Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 167 of 202
Found at i:52238886 original size:58 final size:59
Alignment explanation
Indices: 52238821--52238939 Score: 177
Period size: 60 Copynumber: 2.0 Consensus size: 59
52238811 TTTTTCACTG
* *
52238821 TTTTTCTAGATTTTACAGTTTTGCCACT-TGTTTCCAAAATTTACAGTTCTGCCACTAT
1 TTTTTCTAAATTTTACAATTTTGCCACTGTGTTTCCAAAATTTACAGTTCTGCCACTAT
* * *
52238879 TTTTTCTAAATTTTACAATTTTGCCACTGGTTTTTCCAAATTTTACAGTTTTGCCACTAT
1 TTTTTCTAAATTTTACAATTTTGCCACT-GTGTTTCCAAAATTTACAGTTCTGCCACTAT
52238939 T
1 T
52238940 CTTGAAAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
58 26 0.48
60 28 0.52
ACGTcount: A:0.23, C:0.19, G:0.09, T:0.49
Consensus pattern (59 bp):
TTTTTCTAAATTTTACAATTTTGCCACTGTGTTTCCAAAATTTACAGTTCTGCCACTAT
Found at i:52238955 original size:60 final size:58
Alignment explanation
Indices: 52238833--52238960 Score: 148
Period size: 60 Copynumber: 2.2 Consensus size: 58
52238823 TTTCTAGATT
* *** **
52238833 TTACAGTTTTGCCACTTGTTTCCAAAATTTACAGTTCTGCCACTATTTTTTCTAAATT
1 TTACAGTTTTGCCACTTGTTTCCAAAATTTACAGTTCTGCCACTATTCTTGAAAAAAA
* * * *
52238891 TTACAATTTTGCCACTGGTTTTTCCAAATTTTACAGTTTTGCCACTATTCTTGAAAAAAA
1 TTACAGTTTTGCCACT--TGTTTCCAAAATTTACAGTTCTGCCACTATTCTTGAAAAAAA
52238951 TTACAGTTTT
1 TTACAGTTTT
52238961 ATTGTGACAG
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
58 15 0.26
60 42 0.74
ACGTcount: A:0.27, C:0.19, G:0.09, T:0.45
Consensus pattern (58 bp):
TTACAGTTTTGCCACTTGTTTCCAAAATTTACAGTTCTGCCACTATTCTTGAAAAAAA
Found at i:52239641 original size:136 final size:135
Alignment explanation
Indices: 52239384--52239760 Score: 497
Period size: 136 Copynumber: 2.8 Consensus size: 135
52239374 TGCATTTAAT
* * * ** *
52239384 TGTGCGTTGTGTACCCACAGCAAAAGCATATTCCAACTGCGTCCATTTTACCATGCAAGCACAAC
1 TGTGCGCTGTGTATCCACAGCAAAAGCAGATTCCAACTGCGTCCATTTTACTGTGGAA-CACAAC
*
52239449 CCTCTGACAACTTTTATCTGTGAGTATGTTGTGCTTCCACTGCAATTGACAAATTTTATCTGCAT
65 CCTCTGACAACTTTTATCTGCGAGTATGTTGTGCTTCCACTGCAATTGACAAATTTTATCTGCAT
*
52239514 TATATG
130 TATATA
* *
52239520 TGTGCGCTGTGTATCCACAGAAAAAACAGATTCCAACTGCGTCCATTTTACTGTGTGAACACAAC
1 TGTGCGCTGTGTATCCACAGCAAAAGCAGATTCCAACTGCGTCCATTTTACTGTG-GAACACAAC
* * * * *
52239585 CCTCTGACAGCTTTTTTCTGCGAGTATGTTGTGCTTCCA-TGGCTATTAGA-AGATTTTATTTGC
65 CCTCTGACAACTTTTATCTGCGAGTATGTTGTGCTTCCACT-GCAATT-GACAAATTTTATCTGC
52239648 ATTATATA
128 ATTATATA
* * * * *
52239656 TGTGCGCTGTGTATCCACAGCAAAAGCAGATTCCAAATGCGTCCATTTTATTGTACGAGCAGAAC
1 TGTGCGCTGTGTATCCACAGCAAAAGCAGATTCCAACTGCGTCCATTTTACTGT-GGAACACAAC
* *
52239721 CCTCTGACAACTTTTATCTGCGAGCATGTCGTGCTTCCAC
65 CCTCTGACAACTTTTATCTGCGAGTATGTTGTGCTTCCAC
52239761 GGCCAGTGGC
Statistics
Matches: 210, Mismatches: 26, Indels: 9
0.86 0.11 0.04
Matches are distributed among these distances:
135 1 0.00
136 205 0.98
137 4 0.02
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.33
Consensus pattern (135 bp):
TGTGCGCTGTGTATCCACAGCAAAAGCAGATTCCAACTGCGTCCATTTTACTGTGGAACACAACC
CTCTGACAACTTTTATCTGCGAGTATGTTGTGCTTCCACTGCAATTGACAAATTTTATCTGCATT
ATATA
Found at i:52240149 original size:37 final size:37
Alignment explanation
Indices: 52240065--52240166 Score: 105
Period size: 37 Copynumber: 2.8 Consensus size: 37
52240055 TTTACCATAT
* * * **
52240065 TGAATTGATTGATATGCGAGATTGCTTGTTATTATGT
1 TGAATTGATTGATATGCGAAATTGTTTGTCATTATAC
* * * *
52240102 TAAATAGATTGATATGCGAAACTGTTTGTCATTGTAC
1 TGAATTGATTGATATGCGAAATTGTTTGTCATTATAC
* *
52240139 TGAATTGATTGACATGTGAAATTGTTTG
1 TGAATTGATTGATATGCGAAATTGTTTG
52240167 CTATTACTGT
Statistics
Matches: 51, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.28, C:0.07, G:0.23, T:0.42
Consensus pattern (37 bp):
TGAATTGATTGATATGCGAAATTGTTTGTCATTATAC
Found at i:52241310 original size:3 final size:3
Alignment explanation
Indices: 52241302--52241336 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
52241292 ATATAATTCA
52241302 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
52241337 AAGAAACCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:52241662 original size:19 final size:19
Alignment explanation
Indices: 52241640--52241682 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
52241630 TTTGCAAGTG
52241640 TAAATGGTATTTTTAAATA
1 TAAATGGTATTTTTAAATA
52241659 TAAATGGTATTTTTAAATA
1 TAAATGGTATTTTTAAATA
52241678 TAAAT
1 TAAAT
52241683 TAATACATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (19 bp):
TAAATGGTATTTTTAAATA
Found at i:52250183 original size:9 final size:9
Alignment explanation
Indices: 52250166--52250202 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
52250156 TGAGTTTTCA
52250166 AATTCGAAT
1 AATTCGAAT
*
52250175 AACTCGAAT
1 AATTCGAAT
52250184 AATTCGAAT
1 AATTCGAAT
52250193 AATTCGAAT
1 AATTCGAAT
52250202 A
1 A
52250203 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:52250450 original size:30 final size:31
Alignment explanation
Indices: 52250416--52250475 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
52250406 AAACCTTTTA
*
52250416 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
52250446 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
52250476 TCTCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:52252097 original size:29 final size:29
Alignment explanation
Indices: 52252062--52252118 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
52252052 CCAATTAATT
*
52252062 TTATTTCTCTTAATTTATTTTGCAATCAC
1 TTATTTCGCTTAATTTATTTTGCAATCAC
52252091 TTATTTCGCTTAATTTATTTTGCAATCA
1 TTATTTCGCTTAATTTATTTTGCAATCA
52252119 TGTTTTTACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.25, C:0.16, G:0.05, T:0.54
Consensus pattern (29 bp):
TTATTTCGCTTAATTTATTTTGCAATCAC
Found at i:52257304 original size:37 final size:37
Alignment explanation
Indices: 52257262--52257373 Score: 109
Period size: 37 Copynumber: 3.0 Consensus size: 37
52257252 GCTTACAAGG
52257262 GACCCATAAGAATGTTCCCTTACTGACTCATATTCGA
1 GACCCATAAGAATGTTCCCTTACTGACTCATATTCGA
* *** * *** *
52257299 TACCCATAAGAATGTGGGCTTACCAT-ACTGCTTACAAGG
1 GACCCATAAGAATGTTCCCTTA-C-TGACT-CATATTCGA
52257338 GACCCATAAGAATGTTCCCTTACTGACTCATATTCG
1 GACCCATAAGAATGTTCCCTTACTGACTCATATTCG
52257374 GTAAACTGTG
Statistics
Matches: 54, Mismatches: 17, Indels: 8
0.68 0.22 0.10
Matches are distributed among these distances:
37 23 0.43
38 8 0.15
39 23 0.43
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (37 bp):
GACCCATAAGAATGTTCCCTTACTGACTCATATTCGA
Found at i:52257360 original size:39 final size:39
Alignment explanation
Indices: 52257241--52257360 Score: 129
Period size: 39 Copynumber: 3.1 Consensus size: 39
52257231 GCATTGTGGG
52257241 CTTACCATACTGCTTACAAGGGACCCATAAGAATGTTCC
1 CTTACCATACTGCTTACAAGGGACCCATAAGAATGTTCC
* *** ** ***
52257280 CTTA-C-TGACT-CATATTCGATACCCATAAGAATGTGGG
1 CTTACCAT-ACTGCTTACAAGGGACCCATAAGAATGTTCC
52257317 CTTACCATACTGCTTACAAGGGACCCATAAGAATGTTCC
1 CTTACCATACTGCTTACAAGGGACCCATAAGAATGTTCC
52257356 CTTAC
1 CTTAC
52257361 TGACTCATAT
Statistics
Matches: 59, Mismatches: 18, Indels: 8
0.69 0.21 0.09
Matches are distributed among these distances:
37 23 0.39
38 8 0.14
39 28 0.47
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.28
Consensus pattern (39 bp):
CTTACCATACTGCTTACAAGGGACCCATAAGAATGTTCC
Found at i:52259410 original size:26 final size:26
Alignment explanation
Indices: 52259381--52259430 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
52259371 TGTATTTTTA
*
52259381 ATTTCA-TAATAATATAAAAATATAAT
1 ATTTCATTAAAAAT-TAAAAATATAAT
*
52259407 ATTTTATTAAAAATTAAAAATATA
1 ATTTCATTAAAAATTAAAAATATA
52259431 TAGAATTACT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (26 bp):
ATTTCATTAAAAATTAAAAATATAAT
Found at i:52266537 original size:24 final size:23
Alignment explanation
Indices: 52266501--52266546 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
52266491 GACTAATTAT
*
52266501 AAAAAATATTATTGAATTGAAAA
1 AAAAAATATTATTAAATTGAAAA
*
52266524 AAAAAATTTGTATTAAATTGAAA
1 AAAAAATAT-TATTAAATTGAAA
52266547 TCTAATTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.33
Consensus pattern (23 bp):
AAAAAATATTATTAAATTGAAAA
Found at i:52267651 original size:15 final size:15
Alignment explanation
Indices: 52267615--52267643 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
52267605 TATTTGGCTT
52267615 TATTTTTATTTATTA
1 TATTTTTATTTATTA
52267630 TATTTTTATTTATT
1 TATTTTTATTTATT
52267644 TGTTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TATTTTTATTTATTA
Found at i:52267658 original size:13 final size:14
Alignment explanation
Indices: 52267617--52267650 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
52267607 TTTGGCTTTA
*
52267617 TTTTTATTTATTATA
1 TTTTTATTTATT-TG
52267632 TTTTTATTTATTTG
1 TTTTTATTTATTTG
52267646 TTTTT
1 TTTTT
52267651 TTTTTTTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (14 bp):
TTTTTATTTATTTG
Found at i:52270837 original size:21 final size:21
Alignment explanation
Indices: 52270812--52270853 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
52270802 CATTAATCAG
52270812 ATTGAAGATACATAATTTGGT
1 ATTGAAGATACATAATTTGGT
52270833 ATTGAAGATACATAATTTGGT
1 ATTGAAGATACATAATTTGGT
52270854 TAATTTATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.19, T:0.38
Consensus pattern (21 bp):
ATTGAAGATACATAATTTGGT
Found at i:52271458 original size:16 final size:16
Alignment explanation
Indices: 52271437--52271480 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 16
52271427 CAATTAAAAC
52271437 AAATAATTAAGATAAA-
1 AAATAATTAA-ATAAAG
52271453 AAATAATTAAATAAATG
1 AAATAATTAAATAAA-G
52271470 AAATAATTAAA
1 AAATAATTAAA
52271481 CAAGAACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.19
16 10 0.38
17 11 0.42
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (16 bp):
AAATAATTAAATAAAG
Found at i:52273051 original size:41 final size:40
Alignment explanation
Indices: 52273003--52273102 Score: 137
Period size: 41 Copynumber: 2.5 Consensus size: 40
52272993 GTATTACCGA
* * *
52273003 ATCAATGAAAAGGTTGAAAATGAAGTTATTCGAAAAGTAT
1 ATCAATGAAAAGGTTGAAAAGGAAGTTATCCGAAAAGGAT
* *
52273043 ATCAAATGAAAAGGTTCAAAAGGATGTTATCCGAAAAGGAT
1 ATC-AATGAAAAGGTTGAAAAGGAAGTTATCCGAAAAGGAT
*
52273084 ATCAATGAAAAGGCTGAAA
