Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
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: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 168 of 316
Found at i:53618725 original size:23 final size:23
Alignment explanation
Indices: 53618682--53618731 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
53618672 CTGTATTTGA
53618682 GCATGCCATGTTATATGTATGTT
1 GCATGCCATGTTATATGTATGTT
53618705 GCAT-CCATGTATAATAT-TATGTT
1 GCATGCCATGT-T-ATATGTATGTT
53618728 GCAT
1 GCAT
53618732 TGCATGGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.24
23 15 0.60
24 4 0.16
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (23 bp):
GCATGCCATGTTATATGTATGTT
Found at i:53619629 original size:30 final size:30
Alignment explanation
Indices: 53619595--53619654 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
53619585 TATCATGTCT
53619595 TATGGAAAACACTTCAATGTGGCATCGCCA
1 TATGGAAAACACTTCAATGTGGCATCGCCA
*
53619625 TATGGAAAACACTTCAATGTGGCATTGCCA
1 TATGGAAAACACTTCAATGTGGCATCGCCA
53619655 GATTCGGCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (30 bp):
TATGGAAAACACTTCAATGTGGCATCGCCA
Found at i:53629200 original size:50 final size:50
Alignment explanation
Indices: 53629093--53629245 Score: 148
Period size: 52 Copynumber: 3.0 Consensus size: 50
53629083 CGGAAAAGAT
** * * ** *
53629093 ATGATATGTGCGCCCGTTTAAGACCATAGCTGGGCTATGGCATCAGTGCAAT
1 ATGATATGTGTTCCCGTATAAGACCA-AGCT-GGCTATGGCATCGGTGTGAC
*
53629145 GTGATATGTGTTCCCGTATAAGACC-AGCTGTGCTATGGCATCGGTGTGAC
1 ATGATATGTGTTCCCGTATAAGACCAAGCTG-GCTATGGCATCGGTGTGAC
*
53629195 ATGATAATGTGATT-CCGTATAAGACCATATCTGGCATATGGCATCGGTGTG
1 ATGAT-ATGTG-TTCCCGTATAAGACCA-AGCTGGC-TATGGCATCGGTGTG
53629246 TGATGTGATC
Statistics
Matches: 85, Mismatches: 10, Indels: 11
0.80 0.09 0.10
Matches are distributed among these distances:
49 1 0.01
50 23 0.27
51 17 0.20
52 25 0.29
53 19 0.22
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.29
Consensus pattern (50 bp):
ATGATATGTGTTCCCGTATAAGACCAAGCTGGCTATGGCATCGGTGTGAC
Found at i:53629265 original size:46 final size:47
Alignment explanation
Indices: 53629201--53629295 Score: 122
Period size: 46 Copynumber: 2.0 Consensus size: 47
53629191 TGACATGATA
* * **
53629201 ATGTGATTCCGTATAAGACCATA-TCTGGCATATGGCATCGGTGTGTG
1 ATGTGATTCCATAAAAGACCATAGTAGGGC-TATGGCATCGGTGTGTG
*
53629248 ATGTGA-TCCATAAAAGACCATAGTAGGGCTATGGCTTCGGTGTGTG
1 ATGTGATTCCATAAAAGACCATAGTAGGGCTATGGCATCGGTGTGTG
53629294 AT
1 AT
53629296 ATGTGAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
46 32 0.76
47 10 0.24
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (47 bp):
ATGTGATTCCATAAAAGACCATAGTAGGGCTATGGCATCGGTGTGTG
Found at i:53637897 original size:34 final size:34
Alignment explanation
Indices: 53637853--53637920 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
53637843 GAACAGTTGA
* * *
53637853 ACAGTCTTGGGGCTAAGCCCTTTTCAGTATCAGTG
1 ACAGTCTTGGGCCTAAGCCCATCTCAGTA-CAGTG
*
53637888 ACAGT-TTGGGCCTTAGCCCATCTCAGTACAGTG
1 ACAGTCTTGGGCCTAAGCCCATCTCAGTACAGTG
53637921 TGAAAAATGC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 5 0.17
34 19 0.66
35 5 0.17
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.29
Consensus pattern (34 bp):
ACAGTCTTGGGCCTAAGCCCATCTCAGTACAGTG
Found at i:53643209 original size:9 final size:9
Alignment explanation
Indices: 53643195--53643263 Score: 51
Period size: 9 Copynumber: 8.0 Consensus size: 9
53643185 GACACCTGCA
53643195 ATTAAACAC
1 ATTAAACAC
53643204 ATTAAA-AC
1 ATTAAACAC
*
53643212 ---AAACAT
1 ATTAAACAC
53643218 ATTAAACAC
1 ATTAAACAC
53643227 ATTTAAACAC
1 A-TTAAACAC
53643237 TTATTAAACAC
1 --ATTAAACAC
53643248 A--AAACAC
1 ATTAAACAC
*
53643255 TTTAAACAC
1 ATTAAACAC
53643264 TTATCTTAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 18
0.70 0.04 0.26
Matches are distributed among these distances:
5 3 0.06
6 1 0.02
7 6 0.12
8 2 0.04
9 19 0.40
10 8 0.17
11 8 0.17
12 1 0.02
ACGTcount: A:0.55, C:0.20, G:0.00, T:0.25
Consensus pattern (9 bp):
ATTAAACAC
Found at i:53643243 original size:11 final size:11
Alignment explanation
Indices: 53643195--53643248 Score: 58
Period size: 10 Copynumber: 4.9 Consensus size: 11
53643185 GACACCTGCA
53643195 ATTAAACACAT
1 ATTAAACACAT
*
53643206 -TAAAACAAACAT
1 ATTAAAC--ACAT
53643218 ATTAAACACAT
1 ATTAAACACAT
*
53643229 -TTAAACACTT
1 ATTAAACACAT
53643239 ATTAAACACA
1 ATTAAACACA
53643249 AAACACTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
10 14 0.40
11 12 0.34
12 4 0.11
13 5 0.14
ACGTcount: A:0.56, C:0.19, G:0.00, T:0.26
Consensus pattern (11 bp):
ATTAAACACAT
Found at i:53643243 original size:21 final size:22
Alignment explanation
Indices: 53643195--53643248 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 22
53643185 GACACCTGCA
53643195 ATTAAACACATTAAAACAAACAT
1 ATTAAACACATTAAAAC-AACAT
* *
53643218 ATTAAACACATTTAAAC-ACTT
1 ATTAAACACATTAAAACAACAT
53643239 ATTAAACACA
1 ATTAAACACA
53643249 AAACACTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 13 0.45
23 16 0.55
ACGTcount: A:0.56, C:0.19, G:0.00, T:0.26
Consensus pattern (22 bp):
ATTAAACACATTAAAACAACAT
Found at i:53643254 original size:18 final size:19
Alignment explanation
Indices: 53643217--53643256 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
53643207 AAAACAAACA
53643217 TATTAAACACATTTAAACACT
1 TATTAAACACA--TAAACACT
53643238 TATTAAACACA-AAACACT
1 TATTAAACACATAAACACT
53643256 T
1 T
53643257 TAAACACTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.42
21 11 0.58
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (19 bp):
TATTAAACACATAAACACT
Found at i:53647466 original size:45 final size:45
Alignment explanation
Indices: 53647341--53647555 Score: 253
Period size: 45 Copynumber: 4.9 Consensus size: 45
53647331 TTTTATCAAA
* * * **
53647341 TCACCGGCATT-CAGCCTGCTAGGTTTAAAAACCCGAAT--TCAT-
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAAT-ATC
* *
53647383 TCACCGGCATT-TCGCCTGCTAGGCTC-GAGGCCCGAATAATATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC
* * *
53647426 TCACCAGTATTATAGCCTGCTAGGCTTAAAGGCCCGAATAATATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC
* * *
53647471 TCACTGGCATTATAGCCTGCTAGGGTCAAAGGCCTGAATAATATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC
*
53647516 TCACCGGCATTATAGCCTGCTAGACTCAAAGGCCCGAATA
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATA
53647556 GTACTGTACA
Statistics
Matches: 146, Mismatches: 22, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
41 8 0.05
42 24 0.16
43 10 0.07
44 13 0.09
45 91 0.62
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (45 bp):
TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC
Found at i:53652234 original size:40 final size:39
Alignment explanation
Indices: 53652145--53652406 Score: 309
Period size: 39 Copynumber: 6.6 Consensus size: 39
53652135 TTGAATGATG
* *
53652145 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAATGAC-AAT
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGAT-ACTAAT
*
53652183 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGATACTAAT
*
53652224 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAT
*
53652263 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAT
* * *
53652302 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAT
* *
53652341 TCTGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGA-TACTAAT
* *
53652380 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGT-CCGAAGGCATTTG
53652407 AACGAGGAGC
Statistics
Matches: 200, Mismatches: 16, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
39 131 0.65
40 57 0.28
41 12 0.06
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:53652439 original size:79 final size:79
Alignment explanation
Indices: 53652197--53652431 Score: 241
Period size: 78 Copynumber: 3.0 Consensus size: 79
53652187 GGACTAAGAT
* **
53652197 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGAT-ACTA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAG-TGACTA
* * *
53652261 ATTC-CGGGCT-AAGC
65 AATCTC-GGTTAAATC
* ** *
53652275 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
* *
53652340 ATCTGGGTTAAGTC
66 ATCTCGGTTAAATC
*
53652354 CCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAG
1 CCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-
*
53652416 CTATATC-CGGTTAAAT
62 CTAAATCTCGGTTAAAT
53652432 TTCGAAGGTA
Statistics
Matches: 137, Mismatches: 13, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
77 1 0.01
78 71 0.52
79 41 0.30
80 24 0.18
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
ATCTCGGTTAAATC
Found at i:53660256 original size:39 final size:40
Alignment explanation
Indices: 53660161--53660383 Score: 266
Period size: 39 Copynumber: 5.7 Consensus size: 40
53660151 TTGAATGATG
*
53660161 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
53660199 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
53660240 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
53660279 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
53660318 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
53660357 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
53660384 AACGAGGAGC
Statistics
Matches: 164, Mismatches: 11, Indels: 17
0.85 0.06 0.09
Matches are distributed among these distances:
39 93 0.57
40 59 0.36
41 11 0.07
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:53660347 original size:79 final size:81
Alignment explanation
Indices: 53660161--53660383 Score: 282
Period size: 79 Copynumber: 2.8 Consensus size: 81
53660151 TTGAATGATG
* * *
53660161 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATATCCGGACTAAGATCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACTAATATCCGGGCTAAGACCCGAAGGCAT
*
53660223 TTGTGCGAGATACTAAT
65 TTGTGCGAGATACTAAA
53660240 TCCGGGCTAAG-CCCGAAGGCATTTGTGCG-AGATACTAAT-TCCGGGCTAAG-CCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTAATATCCGGGCTAAGACCCGAAGGCAT
*
53660301 TTGTGCGAGTTACTAAA
65 TTGTGCGAGATACTAAA
* * * * *
53660318 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACT-ATAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATATCCGGGCTAAGACCCGAAGGCATT
53660382 TG
66 TG
53660384 AACGAGGAGC
Statistics
Matches: 127, Mismatches: 9, Indels: 15
0.84 0.06 0.10
Matches are distributed among these distances:
78 46 0.36
79 56 0.44
80 25 0.20
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATATCCGGGCTAAGACCCGAAGGCATT
TGTGCGAGATACTAAA
Found at i:53660405 original size:79 final size:79
Alignment explanation
Indices: 53660161--53660416 Score: 217
Period size: 79 Copynumber: 3.3 Consensus size: 79
53660151 TTGAATGATG
* * * *
53660161 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATATCCGGACTAAGATCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA-CCGGGCTAAG-CCCGAAGGCA
** *
53660222 TTTGTGCGAGAT-ACTAAT
62 TTTGAACGAG-TGACTAAA
* *
53660240 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
** *
53660304 TGCGAGTTACTAAA
66 AACGAGTGACTAAA
*
53660318 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCAT
*
53660381 TTGAACGAG-GAGCTATA
63 TTGAACGAGTGA-CTAAA
* *
53660398 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
53660417 TACGTGATTT
Statistics
Matches: 153, Mismatches: 14, Indels: 20
0.82 0.07 0.11
Matches are distributed among these distances:
77 1 0.01
78 46 0.30
79 69 0.45
80 36 0.24
81 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
AACGAGTGACTAAA
