Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 7 of 295
Found at i:2234989 original size:21 final size:22
Alignment explanation
Indices: 2234949--2234991 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
2234939 TTAAGGCTTG
2234949 ATATTGGTTTGAATTGAATGTGAT
1 ATATTGGTTTG-A-TGAATGTGAT
2234973 ATATTGGTTTG-TGAATGTG
1 ATATTGGTTTGATGAATGTG
2234992 TTAAAGTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
24 11 0.58
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.47
Consensus pattern (22 bp):
ATATTGGTTTGATGAATGTGAT
Found at i:2237175 original size:24 final size:23
Alignment explanation
Indices: 2237142--2237199 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
2237132 AGTTGAAAAG
2237142 TATAA-AATAAAATAAATAATGATA
1 TATAATAATAAAAT-AAT-ATGATA
*
2237166 -ATAATAATAAAATGATATGATA
1 TATAATAATAAAATAATATGATA
2237188 TATATATAATAA
1 TATA-ATAATAA
2237200 TGCTTGATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 6 0.20
23 9 0.30
24 15 0.50
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (23 bp):
TATAATAATAAAATAATATGATA
Found at i:2237552 original size:49 final size:48
Alignment explanation
Indices: 2237470--2237627 Score: 264
Period size: 49 Copynumber: 3.2 Consensus size: 48
2237460 CTTACTTTGA
*
2237470 GAATGTGAAAGTG-TATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTGTTATATATGTGATAGGGCCTAATGGCCGATGTGAT
2237517 GAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTGT-TATATATGTGATAGGGCCTAATGGCCGATGTGAT
*
2237566 GAATGTGAAAGTGTGTATATATGTGATAGGGCCTAATGGCAGATGTGAT
1 GAATGTGAAAGTGT-TATATATGTGATAGGGCCTAATGGCCGATGTGAT
2237615 GAATGTGATAAGT
1 GAATGTGA-AAGT
2237628 CCCGAAGGGC
Statistics
Matches: 105, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
47 13 0.12
49 88 0.84
50 4 0.04
ACGTcount: A:0.32, C:0.07, G:0.31, T:0.30
Consensus pattern (48 bp):
GAATGTGAAAGTGTTATATATGTGATAGGGCCTAATGGCCGATGTGAT
Found at i:2237801 original size:37 final size:37
Alignment explanation
Indices: 2237745--2237823 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
2237735 CCGAGCTCTA
* * *
2237745 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
2237782 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
2237819 AAGAC
1 AAGAC
2237824 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:2243984 original size:18 final size:18
Alignment explanation
Indices: 2243963--2244024 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 18
2243953 ATATATAGAT
2243963 ATATATAATAAGATATAA
1 ATATATAATAAGATATAA
*
2243981 ATATATAATAAGATGATAT
1 ATATATAATAAGAT-ATAA
*
2244000 ATATA-AAT-AGTTAT-A
1 ATATATAATAAGATATAA
2244015 ATA-ATAATAA
1 ATATATAATAA
2244025 TAATAATAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
14 1 0.03
15 6 0.16
16 3 0.08
17 3 0.08
18 17 0.45
19 8 0.21
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (18 bp):
ATATATAATAAGATATAA
Found at i:2244015 original size:35 final size:33
Alignment explanation
Indices: 2243960--2244024 Score: 87
Period size: 35 Copynumber: 1.9 Consensus size: 33
2243950 GAGATATATA
2243960 GATATATATAATAAGATATAAATATATAATAAGAT
1 GATATATATAATAAGATAT-AATA-ATAATAAGAT
*
2243995 GATATATATAA-ATAGTTATAATAATAATAA
1 GATATATATAATA-AGATATAATAATAATAA
2244025 TAATAATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 7 0.25
34 5 0.18
35 16 0.57
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (33 bp):
GATATATATAATAAGATATAATAATAATAAGAT
Found at i:2245875 original size:43 final size:43
Alignment explanation
Indices: 2245819--2245929 Score: 134
Period size: 44 Copynumber: 2.5 Consensus size: 43
2245809 AATCCGCTCT
* * * *
2245819 ACTGTAACTTCAGGGAGATAGGATA-GTGTCTTCGATCTGATCC
1 ACTGTAAC-TCAGGGAGATAAGATATCTGGCTTCAATCTGATCC
* *
2245862 GCTGTAATCTCAGGGAGATAAGATATCTGGCTTCAATCTGCTCC
1 ACTGTAA-CTCAGGGAGATAAGATATCTGGCTTCAATCTGATCC
2245906 ACTGTAACCTCAGGGAGATAAGAT
1 ACTGTAA-CTCAGGGAGATAAGAT
2245930 CTGAAATTCT
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
43 21 0.36
44 37 0.64
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (43 bp):
ACTGTAACTCAGGGAGATAAGATATCTGGCTTCAATCTGATCC
Found at i:2245965 original size:46 final size:45
Alignment explanation
Indices: 2245898--2246144 Score: 187
Period size: 46 Copynumber: 5.7 Consensus size: 45
2245888 CTGGCTTCAA
* *
2245898 TCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTTGG
1 TCTGTTCCACTGTAATCTCAGGGAGATAAGATCTG-AATTCTTTGG
* * * *
2245944 TCTATTCCACTGTAATCTCAGGGAGATAAGACCTG-A---TGTGA
1 TCTGTTCCACTGTAATCTCAGGGAGATAAGATCTGAATTCTTTGG
* * * **
2245985 TCTTTTCTACTGTAA-CTTCAGAGAGATAAGATC------CTTTAA
1 TCTGTTCCACTGTAATC-TCAGGGAGATAAGATCTGAATTCTTTGG
* * * * * * *
2246024 TCCGCTCCATTGTAATCTCAAGGAGATAGGAT-T-ACTATCTTTGA
1 TCTGTTCCACTGTAATCTCAGGGAGATAAGATCTGAAT-TCTTTGG
* *
2246068 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGG
1 TCTGTTCCACTGTAATCTCAGGGAGATAAGATCTG-AATTCTTTGG
2246114 TCTGTTCCACTGTAATCTCAGGGAGATAAGA
1 TCTGTTCCACTGTAATCTCAGGGAGATAAGA
2246145 CCTGTATAAT
Statistics
Matches: 159, Mismatches: 30, Indels: 24
0.75 0.14 0.11
Matches are distributed among these distances:
39 25 0.16
40 2 0.01
41 30 0.19
44 33 0.21
45 1 0.01
46 66 0.42
47 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (45 bp):
TCTGTTCCACTGTAATCTCAGGGAGATAAGATCTGAATTCTTTGG
Found at i:2258563 original size:18 final size:18
Alignment explanation
Indices: 2258542--2258603 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 18
2258532 ATATATAGAT
2258542 ATATATAATAAGATATAA
1 ATATATAATAAGATATAA
*
2258560 ATATATAATAAGATGATAT
1 ATATATAATAAGAT-ATAA
*
2258579 ATATA-AAT-AGTTAT-A
1 ATATATAATAAGATATAA
2258594 ATA-ATAATAA
1 ATATATAATAA
2258604 TAATAATAGG
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
14 1 0.03
15 6 0.16
16 3 0.08
17 3 0.08
18 17 0.45
19 8 0.21
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (18 bp):
ATATATAATAAGATATAA
Found at i:2258594 original size:35 final size:33
Alignment explanation
Indices: 2258539--2258603 Score: 87
Period size: 35 Copynumber: 1.9 Consensus size: 33
2258529 GAGATATATA
2258539 GATATATATAATAAGATATAAATATATAATAAGAT
1 GATATATATAATAAGATAT-AATA-ATAATAAGAT
*
2258574 GATATATATAA-ATAGTTATAATAATAATAA
1 GATATATATAATA-AGATATAATAATAATAA
2258604 TAATAATAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 7 0.25
34 5 0.18
35 16 0.57
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (33 bp):
GATATATATAATAAGATATAATAATAATAAGAT
Found at i:2261584 original size:88 final size:90
Alignment explanation
Indices: 2261466--2261640 Score: 248
Period size: 88 Copynumber: 2.0 Consensus size: 90
2261456 GTCATTGCTT
* * *
2261466 TTTTCTTTTTGTACTCATTTAGATACTTGAACTTTCAAAATGCATAAAAAAAG-CCCTTAAACTT
1 TTTTCTTTTTGCACTCAATTAGATACTTGAACTTTCAAAATGCAT-AAAAAAGTCCCTCAAACTT
** *
2261530 TTT-TGAAAAAGCAATTACGCCCTAC
65 TTTCAAAAAAAGCAATTAAGCCCTAC
* *
2261555 TTTT-TTTTTGCACTCAATTGGATACTTGAACTTTCAAAATGCATCAAAAAGTCCCTCAAACTTT
1 TTTTCTTTTTGCACTCAATTAGATACTTGAACTTTCAAAATGCATAAAAAAGTCCCTCAAACTTT
2261619 TTCAAAAAAAGCAATTAAGCCC
66 TTCAAAAAAAGCAATTAAGCCC
2261641 CCACTTTTAT
Statistics
Matches: 76, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
87 6 0.08
88 50 0.66
89 20 0.26
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.35
Consensus pattern (90 bp):
TTTTCTTTTTGCACTCAATTAGATACTTGAACTTTCAAAATGCATAAAAAAGTCCCTCAAACTTT
TTCAAAAAAAGCAATTAAGCCCTAC
Found at i:2261731 original size:28 final size:26
Alignment explanation
Indices: 2261700--2261751 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
2261690 TACAATTTAT
*
2261700 AAATATTATTAAATTTTAATAAAAATTC
1 AAATATTA--AAAATTTAATAAAAATTC
*
2261728 AAATATTAAAAATTTATTAAAAAT
1 AAATATTAAAAATTTAATAAAAAT
2261752 AGAAAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 14 0.64
28 8 0.36
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (26 bp):
AAATATTAAAAATTTAATAAAAATTC
Found at i:2261766 original size:16 final size:17
Alignment explanation
