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 42 of 186
Found at i:12428823 original size:16 final size:16
Alignment explanation
Indices: 12428798--12428828 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12428788 CCTTCAACTC
*
12428798 TTATATGTAAAAAAAT
1 TTATAAGTAAAAAAAT
12428814 TTATAAGTAAAAAAA
1 TTATAAGTAAAAAAA
12428829 AAGAAAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.32
Consensus pattern (16 bp):
TTATAAGTAAAAAAAT
Found at i:12434554 original size:10 final size:10
Alignment explanation
Indices: 12434528--12434593 Score: 52
Period size: 10 Copynumber: 7.0 Consensus size: 10
12434518 CAAATTTTCG
12434528 ATAATATTTT
1 ATAATATTTT
12434538 -T-ATATTTT
1 ATAATATTTT
12434546 ATAATATTTT
1 ATAATATTTT
*
12434556 AT-CTATCTTT
1 ATAATAT-TTT
12434566 -TAATA-TTT
1 ATAATATTTT
* *
12434574 AAAACATTTT
1 ATAATATTTT
*
12434584 ATGATATTTT
1 ATAATATTTT
12434594 GTAGTTTGTT
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
8 10 0.23
9 9 0.21
10 24 0.56
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.59
Consensus pattern (10 bp):
ATAATATTTT
Found at i:12434571 original size:19 final size:18
Alignment explanation
Indices: 12434528--12434573 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
12434518 CAAATTTTCG
12434528 ATAATATTTTTATATTTT
1 ATAATATTTTTATATTTT
*
12434546 ATAATATTTTATCTATCTTT
1 ATAATATTTT-TATAT-TTT
12434566 -TAATATTT
1 ATAATATTT
12434574 AAAACATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 10 0.40
19 12 0.48
20 3 0.12
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (18 bp):
ATAATATTTTTATATTTT
Found at i:12437905 original size:42 final size:42
Alignment explanation
Indices: 12437846--12437932 Score: 147
Period size: 42 Copynumber: 2.1 Consensus size: 42
12437836 TATCACTTTA
* * *
12437846 TTGATGAAGCAGGGATGACGTTTAATGACTTCTCTGAATTCT
1 TTGATGAAGCAAGGATGACATTTAATGACTTCTCTGAATTAT
12437888 TTGATGAAGCAAGGATGACATTTAATGACTTCTCTGAATTAT
1 TTGATGAAGCAAGGATGACATTTAATGACTTCTCTGAATTAT
12437930 TTG
1 TTG
12437933 TTTACACGTG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.37
Consensus pattern (42 bp):
TTGATGAAGCAAGGATGACATTTAATGACTTCTCTGAATTAT
Found at i:12440031 original size:22 final size:20
Alignment explanation
Indices: 12439997--12440046 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 20
12439987 CTAGTAATTA
12439997 TTATAAATTTTAA-TGATTTT
1 TTATAAATTTTAAGT-ATTTT
*
12440017 TTATAATATTTTTAAGTTTTTT
1 TTATAA-A-TTTTAAGTATTTT
12440039 TTATAAAT
1 TTATAAAT
12440047 CTAGAATGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 7 0.27
21 2 0.08
22 16 0.62
23 1 0.04
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (20 bp):
TTATAAATTTTAAGTATTTT
Found at i:12441886 original size:26 final size:26
Alignment explanation
Indices: 12441857--12441909 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
12441847 GATGTGCCAT
12441857 TACCCCTTAAGCCTATGTCATCACAA
1 TACCCCTTAAGCCTATGTCATCACAA
12441883 TACCCCTTAAGCCTATGTCATCACAA
1 TACCCCTTAAGCCTATGTCATCACAA
12441909 T
1 T
12441910 CTTCTTTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.34, G:0.08, T:0.28
Consensus pattern (26 bp):
TACCCCTTAAGCCTATGTCATCACAA
Found at i:12446506 original size:22 final size:22
Alignment explanation
Indices: 12446481--12446544 Score: 57
Period size: 22 Copynumber: 3.0 Consensus size: 22
12446471 AATTTTAGCT
12446481 ATTAATGTTTAATTT-TTTATTA
1 ATTAAT-TTTAATTTATTTATTA
* *
12446503 ATTAGTTTTTATTTATTTATT-
1 ATTAATTTTAATTTATTTATTA
12446524 -TTAA-TTTAATTTAATTT-TTA
1 ATTAATTTTAATTT-ATTTATTA
12446544 A
1 A
12446545 CTTTTTGAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
19 9 0.26
20 7 0.21
21 7 0.21
22 11 0.32
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (22 bp):
ATTAATTTTAATTTATTTATTA
Found at i:12448835 original size:19 final size:19
Alignment explanation
Indices: 12448804--12448893 Score: 78
Period size: 19 Copynumber: 4.8 Consensus size: 19
12448794 TAAAGGGTCT
*
12448804 TTTTTAT-ACATTTTATAA
1 TTTTTATAAAATTTTATAA
*
12448822 TTTTTATAAAATTTTACAA
1 TTTTTATAAAATTTTATAA
* *
12448841 TTTTT-TAAATTTTTTATGA
1 TTTTTATAAA-ATTTTATAA
* *
12448860 TTTTTAT-AATTTTTCTAA
1 TTTTTATAAAATTTTATAA
* *
12448878 TTTTAACAAAATTTTA
1 TTTTTATAAAATTTTA
12448894 ATATAATTTA
Statistics
Matches: 57, Mismatches: 11, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
18 23 0.40
19 33 0.58
20 1 0.02
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.60
Consensus pattern (19 bp):
TTTTTATAAAATTTTATAA
Found at i:12448845 original size:28 final size:28
Alignment explanation
Indices: 12448805--12448975 Score: 106
Period size: 28 Copynumber: 6.1 Consensus size: 28
12448795 AAAGGGTCTT
12448805 TTTTATACA-TTTTATAATTTTTATAAAA
1 TTTTATA-ATTTTTATAATTTTTATAAAA
* * *
12448833 TTTTACAATTTTT-TAAATTTTT-TATGAT
1 TTTTATAATTTTTAT-AATTTTTATA-AAA
* * *
12448861 TTTTATAATTTTTCTAATTTTAACAAAA
1 TTTTATAATTTTTATAATTTTTATAAAA
*
12448889 TTTTA-ATATAATTTAT-ATTTTTATTAAAA
1 TTTTATA-AT-TTTTATAATTTTTA-TAAAA
* * * * *
12448918 TTTAATAAATTTAATAAATTTAAT-AAA
1 TTTTATAATTTTTATAATTTTTATAAAA
*
12448945 TTTTATTGATTTTTAT--TTTTTATAAAA
1 TTTTA-TAATTTTTATAATTTTTATAAAA
12448972 TTTT
1 TTTT
12448976 TTTACCACAT
Statistics
Matches: 107, Mismatches: 24, Indels: 25
0.69 0.15 0.16
Matches are distributed among these distances:
26 5 0.05
27 19 0.18
28 62 0.58
29 20 0.19
30 1 0.01
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.58
Consensus pattern (28 bp):
TTTTATAATTTTTATAATTTTTATAAAA
Found at i:12448909 original size:56 final size:56
Alignment explanation
Indices: 12448804--12448910 Score: 128
Period size: 56 Copynumber: 1.9 Consensus size: 56
12448794 TAAAGGGTCT
* * **
12448804 TTTTTATACATTTTATAATTTTTATAAAATTTTACAATTTTTTAAATTTTTTATGA
1 TTTTTATACATTTTATAATTTTAACAAAATTTTACAATAATTTAAATTTTTTATGA
* *
12448860 TTTTTATA-ATTTTTCTAATTTTAACAAAATTTTA-ATATAATTTATATTTTT
1 TTTTTATACA-TTTTATAATTTTAACAAAATTTTACA-ATAATTTAAATTTTT
12448911 ATTAAAATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
55 2 0.05
56 41 0.95
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.61
Consensus pattern (56 bp):
TTTTTATACATTTTATAATTTTAACAAAATTTTACAATAATTTAAATTTTTTATGA
Found at i:12448929 original size:9 final size:9
Alignment explanation
Indices: 12448915--12448947 Score: 66
Period size: 9 Copynumber: 3.7 Consensus size: 9
12448905 ATTTTTATTA
12448915 AAATTTAAT
1 AAATTTAAT
12448924 AAATTTAAT
1 AAATTTAAT
12448933 AAATTTAAT
1 AAATTTAAT
12448942 AAATTT
1 AAATTT
12448948 TATTGATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
AAATTTAAT
Found at i:12449331 original size:89 final size:91
Alignment explanation
Indices: 12449137--12449332 Score: 201
Period size: 90 Copynumber: 2.2 Consensus size: 91
12449127 AAAAAAAGAA
* * * *
12449137 CTTAATTGCTTTTTTTTTTAAGTTTGAGGGCTTTTTTATACATTTTGAAAGTCTAAATATCCAAT
1 CTTAATTACTTTTTTTTTTAAGTTTGAGAGCTTTTTTATACATTTTAAAAGTCTAAATACCCAAT
12449202 TGAGTGCAAAAAAAAAAAAGAGCAAGG
66 TGAGTGC-AAAAAAAAAAAGAGCAAGG
* * * *
12449229 C--ACTTAATGTTTTTTTTT-A-TTTGAGAGCATTTTTTATGCATTTTAAAAGT-TCAATTACCC
1 CTTAATTACT-TTTTTTTTTAAGTTTGAGAGC-TTTTTTATACATTTTAAAAGTCT-AAATACCC
* *
12449289 AGTTGAGTGC-AAAAATAAAA-A-CAATGG
63 AATTGAGTGCAAAAAAAAAAAGAGCAA-GG
12449316 CTTAATTACTTTTTTTT
1 CTTAATTACTTTTTTTT
12449333 AAATTAAGAG
Statistics
Matches: 86, Mismatches: 12, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
86 3 0.03
87 4 0.05
88 16 0.19
89 14 0.16
90 39 0.45
91 9 0.10
92 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.42
Consensus pattern (91 bp):
CTTAATTACTTTTTTTTTTAAGTTTGAGAGCTTTTTTATACATTTTAAAAGTCTAAATACCCAAT
TGAGTGCAAAAAAAAAAAGAGCAAGG
Found at i:12449471 original size:3 final size:3
Alignment explanation
Indices: 12449463--12449503 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
12449453 ACAATCACTC
*
12449463 ATT ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
12449504 CATCTCGCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:12450885 original size:21 final size:22
Alignment explanation
Indices: 12450858--12450905 Score: 89
Period size: 21 Copynumber: 2.2 Consensus size: 22
12450848 TGTCACACCA
12450858 GTGGTATAGTGACCCCGTAACT
1 GTGGTATAGTGACCCCGTAACT
12450880 -TGGTATAGTGACCCCGTAACT
1 GTGGTATAGTGACCCCGTAACT
12450901 GTGGT
1 GTGGT
12450906 CTCGTACCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (22 bp):
GTGGTATAGTGACCCCGTAACT
Found at i:12453879 original size:53 final size:53
Alignment explanation
Indices: 12453785--12453921 Score: 150
Period size: 53 Copynumber: 2.6 Consensus size: 53
12453775 TATAAGCCCG
* * * * *
12453785 TAACTGGTTGGTTATGGAATCATATTGAAAAAAGACAATATCGTGCAAGACCGA
1 TAACTGGTGGGTTATGAAATCATATGGAAAAAAGACAATATCATACAAGACC-A
* * * *
12453839 -AACTGGTGGGTTATGAAATCATATGGAAAGAATACCATATCATATAAGACCA
1 TAACTGGTGGGTTATGAAATCATATGGAAAAAAGACAATATCATACAAGACCA
* * *
12453891 TAATTGGTGGATTATGACATCATATGGAAAA
1 TAACTGGTGGGTTATGAAATCATATGGAAAA
12453922 GTTAAGGAAG
Statistics
Matches: 69, Mismatches: 13, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
52 1 0.01
53 68 0.99
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (53 bp):
TAACTGGTGGGTTATGAAATCATATGGAAAAAAGACAATATCATACAAGACCA
Found at i:12455205 original size:35 final size:35
Alignment explanation
Indices: 12455159--12455262 Score: 199
Period size: 35 Copynumber: 3.0 Consensus size: 35
12455149 TAGTGACTAG
12455159 TTTAGATTTTTTACTAAAGTAATTTGTTTTTCTCA
1 TTTAGATTTTTTACTAAAGTAATTTGTTTTTCTCA
12455194 TTTAGATTTTTTACTAAAGTAATTTGTTTTTCTCA
1 TTTAGATTTTTTACTAAAGTAATTTGTTTTTCTCA
*
12455229 TTTAGATTTTTTACTAAAGTAAGTTGTTTTTCTC
1 TTTAGATTTTTTACTAAAGTAATTTGTTTTTCTC
