Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 129 of 175
Found at i:40221761 original size:3 final size:3
Alignment explanation
Indices: 40221755--40221793 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
40221745 TTAATAATAA
* *
40221755 TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
40221794 AATTTCCCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:40222188 original size:18 final size:17
Alignment explanation
Indices: 40222165--40222200 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
40222155 TTTAATTTGA
*
40222165 TATTTGTTTATTTACTTT
1 TATTTGTTGATTT-CTTT
40222183 TATTTGTTGATTTCTTT
1 TATTTGTTGATTTCTTT
40222200 T
1 T
40222201 CATTATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.14, C:0.06, G:0.08, T:0.72
Consensus pattern (17 bp):
TATTTGTTGATTTCTTT
Found at i:40222500 original size:110 final size:110
Alignment explanation
Indices: 40222307--40222854 Score: 945
Period size: 110 Copynumber: 5.0 Consensus size: 110
40222297 TTATCAAAAC
40222307 AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
1 AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
*
40222372 GGGTGTCGATTGTTCTCATTCAACCAAATGGCTAAATATCCTTTT
66 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
40222417 AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
1 AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
*
40222482 GGGTGTTGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
66 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
* *
40222527 AAAAATTTTCAAATAAGGCAATGTATTGCGTTTGGGAAATTCGAGAGAACGTGCCCTAAGGTGCT
1 AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
* *
40222592 GGGTGTCGATTTGTCTCGTTCAACCAAATGGCTAAATATCCTTTT
66 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
*
40222637 AAAAAATTTTCGAAATAAGGCAATGTTTTGCATTTGGGAAATTCGAGAAAACGTGCCCTAAGGTG
1 -AAAAATTTTC-AAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTG
*
40222702 CTGGGTGTCGATTTTTCTCGTTCAACCAAATGGCTAAATATCCTTTT
64 CTGGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
* *
40222749 AAAAATTTTAAAATAAGGCAATGTTTTGCGTTT-GAAAATTCGAGAAAACGTGCCCTAAGGTGCT
1 AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
* * * *
40222813 GGGTGTCGATTTTTCTCATTTAACCGAATAGCCAAATATCCT
66 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCT
40222855 CTTGAATTTC
Statistics
Matches: 417, Mismatches: 19, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
109 67 0.16
110 235 0.56
111 19 0.05
112 96 0.23
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (110 bp):
AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
Found at i:40222757 original size:222 final size:220
Alignment explanation
Indices: 40222307--40222854 Score: 938
Period size: 222 Copynumber: 2.5 Consensus size: 220
40222297 TTATCAAAAC
40222307 AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
1 AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
40222372 GGGTGTCGA-TTGTTCTCATTCAACCAAATGGCTAAATATCCTTTTAAAAATTTTCAAATAAGGC
66 GGGTGTCGATTTG-TCTCATTCAACCAAATGGCTAAATATCCTTTTAAAAATTTTCAAATAAGGC
* *
40222436 AATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTTGATTTTTCTCAT
130 AATGTTTTGCATTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCTCAT
40222501 TCAACCAAATGGCTAAATATCCTTTT
195 TCAACCAAATGGCTAAATATCCTTTT
* *
40222527 AAAAATTTTCAAATAAGGCAATGTATTGCGTTTGGGAAATTCGAGAGAACGTGCCCTAAGGTGCT
1 AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
*
40222592 GGGTGTCGATTTGTCTCGTTCAACCAAATGGCTAAATATCCTTTTAAAAAATTTTCGAAATAAGG
66 GGGTGTCGATTTGTCTCATTCAACCAAATGGCTAAATATCCTTTT-AAAAATTTTC-AAATAAGG
*
40222657 CAATGTTTTGCATTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCTCG
129 CAATGTTTTGCATTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCTCA
40222722 TTCAACCAAATGGCTAAATATCCTTTT
194 TTCAACCAAATGGCTAAATATCCTTTT
* *
40222749 AAAAATTTTAAAATAAGGCAATGTTTTGCGTTT-GAAAATTCGAGAAAACGTGCCCTAAGGTGCT
1 AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
* * * * *
40222813 GGGTGTCGATTTTTCTCATTTAACCGAATAGCCAAATATCCT
66 GGGTGTCGATTTGTCTCATTCAACCAAATGGCTAAATATCCT
40222855 CTTGAATTTC
Statistics
Matches: 309, Mismatches: 16, Indels: 5
0.94 0.05 0.02
Matches are distributed among these distances:
220 103 0.33
221 78 0.25
222 128 0.41
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (220 bp):
AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
GGGTGTCGATTTGTCTCATTCAACCAAATGGCTAAATATCCTTTTAAAAATTTTCAAATAAGGCA
ATGTTTTGCATTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCTCATT
CAACCAAATGGCTAAATATCCTTTT
Found at i:40224407 original size:63 final size:63
Alignment explanation
Indices: 40224322--40224444 Score: 174
Period size: 63 Copynumber: 2.0 Consensus size: 63
40224312 TAATCACACG
* *
40224322 CACGCACACACACACAAAGACATACTTTTTTCAACCCAAACTCTCAATTTGCATAAGTCCACA
1 CACGCACACACACACAAAGACATACTTCTTTCAACCCAAACTATCAATTTGCATAAGTCCACA
* * * * * *
40224385 CACGCACGCACACACAATGACATACTTCTTTCGATCCACACTATGAATTTGCATAAGTCC
1 CACGCACACACACACAAAGACATACTTCTTTCAACCCAAACTATCAATTTGCATAAGTCC
40224445 TATCAAATCC
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
63 52 1.00
ACGTcount: A:0.35, C:0.33, G:0.09, T:0.24
Consensus pattern (63 bp):
CACGCACACACACACAAAGACATACTTCTTTCAACCCAAACTATCAATTTGCATAAGTCCACA
Found at i:40226133 original size:38 final size:37
Alignment explanation
Indices: 40226082--40226231 Score: 203
Period size: 38 Copynumber: 4.0 Consensus size: 37
40226072 AGAAGCATAA
*
40226082 TGTTATTCGGGCTCTGTGCCTAGCAGGCTTTGTGCCAG
1 TGTTATTCAGGCTCTGTGCCTAGCAGGCTTTGTGCC-G
**
40226120 TGTTATTTGGGCTCTGTGCCTAGCAGGCTTTGTGCCG
1 TGTTATTCAGGCTCTGTGCCTAGCAGGCTTTGTGCCG
*
40226157 ATGTTATTCAGGCTCTGTGCCTAGTAGGCTTTGTGCCGG
1 -TGTTATTCAGGCTCTGTGCCTAGCAGGCTTTGTGCC-G
* * *
40226196 TGTTATTCATGCTTTGTGCCTAGTAGGC-TTGTGCCG
1 TGTTATTCAGGCTCTGTGCCTAGCAGGCTTTGTGCCG
40226232 ATATATTGAA
Statistics
Matches: 104, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
36 1 0.01
37 8 0.08
38 94 0.90
39 1 0.01
ACGTcount: A:0.11, C:0.21, G:0.31, T:0.37
Consensus pattern (37 bp):
TGTTATTCAGGCTCTGTGCCTAGCAGGCTTTGTGCCG
Found at i:40226168 original size:22 final size:21
Alignment explanation
Indices: 40226143--40226215 Score: 66
Period size: 22 Copynumber: 3.6 Consensus size: 21
40226133 CTGTGCCTAG
40226143 CAGGCTTTGTGCCGATGTTATT
1 CAGGCTTTGTGCCG-TGTTATT
* *
40226165 CAGGCTCTGTGCC----TAGT
1 CAGGCTTTGTGCCGTGTTATT
40226182 -AGGCTTTGTGCCGGTGTTATT
1 CAGGCTTTGTGCC-GTGTTATT
*
40226203 CATGCTTTGTGCC
1 CAGGCTTTGTGCC
40226216 TAGTAGGCTT
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
16 11 0.28
17 3 0.08
21 3 0.08
22 23 0.57
ACGTcount: A:0.11, C:0.22, G:0.29, T:0.38
Consensus pattern (21 bp):
CAGGCTTTGTGCCGTGTTATT
Found at i:40226214 original size:76 final size:75
Alignment explanation
Indices: 40226081--40226233 Score: 225
Period size: 76 Copynumber: 2.0 Consensus size: 75
40226071 TAGAAGCATA
* **
40226081 ATGTTATTCGGGCTCTGTGCCTAGCAGGCTTTGTGCCAGTGTTATTTGGGCTCTGTGCCTAGCAG
1 ATGTTATTCAGGCTCTGTGCCTAGCAGGCTTTGTGCCAGTGTTATTCAGGCTCTGTGCCTAGCAG
40226146 GCTTTGTGCCG
66 GC-TTGTGCCG
* * * * *
40226157 ATGTTATTCAGGCTCTGTGCCTAGTAGGCTTTGTGCCGGTGTTATTCATGCTTTGTGCCTAGTAG
1 ATGTTATTCAGGCTCTGTGCCTAGCAGGCTTTGTGCCAGTGTTATTCAGGCTCTGTGCCTAGCAG
40226222 GCTTGTGCCG
66 GCTTGTGCCG
40226232 AT
1 AT
40226234 ATATTGAAAG
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
75 10 0.14
76 59 0.86
ACGTcount: A:0.12, C:0.21, G:0.30, T:0.37
Consensus pattern (75 bp):
ATGTTATTCAGGCTCTGTGCCTAGCAGGCTTTGTGCCAGTGTTATTCAGGCTCTGTGCCTAGCAG
GCTTGTGCCG
Found at i:40228150 original size:50 final size:50
Alignment explanation
Indices: 40228075--40228267 Score: 260
Period size: 50 Copynumber: 3.8 Consensus size: 50
40228065 ATTTGGGTAA
*
40228075 AGAGGTCTCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* *
40228125 AGAGGTCTCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** * * * *
40228175 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACTGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** * *
40228225 AGAACATCCCATGTAAGACCACGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
40228268 TGTTATTATT
Statistics
Matches: 126, Mismatches: 16, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
50 93 0.74
51 33 0.26
ACGTcount: A:0.25, C:0.22, G:0.31, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:40233005 original size:38 final size:38
Alignment explanation
Indices: 40232953--40233069 Score: 146
Period size: 38 Copynumber: 3.1 Consensus size: 38
40232943 TAGAAGCATA
* * *
40232953 ATGTTATTCCGGCTCTATACCTAGCAGGCTTTGTGTCG
1 ATGTTATTCAGGCTCTATGCCTAGCAGGCTTTGTGCCG
* *
40232991 ATGTTATTCGGGCTCTATGCCTAGCAGGTTTTGTGCCG
1 ATGTTATTCAGGCTCTATGCCTAGCAGGCTTTGTGCCG
* * * *
40233029 GTGTTATTCAGGCTCTGTGCCTAGTAGGC-TTGTTCCG
1 ATGTTATTCAGGCTCTATGCCTAGCAGGCTTTGTGCCG
40233066 ATGT
1 ATGT
40233070 ATTGAAAGTT
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
37 10 0.15
38 58 0.85
ACGTcount: A:0.14, C:0.21, G:0.27, T:0.38
Consensus pattern (38 bp):
ATGTTATTCAGGCTCTATGCCTAGCAGGCTTTGTGCCG
Found at i:40233801 original size:17 final size:17
Alignment explanation
Indices: 40233779--40233819 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
40233769 GTGTCTCAGT
40233779 CGTGTGTGACACACGGC
1 CGTGTGTGACACACGGC
40233796 CGTGTGTGACACACGGC
1 CGTGTGTGACACACGGC
40233813 CGTGTGT
1 CGTGTGT
40233820 CCCCTGTAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.15, C:0.27, G:0.37, T:0.22
Consensus pattern (17 bp):
CGTGTGTGACACACGGC
Found at i:40234185 original size:19 final size:20
Alignment explanation
Indices: 40234150--40234190 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 20
40234140 TTGTATGGTG
40234150 ATTGAAATGTTTATGTTTTAA
1 ATTGAAATG-TTATGTTTTAA
40234171 ATTGAAATG-TATGTTTTAA
1 ATTGAAATGTTATGTTTTAA
40234190 A
1 A
40234191 GTTGTGTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 11 0.55
21 9 0.45
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.49
Consensus pattern (20 bp):
ATTGAAATGTTATGTTTTAA
Found at i:40234575 original size:55 final size:55
Alignment explanation
Indices: 40234491--40234597 Score: 178
Period size: 55 Copynumber: 1.9 Consensus size: 55
40234481 TTATAGATTA
* * *
40234491 CAAATTAATTATTCATGAGCCCTATTCAAATTAAAAGTGATGATTTATCATCTTG
1 CAAATTAATTATTCATAAGCACTATTCAAATTAAAAGTGATAATTTATCATCTTG
*
40234546 CAAATTAATTATTCATAAGTACTATTCAAATTAAAAGTGATAATTTATCATC
1 CAAATTAATTATTCATAAGCACTATTCAAATTAAAAGTGATAATTTATCATC
40234598 CAATGGATAC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.38
Consensus pattern (55 bp):
CAAATTAATTATTCATAAGCACTATTCAAATTAAAAGTGATAATTTATCATCTTG
Found at i:40237920 original size:55 final size:55
Alignment explanation
Indices: 40237836--40237945 Score: 184
Period size: 55 Copynumber: 2.0 Consensus size: 55
40237826 AAATTATAGA
* * *
40237836 TTGCAAATTAATTATTCATGAGTACTATTCAAATTAAAAGTGATGATTTATCATC
1 TTGCAAATTAATTATTCATAAGCACTATTCAAATTAAAAGTGATGATCTATCATC
*
40237891 TTGCAAATTAATTATTCATAAGCACTATTCAAATTAAAATTGATGATCTATCATC
