Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 85 of 97
Found at i:33560365 original size:73 final size:75
Alignment explanation
Indices: 33560288--33560443 Score: 210
Period size: 73 Copynumber: 2.1 Consensus size: 75
33560278 TTAAATTTTT
* * *
33560288 TATTTATAAAT-GGAATAAATCTTACTAATAATTATAATAAAA-ATATTTCAATGATCATCATTT
1 TATTTATAAATAAGAATAAATCTTACTAATAATTATAATAAAAGATATCTCAATCATCATCATTT
*
33560351 GATGAATACA
66 AATGAATACA
** * * *
33560361 TATTTAT-AATAAGTTTAAATCTTACTAATAATTATAGTAAAAGTTATCTCAATCATCGTCATTT
1 TATTTATAAATAAGAATAAATCTTACTAATAATTATAATAAAAGATATCTCAATCATCATCATTT
33560425 AATGAATACA
66 AATGAATACA
33560435 TATTTATAA
1 TATTTATAA
33560444 GTATAGGTTT
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
72 3 0.04
73 34 0.48
74 33 0.46
75 1 0.01
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.40
Consensus pattern (75 bp):
TATTTATAAATAAGAATAAATCTTACTAATAATTATAATAAAAGATATCTCAATCATCATCATTT
AATGAATACA
Found at i:33560442 original size:74 final size:73
Alignment explanation
Indices: 33560303--33560443 Score: 219
Period size: 74 Copynumber: 1.9 Consensus size: 73
33560293 ATAAATGGAA
* * *
33560303 TAAATCTTACTAATAATTATAATAAAAATATTTCAATGATCATCATTTGATGAATACATATTTAT
1 TAAATCTTACTAATAATTATAATAAAAATATCTCAATCATCATCATTTAATGAATACATATTTAT
33560368 AATAAGTT
66 AATAAGTT
* * *
33560376 TAAATCTTACTAATAATTATAGTAAAAGTTATCTCAATCATCGTCATTTAATGAATACATATTTA
1 TAAATCTTACTAATAATTATAATAAAA-ATATCTCAATCATCATCATTTAATGAATACATATTTA
33560441 TAA
65 TAA
33560444 GTATAGGTTT
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
73 26 0.43
74 35 0.57
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (73 bp):
TAAATCTTACTAATAATTATAATAAAAATATCTCAATCATCATCATTTAATGAATACATATTTAT
AATAAGTT
Found at i:33561689 original size:39 final size:40
Alignment explanation
Indices: 33561635--33561715 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
33561625 GTGTTGTGAA
33561635 AACACCAATCATGGCAAGGTTA-GAAACCTCACTAAGGTG
1 AACACCAATCATGGCAAGGTTAGGAAACCTCACTAAGGTG
* *
33561674 AACACCAATCTTGGCAAGGTTAGGAAACCTTACTAAGGTG
1 AACACCAATCATGGCAAGGTTAGGAAACCTCACTAAGGTG
33561714 AA
1 AA
33561716 TAATGGCCAC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 21 0.54
40 18 0.46
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (40 bp):
AACACCAATCATGGCAAGGTTAGGAAACCTCACTAAGGTG
Found at i:33562427 original size:18 final size:18
Alignment explanation
Indices: 33562406--33562446 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
33562396 TTGCAACAAC
33562406 AACTACTACCACAACCAT
1 AACTACTACCACAACCAT
* * *
33562424 AACTGCTACTACATCCAT
1 AACTACTACCACAACCAT
33562442 AACTA
1 AACTA
33562447 TTGCAACCGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.34, G:0.02, T:0.22
Consensus pattern (18 bp):
AACTACTACCACAACCAT
Found at i:33564340 original size:42 final size:42
Alignment explanation
Indices: 33564281--33564368 Score: 176
Period size: 42 Copynumber: 2.1 Consensus size: 42
33564271 TAACATTCAA
33564281 AAGCATATAGGTTACTTGATTTTAATTCTAATGTTATAGTTT
1 AAGCATATAGGTTACTTGATTTTAATTCTAATGTTATAGTTT
33564323 AAGCATATAGGTTACTTGATTTTAATTCTAATGTTATAGTTT
1 AAGCATATAGGTTACTTGATTTTAATTCTAATGTTATAGTTT
33564365 AAGC
1 AAGC
33564369 TACATATGTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.45
Consensus pattern (42 bp):
AAGCATATAGGTTACTTGATTTTAATTCTAATGTTATAGTTT
Found at i:33566314 original size:12 final size:12
Alignment explanation
Indices: 33566287--33566322 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
33566277 TATTACATAG
*
33566287 TTTTATTAA-CT
1 TTTTATTAATTT
33566298 TTTTATTAATTT
1 TTTTATTAATTT
33566310 TTTTATTAATTT
1 TTTTATTAATTT
33566322 T
1 T
33566323 AAAGAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTTATTAATTT
Found at i:33568897 original size:1 final size:1
Alignment explanation
Indices: 33568891--33568926 Score: 63
Period size: 1 Copynumber: 36.0 Consensus size: 1
33568881 GATGGCTCTG
*
33568891 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
33568927 CTCTGATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:33571168 original size:15 final size:15
Alignment explanation
Indices: 33571147--33571194 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
33571137 ATGTGATAAC
*
33571147 AAATAATATAATTGT
1 AAATAATATGATTGT
* **
33571162 AAGTAATATGATTAC
1 AAATAATATGATTGT
33571177 AAATAATATGATTGT
1 AAATAATATGATTGT
33571192 AAA
1 AAA
33571195 AAAGATAACA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.35
Consensus pattern (15 bp):
AAATAATATGATTGT
Found at i:33571179 original size:30 final size:30
Alignment explanation
Indices: 33571134--33571193 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
33571124 ACTTTACAAT
*
33571134 GTAATGTGATAACAAATAATATAATTGTAA
1 GTAATATGATAACAAATAATATAATTGTAA
* *
33571164 GTAATATGATTACAAATAATATGATTGTAA
1 GTAATATGATAACAAATAATATAATTGTAA
33571194 AAAAGATAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.13, T:0.35
Consensus pattern (30 bp):
GTAATATGATAACAAATAATATAATTGTAA
Found at i:33571440 original size:18 final size:18
Alignment explanation
Indices: 33571419--33571474 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 18
33571409 GTCATATATT
33571419 ATTTTTATTTTTATTATA
1 ATTTTTATTTTTATTATA
*
33571437 A-TTTTA-TATT-TTAT-
1 ATTTTTATTTTTATTATA
*
33571451 ATTTTTATTGTTTAATATA
1 ATTTTTATT-TTTATTATA
33571470 ATTTT
1 ATTTT
33571475 CTATATTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
14 1 0.03
15 9 0.30
16 4 0.13
17 7 0.23
18 4 0.13
19 5 0.17
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.70
Consensus pattern (18 bp):
ATTTTTATTTTTATTATA
Found at i:33571464 original size:7 final size:6
Alignment explanation
Indices: 33571417--33571464 Score: 51
Period size: 6 Copynumber: 7.5 Consensus size: 6
33571407 ATGTCATATA
* *
33571417 TTATTT TTATTT TTATTA TAATTT TATATTT TATATTT TTATTGT TTA
1 TTATTT TTATTT TTATTT TTATTT T-TATTT T-TATTT TTATT-T TTA
33571465 ATATAATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
6 20 0.56
7 16 0.44
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (6 bp):
TTATTT
Found at i:33571484 original size:33 final size:33
Alignment explanation
Indices: 33571418--33571495 Score: 113
Period size: 33 Copynumber: 2.4 Consensus size: 33
33571408 TGTCATATAT
* *
33571418 TATTTTTATT-TTTATTATAATTTTATATTTTA
1 TATTTTTATTGTTTAATATAATTTTATATATTA
*
33571450 TATTTTTATTGTTTAATATAATTTTCTATATTA
1 TATTTTTATTGTTTAATATAATTTTATATATTA
33571483 TATATTTTATTGT
1 TAT-TTTTATTGT
33571496 AATTTTTTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 10 0.24
33 22 0.54
34 9 0.22
ACGTcount: A:0.28, C:0.01, G:0.03, T:0.68
Consensus pattern (33 bp):
TATTTTTATTGTTTAATATAATTTTATATATTA
Found at i:33571673 original size:22 final size:22
Alignment explanation
Indices: 33571645--33571688 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
33571635 AGTAAAAATA
33571645 TTTTTAATAATATTACAAAGTG
1 TTTTTAATAATATTACAAAGTG
33571667 TTTTTAATAATATTACAAAGTG
1 TTTTTAATAATATTACAAAGTG
33571689 CAATACAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (22 bp):
TTTTTAATAATATTACAAAGTG
Found at i:33572159 original size:5 final size:5
Alignment explanation
Indices: 33572149--33572188 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
33572139 ATTTGGATAT
**
33572149 AATAA AATAA AATAA AATAA AATAA ATATTC AATAA AATA
1 AATAA AATAA AATAA AATAA AATAA A-ATAA AATAA AATA
33572189 TTCTATTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 27 0.90
6 3 0.10
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (5 bp):
AATAA
Found at i:33574600 original size:53 final size:55
Alignment explanation
Indices: 33574520--33574642 Score: 146
Period size: 53 Copynumber: 2.3 Consensus size: 55
33574510 TTTTTTATTA
* *
33574520 AAAATAATTTTAAATTACATAATATTATAAATAA-A-AATAATAAT-AATTAAAG
1 AAAATAATTTTAAATTACAAAACATTATAAATAATAGAATAATAATAAATTAAAG
*
33574572 AGAAATAATTTTAAATTTA-AAAACATTATAAATAATAGTAATAATGATAAATTAAAG
1 A-AAATAATTTTAAA-TTACAAAACATTATAAATAATAG-AATAATAATAAATTAAAG
* *
33574629 ATAATTATTTTAAA
1 AAAATAATTTTAAA
33574643 AATCATTATT
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
52 1 0.02
53 27 0.45
54 4 0.07
56 19 0.32
57 9 0.15
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.36
Consensus pattern (55 bp):
AAAATAATTTTAAATTACAAAACATTATAAATAATAGAATAATAATAAATTAAAG
Found at i:33576062 original size:23 final size:25
Alignment explanation
Indices: 33576036--33576088 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 25
33576026 TGACGTTAAA
* *
33576036 TTTACAAAATATT-TT-AAAATTTT
1 TTTAAAAAATATTATTAAAAATATT
33576059 TTTAAAAAATATTATTAAAAATATT
1 TTTAAAAAATATTATTAAAAATATT
33576084 TTTAA
1 TTTAA
33576089 TAGCACATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 12 0.46
24 2 0.08
25 12 0.46
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (25 bp):
TTTAAAAAATATTATTAAAAATATT
Found at i:33576066 original size:12 final size:12
Alignment explanation
Indices: 33576036--33576088 Score: 56
Period size: 12 Copynumber: 4.4 Consensus size: 12
33576026 TGACGTTAAA
33576036 TTTACAAAATA-T
1 TTTA-AAAATATT
*
33576048 TTT-AAAATTTT
1 TTTAAAAATATT
33576059 TTTAAAAAATATT
1 TTT-AAAAATATT
*
33576072 ATTAAAAATATT
1 TTTAAAAATATT
33576084 TTTAA
1 TTTAA
33576089 TAGCACATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
10 5 0.15
11 4 0.12
12 16 0.47
13 9 0.26
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (12 bp):
TTTAAAAATATT
Found at i:33586262 original size:2 final size:2
Alignment explanation
Indices: 33586255--33586283 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
33586245 CAAGATGAAG
33586255 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
33586284 TATATATATA
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:33593323 original size:26 final size:26
Alignment explanation
Indices: 33593263--33593324 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
33593253 ACCATATACC
*
33593263 CATCATCAACATGCACACCATCCCAT
1 CATCATCATCATGCACACCATCCCAT
*
33593289 CATCATCATCATGCACATCATCCCAT
1 CATCATCATCATGCACACCATCCCAT
33593315 CATCATCATC
1 CATCATCATC
33593325 TCATATGCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.32, C:0.40, G:0.03, T:0.24