12455263 GCAATGTAAA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
35 68 1.00
ACGTcount: A:0.25, C:0.09, G:0.10, T:0.57
Consensus pattern (35 bp):
TTTAGATTTTTTACTAAAGTAATTTGTTTTTCTCA
Found at i:12455618 original size:21 final size:23
Alignment explanation
Indices: 12455594--12455641 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
12455584 TCTTATAGCT
12455594 TTAAA-AT-TTTTTAT-ATAATAA
1 TTAAACATATTTTTATAATAA-AA
12455615 TTAAACATATTTTTATAATAAAA
1 TTAAACATATTTTTATAATAAAA
12455638 TTAA
1 TTAA
12455642 TATTAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.21
22 2 0.08
23 13 0.54
24 4 0.17
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TTAAACATATTTTTATAATAAAA
Found at i:12456393 original size:30 final size:30
Alignment explanation
Indices: 12456357--12456418 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
12456347 ACTTATTTTA
*
12456357 TTATTAATTTTGTTATTATTTTAAAGGCAT
1 TTATTAATTTTATTATTATTTTAAAGGCAT
* *
12456387 TTATTAATTTTATTATTATTTTAGAGGTAT
1 TTATTAATTTTATTATTATTTTAAAGGCAT
12456417 TT
1 TT
12456419 GCTTGTTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.60
Consensus pattern (30 bp):
TTATTAATTTTATTATTATTTTAAAGGCAT
Found at i:12463087 original size:6 final size:5
Alignment explanation
Indices: 12463035--12463085 Score: 54
Period size: 5 Copynumber: 10.4 Consensus size: 5
12463025 AATAATAACT
*
12463035 AATAA AAT-- AATAA GAA-AA AATAA AATAA ACTAA AATAA AATAAA AATAA
1 AATAA AATAA AATAA -AATAA AATAA AATAA AATAA AATAA AAT-AA AATAA
12463084 AA
1 AA
12463086 ATTGGGTTGC
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
3 3 0.08
4 2 0.05
5 27 0.69
6 7 0.18
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (5 bp):
AATAA
Found at i:12482916 original size:14 final size:15
Alignment explanation
Indices: 12482883--12482923 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
12482873 ATTGAAAATG
12482883 TTTATAAAAATAAAAA
1 TTTATAAAAAT-AAAA
*
12482899 TTTATAAAAAT-TAA
1 TTTATAAAAATAAAA
12482913 TTTA-AAAAATA
1 TTTATAAAAATA
12482924 GTTAAAAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 6 0.26
14 6 0.26
16 11 0.48
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TTTATAAAAATAAAA
Found at i:12485837 original size:12 final size:12
Alignment explanation
Indices: 12485822--12485851 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
12485812 ACAATAATAC
12485822 TATATATAAATG
1 TATATATAAATG
*
12485834 TATATATATATG
1 TATATATAAATG
12485846 TATATA
1 TATATA
12485852 ATAGAAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (12 bp):
TATATATAAATG
Found at i:12486067 original size:19 final size:21
Alignment explanation
Indices: 12486044--12486094 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
12486034 CTTCTTTCCA
12486044 AAAAAACAAAAAAA-CACCTC
1 AAAAAACAAAAAAACCACCTC
*
12486064 AAAAAAACAAAAAAACCTCCTC
1 -AAAAAACAAAAAAACCACCTC
*
12486086 -CAAAACAAA
1 AAAAAACAAA
12486095 GAACAATCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 8 0.30
21 14 0.52
22 5 0.19
ACGTcount: A:0.69, C:0.25, G:0.00, T:0.06
Consensus pattern (21 bp):
AAAAAACAAAAAAACCACCTC
Found at i:12486089 original size:23 final size:23
Alignment explanation
Indices: 12486021--12486122 Score: 84
Period size: 23 Copynumber: 4.4 Consensus size: 23
12486011 CCTTTCCAAG
*
12486021 AAACAAAAATAACCTTCTTTCCAAAA
1 AAACAAAAA-AACC-TC-CTCCAAAA
*
12486047 AAACAAAAAAA-CACCT-CAAAA
1 AAACAAAAAAACCTCCTCCAAAA
12486068 AAACAAAAAAACCTCCTCCAAAA
1 AAACAAAAAAACCTCCTCCAAAA
* * * *
12486091 CAAA-GAACAATCCTTCTCCAAAA
1 -AAACAAAAAAACCTCCTCCAAAA
*
12486114 AACCAAAAA
1 AAACAAAAA
12486123 CCCACCACCT
Statistics
Matches: 62, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
21 16 0.26
22 7 0.11
23 24 0.39
24 4 0.06
25 2 0.03
26 9 0.15
ACGTcount: A:0.60, C:0.26, G:0.01, T:0.13
Consensus pattern (23 bp):
AAACAAAAAAACCTCCTCCAAAA
Found at i:12486090 original size:22 final size:22
Alignment explanation
Indices: 12486015--12486141 Score: 80
Period size: 22 Copynumber: 5.6 Consensus size: 22
12486005 AACTAGCCTT
* *
12486015 TCCAAGAAACAAAAATAACCTTCTT
1 TCCAAAAAACAAAAA-AACC-TC-C
*
12486040 TCCAAAAAAACAAAAAAA-CACC
1 TCC-AAAAAACAAAAAAACCTCC
*
12486062 TCAAAAAAACAAAAAAACCTCC
1 TCCAAAAAACAAAAAAACCTCC
*
12486084 TCC--AAAACAAAGAACAATCCTTC
1 TCCAAAAAACAAA-AA-AA-CCTCC
* * *
12486107 TCCAAAAAACCAAAAACCCACC
1 TCCAAAAAACAAAAAAACCTCC
* *
12486129 ACCTAAAAACAAA
1 TCCAAAAAACAAA
12486142 GTCTTGAATG
Statistics
Matches: 81, Mismatches: 14, Indels: 17
0.72 0.12 0.15
Matches are distributed among these distances:
20 8 0.10
21 16 0.20
22 22 0.27
23 9 0.11
24 3 0.04
25 12 0.15
26 11 0.14
ACGTcount: A:0.57, C:0.29, G:0.02, T:0.12
Consensus pattern (22 bp):
TCCAAAAAACAAAAAAACCTCC
Found at i:12487786 original size:11 final size:12
Alignment explanation
Indices: 12487746--12487789 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
12487736 CCTTGTTTCC
12487746 CTTTCCCTTCCTT
1 CTTT-CCTTCCTT
*
12487759 CTTTCTTTCCTT
1 CTTTCCTTCCTT
12487771 CTTTCCTTCC-T
1 CTTTCCTTCCTT
12487782 CTTTCCTT
1 CTTTCCTT
12487790 TGTCTTCTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 9 0.31
12 16 0.55
13 4 0.14
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (12 bp):
CTTTCCTTCCTT
Found at i:12488688 original size:14 final size:14
Alignment explanation
Indices: 12488669--12488698 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12488659 TTTTTAAGCG
12488669 GAAAAAAAAGATGA
1 GAAAAAAAAGATGA
*
12488683 GAAAAAAAATATGA
1 GAAAAAAAAGATGA
12488697 GA
1 GA
12488699 CATGGTTAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.20, T:0.10
Consensus pattern (14 bp):
GAAAAAAAAGATGA
Found at i:12491540 original size:29 final size:31
Alignment explanation
Indices: 12491487--12491551 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
12491477 AATAGATTAT
*
12491487 ATTTTTATAATTTTTAAGTTATT-AAATAAA
1 ATTTTTATAATTTTTAAGTGATTAAAATAAA
*
12491517 ATTTTTAT-ATTTTTAAG-GAGTTAAAATATA
1 ATTTTTATAATTTTTAAGTGA-TTAAAATAAA
12491547 ATTTT
1 ATTTT
12491552 ACCTTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 1 0.03
29 11 0.35
30 19 0.61
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (31 bp):
ATTTTTATAATTTTTAAGTGATTAAAATAAA
Found at i:12491552 original size:29 final size:29
Alignment explanation
Indices: 12491484--12491552 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 29
12491474 TTTAATAGAT
* *
12491484 TATATTTTTATAATTTTTAAGTTATTAAA
1 TATAATTTTATAATTTTTAAGTGATTAAA
*
12491513 TAAAATTTT-TATATTTTTAAG-GAGTTAAAA
1 TATAATTTTATA-ATTTTTAAGTGA-TT-AAA
12491543 TATAATTTTA
1 TATAATTTTA
12491553 CCTTTATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
28 3 0.09
29 18 0.56
30 11 0.34
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.54
Consensus pattern (29 bp):
TATAATTTTATAATTTTTAAGTGATTAAA
Found at i:12494513 original size:20 final size:20
Alignment explanation
Indices: 12494465--12494520 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
12494455 AGAATTAAAT
12494465 TATA-AAAAATACAAATATA
1 TATATAAAAATACAAATATA
* * * *
12494484 AAGATTAAAATACATATATA
1 TATATAAAAATACAAATATA
*
12494504 TATATAAAAATATAAAT
1 TATATAAAAATACAAAT
12494521 TTAAAATATA
Statistics
Matches: 27, Mismatches: 9, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (20 bp):
TATATAAAAATACAAATATA
Found at i:12510994 original size:21 final size:22
Alignment explanation
Indices: 12510968--12511015 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
12510958 ACCTTCAACT
*
12510968 TTAAACCTT-AAATCTTGAATC
1 TTAAACCTTCAAACCTTGAATC
12510989 TTAAA-CTTCAAACCTTGAATC
1 TTAAACCTTCAAACCTTGAATC
*
12511010 CTAAAC
1 TTAAAC
12511016 TTGAATTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.40, C:0.23, G:0.04, T:0.33
Consensus pattern (22 bp):
TTAAACCTTCAAACCTTGAATC
Found at i:12516152 original size:31 final size:32
Alignment explanation
Indices: 12516117--12516186 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
12516107 ATTTATTTAA
* *
12516117 ATATATATGA-TTGAATTAAAATTAAAATTTT
1 ATATATATCATTTGAACTAAAATTAAAATTTT
**
12516148 ATATATA-CATTTGAACTGCAATTAAAATTTT
1 ATATATATCATTTGAACTAAAATTAAAATTTT
12516179 ATATATAT
1 ATATATAT
12516187 AATTACATCA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 1 0.03
31 32 0.97
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (32 bp):
ATATATATCATTTGAACTAAAATTAAAATTTT
Found at i:12528185 original size:29 final size:29
Alignment explanation
Indices: 12528102--12528185 Score: 70
Period size: 29 Copynumber: 3.0 Consensus size: 29
12528092 GCGACTAAAT
*
12528102 TAAAAAAAATTG-A-TAT--TTGGTTGAC
1 TAAAAAAAATTGAACTATAGTTGGATGAC
* * * *
12528127 CAAAAAGAAAATAAACAATAGTT-GAGTGAC
1 TAAAAA-AAATTGAACTATAGTTGGA-TGAC
12528157 TAAAAAAAATTGAACTATAGTTGGATGAC
1 TAAAAAAAATTGAACTATAGTTGGATGAC
12528186 CTGTGATGTA
Statistics
Matches: 43, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
25 5 0.12
26 4 0.09
27 1 0.02
28 2 0.05
29 18 0.42
30 13 0.30
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.26
Consensus pattern (29 bp):
TAAAAAAAATTGAACTATAGTTGGATGAC
Found at i:12529069 original size:30 final size:30
Alignment explanation
Indices: 12529023--12529116 Score: 152
Period size: 30 Copynumber: 3.1 Consensus size: 30
12529013 TTTTATTATG
*
12529023 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
12529054 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* *
12529084 CCATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
12529114 CCA
1 CCA
12529117 TAAATATGGA
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
30 53 0.88
31 7 0.12
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.43