1 TTGCAAATTAATTATTCATAAGCACTATTCAAATTAAAAGTGATGATCTATCATC
40237946 CAATGGATAC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (55 bp):
TTGCAAATTAATTATTCATAAGCACTATTCAAATTAAAAGTGATGATCTATCATC
Found at i:40243129 original size:32 final size:31
Alignment explanation
Indices: 40243063--40243139 Score: 127
Period size: 31 Copynumber: 2.5 Consensus size: 31
40243053 ATAAACCTAG
*
40243063 AAAAATATTTTTTAAGATTTGTTATCTGTTA
1 AAAAATATTTTTTAAGATTTGTTATCTATTA
*
40243094 AAAAATATTTTTTAAGATTTTTTATCTATTA
1 AAAAATATTTTTTAAGATTTGTTATCTATTA
40243125 AAAAATATTTGTTTA
1 AAAAATATTT-TTTA
40243140 CTTAACATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
31 39 0.91
32 4 0.09
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (31 bp):
AAAAATATTTTTTAAGATTTGTTATCTATTA
Found at i:40248418 original size:190 final size:187
Alignment explanation
Indices: 40248098--40248459 Score: 501
Period size: 190 Copynumber: 1.9 Consensus size: 187
40248088 TCAATGTTGG
* *** * *
40248098 TTTTTTACTTTGATATTCTTGAAATTTTTATTATTTGTTAAATTTTATTTACTTAATTTTTTTTC
1 TTTTTTACTTTGATATTCTTGAAAATTTTATTATTTGTTAAAACATATTTACTAAATTTATTTTC
* * * * *
40248163 GAAATATATTTTTAAGGTTAATTTGACACTTTTGAGTATTGAGTACAGTGCATTATCAAATCATT
66 AAAATATATTTTTAAGGTTAACTCGACACCTTTGAGTATTGAGTACAATGCATTATCAAATCATT
* *
40248228 ATAAGAATGCATCCATTATATGTCAAGAGAAAAGGATTGTTGTAACGTCCCAATTTT
131 ACAAGAATGCATCCACTATATGTCAAGAGAAAAGGATTGTTGTAACGTCCCAATTTT
* *
40248285 TTTTTTACTTTGATATTGTTGAAAATTTTATTATTTGTTAAAACATATTTGCTCAAAATTTATTT
1 TTTTTTACTTTGATATTCTTGAAAATTTTATTATTTGTTAAAACATATTTACT--AAATTTATTT
* * *
40248350 TCAAAATGCAT-TTTTTAAGGTTAACTCGACACCTTTGAGTGTTGAGTACAATGCGTTGTCAAAT
64 TCAAAAT--ATATTTTTAAGGTTAACTCGACACCTTTGAGTATTGAGTACAATGCATTATCAAAT
* *
40248414 CATTACAAGAGTGCATGCACTATATGTCAAGAGAAAAGGATTGTTG
127 CATTACAAGAATGCATCCACTATATGTCAAGAGAAAAGGATTGTTG
40248460 AAACACCCTA
Statistics
Matches: 151, Mismatches: 20, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
187 47 0.31
189 14 0.09
190 88 0.58
191 2 0.01
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.44
Consensus pattern (187 bp):
TTTTTTACTTTGATATTCTTGAAAATTTTATTATTTGTTAAAACATATTTACTAAATTTATTTTC
AAAATATATTTTTAAGGTTAACTCGACACCTTTGAGTATTGAGTACAATGCATTATCAAATCATT
ACAAGAATGCATCCACTATATGTCAAGAGAAAAGGATTGTTGTAACGTCCCAATTTT
Found at i:40256577 original size:26 final size:27
Alignment explanation
Indices: 40256542--40256594 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
40256532 ACCATAGCAC
40256542 AAATCAGTCATTTACCC-TCGAGGGGCA
1 AAATCAGTCATTTACCCTTC-AGGGGCA
40256569 AAAT-AGTCATTTACCCTTCAGGGGCA
1 AAATCAGTCATTTACCCTTCAGGGGCA
40256595 TTACGGTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 19 0.76
27 6 0.24
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (27 bp):
AAATCAGTCATTTACCCTTCAGGGGCA
Found at i:40263095 original size:22 final size:22
Alignment explanation
Indices: 40263035--40263106 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
40263025 CCACTGATTC
* * *
40263035 GCACTACAGTGCCTACTGTTTA
1 GCACTTCAGTGCCTACTATCTA
* *
40263057 GCATTTC-GATGCTTACTATCTA
1 GCACTTCAG-TGCCTACTATCTA
40263079 GCACTTCAGTGCCTACTAATC-A
1 GCACTTCAGTGCCTACT-ATCTA
40263101 GCACTT
1 GCACTT
40263107 TGATGCCTAC
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
21 1 0.03
22 35 0.88
23 4 0.10
ACGTcount: A:0.24, C:0.28, G:0.15, T:0.33
Consensus pattern (22 bp):
GCACTTCAGTGCCTACTATCTA
Found at i:40272112 original size:44 final size:44
Alignment explanation
Indices: 40272064--40272211 Score: 178
Period size: 43 Copynumber: 3.4 Consensus size: 44
40272054 TGTGTTATCG
* * *
40272064 TGTAAGACCACATCTGGGACATTGGCATCGATTTGTGATTTACG
1 TGTAAGACCATATCTGGGACATTGGCATCGATATGTGATTTACA
* * *
40272108 TGTAAGACCATGTCTGGGACATCGGCATCG-TATATGATTT-CA
1 TGTAAGACCATATCTGGGACATTGGCATCGATATGTGATTTACA
* * *
40272150 TGTAAGACTC-TGTCTGGGACAGTGGCATCGATATGTGA-TAACA
1 TGTAAGAC-CATATCTGGGACATTGGCATCGATATGTGATTTACA
40272193 TGTAAGACCATATCTGGGA
1 TGTAAGACCATATCTGGGA
40272212 TATGGCGTTG
Statistics
Matches: 89, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
42 29 0.33
43 33 0.37
44 27 0.30
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.30
Consensus pattern (44 bp):
TGTAAGACCATATCTGGGACATTGGCATCGATATGTGATTTACA
Found at i:40275306 original size:27 final size:26
Alignment explanation
Indices: 40275250--40275307 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
40275240 AAGCCACCCC
* * **
40275250 TTTTATTTTATTTTGTTTTACTAATT
1 TTTTATTTTATTTTCTTATACTAAGA
*
40275276 TTTTATTTTATTATTCTTATACTTAGA
1 TTTTATTTTATT-TTCTTATACTAAGA
40275303 TTTTA
1 TTTTA
40275308 AATCTATTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 12 0.46
27 14 0.54
ACGTcount: A:0.22, C:0.05, G:0.03, T:0.69
Consensus pattern (26 bp):
TTTTATTTTATTTTCTTATACTAAGA
Found at i:40275432 original size:16 final size:18
Alignment explanation
Indices: 40275400--40275435 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
40275390 TATCATTGAG
40275400 TTTATTATTATTTTATCT
1 TTTATTATTATTTTATCT
40275418 TTTATT-TTA-TTTATCT
1 TTTATTATTATTTTATCT
40275434 TT
1 TT
40275436 CTTTTTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
17 3 0.17
18 6 0.33
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTATTATTATTTTATCT
Found at i:40276453 original size:21 final size:21
Alignment explanation
Indices: 40276429--40276470 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
40276419 TCTTATTTTT
40276429 AAAAGAAGAAAA-AAATCGAAA
1 AAAAGAA-AAAATAAATCGAAA
* *
40276450 AAAATAAAAAATAAATTGAAA
1 AAAAGAAAAAATAAATCGAAA
40276471 TATATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.76, C:0.02, G:0.10, T:0.12
Consensus pattern (21 bp):
AAAAGAAAAAATAAATCGAAA
Found at i:40277366 original size:30 final size:30
Alignment explanation
Indices: 40277325--40277382 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
40277315 TTGGGCATTT
* * *
40277325 CCACACGGGCTGGGCACACGCCCGTGTGAG
1 CCACACAGGCTGGCCACACGCCCATGTGAG
*
40277355 CCACACAGGCTGGCCACACTCCCATGTG
1 CCACACAGGCTGGCCACACGCCCATGTG
40277383 CCAGCTTGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.19, C:0.40, G:0.29, T:0.12
Consensus pattern (30 bp):
CCACACAGGCTGGCCACACGCCCATGTGAG
Found at i:40280864 original size:45 final size:45
Alignment explanation
Indices: 40280769--40280856 Score: 140
Period size: 45 Copynumber: 2.0 Consensus size: 45
40280759 TACAAGAAGC
** **
40280769 GAAGACTTATTAAACAATGGAAAACAAACAAAAACTTCTAAAAGT
1 GAAGACTTATTAAACAATGGAAAACAAACAAAAAAATAGAAAAGT
40280814 GAAGACTTATTAAACAATGGAAAACAAACAAAAAAATAGAAAA
1 GAAGACTTATTAAACAATGGAAAACAAACAAAAAAATAGAAAA
40280857 TTTAAGACAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.60, C:0.11, G:0.11, T:0.17
Consensus pattern (45 bp):
GAAGACTTATTAAACAATGGAAAACAAACAAAAAAATAGAAAAGT
Found at i:40282321 original size:17 final size:17
Alignment explanation
Indices: 40282300--40282333 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40282290 AAAATAAAAA
*
40282300 AAAAACAAAAAAACAGTG
1 AAAAA-AAAACAACAGTG
40282318 AAAAAAAAACAACAGT
1 AAAAAAAAACAACAGT
40282334 TTTTTTTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.74, C:0.12, G:0.09, T:0.06
Consensus pattern (17 bp):
AAAAAAAAACAACAGTG
Found at i:40292169 original size:22 final size:22
Alignment explanation
Indices: 40292122--40292170 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
40292112 TAAATATTTT
* * *
40292122 TAAATAAATTTTTATTTTTATT
1 TAAATAAATGTTTATTTTGATA
40292144 TAAATAAATGTTTATATTTGA-A
1 TAAATAAATGTTTAT-TTTGATA
40292166 TAAAT
1 TAAAT
40292171 TAAAACTCAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (22 bp):
TAAATAAATGTTTATTTTGATA
Found at i:40294911 original size:9 final size:9
Alignment explanation
Indices: 40294892--40294928 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
40294882 TGAGTTTTCG
*
40294892 AATTTGAAT
1 AATTCGAAT
*
40294901 AACTCGAAT
1 AATTCGAAT
40294910 AATTCGAAT
1 AATTCGAAT
40294919 AATTCGAAT
1 AATTCGAAT
40294928 A
1 A
40294929 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:40297599 original size:19 final size:18
Alignment explanation
Indices: 40297577--40297619 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
40297567 AACATAAGTT
40297577 TTAAAA-AATTAATATAATA
1 TTAAAATAATTAA-ATAA-A
40297596 TTAAAATTAATTAAATAAA
1 TTAAAA-TAATTAAATAAA
40297615 TTAAA
1 TTAAA
40297620 CATGTGTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 12 0.55
20 4 0.18
21 6 0.27
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TTAAAATAATTAAATAAA
Found at i:40298982 original size:88 final size:88
Alignment explanation
Indices: 40298880--40299091 Score: 334
Period size: 88 Copynumber: 2.4 Consensus size: 88
40298870 TACTGCTTAA
*
40298880 GGAGATAAGATCTGAAATCTTCAATCTATTCCACTATTGTCCAGAAAAGTAGAATTATTGGCTTC
1 GGAGATAAGATCTGAAATCTTCAATCTATTCCACTATTGTCCAGAAAAGTAGAATTACTGGCTTC
40298945 AATGTACTCCACTGTAACCACAG
66 AATGTACTCCACTGTAACCACAG
* *
40298968 GGAGATAAGATCTGAAATCTTTAATCTATTCCACTGTTGTCCAGAAAAGTAGAATTACTGGCTTC
1 GGAGATAAGATCTGAAATCTTCAATCTATTCCACTATTGTCCAGAAAAGTAGAATTACTGGCTTC
40299033 AATGTACTCCACTGTAACCACAG
66 AATGTACTCCACTGTAACCACAG
* * * ** * *
40299056 GGAGGTAAAATCCGCCATCTTCGATCTGTTCCACTA
1 GGAGATAAGATCTGAAATCTTCAATCTATTCCACTA
40299092 CTGCTTAGGG
Statistics
Matches: 112, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 112 1.00
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (88 bp):
GGAGATAAGATCTGAAATCTTCAATCTATTCCACTATTGTCCAGAAAAGTAGAATTACTGGCTTC
AATGTACTCCACTGTAACCACAG
Found at i:40299002 original size:132 final size:132
Alignment explanation
Indices: 40298669--40298971 Score: 498
Period size: 132 Copynumber: 2.3 Consensus size: 132
40298659 AAGGAGATAT
* * *
40298669 ATTACTAGCTTCAATGTACTCCATTGTAACCACAGGGAGGTAAAATCCGCCATCTTCAATTTGCT
1 ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCAATCTGCT
* * * ** *
40298734 CCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTTTCCAGGGAATTA
66 CCACTACTGCTTAAGGAGATAAGATCTGAAATCTTCAATCTATTCCACTATTGTCCAGAAAAGTA
40298799 GA
131 GA
* *
40298801 ATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
1 ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCAATCTGCT
40298866 CCACTACTGCTTAAGGAGATAAGATCTGAAATCTTCAATCTATTCCACTATTGTCCAGAAAAGTA
66 CCACTACTGCTTAAGGAGATAAGATCTGAAATCTTCAATCTATTCCACTATTGTCCAGAAAAGTA
40298931 GA
131 GA
*
40298933 ATTATTGGCTTCAATGTACTCCACTGTAACCACAGGGAG
1 ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAG
40298972 ATAAGATCTG
Statistics
Matches: 158, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
132 158 1.00
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.29
Consensus pattern (132 bp):
ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCAATCTGCT
CCACTACTGCTTAAGGAGATAAGATCTGAAATCTTCAATCTATTCCACTATTGTCCAGAAAAGTA
GA
Found at i:40299023 original size:220 final size:219
Alignment explanation
Indices: 40298746--40299200 Score: 757
Period size: 220 Copynumber: 2.1 Consensus size: 219
40298736 ACTACTGCTT
* ** *
