Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 129 of 240
Found at i:40096188 original size:21 final size:19
Alignment explanation
Indices: 40096145--40096188 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
40096135 TATCGTTAAT
* *
40096145 AGAAGCTCATAAGCTGAAC
1 AGAAGCTCATAAGCTAAAA
40096164 AGAAGCTCATAAAAGCTAAAA
1 AGAAGCTCAT--AAGCTAAAA
40096185 AGAA
1 AGAA
40096189 ACCCATAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 10 0.48
21 11 0.52
ACGTcount: A:0.52, C:0.16, G:0.18, T:0.14
Consensus pattern (19 bp):
AGAAGCTCATAAGCTAAAA
Found at i:40096237 original size:42 final size:41
Alignment explanation
Indices: 40096186--40096351 Score: 131
Period size: 42 Copynumber: 4.0 Consensus size: 41
40096176 AAGCTAAAAA
* * *
40096186 GAAACCCATAAGGGTTGTACAGAAGCTT-GTAAGAGCTGAAC
1 GAAAACCATAAGGGTTGAACAGAAGCTTAAT-AGAGCTGAAC
* * *
40096227 GAAAAGCCATAAGGGTTAAATAGAAGCTTAATAGAGTTGAAC
1 GAAAA-CCATAAGGGTTGAACAGAAGCTTAATAGAGCTGAAC
* * * *
40096269 GGAAACTCATAAGAGTTGAACAGAAGCTCAATAGAGCTGAGC
1 GAAAAC-CATAAGGGTTGAACAGAAGCTTAATAGAGCTGAAC
* * * *
40096311 -AGAAACTCATATGAGTTAAACAGAAGC-TCATAAGAGCTGAA
1 GA-AAAC-CATAAGGGTTGAACAGAAGCTTAAT-AGAGCTGAA
40096352 TGGAAAGTAA
Statistics
Matches: 101, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
41 7 0.07
42 93 0.92
43 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.19
Consensus pattern (41 bp):
GAAAACCATAAGGGTTGAACAGAAGCTTAATAGAGCTGAAC
Found at i:40096285 original size:21 final size:21
Alignment explanation
Indices: 40096259--40096351 Score: 98
Period size: 21 Copynumber: 4.4 Consensus size: 21
40096249 GAAGCTTAAT
*
40096259 AGAGTTGAACGGAAACTCATA
1 AGAGTTGAACAGAAACTCATA
*
40096280 AGAGTTGAACAGAAGCTCA-A
1 AGAGTTGAACAGAAACTCATA
* *
40096300 TAGAGCTGAGCAGAAACTCATA
1 -AGAGTTGAACAGAAACTCATA
* * *
40096322 TGAGTTAAACAGAAGCTCATA
1 AGAGTTGAACAGAAACTCATA
*
40096343 AGAGCTGAA
1 AGAGTTGAA
40096352 TGGAAAGTAA
Statistics
Matches: 57, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
20 1 0.02
21 55 0.96
22 1 0.02
ACGTcount: A:0.43, C:0.15, G:0.24, T:0.18
Consensus pattern (21 bp):
AGAGTTGAACAGAAACTCATA
Found at i:40096357 original size:84 final size:84
Alignment explanation
Indices: 40096161--40096357 Score: 186
Period size: 84 Copynumber: 2.3 Consensus size: 84
40096151 TCATAAGCTG
* * * * * **
40096161 AACAGAAGCTCATAAAAGCTAAAAAGAAACCCATAAGGGTTGTACAGAAGCTTGTAAGAGCTGAA
1 AACAGAAGCTCATAAGAGCTGAAAGGAAACCCATAAGAGTTGAACAGAAGCTAATAAGAGCTGAA
*
40096226 CGAAAAGCCATAAGGGTTA
66 CGAAAAGCCATAAGAGTTA
* * * * *
40096245 AATAGAAGCTTA-ATAGAGTTGAACGGAAACTCATAAGAGTTGAACAGAAGCTCAAT-AGAGCTG
1 AACAGAAGCTCATA-AGAGCTGAAAGGAAACCCATAAGAGTTGAACAGAAGCT-AATAAGAGCTG
* *
40096308 AGC-AGAAA-CTCATATGAGTTA
64 AACGA-AAAGC-CATAAGAGTTA
*
40096329 AACAGAAGCTCATAAGAGCTGAATGGAAA
1 AACAGAAGCTCATAAGAGCTGAAAGGAAA
40096358 GTAAAACATA
Statistics
Matches: 89, Mismatches: 19, Indels: 10
0.75 0.16 0.08
Matches are distributed among these distances:
83 3 0.03
84 84 0.94
85 2 0.02
ACGTcount: A:0.45, C:0.14, G:0.23, T:0.18
Consensus pattern (84 bp):
AACAGAAGCTCATAAGAGCTGAAAGGAAACCCATAAGAGTTGAACAGAAGCTAATAAGAGCTGAA
CGAAAAGCCATAAGAGTTA
Found at i:40099563 original size:27 final size:27
Alignment explanation
Indices: 40099495--40099568 Score: 71
Period size: 28 Copynumber: 2.7 Consensus size: 27
40099485 GATGATTGAA
40099495 AGGGTTGATGAAATTTTTGAAGTAAAG
1 AGGGTTGATGAAATTTTTGAAGTAAAG
* * *
40099522 AGAGTTGCTGAAAATTTTTGAACG-AAAT
1 AGGGTTGATG-AAATTTTTGAA-GTAAAG
40099550 AGGGTTCG-TGAAATGTTTT
1 AGGGTT-GATGAAAT-TTTT
40099569 AGGGATATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
27 12 0.31
28 25 0.64
29 2 0.05
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.35
Consensus pattern (27 bp):
AGGGTTGATGAAATTTTTGAAGTAAAG
Found at i:40106178 original size:20 final size:20
Alignment explanation
Indices: 40106153--40106230 Score: 86
Period size: 22 Copynumber: 3.9 Consensus size: 20
40106143 TTTAGATTAG
*
40106153 AATTTTGTATGAATATTTTA
1 AATTTTGTATGAATATTATA
40106173 AATTTTTTGTATGAATATTATA
1 AA--TTTTGTATGAATATTATA
* * *
40106195 ATTTTTTTATGAATATTGT-
1 AATTTTGTATGAATATTATA
*
40106214 AATGTTGTATGAATATT
1 AATTTTGTATGAATATT
40106231 GTAATTATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
19 14 0.29
20 17 0.35
22 18 0.37
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (20 bp):
AATTTTGTATGAATATTATA
Found at i:40106342 original size:49 final size:49
Alignment explanation
Indices: 40106289--40106539 Score: 364
Period size: 49 Copynumber: 5.2 Consensus size: 49
40106279 TTTTTATATG
40106289 AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGT
* * ** *
40106338 AATATTATAGTTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGT
* ** *
40106387 AATTTTGTAATTTTGTATGAATATTATATTTTTTTTGAATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGT
* *
40106436 AATATTATAATTTTGTATGAATATTGT-AATTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGT
*
40106484 AATATTGTAATTTTGTATGAATATCAT-AATTTTTT-TATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGT
*
40106531 AATGTTGTA
1 AATATTGTA
40106540 TGAATATTGT
Statistics
Matches: 180, Mismatches: 22, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
47 20 0.11
48 50 0.28
49 110 0.61
ACGTcount: A:0.33, C:0.01, G:0.13, T:0.54
Consensus pattern (49 bp):
AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGT
Found at i:40106357 original size:27 final size:26
Alignment explanation
Indices: 40106321--40106627 Score: 226
Period size: 27 Copynumber: 12.8 Consensus size: 26
40106311 ATTATAAATT
40106321 TTTTGTATGAATATTGTAATATTATA
1 TTTTGTATGAATATTGTAATATTATA
*
40106347 GTTTTGTATGAATATTG-CA-ATT-T-
1 -TTTTGTATGAATATTGTAATATTATA
* *
40106370 TTTTGTATGAATATTGTAATTTTGTAA
1 TTTTGTATGAATATTGTAATATTAT-A
*
40106397 TTTTGTATGAATA-T-T-ATATT-TT
1 TTTTGTATGAATATTGTAATATTATA
*
40106419 TTTTGAATGAATATTGTAATATTATAA
1 TTTTGTATGAATATTGTAATATTAT-A
40106446 TTTTGTATGAATATTGT-A-A-T-T-
1 TTTTGTATGAATATTGTAATATTATA
*
40106467 TTTTGTATGAATATTGTAATATTGTAA
1 TTTTGTATGAATATTGTAATATTAT-A
*
40106494 TTTTGTATGAATA---TCATA--AT-
1 TTTTGTATGAATATTGTAATATTATA
*
40106514 TTTTTTATGAATATTGT------A-A
1 TTTTGTATGAATATTGTAATATTATA
* *
40106533 TGTTGTATGAATATTGTAATATTAGAA
1 TTTTGTATGAATATTGTAATATTA-TA
*
40106560 TTTTGTATGAATATTG---CATT-T-
1 TTTTGTATGAATATTGTAATATTATA
*
40106581 TTTTGTATGAATATTGTAATATTGTAA
1 TTTTGTATGAATATTGTAATATTAT-A
*
40106608 TTTTGTATGAATATTATAAT
1 TTTTGTATGAATATTGTAAT
40106628 GTGGGGATAT
Statistics
Matches: 228, Mismatches: 18, Indels: 68
0.73 0.06 0.22
Matches are distributed among these distances:
19 16 0.07
20 12 0.05
21 33 0.14
22 30 0.13
23 6 0.03
24 20 0.09
25 14 0.06
26 4 0.02
27 93 0.41
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.53
Consensus pattern (26 bp):
TTTTGTATGAATATTGTAATATTATA
Found at i:40106401 original size:98 final size:97
Alignment explanation
Indices: 40106289--40106533 Score: 404
Period size: 98 Copynumber: 2.5 Consensus size: 97
40106279 TTTTTATATG
*
40106289 AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAATATTATAGTTTTGT
1 AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAATATTATAATTTTGT
40106354 ATGAATATTGCAATTTTTTTGTATGAATATTGT
66 ATGAATATTGCAA-TTTTTTGTATGAATATTGT
* ** *
40106387 AATTTTGTAATTTTGTATGAATATTATATTTTTTTTGAATGAATATTGTAATATTATAATTTTGT
1 AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAATATTATAATTTTGT
*
40106452 ATGAATATTGTAATTTTTTGTATGAATATTGT
66 ATGAATATTGCAATTTTTTGTATGAATATTGT
*
40106484 AATATTGTAATTTTGTATGAATATCAT-AATTTTTT-TATGAATATTGTAAT
1 AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAAT
40106534 GTTGTATGAA
Statistics
Matches: 136, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
95 14 0.10
96 6 0.04
97 44 0.32
98 72 0.53
ACGTcount: A:0.33, C:0.01, G:0.12, T:0.54
Consensus pattern (97 bp):
AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAATATTATAATTTTGT
ATGAATATTGCAATTTTTTGTATGAATATTGT
Found at i:40106622 original size:19 final size:19
Alignment explanation
Indices: 40106153--40106552 Score: 154
Period size: 19 Copynumber: 22.2 Consensus size: 19
40106143 TTTAGATTAG
*
40106153 AATTTTGTATGAATATTTT
1 AATTTTGTATGAATATTGT
*
40106172 AAATTTTTTGTATGAATATTAT
1 -AA--TTTTGTATGAATATTGT
*
40106194 AATTTTTTTATGAATATTGT
1 AA-TTTTGTATGAATATTGT
*
40106214 AATGTTGTATGAATATTGT
1 AATTTTGTATGAATATTGT
*
40106233 AATTATTTTAT-AATTAAATTTGT
1 AATT-TTGTATGAA-T--A-TTGT
* * *
40106256 -ATTTATAGTTTTGGAT-TAGT
1 AATTT-T-G-TATGAATATTGT
*
40106276 AATTTTTTATATGAATATTGT
1 AA--TTTTGTATGAATATTGT
*
40106297 AATTTTGTATGAATATTAT
1 AATTTTGTATGAATATTGT
40106316 AAATTTT-T-TG--TA-TG-
1 -AATTTTGTATGAATATTGT
* *
40106330 AATATTG--T-AATATTAT
1 AATTTTGTATGAATATTGT
* *
40106346 AGTTTTGTATGAATATTGC
1 AATTTTGTATGAATATTGT
*
40106365 AATTTT-TTTG--TA-TG-
1 AATTTTGTATGAATATTGT
* *
40106379 AATATTG--T-AATTTTGT
1 AATTTTGTATGAATATTGT
*
40106395 AATTTTGTATGAATATTAT
1 AATTTTGTATGAATATTGT
* *
40106414 -ATTTTTTTTG-A-A-TG-
1 AATTTTGTATGAATATTGT
* *
40106428 AATATTG--T-AATATTAT
1 AATTTTGTATGAATATTGT
40106444 AATTTTGTATGAATATTGT
1 AATTTTGTATGAATATTGT
40106463 AATTTT-T-TG--TA-TG-
1 AATTTTGTATGAATATTGT
*
40106476 AATATTG--T-AATATTGT
1 AATTTTGTATGAATATTGT
**
40106492 AATTTTGTATGAATATCAT
1 AATTTTGTATGAATATTGT
*
40106511 AATTTTTTTATGAATATTGT
1 AA-TTTTGTATGAATATTGT
*
40106531 AATGTTGTATGAATATTGT
1 AATTTTGTATGAATATTGT
40106550 AAT
1 AAT
40106553 ATTAGAATTT
Statistics
Matches: 283, Mismatches: 48, Indels: 99
0.66 0.11 0.23
Matches are distributed among these distances:
13 15 0.05
14 13 0.05
15 16 0.06
16 28 0.10
17 3 0.01
18 18 0.06
19 92 0.33
20 56 0.20
21 9 0.03
22 22 0.08
23 7 0.02
24 3 0.01
25 1 0.00
ACGTcount: A:0.33, C:0.01, G:0.12, T:0.54
Consensus pattern (19 bp):
AATTTTGTATGAATATTGT
Found at i:40106668 original size:114 final size:113
Alignment explanation
Indices: 40106429--40106674 Score: 330
Period size: 114 Copynumber: 2.1 Consensus size: 113
40106419 TTTTGAATGA
* *
40106429 ATATTGTAATATTATAATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATATTGTAA
1 ATATTGTAATATTAGAATTTTGTATGAATATTGCAATTTTTTGTATGAATATTGTAATATTGTAA
** *
40106494 TTTTGTATGAATATCATAATTTTTTTATGAATATTGTAATGTTGTATG
66 TTTTGTATGAATATCATAATTGATATATGAATATTGTAATGTTGTATG
*
40106542 AATATTGTAATATTAGAATTTTGTATGAATATTGCATTTTTTTGTATGAATATTGTAATATTGTA
1 -ATATTGTAATATTAGAATTTTGTATGAATATTGCAATTTTTTGTATGAATATTGTAATATTGTA
* *
40106607 ATTTTGTATGAATATTATAATGTGGGGATATATTGTAATATTGTAATTTTTTGTATG
65 ATTTTGTATGAATATCATAAT-T---GATATA-TG-AATATTGTAA--TGTTGTATG
40106664 AATATTGTAAT
1 -ATATTGTAAT
40106675 TATTTTATAA
Statistics
Matches: 116, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
114 81 0.70
115 1 0.01
118 3 0.03
119 2 0.02
120 10 0.09
122 19 0.16
ACGTcount: A:0.33, C:0.01, G:0.15, T:0.52
Consensus pattern (113 bp):
ATATTGTAATATTAGAATTTTGTATGAATATTGCAATTTTTTGTATGAATATTGTAATATTGTAA
TTTTGTATGAATATCATAATTGATATATGAATATTGTAATGTTGTATG
Found at i:40106758 original size:27 final size:27
Alignment explanation
Indices: 40106727--40106778 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
40106717 ATATTTTGTT
40106727 CACCATTGGCGCCTCCCAAATAGGCAC
1 CACCATTGGCGCCTCCCAAATAGGCAC
* *
40106754 CACCATTGGCGCCTTCCAGATAGGC
1 CACCATTGGCGCCTCCCAAATAGGC
40106779 GCCAATACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.23, C:0.38, G:0.21, T:0.17
Consensus pattern (27 bp):
CACCATTGGCGCCTCCCAAATAGGCAC
Found at i:40108386 original size:11 final size:12
Alignment explanation
Indices: 40108354--40108386 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
40108344 ATTCCCCTCT
40108354 CTTCTCT-TTCC
1 CTTCTCTCTTCC
