Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 27 of 106
Found at i:10758759 original size:23 final size:24
Alignment explanation
Indices: 10758705--10758766 Score: 72
Period size: 26 Copynumber: 2.5 Consensus size: 24
10758695 ATTAACATTA
* *
10758705 TTTTGTATCTTTTCCATATTATTC
1 TTTTGTATCATTTACATATTATTC
10758729 TTTATTGTATCATTTACATATTATTC
1 -TT-TTGTATCATTTACATATTATTC
10758755 -TTTGTATTCATT
1 TTTTGTA-TCATT
10758767 CATGTGATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
23 5 0.15
24 6 0.18
25 2 0.06
26 20 0.61
ACGTcount: A:0.21, C:0.13, G:0.05, T:0.61
Consensus pattern (24 bp):
TTTTGTATCATTTACATATTATTC
Found at i:10759123 original size:92 final size:92
Alignment explanation
Indices: 10758988--10759372 Score: 592
Period size: 92 Copynumber: 4.2 Consensus size: 92
10758978 AATGGTGAGA
* * * *
10758988 ATGGAATCGCGTCACCAGTTGATATTGATTCACTG-GAGTATTTGTTATGAAGTCACACGAGTAC
1 ATGGAATCGCGTCACTAGTTGATATTGATTCGC-GAGAGTATTTGTTATGGAGTCACGCGAGTAC
*
10759052 TAAATGTTGAATCACGTCGGTAGTTAAT
65 TAAATGTTGAATCACGTCGATAGTTAAT
* *
10759080 ATGGAATCGCGTCACTAGTTGATATTGATTCGTGGGAGTATTTGTTATGGAGTCACGCGAGTACT
1 ATGGAATCGCGTCACTAGTTGATATTGATTCGCGAGAGTATTTGTTATGGAGTCACGCGAGTACT
* *
10759145 AAATGTTGAATCATGTCGGTAGTTAAT
66 AAATGTTGAATCACGTCGATAGTTAAT
*
10759172 ATGGAATCGCGTCACTAGTTGATATTGATTCGCGAAAGTATTTGTTATGGAGTCACGCGAGTACT
1 ATGGAATCGCGTCACTAGTTGATATTGATTCGCGAGAGTATTTGTTATGGAGTCACGCGAGTACT
*
10759237 AAATGTTGAATCACATCGATAGTTAAT
66 AAATGTTGAATCACGTCGATAGTTAAT
* * * *
10759264 ATGGAATTGAGTCACTATTTGATATTGATTCGCGAGAGTATTTGTTATGGAGTCACGCAAGTACT
1 ATGGAATCGCGTCACTAGTTGATATTGATTCGCGAGAGTATTTGTTATGGAGTCACGCGAGTACT
* *
10759329 AAATTTTGAATCACGTCGATAGTTAAC
66 AAATGTTGAATCACGTCGATAGTTAAT
*
10759356 ATGGAATCACGTCACTA
1 ATGGAATCGCGTCACTA
10759373 ATCCACATGG
Statistics
Matches: 269, Mismatches: 23, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
91 1 0.00
92 268 1.00
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.33
Consensus pattern (92 bp):
ATGGAATCGCGTCACTAGTTGATATTGATTCGCGAGAGTATTTGTTATGGAGTCACGCGAGTACT
AAATGTTGAATCACGTCGATAGTTAAT
Found at i:10762833 original size:78 final size:78
Alignment explanation
Indices: 10762740--10762907 Score: 255
Period size: 78 Copynumber: 2.2 Consensus size: 78
10762730 TTTGAGAGAG
* * *
10762740 ACATCTTGTGTTTTAGATTTGCTTGTCCCCCAGTTACCACACTCAATTTGCTTCGTTGTACTGGT
1 ACATCTTGTGTTTTAGATTTGCTTGTCCCCCAATCACAACACTCAATTTGCTTCGTTGTACTGGT
10762805 CACAGCTACTACA
66 CACAGCTACTACA
* * *
10762818 ACATCTTGTGTTTTAGATTTGCTTGTCCCCCAATCACAACAGTCATTTTGCTTCGTTGTTCTGGT
1 ACATCTTGTGTTTTAGATTTGCTTGTCCCCCAATCACAACACTCAATTTGCTTCGTTGTACTGGT
* *
10762883 CACAGCTGCTGCA
66 CACAGCTACTACA
*
10762896 ACATCATGTGTT
1 ACATCTTGTGTT
10762908 GCAAATATCA
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
78 81 1.00
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.38
Consensus pattern (78 bp):
ACATCTTGTGTTTTAGATTTGCTTGTCCCCCAATCACAACACTCAATTTGCTTCGTTGTACTGGT
CACAGCTACTACA
Found at i:10766284 original size:118 final size:118
Alignment explanation
Indices: 10766137--10766395 Score: 394
Period size: 118 Copynumber: 2.2 Consensus size: 118
10766127 AACAAGAAGC
* ** * * *
10766137 GAATTGCACAAGTCACGCGCCACTGCTCTCGCAATATATAACAACAGGTCACGTAATATATAAAA
1 GAATTGCACAAGTCAAGCGCCACCACTCTCGCAATACATAACAACAGGTAACGCAATATATAAAA
*
10766202 ACCAATCACTCAAGCCTAAAAAACTACTGAACAAAAGCCTCAAAATAACACAT
66 ACCAATCACGCAAGCCTAAAAAACTACTGAACAAAAGCCTCAAAATAACACAT
* *
10766255 GAATTGCACAAGTCAAGTGCCACCACTCTCGCAATACATAACAGCAGGTAACGCAATATATAAAA
1 GAATTGCACAAGTCAAGCGCCACCACTCTCGCAATACATAACAACAGGTAACGCAATATATAAAA
* *
10766320 ACTAGTCACGCAAGCCTAAAAAACTACTGAACAAAAGCCTCAAAATAACACAT
66 ACCAATCACGCAAGCCTAAAAAACTACTGAACAAAAGCCTCAAAATAACACAT
*
10766373 GAATTACACAAGTCACA-CGCCAC
1 GAATTGCACAAGTCA-AGCGCCAC
10766396 TGTCGTGACG
Statistics
Matches: 127, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
118 126 0.99
119 1 0.01
ACGTcount: A:0.44, C:0.27, G:0.12, T:0.17
Consensus pattern (118 bp):
GAATTGCACAAGTCAAGCGCCACCACTCTCGCAATACATAACAACAGGTAACGCAATATATAAAA
ACCAATCACGCAAGCCTAAAAAACTACTGAACAAAAGCCTCAAAATAACACAT
Found at i:10768492 original size:17 final size:17
Alignment explanation
Indices: 10768470--10768545 Score: 79
Period size: 17 Copynumber: 4.5 Consensus size: 17
10768460 CATCCCGATT
10768470 TTTTATTATTATTA-TTA
1 TTTTATT-TTATTATTTA
10768487 TTTTA-TTTATTTATTTA
1 TTTTATTTTA-TTATTTA
10768504 TTTTATTTTATTTATTTA
1 TTTTATTTTA-TTATTTA
*
10768522 ATTTATATTTA-TATTTA
1 TTTTAT-TTTATTATTTA
10768539 -TTTATTT
1 TTTTATTT
10768546 ATTTTTTTTA
Statistics
Matches: 54, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
15 5 0.09
16 9 0.17
17 19 0.35
18 17 0.31
19 4 0.07
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTATTTTATTATTTA
Found at i:10768497 original size:4 final size:4
Alignment explanation
Indices: 10768488--10768561 Score: 73
Period size: 4 Copynumber: 18.2 Consensus size: 4
10768478 TTATTATTAT
*
10768488 TTTA TTTA TTTA TTTA TTTTA TTTTA TTTA TTTAA TTTA TATT- TATA
1 TTTA TTTA TTTA TTTA -TTTA -TTTA TTTA TTT-A TTTA T-TTA TTTA
*
10768535 TTTA TTTA TTTA TTT- TTT- TTAA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
10768562 GTGTCTACAG
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
3 6 0.10
4 40 0.66
5 15 0.25
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:10768517 original size:9 final size:9
Alignment explanation
Indices: 10768470--10768561 Score: 86
Period size: 9 Copynumber: 10.1 Consensus size: 9
10768460 CATCCCGATT
10768470 TTTTA-TTA
1 TTTTATTTA
10768478 TTATTA-TTA
1 TT-TTATTTA
10768487 TTTTATTTA
1 TTTTATTTA
10768496 -TTTATTTA
1 TTTTATTTA
10768504 TTTTATTT-
1 TTTTATTTA
10768512 TATTTATTTAA
1 T-TTTATTT-A
10768523 TTTATATTTA
1 TTT-TATTTA
10768533 TATTTATTTA
1 T-TTTATTTA
*
10768543 -TTTATTTT
1 TTTTATTTA
10768551 TTTTAATTTA
1 TTTT-ATTTA
10768561 T
1 T
10768562 GTGTCTACAG
Statistics
Matches: 72, Mismatches: 2, Indels: 18
0.78 0.02 0.20
Matches are distributed among these distances:
8 21 0.29
9 28 0.39
10 15 0.21
11 8 0.11
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTTATTTA
Found at i:10770060 original size:22 final size:22
Alignment explanation
Indices: 10770032--10770115 Score: 96
Period size: 22 Copynumber: 3.6 Consensus size: 22
10770022 TAGGTAGCTA
10770032 AAGTCACGCAATGCCTACAAAC
1 AAGTCACGCAATGCCTACAAAC
* *
10770054 AAGTCACGCAATGCTCAACAAAT
1 AAGTCACGCAATGC-CTACAAAC
*
10770077 ATTCAGTCACGCAATACCTACAAAC
1 A---AGTCACGCAATGCCTACAAAC
*
10770102 AGGTCACGCAATGC
1 AAGTCACGCAATGC
10770116 TCAATAAATA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
22 25 0.49
23 7 0.14
25 7 0.14
26 12 0.24
ACGTcount: A:0.39, C:0.30, G:0.14, T:0.17
Consensus pattern (22 bp):
AAGTCACGCAATGCCTACAAAC
Found at i:10770085 original size:26 final size:26
Alignment explanation
Indices: 10770055--10770135 Score: 82
Period size: 26 Copynumber: 3.3 Consensus size: 26
10770045 CCTACAAACA
10770055 AGTCACGCAATGCTCAACAAATATTC
1 AGTCACGCAATGCTCAACAAATATTC
* *
10770081 AGTCACGCAATAC-CTAC-AA-A--C
1 AGTCACGCAATGCTCAACAAATATTC
* *
10770102 AGGTCACGCAATGCTCAATAAATATTT
1 A-GTCACGCAATGCTCAACAAATATTC
10770129 AGTCACG
1 AGTCACG
10770136 TAACACTTGT
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
21 2 0.05
22 11 0.26
23 3 0.07
24 4 0.09
25 4 0.09
26 18 0.42
27 1 0.02
ACGTcount: A:0.38, C:0.26, G:0.14, T:0.22
Consensus pattern (26 bp):
AGTCACGCAATGCTCAACAAATATTC
Found at i:10770108 original size:48 final size:48
Alignment explanation
Indices: 10770033--10770320 Score: 178
Period size: 48 Copynumber: 6.0 Consensus size: 48
10770023 AGGTAGCTAA
*
10770033 AGTCACGCAATGCCTACAAACAAGTCACGCAATGCTCAACAAATATTC
1 AGTCACGCAATACCTACAAACAAGTCACGCAATGCTCAACAAATATTC
* * *
10770081 AGTCACGCAATACCTACAAACAGGTCACGCAATGCTCAATAAATATTT
1 AGTCACGCAATACCTACAAACAAGTCACGCAATGCTCAACAAATATTC
** * * * *
10770129 AGTCACG---TA---AC--ACTTGTCACACAACGCTTAACAAATATTA
1 AGTCACGCAATACCTACAAACAAGTCACGCAATGCTCAACAAATATTC
* * * * * *
10770169 AGTCACGTAATGCCTATAAAGAACTCACGCAATACTCAACAAATATTC
1 AGTCACGCAATACCTACAAACAAGTCACGCAATGCTCAACAAATATTC
* * * * * ** ** *
10770217 AATTAGGTAATATTCAGTCACGTAATACCTGTCACGCAACACTCAACATATATTC
1 AGTCACGCAATA--C-CT-AC--AA-ACAAGTCACGCAATGCTCAACAAATATTC
* * * * *
10770272 AGTCACGTAATGCCTATAAAGAACTCACGCAATGCTCAACAAATATTC
1 AGTCACGCAATACCTACAAACAAGTCACGCAATGCTCAACAAATATTC
10770320 A
1 A
10770321 AGCACCTAAT
Statistics
Matches: 178, Mismatches: 47, Indels: 30
0.70 0.18 0.12
Matches are distributed among these distances:
40 29 0.16
42 2 0.01
43 1 0.01
45 2 0.01
46 1 0.01
48 102 0.57
49 2 0.01
50 1 0.01
51 2 0.01
52 2 0.01
53 1 0.01
54 2 0.01
55 31 0.17
ACGTcount: A:0.40, C:0.25, G:0.11, T:0.24
Consensus pattern (48 bp):
AGTCACGCAATACCTACAAACAAGTCACGCAATGCTCAACAAATATTC
Found at i:10770250 original size:103 final size:103
Alignment explanation
Indices: 10770122--10770321 Score: 319
Period size: 103 Copynumber: 1.9 Consensus size: 103
10770112 ATGCTCAATA
* * * *
10770122 AATATTTAGTCACGTAACACTTGTCACACAACGCTTAACAAATATTAAGTCACGTAATGCCTATA
1 AATATTCAGTCACGTAACACCTGTCACACAACACTCAACAAATATTAAGTCACGTAATGCCTATA
10770187 AAGAACTCACGCAATACTCAACAAATATTCAATTAGGT
66 AAGAACTCACGCAATACTCAACAAATATTCAATTAGGT
* * * *
10770225 AATATTCAGTCACGTAATACCTGTCACGCAACACTCAACATATATTCAGTCACGTAATGCCTATA
1 AATATTCAGTCACGTAACACCTGTCACACAACACTCAACAAATATTAAGTCACGTAATGCCTATA
*
10770290 AAGAACTCACGCAATGCTCAACAAATATTCAA
66 AAGAACTCACGCAATACTCAACAAATATTCAA
10770322 GCACCTAATG
Statistics
Matches: 88, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
103 88 1.00
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.26
Consensus pattern (103 bp):
AATATTCAGTCACGTAACACCTGTCACACAACACTCAACAAATATTAAGTCACGTAATGCCTATA
AAGAACTCACGCAATACTCAACAAATATTCAATTAGGT
Found at i:10782078 original size:21 final size:21
Alignment explanation
