Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 133 of 216
Found at i:42253743 original size:79 final size:80
Alignment explanation
Indices: 42253599--42253815 Score: 330
Period size: 79 Copynumber: 2.7 Consensus size: 80
42253589 TTAAAATTCA
* *
42253599 TATAAACTTA-TAAAATTTATTTAAAAAATCATAAAAACTTATAAATATTATAAAAAATTCTAAT
1 TATAAAATTATTAAAATATATTTAAAAAATCATAAAAACTTATAAATATTATAAAAAATTCTAAT
42253663 AATTTATTAAAACTT
66 AATTTATTAAAACTT
*
42253678 TATGAAATTATTAAAATATATTTAAAAAATCAT-AAAACTTATAAATATTATAAAAAATTCTAAT
1 TATAAAATTATTAAAATATATTTAAAAAATCATAAAAACTTATAAATATTATAAAAAATTCTAAT
42253742 AATTTATTAAAACTT
66 AATTTATTAAAACTT
** * * *
42253757 TATAAAATTATTAAAATATATTTAAAATTTTATAAAAGATTTATAAACATTCATAAAAA
1 TATAAAATTATTAAAATATATTTAAAAAATCATAAAA-ACTTATAAATATT-ATAAAAA
42253816 TTTATAAAAA
Statistics
Matches: 125, Mismatches: 9, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
79 83 0.66
80 24 0.19
81 11 0.09
82 7 0.06
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.39
Consensus pattern (80 bp):
TATAAAATTATTAAAATATATTTAAAAAATCATAAAAACTTATAAATATTATAAAAAATTCTAAT
AATTTATTAAAACTT
Found at i:42253825 original size:10 final size:10
Alignment explanation
Indices: 42253591--42253826 Score: 96
Period size: 10 Copynumber: 23.5 Consensus size: 10
42253581 TAAAAATATT
*
42253591 AAAATTCATA
1 AAAATTTATA
* *
42253601 TAAACTTAT-
1 AAAATTTATA
42253610 AAAATTTATTTA
1 AAAATTTA--TA
* *
42253622 AAAAATCATA
1 AAAATTTATA
*
42253632 AAAACTTATA
1 AAAATTTATA
*
42253642 AATA-TTATA
1 AAAATTTATA
* *
42253651 AAAAATTCTA
1 AAAATTTATA
*
42253661 ATAATTTATTA
1 AAAATTTA-TA
*
42253672 AAACTTTAT-
1 AAAATTTATA
*
42253681 GAAA-TTATTA
1 AAAATTTA-TA
42253691 AAATATATT-TA
1 AAA-AT-TTATA
* *
42253702 AAAAATCAT-
1 AAAATTTATA
*
42253711 AAAACTTATA
1 AAAATTTATA
*
42253721 AATA-TTATA
1 AAAATTTATA
* *
42253730 AAAAATTCTA
1 AAAATTTATA
*
42253740 ATAATTTATTA
1 AAAATTTA-TA
*
42253751 AAACTTTAT-
1 AAAATTTATA
42253760 AAAA-TTATTA
1 AAAATTTA-TA
42253770 AAATATATT-TA
1 AAA-AT-TTATA
*
42253781 AAATTTTATA
1 AAAATTTATA
42253791 AAAGATTTATA
1 AAA-ATTTATA
* *
42253802 AACATTCATA
1 AAAATTTATA
42253812 AAAATTTATA
1 AAAATTTATA
42253822 AAAAT
1 AAAAT
42253827 AATAAATTAT
Statistics
Matches: 166, Mismatches: 39, Indels: 42
0.67 0.16 0.17
Matches are distributed among these distances:
8 6 0.04
9 39 0.23
10 74 0.45
11 37 0.22
12 6 0.04
13 4 0.02
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.39
Consensus pattern (10 bp):
AAAATTTATA
Found at i:42253843 original size:17 final size:16
Alignment explanation
Indices: 42253809--42253841 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
42253799 ATAAACATTC
42253809 ATAAAAATTTATAAAA
1 ATAAAAATTTATAAAA
42253825 ATAATAAA-TTATAAAA
1 ATAA-AAATTTATAAAA
42253841 A
1 A
42253842 ATGTTATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATAAAAATTTATAAAA
Found at i:42254438 original size:19 final size:19
Alignment explanation
Indices: 42254414--42254461 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
42254404 ATTTTATAGC
** *
42254414 AATTTTAATATTTTTTATG
1 AATTTTAATAAGTTTTAGG
* *
42254433 ATTTTTTATAAGTTTTAGG
1 AATTTTAATAAGTTTTAGG
42254452 AATTTTAATA
1 AATTTTAATA
42254462 CATTATTATA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.58
Consensus pattern (19 bp):
AATTTTAATAAGTTTTAGG
Found at i:42256776 original size:13 final size:13
Alignment explanation
Indices: 42256758--42256787 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
42256748 ACTCCTTCTC
42256758 GAAACCATTTTTT
1 GAAACCATTTTTT
42256771 GAAACCATTTTTT
1 GAAACCATTTTTT
42256784 GAAA
1 GAAA
42256788 ATAAAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (13 bp):
GAAACCATTTTTT
Found at i:42257654 original size:15 final size:15
Alignment explanation
Indices: 42257634--42257662 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
42257624 CAAATAGTGT
42257634 ATAAATATATATATC
1 ATAAATATATATATC
42257649 ATAAATATATATAT
1 ATAAATATATATAT
42257663 GTATGGACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
ATAAATATATATATC
Found at i:42257860 original size:3 final size:3
Alignment explanation
Indices: 42257852--42257899 Score: 62
Period size: 3 Copynumber: 16.3 Consensus size: 3
42257842 ATGTATAGGT
* * *
42257852 ATA ATA ATA GTA ATA ATA ATA CTA ATA AT- ATA ATA ATA ATG ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
42257899 A
1 A
42257900 CAAAAATAAC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:42257896 original size:17 final size:17
Alignment explanation
Indices: 42257852--42257898 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
42257842 ATGTATAGGT
*
42257852 ATAATAATAGTAATAATA
1 ATAATAATAAT-ATAATA
*
42257870 ATACTAATAATATAATA
1 ATAATAATAATATAATA
*
42257887 ATAATGATAATA
1 ATAATAATAATA
42257899 ACAAAAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 16 0.64
18 9 0.36
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (17 bp):
ATAATAATAATATAATA
Found at i:42258922 original size:51 final size:51
Alignment explanation
Indices: 42258867--42259124 Score: 174
Period size: 50 Copynumber: 5.1 Consensus size: 51
42258857 TTGCAATGTC
* * *
42258867 AGGGAAACCAGATCCGCCGTCGTAACTTCAATCTATTCCACTGCACCACTA
1 AGGGAAACCAGATCCGCCGTCGTGACTTCAATCTGTTCAACTGCACCACTA
* * * * * * * *
42258918 AGGGAGTA--AGATTCGCCGTTGTGGCTTCAATCTTTTTAAATTGCA--ATGTCA
1 AGGGA-AACCAGATCCGCCGTCGTGACTTCAATC-TGTTCAACTGCACCA-CT-A
* *
42258969 A-GGAAACCAGATCTGCCGTCGTGACTTCAATCTGTTCCACTGCACCACTA
1 AGGGAAACCAGATCCGCCGTCGTGACTTCAATCTGTTCAACTGCACCACTA
* * * * * * * * * *
42259019 AGGGAGTA--AGATCCGCCGTTGTGGCTTCAATCTTTTTAAAT-TACAATGTC
1 AGGGA-AACCAGATCCGCCGTCGTGACTTCAATCTGTTCAACTGCACCA-CTA
* *
42259069 AGGGAAACCAGATCCGCCGTCGTGACTTCAATCTGTTCTACTGCACCGCT-
1 AGGGAAACCAGATCCGCCGTCGTGACTTCAATCTGTTCAACTGCACCACTA
42259119 AGGGAA
1 AGGGAA
42259125 GTAAGATTCG
Statistics
Matches: 150, Mismatches: 43, Indels: 29
0.68 0.19 0.13
Matches are distributed among these distances:
49 6 0.04
50 72 0.48
51 67 0.45
52 5 0.03
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (51 bp):
AGGGAAACCAGATCCGCCGTCGTGACTTCAATCTGTTCAACTGCACCACTA
Found at i:42258950 original size:50 final size:50
Alignment explanation
Indices: 42258892--42259161 Score: 165
Period size: 50 Copynumber: 5.4 Consensus size: 50
42258882 GCCGTCGTAA
*
42258892 CTTCAATCTATTCCACTGCACCACTAAGGGAGTAAGATTCGCCGTTGTGG
1 CTTCAATCTTTTCCACTGCACCACTAAGGGAGTAAGATTCGCCGTTGTGG
** * * * *** * *
42258942 CTTCAATCTTTTTAAATTGCA--ATGTCAAGGAAACCAGA-TCTGCCGTCGTGA
1 CTTCAATC-TTTTCCACTGCACCA-CT-AAGGGAGTAAGATTC-GCCGTTGTGG
* *
42258993 CTTCAATCTGTTCCACTGCACCACTAAGGGAGTAAGATCCGCCGTTGTGG
1 CTTCAATCTTTTCCACTGCACCACTAAGGGAGTAAGATTCGCCGTTGTGG
** * * * * * * * * *
42259043 CTTCAATCTTTTTAAAT-TACAATGTCAGGGA-AACCAGATCCGCCGTCGTGA
1 CTTCAATCTTTTCCACTGCACCA-CTAAGGGAGTA--AGATTCGCCGTTGTGG
* * * *
42259094 CTTCAATCTGTTCTACTGCACCGCT-AGGGAAGTAAGATTCGCCATTGTGG
1 CTTCAATCTTTTCCACTGCACCACTAAGGG-AGTAAGATTCGCCGTTGTGG
*
42259144 CTTCAATCTTTTTCACTG
1 CTTCAATCTTTTCCACTG
42259162 TAATGCCAAA
Statistics
Matches: 157, Mismatches: 50, Indels: 26
0.67 0.21 0.11
Matches are distributed among these distances:
49 5 0.03
50 85 0.54
51 63 0.40
52 4 0.03
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (50 bp):
CTTCAATCTTTTCCACTGCACCACTAAGGGAGTAAGATTCGCCGTTGTGG
Found at i:42259016 original size:101 final size:101
Alignment explanation
Indices: 42258841--42259156 Score: 535
Period size: 101 Copynumber: 3.1 Consensus size: 101
42258831 GTAAGATTGA
* *
42258841 CTTCAATCTTTTTAAATTGCAATGTCAGGGAAACCAGATCCGCCGTCGTAACTTCAATCTATTCC
1 CTTCAATCTTTTTAAATTGCAATGTCAGGGAAACCAGATCCGCCGTCGTGACTTCAATCTGTTCC
42258906 ACTGCACCACTAAGGGAGTAAGATTCGCCGTTGTGG
66 ACTGCACCACTAAGGGAGTAAGATTCGCCGTTGTGG
* *
42258942 CTTCAATCTTTTTAAATTGCAATGTCAAGGAAACCAGATCTGCCGTCGTGACTTCAATCTGTTCC
1 CTTCAATCTTTTTAAATTGCAATGTCAGGGAAACCAGATCCGCCGTCGTGACTTCAATCTGTTCC
*
42259007 ACTGCACCACTAAGGGAGTAAGATCCGCCGTTGTGG
66 ACTGCACCACTAAGGGAGTAAGATTCGCCGTTGTGG
* *
42259043 CTTCAATCTTTTTAAATTACAATGTCAGGGAAACCAGATCCGCCGTCGTGACTTCAATCTGTTCT
1 CTTCAATCTTTTTAAATTGCAATGTCAGGGAAACCAGATCCGCCGTCGTGACTTCAATCTGTTCC
* *
42259108 ACTGCACCGCT-AGGGAAGTAAGATTCGCCATTGTGG
66 ACTGCACCACTAAGGG-AGTAAGATTCGCCGTTGTGG
42259144 CTTCAATCTTTTT
1 CTTCAATCTTTTT
42259157 CACTGTAATG
Statistics
Matches: 202, Mismatches: 12, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
100 4 0.02
101 198 0.98
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (101 bp):
CTTCAATCTTTTTAAATTGCAATGTCAGGGAAACCAGATCCGCCGTCGTGACTTCAATCTGTTCC
ACTGCACCACTAAGGGAGTAAGATTCGCCGTTGTGG
Found at i:42259144 original size:202 final size:193
Alignment explanation
Indices: 42258791--42259156 Score: 545
Period size: 202 Copynumber: 1.8 Consensus size: 193
42258781 ACAAGATTCA
* *
42258791 CCGTTGTGGCTTCAATCTATTCCACTGCACCACTAAGGGAGTAAGATTGACTTCAATCTTTTTAA
1 CCGTCGTGACTTCAATCTATTCCACTGCACCACTAAGGGAGTAAGATTGACTTCAATCTTTTTAA
*
42258856 ATTGCAATGTCAGGGAAACCAGATCCGCCGTCGTAACTTCAATCTATTCCACTGCACCACTAAGG
66 ATTACAATGTCAGGGAAACCAGATCCGCCGTCGTAACTTCAATCTATTCCACTGCACCACTAAGG
*
42258921 GAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAAATTGCAATGTCAAGGAAACCAGATCTG
131 GAGTAAGATTCGCCATTGTGGCTTCAATCTTTTTAAATTGCAATGTCAAGGAAACCAGATCTG
* *
42258984 CCGTCGTGACTTCAATCTGTTCCACTGCACCACTAAGGGAGTAAGATCCGCCGTTGTGGCTTCAA
1 CCGTCGTGACTTCAATCTATTCCACTGCACCACTAAGGGAGTAAGA--------T-TGACTTCAA
* * *
42259049 TCTTTTTAAATTACAATGTCAGGGAAACCAGATCCGCCGTCGTGACTTCAATCTGTTCTACTGCA
57 TCTTTTTAAATTACAATGTCAGGGAAACCAGATCCGCCGTCGTAACTTCAATCTATTCCACTGCA
*
42259114 CCGCT-AGGGAAGTAAGATTCGCCATTGTGGCTTCAATCTTTTT
122 CCACTAAGGG-AGTAAGATTCGCCATTGTGGCTTCAATCTTTTT
42259157 CACTGTAATG
Statistics
Matches: 153, Mismatches: 10, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
193 43 0.28
201 5 0.03
202 105 0.69
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (193 bp):
CCGTCGTGACTTCAATCTATTCCACTGCACCACTAAGGGAGTAAGATTGACTTCAATCTTTTTAA
ATTACAATGTCAGGGAAACCAGATCCGCCGTCGTAACTTCAATCTATTCCACTGCACCACTAAGG
GAGTAAGATTCGCCATTGTGGCTTCAATCTTTTTAAATTGCAATGTCAAGGAAACCAGATCTG
Found at i:42261174 original size:40 final size:39