Found at i:53662347 original size:40 final size:40
Alignment explanation
Indices: 53662158--53662383 Score: 280
Period size: 40 Copynumber: 5.7 Consensus size: 40
53662148 TTGAATGATG
* * * *
53662158 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
53662198 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
53662238 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
53662278 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
53662318 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
53662359 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
53662384 AACGAGGAGC
Statistics
Matches: 168, Mismatches: 14, Indels: 8
0.88 0.07 0.04
Matches are distributed among these distances:
39 1 0.01
40 157 0.93
41 10 0.06
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:53670172 original size:40 final size:40
Alignment explanation
Indices: 53670084--53670309 Score: 266
Period size: 40 Copynumber: 5.7 Consensus size: 40
53670074 TTGAATGATG
* * *
53670084 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAA
* *
53670124 TCCAGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAA
* *
53670164 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAA
*
53670204 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
*
53670244 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTA-AA
*
53670285 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
53670310 AACGAGGAGC
Statistics
Matches: 166, Mismatches: 14, Indels: 12
0.86 0.07 0.06
Matches are distributed among these distances:
39 1 0.01
40 152 0.92
41 12 0.07
42 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
Found at i:53670327 original size:80 final size:79
Alignment explanation
Indices: 53670137--53670342 Score: 215
Period size: 80 Copynumber: 2.6 Consensus size: 79
53670127 AGACTAAGAT
** *
53670137 CCGAAGGCATTTGTGCGAGAT-ACTAAATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC
1 CCGAAGGCATTTGAACGAG-TGACTAAATCCGG-TTAA-ATCCCGAAGGCATTTGTGCGAGATAC
*
53670200 TAATTCCGGGCTAAGTC
63 TAATACCGGGCTAAGTC
** * *
53670217 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT
1 CCGAAGGCATTTGAACGAGTGACTAAATCC-GGTTAAATCCCGAAGGCATTTGTGCGAGA-TACT
*
53670281 -ATAACCGGGCTATGTC
64 AAT-ACCGGGCTAAGTC
* *
53670297 CCGAAGGCATTTGAACGAG-GAGCTATATCCGGTTAAATTCCGAAGG
1 CCGAAGGCATTTGAACGAGTGA-CTAAATCCGGTTAAATCCCGAAGG
53670343 TACGTGATTT
Statistics
Matches: 110, Mismatches: 10, Indels: 13
0.83 0.08 0.10
Matches are distributed among these distances:
79 20 0.18
80 88 0.80
81 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGAACGAGTGACTAAATCCGGTTAAATCCCGAAGGCATTTGTGCGAGATACTAA
TACCGGGCTAAGTC
Found at i:53672538 original size:40 final size:40
Alignment explanation
Indices: 53672483--53672700 Score: 343
Period size: 40 Copynumber: 5.5 Consensus size: 40
53672473 CGGATGATAA
* *
53672483 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
*
53672523 CCGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
53672563 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
53672603 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
53672643 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
53672683 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
53672701 TACTCGGTTT
Statistics
Matches: 168, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
39 17 0.10
40 150 0.89
41 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:53676316 original size:46 final size:46
Alignment explanation
Indices: 53676266--53676436 Score: 204
Period size: 46 Copynumber: 3.7 Consensus size: 46
53676256 TGGTTGAGCA
*
53676266 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * * *
53676312 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
*
53676359 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
53676405 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACT
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT
53676437 AAGGGGCGGG
Statistics
Matches: 104, Mismatches: 14, Indels: 14
0.79 0.11 0.11
Matches are distributed among these distances:
43 5 0.05
45 3 0.03
46 60 0.58
47 29 0.28
48 3 0.03
50 4 0.04
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:53676422 original size:93 final size:93
Alignment explanation
Indices: 53676263--53676433 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
53676253 GGATGGTTGA
* *
53676263 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
53676328 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* *
53676356 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
53676421 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
53676434 ACTAAGGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:53683471 original size:39 final size:40
Alignment explanation
Indices: 53683412--53683626 Score: 316
Period size: 39 Copynumber: 5.5 Consensus size: 40
53683402 CGGATGATAA
* *
53683412 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
53683452 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
53683491 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
53683531 CCGGGCT-AGTCCCGAAGGCATTTGTGTGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
53683570 CCGGGCTAAGT-CCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
53683609 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
53683627 TACTCGGTTT
Statistics
Matches: 162, Mismatches: 8, Indels: 11
0.90 0.04 0.06
Matches are distributed among these distances:
38 9 0.06
39 103 0.64
40 50 0.31
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:53683545 original size:79 final size:80
Alignment explanation
Indices: 53683408--53683626 Score: 324
Period size: 79 Copynumber: 2.8 Consensus size: 80
53683398 ATATCGGATG
* *
53683408 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAG-CCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCCCGAAGGC
53683471 ATTTGTGCGAGTTACT
65 ATTTGTGCGAGTTACT
*
53683487 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCT-AGTCCCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCA
*
53683551 TTTGTGTGAGTTACT
66 TTTGTGCGAGTTACT
* *
53683566 ATAACCGGGCTAAGT-CCGAAGGCATTTGAGCGAG-TAGCTATATCC-GGCTAAATCCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGGGCTAAGTCCCGAAGG
53683627 TACTCGGTTT
Statistics
Matches: 129, Mismatches: 7, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
77 6 0.05
78 38 0.29
79 84 0.65
80 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCA
TTTGTGCGAGTTACT
Found at i:53688193 original size:23 final size:23
Alignment explanation
Indices: 53688161--53688205 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
53688151 TAAATAGATA
53688161 ATAGTATGATAGACTTCACTGAG
1 ATAGTATGATAGACTTCACTGAG
*
53688184 ATAGTGTGATAGACTTCACTGA
1 ATAGTATGATAGACTTCACTGA
53688206 CAATCCCCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.31
Consensus pattern (23 bp):
ATAGTATGATAGACTTCACTGAG
Found at i:53693493 original size:43 final size:43
Alignment explanation
Indices: 53693436--53693561 Score: 137
Period size: 43 Copynumber: 2.9 Consensus size: 43
53693426 TATCGTACAC
* * * * *
53693436 TGCCAACATACCAGACTTGGTCTTACATGTA-ATCACATATCGA
1 TGCCAATATCCCAGACATGGTCTTACACG-AGAACACATATCGA
* *
53693479 TGCCACTATCCCAGACAAGGTCTTACACGAGAACACATATCGA
1 TGCCAATATCCCAGACATGGTCTTACACGAGAACACATATCGA
* * * *
53693522 TGCTAATGTCCTAGACGTGGTCTTACACGAGAACACATAT
1 TGCCAATATCCCAGACATGGTCTTACACGAGAACACATAT
53693562 TGGAAATCCT
Statistics
Matches: 69, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
42 1 0.01
43 68 0.99
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.25
Consensus pattern (43 bp):
TGCCAATATCCCAGACATGGTCTTACACGAGAACACATATCGA
Found at i:53697353 original size:24 final size:24
Alignment explanation
Indices: 53697316--53697410 Score: 113
Period size: 24 Copynumber: 4.0 Consensus size: 24
53697306 TTAAGTTGAT
* *
53697316 AAACAGTAAGCTCTATTAAGCTAA
1 AAACGGTAAGCTCTATTGAGCTAA
*
53697340 AAATGGTAAGCTCTATTGAGCTAA
1 AAACGGTAAGCTCTATTGAGCTAA
53697364 AAACGGTAAGCTCTATTGAGCT--
1 AAACGGTAAGCTCTATTGAGCTAA
* * * *
53697386 GAACAGTAAGCTCCAATGAGCTAA
1 AAACGGTAAGCTCTATTGAGCTAA
53697410 A
1 A
53697411 CAGTAAGCTC
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
22 18 0.30
24 42 0.70
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (24 bp):
AAACGGTAAGCTCTATTGAGCTAA
Found at i:53697397 original size:22 final size:22
Alignment explanation
Indices: 53697315--53697421 Score: 124
Period size: 22 Copynumber: 4.7 Consensus size: 22
53697305 CTTAAGTTGA
*
53697315 TAAACAGTAAGCTCTATTAAGC
1 TAAACAGTAAGCTCTATTGAGC
*
53697337 TAAAAATGGTAAGCTCTATTGAGC
1 TAAACA--GTAAGCTCTATTGAGC
*
53697361 TAAAAACGGTAAGCTCTATTGAGC
1 T--AAACAGTAAGCTCTATTGAGC
* * *
53697385 TGAACAGTAAGCTCCAATGAGC
1 TAAACAGTAAGCTCTATTGAGC
53697407 TAAACAGTAAGCTCT
1 TAAACAGTAAGCTCT
53697422 TACGAGCTAT
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
22 35 0.49
24 33 0.46
26 3 0.04
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (22 bp):
TAAACAGTAAGCTCTATTGAGC
Found at i:53697406 original size:46 final size:47
Alignment explanation
Indices: 53697316--53697421 Score: 128
Period size: 48 Copynumber: 2.3 Consensus size: 47
53697306 TTAAGTTGAT
* *
53697316 AAACAGTAAGCTCTATTAAGCTAAAAATGGTAAGCTCTATTGAGCTAA
1 AAACAGTAAGCTCTATTAAGCTAAAAA-GGTAAGCTCCAATGAGCTAA
* * * *
53697364 AAACGGTAAGCTCTATTGAGCTGAACA-GTAAGCTCCAATGAGCT--
1 AAACAGTAAGCTCTATTAAGCTAAAAAGGTAAGCTCCAATGAGCTAA
53697408 AAACAGTAAGCTCT
1 AAACAGTAAGCTCT
53697422 TACGAGCTAT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
44 13 0.25
46 15 0.29
48 23 0.45
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.25
Consensus pattern (47 bp):
AAACAGTAAGCTCTATTAAGCTAAAAAGGTAAGCTCCAATGAGCTAA
Found at i:53704892 original size:40 final size:40
Alignment explanation
Indices: 53704835--53705052 Score: 289
Period size: 40 Copynumber: 5.5 Consensus size: 40
53704825 CGGATGATAA
* *
53704835 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
* *
53704875 CTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
53704915 CTGGGCTACGTCCCGAAGGCGTTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
53704955 CCGGGCTAAGTCCCGAAGACATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
** *
53704995 CCGGGCTAAGTCCCGAAGGCATTTGAACGAG-TAGCTAGAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
53705035 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
53705053 TACTTGGGTT
Statistics
Matches: 161, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
39 17 0.11
40 143 0.89
41 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:53713107 original size:40 final size:40
Alignment explanation
Indices: 53712949--53713125 Score: 245
Period size: 40 Copynumber: 4.5 Consensus size: 40
53712939 CGGATGATAA
* *
53712949 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
* *
53712989 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
53713029 CCGGGCTACGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
53713069 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
53713109 CC-GGCTAAAT-CCGAAGG
1 CCGGGCTAAGTCCCGAAGG
53713126 TACTTGGGTT
Statistics
Matches: 126, Mismatches: 9, Indels: 6
0.89 0.06 0.04
Matches are distributed among these distances:
38 7 0.06
39 9 0.07
40 109 0.87
41 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:53717777 original size:28 final size:29
Alignment explanation
Indices: 53717743--53717802 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
