Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_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: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 64 of 161
Found at i:19985178 original size:22 final size:21
Alignment explanation
Indices: 19985140--19985180 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
19985130 ATAAATGCTG
*
19985140 TTTTATATTATTATTTTTATA
1 TTTTATATTACTATTTTTATA
*
19985161 TTTTATAATTACTCTTTTTA
1 TTTTAT-ATTACTATTTTTA
19985181 AAAATTGTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTTATATTACTATTTTTATA
Found at i:19987291 original size:17 final size:17
Alignment explanation
Indices: 19987266--19987300 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
19987256 TTGGTTAAAA
* *
19987266 ATTACCCGAATTACCCG
1 ATTAACCGAATTAACCG
19987283 ATTAACCGAATTAACCG
1 ATTAACCGAATTAACCG
19987300 A
1 A
19987301 AAATTACCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.29, G:0.11, T:0.23
Consensus pattern (17 bp):
ATTAACCGAATTAACCG
Found at i:19988604 original size:34 final size:34
Alignment explanation
Indices: 19988555--19988799 Score: 185
Period size: 34 Copynumber: 7.2 Consensus size: 34
19988545 AAATACATGT
* *
19988555 TAAGCAAGTTTATTGCTACTGTATTGATTTATTA
1 TAAGCATGTTAATTGCTACTGTATTGATTTATTA
*
19988589 TAAGCATGTTAATTGCTACTGTATTGACTTGA-TA
1 TAAGCATGTTAATTGCTACTGTATTGA-TTTATTA
* * * ** * *
19988623 TAAACATATTTATTGCTACCATAATGATCTATTA
1 TAAGCATGTTAATTGCTACTGTATTGATTTATTA
* *
19988657 TAAGCATGTTAATTGCTACTGTAGTGACTTGA-TA
1 TAAGCATGTTAATTGCTACTGTATTGA-TTTATTA
* * * * * *
19988691 TAAACATATTTATTGCTACCGTAATGATCTATTA
1 TAAGCATGTTAATTGCTACTGTATTGATTTATTA
* * * * *
19988725 TAAGCATG-AATATTTCTATTGTATCGATTTGTTA
1 TAAGCATGTTA-ATTGCTACTGTATTGATTTATTA
* * *
19988759 TAAGCATGTT-ATTGCTA-TCGTATTAATCTGTTA
1 TAAGCATGTTAATTGCTACT-GTATTGATTTATTA
19988792 TAAGCATG
1 TAAGCATG
19988800 ACATGTTGCA
Statistics
Matches: 162, Mismatches: 42, Indels: 15
0.74 0.19 0.07
Matches are distributed among these distances:
32 1 0.01
33 29 0.18
34 127 0.78
35 5 0.03
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.42
Consensus pattern (34 bp):
TAAGCATGTTAATTGCTACTGTATTGATTTATTA
Found at i:19988656 original size:68 final size:68
Alignment explanation
Indices: 19988563--19988732 Score: 295
Period size: 68 Copynumber: 2.5 Consensus size: 68
19988553 GTTAAGCAAG
* * * *
19988563 TTTATTGCTACTGTATTGATTTATTATAAGCATGTTAATTGCTACTGTATTGACTTGATATAAAC
1 TTTATTGCTACCGTAATGATCTATTATAAGCATGTTAATTGCTACTGTAGTGACTTGATATAAAC
19988628 ATA
66 ATA
*
19988631 TTTATTGCTACCATAATGATCTATTATAAGCATGTTAATTGCTACTGTAGTGACTTGATATAAAC
1 TTTATTGCTACCGTAATGATCTATTATAAGCATGTTAATTGCTACTGTAGTGACTTGATATAAAC
19988696 ATA
66 ATA
19988699 TTTATTGCTACCGTAATGATCTATTATAAGCATG
1 TTTATTGCTACCGTAATGATCTATTATAAGCATG
19988733 AATATTTCTA
Statistics
Matches: 96, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 96 1.00
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (68 bp):
TTTATTGCTACCGTAATGATCTATTATAAGCATGTTAATTGCTACTGTAGTGACTTGATATAAAC
ATA
Found at i:19988761 original size:68 final size:67
Alignment explanation
Indices: 19988563--19988799 Score: 289
Period size: 68 Copynumber: 3.5 Consensus size: 67
19988553 GTTAAGCAAG
* * *
19988563 TTTATTGCTACTGTATTGATTTATTATAAGCATGTTAATTGCTACTGTATTGACTTGATATAAAC
1 TTTATTGCTACCGTAATGATCTATTATAAGCATGTTAATTGCTACTGTA-TGACTTGATATAAAC
19988628 ATA
65 ATA
*
19988631 TTTATTGCTACCATAATGATCTATTATAAGCATGTTAATTGCTACTGTAGTGACTTGATATAAAC
1 TTTATTGCTACCGTAATGATCTATTATAAGCATGTTAATTGCTACTGTA-TGACTTGATATAAAC
19988696 ATA
65 ATA
* * * * * *
19988699 TTTATTGCTACCGTAATGATCTATTATAAGCATG-AATATTTCTATTGTATCGATTTGTTATAAG
1 TTTATTGCTACCGTAATGATCTATTATAAGCATGTTA-ATTGCTACTGTAT-GACTTGATATAAA
19988763 CAT-
64 CATA
* * * * *
19988766 GTTATTGCTATCGTATTAATCTGTTATAAGCATG
1 TTTATTGCTACCGTAATGATCTATTATAAGCATG
19988800 ACATGTTGCA
Statistics
Matches: 150, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
67 31 0.21
68 119 0.79
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (67 bp):
TTTATTGCTACCGTAATGATCTATTATAAGCATGTTAATTGCTACTGTATGACTTGATATAAACA
TA
Found at i:19988885 original size:21 final size:22
Alignment explanation
Indices: 19988861--19988915 Score: 76
Period size: 24 Copynumber: 2.5 Consensus size: 22
19988851 GTTTATCAGG
19988861 AACG-ACTAGTGGTTCATCCAC
1 AACGTACTAGTGGTTCATCCAC
*
19988882 AACGTATTTCAGTGGTTCATCCAC
1 AACGTA-CT-AGTGGTTCATCCAC
19988906 AACGTACTAG
1 AACGTACTAG
19988916 CAGCTTGTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 4 0.14
22 3 0.10
23 2 0.07
24 20 0.69
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.27
Consensus pattern (22 bp):
AACGTACTAGTGGTTCATCCAC
Found at i:19989753 original size:13 final size:14
Alignment explanation
Indices: 19989729--19989762 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
19989719 TCCTCAGAAA
19989729 TTAAAGCAATTG-TT
1 TTAAA-CAATTGTTT
19989743 TTAAACAATTGTTT
1 TTAAACAATTGTTT
19989757 TTAAAC
1 TTAAAC
19989763 TCCGATAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (14 bp):
TTAAACAATTGTTT
Found at i:19990133 original size:3 final size:3
Alignment explanation
Indices: 19990125--19990173 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
19990115 TTAACGTGAC
* *
19990125 ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
19990173 A
1 A
19990174 AAGATACAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:19992135 original size:16 final size:18
Alignment explanation
Indices: 19992112--19992151 Score: 66
Period size: 16 Copynumber: 2.3 Consensus size: 18
19992102 ATTAAGAATT
19992112 TATTTAAATTTT-ATATA
1 TATTTAAATTTTAATATA
19992129 T-TTTAAATTTTAATATA
1 TATTTAAATTTTAATATA
19992146 TATTTA
1 TATTTA
19992152 GGGATAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 10 0.48
17 7 0.33
18 4 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TATTTAAATTTTAATATA
Found at i:19992465 original size:7 final size:7
Alignment explanation
Indices: 19992455--19992486 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
19992445 TCTTAATTAT
19992455 TAAATCC
1 TAAATCC
19992462 TAAATCC
1 TAAATCC
19992469 TAAATCC
1 TAAATCC
*
19992476 TAAACCC
1 TAAATCC
19992483 TAAA
1 TAAA
19992487 ATTAAATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (7 bp):
TAAATCC
Found at i:19992849 original size:54 final size:54
Alignment explanation
Indices: 19992767--19992874 Score: 198
Period size: 54 Copynumber: 2.0 Consensus size: 54
19992757 TAACTTGCAG
*
19992767 CAGCTTCCAACCTGTCTGTACTCCGTACCACCTCCTAATGGACTTACCAATCTT
1 CAGCTTCCAACCTGTCTGCACTCCGTACCACCTCCTAATGGACTTACCAATCTT
*
19992821 CAGCTTCTAACCTGTCTGCACTCCGTACCACCTCCTAATGGACTTACCAATCTT
1 CAGCTTCCAACCTGTCTGCACTCCGTACCACCTCCTAATGGACTTACCAATCTT
19992875 TCTGTGCAAG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.22, C:0.37, G:0.11, T:0.30
Consensus pattern (54 bp):
CAGCTTCCAACCTGTCTGCACTCCGTACCACCTCCTAATGGACTTACCAATCTT
Found at i:20008316 original size:16 final size:16
Alignment explanation
Indices: 20008297--20008327 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20008287 ATTTTAAAAA
*
20008297 ATATAGCTTGGTTCAT
1 ATATAGCTCGGTTCAT
20008313 ATATAGCTCGGTTCA
1 ATATAGCTCGGTTCA
20008328 ACCGGTCCGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (16 bp):
ATATAGCTCGGTTCAT
Found at i:20022375 original size:13 final size:13
Alignment explanation
Indices: 20022357--20022381 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20022347 GGTTTTACCA
20022357 TCTTTTCTTTTTT
1 TCTTTTCTTTTTT
20022370 TCTTTTCTTTTT
1 TCTTTTCTTTTT
20022382 CTTTTTGCCA
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TCTTTTCTTTTTT
Found at i:20030893 original size:15 final size:15
Alignment explanation
Indices: 20030873--20030902 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20030863 GTAAATTTCG
*
20030873 GGTTTTAGGATTAAA
1 GGTTTTAGGACTAAA
20030888 GGTTTTAGGACTAAA
1 GGTTTTAGGACTAAA
20030903 TTAAATAAAG
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:0.33, C:0.03, G:0.27, T:0.37
Consensus pattern (15 bp):
GGTTTTAGGACTAAA
Found at i:20034670 original size:42 final size:42
Alignment explanation
Indices: 20034585--20034703 Score: 98
Period size: 42 Copynumber: 2.8 Consensus size: 42
20034575 TCATATTAGT
* * * * *
20034585 TTCCGTTCAACCATAATGGGTTTCCATTCAGCTCTATTA--AGC
1 TTCCATTCAACCCTTATGAGTTTCCGTTCAGCTC--TTACGAGC
* * *
20034627 TTCTATTTAACCCTTCTGAGTTTCCGTTCAGCTCTTACGAGC
1 TTCCATTCAACCCTTATGAGTTTCCGTTCAGCTCTTACGAGC
* * * *
20034669 TTCCGTTCAACCCTTATGGGTTTCTGTTTAGCTCT
1 TTCCATTCAACCCTTATGAGTTTCCGTTCAGCTCT