40108365 CTTCTCTCTTCC
1 CTTCTCTCTTCC
40108377 C-TCTCTCTTC
1 CTTCTCTCTTC
40108387 TTTTTTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 16 0.76
12 5 0.24
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (12 bp):
CTTCTCTCTTCC
Found at i:40108883 original size:3 final size:3
Alignment explanation
Indices: 40108849--40108914 Score: 60
Period size: 3 Copynumber: 21.3 Consensus size: 3
40108839 AATATCCTTG
* * * *
40108849 TTA TTT TTA TTA GTA TTA TTA GTA TTA CTA TTA TTA TTA TTA TGTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* *
40108895 TTA GTA TATA TTT TTA TTA T
1 TTA TTA T-TA TTA TTA TTA T
40108915 GTACGTGTAT
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
3 43 0.88
4 6 0.12
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:40108911 original size:23 final size:22
Alignment explanation
Indices: 40108856--40108917 Score: 81
Period size: 23 Copynumber: 2.8 Consensus size: 22
40108846 TTGTTATTTT
*
40108856 TATTAGTATTATTA-GTATTAC
1 TATTATTATTATTATGTATTAC
*
40108877 TATTATTATTATTATGTATTAG
1 TATTATTATTATTATGTATTAC
*
40108899 TATATATTTTTATTATGTA
1 TAT-TATTATTATTATGTA
40108918 CGTGTATACA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 13 0.36
22 9 0.25
23 14 0.39
ACGTcount: A:0.32, C:0.02, G:0.08, T:0.58
Consensus pattern (22 bp):
TATTATTATTATTATGTATTAC
Found at i:40108924 original size:23 final size:23
Alignment explanation
Indices: 40108856--40108925 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 23
40108846 TTGTTATTTT
* *
40108856 TATTAGTATTAT-TAGTATTACTA
1 TATTATTATTATGTAGTAGTA-TA
*
40108879 TTATTATTATTATGTATTAGTATA
1 -TATTATTATTATGTAGTAGTATA
*
40108903 TATTTTTATTATGTACGT-GTATA
1 TATTATTATTATGTA-GTAGTATA
40108926 CATATATATA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
23 19 0.49
24 14 0.36
25 6 0.15
ACGTcount: A:0.31, C:0.03, G:0.10, T:0.56
Consensus pattern (23 bp):
TATTATTATTATGTAGTAGTATA
Found at i:40133336 original size:17 final size:18
Alignment explanation
Indices: 40133314--40133347 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
40133304 TAGAATTGAG
40133314 TTGAGAAAATT-ATTTAA
1 TTGAGAAAATTAATTTAA
40133331 TTGAGAAAATTAATTTA
1 TTGAGAAAATTAATTTA
40133348 GTTAACCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (18 bp):
TTGAGAAAATTAATTTAA
Found at i:40135828 original size:113 final size:114
Alignment explanation
Indices: 40135596--40135882 Score: 301
Period size: 113 Copynumber: 2.5 Consensus size: 114
40135586 AATACCTAAT
* * * *
40135596 CCCAACGACTCCGTTTTCTGAGCTTTCGGGAATTTAGCGGCGTTTTTTAAGAAAGTGCCGCTAAG
1 CCCAACGACGCCGTTTTCTGAGCTTTCGGGAATTTAGCGGCG-TTTTTAGGTAAGCGCCGCTAAG
** ** ** *
40135661 CCTCAGGCATTTAGCGGCGTTTTTGAAAAAGTGCCACAAAAAAATGTAAG
65 CCTCAGGCATTTAGCGGCGTTTACGAAAAAGCACCACAAAAAAACATAAC
* * *
40135711 CCCAACGACGCC-ATTTCTGAGCTTTCGGGGATTGAGCGGCGTTTTTAGGTAAGCGCCGCTAA-C
1 CCCAACGACGCCGTTTTCTGAGCTTTCGGGAATTTAGCGGCGTTTTTAGGTAAGCGCCGCTAAGC
** *** *
40135774 GCTCAGGGC-TTTAGCGGCGTTTACGGTAAAGCACTGTAAAGAAACATAAC
66 -CTCA-GGCATTTAGCGGCGTTTACGAAAAAGCACCACAAAAAAACATAAC
* * * *
40135824 CCCAACGACGCCGTTTTCTGAGCTTTTCGCGAATTTAGCAGTGTTTTTAGTTAAGCGCC
1 CCCAACGACGCCGTTTTCTGAGC-TTTCGGGAATTTAGCGGCGTTTTTAGGTAAGCGCC
40135883 ACAAAAATAC
Statistics
Matches: 141, Mismatches: 27, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
112 1 0.01
113 62 0.44
114 38 0.27
115 40 0.28
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.28
Consensus pattern (114 bp):
CCCAACGACGCCGTTTTCTGAGCTTTCGGGAATTTAGCGGCGTTTTTAGGTAAGCGCCGCTAAGC
CTCAGGCATTTAGCGGCGTTTACGAAAAAGCACCACAAAAAAACATAAC
Found at i:40135952 original size:72 final size:74
Alignment explanation
Indices: 40135876--40136011 Score: 195
Period size: 72 Copynumber: 1.9 Consensus size: 74
40135866 GTTTTTAGTT
* * * *
40135876 AAGCGCCACAAAAATACCTAAGCCTAACAACGCCGTTTT-TGAGCTTT-TGGTGATTTAGTGGCA
1 AAGCGCCACAAAAATACCTAAGCCCAACAACGCCGTTTTCGGAGCTTTCGGGGGATTTAGTGGCA
40135939 TTTTTGAGA
66 TTTTTGAGA
** *
40135948 AAGCGCTGCAAAAATACCTAAGCCCAACGACGCCGTTTTCGGAGCTTTCGGGGGATTTAGTGGC
1 AAGCGCCACAAAAATACCTAAGCCCAACAACGCCGTTTTCGGAGCTTTCGGGGGATTTAGTGGC
40136012 GTTTATGGGT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
72 35 0.64
73 7 0.13
74 13 0.24
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.26
Consensus pattern (74 bp):
AAGCGCCACAAAAATACCTAAGCCCAACAACGCCGTTTTCGGAGCTTTCGGGGGATTTAGTGGCA
TTTTTGAGA
Found at i:40136767 original size:29 final size:27
Alignment explanation
Indices: 40136714--40136767 Score: 63
Period size: 29 Copynumber: 1.9 Consensus size: 27
40136704 AGGGGTTAGG
*
40136714 GTTAGGGTTAGGGGTTAGAAGTTAACA
1 GTTAGGGTTAGGGGTTAGAACTTAACA
* *
40136741 GTTAGGGACTTAGGGTTTAGATCTTAA
1 GTTAGGG--TTAGGGGTTAGAACTTAA
40136768 TTAGTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 7 0.32
29 15 0.68
ACGTcount: A:0.28, C:0.06, G:0.33, T:0.33
Consensus pattern (27 bp):
GTTAGGGTTAGGGGTTAGAACTTAACA
Found at i:40137683 original size:85 final size:85
Alignment explanation
Indices: 40137540--40137713 Score: 348
Period size: 85 Copynumber: 2.0 Consensus size: 85
40137530 CCGCTAATGC
40137540 TTAAGCAATAGCGGCGTTTGTACAAGAAACGCCGCAAAAGTGACTTAAAATTTTGGTTGAATGAC
1 TTAAGCAATAGCGGCGTTTGTACAAGAAACGCCGCAAAAGTGACTTAAAATTTTGGTTGAATGAC
40137605 GCCGTTTCTGTCCACGATTT
66 GCCGTTTCTGTCCACGATTT
40137625 TTAAGCAATAGCGGCGTTTGTACAAGAAACGCCGCAAAAGTGACTTAAAATTTTGGTTGAATGAC
1 TTAAGCAATAGCGGCGTTTGTACAAGAAACGCCGCAAAAGTGACTTAAAATTTTGGTTGAATGAC
40137690 GCCGTTTCTGTCCACGATTT
66 GCCGTTTCTGTCCACGATTT
40137710 TTAA
1 TTAA
40137714 CTTAGCATTT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 89 1.00
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (85 bp):
TTAAGCAATAGCGGCGTTTGTACAAGAAACGCCGCAAAAGTGACTTAAAATTTTGGTTGAATGAC
GCCGTTTCTGTCCACGATTT
Found at i:40138498 original size:335 final size:333
Alignment explanation
Indices: 40137766--40138597 Score: 803
Period size: 335 Copynumber: 2.5 Consensus size: 333
40137756 TCAAGAAATG
* * * ** * *
40137766 CCGCAAAAGTGACTTGAAATATTGGCTAAACGTCGACGTCTAACATAAGCAAATTAATTTTTACT
1 CCGCAAAAGTGACTTAAAATATTGCCTAAACGACCTCGTATAACTTAAGCAAATTAATTTTTACT
* * *
40137831 GGCGCTTTAA--AGGAAAACACCAGAACTATGCATTAAATCTTAACAAAACGGCGCCGTTTTGGA
66 GGCG-TTTAATCA-GAAAACGCCAGAACTGTGCATTAAATCTTAATAAAACGGCGCCGTTTTGGA
* * * * * * *
40137894 TTAGAACCTT-CATTCTTTGTGGCACTTGTCTAG-AAACGCCGCAAGTACACAAGCTATAGCGGC
129 TTAGAACTTTAAATT-TTAGTGGCGCTT-TTTAGAAAACGCCGAAAGTA-ACAAGCAATAGCGGC
*
40137957 GTTTGTTCAATAAACGCCACGAAAGTGTCTTAAAATTTTTGCTAAACGGCACCGTCTCTGTACAC
191 GTTTGTTCAATAAACGCCAC-AAAGTGTCTTAAAATTTTTGCTAAACGACACCGTCTCTGTACAC
* * * * * ** * * * *
40138022 ATTTTTATATTTAGAATTTCTCTATATTAATTCAATGGTGCCATTTTTGTTAATTTTTGTGGCGT
255 ATTTTTATACTTACAATTTCTCTAAATTAATCCAACGACGCCATTTCTCTTAATTTTAGTGGCGA
*
40138087 TTTTACACCAAACA
320 TTTTACACAAAACA
* * * * * * * *
40138101 CCGCAAAAGTGACATAAAATGTTGCCTACACGGCTTCGTTTAGCTTAAGCAAATTTATTTTTACT
1 CCGCAAAAGTGACTTAAAATATTGCCTAAACGACCTCGTATAACTTAAGCAAATTAATTTTTACT
* * *
40138166 GGCGTTTAATCAGAAAACGCCAGAAATGTGCATTACATCTTAATAAAACGGTGCCGTTTTGGATT
66 GGCGTTTAATCAGAAAACGCCAGAACTGTGCATTAAATCTTAATAAAACGGCGCCGTTTTGGATT
*
40138231 AGAACTTTAAATTTTAGTGGCGCTTTTTAGAAAACGCCGTAAACGT-GCAAGCAATAGCGGCGTT
131 AGAACTTTAAATTTTAGTGGCGCTTTTTAGAAAACGCCG-AAA-GTAACAAGCAATAGCGGCGTT
** * * ** * *
40138295 TGTTCAGGATGCACTG-TA-AAATTGTCTTAAAA-TTTTGTCTAAACGATGCCGTTTTTGTACTA
194 TGTTCA--ATAAAC-GCCACAAAGTGTCTTAAAATTTTTG-CTAAACGACACCGTCTCTGTAC-A
** * *
40138357 GTTTTTTA-ACTTATCATTTTCTCTAAATTAATCCAACGACGCCGTTTCTCTTAATTTATAGTGG
254 CATTTTTATACTTA-CAATTTCTCTAAATTAATCCAACGACGCCATTTCTCTTAATTT-TAGTGG
*
40138421 C-ATTTTGCACAAAACA
317 CGATTTTACACAAAACA
* * * *
40138437 CCGTAAAA-TGACTTAAAATATTGTCTAAACGACCTCATATAACTTAAGAAAATTAATTTTTACT
1 CCGCAAAAGTGACTTAAAATATTGCCTAAACGACCTCGTATAACTTAAGCAAATTAATTTTTACT
* * * * * *
40138501 -ACGTTT-TTACAAAAAACGCCAGAACTGTGCATTAAAGCTTAATTAAACGGCGCCGTTTCGG-T
66 GGCGTTTAAT-CAGAAAACGCCAGAACTGTGCATTAAATCTTAATAAAACGGCGCCGTTTTGGAT
* *
40138563 TTGAACTTTAATTTTTAGTGGCG-TTTTTCAGAAAA
130 TAGAACTTTAAATTTTAGTGGCGCTTTTT-AGAAAA
40138598 ATGCCACAAA
Statistics
Matches: 407, Mismatches: 75, Indels: 32
0.79 0.15 0.06
Matches are distributed among these distances:
332 5 0.01
333 29 0.07
334 64 0.16
335 230 0.57
336 65 0.16
337 13 0.03
338 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.34
Consensus pattern (333 bp):
CCGCAAAAGTGACTTAAAATATTGCCTAAACGACCTCGTATAACTTAAGCAAATTAATTTTTACT
GGCGTTTAATCAGAAAACGCCAGAACTGTGCATTAAATCTTAATAAAACGGCGCCGTTTTGGATT
AGAACTTTAAATTTTAGTGGCGCTTTTTAGAAAACGCCGAAAGTAACAAGCAATAGCGGCGTTTG
TTCAATAAACGCCACAAAGTGTCTTAAAATTTTTGCTAAACGACACCGTCTCTGTACACATTTTT
ATACTTACAATTTCTCTAAATTAATCCAACGACGCCATTTCTCTTAATTTTAGTGGCGATTTTAC
ACAAAACA
Found at i:40139721 original size:9 final size:9
Alignment explanation
Indices: 40139707--40139740 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
40139697 ATGTCGTGTT
40139707 TTTTTTTTA
1 TTTTTTTTA
40139716 TTTTTTTTA
1 TTTTTTTTA
*
40139725 TTTATTTTA
1 TTTTTTTTA
*
40139734 TATTTTT
1 TTTTTTT
40139741 CATGAGTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:40140113 original size:17 final size:17
Alignment explanation
Indices: 40140093--40140125 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40140083 ATTTTTAATG
40140093 TATATATTTTT-AAAATC
1 TATAT-TTTTTCAAAATC
40140110 TATATTTTTTCAAAAT
1 TATATTTTTTCAAAAT
40140126 TTATCAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (17 bp):
TATATTTTTTCAAAATC
Found at i:40140241 original size:31 final size:30
Alignment explanation
Indices: 40140184--40140304 Score: 88
Period size: 31 Copynumber: 4.0 Consensus size: 30
40140174 TATCATAACT
* * *
40140184 TATATATAAACTTACATAA-TACATATATATA
1 TATATAAAAACTTGCATAACT-TATATA-ATA
40140215 TATATAAAAACTTGCATAACTTATATAATA
1 TATATAAAAACTTGCATAACTTATATAATA
* * * * *
40140245 -ACATAATAAC-T-AATATACAATATATAAACA
1 TATATAAAAACTTGCATA-AC-TTATAT-AATA
*
40140275 TATATAGAAACTTGCATAACTTATATAATA
1 TATATAAAAACTTGCATAACTTATATAATA
40140305 ACATAATAAC
Statistics
Matches: 69, Mismatches: 14, Indels: 15
0.70 0.14 0.15
Matches are distributed among these distances:
27 3 0.04
28 3 0.04
29 13 0.19
30 9 0.13
31 34 0.49
32 4 0.06
33 3 0.04
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.35
Consensus pattern (30 bp):
TATATAAAAACTTGCATAACTTATATAATA
Found at i:40140315 original size:29 final size:29
Alignment explanation
Indices: 40140218--40140315 Score: 87
Period size: 27 Copynumber: 3.3 Consensus size: 29
40140208 ATATATATAT
*
40140218 ATAAAAACTTGCATAACTTATATAATAAC
1 ATAATAACTTGCATAACTTATATAATAAC
* *
40140247 ATAATAAC-T-AATATAC-AATAT-ATAAAC
1 ATAATAACTTGCATA-ACTTATATAAT-AAC
40140274 ATATATAGAAACTTGCATAACTTATATAATAAC
1 ATA-AT---AACTTGCATAACTTATATAATAAC
40140307 ATAATAACT
1 ATAATAACT
40140316 AACATAATAC
Statistics
Matches: 54, Mismatches: 5, Indels: 20
0.68 0.06 0.25
Matches are distributed among these distances:
26 2 0.04
27 13 0.24
28 5 0.09
29 11 0.20
31 3 0.06
32 5 0.09
33 13 0.24
34 2 0.04
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.32
Consensus pattern (29 bp):
ATAATAACTTGCATAACTTATATAATAAC
Found at i:40140321 original size:29 final size:29
Alignment explanation
Indices: 40140229--40140322 Score: 86
Period size: 29 Copynumber: 3.2 Consensus size: 29
40140219 TAAAAACTTG
40140229 CATAACTTATATAATAACATAATAACTAA
1 CATAACTTATATAATAACATAATAACTAA
* * **
40140258 TAT-AC-AATAT-ATAAACATATATAGAAACTTG
1 CATAACTTATATAAT-AACATA-AT---AACTAA
40140289 CATAACTTATATAATAACATAATAACTAA
1 CATAACTTATATAATAACATAATAACTAA
40140318 CATAA
1 CATAA
40140323 TACATAACCT
Statistics
Matches: 49, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
