Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 129432109
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: 129432109
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 138 of 425
Found at i:41627620 original size:98 final size:97
Alignment explanation
Indices: 41627431--41627614 Score: 291
Period size: 98 Copynumber: 1.9 Consensus size: 97
41627421 GCACATCGCC
* *
41627431 TACATATTTCACACTAGCCATTCGGCTTTACCAAATAAACATATCTCATATATATATTTCACATT
1 TACATATTTCACACTAGCCAGTCGGCTTTACCAAATAAACATATCTCA-ATACATATTTCACATT
41627496 GACCATTCGGCTTTACCACATATGCATATCTCA
65 GACCATTCGGCTTTACCACATATGCATATCTCA
* * *
41627529 TACATATTTCACATTAGCCAGTCGGCTTTACCACATATACATATCTC-ATACATATTTCACATT-
1 TACATATTTCACACTAGCCAGTCGGCTTTACCAAATAAACATATCTCAATACATATTTCACATTG
41627592 AGCCATTCGGCTTTACCACATAT
66 A-CCATTCGGCTTTACCACATAT
41627615 ATGCATGTTC
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
95 1 0.01
96 36 0.45
98 43 0.54
ACGTcount: A:0.32, C:0.26, G:0.08, T:0.35
Consensus pattern (97 bp):
TACATATTTCACACTAGCCAGTCGGCTTTACCAAATAAACATATCTCAATACATATTTCACATTG
ACCATTCGGCTTTACCACATATGCATATCTCA
Found at i:41627664 original size:47 final size:47
Alignment explanation
Indices: 41627585--41627919 Score: 481
Period size: 47 Copynumber: 7.1 Consensus size: 47
41627575 CATACATATT
* * *
41627585 TCACATTAGCCATTCGGCTTTACCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * * * * *
41627632 TTACATTCGCCATTCGGCCTTATCTCACATATGAATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * *
41627679 CCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
*
41627726 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * *
41627773 CCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
41627820 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * * **
41627867 TCACATTGTCCATTCGGCCTTATCTCATATATACACATTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
41627914 TCACAT
1 TCACAT
41627920 AAAATCCTAA
Statistics
Matches: 257, Mismatches: 31, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 257 1.00
ACGTcount: A:0.26, C:0.29, G:0.11, T:0.33
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
Found at i:41627920 original size:25 final size:24
Alignment explanation
Indices: 41627841--41627920 Score: 58
Period size: 25 Copynumber: 3.3 Consensus size: 24
41627831 ATTCGGCCTT
**
41627841 ATCACATATATGCATGTTCACATTC
1 ATCACATATAT-CACATTCACATTC
* * *
41627866 ATCACAT-TGTC-CATTCGGCCTT-
1 ATCACATATATCACATTC-ACATTC
*
41627888 ATCTCATATATACACATTCACATTC
1 ATCACATATAT-CACATTCACATTC
41627913 ATCACATA
1 ATCACATA
41627921 AAATCCTAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 10
0.67 0.17 0.17
Matches are distributed among these distances:
22 9 0.22
23 6 0.15
24 6 0.15
25 19 0.47
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (24 bp):
ATCACATATATCACATTCACATTC
Found at i:41629977 original size:54 final size:55
Alignment explanation
Indices: 41629901--41630028 Score: 222
Period size: 54 Copynumber: 2.3 Consensus size: 55
41629891 CTCAAAGCTC
* * *
41629901 TTTTTCCTTCTGTTTCTTTCTTCTATTCGGCCAAGAACAACATGAGAGC-TTTTT
1 TTTTTCTTTCTTTTTCTTTCTTCTATTCAGCCAAGAACAACATGAGAGCTTTTTT
41629955 TTTTTCTTTCTTTTTCTTTCTTCTATTCAGCCAAGAACAACATGAGAGCTTTTTT
1 TTTTTCTTTCTTTTTCTTTCTTCTATTCAGCCAAGAACAACATGAGAGCTTTTTT
41630010 TTTTTCTTTCTTTTTCTTT
1 TTTTTCTTTCTTTTTCTTT
41630029 TTTCATCATC
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
54 46 0.66
55 24 0.34
ACGTcount: A:0.16, C:0.20, G:0.09, T:0.54
Consensus pattern (55 bp):
TTTTTCTTTCTTTTTCTTTCTTCTATTCAGCCAAGAACAACATGAGAGCTTTTTT
Found at i:41631832 original size:40 final size:40
Alignment explanation
Indices: 41631800--41632226 Score: 643
Period size: 40 Copynumber: 10.8 Consensus size: 40
41631790 CCAGCATGAT
* * * *
41631800 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
41631840 TGCTCTTC-GG--TTAGCAC-GAGTATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGA-TACATCACTAGCACGAA
* *
41631877 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACAAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
41631917 TGCTCTTCGGGACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
41631957 TGCTCTTCGAGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
41631997 TGCTCTTCGGGACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
41632037 TGCTCTTCGGGACTTAG-CCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
41632076 TGCTCTTCGGGACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
41632116 TGCTCTTC-GGACTTAGTCCTGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAG-CCCGGATACATCACTAGCACGAA
*
41632156 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
41632196 TGCTCTTC-GGACTTAGCCCGGATATATCACT
1 TGCTCTTCGGGACTTAGCCCGGATACATCACT
41632227 CTCAATTCTC
Statistics
Matches: 358, Mismatches: 21, Indels: 17
0.90 0.05 0.04
Matches are distributed among these distances:
36 2 0.01
37 28 0.08
38 1 0.00
39 72 0.20
40 245 0.68
41 10 0.03
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:41632089 original size:159 final size:158
Alignment explanation
Indices: 41631800--41632226 Score: 668
Period size: 159 Copynumber: 2.7 Consensus size: 158
41631790 CCAGCATGAT
* * *
41631800 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTC-GG--TTAGCAC-GAGT
1 TGCTCTTC-GGACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGGACTTAGC-CGGA-T
*
41631861 ATATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACAAATGCTCTTCG
63 ATATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACAAATGCTCTTCG
41631926 GGACTTAGTCCGGATACATCACTAGCACGAA
128 GGACTTAGTCCGGATACATCACTAGCACGAA
41631957 TGCTCTTCGAGACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGGACTTAGTCCGGATA
1 TGCTCTTCG-GACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGGACTTAG-CCGGATA
* *
41632022 CATCACTAGCACGAATGCTCTTCGGGACTTAG-CCGGATACATCACTAGCACGAATGCTCTTCGG
64 TATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACAAATGCTCTTCGG
41632086 GACTTAGTCCGGATACATCACTAGCACGAA
129 GACTTAGTCCGGATACATCACTAGCACGAA
* *
41632116 TGCTCTTCGGACTTAGTCCTGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATA
1 TGCTCTTCGGACTTAG-CCCGGATATATCACTAGCACGAATGCTCTTCGGGACTTAG-CCGGATA
*
41632181 TATCACTAGCACGAATGCTCTTC-GGACTTAGCCCGGATATATCACT
64 TATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACT
41632227 CTCAATTCTC
Statistics
Matches: 251, Mismatches: 11, Indels: 14
0.91 0.04 0.05
Matches are distributed among these distances:
156 1 0.00
157 43 0.17
158 17 0.07
159 150 0.60
160 37 0.15
161 3 0.01
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (158 bp):
TGCTCTTCGGACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGGACTTAGCCGGATATA
TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACAAATGCTCTTCGGGA
CTTAGTCCGGATACATCACTAGCACGAA
Found at i:41633534 original size:37 final size:37
Alignment explanation
Indices: 41633491--41633561 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
41633481 TAGCTCAACA
*
41633491 AATCTCCACACGA-AGTTATCGGGTCTTACCCGGACAT
1 AATCTCCACAC-ATAGTCATCGGGTCTTACCCGGACAT
41633528 AATCTCCACACATAGTCATCGGGTCTTACCCGGA
1 AATCTCCACACATAGTCATCGGGTCTTACCCGGA
41633562 ATATATTTCC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
36 1 0.03
37 31 0.97
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (37 bp):
AATCTCCACACATAGTCATCGGGTCTTACCCGGACAT
Found at i:41633821 original size:97 final size:96
Alignment explanation
Indices: 41633706--41633888 Score: 314
Period size: 97 Copynumber: 1.9 Consensus size: 96
41633696 GCACATCGCC
* *
41633706 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTTACATT-
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATACATAT-TTCACATTA
41633770 GACCATTCGGCTTTACCACATATGCATATCTCA
65 G-CCATTCGGCTTTACCACATATGCATATCTCA
*
41633803 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAG
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAG
41633868 CCATTCGGCTTTACCACATAT
66 CCATTCGGCTTTACCACATAT
41633889 ATACATGTTC
Statistics
Matches: 82, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
96 28 0.34
97 54 0.66
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.36
Consensus pattern (96 bp):
TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAG
CCATTCGGCTTTACCACATATGCATATCTCA
Found at i:41633836 original size:48 final size:48
Alignment explanation
Indices: 41633706--41633889 Score: 307
Period size: 48 Copynumber: 3.8 Consensus size: 48
41633696 GCACATCGCC
*
41633706 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
* * *
41633754 TATATATATTTACATT-GACCATTCGGCTTTACCACATATGCATATCTCA
1 TACATAT-TTCACATTAG-CCATTCGGCTTTACCACATATACATATCTCA
41633803 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
41633851 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
41633890 TACATGTTCA
Statistics
Matches: 126, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
48 83 0.66
49 43 0.34
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.36
Consensus pattern (48 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
Found at i:41633943 original size:47 final size:47
Alignment explanation
Indices: 41633859--41634193 Score: 508
Period size: 47 Copynumber: 7.1 Consensus size: 47
41633849 CATACATATT
* * * *
41633859 TCACATTAGCCATTCGGCTTTACCACATATATACATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * *
41633906 TCACATTGGCCATTCGGCCTTATCTCACATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * *
41633953 CCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
*
41634000 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * *
41634047 CCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
41634094 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * **
41634141 TCACATTGGCCATTCGGCCTTATCTCATATATACACATTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
41634188 TCACAT
1 TCACAT
41634194 AAAATCCTAA
Statistics
Matches: 262, Mismatches: 26, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 262 1.00
ACGTcount: A:0.26, C:0.30, G:0.11, T:0.33
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
Found at i:41634120 original size:22 final size:22
Alignment explanation
Indices: 41634093--41634164 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
41634083 GCTCACATTC
41634093 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * *
41634115 ATCACATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
41634139 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
41634162 ATC
1 ATC
41634165 TCATATATAC
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
22 13 0.35
23 7 0.19
24 7 0.19
25 10 0.27
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:41636244 original size:53 final size:53
Alignment explanation
Indices: 41636169--41636292 Score: 232
Period size: 53 Copynumber: 2.4 Consensus size: 53
41636159 CTCAAAGCTC
*
41636169 TTTTTCCTTCTTTTTCTTTCTTCTATTCGGCCAAGAACAACATGAGAGCTTTT
1 TTTTTCTTTCTTTTTCTTTCTTCTATTCGGCCAAGAACAACATGAGAGCTTTT
41636222 TTTTTCTTTCTTTTTCTTTCTTCTATTCGGCCAAGAACAACATGAGAGCTTTT
1 TTTTTCTTTCTTTTTCTTTCTTCTATTCGGCCAAGAACAACATGAGAGCTTTT
41636275 TTTTTCTTT-TTTTTCTTT
1 TTTTTCTTTCTTTTTCTTT
41636293 TTCATCATCA
Statistics
