Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 173 of 313
Found at i:53775091 original size:26 final size:26
Alignment explanation
Indices: 53775062--53775120 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 26
53775052 CTATAAGGTA
*
53775062 AAATGACCATAATGCCCTTAGAGGGT
1 AAATGACCATAATGCCCCTAGAGGGT
** ** *
53775088 AAATGAATATTTTGCCCCTCGAGGGT
1 AAATGACCATAATGCCCCTAGAGGGT
53775114 AAATGAC
1 AAATGAC
53775121 TGATTTGTGC
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (26 bp):
AAATGACCATAATGCCCCTAGAGGGT
Found at i:53779155 original size:21 final size:22
Alignment explanation
Indices: 53779130--53779176 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
53779120 ATACTATATA
*
53779130 TTATAAAATATA-TATA-TTTAT
1 TTATAAAAAATATTATAGTTT-T
53779151 TTATAAAAAATATTATAGTTTT
1 TTATAAAAAATATTATAGTTTT
53779173 TTAT
1 TTAT
53779177 CATAACTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 11 0.48
22 9 0.39
23 3 0.13
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
TTATAAAAAATATTATAGTTTT
Found at i:53782442 original size:54 final size:53
Alignment explanation
Indices: 53782341--53782550 Score: 203
Period size: 54 Copynumber: 3.9 Consensus size: 53
53782331 AGTTGTAATG
* * *
53782341 TTAAATCAGT-AGACCACAAGATTATGAAAATCTTGTAAGTACAAGGTTACGATA
1 TTAAATCAGTGA-ACCACAAGATTCT-AAAATCTTGGAAGTGCAAGGTTACGATA
* * * *
53782395 TTAACTCAAG-GAATCACAAGATTCTAATAATTTTGGAAGTGCAAGGTTACGATC
1 TTAAATC-AGTGAACCACAAGATTCTAA-AATCTTGGAAGTGCAAGGTTACGATA
* * *
53782449 TTAAATCAGTGAACCGCAAGATTCTAAAAATCTTAGAAGTGCAAGGTTGCGAT-
1 TTAAATCAGTGAACCACAAGATTCT-AAAATCTTGGAAGTGCAAGGTTACGATA
* * *
53782502 TGTAAATCGGTGAACCGCAAGATTCTAAAAATCATT-AAAGTGCAAGGTT
1 T-TAAATCAGTGAACCACAAGATTCT-AAAATC-TTGGAAGTGCAAGGTT
53782551 GTGATTGTAA
Statistics
Matches: 134, Mismatches: 15, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
53 5 0.04
54 122 0.91
55 7 0.05
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (53 bp):
TTAAATCAGTGAACCACAAGATTCTAAAATCTTGGAAGTGCAAGGTTACGATA
Found at i:53782551 original size:54 final size:53
Alignment explanation
Indices: 53782411--53782695 Score: 224
Period size: 54 Copynumber: 5.3 Consensus size: 53
53782401 CAAGGAATCA
* * * * * *
53782411 CAAGATTCTAATAATTTTGGAAGTGCAAGGTTACGATCT-TAAATCAGTGAACCG
1 CAAGATTCTAAAAATCTT-AAAGTGCAAGGTTGCGAT-TGTAAATCGGTAAACCG
*
53782465 CAAGATTCTAAAAATCTTAGAAGTGCAAGGTTGCGATTGTAAATCGGTGAACCG
1 CAAGATTCTAAAAATCTTA-AAGTGCAAGGTTGCGATTGTAAATCGGTAAACCG
* ** *
53782519 CAAGATTCTAAAAATCATTAAAGTGCAAGGTTGTGATTGTAAA---AAAAACAG
1 CAAGATTCTAAAAATC-TTAAAGTGCAAGGTTGCGATTGTAAATCGGTAAACCG
* ** * * * *
53782570 -AAGTTTCTAAAAATCGTGT-AAGTATAGGGTTGCAATTGTAAATTGGCAAACCG
1 CAAGATTCTAAAAATC-T-TAAAGTGCAAGGTTGCGATTGTAAATCGGTAAACCG
* * * ***
53782623 TAAGATTCTAAAAATCTTGAAACTGCAAGGTTGTGATTGTAAATCAACAAACC-
1 CAAGATTCTAAAAATCTT-AAAGTGCAAGGTTGCGATTGTAAATCGGTAAACCG
53782676 CGAAGATTCTAAAAAATCTT
1 C-AAGATTCT-AAAAATCTT
53782696 GTAAGTATAG
Statistics
Matches: 188, Mismatches: 31, Indels: 23
0.78 0.13 0.10
Matches are distributed among these distances:
50 33 0.18
51 5 0.03
52 1 0.01
53 7 0.04
54 130 0.69
55 12 0.06
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.28
Consensus pattern (53 bp):
CAAGATTCTAAAAATCTTAAAGTGCAAGGTTGCGATTGTAAATCGGTAAACCG
Found at i:53782609 original size:104 final size:108
Alignment explanation
Indices: 53782493--53782731 Score: 326
Period size: 104 Copynumber: 2.2 Consensus size: 108
53782483 AGAAGTGCAA
* ** *
53782493 GGTTGCGATTGTAAATCGGTGAACCGCAAGATTCTAAAAATCATT-AAAGTGCAAGGTTGTGATT
1 GGTTGCAATTGTAAATCGGCAAACCGCAAGATTCTAAAAATC-TTGAAACTGCAAGGTTGTGATT
*
53782557 GTAAA-AA-AAA-CAGAAGTTTCT-AAAAATCGTGTAAGTATAG
65 GTAAACAACAAACCAGAAGATTCTAAAAAATCGTGTAAGTATAG
* *
53782597 GGTTGCAATTGTAAATTGGCAAACCGTAAGATTCTAAAAATCTTGAAACTGCAAGGTTGTGATTG
1 GGTTGCAATTGTAAATCGGCAAACCGCAAGATTCTAAAAATCTTGAAACTGCAAGGTTGTGATTG
* *
53782662 TAAATCAACAAACCCGAAGATTCTAAAAAATCTTGTAAGTATAG
66 TAAA-CAACAAACCAGAAGATTCTAAAAAATCGTGTAAGTATAG
* *
53782706 GGTTGCAATCGTAAATCGACAAACCG
1 GGTTGCAATTGTAAATCGGCAAACCG
53782732 TAAGTGGTTA
Statistics
Matches: 117, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
103 2 0.02
104 60 0.51
106 2 0.02
107 3 0.03
108 9 0.08
109 41 0.35
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.27
Consensus pattern (108 bp):
GGTTGCAATTGTAAATCGGCAAACCGCAAGATTCTAAAAATCTTGAAACTGCAAGGTTGTGATTG
TAAACAACAAACCAGAAGATTCTAAAAAATCGTGTAAGTATAG
Found at i:53782720 original size:55 final size:54
Alignment explanation
Indices: 53782569--53782730 Score: 182
Period size: 54 Copynumber: 3.0 Consensus size: 54
53782559 AAAAAAAACA
* * * *
53782569 GAAGTTTCTAAAAATCGTGTAAGTATAGGGTTGCAATTGTAAATTGGCAAA-CC
1 GAAGATTCTAAAAATCTTGTAAGTATAGGGTTGCAATTGTAAATCGACAAACCC
* * ** * ** *
53782622 GTAAGATTCTAAAAATCTTGAAACTGCAAGGTTGTGATTGTAAATCAACAAACCC
1 G-AAGATTCTAAAAATCTTGTAAGTATAGGGTTGCAATTGTAAATCGACAAACCC
*
53782677 GAAGATTCTAAAAAATCTTGTAAGTATAGGGTTGCAATCGTAAATCGACAAACC
1 GAAGATTCT-AAAAATCTTGTAAGTATAGGGTTGCAATTGTAAATCGACAAACC
53782731 GTAAGTGGTT
Statistics
Matches: 85, Mismatches: 21, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
53 1 0.01
54 46 0.54
55 38 0.45
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (54 bp):
GAAGATTCTAAAAATCTTGTAAGTATAGGGTTGCAATTGTAAATCGACAAACCC
Found at i:53784216 original size:16 final size:16
Alignment explanation
Indices: 53784184--53784217 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
53784174 CTTCAACCTC
*
53784184 TCATTTCCTTCTCATT
1 TCATTTCCTCCTCATT
*
53784200 TCATTTCCTCCTTATT
1 TCATTTCCTCCTCATT
53784216 TC
1 TC
53784218 CTCTCTGTCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.32, G:0.00, T:0.56
Consensus pattern (16 bp):
TCATTTCCTCCTCATT
Found at i:53784839 original size:18 final size:18
Alignment explanation
Indices: 53784816--53784853 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
53784806 CTATCTGCTG
53784816 TTGTTTAAAGTTGTGCAT
1 TTGTTTAAAGTTGTGCAT
53784834 TTGTTTAAAGTTGTGCAT
1 TTGTTTAAAGTTGTGCAT
53784852 TT
1 TT
53784854 TTTCAATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.05, G:0.21, T:0.53
Consensus pattern (18 bp):
TTGTTTAAAGTTGTGCAT
Found at i:53787083 original size:89 final size:86
Alignment explanation
Indices: 53786968--53787162 Score: 275
Period size: 89 Copynumber: 2.2 Consensus size: 86
53786958 CACTTCTTCA
* * *
53786968 AAAAAAGCAATTAAACCCCTTTTTTTTTCCGCTCAATTGGGTACTTGAACTTTCATAATGCATAA
1 AAAAAAGCAATTAAGCCCCTTTTTTTTCCCACTCAATTGGGTACTTGAACTTTCATAATGCATAA
53787033 AAAAAACCTTAAATTTTTTTTTC
66 AAAAAACCTT-AA-TTTTTTTTC
*
53787056 AAAGAAA-CAATTAAGCCTCTATTTTTTTCCCACTCAATTGGGTACTTGAACTTTCATAATGCAT
1 AAA-AAAGCAATTAAGCCCCT-TTTTTTTCCCACTCAATTGGGTACTTGAACTTTCATAATGCAT
* ** *
53787120 CAAAAAGGCCTTTATTTTTTTTC
64 AAAAAAAACCTTAATTTTTTTTC
53787143 AAAAAAGCAATTAAGCCCCT
1 AAAAAAGCAATTAAGCCCCT
53787163 ACTCTTATTA
Statistics
Matches: 95, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
86 3 0.03
87 24 0.25
88 15 0.16
89 53 0.56
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.36
Consensus pattern (86 bp):
AAAAAAGCAATTAAGCCCCTTTTTTTTCCCACTCAATTGGGTACTTGAACTTTCATAATGCATAA
AAAAAACCTTAATTTTTTTTC
Found at i:53789003 original size:50 final size:50
Alignment explanation
Indices: 53788934--53789054 Score: 172
Period size: 50 Copynumber: 2.4 Consensus size: 50
53788924 GCAAGTGTGA
* ** *
53788934 AGTCAATAGACAACTGATAGTCTTAGTCTTTTTTTGTCGAGTT-AAAGTGT
1 AGTCAATAGACAATTGATAGTCTTAG-CCCTTTTTGTCGAGTTAAAAGTAT
*
53788984 AGTCAATAGACAATTGATAGTCTTAGCCCTTTTTGTGGAGTTAAAAGTAT
1 AGTCAATAGACAATTGATAGTCTTAGCCCTTTTTGTCGAGTTAAAAGTAT
*
53789034 AGTCAATAAACAATTGATAGT
1 AGTCAATAGACAATTGATAGT
53789055 TAAATTTGTA
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
49 13 0.20
50 51 0.80
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (50 bp):
AGTCAATAGACAATTGATAGTCTTAGCCCTTTTTGTCGAGTTAAAAGTAT
Found at i:53792737 original size:30 final size:31
Alignment explanation
Indices: 53792703--53792783 Score: 87
Period size: 31 Copynumber: 2.6 Consensus size: 31
53792693 GCCCTCAAAA
*
53792703 TTTTTGAAAATTTTCATTATA-C-CTTTTAATT
1 TTTTTGAAAATTTTCATTA-AGCACTCTTAA-T
*
53792734 TTTTTGAAAATTTTAATTAAGCACTCTTAA-
1 TTTTTGAAAATTTTCATTAAGCACTCTTAAT
* *
53792764 ATTTTGAAAATTCTCATTAA
1 TTTTTGAAAATTTTCATTAA
53792784 TCTCACAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
30 18 0.42
31 19 0.44
32 6 0.14
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.51
Consensus pattern (31 bp):
TTTTTGAAAATTTTCATTAAGCACTCTTAAT
Found at i:53792737 original size:61 final size:61
Alignment explanation
Indices: 53792663--53792782 Score: 152
Period size: 61 Copynumber: 2.0 Consensus size: 61
53792653 TTTGTTTTTT
* * *
53792663 CCTTTAAAATTTTTAGAAAATTTCAATTAGGCCCTC-AAAATTTTTGAAAATTTTCATTATA
1 CCTTTAAAATTTTTAGAAAATTTCAATTAAGCACTCTAAAA-TTTTGAAAATTCTCATTATA
* * * * *
53792724 CCTTTTAATTTTTTTGAAAATTTTAATTAAGCACTCTTAAATTTTGAAAATTCTCATTA
1 CCTTTAAAATTTTTAGAAAATTTCAATTAAGCACTCTAAAATTTTGAAAATTCTCATTA
53792783 ATCTCACAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
61 47 0.94
62 3 0.06
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.46
Consensus pattern (61 bp):
CCTTTAAAATTTTTAGAAAATTTCAATTAAGCACTCTAAAATTTTGAAAATTCTCATTATA
Found at i:53797819 original size:5 final size:5
Alignment explanation
Indices: 53797811--53797836 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
53797801 GAGATGGAAT
53797811 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
53797837 ATATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:53797836 original size:26 final size:26
Alignment explanation
Indices: 53797785--53797836 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
53797775 TGAAGTTTTC
* * *
53797785 TCGAATCGAGTCGAGTGAGATGGAAT
1 TCGAATCGAATCGAATGAGATCGAAT
53797811 TCGAATCGAATCGAATCGA-ATCGAAT
1 TCGAATCGAATCGAAT-GAGATCGAAT
53797837 ATATTTGTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (26 bp):
TCGAATCGAATCGAATGAGATCGAAT
Found at i:53798510 original size:30 final size:31
Alignment explanation
Indices: 53798471--53798530 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
53798461 GGAGGTGGGA
*
53798471 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
53798502 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
53798531 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:53798759 original size:9 final size:9
Alignment explanation
Indices: 53798745--53798781 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
53798735 TATAGTTTGA
53798745 TATTCGAAT
1 TATTCGAAT
53798754 TATTCGAAT
1 TATTCGAAT
*
53798763 TATTCGAGT
1 TATTCGAAT
53798772 TATTCGAAT
1 TATTCGAAT
53798781 T
1 T
53798782 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:53799041 original size:30 final size:29
Alignment explanation
Indices: 53799007--53799115 Score: 130
Period size: 30 Copynumber: 3.7 Consensus size: 29
53798997 GAGAAAGTTT
53799007 AGGGTCAAAATATAATTTTAAAAAATATTA
1 AGGGTCAAAATATAATTTTAAAAAAT-TTA
*
53799037 AGGGTTAAAATATAATTTTATAAAAATTTA
1 AGGGTCAAAATATAATTTTA-AAAAATTTA
* * *
53799067 AGGGTCAAAATGA-AATTTTAGAAAAGTTC
1 AGGGTCAAAAT-ATAATTTTAAAAAATTTA
*
53799096 AGAGGTCAAAATACAATTTT
1 AG-GGTCAAAATATAATTTT
53799116 TAAATTTTTT
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
29 9 0.13
30 54 0.77
31 7 0.10
ACGTcount: A:0.49, C:0.05, G:0.14, T:0.33
Consensus pattern (29 bp):
AGGGTCAAAATATAATTTTAAAAAATTTA