20034704 CATGAATTTC
Statistics
Matches: 60, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
40 3 0.05
42 57 0.95
ACGTcount: A:0.18, C:0.27, G:0.15, T:0.40
Consensus pattern (42 bp):
TTCCATTCAACCCTTATGAGTTTCCGTTCAGCTCTTACGAGC
Found at i:20034684 original size:21 final size:22
Alignment explanation
Indices: 20034635--20034684 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
20034625 GCTTCTATTT
*
20034635 AACCCTT-CTGAGTTTCCGTTC
1 AACCCTTACTGAGCTTCCGTTC
* *
20034656 AGCTCTTAC-GAGCTTCCGTTC
1 AACCCTTACTGAGCTTCCGTTC
20034677 AACCCTTA
1 AACCCTTA
20034685 TGGGTTTCTG
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.18, C:0.34, G:0.14, T:0.34
Consensus pattern (22 bp):
AACCCTTACTGAGCTTCCGTTC
Found at i:20035106 original size:238 final size:238
Alignment explanation
Indices: 20034684--20035160 Score: 882
Period size: 238 Copynumber: 2.0 Consensus size: 238
20034674 TTCAACCCTT
*
20034684 ATGGGTTTCTGTTTAGCTCTCATGAATTTCTGTTCAACCTTCAGGCTTCTGAAAAAGATGTACTC
1 ATGGGTTTCTGTTTAGCTCTCATGAACTTCTGTTCAACCTTCAGGCTTCTGAAAAAGATGTACTC
* * *
20034749 ATATCCGTAAGTCGTTCTTCTAATGGTAAGTTATAAGGAGTTGTCTTGGATGATATATGTATATG
66 ATATCCGTAAGTCGCTCTTCGAATGGTAAGTTATAAGGAGTTGTCTTGGATGATATATGCATATG
*
20034814 AAGAAACAGTAAAAGAATGATATGTATCATGAAATGTATATATATATTTCAATATCTTGATATGT
131 AAGAAACAGTAAAAGAATGATATGTATCATGAAATGTATATATATATATCAATATCTTGATATGT
*
20034879 TGATTCATGGAAATTATGTAAGTTGAAATGAGTAATAAATTCA
196 TGATTCATGGAAATTATGTAAGTTGAAACGAGTAATAAATTCA
*
20034922 ATGGGTTTCTGTTTAGCTCTCATGAGCTTCTGTTCAACCTTCAGGCTTCTGAAAAAGATGTACTC
1 ATGGGTTTCTGTTTAGCTCTCATGAACTTCTGTTCAACCTTCAGGCTTCTGAAAAAGATGTACTC
20034987 ATATCCGTAAGTCGCTCTTCGAATGGTAAGTTATAAGGAGTTGTCTTGGATGATATATGCATATG
66 ATATCCGTAAGTCGCTCTTCGAATGGTAAGTTATAAGGAGTTGTCTTGGATGATATATGCATATG
*
20035052 AAGACACAGTAAAAGAATGATATGTATCATGAAATGTATATATATATATCAATATCTTGATATGT
131 AAGAAACAGTAAAAGAATGATATGTATCATGAAATGTATATATATATATCAATATCTTGATATGT
20035117 TGATTCATGGAAATTATGTAAGTTGAAACGAGTAATAAATTCA
196 TGATTCATGGAAATTATGTAAGTTGAAACGAGTAATAAATTCA
20035160 A
1 A
20035161 GTGTGACATG
Statistics
Matches: 231, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
238 231 1.00
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.36
Consensus pattern (238 bp):
ATGGGTTTCTGTTTAGCTCTCATGAACTTCTGTTCAACCTTCAGGCTTCTGAAAAAGATGTACTC
ATATCCGTAAGTCGCTCTTCGAATGGTAAGTTATAAGGAGTTGTCTTGGATGATATATGCATATG
AAGAAACAGTAAAAGAATGATATGTATCATGAAATGTATATATATATATCAATATCTTGATATGT
TGATTCATGGAAATTATGTAAGTTGAAACGAGTAATAAATTCA
Found at i:20036573 original size:34 final size:33
Alignment explanation
Indices: 20036463--20036707 Score: 185
Period size: 34 Copynumber: 7.2 Consensus size: 33
20036453 TGCAACATGT
* *
20036463 CATGCTTATAACAGATTAATAC-GATAGCAAT-AA
1 CATGCTTATAATA-ATCAATACAG-TAGCAATAAA
* * * * **
20036496 CATGCTTATAACAAATCGATACAATAGAAATATT
1 CATGCTTATAA-TAATCAATACAGTAGCAATAAA
* *
20036530 CATGCTTATAATAGATCATTACGGTAGCAATAAA
1 CATGCTTATAATA-ATCAATACAGTAGCAATAAA
* * * *
20036564 TATGTTTAT-ATCAAGTCACTACAGTAGCAATTAA
1 CATGCTTATAAT-AA-TCAATACAGTAGCAATAAA
*
20036598 CATGCTTATAATAGATCATTAC-GATAGCAATAAA
1 CATGCTTATAATA-ATCAATACAG-TAGCAATAAA
* * *
20036632 TATGTTTAT-ATCAAGTCAATACAGTAGCAATTAA
1 CATGCTTATAAT-AA-TCAATACAGTAGCAATAAA
20036666 CATGCTTATAATAAATCAATACAGTAGCAATAAA
1 CATGCTTATAAT-AATCAATACAGTAGCAATAAA
*
20036700 CTTGCTTA
1 CATGCTTA
20036708 ACATGTATTT
Statistics
Matches: 166, Mismatches: 33, Indels: 25
0.74 0.15 0.11
Matches are distributed among these distances:
33 31 0.19
34 127 0.77
35 8 0.05
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.31
Consensus pattern (33 bp):
CATGCTTATAATAATCAATACAGTAGCAATAAA
Found at i:20036607 original size:68 final size:68
Alignment explanation
Indices: 20036463--20036699 Score: 298
Period size: 68 Copynumber: 3.5 Consensus size: 68
20036453 TGCAACATGT
* * * * * * * * * * *
20036463 CATGCTTATAACAGATTAATACGATAGCAAT-AACATGCTTATAACAAATCGATACAATAG-AAA
1 CATGCTTATAATAGATCATTACGGTAGCAATAAATATGTTTATATCAAGTCAATACAGTAGCAAT
*
20036526 TATT
66 TA-A
*
20036530 CATGCTTATAATAGATCATTACGGTAGCAATAAATATGTTTATATCAAGTCACTACAGTAGCAAT
1 CATGCTTATAATAGATCATTACGGTAGCAATAAATATGTTTATATCAAGTCAATACAGTAGCAAT
20036595 TAA
66 TAA
*
20036598 CATGCTTATAATAGATCATTACGATAGCAATAAATATGTTTATATCAAGTCAATACAGTAGCAAT
1 CATGCTTATAATAGATCATTACGGTAGCAATAAATATGTTTATATCAAGTCAATACAGTAGCAAT
20036663 TAA
66 TAA
* * *
20036666 CATGCTTATAATAAATCAATACAGTAGCAATAAA
1 CATGCTTATAATAGATCATTACGGTAGCAATAAA
20036700 CTTGCTTAAC
Statistics
Matches: 149, Mismatches: 19, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
67 27 0.18
68 118 0.79
69 4 0.03
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.30
Consensus pattern (68 bp):
CATGCTTATAATAGATCATTACGGTAGCAATAAATATGTTTATATCAAGTCAATACAGTAGCAAT
TAA
Found at i:20037920 original size:104 final size:104
Alignment explanation
Indices: 20037802--20037997 Score: 374
Period size: 104 Copynumber: 1.9 Consensus size: 104
20037792 CCGAAAAAAT
*
20037802 TCGGTCGGGGGTCAGTTAATTTTTTTTGATTTTTTCAGTTAACGGTTAAATCGGTTCGAAACCGG
1 TCGGTCGGGGGTCAGTTAATTTTTTTTAATTTTTTCAGTTAACGGTTAAATCGGTTCGAAACCGG
20037867 TCGGTTAACCGAAAAAAATCGGGTAAAGAGTTCGGTTAA
66 TCGGTTAACCGAAAAAAATCGGGTAAAGAGTTCGGTTAA
*
20037906 TCGGTCGGGGGTCAGTTAATTTTTTTTAATTTTTTCGGTTAACGGTTAAATCGGTTCGAAACCGG
1 TCGGTCGGGGGTCAGTTAATTTTTTTTAATTTTTTCAGTTAACGGTTAAATCGGTTCGAAACCGG
20037971 TCGGTTAACCGAAAAAAATCGGGTAAA
66 TCGGTTAACCGAAAAAAATCGGGTAAA
20037998 CTGAATTTTG
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
104 90 1.00
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.34
Consensus pattern (104 bp):
TCGGTCGGGGGTCAGTTAATTTTTTTTAATTTTTTCAGTTAACGGTTAAATCGGTTCGAAACCGG
TCGGTTAACCGAAAAAAATCGGGTAAAGAGTTCGGTTAA
Found at i:20038113 original size:17 final size:17
Alignment explanation
Indices: 20038088--20038122 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
20038078 TGGGTAATTT
* *
20038088 TCGGTTAATTCGGTTAA
1 TCGGGTAATTCGGGTAA
20038105 TCGGGTAATTCGGGTAA
1 TCGGGTAATTCGGGTAA
20038122 T
1 T
20038123 TTTTAACCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.23, C:0.11, G:0.29, T:0.37
Consensus pattern (17 bp):
TCGGGTAATTCGGGTAA
Found at i:20038314 original size:103 final size:104
Alignment explanation
Indices: 20038160--20038358 Score: 382
Period size: 103 Copynumber: 1.9 Consensus size: 104
20038150 TTTCGGTTAA
*
20038160 TTCGGTTAACCGACCTTATTAACCGAAAAAAATTCGGTTCTGTTAATTTTTTTTAAAAAAATTCG
1 TTCGGTTAACCGACCTTATTAACCGAAAAAAATTCGGTTCGGTTAATTTTTTTTAAAAAAATTCG
20038225 GTTCGGTTAACGGTTAAAAATTTTGGAAGGTATATAATT
66 GTTCGGTTAACGGTTAAAAATTTTGGAAGGTATATAATT
20038264 TTCGGTTAACCGACCTTATTAACCG-AAAAAATTCGGTTCGGTTAATTTTTTTTAAAAAAATTCG
1 TTCGGTTAACCGACCTTATTAACCGAAAAAAATTCGGTTCGGTTAATTTTTTTTAAAAAAATTCG
20038328 GTTCGGTTAACGGTTAAAAATTTTGGAAGGT
66 GTTCGGTTAACGGTTAAAAATTTTGGAAGGT
20038359 CGGTTAATTC
Statistics
Matches: 94, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
103 69 0.73
104 25 0.27
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.38
Consensus pattern (104 bp):
TTCGGTTAACCGACCTTATTAACCGAAAAAAATTCGGTTCGGTTAATTTTTTTTAAAAAAATTCG
GTTCGGTTAACGGTTAAAAATTTTGGAAGGTATATAATT
Found at i:20040366 original size:22 final size:21
Alignment explanation
Indices: 20040332--20040372 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
20040322 TGACAATTTT
*
20040332 TAAAAAGAGTAATTATAAAATA
1 TAAAAAGAATAA-TATAAAATA
*
20040354 TAAAAATAATAATATAAAA
1 TAAAAAGAATAATATAAAA
20040373 CAGCATTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (21 bp):
TAAAAAGAATAATATAAAATA
Found at i:20043794 original size:16 final size:16
Alignment explanation
Indices: 20043773--20043808 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
20043763 TTTGGACTGA
20043773 ATTGAATAGAATGAAT
1 ATTGAATAGAATGAAT
*
20043789 ATTGAATAGATTGAAT
1 ATTGAATAGAATGAAT
20043805 -TTGA
1 ATTGA
20043809 TTATTTAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.36
Consensus pattern (16 bp):
ATTGAATAGAATGAAT
Found at i:20044056 original size:9 final size:9
Alignment explanation
Indices: 20044039--20044075 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
20044029 TGAGTTTTCG
20044039 AATTCGAAT
1 AATTCGAAT
*
20044048 AACTCGAAT
1 AATTCGAAT
20044057 AATTCGAAT
1 AATTCGAAT
20044066 AATTCGAAT
1 AATTCGAAT
20044075 A
1 A
20044076 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:20050348 original size:38 final size:38
Alignment explanation
Indices: 20050266--20050350 Score: 154
Period size: 38 Copynumber: 2.2 Consensus size: 38
20050256 CATGTATTCA
20050266 AATATA-AGTATAATATTATTGGTCTTCAAAAATAATAT