Matches: 70, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
52 9 0.13
53 61 0.87
ACGTcount: A:0.16, C:0.20, G:0.10, T:0.54
Consensus pattern (53 bp):
TTTTTCTTTCTTTTTCTTTCTTCTATTCGGCCAAGAACAACATGAGAGCTTTT
Found at i:41643733 original size:123 final size:123
Alignment explanation
Indices: 41643512--41643735 Score: 315
Period size: 123 Copynumber: 1.8 Consensus size: 123
41643502 GAATTATGTG
* * * * * * *
41643512 AAATGAAATATGGATGTGTATTGATTATTGATTTATGTGTGTATGAGTATTTGAATGACACCCGG
1 AAATGAAATATGAATGTCTAATGATTATTGATGTATGTGTGCATGAGCAATTGAATGACACCCGG
* **
41643577 GCTAAGTCCCGAAGGCGATTATGCTAGTGATTATATTGTGTTTGAGCCTTAGTAACGA
66 GCTAAGTCCCGAAGACGATTATGCTAGAAATTATATTGTGTTTGAGCCTTAGTAACGA
* *
41643635 AAATGAAATATGAATGTCTAATGATTATTGATGTATGTGTGCATGAGCAATTGAATGATATCCGG
1 AAATGAAATATGAATGTCTAATGATTATTGATGTATGTGTGCATGAGCAATTGAATGACACCCGG
*
41643700 GCTAAGTCCCGAAGACG-TTATTGCTGGAAATTATAT
66 GCTAAGTCCCGAAGACGATTA-TGCTAGAAATTATAT
41643736 CCGGGTTAAG
Statistics
Matches: 87, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
122 3 0.03
123 84 0.97
ACGTcount: A:0.31, C:0.11, G:0.24, T:0.34
Consensus pattern (123 bp):
AAATGAAATATGAATGTCTAATGATTATTGATGTATGTGTGCATGAGCAATTGAATGACACCCGG
GCTAAGTCCCGAAGACGATTATGCTAGAAATTATATTGTGTTTGAGCCTTAGTAACGA
Found at i:41643857 original size:40 final size:40
Alignment explanation
Indices: 41643730--41643859 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
41643720 TTGCTGGAAA
* * *
41643730 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGCGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * *
41643770 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
41643810 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
41643850 TTATATCCGG
1 TTATATCCGG
41643860 TTGTATTCCG
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 4 0.05
40 73 0.95
ACGTcount: A:0.22, C:0.25, G:0.29, T:0.23
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:41653806 original size:19 final size:18
Alignment explanation
Indices: 41653771--41653817 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
41653761 CCTAAAAGAA
*
41653771 AATTTTCATTTCCATTTT
1 AATTTTTATTTCCATTTT
41653789 AATTTTTATTTCCAATTTT
1 AATTTTTATTTCC-ATTTT
41653808 AA-TTTTATTT
1 AATTTTTATTT
41653818 TTATGTTCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 20 0.74
19 7 0.26
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.64
Consensus pattern (18 bp):
AATTTTTATTTCCATTTT
Found at i:41655280 original size:118 final size:118
Alignment explanation
Indices: 41655072--41655304 Score: 448
Period size: 118 Copynumber: 2.0 Consensus size: 118
41655062 ATCCTGTAGA
41655072 TACTCGTGGAAAAAGAAAAATTACAGAATAGTCCCTGAATTTCTACAACCACTACAATTCAATCT
1 TACTCGTGGAAAAAGAAAAATTACAGAATAGTCCCTGAATTTCTACAACCACTACAATTCAATCT
*
41655137 AGATAAGTTTGTACTATTTAAAATTTTGACATCTATATGAATTGTTGAATTTC
66 AGATAAGTTTGTACGATTTAAAATTTTGACATCTATATGAATTGTTGAATTTC
41655190 TACTCGTGGAAAAAGAAAAATTACAGAATAGTCCCTGAATTTCTACAACCACTACAATTCAATCT
1 TACTCGTGGAAAAAGAAAAATTACAGAATAGTCCCTGAATTTCTACAACCACTACAATTCAATCT
*
41655255 AGATAAGTTTGTACGGTTTAAAATTTTGACATCTATATGAATTGTTGAAT
66 AGATAAGTTTGTACGATTTAAAATTTTGACATCTATATGAATTGTTGAAT
41655305 AGTATAACAT
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
118 113 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (118 bp):
TACTCGTGGAAAAAGAAAAATTACAGAATAGTCCCTGAATTTCTACAACCACTACAATTCAATCT
AGATAAGTTTGTACGATTTAAAATTTTGACATCTATATGAATTGTTGAATTTC
Found at i:41655623 original size:36 final size:36
Alignment explanation
Indices: 41655539--41655624 Score: 113
Period size: 35 Copynumber: 2.4 Consensus size: 36
41655529 TATACTCTCT
* *
41655539 ATTTGGCGTGTTTCAGTTGGACTAATTCTTATGAGC
1 ATTTGGTGTGTTTCAGTTGGACTAACTCTTATGAGC
* *
41655575 A-TTGGTGTGTTTC-GATTGGACTAGCTCTTGTGAGC
1 ATTTGGTGTGTTTCAG-TTGGACTAACTCTTATGAGC
41655610 ATTTGGTGTGTTTCA
1 ATTTGGTGTGTTTCA
41655625 TAGGGATTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
34 1 0.02
35 29 0.67
36 13 0.30
ACGTcount: A:0.16, C:0.13, G:0.28, T:0.43
Consensus pattern (36 bp):
ATTTGGTGTGTTTCAGTTGGACTAACTCTTATGAGC
Found at i:41661617 original size:38 final size:38
Alignment explanation
Indices: 41661572--41661668 Score: 131
Period size: 38 Copynumber: 2.6 Consensus size: 38
41661562 GGCTTAAAGA
* *
41661572 CCCGCAGGCTTCGTGCTGGTAAAATATCTGGGTTAAAT
1 CCCGCAGGCTTCGTGCTGGTAAAATATCAGGGATAAAT
**
41661610 CCCGCAGGCTTCGTGCTGGTATTATATCAGGGATAAAT
1 CCCGCAGGCTTCGTGCTGGTAAAATATCAGGGATAAAT
* * *
41661648 CCCGTAGGCCTAGTGCTGGTA
1 CCCGCAGGCTTCGTGCTGGTA
41661669 TTATTCGGGC
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.22, C:0.23, G:0.28, T:0.28
Consensus pattern (38 bp):
CCCGCAGGCTTCGTGCTGGTAAAATATCAGGGATAAAT
Found at i:41661754 original size:43 final size:43
Alignment explanation
Indices: 41661679--41661907 Score: 332
Period size: 43 Copynumber: 5.3 Consensus size: 43
41661669 TTATTCGGGC
* * *
41661679 CTTCGTGCCGGTGATGTGTATTCGAGCCTTCGTGCCGAGCAGG
1 CTTCATGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGG
* * * *
41661722 TTTCATGACGGTAATGTATATTCGGGCCTTCGTGCCTAGCAGG
1 CTTCATGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGG
*
41661765 CTTCATGCCGGTGATGTATATTCGGGCCTTCGTGCCTAGCAGG
1 CTTCATGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGG
** *
41661808 CTTTGTGCTGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGG
1 CTTCATGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGG
*
41661851 CTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGG
1 CTTCATGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGG
* *
41661894 CGTAATGCCGGTGA
1 CTTCATGCCGGTGA
41661908 AATGATATGT
Statistics
Matches: 167, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 167 1.00
ACGTcount: A:0.13, C:0.24, G:0.33, T:0.31
Consensus pattern (43 bp):
CTTCATGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGG
Found at i:41663474 original size:43 final size:42
Alignment explanation
Indices: 41663411--41663524 Score: 131
Period size: 43 Copynumber: 2.7 Consensus size: 42
41663401 TATCATACCA
* *
41663411 ATGCCATATCCCAGATATGGTCTTACATGGAA-TCTCATATTG
1 ATGCCATAGCCCAGATATGGTCTTACA-CGAAGTCTCATATTG
* **
41663453 ATGCCAATAGCCCAGCTATGGTCTTACACGAAGTCTCATATCA
1 ATGCC-ATAGCCCAGATATGGTCTTACACGAAGTCTCATATTG
* * *
41663496 ATGCCATATCCCAAATATGGTTTTACACG
1 ATGCCATAGCCCAGATATGGTCTTACACG
41663525 TAGTTTCAAC
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
42 28 0.46
43 33 0.54
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.30
Consensus pattern (42 bp):
ATGCCATAGCCCAGATATGGTCTTACACGAAGTCTCATATTG
Found at i:41667123 original size:5 final size:5
Alignment explanation
Indices: 41667113--41667142 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
41667103 GATGCCAACC
*
41667113 ATAAA ATAAA ATAAA ATAAG ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
41667143 TTTTTAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:41671012 original size:132 final size:130
Alignment explanation
Indices: 41670745--41671024 Score: 350
Period size: 132 Copynumber: 2.1 Consensus size: 130
41670735 TTTCCTTTGC
* * *
41670745 TTTAAATGATTTTTAGAAGGTATGCGTGAAATTTTGAAGGGATATTTGATTATTTTAAGCAAACG
1 TTTAAA-GATTTTTA-AAGGCATGAGTGAAATTTCGAAGGGATATTTGATTATTTTAAGCAAACG
* * *
41670810 AGAAATTGCAACCCAACACGTTAGGGCACAATTCCGCGAATTGCCAAATATCGCACATCGCCTTC
64 AGAAATTGCAACCCAACACGTTAGGGCACAATTCCACGAATTGCCAAAGATCGAACATCGCCTTC
*
41670875 GT
129 AT
* *
41670877 TTTAAAGAATTTTTAATAGGCATGAGTGAAATTTCGAAGGGATATTCT-ATTATTTTGAGTAAAC
1 TTTAAAG-ATTTTTAA-AGGCATGAGTGAAATTTCGAAGGGATATT-TGATTATTTTAAGCAAAC
** * *
41670941 GCA-AAATTGCAACCCAACACGTTAGGGCATTATTCCACGAATTGTCAAAGATCGAATC-TCGTC
63 G-AGAAATTGCAACCCAACACGTTAGGGCACAATTCCACGAATTGCCAAAGATCGAA-CATCGCC
41671004 TTCAT
126 TTCAT
*
41671009 TTTAAGGATTTTTAAA
1 TTTAAAGATTTTTAAA
41671025 TGATTGTGTA
Statistics
Matches: 129, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
130 1 0.01
131 10 0.08
132 115 0.89
133 3 0.02
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33
Consensus pattern (130 bp):
TTTAAAGATTTTTAAAGGCATGAGTGAAATTTCGAAGGGATATTTGATTATTTTAAGCAAACGAG
AAATTGCAACCCAACACGTTAGGGCACAATTCCACGAATTGCCAAAGATCGAACATCGCCTTCAT
Found at i:41672223 original size:64 final size:64
Alignment explanation
Indices: 41672150--41672360 Score: 151
Period size: 64 Copynumber: 3.2 Consensus size: 64
41672140 CTGGGCCAGA
*
41672150 GCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
1 GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
* * * *** * ** *
41672214 GCCCATTTCAAAATAC-ATGCAACATCAGTAAACATATGCAAGCCC--ATTTGGGTAACAGTGGT
1 GCCCATTTCAGATTACAAT--AA-A-CTG-GGCCTTA-GC---CCCTTATTCAGATAACA---GT
* *
41672276 ACTGGGCCAGA-
54 A-TGGCCCATAG
*
41672287 GCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
1 GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
41672351 GCCCATTTCA
1 GCCCATTTCA
41672361 AAATACATGC
Statistics
Matches: 103, Mismatches: 27, Indels: 34
0.63 0.16 0.21
Matches are distributed among these distances:
63 9 0.09
64 25 0.24
65 5 0.05
66 1 0.01
67 11 0.11
68 5 0.05
69 5 0.05
70 11 0.11
71 1 0.01
72 5 0.05
73 16 0.16
74 9 0.09
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (64 bp):
GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
Found at i:41672362 original size:137 final size:137
Alignment explanation
Indices: 41672116--41672402 Score: 556
Period size: 137 Copynumber: 2.1 Consensus size: 137
41672106 TATTGGGCCT
**
41672116 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
41672181 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
41672246 CATATGC
131 CATATGC
41672253 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
41672318 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
41672383 CATATGC
131 CATATGC
41672390 AAGCCCATTTGGG
1 AAGCCCATTTGGG
41672403 GAGACTACTC
Statistics
Matches: 148, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
137 148 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.24
Consensus pattern (137 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
CATATGC
Found at i:41672687 original size:25 final size:26
Alignment explanation
Indices: 41672650--41672698 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
41672640 TCAAACATGC
41672650 ATTTAGGTCAATTTAACCCTAGGGGT
1 ATTTAGGTCAATTTAACCCTAGGGGT
* * *
41672676 ATTTCGGT-AATTTATCTCTAGGG
1 ATTTAGGTCAATTTAACCCTAGGG
41672699 TAAAACTGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 13 0.65
26 7 0.35
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.39
Consensus pattern (26 bp):
ATTTAGGTCAATTTAACCCTAGGGGT
Found at i:41674264 original size:25 final size:26
Alignment explanation
Indices: 41674181--41674288 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
41674171 ACATGAATTC
41674181 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
41674207 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
41674233 TTATCATGGAATATTTACCTAA-CCA
1 TTATCATGAAACATTTACCTAACCCA
*
41674258 TTATCATGGAACATTTACCTAA-CCA
1 TTATCATGAAACATTTACCTAACCCA
41674283 TTATCA
1 TTATCA
41674289 ATTTGTATCA
Statistics
Matches: 79, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
25 33 0.42
26 46 0.58
