Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 165 of 186
Found at i:54916483 original size:35 final size:35
Alignment explanation
Indices: 54916415--54916483 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
54916405 TAATTGTGTT
*
54916415 ATTAATTTATTATTTTAGATTTTAAATTTAAATTC
1 ATTAATTTATTATTTTAGATTTTAAATTAAAATTC
*
54916450 ATTAATTT-TTATATTTAGTTTTTAAGA-TAAAATT
1 ATTAATTTATTAT-TTTAGATTTTAA-ATTAAAATT
54916484 TTAAAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 4 0.13
35 25 0.83
36 1 0.03
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (35 bp):
ATTAATTTATTATTTTAGATTTTAAATTAAAATTC
Found at i:54926155 original size:17 final size:18
Alignment explanation
Indices: 54926133--54926173 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
54926123 ATTAAGCTTA
54926133 TATAAAACA-TAATTTAT
1 TATAAAACATTAATTTAT
* *
54926150 TATAAAATATTATTTTAT
1 TATAAAACATTAATTTAT
54926168 TATAAA
1 TATAAA
54926174 CTATTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (18 bp):
TATAAAACATTAATTTAT
Found at i:54926168 original size:18 final size:17
Alignment explanation
Indices: 54926145--54926183 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
54926135 TAAAACATAA
54926145 TTTATTATAAAATATTAT
1 TTTATTATAAAATATT-T
*
54926163 TTTATTATAAACTATTT
1 TTTATTATAAAATATTT
54926180 TTTA
1 TTTA
54926184 AATTTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTATTATAAAATATTT
Found at i:54926278 original size:19 final size:19
Alignment explanation
Indices: 54926256--54926294 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
54926246 TGATTTTAGT
*
54926256 AAAAAAT-TGTTAAACAAA
1 AAAAAATATTTTAAACAAA
*
54926274 AAAAAATATTTTAAGCAAA
1 AAAAAATATTTTAAACAAA
54926293 AA
1 AA
54926295 CCCCAAAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.23
Consensus pattern (19 bp):
AAAAAATATTTTAAACAAA
Found at i:54926352 original size:16 final size:17
Alignment explanation
Indices: 54926331--54926365 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
54926321 AAATAAATCA
54926331 ATTTTCAA-AAAAAAAT
1 ATTTTCAATAAAAAAAT
54926347 ATTTTCAATTAAAAAAAT
1 ATTTTCAA-TAAAAAAAT
54926365 A
1 A
54926366 ATATATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
18 9 0.53
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (17 bp):
ATTTTCAATAAAAAAAT
Found at i:54931679 original size:50 final size:50
Alignment explanation
Indices: 54931620--54931748 Score: 186
Period size: 50 Copynumber: 2.6 Consensus size: 50
54931610 AGTTTCGATA
* * *
54931620 TGTGATCCCATGTAAAACCATATCAGGGACATGGCATTGACATCGATATG
1 TGTGATCCCATGTAAGACCATATCTGGGACATGACATTGACATCGATATG
* * *
54931670 TGTGATCCCATGTAAGACCATGTTTGGGACATGACATTGGCATCGATATG
1 TGTGATCCCATGTAAGACCATATCTGGGACATGACATTGACATCGATATG
* *
54931720 TGTGAACCCATGTAAGACCTTATCTGGGA
1 TGTGATCCCATGTAAGACCATATCTGGGA
54931749 TGCCATTGGC
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 69 1.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (50 bp):
TGTGATCCCATGTAAGACCATATCTGGGACATGACATTGACATCGATATG
Found at i:54931770 original size:50 final size:49
Alignment explanation
Indices: 54931620--54931772 Score: 155
Period size: 50 Copynumber: 3.1 Consensus size: 49
54931610 AGTTTCGATA
* * * * * *
54931620 TGTGATCCCATGTAAAACCATATCAGGGACATGGCATTGACATCGATATG
1 TGTGAACCCATGTAAGACCATATCTGGGA-ATGACATTGGCATCCATATG
* * * *
54931670 TGTGATCCCATGTAAGACCATGTTTGGGACATGACATTGGCATCGATATG
1 TGTGAACCCATGTAAGACCATATCTGGGA-ATGACATTGGCATCCATATG
* *
54931720 TGTGAACCCATGTAAGACCTTATCTGGG-ATGCCATTGGCATCTCACTATG
1 TGTGAACCCATGTAAGACCATATCTGGGAATGACATTGGCATC-CA-TATG
54931770 TGT
1 TGT
54931773 ACGAATTTCC
Statistics
Matches: 89, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
48 13 0.15
49 1 0.01
50 75 0.84
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (49 bp):
TGTGAACCCATGTAAGACCATATCTGGGAATGACATTGGCATCCATATG
Found at i:54934544 original size:96 final size:94
Alignment explanation
Indices: 54934394--54934654 Score: 309
Period size: 95 Copynumber: 2.8 Consensus size: 94
54934384 TATGTGCATC
* *
54934394 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCT-TTGAGACGAGAGCCAGCGTAAGACATGTCT
1 AGTGTAAGACCATGTCTGGGACATGGCATC-G-TATTGAGACGAGAGCTAGTGTAAGACATGTCT
* *
54934456 AGGACATGCACCGGCCTCGA-GAT-ATGCGTACT
64 AGGACATGCACCAGCCTCGATGATGAT-AGT--T
* *
54934488 AGTGTAAGACCATGTCTGGGACATGGCATCAGTATTGAGACGAGTGCTAGTGTAAGACGTGTCTA
1 AGTGTAAGACCATGTCTGGGACATGGCATC-GTATTGAGACGAGAGCTAGTGTAAGACATGTCTA
* *
54934553 GGACACGCATCAGCCTCGATGATGATAGTT
65 GGACATGCACCAGCCTCGATGATGATAGTT
* * *
54934583 AGTGTAAGACCATTTCTGGGACATGGCATCG-ACTTGAGATGTGAGCTAGTGTAAGACCATGTCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGTA-TTGAGACGAGAGCTAGTGTAAGA-CATGTCT
54934647 AGGACATG
64 AGGACATG
54934655 GCATCGGCTT
Statistics
Matches: 145, Mismatches: 15, Indels: 13
0.84 0.09 0.08
Matches are distributed among these distances:
93 1 0.01
94 30 0.21
95 58 0.40
96 49 0.34
97 5 0.03
98 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (94 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGTATTGAGACGAGAGCTAGTGTAAGACATGTCTAG
GACATGCACCAGCCTCGATGATGATAGTT
Found at i:54934666 original size:47 final size:46
Alignment explanation
Indices: 54934394--54934666 Score: 212
Period size: 47 Copynumber: 5.8 Consensus size: 46
54934384 TATGTGCATC
* * * *
54934394 AGTGTAAGACATGTCTGGGACAT-GCATCGGCTTTGAGACGAGAGCC
1 AGTGTAAGACATGTCTAGGACATGGCATCGGC-TTGAGATGTGAGCT
* * * * *
54934440 AGCGTAAGACATGTCTAGGACAT-GCACCGGCCTCGAGATATGCGTACT
1 AGTGTAAGACATGTCTAGGACATGGCATCGG-CTTGAGATGTGAG--CT
* ** * * *
54934488 AGTGTAAGACCATGTCTGGGACATGGCATCAGTATTGAGACGAGTGCT
1 AGTGTAAGA-CATGTCTAGGACATGGCATC-GGCTTGAGATGTGAGCT
* * * * *
54934536 AGTGTAAGACGTGTCTAGGACA-CGCATCAGCCTCGATGATGAT-AGTT
1 AGTGTAAGACATGTCTAGGACATGGCATC-GGCTTGA-GATG-TGAGCT
* * *
54934583 AGTGTAAGACCATTTCTGGGACATGGCATCGACTTGAGATGTGAGCT
1 AGTGTAAGA-CATGTCTAGGACATGGCATCGGCTTGAGATGTGAGCT
54934630 AGTGTAAGACCATGTCTAGGACATGGCATCGGCTTGA
1 AGTGTAAGA-CATGTCTAGGACATGGCATCGGCTTGA
54934667 CATCAGTCAG
Statistics
Matches: 177, Mismatches: 39, Indels: 21
0.75 0.16 0.09
Matches are distributed among these distances:
46 45 0.25
47 67 0.38
48 35 0.20
49 18 0.10
50 11 0.06
51 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTCTAGGACATGGCATCGGCTTGAGATGTGAGCT
Found at i:54937986 original size:50 final size:49
Alignment explanation
Indices: 54937922--54938071 Score: 203
Period size: 50 Copynumber: 3.0 Consensus size: 49
54937912 CGATAAAGTT
* *
54937922 TCGATAT-GTGATCCCATGTAAAACCATGTCGGGGACATGGCATTGGCA
1 TCGATATGGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
* *
54937970 TCGATATGCGTGATCCCATGTAAGACCATGTCTGGTACAGGGCATTGGCA
1 TCGATATG-GTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
* * * *
54938020 TCGATATGTGTGAACCCATGTAAGACCATATCTGGGATATGCCATTGGCA
1 TCGATATG-GTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
54938070 TC
1 TC
54938072 TCACTATGTG
Statistics
Matches: 89, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
48 7 0.08
50 82 0.92
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (49 bp):
TCGATATGGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
Found at i:54940836 original size:23 final size:22
Alignment explanation
Indices: 54940761--54940868 Score: 119
Period size: 22 Copynumber: 4.9 Consensus size: 22
54940751 TTACTATTTT
* *
54940761 AGCTCATTGGAGCTTACCGTTC
1 AGCTCAATAGAGCTTACCGTTC
*
54940783 AGCTCAATAGAGGTTACCGTTC
1 AGCTCAATAGAGCTTACCGTTC
*
54940805 AGCTCAATAGAGCTTGCCGTTTC
1 AGCTCAATAGAGCTTACCG-TTC
* * *
54940828 AACTTAATAGAGCTTACTGTTC
1 AGCTCAATAGAGCTTACCGTTC
*
54940850 AGCTCGAA-GGAGCTTACCG
1 AGCTC-AATAGAGCTTACCG
54940869 ACCATGACTC
Statistics
Matches: 71, Mismatches: 13, Indels: 4
0.81 0.15 0.05
Matches are distributed among these distances:
22 51 0.72
23 20 0.28
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (22 bp):
AGCTCAATAGAGCTTACCGTTC
Found at i:54940852 original size:45 final size:44
Alignment explanation
Indices: 54940746--54940868 Score: 122
Period size: 45 Copynumber: 2.8 Consensus size: 44
54940736 ATAGCTCGTA
* * * * *
54940746 AGAGCTTACTATTTTAGCTCATTGGAGCTTACCGTTCAGCTCAAT
1 AGAGCTTACT-GTTCAGCTCAATAGAGCTTACCGTTCAACTCAAT
* * * *
54940791 AGAGGTTACCGTTCAGCTCAATAGAGCTTGCCGTTTCAACTTAAT
1 AGAGCTTACTGTTCAGCTCAATAGAGCTTACCG-TTCAACTCAAT
*
54940836 AGAGCTTACTGTTCAGCTCGAA-GGAGCTTACCG
1 AGAGCTTACTGTTCAGCTC-AATAGAGCTTACCG
54940869 ACCATGACTC
Statistics
Matches: 63, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
44 18 0.29
45 43 0.68
46 2 0.03
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (44 bp):
AGAGCTTACTGTTCAGCTCAATAGAGCTTACCGTTCAACTCAAT
Found at i:54949940 original size:35 final size:35
Alignment explanation
Indices: 54949894--54949962 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
54949884 ACTGATGTGA
54949894 GTGATGGTAAATTGGTACTTAGAGTAGGTGACGAG
1 GTGATGGTAAATTGGTACTTAGAGTAGGTGACGAG
*
54949929 GTGATGGTAAATTGGTACTTAGGGTAGGTGACGA
1 GTGATGGTAAATTGGTACTTAGAGTAGGTGACGA
54949963 AGAGATTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.28, C:0.06, G:0.38, T:0.29
Consensus pattern (35 bp):
GTGATGGTAAATTGGTACTTAGAGTAGGTGACGAG
Found at i:54954693 original size:25 final size:26
Alignment explanation
Indices: 54954665--54954719 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
54954655 TTATTTTATG
54954665 TTATATT-A-TTACATATATTAA-TATA
1 TTATATTAATTTACATAT-TTAACT-TA
54954690 TTAT-TTAATTTACATATTTAACTTA
1 TTATATTAATTTACATATTTAACTTA
54954715 TTATA
1 TTATA
54954720 AAATATGCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
24 2 0.08
25 15 0.58
26 9 0.35
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (26 bp):
TTATATTAATTTACATATTTAACTTA
Found at i:54968207 original size:39 final size:39
Alignment explanation
Indices: 54968137--54968276 Score: 208
Period size: 39 Copynumber: 3.6 Consensus size: 39
54968127 ATCGTGATCT
* * *
54968137 GAAGCCCGAAGTCTAGCTGAAGCACATAAGTGCTAAACG
1 GAAGCCCAAAGGCTAACTGAAGCACATAAGTGCTAAACG
*
54968176 GAATCCCAAAGGCTAACTGAAGCACATAAGTGCTAAACG
1 GAAGCCCAAAGGCTAACTGAAGCACATAAGTGCTAAACG
* *
54968215 GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