1 AATATAGA-TATAATATTATTGGTCTTCAAAAATAATAT
20050304 AATATAGATATAATATTATTGGTCTTCAAAAATAATAT
1 AATATAGATATAATATTATTGGTCTTCAAAAATAATAT
20050342 AATATAGAT
1 AATATAGAT
20050351 TAACATAATA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
38 45 0.98
39 1 0.02
ACGTcount: A:0.48, C:0.05, G:0.08, T:0.39
Consensus pattern (38 bp):
AATATAGATATAATATTATTGGTCTTCAAAAATAATAT
Found at i:20050469 original size:13 final size:14
Alignment explanation
Indices: 20050440--20050472 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
20050430 AATGGGACTG
20050440 ATTAAAACAATTCA
1 ATTAAAACAATTCA
*
20050454 ATTAAAA-AATTTA
1 ATTAAAACAATTCA
20050467 ATTAAA
1 ATTAAA
20050473 TATTTCTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (14 bp):
ATTAAAACAATTCA
Found at i:20050538 original size:16 final size:17
Alignment explanation
Indices: 20050517--20050565 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
20050507 ATTAAAAAAT
20050517 TATTAAAAATTTATA-A
1 TATTAAAAATTTATAGA
*
20050533 TATTAAAAATATTAAAAGA
1 TATTAAAAAT-TT-ATAGA
*
20050552 TAATAAAAATTTAT
1 TATTAAAAATTTAT
20050566 TTAAATTGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
16 10 0.37
17 3 0.11
18 4 0.15
19 10 0.37
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (17 bp):
TATTAAAAATTTATAGA
Found at i:20050543 original size:9 final size:9
Alignment explanation
Indices: 20050511--20050561 Score: 52
Period size: 9 Copynumber: 5.7 Consensus size: 9
20050501 AATTCAATTA
20050511 AAAAATTATT
1 AAAAA-TATT
20050521 AAAAAT-TT
1 AAAAATATT
*
20050529 -ATAATATT
1 AAAAATATT
20050537 AAAAATATT
1 AAAAATATT
*
20050546 AAAAGATAAT
1 AAAA-ATATT
20050556 AAAAAT
1 AAAAAT
20050562 TTATTTAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
7 4 0.11
8 4 0.11
9 14 0.40
10 13 0.37
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (9 bp):
AAAAATATT
Found at i:20055292 original size:5 final size:5
Alignment explanation
Indices: 20055275--20055349 Score: 80
Period size: 5 Copynumber: 15.0 Consensus size: 5
20055265 TTCTATACAA
* * * *
20055275 ATCAT ATCTT ATCAT ATCAT GA-CAT ATCAT GTCAT GTCAT ATCAA ATCAT
1 ATCAT ATCAT ATCAT ATCAT -ATCAT ATCAT ATCAT ATCAT ATCAT ATCAT
* *
20055325 AGCAT ATCAT ATCAT ATCAA ATCAT
1 ATCAT ATCAT ATCAT ATCAT ATCAT
20055350 TTCCTACCCC
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
4 1 0.02
5 56 0.97
6 1 0.02
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.36
Consensus pattern (5 bp):
ATCAT
Found at i:20055599 original size:14 final size:14
Alignment explanation
Indices: 20055572--20055607 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
20055562 AAACACATGC
20055572 ATATCATA-ATCAT
1 ATATCATACATCAT
20055585 ATATCATACATCAT
1 ATATCATACATCAT
*
20055599 ACATCATAC
1 ATATCATAC
20055608 TTATTTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (14 bp):
ATATCATACATCAT
Found at i:20057537 original size:29 final size:30
Alignment explanation
Indices: 20057476--20057556 Score: 94
Period size: 30 Copynumber: 2.7 Consensus size: 30
20057466 ATTGGACTTG
*
20057476 AATTTTAAAATATAAAAAGTAGAGAGACTA
1 AATTTTAAAATATAAAAAGTAGAAAGACTA
* *
20057506 AATTTCTAAAA-ATAAAAA-TATAAAGATTA
1 AATTT-TAAAATATAAAAAGTAGAAAGACTA
*
20057535 AATTTTAAAATGTTAAAAAGTA
1 AATTTTAAAAT-ATAAAAAGTA
20057557 TAGGGACTCA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
28 5 0.12
29 13 0.30
30 18 0.42
31 7 0.16
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.31
Consensus pattern (30 bp):
AATTTTAAAATATAAAAAGTAGAAAGACTA
Found at i:20058727 original size:25 final size:25
Alignment explanation
Indices: 20058693--20058743 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
20058683 TTAAAATTTT
*
20058693 ACCGGGCCCCGAAAAACTTAGTCCC
1 ACCGGGCCCCAAAAAACTTAGTCCC
20058718 ACCGGGCCCCAAAAAACTTAGTCCC
1 ACCGGGCCCCAAAAAACTTAGTCCC
20058743 A
1 A
20058744 AGATCTACCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.31, C:0.39, G:0.18, T:0.12
Consensus pattern (25 bp):
ACCGGGCCCCAAAAAACTTAGTCCC
Found at i:20059101 original size:5 final size:5
Alignment explanation
Indices: 20059085--20059139 Score: 53
Period size: 5 Copynumber: 11.4 Consensus size: 5
20059075 AGTGAGACTT
* * *
20059085 TTAAA TTAAAA TTAAA TTAAA --AAA -CAAA TCAAA TCAAA TTAAA TTAAA
1 TTAAA TT-AAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA
20059133 TTAAA TT
1 TTAAA TT
20059140 TTTTTTATTT
Statistics
Matches: 46, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
3 3 0.07
4 3 0.07
5 35 0.76
6 5 0.11
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (5 bp):
TTAAA
Found at i:20064826 original size:3 final size:3
Alignment explanation
Indices: 20064818--20064842 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
20064808 CTCACAGAAG
20064818 GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT G
20064843 GTTGTTATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:20064861 original size:15 final size:15
Alignment explanation
Indices: 20064843--20064872 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
20064833 GATGATGATG
20064843 GTTGTTATTGTTATT
1 GTTGTTATTGTTATT
20064858 GTTGTTATTGTTATT
1 GTTGTTATTGTTATT
20064873 ATTTTTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.00, G:0.20, T:0.67
Consensus pattern (15 bp):
GTTGTTATTGTTATT
Found at i:20064874 original size:3 final size:3
Alignment explanation
Indices: 20064847--20064912 Score: 78
Period size: 3 Copynumber: 22.0 Consensus size: 3
20064837 ATGATGGTTG
* * * * * *
20064847 TTA TTG TTA TTG TTG TTA TTG TTA TTA TTT TTA TTA TTG TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
20064895 TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
20064913 CCTGAACATG
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:20069911 original size:12 final size:12
Alignment explanation
Indices: 20069894--20069922 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
20069884 GATCAAAGTA
20069894 AAGGAAATGAAG
1 AAGGAAATGAAG
20069906 AAGGAAATGAAG
1 AAGGAAATGAAG
20069918 AAGGA
1 AAGGA
20069923 CGATTAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.34, T:0.07
Consensus pattern (12 bp):
AAGGAAATGAAG
Found at i:20070681 original size:18 final size:18
Alignment explanation
Indices: 20070655--20070723 Score: 59
Period size: 18 Copynumber: 3.8 Consensus size: 18
20070645 CTGAATTTTT
20070655 TTTTA-CTTTTTTTTAAC
1 TTTTATCTTTTTTTTAAC
* *
20070672 TTTTGTCTTTTTCTTTAATT
1 TTTTATCTTTTT-TTTAA-C
* * *
20070692 TTTTTTCTTTCTTTTAAG
1 TTTTATCTTTTTTTTAAC
*
20070710 TTTTATATTTTTTT
1 TTTTATCTTTTTTT
20070724 CTTATTTTAT
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
17 4 0.10
18 17 0.41
19 10 0.24
20 10 0.24
ACGTcount: A:0.13, C:0.09, G:0.03, T:0.75
Consensus pattern (18 bp):
TTTTATCTTTTTTTTAAC
Found at i:20070707 original size:19 final size:20
Alignment explanation
Indices: 20070651--20070713 Score: 60
Period size: 19 Copynumber: 3.2 Consensus size: 20
20070641 GCTTCTGAAT
*
20070651 TTTTTTTTACTTTTTTTTAAC
1 TTTTTTTT-CTTTCTTTTAAC
*
20070672 TTTTGTCTT-TTTC-TTTAA-
1 TTTT-TTTTCTTTCTTTTAAC
*
20070690 TTTTTTTTCTTTCTTTTAAG
1 TTTTTTTTCTTTCTTTTAAC
20070710 TTTT
1 TTTT
20070714 ATATTTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
17 3 0.09
18 8 0.23
19 10 0.29
20 7 0.20
21 4 0.11
22 3 0.09
ACGTcount: A:0.11, C:0.10, G:0.03, T:0.76
Consensus pattern (20 bp):
TTTTTTTTCTTTCTTTTAAC
Found at i:20070778 original size:17 final size:17
Alignment explanation
Indices: 20070729--20070780 Score: 68
Period size: 17 Copynumber: 3.0 Consensus size: 17
20070719 TTTTTCTTAT
* *
20070729 TTTATTTTGTTTATTTA
1 TTTATTTTATTTAATTA
*
20070746 TTTATTTTTATCTAATTA
1 TTTA-TTTTATTTAATTA
20070764 TTTATTTTATTTAATTA
1 TTTATTTTATTTAATTA
20070781 CTAATTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 16 0.53
18 14 0.47
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (17 bp):
TTTATTTTATTTAATTA
Found at i:20070849 original size:23 final size:22
Alignment explanation
Indices: 20070790--20070856 Score: 64
Period size: 25 Copynumber: 2.9 Consensus size: 22
20070780 ACTAATTTAA
* * *
20070790 AAAAATTTAAA-ATGTATATTTG
1 AAAATTTTAAATAT-TATTTTTC
20070812 AAATATTTTATAATATATATTTTTC
1 AAA-ATTTTA-AATAT-TATTTTTC
20070837 AAAATTTTAAATATTATTTT
1 AAAATTTTAAATATTATTTT
20070857 AAAATTATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
22 9 0.24
23 10 0.26
24 8 0.21
25 11 0.29
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (22 bp):
AAAATTTTAAATATTATTTTTC
Found at i:20070857 original size:36 final size:35
Alignment explanation
Indices: 20070814--20070969 Score: 162
