Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 86 of 210
Found at i:25209799 original size:86 final size:84
Alignment explanation
Indices: 25209694--25209957 Score: 309
Period size: 86 Copynumber: 3.1 Consensus size: 84
25209684 AGGTGTTGGC
25209694 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAAAA
1 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTG-GGAAAA
25209759 AGCGCCACTAAAGATCATAGT
65 AGCGCCACTAAAGATCAT-GT
* * * ***
25209780 CTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGGTCTATT-GCGGCGTTTGAGGGGT
1 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTCT-TTAGCGGCGTTTG-GGAAA
* * *
25209844 AAGCGCCGCTAAAGACCCTGAT
64 AAGCGCCACTAAAGATCATG-T
* *
25209866 CTTTAGTGGCGTTTTTAGG--AGAAGCGCCGCTAAAGATAAGGGTCTTTAACGGCGTTTGAGAGA
1 CTTTAGTGGCGTTTTT-GGTCA-AAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGGGA-A
* *
25209929 GAAGCGCCACTAAAGATCAGGGT
63 AAAGCGCCACTAAAGATCA-TGT
25209952 CTTTAG
1 CTTTAG
25209958 CGGTGCTTCC
Statistics
Matches: 149, Mismatches: 22, Indels: 14
0.81 0.12 0.08
Matches are distributed among these distances:
85 5 0.03
86 139 0.93
87 5 0.03
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (84 bp):
CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGGGAAAAA
GCGCCACTAAAGATCATGT
Found at i:25210039 original size:43 final size:42
Alignment explanation
Indices: 25209715--25210046 Score: 258
Period size: 43 Copynumber: 7.8 Consensus size: 42
25209705 TTTTTGGTCA
* *
25209715 AAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAAA
1 AAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTGT-GAAG
* ** * *
25209758 AAGCGCCACTAAAGATCATAGTCTTTAGTGGCGTTTGTGGTCA-
1 AAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTGT-G-AAG
* * **
25209801 AAGCGCCGCTATAGATCAGGGTCTATT-GCGGCGTTTGAGGGG
1 AAGCGCCGCTAAAGATCAGGGTCT-TTAGCGGCGTTTGTGAAG
* ** * * * *
25209843 TAAGCGCCGCTAAAGACCCTGATCTTTAGTGGCGTTTTTAGGAG
1 -AAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTGT-GAAG
* * *
25209887 AAGCGCCGCTAAAGATAAGGGTCTTTAACGGCGTTTGAGAGAG
1 AAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTGTGA-AG
* * * **
25209930 AAGCGCCACTAAAGATCAGGGTCTTTAGCGGTGCTT-CCACTA-
1 AAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTGTGA--AG
* *** *
25209972 AAGCGCCGCTAAAGGTCTTAGTCTTCAGCGGCGTTTGTGCAAG
1 AAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTGTG-AAG
*
25210015 ATGCGCCGCTAAAGATCAGGGTCTTTAGCGGC
1 AAGCGCCGCTAAAGATCAGGGTCTTTAGCGGC
25210047 ATTTTTTCTA
Statistics
Matches: 221, Mismatches: 57, Indels: 22
0.74 0.19 0.07
Matches are distributed among these distances:
42 34 0.15
43 180 0.81
44 7 0.03
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.25
Consensus pattern (42 bp):
AAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTGTGAAG
Found at i:25210058 original size:85 final size:85
Alignment explanation
Indices: 25209915--25210070 Score: 206
Period size: 85 Copynumber: 1.8 Consensus size: 85
25209905 GGGTCTTTAA
** *
25209915 CGGCGTTTGAGAGAGAAGCGCCACTAAAGATCAGGGTCTTTAGCGGTGCTTCCACTAAAGCGCCG
1 CGGCGTTTGAGAGAGAAGCGCCACTAAAGATCAGGGTCTTTAGCGGCACTTCCACTAAAACGCCG
25209980 CTAAAGGTCTTAGTCTTCAG
66 CTAAAGGTCTTAGTCTTCAG
* * * * ***
25210000 CGGCGTTTGTGCA-AGATGCGCCGCTAAAGATCAGGGTCTTTAGCGGCATTTTTTCTAAAACGCC
1 CGGCGTTTGAG-AGAGAAGCGCCACTAAAGATCAGGGTCTTTAGCGGCACTTCCACTAAAACGCC
25210064 GCTAAAG
65 GCTAAAG
25210071 TTAGCGGCGC
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
85 59 0.98
86 1 0.02
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (85 bp):
CGGCGTTTGAGAGAGAAGCGCCACTAAAGATCAGGGTCTTTAGCGGCACTTCCACTAAAACGCCG
CTAAAGGTCTTAGTCTTCAG
Found at i:25211821 original size:22 final size:21
Alignment explanation
Indices: 25211796--25211839 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
25211786 AAAATGTTAC
*
25211796 AACATGATAATGTAAATACTAA
1 AACATAATAATGTAAATA-TAA
* *
25211818 AACATAATATTTTAAATATAA
1 AACATAATAATGTAAATATAA
25211839 A
1 A
25211840 TAACTAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.32
Consensus pattern (21 bp):
AACATAATAATGTAAATATAA
Found at i:25212492 original size:12 final size:12
Alignment explanation
Indices: 25212477--25212501 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25212467 TAAATTCAAT
25212477 ATTTAATTTTTA
1 ATTTAATTTTTA
25212489 ATTTAATTTTTA
1 ATTTAATTTTTA
25212501 A
1 A
25212502 CATAATTTGG
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTTAATTTTTA
Found at i:25212704 original size:16 final size:17
Alignment explanation
Indices: 25212669--25212706 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
25212659 TTATCTCTAT
*
25212669 ATTTAATTTTTGACATA
1 ATTTAATATTTGACATA
*
25212686 ATTTAATATTT-ATATA
1 ATTTAATATTTGACATA
25212702 ATTTA
1 ATTTA
25212707 CATAATAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (17 bp):
ATTTAATATTTGACATA
Found at i:25214239 original size:13 final size:13
Alignment explanation
Indices: 25214223--25214248 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25214213 AACAATTAAA
25214223 ATAAATTTTATTT
1 ATAAATTTTATTT
25214236 ATAAATTTTATTT
1 ATAAATTTTATTT
25214249 TGAATATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATAAATTTTATTT
Found at i:25215754 original size:33 final size:35
Alignment explanation
Indices: 25215669--25215764 Score: 83
Period size: 35 Copynumber: 2.8 Consensus size: 35
25215659 TTTGTCACTT
* *
25215669 AAATAATTAATTAA-TATTATGATATTTTAGTAAGA
1 AAATAAAT-ATTAATTATTATAATATTTTAGTAAGA
* * *
25215704 ATATAAA-AATAATTTATTATAATATTTT-TTAA-A
1 AAATAAATATTAA-TTATTATAATATTTTAGTAAGA
*
25215737 AAATAAATATTAATTATTTATAAAATTT
1 AAATAAATATTAATTA-TTATAATATTT
25215765 AATTTAAATA
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
33 14 0.29
34 17 0.35
35 18 0.37
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (35 bp):
AAATAAATATTAATTATTATAATATTTTAGTAAGA
Found at i:25215758 original size:34 final size:37
Alignment explanation
Indices: 25215668--25215764 Score: 96
Period size: 34 Copynumber: 2.7 Consensus size: 37
25215658 ATTTGTCACT
* *
25215668 TAAATAATTAATTAATATTATGATATTTTAGTAAGAATA
1 TAAAT-ATTAATT-ATATTATAATATTTTAGTAAGAAAA
* *
25215707 TAAA-AATAATT-TATTATAATATTTT-TTAA-AAAA
1 TAAATATTAATTATATTATAATATTTTAGTAAGAAAA
*
25215740 TAAATATTAATTAT-TTATAAAATTT
1 TAAATATTAATTATATTATAATATTT
25215765 AATTTAAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
33 7 0.14
34 19 0.38
35 14 0.28
37 6 0.12
39 4 0.08
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (37 bp):
TAAATATTAATTATATTATAATATTTTAGTAAGAAAA
Found at i:25215780 original size:20 final size:21
Alignment explanation
Indices: 25215755--25215801 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
25215745 ATTAATTATT
*
25215755 TATAAAATTTAA-TTTAAATA
1 TATAAAATTAAATTTTAAATA
*
25215775 TAT-AAACTAAATTTTAAATA
1 TATAAAATTAAATTTTAAATA
25215795 TA-AAAAT
1 TATAAAAT
25215802 ATAACCAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
TATAAAATTAAATTTTAAATA
Found at i:25216535 original size:25 final size:24
Alignment explanation
Indices: 25216507--25216553 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
25216497 CGGTATTACG
*
25216507 ATTTTTTTAATAAATTTTATTTTTT
1 ATTTTTTTAA-AAATATTATTTTTT
25216532 ATTTTTTTAAAAATATTATTTT
1 ATTTTTTTAAAAATATTATTTT
25216554 ATTAGTGGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (24 bp):
ATTTTTTTAAAAATATTATTTTTT
Found at i:25217908 original size:14 final size:15
Alignment explanation
Indices: 25217891--25217922 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
25217881 ATACTGTTTT
25217891 TTTTTTCATATA-TA
1 TTTTTTCATATATTA
25217905 TTTTTTCATATATTA
1 TTTTTTCATATATTA
25217920 TTT
1 TTT
25217923 AGTTTAAGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTTTCATATATTA
Found at i:25218033 original size:20 final size:21
Alignment explanation
Indices: 25218008--25218048 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
25217998 TGTATATATA
25218008 TGTATA-TATAATGTTAAATT
1 TGTATATTATAATGTTAAATT
* *
25218028 TGTATATTATTATTTTAAATT
1 TGTATATTATAATGTTAAATT
25218049 GCTTCATAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (21 bp):
TGTATATTATAATGTTAAATT
Found at i:25218068 original size:25 final size:25
Alignment explanation
Indices: 25218033--25218097 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 25
25218023 AAATTTGTAT
*
25218033 ATTATTATTTTAAATTGCTTCATAG
1 ATTATTATTTTAAATTACTTCATAG
* * * *
25218058 ATTATTGTTTTAAGTTACTTTATAT
1 ATTATTATTTTAAATTACTTCATAG
25218083 ATTATTTTATTTTAA
1 ATTA--TTATTTTAA
25218098 GTTATTTTAC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
25 24 0.75
27 8 0.25
ACGTcount: A:0.31, C:0.05, G:0.06, T:0.58
Consensus pattern (25 bp):
ATTATTATTTTAAATTACTTCATAG
Found at i:25218121 original size:27 final size:27
Alignment explanation
Indices: 25218065--25218121 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
25218055 TAGATTATTG
* * *
25218065 TTTTAAGTTACTTTATATATTATTTTA
1 TTTTAAGTTACTTTACATATTACTTAA
* *
25218092 TTTTAAGTTATTTTACATATTGCTTAA
1 TTTTAAGTTACTTTACATATTACTTAA
25218119 TTT
1 TTT
25218122 AAAATTAACC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.61
Consensus pattern (27 bp):
TTTTAAGTTACTTTACATATTACTTAA
Found at i:25219658 original size:18 final size:17
Alignment explanation
Indices: 25219628--25219680 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 17
25219618 TAAATAGCAG
*
25219628 AAGG-GAAGGAAGAAGA
1 AAGGAGAAGAAAGAAGA
*
25219644 CAGGGAGAAGAAAGAAAGA
1 -AAGGAGAAGAAAG-AAGA
*
25219663 AAGGAGAAGAAAAAAGA
1 AAGGAGAAGAAAGAAGA
25219680 A
1 A
25219681 GGATAATGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 8 0.27
18 18 0.60
19 4 0.13
ACGTcount: A:0.62, C:0.02, G:0.36, T:0.00
Consensus pattern (17 bp):
AAGGAGAAGAAAGAAGA
Found at i:25223877 original size:29 final size:29
Alignment explanation
Indices: 25223835--25223907 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
25223825 AAAAAATAAA
25223835 ATTAATAACTGAAATGGCATGCCCACAAG
1 ATTAATAACTGAAATGGCATGCCCACAAG
**
25223864 ATTAATAACTGAAATGGCATGCCCATTAG
1 ATTAATAACTGAAATGGCATGCCCACAAG
25223893 ATTAATAACTGAAAT
1 ATTAATAACTGAAAT
25223908 TTTCCATTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.26
Consensus pattern (29 bp):
ATTAATAACTGAAATGGCATGCCCACAAG
Found at i:25223979 original size:32 final size:32
Alignment explanation
Indices: 25223933--25223995 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
25223923 TAAACAAACC
* *
25223933 TTAAATGTGGCTAATTGCTTTATAAGCCCTCT
1 TTAAATGTGACTAATTGCCTTATAAGCCCTCT
*
25223965 TTAAATGTGACTAATTGCCTTGTAAGCCCTC
1 TTAAATGTGACTAATTGCCTTATAAGCCCTC
25223996 CTTATTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (32 bp):
TTAAATGTGACTAATTGCCTTATAAGCCCTCT
Found at i:25226342 original size:11 final size:12
Alignment explanation
Indices: 25226315--25226344 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