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:12529078 original size:15 final size:15
Alignment explanation
Indices: 12529033--12529110 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
12529023 CCAATATCTC
12529033 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
12529048 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
12529063 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
12529078 GACTTTCCAT-TATTT
1 GA-TACCCATATCTTT
12529093 GATACCCATATCTTT
1 GATACCCATATCTTT
12529108 GAT
1 GAT
12529111 TTTCCATAAA
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
14 9 0.19
15 29 0.62
16 9 0.19
ACGTcount: A:0.26, C:0.23, G:0.08, T:0.44
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:12533732 original size:30 final size:31
Alignment explanation
Indices: 12533686--12533749 Score: 112
Period size: 30 Copynumber: 2.1 Consensus size: 31
12533676 TTTTATTATG
12533686 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATATCTCGATACCCATATCTTTGACTTT
*
12533717 CCAATAT-TTGATACCCATATCTTTGACTTT
1 CCAATATCTCGATACCCATATCTTTGACTTT
12533747 CCA
1 CCA
12533750 TAAATATGGA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 25 0.78
31 7 0.22
ACGTcount: A:0.27, C:0.28, G:0.06, T:0.39
Consensus pattern (31 bp):
CCAATATCTCGATACCCATATCTTTGACTTT
Found at i:12533741 original size:15 final size:15
Alignment explanation
Indices: 12533696--12533742 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
12533686 CCAATATCTC
12533696 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
12533711 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
12533726 GATACCCATATCTTT
1 GATACCCATATCTTT
12533741 GA
1 GA
12533743 CTTTCCATAA
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
14 4 0.17
15 16 0.67
16 4 0.17
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:12534370 original size:30 final size:31
Alignment explanation
Indices: 12534334--12534407 Score: 78
Period size: 36 Copynumber: 2.3 Consensus size: 31
12534324 GAATGTATAT
12534334 TTAATAATTG-TTAACATTAATGGAAGACAA
1 TTAATAATTGCTTAACATTAATGGAAGACAA
*
12534364 TTAATAATGGTTGCCATTAACATTAATGGGAGACAA
1 TTAATAA---TTG-C-TTAACATTAATGGAAGACAA
*
12534400 TCAATAAT
1 TTAATAAT
12534408 GACAACCACC
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
30 7 0.19
33 4 0.11
36 25 0.69
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.32
Consensus pattern (31 bp):
TTAATAATTGCTTAACATTAATGGAAGACAA
Found at i:12536848 original size:32 final size:32
Alignment explanation
Indices: 12536803--12536871 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
12536793 TAAAAGAACA
12536803 ATTT-TACCCTTTATTAATTAATCATTATTCT
1 ATTTATACCCTTTATTAATTAATCATTATTCT
12536834 ATTTATACCCTTTATTAATTAATCATTATTCT
1 ATTTATACCCTTTATTAATTAATCATTATTCT
12536866 ATTTAT
1 ATTTAT
12536872 TTTTGTTATC
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 4 0.11
32 33 0.89
ACGTcount: A:0.30, C:0.14, G:0.00, T:0.55
Consensus pattern (32 bp):
ATTTATACCCTTTATTAATTAATCATTATTCT
Found at i:12543571 original size:8 final size:8
Alignment explanation
Indices: 12543552--12543581 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
12543542 GATATTAGAG
12543552 TTATTATTA
1 TTATT-TTA
12543561 TTATTTTA
1 TTATTTTA
12543569 TTATTTTA
1 TTATTTTA
12543577 TTATT
1 TTATT
12543582 CTCAAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 16 0.76
9 5 0.24
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (8 bp):
TTATTTTA
Found at i:12543928 original size:20 final size:20
Alignment explanation
Indices: 12543903--12543946 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
12543893 CTCAATATTG
12543903 AACTGATAAAAATAAATTCA
1 AACTGATAAAAATAAATTCA
12543923 AACTGATAAAAATAAATTCA
1 AACTGATAAAAATAAATTCA
12543943 AACT
1 AACT
12543947 ATCTATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.59, C:0.11, G:0.05, T:0.25
Consensus pattern (20 bp):
AACTGATAAAAATAAATTCA
Found at i:12544711 original size:2 final size:2
Alignment explanation
Indices: 12544704--12544732 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12544694 GGTCTGTTCT
12544704 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
12544733 TTAATGATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:12552732 original size:3 final size:3
Alignment explanation
Indices: 12552724--12552748 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12552714 CAGTATTAAA
12552724 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
12552749 CCTGAGCTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:12563188 original size:20 final size:21
Alignment explanation
Indices: 12563145--12563193 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
12563135 AAGGTTATAA
*
12563145 ATTTATATAAATATATAATAT
1 ATTTATATAAATATAAAATAT
*
12563166 ATTT-TATATAAT-TAAAATTT
1 ATTTATATA-AATATAAAATAT
12563186 ATTTATAT
1 ATTTATAT
12563194 GGACACGTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTTATATAAATATAAAATAT
Found at i:12567678 original size:19 final size:19
Alignment explanation
Indices: 12567633--12567682 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
12567623 GTATAATTAG
12567633 AATTATTTTATAATTGTTT
1 AATTATTTTATAATTGTTT
*
12567652 -ATAAATTTTATAATAT-TTT
1 AAT-TATTTTATAAT-TGTTT
12567671 AATTATTTTATA
1 AATTATTTTATA
12567683 CTTTTATAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 2 0.08
19 21 0.81
20 3 0.12
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
AATTATTTTATAATTGTTT
Found at i:12570892 original size:115 final size:115
Alignment explanation
Indices: 12570690--12570920 Score: 435
Period size: 115 Copynumber: 2.0 Consensus size: 115
12570680 TACTTCATGC
*
12570690 AACCAATATCAAACATGTCAAACTCACTTTTCATTGAACTTTTGAACTTTCCAAACATCTGCTTA
1 AACCAAGATCAAACATGTCAAACTCACTTTTCATTGAACTTTTGAACTTTCCAAACATCTGCTTA
* *
12570755 TTGTTTCCTGTAAAAATAATATCAATGACGTATAAACTTACTATGAGAAT
66 TTGTTTCCTGTAAAAATAATATCAACGACATATAAACTTACTATGAGAAT
12570805 AACCAAGATCAAACATGTCAAACTCACTTTTCATTGAACTTTTGAACTTTCCAAACATCTGCTTA
1 AACCAAGATCAAACATGTCAAACTCACTTTTCATTGAACTTTTGAACTTTCCAAACATCTGCTTA
12570870 TTGTTTCCTGTAAAAATAATATCAACGACATATAAACTTACTATGAGAAT
66 TTGTTTCCTGTAAAAATAATATCAACGACATATAAACTTACTATGAGAAT
12570920 A
1 A
12570921 CCTCCATATT
Statistics
Matches: 113, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
115 113 1.00
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (115 bp):
AACCAAGATCAAACATGTCAAACTCACTTTTCATTGAACTTTTGAACTTTCCAAACATCTGCTTA
TTGTTTCCTGTAAAAATAATATCAACGACATATAAACTTACTATGAGAAT
Found at i:12577516 original size:35 final size:35
Alignment explanation
Indices: 12577493--12577685 Score: 266
Period size: 35 Copynumber: 5.5 Consensus size: 35
12577483 GGCAAAGTGC
*
12577493 GAAATGTAGGTATGGTATTATCCATACCGAGTTGT
1 GAAATGTAGGTATGGTATTATCCATACCGAGTTGA
*
12577528 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
1 GAAATGTAGGTATGGTATTATCCATACCGAGTTGA
* * *
12577563 GAAATATAGGTATGGTATTATCCATACTGAGTTAA
1 GAAATGTAGGTATGGTATTATCCATACCGAGTTGA
* *
12577598 GAAATGTAGGTATGGCATT-TCCCATACCGAGTTGT
1 GAAATGTAGGTATGGTATTAT-CCATACCGAGTTGA
* *
12577633 GAAACGTAGGTATGGTATTTTCCATACCGAGTAT-A
1 GAAATGTAGGTATGGTATTATCCATACCGAGT-TGA
12577668 -AAATGTAGGTATGGTATT
1 GAAATGTAGGTATGGTATT
12577686 TCAATGAGGA
Statistics
Matches: 140, Mismatches: 15, Indels: 7
0.86 0.09 0.04
Matches are distributed among these distances:
34 18 0.13
35 120 0.86
36 2 0.01
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.33
Consensus pattern (35 bp):
GAAATGTAGGTATGGTATTATCCATACCGAGTTGA
Found at i:12577659 original size:105 final size:104
Alignment explanation
Indices: 12577493--12577685 Score: 300
Period size: 105 Copynumber: 1.8 Consensus size: 104
12577483 GGCAAAGTGC
* *
12577493 GAAATGTAGGTATGGTATTATCCATACCGAGTTGTGAAATGTAGGTATGGTATCATCCATACCGA
1 GAAATGTAGGTATGGCATTATCCATACCGAGTTGTGAAACGTAGGTATGGTATCATCCATACCGA
12577558 GT-TGAGAAATATAGGTATGGTATTATCCATACTGAGTTAA
66 GTAT-A-AAATATAGGTATGGTATTATCCATACTGAGTTAA
**
12577598 GAAATGTAGGTATGGCATT-TCCCATACCGAGTTGTGAAACGTAGGTATGGTATTTTCCATACCG
1 GAAATGTAGGTATGGCATTAT-CCATACCGAGTTGTGAAACGTAGGTATGGTATCATCCATACCG
*
12577662 AGTATAAAATGTAGGTATGGTATT
65 AGTATAAAATATAGGTATGGTATT
12577686 TCAATGAGGA
Statistics
Matches: 81, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
104 18 0.22
105 62 0.77
106 1 0.01
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.33
Consensus pattern (104 bp):
GAAATGTAGGTATGGCATTATCCATACCGAGTTGTGAAACGTAGGTATGGTATCATCCATACCGA
GTATAAAATATAGGTATGGTATTATCCATACTGAGTTAA
Found at i:12578937 original size:27 final size:27
Alignment explanation
Indices: 12578913--12578967 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
12578903 GCTACCACAC
*
12578913 GACCCCGACGACGCTCGACCACCACGA
1 GACCCCGACGACGCTCAACCACCACGA
*
12578940 GACCCTGACGACGCTCAACCACCACGA
1 GACCCCGACGACGCTCAACCACCACGA
12578967 G
1 G
12578968 CACTACGAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.27, C:0.45, G:0.22, T:0.05
Consensus pattern (27 bp):
GACCCCGACGACGCTCAACCACCACGA
Found at i:12593861 original size:8 final size:8
Alignment explanation
Indices: 12593848--12593877 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
12593838 AATTATTTCA
*
12593848 AATTCATC
1 AATTCAAC
12593856 AATTCAAC
1 AATTCAAC
12593864 AATTCAAC
1 AATTCAAC
12593872 AATTCA
1 AATTCA
12593878 TATATTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (8 bp):
AATTCAAC
Found at i:12612126 original size:37 final size:38
Alignment explanation
Indices: 12612084--12612168 Score: 95
Period size: 39 Copynumber: 2.3 Consensus size: 38
12612074 AATTAATACA
*
