Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 181 of 185
Found at i:55166780 original size:15 final size:16
Alignment explanation
Indices: 55166748--55166783 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
55166738 TAAAATTGTA
55166748 AATTTATCATTTTAAT
1 AATTTATCATTTTAAT
*
55166764 AATTTAT-ATTTTTAT
1 AATTTATCATTTTAAT
55166779 AATTT
1 AATTT
55166784 TTAAATGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
AATTTATCATTTTAAT
Found at i:55174082 original size:38 final size:40
Alignment explanation
Indices: 55174040--55174131 Score: 116
Period size: 38 Copynumber: 2.3 Consensus size: 40
55174030 AAAAATTATA
* * *
55174040 TTTAATAAAATAAAATATTTATTATATTTAT-TTGTG-TT
1 TTTAATAAAATAAAACATTTATTATATGTATGTAGTGTTT
*
55174078 TTTAATATAATAAAACATTTATTATATGTATGGTAGTGTTT
1 TTTAATAAAATAAAACATTTATTATATGTAT-GTAGTGTTT
55174119 TTTAATATAAATA
1 TTTAATA-AAATA
55174132 CTTTTTAATG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
38 28 0.62
40 4 0.09
41 9 0.20
42 4 0.09
ACGTcount: A:0.40, C:0.01, G:0.08, T:0.51
Consensus pattern (40 bp):
TTTAATAAAATAAAACATTTATTATATGTATGTAGTGTTT
Found at i:55181631 original size:39 final size:39
Alignment explanation
Indices: 55181520--55181634 Score: 94
Period size: 39 Copynumber: 2.9 Consensus size: 39
55181510 TTTTTTCTCA
* *
55181520 AATTTCCACCCAATCTTGATCTAAATTAATATTTCATTC
1 AATTTCCACCCAATCTTGATCTAAATTAACATTTCATGC
** * * **
55181559 AATTT--A-GTAAT-TTAAATGATAAAACAATTCATTTCATGC
1 AATTTCCACCCAATCTT-GAT-CTAAATTAA--CATTTCATGC
55181598 AATTTCCACCCAATCTTGATCTAAATTAACATTTCAT
1 AATTTCCACCCAATCTTGATCTAAATTAACATTTCAT
55181635 CCTGAAACTA
Statistics
Matches: 54, Mismatches: 14, Indels: 16
0.64 0.17 0.19
Matches are distributed among these distances:
35 2 0.04
36 5 0.09
37 7 0.13
39 26 0.48
41 7 0.13
42 5 0.09
43 2 0.04
ACGTcount: A:0.37, C:0.19, G:0.04, T:0.39
Consensus pattern (39 bp):
AATTTCCACCCAATCTTGATCTAAATTAACATTTCATGC
Found at i:55182627 original size:11 final size:13
Alignment explanation
Indices: 55182607--55182638 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
55182597 AATAAATTAA
55182607 TAAAATATCAT-T
1 TAAAATATCATAT
55182619 TAAAA-ATCATAT
1 TAAAATATCATAT
55182631 TAAAATAT
1 TAAAATAT
55182639 TAATAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATATCATAT
Found at i:55185654 original size:5 final size:5
Alignment explanation
Indices: 55185644--55185668 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
55185634 CTGCCCGTGA
55185644 ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT
55185669 TCTGTATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:55186787 original size:17 final size:17
Alignment explanation
Indices: 55186760--55186792 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
55186750 ACTTTATGCT
55186760 TACTCAAATAT-GATCC
1 TACTCAAATATAGATCC
55186776 TACTCGAAATATAGATC
1 TACTC-AAATATAGATC
55186793 TAAAATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.30
Consensus pattern (17 bp):
TACTCAAATATAGATCC
Found at i:55187716 original size:86 final size:86
Alignment explanation
Indices: 55187562--55187720 Score: 205
Period size: 86 Copynumber: 1.8 Consensus size: 86
55187552 TCAAGGAGGC
* * * ***
55187562 CATGGTTGACGTTGACCAACAACACTCAACTTACATAATGTTTTAATCACTAGATCTAGAGGTGA
1 CATGGTTAACGTTGACCAACAACACTCAACTTACATAATGTGTCAATCACTAGATCTAGAGACAA
55187627 ATCTGAGGAGTAGGTGAGGGG
66 ATCTGAGGAGTAGGTGAGGGG
* * *
55187648 CATGGTTAACGTTGACCGACAGCACTCAACTTACATAATGTGTCAATCAC-AGGAT-TCAGTGAC
1 CATGGTTAACGTTGACCAACAACACTCAACTTACATAATGTGTCAATCACTA-GATCT-AGAGAC
55187711 AAATCTGAGG
64 AAATCTGAGG
55187721 GGCTAGCAAG
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
85 2 0.03
86 60 0.97
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (86 bp):
CATGGTTAACGTTGACCAACAACACTCAACTTACATAATGTGTCAATCACTAGATCTAGAGACAA
ATCTGAGGAGTAGGTGAGGGG
Found at i:55188157 original size:17 final size:18
Alignment explanation
Indices: 55188137--55188176 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
55188127 TTTAAAATAA
*
55188137 TAAATAAATCTA-AATTT
1 TAAATAAATCTACAAATT
*
55188154 TAAATAAATTTACAAATT
1 TAAATAAATCTACAAATT
55188172 TAAAT
1 TAAAT
55188177 GTTATAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAATAAATCTACAAATT
Found at i:55188170 original size:25 final size:24
Alignment explanation
Indices: 55188142--55188194 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
55188132 AATAATAAAT
*
55188142 AAATCTAAATTTTA-AATAAATTTAC
1 AAATCTAAATGTTATAA-AAA-TTAC
*
55188167 AAATTTAAATGTTATAAAAATTAC
1 AAATCTAAATGTTATAAAAATTAC
55188191 AAAT
1 AAAT
55188195 ATTCAACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 8 0.32
25 15 0.60
26 2 0.08
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.38
Consensus pattern (24 bp):
AAATCTAAATGTTATAAAAATTAC
Found at i:55188575 original size:18 final size:17
Alignment explanation
Indices: 55188548--55188581 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
55188538 TCCCTTTTAA
55188548 CCTTTCCCTTCCCCTTC
1 CCTTTCCCTTCCCCTTC
55188565 CCTTCTCCCTTCCCCTT
1 CCTT-TCCCTTCCCCTT
55188582 GTGTTGCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (17 bp):
CCTTTCCCTTCCCCTTC
Found at i:55188703 original size:25 final size:27
Alignment explanation
Indices: 55188641--55188703 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 27
55188631 CAGGTAAGGC
55188641 TCCTTCTTCTTCTTCTTCCATTCTTCAT
1 TCCTTC-TCTTCTTCTTCCATTCTTCAT
**
55188669 TCCTT-T-TTCTTCTTCTGTTCTTCA-
1 TCCTTCTCTTCTTCTTCCATTCTTCAT
55188693 T-CTTCTCTTCT
1 TCCTTCTCTTCT
55188704 CAGCATATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
23 3 0.10
24 2 0.06
25 20 0.65
26 1 0.03
28 5 0.16
ACGTcount: A:0.05, C:0.33, G:0.02, T:0.60
Consensus pattern (27 bp):
TCCTTCTCTTCTTCTTCCATTCTTCAT
Found at i:55191513 original size:14 final size:15
Alignment explanation
Indices: 55191491--55191567 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
55191481 CAATCAAACA
55191491 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
55191505 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
55191520 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
55191540 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
55191554 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
55191568 ACTACCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:55191532 original size:20 final size:20
Alignment explanation
Indices: 55191507--55191546 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
55191497 AATATTTTCC
*
55191507 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
55191527 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
55191547 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:55191552 original size:34 final size:35
Alignment explanation
Indices: 55191495--55191561 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
55191485 CAAACACCAG
*
55191495 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
55191530 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
55191562 TATTTTACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:55193025 original size:16 final size:16
Alignment explanation
Indices: 55193004--55193036 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
55192994 TCTCTCACTT
55193004 CAACAATAACTTAATC
1 CAACAATAACTTAATC
55193020 CAACAATAACTTAATC
1 CAACAATAACTTAATC
55193036 C
1 C
55193037 GATCCACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.24
Consensus pattern (16 bp):
CAACAATAACTTAATC
Found at i:55193994 original size:205 final size:204
Alignment explanation
Indices: 55193531--55194246 Score: 891
Period size: 205 Copynumber: 3.5 Consensus size: 204
55193521 GTTAGTTCCA
* * * * *
55193531 TTTCTCCTTCTAGATCTCGCTGTTCGTTTCAAAGTTCATCGATATTTCTGGTTTTTTTAGTTTGA
1 TTTCTCCTTCTAGACCTCGTTATTCATTTCAAAGTTCATCGATATTTCCGGTTTTTTTAGTTTGA
* * *
55193596 TTTGTATTAGTGCTTCTTTGCTGATTAATTTGTTCAATCTTTCGTTCTAGATCTCGCTCTTCGTT
66 TTTGTATTAGTGTTTCTTTGCTGATTAATTTGTTCAAT-TTTCGTTCTAGATCTCGCTATTCATT
** * *
55193661 TATATTTCC-TTTTTAAAAAAAT-ACTTATAATAGTATTTCTTTGCTGATTAGTTTGAATTCATT
130 TATATTTCCTTTTTTAAAAATTTGATTTATAATAGTTTTTCTTTGCTGATTAGTTTGAATTCATT
*
55193724 TTTAGCTCAC
195 TTTAGCTCAT
* * * * *
55193734 TTTCTCCTTCCAGACCTCGTTATTCATTTCGAAGTTCATCTATGTTTCTGGTTTTTTTAGTTTGA
1 TTTCTCCTTCTAGACCTCGTTATTCATTTCAAAGTTCATCGATATTTCCGGTTTTTTTAGTTTGA
* *
55193799 TTTGTATTGGTGTTTCTTTGCTGATTACTTTGTTCAATTTCTCGTTCTAGATCTCGCTATTCATT
66 TTTGTATTAGTGTTTCTTTGCTGATTAATTTGTTCAATTT-TCGTTCTAGATCTCGCTATTCATT
*
55193864 TATATTTCCTTTTTTAAAAATTTGATTTATAATTGTTTTTCTTTGCTGATTAGTTTGAATTCATT
130 TATATTTCCTTTTTTAAAAATTTGATTTATAATAGTTTTTCTTTGCTGATTAGTTTGAATTCATT
*
55193929 TTTAGCTTAT
195 TTTAGCTCAT
*
55193939 TTTCTCCTTCTAGACCTCGTTATTCATTTCAAAGTTCATCGATATTTCCGGTTTTTTTACTTTGA
1 TTTCTCCTTCTAGACCTCGTTATTCATTTCAAAGTTCATCGATATTTCCGGTTTTTTTAGTTTGA
* * * *
55194004 TTTGAATTAGTCTTTCTTTGCTGATTATTTTGTTCAATTTTTCCTTCTAGATCTCGCTATTCATT
66 TTTGTATTAGTGTTTCTTTGCTGATTAATTTGTTCAA-TTTTCGTTCTAGATCTCGCTATTCA-T
***
55194069 TATATATTTCCATTCCTTTTTGTTAATTTGATTTATAATAGTTTTTCTTTGCTGATTAGTTTGAA
129 T-TATATTTCC--T--TTTTTAAAAATTTGATTTATAATAGTTTTTCTTTGCTGATTAGTTTGAA
** **
55194134 TTGGTTTAGAG-TCAT
189 TTCATTTTTAGCTCAT
** * * * ** *
55194149 TTTCTCCTTCTAGACCTCG-TATTGGTTTCGAAGTTCATCAACATTTCCTCTCTCTTTTTAGTTC
1 TTTCTCCTTCTAGACCTCGTTATTCATTTCAAAGTTCATCGATATTTCCGGT-T-TTTTTAGTTT
* * * *
55194213 GATTTTTATTGGTGTTTATTTTCTGATTAATTTG
64 GATTTGTATTAGTGTTTCTTTGCTGATTAATTTG
55194247 AATTGATTTT
Statistics
Matches: 445, Mismatches: 56, Indels: 16
0.86 0.11 0.03
Matches are distributed among these distances:
202 2 0.00
203 123 0.28
204 11 0.02
205 159 0.36
206 5 0.01
207 9 0.02
209 26 0.06
210 23 0.05
211 87 0.20
ACGTcount: A:0.19, C:0.16, G:0.13, T:0.53
Consensus pattern (204 bp):
TTTCTCCTTCTAGACCTCGTTATTCATTTCAAAGTTCATCGATATTTCCGGTTTTTTTAGTTTGA
TTTGTATTAGTGTTTCTTTGCTGATTAATTTGTTCAATTTTCGTTCTAGATCTCGCTATTCATTT
ATATTTCCTTTTTTAAAAATTTGATTTATAATAGTTTTTCTTTGCTGATTAGTTTGAATTCATTT
TTAGCTCAT
Found at i:55194532 original size:114 final size:111
Alignment explanation
Indices: 55194331--55194597 Score: 305
Period size: 112 Copynumber: 2.4 Consensus size: 111
55194321 AAAATAAAAA
55194331 TTGATTTGTGTTAGTATTTCTTTGCTGATAAATTTG-A--ATTTTTAGTTCAATTTCTCGCTCTA
1 TTGATTTGTGTTAGTATTTCTTTGCTGATAAATTTGAATTATTTTTAGTTCAATTTCTCGCTCTA
*
55194393 GATCTCGTTATTCATTTCAAAGTTCACCATTATTGTC-TTTTTTAAAGT
