Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 16 of 199
Found at i:5366842 original size:6 final size:6
Alignment explanation
Indices: 5366810--5366860 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
5366800 AGGGGTTACG
* * * * *
5366810 GGTTCG GGTT-T GGGTCT GGTACT GGTTCA GGTTCT GGTTCT GGTTAT
1 GGTTCT GGTTCT GGTTCT GGTTCT GGTTCT GGTTCT GGTTCT GGTTCT
5366857 GGTT
1 GGTT
5366861 ATGGGAGTGG
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
5 3 0.08
6 33 0.92
ACGTcount: A:0.06, C:0.12, G:0.39, T:0.43
Consensus pattern (6 bp):
GGTTCT
Found at i:5366942 original size:18 final size:18
Alignment explanation
Indices: 5366892--5366943 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 18
5366882 GTGGTGGATA
* *
5366892 TGGTGCTGGAAGTGGAAC
1 TGGTGGTGGAAGTGGTAC
* ** *
5366910 CGGTGGTGGTGGTGGTTC
1 TGGTGGTGGAAGTGGTAC
5366928 TGGTGGTGGAAGTGGT
1 TGGTGGTGGAAGTGGT
5366944 GGTGGTGGTT
Statistics
Matches: 25, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.12, C:0.08, G:0.52, T:0.29
Consensus pattern (18 bp):
TGGTGGTGGAAGTGGTAC
Found at i:5367444 original size:24 final size:24
Alignment explanation
Indices: 5367412--5367459 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
5367402 TTAATTGAGA
5367412 CAATTAATTCTAACGGTGTATAAT
1 CAATTAATTCTAACGGTGTATAAT
*
5367436 CAATTAATTCTGACGGTGTATAAT
1 CAATTAATTCTAACGGTGTATAAT
5367460 GTGATAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (24 bp):
CAATTAATTCTAACGGTGTATAAT
Found at i:5368670 original size:120 final size:120
Alignment explanation
Indices: 5368457--5368700 Score: 488
Period size: 120 Copynumber: 2.0 Consensus size: 120
5368447 AGTGACTGTA
5368457 ATTTATGTGAGATAATAATGTATAACAAACATGGTGATGAGTGAATTTATCATTATTGAACAATA
1 ATTTATGTGAGATAATAATGTATAACAAACATGGTGATGAGTGAATTTATCATTATTGAACAATA
5368522 GTGGATTTTCAATGCTCTTTCAATGTTTAAACAACCTTCTGAATTTTTATTTTTT
66 GTGGATTTTCAATGCTCTTTCAATGTTTAAACAACCTTCTGAATTTTTATTTTTT
5368577 ATTTATGTGAGATAATAATGTATAACAAACATGGTGATGAGTGAATTTATCATTATTGAACAATA
1 ATTTATGTGAGATAATAATGTATAACAAACATGGTGATGAGTGAATTTATCATTATTGAACAATA
5368642 GTGGATTTTCAATGCTCTTTCAATGTTTAAACAACCTTCTGAATTTTTATTTTTT
66 GTGGATTTTCAATGCTCTTTCAATGTTTAAACAACCTTCTGAATTTTTATTTTTT
5368697 ATTT
1 ATTT
5368701 TTGTATGAAA
Statistics
Matches: 124, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 124 1.00
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (120 bp):
ATTTATGTGAGATAATAATGTATAACAAACATGGTGATGAGTGAATTTATCATTATTGAACAATA
GTGGATTTTCAATGCTCTTTCAATGTTTAAACAACCTTCTGAATTTTTATTTTTT
Found at i:5388686 original size:21 final size:20
Alignment explanation
Indices: 5388648--5388686 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
5388638 TCTATCAGAA
*
5388648 AAATGGGATGAGGTAAAAAC
1 AAATGGGATGAGGAAAAAAC
*
5388668 AAATGAGGATGATGAAAAA
1 AAATG-GGATGAGGAAAAA
5388687 TGCATCAACG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.54, C:0.03, G:0.28, T:0.15
Consensus pattern (20 bp):
AAATGGGATGAGGAAAAAAC
Found at i:5390977 original size:20 final size:22
Alignment explanation
Indices: 5390952--5390994 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
5390942 CATAGTGAAG
*
5390952 AAAGAGAGA-ATAAAA-TATAA
1 AAAGAGAAACATAAAACTATAA
5390972 AAAGAGAAACATAAAACTATAA
1 AAAGAGAAACATAAAACTATAA
5390994 A
1 A
5390995 TAGTTTTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 6 0.30
22 6 0.30
ACGTcount: A:0.70, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAAGAGAAACATAAAACTATAA
Found at i:5393508 original size:17 final size:19
Alignment explanation
Indices: 5393486--5393529 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
5393476 ACTTTATACT
5393486 ATTATTTT-T-ATTTTTTA
1 ATTATTTTATAATTTTTTA
5393503 ATTATTTTTATAATTTTTTA
1 ATTA-TTTTATAATTTTTTA
5393523 ATTATTT
1 ATTATTT
5393530 ATACTGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.17
18 4 0.17
19 4 0.17
20 12 0.50
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (19 bp):
ATTATTTTATAATTTTTTA
Found at i:5393516 original size:12 final size:11
Alignment explanation
Indices: 5393493--5393529 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
5393483 ACTATTATTT
5393493 TTATTTTTTAA
1 TTATTTTTTAA
5393504 TTA-TTTTT-A
1 TTATTTTTTAA
*
5393513 TAATTTTTTAA
1 TTATTTTTTAA
5393524 TTATTT
1 TTATTT
5393530 ATACTGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 3 0.14
10 10 0.45
11 9 0.41
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TTATTTTTTAA
Found at i:5398662 original size:12 final size:12
Alignment explanation
Indices: 5398645--5398669 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5398635 TTCTCCTTTG
5398645 ATGAATTTAACA
1 ATGAATTTAACA
5398657 ATGAATTTAACA
1 ATGAATTTAACA
5398669 A
1 A
5398670 CACAAACAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (12 bp):
ATGAATTTAACA
Found at i:5400905 original size:23 final size:23
Alignment explanation
Indices: 5400857--5400906 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
5400847 TATTTATATC
* * *
5400857 ATATAAGAATTAAACATATAATA
1 ATATAAGAAATAAAAATATAAAA
5400880 ATATAA-AAATAAAAATATTAAAA
1 ATATAAGAAATAAAAATA-TAAAA
5400903 ATAT
1 ATAT
5400907 TTACTCTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (23 bp):
ATATAAGAAATAAAAATATAAAA
Found at i:5403920 original size:17 final size:17
Alignment explanation
Indices: 5403894--5403934 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
5403884 AAAACCAAAT
*
5403894 CAGTTTATTAGAAATAA
1 CAGTTCATTAGAAATAA
*
5403911 CAGTTCATTAGACATAA
1 CAGTTCATTAGAAATAA
*
5403928 CAATTCA
1 CAGTTCA
5403935 CACACACAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.32
Consensus pattern (17 bp):
CAGTTCATTAGAAATAA
Found at i:5414602 original size:8 final size:9
Alignment explanation
Indices: 5414573--5414603 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
5414563 AATTTAAAAA
5414573 AAAATATTT
1 AAAATATTT
5414582 AAAATATTT
1 AAAATATTT
5414591 AAAATA-TT
1 AAAATATTT
5414599 AAAAT
1 AAAAT
5414604 CTGTTCAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (9 bp):
AAAATATTT
Found at i:5416515 original size:189 final size:193
Alignment explanation
Indices: 5416050--5416630 Score: 625
Period size: 189 Copynumber: 3.0 Consensus size: 193
5416040 ATGCTAATTT
*** * * *
5416050 ACAAATCCGGATCGAAAACTTGGGCTATAAAGTCGTATATTAGTTGCTCGAAAACTCTGATTTAG
1 ACAAATCCGGATCGAAAACTCATGTTATAAAGTCGTATAGTAGTTGCTCGAAAACTCCGATTTAG
*** * * *
5416115 TGAAAGGAAAAGAAATTTCTCTGGTGATCGATCATACATCGTTTTGAAGCTAGTTTTCTTAATCC
66 TGAAAGGAAAAGAAATTTCTCCACTGATCGATCATACATCGTTTTAAAGCAAG-GTT-TT-AT--
* * * * * *
5416180 GGGGAAGACGATTGAAAGATGTTAATGGTAACATCTTATATAAGCATCTTTAGTTGTTTGTTTAG
126 --TGAAGACGA-CGAAAGATGCTAATGGTAACATCTTGTATAAGCATCTTTAGTTGATTGTATAG
5416245 CTATGA
188 CTATGA
** * *
5416251 ACAAATCCGGATCGAAAACTTGTGTTATAAAGTCGTATATTAGTTGCTCGAAAACTCTGATTTAG
1 ACAAATCCGGATCGAAAACTCATGTTATAAAGTCGTATAGTAGTTGCTCGAAAACTCCGATTTAG
* * *
5416316 TGAAAGGAAAAGAAATTTCTCCACTGATCGATCATGCATCGTTTTAAATCAAGGTTTT-TT-AAT
66 TGAAAGGAAAAGAAATTTCTCCACTGATCGATCATACATCGTTTTAAAGCAAGGTTTTATTGAAG
* *
5416379 CCG-GGAAAGATGCTAATGGTAACATCTTGTATAAGCATCTTTAGTT-ATTGTATAGCTAT-A
131 ACGACGAAAGATGCTAATGGTAACATCTTGTATAAGCATCTTTAGTTGATTGTATAGCTATGA
* ** *
5416439 TACAATTCCGGATCGAAAACTCATGTTATAAAGTTTTATAGTAGTTGCTTGAAAACTCCGATTTA
1 -ACAAATCCGGATCGAAAACTCATGTTATAAAGTCGTATAGTAGTTGCTCGAAAACTCCGATTTA
* * ** * * *
5416504 TTTG-TAGGAAAAGAAATTTCTCCGGTGATCTATCTTACATCGTTTTAAAGCAAGTTTTTAATTC
65 -GTGAAAGGAAAAGAAATTTCTCCACTGATCGATCATACATCGTTTTAAAGCAAGGTTTT-ATT-
*
5416568 GGGGAAGACGACCGAAAGATGCTAATGGTAACATCTTGTATAAGCATCTTTAGTTGTTTGTAT
127 ---GAAGACGA-CGAAAGATGCTAATGGTAACATCTTGTATAAGCATCTTTAGTTGATTGTAT
5416631 CGGTGTTGAA
Statistics
Matches: 329, Mismatches: 39, Indels: 26
0.84 0.10 0.07
Matches are distributed among these distances:
188 1 0.00
189 114 0.35
190 42 0.13
191 2 0.01
192 4 0.01
196 4 0.01
197 1 0.00
198 42 0.13
199 8 0.02
200 2 0.01
201 109 0.33
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (193 bp):
ACAAATCCGGATCGAAAACTCATGTTATAAAGTCGTATAGTAGTTGCTCGAAAACTCCGATTTAG
TGAAAGGAAAAGAAATTTCTCCACTGATCGATCATACATCGTTTTAAAGCAAGGTTTTATTGAAG
ACGACGAAAGATGCTAATGGTAACATCTTGTATAAGCATCTTTAGTTGATTGTATAGCTATGA
Found at i:5417882 original size:17 final size:17
Alignment explanation
Indices: 5417839--5417882 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
5417829 AATAGTAATT
5417839 AAATAAATAATTATAAAA
1 AAATAAA-AATTATAAAA
** *
5417857 TTATGAAAATTATAAAA
1 AAATAAAAATTATAAAA
5417874 AAATAAAAA
1 AAATAAAAA
5417883 AATATATTAA
Statistics
Matches: 20, Mismatches: 6, Indels: 1
0.74 0.22 0.04
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (17 bp):
AAATAAAAATTATAAAA
Found at i:5418687 original size:23 final size:23
Alignment explanation
Indices: 5418660--5418707 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
5418650 ATTGAATGGA
5418660 ATTTTGTTAGGCAGTACAGTACT
1 ATTTTGTTAGGCAGTACAGTACT
5418683 ATTTTGTTAGGCAGTACAGTACT
1 ATTTTGTTAGGCAGTACAGTACT
5418706 AT
1 AT
5418708 ATAAATTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.40
Consensus pattern (23 bp):
ATTTTGTTAGGCAGTACAGTACT
Found at i:5430853 original size:21 final size:20
Alignment explanation
Indices: 5430816--5430855 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
5430806 TTGAAATAAA
*
5430816 TTTAAAAAAATTTTAAATTT
1 TTTAAAAAAATTATAAATTT
*
5430836 TTTAAGAAATATTATAAATT
1 TTTAA-AAAAATTATAAATT
5430856 ATAAAAATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
TTTAAAAAAATTATAAATTT
Found at i:5431904 original size:7 final size:7
Alignment explanation
Indices: 5431892--5431918 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
5431882 TAAAATGCAC
5431892 ATTTATT
1 ATTTATT
5431899 ATTTATT
1 ATTTATT
5431906 ATTTATT
1 ATTTATT
5431913 ATTTAT
1 ATTTAT
5431919 AAATATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
ATTTATT
Found at i:5432378 original size:152 final size:152
Alignment explanation
Indices: 5432097--5432406 Score: 611
Period size: 152 Copynumber: 2.0 Consensus size: 152
5432087 AGAATAGAGA
*
5432097 AATGAGTTGCAGATATTGAAACTCGAAACCTAATTACATGAATTCCCGGATTTCGGATTAGATTC
1 AATGGGTTGCAGATATTGAAACTCGAAACCTAATTACATGAATTCCCGGATTTCGGATTAGATTC
5432162 GGGGAATTGTACAGTACTAGGAATAAGCAACTAGAAGATGGATGCTGTATCAGACAAGCTGATGT
66 GGGGAATTGTACAGTACTAGGAATAAGCAACTAGAAGATGGATGCTGTATCAGACAAGCTGATGT
5432227 TCCGATCTGATCGACTTGTAAC
131 TCCGATCTGATCGACTTGTAAC
5432249 AATGGGTTGCAGATATTGAAACTCGAAACCTAATTACATGAATTCCCGGATTTCGGATTAGATTC
1 AATGGGTTGCAGATATTGAAACTCGAAACCTAATTACATGAATTCCCGGATTTCGGATTAGATTC
5432314 GGGGAATTGTACAGTACTAGGAATAAGCAACTAGAAGATGGATGCTGTATCAGACAAGCTGATGT
66 GGGGAATTGTACAGTACTAGGAATAAGCAACTAGAAGATGGATGCTGTATCAGACAAGCTGATGT
5432379 TCCGATCTGATCGACTTGTAAC
131 TCCGATCTGATCGACTTGTAAC
5432401 AATGGG
1 AATGGG
5432407 GTTTCCTAAA
Statistics
Matches: 157, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
152 157 1.00
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (152 bp):
AATGGGTTGCAGATATTGAAACTCGAAACCTAATTACATGAATTCCCGGATTTCGGATTAGATTC
GGGGAATTGTACAGTACTAGGAATAAGCAACTAGAAGATGGATGCTGTATCAGACAAGCTGATGT
TCCGATCTGATCGACTTGTAAC
Found at i:5439805 original size:31 final size:31
Alignment explanation
Indices: 5439767--5439834 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
5439757 TTTTTTAGTT
** *
5439767 AAATTTGATCATTTATTTTTTAAAAAGAGTC
1 AAATTTGATCATCAATTTTTAAAAAAGAGTC
*
5439798 AAATTTGATCATCAATTTTTAAAAAAGAGTT
1 AAATTTGATCATCAATTTTTAAAAAAGAGTC
5439829 AAATTT
1 AAATTT
5439835 TTAACATCTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.43
