Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 142 of 190
Found at i:41875162 original size:39 final size:40
Alignment explanation
Indices: 41875022--41875164 Score: 123
Period size: 40 Copynumber: 3.5 Consensus size: 40
41875012 ATCCCGCACT
* * * * *
41875022 CTAAGTGCCTTACATAGCCGAAGCTA-TCTCAATCTCGGACA
1 CTAAGTGCCATAAATAGTCGAAGCTATTCTC-A-GTCGAACA
* *
41875063 CTAAGTGCCATATATATAGTCGAAGCTATTCTCAGTTGCACA
1 CTAAGTGCCATA-A-ATAGTCGAAGCTATTCTCAGTCGAACA
*
41875105 CTAAGTGCCATAAATAGTCGAAGCTA-TCTCGAGTCGAATA
1 CTAAGTGCCATAAATAGTCGAAGCTATTCTC-AGTCGAACA
*
41875145 CT-AGTGCTA-AACATAGTCGA
1 CTAAGTGCCATAA-ATAGTCGA
41875165 TTCATCGTCG
Statistics
Matches: 87, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
38 2 0.02
39 18 0.21
40 21 0.24
41 12 0.14
42 17 0.20
43 13 0.15
44 4 0.05
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (40 bp):
CTAAGTGCCATAAATAGTCGAAGCTATTCTCAGTCGAACA
Found at i:41875184 original size:21 final size:21
Alignment explanation
Indices: 41875154--41875193 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
41875144 ACTAGTGCTA
41875154 AACATAGTCG-ATTCATCGTCG
1 AACATAGTCGTATTC-TCGTCG
*
41875175 AACATGGTCGTATTCTCGT
1 AACATAGTCGTATTCTCGT
41875194 GCATACAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.33
Consensus pattern (21 bp):
AACATAGTCGTATTCTCGTCG
Found at i:41877088 original size:25 final size:27
Alignment explanation
Indices: 41877060--41877109 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
41877050 ATTTGTAAAT
41877060 TAGAAAAATATC-TCA-AGAATTTTTC
1 TAGAAAAATATCTTCAGAGAATTTTTC
* *
41877085 TAGAATAATCTCTTCAGAGAATTTT
1 TAGAAAAATATCTTCAGAGAATTTT
41877110 CTCTCTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 10 0.48
26 3 0.14
27 8 0.38
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (27 bp):
TAGAAAAATATCTTCAGAGAATTTTTC
Found at i:41879132 original size:43 final size:43
Alignment explanation
Indices: 41879056--41879185 Score: 149
Period size: 43 Copynumber: 3.0 Consensus size: 43
41879046 CATAGGACCT
* **
41879056 TCGATATGTGTTTTTGTGTAAGACCACGTCTGGGAC-GTCGGCA
1 TCGATATGTGATTACGTGTAAGACCACGTCTGGGACAGT-GGCA
*
41879099 TCGACT-TGTGCTTACGTGTAAGACC-CTGTCTGGGACAGTGGCA
1 TCGA-TATGTGATTACGTGTAAGACCAC-GTCTGGGACAGTGGCA
* * *
41879142 TTGATATGTGATTACATGTAAGACCACGTCTGGGACATTGGCA
1 TCGATATGTGATTACGTGTAAGACCACGTCTGGGACAGTGGCA
41879185 T
1 T
41879186 TGTACGAGTT
Statistics
Matches: 75, Mismatches: 7, Indels: 10
0.82 0.08 0.11
Matches are distributed among these distances:
42 2 0.03
43 69 0.92
44 4 0.05
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (43 bp):
TCGATATGTGATTACGTGTAAGACCACGTCTGGGACAGTGGCA
Found at i:41880514 original size:15 final size:14
Alignment explanation
Indices: 41880493--41880528 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
41880483 ATAATCTTTA
*
41880493 ATAATTATCTTAAT
1 ATAATTATCCTAAT
41880507 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
41880522 ATAATTA
1 ATAATTA
41880529 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:41884925 original size:19 final size:19
Alignment explanation
Indices: 41884901--41884938 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
41884891 AAAGTTAAAA
41884901 ACAAATTTGATTATGGTGG
1 ACAAATTTGATTATGGTGG
41884920 ACAAATTTGATTATGGTGG
1 ACAAATTTGATTATGGTGG
41884939 GTGGCGATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.26, T:0.37
Consensus pattern (19 bp):
ACAAATTTGATTATGGTGG
Found at i:41888021 original size:21 final size:22
Alignment explanation
Indices: 41887974--41888023 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
41887964 TAAAATAATT
*
41887974 AGAATTAAAATTTTAGGTTACG
1 AGAATTAAAATTTAAGGTTACG
41887996 A-AATTAAAA-TTAAGAG-TACG
1 AGAATTAAAATTTAAG-GTTACG
41888016 AGAATTAA
1 AGAATTAA
41888024 TTTGGTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 9 0.36
21 15 0.60
22 1 0.04
ACGTcount: A:0.50, C:0.04, G:0.16, T:0.30
Consensus pattern (22 bp):
AGAATTAAAATTTAAGGTTACG
Found at i:41893818 original size:8 final size:8
Alignment explanation
Indices: 41893801--41893833 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
41893791 AAGAAAAAAA
*
41893801 ATATAAAT
1 ATATACAT
41893809 ATATACAT
1 ATATACAT
41893817 ATATACAT
1 ATATACAT
41893825 ATATACAT
1 ATATACAT
41893833 A
1 A
41893834 AATTATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (8 bp):
ATATACAT
Found at i:41894589 original size:23 final size:22
Alignment explanation
Indices: 41894545--41894659 Score: 61
Period size: 19 Copynumber: 5.6 Consensus size: 22
41894535 AAAAGGTATC
* *
41894545 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
*
41894566 TACAAAATCATATCTTCTACGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
41894589 TGCATATCATA---TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
* *
41894608 TGCATATCATA---TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
* *
41894627 TGCATATCATA---TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
*
41894646 TACATATCATATCT
1 TACAAATCATATCT
41894660 AAGATTGCAT
Statistics
Matches: 82, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
19 55 0.67
21 3 0.04
22 15 0.18
23 9 0.11
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:41894608 original size:19 final size:19
Alignment explanation
Indices: 41894581--41894672 Score: 166
Period size: 19 Copynumber: 4.8 Consensus size: 19
41894571 AATCATATCT
*
41894581 TCTACGATTGCATATCATA
1 TCTAAGATTGCATATCATA
41894600 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
41894619 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
41894638 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
41894657 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
41894673 CTTGAATATT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 70 1.00
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:41894632 original size:38 final size:38
Alignment explanation
Indices: 41894558--41894672 Score: 167
Period size: 38 Copynumber: 2.9 Consensus size: 38
41894548 AAATTAAATC
* *
41894558 TCTAAGATTACAAAATCATATCTTCTACGATTGCATATCATA
1 TCTAAGATTAC-ATATCATA---TCTAAGATTGCATATCATA
*
41894600 TCTAAGATTGCATATCATATCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
41894638 TCTAAGATTACATATCATATCTAAGATTGCATATC
1 TCTAAGATTACATATCATATCTAAGATTGCATATC
41894673 CTTGAATATT
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
38 52 0.75
41 7 0.10
42 10 0.14
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (38 bp):
TCTAAGATTACATATCATATCTAAGATTGCATATCATA
Found at i:41897353 original size:16 final size:16
Alignment explanation
Indices: 41897329--41897366 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
41897319 TTTGGTTCGC
* *
41897329 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
41897345 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
41897361 TGTAAT
1 TGTAAT
41897367 AGCAAATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:41897409 original size:45 final size:44
Alignment explanation
Indices: 41897345--41897439 Score: 145
Period size: 45 Copynumber: 2.1 Consensus size: 44
41897335 GGATTAGAGG
41897345 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAG-AAATCAACTGTTTGGTTGAA
* ***
41897390 TGTAATGGAATAGAGGTGTAATAGTAATCCTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGAAATCAACTGTTTGGTTGAA
41897434 TGTAAT
1 TGTAAT
41897440 AGAAGTGTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
44 22 0.48
45 24 0.52
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.35
Consensus pattern (44 bp):
TGTAATGGAATAGAGGTGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:41897621 original size:18 final size:17
Alignment explanation
Indices: 41897600--41897634 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
41897590 TTATTATTAA
*
41897600 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
41897618 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
41897635 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:41897698 original size:155 final size:157
Alignment explanation
Indices: 41897487--41897801 Score: 544
Period size: 155 Copynumber: 2.0 Consensus size: 157
41897477 TAGAATACCC
* *
41897487 TTAGCATAAATTTGTTTGGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAAAAACTTGTTTGGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
* *
41897552 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
41897617 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
* *
41897644 TTAGCAAAAACTTGTTTTGGTAAATTA-T-TTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAAAAACTTGTTTGGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
* *
41897707 ATATCAGTAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAT
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
41897772 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
41897799 TTA
1 TTA
41897802 ATATTCTTAC
Statistics
Matches: 150, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
155 126 0.84
156 1 0.01
157 23 0.15
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.47
Consensus pattern (157 bp):
TTAGCAAAAACTTGTTTGGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:41897768 original size:15 final size:15
Alignment explanation
Indices: 41897744--41897785 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
41897734 TTTAAACATA
*
41897744 ATTATTATTAAATAT
1 ATTATAATTAAATAT
41897759 ATTATAATTAAAT-T
1 ATTATAATTAAATAT
*
41897773 A-TATAATTTAATA
1 ATTATAATTAAATA
41897786 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 10 0.42
14 2 0.08
15 12 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:41897873 original size:120 final size:121
Alignment explanation
Indices: 41897733--41898028 Score: 456
Period size: 120 Copynumber: 2.5 Consensus size: 121
41897723 ATTTAATCAT
* *
41897733 ATTTAAACATAATTATTATTAAATATATTATAATTAAATTATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* *
41897798 ATTAATATTCTTACATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAA
66 ATTAATATTCTTACATGAATTTACTCAAATCATAATATATGATACTATAAAAGA-AA
*
41897855 A-TT-AACATAATTATTATTAAATATGTTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* * *
41897918 ATTACTATTCTTATATGAATTTATTCAAATCATAATATATGATACTATAAAAGAAA
66 ATTAATATTCTTACATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
* *
41897974 ATTTGAA-ATAATTAATATTAAATATATT-TAAATTAAAATATATGATTTAATAAAA
1 ATTTGAACATAATTATTATTAAATATATTAT-AATTAAAATATATAATTTAATAAAA