26 2 0.04
27 10 0.20
28 4 0.08
29 11 0.22
31 6 0.12
32 4 0.08
33 10 0.20
34 2 0.04
ACGTcount: A:0.54, C:0.13, G:0.02, T:0.31
Consensus pattern (29 bp):
CATAACTTATATAATAACATAATAACTAA
Found at i:40140335 original size:9 final size:9
Alignment explanation
Indices: 40140310--40140773 Score: 554
Period size: 9 Copynumber: 52.7 Consensus size: 9
40140300 TAATAACATA
*
40140310 ATAACTAAC
1 ATAACTTAC
40140319 ATAA--TAC
1 ATAACTTAC
*
40140326 ATAACCTAC
1 ATAACTTAC
40140335 ATAACTTAC
1 ATAACTTAC
* *
40140344 ATAAATTAA
1 ATAACTTAC
40140353 ATAACTTAC
1 ATAACTTAC
40140362 ATAACTTAC
1 ATAACTTAC
40140371 ATAACTTAC
1 ATAACTTAC
* *
40140380 ATAAATTAA
1 ATAACTTAC
40140389 ATAACTTAC
1 ATAACTTAC
*
40140398 ATAACTTAA
1 ATAACTTAC
40140407 ATAACTTAC
1 ATAACTTAC
*
40140416 ACAA--TAC
1 ATAACTTAC
40140423 ATAACCTT-C
1 ATAA-CTTAC
*
40140432 CTAACTTAC
1 ATAACTTAC
* *
40140441 ATTATTTAC
1 ATAACTTAC
*
40140450 ATAA--TAT
1 ATAACTTAC
** *
40140457 ATTGCCTAC
1 ATAACTTAC
40140466 ATAACTTAC
1 ATAACTTAC
* *
40140475 ATAAATTAA
1 ATAACTTAC
40140484 ATAACTTAC
1 ATAACTTAC
*
40140493 ATAACTTAT
1 ATAACTTAC
40140502 ATAACTTAC
1 ATAACTTAC
* *
40140511 ATAAATTAA
1 ATAACTTAC
40140520 ATAACTTAC
1 ATAACTTAC
40140529 ATAACTTAC
1 ATAACTTAC
40140538 ATAACTTAC
1 ATAACTTAC
40140547 ATAACTTAC
1 ATAACTTAC
* *
40140556 ATAAATTAA
1 ATAACTTAC
*
40140565 ATAACTTGC
1 ATAACTTAC
40140574 ATAACTTAC
1 ATAACTTAC
40140583 ATAACTTAC
1 ATAACTTAC
* *
40140592 ATAAATTAA
1 ATAACTTAC
40140601 ATAACTTAC
1 ATAACTTAC
40140610 ATAACTTAC
1 ATAACTTAC
* *
40140619 ATAAATTAA
1 ATAACTTAC
40140628 ATAACTTAC
1 ATAACTTAC
40140637 ATAACTTAC
1 ATAACTTAC
40140646 ATAACTTAC
1 ATAACTTAC
40140655 ATAACTTAC
1 ATAACTTAC
*
40140664 ATAACTTAA
1 ATAACTTAC
40140673 ATAACTTAC
1 ATAACTTAC
40140682 ATAACTTAC
1 ATAACTTAC
* *
40140691 ATAAATTAA
1 ATAACTTAC
40140700 ATAACTTAC
1 ATAACTTAC
40140709 ATAACTTAC
1 ATAACTTAC
*
40140718 ATAACTTAA
1 ATAACTTAC
40140727 ATAACTTAC
1 ATAACTTAC
*
40140736 ATAAATTAC
1 ATAACTTAC
40140745 ATAA--TAC
1 ATAACTTAC
40140752 ATAA--TAC
1 ATAACTTAC
40140759 ATAACTTAC
1 ATAACTTAC
40140768 ATAACT
1 ATAACT
40140774 CATTTATGGT
Statistics
Matches: 386, Mismatches: 59, Indels: 20
0.83 0.13 0.04
Matches are distributed among these distances:
7 30 0.08
8 3 0.01
9 352 0.91
10 1 0.00
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (9 bp):
ATAACTTAC
Found at i:40143593 original size:61 final size:63
Alignment explanation
Indices: 40143474--40143593 Score: 226
Period size: 61 Copynumber: 1.9 Consensus size: 63
40143464 TTATCGTGGG
40143474 TACAAGCACATCGATATGTTCTGTTTGACCATGAATCAATGGAACCTTTACGAAAGTAAGTTC
1 TACAAGCACATCGATATGTTCTGTTTGACCATGAATCAATGGAACCTTTACGAAAGTAAGTTC
40143537 TACAAGCACATCGATATGTTCTG-TTGACCATG-ATCAATGGAACCTTTACGAAAGTAA
1 TACAAGCACATCGATATGTTCTGTTTGACCATGAATCAATGGAACCTTTACGAAAGTAA
40143594 TTACAATTTG
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
61 25 0.44
62 9 0.16
63 23 0.40
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.29
Consensus pattern (63 bp):
TACAAGCACATCGATATGTTCTGTTTGACCATGAATCAATGGAACCTTTACGAAAGTAAGTTC
Found at i:40148611 original size:36 final size:35
Alignment explanation
Indices: 40148564--40148798 Score: 186
Period size: 36 Copynumber: 6.5 Consensus size: 35
40148554 ACATTTGGTT
* *
40148564 AATTACATAACTTACAAAAATTAAATAACTTACATA
1 AATTA-ATAACTTACATAAATTAAATAAATTACATA
* * *
40148600 AATTAAGTAACTTACATAACTTACATAAATTAAATA
1 AATTAA-TAACTTACATAAATTAAATAAATTACATA
** * * *
40148636 TCTTGCATAACTTACATAAATTAAGTAAATTAAATA
1 AATT-AATAACTTACATAAATTAAATAAATTACATA
* * *
40148672 ACTTACATAAATTA-AGTAAATTAAATAACTTACATA
1 AATTA-ATAACTTACA-TAAATTAAATAAATTACATA
* * * * *
40148708 AATTAAGTAAATTAAATAACTTACATAACTTACATA
1 AATTAA-TAACTTACATAAATTAAATAAATTACATA
* * *
40148744 AATTAAATATCTTACATAACTTACATAAATTA-AGTA
1 AATT-AATAACTTACATAAATTAAATAAATTACA-TA
40148780 AATTAAATAACTTACATAA
1 AATT-AATAACTTACATAA
40148799 CTCACATAAT
Statistics
Matches: 166, Mismatches: 25, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
35 4 0.02
36 158 0.95
37 4 0.02
ACGTcount: A:0.52, C:0.11, G:0.03, T:0.34
Consensus pattern (35 bp):
AATTAATAACTTACATAAATTAAATAAATTACATA
Found at i:40148618 original size:27 final size:27
Alignment explanation
Indices: 40148588--40148798 Score: 242
Period size: 27 Copynumber: 7.5 Consensus size: 27
40148578 CAAAAATTAA
40148588 ATAACTTACATAAATTAAGTAACTTAC
1 ATAACTTACATAAATTAAGTAACTTAC
* * *
40148615 ATAACTTACATAAATTAAATATCTTGC
1 ATAACTTACATAAATTAAGTAACTTAC
* *
40148642 ATAACTTACATAAATTAAGTAAATTAA
1 ATAACTTACATAAATTAAGTAACTTAC
* *
40148669 ATAACTTACATAAATTAAGTAAATTAA
1 ATAACTTACATAAATTAAGTAACTTAC
40148696 ATAACTTACATAAATTAAGTAAATTAAATAACTTAC
1 ATAACTTACATAAATTAAG---------TAACTTAC
* *
40148732 ATAACTTACATAAATTAAATATCTTAC
1 ATAACTTACATAAATTAAGTAACTTAC
* *
40148759 ATAACTTACATAAATTAAGTAAATTAA
1 ATAACTTACATAAATTAAGTAACTTAC
40148786 ATAACTTACATAA
1 ATAACTTACATAA
40148799 CTCACATAAT
Statistics
Matches: 159, Mismatches: 16, Indels: 18
0.82 0.08 0.09
Matches are distributed among these distances:
27 135 0.85
36 24 0.15
ACGTcount: A:0.52, C:0.11, G:0.03, T:0.34
Consensus pattern (27 bp):
ATAACTTACATAAATTAAGTAACTTAC
Found at i:40148626 original size:54 final size:53
Alignment explanation
Indices: 40148566--40148776 Score: 262
Period size: 54 Copynumber: 3.9 Consensus size: 53
40148556 ATTTGGTTAA
* * *
40148566 TTACATAACTTACAAAAATTAAATAACTTACATAAATTAAGTAACTTACATAAC
1 TTACATAAATTA-AAAAATTAAATAACTTACATAAATTAAGTAAATTAAATAAC
** **
40148620 TTACATAAATTAAATATCTTGCATAACTTACATAAATTAAGTAAATTAAATAAC
1 TTACATAAATTAAA-AAATTAAATAACTTACATAAATTAAGTAAATTAAATAAC
*
40148674 TTACATAAATTAAGTAAATTAAATAACTTACATAAATTAAGTAAATTAAATAAC
1 TTACATAAATTAA-AAAATTAAATAACTTACATAAATTAAGTAAATTAAATAAC
* * * *
40148728 TTACATAACTTACATAAATTAAATATCTTACATAACTTACA-TAAATTAA
1 TTACATAAATTA-AAAAATTAAATAACTTACATAAATTA-AGTAAATTAA
40148777 GTAAATTAAA
Statistics
Matches: 138, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
53 2 0.01
54 134 0.97
55 2 0.01
ACGTcount: A:0.52, C:0.12, G:0.02, T:0.34
Consensus pattern (53 bp):
TTACATAAATTAAAAAATTAAATAACTTACATAAATTAAGTAAATTAAATAAC
Found at i:40148790 original size:54 final size:54
Alignment explanation
Indices: 40148588--40148798 Score: 278
Period size: 54 Copynumber: 3.7 Consensus size: 54
40148578 CAAAAATTAA
* * *
40148588 ATAACTTACATAAATTAAGTAACTTACATAACTTACATAAATTAAATATCTTGC
1 ATAACTTACATAAATTAAGTAAATTAAATAACTTACATAAATTAAATATCTTAC
* ** *
40148642 ATAACTTACATAAATTAAGTAAATTAAATAACTTACATAAATTAAGTAAATTAA
1 ATAACTTACATAAATTAAGTAAATTAAATAACTTACATAAATTAAATATCTTAC
40148696 ATAACTTACATAAATTAAGTAAATTAAATAACTTACATAACTTACATAAATTAAATATCTTAC
1 ATAACTTACATAAATTAAGTAAA-T---T-A---A-ATAACTTACATAAATTAAATATCTTAC
40148759 ATAACTTACATAAATTAAGTAAATTAAATAACTTACATAA
1 ATAACTTACATAAATTAAGTAAATTAAATAACTTACATAA
40148799 CTCACATAAT
Statistics
Matches: 137, Mismatches: 11, Indels: 18
0.83 0.07 0.11
Matches are distributed among these distances:
54 83 0.61
55 2 0.01
58 2 0.01
59 2 0.01
62 2 0.01
63 46 0.34
ACGTcount: A:0.52, C:0.11, G:0.03, T:0.34
Consensus pattern (54 bp):
ATAACTTACATAAATTAAGTAAATTAAATAACTTACATAAATTAAATATCTTAC
Found at i:40154373 original size:12 final size:12
Alignment explanation
Indices: 40154352--40154412 Score: 65
Period size: 12 Copynumber: 5.3 Consensus size: 12
40154342 AACAGAGGTC
*
40154352 GCAGCAAGAGAA
1 GCAGCGAGAGAA
40154364 GCAGCGAGAGAA
1 GCAGCGAGAGAA
**
40154376 GCA--GAG-GCC
1 GCAGCGAGAGAA
*
40154385 GCAGCGAAAGAA
1 GCAGCGAGAGAA
40154397 GCAGCGAGAGAA
1 GCAGCGAGAGAA
40154409 GCAG
1 GCAG
40154413 AGGTTCAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
9 4 0.10
10 3 0.08
11 2 0.05
12 30 0.77
ACGTcount: A:0.41, C:0.20, G:0.39, T:0.00
Consensus pattern (12 bp):
GCAGCGAGAGAA
Found at i:40154388 original size:33 final size:33
Alignment explanation
Indices: 40154333--40154415 Score: 134
Period size: 33 Copynumber: 2.5 Consensus size: 33
40154323 GCAGCGGCTA
*
40154333 CAGCGAGAGAA-CAGAGGTCGCAGC-AAGAGAAG
1 CAGCGAGAGAAGCAGAGGCCGCAGCGAA-AGAAG
40154365 CAGCGAGAGAAGCAGAGGCCGCAGCGAAAGAAG
1 CAGCGAGAGAAGCAGAGGCCGCAGCGAAAGAAG
40154398 CAGCGAGAGAAGCAGAGG
1 CAGCGAGAGAAGCAGAGG
40154416 TTCAAAAGAA
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
32 11 0.23
33 35 0.73
34 2 0.04
ACGTcount: A:0.40, C:0.19, G:0.40, T:0.01
Consensus pattern (33 bp):
CAGCGAGAGAAGCAGAGGCCGCAGCGAAAGAAG
Found at i:40154884 original size:42 final size:43
Alignment explanation
Indices: 40154819--40154911 Score: 143
Period size: 42 Copynumber: 2.2 Consensus size: 43
40154809 TCAAAACAGT
* *
40154819 GGCGTTTGTGAAATAAGCGCCGCTAAAGAACACTACTTTTAGC
1 GGCGTTTTTGAAATAAGCGCCGCTAAAGAACACTACTTTTAGA
* *
40154862 GGCGTTTTTG-AATAAGCGCCGCTATAGAACATTACTTTTAGA
1 GGCGTTTTTGAAATAAGCGCCGCTAAAGAACACTACTTTTAGA
40154904 GGCGTTTT
1 GGCGTTTT
40154912 CTTCCATGTT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
42 37 0.80
43 9 0.20
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (43 bp):
GGCGTTTTTGAAATAAGCGCCGCTAAAGAACACTACTTTTAGA
Found at i:40154969 original size:67 final size:66
Alignment explanation
Indices: 40154856--40154982 Score: 166
Period size: 67 Copynumber: 1.9 Consensus size: 66
40154846 GAACACTACT
* *
40154856 TTTAGCGGCGTTTTTGAATAAGCGCCGCTATAGAACATTACTTTTAGAGGCGTTTTCTTCCATGT
1 TTTAGCGGCGTTTTTGAATAAGCGCCGCTAAAGAACATGACTTTTAGAGGCGTTTT-TTCCATGT
40154921 TC
65 TC
*** * *
40154923 TTTAGCGGCGTTTTTTCCTAAGCGTCGCTAAAGAACATGA-TCTTTAGCGGCGTTTTTTCC
1 TTTAGCGGCGTTTTTGAATAAGCGCCGCTAAAGAACATGACT-TTTAGAGGCGTTTTTTCC
40154983 TAAGCGCCGC
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
66 5 0.10
67 47 0.90
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (66 bp):
TTTAGCGGCGTTTTTGAATAAGCGCCGCTAAAGAACATGACTTTTAGAGGCGTTTTTTCCATGTT
C
Found at i:40155065 original size:42 final size:42
Alignment explanation
Indices: 40154916--40155064 Score: 253
Period size: 42 Copynumber: 3.5 Consensus size: 42
40154906 CGTTTTCTTC
* *
40154916 CATGTTCTTTAGCGGCGTTTTTTCCTAAGCGTCGCTAAAGAA
1 CATGATCTTTAGCGGCGTTTTTTCCTAAGCGCCGCTAAAGAA
*
40154958 CATGATCTTTAGCGGCGTTTTTTCCTAAGCGCCGCTAAAGAG
1 CATGATCTTTAGCGGCGTTTTTTCCTAAGCGCCGCTAAAGAA
* *
40155000 CATGATCTTTAGCAGCGTTTTTTTCTAAGCGCCGCTAAAGAA
1 CATGATCTTTAGCGGCGTTTTTTCCTAAGCGCCGCTAAAGAA
40155042 CATGATCTTTAGCGGCGTTTTTT
1 CATGATCTTTAGCGGCGTTTTTT
40155065 TATGTAAGCG
Statistics
Matches: 100, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 100 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (42 bp):
CATGATCTTTAGCGGCGTTTTTTCCTAAGCGCCGCTAAAGAA
Found at i:40155180 original size:21 final size:21
Alignment explanation
Indices: 40155154--40155196 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
40155144 TTAGTGGCGT
* * *
40155154 TAAAAAGCTCCGCTAAAGACC
1 TAAAAAACGCCGCTAAAAACC
40155175 TAAAAAACGCCGCTAAAAACC
1 TAAAAAACGCCGCTAAAAACC
40155196 T
1 T
40155197 GTTCTACTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.28, G:0.12, T:0.14
Consensus pattern (21 bp):
TAAAAAACGCCGCTAAAAACC
Found at i:40158870 original size:37 final size:37
Alignment explanation
Indices: 40158820--40158898 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
40158810 TTATTATGAA
* *
40158820 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
40158857 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
40158894 GTCTT
1 GTCTT
40158899 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:40159095 original size:47 final size:47
Alignment explanation
Indices: 40159017--40159510 Score: 790
Period size: 47 Copynumber: 10.5 Consensus size: 47
40159007 CCCTTCGGGA
* * * * * * *