40298746 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTTTCCAGGGAATTAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGAAAAGTAGAATTACTGGCT
40298811 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
66 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
* *
40298876 TTAAGGAGATAAGATCTGAAATCTTCAATCTATTCCACTATTGTCCAGAAAAGTAGAATTATTGG
131 TTAAGGAGATAAGACCTGAAATCTTCAATCTATTCCAC-ATTGTCCAGAAAAGTAGAATTACTGG
40298941 CTTCAATGTACTCCACTGTAACCAC
195 CTTCAATGTACTCCACTGTAACCAC
*
40298966 AGGGAGATAAGATCTGAAATCTTTAATCTATTCCACTGTTGTCCAGAAAAGTAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGAAAAGTAGAATTACTGGCT
* *
40299031 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGTTCCACTACTGC
66 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
* * * **
40299096 TTAGGGAGATAATACCTGAAATCTTCAATCTATTCCACGTTGTCCAGGGAAGTAGAATTACTGGC
131 TTAAGGAGATAAGACCTGAAATCTTCAATCTATTCCACATTGTCCAGAAAAGTAGAATTACTGGC
40299161 TTCAATGTACTCCACTGTAACCAC
196 TTCAATGTACTCCACTGTAACCAC
* *
40299185 AGGGAGGTAAAATCTG
1 AGGGAGATAAGATCTG
40299201 CCATTTTCGA
Statistics
Matches: 219, Mismatches: 16, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
219 61 0.28
220 158 0.72
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (219 bp):
AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGAAAAGTAGAATTACTGGCT
TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
TTAAGGAGATAAGACCTGAAATCTTCAATCTATTCCACATTGTCCAGAAAAGTAGAATTACTGGC
TTCAATGTACTCCACTGTAACCAC
Found at i:40299047 original size:43 final size:42
Alignment explanation
Indices: 40298898--40299047 Score: 101
Period size: 43 Copynumber: 3.5 Consensus size: 42
40298888 GATCTGAAAT
* *
40298898 CTTCAATCTATTCCACTATTGTCCAGAAAAGTAGAATTATTGG
1 CTTCAATCTACTCCACTGTTGTCCAGAAAAGTAGAATTA-TGG
* *** *
40298941 CTTCAATGTACTCCACTGTAACCACAGGGAGATAAGATCTGAA--AT--
1 CTTCAATCTACTCCACTGTTGTC-CA--GA-A-AAG-T-AGAATTATGG
* *
40298986 CTTTAATCTATTCCACTGTTGTCCAGAAAAGTAGAATTACTGG
1 CTTCAATCTACTCCACTGTTGTCCAGAAAAGTAGAATTA-TGG
*
40299029 CTTCAATGTACTCCACTGT
1 CTTCAATCTACTCCACTGT
40299048 AACCACAGGG
Statistics
Matches: 78, Mismatches: 17, Indels: 24
0.66 0.14 0.20
Matches are distributed among these distances:
38 3 0.04
39 1 0.01
40 4 0.05
41 2 0.03
42 2 0.03
43 33 0.42
44 4 0.05
45 17 0.22
46 2 0.03
47 2 0.03
48 4 0.05
49 1 0.01
50 3 0.04
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.32
Consensus pattern (42 bp):
CTTCAATCTACTCCACTGTTGTCCAGAAAAGTAGAATTATGG
Found at i:40299126 original size:132 final size:132
Alignment explanation
Indices: 40298966--40299744 Score: 1326
Period size: 132 Copynumber: 5.9 Consensus size: 132
40298956 CTGTAACCAC
* * **
40298966 AGGGAGATAAGATCTGAAATCTTTAATCTATTCCACTGTTGTCCAGAAAAGTAGAATTACTGGCT
1 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
*
40299031 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGTTCCACTACTGC
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
40299096 TT
131 TT
*
40299098 AGGGAGATAATACCTGAAATCTTCAATCTATTCCAC-GTTGTCCAGGGAAGTAGAATTACTGGCT
1 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
* *
40299162 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATTTTCGATCTGCTCCACTACTGC
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
40299227 TT
131 TT
* *
40299229 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGATGTCTAGGGAAGTAGAATTACTGGCT
1 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
** *
40299294 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTATTCCACTGCTGC
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
40299359 TT
131 TT
*
40299361 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGATGTCCAGGGAAGTAGAATTACTGGCT
1 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
*
40299426 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTACTCCACTACTGC
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
40299491 TT
131 TT
* *
40299493 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTGGTT
1 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
* * *
40299558 TCAATGTACTCCACTATAACCACATGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTATTGC
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
40299623 TT
131 TT
* * *
40299625 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCTAGAGAAGTAGAATTACTGGCT
1 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
* *
40299690 TCAATGTACTCCACTGTAACCACATGGAGGTAAAATTCGCCATCTTCGATCTGCT
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
40299745 TCGCTGTCAA
Statistics
Matches: 613, Mismatches: 33, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
131 125 0.20
132 488 0.80
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (132 bp):
AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
TT
Found at i:40299237 original size:351 final size:352
Alignment explanation
Indices: 40298669--40299354 Score: 1124
Period size: 351 Copynumber: 2.0 Consensus size: 352
40298659 AAGGAGATAT
* *
40298669 ATTACTAGCTTCAATGTACTCCATTGTAACCACAGGGAGGTAAAATCCGCCATCTTCAATTTGCT
1 ATTACTAGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCAATCTGCT
* * *
40298734 CCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTTTCCAGGGAATTA
66 CCACTACTGCTTAGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTA
40298799 GAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTG
131 GAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTG
*
40298864 CTCCACTACTGCTTAAGGAGATAAGATCTGAAATCTTCAATCTATTCCACT-ATTGTCCAGAAAA
196 CTCCACTACTGCTTAAGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGA-TGTCCAGAAAA
* * * *
40298928 GTAGAATTATTGGCTTCAATGTACTCCACTGTAACCACAGGGAGATAAGATCTGAAATCTTTAAT
260 GTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGATAAAATCCGAAATCTTCAAT
40298993 CTATTCCACTGTTGTCCAGAAAAGTAGA
325 CTATTCCACTGTTGTCCAGAAAAGTAGA
* * *
40299021 ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGTT
1 ATTACTAGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCAATCTGCT
*
40299086 CCACTACTGCTTAGGGAGATAATACCTGAAATCTTCAATCTATTCCAC-GTTGTCCAGGGAAGTA
66 CCACTACTGCTTAGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTA
* * *
40299150 GAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATTTTCGATCTG
131 GAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTG
* * **
40299215 CTCCACTACTGCTTAGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGATGTCTAGGGAAG
196 CTCCACTACTGCTTAAGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGATGTCCAGAAAAG
* ** *
40299280 TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATC
261 TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGATAAAATCCGAAATCTTCAATC
40299345 TATTCCACTG
326 TATTCCACTG
40299355 CTGCTTAGGG
Statistics
Matches: 308, Mismatches: 25, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
351 201 0.65
352 107 0.35
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (352 bp):
ATTACTAGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCAATCTGCT
CCACTACTGCTTAGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTA
GAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTG
CTCCACTACTGCTTAAGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGATGTCCAGAAAAG
TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGATAAAATCCGAAATCTTCAATC
TATTCCACTGTTGTCCAGAAAAGTAGA
Found at i:40299541 original size:44 final size:44
Alignment explanation
Indices: 40299229--40299541 Score: 133
Period size: 44 Copynumber: 7.1 Consensus size: 44
40299219 ACTACTGCTT
* * *
40299229 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGATGTCT
1 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGCCC
* * * * * **
40299273 AGGGAAGTAGAATTA-CTG---GCTTCAATGTACTCCACTGTAACCAC
1 AGGG-AG-ATAA-GACCTGAAATCTTCAATCTATTCCACTGTTGCC-C
* * ** * * **
40299317 AGGGAGGTAAAATCC-GCCATCTTCGATCTATTCCACTGCTGCTT
1 AGGGAGATAAGA-CCTGAAATCTTCAATCTATTCCACTGTTGCCC
* *
40299361 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGATGTCC
1 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGCCC
* * * * * **
40299405 AGGGAAGTAGAATTA-CTG---GCTTCAATGTACTCCACTGTAACCAC
1 AGGG-AG-ATAA-GACCTGAAATCTTCAATCTATTCCACTGTTGCC-C
* * ** * * ** **
40299449 AGGGAGGTAAAATCC-GCCATCTTCGATCTACTCCACTACTGCTT
1 AGGGAGATAAGA-CCTGAAATCTTCAATCTATTCCACTGTTGCCC
40299493 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGCCC
1 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGCCC
40299537 AGGGA
1 AGGGA
40299542 AGTAGAATTA
Statistics
Matches: 187, Mismatches: 62, Indels: 40
0.65 0.21 0.14
Matches are distributed among these distances:
41 2 0.01
42 6 0.03
43 44 0.24
44 85 0.45
45 36 0.19
46 12 0.06
47 2 0.01
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (44 bp):
AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGCCC
Found at i:40299660 original size:44 final size:44
Alignment explanation
Indices: 40299467--40299661 Score: 112
Period size: 44 Copynumber: 4.4 Consensus size: 44
40299457 AAAATCCGCC
* * * *
40299467 ATCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGACCTGAA
1 ATCTTCAATCTACTCCACTATTGCTCAGGGAGATAAGATCTGAA
* * *
40299511 ATCTTCAATCTATTCCACTGTTGCCCAGGGA-AGT-AGAATTACTG--
1 ATCTTCAATCTACTCCACTATTGCTCAGGGAGA-TAAG-A-T-CTGAA
* * ** * * * * * **
40299555 GT-TTCAATGTACTCCACTATAACCACATGGAGGTAAAATCCGCC
1 ATCTTCAATCTACTCCACTAT-TGCTCAGGGAGATAAGATCTGAA
* * *
40299599 ATCTTCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGAA
1 ATCTTCAATCTACTCCACTATTGCTCAGGGAGATAAGATCTGAA
*
40299643 ATCTTCAATCTATTCCACT
1 ATCTTCAATCTACTCCACT
40299662 GTTGTCTAGA
Statistics
Matches: 106, Mismatches: 35, Indels: 20
0.66 0.22 0.12
Matches are distributed among these distances:
42 2 0.02
43 19 0.18
44 66 0.62
45 16 0.15
46 3 0.03
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (44 bp):
ATCTTCAATCTACTCCACTATTGCTCAGGGAGATAAGATCTGAA
Found at i:40306254 original size:22 final size:21
Alignment explanation
Indices: 40306219--40306333 Score: 71
Period size: 19 Copynumber: 5.7 Consensus size: 21
40306209 AAAAGGTATC
* *
40306219 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
40306240 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
40306263 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
40306282 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* * *
40306301 TATATAT--TATATCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
40306320 TGCATATCATATCT
1 TACAAATCATATCT
40306334 AAGATTGCAT
Statistics
Matches: 79, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
17 2 0.03
19 45 0.57
21 7 0.09
22 15 0.19
23 10 0.13
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:40306262 original size:23 final size:22
Alignment explanation
Indices: 40306219--40306276 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
40306209 AAAAGGTATC
* *
40306219 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
40306240 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
40306263 TGCATATCATATCT
1 TACAAATCATATCT
40306277 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:40306279 original size:19 final size:19
Alignment explanation