1 GAAGCCCAAAGGCTAACTGAAGCACATAAGTGCTAAACG
* *
54968254 GAAGCCCAAAGCCAAACTGAAGC
1 GAAGCCCAAAGGCTAACTGAAGC
54968277 TTATCAGAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 91 1.00
ACGTcount: A:0.39, C:0.25, G:0.24, T:0.12
Consensus pattern (39 bp):
GAAGCCCAAAGGCTAACTGAAGCACATAAGTGCTAAACG
Found at i:54972391 original size:93 final size:93
Alignment explanation
Indices: 54972281--54972451 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
54972271 GCCCCTAAGT
* *
54972281 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
54972346 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
*
54972374 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
54972439 CGAGTTCGGATGC
66 CGAGTTCGGATGC
54972452 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:54972448 original size:46 final size:46
Alignment explanation
Indices: 54972276--54972448 Score: 210
Period size: 46 Copynumber: 3.7 Consensus size: 46
54972266 AACCCGCCCC
* * *
54972276 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* *
54972322 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
54972370 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
54972415 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
54972449 TGCTCAACCA
Statistics
Matches: 107, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 61 0.57
47 29 0.27
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:54977417 original size:40 final size:41
Alignment explanation
Indices: 54977321--54977425 Score: 117
Period size: 40 Copynumber: 2.6 Consensus size: 41
54977311 TGAATGATGT
* *
54977321 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGGGCTAAGTGACCATAA
* * * *
54977361 CCGGACTAAGAT-CCGAAGGCATTTGGGC-GAGTTACTATAA
1 CCGGGCTAAG-TCCCGAAGGCATTTGGGCTAAGTGACCATAA
*
54977401 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
54977426 AACGAGTAGC
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
39 1 0.02
40 46 0.85
41 7 0.13
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.24
Consensus pattern (41 bp):
CCGGGCTAAGTCCCGAAGGCATTTGGGCTAAGTGACCATAA
Found at i:54984628 original size:33 final size:35
Alignment explanation
Indices: 54984580--54984657 Score: 135
Period size: 33 Copynumber: 2.3 Consensus size: 35
54984570 ACTATACTTG
54984580 TAGA-ATGTATTAAGTGTTGCAATCGG-CCCAACA
1 TAGACATGTATTAAGTGTTGCAATCGGCCCCAACA
54984613 TAGACA-GTATTAAGTGTTGCAATCGGCCCCAACA
1 TAGACATGTATTAAGTGTTGCAATCGGCCCCAACA
54984647 TAGACATGTAT
1 TAGACATGTAT
54984658 GTTCGGCCAC
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
33 24 0.57
34 14 0.33
35 4 0.10
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (35 bp):
TAGACATGTATTAAGTGTTGCAATCGGCCCCAACA
Found at i:54985455 original size:40 final size:40
Alignment explanation
Indices: 54985303--54985448 Score: 172
Period size: 40 Copynumber: 3.6 Consensus size: 40
54985293 TTGAATGATG
* * * *
54985303 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
*
54985343 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
54985383 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
54985424 -CTGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
54985449 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
39 1 0.01
40 81 0.88
41 10 0.11
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:54985455 original size:80 final size:80
Alignment explanation
Indices: 54985303--54985481 Score: 186
Period size: 80 Copynumber: 2.2 Consensus size: 80
54985293 TTGAATGATG
* *
54985303 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
**
54985368 GTGCGAGTTA-CTAAA
66 GAACGAG-TAGCTAAA
* * * * * *
54985383 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACTGGGCTATG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAACCGGACTAAGAT-CCGAAGGCAT
*
54985446 TTGAACGAGTAGCTATA
64 TTGAACGAGTAGCTAAA
* *
54985463 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
54985482 TACGTGATTT
Statistics
Matches: 83, Mismatches: 13, Indels: 7
0.81 0.13 0.07
Matches are distributed among these distances:
79 17 0.20
80 59 0.71
81 7 0.08
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
GAACGAGTAGCTAAA
Found at i:54988177 original size:37 final size:37
Alignment explanation
Indices: 54988127--54988277 Score: 221
Period size: 37 Copynumber: 4.1 Consensus size: 37
54988117 AGACCTTTAG
* *
54988127 CTCAGACAAAATCTCCACACGAAGTTATCGGGTCTTA
1 CTCAGACAAAATCTCCACACGTAGTCATCGGGTCTTA
54988164 CTCAGACAAAATCTCCACACGTAGTCATCGGGTCTTA
1 CTCAGACAAAATCTCCACACGTAGTCATCGGGTCTTA
* * * *
54988201 CCCGGACATAATCTTCACACGTAGTCATCGGGTCTTA
1 CTCAGACAAAATCTCCACACGTAGTCATCGGGTCTTA
* * *
54988238 CCCGGACATAATCTCCACACGTAGTCATCGGGTCTTA
1 CTCAGACAAAATCTCCACACGTAGTCATCGGGTCTTA
54988275 CTC
1 CTC
54988278 GGAATATATT
Statistics
Matches: 106, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 106 1.00
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.25
Consensus pattern (37 bp):
CTCAGACAAAATCTCCACACGTAGTCATCGGGTCTTA
Found at i:54988495 original size:47 final size:47
Alignment explanation
Indices: 54988444--54988713 Score: 432
Period size: 47 Copynumber: 5.7 Consensus size: 47
54988434 TTCACACTAT
* * *
54988444 CCATTCGGCTTTACCACATATATGCATGTTCATATTCATCACATTGG
1 CCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTGG
* * *
54988491 CCATTCGGCATTATCACACATATGCATGCTCACATTCATCACATTGG
1 CCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTGG
54988538 CCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTGG
1 CCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTGG
* * *
54988585 CCATTTGGCCTTATCACACATACGCATGTTCACATTCATCACATTGG
1 CCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTGG
*
54988632 CCATTCGGCCTTATCACATATATGCATGCTCACATTCATCACATTGG
1 CCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTGG
**
54988679 CCATTCGGCCTTATCACATATATGCACATTCACAT
1 CCATTCGGCCTTATCACATATATGCATGTTCACAT
54988714 CACAATTATC
Statistics
Matches: 205, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 205 1.00
ACGTcount: A:0.26, C:0.29, G:0.12, T:0.33
Consensus pattern (47 bp):
CCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTGG
Found at i:54988507 original size:22 final size:22
Alignment explanation
Indices: 54988481--54988556 Score: 59
Period size: 24 Copynumber: 3.3 Consensus size: 22
54988471 GTTCATATTC
54988481 ATCACATTGGCCATTCGGCATT
1 ATCACATTGGCCATTCGGCATT
*
54988503 ATCACACATAT-G-CATGCTC-ACATT
1 AT--CACAT-TGGCCAT--TCGGCATT
*
54988527 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCATT
54988550 ATCACAT
1 ATCACAT
54988557 ATATGCATGT
Statistics
Matches: 42, Mismatches: 3, Indels: 18
0.67 0.05 0.29
Matches are distributed among these distances:
22 12 0.29
23 12 0.29
24 13 0.31
25 5 0.12
ACGTcount: A:0.26, C:0.30, G:0.13, T:0.30
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCATT
Found at i:54988649 original size:22 final size:22
Alignment explanation
Indices: 54988622--54988697 Score: 66
Period size: 22 Copynumber: 3.3 Consensus size: 22
54988612 GTTCACATTC
54988622 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * *
54988644 ATCACATATATG-CATGCTC-ACATT
1 ATCACAT-T-GGCCAT--TCGGCCTT
54988668 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
54988691 ATCACAT
1 ATCACAT
54988698 ATATGCACAT
Statistics
Matches: 41, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
22 16 0.39
23 8 0.20
24 8 0.20
25 9 0.22
ACGTcount: A:0.25, C:0.30, G:0.13, T:0.32
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:55005192 original size:23 final size:23
Alignment explanation
Indices: 55005166--55005214 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
55005156 GTAGGATACC
55005166 ATTAAAATGCATTCTAAACCAAT
1 ATTAAAATGCATTCTAAACCAAT
*
55005189 ATTAAAATGCGTTCTAAACCAAT
1 ATTAAAATGCATTCTAAACCAAT
55005212 ATT
1 ATT
55005215 GGTCACTATG
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:0.45, C:0.16, G:0.06, T:0.33
Consensus pattern (23 bp):
ATTAAAATGCATTCTAAACCAAT
Found at i:55005653 original size:29 final size:29
Alignment explanation
Indices: 55005596--55005654 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
55005586 TTTTCTCTTT
*
55005596 TATTAGGATTGAGATTTACTTTCAGTTTA
1 TATTAGGATTGAGATTTACTTTCAATTTA
* *
55005625 TATTAGGATTTAGATTTACTTTTAATTTA
1 TATTAGGATTGAGATTTACTTTCAATTTA
55005654 T
1 T
55005655 TCTTTGTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.53
Consensus pattern (29 bp):
TATTAGGATTGAGATTTACTTTCAATTTA
Found at i:55008435 original size:16 final size:16
Alignment explanation
Indices: 55008414--55008452 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
55008404 AGTCAGTTTC
*
55008414 TCTATTTACAACAAAT
1 TCTATTCACAACAAAT
55008430 TCTATTCACAACAAAT
1 TCTATTCACAACAAAT
55008446 TCTATTC
1 TCTATTC
55008453 TCTGCTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.38
Consensus pattern (16 bp):
TCTATTCACAACAAAT
Found at i:55015946 original size:30 final size:30
Alignment explanation
Indices: 55015906--55015963 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
55015896 TAAGGATAAC
*
55015906 CCTGATACAAACTCCATAGTAACTCTTTAT
1 CCTGACACAAACTCCATAGTAACTCTTTAT
*
55015936 CCTGACACAAACTCCATAGTATCTCTTT
1 CCTGACACAAACTCCATAGTAACTCTTT
55015964 CCCATTTCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.29, G:0.07, T:0.33
Consensus pattern (30 bp):
CCTGACACAAACTCCATAGTAACTCTTTAT
Found at i:55019975 original size:21 final size:20
Alignment explanation
Indices: 55019947--55019986 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
55019937 CAAAACTTGT
55019947 ATAACTATCATCAAACATTC
1 ATAACTATCATCAAACATTC
*
55019967 ATAATCTATCATCAATCATT
1 ATAA-CTATCATCAAACATT
55019987 AAAATACATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (20 bp):
ATAACTATCATCAAACATTC
Found at i:55049064 original size:40 final size:40
Alignment explanation
Indices: 55049020--55049122 Score: 127
Period size: 40 Copynumber: 2.6 Consensus size: 40
55049010 AATTCAAATA
*
55049020 TATATATGGCACTTAGTGTGCGATTC-AACAAAGCTTCAGC
1 TATATATGGCACTTAGTGTGCGATTCGAA-AAAGATTCAGC
* * * **
55049060 TATATATGGCACTTAGTGTGCGTTTCGGAATAGATTTGGC
