Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 173 of 182
Found at i:52328012 original size:19 final size:18
Alignment explanation
Indices: 52327990--52328026 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
52327980 TTATTTAAGG
52327990 TTTAGGGTTTAGTTATTTA
1 TTTAGGGTTTAGTT-TTTA
52328009 TTTAGGGTTTAGTTTTTA
1 TTTAGGGTTTAGTTTTTA
52328027 GTGATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.19, C:0.00, G:0.22, T:0.59
Consensus pattern (18 bp):
TTTAGGGTTTAGTTTTTA
Found at i:52328024 original size:44 final size:40
Alignment explanation
Indices: 52327849--52328026 Score: 149
Period size: 44 Copynumber: 4.0 Consensus size: 40
52327839 AGGGTTTAGG
* * *
52327849 ATTTAAGATTTAGGGTTTAGGATTTTATTTAAGGTTTAAGGTTTT
1 ATTTAAGGTTTAGGGTTT--TA-TTTATTTAAGG-TT-AGTTTTT
52327894 ATTTAAGGTTTAGGGTTTTATTTGAGATTTAAGGTTAGTGTTTT
1 ATTTAAGGTTTAGGGTTTTATTT---ATTTAAGGTTAGT-TTTT
* *
52327938 ATTTAGGGTTTAAGGTTTTATTTAGGGTTTAAGGTTAGGTTTTT
1 ATTTAAGGTTTAGGGTTTTATTTA---TTTAAGGTTA-GTTTTT
*
52327982 ATTTAAGGTTTAGGGTTTAGTTATTTATTTAGGGTTTAGTTTTT
1 ATTTAAGGTTTAGGG-TT--TTATTTATTTAAGG-TTAGTTTTT
52328026 A
1 A
52328027 GTGATTTATT
Statistics
Matches: 113, Mismatches: 8, Indels: 25
0.77 0.05 0.17
Matches are distributed among these distances:
41 1 0.01
42 3 0.03
43 3 0.03
44 67 0.59
45 32 0.28
47 7 0.06
ACGTcount: A:0.23, C:0.00, G:0.24, T:0.53
Consensus pattern (40 bp):
ATTTAAGGTTTAGGGTTTTATTTATTTAAGGTTAGTTTTT
Found at i:52329487 original size:46 final size:46
Alignment explanation
Indices: 52329420--52329511 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
52329410 AATAGTTAAA
52329420 TGAACTTGAGTAATTTACCCTACTTTTTTATTTTACTTCCAAATAT
1 TGAACTTGAGTAATTTACCCTACTTTTTTATTTTACTTCCAAATAT
52329466 TGAACTTGAGTAATTTACCCTACTTTTTTATTTTACTTCCAAATAT
1 TGAACTTGAGTAATTTACCCTACTTTTTTATTTTACTTCCAAATAT
52329512 AGGATTGAAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.48
Consensus pattern (46 bp):
TGAACTTGAGTAATTTACCCTACTTTTTTATTTTACTTCCAAATAT
Found at i:52338775 original size:12 final size:12
Alignment explanation
Indices: 52338758--52338782 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52338748 ACTTTTAACA
52338758 TTGTTAAATTTT
1 TTGTTAAATTTT
52338770 TTGTTAAATTTT
1 TTGTTAAATTTT
52338782 T
1 T
52338783 CGATGTGACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (12 bp):
TTGTTAAATTTT
Found at i:52341255 original size:180 final size:181
Alignment explanation
Indices: 52340960--52341322 Score: 620
Period size: 180 Copynumber: 2.0 Consensus size: 181
52340950 TCTCTCTATA
52340960 TATATATGATAAATACAAGATTGATCAACATGTGGAAAATTAGGAATAGAAATTGCATAGCTTGG
1 TATATATGATAAATACAAGATTGATCAACATGTGGAAAATTAGGAATAGAAATTGCATAGCTTGG
*
52341025 ATGTGAAGCAACATATAGGAGTGTTGCTTATATCTAGATTTTGATTTGAGTCTTTAGGTTCAGAT
66 ATGTGAAGCAACATATAGGAGTGTTGCTTATATCTAGATTTTGATTTGAGTCTTTAGATTCAGAT
* * * * *
52341090 AATGCTAATTGAGTTTCTTCTTTGATCATATGATGCTTTGTTTCTCGGGTT
131 AATGCTAATTGAGTTTCTCCTTTGATCATATGAAGCTATGTTGCTCGGATT
*
52341141 TATATAT-ATATATACAAGATTGATCAACATGTGGAAAATTAGGAATAGAAATTGCATAGCTTGG
1 TATATATGATAAATACAAGATTGATCAACATGTGGAAAATTAGGAATAGAAATTGCATAGCTTGG
* * *
52341205 ATGTGAAGCAACATATAGGAGTGTTGCTTATATGTGGATTTTGGTTTGAGTCTTTAGATTCAGAT
66 ATGTGAAGCAACATATAGGAGTGTTGCTTATATCTAGATTTTGATTTGAGTCTTTAGATTCAGAT
*
52341270 AATGCTAATTGAGTTTCTCCTTTGATTATATGAAGCTATGTTGCTCGGATT
131 AATGCTAATTGAGTTTCTCCTTTGATCATATGAAGCTATGTTGCTCGGATT
52341321 TA
1 TA
52341323 AGTGTGAGCA
Statistics
Matches: 171, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
180 164 0.96
181 7 0.04
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (181 bp):
TATATATGATAAATACAAGATTGATCAACATGTGGAAAATTAGGAATAGAAATTGCATAGCTTGG
ATGTGAAGCAACATATAGGAGTGTTGCTTATATCTAGATTTTGATTTGAGTCTTTAGATTCAGAT
AATGCTAATTGAGTTTCTCCTTTGATCATATGAAGCTATGTTGCTCGGATT
Found at i:52346134 original size:2 final size:2
Alignment explanation
Indices: 52346127--52346158 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
52346117 GCTAGTAGGC
52346127 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
52346159 GATAGATAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:52346163 original size:4 final size:4
Alignment explanation
Indices: 52346156--52346194 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
52346146 ATATATATAT
52346156 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
52346195 TAAACAACAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:52349141 original size:13 final size:13
Alignment explanation
Indices: 52349125--52349157 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
52349115 ATTAATTTTT
52349125 AAAATTTTTTAAA
1 AAAATTTTTTAAA
52349138 AAAATTTTTTAAA
1 AAAATTTTTTAAA
*
52349151 ACAATTT
1 AAAATTT
52349158 ATATATATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (13 bp):
AAAATTTTTTAAA
Found at i:52354220 original size:21 final size:22
Alignment explanation
Indices: 52354186--52354227 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
52354176 ATTTTGGACG
*
52354186 TATTTTTAAGAGAGATCAATCT
1 TATTTTCAAGAGAGATCAATCT
*
52354208 TATTTTCAA-AGAGATGAATC
1 TATTTTCAAGAGAGATCAATC
52354228 AGATTCTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (22 bp):
TATTTTCAAGAGAGATCAATCT
Found at i:52357641 original size:58 final size:58
Alignment explanation
Indices: 52357522--52357641 Score: 127
Period size: 58 Copynumber: 2.1 Consensus size: 58
52357512 GGATTAATCA
* * * * * *
52357522 TTTTTTACGTATTTAAATTTTAAAATTAATATTTGTTAATATGTACAAATATGATTCT
1 TTTTTTACATATTTAAATTTTAAAATTAACATTTGTAAACATGTACAAATATGAGTAT
* * *
52357580 TTTTTTACATCTTTAGATTTTAAAATTAGCATTTGTCAAACATGTTA-AAATATG-GTAT
1 TTTTTTACATATTTAAATTTTAAAATTAACATTTGT-AAACATG-TACAAATATGAGTAT
52357638 TTTT
1 TTTT
52357642 CGTTATCGAC
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
58 37 0.73
59 12 0.24
60 2 0.04
ACGTcount: A:0.34, C:0.07, G:0.08, T:0.51
Consensus pattern (58 bp):
TTTTTTACATATTTAAATTTTAAAATTAACATTTGTAAACATGTACAAATATGAGTAT
Found at i:52359722 original size:27 final size:26
Alignment explanation
Indices: 52359675--52359728 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
52359665 TGGTTAACAC
* *
52359675 AAAAAACTGATTTAATAATTAACAAAT
1 AAAAAACAGATTAAATAATT-ACAAAT
52359702 AAAAAACAGATTCAAAT-ATTACAAAT
1 AAAAAACAGATT-AAATAATTACAAAT
52359728 A
1 A
52359729 TTCGACCTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 7 0.29
27 14 0.58
28 3 0.12
ACGTcount: A:0.61, C:0.09, G:0.04, T:0.26
Consensus pattern (26 bp):
AAAAAACAGATTAAATAATTACAAAT
Found at i:52361989 original size:6 final size:6
Alignment explanation
Indices: 52361978--52362003 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
52361968 TAGCAAAGAA
52361978 TTCACT TTCACT TTCACT TTCACT TT
1 TTCACT TTCACT TTCACT TTCACT TT
52362004 TTTTTTTCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.31, G:0.00, T:0.54
Consensus pattern (6 bp):
TTCACT
Found at i:52369088 original size:2 final size:2
Alignment explanation
Indices: 52369081--52369105 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
52369071 ACAACCAGAA
52369081 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
52369106 ACATTTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52372476 original size:7 final size:8
Alignment explanation
Indices: 52372460--52372486 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
52372450 AACCGAAAAC
52372460 AAATTAAA
1 AAATTAAA
52372468 AAATTAAA
1 AAATTAAA
52372476 AAATTAAA
1 AAATTAAA
52372484 AAA
1 AAA
52372487 AAATCTGCAA
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:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (8 bp):
AAATTAAA
Found at i:52386846 original size:3 final size:3
Alignment explanation
Indices: 52386838--52386866 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
52386828 CTTGCAAAGG
52386838 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
52386867 TATGGTTCTA
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:52392892 original size:39 final size:39
Alignment explanation
Indices: 52392849--52392924 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
52392839 TATAGGTAAC
52392849 GAGTTTAACTGAGTTTCGAGTTCAGATCGAGGAACTGCT
1 GAGTTTAACTGAGTTTCGAGTTCAGATCGAGGAACTGCT
* *
52392888 GAGTTTAACTGAGTTTCGAGTTCGGATGGAGGAACTG
1 GAGTTTAACTGAGTTTCGAGTTCAGATCGAGGAACTG
52392925 TTTAGCAGGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.25, C:0.13, G:0.32, T:0.30
Consensus pattern (39 bp):
GAGTTTAACTGAGTTTCGAGTTCAGATCGAGGAACTGCT
Found at i:52393685 original size:19 final size:18
Alignment explanation
Indices: 52393662--52393710 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
52393652 ATTTTATAAT
52393662 TCATTGAAAAAATATTAA
1 TCATTGAAAAAATATTAA
*
52393680 TGCATTG-GAAAATATTAAAA
1 T-CATTGAAAAAATATT--AA
52393700 TCATTGAAAAA
1 TCATTGAAAAA
52393711 GATAATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 9 0.36
19 10 0.40
20 6 0.24
ACGTcount: A:0.53, C:0.06, G:0.10, T:0.31
Consensus pattern (18 bp):
TCATTGAAAAAATATTAA
Found at i:52393759 original size:13 final size:13
Alignment explanation
Indices: 52393740--52393786 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
52393730 ATATTCAATC
52393740 AATTTATATTTTT
1 AATTTATATTTTT
* * *
52393753 TATTTATCTTTTA
1 AATTTATATTTTT
*
52393766 AATTTATA-CTTT
1 AATTTATATTTTT
52393778 AATTTATAT
1 AATTTATAT
52393787 GTACCATTCT
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (13 bp):
AATTTATATTTTT
Found at i:52398219 original size:31 final size:31
Alignment explanation