Period size: 36 Copynumber: 4.4 Consensus size: 35
20070804 TATATTTGAA
20070814 ATATTTTATAATATATATTTTTCA-AAATTTTAAATAT
1 ATATTTT-TAA-ATATATTTTT-ATAAATTTTAAATAT
* * *
20070851 -TATTTTAAAAT-TATTTTTTTAAATTTTCAATAT
1 ATATTTTTAAATATATTTTTATAAATTTTAAATAT
*
20070884 ATATTTTTGAAAT-TATTTCTTATAAATTTTAAAAAT
1 ATATTTTT-AAATATATTT-TTATAAATTTTAAATAT
20070920 ATATTTTTGAAACTAT-TTTTTATAAATTTTAAATAT
1 ATATTTTT-AAA-TATATTTTTATAAATTTTAAATAT
20070956 -TATTTTTTAAATAT
1 ATA-TTTTTAAATAT
20070970 TAAATATATT
Statistics
Matches: 104, Mismatches: 8, Indels: 17
0.81 0.06 0.13
Matches are distributed among these distances:
33 19 0.18
34 11 0.11
35 16 0.15
36 53 0.51
37 4 0.04
38 1 0.01
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (35 bp):
ATATTTTTAAATATATTTTTATAAATTTTAAATAT
Found at i:20070866 original size:23 final size:25
Alignment explanation
Indices: 20070812--20070867 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 25
20070802 TGTATATTTG
*
20070812 AAATATTTTATAATATATATTTTTC
1 AAATATTTTATAATATATATTTTTA
20070837 AAA-ATTTTA-AATAT-TA-TTTTA
1 AAATATTTTATAATATATATTTTTA
20070858 AAATTATTTT
1 AAA-TATTTT
20070868 TTTAAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
21 7 0.25
22 2 0.07
23 10 0.36
24 6 0.21
25 3 0.11
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
AAATATTTTATAATATATATTTTTA
Found at i:20070897 original size:35 final size:34
Alignment explanation
Indices: 20070829--20070967 Score: 163
Period size: 36 Copynumber: 4.0 Consensus size: 34
20070819 TTATAATATA
** *
20070829 TATTTTTCAAAATTTTAAATATTA-TTTTAAAAT
1 TATTTTTTTAAATTTTAAATATTATTTTTGAAAT
*
20070862 TATTTTTTTAAATTTTCAATATATATTTTTGAAAT
1 TATTTTTTTAAATTTTAAATAT-TATTTTTGAAAT
* * *
20070897 TATTTCTTATAAATTTTAAAAATATATTTTTGAAAC
1 TATTT-TTTTAAATTTTAAATAT-TATTTTTGAAAT
*
20070933 TATTTTTTATAAATTTTAAATATTATTTTTTAAAT
1 TATTTTTT-TAAATTTTAAATATTATTTTTGAAAT
20070968 ATTAAATATA
Statistics
Matches: 90, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
33 19 0.21
34 2 0.02
35 25 0.28
36 44 0.49
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (34 bp):
TATTTTTTTAAATTTTAAATATTATTTTTGAAAT
Found at i:20070961 original size:21 final size:21
Alignment explanation
Indices: 20070924--20070981 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
20070914 AAAAATATAT
20070924 TTTTGAAACTATT-TTTTATAAA
1 TTTT-AAA-TATTATTTTATAAA
*
20070946 TTTTAAATATTATTTTTTAAA
1 TTTTAAATATTATTTTATAAA
*
20070967 TATTAAATA-TATTTT
1 TTTTAAATATTATTTT
20070982 TAATAATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.30
21 19 0.58
22 4 0.12
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTAAATATTATTTTATAAA
Found at i:20070982 original size:21 final size:22
Alignment explanation
Indices: 20070933--20070991 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
20070923 TTTTTGAAAC
*
20070933 TATTTTTTATAAATTTTAAATA
1 TATTTTTTATAAATATTAAATA
20070955 T-TATTTTT-TAAATATTAAATA
1 TAT-TTTTTATAAATATTAAATA
*
20070976 TATTTTTAAT-AATATT
1 TATTTTTTATAAATATT
20070992 TAAACATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
21 24 0.75
22 8 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TATTTTTTATAAATATTAAATA
Found at i:20070986 original size:18 final size:21
Alignment explanation
Indices: 20070936--20071000 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
20070926 TTGAAACTAT
*
20070936 TTTTTATAAATTTTAAATATTA
1 TTTTT-TAAATATTAAATATTA
20070958 TTTTTTAAATATTAAATA-TA
1 TTTTTTAAATATTAAATATTA
* *
20070978 TTTTTAATAATATTTAAACATTA
1 TTTTTTA-AATA-TTAAATATTA
20071001 AAATTTTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
20 8 0.22
21 16 0.43
22 11 0.30
23 2 0.05
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTTTAAATATTAAATATTA
Found at i:20071000 original size:29 final size:27
Alignment explanation
Indices: 20070961--20071019 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
20070951 AATATTATTT
* * *
20070961 TTTAAATATTAAATATATTTTTAATAATA
1 TTTAAACATTAAA-AT-TTTTAAATAAAA
20070990 TTTAAACATTAAAATTTTTAAATAAAA
1 TTTAAACATTAAAATTTTTAAATAAAA
20071017 TTT
1 TTT
20071020 TTATAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 13 0.48
28 2 0.07
29 12 0.44
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (27 bp):
TTTAAACATTAAAATTTTTAAATAAAA
Found at i:20071017 original size:13 final size:14
Alignment explanation
Indices: 20070999--20071033 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
20070989 ATTTAAACAT
20070999 TAAAATTTTTA-AA
1 TAAAATTTTTATAA
20071012 TAAAATTTTTATAA
1 TAAAATTTTTATAA
20071026 -AAAATTTT
1 TAAAATTTT
20071034 AAAAAGGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 19 0.90
14 2 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TAAAATTTTTATAA
Found at i:20071022 original size:29 final size:29
Alignment explanation
Indices: 20070945--20071014 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
20070935 TTTTTTATAA
*
20070945 ATTTTAAATATTATTTTTTAAATATTAAATAT
1 ATTTTAAATA--A-TTTTTAAACATTAAATAT
* *
20070977 ATTTTTAATAATATTTAAACATTAAA-AT
1 ATTTTAAATAATTTTTAAACATTAAATAT
20071005 -TTTTAAATAA
1 ATTTTAAATAA
20071015 AATTTTTATA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
27 9 0.26
28 2 0.06
29 13 0.38
30 1 0.03
32 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (29 bp):
ATTTTAAATAATTTTTAAACATTAAATAT
Found at i:20071130 original size:12 final size:13
Alignment explanation
Indices: 20071110--20071147 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
20071100 ATTTTAAAGA
*
20071110 TATTTAAAATTTT
1 TATTTAAAAATTT
20071123 TA-TTAAAAATTT
1 TATTTAAAAATTT
20071135 TATTTAAAAATTT
1 TATTTAAAAATTT
20071148 CAAATGTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TATTTAAAAATTT
Found at i:20071281 original size:23 final size:22
Alignment explanation
Indices: 20071240--20071303 Score: 87
Period size: 22 Copynumber: 2.9 Consensus size: 22
20071230 TTTCATATTA
*
20071240 TTAAAAAAT-ATATTT-AATTT
1 TTAAAAAATAATATTTAAAATT
20071260 TTAAAAAATAATATTTAAAATT
1 TTAAAAAATAATATTTAAAATT
20071282 TTAAAAAATATATATTATAAAA
1 TTAAAAAATA-ATATT-TAAAA
20071304 AATTTCAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
20 9 0.23
21 6 0.15
22 14 0.36
23 5 0.13
24 5 0.13
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TTAAAAAATAATATTTAAAATT
Found at i:20071355 original size:9 final size:9
Alignment explanation
Indices: 20071330--20071374 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
20071320 TTCAAATTTT
*
20071330 TAAAATTAA
1 TAAAATAAA
20071339 TAACAATAAA
1 TAA-AATAAA
20071349 TAAAATAAA
1 TAAAATAAA
20071358 T-AAATAAA
1 TAAAATAAA
*
20071366 CAAAATAAA
1 TAAAATAAA
20071375 ATAAGAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
8 7 0.22
9 17 0.53
10 8 0.25
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.22
Consensus pattern (9 bp):
TAAAATAAA
Found at i:20071421 original size:19 final size:19
Alignment explanation
Indices: 20071395--20071449 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
20071385 TATAAAACTT
20071395 AAAAAAAGAAAAAAATTAA
1 AAAAAAAGAAAAAAATTAA
* * *
20071414 AGAAAAAGACAAAAGTTAA
1 AAAAAAAGAAAAAAATTAA
20071433 AAAAAAAGTAAAAAAAT
1 AAAAAAAG-AAAAAAAT
20071450 AAGAAGCAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
19 23 0.79
20 6 0.21
ACGTcount: A:0.78, C:0.02, G:0.09, T:0.11
Consensus pattern (19 bp):
AAAAAAAGAAAAAAATTAA
Found at i:20072250 original size:23 final size:24
Alignment explanation
Indices: 20072216--20072269 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 24
20072206 CCCTACTGTT
* *
20072216 AGTCACCACCATCTGACGTCCACC-
1 AGTCA-CACCATCCGACGTACACCA
20072240 AGTCACACCATCCGACGTACACCA
1 AGTCACACCATCCGACGTACACCA
20072264 AGTCAC
1 AGTCAC
20072270 CATCATCGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.30, C:0.43, G:0.13, T:0.15
Consensus pattern (24 bp):
AGTCACACCATCCGACGTACACCA
Found at i:20072703 original size:1 final size:1
Alignment explanation
Indices: 20072697--20072722 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
20072687 AACTTTGAAA
20072697 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
20072723 CAGACACTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:20074127 original size:40 final size:40
Alignment explanation
Indices: 20074036--20074360 Score: 589
Period size: 40 Copynumber: 8.2 Consensus size: 40
20074026 TCCTCGTTCA
* * * ** *
20074036 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
20074075 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
20074115 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
