Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 16 of 322
Found at i:4426510 original size:19 final size:19
Alignment explanation
Indices: 4426488--4426548 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
4426478 TATAGTTTAG
4426488 ATTAGAATTTTGTATGAAT
1 ATTAGAATTTTGTATGAAT
* *
4426507 ATTATAATTTTTTTATGAAT
1 ATTAGAA-TTTTGTATGAAT
*
4426527 ATT-GTAATGTTGTATGAAT
1 ATTAG-AATTTTGTATGAAT
4426546 ATT
1 ATT
4426549 GTAATTATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 19 0.54
20 16 0.46
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.52
Consensus pattern (19 bp):
ATTAGAATTTTGTATGAAT
Found at i:4426549 original size:19 final size:19
Alignment explanation
Indices: 4426497--4426553 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
4426487 GATTAGAATT
* *
4426497 TTGTATGAATATTATAATTT
1 TTGTATGAATATTGTAA-TG
*
4426517 TTTTATGAATATTGTAATG
1 TTGTATGAATATTGTAATG
4426536 TTGTATGAATATTGTAAT
1 TTGTATGAATATTGTAAT
4426554 TATTTTATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (19 bp):
TTGTATGAATATTGTAATG
Found at i:4426639 original size:41 final size:40
Alignment explanation
Indices: 4426493--4426658 Score: 171
Period size: 41 Copynumber: 4.1 Consensus size: 40
4426483 TTTAGATTAG
4426493 AATTTTGTATGAATATTATAATTTTTT-TATGAATATTGT
1 AATTTTGTATGAATATTATAATTTTTTGTATGAATATTGT
* * * *
4426532 AATGTTGTATGAATATTGTAATTATTTTATAATTAA-ATTTGT
1 AATTTTGTATGAATATTATAATT-TTTTGT-ATGAATA-TTGT
* *
4426574 -ATTTATAGTTTTG--GATTAGTAATTTTTTGTATGAATATTGT
1 AATTT-T-G-TATGAATATTA-TAATTTTTTGTATGAATATTGT
4426615 AATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGT
1 AATTTTGTATGAATATTAT-AATTTTTTGTATGAATATTGT
4426656 AAT
1 AAT
4426659 AATATTATAG
Statistics
Matches: 103, Mismatches: 11, Indels: 24
0.75 0.08 0.17
Matches are distributed among these distances:
39 24 0.23
40 6 0.06
41 42 0.41
42 22 0.21
43 6 0.06
44 3 0.03
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (40 bp):
AATTTTGTATGAATATTATAATTTTTTGTATGAATATTGT
Found at i:4426781 original size:97 final size:97
Alignment explanation
Indices: 4426611--4427207 Score: 1113
Period size: 97 Copynumber: 6.1 Consensus size: 97
4426601 TGTATGAATA
* * *
4426611 TTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAATAATATTATAGTTTTGTA
1 TTGTAATTTTGTATGAATATTAT-ATTTTTTTGTATGAATGTTG---TAATATTATAATTTTGTA
4426676 TGAATATTGCAATTTTTTTGTATGAATATTGTAATT
62 TGAATATTGCAATTTTTTTGTATGAATATTGTAATT
*
4426712 TTGGAATTTTGTATGAATATTATATTTTTTTGTATGAATGTTGTAATATTATAATTTTGTATGAA
1 TTGTAATTTTGTATGAATATTATATTTTTTTGTATGAATGTTGTAATATTATAATTTTGTATGAA
4426777 TATTGCAATTTTTTTGTATGAATATTGTAATT
66 TATTGCAATTTTTTTGTATGAATATTGTAATT
4426809 TTGTAATTTTGTATGAATATTATATTTTTTTGTATGAATGTTGTAATATTATAATTTTGTATGAA
1 TTGTAATTTTGTATGAATATTATATTTTTTTGTATGAATGTTGTAATATTATAATTTTGTATGAA
4426874 TATTGCAATTTTTTTGTATGAATATTGTAATT
66 TATTGCAATTTTTTTGTATGAATATTGTAATT
4426906 TTGTAATTTTGTATGAATATTATATTTTTTTGTATGAATGTTGTAATATTATAATTTTGTATGAA
1 TTGTAATTTTGTATGAATATTATATTTTTTTGTATGAATGTTGTAATATTATAATTTTGTATGAA
4426971 TATTGCAATTTTTTTGTATGAATATTGTAATT
66 TATTGCAATTTTTTTGTATGAATATTGTAATT
4427003 TTGTAATTTTGTATGAATATTATATTTTTTTGTATGAATGTTGTAATATTATAATTTTGTATGAA
1 TTGTAATTTTGTATGAATATTATATTTTTTTGTATGAATGTTGTAATATTATAATTTTGTATGAA
4427068 TATTGCAATTTTTTTGTATGAATATTGTAATT
66 TATTGCAATTTTTTTGTATGAATATTGTAATT
4427100 TTGTAATTTTGTATGAATATTATATTTTTTTGTATGAATGTTGTAATATTATAATTTTGTATGAA
1 TTGTAATTTTGTATGAATATTATATTTTTTTGTATGAATGTTGTAATATTATAATTTTGTATGAA
*
4427165 TATTGCAATTTTTTTGTATGAATATTGTAATA
66 TATTGCAATTTTTTTGTATGAATATTGTAATT
4427197 TTGTAATTTTG
1 TTGTAATTTTG
4427208 CAATTTTTAT
Statistics
Matches: 490, Mismatches: 6, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
97 450 0.92
100 18 0.04
101 22 0.04
ACGTcount: A:0.30, C:0.01, G:0.14, T:0.55
Consensus pattern (97 bp):
TTGTAATTTTGTATGAATATTATATTTTTTTGTATGAATGTTGTAATATTATAATTTTGTATGAA
TATTGCAATTTTTTTGTATGAATATTGTAATT
Found at i:4427168 original size:19 final size:19
Alignment explanation
Indices: 4427144--4427201 Score: 53
Period size: 22 Copynumber: 2.9 Consensus size: 19
4427134 TGAATGTTGT
4427144 AATATTATAATTTTGTATG
1 AATATTATAATTTTGTATG
**
4427163 AATATTGCAATTTTTTTGTATG
1 AATATT---ATAATTTTGTATG
* *
4427185 AATATTGTAATATTGTA
1 AATATTATAATTTTGTA
4427202 ATTTTGCAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
19 13 0.43
22 17 0.57
ACGTcount: A:0.34, C:0.02, G:0.12, T:0.52
Consensus pattern (19 bp):
AATATTATAATTTTGTATG
Found at i:4430426 original size:6 final size:6
Alignment explanation
Indices: 4430407--4430471 Score: 103
Period size: 6 Copynumber: 10.8 Consensus size: 6
4430397 AGAATGTAGT
* *
4430407 TCTGCC TCTCGC TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC
1 TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC
*
4430455 CCTGGC TCTGGC TCTGG
1 TCTGGC TCTGGC TCTGG
4430472 TGCATGATGC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 54 1.00
ACGTcount: A:0.00, C:0.37, G:0.31, T:0.32
Consensus pattern (6 bp):
TCTGGC
Found at i:4432125 original size:16 final size:15
Alignment explanation
Indices: 4432094--4432135 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
4432084 ACAAAATCAA
*
4432094 ATAAAATTTAATTAT
1 ATAAAAGTTAATTAT
4432109 ATAAAAGTTACATTAT
1 ATAAAAGTTA-ATTAT
*
4432125 ATAAAAATTAA
1 ATAAAAGTTAA
4432136 ATAAGTTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (15 bp):
ATAAAAGTTAATTAT
Found at i:4432300 original size:38 final size:38
Alignment explanation
Indices: 4432246--4432319 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
4432236 TAAAAAACCC
*
4432246 AAACTTTTAATAAAATGATTTTTAATTTTTTTATAATT
1 AAACTTTTAATAAAATGATTTTAAATTTTTTTATAATT
*
4432284 AAACTTTTAATGAAATGATTTTAAATTTTTTTATAA
1 AAACTTTTAATAAAATGATTTTAAATTTTTTTATAA
4432320 ACTTTATATG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.53
Consensus pattern (38 bp):
AAACTTTTAATAAAATGATTTTAAATTTTTTTATAATT
Found at i:4432624 original size:22 final size:22
Alignment explanation
Indices: 4432595--4432756 Score: 93
Period size: 20 Copynumber: 7.9 Consensus size: 22
4432585 TATAATATTA
4432595 TTACAATATTCATACAAAAAAT
1 TTACAATATTCATACAAAAAAT
*
4432617 TTATAATATTCATAC---AAA-
1 TTACAATATTCATACAAAAAAT
4432635 TTACAATATTCATACAAAAAA-
1 TTACAATATTCATACAAAAAAT
* * * * *
4432656 TTACTA-ATCCAAAACTATAAA-
1 TTACAATATTC-ATACAAAAAAT
* *
4432677 -TACAA-ATTTAATTATAAAATAA-
1 TTACAATA-TTCA-TACAAAA-AAT
*
4432699 TTACAATATTCATAC--AACA-
1 TTACAATATTCATACAAAAAAT
4432718 TTACAATATTCATA-AAAAAA-
1 TTACAATATTCATACAAAAAAT
*
4432738 TTATAATATTCATACAAAA
1 TTACAATATTCATACAAAA
4432757 TTCTAATCTA
Statistics
Matches: 109, Mismatches: 19, Indels: 25
0.71 0.12 0.16
Matches are distributed among these distances:
18 14 0.13
19 18 0.17
20 27 0.25
21 23 0.21
22 18 0.17
23 8 0.07
24 1 0.01
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.33
Consensus pattern (22 bp):
TTACAATATTCATACAAAAAAT
Found at i:4432638 original size:40 final size:39
Alignment explanation
Indices: 4432594--4432755 Score: 161
Period size: 40 Copynumber: 4.0 Consensus size: 39
4432584 CTATAATATT
4432594 ATTACAATATTCATACAAAAAATTTATAATATTCATACAA
1 ATTACAATATTCATACAAAAAA-TTATAATATTCATACAA
* *
4432634 ATTACAATATTCATACAAAAAATTACT-A-ATCCAAAACTATA
1 ATTACAATATTCATACAAAAAATTA-TAATATTC-ATAC-A-A
* * * *
4432675 AATACAA-ATTTAATTATAAAATAATTACAATATTCATACAA
1 ATTACAATA-TTCA-TACAAAA-AATTATAATATTCATACAA
4432716 CATTACAATATTCATA-AAAAAATTATAATATTCATACAA
1 -ATTACAATATTCATACAAAAAATTATAATATTCATACAA
4432755 A
1 A
4432756 ATTCTAATCT
Statistics
Matches: 100, Mismatches: 11, Indels: 24
0.74 0.08 0.18
Matches are distributed among these distances:
38 4 0.04
39 25 0.25
40 29 0.29
41 13 0.13
42 16 0.16
43 10 0.10
44 3 0.03
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.33
Consensus pattern (39 bp):
ATTACAATATTCATACAAAAAATTATAATATTCATACAA
Found at i:4432644 original size:18 final size:18
Alignment explanation
Indices: 4432594--4432652 Score: 73
Period size: 18 Copynumber: 3.1 Consensus size: 18
4432584 CTATAATATT
4432594 ATTACAATATTCATACAAAAA
1 ATTACAATATTCATAC---AA
*
4432615 ATTTATAATATTCATACAA
1 A-TTACAATATTCATACAA
4432634 ATTACAATATTCATACAA
1 ATTACAATATTCATACAA
4432652 A
1 A
4432653 AAATTACTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 17 0.49
19 3 0.09
21 1 0.03
22 14 0.40
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.34
Consensus pattern (18 bp):
ATTACAATATTCATACAA
Found at i:4432758 original size:19 final size:19
Alignment explanation
Indices: 4432536--4432758 Score: 108
Period size: 19 Copynumber: 11.5 Consensus size: 19
4432526 CATGCAAAAT
*
4432536 TACAATATTACAATATTCA
1 TACAAAATTACAATATTCA
*
4432555 TACAAAAAAATTGCAATATTCA
1 TAC---AAAATTACAATATTCA
* *
4432577 TACAAAACTATAATATT-A
1 TACAAAATTACAATATTCA
*
4432595 TTACAATATT-C-ATA--CA
1 -TACAAAATTACAATATTCA
*
4432611 -A-AAAATTTATAATATTCA
1 TACAAAA-TTACAATATTCA
4432629 TAC-AAATTACAATATTCA
1 TACAAAATTACAATATTCA
* *
4432647 TACAAAAAATTACTA-ATCCAA
1 TAC--AAAATTACAATATTC-A
*
4432668 AACTATAAA-TACAAATTTAATT-A
1 TAC-A-AAATTAC-AA--T-ATTCA
*
4432691 TAAAATAATTACAATATTCA
1 TACAA-AATTACAATATTCA
*
4432711 TACAACATTACAATATTCA
1 TACAAAATTACAATATTCA
* *
4432730 TAAAAAAATTATAATATTCA
1 T-ACAAAATTACAATATTCA
4432750 TACAAAATT
1 TACAAAATT
4432759 CTAATCTAAA
Statistics
Matches: 153, Mismatches: 25, Indels: 52
0.67 0.11 0.23
Matches are distributed among these distances:
13 3 0.02
14 3 0.02
16 4 0.03
17 3 0.02
18 17 0.11
19 49 0.32
20 29 0.19
21 16 0.10
22 22 0.14
23 5 0.03
