Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 97 of 186
Found at i:31781010 original size:46 final size:46
Alignment explanation
Indices: 31780892--31781012 Score: 163
Period size: 46 Copynumber: 2.6 Consensus size: 46
31780882 TGCCATAGTG
* * * *
31780892 TCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACTCA-TTTCATGTCACGCTACCATGGTA
* *
31780938 TATTTCAACCATGGTCTTATTCATTTCATGTCACGCTACCATGGTA
1 TCTTTCAACCATGGTCTTACTCATTTCATGTCACGCTACCATGGTA
*
31780984 TCTTTCAACCATGGTCTTACACATTTCAT
1 TCTTTCAACCATGGTCTTACTCATTTCAT
31781013 ATCAGAGAAC
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
45 4 0.06
46 61 0.94
ACGTcount: A:0.21, C:0.24, G:0.12, T:0.42
Consensus pattern (46 bp):
TCTTTCAACCATGGTCTTACTCATTTCATGTCACGCTACCATGGTA
Found at i:31785420 original size:53 final size:53
Alignment explanation
Indices: 31785237--31785443 Score: 200
Period size: 53 Copynumber: 3.8 Consensus size: 53
31785227 ATTAGGGTTT
* * * *
31785237 AAGGATACCAAGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTTTACAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAG-TTCATAAGGC
* * * * * * * *
31785291 AAGGAAATCATATAAGACCATGTCAAGACATGGCATTGATAAACTACTATAAGTC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGT-AAGTTC-ATAAGGC
* * * *
31785346 AAAGATCCCATGTAAGACCATGCCAAGGCATGGC-TATGGTGAGTTCATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAT-TGGTAAGTTCATAAGGC
* * *
31785399 AAGGATACCACGTAAGACCATGTCAAGACATGGCAATGGTAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT
31785444 TAAAAAGGAA
Statistics
Matches: 118, Mismatches: 31, Indels: 9
0.75 0.20 0.06
Matches are distributed among these distances:
53 43 0.36
54 38 0.32
55 37 0.31
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.21
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCATAAGGC
Found at i:31790609 original size:43 final size:43
Alignment explanation
Indices: 31790551--31790633 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 43
31790541 GACATGGGCA
* * * *
31790551 TGTCTCTTGATCGTGTGTGGCACACGGCCTGACCATATGGGTG
1 TGTCTCTCGACCGTGTGTGGCAAACGGCCTGACCAAATGGGTG
31790594 TGTCTCTCGACCGTGTGTGGCAAACGGCCTGACCAAATGG
1 TGTCTCTCGACCGTGTGTGGCAAACGGCCTGACCAAATGG
31790634 ACGTGTGTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.17, C:0.25, G:0.31, T:0.27
Consensus pattern (43 bp):
TGTCTCTCGACCGTGTGTGGCAAACGGCCTGACCAAATGGGTG
Found at i:31790943 original size:14 final size:14
Alignment explanation
Indices: 31790924--31790958 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
31790914 TCAATTAAGG
31790924 AAATTTTGAGGCCA
1 AAATTTTGAGGCCA
*
31790938 AAATTTCGAGGCCA
1 AAATTTTGAGGCCA
31790952 AAATTTT
1 AAATTTT
31790959 TTATAGGGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.31
Consensus pattern (14 bp):
AAATTTTGAGGCCA
Found at i:31792827 original size:41 final size:41
Alignment explanation
Indices: 31792711--31792976 Score: 430
Period size: 41 Copynumber: 6.6 Consensus size: 41
31792701 ATTAGCGGTA
* *
31792711 TTTTTGACAAAACGCCGCT-AAAAACAGAGCAATAGCGGCG
1 TTTTTGGCAAAGCGCCGCTAAAAAACAGAGCAATAGCGGCG
31792751 TTTTTGGCAAAGCGCCGCT-AAAAACAGAGCAATAGCGGCG
1 TTTTTGGCAAAGCGCCGCTAAAAAACAGAGCAATAGCGGCG
*
31792791 TTTTTGGCAAAGCGCCCCTAAAAAACAGAGCAATAGCGGCG
1 TTTTTGGCAAAGCGCCGCTAAAAAACAGAGCAATAGCGGCG
*
31792832 TTTTTGGCAAAGCGCCGCTAAAAAACATAGCAATAGCGGCG
1 TTTTTGGCAAAGCGCCGCTAAAAAACAGAGCAATAGCGGCG
* *
31792873 TTTTTGTCAAAGCGCCGCTAAAAAATAGAGCAATAGCGGCG
1 TTTTTGGCAAAGCGCCGCTAAAAAACAGAGCAATAGCGGCG
*
31792914 TTTTTGGCAAAGCGCCGCGAAAAAACAGAGCAATAGCGGCG
1 TTTTTGGCAAAGCGCCGCTAAAAAACAGAGCAATAGCGGCG
* *
31792955 TTTTTGGTAAAACG-CGCTAAAA
1 TTTTTGGCAAAGCGCCGCTAAAA
31792977 GTCATATAAC
Statistics
Matches: 211, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
40 63 0.30
41 148 0.70
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.19
Consensus pattern (41 bp):
TTTTTGGCAAAGCGCCGCTAAAAAACAGAGCAATAGCGGCG
Found at i:31793106 original size:46 final size:47
Alignment explanation
Indices: 31792978--31793108 Score: 138
Period size: 46 Copynumber: 2.7 Consensus size: 47
31792968 GCGCTAAAAG
* * * * *
31792978 TCATATAACCTCTAAAACCTTAAACCCCCAAAAGAATCATAGACACTAG
1 TCATATAACCCCTAAAACCCTAAA--CCCAAAAAAACCATAGACACTAA
* * * *
31793027 TCTATATAACCCCTAAAACCCTAGATCCAAAAAAACCCTAGATACTAA
1 TC-ATATAACCCCTAAAACCCTAAACCCAAAAAAACCATAGACACTAA
*
31793075 TC-TATAACCCCTAAAACCCTAAACCCTAAAAAAC
1 TCATATAACCCCTAAAACCCTAAACCCAAAAAAAC
31793109 ATCATATGGA
Statistics
Matches: 69, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
46 29 0.42
48 19 0.28
49 2 0.03
50 19 0.28
ACGTcount: A:0.46, C:0.31, G:0.04, T:0.20
Consensus pattern (47 bp):
TCATATAACCCCTAAAACCCTAAACCCAAAAAAACCATAGACACTAA
Found at i:31793955 original size:6 final size:6
Alignment explanation
Indices: 31793944--31793968 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
31793934 ACCCATATGA
31793944 TCCCTT TCCCTT TCCCTT TCCCTT T
1 TCCCTT TCCCTT TCCCTT TCCCTT T
31793969 GGTTTTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (6 bp):
TCCCTT
Found at i:31794619 original size:7 final size:7
Alignment explanation
Indices: 31794607--31794659 Score: 106
Period size: 7 Copynumber: 7.6 Consensus size: 7
31794597 AATCTTTAAA
31794607 AAAATTG
1 AAAATTG
31794614 AAAATTG
1 AAAATTG
31794621 AAAATTG
1 AAAATTG
31794628 AAAATTG
1 AAAATTG
31794635 AAAATTG
1 AAAATTG
31794642 AAAATTG
1 AAAATTG
31794649 AAAATTG
1 AAAATTG
31794656 AAAA
1 AAAA
31794660 ATAAAAAAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 46 1.00
ACGTcount: A:0.60, C:0.00, G:0.13, T:0.26
Consensus pattern (7 bp):
AAAATTG
Found at i:31794666 original size:14 final size:14
Alignment explanation
Indices: 31794606--31794666 Score: 86
Period size: 14 Copynumber: 4.4 Consensus size: 14
31794596 AAATCTTTAA
31794606 AAAAATTGAAAATT
1 AAAAATTGAAAATT
*
31794620 GAAAATTGAAAATT
1 AAAAATTGAAAATT
*
31794634 GAAAATTGAAAATT
1 AAAAATTGAAAATT
* *
31794648 GAAAATTGAAAAAT
1 AAAAATTGAAAATT
31794662 AAAAA
1 AAAAA
31794667 AATAAAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 44 1.00
ACGTcount: A:0.64, C:0.00, G:0.11, T:0.25
Consensus pattern (14 bp):
AAAAATTGAAAATT
Found at i:31794839 original size:30 final size:26
Alignment explanation
Indices: 31794788--31794842 Score: 74
Period size: 30 Copynumber: 2.0 Consensus size: 26
31794778 TAATCTCAGC
31794788 AAAAAAATTTTAAAAGAAAAAAATAG
1 AAAAAAATTTTAAAAGAAAAAAATAG
31794814 AAAAAAATATGTTAAAAATGAAAAAAATA
1 AAAAAAAT-T-TT-AAAA-GAAAAAAATA
31794843 ATAAAATTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 8 0.32
27 1 0.04
28 2 0.08
29 4 0.16
30 10 0.40
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (26 bp):
AAAAAAATTTTAAAAGAAAAAAATAG
Found at i:31794901 original size:22 final size:22
Alignment explanation
Indices: 31794873--31794917 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
31794863 CGTTTTTAGT
* *
31794873 AAAAACGCCGCAAAAAGTTGAG
1 AAAAACGCCACAAAAAATTGAG
31794895 AAAAACGCCACAAAAAATTGAG
1 AAAAACGCCACAAAAAATTGAG
31794917 A
1 A
31794918 TACAGTGGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.56, C:0.18, G:0.18, T:0.09
Consensus pattern (22 bp):
AAAAACGCCACAAAAAATTGAG
Found at i:31810941 original size:5 final size:5
Alignment explanation
Indices: 31810931--31810959 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
31810921 CATTTTTATG
31810931 AATAT AATAT AATAT AATAT AATAT AATA
1 AATAT AATAT AATAT AATAT AATAT AATA
31810960 GACAAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:31812070 original size:15 final size:14
Alignment explanation
Indices: 31812043--31812069 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
31812033 GGCTATAGTG
31812043 AAATATTAAAAAAT
1 AAATATTAAAAAAT
31812057 AAATATTAAAAAA
1 AAATATTAAAAAA
31812070 AGGAGACATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATATTAAAAAAT
Found at i:31816585 original size:47 final size:47
Alignment explanation
Indices: 31816528--31816737 Score: 305
Period size: 47 Copynumber: 4.4 Consensus size: 47
31816518 ATTGATGTAC
* * *
31816528 AAGTATATATATGTGATAGGGCCGAGTGGCCAATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
*
31816575 AAGTATATATATGCGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
1 AAGTGTATATAT--GTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* *
31816624 ACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
1 A-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* *
31816671 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGG
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
*
31816718 AAGTGTATAAATGTGATAAG
1 AAGTGTATATATGTGATAAG
31816738 TCCCGAAGGG
Statistics
Matches: 149, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
46 1 0.01
47 107 0.72
49 40 0.27
50 1 0.01
ACGTcount: A:0.33, C:0.09, G:0.31, T:0.28
Consensus pattern (47 bp):
AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
Found at i:31816662 original size:22 final size:22
Alignment explanation
Indices: 31816635--31816709 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
31816625 CATGTGTATG
31816635 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * ***
31816657 TGTGATGAATG-TGAAAGTGTATATA
1 TGTGAT-AAGGCCG-AA-TGGCCA-A
31816682 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
31816704 TGTGAT
1 TGTGAT
31816710 GGATGTGGAA
Statistics
Matches: 38, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 14 0.37
23 8 0.21
24 8 0.21
25 8 0.21
ACGTcount: A:0.32, C:0.11, G:0.31, T:0.27
Consensus pattern (22 bp):
TGTGATAAGGCCGAATGGCCAA
Found at i:31816707 original size:94 final size:95
Alignment explanation
Indices: 31816539--31816716 Score: 304
Period size: 96 Copynumber: 1.9 Consensus size: 95
31816529 AGTATATATA
* *
31816539 TGTGATAGGGCCGAGTGGCCAATGTGATGAATGTGAAAGTATATATATGCGTGATAAGGCCGAAT
1 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTATATATAT-CGTGATAAGGCCGAAT
31816604 GGCCAATGTGATGAATGTGAACATGTGTATG
65 GGCCAATGTGATGAATGTGAACATGTGTATG
*
31816635 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATAT-GTGATAAGGCCGAATG
1 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTATATATATCGTGATAAGGCCGAATG
*
31816699 GCCAATGTGATGGATGTG
66 GCCAATGTGATGAATGTG
31816717 GAAGTGTATA
Statistics
Matches: 78, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
94 33 0.42
96 45 0.58
ACGTcount: A:0.30, C:0.10, G:0.33, T:0.27
Consensus pattern (95 bp):
TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTATATATATCGTGATAAGGCCGAATG
GCCAATGTGATGAATGTGAACATGTGTATG
Found at i:31816737 original size:94 final size:94
Alignment explanation
Indices: 31816528--31816737 Score: 298
Period size: 96 Copynumber: 2.2 Consensus size: 94