Consensus pattern (31 bp):
AAATTTGATCATCAATTTTTAAAAAAGAGTC
Found at i:5450681 original size:16 final size:16
Alignment explanation
Indices: 5450662--5450719 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
5450652 TTATGTTATT
*
5450662 TTTATATATTATATAA
1 TTTATATATTATAAAA
5450678 TTTATAGTA-TATAAAA
1 TTTATA-TATTATAAAA
* *
5450694 TTTAAATATATACAAAA
1 TTTATATAT-TATAAAA
*
5450711 TATATATAT
1 TTTATATAT
5450720 ATAGACGGCA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
15 2 0.06
16 17 0.50
17 15 0.44
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (16 bp):
TTTATATATTATAAAA
Found at i:5450791 original size:23 final size:24
Alignment explanation
Indices: 5450729--5450791 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 24
5450719 TATAGACGGC
*
5450729 ATATTATATATAAAAATTTAATAA
1 ATATTAAATATAAAAATTTAATAA
* *
5450753 ATA--AGAATATATAAATTTATTAA
1 ATATTA-AATATAAAAATTTAATAA
5450776 ATATTAAAT-TAAAAAT
1 ATATTAAATATAAAAAT
5450792 AATATAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
22 1 0.03
23 24 0.75
24 6 0.19
25 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (24 bp):
ATATTAAATATAAAAATTTAATAA
Found at i:5456446 original size:18 final size:20
Alignment explanation
Indices: 5456415--5456463 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 20
5456405 GTTTGATAAA
5456415 AATAAATA-TTATTTTT-TT
1 AATAAATATTTATTTTTATT
5456433 AA-AAATATTTATTTTTATT
1 AATAAATATTTATTTTTATT
5456452 AATATAATATTT
1 AATA-AATATTT
5456464 TATATTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 5 0.19
18 10 0.37
19 4 0.15
20 1 0.04
21 7 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
AATAAATATTTATTTTTATT
Found at i:5456460 original size:21 final size:19
Alignment explanation
Indices: 5456415--5456477 Score: 67
Period size: 18 Copynumber: 3.2 Consensus size: 19
5456405 GTTTGATAAA
5456415 AATAAATA-TTATTTTTTT
1 AATAAATATTTATTTTTTT
5456433 AA-AAATATTTATTTTTATT
1 AATAAATATTTATTTTT-TT
5456452 AATATAATATTTTATATTATTTT
1 AATA-AATA-TTTAT-TT-TTTT
5456475 AAT
1 AAT
5456478 TCATTTCGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
17 5 0.13
18 10 0.26
19 4 0.11
20 1 0.03
21 4 0.11
22 5 0.13
23 7 0.18
24 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
AATAAATATTTATTTTTTT
Found at i:5459775 original size:27 final size:27
Alignment explanation
Indices: 5459737--5459788 Score: 88
Period size: 27 Copynumber: 1.9 Consensus size: 27
5459727 TTGAATGTGA
5459737 AAGGGGCTGCTAAGTGCTGATTCCCTC
1 AAGGGGCTGCTAAGTGCTGATTCCCTC
5459764 AAGGGG-TAGCTAAGTGCTGATTCCC
1 AAGGGGCT-GCTAAGTGCTGATTCCC
5459789 CGACTCTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 1 0.04
27 23 0.96
ACGTcount: A:0.21, C:0.23, G:0.31, T:0.25
Consensus pattern (27 bp):
AAGGGGCTGCTAAGTGCTGATTCCCTC
Found at i:5459783 original size:103 final size:103
Alignment explanation
Indices: 5459660--5459864 Score: 365
Period size: 103 Copynumber: 2.0 Consensus size: 103
5459650 TATTGAATAA
* *
5459660 CAAGGGGTTGCTAAGTGCTGATTCCCCGACTTTTTGGTGGTTGCTAAGTGCTGATTCCACCATAT
1 CAAGGGGTAGCTAAGTGCTGATTCCCCGACTCTTTGGTGGTTGCTAAGTGCTGATTCCACCATAT
*
5459725 CTTTGAATGTGAAAGGGGCTGCTAAGTGCTGATTCCCT
66 CCTTGAATGTGAAAGGGGCTGCTAAGTGCTGATTCCCT
*
5459763 CAAGGGGTAGCTAAGTGCTGATTCCCCGACTCTTTGGTGGTTGCTAAGTGTTGATTCCACCATAT
1 CAAGGGGTAGCTAAGTGCTGATTCCCCGACTCTTTGGTGGTTGCTAAGTGCTGATTCCACCATAT
*
5459828 CCTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCC
66 CCTTGAATGTGAAAGGGGCTGCTAAGTGCTGATTCCC
5459865 CGAATCACTG
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 97 1.00
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.32
Consensus pattern (103 bp):
CAAGGGGTAGCTAAGTGCTGATTCCCCGACTCTTTGGTGGTTGCTAAGTGCTGATTCCACCATAT
CCTTGAATGTGAAAGGGGCTGCTAAGTGCTGATTCCCT
Found at i:5459856 original size:76 final size:77
Alignment explanation
Indices: 5459764--5459976 Score: 347
Period size: 76 Copynumber: 2.8 Consensus size: 77
5459754 TGATTCCCTC
* * ** *
5459764 AAGGGGTAGCTAAGTGCTGATTCCCCGACTCTTTGGTGGTTGCTAAGTGTTGATTCCACCATATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGATGATTCCACCATATC
*
5459829 CTTGAATGT-GA
66 CTTGAATGTAAA
5459840 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGATGATTCCACCATATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGATGATTCCACCATATC
5459905 CTTGAATGTAAA
66 CTTGAATGTAAA
* *
5459917 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGAATCCACC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGATGATTCCACC
5459977 GATAACGGTT
Statistics
Matches: 128, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
76 69 0.54
77 59 0.46
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (77 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGATGATTCCACCATATC
CTTGAATGTAAA
Found at i:5459886 original size:33 final size:34
Alignment explanation
Indices: 5459844--5459978 Score: 116
Period size: 33 Copynumber: 3.7 Consensus size: 34
5459834 ATGTGAAAGG
5459844 GGTTGCTAAGTGCTGATTCC-CCGAATCACTGGT
1 GGTTGCTAAGTGCTGATTCCACCGAATCACTGGT
*
5459877 GGTTGCTAAGTGATGATTCCACC-ATATC-CTTGAATGT
1 GGTTGCTAAGTGCTGATTCCACCGA-ATCAC-TG---GT
5459914 AAAAAGGGGTTGCTAAGTGCTGATTCC-CCGAATCACTGGT
1 -------GGTTGCTAAGTGCTGATTCCACCGAATCACTGGT
*
5459954 GGTTGCTAAGTGCTGAATCCACCGA
1 GGTTGCTAAGTGCTGATTCCACCGA
5459979 TAACGGTTAT
Statistics
Matches: 83, Mismatches: 3, Indels: 31
0.71 0.03 0.26
Matches are distributed among these distances:
33 40 0.48
34 11 0.13
37 2 0.02
40 2 0.02
43 7 0.08
44 21 0.25
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (34 bp):
GGTTGCTAAGTGCTGATTCCACCGAATCACTGGT
Found at i:5463136 original size:33 final size:34
Alignment explanation
Indices: 5463090--5463224 Score: 125
Period size: 33 Copynumber: 3.7 Consensus size: 34
5463080 ATAACCGTTA
*
5463090 TCGGTGGATTCAGCACTTAGCAACCACCAGTGAT
1 TCGGTGGAATCAGCACTTAGCAACCACCAGTGAT
5463124 TCGG-GGAATCAGCACTTAGCAACCCCTTTTTACATTCAAG-GAT
1 TCGGTGGAATCAGCACTTAGCAA--CC-----AC---C-AGTGAT
5463167 AT-GGTGGAATCAGCACTTAGCAACCACCAGTGAT
1 -TCGGTGGAATCAGCACTTAGCAACCACCAGTGAT
5463201 TCGG-GGAATCAGCACTTAGCAACC
1 TCGGTGGAATCAGCACTTAGCAACC
5463225 CCTTTCACAT
Statistics
Matches: 85, Mismatches: 1, Indels: 31
0.73 0.01 0.26
Matches are distributed among these distances:
33 40 0.47
34 10 0.12
35 2 0.02
37 2 0.02
40 2 0.02
42 2 0.02
43 6 0.07
44 21 0.25
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (34 bp):
TCGGTGGAATCAGCACTTAGCAACCACCAGTGAT
Found at i:5463219 original size:77 final size:77
Alignment explanation
Indices: 5463092--5463304 Score: 338
Period size: 76 Copynumber: 2.8 Consensus size: 77
5463082 AACCGTTATC
* *
5463092 GGTGGATTCAGCACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCTTTTTAC
1 GGTGGAATCAGCACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCTTTTCAC
5463157 ATTCAAGGATAT
66 ATTCAAGGATAT
5463169 GGTGGAATCAGCACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCC-TTTCAC
1 GGTGGAATCAGCACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCTTTTCAC
5463233 ATTCAAGGATAT
66 ATTCAAGGATAT
* * ** * * *
5463245 GGTGGAATCAACACTTAACAACCACCAAAGAGTCGGGGAATCAACACTTAGCTACCCCTT
1 GGTGGAATCAGCACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCTT
5463305 GAGGGAATCA
Statistics
Matches: 126, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
76 68 0.54
77 58 0.46
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (77 bp):
GGTGGAATCAGCACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCTTTTCAC
ATTCAAGGATAT
Found at i:5463310 original size:27 final size:27
Alignment explanation
Indices: 5463280--5463331 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
5463270 CAAAGAGTCG
*
5463280 GGGAATCAACACTTAGCTACCCCTTGA
1 GGGAATCAACACTTAGCAACCCCTTGA
*
5463307 GGGAATCAGCACTTAGCAACCCCTT
1 GGGAATCAACACTTAGCAACCCCTT
5463332 TCACGTTCAA
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:0.29, C:0.31, G:0.19, T:0.21
Consensus pattern (27 bp):
GGGAATCAACACTTAGCAACCCCTTGA
Found at i:5463322 original size:103 final size:103
Alignment explanation
Indices: 5463204--5463408 Score: 365
Period size: 103 Copynumber: 2.0 Consensus size: 103
5463194 CAGTGATTCG
5463204 GGGAATCAGCACTTAGCAACCCCTTTCACATTCAAGGATATGGTGGAATCAACACTTAACAACCA
1 GGGAATCAGCACTTAGCAACCCCTTTCACATTCAAGGATATGGTGGAATCAACACTTAACAACCA
*
5463269 CCAAAGAGTCGGGGAATCAACACTTAGCTACCCCTTGA
66 CCAAAGAGTCGGGGAATCAACACTTAGCAACCCCTTGA
* * *
5463307 GGGAATCAGCACTTAGCAACCCCTTTCACGTTCAAGGATATGGTGGAATCAGCACTTAGCAACCA
1 GGGAATCAGCACTTAGCAACCCCTTTCACATTCAAGGATATGGTGGAATCAACACTTAACAACCA
*
5463372 CCAAAGAGTCGGGGAATCAGCACTTAGCAACCCCTTG
66 CCAAAGAGTCGGGGAATCAACACTTAGCAACCCCTTG
5463409 TTATTCAATA
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 97 1.00
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.20
Consensus pattern (103 bp):
GGGAATCAGCACTTAGCAACCCCTTTCACATTCAAGGATATGGTGGAATCAACACTTAACAACCA
CCAAAGAGTCGGGGAATCAACACTTAGCAACCCCTTGA
Found at i:5465136 original size:29 final size:30
Alignment explanation
Indices: 5465082--5465141 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
5465072 GACCTGAACT
**
5465082 TTAAAATATAAAAAGTAAAATTTTAAATTC
1 TTAAAATATAAAAAGTAAAAAATTAAATTC
5465112 TTAAAA-ATAAAAA-TATAAAAATTAAATTC
1 TTAAAATATAAAAAGTA-AAAAATTAAATTC
5465141 T
1 T
5465142 AAATTCTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 2 0.07
29 19 0.70
30 6 0.22
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (30 bp):
TTAAAATATAAAAAGTAAAAAATTAAATTC
Found at i:5468557 original size:20 final size:20
Alignment explanation
Indices: 5468519--5468558 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
5468509 AATATTTTCT
* *
5468519 AGTAAATCATTTTATAGAAA
1 AGTAAAACATTTTACAGAAA
*
5468539 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
5468559 TCATTTTAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:5470855 original size:13 final size:13
Alignment explanation
Indices: 5470837--5470861 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5470827 AAAGTATTTT
5470837 AAAAATAAAAAAG
1 AAAAATAAAAAAG
5470850 AAAAATAAAAAA
1 AAAAATAAAAAA
5470862 TATATATTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.04, T:0.08
Consensus pattern (13 bp):
AAAAATAAAAAAG
Found at i:5470859 original size:30 final size:30
Alignment explanation
Indices: 5470801--5470859 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
5470791 ATTAAAAATT
***
5470801 TATTTTAAAAATAAAAAAATATTTTAAAAG
1 TATTTTAAAAATAAAAAAATAAAATAAAAG
5470831 TATTTTAAAAATAAAAAAGA-AAAATAAAA
1 TATTTTAAAAATAAAAAA-ATAAAATAAAA
5470860 AATATATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (30 bp):
TATTTTAAAAATAAAAAAATAAAATAAAAG
Found at i:5473241 original size:15 final size:12
Alignment explanation
Indices: 5473212--5473237 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5473202 TATAAATGTC
5473212 AATTTTATTATA
1 AATTTTATTATA
5473224 AATTTTATTATA
1 AATTTTATTATA
5473236 AA
1 AA
5473238 AAATATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
AATTTTATTATA
Found at i:5481105 original size:31 final size:31
Alignment explanation
Indices: 5481052--5481110 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
5481042 ATTCAAGTTA
* * *
5481052 GGTCTTGAACTTGATAATTATTCCCACACTG
1 GGTCTTGAACTAGACAACTATTCCCACACTG
*
5481083 GGTCTTGAACTAGACAACTATTCTCACA
1 GGTCTTGAACTAGACAACTATTCCCACA
5481111 TTAGAGCTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (31 bp):
GGTCTTGAACTAGACAACTATTCCCACACTG
Found at i:5485643 original size:18 final size:17
Alignment explanation