Alignment explanation
Indices: 42261061--42261246 Score: 205
Period size: 40 Copynumber: 4.6 Consensus size: 39
42261051 TTGAATGATG
* * * *
42261061 TCCGGGCTAAGTCCTGAAGGC-TTTGTGCTAGGTGACCATA
1 TCCGGGCTAAGTCC-GAAGGCATTTGTGCGA-GTTACTAAA
* **
42261101 TCCGGACTAAGATCCGAAGGCATTTGTATGAGTTACTAAA
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
*
42261141 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
*
42261181 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
42261222 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
42261247 AACGAGTAGC
Statistics
Matches: 129, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 117 0.91
41 11 0.09
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:42261253 original size:80 final size:79
Alignment explanation
Indices: 42261114--42261269 Score: 192
Period size: 80 Copynumber: 2.0 Consensus size: 79
42261104 GGACTAAGAT
* **
42261114 CCGAAGGCATTTGTATGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTA-CT
1 CCGAAGGCATTTGTACGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAG-TAGCT
42261178 AAATCCGGGTTAAGTC
65 AAATCC-GGTTAAGTC
* * *
42261194 CCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATG-TCCCGAAGGCATTTGAACGAGTAGC
1 CCGAAGGCATTTGTACGAGTTACTA-AATCCGGACTAAGAT-CCGAAGGCATTTGAACGAGTAGC
*
42261257 TATATCCGGTTAA
64 TAAATCCGGTTAA
42261270 ATTCCAAAGG
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
79 9 0.14
80 55 0.83
81 2 0.03
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.27
Consensus pattern (79 bp):
CCGAAGGCATTTGTACGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGTAGCTA
AATCCGGTTAAGTC
Found at i:42265175 original size:12 final size:12
Alignment explanation
Indices: 42265158--42265184 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
42265148 AGGCTAAGGT
42265158 AGCCAACGCATC
1 AGCCAACGCATC
42265170 AGCCAACGCATC
1 AGCCAACGCATC
42265182 AGC
1 AGC
42265185 TATCTGATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.41, G:0.19, T:0.07
Consensus pattern (12 bp):
AGCCAACGCATC
Found at i:42267331 original size:23 final size:22
Alignment explanation
Indices: 42267305--42267357 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
42267295 TGAACAAAAT
*
42267305 ATGATTATGAAATA-AATAAAAGA
1 ATGATTA-GAAAAAGAAT-AAAGA
42267328 ATGATGTAGAAAAAGAATAAAGA
1 ATGAT-TAGAAAAAGAATAAAGA
*
42267351 ATAATTA
1 ATGATTA
42267358 CTCGAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 2 0.08
23 19 0.73
24 5 0.19
ACGTcount: A:0.60, C:0.00, G:0.15, T:0.25
Consensus pattern (22 bp):
ATGATTAGAAAAAGAATAAAGA
Found at i:42267392 original size:27 final size:26
Alignment explanation
Indices: 42267337--42267392 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
42267327 AATGATGTAG
* *
42267337 AAAAAGAATAAAGAATAATTACTCGA
1 AAAAAGAATAAAGAATAATGACTCAA
* *
42267363 AAAAAGAATGAAAGAATACTGGCTCAA
1 AAAAAGAAT-AAAGAATAATGACTCAA
42267390 AAA
1 AAA
42267393 TACATACGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 9 0.36
27 16 0.64
ACGTcount: A:0.61, C:0.09, G:0.14, T:0.16
Consensus pattern (26 bp):
AAAAAGAATAAAGAATAATGACTCAA
Found at i:42274953 original size:3 final size:3
Alignment explanation
Indices: 42274945--42275003 Score: 66
Period size: 3 Copynumber: 20.0 Consensus size: 3
42274935 ATGTATAGGT
* * *
42274945 ATA ATA ATA GTA ATA ATA ATA CTA ATA AT- ATA ATA ATA ATG ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
42274992 ACA AAA ATA ATA
1 ATA ATA ATA ATA
42275004 GCAGCTTAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:42274989 original size:17 final size:17
Alignment explanation
Indices: 42274945--42274991 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
42274935 ATGTATAGGT
*
42274945 ATAATAATAGTAATAATA
1 ATAATAATAAT-ATAATA
*
42274963 ATACTAATAATATAATA
1 ATAATAATAATATAATA
*
42274980 ATAATGATAATA
1 ATAATAATAATA
42274992 ACAAAAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 16 0.64
18 9 0.36
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (17 bp):
ATAATAATAATATAATA
Found at i:42281560 original size:9 final size:9
Alignment explanation
Indices: 42281548--42281643 Score: 51
Period size: 10 Copynumber: 10.9 Consensus size: 9
42281538 GTAGAGATTT
42281548 TAATTTTTA
1 TAATTTTTA
42281557 TAA-TTTTA
1 TAATTTTTA
*
42281565 T--TTATTA
1 TAATTTTTA
*
42281572 TAATATTTA
1 TAATTTTTA
*
42281581 TAATATATTA
1 TAAT-TTTTA
*
42281591 TTATTCTTTA
1 TAATT-TTTA
*
42281601 TAAGTTTATA
1 TAA-TTTTTA
*
42281611 TCAATTTTAA
1 T-AATTTTTA
42281621 T-A-TTTTA
1 TAATTTTTA
*
42281628 -AATTTTAA
1 TAATTTTTA
42281636 TAATTTTT
1 TAATTTTT
42281644 CTGATATATA
Statistics
Matches: 63, Mismatches: 14, Indels: 20
0.65 0.14 0.21
Matches are distributed among these distances:
7 10 0.16
8 11 0.17
9 18 0.29
10 20 0.32
11 4 0.06
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.60
Consensus pattern (9 bp):
TAATTTTTA
Found at i:42281564 original size:15 final size:16
Alignment explanation
Indices: 42281544--42281580 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
42281534 GATTGTAGAG
42281544 ATTTTAATTT-TTATA
1 ATTTTAATTTATTATA
42281559 ATTTT-ATTTATTATA
1 ATTTTAATTTATTATA
42281574 ATATTTA
1 AT-TTTA
42281581 TAATATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 4 0.21
15 12 0.63
16 3 0.16
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTTTAATTTATTATA
Found at i:42281633 original size:15 final size:16
Alignment explanation
Indices: 42281613--42281642 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
42281603 AGTTTATATC
42281613 AATTTTAAT-ATTTTA
1 AATTTTAATAATTTTA
42281628 AATTTTAATAATTTT
1 AATTTTAATAATTTT
42281643 TCTGATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
AATTTTAATAATTTTA
Found at i:42284769 original size:32 final size:32
Alignment explanation
Indices: 42284726--42284802 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
42284716 CAAAATAAAT
** *
42284726 TATGAAAAGTTACGAATGTGAAGAGGCTTGAA
1 TATGAAAAGTTACGAATGCAAAGAGACTTGAA
* **
42284758 TATGAAGAGTTAATAATGCAAAGAGACTTGAA
1 TATGAAAAGTTACGAATGCAAAGAGACTTGAA
*
42284790 GATGAAAAGTTAC
1 TATGAAAAGTTAC
42284803 ACACATGCAT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.44, C:0.06, G:0.25, T:0.25
Consensus pattern (32 bp):
TATGAAAAGTTACGAATGCAAAGAGACTTGAA
Found at i:42289274 original size:32 final size:32
Alignment explanation
Indices: 42289231--42289307 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
42289221 CAAAATAAAT
** *
42289231 TATGAAAAGTTACGAATGTGAAGAGGCTTGAA
1 TATGAAAAGTTACGAATGCAAAGAGACTTGAA
* **
42289263 TATGAAGAGTTAATAATGCAAAGAGACTTGAA
1 TATGAAAAGTTACGAATGCAAAGAGACTTGAA
*
42289295 GATGAAAAGTTAC
1 TATGAAAAGTTAC
42289308 ACACATGCAT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.44, C:0.06, G:0.25, T:0.25
Consensus pattern (32 bp):
TATGAAAAGTTACGAATGCAAAGAGACTTGAA
Found at i:42294284 original size:20 final size:21
Alignment explanation
Indices: 42294245--42294284 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
42294235 ATGATGACAC
* *
42294245 GGATGTAATTTTGTATTGAGT
1 GGATGTAATTTAGTAATGAGT
42294266 GGAT-TAATTTAGTAATGAG
1 GGATGTAATTTAGTAATGAG
42294285 GTGTGTTACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (21 bp):
GGATGTAATTTAGTAATGAGT
Found at i:42298726 original size:40 final size:40
Alignment explanation
Indices: 42298682--42298760 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
42298672 TCGACCACGT
*
42298682 GCACATAGTGTGTGATATTCTCGAGTATCCAATATTATTA
1 GCACATAGTGTGTGAGATTCTCGAGTATCCAATATTATTA
*
42298722 GCACATAGTGTGTGAGATTCTCGAGTGTCCAATATTATT
1 GCACATAGTGTGTGAGATTCTCGAGTATCCAATATTATT
42298761 CTAGTGGTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (40 bp):
GCACATAGTGTGTGAGATTCTCGAGTATCCAATATTATTA
Found at i:42308167 original size:20 final size:20
Alignment explanation
Indices: 42308138--42308187 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
42308128 AAATCAATAG
* *
42308138 GTATCAATACTTGACTTA-TA
1 GTATCGATACTT-ACTTACAA
*
42308158 GTATCGATACTTCCTTACAA
1 GTATCGATACTTACTTACAA
42308178 GTATCGATAC
1 GTATCGATAC
42308188 CAAATTCTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (20 bp):
GTATCGATACTTACTTACAA
Found at i:42310729 original size:18 final size:18
Alignment explanation
Indices: 42310706--42310747 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
42310696 GTAACATTTT
*
42310706 AAAACTTTAACAGTTGTG
1 AAAACTTTAACAATTGTG
*
42310724 AAAACTTTAACAATTTTG
1 AAAACTTTAACAATTGTG
42310742 AAAACT
1 AAAACT
42310748 AATGCTCGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (18 bp):
AAAACTTTAACAATTGTG
Found at i:42320770 original size:24 final size:24
Alignment explanation
Indices: 42320738--42320786 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
42320728 CAGGAAATAA
42320738 CCCATTATTTCATAACCTTAGATT
1 CCCATTATTTCATAACCTTAGATT
42320762 CCCATTATTTCATAACCTTAGATT
1 CCCATTATTTCATAACCTTAGATT
42320786 C
1 C
42320787 TAGCTCTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.27, G:0.04, T:0.41
Consensus pattern (24 bp):
CCCATTATTTCATAACCTTAGATT
Found at i:42329208 original size:20 final size:19
Alignment explanation
Indices: 42329153--42329197 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
42329143 CATTTCATTG
*
42329153 AGCTCCAATTAGCTCATTTCC
1 AGCTCC-ATGAGCTCATTT-C
*
42329174 AGCTCCATGAACTCATTTC
1 AGCTCCATGAGCTCATTTC
42329193 AGCTC
1 AGCTC
42329198 ATTTGAGCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 6 0.27
20 10 0.45
21 6 0.27
ACGTcount: A:0.24, C:0.33, G:0.11, T:0.31
Consensus pattern (19 bp):
AGCTCCATGAGCTCATTTC
Found at i:42331412 original size:25 final size:25
Alignment explanation
Indices: 42331329--42331412 Score: 69
Period size: 25 Copynumber: 3.4 Consensus size: 25
42331319 GCTCTCTCTC
** **
42331329 GAGCCATATAAAAAGAAGCTCATGT
1 GAGCCATATAACGAGAAGCTCATAA
* * * **
42331354 GAGCCATGTAACGGGAAGCTTATCC
1 GAGCCATATAACGAGAAGCTCATAA
* *
42331379 GGGCTATATAACGAGAAGCTCATAA
1 GAGCCATATAACGAGAAGCTCATAA
42331404 GAGCCATAT
1 GAGCCATAT
42331413 TTAGGAAACT
Statistics
Matches: 43, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.20
Consensus pattern (25 bp):
GAGCCATATAACGAGAAGCTCATAA