Indices: 52398181--52398242 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
52398171 ATTGGTTGTG
*
52398181 GATCGATAATTCGTGTATTCATATCATATTT
1 GATCGATAATTCGTATATTCATATCATATTT
* * *
52398212 GATCGATAATTTGTATGTTCATATTATATTT
1 GATCGATAATTCGTATATTCATATCATATTT
52398243 CATGTATCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.29, C:0.10, G:0.13, T:0.48
Consensus pattern (31 bp):
GATCGATAATTCGTATATTCATATCATATTT
Found at i:52398863 original size:37 final size:36
Alignment explanation
Indices: 52398820--52398900 Score: 92
Period size: 37 Copynumber: 2.2 Consensus size: 36
52398810 CTCAAAAATA
**
52398820 ATATATAATTTATTAAAAAATTTAAAAAAGAT-TATAT
1 ATATATAA-TTACCAAAAAA-TTAAAAAAGATATATAT
* *
52398857 ATATATAATTACCAAGAAATTAAAAATGATACTATAT
1 ATATATAATTACCAAAAAATTAAAAAAGATA-TATAT
52398894 ATATATA
1 ATATATA
52398901 TATATGTGTG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
35 10 0.26
36 8 0.21
37 20 0.53
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (36 bp):
ATATATAATTACCAAAAAATTAAAAAAGATATATAT
Found at i:52400596 original size:20 final size:20
Alignment explanation
Indices: 52400571--52400609 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
52400561 TGATTTGAAA
52400571 ATTTTATAA-TAAAATTTATC
1 ATTTTA-AACTAAAATTTATC
52400591 ATTTTAAACTAAAATTTAT
1 ATTTTAAACTAAAATTTAT
52400610 TTTATTGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTTTAAACTAAAATTTATC
Found at i:52400848 original size:18 final size:17
Alignment explanation
Indices: 52400796--52400848 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 17
52400786 GTTCGACCTG
*
52400796 TTTTTAAATT-TATAAT
1 TTTTTATATTATATAAT
* * *
52400812 ATTTTATATTATGTTAT
1 TTTTTATATTATATAAT
52400829 TTTTATATATTATATAAT
1 TTTT-TATATTATATAAT
52400847 TT
1 TT
52400849 AAAATACATT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
16 8 0.29
17 7 0.25
18 13 0.46
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (17 bp):
TTTTTATATTATATAAT
Found at i:52406641 original size:24 final size:24
Alignment explanation
Indices: 52406614--52406661 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
52406604 ATATGTTACC
*
52406614 ACTTGACCATATATAAGTGGCAAT
1 ACTTCACCATATATAAGTGGCAAT
52406638 ACTTCACCATATATAAGTGGCAAT
1 ACTTCACCATATATAAGTGGCAAT
52406662 TATATGTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.29
Consensus pattern (24 bp):
ACTTCACCATATATAAGTGGCAAT
Found at i:52409548 original size:55 final size:57
Alignment explanation
Indices: 52409414--52409551 Score: 185
Period size: 57 Copynumber: 2.5 Consensus size: 57
52409404 AATGACAAAA
*
52409414 GAAAAAAAA-ATTGAATAATTGAATGATCATTTTGTAACTTTTCATAATTAAATAATC
1 GAAAAAAAATATT-AATAATTAAATGATCATTTTGTAACTTTTCATAATTAAATAATC
* * *
52409471 GAAAACAAATATTAATAATTAAATGCTCATTTTGTAAC-TTTCATAATTGAATAA-C
1 GAAAAAAAATATTAATAATTAAATGATCATTTTGTAACTTTTCATAATTAAATAATC
*
52409526 -AATAAAAAATATTAATAGTTAAATGA
1 GAA-AAAAAATATTAATAATTAAATGA
52409552 CTACTAATAT
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
54 2 0.03
55 21 0.29
56 15 0.21
57 31 0.43
58 3 0.04
ACGTcount: A:0.49, C:0.07, G:0.08, T:0.36
Consensus pattern (57 bp):
GAAAAAAAATATTAATAATTAAATGATCATTTTGTAACTTTTCATAATTAAATAATC
Found at i:52423078 original size:29 final size:29
Alignment explanation
Indices: 52423046--52423101 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
52423036 ATCCTTGTAC
52423046 ACTTCGTAAATTT-GAAATTTAGTCCCTAA
1 ACTT-GTAAATTTAGAAATTTAGTCCCTAA
* * *
52423075 ACTTTTAATTTTAGGAATTTAGTCCCT
1 ACTTGTAAATTTAGAAATTTAGTCCCT
52423102 CTAATTTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 6 0.26
29 17 0.74
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (29 bp):
ACTTGTAAATTTAGAAATTTAGTCCCTAA
Found at i:52425095 original size:30 final size:32
Alignment explanation
Indices: 52425042--52425107 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
52425032 ATTCCTCAAT
52425042 ATTATATATAATAATATAAATAAA-TTTTTAAA
1 ATTATATATAATAATAT-AATAAATTTTTTAAA
*
52425074 ATTATATATATTAATAT-ATAAATTTTTTAAA
1 ATTATATATAATAATATAATAAATTTTTTAAA
52425105 ATT
1 ATT
52425108 CTCTTTATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 5 0.16
31 11 0.34
32 16 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (32 bp):
ATTATATATAATAATATAATAAATTTTTTAAA
Found at i:52425791 original size:25 final size:25
Alignment explanation
Indices: 52425763--52425810 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
52425753 CTCATGTTAC
*
52425763 ATATATTGATATGATTAATTTTTGA
1 ATATATTGATATAATTAATTTTTGA
52425788 ATATATTGATATAATTAATTTTT
1 ATATATTGATATAATTAATTTTT
52425811 AATTGCTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (25 bp):
ATATATTGATATAATTAATTTTTGA
Found at i:52433424 original size:7 final size:7
Alignment explanation
Indices: 52433412--52433436 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
52433402 TTCAAAACCC
52433412 AATTTTA
1 AATTTTA
52433419 AATTTTA
1 AATTTTA
52433426 AATTTTA
1 AATTTTA
52433433 AATT
1 AATT
52433437 ATTGTAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
AATTTTA
Found at i:52433448 original size:23 final size:24
Alignment explanation
Indices: 52433422--52433476 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
52433412 AATTTTAAAT
52433422 TTTAAATTTTAAA-TTATTGTAAC
1 TTTAAATTTTAAACTTATTGTAAC
* * *
52433445 TTTAAA-TTTAAACTTATTTTGAG
1 TTTAAATTTTAAACTTATTGTAAC
52433468 TTTAAATTT
1 TTTAAATTT
52433477 ATTTTGAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 6 0.22
23 19 0.70
24 2 0.07
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.55
Consensus pattern (24 bp):
TTTAAATTTTAAACTTATTGTAAC
Found at i:52433473 original size:17 final size:17
Alignment explanation
Indices: 52433449--52433490 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
52433439 TGTAACTTTA
52433449 AATTTAAACTTATTTTG
1 AATTTAAACTTATTTTG
* *
52433466 AGTTTAAATTTATTTTG
1 AATTTAAACTTATTTTG
52433483 AATTTAAA
1 AATTTAAA
52433491 ATTAAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.52
Consensus pattern (17 bp):
AATTTAAACTTATTTTG
Found at i:52434834 original size:12 final size:13
Alignment explanation
Indices: 52434809--52434833 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52434799 AATGAAAGAA
52434809 GAAATGAATTTTT
1 GAAATGAATTTTT
52434822 GAAATGAATTTT
1 GAAATGAATTTT
52434834 GGGTTTAAAT
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:0.00, G:0.16, T:0.44
Consensus pattern (13 bp):
GAAATGAATTTTT
Found at i:52435355 original size:30 final size:30
Alignment explanation
Indices: 52435319--52435621 Score: 179
Period size: 29 Copynumber: 10.5 Consensus size: 30
52435309 AAAGATCCTT
* *
52435319 AAACTTTCCAAAAATTAAATTTTGACACCC
1 AAACTTTCCAAAAATTACATTTTGACCCCC
* **
52435349 AAACTTTCCAAAAATTATATTTTGA-CCTT
1 AAACTTTCCAAAAATTACATTTTGACCCCC
** * *
52435378 AAACTTTTAAAAAATTCCATTTT--CCCCT
1 AAACTTTCCAAAAATTACATTTTGACCCCC
* * *
52435406 GAAC-TTCCAAAAATCACATTTTTACCCCC
1 AAACTTTCCAAAAATTACATTTTGACCCCC
** * *
52435435 AAACTTTTAAAAAATTTCATTTTTACCCCAC
1 AAACTTTCCAAAAATTACATTTTGACCCC-C
*
52435466 AAAC-TTCCAAAAATTCCATTTTG-CCCCC
1 AAACTTTCCAAAAATTACATTTTGACCCCC
* ** *
52435494 GAAC-TTCCAAAAACCACATTTTTG-CCCTC
1 AAACTTTCCAAAAATTACA-TTTTGACCCCC
* *
52435523 GAAC-TTCCAAAAATCACATATTT-ACCCCC
1 AAACTTTCCAAAAATTACAT-TTTGACCCCC
* * * *
52435552 GAA-TTTCC-AAAATCATATTTTTA-CCCC
1 AAACTTTCCAAAAATTACATTTTGACCCCC
* * *
52435579 TAAC-TTCCAAAAATTTCATTTTTG-CCCAC
1 AAACTTTCCAAAAATTACA-TTTTGACCCCC
*
52435608 GAAC-TTCCAAAAAT
1 AAACTTTCCAAAAAT
52435622 CACTTTTTTA
Statistics
Matches: 220, Mismatches: 39, Indels: 29
0.76 0.14 0.10
Matches are distributed among these distances:
27 27 0.12
28 38 0.17
29 91 0.41
30 59 0.27
31 5 0.02
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33
Consensus pattern (30 bp):
AAACTTTCCAAAAATTACATTTTGACCCCC
Found at i:52435400 original size:29 final size:29
Alignment explanation
Indices: 52435315--52435393 Score: 104
Period size: 30 Copynumber: 2.7 Consensus size: 29
52435305 CCCAAAAGAT
52435315 CCTTAAACTTTCCAAAAATTAAATTTTGA
1 CCTTAAACTTTCCAAAAATTAAATTTTGA
** *
52435344 CACCCAAACTTTCCAAAAATTATATTTTGA
1 C-CTTAAACTTTCCAAAAATTAAATTTTGA
**
52435374 CCTTAAACTTTTAAAAAATT
1 CCTTAAACTTTCCAAAAATT
52435394 CCATTTTCCC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 16 0.38
30 26 0.62
ACGTcount: A:0.42, C:0.19, G:0.03, T:0.37
Consensus pattern (29 bp):
CCTTAAACTTTCCAAAAATTAAATTTTGA
Found at i:52435439 original size:29 final size:29
Alignment explanation
Indices: 52435397--52435665 Score: 235
Period size: 29 Copynumber: 9.3 Consensus size: 29
52435387 AAAAATTCCA
*
52435397 TTTT-CCCCTGAACTTCCAAAAATCACAT
1 TTTTACCCCCGAACTTCCAAAAATCACAT
* ** **
52435425 TTTTACCCCCAAACTTTTAAAAAATTTCAT
1 TTTTACCCCCGAAC-TTCCAAAAATCACAT
*
52435455 TTTTACCCCACAAACTTCCAAAAATTC-CA-
1 TTTTACCCC-CGAACTTCCAAAAA-TCACAT
* *
52435484 TTTTGCCCCCGAACTTCCAAAAACCACAT
1 TTTTACCCCCGAACTTCCAAAAATCACAT
* *
52435513 TTTTGCCCTCGAACTTCCAAAAATCACAT
1 TTTTACCCCCGAACTTCCAAAAATCACAT
* * *
52435542 ATTTACCCCCGAATTTCC-AAAATCATAT
1 TTTTACCCCCGAACTTCCAAAAATCACAT
* **
52435570 TTTTA-CCCCTAACTTCCAAAAATTTCAT
1 TTTTACCCCCGAACTTCCAAAAATCACAT
* * *
52435598 TTTTGCCCACGAACTTCCAAAAATCACTT
1 TTTTACCCCCGAACTTCCAAAAATCACAT
** **
52435627 TTTTA-CCTTGAATCTTCCTAAAAATGGCAT
1 TTTTACCCCCGAA-CTTCC-AAAAATCACAT
52435657 TTTTACCCC
1 TTTTACCCC
52435666 TAAAACTTTC
Statistics
Matches: 192, Mismatches: 38, Indels: 19
0.77 0.15 0.08
Matches are distributed among these distances:
27 11 0.06