20074155 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
20074195 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
20074235 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
20074275 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
20074315 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
20074355 AATGCC
1 AATGCC
20074361 CATTCATATT
Statistics
Matches: 279, Mismatches: 6, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
39 33 0.12
40 246 0.88
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.23
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:20076586 original size:58 final size:58
Alignment explanation
Indices: 20076496--20076611 Score: 223
Period size: 58 Copynumber: 2.0 Consensus size: 58
20076486 AAGCCGTGAG
20076496 ATCCCTTTCGAGTTTCAGTTCGGGCTTCATTCGAGAGGGATATGGGGGGTCACGAGGC
1 ATCCCTTTCGAGTTTCAGTTCGGGCTTCATTCGAGAGGGATATGGGGGGTCACGAGGC
*
20076554 ATCCCTTTCGAGTTTCAGTTCGGGCTTCATTCGAGAGGTATATGGGGGGTCACGAGGC
1 ATCCCTTTCGAGTTTCAGTTCGGGCTTCATTCGAGAGGGATATGGGGGGTCACGAGGC
20076612 GAAAAGAGGG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.17, C:0.21, G:0.34, T:0.28
Consensus pattern (58 bp):
ATCCCTTTCGAGTTTCAGTTCGGGCTTCATTCGAGAGGGATATGGGGGGTCACGAGGC
Found at i:20081147 original size:50 final size:50
Alignment explanation
Indices: 20081072--20081172 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
20081062 CTAGAATCGA
20081072 CTAAACCGTAGCTCTGATACCAATAAAATGTAACACCCCGAACCCGAGAC
1 CTAAACCGTAGCTCTGATACCAATAAAATGTAACACCCCGAACCCGAGAC
20081122 CTAAACCGTAGCTCTGATACCAATAAAATGTAACACCCCGAACCCGAGAC
1 CTAAACCGTAGCTCTGATACCAATAAAATGTAACACCCCGAACCCGAGAC
20081172 C
1 C
20081173 GACACCGGAG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.38, C:0.33, G:0.14, T:0.16
Consensus pattern (50 bp):
CTAAACCGTAGCTCTGATACCAATAAAATGTAACACCCCGAACCCGAGAC
Found at i:20082685 original size:161 final size:161
Alignment explanation
Indices: 20082420--20082724 Score: 610
Period size: 161 Copynumber: 1.9 Consensus size: 161
20082410 TAATATTTAA
20082420 CACATACGTAACATATCCCCATATTGGGATGTTTTTCGAGTATTCGCTGAAATTTTACAGCAAGC
1 CACATACGTAACATATCCCCATATTGGGATGTTTTTCGAGTATTCGCTGAAATTTTACAGCAAGC
20082485 TCATTCATTACCAAATCACGTACCTTCGGGATTTAACCGGATATAGCTCCTCGTTCAAATGCCTT
66 TCATTCATTACCAAATCACGTACCTTCGGGATTTAACCGGATATAGCTCCTCGTTCAAATGCCTT
20082550 CGGGACATAGCCCGGTTTTAGTAACTCACAC
131 CGGGACATAGCCCGGTTTTAGTAACTCACAC
20082581 CACATACGTAACATATCCCCATATTGGGATGTTTTTCGAGTATTCGCTGAAATTTTACAGCAAGC
1 CACATACGTAACATATCCCCATATTGGGATGTTTTTCGAGTATTCGCTGAAATTTTACAGCAAGC
20082646 TCATTCATTACCAAATCACGTACCTTCGGGATTTAACCGGATATAGCTCCTCGTTCAAATGCCTT
66 TCATTCATTACCAAATCACGTACCTTCGGGATTTAACCGGATATAGCTCCTCGTTCAAATGCCTT
20082711 CGGGACATAGCCCG
131 CGGGACATAGCCCG
20082725 ATTTAACAAC
Statistics
Matches: 144, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
161 144 1.00
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (161 bp):
CACATACGTAACATATCCCCATATTGGGATGTTTTTCGAGTATTCGCTGAAATTTTACAGCAAGC
TCATTCATTACCAAATCACGTACCTTCGGGATTTAACCGGATATAGCTCCTCGTTCAAATGCCTT
CGGGACATAGCCCGGTTTTAGTAACTCACAC
Found at i:20082746 original size:39 final size:40
Alignment explanation
Indices: 20082701--20082792 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 40
20082691 GCTCCTCGTT
*
20082701 CAAATGCCTTCGGGACATAGCCC-GATTTAACAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
* * ** *
20082740 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
*
20082780 CAAAGGCCTTCGG
1 CAAATGCCTTCGG
20082793 ATCTTAGTCC
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
39 20 0.45
40 24 0.55
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
Found at i:20082854 original size:41 final size:41
Alignment explanation
Indices: 20082777--20082854 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
20082767 TTAGTATCTC
* * *
20082777 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
20082818 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
20082855 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:20089206 original size:1 final size:1
Alignment explanation
Indices: 20089200--20089228 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
20089190 AACTTTGAAA
20089200 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
20089229 CAGACACTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:20090724 original size:80 final size:80
Alignment explanation
Indices: 20090572--20090764 Score: 221
Period size: 80 Copynumber: 2.4 Consensus size: 80
20090562 CGGTTTTAGT
* * *
20090572 AACTCACACAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTT
1 AACTCGCACAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGACTT
*
20090637 AACCCGGATTTA-AC
66 AACCCGGATATATAC
** *
20090651 AACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTC-GGATC
1 AACTCGCAC-AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGA-C
** *
20090715 TTAGTCCGGATATATTC
64 TTAACCCGGATATATAC
* * *
20090732 -ACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 AAC-TCGCACAATGCCTTCGGGACTTAACCCGGA
20090765 CAGCATTCAA
Statistics
Matches: 97, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
79 11 0.11
80 80 0.82
81 6 0.06
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (80 bp):
AACTCGCACAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGACTT
AACCCGGATATATAC
Found at i:20090725 original size:40 final size:40
Alignment explanation
Indices: 20090542--20090711 Score: 234
Period size: 40 Copynumber: 4.3 Consensus size: 40
20090532 TCCTCGTTCA
* * * ** *
20090542 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
20090581 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
20090621 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
20090661 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
20090701 AAGGCCTTCGG
1 AATGCCTTCGG
20090712 ATCTTAGTCC
Statistics
Matches: 119, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 33 0.28
40 86 0.72
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:20090764 original size:120 final size:119
Alignment explanation
Indices: 20090542--20090764 Score: 272
Period size: 120 Copynumber: 1.9 Consensus size: 119
20090532 TCCTCGTTCA
* * * *
20090542 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGATT
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACTTAACCCGGATA
* *
20090607 TAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
66 TAACAACTAGCACGAAAGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* * * **
20090661 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAGTCCGGA
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGA-CTTAACCCGGA
* *
20090725 TATATTC-ACTTAGCAC-AAAGCCTTCGGGACTTAGCCCGGA
64 TATA-ACAAC-TAGCACGAAAGCCTTCGGGACTTAACCCGGA
20090765 CAGCATTCAA
Statistics
Matches: 87, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
119 37 0.43
120 44 0.51
121 6 0.07
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACTTAACCCGGATA
TAACAACTAGCACGAAAGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:20090773 original size:41 final size:41
Alignment explanation
Indices: 20090696--20090773 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
20090686 TTAGTATCTC
* * *
20090696 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
20090737 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
20090774 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:20095116 original size:35 final size:36
Alignment explanation
Indices: 20095050--20095117 Score: 84
Period size: 36 Copynumber: 1.9 Consensus size: 36
20095040 TATGGAAGAG
* *** *
20095050 AATATATGGGTATGTTATTCATGTTATGTGACAGTA
1 AATATATGAGTATGTTATTCATACCACGTGACAGTA
20095086 AATATATGAGTATGTT-TTCATACCACGTGACA
1 AATATATGAGTATGTTATTCATACCACGTGACA
20095118 ATGATTATAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
35 12 0.44
36 15 0.56
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.38
Consensus pattern (36 bp):
AATATATGAGTATGTTATTCATACCACGTGACAGTA
Found at i:20100744 original size:42 final size:42
Alignment explanation
Indices: 20100681--20100913 Score: 274
Period size: 42 Copynumber: 5.5 Consensus size: 42
20100671 CGTTGGGATT
*
20100681 AGCACTTAGCAACCACC-TTTATATTCAAGGATACGGGGAATC
1 AGCACTTAGCAACC-CCTTTTATAATCAAGGATACGGGGAATC
* *
20100723 AGCACATAGCAACCCCTTTTATAATCAAAGATACGGGGAATC
1 AGCACTTAGCAACCCCTTTTATAATCAAGGATACGGGGAATC
** *
20100765 AGCAAATAGCAACCCCTTTTTTTATAATCTAA-GATACAGGGAATC
1 AGCACTTAGCAACCCC---TTTTATAATC-AAGGATACGGGGAATC
* * * *
20100810 AGTACTTAGCAACCCCTTTGATAATC-AGAATACGAGGAATC