Indices: 10782052--10782167 Score: 94
Period size: 21 Copynumber: 5.5 Consensus size: 21
10782042 TGAGACAGGA
10782052 TAAATTTAAATTTAATTTGTT
1 TAAATTTAAATTTAATTTGTT
**
10782073 TAAATTTAAA-TT-ATCTATCCAT
1 TAAATTTAAATTTAAT-T-T-GTT
**
10782095 TGTATTTAAATTTAATTTGTT
1 TAAATTTAAATTTAATTTGTT
* * **
10782116 TAAATTTAAA-TAAAGATTAAT
1 TAAATTTAAATTTAA-TTTGTT
*
10782137 TATATTTAAATTTAATTTGTT
1 TAAATTTAAATTTAATTTGTT
10782158 TAAATTTAAA
1 TAAATTTAAA
10782168 CATAATATCC
Statistics
Matches: 70, Mismatches: 18, Indels: 14
0.69 0.18 0.14
Matches are distributed among these distances:
19 2 0.03
20 6 0.09
21 44 0.63
22 13 0.19
23 3 0.04
24 2 0.03
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52
Consensus pattern (21 bp):
TAAATTTAAATTTAATTTGTT
Found at i:10782156 original size:42 final size:43
Alignment explanation
Indices: 10782055--10782167 Score: 165
Period size: 42 Copynumber: 2.7 Consensus size: 43
10782045 GACAGGATAA
*** * *
10782055 ATTTAAATTTAATTTGTTTAAATTTAAATTATCTATCCATTGT
1 ATTTAAATTTAATTTGTTTAAATTTAAATTAAAGATCAATTAT
*
10782098 ATTTAAATTTAATTTGTTTAAATTTAAA-TAAAGATTAATTAT
1 ATTTAAATTTAATTTGTTTAAATTTAAATTAAAGATCAATTAT
10782140 ATTTAAATTTAATTTGTTTAAATTTAAA
1 ATTTAAATTTAATTTGTTTAAATTTAAA
10782168 CATAATATCC
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
42 36 0.56
43 28 0.44
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52
Consensus pattern (43 bp):
ATTTAAATTTAATTTGTTTAAATTTAAATTAAAGATCAATTAT
Found at i:10783262 original size:47 final size:47
Alignment explanation
Indices: 10783209--10783304 Score: 156
Period size: 47 Copynumber: 2.0 Consensus size: 47
10783199 ATTTTGTATG
**
10783209 ATTTTACTTATTTGTTAGGTAAAATTTACAAAATGCATGATGTAATT
1 ATTTTACTTATTTGTTACATAAAATTTACAAAATGCATGATGTAATT
* *
10783256 ATTTTACTTATTTGTTACATAAAATTTATAAAATGCATGATGTTATT
1 ATTTTACTTATTTGTTACATAAAATTTACAAAATGCATGATGTAATT
10783303 AT
1 AT
10783305 AAAATGTATG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.36, C:0.06, G:0.10, T:0.47
Consensus pattern (47 bp):
ATTTTACTTATTTGTTACATAAAATTTACAAAATGCATGATGTAATT
Found at i:10783306 original size:20 final size:20
Alignment explanation
Indices: 10783281--10783324 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
10783271 TACATAAAAT
*
10783281 TTATAAAATGCATGATGTTA
1 TTATAAAATGCATGATGTAA
*
10783301 TTATAAAATGTATGATGTAA
1 TTATAAAATGCATGATGTAA
10783321 TTAT
1 TTAT
10783325 TTTCCTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.41, C:0.02, G:0.14, T:0.43
Consensus pattern (20 bp):
TTATAAAATGCATGATGTAA
Found at i:10795190 original size:34 final size:34
Alignment explanation
Indices: 10795147--10795219 Score: 146
Period size: 34 Copynumber: 2.1 Consensus size: 34
10795137 AATGGATATC
10795147 TCAACACAGAAAACATGCTACATCTTCTACATCA
1 TCAACACAGAAAACATGCTACATCTTCTACATCA
10795181 TCAACACAGAAAACATGCTACATCTTCTACATCA
1 TCAACACAGAAAACATGCTACATCTTCTACATCA
10795215 TCAAC
1 TCAAC
10795220 CATCTCAGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.41, C:0.30, G:0.05, T:0.23
Consensus pattern (34 bp):
TCAACACAGAAAACATGCTACATCTTCTACATCA
Found at i:10801821 original size:2 final size:2
Alignment explanation
Indices: 10801816--10801866 Score: 79
Period size: 2 Copynumber: 26.5 Consensus size: 2
10801806 ACACACACAA
*
10801816 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10801858 A- AT AT -T AT A
1 AT AT AT AT AT A
10801867 GTTTCATAGT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.04
2 43 0.96
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:10802406 original size:24 final size:24
Alignment explanation
Indices: 10802368--10802445 Score: 72
Period size: 24 Copynumber: 3.4 Consensus size: 24
10802358 ATAAGCTATG
**
10802368 ATGTTACACACCATGTACAAAAAT
1 ATGTTACACGTCATGTACAAAAAT
** *
10802392 ATGTTACACGTCATG-A-TTAAGT
1 ATGTTACACGTCATGTACAAAAAT
*
10802414 -TGTTACACGTCATGTGCAAAAAT
1 ATGTTACACGTCATGTACAAAAAT
*
10802437 ATGTGACAC
1 ATGTTACAC
10802446 ACTATGGTTA
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
21 14 0.34
22 3 0.07
23 4 0.10
24 20 0.49
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.29
Consensus pattern (24 bp):
ATGTTACACGTCATGTACAAAAAT
Found at i:10802434 original size:45 final size:45
Alignment explanation
Indices: 10802369--10802496 Score: 159
Period size: 45 Copynumber: 2.8 Consensus size: 45
10802359 TAAGCTATGA
*
10802369 TGTTACACACCATGTACAAAAATATGTTACACGTCATGATTAAGT
1 TGTTACACACCATGTACAAAAATATGTGACACGTCATGATTAAGT
** * * * *
10802414 TGTTACACGTCATGTGCAAAAATATGTGACAC-ACTATGGTTAGGT
1 TGTTACACACCATGTACAAAAATATGTGACACGTC-ATGATTAAGT
* *
10802459 TATTACACACCATGTACAAAAACATGTGACACGTCATG
1 TGTTACACACCATGTACAAAAATATGTGACACGTCATG
10802497 TACAGAAATA
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
44 1 0.01
45 66 0.97
46 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (45 bp):
TGTTACACACCATGTACAAAAATATGTGACACGTCATGATTAAGT
Found at i:10802490 original size:24 final size:24
Alignment explanation
Indices: 10802463--10802514 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
10802453 TTAGGTTATT
10802463 ACACACCATGTACAAAAACATGTG
1 ACACACCATGTACAAAAACATGTG
** * *
10802487 ACACGTCATGTACAGAAATATGTG
1 ACACACCATGTACAAAAACATGTG
10802511 ACAC
1 ACAC
10802515 GCAATGATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.19
Consensus pattern (24 bp):
ACACACCATGTACAAAAACATGTG
Found at i:10802515 original size:24 final size:24
Alignment explanation
Indices: 10802469--10802515 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
10802459 TATTACACAC
10802469 CATGTACAAAAACATGTGACACGT
1 CATGTACAAAAACATGTGACACGT
* *
10802493 CATGTACAGAAATATGTGACACG
1 CATGTACAAAAACATGTGACACG
10802516 CAATGATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.21
Consensus pattern (24 bp):
CATGTACAAAAACATGTGACACGT
Found at i:10804773 original size:2 final size:2
Alignment explanation
Indices: 10804762--10804790 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
10804752 CTATCAATAT
10804762 TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
10804791 CTTNTATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:10804800 original size:2 final size:2
Alignment explanation
Indices: 10804795--10804823 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
10804785 TCTCTCCTTN
10804795 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10804824 TATCTTTTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10810501 original size:2 final size:2
Alignment explanation
Indices: 10810494--10810530 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
10810484 TAGTAGTAAT
10810494 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
10810531 ATATATATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:10815239 original size:21 final size:21
Alignment explanation
Indices: 10815214--10815272 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
10815204 TATATTTTTT
*
10815214 AAAAAAGAAATATAAAAAAGTG
1 AAAAAAGAAATATAAAAAAG-C
* *
10815236 AAAATA-AAATATAAGAAAGC
1 AAAAAAGAAATATAAAAAAGC
10815256 AAAAAAG-AATAATAAAA
1 AAAAAAGAAAT-ATAAAA
10815273 GAAATTCAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
20 8 0.27
21 17 0.57
22 5 0.17
ACGTcount: A:0.75, C:0.02, G:0.10, T:0.14
Consensus pattern (21 bp):
AAAAAAGAAATATAAAAAAGC
Found at i:10815473 original size:21 final size:21
Alignment explanation
Indices: 10815429--10815474 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
10815419 GTGCTTAATA
* *
10815429 ATGTTTTTTTTATTCTAAATT
1 ATGTTATTTTTATTCTAAAAT
10815450 ATGTTATTTTTATT-TGAAAAT
1 ATGTTATTTTTATTCT-AAAAT
10815471 ATGT
1 ATGT
10815475 GTAGATTGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.28, C:0.02, G:0.09, T:0.61
Consensus pattern (21 bp):
ATGTTATTTTTATTCTAAAAT
Found at i:10815738 original size:17 final size:16
Alignment explanation
Indices: 10815706--10815737 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
10815696 ATTTCCATTT
10815706 TTTTCTTTCTTTCTTC
1 TTTTCTTTCTTTCTTC
10815722 TTTTCTTT-TTT-TTC
1 TTTTCTTTCTTTCTTC
10815736 TT
1 TT
10815738 CATAATTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 3 0.19
16 8 0.50
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTCTTTCTTTCTTC
Found at i:10815793 original size:18 final size:18
Alignment explanation
Indices: 10815741--10815795 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
10815731 TTTTCTTCAT
* *
10815741 AATTGAAAAATACTAAAAA
1 AATTTAAAAATAC-AAGAA
*
10815760 AATTT-AAAATA-GAGAA
1 AATTTAAAAATACAAGAA
10815776 AATTTAAAAATACAAGAA
1 AATTTAAAAATACAAGAA
10815794 AA
1 AA
10815796 AAAAAGAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
16 8 0.27
17 6 0.20
18 12 0.40
19 4 0.13
ACGTcount: A:0.67, C:0.04, G:0.07, T:0.22
Consensus pattern (18 bp):
AATTTAAAAATACAAGAA
Found at i:10815819 original size:20 final size:21
Alignment explanation
Indices: 10815782--10815826 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
10815772 AGAAAATTTA
10815782 AAAATACAAGAAAAAAAA-AG
1 AAAATACAAGAAAAAAAATAG
*
10815802 AAAATAC-AGAAGACAAAATAG
1 AAAATACAAGAA-AAAAAATAG
10815823 AAAA
1 AAAA
10815827 ATAAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 4 0.18
20 12 0.55
21 6 0.27
ACGTcount: A:0.76, C:0.07, G:0.11, T:0.07
Consensus pattern (21 bp):
AAAATACAAGAAAAAAAATAG
Found at i:10815822 original size:51 final size:48
Alignment explanation
Indices: 10815765--10815860 Score: 115
Period size: 48 Copynumber: 1.9 Consensus size: 48
10815755 AAAAAAATTT
10815765 AAAATAGAGAAAATTTAAAAATACA-AGAAAAAAAAAGAAAAT-ACAGAAGAC
1 AAAATAGA-AAAA--TAAAAATA-ATAGAAAAAAAAA-AAAATAACAGAAGAC
**
10815816 AAAATAGAAAAATAAAAATAATAGAAAATTAAAAAAATAACAGAA
1 AAAATAGAAAAATAAAAATAATAGAAAAAAAAAAAAATAACAGAA
10815861 AATTAGCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
47 6 0.15
48 23 0.56
50 4 0.10
51 8 0.20
ACGTcount: A:0.73, C:0.04, G:0.09, T:0.14
Consensus pattern (48 bp):