28 48 0.25
29 83 0.43
30 42 0.22
31 8 0.04
ACGTcount: A:0.32, C:0.30, G:0.04, T:0.33
Consensus pattern (29 bp):
TTTTACCCCCGAACTTCCAAAAATCACAT
Found at i:52435444 original size:57 final size:58
Alignment explanation
Indices: 52435378--52435680 Score: 178
Period size: 57 Copynumber: 5.2 Consensus size: 58
52435368 TTTTGACCTT
52435378 AAACTTTTAAAAAATTCCA-TTTTCCCCTGAACTTCCAAAAATCACATTTTTACCCCC
1 AAACTTTTAAAAAATTCCATTTTTCCCCTGAACTTCCAAAAATCACATTTTTACCCCC
* ** *
52435435 AAACTTTTAAAAAATTTCATTTTTACCCCACAAACTTCCAAAAATTC-CA-TTTTGCCCCC
1 AAACTTTTAAAAAATTCCATTTTT-CCCC-TGAACTTCCAAAAA-TCACATTTTTACCCCC
* ** * * *
52435494 GAAC-TTCCAAAAA-CCACATTTTTGCCCTCGAACTTCCAAAAATCACATATTTACCCCC
1 AAACTTTTAAAAAATTC-CATTTTTCCCCT-GAACTTCCAAAAATCACATTTTTACCCCC
* ** * ** * *
52435552 GAA--TTTCCAAAA-TCATATTTTTACCCCT-AACTTCCAAAAATTTCATTTTTGCCCAC
1 AAACTTTTAAAAAATTC-CATTTTT-CCCCTGAACTTCCAAAAATCACATTTTTACCCCC
* ** * * * ** *
52435608 GAAC-TTCCAAAAA-TCACTTTTTTACCTTGAATCTTCCTAAAAATGGCATTTTTACCCCTA
1 AAACTTTTAAAAAATTC-CATTTTTCCCCTGAA-CTTCC-AAAAATCACATTTTTACCCC-C
52435668 AAACTTTCTAAAA
1 AAACTTT-TAAAA
52435681 TTAGCTTTTA
Statistics
Matches: 192, Mismatches: 38, Indels: 27
0.75 0.15 0.11
Matches are distributed among these distances:
56 31 0.16
57 67 0.35
58 38 0.20
59 32 0.17
60 17 0.09
61 4 0.02
62 3 0.02
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (58 bp):
AAACTTTTAAAAAATTCCATTTTTCCCCTGAACTTCCAAAAATCACATTTTTACCCCC
Found at i:52435800 original size:29 final size:29
Alignment explanation
Indices: 52435764--52435821 Score: 73
Period size: 31 Copynumber: 2.0 Consensus size: 29
52435754 AATTCTTTAA
52435764 ATTTTTTTAATTCAT-TTTGTATTTTATC
1 ATTTTTTTAATTCATATTTGTATTTTATC
* *
52435792 ATTTATTTTGATTCATAATTTGTTTTTTAT
1 ATTT-TTTTAATTCAT-ATTTGTATTTTAT
52435822 TTTTTCTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 4 0.16
29 10 0.40
31 11 0.44
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.67
Consensus pattern (29 bp):
ATTTTTTTAATTCATATTTGTATTTTATC
Found at i:52436115 original size:97 final size:99
Alignment explanation
Indices: 52435957--52436149 Score: 275
Period size: 97 Copynumber: 2.0 Consensus size: 99
52435947 TCCAAAATAT
* * *
52435957 TTAAAATCGAGGCAATATTTTTTTATTTCGAGTTTTGAAAAATTTGTTCCTTAACTTACTAGGCG
1 TTAAAATCGAGGCAATATTTATTTATCTCGAGTTTTGAAAAATTTGTGCCTTAACTTACTAGGCG
* * *
52436022 CGATTTTTTTTCAAATCGGAATAATCGAATACCC
66 CAACTTTTCTTCAAATCGGAATAATCGAATACCC
*
52436056 TTAAAA-CGAGGCAATGTTTATTTATCTCTG-GTTTTG-AAAATTTGTGCCTTAACTTACTAGGC
1 TTAAAATCGAGGCAATATTTATTTATCTC-GAGTTTTGAAAAATTTGTGCCTTAACTTACTAGGC
* *
52436118 GCAACTTTTCTTCAAATTGGGATAATCGAATA
65 GCAACTTTTCTTCAAATCGGAATAATCGAATA
52436150 TCATTTTCCA
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
97 52 0.62
98 25 0.30
99 7 0.08
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (99 bp):
TTAAAATCGAGGCAATATTTATTTATCTCGAGTTTTGAAAAATTTGTGCCTTAACTTACTAGGCG
CAACTTTTCTTCAAATCGGAATAATCGAATACCC
Found at i:52448185 original size:172 final size:172
Alignment explanation
Indices: 52447835--52448194 Score: 605
Period size: 172 Copynumber: 2.1 Consensus size: 172
52447825 ACTAAATCCC
* *
52447835 TCTTCCTGATGAGATATAGAGAAGCGGATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGATA
1 TCTTCCTGATGAGATATAGAAAAGCGGATTAAAACAAGTGATGCGGTCATCTTCCTAATGAGATA
* *
52447900 CTGAGAAGTAGACCAAATCAATGAAACCAAGCTCAATGTGAGTGAAACTTCAAATCCGAGCTTCC
66 CAGAGAAGTAGACCAAATCAATGAAACCAAGCTCAATGTGAGCGAAACTTCAAATCCGAGCTTCC
* * * **
52447965 TGATGAGATACTGAGAAGCAGGTTGAAGCAATAAAGCAGTGG
131 TAATGAGATACTGAGAAGCAGGTCGAAGCAATAAAACAGTCA
*
52448007 TCTTCCTAATGAGATATAGAAAAGCGGATTAAAACAAGTGATGCGGTCATCTTCCTAATGAGATA
1 TCTTCCTGATGAGATATAGAAAAGCGGATTAAAACAAGTGATGCGGTCATCTTCCTAATGAGATA
*
52448072 CAGAGAAGTAGACCAAATCAATGAAACCAAGCTCAATGTGAGCGAAACTTCGAATCCGAGCTTCC
66 CAGAGAAGTAGACCAAATCAATGAAACCAAGCTCAATGTGAGCGAAACTTCAAATCCGAGCTTCC
52448137 TAATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAC-GATCA
131 TAATGAGATACTGAGAAGCAGGTCGAAGCAATAAAACAG-TCA
52448179 TCTTCCTGATGAGATA
1 TCTTCCTGATGAGATA
52448195 CAGAGAAGTA
Statistics
Matches: 175, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
171 1 0.01
172 174 0.99
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.23
Consensus pattern (172 bp):
TCTTCCTGATGAGATATAGAAAAGCGGATTAAAACAAGTGATGCGGTCATCTTCCTAATGAGATA
CAGAGAAGTAGACCAAATCAATGAAACCAAGCTCAATGTGAGCGAAACTTCAAATCCGAGCTTCC
TAATGAGATACTGAGAAGCAGGTCGAAGCAATAAAACAGTCA
Found at i:52448613 original size:34 final size:34
Alignment explanation
Indices: 52448574--52448706 Score: 216
Period size: 34 Copynumber: 3.9 Consensus size: 34
52448564 TCAAAACCCA
*
52448574 ATTTTAAATTTTAAA-TTATTTTAAGTTTAAATTT
1 ATTTTAAA-TTTAAACTTATTTTGAGTTTAAATTT
52448608 ATTTTAAATTTAAACTTATTTTGAGTTTAAATTT
1 ATTTTAAATTTAAACTTATTTTGAGTTTAAATTT
52448642 ATTTTAAATTTAAACTTATTTTGAGTTTAAATTT
1 ATTTTAAATTTAAACTTATTTTGAGTTTAAATTT
*
52448676 ATTTTAAATTTAAATTTATTTTG-GATTTAAA
1 ATTTTAAATTTAAACTTATTTTGAG-TTTAAA
52448707 ATTAAAAATT
Statistics
Matches: 95, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
33 7 0.07
34 88 0.93
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (34 bp):
ATTTTAAATTTAAACTTATTTTGAGTTTAAATTT
Found at i:52448615 original size:11 final size:12
Alignment explanation
Indices: 52448593--52448693 Score: 59
Period size: 11 Copynumber: 8.8 Consensus size: 12
52448583 TTTAAATTAT
*
52448593 TTTAAGTTTAAA
1 TTTAATTTTAAA
52448605 TTT-ATTTTAAA
1 TTTAATTTTAAA
** *
52448616 TTTAAACTT-AT
1 TTTAATTTTAAA
* *
52448627 TTTGAGTTTAAA
1 TTTAATTTTAAA
52448639 TTT-ATTTTAAA
1 TTTAATTTTAAA
** *
52448650 TTTAAACTT-AT
1 TTTAATTTTAAA
* *
52448661 TTTGAGTTTAAA
1 TTTAATTTTAAA
52448673 TTT-ATTTTAAA
1 TTTAATTTTAAA
*
52448684 TTTAAATTTA
1 TTTAATTTTA
52448694 TTTTGGATTT
Statistics
Matches: 66, Mismatches: 18, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
11 44 0.67
12 22 0.33
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (12 bp):
TTTAATTTTAAA
Found at i:52448706 original size:17 final size:17
Alignment explanation
Indices: 52448574--52448697 Score: 169
Period size: 17 Copynumber: 7.3 Consensus size: 17
52448564 TCAAAACCCA
52448574 ATTTTAAATTTTAAA-TT
1 ATTTTAAA-TTTAAATTT
*
52448591 ATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTT
*
52448608 ATTTTAAATTTAAACTT
1 ATTTTAAATTTAAATTT
* *
52448625 ATTTTGAGTTTAAATTT
1 ATTTTAAATTTAAATTT
*
52448642 ATTTTAAATTTAAACTT
1 ATTTTAAATTTAAATTT
* *
52448659 ATTTTGAGTTTAAATTT
1 ATTTTAAATTTAAATTT
52448676 ATTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
52448693 ATTTT
1 ATTTT
52448698 GGATTTAAAA
Statistics
Matches: 92, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
16 6 0.07
17 86 0.93
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:52450599 original size:29 final size:30
Alignment explanation
Indices: 52450567--52450749 Score: 120
Period size: 29 Copynumber: 6.4 Consensus size: 30
52450557 TTGACTCCCA
* *
52450567 AACTTTTAAAAAATTCAATTTTTCCCCT-G
1 AACTTTCAAAAAATTCAATTTTTACCCTCG
* *
52450596 AAC-TTCCAAAAATTCCATTTTTACCCTCG
1 AACTTTCAAAAAATTCAATTTTTACCCTCG
* * * *
52450625 AAC-TTCCAAAAA-CCATATTTTTGCCCCCG
1 AACTTTCAAAAAATTCA-ATTTTTACCCTCG
* *
52450654 AAC-TTCTAAGAA-TCACATTTTT-CCCTCG
1 AACTTTCAAAAAATTCA-ATTTTTACCCTCG
*
52450682 AA-TTTC-CAAAA-TCATATTTTTACCCTCG
1 AACTTTCAAAAAATTCA-ATTTTTACCCTCG
* * *
52450710 AAC-TTCCAAAAATTCCATTTTT-CCCTCA
1 AACTTTCAAAAAATTCAATTTTTACCCTCG
*
52450738 AACTTCCAAAAA
1 AACTTTCAAAAA
52450750 TCACGTTTTT
Statistics
Matches: 125, Mismatches: 21, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
27 12 0.10
28 50 0.40
29 61 0.49
30 2 0.02
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.34
Consensus pattern (30 bp):
AACTTTCAAAAAATTCAATTTTTACCCTCG
Found at i:52450714 original size:56 final size:57
Alignment explanation
Indices: 52450575--52450779 Score: 240
Period size: 56 Copynumber: 3.6 Consensus size: 57
52450565 CAAACTTTTA
*
52450575 AAAAATTCA-ATTTTTCCCCT-GAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCC
1 AAAAA-TCATATTTTTACCCTCGAACTTCCAAAAATTCCATTTTT-CCCTCGAACTTCC
* * * * * *
52450632 AAAAACCATATTTTTGCCCCCGAACTTCTAAGAA-TCACATTTTTCCCTCGAATTTCC
1 AAAAATCATATTTTTACCCTCGAACTTCCAAAAATTC-CATTTTTCCCTCGAACTTCC
*
52450689 -AAAATCATATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTCCCTCAAACTTCC
1 AAAAATCATATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTCCCTCGAACTTCC
** *
52450745 AAAAATCACGTTTTTA-CCTCGAATCTTCCCAAAAT
1 AAAAATCATATTTTTACCCTCGAA-CTTCCAAAAAT
52450780 AATATTTTTA
Statistics
Matches: 126, Mismatches: 16, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
56 55 0.44
57 53 0.42
58 18 0.14
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.34
Consensus pattern (57 bp):
AAAAATCATATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTCCCTCGAACTTCC
Found at i:52450759 original size:29 final size:29
Alignment explanation
Indices: 52450575--52450792 Score: 218
Period size: 28 Copynumber: 7.7 Consensus size: 29
52450565 CAAACTTTTA
*
52450575 AAAAATTCA-ATTTTTCCCCT-GAACTTCC
1 AAAAA-TCACATTTTTACCCTCGAACTTCC
52450603 AAAAATTC-CATTTTTACCCTCGAACTTCC
1 AAAAA-TCACATTTTTACCCTCGAACTTCC
* * * * *
52450632 AAAAACCATATTTTTGCCCCCGAACTTCT
1 AAAAATCACATTTTTACCCTCGAACTTCC
* *
52450661 AAGAATCACATTTTT-CCCTCGAATTTCC
1 AAAAATCACATTTTTACCCTCGAACTTCC
*
52450689 -AAAATCATATTTTTACCCTCGAACTTCC
1 AAAAATCACATTTTTACCCTCGAACTTCC
*
52450717 AAAAATTC-CATTTTT-CCCTCAAACTTCC
1 AAAAA-TCACATTTTTACCCTCGAACTTCC
*
