 AAACATATAGGGTTTGCATATA
55238625 AACACATATAGGGTTT
1 AA-ACATATAGGGTTT
55238641 TTACAGTACA
Statistics
Matches: 28, Mismatches: 9, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
22 18 0.64
23 10 0.36
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (22 bp):
AAACATATAGGGTTTGCATATA
Found at i:55252975 original size:23 final size:23
Alignment explanation
Indices: 55252940--55252984 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
55252930 TTTTAAATAA
55252940 TTTTGATAATTTTGTAATTTTTC
1 TTTTGATAATTTTGTAATTTTTC
*
55252963 TTTT-ATAATTTTTGTCATTTTT
1 TTTTGATAA-TTTTGTAATTTTT
55252985 GAAGATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.20, C:0.04, G:0.07, T:0.69
Consensus pattern (23 bp):
TTTTGATAATTTTGTAATTTTTC
Found at i:55256593 original size:11 final size:11
Alignment explanation
Indices: 55256579--55256603 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
55256569 CACGTCAAAC
55256579 GAAAAGAAAAA
1 GAAAAGAAAAA
55256590 GAAAAGAAAAA
1 GAAAAGAAAAA
55256601 GAA
1 GAA
55256604 CAAAATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (11 bp):
GAAAAGAAAAA
Found at i:55264801 original size:21 final size:21
Alignment explanation
Indices: 55264771--55264811 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
55264761 TCAGATTTTT
55264771 TTTTATAAAAATGTAAGAAATG
1 TTTTATAAAAATGTAA-AAATG
*
55264793 TTTTA-AAAAATTTAAAAAT
1 TTTTATAAAAATGTAAAAAT
55264812 AAGAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 9 0.50
22 5 0.28
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (21 bp):
TTTTATAAAAATGTAAAAATG
Found at i:55266085 original size:9 final size:9
Alignment explanation
Indices: 55266073--55266140 Score: 50
Period size: 10 Copynumber: 7.4 Consensus size: 9
55266063 TTTTTACTAG
55266073 TTTTTAAAA
1 TTTTTAAAA
*
55266082 TTTTT--AT
1 TTTTTAAAA
*
55266089 TTTTTATAA
1 TTTTTAAAA
55266098 TTTTTAACAA
1 TTTTTAA-AA
*
55266108 TTTCTAATAA
1 TTTTTAA-AA
* *
55266118 TTTTTATAG
1 TTTTTAAAA
55266127 TTTTTAATAA
1 TTTTTAA-AA
55266137 TTTT
1 TTTT
55266141 ATTTTTTTAC
Statistics
Matches: 45, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
7 6 0.13
9 19 0.42
10 20 0.44
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.63
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:55266085 original size:19 final size:19
Alignment explanation
Indices: 55266061--55266140 Score: 87
Period size: 19 Copynumber: 4.3 Consensus size: 19
55266051 CAAGATACAC
55266061 AATTTTTACTAGTTTTTAA-
1 AATTTTTA-TAGTTTTTAAT
55266080 AATTTTTAT--TTTTT-AT
1 AATTTTTATAGTTTTTAAT
* * *
55266096 AATTTTTAACAATTTCTAAT
1 AATTTTT-ATAGTTTTTAAT
55266116 AATTTTTATAGTTTTTAAT
1 AATTTTTATAGTTTTTAAT
55266135 AATTTT
1 AATTTT
55266141 ATTTTTTTAC
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
15 1 0.02
16 12 0.24
17 1 0.02
18 1 0.02
19 27 0.53
20 9 0.18
ACGTcount: A:0.33, C:0.04, G:0.03, T:0.61
Consensus pattern (19 bp):
AATTTTTATAGTTTTTAAT
Found at i:55266740 original size:11 final size:12
Alignment explanation
Indices: 55266719--55266757 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
55266709 ATTTCCATTC
55266719 TATTAAAAAAAT
1 TATTAAAAAAAT
*
55266731 TATTAAAAAATT
1 TATTAAAAAAAT
55266743 TATATAATAAAAAT