1 TATATATGGCACTTAGTGTGCGATTCGAAAAAGATTCAGC
*
55049100 TATATATGGCACTTAGTATGCGA
1 TATATATGGCACTTAGTGTGCGA
55049123 GACCGATATA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
40 53 0.98
41 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (40 bp):
TATATATGGCACTTAGTGTGCGATTCGAAAAAGATTCAGC
Found at i:55053910 original size:30 final size:29
Alignment explanation
Indices: 55053855--55053912 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
55053845 ATGTAATAAC
* *
55053855 TTCCATACACATATCTTTTCTTATGATAT
1 TTCCATAAACATATCATTTCTTATGATAT
55053884 TTCCATATAACATATACATTTC-TATGATA
1 TTCCATA-AACATAT-CATTTCTTATGATA
55053913 AATCATCTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.28
30 13 0.52
31 5 0.20
ACGTcount: A:0.33, C:0.19, G:0.03, T:0.45
Consensus pattern (29 bp):
TTCCATAAACATATCATTTCTTATGATAT
Found at i:55057049 original size:22 final size:22
Alignment explanation
Indices: 55057018--55057065 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
55057008 ATTGATAGTG
55057018 TTGTTCTAGAAAAATCATTTGC
1 TTGTTCTAGAAAAATCATTTGC
*
55057040 TTGTTTTAGAAAAATCATTTGC
1 TTGTTCTAGAAAAATCATTTGC
55057062 TTGT
1 TTGT
55057066 CGCTCTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.10, G:0.15, T:0.46
Consensus pattern (22 bp):
TTGTTCTAGAAAAATCATTTGC
Found at i:55059271 original size:34 final size:34
Alignment explanation
Indices: 55059219--55059294 Score: 80
Period size: 34 Copynumber: 2.2 Consensus size: 34
55059209 CTTAGTCCTC
* * * * * *
55059219 TTTCAGTAGCAGTAGCAGTTTGGGCCTGATCCCG
1 TTTCAGTAACAATAGCAGTCTAGGCCTGAGCCCA
* *
55059253 TTTCAGTAACAATGGCAGTCTAGGCCTTAGCCCA
1 TTTCAGTAACAATAGCAGTCTAGGCCTGAGCCCA
55059287 TTTCAGTA
1 TTTCAGTA
55059295 CAGTATGCAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.30
Consensus pattern (34 bp):
TTTCAGTAACAATAGCAGTCTAGGCCTGAGCCCA
Found at i:55074366 original size:34 final size:34
Alignment explanation
Indices: 55074314--55074394 Score: 92
Period size: 34 Copynumber: 2.4 Consensus size: 34
55074304 TTAGCCCCTC
* * * *
55074314 TTTCAATAGCAGTAGCAGTTTGGGCCTAAGCCCA
1 TTTCAATAACAATAGCAGTCTGGGACTAAGCCCA
* *
55074348 TTTCAATAACAATGGCAGTCTGGGACTTAGCCCA
1 TTTCAATAACAATAGCAGTCTGGGACTAAGCCCA
*
55074382 TTTCAGT-ACAATA
1 TTTCAATAACAATA
55074395 TGCAAGCAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
33 5 0.13
34 34 0.87
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (34 bp):
TTTCAATAACAATAGCAGTCTGGGACTAAGCCCA
Found at i:55079867 original size:40 final size:40
Alignment explanation
Indices: 55079823--55080005 Score: 134
Period size: 41 Copynumber: 4.5 Consensus size: 40
55079813 TGTAAAACAT
*
55079823 AGAGCAATAGTGGCG-TTTTACCAAAAACGTCGCTAAAAAC
1 AGAGCAATAGCGGCGCTTTT-CCAAAAACGTCGCTAAAAAC
*** *
55079863 AGAGCAATAGCGGCGCTTTTGGTAAAACGTCGCTAAAAATA
1 AGAGCAATAGCGGCGCTTTTCCAAAAACGTCGCTAAAAA-C
* * *** * *
55079904 AGAGCATTAACGGCGCTTTTGGTAAAACGCCGCTAAAAATA
1 AGAGCAATAGCGGCGCTTTTCCAAAAACGTCGCTAAAAA-C
* * *** * *
55079945 AGAGCATTAGCGGTGCTTTTGGTAAAACGCCGCTAAAAATA
1 AGAGCAATAGCGGCGCTTTTCCAAAAACGTCGCTAAAAA-C
* *
55079986 AGAGCATTAACGGCGCTTTT
1 AGAGCAATAGCGGCGCTTTT
55080006 GGTAAAATGC
Statistics
Matches: 129, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
40 30 0.23
41 99 0.77
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.23
Consensus pattern (40 bp):
AGAGCAATAGCGGCGCTTTTCCAAAAACGTCGCTAAAAAC
Found at i:55079920 original size:41 final size:41
Alignment explanation
Indices: 55079846--55080024 Score: 279
Period size: 41 Copynumber: 4.4 Consensus size: 41
55079836 CGTTTTACCA
* * * *
55079846 AAAACGTCGCTAAAAA-CAGAGCAATAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAATAAGAGCATTAACGGCGCTTTTGGT
*
55079886 AAAACGTCGCTAAAAATAAGAGCATTAACGGCGCTTTTGGT
1 AAAACGCCGCTAAAAATAAGAGCATTAACGGCGCTTTTGGT
* *
55079927 AAAACGCCGCTAAAAATAAGAGCATTAGCGGTGCTTTTGGT
1 AAAACGCCGCTAAAAATAAGAGCATTAACGGCGCTTTTGGT
55079968 AAAACGCCGCTAAAAATAAGAGCATTAACGGCGCTTTTGGT
1 AAAACGCCGCTAAAAATAAGAGCATTAACGGCGCTTTTGGT
*
55080009 AAAATGCCGCTAAAAA
1 AAAACGCCGCTAAAAA
55080025 GTTTAGGGTT
Statistics
Matches: 129, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
40 16 0.12
41 113 0.88
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.22
Consensus pattern (41 bp):
AAAACGCCGCTAAAAATAAGAGCATTAACGGCGCTTTTGGT
Found at i:55080122 original size:21 final size:22
Alignment explanation
Indices: 55080098--55080141 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
55080088 GGTTTATGTA
*
55080098 TTATGGTTTAAGGGTT-GGGGT
1 TTATGATTTAAGGGTTAGGGGT
55080119 TTATGATTTAAGGGTTAGGGGT
1 TTATGATTTAAGGGTTAGGGGT
55080141 T
1 T
55080142 AGGGGTTAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.18, C:0.00, G:0.39, T:0.43
Consensus pattern (22 bp):
TTATGATTTAAGGGTTAGGGGT
Found at i:55080140 original size:7 final size:7
Alignment explanation
Indices: 55080130--55080156 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
55080120 TATGATTTAA
55080130 GGGTTAG
1 GGGTTAG
55080137 GGGTTAG
1 GGGTTAG
55080144 GGGTTAG
1 GGGTTAG
55080151 GGGTTA
1 GGGTTA
55080157 ATACTTAGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.56, T:0.30
Consensus pattern (7 bp):
GGGTTAG
Found at i:55080404 original size:21 final size:21
Alignment explanation
Indices: 55080378--55080421 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
55080368 TTATGGTTAG
* *
55080378 GGGATATAGTTTAGGGTTTAA
1 GGGATATACTTTAGGGATTAA
55080399 GGGATATACTTTAGGGATTAA
1 GGGATATACTTTAGGGATTAA
55080420 GG
1 GG
55080422 TTATAGGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.02, G:0.34, T:0.34
Consensus pattern (21 bp):
GGGATATACTTTAGGGATTAA
Found at i:55082749 original size:14 final size:13
Alignment explanation
Indices: 55082726--55082755 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
55082716 ATTACTATAA
55082726 TAATTATATGAAG
1 TAATTATATGAAG
55082739 TAATATATATGAAG
1 TAAT-TATATGAAG
55082753 TAA
1 TAA
55082756 AATTATATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (13 bp):
TAATTATATGAAG
Found at i:55083134 original size:183 final size:183
Alignment explanation
Indices: 55082826--55083200 Score: 669
Period size: 183 Copynumber: 2.0 Consensus size: 183
55082816 GATATAGTTC
* * * *
55082826 CATGTGTCTATATTAGTGAATTAATGTTGTATATGTTTCAGTTACTGCTTCCTGCTCCTCCTGCA
1 CATGTGTTTATATTAGTGAATTAATGTTGTATATATTTCAGTTACTACTTCCTGCTCCTCCTACA
55082891 ACTATTGGTTCAACTGAAGCTGCCATTTAATCTTCGAATTAATATTTGGTACTGATATAGATAAA
66 ACTATTGGTTCAACTGAAGCTGCCATTTAATCTTCGAATTAATATTTGGTACTGATATAGATAAA
*
55082956 GTTTTCATATTTGCTTAAACTGAAATATATTTGGTGCTACTCTTATAATCTTA
131 GTTTTCATATTTGCTTAAACTGAAATATATTTGGTGCTACCCTTATAATCTTA
* *
55083009 CATGTGTTTGTATTAGTGAATTAATGTTGTATGTATTTCAGTTACTACTTCCTGCTCCTCCTACA
1 CATGTGTTTATATTAGTGAATTAATGTTGTATATATTTCAGTTACTACTTCCTGCTCCTCCTACA
55083074 ACTATTGGTTCAACTGAAGCTGCCATTTAATCTTCGAATTAATATTTGGTACTGATATAGATAAA
66 ACTATTGGTTCAACTGAAGCTGCCATTTAATCTTCGAATTAATATTTGGTACTGATATAGATAAA
*
55083139 GTTTTTATATTTGCTTAAACTGAAATATATTTGGTGCTACCCTTATAATCTTA
131 GTTTTCATATTTGCTTAAACTGAAATATATTTGGTGCTACCCTTATAATCTTA
*
55083192 CATCTGTTT
1 CATGTGTTT
55083201 TAGGTACTAT
Statistics
Matches: 183, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
183 183 1.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (183 bp):
CATGTGTTTATATTAGTGAATTAATGTTGTATATATTTCAGTTACTACTTCCTGCTCCTCCTACA
ACTATTGGTTCAACTGAAGCTGCCATTTAATCTTCGAATTAATATTTGGTACTGATATAGATAAA
GTTTTCATATTTGCTTAAACTGAAATATATTTGGTGCTACCCTTATAATCTTA
Found at i:55083416 original size:15 final size:15
Alignment explanation
Indices: 55083396--55083424 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
55083386 GGAGTAGACC
55083396 AGGTACGTTTTATTA
1 AGGTACGTTTTATTA
55083411 AGGTACGTTTTATT
1 AGGTACGTTTTATT
55083425 TCAAAATTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.07, G:0.21, T:0.48
Consensus pattern (15 bp):
AGGTACGTTTTATTA
Found at i:55083816 original size:65 final size:65
Alignment explanation
Indices: 55083735--55083862 Score: 229
Period size: 65 Copynumber: 2.0 Consensus size: 65
55083725 CCTGACGGGT
*
55083735 TGCCTTATATCGAGCTGCAAGATATAATGGATTCTCCCTAAGTGTAACAACGCCACGTATGATAA
1 TGCCTTATATCGAGCTGCAAGATATAATGGATCCTCCCTAAGTGTAACAACGCCACGTATGATAA
* *
55083800 TGCCTTATATCGAGCTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGAT
1 TGCCTTATATCGAGCTGCAAGATATAATGGATCCTCCCTAAGTGTAACAACGCCACGTATGAT
55083863 GAATCTTAAA
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:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (65 bp):
TGCCTTATATCGAGCTGCAAGATATAATGGATCCTCCCTAAGTGTAACAACGCCACGTATGATAA
Found at i:55084509 original size:15 final size:15
Alignment explanation
Indices: 55084465--55084520 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
55084455 AACGACATGT
*
55084465 ATATTACTTAATTAAA
1 ATATTATTTAATT-AA
55084481 ATAATT-TTT-A-TAA
1 AT-ATTATTTAATTAA
55084494 ATATTATTTAATTAA
1 ATATTATTTAATTAA
55084509 ATATTATTTAAT
1 ATATTATTTAAT
55084521 CCCGCTACTT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
12 3 0.09
13 7 0.20
14 2 0.06
15 16 0.46
16 4 0.11
17 3 0.09
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
ATATTATTTAATTAA
Found at i:55084664 original size:9 final size:9
Alignment explanation
Indices: 55084624--55084690 Score: 55
Period size: 9 Copynumber: 7.6 Consensus size: 9
55084614 TATTTGATAT
*
55084624 CATAATTTA
1 CATAACTTA
*
55084633 TATAACTTA
1 CATAACTTA
* *
55084642 CAAAACGTA
1 CATAACTTA
55084651 CATAACTTA
1 CATAACTTA
*
55084660 TATAACTTA
1 CATAACTTA
* *
55084669 GATAA-ATA
1 CATAACTTA
*
55084677 TATAACTTA
1 CATAACTTA
55084686 CATAA
1 CATAA
55084691 TACTTAAATA
Statistics
Matches: 44, Mismatches: 13, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
8 6 0.14
9 38 0.86
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.34
Consensus pattern (9 bp):
CATAACTTA
Found at i:55084680 original size:17 final size:17
Alignment explanation
Indices: 55084658--55084775 Score: 65
Period size: 17 Copynumber: 6.4 Consensus size: 17
55084648 GTACATAACT
*
55084658 TATATAACTTAGATAAA
1 TATATAACTTACATAAA
55084675 TATATAACTTACATAATA
1 TATATAACTTACATAA-A
** *
55084693 CTTAAATATATTTTATATTATAA