1 AGCACTTAGCAACCCCTTTTATAATCAAGGATACGGGGAATC
* * * *
20100851 AGCACTTAGTAACCCCTTTGATAATCAAGAATACGGGAAATC
1 AGCACTTAGCAACCCCTTTTATAATCAAGGATACGGGGAATC
20100893 AGCACTTAGCAACCCCTTTTA
1 AGCACTTAGCAACCCCTTTTA
20100914 CATTCAAGAA
Statistics
Matches: 166, Mismatches: 18, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
40 1 0.01
41 36 0.22
42 92 0.55
45 35 0.21
46 2 0.01
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (42 bp):
AGCACTTAGCAACCCCTTTTATAATCAAGGATACGGGGAATC
Found at i:20110009 original size:65 final size:65
Alignment explanation
Indices: 20109905--20110034 Score: 224
Period size: 65 Copynumber: 2.0 Consensus size: 65
20109895 GAAAACCTAT
* *
20109905 AGCTAAGAATCAATAAAAATTACTGAAAACAGAAAACCCGAAAAATTGCAGAGTAACTTGACAAC
1 AGCTAAGAATCAATAAAAATTACTGAAAACAGAAAACCCGAAAAACTGCAGACTAACTTGACAAC
* *
20109970 AGCTAAGAATCAATAAAAATTGCTGAAAACAGAAAACCCGAAAAACTGCGGACTAACTTGACAAC
1 AGCTAAGAATCAATAAAAATTACTGAAAACAGAAAACCCGAAAAACTGCAGACTAACTTGACAAC
20110035 TTCGTTTGAG
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 61 1.00
ACGTcount: A:0.51, C:0.18, G:0.15, T:0.16
Consensus pattern (65 bp):
AGCTAAGAATCAATAAAAATTACTGAAAACAGAAAACCCGAAAAACTGCAGACTAACTTGACAAC
Found at i:20111663 original size:12 final size:12
Alignment explanation
Indices: 20111648--20111741 Score: 57
Period size: 12 Copynumber: 7.5 Consensus size: 12
20111638 CAAAAAATTC
20111648 AAAAAAAGTGAA
1 AAAAAAAGTGAA
20111660 AAAAAATCGAGT-AA
1 AAAAAA---AGTGAA
*
20111674 AAAAAGAGAGAGAA
1 AAAAA-A-AGTGAA
* *
20111688 AGAAAAAAAT-TA
1 A-AAAAAAGTGAA
*
20111700 AAAAAAATTGAA
1 AAAAAAAGTGAA
*
20111712 AAAAAAATTGAA
1 AAAAAAAGTGAA
**
20111724 AAAAAATTTGAA
1 AAAAAAAGTGAA
20111736 AAAAAA
1 AAAAAA
20111742 GAGAAGAGGA
Statistics
Matches: 68, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
11 7 0.10
12 38 0.56
13 4 0.06
14 11 0.16
15 8 0.12
ACGTcount: A:0.73, C:0.01, G:0.13, T:0.13
Consensus pattern (12 bp):
AAAAAAAGTGAA
Found at i:20111706 original size:11 final size:12
Alignment explanation
Indices: 20111690--20111741 Score: 81
Period size: 12 Copynumber: 4.5 Consensus size: 12
20111680 AGAGAGAAAG
20111690 AAAAAAATT--A
1 AAAAAAATTGAA
20111700 AAAAAAATTGAA
1 AAAAAAATTGAA
20111712 AAAAAAATTGAA
1 AAAAAAATTGAA
*
20111724 AAAAAATTTGAA
1 AAAAAAATTGAA
20111736 AAAAAA
1 AAAAAA
20111742 GAGAAGAGGA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
10 9 0.23
12 30 0.77
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (12 bp):
AAAAAAATTGAA
Found at i:20111712 original size:24 final size:25
Alignment explanation
Indices: 20111685--20111741 Score: 84
Period size: 23 Copynumber: 2.4 Consensus size: 25
20111675 AAAAGAGAGA
20111685 GAAAGAAAAAAATT-AAAAAAAA-TT
1 GAAA-AAAAAAATTGAAAAAAAATTT
20111709 G-AAAAAAAAATTGAAAAAAAATTT
1 GAAAAAAAAAATTGAAAAAAAATTT
20111733 GAAAAAAAA
1 GAAAAAAAA
20111742 GAGAAGAGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
22 9 0.30
23 10 0.33
24 4 0.13
25 7 0.23
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.16
Consensus pattern (25 bp):
GAAAAAAAAAATTGAAAAAAAATTT
Found at i:20117438 original size:86 final size:86
Alignment explanation
Indices: 20117328--20117502 Score: 350
Period size: 86 Copynumber: 2.0 Consensus size: 86
20117318 GAAAGGTAAT
20117328 GAAGTTGGAACCAATCCGTGGATGGAATCTTGCAAACCTGAAACAAAGAAAAATCACAAGGTAAT
1 GAAGTTGGAACCAATCCGTGGATGGAATCTTGCAAACCTGAAACAAAGAAAAATCACAAGGTAAT
20117393 TTCGAAAGGGGGTTAGCAAAA
66 TTCGAAAGGGGGTTAGCAAAA
20117414 GAAGTTGGAACCAATCCGTGGATGGAATCTTGCAAACCTGAAACAAAGAAAAATCACAAGGTAAT
1 GAAGTTGGAACCAATCCGTGGATGGAATCTTGCAAACCTGAAACAAAGAAAAATCACAAGGTAAT
20117479 TTCGAAAGGGGGTTAGCAAAA
66 TTCGAAAGGGGGTTAGCAAAA
20117500 GAA
1 GAA
20117503 TTCCTCTCTT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 89 1.00
ACGTcount: A:0.42, C:0.15, G:0.25, T:0.18
Consensus pattern (86 bp):
GAAGTTGGAACCAATCCGTGGATGGAATCTTGCAAACCTGAAACAAAGAAAAATCACAAGGTAAT
TTCGAAAGGGGGTTAGCAAAA
Found at i:20117618 original size:21 final size:21
Alignment explanation
Indices: 20117589--20117725 Score: 51
Period size: 21 Copynumber: 6.7 Consensus size: 21
20117579 CAAGCTCTCT
* *
20117589 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-ATTTC
* **
20117610 TTCTTTTTCAATTTTCATTTC
1 TTCATTTTCTTTTTTCATTTC
20117631 TTCATTTTCTTTTTCTCTCACTTT-
1 TTCATTTTC-TTTT-T-TCA-TTTC
*
20117655 TTCAATTTC-TTTTTC-TTT-
1 TTCATTTTCTTTTTTCATTTC
* *
20117673 TGCAATTTC-TTTTTC-TTT-
1 TTCATTTTCTTTTTTCATTTC
*
20117691 TTCGTTTTCTTTTTGT--TTTC
1 TTCATTTTCTTTTT-TCATTTC
*
20117711 TTTCAATTTCTTTTT
1 -TTCATTTTCTTTTT
20117726 CAATCTCTTT
Statistics
Matches: 92, Mismatches: 15, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
18 26 0.28
19 7 0.08
20 6 0.07
21 33 0.36
22 5 0.05
23 1 0.01
24 11 0.12
25 3 0.03
ACGTcount: A:0.09, C:0.18, G:0.03, T:0.69
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCATTTC
Found at i:20117666 original size:12 final size:12
Alignment explanation
Indices: 20117609--20117735 Score: 55
Period size: 12 Copynumber: 10.6 Consensus size: 12
20117599 TTTTTCGCTT
20117609 TTTCTTTTTCAA
1 TTTCTTTTTCAA
*
20117621 TTTTCATTTCTTCAT
1 -TTTC-TTT-TTCAA
**
20117636 TTTCTTTTTCTC
1 TTTCTTTTTCAA
**
20117648 TCACTTTTTCAA
1 TTTCTTTTTCAA
*
20117660 TTTCTTTTTC-T
1 TTTCTTTTTCAA
** **
20117671 TTTGCAATTTCTT
1 TTT-CTTTTTCAA
**
20117684 TTTCTTTTTCGT
1 TTTCTTTTTCAA
*
20117696 TTTCTTTTT--G
1 TTTCTTTTTCAA
*
20117706 TTT-TCTTTCAA
1 TTTCTTTTTCAA
20117717 TTTCTTTTTCAA
1 TTTCTTTTTCAA
*
20117729 TCTCTTT
1 TTTCTTT
20117736 CTCCTTTTCT
Statistics
Matches: 87, Mismatches: 20, Indels: 15
0.71 0.16 0.12
Matches are distributed among these distances:
9 4 0.05
10 3 0.03
11 6 0.07
12 52 0.60
13 11 0.13
14 7 0.08
15 4 0.05
ACGTcount: A:0.10, C:0.19, G:0.02, T:0.69
Consensus pattern (12 bp):
TTTCTTTTTCAA
Found at i:20117672 original size:18 final size:18
Alignment explanation
Indices: 20117606--20117726 Score: 98
Period size: 18 Copynumber: 6.4 Consensus size: 18
20117596 TCTTTTTTCG
20117606 CTTTTTCTTTTTCAATTTT
1 CTTTTTCTTTTTCAA-TTT
* **
20117625 CATTTCTTCATTTTCTTTTT
1 C-TTT-TTCTTTTTCAATTT
* **
20117645 CTCTCACTTTTTCAATTT
1 CTTTTTCTTTTTCAATTT
*
20117663 CTTTTTCTTTTGCAATTT
1 CTTTTTCTTTTTCAATTT
**
20117681 CTTTTTCTTTTTCGTTTT
1 CTTTTTCTTTTTCAATTT
*
20117699 CTTTTTGTTTTCTTTCAATTT
1 C-TTTT-TCTT-TTTCAATTT
20117720 CTTTTTC
1 CTTTTTC
20117727 AATCTCTTTC
Statistics
Matches: 77, Mismatches: 20, Indels: 10
0.72 0.19 0.09
Matches are distributed among these distances:
18 39 0.51
19 8 0.10
20 14 0.18
21 16 0.21
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.69
Consensus pattern (18 bp):
CTTTTTCTTTTTCAATTT
Found at i:20117726 original size:6 final size:6
Alignment explanation
Indices: 20117606--20117713 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
20117596 TCTTTTTTCG
* * * **
20117606 CTTTTT CTTTTT CAATTTT CATTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
20117657 CAATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
20117705 -GTTTT CTTT
1 CTTTTT CTTT
20117714 CAATTTCTTT
Statistics
Matches: 75, Mismatches: 24, Indels: 6
0.71 0.23 0.06
Matches are distributed among these distances:
5 4 0.05
6 58 0.77
7 10 0.13
8 3 0.04
ACGTcount: A:0.08, C:0.19, G:0.03, T:0.70
Consensus pattern (6 bp):
CTTTTT
Found at i:20118497 original size:8 final size:9
Alignment explanation
Indices: 20118469--20118501 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
20118459 ATTCCCGCAA
20118469 AAAAATAGTC
1 AAAAA-AGTC
20118479 AAAAAAGTC
1 AAAAAAGTC
20118488 AAAAAA-TC
1 AAAAAAGTC
20118496 AAAAAA
1 AAAAAA
20118502 AGACGAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.35
9 10 0.43
10 5 0.22
ACGTcount: A:0.73, C:0.09, G:0.06, T:0.12
Consensus pattern (9 bp):
AAAAAAGTC
Found at i:20126341 original size:40 final size:40
Alignment explanation
Indices: 20126286--20126398 Score: 190
Period size: 40 Copynumber: 2.8 Consensus size: 40
20126276 GAACATTGGA
*
20126286 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTC
20126326 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTC
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTC
* * *
20126366 ATATGTCCGGGTTAAGACCCGAAGGCAAATATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATG
20126399 TTTGCGGCTG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 69 1.00
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTC
Found at i:20130196 original size:20 final size:20
Alignment explanation
Indices: 20130159--20130197 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
20130149 CTTAGATGAC
*