Consensus pattern (26 bp):
CATCATCATCATGCACACCATCCCAT
Found at i:33593515 original size:82 final size:82
Alignment explanation
Indices: 33593373--33593623 Score: 405
Period size: 82 Copynumber: 3.1 Consensus size: 82
33593363 GGAGATCACG
* * * *
33593373 AAGCATCCCCCCCTTCACTCGACAAGAGGTGCACTTCACTCCGGATCATGAAGCAACGGAGCAAT
1 AAGCTTCCCCCCCTTCACTCGGCAAGAGGTGCACTTCACTCCGGATCACGAAGCAACGGAGCAGT
33593438 CCCTTCCCTCCACTTCC
66 CCCTTCCCTCCACTTCC
* *
33593455 AAGCTTCCCCCCCTTCACTCGGTAAGAGGTACACTTCACTCCGGATCACGAAGCAACGGAGCAGT
1 AAGCTTCCCCCCCTTCACTCGGCAAGAGGTGCACTTCACTCCGGATCACGAAGCAACGGAGCAGT
33593520 CCCTTCCCT-CATCTTCC
66 CCCTTCCCTCCA-CTTCC
33593537 AAGCTTCCCCCCCTTCACTCGGCAAGAGGTGCACTTCACTCCGGATCACGAAGCAACGGAGCAGT
1 AAGCTTCCCCCCCTTCACTCGGCAAGAGGTGCACTTCACTCCGGATCACGAAGCAACGGAGCAGT
* * *
33593602 CCCTTCCTTCCTCTTCT
66 CCCTTCCCTCCACTTCC
33593619 AAGCT
1 AAGCT
33593624 CTTGGGCGGA
Statistics
Matches: 156, Mismatches: 11, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
81 2 0.01
82 153 0.98
83 1 0.01
ACGTcount: A:0.22, C:0.39, G:0.17, T:0.22
Consensus pattern (82 bp):
AAGCTTCCCCCCCTTCACTCGGCAAGAGGTGCACTTCACTCCGGATCACGAAGCAACGGAGCAGT
CCCTTCCCTCCACTTCC
Found at i:33596119 original size:68 final size:68
Alignment explanation
Indices: 33595774--33596274 Score: 342
Period size: 69 Copynumber: 7.3 Consensus size: 68
33595764 TACCGATCTT
* * * * *
33595774 AACCCTATGGTATCCTTACCCCCACACTA-GGTTTTTATAAA-GGAAAAATATGGTACATTTACC
1 AACCTTATGGTAT-TTTACCCCCACAC-AGGGCTTTTATAAAGGGAAGAA-ATGGTACATTCACC
33595837 AACCTC
63 AACCTC
* * ** * * * *
33595843 ATTCC-TACT-ATATTCTTACCTTCACATCA-AGCTTTTAT-AAGAAGAAGAGATGGTACATTCT
1 A-ACCTTA-TGGTATT-TTACCCCCACA-CAGGGCTTTTATAAAG-GGAAGAAATGGTACATTCA
33595904 CCAACCT-
61 CCAACCTC
*** * * * * * ** *
33595911 TGTCTCTATGGTATTCTTAACCCCACACCGAGCTTTTAT-AAGTGAAAAAGATGGTATGTTCATC
1 AACCT-TATGGTATT-TTACCCCCACACAGGGCTTTTATAAAGGGAAGAA-ATGGTACATTCACC
33595975 AACCTC
63 AACCTC
* * * *
33595981 AACCTTATGGTATTCTTACCTCCACATTA-GGTTTTTAT-AAGAGGAAGAAATGGTACGTTCACC
1 AACCTTATGGTATT-TTACCCCCACA-CAGGGCTTTTATAAAG-GGAAGAAATGGTACATTCACC
33596044 AACCTC
63 AACCTC
* * * * ** * *
33596050 ATCCCTATGGTACTTTGACCCCCACACCGAACTTTTATAAAGGGAA-AAATGGTACGTTCAACAA
1 AACCTTATGGTA-TTTTACCCCCACACAGGGCTTTTATAAAGGGAAGAAATGGTACATTCACCAA
33596114 CCTC
65 CCTC
* * * * * * *
33596118 ATCCTTATGGTATTTTACCACTACACTGGGCTTTTATAAAGGGAATAGATGGTACATTTACCAAC
1 AACCTTATGGTATTTTACCCCCACACAGGGCTTTTATAAAGGGAAGAAATGGTACATTCACCAAC
33596183 CT-
66 CTC
* * *
33596185 AGACCTTATAGTATTCTTACCCCCACACAGGGCTTTTATAAAAGGAAGAGATGGTACATTCACCA
1 A-ACCTTATGGTATT-TTACCCCCACACAGGGCTTTTATAAAGGGAAGAAATGGTACATTCACCA
33596250 ACCTC
64 ACCTC
33596255 AACCTTATGGTATTCTTACC
1 AACCTTATGGTATT-TTACC
33596275 TCTGTACCAG
Statistics
Matches: 341, Mismatches: 70, Indels: 42
0.75 0.15 0.09
Matches are distributed among these distances:
67 29 0.09
68 68 0.20
69 223 0.65
70 21 0.06
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (68 bp):
AACCTTATGGTATTTTACCCCCACACAGGGCTTTTATAAAGGGAAGAAATGGTACATTCACCAAC
CTC
Found at i:33596766 original size:20 final size:21
Alignment explanation
Indices: 33596735--33596778 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
33596725 TTAATTTAAG
*
33596735 TTATTTTAGTTTAATTTTACT
1 TTATTTTAGTTTAATATTACT
*
33596756 TTATTTT-GTTTTATATTACT
1 TTATTTTAGTTTAATATTACT
33596776 TTA
1 TTA
33596779 AGAATAGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.68
Consensus pattern (21 bp):
TTATTTTAGTTTAATATTACT
Found at i:33598874 original size:29 final size:29
Alignment explanation
Indices: 33598832--33598889 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
33598822 TTTAAGTGCA
33598832 GACAAGTGCAGTGAAGC-TTTTTGGTTTT
1 GACAAGTGCAGTGAAGCTTTTTTGGTTTT
33598860 NGACAAGTGCAGTGAAGCTTTTTTGGTTTT
1 -GACAAGTGCAGTGAAGCTTTTTTGGTTTT
33598890 TCTTCTTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.21, C:0.10, G:0.28, T:0.40
Consensus pattern (29 bp):
GACAAGTGCAGTGAAGCTTTTTTGGTTTT
Found at i:33608555 original size:20 final size:20
Alignment explanation
Indices: 33608530--33608590 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
33608520 TTTTTAAAAC
33608530 TCAAAACCAAGCTCAAATCT
1 TCAAAACCAAGCTCAAATCT
*
33608550 TCAAAA--AATG-TC-NA-C-
1 TCAAAACCAA-GCTCAAATCT
33608565 TCAAAACCAAGCTCAAATCT
1 TCAAAACCAAGCTCAAATCT
33608585 TCAAAA
1 TCAAAA
33608591 AATGGTCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 14
0.67 0.04 0.29
Matches are distributed among these distances:
15 6 0.19
16 2 0.06
17 5 0.16
18 5 0.16
19 2 0.06
20 12 0.38
ACGTcount: A:0.48, C:0.26, G:0.05, T:0.20
Consensus pattern (20 bp):
TCAAAACCAAGCTCAAATCT
Found at i:33608567 original size:35 final size:34
Alignment explanation
Indices: 33608528--33608594 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 34
33608518 TGTTTTTAAA
33608528 ACTCAAAACCAAGCTCAAATCTTCAAAAAATGTC
1 ACTCAAAACCAAGCTCAAATCTTCAAAAAATGTC
33608562 NACTCAAAACCAAGCTCAAATCTTCAAAAAATG
1 -ACTCAAAACCAAGCTCAAATCTTCAAAAAATG
33608595 GTCATTTGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.48, C:0.25, G:0.06, T:0.19
Consensus pattern (34 bp):
ACTCAAAACCAAGCTCAAATCTTCAAAAAATGTC
Found at i:33609419 original size:18 final size:18
Alignment explanation
Indices: 33609369--33609420 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
33609359 TTTAATATAT
*
33609369 TTTAAAA-ATAAAATTTA
1 TTTAAAATATAATATTTA
*
33609386 TTTAAAATATATTATTTA
1 TTTAAAATATAATATTTA
*
33609404 -TTAATATGATAATATTT
1 TTTAAAAT-ATAATATTT
33609421 TTGAGTCAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 13 0.45
18 16 0.55
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
TTTAAAATATAATATTTA
Found at i:33620836 original size:19 final size:19
Alignment explanation
Indices: 33620788--33620842 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
33620778 CCGACTGACA
*
33620788 TCCTTCCTCCCATCCGATG
1 TCCTTCCTCCCATCCGACG
*
33620807 TCTCATCCTCCCATCCGACG
1 TC-CTTCCTCCCATCCGACG
33620827 TCCTTCCTCCCATCCG
1 TCCTTCCTCCCATCCG
33620843 GCATCCAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.11, C:0.51, G:0.09, T:0.29
Consensus pattern (19 bp):
TCCTTCCTCCCATCCGACG
Found at i:33622960 original size:45 final size:45
Alignment explanation
Indices: 33622895--33622985 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 45
33622885 TTGACACTTG
* * * *
33622895 TAAATTTATTTTCTGTTTTAATCCATATCAAATGCTAAAGGATTA
1 TAAATTCATTTCCTATTTTAATCCACATCAAATGCTAAAGGATTA
33622940 TAAATTCATTTCCTATTTTAATCCACATCAAATGCTAAAGGATTA
1 TAAATTCATTTCCTATTTTAATCCACATCAAATGCTAAAGGATTA
33622985 T
1 T
33622986 GAAGGGAAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (45 bp):
TAAATTCATTTCCTATTTTAATCCACATCAAATGCTAAAGGATTA
Found at i:33625061 original size:28 final size:28
Alignment explanation
Indices: 33625008--33625066 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
33624998 ACATTGAAAT
*
33625008 TTTATTTATATTTGATGTAGTGTATTTG
1 TTTATTTATATTTGATGTAATGTATTTG
* *
33625036 TTTATTTATGTTTGGTGTAAAT-TATTTG
1 TTTATTTATATTTGATGT-AATGTATTTG
33625064 TTT
1 TTT
33625067 CTAACATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 25 0.93
29 2 0.07
ACGTcount: A:0.20, C:0.00, G:0.17, T:0.63
Consensus pattern (28 bp):
TTTATTTATATTTGATGTAATGTATTTG
Found at i:33628375 original size:23 final size:23
Alignment explanation
Indices: 33628293--33628376 Score: 64
Period size: 23 Copynumber: 3.7 Consensus size: 23
33628283 AGTGAGAGGT
* * *
33628293 TGTGTCTATTGTCTTTCAACAGA
1 TGTGTCTATTGTATTTTAAAAGA
* *
33628316 TGCGT-TCTT-TATTTTCAAAAGA
1 TGTGTCTATTGTATTTT-AAAAGA
* ** *
33628338 TGTGTCTGTACTATTTTAATAGA
1 TGTGTCTATTGTATTTTAAAAGA
33628361 TGTGTCTATTGTATTT
1 TGTGTCTATTGTATTT
33628377 CGACAGACGT
Statistics
Matches: 46, Mismatches: 12, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
21 4 0.09
22 12 0.26
23 24 0.52
24 6 0.13
ACGTcount: A:0.23, C:0.12, G:0.17, T:0.49
Consensus pattern (23 bp):
TGTGTCTATTGTATTTTAAAAGA
Found at i:33628466 original size:22 final size:23
Alignment explanation
Indices: 33628424--33628473 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
33628414 TTGTAAATAC
**
33628424 TTATTATTTATTTATTTTTAT-T
1 TTATTATTTATTTATAGTTATAT
33628446 TTATTATTT-TTTATGAGTTATAT
1 TTATTATTTATTTAT-AGTTATAT
33628469 TTATT
1 TTATT
33628474 CTTAAACAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 5 0.21
22 13 0.54
23 6 0.25
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (23 bp):
TTATTATTTATTTATAGTTATAT
Found at i:33628958 original size:24 final size:24
Alignment explanation
Indices: 33628925--33628978 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
33628915 ACAGTTGCAC
*
33628925 TGAATGTTCTAGAATGAGGCTATT
1 TGAATATTCTAGAATGAGGCTATT
33628949 TGAATATTCTAGAATGAGGCTATT
1 TGAATATTCTAGAATGAGGCTATT
33628973 T-AATAT
1 TGAATAT
33628979 AAAATTCAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 5 0.17
24 24 0.83
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.39
Consensus pattern (24 bp):
TGAATATTCTAGAATGAGGCTATT
Found at i:33633395 original size:23 final size:22
Alignment explanation
Indices: 33633306--33633397 Score: 64
Period size: 23 Copynumber: 4.0 Consensus size: 22
33633296 AATGAGAGAT
33633306 TGTGTCTGT-TGTCTTTCAACAGA
1 TGTGTCTGTATG--TTTCAACAGA
* *
33633329 TGCGTTCTTTTAT-TTTCAACAGA
1 TGTG-TC-TGTATGTTTCAACAGA
*
33633352 TGTGTCTGTACTGTTTTAACAGA
1 TGTGTCTGTA-TGTTTCAACAGA
*
33633375 TGTGTTTGT-TGTATATCAACAGA
1 TGTGTCTGTATGT-T-TCAACAGA
33633398 CGTATCTATA
Statistics
Matches: 55, Mismatches: 7, Indels: 14
0.72 0.09 0.18
Matches are distributed among these distances:
21 6 0.11
22 4 0.07
23 40 0.73
24 2 0.04
25 2 0.04
26 1 0.02
ACGTcount: A:0.22, C:0.14, G:0.20, T:0.45
Consensus pattern (22 bp):
TGTGTCTGTATGTTTCAACAGA
Found at i:33633459 original size:10 final size:11
Alignment explanation
Indices: 33633438--33633471 Score: 54
Period size: 10 Copynumber: 3.3 Consensus size: 11
33633428 TTGTAAATAC
33633438 TTATTATTTAT
1 TTATTATTTAT
33633449 TTATT-TTTAT
1 TTATTATTTAT
33633459 TTATTATTT-T
1 TTATTATTTAT
33633469 TTA
1 TTA
33633472 AGAGTTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 14 0.64
11 8 0.36