1 --T--ATATAACTTACA-TA-AA
* *
55084716 TTTACATAACTTACATAACT
1 TATA--TAACTTACATAA-A
* *
55084736 TATACAACTTAGATAAA
1 TATATAACTTACATAAA
*
55084753 TATATAATTTACATAAA
1 TATATAACTTACATAAA
55084770 TATATA
1 TATATA
55084776 TCATATCATA
Statistics
Matches: 75, Mismatches: 16, Indels: 20
0.68 0.14 0.18
Matches are distributed among these distances:
17 35 0.47
18 11 0.15
19 3 0.04
20 6 0.08
21 7 0.09
22 9 0.12
23 3 0.04
24 1 0.01
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (17 bp):
TATATAACTTACATAAA
Found at i:55084745 original size:87 final size:87
Alignment explanation
Indices: 55084593--55084751 Score: 237
Period size: 87 Copynumber: 1.8 Consensus size: 87
55084583 TGAAATAAAA
* *
55084593 AACTTACATAATACATAAATATATTTGATATCATAATTTATATAACTTACAAAACGTACATAACT
1 AACTTACATAATACATAAATATATTTGATATCATAATTTACATAACTTACAAAACGTACACAACT
*
55084658 TATATAACTTAGATAAATATAT
66 TAGATAACTTAGATAAATATAT
* * * * * *
55084680 AACTTACATAATACTTAAATATATTTTATATTATAATTTACATAACTTACATAACTTATACAACT
1 AACTTACATAATACATAAATATATTTGATATCATAATTTACATAACTTACAAAACGTACACAACT
55084745 TAGATAA
66 TAGATAA
55084752 ATATATAATT
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 63 1.00
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (87 bp):
AACTTACATAATACATAAATATATTTGATATCATAATTTACATAACTTACAAAACGTACACAACT
TAGATAACTTAGATAAATATAT
Found at i:55090018 original size:13 final size:14
Alignment explanation
Indices: 55090002--55090030 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
55089992 TTCTAAATAT
55090002 TTATAA-TGTTTAA
1 TTATAATTGTTTAA
55090015 TTATAATTGTTTAA
1 TTATAATTGTTTAA
55090029 TT
1 TT
55090031 CAATTCATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TTATAATTGTTTAA
Found at i:55090467 original size:21 final size:21
Alignment explanation
Indices: 55090442--55090500 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
55090432 TTAGAGCGGA
*
55090442 GGCAGCAGAGAGGGAGGCAGC
1 GGCAGCAGCGAGGGAGGCAGC
*
55090463 GGCAGCAGCGAGGGAGGCAGG
1 GGCAGCAGCGAGGGAGGCAGC
*
55090484 GGCAACAGCGAGGGAGG
1 GGCAGCAGCGAGGGAGG
55090501 TAGAGCATAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.27, C:0.19, G:0.54, T:0.00
Consensus pattern (21 bp):
GGCAGCAGCGAGGGAGGCAGC
Found at i:55090905 original size:43 final size:43
Alignment explanation
Indices: 55090857--55090950 Score: 109
Period size: 43 Copynumber: 2.2 Consensus size: 43
55090847 TCTGCCAAAA
* * *
55090857 TTAGCGGTG-TTTGTGGGAAAATGGCCGCTAAAGGCCACGACTT
1 TTAGCGGCGCTTTGTAGGAAAA-CGCCGCTAAAGGCCACGACTT
* ***
55090900 TTAGCGGCGCTTTTTATTCAAACGCCGCTAAAGGCCACGACTT
1 TTAGCGGCGCTTTGTAGGAAAACGCCGCTAAAGGCCACGACTT
55090943 TTAGCGGC
1 TTAGCGGC
55090951 TTTTTTTAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
43 36 0.84
44 7 0.16
ACGTcount: A:0.22, C:0.23, G:0.28, T:0.27
Consensus pattern (43 bp):
TTAGCGGCGCTTTGTAGGAAAACGCCGCTAAAGGCCACGACTT
Found at i:55090957 original size:43 final size:42
Alignment explanation
Indices: 55090880--55090967 Score: 140
Period size: 43 Copynumber: 2.1 Consensus size: 42
55090870 TGGGAAAATG
*
55090880 GCCGCTAAAGGCCACGACTTTTAGCGGCGCTTTTTATTCAAAC
1 GCCGCTAAAGGCCACGACTTTTAGCGGCGCTTTTTAAT-AAAC
**
55090923 GCCGCTAAAGGCCACGACTTTTAGCGGCTTTTTTTAATAAAC
1 GCCGCTAAAGGCCACGACTTTTAGCGGCGCTTTTTAATAAAC
55090965 GCC
1 GCC
55090968 ACCAGTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 7 0.17
43 35 0.83
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.28
Consensus pattern (42 bp):
GCCGCTAAAGGCCACGACTTTTAGCGGCGCTTTTTAATAAAC
Found at i:55098336 original size:12 final size:10
Alignment explanation
Indices: 55098310--55098343 Score: 68
Period size: 10 Copynumber: 3.4 Consensus size: 10
55098300 AAATATCAAC
55098310 CATATATGCA
1 CATATATGCA
55098320 CATATATGCA
1 CATATATGCA
55098330 CATATATGCA
1 CATATATGCA
55098340 CATA
1 CATA
55098344 ATCAAACCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (10 bp):
CATATATGCA
Found at i:55098944 original size:41 final size:40
Alignment explanation
Indices: 55098899--55098982 Score: 100
Period size: 40 Copynumber: 2.1 Consensus size: 40
55098889 AGTGACTTAC
55098899 ATAGCCAAAGCTA-TCTCG-ATCTCGCACACTAAATGCCATAT
1 ATAGCCAAAGCTATTC-CGAAT-T-GCACACTAAATGCCATAT
** *
55098940 ATAGCTGAAGCTATTCCGAATTGCACACTAAGTGCCATAT
1 ATAGCCAAAGCTATTCCGAATTGCACACTAAATGCCATAT
55098980 ATA
1 ATA
55098983 TAGTTGATTC
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
40 20 0.53
41 14 0.37
42 4 0.11
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.26
Consensus pattern (40 bp):
ATAGCCAAAGCTATTCCGAATTGCACACTAAATGCCATAT
Found at i:55099819 original size:22 final size:22
Alignment explanation
Indices: 55099794--55099835 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
55099784 CAATATAACT
55099794 TTAATGAAATACCATTAATACC
1 TTAATGAAATACCATTAATACC
55099816 TTAATGAAATACCATTAATA
1 TTAATGAAATACCATTAATA
55099836 TCATCCACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.33
Consensus pattern (22 bp):
TTAATGAAATACCATTAATACC
Found at i:55103529 original size:27 final size:28
Alignment explanation
Indices: 55103499--55103552 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
55103489 CGAAATTCAT
*
55103499 ACTTTAATTA-TAAAATAATTAATTTTC
1 ACTTAAATTATTAAAATAATTAATTTTC
*
55103526 ACTTAAATTATTAACATAATTAATTTT
1 ACTTAAATTATTAAAATAATTAATTTT
55103553 AATTATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 9 0.38
28 15 0.62
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.48
Consensus pattern (28 bp):
ACTTAAATTATTAAAATAATTAATTTTC
Found at i:55110435 original size:25 final size:25
Alignment explanation
Indices: 55110397--55110447 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
55110387 TAAAATGGTG
*
55110397 TCAATAATCCTAGGAAGGCCTTTCC
1 TCAATAATCATAGGAAGGCCTTTCC
*
55110422 TCAATAATCATAGGAATGCCTTTCC
1 TCAATAATCATAGGAAGGCCTTTCC
55110447 T
1 T
55110448 AGCAACTGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.31
Consensus pattern (25 bp):
TCAATAATCATAGGAAGGCCTTTCC
Found at i:55112386 original size:14 final size:14
Alignment explanation
Indices: 55112367--55112396 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
55112357 GACTGGATTT
55112367 TTATCTATAAATTA
1 TTATCTATAAATTA
55112381 TTATCTATAAATTA
1 TTATCTATAAATTA
55112395 TT
1 TT
55112397 TATGTTTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (14 bp):
TTATCTATAAATTA
Found at i:55112890 original size:102 final size:101
Alignment explanation
Indices: 55112559--55113059 Score: 587
Period size: 102 Copynumber: 5.0 Consensus size: 101
55112549 ATTTTGGTAA
* * ** *
55112559 TTATTTTGTTAGTAATTTATGATTAGGTTATAATTTTTTAGTG--T--TTT-GTGTCCTGTGAGT
1 TTATTTT-TTAGTAATTTATGATTAGGTTATAAATTGTTAGTGTTTAGTTTAGTGTTTTGTGATT
* *
55112619 TTTTAGTAATGTAAA-TTTTGAAAAA-AA-ATTATAG
65 TTTTAGTAATGTAAATTTTTTAAAAATAATTTTATAG
* *
55112653 TTATTTTATTAGTAATTTATGATTAGGTTATAAATTGTTAATGTTTAGTTTAGTGTTTTCTGATT
1 TTATTTT-TTAGTAATTTATGATTAGGTTATAAATTGTTAGTGTTTAGTTTAGTGTTTTGTGATT
* **
55112718 TTTTATTAATGTAAA-TTTAAAAAAATAATTTTATAG
65 TTTTAGTAATGTAAATTTTTTAAAAATAATTTTATAG
* *
55112754 TTATTTTGCTAGTAATTTATGATTAGATTATAAATTGTTAGTGTTTAGTTTAGTGTTTTGTGATT
1 TTATTTT-TTAGTAATTTATGATTAGGTTATAAATTGTTAGTGTTTAGTTTAGTGTTTTGTGATT
55112819 TTTTAGTAATGTAAATTTTTTAAAAATAATTTTATAG
65 TTTTAGTAATGTAAATTTTTTAAAAATAATTTTATAG
* *
55112856 TTATTTTTCTAGTTATTTATGATTAGGTTATAAATTGTTAGTGTTTAGTTTAAG-GTTTTGTGAG
1 TTATTTTT-TAGTAATTTATGATTAGGTTATAAATTGTTAGTGTTTAGTTT-AGTGTTTTGTGAT
*
55112920 TGTTTAGTAATGT-AATTTATTTAAAAAGTAATTTTATAG
64 TTTTTAGTAATGTAAATTT-TTTAAAAA-TAATTTTATAG
* * * **
55112959 TTATATTGTTAGTAATTTATTATTAGGTTATATAAATTGTTGGTGTTTAGTTTAGCATTTTGTGA
1 TTAT-TTTTTAGTAATTTATGATTAGG-T-TATAAATTGTTAGTGTTTAGTTTAGTGTTTTGTGA
* **
55113024 TTTTTT--TAATGTAATTTTTTTATAATGTAATTTTAT
63 TTTTTTAGTAATGTAAATTTTTTA-AAAATAATTTTAT
55113060 TTGACTTTTA
Statistics
Matches: 354, Mismatches: 35, Indels: 27
0.85 0.08 0.06
Matches are distributed among these distances:
94 39 0.11
96 1 0.00
98 3 0.01
99 31 0.09
100 2 0.01
101 85 0.24
102 95 0.27
103 52 0.15
104 12 0.03
105 34 0.10
ACGTcount: A:0.30, C:0.01, G:0.15, T:0.54
Consensus pattern (101 bp):
TTATTTTTTAGTAATTTATGATTAGGTTATAAATTGTTAGTGTTTAGTTTAGTGTTTTGTGATTT
TTTAGTAATGTAAATTTTTTAAAAATAATTTTATAG
Found at i:55113043 original size:13 final size:15
Alignment explanation
Indices: 55113023--55113057 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
55113013 GCATTTTGTG
55113023 ATTTTTT-TAATGTA
1 ATTTTTTATAATGTA
55113037 ATTTTTTTATAATGTA
1 A-TTTTTTATAATGTA
55113053 ATTTT
1 ATTTT
55113058 ATTTGACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 1 0.05
15 10 0.53
16 8 0.42
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.66
Consensus pattern (15 bp):
ATTTTTTATAATGTA
Found at i:55113049 original size:16 final size:15
Alignment explanation
Indices: 55113024--55113057 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
55113014 CATTTTGTGA
55113024 TTTTTTTAATGTAAT
1 TTTTTTTAATGTAAT
55113039 TTTTTTATAATGTAAT
1 TTTTTT-TAATGTAAT
55113055 TTT
1 TTT
55113058 ATTTGACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTTTTAATGTAAT
Found at i:55115379 original size:74 final size:72
Alignment explanation
Indices: 55115263--55115434 Score: 235
Period size: 74 Copynumber: 2.4 Consensus size: 72
55115253 TCAAATCATC
* *
55115263 AATTTTAGGGGGTTTTGT-AATTT-AA-ATAACTTTGTATTTATGTAATGACTTTTTT-CCATTT
1 AATTTTA-GGGGTTTTTTCAATTTAAATATAACTTTATATTTATGTAATGACTTTTTTACCATTT
* *
55115324 TAGTTATT
65 CAATTATT
55115332 AATTTTAGCGGGTTTTTTCAATTTAAATAGTCAACTTTATATTTATGTAATGACTTTTTTACCAT
1 AATTTTAG-GGGTTTTTTCAATTTAAATA-T-AACTTTATATTTATGTAATGACTTTTTTACCAT
55115397 TTCAATTATT
63 TTCAATTATT
*
55115407 AATTTTAGGGGTTTTTGCAATTTAAATA
1 AATTTTAGGGGTTTTTTCAATTTAAATA
55115435 ATAAAGTTTG
Statistics
Matches: 91, Mismatches: 5, Indels: 9
0.87 0.05 0.09
Matches are distributed among these distances:
68 1 0.01
69 15 0.16
70 5 0.05
71 2 0.02
72 1 0.01
73 1 0.01
74 46 0.51
75 20 0.22
ACGTcount: A:0.28, C:0.08, G:0.13, T:0.51
Consensus pattern (72 bp):
AATTTTAGGGGTTTTTTCAATTTAAATATAACTTTATATTTATGTAATGACTTTTTTACCATTTC
AATTATT
Found at i:55118776 original size:25 final size:25