12612084 ATTTTTT-AATTAATAATTAT-AATTTAATTTATATTT
1 ATTTTTTAAATTAATAATTATAAATCTAATTTATATTT
** * *
12612120 ATTTTTTAAATTTGTAATTATCAAATCTATTTTATTTTT
1 ATTTTTTAAATTAATAATTAT-AAATCTAATTTATATTT
12612159 A-TTTTTAAAT
1 ATTTTTTAAAT
12612169 GTGAATTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
36 7 0.17
37 11 0.27
38 9 0.22
39 14 0.34
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.61
Consensus pattern (38 bp):
ATTTTTTAAATTAATAATTATAAATCTAATTTATATTT
Found at i:12612127 original size:18 final size:18
Alignment explanation
Indices: 12612084--12612128 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
12612074 AATTAATACA
12612084 ATTTTTTAATTAATAATT
1 ATTTTTTAATTAATAATT
** * *
12612102 ATAATTTAATTTATATTT
1 ATTTTTTAATTAATAATT
12612120 ATTTTTTAA
1 ATTTTTTAA
12612129 ATTTGTAATT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTTTTAATTAATAATT
Found at i:12612937 original size:18 final size:18
Alignment explanation
Indices: 12612914--12612963 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
12612904 AAGTAGATTT
12612914 TTATATCATGTATACTTC
1 TTATATCATGTATACTTC
*
12612932 TTATATCTATGAATA-TTC
1 TTATATC-ATGTATACTTC
12612950 TT-TATCATGTATAC
1 TTATATCATGTATAC
12612964 CATGGTTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
16 6 0.21
17 4 0.14
18 12 0.43
19 6 0.21
ACGTcount: A:0.30, C:0.14, G:0.06, T:0.50
Consensus pattern (18 bp):
TTATATCATGTATACTTC
Found at i:12614849 original size:397 final size:396
Alignment explanation
Indices: 12614108--12614880 Score: 954
Period size: 397 Copynumber: 1.9 Consensus size: 396
12614098 TCTAATGTCT
12614108 TAAGTGTAGTATTTTCGTCTATGTACACTTGTATTTTTTTGAACATATTAGTTAATAAAATTATT
1 TAAGTGTAGTATTTTCGTCTATGTACACTTGTATTTTTTTGAACATATTAGTTAATAAAATTATT
* * **
12614173 CATGAATTATATTAATATCCTTTGTATATTATCCTCAATGGTTTTTGCATGCAAAGAAAAATGAA
66 CATGAATTACATTAATA-CCTTTGTATAATATCCTCAATGGTTTTTGCACACAAAGAAAAATGAA
* * * *
12614238 AGCAAATATTAGTTCATTGGTTGTCTAATGTTTAACTAATACTAAACGGTATTATGTGATTAGAT
130 AGCAAATATTAGCTCACTGGTTGTCTAATGTTTAACTAATACTAAACGATATTATATGATTAGAT
*
12614303 CGTAATACAGAAAGATAGCTTATATTAGTAGATGAACCTAAAAATATCCTTAGTCTAATCGAAAA
195 CGTAATACAGAAAGATAGCTTATATTAGTAGACGAACCTAAAAATATCCTTAGTCTAATCGAAAA
** * * * *
12614368 TGAGCAAACTGATTAAAAGACTAATTTGTCGTCTATCAAGTTCAATTGGGGAGATGCTTTATCTT
260 TGAGCAAACCAATTAAAAGACAAATATGTCGTCTATCAAGTCCAATTAGGGAGATGCTTTATCTT
* * *
12614433 GGGCATCAGAGCAGATGACTCCCAGAAGATAAAGATATAGATGTGATTGACCAGATGTTGGATCT
325 AGGCATCAGAGCAGATGACTCCCAGAAGATAAAGACATAGATGTGACTGACCAGATGTTGGATCT
12614498 GGTGCCC
390 GGTGCCC
* * **
12614505 TAAGTGTTGTATTTTCGT-TAATGTACGCTTGTAATTTTTTTGAACA-AGTTTA-TTTCTAAAAT
1 TAAGTGTAGTATTTTCGTCT-ATGTACACTTGT-ATTTTTTTGAACATA--TTAGTTAATAAAAT
* * * *
12614567 TATTCATGAATTACGTTAATA-CTTTGTATAATGTCCTC-ATGTGATTTTTGTACACAAAGCAAA
62 TATTCATGAATTACATTAATACCTTTGTATAATATCCTCAATG-G-TTTTTGCACACAAAGAAAA
* * *
12614630 AT-AGGAGCAAATGTT-GCTCACTGGTTGTCTAATGTTTAAACTAATACTAAGCGATATTATATG
125 ATGA-AAGCAAATATTAGCTCACTGGTTGTCTAATGTTT-AACTAATACTAAACGATATTATATG
* * * * ** *
12614693 GTTGGATTGTAATAC-GAAA-ATACATCTTATATTAGTAGACGAACCTAATTATGTCCTTAGTCT
188 ATTAGATCGTAATACAGAAAGAT--AGCTTATATTAGTAGACGAACCTAAAAATATCCTTAGTCT
* * *
12614756 AATCGAAAATGAGTAAACCAATTGAAAGACAAATATGTTGTCTATCAAGTCCAATTAGGGAGATG
251 AATCGAAAATGAGCAAACCAATTAAAAGACAAATATGTCGTCTATCAAGTCCAATTAGGGAGATG
* * ** * * *
12614821 TTTTGTCTTAGGCATC-GAAGTGGATGACTCCTAGAAGATAGAGGCATAGATGTGACTGAC
316 CTTTATCTTAGGCATCAG-AGCAGATGACTCCCAGAAGATAAAGACATAGATGTGACTGAC
12614881 TGGATTGACA
Statistics
Matches: 319, Mismatches: 46, Indels: 22
0.82 0.12 0.06
Matches are distributed among these distances:
395 5 0.02
396 43 0.13
397 228 0.71
398 40 0.13
399 3 0.01
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (396 bp):
TAAGTGTAGTATTTTCGTCTATGTACACTTGTATTTTTTTGAACATATTAGTTAATAAAATTATT
CATGAATTACATTAATACCTTTGTATAATATCCTCAATGGTTTTTGCACACAAAGAAAAATGAAA
GCAAATATTAGCTCACTGGTTGTCTAATGTTTAACTAATACTAAACGATATTATATGATTAGATC
GTAATACAGAAAGATAGCTTATATTAGTAGACGAACCTAAAAATATCCTTAGTCTAATCGAAAAT
GAGCAAACCAATTAAAAGACAAATATGTCGTCTATCAAGTCCAATTAGGGAGATGCTTTATCTTA
GGCATCAGAGCAGATGACTCCCAGAAGATAAAGACATAGATGTGACTGACCAGATGTTGGATCTG
GTGCCC
Found at i:12615677 original size:58 final size:58
Alignment explanation
Indices: 12615613--12615787 Score: 208
Period size: 52 Copynumber: 3.1 Consensus size: 58
12615603 ATAGAAATTG
*
12615613 TGAAAATGGAGAAATTGAAATCATTTGGAAATTATTATGATTTTCTCCAAAATGAAAA
1 TGAAAATGGAGAAATTGAAATCATTTGGAAATGATTATGATTTTCTCCAAAATGAAAA
* * *
12615671 TGAAAATGGAGAAATGGAAA-CATTTGGAAATGATTATGGGTTTTTTCC------AAAA
1 TGAAAATGGAGAAATTGAAATCATTTGGAAATGATTAT-GATTTTCTCCAAAATGAAAA
*
12615723 TGAAAATGGAGAAA-TGGAATCATTTGGAAATGA--ATGTAGTTTTCTCCAAAATGAAAA
1 TGAAAATGGAGAAATTGAAATCATTTGGAAATGATTATG-A-TTTTCTCCAAAATGAAAA
12615780 TGAAAATG
1 TGAAAATG
12615788 AAAATGAAAA
Statistics
Matches: 99, Mismatches: 8, Indels: 21
0.77 0.06 0.16
Matches are distributed among these distances:
49 1 0.01
50 2 0.02
51 10 0.10
52 31 0.31
57 28 0.28
58 27 0.27
ACGTcount: A:0.43, C:0.06, G:0.20, T:0.30
Consensus pattern (58 bp):
TGAAAATGGAGAAATTGAAATCATTTGGAAATGATTATGATTTTCTCCAAAATGAAAA
Found at i:12615800 original size:13 final size:13
Alignment explanation
Indices: 12615770--12615820 Score: 95
Period size: 13 Copynumber: 4.0 Consensus size: 13
12615760 AGTTTTCTCC
12615770 AAAATGAAAATG-
1 AAAATGAAAATGA
12615782 AAAATGAAAATGA
1 AAAATGAAAATGA
12615795 AAAATGAAAATGA
1 AAAATGAAAATGA
12615808 AAAATGAAAATGA
1 AAAATGAAAATGA
12615821 CCTGAAAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 12 0.32
13 26 0.68
ACGTcount: A:0.69, C:0.00, G:0.16, T:0.16
Consensus pattern (13 bp):
AAAATGAAAATGA
Found at i:12615800 original size:19 final size:19
Alignment explanation
Indices: 12615770--12615833 Score: 87
Period size: 18 Copynumber: 3.4 Consensus size: 19
12615760 AGTTTTCTCC
12615770 AAAATGAAAATGAAAATG-
1 AAAATGAAAATGAAAATGA
12615788 AAAATGAAAAATGAAAATGA
1 AAAATG-AAAATGAAAATGA
**
12615808 AAAATGAAAATG-ACCTGA
1 AAAATGAAAATGAAAATGA
12615826 AAAATGAA
1 AAAATGAA
12615834 TTTATGTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
18 18 0.43
19 18 0.43
20 6 0.14
ACGTcount: A:0.66, C:0.03, G:0.16, T:0.16
Consensus pattern (19 bp):
AAAATGAAAATGAAAATGA
Found at i:12615806 original size:52 final size:51
Alignment explanation
Indices: 12615649--12615808 Score: 139
Period size: 52 Copynumber: 3.0 Consensus size: 51
12615639 GGAAATTATT
12615649 ATGA-TTTTCTCCAAAATGAAAATGAAAATGGAGAAATGGAAACATTTGGAAATGA
1 ATGAGTTTTCTCCAAAATGAAAATGAAAAT-GA-AAAT-GAAA-A-TTGGAAATGA
* * * * *
12615704 TTATGGGTTTTTTCCAAAATGAAAATGGAGAAATG-GAAT--CATTTGGAAATGA
1 --ATGAGTTTTCTCCAAAATGAAAAT-GA-AAATGAAAATGAAAATTGGAAATGA
* *
12615756 ATGTAGTTTTCTCCAAAATGAAAATGAAAATGAAAATGAAAAATGAAAATGA
1 ATG-AGTTTTCTCCAAAATGAAAATGAAAATGAAAATGAAAATTGGAAATGA
12615808 A
1 A
12615809 AAATGAAAAT
Statistics
Matches: 84, Mismatches: 12, Indels: 19
0.73 0.10 0.17
Matches are distributed among these distances:
49 5 0.06
50 8 0.10
51 19 0.23
52 20 0.24
54 1 0.01
57 6 0.07
58 18 0.21
59 3 0.04
60 4 0.05
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (51 bp):
ATGAGTTTTCTCCAAAATGAAAATGAAAATGAAAATGAAAATTGGAAATGA
Found at i:12615833 original size:7 final size:6
Alignment explanation
Indices: 12615770--12615820 Score: 84
Period size: 6 Copynumber: 8.2 Consensus size: 6
12615760 AGTTTTCTCC
12615770 AAAATG AAAATG AAAATG AAAATG AAAAATG AAAATG AAAAATG AAAATG
1 AAAATG AAAATG AAAATG AAAATG -AAAATG AAAATG -AAAATG AAAATG
12615820 A
1 A
12615821 CCTGAAAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
6 31 0.72
7 12 0.28
ACGTcount: A:0.69, C:0.00, G:0.16, T:0.16
Consensus pattern (6 bp):
AAAATG
Found at i:12618379 original size:21 final size:21
Alignment explanation
Indices: 12618354--12618425 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
12618344 AGGTCAAACG
* *
12618354 CCCGTATGACTGAGGTACACA
1 CCCGTGTGACTGAGGCACACA
**
12618375 CCCGTGTGAAGGGAGGCACACGA
1 CCCGTGTG-ACTGAGGCACAC-A
12618398 -CCGTGTGACTGAGGCACACA
1 CCCGTGTGACTGAGGCACACA
12618418 CCCGTGTG
1 CCCGTGTG
12618426 GACCAAGGAC
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
20 1 0.02
21 24 0.57
22 16 0.38
23 1 0.02
ACGTcount: A:0.24, C:0.29, G:0.32, T:0.15
Consensus pattern (21 bp):
CCCGTGTGACTGAGGCACACA
Found at i:12618409 original size:43 final size:44
Alignment explanation
Indices: 12618341--12618425 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 44
12618331 TAGGCCGTGT
* *
12618341 GGGAGGTCAAACGCCCGTATGACTGAGGTACACACCCGTGTGAA
1 GGGAGGTCAAACGACCGTATGACTGAGGCACACACCCGTGTGAA
* *
12618385 GGGAGG-CACACGACCGTGTGACTGAGGCACACACCCGTGTG
1 GGGAGGTCAAACGACCGTATGACTGAGGCACACACCCGTGTG
12618426 GACCAAGGAC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 31 0.84
44 6 0.16
ACGTcount: A:0.25, C:0.27, G:0.34, T:0.14
Consensus pattern (44 bp):
GGGAGGTCAAACGACCGTATGACTGAGGCACACACCCGTGTGAA
Found at i:12621542 original size:9 final size:9
Alignment explanation
Indices: 12621528--12621556 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
12621518 CCTAGCAGCC
12621528 CATTTATTT
1 CATTTATTT
12621537 CATTTATTT
1 CATTTATTT
12621546 CATTTATTT
1 CATTTATTT
12621555 CA
1 CA
12621557 CATTTTGACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.24, C:0.14, G:0.00, T:0.62
Consensus pattern (9 bp):
CATTTATTT
Found at i:12622578 original size:46 final size:47
Alignment explanation
Indices: 12622471--12622696 Score: 169
Period size: 46 Copynumber: 4.8 Consensus size: 47
12622461 CCACATTATG
* * * **
12622471 AGAGCTAGTGTAAGACCATGT-TCGGGACATGGCATCAGCGTTGAGACA