25 2 0.01
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (19 bp):
TACAAAATTACAATATTCA
Found at i:4433321 original size:21 final size:20
Alignment explanation
Indices: 4433288--4433326 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
4433278 AAAAATCAGT
*
4433288 AAATATTAGTAATAAATTAC
1 AAATATTACTAATAAATTAC
*
4433308 AAATATTAACTAATTAATT
1 AAATATT-ACTAATAAATT
4433327 TTAATAGGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (20 bp):
AAATATTACTAATAAATTAC
Found at i:4438700 original size:13 final size:13
Alignment explanation
Indices: 4438682--4438720 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
4438672 TATACATCAT
4438682 TTATTTTTTTTTC
1 TTATTTTTTTTTC
* *
4438695 TTATTTTCTATTC
1 TTATTTTTTTTTC
4438708 TTGATTTTTTTTT
1 TT-ATTTTTTTTT
4438721 AGGGTACAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.10, C:0.08, G:0.03, T:0.79
Consensus pattern (13 bp):
TTATTTTTTTTTC
Found at i:4447007 original size:3 final size:3
Alignment explanation
Indices: 4446999--4447041 Score: 77
Period size: 3 Copynumber: 14.0 Consensus size: 3
4446989 ATAGTAATGG
4446999 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TATA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
4447042 CATAATTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:4452401 original size:20 final size:19
Alignment explanation
Indices: 4452378--4452470 Score: 80
Period size: 20 Copynumber: 4.8 Consensus size: 19
4452368 CAAAACTAGA
4452378 TTATGATTTTTTTTTAGTTT
1 TTATGA-TTTTTTTTAGTTT
* * *
4452398 TTAT-AATTTTCTAAGTTT
1 TTATGATTTTTTTTAGTTT
* * *
4452416 TAATAATTTTTTTTGGATTT
1 TTATGATTTTTTTTAG-TTT
*
4452436 TAATGATTTTTTTTAGTTT
1 TTATGATTTTTTTTAGTTT
*
4452455 TTAAGTATTTTTTTTA
1 TTATG-ATTTTTTTTA
4452471 CTTAATTTTG
Statistics
Matches: 58, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
18 13 0.22
19 14 0.24
20 31 0.53
ACGTcount: A:0.23, C:0.01, G:0.09, T:0.68
Consensus pattern (19 bp):
TTATGATTTTTTTTAGTTT
Found at i:4457154 original size:23 final size:23
Alignment explanation
Indices: 4457120--4457163 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
4457110 TAGATTATAA
4457120 CATGTCTGCAAAAGGTTTTTTCT
1 CATGTCTGCAAAAGGTTTTTTCT
*
4457143 CATGTCTTCAAAAGGTTTTTT
1 CATGTCTGCAAAAGGTTTTTT
4457164 TTTTTAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.23, C:0.16, G:0.16, T:0.45
Consensus pattern (23 bp):
CATGTCTGCAAAAGGTTTTTTCT
Found at i:4464764 original size:42 final size:42
Alignment explanation
Indices: 4464683--4464765 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
4464673 AAGTTTGATC
** * *
4464683 TTGAGTATGAAAATTGATAAACAAGTTTAATCGAGTTCGAGT
1 TTGAGTACAAAAATTGATAAACAAGCTTAATCGAATTCGAGT
*
4464725 TTGAGTACAAAAATTGATAAATAAGCTTATAT-GAATTCGAG
1 TTGAGTACAAAAATTGATAAACAAGCTTA-ATCGAATTCGAG
4464766 CTCGAGCAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.33
Consensus pattern (42 bp):
TTGAGTACAAAAATTGATAAACAAGCTTAATCGAATTCGAGT
Found at i:4465813 original size:23 final size:24
Alignment explanation
Indices: 4465761--4465814 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
4465751 CCGTCCAACA
*
4465761 TTTTTAATGATTAGATATAATATG
1 TTTTTAATGATGAGATATAATATG
* *
4465785 TCTTTAAT-ATGAG-TATGAATATT
1 TTTTTAATGATGAGATAT-AATATG
4465808 TTTTTAA
1 TTTTTAA
4465815 AAAAGGTCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
22 3 0.12
23 15 0.60
24 7 0.28
ACGTcount: A:0.35, C:0.02, G:0.11, T:0.52
Consensus pattern (24 bp):
TTTTTAATGATGAGATATAATATG
Found at i:4472197 original size:235 final size:235
Alignment explanation
Indices: 4471777--4472248 Score: 811
Period size: 235 Copynumber: 2.0 Consensus size: 235
4471767 ATTTGAAAGC
* * * **
4471777 TTTCCATAGTGATACAGTGTCTAAAGATGATTTCATTGAACTTTCTAAACATGTTGTAAATTATG
1 TTTCCATACTGATACAGTGCCGAAAGATGATTTCATTGAACTTTCTAAACATGTCATAAATTATG
4471842 CCAGTGGGCTCCCTCTAGCTCTTGAAGTTTTGGGTTCCTTTTTGTGCGGTAGAGATGCGATTCAA
66 CCAGTGGGCTCCCTCTAGCTCTTGAAGTTTTGGGTTCCTTTTTGTGCGGTAGAGATGCGATTCAA
4471907 TGGAGAAGTGCGATTGAAAGACTTAAAAGAGATTCTAATAAAGAAATTCTCGATAAACTTCGAAT
131 TGGAGAAGTGCGATTGAAAGACTTAAAAGAGATTCTAATAAAGAAATTCTCGATAAACTTCGAAT
4471972 CAGCTTTGATGGACTAGAAGAAAGGGAGAAGAATATATTT
196 CAGCTTTGATGGACTAGAAGAAAGGGAGAAGAATATATTT
* * * *
4472012 TTTCCCTACTGATACAGTGCCGAAAGATGATTTCATTGAGCTTTCTGAACATGTCATAGATTATG
1 TTTCCATACTGATACAGTGCCGAAAGATGATTTCATTGAACTTTCTAAACATGTCATAAATTATG
* *
4472077 TTC-GTGGGCTCCCTTTAGCTCTTGAAGTTTTGGGTTCCTTTTTGTGCGGTAGAGATGCGATTCA
66 -CCAGTGGGCTCCCTCTAGCTCTTGAAGTTTTGGGTTCCTTTTTGTGCGGTAGAGATGCGATTCA
4472141 ATGGAGAAGTGCGATTGAAAGACTTAAAAGAGATTCTAATAAAGAAATTCTCGATAAACTTCGAA
130 ATGGAGAAGTGCGATTGAAAGACTTAAAAGAGATTCTAATAAAGAAATTCTCGATAAACTTCGAA
* *
4472206 TCAGTTTTGATGGACTGGAAGAAAGGGAGAAGAATATATTT
195 TCAGCTTTGATGGACTAGAAGAAAGGGAGAAGAATATATTT
4472247 TT
1 TT
4472249 AGATATAGCA
Statistics
Matches: 223, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
235 222 1.00
236 1 0.00
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.33
Consensus pattern (235 bp):
TTTCCATACTGATACAGTGCCGAAAGATGATTTCATTGAACTTTCTAAACATGTCATAAATTATG
CCAGTGGGCTCCCTCTAGCTCTTGAAGTTTTGGGTTCCTTTTTGTGCGGTAGAGATGCGATTCAA
TGGAGAAGTGCGATTGAAAGACTTAAAAGAGATTCTAATAAAGAAATTCTCGATAAACTTCGAAT
CAGCTTTGATGGACTAGAAGAAAGGGAGAAGAATATATTT
Found at i:4472866 original size:25 final size:25
Alignment explanation
Indices: 4472828--4472875 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
4472818 AATGTACTTA
4472828 TTTTTGAAATATTAATGGTATATTT
1 TTTTTGAAATATTAATGGTATATTT
*
4472853 TTTTGTGAAA-ATTAATTGTATAT
1 TTTT-TGAAATATTAATGGTATAT
4472876 ATTTAATGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.54
Consensus pattern (25 bp):
TTTTTGAAATATTAATGGTATATTT
Found at i:4476652 original size:29 final size:28
Alignment explanation
Indices: 4476619--4476678 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 28
4476609 AATGGCCAGC
* *
4476619 CATGCTACTATTATGTTTTTGTTAAAGTG
1 CATGCTACTATGATGATTTTGTT-AAGTG
*
4476648 CATGCTACTATGATGATTTTGTTGAGTG
1 CATGCTACTATGATGATTTTGTTAAGTG
4476676 CAT
1 CAT
4476679 ACAGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 7 0.25
29 21 0.75
ACGTcount: A:0.23, C:0.12, G:0.20, T:0.45
Consensus pattern (28 bp):
CATGCTACTATGATGATTTTGTTAAGTG
Found at i:4480354 original size:13 final size:13
Alignment explanation
Indices: 4480336--4480369 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
4480326 TATACATTAT
*
4480336 TTATTTTATTTTC
1 TTATTTTATGTTC
4480349 TTATTTTATGTTC
1 TTATTTTATGTTC
4480362 TTGATTTT
1 TT-ATTTT
4480370 TTTAGGCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.74
Consensus pattern (13 bp):
TTATTTTATGTTC
Found at i:4483517 original size:39 final size:41
Alignment explanation
Indices: 4483429--4483524 Score: 108
Period size: 39 Copynumber: 2.4 Consensus size: 41
4483419 CGTTTGGACA
* ** *
4483429 AAAAACGCCACTAAAAATCAAGCATTAGTGGCGCTTTTAGG
1 AAAAACGCCGCTAAAAATCAAGCATTACCGACGCTTTTAGG
* *
4483470 -AAAGCGCCGCTAAAAAT-AAGCATTACCGACG-TTTTTGG
1 AAAAACGCCGCTAAAAATCAAGCATTACCGACGCTTTTAGG
*
4483508 AAAAACGCCGCAAAAAA
1 AAAAACGCCGCTAAAAA
4483525 ACCTAAGCCC
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
38 6 0.13
39 25 0.54
40 15 0.33
ACGTcount: A:0.42, C:0.21, G:0.19, T:0.19
Consensus pattern (41 bp):
AAAAACGCCGCTAAAAATCAAGCATTACCGACGCTTTTAGG
Found at i:4483625 original size:41 final size:41
Alignment explanation
Indices: 4483557--4483754 Score: 281
Period size: 41 Copynumber: 4.9 Consensus size: 41
4483547 TTTTGACCTA
* * *** * *
4483557 TCAGGTCTTTAGCGGCATTTAAAAAAAAACGCCGCTAATGT
1 TCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
4483598 TCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
1 TCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
*
4483639 TCAGATCTTTAGCGGCGATTTTG-AAAAGCGCCGCTAATGC
1 TCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
* *
4483679 TCAGATCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATTC
1 TCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
* *
4483720 TCAGAGCTTTAGCGGCGTTTTTGAGAAAGCGCCGC
1 TCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCGC
4483755 AAAAATATTT
Statistics
Matches: 144, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 39 0.27
41 105 0.73
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (41 bp):
TCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
Found at i:4483698 original size:81 final size:81
Alignment explanation
Indices: 4483581--4483754 Score: 285
Period size: 81 Copynumber: 2.1 Consensus size: 81
4483571 GCATTTAAAA
* * *
4483581 AAAAACGCCGCTAATGTTCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGATC
1 AAAAGCGCCGCTAATGCTCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAGC
4483646 TTTAGCGGCGATTTTG
66 TTTAGCGGCGATTTTG
* *
4483662 AAAAGCGCCGCTAATGCTCAGATCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATTCTCAGAGC
1 AAAAGCGCCGCTAATGCTCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAGC
*
4483727 TTTAGCGGCGTTTTTG
66 TTTAGCGGCGATTTTG
4483743 AGAAAGCGCCGC
1 A-AAAGCGCCGC
4483755 AAAAATATTT
Statistics
Matches: 86, Mismatches: 6, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
81 76 0.88
82 10 0.12
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (81 bp):
AAAAGCGCCGCTAATGCTCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAGC
TTTAGCGGCGATTTTG
Found at i:4483893 original size:26 final size:26
Alignment explanation
Indices: 4483848--4483898 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
4483838 TAAATGGATA
** *
4483848 AATTTGAAATAATGACACATAGAAAT