AAAATAGAAAAATAAAAATAATAGAAAAAAAAAAAAATAACAGAAGAC
Found at i:10815853 original size:19 final size:19
Alignment explanation
Indices: 10815829--10815865 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
10815819 ATAGAAAAAT
*
10815829 AAAAATAATAGAAAATTAA
1 AAAAATAACAGAAAATTAA
10815848 AAAAATAACAGAAAATTA
1 AAAAATAACAGAAAATTA
10815866 GCAAAGNTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.19
Consensus pattern (19 bp):
AAAAATAACAGAAAATTAA
Found at i:10815854 original size:16 final size:16
Alignment explanation
Indices: 10815816--10815854 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
10815806 TACAGAAGAC
10815816 AAAATAGAAAAATAAA
1 AAAATAGAAAAATAAA
*
10815832 AATAATAGAAAATTAAA
1 AA-AATAGAAAAATAAA
10815849 AAAATA
1 AAAATA
10815855 ACAGAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (16 bp):
AAAATAGAAAAATAAA
Found at i:10816252 original size:7 final size:7
Alignment explanation
Indices: 10816241--10816271 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
10816231 GAAAAAGGTG
*
10816241 ATTTTGG
1 ATTTTGA
10816248 ATTTTGA
1 ATTTTGA
10816255 ATTTTGA
1 ATTTTGA
10816262 ATTTTGA
1 ATTTTGA
10816269 ATT
1 ATT
10816272 AAAGACTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.16, T:0.58
Consensus pattern (7 bp):
ATTTTGA
Found at i:10817067 original size:30 final size:32
Alignment explanation
Indices: 10817026--10817086 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 32
10817016 AAAAAATTGA
*
10817026 AAAAAAGGGGCAATG-AAGCAAAA-TAAAAAAG
1 AAAAAAGGGGCAA-GAAAACAAAATTAAAAAAG
10817057 AAAAAA-GGGCAAGAAAACAAAATTAAAAAA
1 AAAAAAGGGGCAAGAAAACAAAATTAAAAAA
10817087 AAGAAGGCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
29 1 0.04
30 13 0.48
31 13 0.48
ACGTcount: A:0.69, C:0.07, G:0.18, T:0.07
Consensus pattern (32 bp):
AAAAAAGGGGCAAGAAAACAAAATTAAAAAAG
Found at i:10840035 original size:29 final size:29
Alignment explanation
Indices: 10839980--10840153 Score: 167
Period size: 29 Copynumber: 6.1 Consensus size: 29
10839970 ATATTTTTCG
*
10839980 TAATTCAGATAAG-AAACATGTTTTGTCT
1 TAATTTAGATAAGAAAACATGTTTTGTCT
* * * * *
10840008 TGATTTATATAAGAAAACATATTATGTCA
1 TAATTTAGATAAGAAAACATGTTTTGTCT
*
10840037 TAATTTAGA-AA-AAAACATGTTTTTTCT
1 TAATTTAGATAAGAAAACATGTTTTGTCT
* *
10840064 TAATTTAGATAAGAAAATATGTTTTATCT
1 TAATTTAGATAAGAAAACATGTTTTGTCT
* * *
10840093 TAATTTAGACAA-AAAAAATATGTTTGTCT
1 TAATTTAGATAAGAAAACATGT-TTTGTCT
* **
10840122 TAATTTAGATAAAAAAATTGTGTTTTGTCT
1 TAATTTAGATAAGAAAA-CATGTTTTGTCT
10840152 TA
1 TA
10840154 GTACTTATTT
Statistics
Matches: 118, Mismatches: 22, Indels: 10
0.79 0.15 0.07
Matches are distributed among these distances:
27 21 0.18
28 21 0.18
29 61 0.52
30 13 0.11
31 2 0.02
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.42
Consensus pattern (29 bp):
TAATTTAGATAAGAAAACATGTTTTGTCT
Found at i:10840053 original size:56 final size:57
Alignment explanation
Indices: 10839993--10840138 Score: 177
Period size: 56 Copynumber: 2.6 Consensus size: 57
10839983 TTCAGATAAG
* * *
10839993 AAACATGTTTTGTCTTGATTTATATAAGAAAACATATTATGTCATAATTTAGA-AAA
1 AAACATGTTTTGTCTTAATTTAGATAAGAAAACATATTATATCATAATTTAGACAAA
* * * * *
10840049 AAACATGTTTTTTCTTAATTTAGATAAGAAAATATGTTTTATCTTAATTTAGACAAA
1 AAACATGTTTTGTCTTAATTTAGATAAGAAAACATATTATATCATAATTTAGACAAA
* * *
10840106 AAAAATATGTTTGTCTTAATTTAGATAAAAAAA
1 AAACATGT-TTTGTCTTAATTTAGATAAGAAAA
10840139 TTGTGTTTTG
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
56 45 0.59
57 9 0.12
58 22 0.29
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (57 bp):
AAACATGTTTTGTCTTAATTTAGATAAGAAAACATATTATATCATAATTTAGACAAA
Found at i:10840130 original size:85 final size:85
Alignment explanation
Indices: 10839973--10840137 Score: 208
Period size: 85 Copynumber: 1.9 Consensus size: 85
10839963 CTTTTACATA
* * * * *
10839973 TTTTTCGTAATTCAGATAAGAAACATGTTTTGTCTTGATTTATATAAGAAAACATATTATGTCAT
1 TTTTTCGTAATTCAGATAAGAAACATGTTTTATCTTAATTTAGACAAGAAAAAATATTATGTCAT
10840038 AATTTAGA-AAAAAACATGT
66 AATTTAGATAAAAAACATGT
* * * *
10840057 TTTTTCTTAATTTAGATAAGAAAATATGTTTTATCTTAATTTAGACAA-AAAAAATATGTTTGTC
1 TTTTTCGTAATTCAGATAAG-AAACATGTTTTATCTTAATTTAGACAAGAAAAAATAT-TATGTC
*
10840121 TTAATTTAGATAAAAAA
64 ATAATTTAGATAAAAAA
10840138 ATTGTGTTTT
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
84 26 0.38
85 36 0.53
86 6 0.09
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.41
Consensus pattern (85 bp):
TTTTTCGTAATTCAGATAAGAAACATGTTTTATCTTAATTTAGACAAGAAAAAATATTATGTCAT
AATTTAGATAAAAAACATGT
Found at i:10840625 original size:130 final size:129
Alignment explanation
Indices: 10840481--10840745 Score: 505
Period size: 130 Copynumber: 2.1 Consensus size: 129
10840471 ATATTTCTAA
10840481 AAATT-TATTTTAAGTAAATAAAAAATAAAGTTAAATTTTTTCCATTGTGAACAAAGGAATTTGT
1 AAATTATATTTTAAGTAAATAAAAAATAAAGTTAAATTTTTTCCATTGTGAACAAAGGAATTTGT
*
10840545 GATTAATAGAAAGTTATTTATTAAATACCTTTATGGTAATTTAACCAAAATCAGAAACTTATAT
66 AATTAATAGAAAGTTATTTATTAAATACCTTTATGGTAATTTAACCAAAATCAGAAACTTATAT
10840609 AAATTATNATTTTAAGTAAATAAAAAATAAAGTTAAATTTTTTCCATTGTGAACAAAGGAATTTG
1 AAATTAT-ATTTTAAGTAAATAAAAAATAAAGTTAAATTTTTTCCATTGTGAACAAAGGAATTTG
10840674 TAATTAATAGAAAGTTATTTATTAAATACCTTTATGGTAATTTAACCAAAATCAGAAACTTATAT
65 TAATTAATAGAAAGTTATTTATTAAATACCTTTATGGTAATTTAACCAAAATCAGAAACTTATAT
10840739 AAATTAT
1 AAATTAT
10840746 TTTGTCAAAC
Statistics
Matches: 134, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
128 5 0.04
129 1 0.01
130 128 0.96
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.38
Consensus pattern (129 bp):
AAATTATATTTTAAGTAAATAAAAAATAAAGTTAAATTTTTTCCATTGTGAACAAAGGAATTTGT
AATTAATAGAAAGTTATTTATTAAATACCTTTATGGTAATTTAACCAAAATCAGAAACTTATAT
Found at i:10840921 original size:28 final size:28
Alignment explanation
Indices: 10840889--10840999 Score: 141
Period size: 28 Copynumber: 3.9 Consensus size: 28
10840879 GTCAAACAGG
* *
10840889 TTCTTAATTTAAAGAAGAAAACATATGT
1 TTCTTAATTTAAACAAGAAAACATATTT
*
10840917 GTCTTAATTTAAACAAGAAAACATATTT
1 TTCTTAATTTAAACAAGAAAACATATTT
* *
10840945 TTCTAAATTTAAGACAAGAAAAATATATTTT
1 TTCTTAATTTAA-ACAAG-AAAACATA-TTT
*
10840976 TTCTTAATTTAGACAAGAAAACAT
1 TTCTTAATTTAAACAAGAAAACAT
10841000 GTTTGCTTCA
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
28 35 0.49
29 11 0.15
30 12 0.17
31 13 0.18
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.36
Consensus pattern (28 bp):
TTCTTAATTTAAACAAGAAAACATATTT
Found at i:10842465 original size:17 final size:17
Alignment explanation
Indices: 10842445--10842485 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
10842435 AATTGTCAAC
10842445 ATATTTGTCAAA-AATAT
1 ATATTT-TCAAATAATAT
*
10842462 ATATTTTTAAATAATAT
1 ATATTTTCAAATAATAT
10842479 ATATTTT
1 ATATTTT
10842486 TTATATTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (17 bp):
ATATTTTCAAATAATAT
Found at i:10848280 original size:18 final size:18
Alignment explanation
Indices: 10848243--10848293 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
10848233 CCCAAGTCCA
* *
10848243 AGCCCCAGCTCCTGCTCC
1 AGCCCCAGCCCCTGCCCC
*
10848261 AGTCCCTA-CCCCTGCCCC
1 AG-CCCCAGCCCCTGCCCC
10848279 AGCCCCAGCCCCTGC
1 AGCCCCAGCCCCTGC
10848294 ACCAATTCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
17 4 0.15
18 19 0.70
19 4 0.15
ACGTcount: A:0.12, C:0.59, G:0.16, T:0.14
Consensus pattern (18 bp):
AGCCCCAGCCCCTGCCCC
Found at i:10853184 original size:13 final size:13
Alignment explanation
Indices: 10853166--10853194 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
10853156 GATTGTGATG
10853166 TGACATGGTTATA
1 TGACATGGTTATA
10853179 TGACATGGTTATA
1 TGACATGGTTATA
10853192 TGA
1 TGA
10853195 TCATATTGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.07, G:0.24, T:0.38
Consensus pattern (13 bp):
TGACATGGTTATA
Found at i:10853664 original size:2 final size:2
Alignment explanation
Indices: 10853659--10853685 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10853649 ACACTAAAAA
10853659 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
10853686 ATAAATAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10853823 original size:21 final size:19
Alignment explanation
Indices: 10853776--10853824 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
10853766 TGCGGACGCA
*
10853776 CCTTGCCAGGCACCATCTT
1 CCTTGCCAGGCACCACCTT
* *
10853795 CCCTGCCAGTCACCACCCTCT
1 CCTTGCCAGGCACCA-CCT-T
10853816 CCTTGCCAG
1 CCTTGCCAG
10853825 ACGTGAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 13 0.54
20 2 0.08
21 9 0.38
ACGTcount: A:0.14, C:0.49, G:0.14, T:0.22
Consensus pattern (19 bp):
CCTTGCCAGGCACCACCTT
Found at i:10854242 original size:35 final size:33
Alignment explanation
Indices: 10854162--10854249 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 33
10854152 TTGATTTTTA
* * *
10854162 GGGGGGATAAAGCTTGGGTATTTGCCGTCGGTT
1 GGGGGGATAAAGCTTGGGTAGTTACCGTCGATT
*
10854195 AGAGTGGG-TAAAGCTTGGGTTAGTTACCGTCGATT
1 -G-GGGGGATAAAGCTTGGG-TAGTTACCGTCGATT
10854230 GGGGAGGATAAAGTCTTGGG
1 GGGG-GGATAAAG-CTTGGG
10854250 ACAGTGTTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
33 2 0.05
34 15 0.34
35 21 0.48
36 6 0.14
ACGTcount: A:0.20, C:0.10, G:0.41, T:0.28
Consensus pattern (33 bp):
GGGGGGATAAAGCTTGGGTAGTTACCGTCGATT
Found at i:10855478 original size:4 final size:4
Alignment explanation
Indices: 10855469--10855496 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
10855459 TACATGACAT
10855469 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
10855497 AAAAAAATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:10867826 original size:47 final size:47
Alignment explanation
Indices: 10867756--10867858 Score: 161
Period size: 47 Copynumber: 2.2 Consensus size: 47
10867746 AGGGGCCACA
* * *
10867756 TCTCTTAAATCCTTTGGGTACATTCTAAAGACCTCCGAGCACATTAT
1 TCTCTTAAATCCTATGAGAACATTCTAAAGACCTCCGAGCACATTAT
* *