31816518 ATTGATGTAC
* * *
31816528 AAGTATATATATGTGATAGGGCCGAGTGGCCAATGTGATGAATGTGAAAGTATATATATGCGTGA
1 AAGTGTATA-ATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTATATATAT-CGTGA
31816593 TAAGGCCGAATGGCCAATGTGATGAATGTGA
64 TAAGGCCGAATGGCCAATGTGATGAATGTGA
* *
31816624 ACATGTGTAT-GTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATAT-GTGA
1 A-A-GTGTATAATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTATATATATCGTGA
* *
31816687 TAAGGCCGAATGGCCAATGTGATGGATGTGG
64 TAAGGCCGAATGGCCAATGTGATGAATGTGA
31816718 AAGTGTATAAATGTGATAAG
1 AAGTGTAT-AATGTGATAAG
31816738 TCCCGAAGGG
Statistics
Matches: 102, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
92 6 0.06
93 1 0.01
94 43 0.42
96 46 0.45
97 1 0.01
98 5 0.05
ACGTcount: A:0.33, C:0.09, G:0.31, T:0.28
Consensus pattern (94 bp):
AAGTGTATAATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTATATATATCGTGATA
AGGCCGAATGGCCAATGTGATGAATGTGA
Found at i:31829869 original size:28 final size:28
Alignment explanation
Indices: 31829829--31829940 Score: 109
Period size: 28 Copynumber: 4.0 Consensus size: 28
31829819 GGCCAAGCAA
* * *
31829829 AATATCTCTACAGTGACCAGTGTTACTG
1 AATATCTCTACAGAGACCACTATTACTG
*
31829857 AATATCTCTACAGAGACCACTATTACTT
1 AATATCTCTACAGAGACCACTATTACTG
* ** *
31829885 AATGTCTCTAGGGAGACCACAATTACTG
1 AATATCTCTACAGAGACCACTATTACTG
* * *
31829913 AATGTCTCTTC-GAAGACCACTGTTACTG
1 AATATCTCTACAG-AGACCACTATTACTG
31829941 TATGTGTCAT
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
27 1 0.01
28 69 0.99
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (28 bp):
AATATCTCTACAGAGACCACTATTACTG
Found at i:31837311 original size:12 final size:12
Alignment explanation
Indices: 31837293--31837326 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
31837283 CCATGTGTAG
31837293 CACACGGCTTAC
1 CACACGGCTTAC
* *
31837305 TACACGGCCTAC
1 CACACGGCTTAC
31837317 CACACGGCTT
1 CACACGGCTT
31837327 TGTGACATTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.24, C:0.41, G:0.18, T:0.18
Consensus pattern (12 bp):
CACACGGCTTAC
Found at i:31848406 original size:40 final size:40
Alignment explanation
Indices: 31848347--31848518 Score: 229
Period size: 40 Copynumber: 4.3 Consensus size: 40
31848337 CATTTGAATG
* *
31848347 ATATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
*
31848387 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * * * * *
31848427 TTATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
31848467 AAATCCGGGCTAAGACCCGAAGGCATTTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
31848507 ATATCC-GGCTAA
1 ATATCCGGGCTAA
31848519 ATTCCGAAGA
Statistics
Matches: 114, Mismatches: 18, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
39 6 0.05
40 108 0.95
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.28
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
Found at i:31852286 original size:6 final size:6
Alignment explanation
Indices: 31852275--31852299 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
31852265 GAACCAAAAT
31852275 AAATTA AAATTA AAATTA AAATTA A
1 AAATTA AAATTA AAATTA AAATTA A
31852300 GAAAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATTA
Found at i:31855763 original size:40 final size:42
Alignment explanation
Indices: 31855651--31855786 Score: 131
Period size: 40 Copynumber: 3.4 Consensus size: 42
31855641 TATTATAATC
* *
31855651 TCGCACACTAAGTGCCT-TTCATACCCGAAGCTA-TCTCAATT
1 TCGCACACTAAGTG-CTATTTATAACCGAAGCTATTCTCAATT
** * * *
31855692 TCGCACACTAAGTTTTATATATAACCAAAGCTATTC-CGA-T
1 TCGCACACTAAGTGCTATTTATAACCGAAGCTATTCTCAATT
* **
31855732 TCGCACACTAAGTGCTATTTATAGCCGAAGCTA-TCTCAAAA
1 TCGCACACTAAGTGCTATTTATAACCGAAGCTATTCTCAATT
31855773 T-GCACACTAAGTGC
1 TCGCACACTAAGTGC
31855787 CAAACATAGT
Statistics
Matches: 77, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
39 2 0.03
40 45 0.58
41 28 0.36
42 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (42 bp):
TCGCACACTAAGTGCTATTTATAACCGAAGCTATTCTCAATT
Found at i:31857015 original size:11 final size:11
Alignment explanation
Indices: 31856996--31857027 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
31856986 TGATTTCATG
*
31856996 ATTTTGTGAAA
1 ATTTCGTGAAA
31857007 ATTTCGTGAAA
1 ATTTCGTGAAA
31857018 ATTTCGTGAA
1 ATTTCGTGAA
31857028 GAAATTCTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.34, C:0.06, G:0.19, T:0.41
Consensus pattern (11 bp):
ATTTCGTGAAA
Found at i:31858553 original size:68 final size:63
Alignment explanation
Indices: 31858436--31858688 Score: 192
Period size: 68 Copynumber: 3.9 Consensus size: 63
31858426 ATACAGATGG
* * *
31858436 TATGTAGCTAGGTCACA-GGTGTGGTACTGAGTGCACATCATGT-GTACAAGAGAGCTACAAGAC
1 TATGTAGCTAGGTCGCATGG-GTGGTACT-AGTGAACACCATGTAG-ACAAGAGAGCTAC--GAC
31858499 ATTA
61 A-TA
* * **
31858503 TGATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATA
1 T-ATGTAGCTAGGTCGCATGGGTGGTACTA-GTGAACACCATGTAGACAAGAGAGCTACGACATA
* * * *
31858568 TATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGGCACCATGTAGACAAGAGAGCTACGAGA
1 TATGTAGCTAGGTCGCATGGGTGGTACTA-GTGAA---CACCATGTAGACAAGAGAGCTACGACA
31858633 TA
62 TA
* ** **
31858635 AACTG--GCTAGGTTACATGGGTGGTACTAAGTGCTCACCATGT-GTACAAGAGAGC
1 TA-TGTAGCTAGGTCGCATGGGTGGTACT-AGTGAACACCATGTAG-ACAAGAGAGC
31858689 CGAACTATAT
Statistics
Matches: 155, Mismatches: 21, Indels: 24
0.77 0.10 0.12
Matches are distributed among these distances:
62 1 0.01
63 18 0.12
64 28 0.18
65 3 0.02
66 22 0.14
67 32 0.21
68 48 0.31
69 3 0.02
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.24
Consensus pattern (63 bp):
TATGTAGCTAGGTCGCATGGGTGGTACTAGTGAACACCATGTAGACAAGAGAGCTACGACATA
Found at i:31867217 original size:78 final size:78
Alignment explanation
Indices: 31867086--31867268 Score: 233
Period size: 78 Copynumber: 2.3 Consensus size: 78
31867076 CCAAGCAGAC
* * *
31867086 CCTTTGTTGAAAGTCATCTGTAAATCCCTTGGAGCAAATTATCTAAAAAGCCTATGTCACGTGTT
1 CCTTTGTTGCAAGTCATCTGTAAAGCCCTTGGAGCAAATTATCTAAAAAGCCTATGTCACATGTT
*
31867151 GTTATCTGGAAAG
66 GTTATCTAGAAAG
* * * * * * **
31867164 CCTTTGTGGCAAGTCATCTGTAAAGCCCTTGGGGCTAATTATTTGAAACGCCTATGTGGCATGTT
1 CCTTTGTTGCAAGTCATCTGTAAAGCCCTTGGAGCAAATTATCTAAAAAGCCTATGTCACATGTT
31867229 GTTATCTAGAAAG
66 GTTATCTAGAAAG
*
31867242 CCTTTGTTACAAGTCATCTAG-AAAGCC
1 CCTTTGTTGCAAGTCATCT-GTAAAGCC
31867269 TATATGGCGA
Statistics
Matches: 90, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
78 89 0.99
79 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (78 bp):
CCTTTGTTGCAAGTCATCTGTAAAGCCCTTGGAGCAAATTATCTAAAAAGCCTATGTCACATGTT
GTTATCTAGAAAG
Found at i:31870508 original size:12 final size:12
Alignment explanation
Indices: 31870491--31870516 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
31870481 GTACTACACA
31870491 GACCATTCAGAT
1 GACCATTCAGAT
31870503 GACCATTCAGAT
1 GACCATTCAGAT
31870515 GA
1 GA
31870517 ATTCCACATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (12 bp):
GACCATTCAGAT
Found at i:31899268 original size:6 final size:6
Alignment explanation
Indices: 31899257--31899332 Score: 66
Period size: 6 Copynumber: 12.3 Consensus size: 6
31899247 TATCAAAACT
* * *
31899257 AGAATC AGAATC AGAATC AGAATT AG-GTGAC AGAATC AGAATC AGTATC
1 AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC AGAATC
*
31899306 AGGTAA-C AGAATC AAAATC AGAATC AG
1 A-G-AATC AGAATC AGAATC AGAATC AG
31899333 TATTAGGTAA
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
5 3 0.05
6 46 0.82
7 5 0.09
8 2 0.04
ACGTcount: A:0.47, C:0.14, G:0.20, T:0.18
Consensus pattern (6 bp):
AGAATC
Found at i:31899290 original size:25 final size:25
Alignment explanation
Indices: 31899262--31899332 Score: 106
Period size: 25 Copynumber: 2.8 Consensus size: 25
31899252 AAACTAGAAT
* *
31899262 CAGAATCAGAATCAGAATTAGGTGA
1 CAGAATCAGAATCAGAATCAGGTAA
*
31899287 CAGAATCAGAATCAGTATCAGGTAA
1 CAGAATCAGAATCAGAATCAGGTAA
*
31899312 CAGAATCAAAATCAGAATCAG
1 CAGAATCAGAATCAGAATCAG
31899333 TATTAGGTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.46, C:0.15, G:0.20, T:0.18
Consensus pattern (25 bp):
CAGAATCAGAATCAGAATCAGGTAA
Found at i:31899293 original size:31 final size:30
Alignment explanation
Indices: 31899257--31899361 Score: 112
Period size: 31 Copynumber: 3.6 Consensus size: 30
31899247 TATCAAAACT
* *
31899257 AGAATCAGAATCAGAATCAGAATTAGGTGAC
1 AGAATCAAAATCAGAATCAG-ATTAGGTAAC
* *
31899288 AGAATCAGAATCAG--T---ATCAGGTAAC
1 AGAATCAAAATCAGAATCAGATTAGGTAAC
31899313 AGAATCAAAATCAGAATCAGTATTAGGTAAC
1 AGAATCAAAATCAGAATCAG-ATTAGGTAAC
31899344 AGAATCAAAAATCAGAAT
1 AGAATC-AAAATCAGAAT
31899362 GTGAATGCAA
Statistics
Matches: 63, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
25 21 0.33
27 1 0.02
29 1 0.02
31 29 0.46
32 11 0.17
ACGTcount: A:0.49, C:0.13, G:0.18, T:0.20
Consensus pattern (30 bp):
AGAATCAAAATCAGAATCAGATTAGGTAAC
Found at i:31899349 original size:25 final size:25
Alignment explanation
Indices: 31899262--31899350 Score: 97
Period size: 25 Copynumber: 3.3 Consensus size: 25
31899252 AAACTAGAAT
* *
31899262 CAGAATCAGAATCAGAATTAGGTGA
1 CAGAATCAGAATCAGTATTAGGTAA
*
31899287 CAGAATCAGAATCAGTATCAGGTAA
1 CAGAATCAGAATCAGTATTAGGTAA
31899312 CAGAATCAAAATCAGAATCAGTATTAGGTAA
1 CAG------AATCAGAATCAGTATTAGGTAA
31899343 CAGAATCA
1 CAGAATCA
31899351 AAAATCAGAA
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
25 30 0.56
31 24 0.44
ACGTcount: A:0.46, C:0.15, G:0.19, T:0.20
Consensus pattern (25 bp):
CAGAATCAGAATCAGTATTAGGTAA
Found at i:31900304 original size:27 final size:27
Alignment explanation
Indices: 31900246--31901475 Score: 1490
Period size: 27 Copynumber: 45.3 Consensus size: 27
31900236 AGGGGCAAAA
* * * *
31900246 TGGTAATTTTACCCCACA-AGGTATCT
1 TGGTAATTCTACCCTACAGGGGTATTT
* * *
31900272 CGGTAATTCCACCCTATAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
* *
31900299 TAGTAATTCTACCCTACAGGGGTATTG
1 TGGTAATTCTACCCTACAGGGGTATTT
* * * *
31900326 CGATAATTCTACCCTACAGGCGTATTG
1 TGGTAATTCTACCCTACAGGGGTATTT
* *
31900353 CGATAATTCTACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
* * *
31900380 TCGTAATTCTACCCTACAGGAGTATTC
1 TGGTAATTCTACCCTACAGGGGTATTT
31900407 TGGTAATTCTACCCTACTACCCTACAGGGGTATTT
1 TGGTAA---T----T-CTACCCTACAGGGGTATTT
** * *
31900442 CAGCAATTCTACCCTACAGGGGTATTC
1 TGGTAATTCTACCCTACAGGGGTATTT
31900469 TGGTAATTCTACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
* *
31900496 CGGTAATTCTACCCTACAGGGGTATTC
1 TGGTAATTCTACCCTACAGGGGTATTT
*
31900523 CGGTAATTCTACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
* * *
31900550 CGATAATTCTACCCTACAGGGGTATTC
1 TGGTAATTCTACCCTACAGGGGTATTT
*
31900577 CGGTAATTCTACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