1 AATTTGAAATAAAAAAACATAGAAAT
4483874 AATTTGAAATAAAAAAACATAGAAA
1 AATTTGAAATAAAAAAACATAGAAA
4483899 AATATTTGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.61, C:0.06, G:0.10, T:0.24
Consensus pattern (26 bp):
AATTTGAAATAAAAAAACATAGAAAT
Found at i:4484310 original size:62 final size:63
Alignment explanation
Indices: 4484244--4484373 Score: 165
Period size: 62 Copynumber: 2.1 Consensus size: 63
4484234 TCGATGTCAA
* * * *
4484244 GTTAGGCTTTAGGGTTTAGATTAATTAGTGTGTTTT-AATTT-TTTATGAAATAAGGTTTAGGG
1 GTTAGGCATTAGAGTTTAGATTAATTAATGT-TTTTGAATTTATATATGAAATAAGGTTTAGGG
* * * *
4484306 GTTAGGGATTCGAGTTTAGATTAATTAATGTTTTTGAATTTATATATTAGATAAGGTTTAGGG
1 GTTAGGCATTAGAGTTTAGATTAATTAATGTTTTTGAATTTATATATGAAATAAGGTTTAGGG
4484369 GTTAG
1 GTTAG
4484374 TAGTTTAGGT
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
61 4 0.07
62 31 0.53
63 23 0.40
ACGTcount: A:0.28, C:0.02, G:0.25, T:0.45
Consensus pattern (63 bp):
GTTAGGCATTAGAGTTTAGATTAATTAATGTTTTTGAATTTATATATGAAATAAGGTTTAGGG
Found at i:4484562 original size:21 final size:21
Alignment explanation
Indices: 4484515--4484562 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
4484505 GTAAAAGAGG
4484515 GGTT-AGAGGTTAGAGGTTAA
1 GGTTAAGAGGTTAGAGGTTAA
*
4484535 GAATTAAGA-GTTAGAGGTTAAA
1 G-GTTAAGAGGTTAGAGGTT-AA
4484557 GGTTAA
1 GGTTAA
4484563 TGGCTTGGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
20 1 0.04
21 16 0.70
22 6 0.26
ACGTcount: A:0.38, C:0.00, G:0.33, T:0.29
Consensus pattern (21 bp):
GGTTAAGAGGTTAGAGGTTAA
Found at i:4489742 original size:35 final size:36
Alignment explanation
Indices: 4489703--4489775 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 36
4489693 TTTAATTGTG
4489703 TTATTAATTTATTAT-TTTAAATTTTAAAGCTAA-AT
1 TTATTAATTTATTATATTT-AATTTTAAAGCTAAGAT
* * *
4489738 TTATTAATTTTTTATATTTAGTTTTAAAGTTAAGAT
1 TTATTAATTTATTATATTTAATTTTAAAGCTAAGAT
4489774 TT
1 TT
4489776 TCATAGAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
35 26 0.79
36 7 0.21
ACGTcount: A:0.36, C:0.01, G:0.05, T:0.58
Consensus pattern (36 bp):
TTATTAATTTATTATATTTAATTTTAAAGCTAAGAT
Found at i:4489967 original size:42 final size:42
Alignment explanation
Indices: 4489908--4490226 Score: 119
Period size: 43 Copynumber: 7.5 Consensus size: 42
4489898 AATATTTTTT
* * * * *
4489908 TAAAGGTTATGTTTTTAGCGGCGTT-TTTGCTAGAAGTGTCGC
1 TAAAGGTTATGTCTTTAGCAGCGTTCGTGGCTA-AAGCGTCGC
4489950 TAAAGGTTTAT-TCTTTAGCAGCGTTCGTGGCTAAAGCGTCGC
1 TAAAGG-TTATGTCTTTAGCAGCGTTCGTGGCTAAAGCGTCGC
* * * * **
4489992 TAAAGCTCACGATCTTTAGC-GACGTTTGTATCTAAAGCG-CTGC
1 TAAAGGTTATG-TCTTTAGCAG-CGTTCGTGGCTAAAGCGTC-GC
* * * * * * *
4490035 TAAAGATTACGATCTTTAACGGCGTTTGTGGCTAAAGCGCCGT
1 TAAAGGTTATG-TCTTTAGCAGCGTTCGTGGCTAAAGCGTCGC
* * * * * * *
4490078 TAAAGGTCACGATCTTTAGCGGCGTTTGT-GATAAAAACGCCGC
1 TAAAGGTTATG-TCTTTAGCAGCGTTCGTGGCT-AAAGCGTCGC
* * * * * * * * * *
4490121 TAAATGTCAAGATTTTTAGCGGCATTTGTGGCAAAAGCGCCGT
1 TAAAGGTTATG-TCTTTAGCAGCGTTCGTGGCTAAAGCGTCGC
* * ** *
4490164 TAAAGGTTATGTTCTTTAGCGGCGTTTGT-TATAAAAGCGCCGC
1 TAAAGGTTATG-TCTTTAGCAGCGTTCGTGGCT-AAAGCGTCGC
*
4490207 TAAAGGTCATGATCTTTAGC
1 TAAAGGTTATG-TCTTTAGC
4490227 GGCATTTTTT
Statistics
Matches: 223, Mismatches: 43, Indels: 21
0.78 0.15 0.07
Matches are distributed among these distances:
41 2 0.01
42 35 0.16
43 183 0.82
44 3 0.01
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (42 bp):
TAAAGGTTATGTCTTTAGCAGCGTTCGTGGCTAAAGCGTCGC
Found at i:4490027 original size:43 final size:43
Alignment explanation
Indices: 4489982--4490229 Score: 248
Period size: 43 Copynumber: 5.8 Consensus size: 43
4489972 GTTCGTGGCT
* * * *
4489982 AAAGCGTCGCTAAAGCTCACGATCTTTAGCGACGTTTGTATCT
1 AAAGCGCCGCTAAAGGTCACGATCTTTAGCGGCGTTTGTATCA
* * * * ** *
4490025 AAAGCGCTGCTAAAGATTACGATCTTTAACGGCGTTTGTGGCT
1 AAAGCGCCGCTAAAGGTCACGATCTTTAGCGGCGTTTGTATCA
*
4490068 AAAGCGCCGTTAAAGGTCACGATCTTTAGCGGCGTTTGTGAT-A
1 AAAGCGCCGCTAAAGGTCACGATCTTTAGCGGCGTTTGT-ATCA
* * * * * **
4490111 AAAACGCCGCTAAATGTCAAGATTTTTAGCGGCATTTGTGGCA
1 AAAGCGCCGCTAAAGGTCACGATCTTTAGCGGCGTTTGTATCA
* * * *
4490154 AAAGCGCCGTTAAAGGTTATGTTCTTTAGCGGCGTTTGTTAT-A
1 AAAGCGCCGCTAAAGGTCACGATCTTTAGCGGCGTTTG-TATCA
*
4490197 AAAGCGCCGCTAAAGGTCATGATCTTTAGCGGC
1 AAAGCGCCGCTAAAGGTCACGATCTTTAGCGGC
4490230 ATTTTTTCAC
Statistics
Matches: 165, Mismatches: 37, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
43 164 0.99
44 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.29
Consensus pattern (43 bp):
AAAGCGCCGCTAAAGGTCACGATCTTTAGCGGCGTTTGTATCA
Found at i:4490230 original size:86 final size:86
Alignment explanation
Indices: 4489961--4490233 Score: 323
Period size: 86 Copynumber: 3.2 Consensus size: 86
4489951 AAAGGTTTAT
* * * * * * * *
4489961 TCTTTAGCAGCGTTCGTGGCTAAAGCGTCGCTAAAGCTCACGATCTTTAGCGACGTTTG-TATCT
1 TCTTTAGCGGCATTTGTGGCTAAAGCGCCGTTAAAGGTCACGATCTTTAGCGGCGTTTGTTAT-A
* * * *
4490025 AAAGCGCTGCTAAAGATTACGA
65 AAAGCGCCGCTAAAGGTCATGA
* * *
4490047 TCTTTAACGGCGTTTGTGGCTAAAGCGCCGTTAAAGGTCACGATCTTTAGCGGCGTTTGTGATAA
1 TCTTTAGCGGCATTTGTGGCTAAAGCGCCGTTAAAGGTCACGATCTTTAGCGGCGTTTGTTATAA
* * *
4490112 AAACGCCGCTAAATGTCAAGA
66 AAGCGCCGCTAAAGGTCATGA
* * * * *
4490133 TTTTTAGCGGCATTTGTGGCAAAAGCGCCGTTAAAGGTTATGTTCTTTAGCGGCGTTTGTTATAA
1 TCTTTAGCGGCATTTGTGGCTAAAGCGCCGTTAAAGGTCACGATCTTTAGCGGCGTTTGTTATAA
4490198 AAGCGCCGCTAAAGGTCATGA
66 AAGCGCCGCTAAAGGTCATGA
4490219 TCTTTAGCGGCATTT
1 TCTTTAGCGGCATTT
4490234 TTTCACATAA
Statistics
Matches: 159, Mismatches: 27, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
86 157 0.99
87 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (86 bp):
TCTTTAGCGGCATTTGTGGCTAAAGCGCCGTTAAAGGTCACGATCTTTAGCGGCGTTTGTTATAA
AAGCGCCGCTAAAGGTCATGA
Found at i:4493641 original size:15 final size:15
Alignment explanation
Indices: 4493623--4493652 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4493613 CAATAATAAT
*
4493623 TAAATGTATTTGCCA
1 TAAATGTATTAGCCA
4493638 TAAATGTATTAGCCA
1 TAAATGTATTAGCCA
4493653 CATCAAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (15 bp):
TAAATGTATTAGCCA
Found at i:4500525 original size:9 final size:9
Alignment explanation
Indices: 4500511--4500566 Score: 67
Period size: 9 Copynumber: 6.2 Consensus size: 9
4500501 TTTTCAGTAG
4500511 CATCTGTAT
1 CATCTGTAT
*
4500520 CATCTGTAC
1 CATCTGTAT
*
4500529 CATCGGTAT
1 CATCTGTAT
* *
4500538 CATCAGTAG
1 CATCTGTAT
*
4500547 CATCTGTGT
1 CATCTGTAT
4500556 CATCTGTAT
1 CATCTGTAT
4500565 CA
1 CA
4500567 CTCTCTGCAT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (9 bp):
CATCTGTAT
Found at i:4509301 original size:27 final size:27
Alignment explanation
Indices: 4509271--4509326 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
4509261 TGGCATTGAT
*
4509271 GTTCTCATTAAAAAATCTCTTATAAAA
1 GTTCTCATTAAAAAATCTCTCATAAAA
*
4509298 GTTCTCATTAAAAAATCTCTCATAGAA
1 GTTCTCATTAAAAAATCTCTCATAAAA
4509325 GT
1 GT
4509327 CGATGAACAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (27 bp):
GTTCTCATTAAAAAATCTCTCATAAAA
Found at i:4509311 original size:14 final size:14
Alignment explanation
Indices: 4509271--4509311 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
4509261 TGGCATTGAT
4509271 GTTCTCATTAAAAA
1 GTTCTCATTAAAAA
*
4509285 -ATCTC-TTATAAAA
1 GTTCTCATTA-AAAA
4509298 GTTCTCATTAAAAA
1 GTTCTCATTAAAAA
4509312 ATCTCTCATA
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
12 3 0.14
13 8 0.36
14 8 0.36
15 3 0.14
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.37
Consensus pattern (14 bp):
GTTCTCATTAAAAA
Found at i:4509318 original size:15 final size:15
Alignment explanation
Indices: 4509273--4509320 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
4509263 GCATTGATGT
4509273 TCTCATTAAAAAATC
1 TCTCATTAAAAAATC
* *
4509288 TCTTA-T-AAAAGT-
1 TCTCATTAAAAAATC
4509300 TCTCATTAAAAAATC
1 TCTCATTAAAAAATC
4509315 TCTCAT
1 TCTCAT
4509321 AGAAGTCGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
12 4 0.15
13 6 0.23
14 6 0.23
15 10 0.38
ACGTcount: A:0.42, C:0.19, G:0.02, T:0.38
Consensus pattern (15 bp):
TCTCATTAAAAAATC
Found at i:4512103 original size:9 final size:9
Alignment explanation
Indices: 4512075--4512104 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
4512065 TCTCTTTTCG
4512075 GTAGCATCT
1 GTAGCATCT
*
4512084 GAAGCATCT
1 GTAGCATCT
4512093 GTAGCATCT
1 GTAGCATCT
4512102 GTA
1 GTA
4512105 TCACTCTCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (9 bp):
GTAGCATCT
Found at i:4519917 original size:15 final size:16
Alignment explanation
Indices: 4519897--4519926 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4519887 GCTACCAACA
4519897 AGTATAG-TAGTTGTG
1 AGTATAGATAGTTGTG
4519912 AGTATAGATAGTTGT
1 AGTATAGATAGTTGT
4519927 TCTTCACTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.30, C:0.00, G:0.30, T:0.40
Consensus pattern (16 bp):
AGTATAGATAGTTGTG
Found at i:4525143 original size:61 final size:60
Alignment explanation
Indices: 4525039--4525172 Score: 196
Period size: 61 Copynumber: 2.2 Consensus size: 60
4525029 GGTGGATTCC
* *
4525039 GCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGGGAATTA
1 GCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTCGGGGGAATCA
** * **
4525099 GCACTTAGCAACCACCAAATGGGTCGGGGAGTCAGCACTTAGCAACCCCTCGGGGGAATCA
1 GCACTTAGCAACCACC-AATGAATCGGGGAATCAGCACACAGCAACCCCTCGGGGGAATCA
4525160 GCACTTAGCAACC
1 GCACTTAGCAACC
4525173 CCCTTTCACA
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
60 16 0.24
61 50 0.76
ACGTcount: A:0.31, C:0.30, G:0.25, T:0.15
Consensus pattern (60 bp):
GCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTCGGGGGAATCA
Found at i:4525214 original size:43 final size:42
Alignment explanation
Indices: 4525153--4525367 Score: 214
Period size: 43 Copynumber: 5.5 Consensus size: 42
4525143 ACCCCTCGGG
4525153 GGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATACGGT
1 GGAATCAGCACTTAGCAACCCCC-TTCACATTTAAAATACGGT
* **
4525196 GGAATCAGCACTTAGCAA-CCAC--CA-A--T-AGGTA-GG-
1 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGT
4525229 GGAATCAGCACTTAGCAACCCCCTCTCACATTTAAAATACGGT
1 GGAATCAGCACTTAGCAACCCCCT-TCACATTTAAAATACGGT
* *
4525272 GGAATCAGCACTTAGCAA-CCAC--CA-A--T-AATTA-GG-
1 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGT
*
4525305 GGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATACAGT
1 GGAATCAGCACTTAGCAACCCCC-TTCACATTTAAAATACGGT
*
4525348 GGGATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
4525368 ACCAATGAAT
Statistics
Matches: 140, Mismatches: 12, Indels: 40
0.73 0.06 0.21
Matches are distributed among these distances:
33 36 0.26
34 10 0.07
35 7 0.05
36 2 0.01
37 4 0.03
38 4 0.03
39 4 0.03
40 2 0.01
41 7 0.05
42 9 0.06
43 55 0.39
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.21
Consensus pattern (42 bp):
GGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGT
Found at i:4525238 original size:33 final size:33
Alignment explanation
Indices: 4525187--4525400 Score: 133
Period size: 33 Copynumber: 5.8 Consensus size: 33
4525177 TTCACATTTA
4525187 AAATACGGTGGAATCAGCACTTAGCAACCACCAAT
1 AAATA-GG-GGAATCAGCACTTAGCAACCACCAAT
** *
4525222 AGGTAGGGGAATCAGCACTTAGCAACCCCCTCTCACATTT
1 AAATAGGGGAATCAGCACTTAGCAA---CCAC-CA-A--T
4525262 AAAATACGGTGGAATCAGCACTTAGCAACCACCAAT
1 -AAATA-GG-GGAATCAGCACTTAGCAACCACCAAT
* *
4525298 AATTAGGGGAATCAGCACTTAGCAACCCCCTTTCACATTT
1 AAATAGGGGAATCAGCACTTAGCAA-CCAC---CA-A--T
4525338 AAAATACAGTGGG-ATCAGCACTTAGCAACCACCAAT
1 -AAAT--AG-GGGAATCAGCACTTAGCAACCACCAAT
* * **
4525374 GAATCGGGGAATCAGCACACAGCAACC
1 AAATAGGGGAATCAGCACTTAGCAACC
4525401 CCTTTATATG
Statistics
Matches: 143, Mismatches: 14, Indels: 46
0.70 0.07 0.23
Matches are distributed among these distances:
32 3 0.02
33 52 0.36
34 7 0.05
35 10 0.07
36 5 0.03
37 4 0.03
38 4 0.03
39 4 0.03
40 5 0.03
41 6 0.04
42 5 0.03
43 35 0.24
44 3 0.02
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.19
Consensus pattern (33 bp):
AAATAGGGGAATCAGCACTTAGCAACCACCAAT
Found at i:4525250 original size:76 final size:76
Alignment explanation
Indices: 4525151--4525402 Score: 409
Period size: 76 Copynumber: 3.3 Consensus size: 76
4525141 CAACCCCTCG
4525151 GGGGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACC
*
4525216 ACCAATAGGTA
66 ACCAATAGATA
*
4525227 GGGGAATCAGCACTTAGCAACCCCCTCTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACC
4525292 ACCAATA-ATTA
66 ACCAATAGA-TA
* *
4525303 GGGGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATACAGTGGGATCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACC
*
4525368 ACCAAT-GAATC
66 ACCAATAG-ATA
**
4525379 GGGGAATCAGCACACAGCAACCCC
1 GGGGAATCAGCACTTAGCAACCCC
4525403 TTTATATGCA
Statistics
Matches: 165, Mismatches: 8, Indels: 6
0.92 0.04 0.03
Matches are distributed among these distances:
76 164 0.99
77 1 0.01
ACGTcount: A:0.35, C:0.28, G:0.18, T:0.19
Consensus pattern (76 bp):
GGGGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACC
ACCAATAGATA
Found at i:4529333 original size:13 final size:13
Alignment explanation
Indices: 4529315--4529341 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4529305 CATATGTTGT
4529315 AAATCTTATTTGC
1 AAATCTTATTTGC
4529328 AAATCTTATTTGC
1 AAATCTTATTTGC
4529341 A
1 A
4529342 GATTCATGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.44
Consensus pattern (13 bp):
AAATCTTATTTGC
Found at i:4529934 original size:25 final size:25
Alignment explanation
Indices: 4529892--4529940 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
4529882 TCAAAAGCTA
* *
4529892 CGACAAATGCTTGGAGTTTGCAAGG
1 CGACAAATGCTAGGAGTTAGCAAGG
4529917 CGACAAATGC-AGGAAGTTAGCAAG
1 CGACAAATGCTAGG-AGTTAGCAAG
4529941 ATTTTTTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 19 0.90
ACGTcount: A:0.35, C:0.16, G:0.31, T:0.18
Consensus pattern (25 bp):
CGACAAATGCTAGGAGTTAGCAAGG
Found at i:4534327 original size:18 final size:18
Alignment explanation
Indices: 4534304--4534346 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
4534294 CAATAGGTTT
4534304 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
4534322 TTAATTAAAAAATTTAAA
1 TTAATTAAAAAATTTAAA
4534340 TTAATTA
1 TTAATTA
4534347 CATGTTGAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 6 0.25
18 18 0.75
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:4534464 original size:13 final size:13
Alignment explanation
Indices: 4534429--4534457 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
4534419 AATTATTCTC
4534429 ATCCTAGTTGGAA
1 ATCCTAGTTGGAA
4534442 ATCCTAGTTGGAA
1 ATCCTAGTTGGAA
4534455 ATC
1 ATC
4534458 TAAGTTGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (13 bp):
ATCCTAGTTGGAA
Found at i:4537897 original size:27 final size:25
Alignment explanation
Indices: 4537846--4537893 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
4537836 AATGTATGTA
4537846 TTTTTGAAATATTAATGGTATATTT
1 TTTTTGAAATATTAATGGTATATTT
4537871 TTTTGTGAAA-ATTAATGGTATAT
1 TTTT-TGAAATATTAATGGTATAT
4537894 ATTTAATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (25 bp):
TTTTTGAAATATTAATGGTATATTT
Found at i:4541708 original size:18 final size:18
Alignment explanation
Indices: 4541685--4541727 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
4541675 CAATAGGTTT
4541685 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
4541703 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
4541721 TTAATTA
1 TTAATTA
4541728 CATGTTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:4547354 original size:153 final size:153
Alignment explanation
Indices: 4546940--4547333 Score: 528
Period size: 153 Copynumber: 2.6 Consensus size: 153
4546930 ACTAAGGGAC
* * * * * *
4546940 TGCAATCTTTGTGAAGGAGATATTCCA-CGTGATATTTCTGGTCTATCCTGTTTGGAA-AAACTT
1 TGCACTCTTGGTGAAGCAGATATT-CATAGTGATATTTCTGGTCTATCCTCTTT-GAATAATCTT
* **
4547003 GATCTTAGTGGTAACAATTTCATCAGCATGCCTGCATCTCTTACTCGACTCTTGAAGCTTGCAAA
64 GATCTTAGTGGTAACAATTTCATCAGCATACCTGCATCTCTTACTCGACTCTCAAAGCTTGCAAA
4547068 TCTTATATTGTCAAATTGCAACATG
129 TCTTATATTGTCAAATTGCAACATG
* * * * *
4547093 TGCACTTTTGGTGAAGCAGATACTCATAGTGATATTTCTGGTCTATCCTCTTTGAGTTATCTTAA
1 TGCACTCTTGGTGAAGCAGATATTCATAGTGATATTTCTGGTCTATCCTCTTTGAATAATCTTGA
**
4547158 TCTTAGTGGTAACAATTTCATCAGCATACCTGCATCTCTTACTCGACTCTCAAAGCTT-CATGTT
66 TCTTAGTGGTAACAATTTCATCAGCATACCTGCATCTCTTACTCGACTCTCAAAGCTTGCA-AAT
* *
4547222 CTTGA-CTTGTCAAATTGCAACGTG
130 CTT-ATATTGTCAAATTGCAACATG
*
4547246 TGCACTCTTGGTGAAGCAGATATTCATAGTGATCTTTCTGGTCTATCCTCTTT-AATAAGTCTTG
1 TGCACTCTTGGTGAAGCAGATATTCATAGTGATATTTCTGGTCTATCCTCTTTGAATAA-TCTTG
*
4547310 ATCTTAGTGGTAATAATTTCATCA
65 ATCTTAGTGGTAACAATTTCATCA
4547334 CCATTCCTTT
Statistics
Matches: 211, Mismatches: 25, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
152 9 0.04
153 201 0.95
154 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (153 bp):
TGCACTCTTGGTGAAGCAGATATTCATAGTGATATTTCTGGTCTATCCTCTTTGAATAATCTTGA
TCTTAGTGGTAACAATTTCATCAGCATACCTGCATCTCTTACTCGACTCTCAAAGCTTGCAAATC
TTATATTGTCAAATTGCAACATG
Found at i:4551972 original size:16 final size:16
Alignment explanation
Indices: 4551951--4551989 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
4551941 ATTTTGTTAC
*
4551951 AACAATTATTACAATT
1 AACAATTAATACAATT
4551967 AACAATTAATACAATT
1 AACAATTAATACAATT
*
4551983 AATAATT
1 AACAATT
4551990 TGATAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (16 bp):
AACAATTAATACAATT
Found at i:4552014 original size:16 final size:16
Alignment explanation
Indices: 4551993--4552034 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
4551983 AATAATTTGA
*
4551993 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
4552009 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
4552025 TAGTTTTAAT
1 TAATTTTAAT
4552035 TTTATCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:4559659 original size:5 final size:5
Alignment explanation
Indices: 4559651--4559676 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
4559641 AATAATCAAG
4559651 TTTAT TTTAT TTTAT TTTAT TTTAT T
1 TTTAT TTTAT TTTAT TTTAT TTTAT T
4559677 AAAATTTATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:4581243 original size:100 final size:100
Alignment explanation
Indices: 4581070--4581269 Score: 382
Period size: 100 Copynumber: 2.0 Consensus size: 100
4581060 TATAAGAGTT
4581070 ACAAAAGTAATTTGTCAGTTACCTAATGGTTAACTGCTCCCACTAAATACATAAACAAAACTAAC
1 ACAAAAGTAATTTGTCAGTTACCTAATGGTTAACTGCTCCCACTAAATACATAAACAAAACTAAC
*
4581135 TTAAACTTGTACGCAAAGATAAGCTGACATATTAG
66 TTAAACTTGTACACAAAGATAAGCTGACATATTAG
*
4581170 ACAAAAGTAATTTGTCAGTTACCTAATGGTTAACTGCTCCCACTAAATACATAAATAAAACTAAC
1 ACAAAAGTAATTTGTCAGTTACCTAATGGTTAACTGCTCCCACTAAATACATAAACAAAACTAAC
4581235 TTAAACTTGTACACAAAGATAAGCTGACATATTAG
66 TTAAACTTGTACACAAAGATAAGCTGACATATTAG
4581270 CTATTACATC
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 98 1.00
ACGTcount: A:0.42, C:0.18, G:0.12, T:0.28
Consensus pattern (100 bp):
ACAAAAGTAATTTGTCAGTTACCTAATGGTTAACTGCTCCCACTAAATACATAAACAAAACTAAC
TTAAACTTGTACACAAAGATAAGCTGACATATTAG
Found at i:4582871 original size:16 final size:15
Alignment explanation
