Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 176 of 189
Found at i:52243830 original size:9 final size:9
Alignment explanation
Indices: 52243816--52243936 Score: 154
Period size: 9 Copynumber: 13.4 Consensus size: 9
52243806 GTAGTGATTC
*
52243816 AATTTGGTT
1 AATTCGGTT
*
52243825 AATTTGGTT
1 AATTCGGTT
*
52243834 AATTCGGGT
1 AATTCGGTT
52243843 AATTCGGTT
1 AATTCGGTT
*
52243852 AATTCGGGT
1 AATTCGGTT
*
52243861 AATTCGATT
1 AATTCGGTT
*
52243870 AATTCGGGT
1 AATTCGGTT
*
52243879 AATTCGGGT
1 AATTCGGTT
*
52243888 AATTCGGGT
1 AATTCGGTT
52243897 AATTCGGTT
1 AATTCGGTT
52243906 AATTCGAG-T
1 AATTCG-GTT
52243915 AATTCGGTT
1 AATTCGGTT
52243924 AATTCGGTT
1 AATTCGGTT
52243933 AATT
1 AATT
52243937 TTTAACCAAA
Statistics
Matches: 101, Mismatches: 9, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
8 1 0.01
9 99 0.98
10 1 0.01
ACGTcount: A:0.25, C:0.09, G:0.25, T:0.41
Consensus pattern (9 bp):
AATTCGGTT
Found at i:52243845 original size:18 final size:18
Alignment explanation
Indices: 52243824--52243936 Score: 181
Period size: 18 Copynumber: 6.3 Consensus size: 18
52243814 TCAATTTGGT
*
52243824 TAATTTGGTTAATTCGGG
1 TAATTCGGTTAATTCGGG
52243842 TAATTCGGTTAATTCGGG
1 TAATTCGGTTAATTCGGG
*
52243860 TAATTCGATTAATTCGGG
1 TAATTCGGTTAATTCGGG
*
52243878 TAATTCGGGTAATTCGGG
1 TAATTCGGTTAATTCGGG
*
52243896 TAATTCGGTTAATTCGAG
1 TAATTCGGTTAATTCGGG
*
52243914 TAATTCGGTTAATTCGGT
1 TAATTCGGTTAATTCGGG
52243932 TAATT
1 TAATT
52243937 TTTAACCAAA
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 87 1.00
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.41
Consensus pattern (18 bp):
TAATTCGGTTAATTCGGG
Found at i:52253007 original size:6 final size:6
Alignment explanation
Indices: 52252993--52253027 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
52252983 TCATGTTATA
52252993 TTTGAAT TTTGAT TTTGAT TTTGAT TTTGAT TTTG
1 TTTG-AT TTTGAT TTTGAT TTTGAT TTTGAT TTTG
52253028 TGCAATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 24 0.86
7 4 0.14
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (6 bp):
TTTGAT
Found at i:52255415 original size:44 final size:44
Alignment explanation
Indices: 52255380--52255476 Score: 169
Period size: 44 Copynumber: 2.2 Consensus size: 44
52255370 CAACTCATGT
52255380 TTATCTTCTTCTTTTTTTAAATTCTTTTTTTCAACAACCCAAGA
1 TTATCTTCTTCTTTTTTTAAATTCTTTTTTTCAACAACCCAAGA
* *
52255424 TTATCTTCTCCTTTTTTTTAATTCTTTTTTT-AACAACCCAAGA
1 TTATCTTCTTCTTTTTTTAAATTCTTTTTTTCAACAACCCAAGA
52255467 TTATCTTCTT
1 TTATCTTCTT
52255477 TTTAAAGTCT
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
43 21 0.42
44 29 0.58
ACGTcount: A:0.23, C:0.21, G:0.02, T:0.55
Consensus pattern (44 bp):
TTATCTTCTTCTTTTTTTAAATTCTTTTTTTCAACAACCCAAGA
Found at i:52261811 original size:13 final size:13
Alignment explanation
Indices: 52261793--52261817 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52261783 TAGATTGGAT
52261793 TTGATTATGTAAA
1 TTGATTATGTAAA
52261806 TTGATTATGTAA
1 TTGATTATGTAA
52261818 TCTTGTAAAT
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:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (13 bp):
TTGATTATGTAAA
Found at i:52262630 original size:26 final size:26
Alignment explanation
Indices: 52262600--52262654 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
52262590 AATCACAGCA
52262600 ATTAAATCCACGGTTTGAGCTCGAGC
1 ATTAAATCCACGGTTTGAGCTCGAGC
52262626 ATTAAATCCACGGTTTGAGCTCGAGC
1 ATTAAATCCACGGTTTGAGCTCGAGC
52262652 ATT
1 ATT
52262655 TAAGGCTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (26 bp):
ATTAAATCCACGGTTTGAGCTCGAGC
Found at i:52262709 original size:18 final size:16
Alignment explanation
Indices: 52262686--52262723 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 16
52262676 GCTGTTTATA
52262686 ATATATTATATTATATTT
1 ATATATTAT-TTA-ATTT
52262704 ATATATTATTTAATTT
1 ATATATTATTTAATTT
52262720 ATAT
1 ATAT
52262724 CACAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.40
17 3 0.15
18 9 0.45
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATATATTATTTAATTT
Found at i:52262988 original size:26 final size:26
Alignment explanation
Indices: 52262959--52263010 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
52262949 CTTGAACAAA
52262959 CATAAAATGAAGGTTTGTGTAATGCT
1 CATAAAATGAAGGTTTGTGTAATGCT
52262985 CATAAAATGAAGGTTTGTGTAATGCT
1 CATAAAATGAAGGTTTGTGTAATGCT
52263011 TAAGCTTGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.08, G:0.23, T:0.35
Consensus pattern (26 bp):
CATAAAATGAAGGTTTGTGTAATGCT
Found at i:52279034 original size:49 final size:49
Alignment explanation
Indices: 52278962--52279059 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
52278952 TCTCCAAAAA
52278962 CACATGTGTGATTTTGGTAAAAGGTTTATTGCTATAAATATCATAAATC
1 CACATGTGTGATTTTGGTAAAAGGTTTATTGCTATAAATATCATAAATC
52279011 CACATGTGTGATTTTGGTAAAAGGTTTATTGCTATAAATATCATAAATC
1 CACATGTGTGATTTTGGTAAAAGGTTTATTGCTATAAATATCATAAATC
52279060 AATTCAGTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (49 bp):
CACATGTGTGATTTTGGTAAAAGGTTTATTGCTATAAATATCATAAATC
Found at i:52282062 original size:14 final size:14
Alignment explanation
Indices: 52282039--52282073 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
52282029 AACTAAAAGG
52282039 TTAATTATGTT-AA
1 TTAATTATGTTAAA
52282052 TTAAGTTATGTTAAA
1 TTAA-TTATGTTAAA
52282067 TTAATTA
1 TTAATTA
52282074 ATCTAGGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 4 0.20
14 10 0.50
15 6 0.30
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (14 bp):
TTAATTATGTTAAA
Found at i:52293430 original size:15 final size:17
Alignment explanation
Indices: 52293410--52293441 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
52293400 TTAAAATATT
52293410 CATATAT-TA-TAAAAA
1 CATATATCTATTAAAAA
52293425 CATATATCTATTAAAAA
1 CATATATCTATTAAAAA
52293442 AATGCATGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.34
Consensus pattern (17 bp):
CATATATCTATTAAAAA
Found at i:52296086 original size:16 final size:17
Alignment explanation
Indices: 52296049--52296116 Score: 57
Period size: 17 Copynumber: 3.9 Consensus size: 17
52296039 GATCCGATTG
* *
52296049 AAACACGAGATTTTTTT
1 AAACACGAGAATTTTGT
52296066 AAACACGAGAATTTTGT
1 AAACACGAGAATTTTGT
* * *
52296083 -AACACTATAATAATTTTT
1 AAACACGAGAAT--TTTGT
52296101 GAAACACGAGAATTTT
1 -AAACACGAGAATTTT
52296117 TTTGAAAACA
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
16 9 0.22
17 15 0.38
18 7 0.17
20 9 0.22
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (17 bp):
AAACACGAGAATTTTGT
Found at i:52296106 original size:20 final size:19
Alignment explanation
Indices: 52296077--52296158 Score: 66
Period size: 18 Copynumber: 4.4 Consensus size: 19
52296067 AACACGAGAA
* *
52296077 TTTTGTAACACTATAATAAT
1 TTTTGAAACAC-ATAATATT
*
52296097 TTTTGAAACACGAGAAT-TT
1 TTTTGAAACAC-ATAATATT
52296116 TTTTGAAA-ACATGAA-ATT
1 TTTTGAAACACAT-AATATT
*
52296134 TTTTGAAACACA-AGT-TT
1 TTTTGAAACACATAATATT
52296151 TTTTGAAA
1 TTTTGAAA
52296159 ACGCGAAAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
17 12 0.23
18 14 0.27
19 12 0.23
20 14 0.27
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (19 bp):
TTTTGAAACACATAATATT
Found at i:52296134 original size:36 final size:37
Alignment explanation
Indices: 52296058--52296228 Score: 138
Period size: 36 Copynumber: 4.6 Consensus size: 37
52296048 GAAACACGAG
* * *
52296058 ATTTTTTTAAACACGAGAA-TTTTGT-AACACTATAATA
1 ATTTTTTGAAACACGAGAATTTTTTTGAAAAC-ATAA-A
*
52296095 A-TTTTTGAAACACGAGAATTTTTTTGAAAACATGAA
1 ATTTTTTGAAACACGAGAATTTTTTTGAAAACATAAA
* **
52296131 ATTTTTTGAAACAC-A-AGTTTTTTTGAAAACGCGAAA
1 ATTTTTTGAAACACGAGAATTTTTTTGAAAAC-ATAAA
*** *
52296167 ATTTTTTTTTACATGAGAATTTTTTTGAAAACACTAAA
1 ATTTTTTGAAACACGAGAATTTTTTTGAAAACA-TAAA
* *
52296205 A-TTTTTAAAACACGAACAATTTTT
1 ATTTTTTGAAACACG-AGAATTTTT
52296229 GAAAGCGCGA
Statistics
Matches: 106, Mismatches: 20, Indels: 15
0.75 0.14 0.11
Matches are distributed among these distances:
35 14 0.13
36 31 0.29
37 31 0.29
38 30 0.28
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (37 bp):
ATTTTTTGAAACACGAGAATTTTTTTGAAAACATAAA
Found at i:52296243 original size:18 final size:18
Alignment explanation
Indices: 52296094--52296291 Score: 100
Period size: 18 Copynumber: 10.7 Consensus size: 18
52296084 ACACTATAAT
52296094 AATTTTTG-AAACACGAGA
1 AATTTTTGAAAACACGA-A
* *
52296112 ATTTTTTTGAAAACATGAA
1 A-ATTTTTGAAAACACGAA
*
52296131 ATTTTTTG-AAACAC-AA
1 AATTTTTGAAAACACGAA
** *
52296147 GTTTTTTTGAAAACGCGAA
1 -AATTTTTGAAAACACGAA
**** *
52296166 AATTTTTTTTTACATGAGA
1 AATTTTTGAAAACACGA-A
* *
52296185 ATTTTTTTGAAAACACTAA
1 A-ATTTTTGAAAACACGAA
52296204 AATTTTT-AAAACACGAA
1 AATTTTTGAAAACACGAA
* *
52296221 CAATTTTTGAAAGCGCGAA
1 -AATTTTTGAAAACACGAA
*
52296240 AATTTTTTTAAAACACGAGA
1 AA-TTTTTGAAAACACGA-A
**
52296260 TTTGTTTTTTG-AAACACGAA
1 ---AATTTTTGAAAACACGAA
52296280 AATTTTTGAAAA
1 AATTTTTGAAAA
52296292 GAAGTATCGT
Statistics
Matches: 133, Mismatches: 32, Indels: 30
0.68 0.16 0.15
Matches are distributed among these distances:
16 2 0.02
17 27 0.20
18 39 0.29
19 34 0.26
20 18 0.14
21 8 0.06
22 5 0.04
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (18 bp):
AATTTTTGAAAACACGAA
Found at i:52297025 original size:7 final size:7
Alignment explanation
Indices: 52297013--52297081 Score: 58
Period size: 7 Copynumber: 10.3 Consensus size: 7
52297003 GTGATATTAT
52297013 TTTTTTC
1 TTTTTTC
52297020 TTTTTTC
1 TTTTTTC
*
52297027 --TTCTC
1 TTTTTTC
52297032 -TTTTTC
1 TTTTTTC
52297038 TTTTTTC
1 TTTTTTC
*
52297045 -TTTCTC
1 TTTTTTC
52297051 -TTTTTC