Indices: 5485620--5485654 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5485610 GGCTTGGTTG
5485620 CCTCAGGATCATCTATCT
1 CCTCAGGATCATC-ATCT
*
5485638 CCTCAGGCTCATCATCT
1 CCTCAGGATCATCATCT
5485655 AACCATCCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.20, C:0.37, G:0.11, T:0.31
Consensus pattern (17 bp):
CCTCAGGATCATCATCT
Found at i:5488776 original size:12 final size:12
Alignment explanation
Indices: 5488759--5488787 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
5488749 TTATATTTAT
5488759 TTAATGTTAATG
1 TTAATGTTAATG
5488771 TTAATGTTAATG
1 TTAATGTTAATG
5488783 TTAAT
1 TTAAT
5488788 ATAATATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (12 bp):
TTAATGTTAATG
Found at i:5488857 original size:59 final size:59
Alignment explanation
Indices: 5488794--5488918 Score: 164
Period size: 59 Copynumber: 2.1 Consensus size: 59
5488784 TAATATAATA
* * *
5488794 TAAATTTTAAAT-TTATTATTATATTTTTTTGAAAAATATTTTTCT-TATTTATATATTTT
1 TAAATTTTAAATATTATTATTAT-TTCTTGTCAAAAATATTTTT-TATATTTATATATTTT
* * *
5488853 TAAATTTTATATATTATTATTATTTCTTGTCAACAATATTTTTTATTTTTATATATTTT
1 TAAATTTTAAATATTATTATTATTTCTTGTCAAAAATATTTTTTATATTTATATATTTT
5488912 TAAATTT
1 TAAATTT
5488919 ATTTTTTAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
58 1 0.02
59 47 0.81
60 10 0.17
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (59 bp):
TAAATTTTAAATATTATTATTATTTCTTGTCAAAAATATTTTTTATATTTATATATTTT
Found at i:5489782 original size:9 final size:9
Alignment explanation
Indices: 5489768--5489893 Score: 55
Period size: 9 Copynumber: 13.8 Consensus size: 9
5489758 TTTCCCATAA
5489768 AAAAATTAT
1 AAAAATTAT
*
5489777 AAAAATTCAG
1 AAAAATT-AT
5489787 AAAAATTAT
1 AAAAATTAT
*
5489796 AAAAATATTT
1 AAAAAT-TAT
*
5489806 TAAAATTCAT
1 AAAAATT-AT
*
5489816 TAAAA-T-T
1 AAAAATTAT
*
5489823 AATAATTAAT
1 AAAAATT-AT
**
5489833 AAACCTTAT
1 AAAAATTAT
*
5489842 AAATATTAT
1 AAAAATTAT
5489851 -AAAA-TAT
1 AAAAATTAT
*
5489858 AATAAA-TCT
1 AA-AAATTAT
* *
5489867 AATAATTTT
1 AAAAATTAT
5489876 CAATAAATTAT
1 -AA-AAATTAT
5489887 AAAAATT
1 AAAAATT
5489894 TTATAAGATT
Statistics
Matches: 88, Mismatches: 18, Indels: 22
0.69 0.14 0.17
Matches are distributed among these distances:
7 7 0.08
8 7 0.08
9 39 0.44
10 30 0.34
11 5 0.06
ACGTcount: A:0.58, C:0.05, G:0.01, T:0.37
Consensus pattern (9 bp):
AAAAATTAT
Found at i:5489810 original size:29 final size:30
Alignment explanation
Indices: 5489764--5489823 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
5489754 TTATTTTCCC
5489764 ATAAAAAAATTATAAAAATTCAGAAAAATT
1 ATAAAAAAATTATAAAAATTCAGAAAAATT
* * **
5489794 ATAAAAATATT-TTAAAATTCATTAAAATT
1 ATAAAAAAATTATAAAAATTCAGAAAAATT
5489823 A
1 A
5489824 ATAATTAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (30 bp):
ATAAAAAAATTATAAAAATTCAGAAAAATT
Found at i:5494701 original size:19 final size:19
Alignment explanation
Indices: 5494677--5494713 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
5494667 AAAGTTGTAG
5494677 ATTTAATTTATGTATTTTA
1 ATTTAATTTATGTATTTTA
5494696 ATTTAATTTATGTATTTT
1 ATTTAATTTATGTATTTT
5494714 GTGAAAGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (19 bp):
ATTTAATTTATGTATTTTA
Found at i:5501109 original size:23 final size:23
Alignment explanation
Indices: 5501053--5501103 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
5501043 TTTTTATTAG
**
5501053 ATAATAATTTTAAATATTAAGTT
1 ATAATAATAATAAATATTAAGTT
* *
5501076 ATTATAATAATAAATATTATGTT
1 ATAATAATAATAAATATTAAGTT
5501099 ATAAT
1 ATAAT
5501104 TTTAATTAGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (23 bp):
ATAATAATAATAAATATTAAGTT
Found at i:5508401 original size:24 final size:23
Alignment explanation
Indices: 5508343--5508401 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 23
5508333 CAGTTCTTGT
* *
5508343 ACTCTTCCAATTTTTAAAATTTA
1 ACTCTTCCACTTTTCAAAATTTA
*
5508366 ATCTCTT-GACTTTTCAAATATTTA
1 A-CTCTTCCACTTTTCAAA-ATTTA
*
5508390 ACTCTTCTACTT
1 ACTCTTCCACTT
5508402 ATTTGATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
23 14 0.48
24 15 0.52
ACGTcount: A:0.29, C:0.20, G:0.02, T:0.49
Consensus pattern (23 bp):
ACTCTTCCACTTTTCAAAATTTA
Found at i:5508482 original size:24 final size:23
Alignment explanation
Indices: 5508454--5508498 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
5508444 TTAAGACACA
5508454 TTATAAATAAATTAATAAATAATT
1 TTATAAATAAATTAA-AAATAATT
**
5508478 TTATAAATTCATTAAAAATAA
1 TTATAAATAAATTAAAAATAA
5508499 ATATAACCGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
TTATAAATAAATTAAAAATAATT
Found at i:5514984 original size:11 final size:11
Alignment explanation
Indices: 5514953--5514977 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5514943 TGTTATCATT
5514953 TTGCTATTATA
1 TTGCTATTATA
5514964 TTGCTATTATA
1 TTGCTATTATA
5514975 TTG
1 TTG
5514978 TTGTTATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.08, G:0.12, T:0.56
Consensus pattern (11 bp):
TTGCTATTATA
Found at i:5522096 original size:33 final size:34
Alignment explanation
Indices: 5522058--5522122 Score: 89
Period size: 33 Copynumber: 1.9 Consensus size: 34
5522048 GAAGAAAACA
*
5522058 TAATATTATTAAT-TAATAGTA-AATATTCAATTT
1 TAATATTAAT-ATGTAATAGTATAATATTCAATTT
*
5522091 TAATATTAATATGTAATATTATAATATTCAAT
1 TAATATTAATATGTAATAGTATAATATTCAAT
5522123 AATATTAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 2 0.07
33 16 0.57
34 10 0.36
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (34 bp):
TAATATTAATATGTAATAGTATAATATTCAATTT
Found at i:5522354 original size:23 final size:23
Alignment explanation
Indices: 5522328--5522395 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
5522318 ATAATCTATC
**
5522328 TATATTATAATTTATAAATATTT
1 TATATTATAAAATATAAATATTT
*
5522351 TATAGTATAAAATATAAATATTT
1 TATATTATAAAATATAAATATTT
* *
5522374 TA-ATTACATAAATATAAGTATT
1 TATATTATA-AAATATAAATATT
5522396 GGTTTAAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
22 4 0.11
23 34 0.89
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (23 bp):
TATATTATAAAATATAAATATTT
Found at i:5522569 original size:14 final size:14
Alignment explanation
Indices: 5522530--5522571 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 14
5522520 TATTATGTTT
5522530 ATTTTAGAAAGAATA
1 ATTTTAGAAA-AATA
5522545 ATTTTTA-AAAAATA
1 A-TTTTAGAAAAATA
5522559 ATTTTAGAAAAAT
1 ATTTTAGAAAAAT
5522572 TTGTCAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 5 0.20
14 11 0.44
15 4 0.16
16 5 0.20
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (14 bp):
ATTTTAGAAAAATA
Found at i:5522639 original size:21 final size:22
Alignment explanation
Indices: 5522615--5522657 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
5522605 CATTCAAACA
5522615 TAAGAAAAT-ATCAATTTTTTT
1 TAAGAAAATAATCAATTTTTTT
5522636 TAAGAAAATCAATCAATTTTTT
1 TAAGAAAAT-AATCAATTTTTT
5522658 AAAAAATCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 9 0.45
23 11 0.55
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (22 bp):
TAAGAAAATAATCAATTTTTTT
Found at i:5522658 original size:21 final size:21
Alignment explanation
Indices: 5522615--5522665 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
5522605 CATTCAAACA
5522615 TAAGAAAAT-ATCAATTTTTTT
1 TAAGAAAATCATCAA-TTTTTT
5522636 TAAGAAAATCAATCAA-TTTTT
1 TAAGAAAATC-ATCAATTTTTT
5522657 TAA-AAAATC
1 TAAGAAAATC
5522666 CTTTTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.21
21 17 0.61
23 5 0.18
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.39
Consensus pattern (21 bp):
TAAGAAAATCATCAATTTTTT
Found at i:5534693 original size:12 final size:12
Alignment explanation
Indices: 5534676--5534700 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5534666 TTTTTTTTTT
5534676 AAGTTTCCATTA
1 AAGTTTCCATTA
5534688 AAGTTTCCATTA
1 AAGTTTCCATTA
5534700 A
1 A
5534701 TTATTTTTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (12 bp):
AAGTTTCCATTA
Found at i:5535213 original size:93 final size:93
Alignment explanation
Indices: 5535054--5535231 Score: 225
Period size: 93 Copynumber: 1.9 Consensus size: 93
5535044 GGTGTTACAC
* ** * * * *
5535054 GAAAAGTATAATAACTAGTCATTCTTTAATTAATTATCAAGTCAGGATTTGAAACTGAGATGATA
1 GAAAAGTACAATAACTAAACATTCTTTAATTAATCATCAAGTCAGGAGTTGAAACTGAAATAATA
*
5535119 AAATGAATCAAAATTCGAAATGTCATTT
66 AAATGAATCAAAACTCGAAATGTCATTT
* * *
5535147 GAAAAGTACAATAACTAAACATT-TTCTCATTAATCATCAAGT-TGAGAGTTGAACCTGAAATAA
1 GAAAAGTACAATAACTAAACATTCTT-TAATTAATCATCAAGTCAG-GAGTTGAAACTGAAATAA
5535210 TAAAATGAATCAAAACTCGAAA
64 TAAAATGAATCAAAACTCGAAA
5535232 GTTGGGAATT
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
92 3 0.04
93 69 0.96
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.30
Consensus pattern (93 bp):
GAAAAGTACAATAACTAAACATTCTTTAATTAATCATCAAGTCAGGAGTTGAAACTGAAATAATA
AAATGAATCAAAACTCGAAATGTCATTT
Found at i:5539394 original size:17 final size:17
Alignment explanation
Indices: 5539372--5539417 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 17
5539362 TTTTAAAATA
5539372 TTTATATTATTTTTAAT
1 TTTATATTATTTTTAAT
**
5539389 TTTATA-T-TTACTAAT
1 TTTATATTATTTTTAAT
5539404 TTTAT-TTATTTTTA
1 TTTATATTATTTTTA
5539418 TTTAAATGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 5
0.72 0.12 0.16
Matches are distributed among these distances:
15 12 0.52
16 5 0.22
17 6 0.26
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTATATTATTTTTAAT
Found at i:5541665 original size:30 final size:30
Alignment explanation
Indices: 5541631--5541687 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
5541621 TTTGATTCCC
* *
5541631 AAAAATGATAAAAATTTGATTTAATAATTT
1 AAAAATGATAAAAATTTAAATTAATAATTT
* *
5541661 AAAAATTATAAAGATTTAAATTAATAA
1 AAAAATGATAAAAATTTAAATTAATAA
5541688 AATAATATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (30 bp):
AAAAATGATAAAAATTTAAATTAATAATTT
Found at i:5544933 original size:14 final size:17
Alignment explanation
Indices: 5544902--5544938 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
5544892 ATTATAAAGG
5544902 ATATTATTAAATTAATT
1 ATATTATTAAATTAATT
5544919 ATATTA-TAAA-T-ATT
1 ATATTATTAAATTAATT
5544933 ATATTA
1 ATATTA
5544939 AGAAATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 9 0.45
15 1 0.05
16 4 0.20
17 6 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATTATTAAATTAATT
Found at i:5545149 original size:17 final size:16
Alignment explanation
Indices: 5545127--5545160 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5545117 AAGTTAAAAT
5545127 AAAAGAATAAAAGAAAC
1 AAAAGAA-AAAAGAAAC
*
5545144 AAAAGAAGAAAGAAAC
1 AAAAGAAAAAAGAAAC
5545160 A
1 A
5545161 GAATAGCCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.76, C:0.06, G:0.15, T:0.03
Consensus pattern (16 bp):
AAAAGAAAAAAGAAAC
Found at i:5545878 original size:11 final size:12
Alignment explanation
Indices: 5545855--5545897 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 12
5545845 GAGGTAAGTA
*
5545855 TAATATTAGTAT
1 TAATATTATTAT
5545867 TAAT-TTATTAT
1 TAATATTATTAT
5545878 T-ATATTATTAT
1 TAATATTATTAT
*
5545889 TATTATTAT
1 TAATATTAT
5545898 GAGTGGGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 2 0.07
11 15 0.56
12 10 0.37
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (12 bp):
TAATATTATTAT
Found at i:5546075 original size:22 final size:25
Alignment explanation
Indices: 5546032--5546108 Score: 70
Period size: 27 Copynumber: 3.1 Consensus size: 25
5546022 TGAAAATGTG
* *
5546032 TGAATTTGTGAAATAATTATTG-AT
1 TGAATGTGTGAAATAATGATTGAAT
5546056 TGAATGTG-GAAA-AATGATTGAAT
1 TGAATGTGTGAAATAATGATTGAAT
* **
5546079 TGAAAGTGTGAGAAATTGTGATTGAAT