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:41674275 original size:51 final size:51
Alignment explanation
Indices: 41674181--41674288 Score: 173
Period size: 51 Copynumber: 2.1 Consensus size: 51
41674171 ACATGAATTC
41674181 TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAA-CCA
* * *
41674233 TTATCATGGAATATTTACCTAA-CCATTATCATGGAACATTTACCTAACCA
1 TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCA
41674283 TTATCA
1 TTATCA
41674289 ATTTGTATCA
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
50 9 0.17
51 24 0.45
52 20 0.38
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.33
Consensus pattern (51 bp):
TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCA
Found at i:41678485 original size:25 final size:26
Alignment explanation
Indices: 41678448--41678499 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
41678438 TCAAACATGC
41678448 ATTTAGGTCAATTTAACCCTAGGGGT
1 ATTTAGGTCAATTTAACCCTAGGGGT
* * *
41678474 ATTTCGGT-AATTTATCTCTAGGGGT
1 ATTTAGGTCAATTTAACCCTAGGGGT
41678499 A
1 A
41678500 AAATGTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.38
Consensus pattern (26 bp):
ATTTAGGTCAATTTAACCCTAGGGGT
Found at i:41680012 original size:26 final size:26
Alignment explanation
Indices: 41679976--41680085 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
41679966 ACATGAATTC
41679976 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
41680002 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
41680028 TTATCATGGAATATTTACCTAATCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
41680054 TTGTCATGGAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
41680080 TTATCA
1 TTATCA
41680086 ATTTGTATCA
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.35, C:0.25, G:0.06, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:41680465 original size:24 final size:24
Alignment explanation
Indices: 41680433--41680503 Score: 124
Period size: 24 Copynumber: 3.0 Consensus size: 24
41680423 CTGTCAGGAG
41680433 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
41680457 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
**
41680481 AGGATTTAGGAGCAGATAAGGGA
1 AGGATTTAGGAGTTGATAAGGGA
41680504 GGAAATCTAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.35, C:0.01, G:0.38, T:0.25
Consensus pattern (24 bp):
AGGATTTAGGAGTTGATAAGGGAT
Found at i:41681962 original size:27 final size:27
Alignment explanation
Indices: 41681922--41682033 Score: 129
Period size: 27 Copynumber: 4.1 Consensus size: 27
41681912 AGGAAGCGTC
*
41681922 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
41681949 CTGGTGGCTCTGCCACATATT-TCTGTT
1 CTGGTGGCTCTGCCACA-ATTATCTGAT
*
41681976 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
* * * *
41682004 CTGGTGACTTTGTCAC-ATTATCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGAT
41682030 CTGG
1 CTGG
41682034 CAGCCATGTT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
26 8 0.11
27 49 0.66
28 17 0.23
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:41682028 original size:54 final size:54
Alignment explanation
Indices: 41681922--41682033 Score: 154
Period size: 54 Copynumber: 2.1 Consensus size: 54
41681912 AGGAAGCGTC
* *
41681922 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATTTCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
* * * *
41681976 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTTTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
41682030 CTGG
1 CTGG
41682034 CAGCCATGTT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
54 34 0.67
55 17 0.33
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:41686166 original size:40 final size:40
Alignment explanation
Indices: 41686107--41686314 Score: 209
Period size: 40 Copynumber: 5.2 Consensus size: 40
41686097 CAATTGAATG
* * * * *
41686107 ATATCCGGGTTAAGTCCCGAAGACATTTATGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * * *
41686147 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
41686187 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
41686227 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * **
41686267 CTATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
41686307 ATATCCGG
1 ATATCCGG
41686315 TTGTATTCCG
Statistics
Matches: 143, Mismatches: 25, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 143 1.00
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
Found at i:41689046 original size:7 final size:7
Alignment explanation
Indices: 41689034--41689062 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
41689024 CTTGGTATCA
41689034 TTGATGT
1 TTGATGT
41689041 TTGATGT
1 TTGATGT
41689048 TTGATGT
1 TTGATGT
41689055 TTGATGT
1 TTGATGT
41689062 T
1 T
41689063 GTGGTGGTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.28, T:0.59
Consensus pattern (7 bp):
TTGATGT
Found at i:41689968 original size:29 final size:29
Alignment explanation
Indices: 41689935--41690066 Score: 156
Period size: 29 Copynumber: 4.6 Consensus size: 29
41689925 GTGACGAGAT
*
41689935 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
*
41689964 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
* *
41689993 AGGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
** * **
41690022 TAACACTATGTGTGCAAGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
* **
41690051 CGGCACTGGGTGTGCG
1 TGGCACTAAGTGTGCG
41690067 AGCTCGAAGG
Statistics
Matches: 89, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 89 1.00
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.24
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAAAATA
Found at i:41696666 original size:40 final size:40
Alignment explanation
Indices: 41696607--41696814 Score: 218
Period size: 40 Copynumber: 5.2 Consensus size: 40
41696597 CAATTGAATG
* * * *
41696607 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * * *
41696647 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
41696687 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
41696727 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * **
41696767 CTATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
41696807 ATATCCGG
1 ATATCCGG
41696815 TTGTATTCCG
Statistics
Matches: 142, Mismatches: 26, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 142 1.00
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
Found at i:41696745 original size:80 final size:80
Alignment explanation
Indices: 41696608--41696814 Score: 247
Period size: 80 Copynumber: 2.6 Consensus size: 80
41696598 AATTGAATGA
* * ** * * *
41696608 TATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATTATATCCGGGTTAAGACCCGAAGGCAA
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAA
*
41696673 TTGTGCTAGT-G-AC
66 TTGTGCAAGTCGTAC
* * *
41696686 TACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAAATCCGGGCTAATACCCGAAGGC
1 T--ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGC
* *
41696751 ATTTGTGCAAGTCGTTC
64 AATTGTGCAAGTCGTAC
* *
41696768 TATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTATATCCGG
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGG
41696815 TTGTATTCCG
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
78 1 0.01
80 105 0.96
81 1 0.01
82 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (80 bp):
TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAA
TTGTGCAAGTCGTAC
Found at i:41700356 original size:68 final size:70
Alignment explanation
Indices: 41700284--41700481 Score: 294
Period size: 71 Copynumber: 2.8 Consensus size: 70
41700274 ACACCCTGTA
* * * *
41700284 GTAGCTAGGTCACATGCGTGATA-CGAGATGTA-TC-CCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAG-TGAAGACACCATGTAGACAAGAGAGCTACGTGAAAG
41700346 ATAAAT
65 ATAAAT
*
41700352 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACGTGAAAG
41700417 ATAAAT
65 ATAAAT
*
41700423 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACG
41700482 AGACAAATCG
Statistics
Matches: 121, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
68 24 0.20
69 3 0.02
70 1 0.01
71 93 0.77
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (70 bp):
GTAGCTAGGTCGCATGCGTGATACCAAGTGAAGACACCATGTAGACAAGAGAGCTACGTGAAAGA
TAAAT
Found at i:41700395 original size:41 final size:41
Alignment explanation
Indices: 41700350--41700467 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
41700340 TGAAAGATAA
41700350 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
41700391 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
41700421 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
41700462 ATGTAG
1 ATGTAG
41700468 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:41700407 original size:71 final size:71
Alignment explanation
Indices: 41700318--41700481 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
41700308 GAGATGTATC
41700318 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
41700383 AGGACA
66 AGGACA
41700389 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
41700454 AGGACA
66 AGGACA
41700460 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
41700482 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:41707916 original size:68 final size:70
Alignment explanation
Indices: 41707844--41708041 Score: 294
Period size: 71 Copynumber: 2.8 Consensus size: 70
41707834 ACACCCTGTA
* * * *
41707844 GTAGCTAGGTCACATGCGTGATA-CGAGATGTA-TC-CCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAG-TGAAGACACCATGTAGACAAGAGAGCTACGTGAAAG
41707906 ATAAAT
65 ATAAAT
*
41707912 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACGTGAAAG
41707977 ATAAAT
65 ATAAAT
*
41707983 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACG
41708042 AGACAAATCG
Statistics
Matches: 121, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
68 24 0.20
69 3 0.02
70 1 0.01
71 93 0.77
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (70 bp):
GTAGCTAGGTCGCATGCGTGATACCAAGTGAAGACACCATGTAGACAAGAGAGCTACGTGAAAGA
TAAAT
Found at i:41707955 original size:41 final size:41
Alignment explanation
Indices: 41707910--41708027 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
41707900 TGAAAGATAA
41707910 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
41707951 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
41707981 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
41708022 ATGTAG
1 ATGTAG
41708028 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:41707967 original size:71 final size:71
Alignment explanation
Indices: 41707878--41708041 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
41707868 GAGATGTATC
41707878 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
41707943 AGGACA
66 AGGACA
41707949 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
41708014 AGGACA
66 AGGACA
41708020 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
41708042 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:41709515 original size:44 final size:44
Alignment explanation
Indices: 41709443--41709530 Score: 110
Period size: 44 Copynumber: 2.0 Consensus size: 44
41709433 TAGATTCACC
*
41709443 ATCTTCGATCTGCTCTCTGTTAACACAGAGATGCCAAATCTGCT