Indices: 4582837--4582875 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
4582827 CCATCCATAT
*
4582837 TTAATTTT-TTTAGA
1 TTAATTTTATTTAAA
4582851 TTAATTTTATTTAAAA
1 TTAATTTTATTT-AAA
4582867 TTAATTTTA
1 TTAATTTTA
4582876 AAAATATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.36
15 3 0.14
16 11 0.50
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (15 bp):
TTAATTTTATTTAAA
Found at i:4591599 original size:33 final size:33
Alignment explanation
Indices: 4591562--4591627 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
4591552 TGATAATGAG
4591562 GATGGTTTGAAACAGTCTGTTGAGTCTCCAAGA
1 GATGGTTTGAAACAGTCTGTTGAGTCTCCAAGA
4591595 GATGGTTTGAAACAGTCTGTTGAGTCTCCAAGA
1 GATGGTTTGAAACAGTCTGTTGAGTCTCCAAGA
4591628 TATTCTCAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (33 bp):
GATGGTTTGAAACAGTCTGTTGAGTCTCCAAGA
Found at i:4596068 original size:7 final size:7
Alignment explanation
Indices: 4596056--4596087 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
4596046 AAAATATTTT
4596056 TATTTAA
1 TATTTAA
4596063 TATTTAA
1 TATTTAA
4596070 TATTTAA
1 TATTTAA
4596077 TATTT-A
1 TATTTAA
4596083 TATTT
1 TATTT
4596088 TTTCTTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
TATTTAA
Found at i:4596073 original size:14 final size:13
Alignment explanation
Indices: 4596048--4596087 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
4596038 ATTTTAGAAA
*
4596048 AATATTTTTATTT
1 AATATTTATATTT
4596061 AATATTTAATATTT
1 AATATTT-ATATTT
4596075 AATATTTATATTT
1 AATATTTATATTT
4596088 TTTCTTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:4596073 original size:20 final size:20
Alignment explanation
Indices: 4596048--4596087 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
4596038 ATTTTAGAAA
*
4596048 AATATTTTTATTTAATATTT
1 AATATTTATATTTAATATTT
4596068 AATATTTAATATTT-ATATTT
1 AATATTT-ATATTTAATATTT
4596088 TTTCTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
AATATTTATATTTAATATTT
Found at i:4598016 original size:26 final size:26
Alignment explanation
Indices: 4597986--4598037 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
4597976 ATTTTTAATT
4597986 AGTAAAAGTAAAATAATAAATTGATC
1 AGTAAAAGTAAAATAATAAATTGATC
4598012 AGTAAAAGTAAAATAATAAATTGATC
1 AGTAAAAGTAAAATAATAAATTGATC
4598038 CCTAAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.58, C:0.04, G:0.12, T:0.27
Consensus pattern (26 bp):
AGTAAAAGTAAAATAATAAATTGATC
Found at i:4598043 original size:26 final size:26
Alignment explanation
Indices: 4597988--4598044 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
4597978 TTTTAATTAG
*
4597988 TAAAAGTAAAATAATAAATTGATCAG
1 TAAAAGTAAAATAATAAATTGATCAC
*
4598014 TAAAAGTAAAATAATAAATTGATCCC
1 TAAAAGTAAAATAATAAATTGATCAC
4598040 TAAAA
1 TAAAA
4598045 ATATAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.58, C:0.07, G:0.09, T:0.26
Consensus pattern (26 bp):
TAAAAGTAAAATAATAAATTGATCAC
Found at i:4598336 original size:18 final size:18
Alignment explanation
Indices: 4598305--4598355 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
4598295 AACATACATT
*
4598305 TTAAATAT-TTTTATATTA
1 TTAAATATATATTAT-TTA
*
4598323 TTAAAT-TATATTATTTC
1 TTAAATATATATTATTTA
*
4598340 TTTAATATATATTATT
1 TTAAATATATATTATT
4598356 AACTTTAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 8 0.29
18 20 0.71
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (18 bp):
TTAAATATATATTATTTA
Found at i:4603909 original size:153 final size:153
Alignment explanation
Indices: 4603646--4604011 Score: 549
Period size: 153 Copynumber: 2.4 Consensus size: 153
4603636 GATATTCCAC
* * *
4603646 GTGATATTTCTGGTCTATCCTGTTTGGAA-AAACTTGATCTTAGTGGTAACAATTTCATCAGCAT
1 GTGATATTTCTGGTCTATCCTCTTT-GAATATACTTAATCTTAGTGGTAACAATTTCATCAGCAT
* * *
4603710 ACCTGCATCTCTTACTCGACTCTCGAAGCTTGAAATTCTGCGATTGTCAAATTGTAACATGTGCA
65 ACCTGCATCTCTTACTCGACTCTCGAAGCTGGAAATTCTGAGATTGTCAAATTGCAACATGTGCA
4603775 CTTTTGGTGAAGCAGATACTCATA
130 CTTTTGGTGAAGCAGATACTCATA
*
4603799 GTGATATTTCTGGTCTATCCTCTTTGAATATACTTAATCTTAGTGATAACAATTTCATCAGCATA
1 GTGATATTTCTGGTCTATCCTCTTTGAATATACTTAATCTTAGTGGTAACAATTTCATCAGCATA
* * * * *
4603864 CCTGCATCTCTTACTCGACTGTCGAATCTCGGAAA-TCTTATATTGTCAAATTGCAACATTTGCA
66 CCTGCATCTCTTACTCGACTCTCGAAGCT-GGAAATTCTGAGATTGTCAAATTGCAACATGTGCA
*
4603928 CTTTTGGTGAAGCAGATACTCATG
130 CTTTTGGTGAAGCAGATACTCATA
* *
4603952 GTGATATTTCTGGTCTATCCTCTTTGAGT-TATCTTAATCTTAGTGGTAAGAATTTCATCA
1 GTGATATTTCTGGTCTATCCTCTTTGAATATA-CTTAATCTTAGTGGTAACAATTTCATCA
4604012 CCCTTCCTTT
Statistics
Matches: 194, Mismatches: 16, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
152 5 0.03
153 185 0.95
154 4 0.02
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.38
Consensus pattern (153 bp):
GTGATATTTCTGGTCTATCCTCTTTGAATATACTTAATCTTAGTGGTAACAATTTCATCAGCATA
CCTGCATCTCTTACTCGACTCTCGAAGCTGGAAATTCTGAGATTGTCAAATTGCAACATGTGCAC
TTTTGGTGAAGCAGATACTCATA
Found at i:4604072 original size:153 final size:152
Alignment explanation
Indices: 4603646--4604064 Score: 475
Period size: 153 Copynumber: 2.7 Consensus size: 152
4603636 GATATTCCAC
* * * * *
4603646 GTGATATTTCTGGTCTATCCTGTTTGGAA-AAACTTGATCTTAGTGGTAACAATTTCATCAGCAT
1 GTGATATTTCTGGTCTATCCTCTTT-GAATATACTTAATCTTAGTGATAACAATTTCATCACCAT
* * * * * *** *
4603710 ACCTGCATCTCTTACTCGACTCTCGAAGCTTGAAATTCTGCGATTGTCAAATTGTAACATGTGCA
65 ACCTGCAGCTCTTACTCAACTGTCCAAGCTCGAAA-TCTTAAATTGTCAAATTGCAACATGTGCA
4603775 CTTTTGGTGAAGCAGATACTCATA
129 CTTTTGGTGAAGCAGATACTCATA
*
4603799 GTGATATTTCTGGTCTATCCTCTTTGAATATACTTAATCTTAGTGATAACAATTTCATCAGCATA
1 GTGATATTTCTGGTCTATCCTCTTTGAATATACTTAATCTTAGTGATAACAATTTCATCACCATA
* * * * * *
4603864 CCTGCATCTCTTACTCGACTGTCGAATCTCGGAAATCTTATATTGTCAAATTGCAACATTTGCAC
66 CCTGCAGCTCTTACTCAACTGTCCAAGCTC-GAAATCTTAAATTGTCAAATTGCAACATGTGCAC
*
4603929 TTTTGGTGAAGCAGATACTCATG
130 TTTTGGTGAAGCAGATACTCATA
* * * *
4603952 GTGATATTTCTGGTCTATCCTCTTTGAGT-TATCTTAATCTTAGTGGTAAGAATTTCATCACCCT
1 GTGATATTTCTGGTCTATCCTCTTTGAATATA-CTTAATCTTAGTGATAACAATTTCATCACCAT
* *** * *
4604016 TCCTTTGGCTCTTACTCAACTTTCCAGGCTC-AAATTGCTTAAATTGTCA
65 ACCTGCAGCTCTTACTCAACTGTCCAAGCTCGAAA-T-CTTAAATTGTCA
4604065 GGTTGCAAGA
Statistics
Matches: 232, Mismatches: 29, Indels: 10
0.86 0.11 0.04
Matches are distributed among these distances:
151 3 0.01
152 6 0.03
153 219 0.94
154 4 0.02
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.38
Consensus pattern (152 bp):
GTGATATTTCTGGTCTATCCTCTTTGAATATACTTAATCTTAGTGATAACAATTTCATCACCATA
CCTGCAGCTCTTACTCAACTGTCCAAGCTCGAAATCTTAAATTGTCAAATTGCAACATGTGCACT
TTTGGTGAAGCAGATACTCATA
Found at i:4609698 original size:5 final size:5
Alignment explanation
Indices: 4609690--4609715 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
4609680 AATAATCAAG
4609690 TTTAT TTTAT TTTAT TTTAT TTTAT T
1 TTTAT TTTAT TTTAT TTTAT TTTAT T
4609716 AAAATTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:4614009 original size:20 final size:20
Alignment explanation
Indices: 4613984--4614025 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
4613974 GAATTTCTTC
4613984 AACCTCATTAACTTTTGCTA
1 AACCTCATTAACTTTTGCTA
4614004 AACCTCATTAACTTTTGCTA
1 AACCTCATTAACTTTTGCTA
4614024 AA
1 AA
4614026 GCAACAATGT
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:0.33, C:0.24, G:0.05, T:0.38
Consensus pattern (20 bp):
AACCTCATTAACTTTTGCTA
Found at i:4617574 original size:21 final size:20
Alignment explanation
Indices: 4617550--4617617 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 20
4617540 AACAACGTTA
4617550 AATGTCCAATTAAGCAACACT
1 AATGTCCAATTAAGC-ACACT
* * *
4617571 AATGGT-AAATATAACCACGCT
1 AAT-GTCCAAT-TAAGCACACT
4617592 AAATGTCCAATTAAGGCACACT
1 -AATGTCCAATTAA-GCACACT
4617614 AATG
1 AATG
4617618 GTAGTTATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
21 19 0.53
22 17 0.47
ACGTcount: A:0.43, C:0.21, G:0.13, T:0.24
Consensus pattern (20 bp):
AATGTCCAATTAAGCACACT
Found at i:4617577 original size:43 final size:43
Alignment explanation
Indices: 4617529--4617627 Score: 146
Period size: 43 Copynumber: 2.3 Consensus size: 43
4617519 GGAAAGTTTG
*
4617529 ATGGTAGTTATAACAACGTTAAATGTCCAATTAA-GCAACACTA
1 ATGGTAGTTATAACAACGCTAAATGTCCAATTAAGGC-ACACTA
** *
4617572 ATGGTAAATATAACCACGCTAAATGTCCAATTAAGGCACACTA
1 ATGGTAGTTATAACAACGCTAAATGTCCAATTAAGGCACACTA
4617615 ATGGTAGTTATAA
1 ATGGTAGTTATAA
4617628 GAGAGAGCTA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
43 47 0.96
44 2 0.04
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.27
Consensus pattern (43 bp):
ATGGTAGTTATAACAACGCTAAATGTCCAATTAAGGCACACTA
Found at i:4617615 original size:22 final size:21
Alignment explanation
Indices: 4617548--4617615 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 21
4617538 ATAACAACGT
4617548 TAAATGTCCAATTAAGCAACAC
1 TAAATGTCCAATTAAGC-ACAC
* * *
4617570 T-AATGGT-AAATATAACCACGC
1 TAAAT-GTCCAAT-TAAGCACAC
4617591 TAAATGTCCAATTAAGGCACAC
1 TAAATGTCCAATTAA-GCACAC
4617613 TAA
1 TAA
4617616 TGGTAGTTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
21 15 0.43
22 20 0.57
ACGTcount: A:0.44, C:0.21, G:0.12, T:0.24
Consensus pattern (21 bp):
TAAATGTCCAATTAAGCACAC
Found at i:4620200 original size:3 final size:3
Alignment explanation
Indices: 4620192--4620233 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
4620182 TTTCCCCATT
*
4620192 TTC TTC TTC TT- TTCC TTC TTC TTC CTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TT-C TTC TTC TTC TTC TTC TTC TTC TTC TTC
4620234 ATCATCCTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 31 0.89