* * *
31900604 CGATAATTCTACCCTACAGGGGTATTC
1 TGGTAATTCTACCCTACAGGGGTATTT
*
31900631 CGGTAATTCTACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
* * *
31900658 CGATAATTCTACCCTACAGGGGTATTC
1 TGGTAATTCTACCCTACAGGGGTATTT
*
31900685 CGGTAATTCTACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
* * *
31900712 CGATAATTCTACCCTACAGGGGTATTC
1 TGGTAATTCTACCCTACAGGGGTATTT
*
31900739 CGGTAATTCTACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
* * *
31900766 CGATAATTCTACCCTACAGGGGTATTC
1 TGGTAATTCTACCCTACAGGGGTATTT
*
31900793 CGGTAATTCTACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
* * *
31900820 CGATAATTCTACCCTACAGGGGTATTC
1 TGGTAATTCTACCCTACAGGGGTATTT
*
31900847 CGGTAATTCTACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
* * *
31900874 CGATAATTCTACCCTACAGGGGTATTC
1 TGGTAATTCTACCCTACAGGGGTATTT
*
31900901 CGGTAATTCTACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
* * *
31900928 CGATAATTCTACCCTACAGGGGTATTC
1 TGGTAATTCTACCCTACAGGGGTATTT
*
31900955 CGGTAATTCTACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
* * *
31900982 CGATAATTCTACCCTACAGGGGTATTC
1 TGGTAATTCTACCCTACAGGGGTATTT
*
31901009 CGGTAATTCTACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
* * *
31901036 CGATAATTCTACCCTACAGGGGTATTC
1 TGGTAATTCTACCCTACAGGGGTATTT
*
31901063 CGGTAATTCTACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
* * *
31901090 CGATAATTCTACCCTACAGGGGTATTC
1 TGGTAATTCTACCCTACAGGGGTATTT
*
31901117 CGGTAATTCTACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
* * *
31901144 CGATAATTCTACCCTACAGGGGTATTC
1 TGGTAATTCTACCCTACAGGGGTATTT
*
31901171 CGGTAATTCTACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
* * *
31901198 CGATAATTCTACCCTACAGGGGTATTC
1 TGGTAATTCTACCCTACAGGGGTATTT
*
31901225 CGGTAATTCTACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
* * *
31901252 CGATAATTCTACCCTACAGGGGTATTC
1 TGGTAATTCTACCCTACAGGGGTATTT
*
31901279 CGGTAATTCTACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
* * *
31901306 CGATAATTCTACCCTACAGGGGTATTG
1 TGGTAATTCTACCCTACAGGGGTATTT
* * *
31901333 CGATAATTCTACCCTACAAGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
* * * *
31901360 TGGTAATTTTACTCTATAGGGGTATTG
1 TGGTAATTCTACCCTACAGGGGTATTT
* *
31901387 TGATAATTCTACCTTACAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
* * *
31901414 CGGTAATTCTACCCTATAAGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
* *
31901441 TGGTATTTCTACCCTACATGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
*
31901468 CGGTAATT
1 TGGTAATT
31901476 TTGTAAATCG
Statistics
Matches: 1074, Mismatches: 121, Indels: 17
0.89 0.10 0.01
Matches are distributed among these distances:
26 13 0.01
27 1037 0.97
28 1 0.00
30 1 0.00
32 1 0.00
34 1 0.00
35 20 0.02
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (27 bp):
TGGTAATTCTACCCTACAGGGGTATTT
Found at i:31900341 original size:54 final size:54
Alignment explanation
Indices: 31900247--31901475 Score: 1996
Period size: 54 Copynumber: 22.6 Consensus size: 54
31900237 GGGGCAAAAT
* * * * * * * **
31900247 GGTAATTTTACCCCACA-AGGTATCTCGGTAATTCCACCCTATAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTCC
* * * *
31900300 AGTAATTCTACCCTACAGGGGTATTGCGATAATTCTACCCTACAGGCGTATTGC
1 GGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTCC
* * *
31900354 GATAATTCTACCCTACAGGGGTATTTTCG-TAATTCTACCCTACAGGAGTATTCT
1 GGTAATTCTACCCTACAGGGGTA-TTTCGATAATTCTACCCTACAGGGGTATTCC
* *
31900408 GGTAATTCTACCCTACTACCCTACAGGGGTATTTC-AGCAATTCTACCCTACAGGGGTATTCT
1 GGTAA---T----T-CTACCCTACAGGGGTATTTCGA-TAATTCTACCCTACAGGGGTATTCC
*
31900470 GGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTCC
31900524 GGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTCC
31900578 GGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTCC
31900632 GGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTCC
31900686 GGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTCC
31900740 GGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTCC
31900794 GGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTCC
31900848 GGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTCC
31900902 GGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTCC
31900956 GGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTCC
31901010 GGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTCC
31901064 GGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTCC
31901118 GGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTCC
31901172 GGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTCC
31901226 GGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTCC
*
31901280 GGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTGC
1 GGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTCC
* * * * * * * **
31901334 GATAATTCTACCCTACAAGGGTATTTTGGTAATTTTACTCTATAGGGGTATTGT
1 GGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTCC
* * * * * **
31901388 GATAATTCTACCTTACAGGGGTATTTCGGTAATTCTACCCTATAAGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTCC
* * *
31901442 GGTATTTCTACCCTACATGGGTATTTCGGTAATT
1 GGTAATTCTACCCTACAGGGGTATTTCGATAATT
31901476 TTGTAAATCG
Statistics
Matches: 1118, Mismatches: 45, Indels: 25
0.94 0.04 0.02
Matches are distributed among these distances:
53 14 0.01
54 1048 0.94
55 5 0.00
57 1 0.00
59 1 0.00
61 5 0.00
62 44 0.04
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (54 bp):
GGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTCC
Found at i:31900434 original size:35 final size:35
Alignment explanation
Indices: 31900388--31900458 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 35
31900378 TTTCGTAATT
* *
31900388 CTACCCTACAGGAGTA-TTCTGGTAATTCTACCCTA
1 CTACCCTACAGGAGTATTTC-AGCAATTCTACCCTA
*
31900423 CTACCCTACAGGGGTATTTCAGCAATTCTACCCTA
1 CTACCCTACAGGAGTATTTCAGCAATTCTACCCTA
31900458 C
1 C
31900459 AGGGGTATTC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
35 29 0.91
36 3 0.09
ACGTcount: A:0.25, C:0.31, G:0.14, T:0.30
Consensus pattern (35 bp):
CTACCCTACAGGAGTATTTCAGCAATTCTACCCTA
Found at i:31901526 original size:27 final size:27
Alignment explanation
Indices: 31901496--31901853 Score: 373
Period size: 27 Copynumber: 13.3 Consensus size: 27
31901486 AGGATAAAAC
* *
31901496 GGTAATTTTATAAATCAAGGGTACTTT
1 GGTAATTTTACAAATCAAGGGTATTTT
* * *
31901523 GGTAATTTTACAAGTCGAGGGTATTTC
1 GGTAATTTTACAAATCAAGGGTATTTT
** * * *
31901550 AATAATTTTACAAGTCGAGGGTATTTC
1 GGTAATTTTACAAATCAAGGGTATTTT
* * *
31901577 AGTAATTTCACAAATCAGGGGTATTTT
1 GGTAATTTTACAAATCAAGGGTATTTT
*
31901604 GGTAATTTTACAAA-CTAGGGGTATTTT
1 GGTAATTTTACAAATC-AAGGGTATTTT
*
31901631 GATAATTTTACAAATC-AGGGTATTTT
1 GGTAATTTTACAAATCAAGGGTATTTT
*
31901657 GGTAATTTTACAAACCAAGGGTATTTT
1 GGTAATTTTACAAATCAAGGGTATTTT
* *
31901684 GGTAATTTTATAAA-CAAATGGTATTTT
1 GGTAATTTTACAAATC-AAGGGTATTTT
* * *
31901711 AGTAATTTTACAAACCAGGGGTATTTT
1 GGTAATTTTACAAATCAAGGGTATTTT
** *
31901738 GGTAATTTTGTAAACCAAGGGTATTTT
1 GGTAATTTTACAAATCAAGGGTATTTT
* *
31901765 GGTAATTTCACAAA-CCAGAGGTATTTT
1 GGTAATTTTACAAATCAAG-GGTATTTT
* * *
31901792 GGTAATTTTTCTAATCGAGGGTATTTT
1 GGTAATTTTACAAATCAAGGGTATTTT
* * *
31901819 AGTAATTTTACAAACCAGGGGTATTTT
1 GGTAATTTTACAAATCAAGGGTATTTT
31901846 GGTAATTT
1 GGTAATTT
31901854 GGTAAACTAA
Statistics
Matches: 280, Mismatches: 44, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
26 28 0.10
27 247 0.88
28 5 0.02
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.40
Consensus pattern (27 bp):
GGTAATTTTACAAATCAAGGGTATTTT
Found at i:31901545 original size:81 final size:81
Alignment explanation
Indices: 31901406--31901853 Score: 379
Period size: 81 Copynumber: 5.5 Consensus size: 81
31901396 TACCTTACAG
* ** ** *
31901406 GGGTATTTCGGTAATTCTACCCTAT-AAGGGTATTTTGGT-ATTTCTACCCTAC-ATGGGTATTT
1 GGGTATTTCGGTAATTTTA-CAAATCAAGGGTATTTTGGTAATTT-TA-CAAACGAGGGGTATTT
* **
31901468 CGGTAATTTTGTAAATCGA
63 CGATAATTTTACAAATCGA
* *** * * * *
31901487 GGATAAAACGGTAATTTTATAAATCAAGGGTACTTTGGTAATTTTACAAGTCGA-GGGTATTTCA
1 GGGTATTTCGGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAA-ACGAGGGGTATTTCG
*
31901551 ATAATTTTACAAGTCGA
65 ATAATTTTACAAATCGA
* * * * *
31901568 GGGTATTTCAGTAATTTCACAAATCAGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGA
1 GGGTATTTCGGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAAACGAGGGGTATTTCGA
31901633 TAATTTTACAAATC-A
66 TAATTTTACAAATCGA
* * * * ** *
31901648 GGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTATAAACAAATGGTATTT-TA
1 GGGTATTTCGGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAAACGAGGGGTATTTCGA
*
31901712 GTAATTTTACAAA-CCA
66 -TAATTTTACAAATCGA
* ** * * * * *
31901728 GGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTGGTAATTTCACAAACCAGAGGTATTTTG
1 -GGGTATTTCGGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAAACGAGGGGTATTTCG
* * *
31901793 GTAATTTTTCTAATCGA
65 ATAATTTTACAAATCGA
** * *
31901810 GGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTT
1 GGGTATTTCGGTAATTTTACAAATCAAGGGTATTTTGGTAATTT
31901854 GGTAAACTAA
Statistics
Matches: 300, Mismatches: 57, Indels: 20
0.80 0.15 0.05
Matches are distributed among these distances:
79 2 0.01
80 72 0.24
81 219 0.73
82 7 0.02
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (81 bp):
GGGTATTTCGGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAAACGAGGGGTATTTCGA
TAATTTTACAAATCGA
Found at i:31906346 original size:37 final size:37
Alignment explanation
Indices: 31906296--31906374 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 37
31906286 TTATTACGAA
* * *
31906296 GTCTTACCTGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
31906333 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
31906370 GTCTT
1 GTCTT
31906375 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 35 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:31906571 original size:47 final size:47
Alignment explanation
Indices: 31906493--31906702 Score: 294
Period size: 47 Copynumber: 4.5 Consensus size: 47
31906483 CCCTTCGGGA
* * * * * * *
31906493 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
31906540 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
31906587 CTTATTACATATATACAGTTTCACATTCATCACATCGACTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
31906634 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31906681 CTTATCACATATATACACTTTC
1 CTTATCACATATATACACTTTC
31906703 TTGGCTGAAT
Statistics
Matches: 142, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 142 1.00
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:31921180 original size:42 final size:42