Indices: 40306255--40306346 Score: 157
Period size: 19 Copynumber: 4.8 Consensus size: 19
40306245 AATCATATCT
40306255 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
40306274 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
** *
40306293 TCTAAGATTATATATTATA
1 TCTAAGATTGCATATCATA
40306312 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
40306331 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
40306347 CCTGAAGATT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 67 1.00
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:40307429 original size:23 final size:23
Alignment explanation
Indices: 40307403--40307446 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
40307393 CTCATATTGG
40307403 TAGGGTTAGATTCTTAGAATTAC
1 TAGGGTTAGATTCTTAGAATTAC
40307426 TAGGGTTAGATTCTTAGAATT
1 TAGGGTTAGATTCTTAGAATT
40307447 GCAAATCAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.41
Consensus pattern (23 bp):
TAGGGTTAGATTCTTAGAATTAC
Found at i:40308794 original size:4 final size:4
Alignment explanation
Indices: 40308777--40308822 Score: 56
Period size: 4 Copynumber: 10.8 Consensus size: 4
40308767 AGTTTAATGT
*
40308777 TTAA TTAAA CTTAA TTAAA TTAA TTAA TTAA TTAC TTAA TTAA TTA
1 TTAA TT-AA -TTAA TT-AA TTAA TTAA TTAA TTAA TTAA TTAA TTA
40308823 TCCTTATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
4 27 0.73
5 8 0.22
6 2 0.05
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (4 bp):
TTAA
Found at i:40309692 original size:16 final size:17
Alignment explanation
Indices: 40309671--40309705 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
40309661 TAGGGTTGAA
*
40309671 AAGAAA-GATTTAGAAG
1 AAGAAAGGATTGAGAAG
40309687 AAGAAAGGATTGAGAAG
1 AAGAAAGGATTGAGAAG
40309704 AA
1 AA
40309706 AGAACTGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.57, C:0.00, G:0.29, T:0.14
Consensus pattern (17 bp):
AAGAAAGGATTGAGAAG
Found at i:40318666 original size:19 final size:21
Alignment explanation
Indices: 40318628--40318668 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
40318618 TATTATACTT
*
40318628 TATTTCATTTTTTCTTAAAAA
1 TATTTCATTTTTTCTCAAAAA
40318649 TATTTC-TTTTTT-TCAAAAA
1 TATTTCATTTTTTCTCAAAAA
40318668 T
1 T
40318669 TCCAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 6 0.32
21 6 0.32
ACGTcount: A:0.32, C:0.10, G:0.00, T:0.59
Consensus pattern (21 bp):
TATTTCATTTTTTCTCAAAAA
Found at i:40318667 original size:20 final size:21
Alignment explanation
Indices: 40318628--40318667 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40318618 TATTATACTT
*
40318628 TATTTCATTTTTTCTTAAAAA
1 TATTTCATTTTTTCTAAAAAA
*
40318649 TATTTCTTTTTTTC-AAAAA
1 TATTTCATTTTTTCTAAAAA
40318668 TTCCAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTTCATTTTTTCTAAAAAA
Found at i:40337910 original size:9 final size:9
Alignment explanation
Indices: 40337891--40337927 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
40337881 TGAGTTTTCG
*
40337891 AATTTGAAT
1 AATTCGAAT
*
40337900 AACTCGAAT
1 AATTCGAAT
40337909 AATTCGAAT
1 AATTCGAAT
40337918 AATTCGAAT
1 AATTCGAAT
40337927 A
1 A
40337928 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:40340597 original size:19 final size:18
Alignment explanation
Indices: 40340575--40340617 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
40340565 AACATAAGTT
40340575 TTAAAA-AATTAATATAATA
1 TTAAAATAATTAA-ATAA-A
40340594 TTAAAATTAATTAAATAAA
1 TTAAAA-TAATTAAATAAA
40340613 TTAAA
1 TTAAA
40340618 CATGTGTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 12 0.55
20 4 0.18
21 6 0.27
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TTAAAATAATTAAATAAA
Found at i:40342003 original size:132 final size:132
Alignment explanation
Indices: 40341670--40341972 Score: 498
Period size: 132 Copynumber: 2.3 Consensus size: 132
40341660 AAGGAGATAT
* * *
40341670 ATTACTAGCTTCAATGTACTCCATTGTAACCACAGGGAGGTAAAATCCGCCATCTTCAATTTGCT
1 ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCAATCTGCT
* * * ** *
40341735 CCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTTTCCAGGGAATTA
66 CCACTACTGCTTAAGGAGATAAGATCTGAAATCTTCAATCTATTCCACTATTGTCCAGAAAAGTA
40341800 GA
131 GA
* *
40341802 ATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
1 ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCAATCTGCT
40341867 CCACTACTGCTTAAGGAGATAAGATCTGAAATCTTCAATCTATTCCACTATTGTCCAGAAAAGTA
66 CCACTACTGCTTAAGGAGATAAGATCTGAAATCTTCAATCTATTCCACTATTGTCCAGAAAAGTA
40341932 GA
131 GA
*
40341934 ATTATTGGCTTCAATGTACTCCACTGTAACCACAGGGAG
1 ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAG
40341973 ATAAGATCTG
Statistics
Matches: 158, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
132 158 1.00
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.29
Consensus pattern (132 bp):
ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCAATCTGCT
CCACTACTGCTTAAGGAGATAAGATCTGAAATCTTCAATCTATTCCACTATTGTCCAGAAAAGTA
GA
Found at i:40342023 original size:219 final size:219
Alignment explanation
Indices: 40341747--40342200 Score: 757
Period size: 219 Copynumber: 2.1 Consensus size: 219
40341737 ACTACTGCTT
* * *
40341747 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTTTCCAGGGAATTAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGAAAGTAGAATTACTGGCT
40341812 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
66 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
* *
40341877 TTAAGGAGATAAGATCTGAAATCTTCAATCTATTCCACTATTGTCCAGAAAAGTAGAATTATTGG
131 TTAAGGAGATAAGACCTGAAATCTTCAATCTATTCCAC-ATTGTCCAGAAAAGTAGAATTACTGG
40341942 CTTCAATGTACTCCACTGTAACCAC
195 CTTCAATGTACTCCACTGTAACCAC
*
40341967 AGGGAGATAAGATCTGAAATCTTTAATCTATTCCACTGTTGTCCA-GAAAGTAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGAAAGTAGAATTACTGGCT
* *
40342031 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGTTCCACTACTGC
66 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
* * * **
40342096 TTAGGGAGATAATACCTGAAATCTTCAATCTATTCCACGTTGTCCAGGGAAGTAGAATTACTGGC
131 TTAAGGAGATAAGACCTGAAATCTTCAATCTATTCCACATTGTCCAGAAAAGTAGAATTACTGGC
40342161 TTCAATGTACTCCACTGTAACCAC
196 TTCAATGTACTCCACTGTAACCAC
* *
40342185 AGGGAGGTAAAATCTG
1 AGGGAGATAAGATCTG
40342201 CCATTTTCGA
Statistics
Matches: 219, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
218 61 0.28
219 115 0.53
220 43 0.20
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (219 bp):
AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGAAAGTAGAATTACTGGCT
TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
TTAAGGAGATAAGACCTGAAATCTTCAATCTATTCCACATTGTCCAGAAAAGTAGAATTACTGGC
TTCAATGTACTCCACTGTAACCAC
Found at i:40342038 original size:87 final size:88
Alignment explanation
Indices: 40341881--40342091 Score: 325
Period size: 87 Copynumber: 2.4 Consensus size: 88
40341871 TACTGCTTAA
*
40341881 GGAGATAAGATCTGAAATCTTCAATCTATTCCACTATTGTCCAGAAAAGTAGAATTATTGGCTTC
1 GGAGATAAGATCTGAAATCTTCAATCTATTCCACTATTGTCCAGAAAAGTAGAATTACTGGCTTC
40341946 AATGTACTCCACTGTAACCACAG
66 AATGTACTCCACTGTAACCACAG
* *
40341969 GGAGATAAGATCTGAAATCTTTAATCTATTCCACTGTTGTCCAG-AAAGTAGAATTACTGGCTTC
1 GGAGATAAGATCTGAAATCTTCAATCTATTCCACTATTGTCCAGAAAAGTAGAATTACTGGCTTC
40342033 AATGTACTCCACTGTAACCACAG
66 AATGTACTCCACTGTAACCACAG
* * * ** * *
40342056 GGAGGTAAAATCCGCCATCTTCGATCTGTTCCACTA
1 GGAGATAAGATCTGAAATCTTCAATCTATTCCACTA
40342092 CTGCTTAGGG
Statistics
Matches: 111, Mismatches: 12, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
87 69 0.62
88 42 0.38
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (88 bp):
GGAGATAAGATCTGAAATCTTCAATCTATTCCACTATTGTCCAGAAAAGTAGAATTACTGGCTTC
AATGTACTCCACTGTAACCACAG
Found at i:40342089 original size:132 final size:131
Alignment explanation
Indices: 40341967--40342744 Score: 1281
Period size: 132 Copynumber: 5.9 Consensus size: 131
40341957 CTGTAACCAC
* * *
40341967 AGGGAGATAAGATCTGAAATCTTTAATCTATTCCACTGTTGTCCA-GAAAGTAGAATTACTGGCT
1 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
*
40342031 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGTTCCACTACTGC
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTAC-GC
40342096 TT
130 TT
*
40342098 AGGGAGATAATACCTGAAATCTTCAATCTATTCCAC-GTTGTCCAGGGAAGTAGAATTACTGGCT
1 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
* *
40342162 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATTTTCGATCTGCTCCACTACTGC
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTAC-GC
40342227 TT
130 TT
* *
40342229 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGATGTCTAGGGAAGTAGAATTACTGGCT
1 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
** *
40342294 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTATTCCACTGCTGC
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTAC-GC
40342359 TT
130 TT
*
40342361 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGATGTCCAGGGAAGTAGAATTACTGGCT
1 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
*
40342426 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTACTCCACTACTGC
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTAC-GC
40342491 TT
130 TT
* *
40342493 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTGGTT
1 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
* * *
40342558 TCAATGTACTCCACTATAACCACATGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTATTGC
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTA-CGC
40342623 TT
130 TT
* * *
40342625 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCTAGAGAAGTAGAATTACTGGCT
1 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
* *
40342690 TCAATGTACTCCACTGTAACCACATGGAGGTAAAATTCGCCATCTTCGATCTGCT
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
40342745 TCGCTGTCAA
Statistics
Matches: 612, Mismatches: 32, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
130 8 0.01
131 150 0.25
132 454 0.74
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (131 bp):
AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACGCT
T
Found at i:40342295 original size:350 final size:351
Alignment explanation
Indices: 40341670--40342354 Score: 1122
Period size: 350 Copynumber: 2.0 Consensus size: 351
40341660 AAGGAGATAT
* *
40341670 ATTACTAGCTTCAATGTACTCCATTGTAACCACAGGGAGGTAAAATCCGCCATCTTCAATTTGCT
1 ATTACTAGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCAATCTGCT
* * *
40341735 CCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTTTCCAGGGAATTA
66 CCACTACTGCTTAGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTA
40341800 GAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTG
131 GAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTG
*
40341865 CTCCACTACTGCTTAAGGAGATAAGATCTGAAATCTTCAATCTATTCCACTATTGTCCAGAAAAG
196 CTCCACTACTGCTTAAGGAGATAAGACCTGAAATCTTCAATCTATTCCACTATTGTCCAGAAAAG
* * * *
40341930 TAGAATTATTGGCTTCAATGTACTCCACTGTAACCACAGGGAGATAAGATCTGAAATCTTTAATC
261 TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGATAAAATCCGAAATCTTCAATC
40341995 TATTCCACTGTTGTCCAGAAAGTAGA
326 TATTCCACTGTTGTCCAGAAAGTAGA
* * *