Alignment explanation
Indices: 55118742--55118790 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
55118732 AGTACGAGAT
*
55118742 TAAACTTCAGTATTTCCTTTCACCC
1 TAAACTTCAGTATTGCCTTTCACCC
55118767 TAAACTTCAGTATTGCCTTTCACC
1 TAAACTTCAGTATTGCCTTTCACC
55118791 AGCAAACGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.24, C:0.31, G:0.06, T:0.39
Consensus pattern (25 bp):
TAAACTTCAGTATTGCCTTTCACCC
Found at i:55121374 original size:39 final size:39
Alignment explanation
Indices: 55121331--55121409 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
55121321 CTGCTATGAG
* *
55121331 TATGTTTCTTGGATTTTTATATAATAGTAACAATATTAC
1 TATGTTTCTTGGATTATTATATAATAGTAACAACATTAC
55121370 TATGTTTCTTGGATTATTATATAATAGTAACAACATTAC
1 TATGTTTCTTGGATTATTATATAATAGTAACAACATTAC
55121409 T
1 T
55121410 CATAGTGATA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.47
Consensus pattern (39 bp):
TATGTTTCTTGGATTATTATATAATAGTAACAACATTAC
Found at i:55124795 original size:18 final size:18
Alignment explanation
Indices: 55124772--55124807 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
55124762 TAACCCGCAC
55124772 GAATGCCTTCGGGACTTA
1 GAATGCCTTCGGGACTTA
55124790 GAATGCCTTCGGGACTTA
1 GAATGCCTTCGGGACTTA
55124808 ACCCGATGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (18 bp):
GAATGCCTTCGGGACTTA
Found at i:55124818 original size:21 final size:21
Alignment explanation
Indices: 55124792--55124833 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
55124782 GGGACTTAGA
55124792 ATGCCTTCGGGACTTAACCCG
1 ATGCCTTCGGGACTTAACCCG
55124813 ATGCCTTCGGGACTTAACCCG
1 ATGCCTTCGGGACTTAACCCG
55124834 GTTATAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.33, G:0.24, T:0.24
Consensus pattern (21 bp):
ATGCCTTCGGGACTTAACCCG
Found at i:55124868 original size:40 final size:40
Alignment explanation
Indices: 55124722--55124879 Score: 161
Period size: 40 Copynumber: 4.0 Consensus size: 40
55124712 CGGATGTAAC
* *
55124722 AACCAGCACAAATGCCTTCGGGACTTAACCCGAGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCG-GTTATAAT
*
55124763 AACCCGCACGAATGCCTTCGGGACTTAGAATGCCTTCGG-GACT--T
1 AACCCGCACGAATGCCTTCGGGACTT--AA--CC--CGGTTA-TAAT
55124807 AA--C-C-CG-ATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
55124842 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATA
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATA
55124880 TTTTTTTCTA
Statistics
Matches: 98, Mismatches: 4, Indels: 31
0.74 0.03 0.23
Matches are distributed among these distances:
33 4 0.04
34 1 0.01
35 5 0.05
37 3 0.03
38 1 0.01
39 17 0.17
40 29 0.30
41 25 0.26
42 1 0.01
43 2 0.02
44 3 0.03
45 3 0.03
46 2 0.02
47 2 0.02
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (40 bp):
AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
Found at i:55140807 original size:44 final size:42
Alignment explanation
Indices: 55140759--55140864 Score: 104
Period size: 44 Copynumber: 2.4 Consensus size: 42
55140749 GTGATTTTGC
* * *
55140759 GTAAGACCAAGTCTGGGACATTGGCATCGATTTATGATTTACGT
1 GTAAGACCAA-TCTGGGACAGTGGCATCGATATATGA-TTACAT
* * * *
55140803 GTAAGACCCTATCTGGGATAGTGGTATCGATATGTGATTACAT
1 GTAAGA-CCAATCTGGGACAGTGGCATCGATATATGATTACAT
*
55140846 GTAAGACCACATCTAGGAC
1 GTAAGACCA-ATCTGGGAC
55140865 GTTGGCGTTG
Statistics
Matches: 50, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
42 2 0.04
43 18 0.36
44 27 0.54
45 3 0.06
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (42 bp):
GTAAGACCAATCTGGGACAGTGGCATCGATATATGATTACAT
Found at i:55151880 original size:44 final size:43
Alignment explanation
Indices: 55151813--55151940 Score: 136
Period size: 43 Copynumber: 3.0 Consensus size: 43
55151803 CATAGGGTTC
*
55151813 CGATATGTGATTT-TGTGTAAGACCACATCTGGGACGTTGGCAT
1 CGATATGTGATTTACGTGTAAGACCACATCTGGGACG-TGGCAT
* * *
55151856 CGATTTGTGATTTACGTGTAAGACC-CTGTCTGGGACAGTCGCAT
1 CGATATGTGATTTACGTGTAAGACCAC-ATCTGGGAC-GTGGCAT
* * *
55151900 CGATACGTGA-TTACATGTAAGACCACATTTGGGACGATGGC
1 CGATATGTGATTTACGTGTAAGACCACATCTGGGACG-TGGC
55151941 GTTGTATGAG
Statistics
Matches: 70, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
42 1 0.01
43 36 0.51
44 32 0.46
45 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (43 bp):
CGATATGTGATTTACGTGTAAGACCACATCTGGGACGTGGCAT
Found at i:55151933 original size:43 final size:44
Alignment explanation
Indices: 55151828--55151935 Score: 116
Period size: 44 Copynumber: 2.5 Consensus size: 44
55151818 TGTGATTTTG
* * ** *
55151828 TGTAAGACCACATCTGGGACGTTGGCATCGATTTGTGATTTACG
1 TGTAAGACCACATTTGGGACGTTCGCATCGATACGTGATTTACA
55151872 TGTAAGACC-C-TGTCTGGGACAG-TCGCATCGATACGTGA-TTACA
1 TGTAAGACCACAT-T-TGGGAC-GTTCGCATCGATACGTGATTTACA
55151915 TGTAAGACCACATTTGGGACG
1 TGTAAGACCACATTTGGGACG
55151936 ATGGCGTTGT
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
42 2 0.04
43 20 0.37
44 30 0.56
45 2 0.04
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (44 bp):
TGTAAGACCACATTTGGGACGTTCGCATCGATACGTGATTTACA
Found at i:55161963 original size:21 final size:20
Alignment explanation
Indices: 55161935--55161974 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
55161925 AGATATAATA
55161935 GCCAAGCTTA-ATCATATTCG
1 GCCAAGCTTATAT-ATATTCG
55161955 GCCATAGCTTATATATATTC
1 GCCA-AGCTTATATATATTC
55161975 ACACATTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 12 0.67
22 2 0.11
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (20 bp):
GCCAAGCTTATATATATTCG
Found at i:55164335 original size:18 final size:18
Alignment explanation
Indices: 55164298--55164336 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
55164288 TTGGAAATCA
*
55164298 AAATTATTAAAAGATGAT
1 AAATTATTAAAAGATAAT
55164316 AAATTATTAAATAGA-AAT
1 AAATTATTAAA-AGATAAT
55164334 AAA
1 AAA
55164337 AATCATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (18 bp):
AAATTATTAAAAGATAAT
Found at i:55173566 original size:21 final size:21
Alignment explanation
Indices: 55173542--55173584 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
55173532 TGCATAAGAG
55173542 TGGATTGTTGATATGAAATTA
1 TGGATTGTTGATATGAAATTA
55173563 TGGATTGTTGATATGAAATTA
1 TGGATTGTTGATATGAAATTA
55173584 T
1 T
55173585 TAAAGATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.44
Consensus pattern (21 bp):
TGGATTGTTGATATGAAATTA
Found at i:55175378 original size:40 final size:40
Alignment explanation
Indices: 55175240--55175381 Score: 137
Period size: 41 Copynumber: 3.5 Consensus size: 40
55175230 ATTCGATATC
* *
55175240 TCGCACACTAAGTGCCATATCATAGCCGAAGCTAT-CATAA
1 TCGCACACTAAGTGCCACAT-ATAGCCGAAGCTATCCAGAA
* * * **
55175280 CCTCACACACTAAGTG-CATCACATAGCCAAAGCTATCTCAGTC
1 --TCGCACACTAAGTGCCA-CATATAGCCGAAGCTATC-CAGAA
55175323 TCGCACACTAAGTGCCACATATAGCCGAAGCTACTCCA-AA
1 TCGCACACTAAGTGCCACATATAGCCGAAGCTA-TCCAGAA
*
55175363 TCGTACACTAAGTGCCACA
1 TCGCACACTAAGTGCCACA
55175382 CACATATACA
Statistics
Matches: 82, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
40 18 0.22
41 44 0.54
42 18 0.22
43 2 0.02
ACGTcount: A:0.34, C:0.32, G:0.14, T:0.20
Consensus pattern (40 bp):
TCGCACACTAAGTGCCACATATAGCCGAAGCTATCCAGAA
Found at i:55177407 original size:43 final size:43
Alignment explanation
Indices: 55177348--55177500 Score: 207
Period size: 43 Copynumber: 3.5 Consensus size: 43
55177338 AAAAAGCCAC
* ** * ** *
55177348 AAAAGATCATGACTTTTAGCGGCGTTCATTGGAAAAGTGCCGCT
1 AAAAG-TCATGGCTTTTAGCGGCGTTTGTGGGGGAAGCGCCGCT
*
55177392 AAAAGTCATGGCTTTTAGCGGCGTTTGTGGGGGAAGCGCTGCT
1 AAAAGTCATGGCTTTTAGCGGCGTTTGTGGGGGAAGCGCCGCT
* *
55177435 AAAAGTCTTGGCTTTTAGTGGCGTTTGTGGGGGAAGCGCCGCT
1 AAAAGTCATGGCTTTTAGCGGCGTTTGTGGGGGAAGCGCCGCT
55177478 AAAAGTCATGGCTTTTAGCGGCG
1 AAAAGTCATGGCTTTTAGCGGCG
55177501 CATTTGTTAC
Statistics
Matches: 96, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
43 91 0.95
44 5 0.05
ACGTcount: A:0.22, C:0.17, G:0.33, T:0.28
Consensus pattern (43 bp):
AAAAGTCATGGCTTTTAGCGGCGTTTGTGGGGGAAGCGCCGCT
Found at i:55177655 original size:33 final size:31
Alignment explanation
Indices: 55177572--55177657 Score: 100
Period size: 31 Copynumber: 2.7 Consensus size: 31
55177562 AACCCTTCCT
* * *
55177572 GCATTAAATCCAACCAAAAATAGCAAATATA
1 GCATAAAATCCAACCAAAAACAACAAATATA
* *
55177603 GCATGAAATCCAACCAAAAACAACAAATGTA
1 GCATAAAATCCAACCAAAAACAACAAATATA
*
55177634 GCATAAAAAATACAACCAAAAACA
1 GCAT--AAAATCCAACCAAAAACA
55177658 TTTAATCTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 31 0.66
33 16 0.34
ACGTcount: A:0.58, C:0.21, G:0.07, T:0.14
Consensus pattern (31 bp):
GCATAAAATCCAACCAAAAACAACAAATATA
Found at i:55177916 original size:21 final size:21
Alignment explanation
Indices: 55177892--55177936 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
55177882 TACTGCCATT
55177892 GCTGCTACCT-CTGCCTCCCTC
1 GCTGCT-CCTACTGCCTCCCTC
* *
55177913 GCTGCTGCTACTGTCTCCCTC
1 GCTGCTCCTACTGCCTCCCTC
55177934 GCT
1 GCT
55177937 ACTGCATCCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.04, C:0.47, G:0.18, T:0.31
Consensus pattern (21 bp):
GCTGCTCCTACTGCCTCCCTC
Found at i:55181094 original size:23 final size:23
Alignment explanation
Indices: 55181064--55181109 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
55181054 TAAATTGCAT
55181064 AAAGTCAAAGCGGCTCGATCATG
1 AAAGTCAAAGCGGCTCGATCATG
*
55181087 AAAGTCAAAGTGGCTCGATCATG
1 AAAGTCAAAGCGGCTCGATCATG
55181110 TACTTTCTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.20
Consensus pattern (23 bp):
AAAGTCAAAGCGGCTCGATCATG
Found at i:55183486 original size:9 final size:9
Alignment explanation
Indices: 55183472--55183735 Score: 115
Period size: 9 Copynumber: 30.0 Consensus size: 9
55183462 ATGTATTACA
*
55183472 TAAGTTAAG
1 TAAGTTATG
*
55183481 TAAGTTTTG
1 TAAGTTATG
55183490 TAAGTTATG
1 TAAGTTATG
55183499 TAAGTTATG
1 TAAGTTATG
* *
55183508 ATATGATAT-
1 -TAAGTTATG
* *
55183517 AAATTTATG
1 TAAGTTATG
*
55183526 TAAGGTATG
1 TAAGTTATG
55183535 TAAGTTATG
1 TAAGTTATG
*
55183544 TAAATTATG
1 TAAGTTATG
* ** *
55183553 ATATGAAATA
1 -TAAGTTATG
*
55183563 T-ATTTATG
1 TAAGTTATG
**
55183571 T-A-TTACA
1 TAAGTTATG
55183578 TAAGTTATG
1 TAAGTTATG
55183587 TAAGTTATG
1 TAAGTTATG
55183596 TAAGTTAT-