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTATTATTTAT
Found at i:33633471 original size:14 final size:14
Alignment explanation
Indices: 33633441--33633469 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
33633431 TAAATACTTA
33633441 TTATTTATTTATTT
1 TTATTTATTTATTT
33633455 TTATTTA-TTATTT
1 TTATTTATTTATTT
33633468 TT
1 TT
33633470 TAAGAGTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TTATTTATTTATTT
Found at i:33636835 original size:38 final size:40
Alignment explanation
Indices: 33636793--33636898 Score: 144
Period size: 38 Copynumber: 2.7 Consensus size: 40
33636783 ATAGTGCCTG
*
33636793 TGTGCACGATGTGGGGGGATGTACATGATGGC-ACTGAT-
1 TGTGCACGATGTGGGGGGATGTACATGATGGCGACGGATA
* * * *
33636831 TGTGCACGATGTGGGGAGATGCACATGATGGCGTCGGCTA
1 TGTGCACGATGTGGGGGGATGTACATGATGGCGACGGATA
*
33636871 TGTGCATGATGTGGGGGGATGTACATGA
1 TGTGCACGATGTGGGGGGATGTACATGA
33636899 GCTGGGTGTG
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
38 30 0.52
39 3 0.05
40 25 0.43
ACGTcount: A:0.21, C:0.13, G:0.41, T:0.25
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGTACATGATGGCGACGGATA
Found at i:33642651 original size:19 final size:21
Alignment explanation
Indices: 33642606--33642651 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
33642596 CTCTCCACGA
*
33642606 TTGGTGTCTTTTACAACGTCC
1 TTGGTGTCTTTCACAACGTCC
*
33642627 AT-GTGTC-TTCACAACG-CC
1 TTGGTGTCTTTCACAACGTCC
33642645 TTGGTGT
1 TTGGTGT
33642652 TAGGTTGCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
18 3 0.14
19 12 0.57
20 5 0.24
21 1 0.05
ACGTcount: A:0.15, C:0.24, G:0.22, T:0.39
Consensus pattern (21 bp):
TTGGTGTCTTTCACAACGTCC
Found at i:33643611 original size:40 final size:40
Alignment explanation
Indices: 33643567--33643765 Score: 186
Period size: 40 Copynumber: 4.9 Consensus size: 40
33643557 GATCTTAAAT
* * * *
33643567 ATAAACTTAAATAACGAAAAACAAACATCCATACAATGAC
1 ATAAACTTAAATAACTAAACACAAACATCCAAACAATAAC
* * * *
33643607 ATAAACTTAAATAACTATACACAAATATCCAAATAACAAC
1 ATAAACTTAAATAACTAAACACAAACATCCAAACAATAAC
* *
33643647 ATAAACTTAAATAACTACACACAAAGATCCAAACAAATAAC
1 ATAAACTTAAATAACTAAACACAAACATCCAAAC-AATAAC
* * * * *
33643688 ATAAACTTAAATAACCAAATACATATATCCAAACAACAAC
1 ATAAACTTAAATAACTAAACACAAACATCCAAACAATAAC
* *
33643728 AATATAAATTTAAATAACTAAA-A-ATAATATCCAAACAA
1 ---ATAAACTTAAATAACTAAACACA-AACATCCAAACAA
33643766 CTAGTGTATA
Statistics
Matches: 133, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
40 68 0.51
41 35 0.26
42 13 0.10
43 17 0.13
ACGTcount: A:0.59, C:0.19, G:0.02, T:0.21
Consensus pattern (40 bp):
ATAAACTTAAATAACTAAACACAAACATCCAAACAATAAC
Found at i:33643643 original size:22 final size:21
Alignment explanation
Indices: 33643615--33643688 Score: 57
Period size: 20 Copynumber: 3.6 Consensus size: 21
33643605 ACATAAACTT
33643615 AAATAACTATACACAAATATCC
1 AAATAACTA-ACACAAATATCC
*
33643637 AAATAAC-AACATAAACT-T--
1 AAATAACTAACACAAA-TATCC
*
33643655 AAATAACTACACACAAAGATCC
1 AAATAACTA-ACACAAATATCC
* *
33643677 AAACAAATAACA
1 AAATAACTAACA
33643689 TAAACTTAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 13
0.69 0.08 0.22
Matches are distributed among these distances:
18 7 0.17
19 1 0.02
20 14 0.34
21 5 0.12
22 14 0.34
ACGTcount: A:0.59, C:0.22, G:0.01, T:0.18
Consensus pattern (21 bp):
AAATAACTAACACAAATATCC
Found at i:33643660 original size:18 final size:20
Alignment explanation
Indices: 33643605--33643663 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
33643595 CCATACAATG
33643605 ACATAAACTTAAATAACTAT
1 ACATAAACTTAAATAACTAT
*
33643625 ACACAAA-TATCCAAATAAC-A-
1 ACATAAACT-T--AAATAACTAT
33643645 ACATAAACTTAAATAACTA
1 ACATAAACTTAAATAACTA
33643664 CACACAAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 11
0.71 0.04 0.24
Matches are distributed among these distances:
18 7 0.22
19 2 0.06
20 14 0.44
21 2 0.06
22 7 0.22
ACGTcount: A:0.58, C:0.19, G:0.00, T:0.24
Consensus pattern (20 bp):
ACATAAACTTAAATAACTAT
Found at i:33643719 original size:81 final size:81
Alignment explanation
Indices: 33643567--33643765 Score: 231
Period size: 81 Copynumber: 2.4 Consensus size: 81
33643557 GATCTTAAAT
* * * * *
33643567 ATAAACTTAAATAACGAAAAACAAACATCCATACAATGACATAAACTTAAATAACTATACACAAA
1 ATAAACTTAAATAACTAAAAACAAACATCCAAACAATAACATAAACTTAAATAACCAAACACAAA
*
33643632 TATCCAAATAACAAC-
66 TATCCAAACAACAACA
* * * * *
33643647 ATAAACTTAAATAACTACACACAAAGATCCAAACAAATAACATAAACTTAAATAACCAAATACAT
1 ATAAACTTAAATAACTAAAAACAAACATCCAAAC-AATAACATAAACTTAAATAACCAAACACAA
33643712 ATATCCAAACAACAACAA
65 ATATCCAAACAACAAC-A
* * *
33643730 TATAAATTTAAATAACTAAAAA-TAATATCCAAACAA
1 -ATAAACTTAAATAACTAAAAACAAACATCCAAACAA
33643766 CTAGTGTATA
Statistics
Matches: 99, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
80 29 0.29
81 40 0.40
82 2 0.02
83 10 0.10
84 18 0.18
ACGTcount: A:0.59, C:0.19, G:0.02, T:0.21
Consensus pattern (81 bp):
ATAAACTTAAATAACTAAAAACAAACATCCAAACAATAACATAAACTTAAATAACCAAACACAAA
TATCCAAACAACAACA
Found at i:33643767 original size:21 final size:23
Alignment explanation
Indices: 33643712--33643768 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 23
33643702 CCAAATACAT
33643712 ATATCCAAACAAC-AACAATATA
1 ATATCCAAACAACTAACAATATA
** *
33643734 A-ATTTAAATAACTAA-AA-ATA
1 ATATCCAAACAACTAACAATATA
33643754 ATATCCAAACAACTA
1 ATATCCAAACAACTA
33643769 GTGTATATAC
Statistics
Matches: 27, Mismatches: 6, Indels: 5
0.71 0.16 0.13
Matches are distributed among these distances:
20 4 0.15
21 20 0.74
22 3 0.11
ACGTcount: A:0.60, C:0.18, G:0.00, T:0.23
Consensus pattern (23 bp):
ATATCCAAACAACTAACAATATA
Found at i:33643887 original size:15 final size:17
Alignment explanation
Indices: 33643867--33643899 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
33643857 ATTACAATTA
33643867 ATAA-TTTTATAA-GTT
1 ATAATTTTTATAATGTT
33643882 ATAATTTTTATAATGTT
1 ATAATTTTTATAATGTT
33643899 A
1 A
33643900 ACACAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 8 0.50
17 4 0.25
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (17 bp):
ATAATTTTTATAATGTT
Found at i:33644427 original size:17 final size:18
Alignment explanation
Indices: 33644407--33644446 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
33644397 TAAATATACT
*
33644407 TATATTTAAAGTA-TATA
1 TATATTAAAAGTATTATA
*
33644424 TATACTAAAAGTATTATA
1 TATATTAAAAGTATTATA
33644442 TATAT
1 TATAT
33644447 AATATAGTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (18 bp):
TATATTAAAAGTATTATA
Found at i:33651806 original size:51 final size:51
Alignment explanation
Indices: 33651728--33651858 Score: 201
Period size: 51 Copynumber: 2.6 Consensus size: 51
33651718 CCTTACCAGA
* * *
33651728 AAGAAAAACCTTTAAGCATTTTGAGCATTTTGGAGTGGTTTTTGATATACG
1 AAGAAAAACCTTTGAGCATTTTAAGCATTTTGGAGTGGTTTTTGATACACG
* *
33651779 AAGAAAAACCTTTGA-CAGTTTTAAGCATTTTGGAGTGGTTTTTGATGCATG
1 AAGAAAAACCTTTGAGCA-TTTTAAGCATTTTGGAGTGGTTTTTGATACACG
33651830 AAGAAAAACCTTTGAGCATTTTAAGCATT
1 AAGAAAAACCTTTGAGCATTTTAAGCATT
33651859 CTTCGCTAAG
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
50 2 0.03
51 69 0.95
52 2 0.03
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.36
Consensus pattern (51 bp):
AAGAAAAACCTTTGAGCATTTTAAGCATTTTGGAGTGGTTTTTGATACACG
Found at i:33652049 original size:22 final size:22
Alignment explanation
Indices: 33651982--33652179 Score: 155
Period size: 22 Copynumber: 9.0 Consensus size: 22
33651972 TACATAACTG
* *
33651982 GTTTTTGGGTATTGCGTGACTAA
1 GTTTTTAGGCATTGCGTGACT-A
* * * *
33652005 G-TTTTAAGCATCGCATGATTA
1 GTTTTTAGGCATTGCGTGACTA
**
33652026 GTTTTTAGTTATTGCGTGACTA
1 GTTTTTAGGCATTGCGTGACTA
* *
33652048 GTTTATAGGCATTGTGTGACTA
1 GTTTTTAGGCATTGCGTGACTA
* * **
33652070 GGTTTTAAGCATCACGTGACTA
1 GTTTTTAGGCATTGCGTGACTA
*** *
33652092 GTTTTTAATTATTACGTGACTA
1 GTTTTTAGGCATTGCGTGACTA
*
33652114 GTTTATAGGCATTGCGTGACTA
1 GTTTTTAGGCATTGCGTGACTA
* * *
33652136 GTTAGTAAGGTATTGCGTGACTA
1 GTT-TTTAGGCATTGCGTGACTA
* *
33652159 GTTTTTAGACATTGTGTGACT
1 GTTTTTAGGCATTGCGTGACT
33652180 TAGGCTTTGC
Statistics
Matches: 133, Mismatches: 40, Indels: 5
0.75 0.22 0.03
Matches are distributed among these distances:
21 2 0.02
22 112 0.84
23 19 0.14
ACGTcount: A:0.23, C:0.11, G:0.24, T:0.41
Consensus pattern (22 bp):
GTTTTTAGGCATTGCGTGACTA
Found at i:33652078 original size:66 final size:66
Alignment explanation
Indices: 33651992--33652136 Score: 227
Period size: 66 Copynumber: 2.2 Consensus size: 66
33651982 GTTTTTGGGT
* * * * *
33651992 ATTGCGTGACTAAGTTTTAAGCATCGCATGATTAGTTTTTAGTTATTGCGTGACTAGTTTATAGG
1 ATTGCGTGACTAGGTTTTAAGCATCACATGACTAGTTTTTAATTATTACGTGACTAGTTTATAGG
33652057 C
66 C
* *
33652058 ATTGTGTGACTAGGTTTTAAGCATCACGTGACTAGTTTTTAATTATTACGTGACTAGTTTATAGG
1 ATTGCGTGACTAGGTTTTAAGCATCACATGACTAGTTTTTAATTATTACGTGACTAGTTTATAGG
33652123 C
66 C
33652124 ATTGCGTGACTAG
1 ATTGCGTGACTAG
33652137 TTAGTAAGGT
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 71 1.00
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.40
Consensus pattern (66 bp):
ATTGCGTGACTAGGTTTTAAGCATCACATGACTAGTTTTTAATTATTACGTGACTAGTTTATAGG
C
Found at i:33652213 original size:21 final size:22
Alignment explanation
Indices: 33652187--33652238 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
33652177 ACTTAGGCTT
*
33652187 TGCCTAAAATC-AATCACACAA
1 TGCCTAAAAACTAATCACACAA
* *
33652208 TGCCTAAAAACTAGTCACGCAA
1 TGCCTAAAAACTAATCACACAA
33652230 TGCCTAAAA
1 TGCCTAAAA
33652239 GCCAAAGACA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.44, C:0.27, G:0.10, T:0.19
Consensus pattern (22 bp):
TGCCTAAAAACTAATCACACAA
Found at i:33655092 original size:14 final size:15
Alignment explanation
Indices: 33655069--33655097 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
33655059 TTGGAATAAG
33655069 AAAAGAATAAAAATA
1 AAAAGAATAAAAATA
33655084 AAAAG-ATAAAAATA
1 AAAAGAATAAAAATA
33655098 CCTTTTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (15 bp):
AAAAGAATAAAAATA
Found at i:33655123 original size:20 final size:20
Alignment explanation
Indices: 33655100--33655188 Score: 69
Period size: 20 Copynumber: 4.5 Consensus size: 20
33655090 TAAAAATACC
*
33655100 TTTTATTATATAATTTTAAT-
1 TTTTATT-TATAATATTAATA