Alignment explanation
Indices: 31921059--31921272 Score: 204
Period size: 42 Copynumber: 5.1 Consensus size: 42
31921049 ACACACGATA
* *
31921059 TCATACTAATGCCATATCCCAGATATGGTCTTACATG-GGATC
1 TCATACTAATGCCATATCCCAGATATGGTCTTACACGAAG-TC
* * * * *
31921101 TCGTA-TCGATGCCAATAGCCCAGCTAGGGTCTTACACGACA-TC
1 TCATACT-AATGCC-ATATCCCAGATATGGTCTTACACGA-AGTC
*
31921144 TCATA-TCAATGCCATATCCCAGATATGGTCTGACACGAAGTC
1 TCATACT-AATGCCATATCCCAGATATGGTCTTACACGAAGTC
* * * *
31921186 TCATACTGATGTCATATCCTAGATGTGGTCTTACACGAAGTC
1 TCATACTAATGCCATATCCCAGATATGGTCTTACACGAAGTC
* * *
31921228 TCATACTAACGTCATACCCCAGATATGGTCTTACAC-ATAGTC
1 TCATACTAATGCCATATCCCAGATATGGTCTTACACGA-AGTC
31921270 TCA
1 TCA
31921273 GTAACCCTAA
Statistics
Matches: 142, Mismatches: 23, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
41 3 0.02
42 105 0.74
43 34 0.24
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (42 bp):
TCATACTAATGCCATATCCCAGATATGGTCTTACACGAAGTC
Found at i:31924728 original size:28 final size:27
Alignment explanation
Indices: 31924683--31924749 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
31924673 AAATGTGCAA
*
31924683 AATTATTATA-AAAATAAT-TAAAATT
1 AATTATTTTATAAAATAATCTAAAATT
* *
31924708 CAATATGTTTTATAAAATAATCTTAAATT
1 -AAT-TATTTTATAAAATAATCTAAAATT
31924737 AATTATTTTATAA
1 AATTATTTTATAA
31924750 TAAAAGCATA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
26 3 0.09
27 14 0.41
28 11 0.32
29 6 0.18
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (27 bp):
AATTATTTTATAAAATAATCTAAAATT
Found at i:31932432 original size:46 final size:46
Alignment explanation
Indices: 31932382--31932507 Score: 130
Period size: 46 Copynumber: 2.7 Consensus size: 46
31932372 GACGAGTGCT
* *
31932382 AGTGTAAGACATGTTTGGGACATGCATCGGCCT-CGAGGCG-TAAGCC
1 AGTGTAAGACATGTTTGGGACATGCATC-GACTACGAGACGATAA-CC
* * * **
31932428 AGTGTAAGACATGTCTGGAACATGCGTCGACTACGAGACGATAATT
1 AGTGTAAGACATGTTTGGGACATGCATCGACTACGAGACGATAACC
*
31932474 AGTGTAAGACCATGTTTGGGACATGGCTTCGACT
1 AGTGTAAGA-CATGTTTGGGACAT-GCATCGACT
31932508 TGATATATAA
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
45 3 0.05
46 40 0.61
47 15 0.23
48 8 0.12
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (46 bp):
AGTGTAAGACATGTTTGGGACATGCATCGACTACGAGACGATAACC
Found at i:31940086 original size:46 final size:46
Alignment explanation
Indices: 31939991--31940105 Score: 151
Period size: 46 Copynumber: 2.5 Consensus size: 46
31939981 GTGAGCTAGC
* * * *
31939991 GTAAGACAATGTCTGGGACATGGCATCGGCATTGAGACGAGTGCTAGT
1 GTAAGAC-ATGTCTGGGACAT-GCATCGACATCGAGACGAGAGCCAGT
*
31940039 GTAAGACATGTCTGGGACATGCATCGACCTCGAGACGTA-AGCCAGT
1 GTAAGACATGTCTGGGACATGCATCGACATCGAGACG-AGAGCCAGT
31940085 GTAAGACATGTCTGGGACATG
1 GTAAGACATGTCTGGGACATG
31940106 TGTCGGCTAC
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
46 40 0.66
47 14 0.23
48 7 0.11
ACGTcount: A:0.28, C:0.19, G:0.31, T:0.22
Consensus pattern (46 bp):
GTAAGACATGTCTGGGACATGCATCGACATCGAGACGAGAGCCAGT
Found at i:31941400 original size:21 final size:22
Alignment explanation
Indices: 31941360--31941403 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
31941350 GTCAAATTGA
31941360 TCACACGGGCGTGTTGCCCCTT
1 TCACACGGGCGTGTTGCCCCTT
*
31941382 TCACAGGGGCGTG-TGCCCCTT
1 TCACACGGGCGTGTTGCCCCTT
31941403 T
1 T
31941404 GTCAAATGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.09, C:0.34, G:0.30, T:0.27
Consensus pattern (22 bp):
TCACACGGGCGTGTTGCCCCTT
Found at i:31943347 original size:45 final size:45
Alignment explanation
Indices: 31943296--31943385 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
31943286 TGAAAATTTG
31943296 GATGAAAGATTGTACTCTCTCCCCAAGAAAACAAAAACAAAGGTA
1 GATGAAAGATTGTACTCTCTCCCCAAGAAAACAAAAACAAAGGTA
*
31943341 GATGAAAGATTGTACTCTCTCCCCAAGTAAACAAAAACAAAGGTA
1 GATGAAAGATTGTACTCTCTCCCCAAGAAAACAAAAACAAAGGTA
31943386 ATGGATAACC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.46, C:0.20, G:0.16, T:0.19
Consensus pattern (45 bp):
GATGAAAGATTGTACTCTCTCCCCAAGAAAACAAAAACAAAGGTA
Found at i:31948745 original size:15 final size:13
Alignment explanation
Indices: 31948713--31948737 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31948703 TATATTAATC
31948713 TTTTATCTTATTG
1 TTTTATCTTATTG
31948726 TTTTATCTTATT
1 TTTTATCTTATT
31948738 ATGTTTTAAT
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:0.16, C:0.08, G:0.04, T:0.72
Consensus pattern (13 bp):
TTTTATCTTATTG
Found at i:31954491 original size:13 final size:13
Alignment explanation
Indices: 31954473--31954497 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31954463 CATGGGCGTG
31954473 TGGCCAACCCGTA
1 TGGCCAACCCGTA
31954486 TGGCCAACCCGT
1 TGGCCAACCCGT
31954498 GAAGGCAACG
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:0.20, C:0.40, G:0.24, T:0.16
Consensus pattern (13 bp):
TGGCCAACCCGTA
Found at i:31958941 original size:14 final size:15
Alignment explanation
Indices: 31958922--31958962 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
31958912 TCTTTCATTA
*
31958922 AAAATAACTTTC-GG
1 AAAATAACTTACTGG
31958936 AAAATAA-TTACTGG
1 AAAATAACTTACTGG
31958950 AAAATAACTTACT
1 AAAATAACTTACT
31958963 TTTCTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 3 0.12
14 16 0.67
15 5 0.21
ACGTcount: A:0.49, C:0.12, G:0.10, T:0.29
Consensus pattern (15 bp):
AAAATAACTTACTGG
Found at i:31959587 original size:30 final size:30
Alignment explanation
Indices: 31959527--31959589 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
31959517 AAATATTAAA
*
31959527 TAATTTATTAAAATAATAAATTATATTAAT
1 TAATTTATTAAAATAATAAATTATAATAAT
* * *
31959557 TAATTTATTATATTATTAAA-TATAAATAAT
1 TAATTTATTAAAATAATAAATTAT-AATAAT
31959587 TAA
1 TAA
31959590 ATATGTATGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 3 0.11
30 25 0.89
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
TAATTTATTAAAATAATAAATTATAATAAT
Found at i:31967268 original size:12 final size:12
Alignment explanation
Indices: 31967253--31967310 Score: 50
Period size: 11 Copynumber: 5.0 Consensus size: 12
31967243 ATTTTTCAAA
*
31967253 ATATAATAAATT
1 ATATATTAAATT
31967265 ATAT-TTAAATT
1 ATATATTAAATT
*
31967276 -TATATTAAATA
1 ATATATTAAATT
* *
31967287 AAATAATTATATT
1 ATAT-ATTAAATT
31967300 A-ATATTAAATT
1 ATATATTAAATT
31967311 TAAAAAAAAC
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
10 3 0.08
11 19 0.51
12 8 0.22
13 7 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATATATTAAATT
Found at i:31973294 original size:22 final size:22
Alignment explanation
Indices: 31973262--31973305 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
31973252 TGAGGTAGTG
*
31973262 TAAGACCATGTCTGGGACATGA
1 TAAGACAATGTCTGGGACATGA
31973284 TAAGACAATGTCTGGGACATGA
1 TAAGACAATGTCTGGGACATGA
31973306 CATCGACATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.23
Consensus pattern (22 bp):
TAAGACAATGTCTGGGACATGA
Found at i:31978252 original size:71 final size:71
Alignment explanation
Indices: 31978136--31978280 Score: 281
Period size: 71 Copynumber: 2.0 Consensus size: 71
31978126 TAGTTTCAGG
31978136 GAAAATTTACGGATCTTAATTTAAAGCTCTGTAGCTCGAATTATAAATAATTGAGTGACTATGAC
1 GAAAATTTACGGATCTTAATTTAAAGCTCTGTAGCTCGAATTATAAATAATTGAGTGACTATGAC
31978201 TCGTGT
66 TCGTGT
*
31978207 GAAAATTTACGGATCTTAATTTGAAGCTCTGTAGCTCGAATTATAAATAATTGAGTGACTATGAC
1 GAAAATTTACGGATCTTAATTTAAAGCTCTGTAGCTCGAATTATAAATAATTGAGTGACTATGAC
31978272 TCGTGT
66 TCGTGT
31978278 GAA
1 GAA
31978281 CAGCTTGATG
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 73 1.00
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.34
Consensus pattern (71 bp):
GAAAATTTACGGATCTTAATTTAAAGCTCTGTAGCTCGAATTATAAATAATTGAGTGACTATGAC
TCGTGT
Found at i:31979109 original size:490 final size:490
Alignment explanation
Indices: 31978189--31979163 Score: 1844
Period size: 490 Copynumber: 2.0 Consensus size: 490
31978179 TAAATAATTG
*
31978189 AGTGACTATGACTCGTGTGAAAATTTACGGATCTTAATTTGAAGCTCTGTAGCTCGAATTATAAA
1 AGTGACTATGACTCATGTGAAAATTTACGGATCTTAATTTGAAGCTCTGTAGCTCGAATTATAAA
*
31978254 TAATTGAGTGACTATGACTCGTGTGAACAGCTTGATGTGAGCATTAATAAGTAAATTGTGAAATA
66 TAATTGAGTGACTATGACTCGTGTGAACAACTTGATGTGAGCATTAATAAGTAAATTGTGAAATA
31978319 GTACTTACAAGAATCTTATATACATTAAGGATGTGGAATGGAAAGGAGAAGGAGAAAAATAAATG
131 GTACTTACAAGAATCTTATATACATTAAGGATGTGGAATGGAAAGGAGAAGGAGAAAAATAAATG
*
31978384 ATATATGTTTATAAGAAAACAGTATGAGAATGATGCATATCATGACATGTATATATATAACTAGT
196 ATATATGTTTATAAGAAAACAGTATGAGAATGATACATATCATGACATGTATATATATAACTAGT
31978449 TTCAATATGATGCTTGTTGGGTATGAAGTTGGATTGAAATGTCTCAAGCAAGTATTTTATTATGC
261 TTCAATATGATGCTTGTTGGGTATGAAGTTGGATTGAAATGTCTCAAGCAAGTATTTTATTATGC
31978514 TCATCTGAAATGTGGTATTTTATGAAGATATGATCTAGCTTTAAATATGAATGCTTGATGATTAA
326 TCATCTGAAATGTGGTATTTTATGAAGATATGATCTAGCTTTAAATATGAATGCTTGATGATTAA
*
31978579 GTTGAAAATATTTGGTAAGATGATAATCATGGTATAAAAGTATAAGTGGTACCATAATAGACAAG
391 GCTGAAAATATTTGGTAAGATGATAATCATGGTATAAAAGTATAAGTGGTACCATAATAGACAAG
31978644 GTAAAATGAGTATGAGAGATACATGTATGAGTATA
456 GTAAAATGAGTATGAGAGATACATGTATGAGTATA
31978679 AGTGACTATGACTCATGTGAAAATTTACGGATCTTAATTTGAAGCTCTGTAGCTCGAATTATAAA
1 AGTGACTATGACTCATGTGAAAATTTACGGATCTTAATTTGAAGCTCTGTAGCTCGAATTATAAA
31978744 TAATTGAGTGACTATGACTCGTGTGAACAACTTGATGTGAGCATTAATAAGTAAATTGTGAAATA
66 TAATTGAGTGACTATGACTCGTGTGAACAACTTGATGTGAGCATTAATAAGTAAATTGTGAAATA
* *
31978809 GTACTTACAAGAATCTTATATACATTAAGGATGTGGAATGGAGAGGAGGAGGA-AGAAAATAAAT
131 GTACTTACAAGAATCTTATATACATTAAGGATGTGGAATGGAAAGGAGAAGGAGA-AAAATAAAT
31978873 GATATATGTTTATAAGAAAACAGTATGAGAATGATACATATCATGACATGTATATATATAACTAG
195 GATATATGTTTATAAGAAAACAGTATGAGAATGATACATATCATGACATGTATATATATAACTAG
* *
31978938 TTTCAATATGATGCTTGTTGGGTATGAAGTTGGATTGAAATGTCTCAGGCAAGTATTTTATTCTG
260 TTTCAATATGATGCTTGTTGGGTATGAAGTTGGATTGAAATGTCTCAAGCAAGTATTTTATTATG
31979003 CTCATCTGAAATGTGGTATTTTATGAAGATATGATCTAGCTTTAAATATGAATGCTTGATGATTA
325 CTCATCTGAAATGTGGTATTTTATGAAGATATGATCTAGCTTTAAATATGAATGCTTGATGATTA
*
31979068 AGCTGAAAATATTTGGTAAGATGATAATCATGGTATAAAAGTATAAGTGGTACCATAATAGACAG
390 AGCTGAAAATATTTGGTAAGATGATAATCATGGTATAAAAGTATAAGTGGTACCATAATAGACAA
*
31979133 GGTAAGATGAGTATGAGAGATACATGTATGA
455 GGTAAAATGAGTATGAGAGATACATGTATGA
31979164 TGACATACAA
Statistics
Matches: 474, Mismatches: 10, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
489 1 0.00
490 473 1.00
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.33
Consensus pattern (490 bp):
AGTGACTATGACTCATGTGAAAATTTACGGATCTTAATTTGAAGCTCTGTAGCTCGAATTATAAA
TAATTGAGTGACTATGACTCGTGTGAACAACTTGATGTGAGCATTAATAAGTAAATTGTGAAATA
GTACTTACAAGAATCTTATATACATTAAGGATGTGGAATGGAAAGGAGAAGGAGAAAAATAAATG
ATATATGTTTATAAGAAAACAGTATGAGAATGATACATATCATGACATGTATATATATAACTAGT