40342021 ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGTT
1 ATTACTAGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCAATCTGCT
*
40342086 CCACTACTGCTTAGGGAGATAATACCTGAAATCTTCAATCTATTCCAC-GTTGTCCAGGGAAGTA
66 CCACTACTGCTTAGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTA
* * *
40342150 GAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATTTTCGATCTG
131 GAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTG
* * **
40342215 CTCCACTACTGCTTAGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGA-TGTCTAGGGAA
196 CTCCACTACTGCTTAAGGAGATAAGACCTGAAATCTTCAATCTATTCCACT-ATTGTCCAGAAAA
* ** *
40342279 GTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGAT
260 GTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGATAAAATCCGAAATCTTCAAT
40342344 CTATTCCACTG
325 CTATTCCACTG
40342355 CTGCTTAGGG
Statistics
Matches: 308, Mismatches: 25, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
350 201 0.65
351 107 0.35
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.29
Consensus pattern (351 bp):
ATTACTAGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCAATCTGCT
CCACTACTGCTTAGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTA
GAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTG
CTCCACTACTGCTTAAGGAGATAAGACCTGAAATCTTCAATCTATTCCACTATTGTCCAGAAAAG
TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGATAAAATCCGAAATCTTCAATC
TATTCCACTGTTGTCCAGAAAGTAGA
Found at i:40342541 original size:44 final size:44
Alignment explanation
Indices: 40342229--40342541 Score: 133
Period size: 44 Copynumber: 7.1 Consensus size: 44
40342219 ACTACTGCTT
* * *
40342229 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGATGTCT
1 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGCCC
* * * * * **
40342273 AGGGAAGTAGAATTA-CTG---GCTTCAATGTACTCCACTGTAACCAC
1 AGGG-AG-ATAA-GACCTGAAATCTTCAATCTATTCCACTGTTGCC-C
* * ** * * **
40342317 AGGGAGGTAAAATCC-GCCATCTTCGATCTATTCCACTGCTGCTT
1 AGGGAGATAAGA-CCTGAAATCTTCAATCTATTCCACTGTTGCCC
* *
40342361 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGATGTCC
1 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGCCC
* * * * * **
40342405 AGGGAAGTAGAATTA-CTG---GCTTCAATGTACTCCACTGTAACCAC
1 AGGG-AG-ATAA-GACCTGAAATCTTCAATCTATTCCACTGTTGCC-C
* * ** * * ** **
40342449 AGGGAGGTAAAATCC-GCCATCTTCGATCTACTCCACTACTGCTT
1 AGGGAGATAAGA-CCTGAAATCTTCAATCTATTCCACTGTTGCCC
40342493 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGCCC
1 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGCCC
40342537 AGGGA
1 AGGGA
40342542 AGTAGAATTA
Statistics
Matches: 187, Mismatches: 62, Indels: 40
0.65 0.21 0.14
Matches are distributed among these distances:
41 2 0.01
42 6 0.03
43 44 0.24
44 85 0.45
45 36 0.19
46 12 0.06
47 2 0.01
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (44 bp):
AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGCCC
Found at i:40342660 original size:44 final size:44
Alignment explanation
Indices: 40342467--40342661 Score: 112
Period size: 44 Copynumber: 4.4 Consensus size: 44
40342457 AAAATCCGCC
* * * *
40342467 ATCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGACCTGAA
1 ATCTTCAATCTACTCCACTATTGCTCAGGGAGATAAGATCTGAA
* * *
40342511 ATCTTCAATCTATTCCACTGTTGCCCAGGGA-AGT-AGAATTACTG--
1 ATCTTCAATCTACTCCACTATTGCTCAGGGAGA-TAAG-A-T-CTGAA
* * ** * * * * * **
40342555 GT-TTCAATGTACTCCACTATAACCACATGGAGGTAAAATCCGCC
1 ATCTTCAATCTACTCCACTAT-TGCTCAGGGAGATAAGATCTGAA
* * *
40342599 ATCTTCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGAA
1 ATCTTCAATCTACTCCACTATTGCTCAGGGAGATAAGATCTGAA
*
40342643 ATCTTCAATCTATTCCACT
1 ATCTTCAATCTACTCCACT
40342662 GTTGTCTAGA
Statistics
Matches: 106, Mismatches: 35, Indels: 20
0.66 0.22 0.12
Matches are distributed among these distances:
42 2 0.02
43 19 0.18
44 66 0.62
45 16 0.15
46 3 0.03
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (44 bp):
ATCTTCAATCTACTCCACTATTGCTCAGGGAGATAAGATCTGAA
Found at i:40344169 original size:14 final size:15
Alignment explanation
Indices: 40344146--40344178 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
40344136 GTTGATGCTT
*
40344146 TTCCAGATAAGG-CC
1 TTCCAAATAAGGTCC
40344160 TTCCAAATAAGGTCC
1 TTCCAAATAAGGTCC
40344175 TTCC
1 TTCC
40344179 TAGCTTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.27
Consensus pattern (15 bp):
TTCCAAATAAGGTCC
Found at i:40349265 original size:22 final size:21
Alignment explanation
Indices: 40349230--40349344 Score: 71
Period size: 19 Copynumber: 5.7 Consensus size: 21
40349220 AAAAGGTATC
* *
40349230 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
40349251 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
40349274 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
40349293 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* * *
40349312 TATATAT--TATATCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
40349331 TGCATATCATATCT
1 TACAAATCATATCT
40349345 AAGATTGCAT
Statistics
Matches: 79, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
17 2 0.03
19 45 0.57
21 7 0.09
22 15 0.19
23 10 0.13
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:40349273 original size:23 final size:22
Alignment explanation
Indices: 40349230--40349287 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
40349220 AAAAGGTATC
* *
40349230 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
40349251 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
40349274 TGCATATCATATCT
1 TACAAATCATATCT
40349288 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:40349290 original size:19 final size:19
Alignment explanation
Indices: 40349266--40349357 Score: 157
Period size: 19 Copynumber: 4.8 Consensus size: 19
40349256 AATCATATCT
40349266 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
40349285 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
** *
40349304 TCTAAGATTATATATTATA
1 TCTAAGATTGCATATCATA
40349323 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
40349342 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
40349358 CCTGAAGATT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 67 1.00
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:40351799 original size:4 final size:4
Alignment explanation
Indices: 40351782--40351827 Score: 56
Period size: 4 Copynumber: 10.8 Consensus size: 4
40351772 AGTTTAATGT
*
40351782 TTAA TTAAA CTTAA TTAAA TTAA TTAA TTAA TTAC TTAA TTAA TTA
1 TTAA TT-AA -TTAA TT-AA TTAA TTAA TTAA TTAA TTAA TTAA TTA
40351828 TCCTTATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
4 27 0.73
5 8 0.22
6 2 0.05
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (4 bp):
TTAA
Found at i:40352696 original size:16 final size:17
Alignment explanation
Indices: 40352675--40352709 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
40352665 TAGGGTTGAA
*
40352675 AAGAAA-GATTTAGAAG
1 AAGAAAGGATTGAGAAG
40352691 AAGAAAGGATTGAGAAG
1 AAGAAAGGATTGAGAAG
40352708 AA
1 AA
40352710 AGAACTGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.57, C:0.00, G:0.29, T:0.14
Consensus pattern (17 bp):
AAGAAAGGATTGAGAAG
Found at i:40361648 original size:19 final size:20
Alignment explanation
Indices: 40361610--40361650 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
40361600 TATTATACTT
40361610 TATTTCATTTTTCTTAAAAA
1 TATTTCATTTTTCTTAAAAA
*
40361630 TATTTC-TTTTTTTTCAAAAA
1 TATTTCATTTTTCTT-AAAAA
40361650 T
1 T
40361651 TCCAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.32, C:0.10, G:0.00, T:0.59
Consensus pattern (20 bp):
TATTTCATTTTTCTTAAAAA
Found at i:40372907 original size:17 final size:17
Alignment explanation
Indices: 40372885--40372918 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
40372875 TTGGGTTGGG
40372885 AGCTTAACTCAATTAAC
1 AGCTTAACTCAATTAAC
*
40372902 AGCTTAGCTCAATTAAC
1 AGCTTAACTCAATTAAC
40372919 CTTTACACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.24, G:0.09, T:0.29
Consensus pattern (17 bp):
AGCTTAACTCAATTAAC
Found at i:40373425 original size:103 final size:104
Alignment explanation
Indices: 40373199--40373888 Score: 721
Period size: 104 Copynumber: 6.7 Consensus size: 104
40373189 TAGGTCAAGT
* * * * * *
40373199 TATTTTGGAGTTGCGAGT-TTAACTCTGCTAACTCAAAGAGATATAGGTTGCGATATTAAATCAG
1 TATTTGGGAGTTGCGA-TCTTAAATCAGCTAACTCAGAGAGATATAGGTTGCGATCTTAAATCAA
* * * *
40373263 TTAACCTTTAAACATC-AGTAGGGAATGTAGGTCCGTGAGC
65 CTAACCTTTAAACATCAACT-GGGAACGTAGGTCCGCGAGC
* *
40373303 TATTTGGGAGTTGTGATCTTAAATCAGTTAACTCAGAGAGATATAGGTTGCGATCTTAAATCAAC
1 TATTTGGGAGTTGCGATCTTAAATCAGCTAACTCAGAGAGATATAGGTTGCGATCTTAAATCAAC
* * *
40373368 TAACC-TTAAACATCAACTGGGAATGTAGGTCTGCGAGT
66 TAACCTTTAAACATCAACTGGGAACGTAGGTCCGCGAGC
* * * * * * *
40373406 TATTTGGGAGTTGCAATCTTAAATCAACT-ATTTAGAGAGATATAGGTTGCAATCTTAAGTCAAA
1 TATTTGGGAGTTGCGATCTTAAATCAGCTAACTCAGAGAGATATAGGTTGCGATCTTAAATCAAC
* * * * *
40373470 TAACTTTTAAACATCAACTGAGAACATAGGTCTGCGAGT
66 TAACCTTTAAACATCAACTGGGAACGTAGGTCCGCGAGC
* * * *
40373509 TGTTTGGGAGTTGCGATCTTAAATCAACTAACTCAGAGAGATATAAGTTGCGATATTAAAT-AAG
1 TATTTGGGAGTTGCGATCTTAAATCAGCTAACTCAGAGAGATATAGGTTGCGATCTTAAATCAA-
* * * * **
40373573 CTAACCTTTAAACATCAGCTAGGAACATAGTTCCGTAAGC
65 CTAACCTTTAAACATCAACTGGGAACGTAGGTCCGCGAGC
* * * *
40373613 TATTTGGGAGTTGAGATCTTAATTCAGCTAACTCAGAGAGATTTAGGTTGCGATATTAAATCAAC
1 TATTTGGGAGTTGCGATCTTAAATCAGCTAACTCAGAGAGATATAGGTTGCGATCTTAAATCAAC
* *
40373678 TAACCTTTAAATATCATCTGGGAACGTAGGTCCGCGAGC
66 TAACCTTTAAACATCAACTGGGAACGTAGGTCCGCGAGC
* * * * * *
40373717 TGTTTAGGAGTTGCGATCTTAAAT-ATGTTAACTCAAATAGATTTA-GTTGCGATCTTAAATCAA
1 TATTTGGGAGTTGCGATCTTAAATCA-GCTAACTCAGAGAGATATAGGTTGCGATCTTAAATCAA
* ** * * **
40373780 CTAATCTTTAAACATCAGTTGGAAACGTAAGTTTGCGAGC
65 CTAACCTTTAAACATCAACTGGGAACGTAGGTCCGCGAGC
* * * * * *
40373820 TGTTTAGGAGTTGTGATCTTAAATCTG-TCAACTTAGAGAGATTTAGGTTGCGATCTTAAATCAA
1 TATTTGGGAGTTGCGATCTTAAATCAGCT-AACTCAGAGAGATATAGGTTGCGATCTTAAATCAA
40373884 CTAAC
65 CTAAC
40373889 TCGGAGAGAT
Statistics
Matches: 497, Mismatches: 79, Indels: 20
0.83 0.13 0.03
Matches are distributed among these distances:
102 35 0.07
103 198 0.40
104 262 0.53
105 2 0.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.32
Consensus pattern (104 bp):
TATTTGGGAGTTGCGATCTTAAATCAGCTAACTCAGAGAGATATAGGTTGCGATCTTAAATCAAC
TAACCTTTAAACATCAACTGGGAACGTAGGTCCGCGAGC
Found at i:40380212 original size:15 final size:16
Alignment explanation
Indices: 40380181--40380228 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
40380171 TACACTCAAT
*
40380181 TTTTCACATTCTTTTTC
1 TTTTCTCATT-TTTTTC
40380198 -TTTCTCATTTTTTTC
1 TTTTCTCATTTTTTTC
40380213 TTTTCTCACTTTTTTT
1 TTTTCTCA-TTTTTTT
40380229 TTCATTTTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 6 0.21
16 15 0.54
17 7 0.25
ACGTcount: A:0.08, C:0.21, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTCTCATTTTTTTC
Found at i:40380218 original size:20 final size:20
Alignment explanation
Indices: 40380193--40380275 Score: 62
Period size: 20 Copynumber: 4.0 Consensus size: 20