53717733 CACACGCCTG
* *
53717743 TGTGGGTAGGCTATGTGGTCACA-AGCCA
1 TGTGGGTAGGCCATGTAGTCACACAGCCA
*
53717771 TGTGGGTAGGCCATGTAGTCACACGGCCA
1 TGTGGGTAGGCCATGTAGTCACACAGCCA
53717800 TGT
1 TGT
53717803 CCCTAACCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 21 0.75
29 7 0.25
ACGTcount: A:0.20, C:0.20, G:0.35, T:0.25
Consensus pattern (29 bp):
TGTGGGTAGGCCATGTAGTCACACAGCCA
Found at i:53719772 original size:49 final size:48
Alignment explanation
Indices: 53719699--53719886 Score: 232
Period size: 49 Copynumber: 3.8 Consensus size: 48
53719689 TAGCTGAAGC
*
53719699 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAA
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAA
* * *
53719747 TAATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGATCACAG
1 T-ATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGA-C-CAA
* * * *
53719798 TTTTTAGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACTAA
1 TATCT-GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAA
** *
53719847 TTATCCAGTACACGTAGTAGCCTGCACTTAGTACTACACA
1 -TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACA
53719887 CGTGACCTCA
Statistics
Matches: 118, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
48 1 0.01
49 72 0.61
50 6 0.05
51 39 0.33
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.27
Consensus pattern (48 bp):
TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAA
Found at i:53719818 original size:100 final size:100
Alignment explanation
Indices: 53719704--53719891 Score: 331
Period size: 100 Copynumber: 1.9 Consensus size: 100
53719694 GAAGCTATCT
**
53719704 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCTGGTACACATAGTAGCC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCCAGTACACATAGTAGCC
53719769 TGCACTTAGTACTACACACGTGATCACAGTTTTTA
66 TGCACTTAGTACTACACACGTGATCACAGTTTTTA
* * *
53719804 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACTAATTATCCAGTACACGTAGTAGCC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCCAGTACACATAGTAGCC
53719869 TGCACTTAGTACTACACACGTGA
66 TGCACTTAGTACTACACACGTGA
53719892 CCTCACAATA
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
100 83 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (100 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCCAGTACACATAGTAGCC
TGCACTTAGTACTACACACGTGATCACAGTTTTTA
Found at i:53722050 original size:43 final size:42
Alignment explanation
Indices: 53721988--53722109 Score: 154
Period size: 43 Copynumber: 2.9 Consensus size: 42
53721978 TACCATACCA
* ****
53721988 ATGCCATATCCAAGATATGGTCTTACATGGGATCTCATATAG
1 ATGCCATATCCCAGATATGGTCTTACACAAAATCTCATATAG
* *
53722030 ATGCCATTATCCCAGCTATGGTCTTACACAAAATCTCATATCG
1 ATGCCA-TATCCCAGATATGGTCTTACACAAAATCTCATATAG
**
53722073 ATGCCATATCCCAGATATGGTCTTACACGTAATCTCA
1 ATGCCATATCCCAGATATGGTCTTACACAAAATCTCA
53722110 ACTAACCCTA
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
42 34 0.49
43 35 0.51
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACAAAATCTCATATAG
Found at i:53727177 original size:19 final size:20
Alignment explanation
Indices: 53727140--53727177 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
53727130 ATAAGGTGGT
53727140 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
53727160 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
53727178 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:53733864 original size:46 final size:46
Alignment explanation
Indices: 53733813--53733937 Score: 160
Period size: 46 Copynumber: 2.7 Consensus size: 46
53733803 GGTTAAGCAT
* * * *
53733813 CCGAACTCGTTGATTTGAGTCCGAGTTCACTTATGGATGCAAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCAAACGC
* * *
53733859 TCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATAGATGCGAACGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCAAACGC
* * *
53733905 CCGAGCTCATTGAGTTGAGTCTGAGTTCACTTA
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
53733938 GGGGCGGGTT
Statistics
Matches: 67, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
46 67 1.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCAAACGC
Found at i:53734199 original size:19 final size:20
Alignment explanation
Indices: 53734162--53734199 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
53734152 ATACGGTGGT
53734162 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
53734182 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
53734200 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:53736984 original size:46 final size:46
Alignment explanation
Indices: 53736927--53737101 Score: 169
Period size: 46 Copynumber: 3.8 Consensus size: 46
53736917 TATTTGGGCA
* *
53736927 TCCGAGATCGTTGATTTGAGTCCGAGTTCACTTATGGATACGAATG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAATG
* * * * *
53736973 TCCGAGCTCGTTGAGTTGAGTCCGAGTTC-GTGAGATGTAGTAGGCA--
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACT--TATGGA-TACGAATG
* *
53737019 TCCGAGCTCTTTGAGTTGAGTCTGAGTTCACTTATGGATACGAATG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAATG
* * * *
53737065 -CTTGAGCTCATTGAGTTGAGTTCGAGTTCGCTTATGG
1 TC-CGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
53737102 GCAGGTTACA
Statistics
Matches: 103, Mismatches: 19, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
44 4 0.04
45 6 0.06
46 84 0.82
47 5 0.05
48 4 0.04
ACGTcount: A:0.21, C:0.17, G:0.29, T:0.33
Consensus pattern (46 bp):
TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAATG
Found at i:53737080 original size:92 final size:92
Alignment explanation
Indices: 53736923--53737094 Score: 265
Period size: 92 Copynumber: 1.9 Consensus size: 92
53736913 AGGATATTTG
* *
53736923 GGCATCCGAGATCGTTGATTTGAGTCCGAGTTCACTTATGGATACGAATGTCCGAGCTCGTTGAG
1 GGCATCCGAGATCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAATGTCCGAGCTCATTGAG
53736988 TTGAGTCCGAGTTCGTGAGATGTAGTA
66 TTGAGTCCGAGTTCGTGAGATGTAGTA
* * * *
53737015 GGCATCCGAGCTCTTTGAGTTGAGTCTGAGTTCACTTATGGATACGAATG-CTTGAGCTCATTGA
1 GGCATCCGAGATCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAATGTC-CGAGCTCATTGA
*
53737079 GTTGAGTTCGAGTTCG
65 GTTGAGTCCGAGTTCG
53737095 CTTATGGGCA
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
91 1 0.01
92 71 0.99
ACGTcount: A:0.21, C:0.17, G:0.30, T:0.32
Consensus pattern (92 bp):
GGCATCCGAGATCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAATGTCCGAGCTCATTGAG
TTGAGTCCGAGTTCGTGAGATGTAGTA
Found at i:53739434 original size:65 final size:65
Alignment explanation
Indices: 53739330--53739457 Score: 229
Period size: 65 Copynumber: 2.0 Consensus size: 65
53739320 CCCATGCATT
* *
53739330 AGATAATAATAACATGGCATGCAGTAAATAGTAACAGTCAAACATGCATTCAGGTTAACCTTATC
1 AGATAATAATAACATGGCATGCAGTAAATAGTAACAGTCAAACATGAATTCAGGTCAACCTTATC
*
53739395 AGATAATAATAACATGGCGTGCAGTAAATAGTAACAGTCAAACATGAATTCAGGTCAACCTTA
1 AGATAATAATAACATGGCATGCAGTAAATAGTAACAGTCAAACATGAATTCAGGTCAACCTTA
53739458 ACCCTAGGGG
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 60 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.25
Consensus pattern (65 bp):
AGATAATAATAACATGGCATGCAGTAAATAGTAACAGTCAAACATGAATTCAGGTCAACCTTATC
Found at i:53739516 original size:27 final size:26
Alignment explanation
Indices: 53739460--53739516 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
53739450 CAACCTTAAC
* * *
53739460 CCTAGGGGTATATCAGTAATTTTGCT
1 CCTAGGGGTAAATCAGTAATTTTCCA
*
53739486 CCTAGGGGTAAATCTGTAAATTTTCCA
1 CCTAGGGGTAAATCAGT-AATTTTCCA
53739513 CCTA
1 CCTA
53739517 TAAAGGTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 15 0.58
27 11 0.42
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (26 bp):
CCTAGGGGTAAATCAGTAATTTTCCA
Found at i:53743591 original size:65 final size:65
Alignment explanation
Indices: 53743487--53743614 Score: 247
Period size: 65 Copynumber: 2.0 Consensus size: 65
53743477 CCCATGCATT
*
53743487 AGATAATAATAACATGGCATGCAGTAAATAGTAACAGTCAAATATGCATTCAGGTCAACCTTATC
1 AGATAATAATAACATGGCATGCAGTAAATAGTAACAGTCAAACATGCATTCAGGTCAACCTTATC
53743552 AGATAATAATAACATGGCATGCAGTAAATAGTAACAGTCAAACATGCATTCAGGTCAACCTTA
1 AGATAATAATAACATGGCATGCAGTAAATAGTAACAGTCAAACATGCATTCAGGTCAACCTTA
53743615 ACCCTAGGGG
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 62 1.00
ACGTcount: A:0.42, C:0.17, G:0.16, T:0.25
Consensus pattern (65 bp):
AGATAATAATAACATGGCATGCAGTAAATAGTAACAGTCAAACATGCATTCAGGTCAACCTTATC
Found at i:53751042 original size:46 final size:46
Alignment explanation
Indices: 53750971--53751091 Score: 215
Period size: 46 Copynumber: 2.6 Consensus size: 46
53750961 TATTTGGGCA
*
53750971 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
*
53751017 TCCGAGCTCGTTGAGTTGAGCCCGAGTTCACTTATGGATGCGAACG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
*
53751063 TTCGAGCTCGTTGAGTTGAGTCCGAGTTC
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTC
53751092 GCTTGTGGGC
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 71 1.00
ACGTcount: A:0.18, C:0.21, G:0.31, T:0.30
Consensus pattern (46 bp):
TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:53754058 original size:41 final size:43
Alignment explanation
Indices: 53753960--53754104 Score: 172
Period size: 43 Copynumber: 3.4 Consensus size: 43
53753950 ATATCGTACA
* *
53753960 ATGCCAATGTCCCAGAC-GTGGTCTTACATGCTATCACATATCG
1 ATGCCAATGTCCCAGACAG-GGTCTTACATGCAATCAAATATCG
*
53754003 ATGCCACTGTCCCAGACAGGGTCTTACATG-AATCAAATA-CG
1 ATGCCAATGTCCCAGACAGGGTCTTACATGCAATCAAATATCG
* * *
53754044 ATG-CAGATGTCCCAGACATGGTCTTACACGTAATCACATATATCG
1 ATGCCA-ATGTCCCAGACAGGGTCTTACATGCAATCA-A-ATATCG
53754089 ATGCCAATGTCCCAGA
1 ATGCCAATGTCCCAGA
53754105 TGTGGTCTTA
Statistics
Matches: 89, Mismatches: 6, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
40 2 0.02
41 26 0.29
42 12 0.13
43 28 0.31
44 4 0.04
45 15 0.17
46 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.25
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACAGGGTCTTACATGCAATCAAATATCG
Found at i:53754680 original size:28 final size:30
Alignment explanation
Indices: 53754622--53754684 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 30
53754612 TGTTCATAAA
*
53754622 AGTCCATAAATTTCATTTATTTCATATTTT
1 AGTCCATAAATTTCATTTATTTCATAATTT
* **
53754652 AGTCCCTAAATTT-A-TTATTTTGTAATTT
1 AGTCCATAAATTTCATTTATTTCATAATTT
53754680 AGTCC
1 AGTCC
53754685 TAATTACTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 16 0.55
29 1 0.03
30 12 0.41
ACGTcount: A:0.29, C:0.14, G:0.06, T:0.51
Consensus pattern (30 bp):
AGTCCATAAATTTCATTTATTTCATAATTT
Found at i:53764846 original size:23 final size:23
Alignment explanation
Indices: 53764815--53764863 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
53764805 CGTTATTGAG
53764815 AAAACCCCACCTCCAACATCTGT
1 AAAACCCCACCTCCAACATCTGT
*
53764838 AAAATCCCACCTCCAACATCTGT
1 AAAACCCCACCTCCAACATCTGT
53764861 AAA
1 AAA
53764864 GGGTGTTACA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.39, C:0.39, G:0.04, T:0.18
Consensus pattern (23 bp):
AAAACCCCACCTCCAACATCTGT
Found at i:53769890 original size:47 final size:44
Alignment explanation
Indices: 53769783--53769950 Score: 169
Period size: 44 Copynumber: 3.7 Consensus size: 44
53769773 ATATATGCGT
*
53769783 GCTGATGCATGTCCCAGACATGTCTTACACTAGCACAACTCTTA
1 GCTGATGCATGTCCCAGACATGTCTTACACTGGCACAACTCTTA
* * *
53769827 GCTGATGCGTGTCCCAGACACGTCTTACACTGGC-CATCTCTGTCGA
1 GCTGATGCATGTCCCAGACATGTCTTACACTGGCACAACTCT-T--A
* * * * *