41898029 GTTAAAATAA
Statistics
Matches: 161, Mismatches: 10, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
119 4 0.02
120 152 0.94
121 4 0.02
122 1 0.01
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (121 bp):
ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
ATTAATATTCTTACATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
Found at i:41898172 original size:91 final size:91
Alignment explanation
Indices: 41898046--41898252 Score: 317
Period size: 91 Copynumber: 2.3 Consensus size: 91
41898036 TAATTATAAC
* * * * * *
41898046 TAATAAATTATATTTTATG-ATTTGTATAATTTAAAATAATAAATATTACATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATAAATATTAAATATAATTTAATAAT
41898110 AATATATAATTTCATAAAATTCTTAA
66 AATATATAATTTCATAAAATTCTTAA
*
41898136 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATAAATATTAAATATAATTTAATAAT
*
41898201 GATATATAATTTCATAAAATTCTTAA
66 AATATATAATTTCATAAAATTCTTAA
*
41898227 TAATAAAATGTTCTTATATGAATTTA
1 TAAT-AAATTTTCTTATATGAATTTA
41898253 CTAAAATCAA
Statistics
Matches: 106, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
90 16 0.15
91 70 0.66
92 20 0.19
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (91 bp):
TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATAAATATTAAATATAATTTAATAAT
AATATATAATTTCATAAAATTCTTAA
Found at i:41898212 original size:44 final size:43
Alignment explanation
Indices: 41898070--41898212 Score: 128
Period size: 44 Copynumber: 3.2 Consensus size: 43
41898060 TTATGATTTG
* *
41898070 TATAATTTAAAATAATAAATATTACATATAATTTAATAATAATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
** * * *
41898114 TATAATTTCATAAAATTCTTAATAATAAAT-T-TTCTTATATGAATTTA
1 TATAA-TT--TAAAATAATTAATATTAAATATAAT-TTA-AT-AATATA
*
41898161 TACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
41898205 TATAATTT
1 TATAATTT
41898213 CATAAAATTC
Statistics
Matches: 76, Mismatches: 14, Indels: 18
0.70 0.13 0.17
Matches are distributed among these distances:
43 3 0.04
44 33 0.43
45 7 0.09
46 7 0.09
47 23 0.30
48 3 0.04
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.45
Consensus pattern (43 bp):
TATAATTTAAAATAATTAATATTAAATATAATTTAATAATATA
Found at i:41913257 original size:19 final size:19
Alignment explanation
Indices: 41913233--41913270 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
41913223 AAAGTTAAAA
41913233 ACAAATTTGATTACGGTGG
1 ACAAATTTGATTACGGTGG
*
41913252 ACAAATTTGATTATGGTGG
1 ACAAATTTGATTACGGTGG
41913271 GTGGCGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.08, G:0.26, T:0.34
Consensus pattern (19 bp):
ACAAATTTGATTACGGTGG
Found at i:41921225 original size:17 final size:18
Alignment explanation
Indices: 41921203--41921239 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
41921193 TTTTGGGTTG
41921203 TGTGGG-CCACACGGGCA
1 TGTGGGCCCACACGGGCA
*
41921220 TGTGGGCCCACATGGGCA
1 TGTGGGCCCACACGGGCA
41921238 TG
1 TG
41921240 CAGCATGAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.16, C:0.27, G:0.41, T:0.16
Consensus pattern (18 bp):
TGTGGGCCCACACGGGCA
Found at i:41922561 original size:31 final size:31
Alignment explanation
Indices: 41922523--41922585 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
41922513 CATTCTTCAG
*
41922523 TCAACCTTTCGTAAAGTAGAATAAATTTGAA
1 TCAACCTTTCGTAAAGTAGAATAAATCTGAA
*
41922554 TCAACCTTTGGTAAAGTAGAATAAATCTGAA
1 TCAACCTTTCGTAAAGTAGAATAAATCTGAA
41922585 T
1 T
41922586 GGTTTTCTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (31 bp):
TCAACCTTTCGTAAAGTAGAATAAATCTGAA
Found at i:41923060 original size:11 final size:10
Alignment explanation
Indices: 41923035--41923059 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
41923025 TACTAACATC
41923035 TTTTTCATAG
1 TTTTTCATAG
41923045 TTTTTCATAG
1 TTTTTCATAG
41923055 TTTTT
1 TTTTT
41923060 TATATATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.08, G:0.08, T:0.68
Consensus pattern (10 bp):
TTTTTCATAG
Found at i:41926843 original size:28 final size:27
Alignment explanation
Indices: 41926803--41926899 Score: 133
Period size: 28 Copynumber: 3.5 Consensus size: 27
41926793 AGTATAAAAC
*
41926803 ATACAGTAGCAGTCTGGG-CTTAAGCCCA
1 ATACAGTAACAGT-TGGGCCTT-AGCCCA
*
41926831 ATAAAGTAACAGTTGGGGCCTTAGCCCA
1 ATACAGTAACAGTT-GGGCCTTAGCCCA
41926859 ATACAGTAACAGTGTGGGCCTTAGCCCA
1 ATACAGTAACAGT-TGGGCCTTAGCCCA
41926887 ATACAGTAACAGT
1 ATACAGTAACAGT
41926900 ACAATGCAGT
Statistics
Matches: 63, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
27 1 0.02
28 58 0.92
29 4 0.06
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.22
Consensus pattern (27 bp):
ATACAGTAACAGTTGGGCCTTAGCCCA
Found at i:41927257 original size:27 final size:27
Alignment explanation
Indices: 41927235--41927517 Score: 310
Period size: 27 Copynumber: 10.5 Consensus size: 27
41927225 AGGGGTATAA
*
41927235 CAGTCATTTTACCTTTCGAGGGTATTT
1 CAGTAATTTTACCTTTCGAGGGTATTT
*
41927262 C-GATAATTTTACCCTTCGAGGGTATTT
1 CAG-TAATTTTACCTTTCGAGGGTATTT
* * *
41927289 CAATACTCTTTCCCTTT-GAGGGTATTT
1 CAGTAAT-TTTACCTTTCGAGGGTATTT
*
41927316 CAGTAATTTTACCTTT-TAGGGGTATTT
1 CAGTAATTTTACCTTTCGA-GGGTATTT
41927343 CAGTAATTTTACCTTTCGAGGGTATTT
1 CAGTAATTTTACCTTTCGAGGGTATTT
*
41927370 CAGTAATTTTACCTATCGAGGGTATTT
1 CAGTAATTTTACCTTTCGAGGGTATTT
* *
41927397 TAGTAATTTTACCCTTCGAGGGTATTT
1 CAGTAATTTTACCTTTCGAGGGTATTT
*
41927424 C-GATAATTTTACCCTTCGAGGGTATTT
1 CAG-TAATTTTACCTTTCGAGGGTATTT
* *
41927451 C-GATAATTTTA-CTTATCAACGGTATTT
1 CAG-TAATTTTACCTT-TCGAGGGTATTT
* * *
41927478 TAGTAGTTTTACCCTATCGAGGGTATTT
1 CAGTAATTTTA-CCTTTCGAGGGTATTT
*
41927506 -GGTAATTTTACC
1 CAGTAATTTTACC
41927518 CACGAATCGT
Statistics
Matches: 220, Mismatches: 26, Indels: 21
0.82 0.10 0.08
Matches are distributed among these distances:
26 15 0.07
27 184 0.84
28 19 0.09
29 2 0.01
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (27 bp):
CAGTAATTTTACCTTTCGAGGGTATTT
Found at i:41927362 original size:81 final size:81
Alignment explanation
Indices: 41927235--41927518 Score: 351
Period size: 81 Copynumber: 3.5 Consensus size: 81
41927225 AGGGGTATAA
* *
41927235 CAGTCATTTTACCTTTCGAGGGTATTTCGATAATTTTACCCTTCGAGGGTATTTCAATACTCTTT
1 CAGTAATTTTACCTTTCGAGGGTATTTCGATAATTTTACCCTTCGAGGGTATTTCAATAAT-TTT
* *
41927300 CCCT-TTGAGGGTATTT
65 ACCTATCGAGGGTATTT
* * *
41927316 CAGTAATTTTACCTTT-TAGGGGTATTTC-AGTAATTTTACCTTTCGAGGGTATTTCAGTAATTT
1 CAGTAATTTTACCTTTCGA-GGGTATTTCGA-TAATTTTACCCTTCGAGGGTATTTCAATAATTT
41927379 TACCTATCGAGGGTATTT
64 TACCTATCGAGGGTATTT
* * *
41927397 TAGTAATTTTACCCTTCGAGGGTATTTCGATAATTTTACCCTTCGAGGGTATTTCGATAATTTTA
1 CAGTAATTTTACCTTTCGAGGGTATTTCGATAATTTTACCCTTCGAGGGTATTTCAATAATTTTA
* * *
41927462 CTTATCAACGGTATTT
66 CCTATCGAGGGTATTT
* * * *
41927478 TAGTAGTTTTACCCTATCGAGGGTATTT-GGTAATTTTACCC
1 CAGTAATTTTA-CCTTTCGAGGGTATTTCGATAATTTTACCC
41927519 ACGAATCGTA
Statistics
Matches: 177, Mismatches: 20, Indels: 12
0.85 0.10 0.06
Matches are distributed among these distances:
80 8 0.05
81 153 0.86
82 16 0.09
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.43
Consensus pattern (81 bp):
CAGTAATTTTACCTTTCGAGGGTATTTCGATAATTTTACCCTTCGAGGGTATTTCAATAATTTTA
CCTATCGAGGGTATTT
Found at i:41932425 original size:32 final size:32
Alignment explanation
Indices: 41932338--41932476 Score: 127
Period size: 32 Copynumber: 4.4 Consensus size: 32
41932328 GAATGGCTAC
* * *
41932338 AAGCCATAAGT-ACATTAATATGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * * ** *
41932369 AAACAATCAATAGTAGTAATATGATCGGCATA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * *
41932401 CAGCCATCAGTAACGGTAACATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * *
41932433 AAGCCATCAGTAACAATAATATGATCGGTAAA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
*
41932465 AAACCATCAGTA
1 AAGCCATCAGTA
41932477 GCATCGCAGC
Statistics
Matches: 82, Mismatches: 25, Indels: 1
0.76 0.23 0.01
Matches are distributed among these distances:
31 7 0.09
32 75 0.91
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.22
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTAATATGATCGGCACA
Found at i:41932660 original size:24 final size:24
Alignment explanation
Indices: 41932633--41932681 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
41932623 AGTTATACCA
*
41932633 ATCACAGACAAATCAGTCATTTAC
1 ATCACAGACAAATCAATCATTTAC
* *
41932657 ATCACGGACAAATTAATCATTTAC
1 ATCACAGACAAATCAATCATTTAC
41932681 A
1 A
41932682 CTCGAGGGGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.43, C:0.22, G:0.08, T:0.27
Consensus pattern (24 bp):
ATCACAGACAAATCAATCATTTAC
Found at i:41932702 original size:26 final size:24
Alignment explanation
Indices: 41932633--41932706 Score: 69
Period size: 24 Copynumber: 3.0 Consensus size: 24
41932623 AGTTATACCA
*
41932633 ATCACAGAC-AAATCAGTCATTTAC
1 ATCACGGACAAAAT-AGTCATTTAC
* *
41932657 ATCACGGACAAATTAATCATTTAC
1 ATCACGGACAAAATAGTCATTTAC
* *
41932681 ACTCGAGGGGCAAAATAGTCATTTAC
1 A-TC-ACGGACAAAATAGTCATTTAC
41932707 CCTCTAAGGG
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
24 18 0.45
25 5 0.12
26 17 0.43
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.26
Consensus pattern (24 bp):
ATCACGGACAAAATAGTCATTTAC
Found at i:41932732 original size:27 final size:27
Alignment explanation
Indices: 41932698--41932976 Score: 173
Period size: 27 Copynumber: 10.4 Consensus size: 27
41932688 GGGCAAAATA
*
41932698 GTCA-TTTACCCTCTAAGGGTATTATG
1 GTCATTTTACCCTCTAAGGGTATTACG
* *
41932724 GTCATTTTA-ACTAAC-AAGGGTATTATG
1 GTCATTTTACCCT--CTAAGGGTATTACG
*
41932751 GTTATTTT--CC-CTACAGGGTTATTACG
1 GTCATTTTACCCTCTA-AGGG-TATTACG
* * *
41932777 GTCATTTAACCCTATAGGGGTATTACG
1 GTCATTTTACCCTCTAAGGGTATTACG
* * *
41932804 ATTATTTTACCC-C-ACAGAGGCATTACG
1 GTCATTTTACCCTCTA-AG-GGTATTACG
*
41932831 GTCATTTTACCCTAC-AAGGGTATTACA
1 GTCATTTTACCCT-CTAAGGGTATTACG
* * * *
41932858 GTAATTTAACCCTATGAGGGTATTACG
1 GTCATTTTACCCTCTAAGGGTATTACG
*
41932885 GTCATTTTACCCTAC-AGGGGTATTACG
1 GTCATTTTACCCT-CTAAGGGTATTACG
* * * ** *
41932912 ATCATTTAACCCTATGGGGGTATTACA
1 GTCATTTTACCCTCTAAGGGTATTACG
* * * **
41932939 GTCATTTAACCCTATGAGGGTATTATA
1 GTCATTTTACCCTCTAAGGGTATTACG
41932966 GTCATTTTACC
1 GTCATTTTACC
41932977 TTACAGAGGG
Statistics
Matches: 200, Mismatches: 37, Indels: 31
0.75 0.14 0.12
Matches are distributed among these distances:
23 1 0.00
24 1 0.00
25 5 0.03
26 20 0.10
27 161 0.81
28 8 0.04
29 4 0.02
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCCTCTAAGGGTATTACG
Found at i:41932843 original size:54 final size:54
Alignment explanation
Indices: 41932741--41933030 Score: 261
Period size: 54 Copynumber: 5.4 Consensus size: 54
41932731 TAACTAACAA
* *
41932741 GGGTATTATGGTTATTTT-CCCTACAG-GGTTATTACGGTCATTTAACCCTATAG
1 GGGTATTACGATTATTTTACCCTACAGAGG-TATTACGGTCATTTAACCCTATAG
* * * * *
41932794 GGGTATTACGATTATTTTACCCCACAGAGGCATTACGGTCATTTTACCCTACAA
1 GGGTATTACGATTATTTTACCCTACAGAGGTATTACGGTCATTTAACCCTATAG
* * * * *
41932848 GGGTATTAC-AGTAATTTAACCCTA-TGAGGGTATTACGGTCATTTTACCCTACAG
1 GGGTATTACGA-TTATTTTACCCTACAGA-GGTATTACGGTCATTTAACCCTATAG
* * ** * *
41932902 GGGTATTACGATCATTTAACCCTATGGGGGTATTACAGTCATTTAACCCTAT-G
1 GGGTATTACGATTATTTTACCCTACAGAGGTATTACGGTCATTTAACCCTATAG
* * * * *
41932955 AGGGTATTA-TAGTCATTTTACCTTACAGAGGGCATTACGGTTATTTAACCCTAT-G
1 -GGGTATTACGA-TTATTTTACCCTACAGA-GGTATTACGGTCATTTAACCCTATAG
41933010 GGGATATTACGATTATTTTAC
1 GGG-TATTACGATTATTTTAC
41933031 AACCTTTTCG
Statistics
Matches: 196, Mismatches: 30, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
53 21 0.11
54 135 0.69
55 39 0.20
56 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.36
Consensus pattern (54 bp):
GGGTATTACGATTATTTTACCCTACAGAGGTATTACGGTCATTTAACCCTATAG
Found at i:41932869 original size:81 final size:80
Alignment explanation
Indices: 41932759--41933007 Score: 304
Period size: 81 Copynumber: 3.1 Consensus size: 80
41932749 TGGTTATTTT
* * *
41932759 CCCTACAGGGTTATTACGGTCATTTAACCCTAT-AGGGGTATTACGATTATTTTACCCCACAGAG
1 CCCTACAGGG-TATTACAGTCATTTAACCCTATGA-GGGTATTACGATCATTTTACCCTACAGAG
*
41932823 GCATTACGGTCATTTTA
64 GCATTACGGTCATTTAA
* * *
41932840 CCCTACAAGGGTATTACAGTAATTTAACCCTATGAGGGTATTACGGTCATTTTACCCTACAGGGG
1 CCCTAC-AGGGTATTACAGTCATTTAACCCTATGAGGGTATTACGATCATTTTACCCTACAGAGG
* *
41932905 TATTACGATCATTTAA
65 CATTACGGTCATTTAA
** * *
41932921 CCCTATGGGGGTATTACAGTCATTTAACCCTATGAGGGTATTA-TAGTCATTTTACCTTACAGAG
1 CCCTA-CAGGGTATTACAGTCATTTAACCCTATGAGGGTATTACGA-TCATTTTACCCTACAGA-
*
41932985 GGCATTACGGTTATTTAA
63 GGCATTACGGTCATTTAA
41933003 CCCTA
1 CCCTA
41933008 TGGGGATATT
Statistics
Matches: 144, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
81 119 0.83
82 25 0.17
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (80 bp):
CCCTACAGGGTATTACAGTCATTTAACCCTATGAGGGTATTACGATCATTTTACCCTACAGAGGC
ATTACGGTCATTTAA
Found at i:41933018 original size:27 final size:26
Alignment explanation
Indices: 41932770--41933020 Score: 205
Period size: 27 Copynumber: 9.3 Consensus size: 26
41932760 CCTACAGGGT
41932770 TATTACGGTCATTTAACCCTATAGGGG
1 TATTACGGTCATTTAACCCTAT-GGGG
* * * * * *
41932797 TATTACGATTATTTTACCCCACAGAGG
1 TATTACGGTCATTTAACCCTA-TGGGG
* * **
41932824 CATTACGGTCATTTTACCCTACAAGGG
1 TATTACGGTCATTTAACCCTA-TGGGG
* *
41932851 TATTACAGTAATTTAACCCTATGAGGG
1 TATTACGGTCATTTAACCCTATG-GGG
* *
41932878 TATTACGGTCATTTTACCCTACAGGGG
1 TATTACGGTCATTTAACCCTA-TGGGG
*
41932905 TATTACGATCATTTAACCCTATGGGGG
1 TATTACGGTCATTTAACCCTAT-GGGG
*
41932932 TATTACAGTCATTTAACCCTATGAGGG
1 TATTACGGTCATTTAACCCTATG-GGG
** * * *
41932959 TATTATAGTCATTTTACCTTACAGAGGG
1 TATTACGGTCATTTAACCCTA-TG-GGG
* *
41932987 CATTACGGTTATTTAACCCTATGGGG
1 TATTACGGTCATTTAACCCTATGGGG
41933013 ATATTACG
1 -TATTACG
41933021 ATTATTTTAC
Statistics
Matches: 178, Mismatches: 39, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
26 4 0.02
27 153 0.86
28 21 0.12
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (26 bp):
TATTACGGTCATTTAACCCTATGGGG
Found at i:41933849 original size:32 final size:32
Alignment explanation
Indices: 41933767--41933905 Score: 120
Period size: 32 Copynumber: 4.4 Consensus size: 32
41933757 GAATGGCTAC
* * *
41933767 AAGCCATAAGT-ACATTAATATGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
** *
41933798 AAGCCATCAGTAGTAGTAATATGATCGGCATA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * *
41933830 CAA-CCATCAGTAACGGTAATATGATCGGGAAA
1 -AAGCCATCAGTAACAGTAATATGATCGGCACA
*** * * *
41933862 AATATATTAGTAACAGTAATATAATCGGCTCA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
41933894 AAGCCATCAGTA
1 AAGCCATCAGTA
41933906 GCATCGCAGC
Statistics
Matches: 82, Mismatches: 23, Indels: 5
0.75 0.21 0.05
Matches are distributed among these distances:
31 12 0.15
32 68 0.83
33 2 0.02
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTAATATGATCGGCACA
Found at i:41934204 original size:27 final size:27
Alignment explanation
Indices: 41934174--41934486 Score: 288
Period size: 27 Copynumber: 11.6 Consensus size: 27
41934164 CTCTCAGGGC
* * *
41934174 ATTATGGTCATTTTACCTTACAGGGGT
1 ATTACGGTCATTTTACCCTATAGGGGT
* * * *
41934201 ATTACGATTATTTTATCCTACAGGGGT
1 ATTACGGTCATTTTACCCTATAGGGGT
* * *
41934228 ATTACGGTTATTTAACCCTATATGGGT
1 ATTACGGTCATTTTACCCTATAGGGGT
* * *
41934255 ATTACGATCATTTTACCCTACAGAGGT
1 ATTACGGTCATTTTACCCTATAGGGGT
*
41934282 ATTAAGGTCATTTTACCCTATAGGGGT
1 ATTACGGTCATTTTACCCTATAGGGGT
** *
41934309 ATTATAGTCATTAT-CCCTATAGGGGAT
1 ATTACGGTCATTTTACCCTATAGGGG-T
* *
41934336 ATTACGGTCATTTTACCTTACAGGGGT
1 ATTACGGTCATTTTACCCTATAGGGGT
* * * *
41934363 ATTATGATCATTTAACCCTATGGGGGT
1 ATTACGGTCATTTTACCCTATAGGGGT
* * *
41934390 ATTACGGTTATTTAACCTTATAGGGGT
1 ATTACGGTCATTTTACCCTATAGGGGT
* * *
41934417 ATTACGATCATTTTACCCAATTGGGGCT
1 ATTACGGTCATTTTACCCTATAGGGG-T
* * * *
41934445 -TTACGGTTATTTGACCCTATTGGAGT
1 ATTACGGTCATTTTACCCTATAGGGGT
*
41934471 ATTACGGTTATTTTAC
1 ATTACGGTCATTTTAC
41934487 AACCTTTTCA
Statistics
Matches: 231, Mismatches: 51, Indels: 8
0.80 0.18 0.03
Matches are distributed among these distances:
26 12 0.05
27 209 0.90
28 10 0.04
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (27 bp):
ATTACGGTCATTTTACCCTATAGGGGT
Found at i:41934266 original size:81 final size:81
Alignment explanation
Indices: 41934181--41934433 Score: 337
Period size: 81 Copynumber: 3.1 Consensus size: 81
41934171 GGCATTATGG
* * * *
41934181 TCATTTTACCTTACAGGGGTATTACGATTATTTTATCCTACAGGGGTATTACGGTTATTTAACCC
1 TCATTTTACCTTACAGGGGTATTAAGATCATTTTACCCTATAGGGGTATTACGGTTATTTAACCC
*
41934246 TATATGGGTATTACGA
66 TATAGGGGTATTACGA
* * * ** * *
41934262 TCATTTTACCCTACAGAGGTATTAAGGTCATTTTACCCTATAGGGGTATTATAGTCA-TTATCCC
1 TCATTTTACCTTACAGGGGTATTAAGATCATTTTACCCTATAGGGGTATTACGGTTATTTAACCC
*
41934326 TATAGGGGATATTACGG
66 TATAGGGG-TATTACGA
* * * *
41934343 TCATTTTACCTTACAGGGGTATTATGATCATTTAACCCTATGGGGGTATTACGGTTATTTAACCT
1 TCATTTTACCTTACAGGGGTATTAAGATCATTTTACCCTATAGGGGTATTACGGTTATTTAACCC
41934408 TATAGGGGTATTACGA
66 TATAGGGGTATTACGA
41934424 TCATTTTACC
1 TCATTTTACC
41934434 CAATTGGGGC
Statistics
Matches: 145, Mismatches: 25, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
80 13 0.09
81 119 0.82
82 13 0.09
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (81 bp):
TCATTTTACCTTACAGGGGTATTAAGATCATTTTACCCTATAGGGGTATTACGGTTATTTAACCC
TATAGGGGTATTACGA
Found at i:41934462 original size:81 final size:81
Alignment explanation
Indices: 41934181--41934483 Score: 322
Period size: 81 Copynumber: 3.7 Consensus size: 81
41934171 GGCATTATGG
* * * * * * *
41934181 TCATTTTACCTTACAGGGGTATTACGATTATTTTATCCTACAGGGGTATTACGGTTATTTAACCC
1 TCATTTTACCCTACAGGGGTATTAAGGTCATTTAACCCTATAGGGGTATTACGGTTATTTAACCC
*
41934246 TATATGGGTATTACGA
66 TATAGGGGTATTACGA
* * ** * *
41934262 TCATTTTACCCTACAGAGGTATTAAGGTCATTTTACCCTATAGGGGTATTATAGTCA-TTATCCC
1 TCATTTTACCCTACAGGGGTATTAAGGTCATTTAACCCTATAGGGGTATTACGGTTATTTAACCC
*
41934326 TATAGGGGATATTACGG
66 TATAGGGG-TATTACGA
* * * * *
41934343 TCATTTTACCTTACAGGGGTATTATGATCATTTAACCCTATGGGGGTATTACGGTTATTTAACCT
1 TCATTTTACCCTACAGGGGTATTAAGGTCATTTAACCCTATAGGGGTATTACGGTTATTTAACCC
41934408 TATAGGGGTATTACGA
66 TATAGGGGTATTACGA
* ** * * * * *
41934424 TCATTTTACCCAATTGGGGCT-TTACGGTTATTTGACCCTATTGGAGTATTACGGTTATTT
1 TCATTTTACCCTACAGGGG-TATTAAGGTCATTTAACCCTATAGGGGTATTACGGTTATTT
41934484 TACAACCTTT
Statistics
Matches: 184, Mismatches: 35, Indels: 6
0.82 0.16 0.03
Matches are distributed among these distances:
80 13 0.07
81 157 0.85
82 14 0.08
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (81 bp):
TCATTTTACCCTACAGGGGTATTAAGGTCATTTAACCCTATAGGGGTATTACGGTTATTTAACCC
TATAGGGGTATTACGA
Found at i:41934979 original size:24 final size:23
Alignment explanation
Indices: 41934952--41934996 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
41934942 GCTGTATCGT
41934952 CAGC-TTTCCGACATTTCGACATCC
1 CAGCATTT-CGACATTT-GACATCC
41934976 CAGCATTTCGACATTTGACAT
1 CAGCATTTCGACATTTGACAT
41934997 TCTTAAACGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 5 0.25
24 12 0.60
25 3 0.15
ACGTcount: A:0.24, C:0.31, G:0.13, T:0.31
Consensus pattern (23 bp):
CAGCATTTCGACATTTGACATCC
Found at i:41936433 original size:8 final size:9
Alignment explanation
Indices: 41936420--41936537 Score: 60
Period size: 9 Copynumber: 12.2 Consensus size: 9
41936410 ATAATAAATA
41936420 TTTTT-ATT
1 TTTTTAATT
41936428 TTTTTAATT
1 TTTTTAATT
*
41936437 TTTTAAATT
1 TTTTTAATT
41936446 TTTTTAA-T
1 TTTTTAATT
**
41936454 TTTAAAATACT
1 TTTTTAAT--T
**
41936465 TTTAAAATACT
1 TTTTTAAT--T
*
41936476 TTTTTAAAAT
1 TTTTT-AATT
*
41936486 TTTTTAAAT
1 TTTTTAATT
*
41936495 TTTTAAATT
1 TTTTTAATT
41936504 TTTTTAAAATACT
1 TTTTT--AAT--T
41936517 TTTTTAATTT
1 TTTTTAA-TT
41936527 TTTTTAATT
1 TTTTTAATT
41936536 TT
1 TT
41936538 AAAATATTTT
Statistics
Matches: 90, Mismatches: 10, Indels: 19
0.76 0.08 0.16
Matches are distributed among these distances:
8 11 0.12
9 36 0.40
10 14 0.16
11 20 0.22
12 3 0.03
13 6 0.07
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (9 bp):
TTTTTAATT
Found at i:41936489 original size:40 final size:40
Alignment explanation
Indices: 41936435--41936567 Score: 198
Period size: 41 Copynumber: 3.4 Consensus size: 40
41936425 ATTTTTTTAA
*
41936435 TTTTTTAAATTTTTTTAATTTTAAAATACTTTTAAAATAC
1 TTTTTTAAATTTTTTTAATTTTAAAATATTTTTAAAATAC
* * *
41936475 TTTTTTAAAATTTTTTAAATTTTTAAATTTTTTTAAAATAC
1 TTTTTT-AAATTTTTTTAATTTTAAAATATTTTTAAAATAC
*
41936516 TTTTTTAATTTTTTTTAATTTTAAAATATTTTTAAAATA-
1 TTTTTTAAATTTTTTTAATTTTAAAATATTTTTAAAATAC
41936555 TTTTTT-AATTTTT
1 TTTTTTAAATTTTT
41936568 AAAATAAATT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
38 6 0.07
39 6 0.07
40 35 0.42
41 36 0.43
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (40 bp):
TTTTTTAAATTTTTTTAATTTTAAAATATTTTTAAAATAC
Found at i:41936523 original size:13 final size:11
Alignment explanation
Indices: 41936453--41936519 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