40159017 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
40159064 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCACTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40159111 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
40159158 CTTATTACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40159205 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
40159252 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
40159299 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40159346 CTTATCACATATATATACACTTTCACATTCATCACATCGACCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40159395 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40159442 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40159489 CTTATCACATATATACACTTTC
1 CTTATCACATATATACACTTTC
40159511 TTGGCTGAAT
Statistics
Matches: 421, Mismatches: 24, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
47 377 0.90
49 44 0.10
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:40163542 original size:47 final size:47
Alignment explanation
Indices: 40163501--40164069 Score: 910
Period size: 47 Copynumber: 12.3 Consensus size: 47
40163491 TGTGAGTGTA
40163501 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
40163548 TATATATGTGATGAGGCCTAATGGCCGATGTGATGAA--T----GTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
40163589 -A-A-A-GTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
40163632 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
40163679 TATATATGTGATAAGG-CTAATGG-CGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
40163724 TATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
40163771 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
40163818 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 --TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
40163867 TATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
40163914 TATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
* *
40163961 TATATGTGTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
* * * * * * *
40164008 TATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
40164055 TATAAATGTGATAAG
1 TATATATGTGATAAG
40164070 TCTCGAAGGG
Statistics
Matches: 488, Mismatches: 20, Indels: 28
0.91 0.04 0.05
Matches are distributed among these distances:
37 29 0.06
38 1 0.00
39 2 0.00
40 1 0.00
41 3 0.01
43 3 0.01
44 1 0.00
45 40 0.08
46 14 0.03
47 347 0.71
49 47 0.10
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
Found at i:40163602 original size:37 final size:37
Alignment explanation
Indices: 40163555--40163678 Score: 149
Period size: 37 Copynumber: 3.1 Consensus size: 37
40163545 GTGTATATAT
*
40163555 GTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 GTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
40163592 GTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 GTGATAAGGCCTAATGGCCGATGTGATGAA--T----GTG-A-A-A
40163638 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 -GTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
40163676 GTG
1 GTG
40163679 TATATATGTG
Statistics
Matches: 76, Mismatches: 1, Indels: 20
0.78 0.01 0.21
Matches are distributed among these distances:
37 32 0.42
38 1 0.01
39 2 0.03
40 1 0.01
41 3 0.04
43 3 0.04
44 1 0.01
45 2 0.03
46 1 0.01
47 30 0.39
ACGTcount: A:0.31, C:0.10, G:0.33, T:0.27
Consensus pattern (37 bp):
GTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
Found at i:40170728 original size:12 final size:12
Alignment explanation
Indices: 40170711--40170737 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
40170701 GAGCACAAGC
40170711 ATTTTTAGCTTT
1 ATTTTTAGCTTT
40170723 ATTTTTAGCTTT
1 ATTTTTAGCTTT
40170735 ATT
1 ATT
40170738 CTGGTTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.19, C:0.07, G:0.07, T:0.67
Consensus pattern (12 bp):
ATTTTTAGCTTT
Found at i:40171853 original size:13 final size:13
Alignment explanation
Indices: 40171835--40171868 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
40171825 GAACACTAAA
40171835 TTTTTATAATAAT
1 TTTTTATAATAAT
*
40171848 TTTTTAAAATAAT
1 TTTTTATAATAAT
40171861 TATTTTAT
1 T-TTTTAT
40171869 TTAAATTTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTTATAATAAT
Found at i:40177769 original size:22 final size:21
Alignment explanation
Indices: 40177738--40177779 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
40177728 AGTTAGATAA
40177738 AAAATTAAATA-AATAACTAAG
1 AAAATTAAATAGAAT-ACTAAG
40177759 AAAATTAAAATAGAATACTAA
1 AAAATT-AAATAGAATACTAA
40177780 ATTTACAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 10 0.53
23 3 0.16
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.24
Consensus pattern (21 bp):
AAAATTAAATAGAATACTAAG
Found at i:40207824 original size:95 final size:95
Alignment explanation
Indices: 40207704--40207892 Score: 308
Period size: 95 Copynumber: 2.0 Consensus size: 95
40207694 TAGTGTACAA
*
40207704 TAAGTGTAACCAACACATACCAAATCACGCATTCATTTACACACTAATTATAACATCGACCATAT
1 TAAGTGTAACCAAAACATACCAAATCACGCATTCATTTACACACTAATTATAACATC-ACCATAT
40207769 TCCCATGCTAC-AATGCTCACACAATCAAAG
65 TCCCATGCTACAAATGCTCACACAATCAAAG
* *
40207799 TAAGTGTAATCAAAACATACCAAATCACGCATTCATTTACACACTAATTATAACATCATCATATT
1 TAAGTGTAACCAAAACATACCAAATCACGCATTCATTTACACACTAATTATAACATCACCATATT
* * *
40207864 TCCATGTTACAAATGCTCATACAATCAAA
66 CCCATGCTACAAATGCTCACACAATCAAA
40207893 CATATGTTCC
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
94 15 0.17
95 72 0.83
ACGTcount: A:0.41, C:0.25, G:0.06, T:0.27
Consensus pattern (95 bp):
TAAGTGTAACCAAAACATACCAAATCACGCATTCATTTACACACTAATTATAACATCACCATATT
CCCATGCTACAAATGCTCACACAATCAAAG
Found at i:40217898 original size:20 final size:20
Alignment explanation
Indices: 40217854--40217892 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
40217844 AAAATTAAAG
*
40217854 ACGAGCTCGATTGAGCTGAA
1 ACGAGCTCGATGGAGCTGAA
40217874 ACGAGCTC-ATGGAGCTGAA
1 ACGAGCTCGATGGAGCTGAA
40217893 TTCGAGTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.31, C:0.21, G:0.31, T:0.18
Consensus pattern (20 bp):
ACGAGCTCGATGGAGCTGAA
Found at i:40223250 original size:17 final size:17
Alignment explanation
Indices: 40223228--40223261 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
40223218 ATTTGAATAG
40223228 TACTTATGAATAATTAA
1 TACTTATGAATAATTAA
40223245 TACTTATGAATAATTAA
1 TACTTATGAATAATTAA
40223262 ATTTGTAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (17 bp):
TACTTATGAATAATTAA
Found at i:40227795 original size:33 final size:33
Alignment explanation
Indices: 40227744--40227904 Score: 118
Period size: 33 Copynumber: 4.7 Consensus size: 33
40227734 TTATCCGTTA
* *
40227744 TCGGTGGATTCAGCACTTAGCAACCACCAGTGAT
1 TCGG-GGAATCAGCACTTAGCAACCACCAATGAT
40227778 TCGGGGAATCAGCACTTAGCAACCCCTTTCACATTCAATGAT
1 TCGGGGAATCAGCACTTAGCAA---C---CAC---CAATGAT
* *
40227820 ACAGTGGAATCAGCACTTAGCAACC-CC-----T
1 TC-GGGGAATCAGCACTTAGCAACCACCAATGAT
* *
40227848 TGGGGGAATCAGCACTTAGCAACCACCAATGAA
1 TCGGGGAATCAGCACTTAGCAACCACCAATGAT
*
40227881 TCAGGGAATCAGCACTTAGCAACC
1 TCGGGGAATCAGCACTTAGCAACC
40227905 CCCTTTATAT
Statistics
Matches: 101, Mismatches: 10, Indels: 33
0.70 0.07 0.23
Matches are distributed among these distances:
27 21 0.21
28 3 0.03
33 40 0.40
34 4 0.04
36 2 0.02
37 1 0.01
39 3 0.03
40 1 0.01
42 7 0.07
43 19 0.19
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.20
Consensus pattern (33 bp):
TCGGGGAATCAGCACTTAGCAACCACCAATGAT
Found at i:40232304 original size:7 final size:7
Alignment explanation
Indices: 40232287--40232329 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
40232277 TGAGTCAGAA
40232287 AAAATATG
1 AAAA-ATG
40232295 AAAAATG
1 AAAAATG
40232302 AAAAAATG
1 -AAAAATG
40232310 -AAAATG
1 AAAAATG
*
40232316 AAAAATT
1 AAAAATG
40232323 AAAAATG
1 AAAAATG
40232330 GAGAGGCTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
6 6 0.19
7 14 0.45
8 11 0.35
ACGTcount: A:0.70, C:0.00, G:0.12, T:0.19
Consensus pattern (7 bp):
AAAAATG
Found at i:40233630 original size:44 final size:44
Alignment explanation
Indices: 40233567--40233818 Score: 414
Period size: 44 Copynumber: 5.7 Consensus size: 44
40233557 AAATCATAAA
*
40233567 CCTAGCTCACTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
1 CCTAGCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
*
40233611 CCTAGCTCCCTGACCAGCAGTGGAATAGGTTTAAGATTGCAAGT
1 CCTAGCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
*
40233655 CCTAGCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGAAAGT
1 CCTAGCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
* *
40233699 CCTAGCTCTCTGACCAGCAATGGAATAGGTTGAAGATTGCAAGT
1 CCTAGCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
*
40233743 CCTAGCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAATT
1 CCTAGCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
** **
40233787 CCTATATCCCTGGTCAGCAGTGGAATAGGTTG
1 CCTAGCTCCCTGACCAGCAGTGGAATAGGTTG
40233819 GGAAATTATA
Statistics
Matches: 194, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 194 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (44 bp):
CCTAGCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
Found at i:40233941 original size:129 final size:129
Alignment explanation
Indices: 40233782--40234166 Score: 594
Period size: 129 Copynumber: 3.0 Consensus size: 129
40233772 TTGAAGATTG
* *
40233782 CAATTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTATAGATCTTGTCTCCCTAAGT
1 CAATTCCTATATCCATGGTCAGCAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGT
*
40233847 AGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGTCA
66 AGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCA
* *
40233911 CAATTCCTATATCCATGGTCAGCAGTGGAATAGGTTGGAAAATTACAGATCTTGTCTCCTTAAGT
1 CAATTCCTATATCCATGGTCAGCAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGT
40233976 AGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCA
66 AGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCA
* * * * *
40234040 CAAGTCCTATGTCCTTGGTCAGCAGTGGAATAAGTT-GGAAATTACAGATCTTGTCTCCCTAAGC
1 CAATTCCTATATCCATGGTCAGCAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGT
* * * * ** *
40234104 AGTA-CTGGAGTAGATCGAAGATGGAGAATCCTATCTTCAAGCATAAGGAAGCAGATTGAAGCC
66 AGTAGC-GGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCC
40234167 GATAATCCTA
Statistics
Matches: 236, Mismatches: 19, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
127 1 0.00
128 79 0.33
129 156 0.66
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.26
Consensus pattern (129 bp):
CAATTCCTATATCCATGGTCAGCAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGT
AGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCA
Found at i:40243305 original size:20 final size:20
Alignment explanation
Indices: 40243282--40243332 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
40243272 GTATTCTCTA
40243282 AGAAATTTTGGAATTCCGTT-
1 AGAAATTTTGGAATTCC-TTC
* * *
40243302 AGAATTTTTCGTATTCCTTC
1 AGAAATTTTGGAATTCCTTC
*
40243322 AAAAATTTTGG
1 AGAAATTTTGG
40243333 TTTTGAAATG
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.43
Consensus pattern (20 bp):
AGAAATTTTGGAATTCCTTC
Found at i:40245618 original size:28 final size:28
Alignment explanation
Indices: 40245586--40245640 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
40245576 AATATATAGA
*
40245586 TGCACCGAAGTACAATAACTAAACAAAG
1 TGCACCGAAGTACAATAACAAAACAAAG
* *
40245614 TGCACCGAAGTGCAATATCAAAACAAA
1 TGCACCGAAGTACAATAACAAAACAAA
40245641 ATGGCACTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.49, C:0.22, G:0.15, T:0.15
Consensus pattern (28 bp):
TGCACCGAAGTACAATAACAAAACAAAG