10867803 TCTCTTAAATCCTATGAGAACATTCTGAAGACCTCCGGGCACATTAT
1 TCTCTTAAATCCTATGAGAACATTCTAAAGACCTCCGAGCACATTAT
10867850 TCTCTTAAA
1 TCTCTTAAA
10867859 ACCTCCGAGT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (47 bp):
TCTCTTAAATCCTATGAGAACATTCTAAAGACCTCCGAGCACATTAT
Found at i:10867993 original size:38 final size:38
Alignment explanation
Indices: 10867884--10868241 Score: 294
Period size: 38 Copynumber: 9.2 Consensus size: 38
10867874 GTTTCAAGAC
*
10867884 TTTTAAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTTATTT
1 TTTTAAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCA--T
* * *
10867924 TTTTAAAAAAGGTCTCATTGCCCCAGTTTTGAGGAGTTCAT
1 TTTT--AAAA-GTTTCGTTGCCTCAGTTTTGAGGAGTTCAT
*
10867965 TTTTAAAAGTTTCGTTGCTTCAGTTTTGAGGAGTTCAT
1 TTTTAAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCAT
* * * * *
10868003 TTTAAAAAGTCTCATTGCCTCATTTTTTAGGAGCTT-A-
1 TTTTAAAAGTTTCGTTGCCTCAGTTTTGAGGAG-TTCAT
* * * **
10868040 TTTTAAAAGTGTCATTGTCTCAACTTTGAGGAGTTCAT
1 TTTTAAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCAT
* *
10868078 TTTTAAAA-ATTCGTTGCCTCAGCTTTGAGGAGTTCAT
1 TTTTAAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCAT
* * * *
10868115 TTTTAGAAGTTTCGTTGCCTCAGCTTTGGGGAGTTTTATTT
1 TTTTAAAAGTTTCGTTGCCTCAGTTTTGAGGAG-TTCA--T
* * * *
10868156 TTTTAAAAAAAATTCCGTAGCCTCAATTTTGAGGAGTTCAT
1 TTTT---AAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCAT
** * **
10868197 TACT-AAAGTTTCGTCGCCTCAACTTTGAGGAGTCTCA-
1 TTTTAAAAGTTTCGTTGCCTCAGTTTTGAGGAGT-TCAT
10868234 TTTTAAAA
1 TTTTAAAA
10868242 TTACAACAAA
Statistics
Matches: 258, Mismatches: 45, Indels: 32
0.77 0.13 0.10
Matches are distributed among these distances:
36 2 0.01
37 86 0.33
38 90 0.35
39 9 0.03
40 4 0.02
41 13 0.05
42 4 0.02
43 28 0.11
44 22 0.09
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.42
Consensus pattern (38 bp):
TTTTAAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCAT
Found at i:10868072 original size:37 final size:36
Alignment explanation
Indices: 10867951--10868241 Score: 181
Period size: 37 Copynumber: 7.6 Consensus size: 36
10867941 TTGCCCCAGT
* * **
10867951 TTTGAGGAGTTCATTTTTAAAAGTTTCGTTGCTTCAGT
1 TTTGAGGAGTTCA-TTTTAAAAG-TTCATTGCCTCAAC
**
10867989 TTTGAGGAGTTCATTTTAAAAAGTCTCATTGCCTCATT
1 TTTGAGGAGTTCATTTT-AAAAGT-TCATTGCCTCAAC
* *
10868027 TTTTAGGAGCTT-ATTTTAAAAGTGTCATTGTCTCAAC
1 TTTGAGGAG-TTCATTTTAAAAGT-TCATTGCCTCAAC
* * *
10868064 TTTGAGGAGTTCATTTTTAAAAATTCGTTGCCTCAGC
1 TTTGAGGAGTTCA-TTTTAAAAGTTCATTGCCTCAAC
* * *
10868101 TTTGAGGAGTTCATTTTTAGAAGTTTCGTTGCCTCAGC
1 TTTGAGGAGTTCA-TTTTAAAAG-TTCATTGCCTCAAC
* * * * * *
10868139 TTTGGGGAGTTTTATTTTTTTAAAAAAAATTCCGTAGCCTCAAT
1 TTTGAGGAG-TTCA---TTTT---AAAAGTT-CATTGCCTCAAC
* * *
10868183 TTTGAGGAGTTCATTACT-AAAGTTTCGTCGCCTCAAC
1 TTTGAGGAGTTCATT-TTAAAAG-TTCATTGCCTCAAC
10868220 TTTGAGGAGTCTCATTTTAAAA
1 TTTGAGGAGT-TCATTTTAAAA
10868242 TTACAACAAA
Statistics
Matches: 207, Mismatches: 29, Indels: 34
0.77 0.11 0.13
Matches are distributed among these distances:
36 2 0.01
37 85 0.41
38 82 0.40
39 5 0.02
40 2 0.01
41 6 0.03
43 5 0.02
44 20 0.10
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.42
Consensus pattern (36 bp):
TTTGAGGAGTTCATTTTAAAAGTTCATTGCCTCAAC
Found at i:10868083 original size:76 final size:76
Alignment explanation
Indices: 10867884--10868241 Score: 300
Period size: 81 Copynumber: 4.6 Consensus size: 76
10867874 GTTTCAAGAC
* *
10867884 TTTTAAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTTATTTTTTTAAAAAAGGTCTCATTGCCCCA
1 TTTTAAAAGTTTCGTTG-CTCAGTTTTGAGGAGTTCA--TTTTT-AAAAA-GTCTCATTGCCTCA
10867949 GTTTTGAGGAGTTCAT
61 GTTTTGAGGAGTTCAT
*
10867965 TTTTAAAAGTTTCGTTGCTTCAGTTTTGAGGAGTTCA-TTTTAAAAAGTCTCATTGCCTCATTTT
1 TTTTAAAAGTTTCGTTGC-TCAGTTTTGAGGAGTTCATTTTTAAAAAGTCTCATTGCCTCAGTTT
*
10868029 TTAGGAGCTT-A-
65 TGAGGAG-TTCAT
* * ** * *
10868040 TTTTAAAAGTGTCATTGTCTCAACTTTGAGGAGTTCATTTTTAAAAA-T-TCGTTGCCTCAGCTT
1 TTTTAAAAGTTTCGTTG-CTCAGTTTTGAGGAGTTCATTTTTAAAAAGTCTCATTGCCTCAGTTT
10868103 TGAGGAGTTCAT
65 TGAGGAGTTCAT
* * * * * * *
10868115 TTTTAGAAGTTTCGTTGCCTCAGCTTTGGGGAGTTTTATTTTTTTAAAAAAAAT-TCCGTAGCCT
1 TTTTAAAAGTTTCGTTG-CTCAGTTTTGAGGAG-TTCA--TTTTT--AAAAAGTCT-CATTGCCT
*
10868179 CAATTTTGAGGAGTTCAT
59 CAGTTTTGAGGAGTTCAT
** * **
10868197 TACT-AAAGTTTCGTCGCCTCAACTTTGAGGAGTCTCA-TTTTAAAA
1 TTTTAAAAGTTTCGTTG-CTCAGTTTTGAGGAGT-TCATTTTTAAAA
10868242 TTACAACAAA
Statistics
Matches: 234, Mismatches: 29, Indels: 33
0.79 0.10 0.11
Matches are distributed among these distances:
73 2 0.01
74 19 0.08
75 59 0.25
76 40 0.17
77 7 0.03
78 13 0.06
80 7 0.03
81 62 0.26
82 25 0.11
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.42
Consensus pattern (76 bp):
TTTTAAAAGTTTCGTTGCTCAGTTTTGAGGAGTTCATTTTTAAAAAGTCTCATTGCCTCAGTTTT
GAGGAGTTCAT
Found at i:10870183 original size:22 final size:24
Alignment explanation
Indices: 10870158--10870201 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
10870148 TATATATGAC
10870158 ATTAAATAAA-AA-AATAAAAAAA
1 ATTAAATAAATAATAATAAAAAAA
10870180 ATTAAATAAATAATAATAAAAA
1 ATTAAATAAATAATAATAAAAA
10870202 TCTAAGACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 10 0.50
23 2 0.10
24 8 0.40
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (24 bp):
ATTAAATAAATAATAATAAAAAAA
Found at i:10871679 original size:19 final size:18
Alignment explanation
Indices: 10871642--10871679 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
10871632 TTTTGAGGAA
10871642 AGAAAGAAAAAAAAATAG
1 AGAAAGAAAAAAAAATAG
10871660 AGAAA-AAAAGAAACAATAG
1 AGAAAGAAAA-AAA-AATAG
10871679 A
1 A
10871680 AGACAAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.22
18 8 0.44
19 6 0.33
ACGTcount: A:0.76, C:0.03, G:0.16, T:0.05
Consensus pattern (18 bp):
AGAAAGAAAAAAAAATAG
Found at i:10881175 original size:16 final size:18
Alignment explanation
Indices: 10881136--10881178 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 18
10881126 AAAATACCTT
10881136 ATTTTGTTTCTCCTTTTCC
1 ATTTT-TTTCTCCTTTTCC
*
10881155 CTTTTTTTC-CC-TTTCC
1 ATTTTTTTCTCCTTTTCC
10881171 ATTTTTTT
1 ATTTTTTT
10881179 TTGTTTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 12 0.55
17 2 0.09
18 4 0.18
19 4 0.18
ACGTcount: A:0.05, C:0.26, G:0.02, T:0.67
Consensus pattern (18 bp):
ATTTTTTTCTCCTTTTCC
Found at i:10883461 original size:2 final size:2
Alignment explanation
Indices: 10883454--10883488 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
10883444 TGGGTTTTCT
*
10883454 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10883489 GAACTTTGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:10892070 original size:2 final size:2
Alignment explanation
Indices: 10892063--10892109 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
10892053 TGTATGTATA
10892063 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
10892105 TG TG T
1 TG TG T
10892110 ATAATATTCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:10892203 original size:25 final size:25
Alignment explanation
Indices: 10892169--10892224 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
10892159 GATCACAAAA
10892169 GCCCTCCATATATTGCTTTATTACT
1 GCCCTCCATATATTGCTTTATTACT
10892194 GCCCTCCATATATTGCTTTATTACT
1 GCCCTCCATATATTGCTTTATTACT
*
10892219 ACCCTC
1 GCCCTC
10892225 TAGAGCCCAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.20, C:0.32, G:0.07, T:0.41
Consensus pattern (25 bp):
GCCCTCCATATATTGCTTTATTACT
Found at i:10892845 original size:174 final size:174
Alignment explanation
Indices: 10892548--10892903 Score: 572
Period size: 174 Copynumber: 2.0 Consensus size: 174
10892538 GGTCTTCAAA
* *
10892548 GAACTAGCCCATTATTGGCTAATGAATCAAAAGAAGACCTTCCTGATCTGCTTCTACCATTTTCC
1 GAACTAACCCATTATTGGCTAATAAATCAAAAGAAGACCTTCCTGATCTGCTTCTACCATTTTCC
* *
10892613 TTTTATGCGTTTGATGAATTGCTAAGTGGAGTGAACATTTTCCTGTTTTTCGTTTCAGATTATTT
66 TTTTATGCGTTGGATGAATTGCTAAGTGGAGTGAACATTTTCCTGTATTTCGTTTCAGATTATTT
*
10892678 GATTTCTAGGATA-CATATTTCCAAAATTTAAAACTTGCAGTCCT
131 GATTTCTAGGATATCA-ATTTCCAAAATTTAAAACTCGCAGTCCT
10892722 GAACTAACCCATTATTGGCTAATAAATCAAAAGAAGACCTTCCTGATCTGCTTCTACCATTTTCC
1 GAACTAACCCATTATTGGCTAATAAATCAAAAGAAGACCTTCCTGATCTGCTTCTACCATTTTCC
* * **
10892787 TTTTATGTGTTGGATGGATTGCTAAGTGGAGTGAATGTTTTCCTGATATTT-GTTTCAGATTATT
66 TTTTATGCGTTGGATGAATTGCTAAGTGGAGTGAACATTTTCCTG-TATTTCGTTTCAGATTATT
* *
10892851 TGATTTCTAGGATATGAATTTGCAAAATTTAAAACTCGCAGTCCT
130 TGATTTCTAGGATATCAATTTCCAAAATTTAAAACTCGCAGTCCT
*
10892896 GGACTAAC
1 GAACTAAC
10892904 TTTTGTGATT
Statistics
Matches: 168, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
174 163 0.97
175 5 0.03
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (174 bp):
GAACTAACCCATTATTGGCTAATAAATCAAAAGAAGACCTTCCTGATCTGCTTCTACCATTTTCC
TTTTATGCGTTGGATGAATTGCTAAGTGGAGTGAACATTTTCCTGTATTTCGTTTCAGATTATTT
GATTTCTAGGATATCAATTTCCAAAATTTAAAACTCGCAGTCCT
Found at i:10906935 original size:20 final size:20
Alignment explanation
Indices: 10906910--10906948 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
10906900 TGTCCAATCA
10906910 AAATATATA-AATTAATTATT
1 AAATATATATAA-TAATTATT
10906930 AAATATATATAATAATTAT
1 AAATATATATAATAATTAT
10906949 CTAATTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AAATATATATAATAATTATT
Found at i:10907078 original size:8 final size:8
Alignment explanation
Indices: 10907067--10907095 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
10907057 AAAATTTACA
10907067 AATTTTTT
1 AATTTTTT
10907075 AATTTTTT
1 AATTTTTT
10907083 AA-TTTTT
1 AATTTTTT
10907090 AATTTT
1 AATTTT
10907096 AATTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (8 bp):
AATTTTTT
Found at i:10923403 original size:2 final size:2
Alignment explanation
Indices: 10923393--10923431 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
10923383 GTATATACTT
*