53769873 GGCTGATGTATGTCCCAGACATGTCTTACTCTGGCACTCATAAT-ATG
1 -GCTGATGCATGTCCCAGACATGTCTTACACTGGCA--CA-ACTCTTA
*
53769920 GCTGAAGCATGTCCCAGACATGTCTTACACT
1 GCTGATGCATGTCCCAGACATGTCTTACACT
53769951 AGCCCTTGTC
Statistics
Matches: 101, Mismatches: 15, Indels: 14
0.78 0.12 0.11
Matches are distributed among these distances:
43 6 0.06
44 32 0.32
46 29 0.29
47 30 0.30
49 1 0.01
50 2 0.02
51 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (44 bp):
GCTGATGCATGTCCCAGACATGTCTTACACTGGCACAACTCTTA
Found at i:53769940 original size:46 final size:45
Alignment explanation
Indices: 53769749--53770047 Score: 171
Period size: 47 Copynumber: 6.4 Consensus size: 45
53769739 GCCATATCCT
* *
53769749 AGACATGGTCTTATACTGGCTCTCAT-ATATGCGTGCTGATGCATGTCCC
1 AGACAT-GTCTTACACTGGC-CTCATAATAT--G-GCTGAAGCATGTCCC
* * * * * * *
53769798 AGACATGTCTTACACTAG-CACA-ACTCTTAGCTGATGCGTGTCCC
1 AGACATGTCTTACACTGGCCTCATAAT-ATGGCTGAAGCATGTCCC
* * * * *
53769842 AGACACGTCTTACACTGGCCATC-T-CTGTCGAGGCTGATGTATGTCCC
1 AGACATGTCTTACACTGGCC-TCATAATAT---GGCTGAAGCATGTCCC
*
53769889 AGACATGTCTTACTCTGGCACTCATAATATGGCTGAAGCATGTCCC
1 AGACATGTCTTACACTGGC-CTCATAATATGGCTGAAGCATGTCCC
* ** * *
53769935 AGACATGTCTTACACTAGCC-C-TTGTCTGGATGACGATGCCATGTCCC
1 AGACATGTCTTACACTGGCCTCATAATATGGCTGA--A-G-CATGTCCC
* * ** *
53769982 GGACATGGTCTTATACTGGCTCTCATAATGCGGCCGAAGCATGTCCC
1 AGACAT-GTCTTACACTGGC-CTCATAATATGGCTGAAGCATGTCCC
53770029 AGACATGTCTTACACTGGC
1 AGACATGTCTTACACTGGC
53770048 GCACAAATCA
Statistics
Matches: 194, Mismatches: 37, Indels: 41
0.71 0.14 0.15
Matches are distributed among these distances:
43 8 0.04
44 32 0.16
45 5 0.03
46 49 0.25
47 59 0.30
48 24 0.12
49 10 0.05
50 1 0.01
51 6 0.03
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (45 bp):
AGACATGTCTTACACTGGCCTCATAATATGGCTGAAGCATGTCCC
Found at i:53778603 original size:27 final size:27
Alignment explanation
Indices: 53778573--53778671 Score: 144
Period size: 27 Copynumber: 3.7 Consensus size: 27
53778563 GACCCCTAAA
* *
53778573 TGGTAAAATAACTGTTTTACCCTTATG
1 TGGTAAAATGACTATTTTACCCTTATG
* * *
53778600 TGGTAAAATGATTGTTTTTCCCTTATG
1 TGGTAAAATGACTATTTTACCCTTATG
53778627 TGGTAAAATGACTATTTTACCCTTATG
1 TGGTAAAATGACTATTTTACCCTTATG
*
53778654 TGGTAAAATTACTATTTT
1 TGGTAAAATGACTATTTT
53778672 TTGCCCTTAT
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 65 1.00
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.44
Consensus pattern (27 bp):
TGGTAAAATGACTATTTTACCCTTATG
Found at i:53778645 original size:54 final size:56
Alignment explanation
Indices: 53778573--53778684 Score: 167
Period size: 54 Copynumber: 2.0 Consensus size: 56
53778563 GACCCCTAAA
*
53778573 TGGTAAAATAACTGTTTTACCCTTATGTGGTAAAATGA-T-TGTTTTT-CCCTTATG
1 TGGTAAAATAACTATTTTACCCTTATGTGGTAAAATGACTAT-TTTTTGCCCTTATG
* *
53778627 TGGTAAAATGACTATTTTACCCTTATGTGGTAAAATTACTATTTTTTGCCCTTATG
1 TGGTAAAATAACTATTTTACCCTTATGTGGTAAAATGACTATTTTTTGCCCTTATG
53778683 TG
1 TG
53778685 CAGTATATAT
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
54 35 0.67
55 6 0.12
56 11 0.21
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.45
Consensus pattern (56 bp):
TGGTAAAATAACTATTTTACCCTTATGTGGTAAAATGACTATTTTTTGCCCTTATG
Found at i:53778683 original size:29 final size:29
Alignment explanation
Indices: 53778587--53778684 Score: 134
Period size: 27 Copynumber: 3.5 Consensus size: 29
53778577 AAAATAACTG
53778587 TTTTACCCTTATGTGGTAAAATGA-T-TGT
1 TTTTACCCTTATGTGGTAAAATGACTAT-T
53778615 TTTT-CCCTTATGTGGTAAAATGACTA--
1 TTTTACCCTTATGTGGTAAAATGACTATT
*
53778641 TTTTACCCTTATGTGGTAAAATTACTATT
1 TTTTACCCTTATGTGGTAAAATGACTATT
*
53778670 TTTTGCCCTTATGTG
1 TTTTACCCTTATGTG
53778685 CAGTATATAT
Statistics
Matches: 63, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
26 4 0.06
27 40 0.63
28 5 0.08
29 14 0.22
ACGTcount: A:0.23, C:0.14, G:0.15, T:0.47
Consensus pattern (29 bp):
TTTTACCCTTATGTGGTAAAATGACTATT
Found at i:53780982 original size:27 final size:26
Alignment explanation
Indices: 53780909--53781012 Score: 109
Period size: 27 Copynumber: 3.9 Consensus size: 26
53780899 TAAATGATAG
* * *
53780909 AATGACTAATTTGCCCTTATGAGGTA
1 AATGACTATTTTGCCCTTATGTGGAA
* *
53780935 AATAACTGTTTTGCCCATTATGTGGCAA
1 AATGACTATTTTGCCC-TTATGTGG-AA
*
53780963 AATGACTGTTTTGCCCTTATGTGGTAA
1 AATGACTATTTTGCCCTTATGTGG-AA
* *
53780990 GATGACTATTTTGCCCCTATGTG
1 AATGACTATTTTGCCCTTATGTG
53781013 CAGTATATAT
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
26 13 0.20
27 37 0.56
28 16 0.24
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (26 bp):
AATGACTATTTTGCCCTTATGTGGAA
Found at i:53781011 original size:54 final size:54
Alignment explanation
Indices: 53780909--53781012 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 54
53780899 TAAATGATAG
* *
53780909 AATGACTAATTTGCCCTTATGAGGTAAATAACTGTTTTGCCCATTATGTGGCAA
1 AATGACTAATTTGCCCTTATGAGGTAAATAACTATTTTGCCCACTATGTGGCAA
** * *
53780963 AATGACTGTTTTGCCCTTATGTGGTAAGATGACTATTTTGCCC-CTATGTG
1 AATGACTAATTTGCCCTTATGAGGTAA-ATAACTATTTTGCCCACTATGTG
53781013 CAGTATATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
54 30 0.70
55 13 0.30
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (54 bp):
AATGACTAATTTGCCCTTATGAGGTAAATAACTATTTTGCCCACTATGTGGCAA
Found at i:53782711 original size:24 final size:24
Alignment explanation
Indices: 53782673--53782740 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
53782663 ATGAGCTAAG
* *
53782673 CAGTAAGCTCATACAAGCTGAGAA
1 CAGTAATCTCATACAAGCTGAAAA
*
53782697 CAGTAATCTCTTACAAGCTGAAAA
1 CAGTAATCTCATACAAGCTGAAAA
* *
53782721 CAGCAATCTCATACGAGCTG
1 CAGTAATCTCATACAAGCTG
53782741 CGGTGAGTCT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.21
Consensus pattern (24 bp):
CAGTAATCTCATACAAGCTGAAAA
Found at i:53786252 original size:43 final size:44
Alignment explanation
Indices: 53786081--53786253 Score: 142
Period size: 43 Copynumber: 4.0 Consensus size: 44
53786071 GACATAGGAT
* * * * *
53786081 TCGATATGTG-TTTTCATGTAAGACCTTTTCTAGGACATTGACA
1 TCGATATTTGATTTACATGTAAGACCATGTCTAGGACATTGGCA
* * *
53786124 TCGACT-TATGATTTACGA-GTAAGACCATGTCTGGGACATCGGCA
1 TCGA-TATTTGATTTAC-ATGTAAGACCATGTCTAGGACATTGGCA
** * * * *
53786168 TCG-TATTTGATTT-TGTGTAAGACCCTGTTTAGGATAGTGGCA
1 TCGATATTTGATTTACATGTAAGACCATGTCTAGGACATTGGCA
* *
53786210 TCGATATTTG-TTTACATGTAAGACCATGTCTGGGACGTTGGCA
1 TCGATATTTGATTTACATGTAAGACCATGTCTAGGACATTGGCA
53786253 T
1 T
53786254 TGTACAAGCT
Statistics
Matches: 99, Mismatches: 24, Indels: 14
0.72 0.18 0.10
Matches are distributed among these distances:
42 27 0.27
43 42 0.42
44 29 0.29
45 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (44 bp):
TCGATATTTGATTTACATGTAAGACCATGTCTAGGACATTGGCA
Found at i:53793747 original size:40 final size:40
Alignment explanation
Indices: 53793702--53794091 Score: 681
Period size: 40 Copynumber: 9.8 Consensus size: 40
53793692 CAAGCTCAAT
* * * * *
53793702 TGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCACGAA
1 TGCCTTCGGGTTTTAGCCCGGATATATCAACTCGCACAAA
* * *
53793742 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAT
1 TGCCTTCGGGTTTTAGCCCGGATATATCAACTCGCACAAA
53793782 TGCCTTCGGGTTTTAGCCCGGATATATCAACTCGCACAAA
1 TGCCTTCGGGTTTTAGCCCGGATATATCAACTCGCACAAA
53793822 TGCCTTCGGGTTTTAGCCCGGATATATCAACTCGCACAAA
1 TGCCTTCGGGTTTTAGCCCGGATATATCAACTCGCACAAA
53793862 TGCCTTCGGGTTTTAGCCCGGATATATCAACTCGCACAAA
1 TGCCTTCGGGTTTTAGCCCGGATATATCAACTCGCACAAA
53793902 TGCCTTCGGGTTTTAGCCCGGATATATCAACTCGCACAAA
1 TGCCTTCGGGTTTTAGCCCGGATATATCAACTCGCACAAA
53793942 TGCCTTCGGGTTTTAGCCCGGATATATCAACTCGCACAAA
1 TGCCTTCGGGTTTTAGCCCGGATATATCAACTCGCACAAA
* *
53793982 TGCCTTCGGGTCTTAGCCGGGATATATCAACTCGCACAAA
1 TGCCTTCGGGTTTTAGCCCGGATATATCAACTCGCACAAA
*
53794022 TGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAA
1 TGCCTTCGGGTTTTAGCCCGGATATATCAACTCGCACAAA
53794062 TGCCTTCGGGTTTTAGCCCGGATATATCAA
1 TGCCTTCGGGTTTTAGCCCGGATATATCAA
53794092 TTGCTCATGC
Statistics
Matches: 337, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 337 1.00
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (40 bp):
TGCCTTCGGGTTTTAGCCCGGATATATCAACTCGCACAAA
Found at i:53801974 original size:40 final size:40
Alignment explanation
Indices: 53801954--53802294 Score: 538
Period size: 40 Copynumber: 8.8 Consensus size: 40
53801944 CAAGCTCAAT
* * * *
53801954 TGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCACGAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAA
* *
53801994 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAT
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAA
*
53802034 TGCCTTC-GGTCTTAGCCCGGATATATCAACTTGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAA
53802073 TGCCTTC-GGT-TTAG-CCGGATATATCAACTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAA
*
53802110 TGCCTTCGGGT-TTAGCCCAGATATATCAACTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAA
*
53802149 TGCCTTCGGGTTTTAGCCCGGATATATCAACTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAA
53802189 TGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAA
53802229 TGCCTTCGGGT-TTAGCCCGGATATATCAACTCGCAC-AA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAA
53802267 TGCCTTC-GGT-TTAGCCCGGATATATCAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAA
53802295 TTGCTCATGC
Statistics
Matches: 287, Mismatches: 11, Indels: 9
0.93 0.04 0.03
Matches are distributed among these distances:
37 50 0.17
38 20 0.07
39 99 0.34
40 118 0.41
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (40 bp):
TGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAA
Found at i:53812920 original size:40 final size:40
Alignment explanation
Indices: 53812818--53813031 Score: 310
Period size: 40 Copynumber: 5.4 Consensus size: 40
53812808 GATGATAACC
* *
53812818 GGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCCG
53812858 GGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
53812897 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
* *
53812937 GGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTATAACCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
** *
53812977 GGCTAAGTTTCGAAGGCATTTGAGCGAG-TAGCTATATCC-
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCG
*
53813016 GGCTAAATCCCGAAGG
1 GGCTAAGTCCCGAAGG
53813032 TACTCGGTTT
Statistics
Matches: 159, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
39 50 0.31
40 109 0.69
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
Found at i:53818874 original size:48 final size:47
Alignment explanation
Indices: 53818804--53819029 Score: 168
Period size: 48 Copynumber: 4.7 Consensus size: 47
53818794 TATGTGTGCT
** * *
53818804 AGTGTAAGACCACATCTAGGACATAGCATCGGCCACGATGTGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGG-CACGATGTGAGAGCC
* * *
53818852 AGTGTAAGACCATGTCTGGGACATGGGATTGGCA--ATGTAACGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGATGT---GAGAGCC
* ** * ** *
53818900 AGTGTAAGACCATGTTTGGGACATGGCATCGGCATTAAGACAAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGATG-TGAGAGCC
* * ** *
53818948 AGTGTAAGACCATGTCTGGGACATGGCATTGGCCTCGACATGTGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGG-CACGATGTGAGAGCC
* * ** *
53818996 AATGTAAGACCATGTTTGAAACATGGCATTGGCA
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCA
53819030 ATTCACCCTC
Statistics
Matches: 142, Mismatches: 29, Indels: 15
0.76 0.16 0.08
Matches are distributed among these distances:
45 4 0.03
47 3 0.02
48 131 0.92
49 2 0.01