1 ATCTTCGATCTGCTCTCTGTTAACACAGAGACGCCAAATCTGCT
*
41709487 ATCTTCGATCTGC-C-CT-TTAACAATACAGAGACGTCAAATCTGCT
1 ATCTTCGATCTGCTCTCTGTTAAC---ACAGAGACGCCAAATCTGCT
41709531 CAACGTAAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
41 5 0.13
42 2 0.05
43 1 0.03
44 31 0.79
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (44 bp):
ATCTTCGATCTGCTCTCTGTTAACACAGAGACGCCAAATCTGCT
Found at i:41709603 original size:47 final size:46
Alignment explanation
Indices: 41709549--41709692 Score: 122
Period size: 47 Copynumber: 3.2 Consensus size: 46
41709539 ACACGTGAAA
41709549 GCCAAATCAACTATGTCTTCGATCTGCTCCCTGCCTGATACAGAGAT
1 GCCAAATCAACTATGTCTT-GATCTGCTCCCTGCCTGATACAGAGAT
* * ** * * * *
41709596 GCCAAATCATC-ATG----GATCTGCT-TCAACGT-AAACACGTGAAA
1 GCCAAATCAACTATGTCTTGATCTGCTCCCTGCCTGATACA-GAG-AT
*
41709637 GCCAAATCAGCTATGTCTTTGATCTGCTCCCTGCCTGATACAGAGAT
1 GCCAAATCAACTATGTC-TTGATCTGCTCCCTGCCTGATACAGAGAT
41709684 GCCAAATCA
1 GCCAAATCA
41709693 TCTTGGATCT
Statistics
Matches: 71, Mismatches: 16, Indels: 20
0.66 0.15 0.19
Matches are distributed among these distances:
39 4 0.06
40 5 0.07
41 19 0.27
42 3 0.04
46 3 0.04
47 28 0.39
48 5 0.07
49 4 0.06
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (46 bp):
GCCAAATCAACTATGTCTTGATCTGCTCCCTGCCTGATACAGAGAT
Found at i:41709636 original size:88 final size:88
Alignment explanation
Indices: 41709524--41709777 Score: 447
Period size: 88 Copynumber: 2.9 Consensus size: 88
41709514 GAGACGTCAA
*
41709524 ATCTGC-TCAACGTAAACACGTGAAAGCCAAATCAACTATGTCTTCGATCTGCTCCCTGCCTGAT
1 ATCTGCTTCAACGTAAACACGTGAAAGCCAAATCAGCTATGTCTTCGATCTGCTCCCTGCCTGAT
41709588 ACAGAGATGCCAAATCATCATGG
66 ACAGAGATGCCAAATCATCATGG
*
41709611 ATCTGCTTCAACGTAAACACGTGAAAGCCAAATCAGCTATGTCTTTGATCTGCTCCCTGCCTGAT
1 ATCTGCTTCAACGTAAACACGTGAAAGCCAAATCAGCTATGTCTTCGATCTGCTCCCTGCCTGAT
*
41709676 ACAGAGATGCCAAATCATCTTGG
66 ACAGAGATGCCAAATCATCATGG
* * *
41709699 ATCTACTTCAACGTAAACACGTGAAAGCCAAATCAGCTATGTCTTCGATCTGCTCCCCGTCTGAT
1 ATCTGCTTCAACGTAAACACGTGAAAGCCAAATCAGCTATGTCTTCGATCTGCTCCCTGCCTGAT
41709764 ACAGAGATGCCAAA
66 ACAGAGATGCCAAA
41709778 ACTGCTATCT
Statistics
Matches: 159, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
87 6 0.04
88 153 0.96
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.25
Consensus pattern (88 bp):
ATCTGCTTCAACGTAAACACGTGAAAGCCAAATCAGCTATGTCTTCGATCTGCTCCCTGCCTGAT
ACAGAGATGCCAAATCATCATGG
Found at i:41709641 original size:41 final size:41
Alignment explanation
Indices: 41709596--41709733 Score: 100
Period size: 41 Copynumber: 3.2 Consensus size: 41
41709586 ATACAGAGAT
41709596 GCCAAATCATCATGGATCTGCTTCAACGTAAACACGTGAAA
1 GCCAAATCATCATGGATCTGCTTCAACGTAAACACGTGAAA
* * ** * * * *
41709637 GCCAAATCAGCTATGTCTTTGATCTGCTCCCTGCCTGATACA-GAG-AT
1 GCCAAATCATC-ATG-----GATCTGCT-TCAACGT-AAACACGTGAAA
* *
41709684 GCCAAATCATCTTGGATCTACTTCAACGTAAACACGTGAAA
1 GCCAAATCATCATGGATCTGCTTCAACGTAAACACGTGAAA
41709725 GCCAAATCA
1 GCCAAATCA
41709734 GCTATGTCTT
Statistics
Matches: 69, Mismatches: 18, Indels: 20
0.64 0.17 0.19
Matches are distributed among these distances:
39 4 0.06
40 5 0.07
41 27 0.39
42 3 0.04
46 2 0.03
47 19 0.28
48 5 0.07
49 4 0.06
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.25
Consensus pattern (41 bp):
GCCAAATCATCATGGATCTGCTTCAACGTAAACACGTGAAA
Found at i:41709817 original size:44 final size:44
Alignment explanation
Indices: 41709763--41710095 Score: 380
Period size: 44 Copynumber: 7.6 Consensus size: 44
41709753 CCCCGTCTGA
* * * * *
41709763 TACAGAGATGCCAAAACTGCTATCTTAGATCTACTCTCTGCCAC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTACTCTCTGCCGC
* * * *
41709807 TACAGAGATGCCAAATCTATTATGTTCGATCTACTCTCCGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTACTCTCTGCCGC
* *
41709851 TACAGAGACGCCAAATCTGTTATATTCGATCTTCTCTCTGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTACTCTCTGCCGC
* **
41709895 TACAGAGACGCCAAATCTGTTATCTTCGATCTACT-TTTCGTTGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTACTCTCT-GCCGC
* * * * * ** **
41709939 TATAGAGATGCCAAATCTGTTATCTTTGATCTGCCCTCTAACAA
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTACTCTCTGCCGC
* * *
41709983 TACAGAGACGCCAAATTTGTTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTACTCTCTGCCGC
* * * *
41710027 TACAGATACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCTGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTACTCTCTGCCGC
41710071 TACAGAGACGCCAAATCTGTTATCT
1 TACAGAGACGCCAAATCTGTTATCT
41710096 GCTTCAAGGA
Statistics
Matches: 245, Mismatches: 42, Indels: 4
0.84 0.14 0.01
Matches are distributed among these distances:
43 2 0.01
44 241 0.98
45 2 0.01
ACGTcount: A:0.25, C:0.28, G:0.16, T:0.31
Consensus pattern (44 bp):
TACAGAGACGCCAAATCTGTTATCTTCGATCTACTCTCTGCCGC
Found at i:41711350 original size:5 final size:5
Alignment explanation
Indices: 41711340--41711413 Score: 75
Period size: 5 Copynumber: 15.0 Consensus size: 5
41711330 TTGGCCTCTC
*
41711340 CTTTT CTTTT CTTTT CTTCT -TTTT CTTCTT -TCTTT C-TTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTT-TT CT-TTT CTTTT CTTTT CTTTT
*
41711389 CTTCTT CTTTT CTCTT CTTTT -TTTT
1 CTT-TT CTTTT CTTTT CTTTT CTTTT
41711414 TTTGAAGATC
Statistics
Matches: 59, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
4 11 0.19
5 40 0.68
6 8 0.14
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (5 bp):
CTTTT
Found at i:41711361 original size:13 final size:13
Alignment explanation
Indices: 41711340--41711413 Score: 68
Period size: 13 Copynumber: 5.8 Consensus size: 13
41711330 TTGGCCTCTC
41711340 CTTTTCTTTTCTT
1 CTTTTCTTTTCTT
41711353 -TTCTTCTTTTTCTT
1 CTT-TTC-TTTTCTT
41711367 C-TTTC-TTTCTTT
1 CTTTTCTTTTC-TT
41711379 CTTTTCTTTTCTT
1 CTTTTCTTTTCTT
*
41711392 CTTCTT-TTCTCTT
1 CTT-TTCTTTTCTT
41711405 CTTTT-TTTT
1 CTTTTCTTTT
41711414 TTTGAAGATC
Statistics
Matches: 52, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
11 4 0.08
12 10 0.19
13 24 0.46
14 14 0.27
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
CTTTTCTTTTCTT
Found at i:41711382 original size:34 final size:33
Alignment explanation
Indices: 41711341--41711416 Score: 109
Period size: 34 Copynumber: 2.3 Consensus size: 33
41711331 TGGCCTCTCC
*
41711341 TTTTCTTTTCTTTTCTTCTTTTTCTTCT-TTCTT
1 TTTTCTTTTCTTTTCTTCTTCTT-TTCTCTTCTT
41711374 TCTTTCTTTTCTTTTCTTCTTCTTTTCTCTTCTT
1 T-TTTCTTTTCTTTTCTTCTTCTTTTCTCTTCTT
*
41711408 TTTTTTTTT
1 TTTTCTTTT
41711417 GAAGATCTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
33 12 0.31
34 27 0.69
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (33 bp):
TTTTCTTTTCTTTTCTTCTTCTTTTCTCTTCTT
Found at i:41711409 original size:21 final size:21
Alignment explanation
Indices: 41711343--41711409 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
41711333 GCCTCTCCTT
41711343 TTCTTTTCTTTTCTTCTTTT-TC
1 TTCTTTTC--TTCTTCTTTTCTC
*
41711365 TTC-TTTC-T-TTC-TTTCTT
1 TTCTTTTCTTCTTCTTTTCTC
41711382 TTCTTTTCTTCTTCTTTTCTC
1 TTCTTTTCTTCTTCTTTTCTC
41711403 TTCTTTT
1 TTCTTTT
41711410 TTTTTTTGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
16 3 0.08
17 7 0.18
18 5 0.13
19 1 0.03
20 3 0.08
21 16 0.42
22 3 0.08
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (21 bp):
TTCTTTTCTTCTTCTTTTCTC
Found at i:41713961 original size:19 final size:19
Alignment explanation
Indices: 41713938--41714004 Score: 98
Period size: 19 Copynumber: 3.5 Consensus size: 19
41713928 AGGGAAATCT
*
41713938 AATGCAAATGATGCAATGT
1 AATGCAAATGATGCAATGC
*
41713957 AATGCAAATAATGCAATGC
1 AATGCAAATGATGCAATGC
*
41713976 AATGTAAATGATGCAATGC
1 AATGCAAATGATGCAATGC
*
41713995 AATACAAATG
1 AATGCAAATG
41714005 CATGGGATGA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 42 1.00
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.24
Consensus pattern (19 bp):
AATGCAAATGATGCAATGC
Found at i:41715997 original size:131 final size:132
Alignment explanation
Indices: 41715862--41716186 Score: 322
Period size: 132 Copynumber: 2.5 Consensus size: 132
41715852 TCCAGCATGA
* * * ** * **
41715862 TAGGGCATGATT-CTCGAATTGTCAAACGCCGA-ATATTTCCTTTGTTTTAAATCATTTTTAGA-
1 TAGGGCATGATTCCGCGAATTGTCAAACACC-ACACATCGCCTTCGTTTTAAAGAATTTTTA-AT
* * ** *
41715924 AGGTATGCGTGAAATTTTGAAGGGTTATT-TGATTATTTTAAGAAAACGAGAAATTGCAACCCAA
64 AGGCATGAGTGAAATTTCAAAGGGATATTCT-ATTATTTTAAGAAAACGAGAAATTGCAACCCAA
41715988 CACGT
128 CACGT
* * * *
41715993 TAGGGCACGATTCCGCGAATTGCCAAATATCACACATCGCCTTCGTTTTAAAGAATTTTTAATAG
1 TAGGGCATGATTCCGCGAATTGTCAAACACCACACATCGCCTTCGTTTTAAAGAATTTTTAATAG
* * * *
41716058 GCATGAGTGAAATTTCAAAGGGATATTCTATTATTTTGAGCAAACGCGAAATTGCAATCCAACAC
66 GCATGAGTGAAATTTCAAAGGGATATTCTATTATTTTAAGAAAACGAGAAATTGCAACCCAACAC
41716123 GT
131 GT
* * * *
41716125 TAGGGCACT-ATTCCGCGAATTGTCAAAGATCGA-ATC-TCGTCTTCGTTTTAAAGGATTTTTAA
1 TAGGGCA-TGATTCCGCGAATTGTCAAACA-CCACA-CATCGCCTTCGTTTTAAAGAATTTTTAA
41716187 ATGATTGATT
Statistics
Matches: 159, Mismatches: 28, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
131 13 0.08
132 143 0.90
133 3 0.02
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Consensus pattern (132 bp):
TAGGGCATGATTCCGCGAATTGTCAAACACCACACATCGCCTTCGTTTTAAAGAATTTTTAATAG
GCATGAGTGAAATTTCAAAGGGATATTCTATTATTTTAAGAAAACGAGAAATTGCAACCCAACAC
GT
Found at i:41716072 original size:132 final size:131
Alignment explanation
Indices: 41715900--41716187 Score: 357
Period size: 132 Copynumber: 2.2 Consensus size: 131
41715890 CCGAATATTT
* ** * * ** *
41715900 CCTTTGTTTTAAATCATTTTTAGAAGGTATGCGTGAAATTTTGAAGGGTTATT-TGATTATTTTA
1 CCTTCGTTTTAAAGAATTTTTA-AAGGCATGAGTGAAATTTCAAAGGGATATTCT-ATTATTTTA
*
41715964 AGAAAACGAGAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGAATTGCCAAATATC-ACA-
64 AGAAAACGAGAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGAATTGCCAAAGATCGA-AT
41716027 CATCG
128 C-TCG
*
41716032 CCTTCGTTTTAAAGAATTTTTAATAGGCATGAGTGAAATTTCAAAGGGATATTCTATTATTTTGA
1 CCTTCGTTTTAAAGAATTTTTAA-AGGCATGAGTGAAATTTCAAAGGGATATTCTATTATTTTAA
* * * * *
41716097 GCAAACGCGAAATTGCAATCCAACACGTTAGGGCACTATTCCGCGAATTGTCAAAGATCGAATCT
65 GAAAACGAGAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGAATTGCCAAAGATCGAATCT
41716162 CG
130 CG
* *
41716164 TCTTCGTTTTAAAGGATTTTTAAA
1 CCTTCGTTTTAAAGAATTTTTAAA
41716188 TGATTGATTA
Statistics
Matches: 135, Mismatches: 17, Indels: 9
0.84 0.11 0.06
Matches are distributed among these distances:
131 2 0.01
132 130 0.96
133 3 0.02
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Consensus pattern (131 bp):
CCTTCGTTTTAAAGAATTTTTAAAGGCATGAGTGAAATTTCAAAGGGATATTCTATTATTTTAAG
AAAACGAGAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGAATTGCCAAAGATCGAATCTC
G
Found at i:41716726 original size:2 final size:2
Alignment explanation
Indices: 41716721--41716749 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
41716711 ATAAATAGCA
41716721 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
41716750 AAACATAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41719591 original size:25 final size:25
Alignment explanation
Indices: 41719563--41719619 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
41719553 ACAGATCAAA
*
41719563 ATGCTCGTAGGAACTA-TATAACAGG
1 ATGCTCGTA-GAACGATTATAACAGG
* *