Found at i:42331457 original size:25 final size:25
Alignment explanation
Indices: 42331429--42331482 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 25
42331419 AACTTCGGAT
* *
42331429 AGCCATATATCGGGAAGTTCAAGCG
1 AGCCATATATCGGGAAGATCAAGAG
*
42331454 AGCC--ATATCGGGAAGATCTAGAG
1 AGCCATATATCGGGAAGATCAAGAG
42331477 AGCCAT
1 AGCCAT
42331483 TAATCAAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
23 20 0.83
25 4 0.17
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.19
Consensus pattern (25 bp):
AGCCATATATCGGGAAGATCAAGAG
Found at i:42331465 original size:23 final size:23
Alignment explanation
Indices: 42331435--42331482 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
42331425 GGATAGCCAT
* *
42331435 ATATCGGGAAGTTCAAGCGAGCC
1 ATATCGGGAAGATCAAGAGAGCC
*
42331458 ATATCGGGAAGATCTAGAGAGCC
1 ATATCGGGAAGATCAAGAGAGCC
42331481 AT
1 AT
42331483 TAATCAAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.33, C:0.19, G:0.29, T:0.19
Consensus pattern (23 bp):
ATATCGGGAAGATCAAGAGAGCC
Found at i:42331532 original size:26 final size:26
Alignment explanation
Indices: 42331475--42331524 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
42331465 GAAGATCTAG
42331475 AGAGCCATTAATCAAGAAGCTCACAA
1 AGAGCCATTAATCAAGAAGCTCACAA
* *
42331501 AGAGCCTTTAATCAGGAAGCTCAC
1 AGAGCCATTAATCAAGAAGCTCAC
42331525 GACAAGCCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.18
Consensus pattern (26 bp):
AGAGCCATTAATCAAGAAGCTCACAA
Found at i:42335107 original size:28 final size:26
Alignment explanation
Indices: 42335067--42335151 Score: 73
Period size: 29 Copynumber: 3.0 Consensus size: 26
42335057 TGTTAATGAT
*
42335067 TTTAACAATAAAATCTAAATTTTTAAA
1 TTTAAAAATAAAATCTAAA-TTTTAAA
42335094 TTTAAAAAGTAAAAAAT-TAAAATTTTAAA
1 TTTAAAAA-T--AAAATCT-AAATTTTAAA
**
42335123 AATAAAAATAAAAGTACTAAATTTTAAA
1 TTTAAAAATAAAA-T-CTAAATTTTAAA
42335151 T
1 T
42335152 ATACAAAGAT
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
26 4 0.09
27 8 0.17
28 12 0.26
29 15 0.32
30 8 0.17
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (26 bp):
TTTAAAAATAAAATCTAAATTTTAAA
Found at i:42335108 original size:29 final size:28
Alignment explanation
Indices: 42335076--42335154 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 28
42335066 TTTTAACAAT
*
42335076 AAAATCTAAATTTTTAAATTTAAAAAGTAA
1 AAAATCTAAA-TTTTAAATATAAAAA-TAA
*
42335106 AAAAT-TAAAATTTTAAAAATAAAAAT-A
1 AAAATCT-AAATTTTAAATATAAAAATAA
*
42335133 AAAGTACTAAATTTTAAATATA
1 AAAAT-CTAAATTTTAAATATA
42335155 CAAAGATTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
27 5 0.12
28 14 0.33
29 15 0.36
30 8 0.19
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34
Consensus pattern (28 bp):
AAAATCTAAATTTTAAATATAAAAATAA
Found at i:42335266 original size:17 final size:18
Alignment explanation
Indices: 42335239--42335274 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
42335229 ATCGGAAGTG
*
42335239 GTTGTTATTTTTTTCATT
1 GTTGTTATTTTTCTCATT
42335257 GTTG-TATTTTTCTCATT
1 GTTGTTATTTTTCTCATT
42335274 G
1 G
42335275 GTTAGGGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.11, C:0.08, G:0.14, T:0.67
Consensus pattern (18 bp):
GTTGTTATTTTTCTCATT
Found at i:42338673 original size:140 final size:140
Alignment explanation
Indices: 42338417--42338714 Score: 434
Period size: 140 Copynumber: 2.1 Consensus size: 140
42338407 AATATTTTAA
* *
42338417 TGTCGGCCCAAAAGTATCGGTATAGTATTGAACAAAGCCGACTCTTATTTAAGCATTGCCTTAGG
1 TGTCGGCCCAAAAGTGTCGGCATAGTATTGAACAAAGCCGACTCTTATTTAAGCATTGCCTTAGG
* *
42338482 CATGCATATCCCAACCCTTATACAAAGAGTTGGCCAAAGCGTATGTCGGCAAGTCTATCCCAACA
66 CATGCATATCCCAACCCTTATAAAAAGAGTTGACCAAAGCGTATGTCGGCAAGTCTATCCCAACA
*
42338547 CTAAGGAAAG
131 CTAAGAAAAG
* * * * ** *
42338557 TGTTGGCCCAAAAGTGTCGGCATAGTGTTGGACAAAGTCGACTCTTATTTAAGTGTTGTCTTAGG
1 TGTCGGCCCAAAAGTGTCGGCATAGTATTGAACAAAGCCGACTCTTATTTAAGCATTGCCTTAGG
* * * *
42338622 TATGCATATCTCAACCCTTATAAAAAGATTTGACCAAAGCGTATGTCGGCAAGTCTATCCTAACA
66 CATGCATATCCCAACCCTTATAAAAAGAGTTGACCAAAGCGTATGTCGGCAAGTCTATCCCAACA
*
42338687 CTTAGAAAAG
131 CTAAGAAAAG
*
42338697 TGTCGGACCAAAAGTGTC
1 TGTCGGCCCAAAAGTGTC
42338715 ATCTTAGGAC
Statistics
Matches: 139, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
140 139 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (140 bp):
TGTCGGCCCAAAAGTGTCGGCATAGTATTGAACAAAGCCGACTCTTATTTAAGCATTGCCTTAGG
CATGCATATCCCAACCCTTATAAAAAGAGTTGACCAAAGCGTATGTCGGCAAGTCTATCCCAACA
CTAAGAAAAG
Found at i:42338951 original size:43 final size:43
Alignment explanation
Indices: 42338903--42339025 Score: 192
Period size: 43 Copynumber: 2.9 Consensus size: 43
42338893 GTGTTGCTAA
* *
42338903 CTTTAGCAGCGCTTATCCCACAAACGCCGCTAAAAACCAAGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAAACCAAGAC
* *
42338946 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAATAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAAACCAAGAC
* *
42338989 CTTTAGCGGTGCTTTTCCCACAAACGCCGCCAAAAAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAAAC
42339026 ATGAATTAAA
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 73 1.00
ACGTcount: A:0.30, C:0.35, G:0.15, T:0.20
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAAACCAAGAC
Found at i:42339050 original size:16 final size:16
Alignment explanation
Indices: 42339029--42339059 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42339019 CAAAAACATG
42339029 AATTAAAAAATATTTT
1 AATTAAAAAATATTTT
*
42339045 AATTAAATAATATTT
1 AATTAAAAAATATTT
42339060 ATTTCTATCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTAAAAAATATTTT
Found at i:42339245 original size:18 final size:18
Alignment explanation
Indices: 42339222--42339281 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
42339212 TTAAAACAAG
42339222 TTACATTCTATATTAGAA
1 TTACATTCTATATTAGAA
*** * *
42339240 TTACATAAGAAAATT-G-T
1 TTACAT-TCTATATTAGAA
42339257 TTACATTCTATATTAGAA
1 TTACATTCTATATTAGAA
42339275 TTACATT
1 TTACATT
42339282 AGAATTACAT
Statistics
Matches: 29, Mismatches: 10, Indels: 6
0.64 0.22 0.13
Matches are distributed among these distances:
16 4 0.14
17 7 0.24
18 14 0.48
19 4 0.14
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (18 bp):
TTACATTCTATATTAGAA
Found at i:42343589 original size:52 final size:53
Alignment explanation
Indices: 42343532--42343659 Score: 231
Period size: 52 Copynumber: 2.4 Consensus size: 53
42343522 TATTATTTTT
42343532 CTTTTATTTATTTATTTATCAATAAATAGTTACCTATCC-AATCAATCTGTTG
1 CTTTTATTTATTTATTTATCAATAAATAGTTACCTATCCGAATCAATCTGTTG
* *
42343584 CTTTTATTTATTTATTTGTCAATAAATAGTTACCTATCCGTATCAATCTGTTG
1 CTTTTATTTATTTATTTATCAATAAATAGTTACCTATCCGAATCAATCTGTTG
42343637 CTTTTATTTATTTATTTATCAAT
1 CTTTTATTTATTTATTTATCAAT
42343660 GTTTTTTTTA
Statistics
Matches: 72, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
52 38 0.53
53 34 0.47
ACGTcount: A:0.28, C:0.14, G:0.06, T:0.52
Consensus pattern (53 bp):
CTTTTATTTATTTATTTATCAATAAATAGTTACCTATCCGAATCAATCTGTTG
Found at i:42343948 original size:34 final size:35
Alignment explanation
Indices: 42343897--42343968 Score: 105
Period size: 34 Copynumber: 2.1 Consensus size: 35
42343887 CACTAACTAT
42343897 TAACCTCTAACCTCTAACCCCTAA-CCTTAAACCCC
1 TAACCTCTAACCTCTAACCCCTAACCCTT-AACCCC
42343932 TAACC-CTAA-CTACTAACCCCTAACCCTTAACCCC
1 TAACCTCTAACCT-CTAACCCCTAACCCTTAACCCC
42343966 TAA
1 TAA
42343969 ACATTATTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
33 2 0.06
34 24 0.69
35 9 0.26
ACGTcount: A:0.33, C:0.44, G:0.00, T:0.22
Consensus pattern (35 bp):
TAACCTCTAACCTCTAACCCCTAACCCTTAACCCC
Found at i:42343957 original size:7 final size:7
Alignment explanation
Indices: 42343897--42343968 Score: 67
Period size: 7 Copynumber: 10.4 Consensus size: 7
42343887 CACTAACTAT
*
42343897 TAACCTC
1 TAACCCC
*
42343904 TAACCTC
1 TAACCCC
42343911 TAACCCC
1 TAACCCC
*
42343918 TAA-CCT
1 TAACCCC
42343924 TAAACCCC
1 T-AACCCC
42343932 TAA-CCC
1 TAACCCC
**
42343938 TAACTAC
1 TAACCCC
42343945 TAACCCC
1 TAACCCC
*
42343952 TAACCCT
1 TAACCCC
42343959 TAACCCC
1 TAACCCC
42343966 TAA
1 TAA
42343969 ACATTATTTA
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
6 9 0.17
7 41 0.77
8 3 0.06
ACGTcount: A:0.33, C:0.44, G:0.00, T:0.22
Consensus pattern (7 bp):
TAACCCC
Found at i:42344608 original size:41 final size:41
Alignment explanation
Indices: 42344551--42344825 Score: 372
Period size: 41 Copynumber: 6.7 Consensus size: 41
42344541 AAATGTTTTT
* *
42344551 GCGGCGCTTTTCCAAAAACGCTGGTAAAGGTCT-ATGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGGTCTGA-GCATTA
*
42344592 GCGGCGCTTTTCCAAAAACGCCGCTAAAAGTCTGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGGTCTGAGCATTA
*** * *
42344633 GCGGCGCTTTTTTTAAAATGCCGCTATAGGTCTGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGGTCTGAGCATTA
* * * *
42344674 GCGGCGCTTTTTCAAAAACACCACTAAAGTTCTGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGGTCTGAGCATTA
* * *
42344715 GCGGCACTTTTCCATAAACGCCGCTAAAGGTCTGATCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGGTCTGAGCATTA
*
42344756 GTGGCGCTTTTCCAAAAACGCCGCTAAAGGTCTGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGGTCTGAGCATTA
* *
42344797 GGGGCGCTTTTCCAAAAACGCCACTAAAG
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAG
42344826 CCTCGAAAGG
Statistics
Matches: 204, Mismatches: 29, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
41 203 1.00
42 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (41 bp):
GCGGCGCTTTTCCAAAAACGCCGCTAAAGGTCTGAGCATTA
Found at i:42344907 original size:40 final size:39
Alignment explanation
Indices: 42344863--42344958 Score: 102
Period size: 39 Copynumber: 2.4 Consensus size: 39
42344853 TGGGCTTAGG
* * *
42344863 TTTTTTGCGGCGCTTTTCTAAAAAATGCCGCTAATGCTCA
1 TTTTTAGCGGCG-TTTTCCAAAAAACGCCGCTAATGCTCA
* * *
42344903 TTTTTAGCGGCGTTTTCCAAAAAGCGCCGCTAGTGCTAA
1 TTTTTAGCGGCGTTTTCCAAAAAACGCCGCTAATGCTCA
* *
42344942 TCTTTAGCTGCGATTTT
1 TTTTTAGCGGCG-TTTT
42344959 TGAAAAGCGC
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
39 32 0.68
40 15 0.32
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.38
Consensus pattern (39 bp):
TTTTTAGCGGCGTTTTCCAAAAAACGCCGCTAATGCTCA