50 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.29, T:0.22
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGATGTGAGAGCC
Found at i:53819002 original size:96 final size:96
Alignment explanation
Indices: 53818846--53819029 Score: 246
Period size: 96 Copynumber: 1.9 Consensus size: 96
53818836 CCACGATGTG
* * *
53818846 AGAGCCAGTGTAAGACCATGTCTGGGACATGGGATTGGCAATGTAACGAGAGCTAGTGTAAGACC
1 AGAGCCAGTGTAAGACCATGTCTGGGACATGGCATTGGCAATGTAACGAGAGCCAATGTAAGACC
**
53818911 ATGTTTGGGACATGGCATCGGCATTAAGACA
66 ATGTTTGAAACATGGCATCGGCATTAAGACA
* * * *
53818942 AGAGCTAGTGTAAGACCATGTCTGGGACATGGCATTGGC-CTCG-ACATGTGAGCCAATGTAAGA
1 AGAGCCAGTGTAAGACCATGTCTGGGACATGGCATTGGCAAT-GTA-ACGAGAGCCAATGTAAGA
*
53819005 CCATGTTTGAAACATGGCATTGGCA
64 CCATGTTTGAAACATGGCATCGGCA
53819030 ATTCACCCTC
Statistics
Matches: 76, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
95 2 0.03
96 74 0.97
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.23
Consensus pattern (96 bp):
AGAGCCAGTGTAAGACCATGTCTGGGACATGGCATTGGCAATGTAACGAGAGCCAATGTAAGACC
ATGTTTGAAACATGGCATCGGCATTAAGACA
Found at i:53820244 original size:21 final size:20
Alignment explanation
Indices: 53820220--53820259 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
53820210 GTTAAATAGG
53820220 CACACGAGCGTGTCGCCCTTC
1 CACACGAGCGTGT-GCCCTTC
* *
53820241 CACATGGGCGTGTGCCCTT
1 CACACGAGCGTGTGCCCTT
53820260 ATCTACTTGA
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:0.12, C:0.38, G:0.28, T:0.23
Consensus pattern (20 bp):
CACACGAGCGTGTGCCCTTC
Found at i:53822162 original size:22 final size:22
Alignment explanation
Indices: 53822134--53822198 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
53822124 GTAAATACGT
*
53822134 TTGGCACACAGCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
*
53822156 TTGGCACAGAGCCATATAT-AGG
1 TTGGCACAAAGCCATA-ATCAGG
**
53822178 TTGGTGCAAAGCCATAATCAG
1 TTGGCACAAAGCCATAATCAG
53822199 AATAGTTGGC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.05
22 33 0.89
23 2 0.05
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.22
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:53822397 original size:41 final size:41
Alignment explanation
Indices: 53822340--53822462 Score: 192
Period size: 41 Copynumber: 3.0 Consensus size: 41
53822330 TAAAAGTCAC
* * *
53822340 CGGTGGATTCACGGTCGTCAAGCAACCATACGATCCTTAAT
1 CGGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAAT
*
53822381 CGGTGGATCCACGGTCGTCAAGCAACCATGCGATTCTCAAT
1 CGGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAAT
**
53822422 CGGTGGATCCACAATCGTCAAGCAACCATGCGATCCTCAAT
1 CGGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAAT
53822463 TTCTTCCTCC
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 75 1.00
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (41 bp):
CGGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAAT
Found at i:53822752 original size:27 final size:27
Alignment explanation
Indices: 53822722--53822774 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
53822712 GGTAAATCTA
53822722 CAAACCAAGGGTATTTCAATAATTTTG
1 CAAACCAAGGGTATTTCAATAATTTTG
* *
53822749 CAAACCAATGGTATTTCTATAATTTT
1 CAAACCAAGGGTATTTCAATAATTTT
53822775 TGAAAGTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (27 bp):
CAAACCAAGGGTATTTCAATAATTTTG
Found at i:53822811 original size:27 final size:27
Alignment explanation
Indices: 53822728--53822883 Score: 138
Period size: 27 Copynumber: 5.7 Consensus size: 27
53822718 TCTACAAACC
** * **
53822728 AAGGGTATTTCAATAATTTTGCAAACC
1 AAGGGTATTTCTGTAATTTTGTAAATT
* *
53822755 AATGGTATTTCTATAATTTT-TGAAAGTT
1 AAGGGTATTTCTGTAATTTTGT-AAA-TT
53822783 AAGGGTATTTCTGTAATTTTGTAAATT
1 AAGGGTATTTCTGTAATTTTGTAAATT
* *
53822810 AAGGGTGTTTATGTAATTTTGTAAATT
1 AAGGGTATTTCTGTAATTTTGTAAATT
** *
53822837 -AGGAGTATTTCTGTAATTTTCCAAATC
1 AAGG-GTATTTCTGTAATTTTGTAAATT
*
53822864 AGGGGTATTT-TGGTAATTTT
1 AAGGGTATTTCT-GTAATTTT
53822884 AAAAGTCGAG
Statistics
Matches: 108, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
26 4 0.04
27 80 0.74
28 23 0.21
29 1 0.01
ACGTcount: A:0.30, C:0.06, G:0.19, T:0.45
Consensus pattern (27 bp):
AAGGGTATTTCTGTAATTTTGTAAATT
Found at i:53822880 original size:54 final size:54
Alignment explanation
Indices: 53822822--53823061 Score: 240
Period size: 54 Copynumber: 4.4 Consensus size: 54
53822812 GGGTGTTTAT
**
53822822 GTAATTTTGTAAAT-TAGGAGTATTTCT-GTAATTTTCCAAATCAGGGGTATTTTG
1 GTAATTTTACAAATCTAGG-GTATTT-TGGTAATTTTCCAAATCAGGGGTATTTTG
* * * * *
53822876 GTAATTTTA-AAAGTCGAGGGTATTTTAGTAATTTTCCGAATCAGGGGTGTTTTA
1 GTAATTTTACAAA-TCTAGGGTATTTTGGTAATTTTCCAAATCAGGGGTATTTTG
* * * *
53822930 GTAATTTTACAAGTCAAGGGTATTTTGGTAATTTTACAAA-CTAGGGATATTTTG
1 GTAATTTTACAAATCTAGGGTATTTTGGTAATTTTCCAAATC-AGGGGTATTTTG
***
53822984 GTAATTTTACAAA-CTAGGGGTATTTTGGTAATTTTGTTAATC-GAGGGTATTTTG
1 GTAATTTTACAAATCTA-GGGTATTTTGGTAATTTTCCAAATCAG-GGGTATTTTG
* *
53823038 GTAATTTTACTAATCGAGGGTATT
1 GTAATTTTACAAATCTAGGGTATT
53823062 CAATAATTTT
Statistics
Matches: 156, Mismatches: 21, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
53 8 0.05
54 140 0.90
55 8 0.05
ACGTcount: A:0.28, C:0.07, G:0.22, T:0.42
Consensus pattern (54 bp):
GTAATTTTACAAATCTAGGGTATTTTGGTAATTTTCCAAATCAGGGGTATTTTG
Found at i:53822896 original size:27 final size:26
Alignment explanation
Indices: 53822841--53823061 Score: 173
Period size: 27 Copynumber: 8.2 Consensus size: 26
53822831 TAAATTAGGA
*
53822841 GTATTTCT-GTAATTTTCCAAATC-AGGG
1 GTATTT-TGGTAATTTT-AAAATCGA-GG
53822868 GTATTTTGGTAATTTTAAAAGTCGAGG
1 GTATTTTGGTAATTTTAAAA-TCGAGG
* **
53822895 GTATTTTAGTAATTTTCCGAATC-AGGG
1 GTATTTTGGTAATTTT-AAAATCGA-GG
* * * *
53822922 GTGTTTTAGTAATTTTACAAGTCAAGG
1 GTATTTTGGTAATTTTA-AAATCGAGG
*
53822949 GTATTTTGGTAATTTTACAAA-CTAGG
1 GTATTTTGGTAATTTTA-AAATCGAGG
*
53822975 GATATTTTGGTAATTTTACAAA-CTAGGG
1 G-TATTTTGGTAATTTTA-AAATCGA-GG
**
53823003 GTATTTTGGTAATTTTGTTAATCGAGG
1 GTATTTTGGTAATTTT-AAAATCGAGG
*
53823030 GTATTTTGGTAATTTTACTAATCGAGG
1 GTATTTTGGTAATTTTA-AAATCGAGG
53823057 GTATT
1 GTATT
53823062 CAATAATTTT
Statistics
Matches: 166, Mismatches: 16, Indels: 24
0.81 0.08 0.12
Matches are distributed among these distances:
26 10 0.06
27 147 0.89
28 9 0.05
ACGTcount: A:0.28, C:0.08, G:0.22, T:0.43
Consensus pattern (26 bp):
GTATTTTGGTAATTTTAAAATCGAGG
Found at i:53822907 original size:81 final size:81
Alignment explanation
Indices: 53822703--53823061 Score: 255
Period size: 81 Copynumber: 4.4 Consensus size: 81
53822693 CACCCTACAA
* * * * * * * ** **
53822703 GGGTGTTTTGGTAAATCTACAAACCAAGGGTATTTCAATAATTTTGCAAACCAATGGTATTTCTA
1 GGGTATTTTGGTAATTTTACAAATCGAGGGTATTTTAGTAATTTTGCAAATTAGGGGTATTT-TA
** * *
53822768 -TAATTTTTGAAAGTTAA
65 GTAATTTTACAAA-TCAG
** ** * * *
53822785 GGGTATTTCT-GTAATTTTGTAAATTAAGGGT-GTTTATGTAATTTTGTAAATTAGGAGTATTTC
1 GGGTATTT-TGGTAATTTTACAAATCGAGGGTATTTTA-GTAATTTTGCAAATTAGGGGTATTT-
*
53822848 T-GTAATTTTCCAAATCAG
63 TAGTAATTTTACAAATCAG
* * * *
53822866 GGGTATTTTGGTAATTTTA-AAAGTCGAGGGTATTTTAGTAATTTTCCGAATCAGGGGTGTTTTA
1 GGGTATTTTGGTAATTTTACAAA-TCGAGGGTATTTTAGTAATTTTGCAAATTAGGGGTATTTTA
* *
53822930 GTAATTTTACAAGTCAA
65 GTAATTTTACAAATCAG
* * * * *
53822947 GGGTATTTTGGTAATTTTACAAA-CTAGGGATATTTTGGTAATTTTACAAACTAGGGGTATTTTG
1 GGGTATTTTGGTAATTTTACAAATCGAGGG-TATTTTAGTAATTTTGCAAATTAGGGGTATTTTA
***
53823011 GTAATTTTGTTAATC-G
65 GTAATTTTACAAATCAG
*
53823027 AGGGTATTTTGGTAATTTTACTAATCGAGGGTATT
1 -GGGTATTTTGGTAATTTTACAAATCGAGGGTATT
53823062 CAATAATTTT
Statistics
Matches: 218, Mismatches: 48, Indels: 23
0.75 0.17 0.08
Matches are distributed among these distances:
80 10 0.05
81 143 0.66
82 64 0.29
83 1 0.00
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (81 bp):
GGGTATTTTGGTAATTTTACAAATCGAGGGTATTTTAGTAATTTTGCAAATTAGGGGTATTTTAG
TAATTTTACAAATCAG
Found at i:53823161 original size:27 final size:27
Alignment explanation
Indices: 53823081--53823149 Score: 102
Period size: 27 Copynumber: 2.6 Consensus size: 27
53823071 TGTAAACCAA
*
53823081 GGGTATTTCAATAATTCTACCCTACAG
1 GGGTATTTCAGTAATTCTACCCTACAG
* * *
53823108 GGGCATTTTAGTAATTCTATCCTACAG
1 GGGTATTTCAGTAATTCTACCCTACAG
53823135 GGGTATTTCAGTAAT
1 GGGTATTTCAGTAAT
53823150 AGTAGCCTAC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (27 bp):
GGGTATTTCAGTAATTCTACCCTACAG
Found at i:53825848 original size:32 final size:32
Alignment explanation
Indices: 53825806--53825906 Score: 94
Period size: 32 Copynumber: 3.2 Consensus size: 32
53825796 ATGCAGCTCT
* *
53825806 AAGCCTTCAGTAGCGGTATTATAATTGGCACA
1 AAGCCATCAGTAACGGTATTATAATTGGCACA
* **
53825838 AAGCCATCAGTAACTGTATTATGTTTGGCACA
1 AAGCCATCAGTAACGGTATTATAATTGGCACA
* *** * *
53825870 TAGCCATCAACGACGGTAATATAATCGGCACA
1 AAGCCATCAGTAACGGTATTATAATTGGCACA
*
53825902 CAGCC
1 AAGCC
53825907 TTGGGCAAAT
Statistics
Matches: 54, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
32 54 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (32 bp):
AAGCCATCAGTAACGGTATTATAATTGGCACA
Found at i:53826402 original size:27 final size:27
Alignment explanation
Indices: 53826372--53826458 Score: 131
Period size: 27 Copynumber: 3.2 Consensus size: 27
53826362 CAAAACAGTT
*
53826372 ATTTTACCCTACAAGGGTATTTCGGTA
1 ATTTTACACTACAAGGGTATTTCGGTA
*
53826399 ATTTTACACTACAAAGGTATGTT-GGTA
1 ATTTTACACTACAAGGGTAT-TTCGGTA
*
53826426 AGTTTACACTACAAGGGTATTTCGGTA
1 ATTTTACACTACAAGGGTATTTCGGTA
53826453 ATTTTA
1 ATTTTA
53826459 AAAATTGGGG
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
26 2 0.04
27 49 0.92
28 2 0.04
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (27 bp):
ATTTTACACTACAAGGGTATTTCGGTA
Found at i:53826520 original size:27 final size:26
Alignment explanation
Indices: 53826385--53826549 Score: 102
Period size: 27 Copynumber: 6.2 Consensus size: 26
53826375 TTACCCTACA
* * *
53826385 AGGGTATTTCGGTAATTTTACACTACA
1 AGGGTATTTCGGTAATTTTAAAAT-CG
* * * * *
53826412 AAGGTATGTT-GGTAAGTTTACACTACA
1 AGGGTAT-TTCGGTAATTTTAAAAT-CG
*
53826439 AGGGTATTTCGGTAATTTTAAAAATTG
1 AGGGTATTTCGGTAATTTT-AAAATCG
* * * *
53826466 GGGGCA-TTCAGTAATTTTACAATCCG
1 AGGGTATTTCGGTAATTTTAAAAT-CG
53826492 AGGGTATTTCGGTAATTTTATAAATCG
1 AGGGTATTTCGGTAATTTTA-AAATCG
* * *
53826519 AGAGTATTTTGATAATTTTACAAATCG
1 AGGGTATTTCGGTAATTTTA-AAATCG
53826546 -GGGT
1 AGGGT
53826550 CTTAACGACC
Statistics
Matches: 110, Mismatches: 22, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
25 4 0.04
26 21 0.19
27 77 0.70
28 8 0.07
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (26 bp):
AGGGTATTTCGGTAATTTTAAAATCG
Found at i:53831999 original size:64 final size:64
Alignment explanation
Indices: 53831919--53832102 Score: 178
Period size: 67 Copynumber: 2.8 Consensus size: 64
53831909 AGACATTATG
* * *
53831919 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGTGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * *
53831983 ATGTAGCTAGGTCGCATGCGTGGCT-CCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGA
1 ATGTAGCTAGGTCGCATGGGT-GATACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGA
53832047 TAA
62 TAA
* * * *
53832050 AT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGT-GTACAAGAGAGC
1 ATGTAGCTAGGTCGCATGGGTGATACT-ATGTGTACACCATGTAG-ACAAGAGAGC
53832103 CGAACTCTAT
Statistics
Matches: 97, Mismatches: 16, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
62 1 0.01
63 19 0.20
64 23 0.24
65 4 0.04
66 18 0.19
67 32 0.33
ACGTcount: A:0.28, C:0.17, G:0.31, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:53833391 original size:820 final size:820