Found at i:53803356 original size:17 final size:17
Alignment explanation
Indices: 53803334--53803367 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
53803324 ATCCACTAAT
*
53803334 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
53803351 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
53803368 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:53804827 original size:17 final size:17
Alignment explanation
Indices: 53804805--53804838 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
53804795 ATCCACTAAT
*
53804805 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
53804822 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
53804839 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:53809466 original size:17 final size:17
Alignment explanation
Indices: 53809444--53809477 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
53809434 ATCCACTAAT
*
53809444 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
53809461 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
53809478 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:53809733 original size:3 final size:3
Alignment explanation
Indices: 53809725--53809766 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
53809715 GAAGTGGTGT
53809725 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
53809767 CAACAACAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:53815312 original size:72 final size:72
Alignment explanation
Indices: 53814708--53815295 Score: 887
Period size: 72 Copynumber: 8.1 Consensus size: 72
53814698 TCAGGACCGG
* **
53814708 TTCCAAGATCACT-GGGAACCTCTTGCAACTCACTCATTTAGACTTGTCGCAGAACCAATTGAGT
1 TTCCAAGATCATTGGGGAACCTCTTGCAACTCACTCATTTAGACTTGTCGGTGAACCAATTGAGT
53814772 GGACAAA
66 GGACAAA
* *
53814779 TTCCAAGATTATTGGGGAACCTCTTTCAACTCACTCATTTAGACTTGTC-GTGGAACCAATTGAG
1 TTCCAAGATCATTGGGGAACCTCTTGCAACTCACTCATTTAGACTTGTCGGT-GAACCAATTGAG
53814843 TGGACAAA
65 TGGACAAA
* *
53814851 TTCCAAGATCATTGGGGAACCTCTTGCAACTCACTCATTTAGATTTGTCGATGAACCAATTGAGT
1 TTCCAAGATCATTGGGGAACCTCTTGCAACTCACTCATTTAGACTTGTCGGTGAACCAATTGAGT
53814916 GGACAAA
66 GGACAAA
*
53814923 TTCCAAGATCATTGGGGATCATTGGGGAACATCTTGCAACTCACTCATTT--ACTTGTCGGTGAA
1 TTCC---A--A-----GATCATTGGGGAACCTCTTGCAACTCACTCATTTAGACTTGTCGGTGAA
53814986 CCAATTGAGTGGACAAA
56 CCAATTGAGTGGACAAA
53815003 TTCCAAGATCATTGGGGAACCTCTTGCAACTCACTCATTTAGACTTGTCGGTGAACCAATTGAGT
1 TTCCAAGATCATTGGGGAACCTCTTGCAACTCACTCATTTAGACTTGTCGGTGAACCAATTGAGT
53815068 GGACAAA
66 GGACAAA
* * *
53815075 TTCCGAGATCATTGGGGAACCTCTTGCAACTCACTCATTTAGACTTATCGGTGAACCAATTGAGC
1 TTCCAAGATCATTGGGGAACCTCTTGCAACTCACTCATTTAGACTTGTCGGTGAACCAATTGAGT
53815140 GGACAAA
66 GGACAAA
* * *
53815147 TTCCAAGATCATTGGGGAACCTCTTGCAACTCACTCATTTACAGTTGCCGGTGAACCAATTGAGT
1 TTCCAAGATCATTGGGGAACCTCTTGCAACTCACTCATTTAGACTTGTCGGTGAACCAATTGAGT
*
53815212 GGAAAAA
66 GGACAAA
* * *
53815219 TTCCAAGATCATTGGGGAACCTCTTGCATCTCACTCATTTACACTTGTCGATGAACCAATTGAGT
1 TTCCAAGATCATTGGGGAACCTCTTGCAACTCACTCATTTAGACTTGTCGGTGAACCAATTGAGT
53815284 GGACAAA
66 GGACAAA
53815291 TTCCA
1 TTCCA
53815296 TTGTCAATTC
Statistics
Matches: 474, Mismatches: 28, Indels: 29
0.89 0.05 0.05
Matches are distributed among these distances:
70 33 0.07
71 11 0.02
72 360 0.76
73 1 0.00
75 2 0.00
77 2 0.00
80 32 0.07
82 33 0.07
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (72 bp):
TTCCAAGATCATTGGGGAACCTCTTGCAACTCACTCATTTAGACTTGTCGGTGAACCAATTGAGT
GGACAAA
Found at i:53816892 original size:20 final size:20
Alignment explanation
Indices: 53816867--53816916 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
53816857 TGGCTTAAAA
53816867 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
53816887 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
53816904 GTGGTAGTGGATT
1 TTGGTAGTGGATT
53816917 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:53820176 original size:20 final size:20
Alignment explanation
Indices: 53820151--53820200 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
53820141 TGGCTTAAAA
53820151 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
53820171 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
53820188 GTGGTAGTGGATT
1 TTGGTAGTGGATT
53820201 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:53823898 original size:28 final size:28
Alignment explanation
Indices: 53823862--53823924 Score: 65
Period size: 28 Copynumber: 2.2 Consensus size: 28
53823852 TTACAAAATT
53823862 ATAAAAATTAAAAAT-TAAATGAAAGTAG
1 ATAAAAATTAAAAATATAAAT-AAAGTAG
* **
53823890 ATAAGAATTTCAAATATAAATAAAGTGAG
1 ATAAAAATTAAAAATATAAATAAAGT-AG
*
53823919 AGAAAA
1 ATAAAA
53823925 TGAGGGAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
28 17 0.61
29 11 0.39
ACGTcount: A:0.62, C:0.02, G:0.13, T:0.24
Consensus pattern (28 bp):
ATAAAAATTAAAAATATAAATAAAGTAG
Found at i:53831743 original size:87 final size:87
Alignment explanation
Indices: 53831646--53831866 Score: 205
Period size: 87 Copynumber: 2.5 Consensus size: 87
53831636 AAACTTTTTA
* * * * * * **
53831646 AATGTATCAAAAATATCTTTACACTTCTTAAAAAAAAGCAATTAAATCC-CTA-TTTTTTTCTGC
1 AATGCATCAAAAAGACCTTAACACTTCTTAAAAAAAA-CAATT-AAGCCTCTAGTTTTTTCCCAC
53831709 TCAATTGGGTACTTGAACTGTCAT
64 TCAATTGGGTACTTGAACTGTCAT
*** * * * *
53831733 AATGCATCAAAAAGACCTTAATTTTTTTTCAAAGAAACAATTAAGCCTTTAGTTTTTTCCCACTC
1 AATGCATCAAAAAGACCTTAACACTTCTTAAAAAAAACAATTAAGCCTCTAGTTTTTTCCCACTC
*
53831798 AATTGGGTACTTGAACTTTCAT
66 AATTGGGTACTTGAACTGTCAT
* * * * *
53831820 AATGCATCAAAAAGGCCTTAA-ATTTTTTTCAAAAAAGCAATTAAGCC
1 AATGCATCAAAAAGACCTTAACA-CTTCTTAAAAAAAACAATTAAGCC
53831867 CCTGCTCTTA
Statistics
Matches: 111, Mismatches: 20, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
85 4 0.04
86 7 0.06
87 100 0.90
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.36
Consensus pattern (87 bp):
AATGCATCAAAAAGACCTTAACACTTCTTAAAAAAAACAATTAAGCCTCTAGTTTTTTCCCACTC
AATTGGGTACTTGAACTGTCAT
Found at i:53832046 original size:28 final size:26
Alignment explanation
Indices: 53831989--53832047 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
53831979 CAAATCGTCA
**
53831989 AAAAATAAAAAAATATAAAATTTTAT
1 AAAAATAAAAAAATATAAAATTCCAT
53832015 AAAAATCATAAAAAATATAAAA-TCCAT
1 AAAAAT-A-AAAAAATATAAAATTCCAT
53832042 CAAAAA
1 -AAAAA
53832048 GTCCTTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 6 0.21
27 4 0.14
28 18 0.64
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (26 bp):
AAAAATAAAAAAATATAAAATTCCAT
Found at i:53841353 original size:18 final size:19
Alignment explanation
Indices: 53841327--53841362 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
53841317 TTCTTCTTCA
*
53841327 TTTTCTCTTA-TTTATTTG
1 TTTTATCTTATTTTATTTG
53841345 TTTTATCTTATTTTATTT
1 TTTTATCTTATTTTATTT
53841363 TACTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.14, C:0.08, G:0.03, T:0.75
Consensus pattern (19 bp):
TTTTATCTTATTTTATTTG
Found at i:53842387 original size:20 final size:20
Alignment explanation
Indices: 53842353--53842390 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
53842343 ATATATATAT
53842353 TAATCTATTTATTTGAAACG
1 TAATCTATTTATTTGAAACG
53842373 TAAT-TATTTATTTTGAAA
1 TAATCTATTTA-TTTGAAA
53842391 TGCCTTCACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (20 bp):
TAATCTATTTATTTGAAACG
Found at i:53844350 original size:19 final size:19
Alignment explanation
Indices: 53844326--53844371 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
53844316 CTCTTTTTCT
53844326 TTTGCATTC-ATTCCATGCA
1 TTTGCATTCTATTCCAT-CA
*
53844345 TTTGCATTCTATTGCATCA
1 TTTGCATTCTATTCCATCA
*
53844364 TATGCATT
1 TTTGCATT
53844372 AGAGTTTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.46
Consensus pattern (19 bp):
TTTGCATTCTATTCCATCA
Found at i:53847521 original size:6 final size:6
Alignment explanation
Indices: 53847495--53847544 Score: 50
Period size: 6 Copynumber: 8.5 Consensus size: 6
53847485 CTTCACTTGA
* * *
53847495 AAAAAG AAACA- AAAAAG AAAAAT AAAAAG -AAAAG AAGAATG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AA-AAAG AAAAAG
53847542 AAA
1 AAA
53847545 GGAGAAGCCA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
5 9 0.26
6 21 0.60
7 5 0.14
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:53847521 original size:12 final size:11
Alignment explanation
Indices: 53847494--53847527 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
53847484 ACTTCACTTG
*
53847494 AAAAAAGAAAC
1 AAAAAAGAAAA
53847505 AAAAAAGAAAA
1 AAAAAAGAAAA
53847516 ATAAAAAGAAAA
1 A-AAAAAGAAAA
53847528 GAAGAATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.85, C:0.03, G:0.09, T:0.03
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:53847527 original size:17 final size:18
Alignment explanation
Indices: 53847493--53847544 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
53847483 TACTTCACTT
*
53847493 GAAAAAAGAAACAA-AAAA
1 GAAAAATGAAA-AAGAAAA
53847511 GAAAAAT-AAAAAGAAAA
1 GAAAAATGAAAAAGAAAA
*
53847528 GAAGAATGAAAAAGAAA
1 GAAAAATGAAAAAGAAA
53847545 GGAGAAGCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 2 0.07
17 13 0.43
18 15 0.50
ACGTcount: A:0.79, C:0.02, G:0.15, T:0.04
Consensus pattern (18 bp):
GAAAAATGAAAAAGAAAA
Found at i:53847527 original size:18 final size:19
Alignment explanation
Indices: 53847493--53847544 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 19
53847483 TACTTCACTT
* *
53847493 GAAAAAAGAAACA-AAAAA
1 GAAAAATGAAAAAGAAAAA
53847511 GAAAAAT-AAAAAG-AAAA
1 GAAAAATGAAAAAGAAAAA
*
53847528 GAAGAATGAAAAAGAAA
1 GAAAAATGAAAAAGAAA
53847545 GGAGAAGCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 14 0.50
18 12 0.43
19 2 0.07
ACGTcount: A:0.79, C:0.02, G:0.15, T:0.04
Consensus pattern (19 bp):
GAAAAATGAAAAAGAAAAA
Found at i:53847545 original size:17 final size:17
Alignment explanation
Indices: 53847507--53847544 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
53847497 AAAGAAACAA
*
53847507 AAAAGAAAAATAAAAAG
1 AAAAGAAGAATAAAAAG
53847524 AAAAGAAGAATGAAAAAG
1 AAAAGAAGAAT-AAAAAG
53847542 AAA
1 AAA
53847545 GGAGAAGCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (17 bp):
AAAAGAAGAATAAAAAG
Found at i:53848886 original size:50 final size:50
Alignment explanation
Indices: 53848829--53849389 Score: 238
Period size: 50 Copynumber: 11.3 Consensus size: 50
53848819 GCTATGACGG
* * * *
53848829 CGAATCTTGCTTCTCTGACATTACAATTTAAAAGATTGAAGCCGCAACGA
1 CGAATCTTACTTCCCTGACATTGCAATTGAAAAGATTGAAGCCGCAACGA
* * * * ** * ** * *
53848879 CGAATCTTACTTCCTTGGCGA-TGCAGTGGATCAGATTAAAGCTACGACGG
1 CGAATCTTACTTCCCTGAC-ATTGCAATTGAAAAGATTGAAGCCGCAACGA
* * * * * *
53848929 TGAATCTTGCTTCCCCGACATTGCAATTTAAAATATTGAAGCCGCAACGC
1 CGAATCTTACTTCCCTGACATTGCAATTGAAAAGATTGAAGCCGCAACGA
* * * ** * ** *
53848979 CGAATCTTACTTCCCTGGCGA-TGCAGTGGATCAGATTAAAGCTACGACGA
1 CGAATCTTACTTCCCTGAC-ATTGCAATTGAAAAGATTGAAGCCGCAACGA
* * *
53849029 CGAATCTT-GTTCCCCGACATTGCAATTAAAAAGATTGAAGCCGCAACGA
1 CGAATCTTACTTCCCTGACATTGCAATTGAAAAGATTGAAGCCGCAACGA
* * * * * * ** ** * *
53849078 CAAATTTTACTTCCTTGGCGA-TGCAGTGGATCAGATTGAAGCTACAATGG
1 CGAATCTTACTTCCCTGAC-ATTGCAATTGAAAAGATTGAAGCCGCAACGA
* * * *
53849128 CGAATCTT-GTTCCCCGACATTGCAATTAAAAAAATTGAAGCCGCAACGA
1 CGAATCTTACTTCCCTGACATTGCAATTGAAAAGATTGAAGCCGCAACGA
** * * * * *** *
53849177 CGAATCTTACTTCCCTGGTAGTGCAGTGGAACAGATTGAAGCTATAACGG
1 CGAATCTTACTTCCCTGACATTGCAATTGAAAAGATTGAAGCCGCAACGA
* ** * * * * * *