1 TTTTTTC
*
52297057 TTCTTTC
1 TTTTTTC
52297064 TTTTTCTTC
1 -TTTT-TTC
52297073 TTTTTTC
1 TTTTTTC
52297080 TT
1 TT
52297082 CCTTTTTCTT
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
5 4 0.08
6 14 0.27
7 23 0.45
8 7 0.14
9 3 0.06
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTTTTC
Found at i:52297030 original size:10 final size:10
Alignment explanation
Indices: 52297012--52297093 Score: 80
Period size: 10 Copynumber: 8.0 Consensus size: 10
52297002 TGTGATATTA
52297012 TTTTT-TTCT
1 TTTTTCTTCT
52297021 TTTTTCTTC-
1 TTTTTCTTCT
*
52297030 TCTTT-TTCT
1 TTTTTCTTCT
52297039 TTTTTCTTTCT
1 TTTTTC-TTCT
52297050 CTTTTTCTTCTTT
1 -TTTTTCTTC--T
52297063 CTTTTTCTTCT
1 -TTTTTCTTCT
*
52297074 TTTTTCTTCC
1 TTTTTCTTCT
52297084 TTTTTCTTCT
1 TTTTTCTTCT
52297094 CCTTCTTCTT
Statistics
Matches: 62, Mismatches: 4, Indels: 13
0.78 0.05 0.16
Matches are distributed among these distances:
8 3 0.05
9 13 0.21
10 21 0.34
11 8 0.13
12 6 0.10
13 11 0.18
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTTCTTCT
Found at i:52297042 original size:19 final size:18
Alignment explanation
Indices: 52297014--52297091 Score: 108
Period size: 19 Copynumber: 4.4 Consensus size: 18
52297004 TGATATTATT
52297014 TTTTTCTTTTTTCTTCTC
1 TTTTTCTTTTTTCTTCTC
52297032 TTTTTCTTTTTTCTTTCTC
1 TTTTTCTTTTTTC-TTCTC
*
52297051 TTTTTCTTCTTTCTT-T-
1 TTTTTCTTTTTTCTTCTC
*
52297067 TTCTTCTTTTTTCTTC-C
1 TTTTTCTTTTTTCTTCTC
52297084 TTTTTCTT
1 TTTTTCTT
52297092 CTCCTTCTTC
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
16 13 0.25
17 8 0.15
18 15 0.28
19 17 0.32
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTTCTTTTTTCTTCTC
Found at i:52297046 original size:13 final size:13
Alignment explanation
Indices: 52297013--52297091 Score: 67
Period size: 13 Copynumber: 6.2 Consensus size: 13
52297003 GTGATATTAT
52297013 TTTTTTCTTTTT-
1 TTTTTTCTTTTTC
* *
52297025 TCTTCTCTTTTTC
1 TTTTTTCTTTTTC
*
52297038 TTTTTTCTTTCTC
1 TTTTTTCTTTTTC
52297051 -TTTTTCTTCTTTC
1 TTTTTTCTT-TTTC
52297064 -TTTTTCTTCTTT-
1 TTTTTTCTT-TTTC
*
52297076 TTTCTTCCTTTTTC
1 TTT-TTTCTTTTTC
52297090 TT
1 TT
52297092 CTCCTTCTTC
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
12 18 0.33
13 30 0.55
14 7 0.13
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTTTCTTTTTC
Found at i:52297093 original size:13 final size:13
Alignment explanation
Indices: 52297020--52297103 Score: 50
Period size: 13 Copynumber: 6.5 Consensus size: 13
52297010 TATTTTTTTC
52297020 TTTT-TTCTTCTCT
1 TTTTCTTCTTC-CT
* *
52297033 TTTTCTTTTTTCT
1 TTTTCTTCTTCCT
* *
52297046 TTCTCTT-TTTCT
1 TTTTCTTCTTCCT
*
52297058 TCTTTCTT-TTTCT
1 T-TTTCTTCTTCCT
*
52297071 TCTTTTTTCTTCCT
1 T-TTTCTTCTTCCT
52297085 TTTTCTTC-TCCT
1 TTTTCTTCTTCCT
*
52297097 TCTTCTT
1 TTTTCTT
52297104 TGGGCCGAAC
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
12 16 0.27
13 35 0.58
14 9 0.15
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (13 bp):
TTTTCTTCTTCCT
Found at i:52297756 original size:30 final size:31
Alignment explanation
Indices: 52297722--52297785 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 31
52297712 AAAATACTAG
*
52297722 GGGTCAAGATGAAAATTTAGGAAAAG-TTAA
1 GGGTCAAAATGAAAATTTAGGAAAAGTTTAA
* * **
52297752 GGGTCAAAATGTAATTTTTTGAAAAGTTTAA
1 GGGTCAAAATGAAAATTTAGGAAAAGTTTAA
52297783 GGG
1 GGG
52297786 CTAAACTGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 21 0.75
31 7 0.25
ACGTcount: A:0.41, C:0.03, G:0.27, T:0.30
Consensus pattern (31 bp):
GGGTCAAAATGAAAATTTAGGAAAAGTTTAA
Found at i:52297991 original size:5 final size:5
Alignment explanation
Indices: 52297983--52298008 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
52297973 TATGATATAT
52297983 ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA A
52298009 CATGAAATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:52298271 original size:75 final size:75
Alignment explanation
Indices: 52298167--52299047 Score: 957
Period size: 75 Copynumber: 11.7 Consensus size: 75
52298157 CCTAGCGTAC
* * * * * *
52298167 GACCCGAGGCTCAACTCACCTCACGCATTATGAGTTGATTCTTGAAAAACAGGACTTGAAAATAC
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAATAC
*
52298232 CTCGGCATGC
66 CTCGGCATGT
* * * * * * *
52298242 GGCCCAAGGCTCAACTCACCTCT-GACATTATGAGTTGATATTTGGAAAACAGAAAATAAAGATA
1 GACCCGAGGCTCAACTCACCTCTCG-CAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAATA
*
52298306 CCTTGGCA--T
65 CCTCGGCATGT
* * * *
52298315 GATCC-AGGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAATAGAAATTGAAAA
1 GACCCGA-GGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAGAAATTAAAAA
*
52298379 TACCTCAGC--GT
63 TACCTCGGCATGT
* * * *
52298390 GACCCGAGGCTCAACTCGCTTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTAAAGATAC
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAATAC
*
52298455 CTCGGTATGT
66 CTCGGCATGT
* * * *
52298465 GACCCAAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTGAAAAGCAGAAATTAAAGATAC
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAATAC
*
52298530 CTCGGTATGT
66 CTCGGCATGT
** *
52298540 GACCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAAACAGAAGTTAAAA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA----TTTTTGAAAAACAGAAATT-AAA
*
52298605 AATACCTCGGCGTGT
61 AATACCTCGGCATGT
* * *
52298620 GACCCGAGGCTCAACCCACCTCTGGCAATATGAGTTGATTTTTGAAAAATAGAAATTTAAAAGAA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA-TT--AA-AA
**
52298685 ATACCTCAACATGT
62 ATACCTCGGCATGT
* *
52298699 G-TCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTT--AAAA-A-AAATTGAAAATAC
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAATAC
* *
52298758 CTCAGCGTGT
66 CTCGGCATGT
* *
52298768 GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAATAGAAATTAAAAAA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAGAAATT-AAAAA
*
52298833 TACCTCGGCGTGT
63 TACCTCGGCATGT
*
52298846 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTGTTTTTG-AAAA-A-AAATAAAAGA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTGAAAAACAGAAAT-TAA-A
52298908 AATACCTCGGCATGT
61 AATACCTCGGCATGT
* * * **
52298923 G-TCCGAGGCTCAACTCACCTCTCGCAATACGAGTCGATTTTTGAAAAACAAGATTTTAAAAAAT
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAC-AGAAATT-AAAAAT
* *
52298987 ACCTCGGTATAT
64 ACCTCGGCATGT
52298999 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
52299048 AAAACAGAAA
Statistics
Matches: 693, Mismatches: 78, Indels: 68
0.83 0.09 0.08
Matches are distributed among these distances:
69 15 0.02
70 35 0.05
72 3 0.00
73 74 0.11
74 7 0.01
75 231 0.33
76 72 0.10
77 76 0.11
78 93 0.13
79 38 0.05
80 49 0.07
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.27
Consensus pattern (75 bp):
GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAATAC
CTCGGCATGT
Found at i:52298502 original size:150 final size:149
Alignment explanation
Indices: 52298167--52299048 Score: 934
Period size: 148 Copynumber: 5.8 Consensus size: 149
52298157 CCTAGCGTAC
* * * * * * *
52298167 GACCCGAGGCTCAACTCACCTCACGCATTATGAGTTGATTCTTGAAAAACAGGACTT-GAAAATA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTAAAAAATA
* * * * * *
52298231 CCTCGGCATGCGGCCCAAGGCTCAACTCACCTCT-GACATTATGAGTTGATATTTGGAAAACAGA
66 CCTCGGC-TGTGACCCGAGGCTCAACTCACCTCTCG-CAATATGAGTTGAT-TTTTGAAAAAAGA
* *
52298295 AAATAAAGATACCTTGGCA--T
128 AATTAAAGATACCTCGGCATGT
* * *
52298315 GATCC-AGGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAATAGAAATT-GAAA
1 GACCCGA-GGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAATAGAAATTAAAAA
* * *
52298378 ATACCTCAGC-GTGACCCGAGGCTCAACTCGCTTCTCGCAATATGAGTTGATTTTTGAAAAATAG
63 ATACCTCGGCTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA-AG
*
52298442 AAATTAAAGATACCTCGGTATGT
127 AAATTAAAGATACCTCGGCATGT
* * ** *
52298465 GACCCAAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTGAAAAGCAGAAATT-AAAGATA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTAAAAAATA
* **
52298529 CCTCGGTATGTGACCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAAAC
66 CCTCGG-CTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA----TTTTTGAAAAA-
* * *
52298594 AGAAGTTAAAAAATACCTCGGCGTGT
125 AGAAATT-AAAGATACCTCGGCATGT
* *
52298620 GACCCGAGGCTCAACCCACCTCTGGCAATATGAGTTGATTTTTGAAAAATAGAAATTTAAAAGAA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAA-TT-AAA-AA
** *
52298685 ATACCTCAACATGTG-TCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTT--AAAAA-
63 ATACCTCGGC-TGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAG
* *
52298745 AAATTGAAA-ATACCTCAGCGTGT
127 AAATT-AAAGATACCTCGGCATGT
*
52298768 GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAATAGAAATTAAAAAA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAATAGAAATTAAAAAA
52298833 TACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTGTTTTTG-AAAA
64 TACCTCGGC-TGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTGAAAAA
*
52298897 A-AAATAAAAGAAATACCTCGGCATGT
125 AGAAATTAAAG--ATACCTCGGCATGT
* * * * **
52298923 G-TCCGAGGCTCAACTCACCTCTCGCAATACGAGTCGATTTTTGAAAAACAAGATTTTAAAAAAT
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA-TAGAAATTAAAAAAT
* *
52298987 ACCTCGGTATATGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAA
65 ACCTCGG-CTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAA
52299049 AAACAGAAAT
Statistics
Matches: 630, Mismatches: 70, Indels: 65
0.82 0.09 0.08
Matches are distributed among these distances:
147 23 0.04
148 199 0.32
149 10 0.02
150 122 0.19
151 10 0.02
152 18 0.03
153 72 0.11
154 49 0.08
155 78 0.12
156 2 0.00
158 35 0.06
159 12 0.02
