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 168 of 313
Found at i:52619748 original size:36 final size:36
Alignment explanation
Indices: 52619699--52619809 Score: 102
Period size: 26 Copynumber: 3.4 Consensus size: 36
52619689 ACTCAAAATA
*
52619699 ATACACAAAATAATACACACTAAAATTATTAATTTT
1 ATACTCAAAATAATACACACTAAAATTATTAATTTT
* *
52619735 ATACTC---ATAAT--A-A-T---ATTAATAAATTT
1 ATACTCAAAATAATACACACTAAAATTATTAATTTT
52619761 ATACTCAAAATAATACACACTAAAATTATTAA-TTT
1 ATACTCAAAATAATACACACTAAAATTATTAATTTT
*
52619796 -TACTAAAAATAATA
1 ATACTCAAAATAATA
52619810 ACTAACTAAC
Statistics
Matches: 60, Mismatches: 5, Indels: 22
0.69 0.06 0.25
Matches are distributed among these distances:
26 16 0.27
29 6 0.10
30 1 0.02
31 2 0.03
32 1 0.02
33 6 0.10
34 13 0.22
35 3 0.05
36 12 0.20
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (36 bp):
ATACTCAAAATAATACACACTAAAATTATTAATTTT
Found at i:52619837 original size:62 final size:62
Alignment explanation
Indices: 52619699--52619814 Score: 155
Period size: 62 Copynumber: 1.9 Consensus size: 62
52619689 ACTCAAAATA
* * * * **
52619699 ATACACAAAATAATACACACTAAAATTATTAATTTTATACTCATAATAATATTAATAAATTT
1 ATACTCAAAATAATACACACTAAAATTATTAATTTTATACTAAAAATAATACTAATAAAACT
52619761 ATACTCAAAATAATACACACTAAAATTATTAA-TTT-TACTAAAAATAATAACTAA
1 ATACTCAAAATAATACACACTAAAATTATTAATTTTATACTAAAAATAAT-ACTAA
52619815 CTAACTAACT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
60 11 0.22
61 7 0.14
62 31 0.63
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (62 bp):
ATACTCAAAATAATACACACTAAAATTATTAATTTTATACTAAAAATAATACTAATAAAACT
Found at i:52619977 original size:3 final size:3
Alignment explanation
Indices: 52619969--52620009 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
52619959 TCTTAATACT
52619969 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
52620010 TAATAATAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:52620014 original size:3 final size:3
Alignment explanation
Indices: 52620008--52620041 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
52619998 CAACAACAAC
52620008 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
52620042 CTATTATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:52620111 original size:19 final size:21
Alignment explanation
Indices: 52620087--52620125 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
52620077 ACTAAAACAA
*
52620087 AAAAT-ATTACAA-AATATAC
1 AAAATAATAACAACAATATAC
52620106 AAAATAATAACAACAATATA
1 AAAATAATAACAACAATATA
52620126 ATCAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAATAATAACAACAATATAC
Found at i:52620332 original size:27 final size:27
Alignment explanation
Indices: 52620257--52620324 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
52620247 ATAATACGAG
52620257 TGGTGCCGCCAATTAGTA-TGGCACCAT
1 TGGTGCCGCCAA-TAGTATTGGCACCAT
* * *
52620284 TGGTGCCGCCAATGGTTTTGGCACCTT
1 TGGTGCCGCCAATAGTATTGGCACCAT
52620311 TGGTGCCGCCAATA
1 TGGTGCCGCCAATA
52620325 CCATTGGCGT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
26 3 0.08
27 33 0.92
ACGTcount: A:0.18, C:0.26, G:0.28, T:0.28
Consensus pattern (27 bp):
TGGTGCCGCCAATAGTATTGGCACCAT
Found at i:52620411 original size:27 final size:28
Alignment explanation
Indices: 52620372--52620426 Score: 103
Period size: 27 Copynumber: 2.0 Consensus size: 28
52620362 TTTTTTTTTG
52620372 TTTTTTTTGATATATTTTGGTAAATAAA
1 TTTTTTTTGATATATTTTGGTAAATAAA
52620400 TTTTTTTT-ATATATTTTGGTAAATAAA
1 TTTTTTTTGATATATTTTGGTAAATAAA
52620427 AAAAAGTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 19 0.70
28 8 0.30
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (28 bp):
TTTTTTTTGATATATTTTGGTAAATAAA
Found at i:52622348 original size:27 final size:27
Alignment explanation
Indices: 52622318--52622372 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
52622308 TTGTAAATAC
52622318 ATTTTATATGCATATATCACATGTTTT
1 ATTTTATATGCATATATCACATGTTTT
52622345 ATTTTATATGCATATATCACATGTTTT
1 ATTTTATATGCATATATCACATGTTTT
52622372 A
1 A
52622373 CAAAAATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.31, C:0.11, G:0.07, T:0.51
Consensus pattern (27 bp):
ATTTTATATGCATATATCACATGTTTT
Found at i:52623037 original size:16 final size:16
Alignment explanation
Indices: 52623016--52623047 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
52623006 TAACTGTAGT
52623016 AAATAAAAATTAGCAA
1 AAATAAAAATTAGCAA
52623032 AAATAAAAATTAGCAA
1 AAATAAAAATTAGCAA
52623048 CACAATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (16 bp):
AAATAAAAATTAGCAA
Found at i:52634348 original size:12 final size:12
Alignment explanation
Indices: 52634331--52634360 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
52634321 AGCAACAAGG
*
52634331 TATAAACCAGAT
1 TATAAACCAGAA
52634343 TATAAACCAGAA
1 TATAAACCAGAA
52634355 TATAAA
1 TATAAA
52634361 ATTTCAGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.57, C:0.13, G:0.07, T:0.23
Consensus pattern (12 bp):
TATAAACCAGAA
Found at i:52634398 original size:47 final size:47
Alignment explanation
Indices: 52634343--52634464 Score: 217
Period size: 47 Copynumber: 2.6 Consensus size: 47
52634333 TAAACCAGAT
52634343 TATAAACCAGAATATAAAATTTCAGATATAAAAAAGAAGCAACAAGG
1 TATAAACCAGAATATAAAATTTCAGATATAAAAAAGAAGCAACAAGG
*
52634390 TATAAACCAGAATATAAAATTTCAAATATAAAAAAGAAGCAACAAGG
1 TATAAACCAGAATATAAAATTTCAGATATAAAAAAGAAGCAACAAGG
* *
52634437 TATAAACCAGATTATAAAATTTAAGATA
1 TATAAACCAGAATATAAAATTTCAGATA
52634465 AGAGAAAGTA
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 71 1.00
ACGTcount: A:0.57, C:0.10, G:0.11, T:0.22
Consensus pattern (47 bp):
TATAAACCAGAATATAAAATTTCAGATATAAAAAAGAAGCAACAAGG
Found at i:52634610 original size:14 final size:14
Alignment explanation
Indices: 52634591--52634617 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
52634581 AAATGGAACT
52634591 GTAAGGCAACAACA
1 GTAAGGCAACAACA
52634605 GTAAGGCAACAAC
1 GTAAGGCAACAAC
52634618 GACAGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.22, G:0.22, T:0.07
Consensus pattern (14 bp):
GTAAGGCAACAACA
Found at i:52634644 original size:59 final size:59
Alignment explanation
Indices: 52634574--52634692 Score: 220
Period size: 59 Copynumber: 2.0 Consensus size: 59
52634564 CTTTTGAACG
*
52634574 ACTAAACAAATGGAACTGTAAGGCAACAACAGTAAGGCAACAACGACAGATTATAAACA
1 ACTAAACAAATGGAACTGTAAGGAAACAACAGTAAGGCAACAACGACAGATTATAAACA
*
52634633 ACTAAACAAATGGAATTGTAAGGAAACAACAGTAAGGCAACAACGACAGATTATAAACA
1 ACTAAACAAATGGAACTGTAAGGAAACAACAGTAAGGCAACAACGACAGATTATAAACA
52634692 A
1 A
52634693 GGTTTTGAAC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.52, C:0.17, G:0.17, T:0.14
Consensus pattern (59 bp):
ACTAAACAAATGGAACTGTAAGGAAACAACAGTAAGGCAACAACGACAGATTATAAACA
Found at i:52635543 original size:20 final size:20
Alignment explanation
Indices: 52635520--52635558 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
52635510 ATCAATAATT
52635520 AATTAAATT-TTAAAAATATA
1 AATT-AATTATTAAAAATATA
*
52635540 AATTATTTATTAAAAATAT
1 AATTAATTATTAAAAATAT
52635559 TATTCAACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AATTAATTATTAAAAATATA
Found at i:52640302 original size:34 final size:34
Alignment explanation
Indices: 52640259--52640324 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
52640249 TGGTAGGGTG
* *
52640259 TCTATTATTGT-AAGTGGAGTTCTTTCTTGGCATT
1 TCTATTATTGTCAA-TGGAGTTATTGCTTGGCATT
52640293 TCTATTATTGTCAATGGAGTTATTGCTTGGCA
1 TCTATTATTGTCAATGGAGTTATTGCTTGGCA
52640325 GTAAATGATG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 27 0.93
35 2 0.07
ACGTcount: A:0.20, C:0.12, G:0.21, T:0.47
Consensus pattern (34 bp):
TCTATTATTGTCAATGGAGTTATTGCTTGGCATT
Found at i:52646752 original size:23 final size:22
Alignment explanation
Indices: 52646668--52646751 Score: 100
Period size: 23 Copynumber: 3.8 Consensus size: 22
52646658 ATCAGTATAT
52646668 GACACAT-AAGTGCCTG-AAAC
1 GACACATAAAGTGCCTGAAAAC
* *
52646688 GACACATGAGGTGCCTGAAATAC
1 GACACATAAAGTGCCTGAAA-AC
*
52646711 GACATATAAAGTGCCTGATAAAC
1 GACACATAAAGTGCCTGA-AAAC
*
52646734 GACACATAAAGTGTCTGA
1 GACACATAAAGTGCCTGA
52646752 TCGGCAAGGC
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
20 7 0.13
21 8 0.15
22 2 0.04
23 35 0.65
24 2 0.04
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.19
Consensus pattern (22 bp):
GACACATAAAGTGCCTGAAAAC
Found at i:52647156 original size:3 final size:3
Alignment explanation
Indices: 52647148--52647178 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
52647138 TAGCTACGAA
52647148 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
52647179 CTATTAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:52647702 original size:9 final size:9
Alignment explanation
Indices: 52647690--52647738 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
52647680 CTGGTGTTCT
*
52647690 TTTTGTTTC
1 TTTTCTTTC
52647699 TTTTAC-TTC
1 TTTT-CTTTC
52647708 TTTTCTTTC
1 TTTTCTTTC
52647717 TTTTCTTTC
1 TTTTCTTTC
**
52647726 TTTAGTTTC
1 TTTTCTTTC
52647735 TTTT
1 TTTT
52647739 ATTTACTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
8 1 0.03
9 33 0.97
ACGTcount: A:0.04, C:0.16, G:0.04, T:0.76
Consensus pattern (9 bp):
TTTTCTTTC