TTCAATATGATGCTTGTTGGGTATGAAGTTGGATTGAAATGTCTCAAGCAAGTATTTTATTATGC
TCATCTGAAATGTGGTATTTTATGAAGATATGATCTAGCTTTAAATATGAATGCTTGATGATTAA
GCTGAAAATATTTGGTAAGATGATAATCATGGTATAAAAGTATAAGTGGTACCATAATAGACAAG
GTAAAATGAGTATGAGAGATACATGTATGAGTATA
Found at i:31981633 original size:22 final size:22
Alignment explanation
Indices: 31981573--31981633 Score: 54
Period size: 22 Copynumber: 2.7 Consensus size: 22
31981563 ATTGAATTGA
*
31981573 GAAAGTGAATTATAATTGATACT
1 GAAAGTGAGTTA-AATTGATACT
*
31981596 GAAA-TGAGATAGAAATT-ATACT
1 GAAAGTGAG-T-TAAATTGATACT
31981618 GAAAAGTGAGTTAAAT
1 G-AAAGTGAGTTAAAT
31981634 ACCCTATTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
22 13 0.42
23 13 0.42
24 5 0.16
ACGTcount: A:0.48, C:0.03, G:0.20, T:0.30
Consensus pattern (22 bp):
GAAAGTGAGTTAAATTGATACT
Found at i:31981821 original size:45 final size:45
Alignment explanation
Indices: 31981742--31981852 Score: 150
Period size: 45 Copynumber: 2.5 Consensus size: 45
31981732 CGACTACTGT
* * *
31981742 TACTGTTACCATTACTGTTACCGATTCGATACTTTGTGTGTCAAA
1 TACTGTTACTATTACTGTTACCGATTCAACACTTTGTGTGTCAAA
* * * **
31981787 TACTATTACTATTACCGTTATCGATTCAACACTTTGTGTGTTGAA
1 TACTGTTACTATTACTGTTACCGATTCAACACTTTGTGTGTCAAA
31981832 TACTGTTACTATTACTGTTAC
1 TACTGTTACTATTACTGTTAC
31981853 TGTTCTGGAT
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (45 bp):
TACTGTTACTATTACTGTTACCGATTCAACACTTTGTGTGTCAAA
Found at i:31982149 original size:18 final size:18
Alignment explanation
Indices: 31982077--31982153 Score: 66
Period size: 18 Copynumber: 4.3 Consensus size: 18
31982067 AATTGATCAA
* * *
31982077 TACTGAATAACTGGTTAT
1 TACTGAATAAATGATTGT
* *
31982095 TATTGAATAATTGATTGT
1 TACTGAATAAATGATTGT
* * *
31982113 TACCGAATAACTGACTGT
1 TACTGAATAAATGATTGT
*
31982131 TACTGAATAAATAATTGT
1 TACTGAATAAATGATTGT
31982149 T-CTGA
1 TACTGA
31982154 TTGTTAATGA
Statistics
Matches: 47, Mismatches: 12, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
17 4 0.09
18 43 0.91
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (18 bp):
TACTGAATAAATGATTGT
Found at i:31984270 original size:34 final size:34
Alignment explanation
Indices: 31984223--31984307 Score: 127
Period size: 34 Copynumber: 2.5 Consensus size: 34
31984213 ATACTACATG
31984223 ATGC-TACTGATACTGTGATAGGCTAAGGCCCTA
1 ATGCATACTGATACTGTGATAGGCTAAGGCCCTA
*
31984256 ATGCATACTGATACTGTGATGGGCTAAGGCCCTA
1 ATGCATACTGATACTGTGATAGGCTAAGGCCCTA
* *
31984290 CTGCATATTTGATACTGT
1 ATGCATA-CTGATACTGT
31984308 ACTGAGATGG
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
33 4 0.09
34 34 0.72
35 9 0.19
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.31
Consensus pattern (34 bp):
ATGCATACTGATACTGTGATAGGCTAAGGCCCTA
Found at i:31989107 original size:111 final size:111
Alignment explanation
Indices: 31988912--31989131 Score: 368
Period size: 111 Copynumber: 2.0 Consensus size: 111
31988902 TCTAATCCTA
* *
31988912 TTAAAATTATGACAATTTTACTGTAAAAGAGTCTATGAGAAAATATATTTAATAGTTATATATTC
1 TTAAAATCATGACAATTTTACTGTAAAAGAATCTATGAGAAAATATATTTAATAGTTATATATTC
* * *
31988977 AATGGGCTTATTATGACCAAATGATTTATTTCTATTTTCAAACTCG
66 AATGGGCTTACTATAACCAAATGATTTATTTCCATTTTCAAACTCG
* *
31989023 TTAAAATCATGACAATTTTACTGTAAAAGAATCTATGAGAAAATATATTTAATAGTTCTATATTT
1 TTAAAATCATGACAATTTTACTGTAAAAGAATCTATGAGAAAATATATTTAATAGTTATATATTC
*
31989088 AATGGGTTTACTATAACCAAATGATTTATTTCCATTTTCAAACT
66 AATGGGCTTACTATAACCAAATGATTTATTTCCATTTTCAAACT
31989132 TCATTTAATT
Statistics
Matches: 101, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
111 101 1.00
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.40
Consensus pattern (111 bp):
TTAAAATCATGACAATTTTACTGTAAAAGAATCTATGAGAAAATATATTTAATAGTTATATATTC
AATGGGCTTACTATAACCAAATGATTTATTTCCATTTTCAAACTCG
Found at i:31989289 original size:58 final size:58
Alignment explanation
Indices: 31989168--31989291 Score: 160
Period size: 57 Copynumber: 2.1 Consensus size: 58
31989158 ATTTCCAAGT
* * *
31989168 CATTTTCATTTTTCATTTTGAAGAAAACCACATTCATTTTCAAATGTTTTCATTTCTT
1 CATTTTCATTTTTCATTTTGAAGAAAACCACATTCATTTCCAAATATTTTCATTTCTC
* * * * *
31989226 GATTTTTA-TTTTCATTTTGGAGAAAATCATATTCATTTCCAAATATTTCTCATTTCTC
1 CATTTTCATTTTTCATTTTGAAGAAAACCACATTCATTTCCAAATATTT-TCATTTCTC
31989284 CATTTTCA
1 CATTTTCA
31989292 CAATTTGTAT
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
57 35 0.64
58 20 0.36
ACGTcount: A:0.27, C:0.17, G:0.06, T:0.50
Consensus pattern (58 bp):
CATTTTCATTTTTCATTTTGAAGAAAACCACATTCATTTCCAAATATTTTCATTTCTC
Found at i:31991932 original size:25 final size:25
Alignment explanation
Indices: 31991902--31992023 Score: 83
Period size: 25 Copynumber: 4.9 Consensus size: 25
31991892 AATAACAGGT
31991902 AGCTCTGAAGAGCCATTAATCGAGA
1 AGCTCTGAAGAGCCATTAATCGAGA
* *
31991927 AGCTCTGGATAGCCA-TATATCGAGA
1 AGCTCTGAAGAGCCATTA-ATCGAGA
* *
31991952 AG-T-TCAAGTGAGCCA-T-ATCGGGA
1 AGCTCTGAA--GAGCCATTAATCGAGA
* * *
31991975 AGCTCCGGAGAGCCATTAATCGGGA
1 AGCTCTGAAGAGCCATTAATCGAGA
** *
31992000 AGCTCACAAAGAGCCTTTAATCGA
1 AGCTC-TGAAGAGCCATTAATCGA
31992024 AAAACTCACA
Statistics
Matches: 76, Mismatches: 13, Indels: 15
0.73 0.12 0.14
Matches are distributed among these distances:
23 16 0.21
24 5 0.07
25 41 0.54
26 14 0.18
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.20
Consensus pattern (25 bp):
AGCTCTGAAGAGCCATTAATCGAGA
Found at i:31992019 original size:26 final size:26
Alignment explanation
Indices: 31991968--31992057 Score: 85
Period size: 26 Copynumber: 3.5 Consensus size: 26
31991958 AGTGAGCCAT
** *
31991968 ATCGGGAAGCTC-CGGAGAGCCATTA
1 ATCGGGAAGCTCACAAAGAGCCTTTA
31991993 ATCGGGAAGCTCACAAAGAGCCTTTA
1 ATCGGGAAGCTCACAAAGAGCCTTTA
** * *
31992019 ATCGAAAAACTCACAAAGAGCCATATA
1 ATCGGGAAGCTCACAAAGAGCC-TTTA
*
31992046 A-CGGGACGCTCA
1 ATCGGGAAGCTCA
31992058 TAATAGTTGT
Statistics
Matches: 52, Mismatches: 11, Indels: 3
0.79 0.17 0.05
Matches are distributed among these distances:
25 12 0.23
26 36 0.69
27 4 0.08
ACGTcount: A:0.37, C:0.24, G:0.23, T:0.16
Consensus pattern (26 bp):
ATCGGGAAGCTCACAAAGAGCCTTTA
Found at i:31997938 original size:17 final size:17
Alignment explanation
Indices: 31997918--31997960 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
31997908 ACATCCTGGT
31997918 TGAGCTCACATCTTTGC
1 TGAGCTCACATCTTTGC
* *
31997935 TGAGCTCACATGTTTGG
1 TGAGCTCACATCTTTGC
31997952 TGAGCTCAC
1 TGAGCTCAC
31997961 GGTTGTGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.19, C:0.26, G:0.23, T:0.33
Consensus pattern (17 bp):
TGAGCTCACATCTTTGC
Found at i:31999083 original size:23 final size:23
Alignment explanation
Indices: 31999014--31999088 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 23
31999004 TCTTATGACA
*
31999014 TCCCGTTATTAGCCCTCTCG-AGCT
1 TCCCGTTA-TAGCTCT-TCGAAGCT
* *
31999038 TACCGTATATAGTTCTT-GCAAGCT
1 TCCCGT-TATAGCTCTTCG-AAGCT
*
31999062 TCCCGTTATAGCTCTTCGAAGCG
1 TCCCGTTATAGCTCTTCGAAGCT
31999085 TCCC
1 TCCC
31999089 ATTAGGTTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
22 1 0.02
23 18 0.44
24 20 0.49
25 2 0.05
ACGTcount: A:0.17, C:0.32, G:0.17, T:0.33
Consensus pattern (23 bp):
TCCCGTTATAGCTCTTCGAAGCT
Found at i:31999275 original size:24 final size:24
Alignment explanation
Indices: 31999248--31999391 Score: 105
Period size: 24 Copynumber: 6.0 Consensus size: 24
31999238 AGCTCCCGTT
*
31999248 ATATGGCTCTTTGTGAGCTTCCCG
1 ATATGGCTCTTTATGAGCTTCCCG
* * *
31999272 ATATGGTTCTTTATGAACTTCCTG
1 ATATGGCTCTTTATGAGCTTCCCG
**
31999296 ATTATGGCTC-TTATGAGCTTCCTATT
1 A-TATGGCTCTTTATGAGCTTCC--CG
* *** *
31999322 ATATAGC-CCAGATAAGCTTCCCG
1 ATATGGCTCTTTATGAGCTTCCCG
** *
31999345 ATA-GGCTCTTTGCGGGCTTCCCG
1 ATATGGCTCTTTATGAGCTTCCCG
*
31999368 ATATGGCTCTTTATAAGCTTCCCG
1 ATATGGCTCTTTATGAGCTTCCCG
31999392 TGATAAGGCT
Statistics
Matches: 89, Mismatches: 25, Indels: 12
0.71 0.20 0.10
Matches are distributed among these distances:
22 2 0.02
23 15 0.17
24 49 0.55
25 21 0.24
26 2 0.02
ACGTcount: A:0.19, C:0.24, G:0.20, T:0.37
Consensus pattern (24 bp):
ATATGGCTCTTTATGAGCTTCCCG
Found at i:32001300 original size:44 final size:44
Alignment explanation
Indices: 32001237--32001329 Score: 161
Period size: 44 Copynumber: 2.1 Consensus size: 44
32001227 GAGTGAGTAA
32001237 TTGTAACTATTGGGCATATTTGTT-AGAGTTAAAATTGCTTGTTG
1 TTGTAACTATTGGGCATATTTGTTGAG-GTTAAAATTGCTTGTTG
*
32001281 TTGTAACTATTGGGCATATTTGTTGAGGTTACAATTGCTTGTTG
1 TTGTAACTATTGGGCATATTTGTTGAGGTTAAAATTGCTTGTTG
32001325 TTGTA
1 TTGTA
32001330 GCGGTAAATT
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 45 0.96
45 2 0.04
ACGTcount: A:0.23, C:0.08, G:0.24, T:0.46
Consensus pattern (44 bp):
TTGTAACTATTGGGCATATTTGTTGAGGTTAAAATTGCTTGTTG
Found at i:32002011 original size:137 final size:138
Alignment explanation
Indices: 32001672--32002086 Score: 778
Period size: 138 Copynumber: 3.0 Consensus size: 138
32001662 TTGTGGTGGT
*
32001672 TAGGGTTTGTTTCTTTGGGATTGAGTTGGGCCTTGATTGCCCAAGTATTCATTGTTTGAATTTTT
1 TAGGGTTTGTTTCTTTGGGATTGAGTTGGGCCTTGATTGCTCAAGTATTCATTGTTTGAATTTTT
*
32001737 TTGGACTTTTGAGCCTCCTTATTCAGTGGCT-AAAAAATTGTAAATTAGTCCACTTCAATTTCTT
66 TTGGACTTTTGAGCCTCCTTATTCAGTGGCTAAAAAAATTGCAAATTAGTCCACTTCAATTTCTT
32001801 GAATTTTA
131 GAATTTTA
*
32001809 TAGGGTTTGTTTCTTTGGGATTCAGTTGGGCCTTGATTGCTCAAGTATTCATTGTTTGAATTTTT
1 TAGGGTTTGTTTCTTTGGGATTGAGTTGGGCCTTGATTGCTCAAGTATTCATTGTTTGAATTTTT
32001874 TTGGACTTTTGAGCCTCCTTATTCAGTGGCTAAAAAAATTGCAAATTAGTCCACTTCAATTTCTT
66 TTGGACTTTTGAGCCTCCTTATTCAGTGGCTAAAAAAATTGCAAATTAGTCCACTTCAATTTCTT
32001939 GAATTTTA
131 GAATTTTA
*
32001947 TAGGGTTTGTTTCTTTGGGATTGAGTTAGGCCTTGATTGCTCAAGTATTCATTGTTTGAATTTTT
1 TAGGGTTTGTTTCTTTGGGATTGAGTTGGGCCTTGATTGCTCAAGTATTCATTGTTTGAATTTTT
*
32002012 TTGGACTTTTGAGCCTTCTTATTCAGTGGCTAAAAAAATTGCAAATTAGTCCACTTCAATTTCTT
66 TTGGACTTTTGAGCCTCCTTATTCAGTGGCTAAAAAAATTGCAAATTAGTCCACTTCAATTTCTT
32002077 GAATTTTA
131 GAATTTTA
32002085 TA
1 TA
32002087 ATCATATTTG
Statistics
Matches: 271, Mismatches: 6, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
137 94 0.35
138 177 0.65
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.45
Consensus pattern (138 bp):
TAGGGTTTGTTTCTTTGGGATTGAGTTGGGCCTTGATTGCTCAAGTATTCATTGTTTGAATTTTT
TTGGACTTTTGAGCCTCCTTATTCAGTGGCTAAAAAAATTGCAAATTAGTCCACTTCAATTTCTT
GAATTTTA
Found at i:32004698 original size:27 final size:24
Alignment explanation
Indices: 32004651--32004713 Score: 63
Period size: 27 Copynumber: 2.5 Consensus size: 24
32004641 TTTATATCTC
32004651 TTTTAAATTTTATAACAAAATTATA
1 TTTTAAATTTTATAACAAAATT-TA
***
32004676 TTTTTATAATTTTATAGTTAAATTTA
1 -TTTTA-AATTTTATAACAAAATTTA
32004702 TTTTAAAATTTT
1 TTTT-AAATTTT
32004714 GATCGATCCT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