Found at i:42379329 original size:9 final size:9
Alignment explanation
Indices: 42379315--42379339 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
42379305 CTTGGGTCAG
42379315 AACCTCTTC
1 AACCTCTTC
42379324 AACCTCTTC
1 AACCTCTTC
42379333 AACCTCT
1 AACCTCT
42379340 AATTCCTCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.44, G:0.00, T:0.32
Consensus pattern (9 bp):
AACCTCTTC
Found at i:42379427 original size:21 final size:21
Alignment explanation
Indices: 42379401--42379441 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
42379391 ATCTGCTCAA
* *
42379401 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
42379422 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
42379442 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:42386086 original size:21 final size:20
Alignment explanation
Indices: 42386049--42386087 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
42386039 ATACTTCTTA
*
42386049 TAAAATGAGGAAAAGAAACC
1 TAAAATAAGGAAAAGAAACC
*
42386069 TAAAATAATGGAATAGAAA
1 TAAAATAA-GGAAAAGAAA
42386088 AACTGATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.62, C:0.05, G:0.18, T:0.15
Consensus pattern (20 bp):
TAAAATAAGGAAAAGAAACC
Found at i:42386743 original size:21 final size:21
Alignment explanation
Indices: 42386719--42386759 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
42386709 TCTAAAAAGC
42386719 TCTCAAA-CATCTCTCTAAATT
1 TCTCAAAGC-TCTCTCTAAATT
*
42386740 TCTCAAAGCTCTCTTTAAAT
1 TCTCAAAGCTCTCTCTAAAT
42386760 CACAATTTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.32, C:0.27, G:0.02, T:0.39
Consensus pattern (21 bp):
TCTCAAAGCTCTCTCTAAATT
Found at i:42390222 original size:223 final size:221
Alignment explanation
Indices: 42389830--42390264 Score: 649
Period size: 223 Copynumber: 2.0 Consensus size: 221
42389820 GCAGGATGTA
** * * * *
42389830 CTGTAGAAAAAGAGCATTTAGGTGGGAGACTTTTTCAGTACTTTTGCTGACAATGCATCCTGCTT
1 CTGTAGAAAAAGAGCATCCAGGTGGAAGACTTTTTCAATACTTTTGCTAACAATGCATCCTACTT
* * *
42389895 GAAGCATTTTTTACCCTTTTTTTCAGAACCATCTTCTCAAAATTATTTTGTCAGAAACTATTGTA
66 GAAGCATTTTTTACACTTTTTTTCAAAACCATCTTCTCAAAATTATTTTGTCAGAAACTACTGTA
* * * * * * *
42389960 GAAAAATAGCGTCCAAATGGGAGCTTTTTTTAGTACTTTTGTTGATAGTGCATCCTTCTTGAAGC
131 GAAAAAGAGCGTCCAAATGAGAGCTTTTTTCAATACTTTTGCTGAAAGTGCATCCTGCTTGAAGC
42390025 GTTTTTTATCCTATTTTTTCAGAAACGG
196 GTTTTTTA-CCT-TTTTTTCAGAAACGG
*
42390053 CTGTAGAAAAAGAGTATCCAGGTGGAAG-CATTTTTCAATACTTTTGCTAACAATGCATCCTACT
1 CTGTAGAAAAAGAGCATCCAGGTGGAAGAC-TTTTTCAATACTTTTGCTAACAATGCATCCTACT
42390117 TGAAGCATTTTTTACACTATTTTTTCAAAACCATCTTCTCAAAATTATTTT-TCAGAAACTACTG
65 TGAAGCATTTTTTACACT-TTTTTTCAAAACCATCTTCTCAAAATTATTTTGTCAGAAACTACTG
**
42390181 TAGAAAAAGAGCGTCCAGGTGAGAGCTTTTTTCAATACTTTTGCTGAAAGTGCATCCTGCTTGAA
129 TAGAAAAAGAGCGTCCAAATGAGAGCTTTTTTCAATACTTTTGCTGAAAGTGCATCCTGCTTGAA
42390246 GCGTTTTTTACCTTTTTTT
194 GCGTTTTTTACCTTTTTTT
42390265 AAAATCATAT
Statistics
Matches: 191, Mismatches: 19, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
221 6 0.03
222 4 0.02
223 150 0.79
224 31 0.16
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (221 bp):
CTGTAGAAAAAGAGCATCCAGGTGGAAGACTTTTTCAATACTTTTGCTAACAATGCATCCTACTT
GAAGCATTTTTTACACTTTTTTTCAAAACCATCTTCTCAAAATTATTTTGTCAGAAACTACTGTA
GAAAAAGAGCGTCCAAATGAGAGCTTTTTTCAATACTTTTGCTGAAAGTGCATCCTGCTTGAAGC
GTTTTTTACCTTTTTTTCAGAAACGG
Found at i:42390330 original size:123 final size:124
Alignment explanation
Indices: 42390036--42390472 Score: 583
Period size: 123 Copynumber: 3.5 Consensus size: 124
42390026 TTTTTTATCC
** ** * *
42390036 TATTTTTTCAGAAACGGCTGTAGAAAAAGAGTATCCAGGTGGAAGCATTTTTCAATACTTTTGCT
1 TATTTTTTCAGAAACTACTGTAGAAAAAGAGCGTCCAGGTGGGAGCTTTTTTCAATACTTTTGCT
* *
42390101 AACAATGCATCCTACTTGAAGCATTTTTTACACTATTTTTTCAAAACCATCTTCTCAAAAT
66 GA-AATGCATCCTACTTGAAGCGTTTTTTAC-CTATTTTTTCAAAACCATCTTCTCAAAAT
*
42390162 TA-TTTTTCAGAAACTACTGTAGAAAAAGAGCGTCCAGGTGAGAGCTTTTTTCAATACTTTTGCT
1 TATTTTTTCAGAAACTACTGTAGAAAAAGAGCGTCCAGGTGGGAGCTTTTTTCAATACTTTTGCT
* * *
42390226 GAAAGTGCATCCTGCTTGAAGCGTTTTTTACCT-TTTTTT-AAAATCATATTCTCAAAAT
66 GAAA-TGCATCCTACTTGAAGCGTTTTTTACCTATTTTTTCAAAACCATCTTCTCAAAAT
* **
42390284 TATTTTTTTAGAAACTACTGTAGAAAAAGAGCGTTTAGGTGGGAGCTTTTTTCAATACTTTTGCT
1 TATTTTTTCAGAAACTACTGTAGAAAAAGAGCGTCCAGGTGGGAGCTTTTTTCAATACTTTTGCT
* *
42390349 GACAATGCATCCTACTTGAAGCGTTTTATACCCTATTTTTTCAGAACCATCTTCTCAAAAT
66 GA-AATGCATCCTACTTGAAGCGTTTTTTA-CCTATTTTTTCAAAACCATCTTCTCAAAAT
* * ** ** * *
42390410 TATTTTTTTAGAAACTACTGTAGAAAAATAATGTTTAGCTAGGAGCTTTTTTCAATACTTTTG
1 TATTTTTTCAGAAACTACTGTAGAAAAAGAGCGTCCAGGTGGGAGCTTTTTTCAATACTTTTG
42390473 TTGACTAGAC
Statistics
Matches: 279, Mismatches: 26, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
122 19 0.07
123 89 0.32
124 9 0.03
125 86 0.31
126 76 0.27
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.39
Consensus pattern (124 bp):
TATTTTTTCAGAAACTACTGTAGAAAAAGAGCGTCCAGGTGGGAGCTTTTTTCAATACTTTTGCT
GAAATGCATCCTACTTGAAGCGTTTTTTACCTATTTTTTCAAAACCATCTTCTCAAAAT
Found at i:42394748 original size:54 final size:54
Alignment explanation
Indices: 42394652--42394810 Score: 194
Period size: 54 Copynumber: 2.9 Consensus size: 54
42394642 GTTAAGGAGT
* * **
42394652 CAAACGTCCAATGAATTCTTGAGAATAGATCCATATTGTGATTCCTATTCGAGC
1 CAAACGTCCAATGATTTCTTGAGAAGAGATCCATATCATGATTCCTATTCGAGC
* * *
42394706 CAAATGTCCAATGATTTCTTGAGAAGAGATCTATATCATGATTCCTATTCGAGT
1 CAAACGTCCAATGATTTCTTGAGAAGAGATCCATATCATGATTCCTATTCGAGC
** * * *
42394760 CAAACGTCTTATGATTTCTTGAAAAGAGATCCA-AGTCGTAATTCCTATTCG
1 CAAACGTCCAATGATTTCTTGAGAAGAGATCCATA-TCATGATTCCTATTCG
42394811 TCGAGGAATT
Statistics
Matches: 90, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
53 1 0.01
54 89 0.99
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.33
Consensus pattern (54 bp):
CAAACGTCCAATGATTTCTTGAGAAGAGATCCATATCATGATTCCTATTCGAGC
Found at i:42395686 original size:17 final size:16
Alignment explanation
Indices: 42395658--42395702 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
42395648 GTGCAAAAAC
42395658 AAGAAAAA-AAATAGAA
1 AAGAAAAAGAAATAG-A
*
42395674 AAGAAAAAGAAATTGA
1 AAGAAAAAGAAATAGA
42395690 AAGAAAAGAGAAA
1 AAGAAAA-AGAAA
42395703 GAAAAAGAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 16 0.62
17 10 0.38
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.07
Consensus pattern (16 bp):
AAGAAAAAGAAATAGA
Found at i:42395969 original size:33 final size:33
Alignment explanation
Indices: 42395915--42395988 Score: 105
Period size: 33 Copynumber: 2.3 Consensus size: 33
42395905 AGAGCATGAA
* * *
42395915 AAAAGG-AAGAGAGACTGAAAAAGAAATGAGGG
1 AAAAGGAAAAAGAGACTAAAAAAGAAACGAGGG
*
42395947 AAAAGGAAAAAGAGACTAAAAAAGAAACGAGTG
1 AAAAGGAAAAAGAGACTAAAAAAGAAACGAGGG
42395980 AAAAGGAAA
1 AAAAGGAAA
42395989 GAAAACTTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
32 6 0.16
33 31 0.84
ACGTcount: A:0.62, C:0.04, G:0.28, T:0.05
Consensus pattern (33 bp):
AAAAGGAAAAAGAGACTAAAAAAGAAACGAGGG
Found at i:42401467 original size:46 final size:46
Alignment explanation
Indices: 42401400--42401653 Score: 406
Period size: 46 Copynumber: 5.6 Consensus size: 46
42401390 TTTGAGTACT
42401400 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
42401446 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* * * *
42401492 TCTAATCAAATGACAAAGTGATAAGTGATAGCTTTAACTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* **
42401538 TCTGATCAAGTAACAAAGTGATAAGTAATAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
42401584 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
42401629 TCTGATC-AGGGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
42401654 ATCATATGTA
Statistics
Matches: 194, Mismatches: 14, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
43 12 0.06
44 5 0.03
45 19 0.10
46 158 0.81
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.29
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:42404855 original size:37 final size:37
Alignment explanation
Indices: 42404804--42404916 Score: 117
Period size: 37 Copynumber: 3.1 Consensus size: 37
42404794 ATTCCAAAAA
* *
42404804 TAATATTATTTTAATAGTTTAATATTAAATTAA-ATT
1 TAATATTATCTTAATAGTTTAATATTAATTTAATATT
*
42404840 TAATACTTATCTTAATAGTATT-TTATTAATTTAATATT
1 TAATA-TTATCTTAATAGT-TTAATATTAATTTAATATT
* *
42404878 AAAGTTATTATCTTAATA-TTTAAT-TTAATTTAATTTT
1 TAA--TATTATCTTAATAGTTTAATATTAATTTAATATT
42404915 TA
1 TA
42404917 TCTTGTAGAT
Statistics
Matches: 64, Mismatches: 7, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
36 5 0.08
37 37 0.58
38 9 0.14
39 11 0.17
40 2 0.03
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (37 bp):
TAATATTATCTTAATAGTTTAATATTAATTTAATATT
Found at i:42404977 original size:12 final size:13
Alignment explanation
Indices: 42404947--42404978 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
42404937 TTATTTTAGG
42404947 AATATTTAATATT
1 AATATTTAATATT
42404960 AA-ATTTAATA-T
1 AATATTTAATATT
42404971 AATATTTA
1 AATATTTA
42404979 TCTTGATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.17
12 13 0.72
13 2 0.11
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AATATTTAATATT
Found at i:42409656 original size:12 final size:12
Alignment explanation
Indices: 42409639--42409669 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
42409629 CTCTAGTTTT
42409639 CACACGGCCTAG
1 CACACGGCCTAG
*
42409651 CACACGGCCTGG
1 CACACGGCCTAG
42409663 CACACGG
1 CACACGG
42409670 GCGTGTGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.23, C:0.42, G:0.29, T:0.06
Consensus pattern (12 bp):
CACACGGCCTAG
Found at i:42414503 original size:11 final size:10
Alignment explanation
Indices: 42414487--42414531 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
42414477 TCAATTCATT
42414487 AATATTTATA
1 AATATTTATA
*
42414497 AA-A--TATT
1 AATATTTATA
42414504 AATATTTATAA
1 AATATTTAT-A
42414515 AATATTTATA
1 AATATTTATA
42414525 AATATTT
1 AATATTT
42414532 TAACTTTGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
7 5 0.17
8 1 0.03
9 1 0.03
10 13 0.45
11 9 0.31
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (10 bp):
AATATTTATA
Found at i:42414506 original size:17 final size:17