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (149 bp):
GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTAAAAAATA
CCTCGGCTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAGAAAT
TAAAGATACCTCGGCATGT
Found at i:52319858 original size:16 final size:17
Alignment explanation
Indices: 52319829--52319861 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
52319819 TAAATTTTTA
52319829 AAAATATTAATTTAATAT
1 AAAATATT-ATTTAATAT
52319847 AAAATATT-TTTAATA
1 AAAATATTATTTAATA
52319862 CTATAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAAATATTATTTAATAT
Found at i:52320051 original size:24 final size:23
Alignment explanation
Indices: 52320000--52320053 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
52319990 CTTTAAATCA
* *
52320000 ATATACTAAATTAGTATATTACT
1 ATATACTAAAATAGTATATTAAT
52320023 A-ATACATAAAATAGTA-ATATAAT
1 ATATAC-TAAAATAGTATAT-TAAT
52320046 ATATACTA
1 ATATACTA
52320054 GGATTATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
22 6 0.23
23 16 0.62
24 4 0.15
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (23 bp):
ATATACTAAAATAGTATATTAAT
Found at i:52320534 original size:16 final size:17
Alignment explanation
Indices: 52320515--52320547 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
52320505 TATATAATGT
52320515 ACTACTATTAT-ATATA
1 ACTACTATTATAATATA
*
52320531 ACTATTATTATAATATA
1 ACTACTATTATAATATA
52320548 TATATATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (17 bp):
ACTACTATTATAATATA
Found at i:52320536 original size:13 final size:13
Alignment explanation
Indices: 52320518--52320555 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
52320508 ATAATGTACT
52320518 ACTATTATATATA
1 ACTATTATATATA
52320531 ACTATTAT-TATA
1 ACTATTATATATA
52320543 A-TATATATATATA
1 ACTAT-TATATATA
52320556 TAAGGTAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 3 0.13
12 8 0.35
13 12 0.52
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (13 bp):
ACTATTATATATA
Found at i:52321212 original size:9 final size:9
Alignment explanation
Indices: 52321188--52321224 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
52321178 TGAGTTTTCG
*
52321188 AATTCAAAT
1 AATTCGAAT
*
52321197 AACTCGAAT
1 AATTCGAAT
52321206 AATTCGAAT
1 AATTCGAAT
52321215 AATTCGAAT
1 AATTCGAAT
52321224 A
1 A
52321225 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:52323219 original size:99 final size:100
Alignment explanation
Indices: 52323107--52323298 Score: 260
Period size: 100 Copynumber: 1.9 Consensus size: 100
52323097 TTCGGTGCCA
* * * * *
52323107 CCACTTCACATGGAGTCACCAAAAACAGTAAAAAAAAAT-CATAATGCCTACTCTAGATGTGGCG
1 CCACTTCAAATGGAGTCACCAAAAACAATAAAAAAAAATCCATAATCCCTACTCCAGATATGGCG
*
52323171 GCACCAGTAATTTTTTTTAAAGTTTTTTGGTGTTG
66 GCACCAGTAATTTTTTTAAAAGTTTTTTGGTGTTG
* ** * * *
52323206 CCACTTCAAATGGAGTCACTAAAAACAATAAAAAAATTTCCCTAGTCCCTACTCCAGATATGGTG
1 CCACTTCAAATGGAGTCACCAAAAACAATAAAAAAAAATCCATAATCCCTACTCCAGATATGGCG
*
52323271 GCACCAGTAATTTTTTTAAAATTTTTTT
66 GCACCAGTAATTTTTTTAAAAGTTTTTT
52323299 TATCTCACCA
Statistics
Matches: 79, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
99 34 0.43
100 45 0.57
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.32
Consensus pattern (100 bp):
CCACTTCAAATGGAGTCACCAAAAACAATAAAAAAAAATCCATAATCCCTACTCCAGATATGGCG
GCACCAGTAATTTTTTTAAAAGTTTTTTGGTGTTG
Found at i:52324067 original size:20 final size:20
Alignment explanation
Indices: 52324042--52324085 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
52324032 TCTTTTTTTT
52324042 TTGAAAGGTAAATTCATTAA
1 TTGAAAGGTAAATTCATTAA
52324062 TTGAAAGGTAAATTCATTAA
1 TTGAAAGGTAAATTCATTAA
52324082 TTGA
1 TTGA
52324086 TTCAATTAAT
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:0.05, G:0.16, T:0.36
Consensus pattern (20 bp):
TTGAAAGGTAAATTCATTAA
Found at i:52325691 original size:13 final size:14
Alignment explanation
Indices: 52325675--52325716 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
52325665 TTTCAATTTT
52325675 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
52325688 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
52325703 ATTTTAAATAATAT
1 ATTTT-AATAATAT
52325717 TCTTCACGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:52325701 original size:16 final size:16
Alignment explanation
Indices: 52325679--52325715 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
52325669 AATTTTATTT
52325679 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
52325696 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
52325711 TAATA
1 TAATA
52325716 TTCTTCACGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:52327813 original size:15 final size:15
Alignment explanation
Indices: 52327789--52327818 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52327779 ATAGTTATAG
*
52327789 TAACATTAATAATAA
1 TAACAGTAATAATAA
52327804 TAACAGTAATAATAA
1 TAACAGTAATAATAA
52327819 AAATAGTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.60, C:0.07, G:0.03, T:0.30
Consensus pattern (15 bp):
TAACAGTAATAATAA
Found at i:52329445 original size:31 final size:31
Alignment explanation
Indices: 52329384--52329450 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
52329374 TCGTGACCTT
* ** *
52329384 GTAACCACTGCCAATAGGAACTATTGACCGC
1 GTAACCACTACCAATAAAAACTATTAACCGC
*
52329415 GTAACCACTACCAATAAAAACTCTTAACCGC
1 GTAACCACTACCAATAAAAACTATTAACCGC
52329446 GTAAC
1 GTAAC
52329451 TAATACCCTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.37, C:0.30, G:0.13, T:0.19
Consensus pattern (31 bp):
GTAACCACTACCAATAAAAACTATTAACCGC
Found at i:52330840 original size:5 final size:5
Alignment explanation
Indices: 52330830--52330874 Score: 63
Period size: 5 Copynumber: 9.0 Consensus size: 5
52330820 AACTATTAAT
* * *
52330830 ATATG ATATG ATATG ATATG ATATA ATATA ATATA ATATG ATATG
1 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG
52330875 TGTTAGAGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (5 bp):
ATATG
Found at i:52330984 original size:24 final size:24
Alignment explanation
Indices: 52330952--52331003 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
52330942 TTTCCAGAAG
*
52330952 ATTTAGCATTTATGAGTATAATAT
1 ATTTAGCATTTATGAGAATAATAT
*
52330976 ATTTAGCATTTATTAGAATAATAT
1 ATTTAGCATTTATGAGAATAATAT
52331000 ATTT
1 ATTT
52331004 GACTTTGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (24 bp):
ATTTAGCATTTATGAGAATAATAT
Found at i:52335332 original size:24 final size:24
Alignment explanation
Indices: 52335298--52335350 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
52335288 TTTCTAGAAA
* *
52335298 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAGCATAATAT
*
52335322 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATGAGCATAATAT
52335346 ATTTA
1 ATTTA
52335351 ACTTTGATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (24 bp):
ATTTAGCATTTATGAGCATAATAT
Found at i:52335360 original size:24 final size:24
Alignment explanation
Indices: 52335305--52335361 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
52335295 AAAATTTAGT
* * *
52335305 ATTTATGAGTATAATATATTTAGC
1 ATTTATTAGCATAATATATTTAAC
52335329 ATTTATTAGCATAATATATTTAAC
1 ATTTATTAGCATAATATATTTAAC
52335353 -TTTGATTAG
1 ATTT-ATTAG
52335362 ATTTAAGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 3 0.10
24 26 0.90
ACGTcount: A:0.37, C:0.05, G:0.11, T:0.47
Consensus pattern (24 bp):
ATTTATTAGCATAATATATTTAAC
Found at i:52335703 original size:17 final size:18
Alignment explanation
Indices: 52335681--52335727 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
52335671 TCATTGATGC
52335681 ATATATATAAACTAT-TA
1 ATATATATAAACTATCTA
* *
52335698 ATATATTATATACTATCTG
1 ATATA-TATAAACTATCTA
52335717 ATATGATATAA
1 ATAT-ATATAA
52335728 CATTATAGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 5 0.21
18 9 0.38
19 9 0.38
20 1 0.04
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (18 bp):
ATATATATAAACTATCTA
Found at i:52337854 original size:18 final size:18
Alignment explanation
Indices: 52337823--52337870 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
52337813 TGTCGTTCGT
*
52337823 TTTCAAAACATTATTC-A
1 TTTCAAAACGTTATTCAA
*
52337840 TTTACAAATCGTTATTCAA
1 TTT-CAAAACGTTATTCAA
52337859 TTTCAAAACGTT
1 TTTCAAAACGTT
52337871 TTCTTATTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 3 0.12
18 19 0.73
19 4 0.15
ACGTcount: A:0.38, C:0.17, G:0.04, T:0.42
Consensus pattern (18 bp):
TTTCAAAACGTTATTCAA
Found at i:52342453 original size:13 final size:14
Alignment explanation
Indices: 52342435--52342463 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
52342425 TTACTTTTTG
52342435 TTCAAGCCTAT-TT
1 TTCAAGCCTATATT
52342448 TTCAAGCCTATATT
1 TTCAAGCCTATATT
52342462 TT
1 TT
52342464 TACCCAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.24, C:0.21, G:0.07, T:0.48
Consensus pattern (14 bp):
TTCAAGCCTATATT
Found at i:52355431 original size:34 final size:34
Alignment explanation
Indices: 52355391--52355476 Score: 163
Period size: 34 Copynumber: 2.5 Consensus size: 34
52355381 ATTTAATTAA
*
52355391 ATAATATATTAATAATAATTAAATTAGTTATTTT
1 ATAATATTTTAATAATAATTAAATTAGTTATTTT
52355425 ATAATATTTTAATAATAATTAAATTAGTTATTTT
1 ATAATATTTTAATAATAATTAAATTAGTTATTTT
52355459 ATAATATTTTAATAATAA
1 ATAATATTTTAATAATAA
52355477 AATGATAATA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (34 bp):
ATAATATTTTAATAATAATTAAATTAGTTATTTT
Found at i:52355441 original size:11 final size:11
Alignment explanation
Indices: 52355390--52355475 Score: 59
Period size: 11 Copynumber: 7.6 Consensus size: 11
52355380 TATTTAATTA