Found at i:52647711 original size:18 final size:19
Alignment explanation
Indices: 52647690--52647739 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
52647680 CTGGTGTTCT
52647690 TTTTGTTTCTTTTAC-TTC
1 TTTTGTTTCTTTTACTTTC
*
52647708 TTTTCTTTCTTTT-CTTTC
1 TTTTGTTTCTTTTACTTTC
*
52647726 TTTAGTTTCTTTTA
1 TTTTGTTTCTTTTA
52647740 TTTACTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 1 0.04
18 26 0.96
ACGTcount: A:0.06, C:0.16, G:0.04, T:0.74
Consensus pattern (19 bp):
TTTTGTTTCTTTTACTTTC
Found at i:52647743 original size:14 final size:14
Alignment explanation
Indices: 52647735--52647764 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
52647725 CTTTAGTTTC
52647735 TTTTATTTACTTTA
1 TTTTATTTACTTTA
52647749 TTTTATTTACTTTA
1 TTTTATTTACTTTA
52647763 TT
1 TT
52647765 GTATCTTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTTATTTACTTTA
Found at i:52647845 original size:24 final size:24
Alignment explanation
Indices: 52647796--52647845 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
52647786 AGTAAACCAA
* * *
52647796 TTATTTAATTACATTTGTACATAT
1 TTATATAATTACACTTGTACAAAT
*
52647820 TTATATAATTACACTTGTATAAAT
1 TTATATAATTACACTTGTACAAAT
52647844 TT
1 TT
52647846 TGTACTATAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.08, G:0.04, T:0.52
Consensus pattern (24 bp):
TTATATAATTACACTTGTACAAAT
Found at i:52648069 original size:13 final size:13
Alignment explanation
Indices: 52648051--52648077 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
52648041 CCTTAATTAA
52648051 TAATATCTTCAAT
1 TAATATCTTCAAT
52648064 TAATATCTTCAAT
1 TAATATCTTCAAT
52648077 T
1 T
52648078 CAATCAACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.00, T:0.48
Consensus pattern (13 bp):
TAATATCTTCAAT
Found at i:52653926 original size:23 final size:23
Alignment explanation
Indices: 52653900--52654110 Score: 341
Period size: 23 Copynumber: 9.2 Consensus size: 23
52653890 GTTATTGATT
52653900 AGTGGTAGCTTCGGCTACATATC
1 AGTGGTAGCTTCGGCTACATATC
*
52653923 AGTGGTAGCTTCGGCTACGTATC
1 AGTGGTAGCTTCGGCTACATATC
52653946 AGTGGTAGCTTCGGCTACATATC
1 AGTGGTAGCTTCGGCTACATATC
*
52653969 AGTGGTAGCTTCGGCTACGTATC
1 AGTGGTAGCTTCGGCTACATATC
52653992 AGTGGTAGCTTCGGCTACATATC
1 AGTGGTAGCTTCGGCTACATATC
* *
52654015 AGTGGTAGCTTCGGTTACATACC
1 AGTGGTAGCTTCGGCTACATATC
* *
52654038 AGTGGTAGCTTCGACTACATTTC
1 AGTGGTAGCTTCGGCTACATATC
* * *
52654061 AGTGGTGGCTACGGCTACGTATC
1 AGTGGTAGCTTCGGCTACATATC
52654084 AGTGGTAGCTTCGGCTACATATC
1 AGTGGTAGCTTCGGCTACATATC
52654107 AGTG
1 AGTG
52654111 TGGCACTGAT
Statistics
Matches: 170, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 170 1.00
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.30
Consensus pattern (23 bp):
AGTGGTAGCTTCGGCTACATATC
Found at i:52658693 original size:18 final size:17
Alignment explanation
Indices: 52658660--52658698 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
52658650 TTTTATAAAT
52658660 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
52658678 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
52658695 TGTG
1 TGTG
52658699 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:52658950 original size:23 final size:23
Alignment explanation
Indices: 52658924--52659068 Score: 245
Period size: 23 Copynumber: 6.3 Consensus size: 23
52658914 AGTGTTATTG
52658924 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
52658947 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
52658970 ATCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
52658993 ATTAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * *
52659016 TTCAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
52659039 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
52659062 ATCAGTG
1 ATCAGTG
52659069 TGGCACTTAT
Statistics
Matches: 112, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 112 1.00
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:52660856 original size:9 final size:9
Alignment explanation
Indices: 52660842--52660915 Score: 86
Period size: 9 Copynumber: 8.8 Consensus size: 9
52660832 TTTGGTTAAA
52660842 AATTACCCG
1 AATTACCCG
52660851 AATTACCCG
1 AATTACCCG
52660860 -----CCCG
1 AATTACCCG
52660864 AATTACCCG
1 AATTACCCG
52660873 AATTACCCG
1 AATTACCCG
*
52660882 AATTAACCG
1 AATTACCCG
*
52660891 AATTAACCG
1 AATTACCCG
*
52660900 AATTAACCG
1 AATTACCCG
52660909 AATTACC
1 AATTACC
52660916 GAAAAATACC
Statistics
Matches: 58, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
4 4 0.07
9 54 0.93
ACGTcount: A:0.36, C:0.31, G:0.11, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:52660865 original size:13 final size:13
Alignment explanation
Indices: 52660847--52660872 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52660837 TTAAAAATTA
52660847 CCCGAATTACCCG
1 CCCGAATTACCCG
52660860 CCCGAATTACCCG
1 CCCGAATTACCCG
52660873 AATTACCCGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.46, G:0.15, T:0.15
Consensus pattern (13 bp):
CCCGAATTACCCG
Found at i:52661174 original size:18 final size:18
Alignment explanation
Indices: 52661125--52661175 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
52661115 TTTATTAATT
*
52661125 TTTTCGGTTAACCAAAAA
1 TTTTCGGTTAACCGAAAA
52661143 TTTTCGGTTAACCGAAAA
1 TTTTCGGTTAACCGAAAA
52661161 TTTTCGGTTAACCGA
1 TTTTCGGTTAACCGA
52661176 CCGGTTTCGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (18 bp):
TTTTCGGTTAACCGAAAA
Found at i:52666568 original size:30 final size:31
Alignment explanation
Indices: 52666532--52666591 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
52666522 AAACCTTTTA
*
52666532 TTTTCCCCCAAAATTTTTATTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTATTCCCTTCCCAC
*
52666562 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTATTCCCTTCCCA
52666592 TCCCACCTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTATTCCCTTCCCAC
Found at i:52670766 original size:4 final size:4
Alignment explanation
Indices: 52670757--52670789 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
52670747 CCTCAATTAA
52670757 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT T
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT T
52670790 TTTGCTGTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TCTT
Found at i:52672831 original size:14 final size:15
Alignment explanation
Indices: 52672809--52672846 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
52672799 CAATCAAACA
52672809 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
52672823 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
52672838 ACAGAAAAT
1 CCAGAAAAT
52672847 TAAAACATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:52674751 original size:31 final size:31
Alignment explanation
Indices: 52674716--52674781 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
52674706 AAAATAAAGT
52674716 ATAAGTCATGTGGCGCATAAGCTTTAATAAG
1 ATAAGTCATGTGGCGCATAAGCTTTAATAAG
* *
52674747 ATAAGTCATGTGGTGTATAAGCTTTAATAAG
1 ATAAGTCATGTGGCGCATAAGCTTTAATAAG
52674778 ATAA
1 ATAA
52674782 TTTTCATCGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (31 bp):
ATAAGTCATGTGGCGCATAAGCTTTAATAAG
Found at i:52687177 original size:32 final size:32
Alignment explanation
Indices: 52687141--52687248 Score: 121
Period size: 32 Copynumber: 3.4 Consensus size: 32
52687131 AAAAAAAATA
52687141 TTATTATCATTTAACAAAATTAAAGTTGATAT
1 TTATTATCATTTAACAAAATTAAAGTTGATAT
*
52687173 TTATTATCATTTCAA-AAAATTAAACTTG-TAAT
1 TTATTATCATTT-AACAAAATTAAAGTTGAT-AT
* * * * *
52687205 TTGTTATCATGTCACAAAATGAAAGTTGATAA
1 TTATTATCATTTAACAAAATTAAAGTTGATAT
*
52687237 TTGTTATCATTT
1 TTATTATCATTT
52687249 TATGGAACCA
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
31 2 0.03
32 59 0.92
33 3 0.05
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (32 bp):
TTATTATCATTTAACAAAATTAAAGTTGATAT
Found at i:52692421 original size:29 final size:29
Alignment explanation
Indices: 52692371--52692426 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
52692361 CATTTAATTA
*
52692371 TTTTTAAAATTCAAAAAAATTATAATTTT
1 TTTTTAAAATTCAAAAAAATTAAAATTTT
*
52692400 TTTTTAAAATT-AAAAATTATTAAAATT
1 TTTTTAAAATTCAAAAA-AATTAAAATT
52692427 ATATAAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (29 bp):
TTTTTAAAATTCAAAAAAATTAAAATTTT
Found at i:52694477 original size:29 final size:29
Alignment explanation
Indices: 52694414--52694477 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
52694404 GAAAAATGAA
** *
52694414 TCATTTCGATAAATAATTAAATAATTGGC
1 TCATTTCGATAAATAAAAAAAAAATTGGC
* *
52694443 TGATTTCGATAATTTAAAAAAAAAATTGG-
1 TCATTTCGATAA-ATAAAAAAAAAATTGGC
52694472 TCATTT
1 TCATTT
52694478 ACCCCAGAGT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
29 16 0.57
30 12 0.43
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (29 bp):
TCATTTCGATAAATAAAAAAAAAATTGGC
Found at i:52695435 original size:21 final size:19
Alignment explanation
Indices: 52695370--52695435 Score: 69
Period size: 21 Copynumber: 3.3 Consensus size: 19
52695360 TAAAAAATTA
*
52695370 TTTTTAAAATTTATATATT
1 TTTTTAAATTTTATATATT
* *
52695389 TTTTCTAGATTTTATGTATCT
1 TTTT-TAAATTTTATATAT-T
52695410 TTTTTGAAATTTTATATATT
1 TTTTT-AAATTTTATATATT
52695430 TATTTT
1 T-TTTT