33655120 TTTT-TTTA-AATATTAATA
1 TTTTATTTATAATATTAATA
*
33655138 TTTTATTTATAAT-CTAATCA
1 TTTTATTTATAATATTAAT-A
* * *
33655158 TTAATATTATAAAATACTAATA
1 TT-TTATT-TATAATATTAATA
33655180 TTTTATTTA
1 TTTTATTTA
33655189 ATTTAAATGT
Statistics
Matches: 57, Mismatches: 5, Indels: 14
0.75 0.07 0.18
Matches are distributed among these distances:
17 8 0.14
18 6 0.11
19 10 0.18
20 12 0.21
21 8 0.14
22 8 0.14
23 5 0.09
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTTATTTATAATATTAATA
Found at i:33655949 original size:30 final size:29
Alignment explanation
Indices: 33655906--33655983 Score: 79
Period size: 30 Copynumber: 2.7 Consensus size: 29
33655896 NNNNNATTTA
33655906 AATATGTTATAATTAAAATATAAAAATATT
1 AATATGTTATAATTAAAAT-TAAAAATATT
* * * *
33655936 AATATTTTTTAATTTAAATTTAAAATATT
1 AATATGTTATAATTAAAATTAAAAATATT
*
33655965 AAT-T-TTATAAATTTAAATT
1 AATATGTTAT-AATTAAAATT
33655984 TGTAATTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
27 3 0.07
28 11 0.26
29 12 0.29
30 16 0.38
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (29 bp):
AATATGTTATAATTAAAATTAAAAATATT
Found at i:33655966 original size:14 final size:14
Alignment explanation
Indices: 33655946--33655984 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
33655936 AATATTTTTT
33655946 AATTTAAATTTA-A
1 AATTTAAATTTATA
*
33655959 AATATTAATTTTATA
1 AAT-TTAAATTTATA
33655974 AATTTAAATTT
1 AATTTAAATTT
33655985 GTAATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 3 0.14
14 15 0.68
15 4 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
AATTTAAATTTATA
Found at i:33655984 original size:28 final size:29
Alignment explanation
Indices: 33655906--33655984 Score: 90
Period size: 28 Copynumber: 2.7 Consensus size: 29
33655896 NNNNNATTTA
* *
33655906 AATATGTTAT-AATTAAAATATAAAAATATT
1 AATAT-TTATAAATTTAAAT-TTAAAATATT
* *
33655936 AATATTTTTTAATTTAAATTTAAAATATT
1 AATATTTATAAATTTAAATTTAAAATATT
33655965 AAT-TTTATAAATTTAAATTT
1 AATATTTATAAATTTAAATTT
33655985 GTAATTTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
28 15 0.35
29 15 0.35
30 13 0.30
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (29 bp):
AATATTTATAAATTTAAATTTAAAATATT
Found at i:33655989 original size:22 final size:21
Alignment explanation
Indices: 33655948--33655996 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
33655938 TATTTTTTAA
33655948 TTTAAATTTAAAATATTAATT
1 TTTAAATTTAAAATATTAATT
*
33655969 TTATAAATTT-AAATTTGTAATT
1 TT-TAAATTTAAAATAT-TAATT
33655991 TTTAAA
1 TTTAAA
33655997 AATAAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
TTTAAATTTAAAATATTAATT
Found at i:33656640 original size:45 final size:45
Alignment explanation
Indices: 33656589--33656702 Score: 165
Period size: 45 Copynumber: 2.5 Consensus size: 45
33656579 TCATGGTTAA
* *
33656589 GTTGTTACACGTCATGTACAAAAACATGTTATATACTATGCTTAG
1 GTTGTTACACGTCATGTACAAAAACATATTACATACTATGCTTAG
* * *
33656634 GTTGTTACACGTCATATACAAAAACATATTACATATTATGGTTAG
1 GTTGTTACACGTCATGTACAAAAACATATTACATACTATGCTTAG
* *
33656679 GTTGTTACACGCCATGTTCAAAAA
1 GTTGTTACACGTCATGTACAAAAA
33656703 AAATATTGTT
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 61 1.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (45 bp):
GTTGTTACACGTCATGTACAAAAACATATTACATACTATGCTTAG
Found at i:33656779 original size:53 final size:54
Alignment explanation
Indices: 33656681--33656786 Score: 133
Period size: 53 Copynumber: 2.0 Consensus size: 54
33656671 ATGGTTAGGT
* * **
33656681 TGTTACACGCCATGTTCAAAAAAAATATTGTTGTTACATGCCATATACAAAAACA
1 TGTTACACGCCATGTT-AAAAAAAATATTATTATTACACACCATATACAAAAACA
* * *
33656736 TGTTATACGCCATGTT-TAAAAAATATTATTATTACACACCATATTCAAAAA
1 TGTTACACGCCATGTTAAAAAAAATATTATTATTACACACCATATACAAAAA
33656787 TATTTTGTTA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
53 29 0.66
55 15 0.34
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.32
Consensus pattern (54 bp):
TGTTACACGCCATGTTAAAAAAAATATTATTATTACACACCATATACAAAAACA
Found at i:33657208 original size:23 final size:23
Alignment explanation
Indices: 33657178--33657223 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
33657168 CTTAGTGTCT
33657178 TGAAAGCACAGGAAAGAAAAATC
1 TGAAAGCACAGGAAAGAAAAATC
* *
33657201 TGAAAGCACAGGAGAGAGAAATC
1 TGAAAGCACAGGAAAGAAAAATC
33657224 AGAAGCATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.52, C:0.13, G:0.26, T:0.09
Consensus pattern (23 bp):
TGAAAGCACAGGAAAGAAAAATC
Found at i:33657299 original size:35 final size:35
Alignment explanation
Indices: 33657255--33657325 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
33657245 CGAAGAAAGA
33657255 AAACAATAAAATTAGAAAGAGTGGGATCGTTAGAG
1 AAACAATAAAATTAGAAAGAGTGGGATCGTTAGAG
33657290 AAACAATAAAATTAGAAAGAGTGGGATCGTTAGAG
1 AAACAATAAAATTAGAAAGAGTGGGATCGTTAGAG
33657325 A
1 A
33657326 GAGAAATTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.49, C:0.06, G:0.25, T:0.20
Consensus pattern (35 bp):
AAACAATAAAATTAGAAAGAGTGGGATCGTTAGAG
Found at i:33658270 original size:2 final size:2
Alignment explanation
Indices: 33658263--33658304 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
33658253 GCCAACGTCA
33658263 AT AT AT AT AT AT 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 AT AT AT AT AT AT
33658305 TTTTGATAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33665632 original size:19 final size:19
Alignment explanation
Indices: 33665583--33665632 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
33665573 GCTATAAATA
*
33665583 TCTTCTCCTTCCAGCAGCT
1 TCTTCTTCTTCCAGCAGCT
* *
33665602 TCTTCAAT-TTCCAGTAGCT
1 TCTTC-TTCTTCCAGCAGCT
33665621 TCTTCTTCTTCC
1 TCTTCTTCTTCC
33665633 TCCTTCCATC
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:33666429 original size:2 final size:2
Alignment explanation
Indices: 33666422--33666468 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
33666412 NNNNNNNNNN
33666422 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33666464 TA TA T
1 TA TA T
33666469 GTTGTGCATA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:33666627 original size:38 final size:40
Alignment explanation
Indices: 33666585--33666687 Score: 138
Period size: 38 Copynumber: 2.6 Consensus size: 40
33666575 ATAGTGCCTG
* *
33666585 TGTGCACGATGTGGGGGGATGTACACAATGGCACT-GAT-
1 TGTGCACGATGTGGGGGGATGCACACAATGACACTAGATA
* * *
33666623 TGTGCACGATGTGGGGGGATGCACACGATGACTCTAGCTA
1 TGTGCACGATGTGGGGGGATGCACACAATGACACTAGATA
*
33666663 TGTGCACAATGTGGGGGGATGCACA
1 TGTGCACGATGTGGGGGGATGCACA
33666688 TGAGCTGAGT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
38 31 0.54
39 2 0.04
40 24 0.42
ACGTcount: A:0.23, C:0.17, G:0.37, T:0.22
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGCACACAATGACACTAGATA
Found at i:33685280 original size:2 final size:2
Alignment explanation
Indices: 33685275--33685309 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
33685265 TATATATATA
33685275 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T- TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
33685310 CATAAATAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:33693438 original size:13 final size:12
Alignment explanation
Indices: 33693413--33693469 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
33693403 TGTCATTATT
33693413 ATTTTTTAAAAA
1 ATTTTTTAAAAA
*
33693425 ATTTTTGTATAAA
1 ATTTTT-TAAAAA
* * *
33693438 ATATATT-AAGA
1 ATTTTTTAAAAA
33693449 ATTTTTTAAAAA
1 ATTTTTTAAAAA
*
33693461 ATTTATTAA
1 ATTTTTTAA
33693470 TCCTTTATAG
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
11 7 0.21
12 18 0.53
13 9 0.26
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (12 bp):
ATTTTTTAAAAA
Found at i:33693461 original size:23 final size:24
Alignment explanation
Indices: 33693424--33693469 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
33693414 TTTTTTAAAA
*
33693424 AATTTTTGTATAAAATATATTAAG
1 AATTTTTGTAAAAAATATATTAAG
*
33693448 AATTTTT-TAAAAAATTTATTAA
1 AATTTTTGTAAAAAATATATTAA
33693470 TCCTTTATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
AATTTTTGTAAAAAATATATTAAG
Found at i:33695218 original size:20 final size:19
Alignment explanation
Indices: 33695169--33695255 Score: 63
Period size: 20 Copynumber: 4.5 Consensus size: 19
33695159 TTCCTACAAA
*
33695169 AACATAAAAACTAATAAATAAT
1 AACAT-AAAATTAA-AAA-AAT
33695191 AAC-T-AAATTAAAAAAAT
1 AACATAAAATTAAAAAAAT
*
33695208 AAGCATAAAATTAAAATAACT
1 AA-CATAAAATTAAAA-AAAT
* * *
33695229 AACTTAAAATTATAAAAAC
1 AACATAAAATTAAAAAAAT
33695248 AAC-TAAAA
1 AACATAAAA
33695256 ATAACTAAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
17 5 0.09
18 9 0.16
19 12 0.22
20 20 0.36
21 6 0.11
22 3 0.05
ACGTcount: A:0.67, C:0.09, G:0.01, T:0.23
Consensus pattern (19 bp):
AACATAAAATTAAAAAAAT
Found at i:33695387 original size:2 final size:2
Alignment explanation
Indices: 33695374--33695405 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
33695364 ACATTGTCAA
*
33695374 AT AT AT AC 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 AT
33695406 TAATATGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:33697353 original size:14 final size:15
Alignment explanation
Indices: 33697319--33697352 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
33697309 ATAAGTCTAG
33697319 TTTTTATGATATTTA
1 TTTTTATGATATTTA
33697334 TTTTTATG-TCATTTA
1 TTTTTATGAT-ATTTA
33697349 TTTT
1 TTTT
33697353 ACTTGCACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 1 0.06
15 17 0.94
ACGTcount: A:0.21, C:0.03, G:0.06, T:0.71
Consensus pattern (15 bp):
TTTTTATGATATTTA
Found at i:33700490 original size:43 final size:43
Alignment explanation
Indices: 33700429--33700592 Score: 202
Period size: 43 Copynumber: 3.8 Consensus size: 43
33700419 TTTTAAAAAA
*
33700429 AAAGTTACACAGCCTCATTCTAGATAAAAAGCTTATTCATTTT
1 AAAGTTACACAGCCTCATTCCAGATAAAAAGCTTATTCATTTT
** * * * *
33700472 AAAGTTACACAGCCTCATTCTGGATGAAGAGCTTACTCATTGT
1 AAAGTTACACAGCCTCATTCCAGATAAAAAGCTTATTCATTTT
** *
33700515 AAAGTTACACAGCCTCATTCCAGATAAGGAGCTTATTCCTTTTT
1 AAAGTTACACAGCCTCATTCCAGATAAAAAGCTTATT-CATTTT
** *
33700559 AAAGTTACATTGCCTCATTCCAGATAAAAGGCTT
1 AAAGTTACACAGCCTCATTCCAGATAAAAAGCTT
33700593 TATCTTTGGA
Statistics