40380183 TTCACATTCT
40380193 TTTTCTTTCTCATTTTTTTC
1 TTTTCTTTCTCATTTTTTTC
** *
40380213 TTTTCTCACT-TTTTTTTTC
1 TTTTCTTTCTCATTTTTTTC
*
40380232 ATTTTCTTTCGTGA-TTTTTTC
1 -TTTTCTTTC-TCATTTTTTTC
* *
40380253 TTTCTTTTTTTCATTTTTCTTC
1 TTT-TCTTTCTCATTTTT-TTC
40380275 T
1 T
40380276 CTTTTGTGTT
Statistics
Matches: 48, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
19 8 0.17
20 20 0.42
21 16 0.33
22 4 0.08
ACGTcount: A:0.06, C:0.18, G:0.02, T:0.73
Consensus pattern (20 bp):
TTTTCTTTCTCATTTTTTTC
Found at i:40382371 original size:16 final size:16
Alignment explanation
Indices: 40382351--40382388 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
40382341 TTTTCTTTTT
40382351 ATTTTTTTAATCACG-
1 ATTTTTTTAATCACGA
*
40382366 ATTTTTTTAATTACGA
1 ATTTTTTTAATCACGA
40382382 ATTTTTT
1 ATTTTTT
40382389 ATTTTGAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.26, C:0.08, G:0.05, T:0.61
Consensus pattern (16 bp):
ATTTTTTTAATCACGA
Found at i:40384032 original size:20 final size:20
Alignment explanation
Indices: 40383972--40384033 Score: 52
Period size: 20 Copynumber: 3.0 Consensus size: 20
40383962 TACTAATTAG
* * *
40383972 AACATATTTAATAGACTTAA
1 AACATATTTAACACACATAA
* **
40383992 GACATATTAATAACATGCATAA
1 AACATATT--TAACACACATAA
40384014 AACATATTTAACACACATAA
1 AACATATTTAACACACATAA
40384034 TTAAATTTGT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
20 17 0.53
22 15 0.47
ACGTcount: A:0.52, C:0.15, G:0.05, T:0.29
Consensus pattern (20 bp):
AACATATTTAACACACATAA
Found at i:40392090 original size:12 final size:12
Alignment explanation
Indices: 40392073--40392099 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
40392063 TAATATTTCT
40392073 TTTAAGATATCA
1 TTTAAGATATCA
40392085 TTTAAGATATCA
1 TTTAAGATATCA
40392097 TTT
1 TTT
40392100 TTTTTCAAGT
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:0.37, C:0.07, G:0.07, T:0.48
Consensus pattern (12 bp):
TTTAAGATATCA
Found at i:40398609 original size:13 final size:13
Alignment explanation
Indices: 40398591--40398617 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40398581 CAAGAATCAG
40398591 ATCATAATTTAAC
1 ATCATAATTTAAC
40398604 ATCATAATTTAAC
1 ATCATAATTTAAC
40398617 A
1 A
40398618 ACTTCAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (13 bp):
ATCATAATTTAAC
Found at i:40399519 original size:21 final size:21
Alignment explanation
Indices: 40399463--40399519 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
40399453 TTTGGTTTAA
*
40399463 TAATTGAAT-TTTATATTTTTT
1 TAATTTAATATTTA-ATTTTTT
** *
40399484 TAATTTGGTACTTAATTTTTT
1 TAATTTAATATTTAATTTTTT
40399505 TAATTTAATATTTAA
1 TAATTTAATATTTAA
40399520 ATCTATCAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
21 25 0.89
22 3 0.11
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (21 bp):
TAATTTAATATTTAATTTTTT
Found at i:40401254 original size:11 final size:11
Alignment explanation
Indices: 40401240--40401287 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
40401230 ATATATAAGA
40401240 TAATAATAATT
1 TAATAATAATT
* *
40401251 TAATTATATTT
1 TAATAATAATT
* *
40401262 TAATAATTATA
1 TAATAATAATT
*
40401273 TAATATTAATT
1 TAATAATAATT
40401284 TAAT
1 TAAT
40401288 TATTATTTTT
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TAATAATAATT
Found at i:40401287 original size:19 final size:19
Alignment explanation
Indices: 40401239--40401290 Score: 60
Period size: 14 Copynumber: 3.0 Consensus size: 19
40401229 TATATATAAG
*
40401239 ATAATAATAATTTAATTAT
1 ATAATATTAATTTAATTAT
40401258 AT--T-TTAA--TAATTAT
1 ATAATATTAATTTAATTAT
40401272 ATAATATTAATTTAATTAT
1 ATAATATTAATTTAATTAT
40401291 TATTTTTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
14 9 0.33
16 4 0.15
17 5 0.19
19 9 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATAATATTAATTTAATTAT
Found at i:40414795 original size:15 final size:15
Alignment explanation
Indices: 40414771--40414800 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40414761 TTCCATTTCA
*
40414771 CCACCTAAATCACCT
1 CCACCAAAATCACCT
40414786 CCACCAAAATCACCT
1 CCACCAAAATCACCT
40414801 TTTTTTTCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.47, G:0.00, T:0.17
Consensus pattern (15 bp):
CCACCAAAATCACCT
Found at i:40415808 original size:46 final size:46
Alignment explanation
Indices: 40415741--40415837 Score: 140
Period size: 46 Copynumber: 2.1 Consensus size: 46
40415731 TTCTGTTATT
*
40415741 AATCTTATTCGCATGTTAAGTATGCCACTATATTAATTCGTAATGA
1 AATCTGATTCGCATGTTAAGTATGCCACTATATTAATTCGTAATGA
* * * *
40415787 AATCTGATTCTCATGTTAAGTATGTCACTGTGTTAATTCGTAATGA
1 AATCTGATTCGCATGTTAAGTATGCCACTATATTAATTCGTAATGA
*
40415833 GATCT
1 AATCT
40415838 TCGCATGTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.40
Consensus pattern (46 bp):
AATCTGATTCGCATGTTAAGTATGCCACTATATTAATTCGTAATGA
Found at i:40416069 original size:49 final size:49
Alignment explanation
Indices: 40415989--40416110 Score: 154
Period size: 49 Copynumber: 2.5 Consensus size: 49
40415979 ATATTTGCAA
* * * * * *
40415989 ATCTGGTGGCTTGACCATAATATTCTGTATCTTGCAGTTTGTCTGCATT
1 ATCTGATGGCTTGACCACAATATTCTATATCTGGCAGCTTGTCTGCACT
*
40416038 ATTTGATGGCTTGACCACAATATTCTATATCTGGCAGCTTGTCTGCACT
1 ATCTGATGGCTTGACCACAATATTCTATATCTGGCAGCTTGTCTGCACT
* * *
40416087 ATCTGGTGGCTTAACCACATTATT
1 ATCTGATGGCTTGACCACAATATT
40416111 GGTGTGATAT
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
49 62 1.00
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.39
Consensus pattern (49 bp):
ATCTGATGGCTTGACCACAATATTCTATATCTGGCAGCTTGTCTGCACT
Found at i:40419888 original size:30 final size:31
Alignment explanation
Indices: 40419852--40419911 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
40419842 AAACCTTTTA
*
40419852 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
40419882 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
40419912 TCCCCCTCCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:40425905 original size:9 final size:8
Alignment explanation
Indices: 40425888--40425913 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
40425878 TTTAATTCTG
40425888 TTATTTTT
1 TTATTTTT
40425896 TTATTTTT
1 TTATTTTT
40425904 TTATTTTT
1 TTATTTTT
40425912 TT
1 TT
40425914 CCAGTAACGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTATTTTT
Found at i:40432577 original size:10 final size:10
Alignment explanation
Indices: 40432562--40432586 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
40432552 TAAAGTGATT
40432562 TTGATAGATA
1 TTGATAGATA
40432572 TTGATAGATA
1 TTGATAGATA
40432582 TTGAT
1 TTGAT
40432587 TTTAGGACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.20, T:0.44
Consensus pattern (10 bp):
TTGATAGATA
Found at i:40433288 original size:21 final size:21
Alignment explanation
Indices: 40433197--40433296 Score: 76
Period size: 21 Copynumber: 4.8 Consensus size: 21
40433187 CGAGCTTCTA
* * * *
40433197 TTCAACTCATATGAGTTTTCG
1 TTCAACCCTTATGGGTTTCCG
* *
40433218 TTCAACCCTAATGGGTTTTCG
1 TTCAACCCTTATGGGTTTCCG
* * * * * *
40433239 TTCAGCTCTTTTGAG-CTCTG
1 TTCAACCCTTATGGGTTTCCG
*
40433259 TTTAACCCTTATGGGTTTCCG
1 TTCAACCCTTATGGGTTTCCG
40433280 TTCAACCCTTATGGGTT
1 TTCAACCCTTATGGGTT
40433297 CCTGTTTAGC
Statistics
Matches: 58, Mismatches: 20, Indels: 2
0.73 0.25 0.03
Matches are distributed among these distances:
20 12 0.21
21 46 0.79
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.42
Consensus pattern (21 bp):
TTCAACCCTTATGGGTTTCCG
Found at i:40433312 original size:21 final size:22
Alignment explanation
Indices: 40433256--40433304 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
40433246 CTTTTGAGCT
40433256 CTGTTTAACCCTTATGGGTTTC
1 CTGTTTAACCCTTATGGGTTTC
*
40433278 C-GTTCAACCCTTATGGG-TTC
1 CTGTTTAACCCTTATGGGTTTC
40433298 CTGTTTA
1 CTGTTTA
40433305 GCACTTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 4 0.17
21 19 0.79
22 1 0.04
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (22 bp):
CTGTTTAACCCTTATGGGTTTC
Found at i:40437364 original size:21 final size:23
Alignment explanation
Indices: 40437319--40437365 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
40437309 TCACCTGCAA
* *
40437319 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
40437342 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
40437363 TAA
1 TAA
40437366 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:40442708 original size:16 final size:17
Alignment explanation
Indices: 40442687--40442730 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
40442677 TAGCTTTTTA
40442687 TTTTTTTTTCACG-AAT
1 TTTTTTTTTCACGAAAT
40442703 TTTTTTTTTCACGAAAT
1 TTTTTTTTTCACGAAAT
40442720 TTTTTTTTTCA
1 TTTTTTTTTCA
40442731 ACTTGATATC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 13 0.48
17 14 0.52
ACGTcount: A:0.18, C:0.11, G:0.05, T:0.66
Consensus pattern (17 bp):
TTTTTTTTTCACGAAAT
Found at i:40442785 original size:11 final size:11
Alignment explanation
Indices: 40442769--40442801 Score: 57
Period size: 12 Copynumber: 2.9 Consensus size: 11
40442759 AGGAAACCAA
40442769 TTTTTTTGAAT
1 TTTTTTTGAAT
40442780 TTTTTTTCGAAT
1 TTTTTTT-GAAT
40442792 TTTTTTTGAA
1 TTTTTTTGAA
40442802 GAAACTACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.18, C:0.03, G:0.09, T:0.70
Consensus pattern (11 bp):
TTTTTTTGAAT
Found at i:40443838 original size:21 final size:23
Alignment explanation
Indices: 40443793--40443839 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
40443783 TCACCTGCAA
* *
40443793 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
40443816 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
40443837 TAA
1 TAA
40443840 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:40446273 original size:14 final size:14
Alignment explanation
Indices: 40446254--40446292 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
40446244 TGTTACTGTG
40446254 TTTTAGTTTTAGAC
1 TTTTAGTTTTAGAC
*
40446268 TTTTAGTTTTAGAT
1 TTTTAGTTTTAGAC
*
40446282 TTTTATTTTTA
1 TTTTAGTTTTA
40446293 TTTATTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.21, C:0.03, G:0.10, T:0.67
Consensus pattern (14 bp):
TTTTAGTTTTAGAC
Found at i:40455529 original size:29 final size:29
Alignment explanation
Indices: 40455496--40455552 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
40455486 TTACTTTGTC
*
40455496 ATTTATGTTTGAAATATTACGTTCTAGTT
1 ATTTATGTTTCAAATATTACGTTCTAGTT
* *
40455525 ATTTATGTTTCAAATGTTACGTTTTAGT
1 ATTTATGTTTCAAATATTACGTTCTAGT
40455553 CACATATGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.26, C:0.07, G:0.14, T:0.53
Consensus pattern (29 bp):
ATTTATGTTTCAAATATTACGTTCTAGTT
Found at i:40455560 original size:29 final size:29
Alignment explanation
Indices: 40455499--40455562 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
40455489 CTTTGTCATT
* * **
40455499 TATGTTTGAAATATTACGTTCTAGTTATT
1 TATGTTTCAAATATTACGTTCTAGTCACA
* *
40455528 TATGTTTCAAATGTTACGTTTTAGTCACA
1 TATGTTTCAAATATTACGTTCTAGTCACA
40455557 TATGTT
1 TATGTT