1 ATCAATGAAAAGGTTGAAA
52273103 GGATATCAGT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
40 17 0.33
41 35 0.67
ACGTcount: A:0.48, C:0.08, G:0.21, T:0.23
Consensus pattern (40 bp):
ATCAATGAAAAGGTTGAAAAGGAAGTTATCCGAAAAGGAT
Found at i:52273139 original size:24 final size:24
Alignment explanation
Indices: 52273074--52273192 Score: 154
Period size: 24 Copynumber: 5.0 Consensus size: 24
52273064 GGATGTTATC
52273074 CGAAAAGGATATCAATGAAAAGG-
1 CGAAAAGGATATCAATGAAAAGGT
*
52273097 CTG-AAAGGATATCAGTGAAAAGGT
1 C-GAAAAGGATATCAATGAAAAGGT
* *
52273121 AGAAAAAGATATCAATGAAAAGGT
1 CGAAAAGGATATCAATGAAAAGGT
*
52273145 CGAAAAGGATATCAATTAAAAGGT
1 CGAAAAGGATATCAATGAAAAGGT
* *
52273169 CGAAAGGGATAGCAATG-AAAGGT
1 CGAAAAGGATATCAATGAAAAGGT
52273192 C
1 C
52273193 AATATCTCAT
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
23 28 0.34
24 55 0.66
ACGTcount: A:0.49, C:0.08, G:0.26, T:0.17
Consensus pattern (24 bp):
CGAAAAGGATATCAATGAAAAGGT
Found at i:52274369 original size:26 final size:26
Alignment explanation
Indices: 52274332--52274382 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
52274322 TTTGGCAATG
52274332 CTTTTGAAAAGTGCTGTGGAAAAATA
1 CTTTTGAAAAGTGCTGTGGAAAAATA
* * *
52274358 CTTTTGAGAAGTGCTTTTGAAAAAT
1 CTTTTGAAAAGTGCTGTGGAAAAAT
52274383 TTAACTGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.35
Consensus pattern (26 bp):
CTTTTGAAAAGTGCTGTGGAAAAATA
Found at i:52274376 original size:13 final size:13
Alignment explanation
Indices: 52274330--52274380 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
52274320 AGTTTGGCAA
52274330 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* * *
52274343 TGCTGTGGAAAAA
1 TGCTTTTGAAAAG
* *
52274356 TACTTTTGAGAAG
1 TGCTTTTGAAAAG
52274369 TGCTTTTGAAAA
1 TGCTTTTGAAAA
52274381 ATTTAACTGT
Statistics
Matches: 28, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.33, C:0.08, G:0.24, T:0.35
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:52274641 original size:24 final size:23
Alignment explanation
Indices: 52274612--52274669 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
52274602 TATTTATTAA
52274612 ATTTAATTAGAAT-ATATAAACTAT
1 ATTTAATTAGAATAAT-TAAA-TAT
* *
52274636 ATTTAAATATAATAATTAAATAT
1 ATTTAATTAGAATAATTAAATAT
*
52274659 TTTTAATTAGA
1 ATTTAATTAGA
52274670 TATTGACACA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 11 0.39
24 15 0.54
25 2 0.07
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (23 bp):
ATTTAATTAGAATAATTAAATAT
Found at i:52277827 original size:12 final size:12
Alignment explanation
Indices: 52277788--52277831 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
52277778 CTTAACTCCC
*
52277788 TTTTTTTAAATA
1 TTTTTTAAAATA
* *
52277800 ATTTTAAAAATA
1 TTTTTTAAAATA
52277812 TTTTTTAAAAT-
1 TTTTTTAAAATA
52277823 TTTTTTAAA
1 TTTTTTAAA
52277832 CCGTAAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
11 9 0.33
12 18 0.67
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTTTTTAAAATA
Found at i:52278944 original size:7 final size:7
Alignment explanation
Indices: 52278932--52278963 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
52278922 AGTCGATTGA
52278932 TATTTAG
1 TATTTAG
52278939 TATTTAG
1 TATTTAG
52278946 TATTTAG
1 TATTTAG
52278953 TATTTAG
1 TATTTAG
52278960 TATT
1 TATT
52278964 ATGTATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.59
Consensus pattern (7 bp):
TATTTAG
Found at i:52280311 original size:28 final size:23
Alignment explanation
Indices: 52280142--52280419 Score: 225
Period size: 23 Copynumber: 12.2 Consensus size: 23
52280132 ATTAATACCC
52280142 TTAAATTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
* **
52280165 TTTAATTAAAAACTTTAAACCCT-A
1 TTAAATTAAAAACCCT-AA-CCTAA
* ***
52280189 --AACTTAAAAACCCTAACCCCC
1 TTAAATTAAAAACCCTAACCTAA
* *
52280210 TTAACATAAAAAACTCTAAACCCT-A
1 TTAA-ATTAAAAACCCT-AA-CCTAA
*
52280235 --AACTTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
*
52280256 TTAACTTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
52280279 TTAAATTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
* *
52280302 GTAAATTAAAAACCTTAAACCCT-A
1 TTAAATTAAAAACCCT-AA-CCTAA
* * **
52280326 --AACTTAAAAACCTTAACC-CC
1 TTAAATTAAAAACCCTAACCTAA
*
52280346 TTAACTTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
*
52280369 TTAAATTAAAAACCTTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
* *
52280392 TTTAATTAAAAACCCTAAACTAAA
1 TTAAATTAAAAACCCTAACCT-AA
52280416 TTAA
1 TTAA
52280420 TAATTTTACT
Statistics
Matches: 206, Mismatches: 31, Indels: 35
0.76 0.11 0.13
Matches are distributed among these distances:
20 7 0.03
21 7 0.03
22 49 0.24
23 113 0.55
24 20 0.10
25 8 0.04
26 2 0.01
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (23 bp):
TTAAATTAAAAACCCTAACCTAA
Found at i:52280377 original size:90 final size:91
Alignment explanation
Indices: 52280128--52280411 Score: 312
Period size: 90 Copynumber: 3.1 Consensus size: 91
52280118 GAATTCTACT
**
52280128 AACCATTAATACCCTTAAA-TTAAAAACCCTAACCTAATTTAA-TTAAAAACTTTAAACCCT-A-
1 AACC-TTAA-ACCC-TAAACTTAAAAACCCTAACCTAA-TTAACTTAAAAACCCT-AA-CCTAAT
* ****
52280189 -AACTTAAAAACCCTAACCCCCTTAACA-TAAA
60 TAAATTAAAAACCCTAACCTAAGTAA-ATTAAA
*
52280220 AAACTCTAAACCCTAAACTTAAAAACCCTAACCTAATTAACTTAAAAACCCTAACCTAATTAAAT
1 AACCT-TAAACCCTAAACTTAAAAACCCTAACCTAATTAACTTAAAAACCCTAACCTAATTAAAT
52280285 TAAAAACCCTAACCTAAGTAAATTAAA
65 TAAAAACCCTAACCTAAGTAAATTAAA
* **
52280312 AACCTTAAACCCTAAACTTAAAAACCTTAACC-CCTTAACTTAAAAACCCTAACCTAATTAAATT
1 AACCTTAAACCCTAAACTTAAAAACCCTAACCTAATTAACTTAAAAACCCTAACCTAATTAAATT
* * *
52280376 AAAAACCTTAACCTAATTTAATTAAA
66 AAAAACCCTAACCTAAGTAAATTAAA
*
52280402 AACCCTAAAC
1 AACCTTAAAC
52280412 TAAATTAATA
Statistics
Matches: 169, Mismatches: 16, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
89 3 0.02
90 73 0.43
91 59 0.35
92 34 0.20
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.25
Consensus pattern (91 bp):
AACCTTAAACCCTAAACTTAAAAACCCTAACCTAATTAACTTAAAAACCCTAACCTAATTAAATT
AAAAACCCTAACCTAAGTAAATTAAA
Found at i:52280378 original size:113 final size:113
Alignment explanation
Indices: 52280142--52280415 Score: 365
Period size: 113 Copynumber: 2.4 Consensus size: 113
52280132 ATTAATACCC
** *
52280142 TTAAATTAAAAACCCTAACCTAATTTAATTAAAAACTTTAAACCCT-AAACTTAAAAACCCTAAC
1 TTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCT-AA-CCTAAAAATTAAAAACCCTAAC
* *
52280206 CCCCTTAACATAAAAAACTCTAAACCCTAAACTTAAAAACCCTAACCTAA
64 ACCCTAAACATAAAAAACTCTAAACCCTAAACTTAAAAACCCTAACCTAA
* * *
52280256 TTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAAGTAAATTAAAAACCTTAA-
1 TTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAA--AAATTAAAAACCCTAAC
* * * *
52280320 ACCCTAAACTTAAAAACCT-TAACCCCTTAACTTAAAAACCCTAACCTAA
64 ACCCTAAACATAAAAAACTCTAAACCCTAAACTTAAAAACCCTAACCTAA
* *
52280369 TTAAATTAAAAACCTTAACCTAATTTAATTAAAAACCCTAAACTAAA
1 TTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAAA
52280416 TTAATAATTT
Statistics
Matches: 141, Mismatches: 16, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
111 1 0.01
112 3 0.02
113 73 0.52
114 50 0.35
115 14 0.10
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (113 bp):
TTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAAAAATTAAAAACCCTAACAC
CCTAAACATAAAAAACTCTAAACCCTAAACTTAAAAACCCTAACCTAA
Found at i:52280587 original size:117 final size:117
Alignment explanation
Indices: 52280414--52280777 Score: 647
Period size: 117 Copynumber: 3.1 Consensus size: 117
52280404 CCCTAAACTA
* ** ** **
52280414 AATTAATAATTTTACTTTCACATAATGTTAGATTTGGAAAAATGTTTTTTTCCTGGTACTAACAA
1 AATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAGCGGGTTTTGACTGGTACTAACAA
52280479 TTAATAATTTTATATAATTTGATAATTTTACTAATCATTAATACAATTTATC
66 TTAATAATTTTATATAATTTGATAATTTTACTAATCATTAATACAATTTATC
*
52280531 AATTAATAATTTTACATTCACATAATATTAGATTTGGAAAAGCGGGTTTTGACTGGTACTAACAA
1 AATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAGCGGGTTTTGACTGGTACTAACAA
52280596 TTAATAATTTTATATAATTTGATAATTTTACTAATCATTAATACAATTTATC
66 TTAATAATTTTATATAATTTGATAATTTTACTAATCATTAATACAATTTATC
52280648 AATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAGCGGGTTTTGACTGGTACTAACAA
1 AATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAGCGGGTTTTGACTGGTACTAACAA
52280713 TTAATAATTTTATATAATTTGATAATTTTTACTAATCATTAATACAATTTATC
66 TTAATAATTTTATATAATTTGATAA-TTTTACTAATCATTAATACAATTTATC
52280766 AATTAATAATTT
1 AATTAATAATTT
52280778 CAGAAACTTA
Statistics
Matches: 237, Mismatches: 9, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
117 198 0.84
118 39 0.16
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.44
Consensus pattern (117 bp):
AATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAGCGGGTTTTGACTGGTACTAACAA
TTAATAATTTTATATAATTTGATAATTTTACTAATCATTAATACAATTTATC
Found at i:52284091 original size:123 final size:123
Alignment explanation
Indices: 52283805--52284136 Score: 547
Period size: 123 Copynumber: 2.7 Consensus size: 123
52283795 NNNNNNNGCA
52283805 TCCACGAGGGCGCGATTTTCACAAATTCTTCTCAAATAGCATCCTGCTAGAAGCGATTTTATACT
1 TCCACGAGGGCGCGA-TTTCACAAATTCTTCTCAAATAGCATCCTGCTAGAAGCGATTTTATACT
* * *
52283870 ATTTGCTCAGAAACGTCAAAAAAAAATTGTTTCTTCCATGATCGACTGTAGCAAAAGCGCT
65 ATTTGCTCAGAAACGTC--AAAAAAATTATTTCTTCCATGACCGACTGTAGCAAAAGCGCG
* * *
52283931 TCCACGAGGGCGCAATTTTACAAATTCTTCTCAAATAGAATCCTGCTAGAAGCGATTTTATACTA
1 TCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTAGAAGCGATTTTATACTA
* *
52283996 TTTGCTCAGAAACGTCAAAAAAATTATTTCTTCCATGACCTACTGTAGCCAAAGCGCG
66 TTTGCTCAGAAACGTCAAAAAAATTATTTCTTCCATGACCGACTGTAGCAAAAGCGCG
*
52284054 TCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTAGAAGCGATTCTATACTA
1 TCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTAGAAGCGATTTTATACTA
*
52284119 TTTGATCAGAAACGTCAA
66 TTTGCTCAGAAACGTCAA
52284137 CTCGAAATTA
Statistics
Matches: 193, Mismatches: 13, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
123 115 0.60
125 64 0.33
126 14 0.07
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (123 bp):
TCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTAGAAGCGATTTTATACTA
TTTGCTCAGAAACGTCAAAAAAATTATTTCTTCCATGACCGACTGTAGCAAAAGCGCG