25 10 0.31
26 8 0.25
27 14 0.44
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (24 bp):
TTTTAAATTTTATAACAAAATTTA
Found at i:32004968 original size:17 final size:17
Alignment explanation
Indices: 32004942--32004978 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
32004932 GATAAAAACC
* *
32004942 TATAATAAAATTAATGT
1 TATAAAAAAATTAATAT
32004959 TATAAAAAAATTAATAT
1 TATAAAAAAATTAATAT
32004976 TAT
1 TAT
32004979 TTTTTAGAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
TATAAAAAAATTAATAT
Found at i:32005392 original size:10 final size:9
Alignment explanation
Indices: 32005371--32005429 Score: 52
Period size: 10 Copynumber: 6.6 Consensus size: 9
32005361 TTTTAATTTT
32005371 AAAA-ATTA
1 AAAATATTA
32005379 AAAATATATA
1 AAAATAT-TA
* *
32005389 AAAAAATTT
1 AAAATATTA
32005398 AAAA-ATTA
1 AAAATATTA
32005406 AAAATCATTA
1 AAAAT-ATTA
32005416 AAAAGTA-TA
1 AAAA-TATTA
32005425 AAAAT
1 AAAAT
32005430 TATAAAAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
8 12 0.28
9 13 0.30
10 17 0.40
11 1 0.02
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (9 bp):
AAAATATTA
Found at i:32005395 original size:19 final size:18
Alignment explanation
Indices: 32005371--32005428 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 18
32005361 TTTTAATTTT
32005371 AAAAATTAAAAATATATAA
1 AAAAATTAAAAATATA-AA
32005390 AAAAATTTAAAAAT-TAAA
1 AAAAA-TTAAAAATATAAA
**
32005408 AATCATTAAAAAGTATAAA
1 AAAAATTAAAAA-TATAAA
32005427 AA
1 AA
32005429 TTATAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
17 7 0.21
18 6 0.18
19 13 0.38
20 8 0.24
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26
Consensus pattern (18 bp):
AAAAATTAAAAATATAAA
Found at i:32005403 original size:27 final size:26
Alignment explanation
Indices: 32005368--32005436 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 26
32005358 TTTTTTTAAT
32005368 TTTAAAAATTAAAAAT-ATATAAAAAAA
1 TTTAAAAATTAAAAATCAT-T-AAAAAA
*
32005395 TTTAAAAATTAAAAATCATTAAAAAG
1 TTTAAAAATTAAAAATCATTAAAAAA
*
32005421 TATAAAAATTATAAAA
1 TTTAAAAATTA-AAAA
32005437 AAAATATTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
26 15 0.39
27 21 0.55
28 2 0.05
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (26 bp):
TTTAAAAATTAAAAATCATTAAAAAA
Found at i:32005438 original size:10 final size:9
Alignment explanation
Indices: 32005365--32005437 Score: 55
Period size: 9 Copynumber: 8.2 Consensus size: 9
32005355 TTATTTTTTT
*
32005365 AATTTTAAA
1 AATTATAAA
32005374 AATTA-AAA
1 AATTATAAA
*
32005382 ATATATAAAAA
1 A-AT-TATAAA
32005393 AATT-TAAA
1 AATTATAAA
32005401 AA-T-TAAA
1 AATTATAAA
*
32005408 AATCATTAAA
1 AATTA-TAAA
*
32005418 AAGTATAAA
1 AATTATAAA
32005427 AATTATAAA
1 AATTATAAA
32005436 AA
1 AA
32005438 AAATATTTCT
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
7 7 0.13
8 9 0.17
9 21 0.40
10 11 0.21
11 4 0.08
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (9 bp):
AATTATAAA
Found at i:32006341 original size:23 final size:22
Alignment explanation
Indices: 32006294--32006337 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
32006284 TTCAACATGA
* *
32006294 AAAAAATGGGCTTGATTTTTAT
1 AAAAAATGGGCTTGAATTTGAT
*
32006316 AAAAAATGGGTTTGAATTTGAT
1 AAAAAATGGGCTTGAATTTGAT
32006338 TAAATCCAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.39, C:0.02, G:0.20, T:0.39
Consensus pattern (22 bp):
AAAAAATGGGCTTGAATTTGAT
Found at i:32007446 original size:19 final size:19
Alignment explanation
Indices: 32007400--32007439 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
32007390 TCCATAAGAT
32007400 ATAAATTTTGAATTTTAAA
1 ATAAATTTTGAATTTTAAA
32007419 ATAAATTTTGAATTTTAAA
1 ATAAATTTTGAATTTTAAA
32007438 AT
1 AT
32007440 TCATTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (19 bp):
ATAAATTTTGAATTTTAAA
Found at i:32007480 original size:3 final size:3
Alignment explanation
Indices: 32007472--32007554 Score: 166
Period size: 3 Copynumber: 27.7 Consensus size: 3
32007462 CAATCCAATG
32007472 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
32007520 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
32007555 TTTTTTCTCC
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:32009951 original size:17 final size:18
Alignment explanation
Indices: 32009929--32009967 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
32009919 ATTGAGATAC
32009929 AAATTC-TTAATATTATA
1 AAATTCATTAATATTATA
*
32009946 AAATTCATTATTATTATA
1 AAATTCATTAATATTATA
32009964 AAAT
1 AAAT
32009968 AAGTAGACAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (18 bp):
AAATTCATTAATATTATA
Found at i:32015681 original size:25 final size:25
Alignment explanation
Indices: 32015628--32015743 Score: 117
Period size: 25 Copynumber: 4.6 Consensus size: 25
32015618 GGACACACCA
* * *
32015628 CAGCTTGTATGAGCTTTCCAAT-TT
1 CAGCTTGCATGAGCTTCCCGATATT
*
32015652 ACAGCTTACATGAGCTTCCCGATATT
1 -CAGCTTGCATGAGCTTCCCGATATT
* * *
32015678 CAGCTTGCATGAACTTCCTGTTATT
1 CAGCTTGCATGAGCTTCCCGATATT
* *
32015703 CAGCTTGCATGAGCTTCCTGTTATT
1 CAGCTTGCATGAGCTTCCCGATATT
* *
32015728 CAGCTTGGAAGAGCTT
1 CAGCTTGCATGAGCTT
32015744 ACTGTTTACA
Statistics
Matches: 79, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
25 77 0.97
26 2 0.03
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Consensus pattern (25 bp):
CAGCTTGCATGAGCTTCCCGATATT
Found at i:32015748 original size:25 final size:25
Alignment explanation
Indices: 32015653--32015749 Score: 131
Period size: 25 Copynumber: 3.9 Consensus size: 25
32015643 TTCCAATTTA
* * *
32015653 CAGCTTACATGAGCTTCCCGATATT
1 CAGCTTGCATGAGCTTCCTGTTATT
*
32015678 CAGCTTGCATGAACTTCCTGTTATT
1 CAGCTTGCATGAGCTTCCTGTTATT
32015703 CAGCTTGCATGAGCTTCCTGTTATT
1 CAGCTTGCATGAGCTTCCTGTTATT
* * *
32015728 CAGCTTGGAAGAGCTTACTGTT
1 CAGCTTGCATGAGCTTCCTGTT
32015750 TACAGCTCGT
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 64 1.00
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.36
Consensus pattern (25 bp):
CAGCTTGCATGAGCTTCCTGTTATT
Found at i:32015765 original size:24 final size:25
Alignment explanation
Indices: 32015686--32015765 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
32015676 TTCAGCTTGC
* * * * *
32015686 ATGAACTTCCTGTTATTCAGCTTGC
1 ATGAGCTTACTGTTATACAGCTCGG
* * *
32015711 ATGAGCTTCCTGTTATTCAGCTTGG
1 ATGAGCTTACTGTTATACAGCTCGG
* *
32015736 AAGAGCTTACTGTT-TACAGCTCGT
1 ATGAGCTTACTGTTATACAGCTCGG
32015760 ATGAGC
1 ATGAGC
32015766 ATACATGAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
24 12 0.26
25 35 0.74
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (25 bp):
ATGAGCTTACTGTTATACAGCTCGG
Found at i:32018918 original size:25 final size:26
Alignment explanation
Indices: 32018873--32018954 Score: 82
Period size: 25 Copynumber: 3.2 Consensus size: 26
32018863 CAACTCTTAT
* *
32018873 GAGCGTCTCGA-TATATGGCTCTTCA
1 GAGCTTCTCGATTAAATGGCTCTTCA
*
32018898 GAGCTTCTCGATTAAAT-GCTCTTTGA
1 GAGCTTCTCGATTAAATGGCTC-TTCA
*
32018924 GAGCTTCTTGATT-AATGGCTC-TCTA
1 GAGCTTCTCGATTAAATGGCTCTTC-A
32018949 GAGCTT
1 GAGCTT
32018955 GCTAATATAT
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
24 1 0.02
25 24 0.50
26 23 0.48
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (26 bp):
GAGCTTCTCGATTAAATGGCTCTTCA
Found at i:32019016 original size:24 final size:23
Alignment explanation
Indices: 32018988--32019051 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 23
32018978 TTCCCAATTA
32018988 ATGGCTCTC-TGGAGCTACCTATT
1 ATGGCTCTCAT-GAGCTACCTATT
* *
32019011 ATTGGCTCGCATGAGCTTCCTAGTT
1 A-TGGCTCTCATGAGCTACCTA-TT
*
32019036 ATGGCTCTTATGAGCT
1 ATGGCTCTCATGAGCT
32019052 TCCCGTTATA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
23 1 0.03
24 29 0.85
25 4 0.12
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.36
Consensus pattern (23 bp):
ATGGCTCTCATGAGCTACCTATT
Found at i:32019052 original size:24 final size:24
Alignment explanation
Indices: 32018999--32019054 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
32018989 TGGCTCTCTG
*
32018999 GAGCTACCTATTATTGGCTCGCAT
1 GAGCTTCCTATTATTGGCTCGCAT
**
32019023 GAGCTTCCTAGTTA-TGGCTCTTAT
1 GAGCTTCCTA-TTATTGGCTCGCAT
32019047 GAGCTTCC
1 GAGCTTCC
32019055 CGTTATATGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 25 0.89
25 3 0.11
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.36
Consensus pattern (24 bp):
GAGCTTCCTATTATTGGCTCGCAT
Found at i:32020361 original size:12 final size:12
Alignment explanation
Indices: 32020344--32020368 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
32020334 TATTTTGAGT
32020344 TAAAATGGCATG
1 TAAAATGGCATG
32020356 TAAAATGGCATG
1 TAAAATGGCATG
32020368 T
1 T
32020369 GCATAGGTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.24, T:0.28
Consensus pattern (12 bp):
TAAAATGGCATG
Found at i:32020472 original size:20 final size:20
Alignment explanation
Indices: 32020434--32020472 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
32020424 AAACTCTATC
* *
32020434 TATTTTGGTTTTATTTGAAG
1 TATTTTGGTTCTATATGAAG
32020454 TATTTTGGTTCTATATGAA
1 TATTTTGGTTCTATATGAA
32020473 ATGAATTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.03, G:0.18, T:0.56
Consensus pattern (20 bp):
TATTTTGGTTCTATATGAAG
Found at i:32024190 original size:16 final size:15
Alignment explanation
Indices: 32024141--32024191 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
32024131 AAATTACAAT
32024141 AATATTTAATAA-CA
1 AATATTTAATAATCA
32024155 AGA-ATTTAATAATCA
1 A-ATATTTAATAATCA
*
32024170 AATATTTAATTATCTA
1 AATATTTAATAATC-A
32024186 AATATT
1 AATATT
32024192 ATGCATACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 11 0.34
15 14 0.44
16 7 0.22
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (15 bp):
AATATTTAATAATCA
Found at i:32025879 original size:40 final size:40
Alignment explanation
Indices: 32025826--32025920 Score: 129
Period size: 40 Copynumber: 2.4 Consensus size: 40
32025816 CAGCGTTTTT
* *
32025826 AAAACACCGCTATAGATAGAGAATTAGCGGCGC-TTCATGA
1 AAAACACCGCTATAGATAGAGAATTAACGGCGCTTTC-TCA
* *
32025866 AAAACACCGCTATAGATTGAGCATTAACGGCGCTTTCTCA
1 AAAACACCGCTATAGATAGAGAATTAACGGCGCTTTCTCA
*
32025906 AAAACGCCGCTATAG
1 AAAACACCGCTATAG
32025921 GTCGACCATT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
40 46 0.94
41 3 0.06
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (40 bp):
AAAACACCGCTATAGATAGAGAATTAACGGCGCTTTCTCA
Found at i:32025931 original size:40 final size:40
Alignment explanation
Indices: 32025788--32025955 Score: 123
Period size: 40 Copynumber: 4.3 Consensus size: 40
32025778 CATTTGGACA
* * *
32025788 AAAAACCCCGCTATAGATTGGA-CATTAGCAGCG-TTT-T-