Matches: 103, Mismatches: 17, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
43 70 0.68
44 33 0.32
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32
Consensus pattern (43 bp):
AAAGTTACACAGCCTCATTCCAGATAAAAAGCTTATTCATTTT
Found at i:33700760 original size:17 final size:18
Alignment explanation
Indices: 33700722--33700762 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
33700712 ATCAAATTTT
*
33700722 GAAAATATAAAACATTAA
1 GAAAATATAAAACATGAA
*
33700740 -AAAATATGAAA-ATGAA
1 GAAAATATAAAACATGAA
33700756 GAAAATA
1 GAAAATA
33700763 ACAAAAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.68, C:0.02, G:0.10, T:0.20
Consensus pattern (18 bp):
GAAAATATAAAACATGAA
Found at i:33701659 original size:186 final size:187
Alignment explanation
Indices: 33701288--33701647 Score: 490
Period size: 186 Copynumber: 1.9 Consensus size: 187
33701278 TATGATTCAG
* * *
33701288 ATTTTTATTTTTATTTTTTATTAGGAGTTTAAATAGATTTATGAAAATTCTCCAACGATAAAATA
1 ATTTTTATTTTTATTTTTTATTAAGAATTTAAATAGATTTACGAAAATTCTCCAACGATAAAATA
* ** * *
33701353 TCAAAGACACCAAAAGAGATGGCTTCTTGGCAATTTCTAGGTAAAAAAATCTTTCAAAATTATGC
66 TCAAAGACACCAAAAGAGATGGCTTCTTGGCAATTTCCAAATAAAAAAATCTTCCAAAATTATAC
33701418 CATAAAAGTTTGAAGATTTTAGAAAATTTTCAATACCAAGGATTTCCACAAATATTT
131 CATAAAAGTTTGAAGATTTTAGAAAATTTTCAATACCAAGGATTTCCACAAATATTT
* * * * * *
33701475 ATTTTTGTTTTTA-TTTTTATTAAGAATTTACATAGATTTACGAAAATTCTCCTATGATTAAATC
1 ATTTTTATTTTTATTTTTTATTAAGAATTTAAATAGATTTACGAAAATTCTCCAACGATAAAATA
* * * * * *
33701539 TCAAGGATACCAAAAGAGATGGCTTTTTGGGAATTTCCAAATGAGAAAATCTTCCAAAATTATAC
66 TCAAAGACACCAAAAGAGATGGCTTCTTGGCAATTTCCAAATAAAAAAATCTTCCAAAATTATAC
* * *
33701604 CATAAGAGTTTGAAGATTTT-GAAAAATTTTTAATACTAAGGATT
131 CATAAAAGTTTGAAGATTTTAG-AAAATTTTCAATACCAAGGATT
33701648 CACATAAATA
Statistics
Matches: 149, Mismatches: 23, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
185 1 0.01
186 136 0.91
187 12 0.08
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (187 bp):
ATTTTTATTTTTATTTTTTATTAAGAATTTAAATAGATTTACGAAAATTCTCCAACGATAAAATA
TCAAAGACACCAAAAGAGATGGCTTCTTGGCAATTTCCAAATAAAAAAATCTTCCAAAATTATAC
CATAAAAGTTTGAAGATTTTAGAAAATTTTCAATACCAAGGATTTCCACAAATATTT
Found at i:33702294 original size:61 final size:61
Alignment explanation
Indices: 33702223--33702342 Score: 195
Period size: 61 Copynumber: 2.0 Consensus size: 61
33702213 TTTATATCTG
* * *
33702223 AATCTAGATATAATAATCAAATATAAGAATTTAAATCAGATTACAATCATGTATTTGGCCA
1 AATCTAGATATAATAATCAAATATAAGAATTTAAATCAAATTACAATAATATATTTGGCCA
* *
33702284 AATCTTGATATAATAATCAAATATAAGAATTTAAATCAAATTACACTAATATATTTGGC
1 AATCTAGATATAATAATCAAATATAAGAATTTAAATCAAATTACAATAATATATTTGGC
33702343 TTGTTAGGCT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 54 1.00
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.34
Consensus pattern (61 bp):
AATCTAGATATAATAATCAAATATAAGAATTTAAATCAAATTACAATAATATATTTGGCCA
Found at i:33710705 original size:21 final size:21
Alignment explanation
Indices: 33710681--33710748 Score: 109
Period size: 21 Copynumber: 3.2 Consensus size: 21
33710671 GTTCATGCAA
* *
33710681 TTCATGACAAAAACTGATGCC
1 TTCATGACAAAGACTAATGCC
33710702 TTCATGACAAAGACTAATGCC
1 TTCATGACAAAGACTAATGCC
33710723 TTCATGACAAAGACTAATGCC
1 TTCATGACAAAGACTAATGCC
*
33710744 ATCAT
1 TTCAT
33710749 TCAAAGGCAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (21 bp):
TTCATGACAAAGACTAATGCC
Found at i:33712689 original size:15 final size:15
Alignment explanation
Indices: 33712669--33712715 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
33712659 ACTTTATCTC
* *
33712669 TAGTAATTGTAGTAT
1 TAGTAATAGTAGTAG
33712684 TAGTAATAGTAGTAG
1 TAGTAATAGTAGTAG
* *
33712699 TAGTAGTAGCAGTAG
1 TAGTAATAGTAGTAG
33712714 TA
1 TA
33712716 ACTATATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.36
Consensus pattern (15 bp):
TAGTAATAGTAGTAG
Found at i:33712698 original size:3 final size:3
Alignment explanation
Indices: 33712677--33712715 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
33712667 TCTAGTAATT
* * *
33712677 GTA GTA TTA GTA ATA GTA GTA GTA GTA GTA GCA GTA GTA
1 GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA
33712716 ACTATATTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (3 bp):
GTA
Found at i:33713703 original size:21 final size:21
Alignment explanation
Indices: 33713677--33713744 Score: 84
Period size: 21 Copynumber: 3.2 Consensus size: 21
33713667 GTTCATGCAA
**
33713677 TTCATGACAAAGACTGATGTT
1 TTCATGACAAAGACTGATGCC
33713698 TTCATGACAAAGA-TAGATGCC
1 TTCATGACAAAGACT-GATGCC
*
33713719 TTCATGACAAGGACTGATGCC
1 TTCATGACAAAGACTGATGCC
*
33713740 ATCAT
1 TTCAT
33713745 TCAAAATCAG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.02
21 39 0.95
22 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (21 bp):
TTCATGACAAAGACTGATGCC
Found at i:33715694 original size:3 final size:3
Alignment explanation
Indices: 33715686--33715774 Score: 142
Period size: 3 Copynumber: 29.7 Consensus size: 3
33715676 ACTTTATCTC
* *
33715686 TAG TAG TAG TAG TAA TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAC
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
* *
33715734 TAG TAG TAG TAG TAA TAG TAG CAG TAG TAG TAG TAG TAG TA
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TA
33715775 ACTATATTTA
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.36, C:0.02, G:0.29, T:0.33
Consensus pattern (3 bp):
TAG
Found at i:33722507 original size:21 final size:20
Alignment explanation
Indices: 33722474--33722518 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
33722464 TGTTGAGTAA
33722474 TTAATTTAAGTTATTTTAGT
1 TTAATTTAAGTTATTTTAGT
* *
33722494 TTAATTTTATGTTATTTTATT
1 TTAA-TTTAAGTTATTTTAGT
33722515 TTAA
1 TTAA
33722519 ATTACTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (20 bp):
TTAATTTAAGTTATTTTAGT
Found at i:33729690 original size:26 final size:27
Alignment explanation
Indices: 33729626--33729690 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
33729616 AGCGCCTAAC
* * *
33729626 GGTGTTCTAAGTGCAGAAACACTTAAG
1 GGTGTTCCAAGCGCAGAAACACTCAAG
* * *
33729653 AGTGTTTCAAGCGCAGAAACAC-CCAG
1 GGTGTTCCAAGCGCAGAAACACTCAAG
33729679 GGTGTTCCAAGC
1 GGTGTTCCAAGC
33729691 TCATAATCTA
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
26 12 0.40
27 18 0.60
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.22
Consensus pattern (27 bp):
GGTGTTCCAAGCGCAGAAACACTCAAG
Found at i:33730555 original size:27 final size:27
Alignment explanation
Indices: 33730514--33730611 Score: 117
Period size: 27 Copynumber: 3.7 Consensus size: 27
33730504 ACGGAAGCGT
* *
33730514 CTAA-GGTGTTCCAAGCACAAAAGCGC
1 CTAAGGGTGTTCCAAGCGCAAAAGCAC
*
33730540 CTAAGGGTGTTCCAAGTGCAAAAGCAC
1 CTAAGGGTGTTCCAAGCGCAAAAGCAC
* * * * *
33730567 CCAAGAGTGTTTCAAGCGCAGAAGCAT
1 CTAAGGGTGTTCCAAGCGCAAAAGCAC
33730594 CTAAGGGTGTTCCAAGCG
1 CTAAGGGTGTTCCAAGCG
33730612 TGGAAGCAGA
Statistics
Matches: 59, Mismatches: 12, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
26 4 0.07
27 55 0.93
ACGTcount: A:0.32, C:0.23, G:0.27, T:0.18
Consensus pattern (27 bp):
CTAAGGGTGTTCCAAGCGCAAAAGCAC
Found at i:33730666 original size:27 final size:27
Alignment explanation
Indices: 33730625--33730712 Score: 70
Period size: 27 Copynumber: 3.3 Consensus size: 27
33730615 AAGCAGAGTA
**
33730625 TTCCAAATGTGGAAGCATCC-AGAGGTG
1 TTCCAAATGCAGAAGCATCCAAG-GGTG
* *
33730652 TTCCAAATGCAGAAGCGTTCAAGGGTG
1 TTCCAAATGCAGAAGCATCCAAGGGTG
** * * * *
33730679 TTCCAAGCGGAAAAGCGTCCAAGGGTA
1 TTCCAAATGCAGAAGCATCCAAGGGTG
33730706 TTCCAAA
1 TTCCAAA
33730713 CACGGAAGCG
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
27 47 0.96
28 2 0.04
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.20
Consensus pattern (27 bp):
TTCCAAATGCAGAAGCATCCAAGGGTG
Found at i:33730760 original size:27 final size:27
Alignment explanation
Indices: 33730635--33730776 Score: 101
Period size: 27 Copynumber: 5.3 Consensus size: 27
33730625 TTCCAAATGT
* *
33730635 GGAAGCATCCAGAGGTGTTCCAAATGCA-
1 GGAAGCGTCCAAAGGTGTTCC-AA-GCAG
* *
33730663 -GAAGCGTTCAAGGGTGTTCCAAGC-G
1 GGAAGCGTCCAAAGGTGTTCCAAGCAG
* * * * *
33730688 GAAAAGCGTCCAAGGGTATTCCAAACAC
1 G-GAAGCGTCCAAAGGTGTTCCAAGCAG
* * *
33730716 GGAAGCGGCCCAACGTGTTCCAAGCAG
1 GGAAGCGTCCAAAGGTGTTCCAAGCAG
* * *
33730743 GGAAGCGTTCAAAGGTGTTCCGAGCAT
1 GGAAGCGTCCAAAGGTGTTCCAAGCAG
33730770 GGAAGCG
1 GGAAGCG
33730777 CATTCCAAGC
Statistics
Matches: 87, Mismatches: 23, Indels: 9
0.73 0.19 0.08
Matches are distributed among these distances:
25 2 0.02
26 2 0.02
27 82 0.94
28 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.32, T:0.16
Consensus pattern (27 bp):
GGAAGCGTCCAAAGGTGTTCCAAGCAG
Found at i:33743461 original size:15 final size:15
Alignment explanation
Indices: 33743425--33743481 Score: 78
Period size: 15 Copynumber: 3.7 Consensus size: 15
33743415 TAGATCAAAG
**
33743425 GTTCTTAAGAATTAT
1 GTTCTTAAGAAAAAT
33743440 GGTTCTTAAGAAAAAT
1 -GTTCTTAAGAAAAAT
*
33743456 GTTCTTAAGAAAAAG
1 GTTCTTAAGAAAAAT
33743471 GTTCTTAAGAA
1 GTTCTTAAGAA
33743482 TGCTCTAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
15 25 0.66
16 13 0.34
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.35
Consensus pattern (15 bp):
GTTCTTAAGAAAAAT
Found at i:33748011 original size:23 final size:23
Alignment explanation
Indices: 33747981--33748029 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
33747971 TTAGCTCAAT
33747981 GAATAAGCGACAAAAATGTCCAA
1 GAATAAGCGACAAAAATGTCCAA
33748004 GAATAAGCGACAAAAATGTCCAA
1 GAATAAGCGACAAAAATGTCCAA
33748027 GAA
1 GAA
33748030 AATAGTGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.53, C:0.16, G:0.18, T:0.12
Consensus pattern (23 bp):
GAATAAGCGACAAAAATGTCCAA
Found at i:33750111 original size:118 final size:119
Alignment explanation
Indices: 33749898--33750126 Score: 363
Period size: 118 Copynumber: 1.9 Consensus size: 119
33749888 CATAACTTTC
* * * * *
33749898 CATTAGTAGCTTGTTCTTTTGCTTATCCATAAAAAGATATAAAATCCAAAACAAAATGTATTTTC
1 CATTAATAGCTCGTTATTTTGCTTAACCATAAAAAGACATAAAATCCAAAACAAAATGTATTTTC
* *
33749963 AAATTACCCAATGTATAGTATTTTCTATTTGTTACAAAATAGATATCATTTTTT
66 AAATTACCCAAAGTATAGTATTTTCTATTTGTTACAAAATAAATATCATTTTTT