40455563 ATCGTGTTGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.27, C:0.09, G:0.14, T:0.50
Consensus pattern (29 bp):
TATGTTTCAAATATTACGTTCTAGTCACA
Found at i:40465119 original size:24 final size:24
Alignment explanation
Indices: 40465075--40465125 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
40465065 TACCAATTGC
*
40465075 ATTAATAAAATATTAAATTTATTA
1 ATTAATAAAATATTAAATTTAATA
* *
40465099 ATTAATAAAA-ATTTTATTTTAATA
1 ATTAATAAAATA-TTAAATTTAATA
40465123 ATT
1 ATT
40465126 TTTATTCATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 1 0.04
24 22 0.96
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
ATTAATAAAATATTAAATTTAATA
Found at i:40465991 original size:14 final size:14
Alignment explanation
Indices: 40465972--40466003 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
40465962 ATGTGGAATG
40465972 ATTTTAGTTTTTGT
1 ATTTTAGTTTTTGT
40465986 ATTTTAGTTTTTGT
1 ATTTTAGTTTTTGT
40466000 ATTT
1 ATTT
40466004 CATTTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.12, T:0.72
Consensus pattern (14 bp):
ATTTTAGTTTTTGT
Found at i:40466010 original size:14 final size:14
Alignment explanation
Indices: 40465972--40466010 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
40465962 ATGTGGAATG
*
40465972 ATTTTAGTTTTTGT
1 ATTTCAGTTTTTGT
*
40465986 ATTTTAGTTTTTGT
1 ATTTCAGTTTTTGT
40466000 ATTTCA-TTTTT
1 ATTTCAGTTTTT
40466011 ATTTGTTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 5 0.21
14 19 0.79
ACGTcount: A:0.15, C:0.03, G:0.10, T:0.72
Consensus pattern (14 bp):
ATTTCAGTTTTTGT
Found at i:40466084 original size:4 final size:4
Alignment explanation
Indices: 40466075--40466103 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
40466065 AATTTGTTAC
40466075 ATTT ATTT ATTT ATTT ATTT ATTT ATTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT A
40466104 AATCTAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:40466621 original size:88 final size:89
Alignment explanation
Indices: 40466516--40466690 Score: 262
Period size: 88 Copynumber: 2.0 Consensus size: 89
40466506 CCAAACCCCA
* * * *
40466516 AACCACTAACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAA-CCTAA
1 AACCACTAACCCCTAAACATCATTTAATATATAAATTAAAAAACAATAATCAATCTAAACCCTAA
* *
40466580 ACCCTAACCCGACCCCGAATCCTT
66 ACCCTAACCCGACACCAAATCCTT
* * *
40466604 AACCTCTAACCCTTAAACATCATTTAATATATAAATTAAAACACAATAATCAATCTAAACCCTAA
1 AACCACTAACCCCTAAACATCATTTAATATATAAATTAAAAAACAATAATCAATCTAAACCCTAA
40466669 ACCCTAACCCGACACCAAATCC
66 ACCCTAACCCGACACCAAATCC
40466691 ATAAACCCTA
Statistics
Matches: 77, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
88 52 0.68
89 25 0.32
ACGTcount: A:0.45, C:0.30, G:0.02, T:0.24
Consensus pattern (89 bp):
AACCACTAACCCCTAAACATCATTTAATATATAAATTAAAAAACAATAATCAATCTAAACCCTAA
ACCCTAACCCGACACCAAATCCTT
Found at i:40466781 original size:14 final size:15
Alignment explanation
Indices: 40466764--40466796 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
40466754 CTTAAATCAG
40466764 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
40466778 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
40466793 AATC
1 AATC
40466797 TATAAGCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:40467487 original size:30 final size:30
Alignment explanation
Indices: 40467453--40467515 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
40467443 ACTTAACAAG
* *
40467453 CAAATGCCTCTAAAATAATAACAATATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
*
40467483 CAAATACCTTTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
40467513 CAA
1 CAA
40467516 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.57, C:0.16, G:0.02, T:0.25
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTAA
Found at i:40467570 original size:22 final size:22
Alignment explanation
Indices: 40467545--40467587 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
40467535 TATCCAAACA
40467545 ATAAAAATAAAATAGTAGCAAC
1 ATAAAAATAAAATAGTAGCAAC
* * *
40467567 ATAATAGTAAAATGGTAGCAA
1 ATAAAAATAAAATAGTAGCAA
40467588 AATAGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.07, G:0.14, T:0.21
Consensus pattern (22 bp):
ATAAAAATAAAATAGTAGCAAC
Found at i:40467952 original size:58 final size:60
Alignment explanation
Indices: 40467881--40467997 Score: 175
Period size: 61 Copynumber: 2.0 Consensus size: 60
40467871 GTGATAGAAA
* *
40467881 TTCTAGTGGTTAATAAACAAG-TTGTTTTA-TTTTTCTATGCAATATTAGCCGTGGGAGT
1 TTCTAGTAGTTAATAAACAAGTTTGTTTTATTTTTTCTATACAATATTAGCCGTGGGAGT
* *
40467939 TTCTAGTAGTTAATAAACAAGTTTGTTTTATTTTTTTTTATACAATATTAGCCTTGGGA
1 TTCTAGTAGTTAATAAACAAGTTTGTTTTA-TTTTTTCTATACAATATTAGCCGTGGGA
40467998 CTAGGGAATG
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
58 20 0.38
59 8 0.15
61 24 0.46
ACGTcount: A:0.27, C:0.09, G:0.17, T:0.46
Consensus pattern (60 bp):
TTCTAGTAGTTAATAAACAAGTTTGTTTTATTTTTTCTATACAATATTAGCCGTGGGAGT
Found at i:40468691 original size:23 final size:24
Alignment explanation
Indices: 40468641--40468691 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
40468631 CTAAAATGTG
* *
40468641 ATGTGATGTGTATAAAATGTGCTA
1 ATGTGATGTATATAAAATGTGATA
* *
40468665 ATGTGAT-TATATGAAATGTGATT
1 ATGTGATGTATATAAAATGTGATA
40468688 ATGT
1 ATGT
40468692 CAGAATATGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.33, C:0.02, G:0.24, T:0.41
Consensus pattern (24 bp):
ATGTGATGTATATAAAATGTGATA
Found at i:40470450 original size:19 final size:19
Alignment explanation
Indices: 40470426--40470463 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
40470416 CATGTATTTG
40470426 TGTGGTATGAATGGTGGTT
1 TGTGGTATGAATGGTGGTT
* *
40470445 TGTGGTGTGATTGGTGGTT
1 TGTGGTATGAATGGTGGTT
40470464 GGTAAGCAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.11, C:0.00, G:0.45, T:0.45
Consensus pattern (19 bp):
TGTGGTATGAATGGTGGTT
Found at i:40494103 original size:60 final size:60
Alignment explanation
Indices: 40494029--40494167 Score: 190
Period size: 60 Copynumber: 2.3 Consensus size: 60
40494019 TTTGAATATT
* * *
40494029 AAATTGATAGAATTTGTAAATGTGAAGTGTTAAATTTATT-AATTATTCAGAATTAGGATC
1 AAATTGATAAAATTTGTAAATGTGAAG-ATTAAATTTATTAAATTATTCAAAATTAGGATC
* * *
40494089 AAATTGATAAAATTTATGAATGTGAAGATTAAATTTATTAAATTATTTAAAATTAGGATC
1 AAATTGATAAAATTTGTAAATGTGAAGATTAAATTTATTAAATTATTCAAAATTAGGATC
* *
40494149 AAATTAATAAAATATGTAA
1 AAATTGATAAAATTTGTAA
40494168 GTATTGAGGG
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
59 11 0.16
60 57 0.84
ACGTcount: A:0.46, C:0.02, G:0.13, T:0.39
Consensus pattern (60 bp):
AAATTGATAAAATTTGTAAATGTGAAGATTAAATTTATTAAATTATTCAAAATTAGGATC
Found at i:40494153 original size:30 final size:30
Alignment explanation
Indices: 40494060--40494153 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
40494050 GTGAAGTGTT
*
40494060 AAATTTATT-AATTATTCAGAATTAGGATC
1 AAATTTATTAAATTATTTAGAATTAGGATC
* * *
40494089 AAATTGA-TAAA--ATTTATGAATGTGAAGATT
1 AAATTTATTAAATTATTTA-GAAT-T-AGGATC
*
40494119 AAATTTATTAAATTATTTAAAATTAGGATC
1 AAATTTATTAAATTATTTAGAATTAGGATC
40494149 AAATT
1 AAATT
40494154 AATAAAATAT
Statistics
Matches: 50, Mismatches: 8, Indels: 13
0.70 0.11 0.18
Matches are distributed among these distances:
27 4 0.08
28 5 0.10
29 9 0.18
30 19 0.38
31 5 0.10
32 3 0.06
33 5 0.10
ACGTcount: A:0.46, C:0.03, G:0.11, T:0.40
Consensus pattern (30 bp):
AAATTTATTAAATTATTTAGAATTAGGATC
Found at i:40504412 original size:17 final size:16
Alignment explanation
Indices: 40504383--40504429 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
40504373 AAACAAGTGG
40504383 AAGTGAAGA-AAGTGACC
1 AAGTGAA-ATAAGTG-CC
*
40504400 AAGTGAAATAAGTGCT
1 AAGTGAAATAAGTGCC
*
40504416 AAGAGAAATAAGTG
1 AAGTGAAATAAGTG
40504430 GTAAGCAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 15 0.56
17 12 0.44
ACGTcount: A:0.49, C:0.06, G:0.28, T:0.17
Consensus pattern (16 bp):
AAGTGAAATAAGTGCC
Found at i:40504425 original size:16 final size:16
Alignment explanation
Indices: 40504404--40504434 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40504394 GTGACCAAGT
40504404 GAAATAAGTGCTAAGA
1 GAAATAAGTGCTAAGA
*
40504420 GAAATAAGTGGTAAG
1 GAAATAAGTGCTAAG
40504435 CAAAGTAAGT
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:0.48, C:0.03, G:0.29, T:0.19
Consensus pattern (16 bp):
GAAATAAGTGCTAAGA
Found at i:40518623 original size:25 final size:25
Alignment explanation
Indices: 40518574--40518745 Score: 177
Period size: 25 Copynumber: 6.9 Consensus size: 25
40518564 GAACACACCA
* **
40518574 TAGCTCTCACGAGCTTCTTGATATT
1 TAGCTCTCATGAGCTTCCCGATATT
* * *
40518599 TAGCACTCACGAGCTTCCCGTTATT
1 TAGCTCTCATGAGCTTCCCGATATT
* *
40518624 TAGCTCTTATGAGCATCCCGATATT
1 TAGCTCTCATGAGCTTCCCGATATT
* * *
40518649 TGGCTCTCACGAGCTTTCC-ATTATT
1 TAGCTCTCATGAGCTTCCCGA-TATT
*
40518674 TAGCTCTTATGAGCATT-CCGATATT
1 TAGCTCTCATGAGC-TTCCCGATATT
* *
40518699 TGGCTTTCATGAGCTTCCCGATATT
1 TAGCTCTCATGAGCTTCCCGATATT
*
40518724 TGGCTCTCATGAGCTTCCCGAT
1 TAGCTCTCATGAGCTTCCCGAT
40518746 TAACGGCTCT
Statistics
Matches: 122, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
24 3 0.02
25 116 0.95
26 3 0.02
ACGTcount: A:0.19, C:0.26, G:0.17, T:0.37
Consensus pattern (25 bp):
TAGCTCTCATGAGCTTCCCGATATT
Found at i:40518658 original size:50 final size:50
Alignment explanation
Indices: 40518593--40518745 Score: 207
Period size: 50 Copynumber: 3.1 Consensus size: 50
40518583 CGAGCTTCTT
* *
40518593 GATATTTAGCACTCACGAGCTTCCCGTTATTTAGCTCTTATGAGCATCCC
1 GATATTTGGCTCTCACGAGCTTCCCGTTATTTAGCTCTTATGAGCATCCC
* * *
40518643 GATATTTGGCTCTCACGAGCTTTCCATTATTTAGCTCTTATGAGCATTCC
1 GATATTTGGCTCTCACGAGCTTCCCGTTATTTAGCTCTTATGAGCATCCC
* * * * * *
40518693 GATATTTGGCTTTCATGAGCTTCCCGATATTTGGCTCTCATGAGCTTCCC
1 GATATTTGGCTCTCACGAGCTTCCCGTTATTTAGCTCTTATGAGCATCCC
40518743 GAT
1 GAT
40518746 TAACGGCTCT
Statistics
Matches: 89, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 89 1.00
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.37
Consensus pattern (50 bp):
GATATTTGGCTCTCACGAGCTTCCCGTTATTTAGCTCTTATGAGCATCCC
Found at i:40518699 original size:75 final size:75
Alignment explanation
Indices: 40518576--40518740 Score: 201
Period size: 75 Copynumber: 2.2 Consensus size: 75
40518566 ACACACCATA
** *
40518576 GCTCTCACGAGCTTCTTGATATTTAGCACTCACGAGCTTCCCGTTATTTAGCTCTT-ATGAGCAT
1 GCTCTCACGAGCTTCTCCATATTTAGCACTCACGAGCTTCCCGATATTTAGCT-TTCATGAGCAT
40518640 CCCGATATTTG
65 CCCGATATTTG
* * * * *
40518651 GCTCTCACGAGCTT-TCCATTATTTAGCTCTTATGAGCATT-CCGATATTTGGCTTTCATGAGCT
1 GCTCTCACGAGCTTCTCCA-TATTTAGCACTCACGAGC-TTCCCGATATTTAGCTTTCATGAGCA
40518714 TCCCGATATTTG
64 TCCCGATATTTG
*
40518726 GCTCTCATGAGCTTC
1 GCTCTCACGAGCTTC
40518741 CCGATTAACG
Statistics
Matches: 77, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
74 4 0.05
75 71 0.92
76 2 0.03
ACGTcount: A:0.19, C:0.26, G:0.18, T:0.38
Consensus pattern (75 bp):
GCTCTCACGAGCTTCTCCATATTTAGCACTCACGAGCTTCCCGATATTTAGCTTTCATGAGCATC
CCGATATTTG
Found at i:40518753 original size:25 final size:25
Alignment explanation
Indices: 40518626--40518829 Score: 85