41719588 ATGCTCG-AGAAGGATTTTAACAGG
1 ATGCTCGTAGAACGATTATAACAGG
41719612 ATGCTCGT
1 ATGCTCGT
41719620 TTGAGCTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 4 0.15
24 16 0.59
25 7 0.26
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (25 bp):
ATGCTCGTAGAACGATTATAACAGG
Found at i:41730067 original size:30 final size:30
Alignment explanation
Indices: 41730031--41730131 Score: 118
Period size: 28 Copynumber: 3.5 Consensus size: 30
41730021 GACAAGATTG
* * *
41730031 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* *
41730061 GCACTAAGTGTGCGAGTTT--GATTCTATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* *
41730089 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
41730118 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
41730132 GATTCACTAT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
28 23 0.38
29 19 0.31
30 19 0.31
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGTTTAAAATTATATA
Found at i:41730143 original size:29 final size:28
Alignment explanation
Indices: 41730060--41730135 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 28
41730050 AAAATTGTAC
* *
41730060 AGCACTAAGTGTGCGAGTTTGAT-TCTAT
1 AGCACTAAGTGTGCG-GATTGATATATAT
* *
41730088 AGCACTAAGTGTGC-GAGCTGAAAATATAT
1 AGCACTAAGTGTGCGGA-TTG-ATATATAT
41730117 AGCACTAAGTGTGCGGATT
1 AGCACTAAGTGTGCGGATT
41730136 CACTATATGC
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
26 1 0.03
27 2 0.05
28 15 0.38
29 19 0.49
30 2 0.05
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGGATTGATATATAT
Found at i:41737938 original size:30 final size:30
Alignment explanation
Indices: 41737902--41738002 Score: 118
Period size: 28 Copynumber: 3.5 Consensus size: 30
41737892 GACAAGATTG
* * *
41737902 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* *
41737932 GCACTAAGTGTGCGAGTTT--GATTCTATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* *
41737960 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
41737989 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
41738003 GATTCACTAT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
28 23 0.38
29 19 0.31
30 19 0.31
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGTTTAAAATTATATA
Found at i:41738014 original size:29 final size:28
Alignment explanation
Indices: 41737931--41738006 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 28
41737921 AAAATTGTAC
* *
41737931 AGCACTAAGTGTGCGAGTTTGAT-TCTAT
1 AGCACTAAGTGTGCG-GATTGATATATAT
* *
41737959 AGCACTAAGTGTGC-GAGCTGAAAATATAT
1 AGCACTAAGTGTGCGGA-TTG-ATATATAT
41737988 AGCACTAAGTGTGCGGATT
1 AGCACTAAGTGTGCGGATT
41738007 CACTATATGC
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
26 1 0.03
27 2 0.05
28 15 0.38
29 19 0.49
30 2 0.05
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGGATTGATATATAT
Found at i:41745820 original size:30 final size:30
Alignment explanation
Indices: 41745784--41745884 Score: 118
Period size: 28 Copynumber: 3.5 Consensus size: 30
41745774 GACAAGATTG
* * *
41745784 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* *
41745814 GCACTAAGTGTGCGAGTTT--GATTCTATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* *
41745842 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
41745871 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
41745885 GATTCACTAT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
28 23 0.38
29 19 0.31
30 19 0.31
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGTTTAAAATTATATA
Found at i:41745896 original size:29 final size:28
Alignment explanation
Indices: 41745813--41745888 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 28
41745803 AAAATTGTAC
* *
41745813 AGCACTAAGTGTGCGAGTTTGAT-TCTAT
1 AGCACTAAGTGTGCG-GATTGATATATAT
* *
41745841 AGCACTAAGTGTGC-GAGCTGAAAATATAT
1 AGCACTAAGTGTGCGGA-TTG-ATATATAT
41745870 AGCACTAAGTGTGCGGATT
1 AGCACTAAGTGTGCGGATT
41745889 CACTATATGC
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
26 1 0.03
27 2 0.05
28 15 0.38
29 19 0.49
30 2 0.05
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGGATTGATATATAT
Found at i:41748016 original size:28 final size:28
Alignment explanation
Indices: 41747976--41748032 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
41747966 TGGAATGCCT
41747976 AAGAGCCCTCAAAATTAGCCTTTTGTGA
1 AAGAGCCCTCAAAATTAGCCTTTTGTGA
41748004 AAGAGCCCTCAAAATTAGCCTTTTGTGA
1 AAGAGCCCTCAAAATTAGCCTTTTGTGA
41748032 A
1 A
41748033 TTGGACTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (28 bp):
AAGAGCCCTCAAAATTAGCCTTTTGTGA
Found at i:41749749 original size:80 final size:81
Alignment explanation
Indices: 41749611--41749830 Score: 221
Period size: 80 Copynumber: 2.7 Consensus size: 81
41749601 GAATCACGTA
* * * * * *
41749611 CCTTC-GGAATTTAACCGGATATAGTGACTAGCTCGATTGTCTTCGGGACATT-GCCCGGTTATA
1 CCTTCGGGAATTTACCCGGATTTAGTAACTAGCACGAATGCCTTCGGGAC-TTAGCCCGGTTATA
* * *
41749674 GTGATTCGCAC-AATTG
65 GTAACTCGCACAAAATG
* * * *
41749690 CCTTCGGGAATTTACCCGGATTTAGTAACTCGCACGAATGCCTTCGGGACTTAACCCGGTTTTGG
1 CCTTCGGGAATTTACCCGGATTTAGTAACTAGCACGAATGCCTTCGGGACTTAGCCCGGTTATAG
41749755 TAACTCGCACAAAATG
66 TAACTCGCACAAAATG
* * * * * * *
41749771 CCTTCGGGACTTAACCCAGTTTTAGTCACTTAGCACAAAAGCCTTCGGGACTTAGCCCGG
1 CCTTCGGGAATTTACCCGGATTTAGTAAC-TAGCACGAATGCCTTCGGGACTTAGCCCGG
41749831 ATACCATTCG
Statistics
Matches: 115, Mismatches: 22, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
79 7 0.06
80 54 0.47
81 28 0.24
82 26 0.23
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.28
Consensus pattern (81 bp):
CCTTCGGGAATTTACCCGGATTTAGTAACTAGCACGAATGCCTTCGGGACTTAGCCCGGTTATAG
TAACTCGCACAAAATG
Found at i:41749783 original size:41 final size:40
Alignment explanation
Indices: 41749651--41749830 Score: 191
Period size: 40 Copynumber: 4.5 Consensus size: 40
41749641 GCTCGATTGT
* * * * *
41749651 CTTCGGGACATT-GCCCGGTTATAGTGATTCGCACAATTGC
1 CTTCGGGAC-TTAACCCGGTTTTAGTAACTCGCACAAATGC
* * * *
41749691 CTTCGGGAATTTACCCGGATTTAGTAACTCGCACGAATGC
1 CTTCGGGACTTAACCCGGTTTTAGTAACTCGCACAAATGC
*
41749731 CTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAAATGC
1 CTTCGGGACTTAACCCGGTTTTAGTAACTCGCAC-AAATGC
* * * *
41749772 CTTCGGGACTTAACCCAGTTTTAGTCACTTAGCACAAAAGC
1 CTTCGGGACTTAACCCGGTTTTAGTAAC-TCGCACAAATGC
*
41749813 CTTCGGGACTTAGCCCGG
1 CTTCGGGACTTAACCCGG
41749831 ATACCATTCG
Statistics
Matches: 117, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
39 2 0.02
40 59 0.50
41 51 0.44
42 5 0.04
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (40 bp):
CTTCGGGACTTAACCCGGTTTTAGTAACTCGCACAAATGC
Found at i:41749830 original size:82 final size:80
Alignment explanation
Indices: 41749651--41749830 Score: 200
Period size: 81 Copynumber: 2.2 Consensus size: 80
41749641 GCTCGATTGT
* * * * *
41749651 CTTCGGGACATT-GCCCGGTTATAGTGATTCGCACAATTGCCTTCGGGAATTTACCCGGATTTAG
1 CTTCGGGAC-TTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAATTAACCCAGATTTAG
* * *
41749715 TAACTCGCACGAATGC
65 TAACTAGCACAAAAGC
* * * * *
41749731 CTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAAATGCCTTCGGGACTTAACCCAGTTTTAG
1 CTTCGGGACTTAGCCCGGTTATAGTAACTCGCAC-AAATGCCTTCGGGAATTAACCCAGATTTAG
*
41749796 TCACTTAGCACAAAAGC
65 TAAC-TAGCACAAAAGC
41749813 CTTCGGGACTTAGCCCGG
1 CTTCGGGACTTAGCCCGG
41749831 ATACCATTCG
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
79 2 0.02
80 26 0.32
81 28 0.34
82 26 0.32
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAATTAACCCAGATTTAGT
AACTAGCACAAAAGC
Found at i:41753918 original size:34 final size:34
Alignment explanation
Indices: 41753875--41753963 Score: 151
Period size: 34 Copynumber: 2.6 Consensus size: 34
41753865 ATCTTAGTTA
*
41753875 TTAATTGAGTTTCTAGAATAAATGCTTATCTTAG
1 TTAATTGAGTTGCTAGAATAAATGCTTATCTTAG
41753909 TTAATTGAGTTGCTAGAATAAATGCTTATCTTAG
1 TTAATTGAGTTGCTAGAATAAATGCTTATCTTAG
* *
41753943 TTAATTTAGTTGCTGGAATAA
1 TTAATTGAGTTGCTAGAATAA
41753964 TTTATTGCCA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 52 1.00
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.43
Consensus pattern (34 bp):
TTAATTGAGTTGCTAGAATAAATGCTTATCTTAG
Found at i:41754004 original size:19 final size:19
Alignment explanation
Indices: 41753975--41754049 Score: 109
Period size: 19 Copynumber: 3.9 Consensus size: 19
41753965 TTATTGCCAC
41753975 ATGTG-TTTAATGTGTTTA
1 ATGTGTTTTAATGTGTTTA
41753993 ATGAT-TTTTAATGTGTTTA
1 ATG-TGTTTTAATGTGTTTA
*
41754012 ATGTGTGATTAATGTGTTTA
1 ATGTGT-TTTAATGTGTTTA
41754032 ATGTGTTTTAATGTGTTT
1 ATGTGTTTTAATGTGTTT
41754050 GTTAAATGAA
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
18 4 0.08
19 29 0.57
20 18 0.35
ACGTcount: A:0.23, C:0.00, G:0.21, T:0.56
Consensus pattern (19 bp):
ATGTGTTTTAATGTGTTTA
Found at i:41754023 original size:11 final size:9
Alignment explanation
Indices: 41753975--41754049 Score: 105
Period size: 9 Copynumber: 7.9 Consensus size: 9
41753965 TTATTGCCAC
41753975 ATGTGTTTA
1 ATGTGTTTA
41753984 ATGTGTTTA
1 ATGTGTTTA
*
41753993 ATGATTTTTA
1 ATG-TGTTTA
41754003 ATGTGTTTA
1 ATGTGTTTA
41754012 ATGTGTGATTA
1 ATGTGT--TTA
41754023 ATGTGTTTA
1 ATGTGTTTA
41754032 ATGTGTTTTA
1 ATGTG-TTTA
41754042 ATGTGTTT
1 ATGTGTTT
41754050 GTTAAATGAA
Statistics
Matches: 60, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
9 34 0.57
10 17 0.28
11 9 0.15
ACGTcount: A:0.23, C:0.00, G:0.21, T:0.56
Consensus pattern (9 bp):
ATGTGTTTA
Found at i:41755389 original size:27 final size:26
Alignment explanation
Indices: 41755342--41755392 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
41755332 CGAGGCTGCC
*
41755342 AGATATTGTGACGAAGTCACCAGAAT
1 AGATATTGTGACGAAGCCACCAGAAT
* *
41755368 AGATATATGTGGCGAGGCCACCAGA
1 AGATAT-TGTGACGAAGCCACCAGA
41755393 TTGCAGCGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (26 bp):
AGATATTGTGACGAAGCCACCAGAAT
Found at i:41756019 original size:26 final size:27
Alignment explanation
Indices: 41755990--41756043 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
41755980 TCACACAAGT
*
41755990 TAGTCATTT-ACGCACGAGGGGCAAAA
1 TAGTCATTTAACACACGAGGGGCAAAA
* *
41756016 TAGTCATTTAACACCCTAGGGGCAAAA
1 TAGTCATTTAACACACGAGGGGCAAAA
41756043 T
1 T
41756044 GGTAATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.22
Consensus pattern (27 bp):
TAGTCATTTAACACACGAGGGGCAAAA
Found at i:41756074 original size:27 final size:27
Alignment explanation
Indices: 41756044--41756216 Score: 186
Period size: 27 Copynumber: 6.4 Consensus size: 27
41756034 GGGGCAAAAT
* * *
41756044 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
41756071 GGTAATTCTACCCTA-TAGCGGTATTTT
1 GGTAATTCTACCCTACAAG-GGTATTTC
* *
41756098 AGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
41756125 GGTAATTCTATCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
** * *
41756152 AATAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
41756179 GGTAATTCTACCTTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
41756206 GATAATTCTAC
1 GGTAATTCTAC
41756217 AACTTATCCA
Statistics
Matches: 122, Mismatches: 22, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
26 2 0.02
27 118 0.97
28 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.36
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:41756116 original size:54 final size:54