52695436 TGTTTTTCAT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
19 4 0.11
20 14 0.37
21 20 0.53
ACGTcount: A:0.27, C:0.03, G:0.05, T:0.65
Consensus pattern (19 bp):
TTTTTAAATTTTATATATT
Found at i:52696115 original size:40 final size:40
Alignment explanation
Indices: 52696020--52696115 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 40
52696010 GATGTTAGGG
* *
52696020 GACGTGTC-AGCAAATTGCGTCCACGTAAGCGCGATTACT
1 GACGTGGCAAGCAAATCGCGTCCACGTAAGCGCGATTACT
* ** *
52696059 TACGTGGCAA-CAAATCGCGTCCTTGTAAGCGCGATTTGCT
1 GACGTGGCAAGCAAATCGCGTCCACGTAAGCGCGA-TTACT
52696099 GACGTGG-AAGCAAATCG
1 GACGTGGCAAGCAAATCG
52696116 GGCTTACGTA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
39 29 0.62
40 18 0.38
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (40 bp):
GACGTGGCAAGCAAATCGCGTCCACGTAAGCGCGATTACT
Found at i:52697873 original size:19 final size:20
Alignment explanation
Indices: 52697829--52697873 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
52697819 AGACTTTATA
*
52697829 TATA-ATTTTTATCATTTCT
1 TATACATTTTTATAATTTCT
*
52697848 T-TTCATTTTTATAATTT-T
1 TATACATTTTTATAATTTCT
52697866 TATACATT
1 TATACATT
52697874 ATATACTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (20 bp):
TATACATTTTTATAATTTCT
Found at i:52697883 original size:27 final size:25
Alignment explanation
Indices: 52697852--52697918 Score: 73
Period size: 27 Copynumber: 2.6 Consensus size: 25
52697842 ATTTCTTTTC
52697852 ATTTTTATAATTTTTATACATTATAT
1 ATTTTT-TAATTTTTATACATTATAT
* * *
52697878 ACTTTTTTGAATTTTTTTATATTTTAT
1 A-TTTTTT-AATTTTTATACATTATAT
52697905 A-TTTTTAATTTTTA
1 ATTTTTTAATTTTTA
52697919 ATTTTTTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
24 7 0.20
25 5 0.14
26 2 0.06
27 21 0.60
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.67
Consensus pattern (25 bp):
ATTTTTTAATTTTTATACATTATAT
Found at i:52708906 original size:15 final size:15
Alignment explanation
Indices: 52708877--52708914 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
52708867 CTGTAGCAGC
*
52708877 TTTTGT-TGTTTCTG
1 TTTTGTATGGTTCTG
52708891 TTTTGTATGGTTCTG
1 TTTTGTATGGTTCTG
52708906 TTTTGTATG
1 TTTTGTATG
52708915 TTTGTATTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.05, C:0.05, G:0.24, T:0.66
Consensus pattern (15 bp):
TTTTGTATGGTTCTG
Found at i:52711224 original size:16 final size:15
Alignment explanation
Indices: 52711157--52711232 Score: 50
Period size: 16 Copynumber: 4.9 Consensus size: 15
52711147 GAACAATATA
*
52711157 TAAGAATATCAATTAT
1 TAAGAATAT-TATTAT
*
52711173 TAAGAATATTATGATT
1 TAAGAATATTATTA-T
*
52711189 TGAGTAA-ATTCA-TA-
1 TAAG-AATATT-ATTAT
52711203 TAAGAATATTGATTAT
1 TAAGAATATT-ATTAT
*
52711219 TAAGAATTTTATTA
1 TAAGAATATTATTA
52711233 AATTATATAT
Statistics
Matches: 47, Mismatches: 7, Indels: 13
0.70 0.10 0.19
Matches are distributed among these distances:
13 2 0.04
14 7 0.15
15 9 0.19
16 26 0.55
17 3 0.06
ACGTcount: A:0.45, C:0.03, G:0.11, T:0.42
Consensus pattern (15 bp):
TAAGAATATTATTAT
Found at i:52711258 original size:16 final size:16
Alignment explanation
Indices: 52711237--52711278 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
52711227 TTATTAAATT
*
52711237 ATATATTTTAATTATA
1 ATATATTTTAATAATA
52711253 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
52711268 AT-TATGTTTAA
1 ATATAT-TTTAA
52711279 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:52711263 original size:15 final size:15
Alignment explanation
Indices: 52711228--52711269 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
52711218 TTAAGAATTT
*
52711228 TATTAAATTAT-ATA
1 TATTTAATTATAATA
52711242 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
52711256 TATTTAATAATAAT
1 TATTTAATTATAAT
52711270 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:52713167 original size:3 final size:3
Alignment explanation
Indices: 52713161--52713214 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
52713151 ATTACAATAT
*
52713161 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA TAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
52713209 CAA CAA
1 CAA CAA
52713215 TAATAATAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.31, G:0.00, T:0.02
Consensus pattern (3 bp):
CAA
Found at i:52714724 original size:44 final size:43
Alignment explanation
Indices: 52714664--52714779 Score: 119
Period size: 44 Copynumber: 2.7 Consensus size: 43
52714654 CTAGATGCGT
* *
52714664 TCTGC-TCTCTGCAACTTCTGAGAGATAAGATCTA-AGGTTTTAA
1 TCTGCTTCACTGCAACTTC-GAGAGATAAGAT-TATAGGCTTTAA
* * *
52714707 TCTGCTTCACTGCAACTTCAAGAAGATAGGATTATCGGCTTTAA
1 TCTGCTTCACTGCAACTTCGAG-AGATAAGATTATAGGCTTTAA
* *
52714751 TCTGCTCCACTGCAACTTCAGGGAGATAA
1 TCTGCTTCACTGCAACTTC-GAGAGATAA
52714780 AATTTACCAT
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
43 9 0.15
44 50 0.83
45 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (43 bp):
TCTGCTTCACTGCAACTTCGAGAGATAAGATTATAGGCTTTAA
Found at i:52715140 original size:44 final size:44
Alignment explanation
Indices: 52715086--52715459 Score: 378
Period size: 44 Copynumber: 8.6 Consensus size: 44
52715076 GCTATTTTCC
* * * *
52715086 ACCTACTCCACTGCTGCTCAGGGAGATAGGGTTCACGATCTTCA
1 ACCTATTCCACTGCTGCTCAGGGAGATAGGATTCACAATCTTTA
* *
52715130 ACCTATTCCACTGCTGAC-CAGGGAGATAGGA-CCTACAATCTTCA
1 ACCTATTCCACTGCTG-CTCAGGGAGATAGGATTC-ACAATCTTTA
* * * * * *
52715174 ATCAATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATTTTTA
1 ACCTATTCCACTGCTGCTCAGGGAGATAGGATTCACAATCTTTA
*
52715218 ACCTATTCCACTGCTGAC-CAGGGAAATAGGATTCACAATCTTTA
1 ACCTATTCCACTGCTG-CTCAGGGAGATAGGATTCACAATCTTTA
*
52715262 ACCTATTCCACTGCTG-TCCAGGGAGATAGG-GT-----TCTTTA
1 ACCTATTCCACTGCTGCT-CAGGGAGATAGGATTCACAATCTTTA
* * * * * *
52715300 ATCTATTCCACT-CTTGCCCAAGGAGATAGAATTCTCAATCTTCA
1 ACCTATTCCACTGC-TGCTCAGGGAGATAGGATTCACAATCTTTA
* * *
52715344 ACCTATTCCACTGCTGATCAGGGAGATAAGATTCACAATATTTA
1 ACCTATTCCACTGCTGCTCAGGGAGATAGGATTCACAATCTTTA
*
52715388 ACCTATTCCACTACTG-TCCAGGGAGATAGGATTCACAATCTTTA
1 ACCTATTCCACTGCTGCT-CAGGGAGATAGGATTCACAATCTTTA
52715432 ACCTATTCCACTGCTGAC-CAGGGAGATA
1 ACCTATTCCACTGCTG-CTCAGGGAGATA
52715460 AGGCTGGGGT
Statistics
Matches: 273, Mismatches: 38, Indels: 38
0.78 0.11 0.11
Matches are distributed among these distances:
37 1 0.00
38 29 0.11
39 1 0.00
43 4 0.01
44 234 0.86
45 4 0.01
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.28
Consensus pattern (44 bp):
ACCTATTCCACTGCTGCTCAGGGAGATAGGATTCACAATCTTTA
Found at i:52715307 original size:38 final size:38
Alignment explanation
Indices: 52715256--52715328 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
52715246 GGATTCACAA
* *
52715256 TCTTTAACCTATTCCACTGC-TGTCCAGGGAGATAGGGT
1 TCTTTAACCTATTCCACT-CTTGCCCAAGGAGATAGGGT
*
52715294 TCTTTAATCTATTCCACTCTTGCCCAAGGAGATAG
1 TCTTTAACCTATTCCACTCTTGCCCAAGGAGATAG
52715329 AATTCTCAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 1 0.03
38 30 0.97
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (38 bp):
TCTTTAACCTATTCCACTCTTGCCCAAGGAGATAGGGT
Found at i:52715366 original size:126 final size:128
Alignment explanation
Indices: 52715086--52715418 Score: 447
Period size: 126 Copynumber: 2.6 Consensus size: 128
52715076 GCTATTTTCC
* * * * * *
52715086 ACCTACTCCACTGCTGCTCAGGGAGATAGGGTTCACGATCTTCAACCTATTCCACTGCTGACCAG
1 ACCTATTCCACTGCTGATCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTGTCCAG
* *
52715151 GGAGATAGGACCTACAATCTTCAATCAATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATTTT
66 GGAGATAGGA-CT---ATCTTCAATCAATTCCACTGCTGCCCAAGGAGATAGAATTCTCAATCTT
*
52715216 TA
127 CA
* *
52715218 ACCTATTCCACTGCTGACCAGGGAAATAGGATTCACAATCTTTAACCTATTCCACTGCTGTCCAG
1 ACCTATTCCACTGCTGATCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTGTCCAG
* * *
52715283 GGAGATAGG-GT-TCTTTAATCTATTCCACT-CTTGCCCAAGGAGATAGAATTCTCAATCTTCA
66 GGAGATAGGACTATCTTCAATCAATTCCACTGC-TGCCCAAGGAGATAGAATTCTCAATCTTCA
* * *
52715344 ACCTATTCCACTGCTGATCAGGGAGATAAGATTCACAATATTTAACCTATTCCACTACTGTCCAG
1 ACCTATTCCACTGCTGATCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTGTCCAG
52715409 GGAGATAGGA
66 GGAGATAGGA
52715419 TTCACAATCT
Statistics
Matches: 180, Mismatches: 19, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
125 1 0.01
126 112 0.62
130 1 0.01
132 66 0.37
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.28
Consensus pattern (128 bp):
ACCTATTCCACTGCTGATCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTGTCCAG
GGAGATAGGACTATCTTCAATCAATTCCACTGCTGCCCAAGGAGATAGAATTCTCAATCTTCA
Found at i:52715390 original size:170 final size:173
Alignment explanation
Indices: 52715086--52715459 Score: 492
Period size: 170 Copynumber: 2.2 Consensus size: 173
52715076 GCTATTTTCC
* *
52715086 ACCTACTCCACTGCTGCTCAGGGAGATAGGGTTCACGATCTTCAACCTATTCCACTGCTGACCAG
1 ACCTATTCCACTGCTGC-CAGGGAGATAGGGTT-AC-ATCTTCAACCTATTCCACTGCTGACCAA
* * * * *
52715151 GGAGATAGGACCTACAATCTTCAATCAATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATTTT
63 GGAGATAGAACCTACAATCTTCAACCAATTCCACTGCTGACCAGGGAGATAGAATTCACAATATT
*
52715216 TAACCTATTCCACTGCTGACCAGGGAAATAGGATTCACAATCTTTA
128 TAACCTATTCCACTACTGACCAGGGAAATAGGATTCACAATCTTTA
* *
52715262 ACCTATTCCACTGCTGTCCAGGGAGATAGGGTT-C-T-TT-AATCTATTCCACT-CTTGCCCAAG