33750017 CATTAATAGCTCGTTATTTTGCTTAACCAT-AAAAGACATAAAATCCAAAACAAAATGTATTTTC
1 CATTAATAGCTCGTTATTTTGCTTAACCATAAAAAGACATAAAATCCAAAACAAAATGTATTTTC
*
33750081 AAATTACTCAAAGTATAGTATTTT-TCATTTGTTACAAAATAAATAT
66 AAATTACCCAAAGTATAGTATTTTCT-ATTTGTTACAAAATAAATAT
33750127 TGATAACTCT
Statistics
Matches: 101, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
117 1 0.01
118 74 0.73
119 26 0.26
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.39
Consensus pattern (119 bp):
CATTAATAGCTCGTTATTTTGCTTAACCATAAAAAGACATAAAATCCAAAACAAAATGTATTTTC
AAATTACCCAAAGTATAGTATTTTCTATTTGTTACAAAATAAATATCATTTTTT
Found at i:33750151 original size:118 final size:118
Alignment explanation
Indices: 33749914--33750154 Score: 319
Period size: 118 Copynumber: 2.0 Consensus size: 118
33749904 TAGCTTGTTC
* * *
33749914 TTTTGCTTATCCATAAAAAGATATAAAATCCAAAACAAAATGTATTTTCAAATTACCCAATGTAT
1 TTTTGCTTAACCATAAAAAGACATAAAATCCAAAACAAAATGTATTTTCAAATTACCCAAAGTAT
* ** * *
33749979 AGTATTTTCTATTTGTTACAAAATAGATATCATTTTTTCATTAATAGCTCGTTA
66 AGTATTTTCTATTTGTTACAAAATAAATATCATACTCTCATTAATAGC-AGTTA
*
33750033 TTTTGCTTAACCAT-AAAAGACATAAAATCCAAAACAAAATGTATTTTCAAATTACTCAAAGTAT
1 TTTTGCTTAACCATAAAAAGACATAAAATCCAAAACAAAATGTATTTTCAAATTACCCAAAGTAT
*
33750097 AGTATTTT-TCATTTGTTACAAAATAAATATTGATAACTCT-ATTATATAG-AGTTA
66 AGTATTTTCT-ATTTGTTACAAAATAAATA-TCAT-ACTCTCATTA-ATAGCAGTTA
33750151 TTTT
1 TTTT
33750155 TAACACATTT
Statistics
Matches: 108, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
117 1 0.01
118 81 0.75
119 20 0.19
120 6 0.06
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.40
Consensus pattern (118 bp):
TTTTGCTTAACCATAAAAAGACATAAAATCCAAAACAAAATGTATTTTCAAATTACCCAAAGTAT
AGTATTTTCTATTTGTTACAAAATAAATATCATACTCTCATTAATAGCAGTTA
Found at i:33753234 original size:17 final size:17
Alignment explanation
Indices: 33753205--33753237 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
33753195 TTATTGGTAA
33753205 AATAAAACTTCTTATTG
1 AATAAAACTTCTTATTG
33753222 AATAATAAC-TCTTATT
1 AATAA-AACTTCTTATT
33753238 TTGTTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (17 bp):
AATAAAACTTCTTATTG
Found at i:33753474 original size:29 final size:29
Alignment explanation
Indices: 33753389--33753517 Score: 156
Period size: 30 Copynumber: 4.4 Consensus size: 29
33753379 TCTTATTTTT
33753389 AATTAAGACAAAAATATTTTATCTTGTCTA
1 AATTAAGACAAAAATATTTT-TCTTGTCTA
*
33753419 AATTGAGAC--AAATATGTTTTCTTGTCTA
1 AATTAAGACAAAAATAT-TTTTCTTGTCTA
* *
33753447 GATTAAGATAAAAATATTTTTCTTGTCTTA
1 AATTAAGACAAAAATATTTTTCTTGTC-TA
* *
33753477 AATTAAGACCAAACAT-GTTTTCTTGTCTA
1 AATTAAGA-CAAAAATATTTTTCTTGTCTA
33753506 AATTAAGACAAA
1 AATTAAGACAAA
33753518 CATGTTAAAG
Statistics
Matches: 86, Mismatches: 8, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
28 25 0.29
29 23 0.27
30 33 0.38
31 5 0.06
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.40
Consensus pattern (29 bp):
AATTAAGACAAAAATATTTTTCTTGTCTA
Found at i:33753512 original size:59 final size:58
Alignment explanation
Indices: 33753389--33753517 Score: 197
Period size: 59 Copynumber: 2.2 Consensus size: 58
33753379 TCTTATTTTT
* *
33753389 AATTAAGACAAAAATATTTTATCTTGTCTAAATTGAGACAAATATGTTTTCTTGTCTA
1 AATTAAGACAAAAATATTTTATCTTGTCTAAATTAAGACAAACATGTTTTCTTGTCTA
* *
33753447 GATTAAGATAAAAATATTTT-TCTTGTCTTAAATTAAGACCAAACATGTTTTCTTGTCTA
1 AATTAAGACAAAAATATTTTATCTTGTC-TAAATTAAGA-CAAACATGTTTTCTTGTCTA
33753506 AATTAAGACAAA
1 AATTAAGACAAA
33753518 CATGTTAAAG
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
57 7 0.11
58 27 0.43
59 29 0.46
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.40
Consensus pattern (58 bp):
AATTAAGACAAAAATATTTTATCTTGTCTAAATTAAGACAAACATGTTTTCTTGTCTA
Found at i:33757596 original size:14 final size:12
Alignment explanation
Indices: 33757570--33757605 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 12
33757560 TGAAATTGAG
33757570 AGAAAAAAAAGA
1 AGAAAAAAAAGA
33757582 AGAAAGAAAACAGA
1 AGAAA-AAAA-AGA
33757596 AGAAAAAAAA
1 AGAAAAAAAA
33757606 ATGAAGTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.27
13 8 0.36
14 8 0.36
ACGTcount: A:0.81, C:0.03, G:0.17, T:0.00
Consensus pattern (12 bp):
AGAAAAAAAAGA
Found at i:33757611 original size:14 final size:13
Alignment explanation
Indices: 33757572--33757611 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
33757562 AAATTGAGAG
33757572 AAAAAAAAGAAGA
1 AAAAAAAAGAAGA
*
33757585 AAGAAAACAGAAGA
1 AA-AAAAAAGAAGA
33757599 AAAAAAAATGAAG
1 AAAAAAAA-GAAG
33757612 TGATGAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 7 0.30
14 16 0.70
ACGTcount: A:0.78, C:0.03, G:0.17, T:0.03
Consensus pattern (13 bp):
AAAAAAAAGAAGA
Found at i:33759240 original size:16 final size:16
Alignment explanation
Indices: 33759220--33759268 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
33759210 AAGAATAAAG
33759220 AAATAAAAA-AATATAA
1 AAATAAAAAGAA-ATAA
*
33759236 TAATAAAAAGAAATAA
1 AAATAAAAAGAAATAA
*
33759252 AAATAATAAGTAAATAA
1 AAATAAAAAG-AAATAA
33759269 TAAAATATAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 20 0.71
17 8 0.29
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (16 bp):
AAATAAAAAGAAATAA
Found at i:33759248 original size:26 final size:30
Alignment explanation
Indices: 33759216--33759273 Score: 88
Period size: 26 Copynumber: 2.1 Consensus size: 30
33759206 GGAGAAGAAT
33759216 AAAGAAATAAAAA-AAT-A-T-AATAATAA
1 AAAGAAATAAAAATAATAAGTAAATAATAA
33759242 AAAGAAATAAAAATAATAAGTAAATAATAA
1 AAAGAAATAAAAATAATAAGTAAATAATAA
33759272 AA
1 AA
33759274 TATACATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
26 13 0.46
27 3 0.11
28 1 0.04
29 1 0.04
30 10 0.36
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (30 bp):
AAAGAAATAAAAATAATAAGTAAATAATAA
Found at i:33759250 original size:13 final size:12
Alignment explanation
Indices: 33759216--33759254 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
33759206 GGAGAAGAAT
33759216 AAAGAAATAAAA
1 AAAGAAATAAAA
*
33759228 AAATATAATAATAA
1 AAAGA-AATAA-AA
33759242 AAAGAAATAAAA
1 AAAGAAATAAAA
33759254 A
1 A
33759255 TAATAAGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 7 0.30
13 10 0.43
14 6 0.26
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.15
Consensus pattern (12 bp):
AAAGAAATAAAA
Found at i:33768190 original size:62 final size:62
Alignment explanation
Indices: 33768028--33768628 Score: 812
Period size: 62 Copynumber: 9.9 Consensus size: 62
33768018 CATTAAAGAA
*
33768028 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGAAATTTCAA--TTGT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTTTGT
* * * *
33768088 TTAAATTGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTCAATTTTAT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTTTGT
* * *
33768150 TTAAATTGAATCTGTTGTGAGATAGGTCGAGCGTAGATTAAGTCTAGGAATTTCAA---T-T
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTTTGT
* * *
33768208 TTAAATCAAACCTGTTGTGAGATAAGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTTTGT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTTTGT
* * *
33768270 TTAAATCGAACC-GTTATGAGATAGGTCGAGCCTAAATTAAGTTTAGGAA-TTCAATTTTGT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTTTGT
* * * *
33768330 TTAAATCGAACCTATTGTGAGATAGGTTGAGCCTAGATTAAGTCTAGGAATTTTAATTGTGT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTTTGT
* * * * * *
33768392 TTAAATCGAACCTATTATGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTTAA--TT-C
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTTTGT
* *
33768451 TTAAATTCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAAGAATTTTAATTTTGT
1 TTAAA-TCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTTTGT
* * * * * *
33768514 TTAAATCGAACCTGCTATGAGATAGGTCAAGCCTAAATTAAGT-TTGAGAATTTCAATTTTTT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAG-GAATTTCAATTTTGT
33768576 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTT
33768629 TAATCGAATT
Statistics
Matches: 474, Mismatches: 53, Indels: 26
0.86 0.10 0.05
Matches are distributed among these distances:
58 51 0.11
59 6 0.01
60 121 0.26
61 67 0.14
62 222 0.47
63 7 0.01
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.36
Consensus pattern (62 bp):
TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTTTGT
Found at i:33768364 original size:122 final size:121
Alignment explanation
Indices: 33768028--33768632 Score: 867
Period size: 122 Copynumber: 5.0 Consensus size: 121
33768018 CATTAAAGAA
* * * *
33768028 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGAAATTTCAATTGTTTAAA
1 TTAAATCGAACCTGTTATGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTCAATT-TTTAAA
* * * * *
33768093 TTGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTCAATTTTAT
65 TCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTTTGT
* * * * * *
33768150 TTAAATTGAATCTGTTGTGAGATAGGTCGAGCGTAGATTAAGTCTAGGAATTTCAA-TTTTAAAT
1 TTAAATCGAACCTGTTATGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTCAATTTTTAAAT
* *
33768214 CAAACCTGTTGTGAGATAAGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTTTGT
66 CGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTTTGT
33768270 TTAAATCGAACC-GTTATGAGATAGGTCGAGCCTAAATTAAGTTTAGGAA-TTCAATTTTGTTTA
1 TTAAATCGAACCTGTTATGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTCAA--TT-TTTA
* * *
33768333 AATCGAACCTATTGTGAGATAGGTTGAGCCTAGATTAAGTCTAGGAATTTTAATTGTGT
63 AATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTTTGT
* * *
33768392 TTAAATCGAACCTATTATGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTTAATTCTTAAAT
1 TTAAATCGAACCTGTTATGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTCAATTTTTAAA-
*
33768457 TCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAAGAATTTTAATTTTGT
65 TCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTTTGT
* *
33768514 TTAAATCGAACCTGCTATGAGATAGGTCAAGCCTAAATTAAGTTT-GAGAATTTCAATTTTTTTT
1 TTAAATCGAACCTGTTATGAGATAGGTCGAGCCTAAATTAAGTTTAG-GAATTTCAA---TTTTT
33768578 AAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAAT
62 AAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAAT
33768633 CGAATTTGTT
Statistics
Matches: 437, Mismatches: 35, Indels: 20
0.89 0.07 0.04