Indices: 2261745--2261779 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2261735 AAAAATTTAT
2261745 TAAAAATAG-AAAAAAA
1 TAAAAATAGTAAAAAAA
*
2261761 TAAAAATTGTAAAAAAA
1 TAAAAATAGTAAAAAAA
2261778 TA
1 TA
2261780 TATAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (17 bp):
TAAAAATAGTAAAAAAA
Found at i:2261811 original size:27 final size:27
Alignment explanation
Indices: 2261779--2261854 Score: 93
Period size: 27 Copynumber: 2.8 Consensus size: 27
2261769 GTAAAAAAAT
*
2261779 ATATAAAAATTGTAAAATTTTATA-AA
1 ATATAAAAATTATAAAATTTTATAGAA
*
2261805 ATGATAAAAATTATAAAA-TATATAGAA
1 AT-ATAAAAATTATAAAATTTTATAGAA
*
2261832 ATATAAAAAATTATGAAATTTTA
1 ATAT-AAAAATTATAAAATTTTA
2261855 GAAAGCCGTA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
26 9 0.21
27 30 0.71
28 3 0.07
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (27 bp):
ATATAAAAATTATAAAATTTTATAGAA
Found at i:2261835 original size:10 final size:9
Alignment explanation
Indices: 2261774--2261842 Score: 54
Period size: 9 Copynumber: 7.6 Consensus size: 9
2261764 AAATTGTAAA
2261774 AAAATATAT
1 AAAATATAT
*
2261783 AAAA-ATTGT
1 AAAATA-TAT
*
2261792 AAAATTTTAT
1 AAAA-TATAT
2261802 AAAATGATA-
1 AAAAT-ATAT
2261811 AAAAT-TAT
1 AAAATATAT
2261819 AAAATATAT
1 AAAATATAT
*
2261828 AGAAATATAA
1 A-AAATATAT
2261838 AAAAT
1 AAAAT
2261843 TATGAAATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
7 2 0.04
8 6 0.12
9 24 0.50
10 16 0.33
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (9 bp):
AAAATATAT
Found at i:2262084 original size:19 final size:19
Alignment explanation
Indices: 2262062--2262191 Score: 61
Period size: 19 Copynumber: 6.8 Consensus size: 19
2262052 TTTTTTATGG
2262062 TTTTTATAAAATTTTATTA
1 TTTTTATAAAATTTTATTA
*** *
2262081 -TTTTATTATTTTTTTACTA
1 TTTTTA-TAAAATTTTATTA
** *
2262100 TTTTTATAAAAAAATTATAA
1 TTTTTAT-AAAATTTTATTA
* *
2262120 TTTTTAATAAATTTTTAAT-
1 TTTTT-ATAAAATTTTATTA
* * *
2262139 TTTTTATTGAAATTTAATAA
1 TTTTTA-TAAAATTTTATTA
* *
2262159 ATTTTCTAAAA-TTTATTA
1 TTTTTATAAAATTTTATTA
2262177 TTTATTAT-AAATTTT
1 TTT-TTATAAAATTTT
2262192 TTTCTAATTT
Statistics
Matches: 75, Mismatches: 28, Indels: 16
0.63 0.24 0.13
Matches are distributed among these distances:
18 16 0.21
19 32 0.43
20 25 0.33
21 2 0.03
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.60
Consensus pattern (19 bp):
TTTTTATAAAATTTTATTA
Found at i:2267237 original size:29 final size:32
Alignment explanation
Indices: 2267189--2267259 Score: 94
Period size: 30 Copynumber: 2.3 Consensus size: 32
2267179 AATAATTTAT
* *
2267189 ATTTTTATAATTTTTAAAG-AATTAAACTA-A
1 ATTTTTATTATTTTTAAAGAAATTAAAATATA
2267219 ATTTTTATTATTTTT-AAGAAATTAAAATATA
1 ATTTTTATTATTTTTAAAGAAATTAAAATATA
2267250 ATTTTATATT
1 ATTTT-TATT
2267260 TACTAATTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
29 3 0.08
30 23 0.64
31 6 0.17
32 4 0.11
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (32 bp):
ATTTTTATTATTTTTAAAGAAATTAAAATATA
Found at i:2271411 original size:17 final size:16
Alignment explanation
Indices: 2271377--2271429 Score: 88
Period size: 16 Copynumber: 3.2 Consensus size: 16
2271367 GATTAGCTAT
*
2271377 TACACCACTAATCCAA
1 TACACCTCTAATCCAA
2271393 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
2271410 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
2271426 TACA
1 TACA
2271430 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
16 19 0.54
17 16 0.46
ACGTcount: A:0.40, C:0.38, G:0.00, T:0.23
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:2273015 original size:17 final size:16
Alignment explanation
Indices: 2272988--2273027 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
2272978 TAAATAATTT
2272988 TTTTATATTTTTTAATAA
1 TTTT-TATTTTTTAAT-A
*
2273006 TTTTTATTTTTTGATA
1 TTTTTATTTTTTAATA
2273022 TTTTTA
1 TTTTTA
2273028 AATTTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.33
17 10 0.48
18 4 0.19
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (16 bp):
TTTTTATTTTTTAATA
Found at i:2273483 original size:26 final size:25
Alignment explanation
Indices: 2273454--2273506 Score: 79
Period size: 26 Copynumber: 2.1 Consensus size: 25
2273444 ACTAATAAAC
*
2273454 TATTCTTTTATATTTTTAATAATTTT
1 TATTCTTTTACATTTTTAA-AATTTT
*
2273480 TATTTTTTTACATTTTTAAAATTTT
1 TATTCTTTTACATTTTTAAAATTTT
2273505 TA
1 TA
2273507 AAATTTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (25 bp):
TATTCTTTTACATTTTTAAAATTTT
Found at i:2275345 original size:56 final size:59
Alignment explanation
Indices: 2275249--2275382 Score: 145
Period size: 56 Copynumber: 2.3 Consensus size: 59
2275239 ATGCTTAATT
* *
2275249 TTTTTTTCAAATTAATC-CTTAAATTTAGTAATTGTATTTATAATGAGGA-TT-AA-ATA
1 TTTTTTTCAAATTAATCTCTAAAATTTAGCAATTGTATTTAT-ATGAGGACTTGAACATA
* * *
2275305 TTTTTTTCAAATTAATCTC-AAAATTTAGCAACTT-TTTTTATATTAGGACTTGAACATT
1 TTTTTTTCAAATTAATCTCTAAAATTTAGCAA-TTGTATTTATATGAGGACTTGAACATA
2275363 TTTTTTGTCTAAATTAATCT
1 TTTTTT-TC-AAATTAATCT
2275383 ATGATATTTC
Statistics
Matches: 66, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
55 6 0.09
56 35 0.53
57 5 0.08
58 8 0.12
59 2 0.03
60 10 0.15
ACGTcount: A:0.34, C:0.09, G:0.07, T:0.50
Consensus pattern (59 bp):
TTTTTTTCAAATTAATCTCTAAAATTTAGCAATTGTATTTATATGAGGACTTGAACATA
Found at i:2275918 original size:19 final size:21
Alignment explanation
Indices: 2275890--2275931 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
2275880 TGAATGTGAT
2275890 TTTTTAAAAATAAT-AAAATA
1 TTTTTAAAAATAATAAAAATA
*
2275910 TTTTT-AAAATTATAAAAATA
1 TTTTTAAAAATAATAAAAATA
2275930 TT
1 TT
2275932 AAAAACTCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TTTTTAAAAATAATAAAAATA
Found at i:2278054 original size:24 final size:24
Alignment explanation
Indices: 2278030--2278110 Score: 87
Period size: 24 Copynumber: 3.4 Consensus size: 24
2278020 ATTTTATATT
*
2278030 ATTATTTATATAAATATATAAATTA
1 ATTATATATATAAATAT-TAAATTA
* *
2278055 ATTATAAAGTAT-ATTATTAAATTA
1 ATTATATA-TATAAATATTAAATTA
*
2278079 ATTATAT-TATAAATATTATATT-
1 ATTATATATATAAATATTAAATTA
2278101 ATTATATATA
1 ATTATATATA
2278111 AAAGAAACAA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
22 10 0.21
23 11 0.23
24 13 0.28
25 10 0.21
26 3 0.06
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (24 bp):
ATTATATATATAAATATTAAATTA
Found at i:2278062 original size:11 final size:11
Alignment explanation
Indices: 2278046--2278084 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
2278036 TATATAAATA
2278046 TATAAATTAAT
1 TATAAATTAAT
*
2278057 TATAAAGTATAT
1 TATAAATTA-AT
2278069 TATTAAATTAAT
1 TA-TAAATTAAT
2278081 TATA
1 TATA
2278085 TTATAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 10 0.42
12 8 0.33
13 6 0.25
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (11 bp):
TATAAATTAAT
Found at i:2278086 original size:17 final size:15
Alignment explanation
Indices: 2278029--2278109 Score: 60
Period size: 15 Copynumber: 5.2 Consensus size: 15
2278019 GATTTTATAT
2278029 TATTAT-TTATATAAA
1 TATTATATTAT-TAAA
*
2278044 TATATAAATTAATTATAA
1 TAT-TATATT-ATTA-AA
*
2278062 -AGTATATTATTAAA
1 TATTATATTATTAAA
2278076 TTAATTATATTA-TAAA
1 -T-ATTATATTATTAAA
*
2278092 TATTATATTATTATA
1 TATTATATTATTAAA
2278107 TAT
1 TAT
2278110 AAAAGAAACA
Statistics
Matches: 53, Mismatches: 5, Indels: 16
0.72 0.07 0.22
Matches are distributed among these distances:
14 11 0.21
15 14 0.26
16 11 0.21
17 13 0.25
18 4 0.08
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (15 bp):
TATTATATTATTAAA
Found at i:2278096 original size:14 final size:16
Alignment explanation
Indices: 2278064--2278102 Score: 55
Period size: 14 Copynumber: 2.5 Consensus size: 16
2278054 AATTATAAAG
2278064 TATATTATTAAATTAAT
1 TATATTA-TAAATTAAT
2278081 TATATTATAAA-T-AT
1 TATATTATAAATTAAT
2278095 TATATTAT
1 TATATTAT
2278103 TATATATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 10 0.45
15 1 0.05
16 4 0.18
17 7 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATATTATAAATTAAT
Found at i:2279437 original size:3 final size:3
Alignment explanation
Indices: 2279429--2279473 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
2279419 GTGAGGTAAG
2279429 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2279474 GAGTGGGAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2279657 original size:24 final size:27
Alignment explanation
Indices: 2279625--2279683 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
2279615 CGGATTAATT
2279625 ATTG-ATTGAAAG-GTG-GAAA-AATG
1 ATTGAATTGAAAGTGTGAGAAAGAATG
**
2279648 ATTGAATTGAAAGTGTGAGAAAGTGTG
1 ATTGAATTGAAAGTGTGAGAAAGAATG
2279675 ATTGAATTG
1 ATTGAATTG
2279684 GGATTATATG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 4 0.13
24 8 0.27
25 3 0.10
26 4 0.13
27 11 0.37
ACGTcount: A:0.39, C:0.00, G:0.31, T:0.31
Consensus pattern (27 bp):
ATTGAATTGAAAGTGTGAGAAAGAATG
Found at i:2285923 original size:24 final size:24
Alignment explanation
Indices: 2285899--2285979 Score: 87
Period size: 24 Copynumber: 3.4 Consensus size: 24
2285889 TTTTTATATT
*
2285899 ATTATTTATATAAATATATAAATTA
1 ATTATATATATAAATAT-TAAATTA
* *
2285924 ATTATAAAGTAT-ATTATTAAATTA
1 ATTATATA-TATAAATATTAAATTA
*
2285948 ATTATAT-TATAAATATTATATT-
1 ATTATATATATAAATATTAAATTA
2285970 ATTATATATA
1 ATTATATATA
2285980 AAAGAAACAA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
22 10 0.21
23 11 0.23
24 13 0.28
25 10 0.21
26 3 0.06
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (24 bp):
ATTATATATATAAATATTAAATTA
Found at i:2285931 original size:11 final size:11
Alignment explanation
Indices: 2285915--2285953 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
2285905 TATATAAATA
2285915 TATAAATTAAT
1 TATAAATTAAT
*
2285926 TATAAAGTATAT
1 TATAAATTA-AT
2285938 TATTAAATTAAT
1 TA-TAAATTAAT
2285950 TATA
1 TATA
2285954 TTATAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 10 0.42
12 8 0.33
13 6 0.25
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (11 bp):
TATAAATTAAT
Found at i:2285955 original size:17 final size:15
Alignment explanation
Indices: 2285898--2285978 Score: 60
Period size: 15 Copynumber: 5.2 Consensus size: 15
2285888 ATTTTTATAT
2285898 TATTAT-TTATATAAA
1 TATTATATTAT-TAAA
*
2285913 TATATAAATTAATTATAA
1 TAT-TATATT-ATTA-AA
*
2285931 -AGTATATTATTAAA
1 TATTATATTATTAAA
2285945 TTAATTATATTA-TAAA
1 -T-ATTATATTATTAAA
*
2285961 TATTATATTATTATA
1 TATTATATTATTAAA
2285976 TAT
1 TAT
2285979 AAAAGAAACA
Statistics
Matches: 53, Mismatches: 5, Indels: 16
0.72 0.07 0.22
Matches are distributed among these distances:
14 11 0.21
15 14 0.26
16 11 0.21
17 13 0.25
18 4 0.08
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (15 bp):
TATTATATTATTAAA
Found at i:2285965 original size:14 final size:16
Alignment explanation
Indices: 2285933--2285971 Score: 55
Period size: 14 Copynumber: 2.5 Consensus size: 16
2285923 AATTATAAAG
2285933 TATATTATTAAATTAAT
1 TATATTA-TAAATTAAT
2285950 TATATTATAAA-T-AT
1 TATATTATAAATTAAT
2285964 TATATTAT
1 TATATTAT
2285972 TATATATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 10 0.45
15 1 0.05
16 4 0.18
17 7 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATATTATAAATTAAT
Found at i:2287306 original size:3 final size:3
Alignment explanation
Indices: 2287298--2287345 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
2287288 GTGAGGTAAG
2287298 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2287346 GAGTGGGAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2287529 original size:24 final size:27
Alignment explanation
Indices: 2287497--2287555 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
2287487 CGGATTAATT
2287497 ATTG-ATTGAAAG-GTG-GAAA-AATG
1 ATTGAATTGAAAGTGTGAGAAAGAATG
**
2287520 ATTGAATTGAAAGTGTGAGAAAGTGTG
1 ATTGAATTGAAAGTGTGAGAAAGAATG
2287547 ATTGAATTG
1 ATTGAATTG
2287556 GGATTATATG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 4 0.13
24 8 0.27
25 3 0.10
26 4 0.13
27 11 0.37
ACGTcount: A:0.39, C:0.00, G:0.31, T:0.31
Consensus pattern (27 bp):
ATTGAATTGAAAGTGTGAGAAAGAATG
Found at i:2287759 original size:37 final size:39
Alignment explanation
Indices: 2287700--2287795 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
2287690 CGGATAGATT
* * * *
2287700 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
2287737 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
2287776 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
2287796 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:2292721 original size:29 final size:32
Alignment explanation
Indices: 2292680--2292752 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 32
2292670 TAAAAAAAAC
*
2292680 TAAAAATATTAAAATT-TATAATT-T-ATTTTA
1 TAAAAATATT-AAATTATATAATTATAATTATA
*
2292710 TAAAATTA-TAAATTATATAATTATAATTATA
1 TAAAAATATTAAATTATATAATTATAATTATA
2292741 TAAAAA-ATTAAA
1 TAAAAATATTAAA
2292753 AACCATGTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
28 5 0.14
29 8 0.22
30 9 0.25
31 14 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (32 bp):
TAAAAATATTAAATTATATAATTATAATTATA
Found at i:2295485 original size:16 final size:17
Alignment explanation
Indices: 2295466--2295505 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 17
2295456 CCTTTTTCTT
2295466 TTCCTT-AATGGGAAAA
1 TTCCTTGAATGGGAAAA
2295482 TTCCTTTGAATGGGAAAA
1 TTCC-TTGAATGGGAAAA
2295500 TTCCTT
1 TTCCTT
2295506 TCACTTTCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.18
17 4 0.18
18 14 0.64
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (17 bp):
TTCCTTGAATGGGAAAA
Found at i:2295495 original size:18 final size:18
Alignment explanation
Indices: 2295472--2295506 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2295462 TCTTTTCCTT
2295472 AATGGGAAAATTCCTTTG
1 AATGGGAAAATTCCTTTG
2295490 AATGGGAAAATTCCTTT
1 AATGGGAAAATTCCTTT
2295507 CACTTTCTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (18 bp):
AATGGGAAAATTCCTTTG
Found at i:2300140 original size:39 final size:39
Alignment explanation
Indices: 2300094--2300172 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
2300084 AAATTTTTTC
2300094 TTACAATATACTTAATAATACTTTATGAAAATTCATGTT
1 TTACAATATACTTAATAATACTTTATGAAAATTCATGTT
2300133 TTACAATATACTTAATAATACTTTATGAAAATTCATGTT
1 TTACAATATACTTAATAATACTTTATGAAAATTCATGTT
2300172 T
1 T
2300173 GTCGAGTGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (39 bp):
TTACAATATACTTAATAATACTTTATGAAAATTCATGTT
Found at i:2301376 original size:21 final size:21
Alignment explanation
Indices: 2301350--2301389 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2301340 CTAGGTTTTG
2301350 GGTTTTTACAAGAAAAAACCT
1 GGTTTTTACAAGAAAAAACCT
**
2301371 GGTTTTTACATTAAAAAAC
1 GGTTTTTACAAGAAAAAAC
2301390 TATTTTATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (21 bp):
GGTTTTTACAAGAAAAAACCT
Found at i:2302829 original size:7 final size:7
Alignment explanation
Indices: 2302817--2302841 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2302807 AATAAATCCA
2302817 AAAACTC
1 AAAACTC
2302824 AAAACTC
1 AAAACTC
2302831 AAAACTC
1 AAAACTC
2302838 AAAA
1 AAAA
2302842 TTAATATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.64, C:0.24, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAACTC
Found at i:2303661 original size:33 final size:33
Alignment explanation
Indices: 2303619--2303685 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
2303609 AACTGCTTAA
2303619 GCTCGGAAATCATTGGCGAAAGACGATAGATCG
1 GCTCGGAAATCATTGGCGAAAGACGATAGATCG
2303652 GCTCGGAAATCATTGGCGAAAGACGATAGATCG
1 GCTCGGAAATCATTGGCGAAAGACGATAGATCG
2303685 G
1 G
2303686 ATTCGGAGCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.33, C:0.18, G:0.31, T:0.18
Consensus pattern (33 bp):
GCTCGGAAATCATTGGCGAAAGACGATAGATCG
Found at i:2306428 original size:18 final size:17
Alignment explanation
Indices: 2306395--2306433 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
2306385 TTGTATAAAT
2306395 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