20130159 GAAAAACCTAACGTTTGATT
1 GAAAAACCTAACGCTTGATT
20130179 GAAAAA-CTATACGCTTGAT
1 GAAAAACCTA-ACGCTTGAT
20130198 CAAAAACCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28
Consensus pattern (20 bp):
GAAAAACCTAACGCTTGATT
Found at i:20140061 original size:18 final size:20
Alignment explanation
Indices: 20140038--20140097 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
20140028 ATATATATTT
20140038 ATAATTTGT-ACTTTTT-AA
1 ATAATTTGTAACTTTTTAAA
* *
20140056 ATAATTTTTAATTTTTTAAA
1 ATAATTTGTAACTTTTTAAA
*
20140076 ATAATTTATATA-TTTTTAAA
1 ATAATTTGTA-ACTTTTTAAA
20140096 AT
1 AT
20140098 TTTTAAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 8 0.22
19 6 0.17
20 21 0.58
21 1 0.03
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (20 bp):
ATAATTTGTAACTTTTTAAA
Found at i:20140077 original size:20 final size:20
Alignment explanation
Indices: 20140049--20140097 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
20140039 TAATTTGTAC
*
20140049 TTTTT-AAATAATTTTTA-A
1 TTTTTAAAATAATTTATATA
20140067 TTTTTTAAAATAATTTATATA
1 -TTTTTAAAATAATTTATATA
20140088 TTTTTAAAAT
1 TTTTTAAAAT
20140098 TTTTAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 5 0.19
20 21 0.78
21 1 0.04
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTTAAAATAATTTATATA
Found at i:20140083 original size:29 final size:29
Alignment explanation
Indices: 20140051--20140106 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
20140041 ATTTGTACTT
*
20140051 TTTAAATAATTTTT-AATTTTTTAAAATAA
1 TTTAAAT-ATTTTTAAAATTTTTAAAATAA
*
20140080 TTTATATATTTTTAAAATTTTTAAAAT
1 TTTAAATATTTTTAAAATTTTTAAAAT
20140107 TTTTAGAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (29 bp):
TTTAAATATTTTTAAAATTTTTAAAATAA
Found at i:20140100 original size:8 final size:9
Alignment explanation
Indices: 20140010--20140117 Score: 60
Period size: 9 Copynumber: 11.4 Consensus size: 9
20140000 GCAATTAATT
20140010 AATTTTTAA
1 AATTTTTAA
*
20140019 AATTTTAAA
1 AATTTTTAA
*
20140028 ATATATATTTAT
1 A-AT-T-TTTAA
*
20140040 AATTTGT--
1 AATTTTTAA
*
20140047 ACTTTTTAAA
1 AATTTTT-AA
20140057 TAATTTTT-A
1 -AATTTTTAA
*
20140066 ATTTTTTAA
1 AATTTTTAA
*
20140075 AATAATTTATA
1 AAT-TTTTA-A
*
20140086 TATTTTTAA
1 AATTTTTAA
20140095 AATTTTTAA
1 AATTTTTAA
20140104 AATTTTTAGA
1 AATTTTTA-A
20140114 AATT
1 AATT
20140118 AATTACCTGT
Statistics
Matches: 75, Mismatches: 13, Indels: 21
0.69 0.12 0.19
Matches are distributed among these distances:
7 5 0.07
8 6 0.08
9 32 0.43
10 16 0.21
11 12 0.16
12 4 0.05
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.56
Consensus pattern (9 bp):
AATTTTTAA
Found at i:20143546 original size:18 final size:19
Alignment explanation
Indices: 20143511--20143546 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
20143501 GTGTATTGAG
20143511 TTTAAATCTTATTATATAT
1 TTTAAATCTTATTATATAT
*
20143530 TTTAAATTTTA-TATATA
1 TTTAAATCTTATTATATA
20143547 ATTATAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTAAATCTTATTATATAT
Found at i:20146593 original size:42 final size:42
Alignment explanation
Indices: 20146529--20146612 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
20146519 GATTCATATT
20146529 CTTTACCTAATTCATTAGCTTGTCTTTGCCATCCAGTCAACC
1 CTTTACCTAATTCATTAGCTTGTCTTTGCCATCCAGTCAACC
* *
20146571 CTTTCCCTAATTCTTTAGCTTGTCTTTGCCATCCAGTCAACC
1 CTTTACCTAATTCATTAGCTTGTCTTTGCCATCCAGTCAACC
20146613 ACGTAATTCC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.19, C:0.32, G:0.10, T:0.39
Consensus pattern (42 bp):
CTTTACCTAATTCATTAGCTTGTCTTTGCCATCCAGTCAACC
Found at i:20153986 original size:30 final size:32
Alignment explanation
Indices: 20153939--20153999 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 32
20153929 TTTTAGGGGC
20153939 TAAAATCTTTATAATTTTTAAAAGA-TTAAAT
1 TAAAATCTTTATAATTTTTAAAAGAGTTAAAT
* *
20153970 TAAAAT-TTTATTATTTTTAGAAGAGTTAAA
1 TAAAATCTTTATAATTTTTAAAAGAGTTAAA
20154000 AGGACAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 16 0.59
31 11 0.41
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.46
Consensus pattern (32 bp):
TAAAATCTTTATAATTTTTAAAAGAGTTAAAT
Found at i:20157269 original size:38 final size:37
Alignment explanation
Indices: 20157219--20157359 Score: 156
Period size: 38 Copynumber: 3.7 Consensus size: 37
20157209 CACTGGCACT
*
20157219 AAGCGTGCTAGGCACAAAGCCTAAATAACACTGACACA
1 AAGCCTGCTAGGCACAAAGCCTAAATAACAC-GACACA
** * *
20157257 AAGCCTATTAGGCACAAAGCCTAAATAACACCGGCACT
1 AAGCCTGCTAGGCACAAAGCCTAAATAACA-CGACACA
* * * *
20157295 AAGCCTGCTAGGAATAAAGCCTGAATAACACCAGCACA
1 AAGCCTGCTAGGCACAAAGCCTAAATAACACGA-CACA
* *
20157333 AAGCCTGCTAGGCACAAATCCTGAATA
1 AAGCCTGCTAGGCACAAAGCCTAAATA
20157360 TCAATATAAT
Statistics
Matches: 85, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
37 1 0.01
38 83 0.98
39 1 0.01
ACGTcount: A:0.40, C:0.27, G:0.18, T:0.15
Consensus pattern (37 bp):
AAGCCTGCTAGGCACAAAGCCTAAATAACACGACACA
Found at i:20157345 original size:76 final size:76
Alignment explanation
Indices: 20157208--20157359 Score: 198
Period size: 76 Copynumber: 2.0 Consensus size: 76
20157198 ACTTTTTAAT
* * * * *
20157208 ACACTGGCACTAAGCGTGCTAGGCACAAAGCCTAAATAACACTGACACAAAGCCTATTAGGCACA
1 ACACCGGCACTAAGCCTGCTAGGAACAAAGCCTAAATAACACAGACACAAAGCCTACTAGGCACA
20157273 AAGCCTAAATA
66 AAGCCTAAATA
* * *
20157284 ACACCGGCACTAAGCCTGCTAGGAATAAAGCCTGAATAACACCAG-CACAAAGCCTGCTAGGCAC
1 ACACCGGCACTAAGCCTGCTAGGAACAAAGCCTAAATAACA-CAGACACAAAGCCTACTAGGCAC
* *
20157348 AAATCCTGAATA
65 AAAGCCTAAATA
20157360 TCAATATAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
76 63 0.97
77 2 0.03
ACGTcount: A:0.39, C:0.28, G:0.18, T:0.15
Consensus pattern (76 bp):
ACACCGGCACTAAGCCTGCTAGGAACAAAGCCTAAATAACACAGACACAAAGCCTACTAGGCACA
AAGCCTAAATA
Found at i:20158803 original size:27 final size:27
Alignment explanation
Indices: 20158743--20158803 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
20158733 AGATTCGTTC
* * *
20158743 TTCAAAATTCGCCACAAAGGCTTTTCT
1 TTCAAAAATAGCCACAAAGGCTTTCCT
20158770 TTCCAAAAATAGCCA-AAGAGGCTTTCCT
1 TT-CAAAAATAGCCACAA-AGGCTTTCCT
20158798 TTCAAA
1 TTCAAA
20158804 GTCTAACCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 8 0.28
28 21 0.72
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.30
Consensus pattern (27 bp):
TTCAAAAATAGCCACAAAGGCTTTCCT
Found at i:20158893 original size:29 final size:28
Alignment explanation
Indices: 20158853--20158932 Score: 97
Period size: 29 Copynumber: 2.8 Consensus size: 28
20158843 AATGGCATCC
* *
20158853 TTTAATATAGATAGCCACAAAGATGTCTT
1 TTTAACATAGATAGCCACAAAGA-ATCTT
* *
20158882 TTTCACATAGATAACCACAAATGAATCTT
1 TTTAACATAGATAGCCACAAA-GAATCTT
*
20158911 TTTAACAGAGATAGCCACAAAG
1 TTTAACATAGATAGCCACAAAG
20158933 GCATTCCTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
28 1 0.02
29 40 0.93
30 2 0.05
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.29
Consensus pattern (28 bp):
TTTAACATAGATAGCCACAAAGAATCTT
Found at i:20158943 original size:29 final size:29
Alignment explanation
Indices: 20158825--20159166 Score: 75
Period size: 29 Copynumber: 11.7 Consensus size: 29
20158815 AAGACATCCA
* * * *
20158825 TTTAATAGAGACAACCACAATGGCA-TCC
1 TTTAACAGAGATAGCCACAAAGGCATTCC
* * *
20158853 TTTAATATAGATAGCCACAAA-G-ATGTCTT
1 TTTAACAGAGATAGCCACAAAGGCAT-TC-C
* * * * * *
20158882 TTTCACATAGATAACCACAAATG-AATCTT
1 TTTAACAGAGATAGCCACAAAGGCATTC-C
20158911 TTTAACAGAGATAGCCACAAAGGCATTCC
1 TTTAACAGAGATAGCCACAAAGGCATTCC
* * *
20158940 TTTAACATTAAATACTTGCCACAAAGGCTTTCC
1 TTTAACA-GAGATA---GCCACAAAGGCATTCC
* * * *
20158973 CTT--CAGAGTATCGCCTCAAAGGCATTGCT
1 TTTAACAGAG-ATAGCCACAAAGGCATT-CC
* * **
20159002 TTTAAAAGATATTA-TTACAAAGGC-TTCC
1 TTTAACAGAGA-TAGCCACAAAGGCATTCC
* * *
20159030 ATTTAATAGAGATCA-CAACAAAGTC-TT-C
1 -TTTAACAGAGAT-AGCCACAAAGGCATTCC
* * *
20159058 TATTTACTAGAGATAGCCACAAATGC-TTCAT
1 T-TTAAC-AGAGATAGCCACAAAGGCATTC-C
* * * * **
20159089 TTTAACAGAGATAACTAGAAAGGCTTTTT
1 TTTAACAGAGATAGCCACAAAGGCATTCC
* *
20159118 TTTAACA-AGGATTGCCACAAAGG--TTTC
1 TTTAACAGA-GATAGCCACAAAGGCATTCC
20159145 TGTGTAACAGAGATAGCCACAA
1 T-T-TAACAGAGATAGCCACAA
20159167 TGCTCACTTT
Statistics
Matches: 232, Mismatches: 56, Indels: 51
0.68 0.17 0.15
Matches are distributed among these distances:
26 1 0.00
27 6 0.03
28 40 0.17
29 134 0.58
30 25 0.11
31 9 0.04
33 17 0.07
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (29 bp):
TTTAACAGAGATAGCCACAAAGGCATTCC
Found at i:20171474 original size:27 final size:27
Alignment explanation
Indices: 20171376--20171492 Score: 117
Period size: 28 Copynumber: 4.2 Consensus size: 27