*
52355390 AATAATATATT
1 AATAATATTTT
* *
52355401 AATAATAATTA
1 AATAATATTTT
*
52355412 AATTAGTTATTTT
1 AA-TA-ATATTTT
52355425 -ATAATATTTT
1 AATAATATTTT
* *
52355435 AATAATAATTA
1 AATAATATTTT
*
52355446 AATTAGTTATTTT
1 AA-TA-ATATTTT
52355459 -ATAATATTTT
1 AATAATATTTT
52355469 AATAATA
1 AATAATA
52355476 AAATGATAAT
Statistics
Matches: 56, Mismatches: 13, Indels: 12
0.69 0.16 0.15
Matches are distributed among these distances:
10 12 0.21
11 30 0.54
12 6 0.11
13 8 0.14
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (11 bp):
AATAATATTTT
Found at i:52357161 original size:17 final size:18
Alignment explanation
Indices: 52357141--52357175 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
52357131 TAATTGAGTA
*
52357141 AAAGGATTAAA-TTGAAT
1 AAAGGATAAAAGTTGAAT
52357158 AAAGGATAAAAGTTGAAT
1 AAAGGATAAAAGTTGAAT
52357176 TATAGATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.54, C:0.00, G:0.20, T:0.26
Consensus pattern (18 bp):
AAAGGATAAAAGTTGAAT
Found at i:52357835 original size:9 final size:9
Alignment explanation
Indices: 52357821--52357858 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
52357811 AACAGGGAGA
52357821 AAAGAAAGG
1 AAAGAAAGG
*
52357830 AAAGAAAGA
1 AAAGAAAGG
52357839 AAAGAAA-G
1 AAAGAAAGG
52357847 AAAGAAAGG
1 AAAGAAAGG
52357856 AAA
1 AAA
52357859 AATTAGGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
8 7 0.27
9 19 0.73
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (9 bp):
AAAGAAAGG
Found at i:52357836 original size:4 final size:4
Alignment explanation
Indices: 52357821--52357854 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
52357811 AACAGGGAGA
52357821 AAAG AAAGG AAAG AAAG AAAAG AAAG AAAG AAAG
1 AAAG AAA-G AAAG AAAG -AAAG AAAG AAAG AAAG
52357855 GAAAAATTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:52357839 original size:13 final size:13
Alignment explanation
Indices: 52357821--52357858 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
52357811 AACAGGGAGA
52357821 AAAGAAAGGAAAG
1 AAAGAAAGGAAAG
*
52357834 AAAGAAAAGAAAG
1 AAAGAAAGGAAAG
52357847 AAAGAAAGGAAA
1 AAAGAAAGGAAA
52357859 AATTAGGGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (13 bp):
AAAGAAAGGAAAG
Found at i:52358249 original size:17 final size:18
Alignment explanation
Indices: 52358227--52358260 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
52358217 TAAATGAGTT
52358227 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
52358244 AATTAGGGTATAAATTG
1 AATTAGGATATAAATTG
52358261 AAAAGAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:52358672 original size:13 final size:13
Alignment explanation
Indices: 52358654--52358679 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52358644 TATTTGCTAT
52358654 CTGCTTCACCTCC
1 CTGCTTCACCTCC
52358667 CTGCTTCACCTCC
1 CTGCTTCACCTCC
52358680 AACTTGGTCG
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:0.08, C:0.54, G:0.08, T:0.31
Consensus pattern (13 bp):
CTGCTTCACCTCC
Found at i:52359914 original size:17 final size:17
Alignment explanation
Indices: 52359892--52359925 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
52359882 TTAATCTATA
52359892 ATTCAACTTT-ATCCTTT
1 ATTCAA-TTTAATCCTTT
52359909 ATTCAATTTAATCCTTT
1 ATTCAATTTAATCCTTT
52359926 TACGCAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.26, C:0.21, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTCAATTTAATCCTTT
Found at i:52361343 original size:16 final size:18
Alignment explanation
Indices: 52361311--52361349 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
52361301 ATATTTTTAG
*
52361311 ATTTTTTAAAATTTAT-A
1 ATTTTTTAAAATATATAA
52361328 ATTTTTTAAAA-ATATAA
1 ATTTTTTAAAATATATAA
52361345 ATTTT
1 ATTTT
52361350 AGAATTTCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTTTTAAAATATATAA
Found at i:52361389 original size:20 final size:19
Alignment explanation
Indices: 52361366--52361410 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
52361356 TCTATAAATA
*
52361366 TTTTAAATCTTAAAAATTAT
1 TTTTAAAT-TTAAAAATTAC
*
52361386 TTTTAAAATTTGAAAATTAC
1 TTTT-AAATTTAAAAATTAC
52361406 TTTTA
1 TTTTA
52361411 TTTTTTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 17 0.77
21 4 0.18
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.51
Consensus pattern (19 bp):
TTTTAAATTTAAAAATTAC
Found at i:52362829 original size:3 final size:3
Alignment explanation
Indices: 52362823--52362848 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
52362813 TATAATAATA
52362823 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
52362849 ATAATGGGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:52371578 original size:2 final size:2
Alignment explanation
Indices: 52371573--52371604 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
52371563 CCACTAACCA
*
52371573 AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52371605 CTTAATAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:52378930 original size:3 final size:3
Alignment explanation
Indices: 52378922--52378951 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
52378912 GCTATGATTT
*
52378922 TTA TTA TTA TTA TTA CTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
52378952 CTACCACTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:52378943 original size:15 final size:15
Alignment explanation
Indices: 52378923--52378954 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
52378913 CTATGATTTT
52378923 TATTATTATTATTAC
1 TATTATTATTATTAC
52378938 TATTATTATTATTAC
1 TATTATTATTATTAC
52378953 TA
1 TA
52378955 CCACTATACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.59
Consensus pattern (15 bp):
TATTATTATTATTAC
Found at i:52384949 original size:21 final size:21
Alignment explanation
Indices: 52384923--52384968 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
52384913 GAAGAAGCTT
*
52384923 CGGTTGGAAAGAAGAAGAATG
1 CGGTTGGAAAAAAGAAGAATG
52384944 CGGTTGGAAAAAAGAAGAATG
1 CGGTTGGAAAAAAGAAGAATG
52384965 CGGT
1 CGGT
52384969 CGAACCTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.41, C:0.07, G:0.37, T:0.15
Consensus pattern (21 bp):
CGGTTGGAAAAAAGAAGAATG
Found at i:52390989 original size:89 final size:89
Alignment explanation
Indices: 52390830--52391407 Score: 834
Period size: 89 Copynumber: 6.5 Consensus size: 89
52390820 AGCAGGTTGA
* *
52390830 AAGATAACAGATCTTGTCTTCATATACTGGCGTGAAGTAGATCAGAGATACCAGATCTTGCCTTC
1 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATACCAGATCTTGCCTTC
* *
52390895 CCATACTGGTGGTGAAGCAGATCA
66 CCATACTGGTGGCGAAGCAGATCG
* ** * *
52390919 AAGGAAGTAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATTAGAGATGCCAGATCTTGCCTTC
1 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATACCAGATCTTGCCTTC
*
52390984 CCATACTGGTGGTGAAGCAGATCG
66 CCATACTGGTGGCGAAGCAGATCG
*
52391008 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATAACAGATCTTGCCTTC
1 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATACCAGATCTTGCCTTC
* * *
52391073 CCATACTAGTGGCAAAGCAGATCA
66 CCATACTGGTGGCGAAGCAGATCG
* *
52391097 AAGAAAGCAGATCTTGTCTTCATGTACTGGCGTAAAGTAGATCAGAGATACCAGATCTTGCCTTC
1 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATACCAGATCTTGCCTTC
*
52391162 CCATACTGGTGGCGAAGCAGATTG
66 CCATACTGGTGGCGAAGCAGATCG
* * * * **
52391186 AAGAAAACAGATATTGTCTTCATGTACTGGCGTGAAGCAGATCAAAGATACCAAATCTTGTTTTC
1 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATACCAGATCTTGCCTTC
52391251 CCATACTGGTGGCGAAGCAGATCG
66 CCATACTGGTGGCGAAGCAGATCG
* * * ** *
52391275 AAGAAAACAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAGA-AAAGTAGATCTTGTCTTC
1 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATACCAGATCTTGCCTTC
* *
52391339 CCATACTGGTGGTGAAGTAGATCG
66 CCATACTGGTGGCGAAGCAGATCG
** *
52391363 AAGAAAGTAGATCTTGTCTTCCTGTACTGGCAGTGAAGTAGATCA
1 AAGAAAACAGATCTTGTCTTCATGTACTGGC-GTGAAGTAGATCA
52391408 AATATAGCAG
Statistics
Matches: 437, Mismatches: 51, Indels: 2
0.89 0.10 0.00
Matches are distributed among these distances:
88 62 0.14
89 375 0.86
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.27
Consensus pattern (89 bp):
AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATACCAGATCTTGCCTTC
CCATACTGGTGGCGAAGCAGATCG
Found at i:52391430 original size:45 final size:43
Alignment explanation
Indices: 52390838--52391409 Score: 231
Period size: 45 Copynumber: 12.9 Consensus size: 43
52390828 GAAAGATAAC
* * * **
52390838 AGATCTTGTCTTCATATACTGGC-GTGAAGTAGATCAGAGATACC
1 AGATCTTGTCTTCCTGTACTGGCAGTGAAGTAGATCA-A-AAAGT
* ** ** *
52390882 AGATCTTGCCTTCCCATACTGGTGGTGAAGCAGATCAAAGGAAGT
1 AGATCTTGTCTTCCTGTACTGGCAGTGAAGTAGATCAAA--AAGT
* * * * *
52390927 AGATCTTGTCTTCATGTACTGGC-GTGAAGTAGATTAGAGATGCC
1 AGATCTTGTCTTCCTGTACTGGCAGTGAAGTAGATCA-AAAAG-T
* ** ** * **
52390971 AGATCTTGCCTTCCCATACTGGTGGTGAAGCAGATCGAAGAAAAC
1 AGATCTTGTCTTCCTGTACTGGCAGTGAAGTAGATC-AA-AAAGT
* *
52391016 AGATCTTGTCTTCATGTACTGGC-GTGAAGTAGATCAGAGATAA-C
1 AGATCTTGTCTTCCTGTACTGGCAGTGAAGTAGATCA-A-A-AAGT
* ** * ** ** * *
52391060 AGATCTTGCCTTCCCATACTAGTGGCAAAGCAGATCAAAGAAAGC
1 AGATCTTGTCTTCCTGTACTGGCAGTGAAGTAGATC-AA-AAAGT
* * * **
52391105 AGATCTTGTCTTCATGTACTGGC-GTAAAGTAGATCAGAGATACC
1 AGATCTTGTCTTCCTGTACTGGCAGTGAAGTAGATCA-A-AAAGT
* ** ** * * * **
52391149 AGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATTGAAGAAAAC
1 AGATCTTGTCTTCCTGTACTGGCAGTGAAGTAGA-TCAA-AAAGT
* * * **
52391194 AGATATTGTCTTCATGTACTGGC-GTGAAGCAGATCAAAGATACC
1 AGATCTTGTCTTCCTGTACTGGCAGTGAAGTAGATCAAA-A-AGT
* * ** ** * * **
52391238 AAATCTTGTTTTCCCATACTGGTGGCGAAGCAGATCGAAGAAAAC