Alignment explanation
Indices: 42414484--42414520 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
42414474 TTCTCAATTC
42414484 ATTAATATTTATAAAAT
1 ATTAATATTTATAAAAT
42414501 ATTAATATTTATAAAAT
1 ATTAATATTTATAAAAT
42414518 ATT
1 ATT
42414521 TATAAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTAATATTTATAAAAT
Found at i:42414835 original size:17 final size:16
Alignment explanation
Indices: 42414809--42414876 Score: 52
Period size: 17 Copynumber: 4.2 Consensus size: 16
42414799 TTTTGTTTAA
42414809 ATTT-AATATATAAAAT
1 ATTTAAATATA-AAAAT
*
42414825 ATTTAAATATATCAAAT
1 ATTTAAATATA-AAAAT
* *
42414842 GAATTAGAT-TAAATAAT
1 -ATTTAAATATAAA-AAT
42414859 -TTTAAATATAAAAAT
1 ATTTAAATATAAAAAT
42414874 ATT
1 ATT
42414877 AATTGATTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
15 8 0.20
16 11 0.27
17 16 0.39
18 6 0.15
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.41
Consensus pattern (16 bp):
ATTTAAATATAAAAAT
Found at i:42414885 original size:33 final size:33
Alignment explanation
Indices: 42414826--42414890 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
42414816 ATATAAAATA
**
42414826 TTTAAATATATCAAATGAATTAGATTAAATAAT
1 TTTAAATATAAAAAATGAATTAGATTAAATAAT
* *
42414859 TTTAAATATAAAAATATTAATT-GATTATATAA
1 TTTAAATATAAAAA-ATGAATTAGATTAAATAA
42414891 AATAATTATC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 21 0.78
34 6 0.22
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (33 bp):
TTTAAATATAAAAAATGAATTAGATTAAATAAT
Found at i:42424637 original size:19 final size:19
Alignment explanation
Indices: 42424602--42424640 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
42424592 TTTATTTATG
*
42424602 TTAATTAAGTTAGGTTAAT
1 TTAATTAAGTTAAGTTAAT
42424621 TTAATTAA-TCTAAGTTAAT
1 TTAATTAAGT-TAAGTTAAT
42424640 T
1 T
42424641 AAAGATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 1 0.06
19 17 0.94
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.49
Consensus pattern (19 bp):
TTAATTAAGTTAAGTTAAT
Found at i:42425430 original size:14 final size:14
Alignment explanation
Indices: 42425411--42425439 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
42425401 CTTTTAGTAT
42425411 AAATAGACATATAA
1 AAATAGACATATAA
42425425 AAATAGACATATAA
1 AAATAGACATATAA
42425439 A
1 A
42425440 TTTTTCCGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (14 bp):
AAATAGACATATAA
Found at i:42427293 original size:54 final size:54
Alignment explanation
Indices: 42427208--42427314 Score: 160
Period size: 54 Copynumber: 2.0 Consensus size: 54
42427198 ATCTTATTCT
* * * *
42427208 AGAAAACATCATTGTTCAAGGGGAAGCTACTATTTAAGGGGAGACTACTGTTCC
1 AGAAAACACCATTGTTCAACGGGAAGCTACTACTCAAGGGGAGACTACTGTTCC
* *
42427262 AGAAAACACCATTGTTCAACGGGAAGTTACTACTCAGGGGGAGACTACTGTTC
1 AGAAAACACCATTGTTCAACGGGAAGCTACTACTCAAGGGGAGACTACTGTTC
42427315 AAAAGGAGAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (54 bp):
AGAAAACACCATTGTTCAACGGGAAGCTACTACTCAAGGGGAGACTACTGTTCC
Found at i:42430517 original size:3 final size:3
Alignment explanation
Indices: 42430468--42430497 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
42430458 GTCACCACTG
42430468 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
42430498 CTGCCATCGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:42434334 original size:31 final size:31
Alignment explanation
Indices: 42434249--42434336 Score: 140
Period size: 31 Copynumber: 2.8 Consensus size: 31
42434239 TTTTTGAATA
*
42434249 TTTCCCCCCAAAATTTTACTCCCCCATTTAT
1 TTTCCCCCCAAAATTTTACTCCCTCATTTAT
* *
42434280 TTTTCCTCCAAAATTTTACTCCCTCATTTAT
1 TTTCCCCCCAAAATTTTACTCCCTCATTTAT
*
42434311 TTTCCCCCCAAAATTTTATTCCCTCA
1 TTTCCCCCCAAAATTTTACTCCCTCA
42434337 ACCTTCAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.23, C:0.35, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTCCCCCCAAAATTTTACTCCCTCATTTAT
Found at i:42436846 original size:14 final size:15
Alignment explanation
Indices: 42436813--42436862 Score: 57
Period size: 14 Copynumber: 3.2 Consensus size: 15
42436803 GTAATTTGTT
42436813 TTATATTATATTAAATA
1 TTATA-TATATT-AATA
42436830 TTATATATATTAA-A
1 TTATATATATTAATA
*
42436844 TTATACATATTAATCA
1 TTATATATATTAAT-A
42436860 TTA
1 TTA
42436863 AAATATTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 13 0.43
15 2 0.07
16 10 0.33
17 5 0.17
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (15 bp):
TTATATATATTAATA
Found at i:42442847 original size:13 final size:13
Alignment explanation
Indices: 42442821--42442858 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
42442811 TTATGCTTAT
*
42442821 ATATATATTATAG
1 ATATATAATATAG
42442834 ATA-ATAGATATAG
1 ATATATA-ATATAG
42442847 ATATATAATATA
1 ATATATAATATA
42442859 TGATTAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 3 0.14
13 16 0.73
14 3 0.14
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (13 bp):
ATATATAATATAG
Found at i:42447660 original size:29 final size:29
Alignment explanation
Indices: 42447618--42447684 Score: 109
Period size: 29 Copynumber: 2.3 Consensus size: 29
42447608 TGGAATTGGT
*
42447618 GAACAGAAGTGAGAG-GGTTATAAGTAGGA
1 GAACCGAAGTGAGAGAGG-TATAAGTAGGA
42447647 GAACCGAAGTGAGAGAGGTATAAGTAGGA
1 GAACCGAAGTGAGAGAGGTATAAGTAGGA
42447676 GAACCGAAG
1 GAACCGAAG
42447685 ATGCTATTCT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 34 0.94
30 2 0.06
ACGTcount: A:0.42, C:0.07, G:0.37, T:0.13
Consensus pattern (29 bp):
GAACCGAAGTGAGAGAGGTATAAGTAGGA
Found at i:42449168 original size:21 final size:21
Alignment explanation
Indices: 42449138--42449179 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
42449128 TTTTTCAAAG
* *
42449138 ATGTGTATTGGATTGAATTGA
1 ATGTGAATTGGATTAAATTGA
*
42449159 ATGTGAATTGTATTAAATTGA
1 ATGTGAATTGGATTAAATTGA
42449180 GCTAAATTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.43
Consensus pattern (21 bp):
ATGTGAATTGGATTAAATTGA
Found at i:42449625 original size:24 final size:25
Alignment explanation
Indices: 42449538--42449657 Score: 95
Period size: 25 Copynumber: 4.8 Consensus size: 25
42449528 ATCTAGTTAT
* **
42449538 ATGGCTCTCACGAGCTTTTCGA-TA
1 ATGGCTCTCATGAGCTTCCCGATTA
*
42449562 CGTGGCTCTCATGAGCTTCCCGATTA
1 -ATGGCTCTCATGAGCTTCCCGATTA
* * *
42449588 ATGGCTCTCTTGAGCTTCTC-ATTT
1 ATGGCTCTCATGAGCTTCCCGATTA
42449612 ATGGCTCGT-ATGAGCTTCCCGA-TA
1 ATGGCTC-TCATGAGCTTCCCGATTA
* * *
42449636 ATTGTCTCGCAAGAGCTTCCCG
1 A-TGGCTCTCATGAGCTTCCCG
42449658 TTATACAACT
Statistics
Matches: 76, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
24 21 0.28
25 53 0.70
26 2 0.03
ACGTcount: A:0.17, C:0.28, G:0.22, T:0.33
Consensus pattern (25 bp):
ATGGCTCTCATGAGCTTCCCGATTA
Found at i:42449676 original size:25 final size:25
Alignment explanation
Indices: 42449648--42449705 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
42449638 TGTCTCGCAA
42449648 GAGCTTCCCGTTATACAACTCACAT
1 GAGCTTCCCGTTATACAACTCACAT
*
42449673 GAGCTTCCCGTTATACAACTTACAT
1 GAGCTTCCCGTTATACAACTCACAT
42449698 GAGCTTCC
1 GAGCTTCC
42449706 TATTACATGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.26, C:0.31, G:0.14, T:0.29
Consensus pattern (25 bp):
GAGCTTCCCGTTATACAACTCACAT
Found at i:42451844 original size:332 final size:332
Alignment explanation
Indices: 42451233--42451898 Score: 1233
Period size: 332 Copynumber: 2.0 Consensus size: 332
42451223 TTTCTCAGAT
*
42451233 CATATATGAGCTTATGTATGCTCCAATACTATCCAGAATTTAACTAGGATTAATTTGTAACATTT
1 CATATATGAGCTTATGTATGCTCCAATACTATCCAGAATTTAACTAGGATTAATTTGCAACATTT
*
42451298 TCAAAATTTCAGTTCAATTATAAATCAAAACAATTCATAGCTCAATTTAGTTATCATAAATCAAT
66 TCAAAATTTCAGTTCAATTATAAATCAAAAAAATTCATAGCTCAATTTAGTTATCATAAATCAAT
* *
42451363 AGTCAATCATTATTTATAACATATATGTGAAAATGGAACTTAAATTGGGTTTACGGAACCTTAAA
131 AGTCAATCATTATTCATAACATATATATGAAAATGGAACTTAAATTGGGTTTACGGAACCTTAAA
*
42451428 AATAGTTTGGAAACAACAGGGACTAATCTGAAACAAAATAGAAAAACGTAGAAAAATTTGAAAAC
196 AATAGTTTGGAAACAACAAGGACTAATCTGAAACAAAATAGAAAAACGTAGAAAAATTTGAAAAC
* ** *
42451493 ATGGGTCACACGGCCGTGTGATAGAGCCCAGGCTGTGTGGCTCAGGAACATGGTCATGTGGCCAA
261 AGGGGTCACACAACCGTGTGACAGAGCCCAGGCTGTGTGGCTCAGGAACATGGTCATGTGGCCAA
42451558 CCGTGTA
326 CCGTGTA
*
42451565 CATATATGAGCTTATGTATGCTCTAATACTATCCAGAATTTAACTAGGATTAATTTGCAACATTT
1 CATATATGAGCTTATGTATGCTCCAATACTATCCAGAATTTAACTAGGATTAATTTGCAACATTT
42451630 TCAAAATTTCAGTTCAATTATAAATCAAAAAAATTCATAGCTCAATTTAGTTATCATAAATCAAT
66 TCAAAATTTCAGTTCAATTATAAATCAAAAAAATTCATAGCTCAATTTAGTTATCATAAATCAAT
42451695 AGTCAATCATTATTCATAACATATATATGAAAATGGAACTTAAATTGGGTTTACGGAACCTTAAA
131 AGTCAATCATTATTCATAACATATATATGAAAATGGAACTTAAATTGGGTTTACGGAACCTTAAA
42451760 AATAGTTTGGAAACAACAAGGACTAATCTGAAACAAAATAGAAAAACGTAGAAAAATTTGAAAAC
196 AATAGTTTGGAAACAACAAGGACTAATCTGAAACAAAATAGAAAAACGTAGAAAAATTTGAAAAC
*
42451825 AGGGGTCACACAACCGTGTGACAGAGCCCAGGCTGTGTGGCTCAGGAACATGGTCGTGTGGCCAA
261 AGGGGTCACACAACCGTGTGACAGAGCCCAGGCTGTGTGGCTCAGGAACATGGTCATGTGGCCAA
42451890 CCGTGTA
326 CCGTGTA
42451897 CA
1 CA
42451899 ATTCGAAGTG
Statistics
Matches: 323, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
332 323 1.00
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.29
Consensus pattern (332 bp):
CATATATGAGCTTATGTATGCTCCAATACTATCCAGAATTTAACTAGGATTAATTTGCAACATTT
TCAAAATTTCAGTTCAATTATAAATCAAAAAAATTCATAGCTCAATTTAGTTATCATAAATCAAT
AGTCAATCATTATTCATAACATATATATGAAAATGGAACTTAAATTGGGTTTACGGAACCTTAAA
AATAGTTTGGAAACAACAAGGACTAATCTGAAACAAAATAGAAAAACGTAGAAAAATTTGAAAAC
AGGGGTCACACAACCGTGTGACAGAGCCCAGGCTGTGTGGCTCAGGAACATGGTCATGTGGCCAA
CCGTGTA
Found at i:42467219 original size:21 final size:20
Alignment explanation
Indices: 42467163--42467219 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 20
42467153 TTGCTAAAGT
*
42467163 TTTAATGTCAAACTTCAATGA
1 TTTAAT-TCAAATTTCAATGA
***
42467184 TTTAAGTTGTTATTTCAATGCA
1 TTTAA-TTCAAATTTCAATG-A
42467206 TTTAATTCAAATTT
1 TTTAATTCAAATTT
42467220 ACTATTTTTT
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
21 20 0.74
22 7 0.26
ACGTcount: A:0.33, C:0.11, G:0.09, T:0.47
Consensus pattern (20 bp):
TTTAATTCAAATTTCAATGA
Found at i:42474172 original size:21 final size:21
Alignment explanation
Indices: 42474146--42474205 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