Found at i:40248427 original size:11 final size:11
Alignment explanation
Indices: 40248413--40248445 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
40248403 ATTTTTTTTC
40248413 GAATTAGATAA
1 GAATTAGATAA
40248424 GAATTAGATAA
1 GAATTAGATAA
40248435 GAATTAGATAA
1 GAATTAGATAA
40248446 AATAAATAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.18, T:0.27
Consensus pattern (11 bp):
GAATTAGATAA
Found at i:40254239 original size:51 final size:51
Alignment explanation
Indices: 40254148--40254460 Score: 331
Period size: 51 Copynumber: 6.1 Consensus size: 51
40254138 GAAAGGTCAA
* * * * *
40254148 TGAACTATATATGCAAAGTATCTGCATACTGATTACGTAAAGTTCTATGCG
1 TGAACTATCTATGCAAAGTATGTGCATACTAATTATGTAAAGTTCTATGTG
* * *
40254199 TGAACTATCTATACAAAGTATGTGCGTACTAATTATGTAAAGTTCTATGTT
1 TGAACTATCTATGCAAAGTATGTGCATACTAATTATGTAAAGTTCTATGTG
* * *
40254250 TGAATTATCTATGCAAAGTATGTGCATACTAATTATGTGACA-TTCTATATG
1 TGAACTATCTATGCAAAGTATGTGCATACTAATTATGT-AAAGTTCTATGTG
* * ** * * ** * *
40254301 TGAATTGTCTATAAAAAGTATGTCCGTACTGGTTATGTAAAGTTTTATGTA
1 TGAACTATCTATGCAAAGTATGTGCATACTAATTATGTAAAGTTCTATGTG
* * * *
40254352 TGAACTGTGTATGCAAAGTATATGCATACTAATTATGTAAAGTTTTATGTG
1 TGAACTATCTATGCAAAGTATGTGCATACTAATTATGTAAAGTTCTATGTG
* * * * *
40254403 TGAATTGTCTATGCAAAGGATGTGCGTACTAATTATGTAAAGTTCTATATG
1 TGAACTATCTATGCAAAGTATGTGCATACTAATTATGTAAAGTTCTATGTG
*
40254454 TGCACTA
1 TGAACTA
40254461 GCACTGTAGC
Statistics
Matches: 215, Mismatches: 45, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
50 2 0.01
51 211 0.98
52 2 0.01
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (51 bp):
TGAACTATCTATGCAAAGTATGTGCATACTAATTATGTAAAGTTCTATGTG
Found at i:40254337 original size:102 final size:102
Alignment explanation
Indices: 40254147--40254450 Score: 394
Period size: 102 Copynumber: 3.0 Consensus size: 102
40254137 GGAAAGGTCA
* * * * * *
40254147 ATGAACTATATATGCAAAGTATCTGCATACTGATTACGTAAAGTTCTATGCGTGAACTATCTATA
1 ATGAACTATATATGCAAAGTATATGCATACTAATTATGTAAAGTTCTATGTGTGAATTGTCTATA
40254212 CAAAGTATGTGCGTACTAATTATGTAAAGTTCTATGT
66 CAAAGTATGTGCGTACTAATTATGTAAAGTTCTATGT
* * * * * *
40254249 TTGAATTATCTATGCAAAGTATGTGCATACTAATTATGTGACA-TTCTATATGTGAATTGTCTAT
1 ATGAACTATATATGCAAAGTATATGCATACTAATTATGT-AAAGTTCTATGTGTGAATTGTCTAT
* * ** *
40254313 AAAAAGTATGTCCGTACTGGTTATGTAAAGTTTTATGT
65 ACAAAGTATGTGCGTACTAATTATGTAAAGTTCTATGT
* * * *
40254351 ATGAACTGTGTATGCAAAGTATATGCATACTAATTATGTAAAGTTTTATGTGTGAATTGTCTATG
1 ATGAACTATATATGCAAAGTATATGCATACTAATTATGTAAAGTTCTATGTGTGAATTGTCTATA
*
40254416 CAAAGGATGTGCGTACTAATTATGTAAAGTTCTAT
66 CAAAGTATGTGCGTACTAATTATGTAAAGTTCTAT
40254451 ATGTGCACTA
Statistics
Matches: 169, Mismatches: 31, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
101 2 0.01
102 165 0.98
103 2 0.01
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (102 bp):
ATGAACTATATATGCAAAGTATATGCATACTAATTATGTAAAGTTCTATGTGTGAATTGTCTATA
CAAAGTATGTGCGTACTAATTATGTAAAGTTCTATGT
Found at i:40254358 original size:27 final size:26
Alignment explanation
Indices: 40254332--40254420 Score: 67
Period size: 27 Copynumber: 3.4 Consensus size: 26
40254322 GTCCGTACTG
40254332 GTTATGTAAAGTTTTATGTATGAACT
1 GTTATGTAAAGTTTTATGTATGAACT
* * *
40254358 GTGTATGCAAAG-TATATGCAT--ACT
1 GT-TATGTAAAGTTTTATGTATGAACT
* * *
40254382 AATTATGTAAAGTTTTATGTGTGAATT
1 -GTTATGTAAAGTTTTATGTATGAACT
*
40254409 GTCTATGCAAAG
1 GT-TATGTAAAG
40254421 GATGTGCGTA
Statistics
Matches: 46, Mismatches: 11, Indels: 11
0.68 0.16 0.16
Matches are distributed among these distances:
24 11 0.24
25 7 0.15
26 10 0.22
27 18 0.39
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (26 bp):
GTTATGTAAAGTTTTATGTATGAACT
Found at i:40254440 original size:153 final size:153
Alignment explanation
Indices: 40254174--40254455 Score: 404
Period size: 153 Copynumber: 1.8 Consensus size: 153
40254164 AGTATCTGCA
* * *
40254174 TACTGATTACGTAAAGTTCTATGCGTGAACTATCTATACAAAGTATGTGCGTACTAATTATGTAA
1 TACTGATTACGTAAAGTTCTATGCATGAACTATCTATACAAAGTATATGCATACTAATTATGTAA
* * *
40254239 AGTTCTATGTTTGAATTATCTATGCAAAGTATGTGCATACTAATTATGTGACA-TTCTATATGTG
66 AGTTCTATGTGTGAATTATCTATGCAAAGGATGTGCATACTAATTATGT-AAAGTTCTATATGTG
40254303 AATTGTCTATAAAAAGTATGTCCG
130 AATTGTCTATAAAAAGTATGTCCG
* * * * * * *
40254327 TACTGGTTATGTAAAGTTTTATGTATGAACTGTGTATGCAAAGTATATGCATACTAATTATGTAA
1 TACTGATTACGTAAAGTTCTATGCATGAACTATCTATACAAAGTATATGCATACTAATTATGTAA
* * *
40254392 AGTTTTATGTGTGAATTGTCTATGCAAAGGATGTGCGTACTAATTATGTAAAGTTCTATATGTG
66 AGTTCTATGTGTGAATTATCTATGCAAAGGATGTGCATACTAATTATGTAAAGTTCTATATGTG
40254456 CACTAGCACT
Statistics
Matches: 112, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
152 2 0.02
153 110 0.98
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (153 bp):
TACTGATTACGTAAAGTTCTATGCATGAACTATCTATACAAAGTATATGCATACTAATTATGTAA
AGTTCTATGTGTGAATTATCTATGCAAAGGATGTGCATACTAATTATGTAAAGTTCTATATGTGA
ATTGTCTATAAAAAGTATGTCCG
Found at i:40269566 original size:37 final size:37
Alignment explanation
Indices: 40269503--40269624 Score: 165
Period size: 37 Copynumber: 3.3 Consensus size: 37
40269493 TACTCCCTAT
** *
40269503 TTTGGCGTGTTATCGGGAGGATTAGCTCTTATGAGCA
1 TTTGGCGTGTTATCGGTTGGACTAGCTCTTATGAGCA
*
40269540 TTTGGCGTGTTTTCGGTTGGACTAGCTCTT-TGGAGCA
1 TTTGGCGTGTTATCGGTTGGACTAGCTCTTAT-GAGCA
* *
40269577 ATTGGCGTGTTATCGGTTGGATTAGCTCTTATGAGCA
1 TTTGGCGTGTTATCGGTTGGACTAGCTCTTATGAGCA
*
40269614 TTTGGCATGTT
1 TTTGGCGTGTT
40269625 TTCAGTTCGA
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
36 1 0.01
37 72 0.97
38 1 0.01
ACGTcount: A:0.16, C:0.14, G:0.31, T:0.39
Consensus pattern (37 bp):
TTTGGCGTGTTATCGGTTGGACTAGCTCTTATGAGCA
Found at i:40270858 original size:25 final size:25
Alignment explanation
Indices: 40270756--40270864 Score: 84
Period size: 25 Copynumber: 4.4 Consensus size: 25
40270746 ATACATGTAT
* * *
40270756 GCTCATACGAGCT-CTAGATCGGTAT
1 GCTCTTACGAGCTGATA-ATCGGTAA
*
40270781 GCTCTTACGAGCT-ATAAACGGTAA
1 GCTCTTACGAGCTGATAATCGGTAA
*
40270805 GCT-TCTCCGAGCTGAATAAT-GGTAA
1 GCTCT-TACGAGCTG-ATAATCGGTAA
*
40270830 GCTCTTGCGAGCTGAGT-ATCGGTAA
1 GCTCTTACGAGCTGA-TAATCGGTAA
*
40270855 GCTCATACGA
1 GCTCTTACGA
40270865 ATTGAAATCG
Statistics
Matches: 69, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
23 1 0.01
24 19 0.28
25 44 0.64
26 5 0.07
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.27
Consensus pattern (25 bp):
GCTCTTACGAGCTGATAATCGGTAA
Found at i:40271051 original size:36 final size:36
Alignment explanation
Indices: 40271011--40271083 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
40271001 TCTAATTCAA
*
40271011 TCAAAGCATATAATTACACAATTTAATTACACGAAC
1 TCAAAGCAAATAATTACACAATTTAATTACACGAAC
40271047 TCAAAGCAAATAATTACACAATTTAATTACACGAAC
1 TCAAAGCAAATAATTACACAATTTAATTACACGAAC
40271083 T
1 T
40271084 TACCTCGACG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.48, C:0.19, G:0.05, T:0.27
Consensus pattern (36 bp):
TCAAAGCAAATAATTACACAATTTAATTACACGAAC
Found at i:40271447 original size:17 final size:17
Alignment explanation
Indices: 40271380--40271449 Score: 51
Period size: 17 Copynumber: 4.2 Consensus size: 17
40271370 TATTCACAAA
*
40271380 TTAACACAGTTTTCAAT
1 TTAACACATTTTTCAAT
*
40271397 TTGACACATTTTTCAAAATT
1 TTAACACATTTTTC--AA-T
*
40271417 TTACCACA-----CAAT
1 TTAACACATTTTTCAAT
40271429 TTAACACATTTTTCAAT
1 TTAACACATTTTTCAAT
40271446 TTAA
1 TTAA
40271450 TCCCTAATTG
Statistics
Matches: 40, Mismatches: 5, Indels: 16
0.66 0.08 0.26
Matches are distributed among these distances:
12 8 0.20
13 2 0.05
15 1 0.03
17 20 0.50
19 2 0.05
20 7 0.17
ACGTcount: A:0.37, C:0.19, G:0.03, T:0.41
Consensus pattern (17 bp):
TTAACACATTTTTCAAT
Found at i:40272940 original size:20 final size:20
Alignment explanation
Indices: 40272912--40272952 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
40272902 AAAATAAATG
40272912 CCTTAAGAAATA-TATCGATA
1 CCTTAAGAAA-AGTATCGATA
*
40272932 CCTTCAGAAAAGTATCGATA
1 CCTTAAGAAAAGTATCGATA
40272952 C
1 C
40272953 TGGATCGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (20 bp):
CCTTAAGAAAAGTATCGATA
Found at i:40274889 original size:20 final size:21
Alignment explanation
Indices: 40274845--40274895 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
40274835 CGCAGCCTTA
*
40274845 TGTTGAGCCACAGCAGTCCTG
1 TGTTGAGCCACAGCAGACCTG
* *
40274866 TGTTGAGCCACATCA-ACTTG
1 TGTTGAGCCACAGCAGACCTG
*
40274886 TGTTGTGCCA
1 TGTTGAGCCA
40274896 TAAAGCCTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.29
Consensus pattern (21 bp):
TGTTGAGCCACAGCAGACCTG
Found at i:40285287 original size:19 final size:20
Alignment explanation
Indices: 40285263--40285310 Score: 53
Period size: 23 Copynumber: 2.3 Consensus size: 20
40285253 GATCAGTTGG
40285263 ACCTTT-GATTAATTAACAT
1 ACCTTTGGATTAATTAACAT
40285282 ACCTTTTTTGGATTAATTAACAT
1 ACC---TTTGGATTAATTAACAT
*
40285305 GCCTTT
1 ACCTTT
40285311 TTTTTACTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
19 3 0.12
20 3 0.12
22 3 0.12
23 15 0.62
ACGTcount: A:0.29, C:0.17, G:0.08, T:0.46
Consensus pattern (20 bp):
ACCTTTGGATTAATTAACAT
Found at i:40285295 original size:23 final size:23
Alignment explanation
Indices: 40285269--40285313 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
40285259 TTGGACCTTT
40285269 GATTAATTAACATACCTTTTTTG
1 GATTAATTAACATACCTTTTTTG
*
40285292 GATTAATTAACATGCCTTTTTT
1 GATTAATTAACATACCTTTTTT
40285314 TTACTGATGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.29, C:0.13, G:0.09, T:0.49
Consensus pattern (23 bp):
GATTAATTAACATACCTTTTTTG
Found at i:40287904 original size:49 final size:50
Alignment explanation
Indices: 40287776--40287965 Score: 202
Period size: 49 Copynumber: 3.7 Consensus size: 50
40287766 GGGAATGAGA
* *
40287776 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGTAG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAGATGA-GAG--G
* * **
40287832 TCCCATGTCAGACTATGTCTGGGACATGGTGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * * **
40287882 TCCC-CGTAAGACCATGTCTGGGACATGGCATGGGCACCGACATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* *
40287931 TCCCATGTAAGACCATATCTGGGATATGGCATTGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGG
40287966 TAGTACAGAA
Statistics
Matches: 114, Mismatches: 19, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
49 40 0.35
50 31 0.27
52 3 0.03
53 6 0.05
55 1 0.01
56 33 0.29
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:40287960 original size:50 final size:50
Alignment explanation
Indices: 40287776--40288006 Score: 173
Period size: 49 Copynumber: 4.5 Consensus size: 50
40287766 GGGAATGAGA
* * * * *
40287776 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGTAG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-C----CGA-CATGAGAAC
* * ** * * **
40287832 TCCCATGTCAGACTATGTCTGGGACATGGTGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGACATGAGAAC
*
40287882 TCCC-CGTAAGACCATGTCTGGGACATGGCATGGGCACCGACATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGACATGAGAAC
* * * * *
40287931 TCCCATGTAAGACCATATCTGGGATATGGCATTGGTA--GTACA-GAAAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCG-ACATGAGAAC
* *
40287979 ATCCCATGCAAGACTATGTCTGGGACAT
1 -TCCCATGTAAGACCATGTCTGGGACAT
40288007 AGCTTTGGCA
Statistics
Matches: 145, Mismatches: 27, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
48 6 0.04
49 66 0.46
50 37 0.26
51 2 0.01
55 1 0.01
56 33 0.23
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGACATGAGAAC
Found at i:40288233 original size:12 final size:12
Alignment explanation
Indices: 40288216--40288254 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
40288206 ATGAGTTATT