Period size: 25 Copynumber: 8.2 Consensus size: 25
40518616 CCGTTATTTA
* * **
40518626 GCTCTTATGAGCATCCCGATATTTG
1 GCTCTCATGAGCTTCCCGATATACG
* * ***
40518651 GCTCTCACGAGCTTTCC-ATTATTTA
1 GCTCTCATGAGCTTCCCGA-TATACG
* **
40518676 GCTCTTATGAGCATT-CCGATATTTG
1 GCTCTCATGAGC-TTCCCGATATACG
* **
40518701 GCTTTCATGAGCTTCCCGATATTTG
1 GCTCTCATGAGCTTCCCGATATACG
40518726 GCTCTCATGAGCTTCCCGAT-TAACG
1 GCTCTCATGAGCTTCCCGATAT-ACG
** ** *
40518751 GCTCTTTTGAGCTTCTAGATA-ATTG
1 GCTCTCATGAGCTTCCCGATATA-CG
* * *
40518776 GCTCGT-ATAAGCTTCCCGTTATACA
1 GCTC-TCATGAGCTTCCCGATATACG
* * * *
40518801 ACTCACATGAGCTTCCCGTTATATG
1 GCTCTCATGAGCTTCCCGATATACG
40518826 GCTC
1 GCTC
40518830 GGAAGAGCTT
Statistics
Matches: 138, Mismatches: 31, Indels: 20
0.73 0.16 0.11
Matches are distributed among these distances:
24 5 0.04
25 128 0.93
26 5 0.04
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (25 bp):
GCTCTCATGAGCTTCCCGATATACG
Found at i:40518777 original size:75 final size:75
Alignment explanation
Indices: 40518632--40518778 Score: 181
Period size: 75 Copynumber: 2.0 Consensus size: 75
40518622 TTTAGCTCTT
* ** *
40518632 ATGAGCATCCCGATATTTGGCTCTCACGAGCTTTCCATTATTTAGCTCTTATGAGCATTCCGATA
1 ATGAGCATCCCGATATTTGGCTCTCACGAGCTTCCCATTATACAGCTCTTATGAGCATTCAGATA
*
40518697 TTTGGCTTTC
66 ATTGGCTTTC
* * * *
40518707 ATGAGCTTCCCGATATTTGGCTCTCATGAGCTTCCCGATTA-ACGGCTCTTTTGAGC-TTCTAGA
1 ATGAGCATCCCGATATTTGGCTCTCACGAGCTTCCC-ATTATACAGCTCTTATGAGCATTC-AGA
40518770 TAATTGGCT
64 TAATTGGCT
40518779 CGTATAAGCT
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
74 3 0.05
75 54 0.89
76 4 0.07
ACGTcount: A:0.20, C:0.24, G:0.19, T:0.37
Consensus pattern (75 bp):
ATGAGCATCCCGATATTTGGCTCTCACGAGCTTCCCATTATACAGCTCTTATGAGCATTCAGATA
ATTGGCTTTC
Found at i:40524886 original size:50 final size:50
Alignment explanation
Indices: 40524763--40524899 Score: 177
Period size: 50 Copynumber: 2.7 Consensus size: 50
40524753 ACATACCATA
* * **
40524763 GCTCTCACGAGCTTTCCGTTATTTAGAGCTTATGAGCATCCCGATATTTG
1 GCTCTCACGAGCTTCCCGATATTTAGCTCTTATGAGCATCCCGATATTTG
*
40524813 GCTCTCACAAGCTTCCC-ATTATTTAGCTCTTATGAGCATCCCGATATTTG
1 GCTCTCACGAGCTTCCCGA-TATTTAGCTCTTATGAGCATCCCGATATTTG
* * * *
40524863 GCTTTCATGAGCTTCCCGATATTTGGCTCTCATGAGC
1 GCTCTCACGAGCTTCCCGATATTTAGCTCTTATGAGC
40524900 TTCTCGATTA
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
50 74 0.99
51 1 0.01
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (50 bp):
GCTCTCACGAGCTTCCCGATATTTAGCTCTTATGAGCATCCCGATATTTG
Found at i:40524900 original size:25 final size:25
Alignment explanation
Indices: 40524763--40524907 Score: 143
Period size: 25 Copynumber: 5.8 Consensus size: 25
40524753 ACATACCATA
* * *
40524763 GCTCTCACGAGCTTTCCGTTATTTAG
1 GCTCTCATGAGCTTCCCGATATTT-G
*
40524789 AGCT-T-ATGAGCATCCCGATATTTG
1 -GCTCTCATGAGCTTCCCGATATTTG
** *
40524813 GCTCTCACAAGCTTCCC-ATTATTTA
1 GCTCTCATGAGCTTCCCGA-TATTTG
* *
40524838 GCTCTTATGAGCATCCCGATATTTG
1 GCTCTCATGAGCTTCCCGATATTTG
*
40524863 GCTTTCATGAGCTTCCCGATATTTG
1 GCTCTCATGAGCTTCCCGATATTTG
*
40524888 GCTCTCATGAGCTTCTCGAT
1 GCTCTCATGAGCTTCCCGAT
40524908 TAACGGCTCT
Statistics
Matches: 96, Mismatches: 18, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
23 3 0.03
24 3 0.03
25 85 0.89
26 2 0.02
27 3 0.03
ACGTcount: A:0.19, C:0.26, G:0.18, T:0.37
Consensus pattern (25 bp):
GCTCTCATGAGCTTCCCGATATTTG
Found at i:40524917 original size:75 final size:75
Alignment explanation
Indices: 40524794--40524933 Score: 174
Period size: 75 Copynumber: 1.9 Consensus size: 75
40524784 TTTAGAGCTT
** *
40524794 ATGAGCATCCCGATATTTGGCTCTCACAAGCTTCCCATTATTTAGCTCTTATGAGCATCCCGATA
1 ATGAGCATCCCGATATTTGGCTCTCACAAGCTTCCCATTATACAGCTCTTATGAGCATCCAGATA
40524859 TTTGGCTTTC
66 TTTGGCTTTC
* ** * * * *
40524869 ATGAGCTTCCCGATATTTGGCTCTCATGAGCTTCTCGATTA-ACGGCTCTTTTGAGCTTCCAGAT
1 ATGAGCATCCCGATATTTGGCTCTCACAAGCTTC-CCATTATACAGCTCTTATGAGCATCCAGAT
40524933 A
65 A
40524934 ATTGACTCGT
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
75 49 0.91
76 5 0.09
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.36
Consensus pattern (75 bp):
ATGAGCATCCCGATATTTGGCTCTCACAAGCTTCCCATTATACAGCTCTTATGAGCATCCAGATA
TTTGGCTTTC
Found at i:40525024 original size:25 final size:25
Alignment explanation
Indices: 40524939--40525024 Score: 79
Period size: 25 Copynumber: 3.4 Consensus size: 25
40524929 AGATAATTGA
* *
40524939 CTCGTATAAGCTTCCTGTTATACA-A
1 CTCGTATGAGCTTCCTGTT-TACATG
*
40524964 CTCAG-ATGAGCTTCCTG-TTATATGG
1 CTC-GTATGAGCTTCCTGTTTACAT-G
* *
40524989 CTCGGAAGAGCTTCCTGTTTACATG
1 CTCGTATGAGCTTCCTGTTTACATG
40525014 CTCGTATGAGC
1 CTCGTATGAGC
40525025 ATACATGTAC
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
23 3 0.06
24 2 0.04
25 38 0.78
26 6 0.12
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (25 bp):
CTCGTATGAGCTTCCTGTTTACATG
Found at i:40530015 original size:9 final size:9
Alignment explanation
Indices: 40530001--40530033 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
40529991 TAAGTATAAA
40530001 AATTAACCG
1 AATTAACCG
*
40530010 AATTAACCA
1 AATTAACCG
40530019 AATTAACCG
1 AATTAACCG
40530028 AATTAA
1 AATTAA
40530034 AGCATTGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.52, C:0.18, G:0.06, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:40534060 original size:20 final size:20
Alignment explanation
Indices: 40534035--40534080 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
40534025 CTATGTCTAT
40534035 GTTTTAGTTTTAGACTTTTA
1 GTTTTAGTTTTAGACTTTTA
*
40534055 GTTTTAGTTTTAGATTTTTA
1 GTTTTAGTTTTAGACTTTTA
*
40534075 TTTTTA
1 GTTTTA
40534081 TTTATTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.02, G:0.13, T:0.65
Consensus pattern (20 bp):
GTTTTAGTTTTAGACTTTTA
Found at i:40536752 original size:6 final size:6
Alignment explanation
Indices: 40536741--40536770 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
40536731 GTTATTCATG
40536741 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
40536771 CAAAGCCTAT
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):
AAAAAT
Found at i:40539755 original size:17 final size:17
Alignment explanation
Indices: 40539733--40539765 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40539723 AGGCGTTGCC
40539733 TCATCA-CATCACACAAA
1 TCATCATCATCA-ACAAA
40539750 TCATCATCATCAACAA
1 TCATCATCATCAACAA
40539766 GGGTAACAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.21
Consensus pattern (17 bp):
TCATCATCATCAACAAA
Found at i:40540249 original size:40 final size:42
Alignment explanation
Indices: 40540170--40540260 Score: 152
Period size: 40 Copynumber: 2.2 Consensus size: 42
40540160 GCATGATGTA
*
40540170 CACT-CATGAAATCAACCTAGAAATTTAAAGCAAACAGCCTT
1 CACTGCATGAAATCAACCTAGAAATTTAAAGCAAAAAGCCTT
40540211 CACTGCAT-AAATCAACCTAGAAA-TTAAAGCAAAAAGCCTT
1 CACTGCATGAAATCAACCTAGAAATTTAAAGCAAAAAGCCTT
40540251 CACTGCATGA
1 CACTGCATGA
40540261 TTGATATTCA
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
40 24 0.51
41 20 0.43
42 3 0.06
ACGTcount: A:0.44, C:0.24, G:0.11, T:0.21
Consensus pattern (42 bp):
CACTGCATGAAATCAACCTAGAAATTTAAAGCAAAAAGCCTT
Found at i:40541482 original size:95 final size:93
Alignment explanation
Indices: 40541294--40541616 Score: 447
Period size: 95 Copynumber: 3.5 Consensus size: 93
40541284 GTTTTTAGAT
* * * * * *
40541294 TTTATGGTTTTAAGGAAAAAT-AATAAATAAGGGTTTA-GGTTTCTTAATTCAATTAATTATAAA
1 TTTATGGTTTTAAGAAAAAATCAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAA
40541357 TTTTAAAAAATTAGATTA-GGTTTAGTG
66 TTTTAAAAAATTAGATTAGGGTTTAGTG
*
40541384 TTTATGGTTTTAAGAAAAAATCAAATAAATTAGTGTTTAGGGTTACTTGAGTAAATTAATTATAA
1 TTTATGGTTTTAAGAAAAAATC-AATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAA
*
40541449 ATTTTTAAAAAATTAGATTAGGGTTTAGGG
65 A-TTTTAAAAAATTAGATTAGGGTTTAGTG
* *
40541479 TTTA-GTTTTTTAAGAAAAAATCAAATAAATTAAGGTTTAGGGTTACTTGAGTAAATTAATTATA
1 TTTATG-GTTTTAAGAAAAAATC-AATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATA
* *
40541543 AATTTTAAAAAAATAGATTAGGGTTTTAGTA
64 AATTTTAAAAAATTAGATTAGGG-TTTAGTG
* *
40541574 TTTAGGGTTTTAAGAAAAAATCAATAAATTAGGGTTTGGGGTT
1 TTTATGGTTTTAAGAAAAAATCAATAAATTAGGGTTTAGGGTT
40541617 TAGGGTTAAT
Statistics
Matches: 208, Mismatches: 17, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
90 20 0.10
92 14 0.07
93 22 0.11
94 58 0.28
95 93 0.45
96 1 0.00
ACGTcount: A:0.40, C:0.02, G:0.17, T:0.40
Consensus pattern (93 bp):
TTTATGGTTTTAAGAAAAAATCAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAA
TTTTAAAAAATTAGATTAGGGTTTAGTG
Found at i:40541932 original size:127 final size:126
Alignment explanation
Indices: 40541648--40541939 Score: 405
Period size: 127 Copynumber: 2.3 Consensus size: 126
40541638 TTAATTTAAA
* *
40541648 AAGCTCCCACGTGGACGCTATTTTACTACAGTA--TTCCTAAAAAATAATTTTGAGAAGACGTTT
1 AAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTTCCTAAAAAATAATTTTGAGAAGACGTTT
* * * *
40541711 CTGAGCAAATAGTGTCAAAAACGTTTTAAGCAGGATGCATTGTCAACAAAAGTACTGAAAG
66 CTGAGCAAATAGTGTCAAAAACGCTTCAAGCAGGATGCAATGTCAACAAAAGTACAGAAAG
* * * *
40541772 AAGCT-CCACATGGACGTTCTTTTGCTTACCAGTAGTTTTCTGAAAAAATAATTTTGAGAAGATG
1 AAGCTCCCACGTGGACGCTCTTTTGC-TA-CAGTAGTTTCCT-AAAAAATAATTTTGAGAAGACG
* *
40541836 -TTCTGAGCAAATAGTGTCAAAAACGCTTCAAGTAGGATGCAATGTCAGCAAAAGTACAGAAAG
63 TTTCTGAGCAAATAGTGTCAAAAACGCTTCAAGCAGGATGCAATGTCAACAAAAGTACAGAAAG
40541899 AAGCTCCCCACGTGGACGCTCTTTTGCTACAGTAG-TTCCTA
1 AAGCT-CCCACGTGGACGCTCTTTTGCTACAGTAGTTTCCTA
40541940 TTTGCCTGAG
Statistics
Matches: 146, Mismatches: 15, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
123 16 0.11
124 7 0.05
125 6 0.04
126 4 0.03
127 72 0.49
128 23 0.16
129 18 0.12
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (126 bp):
AAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTTCCTAAAAAATAATTTTGAGAAGACGTTT
CTGAGCAAATAGTGTCAAAAACGCTTCAAGCAGGATGCAATGTCAACAAAAGTACAGAAAG
Found at i:40545984 original size:7 final size:7
Alignment explanation
Indices: 40545974--40546005 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
40545964 TTATATACAT
40545974 AATACTA
1 AATACTA
40545981 AATACTA
1 AATACTA
40545988 AATA-TA
1 AATACTA
40545994 AATACTA
1 AATACTA
40546001 AATAC
1 AATAC
40546006 GAATCAACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:40545997 original size:13 final size:14
Alignment explanation
Indices: 40545974--40546005 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
40545964 TTATATACAT
40545974 AATACTAAATACTA
1 AATACTAAATACTA
40545988 AATA-TAAATACTA
1 AATACTAAATACTA
40546001 AATAC
1 AATAC
40546006 GAATCAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.28
Consensus pattern (14 bp):
AATACTAAATACTA
Found at i:40564855 original size:20 final size:20
Alignment explanation
Indices: 40564830--40564868 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
40564820 AAATATATAT
40564830 ATAATA-ATAATAAATAAAAA
1 ATAATATAT-ATAAATAAAAA
40564850 ATAATATATATAAATAAAA
1 ATAATATATATAAATAAAA
40564869 TGTCCAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
ATAATATATATAAATAAAAA
Done.