Found at i:52287786 original size:24 final size:24
Alignment explanation
Indices: 52287759--52287810 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
52287749 AATCACAGTC
* *
52287759 AAATATATTATGCTAATAAATACT
1 AAATACATTATACTAATAAATACT
*
52287783 AAATACATTATACTCATAAATACT
1 AAATACATTATACTAATAAATACT
52287807 AAAT
1 AAAT
52287811 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.52, C:0.12, G:0.02, T:0.35
Consensus pattern (24 bp):
AAATACATTATACTAATAAATACT
Found at i:52291189 original size:21 final size:22
Alignment explanation
Indices: 52291154--52291196 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
52291144 AAAACAGGTT
**
52291154 TTTAGCGGCGTTTTTTA-TGCC
1 TTTAGCGGCACTTTTTAGTGCC
52291175 TTTAGCGGCACTTTTTAGTGCC
1 TTTAGCGGCACTTTTTAGTGCC
52291197 GCTAAAAGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.12, C:0.21, G:0.23, T:0.44
Consensus pattern (22 bp):
TTTAGCGGCACTTTTTAGTGCC
Found at i:52291313 original size:42 final size:43
Alignment explanation
Indices: 52291254--52291556 Score: 474
Period size: 42 Copynumber: 7.2 Consensus size: 43
52291244 TGTTGCTAAT
*
52291254 GCCGCTATAGATCAGGACCTTTAGCGGCGC-TTCCCCACAAAC
1 GCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCACAAAC
52291296 GCCGCTATAGATCAGGACCTTTAGCGGCGC--TTCCCTACAAAC
1 GCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCC-ACAAAC
*
52291338 GCCGCTATAGATCAAGACCTTTAGCGGCGCTTTT-CCACAAAC
1 GCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCACAAAC
* * *
52291380 GCCGCTATAGCTCAAGATCTTTAGCGGCGCTTTTCCCACAAAC
1 GCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCACAAAC
*
52291423 GCCGCTATAGAGCA-GACCTTTAGCGGCGCTTTTCCCACAAAC
1 GCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCACAAAC
*
52291465 GCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCACACAAAC
1 GCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCACAAAC
* *
52291508 GCCGCTATAGAACA-GACCTTTAGCGGCGCTTTTCACACAAAC
1 GCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCACAAAC
52291550 GCCGCTA
1 GCCGCTA
52291557 AAAACATATC
Statistics
Matches: 246, Mismatches: 10, Indels: 10
0.92 0.04 0.04
Matches are distributed among these distances:
41 4 0.02
42 178 0.72
43 62 0.25
44 2 0.01
ACGTcount: A:0.25, C:0.33, G:0.20, T:0.22
Consensus pattern (43 bp):
GCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCACAAAC
Found at i:52291432 original size:127 final size:127
Alignment explanation
Indices: 52291254--52291556 Score: 479
Period size: 127 Copynumber: 2.4 Consensus size: 127
52291244 TGTTGCTAAT
* * *
52291254 GCCGCTATAGATCAGGACCTTTAGCGGCGC-TTCCCCACAAACGCCGCTATAGATCAGGACCTTT
1 GCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAGCA-GACCTTT
52291318 AGCGGCGC-TTCCCTACAAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTC-CACAAAC
65 AGCGGCGCTTTCCC-ACAAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCACACAAAC
* *
52291380 GCCGCTATAGCTCAAGATCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAGCAGACCTTTA
1 GCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAGCAGACCTTTA
*
52291445 GCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCACACAAAC
66 GCGGCGC-TTTCCCACAAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCACACAAAC
* *
52291508 GCCGCTATAGAAC-AGACCTTTAGCGGCGCTTTTCACACAAACGCCGCTA
1 GCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTA
52291557 AAAACATATC
Statistics
Matches: 163, Mismatches: 10, Indels: 7
0.91 0.06 0.04
Matches are distributed among these distances:
126 42 0.26
127 98 0.60
128 23 0.14
ACGTcount: A:0.25, C:0.33, G:0.20, T:0.22
Consensus pattern (127 bp):
GCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAGCAGACCTTTA
GCGGCGCTTTCCCACAAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCACACAAAC
Found at i:52291487 original size:85 final size:85
Alignment explanation
Indices: 52291254--52291556 Score: 479
Period size: 85 Copynumber: 3.6 Consensus size: 85
52291244 TGTTGCTAAT
*
52291254 GCCGCTATAGATCAGGACCTTTAGCGGCGC-TTCCCCACAAACGCCGCTATAGATCAGGACCTTT
1 GCCGCTATAGATCA-GACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGACCTTT
52291318 AGCGGCGC--TTCCCTACAAAC
65 AGCGGCGCTTTTCCC-ACAAAC
* * *
52291338 GCCGCTATAGATCAAGACCTTTAGCGGCGCTTTT-CCACAAACGCCGCTATAGCTCAAGATCTTT
1 GCCGCTATAGATC-AGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGACCTTT
52291402 AGCGGCGCTTTTCCCACAAAC
65 AGCGGCGCTTTTCCCACAAAC
*
52291423 GCCGCTATAGAGCAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGACCTTTA
1 GCCGCTATAGATCAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGACCTTTA
*
52291488 GCGGCGCTTTTCACACAAAC
66 GCGGCGCTTTTCCCACAAAC
* *
52291508 GCCGCTATAGAACAGACCTTTAGCGGCGCTTTTCACACAAACGCCGCTA
1 GCCGCTATAGATCAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTA
52291557 AAAACATATC
Statistics
Matches: 203, Mismatches: 11, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
84 83 0.41
85 115 0.57
86 5 0.02
ACGTcount: A:0.25, C:0.33, G:0.20, T:0.22
Consensus pattern (85 bp):
GCCGCTATAGATCAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGACCTTTA
GCGGCGCTTTTCCCACAAAC
Found at i:52291628 original size:24 final size:23
Alignment explanation
Indices: 52291587--52291640 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
52291577 ATAATTTTTT
*
52291587 TAAATAATATTTATTTTT-ATGA
1 TAAATAATATTTATTTTTAAGGA
*
52291609 TAAATATTATATTATGTTTTAAGGA
1 TAAATAATAT-TTAT-TTTTAAGGA
52291634 TAAATAA
1 TAAATAA
52291641 AAAATATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 9 0.35
23 4 0.15
24 4 0.15
25 9 0.35
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (23 bp):
TAAATAATATTTATTTTTAAGGA
Found at i:52295157 original size:29 final size:30
Alignment explanation
Indices: 52295091--52295166 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 30
52295081 ATATTATAAA
**
52295091 AATAAAAGTTTAAAATCTTTTTAAAATTTCT
1 AATAAAA-TTTAAAATCTTTTTAAAATTGAT
*
52295122 AAAAAAATTTAAAATC-TTTTAAAATTGAT
1 AATAAAATTTAAAATCTTTTTAAAATTGAT
** *
52295151 TTTAAAATTTTAAATC
1 AATAAAATTTAAAATC
52295167 ACGAAAAATA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 23 0.61
30 9 0.24
31 6 0.16
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (30 bp):
AATAAAATTTAAAATCTTTTTAAAATTGAT
Found at i:52295164 original size:30 final size:30
Alignment explanation
Indices: 52295092--52295147 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
52295082 TATTATAAAA
*
52295092 ATAAAAGTTTAAAATCTTTTTAAAATTTCT
1 ATAAAAATTTAAAATCTTTTTAAAATTTCT
*
52295122 AAAAAAATTTAAAATC-TTTTAAAATT
1 ATAAAAATTTAAAATCTTTTTAAAATT
52295148 GATTTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (30 bp):
ATAAAAATTTAAAATCTTTTTAAAATTTCT
Found at i:52295920 original size:15 final size:15
Alignment explanation
Indices: 52295896--52295930 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
52295886 TCCCAACCTT
*
52295896 TAAA-CCATAATCCC
1 TAAACCCATAATCCA
52295910 TAAACCCATAATCCA
1 TAAACCCATAATCCA
52295925 TAAACC
1 TAAACC
52295931 TTAAAATGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.46, C:0.34, G:0.00, T:0.20
Consensus pattern (15 bp):
TAAACCCATAATCCA
Found at i:52295949 original size:37 final size:36
Alignment explanation
Indices: 52295908--52296020 Score: 103
Period size: 37 Copynumber: 3.2 Consensus size: 36
52295898 AACCATAATC
52295908 CCTAAACCCATAATCCATAAACCTTAAAATGGCAACA
1 CCTAAACCCA-AATCCATAAACCTTAAAATGGCAACA
* * * * *
52295945 CCTAAA-CC--ATGCATATACCCT-AAA--CCAAAGA
1 CCTAAACCCAAATCCATAAACCTTAAAATGGC-AACA
*
52295976 CCTAAACCCAGAATCCATAAACCTTAAAATGGTAACA
1 CCTAAACCCA-AATCCATAAACCTTAAAATGGCAACA
52296013 CCTAAACC
1 CCTAAACC
52296021 TATTTAAACT
Statistics
Matches: 57, Mismatches: 11, Indels: 16
0.68 0.13 0.19
Matches are distributed among these distances:
30 1 0.02
31 9 0.16
32 5 0.09
33 10 0.18
35 10 0.18
36 5 0.09
37 17 0.30
ACGTcount: A:0.45, C:0.31, G:0.06, T:0.18
Consensus pattern (36 bp):
CCTAAACCCAAATCCATAAACCTTAAAATGGCAACA
Found at i:52296137 original size:66 final size:66
Alignment explanation
Indices: 52296060--52296193 Score: 259
Period size: 66 Copynumber: 2.0 Consensus size: 66
52296050 CCCTAAACTA
*
52296060 TAGTGATAATTAATTCAATATTTTAAAATTAATACTATCTCTTTTACGATTATATAAGAAATTAT
1 TAGTGATAATTAATTCAATATTTTAAAATTAATACTATCTCTTTTACAATTATATAAGAAATTAT
52296125 T
66 T
52296126 TAGTGATAATTAATTCAATATTTTAAAATTAATACTATCTCTTTTACAATTATATAAGAAATTAT
1 TAGTGATAATTAATTCAATATTTTAAAATTAATACTATCTCTTTTACAATTATATAAGAAATTAT
52296191 T
66 T
52296192 TA
1 TA
52296194 ATATATAAAT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (66 bp):
TAGTGATAATTAATTCAATATTTTAAAATTAATACTATCTCTTTTACAATTATATAAGAAATTAT
T
Found at i:52296368 original size:41 final size:41
Alignment explanation
Indices: 52296313--52296672 Score: 614
Period size: 41 Copynumber: 8.8 Consensus size: 41
52296303 CCTGAGCATT
*
52296313 ATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGGCCTGGGC
1 ATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCTGGGC
*
52296354 ATTAGCAGCGCTTTCACAAAAACGCCGCTAAAGGCCTGGGC
1 ATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCTGGGC
*
52296395 ATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCT-GAC
1 ATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCTGGGC
*
52296435 ATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCTGGCC
1 ATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCTGGGC
*
52296476 ATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCTGGCC
1 ATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCTGGGC
*
52296517 ATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCTGGAC
1 ATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCTGGGC
*
52296558 ATTAGCGGCGCTTTCACAAAAACGCCACTAAAGGCCTGGGC
1 ATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCTGGGC
* *
52296599 ATTAGCGGCACTTCCACAAAAACGCCGCTAAAGGCCTGGGGC
1 ATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCT-GGGC
*
52296641 ATTAGCGGCGCTTTCCCAAAAACGCCGCTAAA
1 ATTAGCGGCGCTTTCACAAAAACGCCGCTAAA
52296673 TCCCCAAAAG
Statistics
Matches: 303, Mismatches: 14, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
40 39 0.13
41 231 0.76
42 33 0.11
ACGTcount: A:0.28, C:0.31, G:0.24, T:0.17
Consensus pattern (41 bp):
ATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCTGGGC
Found at i:52296530 original size:122 final size:123
Alignment explanation
Indices: 52296313--52296672 Score: 632
Period size: 122 Copynumber: 2.9 Consensus size: 123
52296303 CCTGAGCATT
* *
52296313 ATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGGCCTGGGCATTAGCAGCGCTTTCACAAAAACG
1 ATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCTGGGCATTAGCGGCGCTTTCACAAAAACG
52296378 CCGCTAAAGGCCTGGGCATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCT-GAC
66 CCGCTAAAGGCCTGGGCATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCTGGAC
*
52296435 ATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCTGGCCATTAGCGGCGCTTTCACAAAAACG
1 ATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCTGGGCATTAGCGGCGCTTTCACAAAAACG
*
52296500 CCGCTAAAGGCCTGGCCATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCTGGAC
66 CCGCTAAAGGCCTGGGCATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCTGGAC
* * *
52296558 ATTAGCGGCGCTTTCACAAAAACGCCACTAAAGGCCTGGGCATTAGCGGCACTTCCACAAAAACG
1 ATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCTGGGCATTAGCGGCGCTTTCACAAAAACG
*
52296623 CCGCTAAAGGCCTGGGGCATTAGCGGCGCTTTCCCAAAAACGCCGCTAAA
66 CCGCTAAAGGCCT-GGGCATTAGCGGCGCTTTCACAAAAACGCCGCTAAA
52296673 TCCCCAAAAG
Statistics
Matches: 226, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
122 115 0.51
123 77 0.34
124 34 0.15
ACGTcount: A:0.28, C:0.31, G:0.24, T:0.17
Consensus pattern (123 bp):
ATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCTGGGCATTAGCGGCGCTTTCACAAAAACG
CCGCTAAAGGCCTGGGCATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCTGGAC
Found at i:52296754 original size:39 final size:38
Alignment explanation
Indices: 52296710--52296787 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 38
52296700 TTGGGCTTAG
52296710 ATTTTTTGCGGCGTTTT-ATTGAAAACGCCGCTAATGCTT
1 ATTTTTTGCGGCGTTTTCA-T-AAAACGCCGCTAATGCTT
*
52296749 ATTTTTTGCGGCGTTTTCCATAAAGCGCCGCTAATGCTT
1 ATTTTTTGCGGCGTTTT-CATAAAACGCCGCTAATGCTT
52296788 GATCTTTAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
39 34 0.94
40 1 0.03
41 1 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.40
Consensus pattern (38 bp):
ATTTTTTGCGGCGTTTTCATAAAACGCCGCTAATGCTT
Found at i:52299219 original size:13 final size:13
Alignment explanation
Indices: 52299201--52299234 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
52299191 CTAAAAAATA
*
52299201 AAAATAAGTAATT
1 AAAATAAATAATT
52299214 AAAATAAATAATT
1 AAAATAAATAATT
*
52299227 AAGATAAA
1 AAAATAAA
52299235 AAATAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (13 bp):
AAAATAAATAATT
Found at i:52299240 original size:16 final size:15
Alignment explanation
Indices: 52299196--52299249 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
52299186 CAAATCTAAA
*
52299196 AAAT-AAAAATAAGT
1 AAATAAAAAATAATT
*
52299210 AATTAAAATAAATAATT
1 AAAT-AAA-AAATAATT
52299227 AAGATAAAAAATAATT
1 AA-ATAAAAAATAATT
52299243 AAATAAA
1 AAATAAA
52299250 TCAAATATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
14 3 0.09
15 5 0.15
16 12 0.36
17 12 0.36
18 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (15 bp):
AAATAAAAAATAATT
Found at i:52305285 original size:14 final size:14
Alignment explanation
Indices: 52305260--52305331 Score: 81
Period size: 14 Copynumber: 5.1 Consensus size: 14
52305250 CATGTATGAG
52305260 TATCTGTATCTGTA
1 TATCTGTATCTGTA
* *
52305274 TTTCTGTGTCTGTA
1 TATCTGTATCTGTA
**
52305288 TATCTGTATCCCTA
1 TATCTGTATCTGTA
*
52305302 TATCTGTATTTGTA
1 TATCTGTATCTGTA
* *
52305316 TTTCTATATCTGTA
1 TATCTGTATCTGTA
52305330 TA
1 TA
52305332 CGGGGCGACA
Statistics
Matches: 45, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 45 1.00
ACGTcount: A:0.19, C:0.15, G:0.12, T:0.53
Consensus pattern (14 bp):
TATCTGTATCTGTA
Found at i:52308965 original size:2 final size:2
Alignment explanation
Indices: 52308958--52308985 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
52308948 AATTTCCATA
52308958 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
52308986 TTGGAGTAAG
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:52310613 original size:25 final size:26
Alignment explanation
Indices: 52310585--52310642 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
52310575 CACTTTTGAG
52310585 TTAATAAAA-TTCT-TTGAGT-TTTCTT
1 TTAA-AAAATTTCTCTTGAGTCTTT-TT
52310610 TTAAAAAATTTCTCTTGAGTCTTTTT
1 TTAAAAAATTTCTCTTGAGTCTTTTT
52310636 TTAAAAA
1 TTAAAAA
52310643 TTTAACAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
24 4 0.13
25 8 0.27
26 15 0.50
27 3 0.10
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.52
Consensus pattern (26 bp):
TTAAAAAATTTCTCTTGAGTCTTTTT
Found at i:52311682 original size:20 final size:21
Alignment explanation
Indices: 52311657--52311696 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
52311647 TGTCTTTATC
*
52311657 AATTTT-TATATAAATTTTAA
1 AATTTTCTAAATAAATTTTAA
*
52311677 AATTTTCTAAATAAGTTTTA
1 AATTTTCTAAATAAATTTTA
52311697 CTAATTTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (21 bp):
AATTTTCTAAATAAATTTTAA
Found at i:52313418 original size:10 final size:10
Alignment explanation
Indices: 52313400--52313428 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
52313390 AGAGCCTTTG
52313400 AGAGC-AAAA
1 AGAGCGAAAA
52313409 AGAGCGAAAA
1 AGAGCGAAAA
52313419 AGAGCGAAAA
1 AGAGCGAAAA
52313429 CTGGAAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.26
10 14 0.74
ACGTcount: A:0.62, C:0.10, G:0.28, T:0.00
Consensus pattern (10 bp):
AGAGCGAAAA
Found at i:52315971 original size:13 final size:13
Alignment explanation
Indices: 52315953--52315978 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52315943 GGGTGTAGGC
52315953 CCACATGGGCATG
1 CCACATGGGCATG
52315966 CCACATGGGCATG
1 CCACATGGGCATG
52315979 TAGGTTTTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.31, T:0.15
Consensus pattern (13 bp):
CCACATGGGCATG
Found at i:52318728 original size:21 final size:22
Alignment explanation
Indices: 52318673--52318729 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 22
52318663 TATTAGGTTA
* *
52318673 ATTGAATTGGTATGTTTATATGTG
1 ATTGAA-T-GTATGTTTAAATCTG
*
52318697 ATTGAA-ATATGTTTAAATCT-
1 ATTGAATGTATGTTTAAATCTG
52318717 ATTGAATGTATGT
1 ATTGAATGTATGT
52318730 ACAAATAGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
20 6 0.21
21 16 0.57
24 6 0.21
ACGTcount: A:0.32, C:0.02, G:0.19, T:0.47
Consensus pattern (22 bp):
ATTGAATGTATGTTTAAATCTG
Found at i:52319871 original size:358 final size:354
Alignment explanation
Indices: 52319212--52319919 Score: 1087
Period size: 358 Copynumber: 2.0 Consensus size: 354
52319202 TTTTAATTTT
*
52319212 TCCTTAGATTTTTTGAATTATTTCAAACTAGTCCCGTTTTGATCCCGAAATATTTTTAGGGCCTC
1 TCCTTAGATTTTCTGAATTATTTCAAACTAGTCCCGTTTTGATCCCGAAATATTTTTAGGGCCTC
* *
52319277 GAAATTTTAATTTAAGGCCTAAATGTTTATGTTGGATTTGTATGAGGTTTAAAAAATTAATATTG
66 GAAAATTTAATTTAAGGCCAAAATGTTTATGTTGGATTTGTATGAGGTTTAAAAAATTAATATTG
* **
52319342 AATAGCATTATTAAACTGTTTAAATGTTAATTGTTCTAATTTTTACAGTAATGCTCTGTAACCCT
131 AATAACATTATTAAACTGTTTAAATGTTAATTGTTCTAATTTTTACAGTAATGCTCCATAACCCT
* * *
52319407 AGACCGGCGACGGAAACAGGTTAGGGGTGTTATATTAGGTCGACCTTTTATAGCCACTGCTAGAA
196 AGACCGGCAACGGAAACAGGTTAGGGGTGTTACATTAGGTCGACCCTTTATAGCCACTGCTAGAA
* *
52319472 CTATTATTGATATGGGTACTGGTGAACTTGTGCTTGTGTAGGTGATGAAAAGATTACTTTTCAAG
261 CTATTATTGATATGGGTACTGGTGAACTTGTGCTTGTGTAGGTGATAAAAAGATTACTCTTCAAG
52319537 CACATGATTTTGTGAGAGTCCCTAGAGAA
326 CACATGATTTTGTGAGAGTCCCTAGAGAA
* *
52319566 TCCTTAGATTTTCTGAATTATTTCAAATTAGTCCCGTTTTGATCTC-AAACTATTTTTAGGGCCT
1 TCCTTAGATTTTCTGAATTATTTCAAACTAGTCCCGTTTTGATCCCGAAA-TATTTTTAGGGCCT
* * *
52319630 CGAAAATTTAATTTAAGGCCCAAATATGTATATTTGTTGGATTTTTATGAGGTTTAAATAATTAA
65 CGAAAATTTAATTTAAGG-CCAAA-ATGT-T-TATGTTGGATTTGTATGAGGTTTAAAAAATTAA
* * * *
52319695 TGTTGAATAACATTATTAAATTGTTTAGATGTTAATTGTTCTAATTTTTACGGTAATGCTCCATA
126 TATTGAATAACATTATTAAACTGTTTAAATGTTAATTGTTCTAATTTTTACAGTAATGCTCCATA
** * * *
52319760 ACCCTAGACTTGCAACGGAAACGGGTTAGGGGTGTTACATTAGTTCTACCCTTT-TAGCCACTGC
191 ACCCTAGACCGGCAACGGAAACAGGTTAGGGGTGTTACATTAGGTCGACCCTTTATAGCCACTGC
* * *
52319824 TAGAATTGTTATTGATATGGGTACTGGTGAACTTGTGCTTCGTGTAGGTGATAAAAATATTACTC
256 TAGAACTATTATTGATATGGGTACTGGTGAACTTGTGCTT-GTGTAGGTGATAAAAAGATTACTC
*
52319889 TTCAAGCACGTGATTTTGTGAGAGTCCCTAG
320 TTCAAGCACATGATTTTGTGAGAGTCCCTAG
52319920 TCAGCGAGAT
Statistics
Matches: 319, Mismatches: 29, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
353 3 0.01
354 74 0.23
355 4 0.01
356 4 0.01
357 49 0.15
358 185 0.58
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (354 bp):
TCCTTAGATTTTCTGAATTATTTCAAACTAGTCCCGTTTTGATCCCGAAATATTTTTAGGGCCTC
GAAAATTTAATTTAAGGCCAAAATGTTTATGTTGGATTTGTATGAGGTTTAAAAAATTAATATTG
AATAACATTATTAAACTGTTTAAATGTTAATTGTTCTAATTTTTACAGTAATGCTCCATAACCCT
AGACCGGCAACGGAAACAGGTTAGGGGTGTTACATTAGGTCGACCCTTTATAGCCACTGCTAGAA
CTATTATTGATATGGGTACTGGTGAACTTGTGCTTGTGTAGGTGATAAAAAGATTACTCTTCAAG
CACATGATTTTGTGAGAGTCCCTAGAGAA
Found at i:52321078 original size:19 final size:20
Alignment explanation
Indices: 52321054--52321091 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
52321044 GCCATGTCTT
52321054 TTTTTTTCCTTT-TTAATTC
1 TTTTTTTCCTTTCTTAATTC
*
52321073 TTTTTTTCTTTTCTTAATT
1 TTTTTTTCCTTTCTTAATT
52321092 TATTCTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTTTTCCTTTCTTAATTC
Found at i:52321179 original size:5 final size:6
Alignment explanation
Indices: 52321164--52321248 Score: 62
Period size: 6 Copynumber: 13.7 Consensus size: 6
52321154 TATTTCTATT
* * * * *
52321164 TTTTTG TTTTTG TTTTTA TTTCTA TTTATG TTTTTCTG TTTTTC TTCTTTG
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG -TTTT-TG TTTTTG TT-TTTG
* * * *
52321215 TTTTTG CTTTTG CTTTTG TTTTTA TTTTTA TTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTT
52321249 ATTATGCACT
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
6 52 0.79
7 12 0.18
8 2 0.03
ACGTcount: A:0.06, C:0.07, G:0.09, T:0.78
Consensus pattern (6 bp):
TTTTTG
Found at i:52321186 original size:26 final size:26
Alignment explanation
Indices: 52321154--52321243 Score: 78