1 TG-AA-TGTGTGAAATAATGATTGAAT
5546106 TGA
1 TGA
5546109 GAATATATGT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
22 7 0.16
23 8 0.18
24 9 0.20
25 4 0.09
26 5 0.11
27 11 0.25
ACGTcount: A:0.39, C:0.00, G:0.25, T:0.36
Consensus pattern (25 bp):
TGAATGTGTGAAATAATGATTGAAT
Found at i:5546080 original size:23 final size:24
Alignment explanation
Indices: 5546032--5546089 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
5546022 TGAAAATGTG
* *
5546032 TGAATTTGTGAAATAATTATTGAT
1 TGAATGTGTGAAATAATGATTGAT
5546056 TGAATGTG-GAAA-AATGATTGAAT
1 TGAATGTGTGAAATAATGATTG-AT
*
5546079 TGAAAGTGTGA
1 TGAATGTGTGA
5546090 GAAATTGTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 7 0.24
23 13 0.45
24 9 0.31
ACGTcount: A:0.40, C:0.00, G:0.24, T:0.36
Consensus pattern (24 bp):
TGAATGTGTGAAATAATGATTGAT
Found at i:5546311 original size:37 final size:39
Alignment explanation
Indices: 5546252--5546347 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
5546242 CGGATAGATT
* * * *
5546252 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
5546289 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
5546328 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
5546348 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:5552395 original size:14 final size:17
Alignment explanation
Indices: 5552364--5552400 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
5552354 ATTATAAAGG
5552364 ATATTATTAAATTAATT
1 ATATTATTAAATTAATT
5552381 ATATTA-TAAA-T-ATT
1 ATATTATTAAATTAATT
5552395 ATATTA
1 ATATTA
5552401 AGAAATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 9 0.45
15 1 0.05
16 4 0.20
17 6 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATTATTAAATTAATT
Found at i:5552576 original size:14 final size:14
Alignment explanation
Indices: 5552550--5552600 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
5552540 GAAAACAAAA
5552550 GAAATAAAATAAAG
1 GAAATAAAATAAAG
*
5552564 GAAATAAAGTAAAG
1 GAAATAAAATAAAG
* * *
5552578 CAAGTTAAAATAAAA
1 GAA-ATAAAATAAAG
5552593 G-AATAAAA
1 GAAATAAAA
5552601 GAAACAAAAG
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
13 5 0.17
14 16 0.55
15 8 0.28
ACGTcount: A:0.69, C:0.02, G:0.14, T:0.16
Consensus pattern (14 bp):
GAAATAAAATAAAG
Found at i:5552611 original size:17 final size:16
Alignment explanation
Indices: 5552589--5552622 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5552579 AAGTTAAAAT
5552589 AAAAGAATAAAAGAAAC
1 AAAAGAA-AAAAGAAAC
*
5552606 AAAAGAAGAAAGAAAC
1 AAAAGAAAAAAGAAAC
5552622 A
1 A
5552623 GAATAGCCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.76, C:0.06, G:0.15, T:0.03
Consensus pattern (16 bp):
AAAAGAAAAAAGAAAC
Found at i:5553537 original size:22 final size:25
Alignment explanation
Indices: 5553494--5553570 Score: 70
Period size: 27 Copynumber: 3.1 Consensus size: 25
5553484 TGAAAATGTG
* *
5553494 TGAATTTGTGAAATAATTATTG-AT
1 TGAATGTGTGAAATAATGATTGAAT
5553518 TGAATGTG-GAAA-AATGATTGAAT
1 TGAATGTGTGAAATAATGATTGAAT
* **
5553541 TGAAAGTGTGAGAAATTGTGATTGAAT
1 TG-AA-TGTGTGAAATAATGATTGAAT
5553568 TGA
1 TGA
5553571 GAATATATGT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
22 7 0.16
23 8 0.18
24 9 0.20
25 4 0.09
26 5 0.11
27 11 0.25
ACGTcount: A:0.39, C:0.00, G:0.25, T:0.36
Consensus pattern (25 bp):
TGAATGTGTGAAATAATGATTGAAT
Found at i:5553542 original size:23 final size:24
Alignment explanation
Indices: 5553494--5553551 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
5553484 TGAAAATGTG
* *
5553494 TGAATTTGTGAAATAATTATTGAT
1 TGAATGTGTGAAATAATGATTGAT
5553518 TGAATGTG-GAAA-AATGATTGAAT
1 TGAATGTGTGAAATAATGATTG-AT
*
5553541 TGAAAGTGTGA
1 TGAATGTGTGA
5553552 GAAATTGTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 7 0.24
23 13 0.45
24 9 0.31
ACGTcount: A:0.40, C:0.00, G:0.24, T:0.36
Consensus pattern (24 bp):
TGAATGTGTGAAATAATGATTGAT
Found at i:5553773 original size:37 final size:39
Alignment explanation
Indices: 5553714--5553809 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
5553704 CGGATAGATT
* * * *
5553714 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
5553751 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
5553790 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
5553810 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:5557943 original size:8 final size:9
Alignment explanation
Indices: 5557924--5558015 Score: 60
Period size: 9 Copynumber: 9.4 Consensus size: 9
5557914 AATTTGTTTT
5557924 AAAAATTAA
1 AAAAATTAA
5557933 AAAAATTAA
1 AAAAATTAA
*
5557942 AAAAGTATT-T
1 AAAA--ATTAA
*
5557952 TAAAATTAAA
1 AAAAATT-AA
5557962 AAAAATTTAA
1 AAAAA-TTAA
*
5557972 AAAGTATTTTAA
1 AAA--A-ATTAA
*
5557984 AAAAATTTA
1 AAAAATTAA
*
5557993 AAAATTTAA
1 AAAAATTAA
5558002 AAAAATTTAA
1 AAAAA-TTAA
5558012 AAAA
1 AAAA
5558016 GTATTTTAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 17
0.70 0.11 0.19
Matches are distributed among these distances:
8 3 0.05
9 27 0.42
10 21 0.33
11 5 0.08
12 8 0.12
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (9 bp):
AAAAATTAA
Found at i:5557953 original size:29 final size:29
Alignment explanation
Indices: 5557920--5558005 Score: 111
Period size: 29 Copynumber: 2.9 Consensus size: 29
5557910 CAACAATTTG
5557920 TTTTAAAAATTAAAAAAATTAAAAAAGTA
1 TTTTAAAAATTAAAAAAATTAAAAAAGTA
*
5557949 TTTT-AAAATTAAAAAAAATTTAAAAAGTA
1 TTTTAAAAATT-AAAAAAATTAAAAAAGTA
* *
5557978 TTTTAAAAAAATTTAAAAATTTAAAAAA
1 TTTT--AAAAATTAAAAAAATTAAAAAA
5558006 ATTTAAAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
28 6 0.12
29 25 0.51
31 12 0.24
32 6 0.12
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (29 bp):
TTTTAAAAATTAAAAAAATTAAAAAAGTA
Found at i:5558002 original size:41 final size:41
Alignment explanation
Indices: 5557938--5558045 Score: 155
Period size: 41 Copynumber: 2.6 Consensus size: 41
5557928 ATTAAAAAAA
5557938 TTAAAAAAGTATTTTAAAATTAAAAAAAATTT-AAAAAGTATT
1 TTAAAAAA--ATTTTAAAATTAAAAAAAATTTAAAAAAGTATT
* *
5557980 TTAAAAAAATTTAAAAATTTAAAAAAATTTAAAAAAGTATT
1 TTAAAAAAATTTTAAAATTAAAAAAAATTTAAAAAAGTATT
**
5558021 TTAAAAGTATTTTAAAATTAAAAAA
1 TTAAAAAAATTTTAAAATTAAAAAA
5558046 TAAAAATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
40 20 0.34
41 31 0.53
42 8 0.14
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (41 bp):
TTAAAAAAATTTTAAAATTAAAAAAAATTTAAAAAAGTATT
Found at i:5558008 original size:40 final size:41
Alignment explanation
Indices: 5557938--5558045 Score: 148
Period size: 40 Copynumber: 2.6 Consensus size: 41
5557928 ATTAAAAAAA
*
5557938 TTAAAAAAGTATTTTAAAATTAAAAAAAATTT-AAAAAGTATT
1 TTAAAAAA--ATTTTAAAATTTAAAAAAATTTAAAAAAGTATT
*
5557980 TTAAAAAAATTTAAAAATTTAAAAAAATTTAAAAAAGTATT
1 TTAAAAAAATTTTAAAATTTAAAAAAATTTAAAAAAGTATT
**
5558021 TTAAAAGTATTTTAAAA-TTAAAAAA
1 TTAAAAAAATTTTAAAATTTAAAAAA
5558046 TAAAAATAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
40 28 0.47
41 24 0.40
42 8 0.13
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (41 bp):
TTAAAAAAATTTTAAAATTTAAAAAAATTTAAAAAAGTATT
Found at i:5558009 original size:29 final size:28
Alignment explanation
Indices: 5557924--5558015 Score: 82
Period size: 30 Copynumber: 3.1 Consensus size: 28
5557914 AATTTGTTTT
*
5557924 AAAAATTAAAAAAATTAAAAAAGTATTTTAA
1 AAAAATT-AAAAATTTAAAAAA--ATTTTAA
*
5557955 AATTAAA--AAAAATTTAAAAAGTATTTTAA
1 AA--AAATTAAAAATTTAAAAA-AATTTTAA
5557984 AAAAATTTAAAAATTTAAAAAAA-TTTAA
1 AAAAA-TTAAAAATTTAAAAAAATTTTAA
5558012 AAAA
1 AAAA
5558016 GTATTTTAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 15
0.74 0.04 0.21
Matches are distributed among these distances:
27 3 0.06
28 9 0.17
29 10 0.19
30 25 0.48
31 2 0.04
33 3 0.06
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (28 bp):
AAAAATTAAAAATTTAAAAAAATTTTAA
Found at i:5558026 original size:11 final size:11
Alignment explanation
Indices: 5558012--5558037 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5558002 AAAAATTTAA
5558012 AAAAGTATTTT
1 AAAAGTATTTT
5558023 AAAAGTATTTT
1 AAAAGTATTTT
5558034 AAAA
1 AAAA
5558038 TTAAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:5561319 original size:15 final size:16
Alignment explanation
Indices: 5561290--5561319 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5561280 TTAATTAAAA
5561290 ATTTAAAAGTTTTCAT
1 ATTTAAAAGTTTTCAT
5561306 ATTTAAAA-TTTTCA
1 ATTTAAAAGTTTTCA
5561320 GTACAAGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (16 bp):
ATTTAAAAGTTTTCAT
Found at i:5568507 original size:11 final size:11
Alignment explanation
Indices: 5568491--5568530 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
5568481 TATTAATGCT
5568491 TGAGTTAAACA
1 TGAGTTAAACA
* *
5568502 TGAGTTAATGCT
1 TGAGTTAA-ACA
5568514 TGAGTTAAACA
1 TGAGTTAAACA
5568525 TGAGTT
1 TGAGTT
5568531 GTGATTGAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
11 15 0.62
12 9 0.38
ACGTcount: A:0.35, C:0.07, G:0.23, T:0.35
Consensus pattern (11 bp):
TGAGTTAAACA
Found at i:5568511 original size:23 final size:23
Alignment explanation
Indices: 5568483--5568530 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
5568473 AAACAACATA
5568483 TTAATGCTTGAGTTAAACATGAG
1 TTAATGCTTGAGTTAAACATGAG
5568506 TTAATGCTTGAGTTAAACATGAG
1 TTAATGCTTGAGTTAAACATGAG
5568529 TT
1 TT
5568531 GTGATTGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (23 bp):
TTAATGCTTGAGTTAAACATGAG
Found at i:5568517 original size:12 final size:12
Alignment explanation
Indices: 5568483--5568521 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
5568473 AAACAACATA
5568483 TTAATGCTTGAG
1 TTAATGCTTGAG
* *
5568495 TTAA-ACATGAG
1 TTAATGCTTGAG
5568506 TTAATGCTTGAG
1 TTAATGCTTGAG
5568518 TTAA
1 TTAA
5568522 ACATGAGTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (12 bp):
TTAATGCTTGAG
Found at i:5569793 original size:99 final size:99
Alignment explanation
Indices: 5569617--5569815 Score: 299
Period size: 99 Copynumber: 2.0 Consensus size: 99
5569607 ATAATTACCG
* * * * *
5569617 TTAAAATTAAAAATTTTAAGTGTGAACTTGAGATAGATATCATTATTATACGTTAACTTTGGACC
1 TTAAAACTAAAAATTTTAAGTGTGAACTTGAGATAAATATCATAACTATACATTAACTTTGGACC
* *
5569682 AATGTGCGCTACATGAATTTTAATCTTGTGCGAT
66 AATGTGCACTACATGAACTTTAATCTTGTGCGAT
* *
5569716 TTAAAACTACAAATTTTAAGTGTGAACTTGAGATAAATATCATAACTATATATTAACTTTGGACC
1 TTAAAACTAAAAATTTTAAGTGTGAACTTGAGATAAATATCATAACTATACATTAACTTTGGACC
* *
5569781 AATGTGCACTACATGAGCTTTAATCTTGTGGGAT
66 AATGTGCACTACATGAACTTTAATCTTGTGCGAT
5569815 T
1 T
5569816 AAATTAGAGG
Statistics
Matches: 89, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
99 89 1.00
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (99 bp):
TTAAAACTAAAAATTTTAAGTGTGAACTTGAGATAAATATCATAACTATACATTAACTTTGGACC
AATGTGCACTACATGAACTTTAATCTTGTGCGAT
Found at i:5579854 original size:26 final size:25
Alignment explanation
Indices: 5579815--5579870 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
5579805 ATCTGACTCG
*
5579815 AAAACTCAACTAACACAA-AATAATTC
1 AAAACTCAAATAAC-CAACAA-AATTC
* *
5579841 AAAACTGAAATAACCAACAAATTTC
1 AAAACTCAAATAACCAACAAAATTC
5579866 AAAAC
1 AAAAC
5579871 CTTTGAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 12 0.46
26 14 0.54
ACGTcount: A:0.59, C:0.21, G:0.02, T:0.18
Consensus pattern (25 bp):
AAAACTCAAATAACCAACAAAATTC
Found at i:5594073 original size:171 final size:170
Alignment explanation
Indices: 5593789--5594120 Score: 513
Period size: 171 Copynumber: 1.9 Consensus size: 170
5593779 TGGTTATTTC
* *
5593789 TAAATATTTTTATATGCATATATTAATTTTTTTTCCCAAAAATACGACTAAATCCAAAATGATAC