Matches are distributed among these distances:
118 5 0.01
119 33 0.08
120 66 0.15
121 8 0.02
122 227 0.52
123 36 0.08
124 55 0.13
125 7 0.02
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.36
Consensus pattern (121 bp):
TTAAATCGAACCTGTTATGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTCAATTTTTAAAT
CGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTTTGT
Found at i:33768512 original size:184 final size:183
Alignment explanation
Indices: 33768028--33768632 Score: 857
Period size: 184 Copynumber: 3.3 Consensus size: 183
33768018 CATTAAAGAA
* *
33768028 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGAAATTTCAATTGTTTAAA
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTGTTTAAA
* *
33768093 TT-GAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTCAATTTTATTTAAATT
66 TTCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTCAATTTTGTTTAAATC
* *
33768157 GAATCTGTTGTGAGATAGGTCGAGCGTAGATTAAGTCTAGGAATTTCAA--TT
131 GAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTTT
* *
33768208 TTAAATCAAACCTGTTGTGAGATAAGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTTTGTTTA
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAA--TTGTTTA
*
33768273 AA-TCGAACC-GTTATGAGATAGGTCGAGCCTAAATTAAGTTTAGGAA-TTCAATTTTGTTTAAA
64 AATTCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTCAATTTTGTTTAAA
* * *
33768335 TCGAACCTATTGTGAGATAGGTTGAGCCTAGATTAAGTCTAGGAATTTTAATTGTGT
129 TCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATT-T-T
* * * * *
33768392 TTAAATCGAACCTATTATGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTTAATT-CTTAAA
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTGTTTAAA
* * * *
33768456 TTCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAAGAATTTTAATTTTGTTTAAATC
66 TTCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTCAATTTTGTTTAAATC
* * * * *
33768521 GAACCTGCTATGAGATAGGTCAAGCCTAAATTAAGT-TTGAGAATTTCAATTTTTT
131 GAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAG-GAATTTCAA--TTTT
33768576 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAAT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAAT
33768633 CGAATTTGTT
Statistics
Matches: 376, Mismatches: 36, Indels: 22
0.87 0.08 0.05
Matches are distributed among these distances:
180 112 0.30
181 42 0.11
182 23 0.06
183 36 0.10
184 160 0.43
185 1 0.00
186 2 0.01
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.36
Consensus pattern (183 bp):
TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTGTTTAAA
TTCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTCAATTTTGTTTAAATC
GAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTTT
Found at i:33768713 original size:51 final size:51
Alignment explanation
Indices: 33768579--33768716 Score: 150
Period size: 51 Copynumber: 2.7 Consensus size: 51
33768569 ATTTTTTTTA
* * * * *
33768579 AATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTT
1 AATCGAACTTGTTCTGAGATAGGTCGAGCCTAGATCAAGTCTAGAAATTTC
* * * * * *
33768630 AATCGAATTTGTTCTAATATGGGTCAAACCTAGATCAAGTCTAGAAATTTC
1 AATCGAACTTGTTCTGAGATAGGTCGAGCCTAGATCAAGTCTAGAAATTTC
* * *
33768681 AATCGAACTTATTTTGAGATAAGTCGAGCCTAGATC
1 AATCGAACTTGTTCTGAGATAGGTCGAGCCTAGATC
33768717 GAATTGATTA
Statistics
Matches: 67, Mismatches: 20, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
51 67 1.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (51 bp):
AATCGAACTTGTTCTGAGATAGGTCGAGCCTAGATCAAGTCTAGAAATTTC
Found at i:33768848 original size:17 final size:17
Alignment explanation
Indices: 33768826--33768875 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
33768816 AGACACCTTC
33768826 AAAATAAAATATATAAT
1 AAAATAAAATATATAAT
33768843 AAAATAAAATATGA-AAT
1 AAAATAAAATAT-ATAAT
* *
33768860 AAAATTATATATATAA
1 AAAATAAAATATATAA
33768876 AGAGAGGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 1 0.03
17 27 0.93
18 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (17 bp):
AAAATAAAATATATAAT
Found at i:33769491 original size:24 final size:25
Alignment explanation
Indices: 33769453--33769499 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
33769443 AGAGAAGAAG
*
33769453 AAAGAAAAAGGAAAAGAAAGAAATA
1 AAAGAAAAAGAAAAAGAAAGAAATA
*
33769478 AAAGAAAAA-AAAAAGAAGGAAA
1 AAAGAAAAAGAAAAAGAAAGAAA
33769500 AGGTTTTGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (25 bp):
AAAGAAAAAGAAAAAGAAAGAAATA
Found at i:33769900 original size:16 final size:16
Alignment explanation
Indices: 33769862--33769911 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
33769852 AGAAGAATAA
33769862 AGAAATAAAAA-AATAT
1 AGAAATAAAAAGAA-AT
33769878 A-ATAATAAAAAGAAAT
1 AGA-AATAAAAAGAAAT
*
33769894 AGAAATAATAAGTAAAT
1 AGAAATAAAAAG-AAAT
33769911 A
1 A
33769912 ATAAAATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 1 0.03
16 20 0.69
17 8 0.28
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.20
Consensus pattern (16 bp):
AGAAATAAAAAGAAAT
Found at i:33772282 original size:265 final size:266
Alignment explanation
Indices: 33771808--33772341 Score: 813
Period size: 265 Copynumber: 2.0 Consensus size: 266
33771798 AGATACTTGC
* * * * * *
33771808 TTAATGAACTTAATTTGATCAATTCCTATAGACATGTGGTGAATTAATTAAGTTAGGTCTTTGTA
1 TTAATGAACTTAATTTGATCAATTACTATAAACATATAGTGAACTAATTAAGTTAGGTATTTGTA
*
33771873 CAAGCATCTCGATGGACATTTGTTCATAGCTTTAGATTCTAGGTTAGTAAAACCACACACGAAAG
66 CAAGCATCTCGATGGACACTTGTTCATAGCTTTAGATTCTAGGTTAGTAAAACCACACACGAAAG
* * * * *** *
33771938 ATAAATAATAAGAAAAGTTGGTATCAAATGAAGTGTTGAATAAATTTATGATCCTATGTTTTTAA
131 ATAAATAACAAGAAAAGCTAGTATCAAATGAAGTGTTGAACAAACCAATGATCCTAGGTTTTTAA
*
33772003 TCTATTGCTTTTCTCAATATATTTAATTTTTGTTTATTAA-TTTAGTATTTCTTTTAAATTTTGT
196 TCTATTGCTTTTCTCAATATATTTAATTTTTGTTGATTAATTTTAGTATTTCTTTTAAATTTTGT
33772067 TTTTGA
261 TTTTGA
* *
33772073 TTAATGAACTTAATTTGATCAATTACTATAAACATATAGTGAACTACTTAATTTAGGTATTTGTA
1 TTAATGAACTTAATTTGATCAATTACTATAAACATATAGTGAACTAATTAAGTTAGGTATTTGTA
* *
33772138 C-AGACATCTTGATGGAGACTTG-TCTATAGCTTTAGATTCTAGGTTAGTAAAACCACACACGAA
66 CAAG-CATCTCGATGGACACTTGTTC-ATAGCTTTAGATTCTAGGTTAGTAAAACCACACACGAA
* *
33772201 AGATAAATAACAAGAAAAGCTAGTATTAGATGAAGTGTTGAACAAACCAATGATCCTAGGTTTTT
129 AGATAAATAACAAGAAAAGCTAGTATCAAATGAAGTGTTGAACAAACCAATGATCCTAGGTTTTT
* *
33772266 AATCTATTGTTTTTCTCAATATATTTAATTTTTGTTGGTTAATTTTAGTATTTCTTTTAAATTTT
194 AATCTATTGCTTTTCTCAATATATTTAATTTTTGTTGATTAATTTTAGTATTTCTTTTAAATTTT
33772331 GTTTTTGA
259 GTTTTTGA
33772339 TTA
1 TTA
33772342 GCTTTTTACT
Statistics
Matches: 242, Mismatches: 24, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
264 4 0.02
265 205 0.85
266 33 0.14
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (266 bp):
TTAATGAACTTAATTTGATCAATTACTATAAACATATAGTGAACTAATTAAGTTAGGTATTTGTA
CAAGCATCTCGATGGACACTTGTTCATAGCTTTAGATTCTAGGTTAGTAAAACCACACACGAAAG
ATAAATAACAAGAAAAGCTAGTATCAAATGAAGTGTTGAACAAACCAATGATCCTAGGTTTTTAA
TCTATTGCTTTTCTCAATATATTTAATTTTTGTTGATTAATTTTAGTATTTCTTTTAAATTTTGT
TTTTGA
Found at i:33772685 original size:2 final size:2
Alignment explanation
Indices: 33772678--33772721 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
33772668 CAAAGAGATC
33772678 AT AT AT AT AT AT 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 AT AT AT AT AT AT
33772720 AT
1 AT
33772722 GTAATTATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33779266 original size:2 final size:2
Alignment explanation
Indices: 33779259--33779294 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
33779249 TGTGGCCTTT
33779259 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA CTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
33779295 AATCGAAGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 29 0.91
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:33782170 original size:240 final size:241
Alignment explanation
Indices: 33781745--33782190 Score: 565
Period size: 240 Copynumber: 1.9 Consensus size: 241
33781735 TACAAAAAGA
* * *
33781745 AATAATGCAAATAGTGTTAGAAATACAATTAAGTCAACGACTAACTTTATCTTACACTTTACGAG
1 AATAATGCAAATAGTCTTAGAAATACAATTAAATCAACGACTAACTTTATCTTACACTTTACAAG
* * * * * *
33781810 AGTGAACCGTTAAATATACTTCGAGGGTTTGCAAAGTTATTTGACCTTAGAGCTTACTTTCTACA
66 AGTAAACCGCTAAATATAC-TCAAGGGTTTGCAAAGTCATTCGACCTTAGAACTTACTTTCTACA
* ** * * *
33781875 GCAAGTAAATTATAAGAAATTTATACGTTTTTGTAGTTAATGAAAATTTAAGTGTTTATATTAAT
130 ACAAGTAAATTATAAGAAATTTATACACTTTTATAGTTAATGAAAATTCAAGTGTTTATATAAAT
*
33781940 AGAATACAACACCTTTCTTGCTATTGATTATTCGGTATACGAAGGGG
195 AAAATACAACACCTTTCTTGCTATTGATTATTCGGTATACGAAGGGG
* * * * ** *
33781987 AATAATGCAAATAG-CTTAGAGATACAATTAAATCAATGTCTAACTTTGTCTTGTAGTTTACAAG
1 AATAATGCAAATAGTCTTAGAAATACAATTAAATCAACGACTAACTTTATCTTACACTTTACAAG
* * *
33782051 AGTAAACCGCTAGATATAAC-CAAGGGTTTGTAAAGTCATTCGACCTTAGAACTTACTTTTTACA
66 AGTAAACCGCTAAATAT-ACTCAAGGGTTTGCAAAGTCATTCGACCTTAGAACTTACTTTCTACA
* * * * *
33782115 ACAAGTAGATTATAAGGAATTTGA-ACACTTTTATAGTTGATGAGAATTCAAGTGTTTATGTAAA
130 ACAAGTAAATTATAAGAAATTT-ATACACTTTTATAGTTAATGAAAATTCAAGTGTTTATATAAA
33782179 TAAAATACAACA
194 TAAAATACAACA
33782191 TTTTTCCTAC
Statistics
Matches: 171, Mismatches: 31, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
240 100 0.58
241 55 0.32
242 16 0.09
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (241 bp):
AATAATGCAAATAGTCTTAGAAATACAATTAAATCAACGACTAACTTTATCTTACACTTTACAAG
AGTAAACCGCTAAATATACTCAAGGGTTTGCAAAGTCATTCGACCTTAGAACTTACTTTCTACAA
CAAGTAAATTATAAGAAATTTATACACTTTTATAGTTAATGAAAATTCAAGTGTTTATATAAATA
AAATACAACACCTTTCTTGCTATTGATTATTCGGTATACGAAGGGG
Found at i:33785176 original size:82 final size:82
Alignment explanation
Indices: 33785039--33785203 Score: 312
Period size: 82 Copynumber: 2.0 Consensus size: 82
33785029 TGCACTTTAC
33785039 GAGAGTAGACCGCTAGATACACCCAAGGGTTTATAAAATTGTTTGGCATTAGAGCCTACTTTCTG
1 GAGAGTAGACCGCTAGATACACCCAAGGGTTTATAAAATTGTTTGGCATTAGAGCCTACTTTCTG
33785104 CAACAAGTAGATTATAA
66 CAACAAGTAGATTATAA
* *
33785121 GAGAGTAGACCGCTAGATACACCCAATGGTTTATAAAATTGTTTGGCCTTAGAGCCTACTTTCTG
1 GAGAGTAGACCGCTAGATACACCCAAGGGTTTATAAAATTGTTTGGCATTAGAGCCTACTTTCTG
33785186 CAACAAGTAGATTATAA
66 CAACAAGTAGATTATAA
33785203 G
1 G
33785204 GAATTTGATG
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 81 1.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (82 bp):