4 2 0.06
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
TTC
Found at i:4620286 original size:12 final size:12
Alignment explanation
Indices: 4620193--4620286 Score: 52
Period size: 12 Copynumber: 8.1 Consensus size: 12
4620183 TTCCCCATTT
*
4620193 TCTTCTTCTT-T
1 TCTTCTTCTTCC
4620204 TCCTTCTTCTTCC
1 T-CTTCTTCTTCC
*
4620217 TCTTCTTCTTCT
1 TCTTCTTCTTCC
* *
4620229 TCTTCATCATCC
1 TCTTCTTCTTCC
* * * *
4620241 TCATCATCATCA
1 TCTTCTTCTTCC
* *
4620253 TCATCTTCCTCC
1 TCTTCTTCTTCC
*
4620265 TC-T-TGC-TCC
1 TCTTCTTCTTCC
4620274 TCTTCTTCTTCC
1 TCTTCTTCTTCC
4620286 T
1 T
4620287 TTTTCTCCCC
Statistics
Matches: 66, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
9 5 0.08
10 3 0.05
11 4 0.06
12 53 0.80
13 1 0.02
ACGTcount: A:0.07, C:0.39, G:0.01, T:0.52
Consensus pattern (12 bp):
TCTTCTTCTTCC
Found at i:4626544 original size:29 final size:29
Alignment explanation
Indices: 4626512--4626571 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
4626502 AAGAAAATGT
4626512 AAAATATTATATATTTGGACAAGTGTGAG
1 AAAATATTATATATTTGGACAAGTGTGAG
4626541 AAAATATTATATATTTGGACAAGTGTGAG
1 AAAATATTATATATTTGGACAAGTGTGAG
4626570 AA
1 AA
4626572 TGCTTAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.43, C:0.03, G:0.20, T:0.33
Consensus pattern (29 bp):
AAAATATTATATATTTGGACAAGTGTGAG
Found at i:4632191 original size:16 final size:16
Alignment explanation
Indices: 4632158--4632192 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
4632148 TTGTATTACT
*
4632158 CAACAAGGCTTATGTA
1 CAACAAGGCTTATATA
*
4632174 CAACAAGGCTTTTATA
1 CAACAAGGCTTATATA
4632190 CAA
1 CAA
4632193 ACCAAATACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.26
Consensus pattern (16 bp):
CAACAAGGCTTATATA
Found at i:4632265 original size:103 final size:100
Alignment explanation
Indices: 4632089--4632295 Score: 308
Period size: 103 Copynumber: 2.0 Consensus size: 100
4632079 AGGCACTCAA
* *
4632089 ACAAATCAAATACAAGGAGCTAATATGCAAAGAAAGTGAGTGTAAGACAATGCTATAGCTTGTAT
1 ACAAACCAAATACAAGGAGCTAACATGCAAAGAAAGTGAGTGTAAGACAATGCTATAGCTTGTAT
* * *
4632154 TACTCAACAAGGCTTATGTACAACAAGGCTTTTAT
66 TACTCAACAAAGCTTATATAAAACAAGGCTTTTAT
* *
4632189 ACAAACCAAATACAA-GAGTTAACATGCAAGGAAAGTGAGTGTAAGAGATCTAATGCTATAGCTT
1 ACAAACCAAATACAAGGAGCTAACATGCAAAGAAAGTGAGTGT-A-AGA-C-AATGCTATAGCTT
4632253 GTATTACTCAACAAAGCTTATATAAAACAAGGCTTTTAT
62 GTATTACTCAACAAAGCTTATATAAAACAAGGCTTTTAT
4632292 ACAA
1 ACAA
4632296 TGATTCATGT
Statistics
Matches: 96, Mismatches: 7, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
99 24 0.25
100 15 0.16
101 3 0.03
102 1 0.01
103 53 0.55
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.26
Consensus pattern (100 bp):
ACAAACCAAATACAAGGAGCTAACATGCAAAGAAAGTGAGTGTAAGACAATGCTATAGCTTGTAT
TACTCAACAAAGCTTATATAAAACAAGGCTTTTAT
Found at i:4633677 original size:20 final size:20
Alignment explanation
Indices: 4633652--4633690 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4633642 AAATCAATAC
4633652 AAATCGATTAAACCAACTAA
1 AAATCGATTAAACCAACTAA
* *
4633672 AAATCGATTTAATCAACTA
1 AAATCGATTAAACCAACTA
4633691 TTGAACTGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.18, G:0.05, T:0.26
Consensus pattern (20 bp):
AAATCGATTAAACCAACTAA
Found at i:4636284 original size:10 final size:10
Alignment explanation
Indices: 4636269--4636301 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
4636259 TCTCTCTCTC
4636269 TATATGTATG
1 TATATGTATG
4636279 TATATGTATG
1 TATATGTATG
4636289 --TATGTATG
1 TATATGTATG
4636297 TATAT
1 TATAT
4636302 ATGTACATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
8 8 0.38
10 13 0.62
ACGTcount: A:0.30, C:0.00, G:0.18, T:0.52
Consensus pattern (10 bp):
TATATGTATG
Found at i:4641759 original size:14 final size:14
Alignment explanation
Indices: 4641737--4641774 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
4641727 AGAGTTATAC
4641737 AATAACAACAAAAT
1 AATAACAACAAAAT
*
4641751 AATAGCAACAAAAT
1 AATAACAACAAAAT
*
4641765 AGTAACAACA
1 AATAACAACA
4641775 TAATTGTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.66, C:0.16, G:0.05, T:0.13
Consensus pattern (14 bp):
AATAACAACAAAAT
Found at i:4641829 original size:22 final size:23
Alignment explanation
Indices: 4641783--4641835 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
4641773 CATAATTGTG
*
4641783 AAATAAT-AGCAAAATAGTGAAA
1 AAATAATAAGCAAAATAGTCAAA
4641805 AAATAATAAGCAAAA-AG-CAACA
1 AAATAATAAGCAAAATAGTCAA-A
4641827 AAATAATAA
1 AAATAATAA
4641836 AAAAAGTAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 2 0.07
22 19 0.68
23 7 0.25
ACGTcount: A:0.68, C:0.08, G:0.09, T:0.15
Consensus pattern (23 bp):
AAATAATAAGCAAAATAGTCAAA
Found at i:4641829 original size:33 final size:31
Alignment explanation
Indices: 4641792--4641852 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
4641782 GAAATAATAG
* *
4641792 CAAAATAGTGAAAAAATAATAAGCAAAAAGCAA
1 CAAAATAAT-AAAAAA-AATAAGAAAAAAGCAA
*
4641825 CAAAATAATAAAAAAAGTAAGAAAAAAG
1 CAAAATAATAAAAAAAATAAGAAAAAAG
4641853 AAAAAAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 11 0.44
32 6 0.24
33 8 0.32
ACGTcount: A:0.70, C:0.07, G:0.11, T:0.11
Consensus pattern (31 bp):
CAAAATAATAAAAAAAATAAGAAAAAAGCAA
Found at i:4641851 original size:22 final size:22
Alignment explanation
Indices: 4641783--4641851 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 22
4641773 CATAATTGTG
* *
4641783 AAATAATAGCAAAATAG-TGAAA
1 AAATAATAACAAAA-AGAAGAAA
* *
4641805 AAATAATAAGCAAAAAGCA-ACA
1 AAATAATAA-CAAAAAGAAGAAA
4641827 AAATAATAA-AAAAAGTAAGAAA
1 AAATAATAACAAAAAG-AAGAAA
4641849 AAA
1 AAA
4641852 GAAAAAAGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
20 6 0.16
21 1 0.03
22 26 0.68
23 5 0.13
ACGTcount: A:0.71, C:0.06, G:0.10, T:0.13
Consensus pattern (22 bp):
AAATAATAACAAAAAGAAGAAA
Found at i:4644776 original size:41 final size:40
Alignment explanation
Indices: 4644731--4644858 Score: 116
Period size: 41 Copynumber: 3.1 Consensus size: 40
4644721 TTAAATTATT
* *
4644731 CTAAATCCCTTAGCATTAGCGGCGCTTTATT-AAAATCGCCG
1 CTAAA-CCCTTAGCATTAGCGACGCTTT-TTAAAAAACGCCG
* *
4644772 CTAAAGCCTTGAGCATTAGCGACGCTTTTTAAAAAACGTCG
1 CTAAACCCTT-AGCATTAGCGACGCTTTTTAAAAAACGCCG
* * * * *
4644813 CTACAGCCCTGAGCATTAGCGATGCGTTCTT-AAAAACACCG
1 CTA-AACCCTTAGCATTAGCGACGC-TTTTTAAAAAACGCCG
4644854 CTAAA
1 CTAAA
4644859 GCCACGAAAG
Statistics
Matches: 71, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
40 7 0.10
41 56 0.79
42 8 0.11
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (40 bp):
CTAAACCCTTAGCATTAGCGACGCTTTTTAAAAAACGCCG
Found at i:4645952 original size:9 final size:9
Alignment explanation
Indices: 4645876--4645951 Score: 100
Period size: 9 Copynumber: 8.4 Consensus size: 9
4645866 GTAGTGATTC
*
4645876 AATTTGGTT
1 AATTCGGTT
4645885 AATTCGGTT
1 AATTCGGTT
*
4645894 AATTCGGGT
1 AATTCGGTT
4645903 AATTCGGTT
1 AATTCGGTT
4645912 AATTC-GTGT
1 AATTCGGT-T
*
4645921 AATTCGGCT
1 AATTCGGTT
4645930 AATTCGGTT
1 AATTCGGTT
*
4645939 AATTTGGTT
1 AATTCGGTT
4645948 AATT
1 AATT
4645952 TTTAACCAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
8 2 0.03
9 56 0.95
10 1 0.02
ACGTcount: A:0.24, C:0.09, G:0.22, T:0.45
Consensus pattern (9 bp):
AATTCGGTT
Found at i:4648595 original size:3 final size:3
Alignment explanation
Indices: 4648587--4648627 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
4648577 ATTATTTTAA
4648587 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
4648628 AGAAAAAGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:4653638 original size:14 final size:14
Alignment explanation
Indices: 4653619--4653646 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4653609 AATCCTTTAT
4653619 CCATTTTAATGTGA
1 CCATTTTAATGTGA
4653633 CCATTTTAATGTGA
1 CCATTTTAATGTGA
4653647 GCAAATAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (14 bp):
CCATTTTAATGTGA
Found at i:4659052 original size:16 final size:16
Alignment explanation
Indices: 4659027--4659061 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
4659017 TTATATATAT
*
4659027 TTTTTTTTTCATTCCA
1 TTTTTCTTTCATTCCA
*
4659043 TTTTTCTTTCTTTCCA
1 TTTTTCTTTCATTCCA
4659059 TTT
1 TTT
4659062 CTTTGATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTTCTTTCATTCCA
Found at i:4661557 original size:15 final size:17
Alignment explanation
Indices: 4661530--4661570 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
4661520 AATATAAATA
4661530 TTTATTT-AATTT-GT-
1 TTTATTTAAATTTGGTG
4661544 TTTATTTAAATTTGGTG
1 TTTATTTAAATTTGGTG
4661561 TTT-TTTAAAT
1 TTTATTTAAAT
4661571 AAATATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 7 0.29
15 5 0.21
16 9 0.38
17 3 0.12
ACGTcount: A:0.24, C:0.00, G:0.10, T:0.66
Consensus pattern (17 bp):
TTTATTTAAATTTGGTG
Found at i:4662106 original size:21 final size:21
Alignment explanation
Indices: 4662064--4662106 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
4662054 TTGTAAAAAT
* * **
4662064 AAATATATTATATATTTTTTA
1 AAATATATTAAAAATTAATTA
4662085 AAATATATTAAAAATTAATTA
1 AAATATATTAAAAATTAATTA
4662106 A
1 A
4662107 TTACTTATAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AAATATATTAAAAATTAATTA
Found at i:4670020 original size:20 final size:20
Alignment explanation
Indices: 4669995--4670047 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
4669985 ACAATGTTGT
4669995 AAATTACTAAAGTT-CTTATA
1 AAATTACTAAA-TTGCTTATA
*
4670015 AAATTATTAAATTGCTTATA
1 AAATTACTAAATTGCTTATA
*
4670035 AAATTTCTAAATT
1 AAATTACTAAATT
4670048 TTTTAAAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 2 0.07