52450745 AAAAATCACGTTTTTA-CCTCGAATCTTCC
1 AAAAATCACATTTTTACCCTCGAA-CTTCC
* * *
52450774 CAAAATAATATTTTTACCC
1 AAAAATCACATTTTTACCC
52450793 CTAAAACTTT
Statistics
Matches: 157, Mismatches: 23, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
27 14 0.09
28 70 0.45
29 69 0.44
30 4 0.03
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.35
Consensus pattern (29 bp):
AAAAATCACATTTTTACCCTCGAACTTCC
Found at i:52457748 original size:13 final size:14
Alignment explanation
Indices: 52457730--52457759 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
52457720 TTAAAATATA
52457730 TAAATATTTATT-T
1 TAAATATTTATTAT
52457743 TAAATATTTATTAT
1 TAAATATTTATTAT
52457757 TAA
1 TAA
52457760 GTGGATGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TAAATATTTATTAT
Found at i:52472463 original size:5 final size:5
Alignment explanation
Indices: 52472453--52472482 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
52472443 TGGCTAAAGG
52472453 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
52472483 TTGATGGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:52474119 original size:55 final size:55
Alignment explanation
Indices: 52474031--52474159 Score: 170
Period size: 55 Copynumber: 2.3 Consensus size: 55
52474021 ATTAAACGTG
* * ** *
52474031 TTTAAATATATAAACAATTGATTCAAAAAAAGCAGTATTGCAACATAACAATCGA
1 TTTAAACATATAAACAATTGATTCAAAAAAAGCAATATCACAACATAACAATCAA
* *
52474086 TTTAAACATATAAACAATTGATT-AAAAAGAAGCAATATCACACCATAACAATTAA
1 TTTAAACATATAAACAATTGATTCAAAAA-AAGCAATATCACAACATAACAATCAA
*
52474141 TTTAAACATATAAATAATT
1 TTTAAACATATAAACAATT
52474160 TTTTGGGAGG
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
54 5 0.08
55 60 0.92
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.29
Consensus pattern (55 bp):
TTTAAACATATAAACAATTGATTCAAAAAAAGCAATATCACAACATAACAATCAA
Found at i:52478871 original size:12 final size:12
Alignment explanation
Indices: 52478856--52478899 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
52478846 AATACTTAAC
*
52478856 TTTTAAAATTTA
1 TTTTAAAATATA
52478868 TTTTAAATATATA
1 TTTTAAA-ATATA
* *
52478881 TTGTATAATATA
1 TTTTAAAATATA
52478893 TTTTAAA
1 TTTTAAA
52478900 TAAGTCTATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
12 17 0.65
13 9 0.35
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
TTTTAAAATATA
Found at i:52479537 original size:14 final size:15
Alignment explanation
Indices: 52479513--52479544 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
52479503 ATATTATGTT
52479513 AAAGAAAAAAGAAAG
1 AAAGAAAAAAGAAAG
52479528 AAAG-AAAAAGAAAG
1 AAAGAAAAAAGAAAG
52479542 AAA
1 AAA
52479545 CCCTACTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAAGAAAG
Found at i:52482322 original size:26 final size:27
Alignment explanation
Indices: 52482286--52482338 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
52482276 CAATAAATTA
*
52482286 AAAATTGATAATTTAATT-GAATATTT
1 AAAATTGATAATTTAATTAAAATATTT
*
52482312 AAAATTTATAATTTAATTAAAATATTT
1 AAAATTGATAATTTAATTAAAATATTT
52482339 TATTGATCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (27 bp):
AAAATTGATAATTTAATTAAAATATTT
Found at i:52488364 original size:2 final size:2
Alignment explanation
Indices: 52488357--52488410 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
52488347 TAAGATGATA
52488357 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
52488399 AT AT AT GT AT AT
1 AT AT AT AT AT AT
52488411 CTTTCAATTT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52488721 original size:3 final size:3
Alignment explanation
Indices: 52488713--52488740 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
52488703 TTGTTTTTCA
52488713 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
52488741 CCACAGTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:52492001 original size:26 final size:25
Alignment explanation
Indices: 52491953--52492012 Score: 84
Period size: 26 Copynumber: 2.4 Consensus size: 25
52491943 TCTTAACTCG
*
52491953 ATTAATATAGATATTATTATTATTT
1 ATTAATATAGATAATATTATTATTT
*
52491978 ATTAATATATTATAATATTATTATTT
1 ATTAATATA-GATAATATTATTATTT
*
52492004 ATTATTATA
1 ATTAATATA
52492013 AATTCAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
25 9 0.29
26 22 0.71
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (25 bp):
ATTAATATAGATAATATTATTATTT
Found at i:52493400 original size:14 final size:14
Alignment explanation
Indices: 52493381--52493413 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
52493371 TTATGTGTTC
52493381 TATTTATTTTTAAT
1 TATTTATTTTTAAT
52493395 TATTTATTTTTAAT
1 TATTTATTTTTAAT
52493409 T-TTTA
1 TATTTA
52493414 AATCCACAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TATTTATTTTTAAT
Found at i:52507334 original size:21 final size:22
Alignment explanation
Indices: 52507310--52507361 Score: 52
Period size: 23 Copynumber: 2.4 Consensus size: 22
52507300 ACTTTTCTTC
* *
52507310 ATATGATATAAAT-CATATAAT
1 ATATGATATAAATAAAAATAAT
* *
52507331 ATATAAAATAAATGAAAAATAAT
1 ATATGATATAAAT-AAAAATAAT
52507354 ATATGATA
1 ATATGATA
52507362 AACTTGAAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
21 11 0.48
23 12 0.52
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.33
Consensus pattern (22 bp):
ATATGATATAAATAAAAATAAT
Found at i:52517352 original size:11 final size:11
Alignment explanation
Indices: 52517325--52517355 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
52517315 TTTGTCTCTC
52517325 ATGATTTTTCT
1 ATGATTTTTCT
52517336 AT-ATTTTTCT
1 ATGATTTTTCT
52517346 ATGATTTTTC
1 ATGATTTTTC
52517356 AAAGTCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.19, C:0.10, G:0.06, T:0.65
Consensus pattern (11 bp):
ATGATTTTTCT
Found at i:52524022 original size:22 final size:22
Alignment explanation
Indices: 52523971--52524048 Score: 95
Period size: 22 Copynumber: 3.5 Consensus size: 22
52523961 CTGGGGAAAT
*
52523971 AGTAAGCACACACAGTGCAATCC
1 AGTAGGCACACACAGTGCAAT-C
*
52523994 AGTAGGCACACACAGTGCAATT
1 AGTAGGCACACACAGTGCAATC
* *
52524016 AGTAGGCGCACATAGT-CAAATC
1 AGTAGGCACACACAGTGC-AATC
52524038 AGTAGGCACAC
1 AGTAGGCACAC
52524049 GAGGTGCGAA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
21 1 0.02
22 27 0.56
23 20 0.42
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (22 bp):
AGTAGGCACACACAGTGCAATC
Found at i:52524069 original size:23 final size:23
Alignment explanation
Indices: 52524037--52524113 Score: 118
Period size: 23 Copynumber: 3.3 Consensus size: 23
52524027 ATAGTCAAAT
* *
52524037 CAGTAGGCACACGAGGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
*
52524060 TAGTAAGCACACGAAGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
*
52524083 CAGTAAGCACACAAAGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
52524106 CAGTAAGC
1 CAGTAAGC
52524114 GCGCTAGCGT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.42, C:0.21, G:0.27, T:0.10
Consensus pattern (23 bp):
CAGTAAGCACACGAAGTGCGAAA
Found at i:52526504 original size:14 final size:15
Alignment explanation
Indices: 52526485--52526514 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
52526475 AAGAAATAAA
52526485 AAGAAAAAT-TGTTG
1 AAGAAAAATGTGTTG
52526499 AAGAAAAATGTGTTG
1 AAGAAAAATGTGTTG
52526514 A
1 A
52526515 TGAACTTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.27
Consensus pattern (15 bp):
AAGAAAAATGTGTTG
Found at i:52528963 original size:21 final size:21
Alignment explanation
Indices: 52528921--52528959 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
52528911 TAATAAGATA
* *
52528921 TATGTTAAGTATGATCTGTAT
1 TATGTTAAATATGATATGTAT
52528942 TATG-TAAATATGATATGT
1 TATGTTAAATATGATATGT
52528960 TATTTGCTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.33, C:0.03, G:0.18, T:0.46
Consensus pattern (21 bp):
TATGTTAAATATGATATGTAT
Found at i:52535514 original size:31 final size:30
Alignment explanation
Indices: 52535472--52535538 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 30
52535462 TGATGGAAAA
*
52535472 GGACTGGTTTGTTACATTTTCAAAAGTTGAG
1 GGACTGGTTTGTCACATTTT-AAAAGTTGAG
* * *
52535503 GGACTGTTTTGTCATATTTTTAAAGTTGAG
1 GGACTGGTTTGTCACATTTTAAAAGTTGAG
52535533 GGACTG
1 GGACTG
52535539 AAATGTAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 15 0.47
31 17 0.53
ACGTcount: A:0.24, C:0.09, G:0.27, T:0.40
Consensus pattern (30 bp):
GGACTGGTTTGTCACATTTTAAAAGTTGAG
Found at i:52541128 original size:147 final size:150
Alignment explanation
Indices: 52540775--52541152 Score: 464
Period size: 153 Copynumber: 2.5 Consensus size: 150
52540765 TGCAATATTT
* *
52540775 GTGAAGGAGATATTCCA-CGTGATATTTCTGGTCTATCCTCTTTG-TATCATCTTGATCTTAGTG
1 GTGAAGCAGATATT-CATAGTGATATTTCTGGTCTATCCTCTTTGATA-CATCTTGATCTTAGTG
* *
52540838 GTAATAATTTCACCAGAATACCTGCATCTCTTACTCGACTCTCAAAGCTTGACTTCCTTAAATTG
64 GTAAAAATTTCATCAGAATACCTGCATCTCTTACTCGACTCTCAAAGCTTGACTTCCTTAAA-TG
52540903 TCAAATTGCAACATGAGCACTCTTG
128 T--AATTGCAACATGAGCACTCTTG
* * * **
52540928 GTGAAGCAGACACTCATAGTGATATTTCCGGTCTATCCTCTTTGACGCATCTTGATCTTAGTGGT
1 GTGAAGCAGATATTCATAGTGATATTTCTGGTCTATCCTCTTTGATACATCTTGATCTTAGTGGT
* * * * *
52540993 AACAATTTCATCAGCATACCTGCTTCTCTTACTCGACTCTCAAAGCTTTTG-GTT-CTT-GA-GT
66 AAAAATTTCATCAGAATACCTGCATCTCTTACTCGACTCTCAAAGC--TTGACTTCCTTAAATGT
* *
52541054 -TTTGCAACATGTGCACTCTTG
129 AATTGCAACATGAGCACTCTTG
* * * *
52541075 GTGAAGCAGATATTCATAGTGACATTTCTGATCTATCCTCTTTGATACGTCTTGAACTTAGTGGT
1 GTGAAGCAGATATTCATAGTGATATTTCTGGTCTATCCTCTTTGATACATCTTGATCTTAGTGGT
52541140 AAAAATTTCATCA
66 AAAAATTTCATCA