1 TAAGTTATG
* *
55183604 TATAG-GATA
1 TA-AGTTATG
*
55183613 TATATTTATG
1 TA-AGTTATG
55183623 TAAGTTAT-
1 TAAGTTATG
* *
55183631 TATA-TGATA
1 TA-AGTTATG
*
55183640 TATATTTATG
1 TA-AGTTATG
55183650 T-A-TTATG
1 TAAGTTATG
*
55183657 TAAGTTTTG
1 TAAGTTATG
55183666 TAAGTTATG
1 TAAGTTATG
55183675 TAAGTTAT-
1 TAAGTTATG
* *
55183683 TATA-TGATA
1 TA-AGTTATG
*
55183692 TATATTTATG
1 TA-AGTTATG
55183702 T-A-TTATG
1 TAAGTTATG
* *
55183709 TAAGGTATA
1 TAAGTTATG
55183718 TAAGTTATG
1 TAAGTTATG
55183727 TAAGTTATG
1 TAAGTTATG
55183736 ATATGATATA
Statistics
Matches: 192, Mismatches: 45, Indels: 36
0.70 0.16 0.13
Matches are distributed among these distances:
7 16 0.08
8 27 0.14
9 127 0.66
10 22 0.11
ACGTcount: A:0.36, C:0.00, G:0.17, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Found at i:55183637 original size:79 final size:79
Alignment explanation
Indices: 55183539--55183703 Score: 267
Period size: 79 Copynumber: 2.1 Consensus size: 79
55183529 GGTATGTAAG
55183539 TTATGTAAATTATGATATGAAATATATTTATGTATTACATAAGTTATGTAAGTTATGTAAGTTAT
1 TTATGTAAATTATGATATGAAATATATTTATGTATTACATAAGTTATGTAAGTTATGTAAGTTAT
55183604 TATAGGATATATAT
66 TATAGGATATATAT
* * * ** *
55183618 TTATGTAAGTTATTATATGATATATATTTATGTATTATGTAAGTTTTGTAAGTTATGTAAGTTAT
1 TTATGTAAATTATGATATGAAATATATTTATGTATTACATAAGTTATGTAAGTTATGTAAGTTAT
*
55183683 TATATGATATATAT
66 TATAGGATATATAT
55183697 TTATGTA
1 TTATGTA
55183704 TTATGTAAGG
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.36, C:0.01, G:0.14, T:0.49
Consensus pattern (79 bp):
TTATGTAAATTATGATATGAAATATATTTATGTATTACATAAGTTATGTAAGTTATGTAAGTTAT
TATAGGATATATAT
Found at i:55183674 original size:52 final size:52
Alignment explanation
Indices: 55183618--55183751 Score: 232
Period size: 52 Copynumber: 2.6 Consensus size: 52
55183608 GGATATATAT
* * *
55183618 TTATGTAAGTTATTATATGATATATATTTATGTATTATGTAAGTTTTGTAAG
1 TTATGTAAGTTATTATATGATATATATTTATGTATTATGTAAGGTATATAAG
55183670 TTATGTAAGTTATTATATGATATATATTTATGTATTATGTAAGGTATATAAG
1 TTATGTAAGTTATTATATGATATATATTTATGTATTATGTAAGGTATATAAG
*
55183722 TTATGTAAGTTATGATATGATATATATTTA
1 TTATGTAAGTTATTATATGATATATATTTA
55183752 ACATTAAGAT
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 78 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (52 bp):
TTATGTAAGTTATTATATGATATATATTTATGTATTATGTAAGGTATATAAG
Found at i:55183735 original size:79 final size:79
Alignment explanation
Indices: 55183539--55183728 Score: 235
Period size: 79 Copynumber: 2.4 Consensus size: 79
55183529 GGTATGTAAG
* * * * * **
55183539 TTATGTAAATTATGATATGAAATATATTTATGTATTACATAAGTTATGTAAGTTATGTAAGTTAT
1 TTATGTAAGTTATTATAGGATATATAGTTATGTATTATGTAAGTTATGTAAGTTATGTAAGTTAT
55183604 TATAGGATATATAT
66 TATAGGATATATAT
* * *
55183618 TTATGTAAGTTATTATATGATATATATTTATGTATTATGTAAGTTTTGTAAGTTATGTAAGTTAT
1 TTATGTAAGTTATTATAGGATATATAGTTATGTATTATGTAAGTTATGTAAGTTATGTAAGTTAT
*
55183683 TATATGATATATAT
66 TATAGGATATATAT
55183697 TTATGT-A-TTATGTA-AGG-TATATAAGTTATGTA
1 TTATGTAAGTTAT-TATAGGATATAT-AGTTATGTA
55183729 AGTTATGATA
Statistics
Matches: 100, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
76 5 0.05
77 14 0.14
78 3 0.03
79 78 0.78
ACGTcount: A:0.36, C:0.01, G:0.15, T:0.48
Consensus pattern (79 bp):
TTATGTAAGTTATTATAGGATATATAGTTATGTATTATGTAAGTTATGTAAGTTATGTAAGTTAT
TATAGGATATATAT
Found at i:55186829 original size:114 final size:115
Alignment explanation
Indices: 55186668--55186923 Score: 345
Period size: 115 Copynumber: 2.2 Consensus size: 115
55186658 TTTTTGCGGG
* * *
55186668 CTAATGCTAATCTATTGCAGCGTTTTTCACCCTAGCCCCGCTAAAGCCACCAAAGATGCATCACA
1 CTAATGCTAATCTATTGC-GGGGTTTTCACCCTAGCCCCGCTAAAGCCACCAAAAATGCATCA-A
* * *
55186733 AA-ACGGCGTCGTTTTAATA-TTGTTTTTGTGGCGTTTTAAAAAAAACGCCA
64 AAGACGGCGTCATTTTAATATTTCTTTTTGGGGCGTTTTAAAAAAAACGCCA
* *
55186783 CTAATGCTAATCTATTGCGGGGTTTTCACCCTAGCGCCGCTAAAGCCACTAAAAATGCATCAAAA
1 CTAATGCTAATCTATTGCGGGGTTTTCACCCTAGCCCCGCTAAAGCCACCAAAAATGCATCAAAA
* ** * *
55186848 GACGGCGTCATTTTATTATTTCTTTTTGGGGCGTTTTTTAACAAACGCCG
66 GACGGCGTCATTTTAATATTTCTTTTTGGGGCGTTTTAAAAAAAACGCCA
* *
55186898 CTAATGCTAATCTATTGTGGTGTTTT
1 CTAATGCTAATCTATTGCGGGGTTTT
55186924 TTAACAAACG
Statistics
Matches: 124, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
113 3 0.02
114 54 0.44
115 67 0.54
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (115 bp):
CTAATGCTAATCTATTGCGGGGTTTTCACCCTAGCCCCGCTAAAGCCACCAAAAATGCATCAAAA
GACGGCGTCATTTTAATATTTCTTTTTGGGGCGTTTTAAAAAAAACGCCA
Found at i:55186963 original size:39 final size:39
Alignment explanation
Indices: 55186881--55186963 Score: 130
Period size: 39 Copynumber: 2.1 Consensus size: 39
55186871 TTTTGGGGCG
* **
55186881 TTTTTTAACAAACGCCGCTAATGCTAATCTATTGTGGTG
1 TTTTTTAACAAACGCCGCTAATGCTAATCTATTGCGGCA
*
55186920 TTTTTTAACAAACGTCGCTAATGCTAATCTATTGCGGCA
1 TTTTTTAACAAACGCCGCTAATGCTAATCTATTGCGGCA
55186959 TTTTT
1 TTTTT
55186964 CACCATTGGC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41
Consensus pattern (39 bp):
TTTTTTAACAAACGCCGCTAATGCTAATCTATTGCGGCA
Found at i:55186976 original size:154 final size:154
Alignment explanation
Indices: 55186783--55187071 Score: 368
Period size: 154 Copynumber: 1.9 Consensus size: 154
55186773 AAAAACGCCA
* * *
55186783 CTAATGCTAATCTATTGCGGGGTTTTCACCCTAGCGCCGCTAAAGCCACTAAAAATGCATCAAAA
1 CTAATGCTAATCTATTGCGGAGTTTTCACCATAGCGCCGCAAAAGCCACTAAAAATGCATCAAAA
* ** * * * *
55186848 GACGGCGTCATTTTATTATT-TCTTTTTGGGGCGTTTT-TTAACAAACGCCGCTAATGCTAATCT
66 GACGGAGTCATTTTAAAATTGT-TTTTTGCGACGTTTTCGT-ACAAACACCGCTAATGCTAATCT
55186911 ATTGTGGTGTTTTTTAACAAACGTCG
129 ATTGTGGTGTTTTTTAACAAACGTCG
* * * * *
55186937 CTAATGCTAATCTATTGCGGCATTTTTCACCATTG-GCCGCAAAAGCCATTAAAGATGCATCACA
1 CTAATGCTAATCTATTGCGG-AGTTTTCACCATAGCGCCGCAAAAGCCACTAAAAATGCATCAAA
* * *
55187001 AGACGGAGTCGTTTTAAAATTGTTTTTTGCGACGTTTTCGTAGAAACACGGCTAATGCTAATCTA
65 AGACGGAGTCATTTTAAAATTGTTTTTTGCGACGTTTTCGTACAAACACCGCTAATGCTAATCTA
55187066 TTGTGG
130 TTGTGG
55187072 CATTTGGCGT
Statistics
Matches: 114, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
154 102 0.89
155 12 0.11
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (154 bp):
CTAATGCTAATCTATTGCGGAGTTTTCACCATAGCGCCGCAAAAGCCACTAAAAATGCATCAAAA
GACGGAGTCATTTTAAAATTGTTTTTTGCGACGTTTTCGTACAAACACCGCTAATGCTAATCTAT
TGTGGTGTTTTTTAACAAACGTCG
Found at i:55187397 original size:21 final size:21
Alignment explanation
Indices: 55187373--55187466 Score: 53
Period size: 21 Copynumber: 4.1 Consensus size: 21
55187363 TAAACCCAAT
55187373 ACCCGATACCCTAAACCTTAA
1 ACCCGATACCCTAAACCTTAA
* * *
55187394 ACCCAATACCGAATACCTTAAAACCTAA
1 A--C----CCG-ATACCCTAAACCTTAA
* ** *
55187422 ACCCTATAAACTAAACCATAA
1 ACCCGATACCCTAAACCTTAA
*
55187443 ACCCAATACCCTAAACCTTAA
1 ACCCGATACCCTAAACCTTAA
55187464 ACC
1 ACC
55187467 TAAATTCTAA
Statistics
Matches: 53, Mismatches: 13, Indels: 14
0.66 0.16 0.17
Matches are distributed among these distances:
21 32 0.60
22 2 0.04
23 1 0.02
26 1 0.02
27 3 0.06
28 14 0.26
ACGTcount: A:0.45, C:0.35, G:0.02, T:0.18
Consensus pattern (21 bp):
ACCCGATACCCTAAACCTTAA
Found at i:55187403 original size:28 final size:28
Alignment explanation
Indices: 55187363--55187425 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 28
55187353 AATTAATTTG
55187363 TAAACCCAATACCCG-ATACCCT-AAACC
1 TAAACCCAATA-CCGAATACCCTAAAACC
*
55187390 TTAAACCCAATACCGAATACCTTAAAACC
1 -TAAACCCAATACCGAATACCCTAAAACC
55187419 TAAACCC
1 TAAACCC
55187426 TATAAACTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 3 0.09
28 24 0.75
29 5 0.16
ACGTcount: A:0.43, C:0.37, G:0.03, T:0.17
Consensus pattern (28 bp):
TAAACCCAATACCGAATACCCTAAAACC
Found at i:55187490 original size:14 final size:14
Alignment explanation
Indices: 55187408--55187490 Score: 57
Period size: 14 Copynumber: 6.0 Consensus size: 14
55187398 AATACCGAAT
*
55187408 ACCTTAAAACCTAA
1 ACCTTAAACCCTAA
55187422 ACCCTATAAA--CTAA
1 A-CCT-TAAACCCTAA
*
55187436 ACCATAAACCC-AA
1 ACCTTAAACCCTAA
* *
55187449 TACCCTAAACCTTAA
1 -ACCTTAAACCCTAA
**
55187464 ACC-TAAATTCTAA
1 ACCTTAAACCCTAA
55187477 ACCTTAAACCCTAA
1 ACCTTAAACCCTAA
55187491 TTTCATGCAC
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
12 4 0.07
13 14 0.26
14 27 0.50
15 5 0.09
16 4 0.07
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.22
Consensus pattern (14 bp):
ACCTTAAACCCTAA
Found at i:55187977 original size:21 final size:22
Alignment explanation
Indices: 55187953--55187993 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
55187943 GTTTTTAGAA
*
55187953 TTTAGGGTTTA-GGGTTTAATG
1 TTTAAGGTTTAGGGGTTTAATG
55187974 TTTAAGGTTTAGGGGTTTAA
1 TTTAAGGTTTAGGGGTTTAA
55187994 AGAAACCCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.22, C:0.00, G:0.32, T:0.46
Consensus pattern (22 bp):
TTTAAGGTTTAGGGGTTTAATG
Found at i:55188332 original size:41 final size:40
Alignment explanation
Indices: 55188287--55188376 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 40
55188277 ATAGATCAAC
* *
55188287 TTTTT-GCGGCGTTTGTAACAAAAAACGCCGCTATTGCTTAG
1 TTTTTAGCGGCGTTTG-AAC-AAAAACGCCGCCATTGCTCAG
* * * *
55188328 TTTTTAGTGGTGTTTGGACAAAAACGCCGCCATTTCTCAG
1 TTTTTAGCGGCGTTTGAACAAAAACGCCGCCATTGCTCAG
55188368 TTTTTAGCG
1 TTTTTAGCG
55188377 CTATTGCTCA
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
40 26 0.63
41 7 0.17
42 8 0.20
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTGAACAAAAACGCCGCCATTGCTCAG
Found at i:55188392 original size:60 final size:61
Alignment explanation
Indices: 55188315--55188435 Score: 154
Period size: 61 Copynumber: 2.0 Consensus size: 61
55188305 CAAAAAACGC
* * * * * *
55188315 CGCTATTGCTTAGTTTTTAGTGGTG-TTTGGACAAAAACGCCGCCATTTCTCAGTTTTTAG
1 CGCTATTGCTCAATTTTTAGTGGCGTTTTGAACAAAAACACCGCCATTGCTCAGTTTTTAG
* * *
55188375 CGCTATTGCTCAATTTTTAGTGGCGTTTTGAACAAAAATACCTCTATTGCTCAGTTTTTAG
1 CGCTATTGCTCAATTTTTAGTGGCGTTTTGAACAAAAACACCGCCATTGCTCAGTTTTTAG
55188436 TGGTGTTTTG
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
60 22 0.43
61 29 0.57
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.40
Consensus pattern (61 bp):
CGCTATTGCTCAATTTTTAGTGGCGTTTTGAACAAAAACACCGCCATTGCTCAGTTTTTAG