41936443 ATTTTTTTAA
41936453 TTTTAAAATAC
1 TTTTAAAATAC
41936464 TTTTAAAATAC
1 TTTTAAAATAC
41936475 TTTTTTAAAAT--
1 --TTTTAAAATAC
*
41936486 TTTTTAAAT--
1 TTTTAAAATAC
**
41936495 TTTT-AAATTT
1 TTTTAAAATAC
41936505 TTTTAAAATAC
1 TTTTAAAATAC
41936516 TTTT
1 TTTT
41936520 TTAATTTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
8 4 0.08
9 12 0.25
10 4 0.08
11 19 0.40
13 9 0.19
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:41936548 original size:11 final size:11
Alignment explanation
Indices: 41936534--41936559 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
41936524 TTTTTTTTAA
41936534 TTTTAAAATAT
1 TTTTAAAATAT
41936545 TTTTAAAATAT
1 TTTTAAAATAT
41936556 TTTT
1 TTTT
41936560 TAATTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:41936579 original size:20 final size:19
Alignment explanation
Indices: 41936543--41936580 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
41936533 ATTTTAAAAT
*
41936543 ATTTTTAAAATATTTTTTA
1 ATTTTTAAAATAATTTTTA
41936562 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAAT-AATTTTT
41936581 GGTATTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTTAAAATAATTTTTA
Found at i:41939716 original size:28 final size:28
Alignment explanation
Indices: 41939685--41939800 Score: 142
Period size: 28 Copynumber: 4.1 Consensus size: 28
41939675 CATGCAGTAG
* * *
41939685 CAGTCTGGGCCTGAGCCCAATACAACAA
1 CAGTGTGGGCCTTAGCCCAATACAATAA
* *
41939713 CAGTGTGGGCCTTAGCCTAATACAGTAA
1 CAGTGTGGGCCTTAGCCCAATACAATAA
* * *
41939741 CAGTGTAGGCATTAGCCCAATACAGTAA
1 CAGTGTGGGCCTTAGCCCAATACAATAA
* *
41939769 CAGTGTGAGCCTTAGGCCAATACAATAA
1 CAGTGTGGGCCTTAGCCCAATACAATAA
41939797 CAGT
1 CAGT
41939801 ACAATGCAGT
Statistics
Matches: 75, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 75 1.00
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.21
Consensus pattern (28 bp):
CAGTGTGGGCCTTAGCCCAATACAATAA
Found at i:41940193 original size:27 final size:27
Alignment explanation
Indices: 41940163--41940494 Score: 411
Period size: 27 Copynumber: 12.3 Consensus size: 27
41940153 TATTTTAGCT
* * *
41940163 ATTTTACCCTTTGGGGGTATTTCAATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
41940190 ATTTTACCCTT-GAAGGGTATTTCG-TA
1 ATTTTACCCTTCG-AGGGTATTTCGATA
* ** *
41940216 ATCTTACCCTTTAAGGGTATTTCGGTA
1 ATTTTACCCTTCGAGGGTATTTCGATA
* * *
41940243 ATCTTACCCTTTGAGGGTATTTCGGTA
1 ATTTTACCCTTCGAGGGTATTTCGATA
41940270 ATTTTACCCTTCGAGGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
* * *
41940297 ATTTTACCCTTCGAGGATATTTTGGTA
1 ATTTTACCCTTCGAGGGTATTTCGATA
* * *
41940324 AATTTAGCCTTCGAGGGTATTT-TAGTA
1 ATTTTACCCTTCGAGGGTATTTCGA-TA
41940351 ATTTTACCCATT-GAGGGTATTTCGATA
1 ATTTTACCC-TTCGAGGGTATTTCGATA
* * *
41940378 GTTTTACCATTCGAAGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
41940405 ATTTTACCCTTCGAGGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
41940432 ATTTTACCCTTCGAGGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
* * *
41940459 ATTTTACCCTTCGAGGTTAGTTCAATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
41940486 ATTTTACCC
1 ATTTTACCC
41940495 ACGAATCGCA
Statistics
Matches: 270, Mismatches: 28, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
26 26 0.10
27 241 0.89
28 3 0.01
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42
Consensus pattern (27 bp):
ATTTTACCCTTCGAGGGTATTTCGATA
Found at i:41942106 original size:42 final size:42
Alignment explanation
Indices: 41942058--41942157 Score: 164
Period size: 42 Copynumber: 2.4 Consensus size: 42
41942048 GCTTTCGGTA
* *
41942058 TCGCACACTTAGTGCCCGTTATTCAACATCATCATTTTAATT
1 TCGCACACTTAGTGCCCATTATCCAACATCATCATTTTAATT
* *
41942100 TCGCACACTTAGTGCCTATTATCCAACATCATTATTTTAATT
1 TCGCACACTTAGTGCCCATTATCCAACATCATCATTTTAATT
41942142 TCGCACACTTAGTGCC
1 TCGCACACTTAGTGCC
41942158 GTTCATATAG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.26, C:0.27, G:0.10, T:0.37
Consensus pattern (42 bp):
TCGCACACTTAGTGCCCATTATCCAACATCATCATTTTAATT
Found at i:41947858 original size:29 final size:29
Alignment explanation
Indices: 41947629--41947858 Score: 173
Period size: 29 Copynumber: 8.0 Consensus size: 29
41947619 TTTTTTGTAG
* *
41947629 AATAGTGGTAAAACTGTAAAATCT-AAAA
1 AATAGTGGCAAAACTGTAAAATCTGGAAA
* *
41947657 AATAGTGGAAAAACTGTAAAATCTAGAAA
1 AATAGTGGCAAAACTGTAAAATCTGGAAA
* * *
41947686 AATAATGGC-AAATTATAAAATCTGGAAA
1 AATAGTGGCAAAACTGTAAAATCTGGAAA
** *
41947714 ACCAGTGGCAAAACTGTAAAATTTAGG-AA
1 AATAGTGGCAAAACTGTAAAATCT-GGAAA
* * *
41947743 AATTGTGGTAGAACTGTAAAAT-TGGGAAA
1 AATAGTGGCAAAACTGTAAAATCT-GGAAA
* * ** *
41947772 AATAGTGGCAGAACTATAAAAGATGTAAA
1 AATAGTGGCAAAACTGTAAAATCTGGAAA
** * *
41947801 ACCAGTGGCAAAATTGTAAAAT-TTGAAA
1 AATAGTGGCAAAACTGTAAAATCTGGAAA
* * * *
41947829 AACAGTGGCAGAACTATAAAATCTGTAAA
1 AATAGTGGCAAAACTGTAAAATCTGGAAA
41947858 A
1 A
41947859 TGGCAGTACA
Statistics
Matches: 158, Mismatches: 38, Indels: 11
0.76 0.18 0.05
Matches are distributed among these distances:
28 70 0.44
29 85 0.54
30 3 0.02
ACGTcount: A:0.50, C:0.09, G:0.19, T:0.23
Consensus pattern (29 bp):
AATAGTGGCAAAACTGTAAAATCTGGAAA
Found at i:41950892 original size:65 final size:65
Alignment explanation
Indices: 41950783--41950913 Score: 235
Period size: 65 Copynumber: 2.0 Consensus size: 65
41950773 TTTTAAAAAG
*
41950783 ATTACTTTCCATCTTGCTTGATAGACATGAGATACACTGACAATTACCATAAAGTATTATTAGTC
1 ATTAATTTCCATCTTGCTTGATAGACATGAGATACACTGACAATTACCATAAAGTATTATTAGTC
* *
41950848 ATTAATTTCCATCTTTCTTGATAGACATGAGATACACTGACAATTACCGTAAAGTATTATTAGTC
1 ATTAATTTCCATCTTGCTTGATAGACATGAGATACACTGACAATTACCATAAAGTATTATTAGTC
41950913 A
1 A
41950914 AGAACCTACT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (65 bp):
ATTAATTTCCATCTTGCTTGATAGACATGAGATACACTGACAATTACCATAAAGTATTATTAGTC
Found at i:41955870 original size:13 final size:13
Alignment explanation
Indices: 41955839--41955876 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
41955829 AATTTCAAGT
41955839 ATTGT-ATAAAAA
1 ATTGTGATAAAAA
41955851 ATATGTGATAAAAA
1 AT-TGTGATAAAAA
*
41955865 CTTGTGATAAAA
1 ATTGTGATAAAA
41955877 TTAATATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 2 0.09
13 13 0.57
14 8 0.35
ACGTcount: A:0.53, C:0.03, G:0.13, T:0.32
Consensus pattern (13 bp):
ATTGTGATAAAAA
Found at i:41957562 original size:19 final size:19
Alignment explanation
Indices: 41957538--41957576 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
41957528 AGCAGACCAA
*
41957538 TTAAGTCTGTTGGGGTTGT
1 TTAAGTCTGTTAGGGTTGT
*
41957557 TTAAGTTTGTTAGGGTTGT
1 TTAAGTCTGTTAGGGTTGT
41957576 T
1 T
41957577 AACTTCAGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.13, C:0.03, G:0.33, T:0.51
Consensus pattern (19 bp):
TTAAGTCTGTTAGGGTTGT
Found at i:41963214 original size:27 final size:26
Alignment explanation
Indices: 41963170--41963501 Score: 278
Period size: 27 Copynumber: 12.3 Consensus size: 26
41963160 GTAATGGGCC
*
41963170 TAAAATGACAGAAATACCCTCGAAGGG
1 TAAAATGAC-CAAATACCCTCGAAGGG
* *
41963197 TAAAATAACCAAACTACCCTCGAAAGG
1 TAAAATGACCAAA-TACCCTCGAAGGG
* *
41963224 TAAAATGATCGAAATACCCCCGAAGGG
1 TAAAATGA-CCAAATACCCTCGAAGGG
* * * *
41963251 TCAAATGACTGAAATACCCTCAAAGGA
1 TAAAATGAC-CAAATACCCTCGAAGGG
* * *
41963278 TAAAATGACCGAAATACCTTCAAAGGT
1 TAAAATGACC-AAATACCCTCGAAGGG
* *
41963305 TAAAATGACTGAAATACCC-CTAAAGGG
1 TAAAATGAC-CAAATACCCTC-GAAGGG
* * *
41963332 TAAAAAGACTAAAATATCCTCGAAGGG
1 TAAAATGAC-CAAATACCCTCGAAGGG
*
41963359 TAAAATGACTGAAATACCCTCGAAGGG
1 TAAAATGAC-CAAATACCCTCGAAGGG
41963386 TAAAATGACCGAAATACTCC-CGAAGGG
1 TAAAATGACC-AAATAC-CCTCGAAGGG
* *
41963413 TAAAACGACCGAAATA-CCTCCGAAAGG
1 TAAAATGACC-AAATACCCT-CGAAGGG
*
41963440 TAAAATGATCGAAATACCC-CTGAAGGG
1 TAAAATGA-CCAAATACCCTC-GAAGGG
* *
41963467 TAAAATGACAGAAATACCC-CGAAGGA
1 TAAAATGAC-CAAATACCCTCGAAGGG
41963493 TAAAATGAC
1 TAAAATGAC
41963502 TATTATAGCC
Statistics
Matches: 258, Mismatches: 32, Indels: 31
0.80 0.10 0.10
Matches are distributed among these distances:
25 2 0.01
26 21 0.08
27 225 0.87
28 10 0.04
ACGTcount: A:0.45, C:0.20, G:0.19, T:0.17
Consensus pattern (26 bp):
TAAAATGACCAAATACCCTCGAAGGG
Found at i:41963269 original size:54 final size:53
Alignment explanation
Indices: 41963170--41963501 Score: 352
Period size: 54 Copynumber: 6.2 Consensus size: 53
41963160 GTAATGGGCC
* * *
41963170 TAAAATGACAGAAATACCCTCGAAGGGTAAAATAAC-CAAACTACCCTCGAAAGG
1 TAAAATGAC-GAAATACCCCCGAAGGGTAAAATGACTGAAA-TACCCTCGAAAGG
*
41963224 TAAAATGATCGAAATACCCCCGAAGGGTCAAATGACTGAAATACCCTC-AAAGG
1 TAAAATGA-CGAAATACCCCCGAAGGGTAAAATGACTGAAATACCCTCGAAAGG
** * * *
41963277 ATAAAATGACCGAAATACCTTCAAAGGTTAAAATGACTGAAATACCC-CTAAAGGG
1 -TAAAATGA-CGAAATACCCCCGAAGGGTAAAATGACTGAAATACCCTCGAAA-GG
* * * * *
41963332 TAAAAAGACTAAAATATCCTCGAAGGGTAAAATGACTGAAATACCCTCGAAGGG
1 TAAAATGAC-GAAATACCCCCGAAGGGTAAAATGACTGAAATACCCTCGAAAGG
* * *
41963386 TAAAATGACCGAAATACTCCCGAAGGGTAAAACGACCGAAATA-CCTCCGAAAGG
1 TAAAATGA-CGAAATACCCCCGAAGGGTAAAATGACTGAAATACCCT-CGAAAGG
* *
41963440 TAAAATGATCGAAATACCCCTGAAGGGTAAAATGACAGAAATACCC-CG-AAGG
1 TAAAATGA-CGAAATACCCCCGAAGGGTAAAATGACTGAAATACCCTCGAAAGG
41963492 ATAAAATGAC
1 -TAAAATGAC
41963502 TATTATAGCC
Statistics
Matches: 236, Mismatches: 31, Indels: 24
0.81 0.11 0.08
Matches are distributed among these distances:
52 5 0.02
53 20 0.08
54 199 0.84
55 12 0.05
ACGTcount: A:0.45, C:0.20, G:0.19, T:0.17
Consensus pattern (53 bp):
TAAAATGACGAAATACCCCCGAAGGGTAAAATGACTGAAATACCCTCGAAAGG
Found at i:41963309 original size:81 final size:82
Alignment explanation
Indices: 41963170--41963502 Score: 362
Period size: 81 Copynumber: 4.1 Consensus size: 82
41963160 GTAATGGGCC
* * *
41963170 TAAAATGACAGAAATACCCTCGAAGGGTAAAATAACC-AAACTACCCTCGAAA-GGTAAAATGAT
1 TAAAATGACTGAAATACCCTCAAAGGGTAAAATGACCGAAA-TACCCTCGAAAGGGTAAAATGA-
41963233 C-GAAATACCCCCGAAGGG
64 CAGAAATACCCCCGAAGGG
* * * * *
41963251 TCAAATGACTGAAATACCCTCAAAGGATAAAATGACCGAAATACCTTC-AAAGGTTAAAATGACT
1 TAAAATGACTGAAATACCCTCAAAGGGTAAAATGACCGAAATACCCTCGAAAGGGTAAAATGACA
**
41963315 GAAATACCCCTAAAGGG
66 GAAATACCCCCGAAGGG
* * * * * *
41963332 TAAAAAGACTAAAATATCCTCGAAGGGTAAAATGACTGAAATACCCTCG-AAGGGTAAAATGACC
1 TAAAATGACTGAAATACCCTCAAAGGGTAAAATGACCGAAATACCCTCGAAAGGGTAAAATGACA
*
41963396 GAAATACTCCCGAAGGG
66 GAAATACCCCCGAAGGG
* * *
41963413 TAAAACGACCGAAATA-CCTCCGAAA-GGTAAAATGATCGAAATACCC-CTG-AAGGGTAAAATG
1 TAAAATGACTGAAATACCCT-C-AAAGGGTAAAATGACCGAAATACCCTC-GAAAGGGTAAAATG
*
41963474 ACAGAAATA-CCCCGAAGGA