52541153 CCATTCATTT
Statistics
Matches: 196, Mismatches: 25, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
147 87 0.44
150 2 0.01
152 3 0.02
153 99 0.51
154 2 0.01
155 3 0.02
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.37
Consensus pattern (150 bp):
GTGAAGCAGATATTCATAGTGATATTTCTGGTCTATCCTCTTTGATACATCTTGATCTTAGTGGT
AAAAATTTCATCAGAATACCTGCATCTCTTACTCGACTCTCAAAGCTTGACTTCCTTAAATGTAA
TTGCAACATGAGCACTCTTG
Found at i:52541169 original size:147 final size:146
Alignment explanation
Indices: 52540908--52541173 Score: 372
Period size: 147 Copynumber: 1.8 Consensus size: 146
52540898 AATTGTCAAA
* *
52540908 TTGCAACATGAGCACTCTTGGTGAAGCAGACACTCATAGTGATATTTCCGGTCTATCCTCTTTGA
1 TTGCAACATGAGCACTCTTGGTGAAGCAGACACTCATAGTGACATTTCCGATCTATCCTCTTTGA
* * * * *
52540973 CGCATCTTGATCTTAGTGGTAACAATTTCATCAGCATACCTGCTTCTCTTACTCGACTCTCAAAG
66 CACATCTTGAACTTAGTGGTAAAAATTTCATCACCATACAT-CTTCTCTTACTCGACTCTCAAAG
52541038 CTTTTGGTTCTTGAGTT
130 CTTTTGGTTCTTGAGTT
* * * *
52541055 TTGCAACATGTGCACTCTTGGTGAAGCAGATATTCATAGTGACATTTCTGATCTATCCTCTTTGA
1 TTGCAACATGAGCACTCTTGGTGAAGCAGACACTCATAGTGACATTTCCGATCTATCCTCTTTGA
* * *
52541120 TACGTCTTGAACTTAGTGGTAAAAATTTCATCACCATTCAT-TTGGCTCTTACTC
66 CACATCTTGAACTTAGTGGTAAAAATTTCATCACCATACATCTT--CTCTTACTC
52541174 AACTTTCCAG
Statistics
Matches: 103, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
145 2 0.02
147 101 0.98
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.37
Consensus pattern (146 bp):
TTGCAACATGAGCACTCTTGGTGAAGCAGACACTCATAGTGACATTTCCGATCTATCCTCTTTGA
CACATCTTGAACTTAGTGGTAAAAATTTCATCACCATACATCTTCTCTTACTCGACTCTCAAAGC
TTTTGGTTCTTGAGTT
Found at i:52550702 original size:47 final size:46
Alignment explanation
Indices: 52550640--52550733 Score: 136
Period size: 47 Copynumber: 2.0 Consensus size: 46
52550630 ATATCCAATC
* *
52550640 TATATGATATAAATTCAAAGCTTAGTCGAATT-GATTGATACAATCAA
1 TATATGATATAAATTCAAAACTTAATCGAATTAG-TTGATACAA-CAA
*
52550687 TATATGATATAAATTCAAAACTTAATCTAATTAGTTGATACAACAA
1 TATATGATATAAATTCAAAACTTAATCGAATTAGTTGATACAACAA
52550733 T
1 T
52550734 CCTTGAAAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
46 4 0.09
47 38 0.88
48 1 0.02
ACGTcount: A:0.45, C:0.11, G:0.10, T:0.35
Consensus pattern (46 bp):
TATATGATATAAATTCAAAACTTAATCGAATTAGTTGATACAACAA
Found at i:52551370 original size:18 final size:18
Alignment explanation
Indices: 52551322--52551377 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 18
52551312 CTAAGTCACT
*
52551322 TCATTTCTTTTTGTCTAAAC
1 TCATTTCCTTTT-TCT-AAC
*
52551342 T-ACTTTTCTTTTTCTAAC
1 TCA-TTTCCTTTTTCTAAC
52551360 TCATTTCCTTTTTGCTAA
1 TCATTTCCTTTTT-CTAA
52551378 GAAACTATAG
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
18 13 0.43
19 9 0.30
20 8 0.27
ACGTcount: A:0.18, C:0.21, G:0.04, T:0.57
Consensus pattern (18 bp):
TCATTTCCTTTTTCTAAC
Found at i:52564181 original size:91 final size:91
Alignment explanation
Indices: 52564062--52564305 Score: 348
Period size: 91 Copynumber: 2.7 Consensus size: 91
52564052 CACCATTATG
* * *
52564062 TCTTAATGATTAATATGATCACTATCAACTAATAATTGTGATAAATTACTCACTTGAGAACAAGC
1 TCTTAATGATTTATATGATCACTATCAACTAATGATTGTGATAAATTACTCACTTGAGAACAAGA
52564127 AACCACTTTCAACAACCATTATGTCT
66 AACCACTTTCAACAACCATTATGTCT
* * * **
52564153 TCTTCATGATTTATATAAGCACTATCAACTAATGATTGTGATAAATTACT-TGTTCGAGAACAAG
1 TCTTAATGATTTATATGATCACTATCAACTAATGATTGTGATAAATTACTCACTT-GAGAACAAG
*
52564217 AAACCACTTTCAACAACCATTGTGTCT
65 AAACCACTTTCAACAACCATTATGTCT
* * * *
52564244 TTTTAATGATTTATATGATCACTGTTAACTAATGATTGTGATAAA-TACTCATTTGAGAACAA
1 TCTTAATGATTTATATGATCACTATCAACTAATGATTGTGATAAATTACTCACTTGAGAACAA
52564306 ATAATTCTAT
Statistics
Matches: 134, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
90 14 0.10
91 120 0.90
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (91 bp):
TCTTAATGATTTATATGATCACTATCAACTAATGATTGTGATAAATTACTCACTTGAGAACAAGA
AACCACTTTCAACAACCATTATGTCT
Found at i:52567028 original size:24 final size:24
Alignment explanation
Indices: 52566996--52567042 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
52566986 AGAAATAATC
52566996 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
*
52567020 TTTCAATTAAACTTTGTTTATTT
1 TTTCAATTAAACTCTGTTTATTT
52567043 ATTTGAGACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.26, C:0.11, G:0.06, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:52569030 original size:24 final size:24
Alignment explanation
Indices: 52568979--52569033 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
52568969 TCTTTTACTT
*
52568979 AAACTCTATTTATTTGTTTCAATT
1 AAACTCTATTTATTTGTTTCAATC
* * *
52569003 AAACTCTGTTTATTTGTTTGAGTC
1 AAACTCTATTTATTTGTTTCAATC
52569027 AAACTCT
1 AAACTCT
52569034 TATTAGTCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.27, C:0.15, G:0.09, T:0.49
Consensus pattern (24 bp):
AAACTCTATTTATTTGTTTCAATC
Found at i:52571523 original size:41 final size:42
Alignment explanation
Indices: 52571447--52571525 Score: 124
Period size: 41 Copynumber: 1.9 Consensus size: 42
52571437 TAACATAGTT
* * *
52571447 TTTTTTATACCATTTAAAATTTTAGTCATTTAATTCATATAG
1 TTTTTTATACCATTTAAAATTTTAGTAACTCAATTCATATAG
52571489 TTTTTT-TACCATTTAAAATTTTAGTAACTCAATTCAT
1 TTTTTTATACCATTTAAAATTTTAGTAACTCAATTCAT
52571526 TCCTTTTTAC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
41 28 0.82
42 6 0.18
ACGTcount: A:0.33, C:0.11, G:0.04, T:0.52
Consensus pattern (42 bp):
TTTTTTATACCATTTAAAATTTTAGTAACTCAATTCATATAG
Found at i:52580554 original size:39 final size:39
Alignment explanation
Indices: 52580469--52580554 Score: 136
Period size: 39 Copynumber: 2.2 Consensus size: 39
52580459 AATTCAAGGA
* *
52580469 AATGGTTCGATATTATTATGCCTGGAAGTGAAATCCCAG
1 AATGGTTTGATATTATTATGCCCGGAAGTGAAATCCCAG
* *
52580508 AATGGTTTGATATTATTATGCCCGGAAGTGGAATCTCAG
1 AATGGTTTGATATTATTATGCCCGGAAGTGAAATCCCAG
52580547 AATGGTTT
1 AATGGTTT
52580555 AGCCAACAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.34
Consensus pattern (39 bp):
AATGGTTTGATATTATTATGCCCGGAAGTGAAATCCCAG
Found at i:52581446 original size:6 final size:6
Alignment explanation
Indices: 52581430--52581459 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
52581420 GGAGTAGCAA
52581430 TATCA- TATCAG TATCAG TATCAG TATCAG T
1 TATCAG TATCAG TATCAG TATCAG TATCAG T
52581460 TTCAAGTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (6 bp):
TATCAG
Found at i:52589211 original size:152 final size:152
Alignment explanation
Indices: 52588826--52589190 Score: 500
Period size: 152 Copynumber: 2.4 Consensus size: 152
52588816 GATATTCCAC
**** * *
52588826 GTGATATTTCTGGTCTATCCTCTTTTTTTCATCTTGATCTTAGTGGTAATAATTTCACCAGCATA
1 GTGATATTTCTGGTCTATCCTC-TTTGAGAATCTTGATCTTAGTGGTAACAATTTCATCAGCATA
*
52588891 CCTGCACCTCTTACTCAACTCCCAAAGCTTAACTTCCTTGAATTGTCAAATTGCAACATGTGCAC
65 CCTGCACCTCTTACTCAACTCCCAAAGCTTAACGTCCTTGAATTGTCAAATTGCAACATGTGCAC
52588956 TCTTGGTGAAGCAGACACTCATA
130 TCTTGGTGAAGCAGACACTCATA
* *
52588979 GTGATATTTCTGGTCTATCCTCTTTGAGAAATCTTTATCTTTGTGGTAACAATTTCATCAGCATA
1 GTGATATTTCTGGTCTATCCTCTTTGAG-AATCTTGATCTTAGTGGTAACAATTTCATCAGCATA
* * * * * *
52589044 CCTGCATCTCTTACTCGACTCTCAAAGC-TGAGGTCCTT-AATTTGTCAAATTGCAGCATGTGCA
65 CCTGCACCTCTTACTCAACTCCCAAAGCTTAACGTCCTTGAA-TTGTCAAATTGCAACATGTGCA
* *
52589107 CTCTTGGTGAAGCAGATATTCATA
129 CTCTTGGTGAAGCAGACACTCATA
* * *
52589131 GTGACATTTCTGGTCTATCCTCTTTGAAGAATCTTGCTCTTAGTGGTAAGAATTTCATCA
1 GTGATATTTCTGGTCTATCCTCTTTG-AGAATCTTGATCTTAGTGGTAACAATTTCATCA
52589191 CCATTCCTTT
Statistics
Matches: 187, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
151 2 0.01
152 105 0.56
153 80 0.43
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (152 bp):
GTGATATTTCTGGTCTATCCTCTTTGAGAATCTTGATCTTAGTGGTAACAATTTCATCAGCATAC
CTGCACCTCTTACTCAACTCCCAAAGCTTAACGTCCTTGAATTGTCAAATTGCAACATGTGCACT
CTTGGTGAAGCAGACACTCATA
Found at i:52590818 original size:25 final size:23
Alignment explanation
Indices: 52590790--52590835 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
52590780 GTTGGATCCA
52590790 AATTAAATTCTAAAAACATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
52590815 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
52590836 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:52590927 original size:13 final size:13
Alignment explanation
Indices: 52590906--52590939 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
52590896 ACAATATAAC
52590906 AATAATAATCCTA
1 AATAATAATCCTA
*
52590919 AATATTAATCCTA
1 AATAATAATCCTA
*
52590932 AAAAATAA
1 AATAATAA
52590940 AATTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:52591498 original size:39 final size:39
Alignment explanation
Indices: 52591382--52591490 Score: 164
Period size: 39 Copynumber: 2.8 Consensus size: 39
52591372 TACGGGTAAT
* * *
52591382 AGATTGCTAAGATGAGGAGTGCGATGAGCATGAGCTGTC
1 AGATTGCTCAGATGAGGAATGCGATGAGCTTGAGCTGTC
* *
52591421 AGATTTCTCAGATGAGGAACGCGATGAGCTTGAGCTGTC
1 AGATTGCTCAGATGAGGAATGCGATGAGCTTGAGCTGTC
*
52591460 AGATTGCTCAGATGAGGAATGCTATGAGCTT
1 AGATTGCTCAGATGAGGAATGCGATGAGCTT
52591491 CAACTGTCTT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 62 1.00
ACGTcount: A:0.28, C:0.15, G:0.32, T:0.26
Consensus pattern (39 bp):
AGATTGCTCAGATGAGGAATGCGATGAGCTTGAGCTGTC
Found at i:52597562 original size:15 final size:16
Alignment explanation
Indices: 52597537--52597566 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
52597527 GAATTAAAAA
52597537 TAAAAGAAAATAGAAT
1 TAAAAGAAAATAGAAT
52597553 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