66 GATCTCGTTATTCATTTCAAAGTTCACCA--A-TGCCATTTTTTAAAGT
* * *
55194441 TTGATTTGTGTTAGTATTTCTTTGGTGATTAATTTGAATTGATTTTTAGTTC-ATTGTGTC-CTT
1 TTGATTTGTGTTAGTATTTCTTTGCTGATAAATTTGAATT-ATTTTTAGTTCAATT-TCTCGC-T
* * * ** *
55194504 CTTGATCTCGCTT-TTCATTTTAAAGTTCATCAATGCCATTTTTTTTATT
63 CTAGATCTCG-TTATTCATTTCAAAGTTCACCAATGCCATTTTTTAAAGT
* *
55194553 TTGATTTGTATTAGTGTTTCTTTGCTGATAAATTTGAATTTATTT
1 TTGATTTGTGTTAGTATTTCTTTGCTGATAAATTTGAA-TTATTT
55194598 CAGAGCAAAT
Statistics
Matches: 134, Mismatches: 14, Indels: 16
0.82 0.09 0.10
Matches are distributed among these distances:
110 34 0.25
111 4 0.03
112 47 0.35
113 6 0.04
114 41 0.31
115 2 0.01
ACGTcount: A:0.21, C:0.11, G:0.14, T:0.54
Consensus pattern (111 bp):
TTGATTTGTGTTAGTATTTCTTTGCTGATAAATTTGAATTATTTTTAGTTCAATTTCTCGCTCTA
GATCTCGTTATTCATTTCAAAGTTCACCAATGCCATTTTTTAAAGT
Found at i:55198980 original size:22 final size:21
Alignment explanation
Indices: 55198940--55198980 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
55198930 CAAATTTCTT
* *
55198940 AATTTTAACACTTCTAAGCAG
1 AATTTTAACACTCCCAAGCAG
55198961 AATTTTAAACACTCCCAAGC
1 AATTTT-AACACTCCCAAGC
55198981 TTTTCAAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.39, C:0.24, G:0.07, T:0.29
Consensus pattern (21 bp):
AATTTTAACACTCCCAAGCAG
Found at i:55208752 original size:124 final size:124
Alignment explanation
Indices: 55208532--55208875 Score: 564
Period size: 124 Copynumber: 2.8 Consensus size: 124
55208522 CGACTTGATG
** *
55208532 TTTCTGATAAAATAGTATAAAATCGCTTTTAGCAGGATGCTTTTTGAGAAGAATTTGTGAAATCG
1 TTTCTGACCAAATAGTATAAAATCGCTTTTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCG
* * *
55208597 CGGCCTCGTGGGCGCGCTTTTGCTACAGTAGGTCATGTAAGAAATATTTTTTTTTTACT
66 CGGCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTTGACT
*
55208656 TTTCTGAGCAAATAGTATAAAATCGCTTTTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCG
1 TTTCTGACCAAATAGTATAAAATCGCTTTTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCG
*
55208721 CGGCCTCGTGGACGCGCTTTTGCTATAGTAGGTCATGTAAGAAATAATTTTTTTTGACT
66 CGGCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTTGACT
** *
55208780 TTTCTGACCAAATAGTATAAAATCGCTTCAAGCAGGATGCTATTTGAGAAGAATTTGTGAAATTG
1 TTTCTGACCAAATAGTATAAAATCGCTTTTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCG
*
55208845 CGGCCTCGT-GAGCGCGTTTTTGCTACAGTAG
66 CGGCCTCGTGGA-CGCGCTTTTGCTACAGTAG
55208876 CATGTTTGGG
Statistics
Matches: 206, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
123 2 0.01
124 204 0.99
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.35
Consensus pattern (124 bp):
TTTCTGACCAAATAGTATAAAATCGCTTTTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCG
CGGCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTTGACT
Found at i:55211893 original size:37 final size:37
Alignment explanation
Indices: 55211851--55212052 Score: 377
Period size: 37 Copynumber: 5.5 Consensus size: 37
55211841 TTGTATTAAC
*
55211851 TCAAATTATATAAAATTATAAATGGTTACTAAAATTA
1 TCAAATTATATAAAATTATAAATGGTTAGTAAAATTA
*
55211888 TCAAATTATATAAAATTATTAATGGTTAGTAAAATTA
1 TCAAATTATATAAAATTATAAATGGTTAGTAAAATTA
*
55211925 TCAAATTATATAAAATTATTAATGGTTAGTAAAATTA
1 TCAAATTATATAAAATTATAAATGGTTAGTAAAATTA
55211962 TCAAATTATATAAAATTATAAATGGTTAGTAAAATTA
1 TCAAATTATATAAAATTATAAATGGTTAGTAAAATTA
55211999 TCAAATTATATAAAATTATAAATGGTTAGTAAAATTA
1 TCAAATTATATAAAATTATAAATGGTTAGTAAAATTA
55212036 TCAAATTATATAAAATT
1 TCAAATTATATAAAATT
55212053 GGGTTAGGGT
Statistics
Matches: 162, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 162 1.00
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.39
Consensus pattern (37 bp):
TCAAATTATATAAAATTATAAATGGTTAGTAAAATTA
Found at i:55212819 original size:35 final size:29
Alignment explanation
Indices: 55212048--55212849 Score: 1092
Period size: 29 Copynumber: 27.6 Consensus size: 29
55212038 AAATTATATA
*
55212048 AAATTGGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
* *
55212077 AAGTTAGGTTAGGGTTATGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
* *
55212106 AAGTTTGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
* *
55212135 AAGTTTGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
* *
55212164 AAGTTTGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
* *
55212193 GAATTGGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
*
55212222 AAATTAGGTTAGGGTTAGTGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
* *
55212251 AAGTTTGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
*
55212280 AAATTAGGTTAGGGTTAGAGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
* *
55212309 AAGTTTGGTTAGGGTTAGGG-TTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
* *
55212337 GAATTGGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
* *
55212366 AAGTTTGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
* *
55212395 -AATTAAGTTAGGGTTA-GGATTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
* *
55212422 AAGTTAGGTTAAGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
* *
55212451 AAGTTTGGTTAGGGTTAGGG-TTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
* *
55212479 GAATTGGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
* *
55212508 GAATTTGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
* *
55212537 GAATTGGGTTAGGGTTAGAGTTAGGGTTTTTAATT
1 -AA----ATTA-GGTTAGGGTTAGGGTTTTTAATT
* *
55212572 GAATTGGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
*
55212601 GAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
* *
55212630 AAGTTTGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
* * *
55212659 GAATTGGGTTAGGGTTAAGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
55212688 AAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
* *
55212717 GAATTGGGTTAGGGTTAGGG-TTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
*
55212745 GAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
55212774 AAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
* *
55212803 GAATTTGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
*
55212832 AAATTTGGTTAGGGTTAG
1 AAATTAGGTTAGGGTTAG
55212850 AAATAAACAT
Statistics
Matches: 696, Mismatches: 66, Indels: 22
0.89 0.08 0.03
Matches are distributed among these distances:
27 10 0.01
28 103 0.15
29 555 0.80
30 3 0.00
34 3 0.00
35 22 0.03
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (29 bp):
AAATTAGGTTAGGGTTAGGGTTTTTAATT
Found at i:55214041 original size:7 final size:7
Alignment explanation
Indices: 55214029--55214054 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
55214019 TATACATAAT
55214029 AATACTA
1 AATACTA
55214036 AATACTA
1 AATACTA
55214043 AATACTA
1 AATACTA
55214050 AATAC
1 AATAC
55214055 CAATCGACTA
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:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:55215259 original size:22 final size:22
Alignment explanation
Indices: 55215231--55215278 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
55215221 TATGGATTTG
55215231 AGAGAATTTTGGAAGGAAATTA
1 AGAGAATTTTGGAAGGAAATTA
*
55215253 AGAGAATTTTGGAAGGAAATTG
1 AGAGAATTTTGGAAGGAAATTA
55215275 AGAG
1 AGAG
55215279 GAAATTGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.31, T:0.25
Consensus pattern (22 bp):
AGAGAATTTTGGAAGGAAATTA
Found at i:55215274 original size:73 final size:73
Alignment explanation
Indices: 55215191--55215356 Score: 287
Period size: 73 Copynumber: 2.3 Consensus size: 73
55215181 TCATTTTAAA
*
55215191 AAAGGAAATTGAGAGGAAATTGAAATCAAATATGGATTTGAGAGAATTTTGGAAGGAAATTAAGA
1 AAAGGAAATTGAGAGGAAATTGAAATCAAATATGGATTTGAGAGAATTTTGGAAGGAAATCAAGA
55215256 GAATTTTG
66 GAATTTTG
* * *
55215264 GAAGGAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAGGAAATCGAGA
1 AAAGGAAATTGAGAGGAAATTGAAATCAAATATGGATTTGAGAGAATTTTGGAAGGAAATCAAGA
55215329 GAATTTTG
66 GAATTTTG
*
55215337 AAAAGAAATTGAGAGGAAAT
1 AAAGGAAATTGAGAGGAAAT
55215357 ATGAGAGAGG
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 87 1.00
ACGTcount: A:0.46, C:0.01, G:0.27, T:0.26
Consensus pattern (73 bp):
AAAGGAAATTGAGAGGAAATTGAAATCAAATATGGATTTGAGAGAATTTTGGAAGGAAATCAAGA
GAATTTTG
Found at i:55215328 original size:22 final size:22
Alignment explanation
Indices: 55215303--55215351 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
55215293 ATATGGATTT
* *
55215303 GAGAGAATTTTGGAAGGAAATC
1 GAGAGAATTTTGAAAAGAAATC
*
55215325 GAGAGAATTTTGAAAAGAAATT
1 GAGAGAATTTTGAAAAGAAATC
55215347 GAGAG
1 GAGAG
55215352 GAAATATGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.45, C:0.02, G:0.31, T:0.22
Consensus pattern (22 bp):
GAGAGAATTTTGAAAAGAAATC
Found at i:55216369 original size:175 final size:175
Alignment explanation
Indices: 55216078--55216790 Score: 984
Period size: 175 Copynumber: 4.1 Consensus size: 175
55216068 CGGTTAGCTA
* * * * * * ** *
55216078 CCACTTGGTGGTTGACGATGTTTTCTTTTTCAACGTTTGTTCACGAAGCAATTGGTCTGCCGACA
1 CCACTTGGTGGTTGGCGACGTTTTCTTTTTGAACATTTGTCCTCGAAGTGATTGGTATGCCGACA
* * * * *
55216143 TTTTATTGATAGAGAATGTTTTATGGAGATGTGGTGAAGTTGATTAATTATTTAGTGGTTTGTCG
66 TTTTATTGACAGAGAATGTTTTATGAAGACGTGGTGAAATTGATTAATTATTTAGTGGTTTGTCA
*
55216208 TATTATCATGTTTGCTTTTTACTATGTTAGGAATTTGTTTCTTAC
131 TATTATCATGTTTGCTTTTTACTATGTTAGGAATTTGTTTCCTAC
55216253 CCACTTGGTGGTTGGCGACGTTTTCTTTTTGAACATTTGTCCTCGAAGTGATTGGTATGCCGACA
1 CCACTTGGTGGTTGGCGACGTTTTCTTTTTGAACATTTGTCCTCGAAGTGATTGGTATGCCGACA
* * * * *
55216318 TTTTATTGACAGAGAAAGTTTTATGAAGATGTGGTGAAACTGATTAATTATTCAGTGGTCTGTC-
66 TTTTATTGACAGAGAATGTTTTATGAAGACGTGGTGAAATTGATTAATTATTTAGTGGTTTGTCA
*
55216382 -ATTATCATGTTTGCTTTTTACTATGTTAGGAATTTGTTTCCTGC
131 TATTATCATGTTTGCTTTTTACTATGTTAGGAATTTGTTTCCTAC
* * * * * * * *
55216426 CCTCTTGGTGGTTGGCGAAGTTTTCTTTTTGAACATCTGTTCGCGAAGTGATTGGTATGTCTATA
1 CCACTTGGTGGTTGGCGACGTTTTCTTTTTGAACATTTGTCCTCGAAGTGATTGGTATGCCGACA
55216491 TTTTATTGACAGAGAATGTTTTATGAAGACGTGGTGAAATTGATTAATTATTTAGTGGTTTGTCA
66 TTTTATTGACAGAGAATGTTTTATGAAGACGTGGTGAAATTGATTAATTATTTAGTGGTTTGTCA
55216556 TATTATCATGTTTGCTTTTTACTATGTTAGGAATTTGTTTCCTAC
131 TATTATCATGTTTGCTTTTTACTATGTTAGGAATTTGTTTCCTAC
* * *
55216601 CCACTTGGCGATTGGCGACGTTTTCTTTTTGAACATTTGTTCGT-GAAGTGATTGGTATGCCGAC
1 CCACTTGGTGGTTGGCGACGTTTTCTTTTTGAACATTTG-TCCTCGAAGTGATTGGTATGCCGAC
* * * * * *
55216665 ATTTTATTGACAGAGCATGTTTTTTGAAAACGTGGTGAAATTGATTAATT-TTTCAATGGCTCGT
65 ATTTTATTGACAGAGAATGTTTTATGAAGACGTGGTGAAATTGATTAATTATTT-AGTGGTTTGT