63 ACAGAAATACCCCCGAAGGG
41963493 TAAAATGACT
1 TAAAATGACT
41963503 ATTATAGCCC
Statistics
Matches: 212, Mismatches: 33, Indels: 15
0.82 0.13 0.06
Matches are distributed among these distances:
80 24 0.11
81 183 0.86
82 5 0.02
ACGTcount: A:0.44, C:0.20, G:0.19, T:0.17
Consensus pattern (82 bp):
TAAAATGACTGAAATACCCTCAAAGGGTAAAATGACCGAAATACCCTCGAAAGGGTAAAATGACA
GAAATACCCCCGAAGGG
Found at i:41963737 original size:26 final size:26
Alignment explanation
Indices: 41963681--41963751 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
41963671 ACATATACTA
* **
41963681 TTACTGGCAGCTTTACTGCATTGCTG
1 TTACTGGCAGCTTTGCTGCATCACTG
*
41963707 TTACTGGCAGCTTTGCTGCATCATTAG
1 TTACTGGCAGCTTTGCTGCATCACT-G
* *
41963734 -TACTGGTAACTTTGCTGC
1 TTACTGGCAGCTTTGCTGC
41963752 GATTTTGGTG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 37 0.97
27 1 0.03
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.38
Consensus pattern (26 bp):
TTACTGGCAGCTTTGCTGCATCACTG
Found at i:41987523 original size:15 final size:16
Alignment explanation
Indices: 41987503--41987532 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41987493 GAGTATAGTA
41987503 AAATA-TTAAAAAAAT
1 AAATATTTAAAAAAAT
41987518 AAATATTTAAAAAAA
1 AAATATTTAAAAAAA
41987533 GAGATATCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AAATATTTAAAAAAAT
Found at i:41988311 original size:18 final size:19
Alignment explanation
Indices: 41988288--41988324 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
41988278 TTTTTAAAAA
41988288 TATAAAT-TTTAGAATTTT
1 TATAAATATTTAGAATTTT
41988306 TATAAATATTTAGAATTTT
1 TATAAATATTTAGAATTTT
41988325 AAAAATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
TATAAATATTTAGAATTTT
Found at i:41988325 original size:18 final size:18
Alignment explanation
Indices: 41988288--41988341 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
41988278 TTTTTAAAAA
41988288 TATAAAT-TTTAGAATTTT
1 TATAAATATTTAGAA-TTT
41988306 TATAAATATTTAGAATTT
1 TATAAATATTTAGAATTT
* *
41988324 TAAAAATTATTTTGAATT
1 TATAAA-TATTTAGAATT
41988342 ATTTTGTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
18 15 0.47
19 17 0.53
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.52
Consensus pattern (18 bp):
TATAAATATTTAGAATTT
Found at i:41989814 original size:30 final size:30
Alignment explanation
Indices: 41989780--41989886 Score: 114
Period size: 30 Copynumber: 3.6 Consensus size: 30
41989770 ACCCCTTAAT
* *
41989780 TTTCTTTAAATTGTATTTTGGACCCTAAAC
1 TTTCTTAAAATTATATTTTGGACCCTAAAC
*
41989810 TTTCTTAAAATT-TCATTTT-GACCCCTTAAC
1 TTTCTTAAAATTAT-ATTTTGGA-CCCTAAAC
* * *
41989840 TTTCTAAAAATTATATTTTGG-CCC-ATAT
1 TTTCTTAAAATTATATTTTGGACCCTAAAC
41989868 TTTCTTAAAATTATATTTT
1 TTTCTTAAAATTATATTTT
41989887 TCTCCAGAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
28 19 0.29
29 6 0.09
30 39 0.59
31 2 0.03
ACGTcount: A:0.29, C:0.16, G:0.06, T:0.50
Consensus pattern (30 bp):
TTTCTTAAAATTATATTTTGGACCCTAAAC
Found at i:41990488 original size:16 final size:16
Alignment explanation
Indices: 41990452--41990501 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
41990442 TTCGGGAAAA
*
41990452 AGAGAAGAGAGAA-AG
1 AGAGAAGAGAGAAGGG
*
41990467 -GAGAAGGGA-AAGGGG
1 AGAGAAGAGAGAA-GGG
41990482 AGAGAAGAGAGAAGGG
1 AGAGAAGAGAGAAGGG
41990498 AGAG
1 AGAG
41990502 TCCGGCCACC
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
13 2 0.07
14 8 0.29
15 1 0.04
16 15 0.54
17 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (16 bp):
AGAGAAGAGAGAAGGG
Found at i:41990592 original size:20 final size:20
Alignment explanation
Indices: 41990565--41990619 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
41990555 TAGGGTTTTT
41990565 GAAAGAAGAAAAAAGTAGAA
1 GAAAGAAGAAAAAAGTAGAA
* *
41990585 GGAAGAAG-AAAAAGAAGAA
1 GAAAGAAGAAAAAAGTAGAA
41990604 GAAAGAA-AAGAAAAGT
1 GAAAGAAGAA-AAAAGT
41990620 TTAAAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.69, C:0.00, G:0.27, T:0.04
Consensus pattern (20 bp):
GAAAGAAGAAAAAAGTAGAA
Found at i:41990609 original size:16 final size:16
Alignment explanation
Indices: 41990567--41990612 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
41990557 GGGTTTTTGA
*
41990567 AAGAAGAAA-AAAGTAG
1 AAGAAGAAAGAAA-AAG
41990583 AAGGAAG-AAGAAAAAG
1 AA-GAAGAAAGAAAAAG
41990599 AAGAAGAAAGAAAA
1 AAGAAGAAAGAAAA
41990613 GAAAAGTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 4 0.15
16 15 0.58
17 7 0.27
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (16 bp):
AAGAAGAAAGAAAAAG
Found at i:41998853 original size:77 final size:78
Alignment explanation
Indices: 41998724--41999094 Score: 380
Period size: 77 Copynumber: 4.7 Consensus size: 78
41998714 TCAAGAATTA
41998724 TATTTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
1 TATTTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
41998789 CTATACACCGAGG
66 CTATACACCGAGG
* * * * *
41998802 TA-TTTTCAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTAAGCCTCAGG
1 TATTTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
** * *
41998866 CTGCACGCTGAGG
66 CTATACACCGAGG
* * * *
41998879 TATTTTTTAATTTATTTTTTAAAAAATCAAATCAAAACCAACTCATAATGCGAGAGGTGAGTTGA
1 TATTTTTCAATTTCTGTTTT------TCAAA--AAAATCAACTCATAATGCGAGAGGTGAGTTGA
*
41998944 GCCTCGGGCTATACACTGAGG
58 GCCTCGGGCTATACACCGAGG
* * * *
41998965 TATTTTT-AATTTTTGTTTTTC--AAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTTGGG
1 TATTTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
**
41999027 -TCATATGCCGAGG
66 CT-ATACACCGAGG
* ** *
41999040 TATTTTTCAATTTCTATTTTTC--AAAGGTCAACTCATAAT-CTGAGAAGTGAGTTGA
1 TATTTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGC-GAGAGGTGAGTTGA
41999095 ACATCGAATC
Statistics
Matches: 244, Mismatches: 37, Indels: 26
0.79 0.12 0.08
Matches are distributed among these distances:
74 1 0.00
75 52 0.21
76 38 0.16
77 69 0.28
78 15 0.06
79 2 0.01
84 5 0.02
85 10 0.04
86 52 0.21
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (78 bp):
TATTTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
CTATACACCGAGG
Found at i:41998963 original size:86 final size:86
Alignment explanation
Indices: 41998826--41998994 Score: 232
Period size: 86 Copynumber: 2.0 Consensus size: 86
41998816 GCTTTTCAAA
* * * *
41998826 AAAATCAACTCATATTGCGAGAAGTGAGTTAAGCCTCAGGCTGCACGCTGAGGTATTTTTTAATT
1 AAAACCAACTCATAATGCGAGAAGTGAGTTAAGCCTCAGGCTACACACTGAGGTA-TTTTTAATT
41998891 TAT-TTTTTAAAAAATCAAATC
65 TATGTTTTTAAAAAATCAAATC
* * * *
41998912 AAAACCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCTATACACTGAGGTATTTTTAATTT
1 AAAACCAACTCATAATGCGAGAAGTGAGTTAAGCCTCAGGCTACACACTGAGGTATTTTTAATTT
* *
41998977 TTGTTTTTCAAAAATCAA
66 ATGTTTTTAAAAAATCAA
41998995 CTTATATTGC
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
85 11 0.15
86 61 0.85
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (86 bp):
AAAACCAACTCATAATGCGAGAAGTGAGTTAAGCCTCAGGCTACACACTGAGGTATTTTTAATTT
ATGTTTTTAAAAAATCAAATC
Found at i:41999013 original size:75 final size:76
Alignment explanation
Indices: 41998912--41999094 Score: 212
Period size: 75 Copynumber: 2.4 Consensus size: 76
41998902 AAATCAAATC
41998912 AAAACCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG-C-TATACACTGAGGTATTTTT-AA
1 AAAACCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCATATAC-C-GAGGTATTTTTCAA
* *
41998974 TTTTTGTTTTTCA
64 TTTCTATTTTTCA
* * * * *
41998987 AAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTTGGGTCATATGCCGAGGTATTTTTCAATT
1 AAAACCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCATATACCGAGGTATTTTTCAATT
41999052 TCTATTTTTCA
66 TCTATTTTTCA
*** *
41999063 AAGGTCAACTCATAAT-CTGAGAAGTGAGTTGA
1 AAAACCAACTCATAATGC-GAGAGGTGAGTTGA
41999095 ACATCGAATC
Statistics
Matches: 92, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
75 48 0.52
76 40 0.43
77 4 0.04
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (76 bp):
AAAACCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCATATACCGAGGTATTTTTCAATT
TCTATTTTTCA
Found at i:41999060 original size:163 final size:161
Alignment explanation
Indices: 41998749--41999052 Score: 441
Period size: 163 Copynumber: 1.9 Consensus size: 161
41998739 GTTTTTCAAA
*
41998749 AAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCTATACACCGAGGTATTTTCAATTT
1 AAAACCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCTATACACCGAGGTATTTTCAATTT
*
41998814 CTGCTTTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTAAGCCTCAGGCTGCACGCTGAGG
66 CTGCTTTTC-AAAAAATCAACTCATATTGCGAGAAGTGAGTTAAGCCTCAGGCT-CACGCCGAGG
*
41998879 TATTTTTTAATTTATTTTTTAAAAAATCAAATC
129 TATTTTTCAATTTATTTTTTAAAAAATCAAATC
* *
41998912 AAAACCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCTATACACTGAGGTATTTTTAATTT
1 AAAACCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCTATACACCGAGGTATTTTCAATTT
* * * * * * * *
41998977 TTGTTTTTC-AAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCT-TGGGTCATATGCCGAGG
66 CTGCTTTTCAAAAAATCAACTCATATTGCGAGAAGTGAGTTAAGCCTCAGGCTC--ACGCCGAGG
41999040 TATTTTTCAATTT
129 TATTTTTCAATTT
41999053 CTATTTTTCA
Statistics
Matches: 126, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
159 1 0.01
160 3 0.02
161 53 0.42
163 69 0.55
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.33
Consensus pattern (161 bp):
AAAACCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCTATACACCGAGGTATTTTCAATTT
CTGCTTTTCAAAAAATCAACTCATATTGCGAGAAGTGAGTTAAGCCTCAGGCTCACGCCGAGGTA
TTTTTCAATTTATTTTTTAAAAAATCAAATC
Found at i:42000308 original size:10 final size:10
Alignment explanation
Indices: 42000290--42000354 Score: 53
Period size: 10 Copynumber: 6.3 Consensus size: 10
42000280 AGGGTTTCCG
42000290 AAAGAAGAAA
1 AAAGAAGAAA
* *
42000300 AAAGTAGAAG
1 AAAGAAGAAA
*
42000310 GAAGAAGAAAA
1 AAAGAAG-AAA
42000321 AGAAGAAGAAAGA
1 A-AAGAAG-AA-A
42000334 AAAGAA-AAA
1 AAAGAAGAAA
42000343 AAAG-AGAAA
1 AAAGAAGAAA
42000352 AAA
1 AAA
42000355 AATTTAAATC
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
8 1 0.02
9 11 0.24
10 15 0.33
11 2 0.04
12 14 0.31
13 2 0.04
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (10 bp):
AAAGAAGAAA
Found at i:42000322 original size:19 final size:20
Alignment explanation
Indices: 42000289--42000351 Score: 69
Period size: 19 Copynumber: 3.2 Consensus size: 20
42000279 TAGGGTTTCC
*
42000289 GAAAGAAGAAAAAAGTAGAA
1 GAAAGAAGAAAAAAGAAGAA
*
42000309 GGAAGAAG-AAAAAGAAGAA
1 GAAAGAAGAAAAAAGAAGAA