Period size: 26 Copynumber: 3.5 Consensus size: 26
52321144 TTTCTATTTC
52321154 TATTTCTATTTTTTTGTTTTTGTTTT
1 TATTTCTATTTTTTTGTTTTTGTTTT
* *
52321180 TATTTCTATTTATGTT-TTTCTGTTTT
1 TATTTCTATTT-TTTTGTTTTTGTTTT
* * *
52321206 T-CTTCT-TTGTTTTTGCTTTTGCTTT
1 TATTTCTATT-TTTTTGTTTTTGTTTT
* *
52321231 TGTTTTTATTTTT
1 TATTTCTATTTTT
52321244 ATTTTATTAT
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
24 5 0.10
25 13 0.26
26 27 0.54
27 5 0.10
ACGTcount: A:0.07, C:0.08, G:0.09, T:0.77
Consensus pattern (26 bp):
TATTTCTATTTTTTTGTTTTTGTTTT
Found at i:52321206 original size:38 final size:39
Alignment explanation
Indices: 52321140--52321219 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 39
52321130 TTATATTTTA
* * *
52321140 TTTATTTCTATTTCTATTTCTATTTTTTTGTT-TTTGTT
1 TTTATTTCTATTTATATTTCTATGTTTTTCTTCTTTGTT
* * *
52321178 TTTATTTCTATTTATGTTTTTCTGTTTTTCTTCTTTGTT
1 TTTATTTCTATTTATATTTCTATGTTTTTCTTCTTTGTT
52321217 TTT
1 TTT
52321220 GCTTTTGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
38 26 0.74
39 9 0.26
ACGTcount: A:0.09, C:0.09, G:0.06, T:0.76
Consensus pattern (39 bp):
TTTATTTCTATTTATATTTCTATGTTTTTCTTCTTTGTT
Found at i:52331154 original size:27 final size:28
Alignment explanation
Indices: 52331103--52331162 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 28
52331093 AATAAACACC
52331103 AAAAAAATATTTTAAATATAAAAAGAAT
1 AAAAAAATATTTTAAATATAAAAAGAAT
*
52331131 AAAAAAAGTATTTTAAA-AT-TAAAGAAT
1 AAAAAAA-TATTTTAAATATAAAAAGAAT
52331158 AAAAA
1 AAAAA
52331163 TTATTTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 12 0.40
28 9 0.30
29 9 0.30
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (28 bp):
AAAAAAATATTTTAAATATAAAAAGAAT
Found at i:52332072 original size:17 final size:16
Alignment explanation
Indices: 52332027--52332074 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
52332017 AATTGACATT
*
52332027 TTATTTAAATTTTTTA
1 TTATTTCAATTTTTTA
*
52332043 TTATTTGC-TTTTTTTA
1 TTATTT-CAATTTTTTA
52332059 TATATTTCAATTTTTT
1 T-TATTTCAATTTTTT
52332075 TTTAAAAGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 15 0.58
17 11 0.42
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (16 bp):
TTATTTCAATTTTTTA
Found at i:52332548 original size:9 final size:9
Alignment explanation
Indices: 52332534--52332566 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
52332524 TTAAGAAATA
52332534 TAAAATATC
1 TAAAATATC
52332543 TAAAAT-TC
1 TAAAATATC
52332551 TTAAAATATC
1 -TAAAATATC
52332561 TAAAAT
1 TAAAAT
52332567 TCAGAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 2 0.09
9 18 0.82
10 2 0.09
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (9 bp):
TAAAATATC
Found at i:52332557 original size:18 final size:18
Alignment explanation
Indices: 52332534--52332568 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
52332524 TTAAGAAATA
52332534 TAAAATATCTAAAATTCT
1 TAAAATATCTAAAATTCT
52332552 TAAAATATCTAAAATTC
1 TAAAATATCTAAAATTC
52332569 AGAATAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.37
Consensus pattern (18 bp):
TAAAATATCTAAAATTCT
Found at i:52335789 original size:25 final size:25
Alignment explanation
Indices: 52335755--52335809 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
52335745 TTGAATGATA
52335755 AAGAATGAATTCCCATGACTCCTTG
1 AAGAATGAATTCCCATGACTCCTTG
52335780 AAGAATGAATTCCCATGACTCCTTG
1 AAGAATGAATTCCCATGACTCCTTG
52335805 AAGAA
1 AAGAA
52335810 AATTGAGAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.25
Consensus pattern (25 bp):
AAGAATGAATTCCCATGACTCCTTG
Found at i:52339297 original size:18 final size:18
Alignment explanation
Indices: 52339259--52339329 Score: 60
Period size: 18 Copynumber: 4.1 Consensus size: 18
52339249 AAATCGGGAT
52339259 AATGATATTGAAATGGAA
1 AATGATATTGAAATGGAA
* *
52339277 AATTATATTGAAGT-GACA
1 AATGATATTGAAATGGA-A
*
52339295 AATGATA-TGGAAT-G-A
1 AATGATATTGAAATGGAA
*
52339310 AATGAAATGTGAAATGGAA
1 AATGATAT-TGAAATGGAA
52339329 A
1 A
52339330 TCAAAATGGT
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
15 7 0.17
17 12 0.29
18 20 0.49
19 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.23, T:0.27
Consensus pattern (18 bp):
AATGATATTGAAATGGAA
Found at i:52340435 original size:30 final size:30
Alignment explanation
Indices: 52340400--52340459 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
52340390 CCTGGCACAT
* * *
52340400 GGTCGTGTGCCATACATGGGCTTATGGCAC
1 GGTCGTCTGCCATACACGAGCTTATGGCAC
52340430 GGTCGTCTGCCATACACGAGCTTATGGCAC
1 GGTCGTCTGCCATACACGAGCTTATGGCAC
52340460 AACCGTTTAG
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:0.18, C:0.27, G:0.30, T:0.25
Consensus pattern (30 bp):
GGTCGTCTGCCATACACGAGCTTATGGCAC
Found at i:52341537 original size:13 final size:13
Alignment explanation
Indices: 52341519--52341543 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52341509 TCCATTGGCT
52341519 TTTCTAATAAAGG
1 TTTCTAATAAAGG
52341532 TTTCTAATAAAG
1 TTTCTAATAAAG
52341544 CAACTTAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (13 bp):
TTTCTAATAAAGG
Found at i:52341960 original size:21 final size:21
Alignment explanation
Indices: 52341920--52341960 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
52341910 GCATGAATTT
*
52341920 AATTATTTGAAATTTACAATG
1 AATTATTTAAAATTTACAATG
52341941 AATTATTTTAAAATTT-CAAT
1 AATTA-TTTAAAATTTACAAT
52341961 TAACAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (21 bp):
AATTATTTAAAATTTACAATG
Found at i:52345687 original size:19 final size:19
Alignment explanation
Indices: 52345663--52345699 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
52345653 TAACATGGAA
52345663 TTAAAC-ATACATACCACAT
1 TTAAACTAT-CATACCACAT
52345682 TTAAACTATCATACCACA
1 TTAAACTATCATACCACA
52345700 ACATCAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.27
Consensus pattern (19 bp):
TTAAACTATCATACCACAT
Found at i:52346219 original size:34 final size:33
Alignment explanation
Indices: 52346174--52346293 Score: 170
Period size: 34 Copynumber: 3.5 Consensus size: 33
52346164 ACATGATTAA
52346174 CCATCCAACACACTAAATGCTCGTATGAGCTAAT
1 CCATCC-ACACACTAAATGCTCGTATGAGCTAAT
52346208 CCATCCGACACACTAAATGCTCGTATGTA-CTAAT
1 CCATCC-ACACACTAAATGCTCGTATG-AGCTAAT
*
52346242 CCATCCAGCACACCAAATGCTCGTATGAGCTAAT
1 CCATCCA-CACACTAAATGCTCGTATGAGCTAAT
*
52346276 CCATCCAGCACACCAAAT
1 CCATCCA-CACACTAAAT
52346294 AACACTATAA
Statistics
Matches: 81, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
33 2 0.02
34 78 0.96
35 1 0.01
ACGTcount: A:0.34, C:0.33, G:0.12, T:0.22
Consensus pattern (33 bp):
CCATCCACACACTAAATGCTCGTATGAGCTAAT
Found at i:52354059 original size:27 final size:27
Alignment explanation
Indices: 52354005--52354059 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
52353995 AATATATAAT
*
52354005 AATTATTAAATAATTAAATTGTACTTA
1 AATTATTAAATAATTAAATTGTAATTA
* *
52354032 AATTATTAACAT-ATTTAATTTTAATTA
1 AATTATTAA-ATAATTAAATTGTAATTA
52354059 A
1 A
52354060 TTTTATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 22 0.92
28 2 0.08
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (27 bp):
AATTATTAAATAATTAAATTGTAATTA
Found at i:52362430 original size:25 final size:26
Alignment explanation
Indices: 52362377--52362430 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
52362367 TTCTCCTGAA
* *
52362377 TTTCAATTTTATTTAATTATTTAATT
1 TTTCAATTTTATTGAATTAGTTAATT
52362403 TTTCAA-TTTATTGAATT-GTTAATAT
1 TTTCAATTTTATTGAATTAGTTAAT-T
52362428 TTT
1 TTT
52362431 ATACTAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 5 0.20
25 14 0.56
26 6 0.24
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.63
Consensus pattern (26 bp):
TTTCAATTTTATTGAATTAGTTAATT
Found at i:52367876 original size:40 final size:40
Alignment explanation
Indices: 52367832--52367912 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
52367822 TTTTTCCAGC
* *
52367832 CTTAACTTGAGTTCTTTAACCCTCCTAATCAACTTTTAAA
1 CTTAAATTGAGTTCTTTAACCCTCCTAATCAACCTTTAAA
52367872 CTTAAATTGAGTTCTTTAACCCTCCTAATCAACCTTTAAA
1 CTTAAATTGAGTTCTTTAACCCTCCTAATCAACCTTTAAA
52367912 C
1 C
52367913 CCATTTCAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.31, C:0.26, G:0.05, T:0.38
Consensus pattern (40 bp):
CTTAAATTGAGTTCTTTAACCCTCCTAATCAACCTTTAAA
Found at i:52371879 original size:16 final size:17
Alignment explanation
Indices: 52371858--52371891 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
52371848 AATCATGTCT
52371858 ATAGCTAGCCATT-TCA
1 ATAGCTAGCCATTATCA
*
52371874 ATAGCTAGTCATTATCA
1 ATAGCTAGCCATTATCA
52371891 A
1 A
52371892 ATATTTACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (17 bp):
ATAGCTAGCCATTATCA
Found at i:52375808 original size:19 final size:19
Alignment explanation
Indices: 52375748--52375809 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
52375738 TAAAAAAAAA
*
52375748 TTTTACAACTTTT-TAATAT
1 TTTTACAATTTTTATAAT-T
*
52375767 TTTTA-ATATATTTTA-AATA
1 TTTTACA-AT-TTTTATAATT
52375786 TTTTACAATTTTTATAATT
1 TTTTACAATTTTTATAATT
52375805 TTTTA
1 TTTTA
52375810 AGTTTTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
18 6 0.17
19 21 0.60
20 8 0.23
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTACAATTTTTATAATT
Found at i:52382098 original size:19 final size:20
Alignment explanation
Indices: 52382076--52382115 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
52382066 AAAAATATTA
52382076 ACTC-TTTTAAATA-ATAAAT
1 ACTCTTTTTAAA-ACATAAAT
52382095 ACTCTTTTTAAAACATAAAT
1 ACTCTTTTTAAAACATAAAT
52382115 A
1 A
52382116 TTAACTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTCTTTTTAAAACATAAAT
Found at i:52383445 original size:5 final size:5
Alignment explanation
Indices: 52383435--52383462 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
52383425 TTTTCACCCA
52383435 AAACC AAACC AAACC AAACC AAACC AAA
1 AAACC AAACC AAACC AAACC AAACC AAA
52383463 ACCTTTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.64, C:0.36, G:0.00, T:0.00
Consensus pattern (5 bp):
AAACC
Found at i:52389531 original size:33 final size:35
Alignment explanation
Indices: 52389468--52389548 Score: 96
Period size: 36 Copynumber: 2.3 Consensus size: 35
52389458 ATTATATATG
* *
52389468 CATTATTATTTATTAGCATGATTATGATTTTATTCT