1 AGATCTTGTCTTCCTGTACTGGCAGTGAAGTAGATC-AA-AAAGT
* *
52391283 AGATCTTGTCTTCATGTATTGGCA-TGAAGTAGATCAGAAAAGT
1 AGATCTTGTCTTCCTGTACTGGCAGTGAAGTAGATCA-AAAAGT
** **
52391326 AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAGT
1 AGATCTTGTCTTCCTGTACTGGCAGTGAAGTAGATC-AA-AAAGT
52391371 AGATCTTGTCTTCCTGTACTGGCAGTGAAGTAGATCAAA
1 AGATCTTGTCTTCCTGTACTGGCAGTGAAGTAGATCAAA
52391410 TATAGCAGGT
Statistics
Matches: 399, Mismatches: 104, Indels: 51
0.72 0.19 0.09
Matches are distributed among these distances:
42 1 0.00
43 32 0.08
44 167 0.42
45 190 0.48
46 8 0.02
47 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (43 bp):
AGATCTTGTCTTCCTGTACTGGCAGTGAAGTAGATCAAAAAGT
Found at i:52393062 original size:3 final size:3
Alignment explanation
Indices: 52393054--52393086 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
52393044 GCTATGATTT
*
52393054 TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
52393087 CTACCACTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:52396227 original size:15 final size:15
Alignment explanation
Indices: 52396204--52396237 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
52396194 GATTTTATTT
* *
52396204 TTTATTATATTGACA
1 TTTACTATATTGAAA
52396219 TTTACTATATTGAAA
1 TTTACTATATTGAAA
52396234 TTTA
1 TTTA
52396238 TTTTTTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (15 bp):
TTTACTATATTGAAA
Found at i:52402295 original size:16 final size:17
Alignment explanation
Indices: 52402261--52402301 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
52402251 AGATGGAGAT
52402261 AATAAATAAACCCCAAA
1 AATAAATAAACCCCAAA
52402278 AATAAAT-AACCCTCAAA
1 AATAAATAAACCC-CAAA
52402295 ACATAAA
1 A-ATAAA
52402302 CACAAAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.23
17 12 0.55
18 5 0.23
ACGTcount: A:0.63, C:0.22, G:0.00, T:0.15
Consensus pattern (17 bp):
AATAAATAAACCCCAAA
Found at i:52405642 original size:75 final size:75
Alignment explanation
Indices: 52405552--52405716 Score: 312
Period size: 75 Copynumber: 2.2 Consensus size: 75
52405542 TTTTCTGCTT
*
52405552 CTTTCATGCATGCTGGTTCACGGGTCCATTATTTCTTTGCTCTGCTACATGCAAACAAAACACTA
1 CTTTCATGCATGCTGGTTCAAGGGTCCATTATTTCTTTGCTCTGCTACATGCAAACAAAACACTA
52405617 CATTTTCCTG
66 CATTTTCCTG
*
52405627 CTTTCATGCATGCTGGTTCAAGGGTTCATTATTTCTTTGCTCTGCTACATGCAAACAAAACACTA
1 CTTTCATGCATGCTGGTTCAAGGGTCCATTATTTCTTTGCTCTGCTACATGCAAACAAAACACTA
52405692 CATTTTCCTG
66 CATTTTCCTG
52405702 CTTTCATGCATGCTG
1 CTTTCATGCATGCTG
52405717 CCACGGGTTC
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
75 88 1.00
ACGTcount: A:0.22, C:0.25, G:0.15, T:0.37
Consensus pattern (75 bp):
CTTTCATGCATGCTGGTTCAAGGGTCCATTATTTCTTTGCTCTGCTACATGCAAACAAAACACTA
CATTTTCCTG
Found at i:52410053 original size:16 final size:16
Alignment explanation
Indices: 52410032--52410063 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
52410022 AAATGTCAAT
52410032 TTGAAAATGTTAAAAA
1 TTGAAAATGTTAAAAA
52410048 TTGAAAATGTTAAAAA
1 TTGAAAATGTTAAAAA
52410064 AAATAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.31
Consensus pattern (16 bp):
TTGAAAATGTTAAAAA
Found at i:52410407 original size:16 final size:16
Alignment explanation
Indices: 52410386--52410426 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
52410376 ATATTTGATA
52410386 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
52410402 TAATTTCAATAACAAT
1 TAATTTTAATAACAAT
*
52410418 TAGTTTTAA
1 TAATTTTAA
52410427 GTAAAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.44
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:52411317 original size:42 final size:43
Alignment explanation
Indices: 52411252--52411414 Score: 222
Period size: 43 Copynumber: 3.8 Consensus size: 43
52411242 TTTTAGAAAT
* * * *
52411252 AAACGCTGCTATAGATCATGACCTTTAGCGGCGCTTTT-GCAT
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* *
52411294 AAACGCCGCTATAGGTCAAGACCTTTAGCGGTGCTTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* *
52411337 AAACGCCGCTATAGCTCGAGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* *
52411380 AAACGCCGCTATAGAACAA-ACCTTTAGCGACGCTT
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTT
52411415 CTCGTAAAAA
Statistics
Matches: 107, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
42 49 0.46
43 58 0.54
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
Found at i:52411365 original size:85 final size:85
Alignment explanation
Indices: 52411252--52411408 Score: 228
Period size: 85 Copynumber: 1.8 Consensus size: 85
52411242 TTTTAGAAAT
* * * **
52411252 AAACGCTGCTATAGATCATGACCTTTAGCGGCGCTTTT-GCATAAACGCCGCTATAGGTCAAGAC
1 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAACAA-AC
52411316 CTTTAGCGGTGCTTTTCCCAC
65 CTTTAGCGGTGCTTTTCCCAC
*
52411337 AAACGCCGCTATAGCTCGA-GACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAACAAAC
1 AAACGCCGCTATAGATC-ATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAACAAAC
52411401 CTTTAGCG
65 CTTTAGCG
52411409 ACGCTTCTCG
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
85 44 0.69
86 20 0.31
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.25
Consensus pattern (85 bp):
AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAACAAACC
TTTAGCGGTGCTTTTCCCAC
Found at i:52411426 original size:85 final size:85
Alignment explanation
Indices: 52411252--52411428 Score: 214
Period size: 85 Copynumber: 2.1 Consensus size: 85
52411242 TTTTAGAAAT
* * * **
52411252 AAACGCTGCTATAGATCATGACCTTTAGCGGCGCTTTTGCATAAACGCCGCTATAGGTCAAGACC
1 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTCCACAAACGCCGCTATAGAACAAGACC
** * *
52411317 TTTAGCGGTGCTTTTCCCAC
66 TTTAGCGACGCTTCTCCCAA
*
52411337 AAACGCCGCTATAGCTCGA-GACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAACAA-A
1 AAACGCCGCTATAGATC-ATGACCTTTAGCGGCGCTTTT-CCACAAACGCCGCTATAGAACAAGA
**
52411400 CCTTTAGCGACGCTTCTCGTAA
64 CCTTTAGCGACGCTTCTCCCAA
52411422 AAACGCC
1 AAACGCC
52411429 ACTAAAAACA
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
85 58 0.74
86 20 0.26
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (85 bp):
AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTCCACAAACGCCGCTATAGAACAAGACC
TTTAGCGACGCTTCTCCCAA
Found at i:52413627 original size:22 final size:22
Alignment explanation
Indices: 52413599--52413654 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
52413589 TTACTAGCAC
*
52413599 GCTCTCTGTTTAGCACATTCGT
1 GCTCTCTGTTTAGCACATTAGT
* *
52413621 GCTCTCTGTATAGCACTTTAGT
1 GCTCTCTGTTTAGCACATTAGT
52413643 GCTCTCTGTTTA
1 GCTCTCTGTTTA
52413655 ATAGTGCATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.43
Consensus pattern (22 bp):
GCTCTCTGTTTAGCACATTAGT
Found at i:52414949 original size:47 final size:50
Alignment explanation
Indices: 52414890--52414993 Score: 126
Period size: 47 Copynumber: 2.1 Consensus size: 50
52414880 AAAATATGAT
* * *
52414890 TATGTGATTTCCGGGTAAGACCATATCTGGGA-TATGGCATC-G-GTGTGA
1 TATGTGATTTCCGGATAAGACCATAGCT-GGACTATAGCATCGGTGTGTGA
* *
52414938 TATGTG-TTTCCGTATAAGACCATAGCTGGACTATAGCTTCGGTGTGTGA
1 TATGTGATTTCCGGATAAGACCATAGCTGGACTATAGCATCGGTGTGTGA
52414987 TATGTGA
1 TATGTGA
52414994 CAATGTGCAA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
46 3 0.06
47 25 0.53
48 7 0.15
49 12 0.26
ACGTcount: A:0.23, C:0.14, G:0.29, T:0.34
Consensus pattern (50 bp):
TATGTGATTTCCGGATAAGACCATAGCTGGACTATAGCATCGGTGTGTGA
Found at i:52420859 original size:20 final size:20
Alignment explanation
Indices: 52420834--52420873 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
52420824 AATATTTTTC
*
52420834 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
* *
52420854 AGTAAAACCTTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
52420874 TCATTTTACG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.15, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:52421142 original size:19 final size:21
Alignment explanation
Indices: 52421113--52421154 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
52421103 AAGTTGTCGT
52421113 AAATATTAAAAT-AAAAATAA
1 AAATATTAAAATCAAAAATAA
*
52421133 AAAT-TTAAAATCAAAACTAA
1 AAATATTAAAATCAAAAATAA
52421153 AA
1 AA
52421155 TAAATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
AAATATTAAAATCAAAAATAA
Found at i:52424656 original size:19 final size:19
Alignment explanation
Indices: 52424632--52424680 Score: 89
Period size: 19 Copynumber: 2.5 Consensus size: 19
52424622 TAATATTATA
52424632 ATTTTTAGTTTTTGTATTTC
1 ATTTTTA-TTTTTGTATTTC
52424652 ATTTTTATTTTTGTATTTC
1 ATTTTTATTTTTGTATTTC
52424671 ATTTTTATTT
1 ATTTTTATTT
52424681 GTTATAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 22 0.76
20 7 0.24
ACGTcount: A:0.16, C:0.04, G:0.06, T:0.73
Consensus pattern (19 bp):
ATTTTTATTTTTGTATTTC
Found at i:52425105 original size:7 final size:7
Alignment explanation
Indices: 52425092--52425153 Score: 63
Period size: 7 Copynumber: 8.9 Consensus size: 7
52425082 AAACATAAAT
52425092 CCTTAAC
1 CCTTAAC
*
52425099 CCCTAAC
1 CCTTAAC
*
52425106 CCATAAC
1 CCTTAAC
*
52425113 CCATAAC
1 CCTTAAC
52425120 CCTTAAC
1 CCTTAAC
*
52425127 CCTTAAA
1 CCTTAAC
52425134 CCTTAAAC
1 CCTT-AAC
52425142 CC-TAAC
1 CCTTAAC
*
52425148 CTTTAA
1 CCTTAA
52425154 ACCATAAATC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
6 4 0.09
7 39 0.83
8 4 0.09
ACGTcount: A:0.35, C:0.40, G:0.00, T:0.24
Consensus pattern (7 bp):
CCTTAAC
Found at i:52425114 original size:14 final size:14
Alignment explanation
Indices: 52425092--52425153 Score: 70
Period size: 14 Copynumber: 4.4 Consensus size: 14
52425082 AAACATAAAT
52425092 CCTTAACCCCTAAC
1 CCTTAACCCCTAAC