2306413 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
2306430 TGTG
1 TGTG
2306434 GAAGGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:2306530 original size:76 final size:75
Alignment explanation
Indices: 2306438--2306586 Score: 280
Period size: 76 Copynumber: 2.0 Consensus size: 75
2306428 AATGTGGAAG
2306438 GAAAGTTGTTCATGAATTATTCAAGTGATAAAGTGTTGAAAATAAAGTGTTAAGTGTAAATTCCC
1 GAAAGTTGTTCATGAATTATTCAAGTGATAAAGTGTTGAAAATAAAGTGTTAAGTGTAAATTCCC
*
2306503 TTGTTGAACAT
66 -GGTTGAACAT
2306514 GAAAGTTGTTCATGAATTATTCAAGTGATAAAGTGTTGAAAATAAAGTGTTAAGTGTAAATTCCC
1 GAAAGTTGTTCATGAATTATTCAAGTGATAAAGTGTTGAAAATAAAGTGTTAAGTGTAAATTCCC
2306579 GGTTGAAC
66 GGTTGAAC
2306587 TTAGGAATAG
Statistics
Matches: 72, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
75 7 0.10
76 65 0.90
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.34
Consensus pattern (75 bp):
GAAAGTTGTTCATGAATTATTCAAGTGATAAAGTGTTGAAAATAAAGTGTTAAGTGTAAATTCCC
GGTTGAACAT
Found at i:2306762 original size:23 final size:23
Alignment explanation
Indices: 2306735--2306832 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
2306725 AGTGTTATTG
2306735 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
2306758 TTCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
2306781 -CCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
2306803 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
2306826 ATCAGTG
1 ATCAGTG
2306833 TGGCACTTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:2306801 original size:45 final size:45
Alignment explanation
Indices: 2306737--2306825 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
2306727 TGTTATTGAT
* *
2306737 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTTGGCTACATC
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
2306782 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
2306826 ATCAGTGTGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.19, C:0.22, G:0.27, T:0.31
Consensus pattern (45 bp):
CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
Found at i:2311055 original size:22 final size:22
Alignment explanation
Indices: 2311030--2311091 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
2311020 ATTTTTTTTA
2311030 AAATTTTTAATAATTTTAAATT
1 AAATTTTTAATAATTTTAAATT
* *
2311052 AAATGTTTAAT--GTTT-AATT
1 AAATTTTTAATAATTTTAAATT
* *
2311071 ATTATTTTTAATAATTGTAAA
1 A-AATTTTTAATAATTTTAAA
2311092 AGTTTAGTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
19 5 0.17
20 11 0.37
22 12 0.40
23 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (22 bp):
AAATTTTTAATAATTTTAAATT
Found at i:2316371 original size:26 final size:24
Alignment explanation
Indices: 2316330--2316397 Score: 84
Period size: 26 Copynumber: 2.8 Consensus size: 24
2316320 TGTATAAGAG
* *
2316330 TTTTAAAATGTTTAAAAATATTTATT
1 TTTTAAAAT-TTTAAAAATATGTA-A
2316356 TTTATAAAATTTTAAAAATATGTAA
1 TTT-TAAAATTTTAAAAATATGTAA
2316381 TTTT-AAATTTTAAAAAT
1 TTTTAAAATTTTAAAAAT
2316398 TCAAAATAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
23 13 0.33
24 1 0.03
25 3 0.08
26 16 0.41
27 6 0.15
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (24 bp):
TTTTAAAATTTTAAAAATATGTAA
Found at i:2316632 original size:14 final size:14
Alignment explanation
Indices: 2316607--2316649 Score: 56
Period size: 13 Copynumber: 3.2 Consensus size: 14
2316597 ACTTAATTCT
2316607 TTTGTA-AATTTTA
1 TTTGTATAATTTTA
2316620 TTTGTATAATTTTA
1 TTTGTATAATTTTA
2316634 -TT-TATAATTTATA
1 TTTGTATAATTT-TA
2316647 TTT
1 TTT
2316650 TTTTTCTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 8 0.30
13 10 0.37
14 9 0.33
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (14 bp):
TTTGTATAATTTTA
Found at i:2316682 original size:20 final size:21
Alignment explanation
Indices: 2316641--2316692 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 21
2316631 TTATTTATAA
*
2316641 TTTATATTTTTTTTCTAGA-T
1 TTTATATATTTTTTCTAGATT
2316661 TTTATATATTTTTTCT-GAATT
1 TTTATATATTTTTTCTAG-ATT
2316682 TTTATATATTT
1 TTTATATATTT
2316693 ATTTTTTTAC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 1 0.03
20 16 0.55
21 12 0.41
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.69
Consensus pattern (21 bp):
TTTATATATTTTTTCTAGATT
Found at i:2333186 original size:3 final size:3
Alignment explanation
Indices: 2333178--2333225 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
2333168 TCACTACCTG
2333178 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
2333226 AATGACTGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:2334824 original size:21 final size:22
Alignment explanation
Indices: 2334798--2334844 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
2334788 CTCTGCTCAA
*
2334798 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
2334819 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
2334841 ACTC
1 ACTC
2334845 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:2342748 original size:39 final size:40
Alignment explanation
Indices: 2342602--2342749 Score: 237
Period size: 40 Copynumber: 3.7 Consensus size: 40
2342592 TATTTGGATG
* *
2342602 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAACT
* *
2342642 ATATA-CGGGCTAAGTTCCGAAGGCATTTGTGCGAGTTACT
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAACT
2342682 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAACT
2342722 ATAACCGGGCT-AGTCCCGAAGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
2342750 AACAAGTAGC
Statistics
Matches: 101, Mismatches: 5, Indels: 5
0.91 0.05 0.05
Matches are distributed among these distances:
39 18 0.18
40 82 0.81
41 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAACT
Found at i:2352502 original size:13 final size:13
Alignment explanation
Indices: 2352484--2352513 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2352474 ATATTATATT
2352484 TATACACTGATAA
1 TATACACTGATAA
2352497 TATACACTGATAA
1 TATACACTGATAA
2352510 TATA
1 TATA
2352514 TAATTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (13 bp):
TATACACTGATAA
Found at i:2354260 original size:6 final size:6
Alignment explanation
Indices: 2354249--2354278 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
2354239 GAACATTGGT
2354249 CCCATC CCCATC CCCATC CCCATC CCCATC
1 CCCATC CCCATC CCCATC CCCATC CCCATC
2354279 TTCAACCAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.67, G:0.00, T:0.17
Consensus pattern (6 bp):
CCCATC
Found at i:2356394 original size:17 final size:17
Alignment explanation
Indices: 2356369--2356407 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
2356359 AATTTTTAAA
*
2356369 TCAAATAAATAATGGAT
1 TCAATTAAATAATGGAT
* *
2356386 TCAATTAAATTATTGAT
1 TCAATTAAATAATGGAT
2356403 TCAAT
1 TCAAT
2356408 CCATTGTATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (17 bp):
TCAATTAAATAATGGAT
Found at i:2362014 original size:22 final size:22
Alignment explanation
Indices: 2361962--2362015 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
2361952 TGAAATTATT
*
2361962 AATTAAAATATAATAACTATTA
1 AATTAAAATATAATAACTATAA
* * *
2361984 ATTTTAAATATAATTA-TATAAA
1 AATTAAAATATAATAACTAT-AA
2362006 AATTAAAATA
1 AATTAAAATA
2362016 GTTAACCACA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 3 0.12
22 22 0.88
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTAAAATATAATAACTATAA
Found at i:2362286 original size:25 final size:26
Alignment explanation
Indices: 2362258--2362311 Score: 83
Period size: 25 Copynumber: 2.1 Consensus size: 26
2362248 GGCAAACAAT
*
2362258 TTTTTATATTTAATATCTTTAAA-TA
1 TTTTTAAATTTAATATCTTTAAACTA
*
2362283 TTTTTAAATTTAATTTCTTTAAACTA
1 TTTTTAAATTTAATATCTTTAAACTA
2362309 TTT
1 TTT
2362312 AAATCAATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 21 0.81
26 5 0.19
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (26 bp):
TTTTTAAATTTAATATCTTTAAACTA
Found at i:2375239 original size:14 final size:14