42000328 GAAAGAAAAGAAAAAA-AAG-A
1 GAAAG--AAGAAAAAAGAAGAA
42000348 GAAA
1 GAAA
42000352 AAAAATTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
19 14 0.38
20 12 0.32
21 6 0.16
22 5 0.14
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (20 bp):
GAAAGAAGAAAAAAGAAGAA
Found at i:42000327 original size:12 final size:12
Alignment explanation
Indices: 42000310--42000355 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
42000300 AAAGTAGAAG
42000310 GAAGAAGAAAAA
1 GAAGAAGAAAAA
42000322 GAAGAAGAAAGAA
1 GAAGAAGAAA-AA
*
42000335 -AAGAAAAAAAA
1 GAAGAAGAAAAA
42000346 G-AGAA-AAAAA
1 GAAGAAGAAAAA
42000356 ATTTAAATCA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
10 5 0.16
11 6 0.19
12 18 0.58
13 2 0.06
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:42000333 original size:16 final size:16
Alignment explanation
Indices: 42000291--42000336 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
42000281 GGGTTTCCGA
*
42000291 AAGAAGAAA-AAAGTAG
1 AAGAAGAAAGAAA-AAG
42000307 AAGGAAG-AAGAAAAAG
1 AA-GAAGAAAGAAAAAG
42000323 AAGAAGAAAGAAAA
1 AAGAAGAAAGAAAA
42000337 GAAAAAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 4 0.15
16 15 0.58
17 7 0.27
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (16 bp):
AAGAAGAAAGAAAAAG
Found at i:42000672 original size:16 final size:16
Alignment explanation
Indices: 42000651--42000687 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
42000641 CGGCAGCAGC
42000651 AAAAAAAA-GAGAAAAG
1 AAAAAAAAGGA-AAAAG
42000667 AAAAAAAAGGAAAAAG
1 AAAAAAAAGGAAAAAG
42000683 AAAAA
1 AAAAA
42000688 GAAAAAGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 18 0.90
17 2 0.10
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAAAAAGGAAAAAG
Found at i:42000698 original size:7 final size:6
Alignment explanation
Indices: 42000654--42000694 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
42000644 CAGCAGCAAA
*
42000654 AAAAAG AGAAAAG -AAAA- AAAAGG AAAAAG AAAAAG AAAAAG
1 AAAAAG A-AAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
42000695 GAAAGGCCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
5 7 0.23
6 18 0.60
7 5 0.17
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:42001279 original size:18 final size:18
Alignment explanation
Indices: 42001159--42001338 Score: 116
Period size: 17 Copynumber: 10.2 Consensus size: 18
42001149 AAAAATCAAT
42001159 AAAA-TTTCGTG-TTTCA
1 AAAATTTTCGTGTTTTCA
*
42001175 AAAATCTTT-GTG-TTTCC
1 AAAAT-TTTCGTGTTTTCA
42001192 AAAA-TTTCG-GTATTTCA
1 AAAATTTTCGTGT-TTTCA
*
42001209 AAAATTTTCCGTATTTTCA
1 AAAATTTT-CGTGTTTTCA
*
42001228 AAAATTTCCGTG-TTTCA
1 AAAATTTTCGTGTTTTCA
*
42001245 AAAATTTTTTTTTGTGTTTTCA
1 AAAA----TTTTCGTGTTTTCA
*
42001267 ACAATTTTCGTG--TT-A
1 AAAATTTTCGTGTTTTCA
*
42001282 AAAA-ATTCGTG-TTTCAA
1 AAAATTTTCGTGTTTTC-A
*
42001299 AATAATTCTCGTG-TTTCA
1 AA-AATTTTCGTGTTTTCA
*
42001317 TAAATTTTCGTGTTTTCA
1 AAAATTTTCGTGTTTTCA
42001335 AAAA
1 AAAA
42001339 AAAAATTCCC
Statistics
Matches: 129, Mismatches: 16, Indels: 36
0.71 0.09 0.20
Matches are distributed among these distances:
14 6 0.05
15 10 0.08
16 7 0.05
17 40 0.31
18 28 0.22
19 23 0.18
20 1 0.01
21 6 0.05
22 8 0.06
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.46
Consensus pattern (18 bp):
AAAATTTTCGTGTTTTCA
Found at i:42001402 original size:16 final size:16
Alignment explanation
Indices: 42001348--42001402 Score: 56
Period size: 17 Copynumber: 3.3 Consensus size: 16
42001338 AAAAAATTCC
* *
42001348 CGTGCTTCGAAAATTT
1 CGTGTTTCGAAATTTT
*
42001364 CGTGTTTTCAAAAGTTTT
1 CGTG-TTTCGAAA-TTTT
*
42001382 TGTGTTTCGAAATTTT
1 CGTGTTTCGAAATTTT
42001398 CGTGT
1 CGTGT
42001403 CTCAATAAAC
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
16 12 0.39
17 13 0.42
18 6 0.19
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.47
Consensus pattern (16 bp):
CGTGTTTCGAAATTTT
Found at i:42007085 original size:6 final size:6
Alignment explanation
Indices: 42007074--42007103 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
42007064 GATGATTTGA
42007074 GCCCTT GCCCTT GCCCTT GCCCTT GCCCTT
1 GCCCTT GCCCTT GCCCTT GCCCTT GCCCTT
42007104 AGGCTCCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.17, T:0.33
Consensus pattern (6 bp):
GCCCTT
Found at i:42015062 original size:14 final size:14
Alignment explanation
Indices: 42015045--42015073 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
42015035 ATTTAATTTC
42015045 TTTGAATTAATATT
1 TTTGAATTAATATT
42015059 TTTGAATTAATATT
1 TTTGAATTAATATT
42015073 T
1 T
42015074 AATTGATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TTTGAATTAATATT
Found at i:42018228 original size:89 final size:88
Alignment explanation
Indices: 42018024--42018251 Score: 289
Period size: 89 Copynumber: 2.6 Consensus size: 88
42018014 AAGCCCATTT
* * * *
42018024 TTTTTGTTTGCACTCAATTGGGTATTTGAACTTTCAAAATGCATCAAAAAAGCTCTCAAACTATT
1 TTTTT-TTTGCACTCAATTGGGTACTTGAACTTTCAAAATGCAT-TAAAAAGCCCGCAAAC-ATT
* *
42018089 TAAAAAAAAAGCAATTAAGCCCCTAC
63 TAAAAAAAAAACAATTAAGCCACTAC
42018115 TTTTTTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGCATTAAAAAGCCCGCAAAC-TTTAA
1 TTTTTTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGCATTAAAAAGCCCGCAAACATTTAA
* *
42018179 AAAATAAAACAATTAAGCCATTGAG
66 AAAA-AAAACAATTAAGCCACT-AC
* ** *
42018204 TTTTTTTGGCACTCAATTTAGTACTTGAACTGT-AAAATGCATTAAAAA
1 TTTTTTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGCATTAAAAA
42018252 TACTCTCTGA
Statistics
Matches: 123, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
87 9 0.07
88 29 0.24
89 43 0.35
90 37 0.30
91 5 0.04
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (88 bp):
TTTTTTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGCATTAAAAAGCCCGCAAACATTTAA
AAAAAAAACAATTAAGCCACTAC
Found at i:42020214 original size:27 final size:27
Alignment explanation
Indices: 42020163--42020715 Score: 590
Period size: 27 Copynumber: 20.5 Consensus size: 27
42020153 AAAGGTTGTT
* **
42020163 AAATGACCATAATGTCCTTTGTAGGGTA
1 AAATGACCGTAATG-CCCCTGTAGGGTA
* * *
42020191 AAATAACCGTAATACCCCTATAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
* ***
42020218 AAATGACCGTAATACCCCCAAAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
* * * **
42020245 AAATAACCGTAATACTCCC-ATAGAATA
1 AAATGACCGTAATGC-CCCTGTAGGGTA
* *
42020272 AAATAACCGTAATACCCC-GATAGGGTA
1 AAATGACCGTAATGCCCCTG-TAGGGTA
*
42020299 AAATAACCGTAATGCCCCTGTAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
* * *** * * *
42020326 AATTAATTATAATACCTCTATAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
* * *
42020353 AAATGATCGTAATACCCTTGTAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
**
42020380 AAATGACCGTAATGCCATTGTAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
*
42020407 AAATGACCGTAATGCCCCTGTAAGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
* * * *
42020434 AAATGTCCATAATGCCTCTGTAAGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
*
42020461 AAATGACCGTAATGCCTCTGTAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
* * *
42020488 AAATAATCGTAATGTCCCTGTAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
* *
42020515 AAATGACC-TAATGCCCTTGTAAGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
*
42020541 AAATGACCATAATGCCCCTGTAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
**
42020568 AAATGACCGTAATGCCCCTAAAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
**
42020595 AAATGACTATAATGCCCCTGTAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
*
42020622 AAATGATCGTAATGCCCCTGTAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
* * *
42020649 AAATGATCGTAATGCCCTTGTAAGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
*
42020676 AAATGACCGTAATGCCCCTGTAAGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
42020703 AAATGACCGTAAT
1 AAATGACCGTAAT
42020716 ACCTTCGAGG
Statistics
Matches: 453, Mismatches: 68, Indels: 9
0.85 0.13 0.02
Matches are distributed among these distances:
26 26 0.06
27 412 0.91
28 15 0.03
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (27 bp):
AAATGACCGTAATGCCCCTGTAGGGTA
Found at i:42020990 original size:26 final size:26
Alignment explanation
Indices: 42020935--42020990 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
42020925 TATATTATAT
* * *
42020935 TGGCAGCTTTGCTGCGATACTGCTGC
1 TGGCAACTTTGCTGCGATACTACTGA
* *
42020961 TGGCAACTTTGTTGCGATGCTACTGA
1 TGGCAACTTTGCTGCGATACTACTGA
42020987 TGGC
1 TGGC
42020991 TTTGTGCTGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.14, C:0.23, G:0.30, T:0.32
Consensus pattern (26 bp):
TGGCAACTTTGCTGCGATACTACTGA
Found at i:42021023 original size:32 final size:32
Alignment explanation
Indices: 42020981--42021183 Score: 255
Period size: 32 Copynumber: 6.4 Consensus size: 32
42020971 GTTGCGATGC
* * *
42020981 TACTGATGGCTTTGTGCTGATCATATTATCAT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* *
42021013 CACTGATGGCTTTGTGCCAATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* *
42021045 TATTGATGGTTTTGTGCCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
*
42021077 TACTGATGGCTTTGTACCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* * * *
42021109 TACTGATGGCTGTGTGCCGATCATATCACTGC
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* * *
42021141 TACTGATGGCTTTGTGCCAAACATATTACTG-
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
*
42021172 TACTTATGGCTT
1 TACTGATGGCTT
42021184 GTAGCCATTC
Statistics
Matches: 149, Mismatches: 22, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
31 11 0.07
32 138 0.93
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.38
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATTACCGT
Found at i:42021200 original size:22 final size:21
Alignment explanation
Indices: 42021175--42021236 Score: 52
Period size: 22 Copynumber: 2.8 Consensus size: 21
42021165 ATTACTGTAC
42021175 TTATGGCTTGTAGCCATTCTGT
1 TTATGGCTT-TAGCCATTCTGT
* ** *
42021197 TTATAGCTTATAGTTATCCTGT
1 TTATGGCTT-TAGCCATTCTGT
*
42021219 TTACGGCTCTTAGCCATT
1 TTATGGCT-TTAGCCATT
42021237 TTGACTACTG
Statistics
Matches: 29, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
22 28 0.97
23 1 0.03
ACGTcount: A:0.18, C:0.19, G:0.18, T:0.45
Consensus pattern (21 bp):
TTATGGCTTTAGCCATTCTGT
Found at i:42022198 original size:21 final size:21
Alignment explanation
Indices: 42022163--42022221 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
42022153 ATAAAAATAT
*