* *
52425106 CCATAACCCATAAC
1 CCTTAACCCCTAAC
* *
52425120 CCTTAACCCTTAAA
1 CCTTAACCCCTAAC
*
52425134 CCTTAAACCCTAAC
1 CCTTAACCCCTAAC
*
52425148 CTTTAA
1 CCTTAA
52425154 ACCATAAATC
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 39 1.00
ACGTcount: A:0.35, C:0.40, G:0.00, T:0.24
Consensus pattern (14 bp):
CCTTAACCCCTAAC
Found at i:52425120 original size:21 final size:21
Alignment explanation
Indices: 52425085--52425160 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
52425075 AATTATAAAA
*
52425085 CATAAATCCTTAACCCCTAACC
1 CATAAA-CCATAACCCCTAACC
* *
52425107 CATAACCCATAACCCTTAACC
1 CATAAACCATAACCCCTAACC
* * *
52425128 CTTAAACCTTAAACCCTAACC
1 CATAAACCATAACCCCTAACC
**
52425149 TTTAAACCATAA
1 CATAAACCATAA
52425161 ATCATAAACC
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
21 39 0.89
22 5 0.11
ACGTcount: A:0.39, C:0.37, G:0.00, T:0.24
Consensus pattern (21 bp):
CATAAACCATAACCCCTAACC
Found at i:52425161 original size:21 final size:21
Alignment explanation
Indices: 52425099--52425161 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
52425089 AATCCTTAAC
* *
52425099 CCCTAACCCATAACCCAT-AA
1 CCCTAACCCTTAAACCATAAA
*
52425119 CCCTTAACCCTTAAACCTTAAA
1 CCC-TAACCCTTAAACCATAAA
*
52425141 CCCTAACCTTTAAACCATAAA
1 CCCTAACCCTTAAACCATAAA
52425162 TCATAAACCA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
20 3 0.08
21 28 0.78
22 5 0.14
ACGTcount: A:0.40, C:0.38, G:0.00, T:0.22
Consensus pattern (21 bp):
CCCTAACCCTTAAACCATAAA
Found at i:52425168 original size:14 final size:14
Alignment explanation
Indices: 52425151--52425186 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
52425141 CCCTAACCTT
52425151 TAAACCATAAATCA-
1 TAAACCAT-AATCAC
52425165 TAAACCATAATCAC
1 TAAACCATAATCAC
52425179 TAAACCAT
1 TAAACCAT
52425187 CAGAGTAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 5 0.24
14 16 0.76
ACGTcount: A:0.53, C:0.25, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAACCATAATCAC
Found at i:52426227 original size:40 final size:41
Alignment explanation
Indices: 52426183--52426259 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
52426173 TTAAATCCCT
* * * *
52426183 GAGCATTAGTGGCACTTT-TTAGAAAACGCCGCTAAAAATA
1 GAGCATTAGCGACACTTTCTCAAAAAACGCCGCTAAAAATA
*
52426223 GAGCATTAGCGACGCTTTCTCAAAAAACGCCGCTAAA
1 GAGCATTAGCGACACTTTCTCAAAAAACGCCGCTAAA
52426260 GCCCTGAGCA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
40 15 0.48
41 16 0.52
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.22
Consensus pattern (41 bp):
GAGCATTAGCGACACTTTCTCAAAAAACGCCGCTAAAAATA
Found at i:52426290 original size:41 final size:41
Alignment explanation
Indices: 52426223--52426418 Score: 216
Period size: 41 Copynumber: 4.8 Consensus size: 41
52426213 GCTAAAAATA
* *
52426223 GAGCATTAGCGACGCTTTCTCAAAAAACGCCGCTAAAGCCCT
1 GAGCATTAGCGGCGCTTCCTC-AAAAACGCCGCTAAAGCCCT
* *
52426265 GAGCATTTGCGGCGCTTCCTCAAAAACGCTGCTAAAGCCCT
1 GAGCATTAGCGGCGCTTCCTCAAAAACGCCGCTAAAGCCCT
* * * * *
52426306 -AGCATTAGCGGAGCCTCCTCAAAAACGCCTCTAAATCCCC
1 GAGCATTAGCGGCGCTTCCTCAAAAACGCCGCTAAAGCCCT
* * *
52426346 GAGCATTAGCGGCTCCTT-CACAAAAACGCCGCTATAGCCCT
1 GAGCATTAGCGGC-GCTTCCTCAAAAACGCCGCTAAAGCCCT
* ** *
52426387 GAGCATTAGCGACGCTTTATTAAAAACGCCGC
1 GAGCATTAGCGGCGCTTCCTCAAAAACGCCGC
52426419 AAAATCCCCG
Statistics
Matches: 127, Mismatches: 24, Indels: 7
0.80 0.15 0.04
Matches are distributed among these distances:
40 36 0.28
41 71 0.56
42 20 0.16
ACGTcount: A:0.29, C:0.32, G:0.19, T:0.20
Consensus pattern (41 bp):
GAGCATTAGCGGCGCTTCCTCAAAAACGCCGCTAAAGCCCT
Found at i:52426327 original size:82 final size:83
Alignment explanation
Indices: 52426223--52426429 Score: 217
Period size: 81 Copynumber: 2.5 Consensus size: 83
52426213 GCTAAAAATA
* * * * * *
52426223 GAGCATTAGC-GACGCTTTCTCAAAAAACGCCGCTAAAGCCCTGAGCATTTGCGGC-GCTTCCTC
1 GAGCATTAGCGGACGCCTCCTC-AAAAACGCCGCTAAAGCCCCGAGCATTAGCGGCTCCTT-CAC
*
52426286 AAAAACGCTGCTAAAGCCCT
64 AAAAACGCCGCTAAAGCCCT
* *
52426306 -AGCATTAGCGGA-GCCTCCTCAAAAACGCCTCTAAATCCCCGAGCATTAGCGGCTCCTTCACAA
1 GAGCATTAGCGGACGCCTCCTCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGGCTCCTTCACAA
*
52426369 AAACGCCGCTATAGCCCT
66 AAACGCCGCTAAAGCCCT
* ** * * *
52426387 GAGCATTAGC-GACGCTTTATTAAAAACGCCGCAAAATCCCCGA
1 GAGCATTAGCGGACGCCTCCTCAAAAACGCCGCTAAAGCCCCGA
52426430 AAGCTTAGAA
Statistics
Matches: 104, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
81 51 0.49
82 51 0.49
83 2 0.02
ACGTcount: A:0.29, C:0.32, G:0.19, T:0.19
Consensus pattern (83 bp):
GAGCATTAGCGGACGCCTCCTCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGGCTCCTTCACAA
AAACGCCGCTAAAGCCCT
Found at i:52426533 original size:39 final size:40
Alignment explanation
Indices: 52426481--52426596 Score: 128
Period size: 40 Copynumber: 3.0 Consensus size: 40
52426471 CGCTTTCTGG
* * *
52426481 AAAA-CGCCTCTAATGCT-TATTTTTAGCGGCGTTTTTCA
1 AAAAGCGCCGCTAATGCTAGATCTTTAGCGGCGTTTTTCA
* * * * *
52426519 TAATGCGCCGCTAATGCTAGATCTTTAACGGCATTTTCCA
1 AAAAGCGCCGCTAATGCTAGATCTTTAGCGGCGTTTTTCA
* *
52426559 AAAAGCGCCGCTAATGCTCGATCTTTAGCGGTGTTTTT
1 AAAAGCGCCGCTAATGCTAGATCTTTAGCGGCGTTTTT
52426597 TATCCAAACG
Statistics
Matches: 61, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
38 2 0.03
39 12 0.20
40 47 0.77
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.35
Consensus pattern (40 bp):
AAAAGCGCCGCTAATGCTAGATCTTTAGCGGCGTTTTTCA
Found at i:52427287 original size:13 final size:13
Alignment explanation
Indices: 52427254--52427278 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52427244 CAACCTCAAT
52427254 GTTAAACACTAGG
1 GTTAAACACTAGG
52427267 GTTAAACACTAG
1 GTTAAACACTAG
52427279 AGGTGAACAT
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:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (13 bp):
GTTAAACACTAGG
Found at i:52429376 original size:19 final size:20
Alignment explanation
Indices: 52429338--52429377 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
52429328 TATTAATAAC
*
52429338 ATTTATCAAATTAAATTTAT
1 ATTTATCAAATTAAAATTAT
*
52429358 ATTTTTCAAA-TAAAATTAT
1 ATTTATCAAATTAAAATTAT
52429377 A
1 A
52429378 GTTAATTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTTATCAAATTAAAATTAT
Found at i:52431518 original size:22 final size:23
Alignment explanation
Indices: 52431485--52431543 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
52431475 AGAATGATAC
*
52431485 ATGA-AAACTTAAAATAAT-TAT
1 ATGATAAATTTAAAATAATATAT
52431506 ATGATAAATTTAAAATAATAATAT
1 ATGATAAATTTAAAATAAT-ATAT
*
52431530 GTGATAAATTTAAA
1 ATGATAAATTTAAA
52431544 CAACATTCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 4 0.12
22 13 0.39
24 16 0.48
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.36
Consensus pattern (23 bp):
ATGATAAATTTAAAATAATATAT
Found at i:52434151 original size:6 final size:6
Alignment explanation
Indices: 52434140--52434166 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
52434130 TCCCCACCAT
52434140 AAATAA AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAA
52434167 ATACATCCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:52434357 original size:251 final size:251
Alignment explanation
Indices: 52434074--52435415 Score: 2614
Period size: 251 Copynumber: 5.3 Consensus size: 251
52434064 GCCACATAAT
52434074 CAAAATAATTAAACTCCACAAAACGTAAACCTAACCCTGATTAAAAAGAAAACCGGTCCCCACCA
1 CAAAATAATTAAACTCCACAAAACGTAAACCTAACCCTGATTAAAAAGAAAACCGGTCCCCACCA
52434139 TAAATAAAAATAAAAATAAAAATAAAAAATACATCCCACAACTACATGAGTTAGGGTCAAATGGT
66 TAAATAAAAATAAAAATAAAAATAAAAAATACATCCCACAACTACATGAGTTAGGGTCAAATGGT
52434204 AAAGAGTCTCCCCTCTCTTAATTAATAGTTTGAGAGTTGGATCTCACTTCAGATATGAAACAAAT
131 AAAGAGTCTCCCCTCTCTTAATTAATAGTTTGAGAGTTGGATCTCACTTCAGATATGAAACAAAT
52434269 TTAAAACTGGTGGTCATAGAATAAAGTAGTCAATGTCCAACCGTCTCAATCCTAAG
196 TTAAAACTGGTGGTCATAGAATAAAGTAGTCAATGTCCAACCGTCTCAATCCTAAG
52434325 CAAAATAATTAAACTCCACAAAACGTAAACCTAACCCTGATTAAAAAGAAAACCGGTCCCCACCA
1 CAAAATAATTAAACTCCACAAAACGTAAACCTAACCCTGATTAAAAAGAAAACCGGTCCCCACCA
52434390 TAAATAAAAATAAAAATAAAAATAAAAAATACATCCCACAACTACATGAGTTAGGGTCAAATGGT
66 TAAATAAAAATAAAAATAAAAATAAAAAATACATCCCACAACTACATGAGTTAGGGTCAAATGGT
52434455 AAAGAGTCTCCCCTCTCTTAATTAATAGTTTGAGAGTTGGATCTCACTTCAGATATGAAACAAAT
131 AAAGAGTCTCCCCTCTCTTAATTAATAGTTTGAGAGTTGGATCTCACTTCAGATATGAAACAAAT
52434520 TTAAAACTGGTGGTCATAGAATAAAGTAGTCAATGTCCAACCGTCTCAATCCTAAG
196 TTAAAACTGGTGGTCATAGAATAAAGTAGTCAATGTCCAACCGTCTCAATCCTAAG
52434576 CAAAATAATTAAACTCCACAAAACGTAAACCTAACCCTGATTAAAAAGAAAACCGGTCCCCACCA
1 CAAAATAATTAAACTCCACAAAACGTAAACCTAACCCTGATTAAAAAGAAAACCGGTCCCCACCA
52434641 TAAATAAAAATAAAAATAAAAATAAAAAATACATCCCACAACTACATGAGTTAGGGTCAAATGGT
66 TAAATAAAAATAAAAATAAAAATAAAAAATACATCCCACAACTACATGAGTTAGGGTCAAATGGT
52434706 AAAGAGTCTCCCCTCTCTTAATTAATAGTTTGAGAGTTGGATCTCACTTCAGATATGAAACAAAT
131 AAAGAGTCTCCCCTCTCTTAATTAATAGTTTGAGAGTTGGATCTCACTTCAGATATGAAACAAAT
52434771 TTAAAACTGGTGGTCATAGAATAAAGTAGTCAATGTCCAACCGTCTCAATCCTAAG
196 TTAAAACTGGTGGTCATAGAATAAAGTAGTCAATGTCCAACCGTCTCAATCCTAAG
52434827 CAAAATAATTAAACTCCACAAAACGTAAACCTAACCCTGATTAAAAAGAAAACCGGTCCCCACCA
1 CAAAATAATTAAACTCCACAAAACGTAAACCTAACCCTGATTAAAAAGAAAACCGGTCCCCACCA
52434892 TAAATAAAAATAAAAATAAAAATAAAAAATACATCCCACAACTACATGAGTTAGGGTCAAATGGT
66 TAAATAAAAATAAAAATAAAAATAAAAAATACATCCCACAACTACATGAGTTAGGGTCAAATGGT
52434957 AAAGAGTCTCCCCTCTCTTAATTAATAGTTTGAGAGTTGGATCTCACTTCAGATATGAAACAAAT
131 AAAGAGTCTCCCCTCTCTTAATTAATAGTTTGAGAGTTGGATCTCACTTCAGATATGAAACAAAT
52435022 TTAAAACTGGTGGTCATAGAATAAAGTAGTCAATGTCCAACCGTCTCAATCCTAAG
196 TTAAAACTGGTGGTCATAGAATAAAGTAGTCAATGTCCAACCGTCTCAATCCTAAG