53849227 TGAATC-TGGTTCCCCGATATTGCAATTAAAAAGATTGAAGCCACGACGG
1 CGAATCTTACTTCCCTGACATTGCAATTGAAAAGATTGAAGCCGCAACGA
* * ** * * * ** * *
53849276 TGAATCTTACTTCCCTGGCGGTGCAGTGGAGCAA-ATTGAAGCTACGACGG
1 CGAATCTTACTTCCCTGACATTGCAATTGA-AAAGATTGAAGCCGCAACGA
* * * * * * * *
53849326 TGAATCTTGCTTCCCAGAGATTGTAATTAAAAAGATTGAAGCCACGAC-A
1 CGAATCTTACTTCCCTGACATTGCAATTGAAAAGATTGAAGCCGCAACGA
53849375 GCGAATCTTACTTCC
1 -CGAATCTTACTTCC
53849390 TTGGCGGTGC
Statistics
Matches: 356, Mismatches: 143, Indels: 24
0.68 0.27 0.05
Matches are distributed among these distances:
48 2 0.01
49 106 0.30
50 243 0.68
51 5 0.01
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.26
Consensus pattern (50 bp):
CGAATCTTACTTCCCTGACATTGCAATTGAAAAGATTGAAGCCGCAACGA
Found at i:53849097 original size:99 final size:99
Alignment explanation
Indices: 53848810--53849454 Score: 794
Period size: 99 Copynumber: 6.5 Consensus size: 99
53848800 TATAGTAGAG
* * * * *
53848810 CAGATTGAAGCTATGACGGCGAATCTTGCTTCTCTGACATTACAATTTAAAAGATTGAAGCCGCA
1 CAGATTGAAGCTACGACGGCGAATCTTG-TTCCCCGACATTGCAATTAAAAAGATTGAAGCCGCA
*
53848875 ACGACGAATCTTACTTCCTTGGCGATGCAGTGGAT
65 ACGACGAATCTTACTTCCCTGGCGATGCAGTGGAT
* * * *
53848910 CAGATTAAAGCTACGACGGTGAATCTTGCTTCCCCGACATTGCAATTTAAAATATTGAAGCCGCA
1 CAGATTGAAGCTACGACGGCGAATCTTG-TTCCCCGACATTGCAATTAAAAAGATTGAAGCCGCA
*
53848975 ACGCCGAATCTTACTTCCCTGGCGATGCAGTGGAT
65 ACGACGAATCTTACTTCCCTGGCGATGCAGTGGAT
* *
53849010 CAGATTAAAGCTACGACGACGAATCTTGTTCCCCGACATTGCAATTAAAAAGATTGAAGCCGCAA
1 CAGATTGAAGCTACGACGGCGAATCTTGTTCCCCGACATTGCAATTAAAAAGATTGAAGCCGCAA
* * *
53849075 CGACAAATTTTACTTCCTTGGCGATGCAGTGGAT
66 CGACGAATCTTACTTCCCTGGCGATGCAGTGGAT
* * *
53849109 CAGATTGAAGCTACAATGGCGAATCTTGTTCCCCGACATTGCAATTAAAAAAATTGAAGCCGCAA
1 CAGATTGAAGCTACGACGGCGAATCTTGTTCCCCGACATTGCAATTAAAAAGATTGAAGCCGCAA
* *
53849174 CGACGAATCTTACTTCCCTGG-TAGTGCAGTGGAA
66 CGACGAATCTTACTTCCCTGGCGA-TGCAGTGGAT
** * * * * *
53849208 CAGATTGAAGCTATAACGGTGAATCTGGTTCCCCGATATTGCAATTAAAAAGATTGAAGCCACGA
1 CAGATTGAAGCTACGACGGCGAATCTTGTTCCCCGACATTGCAATTAAAAAGATTGAAGCCGCAA
** * *
53849273 CGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAG
66 CGACGAATCTTACTTCCCTGGCGATGCAGTGGAT
* * * * * * *
53849307 CAAATTGAAGCTACGACGGTGAATCTTGCTTCCCAGAGATTGTAATTAAAAAGATTGAAGCCACG
1 CAGATTGAAGCTACGACGGCGAATCTTG-TTCCCCGACATTGCAATTAAAAAGATTGAAGCCGCA
* * *
53849372 AC-AGCGAATCTTACTTCCTTGGCGGTGCAGTGGAG
65 ACGA-CGAATCTTACTTCCCTGGCGATGCAGTGGAT
* * *
53849407 CATATTGAAG-T-CGCAACGGCAAATCTTGTTCCCCGACATTGCAGTTAA
1 CAGATTGAAGCTACG--ACGGCGAATCTTGTTCCCCGACATTGCAATTAA
53849455 TTTGACAGAA
Statistics
Matches: 482, Mismatches: 57, Indels: 13
0.87 0.10 0.02
Matches are distributed among these distances:
98 3 0.01
99 278 0.58
100 201 0.42
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (99 bp):
CAGATTGAAGCTACGACGGCGAATCTTGTTCCCCGACATTGCAATTAAAAAGATTGAAGCCGCAA
CGACGAATCTTACTTCCCTGGCGATGCAGTGGAT
Found at i:53849414 original size:50 final size:50
Alignment explanation
Indices: 53849260--53849416 Score: 156
Period size: 50 Copynumber: 3.1 Consensus size: 50
53849250 AATTAAAAAG
53849260 ATTGAAGCCACGACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAGCAA
1 ATTGAAGCCACGACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAGCAA
* * * ** * * * **
53849310 ATTGAAGCTACGACGGTGAATCTTGCTTCCCAGAG-ATTGTAAT-TAAAAA
1 ATTGAAGCCACGACGGTGAATCTTACTTCCCTG-GCGGTGCAGTGGAGCAA
* * * *
53849359 GATTGAAGCCACGACAGCGAATCTTACTTCCTTGGCGGTGCAGTGGAGCAT
1 -ATTGAAGCCACGACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAGCAA
53849410 ATTGAAG
1 ATTGAAG
53849417 TCGCAACGGC
Statistics
Matches: 79, Mismatches: 24, Indels: 8
0.71 0.22 0.07
Matches are distributed among these distances:
49 4 0.05
50 72 0.91
51 3 0.04
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (50 bp):
ATTGAAGCCACGACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAGCAA
Found at i:53849558 original size:40 final size:40
Alignment explanation
Indices: 53849514--53850122 Score: 452
Period size: 40 Copynumber: 14.7 Consensus size: 40
53849504 AAACCACAGA
* *
53849514 TCTTATCTCCCTAAGCAGTAGTTGAGCAGATCGCATCCAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAATCCAG
* *
53849554 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGTAGAAAT-CAA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAG--A-TCG-AATCCAG
* ** *** * * ** *
53849597 TCCTATCTCTTTGAAATTGCAGTGGAGCGGATTAAAACCACAG
1 TCTTATCTCCCT-AAGCAGTAGTGGAGCAGA-TCGAATC-CAG
* * * * * *
53849640 ATCTTATCTCCTTAAGCAATAGTGGAGCAAATCGCATCAAA
1 -TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAATCCAG
* * * *
53849681 TCTTATCTCTCTAAGCAGTAGTGGAGCAAATCGCATCAAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAATCCAG
** * *
53849721 TCTTATCTCCCTAAGCAGTAGTGGAGCAAATGAAAGAAACCAA
1 TCTTATCTCCCTAAGCAGTAGTGGAGC--A-GATCGAATCCAG
* ** * ** *
53849764 TCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAG
1 TCTTATCTCCCT-AAGCAGTAGTGGAGCAGA-TCGAATC-CAG
* * **
53849807 ATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGCATAAAG
1 -TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAATCCAG
*
53849848 TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CAGAACCACAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-GAATC-CAG
* * * *
53849889 ATCTTATCTCCCTAAGCAGTAGTAGAGCAGATTGCATCGAG
1 -TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAATCCAG
* *
53849930 TCTTATCTCCCTAAGCAGTAGTAGAGCAGA-CAGAACCACAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-GAATC-CAG
* ** * *
53849971 ATCTTATCTCCCTAAGTAGTAGCAGAGCAGATCGCATCAAG
1 -TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAATCCAG
*
53850012 TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CAGAACCACAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-GAATC-CAG
* ** *
53850053 ATCTTATCTCCCTAAGCAGTAATGGAGCAGATCGCCTCAAG
1 -TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAATCCAG
*
53850094 TCTTATCTCCCTAAGTAGTAGTGGAGCAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAG
53850123 GTTGAAGATA
Statistics
Matches: 448, Mismatches: 94, Indels: 54
0.75 0.16 0.09
Matches are distributed among these distances:
39 2 0.00
40 211 0.47
41 19 0.04
42 109 0.24
43 60 0.13
44 47 0.10
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (40 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAATCCAG
Found at i:53849656 original size:87 final size:85
Alignment explanation
Indices: 53849554--53849917 Score: 286
Period size: 87 Copynumber: 4.3 Consensus size: 85
53849544 TCGCATCCAG
*
53849554 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGTAGAAATCAATCCTATCTCTTTGAAATTGCAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCA-A-AGTAGAAATCAATCCTATCTCTCTGAAATTGCAG
53849619 TGGAGCGGATTAAAACCACAGA
64 TGGAGCGGATTAAAACCACAGA
* * * * *
53849641 TCTTATCTCCTTAAGCAATAGTGGAGCAAA-TCG-CATCAAATCTTATCTCTCT--AA--GCAGT
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAAAGTAGAAATC-AATCCTATCTCTCTGAAATTGCAGT
* ** *
53849700 --AGTGGAGCAAATCGCATCA-A
65 GGAGCGGATTAAAAC-CA-CAGA
* * * *
53849720 GTCTTATCTCCCTAAGCAGTAGTGGAGCAAATGAAAGAAACCAATCCTATCTCCCTGAAGTTGCA
1 -TCTTATCTCCCTAAGCAGTAGTGGAGCAAA-G-TAGAAATCAATCCTATCTCTCTGAAATTGCA
*
53849785 GTGGAGCAGATTAAAACCACAGA
63 GTGGAGCGGATTAAAACCACAGA
* * * * * * * *** *
53849808 TCTTATCTCCCTAAGCAGTAGCGGAGCAGA-TCG-CATAAAGTCTTATCTCCCT-AAGCAGTAGT
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAAAGTAGAAATCAA-TCCTATCTCTCTGAAATTGCAGT
* * *
53849870 GGAGCAGA-CAGAACCACAGA
65 GGAGCGGATTAAAACCACAGA
*
53849890 TCTTATCTCCCTAAGCAGTAGTAGAGCA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCA
53849918 GATTGCATCG
Statistics
Matches: 222, Mismatches: 39, Indels: 37
0.74 0.13 0.12
Matches are distributed among these distances:
78 9 0.04
79 3 0.01
80 35 0.16
82 38 0.17
83 34 0.15
84 28 0.13
85 2 0.01
86 1 0.00
87 61 0.27
88 3 0.01
89 8 0.04
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (85 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAAAGTAGAAATCAATCCTATCTCTCTGAAATTGCAGTG
GAGCGGATTAAAACCACAGA
Found at i:53849697 original size:167 final size:168
Alignment explanation
Indices: 53849513--53850083 Score: 700
Period size: 167 Copynumber: 3.4 Consensus size: 168
53849503 AAAACCACAG
* * *
53849513 ATCTTATCTCCCTAAGCAGTAGTTGAGCAGATC-GCATC-CAG-TCTTATCTCCCTAAGCAGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CAGAACCACAGATCTTATCTCCCTAAGCAGTAG
** * *
53849575 TGGAGCAGACAGTAGAAATCAATCCTATCTCTTTGAAATTGCAGTGGAGCGGATTAAAACCACAG
65 TGGAGCAGA-AGTAGAAATCAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAG
* * * *
53849640 ATCTTATCTCCTTAAGCAATAGTGGAGCAAATCGCATCAA
129 ATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGCATCAA
* * * *
53849680 ATCTTATCTCTCTAAGCAGTAGTGGAGCAAATC-GCATCA-AG-TCTTATCTCCCTAAGCAGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CAGAACCACAGATCTTATCTCCCTAAGCAGTAG
* *
53849742 TGGAGCA-AATGAAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACA
65 TGGAGCAGAA-G-TAGAAATCAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACA
53849806 GATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGCAT-AA
128 GATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGCATCAA
53849846 AGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGAACCACAGATCTTATCTCCCTAAGCAGTAG
1 A-TCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGAACCACAGATCTTATCTCCCTAAGCAGTAG
* * * * * ** * * * *
53849911 TAGAGCAG-A-TTG-CATCGAGTCTTATCTCCCT-AAGCAGTAGTAGAGCAGA-CAGAACCACAG
65 TGGAGCAGAAGTAGAAATC-AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAG
* *
53849971 ATCTTATCTCCCTAAGTAGTAGCAGAGCAGATCGCATCAA
129 ATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGCATCAA
* *
53850011 GTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGAACCACAGATCTTATCTCCCTAAGCAGTAAT
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGAACCACAGATCTTATCTCCCTAAGCAGTAGT
53850076 GGAGCAGA
66 GGAGCAGA
53850084 TCGCCTCAAG
Statistics
Matches: 358, Mismatches: 35, Indels: 24
0.86 0.08 0.06
Matches are distributed among these distances:
164 113 0.32
165 19 0.05
166 19 0.05
167 177 0.49
168 2 0.01
169 28 0.08
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (168 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGAACCACAGATCTTATCTCCCTAAGCAGTAGT
GGAGCAGAAGTAGAAATCAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGAT
CTTATCTCCCTAAGCAGTAGCGGAGCAGATCGCATCAA
Found at i:53849907 original size:82 final size:82
Alignment explanation
Indices: 53849514--53850122 Score: 599
Period size: 82 Copynumber: 7.4 Consensus size: 82
53849504 AAACCACAGA
* * *
53849514 TCTTATCTCCCTAAGCAGTAGTTGAGCAGATC-GCATC-CAG-TCTTATCTCCCTAAGCAGTAGT
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CAGAACCACAGATCTTATCTCCCTAAGCAGTAGT
* *
53849576 GGAGCAGA-CAGTAGAAA-
65 GGAGCAGATC-GCATAAAG
** *** * * * * *
53849593 TCAATCCTATCTCTTTGAAATTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCCTTAAGCA
1 TC--T--TATCTCCCT-AAGCAGTAGTGGAGCAGA-CAGAACCACAGATCTTATCTCCCTAAGCA
* *
53849658 ATAGTGGAGCAAATCGCATCAAA-
60 GTAGTGGAGCAGATCGCAT-AAAG
* * * *
53849681 TCTTATCTCTCTAAGCAGTAGTGGAGCAAATC-GCATCA-AG-TCTTATCTCCCTAAGCAGTAGT
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CAGAACCACAGATCTTATCTCCCTAAGCAGTAGT
* * * *
53849743 GGAGCAAAT-GAAAGAAACCAA
65 GGAGCAGATCG-CA-TAA--AG
* ** * * *
53849764 TCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCTCCCTAAGCAGTAG
1 TCTTATCTCCCT-AAGCAGTAGTGGAGCAGA-CAGAACCACAGATCTTATCTCCCTAAGCAGTAG
*
53849829 CGGAGCAGATCGCATAAAG
64 TGGAGCAGATCGCATAAAG
*
53849848 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGAACCACAGATCTTATCTCCCTAAGCAGTAGTA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGAACCACAGATCTTATCTCCCTAAGCAGTAGTG
* **
53849913 GAGCAGATTGCATCGAG
66 GAGCAGATCGCATAAAG
* * **
53849930 TCTTATCTCCCTAAGCAGTAGTAGAGCAGACAGAACCACAGATCTTATCTCCCTAAGTAGTAGCA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGAACCACAGATCTTATCTCCCTAAGCAGTAGTG
*
53849995 GAGCAGATCGCATCAAG
66 GAGCAGATCGCATAAAG
*
53850012 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGAACCACAGATCTTATCTCCCTAAGCAGTAATG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGAACCACAGATCTTATCTCCCTAAGCAGTAGTG
* *
53850077 GAGCAGATCGCCTCAAG
66 GAGCAGATCGCATAAAG
*
53850094 TCTTATCTCCCTAAGTAGTAGTGGAGCAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAG
53850123 GTTGAAGATA
Statistics
Matches: 440, Mismatches: 70, Indels: 37
0.80 0.13 0.07
Matches are distributed among these distances:
79 3 0.01
80 32 0.07
81 3 0.01
82 230 0.52
83 45 0.10
84 48 0.11
85 5 0.01
86 8 0.02
87 59 0.13
88 7 0.02
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (82 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGAACCACAGATCTTATCTCCCTAAGCAGTAGTG
GAGCAGATCGCATAAAG
Found at i:53851883 original size:20 final size:20
Alignment explanation
Indices: 53851860--53851905 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
53851850 GTTTCCATTA
*
53851860 TTATTTATTTATTG-TCTAAT
1 TTATTTATATATTGATCT-AT
*
53851880 TTATATATATATTGATCTAT
1 TTATTTATATATTGATCTAT
53851900 TTATTT
1 TTATTT
53851906 GAAACGTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.63
Consensus pattern (20 bp):
TTATTTATATATTGATCTAT
Found at i:53853902 original size:19 final size:19
Alignment explanation
Indices: 53853878--53853942 Score: 76
Period size: 19 Copynumber: 3.3 Consensus size: 19
53853868 TTTCTATATA
53853878 TTTTATAATTTTTTAAAAT
1 TTTTATAATTTTTTAAAAT
** *
53853897 TTTTATAAAATTTTACAAT
1 TTTTATAATTTTTTAAAAT
53853916 TTTTATATATTTTTTAATAAAT
1 TTTTATA-ATTTTTT-A-AAAT
53853938 TTTTA
1 TTTTA
53853943 ATATTTGAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
19 23 0.62
20 5 0.14
21 1 0.03
22 8 0.22
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTATAATTTTTTAAAAT
Found at i:53853929 original size:10 final size:10
Alignment explanation
Indices: 53853864--53853948 Score: 54
Period size: 9 Copynumber: 8.7 Consensus size: 10
53853854 TATAAAATTT
*
53853864 TATATTTCTA
1 TATATTTTTA
53853874 TATA-TTTTA
1 TATATTTTTA
53853883 TA-ATTTTT-
1 TATATTTTTA
*
53853891 TAAAATTTTTA
1 T-ATATTTTTA
* *
53853902 TAAAATTTTA
1 TATATTTTTA
*
53853912 CA-ATTTTTA
1 TATATTTTTA
53853921 TATATTTTTTAA
1 TATA-TTTTT-A
*
53853933 TAAATTTTTA
1 TATATTTTTA
53853943 -ATATTT
1 TATATTT
53853949 GAATTTTTTA
Statistics
Matches: 61, Mismatches: 7, Indels: 15
0.73 0.08 0.18
Matches are distributed among these distances:
8 2 0.03
9 23 0.38
10 21 0.34
11 11 0.18
12 4 0.07
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (10 bp):
TATATTTTTA
Found at i:53854110 original size:89 final size:91
Alignment explanation
Indices: 53854017--53854199 Score: 219
Period size: 91 Copynumber: 2.0 Consensus size: 91
53854007 CATTTTTAAT
* ** ** * *
53854017 AAAAGTAGG-GACTTAATTGCTTTTTTT-TTAA-GTTTGAGGGTGTTTTTGATGCATTTTGAGAG
1 AAAAGTAGGAG-CTTAATTACTTTTTTTGAAAATGTTTGAGGGCCTTTTAGATGCATTTTGAAAG
* *
53854079 TTTAAGTACCCAATTGAGTGCAAAAAA
65 TTCAAGTACCCAAATGAGTGCAAAAAA
* *
53854106 AAAAGTAGGAGCTTAATTACTTTTTTTGAAAATTTTTGAGGGCCTTTTAGATGTATTTTGAAAGT
1 AAAAGTAGGAGCTTAATTACTTTTTTTGAAAATGTTTGAGGGCCTTTTAGATGCATTTTGAAAGT
* *
53854171 TCAAGTCCCCAAATGAGTGTAAAAAA
66 TCAAGTACCCAAATGAGTGCAAAAAA
53854197 AAA
1 AAA
53854200 GAACAGGGGT
Statistics
Matches: 78, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
89 24 0.31
90 3 0.04
91 51 0.65
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.37
Consensus pattern (91 bp):
AAAAGTAGGAGCTTAATTACTTTTTTTGAAAATGTTTGAGGGCCTTTTAGATGCATTTTGAAAGT
TCAAGTACCCAAATGAGTGCAAAAAA
Found at i:53854917 original size:19 final size:20
Alignment explanation
Indices: 53854880--53854917 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
53854870 GGGTTAAAAA
*
53854880 TATTTTTTTTAAAATATTTT
1 TATTTTTATTAAAATATTTT
53854900 TATTTTTATTAAAA-ATTT
1 TATTTTTATTAAAATATTT
53854918 AGAATTAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TATTTTTATTAAAATATTTT
Found at i:53855414 original size:28 final size:29
Alignment explanation
Indices: 53855381--53855442 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
53855371 TACAAAATTC
53855381 TAAAAATTAAAAAT-TAAATGAAAGT-AGA
1 TAAAAATTAAAAATATAAAT-AAAGTGAGA
**
53855409 TAAAAATTTCAAATATAAATAAAGTGAGA
1 TAAAAATTAAAAATATAAATAAAGTGAGA
*
53855438 GAAAA
1 TAAAA
53855443 TGAGGGAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 17 0.59
29 12 0.41
ACGTcount: A:0.63, C:0.02, G:0.11, T:0.24
Consensus pattern (29 bp):
TAAAAATTAAAAATATAAATAAAGTGAGA
Found at i:53857704 original size:72 final size:72
Alignment explanation
Indices: 53857626--53857774 Score: 253
Period size: 72 Copynumber: 2.1 Consensus size: 72
53857616 TCAGGAACGG
* **
53857626 TTCCAAGATCACTGGGGAACCTCTTGCAACTCACTCATTTAGACTTGTCGGGGAACCAATTGAGT
1 TTCCAAGATCACTGGGGAACCACTTGCAACTCACTCATTTAGACTTGTCGCAGAACCAATTGAGT
53857691 GGACAAA
66 GGACAAA
* *
53857698 TTCCAAGATCATTGGGGAACCACTTGCAACTCACTCTTTTAGACTTGTCGCAGAACCAATTGAGT
1 TTCCAAGATCACTGGGGAACCACTTGCAACTCACTCATTTAGACTTGTCGCAGAACCAATTGAGT
53857763 GGACAAA
66 GGACAAA
53857770 TTCCA
1 TTCCA
53857775 TCGTCAATTC
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (72 bp):
TTCCAAGATCACTGGGGAACCACTTGCAACTCACTCATTTAGACTTGTCGCAGAACCAATTGAGT
GGACAAA
Found at i:53866778 original size:23 final size:25
Alignment explanation
Indices: 53866742--53866790 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
53866732 AGAATAAAAA
*
53866742 AATAACATCTTAATTT-AAATAATT
1 AATAACATCTTAATTTGAAAAAATT
*
53866766 AATAA-ATTTTAATTTGAAAAAATT
1 AATAACATCTTAATTTGAAAAAATT
53866790 A
1 A
53866791 TTTTGAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (25 bp):
AATAACATCTTAATTTGAAAAAATT
Found at i:53870560 original size:20 final size:20
Alignment explanation
Indices: 53870535--53870584 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
53870525 TGGCTTAAAA
53870535 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
53870555 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
53870572 GTGGTAGTGGATT
1 TTGGTAGTGGATT
53870585 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:53871020 original size:20 final size:20
Alignment explanation
Indices: 53870995--53871044 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
53870985 TGGCTTAAAA
53870995 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
53871015 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
53871032 GTGGTAGTGGATT
1 TTGGTAGTGGATT
53871045 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:53875659 original size:20 final size:20
Alignment explanation
Indices: 53875634--53875683 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
53875624 TGGCTTAAAA
53875634 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
53875654 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
53875671 GTGGTAGTGGATT
1 TTGGTAGTGGATT
53875684 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:53876395 original size:22 final size:22
Alignment explanation
Indices: 53876354--53876396 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
53876344 CAACAAAATC
*
53876354 TAAATCTATTATTCATAACAAT
1 TAAATCTATTATCCATAACAAT
53876376 TAAAGTCTATTATCCA-AACAA
1 TAAA-TCTATTATCCATAACAA
53876397 CCATTACCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.35
Consensus pattern (22 bp):
TAAATCTATTATCCATAACAAT
Found at i:53879881 original size:48 final size:48
Alignment explanation
Indices: 53879825--53879969 Score: 290
Period size: 48 Copynumber: 3.0 Consensus size: 48
53879815 ACTTTTTGGC
53879825 TTAACGTACAAGGATAAATTTATTCATTTTTTAATTAAAGGGGTACAA
1 TTAACGTACAAGGATAAATTTATTCATTTTTTAATTAAAGGGGTACAA
53879873 TTAACGTACAAGGATAAATTTATTCATTTTTTAATTAAAGGGGTACAA
1 TTAACGTACAAGGATAAATTTATTCATTTTTTAATTAAAGGGGTACAA
53879921 TTAACGTACAAGGATAAATTTATTCATTTTTTAATTAAAGGGGTACAA
1 TTAACGTACAAGGATAAATTTATTCATTTTTTAATTAAAGGGGTACAA
53879969 T
1 T
53879970 ATAATCTGAT
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 97 1.00
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.38
Consensus pattern (48 bp):
TTAACGTACAAGGATAAATTTATTCATTTTTTAATTAAAGGGGTACAA
Found at i:53880293 original size:16 final size:16
Alignment explanation
Indices: 53880272--53880313 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
53880262 TTTTGCTCTT
53880272 AAGAAAATAATT-ATAA
1 AAGAAAA-AATTGATAA
*
53880288 AAGAAAAAGTTGATAA
1 AAGAAAAAATTGATAA
53880304 AAGAGAAAAA
1 AAGA-AAAAA
53880314 CAAAATTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 3 0.14
16 15 0.68
17 4 0.18
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (16 bp):
AAGAAAAAATTGATAA
Found at i:53880356 original size:61 final size:61
Alignment explanation
Indices: 53880170--53880356 Score: 297
Period size: 61 Copynumber: 3.1 Consensus size: 61
53880160 AAATCAGTTG
**
53880170 AAAAGTTGATAAAAGAGAAAATAC-AAATTCTTTTTGCTCTTAAGAAAATAATTATAAAGGG
1 AAAAGTTGATAAAAGAGAAAA-ACAAAATTCTTTTTGCTCTTAAGAAAATAATTATAAAGAA
* *
53880231 AAAAGTTAATAAAAGAGAAAAGCAAAATTCTTTTTGCTCTTAAGAAAATAATTATAAA-AGA
1 AAAAGTTGATAAAAGAGAAAAACAAAATTCTTTTTGCTCTTAAGAAAATAATTATAAAGA-A
*
53880292 AAAAGTTGATAAAAGAGAAAAACAAAATTCTTTTTGCTCTTAAGTAAATAATTATAAAGAA
1 AAAAGTTGATAAAAGAGAAAAACAAAATTCTTTTTGCTCTTAAGAAAATAATTATAAAGAA
53880353 AAAA
1 AAAA
53880357 AAATAAAGAA
Statistics
Matches: 116, Mismatches: 7, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
60 1 0.01
61 114 0.98
62 1 0.01
ACGTcount: A:0.53, C:0.06, G:0.12, T:0.28
Consensus pattern (61 bp):
AAAAGTTGATAAAAGAGAAAAACAAAATTCTTTTTGCTCTTAAGAAAATAATTATAAAGAA
Found at i:53906100 original size:28 final size:28
Alignment explanation
Indices: 53906068--53906124 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
53906058 AACAATAACA
53906068 TAGCAACCTAAGTTTCAAGTGGAAAAAG
1 TAGCAACCTAAGTTTCAAGTGGAAAAAG
53906096 TAGCAACCTAAGTTTCAAGTGGAAAAAG
1 TAGCAACCTAAGTTTCAAGTGGAAAAAG
53906124 T
1 T
53906125 TATGTTCTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.23
Consensus pattern (28 bp):
TAGCAACCTAAGTTTCAAGTGGAAAAAG
Found at i:53909701 original size:21 final size:21
Alignment explanation
Indices: 53909676--53909717 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
53909666 GGCATGTACA
53909676 TAGGCTTAGAATCATGTGTAT
1 TAGGCTTAGAATCATGTGTAT
53909697 TAGGCTTAGAATCATGTGTAT
1 TAGGCTTAGAATCATGTGTAT
53909718 CGTTGTAGTA
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:0.29, C:0.10, G:0.24, T:0.38
Consensus pattern (21 bp):
TAGGCTTAGAATCATGTGTAT
Found at i:53911206 original size:2 final size:2
Alignment explanation
Indices: 53911199--53911272 Score: 139
Period size: 2 Copynumber: 37.0 Consensus size: 2
53911189 ATCCCAATTT
*
53911199 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA TA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
53911241 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
53911273 TACATATAAC