1 ACCTATTCCACTGCTG-CCAGGGAGATAGGGTTACATCTTCAACCTATTCCACTGC-TGACCAAG
* * *
52715322 GAGATAGAATTCT-CAATCTTCAACCTATTCCACTGCTGATCAGGGAGATA-AGATTCACAATAT
64 GAGATAGAA-CCTACAATCTTCAACCAATTCCACTGCTGACCAGGGAGATAGA-ATTCACAATAT
* *
52715385 TTAACCTATTCCACTACTGTCCAGGGAGATAGGATTCACAATCTTTA
127 TTAACCTATTCCACTACTGACCAGGGAAATAGGATTCACAATCTTTA
52715432 ACCTATTCCACTGCTGACCAGGGAGATA
1 ACCTATTCCACTGCTG-CCAGGGAGATA
52715460 AGGCTGGGGT
Statistics
Matches: 178, Mismatches: 16, Indels: 14
0.86 0.08 0.07
Matches are distributed among these distances:
169 2 0.01
170 139 0.78
171 4 0.02
172 1 0.01
174 1 0.01
176 30 0.17
177 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.28
Consensus pattern (173 bp):
ACCTATTCCACTGCTGCCAGGGAGATAGGGTTACATCTTCAACCTATTCCACTGCTGACCAAGGA
GATAGAACCTACAATCTTCAACCAATTCCACTGCTGACCAGGGAGATAGAATTCACAATATTTAA
CCTATTCCACTACTGACCAGGGAAATAGGATTCACAATCTTTA
Found at i:52716521 original size:44 final size:43
Alignment explanation
Indices: 52716461--52716576 Score: 119
Period size: 44 Copynumber: 2.7 Consensus size: 43
52716451 CTAGATGCGT
* *
52716461 TCTGC-TCTCTGCAACTTCTGAGAGATAAGATCTA-AGGTTTTAA
1 TCTGCTTCACTGCAACTTC-GAGAGATAAGAT-TATAGGCTTTAA
* * *
52716504 TCTGCTTCACTGCAACTTCAAGAAGATAGGATTATCGGCTTTAA
1 TCTGCTTCACTGCAACTTCGAG-AGATAAGATTATAGGCTTTAA
* *
52716548 TCTGCTCCACTGCAACTTCAGGGAGATAA
1 TCTGCTTCACTGCAACTTC-GAGAGATAA
52716577 AATTTACCAT
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
43 9 0.15
44 50 0.83
45 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (43 bp):
TCTGCTTCACTGCAACTTCGAGAGATAAGATTATAGGCTTTAA
Found at i:52716949 original size:44 final size:44
Alignment explanation
Indices: 52716883--52717256 Score: 415
Period size: 44 Copynumber: 8.6 Consensus size: 44
52716873 GCTATTTTCC
* * * * *
52716883 ACCTACTCGACTGCTG-CTCAGGGAGATAGGGTTCACGATCTTCA
1 ACCTATTCCACTGCTGAC-CAGGGAGATAGGATTCACAATCTTTA
* *
52716927 ACCTATTCCACTGCTGACCAGGGAGATAGGA-CCTACAATCTTCA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTC-ACAATCTTTA
* * * * * *
52716971 ATCAATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATTTTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTA
*
52717015 ACCTATTCCACTGCTGACCAGGGAAATAGGATTCACAATCTTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTA
* *
52717059 ACCTATTCCACTGCTGTCCAGGGAGATAGG-GT-----TCTTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTA
* * * * * *
52717097 ATCTATTCCACT-CTTGCCCAAGGAGATAGAATTCTCAATCTTCA
1 ACCTATTCCACTGC-TGACCAGGGAGATAGGATTCACAATCTTTA
* * *
52717141 ACCTATTCCACTGCTGATCAGGGAGATAAGATTCACAATATTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTA
* *
52717185 ACCTATTCCACTACTGTCCAGGGAGATAGGATTCACAATCTTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTA
52717229 ACCTATTCCACTGCTGACCAGGGAGATA
1 ACCTATTCCACTGCTGACCAGGGAGATA
52717257 AGGCTGGGGT
Statistics
Matches: 274, Mismatches: 45, Indels: 22
0.80 0.13 0.06
Matches are distributed among these distances:
37 1 0.00
38 30 0.11
39 1 0.00
43 2 0.01
44 237 0.86
45 3 0.01
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (44 bp):
ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTA
Found at i:52717104 original size:38 final size:38
Alignment explanation
Indices: 52717053--52717125 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
52717043 GGATTCACAA
* *
52717053 TCTTTAACCTATTCCACTGC-TGTCCAGGGAGATAGGGT
1 TCTTTAACCTATTCCACT-CTTGCCCAAGGAGATAGGGT
*
52717091 TCTTTAATCTATTCCACTCTTGCCCAAGGAGATAG
1 TCTTTAACCTATTCCACTCTTGCCCAAGGAGATAG
52717126 AATTCTCAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 1 0.03
38 30 0.97
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (38 bp):
TCTTTAACCTATTCCACTCTTGCCCAAGGAGATAGGGT
Found at i:52717124 original size:170 final size:170
Alignment explanation
Indices: 52716929--52717256 Score: 482
Period size: 170 Copynumber: 1.9 Consensus size: 170
52716919 GATCTTCAAC
* * * *
52716929 CTATTCCACTGCTGACCAGGGAGATAGGA-CCTACAATCTTCAATCAATTCCACTGCTGCCCAGG
1 CTATTCCACTGCTGACCAAGGAGATAGAATCCT-CAATCTTCAACCAATTCCACTGCTGACCAGG
* * *
52716993 GAGAT-AGAATTCTCAATTTTTAACCTATTCCACTGCTGACCAGGGAAATAGGATTCACAATCTT
65 GAGATAAG-ATTCACAATATTTAACCTATTCCACTACTGACCAGGGAAATAGGATTCACAATCTT
*
52717057 TAACCTATTCCACTGCTGTCCAGGGAGATAGGGTTCTTTAAT
129 TAACCTATTCCACTGCTGACCAGGGAGATAGGGTTCTTTAAT
* * * *
52717099 CTATTCCACT-CTTGCCCAAGGAGATAGAATTCTCAATCTTCAACCTATTCCACTGCTGATCAGG
1 CTATTCCACTGC-TGACCAAGGAGATAGAATCCTCAATCTTCAACCAATTCCACTGCTGACCAGG
* *
52717163 GAGATAAGATTCACAATATTTAACCTATTCCACTACTGTCCAGGGAGATAGGATTCACAATCTTT
65 GAGATAAGATTCACAATATTTAACCTATTCCACTACTGACCAGGGAAATAGGATTCACAATCTTT
52717228 AACCTATTCCACTGCTGACCAGGGAGATA
130 AACCTATTCCACTGCTGACCAGGGAGATA
52717257 AGGCTGGGGT
Statistics
Matches: 141, Mismatches: 14, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
169 1 0.01
170 136 0.96
171 4 0.03
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (170 bp):
CTATTCCACTGCTGACCAAGGAGATAGAATCCTCAATCTTCAACCAATTCCACTGCTGACCAGGG
AGATAAGATTCACAATATTTAACCTATTCCACTACTGACCAGGGAAATAGGATTCACAATCTTTA
ACCTATTCCACTGCTGACCAGGGAGATAGGGTTCTTTAAT
Found at i:52717163 original size:126 final size:128
Alignment explanation
Indices: 52716883--52717215 Score: 438
Period size: 126 Copynumber: 2.6 Consensus size: 128
52716873 GCTATTTTCC
* * * * * * *
52716883 ACCTACTCGACTGCTGCTCAGGGAGATAGGGTTCACGATCTTCAACCTATTCCACTGCTGACCAG
1 ACCTATTCCACTGCTGATCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTGTCCAG
* *
52716948 GGAGATAGGACCTACAATCTTCAATCAATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATTTT
66 GGAGATAGGA-CT---ATCTTCAATCAATTCCACTGCTGCCCAAGGAGATAGAATTCTCAATCTT
*
52717013 TA
127 CA
* *
52717015 ACCTATTCCACTGCTGACCAGGGAAATAGGATTCACAATCTTTAACCTATTCCACTGCTGTCCAG
1 ACCTATTCCACTGCTGATCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTGTCCAG
* * *
52717080 GGAGATAGG-GT-TCTTTAATCTATTCCACT-CTTGCCCAAGGAGATAGAATTCTCAATCTTCA
66 GGAGATAGGACTATCTTCAATCAATTCCACTGC-TGCCCAAGGAGATAGAATTCTCAATCTTCA
* * *
52717141 ACCTATTCCACTGCTGATCAGGGAGATAAGATTCACAATATTTAACCTATTCCACTACTGTCCAG
1 ACCTATTCCACTGCTGATCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTGTCCAG
52717206 GGAGATAGGA
66 GGAGATAGGA
52717216 TTCACAATCT
Statistics
Matches: 179, Mismatches: 20, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
125 1 0.01
126 112 0.63
130 1 0.01
132 65 0.36
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (128 bp):
ACCTATTCCACTGCTGATCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTGTCCAG
GGAGATAGGACTATCTTCAATCAATTCCACTGCTGCCCAAGGAGATAGAATTCTCAATCTTCA
Found at i:52717317 original size:88 final size:87
Alignment explanation
Indices: 52717225--52717492 Score: 329
Period size: 88 Copynumber: 3.0 Consensus size: 87
52717215 ATTCACAATC
** * ** * * *
52717225 TTTAACCTATTCCACTGCTGACCAGGGAGATAAGGCTGGGGTCATCAATTTGCTTCGTTGTCGGT
1 TTTAACCTGCTCCACTGC-AACCAGGGAGGCAAGGCTGGTGTCTTCGATTTGCTTCGTTGTCGGT
52717290 GCAGGAAGGCAAGATCTGCTATT
65 GCAGGAAGGCAAGATCTGCTATT
* * * * *
52717313 TTTAACCTGCTCCGCTGCAACCCAAGGAGGCAAGGTTGGTGTCTTCGATCTGCTTCGTTATCGGT
1 TTTAACCTGCTCCACTGCAA-CCAGGGAGGCAAGGCTGGTGTCTTCGATTTGCTTCGTTGTCGGT
*
52717378 GCAGGAAGGCAAGATCTACTATT
65 GCAGGAAGGCAAGATCTGCTATT
* * ***
52717401 TTTAACCTGCTACACTGCAACCTAGGGAGGCAAGGCTGGTGTCTTTGATTTGCTTTACTGTCGGT
1 TTTAACCTGCTCCACTGCAACC-AGGGAGGCAAGGCTGGTGTCTTCGATTTGCTTCGTTGTCGGT
*
52717466 GTAGGAAGGCAAGATCTGCTATT
65 GCAGGAAGGCAAGATCTGCTATT
52717489 TTTA
1 TTTA
52717493 CTGATCTGCT
Statistics
Matches: 152, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
87 3 0.02
88 149 0.98
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.31
Consensus pattern (87 bp):
TTTAACCTGCTCCACTGCAACCAGGGAGGCAAGGCTGGTGTCTTCGATTTGCTTCGTTGTCGGTG
CAGGAAGGCAAGATCTGCTATT
Found at i:52726529 original size:3 final size:3
Alignment explanation
Indices: 52726523--52726570 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
52726513 ATTACAATAT
*
52726523 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA TAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
52726571 TAATAATAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.31, G:0.00, T:0.02
Consensus pattern (3 bp):
CAA
Found at i:52728677 original size:19 final size:18
Alignment explanation
Indices: 52728655--52728693 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
52728645 AATTTGGAAC
*
52728655 AAATGAGAAAATTTTGGGA
1 AAATGAGAAAA-ATTGGGA
*
52728674 AAATGTGAAAAATTGGGA
1 AAATGAGAAAAATTGGGA
52728692 AA
1 AA
52728694 CAGGGGTCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.51, C:0.00, G:0.26, T:0.23
Consensus pattern (18 bp):
AAATGAGAAAAATTGGGA
Found at i:52731405 original size:62 final size:62
Alignment explanation
Indices: 52731305--52731428 Score: 205
Period size: 62 Copynumber: 2.0 Consensus size: 62
52731295 CGAGGTCCCA
* *
52731305 ATACCTCATTTTTTAAAACCGCTTGACTTTAAAGATTTACCACTTGAACCTAATTACTCATT
1 ATACCTCATTTTCTAAAACCACTTGACTTTAAAGATTTACCACTTGAACCTAATTACTCATT
*
52731367 ATACCTTATTTTCTAAAACCACTTGACTTT-AAGTATTTACCACTTGAACCTAATTACTCATT
1 ATACCTCATTTTCTAAAACCACTTGACTTTAAAG-ATTTACCACTTGAACCTAATTACTCATT
52731429 CAATTAACAT
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