* * * * *
55216729 TATATTATAATGTTTGCTTCTTACTATGTTAGGAATTTTTTTTCCTGC
129 CATATTATCATGTTTGCTTTTTACTATGTTAGGAA-TTTGTTTCCTAC
55216777 CCACTTGGTGGTTG
1 CCACTTGGTGGTTG
55216791 ATGATGTTCG
Statistics
Matches: 477, Mismatches: 56, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
173 158 0.33
174 3 0.01
175 293 0.61
176 23 0.05
ACGTcount: A:0.22, C:0.13, G:0.22, T:0.44
Consensus pattern (175 bp):
CCACTTGGTGGTTGGCGACGTTTTCTTTTTGAACATTTGTCCTCGAAGTGATTGGTATGCCGACA
TTTTATTGACAGAGAATGTTTTATGAAGACGTGGTGAAATTGATTAATTATTTAGTGGTTTGTCA
TATTATCATGTTTGCTTTTTACTATGTTAGGAATTTGTTTCCTAC
Found at i:55217068 original size:25 final size:24
Alignment explanation
Indices: 55217040--55217095 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
55217030 ACATAAACTC
* *
55217040 TAAATCTGAAACCTAAAGCTCTATA
1 TAAATCT-AAACCTAAAACTCAATA
* *
55217065 TAAACCCTAAATCTAAAACTCAATA
1 TAAA-TCTAAACCTAAAACTCAATA
55217090 TAAATC
1 TAAATC
55217096 CTAACTCAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
24 1 0.04
25 22 0.88
26 2 0.08
ACGTcount: A:0.48, C:0.21, G:0.04, T:0.27
Consensus pattern (24 bp):
TAAATCTAAACCTAAAACTCAATA
Found at i:55217098 original size:25 final size:25
Alignment explanation
Indices: 55217052--55217109 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
55217042 AATCTGAAAC
* *
55217052 CTAAAGCTCTATATAAACCCTAAAT
1 CTAAAACTCAATATAAACCCTAAAT
* *
55217077 CTAAAACTCAATATAAATCCTAACT
1 CTAAAACTCAATATAAACCCTAAAT
55217102 C-AAAACTC
1 CTAAAACTC
55217110 GAGAAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 7 0.24
25 22 0.76
ACGTcount: A:0.47, C:0.26, G:0.02, T:0.26
Consensus pattern (25 bp):
CTAAAACTCAATATAAACCCTAAAT
Found at i:55220171 original size:31 final size:31
Alignment explanation
Indices: 55220094--55220161 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
55220084 GCCATAAGTG
*
55220094 CCAAATTAAACATTAAAACAAAACTCAGGTA
1 CCAAATTAAATATTAAAACAAAACTCAGGTA
* *
55220125 TCAAATTAAATATTAAAACCAAACTCAGGTA
1 CCAAATTAAATATTAAAACAAAACTCAGGTA
55220156 CCAAAT
1 CCAAAT
55220162 AGTATATTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.53, C:0.19, G:0.06, T:0.22
Consensus pattern (31 bp):
CCAAATTAAATATTAAAACAAAACTCAGGTA
Found at i:55223871 original size:11 final size:10
Alignment explanation
Indices: 55223843--55223879 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
55223833 AATTTAATTC
55223843 TTTTCTTTTA
1 TTTTCTTTTA
*
55223853 TGTTCTTTTAA
1 TTTTCTTTT-A
55223864 TTTTCTTTTA
1 TTTTCTTTTA
55223874 TTTTCT
1 TTTTCT
55223880 ATTCTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 15 0.62
11 9 0.38
ACGTcount: A:0.11, C:0.11, G:0.03, T:0.76
Consensus pattern (10 bp):
TTTTCTTTTA
Found at i:55223888 original size:21 final size:20
Alignment explanation
Indices: 55223839--55223887 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
55223829 GAGCAATTTA
55223839 ATTCTTTTCTTTTATGTTCT
1 ATTCTTTTCTTTTATGTTCT
* * *
55223859 TTTAATTTTCTTTTATTTTCT
1 ATT-CTTTTCTTTTATGTTCT
55223880 ATTCTTTT
1 ATTCTTTT
55223888 TTACTTCTCT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.12, C:0.12, G:0.02, T:0.73
Consensus pattern (20 bp):
ATTCTTTTCTTTTATGTTCT
Found at i:55240366 original size:31 final size:31
Alignment explanation
Indices: 55240328--55240391 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
55240318 AGTTTTTAAA
55240328 AATTTATTTAACTAAAATCAGATCGGTCATC
1 AATTTATTTAACTAAAATCAGATCGGTCATC
55240359 AATTTATTTAACTAAAATCAGATCGGTCATC
1 AATTTATTTAACTAAAATCAGATCGGTCATC
55240390 AA
1 AA
55240392 AGTCATGGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (31 bp):
AATTTATTTAACTAAAATCAGATCGGTCATC
Found at i:55242050 original size:25 final size:26
Alignment explanation
Indices: 55242022--55242072 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
55242012 AAGAGGAAAG
55242022 TTTAAAGAACATAAAA-GAAAAAAAT
1 TTTAAAGAACATAAAACGAAAAAAAT
** *
55242047 TTTAAATTACTTAAAACGAAAAAAAT
1 TTTAAAGAACATAAAACGAAAAAAAT
55242073 ATGGGGATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.63, C:0.06, G:0.06, T:0.25
Consensus pattern (26 bp):
TTTAAAGAACATAAAACGAAAAAAAT
Found at i:55242220 original size:15 final size:15
Alignment explanation
Indices: 55242200--55242250 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
55242190 ATAACATGAT
55242200 AACGTAAATGACTAA
1 AACGTAAATGACTAA
* *
55242215 AACGTAACAT--TTCA
1 AACGTAA-ATGACTAA
*
55242229 AACATAAATGACTAA
1 AACGTAAATGACTAA
55242244 AACGTAA
1 AACGTAA
55242251 CCTAAGGTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 15 0.56
16 2 0.07
ACGTcount: A:0.53, C:0.16, G:0.10, T:0.22
Consensus pattern (15 bp):
AACGTAAATGACTAA
Found at i:55251265 original size:13 final size:13
Alignment explanation
Indices: 55251249--55251273 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55251239 AAAATTAATA
55251249 AACCCAATTACCC
1 AACCCAATTACCC
55251262 AACCCAATTACC
1 AACCCAATTACC
55251274 ATTTACCAAC
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:0.44, G:0.00, T:0.16
Consensus pattern (13 bp):
AACCCAATTACCC
Found at i:55251284 original size:19 final size:19
Alignment explanation
Indices: 55251260--55251376 Score: 63
Period size: 19 Copynumber: 5.5 Consensus size: 19
55251250 ACCCAATTAC
*
55251260 CCAACCCAATTACCATTTA
1 CCAACCCAATTACAATTTA
* *
55251279 CCAACCCAATAAACTAAAGTCTA
1 CCAACCCAAT-TAC--AA-TTTA
*
55251302 CCCAAACCCAATTACTATTTA
1 -CC-AACCCAATTACAATTTA
* *
55251323 CCAACCCAATAAACTAAAGTCTA
1 CCAACCCAAT-TAC--AA-TTTA
*
55251346 TCCAAACCCAATTACCATTTA
1 -CC-AACCCAATTACAATTTA
55251367 CCAACCCAAT
1 CCAACCCAAT
55251377 AAAACAAACA
Statistics
Matches: 74, Mismatches: 12, Indels: 24
0.67 0.11 0.22
Matches are distributed among these distances:
19 26 0.35
20 8 0.11
21 6 0.08
22 4 0.05
23 6 0.08
24 8 0.11
25 16 0.22
ACGTcount: A:0.42, C:0.34, G:0.02, T:0.22
Consensus pattern (19 bp):
CCAACCCAATTACAATTTA
Found at i:55251311 original size:25 final size:24
Alignment explanation
Indices: 55251277--55251357 Score: 84
Period size: 25 Copynumber: 3.5 Consensus size: 24
55251267 AATTACCATT
55251277 TACC-AACCCAATAAACTAAAGTC
1 TACCAAACCCAATAAACTAAAGTC
* *
55251300 TACCCAAACCCAAT-TACT--A-TT
1 TA-CCAAACCCAATAAACTAAAGTC
55251321 TACC-AACCCAATAAACTAAAGTC
1 TACCAAACCCAATAAACTAAAGTC
55251344 TATCCAAACCCAAT
1 TA-CCAAACCCAAT
55251358 TACCATTTAC
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
19 8 0.17
20 5 0.11
21 3 0.07
22 2 0.04
23 5 0.11
24 7 0.15
25 16 0.35
ACGTcount: A:0.44, C:0.32, G:0.02, T:0.21
Consensus pattern (24 bp):
TACCAAACCCAATAAACTAAAGTC
Found at i:55251312 original size:44 final size:44
Alignment explanation
Indices: 55251257--55251379 Score: 221
Period size: 44 Copynumber: 2.8 Consensus size: 44
55251247 TAAACCCAAT
55251257 TACCC-AACCCAATTACCATTTACCAACCCAATAAACTAAAGTC
1 TACCCAAACCCAATTACCATTTACCAACCCAATAAACTAAAGTC
*
55251300 TACCCAAACCCAATTACTATTTACCAACCCAATAAACTAAAGTC
1 TACCCAAACCCAATTACCATTTACCAACCCAATAAACTAAAGTC
*
55251344 TATCCAAACCCAATTACCATTTACCAACCCAATAAA
1 TACCCAAACCCAATTACCATTTACCAACCCAATAAA
55251380 ACAAACAGCT
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
43 5 0.07
44 71 0.93
ACGTcount: A:0.43, C:0.33, G:0.02, T:0.22
Consensus pattern (44 bp):
TACCCAAACCCAATTACCATTTACCAACCCAATAAACTAAAGTC
Found at i:55274850 original size:13 final size:13
Alignment explanation
Indices: 55274832--55274869 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
55274822 ACACTCAAAA
55274832 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
55274845 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
55274858 TTCTCAAAAGCA
1 TTCTCAAAAGCA
55274870 ATGAAGAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.39, C:0.29, G:0.08, T:0.24
Consensus pattern (13 bp):
TTCTCAAAAGCAC
Found at i:55276235 original size:88 final size:87
Alignment explanation
Indices: 55275988--55276242 Score: 327
Period size: 87 Copynumber: 2.9 Consensus size: 87
55275978 AATTCCTATT
* * * *
55275988 CAACATAAAAGAATCTAGAAAAAAAGGTA-T-CGAGTAACTTCAACTACTTAAACACGAAGTGAA
1 CAACATAAAAGAATCTAGAAAAAAAGATAGTGCAAGTAATTTCAACTACTTAAACACAAAGTGAA
*
55276051 TCAGTTCCTTACTAATCGTATG
66 TCAGTTCCTTACTAATCATATG
* * * * *
55276073 CAACATAAAAAAATCTAGAGAAAAAGA-AGTGCAGACTAATTGCAACTACTTAAACACAAAGTAA
1 CAACATAAAAGAATCTAGAAAAAAAGATAGTGCA-AGTAATTTCAACTACTTAAACACAAAGTGA
*
55276137 ATCAGCTCCTTACTAATCATATG
65 ATCAGTTCCTTACTAATCATATG
* * * *
55276160 CAACATAAAAGAATCTAGAAAAAAAAATAGTGCCAAGTAATTTCAACTGCCTCAACACAAAGTGA
1 CAACATAAAAGAATCTAGAAAAAAAGATAGTG-CAAGTAATTTCAACTACTTAAACACAAAGTGA
*
55276225 ATCAATTCCTTACTAATC
65 ATCAGTTCCTTACTAATC
55276243 GTTGTAAGAT
Statistics
Matches: 143, Mismatches: 22, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
84 1 0.01
85 25 0.17
86 1 0.01
87 70 0.49
88 44 0.31
89 2 0.01
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.23
Consensus pattern (87 bp):
CAACATAAAAGAATCTAGAAAAAAAGATAGTGCAAGTAATTTCAACTACTTAAACACAAAGTGAA
TCAGTTCCTTACTAATCATATG
Found at i:55280770 original size:31 final size:31
Alignment explanation
Indices: 55280694--55280793 Score: 94
Period size: 31 Copynumber: 3.2 Consensus size: 31
55280684 ATTTAGGGTT
* *
55280694 TGAACTTGGCAACTATTCCCACATTGGGACC
1 TGAACTTGGCAATTGTTCCCACATTGGGACC
** *
55280725 TGAACTTGATAATTGTTCCCATATTGTGG-CC
1 TGAACTTGGCAATTGTTCCCACATTG-GGACC
* ** * *
55280756 TGAACTAGGCAATTGTTCTTACATTGGGGCT
1 TGAACTTGGCAATTGTTCCCACATTGGGACC
55280787 TGAACTT
1 TGAACTT
55280794 TTTTTGTCCA
Statistics
Matches: 54, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
30 2 0.04
31 50 0.93
32 2 0.04
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (31 bp):
TGAACTTGGCAATTGTTCCCACATTGGGACC
Found at i:55287332 original size:12 final size:15
Alignment explanation
Indices: 55287303--55287335 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
55287293 TGAGGATTTA
55287303 GCTGCTTCCTTTTCT
1 GCTGCTTCCTTTTCT
55287318 GCTGCTT-CTTTTGCT
1 GCTGCTTCCTTTT-CT
55287333 GCT
1 GCT
55287336 ATCCTCTCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.00, C:0.30, G:0.18, T:0.52
Consensus pattern (15 bp):
GCTGCTTCCTTTTCT
Found at i:55290597 original size:18 final size:18
Alignment explanation
Indices: 55290561--55290599 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
55290551 TGAAAAATAT
*
55290561 TAAAAAATATATTTTTTA
1 TAAAAAATATATTTATTA
55290579 TAAAAAAT-TATATTATTA
1 TAAAAAATATAT-TTATTA