25226305 CGTGAGTAAC
*
25226315 AAAAAACACAGT
1 AAAAAACACAAT
25226327 AAAAAACACAAT
1 AAAAAACACAAT
25226339 AAAAAA
1 AAAAAA
25226345 ATCTCATAAT
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:0.77, C:0.13, G:0.03, T:0.07
Consensus pattern (12 bp):
AAAAAACACAAT
Found at i:25227137 original size:106 final size:108
Alignment explanation
Indices: 25226758--25227242 Score: 591
Period size: 108 Copynumber: 4.4 Consensus size: 108
25226748 AAAATAATTA
*
25226758 AAAAAATTTACATTCATAACAAATCACAATAAACACTAAACTAAACACAAACAATTTATAACCTA
1 AAAAAATTTACATTCATAAAAAATCAC-A-AAACACTAAACTAAACACAAACAATTTATAACCTA
* * * *
25226823 ATCATAAATTACTAACAAAATAAACTTTCAAACAATTAAAAAAAAAC
64 ATCATAAATTAATAACAAAATTAACTTTAAAATAATT--AAAAAAAC
*
25226870 AAAAAATTTTACATTCATAAAAAATCACAGTAAACATTAAACTAAACACACACAAACAATTTATA
1 AAAAAA-TTTACATTCATAAAAAATCACA--AAACACTAAACT--A-A-ACACAAACAATTTATA
* *
25226935 ACCTAACCATAAATTAATAGCAAAA-TAACTTTAAAATAATTTAAAAAATAC
59 ACCTAATCATAAATTAATAACAAAATTAACTTTAAAATAA-TTAAAAAA-AC
* * * *
25226986 AAAAAAATTACATTCATAAGAAATCACAAAACACTAAACTAAACACAAATAATTTATAACATAAT
1 AAAAAATTTACATTCATAAAAAATCACAAAACACTAAACTAAACACAAACAATTTATAACCTAAT
* *
25227051 CA-AAATTAATAACAAAATTAA-TATAAAATAATTAAGAAAAC
66 CATAAATTAATAACAAAATTAACTTTAAAATAATTAAAAAAAC
* * * * *
25227092 AAAAAATGTAAATTAATAAAAAATCACAAAACACTAAATTCAACACAAACAATTTATAACCTAAT
1 AAAAAATTTACATTCATAAAAAATCACAAAACACTAAACTAAACACAAACAATTTATAACCTAAT
* * * *
25227157 AAAAAATTACTAACAAAAATAACTTTAAAATAATTAAAAAATA-
66 CATAAATTAATAACAAAATTAACTTTAAAATAATTAAAAAA-AC
* *
25227200 AAAAAATTTACTTTCATAACAAATCACAAAACACTAAACTAAA
1 AAAAAATTTACATTCATAAAAAATCACAAAACACTAAACTAAA
25227243 TAAAAAAACT
Statistics
Matches: 323, Mismatches: 38, Indels: 28
0.83 0.10 0.07
Matches are distributed among these distances:
106 59 0.18
107 24 0.07
108 75 0.23
109 26 0.08
110 1 0.00
111 1 0.00
112 7 0.02
113 43 0.13
115 27 0.08
116 20 0.06
117 40 0.12
ACGTcount: A:0.60, C:0.15, G:0.01, T:0.24
Consensus pattern (108 bp):
AAAAAATTTACATTCATAAAAAATCACAAAACACTAAACTAAACACAAACAATTTATAACCTAAT
CATAAATTAATAACAAAATTAACTTTAAAATAATTAAAAAAAC
Found at i:25243698 original size:13 final size:13
Alignment explanation
Indices: 25243682--25243745 Score: 74
Period size: 13 Copynumber: 4.9 Consensus size: 13
25243672 TTTAAACCAA
25243682 ACTTTTCAAAAGT
1 ACTTTTCAAAAGT
* *
25243695 ACTTCTCAAAAGC
1 ACTTTTCAAAAGT
* * **
25243708 ATTTTTCCACTGT
1 ACTTTTCAAAAGT
25243721 ACTTTTCAAAAGT
1 ACTTTTCAAAAGT
25243734 ACTTTTCAAAAG
1 ACTTTTCAAAAG
25243746 CAATGAAGAA
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
13 39 1.00
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.38
Consensus pattern (13 bp):
ACTTTTCAAAAGT
Found at i:25246514 original size:19 final size:19
Alignment explanation
Indices: 25246490--25246554 Score: 58
Period size: 19 Copynumber: 3.2 Consensus size: 19
25246480 ATTCCAAAAA
25246490 TAATATTATTTTAATAATT
1 TAATATTATTTTAATAATT
**
25246509 TAATATTAAATTAATACTTATCT
1 TAATATTATTTTAATA---AT-T
* *
25246532 TAATAATATTTTATTAATT
1 TAATATTATTTTAATAATT
25246551 TAAT
1 TAAT
25246555 GTTCACTTTG
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
19 19 0.53
20 2 0.06
22 2 0.06
23 13 0.36
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (19 bp):
TAATATTATTTTAATAATT
Found at i:25248118 original size:16 final size:18
Alignment explanation
Indices: 25248092--25248124 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
25248082 CTCAACCATA
25248092 ATCACTTTCAT-GATATT
1 ATCACTTTCATAGATATT
25248109 ATCA-TTTCATAGATAT
1 ATCACTTTCATAGATAT
25248125 ATACCTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.33, C:0.15, G:0.06, T:0.45
Consensus pattern (18 bp):
ATCACTTTCATAGATATT
Found at i:25249168 original size:28 final size:28
Alignment explanation
Indices: 25249126--25249190 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
25249116 CAGTGACAGT
*
25249126 ACAGTGTGGGCCTTAGCCCAATACAATA
1 ACAGTGTAGGCCTTAGCCCAATACAATA
* *
25249154 ATAGTGTAGGCCTTAGCCCAATACAGTA
1 ACAGTGTAGGCCTTAGCCCAATACAATA
25249182 ACAGTGTAG
1 ACAGTGTAG
25249191 TGCAATAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.23
Consensus pattern (28 bp):
ACAGTGTAGGCCTTAGCCCAATACAATA
Found at i:25249549 original size:27 final size:27
Alignment explanation
Indices: 25249517--25249572 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
25249507 ACATAAGGCC
* *
25249517 ATAATAGTCATTTTATCTCT-TAGGGGT
1 ATAATAGTAATTTTA-CCCTATAGGGGT
25249544 ATAATAGTAATTTTACCCTATAGGGGT
1 ATAATAGTAATTTTACCCTATAGGGGT
25249571 AT
1 AT
25249573 TTCTGTCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 3 0.12
27 23 0.88
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.41
Consensus pattern (27 bp):
ATAATAGTAATTTTACCCTATAGGGGT
Found at i:25249583 original size:27 final size:26
Alignment explanation
Indices: 25249553--25249638 Score: 127
Period size: 27 Copynumber: 3.2 Consensus size: 26
25249543 TATAATAGTA
25249553 ATTTTACCCTATAGGGGTATTTCTGTC
1 ATTTTACCCTAT-GGGGTATTTCTGTC
* *
25249580 ATTTTACCTTATGGGAGTATTTCGGTC
1 ATTTTACCCTATGGG-GTATTTCTGTC
25249607 ATTTTACCCTATGGGGGTATTTCTGTC
1 ATTTTACCCTAT-GGGGTATTTCTGTC
25249634 ATTTT
1 ATTTT
25249639 CATCTATTAG
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
26 3 0.06
27 47 0.89
28 3 0.06
ACGTcount: A:0.17, C:0.16, G:0.20, T:0.47
Consensus pattern (26 bp):
ATTTTACCCTATGGGGTATTTCTGTC
Found at i:25253495 original size:24 final size:25
Alignment explanation
Indices: 25253468--25253515 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
25253458 GTTAGTGCTA
* *
25253468 AATATGATTTATG-TACGTATGATT
1 AATATGATATATGCTAAGTATGATT
*
25253492 AATATGCTATATGCTAAGTATGAT
1 AATATGATATATGCTAAGTATGAT
25253516 CTGTATTATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (25 bp):
AATATGATATATGCTAAGTATGATT
Found at i:25253560 original size:21 final size:21
Alignment explanation
Indices: 25253501--25253560 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
25253491 TAATATGCTA
*
25253501 TATGCTAAGTATGATCTGTAT
1 TATGCTAAGTATGATTTGTAT
* *
25253522 TATGTTAAGTATGCTTTGTTAT
1 TATGCTAAGTATGATTTG-TAT
*
25253544 T-TGCTAAGCATGATTTG
1 TATGCTAAGTATGATTTG
25253561 AATTCTGCAG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
21 28 0.88
22 4 0.12
ACGTcount: A:0.25, C:0.08, G:0.20, T:0.47
Consensus pattern (21 bp):
TATGCTAAGTATGATTTGTAT
Found at i:25256814 original size:125 final size:124
Alignment explanation
Indices: 25256575--25257071 Score: 667
Period size: 125 Copynumber: 4.0 Consensus size: 124
25256565 GGATTTTTCG
* * *
25256575 GGTCCTGAA-AAATTATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACACTTAAAGCAG
1 GGTCCTGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTAT-AAAAACGCTTCAAGCAG
* * * * *
25256639 AATGCTATT-TGAGAAGAATTTCTGAAATTGCACCCTCGTGGACGCACTTTTGCTATAGTT
65 GATGCT-TTATGAGAAGAATTTCTGAAATTGCGCCCACGTGGACGCGCTTTTGCTACAGTT
* * * *
25256699 GGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATATTATAAAATCGCTTCTACCAG
1 GGTCCT-GAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCAG
* * * *
25256764 GATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACTCGCTTTTGCTACAGTA
65 GATGCTTTATGAGAAGAATTTCTGAAATTGCGCCCACGTGGACGCGCTTTTGCTACAGTT
* * *
25256824 GGTCCTGAAAAAATTATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCAGG
1 GGTCCTGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCAGG
** * * *
25256889 ATGCGATCTGAGAAGAATTTCTGAAATTGCGCCCTCGTGGACGCTCTTTTGCTACAGTT
66 ATGCTTTATGAGAAGAATTTCTGAAATTGCGCCCACGTGGACGCGCTTTTGCTACAGTT
* *
25256948 GGTCCTGAAAGAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAA-CA
1 GGTCCTG-AAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAACGCTTC-AAGCA
* * *
25257012 GGATGCTTTATGAGAAGAATTTGTGAAATTGAGCCCACGTAGACGCGCTTTTGCTACAGT
64 GGATGCTTTATGAGAAGAATTTCTGAAATTGCGCCCACGTGGACGCGCTTTTGCTACAGT
25257072 AGCATGTTTG
Statistics
Matches: 325, Mismatches: 43, Indels: 9
0.86 0.11 0.02
Matches are distributed among these distances:
124 117 0.36
125 171 0.53
126 37 0.11
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Consensus pattern (124 bp):
GGTCCTGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCAGG
ATGCTTTATGAGAAGAATTTCTGAAATTGCGCCCACGTGGACGCGCTTTTGCTACAGTT
Found at i:25257016 original size:249 final size:249
Alignment explanation
Indices: 25256575--25257073 Score: 829
Period size: 249 Copynumber: 2.0 Consensus size: 249
25256565 GGATTTTTCG
25256575 GGTCCTGAAAAATTATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACACTTAAAGCAGA
1 GGTCCTGAAAAATTATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACACTTAAAGCAGA
* * *
25256640 ATGCTATTTGAGAAGAATTTCTGAAATTGCACCCTCGTGGACGCACTTTTGCTATAGTTGGTCCT
66 ATGCGATCTGAGAAGAATTTCTGAAATTGCACCCTCGTGGACGCACTTTTGCTACAGTTGGTCCT
* * *
25256705 GGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATATTATAAAATCGCTTCTACCAGGATGCT
131 GAAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAACAGGATGCT
* * *
25256770 TTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACTCGCTTTTGCTACAGTA
196 TTATGAGAAGAATTTGTGAAATCGAGCCCACGTAGACGCGCTTTTGCTACAGTA
* * *
25256824 GGTCCTGAAAAAATTATTTTGAGTTGACGTTTCTGAGCAAATAGTAT-AAAAACGCTTCAAGCAG
1 GGTCCTG-AAAAATTATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACACTTAAAGCAG
* * *
25256888 GATGCGATCTGAGAAGAATTTCTGAAATTGCGCCCTCGTGGACGCTCTTTTGCTACAGTTGGTCC
65 AATGCGATCTGAGAAGAATTTCTGAAATTGCACCCTCGTGGACGCACTTTTGCTACAGTTGGTCC
*
25256953 TGAAAGAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAACAGGATGC
130 TGAAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAACAGGATGC
*
25257018 TTTATGAGAAGAATTTGTGAAATTGAGCCCACGTAGACGCGCTTTTGCTACAGTA
195 TTTATGAGAAGAATTTGTGAAATCGAGCCCACGTAGACGCGCTTTTGCTACAGTA
25257073 G
1 G
25257074 CATGTTTGGA
Statistics
Matches: 232, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
249 194 0.84
250 38 0.16
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Consensus pattern (249 bp):
GGTCCTGAAAAATTATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACACTTAAAGCAGA
ATGCGATCTGAGAAGAATTTCTGAAATTGCACCCTCGTGGACGCACTTTTGCTACAGTTGGTCCT
GAAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAACAGGATGCT
TTATGAGAAGAATTTGTGAAATCGAGCCCACGTAGACGCGCTTTTGCTACAGTA
Found at i:25260313 original size:22 final size:22
Alignment explanation
Indices: 25260279--25260600 Score: 368
Period size: 22 Copynumber: 14.9 Consensus size: 22
25260269 TTTATGTTAG
*
25260279 GGTTTTTAGGTTAAGGGTTTAT
1 GGTTTTTAAGTTAAGGGTTTAT
*** * *
25260301 GAAATTTAAGTTAAGAGTTTAG
1 GGTTTTTAAGTTAAGGGTTTAT
* *
25260323 GGTTTTTAAGTTGAGGG-TTAA
1 GGTTTTTAAGTTAAGGGTTTAT
* *
25260344 GGTTTTTAGGTTAAGGG-TTAG
1 GGTTTTTAAGTTAAGGGTTTAT
* * *
25260365 GGGTTTTATGTTAAGAGTTTA-
1 GGTTTTTAAGTTAAGGGTTTAT
*
25260386 GAGTTTTTAAGTTAAGGGTTTAG
1 G-GTTTTTAAGTTAAGGGTTTAT
*
25260409 GGTTTTTAGGTTAAGGGTTTAT