42474136 TAAAATACCC
42474146 TAATTAAAAAATTAAAATCAA
1 TAATTAAAAAATTAAAATCAA
* *
42474167 TAATTAAAAATACTAAAATGAA
1 TAATTAAAAA-ATTAAAATCAA
* *
42474189 -AGTTAAGAAATTAAAAT
1 TAATTAAAAAATTAAAAT
42474206 TAAAAGAAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
20 7 0.21
21 17 0.52
22 9 0.27
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.28
Consensus pattern (21 bp):
TAATTAAAAAATTAAAATCAA
Found at i:42474211 original size:21 final size:20
Alignment explanation
Indices: 42474152--42474211 Score: 52
Period size: 20 Copynumber: 2.9 Consensus size: 20
42474142 ACCCTAATTA
*
42474152 AAAAATTAAAATCAATAA-TT
1 AAAAATTAAAATTAA-AAGTT
*
42474172 AAAAATACTAAAA-TGAAAGTT
1 AAAAAT--TAAAATTAAAAGTT
42474193 AAGAAATTAAAATTAAAAG
1 AA-AAATTAAAATTAAAAG
42474212 AAACTTATAC
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
20 13 0.41
21 10 0.31
22 9 0.28
ACGTcount: A:0.65, C:0.03, G:0.07, T:0.25
Consensus pattern (20 bp):
AAAAATTAAAATTAAAAGTT
Found at i:42474690 original size:24 final size:24
Alignment explanation
Indices: 42474639--42474691 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
42474629 AGTGGTCAAT
* *
42474639 TCTACTTCTACATCTACTATTAGG
1 TCTACTTCTACATCTACTACTAGA
* * *
42474663 TCTACTTCTCCATCTACTGCTATA
1 TCTACTTCTACATCTACTACTAGA
42474687 TCTAC
1 TCTAC
42474692 AGCTAAGTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.23, C:0.30, G:0.06, T:0.42
Consensus pattern (24 bp):
TCTACTTCTACATCTACTACTAGA
Found at i:42494666 original size:12 final size:12
Alignment explanation
Indices: 42494649--42494678 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
42494639 TCAAGCTGTT
42494649 ACACGGCCTAGC
1 ACACGGCCTAGC
*
42494661 ACACGGCCTGGC
1 ACACGGCCTAGC
42494673 ACACGG
1 ACACGG
42494679 ATGTGTGGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.40, G:0.30, T:0.07
Consensus pattern (12 bp):
ACACGGCCTAGC
Found at i:42497541 original size:16 final size:16
Alignment explanation
Indices: 42497520--42497568 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
42497510 ATTTCTAGTA
*
42497520 ACAACAGAAATCAAAT
1 ACAACAGAAATCGAAT
*
42497536 ACAACAGAAATTGAAT
1 ACAACAGAAATCGAAT
42497552 ACAACAGAAATCGAAT
1 ACAACAGAAATCGAAT
42497568 A
1 A
42497569 AATTCTATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.59, C:0.16, G:0.10, T:0.14
Consensus pattern (16 bp):
ACAACAGAAATCGAAT
Found at i:42497743 original size:78 final size:77
Alignment explanation
Indices: 42497584--42497869 Score: 362
Period size: 78 Copynumber: 3.7 Consensus size: 77
42497574 TATTGAATGG
* * * *
42497584 CAGGAA-AAGAATCCTAAAATAGAATTATTCAATTGA-TTTCTGTTTGAAACAAAAAAACCAAAC
1 CAGGAATAA-AATCCTGAAACA-AATTGTTCAATTGATTTTCTGTTTGAAAC--AAAAATCAAAC
* *
42497647 AAATCTTGTTAAATGA
62 AAATCCTGTTAAACGA
*
42497663 CAGGAATAAAATCTTGAAACAAATTTGTTCAATTGATTTTCTGTTTGAAACAAAAATCAAACAAA
1 CAGGAATAAAATCCTGAAACAAA-TTGTTCAATTGATTTTCTGTTTGAAACAAAAATCAAACAAA
*
42497728 TCCTATTAAACGA
65 TCCTGTTAAACGA
* *
42497741 CAGGAATAAAATCCTAAAACAAGATTGTTCAATTGATTTTCTGTTTGAAACAAAAATTAAACAAA
1 CAGGAATAAAATCCTGAAACAA-ATTGTTCAATTGATTTTCTGTTTGAAACAAAAATCAAACAAA
*
42497806 TCCTGTTAAACAA
65 TCCTGTTAAACGA
* * *
42497819 CAAGAAT-AAATCCTGAAACAGGATTGTTCAATTGAATTTCTGTTTGAAACA
1 CAGGAATAAAATCCTGAAACA-AATTGTTCAATTGATTTTCTGTTTGAAACA
42497870 GAATACAATT
Statistics
Matches: 185, Mismatches: 17, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
77 40 0.22
78 102 0.55
79 27 0.15
80 16 0.09
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.30
Consensus pattern (77 bp):
CAGGAATAAAATCCTGAAACAAATTGTTCAATTGATTTTCTGTTTGAAACAAAAATCAAACAAAT
CCTGTTAAACGA
Found at i:42500211 original size:30 final size:30
Alignment explanation
Indices: 42500177--42500274 Score: 74
Period size: 30 Copynumber: 3.2 Consensus size: 30
42500167 TATGATATCT
42500177 TATATAACTAATGGTACCATTAATGTTGAC
1 TATATAACTAATGGTACCATTAATGTTGAC
* * * ** * *
42500207 TATAT-TCAAAGCGGTGATAATCATATGAT-ATC
1 TATATAACTAA-TGGT-ACCATTA-ATGTTGA-C
42500239 TTATATAACTAATGGTACCATTAATGTTGAC
1 -TATATAACTAATGGTACCATTAATGTTGAC
42500270 TATAT
1 TATAT
42500275 TCAAAGCGGT
Statistics
Matches: 47, Mismatches: 14, Indels: 14
0.63 0.19 0.19
Matches are distributed among these distances:
29 3 0.06
30 13 0.28
31 10 0.21
32 10 0.21
33 8 0.17
34 3 0.06
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (30 bp):
TATATAACTAATGGTACCATTAATGTTGAC
Found at i:42500242 original size:63 final size:63
Alignment explanation
Indices: 42500165--42500291 Score: 254
Period size: 63 Copynumber: 2.0 Consensus size: 63
42500155 ACTGCAATGC
42500165 CATATGATATCTTATATAACTAATGGTACCATTAATGTTGACTATATTCAAAGCGGTGATAAT
1 CATATGATATCTTATATAACTAATGGTACCATTAATGTTGACTATATTCAAAGCGGTGATAAT
42500228 CATATGATATCTTATATAACTAATGGTACCATTAATGTTGACTATATTCAAAGCGGTGATAAT
1 CATATGATATCTTATATAACTAATGGTACCATTAATGTTGACTATATTCAAAGCGGTGATAAT
42500291 C
1 C
42500292 TTACATATCA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.36
Consensus pattern (63 bp):
CATATGATATCTTATATAACTAATGGTACCATTAATGTTGACTATATTCAAAGCGGTGATAAT
Found at i:42501916 original size:15 final size:16
Alignment explanation
Indices: 42501885--42501917 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
42501875 ATTTGGTAAG
*
42501885 GAAGAAAAGTGAGAGA
1 GAAGAAAAGTAAGAGA
42501901 GAAGAAAA-TAAGAGA
1 GAAGAAAAGTAAGAGA
42501916 GA
1 GA
42501918 TAATCATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.61, C:0.00, G:0.33, T:0.06
Consensus pattern (16 bp):
GAAGAAAAGTAAGAGA
Found at i:42505726 original size:6 final size:6
Alignment explanation
Indices: 42505715--42505742 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
42505705 CGTTTTGTTC
42505715 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
42505743 TCGAAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTAT
Found at i:42506565 original size:33 final size:30
Alignment explanation
Indices: 42506507--42506590 Score: 80
Period size: 31 Copynumber: 2.7 Consensus size: 30
42506497 TATTTATATC
42506507 TATATATATATACATACATACATTTTCATAA
1 TATATATATATACATACATACATTTT-ATAA
* * *
42506538 TATATATATGTACACGTATATATATTTTATAA
1 TATATATATATACA--TACATACATTTTATAA
* *
42506570 CT-TATTTATATATATACATAC
1 -TATATATATATACATACATAC
42506591 TTATATTTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
30 5 0.12
31 13 0.31
32 13 0.31
33 11 0.26
ACGTcount: A:0.42, C:0.11, G:0.02, T:0.45
Consensus pattern (30 bp):
TATATATATATACATACATACATTTTATAA
Found at i:42506671 original size:30 final size:31
Alignment explanation
Indices: 42506614--42506672 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
42506604 TATTTTATAA
* *
42506614 TTTTATATACGTATATATATACATACACATC
1 TTTTATATACGTATATAGACACATACACATC
* *
42506645 TTTTATA-ATGTATATAGACACGTACACA
1 TTTTATATACGTATATAGACACATACACA
42506673 CACAATTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 17 0.71
31 7 0.29
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (31 bp):
TTTTATATACGTATATAGACACATACACATC
Found at i:42509195 original size:21 final size:21
Alignment explanation
Indices: 42509169--42509208 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
42509159 AGAAAATTTG
* *
42509169 ATAATTGAGTGAAAGAAAACA
1 ATAATTAAGGGAAAGAAAACA
42509190 ATAATTAAGGGAAAGAAAA
1 ATAATTAAGGGAAAGAAAA
42509209 AAAAATGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.60, C:0.03, G:0.20, T:0.17
Consensus pattern (21 bp):
ATAATTAAGGGAAAGAAAACA
Found at i:42526509 original size:23 final size:21
Alignment explanation
Indices: 42526484--42526523 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
42526474 ATTCAAAGAT
*
42526484 ATATATAATTTAGAAAAATTA
1 ATATATAAATTAGAAAAATTA
*
42526505 ATATATAAATTATAAAAAT
1 ATATATAAATTAGAAAAAT
42526524 AAAATTTACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (21 bp):
ATATATAAATTAGAAAAATTA
Found at i:42528113 original size:40 final size:40
Alignment explanation
Indices: 42528057--42528135 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
42528047 AGTGGGTGTC
*
42528057 TATTAGGATAAAAAGTTTGATATATTTTAGGACTCTAATT
1 TATTAGGATAAAAAGTTTGATATATTTTAAGACTCTAATT
*
42528097 TATTAGGATAAGAAGTTTGATATATTTTAAGACTCTAAT
1 TATTAGGATAAAAAGTTTGATATATTTTAAGACTCTAAT
42528136 GTTGGTTAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (40 bp):
TATTAGGATAAAAAGTTTGATATATTTTAAGACTCTAATT
Found at i:42537937 original size:6 final size:6
Alignment explanation
Indices: 42537926--42537955 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
42537916 AGAAATGCTG
42537926 AAAATA AAAATA AAAATA AAAATA AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA
42537956 GGGGGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:42540515 original size:15 final size:15
Alignment explanation
Indices: 42540495--42540529 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
42540485 ATCGTTCGGC
42540495 TCCTCGAAAAATAAT
1 TCCTCGAAAAATAAT
42540510 TCCTCGAAAAATAAT
1 TCCTCGAAAAATAAT
42540525 TCCTC
1 TCCTC
42540530 CACCACGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.40, C:0.26, G:0.06, T:0.29
Consensus pattern (15 bp):
TCCTCGAAAAATAAT
Found at i:42548275 original size:87 final size:87
Alignment explanation
Indices: 42548128--42548301 Score: 312
Period size: 87 Copynumber: 2.0 Consensus size: 87
42548118 CTTCCTAGGG
**
42548128 GCCTTCTAATCATGGGAGGAAGAATGGGTTCCATGTCCCTCACATGTTCCCATTGCATAGGACCT
1 GCCTTCTAATCATGGGAGGAAGAATGGGTTCCATGTCCCTCACATGTGACCATTGCATAGGACCT
42548193 ATACGCAAAAATTTAAAGATGT
66 ATACGCAAAAATTTAAAGATGT
*
42548215 GCCTTCTAATCATGGGAGGAAGAATGGGTTCCATGTCCCTCACATGTGACCATTGTATAGGACCT
1 GCCTTCTAATCATGGGAGGAAGAATGGGTTCCATGTCCCTCACATGTGACCATTGCATAGGACCT
*
42548280 ATTCGCAAAAATTTAAAGATGT
66 ATACGCAAAAATTTAAAGATGT
42548302 CAAACATATT
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 83 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (87 bp):
GCCTTCTAATCATGGGAGGAAGAATGGGTTCCATGTCCCTCACATGTGACCATTGCATAGGACCT
ATACGCAAAAATTTAAAGATGT
Found at i:42550728 original size:57 final size:57
Alignment explanation
Indices: 42550653--42550765 Score: 136
Period size: 57 Copynumber: 2.0 Consensus size: 57
42550643 CCATTATTCA
* *** * *