1 AGAGCCAGTGTAAGA-CATGTCT-GGGACATGGCATCAGCCTCGAGATT
* *
12622519 AGAGCTAGGGTAAGACATGTCTGGGACAT-GCATCAGCCTCGAGACTT
1 AGAGCCAGTGTAAGACATGTCTGGGACATGGCATCAGCCTCGAGA-TT
* * * * *
12622566 A-AGCCAGTGTAAGACACGTCTGGGACAT-GCAT-TGGCTACAAGATG
1 AGAGCCAGTGTAAGACATGTCTGGGACATGGCATCAGCCT-CGAGATT
* * * * * *
12622611 ATAGTCAGTGTAAAACCATGTCTGAGACATGGCATC-GACTTGAGA-T
1 AGAGCCAGTGTAAGA-CATGTCTGGGACATGGCATCAGCCTCGAGATT
*
12622657 ATGAGCCAGTGTAAGAACATGTCTGGTACATGGCATCAGC
1 A-GAGCCAGTGTAAG-ACATGTCTGGGACATGGCATCAGC
12622697 ACCTTACCCA
Statistics
Matches: 142, Mismatches: 26, Indels: 20
0.76 0.14 0.11
Matches are distributed among these distances:
45 5 0.04
46 57 0.40
47 56 0.39
48 24 0.17
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.22
Consensus pattern (47 bp):
AGAGCCAGTGTAAGACATGTCTGGGACATGGCATCAGCCTCGAGATT
Found at i:12629095 original size:46 final size:46
Alignment explanation
Indices: 12629042--12629217 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
12629032 ACATTATGAG
*
12629042 AGCCAGTGTAAGACATGTCTAGGACAT-GCATCGGCCTCGAGACAT
1 AGCCAGTGTAAGACATGTCTGGGACATGGCATCGGCCTCGAGACAT
*
12629087 AAGCCAGTGTAAGACATGTCTGGGACAT-GCATCGG-CTACGAGATGAT
1 -AGCCAGTGTAAGACATGTCTGGGACATGGCATCGGCCT-CGAGA-CAT
* * * *
12629134 AGTCAGTGTAAGATCATGTCTGGGACATGGCATC-GACTTGAGATAT
1 AGCCAGTGTAAGA-CATGTCTGGGACATGGCATCGGCCTCGAGACAT
12629180 GAGCCAGTGTAAGACTATGTCTGGGACATGGCATCGGC
1 -AGCCAGTGTAAGAC-ATGTCTGGGACATGGCATCGGC
12629218 ACCTTACCCA
Statistics
Matches: 115, Mismatches: 7, Indels: 14
0.85 0.05 0.10
Matches are distributed among these distances:
45 2 0.02
46 53 0.46
47 52 0.45
48 8 0.07
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.23
Consensus pattern (46 bp):
AGCCAGTGTAAGACATGTCTGGGACATGGCATCGGCCTCGAGACAT
Found at i:12629177 original size:47 final size:45
Alignment explanation
Indices: 12629042--12629215 Score: 215
Period size: 47 Copynumber: 3.7 Consensus size: 45
12629032 ACATTATGAG
* * *
12629042 AGCCAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGACATA
1 AGCCAGTGTAAGACATGTCTGGGACATGCATC-GACTCGAGATATA
*
12629088 AGCCAGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGAT-
1 AGCCAGTGTAAGACATGTCTGGGACATGCATCGACT-CGAGAT-ATA
* * *
12629134 AGTCAGTGTAAGATCATGTCTGGGACATGGCATCGACTTGAGATATG
1 AGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGACTCGAGATATA
12629181 AGCCAGTGTAAGACTATGTCTGGGACATGGCATCG
1 AGCCAGTGTAAGAC-ATGTCTGGGACAT-GCATCG
12629216 GCACCTTACC
Statistics
Matches: 115, Mismatches: 7, Indels: 11
0.86 0.05 0.08
Matches are distributed among these distances:
45 3 0.03
46 51 0.44
47 53 0.46
48 8 0.07
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (45 bp):
AGCCAGTGTAAGACATGTCTGGGACATGCATCGACTCGAGATATA
Found at i:12629187 original size:93 final size:92
Alignment explanation
Indices: 12628996--12629217 Score: 258
Period size: 93 Copynumber: 2.4 Consensus size: 92
12628986 GTCATTTATT
* * * *
12628996 TATGAGCTATTGTAAGACATGTCTGGG--A--CATCGACTACATTATGAGAGCCAGTGTAAGACA
1 TATGAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCTACATGATGAGAGCCAGTGTAAGACA
*
12629057 TGTCTAGGACATGCATCGGCCTCGAGA
66 TGTCTAGGACATGCATCGGACTCGAGA
* * * *
12629084 CATAAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCTACGA-GATGATAGTCAGTGTAAGAT
1 TATGAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCTAC-ATGATGAGAGCCAGTGTAAGA-
* *
12629148 CATGTCTGGGACATGGCATC-GACTTGAGA
64 CATGTCTAGGACAT-GCATCGGACTCGAGA
12629177 TATGAGCCAGTGTAAGACTATGTCTGGGACATGGCATCGGC
1 TATGAGCCAGTGTAAGAC-ATGTCTGGGACAT-GCATCGGC
12629218 ACCTTACCCA
Statistics
Matches: 112, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
88 23 0.21
90 1 0.01
92 25 0.22
93 37 0.33
94 18 0.16
95 8 0.07
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.24
Consensus pattern (92 bp):
TATGAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCTACATGATGAGAGCCAGTGTAAGACA
TGTCTAGGACATGCATCGGACTCGAGA
Found at i:12635657 original size:16 final size:16
Alignment explanation
Indices: 12635638--12635668 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12635628 CTTCTTCACT
12635638 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
12635654 TACTTACTTACTTAA
1 TACTCACTTACTTAA
12635669 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:12635674 original size:20 final size:20
Alignment explanation
Indices: 12635635--12635674 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
12635625 AAACTTCTTC
* *
12635635 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
12635655 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
12635675 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:12636062 original size:55 final size:53
Alignment explanation
Indices: 12635909--12636111 Score: 201
Period size: 55 Copynumber: 3.8 Consensus size: 53
12635899 CCTTTTGAAA
* * *
12635909 CTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-GAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGATAT-CTTGCCTTATAGAC
* * * ** *
12635962 CTAACCAATGTCATGTCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGTAC
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGATATC-TTGCCTTATAG-AC
** * * *
12636017 CTTATGAATGCCATGTCTTGACATGGTCTTACATGATTTGCTTGCCTTAGAAAC
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGATAT-CTTGCCTTATAGAC
* * *
12636071 CTTACCAATTTCCATGCCTTGGCATGGTCTTACATGATATC
1 CTTACCAA-TGCCATGTCTTGACATGGTCTTACATGATATC
12636112 CTTAAACCCT
Statistics
Matches: 121, Mismatches: 24, Indels: 9
0.79 0.16 0.06
Matches are distributed among these distances:
52 1 0.01
53 42 0.35
54 10 0.08
55 67 0.55
56 1 0.01
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (53 bp):
CTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCTTGCCTTATAGAC
Found at i:12640696 original size:46 final size:46
Alignment explanation
Indices: 12640629--12641041 Score: 520
Period size: 46 Copynumber: 8.6 Consensus size: 46
12640619 TAAGTGTAGC
* *
12640629 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
* *
12640675 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
* * * *
12640721 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGTAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
12640767 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
* *
12640819 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
*
12640865 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
* *
12640917 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
* * *
12640963 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
12641015 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
12641042 AGTACTCAAA
Statistics
Matches: 327, Mismatches: 22, Indels: 36
0.85 0.06 0.09
Matches are distributed among these distances:
46 198 0.61
48 2 0.01
49 2 0.01
50 2 0.01
52 123 0.38
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.36
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
Found at i:12640829 original size:98 final size:98
Alignment explanation
Indices: 12640629--12641041 Score: 667
Period size: 98 Copynumber: 4.3 Consensus size: 98
12640619 TAAGTGTAGC
* * **
12640629 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCAC--T----TT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTT
*
12640688 GTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
66 GTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
* * *
12640721 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGTAGCTATCACTTATCACTTTTCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTT
*
12640786 GTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
66 GTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
*
12640819 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTT
*
12640884 GTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
66 GTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
*
12640917 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTT
*
12640982 GTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
66 GTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
12641015 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
12641042 AGTACTCAAA
Statistics
Matches: 303, Mismatches: 12, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
92 52 0.17
94 1 0.00
98 250 0.83
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.36
Consensus pattern (98 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTT
GTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
Found at i:12645605 original size:16 final size:16
Alignment explanation
Indices: 12645586--12645616 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12645576 CTTCTTCACT
12645586 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
12645602 TACTTACTTACTTAA
1 TACTCACTTACTTAA
12645617 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:12645622 original size:20 final size:20
Alignment explanation
Indices: 12645583--12645622 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
12645573 AAACTTCTTC
* *
12645583 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
12645603 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
12645623 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:12645998 original size:55 final size:53
Alignment explanation
Indices: 12645873--12646062 Score: 197
Period size: 55 Copynumber: 3.5 Consensus size: 53
12645863 ATTTCCATCT
*
12645873 CTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATGCCATGC
1 CTTGACATGGTCTTACATGGGATCCTTGCCTTATGAACTCACCAATGCCATGC
* * * *
12645926 ATTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAACTTATCAATGCCATGC
1 CTTGACATGGTCTTACATGGGATCC-TTGCCTTAT-G-AACTCACCAATGCCATGC
*** * *
12645981 CTTGACATGGTCTTACATGATTTCCTTGCCTTA-GAAACCTTACCAATTACCATGC
1 CTTGACATGGTCTTACATGGGATCCTTGCCTTATG-AA-CTCACCAA-TGCCATGC
*
12646036 CTCTG-CATGGTCTTACATGGCATCCTT
1 CT-TGACATGGTCTTACATGGGATCCTT
12646063 AAACCCTAAA
Statistics
Matches: 114, Mismatches: 16, Indels: 12
0.80 0.11 0.08
Matches are distributed among these distances:
52 2 0.02
53 31 0.27
54 8 0.07
55 69 0.61
56 4 0.04
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (53 bp):
CTTGACATGGTCTTACATGGGATCCTTGCCTTATGAACTCACCAATGCCATGC
Found at i:12657659 original size:14 final size:13
Alignment explanation
Indices: 12657639--12657670 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
12657629 AATATTTAAC
12657639 TTGTTCTTAATTA
1 TTGTTCTTAATTA
12657652 TATGTTCTTAATTA
1 T-TGTTCTTAATTA
12657666 TTGTT
1 TTGTT
12657671 TTGATATCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.22, C:0.06, G:0.09, T:0.62
Consensus pattern (13 bp):
TTGTTCTTAATTA
Found at i:12659502 original size:13 final size:13
Alignment explanation
Indices: 12659484--12659511 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
12659474 ACAAATGATA
12659484 AAAATTTTCACAC
1 AAAATTTTCACAC
12659497 AAAATTTTCACAC
1 AAAATTTTCACAC
12659510 AA
1 AA
12659512 GTCACATATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (13 bp):
AAAATTTTCACAC
Found at i:12666186 original size:23 final size:23
Alignment explanation
Indices: 12666160--12666283 Score: 117
Period size: 23 Copynumber: 5.4 Consensus size: 23
12666150 CTGCTCATTT
* *
12666160 GAGCTTACCGATTCAGCTCGTAA
1 GAGCTTACTGATTCAGCTCATAA
* * **
12666183 GAGCTTAATGTTTCAGCTCATTG
1 GAGCTTACTGATTCAGCTCATAA
*
12666206 GAGCTTACTGATTCAGCTCGTAA
1 GAGCTTACTGATTCAGCTCATAA
**
12666229 GAGCTTACTG-TTCAGCTCATTG
1 GAGCTTACTGATTCAGCTCATAA
* * *
12666251 GAACTTACCGTTTCAGCTCA-ATA
1 GAGCTTACTGATTCAGCTCATA-A
12666274 GAGCTTACTG
1 GAGCTTACTG
12666284 TCCATCAACT
Statistics
Matches: 79, Mismatches: 20, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
22 17 0.22
23 62 0.78
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (23 bp):
GAGCTTACTGATTCAGCTCATAA
Found at i:12666219 original size:46 final size:45
Alignment explanation
Indices: 12666152--12666269 Score: 182
Period size: 46 Copynumber: 2.6 Consensus size: 45
12666142 ACTCACCACT
*
12666152 GCTCATTTGAGCTTACCGATTCAGCTCGTAAGAGCTTAATGTTTCA
1 GCTCATTGGAGCTTACCGATTCAGCTCGTAAGAGCTTAATG-TTCA
* *
12666198 GCTCATTGGAGCTTACTGATTCAGCTCGTAAGAGCTTACTGTTCA
1 GCTCATTGGAGCTTACCGATTCAGCTCGTAAGAGCTTAATGTTCA
* *
12666243 GCTCATTGGAACTTACCGTTTCAGCTC
1 GCTCATTGGAGCTTACCGATTCAGCTC
12666270 AATAGAGCTT
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
45 28 0.42
46 38 0.58
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (45 bp):
GCTCATTGGAGCTTACCGATTCAGCTCGTAAGAGCTTAATGTTCA
Found at i:12666258 original size:45 final size:45
Alignment explanation
Indices: 12666152--12666284 Score: 187
Period size: 45 Copynumber: 2.9 Consensus size: 45
12666142 ACTCACCACT
* *
12666152 GCTCATTTGAGCTTACCGATTCAGCTCGTAAGAGCTTAATGTTTCA
1 GCTCATTGGAGCTTACCGATTCAGCTCGTAAGAGCTTACTG-TTCA
*
12666198 GCTCATTGGAGCTTACTGATTCAGCTCGTAAGAGCTTACTGTTCA
1 GCTCATTGGAGCTTACCGATTCAGCTCGTAAGAGCTTACTGTTCA
* * *
12666243 GCTCATTGGAACTTACCGTTTCAGCTC-AATAGAGCTTACTGT
1 GCTCATTGGAGCTTACCGATTCAGCTCGTA-AGAGCTTACTGT
12666285 CCATCAACTC
Statistics
Matches: 79, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
44 1 0.01
45 40 0.51
46 38 0.48
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (45 bp):
GCTCATTGGAGCTTACCGATTCAGCTCGTAAGAGCTTACTGTTCA
Found at i:12677297 original size:59 final size:57
Alignment explanation
Indices: 12677194--12677320 Score: 132
Period size: 59 Copynumber: 2.2 Consensus size: 57
12677184 CAATAATGGA
* * * * *
12677194 TTTTTTTTATTACCCTACTATGAAAAGTTAGAAAATAATTACTCAATTATTAGTAAT
1 TTTTTTTTATTAACCTACTATAAAAAGTTACAAAATAATCACTCAACTATTAGTAAT
* **
12677251 TTTTTTTTTTGTAACCTAACTATAAAAAGTTACAAAATGGTCACTCAACTATT--TAAT
1 TTTTTTTTAT-TAACCT-ACTATAAAAAGTTACAAAATAATCACTCAACTATTAGTAAT
12677308 TGTCTTTTTTATT
1 T-T-TTTTTTATT
12677321 CACCCAACTA
Statistics
Matches: 57, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
57 14 0.25
58 7 0.12
59 36 0.63
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.46
Consensus pattern (57 bp):
TTTTTTTTATTAACCTACTATAAAAAGTTACAAAATAATCACTCAACTATTAGTAAT
Found at i:12677592 original size:2 final size:2
Alignment explanation
Indices: 12677585--12677613 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12677575 TTGGAAAACA
12677585 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12677614 ATAGGAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12678470 original size:41 final size:41
Alignment explanation
Indices: 12678425--12678534 Score: 211
Period size: 41 Copynumber: 2.7 Consensus size: 41
12678415 AAATAAAAAA
12678425 TTGATATGTTTAGTAAATAATTATATTTAATAAACAGAAAT
1 TTGATATGTTTAGTAAATAATTATATTTAATAAACAGAAAT
12678466 TTGATATGTTTAGTAAATAATTATATTTAATAAACAGAAAT
1 TTGATATGTTTAGTAAATAATTATATTTAATAAACAGAAAT
*
12678507 TTGATATGTTTAGTAAATAATTTTATTT
1 TTGATATGTTTAGTAAATAATTATATTT
12678535 GATTAAAAAT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 68 1.00
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (41 bp):
TTGATATGTTTAGTAAATAATTATATTTAATAAACAGAAAT
Found at i:12680293 original size:150 final size:149
Alignment explanation
Indices: 12679975--12680563 Score: 844
Period size: 150 Copynumber: 3.9 Consensus size: 149
12679965 TAGGCGATCT
* * * *
12679975 GGAGGCACATTCCACTGAGGATCTAATACTACCCATCACATTGGATGGAGAAGAGTGCGGAATTC
1 GGAGGCACCTTCCACTGAGGATCTACTACTACCCATCACATTGGACGGAGAAGAGTGAGGAATTC
** * *
12680040 CACTGTATGTCTCACTTCTAGGAGTCC-T--TCCACTCTTCTTATTAGTTTTCCTTCCAAGATTT
66 CACCATGTGTCTCACTTCTAGGAGTCCTTCCTCCACTCTT-TTATCAGTTTTCCTTCCAAGATTT
**
12680102 TCTTCAGAGTGCAATTTGGA
130 TCTTCACTGTGCAATTTGGA
* * * *
12680122 AGAGGCACCTTCCACTGAGGATCTACTACTACCCATCACGTTGTACGGAGAAGAGTGGGGAATTC
1 GGAGGCACCTTCCACTGAGGATCTACTACTACCCATCACATTGGACGGAGAAGAGTGAGGAATTC
*
12680187 CACCGTGTGTCTCACTTCTAGGAGTCCTTCCTCCACTCATTTTATCAGTTTTCCTTCCAAGATTT
66 CACCATGTGTCTCACTTCTAGGAGTCCTTCCTCCACTC-TTTTATCAGTTTTCCTTCCAAGATTT
*
12680252 TCTTCACTGTGCAATTTGGG
130 TCTTCACTGTGCAATTTGGA
*
12680272 GGAGGCACCTTTCACTGAGGATCTACTACTACCCATCACATTGGACGGAGAAGAGTGAGGAATTC
1 GGAGGCACCTTCCACTGAGGATCTACTACTACCCATCACATTGGACGGAGAAGAGTGAGGAATTC
* ** * *
12680337 CACTATGCATCTCACTTCTAGGAGTCCTTCCTCCACCCTTTATATCAGTTTTCCTTACAAGATTT
66 CACCATGTGTCTCACTTCTAGGAGTCCTTCCTCCACTCTTT-TATCAGTTTTCCTTCCAAGATTT
12680402 TCTTCACTGTGCAATTTGGA
130 TCTTCACTGTGCAATTTGGA
* * *
12680422 GGAGGCACCTTCCACCGAGGATCTACTACTACCCATCACATTGAATGGAGAAGAGTGAGGAATTC
1 GGAGGCACCTTCCACTGAGGATCTACTACTACCCATCACATTGGACGGAGAAGAGTGAGGAATTC
* * **
12680487 CATCATGTGTCTCGCTTCTAGGAGT-CTGTCCTCCACTCTTTTTATCAGTTTTCCTTCCATCATT
66 CACCATGTGTCTCACTTCTAGGAGTCCT-TCCTCCACTC-TTTTATCAGTTTTCCTTCCAAGATT
12680551 TTCTTCACTGTGC
129 TTCTTCACTGTGC
12680564 TTTCTCTTCT
Statistics
Matches: 397, Mismatches: 38, Indels: 11
0.89 0.09 0.02
Matches are distributed among these distances:
147 83 0.21
148 1 0.00
149 5 0.01
150 303 0.76
151 5 0.01
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (149 bp):
GGAGGCACCTTCCACTGAGGATCTACTACTACCCATCACATTGGACGGAGAAGAGTGAGGAATTC
CACCATGTGTCTCACTTCTAGGAGTCCTTCCTCCACTCTTTTATCAGTTTTCCTTCCAAGATTTT
CTTCACTGTGCAATTTGGA
Found at i:12682831 original size:36 final size:36
Alignment explanation
Indices: 12682791--12682864 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
12682781 AGAAATAGGA
*
12682791 CAAAGCATTGTTTTTGCAATGACACAAAAATAAAAT
1 CAAAGCATTGTTTTTGCAATGAAACAAAAATAAAAT
12682827 CAAAGCATTGTTTTTGCAATGAAACAAAAATAAAAT
1 CAAAGCATTGTTTTTGCAATGAAACAAAAATAAAAT
12682863 CA
1 CA
12682865 TACTCCCTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.27
Consensus pattern (36 bp):
CAAAGCATTGTTTTTGCAATGAAACAAAAATAAAAT
Found at i:12685178 original size:3 final size:3
Alignment explanation
Indices: 12685164--12685197 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
12685154 ATCATACAAG
* *
12685164 TCA TCT TCA TCA TCA TCA TTA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
12685198 TATTGGAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.41
Consensus pattern (3 bp):
TCA
Found at i:12685198 original size:15 final size:15
Alignment explanation
Indices: 12685170--12685200 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
12685160 CAAGTCATCT
12685170 TCATCATCATCATTA
1 TCATCATCATCATTA
12685185 TCATCATCATCATTA
1 TCATCATCATCATTA
12685200 T
1 T
12685201 TGGAATCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.26, G:0.00, T:0.42
Consensus pattern (15 bp):
TCATCATCATCATTA
Found at i:12688469 original size:16 final size:16
Alignment explanation
Indices: 12688448--12688515 Score: 109
Period size: 16 Copynumber: 4.2 Consensus size: 16
12688438 TTTGGTTCGC
*
12688448 TGTATTGGATTAAAGG
1 TGTATTGGATTAGAGG
12688464 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
12688480 TGTAATGGATTAGAGG
1 TGTATTGGATTAGAGG
*
12688496 TGTATTGGAATAGAGG
1 TGTATTGGATTAGAGG
12688512 TGTA
1 TGTA
12688516 ATAGCAAATC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.29, C:0.00, G:0.35, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:12688772 original size:18 final size:17
Alignment explanation
Indices: 12688751--12688785 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12688741 TTATTATTAA
*
12688751 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
12688769 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