Alignment explanation
Indices: 2375217--2375259 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
2375207 AGGTAAGTAA
2375217 TTAAAATATAATAT
1 TTAAAATATAATAT
* *
2375231 TTTAAATATAAATAA
1 TTAAAATAT-AATAT
2375246 TTAAAATATAATAT
1 TTAAAATATAATAT
2375260 GAGTTAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TTAAAATATAATAT
Found at i:2375244 original size:15 final size:15
Alignment explanation
Indices: 2375214--2375256 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
2375204 TTAAGGTAAG
2375214 TAATTAAAATAT-AA
1 TAATTAAAATATAAA
* *
2375228 TATTTTAAATATAAA
1 TAATTAAAATATAAA
2375243 TAATTAAAATATAA
1 TAATTAAAATATAA
2375257 TATGAGTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TAATTAAAATATAAA
Found at i:2382420 original size:54 final size:54
Alignment explanation
Indices: 2382337--2382445 Score: 155
Period size: 54 Copynumber: 2.0 Consensus size: 54
2382327 GATTTATAAG
* * *
2382337 TCAATCGATCTGACGCCTCTCTTAGATTGATACCTTGACTAATTCCCGATTCAA
1 TCAATCGATCTAACGCCTCTCTTAAATTGATACCTTGACTAATTCCCAATTCAA
* * * *
2382391 TCAATTGATCTAATGCCTCTTTTAAATTGATACCTTGACTAATTCTCAATTCAA
1 TCAATCGATCTAACGCCTCTCTTAAATTGATACCTTGACTAATTCCCAATTCAA
2382445 T
1 T
2382446 TGGCAAGTTC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.38
Consensus pattern (54 bp):
TCAATCGATCTAACGCCTCTCTTAAATTGATACCTTGACTAATTCCCAATTCAA
Found at i:2384450 original size:21 final size:21
Alignment explanation
Indices: 2384424--2384465 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2384414 AGGCAAAATA
2384424 CAATTTGACTTCTTGTACAGG
1 CAATTTGACTTCTTGTACAGG
2384445 CAATTTGACTTCTTGTACAGG
1 CAATTTGACTTCTTGTACAGG
2384466 ACCTACATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (21 bp):
CAATTTGACTTCTTGTACAGG
Found at i:2384824 original size:26 final size:26
Alignment explanation
Indices: 2384801--2384854 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
2384791 GACAAGTACT
*
2384801 AATTTGCTATTTTTTAATAGAGTAGC
1 AATTTACTATTTTTTAATAGAGTAGC
2384827 AATTTACTATTTTTTAATAGAGTAGC
1 AATTTACTATTTTTTAATAGAGTAGC
2384853 AA
1 AA
2384855 AATGCAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.44
Consensus pattern (26 bp):
AATTTACTATTTTTTAATAGAGTAGC
Found at i:2386203 original size:24 final size:24
Alignment explanation
Indices: 2386175--2386224 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
2386165 TTTCACATTA
* *
2386175 ATCATCCATTATTTTTAAAATAAC
1 ATCATCCATTATTTTAAAAAGAAC
2386199 ATCATCCATTATTTTAAAAAGAAC
1 ATCATCCATTATTTTAAAAAGAAC
2386223 AT
1 AT
2386225 AATGTAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.44, C:0.16, G:0.02, T:0.38
Consensus pattern (24 bp):
ATCATCCATTATTTTAAAAAGAAC
Found at i:2386659 original size:16 final size:15
Alignment explanation
Indices: 2386640--2386670 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
2386630 TGTAATTATA
2386640 TTTTTTCCGAATTTTC
1 TTTTTTCC-AATTTTC
2386656 TTTTTTCCAATTTTC
1 TTTTTTCCAATTTTC
2386671 AAATTCTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.13, C:0.19, G:0.03, T:0.65
Consensus pattern (15 bp):
TTTTTTCCAATTTTC
Found at i:2387723 original size:42 final size:42
Alignment explanation
Indices: 2387663--2387785 Score: 149
Period size: 42 Copynumber: 2.9 Consensus size: 42
2387653 CGCTTTACTT
*
2387663 AGTTTAATTTTTGAATTCGAAGTAAGGTTAATAGTATGTTTC
1 AGTTTAATTTTTGAATTCGAAGTAAGATTAATAGTATGTTTC
* ** **
2387705 AGTTTACTTTTTTTATTCGAAGTAAGATTCTTAGTATGTTTC
1 AGTTTAATTTTTGAATTCGAAGTAAGATTAATAGTATGTTTC
* * *
2387747 AGTTTAATTTTCGGATT-GCAAGTAAGATTAATAATATGT
1 AGTTTAATTTTTGAATTCG-AAGTAAGATTAATAGTATGT
2387786 GTGATTAAAT
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
41 1 0.01
42 66 0.99
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (42 bp):
AGTTTAATTTTTGAATTCGAAGTAAGATTAATAGTATGTTTC
Found at i:2387992 original size:42 final size:42
Alignment explanation
Indices: 2387933--2388015 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
2387923 CTTAGTTCTA
*
2387933 TTTTTGGATTCGAAGTAAGATTAATAGTATGTTTCAGTTTAC
1 TTTTTGGATTCGAAGTAAGATTAAGAGTATGTTTCAGTTTAC
* *
2387975 TTTTTGGATTCGAAGTAAGATTTAGAGTATGTTTCGGTTTA
1 TTTTTGGATTCGAAGTAAGATTAAGAGTATGTTTCAGTTTA
2388016 TATTTGATCA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.27, C:0.06, G:0.22, T:0.46
Consensus pattern (42 bp):
TTTTTGGATTCGAAGTAAGATTAAGAGTATGTTTCAGTTTAC
Found at i:2388140 original size:96 final size:96
Alignment explanation
Indices: 2387970--2388228 Score: 267
Period size: 96 Copynumber: 2.7 Consensus size: 96
2387960 TATGTTTCAG
* * * * *
2387970 TTTACTTTTTGGATTCGAAGTAAGATTTA-GAGTATGTTTCGGTTTATATTTGATCAAATT-CCT
1 TTTAATTTTTGGATTTGAAGTAAGATTCATGA-TATG-TTC--TTT-TGTTTGATTAAATTACCT
** * * *
2388033 CATAG--TT-CATTTCTGTATGTATTCGTTATTTAG
61 CATAGCTTTACATTTCTACATGTACTCGTTACTTAA
* * *
2388066 TTTAATTTTTGGATTTGAAGTAAGATTCATGATATGTTCTTTTGTTTGATTAAGTTATCTCGTAG
1 TTTAATTTTTGGATTTGAAGTAAGATTCATGATATGTTCTTTTGTTTGATTAAATTACCTCATAG
* * *
2388131 CTTTACATTTCTACATTTCCTCTTTACTTAA
66 CTTTACATTTCTACATGTACTCGTTACTTAA
* * *
2388162 TTTAATTTTTTGATTTGATGTAAGATTCATGATATTTTCTTTTGTTTGATTAAATTACCTCATAG
1 TTTAATTTTTGGATTTGAAGTAAGATTCATGATATGTTCTTTTGTTTGATTAAATTACCTCATAG
2388227 CT
66 CT
2388229 CTTCGTTTCC
Statistics
Matches: 136, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
92 11 0.08
93 9 0.07
95 5 0.04
96 109 0.80
97 2 0.01
ACGTcount: A:0.24, C:0.11, G:0.14, T:0.51
Consensus pattern (96 bp):
TTTAATTTTTGGATTTGAAGTAAGATTCATGATATGTTCTTTTGTTTGATTAAATTACCTCATAG
CTTTACATTTCTACATGTACTCGTTACTTAA
Found at i:2388245 original size:96 final size:96
Alignment explanation
Indices: 2388066--2388255 Score: 283
Period size: 96 Copynumber: 2.0 Consensus size: 96
2388056 CGTTATTTAG
* * *
2388066 TTTAATTTTTGGATTTGAAGTAAGATTCATGATATGTTCTTTTGTTTGATTAAGTTATCTCGTAG
1 TTTAATTTTTGGATTTGAAGTAAGATTCATGATATGTTCTTTTGTTTGATTAAATTACCTCATAG
*
2388131 CTTTACATTTCTACATTTCCTCTTTACTTAA
66 CTTTACATTTCCACATTTCCTCTTTACTTAA
* * *
2388162 TTTAATTTTTTGATTTGATGTAAGATTCATGATATTTTCTTTTGTTTGATTAAATTACCTCATAG
1 TTTAATTTTTGGATTTGAAGTAAGATTCATGATATGTTCTTTTGTTTGATTAAATTACCTCATAG
* *
2388227 CTCTT-CGTTTCCATATTTCCTCTTTACTT
66 CT-TTACATTTCCACATTTCCTCTTTACTT
2388256 TGGTGTTCTT
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
96 82 0.98
97 2 0.02
ACGTcount: A:0.23, C:0.14, G:0.11, T:0.53
Consensus pattern (96 bp):
TTTAATTTTTGGATTTGAAGTAAGATTCATGATATGTTCTTTTGTTTGATTAAATTACCTCATAG
CTTTACATTTCCACATTTCCTCTTTACTTAA
Found at i:2394461 original size:16 final size:16
Alignment explanation
Indices: 2394422--2394472 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
2394412 ATTCTTTTAG
2394422 TAATATTTAATT-TTAAT
1 TAAT-TTTAATTATT-AT
2394439 TATATTTTAATTATTAT
1 TA-ATTTTAATTATTAT
2394456 TAATTTCT-ATTATTAT
1 TAATTT-TAATTATTAT
2394472 T
1 T
2394473 TTAGGAAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
16 13 0.42
17 14 0.45
18 4 0.13
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (16 bp):
TAATTTTAATTATTAT
Found at i:2394519 original size:18 final size:17
Alignment explanation
Indices: 2394495--2394542 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
2394485 ACATGTTGAA
2394495 TAATTATATTTTAAT-TT
1 TAATTAT-TTTTAATATT
*
2394512 TAAATTATTTTTTACTATT
1 T-AATTA-TTTTTAATATT
2394531 TAATTATTTTTA
1 TAATTATTTTTA
2394543 GTTGAAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 7 0.26
18 16 0.59
19 4 0.15
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (17 bp):
TAATTATTTTTAATATT
Found at i:2397334 original size:20 final size:20
Alignment explanation
Indices: 2397309--2397350 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
2397299 AAAAAATTAA
2397309 ATTATTTTTTAAACGAAAAT
1 ATTATTTTTTAAACGAAAAT
2397329 ATTATTTTTTAAACGAAAAT
1 ATTATTTTTTAAACGAAAAT
2397349 AT
1 AT
2397351 AAAGTAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (20 bp):
ATTATTTTTTAAACGAAAAT
Found at i:2402864 original size:21 final size:22
Alignment explanation