40288216 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
40288228 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
40288240 TAAGTGAGTAAG
1 TAAGTAAGCAAG
40288252 TAA
1 TAA
40288255 AGAAGCGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:40291545 original size:23 final size:23
Alignment explanation
Indices: 40291519--40291593 Score: 114
Period size: 23 Copynumber: 3.3 Consensus size: 23
40291509 ATAAGTGCCA
**
40291519 CACTGATATGTAGCTAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
40291542 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
40291565 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
40291588 CACTGA
1 CACTGA
40291594 GCAATAACAT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:40293501 original size:14 final size:14
Alignment explanation
Indices: 40293484--40293516 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
40293474 GTTTTAGGTA
40293484 GGTTTA-GGATTTAT
1 GGTTTATGG-TTTAT
40293498 GGTTTATGGTTTAT
1 GGTTTATGGTTTAT
40293512 GGTTT
1 GGTTT
40293517 TTTTTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 16 0.89
15 2 0.11
ACGTcount: A:0.15, C:0.00, G:0.30, T:0.55
Consensus pattern (14 bp):
GGTTTATGGTTTAT
Found at i:40293538 original size:33 final size:33
Alignment explanation
Indices: 40293501--40293610 Score: 114
Period size: 33 Copynumber: 3.3 Consensus size: 33
40293491 GATTTATGGT
**
40293501 TTATGGTTTATGGTTTTTTTTAAAATAATTAAA
1 TTATGGTTTATGGTTTTTAATAAAATAATTAAA
* * * *
40293534 TTAT-GTTTTTGGGCTTTAAATAAATTAATTAAA
1 TTATGGTTTAT-GGTTTTTAATAAAATAATTAAA
* * *
40293567 TTAGGGTTTAGGGTTTTTAAAAAAATTAATTAAA
1 TTATGGTTTATGGTTTTTAATAAAA-TAATTAAA
40293601 TTATGGTTTA
1 TTATGGTTTA
40293611 GTTTTTTTAA
Statistics
Matches: 60, Mismatches: 14, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
32 5 0.08
33 34 0.57
34 21 0.35
ACGTcount: A:0.35, C:0.01, G:0.15, T:0.49
Consensus pattern (33 bp):
TTATGGTTTATGGTTTTTAATAAAATAATTAAA
Found at i:40293593 original size:34 final size:34
Alignment explanation
Indices: 40293501--40293621 Score: 129
Period size: 34 Copynumber: 3.6 Consensus size: 34
40293491 GATTTATGGT
* ***
40293501 TTATGGTTTATGGTTTTTTTTAAAA-TAATTAAA
1 TTATGGTTTAGGGTTTTTAAAAAAATTAATTAAA
* * * *
40293534 TTATGTTTTTGGG-CTTTAAATAAATTAATTAAA
1 TTATGGTTTAGGGTTTTTAAAAAAATTAATTAAA
*
40293567 TTAGGGTTTAGGGTTTTTAAAAAAATTAATTAAA
1 TTATGGTTTAGGGTTTTTAAAAAAATTAATTAAA
**
40293601 TTATGGTTTAGTTTTTTTAAA
1 TTATGGTTTAGGGTTTTTAAA
40293622 TAATTTGGTG
Statistics
Matches: 70, Mismatches: 16, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
32 6 0.09
33 28 0.40
34 36 0.51
ACGTcount: A:0.35, C:0.01, G:0.14, T:0.50
Consensus pattern (34 bp):
TTATGGTTTAGGGTTTTTAAAAAAATTAATTAAA
Found at i:40293934 original size:126 final size:126
Alignment explanation
Indices: 40293694--40294089 Score: 571
Period size: 126 Copynumber: 3.1 Consensus size: 126
40293684 CTTTTGTTTT
* * * **
40293694 TTTTTCTACAGTTGTTCCTAAAAAAATAATTTTGAGAAGACGGTTCTGAAA-AGATAATGTCAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCT-AAACAAATGGTGTC-AA
* ** *
40293758 AAACGCTTCAAGCAGGATGCAGTGTCAACAAAATT-ACTAAAAAAAGCTCCCACGTGGACGCTC
64 AAACGCTTCAAGCAGGATGCACTGTCAGTAAAATTGA-TGAAAAAAGCTCCCACGTGGACGCTC
* * *
40293821 TTTTTCTACAGTAGATCCTGAAAAAATAATTTTGAGATGAAGGTTCTAAACAAATGGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTAAACAAATGGTGTCAAAA
* * *
40293886 ACACTTCAAGCAGGATGCACTGTCAGTAAAATTGATGAAAAAAGCTCCCACGTAGACTCTC
66 ACGCTTCAAGCAGGATGCACTGTCAGTAAAATTGATGAAAAAAGCTCCCACGTGGACGCTC
*
40293947 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATGGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTAAACAAATGGTGTCAAAA
* * *
40294012 ACGCTTCAAGCAAGATGCACTATCAGTAAAATTGATGGAAAAAGCTCCCACGTGGACGCTC
66 ACGCTTCAAGCAGGATGCACTGTCAGTAAAATTGATGAAAAAAGCTCCCACGTGGACGCTC
*
40294073 TTTTTCTATAGTAGTTC
1 TTTTTCTACAGTAGTTC
40294090 ATGTTTGGCC
Statistics
Matches: 241, Mismatches: 26, Indels: 5
0.89 0.10 0.02
Matches are distributed among these distances:
126 191 0.79
127 50 0.21
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.28
Consensus pattern (126 bp):
TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTAAACAAATGGTGTCAAAA
ACGCTTCAAGCAGGATGCACTGTCAGTAAAATTGATGAAAAAAGCTCCCACGTGGACGCTC
Found at i:40299902 original size:103 final size:104
Alignment explanation
Indices: 40299723--40299987 Score: 417
Period size: 103 Copynumber: 2.6 Consensus size: 104
40299713 AACCGTTATT
* * * *
40299723 GGTGGATCTCGCACTTAGCACCACCACTTAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
** *
40299788 ATCAGCACATAGCAACCCCCTTT-TTATTTCAGAGATAC
66 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
40299826 GGTGGATATCGCACTTAGCACCACCAATGAA-CTGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 GGTGGATATCGCACTTAGCACCACCAATGAATC-GGGGAATCAGCACTTAGCAACCCCTCGGGGG
40299890 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
65 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
* **
40299930 GGTGGATATCGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
40299988 TTATGTACAA
Statistics
Matches: 149, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
102 1 0.01
103 82 0.55
104 65 0.44
105 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.20
Consensus pattern (104 bp):
GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
Found at i:40300348 original size:29 final size:29
Alignment explanation
Indices: 40300315--40300378 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
40300305 TAATCCACCA
40300315 CCCAACTTTTTGAAAAATTACAATTTTG-C
1 CCCAAC-TTTTGAAAAATTACAATTTTGTC
* * *
40300344 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGAAAAATTACAATTTTGTC
40300374 CCCAA
1 CCCAA
40300379 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 23 0.77
30 7 0.23
ACGTcount: A:0.31, C:0.27, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGAAAAATTACAATTTTGTC
Found at i:40300352 original size:30 final size:30
Alignment explanation
Indices: 40300322--40300378 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
40300312 CCACCCAACT
40300322 TTTTGAAAAATTACAATTTTG-CCCCAAAC
1 TTTTGAAAAATTACAATTTTGTCCCCAAAC
* * *
40300351 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGTCCCCAA
40300379 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGTCCCCAAAC
Found at i:40303212 original size:24 final size:24
Alignment explanation
Indices: 40303160--40303211 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 24
40303150 GACTGTTATA
40303160 AAAATTATA-AAATAAAAAGTAATT
1 AAAATTATATAAATAAAAAG-AATT
*
40303184 AAAATTATATAAATAAAAAAATATT
1 AAAATTATATAAATAAAAAGA-ATT
40303209 AAA
1 AAA
40303212 TAATATTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (24 bp):
AAAATTATATAAATAAAAAGAATT
Found at i:40303863 original size:50 final size:50
Alignment explanation
Indices: 40303809--40303938 Score: 181
Period size: 50 Copynumber: 2.6 Consensus size: 50
40303799 TTAATAAAGT
* * *
40303809 CATGCATTATGTAACTTTCCTGTTAGTTAAG-TATGCATCATAAATAATGA
1 CATGCATTATGTAACTCTCATGTTAGTTAAGAT-TACATCATAAATAATGA
* *
40303859 CATGCATTATGTAACTCTCATGTTAGTTAAGATTACATCATAAATTATGT
1 CATGCATTATGTAACTCTCATGTTAGTTAAGATTACATCATAAATAATGA
* *
40303909 CATGCATTATGTAACTCCCATGTCAGTTAA
1 CATGCATTATGTAACTCTCATGTTAGTTAA
40303939 AGTTTGCATC
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
50 71 0.99
51 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (50 bp):
CATGCATTATGTAACTCTCATGTTAGTTAAGATTACATCATAAATAATGA
Found at i:40303975 original size:52 final size:50
Alignment explanation
Indices: 40303805--40303977 Score: 163
Period size: 50 Copynumber: 3.4 Consensus size: 50
40303795 GCATTTAATA
* * *
40303805 AAGTCATGCATTATGTAACTTTCC-TGTTAGTTAAG-TATGCATCATAAAT-
1 AAGTCATGCATTATGTAAC-TCCCATGTCAGTTAAGAT-TACATCATAAATG
* * * *
40303854 AATGACATGCATTATGTAACTCTCATGTTAGTTAAGATTACATCATAAATT
1 AA-GTCATGCATTATGTAACTCCCATGTCAGTTAAGATTACATCATAAATG
* * * *
40303905 ATGTCATGCATTATGTAACTCCCATGTCAGTTAAAGTTTGCATCTTTAAATG
1 AAGTCATGCATTATGTAACTCCCATGTCAGTT-AAGATTACATC-ATAAATG
* *
40303957 AAGTCGTGCATTAAGTAACTC
1 AAGTCATGCATTATGTAACTC
40303978 ATTGTCCATT
Statistics
Matches: 103, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
49 4 0.04
50 65 0.63
51 11 0.11
52 23 0.22
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (50 bp):
AAGTCATGCATTATGTAACTCCCATGTCAGTTAAGATTACATCATAAATG
Found at i:40318482 original size:101 final size:101
Alignment explanation
Indices: 40318330--40318534 Score: 356
Period size: 101 Copynumber: 2.0 Consensus size: 101
40318320 TAAGTTTTCA
*
40318330 TAAATTAGTAGTATATATGATGAATAGTGATTAAACAACTCATGTTGAGATTCGTTAGCAAATTA
1 TAAATTAGTAGTATATATGAGGAATAGTGATTAAACAACTCATGTTGAGATTCGTTAGCAAATTA
* *
40318395 ATAAAGAGATAATTTAAGTGATAAATTTTGAATAAT
66 ATAAAGAGATAATTTAAATGATAAATTTCGAATAAT
* * *
40318431 TAAATTAGTAGTATATATGAGGAATAGTGATTAAACAGCTCATGTTGAGATTTGTTAGCAAGTTA
1 TAAATTAGTAGTATATATGAGGAATAGTGATTAAACAACTCATGTTGAGATTCGTTAGCAAATTA
40318496 ATAAAGAGATAATTTAAATGATAAATTTCGAATAAT
66 ATAAAGAGATAATTTAAATGATAAATTTCGAATAAT
40318532 TAA
1 TAA
40318535 GTGGTTAAAT
Statistics
Matches: 98, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
101 98 1.00
ACGTcount: A:0.43, C:0.05, G:0.17, T:0.35
Consensus pattern (101 bp):
TAAATTAGTAGTATATATGAGGAATAGTGATTAAACAACTCATGTTGAGATTCGTTAGCAAATTA
ATAAAGAGATAATTTAAATGATAAATTTCGAATAAT
Found at i:40319829 original size:18 final size:19
Alignment explanation
Indices: 40319795--40319835 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
40319785 TTTGATTGCT
40319795 GGGTCGTTGCCAAGTTT-C
1 GGGTCGTTGCCAAGTTTAC
**
40319813 GGGTCGTTGCCGGGTTTAC
1 GGGTCGTTGCCAAGTTTAC
40319832 GGGT
1 GGGT
40319836 TTTGAGGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.07, C:0.20, G:0.41, T:0.32
Consensus pattern (19 bp):
GGGTCGTTGCCAAGTTTAC
Found at i:40320879 original size:89 final size:89
Alignment explanation
Indices: 40320728--40320907 Score: 342
Period size: 89 Copynumber: 2.0 Consensus size: 89
40320718 TACTCAATGC
*
40320728 AGAAGATTTTTTGTACATGGATATCCGACAAATGCGAATCACTGAGTCCCATAAATGAAACATTT
1 AGAAGATTTTTTGTACATGGATATCCAACAAATGCGAATCACTGAGTCCCATAAATGAAACATTT
40320793 AACTGTAGCAAAAACCAGTAGTTT
66 AACTGTAGCAAAAACCAGTAGTTT
*
40320817 AGAAGATTTTTTGTACATGGATATCCAACAAATGCGAATCACTGAGTCTCATAAATGAAACATTT
1 AGAAGATTTTTTGTACATGGATATCCAACAAATGCGAATCACTGAGTCCCATAAATGAAACATTT
40320882 AACTGTAGCAAAAACCAGTAGTTT
66 AACTGTAGCAAAAACCAGTAGTTT
40320906 AG
1 AG
40320908 TCTTTGTGTT
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 89 1.00
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (89 bp):
AGAAGATTTTTTGTACATGGATATCCAACAAATGCGAATCACTGAGTCCCATAAATGAAACATTT
AACTGTAGCAAAAACCAGTAGTTT
Found at i:40325573 original size:4 final size:4
Alignment explanation
Indices: 40325564--40325597 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
40325554 AGGATGTACT
* *
40325564 TGGA TGGA TGGA TGGA TGGG TGGA TGGA AGGA TG
1 TGGA TGGA TGGA TGGA TGGA TGGA TGGA TGGA TG
40325598 AAAAGAGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.24, C:0.00, G:0.53, T:0.24
Consensus pattern (4 bp):
TGGA
Found at i:40328854 original size:28 final size:28
Alignment explanation
Indices: 40328814--40328869 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
40328804 AAAAAAATTG
40328814 CAACTAAAATGTTAACAAACGCAAGGCT
1 CAACTAAAATGTTAACAAACGCAAGGCT
*
40328842 CAACTAAAATGTTAACAAATGCAAGGCT
1 CAACTAAAATGTTAACAAACGCAAGGCT
40328870 GTTTAGAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.46, C:0.20, G:0.14, T:0.20
Consensus pattern (28 bp):
CAACTAAAATGTTAACAAACGCAAGGCT
Found at i:40329067 original size:18 final size:18
Alignment explanation