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.49, G:0.00, T:0.01
Consensus pattern (2 bp):
CA
Found at i:53914395 original size:46 final size:46
Alignment explanation
Indices: 53914328--53914419 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
53914318 GCCATTGACG
53914328 TGGGAGGCGCATACCTTTGATTAGCCTATGGACGGCAGCGATGCCA
1 TGGGAGGCGCATACCTTTGATTAGCCTATGGACGGCAGCGATGCCA
53914374 TGGGAGGCGCATACCTTTGATTAGCCTATGGACGGCAGCGATGCCA
1 TGGGAGGCGCATACCTTTGATTAGCCTATGGACGGCAGCGATGCCA
53914420 CGACTATAGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.22, C:0.24, G:0.33, T:0.22
Consensus pattern (46 bp):
TGGGAGGCGCATACCTTTGATTAGCCTATGGACGGCAGCGATGCCA
Found at i:53919713 original size:705 final size:705
Alignment explanation
Indices: 53918364--53919761 Score: 2679
Period size: 705 Copynumber: 2.0 Consensus size: 705
53918354 GTTACGGCAA
53918364 GTTTTTGAAGAGGGCTGCTAACTGGCAGTCAAAAGTGGCCATTTCCATCATTTATGCAATAGTAT
1 GTTTTTGAAGAGGGCTGCTAACTGGCAGTCAAAAGTGGCCATTTCCATCATTTATGCAATAGTAT
53918429 GCTAACTTGCCATATTTGGAGTTGGCAATGCATTAAAACAAAATCTTTAGGCATTGAATTGTGTT
66 GCTAACTTGCCATATTTGGAGTTGGCAATGCATTAAAACAAAATCTTTAGGCATTGAATTGTGTT
* *
53918494 AATATTGTGGATGTGTGGAAGCCTGACTTTGAAAACCAATCATTTAAAGTAATTATCCTTGAAGA
131 AATATTGTGGATGTGTGGAAGCCTGACTTTGAAAACCAATCAATTAAAGTAACTATCCTTGAAGA
*
53918559 GCCCAACTATTTTTGTAAAAGCCTTAAGTTGCGAAGAACTAGGTTAATCTTCCACCAAACGTGTG
196 GCCCAACTATTTTTGTAAAAGCCTTAAGTTGCGAAGAACTAGGTTAATCTTCCACCAAACATGTG
53918624 TTGATAAAGTCAGATAAGAAGTTAACAACTCACCACGATGTTTTTTTCCATTACTATAGTAAACT
261 TTGATAAAGTCAGATAAGAAGTTAACAACTCACCACGATGTTTTTTTCCATTACTATAGTAAACT
53918689 TGGACACATAATACCATAGTGTACCAAAATACTACATGATCTAAGATAGTGACGCATGGTGCCAG
326 TGGACACATAATACCATAGTGTACCAAAATACTACATGATCTAAGATAGTGACGCATGGTGCCAG
*
53918754 TTGAAGTGCCCACTTTACGTGGCTCATTGTCTGTGAAGAAGTAAAAGATTGTTTGGAAGAAGAAT
391 TTGAAGTGCCCACTTTACGTGGCTCATTGTCTGTGAAGAAGCAAAAGATTGTTTGGAAGAAGAAT
*
53918819 GAGCCAAAGTGTTTACTTGTATCTAATTAATATTTGAAGAATTCTTTAGATAATGTGTGGTACTT
456 GAGCCAAAGTGTTTACTTGCATCTAATTAATATTTGAAGAATTCTTTAGATAATGTGTGGTACTT
53918884 CAATAGTGGATCCTCTAGACACATGACAGATAATCAAAACTACTTATCTAACTTTGAACATTGCC
521 CAATAGTGGATCCTCTAGACACATGACAGATAATCAAAACTACTTATCTAACTTTGAACATTGCC
53918949 ATGTTAGACGAGTCACCTTTGGAGATGGCAAAAAGGGGCACATACTTTGGAAAGGCAAACTTGAT
586 ATGTTAGACGAGTCACCTTTGGAGATGGCAAAAAGGGGCACATACTTTGGAAAGGCAAACTTGAT
*
53919014 GTCCTAGGATGCTAGAACAAAATAATGTGCTTTTTATGGATGCACAAAATAATGT
651 GTACTAGGATGCTAGAACAAAATAATGTGCTTTTTATGGATGCACAAAATAATGT
* *
53919069 GTTTTTGAAGAGGGCTGCTAATTGGCAGTCAAAAGTGGCCATTTCCATCGTTTATGCAATAGTAT
1 GTTTTTGAAGAGGGCTGCTAACTGGCAGTCAAAAGTGGCCATTTCCATCATTTATGCAATAGTAT
53919134 GCTAACTTGCCATATTTGGAGTTGGCAATGCATTAAAACAAAATCTTTAGGCATTGAATTGTGTT
66 GCTAACTTGCCATATTTGGAGTTGGCAATGCATTAAAACAAAATCTTTAGGCATTGAATTGTGTT
53919199 AATATTGTGGATGTGTGGAAGCCTGACTTTGAAAACCAATCAATTAAAGTAACTATCCTTGAAGA
131 AATATTGTGGATGTGTGGAAGCCTGACTTTGAAAACCAATCAATTAAAGTAACTATCCTTGAAGA
*
53919264 GCCCAACTATTTTTGTAAAAGCCTTAAGTTGCGAAGAACTAGGTTAATGTTCCACCAAACATGTG
196 GCCCAACTATTTTTGTAAAAGCCTTAAGTTGCGAAGAACTAGGTTAATCTTCCACCAAACATGTG
*
53919329 TTGATAAAGTCAGATAAGAAGTTAACAACTCACCACGATGTTTTTTTCCATTACTATAGTACACT
261 TTGATAAAGTCAGATAAGAAGTTAACAACTCACCACGATGTTTTTTTCCATTACTATAGTAAACT
*
53919394 TGGACACATAATACCATAGTGTACCAAAATACTACATGATCTGAGATAGTGACGCATGGTGCCAG
326 TGGACACATAATACCATAGTGTACCAAAATACTACATGATCTAAGATAGTGACGCATGGTGCCAG
53919459 TTGAAGTGCCCACTTTACGTGGCTCATTGTCTGTGAAGAAGCAAAAGATTGTTTGGAAGAAGAAT
391 TTGAAGTGCCCACTTTACGTGGCTCATTGTCTGTGAAGAAGCAAAAGATTGTTTGGAAGAAGAAT
*
53919524 GAGCCAAAGTGTTTGCTTGCATCTAATTAATATTTGAAGAATTCTTTAGATAATGTGTGGTACTT
456 GAGCCAAAGTGTTTACTTGCATCTAATTAATATTTGAAGAATTCTTTAGATAATGTGTGGTACTT
53919589 CAATAGTGGATCCTCTAGACACATGACAGATAATCAAAACTACTTATCTAACTTTGAACATTGCC
521 CAATAGTGGATCCTCTAGACACATGACAGATAATCAAAACTACTTATCTAACTTTGAACATTGCC
*
53919654 ATTTTAGACGAGTCACCTTTGGAGATGGCAAAAAGGGGCACATACTTTGGAAAGGCAAACTTGAT
586 ATGTTAGACGAGTCACCTTTGGAGATGGCAAAAAGGGGCACATACTTTGGAAAGGCAAACTTGAT
53919719 GTACTAGGATGCTAGAACAAAATAATGTGCTTTTTATGGATGC
651 GTACTAGGATGCTAGAACAAAATAATGTGCTTTTTATGGATGC
53919762 CCTGAAGTCT
Statistics
Matches: 680, Mismatches: 13, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
705 680 1.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (705 bp):
GTTTTTGAAGAGGGCTGCTAACTGGCAGTCAAAAGTGGCCATTTCCATCATTTATGCAATAGTAT
GCTAACTTGCCATATTTGGAGTTGGCAATGCATTAAAACAAAATCTTTAGGCATTGAATTGTGTT
AATATTGTGGATGTGTGGAAGCCTGACTTTGAAAACCAATCAATTAAAGTAACTATCCTTGAAGA
GCCCAACTATTTTTGTAAAAGCCTTAAGTTGCGAAGAACTAGGTTAATCTTCCACCAAACATGTG
TTGATAAAGTCAGATAAGAAGTTAACAACTCACCACGATGTTTTTTTCCATTACTATAGTAAACT
TGGACACATAATACCATAGTGTACCAAAATACTACATGATCTAAGATAGTGACGCATGGTGCCAG
TTGAAGTGCCCACTTTACGTGGCTCATTGTCTGTGAAGAAGCAAAAGATTGTTTGGAAGAAGAAT
GAGCCAAAGTGTTTACTTGCATCTAATTAATATTTGAAGAATTCTTTAGATAATGTGTGGTACTT
CAATAGTGGATCCTCTAGACACATGACAGATAATCAAAACTACTTATCTAACTTTGAACATTGCC
ATGTTAGACGAGTCACCTTTGGAGATGGCAAAAAGGGGCACATACTTTGGAAAGGCAAACTTGAT
GTACTAGGATGCTAGAACAAAATAATGTGCTTTTTATGGATGCACAAAATAATGT
Found at i:53920218 original size:20 final size:20
Alignment explanation
Indices: 53920193--53920233 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
53920183 AATGTTTCTG
53920193 TGTATGCTAATTTTATAAAC
1 TGTATGCTAATTTTATAAAC
53920213 TGTATGCTAATTTTATAAAC
1 TGTATGCTAATTTTATAAAC
53920233 T
1 T
53920234 ATTTTGTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (20 bp):
TGTATGCTAATTTTATAAAC
Found at i:53922466 original size:53 final size:53
Alignment explanation
Indices: 53922406--53922518 Score: 172
Period size: 53 Copynumber: 2.1 Consensus size: 53
53922396 GTCTTACACA
* * * *
53922406 CTTCTTTTTATATGGTGTCATAACTCACTAGTTACGATCTTACATGATATGGT
1 CTTCTTTTCATATGATGTCATAACCCACTAGTTACGATCTTACATGATATGAT
* *
53922459 CTTCTTTTCATATGATGTCATAACCCACTAGTTATGGTCTTACATGATATGAT
1 CTTCTTTTCATATGATGTCATAACCCACTAGTTACGATCTTACATGATATGAT
53922512 CTTCTTT
1 CTTCTTT
53922519 AGTGACATTG
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.44
Consensus pattern (53 bp):
CTTCTTTTCATATGATGTCATAACCCACTAGTTACGATCTTACATGATATGAT
Found at i:53933676 original size:87 final size:87
Alignment explanation
Indices: 53933555--53933716 Score: 209
Period size: 87 Copynumber: 1.9 Consensus size: 87
53933545 AGACCTGATG
* * * * * *
53933555 CGATCTACTCTGCTGTAACCTCAGAGAGATAAGATC-CTTTATTTTAATCCGCTCCACTGTAACT
1 CGATCTACTCCGCTGTAACCTCAGAGAGACAAGATCTC-TGACTTCAATCCGCTCCACTGTAACC
53933619 TCAGGGAGATAGGATAGTGTCTT
65 TCAGGGAGATAGGATAGTGTCTT
* * * * *
53933642 CGATCTGCTCCGCTGTAATCTCAGGGAGACAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCT
1 CGATCTACTCCGCTGTAACCTCAGAGAGACAAGATCTCTGACTTCAATCCGCTCCACTGTAACCT
53933707 CAGGGAGATA
66 CAGGGAGATA
53933717 AGATCTGAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
87 62 0.98
88 1 0.02
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (87 bp):
CGATCTACTCCGCTGTAACCTCAGAGAGACAAGATCTCTGACTTCAATCCGCTCCACTGTAACCT
CAGGGAGATAGGATAGTGTCTT
Found at i:53933709 original size:44 final size:44
Alignment explanation
Indices: 53933567--53934047 Score: 170
Period size: 44 Copynumber: 11.1 Consensus size: 44
53933557 ATCTACTCTG
* *** * *
53933567 CTGTAACCTCAGAGAGATAAGATC-CTTTATTTTAATCCGCTCCA
1 CTGTAACCTCAGGGAGATAAGATCTC-TGGCTTCAATCTGCTCCA
* * ** * * *
53933611 CTGTAACTTCAGGGAGATAGGAT-AGTGTCTTCGATCTGCTCCG
1 CTGTAACCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCA
* *
53933654 CTGTAATCTCAGGGAGACAAGATCTCTGGCTTCAATCTGCTCCA
1 CTGTAACCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCA
***** ** *
53933698 CTGTAACCTCAGGGAGATAAGATCTGAAATTCTCTGTTCTACTCCA
1 CTGTAACCTCAGGGAGATAAGATCTCTGGCT-TC-AATCTGCTCCA
* * * * *
53933744 CTGTAACCTCAGGGAAATAAGA-C-CT-GATGT-GATCTTCTCTA
1 CTGTAACCTCAGGGAGATAAGATCTCTGGCT-TCAATCTGCTCCA
* * *
53933785 CTGTAACTTCAGAGAGATAAGATC-CT---TT-AATCCGCTCCA
1 CTGTAACCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCA
* * * * ** ** *
53933824 TTGTAATCTCAAGGAGATAGGAT-TACTATCTTTGATCTGCTCCG
1 CTGTAACCTCAGGGAGATAAGATCT-CTGGCTTCAATCTGCTCCA
* ** * ** *
53933868 CTG-ATATCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTACTCCA
1 CTGTA-ACCTCAGGGAGATAAGATCT--CTGGCTTCAATCTGCTCCA
* * **
53933914 CTGTAACCTCAGGGAGATAAGA-C-CTGG-TGCGATCTGCTCTG
1 CTGTAACCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCA
* * * *** * *
53933955 CTGTAACTTCAGAGAAATAAGATC-CTTTATTTTAATCCGCTCCA
1 CTGTAACCTCAGGGAGATAAGATCTC-TGGCTTCAATCTGCTCCA
* * * * * *
53933999 CTGTAACTTCAGGGAGATAGGAT-TATGTCTTCGATCTGCTCCG
1 CTGTAACCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCA
53934042 CTGTAA
1 CTGTAA
53934048 TTTCAGGGGA
Statistics
Matches: 322, Mismatches: 96, Indels: 39
0.70 0.21 0.09
Matches are distributed among these distances:
39 25 0.08
40 3 0.01
41 55 0.17
42 6 0.02
43 53 0.16
44 113 0.35
45 5 0.02
46 61 0.19
47 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (44 bp):
CTGTAACCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCA
Found at i:53933866 original size:170 final size:170
Alignment explanation
Indices: 53933683--53934047 Score: 495
Period size: 170 Copynumber: 2.1 Consensus size: 170
53933673 AGATCTCTGG
* * * *
53933683 CTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTC-TCTGTTCTACTCCACTG
1 CTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAAGTCTTC-GGTCTACTCCACTG
* * *
53933747 TAACCTCAGGGAAATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCC-T
65 TAACCTCAGGGAAATAAGACCTGATGCGATCTGCTCTACTGTAACTTCAGAGAAATAAGATCCTT
*
53933811 TTAATCCGCTCCATTGTAA-TCTCAAGGAGATAGGATTACTAT
130 TTAATCCGCTCCACTGTAACT-TCAAGGAGATAGGATTA-TAT
* *
53933853 CTTTGATCTGCTCCGCTG-ATATCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTACTCCACTG
1 CTTCGATCTGCTCCGCTGTA-ACCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTACTCCACTG
* * *
53933917 TAACCTCAGGGAGATAAGACCTGGTGCGATCTGCTCTGCTGTAACTTCAGAGAAATAAGATCCTT
65 TAACCTCAGGGAAATAAGACCTGATGCGATCTGCTCTACTGTAACTTCAGAGAAATAAGATCC--
* *
53933982 TATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTATGT
128 --TTTTAATCCGCTCCACTGTAACTTCAAGGAGATAGGATTATAT
53934027 CTTCGATCTGCTCCGCTGTAA
1 CTTCGATCTGCTCCGCTGTAA
53934048 TTTCAGGGGA
Statistics
Matches: 170, Mismatches: 16, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
169 1 0.01
170 110 0.65
171 2 0.01
174 20 0.12
175 36 0.21
176 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (170 bp):
CTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTACTCCACTGT
AACCTCAGGGAAATAAGACCTGATGCGATCTGCTCTACTGTAACTTCAGAGAAATAAGATCCTTT
TAATCCGCTCCACTGTAACTTCAAGGAGATAGGATTATAT
Found at i:53934071 original size:87 final size:85
Alignment explanation
Indices: 53933909--53934068 Score: 205
Period size: 87 Copynumber: 1.9 Consensus size: 85
53933899 CTTCGGTCTA
* * *
53933909 CTCCACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCTGCTCTGCTGTAACTTCAGAGAAATA
1 CTCCACTGTAACCTCAGGGAGATAAGACATGCTGCGATCTGCTCCGCTGTAACTTCAGAGAAATA
53933974 AGATCCTTTATTTTAATCCG
66 AGATCCTTTATTTTAATCCG
* * * * * * *
53933994 CTCCACTGTAACTTCAGGGAGATAGGATTATGTCTTCGATCTGCTCCGCTGTAATTTCAGGGGAA
1 CTCCACTGTAACCTCAGGGAGATAAGA-CATG-CTGCGATCTGCTCCGCTGTAACTTCAGAGAAA
53934059 TAAGA-CCTTT
64 TAAGATCCTTT
53934069 TATAATGAAC
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
85 25 0.40
86 7 0.11
87 31 0.49
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.31
Consensus pattern (85 bp):
CTCCACTGTAACCTCAGGGAGATAAGACATGCTGCGATCTGCTCCGCTGTAACTTCAGAGAAATA