10923393 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10923432 TCACACATAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:10924574 original size:87 final size:89
Alignment explanation
Indices: 10924415--10924588 Score: 201
Period size: 87 Copynumber: 2.0 Consensus size: 89
10924405 TCTAATCTCT
* * *
10924415 TAAGTTTTGATATTATTTTGTTTTCATCATTTTCAAGCTTCAAAAGGATTTCAGTGATTGATCTA
1 TAAGTGTTGATATTATTTTGTTTTCATCA-TTTCAAGCTTCAAAAGAATTTCAATGATTGATCTA
* * * *
10924480 TGATTTCTGGTTTTAGCAAATCAGG
65 TAATTTCTAGTTGTAACAAATCAGG
* * * * *
10924505 TAAGTGTTGGTATTATTTTGTTTTCATC-TTT-AAGCTTTAAAAGAATTTCAAT-ATTTGGTTTT
1 TAAGTGTTGATATTATTTTGTTTTCATCATTTCAAGCTTCAAAAGAATTTCAATGA-TTGATCTA
10924567 TAATTTCTAGTTGTAACAAATC
65 TAATTTCTAGTTGTAACAAATC
10924589 GAGTAAACGA
Statistics
Matches: 71, Mismatches: 12, Indels: 5
0.81 0.14 0.06
Matches are distributed among these distances:
86 1 0.01
87 41 0.58
88 3 0.04
90 26 0.37
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.48
Consensus pattern (89 bp):
TAAGTGTTGATATTATTTTGTTTTCATCATTTCAAGCTTCAAAAGAATTTCAATGATTGATCTAT
AATTTCTAGTTGTAACAAATCAGG
Found at i:10925216 original size:64 final size:64
Alignment explanation
Indices: 10925096--10925216 Score: 163
Period size: 64 Copynumber: 1.9 Consensus size: 64
10925086 TGATATGTTG
* * * * *
10925096 TTGATTTTCTTGTCTACCCTGAAAAGGGAATTGATCATATGATTAGTAATGTAAATACCTATTA
1 TTGATTTTCTTGTCCACCATGAAAAGAGAATTGATCATATGATTAGTAAAGGAAATACCTATTA
* *
10925160 TTGATTTTCTTGTCCATCATG-AAAGAAGAATTGATCATTTGATTAGTAAAGGAAATA
1 TTGATTTTCTTGTCCACCATGAAAAG-AGAATTGATCATATGATTAGTAAAGGAAATA
10925217 TCCAAGAATA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
63 4 0.08
64 45 0.92
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.38
Consensus pattern (64 bp):
TTGATTTTCTTGTCCACCATGAAAAGAGAATTGATCATATGATTAGTAAAGGAAATACCTATTA
Found at i:10929205 original size:71 final size:71
Alignment explanation
Indices: 10929116--10929284 Score: 275
Period size: 71 Copynumber: 2.4 Consensus size: 71
10929106 TGGCACTGAT
10929116 TGTGCACGATGTGGGGGGATGCACATGCCGGTGATGATGGCAGTGTGGGAGATGGATAATGATAG
1 TGTGCACGATGTGGGGGGATGCACATGCCGGTGATGATGGCAGTGTGGGAGATGGATAATGATAG
10929181 TGCCCG
66 TGCCCG
* * *
10929187 TGTGCACGATGTGGGGGGATGCACATACCTGTGATGATGGCGGTGTGGGAGATGGATAATGATAG
1 TGTGCACGATGTGGGGGGATGCACATGCCGGTGATGATGGCAGTGTGGGAGATGGATAATGATAG
*
10929252 TGCCTG
66 TGCCCG
* * *
10929258 TGTACACGATGTGAGGGGATGTACATG
1 TGTGCACGATGTGGGGGGATGCACATG
10929285 AGTCGGGTGT
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
71 90 1.00
ACGTcount: A:0.22, C:0.13, G:0.41, T:0.24
Consensus pattern (71 bp):
TGTGCACGATGTGGGGGGATGCACATGCCGGTGATGATGGCAGTGTGGGAGATGGATAATGATAG
TGCCCG
Found at i:10930618 original size:2 final size:2
Alignment explanation
Indices: 10930611--10930638 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
10930601 CTTAATAATG
10930611 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10930639 GAAAATCACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10936754 original size:19 final size:19
Alignment explanation
Indices: 10936705--10936754 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
10936695 GCTATAAATA
* *
10936705 TCTTCTCCTTCTAGCAGCT
1 TCTTCTTCTTCCAGCAGCT
*
10936724 TCTTCAAT-TTCCAGCAGCT
1 TCTTC-TTCTTCCAGCAGCT
10936743 TCTTCTTCTTCC
1 TCTTCTTCTTCC
10936755 TTCTTCCATC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 1 0.04
19 24 0.96
ACGTcount: A:0.12, C:0.36, G:0.08, T:0.44
Consensus pattern (19 bp):
TCTTCTTCTTCCAGCAGCT
Found at i:10937657 original size:38 final size:39
Alignment explanation
Indices: 10937612--10937713 Score: 125
Period size: 38 Copynumber: 2.6 Consensus size: 39
10937602 TAATATCCCT
* *
10937612 GTGCACGATGTGGGGGGATGTACACGATGGCACTGACTA
1 GTGCACGATGTGGGGGGATGCACACGATGACACTGACTA
* * *
10937651 -TGCACGATGTGGGGAGATGCACACGATGACTCTGGCTA
1 GTGCACGATGTGGGGGGATGCACACGATGACACTGACTA
* *
10937689 TGTGCATGATGTGGGGGAATGCACA
1 -GTGCACGATGTGGGGGGATGCACA
10937714 TGAGCTGGGT
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
38 33 0.62
40 20 0.38
ACGTcount: A:0.24, C:0.18, G:0.37, T:0.22
Consensus pattern (39 bp):
GTGCACGATGTGGGGGGATGCACACGATGACACTGACTA
Found at i:10938695 original size:2 final size:2
Alignment explanation
Indices: 10938688--10938734 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
10938678 CCTCAATAAC
10938688 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10938729 TA TA TA
1 TA TA TA
10938735 AAGACCTAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:10945636 original size:14 final size:14
Alignment explanation
Indices: 10945617--10945788 Score: 57
Period size: 15 Copynumber: 11.6 Consensus size: 14
10945607 TAATGTTATA
10945617 ATTAAAATAAAAAT
1 ATTAAAATAAAAAT
10945631 ATTAAAATAAAATATAT
1 ATTAAAAT-AAA-A-AT
*
10945648 AATATAAGAATTAAAA-
1 -AT-TAA-AATAAAAAT
*
10945664 ATTAAAATAAAATAA
1 ATTAAAATAAAA-AT
*
10945679 AATAAAATATAAGAA-
1 ATTAAAATA-AA-AAT
* **
10945694 ATTAAATTCATATGAT
1 ATTAAAAT-A-AAAAT
* * *
10945710 AATATAAGTAAAAAA
1 ATTA-AAATAAAAAT
10945725 ATTAAAATAAAATAT
1 ATTAAAATAAAA-AT
*
10945740 ATATAATATAAAAA-
1 AT-TAAAATAAAAAT
* *
10945754 ATTATATTAAAAA-
1 ATTAAAATAAAAAT
*
10945767 ATAAAAAT-AAAAT
1 ATTAAAATAAAAAT
10945780 ATTTAAAAT
1 A-TTAAAAT
10945789 TATAATAAGA
Statistics
Matches: 118, Mismatches: 23, Indels: 34
0.67 0.13 0.19
Matches are distributed among these distances:
12 4 0.03
13 20 0.17
14 27 0.23
15 29 0.25
16 20 0.17
17 7 0.06
18 3 0.03
19 5 0.04
20 3 0.03
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30
Consensus pattern (14 bp):
ATTAAAATAAAAAT
Found at i:10945641 original size:5 final size:5
Alignment explanation
Indices: 10945619--10945687 Score: 52
Period size: 5 Copynumber: 13.4 Consensus size: 5
10945609 ATGTTATAAT
* * * *
10945619 TAAAA TAAAA -ATAT TAAAA TAAAA T-ATA TAATA TAAGAA TTAAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAA-AA -T-AAAA
10945665 TTAAAA TAAAA TAAAA TAAAA TA
1 -TAAAA TAAAA TAAAA TAAAA TA
10945688 TAAGAAATTA
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
4 5 0.09
5 36 0.68
6 5 0.09
7 5 0.09
8 2 0.04
ACGTcount: A:0.71, C:0.00, G:0.01, T:0.28
Consensus pattern (5 bp):
TAAAA
Found at i:10945769 original size:22 final size:22
Alignment explanation
Indices: 10945720--10945787 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 22
10945710 AATATAAGTA
* *
10945720 AAAAAATTAAAATAAAATATAT
1 AAAAAATAAAAATAAAATATTT
* * **
10945742 ATAATATAAAAA-ATTATA-TT
1 AAAAAATAAAAATAAAATATTT
10945762 AAAAAATAAAAATAAAATATTT
1 AAAAAATAAAAATAAAATATTT
10945784 AAAA
1 AAAA
10945788 TTATAATAAG
Statistics
Matches: 34, Mismatches: 10, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
20 11 0.32
21 8 0.24
22 15 0.44
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAAAATAAAAATAAAATATTT
Found at i:10945778 original size:56 final size:60
Alignment explanation
Indices: 10945660--10945788 Score: 140
Period size: 56 Copynumber: 2.2 Consensus size: 60
10945650 TATAAGAATT
* * * *
10945660 AAAAATTAAAATAAAATAAAATAAAATATAAGAAATTAAATTCATATGATAATATAAGTAA
1 AAAAATTAAAATAAAATAAAATAAAATATAAAAAATTAAATTCATA-GAAAATAAAAATAA
* * *
10945721 AAAAATTAAAATAAAAT-ATATATAATATAAAAAATTATATT-A-A-AAAATAAAAATAA
1 AAAAATTAAAATAAAATAAAATAAAATATAAAAAATTAAATTCATAGAAAATAAAAATAA
* *
10945777 AATATTTAAAAT
1 AAAAATTAAAAT
10945789 TATAATAAGA
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
56 20 0.34
58 1 0.02
59 1 0.02
60 20 0.34
61 17 0.29
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.29
Consensus pattern (60 bp):
AAAAATTAAAATAAAATAAAATAAAATATAAAAAATTAAATTCATAGAAAATAAAAATAA
Found at i:10945788 original size:33 final size:33
Alignment explanation
Indices: 10945728--10945815 Score: 104
Period size: 33 Copynumber: 2.6 Consensus size: 33
10945718 TAAAAAAATT
*
10945728 AAAATAAAATATATATAATATAAAAAATTATATTAA
1 AAAATAAAA-ATA-A-AATATAAAAAATTATAATAA
**
10945764 AAAATAAAAATAAAATATTTAAAATTATAATAA
1 AAAATAAAAATAAAATATAAAAAATTATAATAA
* *
10945797 GAAATGAAAATAAAATATA
1 AAAATAAAAATAAAATATA
10945816 TGACATTAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
33 33 0.72
34 1 0.02
35 3 0.07
36 9 0.20
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (33 bp):
AAAATAAAAATAAAATATAAAAAATTATAATAA
Found at i:10946051 original size:15 final size:15
Alignment explanation
Indices: 10946030--10946103 Score: 67
Period size: 15 Copynumber: 4.9 Consensus size: 15
10946020 TGTTATTTTG
*
10946030 CTTGCAATCATATTG
1 CTTGCAATCATATTA
* *
10946045 TTTGCAATCACATTA
1 CTTGCAATCATATTA
*
10946060 CTTGCAATTATATTA
1 CTTGCAATCATATTA
* * *
10946075 CCTGTAATTATATTA
1 CTTGCAATCATATTA
* *
10946090 CCTGTAATCATATT
1 CTTGCAATCATATT
10946104 GCATTGTAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 50 1.00
ACGTcount: A:0.31, C:0.18, G:0.08, T:0.43
Consensus pattern (15 bp):
CTTGCAATCATATTA
Found at i:10946520 original size:27 final size:27
Alignment explanation
Indices: 10946482--10946589 Score: 92
Period size: 27 Copynumber: 4.0 Consensus size: 27
10946472 AGCGCTTTAT
*
10946482 GAGCA-CGAAAGCACCCAAGAGCTTTTC
1 GAGCACCG-AAGCACCCAAGAGCTTTCC
** * * *
10946509 GAGCACCGAAGCTTCTAAGGGCATTCC
1 GAGCACCGAAGCACCCAAGAGCTTTCC
* * *
10946536 CAACACGGAAGCACCCAAGAGCTTTCC
1 GAGCACCGAAGCACCCAAGAGCTTTCC
* * *
10946563 AAGCGCGGAAGCACCCAAGAGCTTTCC
1 GAGCACCGAAGCACCCAAGAGCTTTCC
10946590 AAGTGCGGAA
Statistics
Matches: 63, Mismatches: 17, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
27 61 0.97
28 2 0.03
ACGTcount: A:0.31, C:0.32, G:0.23, T:0.14
Consensus pattern (27 bp):
GAGCACCGAAGCACCCAAGAGCTTTCC
Found at i:10946590 original size:27 final size:27
Alignment explanation
Indices: 10946541--10946609 Score: 120
Period size: 27 Copynumber: 2.6 Consensus size: 27
10946531 ATTCCCAACA
10946541 CGGAAGCACCCAAGAGCTTTCCAAGCG
1 CGGAAGCACCCAAGAGCTTTCCAAGCG
*
10946568 CGGAAGCACCCAAGAGCTTTCCAAGTG
1 CGGAAGCACCCAAGAGCTTTCCAAGCG
*
10946595 CGGAAACACCCAAGA