Indices: 2402840--2402886 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
2402830 AATCACACCT
*
2402840 AAATCAAAATA-AATATGAACA
1 AAATCAAAATATAATATGAAAA
* *
2402861 AAATCCACATATAATATGAAAA
1 AAATCAAAATATAATATGAAAA
2402883 AAAT
1 AAAT
2402887 GATCTACATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.64, C:0.11, G:0.04, T:0.21
Consensus pattern (22 bp):
AAATCAAAATATAATATGAAAA
Found at i:2403927 original size:7 final size:6
Alignment explanation
Indices: 2403909--2403938 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
2403899 ACTTGACATT
2403909 ATAAAA ATAAAA ATAAAA ATAAAA ACTAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA A-TAAA
2403939 TTTTGTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.83
7 4 0.17
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (6 bp):
ATAAAA
Found at i:2407224 original size:17 final size:17
Alignment explanation
Indices: 2407200--2407233 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2407190 ATTCATTGAC
2407200 CTAACCAATTC-AAAAA
1 CTAACCAATTCTAAAAA
2407216 CTAATCCAATTCTAAAAA
1 CTAA-CCAATTCTAAAAA
2407234 TTTTGATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 7 0.44
18 5 0.31
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.24
Consensus pattern (17 bp):
CTAACCAATTCTAAAAA
Found at i:2408564 original size:23 final size:23
Alignment explanation
Indices: 2408520--2408573 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
2408510 ATCAACAAAT
* **
2408520 TTAATAAAAGAATTTTTGCAGTA
1 TTAACAAAAGAATTTTAACAGTA
2408543 TTAACAAAAGAATTTTAACAGTA
1 TTAACAAAAGAATTTTAACAGTA
*
2408566 TGAACAAA
1 TTAACAAA
2408574 TTGACCTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.50, C:0.07, G:0.11, T:0.31
Consensus pattern (23 bp):
TTAACAAAAGAATTTTAACAGTA
Found at i:2411619 original size:34 final size:33
Alignment explanation
Indices: 2411556--2411691 Score: 87
Period size: 36 Copynumber: 3.9 Consensus size: 33
2411546 ACACAATATG
* *
2411556 GTATTTAAAATATATATATATGTATATATAATA
1 GTATTTAAAATATATACATAAGTATATATAATA
*
2411589 GTATTTAAGAATATATACATAAGATGATATAAAATA
1 GTATTTAA-AATATATACATAAG-T-ATATATAATA
* ** * * * *
2411625 CATACATAGAATAGTATA-AGAAATATATAACTAATG
1 -GTATTTAAAATA-TATACATAAGTATAT-A-TAATA
*
2411661 GTATTAAAAAATATATACATAA-TATATATAA
1 GTATT-TAAAATATATACATAAGTATATATAA
2411692 AATACATATA
Statistics
Matches: 77, Mismatches: 17, Indels: 18
0.69 0.15 0.16
Matches are distributed among these distances:
33 11 0.14
34 17 0.22
35 14 0.18
36 27 0.35
37 8 0.10
ACGTcount: A:0.53, C:0.04, G:0.08, T:0.35
Consensus pattern (33 bp):
GTATTTAAAATATATACATAAGTATATATAATA
Found at i:2411695 original size:11 final size:11
Alignment explanation
Indices: 2411668--2411710 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
2411658 ATGGTATTAA
*
2411668 AAAATATATAC
1 AAAATATATAT
*
2411679 ATAATATATAT
1 AAAATATATAT
*
2411690 AAAATACATAT
1 AAAATATATAT
*
2411701 AATATATATA
1 AAAATATATA
2411711 CGTATTAGAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (11 bp):
AAAATATATAT
Found at i:2412859 original size:17 final size:17
Alignment explanation
Indices: 2412817--2412864 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
2412807 TTTCTTGATT
*
2412817 TTTTTTTTTGAGTTAGG
1 TTTTTTTTTGGGTTAGG
*
2412834 ATTTTTTTTGGGTTAGG
1 TTTTTTTTTGGGTTAGG
*
2412851 TTTTTTTTTTGGTT
1 TTTTTTTTTGGGTT
2412865 TAATAGGCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.08, C:0.00, G:0.23, T:0.69
Consensus pattern (17 bp):
TTTTTTTTTGGGTTAGG
Found at i:2413142 original size:16 final size:17
Alignment explanation
Indices: 2413120--2413163 Score: 65
Period size: 15 Copynumber: 2.7 Consensus size: 17
2413110 CCATTAAACT
2413120 CCCCAAAAAAAACCTAA
1 CCCCAAAAAAAACCTAA
*
2413137 -CCC-AAAAAAATCTAA
1 CCCCAAAAAAAACCTAA
2413152 CCCCAAAAAAAA
1 CCCCAAAAAAAA
2413164 ATCAAAAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 11 0.46
16 6 0.25
17 7 0.29
ACGTcount: A:0.61, C:0.32, G:0.00, T:0.07
Consensus pattern (17 bp):
CCCCAAAAAAAACCTAA
Found at i:2413145 original size:15 final size:16
Alignment explanation
Indices: 2413120--2413162 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
2413110 CCATTAAACT
2413120 CCCCAAAAAAAACCTAA
1 CCCC-AAAAAAACCTAA
*
2413137 -CCCAAAAAAATCTAA
1 CCCCAAAAAAACCTAA
2413152 CCCCAAAAAAA
1 CCCCAAAAAAA
2413163 AATCAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.60, C:0.33, G:0.00, T:0.07
Consensus pattern (16 bp):
CCCCAAAAAAACCTAA
Found at i:2414296 original size:11 final size:11
Alignment explanation
Indices: 2414272--2414314 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
2414262 TTCTAATACG
*
2414272 TATATATATTA
1 TATATATTTTA
*
2414283 TATGTATTTTA
1 TATATATTTTA
* *
2414294 TATATATTATG
1 TATATATTTTA
2414305 TATATATTTT
1 TATATATTTT
2414315 TTAATGCCAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (11 bp):
TATATATTTTA
Found at i:2415702 original size:8 final size:8
Alignment explanation
Indices: 2415668--2415719 Score: 52
Period size: 8 Copynumber: 6.5 Consensus size: 8
2415658 TAGTGATGTG
*
2415668 AATAATAA
1 AATATTAA
*
2415676 AGTATATAA
1 AATAT-TAA
2415685 AATA-TAA
1 AATATTAA
2415692 AATATTAA
1 AATATTAA
*
2415700 AATATCAA
1 AATATTAA
*
2415708 AATATTAG
1 AATATTAA
2415716 AATA
1 AATA
2415720 ATAATAATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
7 7 0.19
8 23 0.64
9 6 0.17
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:2415709 original size:16 final size:15
Alignment explanation
Indices: 2415672--2415719 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
2415662 GATGTGAATA
*
2415672 ATAAAGTATATAAAAT
1 ATAAAATAT-TAAAAT
2415688 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
2415703 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
2415719 A
1 A
2415720 ATAATAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 8 0.28
16 21 0.72
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:2415780 original size:21 final size:20
Alignment explanation
Indices: 2415738--2415790 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
2415728 TAATATTGAC
2415738 AAATAAAAA-AATAAAATAG
1 AAATAAAAATAATAAAATAG
* *
2415757 AAATAAAAATATATATATTAG
1 AAATAAAAATA-ATAAAATAG
*
2415778 AAATAATAATAAT
1 AAATAAAAATAAT
2415791 GTTTAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 9 0.31
20 3 0.10
21 17 0.59
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (20 bp):
AAATAAAAATAATAAAATAG
Found at i:2415919 original size:22 final size:24
Alignment explanation
Indices: 2415860--2416008 Score: 79
Period size: 25 Copynumber: 5.9 Consensus size: 24
2415850 GTGATAATAT
* *
2415860 TAAAAATATGTACATAATATAGTG
1 TAAAAATATATACATAATATAATG
*
2415884 TAAAAAATACATACATAATATAAT-
1 T-AAAAATATATACATAATATAATG
*
2415908 T-AAAATATATACATAAGATAACATG
1 TAAAAATATATACATAATAT-A-ATG
* *
2415933 TAGAAAAAAAAATATAAATAATATAGTAT-
1 T----AAAAATATATACATAATATA--ATG
* * * *
2415962 TAAAGATATATACATAAAATAGTA
1 TAAAAATATATACATAATATAATG
* *
2415986 TAATATATATATACGTAATATAA
1 TAA-AAATATATACATAATATAA
2416009 AATTTAGAAT
Statistics
Matches: 95, Mismatches: 18, Indels: 23
0.70 0.13 0.17
Matches are distributed among these distances:
22 16 0.17
23 2 0.02
24 7 0.07
25 51 0.54
29 2 0.02
30 17 0.18
ACGTcount: A:0.58, C:0.05, G:0.07, T:0.31
Consensus pattern (24 bp):
TAAAAATATATACATAATATAATG
Found at i:2415972 original size:25 final size:24
Alignment explanation
Indices: 2415943--2416073 Score: 85
Period size: 25 Copynumber: 5.5 Consensus size: 24
2415933 TAGAAAAAAA
* *
2415943 AATATAAATAATATAGTATTAAAG
1 AATATACATAATATAATATTAAAG
* * *
2415967 ATATATACATAAAATAGTA-TAATAT
1 A-ATATACATAATATAATATTAA-AG
* * *
2415992 ATATATACGTAATATAAAATT-TAG
1 A-ATATACATAATATAATATTAAAG
* *
2416016 AATATACCTAATAT-AT-TAAAAG
1 AATATACATAATATAATATTAAAG
*
2416038 AATATATATAATATAATATT-AAG
1 AATATACATAATATAATATTAAAG
2416061 AAATATA-ATAATA
1 -AATATACATAATA
2416074 ACAAAAAAAA
Statistics
Matches: 84, Mismatches: 16, Indels: 15
0.73 0.14 0.13