Indices: 40329044--40329086 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
40329034 TGTTTGGCTA
*
40329044 CCCTTCTTCTCCCCTTTC
1 CCCTTCCTCTCCCCTTTC
*
40329062 CCCTTCCTCTTCCCTTTC
1 CCCTTCCTCTCCCCTTTC
40329080 CCCTTCC
1 CCCTTCC
40329087 CCTTGGGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (18 bp):
CCCTTCCTCTCCCCTTTC
Found at i:40331932 original size:12 final size:12
Alignment explanation
Indices: 40331904--40331936 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
40331894 ATGCAACAGG
40331904 AAACCAGC-TGC
1 AAACCAGCATGC
40331915 AAACCAGCATGC
1 AAACCAGCATGC
*
40331927 AGACCAGCAT
1 AAACCAGCAT
40331937 CCAAGCTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.39, C:0.33, G:0.18, T:0.09
Consensus pattern (12 bp):
AAACCAGCATGC
Found at i:40332456 original size:19 final size:18
Alignment explanation
Indices: 40332418--40332464 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
40332408 AATATAATTG
40332418 TAATAATTTTTAATCATT
1 TAATAATTTTTAATCATT
* **
40332436 TATTAATTTTGTAATTGTT
1 TAATAATTTT-TAATCATT
40332455 TAATAATTTT
1 TAATAATTTT
40332465 AAAAACTTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (18 bp):
TAATAATTTTTAATCATT
Found at i:40335540 original size:40 final size:40
Alignment explanation
Indices: 40335496--40335577 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
40335486 GTTAAAGGTA
40335496 GGCTTGTATATTTTGTTGTGTGGCCGGGGTTTTAAGTGTT
1 GGCTTGTATATTTTGTTGTGTGGCCGGGGTTTTAAGTGTT
40335536 GGCTTGTATATTTTGTTGTGTGGCCGGGGTTTTAAGTGTT
1 GGCTTGTATATTTTGTTGTGTGGCCGGGGTTTTAAGTGTT
40335576 GG
1 GG
40335578 AATCAGGTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.10, C:0.07, G:0.37, T:0.46
Consensus pattern (40 bp):
GGCTTGTATATTTTGTTGTGTGGCCGGGGTTTTAAGTGTT
Found at i:40335559 original size:21 final size:21
Alignment explanation
Indices: 40335496--40335559 Score: 53
Period size: 20 Copynumber: 3.1 Consensus size: 21
40335486 GTTAAAGGTA
40335496 GGCTTGTATATTTTGTTGTGT
1 GGCTTGTATATTTTGTTGTGT
** ** *
40335517 GGCCGGGGT-TTTAAG-TGT-T
1 GGCTTGTATATTT-TGTTGTGT
40335536 GGCTTGTATATTTTGTTGTGT
1 GGCTTGTATATTTTGTTGTGT
40335557 GGC
1 GGC
40335560 CGGGGTTTTA
Statistics
Matches: 29, Mismatches: 10, Indels: 8
0.62 0.21 0.17
Matches are distributed among these distances:
19 7 0.24
20 12 0.41
21 10 0.34
ACGTcount: A:0.09, C:0.08, G:0.34, T:0.48
Consensus pattern (21 bp):
GGCTTGTATATTTTGTTGTGT
Found at i:40336401 original size:2 final size:2
Alignment explanation
Indices: 40336396--40336438 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
40336386 TTATATATAG
* * *
40336396 AC AC AC AC AC AC AC AC AC AC AC AC AC GC AC AC AT AC AC TC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
40336438 A
1 A
40336439 AATACAATGA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.47, C:0.47, G:0.02, T:0.05
Consensus pattern (2 bp):
AC
Found at i:40340038 original size:43 final size:44
Alignment explanation
Indices: 40339962--40340044 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 44
40339952 CAATCGCAGG
* * *
40339962 AATTAGTAGAATACTCTATTGAGGCTTTATTTTTT-TCCCCCAC
1 AATTAGTAGAATACTCAACTGAGCCTTTATTTTTTCTCCCCCAC
* * *
40340005 AATTTGTAGAATATTCAACTGAGCCTTTCTTTTTTCTCCC
1 AATTAGTAGAATACTCAACTGAGCCTTTATTTTTTCTCCC
40340045 AAAAATTTTG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
43 29 0.88
44 4 0.12
ACGTcount: A:0.24, C:0.22, G:0.11, T:0.43
Consensus pattern (44 bp):
AATTAGTAGAATACTCAACTGAGCCTTTATTTTTTCTCCCCCAC
Found at i:40341790 original size:44 final size:44
Alignment explanation
Indices: 40341736--40341851 Score: 130
Period size: 44 Copynumber: 2.6 Consensus size: 44
40341726 GATTATTGTT
* *
40341736 ATTAAATTTTAATAGAATTATTATTTAATAA-AA-ATAAAAATTTA
1 ATTATATTTTAATATAATTATTATTTAA-AATAACAT-AAAATTTA
* *
40341780 ATTATATTTTAATATAATTATTAAATTAAAATAACATATAATTTA
1 ATTATATTTTAATATAATTATT-ATTTAAAATAACATAAAATTTA
*
40341825 ATAATATTCTTAATATAATTATT-TTTA
1 ATTATATT-TTAATATAATTATTATTTA
40341852 TCCAAAATTA
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
44 25 0.40
45 21 0.34
46 16 0.26
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (44 bp):
ATTATATTTTAATATAATTATTATTTAAAATAACATAAAATTTA
Found at i:40343900 original size:20 final size:21
Alignment explanation
Indices: 40343847--40343900 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
40343837 GTAGCATAAA
*
40343847 GATTCAAAGCATCAAACAATC
1 GATTTAAAGCATCAAACAATC
*
40343868 GATTTAAA-TATCAAACAAT-
1 GATTTAAAGCATCAAACAATC
*
40343887 TATTTAAAGCATCA
1 GATTTAAAGCATCA
40343901 TTCAATCAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 7 0.25
20 14 0.50
21 7 0.25
ACGTcount: A:0.48, C:0.17, G:0.07, T:0.28
Consensus pattern (21 bp):
GATTTAAAGCATCAAACAATC
Found at i:40345037 original size:3 final size:3
Alignment explanation
Indices: 40345031--40345069 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
40345021 TATATAGTAG
* *
40345031 TAA TAA TAA TAA TAA CAA TAA TAA TAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
40345070 AATCATAGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:40346767 original size:41 final size:40
Alignment explanation
Indices: 40346693--40346773 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 40
40346683 ATCCCGAACC
* *
40346693 GACAAAATTCTCCTGCCCCTAATTGTGCCCCTTTTATATG
1 GACAAAATTCTCATGCCCCTAATTATGCCCCTTTTATATG
* *
40346733 GACAAAATTCTCATGCTCCCTAATTATTCTCCTTTTATATG
1 GACAAAATTCTCATGC-CCCTAATTATGCCCCTTTTATATG
40346774 CCCCTCCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 15 0.42
41 21 0.58
ACGTcount: A:0.25, C:0.27, G:0.10, T:0.38
Consensus pattern (40 bp):
GACAAAATTCTCATGCCCCTAATTATGCCCCTTTTATATG
Found at i:40346968 original size:21 final size:21
Alignment explanation
Indices: 40346944--40346984 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
40346934 CTTTTTTACC
*
40346944 AAAATATTACAAA-AAAATAAA
1 AAAATATCA-AAATAAAATAAA
40346965 AAAATATCAAAATAAAATAA
1 AAAATATCAAAATAAAATAA
40346985 TTTTTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.20
Consensus pattern (21 bp):
AAAATATCAAAATAAAATAAA
Found at i:40347166 original size:22 final size:20
Alignment explanation
Indices: 40347140--40347183 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
40347130 CATAATGTAC
40347140 TAAAATAATTAATACATTATAT
1 TAAAATAA-T-ATACATTATAT
*
40347162 TAAAATAATGTACATTATAT
1 TAAAATAATATACATTATAT
40347182 TA
1 TA
40347184 TTTTTTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.57
21 1 0.05
22 8 0.38
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (20 bp):
TAAAATAATATACATTATAT
Found at i:40347670 original size:155 final size:151
Alignment explanation
Indices: 40347212--40347900 Score: 935
Period size: 153 Copynumber: 4.5 Consensus size: 151
40347202 GTACTAAAGT
*
40347212 AACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAGTAT-TTTTTTTAAAGTAAT
1 AACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTTTAAAGTAAT
* * *
40347276 AAAATCCAGGAAAAAAAATACGAATAAAGGGCCGAAATAAGAG-TTTTTTTAAATTTA-TTAAAA
66 AAAAT-CTGGGAAAAAAATACGAACAAAGGGCCGAAATAA-AGTTTTTTTTAAATTTATTTAAAA
*
40347339 AAACAGTAAATTAATACATTTCA
129 AAACACTAAATTAATACATTTCA
40347362 AACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAAT-AT-TATTTTTTTAAAAGTAA
1 AACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTTT-AAAGTAA
* * * *
40347425 TAAAAT-TCGGGGAAAAAATACTAACAAAGGGCCGAAATAATGATTTTTTTAAAAATTTATTTAT
65 TAAAATCT-GGGAAAAAAATACGAACAAAGGGCCGAAATAAAG-TTTTTTT-TAAATTTATTTA-
* * *
40347489 AAAACACAATAAATTAATATATTTCA
126 AAAAAACACTAAATTAATACATTTCA
* * *
40347515 AACATAATTTACTAAAATAATGTAAAACAATAAAATAAGAAAATAATATATTTTTTTAAAGTAAT
1 AACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTTTAAAGTAAT
* *
40347580 AAACTCTGGAGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTTTTTAAATTTATTTAA
66 AAAATCTGG-GAAAAAAATACGAACAAAGGGCCGAAATAA-AG--TTTTTTTTAAATTTATTTAA
40347645 AAAAACACTAAATTAATACATTTCA
127 AAAAACACTAAATTAATACATTTCA
* * *
40347670 AACTTGATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAGTATATTTTTATTGAAAGTA
1 AACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTT-TT-AAAGTA
* *
40347735 ATAAAATCCGGGAAAAAAATACGAACAAAGGGCCGAAATAAAGATTTTTTT-AATTTATTTAAAA
64 ATAAAATCTGGGAAAAAAATACGAACAAAGGGCCGAAATAAAGTTTTTTTTAAATTTATTTAAAA
* * *
40347799 AACAAACTAAATTAATACCTTTAA
129 AA-ACACTAAATTAATACATTTCA
* * * *
40347823 AATATAATGTATTAAAATAATGTAAAATAA-AAAATTAGAAAATATTATATTTTTTAAAAGTAAT
1 AACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTTTAAAGTAAT
40347887 AAAATCTGGGAAAA
66 AAAATCTGGGAAAA
40347901 GTTTATATTA
Statistics
Matches: 479, Mismatches: 43, Indels: 34
0.86 0.08 0.06
Matches are distributed among these distances:
148 2 0.00
149 36 0.08
150 84 0.18
151 8 0.02
152 41 0.09
153 115 0.24
154 16 0.03
155 111 0.23
156 44 0.09
157 22 0.05
ACGTcount: A:0.52, C:0.07, G:0.09, T:0.32
Consensus pattern (151 bp):
AACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTTTAAAGTAAT
AAAATCTGGGAAAAAAATACGAACAAAGGGCCGAAATAAAGTTTTTTTTAAATTTATTTAAAAAA
ACACTAAATTAATACATTTCA
Found at i:40347792 original size:308 final size:302
Alignment explanation
Indices: 40347212--40347900 Score: 1021
Period size: 308 Copynumber: 2.3 Consensus size: 302
40347202 GTACTAAAGT
*
40347212 AACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAGTAT-TTTTTTTAAAGTAAT
1 AACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTTTAAAGTAAT
* *
40347276 AAAATCCAGGA-AAAAAAATACGAATAAAGGGCCGAAATAAGAGTTTTTTTAAATTTATTAAAAA
66 AAAAT-CTGGAGAAAAAAATACGAACAAAGGGCCGAAATAAGAGTTTTTTTAAATTTATTAAAAA
*
40347340 AACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAA
130 AACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAA
* * * *
40347405 TATTATTTTTTTAAAAGTAATAAAATTCGGGGAAAAAATACTAACAAAGGGCCGAAATAATGATT
195 TATTATTTTTTTAAAAGTAATAAAATCCGGGAAAAAAATACGAACAAAGGGCCGAAATAAAGATT
* * *
40347470 TTTTTAAAAATTTATTTATAAAACACAA-TAAATTAATATATTTCA
260 TTTTT--AAATTTATTTAAAAAACA-AACTAAATTAATACATTTAA
* * *
40347515 AACATAATTTACTAAAATAATGTAAAACAATAAAATAAGAAAATAATATATTTTTTTAAAGTAAT
1 AACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTTTAAAGTAAT
* *
40347580 AAACTCTGGAGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTTTTTAAATTTATTTAA
66 AAAATCTGGAGAAAAAAATACGAACAAAGGGCCGAAATAAGAG---TTTTTTTAAATTTA-TTAA
* *
40347645 AAAAACACTAAATTAATACATTTCAAACTTGATGTACTAAAATAATGTAAAATAATAAAATTAGA
127 AAAAACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGA
*
40347710 AAATAGTATATTTTTATTGAAAGTAATAAAATCCGGGAAAAAAATACGAACAAAGGGCCGAAATA
192 AAATA-T-TATTTTT-TTAAAAGTAATAAAATCCGGGAAAAAAATACGAACAAAGGGCCGAAATA
*
40347775 AAGATTTTTTT-AATTTATTTAAAAAACAAACTAAATTAATACCTTTAA
254 AAGATTTTTTTAAATTTATTTAAAAAACAAACTAAATTAATACATTTAA
* * * *
40347823 AATATAATGTATTAAAATAATGTAAAATAA-AAAATTAGAAAATATTATATTTTTTAAAAGTAAT
1 AACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTTTAAAGTAAT
40347887 AAAATCTGG-GAAAA
66 AAAATCTGGAGAAAA
40347901 GTTTATATTA
Statistics
Matches: 348, Mismatches: 28, Indels: 17
0.89 0.07 0.04
Matches are distributed among these distances:
303 49 0.14
304 49 0.14
306 5 0.01
307 55 0.16
308 127 0.36
309 1 0.00
310 7 0.02
311 55 0.16
ACGTcount: A:0.52, C:0.07, G:0.09, T:0.32
Consensus pattern (302 bp):
AACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTTTAAAGTAAT
AAAATCTGGAGAAAAAAATACGAACAAAGGGCCGAAATAAGAGTTTTTTTAAATTTATTAAAAAA
ACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAAT
ATTATTTTTTTAAAAGTAATAAAATCCGGGAAAAAAATACGAACAAAGGGCCGAAATAAAGATTT
TTTTAAATTTATTTAAAAAACAAACTAAATTAATACATTTAA
Found at i:40348598 original size:21 final size:20
Alignment explanation