61 3 0.05
62 55 0.95
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.40
Consensus pattern (62 bp):
ATACCTCATTTTCTAAAACCACTTGACTTTAAAGATTTACCACTTGAACCTAATTACTCATT
Found at i:52739904 original size:17 final size:18
Alignment explanation
Indices: 52739871--52739903 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
52739861 GAAAAATTAT
52739871 TTTATCTTTTTAATTTTC
1 TTTATCTTTTTAATTTTC
52739889 TTTAT-TTTTT-ATTTT
1 TTTATCTTTTTAATTTT
52739904 TAGTTCATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTATCTTTTTAATTTTC
Found at i:52747056 original size:16 final size:16
Alignment explanation
Indices: 52747035--52747106 Score: 69
Period size: 15 Copynumber: 4.6 Consensus size: 16
52747025 GGAATTAATG
52747035 AATTTTTATTTTTTAT
1 AATTTTTATTTTTTAT
52747051 AATTTTTA-TTTTTAT
1 AATTTTTATTTTTTAT
* * *
52747066 ACTTTTTATTATGTAT
1 AATTTTTATTTTTTAT
*
52747082 -ATTTTCTAAATTTTTAT
1 AATTTT-T-ATTTTTTAT
52747099 -ATTTTTAT
1 AATTTTTAT
52747107 AATTTTTTAA
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
15 19 0.42
16 15 0.33
17 11 0.24
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.69
Consensus pattern (16 bp):
AATTTTTATTTTTTAT
Found at i:52747058 original size:9 final size:8
Alignment explanation
Indices: 52747036--52747113 Score: 72
Period size: 9 Copynumber: 9.8 Consensus size: 8
52747026 GAATTAATGA
52747036 ATTTTTAT
1 ATTTTTAT
52747044 -TTTTTAT
1 ATTTTTAT
*
52747051 AATTTT-T
1 ATTTTTAT
52747058 ATTTTTAT
1 ATTTTTAT
52747066 ACTTTTTAT
1 A-TTTTTAT
* *
52747075 -TATGTAT
1 ATTTTTAT
*
52747082 ATTTTCTAA
1 ATTTT-TAT
52747091 ATTTTTAT
1 ATTTTTAT
52747099 ATTTTTAT
1 ATTTTTAT
52747107 AATTTTT
1 -ATTTTT
52747114 TAAAATTGAT
Statistics
Matches: 56, Mismatches: 8, Indels: 11
0.75 0.11 0.15
Matches are distributed among these distances:
7 18 0.32
8 18 0.32
9 20 0.36
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.71
Consensus pattern (8 bp):
ATTTTTAT
Found at i:52747071 original size:24 final size:22
Alignment explanation
Indices: 52747036--52747106 Score: 72
Period size: 24 Copynumber: 3.1 Consensus size: 22
52747026 GAATTAATGA
52747036 ATTTTTAT-TTTTTATAATTTTT
1 ATTTTTATATTTTTAT-ATTTTT
* *
52747058 ATTTTTATACTTTTTATTATGTAT
1 ATTTTTATA-TTTTTA-TATTTTT
*
52747082 ATTTTCTAAATTTTTATATTTTT
1 ATTTT-TATATTTTTATATTTTT
52747105 AT
1 AT
52747107 AATTTTTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
22 8 0.20
23 7 0.17
24 21 0.52
25 4 0.10
ACGTcount: A:0.25, C:0.03, G:0.01, T:0.70
Consensus pattern (22 bp):
ATTTTTATATTTTTATATTTTT
Found at i:52747700 original size:144 final size:144
Alignment explanation
Indices: 52747440--52747722 Score: 566
Period size: 144 Copynumber: 2.0 Consensus size: 144
52747430 CCAATTTAAT
52747440 TATCATGTTTAAACTAGAGGTGTTTATGGGTTGGACTGAGCACGATATTAATATACTTTATATTT
1 TATCATGTTTAAACTAGAGGTGTTTATGGGTTGGACTGAGCACGATATTAATATACTTTATATTT
52747505 GCCCAAACTTGATCCGACCTAAAATATGGGCCTAAAATTTTGTTGAAGTCTGCCAATATTTGCAA
66 GCCCAAACTTGATCCGACCTAAAATATGGGCCTAAAATTTTGTTGAAGTCTGCCAATATTTGCAA
52747570 AAGATTAACCCAAA
131 AAGATTAACCCAAA
52747584 TATCATGTTTAAACTAGAGGTGTTTATGGGTTGGACTGAGCACGATATTAATATACTTTATATTT
1 TATCATGTTTAAACTAGAGGTGTTTATGGGTTGGACTGAGCACGATATTAATATACTTTATATTT
52747649 GCCCAAACTTGATCCGACCTAAAATATGGGCCTAAAATTTTGTTGAAGTCTGCCAATATTTGCAA
66 GCCCAAACTTGATCCGACCTAAAATATGGGCCTAAAATTTTGTTGAAGTCTGCCAATATTTGCAA
52747714 AAGATTAAC
131 AAGATTAAC
52747723 TCAATCCCAT
Statistics
Matches: 139, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
144 139 1.00
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Consensus pattern (144 bp):
TATCATGTTTAAACTAGAGGTGTTTATGGGTTGGACTGAGCACGATATTAATATACTTTATATTT
GCCCAAACTTGATCCGACCTAAAATATGGGCCTAAAATTTTGTTGAAGTCTGCCAATATTTGCAA
AAGATTAACCCAAA
Found at i:52750061 original size:21 final size:22
Alignment explanation
Indices: 52750015--52750055 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
52750005 CCAATATCAG
*
52750015 TAAATAGATAGCTTGAACTAAC
1 TAAATACATAGCTTGAACTAAC
*
52750037 TAAATACATA-CTTTAACTA
1 TAAATACATAGCTTGAACTA
52750056 CTTAAACTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.32
Consensus pattern (22 bp):
TAAATACATAGCTTGAACTAAC
Found at i:52751699 original size:20 final size:20
Alignment explanation
Indices: 52751674--52751713 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
52751664 CAATTTCAGC
52751674 ATAAAAGGTGTTGCCTTGAG
1 ATAAAAGGTGTTGCCTTGAG
52751694 ATAAAAGGTGTTGCCTTGAG
1 ATAAAAGGTGTTGCCTTGAG
52751714 GGAGAGAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.10, G:0.30, T:0.30
Consensus pattern (20 bp):
ATAAAAGGTGTTGCCTTGAG
Found at i:52757447 original size:13 final size:13
Alignment explanation
Indices: 52757429--52757458 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
52757419 AGCTCAAACT
52757429 CAATTACCCAACC
1 CAATTACCCAACC
52757442 CAATTACCCAACC
1 CAATTACCCAACC
52757455 CAAT
1 CAAT
52757459 AAAACTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.43, G:0.00, T:0.17
Consensus pattern (13 bp):
CAATTACCCAACC
Found at i:52757616 original size:9 final size:9
Alignment explanation
Indices: 52757604--52757675 Score: 65
Period size: 9 Copynumber: 7.9 Consensus size: 9
52757594 AAAAAATTTT
52757604 GGGTAATTC
1 GGGTAATTC
*
52757613 GGGTATTTTTC
1 GGGTA--ATTC
*
52757624 -GGTAATTT
1 GGGTAATTC
* *
52757632 GGTTAATTT
1 GGGTAATTC
*
52757641 GGTTAATTC
1 GGGTAATTC
*
52757650 GGTTAATTC
1 GGGTAATTC
52757659 GGGTAATTC
1 GGGTAATTC
52757668 GGGTAATT
1 GGGTAATT
52757676 TTTAACCAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
8 2 0.04
9 45 0.83
10 4 0.07
11 3 0.06
ACGTcount: A:0.21, C:0.07, G:0.28, T:0.44
Consensus pattern (9 bp):
GGGTAATTC
Found at i:52757653 original size:18 final size:18
Alignment explanation
Indices: 52757601--52757676 Score: 80
Period size: 18 Copynumber: 4.2 Consensus size: 18
52757591 ATAAAAAAAT
* *
52757601 TTTGGGTAATTCGGGTATT
1 TTTGGGTAATTCGGTTA-A
* *
52757620 TTTCGGTAATTTGGTTAA
1 TTTGGGTAATTCGGTTAA
*
52757638 TTTGGTTAATTCGGTTAA
1 TTTGGGTAATTCGGTTAA
* *
52757656 TTCGGGTAATTCGGGTAA
1 TTTGGGTAATTCGGTTAA
52757674 TTT
1 TTT
52757677 TTAACCAAAA
Statistics
Matches: 46, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
18 32 0.70
19 14 0.30
ACGTcount: A:0.20, C:0.07, G:0.26, T:0.47
Consensus pattern (18 bp):
TTTGGGTAATTCGGTTAA
Found at i:52757665 original size:27 final size:26
Alignment explanation
Indices: 52757604--52757675 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 26
52757594 AAAAAATTTT
* *
52757604 GGGTAATTCGGGTATTTTTCGGTAATTT
1 GGGTAATTCGGGTA--ATTCGGTAATTC
* * *
52757632 GGTTAATTTGGTTAATTCGGTTAATTC
1 GGGTAATTCGGGTAATTCGG-TAATTC
52757659 GGGTAATTCGGGTAATT
1 GGGTAATTCGGGTAATT
52757676 TTTAACCAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
26 5 0.14
27 19 0.54
28 11 0.31
ACGTcount: A:0.21, C:0.07, G:0.28, T:0.44
Consensus pattern (26 bp):
GGGTAATTCGGGTAATTCGGTAATTC
Found at i:52758956 original size:14 final size:14
Alignment explanation
Indices: 52758939--52758965 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
52758929 GTTAAGGACT
52758939 CATACTAATGATGA
1 CATACTAATGATGA
52758953 CATACTAATGATG
1 CATACTAATGATG
52758966 GCAGCACGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (14 bp):
CATACTAATGATGA
Found at i:52761128 original size:20 final size:19
Alignment explanation
Indices: 52761097--52761142 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
52761087 AAATATTTTT
52761097 ATTTTAAATTTTTTT-ATAA
1 ATTTTAAATTTTTTTGA-AA
52761116 ATTTTACAATTTTTTTGAAA
1 ATTTTA-AATTTTTTTGAAA
52761136 ATTTTAA
1 ATTTTAA
52761143 TTAATATGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.28
20 17 0.68
21 1 0.04
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (19 bp):
ATTTTAAATTTTTTTGAAA
Found at i:52767745 original size:9 final size:10
Alignment explanation
Indices: 52767694--52767751 Score: 68
Period size: 11 Copynumber: 5.9 Consensus size: 10
52767684 AGATATTTAC
52767694 AAAATTATAA
1 AAAATTATAA
52767704 AAAATATATAA
1 AAAAT-TATAA
52767715 AAAAGTTATAA
1 AAAA-TTATAA
52767726 AAAATT-T--
1 AAAATTATAA
*
52767733 AAAATTAAAA
1 AAAATTATAA
52767743 AAAATTATA
1 AAAATTATA
52767752 TTAAAAAAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
7 6 0.15
9 1 0.02
10 15 0.37
11 18 0.44
12 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (10 bp):
AAAATTATAA
Found at i:52770007 original size:3 final size:3
Alignment explanation
Indices: 52770001--52770029 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
52769991 CATTAATTGA
52770001 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
52770030 AGCGCACGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:52781833 original size:2 final size:2
Alignment explanation
Indices: 52781826--52781861 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
52781816 ATAACTAAAC
*
52781826 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
52781862 ACTTTTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:52783158 original size:3 final size:3
Alignment explanation
Indices: 52783137--52783228 Score: 125
Period size: 3 Copynumber: 31.3 Consensus size: 3
52783127 TAATAGCTCC
* * ** *