42022163 AAAAATATTATTAAAATTAGGA
1 AAAAAAATTA-TAAAATTAGGA
* * *
42022185 AAAAAAATTATAAAAATCGTA
1 AAAAAAATTATAAAATTAGGA
*
42022206 AAAGAAATTATAAAAT
1 AAAAAAATTATAAAAT
42022222 ATTGTAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
21 22 0.71
22 9 0.29
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.27
Consensus pattern (21 bp):
AAAAAAATTATAAAATTAGGA
Found at i:42022199 original size:9 final size:9
Alignment explanation
Indices: 42022187--42022258 Score: 63
Period size: 9 Copynumber: 7.4 Consensus size: 9
42022177 AATTAGGAAA
42022187 AAAAATTAT
1 AAAAATTAT
*
42022196 AAAAATCGTAA
1 AAAAAT--TAT
42022207 AAGAAATTAT
1 AA-AAATTAT
*
42022217 AAAATATTGT
1 AAAA-ATTAT
42022227 AAAAATTTAT
1 AAAAA-TTAT
* *
42022237 AAAAGTCAT
1 AAAAATTAT
42022246 AAAAATTAT
1 AAAAATTAT
42022255 AAAA
1 AAAA
42022259 GGCATCAAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
9 23 0.46
10 19 0.38
11 4 0.08
12 4 0.08
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (9 bp):
AAAAATTAT
Found at i:42022236 original size:20 final size:20
Alignment explanation
Indices: 42022185--42022258 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
42022175 AAAATTAGGA
42022185 AAAAAAATTATAAAAATCGT
1 AAAAAAATTATAAAAATCGT
*
42022205 AAAAGAAATTATAAAATATTGT
1 AAAA-AAATTATAAAA-ATCGT
* *
42022227 -AAAAATTTATAAAAGTC--
1 AAAAAAATTATAAAAATCGT
*
42022244 ATAAAAATTATAAAA
1 AAAAAAATTATAAAA
42022259 GGCATCAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
18 12 0.27
19 1 0.02
20 14 0.31
21 14 0.31
22 4 0.09
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
AAAAAAATTATAAAAATCGT
Found at i:42022268 original size:19 final size:19
Alignment explanation
Indices: 42022226--42022269 Score: 63
Period size: 18 Copynumber: 2.3 Consensus size: 19
42022216 TAAAATATTG
*
42022226 TAAAAATTTATAAAAGTCA
1 TAAAAATTTATAAAAGGCA
42022245 TAAAAA-TTATAAAAGGCA
1 TAAAAATTTATAAAAGGCA
42022263 TCAAAAA
1 T-AAAAA
42022270 GACTAACGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.61, C:0.07, G:0.07, T:0.25
Consensus pattern (19 bp):
TAAAAATTTATAAAAGGCA
Found at i:42022441 original size:9 final size:10
Alignment explanation
Indices: 42022410--42022607 Score: 84
Period size: 9 Copynumber: 20.6 Consensus size: 10
42022400 AGTACGATAA
42022410 TTTTATAATT
1 TTTTATAATT
42022420 TTTTATGAA--
1 TTTTAT-AATT
42022429 TTTTAT-ATT
1 TTTTATAATT
42022438 TTTTATAATT
1 TTTTATAATT
*
42022448 TTCTTACAA--
1 TT-TTATAATT
* **
42022457 CTTTATAAAA
1 TTTTATAATT
42022467 TTTTATAATT
1 TTTTATAATT
42022477 TTTTAT-A-T
1 TTTTATAATT
* *
42022485 TTCTAT-ATA
1 TTTTATAATT
*
42022494 TTTTCTAA-T
1 TTTTATAATT
*
42022503 TTTTATGA-T
1 TTTTATAATT
**
42022512 TTTTATAAAA
1 TTTTATAATT
*
42022522 TTTTACAA-T
1 TTTTATAATT
42022531 TTTTATATATT
1 TTTTATA-ATT
42022542 TTTTA-AGA-T
1 TTTTATA-ATT
*
42022551 TTTCATAACTT
1 TTTTATAA-TT
* *
42022562 TTTTGTAATA
1 TTTTATAATT
*
42022572 TTTAATAA-T
1 TTTTATAATT
42022581 TTTTA-AATAT
1 TTTTATAAT-T
*
42022591 TATTATATATT
1 TTTTATA-ATT
42022602 TTTTAT
1 TTTTAT
42022608 TAAAATTTAA
Statistics
Matches: 140, Mismatches: 29, Indels: 37
0.68 0.14 0.18
Matches are distributed among these distances:
7 1 0.01
8 14 0.10
9 48 0.34
10 48 0.34
11 27 0.19
12 2 0.01
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (10 bp):
TTTTATAATT
Found at i:42022545 original size:20 final size:19
Alignment explanation
Indices: 42022522--42022606 Score: 66
Period size: 20 Copynumber: 4.3 Consensus size: 19
42022512 TTTTATAAAA
42022522 TTTTACAATTTTTATATATT
1 TTTTA-AATTTTTATATATT
*
42022542 TTTTAAGATTTTCATA-ACTT
1 TTTTAA-ATTTTTATATA-TT
* * *
42022562 TTTTGTAATATTTA-ATAAT
1 TTTT-AAATTTTTATATATT
42022581 TTTTAAATATTATTATATATT
1 TTTTAAAT-TT-TTATATATT
42022602 TTTTA
1 TTTTA
42022607 TTAAAATTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 13
0.70 0.11 0.18
Matches are distributed among these distances:
18 3 0.06
19 9 0.18
20 28 0.56
21 10 0.20
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTTAAATTTTTATATATT
Found at i:42026080 original size:13 final size:13
Alignment explanation
Indices: 42026057--42026081 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42026047 TTTATTTTAG
42026057 TATTTTATTTACT
1 TATTTTATTTACT
42026070 TATTTTATTTAC
1 TATTTTATTTAC
42026082 AGTTATACTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (13 bp):
TATTTTATTTACT
Found at i:42026182 original size:16 final size:16
Alignment explanation
Indices: 42026157--42026191 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
42026147 TAATTCTCAT
*
42026157 TTTATTTATTTACGTA
1 TTTATCTATTTACGTA
*
42026173 TTTATCTATTTACTTA
1 TTTATCTATTTACGTA
42026189 TTT
1 TTT
42026192 TTACAATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.23, C:0.09, G:0.03, T:0.66
Consensus pattern (16 bp):
TTTATCTATTTACGTA
Found at i:42048553 original size:60 final size:60
Alignment explanation
Indices: 42048460--42048591 Score: 237
Period size: 60 Copynumber: 2.2 Consensus size: 60
42048450 TAAACGTGAG
* * *
42048460 ATTTATGTAAATCAAATGGTATATGATTTTTTTTATTCTGATCGTAATATTTAACACTTC
1 ATTTATGTAAATAAAATGCTATATGATTTTTTTTATTCTGATCGTAATATTGAACACTTC
42048520 ATTTATGTAAATAAAATGCTATATGATTTTTTTTATTCTGATCGTAATATTGAACACTTC
1 ATTTATGTAAATAAAATGCTATATGATTTTTTTTATTCTGATCGTAATATTGAACACTTC
42048580 ATTTATGTAAAT
1 ATTTATGTAAAT
42048592 CGTGTTTAAA
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 69 1.00
ACGTcount: A:0.33, C:0.09, G:0.10, T:0.48
Consensus pattern (60 bp):
ATTTATGTAAATAAAATGCTATATGATTTTTTTTATTCTGATCGTAATATTGAACACTTC
Found at i:42053205 original size:82 final size:82
Alignment explanation
Indices: 42053056--42053211 Score: 267
Period size: 82 Copynumber: 1.9 Consensus size: 82
42053046 CCACCTAATT
* *
42053056 TGGAGTAGAAGTTGAGATTTCTTTGTTTTCATTGGTTTTCTATGCTTTCTTGCATCTGTTCCAAA
1 TGGAGTAGAAGTTGAGATTTATTTGTTTTCATTGGTTTTCTATGCTTTCTTGCATCTATTCCAAA
42053121 ATGCGTTTTTTAGTCCC
66 ATGCGTTTTTTAGTCCC
* *
42053138 TGGAGTAGAAGTTGAGATTTATTTGTTTTCATTGGTTTTCTATGCTTTCTTGCATTTATTCCGAA
1 TGGAGTAGAAGTTGAGATTTATTTGTTTTCATTGGTTTTCTATGCTTTCTTGCATCTATTCCAAA
*
42053203 ATGGGTTTT
66 ATGCGTTTT
42053212 AATTCTTCTA
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
82 69 1.00
ACGTcount: A:0.18, C:0.13, G:0.21, T:0.49
Consensus pattern (82 bp):
TGGAGTAGAAGTTGAGATTTATTTGTTTTCATTGGTTTTCTATGCTTTCTTGCATCTATTCCAAA
ATGCGTTTTTTAGTCCC
Found at i:42053562 original size:6 final size:6
Alignment explanation
Indices: 42053551--42053589 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
42053541 GATAACTCTC
* *
42053551 TTTCCG TTTCCG TTTCCG TTTCCT TTTCCT TTATCCG TT
1 TTTCCG TTTCCG TTTCCG TTTCCG TTTCCG TT-TCCG TT
42053590 ACTCCTTGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 25 0.83
7 5 0.17
ACGTcount: A:0.03, C:0.31, G:0.10, T:0.56
Consensus pattern (6 bp):
TTTCCG
Found at i:42054917 original size:14 final size:14
Alignment explanation
Indices: 42054898--42054926 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
42054888 CAAAAAAAAT
42054898 AAATTCATTTTCTA
1 AAATTCATTTTCTA
42054912 AAATTCATTTTCTA
1 AAATTCATTTTCTA
42054926 A
1 A
42054927 CCAGAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATTCATTTTCTA
Found at i:42054980 original size:59 final size:59
Alignment explanation
Indices: 42054867--42054981 Score: 203
Period size: 59 Copynumber: 1.9 Consensus size: 59
42054857 TCATCTAAAT
*
42054867 ACCAGAAAATATTAACTTTTTCAAAAAAAATAAATTCATTTTCTAAAATTCATTTTCTA
1 ACCAGAAAATATTAACTTTTCCAAAAAAAATAAATTCATTTTCTAAAATTCATTTTCTA
* *
42054926 ACCAGAAAATATTAGCTTTTCCAAAAAAAGTAAATTCATTTTCTAAAATTCATTTT
1 ACCAGAAAATATTAACTTTTCCAAAAAAAATAAATTCATTTTCTAAAATTCATTTT
42054982 TCGGAAACTA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.44, C:0.14, G:0.03, T:0.38
Consensus pattern (59 bp):
ACCAGAAAATATTAACTTTTCCAAAAAAAATAAATTCATTTTCTAAAATTCATTTTCTA
Found at i:42057617 original size:2 final size:2
Alignment explanation
Indices: 42057610--42057640 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
42057600 TAGGATGCGT
42057610 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42057641 TAACCATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42061407 original size:2 final size:2
Alignment explanation
Indices: 42061400--42061424 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
42061390 CGTACTTATT
42061400 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
42061425 CTTTATCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42063647 original size:6 final size:6
Alignment explanation
Indices: 42063636--42063669 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
42063626 GTGAGTTTGA
42063636 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCT
42063670 AGTTCTGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TTCTTT
Found at i:42063675 original size:18 final size:18
Alignment explanation
Indices: 42063636--42063675 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
42063626 GTGAGTTTGA
**
42063636 TTCTTTTTCTTTTTCTTT
1 TTCTTTTTCTTTTTCTAG
42063654 TTCTTTTTCTTTTTCTAG
1 TTCTTTTTCTTTTTCTAG
42063672 TTCT
1 TTCT
42063676 GTTTGGATGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.78
Consensus pattern (18 bp):
TTCTTTTTCTTTTTCTAG
Found at i:42069051 original size:23 final size:23
Alignment explanation
Indices: 42069025--42069075 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
42069015 TGGAAAGAAG
* *
42069025 TGTAATATCCTGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
42069048 TGTAATACCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
*
42069071 AGTAA
1 TGTAA
42069076 GAAAGTACGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (23 bp):
TGTAATACCCCGAAAATTACTAC
Found at i:42069570 original size:8 final size:8
Alignment explanation
Indices: 42069557--42069591 Score: 52
Period size: 8 Copynumber: 4.1 Consensus size: 8
42069547 TTTTAAATAA
42069557 TATTTTAT
1 TATTTTAT
42069565 TATTTTTTAT
1 TA--TTTTAT
42069575 TATTTTAT
1 TATTTTAT
42069583 TATTTTAT
1 TATTTTAT
42069591 T
1 T
42069592 TAGTATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 17 0.68
10 8 0.32
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (8 bp):
TATTTTAT
Found at i:42080074 original size:20 final size:19
Alignment explanation
Indices: 42080029--42080075 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
42080019 AGCCCATTCC
*
42080029 AATTTAA-AAATTAATATA
1 AATTTAATAAATTAATAAA
**
42080047 AAGATAATAATATTAATAAA
1 AATTTAATAA-ATTAATAAA