12688786 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:12688838 original size:157 final size:157
Alignment explanation
Indices: 12688645--12688951 Score: 578
Period size: 157 Copynumber: 2.0 Consensus size: 157
12688635 CCCTTATCAT
*
12688645 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTATTATCAA
1 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
*
12688710 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAA
66 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
12688775 TTTAATAAAATTCTTAATAATTAGCAG
131 TTTAATAAAATTCTTAATAATTAGCAG
* *
12688802 AAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAATTTTTAATAAGATTATTAATATCAA
1 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
12688867 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
66 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
12688932 TTTAATAAAATTCTTAATAA
131 TTTAATAAAATTCTTAATAA
12688952 CTAATATTCT
Statistics
Matches: 146, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 146 1.00
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.48
Consensus pattern (157 bp):
AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
TTTAATAAAATTCTTAATAATTAGCAG
Found at i:12688925 original size:16 final size:16
Alignment explanation
Indices: 12688888--12688929 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
12688878 TTAATCATAT
*
12688888 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
12688904 TT-AAATATATTATAA
1 TTAAAATATATTATAA
12688919 TTAAAATATAT
1 TTAAAATATAT
12688930 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:12688936 original size:14 final size:15
Alignment explanation
Indices: 12688897--12688938 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
12688887 TTTAAACATA
*
12688897 ATTATTATTAAATAT
1 ATTATAATTAAATAT
12688912 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
12688926 A-TATAATTTAATA
1 ATTATAATTAAATA
12688939 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:12689384 original size:13 final size:13
Alignment explanation
Indices: 12689366--12689390 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12689356 GCCTTAACAA
12689366 GAGCAGCACTCAT
1 GAGCAGCACTCAT
12689379 GAGCAGCACTCA
1 GAGCAGCACTCA
12689391 AAACAGATTT
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:0.32, C:0.32, G:0.24, T:0.12
Consensus pattern (13 bp):
GAGCAGCACTCAT
Found at i:12696600 original size:15 final size:14
Alignment explanation
Indices: 12696552--12696610 Score: 59
Period size: 14 Copynumber: 4.3 Consensus size: 14
12696542 TTTTCTTCTG
*
12696552 ATTATATTTTAGTT
1 ATTATATTTTAATT
* *
12696566 ATTTATATTTAAAAT
1 A-TTATATTTTAATT
12696581 ATTATATTTTAATT
1 ATTATATTTTAATT
*
12696595 AGT-TATTTT-ATT
1 ATTATATTTTAATT
12696607 ATTA
1 ATTA
12696611 AGTTTTGTTA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
12 5 0.14
13 6 0.17
14 14 0.39
15 11 0.31
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (14 bp):
ATTATATTTTAATT
Found at i:12699905 original size:38 final size:38
Alignment explanation
Indices: 12699845--12699917 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 38
12699835 CTGAGCACAC
*
12699845 GCCCGTGTCGATATCGCTCCAGGTTTTCCAAATACGCG
1 GCCCATGTCGATATCGCTCCAGGTTTTCCAAATACGCG
* *
12699883 GCCCATGTGGATATTGCTCCAGGTTTTCCAAATAC
1 GCCCATGTCGATATCGCTCCAGGTTTTCCAAATAC
12699918 ACAGAAAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.29
Consensus pattern (38 bp):
GCCCATGTCGATATCGCTCCAGGTTTTCCAAATACGCG
Found at i:12701300 original size:16 final size:15
Alignment explanation
Indices: 12701270--12701299 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
12701260 GGATGGTGGG
12701270 GGGAATTCATTTTTT
1 GGGAATTCATTTTTT
12701285 GGGAATTCATTTTTT
1 GGGAATTCATTTTTT
12701300 TTTTCATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.20, T:0.53
Consensus pattern (15 bp):
GGGAATTCATTTTTT
Found at i:12704673 original size:17 final size:17
Alignment explanation
Indices: 12704650--12704691 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
12704640 GAGGCCTTAG
*
12704650 TATTGATT-TATTTATA
1 TATTGATTATATATATA
12704666 TGATTGATTATATATATA
1 T-ATTGATTATATATATA
12704684 TATTGATT
1 TATTGATT
12704692 GTAACTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 1 0.04
17 14 0.61
18 8 0.35
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (17 bp):
TATTGATTATATATATA
Found at i:12706019 original size:27 final size:27
Alignment explanation
Indices: 12705981--12706034 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
12705971 GCTTTGTGTA
12705981 GTCTAACCAAAACAATATATAATCTAC
1 GTCTAACCAAAACAATATATAATCTAC
12706008 GTCTAACCAAAACAATATATAATCTAC
1 GTCTAACCAAAACAATATATAATCTAC
12706035 TTATTTGCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.22, G:0.04, T:0.26
Consensus pattern (27 bp):
GTCTAACCAAAACAATATATAATCTAC
Found at i:12708582 original size:26 final size:24
Alignment explanation
Indices: 12708548--12708596 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
12708538 TAAATACAAA
* *
12708548 ATTTTAAAATATAATAAATCAAATAC
1 ATTTAAAAACATAA-AAA-CAAATAC
12708574 ATTTAAAAACATAAAAACAAATA
1 ATTTAAAAACATAAAAACAAATA
12708597 TTAAAACAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.29
25 3 0.14
26 12 0.57
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (24 bp):
ATTTAAAAACATAAAAACAAATAC
Found at i:12708662 original size:41 final size:40
Alignment explanation
Indices: 12708587--12708671 Score: 98
Period size: 41 Copynumber: 2.1 Consensus size: 40
12708577 TAAAAACATA
*
12708587 AAAACAAATATTAAAACAAGAAACAAATAAAAAATGATACT
1 AAAACAAATATTAAAACAAGAAACAAATAAAAAAT-ATAAT
* * * * **
12708628 AAAACAATTCTTAAAACAATACACAAATTGAAAATATAAT
1 AAAACAAATATTAAAACAAGAAACAAATAAAAAATATAAT
12708668 AAAA
1 AAAA
12708672 AGTGGTCATA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
40 8 0.22
41 29 0.78
ACGTcount: A:0.66, C:0.11, G:0.04, T:0.20
Consensus pattern (40 bp):
AAAACAAATATTAAAACAAGAAACAAATAAAAAATATAAT
Found at i:12714255 original size:31 final size:30
Alignment explanation
Indices: 12714220--12714277 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
12714210 AATAATACTT
*
12714220 ATAAATTAT-TGAAATTATATTTATATTTTTA
1 ATAAAATATGTGAAATT-TATTT-TATTTTTA
*
12714251 ATAAAATATGTTAAATTTATTTTATTT
1 ATAAAATATGTGAAATTTATTTTATTT
12714278 AAATAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 5 0.21
31 13 0.54
32 6 0.25
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (30 bp):
ATAAAATATGTGAAATTTATTTTATTTTTA
Found at i:12714285 original size:27 final size:26
Alignment explanation
Indices: 12714232--12714293 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
12714222 AAATTATTGA
*
12714232 AATTATATTTATATTTTTAATAAAAT
1 AATTAAATTTATATTTTTAATAAAAT
* * *
12714258 ATGTTAAATTTATTTTATTTAA-ATAAT
1 A-ATTAAATTTATATT-TTTAATAAAAT
12714285 AATTAAATT
1 AATTAAATT
12714294 ACATGTATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
26 8 0.28
27 16 0.55
28 5 0.17
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
AATTAAATTTATATTTTTAATAAAAT
Found at i:12714870 original size:42 final size:42
Alignment explanation
Indices: 12714818--12714901 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
12714808 TATCTAAAAT
* * *
12714818 AATATAAAATATTATATTACTAAGATTCAAATTAGAAATAAA
1 AATATAAAATATTATATTAATAAGATTAAAATTAAAAATAAA
*
12714860 AATATAAAATATTATATTAATAAGGTTAAAATTAAAAATAAA
1 AATATAAAATATTATATTAATAAGATTAAAATTAAAAATAAA
12714902 TAATCTTTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (42 bp):
AATATAAAATATTATATTAATAAGATTAAAATTAAAAATAAA
Found at i:12715015 original size:16 final size:15
Alignment explanation
Indices: 12714994--12715038 Score: 65
Period size: 14 Copynumber: 3.0 Consensus size: 15
12714984 TTTTTAATAT
12714994 AAATTTAGTACTTATA
1 AAATTTAGTACTTA-A
*
12715010 AAATTTAGCAC-TAA
1 AAATTTAGTACTTAA
12715024 AAATTTAGTACTTAA
1 AAATTTAGTACTTAA
12715039 TTTTTTCAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 11 0.42
15 5 0.19
16 10 0.38
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.38
Consensus pattern (15 bp):
AAATTTAGTACTTAA
Found at i:12716272 original size:28 final size:28
Alignment explanation
Indices: 12716240--12716296 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 28
12716230 TGTTCCCCTG
12716240 ATTTCAACATTAATTTTTTTTA-AAT-GTA
1 ATTTC-ACA-TAATTTTTTTTATAATAGTA
*
12716268 ATTTCACATGATTTTTTTTATAATAGTA
1 ATTTCACATAATTTTTTTTATAATAGTA
12716296 A
1 A
12716297 GCATCCTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 11 0.42
27 6 0.23
28 9 0.35
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (28 bp):
ATTTCACATAATTTTTTTTATAATAGTA
Found at i:12716990 original size:9 final size:7
Alignment explanation
Indices: 12716963--12716989 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
12716953 TTTATCTCAT
12716963 ATATATC
1 ATATATC
12716970 ATATATC
1 ATATATC
12716977 ATATATC
1 ATATATC
12716984 ATATAT
1 ATATAT
12716990 ACTATTACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (7 bp):
ATATATC
Found at i:12720401 original size:20 final size:20
Alignment explanation
Indices: 12720376--12720413 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12720366 TTAAAATTGA
12720376 CAAAAATAAAAAAATGTTTT
1 CAAAAATAAAAAAATGTTTT
* *
12720396 CAAAAATTAAAAATTGTT
1 CAAAAATAAAAAAATGTT
12720414 AAAATTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (20 bp):
CAAAAATAAAAAAATGTTTT
Found at i:12728227 original size:24 final size:24
Alignment explanation
Indices: 12728195--12728244 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
12728185 CTACAGAAGA
* *
12728195 AAATAACAAAGATTTTATGCTAAT