1 CATTATTATTTACTAGCATGAGTATGATTTTATT-T
52389504 CATTATTATTTACTAGCATG-GT-T-ATTTTATTT
1 CATTATTATTTACTAGCATGAGTATGATTTTATTT
*
52389536 TATTATTTATTTA
1 CATTA-TTATTTA
52389549 TTTATTATTC
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
32 5 0.12
33 15 0.37
34 1 0.02
35 1 0.02
36 19 0.46
ACGTcount: A:0.27, C:0.07, G:0.07, T:0.58
Consensus pattern (35 bp):
CATTATTATTTACTAGCATGAGTATGATTTTATTT
Found at i:52395297 original size:17 final size:17
Alignment explanation
Indices: 52395275--52395312 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
52395265 CCCAAGGTGC
52395275 TCAACCACCATACCGAA
1 TCAACCACCATACCGAA
* *
52395292 TCAACCATCATACTGAA
1 TCAACCACCATACCGAA
52395309 TCAA
1 TCAA
52395313 ATCTTTTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.34, G:0.05, T:0.18
Consensus pattern (17 bp):
TCAACCACCATACCGAA
Found at i:52397410 original size:21 final size:21
Alignment explanation
Indices: 52397386--52397436 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
52397376 TTCTTTTGAA
*
52397386 CCTCTGCTTCTCTCGCTGCAG
1 CCTCTGCTTCCCTCGCTGCAG
* *
52397407 CCTCTACTTCCCTCGCTGCCG
1 CCTCTGCTTCCCTCGCTGCAG
52397428 CCTCTGCTT
1 CCTCTGCTT
52397437 TAAGTTGTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.04, C:0.47, G:0.16, T:0.33
Consensus pattern (21 bp):
CCTCTGCTTCCCTCGCTGCAG
Found at i:52397489 original size:87 final size:87
Alignment explanation
Indices: 52397321--52397480 Score: 239
Period size: 87 Copynumber: 1.8 Consensus size: 87
52397311 TTTTGCTCTG
* * *
52397321 CTCTGCTTCTCTCGATGCCGCATCTACTTTAAGTTGTAGCTGGAGTTCTTCATATTTCTTTTGAA
1 CTCTACTTCCCTCGATGCCGCATCTACTTTAAGTTGTAGCTGGAGTTCTTCATATTTCCTTTGAA
** *
52397386 CCTCTGCTTCTCTCGCTGCAGC
66 CCTCAACTTCGCTCGCTGCAGC
* * *
52397408 CTCTACTTCCCTCGCTGCCGCCTCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATTTCCTTTGAA
1 CTCTACTTCCCTCGATGCCGCATCTACTTTAAGTTGTAGCTGGAGTTCTTCATATTTCCTTTGAA
52397473 CCTCAACT
66 CCTCAACT
52397481 GTGGTCGCTT
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
87 65 1.00
ACGTcount: A:0.14, C:0.30, G:0.16, T:0.39
Consensus pattern (87 bp):
CTCTACTTCCCTCGATGCCGCATCTACTTTAAGTTGTAGCTGGAGTTCTTCATATTTCCTTTGAA
CCTCAACTTCGCTCGCTGCAGC
Found at i:52403063 original size:94 final size:93
Alignment explanation
Indices: 52402924--52403095 Score: 256
Period size: 94 Copynumber: 1.8 Consensus size: 93
52402914 AAATTATGTT
* * * *
52402924 ATTAGAAATTAATATTATATAAGTAATCTTAATTAGAAATTTTATCTTAATATTGTATAAGTTAT
1 ATTAGAAATTAATATTAAACAAGTAATCGTAATTAGAAATTTTATCTTAATATTATATAAGTTAT
52402989 CTAAAATTAGAAATTGATGTGTACTTAGAA
66 CT--AATTAGAAATTGATGTGTACTTAGAA
* *
52403019 ATTAGAAATTAATATTAAACGAGTTAT-GTAATTAGAAATTTTATCTTAATATTATATAAGTTAT
1 ATTAGAAATTAATATTAAACAAGTAATCGTAATTAGAAATTTTATCTTAATATTATATAAGTTAT
*
52403083 GTAATTAGAAATT
66 CTAATTAGAAATT
52403096 TTATCTTCAT
Statistics
Matches: 70, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
92 11 0.16
94 36 0.51
95 23 0.33
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.42
Consensus pattern (93 bp):
ATTAGAAATTAATATTAAACAAGTAATCGTAATTAGAAATTTTATCTTAATATTATATAAGTTAT
CTAATTAGAAATTGATGTGTACTTAGAA
Found at i:52403068 original size:37 final size:37
Alignment explanation
Indices: 52403027--52403119 Score: 132
Period size: 37 Copynumber: 2.5 Consensus size: 37
52403017 AAATTAGAAA
*
52403027 TTAATATTAAACGAGTTATGTAATTAGAAATTTTATC
1 TTAATATTAAACAAGTTATGTAATTAGAAATTTTATC
* *
52403064 TTAATATTATATAAGTTATGTAATTAGAAATTTTATC
1 TTAATATTAAACAAGTTATGTAATTAGAAATTTTATC
* * *
52403101 TTCATATTATATAAGTTAT
1 TTAATATTAAACAAGTTAT
52403120 CTTAATTTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (37 bp):
TTAATATTAAACAAGTTATGTAATTAGAAATTTTATC
Found at i:52403082 original size:20 final size:20
Alignment explanation
Indices: 52403059--52403130 Score: 62
Period size: 20 Copynumber: 3.8 Consensus size: 20
52403049 ATTAGAAATT
52403059 TTATCTTAATATTATATAAG
1 TTATCTTAATATTATATAAG
* * *
52403079 TTAT-GT-A-ATTAGA-AATT
1 TTATCTTAATATTATATAA-G
*
52403096 TTATCTTCATATTATATAAG
1 TTATCTTAATATTATATAAG
*
52403116 TTATCTTAATTTTAT
1 TTATCTTAATATTAT
52403131 GTAATTAGAA
Statistics
Matches: 39, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
16 2 0.05
17 9 0.23
18 2 0.05
19 2 0.05
20 22 0.56
21 2 0.05
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.53
Consensus pattern (20 bp):
TTATCTTAATATTATATAAG
Found at i:52403470 original size:10 final size:10
Alignment explanation
Indices: 52403455--52403511 Score: 60
Period size: 10 Copynumber: 5.5 Consensus size: 10
52403445 TAAATTTATA
52403455 ATTCATTGAC
1 ATTCATTGAC
52403465 ATTCATTGAC
1 ATTCATTGAC
**
52403475 AATTCACCGAC
1 -ATTCATTGAC
52403486 ATTCATTGAC
1 ATTCATTGAC
**
52403496 AATTCACCGAC
1 -ATTCATTGAC
52403507 ATTCA
1 ATTCA
52403512 ATCAATTAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
10 23 0.59
11 16 0.41
ACGTcount: A:0.33, C:0.26, G:0.09, T:0.32
Consensus pattern (10 bp):
ATTCATTGAC
Found at i:52403478 original size:21 final size:21
Alignment explanation
Indices: 52403462--52403511 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
52403452 ATAATTCATT
52403462 GACATTCATTGACAATTCACC
1 GACATTCATTGACAATTCACC
52403483 GACATTCATTGACAATTCACC
1 GACATTCATTGACAATTCACC
52403504 GACATTCA
1 GACATTCA
52403512 ATCAATTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.34, C:0.28, G:0.10, T:0.28
Consensus pattern (21 bp):
GACATTCATTGACAATTCACC
Found at i:52404312 original size:18 final size:18
Alignment explanation
Indices: 52404289--52404323 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
52404279 CTTGCCCTTA
*
52404289 GTAATCGGCAGAGGCAAC
1 GTAATCGACAGAGGCAAC
52404307 GTAATCGACAGAGGCAA
1 GTAATCGACAGAGGCAA
52404324 ACCCTAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.20, G:0.31, T:0.11
Consensus pattern (18 bp):
GTAATCGACAGAGGCAAC
Found at i:52405556 original size:21 final size:21
Alignment explanation
Indices: 52405532--52405576 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
52405522 TATAAGCCTT
* *
52405532 AACTGCAAATCATAAACCCCA
1 AACTACAAACCATAAACCCCA
* *
52405553 AACTATAAACCCTAAACCCCA
1 AACTACAAACCATAAACCCCA
52405574 AAC
1 AAC
52405577 CGTAAACCTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.49, C:0.36, G:0.02, T:0.13
Consensus pattern (21 bp):
AACTACAAACCATAAACCCCA
Found at i:52405568 original size:7 final size:7
Alignment explanation
Indices: 52405544--52405606 Score: 54
Period size: 7 Copynumber: 9.0 Consensus size: 7
52405534 CTGCAAATCA
52405544 TAAACCC
1 TAAACCC
* **
52405551 CAAACTA
1 TAAACCC
52405558 TAAACCC
1 TAAACCC
52405565 TAAACCC
1 TAAACCC
* *
52405572 CAAACCG
1 TAAACCC
*
52405579 TAAACCT
1 TAAACCC
* *
52405586 TAAATCT
1 TAAACCC
52405593 TAAACCC
1 TAAACCC
52405600 TAAACCC
1 TAAACCC
52405607 ATCAATTAAT
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
7 43 1.00
ACGTcount: A:0.44, C:0.37, G:0.02, T:0.17
Consensus pattern (7 bp):
TAAACCC
Found at i:52405582 original size:21 final size:21
Alignment explanation
Indices: 52405544--52405589 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
52405534 CTGCAAATCA
*
52405544 TAAACCCCAAACTATAAACCC
1 TAAACCCCAAACCATAAACCC
* *
52405565 TAAACCCCAAACCGTAAACCT
1 TAAACCCCAAACCATAAACCC
52405586 TAAA
1 TAAA
52405590 TCTTAAACCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.48, C:0.35, G:0.02, T:0.15
Consensus pattern (21 bp):
TAAACCCCAAACCATAAACCC
Found at i:52406653 original size:227 final size:229
Alignment explanation
Indices: 52406415--52406887 Score: 523
Period size: 227 Copynumber: 2.1 Consensus size: 229
52406405 TTTTTAGTTA
* * * *
52406415 AGCGTCGCTAATTTC-G-GGAAATAGCGGCGTTTTGTAAAAACCGCCGCT-ATTGGCT-CTATAG
1 AGCGCCGCTAATTACTGTGGAAATA--GGCGTTTT-TAAAAACCGCCACTAATT--CTGCTATAC
* * * * * *
52406476 CTGAAGAC-CAAATGTTGCG-TTTCAGTTAAGATATTTTGCGGCGCTTTTTATATTGTGCCGCTA
61 CTCAAGACAAAAACGCTGCGTTTTCAGTTAAGATATTTTGCGGCGCTTTTTATATAGCGCCGCTA
* * * *
52406539 ATACTGTGATTTAGCGGCGAGTTTCATAAGCGCCACTAATTCTAATATGCCTGAAGACC-AAACG
126 ATACTGTGATTTAGCGGCGAGTTTCATAAGCGCCAATAATTCTAATATACCTCAAGACCAAAACA
* *
52406603 CTGCATTTTGGTTAAGATATTTTGCGGCGCTTTTTATAT
191 CAGCATTTTGGTTAAGATATTTTACGGCGCTTTTTATAT
**** * * * *
52406642 AGCGCCGCTAA-TACTGTGTTTTTAGGCGTTTTTCATAAGCGCCACTAATTCTGGTATACCTCAA
1 AGCGCCGCTAATTACTGTGGAAATAGGCGTTTTTAAAAACCGCCACTAATTCTGCTATACCTCAA
* * *
52406706 GACAAAAACGCTGCGTTTTTAGTTAAGATATTTTTCGGCGCTTTTTTTATAGCGCCGCTAATACT
66 GACAAAAACGCTGCGTTTTCAGTTAAGATATTTTGCGGCGCTTTTTATATAGCGCCGCTAATACT
* * ** * * *
52406771 GTGCTTTAGCGGTGTTTTTCGTAAGCGCCAATAATTCTGATATACCTCAAGACCAAAACACAGCG
131 GTGATTTAGCGGCGAGTTTCATAAGCGCCAATAATTCTAATATACCTCAAGACCAAAACACAGCA
52406836 TTTTGGTTAAGATATTTTACGGCGCTTTTTATAT
196 TTTTGGTTAAGATATTTTACGGCGCTTTTTATAT
*
52406870 TGCGCCGCTAA-TACTGTG
1 AGCGCCGCTAATTACTGTG
52406888 CTTTAGCGGC
Statistics
Matches: 204, Mismatches: 35, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
224 2 0.01
225 21 0.10
226 21 0.10
227 100 0.49
228 60 0.29
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.35
Consensus pattern (229 bp):
AGCGCCGCTAATTACTGTGGAAATAGGCGTTTTTAAAAACCGCCACTAATTCTGCTATACCTCAA
GACAAAAACGCTGCGTTTTCAGTTAAGATATTTTGCGGCGCTTTTTATATAGCGCCGCTAATACT
GTGATTTAGCGGCGAGTTTCATAAGCGCCAATAATTCTAATATACCTCAAGACCAAAACACAGCA
TTTTGGTTAAGATATTTTACGGCGCTTTTTATAT
Found at i:52406829 original size:115 final size:114
Alignment explanation
Indices: 52406491--52406936 Score: 601
Period size: 114 Copynumber: 3.9 Consensus size: 114
52406481 GACCAAATGT
* * * *
52406491 TGCGTTTCAGTTAAGATATTTTGCGGCGCTTTTTATATTGTGCCGCTAATACTGTGATTTAGCGG
1 TGCGTTTTAGTTAAGATATTTTGCGGCGCTTTTTATATAGCGCCGCTAATACTGTGCTTTAGCGG
** * *
52406556 CGAGTTTCATAAGCGCCACTAATTCTAATATGCCTGAAGACC-AAACGC
66 CGTTTTTCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAAACGC
* * *
52406604 TGCATTTTGGTTAAGATATTTTGCGGCGCTTTTTATATAGCGCCGCTAATACTGTGTTTTTA--G
1 TGCGTTTTAGTTAAGATATTTTGCGGCGCTTTTTATATAGCGCCGCTAATACTGTG-CTTTAGCG
** *
52406667 GCGTTTTTCATAAGCGCCACTAATTCTGGTATACCTCAAGACAAAAACGC
65 GCGTTTTTCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAAACGC
* *
52406717 TGCGTTTTTAGTTAAGATATTTTTCGGCGCTTTTTTTATAGCGCCGCTAATACTGTGCTTTAGCG