20 27 0.93
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (20 bp):
AAATTACTAAATTGCTTATA
Found at i:4689416 original size:12 final size:13
Alignment explanation
Indices: 4689399--4689430 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
4689389 TAACTTCTCA
4689399 TTTGTTT-TTTTT
1 TTTGTTTCTTTTT
4689411 TTTGTTTCTTTTT
1 TTTGTTTCTTTTT
4689424 TTT-TTTC
1 TTTGTTTC
4689431 GAGTGCATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.88
Consensus pattern (13 bp):
TTTGTTTCTTTTT
Found at i:4690709 original size:17 final size:19
Alignment explanation
Indices: 4690674--4690716 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
4690664 ATTAGTTTAA
* *
4690674 TTAAAAATTAGATTTA-TT
1 TTAAAAATTAGAGTAATTT
4690692 TTAAAAATT-GAGTAATTT
1 TTAAAAATTAGAGTAATTT
4690710 TTAAAAA
1 TTAAAAA
4690717 ATAATAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (19 bp):
TTAAAAATTAGAGTAATTT
Found at i:4696369 original size:18 final size:18
Alignment explanation
Indices: 4696342--4696380 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
4696332 TAATAAATAA
* *
4696342 AATTATCCAACCCAACTC
1 AATTACCCAACCCAACCC
4696360 AATTACCCAACCCAACCC
1 AATTACCCAACCCAACCC
4696378 AAT
1 AAT
4696381 AAAACTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.41, G:0.00, T:0.18
Consensus pattern (18 bp):
AATTACCCAACCCAACCC
Found at i:4696571 original size:37 final size:37
Alignment explanation
Indices: 4696530--4696604 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
4696520 TGTTAATTTC
4696530 AAGACTTACGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGACTTACGTAATGTTTTTAATTATGTAGTGATTCA
*
4696567 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGACTTACGTAATGTTTTTAATTATGTAGTGATTCA
4696604 A
1 A
4696605 TTCGGGTAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (37 bp):
AAGACTTACGTAATGTTTTTAATTATGTAGTGATTCA
Found at i:4696594 original size:17 final size:17
Alignment explanation
Indices: 4696539--4696595 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
4696529 CAAGACTTAC
4696539 GTAATGTTTTTAATTAT
1 GTAATGTTTTTAATTAT
* ***
4696556 GTAGTGATTCAAAGACTTAT
1 GTAATG-TTTTTA-A-TTAT
4696576 GTAATGTTTTTAATTAT
1 GTAATGTTTTTAATTAT
4696593 GTA
1 GTA
4696596 GTGATTCAAT
Statistics
Matches: 29, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
17 12 0.41
18 4 0.14
19 4 0.14
20 9 0.31
ACGTcount: A:0.32, C:0.04, G:0.16, T:0.49
Consensus pattern (17 bp):
GTAATGTTTTTAATTAT
Found at i:4696640 original size:9 final size:9
Alignment explanation
Indices: 4696603--4696642 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
4696593 GTAGTGATTC
*
4696603 AATTCGGGT
1 AATTCGGTT
4696612 AATTCGGTT
1 AATTCGGTT
**
4696621 AATTCAATT
1 AATTCGGTT
4696630 AATTCGGTT
1 AATTCGGTT
4696639 AATT
1 AATT
4696643 TTTAACCAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:4704607 original size:24 final size:22
Alignment explanation
Indices: 4704575--4704636 Score: 79
Period size: 24 Copynumber: 2.7 Consensus size: 22
4704565 AGTGTATTGT
4704575 ATATTATTATTTTAGATTTATCA
1 ATATTATTATTTTA-ATTTATCA
* *
4704598 TGTTTTATTATTTGTAATTTATCA
1 -ATATTATTATTT-TAATTTATCA
4704622 ATATTATTATTTTAA
1 ATATTATTATTTTAA
4704637 ATTCATCTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 3 0.09
23 10 0.30
24 18 0.55
25 2 0.06
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.60
Consensus pattern (22 bp):
ATATTATTATTTTAATTTATCA
Found at i:4704639 original size:23 final size:23
Alignment explanation
Indices: 4704575--4704696 Score: 86
Period size: 23 Copynumber: 5.2 Consensus size: 23
4704565 AGTGTATTGT
*
4704575 ATATTATTATTTTAGATTTATCA
1 ATATTATTATTTTAAATTTATCA
* *
4704598 TGTTTTATTATTTGT-AATTTATCA
1 -ATATTATTATTT-TAAATTTATCA
* *
4704622 ATATTATTATTTTAAATTCATCT
1 ATATTATTATTTTAAATTTATCA
* ** *
4704645 TTAACATTATCTTAAATTTATC-
1 ATATTATTATTTTAAATTTATCA
* *
4704667 ATGTATATCTATTTCAAATTTATCA
1 ATAT-TAT-TATTTTAAATTTATCA
*
4704692 TTATT
1 ATATT
4704697 TTTAAATTTA
Statistics
Matches: 73, Mismatches: 20, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
22 2 0.03
23 36 0.49
24 32 0.44
25 3 0.04
ACGTcount: A:0.33, C:0.08, G:0.03, T:0.56
Consensus pattern (23 bp):
ATATTATTATTTTAAATTTATCA
Found at i:4704766 original size:33 final size:33
Alignment explanation
Indices: 4704729--4704796 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
4704719 TTTTGGATTT
4704729 ATCACGTATGATTATTCTAGAATTACCATCAAA
1 ATCACGTATGATTATTCTAGAATTACCATCAAA
*
4704762 ATCACGTATGATTATTCTAGAATTATCATCAAA
1 ATCACGTATGATTATTCTAGAATTACCATCAAA
4704795 AT
1 AT
4704797 TTTTAAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (33 bp):
ATCACGTATGATTATTCTAGAATTACCATCAAA
Found at i:4704856 original size:24 final size:23
Alignment explanation
Indices: 4704798--4704856 Score: 59
Period size: 24 Copynumber: 2.4 Consensus size: 23
4704788 CATCAAAATT
4704798 TTTAAATT-TTATATGTATTATTA
1 TTTAAATTATTATA-GTATTATTA
4704821 TTTCAAATTTATTATA-TATTATTTA
1 TTT-AAA-TTATTATAGTATTA-TTA
4704846 TTGTAAATTAT
1 TT-TAAATTAT
4704857 CCAATTCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
23 3 0.10
24 12 0.39
25 10 0.32
26 6 0.19
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (23 bp):
TTTAAATTATTATAGTATTATTA
Found at i:4706165 original size:14 final size:14
Alignment explanation
Indices: 4706146--4706175 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4706136 ACAAATTGAC
*
4706146 ATGATATTACATAT
1 ATGATAATACATAT
4706160 ATGATAATACATAT
1 ATGATAATACATAT
4706174 AT
1 AT
4706176 ACCATATCTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (14 bp):
ATGATAATACATAT
Found at i:4708105 original size:6 final size:6
Alignment explanation
Indices: 4708094--4708119 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
4708084 CTTTCTAGCC
4708094 ATTATA ATTATA ATTATA ATTATA AT
1 ATTATA ATTATA ATTATA ATTATA AT
4708120 GGTAAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTATA
Found at i:4711283 original size:12 final size:12
Alignment explanation
Indices: 4711260--4711299 Score: 57
Period size: 13 Copynumber: 3.4 Consensus size: 12
4711250 AATTTGCTCA
4711260 TTTTTTTT--AT
1 TTTTTTTTAAAT
4711270 TTTTTTTTAAAT
1 TTTTTTTTAAAT
4711282 TTTTTATTTAAAT
1 TTTTT-TTTAAAT
4711295 TTTTT
1 TTTTT
4711300 ATTTTGTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 8 0.30
12 7 0.26
13 12 0.44
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTTTTTAAAT
Found at i:4711286 original size:14 final size:13
Alignment explanation
Indices: 4711269--4711304 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
4711259 ATTTTTTTTA
4711269 TTTTTTTTTAAAT
1 TTTTTTTTTAAAT
*
4711282 TTTTTATTTAAAT
1 TTTTTTTTTAAAT
4711295 TTTTTATTTT
1 TTTTT-TTTT
4711305 GTTGTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 17 0.85
14 3 0.15
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTTTTTTAAAT
Found at i:4714502 original size:5 final size:5
Alignment explanation
Indices: 4714490--4714523 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
4714480 ATTTTTGGGA
* *
4714490 AAAAT AGAAT AGAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
4714524 AGATTAAGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:4715741 original size:19 final size:20
Alignment explanation
Indices: 4715714--4715764 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 20
4715704 AAATATAAAA
4715714 TTTGAAATTTTT-ATAAA-TAT
1 TTTG-AATTTTTGA-AAATTAT
4715734 TTTGAATTTTTGAAAATTAT
1 TTTGAATTTTTGAAAATTAT
4715754 TTTGAATTTTT
1 TTTGAATTTTT
4715765 TTTTGTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.34
20 19 0.66
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (20 bp):
TTTGAATTTTTGAAAATTAT
Found at i:4717522 original size:24 final size:24
Alignment explanation
Indices: 4717492--4717539 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
4717482 GAAAGTTGAA
* *
4717492 AATAAAT-AAATAAAATAACAAAAT
1 AATAAATGAAA-AAAAGAAAAAAAT
4717516 AATAAATGAAAAAAAGAAAAAAAT
1 AATAAATGAAAAAAAGAAAAAAAT
4717540 TTGAAGTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.77, C:0.02, G:0.04, T:0.17
Consensus pattern (24 bp):
AATAAATGAAAAAAAGAAAAAAAT
Found at i:4723441 original size:43 final size:44
Alignment explanation
Indices: 4723338--4723450 Score: 135
Period size: 44 Copynumber: 2.6 Consensus size: 44
4723328 TGTGTTATCG
* *
4723338 TGTAAGACCACATCTGAGAC-GTTGACATCGACTTGTGACTTACA
1 TGTAAGACCACATCTGGGACAG-TGGCATCGACTTGTGACTTACA
*
4723382 TGTAAGACC-CTGTCTGGGACAGTGGCATCGA-TATGTGA-TTACA
1 TGTAAGACCAC-ATCTGGGACAGTGGCATCGACT-TGTGACTTACA
*
4723425 TGTAAGACCACATCTGGGACAATGGC
1 TGTAAGACCACATCTGGGACAGTGGC
4723451 GTTGTACGAA
Statistics
Matches: 60, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
43 29 0.48
44 30 0.50
45 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (44 bp):
TGTAAGACCACATCTGGGACAGTGGCATCGACTTGTGACTTACA
Found at i:4727120 original size:36 final size:36
Alignment explanation
Indices: 4727073--4727391 Score: 215
Period size: 36 Copynumber: 8.0 Consensus size: 36
4727063 GCTAAGCTAC
4727073 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
*
4727109 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAG
1 CACTTATCACTTTGTCACTTGATCAGATAA--GTA--T--AG
* * * *
4727151 CTACCACTTATCACTTTGTCTCTTAATCAGATAAGTGTTG
1 ----CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
*
4727191 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAG
1 CACTTATCACTTTGTCACTTGATCAGATAA--GTA--T--AG
* * * *
4727233 CTACCACTTATCACTTTGTCTCTTAATCAGATAAGTGTTG