Alignment explanation
Indices: 53831811--53833453 Score: 3241
Period size: 820 Copynumber: 2.0 Consensus size: 820
53831801 AGAGAGAAAT
53831811 CCCGGTTGAACCTTCGGAAAGATTGGATGATACAGATAGTATGTAGCTAGGTCACATGTATGGTG
1 CCCGGTTGAACCTTCGGAAAGATTGGATGATACAGATAGTATGTAGCTAGGTCACATGTATGGTG
53831876 CTGAGTGCACATCATGTGTACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTG
66 CTGAGTGCACATCATGTGTACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTG
53831941 ATACTATGTGTACACCATGTAGACAAGAGTGCTACGGGATATATGTAGCTAGGTCGCATGCGTGG
131 ATACTATGTGTACACCATGTAGACAAGAGTGCTACGGGATATATGTAGCTAGGTCGCATGCGTGG
*
53832006 CTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGATAAATTGGCTAGGTCACATGGGTG
196 CTCCAGGTGAAGGACACCATGTAAACAAGAGAGCTACGAGATAAATTGGCTAGGTCACATGGGTG
53832071 GTACTGAGTGTTCACCATGTGTACAAGAGAGCCGAACTCTATGATGGGTGGAGCTATGTGCTGAA
261 GTACTGAGTGTTCACCATGTGTACAAGAGAGCCGAACTCTATGATGGGTGGAGCTATGTGCTGAA
53832136 ACCACCAAGTATCGAGGATTGGTCCGAAGTGTTCAACGGGAGACTCTCTATGTATTACTTTGTGA
326 ACCACCAAGTATCGAGGATTGGTCCGAAGTGTTCAACGGGAGACTCTCTATGTATTACTTTGTGA
53832201 GTTTTGTGATGAATAAGTGCATGAACTTGGTTATGTGAATGACGTGTTCATTAAGTGACCAGGAT
391 GTTTTGTGATGAATAAGTGCATGAACTTGGTTATGTGAATGACGTGTTCATTAAGTGACCAGGAT
53832266 GTGGTAAGGTTATAAACAAGTAAGTTATACATGAGGATGATTTTATGGTGACCTTGTGATCATGG
456 GTGGTAAGGTTATAAACAAGTAAGTTATACATGAGGATGATTTTATGGTGACCTTGTGATCATGG
* *
53832331 GCCTATACTTGTGATGTATGAAATGTGGTGAAAATGATTTGTGATATGTATGTTAAAATGATATT
521 GCCTATACTTCTGATGTATGAAATGTGGTGAAAATGATTTGTGATATGTATGTTAAAATGAGATT
53832396 AATAAAAAGAAAGTGTGAAAGAGTGAATTAGCAATAAAACTGTTTTGGATAGTAGTAATGACGTG
586 AATAAAAAGAAAGTGTGAAAGAGTGAATTAGCAATAAAACTGTTTTGGATAGTAGTAATGACGTG
53832461 ATTTTGAAAAATCACCAAAAATAGTAGAAATTGAATCAGAGACTGAATGAGATAGTAAATTAAAT
651 ATTTTGAAAAATCACCAAAAATAGTAGAAATTGAATCAGAGACTGAATGAGATAGTAAATTAAAT
53832526 CTTAATGAGTCTATTTTCATATAAAAGAAACAGAGCAAGAAAAGGAGTTCTATATTTTGACATAT
716 CTTAATGAGTCTATTTTCATATAAAAGAAACAGAGCAAGAAAAGGAGTTCTATATTTTGACATAT
53832591 TTATGTTTTTGTGAGACTGGTTTAGAATGATTACGTGATC
781 TTATGTTTTTGTGAGACTGGTTTAGAATGATTACGTGATC
53832631 CCCGGTTGAACCTTCGGAAAGATTGGATGATACAGATAGTATGTAGCTAGGTCACATGTATGGTG
1 CCCGGTTGAACCTTCGGAAAGATTGGATGATACAGATAGTATGTAGCTAGGTCACATGTATGGTG
53832696 CTGAGTGCACATCATGTGTACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTG
66 CTGAGTGCACATCATGTGTACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTG
53832761 ATACTATGTGTACACCATGTAGACAAGAGTGCTACGGGATATATGTAGCTAGGTCGCATGCGTGG
131 ATACTATGTGTACACCATGTAGACAAGAGTGCTACGGGATATATGTAGCTAGGTCGCATGCGTGG
53832826 CTCCAGGTGAAGGACACCATGTAAACAAGAGAGCTACGAGATAAATTGGCTAGGTCACATGGGTG
196 CTCCAGGTGAAGGACACCATGTAAACAAGAGAGCTACGAGATAAATTGGCTAGGTCACATGGGTG
53832891 GTACTGAGTGTTCACCATGTGTACAAGAGAGCCGAACTCTATGATGGGTGGAGCTATGTGCTGAA
261 GTACTGAGTGTTCACCATGTGTACAAGAGAGCCGAACTCTATGATGGGTGGAGCTATGTGCTGAA
53832956 ACCACCAAGTATCGAGGATTGGTCCGAAGTGTTCAACGGGAGACTCTCTATGTATTACTTTGTGA
326 ACCACCAAGTATCGAGGATTGGTCCGAAGTGTTCAACGGGAGACTCTCTATGTATTACTTTGTGA
53833021 GTTTTGTGATGAATAAGTGCATGAACTTGGTTATGTGAATGACGTGTTCATTAAGTGACCAGGAT
391 GTTTTGTGATGAATAAGTGCATGAACTTGGTTATGTGAATGACGTGTTCATTAAGTGACCAGGAT
53833086 GTGGTAAGGTTATAAACAAGTAAGTTATACATGAGGATGATTTTATGGTGACCTTGTGATCATGG
456 GTGGTAAGGTTATAAACAAGTAAGTTATACATGAGGATGATTTTATGGTGACCTTGTGATCATGG
53833151 GCCTATACTTCTGATGTATGAAATGTGGTGAAAATGATTTGTGATATGTATGTTAAAATGAGATT
521 GCCTATACTTCTGATGTATGAAATGTGGTGAAAATGATTTGTGATATGTATGTTAAAATGAGATT
53833216 AATAAAAAGAAAGTGTGAAAGAGTGAATTAGCAATAAAACTGTTTTGGATAGTAGTAATGACGTG
586 AATAAAAAGAAAGTGTGAAAGAGTGAATTAGCAATAAAACTGTTTTGGATAGTAGTAATGACGTG
*
53833281 ATTTTGAAAAATCACCAAAAATAGTAGAAATTGAATCAGAGACTGAATGAGATATTAAATTAAAT
651 ATTTTGAAAAATCACCAAAAATAGTAGAAATTGAATCAGAGACTGAATGAGATAGTAAATTAAAT
*
53833346 CTTAATGAGTCTATTTTCATATAAAAGAAACAGAGCAAGAAAAGGAGTTCTATATTTTGATATAT
716 CTTAATGAGTCTATTTTCATATAAAAGAAACAGAGCAAGAAAAGGAGTTCTATATTTTGACATAT
53833411 TTATGTTTTTGTGAGACTGGTTTAGAATGATTACGTGATC
781 TTATGTTTTTGTGAGACTGGTTTAGAATGATTACGTGATC
53833451 CCC
1 CCC
53833454 TGTTCTAACT
Statistics
Matches: 818, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
820 818 1.00
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (820 bp):
CCCGGTTGAACCTTCGGAAAGATTGGATGATACAGATAGTATGTAGCTAGGTCACATGTATGGTG
CTGAGTGCACATCATGTGTACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTG
ATACTATGTGTACACCATGTAGACAAGAGTGCTACGGGATATATGTAGCTAGGTCGCATGCGTGG
CTCCAGGTGAAGGACACCATGTAAACAAGAGAGCTACGAGATAAATTGGCTAGGTCACATGGGTG
GTACTGAGTGTTCACCATGTGTACAAGAGAGCCGAACTCTATGATGGGTGGAGCTATGTGCTGAA
ACCACCAAGTATCGAGGATTGGTCCGAAGTGTTCAACGGGAGACTCTCTATGTATTACTTTGTGA
GTTTTGTGATGAATAAGTGCATGAACTTGGTTATGTGAATGACGTGTTCATTAAGTGACCAGGAT
GTGGTAAGGTTATAAACAAGTAAGTTATACATGAGGATGATTTTATGGTGACCTTGTGATCATGG
GCCTATACTTCTGATGTATGAAATGTGGTGAAAATGATTTGTGATATGTATGTTAAAATGAGATT
AATAAAAAGAAAGTGTGAAAGAGTGAATTAGCAATAAAACTGTTTTGGATAGTAGTAATGACGTG
ATTTTGAAAAATCACCAAAAATAGTAGAAATTGAATCAGAGACTGAATGAGATAGTAAATTAAAT
CTTAATGAGTCTATTTTCATATAAAAGAAACAGAGCAAGAAAAGGAGTTCTATATTTTGACATAT
TTATGTTTTTGTGAGACTGGTTTAGAATGATTACGTGATC
Found at i:53837259 original size:46 final size:46
Alignment explanation
Indices: 53837206--53837377 Score: 201
Period size: 46 Copynumber: 3.7 Consensus size: 46
53837196 TGGGTATCCA
53837206 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATGTCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATGTCCG
*
53837252 AACTCGTTGAGTTGAGTCCGAGTT--C-GA-GAGATGT-AACTAGGCATCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGTGAA-T--G--TCCG
* * * *
53837299 AGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATGTCCG
*
53837345 AGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
53837378 GCGTGTTACA
Statistics
Matches: 109, Mismatches: 6, Indels: 22
0.80 0.04 0.16
Matches are distributed among these distances:
42 3 0.03
43 7 0.06
44 1 0.01
45 1 0.01
46 60 0.55
47 27 0.25
48 1 0.01
49 1 0.01
50 5 0.05
51 3 0.03
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.29
Consensus pattern (46 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATGTCCG
Found at i:53840987 original size:13 final size:13
Alignment explanation
Indices: 53840969--53840993 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53840959 TTTCTGTGAA
53840969 AGTAGTAAAAATG
1 AGTAGTAAAAATG
53840982 AGTAGTAAAAAT
1 AGTAGTAAAAAT
53840994 CTGAATTGAA
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:0.56, C:0.00, G:0.20, T:0.24
Consensus pattern (13 bp):
AGTAGTAAAAATG
Found at i:53841621 original size:48 final size:48
Alignment explanation
Indices: 53841414--53841644 Score: 217
Period size: 48 Copynumber: 4.9 Consensus size: 48
53841404 GGGACATGCA
*
53841414 TGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAAAATG
1 TGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATATG
* * *
53841462 TGACCCCATGTAAGACCATCTATGGGACATGGCATTGGCATCAATATG
1 TGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATATG
* *** * *
53841510 AGA-CATTGTGTAAGACCATAG-CTGGG-CTAT--CA---GCTTCGATATG
1 TGATC-CCATGTAAGACCAT-GTCTGGGAC-ATGGCATTGGCATCAATATG
* *
53841553 CATGATCCCATGTTAGACCATGTCTGGGACATGGCATTGGCATCGATATG
1 --TGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATATG
* * * *
53841603 TGATCCCATGTAATACCATATCTGGGATATGGAATTGGCATC
1 TGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATC
53841645 CTACTATGTG
Statistics
Matches: 147, Mismatches: 23, Indels: 26
0.75 0.12 0.13
Matches are distributed among these distances:
43 9 0.06
44 1 0.01
45 19 0.13
46 4 0.03
47 4 0.03
48 100 0.68
50 10 0.07
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (48 bp):
TGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATATG
Found at i:53844415 original size:24 final size:24
Alignment explanation
Indices: 53844326--53844418 Score: 84
Period size: 24 Copynumber: 3.9 Consensus size: 24
53844316 GAGCTAACGG
53844326 ACAGTAAGCTC-TACTGAGCTG-AA
1 ACAGTAAGCTCTTAC-GAGCTGAAA
* *
53844349 ACGGTAAGCT-TTGACGAGCTGGAA
1 ACAGTAAGCTCTT-ACGAGCTGAAA
* ** *
53844373 ATAGTAAGCTCCAATGAGCTGAAA
1 ACAGTAAGCTCTTACGAGCTGAAA
*
53844397 ACAATAAGCTCTTACGAGCTGA
1 ACAGTAAGCTCTTACGAGCTGA
53844419 TATATCGGTA
Statistics
Matches: 54, Mismatches: 12, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
23 16 0.30
24 38 0.70
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.22
Consensus pattern (24 bp):
ACAGTAAGCTCTTACGAGCTGAAA
Found at i:53848434 original size:35 final size:35
Alignment explanation
Indices: 53848391--53848504 Score: 133
Period size: 35 Copynumber: 3.3 Consensus size: 35
53848381 CATAGGTAAG
53848391 TACATGTGAGCTTATATTGAACTTGTATATTCGGC
1 TACATGTGAGCTTATATTGAACTTGTATATTCGGC
* * **
53848426 TGCATGTGAGGTTATATTGAACTTG-AGTATAT-GAT
1 TACATGTGAGCTTATATTGAACTTGTA-TAT-TCGGC
* *
53848461 TACATGTGAGCTTATATTGAACTGGTATATTCGGT
1 TACATGTGAGCTTATATTGAACTTGTATATTCGGC
*
53848496 TATATGTGA
1 TACATGTGA
53848505 AGTTATCTTG
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
34 2 0.03
35 62 0.94
36 2 0.03
ACGTcount: A:0.27, C:0.10, G:0.23, T:0.40
Consensus pattern (35 bp):
TACATGTGAGCTTATATTGAACTTGTATATTCGGC
Found at i:53851187 original size:47 final size:47
Alignment explanation
Indices: 53851133--53851370 Score: 359
Period size: 47 Copynumber: 5.1 Consensus size: 47
53851123 TTAGGATTTT
** * * *
53851133 ATGTGATGAATGTGAATGTGTATATATGAGATGAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
53851180 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
53851227 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
53851274 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
53851321 ATGTGATGAATGTGAACATGTATATATGTGGTAAGGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
53851368 ATG
1 ATG
53851371 CGAAACGTGT
Statistics
Matches: 179, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 179 1.00
ACGTcount: A:0.32, C:0.11, G:0.31, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:53851257 original size:25 final size:25
Alignment explanation
Indices: 53851228--53851305 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 25
53851218 GAATGGCCAA
53851228 TGTGATGAATGTGAACATGCGTATG
1 TGTGATGAATGTGAACATGCGTATG
* * * *
53851253 TGTGAT-AAGGCCG-A-ATG-GCCA-A
1 TGTGATGAATG-TGAACATGCG-TATG
53851275 TGTGATGAATGTGAACATGCGTATG
1 TGTGATGAATGTGAACATGCGTATG
53851300 TGTGAT
1 TGTGAT
53851306 AAGGCCGAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 14
0.63 0.13 0.23
Matches are distributed among these distances:
22 8 0.21
23 8 0.21
24 8 0.21
25 14 0.37
ACGTcount: A:0.28, C:0.10, G:0.32, T:0.29
Consensus pattern (25 bp):
TGTGATGAATGTGAACATGCGTATG
Found at i:53851410 original size:46 final size:46
Alignment explanation
Indices: 53851344--53851434 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
53851334 GAACATGTAT
* * *
53851344 ATATGTGGTAAGGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTATGAGATGG
* * *
53851390 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTATGAGATG
53851435 TGTATATATA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.33, C:0.09, G:0.32, T:0.26
Consensus pattern (46 bp):
ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTATGAGATGG
Found at i:53859449 original size:15 final size:15
Alignment explanation
Indices: 53859429--53859459 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
53859419 GCAAGTTTTA
53859429 TGCCGGTGATTTATT
1 TGCCGGTGATTTATT
53859444 TGCCGGTGATTTATT
1 TGCCGGTGATTTATT