Indices: 40348554--40348606 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
40348544 ATAATTACGT
*
40348554 TTATTTTTTTAAATTAAGAG
1 TTATTTTTTTAAATTAAGAA
* *
40348574 TTATTTTTTTAACTTCATGAA
1 TTATTTTTTTAAATT-AAGAA
40348595 TTATTTATTTTA
1 TTATTT-TTTTA
40348607 TTATTTTCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 14 0.50
21 9 0.32
22 5 0.18
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (20 bp):
TTATTTTTTTAAATTAAGAA
Found at i:40349952 original size:21 final size:19
Alignment explanation
Indices: 40349927--40349966 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
40349917 CCGGCCCGAT
40349927 TTTTAATAAACACAAAAAATA
1 TTTTAA-AAACA-AAAAAATA
*
40349948 TTTTAAAAATAAAAAAATA
1 TTTTAAAAACAAAAAAATA
40349967 AAAAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 4 0.22
21 6 0.33
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (19 bp):
TTTTAAAAACAAAAAAATA
Found at i:40351312 original size:20 final size:20
Alignment explanation
Indices: 40351289--40351330 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
40351279 TATTTATATA
40351289 CTTTAGAATGCCCAAAAAGC
1 CTTTAGAATGCCCAAAAAGC
40351309 CTTTAGAATGCCCAAAAAGC
1 CTTTAGAATGCCCAAAAAGC
40351329 CT
1 CT
40351331 AAAACTTGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.26, G:0.14, T:0.21
Consensus pattern (20 bp):
CTTTAGAATGCCCAAAAAGC
Found at i:40352055 original size:15 final size:17
Alignment explanation
Indices: 40352037--40352077 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
40352027 ATTAATTTAT
*
40352037 TATTTTTTAAATAT-A-
1 TATTTTTAAAATATGAG
40352052 TATTTTTAAAATATGAG
1 TATTTTTAAAATATGAG
40352069 TATTTTTAA
1 TATTTTTAA
40352078 GGTGTATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.57
16 1 0.04
17 9 0.39
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (17 bp):
TATTTTTAAAATATGAG
Found at i:40352757 original size:3 final size:3
Alignment explanation
Indices: 40352749--40352834 Score: 172
Period size: 3 Copynumber: 28.7 Consensus size: 3
40352739 AATCTAAGTA
40352749 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
40352797 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
40352835 AGAATTAGTA
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 83 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:40353284 original size:28 final size:28
Alignment explanation
Indices: 40353242--40353301 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
40353232 GTGTTCCCTG
40353242 TTTTTCAAAATTTACAATTTTGCCCATA
1 TTTTTCAAAATTTACAATTTTGCCCATA
* * *
40353270 TTTTTC-AAATGTTACAGTTTTGCGCATG
1 TTTTTCAAAAT-TTACAATTTTGCCCATA
40353298 TTTT
1 TTTT
40353302 CTAGGTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 4 0.14
28 24 0.86
ACGTcount: A:0.25, C:0.15, G:0.10, T:0.50
Consensus pattern (28 bp):
TTTTTCAAAATTTACAATTTTGCCCATA
Found at i:40354983 original size:40 final size:40
Alignment explanation
Indices: 40354935--40355162 Score: 402
Period size: 40 Copynumber: 5.7 Consensus size: 40
40354925 GCAAACACAG
* * * *
40354935 TTGCCTTCGGGTCTTAACTCGGACATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
40354975 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
40355015 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
40355055 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
40355095 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
40355135 TTGCCTTCGGGTTTTAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
40355163 TCCAATGCTC
Statistics
Matches: 181, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 181 1.00
ACGTcount: A:0.21, C:0.26, G:0.20, T:0.32
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:40369365 original size:17 final size:17
Alignment explanation
Indices: 40369339--40369371 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
40369329 GTTAGTGCAC
*
40369339 ATTGTTGTTGCATTTTT
1 ATTGTCGTTGCATTTTT
40369356 ATTGTCGTTGCATTTT
1 ATTGTCGTTGCATTTT
40369372 AATGTTAGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.09, G:0.18, T:0.61
Consensus pattern (17 bp):
ATTGTCGTTGCATTTTT
Found at i:40372625 original size:23 final size:23
Alignment explanation
Indices: 40372592--40372645 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
40372582 CAAGTCAACG
*
40372592 ATGAG-AGGATCAAATTTGTTGA
1 ATGAGAAGGATCAAATCTGTTGA
40372614 ATGAGAAGGATCAAATCTGTTGA
1 ATGAGAAGGATCAAATCTGTTGA
40372637 ATGAGAAGG
1 ATGAGAAGG
40372646 TTGGGATTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 5 0.17
23 25 0.83
ACGTcount: A:0.39, C:0.06, G:0.30, T:0.26
Consensus pattern (23 bp):
ATGAGAAGGATCAAATCTGTTGA
Found at i:40387165 original size:26 final size:26
Alignment explanation
Indices: 40387127--40387180 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
40387117 CACATATAAG
*
40387127 AATGATCAGATAATGAATCTTTCACT
1 AATGATCAAATAATGAATCTTTCACT
40387153 AATGATCAAATAATGAATCTTTCACT
1 AATGATCAAATAATGAATCTTTCACT
40387179 AA
1 AA
40387181 CTCAAGGAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.33
Consensus pattern (26 bp):
AATGATCAAATAATGAATCTTTCACT
Found at i:40391642 original size:17 final size:17
Alignment explanation
Indices: 40391617--40391653 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
40391607 TAAAAAAAAC
40391617 ATTAGTATTGTTATCAA
1 ATTAGTATTGTTATCAA
* *
40391634 ATTATTATTTTTATCAA
1 ATTAGTATTGTTATCAA
40391651 ATT
1 ATT
40391654 TTGCTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.54
Consensus pattern (17 bp):
ATTAGTATTGTTATCAA
Found at i:40394251 original size:22 final size:22
Alignment explanation
Indices: 40394226--40394282 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 22
40394216 TACAAATTAA
40394226 ATCTCTAAGATTACAAAATCAT
1 ATCTCTAAGATTACAAAATCAT
* *
40394248 ATCTTCTAAGATTGC-ATATCAT
1 ATC-TCTAAGATTACAAAATCAT
40394270 A--TCTAAGATTACA
1 ATCTCTAAGATTACA
40394283 TATCCTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 10 0.33
22 10 0.33
23 10 0.33
ACGTcount: A:0.40, C:0.18, G:0.07, T:0.35
Consensus pattern (22 bp):
ATCTCTAAGATTACAAAATCAT
Found at i:40394259 original size:23 final size:22
Alignment explanation
Indices: 40394216--40394273 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
40394206 AAAGGGTATC
* *
40394216 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
40394237 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
40394260 TGCATATCATATCT
1 TACAAATCATATCT
40394274 AAGATTACAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:40395439 original size:150 final size:150
Alignment explanation
Indices: 40395227--40395507 Score: 427
Period size: 150 Copynumber: 1.9 Consensus size: 150
40395217 ATCTTCAGTA
* *
40395227 TTTTAAATTGCAATGTTGGGGAAACAAGATTCGTTGTCGTAGTTTCAATCTATTCCACTACACCA
1 TTTTAAATTGCAATGTTGGGGAAACAAGATTCGTCGTCGTAGCTTCAATCTATTCCACTACACCA
* * * *
40395292 CCAGAGGAGTAAGATTCGTCGTTGCAGCTTTAATTTGCTCCACTGTAATGCCAAAGAAATAAGAT
66 CCAGAGGAATAAGATTCGCCATTGCAGCTTTAATCTGCTCCACTGTAATGCCAAAGAAATAAGAT
40395357 TAGTCGTTGCGACTTCAATC
131 TAGTCGTTGCGACTTCAATC
* * *
40395377 TTTTAAATTGCATTGTTGGGGAAACGAGATTCGTCGTCGTAGCTTCAATCTGTTCCACTACACCA
1 TTTTAAATTGCAATGTTGGGGAAACAAGATTCGTCGTCGTAGCTTCAATCTATTCCACTACACCA
* ** * * *
40395442 CCAGGGGAATAAGATTCGCCATTGTGGCTTTAATCTGCTCCATTGTAATGCCAAAGAGATAGGAT
66 CCAGAGGAATAAGATTCGCCATTGCAGCTTTAATCTGCTCCACTGTAATGCCAAAGAAATAAGAT
40395507 T
131 T
40395508 CGCTGCCCAC
Statistics
Matches: 116, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
150 116 1.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.32
Consensus pattern (150 bp):
TTTTAAATTGCAATGTTGGGGAAACAAGATTCGTCGTCGTAGCTTCAATCTATTCCACTACACCA
CCAGAGGAATAAGATTCGCCATTGCAGCTTTAATCTGCTCCACTGTAATGCCAAAGAAATAAGAT
TAGTCGTTGCGACTTCAATC
Found at i:40395796 original size:266 final size:267
Alignment explanation
Indices: 40395347--40395890 Score: 847
Period size: 266 Copynumber: 2.0 Consensus size: 267
40395337 TAATGCCAAA
* * *
40395347 GAAATAAGATTAGTCGTTGCGACTTCAATCTTTTAAATTGCATTGTTGGGGAAACGAGATTCGTC
1 GAAATAAGATTAGCCATTGCGACTTCAATCTTTTAAATTGCAATGTTGGGGAAACGAGATTCGTC
*
40395412 GTCGTAGCTTCAATCTGTTCCACTACACCACCAGGGGAATAAGATTCGCCATTGTGGCTTTAATC
66 GTCGTAGCTTCAATCTGTTCCACTACACCACCAGGGGAATAAGATTCGCCATTGCGGCTTTAATC
* * * * *
40395477 TGCTCCATTGTAATGCCAAAGAGATAGGATTCGCTGCCCACAGCTTCAATCCGCTCCACTTCAGC
131 TGCTCCACTGTAACGACAAAGAGATAGGATTCACTGCCCACAACTTCAATCCGCTCCACTTCAGC
** * * * *
40395542 TAATCCAAGCCTTAATGCCAGGGAGATAAGATTCGCCGT-TTGGCTTTAATCTGCTCTGCTACAA
196 TAATCCAAGCCTTAACACCAAGGAGATAAGATTCGCCGTCGTGGCTTCAATCTGCTCTACTACAA
40395606 CGCTAGG
261 CGCTAGG
* * * *
40395613 GAAATAAGATTTGCCATTGCGGCTTCACTCTTTTAACTTGCAATGTTGGGGAAACGAGATTCGTC
1 GAAATAAGATTAGCCATTGCGACTTCAATCTTTTAAATTGCAATGTTGGGGAAACGAGATTCGTC
* * * *
40395678 GTCGTAGCTTGAATCTGTTCCACTACACCGCCAGGGGAGTAAGATTCGCCGTTGCGGCTTTAATC
66 GTCGTAGCTTCAATCTGTTCCACTACACCACCAGGGGAATAAGATTCGCCATTGCGGCTTTAATC
*
40395743 TGCTCCACTGTAACGACAAAGAGATAGGATTCACTGCCCACAACTTTAATCCGCTCCACTTCAGC
131 TGCTCCACTGTAACGACAAAGAGATAGGATTCACTGCCCACAACTTCAATCCGCTCCACTTCAGC
* *
40395808 TAATCCAAGCCTTAACACCAAGGAGATAAGATTCGTCGTCGTGGCTTCAATCTGTTCTACTACAA
196 TAATCCAAGCCTTAACACCAAGGAGATAAGATTCGCCGTCGTGGCTTCAATCTGCTCTACTACAA
40395873 CGCTAGG
261 CGCTAGG
40395880 GAAATAAGATT
1 GAAATAAGATT
40395891 CACCGTTGTG
Statistics
Matches: 251, Mismatches: 26, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
266 212 0.84
267 39 0.16
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (267 bp):
GAAATAAGATTAGCCATTGCGACTTCAATCTTTTAAATTGCAATGTTGGGGAAACGAGATTCGTC
GTCGTAGCTTCAATCTGTTCCACTACACCACCAGGGGAATAAGATTCGCCATTGCGGCTTTAATC
TGCTCCACTGTAACGACAAAGAGATAGGATTCACTGCCCACAACTTCAATCCGCTCCACTTCAGC
TAATCCAAGCCTTAACACCAAGGAGATAAGATTCGCCGTCGTGGCTTCAATCTGCTCTACTACAA
CGCTAGG
Found at i:40396041 original size:44 final size:44
Alignment explanation
Indices: 40395992--40396111 Score: 161
Period size: 44 Copynumber: 2.7 Consensus size: 44
40395982 ATCTGCTATT
* * * *
40395992 TTCAACCTACTCCACTGCTGCCCAGGGAGATAGGA-TTCATAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGAACTT-ACAATC
40396036 TTCAACCTATTCCACTGCTGACCAGGGAGATAGAACTTACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGAACTTACAATC
** *
40396080 TTCAATATATTCCACTGCTGACCAGGTAGATA
1 TTCAACCTATTCCACTGCTGACCAGGGAGATA
40396112 AAGCTTTGTG
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 66 0.97
45 2 0.03
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.27
Consensus pattern (44 bp):
TTCAACCTATTCCACTGCTGACCAGGGAGATAGAACTTACAATC
Found at i:40398394 original size:32 final size:33
Alignment explanation
Indices: 40398354--40398438 Score: 127
Period size: 36 Copynumber: 2.5 Consensus size: 33
40398344 AAGAAAATCC
40398354 AAAAGAATGAAAGAATAAAAAATAATTATTCGT
1 AAAAGAATGAAAGAATAAAAAATAATTATTCGT
40398387 AAAGAATGAATGAAAGAATAAAAAATAATTATTCGT
1 -AA-AA-GAATGAAAGAATAAAAAATAATTATTCGT
*
40398423 -AAAGAATGAAAAAATA
1 AAAAGAATGAAAGAATA
40398439 TTGGCTCAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
32 12 0.25
33 2 0.04
34 3 0.06
35 2 0.04
36 29 0.60
ACGTcount: A:0.62, C:0.02, G:0.13, T:0.22
Consensus pattern (33 bp):
AAAAGAATGAAAGAATAAAAAATAATTATTCGT
Found at i:40398403 original size:36 final size:36
Alignment explanation
Indices: 40398358--40398432 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
40398348 AAATCCAAAA
40398358 GAATGAAAGAATAAAAAATAATTATTCGTAAAGAAT
1 GAATGAAAGAATAAAAAATAATTATTCGTAAAGAAT
40398394 GAATGAAAGAATAAAAAATAATTATTCGTAAAGAAT
1 GAATGAAAGAATAAAAAATAATTATTCGTAAAGAAT
40398430 GAA
1 GAA
40398433 AAAATATTGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.59, C:0.03, G:0.15, T:0.24
Consensus pattern (36 bp):
GAATGAAAGAATAAAAAATAATTATTCGTAAAGAAT
Done.