AGATCCTTTATTTTAATCCG
Found at i:53943039 original size:66 final size:66
Alignment explanation
Indices: 53942958--53943089 Score: 255
Period size: 66 Copynumber: 2.0 Consensus size: 66
53942948 ACGATTACAG
53942958 TACTGGTGAAGCGATCTTTCTAGTTCAGTTATCCGGACCTTAAACTCCGTCTTCTCATCTTGGCA
1 TACTGGTGAAGCGATCTTTCTAGTTCAGTTATCCGGACCTTAAACTCCGTCTTCTCATCTTGGCA
53943023 A
66 A
*
53943024 TACTGGTGAAGCGATCTTTCTAGTTCAGTTATCCGGACCTTCAACTCCGTCTTCTCATCTTGGCA
1 TACTGGTGAAGCGATCTTTCTAGTTCAGTTATCCGGACCTTAAACTCCGTCTTCTCATCTTGGCA
53943089 A
66 A
53943090 ACTAGTAGAC
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.35
Consensus pattern (66 bp):
TACTGGTGAAGCGATCTTTCTAGTTCAGTTATCCGGACCTTAAACTCCGTCTTCTCATCTTGGCA
A
Found at i:53944762 original size:50 final size:50
Alignment explanation
Indices: 53944687--53944786 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
53944677 CGTTGTGTCG
53944687 TTTCAGCCCATATTCGCACAGCCGCATTATCCTCTACTTTATCAACAAAC
1 TTTCAGCCCATATTCGCACAGCCGCATTATCCTCTACTTTATCAACAAAC
53944737 TTTCAGCCCATATTCGCACAGCCGCATTATCCTCTACTTTATCAACAAAC
1 TTTCAGCCCATATTCGCACAGCCGCATTATCCTCTACTTTATCAACAAAC
53944787 CCCTTTTCCA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.28, C:0.34, G:0.08, T:0.30
Consensus pattern (50 bp):
TTTCAGCCCATATTCGCACAGCCGCATTATCCTCTACTTTATCAACAAAC
Found at i:53945649 original size:29 final size:29
Alignment explanation
Indices: 53945616--53945673 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
53945606 TTGGTCTACG
53945616 AAATTTAGAAAACGGGTTCAGGAGTCGGT
1 AAATTTAGAAAACGGGTTCAGGAGTCGGT
* *
53945645 AAATTTAGAAAATGGGTTCGGGAGTCGGT
1 AAATTTAGAAAACGGGTTCAGGAGTCGGT
53945674 TACGCACGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.33, C:0.09, G:0.33, T:0.26
Consensus pattern (29 bp):
AAATTTAGAAAACGGGTTCAGGAGTCGGT
Found at i:53948565 original size:113 final size:114
Alignment explanation
Indices: 53948049--53948692 Score: 967
Period size: 114 Copynumber: 5.7 Consensus size: 114
53948039 AAAACACCCC
* * * * * * *
53948049 AAAAAACCTAAGCCCAACGACGTCGTTTCCCGAGCTTTAGGGGATTTAGCAGCGTTTCTAAAAAA
1 AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTGAAAAA
*
53948114 GCGCCGCTAATGTTCAGGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCA
66 GCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCA
* * * *
53948163 AAAAAACCTAATCTCAACAACGCCGTTTTCTAAGCTTTCGGGGATTTAGCGGCGTTTTT-AAGAA
1 AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTGAA-AA
*
53948227 AGCGCAGCTAATGCTCAGGGCTTTAGCGGCGTTTTT-GAGAAAGCGCCGCA
65 AGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGA-AAAGCGCCGCA
* **
53948277 AAAAAACCTAAGACCAACGACGCCGTTTTCTGAGCTTTCTTGGATTTAGCGGCGTTTTT-AAGAA
1 AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTGAA-AA
*
53948341 AGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTT-GAGAAAGCGCCGCAA
65 AGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGA-AAAGCGCCGC-A
* * *
53948392 AAAAAACTTAAGCCCAACGATGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTGGAAAA
1 AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTGAAAAA
* *
53948457 GCGCCGCTAATGCCCAGGGCTTTAGCGGCATTTTTGGAAAAGCGCCGC-
66 GCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCA
*
53948505 AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTGGAAAA
1 AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTGAAAAA
* *
53948570 GCGCCGCTAATGCCCAGGGCTTTAGCGGCATTTTTGGAAAAGCGCCGC-
66 GCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCA
*
53948618 AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTGGAAAA
1 AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTGAAAAA
53948683 GCGCCGCTAA
66 GCGCCGCTAA
53948693 AATTTTTTTA
Statistics
Matches: 493, Mismatches: 32, Indels: 11
0.92 0.06 0.02
Matches are distributed among these distances:
113 190 0.39
114 200 0.41
115 100 0.20
116 3 0.01
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (114 bp):
AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTGAAAAA
GCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCA
Found at i:53949034 original size:22 final size:23
Alignment explanation
Indices: 53948989--53949042 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 23
53948979 TGGGATTTAA
* *
53948989 GGTTTAGGGGTTAAAGGGTTAGG
1 GGTTTAGGGATTAAAGAGTTAGG
53949012 GGTTTAGGGATTAAA-AGTTAGG
1 GGTTTAGGGATTAAAGAGTTAGG
*
53949034 GATTTAGGG
1 GGTTTAGGG
53949043 GTCGAGTTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.26, C:0.00, G:0.43, T:0.31
Consensus pattern (23 bp):
GGTTTAGGGATTAAAGAGTTAGG
Found at i:53949272 original size:14 final size:15
Alignment explanation
Indices: 53949253--53949290 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
53949243 GGGATTACGG
53949253 TTTAAGGGTT-GGGA
1 TTTAAGGGTTAGGGA
*
53949267 TTTAAGGTTTAGGGA
1 TTTAAGGGTTAGGGA
*
53949282 TTCAAGGGT
1 TTTAAGGGT
53949291 CGAGTTAAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.24, C:0.03, G:0.37, T:0.37
Consensus pattern (15 bp):
TTTAAGGGTTAGGGA
Found at i:53950245 original size:149 final size:150
Alignment explanation
Indices: 53949920--53950304 Score: 543
Period size: 149 Copynumber: 2.6 Consensus size: 150
53949910 AAATAGCTTA
* * *
53949920 AAAAACGCCGCAAAAAATAAATCAACTTAT---AAA-AAAATAAAAAAATTTTATAATAGCAAAA
1 AAAAACGCCGCAAAAAATAAATCAATTTATAAAAAATAAAATAAAAAATTTTTAAAATAGCAAAA
* * *
53949981 CGGCGCCGTTTTGTTCAAAATGAAAAAAAATTGCGGCGCATTATAAGAAGCGCCGCTAAAGGTAA
66 CGGCGTCGTTTTGTTCAAAATGAAAAAAAATTGCAGCGCATTATAAGAAACGCCGCTAAAGGTAA
*
53950046 GCAATAGCGGCGTTTTCTAT
131 GCAATAGCAGCGTTTTCTAT
*
53950066 AAAAACGCCGCAAAAAATAAATCAATTTATAAAAAATAAAATAAAAAATTTTTAAAACAGCAAAA
1 AAAAACGCCGCAAAAAATAAATCAATTTATAAAAAATAAAATAAAAAATTTTTAAAATAGCAAAA
* * **
53950131 TGGCGTCGTTTTGTTCAAAATGAAAAAAATTTTGCAGCGTTTCTATGAA-AAACGCCGCTAAAGG
66 CGGCGTCGTTTTGTTCAAAATGAAAAAAA-ATTGCAGCGCAT-TAT-AAGAAACGCCGCTAAAGG
53950195 T-AGCAATAGCAGCGTTTT-T-T
128 TAAGCAATAGCAGCGTTTTCTAT
**
53950215 AAAAACGCCGCAAAAAATAAATCAATTTATAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAA
1 AAAAACGCCGCAAAAAATAAATCAATTTATAAAAAATAAAATAAAAAATTTTTAAAATAGCAAAA
* *
53950280 CGGTGTCATTTTGTTCAAAATGAAA
66 CGGCGTCGTTTTGTTCAAAATGAAA
53950305 TAGAAAAAAC
Statistics
Matches: 214, Mismatches: 18, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
146 29 0.14
149 88 0.41
150 53 0.25
151 24 0.11
152 18 0.08
153 2 0.01
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.25
Consensus pattern (150 bp):
AAAAACGCCGCAAAAAATAAATCAATTTATAAAAAATAAAATAAAAAATTTTTAAAATAGCAAAA
CGGCGTCGTTTTGTTCAAAATGAAAAAAAATTGCAGCGCATTATAAGAAACGCCGCTAAAGGTAA
GCAATAGCAGCGTTTTCTAT
Found at i:53950328 original size:94 final size:94
Alignment explanation
Indices: 53950215--53950398 Score: 314
Period size: 94 Copynumber: 2.0 Consensus size: 94
53950205 AGCGTTTTTT
* * *
53950215 AAAAACGCCGCAAAAAATAAATCAATTTATAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAA
1 AAAAACACCGCAAAAAATAAATCAATTTATAAAAAACAAAATAAAAAATTTTTAGAATAGCAAAA
*
53950280 CGGTGTCATTTTGTTCAAAATGAAATAGA
66 CGGCGTCATTTTGTTCAAAATGAAATAGA
*
53950309 AAAAACACCGTAAAAAATAAATCAATTTATAAAAAACAAAATAAAAAATTTTTAGAATAGCAAAA
1 AAAAACACCGCAAAAAATAAATCAATTTATAAAAAACAAAATAAAAAATTTTTAGAATAGCAAAA
*
53950374 CGGCGTCGTTTTGTTCAAAATGAAA
66 CGGCGTCATTTTGTTCAAAATGAAA
53950399 AAAAATTTGC
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
94 84 1.00
ACGTcount: A:0.54, C:0.11, G:0.10, T:0.25
Consensus pattern (94 bp):
AAAAACACCGCAAAAAATAAATCAATTTATAAAAAACAAAATAAAAAATTTTTAGAATAGCAAAA
CGGCGTCATTTTGTTCAAAATGAAATAGA
Found at i:53950449 original size:136 final size:139
Alignment explanation
Indices: 53950309--53950686 Score: 483
Period size: 152 Copynumber: 2.6 Consensus size: 139
53950299 ATGAAATAGA
* * *
53950309 AAAAACACCGTAAAAAATAAATCAATTTATAAAAAACAAAATAAAAAATTTTTAGAATAGCAAAA
1 AAAAACGCCGCAAAAAATAAATCAATTTATAAAAAATAAAATAAAAAATTTTTAGAATAGCAAAA
* *
53950374 CGGCGTCGTTTTGTTCAAAATGAAAAAAAATTT-G-C-ACGCCGCTAAAGGTAAGCAATAGCGGC
66 CGGTGTCATTTTGTTCAAAATGAAAAAAAATTTGGTCAACGCCGCTAAAGGTAAGCAATAGCGGC
53950436 GTTTTCTAT
131 GTTTTCTAT
* * *
53950445 AAAAACGCCACAAAAAGTAAATCAATTTATAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAA
1 AAAAACGCCGCAAAAAATAAATCAATTTATAAAAAATAAAATAAAAAATTTTTAGAATAGCAAAA
* *
53950510 CGGTGTCATTTTGTTCAAAATGAAAAAAATTTTGCGGCGTTTCTATGAAAAACGCTGCTAAAGGT
66 CGGTGTCATTTTGTTCAAAATGAAAAAAAATTT---G-G--TC-------AACGCCGCTAAAGGT
53950575 AAGCAATAGCGGCGTTTTCTAT
118 AAGCAATAGCGGCGTTTTCTAT
* * *
53950597 AAAAACGCCGCAAAAAATTAATCAATTTATAAAAAATAAAATAAAAAATTTTTCGAATAGTAAAA
1 AAAAACGCCGCAAAAAATAAATCAATTTATAAAAAATAAAATAAAAAATTTTTAGAATAGCAAAA
* *
53950662 CGGTGTCATTTTATTCAAAAGGAAA
66 CGGTGTCATTTTGTTCAAAATGAAA
53950687 TAGCGGTGTT
Statistics
Matches: 208, Mismatches: 18, Indels: 16
0.86 0.07 0.07
Matches are distributed among these distances:
136 89 0.43
141 1 0.00
144 1 0.00
152 117 0.56
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.26
Consensus pattern (139 bp):
AAAAACGCCGCAAAAAATAAATCAATTTATAAAAAATAAAATAAAAAATTTTTAGAATAGCAAAA
CGGTGTCATTTTGTTCAAAATGAAAAAAAATTTGGTCAACGCCGCTAAAGGTAAGCAATAGCGGC
GTTTTCTAT
Found at i:53950553 original size:379 final size:384
Alignment explanation
Indices: 53949841--53950791 Score: 1355
Period size: 379 Copynumber: 2.5 Consensus size: 384
53949831 ATTTTATAAA
53949841 AAATCAATTTATAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACGGTGTCATTTTGTTCAA
1 AAATCAATTTATAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACGGTGTCATTTTGTTCAA
* * *
53949906 AATGAAATAGCTTAAAAAACGCCGCAAAAAATAAATCAACTTAT---AAA-AAAATAAAAAAATT
66 AATGAAATAG---AAAAAACACCGCAAAAAATAAATCAATTTATAAAAAACAAAATAAAAAATTT
* *
53949967 TTATAATAGCAAAACGGCGCCGTTTTGTTCAAAATGAAAAAAAATTGCGGCGCATTATAAGAAGC
128 TTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATG-AAAAAAA---------ATT-T-AGAAGC
*
53950032 GCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAATCAATTTATA
181 GCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCACAAAAAATAAATCAATTTATA
* *
53950097 AAAAATAAAATAAAAAATTTTTAAAACAGCAAAATGGCGTCGTTTTGTTCAAAATGAAAAAAATT
246 AAAAATAAAATAAAAAATTTTTAAAACAGCAAAACGGCGTCATTTTGTTCAAAATGAAAAAAATT
53950162 TTGCAGCGTTTCTATGAAAAACGCCGCTAAAGGT-AGCAATAGCAGCGTTTT-T-TAAAAACGCC
311 TTGCAGCGTTTCTATGAAAAACGCCGCTAAAGGTAAGCAATAGCAGCGTTTTCTATAAAAACGCC
53950224 GCAAAAAAT
376 GCAAAAAAT
53950233 AAATCAATTTATAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACGGTGTCATTTTGTTCAA
1 AAATCAATTTATAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACGGTGTCATTTTGTTCAA
*
53950298 AATGAAATAGAAAAAACACCGTAAAAAATAAATCAATTTATAAAAAACAAAATAAAAAATTTTTA
66 AATGAAATAGAAAAAACACCGCAAAAAATAAATCAATTTATAAAAAACAAAATAAAAAATTTTTA
*
53950363 GAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAAAATTT-GCA-CGCCGCTAAAGGTAAG
131 GAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAAAATTTAGAAGCGCCGCTAAAGGTAAG
*
53950426 CAATAGCGGCGTTTTCTATAAAAACGCCACAAAAAGTAAATCAATTTATAAAAAATAAAATAAAA
196 CAATAGCGGCGTTTTCTATAAAAACGCCACAAAAAATAAATCAATTTATAAAAAATAAAATAAAA
** * * *
53950491 AATTTTTAGCATAGCAAAACGGTGTCATTTTGTTCAAAATGAAAAAAATTTTGCGGCGTTTCTAT
261 AATTTTTAAAACAGCAAAACGGCGTCATTTTGTTCAAAATGAAAAAAATTTTGCAGCGTTTCTAT
* *
53950556 GAAAAACGCTGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGCAAAAAAT
326 GAAAAACGCCGCTAAAGGTAAGCAATAGCAGCGTTTTCTATAAAAACGCCGCAAAAAAT
* * * * *
53950615 TAATCAATTTATAAAAAATAAAATAAAAAATTTTTCGAATAGTAAAACGGTGTCATTTTATTCAA