55290597 TAA
1 TAA
55290600 GGGTATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TAAAAAATATATTTATTA
Found at i:55295611 original size:10 final size:9
Alignment explanation
Indices: 55295581--55295605 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
55295571 TTAAAATAAT
55295581 ATTTTAAAA
1 ATTTTAAAA
55295590 ATTTTAAAA
1 ATTTTAAAA
55295599 ATTTTAA
1 ATTTTAA
55295606 TTAATTGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
ATTTTAAAA
Found at i:55295905 original size:69 final size:69
Alignment explanation
Indices: 55295805--55295942 Score: 224
Period size: 69 Copynumber: 2.0 Consensus size: 69
55295795 TTTAAATAAT
*
55295805 CGAATTTACTTGTGGAGTTTAAAAAACTTCATCTACACCGAA-TAATTTATTATTATCGTTTAAT
1 CGAATTTACTTGTGGAGTTTAAAAAACTTCATCTACACC-AATTAATTTATTATTATAGTTTAAT
55295869 TTTTC
65 TTTTC
* **
55295874 CGAATTTATTTGTGGAGTTTAAAAAGTTTCATCTACACCAATTAATTTATTATTATAGTTTAATT
1 CGAATTTACTTGTGGAGTTTAAAAAACTTCATCTACACCAATTAATTTATTATTATAGTTTAATT
55295939 TTTC
66 TTTC
55295943 TTAGTCAATC
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
68 2 0.03
69 62 0.97
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.46
Consensus pattern (69 bp):
CGAATTTACTTGTGGAGTTTAAAAAACTTCATCTACACCAATTAATTTATTATTATAGTTTAATT
TTTC
Found at i:55296484 original size:19 final size:18
Alignment explanation
Indices: 55296443--55296487 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
55296433 TACTCTGTAC
*
55296443 TTTATAGAGAAATCTTAT
1 TTTATAGAGAAATCCTAT
*
55296461 TTTATTGAGAAATCCTATT
1 TTTATAGAGAAATCCTA-T
55296480 TTTATAGA
1 TTTATAGA
55296488 AATTTTAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.47
Consensus pattern (18 bp):
TTTATAGAGAAATCCTAT
Found at i:55301939 original size:30 final size:31
Alignment explanation
Indices: 55301885--55301943 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
55301875 TAATGTCAAG
* *
55301885 TATTAAATTGAACATTGAAGCCAAACTCATA
1 TATTAAATTGAACATTAAAACCAAACTCATA
55301916 TATTAAATTG-ACATTAAAACCAAACTCA
1 TATTAAATTGAACATTAAAACCAAACTCA
55301944 ATTACTGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.47, C:0.17, G:0.07, T:0.29
Consensus pattern (31 bp):
TATTAAATTGAACATTAAAACCAAACTCATA
Found at i:55303630 original size:3 final size:3
Alignment explanation
Indices: 55303622--55303652 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
55303612 TTAATCAATC
55303622 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
55303653 GCAACGTGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:55305324 original size:23 final size:23
Alignment explanation
Indices: 55305295--55305356 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
55305285 GCCCGGCCCG
* *
55305295 TTTTTAATTAAAATTAAAATTAT
1 TTTTTAATTAAAATTAAAACTAA
*
55305318 TTTTTAAATAAAATTAAAACTAA
1 TTTTTAATTAAAATTAAAACTAA
*
55305341 TTGTT-ATTAAAATTAA
1 TTTTTAATTAAAATTAA
55305357 TTGTTAGTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 10 0.29
23 24 0.71
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
TTTTTAATTAAAATTAAAACTAA
Found at i:55305369 original size:16 final size:16
Alignment explanation
Indices: 55305332--55305371 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
55305322 TAAATAAAAT
* *
55305332 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
55305348 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
55305364 TAAAATTA
1 TAAAATTA
55305372 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:55305450 original size:59 final size:59
Alignment explanation
Indices: 55305382--55305551 Score: 295
Period size: 59 Copynumber: 2.9 Consensus size: 59
55305372 TCAAATTATT
*
55305382 AATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
* * *
55305441 AATTATTAATTGTATTAATTGTTGTAATAAAATTTATCACTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
*
55305500 AATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAA
55305552 ACAAACTTGA
Statistics
Matches: 103, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 103 1.00
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.45
Consensus pattern (59 bp):
AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
Found at i:55305507 original size:20 final size:20
Alignment explanation
Indices: 55305422--55305500 Score: 58
Period size: 20 Copynumber: 4.0 Consensus size: 20
55305412 AATCTAACAT
55305422 TTGATTAGTAAATTTATCAA
1 TTGATTAGTAAATTTATCAA
* *
55305442 ---ATTA-TTAATTGTATTAA
1 TTGATTAGTAAATT-TATCAA
* * *
55305459 TTGTTGTAATAAAATTTATCAC
1 TTGAT-TAGT-AAATTTATCAA
55305481 TTGATTAGTAAATTTATCAA
1 TTGATTAGTAAATTTATCAA
55305501 ATTATTAATT
Statistics
Matches: 43, Mismatches: 9, Indels: 14
0.65 0.14 0.21
Matches are distributed among these distances:
16 5 0.12
17 9 0.21
20 11 0.26
21 5 0.12
22 9 0.21
23 4 0.09
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.47
Consensus pattern (20 bp):
TTGATTAGTAAATTTATCAA
Found at i:55305658 original size:22 final size:24
Alignment explanation
Indices: 55305618--55305661 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
55305608 AAATAAACTT
55305618 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
55305642 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAACTATTATATTT
55305662 AATATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:55307234 original size:30 final size:30
Alignment explanation
Indices: 55307208--55307295 Score: 126
Period size: 30 Copynumber: 2.9 Consensus size: 30
55307198 ATATTTTTAC
55307208 ATACTTTTTTAAAATTTTTTTAATTTTAAA
1 ATACTTTTTTAAAATTTTTTTAATTTTAAA
*
55307238 ATACTTTTTTTAAATTTTTTTAATTTTAAA
1 ATACTTTTTTAAAATTTTTTTAATTTTAAA
55307268 ATA--TTTTTAAAATACTTTTTTAAATTTT
1 ATACTTTTTTAAAAT--TTTTTT-AATTTT
55307296 TTAAAATAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
28 9 0.17
30 38 0.72
31 6 0.11
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (30 bp):
ATACTTTTTTAAAATTTTTTTAATTTTAAA
Found at i:55307238 original size:40 final size:39
Alignment explanation
Indices: 55307181--55307297 Score: 135
Period size: 40 Copynumber: 3.2 Consensus size: 39
55307171 AAATATATTT
*
55307181 ATTTTTTTAATTGTAAAATATTTTTACATACTTTTTTAAA
1 ATTTTTTTAATTTTAAAATATTTTTACATACTTTTTT-AA
55307221 ATTTTTTTAATTTT-AAA-A----TAC-T--TTTTTTAA
1 ATTTTTTTAATTTTAAAATATTTTTACATACTTTTTTAA
*
55307251 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAA
1 ATTTTTTTAATTTTAAAATATTTTT-ACATACTTTTTTAA
55307291 ATTTTTT
1 ATTTTTT
55307298 AAAATAAAAA
Statistics
Matches: 65, Mismatches: 2, Indels: 20
0.75 0.02 0.23
Matches are distributed among these distances:
30 16 0.25
31 9 0.14
32 1 0.02
33 1 0.02
34 3 0.05
36 1 0.02
37 1 0.02
38 2 0.03
39 3 0.05
40 28 0.43
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (39 bp):
ATTTTTTTAATTTTAAAATATTTTTACATACTTTTTTAA
Found at i:55307292 original size:12 final size:11
Alignment explanation
Indices: 55307261--55307303 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
55307251 ATTTTTTTAA
55307261 TTTTAAAATAT
1 TTTTAAAATAT
55307272 TTTTAAAATACT
1 TTTTAAAATA-T
*
55307284 TTTTTAAAT-T
1 TTTTAAAATAT
55307294 TTTTAAAATA
1 TTTTAAAATA
55307304 AAAATGGGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 9 0.32
11 10 0.36
12 9 0.32
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:55315754 original size:132 final size:131
Alignment explanation
Indices: 55315602--55315864 Score: 359
Period size: 132 Copynumber: 2.0 Consensus size: 131
55315592 TTTTTCTGTA
* *
55315602 AGCACTTGTTCATGCTTGTATATACTTGTAATTAATTTGTTAATTTATAATA-GGCATAGATGAG
1 AGCACTTGTTCATGCTTGTATATACTTGTAATCAATATGTTAATTTATAATAGGGCATAGATGAG
55315666 CTAGATACAAATTGTAACATAGTGTTT-CTGATCCAGCTGTAACCATGGATGTAACATAAATGCT
66 CTAGATACAAATTGTAACATAG-GTTTGCTGATCC--CTGTAACCATGGATGTAACATAAATGCT
55315730 CCCC
128 CCCC
* * *
55315734 AGCACTTGTTCATGCTTGTATATACTTGTAATCGATATGTTAGTTTGTAATAGGGGCATAGATGA
1 AGCACTTGTTCATGCTTGTATATACTTGTAATCAATATGTTAATTTATAATA-GGGCATAGATGA
* * * * * * * *
55315799 GCTTGATGCGAATTGTAACATAGGTTTGCTGATCCTTGTAACCGTTGATGTAGCATACATGCTCC
65 GCTAGATACAAATTGTAACATAGGTTTGCTGATCCCTGTAACCATGGATGTAACATAAATGCTCC
55315864 C
130 C
55315865 TTTTTCTGTA
Statistics
Matches: 115, Mismatches: 13, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
132 73 0.63
133 4 0.03
134 38 0.33
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.36
Consensus pattern (131 bp):
AGCACTTGTTCATGCTTGTATATACTTGTAATCAATATGTTAATTTATAATAGGGCATAGATGAG
CTAGATACAAATTGTAACATAGGTTTGCTGATCCCTGTAACCATGGATGTAACATAAATGCTCCC
C
Found at i:55316358 original size:10 final size:10
Alignment explanation
Indices: 55316343--55316371 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
55316333 ATGTAACATA
55316343 CATGCTTGTT
1 CATGCTTGTT
55316353 CATGCTTGTT
1 CATGCTTGTT
55316363 CATGCTTGT
1 CATGCTTGT
55316372 ATACGCTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.10, C:0.21, G:0.21, T:0.48
Consensus pattern (10 bp):
CATGCTTGTT
Found at i:55316379 original size:20 final size:20
Alignment explanation
Indices: 55316343--55316381 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
55316333 ATGTAACATA
*
55316343 CATGCTTGTTCATGCTTGTT
1 CATGCTTGTTCACGCTTGTT
55316363 CATGCTTGTAT-ACGCTTGT
1 CATGCTTGT-TCACGCTTGT
55316382 AATTGATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.46
Consensus pattern (20 bp):
CATGCTTGTTCACGCTTGTT
Found at i:55321650 original size:18 final size:19
Alignment explanation
Indices: 55321629--55321671 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
55321619 TTAAGTTTTG
55321629 TTTTAATATTT-TTAT-ATA
1 TTTTAAT-TTTATTATCATA
55321647 TTTTAATTTTATTATGCATA
1 TTTTAATTTTATTAT-CATA
55321667 TTTTA
1 TTTTA
55321672 TTACCTCCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.14
18 11 0.50
20 8 0.36
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (19 bp):
TTTTAATTTTATTATCATA
Found at i:55329501 original size:24 final size:24
Alignment explanation
Indices: 55329457--55329503 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
55329447 AAAATAAAAA
* **
55329457 ATATTTATAAAAATTCCAAAATTT
1 ATATTTAAAAAAATTAAAAAATTT
55329481 ATATTTAAAAAAATTAAAAAATT
1 ATATTTAAAAAAATTAAAAAATT
55329504 CTAAAGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (24 bp):
ATATTTAAAAAAATTAAAAAATTT
Found at i:55329519 original size:11 final size:9
Alignment explanation
Indices: 55329485--55329529 Score: 54
Period size: 9 Copynumber: 4.7 Consensus size: 9
55329475 AAATTTATAT