52783137 ATT ATT TTT ATT ATC ATT ATT ATT -TT ATT ATT AGC CTT -TT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
52783183 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
52783229 CTTACTTACT
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
2 4 0.05
3 74 0.95
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:52783235 original size:4 final size:4
Alignment explanation
Indices: 52783226--52783266 Score: 73
Period size: 4 Copynumber: 10.2 Consensus size: 4
52783216 ATTATTATTA
*
52783226 TTAC TTAC TTAC TTAC TTAC TTAC TTAC TAAC TTAC TTAC T
1 TTAC TTAC TTAC TTAC TTAC TTAC TTAC TTAC TTAC TTAC T
52783267 AGTTCTATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.27, C:0.24, G:0.00, T:0.49
Consensus pattern (4 bp):
TTAC
Found at i:52783764 original size:66 final size:66
Alignment explanation
Indices: 52783680--52783812 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
52783670 ATATTCTTAA
52783680 TGTATTATTATTAATCTCATTTTTCTTAATACATACTTTTTACACACATCACTTATTTTGATTTT
1 TGTATTATTATTAATCTCATTTTTCTTAATACATACTTTTTACACACATCACTTATTTTGATTTT
52783745 C
66 C
52783746 TGTATTATTATTAATCTCATTTTTCTTAATACATACTTTTTACACACATCACTTATTTTGATTTT
1 TGTATTATTATTAATCTCATTTTTCTTAATACATACTTTTTACACACATCACTTATTTTGATTTT
52783811 C
66 C
52783812 T
1 T
52783813 TCCTATATAG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.27, C:0.17, G:0.03, T:0.53
Consensus pattern (66 bp):
TGTATTATTATTAATCTCATTTTTCTTAATACATACTTTTTACACACATCACTTATTTTGATTTT
C
Found at i:52799283 original size:3 final size:3
Alignment explanation
Indices: 52799271--52799340 Score: 61
Period size: 3 Copynumber: 23.3 Consensus size: 3
52799261 ATTAATATAT
* * ** *
52799271 ATA A-A ATA ATA ATA CTA ATA ATA ATA ATA AAA ATA ACG ATA GTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
52799318 ATA GTA ATAA ATA ATA ATG ATA A
1 ATA ATA AT-A ATA ATA ATA ATA A
52799341 ATTAATATTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
2 2 0.04
3 46 0.90
4 3 0.06
ACGTcount: A:0.63, C:0.03, G:0.06, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:52803434 original size:18 final size:18
Alignment explanation
Indices: 52803408--52803442 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
52803398 TTTTAAGCAA
*
52803408 GATGTTTTGTTAGCAGAG
1 GATGCTTTGTTAGCAGAG
52803426 GATGCTTTGTTAGCAGA
1 GATGCTTTGTTAGCAGA
52803443 AGTACTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.09, G:0.31, T:0.37
Consensus pattern (18 bp):
GATGCTTTGTTAGCAGAG
Found at i:52804065 original size:82 final size:82
Alignment explanation
Indices: 52803928--52804090 Score: 326
Period size: 82 Copynumber: 2.0 Consensus size: 82
52803918 CAGAACTTCG
52803928 TAAAAGAATTAGGCGTAAAATATTCGGAACGACGCCAATGAAAGTTCTGTCTATTACGTATCGAT
1 TAAAAGAATTAGGCGTAAAATATTCGGAACGACGCCAATGAAAGTTCTGTCTATTACGTATCGAT
52803993 TTTGCTCTTCTGTTGAC
66 TTTGCTCTTCTGTTGAC
52804010 TAAAAGAATTAGGCGTAAAATATTCGGAACGACGCCAATGAAAGTTCTGTCTATTACGTATCGAT
1 TAAAAGAATTAGGCGTAAAATATTCGGAACGACGCCAATGAAAGTTCTGTCTATTACGTATCGAT
52804075 TTTGCTCTTCTGTTGA
66 TTTGCTCTTCTGTTGA
52804091 TCCGGTGACA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 81 1.00
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.33
Consensus pattern (82 bp):
TAAAAGAATTAGGCGTAAAATATTCGGAACGACGCCAATGAAAGTTCTGTCTATTACGTATCGAT
TTTGCTCTTCTGTTGAC
Found at i:52804273 original size:34 final size:35
Alignment explanation
Indices: 52804229--52804296 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 35
52804219 TGTAAAAGTA
* *
52804229 AATTTCTATTTTAGTACATGAAATAATAT-AAAAG
1 AATTTATATTTTAGTACATCAAATAATATCAAAAG
*
52804263 AATTTATATTTTATTACATCAAATAATATCAAAA
1 AATTTATATTTTAGTACATCAAATAATATCAAAA
52804297 TATTCAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 26 0.87
35 4 0.13
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (35 bp):
AATTTATATTTTAGTACATCAAATAATATCAAAAG
Found at i:52804335 original size:23 final size:22
Alignment explanation
Indices: 52804292--52804335 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
52804282 CAAATAATAT
*
52804292 CAAAATATTCAAAATGTTTCTA
1 CAAAATATTCAAAATGCTTCTA
52804314 CAAATATATT-AAAATAGCTTCT
1 CAAA-ATATTCAAAAT-GCTTCT
52804336 CAATCTCCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (22 bp):
CAAAATATTCAAAATGCTTCTA
Found at i:52804452 original size:21 final size:20
Alignment explanation
Indices: 52804422--52804475 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
52804412 CTTCCGGCGG
*
52804422 GGGTTGTGGTTGATCCGGCA
1 GGGTTCTGGTTGATCCGGCA
** *
52804442 GGGATTCTGGTTCCTCCGGTA
1 GGG-TTCTGGTTGATCCGGCA
52804463 GGGTATCTGGTTG
1 GGGT-TCTGGTTG
52804476 TCGGTGTTGG
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.09, C:0.17, G:0.41, T:0.33
Consensus pattern (20 bp):
GGGTTCTGGTTGATCCGGCA
Found at i:52805418 original size:7 final size:7
Alignment explanation
Indices: 52805406--52805434 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
52805396 TTATATATAT
52805406 AATACTA
1 AATACTA
52805413 AATACTA
1 AATACTA
52805420 AATACTA
1 AATACTA
52805427 AATACTA
1 AATACTA
52805434 A
1 A
52805435 TCAACTAGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:52806625 original size:40 final size:40
Alignment explanation
Indices: 52806575--52806652 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 40
52806565 AAATAATTAA
52806575 AAATAGGGATTTAAGAGAAATTT-GAGAGGAAATTGAGATT
1 AAATAGGGATTTAAGAGAAATTTGGA-AGGAAATTGAGATT
* * *
52806615 AAATATGGATTTGAGATAAATTTGGAAGGAAATTGAGA
1 AAATAGGGATTTAAGAGAAATTTGGAAGGAAATTGAGA
52806653 GCAAATTGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 32 0.94
41 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.27, T:0.28
Consensus pattern (40 bp):
AAATAGGGATTTAAGAGAAATTTGGAAGGAAATTGAGATT
Found at i:52806640 original size:17 final size:18
Alignment explanation
Indices: 52806607--52806640 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
52806597 TGAGAGGAAA
52806607 TTGAGATTAAATATGGAT
1 TTGAGATTAAATATGGAT
*
52806625 TTGAGA-TAAATTTGGA
1 TTGAGATTAAATATGGA
52806641 AGGAAATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.38, C:0.00, G:0.24, T:0.38
Consensus pattern (18 bp):
TTGAGATTAAATATGGAT
Found at i:52806660 original size:11 final size:11
Alignment explanation
Indices: 52806641--52806697 Score: 78
Period size: 11 Copynumber: 5.1 Consensus size: 11
52806631 TAAATTTGGA
52806641 AGGAAATTGAG
1 AGGAAATTGAG
* *
52806652 AGCAAATTGAA
1 AGGAAATTGAG
52806663 AGGAAATTGAG
1 AGGAAATTGAG
52806674 AGGAAATTGAG
1 AGGAAATTGAG
*
52806685 AGAATAATTGAG
1 AGGA-AATTGAG
52806697 A
1 A
52806698 AAGCATTAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
11 32 0.80
12 8 0.20
ACGTcount: A:0.49, C:0.02, G:0.30, T:0.19
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:52807598 original size:25 final size:23
Alignment explanation
Indices: 52807558--52807609 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 23
52807548 TTTATTTTTA
*
52807558 ATTTTATATTTTAATTTTGTG-AT
1 ATTTTATATTTAAATTTT-TGAAT
52807581 ATTTTATAATTATAAATTTTTGAAT
1 ATTTTAT-ATT-TAAATTTTTGAAT
52807606 ATTT
1 ATTT
52807610 AGAATAATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 7 0.28
24 5 0.20
25 13 0.52
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.62
Consensus pattern (23 bp):
ATTTTATATTTAAATTTTTGAAT
Found at i:52808303 original size:16 final size:18
Alignment explanation
Indices: 52808270--52808303 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
52808260 TTTTATTTTA
52808270 TTTTCGTAATTAATTAAT
1 TTTTCGTAATTAATTAAT
52808288 TTTTCGT-ATT-ATTAAT
1 TTTTCGTAATTAATTAAT
52808304 GTAAAAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 3 0.19
18 7 0.44
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.59
Consensus pattern (18 bp):
TTTTCGTAATTAATTAAT
Found at i:52809294 original size:17 final size:17
Alignment explanation
Indices: 52809256--52809298 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
52809246 AAAATTTATT
52809256 TATAAAA-A-TTAAAAA
1 TATAAAATATTTAAAAA
*
52809271 TATTAAAATATTTAAAAG
1 TA-TAAAATATTTAAAAA
52809289 TATAAAATAT
1 TATAAAATAT
52809299 ATTTTTTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 2 0.08
16 5 0.21
17 9 0.38
18 8 0.33
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (17 bp):
TATAAAATATTTAAAAA
Found at i:52812049 original size:27 final size:27
Alignment explanation
Indices: 52812010--52812086 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
52812000 TCAGGTTAAT
52812010 TAAATTGGCGGCAACAAAT-GTGCCAAA
1 TAAATTGGCGGC-ACAAATGGTGCCAAA
* *
52812037 TAAATTGGTGGCACCAATGGTGCCAAA
1 TAAATTGGCGGCACAAATGGTGCCAAA
* *
52812064 GT-CATTGGCGGCAC-CATGGTGCC
1 -TAAATTGGCGGCACAAATGGTGCC
52812087 GAAGGAAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
26 13 0.30
27 29 0.67
28 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (27 bp):
TAAATTGGCGGCACAAATGGTGCCAAA
Found at i:52812188 original size:19 final size:19
Alignment explanation
Indices: 52812155--52812227 Score: 96
Period size: 19 Copynumber: 3.9 Consensus size: 19
52812145 ATTTCCCTTC
*
52812155 AACTCT-TTTTTATTTAAT
1 AACTCTATTTTAATTTAAT
52812173 AACTCTATTTTAATTTAAT
1 AACTCTATTTTAATTTAAT
* * *
52812192 AA-ACTATTATCATTTAAT
1 AACTCTATTTTAATTTAAT