1 TAAATATTTTTATATGCATACATTAAATTTTTTTCCCAAAAATACGACTAAATCCAAAATGATAC
* *
5593854 ACCAAAACGGACCAATACTAATACACATCAGTTCCAATAAAAAAATGATGCATCCACTAGTACAA
66 ACCAAAACAGACCAATACCAATACACATCAGTTCCAATAAAAAAATGATGCATCCACTAGTACAA
*
5593919 TATGAATTACTTTGAGTAAAATTGTAAACCACATCAACCT
131 TATGAATTACCTTGAGTAAAATTGTAAACCACATCAACCT
*
5593959 TAAATATTTTTATATGCATACATTAAAAATTTTTTTCCC-AAAATATGACTAAATCCAAAATGAT
1 TAAATATTTTTATATGCATACATT--AAATTTTTTTCCCAAAAATACGACTAAATCCAAAATGAT
* ** * * *
5594023 ACACCGAATTAGACCAATACCAATACACATCAGTTTCAATAGAAAAATGATGCATTCACTAGTAC
64 ACACCAAAACAGACCAATACCAATACACATCAGTTCCAATAAAAAAATGATGCATCCACTAGTAC
* *
5594088 AATATTAATTACCTTGAGTAAAATTGTAGACCA
129 AATATGAATTACCTTGAGTAAAATTGTAAACCA
5594121 ACATTAAAAA
Statistics
Matches: 146, Mismatches: 14, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
170 23 0.16
171 111 0.76
172 12 0.08
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.31
Consensus pattern (170 bp):
TAAATATTTTTATATGCATACATTAAATTTTTTTCCCAAAAATACGACTAAATCCAAAATGATAC
ACCAAAACAGACCAATACCAATACACATCAGTTCCAATAAAAAAATGATGCATCCACTAGTACAA
TATGAATTACCTTGAGTAAAATTGTAAACCACATCAACCT
Found at i:5594830 original size:91 final size:91
Alignment explanation
Indices: 5594675--5595175 Score: 637
Period size: 91 Copynumber: 5.5 Consensus size: 91
5594665 CATCGCTGTA
* *
5594675 GGACCTCAACGAGGCAGCTAAATGTTCATTTCTATGAGCTGAAAATTGAAACAAATATGAGTTGG
1 GGACCTCAATGAGGCAGCTAAATGTTCATTTCTTTGAGCTGAAAATTGAAACAAATATGAGTTGG
**
5594740 CTACTTCTAACCTACTGATACGAAAT
66 CTACTTCTAACCTACCAATACGAAAT
* *
5594766 GGACCTCAATGAGACAGCTAAATGTTCATTTCTATGAGCTGAAAATTGAAACAAATATGAGTTGG
1 GGACCTCAATGAGGCAGCTAAATGTTCATTTCTTTGAGCTGAAAATTGAAACAAATATGAGTTGG
*
5594831 CTACTTCTAACCTACCACTACGAAAT
66 CTACTTCTAACCTACCAATACGAAAT
** * * * * * **
5594857 ATATCTCAATGAGTCAGCTAAATGTTCATTTCTTTGAGCTGAAAGA-CGAAGCAAATATGCGTCA
1 GGACCTCAATGAGGCAGCTAAATGTTCATTTCTTTGAGCTGAAA-ATTGAAACAAATATGAGTTG
*
5594921 GCTACTTCTAAGCTACCAATACGAAAT
65 GCTACTTCTAACCTACCAATACGAAAT
* * * * * *
5594948 GGATCTCAACGACGCAGCTAAATGTTCATTTCTTTGAGCTGAAAATGGAAGCAAATATGAGTCGG
1 GGACCTCAATGAGGCAGCTAAATGTTCATTTCTTTGAGCTGAAAATTGAAACAAATATGAGTTGG
*
5595013 CTACTTCTAAGCTACCAATACGAAAT
66 CTACTTCTAACCTACCAATACGAAAT
* * * * *
5595039 GGACCTCAATGAGGCAGCTACATATTCAATTCTGTGAGCTGAAAATTGAAACAAATATGAGTTGA
1 GGACCTCAATGAGGCAGCTAAATGTTCATTTCTTTGAGCTGAAAATTGAAACAAATATGAGTTGG
* ***
5595104 CTACTTTTAACCTACTGCTACGAAACT
66 CTACTTCTAACCTACCAATACGAAA-T
** * *
5595131 -GACCTTGATGTGGCAGCTAAATGTTCATTTCTTTGAGTTGAAAAT
1 GGACCTCAATGAGGCAGCTAAATGTTCATTTCTTTGAGCTGAAAAT
5595176 CGAGAGTGAA
Statistics
Matches: 358, Mismatches: 49, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
90 1 0.00
91 355 0.99
92 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (91 bp):
GGACCTCAATGAGGCAGCTAAATGTTCATTTCTTTGAGCTGAAAATTGAAACAAATATGAGTTGG
CTACTTCTAACCTACCAATACGAAAT
Found at i:5595166 original size:273 final size:273
Alignment explanation
Indices: 5594679--5595173 Score: 758
Period size: 273 Copynumber: 1.8 Consensus size: 273
5594669 GCTGTAGGAC
* * *
5594679 CTCAACGAGGCAGCTAAATGTTCATTTCTATGAGCTGAAAATTGAAACAAATATGAGTTGGCTAC
1 CTCAACGACGCAGCTAAATGTTCATTTCTATGAGCTGAAAATGGAAACAAATATGAGTCGGCTAC
** * *
5594744 TTCTAACCTACTGATACGAAATGGACCTCAATGAGACAGCTAAATGTTCATTTCTATGAGCTGAA
66 TTCTAACCTACCAATACGAAATGGACCTCAATGAGACAGCTAAATATTCAATTCTATGAGCTGAA
* * * *
5594809 AATTGAAACAAATATGAGTTGGCTACTTCTAACCTACCACTACGAAATATATCTCAATGAGTCAG
131 AATTGAAACAAATATGAGTTGACTACTTCTAACCTACCACTACGAAATAGACCTCAATGAGGCAG
5594874 CTAAATGTTCATTTCTTTGAGCTGAAAGACGAAGCAAATATGCGTCAGCTACTTCTAAGCTACCA
196 CTAAATGTTCATTTCTTTGAGCTGAAAGACGAAGCAAATATGCGTCAGCTACTTCTAAGCTACCA
5594939 ATACGAAATGGAT
261 ATACGAAATGGAT
* *
5594952 CTCAACGACGCAGCTAAATGTTCATTTCTTTGAGCTGAAAATGGAAGCAAATATGAGTCGGCTAC
1 CTCAACGACGCAGCTAAATGTTCATTTCTATGAGCTGAAAATGGAAACAAATATGAGTCGGCTAC
* * * *
5595017 TTCTAAGCTACCAATACGAAATGGACCTCAATGAGGCAGCTACATATTCAATTCTGTGAGCTGAA
66 TTCTAACCTACCAATACGAAATGGACCTCAATGAGACAGCTAAATATTCAATTCTATGAGCTGAA
* ** ** *
5595082 AATTGAAACAAATATGAGTTGACTACTTTTAACCTACTGCTACGAAACT-GACCTTGATGTGGCA
131 AATTGAAACAAATATGAGTTGACTACTTCTAACCTACCACTACGAAA-TAGACCTCAATGAGGCA
*
5595146 GCTAAATGTTCATTTCTTTGAGTTGAAA
195 GCTAAATGTTCATTTCTTTGAGCTGAAA
5595174 ATCGAGAGTG
Statistics
Matches: 197, Mismatches: 24, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
273 196 0.99
274 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (273 bp):
CTCAACGACGCAGCTAAATGTTCATTTCTATGAGCTGAAAATGGAAACAAATATGAGTCGGCTAC
TTCTAACCTACCAATACGAAATGGACCTCAATGAGACAGCTAAATATTCAATTCTATGAGCTGAA
AATTGAAACAAATATGAGTTGACTACTTCTAACCTACCACTACGAAATAGACCTCAATGAGGCAG
CTAAATGTTCATTTCTTTGAGCTGAAAGACGAAGCAAATATGCGTCAGCTACTTCTAAGCTACCA
ATACGAAATGGAT
Found at i:5595515 original size:122 final size:122
Alignment explanation
Indices: 5595088--5596589 Score: 1849
Period size: 122 Copynumber: 12.3 Consensus size: 122
5595078 TGAAAATTGA
* * * * * * ** *
5595088 AACAAATATGAGTTGACTACTTTTAACCTACTGCTACGAAACT-GACCTTGATGTGGCAGCTAAA
1 AACAAATATGAATTGGCTACTTCTAACCTACCGATAC-AAAATGGACCTCAATGAGGCAGCTAAA
* * * * *
5595152 TGTTCATTTCTTTGAGTTGAAAATCGAGAGTGAATAGGTTTTTTTGTTTCTGTAGCTCTG
65 TGTTCATTTCTGTGAGCTGAAAA-CCAAAGTGAATAGG-TTTTATGTTTCTGTAGCTCTG
* * * *
5595212 AACAAATATGAATTGGCTAGTTCTAACCTACCAATACGAAATGGACCTCAAAGAGGCAGCTAAAT
1 AACAAATATGAATTGGCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAAT
*
5595277 GTTCGTTTCTGTGAGCTG-AAACCAAAGTGAATAGGTTTTATGTTTCTGTAGCTCTG
66 GTTCATTTCTGTGAGCTGAAAACCAAAGTGAATAGGTTTTATGTTTCTGTAGCTCTG
* * * *
5595333 AACAAATATGAATTGGCTAGTTCTAACCTACCAATACGAAATGGACCTCAAAGAGGCAGCTAAAT
1 AACAAATATGAATTGGCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAAT
* *
5595398 GTTCGTTTCTGTGAGCTGAAAACCAAAGTGAATAGGTTTTATGTTTATGTAGCTCTG
66 GTTCATTTCTGTGAGCTGAAAACCAAAGTGAATAGGTTTTATGTTTCTGTAGCTCTG
* *
5595455 AACAAATATGAATTGCCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGTCAGCTAAAT
1 AACAAATATGAATTGGCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAAT
** * * * * *
5595520 GTTCATTTCCATGAGCTGAAAATCAAAGTGAATAGATTTTATGTTTCCGTAACCCTG
66 GTTCATTTCTGTGAGCTGAAAACCAAAGTGAATAGGTTTTATGTTTCTGTAGCTCTG
* * * *
5595577 AACAAATATGAATTGGCTACTTCTGACCTATCGATACGAAATGTACCTCAATGAGGCAGCTAAAT
1 AACAAATATGAATTGGCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAAT
*
5595642 GTTCATTTCTGTGAGCTGAAAATCAAAGTGAATAGGTTTTTATGTTTCTGTAGCTCTG
66 GTTCATTTCTGTGAGCTGAAAACCAAAGTGAATAGG-TTTTATGTTTCTGTAGCTCTG
* *
5595700 AACAAATATGAATTGCCTACTTCTAACCTACTGATACAAAATGGACCTCAATGAGGCAGCTAAAT
1 AACAAATATGAATTGGCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAAT
* ** * * * *
5595765 GTTCACTTCCATGAGCTGAAAACC-AA---AATAGATTTTATGTTTCAGTAACCCTG
66 GTTCATTTCTGTGAGCTGAAAACCAAAGTGAATAGGTTTTATGTTTCTGTAGCTCTG
* * * * * *
5595818 AACAAATATGTATTGGCTACTTCTGACCTACCGATACGAAATGTACCTCAATGAAGCGGCTAAAT
1 AACAAATATGAATTGGCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAAT
* *
5595883 GTTCATTTCTGTGAGCTGAAAATCAAAAGCGAATAGGTTTTTATGTTTTCTGTAGCTCTG
66 GTTCATTTCTGTGAGCTGAAAA-CCAAAGTGAATAGG-TTTTATG-TTTCTGTAGCTCTG
* * ** * * *
5595943 AACTAATAATGAATTGGCTACTTCTAACCAACCGATATGAAATAGACCTAAATGAGGCAGCAAAA
1 AACAAAT-ATGAATTGGCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAA
* * * * *
5596008 CGTTCATTTCTGTGAGATGAAAATCGAAGTGAATAGGTTTTATGTTTCTGTAGCTCTC
65 TGTTCATTTCTGTGAGCTGAAAACCAAAGTGAATAGGTTTTATGTTTCTGTAGCTCTG
** * ** * * *
5596066 AACAAATATGAATTTCCTACTTCTAACCTACCAATACAAAACAGCCCTCAATAAGCCAGCTAAAT
1 AACAAATATGAATTGGCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAAT
* * * * * *
5596131 GTTCATTCCTGTGAGCTGAAAATCGAAA-TGAATAGATTTCATGTTTCTGTAGTTGTG
66 GTTCATTTCTGTGAGCTGAAAA-CCAAAGTGAATAGGTTTTATGTTTCTGTAGCTCTG
*
5596188 AACAAATATGAATTGGCTACTTCTAACCTACCGATACGAAATGGACCTCAATGAGGCAGCTAAAT
1 AACAAATATGAATTGGCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAAT
* * *
5596253 GTTCATTTCTATGAGCT-AAAATCAAAGTGAATAGGTTTTTATGTTTCTGCAGCTCTG
66 GTTCATTTCTGTGAGCTGAAAACCAAAGTGAATAGG-TTTTATGTTTCTGTAGCTCTG
* * *
5596310 GACAAATATGAATTGGCTACTTCTAAGCTACTGATACAAAATGGACCTCAATGAGGCAGCTAAAT
1 AACAAATATGAATTGGCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAAT
*
5596375 GTTCATTTCTGTGAGCTGAAAATCAAAGTGAATAGGGTTTTATGTTTCTGTAGCTCTG
66 GTTCATTTCTGTGAGCTGAAAACCAAAGTGAATA-GGTTTTATGTTTCTGTAGCTCTG
* * * *
5596433 AACTAATATGAATTGGCTACCTCTAACCTACCCATAC-AAATGGAACTCAATGAGGCAGCTAAAT
1 AACAAATATGAATTGGCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAAT
* * * * * * * * **
5596497 GTTAATTTCTATGAGCTG-AAATCGAAGTAAATAGGTCTTATGTTTCTATA-ATCCA
66 GTTCATTTCTGTGAGCTGAAAACCAAAGTGAATAGGTTTTATGTTTCTGTAGCTCTG
* * *
5596552 AACGAATATGAATCT-GTTACTTCTAACCTATCGATACA
1 AACAAATATGAAT-TGGCTACTTCTAACCTACCGATACA
5596590 GAATAGGCAT
Statistics
Matches: 1196, Mismatches: 164, Indels: 40
0.85 0.12 0.03
Matches are distributed among these distances:
118 94 0.08
119 38 0.03
120 21 0.02
121 127 0.11
122 546 0.46
123 196 0.16
124 79 0.07
125 27 0.02
126 68 0.06
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (122 bp):
AACAAATATGAATTGGCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAAT
GTTCATTTCTGTGAGCTGAAAACCAAAGTGAATAGGTTTTATGTTTCTGTAGCTCTG
Found at i:5596165 original size:733 final size:729
Alignment explanation
Indices: 5595146--5596517 Score: 2097
Period size: 733 Copynumber: 1.9 Consensus size: 729
5595136 TGATGTGGCA
* * * * * *
5595146 GCTAAATGTTCATTTCTTTGAGTTGAAAATCGAGAGTGAATAGGTTTTTTTGTTTCTGTAGCTCT
1 GCTAAATGTTCATTTCTGTGAGCTGAAAATCAAAAGCGAATAGGTTTTTATGTTTCTGTAGCTCT
* * * *
5595211 GAACAAATATGAATTGGCTAGTTCTAACCTACCAATACGAAATGGACCTCAAAGAGGCAGCTAAA
66 GAACAAATATGAATTGGCTACTTCTAACCAACCAATACGAAATAGACCTCAAAGAGGCAGCAAAA
* * * *
5595276 TGTTCGTTTCTGTGAGCTGAAACCAAAGTGAATAGGTTTTATGTTTCTGTAGCTCTGAACAAATA
131 CGTTCATTTCTGTGAGATGAAACCAAAGTGAATAGGTTTTATGTTTCTGTAGCTCTCAACAAATA
* * * ** * * *
5595341 TGAATTGGCTAGTTCTAACCTACCAATACGAAATGGACCTCAAAGAGGCAGCTAAATGTTCGTTT
196 TGAATTGCCTACTTCTAACCTACCAATACAAAACAGACCTCAAAGAGCCAGCTAAATGTTCATTC
* *
5595406 CTGTGAGCTGAAAACCAAAGTGAATAGGTTTTATGTTTATGTAGCTCTGAACAAATATGAATTGC
261 CTGTGAGCTGAAAACCAAAGTGAATAGATTTCATGTTTATGTAGCTCTGAACAAATATGAATTGC
*
5595471 CTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGTCAGCTAAATGTTCATTTCCATGAGC
326 CTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAATGTTCATTTCCATGAGC
*
5595536 TGAAAATCAAAGTGAATA-GATTTTATGTTTCCGTAACCCTGAACAAATATGAATTGGCTACTTC
391 T-AAAATCAAAGTGAATAGGATTTTATGTTTCCGCAACCCTGAACAAATATGAATTGGCTACTTC
* * *
5595600 TGACCTA-TCGATACGAAATGTACCTCAATGAGGCAGCTAAATGTTCATTTCTGTGAGCTGAAAA
455 TAACCTACT-GATACAAAATGGACCTCAATGAGGCAGCTAAATGTTCATTTCTGTGAGCTGAAAA
* *
5595664 TCAAAGTGAATAGGTTTTTATGTTTCTGTAGCTCTGAACAAATATGAATTGCCTACTTCTAACCT
519 TCAAAGTGAATAGGGTTTTATGTTTCTGTAGCTCTGAACAAATATGAATTGCCTACCTCTAACCT
** * *
5595729 ACTGATACAAAATGGACCTCAATGAGGCAGCTAAATGTTCACTTCCATGAGCTGAAAACCAAAAT
584 ACCCATAC-AAATGGAACTCAATGAGGCAGCTAAATGTTAACTTCCATGAGCTGAAAACCAAAAT
5595794 AGATTTTATGTTTCAGTAACCCTGAACAAATATGTATTGGCTACTTCTGACCTACCGATACGAAA
648 AGATTTTATGTTTCAGTAACCCTGAACAAATATGTATTGGCTACTTCTGACCTACCGATACGAAA
5595859 TGTACCTCAATGAAGCG
713 TGTACCTCAATGAAGCG
5595876 GCTAAATGTTCATTTCTGTGAGCTGAAAATCAAAAGCGAATAGGTTTTTATGTTTTCTGTAGCTC
1 GCTAAATGTTCATTTCTGTGAGCTGAAAATCAAAAGCGAATAGGTTTTTATG-TTTCTGTAGCTC
* * *
5595941 TGAACTAATAATGAATTGGCTACTTCTAACCAACCGATATGAAATAGACCT-AAATGAGGCAGCA
65 TGAACAAAT-ATGAATTGGCTACTTCTAACCAACCAATACGAAATAGACCTCAAA-GAGGCAGCA
* *
5596005 AAACGTTCATTTCTGTGAGATGAAAATCGAAGTGAATAGGTTTTATGTTTCTGTAGCTCTCAACA