55329485 TTAAAAAAA
1 TTAAAAAAA
*
55329494 TTAAAAAAT
1 TTAAAAAAA
55329503 TCTAAAGAAAA
1 T-TAAA-AAAA
55329514 TATAAAAAAA
1 T-TAAAAAAA
55329524 TTAAAA
1 TTAAAA
55329530 TTTTTAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
9 14 0.45
10 9 0.29
11 8 0.26
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (9 bp):
TTAAAAAAA
Found at i:55334727 original size:31 final size:30
Alignment explanation
Indices: 55334692--55334753 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
55334682 AGAGTTAGAG
* *
55334692 AAAAAAAATTTTAAGTCCCTTAAAAGTTGGT
1 AAAAAAAAATTT-AGACCCTTAAAAGTTGGT
*
55334723 AAAAAAAAATTTAGACGCTTAAAAGTTGGT
1 AAAAAAAAATTTAGACCCTTAAAAGTTGGT
55334753 A
1 A
55334754 TTTCTTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 17 0.61
31 11 0.39
ACGTcount: A:0.48, C:0.08, G:0.15, T:0.29
Consensus pattern (30 bp):
AAAAAAAAATTTAGACCCTTAAAAGTTGGT
Found at i:55337682 original size:11 final size:11
Alignment explanation
Indices: 55337666--55337691 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
55337656 AGATCTACTA
55337666 TTTTCTTGTTG
1 TTTTCTTGTTG
55337677 TTTTCTTGTTG
1 TTTTCTTGTTG
55337688 TTTT
1 TTTT
55337692 ACTACTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.15, T:0.77
Consensus pattern (11 bp):
TTTTCTTGTTG
Found at i:55338952 original size:58 final size:59
Alignment explanation
Indices: 55338831--55338983 Score: 159
Period size: 58 Copynumber: 2.6 Consensus size: 59
55338821 GGTTAAATCA
* * * * *
55338831 CTGAATTTGACAATTGTTCCCAACATTAGGACCTGAACTCTTTTTAGTCCAAGTTAGTAC
1 CTGAACTTAACAACTGTTCCC-ACATTAGGACCTAAACTCTTTTTAGTCCAAATTAGTAC
* * *
55338891 CTGAAC-TAGGCAACTGTTCCCACATTA-GAGCCTAAATTCTTTTT-GTCCAAATTAGTCC
1 CTGAACTTA-ACAACTGTTCCCACATTAGGA-CCTAAACTCTTTTTAGTCCAAATTAGTAC
* * *
55338949 CTGAACTTAACAATTGTTCCCACATTGGGAACTAA
1 CTGAACTTAACAACTGTTCCCACATTAGGACCTAA
55338984 TCATTTTGCT
Statistics
Matches: 77, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
58 39 0.51
59 23 0.30
60 15 0.19
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (59 bp):
CTGAACTTAACAACTGTTCCCACATTAGGACCTAAACTCTTTTTAGTCCAAATTAGTAC
Found at i:55343051 original size:262 final size:262
Alignment explanation
Indices: 55342572--55343197 Score: 923
Period size: 262 Copynumber: 2.4 Consensus size: 262
55342562 TCAAAGCTTG
* * * *
55342572 AAAG-TTGAAACTCAACAGAAGCTCAATTGAGTTCCACTTTTAAAGCTTAACTCTCATGCTCAAT
1 AAAGCTTGAAACTCAACAGAAGCTCAATCGAGTTCCACATTTAAAGCTAAACTCTCATGCTCGAT
* ** * * * * *
55342636 TTCAAGCTCAATTATTAGTACTGGAGCTAGAATTCAGTGTTTAAATGTTTACATTGAAGTTTTTC
66 TTCAAGCTCAATTATTAGTGCTCAAACTAGAACTC-GTGTTTAAATGTTCAAATTGAAGTTTCTC
* * * *
55342701 AATACTCATTAAATATAGAAAAAAGCTGGATTAAGCTGATAACGTACTCAGATAAAGTATTAGTA
130 AATACTCATTAAACATAGAAAAAAGCTGGACTAAGCTGATAACGTACACAAATAAAGTATTAGTA
* *
55342766 TACTCAAATTTGACCACTTCAACAGCTCAAGCCCTAAGAAGCTTGAGCTCAAGTTTGACTTGAAA
195 TACTCAAATTCGACCACTTCAACAGCTCAAGCCATAAGAAGCTTGAGCTCAAGTTTGACTTGAAA
55342831 ATC
260 ATC
*
55342834 AAAGCTTGAAACTCAACAGAAGCTCAATCGAGTTCCACATTTAAAGCTCAACTCTCATGCTCGAT
1 AAAGCTTGAAACTCAACAGAAGCTCAATCGAGTTCCACATTTAAAGCTAAACTCTCATGCTCGAT
** ** *
55342899 TTCAATTTCAATTATTAGTGCTTTAACTTGAACTCGTGTTTAAATGTTCAAATTGAAGTTTCTCA
66 TTCAAGCTCAATTATTAGTGCTCAAACTAGAACTCGTGTTTAAATGTTCAAATTGAAGTTTCTCA
55342964 ATACTCATTAAACATAGAAAAAAGCTGGACTAAGCTGATAA-GCTACACAAATAAAGTATTAGTA
131 ATACTCATTAAACATAGAAAAAAGCTGGACTAAGCTGATAACG-TACACAAATAAAGTATTAGTA
*
55343028 TACTCAAATTCGACCAGTTCAACAGCTCAAGCCATAAGAAGCTTGAGCTCAAGTTTGACTTGAAA
195 TACTCAAATTCGACCACTTCAACAGCTCAAGCCATAAGAAGCTTGAGCTCAAGTTTGACTTGAAA
*
55343093 CTC
260 ATC
* * **
55343096 GAAGCCTGAAACTCAACAGAAGCTCAATCGAGTTCCATGTTTAAAGCTAAACTCTCATGCTCGAT
1 AAAGCTTGAAACTCAACAGAAGCTCAATCGAGTTCCACATTTAAAGCTAAACTCTCATGCTCGAT
* * *
55343161 TTCCAGCTCAATGATTAGTGCTCAAACTCGAACTCGT
66 TTCAAGCTCAATTATTAGTGCTCAAACTAGAACTCGT
55343198 AGAATAGAAA
Statistics
Matches: 327, Mismatches: 35, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
261 1 0.00
262 243 0.74
263 83 0.25
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.30
Consensus pattern (262 bp):
AAAGCTTGAAACTCAACAGAAGCTCAATCGAGTTCCACATTTAAAGCTAAACTCTCATGCTCGAT
TTCAAGCTCAATTATTAGTGCTCAAACTAGAACTCGTGTTTAAATGTTCAAATTGAAGTTTCTCA
ATACTCATTAAACATAGAAAAAAGCTGGACTAAGCTGATAACGTACACAAATAAAGTATTAGTAT
ACTCAAATTCGACCACTTCAACAGCTCAAGCCATAAGAAGCTTGAGCTCAAGTTTGACTTGAAAA
TC
Found at i:55346447 original size:22 final size:22
Alignment explanation
Indices: 55346396--55346441 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
55346386 CCTCCTTGCC
55346396 TTAGGTTTTAGATGACCAATTA
1 TTAGGTTTTAGATGACCAATTA
55346418 TTAGGTTTTAGATGACCAATTA
1 TTAGGTTTTAGATGACCAATTA
55346440 TT
1 TT
55346442 GAGTTTATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.43
Consensus pattern (22 bp):
TTAGGTTTTAGATGACCAATTA
Found at i:55356456 original size:2 final size:2
Alignment explanation
Indices: 55356449--55356476 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
55356439 TCTCTGGTTT
55356449 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
55356477 CTTTTTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:55357484 original size:8 final size:8
Alignment explanation
Indices: 55357471--55357520 Score: 56
Period size: 8 Copynumber: 6.9 Consensus size: 8
55357461 ACTAACATGA
55357471 AATTTTTT
1 AATTTTTT
55357479 AATTTTTT
1 AATTTTTT
*
55357487 AATTTGTT
1 AATTTTTT
55357495 AA-TTTTT
1 AATTTTTT
55357502 -A-TTTTT
1 AATTTTTT
55357508 --TTTTTT
1 AATTTTTT
55357514 AATTTTT
1 AATTTTT
55357521 ATAAAGTACG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
6 11 0.30
7 4 0.11
8 22 0.59
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (8 bp):
AATTTTTT
Found at i:55358844 original size:24 final size:24
Alignment explanation
Indices: 55358799--55358844 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
55358789 GTTAATATCC
* *
55358799 TAATAAATTATACTATACTATAAT
1 TAATAAATTAAACTATAATATAAT
55358823 TAATAATATTAAAC-ATAATATA
1 TAATAA-ATTAAACTATAATATA
55358845 TATATCATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (24 bp):
TAATAAATTAAACTATAATATAAT
Found at i:55361828 original size:96 final size:95
Alignment explanation
Indices: 55361633--55361815 Score: 246
Period size: 96 Copynumber: 1.9 Consensus size: 95
55361623 TAAAAAAGTG
* * * *
55361633 AATATGCAATGAAAAATAATTATTTGCATTAGACACCCCTAAATTATAACTAAAATTCTTAATTT
1 AATATGCAATAAAAAATAATTATTT-CACTAAACACCCCTAAACTATAACTAAAATTCTTAATTT
*
55361698 AGTCTCAAACTTCAAAACGTTGACTTACCAA
65 AGTCTCAAACATCAAAACGTTGACTTACCAA
55361729 AATATGCAATAAAAAAATAATTAATTT-ACTAAACA-CCCTCAAACTATAACTAAAATT-TTAAT
1 AATATGCAAT-AAAAAATAATT-ATTTCACTAAACACCCCT-AAACTATAACTAAAATTCTTAAT
* *
55361791 TTAGTCTCGAACATCAAAATGTTGA
63 TTAGTCTCAAACATCAAAACGTTGA
55361816 GTTAATCAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
95 31 0.40
96 32 0.42
97 10 0.13
98 4 0.05
ACGTcount: A:0.45, C:0.16, G:0.07, T:0.32
Consensus pattern (95 bp):
AATATGCAATAAAAAATAATTATTTCACTAAACACCCCTAAACTATAACTAAAATTCTTAATTTA
GTCTCAAACATCAAAACGTTGACTTACCAA
Found at i:55369894 original size:4 final size:4
Alignment explanation
Indices: 55369885--55369918 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
55369875 ATCAATGAGT
*
55369885 TTAA TTAA TTAA TTAA TTAA CTAA TTATA TTAA T
1 TTAA TTAA TTAA TTAA TTAA TTAA TTA-A TTAA T
55369919 AAAAAAAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (4 bp):
TTAA
Found at i:55372954 original size:25 final size:27
Alignment explanation
Indices: 55372924--55372992 Score: 72
Period size: 26 Copynumber: 2.6 Consensus size: 27
55372914 TTTGATTTAC
55372924 TATTTTAAATAATAAAAAT-TAA-AAA
1 TATTTTAAATAATAAAAATATAATAAA
* * *
55372949 TATTTTATATTAAT-ATAATATAATATA
1 TATTTTA-AATAATAAAAATATAATAAA
*
55372976 TTTTTTAAATAATAAAA
1 TATTTTAAATAATAAAA
55372993 CAAAATTTTC
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
25 11 0.32
26 13 0.38
27 10 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
TATTTTAAATAATAAAAATATAATAAA
Found at i:55383119 original size:147 final size:147
Alignment explanation
Indices: 55382852--55383196 Score: 541
Period size: 147 Copynumber: 2.3 Consensus size: 147
55382842 TATACAGGAG
* * *
55382852 AAATGGTTACAGATGTTGGGATTCGAATCCCGAACCTACTGCATATCAGGGTGGTTGAATAAACC
1 AAATGGTTGCATATGTTGGGATTCGAATCCCGAACCTACTGCATATCGGGGTGGTTGAATAAACC
* * * *
55382917 AACTTAGCTTAACTCCGGGCTTTTCTCAAATTATCCGGTTTCATTGGATCCTTGCAGCAGCATAT
66 AACTGAGCTTAACTCCGAGCTTTTCTCAAATTATCCGGTTTCACTGGATCCTTGCAGCAGCATAC
55382982 GGATCAAGACATAGGGA
131 GGATCAAGACATAGGGA
* * *
55382999 AAATGGTTGCATATGTTGCGATTCGAATCCCGAACTTGCTGCATATCGGGGTGGTTGAATAAACC
1 AAATGGTTGCATATGTTGGGATTCGAATCCCGAACCTACTGCATATCGGGGTGGTTGAATAAACC
*
55383064 AACTGAGCTTAACTCCGAG-TTCTTCTCAAATTATCCGGTTTCAGCT-GATCTTTGCAGCAGCAT
66 AACTGAGCTTAACTCCGAGCTT-TTCTCAAATTATCCGGTTTCA-CTGGATCCTTGCAGCAGCAT
55383127 ACGGATCAAGACATAGGGA
129 ACGGATCAAGACATAGGGA
* *
55383146 AAATGGTTGCATATGTTGGGATTCGAATCCCAAACCTACTGAATATCGGGG
1 AAATGGTTGCATATGTTGGGATTCGAATCCCGAACCTACTGCATATCGGGG
55383197 AGGTAACTGT
Statistics
Matches: 180, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
146 2 0.01
147 177 0.98
148 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.28
Consensus pattern (147 bp):
AAATGGTTGCATATGTTGGGATTCGAATCCCGAACCTACTGCATATCGGGGTGGTTGAATAAACC
AACTGAGCTTAACTCCGAGCTTTTCTCAAATTATCCGGTTTCACTGGATCCTTGCAGCAGCATAC
GGATCAAGACATAGGGA
Found at i:55390407 original size:12 final size:12
Alignment explanation
Indices: 55390390--55390424 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
55390380 TGGAAACCTC
*
55390390 GAAGAACAAGAA
1 GAAGAATAAGAA
55390402 GAAGAATAAGAA
1 GAAGAATAAGAA
55390414 GAAGAATAAGA
1 GAAGAATAAGA
55390425 GTGGAAGGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.66, C:0.03, G:0.26, T:0.06
Consensus pattern (12 bp):
GAAGAATAAGAA
Found at i:55394505 original size:30 final size:30
Alignment explanation
Indices: 55394470--55394529 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
55394460 TTATAGGGAC
*
55394470 TGGATCAA-ATTAGTCCCTCTATTTATTAAA
1 TGGATCAATATTAGTCCCTATA-TTATTAAA
* *
55394500 TGGATCAATTTTGGTCCCTATATTATTAAA
1 TGGATCAATATTAGTCCCTATATTATTAAA
55394530 AAGAACCCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.42
Consensus pattern (30 bp):
TGGATCAATATTAGTCCCTATATTATTAAA
Found at i:55397817 original size:16 final size:16
Alignment explanation