Matches are distributed among these distances:
21 1 0.01
22 15 0.18
23 23 0.27
24 13 0.15
25 31 0.37
26 1 0.01
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.35
Consensus pattern (24 bp):
AATATACATAATATAATATTAAAG
Found at i:2416066 original size:22 final size:22
Alignment explanation
Indices: 2416001--2416073 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 22
2415991 TATATATACG
* *
2416001 TAATATAAAATTTAG-AATATA
1 TAATATAATATTAAGAAATATA
* *
2416022 CCTAATATATTA-AAAGAATATATA
1 --TAATATAATATTAAGAA-ATATA
2416046 TAATATAATATTAAGAAATATAA
1 TAATATAATATTAAGAAATAT-A
2416069 TAATA
1 TAATA
2416074 ACAAAAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
22 15 0.38
23 20 0.50
24 5 0.12
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.36
Consensus pattern (22 bp):
TAATATAATATTAAGAAATATA
Found at i:2416482 original size:15 final size:14
Alignment explanation
Indices: 2416462--2416512 Score: 57
Period size: 15 Copynumber: 3.5 Consensus size: 14
2416452 CCCCCCCCCC
2416462 CAAAAAAACCTTCTT
1 CAAAAAAACCTTC-T
**
2416477 CAAAAAAAAATTCT
1 CAAAAAAACCTTCT
*
2416491 CAAAAAAAACCTCCT
1 C-AAAAAAACCTTCT
2416506 CAAAAAA
1 CAAAAAA
2416513 CCCCAATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
14 8 0.27
15 22 0.73
ACGTcount: A:0.59, C:0.24, G:0.00, T:0.18
Consensus pattern (14 bp):
CAAAAAAACCTTCT
Found at i:2418268 original size:32 final size:33
Alignment explanation
Indices: 2418227--2418299 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 33
2418217 CAGTTTTCCT
2418227 AAAATATTTT-CA-AGAAATC-TGCCAAACAACAG
1 AAAATATTTTACACAG-AATCAT-CCAAACAACAG
* *
2418259 AAAATATTTTACACAGATTCATCCAAACACCAG
1 AAAATATTTTACACAGAATCATCCAAACAACAG
2418292 AAAATATT
1 AAAATATT
2418300 AACTTTTCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
32 10 0.28
33 23 0.64
34 3 0.08
ACGTcount: A:0.49, C:0.19, G:0.07, T:0.25
Consensus pattern (33 bp):
AAAATATTTTACACAGAATCATCCAAACAACAG
Found at i:2420796 original size:4 final size:4
Alignment explanation
Indices: 2420789--2420817 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
2420779 TACACTTATG
2420789 TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
2420818 AAATTTGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:2424929 original size:11 final size:11
Alignment explanation
Indices: 2424913--2424937 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2424903 TATTTCACTT
2424913 TCATATCATAA
1 TCATATCATAA
2424924 TCATATCATAA
1 TCATATCATAA
2424935 TCA
1 TCA
2424938 CATGTAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.20, G:0.00, T:0.36
Consensus pattern (11 bp):
TCATATCATAA
Found at i:2425722 original size:27 final size:28
Alignment explanation
Indices: 2425691--2425743 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
2425681 TAAAATTCTA
*
2425691 ATTCAATTGATTTA-ATTATTTTTTTCG
1 ATTCAATTGATTTATATTAATTTTTTCG
2425718 ATTCAATTGATTTATATTAATTTTTT
1 ATTCAATTGATTTATATTAATTTTTT
2425744 GGTCAATCGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 14 0.58
28 10 0.42
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.60
Consensus pattern (28 bp):
ATTCAATTGATTTATATTAATTTTTTCG
Found at i:2425749 original size:26 final size:27
Alignment explanation
Indices: 2425693--2425755 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
2425683 AAATTCTAAT
* *
2425693 TCAATTGATTTAATTATTTTTTTCGAT
1 TCAATTGATTTAATTAATTTTTTCGAG
2425720 TCAATTGATTTATATTAATTTTTT-G-G
1 TCAATTGATTTA-ATTAATTTTTTCGAG
*
2425746 TCAATCGATT
1 TCAATTGATT
2425756 AAATACCCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 9 0.28
27 13 0.41
28 10 0.31
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.56
Consensus pattern (27 bp):
TCAATTGATTTAATTAATTTTTTCGAG
Found at i:2444323 original size:21 final size:21
Alignment explanation
Indices: 2444297--2444340 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2444287 CTAGTTTTCT
*
2444297 TTTTTTTAATTA-TTATTATAA
1 TTTTTTTAATAATTTATT-TAA
2444318 TTTTTTTAATAATTTATTTAA
1 TTTTTTTAATAATTTATTTAA
2444339 TT
1 TT
2444341 AAAATCGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTTTTTAATAATTTATTTAA
Found at i:2444621 original size:7 final size:7
Alignment explanation
Indices: 2444609--2444641 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
2444599 TCTTTCAAAT
2444609 TTTTAAA
1 TTTTAAA
2444616 TTTTAAA
1 TTTTAAA
2444623 TTTTAAA
1 TTTTAAA
*
2444630 -TTTAAT
1 TTTTAAA
2444636 TTTTAA
1 TTTTAA
2444642 CATCATTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (7 bp):
TTTTAAA
Found at i:2444639 original size:13 final size:14
Alignment explanation
Indices: 2444606--2444641 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
2444596 TAATCTTTCA
2444606 AATTTTTAAATTTT
1 AATTTTTAAATTTT
*
2444620 AAATTTTAAA-TTT
1 AATTTTTAAATTTT
2444633 AATTTTTAA
1 AATTTTTAA
2444642 CATCATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
AATTTTTAAATTTT
Found at i:2449049 original size:22 final size:22
Alignment explanation
Indices: 2449001--2449049 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2448991 TCTAACTCGA
* **
2449001 ATTTTTCTACTATTTTCTTGTT
1 ATTTTCCTACTATTTTCTCATT
*
2449023 GTTTTCCTACTATTTTCTCATT
1 ATTTTCCTACTATTTTCTCATT
2449045 ATTTT
1 ATTTT
2449050 GTTATTATTG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.14, C:0.16, G:0.04, T:0.65
Consensus pattern (22 bp):
ATTTTCCTACTATTTTCTCATT
Found at i:2451232 original size:13 final size:13
Alignment explanation
Indices: 2451182--2451234 Score: 54
Period size: 13 Copynumber: 4.1 Consensus size: 13
2451172 AGTTTGGCAA
*
2451182 TGCTTTTGAAAAA
1 TGCTTTTGAAAAG
* *
2451195 CGCTTTTGAAGAG
1 TGCTTTTGAAAAG
*
2451208 TGC-TGTGAAAAAG
1 TGCTTTTG-AAAAG
2451221 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
2451234 T
1 T
2451235 TTGGTTTAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
12 3 0.10
13 25 0.81
14 3 0.10
ACGTcount: A:0.32, C:0.09, G:0.25, T:0.34
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:2452704 original size:19 final size:19
Alignment explanation
Indices: 2452669--2452738 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 19
2452659 GAAAAAAATA
**
2452669 AATAATTTTTATGTTTTTT
1 AATAATTTTTAAATTTTTT
**
2452688 AATAATTTTTAAATTTTAAA
1 AATAATTTTTAAATTTT-TT
*
2452708 AATATTTTTTAAATTTTTT
1 AATAATTTTTAAATTTTTT
*
2452727 AA-ATTTTTTAAA
1 AATAATTTTTAAA
2452739 ACTTAATTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
18 10 0.23
19 17 0.40
20 16 0.37
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (19 bp):
AATAATTTTTAAATTTTTT
Found at i:2452723 original size:9 final size:9
Alignment explanation
Indices: 2452682--2452738 Score: 60
Period size: 9 Copynumber: 6.0 Consensus size: 9
2452672 AATTTTTATG
2452682 TTTTTTAATA
1 TTTTTTAA-A
*
2452692 ATTTTTAAA
1 TTTTTTAAA
**
2452701 TTTTAAAAATA
1 TTTT-TTAA-A
2452712 TTTTTTAAA
1 TTTTTTAAA
2452721 TTTTTTAAA
1 TTTTTTAAA
2452730 TTTTTTAAA
1 TTTTTTAAA
2452739 ACTTAATTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
9 23 0.59
10 11 0.28
11 5 0.13
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:2452730 original size:20 final size:20
Alignment explanation
Indices: 2452667--2452738 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
2452657 GTGAAAAAAA
**
2452667 TAAATAATTTTTATGTTTTT
1 TAAATAATTTTTAAATTTTT
*
2452687 T-AATAATTTTTAAATTTTA
1 TAAATAATTTTTAAATTTTT
* *
2452706 AAAATATTTTTTAAATTTTT
1 TAAATAATTTTTAAATTTTT
2452726 TAAAT--TTTTTAAA
1 TAAATAATTTTTAAA
2452739 ACTTAATTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
18 8 0.18
19 15 0.34
20 21 0.48
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (20 bp):
TAAATAATTTTTAAATTTTT
Found at i:2456206 original size:21 final size:21
Alignment explanation
Indices: 2456180--2456220 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2456170 ATCTGCTCAA
* *
2456180 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
2456201 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