1 CGGAAGCACCCAAGA
10946610 ATAAGCATGG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.33, C:0.32, G:0.25, T:0.10
Consensus pattern (27 bp):
CGGAAGCACCCAAGAGCTTTCCAAGCG
Found at i:10967115 original size:2 final size:2
Alignment explanation
Indices: 10967100--10967138 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
10967090 AATTAATACA
*
10967100 AT AT AT AG AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10967139 TAAAAGACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 33 0.97
3 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:10972054 original size:13 final size:13
Alignment explanation
Indices: 10972036--10972091 Score: 60
Period size: 13 Copynumber: 4.1 Consensus size: 13
10972026 GTTTGTGAAG
10972036 TTTATTTTTATTA
1 TTTATTTTTATTA
10972049 TTTATTTTTATTTA
1 TTTATTTTTA-TTA
*
10972063 TTATATTTTTTTGTTA
1 TT-TA--TTTTTATTA
10972079 TTTATTTTT-TTA
1 TTTATTTTTATTA
10972091 T
1 T
10972092 CTTTTTCATT
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
12 4 0.11
13 15 0.39
14 5 0.13
15 4 0.11
16 5 0.13
17 5 0.13
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.79
Consensus pattern (13 bp):
TTTATTTTTATTA
Found at i:10972064 original size:17 final size:16
Alignment explanation
Indices: 10972040--10972089 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
10972030 GTGAAGTTTA
10972040 TTTTTATTATTTATTT
1 TTTTTATTATTTATTT
10972056 TTATTTATTA--TA-TT
1 TT-TTTATTATTTATTT
*
10972070 TTTTTGTTATTTATTT
1 TTTTTATTATTTATTT
10972086 TTTT
1 TTTT
10972090 ATCTTTTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
13 6 0.21
14 4 0.14
15 4 0.14
16 8 0.28
17 7 0.24
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (16 bp):
TTTTTATTATTTATTT
Found at i:10972079 original size:20 final size:20
Alignment explanation
Indices: 10972036--10972096 Score: 67
Period size: 19 Copynumber: 3.1 Consensus size: 20
10972026 GTTTGTGAAG
10972036 TTTATTT-TTATTATTTATT
1 TTTATTTATTATTATTTATT
*
10972055 TTTATTTATTA-TATTTTTT
1 TTTATTTATTATTATTTATT
10972074 TGTTATTTATT-TT-TTTATCT
1 T-TTATTTATTATTATTTAT-T
10972094 TTT
1 TTT
10972097 TCATTCTAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
19 21 0.58
20 15 0.42
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.79
Consensus pattern (20 bp):
TTTATTTATTATTATTTATT
Found at i:10973758 original size:15 final size:16
Alignment explanation
Indices: 10973732--10973765 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
10973722 TTTTTTTCTC
10973732 ATTATGTTATTTTATT
1 ATTATGTTATTTTATT
10973748 ATTAT-TTATTTTATT
1 ATTATGTTATTTTATT
10973763 ATT
1 ATT
10973766 TTTTTGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (16 bp):
ATTATGTTATTTTATT
Found at i:10973763 original size:12 final size:11
Alignment explanation
Indices: 10973738--10973780 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
10973728 TCTCATTATG
*
10973738 TTATTTTATTA
1 TTATTTTTTTA
10973749 TTATTTATTTTA
1 TTATTT-TTTTA
10973761 TTATTTTTTTGA
1 TTATTTTTTT-A
10973773 TT-TTTTTT
1 TTATTTTTT
10973781 AAATGGGTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 16 0.55
12 13 0.45
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (11 bp):
TTATTTTTTTA
Found at i:10976447 original size:10 final size:10
Alignment explanation
Indices: 10976419--10976480 Score: 72
Period size: 10 Copynumber: 6.0 Consensus size: 10
10976409 CCTCACCAAA
10976419 CATCAAATAT
1 CATCAAATAT
*
10976429 CACCAAAATAT
1 CATC-AAATAT
*
10976440 CATGAAATAT
1 CATCAAATAT
10976450 CATCAAATAT
1 CATCAAATAT
10976460 CATCAAAT-T
1 CATCAAATAT
10976469 CAGTCAGAATAT
1 CA-TCA-AATAT
10976481 TCTCCCTAGG
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
9 3 0.07
10 29 0.66
11 11 0.25
12 1 0.02
ACGTcount: A:0.48, C:0.19, G:0.05, T:0.27
Consensus pattern (10 bp):
CATCAAATAT
Found at i:10977071 original size:28 final size:27
Alignment explanation
Indices: 10977032--10977085 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
10977022 ATGTCCTGGT
*
10977032 GGTGGAAAATTA-CTATTTTGCCCCTAG
1 GGTGGAAAATTATC-ATTTTACCCCTAG
10977059 GGTGGCAAAATTATCATTTTACCCCTA
1 GGTGG-AAAATTATCATTTTACCCCTA
10977086 TGCTCCGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 5 0.21
28 18 0.75
29 1 0.04
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (27 bp):
GGTGGAAAATTATCATTTTACCCCTAG
Found at i:10978218 original size:27 final size:27
Alignment explanation
Indices: 10978122--10978319 Score: 193
Period size: 27 Copynumber: 7.3 Consensus size: 27
10978112 CTTCACTACT
* *
10978122 CATTCA-TTTTGGTGGGTAAAAGTATC
1 CATTCACTTCTGGTGGGTAAAGGTATC
*
10978148 CATTTCACTTCTGGTGGGTATAGGTATC
1 CA-TTCACTTCTGGTGGGTAAAGGTATC
* * * *
10978176 GA-TCAGCTTCTAGTGGATAATGGTATC
1 CATTCA-CTTCTGGTGGGTAAAGGTATC
* * *
10978203 CATTCACTTTTGGTGGGTAAATGTATT
1 CATTCACTTCTGGTGGGTAAAGGTATC
* *
10978230 TATTCACTTCTGGTGGGTAAAGGTATT
1 CATTCACTTCTGGTGGGTAAAGGTATC
*
10978257 TATTCACTTCTGGTGGGTAAAGGTATC
1 CATTCACTTCTGGTGGGTAAAGGTATC
* * * * * *
10978284 CATCCACTTTTGATGGGAAAAAGTATT
1 CATTCACTTCTGGTGGGTAAAGGTATC
10978311 CATTCACTT
1 CATTCACTT
10978320 TTAGTGGTTG
Statistics
Matches: 141, Mismatches: 27, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
26 5 0.04
27 115 0.82
28 21 0.15
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
CATTCACTTCTGGTGGGTAAAGGTATC
Found at i:10978267 original size:81 final size:81
Alignment explanation
Indices: 10978122--10978319 Score: 256
Period size: 81 Copynumber: 2.4 Consensus size: 81
10978112 CTTCACTACT
* *
10978122 CATTCA-TTTTGGTGGGTAAAAGTATCCATTTCACTTCTGGTGGGTATAGGTATCGATCAGCTTC
1 CATTCACTTTTGGTGGGTAAAAGTATTCA-TTCACTTCTGGTGGGTAAAGGTATCGATCAGCTTC
*
10978186 TAGTGGATAATGGTATC
65 TAGTGGATAAAGGTATC
* * **
10978203 CATTCACTTTTGGTGGGTAAATGTATTTATTCACTTCTGGTGGGTAAAGGTATTTATTCA-CTTC
1 CATTCACTTTTGGTGGGTAAAAGTATTCATTCACTTCTGGTGGGTAAAGGTATCGA-TCAGCTTC
* *
10978267 TGGTGGGTAAAGGTATC
65 TAGTGGATAAAGGTATC
* * *
10978284 CATCCACTTTTGATGGGAAAAAGTATTCATTCACTT
1 CATTCACTTTTGGTGGGTAAAAGTATTCATTCACTT
10978320 TTAGTGGTTG
Statistics
Matches: 101, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
81 79 0.78
82 22 0.22
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.38
Consensus pattern (81 bp):
CATTCACTTTTGGTGGGTAAAAGTATTCATTCACTTCTGGTGGGTAAAGGTATCGATCAGCTTCT
AGTGGATAAAGGTATC
Found at i:10982001 original size:15 final size:15
Alignment explanation
Indices: 10981981--10982012 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
10981971 CAATGTTATA
10981981 ATTAAAATAAAAAAT
1 ATTAAAATAAAAAAT
*
10981996 ATTAAAATAAAATAT
1 ATTAAAATAAAAAAT
10982011 AT
1 AT
10982013 AATATAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
ATTAAAATAAAAAAT
Found at i:10982402 original size:15 final size:15
Alignment explanation
Indices: 10982382--10982412 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
10982372 TGTTATTTTT
10982382 CTTGCAATCACATTG
1 CTTGCAATCACATTG
10982397 CTTGCAATCACATTG
1 CTTGCAATCACATTG
10982412 C
1 C
10982413 ATTGTAAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.29, G:0.13, T:0.32
Consensus pattern (15 bp):
CTTGCAATCACATTG
Found at i:10992934 original size:19 final size:19
Alignment explanation
Indices: 10992910--10992947 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
10992900 CTGCCAAACC
* *
10992910 CTCAAATTATACTTCAATA
1 CTCAAATCATACTCCAATA
10992929 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
10992948 AGTCAAATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.42, C:0.26, G:0.00, T:0.32
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:10995764 original size:22 final size:22
Alignment explanation
Indices: 10995721--10995764 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
10995711 TTTAAAACAA
* *
10995721 CTTTAAAACTAAAAACTTTGAT
1 CTTTAAAACCAAAAACTCTGAT
**
10995743 CTTTAAAACCAAAGGCTCTGAT
1 CTTTAAAACCAAAAACTCTGAT
10995765 ACCAATTGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (22 bp):
CTTTAAAACCAAAAACTCTGAT
Found at i:10998184 original size:28 final size:28
Alignment explanation
Indices: 10998142--10998195 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
10998132 GGAAAAATAT
10998142 CCTAGTAGTGGAAAATTACAATTTTACC
1 CCTAGTAGTGGAAAATTACAATTTTACC
*
10998170 CCTAG-AGTGGCAAAATTACCATTTTA
1 CCTAGTAGTGG-AAAATTACAATTTTA
10998196 ACCTTTTACT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (28 bp):
CCTAGTAGTGGAAAATTACAATTTTACC
Found at i:10998991 original size:31 final size:31
Alignment explanation
Indices: 10998956--10999032 Score: 129
Period size: 31 Copynumber: 2.5 Consensus size: 31
10998946 CCAATAAACG
*
10998956 GGTTCGGGTAGTGATTTCATTACCCGAATCA
1 GGTTCGGGTAGTGATTTCACTACCCGAATCA
10998987 GGTTCGGGTAGTGATTTCACTACCCGAATCA
1 GGTTCGGGTAGTGATTTCACTACCCGAATCA
*
10999018 GGTTTGGGTAG-GATT
1 GGTTCGGGTAGTGATT
10999033 CTGGTATCAC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
30 4 0.09
31 40 0.91
ACGTcount: A:0.21, C:0.17, G:0.30, T:0.32
Consensus pattern (31 bp):
GGTTCGGGTAGTGATTTCACTACCCGAATCA
Found at i:11007642 original size:15 final size:16
Alignment explanation
Indices: 11007610--11007640 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11007600 AAGAGAAATT
*
11007610 TTTTTAAATAAAAAAA
1 TTTTAAAATAAAAAAA
11007626 TTTTAAAATAAAAAA
1 TTTTAAAATAAAAAA
11007641 TTATAATTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TTTTAAAATAAAAAAA
Found at i:11008841 original size:2 final size:2
Alignment explanation
Indices: 11008834--11008863 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11008824 GGATATTAGA
11008834 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11008864 TGTCCTAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11010007 original size:22 final size:22
Alignment explanation
Indices: 11009980--11010035 Score: 112
Period size: 22 Copynumber: 2.5 Consensus size: 22
11009970 TAATTAAGTA
11009980 TCCTAATTACCTAATTAGTTAC