1 AAAAACGCCGCTATAGA-TCGACCATTAGCGGCGCTTTCTC
* * * ** *
32025825 TAAAACACCGCTATAGATAGAGAATTAGCGGCGC-TTCATG
1 AAAAACGCCGCTATAGATCGACCATTAGCGGCGCTTTC-TC
* * * *
32025865 AAAAACACCGCTATAGATTGAGCATTAACGGCGCTTTCTC
1 AAAAACGCCGCTATAGATCGACCATTAGCGGCGCTTTCTC
* * *
32025905 AAAAACGCCGCTATAGGTCGACCATTAGTGGCG-TTTATC
1 AAAAACGCCGCTATAGATCGACCATTAGCGGCGCTTTCTC
32025944 AAAAAACGCCGC
1 -AAAAACGCCGC
32025956 AAAAAATTTA
Statistics
Matches: 107, Mismatches: 17, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
36 3 0.03
37 26 0.24
39 6 0.06
40 69 0.64
41 3 0.03
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Consensus pattern (40 bp):
AAAAACGCCGCTATAGATCGACCATTAGCGGCGCTTTCTC
Found at i:32026159 original size:152 final size:153
Alignment explanation
Indices: 32025848--32026267 Score: 497
Period size: 152 Copynumber: 2.7 Consensus size: 153
32025838 TAGATAGAGA
* * *
32025848 ATTAGCGGCGC-TTCATGAAAAACACCGCTATAGATTGAGCATTAACGGCGCTTTCTCAAAAACG
1 ATTAGCGGCGCTTTC-TGAAAAACACCGCTATAGATCGAGCATTAGCGGCGCTTT-TTAAAAACG
* * * *
32025912 CCGCTATAGGTCGACCATTAGT-GGCGTTTATCAAAAAACGCCGCAAAAAATTTAAGCACAACGG
64 CCGCTATAGGTCGACCATTA-TCGGCG-TTATTAGAAAACGCCACAAAAAATTTAAGCACAACGC
*
32025976 CGTCGTTTTATGTTGAGCTTTAGTGTC
127 CCTCGTTTTATGTTGAGCTTTAGTGTC
* * * *
32026003 ATTAGCGGCGCTTTCTCAAAAACGCCGCTATAGATCGAGCATTAGTGGC-ATTTTTAAAAACGCC
1 ATTAGCGGCGCTTTCTGAAAAACACCGCTATAGATCGAGCATTAGCGGCGCTTTTTAAAAACGCC
* * *
32026067 GCTATAGGTCAACCATTATCGGCGCTTCTTGGAAAACGCCACAAAAAA-TTAAGCACAACGCCCT
66 GCTATAGGTCGACCATTATCGGCG-TTATTAGAAAACGCCACAAAAAATTTAAGCACAACGCCCT
* *
32026131 CGTTTTATGTTGGGCTTTAGTGTT
130 CGTTTTATGTTGAGCTTTAGTGTC
* * * * * *
32026155 ATTAGCGGCGCTTTTTGAAAAACACCGCTACAAATCGAGCATTAGCGGCTCTTTTTGGAAAATGC
1 ATTAGCGGCGCTTTCTGAAAAACACCGCTATAGATCGAGCATTAGCGGCGCTTTTT-AAAAACGC
* * * * *
32026220 CGTTATAGGTCGACCTTTAGCAGCGTTTTCTAGAAAACGCCACAAAAA
65 CGCTATAGGTCGACCATTATCGGCGTTAT-TAGAAAACGCCACAAAAA
32026268 TTCAGTGTCA
Statistics
Matches: 226, Mismatches: 34, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
152 80 0.35
153 57 0.25
154 46 0.20
155 40 0.18
156 3 0.01
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (153 bp):
ATTAGCGGCGCTTTCTGAAAAACACCGCTATAGATCGAGCATTAGCGGCGCTTTTTAAAAACGCC
GCTATAGGTCGACCATTATCGGCGTTATTAGAAAACGCCACAAAAAATTTAAGCACAACGCCCTC
GTTTTATGTTGAGCTTTAGTGTC
Found at i:32026617 original size:14 final size:14
Alignment explanation
Indices: 32026595--32026639 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
32026585 TTAATTATCA
*
32026595 TTATAGTTTAGAGT
1 TTATGGTTTAGAGT
32026609 TTATGGTTTA-AGGT
1 TTATGGTTTAGA-GT
*
32026623 ATATGGTTTAGAGT
1 TTATGGTTTAGAGT
32026637 TTA
1 TTA
32026640 AAGTTTATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 1 0.04
14 24 0.92
15 1 0.04
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (14 bp):
TTATGGTTTAGAGT
Found at i:32026765 original size:7 final size:7
Alignment explanation
Indices: 32026755--32026796 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
32026745 TAAGGGTATT
32026755 GGGTTAG
1 GGGTTAG
32026762 GGGTTAG
1 GGGTTAG
*
32026769 GTGTTA-
1 GGGTTAG
32026775 GGGTTAG
1 GGGTTAG
32026782 GGGTTTAG
1 GGG-TTAG
*
32026790 GGTTTAG
1 GGGTTAG
32026797 ATTAATTAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
6 5 0.17
7 19 0.63
8 6 0.20
ACGTcount: A:0.14, C:0.00, G:0.50, T:0.36
Consensus pattern (7 bp):
GGGTTAG
Found at i:32026774 original size:14 final size:14
Alignment explanation
Indices: 32026755--32026796 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
32026745 TAAGGGTATT
32026755 GGGTTAGGGGTTAG
1 GGGTTAGGGGTTAG
*
32026769 GTGTTA-GGGTTAG
1 GGGTTAGGGGTTAG
*
32026782 GGGTTTAGGGTTTAG
1 GGG-TTAGGGGTTAG
32026797 ATTAATTAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 9 0.39
14 8 0.35
15 6 0.26
ACGTcount: A:0.14, C:0.00, G:0.50, T:0.36
Consensus pattern (14 bp):
GGGTTAGGGGTTAG
Found at i:32026796 original size:21 final size:21
Alignment explanation
Indices: 32026707--32026796 Score: 80
Period size: 21 Copynumber: 4.3 Consensus size: 21
32026697 ATGTTTTAAT
*
32026707 GGTTTAAGGGTT-GGGGTTTAA
1 GGTTT-AGGGTTAGGGGTTTAG
* * * *
32026728 GGTCTAGGGGTAGTGGTTAAG
1 GGTTTAGGGTTAGGGGTTTAG
32026749 GGTATT-GGGTTAGGGG-TTA-
1 GGT-TTAGGGTTAGGGGTTTAG
32026768 GGTGTTAGGGTTAGGGGTTTAG
1 GGT-TTAGGGTTAGGGGTTTAG
32026790 GGTTTAG
1 GGTTTAG
32026797 ATTAATTAGT
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
19 5 0.09
20 17 0.31
21 28 0.52
22 4 0.07
ACGTcount: A:0.17, C:0.01, G:0.47, T:0.36
Consensus pattern (21 bp):
GGTTTAGGGTTAGGGGTTTAG
Found at i:32027213 original size:14 final size:15
Alignment explanation
Indices: 32027196--32027254 Score: 63
Period size: 14 Copynumber: 4.1 Consensus size: 15
32027186 TATATGATAG
32027196 GGTTT-TGAGTTTAA
1 GGTTTATGAGTTTAA
*
32027210 GGTTT-TGAGATTTAG
1 GGTTTATGAG-TTTAA
*
32027225 GGTTTAT-AGTTTGA
1 GGTTTATGAGTTTAA
32027239 GGTTTATG-GTTTAA
1 GGTTTATGAGTTTAA
32027253 GG
1 GG
32027255 GTAGAGTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
14 26 0.68
15 11 0.29
16 1 0.03
ACGTcount: A:0.20, C:0.00, G:0.32, T:0.47
Consensus pattern (15 bp):
GGTTTATGAGTTTAA
Found at i:32030268 original size:13 final size:14
Alignment explanation
Indices: 32030252--32030283 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
32030242 TTATTATAAA
32030252 TAATTATAAT-GTT
1 TAATTATAATGGTT
32030265 TAATTATAATGGTT
1 TAATTATAATGGTT
32030279 TAATT
1 TAATT
32030284 CGTCGTTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (14 bp):
TAATTATAATGGTT
Found at i:32030996 original size:32 final size:31
Alignment explanation
Indices: 32030960--32031037 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
32030950 TTCATTTAAC
* * *
32030960 ATTTTTTGTTGTATTTTTATGCTACATTTGCT
1 ATTTTTGGTTGGA-TTTCATGCTACATTTGCT
* *
32030992 ATTTTTGGTTGGATTTCATGTTATATTTGCT
1 ATTTTTGGTTGGATTTCATGCTACATTTGCT
*
32031023 GTTTTTGGTTGGATT
1 ATTTTTGGTTGGATT
32031038 AAATGCAGGA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 29 0.73
32 11 0.28
ACGTcount: A:0.14, C:0.06, G:0.19, T:0.60
Consensus pattern (31 bp):
ATTTTTGGTTGGATTTCATGCTACATTTGCT
Found at i:32031236 original size:44 final size:44
Alignment explanation
Indices: 32031127--32031289 Score: 190
Period size: 43 Copynumber: 3.8 Consensus size: 44
32031117 TCACTAAATT
* * * *
32031127 CCATGACTTTTAG-TAGCGCTTTTCCCTCAAATGCCGTTAAAAA-
1 CCATGACTTTTAGCGA-CGCTTTTCCCACAAACGCCGCTAAAAAG
* * *
32031170 CCAT-ACTTTCAGTGGCGCTTTTCCCACAAACGCCGCTAAAAAG
1 CCATGACTTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAAAG
*
32031213 CCATGACTTTTAGCGATGCTTTTCCCACAAACGCCGCT-AAAAG
1 CCATGACTTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAAAG
* * *
32031256 CCATGACTTTTAGCGGCACTTTTCCCACAGACGC
1 CCATGACTTTTAGCGACGCTTTTCCCACAAACGC
32031290 GCTTGTGAAA
Statistics
Matches: 103, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
42 31 0.30
43 43 0.42
44 29 0.28
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (44 bp):
CCATGACTTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAAAG
Found at i:32031871 original size:20 final size:19
Alignment explanation
Indices: 32031846--32031890 Score: 74
Period size: 18 Copynumber: 2.4 Consensus size: 19
32031836 TAATTAATGG
32031846 TAAACTACACCATTAATCAC
1 TAAACTA-ACCATTAATCAC
32031866 TAAACT-ACCATTAATCAC
1 TAAACTAACCATTAATCAC
32031884 TAAACTA
1 TAAACTA
32031891 TGTTAAGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 18 0.75
20 6 0.25
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.27
Consensus pattern (19 bp):
TAAACTAACCATTAATCAC
Found at i:32032213 original size:73 final size:73
Alignment explanation
Indices: 32032127--32032271 Score: 281
Period size: 73 Copynumber: 2.0 Consensus size: 73
32032117 AAGGGTTGTT
*
32032127 TAAATTTTGATTCGTAGATTCATGACATTCAAAGTTGTTTGATACACAAAATTAAAGTGTAAAAG
1 TAAATTTTAATTCGTAGATTCATGACATTCAAAGTTGTTTGATACACAAAATTAAAGTGTAAAAG
32032192 AAAAGAGA
66 AAAAGAGA
32032200 TAAATTTTAATTCGTAGATTCATGACATTCAAAGTTGTTTGATACACAAAATTAAAGTGTAAAAG
1 TAAATTTTAATTCGTAGATTCATGACATTCAAAGTTGTTTGATACACAAAATTAAAGTGTAAAAG
32032265 AAAAGAG
66 AAAAGAG
32032272 GAAAGAAAAC
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (73 bp):
TAAATTTTAATTCGTAGATTCATGACATTCAAAGTTGTTTGATACACAAAATTAAAGTGTAAAAG
AAAAGAGA
Found at i:32035820 original size:22 final size:20
Alignment explanation
Indices: 32035795--32035842 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 20
32035785 ATAAGAACAA
32035795 AATTAATTTAA-AATAATTTTAT
1 AATTAA-TTAAGAATAA--TTAT
*
32035817 AATTTATTAAGAATAATTAT
1 AATTAATTAAGAATAATTAT
32035837 AATTAA
1 AATTAA
32035843 CGGTTATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 9 0.39
21 4 0.17
22 10 0.43
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
AATTAATTAAGAATAATTAT
Found at i:32039200 original size:9 final size:9
Alignment explanation
Indices: 32039182--32039274 Score: 132
Period size: 9 Copynumber: 10.3 Consensus size: 9
32039172 TCAGTTGAAC
32039182 TAAATCGGT
1 TAAATCGGT
*
32039191 TAAGTCGGT
1 TAAATCGGT
*
32039200 TAAGTCGGT
1 TAAATCGGT
32039209 TAAATCGGT
1 TAAATCGGT
*
32039218 TAAATTGGT
1 TAAATCGGT
*
32039227 TAAGTCGGT
1 TAAATCGGT
*
32039236 TAAATCAGT
1 TAAATCGGT
32039245 TAAATCGGT
1 TAAATCGGT
*
32039254 TAAGTCGGT
1 TAAATCGGT
32039263 TAAATCGGT
1 TAAATCGGT
32039272 TAA
1 TAA
32039275 TTTTTAACCA
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 74 1.00
ACGTcount: A:0.31, C:0.10, G:0.25, T:0.34
Consensus pattern (9 bp):
TAAATCGGT
Found at i:32039212 original size:27 final size:27
Alignment explanation
Indices: 32039182--32039274 Score: 159
Period size: 27 Copynumber: 3.4 Consensus size: 27
32039172 TCAGTTGAAC
*
32039182 TAAATCGGTTAAGTCGGTTAAGTCGGT
1 TAAATCGGTTAAATCGGTTAAGTCGGT
*
32039209 TAAATCGGTTAAATTGGTTAAGTCGGT
1 TAAATCGGTTAAATCGGTTAAGTCGGT
*
32039236 TAAATCAGTTAAATCGGTTAAGTCGGT
1 TAAATCGGTTAAATCGGTTAAGTCGGT
32039263 TAAATCGGTTAA
1 TAAATCGGTTAA
32039275 TTTTTAACCA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 61 1.00
ACGTcount: A:0.31, C:0.10, G:0.25, T:0.34
Consensus pattern (27 bp):
TAAATCGGTTAAATCGGTTAAGTCGGT
Found at i:32040261 original size:15 final size:15
Alignment explanation
Indices: 32040237--32040267 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
32040227 GCACTAAATT
32040237 ATATTATATATATAA
1 ATATTATATATATAA
*
32040252 ATATTTTATATATAA
1 ATATTATATATATAA
32040267 A
1 A
32040268 AAATAAGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATATTATATATATAA
Found at i:32040493 original size:34 final size:34
Alignment explanation
Indices: 32040455--32040522 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
32040445 ACATCACATG
*