1 GGTTTTTAAGTTAAGGGTTTAT
* *
25260431 GGTTTTTAAGTTGAGGG-TTAG
1 GGTTTTTAAGTTAAGGGTTTAT
*
25260452 GGTTTTTAGGTTAAGGGTTTAT
1 GGTTTTTAAGTTAAGGGTTTAT
*
25260474 GGTTTTTAAGTTAAGGGTTTAG
1 GGTTTTTAAGTTAAGGGTTTAT
25260496 GGTTTTTAAGTTAAGGG-TTAT
1 GGTTTTTAAGTTAAGGGTTTAT
*
25260517 GGTTTTTAGGTTAAGGGTTTAT
1 GGTTTTTAAGTTAAGGGTTTAT
**
25260539 GGAATTTAAGTTAAGGGTTTAT
1 GGTTTTTAAGTTAAGGGTTTAT
* *
25260561 GGTTTTTAAGTTAATGG-TTAG
1 GGTTTTTAAGTTAAGGGTTTAT
*
25260582 GGTTTTTAGGTTAAGGGTT
1 GGTTTTTAAGTTAAGGGTT
25260601 AGGAATAGGG
Statistics
Matches: 252, Mismatches: 42, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
21 91 0.36
22 160 0.63
23 1 0.00
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (22 bp):
GGTTTTTAAGTTAAGGGTTTAT
Found at i:25260350 original size:65 final size:65
Alignment explanation
Indices: 25260275--25260600 Score: 413
Period size: 65 Copynumber: 5.0 Consensus size: 65
25260265 AGCCTTTATG
*** * * *
25260275 TTAGGGTTTTTAGGTTAAGGGTTTATGAAATTTAAGTTAAGAGTTTAGGGTTTTTAAGTTGAGGG
1 TTAGGGTTTTTAGGTTAAGGGTTTATGGTTTTTAAGTTAAG-GGTTAGGGTTTTTAGGTTAAGGG
25260340 -
65 T
* * * * * * *
25260340 TTAAGGTTTTTAGGTTAAGGG-TTAGGGGTTTTATGTTAAGAGTTTAGAGTTTTTAAGTTAAGGG
1 TTAGGGTTTTTAGGTTAAGGGTTTATGGTTTTTAAGTTAAG-GGTTAGGGTTTTTAGGTTAAGGG
25260404 T
65 T
*
25260405 TTAGGGTTTTTAGGTTAAGGGTTTATGGTTTTTAAGTTGAGGGTTAGGGTTTTTAGGTTAAGGGT
1 TTAGGGTTTTTAGGTTAAGGGTTTATGGTTTTTAAGTTAAGGGTTAGGGTTTTTAGGTTAAGGGT
* * * *
25260470 TTATGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTATGGTTTTTAGGTTAAGGGT
1 TTAGGGTTTTTAGGTTAAGGGTTTATGGTTTTTAAGTTAAGGGTTAGGGTTTTTAGGTTAAGGGT
* ** * *
25260535 TTATGGAATTTAAGTTAAGGGTTTATGGTTTTTAAGTTAATGGTTAGGGTTTTTAGGTTAAGGGT
1 TTAGGGTTTTTAGGTTAAGGGTTTATGGTTTTTAAGTTAAGGGTTAGGGTTTTTAGGTTAAGGGT
25260600 T
1 T
25260601 AGGAATAGGG
Statistics
Matches: 233, Mismatches: 26, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
64 36 0.15
65 182 0.78
66 15 0.06
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (65 bp):
TTAGGGTTTTTAGGTTAAGGGTTTATGGTTTTTAAGTTAAGGGTTAGGGTTTTTAGGTTAAGGGT
Found at i:25260371 original size:43 final size:42
Alignment explanation
Indices: 25260274--25260601 Score: 379
Period size: 43 Copynumber: 7.6 Consensus size: 42
25260264 AAGCCTTTAT
* ***
25260274 GTTAGGGTTTTTAGGTTAAGGGTTTATGAAATTTAAGTTAAGAG
1 GTTAGGGTTTTTAAGTTAAGGG-TTATGGTTTTTAAGTTAAG-G
* * * *
25260318 TTTAGGGTTTTTAAGTTGAGGGTTAAGGTTTTTAGGTTAAGG
1 GTTAGGGTTTTTAAGTTAAGGGTTATGGTTTTTAAGTTAAGG
* * *
25260360 GTTAGGGGTTTTATGTTAAGAGTT-TAGAGTTTTTAAGTTAAGG
1 GTTAGGGTTTTTAAGTTAAGGGTTAT-G-GTTTTTAAGTTAAGG
* *
25260403 GTTTAGGGTTTTTAGGTTAAGGGTTTATGGTTTTTAAGTTGAGG
1 G-TTAGGGTTTTTAAGTTAAGGG-TTATGGTTTTTAAGTTAAGG
*
25260447 GTTAGGGTTTTTAGGTTAAGGGTTTATGGTTTTTAAGTTAAGG
1 GTTAGGGTTTTTAAGTTAAGGG-TTATGGTTTTTAAGTTAAGG
*
25260490 GTTTAGGGTTTTTAAGTTAAGGGTTATGGTTTTTAGGTTAAGG
1 G-TTAGGGTTTTTAAGTTAAGGGTTATGGTTTTTAAGTTAAGG
* ** *
25260533 GTTTATGGAATTTAAGTTAAGGGTTTATGGTTTTTAAGTTAATG
1 G-TTAGGGTTTTTAAGTTAAGGG-TTATGGTTTTTAAGTTAAGG
*
25260577 GTTAGGGTTTTTAGGTTAAGGGTTA
1 GTTAGGGTTTTTAAGTTAAGGGTTA
25260602 GGAATAGGGT
Statistics
Matches: 246, Mismatches: 31, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
42 24 0.10
43 127 0.52
44 91 0.37
45 3 0.01
46 1 0.00
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.45
Consensus pattern (42 bp):
GTTAGGGTTTTTAAGTTAAGGGTTATGGTTTTTAAGTTAAGG
Found at i:25261207 original size:18 final size:18
Alignment explanation
Indices: 25261184--25261223 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
25261174 GACTCGGAAA
* *
25261184 AGGATACATATAAGGGTT
1 AGGATACATAAAAGGGCT
25261202 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
25261220 AGGA
1 AGGA
25261224 AACGCACCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.07, G:0.30, T:0.20
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:25263133 original size:51 final size:51
Alignment explanation
Indices: 25263071--25263168 Score: 135
Period size: 51 Copynumber: 1.9 Consensus size: 51
25263061 AAGAATAGGG
** *
25263071 ATTTAAGAGAAATTT-AAAAGGAAATTGAGAGCTAATTGAGATTAAATATGA
1 ATTTAAGAGAAATTTGAAAA-GAAATTGAGAGAAAATTGAGATAAAATATGA
* *
25263122 ATTTGAGAGAAATTTGGAAAGAAATTGAGAGAAAATTGAGATAAAAT
1 ATTTAAGAGAAATTTGAAAAGAAATTGAGAGAAAATTGAGATAAAAT
25263169 TTGAGAGAGG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
51 38 0.93
52 3 0.07
ACGTcount: A:0.50, C:0.01, G:0.21, T:0.28
Consensus pattern (51 bp):
ATTTAAGAGAAATTTGAAAAGAAATTGAGAGAAAATTGAGATAAAATATGA
Found at i:25263137 original size:11 final size:11
Alignment explanation
Indices: 25263121--25263176 Score: 60
Period size: 12 Copynumber: 5.0 Consensus size: 11
25263111 ATTAAATATG
25263121 AATTTGAGAGA
1 AATTTGAGAGA
*
25263132 AATTTGGAAAGA
1 AATTT-GAGAGA
25263144 AA-TTGAGAGA
1 AATTTGAGAGA
* *
25263154 AAATTGAGATAA
1 AATTTGAGA-GA
25263166 AATTTGAGAGA
1 AATTTGAGAGA
25263177 GGATTTGTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
10 7 0.19
11 14 0.38
12 16 0.43
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (11 bp):
AATTTGAGAGA
Found at i:25263168 original size:22 final size:23
Alignment explanation
Indices: 25263121--25263176 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
25263111 ATTAAATATG
*
25263121 AATTTGAGAGAAATTTGGAAAGA
1 AATTTGAGAGAAAATTGGAAAGA
*
25263144 AA-TTGAGAGAAAATTGAGATA-A
1 AATTTGAGAGAAAATTG-GAAAGA
25263166 AATTTGAGAGA
1 AATTTGAGAGA
25263177 GGATTTGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 16 0.55
23 13 0.45
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (23 bp):
AATTTGAGAGAAAATTGGAAAGA
Found at i:25266939 original size:17 final size:16
Alignment explanation
Indices: 25266908--25266942 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
25266898 TTCATTTTTC
*
25266908 TTGGGTTTTTTTTCTT
1 TTGGGTTTTTCTTCTT
25266924 TTGGGTTTTTGCTTCTT
1 TTGGGTTTTT-CTTCTT
25266941 TT
1 TT
25266943 CTTTGTCGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.00, C:0.09, G:0.20, T:0.71
Consensus pattern (16 bp):
TTGGGTTTTTCTTCTT
Found at i:25272979 original size:23 final size:24
Alignment explanation
Indices: 25272964--25273009 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
25272954 TGCACCGAAA
*
25272964 TGCCAGTGTCACTTGCAC-AAGAG
1 TGCCACTGTCACTTGCACGAAGAG
25272987 TGCCACTGTCACTTGCATCGAAG
1 TGCCACTGTCACTTGCA-CGAAG
25273010 TGTCATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 16 0.80
24 1 0.05
25 3 0.15
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (24 bp):
TGCCACTGTCACTTGCACGAAGAG
Found at i:25273011 original size:23 final size:22
Alignment explanation
Indices: 25272953--25273011 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 22
25272943 AATAAATAAT
* *
25272953 TTGCACCGAAATGCCAGTGTCAC
1 TTGCA-CGAAGTGCCACTGTCAC
*
25272976 TTGCACAAGAGTGCCACTGTCAC
1 TTGCACGA-AGTGCCACTGTCAC
25272999 TTGCATCGAAGTG
1 TTGCA-CGAAGTG
25273012 TCATTATTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
22 2 0.07
23 26 0.87
24 2 0.07
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (22 bp):
TTGCACGAAGTGCCACTGTCAC
Found at i:25274938 original size:25 final size:25
Alignment explanation
Indices: 25274904--25274967 Score: 110
Period size: 25 Copynumber: 2.6 Consensus size: 25
25274894 TAACCCATAA
25274904 CTTGTGTGAGCATTTATAGTCACAG
1 CTTGTGTGAGCATTTATAGTCACAG
* *
25274929 CTTGTGTGAGCATTTATCGTCATAG
1 CTTGTGTGAGCATTTATAGTCACAG
25274954 CTTGTGTGAGCATT
1 CTTGTGTGAGCATT
25274968 ATTCCCGTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.39
Consensus pattern (25 bp):
CTTGTGTGAGCATTTATAGTCACAG
Found at i:25275029 original size:13 final size:13
Alignment explanation
Indices: 25275011--25275082 Score: 74
Period size: 13 Copynumber: 5.5 Consensus size: 13
25275001 TCATTAGGTG
25275011 GAAATGGATATAT
1 GAAATGGATATAT
*
25275024 GAAATGGTTATAT
1 GAAATGGATATAT
*
25275037 GAAAATGGATATTT
1 G-AAATGGATATAT
*
25275051 GAAATGGAT-TCTT
1 GAAATGGATAT-AT
* *
25275064 GAAATGGAAATGT
1 GAAATGGATATAT
25275077 GAAATG
1 GAAATG
25275083 TTAAATGAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
12 1 0.02
13 38 0.75
14 12 0.24
ACGTcount: A:0.42, C:0.01, G:0.25, T:0.32
Consensus pattern (13 bp):
GAAATGGATATAT
Found at i:25275048 original size:27 final size:27
Alignment explanation
Indices: 25275012--25275091 Score: 85
Period size: 27 Copynumber: 3.0 Consensus size: 27
25275002 CATTAGGTGG
25275012 AAATGGATATATGAAATGGTTATATGA
1 AAATGGATATATGAAATGGTTATATGA
* *
25275039 AAATGGATATTTGAAATGGATTCT-TG-
1 AAATGGATATATGAAATGG-TTATATGA
* * *
25275065 AAATGGAAATGTGAAAT-GTTAAATGA
1 AAATGGATATATGAAATGGTTATATGA
25275091 A
1 A
25275092 TATGTGATGG
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
24 2 0.05
25 3 0.07
26 16 0.36
27 20 0.45
28 3 0.07
ACGTcount: A:0.44, C:0.01, G:0.23, T:0.33
Consensus pattern (27 bp):
AAATGGATATATGAAATGGTTATATGA
Found at i:25282113 original size:38 final size:37
Alignment explanation
Indices: 25282043--25282115 Score: 96
Period size: 37 Copynumber: 1.9 Consensus size: 37
25282033 CTTTCATAAT
*
25282043 TTCACTTTTTCACTTTCAATCATAATTCAATTCAAAA
1 TTCACTTTTCCACTTTCAATCATAATTCAATTCAAAA
25282080 TTCACTTTTCCA-TTTCTAAGTCGAT-ATTCAATTCAA
1 TTCACTTTTCCACTTTC-AA-TC-ATAATTCAATTCAA
25282116 TTCCACACCT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
36 4 0.12
37 13 0.41
38 13 0.41
39 2 0.06
ACGTcount: A:0.32, C:0.22, G:0.03, T:0.44
Consensus pattern (37 bp):
TTCACTTTTCCACTTTCAATCATAATTCAATTCAAAA
Found at i:25282146 original size:23 final size:22
Alignment explanation
Indices: 25282103--25282146 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
25282093 TTCTAAGTCG
25282103 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
25282126 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
25282147 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:25282260 original size:45 final size:45
Alignment explanation
Indices: 25282191--25282284 Score: 134
Period size: 45 Copynumber: 2.1 Consensus size: 45
25282181 AGCAAATACT
* * * *
25282191 CGGTGGATTCAGTACATAGTAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAATACATAGCAACCACCTTACTAATCAATGATGTC
* *
25282236 CGGTGGAATCAATACATAGCAACCACCTTACTAATTAATGATGTT
1 CGGTGGAATCAATACATAGCAACCACCTTACTAATCAATGATGTC
25282281 CGGT
1 CGGT
25282285 TCACATAGTA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (45 bp):
CGGTGGAATCAATACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:25287794 original size:67 final size:67
Alignment explanation
Indices: 25287686--25287816 Score: 244
Period size: 67 Copynumber: 2.0 Consensus size: 67
25287676 TTTCTAATTC
*
25287686 AGAGAGCACACTCCCGCGAACCTCATTTCTTATAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
1 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
25287751 CA
66 CA
*
25287753 AGAGAGCACACTCTCGCGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCT
1 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCT
25287817 ATAATATAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.27, C:0.33, G:0.19, T:0.21
Consensus pattern (67 bp):
AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
CA
Found at i:25303767 original size:28 final size:29
Alignment explanation
Indices: 25303651--25303767 Score: 179
Period size: 28 Copynumber: 4.2 Consensus size: 29
25303641 AGTGACAGTA
*
25303651 CAGTGTGGGCCTTAGCCCAATACAATAA-
1 CAGTGTGGGCCTTAGCCCAATACAGTAAT
*
25303679 CAATGTGGGCCTTAGCCCAATACAG-AAT
1 CAGTGTGGGCCTTAGCCCAATACAGTAAT
*
25303707 CAGTGTGGGCCTTAGCCCAATACA-AAAT
1 CAGTGTGGGCCTTAGCCCAATACAGTAAT
25303735 CAGTGTGGGCCTTAGCCCAATACAGTAAT
1 CAGTGTGGGCCTTAGCCCAATACAGTAAT
25303764 -AGTG
1 CAGTG
25303768 CAGTGCAATA
Statistics
Matches: 82, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
27 2 0.02
28 77 0.94
29 3 0.04
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.22
Consensus pattern (29 bp):
CAGTGTGGGCCTTAGCCCAATACAGTAAT
Found at i:25303898 original size:26 final size:27
Alignment explanation
Indices: 25303869--25303947 Score: 110
Period size: 26 Copynumber: 3.0 Consensus size: 27
25303859 TACACACCAA
*
25303869 TATCGCAGCAGAGCTTCCAGTAAT-AG
1 TATCGCAGCAGAGCTACCAGTAATCAG
25303895 TATCGCAGCAGAGCTACCAGT-ATCAG
1 TATCGCAGCAGAGCTACCAGTAATCAG
* *
25303921 TATCGCAGCAAAGCTGCCAGTAA-CAG
1 TATCGCAGCAGAGCTACCAGTAATCAG
25303947 T
1 T
25303948 GTATGTGGCA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
25 2 0.04
26 45 0.94
27 1 0.02
ACGTcount: A:0.32, C:0.25, G:0.23, T:0.20
Consensus pattern (27 bp):
TATCGCAGCAGAGCTACCAGTAATCAG
Found at i:25304159 original size:27 final size:27
Alignment explanation
Indices: 25304128--25304758 Score: 246
Period size: 27 Copynumber: 23.4 Consensus size: 27
25304118 TAGAGCAAAT
* * *
25304128 CAGTCATTTTATCTTCTAGGGGTATAA
1 CAGTCATTTTACCTTATAGGGGTATTA
* **
25304155 CAGTCATTTTATCTCCTAGGGGTA-TA
1 CAGTCATTTTACCTTATAGGGGTATTA
* *
25304181 CAGTCATTTTACCCTATAGGGGTATTT
1 CAGTCATTTTACCTTATAGGGGTATTA
** * * *
25304208 TGGTCATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCTTATAGGGGTATTA
*
25304235 CAGTCATTTTACCTTATAGGGGTATTT
1 CAGTCATTTTACCTTATAGGGGTATTA
**
25304262 TGGTCATTTTACCTTAT-GAGGGTATT-
1 CAGTCATTTTACCTTATAG-GGGTATTA
** * * *
25304288 TTGATCATTTTACCCTATGGGGGTATTT
1 CAG-TCATTTTACCTTATAGGGGTATTA
** * * * *
25304316 TGGTTATTTTACCCTATAAGGGTATTT
1 CAGTCATTTTACCTTATAGGGGTATTA
** * * * *
25304343 TGGTTATTTTACCCTAT-GAGAGTATTT
1 CAGTCATTTTACCTTATAG-GGGTATTA
** * * * *
25304370 TGGTTATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCTTATAGGGGTATTA
* **
25304397 CAGTCATTTT-CATCTATTAGGGGTAAAA
1 CAGTCATTTTACCT-TA-TAGGGGTATTA
* * *
25304425 TAGTCATTTTACCTT-TCAAGGGTATTT
1 CAGTCATTTTACCTTAT-AGGGGTATTA
* * *
25304452 TAGTCATTTTACCCTAT-GGGGTATTT
1 CAGTCATTTTACCTTATAGGGGTATTA
* *
25304478 CAGTCATTTTACCCTATAGGGGTATTT
1 CAGTCATTTTACCTTATAGGGGTATTA
**
25304505 TGGTCATTTTACCTTAT-GAGGGTATT-
1 CAGTCATTTTACCTTATAG-GGGTATTA
** *
25304531 TTGATCATTTTACCCTAT-GAGGGTATT-
1 CAG-TCATTTTACCTTATAG-GGGTATTA
** * * *
25304558 TTGATCATTTTACCCTATGGGGGTATTT
1 CAG-TCATTTTACCTTATAGGGGTATTA
** * * * *
25304586 TGGTTATTTTACCCTATAAGGGTATTT
1 CAGTCATTTTACCTTATAGGGGTATTA
** * * *
25304613 TGGTCATTTTACCCTAT-GAGAGTATTT
1 CAGTCATTTTACCTTATAG-GGGTATTA
** * * * *
25304640 TGGTTATTTTACCATATGGGGGTATTT
1 CAGTCATTTTACCTTATAGGGGTATTA
* **
25304667 CAGTCATTTT-CATTTATTAGGGGTAAAA
1 CAGTCATTTTAC-CTTA-TAGGGGTATTA
* * *
25304695 TAGTCATTTTACCTT-TCAAGGGTATTT
1 CAGTCATTTTACCTTAT-AGGGGTATTA
* * * *
25304722 TAGTCATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCTTATAGGGGTATTA
*
25304749 CAGTTATTTT
1 CAGTCATTTT
25304759 TATCTATTAG
Statistics
Matches: 502, Mismatches: 78, Indels: 48
0.80 0.12 0.08
Matches are distributed among these distances:
26 55 0.11
27 399 0.79
28 45 0.09
29 3 0.01
ACGTcount: A:0.22, C:0.14, G:0.20, T:0.45
Consensus pattern (27 bp):
CAGTCATTTTACCTTATAGGGGTATTA
Found at i:25304258 original size:54 final size:54
Alignment explanation
Indices: 25304181--25304748 Score: 526
Period size: 54 Copynumber: 10.5 Consensus size: 54
25304171 TAGGGGTATA
**
25304181 CAGTCATTTTACCCTATAGGGGTATTTTGGTCATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTATAGGGGTATTTTGGTCATTTTACCCTATAAGGGTATTT
* * *
25304235 CAGTCATTTTACCTTATAGGGGTATTTTGGTCATTTTACCTTATGAGGGTATTT
1 CAGTCATTTTACCCTATAGGGGTATTTTGGTCATTTTACCCTATAAGGGTATTT
* * *
25304289 -TGATCATTTTACCCTATGGGGGTATTTTGGTTATTTTACCCTATAAGGGTATTT
1 CAG-TCATTTTACCCTATAGGGGTATTTTGGTCATTTTACCCTATAAGGGTATTT
** * * * **
25304343 TGGTTATTTTACCCTAT-GAGAGTATTTTGGTTATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTATAG-GGGTATTTTGGTCATTTTACCCTATAAGGGTATTT
* *** * *
25304397 CAGTCATTTT-CATCTATTAGGGGTAAAATAGTCATTTTA-CCTTTCAAGGGTATTT
1 CAGTCATTTTAC-CCTA-TAGGGGTATTTTGGTCATTTTACCCTAT-AAGGGTATTT
* ** *
25304452 TAGTCATTTTACCCTAT-GGGGTATTTCAGTCATTTTACCCTATAGGGGTATTT
1 CAGTCATTTTACCCTATAGGGGTATTTTGGTCATTTTACCCTATAAGGGTATTT
** * * *
25304505 TGGTCATTTTACCTTAT-GAGGGTATTTTGATCATTTTACCCTATGAGGGTATTT
1 CAGTCATTTTACCCTATAG-GGGTATTTTGGTCATTTTACCCTATAAGGGTATTT
* * *
25304559 -TGATCATTTTACCCTATGGGGGTATTTTGGTTATTTTACCCTATAAGGGTATTT
1 CAG-TCATTTTACCCTATAGGGGTATTTTGGTCATTTTACCCTATAAGGGTATTT
** * * * **
25304613 TGGTCATTTTACCCTAT-GAGAGTATTTTGGTTATTTTACCATATGGGGGTATTT
1 CAGTCATTTTACCCTATAG-GGGTATTTTGGTCATTTTACCCTATAAGGGTATTT
** *** * *
25304667 CAGTCATTTT-CATTTATTAGGGGTAAAATAGTCATTTTA-CCTTTCAAGGGTATTT
1 CAGTCATTTTAC-CCTA-TAGGGGTATTTTGGTCATTTTACCCTAT-AAGGGTATTT
* *
25304722 TAGTCATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTATAGGGGTATTT
25304749 CAGTTATTTT
Statistics
Matches: 422, Mismatches: 73, Indels: 38
0.79 0.14 0.07
Matches are distributed among these distances:
53 47 0.11
54 301 0.71
55 70 0.17
56 4 0.01
ACGTcount: A:0.21, C:0.14, G:0.20, T:0.45
Consensus pattern (54 bp):
CAGTCATTTTACCCTATAGGGGTATTTTGGTCATTTTACCCTATAAGGGTATTT
Found at i:25304298 original size:81 final size:81
Alignment explanation
Indices: 25304183--25304676 Score: 586
Period size: 81 Copynumber: 6.1 Consensus size: 81
25304173 GGGGTATACA
*
25304183 GTCATTTTACCCTAT-AGGGGTATTTTGGTCATTTTACCCTATGGGGGTATTTCAGTCATTTTAC
1 GTCATTTTACCCTATGA-GGGTATTTTGATCATTTTACCCTATGGGGGTATTTCAGTCATTTTAC
*
25304247 CTTATAGGGGTATTTTG
65 CCTATAGGGGTATTTTG
* ** *
25304264 GTCATTTTACCTTATGAGGGTATTTTGATCATTTTACCCTATGGGGGTATTTTGGTTATTTTACC
1 GTCATTTTACCCTATGAGGGTATTTTGATCATTTTACCCTATGGGGGTATTTCAGTCATTTTACC
*
25304329 CTATAAGGGTATTTTG
66 CTATAGGGGTATTTTG
* * * *
25304345 GTTATTTTACCCTATGAGAGTATTTTGGTTATTTTACCCTATGGGGGTATTTCAGTCATTTT-CA
1 GTCATTTTACCCTATGAGGGTATTTTGATCATTTTACCCTATGGGGGTATTTCAGTCATTTTAC-
* *** *
25304409 TCTATTAGGGGTAAAATA
65 CCTA-TAGGGGTATTTTG
* *
25304427 GTCATTTTA-CCTTTCAAGGGTATTTT-AGTCATTTTACCCTAT-GGGGTATTTCAGTCATTTTA
1 GTCATTTTACCCTAT-GAGGGTATTTTGA-TCATTTTACCCTATGGGGGTATTTCAGTCATTTTA
25304489 CCCTATAGGGGTATTTTG
64 CCCTATAGGGGTATTTTG
* * *
25304507 GTCATTTTACCTTATGAGGGTATTTTGATCATTTTACCCTATGAGGGTATTT-TGATCATTTTAC
1 GTCATTTTACCCTATGAGGGTATTTTGATCATTTTACCCTATGGGGGTATTTCAG-TCATTTTAC
*
25304571 CCTATGGGGGTATTTTG
65 CCTATAGGGGTATTTTG
* * * * * ** *
25304588 GTTATTTTACCCTATAAGGGTATTTTGGTCATTTTACCCTATGAGAGTATTTTGGTTATTTTACC
1 GTCATTTTACCCTATGAGGGTATTTTGATCATTTTACCCTATGGGGGTATTTCAGTCATTTTACC
* * **
25304653 ATATGGGGGTATTTCA
66 CTATAGGGGTATTTTG
25304669 GTCATTTT
1 GTCATTTT
25304677 CATTTATTAG
Statistics
Matches: 353, Mismatches: 49, Indels: 22
0.83 0.12 0.05
Matches are distributed among these distances:
80 44 0.12
81 268 0.76
82 41 0.12
ACGTcount: A:0.21, C:0.14, G:0.20, T:0.46
Consensus pattern (81 bp):
GTCATTTTACCCTATGAGGGTATTTTGATCATTTTACCCTATGGGGGTATTTCAGTCATTTTACC
CTATAGGGGTATTTTG
Found at i:25304625 original size:270 final size:271
Alignment explanation
Indices: 25304127--25304758 Score: 1024
Period size: 270 Copynumber: 2.3 Consensus size: 271
25304117 ATAGAGCAAA
* * * * * **
25304127 TCAGTCATTTT-ATCT-TCTAGGGGTATAACAGTCATTTTATC-TCCTAGGGGTA-TACAGTCAT
1 TCAGTCATTTTCATCTAT-TAGGGGTAAAATAGTCATTTTACCTTTC-AAGGGTATTTTAGTCAT
** *
25304188 TTTACCCTATAGGGGTATTTTGGTCATTTTACCCTATGGGGGTATTTCAGTCATTTTACCTTATA
64 TTTACCCTATAGGGGTATTTCAGTCATTTTACCCTATAGGGGTATTTCAGTCATTTTACCTTATA
* *
25304253 GGGGTATTTTGGTCATTTTACCTTATGAGGGTATTTTGATCATTTTACCCTATGGGGGTATTTTG
129 GGGGTATTTTGATCATTTTACCCTATGAGGGTATTTTGATCATTTTACCCTATGGGGGTATTTTG
*
25304318 GTTATTTTACCCTATAAGGGTATTTTGGTTATTTTACCCTATGAGAGTATTTTGGTTATTTTACC
194 GTTATTTTACCCTATAAGGGTATTTTGGTCATTTTACCCTATGAGAGTATTTTGGTTATTTTACC
*
25304383 CTATGGGGGTATT
259 ATATGGGGGTATT
25304396 TCAGTCATTTTCATCTATTAGGGGTAAAATAGTCATTTTACCTTTCAAGGGTATTTTAGTCATTT
1 TCAGTCATTTTCATCTATTAGGGGTAAAATAGTCATTTTACCTTTCAAGGGTATTTTAGTCATTT
**
25304461 TACCCTAT-GGGGTATTTCAGTCATTTTACCCTATAGGGGTATTTTGGTCATTTTACCTTAT-GA
66 TACCCTATAGGGGTATTTCAGTCATTTTACCCTATAGGGGTATTTCAGTCATTTTACCTTATAG-
25304524 GGGTATTTTGATCATTTTACCCTATGAGGGTATTTTGATCATTTTACCCTATGGGGGTATTTTGG
130 GGGTATTTTGATCATTTTACCCTATGAGGGTATTTTGATCATTTTACCCTATGGGGGTATTTTGG
25304589 TTATTTTACCCTATAAGGGTATTTTGGTCATTTTACCCTATGAGAGTATTTTGGTTATTTTACCA
195 TTATTTTACCCTATAAGGGTATTTTGGTCATTTTACCCTATGAGAGTATTTTGGTTATTTTACCA
25304654 TATGGGGGTATT
260 TATGGGGGTATT
*
25304666 TCAGTCATTTTCATTTATTAGGGGTAAAATAGTCATTTTACCTTTCAAGGGTATTTTAGTCATTT
1 TCAGTCATTTTCATCTATTAGGGGTAAAATAGTCATTTTACCTTTCAAGGGTATTTTAGTCATTT
* *
25304731 TACCCTATGGGGGTATTTCAGTTATTTT
66 TACCCTATAGGGGTATTTCAGTCATTTT
25304759 TATCTATTAG
Statistics
Matches: 339, Mismatches: 18, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
269 12 0.04
270 289 0.85
271 38 0.11
ACGTcount: A:0.22, C:0.14, G:0.20, T:0.45
Consensus pattern (271 bp):
TCAGTCATTTTCATCTATTAGGGGTAAAATAGTCATTTTACCTTTCAAGGGTATTTTAGTCATTT
TACCCTATAGGGGTATTTCAGTCATTTTACCCTATAGGGGTATTTCAGTCATTTTACCTTATAGG
GGTATTTTGATCATTTTACCCTATGAGGGTATTTTGATCATTTTACCCTATGGGGGTATTTTGGT
TATTTTACCCTATAAGGGTATTTTGGTCATTTTACCCTATGAGAGTATTTTGGTTATTTTACCAT
ATGGGGGTATT
Found at i:25304731 original size:82 final size:81
Alignment explanation
Indices: 25304535--25304816 Score: 289
Period size: 82 Copynumber: 3.4 Consensus size: 81
25304525 GGTATTTTGA
* * * * * ** * *
25304535 TCATTTTACCCTATGAGGGTATTTTGATCATTTTACCCTATGGGGGTATTTTGGTTATTTT-ACC
1 TCATTTTA-CCTTTCAGGGTATTTTGGTTATTTTACCATATGGGGGTATTTCAGTCATTTTCA-T
* *** *
25304599 CTA-TAAGGGTATTTTGG
64 CTATTAGGGGTAAAATAG
* * * *
25304616 TCATTTTACCCTATGAGAGTATTTTGGTTATTTTACCATATGGGGGTATTTCAGTCATTTTCATT
1 TCATTTTA-CCTTTCAGGGTATTTTGGTTATTTTACCATATGGGGGTATTTCAGTCATTTTCATC
25304681 TATTAGGGGTAAAATAG
65 TATTAGGGGTAAAATAG
* * * * *
25304698 TCATTTTACCTTTCAAGGGTATTTTAGTCATTTTACCCTATGGGGGTATTTCAGTTATTTTTATC
1 TCATTTTACCTTTC-AGGGTATTTTGGTTATTTTACCATATGGGGGTATTTCAGTCATTTTCATC
25304763 TATTAGGGGTAAAATAG
65 TATTAGGGGTAAAATAG
*
25304780 TCATTTTATCTTTCAGGGTTATTTTGGTTATTTTACC