1 TCCTAATTACCTAATTAGTTAC
11010002 TCCTAATTACCTAATTAGTTAC
1 TCCTAATTACCTAATTAGTTAC
11010024 TCCTAATTACCT
1 TCCTAATTACCT
11010036 GTATATATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.30, C:0.25, G:0.04, T:0.41
Consensus pattern (22 bp):
TCCTAATTACCTAATTAGTTAC
Found at i:11024640 original size:16 final size:17
Alignment explanation
Indices: 11024602--11024640 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
11024592 AAATTCTTGA
*
11024602 AAAAAAGTAACTTTTTT
1 AAAAAAGTAAATTTTTT
*
11024619 TAAAAA-TAAATTTTTT
1 AAAAAAGTAAATTTTTT
11024635 AAAAAA
1 AAAAAA
11024641 AGCTTAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (17 bp):
AAAAAAGTAAATTTTTT
Found at i:11026045 original size:724 final size:721
Alignment explanation
Indices: 11024620--11026065 Score: 2673
Period size: 724 Copynumber: 2.0 Consensus size: 721
11024610 AACTTTTTTT
11024620 AAAAATAAATTTTTTAAAAAAAGCTTAAAAAAAACTCCTAATAAGATCTTTCTTTTCTCTTTTTT
1 AAAAATAAATTTTTTAAAAAAAGCTTAAAAAAAACTCCTAATAAGATCTTTCTTTTCTC-----T
11024685 TTTTTTTTCAAAAAAAGGCCAATTTTTTAGGAGTGTTATTTTTTTACAAAACGATCCTCTTTCAA
61 TTTTTTTTCAAAAAAAGGCCAATTTTTTAGGAGTGTTATTTTTTTACAAAACGATCCTCTTTCAA
11024750 AAAATTCCCCCTTCCTCTCTCCTTATCGATTTTCTTCTCCTCTTCCCCTTACTACAAATCATCCT
126 AAAATTCCCCCTTCCTCTCTCCTTATCGATTTTCTTCTCCTCTTCCCCTTACTACAAATCATCCT
*
11024815 TCTAGGGTTTTTTTTTATTCCTAAAAAGATTAAGAGAACAAAAGATCTAAAATTCAAAATTGCAT
191 TCTAGGGTTTTTTTTTATTCCTAAAAAGATTAAGAGAACAAAAGATCTAAAATTCAAAACTGCAT
11024880 TCAGATATTATTTCTTCTTTTTCTTTTTGTTTTGAAAACTCTCTTTATTATTTGATATGACAATT
256 TCAGATATTATTTCTTCTTTTTCTTTTTGTTTTGAAAACTCTCTTTATTATTTGATATGACAATT
11024945 ATGTGATGTTTATTTATTTTTAACTTCTTTCTAGTGTATATAATATTTGTTGATTATGATTGAAA
321 ATGTGATGTTTATTTATTTTTAACTTCTTTCTAGTGTATATAATATTTGTTGATTATGATTGAAA
* * * *
11025010 TAATTAGTCAAATAGGTCAATGGCTGTTGAGATACATGAGATAAAAATTGAGAAGTTAATATTTG
386 TAATTAATCAAAAAGGCCAATGGCTGTTGAGATAAATGAGATAAAAATTGAGAAGTTAATATTTG
11025075 TACTTATTTGTGTTAACTCAGTTTTGAAAAATTTTTTCTTTTAGGTATAACAATAGACGGCACTA
451 TACTTATTTGTGTTAACTCAGTTTTGAAAAATTTTTTCTTTTAGGTATAACAATAGACGGCACTA
11025140 CAAAAAAATTGAAATAAACTTTAATTCCTTTAGCAACAGGAATTGCAAAATTCCTAAATTTCTTA
516 CAAAAAAATTGAAATAAACTTTAATTCCTTTAGCAACAGGAATTGCAAAATTCCTAAATTTCTTA
11025205 ATAATGAATATCACATTTGAGCTAACAATACCTAATAGATGATGTGGCACTTCTTGACAAAATAA
581 ATAATGAATATCACATTTGAGCTAACAATACCTAATAGATGATGTGGCACTTCTTGACAAAATAA
11025270 ATAACCCATTAAGAAAATCAACAAAATTTGTCTAAAATAATGGGAAAAAAAATAAAAGCCAAAAC
646 ATAACCCATTAAGAAAATCAACAAAATTTGTCTAAAATAATGGGAAAAAAAATAAAAGCCAAAAC
11025335 CTTTNTTTTAAA
711 CTTT-TTTTAAA
11025347 AAAAATAAATTTTTTTAAAAAAAAAGCTTAAAAAAAACTCCTAATAAGATCTTTCTTTTCTC-TT
1 AAAAATAAA-TTTTTT--AAAAAAAGCTTAAAAAAAACTCCTAATAAGATCTTTCTTTTCTCTTT
*
11025411 TTTTTTCAAAAAAAGGCCAATTTTTTAGGAGTGTTATTTTTTTCCAAAACGATCCTCTTTCAAAA
63 TTTTTTCAAAAAAAGGCCAATTTTTTAGGAGTGTTATTTTTTTACAAAACGATCCTCTTTCAAAA
*
11025476 AATTCCCCCTTCCTCTCTCCTTATCGATTTTCTTCTCCTCTTCCCCTTTCTACAAATCATCCTTC
128 AATTCCCCCTTCCTCTCTCCTTATCGATTTTCTTCTCCTCTTCCCCTTACTACAAATCATCCTTC
11025541 TAGGGGTTTTTTTTTATTCCTAAAAAGATTAAGAGAACAAAAGATCT-AAATTCAAAACTGCATT
193 TA-GGGTTTTTTTTTATTCCTAAAAAGATTAAGAGAACAAAAGATCTAAAATTCAAAACTGCATT
11025605 CATG-TATTATTTCTTCTTTTTCTTTTTGTTTTGAAAACTCTCTTTATTATTTGATATGACAATT
257 CA-GATATTATTTCTTCTTTTTCTTTTTGTTTTGAAAACTCTCTTTATTATTTGATATGACAATT
11025669 ATGTGATGTTTATTTATTTTTAACTTCTTTCTAGTGTATATAATATTTGTTGATTATGATTGAAA
321 ATGTGATGTTTATTTATTTTTAACTTCTTTCTAGTGTATATAATATTTGTTGATTATGATTGAAA
* * *
11025734 TAATTAATCAAAAAGGCCAATGGTTGTTGAGATAAATTAGATGAAAATTGAGAAGTTAATATTTG
386 TAATTAATCAAAAAGGCCAATGGCTGTTGAGATAAATGAGATAAAAATTGAGAAGTTAATATTTG
11025799 TAACTTATTTGTGTTAACTCAGTTTTGAAAAATTTTTTCTTTTAGGTATAACAATAGACGGCACT
451 T-ACTTATTTGTGTTAACTCAGTTTTGAAAAATTTTTTCTTTTAGGTATAACAATAGACGGCACT
11025864 ACAAAAAAATTGAAATAAACTTTAATTCCTTTAGCAACAGGAATTGCAAAATTCCTAAATTTCTT
515 ACAAAAAAATTGAAATAAACTTTAATTCCTTTAGCAACAGGAATTGCAAAATTCCTAAATTTCTT
11025929 AATAATGAATATCACATTTGAGCTAACAATACCTAATAGATGATGTGGCACTTCTTGACAAAATA
580 AATAATGAATATCACATTTGAGCTAACAATACCTAATAGATGATGTGGCACTTCTTGACAAAATA
11025994 AATAACCCATTAAGAAAATCAACAAAATTTGTCTAAAATAATGGGAAAAAAAATAAAAGCCAAAA
645 AATAACCCATTAAGAAAATCAACAAAATTTGTCTAAAATAATGGGAAAAAAAATAAAAGCCAAAA
11026059 CCTTTTT
710 CCTTTTT
11026066 GTTCATGGAG
Statistics
Matches: 703, Mismatches: 10, Indels: 15
0.97 0.01 0.02
Matches are distributed among these distances:
724 336 0.48
725 308 0.44
727 9 0.01
728 6 0.01
730 44 0.06
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.39
Consensus pattern (721 bp):
AAAAATAAATTTTTTAAAAAAAGCTTAAAAAAAACTCCTAATAAGATCTTTCTTTTCTCTTTTTT
TTTCAAAAAAAGGCCAATTTTTTAGGAGTGTTATTTTTTTACAAAACGATCCTCTTTCAAAAAAT
TCCCCCTTCCTCTCTCCTTATCGATTTTCTTCTCCTCTTCCCCTTACTACAAATCATCCTTCTAG
GGTTTTTTTTTATTCCTAAAAAGATTAAGAGAACAAAAGATCTAAAATTCAAAACTGCATTCAGA
TATTATTTCTTCTTTTTCTTTTTGTTTTGAAAACTCTCTTTATTATTTGATATGACAATTATGTG
ATGTTTATTTATTTTTAACTTCTTTCTAGTGTATATAATATTTGTTGATTATGATTGAAATAATT
AATCAAAAAGGCCAATGGCTGTTGAGATAAATGAGATAAAAATTGAGAAGTTAATATTTGTACTT
ATTTGTGTTAACTCAGTTTTGAAAAATTTTTTCTTTTAGGTATAACAATAGACGGCACTACAAAA
AAATTGAAATAAACTTTAATTCCTTTAGCAACAGGAATTGCAAAATTCCTAAATTTCTTAATAAT
GAATATCACATTTGAGCTAACAATACCTAATAGATGATGTGGCACTTCTTGACAAAATAAATAAC
CCATTAAGAAAATCAACAAAATTTGTCTAAAATAATGGGAAAAAAAATAAAAGCCAAAACCTTTT
TTTAAA
Found at i:11027915 original size:2 final size:2
Alignment explanation
Indices: 11027908--11027942 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
11027898 TTTCTATAAC
11027908 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11027943 CATACATACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11028056 original size:43 final size:43
Alignment explanation
Indices: 11027983--11028109 Score: 132
Period size: 43 Copynumber: 3.0 Consensus size: 43
11027973 CCCGCCACAC
* * * *
11027983 TCAGCTTATGTGCACTCTGTAC-TCGCACATAGCCAGGTTATCA
1 TCAGCTCATGTGCACTCT-CACACCGCACATAGCCAGGTCATCA
* ***
11028026 TCAGCTCATGTGCACTCTCACACCGTACATAGTTGGGTCATCA
1 TCAGCTCATGTGCACTCTCACACCGCACATAGCCAGGTCATCA
* *
11028069 TCATCTCATGTGCACTCCCACACCGCACATAGCTC-GGTCAT
1 TCAGCTCATGTGCACTCTCACACCGCACATAGC-CAGGTCAT
11028110 TATTATCACA
Statistics
Matches: 69, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
42 2 0.03
43 67 0.97
ACGTcount: A:0.23, C:0.32, G:0.17, T:0.28
Consensus pattern (43 bp):
TCAGCTCATGTGCACTCTCACACCGCACATAGCCAGGTCATCA
Found at i:11029079 original size:16 final size:17
Alignment explanation
Indices: 11029058--11029090 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
11029048 AAGTTTGGAG
*
11029058 AAGAAA-GAAGTAAAAA
1 AAGAAAGGAAATAAAAA
11029074 AAGAAAGGAAATAAAAA
1 AAGAAAGGAAATAAAAA
11029091 GAAATAAGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (17 bp):
AAGAAAGGAAATAAAAA
Found at i:11036028 original size:26 final size:26
Alignment explanation
Indices: 11035999--11036050 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
11035989 ATAAAGGTTA
* *
11035999 TTTATAAGGTGCTAACTGGAAAAAAT
1 TTTATAAGATGCTAACTAGAAAAAAT
*
11036025 TTTATAAGATGCTAATTAGAAAAAAT
1 TTTATAAGATGCTAACTAGAAAAAAT
11036051 ATCTAAGCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.46, C:0.06, G:0.15, T:0.33
Consensus pattern (26 bp):
TTTATAAGATGCTAACTAGAAAAAAT
Found at i:11046402 original size:21 final size:21
Alignment explanation
Indices: 11046378--11046417 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
11046368 AAAATAAAAA
11046378 TATTATGTTATT-TTTTAATAT
1 TATTAT-TTATTATTTTAATAT
11046399 TATTATTTATTATTTTAAT
1 TATTATTTATTATTTTAAT
11046418 TGCTTAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (21 bp):
TATTATTTATTATTTTAATAT
Found at i:11052472 original size:22 final size:22
Alignment explanation
Indices: 11052428--11052472 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
11052418 GCACGTGTGA
* *
11052428 ACGCAGACAGGTGAAGTGCTAC
1 ACGCACACAGGTGAAGTGATAC
*
11052450 ACGCACACAGGTGAATTGATAC
1 ACGCACACAGGTGAAGTGATAC
11052472 A
1 A
11052473 TAGACTGGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.22, G:0.27, T:0.16
Consensus pattern (22 bp):
ACGCACACAGGTGAAGTGATAC
Found at i:11054499 original size:19 final size:21
Alignment explanation
Indices: 11054477--11054524 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
11054467 ACCAAATTTT
11054477 TATTATT-TTTAAAAATT-AA
1 TATTATTATTTAAAAATTAAA
* *
11054496 TATT-TTATTTATAATTTAAA
1 TATTATTATTTAAAAATTAAA
11054516 TATTATTAT
1 TATTATTAT
11054525 GATTATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 2 0.08
19 12 0.50
20 6 0.25
21 4 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TATTATTATTTAAAAATTAAA
Found at i:11054520 original size:26 final size:26
Alignment explanation
Indices: 11054484--11054732 Score: 141
Period size: 26 Copynumber: 9.6 Consensus size: 26
11054474 TTTTATTATT
*
11054484 TTTAAAAATTAATATTTTATTTATAA
1 TTTAAATATTAATATTTTATTTATAA
* * *
11054510 TTTAAATATTATTATGATTATTTAT-T
1 TTTAAATATTAATAT-TTTATTTATAA
11054536 TTTAAATATTAATAATTTTAATTTAT--
1 TTTAAATATTAAT-ATTTT-ATTTATAA
* * *
11054562 TTTAAAGTATTAA-A---AATTGATAC
1 TTTAAA-TATTAATATTTTATTTATAA
11054585 TTTAAATATTAATATTTTATTTATAA
1 TTTAAATATTAATATTTTATTTATAA
* * * **
11054611 -TTAATTTGTTACTAAGGTTATTTATTATA
1 TTTAA-ATATTAAT-ATTTTATTTA-TA-A
11054640 TTTTTAAATATTAATAATTTATATTT-T-A
1 --TTTAAATATTAAT-ATTT-TATTTATAA
*
11054668 TTTAAAATATTAATA----ATTTATCA
1 TTT-AAATATTAATATTTTATTTATAA
*
11054691 TTTAAATATTAATATTTTATTTAAAA
1 TTTAAATATTAATATTTTATTTATAA
11054717 TTT-AATCATTAATATT
1 TTTAAAT-ATTAATATT
11054733 ATAAAATACT
Statistics
Matches: 174, Mismatches: 23, Indels: 52
0.70 0.09 0.21
Matches are distributed among these distances:
21 9 0.05
22 18 0.10
23 11 0.06
25 8 0.05
26 66 0.38
27 40 0.23
28 3 0.02
29 1 0.01
30 1 0.01
31 8 0.05
32 9 0.05
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (26 bp):
TTTAAATATTAATATTTTATTTATAA
Found at i:11054679 original size:42 final size:42