42550653 CATTTTGACAACATAAATATGTGCATTAAGAGACATTATGACAGCAGCTGTAAATTG
1 CATTTGGACAACATAAATATACACATTAAAAGACATTATGACAGCAACTGTAAATTG
* * * *
42550710 CATTTGGACAGCATAAATATACACATTAAAAGATATTTTGGCAGCAACTGTAAATT
1 CATTTGGACAACATAAATATACACATTAAAAGACATTATGACAGCAACTGTAAATT
42550766 ACAAGTGCAA
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
57 46 1.00
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (57 bp):
CATTTGGACAACATAAATATACACATTAAAAGACATTATGACAGCAACTGTAAATTG
Found at i:42551914 original size:305 final size:304
Alignment explanation
Indices: 42551218--42552069 Score: 1198
Period size: 305 Copynumber: 2.8 Consensus size: 304
42551208 AATTACAAAA
* * * * * *
42551218 GAATAAAAAGGAAAGCCATTTTCACCAGTAGTAACATGAAGAGTGAAGAAATAAAATGATTTTAG
1 GAATAAAAAGGAAGGCCCTTTTCACCAGCAGTAACATGCAGAGCGAAGAAATAAAACGATTTTAG
* *
42551283 ATCCAAATCTGAGTAAAACCAAGTTCTTAGCAGAAATTATGCAAAACCCACATCAGAAATACAAT
66 ATCCAAATTTGAGTAAAACCAAGTTGTTAGCAGAAATTATGCAAAACCCACATCAGAAATACAAT
* * * *
42551348 TAATCATGTAGAGTCTCCAAGTACCAAGCAGAT-AAACTAATAGCATAGAGATATGGTTTAAAGA
131 TAATAATGTAGAGTCTCCAAGTACCAAGCAGATAAAACTAATAACATAGAAATATAGTTTAAAGA
**
42551412 AAACAAAAGCTACTAACCAATTAGCTCTGAACCAAAATTTACCCAAGACCAGCAAAAAAAAATTG
196 AAACAAAAGCTACTAACCAATTAGCTCTGAACCAAAACCTACCCAAGACCAGCAAAAAAAAATTG
42551477 CAAGGTAGTTCAACACAAAATCAAAAGAAAGAAAGAATAATCTG
261 CAAGGTAGTTCAACACAAAATCAAAAGAAAGAAAGAATAATCTG
* * *
42551521 GAATAAAAAGGAAGGCCCTTTTCACCAGCAATAACATGCAAAGCGAAAAAATAAAACGATTTTAG
1 GAATAAAAAGGAAGGCCCTTTTCACCAGCAGTAACATGCAGAGCGAAGAAATAAAACGATTTTAG
* *
42551586 ATCCAAATTTGAGTAAAACCAAGTTGTTAGCAGAAATTATGCAAAACCCACATAAGATATACAAT
66 ATCCAAATTTGAGTAAAACCAAGTTGTTAGCAGAAATTATGCAAAACCCACATCAGAAATACAAT
* * *
42551651 TAATAATGTAGAGTCTCAAAGTACCAAGCAAATAAAACTAATAACATAAAAATATAGTTTAAAGA
131 TAATAATGTAGAGTCTCCAAGTACCAAGCAGATAAAACTAATAACATAGAAATATAGTTTAAAGA
* * * * *
42551716 ATACAAAAGCTAGTAACTAATTAGCT-TGAACCAAAACCTATCCAATACCAGCAAAAAGAAAGAT
196 AAACAAAAGCTACTAACCAATTAGCTCTGAACCAAAACCTACCCAAGACCAGCAAAAA-AAA-AT
* * * *
42551780 TGGAAGGT-GATTCAGCACAAAATCAACAA-TAAGAAAGAATAATTTG
259 TGCAAGGTAG-TTCAACACAAAATCAA-AAGAAAGAAAGAATAATCTG
* * *
42551826 GAATAAAAAGGAAGGCCCTTTTCACTAGCAGTAATATGCAGAGCGAAGAAATAAAACGGTTTTAG
1 GAATAAAAAGGAAGGCCCTTTTCACCAGCAGTAACATGCAGAGCGAAGAAATAAAACGATTTTAG
*
42551891 ATCCAAATTTGAGTAAGACCAAGTTGTTAGCAGAAATTATGCAAAACCCACATCAGAAATACAAT
66 ATCCAAATTTGAGTAAAACCAAGTTGTTAGCAGAAATTATGCAAAACCCACATCAGAAATACAAT
*
42551956 TAATAATGTAGAGTCTCCAAGTACTAAGCAGATAAAACTAATAACATAG--A-A-A---T-----
131 TAATAATGTAGAGTCTCCAAGTACCAAGCAGATAAAACTAATAACATAGAAATATAGTTTAAAGA
* * *
42552009 AAA-AAAAGCTACTAACCAATTAGCTCTGAACCAAAACTTACCTAAGATCAGCAAAAAAAAA
196 AAACAAAAGCTACTAACCAATTAGCTCTGAACCAAAACCTACCCAAGACCAGCAAAAAAAAA
42552070 AGATACTGGA
Statistics
Matches: 491, Mismatches: 52, Indels: 24
0.87 0.09 0.04
Matches are distributed among these distances:
291 1 0.00
292 23 0.05
293 28 0.06
298 1 0.00
301 1 0.00
302 1 0.00
303 175 0.36
304 54 0.11
305 205 0.42
306 2 0.00
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.21
Consensus pattern (304 bp):
GAATAAAAAGGAAGGCCCTTTTCACCAGCAGTAACATGCAGAGCGAAGAAATAAAACGATTTTAG
ATCCAAATTTGAGTAAAACCAAGTTGTTAGCAGAAATTATGCAAAACCCACATCAGAAATACAAT
TAATAATGTAGAGTCTCCAAGTACCAAGCAGATAAAACTAATAACATAGAAATATAGTTTAAAGA
AAACAAAAGCTACTAACCAATTAGCTCTGAACCAAAACCTACCCAAGACCAGCAAAAAAAAATTG
CAAGGTAGTTCAACACAAAATCAAAAGAAAGAAAGAATAATCTG
Found at i:42553581 original size:30 final size:30
Alignment explanation
Indices: 42553540--42553736 Score: 268
Period size: 30 Copynumber: 6.6 Consensus size: 30
42553530 TAAGGTTACT
42553540 CACAAGCTGACATTATAATAGAATTGCTCA
1 CACAAGCTGACATTATAATAGAATTGCTCA
* ** *
42553570 CACAAGTTGACATTATAATAGGTTTTCTCA
1 CACAAGCTGACATTATAATAGAATTGCTCA
* *
42553600 CACAAGCTGATATTATAATAGAATTTCTCA
1 CACAAGCTGACATTATAATAGAATTGCTCA
* * * *
42553630 CACAAGTTGACATTATAATTGATTTGCTTA
1 CACAAGCTGACATTATAATAGAATTGCTCA
* *
42553660 CACAAGCTAACATTATAATAGAATTTCTCA
1 CACAAGCTGACATTATAATAGAATTGCTCA
* *
42553690 CACAAGTTGACATTATAATAGATTTGCTCA
1 CACAAGCTGACATTATAATAGAATTGCTCA
42553720 CACAAGCTGACATTATA
1 CACAAGCTGACATTATA
42553737 TCGAGATTAC
Statistics
Matches: 142, Mismatches: 25, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 142 1.00
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (30 bp):
CACAAGCTGACATTATAATAGAATTGCTCA
Found at i:42553616 original size:60 final size:60
Alignment explanation
Indices: 42553540--42553736 Score: 331
Period size: 60 Copynumber: 3.3 Consensus size: 60
42553530 TAAGGTTACT
* * *
42553540 CACAAGCTGACATTATAATAGAATTGCTCACACAAGTTGACATTATAATAGGTTTTCTCA
1 CACAAGCTGACATTATAATAGAATTTCTCACACAAGTTGACATTATAATAGATTTGCTCA
* * *
42553600 CACAAGCTGATATTATAATAGAATTTCTCACACAAGTTGACATTATAATTGATTTGCTTA
1 CACAAGCTGACATTATAATAGAATTTCTCACACAAGTTGACATTATAATAGATTTGCTCA
*
42553660 CACAAGCTAACATTATAATAGAATTTCTCACACAAGTTGACATTATAATAGATTTGCTCA
1 CACAAGCTGACATTATAATAGAATTTCTCACACAAGTTGACATTATAATAGATTTGCTCA
42553720 CACAAGCTGACATTATA
1 CACAAGCTGACATTATA
42553737 TCGAGATTAC
Statistics
Matches: 126, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 126 1.00
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (60 bp):
CACAAGCTGACATTATAATAGAATTTCTCACACAAGTTGACATTATAATAGATTTGCTCA
Found at i:42554147 original size:5 final size:5
Alignment explanation
Indices: 42554137--42554184 Score: 96
Period size: 5 Copynumber: 9.6 Consensus size: 5
42554127 GAGCACAAAT
42554137 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAA
42554185 AGTAGTAAGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 43 1.00
ACGTcount: A:0.60, C:0.19, G:0.00, T:0.21
Consensus pattern (5 bp):
TAACA
Found at i:42554913 original size:15 final size:15
Alignment explanation
Indices: 42554895--42554957 Score: 72
Period size: 15 Copynumber: 4.2 Consensus size: 15
42554885 TTATATACTT
42554895 TTAATTAAAACTTAA
1 TTAATTAAAACTTAA
* * * *
42554910 TTAATCATAATTTAT
1 TTAATTAAAACTTAA
*
42554925 TTAATTAAACCTTAA
1 TTAATTAAAACTTAA
*
42554940 TTAATTAAAAATTAA
1 TTAATTAAAACTTAA
42554955 TTA
1 TTA
42554958 TAATTAACCA
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 37 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.44
Consensus pattern (15 bp):
TTAATTAAAACTTAA
Found at i:42559175 original size:41 final size:41
Alignment explanation
Indices: 42559117--42559325 Score: 267
Period size: 41 Copynumber: 5.1 Consensus size: 41
42559107 AACAAGTGCT
* * *
42559117 TTCAGGGGCACTAAAGTACAAACAGGGGCACACATGTGCAA
1 TTCAGGGGTACCAAAGTACAAACAGGGGCACATATGTGCAA
* * * *
42559158 TTCGGGGGTAGCAAAGTAAAAACAGGGGCGCATATGTGCAA
1 TTCAGGGGTACCAAAGTACAAACAGGGGCACATATGTGCAA
*
42559199 TTCAGGGGTACCAAAGTACAAATAGGGGCA-ACTATGTGCAA
1 TTCAGGGGTACCAAAGTACAAACAGGGGCACA-TATGTGCAA
* ** * *
42559240 TTCAAGGGTACTGAAGTACAAACAGGGGCACGTAAGTGCAA
1 TTCAGGGGTACCAAAGTACAAACAGGGGCACATATGTGCAA
* *
42559281 TTCAGGGGTACCGAAGTACAAACAGGGGCACATATGTGTAA
1 TTCAGGGGTACCAAAGTACAAACAGGGGCACATATGTGCAA
42559322 TTCA
1 TTCA
42559326 AAAATATTCT
Statistics
Matches: 143, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
40 1 0.01
41 142 0.99
ACGTcount: A:0.35, C:0.18, G:0.29, T:0.18
Consensus pattern (41 bp):
TTCAGGGGTACCAAAGTACAAACAGGGGCACATATGTGCAA
Found at i:42559297 original size:21 final size:21
Alignment explanation
Indices: 42559193--42559297 Score: 72
Period size: 21 Copynumber: 5.1 Consensus size: 21
42559183 GGGCGCATAT
*
42559193 GTGCAATTCAGGGGTACCAAA
1 GTGCAATTCAGGGGTACCGAA
* * * * * *
42559214 GTACAAAT-AGGGGCAACTAT
1 GTGCAATTCAGGGGTACCGAA
* *
42559234 GTGCAATTCAAGGGTACTGAA
1 GTGCAATTCAGGGGTACCGAA
* * *
42559255 GTACAA-ACAGGGGCA-CGTAA
1 GTGCAATTCAGGGGTACCG-AA
42559275 GTGCAATTCAGGGGTACCGAA
1 GTGCAATTCAGGGGTACCGAA
42559296 GT
1 GT
42559298 ACAAACAGGG
Statistics
Matches: 58, Mismatches: 22, Indels: 8
0.66 0.25 0.09
Matches are distributed among these distances:
19 1 0.02
20 27 0.47
21 28 0.48
22 2 0.03
ACGTcount: A:0.34, C:0.17, G:0.30, T:0.19
Consensus pattern (21 bp):
GTGCAATTCAGGGGTACCGAA
Found at i:42559308 original size:20 final size:20
Alignment explanation
Indices: 42559245--42559308 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
42559235 TGCAATTCAA
*
42559245 GGGTACTGAAGTACAAACAG
1 GGGTACCGAAGTACAAACAG
* * *
42559265 GGGCA-CGTAAGTGCAATTCAG
1 GGGTACCG-AAGTACAA-ACAG
42559286 GGGTACCGAAGTACAAACAG
1 GGGTACCGAAGTACAAACAG
42559306 GGG
1 GGG
42559309 CACATATGTG
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
19 1 0.03
20 17 0.50
21 14 0.41
22 2 0.06
ACGTcount: A:0.34, C:0.17, G:0.34, T:0.14
Consensus pattern (20 bp):
GGGTACCGAAGTACAAACAG
Found at i:42566157 original size:54 final size:54
Alignment explanation
Indices: 42566075--42566183 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
42566065 AAACATTTGT
42566075 TTCTTTTAAAAACTGAAGTTTCCTACTACTAGCAATTGTAATCCATAAGGTAAA
1 TTCTTTTAAAAACTGAAGTTTCCTACTACTAGCAATTGTAATCCATAAGGTAAA
42566129 TTCTTTTAAAAACTGAAGTTTCCTACTACTAGCAATTGTAATCCATAAGGTAAA
1 TTCTTTTAAAAACTGAAGTTTCCTACTACTAGCAATTGTAATCCATAAGGTAAA
42566183 T
1 T
42566184 ATAATTAAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.36
Consensus pattern (54 bp):
TTCTTTTAAAAACTGAAGTTTCCTACTACTAGCAATTGTAATCCATAAGGTAAA
Found at i:42566192 original size:54 final size:54
Alignment explanation
Indices: 42566080--42566195 Score: 198
Period size: 54 Copynumber: 2.1 Consensus size: 54
42566070 TTTGTTTCTT
**
42566080 TTAAAAACTGAAGTTTCCTACTACTAGCAATTGTAATCCATAAGGTAAATTCTT
1 TTAAAAACTGAAGTTTCCTACTACTAGCAATTGTAATCCATAAGGTAAATTCAA
42566134 TTAAAAACTGAAGTTTCCTACTACTAGCAATTGTAATCCATAAGGTAAATAT-AA
1 TTAAAAACTGAAGTTTCCTACTACTAGCAATTGTAATCCATAAGGTAAAT-TCAA
42566188 TTAAAAAC
1 TTAAAAAC
42566196 CAAAACCAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
54 58 0.98
55 1 0.02
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (54 bp):
TTAAAAACTGAAGTTTCCTACTACTAGCAATTGTAATCCATAAGGTAAATTCAA
Found at i:42580637 original size:17 final size:17
Alignment explanation
Indices: 42580598--42580638 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
42580588 CACATCTTTC
* *
42580598 TCATTTTCTCTTTTTTT
1 TCATTTTTTCATTTTTT
42580615 TC-TTTTTTCATTTTTT