1 TGCG-TTTTAGTTAAGATATTTTGCGGCGCTTTTTATATAGCGCCGCTAATACTGTGCTTTAGCG
* * * * *
52406782 GTGTTTTTCGTAAGCGCCAATAATTCTGATATACCTCAAGACCAAAACAC
65 GCGTTTTTCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAAACGC
* * * *
52406832 AGCGTTTTGGTTAAGATATTTTACGGCGCTTTTTATATTGCGCCGCTAATACTGTGCTTTAGCGG
1 TGCGTTTTAGTTAAGATATTTTGCGGCGCTTTTTATATAGCGCCGCTAATACTGTGCTTTAGCGG
* *
52406897 CGTTTTTGCATAAGCGCCACTAATTTTAATATACTTCAAG
66 CGTTTTT-CATAAGCGCCACTAATTCTAATATACCTCAAG
52406937 CTCGTACGCT
Statistics
Matches: 292, Mismatches: 35, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
112 37 0.13
113 64 0.22
114 116 0.40
115 75 0.26
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.37
Consensus pattern (114 bp):
TGCGTTTTAGTTAAGATATTTTGCGGCGCTTTTTATATAGCGCCGCTAATACTGTGCTTTAGCGG
CGTTTTTCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAAACGC
Found at i:52406951 original size:114 final size:113
Alignment explanation
Indices: 52406479--52406976 Score: 599
Period size: 114 Copynumber: 4.4 Consensus size: 113
52406469 TCTATAGCTG
* * ** * *
52406479 AAGACCAAATGTTGCGTTTCAGTTAAGATATTTTGCGGCGCTTTTTATATTGTGCCGCTAATACT
1 AAGACCAAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTTATATAGCGCCGCTAATACT
* ** * *
52406544 GTGATTTAGCGGCGAGTTTCATAAGCGCCACTAATTCTAATATGCCTG
66 GTGCTTTAGCGGCGTTTTTCATAAGCGCCACTAATTCTAATATACCTC
*
52406592 AAGACCAAACGCTGCATTTTGGTTAAGATATTTTGCGGCGCTTTTTATATAGCGCCGCTAATACT
1 AAGACCAAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTTATATAGCGCCGCTAATACT
* **
52406657 GTGTTTTTA--GGCGTTTTTCATAAGCGCCACTAATTCTGGTATACCTC
66 GTG-CTTTAGCGGCGTTTTTCATAAGCGCCACTAATTCTAATATACCTC
* * * *
52406704 AAGACAAAAACGCTGCGTTTTTAGTTAAGATATTTTTCGGCGCTTTTTTTATAGCGCCGCTAATA
1 AAGAC-CAAACGCTGCG-TTTTGGTTAAGATATTTTGCGGCGCTTTTTATATAGCGCCGCTAATA
* * * *
52406769 CTGTGCTTTAGCGGTGTTTTTCGTAAGCGCCAATAATTCTGATATACCTC
64 CTGTGCTTTAGCGGCGTTTTTCATAAGCGCCACTAATTCTAATATACCTC
* * * *
52406819 AAGACCAAAACACAGCGTTTTGGTTAAGATATTTTACGGCGCTTTTTATATTGCGCCGCTAATAC
1 AAGACC-AAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTTATATAGCGCCGCTAATAC
* *
52406884 TGTGCTTTAGCGGCGTTTTTGCATAAGCGCCACTAATTTTAATATACTTC
65 TGTGCTTTAGCGGCGTTTTT-CATAAGCGCCACTAATTCTAATATACCTC
** * * *
52406934 AAG-CTCGTACGCTGCGTTTTGTTTAACAT-TTTCTGCAGCGCTT
1 AAGAC-CAAACGCTGCGTTTTGGTTAAGATATTT-TGCGGCGCTT
52406977 ACAAATAAAC
Statistics
Matches: 331, Mismatches: 45, Indels: 17
0.84 0.11 0.04
Matches are distributed among these distances:
112 37 0.11
113 77 0.23
114 142 0.43
115 75 0.23
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.37
Consensus pattern (113 bp):
AAGACCAAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTTATATAGCGCCGCTAATACT
GTGCTTTAGCGGCGTTTTTCATAAGCGCCACTAATTCTAATATACCTC
Found at i:52408440 original size:13 final size:13
Alignment explanation
Indices: 52408422--52408447 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52408412 AGAAACACAT
52408422 ATATCATATCAGA
1 ATATCATATCAGA
52408435 ATATCATATCAGA
1 ATATCATATCAGA
52408448 CCATAACAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
ATATCATATCAGA
Found at i:52410486 original size:42 final size:43
Alignment explanation
Indices: 52410375--52410680 Score: 334
Period size: 43 Copynumber: 7.2 Consensus size: 43
52410365 TTTCAAAAAT
* * *
52410375 AAACACCGCTATAGA-CCATGACCTTTAGCGGTGCTTTTCCCAC
1 AAACGCCGCTATAGATCGA-GACCTTTAGCGGCGCTTTTCCCAC
* * *
52410418 AAACGCCGCTAAAGATC-AGGACCTTTAGCGGTGCTTTT-GCAC
1 AAACGCCGCTATAGATCGA-GACCTTTAGCGGCGCTTTTCCCAC
* * * *
52410460 AAGCGCTGTTATAGATCGAGATCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCGAGACCTTTAGCGGCGCTTTTCCCAC
52410503 AAACGCCGCTATAGATCGAGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCGAGACCTTTAGCGGCGCTTTTCCCAC
* * * *
52410546 AAACACCGCTATAGATC-ATGACATTTAGCGGCACTTTTTCCAC
1 AAACGCCGCTATAGATCGA-GACCTTTAGCGGCGCTTTTCCCAC
* * * *
52410589 AAATGCCGCTATAGCTCAAGACCTTTAGTGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCGAGACCTTTAGCGGCGCTTTTCCCAC
* * * * * *
52410632 AAACGCCGCTATAGAAC-AAACCTTTAGCGACGCTTCTCGCAA
1 AAACGCCGCTATAGATCGAGACCTTTAGCGGCGCTTTTCCCAC
52410674 AAACGCC
1 AAACGCC
52410681 ACTAAAAACA
Statistics
Matches: 223, Mismatches: 35, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
42 60 0.27
43 161 0.72
44 2 0.01
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTATAGATCGAGACCTTTAGCGGCGCTTTTCCCAC
Found at i:52410528 original size:128 final size:127
Alignment explanation
Indices: 52410375--52410666 Score: 361
Period size: 128 Copynumber: 2.3 Consensus size: 127
52410365 TTTCAAAAAT
* * *
52410375 AAACACCGCTATAGACCATGACCTTTAGCGGTGCTTTTCCCACAAACGCCGCTAAAGATCAGGAC
1 AAACGCCGCTATAGA-CA-GACCTTTAGCGGCGCTTTTCCCACAAACACCGCTAAAGATCAGGAC
* ** * * * * * *
52410440 CTTTAGCGGTGC-TTTTGCACAAGCGCTGTTATAGATCGAGATCTTTAGCGGCGCTTTTCCCAC
64 ATTTAGCGGCACTTTTTCCACAAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* *
52410503 AAACGCCGCTATAGATCGAGACCTTTAGCGGCGCTTTTCCCACAAACACCGCTATAGATCATGAC
1 AAACGCCGCTATAGA-C-AGACCTTTAGCGGCGCTTTTCCCACAAACACCGCTAAAGATCAGGAC
* * *
52410568 ATTTAGCGGCACTTTTTCCACAAATGCCGCTATAGCTCAAGACCTTTAGTGGCGCTTTTCCCAC
64 ATTTAGCGGCACTTTTTCCACAAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* *
52410632 AAACGCCGCTATAGAACAAACCTTTAGCGACGCTT
1 AAACGCCGCTATAG-ACAGACCTTTAGCGGCGCTT
52410667 CTCGCAAAAA
Statistics
Matches: 141, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
128 82 0.58
129 58 0.41
130 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (127 bp):
AAACGCCGCTATAGACAGACCTTTAGCGGCGCTTTTCCCACAAACACCGCTAAAGATCAGGACAT
TTAGCGGCACTTTTTCCACAAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
Found at i:52411655 original size:22 final size:22
Alignment explanation
Indices: 52411543--52411648 Score: 158
Period size: 22 Copynumber: 4.8 Consensus size: 22
52411533 TGTTGATAGT
*
52411543 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
52411565 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
52411587 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
* * * **
52411609 ACGAACTAAACCCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
52411631 ACGTACTAAGCTCTCATG
1 ACGTACTAAGCTCTCATG
52411649 GCTAACGCAC
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 75 1.00
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.31
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTA
Found at i:52412240 original size:5 final size:5
Alignment explanation
Indices: 52412230--52412255 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
52412220 ACTTGGTTTG
52412230 TATTT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT T
52412256 CAAATTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:52413337 original size:12 final size:12
Alignment explanation
Indices: 52413320--52413374 Score: 62
Period size: 12 Copynumber: 4.7 Consensus size: 12
52413310 CAAATTATTT
52413320 TATTTAAACTAA
1 TATTTAAACTAA
52413332 TATTTAAACT--
1 TATTTAAACTAA
*
52413342 TATTTATTAA-TAC
1 TATTTA--AACTAA
52413355 TATTTAAACTAA
1 TATTTAAACTAA
52413367 TATTTAAA
1 TATTTAAA
52413375 TGTTTAAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
10 6 0.16
11 3 0.08
12 22 0.59
13 6 0.16
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.47
Consensus pattern (12 bp):
TATTTAAACTAA
Found at i:52413394 original size:35 final size:36
Alignment explanation
Indices: 52413311--52413399 Score: 105
Period size: 35 Copynumber: 2.6 Consensus size: 36
52413301 TTTTGAACAC
52413311 AAAT-TATTTTATTTAAACTAATATTTAAACTTATT
1 AAATATATTTTATTTAAACTAATATTTAAACTTATT
* * **
52413346 TATTA-ATACTATTTAAACTAATATTTAAA-TGT-TT
1 AAATATATTTTATTTAAACTAATATTTAAACT-TATT
52413380 AAATATATTTTATTTAAACT
1 AAATATATTTTATTTAAACT
52413400 TATTTATTAA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
34 6 0.14
35 37 0.86
ACGTcount: A:0.43, C:0.06, G:0.01, T:0.51
Consensus pattern (36 bp):
AAATATATTTTATTTAAACTAATATTTAAACTTATT
Found at i:52413455 original size:58 final size:58
Alignment explanation
Indices: 52413335--52413455 Score: 154
Period size: 58 Copynumber: 2.1 Consensus size: 58
52413325 AAACTAATAT
* * * *
52413335 TTAAACTTATTTATTAATACTATTTAAACTAATATTTAAATGTTTAAATATATTTTAT
1 TTAAACTTATTTATTAATACTATTTAAACTAATATTTAAATATATAAATATAGTTTAA
* * * *
52413393 TTAAACTTATTTATTAATTCTATTTAACCTAATATTTAAATATATCAA-ATGGTTTAGA
1 TTAAACTTATTTATTAATACTATTTAAACTAATATTTAAATATATAAATATAGTTTA-A
52413451 TTAAA
1 TTAAA
52413456 TTTTTTTAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
57 6 0.11
58 48 0.89
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.49
Consensus pattern (58 bp):
TTAAACTTATTTATTAATACTATTTAAACTAATATTTAAATATATAAATATAGTTTAA
Found at i:52413713 original size:15 final size:15
Alignment explanation
Indices: 52413693--52413730 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
52413683 TCGACCCCTG
52413693 AATCCCTAAAC-CTT
1 AATCCCTAAACTCTT
52413707 AAATCCCT-AACTCTT
1 -AATCCCTAAACTCTT
52413722 AATCCCTAA
1 AATCCCTAA
52413731 CATCTAGCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.37, C:0.34, G:0.00, T:0.29
Consensus pattern (15 bp):
AATCCCTAAACTCTT
Found at i:52413727 original size:14 final size:14
Alignment explanation
Indices: 52413693--52413731 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
52413683 TCGACCCCTG
52413693 AATCCCTAAACCTTA
1 AATCCCT-AACCTTA
52413708 AATCCCTAACTCTT-
1 AATCCCTAAC-CTTA
52413722 AATCCCTAAC
1 AATCCCTAAC
52413732 ATCTAGCCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.28
Consensus pattern (14 bp):
AATCCCTAACCTTA
Found at i:52414005 original size:14 final size:14
Alignment explanation
Indices: 52413986--52414048 Score: 65
Period size: 14 Copynumber: 4.4 Consensus size: 14
52413976 AACCTTAAAT
52413986 CCCTAAC-TCTTAAC
1 CCCTAACGTC-TAAC
*
52414000 CCCTAACGTCAAAC
1 CCCTAACGTCTAAC
52414014 CCCTAACGTCTAAC
1 CCCTAACGTCTAAC
* **
52414028 CCTTAAACCCCTAAC
1 CCCT-AACGTCTAAC
52414043 CCCTAA
1 CCCTAA
52414049 ACTTTAAATC
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
14 28 0.68
15 13 0.32
ACGTcount: A:0.32, C:0.44, G:0.03, T:0.21
Consensus pattern (14 bp):
CCCTAACGTCTAAC
Found at i:52414070 original size:21 final size:22
Alignment explanation