53859459 T
1 T
53859460 CAACTCTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.13, G:0.26, T:0.48
Consensus pattern (15 bp):
TGCCGGTGATTTATT
Found at i:53859663 original size:35 final size:33
Alignment explanation
Indices: 53859553--53859663 Score: 123
Period size: 35 Copynumber: 3.2 Consensus size: 33
53859543 AGGTAAGTAC
**
53859553 ATGTGAGCTTATATTGAACTTGTATATTCGGCTGC
1 ATGTGAGCTTATATTGAACTTG-ATATTCGG-TTA
* * *
53859588 ATGTGAGGTTATATTGAACTTGAGTATTTGATTA
1 ATGTGAGCTTATATTGAACTTGA-TATTCGGTTA
53859622 ATTGTGAGCTTATATTGAACTTGCATATTCGGTTA
1 A-TGTGAGCTTATATTGAACTTG-ATATTCGGTTA
53859657 TATGTGA
1 -ATGTGA
53859664 AGTTATCTTG
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
34 3 0.05
35 59 0.92
36 2 0.03
ACGTcount: A:0.26, C:0.09, G:0.23, T:0.42
Consensus pattern (33 bp):
ATGTGAGCTTATATTGAACTTGATATTCGGTTA
Found at i:53862330 original size:40 final size:40
Alignment explanation
Indices: 53862275--53862433 Score: 259
Period size: 40 Copynumber: 4.0 Consensus size: 40
53862265 GATTTATTGA
*
53862275 CATTTGTGCTAGTGACTATATCTGGGCTAAGTCCCGAAGG
1 CATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGG
53862315 CATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGG
1 CATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGG
*
53862355 CATTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGG
1 CATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGG
* *
53862395 CATTTGTGCGAGTTG-CTATATCC-GGCTAAATCCCGAAGG
1 CATTTGTGCTAG-TGACTATATCCGGGCTAAGTCCCGAAGG
53862434 TACTTGGGTT
Statistics
Matches: 113, Mismatches: 5, Indels: 3
0.93 0.04 0.02
Matches are distributed among these distances:
39 14 0.12
40 97 0.86
41 2 0.02
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (40 bp):
CATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGG
Found at i:53866489 original size:68 final size:68
Alignment explanation
Indices: 53866344--53866495 Score: 172
Period size: 68 Copynumber: 2.3 Consensus size: 68
53866334 CACCTCGAAC
* * * *
53866344 CACACATGCAACCTAGCTACATC--AA--TCTCGTAGCTCTCTTGTCTACATGGTGTACACATAG
1 CACACATGCGACCTAGCTACCTCATAATGTCTCGTAGCTCTCTTGTCTACATGGTATACACACAG
53866405 TAT
66 TAT
*
53866408 CACCCATGCGACCTAGCTACCTCATAATGTCTCGTAGCTCTCTTGTAC-ACATGGTATACATC-C
1 CACACATGCGACCTAGCTACCTCATAATGTCTCGTAGCTCTCTTGT-CTACATGGTATACA-CAC
*
53866471 CGTAT
64 AGTAT
* *
53866476 TACACATGTGACCTAGCTAC
1 CACACATGCGACCTAGCTAC
53866496 ATACCATCTG
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
64 20 0.27
66 2 0.03
68 49 0.67
69 2 0.03
ACGTcount: A:0.26, C:0.30, G:0.14, T:0.29
Consensus pattern (68 bp):
CACACATGCGACCTAGCTACCTCATAATGTCTCGTAGCTCTCTTGTCTACATGGTATACACACAG
TAT
Found at i:53866992 original size:30 final size:30
Alignment explanation
Indices: 53866958--53867018 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
53866948 TCCTTAACCC
53866958 AAACTTTGGAAAAATTACAATTTTTCCCCT
1 AAACTTTGGAAAAATTACAATTTTTCCCCT
* * * * *
53866988 AAACTTTTGCATATTTACACTTTTTCCCCT
1 AAACTTTGGAAAAATTACAATTTTTCCCCT
53867018 A
1 A
53867019 GGCTCGAGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.41
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTTCCCCT
Found at i:53872840 original size:36 final size:36
Alignment explanation
Indices: 53872791--53872865 Score: 123
Period size: 36 Copynumber: 2.1 Consensus size: 36
53872781 AAAACCATGC
*
53872791 AAAGAAAACGAATTTTATAGCGCTCTATTCTAATGT
1 AAAGAAAACGAATTTTATAGCGCTCTAATCTAATGT
* *
53872827 AAAGAAAATGAATTTTATAGCTCTCTAATCTAATGT
1 AAAGAAAACGAATTTTATAGCGCTCTAATCTAATGT
53872863 AAA
1 AAA
53872866 TGGTGTGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (36 bp):
AAAGAAAACGAATTTTATAGCGCTCTAATCTAATGT
Found at i:53886224 original size:43 final size:43
Alignment explanation
Indices: 53886105--53886224 Score: 116
Period size: 43 Copynumber: 2.8 Consensus size: 43
53886095 ATTAGGTTAT
* * * *
53886105 CGATATGTGCTTACATGTAAGACCATGTCTAGGACATTGGCAT
1 CGATATGTGATTACATGTAAGACCATGTCTGGGACAGTGGCAC
* * * * * *
53886148 CGTTAAT-CGATTTCGTGTAAGACCTTGTTTGGGACAGTGGCAC
1 CGAT-ATGTGATTACATGTAAGACCATGTCTGGGACAGTGGCAC
* *
53886191 CGATATGTGATAACATGTAAGACCATATCTGGGA
1 CGATATGTGATTACATGTAAGACCATGTCTGGGA
53886225 TATGGCATTA
Statistics
Matches: 57, Mismatches: 18, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
42 2 0.04
43 53 0.93
44 2 0.04
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (43 bp):
CGATATGTGATTACATGTAAGACCATGTCTGGGACAGTGGCAC
Found at i:53891693 original size:28 final size:28
Alignment explanation
Indices: 53891661--53891716 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
53891651 TTGAATAAGA
53891661 GTAAATTGTACAATTATGATGTTTTACC
1 GTAAATTGTACAATTATGATGTTTTACC
53891689 GTAAATTGTACAATTATGATGTTTTACC
1 GTAAATTGTACAATTATGATGTTTTACC
53891717 TTTAAATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (28 bp):
GTAAATTGTACAATTATGATGTTTTACC
Found at i:53896523 original size:29 final size:29
Alignment explanation
Indices: 53896468--53896523 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
53896458 ATTTACGAGC
*
53896468 CTAGGGGAAAAATGTAATTTTGACAAAGT
1 CTAGGGGAAAAATGTAATTGTGACAAAGT
*
53896497 CTAGGGGCAAAATTGTAATTGTG-CAAA
1 CTAGGGG-AAAAATGTAATTGTGACAAA
53896524 AATATGATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 11 0.46
30 13 0.54
ACGTcount: A:0.39, C:0.09, G:0.25, T:0.27
Consensus pattern (29 bp):
CTAGGGGAAAAATGTAATTGTGACAAAGT
Found at i:53898182 original size:28 final size:28
Alignment explanation
Indices: 53898150--53898205 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
53898140 TTGAACAAGA
*
53898150 GTAAATTGTACAATTATGATGTTTTACC
1 GTAAATTGTACAATCATGATGTTTTACC
53898178 GTAAATTGTACAATCATGATGTTTTACC
1 GTAAATTGTACAATCATGATGTTTTACC
53898206 TTTAAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.41
Consensus pattern (28 bp):
GTAAATTGTACAATCATGATGTTTTACC
Found at i:53904174 original size:14 final size:11
Alignment explanation
Indices: 53904141--53904168 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
53904131 GGTTGAAAAT
53904141 TTATTTTAATA
1 TTATTTTAATA
53904152 TTATTTTAATA
1 TTATTTTAATA
53904163 TTATTT
1 TTATTT
53904169 CGTTAAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTATTTTAATA
Found at i:53915945 original size:13 final size:13
Alignment explanation
Indices: 53915910--53915957 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
53915900 ATTTAATTAA
53915910 ATGCTAAATATAT
1 ATGCTAAATATAT
53915923 ATGCTGAAATGATAT
1 ATGCT-AAAT-ATAT
53915938 ATG-TAAATTTATAT
1 ATGCTAAA--TATAT
53915952 ATGCTA
1 ATGCTA
53915958 TAGCCGAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
13 8 0.27
14 12 0.40
15 10 0.33
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.40
Consensus pattern (13 bp):
ATGCTAAATATAT
Found at i:53916197 original size:43 final size:43
Alignment explanation
Indices: 53916105--53916186 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
53916095 GAGTAAGACC
**
53916105 ATGGCATCCATATGTGTTTACGAGTAAGACCCTGTCTGGAACA
1 ATGGCATCCATATGTGACTACGAGTAAGACCCTGTCTGGAACA
*
53916148 ATGGCATCGATATGTGACTAC-ATGTAAGACCAC-GTCTGG
1 ATGGCATCCATATGTGACTACGA-GTAAGACC-CTGTCTGG
53916187 GACGTTGGCA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
42 1 0.03
43 32 0.94
44 1 0.03
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (43 bp):
ATGGCATCCATATGTGACTACGAGTAAGACCCTGTCTGGAACA
Found at i:53919197 original size:29 final size:29
Alignment explanation
Indices: 53919157--53919244 Score: 115
Period size: 29 Copynumber: 3.1 Consensus size: 29
53919147 ATGTGACTGA
*
53919157 GCCTAACGGGCCATATAAATGTGATTTGG
1 GCCTAATGGGCCATATAAATGTGATTTGG
* *
53919186 GCCTAATGGGCCATATATAGGTGATTTGG
1 GCCTAATGGGCCATATAAATGTGATTTGG
* * *
53919215 GTCTAATGGGCCATATGAATATGA-TTGG
1 GCCTAATGGGCCATATAAATGTGATTTGG
53919243 GC
1 GC
53919245 TTAGTAGGCC
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 5 0.10
29 45 0.90
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.30
Consensus pattern (29 bp):
GCCTAATGGGCCATATAAATGTGATTTGG
Found at i:53920380 original size:17 final size:18
Alignment explanation
Indices: 53920347--53920381 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
53920337 ATTTAAGAAG
*
53920347 GGTTTTCATTGAAAACAC
1 GGTTTTCACTGAAAACAC
53920365 GGTTTTCACT-AAAACAC
1 GGTTTTCACTGAAAACAC
53920382 TTCAATGTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.31
Consensus pattern (18 bp):
GGTTTTCACTGAAAACAC
Found at i:53926990 original size:38 final size:37
Alignment explanation
Indices: 53926935--53927006 Score: 126
Period size: 38 Copynumber: 1.9 Consensus size: 37
53926925 ACTATGTCCG
53926935 AAAACCCCGTATGAACCTTAGGAATAGATAGGATTCA
1 AAAACCCCGTATGAACCTTAGGAATAGATAGGATTCA
*
53926972 AAAAGCCCCGTATGAACCTTAGGAATAGTTAGGAT
1 AAAA-CCCCGTATGAACCTTAGGAATAGATAGGAT
53927007 ACATATGTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
37 4 0.12
38 29 0.88
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.22
Consensus pattern (37 bp):
AAAACCCCGTATGAACCTTAGGAATAGATAGGATTCA
Found at i:53927815 original size:12 final size:12
Alignment explanation
Indices: 53927798--53927823 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
53927788 ATTATGATAC
53927798 TATAATTTAGTT
1 TATAATTTAGTT
53927810 TATAATTTAGTT
1 TATAATTTAGTT
53927822 TA
1 TA
53927824 GTTTAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (12 bp):
TATAATTTAGTT
Found at i:53933686 original size:5 final size:5
Alignment explanation
Indices: 53933676--53933706 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
53933666 TAACTTATAC
53933676 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA G
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA G
53933707 CTTATTTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:53939077 original size:47 final size:47
Alignment explanation
Indices: 53939023--53939264 Score: 331
Period size: 47 Copynumber: 5.1 Consensus size: 47
53939013 TTAGGATTTT
** * *
53939023 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCAA
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
*
53939070 ATGTGATGAATGTGAACCTGTATATATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATG--TATATA--TGTGATAAGGCCGAATGGCCA
** *
53939121 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
* *
53939168 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
* * *
53939215 ATGTGATGAATGTGAACATGTATATATGTGGTAAGGCTGAATGGCTA
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
53939262 ATG
1 ATG
53939265 CGAAACGTGT
Statistics
Matches: 175, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
47 128 0.73
49 9 0.05
51 38 0.22
ACGTcount: A:0.33, C:0.10, G:0.29, T:0.28
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
Found at i:53939125 original size:24 final size:24
Alignment explanation
Indices: 53939097--53939172 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
53939087 CTGTATATAT
53939097 ATGTGTGATAAGGCCGAATGGCCA
1 ATGTGTGATAAGGCCGAATGGCCA
* * **
53939121 ATGTGATGA-ATGTG--AACAT-GCGT
1 ATGTG-TGATAAG-GCCGA-ATGGCCA
53939144 ATGTGTGATAAGGCCGAATGGCCA
1 ATGTGTGATAAGGCCGAATGGCCA
53939168 ATGTG
1 ATGTG
53939173 ATGAATGTGA
Statistics
Matches: 37, Mismatches: 8, Indels: 14
0.63 0.14 0.24
Matches are distributed among these distances:
22 4 0.11
23 12 0.32
24 17 0.46
25 4 0.11
ACGTcount: A:0.29, C:0.13, G:0.33, T:0.25
Consensus pattern (24 bp):
ATGTGTGATAAGGCCGAATGGCCA
Found at i:53939304 original size:46 final size:46