1 TAT-TAA-AAAAAT
55266757 T
1 T
55266758 TAAAATTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 14 0.61
13 3 0.13
14 6 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TATTAAAAAAAT
Found at i:55267458 original size:8 final size:8
Alignment explanation
Indices: 55267445--55267492 Score: 51
Period size: 8 Copynumber: 5.5 Consensus size: 8
55267435 TTTATAAGTA
55267445 ATATATTT
1 ATATATTT
55267453 ATATATTT
1 ATATATTT
55267461 ATATATTTT
1 ATATA-TTT
*
55267470 AATCAAATTT
1 -AT-ATATTT
55267480 ATTATATTT
1 A-TATATTT
55267489 ATAT
1 ATAT
55267493 TAAGTATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
8 16 0.47
9 10 0.29
10 6 0.18
11 2 0.06
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (8 bp):
ATATATTT
Found at i:55271133 original size:23 final size:22
Alignment explanation
Indices: 55271077--55271134 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 22
55271067 AATCTTCAAG
55271077 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
55271096 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
55271118 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
55271135 GAATTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.39
22 8 0.24
23 12 0.36
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:55271147 original size:21 final size:23
Alignment explanation
Indices: 55271090--55271147 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 23
55271080 ATGCAATCTT
* *
55271090 AGATATG-ATATGCAATCTTAGA
1 AGATATGAATTTGTAATCTTAGA
*
55271112 AGATATGATTTTGTAATCTTAG-
1 AGATATGAATTTGTAATCTTAGA
*
55271134 AGA-ATTAATTTGTA
1 AGATATGAATTTGTA
55271148 GATACCCTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 9 0.30
22 10 0.33
23 11 0.37
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (23 bp):
AGATATGAATTTGTAATCTTAGA
Found at i:55271250 original size:15 final size:15
Alignment explanation
Indices: 55271230--55271262 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
55271220 AGGCCTTTCC
55271230 CTTCATTGTAAAACA
1 CTTCATTGTAAAACA
55271245 CTTCATTGTAAAACA
1 CTTCATTGTAAAACA
55271260 CTT
1 CTT
55271263 GAGTTTGGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.36
Consensus pattern (15 bp):
CTTCATTGTAAAACA
Found at i:55272815 original size:16 final size:16
Alignment explanation
Indices: 55272794--55272844 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
55272784 TGTTGTGTTT
*
55272794 CATTTTGATTGCATGA
1 CATTTTGACTGCATGA
**
55272810 CATTTTGACTGCACAA
1 CATTTTGACTGCATGA
55272826 CATTTTGACTGCATGA
1 CATTTTGACTGCATGA
55272842 CAT
1 CAT
55272845 GCTCATCATA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (16 bp):
CATTTTGACTGCATGA
Found at i:55278236 original size:132 final size:132
Alignment explanation
Indices: 55277998--55278518 Score: 663
Period size: 132 Copynumber: 4.0 Consensus size: 132
55277988 CTGAGTTTGC
* *
55277998 AGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGTAGATCAAAGACGG
1 AGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTAGAGCAGATCAAAGACGG
* * * *
55278063 TGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAAATCTAAGCCACCAGTCCTATCTCCCTGAGTA
66 CGAATCTTATCTTCCCAAGGTAGTAAGGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTGAGTA
*
55278128 AT
131 GT
* * * * * *
55278130 AGTGGAGTAGGTTGAAGATTGTAAATCCTGTCTCCCTAAGCAATAGTAGAGCAAATAAAAAATGG
1 AGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTAGAGCAGATCAAAGACGG
* * *
55278195 CGAATCTTATTTTCCCAAGGTAGTAAGGAAGCAGATTTAAGCCATCAATCCTATCTCCCTGAGTA
66 CGAATCTTATCTTCCCAAGGTAGTAAGGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTGAGTA
*
55278260 GC
131 GT
* * * **
55278262 AGTGGAGTAGGTTAAAGA-TATAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGG
1 AGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTAGAGCAGATCAAAGACGG
* * * * * * * *
55278326 TGAATCTTATCTTCTCGAGATAGT-AGGAAGCAGATTTAAGCCACTAGTCTTATCTCCCTAAGCA
66 CGAATCTTATCTTCCCAAGGTAGTAAGGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTGAGTA
55278390 GT
131 GT
* * *
55278392 AGTGGAGTAGGTTGAAGATTGTATATTCTATCTCCCTAAGCAGTAGTAGAGCAGATCAAAGACGG
1 AGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTAGAGCAGATCAAAGACGG
* * * *
55278457 C-AAGTCTTATCTTTCCGAGGTAGTGAGGAAGCAGATTTAAGCCACTAG-CCTTATCTCCCTGA
66 CGAA-TCTTATCTTCCCAAGGTAGTAAGGAAGCAGATTTAAGCCACCAGTCC-TATCTCCCTGA
55278519 AGTTGCAACG
Statistics
Matches: 332, Mismatches: 53, Indels: 8
0.84 0.13 0.02
Matches are distributed among these distances:
130 54 0.16
131 113 0.34
132 165 0.50
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.27
Consensus pattern (132 bp):
AGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTAGAGCAGATCAAAGACGG
CGAATCTTATCTTCCCAAGGTAGTAAGGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTGAGTA
GT
Found at i:55278468 original size:44 final size:45
Alignment explanation
Indices: 55278370--55278468 Score: 103
Period size: 44 Copynumber: 2.2 Consensus size: 45
55278360 TTTAAGCCAC
* * * ** ** *
55278370 TAGTCTTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGTA
1 TAGTCTTATCTCCCTAAGCAGTAGTAGAGCAGATCAAAGACGGCA
*
55278415 TATTC-TATCTCCCTAAGCAGTAGTAGAGCAGATCAAAGACGGCA
1 TAGTCTTATCTCCCTAAGCAGTAGTAGAGCAGATCAAAGACGGCA
55278459 -AGTCTTATCT
1 TAGTCTTATCT
55278469 TTCCGAGGTA
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
43 3 0.07
44 36 0.84
45 4 0.09
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.30
Consensus pattern (45 bp):
TAGTCTTATCTCCCTAAGCAGTAGTAGAGCAGATCAAAGACGGCA
Found at i:55278488 original size:262 final size:264
Alignment explanation
Indices: 55277996--55278518 Score: 741
Period size: 262 Copynumber: 2.0 Consensus size: 264
55277986 TTCTGAGTTT
* * *
55277996 GCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGTAGATCAAAGAC
1 GCAGTGGAGTAGGTTAAAGATTATAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
* *
55278061 GGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAAATCTAAGCCACCAGTCCTATCTCCCTGAG
66 GGTGAATCTTATCTTCCCAAGATAGTAGGGAAGCAAATCTAAGCCACCAGTCCTATCTCCCTAAG
* *
55278126 TAATAGTGGAGTAGGTTGAAGATTGTAAATCCTGTCTCCCTAAGCAATAGTAGAGCAAATAAAAA
131 CAATAGTGGAGTAGGTTGAAGATTGTAAATCCTATCTCCCTAAGCAATAGTAGAGCAAATAAAAA
* *
55278191 ATGGCGAATCTTATTTTCCCAAGGTAGTAAGGAAGCAGATTTAAGCCATCAATCC-TATCTCCCT
196 ACGGCGAATCTTATTTTCCCAAGGTAGTAAGGAAGCAGATTTAAGCCA-CAAGCCTTATCTCCCT
55278255 GAGTA
260 GAGTA
**
55278260 GCAGTGGAGTAGGTTAAAGA-TATAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATTGAAGAC
1 GCAGTGGAGTAGGTTAAAGATTATAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
* * * * * *
55278324 GGTGAATCTTATCTTCTCGAGATAGTA-GGAAGCAGATTTAAGCCACTAGTCTTATCTCCCTAAG
66 GGTGAATCTTATCTTCCCAAGATAGTAGGGAAGCAAATCTAAGCCACCAGTCCTATCTCCCTAAG
* * * * * * *
55278388 CAGTAGTGGAGTAGGTTGAAGATTGTATATTCTATCTCCCTAAGCAGTAGTAGAGCAGATCAAAG
131 CAATAGTGGAGTAGGTTGAAGATTGTAAATCCTATCTCCCTAAGCAATAGTAGAGCAAATAAAAA
* * *
55278453 ACGGC-AAGTCTTATCTTT-CCGAGGTAGTGAGGAAGCAGATTTAAGCCACTAGCCTTATCTCCC
196 ACGGCGAA-TCTTAT-TTTCCCAAGGTAGTAAGGAAGCAGATTTAAGCCACAAGCCTTATCTCCC
55278516 TGA
259 TGA
55278519 AGTTGCAACG
Statistics
Matches: 229, Mismatches: 27, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
261 6 0.03
262 137 0.60
263 67 0.29
264 19 0.08
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.27
Consensus pattern (264 bp):
GCAGTGGAGTAGGTTAAAGATTATAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
GGTGAATCTTATCTTCCCAAGATAGTAGGGAAGCAAATCTAAGCCACCAGTCCTATCTCCCTAAG
CAATAGTGGAGTAGGTTGAAGATTGTAAATCCTATCTCCCTAAGCAATAGTAGAGCAAATAAAAA
ACGGCGAATCTTATTTTCCCAAGGTAGTAAGGAAGCAGATTTAAGCCACAAGCCTTATCTCCCTG
AGTA
Found at i:55278761 original size:44 final size:44
Alignment explanation
Indices: 55278650--55278765 Score: 153
Period size: 44 Copynumber: 2.6 Consensus size: 44
55278640 ATCTTATCCT
*
55278650 CCTAAAGTTGCAGTGGAGTAGATTAAAGCCAATAATCCTATCTC
1 CCTAAAGTTGCAGTGGAGTGGATTAAAGCCAATAATCCTATCTC
** * * *
55278694 CCTAAAGTTATAGTAGAGCGGATTGAAA-CCACTAATCCTATCTC
1 CCTAAAGTTGCAGTGGAGTGGATT-AAAGCCAATAATCCTATCTC
*
55278738 CCTGAAGTTGCAGTGGAGTGGATTAAAG
1 CCTAAAGTTGCAGTGGAGTGGATTAAAG
55278766 ACACAAGTCT
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
43 3 0.05
44 53 0.90
45 3 0.05
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.27
Consensus pattern (44 bp):
CCTAAAGTTGCAGTGGAGTGGATTAAAGCCAATAATCCTATCTC
Found at i:55278780 original size:44 final size:43
Alignment explanation
Indices: 55278650--55278782 Score: 142
Period size: 44 Copynumber: 3.0 Consensus size: 43
55278640 ATCTTATCCT
* *
55278650 CCTAAAGTTGCAGTGGAGTAGATTAAAGCCAATAATCCTATCTC
1 CCTAAAGTTGCAGTGGAGTGGATTAAAGCC-ACAATCCTATCTC
** * *
55278694 CCTAAAGTTATAGTAGAGCGGATTGAAA-CCACTAATCCTATCTC
1 CCTAAAGTTGCAGTGGAGTGGATT-AAAGCCAC-AATCCTATCTC
* * *
55278738 CCTGAAGTTGCAGTGGAGTGGATTAAAGACACAAGTCTTATCTC
1 CCTAAAGTTGCAGTGGAGTGGATTAAAGCCACAA-TCCTATCTC
55278782 C
1 C
55278783 TTGGCATTAT
Statistics
Matches: 72, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
43 6 0.08
44 63 0.88
45 3 0.04
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (43 bp):
CCTAAAGTTGCAGTGGAGTGGATTAAAGCCACAATCCTATCTC
Found at i:55278986 original size:51 final size:51
Alignment explanation
Indices: 55278900--55279000 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 51
55278890 GTTAAGACTG
55278900 AAGGAAGCAAATCTTATTTCCCTGGCATTGCAGTGGAACAGATTAAAGCTA
1 AAGGAAGCAAATCTTATTTCCCTGGCATTGCAGTGGAACAGATTAAAGCTA
* * * * * *
55278951 AAGGTAGCGAATCTTGTTTCCCTTGCATTGTAGTGGAATAGATTAAAGCT
1 AAGGAAGCAAATCTTATTTCCCTGGCATTGCAGTGGAACAGATTAAAGCT
55279001 GAAATGGAGC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.30
Consensus pattern (51 bp):
AAGGAAGCAAATCTTATTTCCCTGGCATTGCAGTGGAACAGATTAAAGCTA
Done.