52597567 AATAGGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAATAGAAT
Found at i:52597569 original size:22 final size:22
Alignment explanation
Indices: 52597512--52597571 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
52597502 ATCTAAGGAA
52597512 AAAAAT-AAA-AAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
52597532 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
52597554 AAAAGA-AATAGAAAATAG
1 AAAA-ATAAAAGAAAATAG
52597572 GGAAGTCAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
20 6 0.17
21 3 0.08
22 26 0.72
23 1 0.03
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:52598359 original size:14 final size:14
Alignment explanation
Indices: 52598342--52598371 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
52598332 TTTAAACTCT
*
52598342 AAAAGATAAATATA
1 AAAAGATAAACATA
52598356 AAAAGATAAACATA
1 AAAAGATAAACATA
52598370 AA
1 AA
52598372 TTAAATACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.73, C:0.03, G:0.07, T:0.17
Consensus pattern (14 bp):
AAAAGATAAACATA
Found at i:52598395 original size:19 final size:19
Alignment explanation
Indices: 52598373--52598415 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
52598363 AAACATAAAT
52598373 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
52598392 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
52598411 TAAAT
1 TAAAT
52598416 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:52607510 original size:91 final size:91
Alignment explanation
Indices: 52607396--52607565 Score: 277
Period size: 91 Copynumber: 1.9 Consensus size: 91
52607386 TCTCATTGTC
**
52607396 ACCATTGTGTCTCCTTAATGATTAATATGATCACTATCAACTAATGATTGTGATAAATTGTTCGT
1 ACCATTGTGTCTCCTTAATGATTAATATGATCACTATCAACTAATGATTGTGATAAATTACTCGT
*
52607461 TCGAGAACAAGCAACCACTTTCAGCA
66 TCAAGAACAAGCAACCACTTTCAGCA
** *
52607487 ACCATTGTGTCTTTTTAATGATTAATATGATCACTATTAACTAATGATTGTGATAAATTACTCGT
1 ACCATTGTGTCTCCTTAATGATTAATATGATCACTATCAACTAATGATTGTGATAAATTACTCGT
*
52607552 TCAAGAACTAGCAA
66 TCAAGAACAAGCAA
52607566 TTCTATTTTA
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
91 72 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (91 bp):
ACCATTGTGTCTCCTTAATGATTAATATGATCACTATCAACTAATGATTGTGATAAATTACTCGT
TCAAGAACAAGCAACCACTTTCAGCA
Found at i:52611128 original size:24 final size:24
Alignment explanation
Indices: 52611094--52611168 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
52611084 AAAAATAATC
*
52611094 TTTCACTTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
* * *
52611118 TTTTAATTAAACTCTATTTTTTTG
1 TTTCAATTAAACTCTGTTTATTTG
*
52611142 TTTCAATTAAACTCTGTTTAGTTG
1 TTTCAATTAAACTCTGTTTATTTG
52611166 TTT
1 TTT
52611169 GAGTCAAATT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.23, C:0.12, G:0.08, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:52627074 original size:30 final size:31
Alignment explanation
Indices: 52627040--52627099 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
52627030 ATATGTATTA
* * *
52627040 TTAAATCAAAATTAAAGTTT-ATGTTTACAT
1 TTAAACCAAAATCAAAGTTTCATGTGTACAT
*
52627070 TTAAACCATAATCAAAGTTTCATGTGTACA
1 TTAAACCAAAATCAAAGTTTCATGTGTACA
52627100 ATTGCATCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (31 bp):
TTAAACCAAAATCAAAGTTTCATGTGTACAT
Found at i:52627391 original size:7 final size:7
Alignment explanation
Indices: 52627371--52627407 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
52627361 TTATACACCA
52627371 TTTATTT
1 TTTATTT
*
52627378 TAT-TTT
1 TTTATTT
52627384 TTTATTT
1 TTTATTT
52627391 TTTATTT
1 TTTATTT
52627398 TTTATTT
1 TTTATTT
52627405 TTT
1 TTT
52627408 TAGGCTACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 5 0.19
7 22 0.81
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTATTT
Found at i:52630860 original size:22 final size:21
Alignment explanation
Indices: 52630829--52630871 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
52630819 TTAGTATATC
52630829 TTTATGTATTGTAAATAATGAT
1 TTTATGTATTGTAAAT-ATGAT
* *
52630851 TTTATTTATTTTAAATATGAT
1 TTTATGTATTGTAAATATGAT
52630872 AAGAAACAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (21 bp):
TTTATGTATTGTAAATATGAT
Found at i:52638331 original size:14 final size:12
Alignment explanation
Indices: 52638294--52638360 Score: 52
Period size: 14 Copynumber: 5.6 Consensus size: 12
52638284 TACTTTAGCC
52638294 ATTTTTTA-TT-
1 ATTTTTTATTTA
*
52638304 ATTTGTT-TTT-
1 ATTTTTTATTTA
52638314 ATTTTATTATTTGA
1 ATTTT-TTATTT-A
*
52638328 ATTTTTAATTTA
1 ATTTTTTATTTA
52638340 ATTTTTCTATTTTA
1 ATTTTT-TA-TTTA
52638354 ATTTTTT
1 ATTTTTT
52638361 CCCTTTTATT
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
10 12 0.26
11 2 0.04
12 10 0.22
13 7 0.15
14 15 0.33
ACGTcount: A:0.22, C:0.01, G:0.03, T:0.73
Consensus pattern (12 bp):
ATTTTTTATTTA
Found at i:52638333 original size:21 final size:18
Alignment explanation
Indices: 52638297--52638358 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 18
52638287 TTTAGCCATT
*
52638297 TTTTATTATTTGTTTTTA
1 TTTTATTATTTGTTTTAA
52638315 TTTTATTATTTGAATTTTTAA
1 TTTTATTATTTG---TTTTAA
* * *
52638336 TTTAATTTTTCTATTTTAA
1 TTTTATTATT-TGTTTTAA
52638355 TTTT
1 TTTT
52638359 TTCCCTTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
18 12 0.34
19 9 0.26
21 13 0.37
22 1 0.03
ACGTcount: A:0.23, C:0.02, G:0.03, T:0.73
Consensus pattern (18 bp):
TTTTATTATTTGTTTTAA
Found at i:52640591 original size:25 final size:23
Alignment explanation
Indices: 52640550--52640595 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
52640540 CCAATTAGGG
52640550 AATTATTATTTAGATTTAATTCA
1 AATTATTATTTAGATTTAATTCA
*
52640573 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TATTTAG-ATTTAATT
52640596 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (23 bp):
AATTATTATTTAGATTTAATTCA
Found at i:52654663 original size:40 final size:40
Alignment explanation
Indices: 52654608--52654724 Score: 139
Period size: 40 Copynumber: 2.9 Consensus size: 40
52654598 TGTGGACAGA
* * **
52654608 AAACGCCGCAAAAGGTAAATCAATAGCGGTGTTTTTTGAT
1 AAACGACGCAAAAGGTAAAGCAATAGCGGTGTTTTTAAAT
* *
52654648 AAACGACGCAAAAGGTAAAGCAATAGC-ATCGTTTCTAAAT
1 AAACGACGCAAAAGGTAAAGCAATAGCGGT-GTTTTTAAAT
*
52654688 AAAC-ACCGCAAAAGGTAAAGCAATAGCGGCGTTTTTA
1 AAACGA-CGCAAAAGGTAAAGCAATAGCGGTGTTTTTA
52654725 CACAAGCGCC
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
39 2 0.03
40 63 0.97
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.22
Consensus pattern (40 bp):
AAACGACGCAAAAGGTAAAGCAATAGCGGTGTTTTTAAAT
Found at i:52654758 original size:40 final size:41
Alignment explanation
Indices: 52654711--52654884 Score: 124
Period size: 41 Copynumber: 4.3 Consensus size: 41
52654701 GGTAAAGCAA
* * *
52654711 TAGCGGCGTTTTTACACAAGCGCCACTAAAGGTCGGGTCAT
1 TAGCGGCGCTTATACACAAGCGCCACTAAAGGTCAGGTCAT
* * * *
52654752 TA-CGGCGCTTATCCATAAGTGCCGCTAAAGGTCAGGTCAT
1 TAGCGGCGCTTATACACAAGCGCCACTAAAGGTCAGGTCAT
* * ** * *
52654792 TAGCGGCGCTT-TCCCAAAAATGCCGCTAAAAGTCATGG-CAT
1 TAGCGGCGCTTAT-ACACAAGCGCCACTAAAGGTCA-GGTCAT
* * * *
52654833 TAGCGACGCTT-TCCCACAAGCGCCGCTAAAGGTTAGGGT-AT
1 TAGCGGCGCTTAT-ACACAAGCGCCACTAAAGGTCA-GGTCAT
52654874 TAGCGGCGCTT
1 TAGCGGCGCTT
52654885 CTTCATACAC
Statistics
Matches: 111, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
40 34 0.31
41 75 0.68
42 2 0.02
ACGTcount: A:0.25, C:0.26, G:0.26, T:0.24
Consensus pattern (41 bp):
TAGCGGCGCTTATACACAAGCGCCACTAAAGGTCAGGTCAT
Found at i:52654816 original size:41 final size:42
Alignment explanation
Indices: 52654736--52654884 Score: 175
Period size: 41 Copynumber: 3.7 Consensus size: 42
52654726 ACAAGCGCCA
*
52654736 CTAAAGGTC-GGGTCATTA-CGGCGCTTAT-CCATAAGTGCCG
1 CTAAAGGTCAGGGTCATTAGCGGCGCTT-TCCCAAAAGTGCCG
*
52654776 CTAAAGGTCA-GGTCATTAGCGGCGCTTTCCCAAAAATGCCG
1 CTAAAGGTCAGGGTCATTAGCGGCGCTTTCCCAAAAGTGCCG
* * * * *
52654817 CTAAAAGTCATGG-CATTAGCGACGCTTTCCCACAAGCGCCG
1 CTAAAGGTCAGGGTCATTAGCGGCGCTTTCCCAAAAGTGCCG
*
52654858 CTAAAGGTTAGGGT-ATTAGCGGCGCTT
1 CTAAAGGTCAGGGTCATTAGCGGCGCTT
52654885 CTTCATACAC
Statistics
Matches: 93, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
40 18 0.19
41 73 0.78
42 2 0.02
ACGTcount: A:0.25, C:0.26, G:0.26, T:0.23
Consensus pattern (42 bp):
CTAAAGGTCAGGGTCATTAGCGGCGCTTTCCCAAAAGTGCCG
Found at i:52654946 original size:42 final size:42
Alignment explanation
Indices: 52654896--52654986 Score: 128
Period size: 42 Copynumber: 2.2 Consensus size: 42
52654886 TTCATACACA
* * * * *
52654896 CCGCTAATGCTCTGACTTTTAGCGGCGTTTATTGTAGAAGCG
1 CCGCTAATGATCTAACCTTTAGCGGCGTTTATTGTAAAAACG
*
52654938 CCGCTAATGATCTAACCTTTAGCGGCGTTTATTTTAAAAACG
1 CCGCTAATGATCTAACCTTTAGCGGCGTTTATTGTAAAAACG
52654980 CCGCTAA
1 CCGCTAA
52654987 AAATTAAGTA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (42 bp):
CCGCTAATGATCTAACCTTTAGCGGCGTTTATTGTAAAAACG
Found at i:52660540 original size:21 final size:21
Alignment explanation
Indices: 52660514--52660555 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
52660504 AAAAAGAACA
52660514 TGTTCTTTAGCGGCGTTTGTG
1 TGTTCTTTAGCGGCGTTTGTG
52660535 TGTTCTTTAGCGGCGTTTGTG
1 TGTTCTTTAGCGGCGTTTGTG
52660556 GGTAAAGCGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.05, C:0.14, G:0.33, T:0.48
Consensus pattern (21 bp):
TGTTCTTTAGCGGCGTTTGTG
Found at i:52660596 original size:43 final size:43
Alignment explanation
Indices: 52660535--52660633 Score: 155
Period size: 43 Copynumber: 2.3 Consensus size: 43
52660525 GGCGTTTGTG
* *