1 AAATCAATTTATAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACGGTGTCATTTTGTTCAA
* ******* **
53950680 AAGGAAATAGCGGTGTTTTTATAGCAAAAAATAAATCAATTTATAAAAAACAAAAT-AAAAATTT
66 AATGAAATA---GAAAAAACACCGCAAAAAATAAATCAATTTATAAAAAACAAAATAAAAAATTT
* *
53950744 TTAGAATAGCAAAAAGGCGTTGTTTTGTTCAAAATGAAAAAAAATTTA
128 TTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAAAATTTA
53950792 CGACATTTTT
Statistics
Matches: 512, Mismatches: 36, Indels: 29
0.89 0.06 0.05
Matches are distributed among these distances:
379 155 0.30
380 18 0.04
381 1 0.00
382 88 0.17
383 3 0.01
384 53 0.10
385 34 0.07
389 28 0.05
392 85 0.17
393 47 0.09
ACGTcount: A:0.48, C:0.12, G:0.13, T:0.27
Consensus pattern (384 bp):
AAATCAATTTATAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACGGTGTCATTTTGTTCAA
AATGAAATAGAAAAAACACCGCAAAAAATAAATCAATTTATAAAAAACAAAATAAAAAATTTTTA
GAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAAAATTTAGAAGCGCCGCTAAAGGTAAG
CAATAGCGGCGTTTTCTATAAAAACGCCACAAAAAATAAATCAATTTATAAAAAATAAAATAAAA
AATTTTTAAAACAGCAAAACGGCGTCATTTTGTTCAAAATGAAAAAAATTTTGCAGCGTTTCTAT
GAAAAACGCCGCTAAAGGTAAGCAATAGCAGCGTTTTCTATAAAAACGCCGCAAAAAAT
Found at i:53954584 original size:80 final size:80
Alignment explanation
Indices: 53954451--53954610 Score: 302
Period size: 80 Copynumber: 2.0 Consensus size: 80
53954441 ATCAACTACT
*
53954451 TTCGAAGGCCTTACTAGGAATTGAAATGGTGTGCAAAGAGATTGCTTCTTCTGATCTGATTTTTC
1 TTCGAAGGCCTTAATAGGAATTGAAATGGTGTGCAAAGAGATTGCTTCTTCTGATCTGATTTTTC
53954516 GATATAAATACTGGA
66 GATATAAATACTGGA
*
53954531 TTCGAAGGCCTTAATAGGAATTGAAATGTTGTGCAAAGAGATTGCTTCTTCTGATCTGATTTTTC
1 TTCGAAGGCCTTAATAGGAATTGAAATGGTGTGCAAAGAGATTGCTTCTTCTGATCTGATTTTTC
53954596 GATATAAATACTGGA
66 GATATAAATACTGGA
53954611 CAAAGTATGG
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
80 78 1.00
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.36
Consensus pattern (80 bp):
TTCGAAGGCCTTAATAGGAATTGAAATGGTGTGCAAAGAGATTGCTTCTTCTGATCTGATTTTTC
GATATAAATACTGGA
Found at i:53954784 original size:27 final size:26
Alignment explanation
Indices: 53954754--53954810 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
53954744 AATTTCGAGG
*
53954754 TTTACAATTTT-TAATTTTTATTAATT
1 TTTAC-ATTTTCTAACTTTTATTAATT
* *
53954780 ATTTACGTTTTCTCACTTTTATTAATT
1 -TTTACATTTTCTAACTTTTATTAATT
53954807 TTTA
1 TTTA
53954811 TTATTATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.26, C:0.09, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTACATTTTCTAACTTTTATTAATT
Found at i:53955219 original size:22 final size:22
Alignment explanation
Indices: 53955191--53955234 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
53955181 TAGCGGCGCT
*
53955191 AAAAAGCGCAGCTAAAGGCCTA
1 AAAAAGCGCAGCTAAAAGCCTA
*
53955213 AAAAAGCGCCGCTAAAAGCCTA
1 AAAAAGCGCAGCTAAAAGCCTA
53955235 TTTTGGTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.45, C:0.25, G:0.20, T:0.09
Consensus pattern (22 bp):
AAAAAGCGCAGCTAAAAGCCTA
Found at i:53957187 original size:7 final size:7
Alignment explanation
Indices: 53957175--53957208 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
53957165 TCCTATATTC
53957175 TCAATCT
1 TCAATCT
53957182 TCAATCT
1 TCAATCT
53957189 TCAATCT
1 TCAATCT
*
53957196 TCAATCC
1 TCAATCT
53957203 TCAATC
1 TCAATC
53957209 CCATTTTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.38
Consensus pattern (7 bp):
TCAATCT
Found at i:53957223 original size:7 final size:7
Alignment explanation
Indices: 53957213--53957265 Score: 56
Period size: 7 Copynumber: 7.6 Consensus size: 7
53957203 TCAATCCCAT
53957213 TTTTCAA
1 TTTTCAA
53957220 TTTT-ATA
1 TTTTCA-A
53957227 TTTTCAA
1 TTTTCAA
*
53957234 TCTTCAAA
1 TTTTC-AA
53957242 TTTT-AA
1 TTTTCAA
53957248 TTTTCAA
1 TTTTCAA
*
53957255 TTTTTAA
1 TTTTCAA
53957262 TTTT
1 TTTT
53957266 TAATCCTCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
6 7 0.18
7 26 0.67
8 6 0.15
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.62
Consensus pattern (7 bp):
TTTTCAA
Found at i:53957250 original size:21 final size:21
Alignment explanation
Indices: 53957218--53957269 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
53957208 CCCATTTTTC
53957218 AATTTTATATTTTCAATCTTCA
1 AATTTTA-ATTTTCAATCTTCA
* *
53957240 AATTTTAATTTTCAATTTTTA
1 AATTTTAATTTTCAATCTTCA
*
53957261 ATTTTTAAT
1 AATTTTAAT
53957270 CCTCAATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 20 0.74
22 7 0.26
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.60
Consensus pattern (21 bp):
AATTTTAATTTTCAATCTTCA
Found at i:53957319 original size:15 final size:15
Alignment explanation
Indices: 53957299--53957328 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
53957289 TATTTTTTGA
53957299 ATTTTATTATCTTCT
1 ATTTTATTATCTTCT
*
53957314 ATTTTATTATTTTCT
1 ATTTTATTATCTTCT
53957329 TATAAATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTTTATTATCTTCT
Found at i:53958728 original size:24 final size:23
Alignment explanation
Indices: 53958697--53958743 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
53958687 TATTCACACA
53958697 TATTCTTAC-TTAATTTCAAATGT
1 TATTCTTACATTAATTT-AAATGT
*
53958720 TATTACTTACATTACTTTAAATGT
1 TATT-CTTACATTAATTTAAATGT
53958744 CTCATGATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 11 0.52
25 6 0.29
ACGTcount: A:0.32, C:0.13, G:0.04, T:0.51
Consensus pattern (23 bp):
TATTCTTACATTAATTTAAATGT
Found at i:53959024 original size:22 final size:24
Alignment explanation
Indices: 53958982--53959025 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
53958972 TAACTAAGCT
53958982 TACTTACTTTTCTAACTTAATTCA
1 TACTTACTTTTCTAACTTAATTCA
53959006 TACTT-CTTTTCT-ACTTAATT
1 TACTTACTTTTCTAACTTAATT
53959026 TCTTGCCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.40
23 7 0.35
24 5 0.25
ACGTcount: A:0.25, C:0.20, G:0.00, T:0.55
Consensus pattern (24 bp):
TACTTACTTTTCTAACTTAATTCA
Found at i:53959645 original size:13 final size:11
Alignment explanation
Indices: 53959625--53959692 Score: 57
Period size: 13 Copynumber: 5.7 Consensus size: 11
53959615 AGTTTATTTA
53959625 ATATATAATAAT
1 ATATATAAT-AT
53959637 ATGATATAATAT
1 AT-ATATAATAT
53959649 AATTATATAATAT
1 -A-TATATAATAT
*
53959662 AT-TATATTAT
1 ATATATAATAT
*
53959672 ATAATAAAATAAT
1 AT-ATATAAT-AT
53959685 ATATATAA
1 ATATATAA
53959693 AACATAAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
10 9 0.20
11 1 0.02
12 14 0.30
13 21 0.46
14 1 0.02
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (11 bp):
ATATATAATAT
Found at i:53959648 original size:5 final size:5
Alignment explanation
Indices: 53959623--53959692 Score: 53
Period size: 5 Copynumber: 14.6 Consensus size: 5
53959613 TTAGTTTATT
*
53959623 TAATA T-ATAA TAATA TGATA TAATA TAAT- T-ATA TAATA TATTATA
1 TAATA TAAT-A TAATA TAATA TAATA TAATA TAATA TAATA TA--ATA
*
53959668 TTATA TAATA -AA-A TAATA T-ATA TAA
1 TAATA TAATA TAATA TAATA TAATA TAA
53959693 AACATAAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 18
0.70 0.05 0.24
Matches are distributed among these distances:
3 3 0.06
4 12 0.23
5 31 0.60
6 2 0.04
7 4 0.08
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (5 bp):
TAATA
Found at i:53959676 original size:30 final size:29
Alignment explanation
Indices: 53959623--53959691 Score: 86
Period size: 30 Copynumber: 2.4 Consensus size: 29
53959613 TTAGTTTATT
* *
53959623 TAATATATA-ATAATATGATATAATATAA
1 TAATATATATATTATATGATATAATAAAA
* *
53959651 TTATATAATATATTATATTATATAATAAAA
1 TAATAT-ATATATTATATGATATAATAAAA
53959681 TAATATATATA
1 TAATATATATA
53959692 AAACATAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 5 0.15
29 8 0.24
30 21 0.62
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (29 bp):
TAATATATATATTATATGATATAATAAAA
Found at i:53959815 original size:23 final size:23
Alignment explanation
Indices: 53959789--53959833 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
53959779 ATTAATCTAT
53959789 AATTCAACT-TTTACTCCTAATTC
1 AATTCAACTCTTT-CTCCTAATTC
* *
53959812 AATTTAACTCTTTTTCCTAATT
1 AATTCAACTCTTTCTCCTAATT
53959834 TCTCTTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.29, C:0.22, G:0.00, T:0.49
Consensus pattern (23 bp):
AATTCAACTCTTTCTCCTAATTC
Found at i:53966489 original size:21 final size:23
Alignment explanation
Indices: 53966460--53966506 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
53966450 CGTGAATTAA
53966460 GTTTATAATA-TT-TAATCTATT
1 GTTTATAATAGTTATAATCTATT
* *
53966481 GTTTTTAATAGTTATAATGTATT
1 GTTTATAATAGTTATAATCTATT
53966504 GTT
1 GTT
53966507 ACAATAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 2 0.09
23 11 0.50
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (23 bp):
GTTTATAATAGTTATAATCTATT
Found at i:53969460 original size:17 final size:18
Alignment explanation
Indices: 53969429--53969463 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
53969419 ATTTAATTAT
53969429 CAATTTATACAAATTTTG
1 CAATTTATACAAATTTTG
*
53969447 CAATTTATTC-AATTTTG
1 CAATTTATACAAATTTTG
53969464 TCCCTAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.34, C:0.11, G:0.06, T:0.49
Consensus pattern (18 bp):
CAATTTATACAAATTTTG
Found at i:53980998 original size:30 final size:29
Alignment explanation
Indices: 53980964--53981041 Score: 93
Period size: 31 Copynumber: 2.6 Consensus size: 29
53980954 ATAAAAGTAG
* *
53980964 AAAATTATAAAAATTATAGAATAACTATAA
1 AAAATTATAAAAATTATACAA-AACTACAA
*
53980994 AAAATTATAAAAATATTATACAAAATTACAA
1 AAAATTAT-AAAA-ATTATACAAAACTACAA
*
53981025 AAAAATATAAAAATTAT
1 AAAATTATAAAAATTAT
53981042 TAATATATTA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 5 0.12
30 12 0.29
31 17 0.40
32 8 0.19
ACGTcount: A:0.65, C:0.04, G:0.01, T:0.29
Consensus pattern (29 bp):
AAAATTATAAAAATTATACAAAACTACAA
Found at i:53981006 original size:11 final size:11
Alignment explanation
Indices: 53980964--53981037 Score: 59
Period size: 10 Copynumber: 7.2 Consensus size: 11
53980954 ATAAAAGTAG
53980964 AAAATTAT--A
1 AAAATTATAAA
*
53980973 AAAATTATAGA
1 AAAATTATAAA
* *
53980984 ATAACTAT-AA
1 AAAATTATAAA
53980994 AAAATTATAAA
1 AAAATTATAAA
* *
53981005 AATATTAT-AC
1 AAAATTATAAA
*
53981015 AAAATTACAAA
1 AAAATTATAAA
53981026 AAAA-TATAAA
1 AAAATTATAAA
53981036 AA
1 AA
53981038 TTATTAATAT
Statistics
Matches: 50, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
9 8 0.16
10 21 0.42
11 21 0.42
ACGTcount: A:0.68, C:0.04, G:0.01, T:0.27
Consensus pattern (11 bp):
AAAATTATAAA
Found at i:53981013 original size:21 final size:21
Alignment explanation
Indices: 53980967--53981077 Score: 88
Period size: 21 Copynumber: 5.5 Consensus size: 21
53980957 AAAGTAGAAA
*
53980967 ATTAT-AAAAATTAT-AGAAT
1 ATTATAAAAAATTATAAAAAT
*
53980986 AACTATAAAAAATTATAAAAAT
1 -ATTATAAAAAATTATAAAAAT
* *
53981008 ATTATACAAAATTACAAAAA-
1 ATTATAAAAAATTATAAAAAT
* * *
53981028 AATAT-AAAAATTATTAATAT
1 ATTATAAAAAATTATAAAAAT
* **
53981048 ATTATGAAAAA-TATGCAAAT
1 ATTATAAAAAATTATAAAAAT
53981068 ATTATAAAAA
1 ATTATAAAAA
53981078 CTAGAATTAT
Statistics
Matches: 72, Mismatches: 15, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
19 10 0.14
20 27 0.38
21 31 0.43
22 4 0.06
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.32
Consensus pattern (21 bp):
ATTATAAAAAATTATAAAAAT
Found at i:53981125 original size:11 final size:11
Alignment explanation
Indices: 53981109--53981141 Score: 52
Period size: 10 Copynumber: 3.2 Consensus size: 11
53981099 TAAAGTATAT
53981109 AAAATTGATAA