GAGAGTAGACCGCTAGATACACCCAAGGGTTTATAAAATTGTTTGGCATTAGAGCCTACTTTCTG
CAACAAGTAGATTATAA
Found at i:33789056 original size:46 final size:47
Alignment explanation
Indices: 33788943--33789065 Score: 212
Period size: 47 Copynumber: 2.6 Consensus size: 47
33788933 AAGAAAAATG
33788943 TAGACAAGAAAAGTGTAAAAGGGCAAACATGACTACCTACAAAACAA
1 TAGACAAGAAAAGTGTAAAAGGGCAAACATGACTACCTACAAAACAA
* *
33788990 TAGACAAGAAAAGTGTAAAAGGGCAAACATGACTATCTACAAAGC-A
1 TAGACAAGAAAAGTGTAAAAGGGCAAACATGACTACCTACAAAACAA
*
33789036 TAGACAAGAAAAGTGTAAAAGGGAAAACAT
1 TAGACAAGAAAAGTGTAAAAGGGCAAACAT
33789066 ATGCCTACCT
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
46 30 0.41
47 43 0.59
ACGTcount: A:0.53, C:0.14, G:0.20, T:0.14
Consensus pattern (47 bp):
TAGACAAGAAAAGTGTAAAAGGGCAAACATGACTACCTACAAAACAA
Found at i:33801452 original size:87 final size:87
Alignment explanation
Indices: 33801330--33801505 Score: 280
Period size: 87 Copynumber: 2.0 Consensus size: 87
33801320 TTAGCGGTAA
* * **
33801330 ATACGCTACCCTCGAGACTTTATTTTCAGAAGACAAATTAATTAATCATGATACGCGTCTTAATT
1 ATACGCTACCCTCGACACTTTATTTTCAGAAGACAAATTAAATAATCATGATACGCACCTTAATT
33801395 TGATTTAATATTACCTTTAATT
66 TGATTTAATATTACCTTTAATT
* * *
33801417 ATACGTTACCCTCGACACTTTATTTTCAGGAGACAAATTAAATAATCATGATACGCACCTTACTT
1 ATACGCTACCCTCGACACTTTATTTTCAGAAGACAAATTAAATAATCATGATACGCACCTTAATT
*
33801482 TGATTTAATATTACTTTTAATT
66 TGATTTAATATTACCTTTAATT
33801504 AT
1 AT
33801506 TTTTAATTAA
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 81 1.00
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.39
Consensus pattern (87 bp):
ATACGCTACCCTCGACACTTTATTTTCAGAAGACAAATTAAATAATCATGATACGCACCTTAATT
TGATTTAATATTACCTTTAATT
Found at i:33802087 original size:21 final size:21
Alignment explanation
Indices: 33802063--33802105 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
33802053 TACTTAAGCC
33802063 TGCAATTTTGTGTACCAGACA
1 TGCAATTTTGTGTACCAGACA
33802084 TGCAATTTTGTGTACCAGACA
1 TGCAATTTTGTGTACCAGACA
33802105 T
1 T
33802106 ATAGACCTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (21 bp):
TGCAATTTTGTGTACCAGACA
Found at i:33802308 original size:14 final size:15
Alignment explanation
Indices: 33802289--33802319 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
33802279 TTATTTTTAT
33802289 AATTTT-AATTAATA
1 AATTTTCAATTAATA
33802303 AATTTTCAATTAATA
1 AATTTTCAATTAATA
33802318 AA
1 AA
33802320 ATTATTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTTTCAATTAATA
Found at i:33802370 original size:21 final size:22
Alignment explanation
Indices: 33802333--33802375 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
33802323 ATTTTATGAC
*
33802333 TTAATTGATAAATTAAA-ATTA
1 TTAATTGATAAAGTAAATATTA
33802354 TTAATTTGAT-AAGTAAATATTA
1 TTAA-TTGATAAAGTAAATATTA
33802376 AATATATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (22 bp):
TTAATTGATAAAGTAAATATTA
Found at i:33802440 original size:22 final size:22
Alignment explanation
Indices: 33802412--33802480 Score: 75
Period size: 22 Copynumber: 2.9 Consensus size: 22
33802402 AATATTATTG
*
33802412 ATAATTAAATTATTAATTTTAT
1 ATAATTAAATTATTAATTTTAA
*
33802434 ATAATTAAATATATAAAATTATTAA
1 ATAATTAAAT-TAT-TAATT-TTAA
33802459 ATTAATTAAAATTATTAATTTT
1 A-TAATT-AAATTATTAATTTT
33802481 TTAAATTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
22 10 0.26
23 3 0.08
24 6 0.15
25 8 0.21
26 8 0.21
27 4 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATAATTAAATTATTAATTTTAA
Found at i:33802484 original size:26 final size:24
Alignment explanation
Indices: 33802413--33802487 Score: 73
Period size: 26 Copynumber: 3.0 Consensus size: 24
33802403 ATATTATTGA
*
33802413 TAATTAAATTATTAA-TTTTATA-
1 TAATTAAATTATTAATTTTTAAAT
* *
33802435 TAATTAAATATATAAAATTATTAAAT
1 TAATTAAAT-TAT-TAATTTTTAAAT
33802461 TAATTAAAATTATTAATTTTTTAAAT
1 TAATT-AAATTATTAA-TTTTTAAAT
33802487 T
1 T
33802488 TATAAAGCTA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
22 9 0.21
23 3 0.07
24 2 0.05
25 7 0.17
26 17 0.40
27 4 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TAATTAAATTATTAATTTTTAAAT
Found at i:33802485 original size:17 final size:17
Alignment explanation
Indices: 33802346--33802478 Score: 64
Period size: 17 Copynumber: 7.8 Consensus size: 17
33802336 ATTGATAAAT
33802346 TAAAATTATTAATT-TGA
1 TAAAATTATTAATTAT-A
* *
33802363 TAAGTAAATATTAAATATA
1 TAA--AATTATTAATTATA
* * *
33802382 TTAAAATATATAAAATAAA
1 -TAAAAT-TATTAATTATA
* *
33802401 TAATATTATTGA-TA-A
1 TAAAATTATTAATTATA
* *
33802416 TTAAATTATTAATTTTA
1 TAAAATTATTAATTATA
*
33802433 TATAATTA--AA-TATA
1 TAAAATTATTAATTATA
33802447 TAAAATTATTAAATTA-A
1 TAAAATTATT-AATTATA
33802464 TTAAAATTATTAATT
1 -TAAAATTATTAATT
33802479 TTTTAAATTT
Statistics
Matches: 88, Mismatches: 16, Indels: 24
0.69 0.12 0.19
Matches are distributed among these distances:
14 10 0.11
15 12 0.14
16 3 0.03
17 21 0.24
18 19 0.22
19 19 0.22
20 4 0.05
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
TAAAATTATTAATTATA
Found at i:33812036 original size:27 final size:26
Alignment explanation
Indices: 33812006--33812063 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
33811996 AGGAACAAGT
* * *
33812006 AAAATGAACATCAACAGGAACAAACAG
1 AAAATAAAAATCAACAGCAACAAA-AG
*
33812033 AAAATAAAAATCAACATCAACAAAAG
1 AAAATAAAAATCAACAGCAACAAAAG
33812059 AAAAT
1 AAAAT
33812064 CCGACAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 7 0.26
27 20 0.74
ACGTcount: A:0.66, C:0.16, G:0.09, T:0.10
Consensus pattern (26 bp):
AAAATAAAAATCAACAGCAACAAAAG
Found at i:33825669 original size:8 final size:8
Alignment explanation
Indices: 33825656--33825713 Score: 53
Period size: 8 Copynumber: 6.5 Consensus size: 8
33825646 TGCAATTGTC
33825656 TATTTTTT
1 TATTTTTT
33825664 TATTTTTT
1 TATTTTTT
33825672 TATTATTTAAT
1 TATT-TTT--T
33825683 TATTATTTT
1 TATT-TTTT
*
33825692 CATTTTATTT
1 TA-TTT-TTT
33825702 TATTTTTT
1 TATTTTTT
33825710 TATT
1 TATT
33825714 ATCATATTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
8 19 0.44
9 9 0.21
10 6 0.14
11 9 0.21
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.78
Consensus pattern (8 bp):
TATTTTTT
Found at i:33825697 original size:27 final size:26
Alignment explanation
Indices: 33825656--33825748 Score: 71
Period size: 27 Copynumber: 3.3 Consensus size: 26
33825646 TGCAATTGTC
* *
33825656 TATTTTTTTATTTTTTTATTATTTAAT
1 TATTATTTTCTTTTTTTATT-TTTAAT
*
33825683 TATTATTTTCATTTTATTTTATTTTTTTAT
1 TATTATTTTC--TTT-TTTTA-TTTTTAAT
* *
33825713 TATCATATTTTC-TATTTTATTTCTAAT
1 TAT--TATTTTCTTTTTTTATTTTTAAT
33825740 TATTATTTT
1 TATTATTTT
33825749 TCATACTTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
25 6 0.11
27 17 0.31
28 5 0.09
29 4 0.07
30 13 0.24
31 2 0.04
32 7 0.13
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (26 bp):
TATTATTTTCTTTTTTTATTTTTAAT
Found at i:33825699 original size:33 final size:32
Alignment explanation
Indices: 33825669--33825734 Score: 91
Period size: 30 Copynumber: 2.1 Consensus size: 32
33825659 TTTTTTATTT
* *
33825669 TTTTATTATTTAATTAT-TATTTTC-ATTTTA
1 TTTTATTTTTTTATTATATATTTTCTATTTTA
33825699 TTTTATTTTTTTATTATCATATTTTCTATTTTA
1 TTTTATTTTTTTATTAT-ATATTTTCTATTTTA
33825732 TTT
1 TTT
33825735 CTAATTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 15 0.48
32 7 0.23
33 9 0.29
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.73
Consensus pattern (32 bp):
TTTTATTTTTTTATTATATATTTTCTATTTTA
Found at i:33825743 original size:38 final size:38
Alignment explanation
Indices: 33825663--33825749 Score: 90
Period size: 38 Copynumber: 2.3 Consensus size: 38
33825653 GTCTATTTTT
* *
33825663 TTATTTTTTTATTATTTAATTATTATTTTCATTTTATT
1 TTATTTTTTTATTATATAATTATTATTTTCATTTTATA
*
33825701 TTATTTTTTTATTATCAT-ATTTTCTATTTT-ATTTCTA-A
1 TTATTTTTTTATTAT-ATAATTAT-TATTTTCATTT-TATA
33825739 TTATTATTTTT
1 TTATT-TTTTT
33825750 CATACTTTAC
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
38 28 0.67
39 14 0.33
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (38 bp):
TTATTTTTTTATTATATAATTATTATTTTCATTTTATA
Found at i:33839993 original size:34 final size:33
Alignment explanation
Indices: 33839947--33840550 Score: 466
Period size: 34 Copynumber: 17.5 Consensus size: 33
33839937 AGCAGATAAC
* * *
33839947 CCAGCTTCAACTCTCCGTAACCGGCGGCAAGCAT
1 CCAGCTTTAACTCTCC-TAACCGGCGGCAAACAA
* * *
33839981 CCAGCTTTAACTCTCCCTCACCAGCAGCAAAACAAA
1 CCAGCTTTAACTCT-CCTAACCGGCGGC-AAAC-AA
* *
33840017 CCAGCTTTTACTCCTCCTAACCGGCGACCAAA-AA
1 CCAGCTTTAACT-CTCCTAACCGGCG-GCAAACAA
* ** *
33840051 CCAGCTTTTACTCCTCCTAACCGGCGGCATGCAT
1 CCAGCTTTAACT-CTCCTAACCGGCGGCAAACAA
** *
33840085 CCAGCTTTTAACTCTCCTAACCGGCGGCATGCAT
1 CCAGC-TTTAACTCTCCTAACCGGCGGCAAACAA
* * ** *
33840119 CCAGCTTTTACTCCTCCTAACCGGAGGCATGCAT
1 CCAGCTTTAACT-CTCCTAACCGGCGGCAAACAA
* * *
33840153 CCAGCTTTAACTCTCCCTCACCAGCAGCAAACAAA
1 CCAGCTTTAACTCT-CCTAACCGGCGGCAAAC-AA
**
33840188 CCAGCTTTTGCTCCTCCTAACCGGCGGCCAAA-AA
1 CCAGCTTTAACT-CTCCTAACCGGCGG-CAAACAA
* * *
33840222 CCAGCTTTAACTCTCCCTCACCAGCAGCAAACAAA
1 CCAGCTTTAACTCT-CCTAACCGGCGGCAAAC-AA
* * *
33840257 CCAGCTTTTACTCCTCCTAAACGGCGGTC-AAGAA
1 CCAGCTTTAACT-CTCCTAACCGGCGG-CAAACAA
33840291 CCAGCTTTTAACTCTCCTAACCGGCGGCAAACAA
1 CCAGC-TTTAACTCTCCTAACCGGCGGCAAACAA
* * *
33840325 CCCAGCTTTTACCTCTCCTAACCGGCTGTAAA-AA
1 -CCAGC-TTTAACTCTCCTAACCGGCGGCAAACAA
* * *
33840359 CCAGCTTTTAACTCTCCCTCACCAGCAGCAAAACAAA
1 CCAGC-TTTAACTCT-CCTAACCGGCGGC-AAAC-AA
* * *
33840396 CCAGCTTTTACTCCTCCTAAACGGCGGTC-AAGAA
1 CCAGCTTTAACT-CTCCTAACCGGCGG-CAAACAA
33840430 CCAGCTTTTAACTCTCCTAACCGGCGGCAAA-AA
1 CCAGC-TTTAACTCTCCTAACCGGCGGCAAACAA
* * *
33840463 CCAACTTTTAAGTCTCCCTCACCGGCGGCAAACAA
1 CCAGC-TTTAACTCT-CCTAACCGGCGGCAAACAA
*
33840498 CCCAGCTTTTACCTCTCCTAACCGGCGGCAAA-AA
1 -CCAGC-TTTAACTCTCCTAACCGGCGGCAAACAA
33840532 CCCAGCTTTTAACTCTCCT
1 -CCAGC-TTTAACTCTCCT
33840551 GCACCCACCC
Statistics
Matches: 470, Mismatches: 69, Indels: 62
0.78 0.11 0.10
Matches are distributed among these distances:
33 47 0.10
34 236 0.50
35 116 0.25
36 58 0.12
37 13 0.03
ACGTcount: A:0.27, C:0.37, G:0.14, T:0.22
Consensus pattern (33 bp):
CCAGCTTTAACTCTCCTAACCGGCGGCAAACAA
Done.