32040455 AGTAAGAAAACTAGTAAGTATATAAATGAGATTT
1 AGTAAGAAAACTAGTAAATATATAAATGAGATTT
32040489 AGTAAGAAAACTAGTAAATATATAAATGAGATTT
1 AGTAAGAAAACTAGTAAATATATAAATGAGATTT
32040523 TTTAAAAAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.16, T:0.29
Consensus pattern (34 bp):
AGTAAGAAAACTAGTAAATATATAAATGAGATTT
Found at i:32044554 original size:20 final size:21
Alignment explanation
Indices: 32044520--32044573 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
32044510 TGATGATATT
*
32044520 TTATGATTA-TTTAATTAGATA
1 TTAT-ATTATTTTAATAAGATA
32044541 -TATATTATTTTAATAAGATA
1 TTATATTATTTTAATAAGATA
*
32044561 TTTTATTATTTTA
1 TTATATTATTTTA
32044574 TTATTATTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.14
20 14 0.48
21 11 0.38
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (21 bp):
TTATATTATTTTAATAAGATA
Found at i:32044577 original size:3 final size:3
Alignment explanation
Indices: 32044559--32044607 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
32044549 TTTAATAAGA
*
32044559 TAT T-T TAT TAT T-T TAT TAT TAT T-T CAT TAT TAT T-T TAT TAT TAAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT
32044604 TAT T
1 TAT T
32044608 TAGTATAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
2 7 0.18
3 29 0.74
4 3 0.08
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:32044579 original size:11 final size:11
Alignment explanation
Indices: 32044563--32044601 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
32044553 ATAAGATATT
32044563 TTATTATTTTA
1 TTATTATTTTA
*
32044574 TTATTATTTCA
1 TTATTATTTTA
32044585 TTATTATTTTA
1 TTATTATTTTA
32044596 TTATTA
1 TTATTA
32044602 ATTATTTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:32044587 original size:19 final size:19
Alignment explanation
Indices: 32044559--32044600 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
32044549 TTTAATAAGA
*
32044559 TATTTTATTATT-TTATTAT
1 TATTTCATTATTATT-TTAT
32044578 TATTTCATTATTATTTTAT
1 TATTTCATTATTATTTTAT
32044597 TATT
1 TATT
32044601 AATTATTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (19 bp):
TATTTCATTATTATTTTAT
Found at i:32046792 original size:46 final size:46
Alignment explanation
Indices: 32046740--32046965 Score: 317
Period size: 46 Copynumber: 4.9 Consensus size: 46
32046730 TCTCTAATAT
* * *
32046740 GAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCGTGACAG
1 GAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAG
* *
32046786 GAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACGG
1 GAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAG
* * *
32046832 GAAATGAATAAGACCATGGTTGAAAGATACCATGGCAGCGTGACAG
1 GAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAG
* *
32046878 GAAATGAATAAGACCATGGTTGAAAGATACCATGACAACATGACAG
1 GAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAG
* * * * *
32046924 AAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 GAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATG
32046966 TCAAAGATAA
Statistics
Matches: 162, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 162 1.00
ACGTcount: A:0.40, C:0.15, G:0.26, T:0.19
Consensus pattern (46 bp):
GAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAG
Found at i:32051229 original size:6 final size:6
Alignment explanation
Indices: 32051215--32051245 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
32051205 ACAAATCTGG
*
32051215 AACAAT AACAGT AACAGT AACAGT AACAGT A
1 AACAGT AACAGT AACAGT AACAGT AACAGT A
32051246 TGGCACACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.55, C:0.16, G:0.13, T:0.16
Consensus pattern (6 bp):
AACAGT
Found at i:32051556 original size:22 final size:22
Alignment explanation
Indices: 32051511--32051556 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
32051501 TCCCTCTTTC
*
32051511 TTTCTTTTATTTCTTTATTCTA
1 TTTCTTTTATTTCTTTAATCTA
32051533 TTTCTTTTATTTACTTTAAT-TA
1 TTTCTTTTATTT-CTTTAATCTA
32051555 TT
1 TT
32051557 AAATTATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTCTTTTATTTCTTTAATCTA
Found at i:32051569 original size:3 final size:3
Alignment explanation
Indices: 32051559--32051603 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
32051549 TAATTATTAA
*
32051559 ATT A-T ATT ATT ATT A-T ATT -TT AGTA ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT
32051602 AT
1 AT
32051604 AATATTTTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
2 6 0.17
3 28 0.78
4 2 0.06
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:32051609 original size:32 final size:32
Alignment explanation
Indices: 32051549--32051612 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
32051539 TTATTTACTT
*
32051549 TAATTATTAAATTATATTATTATTATATTTTAG
1 TAATTATT-AATTATATTATTATAATATTTTAG
32051582 TAATTATT-ATTATTATTATTATAATATTTTA
1 TAATTATTAATTA-TATTATTATAATATTTTA
32051613 CTTAAATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 4 0.14
32 17 0.59
33 8 0.28
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (32 bp):
TAATTATTAATTATATTATTATAATATTTTAG
Found at i:32056365 original size:26 final size:26
Alignment explanation
Indices: 32056329--32056378 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
32056319 AAAAAAGACG
*
32056329 GAATAGTTTTCGAGTATTATTACACA
1 GAATAGTTTTCGAGCATTATTACACA
32056355 GAATAGTTTTCGAGCATTATTACA
1 GAATAGTTTTCGAGCATTATTACA
32056379 AACCTTTGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (26 bp):
GAATAGTTTTCGAGCATTATTACACA
Found at i:32059018 original size:24 final size:23
Alignment explanation
Indices: 32058969--32059016 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
32058959 CAGGAAGGTC
32058969 TTCCTGCATTGTGGGTTTTTTAT
1 TTCCTGCATTGTGGGTTTTTTAT
32058992 TTCCTGCATTGTGGGTTTTTTAT
1 TTCCTGCATTGTGGGTTTTTTAT
32059015 TT
1 TT
32059017 TCATTATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.08, C:0.12, G:0.21, T:0.58
Consensus pattern (23 bp):
TTCCTGCATTGTGGGTTTTTTAT
Found at i:32060909 original size:37 final size:38
Alignment explanation
Indices: 32060859--32060933 Score: 143
Period size: 37 Copynumber: 2.0 Consensus size: 38
32060849 CTCTCTTCCC
32060859 CTATTCAGAGAGTTTCGAAC-TTTTTTTTAAAGAATGG
1 CTATTCAGAGAGTTTCGAACTTTTTTTTTAAAGAATGG
32060896 CTATTCAGAGAGTTTCGAACTTTTTTTTTAAAGAATGG
1 CTATTCAGAGAGTTTCGAACTTTTTTTTTAAAGAATGG
32060934 TGTAAAATGA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 20 0.54
38 17 0.46
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.41
Consensus pattern (38 bp):
CTATTCAGAGAGTTTCGAACTTTTTTTTTAAAGAATGG
Found at i:32061696 original size:44 final size:47
Alignment explanation
Indices: 32061584--32061698 Score: 119
Period size: 47 Copynumber: 2.4 Consensus size: 47
32061574 TATACTATTC
* * *
32061584 TATTATTTTACATTTTAATAATATATTATTTCATATTATTATTTATTATA
1 TATTATTTTACA--TTAATTAT-TATTATTTCAAATTATTATCTATTATA
** *
32061634 TATTATTTTACACAAATTATTATTATTTTAAATTATTATCTA-TATA
1 TATTATTTTACATTAATTATTATTATTTCAAATTATTATCTATTATA
*
32061680 TATT-TTTT-TATTAATTATT
1 TATTATTTTACATTAATTATT
32061699 TGTACATATT
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
44 8 0.14
45 4 0.07
46 8 0.14
47 19 0.34
48 5 0.09
50 12 0.21
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (47 bp):
TATTATTTTACATTAATTATTATTATTTCAAATTATTATCTATTATA
Found at i:32064428 original size:37 final size:37
Alignment explanation
Indices: 32064380--32064451 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
32064370 AAAATTTGTT
32064380 GAGAAACATTTGTTTTAATATTTTTAATGCATTTTTA
1 GAGAAACATTTGTTTTAATATTTTTAATGCATTTTTA
* * * * *
32064417 GAGAAATATTTGTTTTGATGTTTTTACTGTATTTT
1 GAGAAACATTTGTTTTAATATTTTTAATGCATTTT
32064452 ATATATTATA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.28, C:0.04, G:0.14, T:0.54
Consensus pattern (37 bp):
GAGAAACATTTGTTTTAATATTTTTAATGCATTTTTA
Found at i:32067465 original size:41 final size:41
Alignment explanation
Indices: 32067407--32067489 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
32067397 TCTTATTGGT
32067407 AACACGAATAAACAGAGAGGCATCAGACTTTGAAAGAACAA
1 AACACGAATAAACAGAGAGGCATCAGACTTTGAAAGAACAA
*
32067448 AACACGAATAAATAGAGAGGCATCAGACTTTGAAAGAACAA
1 AACACGAATAAACAGAGAGGCATCAGACTTTGAAAGAACAA
32067489 A
1 A
32067490 CCCTAATGAG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.52, C:0.16, G:0.19, T:0.13
Consensus pattern (41 bp):
AACACGAATAAACAGAGAGGCATCAGACTTTGAAAGAACAA
Found at i:32073620 original size:39 final size:39
Alignment explanation
Indices: 32073566--32073660 Score: 111
Period size: 40 Copynumber: 2.4 Consensus size: 39
32073556 AAACCAAGTA
* *
32073566 CCTTCGGGATTTAGCCAGACATAGCT-ACCCGCTCAAATG
1 CCTTCGGGACTTAGCCAGACATAG-TAACCCGCACAAATG
* * **
32073605 CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATG
1 CCTTCGGGACTTAG-CCAGACATAGTAACCCGCACAAATG
32073645 CCTTCGGGACTTAGCC
1 CCTTCGGGACTTAGCC
32073661 CGGATATAGT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
39 16 0.33
40 32 0.67
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.24
Consensus pattern (39 bp):
CCTTCGGGACTTAGCCAGACATAGTAACCCGCACAAATG
Found at i:32073652 original size:40 final size:40
Alignment explanation
Indices: 32073599--32073674 Score: 152
Period size: 40 Copynumber: 1.9 Consensus size: 40
32073589 GCTACCCGCT
32073599 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTTGCA
32073639 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACT
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACT
32073675 ATATTCATGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTTGCA
Found at i:32087955 original size:11 final size:12
Alignment explanation
Indices: 32087939--32087967 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
32087929 CGAAATAATA
32087939 TTTTTTTGAATT
1 TTTTTTTGAATT
32087951 TTTTTTTGAATT
1 TTTTTTTGAATT
32087963 TTTTT
1 TTTTT
32087968 CACAAACCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (12 bp):
TTTTTTTGAATT
Found at i:32093529 original size:40 final size:40
Alignment explanation
Indices: 32093472--32093649 Score: 218
Period size: 40 Copynumber: 4.5 Consensus size: 40
32093462 CGGATGATAA
* * * *
32093472 CCGGGCTAGGTCCCGAAGGCCTTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
*
32093512 CCGGGCTAAGTCACGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
32093552 CTGGGCTAGGTCCCAAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
32093592 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
32093632 CC-GGCAAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
32093650 TACTTGGTTT
Statistics
Matches: 121, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
39 16 0.13
40 104 0.86
41 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Done.