1 TCATTTTACCTTTCAGGG-TATTTTGGTTATTTTACC
25304817 TATTTTGGGG
Statistics
Matches: 171, Mismatches: 26, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
81 64 0.37
82 107 0.63
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.46
Consensus pattern (81 bp):
TCATTTTACCTTTCAGGGTATTTTGGTTATTTTACCATATGGGGGTATTTCAGTCATTTTCATCT
ATTAGGGGTAAAATAG
Found at i:25304786 original size:27 final size:27
Alignment explanation
Indices: 25304668--25304790 Score: 81
Period size: 27 Copynumber: 4.5 Consensus size: 27
25304658 GGGGTATTTC
*
25304668 AGTCATTTTCATTTATTAGGGGTAAAAT
1 AGTCATTTT-ATCTATTAGGGGTAAAAT
* * ***
25304696 AGTCATTTTACCT-TTCAAGGGTATTTT
1 AGTCATTTTATCTATT-AGGGGTAAAAT
* * **
25304723 AGTCATTTTACCCTA-TGGGGGT-ATTT
1 AGTCATTTTA-TCTATTAGGGGTAAAAT
*
25304749 CAGTTATTTTTATCTATTAGGGGTAAAAT
1 -AGTCA-TTTTATCTATTAGGGGTAAAAT
25304778 AGTCATTTTATCT
1 AGTCATTTTATCT
25304791 TTCAGGGTTA
Statistics
Matches: 73, Mismatches: 15, Indels: 15
0.71 0.15 0.15
Matches are distributed among these distances:
26 5 0.07
27 38 0.52
28 28 0.38
29 2 0.03
ACGTcount: A:0.26, C:0.11, G:0.17, T:0.46
Consensus pattern (27 bp):
AGTCATTTTATCTATTAGGGGTAAAAT
Found at i:25305067 original size:17 final size:18
Alignment explanation
Indices: 25305045--25305079 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
25305035 TATCCGTATA
25305045 GGGCCCACA-AGCCCATT
1 GGGCCCACACAGCCCATT
25305062 GGGCCCACACAGCCCATT
1 GGGCCCACACAGCCCATT
25305080 TCAGCCCAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.23, C:0.43, G:0.23, T:0.11
Consensus pattern (18 bp):
GGGCCCACACAGCCCATT
Found at i:25305086 original size:19 final size:19
Alignment explanation
Indices: 25305047--25305105 Score: 52
Period size: 20 Copynumber: 3.2 Consensus size: 19
25305037 TCCGTATAGG
**
25305047 GCCCACA-AGCCCA-TTGG
1 GCCCACACAGCCCATTTCA
25305064 GCCCACACAGCCCATTTCA
1 GCCCACACAGCCCATTTCA
*
25305083 GCCCA-ACGTGGCCCATTTCA
1 GCCCACAC--AGCCCATTTCA
25305103 GCC
1 GCC
25305106 TAAGCCCATG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
17 7 0.20
18 8 0.23
19 7 0.20
20 13 0.37
ACGTcount: A:0.22, C:0.44, G:0.19, T:0.15
Consensus pattern (19 bp):
GCCCACACAGCCCATTTCA
Found at i:25308552 original size:26 final size:26
Alignment explanation
Indices: 25308490--25308553 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 26
25308480 TTTACCCCAA
*
25308490 TAAAATTTTGATGATTTTACCCTCGG
1 TAAAATTTTGATGAATTTACCCTCGG
*
25308516 TAAAGTTTTTGATGAATTTA-CCTCTGG
1 TAAA-ATTTTGATGAATTTACCCTC-GG
25308543 TAAAATTTTGA
1 TAAAATTTTGA
25308554 AAAAATATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 14 0.42
27 19 0.58
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.44
Consensus pattern (26 bp):
TAAAATTTTGATGAATTTACCCTCGG
Found at i:25311187 original size:18 final size:18
Alignment explanation
Indices: 25311149--25311187 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
25311139 AGCGTGTAGG
*
25311149 CCACACGGGCATGTGGAC
1 CCACACGGGCATATGGAC
*
25311167 CCACACGGGCATATGGCC
1 CCACACGGGCATATGGAC
25311185 CCA
1 CCA
25311188 AAATTTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.23, C:0.38, G:0.28, T:0.10
Consensus pattern (18 bp):
CCACACGGGCATATGGAC
Found at i:25318018 original size:23 final size:23
Alignment explanation
Indices: 25317992--25318049 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
25317982 CCAAAGTGTA
*
25317992 AATAACAAAAGTAATGAAGTACT
1 AATAACAAAAGTAATGAACTACT
* * *
25318015 AATAACAGAAGTAATGTACTATT
1 AATAACAAAAGTAATGAACTACT
*
25318038 AGTAACAAAAGT
1 AATAACAAAAGT
25318050 CTGCTATTGG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.53, C:0.09, G:0.14, T:0.24
Consensus pattern (23 bp):
AATAACAAAAGTAATGAACTACT
Found at i:25321152 original size:22 final size:22
Alignment explanation
Indices: 25321096--25321154 Score: 91
Period size: 22 Copynumber: 2.7 Consensus size: 22
25321086 TATATTTCCA
**
25321096 TAAGCTCTCATGGCTAACGTAC
1 TAAGCTCTCATGTTTAACGTAC
*
25321118 TAAGCTCTCATGTTTCACGTAC
1 TAAGCTCTCATGTTTAACGTAC
25321140 TAAGCTCTCATGTTT
1 TAAGCTCTCATGTTT
25321155 GAACAATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.36
Consensus pattern (22 bp):
TAAGCTCTCATGTTTAACGTAC
Found at i:25323048 original size:22 final size:23
Alignment explanation
Indices: 25322998--25323060 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 23
25322988 TTCCTAATAT
25322998 GTTCCTTGATTCTCTCTCAGTGA
1 GTTCCTTGATTCTCTCTCAGTGA
*
25323021 TTTTCCTTGATTCTCTCT-AGCTG-
1 -GTTCCTTGATTCTCTCTCAG-TGA
* *
25323044 GTTCCTTCATTTTCTCT
1 GTTCCTTGATTCTCTCT
25323061 TCCTCCAAGC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
22 14 0.41
23 2 0.06
24 18 0.53
ACGTcount: A:0.10, C:0.27, G:0.13, T:0.51
Consensus pattern (23 bp):
GTTCCTTGATTCTCTCTCAGTGA
Found at i:25329701 original size:88 final size:87
Alignment explanation
Indices: 25329552--25329716 Score: 242
Period size: 88 Copynumber: 1.9 Consensus size: 87
25329542 CTATAACCTT
* * *
25329552 CCTTTTCTCTTCTCTTTGAGGACAATTAACCTTCCTGTTCACTCAGGGCCTCCATGAAACACATC
1 CCTTTTCTCTTCTCTTT-AGGACAAGTAACCTTCCTGTTCACTCAAGGCCTCCATGAAACACATA
25329617 CAAATATCACACTGGACAGTAAC
65 CAAATATCACACTGGACAGTAAC
* * *
25329640 CCTTTTCTCTTTTCTCTTT-GGACAAGTAACCTTCCTGTTCTCTCAATGCTTCCATGAAACACAT
1 CCTTTTCTC--TTCTCTTTAGGACAAGTAACCTTCCTGTTCACTCAAGGCCTCCATGAAACACAT
25329704 ACAAATATCACAC
64 ACAAATATCACAC
25329717 CAGACAGTGC
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
88 61 0.88
90 8 0.12
ACGTcount: A:0.27, C:0.30, G:0.10, T:0.33
Consensus pattern (87 bp):
CCTTTTCTCTTCTCTTTAGGACAAGTAACCTTCCTGTTCACTCAAGGCCTCCATGAAACACATAC
AAATATCACACTGGACAGTAAC
Found at i:25331371 original size:20 final size:20
Alignment explanation
Indices: 25331346--25331431 Score: 84
Period size: 20 Copynumber: 4.2 Consensus size: 20
25331336 TATTTTTAGG
25331346 GATTTACCAAAATTTATAAA
1 GATTTACCAAAATTTATAAA
* *
25331366 GCTTTACCAAAAAATTAT-AA
1 GATTTACC-AAAATTTATAAA
* * *
25331386 GAATTTACCAATACTTCTAAA
1 G-ATTTACCAAAATTTATAAA
* *
25331407 GATTTACCAATATTTTTAAA
1 GATTTACCAAAATTTATAAA
25331427 GATTT
1 GATTT
25331432 TCTTGGTGCC
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
20 38 0.69
21 17 0.31
ACGTcount: A:0.44, C:0.13, G:0.06, T:0.37
Consensus pattern (20 bp):
GATTTACCAAAATTTATAAA
Found at i:25331514 original size:20 final size:20
Alignment explanation
Indices: 25331470--25331515 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
25331460 ACATTTTGGC
25331470 ATACCAAAATTCCTAAAGATT
1 ATACCAAAATT-CTAAAGATT
*
25331491 -TACCAAAATT-TATAAGGTT
1 ATACCAAAATTCTA-AAGATT
25331510 ATACCA
1 ATACCA
25331516 GATAATACCT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 2 0.09
19 5 0.23
20 15 0.68
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.30
Consensus pattern (20 bp):
ATACCAAAATTCTAAAGATT
Found at i:25332316 original size:31 final size:31
Alignment explanation
Indices: 25332281--25332343 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
25332271 ATGATGCTGC
25332281 ATACTACATAAGTCGTATACCCAATGCACTA
1 ATACTACATAAGTCGTATACCCAATGCACTA
25332312 ATACTACATAAGTCGTATACCCAATGCACTA
1 ATACTACATAAGTCGTATACCCAATGCACTA
25332343 A
1 A
25332344 CTTTCGATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (31 bp):
ATACTACATAAGTCGTATACCCAATGCACTA
Found at i:25332368 original size:34 final size:34
Alignment explanation
Indices: 25332325--25332393 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
25332315 CTACATAAGT
25332325 CGTATACCCAATGCACTAACTTTCGATTCCTTAG
1 CGTATACCCAATGCACTAACTTTCGATTCCTTAG
25332359 CGTATACCCAATGCACTAACTTTCGATTCCTTAG
1 CGTATACCCAATGCACTAACTTTCGATTCCTTAG
25332393 C
1 C
25332394 TATTTGAACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.26, C:0.30, G:0.12, T:0.32
Consensus pattern (34 bp):
CGTATACCCAATGCACTAACTTTCGATTCCTTAG
Found at i:25335187 original size:26 final size:26
Alignment explanation
Indices: 25335144--25335219 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 26
25335134 TCTCATCCCT
* *
25335144 ATTTTACCCGTAGCAAAATTTTAAAG
1 ATTTTACCCCTAGTAAAATTTTAAAG
* **
25335170 ATTTTACCCCTAGTAAAATTTTGACT
1 ATTTTACCCCTAGTAAAATTTTAAAG
* **
25335196 ATTTTTCCTTTAGTAAAATTTTAA
1 ATTTTACCCCTAGTAAAATTTTAA
25335220 GAAAATATAT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.43
Consensus pattern (26 bp):
ATTTTACCCCTAGTAAAATTTTAAAG
Found at i:25340940 original size:24 final size:26
Alignment explanation
Indices: 25340916--25340965 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
25340906 ACAACTCATT
25340916 AATTAAAAATATT-TTTAAATAATTAA
1 AATTAAAAATATTATTTAAATAATT-A
*
25340942 AATTAAAAATATTATTTTAATAAT
1 AATTAAAAATATTATTTAAATAAT
25340966 ATTACATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
AATTAAAAATATTATTTAAATAATTA
Found at i:25341458 original size:24 final size:26
Alignment explanation
Indices: 25341434--25341483 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
25341424 ACAACTCATT
25341434 AATTAAAAATATT-TTTAAATAATTAA
1 AATTAAAAATATTATTTAAATAATT-A
*
25341460 AATTAAAAATATTATTTTAATAAT
1 AATTAAAAATATTATTTAAATAAT
25341484 ATTACATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
AATTAAAAATATTATTTAAATAATTA
Found at i:25341635 original size:64 final size:64
Alignment explanation
Indices: 25341551--25341671 Score: 215
Period size: 64 Copynumber: 1.9 Consensus size: 64
25341541 AAATAAAATA
*
25341551 AAAATTTGATAATTAGATATAATCAAGTAAACAACTTGATTAAAAAACAAATATTCAATATATT
1 AAAATTGGATAATTAGATATAATCAAGTAAACAACTTGATTAAAAAACAAATATTCAATATATT
* *
25341615 AAAATTGGATCATTAGATATAATCAAGTAAACAACTTGATTAAAACACAAATATTCA
1 AAAATTGGATAATTAGATATAATCAAGTAAACAACTTGATTAAAAAACAAATATTCA
25341672 TTGTTATTAT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 54 1.00
ACGTcount: A:0.52, C:0.10, G:0.07, T:0.31
Consensus pattern (64 bp):
AAAATTGGATAATTAGATATAATCAAGTAAACAACTTGATTAAAAAACAAATATTCAATATATT
Found at i:25344533 original size:91 final size:91
Alignment explanation
Indices: 25344401--25344698 Score: 508
Period size: 91 Copynumber: 3.3 Consensus size: 91
25344391 ATGATTTTAG
* *
25344401 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
*
25344466 ATTTAATATTAATTATTTTAAATTGTA
65 ATTTAATATTAATTATTTTAAATTATA
*
25344493 TAAATTCATATAAGAAAATTTATTATCAAGAAATTTATGAAATTATATATCATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
25344558 TTTAATATTAATTATTTTAAATTATA
66 TTTAATATTAATTATTTTAAATTATA
*
25344584 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
* *
25344649 -ATAATAATAATTATTTTAAATTATA
66 TTTAATATTAATTATTTTAAATTATA
*
25344674 CAAATTCATATAAGAAAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
25344699 GTTATAATTA
Statistics
Matches: 197, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
90 47 0.24
91 134 0.68
92 16 0.08
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TTTAATATTAATTATTTTAAATTATA