Alignment explanation
Indices: 11054660--11054763 Score: 115
Period size: 42 Copynumber: 2.5 Consensus size: 42
11054650 TTAATAATTT
*
11054660 ATATTTTATTTAAAATATTAATAATTTATCATTTAAATATTA
1 ATATTTTATTTAAAATATTAATAATTTATAATTTAAATATTA
* * *
11054702 ATATTTTATTTAAAAT-TTAATCATTAAT-ATTATAAAATACTA
1 ATATTTTATTTAAAATATTAATAATTTATAATT-T-AAATATTA
* *
11054744 TTATTTTATTTATAAT-TTAA
1 ATATTTTATTTAAAATATTAA
11054764 ATATTATTAT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
40 3 0.05
41 11 0.20
42 41 0.75
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (42 bp):
ATATTTTATTTAAAATATTAATAATTTATAATTTAAATATTA
Found at i:11054679 original size:106 final size:105
Alignment explanation
Indices: 11054527--11054718 Score: 298
Period size: 106 Copynumber: 1.8 Consensus size: 105
11054517 ATTATTATGA
*
11054527 TTATTTATTTTTAAATATTAATAATTTTAATTTATTTTAAAGTATTAAAAATTGAT-ACTTTAAA
1 TTATTTATTTTTAAATATTAATAATTTTAATTTATTTTAAAATATTAAAAATTGATCA-TTTAAA
*
11054591 TATTAATATTTTATTTATAATTAATTTGTTACTAAGGTTAT
65 TATTAATATTTTATTTAAAATTAATTTGTTACTAAGGTTAT
* * *
11054632 TTATTATATTTTTAAATATTAATAATTTATATTTTA-TTTAAAATATTAATAATTTATCATTTAA
1 TTATT-TATTTTTAAATATTAATAATTT-TAATTTATTTTAAAATATTAAAAATTGATCATTTAA
11054696 ATATTAATATTTTATTTAAAATT
64 ATATTAATATTTTATTTAAAATT
11054719 TAATCATTAA
Statistics
Matches: 79, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
105 5 0.06
106 67 0.85
107 7 0.09
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.55
Consensus pattern (105 bp):
TTATTTATTTTTAAATATTAATAATTTTAATTTATTTTAAAATATTAAAAATTGATCATTTAAAT
ATTAATATTTTATTTAAAATTAATTTGTTACTAAGGTTAT
Found at i:11054751 original size:106 final size:103
Alignment explanation
Indices: 11054484--11054751 Score: 264
Period size: 106 Copynumber: 2.6 Consensus size: 103
11054474 TTTTATTATT
* * *
11054484 TTTAAAAATTAATATTTTATTTATAATTTAA-A-TATTATTATGATTAT-TTATTTTTAAATATT
1 TTTAAATATTAATATTTTATTTATAATTTAATATTAATATTATAATTATATTA-TTTTAAATATT
*
11054546 AATAATTTTAATTTATTTTAAAGTATTAAAAATTGATAC
65 AATAATTTTAATTTATTTTAAAATATTAAAAATTGATAC
* * *
11054585 TTTAAATATTAATATTTTATTTATAA-TTAATTTGTTACTAAGGTTATTTATTATA-T-TTTTAA
1 TTTAAATATTAATATTTTATTTATAATTTAA--TATTAAT-A--TTA-TAATTATATTATTTTAA
* * *
11054647 ATATTAATAATTTATATTTTA-TTTAAAATATTAATAATTTAT-C
60 ATATTAATAATTT-TAATTTATTTTAAAATATTAAAAATTGATAC
* *
11054690 ATTTAAATATTAATATTTTATTTAAAATTTAATCATTAATATTATAAAATACTATTATTTTA
1 -TTTAAATATTAATATTTTATTTATAATTTAAT-ATTAATATTAT-AATTA-TATTATTTTA
11054752 TTTATAATTT
Statistics
Matches: 137, Mismatches: 13, Indels: 29
0.77 0.07 0.16
Matches are distributed among these distances:
100 4 0.03
101 25 0.18
102 1 0.01
103 6 0.04
104 5 0.04
105 5 0.04
106 71 0.52
107 13 0.09
108 7 0.05
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (103 bp):
TTTAAATATTAATATTTTATTTATAATTTAATATTAATATTATAATTATATTATTTTAAATATTA
ATAATTTTAATTTATTTTAAAATATTAAAAATTGATAC
Found at i:11066597 original size:16 final size:16
Alignment explanation
Indices: 11066562--11066605 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
11066552 ATGAAAATTT
*
11066562 ATTAATTAATTAAGAT
1 ATTAATTAATTAAGAA
* *
11066578 ATTATTTAATTACGAA
1 ATTAATTAATTAAGAA
11066594 ATTAA-TAATTAA
1 ATTAATTAATTAA
11066606 TTAAAAAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (16 bp):
ATTAATTAATTAAGAA
Found at i:11070457 original size:10 final size:10
Alignment explanation
Indices: 11070444--11070480 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
11070434 ATATGTATAC
11070444 ATATATACAT
1 ATATATACAT
11070454 ATATATACAT
1 ATATATACAT
*
11070464 ATATATATAT
1 ATATATACAT
11070474 ATATATA
1 ATATATA
11070481 ATTTTGATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (10 bp):
ATATATACAT
Found at i:11070460 original size:18 final size:18
Alignment explanation
Indices: 11070434--11070478 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
11070424 AGTCATGTGT
*
11070434 ATATGTATACATATATAC
1 ATATATATACATATATAC
*
11070452 ATATATATACATATATAT
1 ATATATATACATATATAC
11070470 ATATATATA
1 ATATATATA
11070479 TAATTTTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (18 bp):
ATATATATACATATATAC
Found at i:11070477 original size:8 final size:8
Alignment explanation
Indices: 11070433--11070480 Score: 60
Period size: 8 Copynumber: 6.0 Consensus size: 8
11070423 GAGTCATGTG
*
11070433 TATATGTA
1 TATATATA
*
11070441 TACATATA
1 TATATATA
*
11070449 TACATATA
1 TATATATA
*
11070457 TATACATA
1 TATATATA
11070465 TATATATA
1 TATATATA
11070473 TATATATA
1 TATATATA
11070481 ATTTTGATGT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 35 1.00
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (8 bp):
TATATATA
Found at i:11070479 original size:6 final size:6
Alignment explanation
Indices: 11070433--11070480 Score: 60
Period size: 6 Copynumber: 8.0 Consensus size: 6
11070423 GAGTCATGTG
* * * *
11070433 TATATG TATACA TATATA CATATA TATACA TATATA TATATA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
11070481 ATTTTGATGT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (6 bp):
TATATA
Found at i:11073508 original size:17 final size:17
Alignment explanation
Indices: 11073486--11073547 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
11073476 ACGCCATCGA
11073486 TTGGGGAGAGCCGACCG
1 TTGGGGAGAGCCGACCG
*
11073503 TTGGGGAGCGACGCCG-TCG
1 TTGGGGA--GA-GCCGACCG
*
11073522 ATTAGGGAGAGCCGACCG
1 -TTGGGGAGAGCCGACCG
11073540 TTGGGGAG
1 TTGGGGAG
11073548 CGACGCTGGA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
17 18 0.50
18 4 0.11
19 4 0.11
20 10 0.28
ACGTcount: A:0.18, C:0.21, G:0.47, T:0.15
Consensus pattern (17 bp):
TTGGGGAGAGCCGACCG
Found at i:11073516 original size:37 final size:37
Alignment explanation
Indices: 11073475--11073553 Score: 140
Period size: 37 Copynumber: 2.1 Consensus size: 37
11073465 AGCCGATTTG
*
11073475 GACGCCATCGATTGGGGAGAGCCGACCGTTGGGGAGC
1 GACGCCATCGATTAGGGAGAGCCGACCGTTGGGGAGC
*
11073512 GACGCCGTCGATTAGGGAGAGCCGACCGTTGGGGAGC
1 GACGCCATCGATTAGGGAGAGCCGACCGTTGGGGAGC
11073549 GACGC
1 GACGC
11073554 TGGAATGAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.19, C:0.25, G:0.43, T:0.13
Consensus pattern (37 bp):
GACGCCATCGATTAGGGAGAGCCGACCGTTGGGGAGC
Found at i:11073614 original size:2 final size:2
Alignment explanation
Indices: 11073607--11073645 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
11073597 GAATGGCAGT
*
11073607 GA GA GA GA GA GA GA GA GA GA GA GA AA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
11073646 GATTCGGCTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:11074920 original size:13 final size:13
Alignment explanation
Indices: 11074902--11074993 Score: 61
Period size: 13 Copynumber: 7.2 Consensus size: 13
11074892 TTAATTACTT
*
11074902 AATAAAAATAACA
1 AATAAAAATAATA
*
11074915 AATAAATAACAATA
1 AATAAA-AATAATA
*
11074929 GATAAAAA-AA-A
1 AATAAAAATAATA
11074940 AGGATAAAAATAATA
1 A--ATAAAAATAATA
11074955 AATAAAAA-AAT-
1 AATAAAAATAATA
**
11074966 AATTCAAAT-ATA
1 AATAAAAATAATA
11074978 CAAT-AAAATAATA
1 -AATAAAAATAATA
11074991 AAT
1 AAT
11074994 TTATAAAAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 19
0.71 0.08 0.21
Matches are distributed among these distances:
11 9 0.14
12 12 0.19
13 28 0.44
14 12 0.19
15 2 0.03
ACGTcount: A:0.72, C:0.04, G:0.03, T:0.21
Consensus pattern (13 bp):
AATAAAAATAATA
Found at i:11074946 original size:23 final size:23
Alignment explanation
Indices: 11074920--11074963 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
11074910 TAACAAATAA
*
11074920 ATAACAATAGATAAA-AAAAAAGG
1 ATAAAAATA-ATAAATAAAAAAGG
11074943 ATAAAAATAATAAATAAAAAA
1 ATAAAAATAATAAATAAAAAA
11074964 ATAATTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.16
Consensus pattern (23 bp):
ATAAAAATAATAAATAAAAAAGG
Found at i:11075251 original size:15 final size:14
Alignment explanation
Indices: 11075213--11075282 Score: 51
Period size: 15 Copynumber: 5.1 Consensus size: 14
11075203 AAGATATAAA
11075213 AAAATA-ATAAGTAG
1 AAAATATATAA-TAG
11075227 -AAATA-A-AATAG
1 AAAATATATAATAG
*
11075238 AAAATATGATAATAA
1 AAAATAT-ATAATAG
*
11075253 AAAATATAATAAAATG
1 AAAATAT-ATAATA-G
11075269 AAAATA-ATAATAG
1 AAAATATATAATAG
11075282 A
1 A
11075283 CAATTGCATT
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
11 3 0.07
12 7 0.15
13 8 0.17
14 6 0.13
15 16 0.35
16 6 0.13
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.23
Consensus pattern (14 bp):
AAAATATATAATAG
Found at i:11075278 original size:17 final size:16
Alignment explanation
Indices: 11075228--11075280 Score: 56
Period size: 15 Copynumber: 3.2 Consensus size: 16
11075218 AATAAGTAGA
11075228 AATAAAATAGAAAATAT
1 AATAAAAT-GAAAATAT
*
11075245 GATAATAA--AAAATAT
1 AATAA-AATGAAAATAT
11075260 AATAAAATGAAAATAAT
1 AATAAAATGAAAAT-AT
11075277 AATA
1 AATA
11075281 GACAATTGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
14 2 0.07
15 11 0.37
16 5 0.17
17 10 0.33
18 2 0.07
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.25
Consensus pattern (16 bp):
AATAAAATGAAAATAT
Found at i:11078854 original size:83 final size:83
Alignment explanation
Indices: 11078715--11078874 Score: 275
Period size: 83 Copynumber: 1.9 Consensus size: 83
11078705 TTCTTCTGAA
11078715 GGATGAATTGAGTGAGCAGTTGATCGATCACCTCAAGATGGTTAGGGACCAATATGACAAAGTTG
1 GGATGAATTGAGTGAGCAGTTGATCGATCACCTCAAGATGGTTAGGGACCAATATGACAAAGTTG
*
11078780 GTTTTTCNTTTTTTCGAG
66 GTTTTTCCTTTTTTCGAG
** * *
11078798 GGATGAATTGAGTGAGTGGTTGATCGATCACCTCATGATGGTTAGGGACCAATATGACTAAGTTG
1 GGATGAATTGAGTGAGCAGTTGATCGATCACCTCAAGATGGTTAGGGACCAATATGACAAAGTTG
11078863 GTTTTTCCTTTT
66 GTTTTTCCTTTT
11078875 GGTAGTTATG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 72 1.00
ACGTcount: A:0.25, C:0.13, G:0.27, T:0.34
Consensus pattern (83 bp):
GGATGAATTGAGTGAGCAGTTGATCGATCACCTCAAGATGGTTAGGGACCAATATGACAAAGTTG
GTTTTTCCTTTTTTCGAG
Done.