Alignment explanation
Indices: 41756048--41756216 Score: 214
Period size: 54 Copynumber: 3.1 Consensus size: 54
41756038 CAAAATGGTA
* * * * * *
41756048 ATTT-TACCCCACAAGGGTATCTCGGTAATTCTACCCTATAGCGGTATTTTAGT
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAAT
*
41756101 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTATCCTACAGGGGTATTTCAAT
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAAT
* * * * *
41756155 AATTCTACCCTATAGGGGTATTTCGGTAATTCTACCTTACAGGGGTATTTCGAT
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAAT
*
41756209 AATTCTAC
1 ATTTCTAC
41756217 AACTTATCCA
Statistics
Matches: 102, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
53 4 0.04
54 98 0.96
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (54 bp):
ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAAT
Found at i:41762863 original size:2 final size:2
Alignment explanation
Indices: 41762856--41762887 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
41762846 ACCAGAACAG
41762856 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41762888 GTGGCAAAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41763653 original size:27 final size:27
Alignment explanation
Indices: 41763623--41763822 Score: 274
Period size: 27 Copynumber: 7.4 Consensus size: 27
41763613 AGGGCAAAAT
* * *
41763623 GGTAATTTTACCCTACAAGGGTATCTC
1 GGTAATTCTACCCTACAGGGGTATTTC
41763650 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * * *
41763677 AGTATTTCTACCTTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
41763704 GGTAATTCTATCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
41763731 GGTAATTCTATCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
**
41763758 AATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
41763785 AGTAATTCTACCTTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
41763812 GGTAATTCTAC
1 GGTAATTCTAC
41763823 AACTTATCCT
Statistics
Matches: 155, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 155 1.00
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:41766082 original size:43 final size:43
Alignment explanation
Indices: 41766001--41766085 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
41765991 ATCGGTATCT
* *** *
41766001 TATTTGATTTCATGTAAGACCTTGTCTGGGATAGTGGCATTGA
1 TATTTGATTACATGTAAGACCACATCTGAGATAGTGGCATTGA
41766044 TATTTGATTACATGTAAGACCACATCTGAGAT-GTTGGCATTG
1 TATTTGATTACATGTAAGACCACATCTGAGATAG-TGGCATTG
41766086 TACGAGCTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 1 0.03
43 35 0.97
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.38
Consensus pattern (43 bp):
TATTTGATTACATGTAAGACCACATCTGAGATAGTGGCATTGA
Found at i:41771248 original size:34 final size:34
Alignment explanation
Indices: 41771205--41771293 Score: 160
Period size: 34 Copynumber: 2.6 Consensus size: 34
41771195 ATCTTAGTTA
41771205 TTAATTGAGTTGCTAGAATAAATGCTTATCTTAG
1 TTAATTGAGTTGCTAGAATAAATGCTTATCTTAG
41771239 TTAATTGAGTTGCTAGAATAAATGCTTATCTTAG
1 TTAATTGAGTTGCTAGAATAAATGCTTATCTTAG
* *
41771273 TTAATTTAGTTGCTGGAATAA
1 TTAATTGAGTTGCTAGAATAA
41771294 TTTATTGTTA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 53 1.00
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.42
Consensus pattern (34 bp):
TTAATTGAGTTGCTAGAATAAATGCTTATCTTAG
Found at i:41771317 original size:9 final size:9
Alignment explanation
Indices: 41771305--41771366 Score: 70
Period size: 9 Copynumber: 6.4 Consensus size: 9
41771295 TTATTGTTAC
41771305 ATGTGTTTA
1 ATGTGTTTA
41771314 ATGTGTTTA
1 ATGTGTTTA
*
41771323 ATGTTTTTTA
1 ATG-TGTTTA
41771333 ATGTGTGATTA
1 ATGTGT--TTA
41771344 ATGTGTTTA
1 ATGTGTTTA
*
41771353 ATTTGTTTTA
1 ATGTG-TTTA
41771363 ATGT
1 ATGT
41771367 CTTTGTTAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
9 21 0.47
10 15 0.33
11 9 0.20
ACGTcount: A:0.23, C:0.00, G:0.19, T:0.58
Consensus pattern (9 bp):
ATGTGTTTA
Found at i:41771334 original size:19 final size:19
Alignment explanation
Indices: 41771308--41771366 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 19
41771298 TTGTTACATG
41771308 TGTTTAATGTGTTTAATGT
1 TGTTTAATGTGTTTAATGT
*
41771327 TTTTTAATGTGTGATTAATG-
1 TGTTTAATGTGT--TTAATGT
*
41771347 TGTTTAATTTGTTTTAATGT
1 TGTTTAATGTG-TTTAATGT
41771367 CTTTGTTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 17 0.52
20 9 0.27
21 7 0.21
ACGTcount: A:0.22, C:0.00, G:0.19, T:0.59
Consensus pattern (19 bp):
TGTTTAATGTGTTTAATGT
Found at i:41771346 original size:30 final size:30
Alignment explanation
Indices: 41771306--41771366 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
41771296 TATTGTTACA
*
41771306 TGTGTTTAATGTGTTTAATGTT-TTTTAATG
1 TGTGATTAATGTGTTTAAT-TTGTTTTAATG
41771336 TGTGATTAATGTGTTTAATTTGTTTTAATG
1 TGTGATTAATGTGTTTAATTTGTTTTAATG
41771366 T
1 T
41771367 CTTTGTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 2 0.07
30 27 0.93
ACGTcount: A:0.21, C:0.00, G:0.20, T:0.59
Consensus pattern (30 bp):
TGTGATTAATGTGTTTAATTTGTTTTAATG
Found at i:41775094 original size:40 final size:40
Alignment explanation
Indices: 41775050--41775131 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
41775040 ATGGCATGTA
*
41775050 TAACTAGATTCACATTCGCTTCCTTAGTCCTAGAATCGAC
1 TAACTAGATTCACATTCACTTCCTTAGTCCTAGAATCGAC
41775090 TAACTAGATTCACATTCACTTCCTTAGTCCTAGAATCGAC
1 TAACTAGATTCACATTCACTTCCTTAGTCCTAGAATCGAC
41775130 TA
1 TA
41775132 GATTGTAGCT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.33
Consensus pattern (40 bp):
TAACTAGATTCACATTCACTTCCTTAGTCCTAGAATCGAC
Found at i:41782191 original size:16 final size:18
Alignment explanation
Indices: 41782170--41782202 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
41782160 TTTGGTGCAT
41782170 TAAAAGC-TCG-TACCAG
1 TAAAAGCATCGATACCAG
41782186 TAAAAGCATCGATACCA
1 TAAAAGCATCGATACCA
41782203 TGTATGACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.42, C:0.24, G:0.15, T:0.18
Consensus pattern (18 bp):
TAAAAGCATCGATACCAG
Found at i:41788772 original size:35 final size:35
Alignment explanation
Indices: 41788732--41788851 Score: 134
Period size: 35 Copynumber: 3.4 Consensus size: 35
41788722 AGGTATGTAT
* * * *
41788732 ATATGTGATGTTATATCTAACTTGTATGTTTGGCC
1 ATATGTGATGATATATCTAACTTGTATATTCGACC
* * *
41788767 ATATGTGATGATATAT-TGAATTTGTAAATTCGACT
1 ATATGTGATGATATATCT-AACTTGTATATTCGACC
* * *
41788802 ACATGTGATGTTCTATCTAACTTGTATATTCGACC
1 ATATGTGATGATATATCTAACTTGTATATTCGACC
41788837 ATATGTGATGATATA
1 ATATGTGATGATATA
41788852 ATGAACCTTG
Statistics
Matches: 67, Mismatches: 16, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
34 1 0.01
35 65 0.97
36 1 0.01
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.42
Consensus pattern (35 bp):
ATATGTGATGATATATCTAACTTGTATATTCGACC
Found at i:41793515 original size:6 final size:6
Alignment explanation
Indices: 41793506--41793630 Score: 94
Period size: 6 Copynumber: 20.3 Consensus size: 6
41793496 TATTAGAACT
* * * *
41793506 AGAATC AGAATC AAAATC AGAATC AG-GTGAC AAAATC AGAATC AGTATC
1 AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC AGAATC
* * *
41793555 AGGTAAT- AGAATC AAAATC AGAATC AGTATC AGGTAA-C AGAATC AAAATC
1 A-G-AATC AGAATC AGAATC AGAATC AGAATC A-G-AATC AGAATC AGAATC
* *
41793605 AGAATC AAAATC AGAATC AGTATC AG
1 AGAATC AGAATC AGAATC AGAATC AG
41793631 GTAACAGAAT
Statistics
Matches: 93, Mismatches: 17, Indels: 18
0.73 0.13 0.14
Matches are distributed among these distances:
5 6 0.06
6 76 0.82
7 7 0.08
8 4 0.04
ACGTcount: A:0.50, C:0.15, G:0.16, T:0.19
Consensus pattern (6 bp):
AGAATC
Found at i:41793542 original size:25 final size:25
Alignment explanation
Indices: 41793514--41793653 Score: 99
Period size: 25 Copynumber: 5.6 Consensus size: 25
41793504 CTAGAATCAG
*
41793514 AATCAAAATCAGAATCAGGTGACAA
1 AATCAAAATCAGAATCAGGTAACAA
* * * *
41793539 AATCAGAATCAGTATCAGGTAATAG
1 AATCAAAATCAGAATCAGGTAACAA
* *
41793564 AATCAAAATCAGAATCA-GTATCAGGT
1 AATCAAAATCAGAATCAGGTAACA--A
* *
41793590 AA-CAGAATCAAAATCA-G-AATCAA
1 AATCAAAATCAGAATCAGGTAA-CAA
* * *
41793613 AATCAGAATCAGTATCAGGTAACAG
1 AATCAAAATCAGAATCAGGTAACAA
*
41793638 AATAAAAAATCAGAAT
1 AAT-CAAAATCAGAAT
41793654 GTGAATGCAA
Statistics
Matches: 88, Mismatches: 20, Indels: 13
0.73 0.17 0.11
Matches are distributed among these distances:
23 2 0.02
24 17 0.19
25 56 0.64
26 13 0.15
ACGTcount: A:0.51, C:0.14, G:0.15, T:0.19
Consensus pattern (25 bp):
AATCAAAATCAGAATCAGGTAACAA
Found at i:41793544 original size:31 final size:32
Alignment explanation
Indices: 41793536--41793618 Score: 116
Period size: 31 Copynumber: 2.7 Consensus size: 32
41793526 AATCAGGTGA
**
41793536 CAAAATCAGAATCAGTATCAGGTAAT-AGAAT
1 CAAAATCAGAATCAAAATCAGGTAATCAGAAT
**
41793567 CAAAATCAGAATCAGTATCAGGTAA-CAGAAT
1 CAAAATCAGAATCAAAATCAGGTAATCAGAAT
41793598 CAAAATCAGAATCAAAATCAG
1 CAAAATCAGAATCAAAATCAG
41793619 AATCAGTATC
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.51, C:0.16, G:0.14, T:0.19
Consensus pattern (32 bp):
CAAAATCAGAATCAAAATCAGGTAATCAGAAT
Found at i:41793610 original size:43 final size:44
Alignment explanation
Indices: 41793562--41793653 Score: 168
Period size: 43 Copynumber: 2.1 Consensus size: 44
41793552 ATCAGGTAAT
*
41793562 AGAATCAAAATCAGAATCAGTATCAGGTAACAGAAT-CAAAATC
1 AGAATCAAAATCAGAATCAGTATCAGGTAACAGAATAAAAAATC
41793605 AGAATCAAAATCAGAATCAGTATCAGGTAACAGAATAAAAAATC
1 AGAATCAAAATCAGAATCAGTATCAGGTAACAGAATAAAAAATC
41793649 AGAAT
1 AGAAT
41793654 GTGAATGCAA
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
43 36 0.77
44 11 0.23
ACGTcount: A:0.53, C:0.14, G:0.14, T:0.18
Consensus pattern (44 bp):
AGAATCAAAATCAGAATCAGTATCAGGTAACAGAATAAAAAATC
Found at i:41793853 original size:26 final size:27
Alignment explanation
Indices: 41793790--41793863 Score: 105
Period size: 27 Copynumber: 2.8 Consensus size: 27
41793780 ACTCAGTTAT
* *
41793790 CAGATATTGTGACAGAGTCACCAGATA
1 CAGATATTGTGGCAGAGCCACCAGATA
41793817 CAGATATTGTGGCAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
* *
41793843 CAGATAATGTGGCAAAGCCAC
1 CAGATATTGTGGCAGAGCCAC
41793864 TTAACAGAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
26 20 0.47
27 23 0.53
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:41794050 original size:22 final size:23
Alignment explanation
Indices: 41794022--41794083 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 23
41794012 GCAAATACGT
*
41794022 TTGGCACACAGCCATAAT-TAGA
1 TTGGCACAAAGCCATAATGTAGA
* *
41794044 TTGGCACAGAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAATGTAGA
*
41794066 TTGACACAAAGCCATAAT
1 TTGGCACAAAGCCATAAT
41794084 CAGAAGGCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 2 0.06
22 30 0.88
23 2 0.06
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (23 bp):
TTGGCACAAAGCCATAATGTAGA
Found at i:41796224 original size:40 final size:40
Alignment explanation
Indices: 41796130--41796349 Score: 238
Period size: 40 Copynumber: 5.5 Consensus size: 40
41796120 TATTCGAATG
*
41796130 ATATCCGGGCTAAG-TCCCGAAGGCTTTTGTGCTAGGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTA-GTGACT
* * * *
41796171 ATAACCGGACTAAGATCCGAAGGCATTCGTGCGAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAG-TGACT