52660535 TGTTCTTTAGCGGCGTTTGTGGGTAAAGCG-TCGCTAAAGACTA
1 TGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCT-GCTAAAGACCA
*
52660578 TGTTCTTTAGCGGCGTTTGTTGGAAAAGCGCTGCTAAAGACCA
1 TGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCTGCTAAAGACCA
52660621 TGTTCTTTAGCGG
1 TGTTCTTTAGCGG
52660634 TATTTTTCTT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
43 51 0.98
44 1 0.02
ACGTcount: A:0.20, C:0.17, G:0.29, T:0.33
Consensus pattern (43 bp):
TGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCTGCTAAAGACCA
Found at i:52671374 original size:14 final size:14
Alignment explanation
Indices: 52671355--52671382 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
52671345 ATAATAGATT
52671355 TTTAATTAATTAAA
1 TTTAATTAATTAAA
52671369 TTTAATTAATTAAA
1 TTTAATTAATTAAA
52671383 CTTTTTAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTAATTAATTAAA
Found at i:52671744 original size:14 final size:14
Alignment explanation
Indices: 52671725--52671752 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
52671715 ATTTAAAATT
52671725 TTTAATTAATTAAA
1 TTTAATTAATTAAA
52671739 TTTAATTAATTAAA
1 TTTAATTAATTAAA
52671753 AATTTATTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTAATTAATTAAA
Found at i:52673190 original size:153 final size:153
Alignment explanation
Indices: 52672898--52673200 Score: 378
Period size: 153 Copynumber: 2.0 Consensus size: 153
52672888 ATCTAAGGGA
* * * *
52672898 CTGCAATCTTTGTGAAGGAGATATTCCAGCTGATATTACTGGTCTATCCTGTTTGACACGTCTTG
1 CTGCAATCTTGGTGAAGGAGATATTCCAGCTGATATTACTGGTCTATCCTCTTTGACACATCTTC
* * *
52672963 ATCTTAGTGATAATAATTTCATCAGCATACCTGCATCTCTTACTCGACTCTCAAAGCTTGAGTTC
66 ATCTTAGGGATAACAATTTCATCAGCATACCTGCATCTATTACTCGACTCTCAAAGCTTGAGTTC
*
52673028 CTTAAATTGTCAA-ATTGCAACAT
131 ATTAAATTGT-AAGATTGCAACAT
* * ***
52673051 CTGCACTCTTGGTGAAGGAGATATTCCTAG-TGATATTTCTGGTCTATCCTCTTTGAGGTATCTT
1 CTGCAATCTTGGTGAAGGAGATATTCC-AGCTGATATTACTGGTCTATCCTCTTTGACACATCTT
* * * * * *
52673115 CTTCTTAGGGGTAACAATTTCATCAGCATACCTGCATCTATTATTCGACTTTCCAAGCTTTA-TT
65 CATCTTAGGGATAACAATTTCATCAGCATACCTGCATCTATTACTCGACTCTCAAAGCTTGAGTT
*
52673179 CTATTAGATTGTAAGATTGCAA
130 C-ATTAAATTGTAAGATTGCAA
52673201 GATGCTTAAA
Statistics
Matches: 127, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
152 5 0.04
153 120 0.94
154 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (153 bp):
CTGCAATCTTGGTGAAGGAGATATTCCAGCTGATATTACTGGTCTATCCTCTTTGACACATCTTC
ATCTTAGGGATAACAATTTCATCAGCATACCTGCATCTATTACTCGACTCTCAAAGCTTGAGTTC
ATTAAATTGTAAGATTGCAACAT
Found at i:52680651 original size:47 final size:47
Alignment explanation
Indices: 52680561--52680652 Score: 123
Period size: 47 Copynumber: 2.0 Consensus size: 47
52680551 ATATCTAATC
* * **
52680561 TATATGATATAAATTCAAAGCTTAGTCTAATTGATTGATACAATCAA
1 TATATGATATAAATTCAAAACTTAATCTAATTGATACATACAATCAA
*
52680608 TATATGATATAAATTCAAAACTTAATCATAGTTGATACA-ACAATC
1 TATATGATATAAATTCAAAACTTAATC-TAATTGATACATACAATC
52680653 CTTAAAAAGT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
47 31 0.79
48 8 0.21
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.35
Consensus pattern (47 bp):
TATATGATATAAATTCAAAACTTAATCTAATTGATACATACAATCAA
Found at i:52682326 original size:24 final size:24
Alignment explanation
Indices: 52682278--52682326 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
52682268 TTTTAGCTTA
* *
52682278 TTTTAATATAAATTATTTAAATTT
1 TTTTAATATAAATGATTGAAATTT
* *
52682302 TTTTAGTATAAATGATTGAACTTT
1 TTTTAATATAAATGATTGAAATTT
52682326 T
1 T
52682327 ATCAAGGTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (24 bp):
TTTTAATATAAATGATTGAAATTT
Found at i:52683417 original size:153 final size:153
Alignment explanation
Indices: 52683013--52683396 Score: 578
Period size: 153 Copynumber: 2.5 Consensus size: 153
52683003 TGCAATCTTT
* * * *
52683013 GTGAAGGAGATATTCCA-CGTGATATTTCTGGTCTACCCTCTTTGATACGTTTTGATCTTAGTGG
1 GTGAAGCAGATATT-CATAGTGATATTTCTGGTCTATCCTCTTTGATACGTCTTGATCTTAGTGG
* *
52683077 TAACAATTTCATCAGCATGCCTGCATCTCTTACTCGACTCTCCAAGCTTGAAGATCTTATATTGT
65 TAACAATTTCATCAGCATACCTGCATCTCTTACTCGACTCTCCAAGCTTGAAGATCTTATAATGT
*
52683142 CAAATTGCAACATGTGCACTCTTG
130 CAAATTGCAACATGTGCACTCCTG
* **
52683166 GTGAAGCAGATACTCATAGTGATATTTCTGGTCTATCCTCTTTG-TGGTGTCTTGATCTTAGTGG
1 GTGAAGCAGATATTCATAGTGATATTTCTGGTCTATCCTCTTTGAT-ACGTCTTGATCTTAGTGG
* *
52683230 TAACAATTTCATCAGCATACCTGCATCTCTTACTCGACTCTCCAAGCTT-CAGTTTCTT-TACAT
65 TAACAATTTCATCAGCATACCTGCATCTCTTACTCGACTCTCCAAGCTTGAAG-ATCTTATA-AT
52683293 GTCAAATTGCAACATGTGCACTCCTG
128 GTCAAATTGCAACATGTGCACTCCTG
*
52683319 GTGAAGCAGATATTCATAGTGACATTTCTGGTCTATCCTCTTTGATACGTCTTGATCTTAGTGGT
1 GTGAAGCAGATATTCATAGTGATATTTCTGGTCTATCCTCTTTGATACGTCTTGATCTTAGTGGT
*
52683384 AAGAATTTCATCA
66 AACAATTTCATCA
52683397 CCATTCCTTT
Statistics
Matches: 209, Mismatches: 17, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
152 7 0.03
153 201 0.96
154 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.37
Consensus pattern (153 bp):
GTGAAGCAGATATTCATAGTGATATTTCTGGTCTATCCTCTTTGATACGTCTTGATCTTAGTGGT
AACAATTTCATCAGCATACCTGCATCTCTTACTCGACTCTCCAAGCTTGAAGATCTTATAATGTC
AAATTGCAACATGTGCACTCCTG
Found at i:52684684 original size:15 final size:15
Alignment explanation
Indices: 52684637--52684687 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
52684627 TTGCTTTAGA
*
52684637 TTACATTTTAATCAC
1 TTACATTTTAATTAC
* * * *
52684652 TTATATTTAAAAT-G
1 TTACATTTTAATTAC
52684666 TTACATTTTAATTAC
1 TTACATTTTAATTAC
52684681 TTACATT
1 TTACATT
52684688 ATCGTCTTGT
Statistics
Matches: 26, Mismatches: 9, Indels: 2
0.70 0.24 0.05
Matches are distributed among these distances:
14 10 0.38
15 16 0.62
ACGTcount: A:0.35, C:0.12, G:0.02, T:0.51
Consensus pattern (15 bp):
TTACATTTTAATTAC
Found at i:52692943 original size:153 final size:153
Alignment explanation
Indices: 52692558--52692923 Score: 558
Period size: 153 Copynumber: 2.4 Consensus size: 153
52692548 GATATTCCAG
*
52692558 GTGATATTTCTGTTCTATCCTCTTTG-GAACGTCTTGATCTTAGTGGTAACAATTTCATCAGCAT
1 GTGATATTTCTGGTCTATCCTCTTTGAG-ACGTCTTGATCTTAGTGGTAACAATTTCATCAGCAT
* * * ***
52692622 ACCTGCATCTCTTACTCGACTCTCGAAGCTTTGGTTTCTTGGTTTGTCAAATTGCAACATGTGCA
65 ACCTGCATCTCTTACTAGACTCTCAAAGCTTTGGGTTCTTAACTTGTCAAATTGCAACATGTGCA
*
52692687 CTCTTGATGAAGCAGATACTCATA
130 CTCTTGATGAAGAAGATACTCATA
* *
52692711 GTGATATTTCTGGTCTATCCTCCTTGAGA-GATCTTGATCTTCGTGGTAACAATTTCATCAGCAT
1 GTGATATTTCTGGTCTATCCTCTTTGAGACG-TCTTGATCTTAGTGGTAACAATTTCATCAGCAT
52692775 ACCTGCATCTCTTACTAGACTCTCAAAGC-TTGAGGTTCTTAACTTGTCAAATTGCAACATGTGC
65 ACCTGCATCTCTTACTAGACTCTCAAAGCTTTG-GGTTCTTAACTTGTCAAATTGCAACATGTGC
* * *
52692839 ACTCTTGGTGAAGAAGATATTCGTA
129 ACTCTTGATGAAGAAGATACTCATA
*
52692864 GTGATATTTCTGGTCTATCCTCTTTGAGACGTCTTGATCTTAGTGGTAAGAATTTCATCA
1 GTGATATTTCTGGTCTATCCTCTTTGAGACGTCTTGATCTTAGTGGTAACAATTTCATCA
52692924 CCATTCCTTT
Statistics
Matches: 193, Mismatches: 16, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
152 4 0.02
153 187 0.97
154 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.37
Consensus pattern (153 bp):
GTGATATTTCTGGTCTATCCTCTTTGAGACGTCTTGATCTTAGTGGTAACAATTTCATCAGCATA
CCTGCATCTCTTACTAGACTCTCAAAGCTTTGGGTTCTTAACTTGTCAAATTGCAACATGTGCAC
TCTTGATGAAGAAGATACTCATA
Found at i:52697663 original size:15 final size:16
Alignment explanation
Indices: 52697643--52697672 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52697633 TTCGGACACA
52697643 TTAAAA-AAATAAAAT
1 TTAAAATAAATAAAAT
52697658 TTAAAATAAATAAAA
1 TTAAAATAAATAAAA
52697673 AAAATCAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
TTAAAATAAATAAAAT
Found at i:52701131 original size:44 final size:44
Alignment explanation
Indices: 52701068--52701155 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
52701058 TCTTCCTTTG
52701068 CCATTGATCGATTTAAAGCTTTACTCACTTATGACCAAACACAT
1 CCATTGATCGATTTAAAGCTTTACTCACTTATGACCAAACACAT
52701112 CCATTGATCGATTTAAAGCTTTACTCACTTATGACCAAACACAT
1 CCATTGATCGATTTAAAGCTTTACTCACTTATGACCAAACACAT
52701156 TGGCAACATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.34, C:0.25, G:0.09, T:0.32
Consensus pattern (44 bp):
CCATTGATCGATTTAAAGCTTTACTCACTTATGACCAAACACAT
Found at i:52707550 original size:3 final size:3
Alignment explanation
Indices: 52707542--52707580 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
52707532 TTTCCCCATT
*
52707542 TTC TTC TTC TT- TTCC TTC TTC TTC TTC CTC TTC TTC TTC
1 TTC TTC TTC TTC TT-C TTC TTC TTC TTC TTC TTC TTC TTC
52707581 ATCATCTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 28 0.88
4 2 0.06
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
TTC
Found at i:52707577 original size:12 final size:13
Alignment explanation
Indices: 52707544--52707580 Score: 60
Period size: 12 Copynumber: 3.0 Consensus size: 13
52707534 TCCCCATTTT
52707544 CTTCTTCTT-TTC
1 CTTCTTCTTCTTC
52707556 CTTCTTCTTCTTC
1 CTTCTTCTTCTTC
52707569 C-TCTTCTTCTTC
1 CTTCTTCTTCTTC
52707581 ATCATCTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 20 0.83
13 4 0.17
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (13 bp):
CTTCTTCTTCTTC
Found at i:52707585 original size:3 final size:3
Alignment explanation
Indices: 52707579--52707610 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
52707569 CTCTTCTTCT
*
52707579 TCA TCA TCT TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
52707611 GTCCTCCTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.28, C:0.34, G:0.00, T:0.38
Consensus pattern (3 bp):
TCA