1 AAATAACAAAGATATTATACTAAT
*
12728219 AAATAACAAATATATTATACTAAT
1 AAATAACAAAGATATTATACTAAT
12728243 AA
1 AA
12728245 TTTTTAAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.32
Consensus pattern (24 bp):
AAATAACAAAGATATTATACTAAT
Found at i:12738745 original size:18 final size:19
Alignment explanation
Indices: 12738718--12738755 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
12738708 TAAATAAATA
*
12738718 ATTATATATTTTTAAAGAC
1 ATTATATATTTTGAAAGAC
12738737 ATTAT-TATTTTGAAAGAC
1 ATTATATATTTTGAAAGAC
12738755 A
1 A
12738756 CCTATTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (19 bp):
ATTATATATTTTGAAAGAC
Found at i:12740871 original size:17 final size:18
Alignment explanation
Indices: 12740845--12740889 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
12740835 TTTCTTGAAG
*
12740845 TTTTTGTTTTCTGT-T-T
1 TTTTTCTTTTCTGTGTAT
12740861 TTATTTCTTTTCTGTGTAT
1 TT-TTTCTTTTCTGTGTAT
12740880 TTTTTCTTTT
1 TTTTTCTTTT
12740890 TTAAAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 2 0.08
17 11 0.44
18 9 0.36
19 3 0.12
ACGTcount: A:0.04, C:0.09, G:0.09, T:0.78
Consensus pattern (18 bp):
TTTTTCTTTTCTGTGTAT
Found at i:12741710 original size:92 final size:92
Alignment explanation
Indices: 12741552--12741753 Score: 314
Period size: 92 Copynumber: 2.2 Consensus size: 92
12741542 TCCAACCCAT
* * * * * *
12741552 TGCAACTTCGGGTAGATATTTGTCTCTTCAACCTATTTCACTGCAACTTCAGGGAGATAAGATCT
1 TGCAACTTTGGGGAGATATTCGTATCCTCAACCTATTCCACTGCAACTTCAGGGAGATAAGATCT
12741617 GTAGCTTATAGCTTTAGTTTATTCCAC
66 GTAGCTTATAGCTTTAGTTTATTCCAC
*
12741644 TGCAACTTTGGGGAGATATTCGTATCCTCAACCTATTCCACTGCAACTTCAGGGAGATAAGGTCT
1 TGCAACTTTGGGGAGATATTCGTATCCTCAACCTATTCCACTGCAACTTCAGGGAGATAAGATCT
*
12741709 GTAGCTTGTAGCTTTAGTTTATTCCAC
66 GTAGCTTATAGCTTTAGTTTATTCCAC
* *
12741736 TGTAACTTTAGGGAGATA
1 TGCAACTTTGGGGAGATA
12741754 AGACTTGCTG
Statistics
Matches: 100, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
92 100 1.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (92 bp):
TGCAACTTTGGGGAGATATTCGTATCCTCAACCTATTCCACTGCAACTTCAGGGAGATAAGATCT
GTAGCTTATAGCTTTAGTTTATTCCAC
Found at i:12741915 original size:89 final size:89
Alignment explanation
Indices: 12741814--12742070 Score: 270
Period size: 89 Copynumber: 2.9 Consensus size: 89
12741804 GGACTTGTCG
* * *
12741814 CTTCAATCTGCTCCACTCCAACTTCAAGGAGATAAGATTTGTAATCTTCAATCTGCTCCACTATA
1 CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTAT-AGCTTCAATCTGCTCCACTATA
** ***
12741879 ACT-TCA-AGTAGATAAGTTTTGTGA-
65 ACTAT-AGAG-AGATAAAATTTACCAT
* * * *
12741903 CTTCAA-CTTGCTCCATTGCAACTTCAAGGAGATAAGGTTTATAGCTTTAATCTGCTCCACTGTA
1 CTTCAATC-TGCTCCACTGCAACTTCAAGGAGATAAGATTTATAGCTTCAATCTGCTCCACTATA
12741967 ACTATAGAGAGATAAAATTTACCAT
65 ACTATAGAGAGATAAAATTTACCAT
* * * * * **
12741992 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTATGGCTTCAACCTACTCCATTGCAA
1 CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTATAGCTTCAATCTGCTCCACTATAA
*
12742057 CTTTAGAGAGATAA
66 CTATAGAGAGATAA
12742071 GGTTTATAAC
Statistics
Matches: 141, Mismatches: 22, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
88 34 0.24
89 106 0.75
90 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (89 bp):
CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTATAGCTTCAATCTGCTCCACTATAA
CTATAGAGAGATAAAATTTACCAT
Found at i:12741926 original size:44 final size:45
Alignment explanation
Indices: 12741814--12742031 Score: 203
Period size: 45 Copynumber: 4.9 Consensus size: 45
12741804 GGACTTGTCG
*
12741814 CTTCAATCTGCTCCACTCCAACTTCAAGGAGATAAGATTTGTAAT
1 CTTCAATCTGCTCCACTACAACTTCAAGGAGATAAGATTTGTAAT
* * * *
12741859 CTTCAATCTGCTCCACTATAACTTCAAGTAGATAAGTTTTGTGA-
1 CTTCAATCTGCTCCACTACAACTTCAAGGAGATAAGATTTGTAAT
* * * * *
12741903 CTTCAA-CTTGCTCCATTGCAACTTCAAGGAGATAAGGTTTAT-AG
1 CTTCAATC-TGCTCCACTACAACTTCAAGGAGATAAGATTTGTAAT
* ** * ***
12741947 CTTTAATCTGCTCCACTGTAAC-T-ATAGAGAGATAAAATTTACCAT
1 CTTCAATCTGCTCCACTACAACTTCA-AG-GAGATAAGATTTGTAAT
* *
12741992 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTT
1 CTTCAATCTGCTCCACTACAACTTCAAGGAGATAAGATTT
12742032 ATGGCTTCAA
Statistics
Matches: 143, Mismatches: 22, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
42 1 0.01
43 5 0.03
44 62 0.43
45 72 0.50
46 2 0.01
47 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.33
Consensus pattern (45 bp):
CTTCAATCTGCTCCACTACAACTTCAAGGAGATAAGATTTGTAAT
Found at i:12742056 original size:44 final size:44
Alignment explanation
Indices: 12741813--12742078 Score: 236
Period size: 44 Copynumber: 6.0 Consensus size: 44
12741803 AGGACTTGTC
* *
12741813 GCTTCAATCTGCTCCACTCCAACTTCAAGGAGATAAGATTTGTAA
1 GCTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTAT-A
* ** * * *
12741858 TCTTCAATCTGCTCCACTATAACTTCAAGTAGATAAGTTTTGT-
1 GCTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTATA
* *
12741901 GACTTCAA-CTTGCTCCATTGCAACTTCAAGGAGATAAGGTTTATA
1 G-CTTCAATC-TGCTCCACTGCAACTTCAAGGAGATAAGATTTATA
* * * *
12741946 GCTTTAATCTGCTCCACTGTAAC-T-ATAGAGAGATAAAATTTACCA
1 GCTTCAATCTGCTCCACTGCAACTTCA-AG-GAGATAAGATTTA-TA
* * *
12741991 TCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTATG
1 GCTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTATA
* * * * *
12742035 GCTTCAACCTACTCCATTGCAACTT-TAGAGAGATAAGGTTTATA
1 GCTTCAATCTGCTCCACTGCAACTTCAAG-GAGATAAGATTTATA
12742079 ACTTGTAGCT
Statistics
Matches: 178, Mismatches: 33, Indels: 21
0.77 0.14 0.09
Matches are distributed among these distances:
42 1 0.01
43 5 0.03
44 96 0.54
45 73 0.41
46 2 0.01
47 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.32
Consensus pattern (44 bp):
GCTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTATA
Found at i:12745519 original size:50 final size:50
Alignment explanation
Indices: 12745395--12745643 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
12745385 GATAATAACA
* * ** * *
12745395 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
12745446 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
12745496 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
12745546 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
12745601 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
12745644 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:12745573 original size:100 final size:104
Alignment explanation
Indices: 12745394--12745643 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
12745384 TGATAATAAC
**
12745394 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
12745459 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
12745496 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
12745559 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
12745601 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
12745644 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:12745759 original size:13 final size:13
Alignment explanation
Indices: 12745738--12745769 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
12745728 GCTTGGATCA
*
12745738 TCATCAAATAAAT
1 TCATAAAATAAAT
12745751 TCATAAAATAAAT
1 TCATAAAATAAAT
12745764 TCATAA
1 TCATAA
12745770 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:12746016 original size:30 final size:30
Alignment explanation
Indices: 12745981--12746038 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
12745971 CCTCGACTCT
*
12745981 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
12746011 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
12746039 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:12757276 original size:29 final size:29
Alignment explanation
Indices: 12757230--12757288 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
12757220 TTTTATTATC
*
12757230 TAACATCTATCTTCGTACATTGAGGGCAA
1 TAACATCTATCTTCGTACATTGACGGCAA
*
12757259 TAACATCTATCTTTGTACATTGACGGCAA
1 TAACATCTATCTTCGTACATTGACGGCAA
12757288 T
1 T
12757289 GTACATATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (29 bp):
TAACATCTATCTTCGTACATTGACGGCAA
Found at i:12767431 original size:10 final size:10
Alignment explanation
Indices: 12767416--12767450 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
12767406 TCATTTAATT
*
12767416 AATTTTTTTA
1 AATTTTTTAA
12767426 AA-TTTTTAA
1 AATTTTTTAA
12767435 AATTTTTTAA
1 AATTTTTTAA
12767445 AATTTT
1 AATTTT
12767451 AATAATTCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
AATTTTTTAA
Found at i:12767457 original size:19 final size:19
Alignment explanation
Indices: 12767409--12767457 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 19
12767399 CATATTATCA
*
12767409 TTTAATTAATTTTTTTAAATT
1 TTTAA-TAA-TTTTTTAAAAT
12767430 TTTAA-AATTTTTTAAAAT
1 TTTAATAATTTTTTAAAAT
12767448 TTTAATAATT
1 TTTAATAATT
12767458 CTAATTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 15 0.58
19 6 0.23
21 5 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTAATAATTTTTTAAAAT
Found at i:12790194 original size:58 final size:59
Alignment explanation
Indices: 12790096--12790210 Score: 196
Period size: 58 Copynumber: 2.0 Consensus size: 59
12790086 TCATTGCAAC
**
12790096 AAGTAATTGGATACCTTACCATTTAACATACACGTAATTTTGTGGGT-TTTTTTTTTAT
1 AAGTAATTGGATACCTTACCATTTAACATACAAATAATTTTGTGGGTGTTTTTTTTTAT
*
12790154 AAGTAATTGGATACCTTACCATTTAACATACAAATGATTTTGTGGGTGTTTTTTTTT
1 AAGTAATTGGATACCTTACCATTTAACATACAAATAATTTTGTGGGTGTTTTTTTTT
12790211 TTGATAAATT
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
58 44 0.83
59 9 0.17
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.46
Consensus pattern (59 bp):
AAGTAATTGGATACCTTACCATTTAACATACAAATAATTTTGTGGGTGTTTTTTTTTAT
Done.