* *
41796211 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
*
41796251 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTAGTGACT
* * * *
41796291 ATATCCGGGCTAAGACCCGAAGGC-CTTGTGCAAGT-AGTT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGA-CT
41796330 ATATCC-GGCTAA-ATCCGAAG
1 ATATCCGGGCTAAGATCCGAAG
41796350 ATTACTTGAG
Statistics
Matches: 153, Mismatches: 20, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
37 7 0.05
38 7 0.05
39 16 0.10
40 93 0.61
41 29 0.19
42 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
Found at i:41804257 original size:40 final size:40
Alignment explanation
Indices: 41804163--41804382 Score: 238
Period size: 40 Copynumber: 5.5 Consensus size: 40
41804153 TATTCGAATG
*
41804163 ATATCCGGGCTAAG-TCCCGAAGGCTTTTGTGCTAGGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTA-GTGACT
* * * *
41804204 ATAACCGGACTAAGATCCGAAGGCATTCGTGCGAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAG-TGACT
* *
41804244 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
*
41804284 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTAGTGACT
* * * *
41804324 ATATCCGGGCTAAGACCCGAAGGC-CTTGTGCAAGT-AGTT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGA-CT
41804363 ATATCC-GGCTAA-ATCCGAAG
1 ATATCCGGGCTAAGATCCGAAG
41804383 ATTACTTGAG
Statistics
Matches: 153, Mismatches: 20, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
37 7 0.05
38 7 0.05
39 16 0.10
40 93 0.61
41 29 0.19
42 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
Found at i:41812263 original size:40 final size:40
Alignment explanation
Indices: 41812169--41812388 Score: 238
Period size: 40 Copynumber: 5.5 Consensus size: 40
41812159 TATTCGAATG
*
41812169 ATATCCGGGCTAAG-TCCCGAAGGCTTTTGTGCTAGGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTA-GTGACT
* * * *
41812210 ATAACCGGACTAAGATCCGAAGGCATTCGTGCGAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAG-TGACT
* *
41812250 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
*
41812290 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTAGTGACT
* * * *
41812330 ATATCCGGGCTAAGACCCGAAGGC-CTTGTGCAAGT-AGTT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGA-CT
41812369 ATATCC-GGCTAA-ATCCGAAG
1 ATATCCGGGCTAAGATCCGAAG
41812389 ATTACTTGAG
Statistics
Matches: 153, Mismatches: 20, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
37 7 0.05
38 7 0.05
39 16 0.10
40 93 0.61
41 29 0.19
42 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
Found at i:41813897 original size:27 final size:27
Alignment explanation
Indices: 41813858--41814408 Score: 732
Period size: 27 Copynumber: 20.5 Consensus size: 27
41813848 ACCCCACAAT
* * * * *
41813858 GTATCTCGCTAATTCCATCCTATAGGG
1 GTATTTCGGTAATTCTACCCTACAGGG
**
41813885 GTATTTTAGTAATTCTACCCTACAGGG
1 GTATTTCGGTAATTCTACCCTACAGGG
* * *
41813912 GTGTTTTGGTAATTCTACCCTATAGGG
1 GTATTTCGGTAATTCTACCCTACAGGG
* *
41813939 GTATTGCGATAATTCTACCCTACAGGG
1 GTATTTCGGTAATTCTACCCTACAGGG
41813966 GTATTTCGGTAATTCTACCCTACA-GG
1 GTATTTCGGTAATTCTACCCTACAGGG
* * *
41813992 GTATTGCGGTAATTCTTCCCTATAGGG
1 GTATTTCGGTAATTCTACCCTACAGGG
41814019 GTATTTCGGTAATTCTACCCTACAGGG
1 GTATTTCGGTAATTCTACCCTACAGGG
* *
41814046 GTATCTCGGTAATTCTACCCTACAAGG
1 GTATTTCGGTAATTCTACCCTACAGGG
* * * *
41814073 GTATTCCGATTATTCTACCCTACAAGG
1 GTATTTCGGTAATTCTACCCTACAGGG
*
41814100 GTATTTCGGTAATTCTACCCTACATGG
1 GTATTTCGGTAATTCTACCCTACAGGG
* * *
41814127 GTATTGCGATAATTCTACCTTACAGGG
1 GTATTTCGGTAATTCTACCCTACAGGG
*
41814154 GTATTTCGGTAATTCTACCCTACATGG
1 GTATTTCGGTAATTCTACCCTACAGGG
*
41814181 GTATTTTGGTAATTCTACCCTACAGGG
1 GTATTTCGGTAATTCTACCCTACAGGG
*
41814208 GTATTTCGGTAAGTCTACCCTACAGGG
1 GTATTTCGGTAATTCTACCCTACAGGG
*
41814235 GTATTGCGGTAATTCTA-CCTACAGGG
1 GTATTTCGGTAATTCTACCCTACAGGG
41814261 GTATTTCAGG-AATTCTACCCTACAGGG
1 GTATTTC-GGTAATTCTACCCTACAGGG
* * *
41814288 TTATTGCGATAATTCTACCCTACA-GG
1 GTATTTCGGTAATTCTACCCTACAGGG
* * *
41814314 GTATTGCGATAATTCTACCCTACAAGG
1 GTATTTCGGTAATTCTACCCTACAGGG
41814341 GTATTTCGGTAATTCTACCCTACAGGG
1 GTATTTCGGTAATTCTACCCTACAGGG
*
41814368 GTATTGCGGTAATTCTACCCTACAGGG
1 GTATTTCGGTAATTCTACCCTACAGGG
*
41814395 GTATTTCGATAATT
1 GTATTTCGGTAATT
41814409 TTACAAACCA
Statistics
Matches: 461, Mismatches: 58, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
26 71 0.15
27 390 0.85
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (27 bp):
GTATTTCGGTAATTCTACCCTACAGGG
Found at i:41816407 original size:6 final size:6
Alignment explanation
Indices: 41816389--41816479 Score: 53
Period size: 6 Copynumber: 14.8 Consensus size: 6
41816379 AAGAAACATT
* * *
41816389 ATCAGA A-CTAGA ATCAGA ATCAAA ATCAG- GTGACAGA ATTAGA ATCAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA ATCAGA
* * * *
41816438 ATCAGT ATCAGGTA AT-AGA ATCAAA ATCAAA ATCAGT ATCAG
1 ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAGA ATCAG
41816480 GTAACAGAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
5 5 0.08
6 52 0.79
7 6 0.09
8 3 0.05
ACGTcount: A:0.48, C:0.14, G:0.16, T:0.21
Consensus pattern (6 bp):
ATCAGA
Found at i:41816432 original size:25 final size:24
Alignment explanation
Indices: 41816398--41816466 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 24
41816388 TATCAGAACT
*
41816398 AGAATCAGAATCAAAATCAGGTGA-C
1 AGAATTAGAATCAAAATCA-GT-ATC
*
41816423 AGAATTAGAATCAGAATCAGTATC
1 AGAATTAGAATCAAAATCAGTATC
41816447 AGGTAA-TAGAATCAAAATCA
1 A-G-AATTAGAATCAAAATCA
41816467 AAATCAGTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
23 1 0.03
24 4 0.11
25 31 0.82
26 2 0.05
ACGTcount: A:0.49, C:0.13, G:0.17, T:0.20
Consensus pattern (24 bp):
AGAATTAGAATCAAAATCAGTATC
Found at i:41816432 original size:31 final size:31
Alignment explanation
Indices: 41816391--41816489 Score: 126
Period size: 31 Copynumber: 3.2 Consensus size: 31
41816381 GAAACATTAT
* ** *
41816391 CAGAACTAGAATCAGAATCAAAATCAGGTGA
1 CAGAATTAGAATCAGAATCAGTATCAGGTAA
41816422 CAGAATTAGAATCAGAATCAGTATCAGGTAA
1 CAGAATTAGAATCAGAATCAGTATCAGGTAA
* * * *
41816453 TAGAATCAAAATCAAAATCAGTATCAGGTAA
1 CAGAATTAGAATCAGAATCAGTATCAGGTAA
41816484 CAGAAT
1 CAGAAT
41816490 AAAAAATCAG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 59 1.00
ACGTcount: A:0.48, C:0.14, G:0.17, T:0.20
Consensus pattern (31 bp):
CAGAATTAGAATCAGAATCAGTATCAGGTAA
Found at i:41816681 original size:27 final size:26
Alignment explanation
Indices: 41816646--41816739 Score: 107
Period size: 27 Copynumber: 3.5 Consensus size: 26
41816636 TATCAAATAT
* * *
41816646 TGTGACAGAGTCACCAGATACAGATAT
1 TGTGGCAGAGCCACCAGA-ACAGATAA
*
41816673 TGTGGCAGAGCCACCAGAACAAATAA
1 TGTGGCAGAGCCACCAGAACAGATAA
* *
41816699 TGTGGCAAAGCCAACTAGAACAGATAA
1 TGTGGCAGAGCC-ACCAGAACAGATAA
*
41816726 TGTGGCAAAGCCAC
1 TGTGGCAGAGCCAC
41816740 TTAACAGAAT
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
26 19 0.32
27 40 0.68
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (26 bp):
TGTGGCAGAGCCACCAGAACAGATAA
Found at i:41816923 original size:22 final size:21
Alignment explanation
Indices: 41816898--41816962 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
41816888 GCAAATACGT
41816898 TTGGCACACAACCATAATCAGG
1 TTGGCACA-AACCATAATCAGG
* *
41816920 TTGGCACAGAGCCAT-ATGTAGG
1 TTGGCACA-AACCATAAT-CAGG
*
41816942 TTGACACAAAGCCATAATCAG
1 TTGGCACAAA-CCATAATCAG
41816963 AAGGCTTTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
21 3 0.09
22 29 0.85
23 2 0.06
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (21 bp):
TTGGCACAAACCATAATCAGG
Found at i:41817454 original size:27 final size:27
Alignment explanation
Indices: 41817389--41817771 Score: 441
Period size: 27 Copynumber: 14.3 Consensus size: 27
41817379 GAGGCAAAAG
* * * *
41817389 GGTAATTTTACCCCACA-AGGTATCTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
41817415 GGTATTTCCACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
*
41817442 AGTAATTCTACCCTACA-GGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
41817468 GGTAATTATACCCTACAGGGTTATTGC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
41817495 GATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
41817522 GGTAATTCTACCCTACTGGGGTAATTC
1 GGTAATTCTACCCTACAGGGGTATTTC
41817549 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
41817576 AGTAATTCTACCCTAGAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
41817603 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
41817630 GATAATTCTACCCTACAGGGGTATTGC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
41817657 GATAATTCTACCCTACAGGGGTATTGC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
41817684 GGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * ** *
41817711 GATAATTTTA-CAAACCAGGGGTATTTT
1 GGTAATTCTACCCTA-CAGGGGTATTTC
* ** *
41817738 GGTAATTTTA-CAAACCAGGGGTATTTT
1 GGTAATTCTACCCTA-CAGGGGTATTTC
41817765 GGTAATT
1 GGTAATT
41817772 TGGTAAACTA
Statistics
Matches: 312, Mismatches: 42, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
26 38 0.12
27 274 0.88
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.34
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:41819104 original size:41 final size:41
Alignment explanation
Indices: 41819028--41819105 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
41819018 ATTGTGATAT
*
41819028 TCGGGCTTTGAGCCTAGCAAGCCTTGTGCTAGTGAATTTGA
1 TCGGGCTTTGAGCCTAGCAAGCCTTGTGCCAGTGAATTTGA
* * *
41819069 TCGGGCTTTGTGCCTAGC-AGGCTTAGTGCCGGTGAAT
1 TCGGGCTTTGAGCCTAGCAAGCCTT-GTGCCAGTGAAT
41819106 AAATATCAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 5 0.16
41 27 0.84
ACGTcount: A:0.17, C:0.21, G:0.32, T:0.31
Consensus pattern (41 bp):
TCGGGCTTTGAGCCTAGCAAGCCTTGTGCCAGTGAATTTGA
Found at i:41819330 original size:35 final size:35
Alignment explanation
Indices: 41819291--41819411 Score: 136
Period size: 35 Copynumber: 3.5 Consensus size: 35
41819281 CAGGTATGTA
* * *
41819291 CATATGTGATGTTATATCTAACTTGTATATTCGAC
1 CATATGTGATGATATATCTAACTTGTATATTTGGC
* * *
41819326 CATATATGATGATATAT-TGAATTTGTAAATTTGGC
1 CATATGTGATGATATATCT-AACTTGTATATTTGGC
* * * *
41819361 TACATGTGATGTTCTATCTAACTTGTATATTTGGC
1 CATATGTGATGATATATCTAACTTGTATATTTGGC
41819396 CATATGTGATGATATA
1 CATATGTGATGATATA
41819412 ATGAACCTTG
Statistics
Matches: 67, Mismatches: 17, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
34 1 0.01
35 65 0.97
36 1 0.01
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.43
Consensus pattern (35 bp):
CATATGTGATGATATATCTAACTTGTATATTTGGC
Found at i:41823294 original size:13 final size:15
Alignment explanation
Indices: 41823276--41823307 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
41823266 TATAAATTAA
41823276 ATATTATT-ATAT-T
1 ATATTATTAATATAT
41823289 ATATTATTAATATAT
1 ATATTATTAATATAT
41823304 ATAT
1 ATAT
41823308 ATATGAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 4 0.24
15 5 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATATTATTAATATAT
Found at i:41823886 original size:24 final size:23
Alignment explanation
Indices: 41823854--41823898 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
41823844 GTGATGAAAT
*
41823854 AAATATGAATATGTGATTATTGTG