Indices: 55397778--55397829 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
55397768 TTTGAAAAAA
*
55397778 ATTTATTT-TTTTATT
1 ATTTATTTATTGTATT
*
55397793 TTTTAATTTCA-TGTATT
1 ATTT-ATTT-ATTGTATT
55397810 ATTTATTTATTGTATT
1 ATTTATTTATTGTATT
55397826 ATTT
1 ATTT
55397830 TTCACATGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
15 4 0.13
16 18 0.60
17 8 0.27
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.71
Consensus pattern (16 bp):
ATTTATTTATTGTATT
Found at i:55400577 original size:6 final size:6
Alignment explanation
Indices: 55400566--55400597 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
55400556 AGGGTTCTAT
55400566 ATATAC ATATAC ATATAC ATATAC ATATAC AT
1 ATATAC ATATAC ATATAC ATATAC ATATAC AT
55400598 TATCGAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAC
Found at i:55402124 original size:16 final size:16
Alignment explanation
Indices: 55402103--55402135 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
55402093 AATAGCTGAA
55402103 ATTATTA-AGAAATTTT
1 ATTATTAGAG-AATTTT
55402119 ATTATTAGAGAATTTT
1 ATTATTAGAGAATTTT
55402135 A
1 A
55402136 AACCCAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.48
Consensus pattern (16 bp):
ATTATTAGAGAATTTT
Found at i:55404892 original size:19 final size:16
Alignment explanation
Indices: 55404870--55404920 Score: 50
Period size: 15 Copynumber: 3.1 Consensus size: 16
55404860 TAATTTTTTT
55404870 TATTTTTAAAAATATTTAA
1 TATTTTT-AAAATA-TT-A
*
55404889 TATTATTAAAATATTA
1 TATTTTTAAAATATTA
*
55404905 TATTTTT-CAATATTA
1 TATTTTTAAAATATTA
55404920 T
1 T
55404921 TAAACATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 8 0.28
16 7 0.24
17 2 0.07
18 6 0.21
19 6 0.21
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTTTTAAAATATTA
Found at i:55404942 original size:24 final size:25
Alignment explanation
Indices: 55404885--55404938 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
55404875 TTAAAAATAT
* *
55404885 TTAATATTATTAAAATATTATATTT
1 TTAATATTATTAAAACATTATATTC
55404910 TTCAATATTATT-AAACA-TATATTC
1 TT-AATATTATTAAAACATTATATTC
55404934 TTAAT
1 TTAAT
55404939 TATTTATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 3 0.12
24 8 0.31
25 6 0.23
26 9 0.35
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.52
Consensus pattern (25 bp):
TTAATATTATTAAAACATTATATTC
Found at i:55405013 original size:20 final size:22
Alignment explanation
Indices: 55404973--55405014 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
55404963 AATATTAATA
*
55404973 TAATAAATATAATTTATTATTT
1 TAATAAATATAATTTAATATTT
55404995 TAATAAAT-T-ATTTAATATTT
1 TAATAAATATAATTTAATATTT
55405015 CAATTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 1 0.05
22 8 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TAATAAATATAATTTAATATTT
Found at i:55405098 original size:15 final size:15
Alignment explanation
Indices: 55405080--55405136 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 15
55405070 ATTAAATATT
55405080 AATATTTTAATAATA
1 AATATTTTAATAATA
*
55405095 AATAATTATTACAATTATA
1 AAT-ATT-TT--AATAATA
*
55405114 AATATATTAATAATA
1 AATATTTTAATAATA
55405129 AATATTTT
1 AATATTTT
55405137 GTCGTATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 16 0.47
16 3 0.09
17 4 0.12
18 2 0.06
19 9 0.26
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:55406445 original size:23 final size:24
Alignment explanation
Indices: 55406419--55406473 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
55406409 CTCGGTTAAT
* *
55406419 AATTTAATTAATTTTTTT-TATAA
1 AATTTAATCAATTTTTTTATAGAA
*
55406442 AATTGAATCAATTTTTTTATAGAA
1 AATTTAATCAATTTTTTTATAGAA
55406466 AAGTTTAA
1 AA-TTTAA
55406474 AGTGATAATC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 16 0.62
24 6 0.23
25 4 0.15
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (24 bp):
AATTTAATCAATTTTTTTATAGAA
Found at i:55408883 original size:15 final size:15
Alignment explanation
Indices: 55408844--55408884 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
55408834 ATAATTTAAA
*
55408844 TTCAGCATTTATTTT
1 TTCAACATTTATTTT
* *
55408859 TTTAATATTTATTTT
1 TTCAACATTTATTTT
55408874 TTCAACATTTA
1 TTCAACATTTA
55408885 AAATTTTCAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.27, C:0.10, G:0.02, T:0.61
Consensus pattern (15 bp):
TTCAACATTTATTTT
Found at i:55411011 original size:25 final size:25
Alignment explanation
Indices: 55410961--55411012 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
55410951 AATATATATT
* * *
55410961 AATATTTATATTAATATTAAACAAA
1 AATAATTATATTAAAATAAAACAAA
*
55410986 AATAATTATATTAAAATAAAATAAA
1 AATAATTATATTAAAATAAAACAAA
55411011 AA
1 AA
55411013 ATCCTCCCCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (25 bp):
AATAATTATATTAAAATAAAACAAA
Found at i:55411065 original size:21 final size:23
Alignment explanation
Indices: 55411037--55411099 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 23
55411027 CTCCCCCTCC
55411037 CCCT-TCCCACCCTGTCCCT-CT
1 CCCTCTCCCACCCTGTCCCTGCT
*
55411058 -CCTCTCCC-CACT-TGCCCTGCT
1 CCCTCTCCCACCCTGT-CCCTGCT
*
55411079 CCCTCTCCCACCTTCGTCCCT
1 CCCTCTCCCACCCT-GTCCCT
55411100 TTTCAAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 11
0.70 0.07 0.24
Matches are distributed among these distances:
19 1 0.03
20 10 0.31
21 6 0.19
22 8 0.25
23 2 0.06
24 4 0.12
25 1 0.03
ACGTcount: A:0.05, C:0.60, G:0.06, T:0.29
Consensus pattern (23 bp):
CCCTCTCCCACCCTGTCCCTGCT
Found at i:55412300 original size:18 final size:18
Alignment explanation
Indices: 55412258--55412300 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
55412248 CCAACTCATT
55412258 TTTTAT-TTATTTATATA
1 TTTTATATTATTTATATA
* * *
55412275 TATCATATTATTTTTATA
1 TTTTATATTATTTATATA
55412293 TTTTATAT
1 TTTTATAT
55412301 AAATTATAAG
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTATATTATTTATATA
Found at i:55412673 original size:21 final size:22
Alignment explanation
Indices: 55412644--55412688 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
55412634 TTGGTGAAGG
*
55412644 AAGAGCTTAAT-AGATAC-TTTT
1 AAGAACTTAATCAGA-ACATTTT
55412665 AAGAACTTAATCAGAACATTTT
1 AAGAACTTAATCAGAACATTTT
55412687 AA
1 AA
55412689 CCTTTTAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (22 bp):
AAGAACTTAATCAGAACATTTT
Found at i:55420589 original size:23 final size:22
Alignment explanation
Indices: 55420537--55420589 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
55420527 TCCACGTCTT
*
55420537 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
55420559 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
55420582 TTTCTTTT
1 TTTCTTTT
55420590 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:55435819 original size:110 final size:110
Alignment explanation
Indices: 55435626--55435838 Score: 282
Period size: 110 Copynumber: 1.9 Consensus size: 110
55435616 ACATTCTCCG
* *
55435626 AATATAATCATACAAGCATCCAATACTTACCCCAAGTCCAAGTAACAAAGTAGCATTCCTAATGT
1 AATATAATCATACAAGCATCCAATACTCACCCCAAGTCCAAGTAACAAAGTAGCATTCCTAAAGT
55435691 ATACATATATTATACAAAACTGACATTGAACATACCCTTATCAGA
66 ATACATATATTATACAAAACTGACATTGAACATACCCTTATCAGA
* * * * ** * * * **
55435736 AATATACTCATACACGTATCCAATACTCACCCCAAGTTCGGGTAACGAATTGGCATTGGTAAAGT
1 AATATAATCATACAAGCATCCAATACTCACCCCAAGTCCAAGTAACAAAGTAGCATTCCTAAAGT
* * *
55435801 ATGCATATATTATACAAAACTTAGATTGAACATACCCT
66 ATACATATATTATACAAAACTGACATTGAACATACCCT
55435839 CATTGGACTG
Statistics
Matches: 87, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
110 87 1.00
ACGTcount: A:0.40, C:0.22, G:0.11, T:0.27
Consensus pattern (110 bp):
AATATAATCATACAAGCATCCAATACTCACCCCAAGTCCAAGTAACAAAGTAGCATTCCTAAAGT
ATACATATATTATACAAAACTGACATTGAACATACCCTTATCAGA
Found at i:55438138 original size:15 final size:18
Alignment explanation
Indices: 55438092--55438141 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
55438082 TAAAAGAAAT
*
55438092 ACTGATTTAATTGATTGA
1 ACTGATTAAATTGATTGA
55438110 ACTGATTAATATTGATT-A
1 ACTGATTAA-ATTGATTGA
55438128 A-TG-TTAAATTGATT
1 ACTGATTAAATTGATT
55438142 CAGTTAGATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
15 7 0.23
16 4 0.13
17 2 0.07
18 10 0.33
19 7 0.23
ACGTcount: A:0.36, C:0.04, G:0.14, T:0.46
Consensus pattern (18 bp):
ACTGATTAAATTGATTGA
Found at i:55441687 original size:16 final size:15
Alignment explanation
Indices: 55441659--55441700 Score: 66
Period size: 16 Copynumber: 2.7 Consensus size: 15
55441649 AAAAGTGTTC
55441659 CTGACCTGAAATGGT
1 CTGACCTGAAATGGT
*
55441674 CTGAACCTGCAATGGT
1 CTG-ACCTGAAATGGT
55441690 CTGACCTGAAA
1 CTGACCTGAAA
55441701 ATTTGGCCCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (15 bp):
CTGACCTGAAATGGT
Found at i:55443086 original size:14 final size:15
Alignment explanation
Indices: 55443054--55443085 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
55443044 ACAAATTTAC
55443054 TTTTATAAGATAAAT
1 TTTTATAAGATAAAT
55443069 TTTTA-AAG-TAAAT
1 TTTTATAAGATAAAT
55443082 TTTT
1 TTTT
55443086 TCTAAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 3 0.18
15 5 0.29
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (15 bp):
TTTTATAAGATAAAT
Found at i:55444717 original size:90 final size:90
Alignment explanation
Indices: 55444440--55444790 Score: 438
Period size: 90 Copynumber: 3.8 Consensus size: 90
55444430 CACCGAGTTG
* * * *
55444440 AGTGTCGGCCTGTCGGGTACAATATGCATTCCCCATGTCCGAATGTGTATTGAAAATTGTTAGTT
1 AGTGTCGACCTGTCGGGTACAATATGCATTCCCCATGTCTGAATATGTATTGACAATTGTTAGTT
55444505 GCAATGTTACTAGGAGTCTAGTGTTAGTGTT
66 GCAATGTTACTAGGAGTC--GTG-TA---TT
* * * * * *
55444536 AGTGTCGGCCTGTCAGGG-ATAATATGCATTCCCCGTATC-GAGTATGTATTGACAATTGTTAGC
1 AGTGTCGACCTGTC-GGGTACAATATGCATTCCCCATGTCTGAATATGTATTGACAATTGTTAGT
* * * *
55444599 TGCAATGCTACTTGGAGTCGAGTGTT
65 TGCAATGTTACTAGGAGTCGTGTATT
* *
55444625 AGTGTCGACCTGTCGGGTACAATATGCATTCCCCATGTCTGAATATGCATTGACGATTGTTAGTT
1 AGTGTCGACCTGTCGGGTACAATATGCATTCCCCATGTCTGAATATGTATTGACAATTGTTAGTT
*
55444690 GCAATGTTACTCGGAGTCGTGTATT
66 GCAATGTTACTAGGAGTCGTGTATT
* *
55444715 AGTGTC-AGCCTGTCGGGTGCAATATGCATTCCCCATGTCTGAGTATGTATTGACAATTGTTAGT
1 AGTGTCGA-CCTGTCGGGTACAATATGCATTCCCCATGTCTGAATATGTATTGACAATTGTTAGT
55444779 TGCAATGTTACT
65 TGCAATGTTACT
55444791 TTCCTGTTGG
Statistics
Matches: 224, Mismatches: 27, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
88 3 0.01
89 34 0.15
90 112 0.50
92 1 0.00
93 2 0.01
95 37 0.17
96 32 0.14