Found at i:55188434 original size:41 final size:42
Alignment explanation
Indices: 55188377--55188485 Score: 150
Period size: 41 Copynumber: 2.6 Consensus size: 42
55188367 GTTTTTAGCG
* *
55188377 CTATTGCTCAATTTTTAGTGGCGTTTTGAACAAAAATACC-T
1 CTATTGCTCAGTTTTTAGTGGCGTTTTGAACAAAAACACCGT
*
55188418 CTATTGCTCAGTTTTTAGTGGTGTTTTGAACAAAAACACCGT
1 CTATTGCTCAGTTTTTAGTGGCGTTTTGAACAAAAACACCGT
* * *
55188460 -TATTGCTTAGTTTTTTGCGGCGTTTT
1 CTATTGCTCAGTTTTTAGTGGCGTTTT
55188486 ATTGCAAACG
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
41 59 0.98
42 1 0.02
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (42 bp):
CTATTGCTCAGTTTTTAGTGGCGTTTTGAACAAAAACACCGT
Found at i:55201971 original size:27 final size:27
Alignment explanation
Indices: 55201936--55201990 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
55201926 GTTCATATTT
55201936 CGTCACTGAAATTCGGCCTTGCTTTAG
1 CGTCACTGAAATTCGGCCTTGCTTTAG
* * *
55201963 CGTCCCTGAAATTTGGCGTTGCTTTAG
1 CGTCACTGAAATTCGGCCTTGCTTTAG
55201990 C
1 C
55201991 TCTAGGAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (27 bp):
CGTCACTGAAATTCGGCCTTGCTTTAG
Found at i:55204252 original size:94 final size:94
Alignment explanation
Indices: 55204132--55204304 Score: 258
Period size: 94 Copynumber: 1.8 Consensus size: 94
55204122 ATCTCAAGTC
* *
55204132 GATGCCATGTCTCAGACATGGTCTTACACTGACTATCAT-ATCGTAGCCAATGTATGTCCCAGAC
1 GATGCCATGTCCCAGACATGGTCTTACACTGACTATCATAAT-GTAGCCAATGCATGTCCCAGAC
55204196 ATGTCTTACACTAGCTCTCGTCTCAATGCT
65 ATGTCTTACACTAGCTCTCGTCTCAATGCT
* * * * *
55204226 GATGCCATGTCCCAGACATGGTCTTACATTGGCTCTCATAATGTGGCCGATGCATGTCCCAGACA
1 GATGCCATGTCCCAGACATGGTCTTACACTGACTATCATAATGTAGCCAATGCATGTCCCAGACA
*
55204291 TGTTTTACACTAGC
66 TGTCTTACACTAGC
55204305 CAACAATAAC
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
94 68 0.97
95 2 0.03
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (94 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGACTATCATAATGTAGCCAATGCATGTCCCAGACA
TGTCTTACACTAGCTCTCGTCTCAATGCT
Found at i:55204282 original size:47 final size:47
Alignment explanation
Indices: 55204080--55204301 Score: 167
Period size: 47 Copynumber: 4.7 Consensus size: 47
55204070 CGTGGGTAAG
* *
55204080 GTGCCGATGCCATGTCCTAGACATGGTCTTACACTGACT-T-AT-AT
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT
* * * * *
55204124 CTCAAGTCGATGCCATGTCTCAGACATGGTCTTACACTGACTATCAT-AT
1 GT---GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT
* * * *
55204173 CGTAGCCAATG-TATGTCCCAGACAT-GTCTTACACTAGCTCTCGTCTCAA-
1 -GT-GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTC--AT-AAT
* *
55204222 -TGCTGATGCCATGTCCCAGACATGGTCTTACATTGGCTCTCATAAT
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT
*
55204268 GTGGCCGATG-CATGTCCCAGACAT-GTTTTACACT
1 GT-GCCGATGCCATGTCCCAGACATGGTCTTACACT
55204302 AGCCAACAAT
Statistics
Matches: 141, Mismatches: 22, Indels: 28
0.74 0.12 0.15
Matches are distributed among these distances:
44 1 0.01
45 2 0.01
46 28 0.20
47 75 0.53
48 29 0.21
49 4 0.03
50 2 0.01
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (47 bp):
GTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT
Found at i:55206983 original size:41 final size:40
Alignment explanation
Indices: 55206938--55207014 Score: 118
Period size: 41 Copynumber: 1.9 Consensus size: 40
55206928 ACACACCGAT
*
55206938 ACGAAGCCTGCTAGGCACCAAGCCTGATATAATACACTGGC
1 ACGAAGCCTGCTAGGCACAAAGCCT-ATATAATACACTGGC
* *
55206979 ACGAAGCTTGCTAGGCATAAAGCCTATATAATACAC
1 ACGAAGCCTGCTAGGCACAAAGCCTATATAATACAC
55207015 CACAACATCA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 11 0.33
41 22 0.67
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (40 bp):
ACGAAGCCTGCTAGGCACAAAGCCTATATAATACACTGGC
Found at i:55207435 original size:45 final size:45
Alignment explanation
Indices: 55207386--55207489 Score: 100
Period size: 45 Copynumber: 2.3 Consensus size: 45
55207376 TCATCTCTTG
* ** * *
55207386 TCTTACTCGTTTTTGGTATGGTGCCATAGTGTCTTTCAACTTTTT
1 TCTTACTCATTTCCGGTATAGTGCCATAGAGTCTTTCAACTTTTT
* * * * **
55207431 TCTTATTTATTTCCGGTATATTGCCATAGAGTCTTTCAACTATGG
1 TCTTACTCATTTCCGGTATAGTGCCATAGAGTCTTTCAACTTTTT
*
55207476 TCTTAATCATTTCC
1 TCTTACTCATTTCC
55207490 TTCAAGCCAA
Statistics
Matches: 46, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.18, C:0.19, G:0.14, T:0.48
Consensus pattern (45 bp):
TCTTACTCATTTCCGGTATAGTGCCATAGAGTCTTTCAACTTTTT
Found at i:55208102 original size:13 final size:13
Alignment explanation
Indices: 55208084--55208110 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
55208074 TCTAGATTAG
55208084 CTAGATTAAGCTA
1 CTAGATTAAGCTA
55208097 CTAGATTAAGCTA
1 CTAGATTAAGCTA
55208110 C
1 C
55208111 AATGATCACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.30
Consensus pattern (13 bp):
CTAGATTAAGCTA
Found at i:55214706 original size:43 final size:42
Alignment explanation
Indices: 55214636--55214771 Score: 148
Period size: 43 Copynumber: 3.2 Consensus size: 42
55214626 TAAGACCGCG
* *
55214636 TCTGGGACATTGGCATTGTATTGTGATTATGTGTAAGACCATG
1 TCTGGGACATTGGCATCGTA-TGTGATTATGTGTAAGACCATA
* *
55214679 TCTGGGACATTGGCATCGTTATATGATT-TCGTGTAAGACCCTA
1 TCTGGGACATTGGCATCG-TATGTGATTAT-GTGTAAGACCATA
* * * **
55214722 TCTGGGGCAATGGCATCGATATGTGATAACATGTAAGACCATA
1 TCTGGGACATTGGCATCG-TATGTGATTATGTGTAAGACCATA
55214765 TCTGGGA
1 TCTGGGA
55214772 TGTGGCATTG
Statistics
Matches: 77, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
42 1 0.01
43 74 0.96
44 2 0.03
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.32
Consensus pattern (42 bp):
TCTGGGACATTGGCATCGTATGTGATTATGTGTAAGACCATA
Found at i:55225442 original size:21 final size:21
Alignment explanation
Indices: 55225416--55225521 Score: 65
Period size: 21 Copynumber: 5.1 Consensus size: 21
55225406 GTGCCTCTGT
*
55225416 TTGTACTTCGGTACCCTTGAA
1 TTGTACTTCGGTACCCCTGAA
* * *
55225437 TTGTACATAC-GTCCCCCT-AT
1 TTGTAC-TTCGGTACCCCTGAA
* * *
55225457 TTGTACGTCGGTACACTTGAA
1 TTGTACTTCGGTACCCCTGAA
* * ** * *
55225478 TTGCACATATGTTCCCCT-AT
1 TTGTACTTCGGTACCCCTGAA
55225498 TTGTACTTCGGTACCCCTGAA
1 TTGTACTTCGGTACCCCTGAA
55225519 TTG
1 TTG
55225522 CACATACGTG
Statistics
Matches: 57, Mismatches: 24, Indels: 8
0.64 0.27 0.09
Matches are distributed among these distances:
19 1 0.02
20 26 0.46
21 28 0.49
22 2 0.04
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.37
Consensus pattern (21 bp):
TTGTACTTCGGTACCCCTGAA
Found at i:55225633 original size:41 final size:41
Alignment explanation
Indices: 55225387--55225618 Score: 313
Period size: 41 Copynumber: 5.7 Consensus size: 41
55225377 TAATTAATTA
* *
55225387 TACCC-TGAATTGCACATACGTGCCTCTGTTTGTACTTCGG
1 TACCCTTGAATTGCACATACGTGCCCCTATTTGTACTTCGG
* * *
55225427 TACCCTTGAATTGTACATACGTCCCCCTATTTGTACGTCGG
1 TACCCTTGAATTGCACATACGTGCCCCTATTTGTACTTCGG
* * *
55225468 TACACTTGAATTGCACATATGTTCCCCTATTTGTACTTCGG
1 TACCCTTGAATTGCACATACGTGCCCCTATTTGTACTTCGG
* *
55225509 TACCCCTGAATTGCACATACGTGCCCCTATTTTTACTTCGG
1 TACCCTTGAATTGCACATACGTGCCCCTATTTGTACTTCGG
* * * *
55225550 TACCCTTAAATAGCACATCCGTGCCCCTATTTGTACTTTGG
1 TACCCTTGAATTGCACATACGTGCCCCTATTTGTACTTCGG
* *
55225591 TACCCTTAAATAGCACATACGTGCCCCT
1 TACCCTTGAATTGCACATACGTGCCCCT
55225619 GTTTATATTC
Statistics
Matches: 169, Mismatches: 22, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
40 5 0.03
41 164 0.97
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.34
Consensus pattern (41 bp):
TACCCTTGAATTGCACATACGTGCCCCTATTTGTACTTCGG
Found at i:55236765 original size:39 final size:39
Alignment explanation
Indices: 55236704--55236847 Score: 200
Period size: 39 Copynumber: 3.7 Consensus size: 39
55236694 ACCAGCTCGA
* * * * *
55236704 AGCCTGCGAGA-CTTTAGCCCGGACATATTTCCAGCACGT
1 AGCCTGCG-GACCTTAAGTCCGGATATAATTCCAGCACAT
*
55236743 AGCCTGTGGACCTTAAGTCCGGATATAATTCCAGCACAT
1 AGCCTGCGGACCTTAAGTCCGGATATAATTCCAGCACAT
* *
55236782 AGCCTGCGGACCCTAAGTCCGGATATAATTCTAGCACAT
1 AGCCTGCGGACCTTAAGTCCGGATATAATTCCAGCACAT
55236821 AGCCTGCGGACCTTAAGTCCGGATATA
1 AGCCTGCGGACCTTAAGTCCGGATATA
55236848 CATCACTGAA
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
38 2 0.02
39 92 0.98
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (39 bp):
AGCCTGCGGACCTTAAGTCCGGATATAATTCCAGCACAT
Found at i:55244550 original size:17 final size:17
Alignment explanation
Indices: 55244528--55244561 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
55244518 GAAAATAACA
55244528 AAGGAAA-TAACAAAAAT
1 AAGGAAATTAA-AAAAAT
55244545 AAGGAAATTAAAAAAAT
1 AAGGAAATTAAAAAAAT
55244562 GATAAAGGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.71, C:0.03, G:0.12, T:0.15
Consensus pattern (17 bp):
AAGGAAATTAAAAAAAT
Found at i:55250408 original size:31 final size:31
Alignment explanation
Indices: 55250368--55250429 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
55250358 TGGTCATGGT
55250368 GGTTCGAGGAGTTTATACTCCTCATTCCTGC
1 GGTTCGAGGAGTTTATACTCCTCATTCCTGC
* *
55250399 GGTTTGAGGAGTTTATACTCCTTATTCCTGC
1 GGTTCGAGGAGTTTATACTCCTCATTCCTGC
55250430 TATCAATCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.39
Consensus pattern (31 bp):
GGTTCGAGGAGTTTATACTCCTCATTCCTGC
Found at i:55256140 original size:16 final size:16
Alignment explanation
Indices: 55256108--55256149 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
55256098 TGCTACTGTC
55256108 CAAAATTGTC-TTATTA
1 CAAAATT-TCATTATTA
*
55256124 CAAAATTTCATTTTTA
1 CAAAATTTCATTATTA
*
55256140 CATAATTTCA
1 CAAAATTTCA
55256150 CTTACTCTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 2 0.09
16 21 0.91
ACGTcount: A:0.38, C:0.14, G:0.02, T:0.45
Consensus pattern (16 bp):
CAAAATTTCATTATTA
Found at i:55256426 original size:50 final size:49
Alignment explanation
Indices: 55256363--55256540 Score: 171
Period size: 50 Copynumber: 3.6 Consensus size: 49
55256353 TGGTAAGCAC
*
55256363 AGTAGCCTACACTTAGTACTACACATGCGACCTACCAATCTGGTACATGT
1 AGTAGCCTACACTTAGTACTACACATGCGACCTA-CAATCTGGTACACGT
* * * * * * *
55256413 AGTAGCCTGCACTTAGTACTACACACGTGA--TAGAAGTTAACGGGTACGCAT
1 AGTAGCCTACACTTAGTACTACACATGCGACCTACAA--T--CTGGTACACGT
* * *
55256464 AGTAGCCTGCACTTAGTACTACACATACGACCTATCAATTTGGTACACGT