Found at i:25344842 original size:120 final size:120
Alignment explanation
Indices: 25344714--25345131 Score: 721
Period size: 120 Copynumber: 3.5 Consensus size: 120
25344704 AATTATTTTA
* *
25344714 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATATTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATATTT
*
25344778 TATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
* * *
25344834 AGTTTTATTAAATTATATAGTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
* *
25344899 ATAGTATCATATATTATGATTTGAGTAAATTCATATAATAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
*
25344954 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
25345019 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
*
25345074 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATG-TTAAAT
25345132 ATGATTAAAT
Statistics
Matches: 282, Mismatches: 14, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
120 274 0.97
121 8 0.03
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
Found at i:25344861 original size:18 final size:18
Alignment explanation
Indices: 25344834--25344869 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
25344824 GATTATTAAG
* *
25344834 AGTTTTATTAAATTATAT
1 AGTTTAATTAAAATATAT
25344852 AGTTTAATTAAAATATAT
1 AGTTTAATTAAAATATAT
25344870 TTAATAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (18 bp):
AGTTTAATTAAAATATAT
Found at i:25344989 original size:16 final size:16
Alignment explanation
Indices: 25344968--25345014 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
25344958 TTATTAAATT
25344968 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
25344984 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
25344999 AT-TATGTTAAATTATA
1 ATATAT-TTTAATTATA
25345015 TTTTATAGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 11 0.42
16 13 0.50
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:25345092 original size:61 final size:61
Alignment explanation
Indices: 25344907--25345094 Score: 192
Period size: 61 Copynumber: 3.1 Consensus size: 61
25344897 TTATAGTATC
*
25344907 ATATATTATGATTTGAGTAAATTCATATAATAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAATAATATTGATTATTAAGAATTTTATTAAATT
* * * * * * *
25344968 ATATATTTTAATTAT-AATATATTTA-ATAATAAT-TATG-TTAAATT-A-TATTTTA-TAGTAT
1 ATATATTATGATT-TGAGTAAATTCATATAATAATAT-TGATT--ATTAAGAATTTTATTA-AAT
*
25345026 C
61 T
*
25345027 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAATAATATTGATTATTAAGAATTTTATTAAATT
25345088 ATATATT
1 ATATATT
25345095 TTAATTATAA
Statistics
Matches: 97, Mismatches: 18, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
58 3 0.03
59 32 0.33
60 20 0.21
61 39 0.40
62 3 0.03
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (61 bp):
ATATATTATGATTTGAGTAAATTCATATAATAATATTGATTATTAAGAATTTTATTAAATT
Found at i:25345109 original size:16 final size:16
Alignment explanation
Indices: 25345088--25345129 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
25345078 TTATTAAATT
*
25345088 ATATATTTTAATTATA
1 ATATATTTTAATAATA
25345104 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
25345119 AT-TATGTTTAA
1 ATATAT-TTTAA
25345130 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:25345114 original size:15 final size:15
Alignment explanation
Indices: 25345079--25345120 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
25345069 TTAAGAATTT
*
25345079 TATTAAATTAT-ATA
1 TATTTAATTATAATA
25345093 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
25345107 TATTTAATAATAAT
1 TATTTAATTATAAT
25345121 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:25345597 original size:45 final size:45
Alignment explanation
Indices: 25345546--25345679 Score: 119
Period size: 50 Copynumber: 2.9 Consensus size: 45
25345536 TATTTTGTAC
*
25345546 TGGTATTAATTAGATTCTATTTTATAGTTGCTTGAACATATATTT
1 TGGTATTAATTTGATTCTATTTTATAGTTGCTTGAACATATATTT
* * * *
25345591 TGGTATTGGTTTGATTTGATTATATTTTATAGTT-ATTCGAATATATATTT
1 TGGTA-----TTAATTTGATTCTATTTTATAGTTGCTT-GAACATATATTT
* * *
25345641 TAGTATTAATTTGATTCTATTTAATA-TGTGCTCGAACAT
1 TGGTATTAATTTGATTCTATTTTATAGT-TGCTTGAACAT
25345680 GCATTTATAA
Statistics
Matches: 69, Mismatches: 12, Indels: 16
0.71 0.12 0.16
Matches are distributed among these distances:
44 1 0.01
45 29 0.42
46 1 0.01
49 2 0.03
50 36 0.52
ACGTcount: A:0.28, C:0.06, G:0.14, T:0.51
Consensus pattern (45 bp):
TGGTATTAATTTGATTCTATTTTATAGTTGCTTGAACATATATTT
Found at i:25345617 original size:50 final size:49
Alignment explanation
Indices: 25345536--25345656 Score: 127
Period size: 50 Copynumber: 2.4 Consensus size: 49
25345526 GTTATTAGTT
* * * *
25345536 TATTTTGTACTGGTATTAATTAGATTCTATTTTATAGTTGCTT-GAACATA
1 TATTTTGTATTGGT-TTGATTAGATTATATTTTATAGTT-ATTCGAACATA
* *
25345586 TATTTTGGTATTGGTTTGATTTGATTATATTTTATAGTTATTCGAATATA
1 TATTTT-GTATTGGTTTGATTAGATTATATTTTATAGTTATTCGAACATA
**
25345636 TATTTTAGTATTAATTTGATT
1 TATTTT-GTATTGGTTTGATT
25345657 CTATTTAATA
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
49 2 0.03
50 51 0.85
51 7 0.12
ACGTcount: A:0.27, C:0.04, G:0.14, T:0.55
Consensus pattern (49 bp):
TATTTTGTATTGGTTTGATTAGATTATATTTTATAGTTATTCGAACATA
Found at i:25356663 original size:23 final size:23
Alignment explanation
Indices: 25356633--25356679 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
25356623 TTCTTGCTTG
25356633 AGGCCAACTACATTTCCCATTAT
1 AGGCCAACTACATTTCCCATTAT
25356656 AGGCCAACTACATTTCCCATTAT
1 AGGCCAACTACATTTCCCATTAT
25356679 A
1 A
25356680 ATCTTTCCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.30, G:0.09, T:0.30
Consensus pattern (23 bp):
AGGCCAACTACATTTCCCATTAT
Found at i:25361178 original size:20 final size:20
Alignment explanation
Indices: 25361128--25361179 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
25361118 TTGGAACATG
* *
25361128 AATATCGATACCTTAGGAAA
1 AATATCGATACTTTAAGAAA
* * *
25361148 TATGTCAATACTTTAAGAAA
1 AATATCGATACTTTAAGAAA
25361168 AATATCGATACT
1 AATATCGATACT
25361180 GGATCGATAT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.31
Consensus pattern (20 bp):
AATATCGATACTTTAAGAAA
Found at i:25361505 original size:17 final size:17
Alignment explanation
Indices: 25361485--25361519 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
25361475 AATAACAGAG
* *
25361485 GTAATGTAATAGGTAAA
1 GTAATGCAATAGATAAA
25361502 GTAATGCAATAGATAAA
1 GTAATGCAATAGATAAA
25361519 G
1 G
25361520 AATTACCTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.49, C:0.03, G:0.23, T:0.26
Consensus pattern (17 bp):
GTAATGCAATAGATAAA
Found at i:25366273 original size:15 final size:15
Alignment explanation
Indices: 25366255--25366331 Score: 56
Period size: 15 Copynumber: 5.3 Consensus size: 15
25366245 AATTCATATT
25366255 TTAATAATTATTATA
1 TTAATAATTATTATA
*
25366270 TTAATAATGTTATTAAA
1 TTAATAA--TTATTATA
*
25366287 TT-ATATATTATTTTA
1 TTAATA-ATTATTATA
25366302 TT-A-AATTA-TAT-
1 TTAATAATTATTATA
* *
25366313 TTAATAATAATTATG
1 TTAATAATTATTATA
25366328 TTAA
1 TTAA
25366332 AAAATGATTA
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
11 2 0.04
12 3 0.06
13 8 0.16
14 4 0.08
15 20 0.40
16 3 0.06
17 10 0.20
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
TTAATAATTATTATA
Found at i:25366292 original size:61 final size:57
Alignment explanation
Indices: 25366225--25366362 Score: 145
Period size: 58 Copynumber: 2.3 Consensus size: 57
25366215 TTTTTATAAT
* * *
25366225 ATTATATATTATGATTTTTTAATTCATATTTTAATAATTATTATATT-AATAATGTTATTAA
1 ATTATATATTAT-ATTTTTAAATT-ATA-TTTAATAATAATTATATTAAAAAATG--ATTAA
*
25366286 ATTATATATTAT-TTTATTAAATTATATTTAATAATAATTATGTTAAAAAATGATTAA
1 ATTATATATTATATTT-TTAAATTATATTTAATAATAATTATATTAAAAAATGATTAA
* *
25366343 ATTATTTATTTTTATTTTTA
1 ATTATATA-TTATATTTTTA
25366363 TTAAAATATA
Statistics
Matches: 67, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
57 12 0.18
58 22 0.33
59 15 0.22
60 6 0.09
61 12 0.18
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.56
Consensus pattern (57 bp):
ATTATATATTATATTTTTAAATTATATTTAATAATAATTATATTAAAAAATGATTAA
Found at i:25371515 original size:21 final size:21
Alignment explanation
Indices: 25371470--25371515 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
25371460 TAGAAGTATA
* *
25371470 AAAATAATATATATATATTAT
1 AAAATAATATATATATATAAG
25371491 AAAATAATATA-AGTATATAAG
1 AAAATAATATATA-TATATAAG
25371512 AAAA
1 AAAA
25371516 CAAGTGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (21 bp):
AAAATAATATATATATATAAG
Found at i:25373008 original size:44 final size:44
Alignment explanation
Indices: 25372951--25373076 Score: 216
Period size: 44 Copynumber: 2.9 Consensus size: 44
25372941 TAAGATTCGT
* *
25372951 AATCTTCAACCTATTCCACTGCTAACCAGGGAGATAGGATTCAC
1 AATCTTCAGCCTATTCCACTGCTGACCAGGGAGATAGGATTCAC
25372995 AATCTTCAGCCTATTCCACTGCTGACCAGGGAGATAGGATTCAC
1 AATCTTCAGCCTATTCCACTGCTGACCAGGGAGATAGGATTCAC
* *
25373039 AATCTTCAGCCTATTCCACTACTGTCCAGGGAGATAGG
1 AATCTTCAGCCTATTCCACTGCTGACCAGGGAGATAGG
25373077 GTTGGGGTTA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 78 1.00
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (44 bp):
AATCTTCAGCCTATTCCACTGCTGACCAGGGAGATAGGATTCAC
Found at i:25373190 original size:43 final size:43
Alignment explanation
Indices: 25373137--25373278 Score: 133
Period size: 43 Copynumber: 3.3 Consensus size: 43
25373127 TATTTTTAAC
25373137 CTGCTTCGCTGCAACCCAAGGAGGCAAGGCTGGTGTCTTCAAT
1 CTGCTTCGCTGCAACCCAAGGAGGCAAGGCTGGTGTCTTCAAT
**** * * * * * *
25373180 CTGCTTCGCTGTCGGTGC-AGGAAGGCAAGATCTGCTATTTTTAAC
1 CTGCTTCGCTG-CAACCCAAGG-AGGCAAG-GCTGGTGTCTTCAAT
* * *
25373225 CTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGAT
1 CTGCTTCGCTGCAACCCAAGGAGGCAAGGCTGGTGTCTTCAAT
25373268 CTGCTTCGCTG
1 CTGCTTCGCTG
25373279 TTGGTGCAGG
Statistics
Matches: 71, Mismatches: 24, Indels: 8
0.69 0.23 0.08
Matches are distributed among these distances:
43 32 0.45
44 18 0.25
45 21 0.30
ACGTcount: A:0.18, C:0.27, G:0.29, T:0.26
Consensus pattern (43 bp):
CTGCTTCGCTGCAACCCAAGGAGGCAAGGCTGGTGTCTTCAAT
Found at i:25373235 original size:45 final size:45
Alignment explanation
Indices: 25373092--25373323 Score: 186
Period size: 45 Copynumber: 5.2 Consensus size: 45
25373082 GGTTATCGAT
*
25373092 CTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTACTATTTTTAAC
1 CTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAAC
**** * * * * * *
25373137 CTGCTTCGCTG-CAACCCAAGG-AGGCAAG-GCTGGTGTCTTCAAT
1 CTGCTTCGCTGTCGGTGC-AGGAAGGCAAGATCTGCTATTTTTAAC
25373180 CTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAAC
1 CTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAAC
* **** * * * * * ** *
25373225 CTGCTCCGCTG-CAACCCAGGGAGGCAAG-GCTGGTGTCTTCGAT
1 CTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAAC
*
25373268 CTGCTTCGCTGTTGGTGCAGGAAGGCAAGATCTGCTATTTTTAAC
1 CTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAAC
*
25373313 CTGCTCCGCTG
1 CTGCTTCGCTG
25373324 CAACCCAGGG
Statistics
Matches: 132, Mismatches: 49, Indels: 12
0.68 0.25 0.06
Matches are distributed among these distances:
43 40 0.30
44 41 0.31
45 51 0.39
ACGTcount: A:0.19, C:0.25, G:0.28, T:0.28
Consensus pattern (45 bp):
CTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAAC
Found at i:25373239 original size:88 final size:88
Alignment explanation
Indices: 25373090--25373740 Score: 786
Period size: 88 Copynumber: 7.4 Consensus size: 88
25373080 GGGGTTATCG
* * *
25373090 ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTACTATTTTTAACCTGCTTCGCTGCAACCCA
1 ATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA
* *
25373155 AGGAGGCAAGGCTGGTGTCTTCA
66 GGGAGGCAAGGCTAGTGTCTTCA
*
25373178 ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA
1 ATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA
* *
25373243 GGGAGGCAAGGCTGGTGTCTTCG
66 GGGAGGCAAGGCTAGTGTCTTCA
* *
25373266 ATCTGCTTCGCTGTTGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA
1 ATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA
25373331 GGGAGGCAAGGCTAGTGTCTTCA
66 GGGAGGCAAGGCTAGTGTCTTCA
* * * * * * * * *
25373354 ATCTACTTCACTGTCAGTACAGGAAGGCAAGATCTGTTATCTTTAACCTACTCTGCTGCCACCGA
1 ATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA
25373419 GGGAGGCAAGGCTAGTGTCTTCA
66 GGGAGGCAAGGCTAGTGTCTTCA
** * * * * *
25373442 ATCTGCTTCACTGTTAGTACAGGAAGGCAAGATCTGCTATCTTTAACCTGTTCCGCTGCCACCGA
1 ATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA
25373507 GGGAGGCAAGGCTAGTGTCTTCA
66 GGGAGGCAAGGCTAGTGTCTTCA
* * * * * * * * *
25373530 ATCTGCTTCACTGTCAGTACAGGAGGGTAAGATCTGCTATCTTTAACCTGCTCTGCTACCACCGA
1 ATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA
* *
25373595 GGGAGGCAAGGCTAGTGCCTTCG
66 GGGAGGCAAGGCTAGTGTCTTCA
* * * * * * ** * * *
25373618 ATCTACTCCACT-ACTGAT-TAGGGAGATAAGATCTG-TAATTTTCAACTTGCTCTGCTGCAACC
1 ATCTGCTTCACTGTC-GGTGCAGGAAGGCAAGATCTGCT-ATTTTTAACCTGCTCCGCTGCAACC
* **
25373680 CAGGGAGGCAAGGCTGGTGTCTTTG
64 CAGGGAGGCAAGGCTAGTGTCTTCA
* *
25373705 ATCTGCTTCGCTGTCGGTGTAGGAAGGCAAGATCTG
1 ATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTG
25373741 TTATCTTCAC
Statistics
Matches: 501, Mismatches: 58, Indels: 8
0.88 0.10 0.01
Matches are distributed among these distances:
86 1 0.00
87 66 0.13
88 434 0.87
ACGTcount: A:0.22, C:0.25, G:0.26, T:0.27
Consensus pattern (88 bp):
ATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA
GGGAGGCAAGGCTAGTGTCTTCA
Found at i:25375905 original size:26 final size:25
Alignment explanation
Indices: 25375870--25375937 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 25
25375860 GAAGAAAATC
*
25375870 CAAAA-GAATGAAAGAATAATTATTT
1 CAAAATGAATGAAAGAAT-ATTAGTT
* *
25375895 CAAAATGAATGAAAAAATATTGGTT
1 CAAAATGAATGAAAGAATATTAGTT
25375920 CAAAAATGAATGCAAAGA
1 C-AAAATGAATG-AAAGA
25375938 TGTATTTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
25 11 0.31
26 21 0.58
27 4 0.11
ACGTcount: A:0.56, C:0.06, G:0.15, T:0.24
Consensus pattern (25 bp):
CAAAATGAATGAAAGAATATTAGTT
Found at i:25381159 original size:6 final size:6
Alignment explanation
Indices: 25381148--25381178 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
25381138 CATGATAATA
*
25381148 AAAAAT AAAAAT AAAAAT AAAAGT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT A
25381179 GGACCAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:25384802 original size:3 final size:3
Alignment explanation
Indices: 25384788--25384855 Score: 66
Period size: 3 Copynumber: 23.0 Consensus size: 3
25384778 CTTGAGCTTC
* * * * *
25384788 ATT ATT ACT ATT ATT ATT GTT AAT ATT ATT ATT ATT ATT ATT ACT ACT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
25384836 ACT ATT ATT A-T ATT TTT ATT
1 ATT ATT ATT ATT ATT ATT ATT
25384856 GATCTAACAT
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
2 2 0.04
3 52 0.96
ACGTcount: A:0.32, C:0.06, G:0.01, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:25384814 original size:21 final size:21
Alignment explanation
Indices: 25384790--25384846 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
25384780 TGAGCTTCAT
*
25384790 TATTACTATTATTATTGTTAA
1 TATTACTATTATTATTATTAA
* *
25384811 TATTATTATTATTATTATTAC
1 TATTACTATTATTATTATTAA
*
25384832 TACTACTATTATTAT
1 TATTACTATTATTAT
25384847 ATTTTTATTG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (21 bp):
TATTACTATTATTATTATTAA
Found at i:25388945 original size:27 final size:27
Alignment explanation
Indices: 25388907--25388960 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
25388897 AGGGAAAGGC
25388907 CCTATGGCCAACCCCAGTGAGGATAAG
1 CCTATGGCCAACCCCAGTGAGGATAAG
25388934 CCTATGGCCAACCCCAGTGAGGATAAG
1 CCTATGGCCAACCCCAGTGAGGATAAG
25388961 GATGAGCCAC
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:0.30, C:0.30, G:0.26, T:0.15
Consensus pattern (27 bp):
CCTATGGCCAACCCCAGTGAGGATAAG
Found at i:25398739 original size:24 final size:24
Alignment explanation
Indices: 25398680--25398739 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
25398670 AGATAATGAA
25398680 TTTAATCTTTTATATTTTATTTATT
1 TTTAAT-TTTTATATTTTATTTATT
* * *
25398705 ATTAGTGTTTATTATTTTA-TTATT
1 TTTAATTTTTA-TATTTTATTTATT
25398729 TTTAATTTTTA
1 TTTAATTTTTA
25398740 ATTAATCTCC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
24 17 0.61
25 11 0.39
ACGTcount: A:0.25, C:0.02, G:0.03, T:0.70
Consensus pattern (24 bp):
TTTAATTTTTATATTTTATTTATT
Found at i:25408159 original size:25 final size:25
Alignment explanation
Indices: 25408131--25408183 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
25408121 AAACTGAATG
*
25408131 GAGCAGAACAAAACCA-AACAAAGCA
1 GAGCAAAACAAAA-CAGAACAAAGCA
* *
25408156 GAGCAAAACAGAACAGAGCAAAGCA
1 GAGCAAAACAAAACAGAACAAAGCA
25408181 GAG
1 GAG
25408184 GATGTGTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 2 0.08
25 22 0.92
ACGTcount: A:0.57, C:0.21, G:0.23, T:0.00
Consensus pattern (25 bp):
GAGCAAAACAAAACAGAACAAAGCA
Found at i:25408175 original size:20 final size:20
Alignment explanation
Indices: 25408131--25408180 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
25408121 AAACTGAATG
*
25408131 GAGCAGAACAAAACCAAACA
1 GAGCAGAGCAAAACCAAACA
*
25408151 AAGCAGAGCAAAA-CAGAACA
1 GAGCAGAGCAAAACCA-AACA
*
25408171 GAGCAAAGCA
1 GAGCAGAGCA
25408181 GAGGATGTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.58, C:0.22, G:0.20, T:0.00
Consensus pattern (20 bp):
GAGCAGAGCAAAACCAAACA
Found at i:25416733 original size:17 final size:17
Alignment explanation
Indices: 25416711--25416744 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
25416701 CCATAAGAAA
25416711 GATTATAAATGAAAACT
1 GATTATAAATGAAAACT
25416728 GATTATAAATGAAAACT
1 GATTATAAATGAAAACT
25416745 TAATAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.12, T:0.29
Consensus pattern (17 bp):
GATTATAAATGAAAACT
Found at i:25419169 original size:16 final size:16
Alignment explanation
Indices: 25419148--25419179 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
25419138 GTTTTGTTGC
*
25419148 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
25419164 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
25419180 CTTTTAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:25419530 original size:50 final size:51
Alignment explanation
Indices: 25419397--25419533 Score: 152
Period size: 50 Copynumber: 2.7 Consensus size: 51
25419387 ATTAATGATA
* * * *
25419397 CCGGTTCACGTACTAGCCTGCACATAGTACTACACATGTGATCGAAGCTAT
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACATGCGATCCAAGCTAT
** * * * *
25419448 CCGGTATGCATAGTATCCTGCACATAGTACTACACATGCGA-CCTATC-ATT
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACATGCGATCCAAGCTA-T
*
25419498 CTGGTACACGTAGTAGCCTGCACATAGTACTACACA
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACA
25419534 CGTGACCATC
Statistics
Matches: 70, Mismatches: 15, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
49 1 0.01
50 35 0.50
51 34 0.49
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (51 bp):
CCGGTACACGTAGTAGCCTGCACATAGTACTACACATGCGATCCAAGCTAT
Found at i:25423087 original size:2 final size:2
Alignment explanation
Indices: 25423076--25423111 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
25423066 CCATATTATT
25423076 TC TC -C TC 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 TC TC TC TC T
25423112 TGCCTCTACT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:25433867 original size:20 final size:20
Alignment explanation
Indices: 25433844--25433882 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
25433834 CCATTACAAA
*
25433844 TAACCAATTT-CCGTTTCATC
1 TAACC-ATTTGCCATTTCATC
25433864 TAACCATTTGCCATTTCAT
1 TAACCATTTGCCATTTCAT
25433883 ATATCCAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.26, C:0.28, G:0.05, T:0.41
Consensus pattern (20 bp):
TAACCATTTGCCATTTCATC
Found at i:25456506 original size:147 final size:147
Alignment explanation
Indices: 25456234--25456536 Score: 536
Period size: 147 Copynumber: 2.1 Consensus size: 147
25456224 TATTGAAACC
*
25456234 GGTACCCCATGCAGTCTCACTATCTCAGACACATACAATTTAGCCAGCTTCTGCAGAGAGTAGTT
1 GGTAACCCATGCAGTCTCACTATCTCAGACACATACAATTTAGCCAGCTTCTGCAGAGAGTAGTT
*
25456299 AGTATGAATCGGTATGAAGTGGGTGGATTTGGTCAATCGATCCACGATGACCCATACAGAATCCT
66 AGTATGAACCGGTATGAAGTGGGTGGATTTGGTCAATCGATCCACGATGACCCATACAGAATCCT
**
25456364 TCTTGTTAGGTGTGAGG
131 TCTTCCTAGGTGTGAGG
*
25456381 GGTAACCCATGCAGTCTCACTATCTCAGACACATACAATTTAGCCAGCTTCTGCAGATAGTAGTT
1 GGTAACCCATGCAGTCTCACTATCTCAGACACATACAATTTAGCCAGCTTCTGCAGAGAGTAGTT
25456446 AGT-TCGAACCGGTATGAAGTGGGTGGATTTGGTCAATCGATCCACGATGACCCATACAGAATCC
66 AGTAT-GAACCGGTATGAAGTGGGTGGATTTGGTCAATCGATCCACGATGACCCATACAGAATCC
25456510 TTCTTCCTAGGTGTGAGG
130 TTCTTCCTAGGTGTGAGG
*
25456528 CGTAACCCA
1 GGTAACCCA
25456537 CCTACGAAGT
Statistics
Matches: 149, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
146 1 0.01
147 148 0.99
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (147 bp):
GGTAACCCATGCAGTCTCACTATCTCAGACACATACAATTTAGCCAGCTTCTGCAGAGAGTAGTT
AGTATGAACCGGTATGAAGTGGGTGGATTTGGTCAATCGATCCACGATGACCCATACAGAATCCT
TCTTCCTAGGTGTGAGG
Found at i:25471985 original size:94 final size:94
Alignment explanation
Indices: 25471824--25472028 Score: 248
Period size: 94 Copynumber: 2.2 Consensus size: 94
25471814 AAATGAGGTT
* ** * * *
25471824 TAATGTGTAAGACTATGGTTTGGCTACGGTAGCATATAGAGCCCGTCGAGACAATAAACACGAGG
1 TAATGTGTAAGACCATGGTTCAGCTACGGCAACATATAGAGCCCATCGAGACAATAAACACGAGG
*
25471889 TAGTCCGCCAGAACATTAAACATAGGGAA
66 TAGTCCACCAGAACATTAAACATAGGGAA
* * * * * *
25471918 TAATGTGTAAGACCATGGTTCAGCTATGGCAACATATGGAGTCCATCGGGACAATAAATACGGGG
1 TAATGTGTAAGACCATGGTTCAGCTACGGCAACATATAGAGCCCATCGAGACAATAAACACGAGG
* * * *
25471983 TAGTCTACCTGGACATTAAACATGGGGAA
66 TAGTCCACCAGAACATTAAACATAGGGAA
*