Indices: 52413996--52414071 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 22
52413986 CCCTAACTCT
* *
52413996 TAACCCCT-AACGTCAAACCCC
1 TAACCCCTAAACTTTAAACCCC
** * *
52414017 TAACGTCTAACCCTTAAACCCC
1 TAACCCCTAAACTTTAAACCCC
*
52414039 TAACCCCTAAACTTTAAATCCC
1 TAACCCCTAAACTTTAAACCCC
*
52414061 -AACCCTTAAAC
1 TAACCCCTAAAC
52414072 CATAATCCCT
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
21 16 0.37
22 27 0.63
ACGTcount: A:0.36, C:0.41, G:0.03, T:0.21
Consensus pattern (22 bp):
TAACCCCTAAACTTTAAACCCC
Found at i:52414088 original size:14 final size:14
Alignment explanation
Indices: 52414071--52414112 Score: 66
Period size: 14 Copynumber: 2.9 Consensus size: 14
52414061 AACCCTTAAA
52414071 CCATAATCCCTAAT
1 CCATAATCCCTAAT
52414085 CCATAATCCCTAAAT
1 CCATAATCCCT-AAT
*
52414100 CCATACTCCCTAA
1 CCATAATCCCTAA
52414113 ACCTTAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 13 0.50
15 13 0.50
ACGTcount: A:0.36, C:0.38, G:0.00, T:0.26
Consensus pattern (14 bp):
CCATAATCCCTAAT
Found at i:52414100 original size:15 final size:15
Alignment explanation
Indices: 52414067--52414113 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
52414057 TCCCAACCCT
52414067 TAAA-CCATAATCCC
1 TAAATCCATAATCCC
52414081 T-AATCCATAATCCC
1 TAAATCCATAATCCC
*
52414095 TAAATCCATACTCCC
1 TAAATCCATAATCCC
52414110 TAAA
1 TAAA
52414114 CCTTAAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 2 0.07
14 12 0.40
15 16 0.53
ACGTcount: A:0.40, C:0.34, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:52414252 original size:57 final size:57
Alignment explanation
Indices: 52414188--52414302 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
52414178 ACCTTAAACT
52414188 ATAGTGATAATTAATTCAACATTTTAAAATTAATACTATCTCCTTTACGATTATATA
1 ATAGTGATAATTAATTCAACATTTTAAAATTAATACTATCTCCTTTACGATTATATA
52414245 ATAGTGATAATTAATTCAACATTTTAAAATTAATACTATCTCCTTTACGATTATATA
1 ATAGTGATAATTAATTCAACATTTTAAAATTAATACTATCTCCTTTACGATTATATA
52414302 A
1 A
52414303 GAAATTTTTT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.42
Consensus pattern (57 bp):
ATAGTGATAATTAATTCAACATTTTAAAATTAATACTATCTCCTTTACGATTATATA
Found at i:52414573 original size:41 final size:41
Alignment explanation
Indices: 52414516--52414714 Score: 310
Period size: 41 Copynumber: 4.9 Consensus size: 41
52414506 TAAAAAGCTT
* *
52414516 TTAGCGGTGCTTTATCAAAAACGCCGCTAAAGCCCAGAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCAGAGCA
* * *
52414557 TTAGCGGCGCTTTATCAAAAACGCTGCTAAATCCCAGAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCAGAGCA
* *
52414598 TTAGCGGCGCTTTTTCAAAAAAGCCGCTAAAGCCCCGAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCAGAGCA
52414639 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCC-GAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAA-GCCCAGAGCA
*
52414680 TTAGCGGCGCTTTTTCAAAATCGCCGCTAAAGCCC
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCCC
52414715 CAAAAGGTCA
Statistics
Matches: 147, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
40 4 0.03
41 139 0.95
42 4 0.03
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.21
Consensus pattern (41 bp):
TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCAGAGCA
Found at i:52414755 original size:43 final size:43
Alignment explanation
Indices: 52414707--52414793 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
52414697 AAATCGCCGC
* *
52414707 TAAAGCCCCAAAAGGTCAGAAGACGGCGTCGTTGGGCTTATGT
1 TAAAGCCCCAAAAGGTCAGAAAACAGCGTCGTTGGGCTTATGT
52414750 TAAAGCCCCAAAAGGTCAGAAAACAGCGTCGTTGGGCTTATGT
1 TAAAGCCCCAAAAGGTCAGAAAACAGCGTCGTTGGGCTTATGT
52414793 T
1 T
52414794 TTTTGCGGCG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.30, C:0.21, G:0.28, T:0.22
Consensus pattern (43 bp):
TAAAGCCCCAAAAGGTCAGAAAACAGCGTCGTTGGGCTTATGT
Found at i:52414879 original size:40 final size:39
Alignment explanation
Indices: 52414808--52414922 Score: 149
Period size: 40 Copynumber: 2.9 Consensus size: 39
52414798 GCGGCGCCAG
* * * *
52414808 AAAGCGCCGCTAATGCTTATTTTTAGCGGCGTTTTCCAT
1 AAAGCACCGCTAATGCTAATCTTTAGCGGCGTTTTCCAA
**
52414847 AATTCACCGCTAATGCTAGATCTTTAGCGGCGTTTTCCAA
1 AAAGCACCGCTAATGCTA-ATCTTTAGCGGCGTTTTCCAA
*
52414887 AAAGCGCCGCTAATGCTCAATCTTTAGCGGCGTTTT
1 AAAGCACCGCTAATGCT-AATCTTTAGCGGCGTTTT
52414923 TTATCCAAAC
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
39 14 0.22
40 50 0.77
41 1 0.02
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (39 bp):
AAAGCACCGCTAATGCTAATCTTTAGCGGCGTTTTCCAA
Found at i:52414949 original size:12 final size:12
Alignment explanation
Indices: 52414932--52414956 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52414922 TTTATCCAAA
52414932 CGCCGCTAAAAG
1 CGCCGCTAAAAG
52414944 CGCCGCTAAAAG
1 CGCCGCTAAAAG
52414956 C
1 C
52414957 CTATTTTGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.36, G:0.24, T:0.08
Consensus pattern (12 bp):
CGCCGCTAAAAG
Found at i:52415685 original size:27 final size:29
Alignment explanation
Indices: 52415644--52415703 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
52415634 ATTATATTTG
* *
52415644 TAAAATTTTATAAATAT-TTTTAATAAAA
1 TAAAATTTTAAAAATATATTATAATAAAA
*
52415672 TAAAA-TTTAAAAATATATTATAATTAAA
1 TAAAATTTTAAAAATATATTATAATAAAA
52415700 TAAA
1 TAAA
52415704 TATTATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 10 0.36
28 18 0.64
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
TAAAATTTTAAAAATATATTATAATAAAA
Found at i:52416338 original size:30 final size:29
Alignment explanation
Indices: 52416270--52416344 Score: 71
Period size: 30 Copynumber: 2.5 Consensus size: 29
52416260 AAGAAATTTG
*
52416270 TTAAAAGGGTATAAATTGAATTATTAATTT
1 TTAAAAGGGTA-AAATTGAATTATTAATTA
** *
52416300 TTTTAAGGGCTAAAA-TGTAATTTTTAATTA
1 TTAAAAGGG-TAAAATTG-AATTATTAATTA
52416330 TTAAAAGGGTTAAAA
1 TTAAAAGGG-TAAAA
52416345 AGCTTAAATT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
29 2 0.06
30 32 0.89
31 2 0.06
ACGTcount: A:0.43, C:0.01, G:0.15, T:0.41
Consensus pattern (29 bp):
TTAAAAGGGTAAAATTGAATTATTAATTA
Found at i:52422854 original size:27 final size:27
Alignment explanation
Indices: 52422812--52422875 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
52422802 CATCCTATCA
* * *
52422812 GCCTTTGTGGCGTACTCTGAATGAATT
1 GCCTTTGTGGCATACTCTAAATGAATC
*
52422839 GCCTTTGTGGCATACTCTAAATGGATC
1 GCCTTTGTGGCATACTCTAAATGAATC
*
52422866 GCCTTAGTGG
1 GCCTTTGTGG
52422876 TGTACCTTAC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.19, C:0.20, G:0.27, T:0.34
Consensus pattern (27 bp):
GCCTTTGTGGCATACTCTAAATGAATC
Found at i:52437745 original size:15 final size:15
Alignment explanation
Indices: 52437726--52437763 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
52437716 TAATTAAGGT
52437726 TTAATTAAATAATT-
1 TTAATTAAATAATTA
*
52437740 TATAATTAATTAATTA
1 T-TAATTAAATAATTA
52437756 TTAATTAA
1 TTAATTAA
52437764 GGTATATAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 19 0.90
16 1 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAATTAAATAATTA
Found at i:52440914 original size:13 final size:14
Alignment explanation
Indices: 52440896--52440928 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
52440886 TTAGCTTATT
*
52440896 AAATATAAATA-AA
1 AAATATAAACATAA
52440909 AAATATAAACATAA
1 AAATATAAACATAA
52440923 AAATAT
1 AAATAT
52440929 TACAAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (14 bp):
AAATATAAACATAA
Found at i:52441518 original size:32 final size:34
Alignment explanation
Indices: 52441481--52441554 Score: 107
Period size: 34 Copynumber: 2.2 Consensus size: 34
52441471 CTATGTTATA
*
52441481 GTTTATGCTAATT-ATATTTTTATAATAAGG-AT
1 GTTTATGCTAATTGATATTATTATAATAAGGAAT
*
52441513 TTTTATGCTAATTGGATATTATTATAATAAGGAAT
1 GTTTATGCTAATT-GATATTATTATAATAAGGAAT
52441548 GTTTATG
1 GTTTATG
52441555 GGATTGAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
32 12 0.33
34 16 0.44
35 8 0.22
ACGTcount: A:0.34, C:0.03, G:0.15, T:0.49
Consensus pattern (34 bp):
GTTTATGCTAATTGATATTATTATAATAAGGAAT
Found at i:52441711 original size:6 final size:6
Alignment explanation
Indices: 52441700--52441726 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
52441690 GCATATAATT
52441700 ATTATA ATTATA ATTATA ATTATA ATT
1 ATTATA ATTATA ATTATA ATTATA ATT
52441727 TAAGGTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
ATTATA
Found at i:52454499 original size:38 final size:38
Alignment explanation
Indices: 52454456--52454530 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
52454446 ACTATTTACC
* *
52454456 AAACTTAATCAACCTTTCAAGATATATTCTATTTTTTT
1 AAACTTAATCAACCTTCCAAGATATATTCTAATTTTTT
52454494 AAACTTAATCAACCTTCCAAGATATATTCTAATTTTT
1 AAACTTAATCAACCTTCCAAGATATATTCTAATTTTT
52454531 AGTGCAACCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.36, C:0.17, G:0.03, T:0.44
Consensus pattern (38 bp):
AAACTTAATCAACCTTCCAAGATATATTCTAATTTTTT
Found at i:52455274 original size:2 final size:2
Alignment explanation
Indices: 52455267--52455304 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
52455257 AATAATAAGA
52455267 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
52455305 TGAAATTGGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52459997 original size:35 final size:35
Alignment explanation
Indices: 52459958--52460145 Score: 102
Period size: 37 Copynumber: 5.2 Consensus size: 35
52459948 TTTGCAATCG
52459958 CAACTTCATTTAAACAGCTCGTTGATTTACGATCA
1 CAACTTCATTTAAACAGCTCGTTGATTTACGATCA
* ** *
52459993 CAACTGTCATTTTTTAA-AGCTCACTAATTTACGATCTTGA
1 CAACT-TCA--TTTAAACAGCTCGTTGATTTACGATC---A
* * *
52460033 -ACACTTCA-TT-AAGAGTTCGTTGATTTACGA-CTG
1 CA-ACTTCATTTAAACAGCTCGTTGATTTACGATC-A
* * ** *
52460066 CAACTCCATTTAAACAGTTCACTGATTTATGATCA
1 CAACTTCATTTAAACAGCTCGTTGATTTACGATCA
52460101 CAACTTTCATTTTTCAAAC--CTCGTTGATTTACGATCA
1 CAAC-TTCA--TTT-AAACAGCTCGTTGATTTACGATCA
*
52460138 CAGCTTCA
1 CAACTTCA
52460146 GTTCATTGAT
Statistics
Matches: 115, Mismatches: 22, Indels: 31
0.68 0.13 0.18
Matches are distributed among these distances:
33 5 0.04
34 3 0.03
35 28 0.24
36 26 0.23
37 33 0.29
38 8 0.07
39 8 0.07
40 4 0.03
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (35 bp):
CAACTTCATTTAAACAGCTCGTTGATTTACGATCA
Done.