1 AAAATTGATAA
53981120 AAAATTG-TAA
1 AAAATTGATAA
53981130 AAAATT-ATAA
1 AAAATTGATAA
53981140 AA
1 AA
53981142 CTATATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 14 0.67
11 7 0.33
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (11 bp):
AAAATTGATAA
Found at i:53981437 original size:8 final size:8
Alignment explanation
Indices: 53981424--53981450 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
53981414 TAAAAATTAT
53981424 TTAAAATA
1 TTAAAATA
53981432 TTAAAATA
1 TTAAAATA
53981440 TTAAAATA
1 TTAAAATA
53981448 TTA
1 TTA
53981451 TGAAATTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
TTAAAATA
Found at i:53981582 original size:20 final size:21
Alignment explanation
Indices: 53981557--53981602 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
53981547 TGATTTTATG
53981557 ATTTTA-ATAAATTTTAA-ATA
1 ATTTTATAT-AATTTTAACATA
*
53981577 ATTTTATATCATTTTAACATA
1 ATTTTATATAATTTTAACATA
53981598 ATTTT
1 ATTTT
53981603 CTATGACTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTTTATATAATTTTAACATA
Found at i:53982105 original size:4 final size:4
Alignment explanation
Indices: 53982096--53982172 Score: 136
Period size: 4 Copynumber: 19.2 Consensus size: 4
53982086 ATCTAACCTC
* *
53982096 GTAT GTAT GTAT GTAC GTAC GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
53982144 GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
53982173 AGTTTAGAGA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 71 1.00
ACGTcount: A:0.25, C:0.03, G:0.26, T:0.47
Consensus pattern (4 bp):
GTAT
Found at i:53985165 original size:16 final size:17
Alignment explanation
Indices: 53985146--53985177 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
53985136 GTTAAAGAAC
53985146 TAGTGT-AATAAAAATA
1 TAGTGTGAATAAAAATA
53985162 TAGTGTGAATAAAAAT
1 TAGTGTGAATAAAAAT
53985178 GAAGAACGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.31
Consensus pattern (17 bp):
TAGTGTGAATAAAAATA
Found at i:53991644 original size:15 final size:15
Alignment explanation
Indices: 53991624--53991656 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
53991614 TTCCAAATGT
53991624 TAGTTGTTCTCAACA
1 TAGTTGTTCTCAACA
*
53991639 TAGTTGTTCTCAATA
1 TAGTTGTTCTCAACA
53991654 TAG
1 TAG
53991657 AGATTGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (15 bp):
TAGTTGTTCTCAACA
Found at i:53991762 original size:16 final size:16
Alignment explanation
Indices: 53991741--53991800 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
53991731 GGAAAAAAAA
53991741 TTGTTCTAAATACA-AG
1 TTGTTCTAAA-ACATAG
* *
53991757 TTGTTCCAAAACATGG
1 TTGTTCTAAAACATAG
53991773 TTGTTCT-AAACATAG
1 TTGTTCTAAAACATAG
*
53991788 TTATTCCTAAAAC
1 TTGTT-CTAAAAC
53991801 GTCATTATTC
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
15 14 0.39
16 18 0.50
17 4 0.11
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.37
Consensus pattern (16 bp):
TTGTTCTAAAACATAG
Found at i:54001575 original size:23 final size:22
Alignment explanation
Indices: 54001533--54001575 Score: 52
Period size: 22 Copynumber: 1.9 Consensus size: 22
54001523 TATAAGACAA
*
54001533 AAAAAATTCAAGTATCAATTTG
1 AAAAAATTCAAGTATAAATTTG
54001555 AAAAAATT-AAGGTACTAAATT
1 AAAAAATTCAA-GTA-TAAATT
54001576 AAATATTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 2 0.11
22 11 0.61
23 5 0.28
ACGTcount: A:0.53, C:0.07, G:0.09, T:0.30
Consensus pattern (22 bp):
AAAAAATTCAAGTATAAATTTG
Found at i:54004992 original size:15 final size:16
Alignment explanation
Indices: 54004967--54004996 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
54004957 TAATTACAAT
54004967 TTGTAATCATCAAGCC
1 TTGTAATCATCAAGCC
54004983 TTGT-ATCATCAAGC
1 TTGTAATCATCAAGC
54004997 TAAACACATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.33
Consensus pattern (16 bp):
TTGTAATCATCAAGCC
Found at i:54011788 original size:25 final size:25
Alignment explanation
Indices: 54011707--54011813 Score: 121
Period size: 25 Copynumber: 4.3 Consensus size: 25
54011697 CTATAGCTCT
*
54011707 TATGAGCTTATCGATTCTCAACTCG
1 TATGAGCTTACCGATTCTCAACTCG
*
54011732 TATGAGCTTACTGATTCTCAACTCG
1 TATGAGCTTACCGATTCTCAACTCG
*
54011757 TATGAGCTTACCGATT-TACAACTCA
1 TATGAGCTTACCGATTCT-CAACTCG
* *
54011782 TGA-GAGCATACCGATTCAT-AGCTCG
1 T-ATGAGCTTACCGATTC-TCAACTCG
54011807 TATGAGC
1 TATGAGC
54011814 ATACATGTAC
Statistics
Matches: 70, Mismatches: 7, Indels: 10
0.80 0.08 0.11
Matches are distributed among these distances:
24 2 0.03
25 66 0.94
26 1 0.01
27 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (25 bp):
TATGAGCTTACCGATTCTCAACTCG
Found at i:54012483 original size:21 final size:21
Alignment explanation
Indices: 54012444--54012488 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
54012434 TATTTGAGCT
*
54012444 AATGAAAGTAAATGCAATGGA
1 AATGAAAGTAAATGCAATGAA
*
54012465 AATGAATG-AAATGCAAATGAA
1 AATGAAAGTAAATGC-AATGAA
54012486 AAT
1 AAT
54012489 AAGAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.56, C:0.04, G:0.20, T:0.20
Consensus pattern (21 bp):
AATGAAAGTAAATGCAATGAA
Found at i:54016594 original size:13 final size:13
Alignment explanation
Indices: 54016576--54016617 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
54016566 AACAGGTAAC
* *
54016576 AAAAAACAATTTA
1 AAAAAAAAATCTA
54016589 AAAAAAAAATCTA
1 AAAAAAAAATCTA
*
54016602 AAAAATAAA-CTA
1 AAAAAAAAATCTA
54016614 AAAA
1 AAAA
54016618 CAACTTACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 7 0.27
13 19 0.73
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.17
Consensus pattern (13 bp):
AAAAAAAAATCTA
Found at i:54020326 original size:18 final size:18
Alignment explanation
Indices: 54020303--54020340 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
54020293 TTATTAACCA
54020303 AGCGAGACTCCACAAAGT
1 AGCGAGACTCCACAAAGT
54020321 AGCGAGACTCCACAAAGT
1 AGCGAGACTCCACAAAGT
54020339 AG
1 AG
54020341 GATTTGTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.26, G:0.24, T:0.11
Consensus pattern (18 bp):
AGCGAGACTCCACAAAGT
Found at i:54028889 original size:24 final size:24
Alignment explanation
Indices: 54028862--54028907 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
54028852 AATCTGCGTC
* *
54028862 TGCATTTGTATCTAAATTTGAATA
1 TGCATATGTATCTAAATCTGAATA
54028886 TGCATATGTATCTAAATCTGAA
1 TGCATATGTATCTAAATCTGAA
54028908 AATACATCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.41
Consensus pattern (24 bp):
TGCATATGTATCTAAATCTGAATA
Found at i:54030364 original size:21 final size:21
Alignment explanation
Indices: 54030320--54030364 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
54030310 TTTGTAGAAA
*
54030320 TTAAAAATATTTGAAATTTCT
1 TTAAAAATATTAGAAATTTCT
*
54030341 TTAAAAACTATTAGAACTTT-T
1 TTAAAAA-TATTAGAAATTTCT
54030362 TTA
1 TTA
54030365 GAACTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (21 bp):
TTAAAAATATTAGAAATTTCT
Found at i:54030453 original size:11 final size:11
Alignment explanation
Indices: 54030439--54030464 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
54030429 TTTAGTTGAA
54030439 TTTTTTTCTAT
1 TTTTTTTCTAT
54030450 TTTTTTTCTAT
1 TTTTTTTCTAT
54030461 TTTT
1 TTTT
54030465 ATAATTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTCTAT
Found at i:54030988 original size:18 final size:19
Alignment explanation
Indices: 54030953--54030991 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
54030943 TTTTAATAAC
**
54030953 TTTTTATATATTTTTAAAA
1 TTTTTATATATTAATAAAA
54030972 TTTTTATA-ATTAATAAAA
1 TTTTTATATATTAATAAAA
54030990 TT
1 TT
54030992 ATATCTCGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTTATATATTAATAAAA
Found at i:54031348 original size:9 final size:9
Alignment explanation
Indices: 54031330--54031369 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
54031320 TTTGGTTAAA
54031330 AATTAACCG
1 AATTAACCG
*
54031339 AATTACCCG
1 AATTAACCG
*
54031348 AATTAACTG
1 AATTAACCG
54031357 AATTAACCG
1 AATTAACCG
54031366 AATT
1 AATT
54031370 GAATCACTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:54031420 original size:6 final size:6
Alignment explanation
Indices: 54031389--54031437 Score: 62
Period size: 6 Copynumber: 7.7 Consensus size: 6
54031379 CATAATTAAA
*
54031389 TTAGTT TTAGACTT TTAGACT TTAGTT TTAGTT TTAGTT TTAGTT TTAG
1 TTAGTT TTAG--TT TTAG-TT TTAGTT TTAGTT TTAGTT TTAGTT TTAG
54031438 AATTTTATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
6 27 0.71
7 5 0.13
8 6 0.16
ACGTcount: A:0.20, C:0.04, G:0.16, T:0.59
Consensus pattern (6 bp):
TTAGTT
Found at i:54031518 original size:18 final size:18
Alignment explanation
Indices: 54031478--54031521 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
54031468 AATTTTTATG
**
54031478 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
54031496 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
54031514 TTTGGGTT
1 ATTGGGTT
54031522 TGGATTGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.00, G:0.43, T:0.43
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:54056028 original size:11 final size:11
Alignment explanation
Indices: 54055998--54056043 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
54055988 ATATTCAAAC
*
54055998 AATAATAACAA
1 AATAATAGCAA
*
54056009 AATAGTAGCAA
1 AATAATAGCAA
*
54056020 TATAATAGCAA
1 AATAATAGCAA
*
54056031 AATAATAGTAA
1 AATAATAGCAA
54056042 AA
1 AA
54056044 CGGCAACAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.63, C:0.07, G:0.09, T:0.22
Consensus pattern (11 bp):
AATAATAGCAA
Found at i:54078475 original size:19 final size:20
Alignment explanation
Indices: 54078432--54078479 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
54078422 ATTAAAATTT
54078432 TAAAT-TTAAAAAAATATAA
1 TAAATATTAAAAAAATATAA
*
54078451 -AGATATTAAAAAAATA-AA
1 TAAATATTAAAAAAATATAA
54078469 TAAATA-TAAAA
1 TAAATATTAAAA
54078480 TATAAGCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (20 bp):
TAAATATTAAAAAAATATAA
Found at i:54086810 original size:37 final size:37
Alignment explanation
Indices: 54086731--54086832 Score: 100
Period size: 37 Copynumber: 2.8 Consensus size: 37
54086721 AAGGAGCTAT
* * *
54086731 GCTCAAAATTTAGTGAG-TAGAATCTGAGAAGGTATAA
1 GCTCAAAATTTAGTGAGTTATACT-TGAGAAGGTACAA
* *
54086768 ACTCAAAATTTAGTGAGTTATACTTGAGAAGGTACGA
1 GCTCAAAATTTAGTGAGTTATACTTGAGAAGGTACAA
** *
54086805 GCTCAATTTTTAAG-GAGTTGTACTTGAG
1 GCTCAAAATTT-AGTGAGTTATACTTGAG
54086833 GTGTAAACTA
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
37 48 0.89
38 6 0.11
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.31
Consensus pattern (37 bp):
GCTCAAAATTTAGTGAGTTATACTTGAGAAGGTACAA
Found at i:54086854 original size:71 final size:71
Alignment explanation
Indices: 54086760--54086897 Score: 168
Period size: 71 Copynumber: 1.9 Consensus size: 71
54086750 GAATCTGAGA
* * * * * * *
54086760 AGGTATAAACTCAAAATTTAGTGAGTTATACTTGAGAAGGTACGAGCTCAATTTTTAAGGAGTTG
1 AGGTATAAACTAAAAACTTAGTGAGATATACCTGAAAAGGTACGAGCTCAAATTTTAAGGACTTG
54086825 TACTTG
66 TACTTG
* * ** *
54086831 AGGTGTAAACTAAAAACTTAGTGAGATGTACCTGAAAAGGTGTGAGCTCAAATTTTAGGGACTTG
1 AGGTATAAACTAAAAACTTAGTGAGATATACCTGAAAAGGTACGAGCTCAAATTTTAAGGACTTG
54086896 TA
66 TA
54086898 TTTAGGAAGG
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
71 55 1.00
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.31
Consensus pattern (71 bp):
AGGTATAAACTAAAAACTTAGTGAGATATACCTGAAAAGGTACGAGCTCAAATTTTAAGGACTTG
TACTTG
Done.