25472012 TAATATGTAAGACCATG
1 TAATGTGTAAGACCATG
25472029 TCTCGGCTAT
Statistics
Matches: 93, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
94 93 1.00
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (94 bp):
TAATGTGTAAGACCATGGTTCAGCTACGGCAACATATAGAGCCCATCGAGACAATAAACACGAGG
TAGTCCACCAGAACATTAAACATAGGGAA
Found at i:25472079 original size:94 final size:94
Alignment explanation
Indices: 25471856--25472080 Score: 240
Period size: 94 Copynumber: 2.4 Consensus size: 94
25471846 GCTACGGTAG
* * * *
25471856 CATATAGAGCCCGTCGAGACAATAAACACGAGGTAGTCCGCCAGAACATTAAACATAGGGAATAA
1 CATATAGAGTCCATCGGGACAATAAACACGAGGTAGTCCACCAGAACATTAAACATAGGGAATAA
* *
25471921 TGTGTAAGACCATGGTTCAGCTATGGCAA
66 TATGTAAGACCATGGTTCAGCTATGACAA
* * * * * * *
25471950 CATATGGAGTCCATCGGGACAATAAATACGGGGTAGTCTACCTGGACATTAAACATGGGGAATAA
1 CATATAGAGTCCATCGGGACAATAAACACGAGGTAGTCCACCAGAACATTAAACATAGGGAATAA
* *
25472015 TATGTAAGACCAT-GTCTCGGCTATGACAG
66 TATGTAAGACCATGGT-TCAGCTATGACAA
* * *
25472044 TATATAGAGTTCGC-T-GGGATACTAAACACGAGGTAGT
1 CATATAGAG-TC-CATCGGGACAATAAACACGAGGTAGT
25472081 TCGCAAGGAC
Statistics
Matches: 107, Mismatches: 21, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
93 2 0.02
94 101 0.94
95 3 0.03
96 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (94 bp):
CATATAGAGTCCATCGGGACAATAAACACGAGGTAGTCCACCAGAACATTAAACATAGGGAATAA
TATGTAAGACCATGGTTCAGCTATGACAA
Found at i:25474150 original size:12 final size:11
Alignment explanation
Indices: 25474135--25474233 Score: 51
Period size: 11 Copynumber: 9.6 Consensus size: 11
25474125 AAAAATTAAA
25474135 AAAAAGTATTTT
1 AAAAA-TATTTT
25474147 AAAAATATTTT
1 AAAAATATTTT
25474158 --AAA-A--TT
1 AAAAATATTTT
*
25474164 AAAAA-AATTT
1 AAAAATATTTT
25474174 AAAAAGTATTTT
1 AAAAA-TATTTT
25474186 AAAACA-ATTTT
1 AAAA-ATATTTT
25474197 ---AA-ATTTT
1 AAAAATATTTT
*
25474204 AAAAA-ATTTAA
1 AAAAATATTT-T
25474215 AAAAAGTATTTT
1 AAAAA-TATTTT
25474227 AAAAATA
1 AAAAATA
25474234 AAAAAATAAA
Statistics
Matches: 71, Mismatches: 3, Indels: 27
0.70 0.03 0.27
Matches are distributed among these distances:
6 2 0.03
7 6 0.08
8 6 0.08
9 3 0.04
10 13 0.18
11 18 0.25
12 18 0.25
13 5 0.07
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:25474168 original size:39 final size:41
Alignment explanation
Indices: 25474125--25474233 Score: 145
Period size: 39 Copynumber: 2.7 Consensus size: 41
25474115 AAATTAAAAC
25474125 AAAAATTAAAAAAAAGTATTTTAAAAATATTTTAAA-ATTAA
1 AAAAATTAAAAAAAAGTATTTTAAAAATATTTTAAATATT-A
* *
25474166 AAAAATT--TAAAAAGTATTTTAAAACA-ATTTTAAATTTTA
1 AAAAATTAAAAAAAAGTATTTTAAAA-ATATTTTAAATATTA
*
25474205 AAAAATTTAAAAAAAGTATTTTAAAAATA
1 AAAAATTAAAAAAAAGTATTTTAAAAATA
25474234 AAAAAATAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
39 32 0.53
40 4 0.07
41 24 0.40
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.36
Consensus pattern (41 bp):
AAAAATTAAAAAAAAGTATTTTAAAAATATTTTAAATATTA
Found at i:25474178 original size:17 final size:17
Alignment explanation
Indices: 25474145--25474178 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
25474135 AAAAAGTATT
* *
25474145 TTAAAAATATTTTAAAA
1 TTAAAAAAATTTAAAAA
25474162 TTAAAAAAATTTAAAAA
1 TTAAAAAAATTTAAAAA
25474179 GTATTTTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAAAAAAATTTAAAAA
Found at i:25474675 original size:15 final size:17
Alignment explanation
Indices: 25474640--25474677 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
25474630 TGTATAACAT
25474640 AATTATGAAATGTCTTG
1 AATTATGAAATGTCTTG
25474657 -ATTAT-AAATG-CTTG
1 AATTATGAAATGTCTTG
25474671 AATTATG
1 AATTATG
25474678 GTGTAATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
14 4 0.21
15 10 0.53
16 5 0.26
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (17 bp):
AATTATGAAATGTCTTG
Found at i:25476726 original size:16 final size:17
Alignment explanation
Indices: 25476703--25476756 Score: 56
Period size: 17 Copynumber: 3.0 Consensus size: 17
25476693 TAATGTGGTT
*
25476703 ATAAAAATAATTAAAAT
1 ATAAAAATAATTAAAAA
25476720 A-AAAAATACATTAGTTAAAA
1 ATAAAAATA-ATTA---AAAA
25476740 ATAAAAATAATTAAAAA
1 ATAAAAATAATTAAAAA
25476757 TATCATCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
16 7 0.23
17 9 0.29
20 8 0.26
21 7 0.23
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (17 bp):
ATAAAAATAATTAAAAA
Found at i:25476757 original size:16 final size:16
Alignment explanation
Indices: 25476703--25476758 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 16
25476693 TAATGTGGTT
25476703 ATAAAAATAATT-AAA
1 ATAAAAATAATTAAAA
25476718 ATAAAAAATACATTAGTTAAAA
1 AT-AAAAAT--A--A-TTAAAA
25476740 ATAAAAATAATTAAAA
1 ATAAAAATAATTAAAA
25476756 ATA
1 ATA
25476759 TCATCAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
15 2 0.06
16 15 0.44
17 1 0.03
18 1 0.03
19 1 0.03
20 1 0.03
21 8 0.24
22 5 0.15
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.27
Consensus pattern (16 bp):
ATAAAAATAATTAAAA
Found at i:25477005 original size:136 final size:134
Alignment explanation
Indices: 25476844--25477257 Score: 379
Period size: 146 Copynumber: 2.9 Consensus size: 134
25476834 ACAACCTCAT
* * * * *
25476844 ACTCAAGGATGTAATCACAATTATCTAACCACCTAAAGAAATGAGCTAATATGTTAAAAATATTA
1 ACTCAAGGATGTAATTACAACTATCTAACCATCTAACGAAA-GAACTAATATGTTAAAAATATTA
*
25476909 ATTAAAAAAAACTTGAAGCAACATGAAATAAAAAAAATATAAATCTGAGTAGTACAGGAATCAAA
65 ATTAAAAAAAACTTGAAGCAACATGAAATAAAAAAAATATAAATCTGAGTAG-AGAGGAATCAAA
*
25476974 CTCGAG
129 CTCAAG
* *
25476980 AC-CTAAGGATGTAATTACAACTATCTAACCTTCTAACGAAAGAACTAAAATGTTAAAAAATATT
1 ACTC-AAGGATGTAATTACAACTATCTAACCATCTAACGAAAGAACTAATATGTT--AAAA-A-T
* * *
25477044 AATTAAAATTTTTTTTAAAAAAAACTTGAAGTAACATGAAAT--AAAAAATACAAATATGAGTAA
61 -ATT--AA------TTAAAAAAAACTTGAAGCAACATGAAATAAAAAAAATATAAATCTGAGT-A
*
25477107 GAGAAGAATCAAACTCAAG
116 GAGAGGAATCAAACTCAAG
* * * * *
25477126 ACTCAAAGATATAGTTGCAACTATCTAACCATCTAACCAAAGAACTAATATGTTAAAAA-ATTAA
1 ACTCAAGGATGTAATTACAACTATCTAACCATCTAACGAAAGAACTAATATGTTAAAAATATTAA
* *
25477190 TTAAAAATTTTAAAAACTTGAAGCAGCATGAAATAAAAAAAA-ATACAAACGTGAGTAGGAGAGG
66 TT--AAA----AAAAACTTGAAGCAACATGAAATAAAAAAAATATA-AATC-TGAGTA-GAGAGG
25477254 AATC
122 AATC
25477258 GAATGTGGGA
Statistics
Matches: 225, Mismatches: 26, Indels: 49
0.75 0.09 0.16
Matches are distributed among these distances:
132 2 0.01
134 3 0.01
135 12 0.05
136 34 0.15
137 4 0.02
138 24 0.11
139 3 0.01
140 15 0.07
141 14 0.06
142 2 0.01
143 1 0.00
144 4 0.02
146 77 0.34
147 3 0.01
148 27 0.12
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.25
Consensus pattern (134 bp):
ACTCAAGGATGTAATTACAACTATCTAACCATCTAACGAAAGAACTAATATGTTAAAAATATTAA
TTAAAAAAAACTTGAAGCAACATGAAATAAAAAAAATATAAATCTGAGTAGAGAGGAATCAAACT
CAAG
Found at i:25477062 original size:148 final size:142
Alignment explanation
Indices: 25476910--25477257 Score: 404
Period size: 146 Copynumber: 2.4 Consensus size: 142
25476900 AAAATATTAA
*
25476910 TTAAAAAAAACTTGAAGCAACATGAAATAAAAAAAATATAAATCTGAGTAGTACAGGAATCAAAC
1 TTAAAAAAAACTTGAAGCAACATGAAATAAAAAAAATATAAATCTGAGTAG-AGAGGAATCAAAC
* * * * *
25476975 TCGAGAC-CTAAGGATGTAATTACAACTATCTAACCTTCTAACGAAAGAACTAAAATGTTAAAAA
65 TCAAGACTC-AAAGATATAATTACAACTATCTAACCATCTAACCAAAGAACTAAAATGTT-AAAA
*
25477039 ATATTAATTAAAATTTTTT
128 A-ATTAATTAAAA---ATT
* * * *
25477058 TTAAAAAAAACTTGAAGTAACATGAAAT--AAAAAATACAAATATGAGTAAGAGAAGAATCAAAC
1 TTAAAAAAAACTTGAAGCAACATGAAATAAAAAAAATATAAATCTGAGT-AGAGAGGAATCAAAC
* * *
25477121 TCAAGACTCAAAGATATAGTTGCAACTATCTAACCATCTAACCAAAGAACTAATATGTTAAAAAA
65 TCAAGACTCAAAGATATAATTACAACTATCTAACCATCTAACCAAAGAACTAAAATGTTAAAAAA
25477186 TTAATTAAAAATT
130 TTAATTAAAAATT
* *
25477199 TT---AAAAACTTGAAGCAGCATGAAATAAAAAAAA-ATACAAACGTGAGTAGGAGAGGAATC
1 TTAAAAAAAACTTGAAGCAACATGAAATAAAAAAAATATA-AATC-TGAGTA-GAGAGGAATC
25477258 GAATGTGGGA
Statistics
Matches: 173, Mismatches: 20, Indels: 21
0.81 0.09 0.10
Matches are distributed among these distances:
138 21 0.12
139 2 0.01
140 9 0.05
141 18 0.10
144 11 0.06
145 5 0.03
146 77 0.45
147 3 0.02
148 27 0.16
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.24
Consensus pattern (142 bp):
TTAAAAAAAACTTGAAGCAACATGAAATAAAAAAAATATAAATCTGAGTAGAGAGGAATCAAACT
CAAGACTCAAAGATATAATTACAACTATCTAACCATCTAACCAAAGAACTAAAATGTTAAAAAAT
TAATTAAAAATT
Found at i:25483634 original size:19 final size:18
Alignment explanation
Indices: 25483606--25483648 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
25483596 ATTTAAGAGG
*
25483606 GAATTGAGAGAGATTTGA
1 GAATTGAGAGAGAATTGA
25483624 GAATGTGAGAGAGAATTGA
1 GAAT-TGAGAGAGAATTGA
25483643 -AATTGA
1 GAATTGA
25483649 ATTGGAAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 3 0.13
18 7 0.30
19 13 0.57
ACGTcount: A:0.42, C:0.00, G:0.33, T:0.26
Consensus pattern (18 bp):
GAATTGAGAGAGAATTGA
Found at i:25485614 original size:5 final size:5
Alignment explanation
Indices: 25485604--25485643 Score: 57
Period size: 5 Copynumber: 8.2 Consensus size: 5
25485594 ATCGGGGGGG
25485604 TTTTC TTTTC TTTTC TTTTC TTTT- TTCTTC -TTTC TTTTC T
1 TTTTC TTTTC TTTTC TTTTC TTTTC TT-TTC TTTTC TTTTC T
25485644 CGGCTAAAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
4 5 0.16
5 27 0.84
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:25486929 original size:14 final size:14
Alignment explanation
Indices: 25486912--25486939 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
25486902 TTACACTGTT
25486912 TTACTTTATAATAC
1 TTACTTTATAATAC
25486926 TTACTTTATAATAC
1 TTACTTTATAATAC
25486940 GCATGTTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (14 bp):
TTACTTTATAATAC
Found at i:25492041 original size:15 final size:15
Alignment explanation
Indices: 25492021--25492051 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
25492011 GCAGCATCTG
25492021 AAAATTCACCAAACT
1 AAAATTCACCAAACT
25492036 AAAATTCACCAAACT
1 AAAATTCACCAAACT
25492051 A
1 A
25492052 CCTATCTCCA
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:0.55, C:0.26, G:0.00, T:0.19
Consensus pattern (15 bp):
AAAATTCACCAAACT
Found at i:25494649 original size:9 final size:9
Alignment explanation
Indices: 25494635--25494667 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
25494625 GAGTTAGACG
25494635 ATTCGAGTT
1 ATTCGAGTT
25494644 ATTCGAGTT
1 ATTCGAGTT
*
25494653 AATCGAGTT
1 ATTCGAGTT
25494662 ATTCGA
1 ATTCGA
25494668 ATCAAATCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.39
Consensus pattern (9 bp):
ATTCGAGTT
Found at i:25494677 original size:19 final size:18
Alignment explanation
Indices: 25494637--25494677 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
25494627 GTTAGACGAT
* *
25494637 TCGAGTTATTCGAGTTAA
1 TCGAGTTATTCGAATAAA
25494655 TCGAGTTATTCGAATCAAA
1 TCGAGTTATTCGAAT-AAA
25494674 TCGA
1 TCGA
25494678 TTTTTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.34
Consensus pattern (18 bp):
TCGAGTTATTCGAATAAA
Done.