1 AAATATGAATATATG-TTATTGTG
*
41823878 AAATTTGAATATATGTTATTG
1 AAATATGAATATATGTTATTG
41823899 AAAATGTAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (23 bp):
AAATATGAATATATGTTATTGTG
Found at i:41828011 original size:27 final size:27
Alignment explanation
Indices: 41827942--41828013 Score: 117
Period size: 27 Copynumber: 2.7 Consensus size: 27
41827932 AAAATGTCAA
* * *
41827942 AAAAGAATGGCCTTTATGATGTATTGC
1 AAAAGAATAGCCTTTGTGATGTATTAC
41827969 AAAAGAATAGCCTTTGTGATGTATTAC
1 AAAAGAATAGCCTTTGTGATGTATTAC
41827996 AAAAGAATAGCCTTTGTG
1 AAAAGAATAGCCTTTGTG
41828014 GAAAAGTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (27 bp):
AAAAGAATAGCCTTTGTGATGTATTAC
Found at i:41828029 original size:54 final size:53
Alignment explanation
Indices: 41827969--41828122 Score: 182
Period size: 54 Copynumber: 2.8 Consensus size: 53
41827959 GATGTATTGC
*
41827969 AAAAGAATAGCCTTTGTGATGTATTACAAAAGAATAGCCTTTGTGGAAAAGTTT
1 AAAAGAATAGCC-TTGTGATGTATTACAAAAGAATAGCCTTTGTGGAAAAGTCT
* *** * * *
41828023 AGAAGAATAGCCCTTGTGGCATATTACAAAAGAGTAGCCTTTATGGCAAAGTCT
1 AAAAGAATAG-CCTTGTGATGTATTACAAAAGAATAGCCTTTGTGGAAAAGTCT
* * *
41828077 AAAAGAATAGGCCTTGAGTTGTATTACGAAAGAATAGCCTTTGTGG
1 AAAAGAATA-GCCTTGTGATGTATTACAAAAGAATAGCCTTTGTGG
41828123 GGAACTCTGG
Statistics
Matches: 82, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
54 79 0.96
55 3 0.04
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (53 bp):
AAAAGAATAGCCTTGTGATGTATTACAAAAGAATAGCCTTTGTGGAAAAGTCT
Found at i:41828055 original size:27 final size:27
Alignment explanation
Indices: 41827963--41828122 Score: 112
Period size: 27 Copynumber: 5.9 Consensus size: 27
41827953 CTTTATGATG
* ***
41827963 TATTGCAAAAGAATAGCCTTTGTGATG
1 TATTACAAAAGAATAGCCTTTGTGGCA
*
41827990 TATTACAAAAGAATAGCCTTTGTGGAA
1 TATTACAAAAGAATAGCCTTTGTGGCA
* * * *
41828017 AAGTT-TAGAAGAATAGCCCTTGTGGCA
1 TA-TTACAAAAGAATAGCCTTTGTGGCA
* *
41828044 TATTACAAAAGAGTAGCCTTTATGGCA
1 TATTACAAAAGAATAGCCTTTGTGGCA
* * * *
41828071 AAGT-CTAAAAGAATAGGCCTTGAGTTG--
1 TATTAC-AAAAGAATA-GCCTT-TGTGGCA
*
41828098 TATTACGAAAGAATAGCCTTTGTGG
1 TATTACAAAAGAATAGCCTTTGTGG
41828123 GGAACTCTGG
Statistics
Matches: 101, Mismatches: 26, Indels: 14
0.72 0.18 0.10
Matches are distributed among these distances:
25 3 0.03
26 8 0.08
27 80 0.79
28 8 0.08
29 2 0.02
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (27 bp):
TATTACAAAAGAATAGCCTTTGTGGCA
Found at i:41834817 original size:19 final size:19
Alignment explanation
Indices: 41834793--41834833 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
41834783 TTGATGATGG
41834793 AGAATGAATAATTGTTAAT
1 AGAATGAATAATTGTTAAT
41834812 AGAATGAATAATTGTTAAT
1 AGAATGAATAATTGTTAAT
41834831 AGA
1 AGA
41834834 TTTTAATGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.34
Consensus pattern (19 bp):
AGAATGAATAATTGTTAAT
Found at i:41837198 original size:47 final size:47
Alignment explanation
Indices: 41837147--41837495 Score: 520
Period size: 47 Copynumber: 7.4 Consensus size: 47
41837137 CCCTTCGGGA
* * * * * *
41837147 CTTATCACATTTAAACACTTTCACATCCATAACATTGGCCATTCGGC
1 CTTATCACATATACACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
41837194 CTTATCACATATATACACCTTCACATCCATCACATCGGCCATTAGGT
1 CTTATCACATATACACACTTTCACATTCATCACATCGGCCATTAGGC
* * * * * *
41837241 CTTATCTCATATATACACCTTCACATTCATCACGTTGGCCATTCGGC
1 CTTATCACATATACACACTTTCACATTCATCACATCGGCCATTAGGC
*
41837288 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATACACACTTTCACATTCATCACATCGGCCATTAGGC
41837335 CTTATCACATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATACACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41837382 CTTATCACATATACACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATACACACTTTCACATTCATCACATCGGCCATTAGGC
41837429 CTTATCACATATA-ACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATACACACTTTCACATTCATCACATCGGCCATTAGGC
41837475 CTTATCACATATACACACTTT
1 CTTATCACATATACACACTTT
41837496 GTACATCAAT
Statistics
Matches: 278, Mismatches: 23, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
46 44 0.16
47 234 0.84
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATACACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:41837344 original size:22 final size:22
Alignment explanation
Indices: 41837316--41837391 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
41837306 TTTCACATTC
41837316 ATCACATCGGCCATTAGGCCTT
1 ATCACATCGGCCATTAGGCCTT
*** *** *
41837338 ATCACATATACACACTTTCACATT
1 ATCACATCGGC-CA-TTAGGCCTT
41837362 CATCACATCGGCCATTAGGCCTT
1 -ATCACATCGGCCATTAGGCCTT
41837385 ATCACAT
1 ATCACAT
41837392 ATACACACTT
Statistics
Matches: 37, Mismatches: 14, Indels: 6
0.65 0.25 0.11
Matches are distributed among these distances:
22 15 0.41
23 7 0.19
24 7 0.19
25 8 0.22
ACGTcount: A:0.29, C:0.32, G:0.11, T:0.29
Consensus pattern (22 bp):
ATCACATCGGCCATTAGGCCTT
Found at i:41842378 original size:30 final size:30
Alignment explanation
Indices: 41842323--41842485 Score: 249
Period size: 30 Copynumber: 5.5 Consensus size: 30
41842313 ATAGTGAATC
41842323 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
41842352 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
41842382 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
*
41842412 CGCACACTTAGTGCTATAT-ATTTTCAGTT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
* * * * *
41842441 CGCACACTTAGTGCTGTACAATTTTTAAACC
1 CGCACACTTAGTGCTATATAA-TTTTCAGCT
41842472 CGCACACTTAGTGC
1 CGCACACTTAGTGC
41842486 CAATCTTGTC
Statistics
Matches: 124, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
29 45 0.36
30 60 0.48
31 19 0.15
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.36
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAGCT
Found at i:41846612 original size:39 final size:39
Alignment explanation
Indices: 41846558--41846757 Score: 301
Period size: 39 Copynumber: 5.1 Consensus size: 39
41846548 TGTATGAATA
* *
41846558 TGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAATG
1 TGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAATTG
*
41846597 TGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAATTG
1 TGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAATTG
* *
41846636 TGCGAGTTATGATATCCGGGCTAAGCCTGAAGGCAATTG
1 TGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAATTG
*
41846675 TGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAATTG
1 TGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAATTG
* * * *
41846714 TGCGGGTTGTGATACCCGGGTTAAGTCCCGAAGGCATTTG
1 TGCGAGTTGTGATATCCGGGCTAAG-CCCGAAGGCAATTG
41846754 TGCG
1 TGCG
41846758 GGTTACCACA
Statistics
Matches: 150, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 133 0.89
40 17 0.11
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.24
Consensus pattern (39 bp):
TGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAATTG
Found at i:41853722 original size:47 final size:47
Alignment explanation
Indices: 41853669--41853798 Score: 190
Period size: 47 Copynumber: 2.8 Consensus size: 47
41853659 GTGCGAATAA
* * *
41853669 TACCTTGATTTGGCTACGGGCCATTGTATAGGTATTC-AGAGATGAGT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCTAG-GATAAGT
* *
41853716 TACCTTGATTTGGCTATGGGTCATGGTATAGGTACTCTAGGATAAGT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCTAGGATAAGT
*
41853763 TACCTTGATTTGGCTACGGGCTATGGTATAGGTACT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACT
41853799 TATCGATTGT
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
47 72 0.97
48 2 0.03
ACGTcount: A:0.22, C:0.15, G:0.28, T:0.35
Consensus pattern (47 bp):
TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCTAGGATAAGT
Found at i:41855868 original size:22 final size:22
Alignment explanation
Indices: 41855824--41855873 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
41855814 GTGGTTTAAT
* *
41855824 GGTGGTGATATGTTAGTTTTTG
1 GGTGGTGATATGATAGTTGTTG
*
41855846 GGTGGTGATATGATGGTTGTTG
1 GGTGGTGATATGATAGTTGTTG
41855868 GGTGGT
1 GGTGGT
41855874 ATTTCGGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.12, C:0.00, G:0.44, T:0.44
Consensus pattern (22 bp):
GGTGGTGATATGATAGTTGTTG
Found at i:41858741 original size:46 final size:46
Alignment explanation
Indices: 41858673--41858801 Score: 136
Period size: 46 Copynumber: 2.8 Consensus size: 46
41858663 AAAACACACC
*
41858673 AACATATA--TGTGGACGAAGCCACCAAATTTGCAGACAAGCTACTAA
1 AACATATAGTTGTGGAC--AGCCACCAAATTTGCAGACAAGCTACCAA
* ** *
41858719 TACATATAGTTGTGGACAGCCACCAAATTCACAGACAAGCTGCCAA
1 AACATATAGTTGTGGACAGCCACCAAATTTGCAGACAAGCTACCAA
* * *
41858765 AACATGTAGGTTGTGGATAAACCACCAAATTTGCAGA
1 AACATATA-GTTGTGGA-CAGCCACCAAATTTGCAGA
41858802 TTATTACTAC
Statistics
Matches: 68, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
46 38 0.56
47 8 0.12
48 22 0.32
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.21
Consensus pattern (46 bp):
AACATATAGTTGTGGACAGCCACCAAATTTGCAGACAAGCTACCAA
Found at i:41859856 original size:24 final size:24
Alignment explanation
Indices: 41859824--41859873 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
41859814 TCACTTCGAT
41859824 TGGTAAATTTCTAATTATGGGTGC
1 TGGTAAATTTCTAATTATGGGTGC
41859848 TGGTAAATTTCTAATTATGGGTGC
1 TGGTAAATTTCTAATTATGGGTGC
41859872 TG
1 TG
41859874 TGACGCAGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.08, G:0.26, T:0.42
Consensus pattern (24 bp):
TGGTAAATTTCTAATTATGGGTGC
Found at i:41859971 original size:32 final size:32
Alignment explanation
Indices: 41859925--41859991 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
41859915 ACAACTCCTT
*
41859925 TTGCTGATTCGATATTTTCAAAATTGAATCAA
1 TTGCCGATTCGATATTTTCAAAATTGAATCAA
41859957 TTGCCGATTCGATATTTTCAAAATTGAATCAA
1 TTGCCGATTCGATATTTTCAAAATTGAATCAA
41859989 TTG
1 TTG
41859992 TCAAAGATTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (32 bp):
TTGCCGATTCGATATTTTCAAAATTGAATCAA
Found at i:41860129 original size:29 final size:29
Alignment explanation
Indices: 41860087--41860145 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
41860077 ATTTTTTATA
41860087 CTTAAAATTTATTCAATTGTTAATTAAAC
1 CTTAAAATTTATTCAATTGTTAATTAAAC
41860116 CTTAAAATTTATTCAATTGTTAATTAAAC
1 CTTAAAATTTATTCAATTGTTAATTAAAC
41860145 C
1 C
41860146 AATTTTTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.41, C:0.12, G:0.03, T:0.44
Consensus pattern (29 bp):
CTTAAAATTTATTCAATTGTTAATTAAAC
Found at i:41860192 original size:17 final size:17
Alignment explanation
Indices: 41860170--41860206 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
41860160 TTCAATTGGT
41860170 CCATATTGATTCACAAG
1 CCATATTGATTCACAAG
41860187 CCATATTGATTCACAAG
1 CCATATTGATTCACAAG
41860204 CCA
1 CCA
41860207 ACTAATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.35, C:0.27, G:0.11, T:0.27
Consensus pattern (17 bp):
CCATATTGATTCACAAG
Found at i:41860588 original size:10 final size:9
Alignment explanation
Indices: 41860571--41860596 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
41860561 AGTAACCACC
41860571 ATAAAAAAA
1 ATAAAAAAA
41860580 ATAAAAAAA
1 ATAAAAAAA
41860589 ATAAAAAA
1 ATAAAAAA
41860597 TAAAAACCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
ATAAAAAAA
Done.