128 AAACGTTCATTTCTGTGAGATG-AAACCAAAGTGAATAGGTTTTATGTTTCTGTAGCTCTCAACA
* *
5596070 AATATGAATTTCCTACTTCTAACCTACCAATACAAAACAGCCCTCAATA-AGCCAGCTAAATGTT
192 AATATGAATTGCCTACTTCTAACCTACCAATACAAAACAGACCTCAA-AGAGCCAGCTAAATGTT
* * * *
5596134 CATTCCTGTGAGCTGAAAATCGAAA-TGAATAGATTTCATGTTTCTGTAGTTGTGAACAAATATG
256 CATTCCTGTGAGCTGAAAA-CCAAAGTGAATAGATTTCATGTTTATGTAGCTCTGAACAAATATG
* * *
5596198 AATTGGCTACTTCTAACCTACCGATACGAAATGGACCTCAATGAGGCAGCTAAATGTTCATTTCT
320 AATTGCCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAATGTTCATTTCC
* * * * *
5596263 ATGAGCTAAAATCAAAGTGAATAGGTTTTTATGTTTCTGCAGCTCTGGACAAATATGAATTGGCT
385 ATGAGCTAAAATCAAAGTGAATAGGATTTTATGTTTCCGCAACCCTGAACAAATATGAATTGGCT
*
5596328 ACTTCTAAGCTACTGATACAAAATGGACCTCAATGAGGCAGCTAAATGTTCATTTCTGTGAGCTG
450 ACTTCTAACCTACTGATACAAAATGGACCTCAATGAGGCAGCTAAATGTTCATTTCTGTGAGCTG
* *
5596393 AAAATCAAAGTGAATAGGGTTTTATGTTTCTGTAGCTCTGAACTAATATGAATTGGCTACCTCTA
515 AAAATCAAAGTGAATAGGGTTTTATGTTTCTGTAGCTCTGAACAAATATGAATTGCCTACCTCTA
* *
5596458 ACCTACCCATACAAATGGAACTCAATGAGGCAGCTAAATGTTAATTTCTATGAGCTGAAA
580 ACCTACCCATACAAATGGAACTCAATGAGGCAGCTAAATGTTAACTTCCATGAGCTGAAA
5596518 TCGAAGTAAA
Statistics
Matches: 575, Mismatches: 59, Indels: 14
0.89 0.09 0.02
Matches are distributed among these distances:
730 46 0.08
731 23 0.04
732 123 0.21
733 377 0.66
734 6 0.01
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (729 bp):
GCTAAATGTTCATTTCTGTGAGCTGAAAATCAAAAGCGAATAGGTTTTTATGTTTCTGTAGCTCT
GAACAAATATGAATTGGCTACTTCTAACCAACCAATACGAAATAGACCTCAAAGAGGCAGCAAAA
CGTTCATTTCTGTGAGATGAAACCAAAGTGAATAGGTTTTATGTTTCTGTAGCTCTCAACAAATA
TGAATTGCCTACTTCTAACCTACCAATACAAAACAGACCTCAAAGAGCCAGCTAAATGTTCATTC
CTGTGAGCTGAAAACCAAAGTGAATAGATTTCATGTTTATGTAGCTCTGAACAAATATGAATTGC
CTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAATGTTCATTTCCATGAGC
TAAAATCAAAGTGAATAGGATTTTATGTTTCCGCAACCCTGAACAAATATGAATTGGCTACTTCT
AACCTACTGATACAAAATGGACCTCAATGAGGCAGCTAAATGTTCATTTCTGTGAGCTGAAAATC
AAAGTGAATAGGGTTTTATGTTTCTGTAGCTCTGAACAAATATGAATTGCCTACCTCTAACCTAC
CCATACAAATGGAACTCAATGAGGCAGCTAAATGTTAACTTCCATGAGCTGAAAACCAAAATAGA
TTTTATGTTTCAGTAACCCTGAACAAATATGTATTGGCTACTTCTGACCTACCGATACGAAATGT
ACCTCAATGAAGCG
Found at i:5598651 original size:26 final size:26
Alignment explanation
Indices: 5598631--5598687 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
5598621 TTTCATATTA
5598631 ATTTTTTATTTTGAAATTTCAAACTT
1 ATTTTTTATTTTGAAATTTCAAACTT
* *
5598657 ATTTTTTATTTTGAATTTTCAGACTT
1 ATTTTTTATTTTGAAATTTCAAACTT
5598683 ATTTT
1 ATTTT
5598688 GATAAAATAT
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:0.26, C:0.07, G:0.05, T:0.61
Consensus pattern (26 bp):
ATTTTTTATTTTGAAATTTCAAACTT
Found at i:5598847 original size:21 final size:21
Alignment explanation
Indices: 5598808--5598848 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5598798 ATTTTCGCCA
5598808 TTTTAAATATAAAATATTTAT
1 TTTTAAATATAAAATATTTAT
*
5598829 TTTTATATCATAAAA-ATTTA
1 TTTTAAAT-ATAAAATATTTA
5598849 AAATTAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTTAAATATAAAATATTTAT
Found at i:5601120 original size:126 final size:124
Alignment explanation
Indices: 5600872--5601123 Score: 405
Period size: 126 Copynumber: 2.0 Consensus size: 124
5600862 CTTCTAATTC
* * *
5600872 CCAATCAACAAAGCACAGTTCATTGCAATTGAATCTGAGAAATGGATAAAATTTCATTCATTTGT
1 CCAATCAACAAAGCACAGTTCATTACAATTGAATCTAAGAAACGGATAAAATTTCATTCATTTGT
* * *
5600937 TGAAGCAAACACTTAAATTGGATCATTCAATAAGCATTCATTACTTAAGATTCAATTAT
66 TGAAGAAAACACTTAAATCGGATCATTCAATAAGCATTCATTACTTAAAATTCAATTAT
*
5600996 CCAATCAACAAAGCACAGTTCATTACAATTGAATCTAAGAAACGTATAAAATTTTCATTCATTTG
1 CCAATCAACAAAGCACAGTTCATTACAATTGAATCTAAGAAACGGATAAAA-TTTCATTCATTTG
* *
5601061 TTGAAATAAAACACTTAAATCGGATCATTCACTAAGCATTCATTACTTAAAATTCAATTAT
65 TTG-AAGAAAACACTTAAATCGGATCATTCAATAAGCATTCATTACTTAAAATTCAATTAT
5601122 CC
1 CC
5601124 CAACAATAAT
Statistics
Matches: 117, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
124 47 0.40
125 16 0.14
126 54 0.46
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.32
Consensus pattern (124 bp):
CCAATCAACAAAGCACAGTTCATTACAATTGAATCTAAGAAACGGATAAAATTTCATTCATTTGT
TGAAGAAAACACTTAAATCGGATCATTCAATAAGCATTCATTACTTAAAATTCAATTAT
Found at i:5605811 original size:44 final size:44
Alignment explanation
Indices: 5605697--5605813 Score: 114
Period size: 44 Copynumber: 2.7 Consensus size: 44
5605687 TTTTAACCCA
* * ** * *
5605697 CTCCACTGTAACTTCAGGGAGATAGGAT-AGTGTCTTCGATCTG
1 CTCCACTGTAACTTCAGGGGGATAAGATCTCTGGCTTCAATCTG
**
5605740 CTCTGCTGTAA-TCTC-GGGGAGATAAGATCTCTGGCTTCAATCTG
1 CTCCACTGTAACT-TCAGGGG-GATAAGATCTCTGGCTTCAATCTG
*
5605784 CTCCACTGTAACTTCAGGGGGACAAGATCT
1 CTCCACTGTAACTTCAGGGGGATAAGATCT
5605814 GTAATTTCCA
Statistics
Matches: 58, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
42 4 0.07
43 18 0.31
44 31 0.53
45 5 0.09
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (44 bp):
CTCCACTGTAACTTCAGGGGGATAAGATCTCTGGCTTCAATCTG
Found at i:5606109 original size:88 final size:88
Alignment explanation
Indices: 5605965--5606470 Score: 836
Period size: 88 Copynumber: 5.8 Consensus size: 88
5605955 AGCTCCAATG
** * *
5605965 CAACCGATGGAGGCAAGGCTTTGT-T-TTCGATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATC
1 CAACCGAAAGAGGCAAGG-TTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATC
5606028 TTTTGTCTTCAACCAGCTCTATCA
65 TTTTGTCTTCAACCAGCTCTATCA
* *
5606052 CAATCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAAAGGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
5606117 TTTGTCTTCAACCAGCTCTATCA
66 TTTGTCTTCAACCAGCTCTATCA
* * *
5606140 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAAAAGCAAGATGT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
*
5606205 TTTGTCTTCAACCAGCTCCATCA
66 TTTGTCTTCAACCAGCTCTATCA
*
5606228 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
*
5606293 TTTGTCTTCAACCAGCTCCATCA
66 TTTGTCTTCAACCAGCTCTATCA
*
5606316 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
5606381 TTTGTCTTCAACCAGCTCTATCA
66 TTTGTCTTCAACCAGCTCTATCA
* * * *
5606404 CAACCGAAAGAGGCAAGGTTTATGTCTTCGACCTGCTTCACTATCAATGCAGGAAGGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
5606469 TT
66 TT
5606471 AACTTCATTG
Statistics
Matches: 397, Mismatches: 20, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
86 5 0.01
87 16 0.04
88 376 0.95
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (88 bp):
CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
TTTGTCTTCAACCAGCTCTATCA
Found at i:5611039 original size:19 final size:20
Alignment explanation
Indices: 5611010--5611058 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
5611000 CACTTCGTGA
* *
5611010 AAATCTAATGCATATG-ATG
1 AAATGTAATGCAAATGCATG
*
5611029 CAATGTAATGCAAATGCATG
1 AAATGTAATGCAAATGCATG
5611049 AAATG-AATGC
1 AAATGTAATGC
5611059 CTAAAGAGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (20 bp):
AAATGTAATGCAAATGCATG
Found at i:5612652 original size:18 final size:18
Alignment explanation
Indices: 5612612--5612654 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
5612602 TTCCAAACGC
5612612 AAAATATTGCCCTATTTG
1 AAAATATTGCCCTATTTG
* * * *
5612630 GAAATATTTCCCTTTTTT
1 AAAATATTGCCCTATTTG
5612648 AAAATAT
1 AAAATAT
5612655 GATATTCATG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.35, C:0.14, G:0.07, T:0.44
Consensus pattern (18 bp):
AAAATATTGCCCTATTTG
Found at i:5613165 original size:8 final size:8
Alignment explanation
Indices: 5613066--5613177 Score: 52
Period size: 8 Copynumber: 14.0 Consensus size: 8
5613056 ATATATGCAT
5613066 TATA-AAA
1 TATATAAA
*
5613073 TATATATA
1 TATATAAA
*
5613081 TATATATA
1 TATATAAA
5613089 TATAAGTAAA
1 TAT-A-TAAA
* *
5613099 TATGTACA
1 TATATAAA
**
5613107 TATATACG
1 TATATAAA
**
5613115 TATATACG
1 TATATAAA
*
5613123 TATATAAC
1 TATATAAA
5613131 TATCATAAA
1 TAT-ATAAA
5613140 -ATATAAA
1 TATATAAA
**
5613147 -A-AGTATG
1 TATA-TAAA
5613154 TATATAAA
1 TATATAAA
5613162 TATATAAA
1 TATATAAA
*
5613170 AATATAAA
1 TATATAAA
5613178 AAATATATAC
Statistics
Matches: 84, Mismatches: 14, Indels: 13
0.76 0.13 0.12
Matches are distributed among these distances:
6 1 0.01
7 12 0.14
8 59 0.70
9 6 0.07
10 6 0.07
ACGTcount: A:0.54, C:0.04, G:0.05, T:0.36
Consensus pattern (8 bp):
TATATAAA
Found at i:5613181 original size:9 final size:10
Alignment explanation
Indices: 5613140--5613186 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
5613130 CTATCATAAA
5613140 ATATAAAAAGT
1 ATATAAAAA-T
*
5613151 ATGTATATAAAT
1 A--TATAAAAAT
5613163 ATATAAAAAT
1 ATATAAAAAT
5613173 ATA-AAAAAT
1 ATATAAAAAT
5613182 ATATA
1 ATATA
5613187 CTCCTATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
9 9 0.29
10 12 0.39
11 1 0.03
12 2 0.06
13 7 0.23
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (10 bp):
ATATAAAAAT
Found at i:5613340 original size:30 final size:30
Alignment explanation
Indices: 5613266--5613342 Score: 75
Period size: 30 Copynumber: 2.6 Consensus size: 30
5613256 AAAAGTGTTA
* * **
5613266 AAAAGGGACTAGATCG-AAGTAAAAGCAAC
1 AAAAGGGACTAAATCGAAAATAAAAAAAAC
* * *
5613295 AACACGGGGCAAAATCGAAAATAAAAAAAAC
1 AA-AAGGGACTAAATCGAAAATAAAAAAAAC
5613326 AAAAGGGACTAAATCGA
1 AAAAGGGACTAAATCGA
5613343 GAGAAAAGTA
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
29 2 0.06
30 22 0.61
31 12 0.33
ACGTcount: A:0.56, C:0.14, G:0.21, T:0.09
Consensus pattern (30 bp):
AAAAGGGACTAAATCGAAAATAAAAAAAAC
Found at i:5617565 original size:57 final size:57
Alignment explanation
Indices: 5617502--5617613 Score: 206
Period size: 57 Copynumber: 2.0 Consensus size: 57
5617492 AAACTAAGTG
* *
5617502 TAATGAAACATTTAAAATACAAAAAGAATTTTCATGTCACCTGTTACATATCAGTCA
1 TAATGAAACATTTAAAATAAAAAAAGAATTTTCATGACACCTGTTACATATCAGTCA
5617559 TAATGAAACATTTAAAATAAAAAAAGAATTTTCATGACACCTGTTACATATCAGT
1 TAATGAAACATTTAAAATAAAAAAAGAATTTTCATGACACCTGTTACATATCAGT
5617614 ATTTTAATTA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (57 bp):
TAATGAAACATTTAAAATAAAAAAAGAATTTTCATGACACCTGTTACATATCAGTCA
Found at i:5617793 original size:27 final size:25
Alignment explanation
Indices: 5617766--5617815 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
5617756 AAATTTAAAT
*
5617766 TTAGATACTAAATTAAATAAAAAAAA
1 TTAGATACCAAATTAAA-AAAAAAAA
* *
5617792 TTAGGTGCCAAATTAAAAAAAAAA
1 TTAGATACCAAATTAAAAAAAAAA
5617816 TTGTCAAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.62, C:0.06, G:0.08, T:0.24
Consensus pattern (25 bp):
TTAGATACCAAATTAAAAAAAAAAA
Found at i:5618675 original size:304 final size:298
Alignment explanation
Indices: 5618059--5618967 Score: 940
Period size: 304 Copynumber: 3.0 Consensus size: 298
5618049 TATAATAAAT
* * * * * * *
5618059 AATGAAGTTTTGATTGAGTGATAAATTTAAAGTTTTACTAATACATTTAGAGCGA-GTCCAACCC
1 AATGAAGTTTTGGTTGAGTGATAAATTTAAAATTTTACTAATGCAATT-G-GTGAGGTTCAA--A
* * * * *
5618123 GCACCATATGCATATTTTTATTGGTTTTTGTTAAAATAAAAAGATTAAAATACCCTCGAATAAT-
62 TCACCATATGCAAATTTTTATTGGTTTTTGTTAAAATGAAAAGACTAAAATA-CCTTGAATAATA
* * * * * * *
5618187 -ATGACTTTGATCACGGAA-GACATTTTCGTAATTTCTCTAACCGAGTTGGTGTATGGTTGACTT
126 GATTACTTTAATTACGAAAGGACATTTTCGTAATTTTTCTAATCGAGTTGGTGTATGGTTGACTC
* * *
5618250 GTGACACCAACTCAATCAGAGATTTTATT--AAT-AG--TACAT--ATATACAACTGATGGAAAT
191 GTGACACCAACTCAGTTAGAGATTTTATTAAAATAAGTATATATAGATATACAACTGAT-GAAAT
* * **
5618308 AGTAAATTGTGCATATTAAAATAAAAATGTATAGAATATACAAA
255 AATAAATTGTGCATATTAAAATAAAAATGTATAAAATATATTAA
* ** *
5618352 AATGAAATTTCAGTTGAGTGATAAATTTAAAATTTTACTAATGCAATTGGTGAGGTTCAATTTTC
1 AATGAAGTTTTGGTTGAGTGATAAATTTAAAATTTTACTAATGCAATTGGTGAGGTTCAA--ATC
* * * * *