1 ----CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
*
4727273 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAG
1 CACTTATCACTTTGTCACTTGATCAGATAA--GTA--T--AG
* * * *
4727315 CTACCACTTATCACTTTGTCTCTTAATCAGATAAGTGTTG
1 ----CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
* *
4727355 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
4727391 C
1 C
4727392 TAAAGCTACC
Statistics
Matches: 223, Mismatches: 30, Indels: 60
0.71 0.10 0.19
Matches are distributed among these distances:
36 116 0.52
38 7 0.03
40 6 0.03
42 7 0.03
44 6 0.03
46 81 0.36
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (36 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
Found at i:4727160 original size:46 final size:46
Alignment explanation
Indices: 4727109--4727427 Score: 329
Period size: 46 Copynumber: 7.6 Consensus size: 46
4727099 ATAAGTATAG
4727109 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* * *
4727155 CACTTATCACTTTGTCTCTTAATCAGATAAGTGT---T---G----
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
4727191 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* * *
4727237 CACTTATCACTTTGTCTCTTAATCAGATAAGTGT---T---G----
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
4727273 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* * *
4727319 CACTTATCACTTTGTCTCTTAATCAGATAAGTGT---T---G----
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
4727355 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
4727401 CACTTATCACTTTATCTCTTGATCAGA
1 CACTTATCACTTTTTCACTTGATCAGA
4727428 AGTACTCAAA
Statistics
Matches: 223, Mismatches: 20, Indels: 60
0.74 0.07 0.20
Matches are distributed among these distances:
36 93 0.42
39 3 0.01
40 3 0.01
42 3 0.01
43 3 0.01
46 118 0.53
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (46 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:4727168 original size:82 final size:82
Alignment explanation
Indices: 4727030--4727427 Score: 703
Period size: 82 Copynumber: 4.9 Consensus size: 82
4727020 TACGTATGAT
* * *
4727030 CACTTATCA-TTTGTC-CCTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTTGTCACT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
* * *
4727092 TGATCAGATAAGTATAG
66 TAATCAGATAAGTGTTG
4727109 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
4727174 TAATCAGATAAGTGTTG
66 TAATCAGATAAGTGTTG
4727191 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
4727256 TAATCAGATAAGTGTTG
66 TAATCAGATAAGTGTTG
4727273 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
4727338 TAATCAGATAAGTGTTG
66 TAATCAGATAAGTGTTG
*
4727355 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCTCT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
*
4727420 TGATCAGA
66 TAATCAGA
4727428 AGTACTCAAA
Statistics
Matches: 308, Mismatches: 8, Indels: 3
0.97 0.03 0.01
Matches are distributed among these distances:
79 9 0.03
80 5 0.02
81 20 0.06
82 274 0.89
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.37
Consensus pattern (82 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
TAATCAGATAAGTGTTG
Found at i:4727901 original size:13 final size:13
Alignment explanation
Indices: 4727885--4727912 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4727875 AACCGCAACA
4727885 CCAAACCCTAATT
1 CCAAACCCTAATT
4727898 CCAAACCCTAATT
1 CCAAACCCTAATT
4727911 CC
1 CC
4727913 CAACTTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.43, G:0.00, T:0.21
Consensus pattern (13 bp):
CCAAACCCTAATT
Found at i:4729269 original size:21 final size:21
Alignment explanation
Indices: 4729240--4729280 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
4729230 ATTTCTGATG
4729240 GTAAAGTGTGATGGCTTGCTA
1 GTAAAGTGTGATGGCTTGCTA
*
4729261 GTAAGGTGTGATGGCTTGCT
1 GTAAAGTGTGATGGCTTGCT
4729281 GTTCAGAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.10, G:0.37, T:0.34
Consensus pattern (21 bp):
GTAAAGTGTGATGGCTTGCTA
Found at i:4733264 original size:61 final size:60
Alignment explanation
Indices: 4733169--4733288 Score: 204
Period size: 61 Copynumber: 2.0 Consensus size: 60
4733159 CTAAGCTGAT
* *
4733169 TGCATTGTAAGCGTGGTCTGATCACAGGAAGCCAACAGCATCTGGCATGGTCCATTACCAA
1 TGCATTGTAAGCGTGGTATGATCACAGGAAGCCAACAGCATCGGGCAT-GTCCATTACCAA
*
4733230 TGCATTGTAAGTGTGGTATGATCACAGGAAGCCAACAGCATCGGGCATGTCCATTACCA
1 TGCATTGTAAGCGTGGTATGATCACAGGAAGCCAACAGCATCGGGCATGTCCATTACCA
4733289 TCCGGACTCA
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
60 11 0.20
61 45 0.80
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.23
Consensus pattern (60 bp):
TGCATTGTAAGCGTGGTATGATCACAGGAAGCCAACAGCATCGGGCATGTCCATTACCAA
Found at i:4750282 original size:3 final size:3
Alignment explanation
Indices: 4750274--4750299 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4750264 GAGGGAGAAT
4750274 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
4750300 CATTGAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:4754277 original size:247 final size:252
Alignment explanation
Indices: 4753824--4754280 Score: 753
Period size: 247 Copynumber: 1.8 Consensus size: 252
4753814 TAAATTACTG
*
4753824 AAATATTGGTATTATGTGGGTTCTTTATAGATTTAGTTTCTTTCTAATCCCTATATTTTCTTAAA
1 AAATATTGGTATTA-GTGGGTTCATTATAGATTTAGTTTCTTTCTAAT--CTATATTTTCTTAAA
*
4753889 TGTGAATTTTTGATTATGAGACACATTCTTTGTTAAATAATTTCACGATATATACATCTAAATAA
63 TGTGAATTTTAGATTATGAGACACATTCTTTGTTAAATAATTTCACGATATATACATCTAAATAA
** *
4753954 TTTTTACAATTTTTTTTGTACATTTAAGAAAAGACACGAAAGATGCTGACATACAAATGCTGCAT
128 TTTTTACAATCCTTTTTGTACATTTAAGAAAAGACACGAAAGATGCCGACATACAAATGCTGCAT
*
4754019 TATGCCATGTTTAATCATTGAGTTCTTATTTGATCATTTCACTGTTAATTGGTCACAATT
193 TATGACATGTTTAATCATTGAGTTCTTATTTGATCATTTCACTGTTAATTGGTCACAATT
4754079 AAATATTGGTATTA-TGGGTTCATTATAGATTTAGTTTCTTTCT-AT-TATATTTTCTTAAATGT
1 AAATATTGGTATTAGTGGGTTCATTATAGATTTAGTTTCTTTCTAATCTATATTTTCTTAAATGT
* * *
4754141 GAATTTTAGATTATGAGACA-TTTTTTTGTTAAATAATTTCACGATATATACATCTAAATATTTT
66 GAATTTTAGATTATGAGACACATTCTTTGTTAAATAATTTCACGATATATACATCTAAATAATTT
* *
4754205 TTACAA-CCTTTTTGTACATTTAAGAAAAGACACGAAAGATGCCGAGATATAAATGCTGCATTAT
131 TTACAATCCTTTTTGTACATTTAAGAAAAGACACGAAAGATGCCGACATACAAATGCTGCATTAT
4754269 GACATGTTTAAT
196 GACATGTTTAAT
4754281 AAGCCATGTT
Statistics
Matches: 191, Mismatches: 11, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
247 64 0.34
248 47 0.25
249 36 0.19
252 2 0.01
253 28 0.15
255 14 0.07
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (252 bp):
AAATATTGGTATTAGTGGGTTCATTATAGATTTAGTTTCTTTCTAATCTATATTTTCTTAAATGT
GAATTTTAGATTATGAGACACATTCTTTGTTAAATAATTTCACGATATATACATCTAAATAATTT
TTACAATCCTTTTTGTACATTTAAGAAAAGACACGAAAGATGCCGACATACAAATGCTGCATTAT
GACATGTTTAATCATTGAGTTCTTATTTGATCATTTCACTGTTAATTGGTCACAATT
Found at i:4761699 original size:88 final size:88
Alignment explanation
Indices: 4761550--4761722 Score: 233
Period size: 88 Copynumber: 2.0 Consensus size: 88
4761540 TTTTTAATAT
* *
4761550 GAGAAGATAATAACTAAATTTCAATTCTAATTCCTCTAGTTTCTATGGTTAAATTTCAGTTTTGA
1 GAGAAGATAATAACTAAATTTCAATTCTAATTCCTCAAATTTCTATGGTTAAATTTCAGTTTTGA
*
4761615 TCCTTATATATCACTCAAATTTC
66 TCCCTATATATCACTCAAATTTC
** * *
4761638 GAGAAGATAATTGCTAAATTTCAATTCTAA-TCATTCAAATTTTTATGGTTAAATATT-AGTTTT
1 GAGAAGATAATAACTAAATTTCAATTCTAATTC-CTCAAATTTCTATGGTTAAAT-TTCAGTTTT
* *
4761701 GATCCCTATATTTCAGTCAAAT
64 GATCCCTATATATCACTCAAAT
4761723 CTATAACCCT
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
87 2 0.03
88 70 0.95
89 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (88 bp):
GAGAAGATAATAACTAAATTTCAATTCTAATTCCTCAAATTTCTATGGTTAAATTTCAGTTTTGA
TCCCTATATATCACTCAAATTTC
Found at i:4764225 original size:30 final size:31
Alignment explanation
Indices: 4764153--4764230 Score: 88
Period size: 30 Copynumber: 2.5 Consensus size: 31
4764143 ATTCTATATT
*
4764153 AAATATAAATATAAATTTATTATTATTTAATCA
1 AAATATAATTAT-AA-TTATTATTATTTAATCA
*
4764186 AAATGTAATTATAATT-TTATTATTTAAT-A
1 AAATATAATTATAATTATTATTATTTAATCA
*
4764215 CAAATATAATTTTAAT
1 -AAATATAATTATAAT
4764231 AATTTGAAGT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 1 0.03
30 25 0.62
31 2 0.05
32 2 0.05
33 10 0.25
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (31 bp):
AAATATAATTATAATTATTATTATTTAATCA
Found at i:4766383 original size:14 final size:15
Alignment explanation
Indices: 4766364--4766393 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4766354 TCGGCTCTCC
4766364 ACTTA-TTAATTACA
1 ACTTATTTAATTACA
4766378 ACTTATTTAATTACA
1 ACTTATTTAATTACA
4766393 A
1 A
4766394 AGTTATTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.43
Consensus pattern (15 bp):
ACTTATTTAATTACA
Found at i:4774364 original size:20 final size:20
Alignment explanation
Indices: 4774339--4774379 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
4774329 GCTTTCTCTT
4774339 TCCTTGTGTACTTTTTGGTA
1 TCCTTGTGTACTTTTTGGTA
4774359 TCCTTGTGTACTTTTTGGTA
1 TCCTTGTGTACTTTTTGGTA
4774379 T
1 T
4774380 AATATGTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.10, C:0.15, G:0.20, T:0.56
Consensus pattern (20 bp):
TCCTTGTGTACTTTTTGGTA
Found at i:4774387 original size:19 final size:20
Alignment explanation
Indices: 4774345--4774388 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
4774335 TCTTTCCTTG
** *
4774345 TGTACTTTTTGGTATCCTTG
1 TGTACTTTTTGGTATCAATA
4774365 TGTACTTTTTGGTAT-AATA
1 TGTACTTTTTGGTATCAATA
4774384 TGTAC
1 TGTAC
4774389 ATCCAAGGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.18, C:0.11, G:0.18, T:0.52
Consensus pattern (20 bp):
TGTACTTTTTGGTATCAATA
Done.