2456221 TAGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:2460746 original size:30 final size:30
Alignment explanation
Indices: 2460712--2460771 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
2460702 TATTTTATTA
*
2460712 TTAATTTTGTTATTATTTTAAAGGCATTTG
1 TTAATTTAGTTATTATTTTAAAGGCATTTG
* *
2460742 TTAATTTAGTTATTATTTTACAGGTATTTG
1 TTAATTTAGTTATTATTTTAAAGGCATTTG
2460772 CTTGTTAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.27, C:0.03, G:0.13, T:0.57
Consensus pattern (30 bp):
TTAATTTAGTTATTATTTTAAAGGCATTTG
Found at i:2461672 original size:16 final size:15
Alignment explanation
Indices: 2461653--2461692 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
2461643 TAATTTTTAC
*
2461653 AATTTTTGTTTTTTGT
1 AATTTTTATTTTTT-T
*
2461669 AATTTATATTTTTTT
1 AATTTTTATTTTTTT
2461684 AATTTTTAT
1 AATTTTTAT
2461693 AAAATTTGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (15 bp):
AATTTTTATTTTTTT
Found at i:2465741 original size:21 final size:19
Alignment explanation
Indices: 2465715--2465754 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
2465705 CATAATATCC
*
2465715 TATTTAACATATATATTTTAT
1 TATTTAAAAT-TAT-TTTTAT
2465736 TATTTAAAATTATTTTTAT
1 TATTTAAAATTATTTTTAT
2465755 AATAATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 3 0.17
21 9 0.50
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTTAAAATTATTTTTAT
Found at i:2472635 original size:5 final size:5
Alignment explanation
Indices: 2472625--2472652 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
2472615 TAGTAAACTA
2472625 ATAAT ATAAT ATAAT ATAAT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATA
2472653 GGTAATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:2473191 original size:22 final size:22
Alignment explanation
Indices: 2473142--2473198 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
2473132 AGAAATGAGT
*
2473142 AAAAATAATATACATAATAATA
1 AAAAATATTATACATAATAATA
* *
2473164 AGAAATATTATA-ATAAGTACTA
1 AAAAATATTATACATAA-TAATA
2473186 AAAAATATCTATA
1 AAAAATAT-TATA
2473199 TTTATATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 4 0.14
22 21 0.72
23 4 0.14
ACGTcount: A:0.61, C:0.05, G:0.04, T:0.30
Consensus pattern (22 bp):
AAAAATATTATACATAATAATA
Found at i:2474557 original size:16 final size:16
Alignment explanation
Indices: 2474538--2474595 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
2474528 TAGATTGTAA
2474538 TGGGTTTAGGGGTATT
1 TGGGTTTAGGGGTATT
*** **
2474554 TGGGTTTTATTTGTAAA
1 TGGG-TTTAGGGGTATT
*
2474571 TAGGTTTAGGGGTATT
1 TGGGTTTAGGGGTATT
2474587 TGGGTTTAG
1 TGGGTTTAG
2474596 AGGTTGTTTA
Statistics
Matches: 29, Mismatches: 12, Indels: 2
0.67 0.28 0.05
Matches are distributed among these distances:
16 19 0.66
17 10 0.34
ACGTcount: A:0.17, C:0.00, G:0.36, T:0.47
Consensus pattern (16 bp):
TGGGTTTAGGGGTATT
Found at i:2474578 original size:33 final size:32
Alignment explanation
Indices: 2474532--2474593 Score: 106
Period size: 33 Copynumber: 1.9 Consensus size: 32
2474522 ATGGGTTAGA
*
2474532 TTGTAATGGGTTTAGGGGTATTTGGGTTTTAT
1 TTGTAATAGGTTTAGGGGTATTTGGGTTTTAT
2474564 TTGTAAATAGGTTTAGGGGTATTTGGGTTT
1 TTGT-AATAGGTTTAGGGGTATTTGGGTTT
2474594 AGAGGTTGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 4 0.14
33 24 0.86
ACGTcount: A:0.18, C:0.00, G:0.34, T:0.48
Consensus pattern (32 bp):
TTGTAATAGGTTTAGGGGTATTTGGGTTTTAT
Found at i:2475269 original size:21 final size:22
Alignment explanation
Indices: 2475227--2475270 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
2475217 CGATTATGTC
* *
2475227 AATTAATTCATTTTATTATTAA
1 AATTAATTAATTTAATTATTAA
*
2475249 AATT-ATTAATTTAATTGTTAA
1 AATTAATTAATTTAATTATTAA
2475270 A
1 A
2475271 TAATATATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (22 bp):
AATTAATTAATTTAATTATTAA
Found at i:2475922 original size:11 final size:11
Alignment explanation
Indices: 2475908--2475960 Score: 63
Period size: 11 Copynumber: 4.7 Consensus size: 11
2475898 AAGAGAAAAA
*
2475908 AAGAATAAGAG
1 AAGAAGAAGAG
2475919 AAGAA-ACAGAG
1 AAGAAGA-AGAG
2475930 AAGAAGAAGAAG
1 AAGAAGAAG-AG
*
2475942 AAGAAGAGGAG
1 AAGAAGAAGAG
2475953 AAGAAGAA
1 AAGAAGAA
2475961 ATAAGAGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
10 1 0.03
11 25 0.68
12 11 0.30
ACGTcount: A:0.64, C:0.02, G:0.32, T:0.02
Consensus pattern (11 bp):
AAGAAGAAGAG
Found at i:2475923 original size:3 final size:3
Alignment explanation
Indices: 2475890--2475960 Score: 55
Period size: 3 Copynumber: 25.3 Consensus size: 3
2475880 CTTGGACAGT
* * *
2475890 AGA AGA AAA AG- AGA A-A AAA AGA ATA AG- AGA AGA A-A CAG- AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA -AGA AGA
*
2475931 AGA AGA AGA AGA AGA AG- AGG AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
2475961 ATAAGAGAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
2 11 0.20
3 44 0.80
ACGTcount: A:0.68, C:0.01, G:0.30, T:0.01
Consensus pattern (3 bp):
AGA
Found at i:2478806 original size:21 final size:21
Alignment explanation
Indices: 2478782--2478822 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2478772 ATCTGCTCAA
* *
2478782 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
2478803 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
2478823 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:2482466 original size:21 final size:21
Alignment explanation
Indices: 2482442--2482481 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2482432 CTACGTGGCA
2482442 AGTTAACTGGCCACGTCAGCT
1 AGTTAACTGGCCACGTCAGCT
* *
2482463 AGTTAACTTGCCATGTCAG
1 AGTTAACTGGCCACGTCAG
2482482 TGCTCCTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (21 bp):
AGTTAACTGGCCACGTCAGCT
Found at i:2484824 original size:24 final size:24
Alignment explanation
Indices: 2484788--2484835 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
2484778 CATGTCAGGG
2484788 AAAGCGCGCCGAGCTGTACATGTT
1 AAAGCGCGCCGAGCTGTACATGTT
*
2484812 AAAGCGCGTCGAGCTGTACATGTT
1 AAAGCGCGCCGAGCTGTACATGTT
2484836 TTCTTTGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.25, C:0.23, G:0.29, T:0.23
Consensus pattern (24 bp):
AAAGCGCGCCGAGCTGTACATGTT
Found at i:2487791 original size:23 final size:24
Alignment explanation
Indices: 2487761--2487807 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
2487751 GAATATACTT
*
2487761 TAAAAATA-ATATTTTTTAAAAAA
1 TAAAAATACATAATTTTTAAAAAA
2487784 TAAAAATACTATAATTTTTAAAAA
1 TAAAAATAC-ATAATTTTTAAAAA
2487808 GAAATTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.38
25 13 0.62
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (24 bp):
TAAAAATACATAATTTTTAAAAAA
Found at i:2490133 original size:24 final size:23
Alignment explanation
Indices: 2490106--2490155 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
2490096 ATTATATTAA
*
2490106 AAAATAAAATTATT-TAAATTTTAG
1 AAAA-AAAATAATTATAAATTTT-G
*
2490130 AAAAGAAATAATTATAAATTTTG
1 AAAAAAAATAATTATAAATTTTG
2490153 AAA
1 AAA
2490156 TAATTAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (23 bp):
AAAAAAAATAATTATAAATTTTG
Found at i:2490138 original size:23 final size:23
Alignment explanation
Indices: 2490112--2490155 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2490102 TTAAAAAATA
*
2490112 AAATTATT-TAAATTTTAGAAAAG
1 AAATAATTATAAATTTT-GAAAAG
2490135 AAATAATTATAAATTTTGAAA
1 AAATAATTATAAATTTTGAAA
2490156 TAATTAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.39
Consensus pattern (23 bp):
AAATAATTATAAATTTTGAAAAG
Found at i:2491382 original size:24 final size:24
Alignment explanation
Indices: 2491346--2491393 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
2491336 CAAAGCCTCG
*
2491346 CTCTTCACGTTGGGTTTGTTCTAC
1 CTCTTCACCTTGGGTTTGTTCTAC
2491370 CTCTTCACCTTGGGTTTGTTCTAC
1 CTCTTCACCTTGGGTTTGTTCTAC
2491394 TTGTTCGGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.08, C:0.27, G:0.19, T:0.46
Consensus pattern (24 bp):
CTCTTCACCTTGGGTTTGTTCTAC
Done.