Found at i:52707727 original size:26 final size:28
Alignment explanation
Indices: 52707698--52707759 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 28
52707688 CCTTTTTCTT
*
52707698 CTCCTTCACACT-ACCCCCTCTTCC-TC
1 CTCCTTCACACTGACACCCTCTTCCTTC
*
52707724 CTCCTTCACTCTGAGACACCCTCTTCCTTC
1 CTCCTTCACACT--GACACCCTCTTCCTTC
52707754 CTCCTT
1 CTCCTT
52707760 TCATTTCTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 11 0.37
29 11 0.37
30 8 0.27
ACGTcount: A:0.11, C:0.52, G:0.03, T:0.34
Consensus pattern (28 bp):
CTCCTTCACACTGACACCCTCTTCCTTC
Found at i:52716623 original size:3 final size:3
Alignment explanation
Indices: 52716569--52716604 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
52716559 TTGGGGGATA
52716569 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC
52716605 GCCTTCAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (3 bp):
TCC
Found at i:52720153 original size:28 final size:27
Alignment explanation
Indices: 52720107--52720190 Score: 91
Period size: 28 Copynumber: 3.0 Consensus size: 27
52720097 TTTTAGGTAC
52720107 TCGGGGATAAAATCGTAATTTTGGGAAAG
1 TCGGGG-TAAAATCGTAATTTT-GGAAAG
52720136 TTCGGGGTAAAAT-GTAATTTTGG-AAG
1 -TCGGGGTAAAATCGTAATTTTGGAAAG
*
52720162 TCTGAGGGTAAAATGGTAATTTTTGGAAA
1 TC-G-GGGTAAAATCGTAA-TTTTGGAAA
52720191 AAAATCGAGG
Statistics
Matches: 49, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
25 2 0.04
26 4 0.08
27 11 0.22
28 12 0.24
29 12 0.24
30 8 0.16
ACGTcount: A:0.33, C:0.05, G:0.30, T:0.32
Consensus pattern (27 bp):
TCGGGGTAAAATCGTAATTTTGGAAAG
Found at i:52720320 original size:58 final size:59
Alignment explanation
Indices: 52720144--52720422 Score: 223
Period size: 57 Copynumber: 4.7 Consensus size: 59
52720134 AGTTCGGGGT
* * * **
52720144 AAAATGTAATTTTGGAAGTCTGAGGGTAAAATGGTAATTTTTGGAAAAAAATCGAGGTCA
1 AAAATGGAATTTTGGAAGTCCGAGGGTAAAATGGTAATTTTT-GATAAGTATCGAGGTCA
* * * * *
52720204 AAAATGGAGTTTTTGAAAGTTCGAGGGTAAAATAGTAATTTTTGATGAA--ATCGGGGTCA
1 AAAATGGA-ATTTTGGAAGTCCGAGGGTAAAATGGTAATTTTTGAT-AAGTATCGAGGTCA
* * *
52720263 AAAATAGAATTTTGGACA-TCCGAGGGTAAAATGGTAATTTTTG-TAAGTTTCAAGGTCA
1 AAAATGGAATTTTGGA-AGTCCGAGGGTAAAATGGTAATTTTTGATAAGTATCGAGGTCA
** * * * * * *
52720321 AAAATGGAA-TTTGGAAGTTTGAGGGCAAAATGGTAATTTTTG-GAAGTTTTGGGGTTA
1 AAAATGGAATTTTGGAAGTCCGAGGGTAAAATGGTAATTTTTGATAAGTATCGAGGTCA
* **
52720378 AAAATGGAAGTTTTAGAAGTTTG-GGGTTAAAAAT-GTAATTTTTGA
1 AAAATGGAA-TTTTGGAAGTCCGAGGG-T-AAAATGGTAATTTTTGA
52720423 AAGGTTAGGG
Statistics
Matches: 181, Mismatches: 27, Indels: 22
0.79 0.12 0.10
Matches are distributed among these distances:
56 3 0.02
57 48 0.27
58 47 0.26
59 38 0.21
60 14 0.08
61 31 0.17
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.33
Consensus pattern (59 bp):
AAAATGGAATTTTGGAAGTCCGAGGGTAAAATGGTAATTTTTGATAAGTATCGAGGTCA
Found at i:52720434 original size:59 final size:59
Alignment explanation
Indices: 52720334--52720528 Score: 236
Period size: 59 Copynumber: 3.3 Consensus size: 59
52720324 ATGGAATTTG
* * * *
52720334 GAAGTTTGAGGG--CAAAATGGTAATTTTTGGAAGTTTTGGGGTTAAAAATGGAAGTTTTA
1 GAAGTTTGAGGGTTAAAAAT-GTAATTTTTGGAAGTTTAGGGGTT-AAAATGTAAATTTTA
* *
52720393 GAAGTTTG-GGGTTAAAAATGTAATTTTTGAAAGGTTAGGGGTTAAAATGTAAATTTTA
1 GAAGTTTGAGGGTTAAAAATGTAATTTTTGGAAGTTTAGGGGTTAAAATGTAAATTTTA
* * *
52720451 AAAGTTTGAGGG-TAAAAATGTAATTTTTAGGAAGTTTAGGGGTCAAAATGTAATTTTTA
1 GAAGTTTGAGGGTTAAAAATGTAATTTTT-GGAAGTTTAGGGGTTAAAATGTAAATTTTA
*
52720510 GGAAGTTTGAGGGTCAAAA
1 -GAAGTTTGAGGGTTAAAA
52720529 TATAATTGAT
Statistics
Matches: 117, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
58 39 0.33
59 58 0.50
60 16 0.14
61 4 0.03
ACGTcount: A:0.35, C:0.02, G:0.28, T:0.35
Consensus pattern (59 bp):
GAAGTTTGAGGGTTAAAAATGTAATTTTTGGAAGTTTAGGGGTTAAAATGTAAATTTTA
Found at i:52720524 original size:30 final size:29
Alignment explanation
Indices: 52720115--52720535 Score: 223
Period size: 29 Copynumber: 14.4 Consensus size: 29
52720105 ACTCGGGGAT
* *
52720115 AAAATCGTAATTTTGGGAAAGTTCG-GGGT-
1 AAAAT-GTAATTTTTGG-AAGTTTGAGGGTC
*
52720144 AAAATGTAA-TTTTGGAAGTCTGAGGGT-
1 AAAATGTAATTTTTGGAAGTTTGAGGGTC
** *
52720171 AAAATGGTAATTTTTGGAAAAAAATCGA-GGTC
1 AAAAT-GTAATTTTTGG---AAGTTTGAGGGTC
* * * *
52720203 AAAAATGGAGTTTTTGAAAGTTCGAGGGT-
1 -AAAATGTAATTTTTGGAAGTTTGAGGGTC
* *
52720232 AAAATAGTAATTTTTGATGAA-ATCG-GGGTC
1 AAAAT-GTAATTTTTG--GAAGTTTGAGGGTC
**
52720262 AAAAATAG-AA-TTTTGGACA-TCCGAGGGT-
1 -AAAAT-GTAATTTTTGGA-AGTTTGAGGGTC
* * *
52720290 AAAATGGTAATTTTTGTAAGTTTCAAGGTC
1 AAAAT-GTAATTTTTGGAAGTTTGAGGGTC
*
52720320 AAAAATGGAA--TTTGGAAGTTTGAGGG-C
1 -AAAATGTAATTTTTGGAAGTTTGAGGGTC
*
52720347 AAAATGGTAATTTTTGGAAGTTTTG-GGGTTA
1 AAAAT-GTAATTTTTGGAAG-TTTGAGGG-TC
* * * *
52720378 AAAATGGAAGTTTTAGAAGTTTG-GGGTTA
1 AAAATGTAATTTTTGGAAGTTTGAGGG-TC
* * *
52720407 AAAATGTAATTTTTGAAAGGTT-AGGGGTT
1 AAAATGTAATTTTTGGAAGTTTGA-GGGTC
* ** *
52720436 AAAATGTAAATTTTAAAAGTTTGAGGGTA
1 AAAATGTAATTTTTGGAAGTTTGAGGGTC
52720465 AAAATGTAATTTTTAGGAAGTTT-AGGGGTC
1 AAAATGTAATTTTT-GGAAGTTTGA-GGGTC
52720495 AAAATGTAATTTTTAGGAAGTTTGAGGGTC
1 AAAATGTAATTTTT-GGAAGTTTGAGGGTC
*
52720525 AAAATATAATT
1 AAAATGTAATT
52720536 GATTGATAGC
Statistics
Matches: 311, Mismatches: 48, Indels: 65
0.73 0.11 0.15
Matches are distributed among these distances:
26 10 0.03
27 26 0.08
28 32 0.10
29 125 0.40
30 78 0.25
31 23 0.07
32 12 0.04
33 5 0.02
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (29 bp):
AAAATGTAATTTTTGGAAGTTTGAGGGTC
Found at i:52721632 original size:9 final size:9
Alignment explanation
Indices: 52721620--52721675 Score: 53
Period size: 9 Copynumber: 6.2 Consensus size: 9
52721610 TTATTACTGT
52721620 TATTATTAA
1 TATTATTAA
*
52721629 TATTATT-C
1 TATTATTAA
*
52721637 TCATTAAT-A
1 T-ATTATTAA
52721646 TCATTATTAA
1 T-ATTATTAA
*
52721656 TATTATTGA
1 TATTATTAA
52721665 TATTATTAA
1 TATTATTAA
52721674 TA
1 TA
52721676 AAATTATTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
8 1 0.03
9 36 0.92
10 2 0.05
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (9 bp):
TATTATTAA
Found at i:52721634 original size:12 final size:12
Alignment explanation
Indices: 52721590--52721662 Score: 65
Period size: 12 Copynumber: 5.6 Consensus size: 12
52721580 AACATTTATT
52721590 TATTATTATTAA
1 TATTATTATTAA
*
52721602 TAAATTTATTATTAC
1 T--A-TTATTATTAA
*
52721617 TGTTATTATTAA
1 TATTATTATTAA
52721629 TATTATTCTCATTAA
1 TATTA-T-T-ATTAA
*
52721644 TATCATTATTAA
1 TATTATTATTAA
52721656 TATTATT
1 TATTATT
52721663 GATATTATTA
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
12 25 0.51
13 2 0.04
14 3 0.06
15 19 0.39
ACGTcount: A:0.37, C:0.05, G:0.01, T:0.56
Consensus pattern (12 bp):
TATTATTATTAA
Found at i:52721667 original size:21 final size:21
Alignment explanation
Indices: 52721643--52721683 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
52721633 ATTCTCATTA
* *
52721643 ATATCATTATTAATATTATTG
1 ATATCATTAATAAAATTATTG
*
52721664 ATATTATTAATAAAATTATT
1 ATATCATTAATAAAATTATT
52721684 TAACACTGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
ATATCATTAATAAAATTATTG
Found at i:52722383 original size:17 final size:17
Alignment explanation
Indices: 52722363--52722397 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
52722353 GTTTTTAATT
*
52722363 TTATATTAAGTTTAAAA
1 TTATATTAAATTTAAAA
*
52722380 TTATTTTAAATTTAAAA
1 TTATATTAAATTTAAAA
52722397 T
1 T
52722398 AAATTTAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (17 bp):
TTATATTAAATTTAAAA
Found at i:52722404 original size:17 final size:17
Alignment explanation
Indices: 52722368--52722406 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
52722358 TAATTTTATA
* * *
52722368 TTAAGTTTAAAATTATT
1 TTAAATTTAAAATAAAT
52722385 TTAAATTTAAAATAAAT
1 TTAAATTTAAAATAAAT
52722402 TTAAA
1 TTAAA
52722407 CCTAAATTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
TTAAATTTAAAATAAAT
Found at i:52724295 original size:92 final size:93
Alignment explanation
Indices: 52724138--52724306 Score: 286
Period size: 92 Copynumber: 1.8 Consensus size: 93
52724128 GCTAATATTC
* * * *
52724138 AAGGAAAGTGAGTGTAAGACAATGCTATAGCTTGTATTACTCAACAAAGCTTATGTACAACAAGG
1 AAGGAAAGTGAGTGTAAAACAATGCTATAGCTTCTATTACTCAACAAAGATTATGTAAAACAAGG
52724203 C-TTTTATACAAACCAAATACAAGACTT
66 CTTTTTATACAAACCAAATACAAGACTT
*
52724230 AAGGAAAGTGAGTGTAAAAGAATGCTATAGCTTCTATTACTCAACAAAGATTATGTAAAACAAGG
1 AAGGAAAGTGAGTGTAAAACAATGCTATAGCTTCTATTACTCAACAAAGATTATGTAAAACAAGG
52724295 CTTTTTATACAA
66 CTTTTTATACAA
52724307 TGATTCATGT
Statistics
Matches: 71, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
92 61 0.86
93 10 0.14
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (93 bp):
AAGGAAAGTGAGTGTAAAACAATGCTATAGCTTCTATTACTCAACAAAGATTATGTAAAACAAGG
CTTTTTATACAAACCAAATACAAGACTT
Found at i:52738235 original size:15 final size:16
Alignment explanation
Indices: 52738215--52738249 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
52738205 TTTAATTTTT
52738215 TAAATTATAAAAAT-A
1 TAAATTATAAAAATAA
*
52738230 TAAATTATTAAAATAA
1 TAAATTATAAAAATAA
52738246 TAAA
1 TAAA
52738250 AATATCTCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TAAATTATAAAAATAA
Found at i:52741361 original size:22 final size:21
Alignment explanation
Indices: 52741318--52741356 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
52741308 CTCTAGAAAC
52741318 TTTTTATTAAAATAATATTAA
1 TTTTTATTAAAATAATATTAA
*
52741339 TTTTT-TTAAAATTATATT
1 TTTTTATTAAAATAATATT
52741357 TTAATAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTTTATTAAAATAATATTAA
Done.