5618417 ACCTTATGCAAATTTTTATTGGTTTTTGTCAGAATGAAATGGCTAAAATACACTTGAATAATACG
64 ACCATATGCAAATTTTTATTGGTTTTTGTTAAAATGAAAAGACTAAAATAC-CTTGAATAATA-G
* * * *
5618482 ATTACTTTAATTACGAAAGGACATTTTTGTAATTTTTCTAATCGAGTTTGTGTTTGGTTGACTCA
127 ATTACTTTAATTACGAAAGGACATTTTCGTAATTTTTCTAATCGAGTTGGTGTATGGTTGACTCG
*
5618547 TGACACCAACTCAGTTAGAGGTTTTATTAAAATTAAGTATATATAGATATACAACTGATGAATAT
192 TGACACCAACTCAGTTAGAGATTTTATTAAAA-TAAGTATATATAGATATACAACTGATGAA-AT
* * * *
5618612 AATAAAATGTGCATAGTAAAATAAGAATGCATAAAATATATTAA
255 AATAAATTGTGCATATTAAAATAAAAATGTATAAAATATATTAA
* * ** * *
5618656 AATGAAGTTTTGGTTGAGTGGTAAATTTAAGATTTTACTAATGCAATTATTGCGGGTTCAAATCC
1 AATGAAGTTTTGGTTGAGTGATAAATTTAAAATTTTACTAATGCAATTGGTG-AGGTTCAAATCA
* * *
5618721 CCCTATGCAAATTTTAATTGGTTTTTGTTAAAATGAAAAGACTAAAATGCCTTCGAATAATATGG
65 CCATATGCAAATTTTTATTGGTTTTTGTTAAAATGAAAAGACTAAAATACCTT-GAATAATA--G
* * * *****
5618786 CTTACTTTAATTACGAAAGGGCATTTTCATAATTTTTCTAATCGAGTTGGTACCCAGTTGACTCG
127 ATTACTTTAATTACGAAAGGACATTTTCGTAATTTTTCTAATCGAGTTGGTGTATGGTTGACTCG
* * * * *
5618851 TGACACCAACTTAGTTAGCGATTTTATTAATAGTAAGTATAGATATAGATATACAACTAATGGAG
192 TGACACCAACTCAGTTAGAGATTTTATTAA-AATAAGTAT--ATATAGATATACAACTGAT-GAA
* * *
5618916 ATAATAATTTGTACATATTAAAATAAAAATATATAAAATATATTAA
253 ATAATAAATTGTGCATATTAAAATAAAAATGTATAAAATATATTAA
5618962 AATGAA
1 AATGAA
5618968 ACGTTAGTTG
Statistics
Matches: 507, Mismatches: 87, Indels: 31
0.81 0.14 0.05
Matches are distributed among these distances:
291 4 0.01
292 58 0.11
293 41 0.08
295 14 0.03
296 64 0.13
298 2 0.00
299 1 0.00
300 2 0.00
302 7 0.01
303 56 0.11
304 185 0.36
305 8 0.02
306 63 0.12
307 2 0.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (298 bp):
AATGAAGTTTTGGTTGAGTGATAAATTTAAAATTTTACTAATGCAATTGGTGAGGTTCAAATCAC
CATATGCAAATTTTTATTGGTTTTTGTTAAAATGAAAAGACTAAAATACCTTGAATAATAGATTA
CTTTAATTACGAAAGGACATTTTCGTAATTTTTCTAATCGAGTTGGTGTATGGTTGACTCGTGAC
ACCAACTCAGTTAGAGATTTTATTAAAATAAGTATATATAGATATACAACTGATGAAATAATAAA
TTGTGCATATTAAAATAAAAATGTATAAAATATATTAA
Found at i:5620528 original size:22 final size:21
Alignment explanation
Indices: 5620501--5620587 Score: 99
Period size: 22 Copynumber: 4.2 Consensus size: 21
5620491 TAGATTAGAA
*
5620501 TTTTGTATGAATATTTTAAATT
1 TTTTGTATGAATATTAT-AATT
5620523 TTTTGTATGAATATTATAATT
1 TTTTGTATGAATATTATAATT
*
5620544 TTTT-TATGAATATTGTAA--
1 TTTTGTATGAATATTATAATT
* *
5620562 TGTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTATAATT
5620583 ATTTT
1 -TTTT
5620588 ATAATTAAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
18 3 0.05
19 14 0.25
20 13 0.23
21 8 0.14
22 19 0.33
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.57
Consensus pattern (21 bp):
TTTTGTATGAATATTATAATT
Found at i:5620572 original size:19 final size:19
Alignment explanation
Indices: 5620525--5620581 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
5620515 TTTAAATTTT
* *
5620525 TTGTATGAATATTATAATTT
1 TTGTATGAATATTGTAA-TG
*
5620545 TTTTATGAATATTGTAATG
1 TTGTATGAATATTGTAATG
5620564 TTGTATGAATATTGTAAT
1 TTGTATGAATATTGTAAT
5620582 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:5620668 original size:19 final size:19
Alignment explanation
Indices: 5620646--5620703 Score: 55
Period size: 22 Copynumber: 2.9 Consensus size: 19
5620636 ATATTGTAAT
*
5620646 AATATTATAGTTTTGTATG
1 AATATTATAATTTTGTATG
5620665 AATATTGCA-AATTTTTTGTATG
1 AATATT--ATAA--TTTTGTATG
*
5620687 AATATTGTAATTTTGTA
1 AATATTATAATTTTGTA
5620704 ATTTTGTATG
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
19 13 0.41
20 1 0.03
21 3 0.09
22 15 0.47
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.52
Consensus pattern (19 bp):
AATATTATAATTTTGTATG
Found at i:5620698 original size:21 final size:21
Alignment explanation
Indices: 5620656--5620793 Score: 114
Period size: 21 Copynumber: 6.0 Consensus size: 21
5620646 AATATTATAG
*
5620656 TTTTGTATGAATATTGCAAATT
1 TTTTGTATGAATATTG-TAATT
5620678 TTTTGTATGAATATTGTAATTTTGT
1 TTTTGTATGAATATTGTAA---T-T
* *
5620703 AATTTTGTATGAATATTATATTT
1 --TTTTGTATGAATATTGTAATT
*
5620726 TTTTGTATGAATGTTGTAATATTAT
1 TTTTGTATGAATATTGT-A-A-T-T
*
5620751 AATTTTGTATGAATATTGCAATT
1 --TTTTGTATGAATATTGTAATT
5620774 TTTTGTATGAATATTGTAAT
1 TTTTGTATGAATATTGTAAT
5620794 ATTGTAAATT
Statistics
Matches: 95, Mismatches: 9, Indels: 25
0.74 0.07 0.19
Matches are distributed among these distances:
21 36 0.38
22 17 0.18
23 2 0.02
24 4 0.04
25 3 0.03
26 1 0.01
27 32 0.34
ACGTcount: A:0.30, C:0.01, G:0.14, T:0.54
Consensus pattern (21 bp):
TTTTGTATGAATATTGTAATT
Found at i:5620754 original size:48 final size:47
Alignment explanation
Indices: 5620622--5620805 Score: 233
Period size: 48 Copynumber: 3.8 Consensus size: 47
5620612 TTGGATTAGT
*
5620622 AATTTTTTGTATGAATATTGTAATAATATTATAGTTTTGTATGAATATTGCA
1 AATTTTTTGTATGAATATTG---TAATATTATAATTTTGTATGAATATT--A
* *
5620674 AATTTTTTGTATGAATATTGTAATTTTGTAATTTTGTATGAATATTA
1 AATTTTTTGTATGAATATTGTAATATTATAATTTTGTATGAATATTA
* * *
5620721 TATTTTTTTGTATGAATGTTGTAATATTATAATTTTGTATGAATATTGC
1 -AATTTTTTGTATGAATATTGTAATATTATAATTTTGTATGAATATT-A
* *
5620770 AATTTTTTGTATGAATATTGTAATATTGTAAATTTG
1 AATTTTTTGTATGAATATTGTAATATTATAATTTTG
5620806 CAATTTTTAT
Statistics
Matches: 118, Mismatches: 12, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
47 1 0.01
48 74 0.63
49 23 0.19
52 20 0.17
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.53
Consensus pattern (47 bp):
AATTTTTTGTATGAATATTGTAATATTATAATTTTGTATGAATATTA
Found at i:5620767 original size:19 final size:19
Alignment explanation
Indices: 5620743--5620799 Score: 69
Period size: 21 Copynumber: 2.9 Consensus size: 19
5620733 TGAATGTTGT
*
5620743 AATATTATAATTTTGTATG
1 AATATTGTAATTTTGTATG
*
5620762 AATATTGCAATTTTTTGTATG
1 AATATTGTAA--TTTTGTATG
*
5620783 AATATTGTAATATTGTA
1 AATATTGTAATTTTGTA
5620800 AATTTGCAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 14 0.44
21 18 0.56
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.51
Consensus pattern (19 bp):
AATATTGTAATTTTGTATG
Found at i:5620769 original size:97 final size:97
Alignment explanation
Indices: 5620624--5620805 Score: 294
Period size: 96 Copynumber: 1.9 Consensus size: 97
5620614 GGATTAGTAA
*
5620624 TTTTTTGTATGAATATTGTAATAATATTATAGTTTTGTATGAATATTGCAAATTTTTTGTATGAA
1 TTTTTTGTATGAATATTG--ATAATATTATAATTTTGTATGAATATTGC-AATTTTTTGTATGAA
* *
5620689 TATTGTAATTTTGTAATTTTGTATGAATATTATAT
63 TATTGTAATATTGTAAATTTGTATGAATATTATAT
*
5620724 TTTTTTGTATGAATGTTG-TAATATTATAATTTTGTATGAATATTGCAATTTTTTGTATGAATAT
1 TTTTTTGTATGAATATTGATAATATTATAATTTTGTATGAATATTGCAATTTTTTGTATGAATAT
5620788 TGTAATATTGTAAATTTG
66 TGTAATATTGTAAATTTG
5620806 CAATTTTTAT
Statistics
Matches: 78, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
96 34 0.44
97 27 0.35
100 17 0.22
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.54
Consensus pattern (97 bp):
TTTTTTGTATGAATATTGATAATATTATAATTTTGTATGAATATTGCAATTTTTTGTATGAATAT
TGTAATATTGTAAATTTGTATGAATATTATAT
Found at i:5625073 original size:16 final size:15
Alignment explanation
Indices: 5625042--5625083 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
5625032 ACAAAATCAA
*
5625042 ATAAAATTTAATTAT
1 ATAAAAGTTAATTAT
5625057 ATAAAAGTTACATTAT
1 ATAAAAGTTA-ATTAT
*
5625073 ATAAAAATTAA
1 ATAAAAGTTAA
5625084 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:5625491 original size:27 final size:26
Alignment explanation
Indices: 5625458--5625653 Score: 193
Period size: 27 Copynumber: 7.8 Consensus size: 26
5625448 ATATCCTCAC
*
5625458 ATTACAATATTCATGCAAAATTACAAT
1 ATTACAATATTCATACAAAATTA-AAT
5625485 ATTACAATATTCATAC-AAA--AAA-
1 ATTACAATATTCATACAAAATTAAAT
*
5625507 ATTGCAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTA-AAT
*
5625534 ATTACAACATTCATACAAAA--AAAT
1 ATTACAATATTCATACAAAATTAAAT
*
5625558 A-T--AATATTCATACAAAATTACAAA
1 ATTACAATATTCATACAAAATTA-AAT
5625582 ATTACAATATTCATAC-AAA--AAA-
1 ATTACAATATTCATACAAAATTAAAT
*
5625604 ATTGCAATATTCATACAAAACTATAATATT
1 ATTACAATATTCATACAAAA-T-TAA-A-T
5625634 ATTACAATATTCATACAAAA
1 ATTACAATATTCATACAAAA
5625654 AATTACTAAT
Statistics
Matches: 142, Mismatches: 8, Indels: 35
0.77 0.04 0.19
Matches are distributed among these distances:
21 14 0.10
22 30 0.21
23 12 0.08
24 9 0.06
25 3 0.02
26 8 0.06
27 46 0.32
28 1 0.01
30 19 0.13
ACGTcount: A:0.54, C:0.14, G:0.02, T:0.31
Consensus pattern (26 bp):
ATTACAATATTCATACAAAATTAAAT
Found at i:5625526 original size:49 final size:49
Alignment explanation
Indices: 5625462--5625655 Score: 286
Period size: 49 Copynumber: 3.9 Consensus size: 49
5625452 CCTCACATTA
*
5625462 CAATATTCATGCAAAATTACAATATTACAATATTCATACAAAAAAATTG
1 CAATATTCATACAAAATTACAATATTACAATATTCATACAAAAAAATTG
* *
5625511 CAATATTCATACAAAATTATAATATTACAACATTCATACAAAAAAATAT-
1 CAATATTCATACAAAATTACAATATTACAATATTCATACAAAAAAAT-TG
*
5625560 -AATATTCATACAAAATTACAAAATTACAATATTCATACAAAAAAATTG
1 CAATATTCATACAAAATTACAATATTACAATATTCATACAAAAAAATTG
5625608 CAATATTCATACAAAACTATA-ATATTATTACAATATTCATACAAAAAA
1 CAATATTCATACAAAA-T-TACA-A-TATTACAATATTCATACAAAAAA
5625656 TTACTAATCC
Statistics
Matches: 131, Mismatches: 7, Indels: 11
0.88 0.05 0.07
Matches are distributed among these distances:
47 1 0.01
48 43 0.33
49 59 0.45
50 3 0.02
51 3 0.02
52 22 0.17
ACGTcount: A:0.54, C:0.14, G:0.02, T:0.30
Consensus pattern (49 bp):
CAATATTCATACAAAATTACAATATTACAATATTCATACAAAAAAATTG
Found at i:5625576 original size:97 final size:100
Alignment explanation
Indices: 5625463--5625655 Score: 329
Period size: 97 Copynumber: 2.0 Consensus size: 100
5625453 CTCACATTAC
* *
5625463 AATATTCATGCAAAATTACAATATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAA-
1 AATATTCATACAAAATTACAAAATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAAC
5625527 T-T-ATAATATTACAACATTCATACAAAAAAATAT
66 TATAATAATATTACAACATTCATACAAAAAAATAT
5625560 AATATTCATACAAAATTACAAAATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAAC
1 AATATTCATACAAAATTACAAAATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAAC
* *
5625625 TATAATATTATTACAATATTCATACAAAAAA
66 TATAATAATATTACAACATTCATACAAAAAA
5625656 TTACTAATCC
Statistics
Matches: 89, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
97 62 0.70
98 1 0.01
99 1 0.01
100 25 0.28
ACGTcount: A:0.54, C:0.13, G:0.02, T:0.31
Consensus pattern (100 bp):
AATATTCATACAAAATTACAAAATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAAC
TATAATAATATTACAACATTCATACAAAAAAATAT
Found at i:5625600 original size:19 final size:19
Alignment explanation
Indices: 5625479--5625536 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 19
5625469 CATGCAAAAT
*
5625479 TACAATATTACAATATTCA
1 TACAAAATTACAATATTCA
*
5625498 TACAAAAAAATTGCAATATTCA
1 TAC---AAAATTACAATATTCA
*
5625520 TACAAAATTATAATATT
1 TACAAAATTACAATATT
5625537 ACAACATTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
19 15 0.47
22 17 0.53
ACGTcount: A:0.52, C:0.12, G:0.02, T:0.34
Consensus pattern (19 bp):
TACAAAATTACAATATTCA
Found at i:5625601 original size:19 final size:19
Alignment explanation
Indices: 5625576--5625633 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 19
5625566 CATACAAAAT
5625576 TACAAAATTACAATATTCA
1 TACAAAATTACAATATTCA
*
5625595 TACAAAAAAATTGCAATATTCA
1 TAC---AAAATTACAATATTCA
* *
5625617 TACAAAACTATAATATT
1 TACAAAATTACAATATT
5625634 ATTACAATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
19 14 0.44
22 18 0.56
ACGTcount: A:0.53, C:0.14, G:0.02, T:0.31
Consensus pattern (19 bp):
TACAAAATTACAATATTCA
Found at i:5625767 original size:22 final size:21
Alignment explanation