42080067 AATTTAATA
1 AATTTAATA
42080076 TCAATAAAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
18 5 0.23
19 2 0.09
20 15 0.68
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
AATTTAATAAATTAATAAA
Found at i:42089765 original size:25 final size:26
Alignment explanation
Indices: 42089724--42089855 Score: 113
Period size: 25 Copynumber: 5.3 Consensus size: 26
42089714 TCCCGTTATG
*
42089724 TGGCTCTC-ACGAGCTTCTCGATTAA
1 TGGCTCTCTATGAGCTTCTCGATTAA
* * *
42089749 TGGCTCTCT-TGAACTTC-CCATTTA
1 TGGCTCTCTATGAGCTTCTCGATTAA
*
42089773 TGGCT-TGTATGAGCTT-TCCGA-TAA
1 TGGCTCTCTATGAGCTTCT-CGATTAA
42089797 TTGGCTCTCTA-GAGCTTCTCGA-TAA
1 -TGGCTCTCTATGAGCTTCTCGATTAA
42089822 TTGGCTCT-TATGAGCTT-TCCGATTAA
1 -TGGCTCTCTATGAGCTTCT-CGATTAA
42089848 TGGCTCTC
1 TGGCTCTC
42089856 CGGAGCTTCC
Statistics
Matches: 87, Mismatches: 9, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
23 2 0.02
24 21 0.24
25 57 0.66
26 7 0.08
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.38
Consensus pattern (26 bp):
TGGCTCTCTATGAGCTTCTCGATTAA
Found at i:42089908 original size:25 final size:25
Alignment explanation
Indices: 42089879--42089926 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
42089869 TATTAGCTCG
*
42089879 CATGAACTTCCTGTTACATGGCTTA
1 CATGAACTTCATGTTACATGGCTTA
* *
42089904 CATGAGCTTCATGTTATATGGCT
1 CATGAACTTCATGTTACATGGCT
42089927 CAAAAGAGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.38
Consensus pattern (25 bp):
CATGAACTTCATGTTACATGGCTTA
Found at i:42098412 original size:25 final size:25
Alignment explanation
Indices: 42098384--42098436 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
42098374 ATGACAATCT
42098384 AATCCTTATTCAATCTATATCCTTA
1 AATCCTTATTCAATCTATATCCTTA
42098409 AATCCTTATTCAATCTATATCCTTA
1 AATCCTTATTCAATCTATATCCTTA
42098434 AAT
1 AAT
42098437 ATGGAAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.34, C:0.23, G:0.00, T:0.43
Consensus pattern (25 bp):
AATCCTTATTCAATCTATATCCTTA
Found at i:42101701 original size:2 final size:2
Alignment explanation
Indices: 42101694--42101724 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
42101684 AATAAAATGA
42101694 AT 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 AT A
42101725 GTCATGATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42102119 original size:7 final size:6
Alignment explanation
Indices: 42102074--42102103 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
42102064 TAAAAATCAA
42102074 AAAATC AAAATC AAAATC AAAATTC AAAAT
1 AAAATC AAAATC AAAATC AAAA-TC AAAAT
42102104 ATATAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.67, C:0.13, G:0.00, T:0.20
Consensus pattern (6 bp):
AAAATC
Found at i:42105617 original size:18 final size:19
Alignment explanation
Indices: 42105580--42105619 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
42105570 TATTTTGTAT
42105580 AAATTAAATATAAGATTAA
1 AAATTAAATATAAGATTAA
42105599 AAATTGAAA-ATAA-ATTAA
1 AAATT-AAATATAAGATTAA
42105617 AAA
1 AAA
42105620 CATATAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.40
19 9 0.45
20 3 0.15
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (19 bp):
AAATTAAATATAAGATTAA
Found at i:42107175 original size:2 final size:2
Alignment explanation
Indices: 42107168--42107193 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42107158 GAAAAACAAG
42107168 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
42107194 GTGTTGTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42107644 original size:2 final size:2
Alignment explanation
Indices: 42107632--42107663 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
42107622 GAATTACTAG
*
42107632 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42107664 AAATTAACCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:42124299 original size:15 final size:16
Alignment explanation
Indices: 42124271--42124301 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
42124261 AGGGGTTAAG
42124271 GGTTTAATGATTTTGA
1 GGTTTAATGATTTTGA
42124287 GGTTTAA-GATTTTGA
1 GGTTTAATGATTTTGA
42124302 TTTTAAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (16 bp):
GGTTTAATGATTTTGA
Found at i:42124393 original size:62 final size:61
Alignment explanation
Indices: 42124273--42124401 Score: 134
Period size: 61 Copynumber: 2.1 Consensus size: 61
42124263 GGGTTAAGGG
* ** * * * * *
42124273 TTTAATGATTTTGAGGTTTAAGATTTTGATTTTAAGTTTAGGAATGGTAATTAGGTTTAATA
1 TTTAATGATTTTAAGGTTTAAGAGGTTGATTTCAAGGTTAGGAACGATAATTAAGTTT-ATA
* *
42124335 TTTAATGATTTTAAGGTTTAAG-GGTTGATTTCGAGGTTAGGGACGATAATGTAAGTTTATA
1 TTTAATGATTTTAAGGTTTAAGAGGTTGATTTCAAGGTTAGGAACGATAAT-TAAGTTTATA
*
42124396 ATTAAT
1 TTTAAT
42124402 TTTTTAAATA
Statistics
Matches: 55, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
61 28 0.51
62 27 0.49
ACGTcount: A:0.31, C:0.02, G:0.22, T:0.45
Consensus pattern (61 bp):
TTTAATGATTTTAAGGTTTAAGAGGTTGATTTCAAGGTTAGGAACGATAATTAAGTTTATA
Found at i:42126134 original size:11 final size:11
Alignment explanation
Indices: 42126120--42126205 Score: 62
Period size: 11 Copynumber: 8.4 Consensus size: 11
42126110 TATTTTTTTA
42126120 TTTTAAAATAT
1 TTTTAAAATAT
*
42126131 TTTTAAAATAC
1 TTTTAAAATAT
*
42126142 TTTCAAAAT-T
1 TTTTAAAATAT
*
42126152 TTTT----TAA
1 TTTTAAAATAT
42126159 TTTTAAAATAT
1 TTTTAAAATAT
42126170 TTTTAAAATACT
1 TTTTAAAATA-T
*
42126182 TTTT--TA-AT
1 TTTTAAAATAT
42126190 TTTTAAAATAAT
1 TTTTAAAAT-AT
42126202 TTTT
1 TTTT
42126206 TTGTATTTAT
Statistics
Matches: 57, Mismatches: 8, Indels: 19
0.68 0.10 0.23
Matches are distributed among these distances:
6 1 0.02
7 4 0.07
8 5 0.09
9 1 0.02
10 5 0.09
11 30 0.53
12 11 0.19
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:42126191 original size:39 final size:39
Alignment explanation
Indices: 42126069--42126193 Score: 189
Period size: 39 Copynumber: 3.2 Consensus size: 39
42126059 TTATTTTTAA
*
42126069 AATTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTT
1 AATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTT
***
42126108 ATTATTTTTTT-ATTTTAAAATATTTTTAAAATACTTTCAA
1 A--ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTT
42126148 AATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTT
1 AATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTT
42126187 AATTTTT
1 AATTTTT
42126194 AAAATAATTT
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
38 8 0.11
39 34 0.45
40 27 0.36
41 7 0.09
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (39 bp):
AATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTT
Found at i:42126207 original size:21 final size:20
Alignment explanation
Indices: 42126168--42126206 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
42126158 ATTTTAAAAT
42126168 ATTTTTAAAATACTTTTTTA
1 ATTTTTAAAATACTTTTTTA
*
42126188 ATTTTTAAAATAATTTTTT
1 ATTTTTAAAATACTTTTTT
42126207 TGTATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTTTAAAATACTTTTTTA
Found at i:42127854 original size:3 final size:3
Alignment explanation
Indices: 42127846--42127916 Score: 133
Period size: 3 Copynumber: 23.3 Consensus size: 3
42127836 TTATCATCTT
42127846 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
42127894 TTA TTA TTA TTA TTA TTA CTTA T
1 TTA TTA TTA TTA TTA TTA -TTA T
42127917 ATATATACGC
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 64 0.96
4 3 0.04
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:42128014 original size:15 final size:15
Alignment explanation
Indices: 42127996--42128044 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
42127986 CGTTATTTCA
42127996 TTTATGTTTTCTTT-T
1 TTTAT-TTTTCTTTAT
*
42128011 TTTATTATTTATTTAT
1 TTTATT-TTTCTTTAT
*
42128027 TTTATTTTTCTTTCT
1 TTTATTTTTCTTTAT
42128042 TTT
1 TTT
42128045 CTAAAAAGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 1 0.03
15 21 0.72
16 7 0.24
ACGTcount: A:0.12, C:0.06, G:0.02, T:0.80
Consensus pattern (15 bp):
TTTATTTTTCTTTAT
Found at i:42128038 original size:30 final size:33
Alignment explanation
Indices: 42127979--42128044 Score: 86
Period size: 31 Copynumber: 2.1 Consensus size: 33
42127969 AGTATTATTA
42127979 TTATTATCGTTATTTCATTTATGTTTTCTTT-TT
1 TTATTATC-TTATTTCATTTATGTTTTCTTTCTT
42128012 TTATTAT-TTATTT-ATTTTAT-TTTTCTTTCTT
1 TTATTATCTTATTTCA-TTTATGTTTTCTTTCTT
42128043 TT
1 TT
42128045 CTAAAAAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
30 9 0.29
31 15 0.48
33 7 0.23
ACGTcount: A:0.15, C:0.08, G:0.03, T:0.74
Consensus pattern (33 bp):
TTATTATCTTATTTCATTTATGTTTTCTTTCTT
Found at i:42134704 original size:29 final size:29
Alignment explanation
Indices: 42134662--42134720 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
42134652 ATATAAAAAC
42134662 TAAAAAGCAAAGCAAAATGATGGTGGAGA
1 TAAAAAGCAAAGCAAAATGATGGTGGAGA
42134691 TAAAAAGCAAAGCAAAATGATGGTGGAGA
1 TAAAAAGCAAAGCAAAATGATGGTGGAGA
42134720 T
1 T
42134721 TTAGATTAAA
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:0.51, C:0.07, G:0.27, T:0.15
Consensus pattern (29 bp):
TAAAAAGCAAAGCAAAATGATGGTGGAGA
Found at i:42136860 original size:29 final size:28
Alignment explanation
Indices: 42136789--42136860 Score: 74
Period size: 27 Copynumber: 2.5 Consensus size: 28
42136779 AAGAACTAGA
* *
42136789 TAAAATATATATAGTTTTTGATGAATTGG
1 TAAAATATA-ATATTTTTTGATGAAATGG
* * *
42136818 TAAAAT-CACTATTTTTTTATGAAATGG
1 TAAAATATAATATTTTTTGATGAAATGG
42136845 TAAAAATATAATATTT
1 T-AAAATATAATATTT
42136861 GAGTTTGTAG
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
27 16 0.47
28 6 0.18
29 12 0.35
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.44
Consensus pattern (28 bp):
TAAAATATAATATTTTTTGATGAAATGG
Found at i:42138213 original size:13 final size:13
Alignment explanation
Indices: 42138195--42138219 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42138185 CCCAATTGGT
42138195 AATTGAACTTGAA
1 AATTGAACTTGAA
42138208 AATTGAACTTGA
1 AATTGAACTTGA
42138220 GATCGTAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (13 bp):
AATTGAACTTGAA
Found at i:42138493 original size:26 final size:26
Alignment explanation
Indices: 42138457--42138508 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
42138447 TTAATGATTG
42138457 AGTGGTGGAAGAATTACACTCCTACT
1 AGTGGTGGAAGAATTACACTCCTACT
42138483 AGTGGTGGAAGAATTACACTCCTACT
1 AGTGGTGGAAGAATTACACTCCTACT
42138509 TAGACTCTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (26 bp):
AGTGGTGGAAGAATTACACTCCTACT
Done.