52812210 AACTCTATTTTAATTTAA
1 AACTCTATTTTAATTTAA
52812228 AAAAATTAAG
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
18 21 0.46
19 25 0.54
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (19 bp):
AACTCTATTTTAATTTAAT
Found at i:52812545 original size:37 final size:37
Alignment explanation
Indices: 52812498--52812568 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
52812488 AGTATTACTT
*
52812498 AATATTTTATTAAATTAAAATAGAGTTATTAAATGAG
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
52812535 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
52812569 AAAAAATTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (37 bp):
AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
Found at i:52812573 original size:19 final size:19
Alignment explanation
Indices: 52812504--52812572 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
52812494 ACTTAATATT
52812504 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
* * *
52812523 TTATTAAATGAGAATAG-T
1 TTATTAAATTAAAATAGAG
52812541 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
52812560 TTATTAAA-TAAAA
1 TTATTAAATTAAAA
52812573 AATTGAGTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
18 20 0.47
19 23 0.53
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (19 bp):
TTATTAAATTAAAATAGAG
Found at i:52812841 original size:36 final size:37
Alignment explanation
Indices: 52812790--52812859 Score: 133
Period size: 36 Copynumber: 1.9 Consensus size: 37
52812780 AGTATTACTT
52812790 AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
52812827 AATA-TTTATTAAATTAAAATAGAGTTATTAAAT
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
52812860 AAAAAAAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 29 0.88
37 4 0.12
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (37 bp):
AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
Found at i:52812847 original size:17 final size:17
Alignment explanation
Indices: 52812790--52812847 Score: 62
Period size: 17 Copynumber: 3.2 Consensus size: 17
52812780 AGTATTACTT
52812790 AATAGTTTATTAAATTAA
1 AATA-TTTATTAAATTAA
* * *
52812808 AATAGAGTTATTAAATGAG
1 AAT--ATTTATTAAATTAA
52812827 AATATTTATTAAATTAA
1 AATATTTATTAAATTAA
52812844 AATA
1 AATA
52812848 GAGTTATTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
17 15 0.47
18 3 0.09
19 13 0.41
20 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.40
Consensus pattern (17 bp):
AATATTTATTAAATTAA
Found at i:52812864 original size:19 final size:19
Alignment explanation
Indices: 52812796--52812863 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
52812786 ACTTAATAGT
52812796 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
* * *
52812815 TTATTAAATGAGAAT--AT
1 TTATTAAATTAAAATAGAG
52812832 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
52812851 TTATTAAA-TAAAA
1 TTATTAAATTAAAA
52812864 AAAACTTGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
17 14 0.34
18 5 0.12
19 22 0.54
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (19 bp):
TTATTAAATTAAAATAGAG
Found at i:52812984 original size:27 final size:27
Alignment explanation
Indices: 52812935--52813007 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
52812925 TTTTTTTTTC
* * *
52812935 CTTTGGCACCATGGTGACGCCAA-TGA
1 CTTTGGCACTATGGTGCCACCAATTGA
*
52812961 CTTTGGCACTATTGGTGCCACCAATTTA
1 CTTTGGCACTA-TGGTGCCACCAATTGA
52812989 -TTTGGCATCTATGGTGCCA
1 CTTTGGCA-CTATGGTGCCA
52813008 GAAATTTAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
26 10 0.25
27 25 0.62
28 5 0.12
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.32
Consensus pattern (27 bp):
CTTTGGCACTATGGTGCCACCAATTGA
Found at i:52813013 original size:27 final size:27
Alignment explanation
Indices: 52812962--52813021 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
52812952 CGCCAATGAC
*
52812962 TTTGGCACTATTGGTGCCACCAATTTA
1 TTTGGCACTATTGGTGCCACAAATTTA
*
52812989 TTTGGCATCTA-TGGTGCCAGAAATTTA
1 TTTGGCA-CTATTGGTGCCACAAATTTA
*
52813016 ATTGGC
1 TTTGGC
52813022 CTGATCAGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 26 0.90
28 3 0.10
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (27 bp):
TTTGGCACTATTGGTGCCACAAATTTA
Found at i:52813090 original size:23 final size:23
Alignment explanation
Indices: 52813064--52813114 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
52813054 TTTATTTTTG
52813064 ATATATTTTGGTAAATAAAAAAA
1 ATATATTTTGGTAAATAAAAAAA
52813087 ATATATTTTGGTAAATAAAAAAA
1 ATATATTTTGGTAAATAAAAAAA
*
52813110 TTATA
1 ATATA
52813115 ACATTTTAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (23 bp):
ATATATTTTGGTAAATAAAAAAA
Found at i:52814974 original size:16 final size:14
Alignment explanation
Indices: 52814935--52814966 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
52814925 AAAAATCAAG
*
52814935 TTGATTCAATTAAT
1 TTGATTCAAATAAT
52814949 TTGATTCAAATAAT
1 TTGATTCAAATAAT
52814963 TTGA
1 TTGA
52814967 CATTCAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (14 bp):
TTGATTCAAATAAT
Found at i:52816868 original size:54 final size:54
Alignment explanation
Indices: 52816804--52816965 Score: 324
Period size: 54 Copynumber: 3.0 Consensus size: 54
52816794 GGAGGAATGA
52816804 GTGGATTGAAATGGGAATTCAAGGAAGTAAGATGACATCGCGGAGATGATTAGC
1 GTGGATTGAAATGGGAATTCAAGGAAGTAAGATGACATCGCGGAGATGATTAGC
52816858 GTGGATTGAAATGGGAATTCAAGGAAGTAAGATGACATCGCGGAGATGATTAGC
1 GTGGATTGAAATGGGAATTCAAGGAAGTAAGATGACATCGCGGAGATGATTAGC
52816912 GTGGATTGAAATGGGAATTCAAGGAAGTAAGATGACATCGCGGAGATGATTAGC
1 GTGGATTGAAATGGGAATTCAAGGAAGTAAGATGACATCGCGGAGATGATTAGC
52816966 TAATGGTACG
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 108 1.00
ACGTcount: A:0.35, C:0.09, G:0.33, T:0.22
Consensus pattern (54 bp):
GTGGATTGAAATGGGAATTCAAGGAAGTAAGATGACATCGCGGAGATGATTAGC
Found at i:52820911 original size:18 final size:18
Alignment explanation
Indices: 52820888--52820926 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
52820878 CCAATATGCT
52820888 CAACAATCTCCTACGGTC
1 CAACAATCTCCTACGGTC
*
52820906 CAACAATCTCGTACGGTC
1 CAACAATCTCCTACGGTC
52820924 CAA
1 CAA
52820927 TAAATCTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.31, C:0.36, G:0.13, T:0.21
Consensus pattern (18 bp):
CAACAATCTCCTACGGTC
Found at i:52825578 original size:25 final size:25
Alignment explanation
Indices: 52825526--52825641 Score: 107
Period size: 25 Copynumber: 4.7 Consensus size: 25
52825516 TCCTGATATA
* * *
52825526 TGGCTCTCCTGAGCTTGC-CGTTATT
1 TGGCTCTCATGAGCTT-CTCGATAAT
52825551 TGGCTCTCATGAGCTTCTCGATAAT
1 TGGCTCTCATGAGCTTCTCGATAAT
* *
52825576 TGGCTCTTATAAGCTTCTCGATTAA-
1 TGGCTCTCATGAGCTTCTCGA-TAAT
*
52825601 TGGCTCTCCA-GAGCTTCTCAAT-AT
1 TGGCTCT-CATGAGCTTCTCGATAAT
52825625 TGGCTCAT-ATGAGCTTC
1 TGGCTC-TCATGAGCTTC
52825642 CTGATTTACA
Statistics
Matches: 77, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
23 2 0.03
24 15 0.19
25 56 0.73
26 4 0.05
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.37
Consensus pattern (25 bp):
TGGCTCTCATGAGCTTCTCGATAAT
Found at i:52825656 original size:49 final size:50
Alignment explanation
Indices: 52825553--52825665 Score: 124
Period size: 49 Copynumber: 2.3 Consensus size: 50
52825543 CCGTTATTTG
* * **
52825553 GCTCTCATGAGCTTCTCGATAATTGGCTCTTATAAGCTTCTCGATTAATG
1 GCTCTCATGAGCTTCTCAATAATTGGCTCATATAAGCTTCTCGATTAACA
* *
52825603 GCTCTCCA-GAGCTTCTCAAT-ATTGGCTCATATGAGCTTC-CTGATTTACA
1 GCTCT-CATGAGCTTCTCAATAATTGGCTCATATAAGCTTCTC-GATTAACA
*
52825652 GCTCTTATGAGCTT
1 GCTCTCATGAGCTT
52825666 ATTGATTCTC
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
48 2 0.04
49 33 0.62
50 16 0.30
51 2 0.04
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.37
Consensus pattern (50 bp):
GCTCTCATGAGCTTCTCAATAATTGGCTCATATAAGCTTCTCGATTAACA
Found at i:52825660 original size:25 final size:25
Alignment explanation
Indices: 52825627--52825692 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
52825617 CTCAATATTG
52825627 GCTCATATGAGCTTCCTGATT-TACA
1 GCTCATATGAGCTTCCTGATTCT-CA
* **
52825652 GCTCTTATGAGCTTATTGATTCTCA
1 GCTCATATGAGCTTCCTGATTCTCA
*
52825677 GCTCAAATGAGCTTCC
1 GCTCATATGAGCTTCC
52825693 CTTTATACTG
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
25 32 0.97
26 1 0.03
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.36
Consensus pattern (25 bp):
GCTCATATGAGCTTCCTGATTCTCA
Found at i:52830315 original size:27 final size:27
Alignment explanation
Indices: 52830285--52830630 Score: 267
Period size: 27 Copynumber: 12.9 Consensus size: 27
52830275 GCAAATGACT
* * *
52830285 GAAATACCCTCGATGGGTAAAATGATC
1 GAAATACCCTCAAAGGGTAAAATTATC
*
52830312 GAAATA-CCTCTAAAGGGTAAAATGA-C
1 GAAATACCCTC-AAAGGGTAAAATTATC
* * *
52830338 TAAAATACCC-CTAAAGGGTAAAATAACC
1 -GAAATACCCTC-AAAGGGTAAAATTATC
* * * *
52830366 AAAATACCCTTAAAGGGTAAAATAACC
1 GAAATACCCTCAAAGGGTAAAATTATC
**
52830393 GAAATA-CCTTGAAGGGTAAAATTATC
1 GAAATACCCTCAAAGGGTAAAATTATC
* * * *
52830419 GAAATAACCTTAAAGGATAAATTTATC
1 GAAATACCCTCAAAGGGTAAAATTATC
*
52830446 GAAATACCCTCAAAGGGTAAAATTACC
1 GAAATACCCTCAAAGGGTAAAATTATC
* *
52830473 GAAATACCCTTAAAGAGTAAAATTA-C
1 GAAATACCCTCAAAGGGTAAAATTATC
* * *
52830499 TGAAACACCCTCGAAGGGTAAAATTACC
1 -GAAATACCCTCAAAGGGTAAAATTATC