Alignment explanation
Indices: 53939238--53939328 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 46
53939228 GAACATGTAT
* ** *
53939238 ATATGTGGTAAGGCTGAATGGCTAATGCGAAACGTGTATGAGATGG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTATGAGATGG
* * *
53939284 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTATGAGATG
53939329 TGTATATATA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.33, C:0.08, G:0.32, T:0.27
Consensus pattern (46 bp):
ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTATGAGATGG
Found at i:53942959 original size:40 final size:41
Alignment explanation
Indices: 53942900--53943051 Score: 211
Period size: 40 Copynumber: 3.8 Consensus size: 41
53942890 CATTTGAATG
* * *
53942900 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATT
*
53942940 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATT
*
53942980 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATT
* * *
53943020 ATACCCGGGTTAAGACCCGAAGGCAATTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGC
53943052 TTGTGGTTAT
Statistics
Matches: 102, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
40 99 0.97
41 3 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (41 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATT
Found at i:53943063 original size:80 final size:80
Alignment explanation
Indices: 53942900--53943071 Score: 213
Period size: 80 Copynumber: 2.2 Consensus size: 80
53942890 CATTTGAATG
* * * * *
53942900 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTGACTATACCCGGGCTAAGACCCGAAGGCA
* *
53942965 TTTGTGCGAGTTGAT
66 ATTGTGCGAGTGGAT
* *
53942980 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATACCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAG-TGACTATACCCGGGCTAAGACCCGAAGGC
** *
53943044 AATTGTGCTTGTGGTT
65 AATTGTGCGAGTGGAT
53943060 ATATCC-GGCTAA
1 ATATCCGGGCTAA
53943072 ATTCTGAAGA
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
79 6 0.08
80 71 0.90
81 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTGACTATACCCGGGCTAAGACCCGAAGGCA
ATTGTGCGAGTGGAT
Found at i:53951017 original size:40 final size:41
Alignment explanation
Indices: 53950958--53951109 Score: 211
Period size: 40 Copynumber: 3.8 Consensus size: 41
53950948 CATTTGAATG
* * *
53950958 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATT
*
53950998 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATT
*
53951038 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATT
* * *
53951078 ATACCCGGGTTAAGACCCGAAGGCAATTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGC
53951110 TTGTGGTTAT
Statistics
Matches: 102, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
40 99 0.97
41 3 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (41 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATT
Found at i:53951121 original size:80 final size:80
Alignment explanation
Indices: 53950958--53951129 Score: 213
Period size: 80 Copynumber: 2.2 Consensus size: 80
53950948 CATTTGAATG
* * * * *
53950958 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTGACTATACCCGGGCTAAGACCCGAAGGCA
* *
53951023 TTTGTGCGAGTTGAT
66 ATTGTGCGAGTGGAT
* *
53951038 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATACCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAG-TGACTATACCCGGGCTAAGACCCGAAGGC
** *
53951102 AATTGTGCTTGTGGTT
65 AATTGTGCGAGTGGAT
53951118 ATATCC-GGCTAA
1 ATATCCGGGCTAA
53951130 ATTCTGAAGA
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
79 6 0.08
80 71 0.90
81 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTGACTATACCCGGGCTAAGACCCGAAGGCA
ATTGTGCGAGTGGAT
Found at i:53954581 original size:10 final size:10
Alignment explanation
Indices: 53954566--53954595 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
53954556 ATAAGAGAAT
53954566 GAAAAATAAA
1 GAAAAATAAA
53954576 GAAAAATAAA
1 GAAAAATAAA
*
53954586 GAAAGATAAA
1 GAAAAATAAA
53954596 AGAACCAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (10 bp):
GAAAAATAAA
Found at i:53956723 original size:12 final size:12
Alignment explanation
Indices: 53956706--53956736 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
53956696 TTAAAAATAA
53956706 AAAAATATTTTT
1 AAAAATATTTTT
53956718 AAAAATATTTTT
1 AAAAATATTTTT
53956730 AAAAATA
1 AAAAATA
53956737 AAAAATCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
AAAAATATTTTT
Found at i:53974003 original size:26 final size:26
Alignment explanation
Indices: 53973974--53974029 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
53973964 TGATACAAAT
53973974 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
53974000 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
53974026 TGAT
1 TGAT
53974030 GGAATTTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:53980983 original size:26 final size:26
Alignment explanation
Indices: 53980953--53981052 Score: 191
Period size: 26 Copynumber: 3.8 Consensus size: 26
53980943 AATTGAGAAT
53980953 GGTTAGGTAAATGTTCCATGATAATG
1 GGTTAGGTAAATGTTCCATGATAATG
*
53980979 GGTTAGGTAAATGTTTCATGATAATG
1 GGTTAGGTAAATGTTCCATGATAATG
53981005 GGTTAGGTAAATGTTCCATGATAATG
1 GGTTAGGTAAATGTTCCATGATAATG
53981031 GGTTAGGTAAATGTTCCATGAT
1 GGTTAGGTAAATGTTCCATGAT
53981053 GGGAATTTCA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 72 1.00
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.36
Consensus pattern (26 bp):
GGTTAGGTAAATGTTCCATGATAATG
Found at i:53982568 original size:26 final size:26
Alignment explanation
Indices: 53982539--53982591 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
53982529 TTTACAATTT
53982539 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* * *
53982565 TACCCTTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
53982591 T
1 T
53982592 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:53988751 original size:14 final size:14
Alignment explanation
Indices: 53988732--53988763 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
53988722 TCCAATCACC
53988732 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
53988746 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
53988760 GGGC
1 GGGC
53988764 TAAATGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.16, G:0.47, T:0.31
Consensus pattern (14 bp):
GGGCCAGTTTGGTT
Found at i:53993876 original size:14 final size:14
Alignment explanation
Indices: 53993857--53993888 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
53993847 TCCAATCACC
53993857 GGGCCAATTTGGTT
1 GGGCCAATTTGGTT
*
53993871 GGGCCAGTTTGGTT
1 GGGCCAATTTGGTT
53993885 GGGC
1 GGGC
53993889 TAAATGACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.16, G:0.44, T:0.31
Consensus pattern (14 bp):
GGGCCAATTTGGTT
Found at i:54006318 original size:43 final size:42
Alignment explanation
Indices: 54006255--54006393 Score: 129
Period size: 43 Copynumber: 3.3 Consensus size: 42
54006245 GGCATCAAGG
*
54006255 TGCCAATGGTGTCTGAGGCTCCAGTACGATCAAGGGCCTAAGT
1 TGCCAATGGTGTTTGAGGCTCC-GTACGATCAAGGGCCTAAGT
* * * * *
54006298 TACCAATGGTGTTTGAGGCTCCCGCAC-ATCCA-GGCACCAAGG
1 TGCCAATGGTGTTTGAGGCT-CCGTACGATCAAGGGC-CTAAGT
* * * *
54006340 TGCCGATGGTGCTTGAGGCTCTCGTACGACCAAGGGCCTAGGT
1 TGCCAATGGTGTTTGAGGCTC-CGTACGATCAAGGGCCTAAGT
*
54006383 TGCCGATGGTG
1 TGCCAATGGTG
54006394 CCTGAGTGTG
Statistics
Matches: 76, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
41 4 0.05
42 29 0.38
43 38 0.50
44 5 0.07
ACGTcount: A:0.20, C:0.26, G:0.32, T:0.22
Consensus pattern (42 bp):
TGCCAATGGTGTTTGAGGCTCCGTACGATCAAGGGCCTAAGT
Found at i:54006356 original size:42 final size:41
Alignment explanation
Indices: 54006234--54006360 Score: 121
Period size: 43 Copynumber: 3.0 Consensus size: 41
54006224 TTCTTTAGCT
*
54006234 CGCACATCCGAGGCATCAAGGTGCCAATGGTGTCTGAGGCTCC
1 CGCACATCC-AGGCACCAAGGTGCCAATGGTGT-TGAGGCTCC
* * * * * *
54006277 AGTACGATCAAGGGC-CTAAGTTACCAATGGTGTTTGAGGCTCC
1 CGCAC-ATCCA-GGCACCAAGGTGCCAATGGTG-TTGAGGCTCC
*
54006320 CGCACATCCAGGCACCAAGGTGCCGATGGTGCTTGAGGCTC
1 CGCACATCCAGGCACCAAGGTGCCAATGGTG-TTGAGGCTC
54006361 TCGTACGACC
Statistics
Matches: 65, Mismatches: 15, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
41 3 0.05
42 26 0.40
43 29 0.45
44 7 0.11
ACGTcount: A:0.22, C:0.28, G:0.30, T:0.20
Consensus pattern (41 bp):
CGCACATCCAGGCACCAAGGTGCCAATGGTGTTGAGGCTCC
Found at i:54006392 original size:85 final size:86
Alignment explanation
Indices: 54006234--54006393 Score: 227
Period size: 85 Copynumber: 1.9 Consensus size: 86
54006224 TTCTTTAGCT
* *
54006234 CGCACATCCGAGGCATCAAGGTGCCAATGGTGTCTGAGGCTCCAGTACGATCAAGGGCCTAAGTT
1 CGCACATCCGAGGCACCAAGGTGCCAATGGTGTCTGAGGCTCCAGTACGACCAAGGGCCTAAGTT
54006299 ACCAATGGTGTTTGAGGCTCC
66 ACCAATGGTGTTTGAGGCTCC
* *
54006320 CGCACATCC-AGGCACCAAGGTGCCGATGGTG-CTTGAGGCTCTC-GTACGACCAAGGGCCTAGG
1 CGCACATCCGAGGCACCAAGGTGCCAATGGTGTC-TGAGGCTC-CAGTACGACCAAGGGCCTAAG
* *
54006382 TTGCCGATGGTG
64 TTACCAATGGTG
54006394 CCTGAGTGTG
Statistics
Matches: 66, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
84 1 0.02
85 55 0.83
86 10 0.15
ACGTcount: A:0.21, C:0.27, G:0.31, T:0.21
Consensus pattern (86 bp):
CGCACATCCGAGGCACCAAGGTGCCAATGGTGTCTGAGGCTCCAGTACGACCAAGGGCCTAAGTT
ACCAATGGTGTTTGAGGCTCC
Found at i:54008512 original size:39 final size:39
Alignment explanation
Indices: 54008458--54008569 Score: 152
Period size: 39 Copynumber: 2.9 Consensus size: 39
54008448 CAGTGATGTT
54008458 TATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTA
1 TATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTA
* * * *
54008497 TATCCAGACTTAGGGTGCGCAAGCTATGTGCTAGAATTA
1 TATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTA
* * * *
54008536 TAACCGGACTTAAGGTCCGCAGGTTACGTGCTGG
1 TATCCGGACTTAGGGTCCGCAGGCTATGTGCTGG
54008570 TAATATGTCT
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 61 1.00
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (39 bp):
TATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTA
Found at i:54009728 original size:52 final size:52
Alignment explanation
Indices: 54009650--54009751 Score: 177
Period size: 52 Copynumber: 2.0 Consensus size: 52
54009640 GTGTTAATAC
* *
54009650 GATAGTGTGATGATTTTTGACAGTTAAAAATGTGTTTCTGTATAGTAATGAT
1 GATAGTGTGATGATTTCTGACAGTTAAAAATGTGTTTCTATATAGTAATGAT
*
54009702 GATAGTGTGATGATTTCTGACAGTTAAAAATGTGTTTTTATATAGTAATG
1 GATAGTGTGATGATTTCTGACAGTTAAAAATGTGTTTCTATATAGTAATG
54009752 GATCCCAATC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.31, C:0.04, G:0.23, T:0.42
Consensus pattern (52 bp):
GATAGTGTGATGATTTCTGACAGTTAAAAATGTGTTTCTATATAGTAATGAT
Found at i:54017206 original size:27 final size:27
Alignment explanation
Indices: 54017176--54017353 Score: 162
Period size: 27 Copynumber: 6.6 Consensus size: 27
54017166 ATATTGAGCC
* *
54017176 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * *
54017203 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
54017230 CGCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCTACATAATCA-ACT
** ** *
54017258 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
54017285 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
54017312 CGTACAATTAGTGCAACATAATCGAA-T
1 CGCACACTTAGTGCTACATAATC-AACT
54017339 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54017354 GTACAATTTA
Statistics
Matches: 123, Mismatches: 24, Indels: 8
0.79 0.15 0.05
Matches are distributed among these distances:
27 98 0.80
28 25 0.20
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Done.