1 AGTAGCCTACACTTAGTACTACACATGCGACCTA-CAATCTGGTACACGT
**
55256514 AGTAGTTTACACTTAGTACTACACATG
1 AGTAGCCTACACTTAGTACTACACATG
55256541 TGACTCACAA
Statistics
Matches: 101, Mismatches: 20, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
47 2 0.02
48 2 0.02
49 1 0.01
50 57 0.56
51 34 0.34
52 1 0.01
53 2 0.02
54 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (49 bp):
AGTAGCCTACACTTAGTACTACACATGCGACCTACAATCTGGTACACGT
Found at i:55256538 original size:101 final size:101
Alignment explanation
Indices: 55256354--55256543 Score: 281
Period size: 101 Copynumber: 1.9 Consensus size: 101
55256344 AAAGCTCTCT
* *
55256354 GGTAAGCACAGTAGCCTACACTTAGTACTACACATGCGACCTACCAATCTGGTACATGTAGTAGC
1 GGTAAGCACAGTAGCCTACACTTAGTACTACACATACGACCTACCAATCTGGTACACGTAGTAGC
*
55256419 CTGCACTTAGTACTACACACGTGATAGAAGTTAACG
66 CTACACTTAGTACTACACACGTGATAGAAGTTAACG
* * * * * *
55256455 GGTACGCATAGTAGCCTGCACTTAGTACTACACATACGACCTATCAATTTGGTACACGTAGTAGT
1 GGTAAGCACAGTAGCCTACACTTAGTACTACACATACGACCTACCAATCTGGTACACGTAGTAGC
* *
55256520 TTACACTTAGTACTACACATGTGA
66 CTACACTTAGTACTACACACGTGA
55256544 CTCACAACGA
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
101 78 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (101 bp):
GGTAAGCACAGTAGCCTACACTTAGTACTACACATACGACCTACCAATCTGGTACACGTAGTAGC
CTACACTTAGTACTACACACGTGATAGAAGTTAACG
Found at i:55264048 original size:21 final size:21
Alignment explanation
Indices: 55264009--55264048 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
55263999 GTAATTTTGT
* * *
55264009 TTAGAACATTAATTGAATGTA
1 TTAGAACATGAAATAAATGTA
55264030 TTAGAACATGAAATAAATG
1 TTAGAACATGAAATAAATG
55264049 AAAACAACGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.05, G:0.15, T:0.33
Consensus pattern (21 bp):
TTAGAACATGAAATAAATGTA
Found at i:55265911 original size:10 final size:10
Alignment explanation
Indices: 55265892--55266043 Score: 51
Period size: 10 Copynumber: 16.1 Consensus size: 10
55265882 TTATAACCAA
55265892 AATATATAAT
1 AATATATAAT
*
55265902 -A-ATAT-GT
1 AATATATAAT
*
55265909 AATATGTAAT
1 AATATATAAT
*
55265919 AAAATATAAT
1 AATATATAAT
55265929 GAA-ATATGAAT
1 -AATATAT-AAT
*
55265940 ACTATA-AAT
1 AATATATAAT
**
55265949 AA-GGATAAT
1 AATATATAAT
*
55265958 AATACATAAT
1 AATATATAAT
*
55265968 AA-A-AAAAT
1 AATATATAAT
55265976 AATAT-T-AT
1 AATATATAAT
55265984 -ATATATAAT
1 AATATATAAT
*
55265993 AAAATATAAT
1 AATATATAAT
* *
55266003 AACATGTAAT
1 AATATATAAT
*
55266013 -TTATA-AAT
1 AATATATAAT
* *
55266021 AAATAATAAAAA
1 -AAT-ATATAAT
55266033 AATATATAAT
1 AATATATAAT
55266043 A
1 A
55266044 TAATGAATGT
Statistics
Matches: 102, Mismatches: 23, Indels: 34
0.64 0.14 0.21
Matches are distributed among these distances:
7 5 0.05
8 18 0.18
9 19 0.19
10 44 0.43
11 14 0.14
12 2 0.02
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.33
Consensus pattern (10 bp):
AATATATAAT
Found at i:55265977 original size:21 final size:24
Alignment explanation
Indices: 55265953--55266004 Score: 65
Period size: 21 Copynumber: 2.3 Consensus size: 24
55265943 ATAAATAAGG
55265953 ATAATAATACATA-ATAA-AAAA-
1 ATAATAATACATATATAATAAAAT
* *
55265974 ATAATATTATATATATAATAAAAT
1 ATAATAATACATATATAATAAAAT
55265998 ATAATAA
1 ATAATAA
55266005 CATGTAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 11 0.44
22 4 0.16
23 4 0.16
24 6 0.24
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (24 bp):
ATAATAATACATATATAATAAAAT
Found at i:55266105 original size:21 final size:20
Alignment explanation
Indices: 55266077--55266134 Score: 55
Period size: 21 Copynumber: 2.9 Consensus size: 20
55266067 TATTTTATAC
* *
55266077 AATTAATATTTTTTAAAAAA
1 AATTAATAATATTTAAAAAA
*
55266097 AATTGAATAATATTTAAAATA
1 AATT-AATAATATTTAAAAAA
* *
55266118 AACTAA-AATATATAAAA
1 AATTAATAATATTTAAAA
55266135 GGATTAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
19 10 0.31
20 6 0.19
21 16 0.50
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (20 bp):
AATTAATAATATTTAAAAAA
Found at i:55267945 original size:87 final size:87
Alignment explanation
Indices: 55267814--55268380 Score: 1062
Period size: 87 Copynumber: 6.5 Consensus size: 87
55267804 AGTCAGATCT
* * * *
55267814 GCTATGTTTTCGATTTGCTCCCCGCCAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACG
1 GCTATGTCTTCGATCTGCTCCCTGCCAATACAGAGACGCCAAATCATCTTAGATTTGCTTCAACG
55267879 TAAACACGTGAAAGCTAAATCA
66 TAAACACGTGAAAGCTAAATCA
55267901 GCTATGTCTTCGATCTGCTCCCTGCCAATACAGAGACGCCAAATCATCTTAGATTTGCTTCAACG
1 GCTATGTCTTCGATCTGCTCCCTGCCAATACAGAGACGCCAAATCATCTTAGATTTGCTTCAACG
55267966 TAAACACGTGAAAGCTAAATCA
66 TAAACACGTGAAAGCTAAATCA
55267988 GCTATGTCTTCGATCTGCTCCCTGCCAATACAGAGACGCCAAATCATCTTAGATTTGCTTCAACG
1 GCTATGTCTTCGATCTGCTCCCTGCCAATACAGAGACGCCAAATCATCTTAGATTTGCTTCAACG
55268053 TAAACACGTGAAAGCTAAATCA
66 TAAACACGTGAAAGCTAAATCA
55268075 GCTATGTCTTCGATCTGCTCCCTGCCAATACAGAGACGCCAAATCATCTTAGATTTGCTTCAACG
1 GCTATGTCTTCGATCTGCTCCCTGCCAATACAGAGACGCCAAATCATCTTAGATTTGCTTCAACG
55268140 TAAACACGTGAAAGCTAAATCA
66 TAAACACGTGAAAGCTAAATCA
55268162 GCTATGTCTTCGATCTGCTCCCTGCCAATACAGAGACGCCAAATCATCTTAGATTTGCTTCAACG
1 GCTATGTCTTCGATCTGCTCCCTGCCAATACAGAGACGCCAAATCATCTTAGATTTGCTTCAACG
55268227 TAAACACGTGAAAGCTAAATCA
66 TAAACACGTGAAAGCTAAATCA
55268249 GCTATGTCTTCGATCTGCTCCCTGCCAATACAGAGACGCCAAATCATCTTAGATTTGCTTCAACG
1 GCTATGTCTTCGATCTGCTCCCTGCCAATACAGAGACGCCAAATCATCTTAGATTTGCTTCAACG
*
55268314 TAAACACGTGAAAGCCAAATCA
66 TAAACACGTGAAAGCTAAATCA
* * *
55268336 GCTATGTCTTCGATTTGCTCCCTGCCAGTACAGAGATGCCAAATC
1 GCTATGTCTTCGATCTGCTCCCTGCCAATACAGAGACGCCAAATC
55268381 TGTTATCTTC
Statistics
Matches: 472, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
87 472 1.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (87 bp):
GCTATGTCTTCGATCTGCTCCCTGCCAATACAGAGACGCCAAATCATCTTAGATTTGCTTCAACG
TAAACACGTGAAAGCTAAATCA
Found at i:55268393 original size:44 final size:44
Alignment explanation
Indices: 55268327--55268464 Score: 186
Period size: 44 Copynumber: 3.1 Consensus size: 44
55268317 ACACGTGAAA
* * *
55268327 GCCAAATCAGCTATGTCTTCGATTTGCTCCCTGCCAGTACAGAGAT
1 GCCAAATCTGCTA--TCTTCGATTTGCTCTCTGCCAATACAGAGAT
* *
55268373 GCCAAATCTGTTATCTTCGATCTGCTCTCTGCCAATACAGAGAT
1 GCCAAATCTGCTATCTTCGATTTGCTCTCTGCCAATACAGAGAT
* * *
55268417 GCCAAATCTGCTATCTTCGATTTGTTCTCTGACAATACAAAGAT
1 GCCAAATCTGCTATCTTCGATTTGCTCTCTGCCAATACAGAGAT
55268461 GCCA
1 GCCA
55268465 GATCATCTTG
Statistics
Matches: 82, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
44 71 0.87
46 11 0.13
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.30
Consensus pattern (44 bp):
GCCAAATCTGCTATCTTCGATTTGCTCTCTGCCAATACAGAGAT
Found at i:55270504 original size:43 final size:41
Alignment explanation
Indices: 55270443--55270532 Score: 126
Period size: 43 Copynumber: 2.1 Consensus size: 41
55270433 CTGGCATTAC
*
55270443 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACTAA
1 GCCTGCTAGGCACGAAGGCCCGAATACA-AT-ACCAGCACTAA
* * *
55270486 GCCTGCTAGGCAGGAAGGCCCGAATATAATACCAGCACTAG
1 GCCTGCTAGGCACGAAGGCCCGAATACAATACCAGCACTAA
55270527 GCCTGC
1 GCCTGC
55270533 GGGATTTATC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
41 15 0.35
42 2 0.05
43 26 0.60
ACGTcount: A:0.29, C:0.32, G:0.26, T:0.13
Consensus pattern (41 bp):
GCCTGCTAGGCACGAAGGCCCGAATACAATACCAGCACTAA
Found at i:55270558 original size:38 final size:38
Alignment explanation
Indices: 55270504--55270587 Score: 116
Period size: 38 Copynumber: 2.2 Consensus size: 38
55270494 GGCAGGAAGG
* * *
55270504 CCCGAATATAATACCAGCACT-AGGCCTGCGGGATTTAT
1 CCCGAATATAATACCAGCA-TGAAGCCTGCGAGATTTAA
*
55270542 CCCGGATATAATACCAGCATGAAGCCTGCGAGATTTAA
1 CCCGAATATAATACCAGCATGAAGCCTGCGAGATTTAA
55270580 CCCGAATA
1 CCCGAATA
55270588 CACATCAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
37 1 0.03
38 39 0.98
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.21
Consensus pattern (38 bp):
CCCGAATATAATACCAGCATGAAGCCTGCGAGATTTAA
Found at i:55275741 original size:32 final size:32
Alignment explanation
Indices: 55275703--55275766 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
55275693 AACAAGTATT
*
55275703 GTTTGACCTGTTCAAAAGCATTCCGGCATTCC
1 GTTTGACCTGTTCAAAAGCATTCCGACATTCC
* *
55275735 GTTTGACCTTTTCAAAAGCATTCTGACATTCC
1 GTTTGACCTGTTCAAAAGCATTCCGACATTCC
55275767 TTATCCCAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.23, C:0.27, G:0.16, T:0.34
Consensus pattern (32 bp):
GTTTGACCTGTTCAAAAGCATTCCGACATTCC
Found at i:55280534 original size:15 final size:15
Alignment explanation
Indices: 55280510--55280539 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
55280500 GTTCCATACT
55280510 GATGCATAGCTTCCA
1 GATGCATAGCTTCCA
*
55280525 GATGCGTAGCTTCCA
1 GATGCATAGCTTCCA
55280540 CGTTTTCTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (15 bp):
GATGCATAGCTTCCA
Found at i:55282214 original size:17 final size:19
Alignment explanation
Indices: 55282192--55282234 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
55282182 ATGGAAATAT
55282192 AATCTT-CA-ATGATATGC
1 AATCTTACATATGATATGC
*
55282209 AATCTTAGATATGATATGC
1 AATCTTACATATGATATGC
55282228 AATCTTA
1 AATCTTA
55282235 GAAGATATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.26
18 1 0.04
19 16 0.70
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (19 bp):
AATCTTACATATGATATGC
Found at i:55282245 original size:22 final size:19
Alignment explanation
Indices: 55282200--55282236 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
55282190 ATAATCTTCA
55282200 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
55282219 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
55282237 AGATATGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:55282262 original size:22 final size:22
Alignment explanation
Indices: 55282200--55282245 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 22
55282190 ATAATCTTCA
55282200 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
55282219 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
55282241 ATGAT
1 ATGAT
55282246 TTTGTAATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.62
22 9 0.38
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Done.