97 3 0.01
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (90 bp):
AGTGTCGACCTGTCGGGTACAATATGCATTCCCCATGTCTGAATATGTATTGACAATTGTTAGTT
GCAATGTTACTAGGAGTCGTGTATT
Found at i:55444840 original size:70 final size:70
Alignment explanation
Indices: 55444723--55444861 Score: 188
Period size: 70 Copynumber: 2.0 Consensus size: 70
55444713 TTAGTGTCAG
* * * * * *
55444723 CCTGTCGGGTGCAATATGCATTCCCCATGTCTGAGTATGTATTGACAATTGTTAGTTGCAATGTT
1 CCTGTCGGGTACAATATGCATTCCCCATGTCCGAGTATGCATAGACAATTGTTAATTACAATGTT
55444788 ACTTT
66 ACTTT
* * * *
55444793 CCTGTTGGGTACAATATTCATTCCCCGTGTCCGAGTATGCATAGACAATTGTTAATTACGATGTT
1 CCTGTCGGGTACAATATGCATTCCCCATGTCCGAGTATGCATAGACAATTGTTAATTACAATGTT
55444858 ACTT
66 ACTT
55444862 GGAGCCGAGT
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
70 59 1.00
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.37
Consensus pattern (70 bp):
CCTGTCGGGTACAATATGCATTCCCCATGTCCGAGTATGCATAGACAATTGTTAATTACAATGTT
ACTTT
Found at i:55471391 original size:20 final size:20
Alignment explanation
Indices: 55471366--55471406 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
55471356 TTCATCTCAT
55471366 GCATCGCATCATATGCATTA
1 GCATCGCATCATATGCATTA
*
55471386 GCATCGCATTATATGCATTA
1 GCATCGCATCATATGCATTA
55471406 G
1 G
55471407 AGACCTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (20 bp):
GCATCGCATCATATGCATTA
Found at i:55474218 original size:30 final size:30
Alignment explanation
Indices: 55474178--55474339 Score: 163
Period size: 30 Copynumber: 5.4 Consensus size: 30
55474168 AATATGGGCC
*
55474178 AAAATGTAATTTATTG-AAAGTTTAGGGGTT
1 AAAATGTAATTT-TAGAAAAGTTTAGGGGTT
* * *
55474208 AAAGTGTAATTTT-GAGAAAGGTTAAGGGTT
1 AAAATGTAATTTTAGA-AAAGTTTAGGGGTT
* *
55474238 GAAATGTAATTTTAGAAAAGTTT-GGGGTC
1 AAAATGTAATTTTAGAAAAGTTTAGGGGTT
*
55474267 AAAATGTAAATTTTAGAAAAGTTTA-AGGTT
1 AAAATGT-AATTTTAGAAAAGTTTAGGGGTT
* **
55474297 AAAATGTAAATTTCA-AAAAGTACAGGGGTT
1 AAAATGT-AATTTTAGAAAAGTTTAGGGGTT
55474327 AAAATGTAATTTT
1 AAAATGTAATTTT
55474340 TATTTTTTTG
Statistics
Matches: 110, Mismatches: 16, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
28 1 0.01
29 23 0.21
30 84 0.76
31 2 0.02
ACGTcount: A:0.41, C:0.02, G:0.22, T:0.35
Consensus pattern (30 bp):
AAAATGTAATTTTAGAAAAGTTTAGGGGTT
Found at i:55474305 original size:89 final size:89
Alignment explanation
Indices: 55474148--55474339 Score: 205
Period size: 89 Copynumber: 2.1 Consensus size: 89
55474138 CTTTTGGGGC
* * *
55474148 AAAAGTGTAATTTTAGCAAAAATATGGGCCAAAATGTAATTTATTGAAAGTTTAGGGGTTAAAGT
1 AAAA-TGTAATTTTAGCAAAAATATGGGCCAAAATGTAATTTATAGAAAGTTTAGAGGTTAAAAT
* * *
55474213 GTAATTTTGAGAAAGGTTA-A-GGGTT
65 GTAAATTTCA-AAAAG-TACAGGGGTT
* * * *
55474238 GAAATGTAATTTTAG-AAAAGTTTGGGGTCAAAATGTAAATTT-TAGAAAAGTTTA-AGGTTAAA
1 AAAATGTAATTTTAGCAAAAATAT-GGGCCAAAATGT-AATTTATAG-AAAGTTTAGAGGTTAAA
55474300 ATGTAAATTTCAAAAAGTACAGGGGTT
63 ATGTAAATTTCAAAAAGTACAGGGGTT
55474327 AAAATGTAATTTT
1 AAAATGTAATTTT
55474340 TATTTTTTTG
Statistics
Matches: 86, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
87 2 0.02
88 11 0.13
89 57 0.66
90 16 0.19
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.34
Consensus pattern (89 bp):
AAAATGTAATTTTAGCAAAAATATGGGCCAAAATGTAATTTATAGAAAGTTTAGAGGTTAAAATG
TAAATTTCAAAAAGTACAGGGGTT
Found at i:55474341 original size:60 final size:59
Alignment explanation
Indices: 55474201--55474341 Score: 160
Period size: 59 Copynumber: 2.4 Consensus size: 59
55474191 TTGAAAGTTT
* * * * *
55474201 AGGGGTTAAAGTGTAATTTTGAGAAAGGTTAAGGGTTGAAATGTAATTTTAGAAAAGTT
1 AGGGGTTAAAATGTAATTTTTAGAAAGGTTAAGGGTTAAAATGTAATTTCAGAAAAGTC
* * * *
55474260 TGGGGTCAAAATGTAAATTTTAGAAAAGTTTAA-GGTTAAAATGTAAATTTCA-AAAAGTAC
1 AGGGGTTAAAATGTAATTTTTAG-AAAGGTTAAGGGTTAAAATGT-AATTTCAGAAAAGT-C
55474320 AGGGGTTAAAATGTAATTTTTA
1 AGGGGTTAAAATGTAATTTTTA
55474342 TTTTTTTGCC
Statistics
Matches: 67, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
59 34 0.51
60 33 0.49
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.34
Consensus pattern (59 bp):
AGGGGTTAAAATGTAATTTTTAGAAAGGTTAAGGGTTAAAATGTAATTTCAGAAAAGTC
Found at i:55474731 original size:75 final size:74
Alignment explanation
Indices: 55474652--55475600 Score: 1296
Period size: 75 Copynumber: 12.6 Consensus size: 74
55474642 GATCCAAAGT
* ** * *
55474652 TCAACTCACTTCTCAG-ATTATGAGTTGA-CCTTTG-AAAAATAGATATTGAAAATACCTCGATG
1 TCAACTCACCTCTC-GCATTATGAGTTGATTTTTTGAAAAAACAGAAATTGAAAATACCTC-A-G
55474714 TGTGACCCGAGGC
63 -GTGACCCGAGGC
*
55474727 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAAAACAGAAATTAAAAATACCTCAGCG
1 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTG-AAAAAACAGAAATTGAAAATACCTCAG-G
55474792 TGACCCGAGGC
64 TGACCCGAGGC
*
55474803 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAAACAGAAATTAAAAATACCTCAGCGT
1 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAAACAGAAATTGAAAATACCTCAG-GT
55474868 GACCCGAGGC
65 GACCCGAGGC
*
55474878 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAAAACAGAAATTAAAAATACCTCAGCG
1 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTG-AAAAAACAGAAATTGAAAATACCTCAG-G
55474943 TGACCCGAGGC
64 TGACCCGAGGC
*
55474954 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAAACAGAAATTAAAAATACCTCAGCGT
1 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAAACAGAAATTGAAAATACCTCAG-GT
55475019 GACCCGAGGC
65 GACCCGAGGC
55475029 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAAACAGAAATT-AAAATACCTCAGCGT
1 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAAACAGAAATTGAAAATACCTCAG-GT
55475093 GACCCGAGGC
65 GACCCGAGGC
* *
55475103 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTTG--AAAATATAAATTGAAAATACCTCAGGA
1 TCAACTCACCTCTCGCATTATGAGTTGA-TTTTTTGAAAAAACAGAAATTGAAAATACCTCAGG-
55475166 TGACCCGAGGC
64 TGACCCGAGGC
* * * *
55475177 TCAACTCACTTCTCGCAATATGAATTGATTTTTTTG-AAAAACATAAATTGAAAATACCTCAGGA
1 TCAACTCACCTCTCGCATTATGAGTTGA-TTTTTTGAAAAAACAGAAATTGAAAATACCTCAGG-
*
55475241 TGACTCGAGGC
64 TGACCCGAGGC
* * *
55475252 TCAACTCACTTCTCGCATTATGAGTTGATTTTTTTTG-AAAAATATAAATTGAAAATACCTCAGG
1 TCAACTCACCTCTCGCATTATGAGTTGA--TTTTTTGAAAAAACAGAAATTGAAAATACCTCAGG
55475316 ATGACCCGAGGC
64 -TGACCCGAGGC
* *
55475328 TCAACTCACTTCTCGTATTATGAGTTGATTTTTTTG-AAAAACAGAAATTGAAAATACCTCAGGA
1 TCAACTCACCTCTCGCATTATGAGTTGA-TTTTTTGAAAAAACAGAAATTGAAAATACCTCAGG-
* *
55475392 TGACCTGAGGT
64 TGACCCGAGGC
* *
55475403 TCAACTCACCTCTCGCATTATGAGTTGA-TTTTTG-AAAAACAGAAAATGAAAATACCTTAGGAT
1 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAAACAGAAATTGAAAATACCTCAGG-T
*
55475466 CACCCGAGGC
65 GACCCGAGGC
* *
55475476 TCAACTCACTTCTCGCAATATGAGTTGA-TTTTTGAAAAAAACAGAAATTGAAAAATACCTCGAC
1 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTG-AAAAAACAGAAATTG-AAAATACCTC-A-
55475540 GTGTGACCCGAGGC
62 G-GTGACCCGAGGC
*
55475554 TCAACTCACCTCTCGCAATATGAGTTGATTTTTT--AAAAACAGCAAAT
1 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAAACAG-AAAT
55475601 AAAAAATTTG
Statistics
Matches: 820, Mismatches: 36, Indels: 34
0.92 0.04 0.04
Matches are distributed among these distances:
73 83 0.10
74 110 0.13
75 340 0.41
76 216 0.26
77 6 0.01
78 59 0.07
79 6 0.01
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (74 bp):
TCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAAACAGAAATTGAAAATACCTCAGGTG
ACCCGAGGC
Found at i:55474877 original size:151 final size:149
Alignment explanation
Indices: 55474652--55475600 Score: 1332
Period size: 151 Copynumber: 6.3 Consensus size: 149
55474642 GATCCAAAGT
* ** * *
55474652 TCAACTCACTTCTCAG-ATTATGAGTTGA-CCTTTGAAAAATAGATATTGAAAATACCTCGATGT
1 TCAACTCACCTCTC-GCATTATGAGTTGATTTTTTGAAAAACAGAAATTGAAAATACCTC-A-G-
55474715 G-TGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAAAACAGAAATTAA
62 GATGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTG-AAAAAACAGAAATTAA
55474779 AAATACCTCAGCGTGACCCGAGGC
126 AAATACCTCAGCGTGACCCGAGGC
*
55474803 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAAACAGAAATTAAAAATACCTCAGCG-
1 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTG-AAAAACAGAAATTGAAAATACCTCAG-GA
55474867 TGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAAAACAGAAATTAAAA
64 TGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTG-AAAAAACAGAAATTAAAA
55474932 ATACCTCAGCGTGACCCGAGGC
128 ATACCTCAGCGTGACCCGAGGC
*
55474954 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAAACAGAAATTAAAAATACCTCAGCG-
1 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTG-AAAAACAGAAATTGAAAATACCTCAG-GA
55475018 TGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAAACAGAAATT-AAAA
64 TGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAAACAGAAATTAAAAA
55475082 TACCTCAGCGTGACCCGAGGC
129 TACCTCAGCGTGACCCGAGGC
* *
55475103 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTTG-AAAATATAAATTGAAAATACCTCAGGAT
1 TCAACTCACCTCTCGCATTATGAGTTGA-TTTTTTGAAAAACAGAAATTGAAAATACCTCAGGAT
* * * * *
55475167 GACCCGAGGCTCAACTCACTTCTCGCAATATGAATTGATTTTTTTG-AAAAACATAAATTGAAAA
65 GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA-TTTTTTGAAAAAACAGAAATTAAAAA
*
55475231 TACCTCAG-GATGACTCGAGGC
129 TACCTCAGCG-TGACCCGAGGC
* * *
55475252 TCAACTCACTTCTCGCATTATGAGTTGATTTTTTTTGAAAAATATAAATTGAAAATACCTCAGGA
1 TCAACTCACCTCTCGCATTATGAGTTGA--TTTTTTGAAAAACAGAAATTGAAAATACCTCAGGA
* * *
55475317 TGACCCGAGGCTCAACTCACTTCTCGTATTATGAGTTGATTTTTTTG-AAAAACAGAAATTGAAA
64 TGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA-TTTTTTGAAAAAACAGAAATTAAAA
* *
55475381 ATACCTCAG-GATGACCTGAGGT
128 ATACCTCAGCG-TGACCCGAGGC
* * *
55475403 TCAACTCACCTCTCGCATTATGAGTTGA-TTTTTGAAAAACAGAAAATGAAAATACCTTAGGATC
1 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAACAGAAATTGAAAATACCTCAGGATG
* *
55475467 ACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGA-TTTTTGAAAAAAACAGAAATTGAAAAA
66 ACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTG-AAAAAACAGAAATT-AAAAA
*
55475531 TACCTCGACGTGTGACCCGAGGC
129 TACCTC-A-GCGTGACCCGAGGC
*
55475554 TCAACTCACCTCTCGCAATATGAGTTGATTTTTT-AAAAACAGCAAAT
1 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAACAG-AAAT
55475601 AAAAAATTTG
Statistics
Matches: 744, Mismatches: 36, Indels: 35
0.91 0.04 0.04
Matches are distributed among these distances:
146 6 0.01
147 1 0.00
148 150 0.20
149 119 0.16
150 31 0.04
151 402 0.54
152 14 0.02
153 21 0.03
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (149 bp):
TCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAACAGAAATTGAAAATACCTCAGGATG
ACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAAACAGAAATTAAAAATA
CCTCAGCGTGACCCGAGGC
Found at i:55476479 original size:1 final size:1
Alignment explanation
Indices: 55476469--55476549 Score: 63
Period size: 1 Copynumber: 81.0 Consensus size: 1
55476459 TTCATCTTGA
* * * * * * * * *
55476469 TTTTTCTTTTTCTTTTCTTTCTTTTTTTGTTTTTTTTGTTTTTTTGTTTTTTTGTTTTTTTGTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
55476534 TTTTTATTGTTTTTTT
1 TTTTTTTTTTTTTTTT
55476550 AGGCATAACA
Statistics
Matches: 58, Mismatches: 22, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
1 58 1.00
ACGTcount: A:0.01, C:0.05, G:0.07, T:0.86
Consensus pattern (1 bp):
T
Found at i:55476538 original size:17 final size:17
Alignment explanation
Indices: 55476475--55476538 Score: 94
Period size: 17 Copynumber: 3.8 Consensus size: 17
55476465 TTGATTTTTC
* * *
55476475 TTTTTCTTTTCTTTCTT
1 TTTTTGTTTTTTTTGTT
55476492 TTTTTGTTTTTTTTGTT
1 TTTTTGTTTTTTTTGTT
55476509 TTTTTG-TTTTTTTGTT
1 TTTTTGTTTTTTTTGTT
55476525 TTTTTGTTTTTTTT
1 TTTTTGTTTTTTTT
55476539 ATTGTTTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
16 16 0.37
17 27 0.63
ACGTcount: A:0.00, C:0.05, G:0.08, T:0.88
Consensus pattern (17 bp):
TTTTTGTTTTTTTTGTT
Found at i:55476547 original size:9 final size:8
Alignment explanation
Indices: 55476475--55476537 Score: 90
Period size: 8 Copynumber: 7.6 Consensus size: 8
55476465 TTGATTTTTC
*
55476475 TTTTTCTT
1 TTTTTGTT
*
55476483 TTCTTTCTT
1 TT-TTTGTT
55476492 TTTTTGTTT
1 TTTTTG-TT
55476501 TTTTTGTT
1 TTTTTGTT
55476509 TTTTTGTT
1 TTTTTGTT
55476517 TTTTTGTT
1 TTTTTGTT
55476525 TTTTTGTT
1 TTTTTGTT
55476533 TTTTT
1 TTTTT
55476538 TATTGTTTTT
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
8 36 0.69
9 16 0.31
ACGTcount: A:0.00, C:0.05, G:0.08, T:0.87
Consensus pattern (8 bp):
TTTTTGTT
Found at i:55480519 original size:4 final size:4
Alignment explanation
Indices: 55480510--55480534 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
55480500 ATGTACATGC
55480510 AATG AATG AATG AATG AATG AATG A
1 AATG AATG AATG AATG AATG AATG A
55480535 CCAATGGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (4 bp):
AATG
Found at i:55482240 original size:17 final size:16
Alignment explanation
Indices: 55482220--55482311 Score: 69
Period size: 17 Copynumber: 5.3 Consensus size: 16
55482210 AATACGATTT
55482220 TTTTTAAAACACAAAGA
1 TTTTTAAAACACAAA-A
* **
55482237 TTTTTGAAACA-ATTATT
1 TTTTTAAAACACA--AAA
55482254 TTTTTGAAAACACGAAAAA
1 TTTTT-AAAACAC--AAAA
*
55482273 TTTTTAAAACACGGAAA
1 TTTTTAAAACAC-AAAA
55482290 TTTTTAAAACACAGAAA
1 TTTTTAAAACACA-AAA
55482307 TTTTT
1 TTTTT
55482312 TGAAAACATG
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
16 1 0.02
17 38 0.64
18 13 0.22
19 6 0.10
21 1 0.02
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.37
Consensus pattern (16 bp):
TTTTTAAAACACAAAA
Found at i:55482264 original size:35 final size:36
Alignment explanation
Indices: 55482216--55482283 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 36
55482206 TCAAAATACG
* * *
55482216 ATTTTTTTTAAAACAC-AAAGATTTTTGAAACAATT
1 ATTTTTTTGAAAACACGAAAAATTTTTAAAACAATT
55482251 ATTTTTTTGAAAACACGAAAAATTTTTAAAACA
1 ATTTTTTTGAAAACACGAAAAATTTTTAAAACA
55482284 CGGAAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 15 0.52
36 14 0.48
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.40
Consensus pattern (36 bp):
ATTTTTTTGAAAACACGAAAAATTTTTAAAACAATT
Found at i:55482276 original size:18 final size:18
Alignment explanation
Indices: 55482255--55482333 Score: 88
Period size: 18 Copynumber: 4.4 Consensus size: 18
55482245 ACAATTATTT
55482255 TTTTGAAAACACGAAAAA
1 TTTTGAAAACACGAAAAA
* *
55482273 TTTTTAAAACACG-GAAA
1 TTTTGAAAACACGAAAAA
* **
55482290 TTTTTAAAACACAGAAATT
1 TTTTGAAAACAC-GAAAAA
*
55482309 TTTTGAAAACATGAAAAA
1 TTTTGAAAACACGAAAAA
55482327 TTTTGAA
1 TTTTGAA
55482334 TAACGGATGC
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
17 15 0.30
18 24 0.48
19 11 0.22
ACGTcount: A:0.49, C:0.09, G:0.10, T:0.32
Consensus pattern (18 bp):
TTTTGAAAACACGAAAAA
Found at i:55482542 original size:19 final size:19
Alignment explanation
Indices: 55482509--55482565 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
55482499 CGTTGCATTA
55482509 TTTTTGAAAACACGAATATT
1 TTTTTGAAAACACGAA-ATT
*
55482529 TTTTTG-AAATACGAAATTT
1 TTTTTGAAAACACGAAA-TT
*
55482548 TTTTCTGAAGACACGAAA
1 TTTT-TGAAAACACGAAA
55482566 ATTTCAAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 1 0.03
19 14 0.45
20 8 0.26
21 8 0.26
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.39
Consensus pattern (19 bp):
TTTTTGAAAACACGAAATT
Found at i:55482609 original size:13 final size:11
Alignment explanation
Indices: 55482581--55482605 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
55482571 AAAACACGAA
55482581 AATTTTTTTTG
1 AATTTTTTTTG
55482592 AATTTTTTTTG
1 AATTTTTTTTG
55482603 AAT
1 AAT
55482606 ATTTACAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (11 bp):
AATTTTTTTTG
Found at i:55482747 original size:16 final size:16
Alignment explanation
Indices: 55482726--55482763 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
55482716 TTAAAATTAT
55482726 TTAAAA-TAACATTAAA
1 TTAAAATTAA-ATTAAA
*
55482742 TTAAAATTGAATTAAA
1 TTAAAATTAAATTAAA
55482758 TTAAAA
1 TTAAAA
55482764 ATATAATTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 18 0.90
17 2 0.10
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34
Consensus pattern (16 bp):
TTAAAATTAAATTAAA
Found at i:55482955 original size:17 final size:17
Alignment explanation
Indices: 55482933--55482975 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
55482923 GAACCCTTTT
*
55482933 TTTTCTCTTTTTCTCTC
1 TTTTCTCTTTTTATCTC
*
55482950 TTTTCTTTTTTTATCTC
1 TTTTCTCTTTTTATCTC
*
55482967 TTTTTTCTT
1 TTTTCTCTT
55482976 CTGTTTTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTCTCTTTTTATCTC
Found at i:55482966 original size:19 final size:18
Alignment explanation
Indices: 55482940--55482975 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
55482930 TTTTTTTCTC
55482940 TTTTTCTCTCTTTTCTTT
1 TTTTTCTCTCTTTTCTTT
*
55482958 TTTTATCTCTTTTTTCTT
1 TTTT-TCTCTCTTTTCTT
55482976 CTGTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTTCTCTCTTTTCTTT
Found at i:55482966 original size:27 final size:26
Alignment explanation
Indices: 55482928--55482987 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
55482918 AAATTGAACC
*
55482928 CTTTTTTTTCTC-TTTTTCTCTCTTTT
1 CTTTTTTTTCTCTTTTTTCT-TCTGTT
55482954 CTTTTTTTATCTCTTTTTTCTTCTGTT
1 CTTTTTTT-TCTCTTTTTTCTTCTGTT
55482981 -TTTTTTT
1 CTTTTTTT
55482988 CTGGCCTGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 15 0.48
27 9 0.29
28 7 0.23
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (26 bp):
CTTTTTTTTCTCTTTTTTCTTCTGTT
Found at i:55483066 original size:27 final size:28
Alignment explanation
Indices: 55483015--55483072 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 28
55483005 GGCCTGCTGG
55483015 GCCTGCACACTGCTGGCTGCTGTTGGGCT
1 GCCTGCACACTGC-GGCTGCTGTTGGGCT
*
55483044 GCCTGCGCACTG-GGCTGCTGTTGGGCT
1 GCCTGCACACTGCGGCTGCTGTTGGGCT
55483071 GC
1 GC
55483073 TGCTGGGTCG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
27 17 0.61
29 11 0.39
ACGTcount: A:0.05, C:0.31, G:0.38, T:0.26
Consensus pattern (28 bp):
GCCTGCACACTGCGGCTGCTGTTGGGCT
Found at i:55483175 original size:3 final size:3
Alignment explanation
Indices: 55483169--55483226 Score: 61
Period size: 3 Copynumber: 20.3 Consensus size: 3
55483159 TTATTTTTCT
* *
55483169 TTC TTC TTC TTC TTT TTC TTCC TTC TT- TTC TAC -TC TT- TT- TTC
1 TTC TTC TTC TTC TTC TTC TT-C TTC TTC TTC TTC TTC TTC TTC TTC
55483211 TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC T
55483227 CTGTTCGGCC
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
2 7 0.15
3 37 0.79
4 3 0.06
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:55483361 original size:28 final size:27
Alignment explanation
Indices: 55483329--55483410 Score: 76
Period size: 28 Copynumber: 2.9 Consensus size: 27
55483319 TCCCTCTCTT
*
55483329 CTTTTCTTTTTCTTTTTCTTTTTCGACA
1 CTTTTCTTTTTCTTTTTCTTTTT-GAAA
*
55483357 CTTTT-TTTTCTCTTTTTCTCTTTGAAA
1 CTTTTCTTTT-TCTTTTTCTTTTTGAAA
*
55483384 ATTTTCCTTTGCTTACTTTTTCTTTTT
1 CTTTT-CTTT--TT-CTTTTTCTTTTT
55483411 TGCTTTGGCT
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
27 11 0.25
28 17 0.39
29 3 0.07
30 1 0.02
31 12 0.27
ACGTcount: A:0.09, C:0.20, G:0.04, T:0.68
Consensus pattern (27 bp):
CTTTTCTTTTTCTTTTTCTTTTTGAAA
Found at i:55483942 original size:30 final size:28
Alignment explanation
Indices: 55483893--55484054 Score: 144
Period size: 30 Copynumber: 5.5 Consensus size: 28
55483883 AATATGGGCC
*
55483893 AAAATGTAATTTCTTGAAAGTTTAGGTGTT
1 AAAATGTAATTT-TAGAAAGTTTAGG-GTT
* *
55483923 AAAGTGTAATTTTGAGAAAGGTTAAGGGTT
1 AAAATGTAATTTT-AGAAA-GTTTAGGGTT
* * *
55483953 GAAATGTAATTTTAGCAAAGTTTGGGGTC
1 AAAATGTAATTTTAG-AAAGTTTAGGGTT
* * *
55483982 AAAATGTAAATTTTGGAAAAGTTTAAGGTC
1 AAAATGT-AATTTTAG-AAAGTTTAGGGTT
* *
55484012 AAAATGTAAATTTTAAAAAGTATAGGGGTT
1 AAAATGT-AATTTTAGAAAGTTTA-GGGTT
55484042 AAAATGTAATTTT
1 AAAATGTAATTTT
55484055 TATTTTTTTG
Statistics
Matches: 109, Mismatches: 18, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
29 29 0.27
30 74 0.68
31 6 0.06
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.36
Consensus pattern (28 bp):
AAAATGTAATTTTAGAAAGTTTAGGGTT
Found at i:55483973 original size:60 final size:58
Alignment explanation
Indices: 55483892--55484054 Score: 177
Period size: 60 Copynumber: 2.7 Consensus size: 58
55483882 AAATATGGGC
* * *
55483892 CAAAATGTAATTTCTTGAAAGTTTAGGTGTTAAAGTGTAATTTT-GAGAAAGGTTAAGGGT
1 CAAAATGTAATTT-TAGAAAGTTTAGGGGTTAAAATGTAATTTTGGA-AAAGGTTAA-GGT
** * *
55483952 TGAAATGTAATTTTAGCAAAGTTT-GGGGTCAAAATGTAAATTTTGGAAAAGTTTAAGGT
1 CAAAATGTAATTTTAG-AAAGTTTAGGGGTTAAAATGT-AATTTTGGAAAAGGTTAAGGT
* *
55484011 CAAAATGTAAATTTTAAAAAGTATAGGGGTTAAAATGTAATTTT
1 CAAAATGT-AATTTTAGAAAGTTTAGGGGTTAAAATGTAATTTT
55484055 TATTTTTTTG
Statistics
Matches: 86, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
59 33 0.38
60 51 0.59
61 2 0.02
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (58 bp):
CAAAATGTAATTTTAGAAAGTTTAGGGGTTAAAATGTAATTTTGGAAAAGGTTAAGGT
Done.