Indices: 5625692--5625778 Score: 99
Period size: 20 Copynumber: 4.2 Consensus size: 21
5625682 ATTTAATTAT
*
5625692 AAAATAATTACAATATTCATAC
1 AAAA-AATTAAAATATTCATAC
* *
5625714 --AACATTACAATATTCATA-
1 AAAAAATTAAAATATTCATAC
*
5625732 AAAAAATTATAATATTCATAC
1 AAAAAATTAAAATATTCATAC
5625753 AAAAAATTTAAAATATTCATAC
1 AAAAAA-TTAAAATATTCATAC
5625775 AAAA
1 AAAA
5625779 TTCTAATCTA
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
19 15 0.26
20 18 0.32
21 6 0.11
22 18 0.32
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAAAATTAAAATATTCATAC
Found at i:5635637 original size:17 final size:18
Alignment explanation
Indices: 5635610--5635643 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5635600 GTAACTTTTA
*
5635610 AAAGTTAAAACTAAAAAT
1 AAAGTTAAAACCAAAAAT
5635628 AAAG-TAAAACCAAAAA
1 AAAGTTAAAACCAAAAA
5635644 AAGAGAAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.71, C:0.09, G:0.06, T:0.15
Consensus pattern (18 bp):
AAAGTTAAAACCAAAAAT
Found at i:5650410 original size:42 final size:42
Alignment explanation
Indices: 5650203--5650807 Score: 259
Period size: 42 Copynumber: 14.3 Consensus size: 42
5650193 AGTGGATCAA
* *** *
5650203 AGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATC-C
1 AGATACAGATCTTGTCTTCATGTATTGG-CG-GAAGTAGATCGC
* * *
5650246 AGAAAGCAGATCTTGTCTTCATGTATTGGCTGAAGTAGATCGA
1 AGATA-CAGATCTTGTCTTCATGTATTGGCGGAAGTAGATCGC
* * * * * *
5650289 AGATAGCAGATCCTATCTTCCTATATTGGTAGGAAGTGGATCG-
1 AGATA-CAGATCTTGTCTTCATGTATTGG-CGGAAGTAGATCGC
** * **
5650332 ACGACGCAGATCTTGTCTTCCCATATGGTGGC-GAAGTAGATCGC
1 A-GATACAGATCTTGTCTT--CATGTATTGGCGGAAGTAGATCGC
* * *
5650376 AGA-AAAGATCTTATCTTCATGTATTGGCGTGAAGTAGATCGA
1 AGATACAGATCTTGTCTTCATGTATTGGCG-GAAGTAGATCGC
* * * * * *
5650418 AGATAGCAGGTCCTATCTTCCTATATTGGTAGGAAGT-GAT--C
1 AGATA-CAGATCTTGTCTTCATGTATTGG-CGGAAGTAGATCGC
*
5650459 AGATGCAGATCTTGTCTTCCCTACTG-A-TGGC-GAAGTAGATCG-
1 AGATACAGATCTTGTCTT--C-A-TGTATTGGCGGAAGTAGATCGC
* * *
5650501 AAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAA
1 AGATACAGATCTTGTCTTCATGTATTGGCG-GAAGTAGATCG-C
* * * * * * *
5650545 AGATAGCA-AGTCCTATCTTCCTATA-TGGAGGAA-TGGAT--A
1 AGATA-CAGA-TCTTGTCTTCATGTATTGGCGGAAGTAGATCGC
* *
5650584 AGATGCAGATCTTG-CTTCCATATGA-TGGC-GAA-TAGATCG-
1 AGATACAGATCTTGTCTT-CATGT-ATTGGCGGAAGTAGATCGC
* *
5650623 AGAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGA
1 AGATACAGATCTTGTCTTCATGTATTGGCG-GAAGTAGATCGC
* * * * * *
5650666 AGATAGCAG-TCCTATCTTC-TATATTGGTAGGAAGTGGATCGA
1 AGATA-CAGATCTTGTCTTCATGTATTGG-CGGAAGTAGATCGC
** * **
5650708 AGACGCAGATCTTGTCTTCCCATATGGTGGC-GAAGTAGATCGC
1 AGATACAGATCTTGTCTT--CATGTATTGGCGGAAGTAGATCGC
* * *
5650751 AGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAAATCGA
1 AGATA-CAGATCTTGTCTTCATGTATTGGCG-GAAGTAGATCGC
*
5650795 AGGTAGCAGATCT
1 AGATA-CAGATCT
5650808 ACTTCCTATA
Statistics
Matches: 425, Mismatches: 90, Indels: 93
0.70 0.15 0.15
Matches are distributed among these distances:
37 3 0.01
38 19 0.04
39 32 0.08
40 31 0.07
41 13 0.03
42 112 0.26
43 85 0.20
44 103 0.24
45 27 0.06
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.29
Consensus pattern (42 bp):
AGATACAGATCTTGTCTTCATGTATTGGCGGAAGTAGATCGC
Found at i:5650410 original size:85 final size:86
Alignment explanation
Indices: 5650224--5650889 Score: 216
Period size: 83 Copynumber: 7.9 Consensus size: 86
5650214 TTGTCTTCCC
* * * * *
5650224 ATATTGGTGGCGAAGTAGATCCA-GAAAGCAGATCTTGTCTTCATGTATTGGCTGAAGTAGATCG
1 ATATTGGTAG-GAAGTAGATCGACG-ACGCAGATCTTGTCTTCATATAGTGGCTGAAGTAGATCG
* *
5650288 AAGATAGCAGATCCTATCTTCCT
64 AAGATAGAAGATCCTATCTTCAT
* *
5650311 ATATTGGTAGGAAGTGGATCGACGACGCAGATCTTGTCTTCCCATATGGTGGC-GAAGTAGATCG
1 ATATTGGTAGGAAGTAGATCGACGACGCAGATCTTGTCTT--CATATAGTGGCTGAAGTAGATCG
* *
5650375 CAGA-A-AAGATCTTATCTTCAT
64 AAGATAGAAGATCCTATCTTCAT
* * * * * * * * *
5650396 GTATTGG-CGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTATATTGG-TAGGAAGT-GAT
1 ATATTGGTAG-GAAGTAGATCGACGA-CGCAGATCTTGTCTTCATATAGTGGCT--GAAGTAGAT
* * * *
5650458 C--AGAT-GCAGATCTTGTCTTC-C
62 CGAAGATAGAAGATCCTATCTTCAT
* * * * * ** * *
5650479 CTACTGATGGCGAAGTAGATCGA-AAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCG
1 ATATTGGTAG-GAAGTAGATCGACGACGCAGATCTTGTCTTCATATAGTGGC-TGAAGTAGATCG
*
5650543 AAAGATAGCAAG-TCCTATCTTCCT
64 -AAGATAG-AAGATCCTATCTTCAT
* * *
5650567 ATA-TGG-AGGAA-TGGAT--AAGATGCAGATCTTG-CTTCCATAT-GATGGC-GAA-TAGATCG
1 ATATTGGTAGGAAGTAGATCGACGACGCAGATCTTGTCTT-CATATAG-TGGCTGAAGTAGATCG
* *
5650623 -AGA-A-ACAGATCTTGTCTTCAT
64 AAGATAGA-AGATCCTATCTTCAT
* * * * * * * *
5650644 GTATTGG-CGTGAAGTAGATCGAAGATAGCAG-TCCTATCTTC-TATATTGG-TAGGAAGTGGAT
1 ATATTGGTAG-GAAGTAGATCGACGA-CGCAGATCTTGTCTTCATATAGTGGCT--GAAGTAGAT
* * * * **
5650705 CGAAGA-CGCAGATCTTGTCTTCCC
62 CGAAGATAGAAGATCCTATCTTCAT
* * * * *
5650729 ATA-TGGTGGCGAAGTAGATCG-CAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAAAT
1 ATATTGGTAG-GAAGTAGATCGAC-G-ACGCAGATCTTGTCTTCATATAGTGGC-TGAAGTAGAT
* * *
5650792 CGAAGGTAGCAGAT-CTA-CTTCCT
62 CGAAGATAGAAGATCCTATCTTCAT
* * * ** ** * *
5650815 ATA-TGATAGGAAGT-GATCCAAGATACAGATCTTGTCTTCCCATACTGGTGTGAAGTAGATCGA
1 ATATTGGTAGGAAGTAGATCGACGACGCAGATCTTGTCTTCATATAGTGG-CTGAAGTAGATCGA
* *
5650878 AGAAAGCAGATC
65 AGATAGAAGATC
5650890 GACGATGGGG
Statistics
Matches: 436, Mismatches: 93, Indels: 103
0.69 0.15 0.16
Matches are distributed among these distances:
75 1 0.00
76 2 0.00
77 12 0.03
78 7 0.02
79 3 0.01
80 11 0.03
81 9 0.02
82 36 0.08
83 81 0.19
84 52 0.12
85 80 0.18
86 68 0.16
87 55 0.13
88 18 0.04
89 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (86 bp):
ATATTGGTAGGAAGTAGATCGACGACGCAGATCTTGTCTTCATATAGTGGCTGAAGTAGATCGAA
GATAGAAGATCCTATCTTCAT
Found at i:5650441 original size:129 final size:130
Alignment explanation
Indices: 5650165--5650889 Score: 1032
Period size: 129 Copynumber: 5.7 Consensus size: 130
5650155 ATAAAAGAAT
* *
5650165 AGGTCCTATTCTTCCTATATTAGTAGGAAGTGGATCAAAGATGCAGATCTTGTCTTCCCATATTG
1 AGGTCCTA-TCTTCCTATATTGGTAGGAAGTGGATC-AAGATGCAGATCTTGTCTTCCCATACTG
5650230 GTGGCGAAGTAGATC-CAGAAAGCAGATCTTGTCTTCATGTATTGGC-TGAAGTAGATCGAAGAT
64 GTGGCGAAGTAGATCGCAGAAA-CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAT
5650293 AGC
128 AGC
* * *
5650296 AGATCCTATCTTCCTATATTGGTAGGAAGTGGATCGACGACGCAGATCTTGTCTTCCCATA-TGG
1 AGGTCCTATCTTCCTATATTGGTAGGAAGTGGATC-AAGATGCAGATCTTGTCTTCCCATACTGG
*
5650360 TGGCGAAGTAGATCGCAGAAA-AGATCTTATCTTCATGTATTGGCGTGAAGTAGATCGAAGATAG
65 TGGCGAAGTAGATCGCAGAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAG
5650424 C
130 C
*
5650425 AGGTCCTATCTTCCTATATTGGTAGGAAGT-GATC-AGATGCAGATCTTGTCTTCCC-TACTGAT
1 AGGTCCTATCTTCCTATATTGGTAGGAAGTGGATCAAGATGCAGATCTTGTCTTCCCATACTGGT
*
5650487 GGCGAAGTAGATCG-AAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAAGATAG
66 GGCGAAGTAGATCGCAGAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCG-AAGATAG
5650551 C
130 C
* *
5650552 AAGTCCTATCTTCCTATA-TGG-AGGAA-TGGAT-AAGATGCAGATCTTG-CTT-CCATA-TGAT
1 AGGTCCTATCTTCCTATATTGGTAGGAAGTGGATCAAGATGCAGATCTTGTCTTCCCATACTGGT
5650610 GGCGAA-TAGATCG-AGAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGC
66 GGCGAAGTAGATCGCAGAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGC
*
5650673 A-GTCCTATCTT-CTATATTGGTAGGAAGTGGATCGAAGACGCAGATCTTGTCTTCCCATA-TGG
1 AGGTCCTATCTTCCTATATTGGTAGGAAGTGGATC-AAGATGCAGATCTTGTCTTCCCATACTGG
* *
5650735 TGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAAATCGAAGGTA
65 TGGCGAAGTAGATCGCAGAAA-CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATA
5650800 GC
129 GC
* * *
5650802 AGAT-CTA-CTTCCTATA-TGATAGGAAGT-GATCCAAGATACAGATCTTGTCTTCCCATACTGG
1 AGGTCCTATCTTCCTATATTGGTAGGAAGTGGAT-CAAGATGCAGATCTTGTCTTCCCATACTGG
* *
5650863 T-GTGAAGTAGATCGAAGAAAGCAGATC
65 TGGCGAAGTAGATCGCAGAAA-CAGATC
5650890 GACGATGGGG
Statistics
Matches: 548, Mismatches: 24, Indels: 48
0.88 0.04 0.08
Matches are distributed among these distances:
119 5 0.01
120 13 0.02
121 14 0.03
122 53 0.10
123 12 0.02
124 20 0.04
125 31 0.06
126 88 0.16
127 82 0.15
128 49 0.09
129 118 0.22
130 56 0.10
131 7 0.01
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (130 bp):
AGGTCCTATCTTCCTATATTGGTAGGAAGTGGATCAAGATGCAGATCTTGTCTTCCCATACTGGT
GGCGAAGTAGATCGCAGAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGC
Found at i:5662001 original size:44 final size:44
Alignment explanation
Indices: 5661887--5662003 Score: 114
Period size: 44 Copynumber: 2.7 Consensus size: 44
5661877 TTTTAACCCA
* * ** * *
5661887 CTCCACTGTAACTTCAGGGAGATAGGAT-AGTGTCTTCGATCTG
1 CTCCACTGTAACTTCAGGGGGATAAGATCTCTGGCTTCAATCTG
**
5661930 CTCTGCTGTAA-TCTC-GGGGAGATAAGATCTCTGGCTTCAATCTG
1 CTCCACTGTAACT-TCAGGGG-GATAAGATCTCTGGCTTCAATCTG
*
5661974 CTCCACTGTAACTTCAGGGGGACAAGATCT
1 CTCCACTGTAACTTCAGGGGGATAAGATCT
5662004 GTAATTTCCA
Statistics
Matches: 58, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
42 4 0.07
43 18 0.31
44 31 0.53
45 5 0.09
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (44 bp):
CTCCACTGTAACTTCAGGGGGATAAGATCTCTGGCTTCAATCTG
Found at i:5662299 original size:88 final size:88
Alignment explanation
Indices: 5662155--5662659 Score: 827
Period size: 88 Copynumber: 5.8 Consensus size: 88
5662145 AGCTCCAATG
** * *
5662155 CAACCGATGGAGGCAAGGCTTTGT-T-TTCGATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATC
1 CAACCGAAAGAGGCAAGG-TTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATC
5662218 TTTTGTCTTCAACCAGCTCTATCA
65 TTTTGTCTTCAACCAGCTCTATCA
* *
5662242 CAATCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAAAGGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
5662307 TTTGTCTTCAACCAGCTCTATCA
66 TTTGTCTTCAACCAGCTCTATCA
* * *
5662330 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAAAAGCAAGATGT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
*
5662395 TTTGTCTTCAACCAGCTCCATCA
66 TTTGTCTTCAACCAGCTCTATCA
*
5662418 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
*
5662483 TTTGTCTTCAACCAGCTCCATCA
66 TTTGTCTTCAACCAGCTCTATCA
*
5662506 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
5662571 TTTGTCTTCAACCAGCTCTATCA
66 TTTGTCTTCAACCAGCTCTATCA
* * * *
5662594 CAA-CGAAAGAGGCAAGGTTTATGTCTTCGACCTGCTTCACTATCAATGCAGGAAGGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
5662658 TT
66 TT
5662660 AACTTCATTG
Statistics
Matches: 396, Mismatches: 20, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
86 5 0.01
87 74 0.19
88 317 0.80
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (88 bp):
CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
TTTGTCTTCAACCAGCTCTATCA
Found at i:5664398 original size:18 final size:19
Alignment explanation
Indices: 5664362--5664417 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 19
5664352 TTTCTTTTTC
* *
5664362 TCATTTTCATTTTGA-TCT
1 TCATTTTGATTTTTATTCT
*
5664380 TGATTTTGATTTTT-TTCT
1 TCATTTTGATTTTTATTCT
* *
5664398 TCTTTTTGTTTTTTATTCT
1 TCATTTTGATTTTTATTCT
5664417 T
1 T
5664418 AAGCCTTTTG
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 25 0.83
19 5 0.17
ACGTcount: A:0.11, C:0.11, G:0.07, T:0.71
Consensus pattern (19 bp):
TCATTTTGATTTTTATTCT
Found at i:5666918 original size:19 final size:20
Alignment explanation
Indices: 5666889--5666937 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
5666879 CACTTCGTGA
* *
5666889 AAATCTAATGCATATG-ATG
1 AAATGTAATGCAAATGCATG
*
5666908 CAATGTAATGCAAATGCATG
1 AAATGTAATGCAAATGCATG
5666928 AAATG-AATGC
1 AAATGTAATGC
5666938 CTAAAGAGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (20 bp):
AAATGTAATGCAAATGCATG
Done.