1 TCATTTTTTCATTTTTT
42580631 TCATTTTT
1 TCATTTTT
42580639 CTTTCCTACC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (17 bp):
TCATTTTTTCATTTTTT
Found at i:42580956 original size:13 final size:13
Alignment explanation
Indices: 42580938--42580962 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42580928 TCGAAACGAC
42580938 CCTTTAACCATTA
1 CCTTTAACCATTA
42580951 CCTTTAACCATT
1 CCTTTAACCATT
42580963 GACCGTTAAA
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:0.28, C:0.32, G:0.00, T:0.40
Consensus pattern (13 bp):
CCTTTAACCATTA
Found at i:42581255 original size:10 final size:9
Alignment explanation
Indices: 42581210--42581280 Score: 56
Period size: 10 Copynumber: 7.7 Consensus size: 9
42581200 TTTCTATATA
42581210 TTTTATAAT
1 TTTTATAAT
42581219 TTTTA-AGAT
1 TTTTATA-AT
*
42581228 TTTTATAAAA
1 TTTTAT-AAT
42581238 TTTTATAAT
1 TTTTATAAT
42581247 TTTTAATAAT
1 TTTT-ATAAT
*
42581257 ATTTA-AAT
1 TTTTATAAT
* *
42581265 ATTTAAATAT
1 TTTTATA-AT
42581275 TTTTAT
1 TTTTAT
42581281 TAAAATTTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
8 9 0.18
9 20 0.39
10 21 0.41
11 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (9 bp):
TTTTATAAT
Found at i:42581268 original size:28 final size:28
Alignment explanation
Indices: 42581207--42581307 Score: 98
Period size: 28 Copynumber: 3.6 Consensus size: 28
42581197 ATATTTCTAT
* *
42581207 ATATTTTATAATTTTTAA-GATTTTTATA
1 ATATTTTATAATTTTTAATAATATTTA-A
*
42581235 AAATTTTATAATTTTTAATAATATTTAA
1 ATATTTTATAATTTTTAATAATATTTAA
* * *
42581263 ATA-TTTAAATATTTTTATTAAAATTTAA
1 ATATTTTATA-ATTTTTAATAATATTTAA
* *
42581291 TTATTTTATAACTTTTA
1 ATATTTTATAATTTTTA
42581308 TTTTTATTTT
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
27 5 0.08
28 44 0.73
29 11 0.18
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (28 bp):
ATATTTTATAATTTTTAATAATATTTAA
Found at i:42581290 original size:20 final size:21
Alignment explanation
Indices: 42581259--42581297 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
42581249 TTAATAATAT
42581259 TTAAATATTTAAATATTTTTA
1 TTAAATATTTAAATATTTTTA
*
42581280 TTAAA-ATTTAATTATTTT
1 TTAAATATTTAAATATTTT
42581298 ATAACTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTAAATATTTAAATATTTTTA
Found at i:42581601 original size:92 final size:89
Alignment explanation
Indices: 42581430--42581603 Score: 197
Period size: 92 Copynumber: 1.9 Consensus size: 89
42581420 AAGAGCAATG
* * *
42581430 GCTTAATTGCTTTTTTGAAAAAGTTTAAGGGTCTTTTTGATGCATTTTGAAAGTTCAAATACCCA
1 GCTTAATTACTTTTTTGAAAAAGTTTAAGGGTCTTTTTAATGCATTATGAAAGTTCAAATACCCA
* **
42581495 ATTGCGTGTAAAAAAAAAGTAGGA
66 ATTGAGTACAAAAAAAAAGTAGGA
* * * **
42581519 GCTTAATTACTTTTTCTGAAAAAAGTTTGAGGGTTTTTTTTAATGCATTATGAAAGTTTAGGTAC
1 GCTTAATTACTTTTT-TG-AAAAAGTTTAAGGG-TCTTTTTAATGCATTATGAAAGTTCAAATAC
*
42581584 CCAAGTT-AGTACCAAAAAAA
63 CCAA-TTGAGTACAAAAAAAA
42581604 GAGACTTAAT
Statistics
Matches: 69, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
89 14 0.20
90 2 0.03
91 13 0.19
92 38 0.55
93 2 0.03
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (89 bp):
GCTTAATTACTTTTTTGAAAAAGTTTAAGGGTCTTTTTAATGCATTATGAAAGTTCAAATACCCA
ATTGAGTACAAAAAAAAAGTAGGA
Found at i:42582918 original size:23 final size:23
Alignment explanation
Indices: 42582875--42582918 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
42582865 AAAGGTTAAG
**
42582875 ATTTTGTTGAATTTTTTTATATT
1 ATTTTGTTGAATTTTCCTATATT
42582898 ATTTTG-TGAATTATTCCTATA
1 ATTTTGTTGAATT-TTCCTATA
42582919 AAATTTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.25, C:0.05, G:0.09, T:0.61
Consensus pattern (23 bp):
ATTTTGTTGAATTTTCCTATATT
Found at i:42589468 original size:30 final size:28
Alignment explanation
Indices: 42589432--42589491 Score: 86
Period size: 27 Copynumber: 2.1 Consensus size: 28
42589422 GTGGAAAGGA
42589432 AAAGATCACTGAGTAGACGTCTTC-ATTCAT
1 AAAGATCACT--G-AGACGTCTTCGATTCAT
42589462 AAAGATCACTGAGACGTCTTCGATTCAT
1 AAAGATCACTGAGACGTCTTCGATTCAT
42589490 AA
1 AA
42589492 CATCCATCGT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
27 10 0.34
28 9 0.31
30 10 0.34
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (28 bp):
AAAGATCACTGAGACGTCTTCGATTCAT
Found at i:42589717 original size:40 final size:36
Alignment explanation
Indices: 42589660--42589799 Score: 104
Period size: 40 Copynumber: 3.7 Consensus size: 36
42589650 GTGACAATTT
* *
42589660 GTTGGTTAAACCAACTAGAGTTGGGCTCACATTTAATATC
1 GTTGGTTTATCCAACTAGAGTTGGG-TCACA---AATATC
* *
42589700 GTTGGTTTATCCGACTAGCA-CTGGG-CACAAATATC
1 GTTGGTTTATCCAACTAG-AGTTGGGTCACAAATATC
* *
42589735 GTTGGTTTATCCAACTAAAGTTGGGTTCACTAATCATTTC
1 GTTGGTTTATCCAACTAGAGTTGGG-TCAC-AA--ATATC
** *
42589775 GTCAGTTTATCCAACTAGCGTTGGG
1 GTTGGTTTATCCAACTAGAGTTGGG
42589800 CGCAATTTCC
Statistics
Matches: 81, Mismatches: 12, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
34 1 0.01
35 26 0.32
37 3 0.04
38 6 0.07
40 44 0.54
41 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (36 bp):
GTTGGTTTATCCAACTAGAGTTGGGTCACAAATATC
Found at i:42589922 original size:69 final size:68
Alignment explanation
Indices: 42589779--42589941 Score: 191
Period size: 69 Copynumber: 2.4 Consensus size: 68
42589769 CATTTCGTCA
* * * * * * *
42589779 GTTTATCCAACTAGCGTTGGGCGCAATTTCCGTTAGTTTATCTGACAGTGCTAGGCACACATTTG
1 GTTTATCTAACTAGCGCTGGGCGCAACTTCCGTCAGTTTATCTAACAGTGCTAGGCACACAATTA
42589844 TCG
66 TCG
* * * * *
42589847 GTTTATCTGACTAGCGCTGGGTGCAACTTCCGTCAGTTTGTCTAACTATTGCTGGGCACACAATT
1 GTTTATCTAACTAGCGCTGGGCGCAACTTCCGTCAGTTTATCTAAC-AGTGCTAGGCACACAATT
42589912 ATCG
65 ATCG
**
42589916 GTTTATCTAACTAGCATTGGGCGCAA
1 GTTTATCTAACTAGCGCTGGGCGCAA
42589942 ACTCTTTCAC
Statistics
Matches: 78, Mismatches: 16, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
68 38 0.49
69 40 0.51
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.33
Consensus pattern (68 bp):
GTTTATCTAACTAGCGCTGGGCGCAACTTCCGTCAGTTTATCTAACAGTGCTAGGCACACAATTA
TCG
Found at i:42595401 original size:85 final size:85
Alignment explanation
Indices: 42595258--42595436 Score: 340
Period size: 85 Copynumber: 2.1 Consensus size: 85
42595248 GGCCGGCCAT
42595258 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
42595323 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
*
42595343 GAGCATGGGTGGACAAGATGTTATGGCTAAAAATATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
42595408 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
*
42595428 GGGCATGGG
1 GAGCATGGG
42595437 CAATAAAATA
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 92 1.00
ACGTcount: A:0.37, C:0.08, G:0.28, T:0.27
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
GTAAGGATTAATAAAATAAA
Found at i:42597630 original size:47 final size:47
Alignment explanation
Indices: 42597576--42598217 Score: 1022
Period size: 47 Copynumber: 13.6 Consensus size: 47
42597566 TATTTGAATA
42597576 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
42597623 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
42597672 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
42597719 AATGTGAAAGTGTATATATATGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
42597766 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
42597815 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCC-A-ATG-TG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
42597859 -ATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
42597907 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
**
42597956 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAACCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
42598003 AATGTGAAAGTGTATATTTGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
42598050 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
42598097 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * * *
42598144 AATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
42598191 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
42598218 TCCCGAAGGG
Statistics
Matches: 558, Mismatches: 27, Indels: 20
0.92 0.04 0.03
Matches are distributed among these distances:
43 11 0.02
44 2 0.00
45 28 0.05
46 2 0.00
47 364 0.65
48 2 0.00
49 149 0.27
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:42603514 original size:50 final size:50
Alignment explanation
Indices: 42603398--42603690 Score: 462
Period size: 50 Copynumber: 5.8 Consensus size: 50
42603388 GATAATAACA
* ** *
42603398 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTACTCATGTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCT-CTCATCTCGG
*
42603449 TGCCCATGCCATGTCCCAGACATGGTCTTACGA-GGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTAC-ATGGGACCTCTCATCTCGG
* * * *
42603499 TGCCAATGCCATGTCCTAGACATGGTCTTACATAGGACCTCTCATTTCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
42603549 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
42603599 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
42603649 TGCCAATGCCATGTCCCATACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
42603691 TTACCCCAAT
Statistics
Matches: 224, Mismatches: 16, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
49 1 0.00
50 188 0.84
51 34 0.15
52 1 0.00
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:42603806 original size:13 final size:13
Alignment explanation
Indices: 42603785--42603814 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
42603775 GCTTGGATCA
42603785 TCATCAAATAAAT
1 TCATCAAATAAAT
*
42603798 TCATGAAATAAAT
1 TCATCAAATAAAT
42603811 TCAT
1 TCAT
42603815 TATTTCTGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.13, G:0.03, T:0.33
Consensus pattern (13 bp):
TCATCAAATAAAT
Found at i:42605843 original size:22 final size:24
Alignment explanation
Indices: 42605800--42605843 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
42605790 GCATGATATT
42605800 TCAATAAACAAACAATTCAATGAA
1 TCAATAAACAAACAATTCAATGAA
*
42605824 TCAATAAA-AAA-AATTGAATG
1 TCAATAAACAAACAATTCAATG
42605844 TAGGAACCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 3 0.16
24 8 0.42
ACGTcount: A:0.59, C:0.11, G:0.07, T:0.23
Consensus pattern (24 bp):
TCAATAAACAAACAATTCAATGAA
Done.