52435078 CAAAATAATTAAACTCCACAAAACGTAAACCTAACCCTGATTAAAAAGAAAACCGGTCCCCACCA
1 CAAAATAATTAAACTCCACAAAACGTAAACCTAACCCTGATTAAAAAGAAAACCGGTCCCCACCA
52435143 TAAATAAAAATAAAAATAAAAATAAAAAATACATCCCACAACTACATGAGTTAGGGTCAAATGGT
66 TAAATAAAAATAAAAATAAAAATAAAAAATACATCCCACAACTACATGAGTTAGGGTCAAATGGT
52435208 AAAGAGTCTCCCCTCTCTTAATTAATAGTTTGAGAGTTGGATCTCACTTCAGATATGAAACAAAT
131 AAAGAGTCTCCCCTCTCTTAATTAATAGTTTGAGAGTTGGATCTCACTTCAGATATGAAACAAAT
* *
52435273 TTAAAACTGGTGATCATAGAATAAAGTAGTCAATGTCCAACCGTCTCCATCCTAAG
196 TTAAAACTGGTGGTCATAGAATAAAGTAGTCAATGTCCAACCGTCTCAATCCTAAG
* * *
52435329 CAAAATAATTAAACTCCACAAAACGTAAACCTAACCCTGGTTAAAAAGAAAACCTGTCCCCGCCA
1 CAAAATAATTAAACTCCACAAAACGTAAACCTAACCCTGATTAAAAAGAAAACCGGTCCCCACCA
*
52435394 -AATTTAAAAATAAAAATAAAAA
66 TAA-ATAAAAATAAAAATAAAAA
52435416 CAAGAAACAA
Statistics
Matches: 1084, Mismatches: 6, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
250 2 0.00
251 1082 1.00
ACGTcount: A:0.44, C:0.20, G:0.12, T:0.24
Consensus pattern (251 bp):
CAAAATAATTAAACTCCACAAAACGTAAACCTAACCCTGATTAAAAAGAAAACCGGTCCCCACCA
TAAATAAAAATAAAAATAAAAATAAAAAATACATCCCACAACTACATGAGTTAGGGTCAAATGGT
AAAGAGTCTCCCCTCTCTTAATTAATAGTTTGAGAGTTGGATCTCACTTCAGATATGAAACAAAT
TTAAAACTGGTGGTCATAGAATAAAGTAGTCAATGTCCAACCGTCTCAATCCTAAG
Found at i:52434402 original size:6 final size:6
Alignment explanation
Indices: 52434391--52434417 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
52434381 TCCCCACCAT
52434391 AAATAA AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAA
52434418 ATACATCCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:52434653 original size:6 final size:6
Alignment explanation
Indices: 52434642--52434668 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
52434632 TCCCCACCAT
52434642 AAATAA AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAA
52434669 ATACATCCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:52434904 original size:6 final size:6
Alignment explanation
Indices: 52434893--52434919 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
52434883 TCCCCACCAT
52434893 AAATAA AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAA
52434920 ATACATCCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:52435155 original size:6 final size:6
Alignment explanation
Indices: 52435144--52435170 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
52435134 TCCCCACCAT
52435144 AAATAA AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAA
52435171 ATACATCCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:52454332 original size:25 final size:26
Alignment explanation
Indices: 52454300--52454354 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
52454290 TTATTAAATT
*
52454300 ATATATTTTAATTATAA-TATATTTA
1 ATATATTTTAATAATAATTATATTTA
*
52454325 ATATA-TTTAATAATAATTATGTTTA
1 ATATATTTTAATAATAATTATATTTA
52454350 A-ATAT
1 ATATAT
52454355 GATTAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
ATATATTTTAATAATAATTATATTTA
Found at i:52454541 original size:44 final size:45
Alignment explanation
Indices: 52454492--52454586 Score: 129
Period size: 45 Copynumber: 2.1 Consensus size: 45
52454482 TTACACCTCT
* *
52454492 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
** *
52454536 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
*
52454581 AATACA
1 ATTACA
52454587 CCTCTAATCC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 18 0.41
45 26 0.59
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.34
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
Found at i:52454588 original size:16 final size:16
Alignment explanation
Indices: 52454567--52454602 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
52454557 GATTTGCTAT
*
52454567 TACACCTCTATTCCAA
1 TACACCTCTAATCCAA
52454583 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
52454599 TACA
1 TACA
52454603 GCGAACCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:52457675 original size:45 final size:45
Alignment explanation
Indices: 52457611--52457732 Score: 226
Period size: 45 Copynumber: 2.7 Consensus size: 45
52457601 GCCATATCCT
52457611 TCTTCCTCGGATCTACCATAACTTGGCTTCCTATATCCTTCTGCC
1 TCTTCCTCGGATCTACCATAACTTGGCTTCCTATATCCTTCTGCC
*
52457656 TCTTCCTCGGATCTACCATAACTTGGCTTCCTATATCCTTCTTCC
1 TCTTCCTCGGATCTACCATAACTTGGCTTCCTATATCCTTCTGCC
*
52457701 TCTTCCTCGGATCTACCATAACTTGGTTTCCT
1 TCTTCCTCGGATCTACCATAACTTGGCTTCCT
52457733 CTCATACCCG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 75 1.00
ACGTcount: A:0.16, C:0.34, G:0.11, T:0.39
Consensus pattern (45 bp):
TCTTCCTCGGATCTACCATAACTTGGCTTCCTATATCCTTCTGCC
Found at i:52458049 original size:54 final size:54
Alignment explanation
Indices: 52457984--52458095 Score: 172
Period size: 54 Copynumber: 2.1 Consensus size: 54
52457974 TGTTCGCCAT
*
52457984 ATTCGGGTCTCCGGCCATACCCAGATT-CAAATTCAGGAGGCGGAGGCTGCTCAA
1 ATTCGGGTCTCCGGCCATACCCAG-TTCCAAACTCAGGAGGCGGAGGCTGCTCAA
* * *
52458038 ATTCGGGTCTCCGTCGATACCCAGTTCCAAACTCAGGCGGCGGAGGCTGCTCAA
1 ATTCGGGTCTCCGGCCATACCCAGTTCCAAACTCAGGAGGCGGAGGCTGCTCAA
52458092 ATTC
1 ATTC
52458096 TGATCTACGG
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
53 2 0.04
54 51 0.96
ACGTcount: A:0.22, C:0.29, G:0.27, T:0.21
Consensus pattern (54 bp):
ATTCGGGTCTCCGGCCATACCCAGTTCCAAACTCAGGAGGCGGAGGCTGCTCAA
Found at i:52462128 original size:30 final size:30
Alignment explanation
Indices: 52462094--52462198 Score: 86
Period size: 30 Copynumber: 3.5 Consensus size: 30
52462084 AATGTGACCA
*
52462094 ATTACAGGCTATGACAGGCAAATGCAAATG
1 ATTACAGGCTATGACAGGAAAATGCAAATG
* ** ****
52462124 ATTACAAGG-TATGAAAATAAAAATGTGTCTG
1 ATTAC-AGGCTATG-ACAGGAAAATGCAAATG
*
52462155 ATTACAGGCTATGACAGGTAAATGCAAATG
1 ATTACAGGCTATGACAGGAAAATGCAAATG
* *
52462185 ATTGCAGGGTATGA
1 ATTACAGGCTATGA
52462199 TAATGCAAAT
Statistics
Matches: 54, Mismatches: 18, Indels: 6
0.69 0.23 0.08
Matches are distributed among these distances:
30 33 0.61
31 21 0.39
ACGTcount: A:0.40, C:0.11, G:0.24, T:0.25
Consensus pattern (30 bp):
ATTACAGGCTATGACAGGAAAATGCAAATG
Found at i:52462165 original size:61 final size:61
Alignment explanation
Indices: 52462065--52462198 Score: 214
Period size: 61 Copynumber: 2.2 Consensus size: 61
52462055 TAGTACAGTG
52462065 TACAGGGTATGAAAATAAAAATGTGACCAATTACAGGCTATGACAGGCAAATGCAAATGAT
1 TACAGGGTATGAAAATAAAAATGTGACCAATTACAGGCTATGACAGGCAAATGCAAATGAT
* * ** *
52462126 TACAAGGTATGAAAATAAAAATGTGTCTGATTACAGGCTATGACAGGTAAATGCAAATGAT
1 TACAGGGTATGAAAATAAAAATGTGACCAATTACAGGCTATGACAGGCAAATGCAAATGAT
*
52462187 TGCAGGGTATGA
1 TACAGGGTATGA
52462199 TAATGCAAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 66 1.00
ACGTcount: A:0.42, C:0.11, G:0.23, T:0.24
Consensus pattern (61 bp):
TACAGGGTATGAAAATAAAAATGTGACCAATTACAGGCTATGACAGGCAAATGCAAATGAT
Found at i:52465201 original size:13 final size:13
Alignment explanation
Indices: 52465183--52465208 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52465173 TTAAATTCTT
52465183 AAAAATAAAAATA
1 AAAAATAAAAATA
52465196 AAAAATAAAAATA
1 AAAAATAAAAATA
52465209 TTAATTATTT
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAATAAAAATA
Found at i:52476199 original size:13 final size:13
Alignment explanation
Indices: 52476181--52476207 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
52476171 ATATATTTTT
52476181 AGATTTAAAATTA
1 AGATTTAAAATTA
52476194 AGATTTAAAATTA
1 AGATTTAAAATTA
52476207 A
1 A
52476208 CAATAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (13 bp):
AGATTTAAAATTA
Found at i:52476372 original size:43 final size:43
Alignment explanation
Indices: 52476312--52476398 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
52476302 TTTCCCTTTG
52476312 TTTTTACAGGATTTCCCTCTTGTATCATCAAATCATCATCCAT
1 TTTTTACAGGATTTCCCTCTTGTATCATCAAATCATCATCCAT
52476355 TTTTTACAGGATTTCCCTCTTGTATCATCAAATCATCATCCAT
1 TTTTTACAGGATTTCCCTCTTGTATCATCAAATCATCATCCAT
52476398 T
1 T
52476399 AATATAACAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.25, C:0.25, G:0.07, T:0.43
Consensus pattern (43 bp):
TTTTTACAGGATTTCCCTCTTGTATCATCAAATCATCATCCAT
Found at i:52482552 original size:11 final size:11
Alignment explanation
Indices: 52482527--52482566 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
52482517 TTCACACATT
52482527 ATTTCT-TTAA
1 ATTTCTCTTAA
*
52482537 TTTTCTCTTAA
1 ATTTCTCTTAA
52482548 ATTTCTCTCTAA
1 ATTTCTCT-TAA
52482560 ATTTCTC
1 ATTTCTC
52482567 AAAGCTTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 5 0.19
11 11 0.42
12 10 0.38
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (11 bp):
ATTTCTCTTAA
Found at i:52484358 original size:18 final size:18
Alignment explanation
Indices: 52484335--52484377 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
52484325 TGCCAGGTGC
**
52484335 GTATCCTAGTCCTTATAT
1 GTATCCTAACCCTTATAT
52484353 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
52484371 GTTTCCT
1 GTATCCT
52484378 TTTTTCAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.21, C:0.26, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:52484875 original size:93 final size:92
Alignment explanation
Indices: 52484716--52484909 Score: 352
Period size: 93 Copynumber: 2.1 Consensus size: 92
52484706 CAACATTGAT
* * *
52484716 TTTTTAATATATTTGTACAAACTATTTTTATATTGTTTTATTTAGTAAAATAAAAGTTGTTTTTA
1 TTTTTAATATATTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAATAAAAGTTATTTTTA
52484781 ATATTTTAATAGTAATTTATTTTTTATA
66 ATATTTTAATAGTAATTTA-TTTTTATA
52484809 TTTTTAATATATTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAATAAAAGTTATTTTTA
1 TTTTTAATATATTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAATAAAAGTTATTTTTA
52484874 ATATTTTAATAGTAATTTATTTTTATA
66 ATATTTTAATAGTAATTTATTTTTATA
52484901 TTTTTAATA
1 TTTTTAATA
52484910 AAATAGAAGT
Statistics
Matches: 98, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
92 17 0.17
93 81 0.83
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.57
Consensus pattern (92 bp):
TTTTTAATATATTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAATAAAAGTTATTTTTA
ATATTTTAATAGTAATTTATTTTTATA
Found at i:52484951 original size:8 final size:9
Alignment explanation
Indices: 52484935--52484964 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
52484925 TGAATAAGAC
52484935 AATATTTTT
1 AATATTTTT
52484944 AATATTTTT
1 AATATTTTT
52484953 -ATATTTTT
1 AATATTTTT
52484961 AATA
1 AATA
52484965 AAATAGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
AATATTTTT
Found at i:52488231 original size:126 final size:126
Alignment explanation
Indices: 52488000--52488398 Score: 550
Period size: 126 Copynumber: 3.2 Consensus size: 126
52487990 GCCAAGCAGG
* ** * *
52488000 AACTACTGTAGAAAAAGAGCGCCCACGTGGGAGCTTTTTTTAGTAATTTTGTTGACAGTGCATCC
1 AACTACTGTAGAAAAAGAACATCCACATGGGAGCTTTTTTTAGTAATTTTGCTGACAGTGCATCC
* * * *
52488065 TGCTTAAAGCATTTTTGACACTATTTGTTCAAAACCGTCTTCTCAAAATTATTTTTTTAGA
66 TGCTTGAAGCATTTTTTACACTATTTGTTCAGAACTGTCTTCTCAAAATTATTTTTTTAGA
52488126 AACTACTGTAGAAAAAGAACATCCACATGGGAGCTTTTTTTAGTAATTTTGCTGACAGTGCATCC
1 AACTACTGTAGAAAAAGAACATCCACATGGGAGCTTTTTTTAGTAATTTTGCTGACAGTGCATCC
* *
52488191 TGCTTGAAGCATTTTTTACACTATTTGTTCAGAACTGTCTTCTCAAAATTATTTTTTCAGG
66 TGCTTGAAGCATTTTTTACACTATTTGTTCAGAACTGTCTTCTCAAAATTATTTTTTTAGA
** * * *
52488252 AACTACTGTAGAAAAAGAGTATCCA-AGTGGAAGCTTTTTTCAGTAATTTTGCTAACAGTGCATC
1 AACTACTGTAGAAAAAGAACATCCACA-TGGGAGCTTTTTTTAGTAATTTTGCTGACAGTGCATC
* * * * * *
52488316 CTGCTTGAAGCGTTTTTTACATTATCTT-TTTAGAATTATTTTCTCAAAATTATTTTTTTAGA
65 CTGCTTGAAGCATTTTTTACACTAT-TTGTTCAGAACTGTCTTCTCAAAATTATTTTTTTAGA
* *
52488378 AACTAATGTAGAAAAAAAACA
1 AACTACTGTAGAAAAAGAACA
52488399 AAAAAATTTA
Statistics
Matches: 243, Mismatches: 28, Indels: 4
0.88 0.10 0.01
Matches are distributed among these distances:
125 1 0.00
126 240 0.99
127 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (126 bp):
AACTACTGTAGAAAAAGAACATCCACATGGGAGCTTTTTTTAGTAATTTTGCTGACAGTGCATCC
TGCTTGAAGCATTTTTTACACTATTTGTTCAGAACTGTCTTCTCAAAATTATTTTTTTAGA
Found at i:52488494 original size:34 final size:32
Alignment explanation
Indices: 52488448--52488563 Score: 128
Period size: 34 Copynumber: 3.5 Consensus size: 32
52488438 TTAAACACAA
52488448 AATTATTTTAAAAAAACTAAACCATAATTTAATT
1 AATT-TTTTAAAAAAACTAAACC-TAATTTAATT
**
52488482 AATTTTCTTAAAAATCCTAAACCCTAATTTAATT
1 AATTTT-TTAAAAAAACTAAA-CCTAATTTAATT
**
52488516 AATTTATTT-AAAACCCTAAAACCTAATTTAATT
1 AATTT-TTTAAAAAAACT-AAACCTAATTTAATT
52488549 AA-TTTTTAAAAAAAC
1 AATTTTTTAAAAAAAC
52488564 CTTAAACTAC
Statistics
Matches: 72, Mismatches: 5, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
31 3 0.04
32 7 0.10
33 23 0.32
34 36 0.50
35 3 0.04
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (32 bp):
AATTTTTTAAAAAAACTAAACCTAATTTAATT
Found at i:52488564 original size:34 final size:33
Alignment explanation
Indices: 52488453--52488570 Score: 125
Period size: 33 Copynumber: 3.6 Consensus size: 33
52488443 CACAAAATTA
*
52488453 TTTTAAAAAA-ACT-AAACCATAATTTAATTAAT
1 TTTTAAAAAACCCTAAAACC-TAATTTAATTAAT
* * *
52488485 TTTCTTAAAAATCCTAAACCCTAATTTAATTAAT
1 TTT-TAAAAAACCCTAAAACCTAATTTAATTAAT
*
52488519 TTATT-TAAAACCCTAAAACCTAATTTAATTAAT
1 TT-TTAAAAAACCCTAAAACCTAATTTAATTAAT
* *
52488552 TTTTAAAAAAACCTTAAAC
1 TTTTAAAAAACCCTAAAAC
52488571 TACTAAAAAC
Statistics
Matches: 72, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
32 5 0.07
33 44 0.61
34 18 0.25
35 5 0.07
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.38
Consensus pattern (33 bp):
TTTTAAAAAACCCTAAAACCTAATTTAATTAAT
Found at i:52492431 original size:11 final size:11
Alignment explanation
Indices: 52492413--52492442 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
52492403 CTAAAAATTC
52492413 AAAA-AAAATA
1 AAAACAAAATA
52492423 AAAACAAAATA
1 AAAACAAAATA
52492434 AAAACAAAA
1 AAAACAAAA
52492443 ACACATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.21
11 15 0.79
ACGTcount: A:0.87, C:0.07, G:0.00, T:0.07
Consensus pattern (11 bp):
AAAACAAAATA
Found at i:52493447 original size:46 final size:47
Alignment explanation
Indices: 52493397--52493488 Score: 125
Period size: 47 Copynumber: 2.0 Consensus size: 47
52493387 CGAATATAAT
52493397 AAATATATATTTT-TTATTTTTA-TTTTTTAATTTTAAAATACTTTTA
1 AAATAT-TATTTTATTATTTTTATTTTTTTAATTTTAAAATACTTTTA
* * * *
52493443 AAATATTTTTTTATTTTTTTTATTTTTTTATTTTTAAAATATTTTT
1 AAATATTATTTTATTATTTTTATTTTTTTAATTTTAAAATACTTTT
52493489 TAATGTTTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
45 5 0.12
46 14 0.35
47 21 0.52
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.68
Consensus pattern (47 bp):
AAATATTATTTTATTATTTTTATTTTTTTAATTTTAAAATACTTTTA
Found at i:52493461 original size:7 final size:8
Alignment explanation
Indices: 52493446--52493477 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
52493436 ACTTTTAAAA
52493446 TATTTTTT
1 TATTTTTT
52493454 TATTTTTTT
1 TA-TTTTTT
52493463 TATTTTTT
1 TATTTTTT
52493471 TATTTTT
1 TATTTTT
52493478 AAAATATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TATTTTTT
Found at i:52493462 original size:9 final size:9
Alignment explanation
Indices: 52493448--52493477 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
52493438 TTTTAAAATA
52493448 TTTTTTTAT
1 TTTTTTTAT
52493457 TTTTTTTA-
1 TTTTTTTAT
52493465 TTTTTTTAT
1 TTTTTTTAT
52493474 TTTT
1 TTTT
52493478 AAAATATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:52494989 original size:18 final size:18
Alignment explanation
Indices: 52494966--52495000 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
52494956 TCTGACAAAA
*
52494966 AAAACTGTTAAAATAAAT
1 AAAACTATTAAAATAAAT
52494984 AAAACTATTAAAATAAA
1 AAAACTATTAAAATAAA
52495001 CTGATGGGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.66, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAACTATTAAAATAAAT
Found at i:52495068 original size:27 final size:27
Alignment explanation
Indices: 52495038--52495155 Score: 155
Period size: 27 Copynumber: 4.4 Consensus size: 27
52495028 CTTAGGGAAG
* ***
52495038 AGGCGGCACCAGTCACGCCTTTTTCAT
1 AGGCGGCACCGGTCACGCCTTCCCCAT
52495065 AGGCGGCACCGGTCACGCCTTCCCCAT
1 AGGCGGCACCGGTCACGCCTTCCCCAT
* * *
52495092 AGGCAGCACCGGTCACGCCATCCCCAA
1 AGGCGGCACCGGTCACGCCTTCCCCAT
* *
52495119 AGGCGGCACCGATTACGCCTTCCCCAT
1 AGGCGGCACCGGTCACGCCTTCCCCAT
52495146 AGGCGGCACC
1 AGGCGGCACC
52495156 CACTCCCCCA
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 79 1.00
ACGTcount: A:0.19, C:0.41, G:0.25, T:0.15
Consensus pattern (27 bp):
AGGCGGCACCGGTCACGCCTTCCCCAT
Found at i:52495239 original size:4 final size:4
Alignment explanation
Indices: 52495230--52495281 Score: 56
Period size: 4 Copynumber: 13.5 Consensus size: 4
52495220 GGGAGAATAG
* *
52495230 AAGA AAGA AAGAA AAGA AA-A TAGA AAGA AAGA AAGA AA-A TAG- AAGA
1 AAGA AAGA AAG-A AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
52495276 AAGA AA
1 AAGA AA
52495282 ATGTATTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
3 6 0.15
4 30 0.75
5 4 0.10
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (4 bp):
AAGA
Found at i:52495266 original size:19 final size:19
Alignment explanation
Indices: 52495231--52495281 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
52495221 GGAGAATAGA
52495231 AGAAAGAAAGAAAAGAAAAT
1 AGAAAGAAAG-AAAGAAAAT
52495251 AGAAAGAAAGAAAGAAAAT
1 AGAAAGAAAGAAAGAAAAT
52495270 AG-AAGAAAGAAA
1 AGAAAGAAAGAAA
52495282 ATGTATTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.32
19 11 0.35
20 10 0.32
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.04
Consensus pattern (19 bp):
AGAAAGAAAGAAAGAAAAT
Found at i:52498351 original size:14 final size:14
Alignment explanation
Indices: 52498332--52498360 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
52498322 TAATGTATTT
52498332 AATTTATATTACAA
1 AATTTATATTACAA
52498346 AATTTATATTACAA
1 AATTTATATTACAA
52498360 A
1 A
52498361 GTTGGTTCCA
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:52522174 original size:59 final size:60
Alignment explanation
Indices: 52522041--52522194 Score: 238
Period size: 59 Copynumber: 2.6 Consensus size: 60
52522031 TGCACACCTC
** * * *
52522041 TATCTAGATAGCATTTTATTAATTTAATATTAATATGAGATATTAAATTTAATTTAATATT
1 TATCTAGATAATATTTTATTAATTTAATATTAATATGAGA-ATTAAATTAAATTAAATAAT
52522102 TATCTAGATAATATTTTATTAATTTAATATTAATATGAG-ATTAAATTAAATTAAATAAT
1 TATCTAGATAATATTTTATTAATTTAATATTAATATGAGAATTAAATTAAATTAAATAAT
*
52522161 TATCTTGATAATATTTTATTAATTTAATATTAAT
1 TATCTAGATAATATTTTATTAATTTAATATTAAT
52522195 GTAATTAATT
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
59 50 0.57
61 37 0.43
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (60 bp):
TATCTAGATAATATTTTATTAATTTAATATTAATATGAGAATTAAATTAAATTAAATAAT
Found at i:52529778 original size:7 final size:7
Alignment explanation
Indices: 52529766--52529791 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
52529756 GAATGAATAG
52529766 GAAATGA
1 GAAATGA
52529773 GAAATGA
1 GAAATGA
52529780 GAAATGA
1 GAAATGA
52529787 GAAAT
1 GAAAT
52529792 ATTTAGGAAT
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:0.58, C:0.00, G:0.27, T:0.15
Consensus pattern (7 bp):
GAAATGA
Done.