* ** * *
52830527 AAAATAGCATTGAAA-GGTAAAATTATT
1 GAAATA-CCCTCAAAGGGTAAAATTATC
*
52830554 GAAATACCTTCAAAGGGTAAAATTATC
1 GAAATACCCTCAAAGGGTAAAATTATC
* * * *
52830581 AAAATACCGCT-GAAGGGTAAAATGAGC
1 GAAATACC-CTCAAAGGGTAAAATTATC
*
52830608 GAAATACTCCT-ATAGGGTAAAAT
1 GAAATAC-CCTCAAAGGGTAAAAT
52830631 AACCGTTATA
Statistics
Matches: 264, Mismatches: 43, Indels: 24
0.80 0.13 0.07
Matches are distributed among these distances:
26 35 0.13
27 219 0.83
28 10 0.04
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.22
Consensus pattern (27 bp):
GAAATACCCTCAAAGGGTAAAATTATC
Found at i:52830344 original size:54 final size:54
Alignment explanation
Indices: 52830277--52830630 Score: 296
Period size: 54 Copynumber: 6.6 Consensus size: 54
52830267 ATTCGTAGGC
* * * * *
52830277 AAATGACTGAAATACCCTCGATGGGTAAAATGATCGAAATACCTCTAAAGGGTA
1 AAATGACTGAAATACCCTCAAAGGGTAAAATTACCAAAATACCTCTAAAGGGTA
* *
52830331 AAATGACTAAAATACCC-CTAAAGGGTAAAATAACCAAAATACC-CTTAAAGGGTA
1 AAATGACTGAAATACCCTC-AAAGGGTAAAATTACCAAAATACCTC-TAAAGGGTA
* * ** * * *
52830385 AAATAACCGAAATA-CCTTGAAGGGTAAAATTATCGAAATAACCT-TAAAGGATA
1 AAATGACTGAAATACCCTCAAAGGGTAAAATTACCAAAAT-ACCTCTAAAGGGTA
* * * *
52830438 AATTTA-TCGAAATACCCTCAAAGGGTAAAATTACCGAAATACC-CTTAAAGAGTA
1 AAATGACT-GAAATACCCTCAAAGGGTAAAATTACCAAAATACCTC-TAAAGGGTA
* * * *
52830492 AAATTACTGAAACACCCTCGAAGGGTAAAATTACCAAAATAGCAT-TGAAA-GGTA
1 AAATGACTGAAATACCCTCAAAGGGTAAAATTACCAAAATA-CCTCT-AAAGGGTA
* * * * * *
52830546 AAATTATTGAAATACCTTCAAAGGGTAAAATTATCAAAATACCGCTGAAGGGTA
1 AAATGACTGAAATACCCTCAAAGGGTAAAATTACCAAAATACCTCTAAAGGGTA
*
52830600 AAATGAGC-GAAATACTCCT-ATAGGGTAAAAT
1 AAATGA-CTGAAATAC-CCTCAAAGGGTAAAAT
52830631 AACCGTTATA
Statistics
Matches: 242, Mismatches: 41, Indels: 34
0.76 0.13 0.11
Matches are distributed among these distances:
53 45 0.19
54 190 0.79
55 7 0.03
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.22
Consensus pattern (54 bp):
AAATGACTGAAATACCCTCAAAGGGTAAAATTACCAAAATACCTCTAAAGGGTA
Found at i:52830642 original size:81 final size:79
Alignment explanation
Indices: 52830286--52830635 Score: 303
Period size: 81 Copynumber: 4.3 Consensus size: 79
52830276 CAAATGACTG
* * * * *
52830286 AAATACCCTCGATGGGTAAAATGATCGAAATACCTCTAAAGGGTAAAATGACTAAAATACCCCTA
1 AAATACCCTCAAAGGGTAAAATAACCGAAATACCT-TAAAGGGTAAAATTACTAAAATA-CCCTA
*
52830351 AAGGGTAAAATAACCA
64 AAGGGTAAAATTACCA
* * * *
52830367 AAATACCCTTAAAGGGTAAAATAACCGAAATACCTTGAAGGGTAAAATTA-TCGAAATAACCTTA
1 AAATACCCTCAAAGGGTAAAATAACCGAAATACCTTAAAGGGTAAAATTACT-AAAAT-ACCCTA
* * * *
52830431 AAGGATAAATTTATCG
64 AAGGGTAAAATTACCA
* * * * *
52830447 AAATACCCTCAAAGGGTAAAATTACCGAAATACCCTTAAAGAGTAAAATTACTGAAACACCCTCG
1 AAATACCCTCAAAGGGTAAAATAACCGAAATA-CCTTAAAGGGTAAAATTACTAAAATACCCT-A
52830512 AAGGGTAAAATTACCA
64 AAGGGTAAAATTACCA
** * * **
52830528 AAATAGCATTGAAA-GGTAAAATTATTGAAATACCTTCAAAGGGTAAAATTA-TCAAAATACCGC
1 AAATA-CCCTCAAAGGGTAAAATAACCGAAATACCTT-AAAGGGTAAAATTACT-AAAATACC-C
* * * *
52830591 TGAAGGGTAAAATGAGCG
62 TAAAGGGTAAAATTACCA
*
52830609 AAATACTCCT-ATAGGGTAAAATAACCG
1 AAATAC-CCTCAAAGGGTAAAATAACCG
52830636 TTATACCCCT
Statistics
Matches: 216, Mismatches: 42, Indels: 22
0.77 0.15 0.08
Matches are distributed among these distances:
79 1 0.00
80 74 0.34
81 133 0.62
82 8 0.04
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.22
Consensus pattern (79 bp):
AAATACCCTCAAAGGGTAAAATAACCGAAATACCTTAAAGGGTAAAATTACTAAAATACCCTAAA
GGGTAAAATTACCA
Found at i:52830853 original size:26 final size:26
Alignment explanation
Indices: 52830824--52830873 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
52830814 ATGCCACATA
* *
52830824 TACTGTTACTGGCAGCTTTGCTGCGT
1 TACTATTACTGGCAACTTTGCTGCGT
52830850 TACTATTACTGGCAACTTTGCTGC
1 TACTATTACTGGCAACTTTGCTGC
52830874 AATTCTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (26 bp):
TACTATTACTGGCAACTTTGCTGCGT
Found at i:52830881 original size:26 final size:26
Alignment explanation
Indices: 52830824--52830885 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
52830814 ATGCCACATA
* * *
52830824 TACTGTTACTGGCAGCTTTGCTGCGT
1 TACTATTACTGGCAACTTTGCTGCAT
52830850 TACTATTACTGGCAACTTTGCTGCAAT
1 TACTATTACTGGCAACTTTGCTGC-AT
52830877 T-CTATTACT
1 TACTATTACT
52830886 AGCAGTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
26 30 0.94
27 2 0.06
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.40
Consensus pattern (26 bp):
TACTATTACTGGCAACTTTGCTGCAT
Found at i:52831568 original size:20 final size:20
Alignment explanation
Indices: 52831543--52831585 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
52831533 TTCCAAACTT
* *
52831543 AAGAAATGATTTTTATCAAC
1 AAGAAACGAGTTTTATCAAC
52831563 AAGAAACGAGTTTTATCAAC
1 AAGAAACGAGTTTTATCAAC
52831583 AAG
1 AAG
52831586 TCTAAGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.47, C:0.12, G:0.14, T:0.28
Consensus pattern (20 bp):
AAGAAACGAGTTTTATCAAC
Found at i:52833373 original size:41 final size:40
Alignment explanation
Indices: 52833265--52833379 Score: 115
Period size: 41 Copynumber: 2.8 Consensus size: 40
52833255 GAATAATAAA
* * * **
52833265 GAATTGCACATACGTGCCCCTATTTGAACTTTGGTACCCCT
1 GAATTGCACATACGTG-CCATATTTGTACTTCGAAACCCCT
* *
52833306 GAATTGCACATACATGTCCTTATTTGTACTTCGAAACCCCT
1 GAATTGCACATACGTG-CCATATTTGTACTTCGAAACCCCT
*
52833347 -AGATTGCACATACGTGCACATGTTTGTACTTCG
1 GA-ATTGCACATACGTGC-CATATTTGTACTTCG
52833380 GTACTCCTGG
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
40 2 0.03
41 60 0.97
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (40 bp):
GAATTGCACATACGTGCCATATTTGTACTTCGAAACCCCT
Found at i:52835439 original size:18 final size:19
Alignment explanation
Indices: 52835403--52835440 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
52835393 AGAGTCCCAA
* *
52835403 AAATTACAAACTTTCAAAT
1 AAATTACAAAATTTAAAAT
52835422 AAATT-CAAAATTTAAAAT
1 AAATTACAAAATTTAAAAT
52835440 A
1 A
52835441 CCGAAACTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.32
Consensus pattern (19 bp):
AAATTACAAAATTTAAAAT
Found at i:52839911 original size:30 final size:29
Alignment explanation
Indices: 52839871--52839929 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
52839861 TATAAAAATA
*
52839871 TTTTACATAAATATATATTTTTATTTTTAT
1 TTTTACATAAATATATATTTAT-TTTTTAT
*
52839901 TTTTATATAAATATATATTTATTTTTTAT
1 TTTTACATAAATATATATTTATTTTTTAT
52839930 AAAAATTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 7 0.26
30 20 0.74
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (29 bp):
TTTTACATAAATATATATTTATTTTTTAT
Found at i:52839987 original size:59 final size:59
Alignment explanation
Indices: 52839895--52840016 Score: 235
Period size: 59 Copynumber: 2.1 Consensus size: 59
52839885 ATATTTTTAT
*
52839895 TTTTATTTTTATATAAATATATATTTATTTTTTATAAAAATTATGTGTCGTAATGAATG
1 TTTTATTTTTATATAAATATATATTTATTTTTTATAAAAATTATGTGTAGTAATGAATG
52839954 TTTTATTTTTATATAAATATATATTTATTTTTTATAAAAATTATGTGTAGTAATGAATG
1 TTTTATTTTTATATAAATATATATTTATTTTTTATAAAAATTATGTGTAGTAATGAATG
52840013 TTTT
1 TTTT
52840017 CATGATTTTA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.35, C:0.01, G:0.08, T:0.56
Consensus pattern (59 bp):
TTTTATTTTTATATAAATATATATTTATTTTTTATAAAAATTATGTGTAGTAATGAATG
Found at i:52840179 original size:24 final size:24
Alignment explanation
Indices: 52840152--52840250 Score: 67
Period size: 24 Copynumber: 4.0 Consensus size: 24
52840142 TAAAATGTAA
52840152 TTAATTTTTATATAATTTTAAATT
1 TTAATTTTTATATAATTTTAAATT
* * * *
52840176 TTAATTTATATTTTATTTT-TATT
1 TTAATTTTTATATAATTTTAAATT
* *
52840199 TATAAAACTTTT-TATAATTTTAATTTT
1 T-T--AATTTTTATATAATTTTAA-ATT
*
52840226 TTAGATTTTTTTATAATTTTCAAAT
1 TTA-ATTTTTATATAATTTT-AAAT
52840251 AATAATGTCC
Statistics
Matches: 55, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
23 4 0.07
24 18 0.33
25 12 0.22
26 16 0.29
27 5 0.09
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (24 bp):
TTAATTTTTATATAATTTTAAATT
Found at i:52840485 original size:19 final size:20
Alignment explanation
Indices: 52840444--52840485 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
52840434 TTACACGTTT
* * *
52840444 AATTTTTAATTCATTATTCA
1 AATTTTTAAATCATAATTAA
52840464 AATTTTTAAAT-ATAATTAA
1 AATTTTTAAATCATAATTAA
52840483 AAT
1 AAT
52840486 ATATTATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (20 bp):
AATTTTTAAATCATAATTAA
Found at i:52840874 original size:23 final size:23
Alignment explanation
Indices: 52840848--52840892 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
52840838 AATTGACCAT
52840848 AATA-ATTCATATAAATATATTAC
1 AATAGATT-ATATAAATATATTAC
*
52840871 AATAGATTATATAAATTTATTA
1 AATAGATTATATAAATATATTA
52840893 TTTAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.42
Consensus pattern (23 bp):
AATAGATTATATAAATATATTAC
Found at i:52841134 original size:24 final size:23
Alignment explanation
Indices: 52841092--52841138 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
52841082 GGTTTCATCA
52841092 AAATTATCACATAACAATACTAAT
1 AAATTATCACATAACAATA-TAAT
* * *
52841116 AAATTATTACTTAATAATATAAT
1 AAATTATCACATAACAATATAAT
52841139 TAAAAAGTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (23 bp):
AAATTATCACATAACAATATAAT
Done.