20171366 GGTGTTACAG
*
20171376 ATAGTCCATACAGGCACTTGCTTGAAGA
1 ATAGTCCATACAGACACTTGCTTGAA-A
** * * *
20171404 ATAGTCTTTCCAGACTCTTTCTTGAAA
1 ATAGTCCATACAGACACTTGCTTGAAA
* * *
20171431 GATAGTCCATGCGGACAATTGCTTGAAA
1 -ATAGTCCATACAGACACTTGCTTGAAA
*
20171459 ATTGTCCATACAGACACTTGCTTGAAA
1 ATAGTCCATACAGACACTTGCTTGAAA
20171486 GATAGTC
1 -ATAGTC
20171493 GGTAAGGACT
Statistics
Matches: 69, Mismatches: 18, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
27 24 0.35
28 45 0.65
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.30
Consensus pattern (27 bp):
ATAGTCCATACAGACACTTGCTTGAAA
Found at i:20173828 original size:28 final size:27
Alignment explanation
Indices: 20173796--20173849 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
20173786 ATGAAAATGC
* *
20173796 AGGAAGGCTCTGTGGCTAATCTATGAAA
1 AGGAAGCCTCTGTGAC-AATCTATGAAA
*
20173824 AGGAAGCCTTTGTGACAATCTATGAA
1 AGGAAGCCTCTGTGACAATCTATGAA
20173850 GAAATTGTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (27 bp):
AGGAAGCCTCTGTGACAATCTATGAAA
Found at i:20180163 original size:23 final size:23
Alignment explanation
Indices: 20180136--20180183 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
20180126 TTATGTCACC
20180136 CCACACTTTATTTTGCACATTGT
1 CCACACTTTATTTTGCACATTGT
20180159 CCACACTTTATTTTGCACATTGT
1 CCACACTTTATTTTGCACATTGT
20180182 CC
1 CC
20180184 CCAATGTGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.21, C:0.29, G:0.08, T:0.42
Consensus pattern (23 bp):
CCACACTTTATTTTGCACATTGT
Found at i:20180345 original size:5 final size:5
Alignment explanation
Indices: 20180335--20180372 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
20180325 GATTTTTTAT
20180335 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAA
20180373 CACACAAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:20183567 original size:20 final size:21
Alignment explanation
Indices: 20183524--20183568 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
20183514 AGACTAATTT
*
20183524 AAAACAAATCAAAGAATTTGG
1 AAAAAAAATCAAAGAATTTGG
* *
20183545 AAAAAAAATTAAA-AATTTTG
1 AAAAAAAATCAAAGAATTTGG
20183565 AAAA
1 AAAA
20183569 TAGGGGTCGC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.64, C:0.04, G:0.09, T:0.22
Consensus pattern (21 bp):
AAAAAAAATCAAAGAATTTGG
Found at i:20190382 original size:42 final size:42
Alignment explanation
Indices: 20190323--20190406 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
20190313 AAATATCAAG
20190323 GTAACTCAGGTAAGAAATGATGGAAACTTTCTCTTTCTTCTT
1 GTAACTCAGGTAAGAAATGATGGAAACTTTCTCTTTCTTCTT
*
20190365 GTAACTCAGGTAAGAAATTATGGAAACTTTCTCTTTCTTCTT
1 GTAACTCAGGTAAGAAATGATGGAAACTTTCTCTTTCTTCTT
20190407 CAAGAAGAGA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (42 bp):
GTAACTCAGGTAAGAAATGATGGAAACTTTCTCTTTCTTCTT
Found at i:20191371 original size:58 final size:58
Alignment explanation
Indices: 20191233--20191416 Score: 194
Period size: 58 Copynumber: 3.2 Consensus size: 58
20191223 ATAAAAGTGA
* * * *
20191233 GCCTTTGTGGATATCTCTGTTAAATAGAGA-A-ATTTGTGGCTATCTCTG-TAAAAGAAC
1 GCCTTTGTGGCTATCTCTATTAAA-AGA-ACACCTTTGTGGCTATCTCTGTTAATAGAAC
* * * *
20191290 ACCTTTGTGGCTATCTCTATTAAAGGTACACCTTTGTGGCTATCTCTGTTAATGGAAC
1 GCCTTTGTGGCTATCTCTATTAAAAGAACACCTTTGTGGCTATCTCTGTTAATAGAAC
* * * * * * *
20191348 GCCTTTGTGGCTATCTTTCTTAAAAGAACACTTTTATGGCTATCTATGTTAATTGAAT
1 GCCTTTGTGGCTATCTCTATTAAAAGAACACCTTTGTGGCTATCTCTGTTAATAGAAC
20191406 GCCTTTGTGGC
1 GCCTTTGTGGC
20191417 AATACTCTGA
Statistics
Matches: 106, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
55 1 0.01
56 2 0.02
57 37 0.35
58 66 0.62
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (58 bp):
GCCTTTGTGGCTATCTCTATTAAAAGAACACCTTTGTGGCTATCTCTGTTAATAGAAC
Found at i:20191399 original size:29 final size:29
Alignment explanation
Indices: 20191234--20191399 Score: 176
Period size: 29 Copynumber: 5.8 Consensus size: 29
20191224 TAAAAGTGAG
*
20191234 CCTTTGTGGATATCTCTGTTAAATAGAGA-A
1 CCTTTGTGGCTATCTCTGTTAAA-AGA-ACA
*
20191264 -ATTTGTGGCTATCTCTG-TAAAAGAACA
1 CCTTTGTGGCTATCTCTGTTAAAAGAACA
* * *
20191291 CCTTTGTGGCTATCTCTATTAAAGGTACA
1 CCTTTGTGGCTATCTCTGTTAAAAGAACA
** *
20191320 CCTTTGTGGCTATCTCTGTTAATGGAACG
1 CCTTTGTGGCTATCTCTGTTAAAAGAACA
* *
20191349 CCTTTGTGGCTATCTTTCTTAAAAGAACA
1 CCTTTGTGGCTATCTCTGTTAAAAGAACA
* * *
20191378 CTTTTATGGCTATCTATGTTAA
1 CCTTTGTGGCTATCTCTGTTAA
20191400 TTGAATGCCT
Statistics
Matches: 114, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
26 1 0.01
27 4 0.04
28 19 0.17
29 90 0.79
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.39
Consensus pattern (29 bp):
CCTTTGTGGCTATCTCTGTTAAAAGAACA
Found at i:20191414 original size:87 final size:85
Alignment explanation
Indices: 20191265--20191444 Score: 202
Period size: 87 Copynumber: 2.1 Consensus size: 85
20191255 AATAGAGAAA
* * *
20191265 TTTGTGGCTATCTCTGTAAAAGAACACCTTTGTGGCTATCTCTATTAAAGGTACACCTTTGTGGC
1 TTTGTGGCTATCTCTGTAAAAGAACACCTTTATGGCTATCTATATTAAAGGAACACCTTTGTGGC
* * *
20191330 TAT-CTCTGTTAATGGAACGCC
66 AATACTCTG--AAGGGAAAGCC
* * ** **
20191351 TTTGTGGCTATCTTTCT-TAAAAGAACACTTTTATGGCTATCTATGTTAATTGAATGCCTTTGTG
1 TTTGTGGCTATC--TCTGTAAAAGAACACCTTTATGGCTATCTATATTAAAGGAACACCTTTGTG
20191415 GCAATACTCTGAAGGGAAAGCC
64 GCAATACTCTGAAGGGAAAGCC
20191437 TTTGTGGC
1 TTTGTGGC
20191445 GAGTACTGAA
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
86 29 0.37
87 42 0.53
88 8 0.10
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (85 bp):
TTTGTGGCTATCTCTGTAAAAGAACACCTTTATGGCTATCTATATTAAAGGAACACCTTTGTGGC
AATACTCTGAAGGGAAAGCC
Found at i:20191416 original size:29 final size:29
Alignment explanation
Indices: 20191265--20191416 Score: 128
Period size: 29 Copynumber: 5.3 Consensus size: 29
20191255 AATAGAGAAA
* * *
20191265 TTTGTGGCTATCTCTG-TAAAAGAACACC
1 TTTGTGGCTATCTATGTTAATAGAACGCC
* * * *
20191293 TTTGTGGCTATCTCTATTAA-AGGTACACC
1 TTTGTGGCTATCTATGTTAATA-GAACGCC
* *
20191322 TTTGTGGCTATCTCTGTTAATGGAACGCC
1 TTTGTGGCTATCTATGTTAATAGAACGCC
* * * * *
20191351 TTTGTGGCTATCTTTCTTAAAAGAACACT
1 TTTGTGGCTATCTATGTTAATAGAACGCC
* * *
20191380 TTTATGGCTATCTATGTTAATTGAATGCC
1 TTTGTGGCTATCTATGTTAATAGAACGCC
20191409 TTTGTGGC
1 TTTGTGGC
20191417 AATACTCTGA
Statistics
Matches: 100, Mismatches: 21, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
28 16 0.16
29 84 0.84
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.39
Consensus pattern (29 bp):
TTTGTGGCTATCTATGTTAATAGAACGCC
Found at i:20206576 original size:35 final size:35
Alignment explanation
Indices: 20206530--20206599 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
20206520 AGATATAAAA
20206530 ACAGAACTACCACTTTCCCTCATAAATAGCATATG
1 ACAGAACTACCACTTTCCCTCATAAATAGCATATG
20206565 ACAGAACTACCACTTTCCCTCATAAATAGCATATG
1 ACAGAACTACCACTTTCCCTCATAAATAGCATATG
20206600 TTTGGCTCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.37, C:0.29, G:0.09, T:0.26
Consensus pattern (35 bp):
ACAGAACTACCACTTTCCCTCATAAATAGCATATG
Found at i:20211061 original size:27 final size:27
Alignment explanation
Indices: 20211031--20211083 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
20211021 AATGATACTT
*
20211031 TTTCATATTGCGCTACAAAGGCATTCC
1 TTTCATATTACGCTACAAAGGCATTCC
*
20211058 TTTCATATTACGCTACAAATGCATTC
1 TTTCATATTACGCTACAAAGGCATTC
20211084 GTTTAGGGTT
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:0.28, C:0.25, G:0.11, T:0.36
Consensus pattern (27 bp):
TTTCATATTACGCTACAAAGGCATTCC
Found at i:20212784 original size:27 final size:25
Alignment explanation
Indices: 20212744--20212827 Score: 116
Period size: 27 Copynumber: 3.3 Consensus size: 25
20212734 TTTTATCATC
20212744 ATTTATTTTAAGTTTTTATATATATT
1 ATTTATTTTAAGTTTTT-TATATATT
*
20212770 ATTTATTTTTAAGTTGTTTTACATATT
1 ATTTA-TTTTAAGTT-TTTTATATATT
*
20212797 ATTTA-TTTAAATTTTTTATATATT
1 ATTTATTTTAAGTTTTTTATATATT
20212821 ATTTATT
1 ATTTATT
20212828 GTAAACTATT
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
24 15 0.29
25 8 0.15
26 5 0.10
27 21 0.40
28 3 0.06
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.65
Consensus pattern (25 bp):
ATTTATTTTAAGTTTTTTATATATT
Found at i:20212839 original size:24 final size:24
Alignment explanation
Indices: 20212792--20212876 Score: 72
Period size: 24 Copynumber: 3.7 Consensus size: 24
20212782 GTTGTTTTAC
* *
20212792 ATATTATTTATTTAAATTTTTTAT
1 ATATTATTTATTTAAATCTATTAT
20212816 ATATTATTTATTGTAAA-CTATTAT
1 ATATTATTTATT-TAAATCTATTAT
* * *
20212840 ATA-TATCT-TTCAAAT-TTTTAT
1 ATATTATTTATTTAAATCTATTAT
20212861 ATATATATTT-TTTAAA
1 ATAT-TATTTATTTAAA
20212877 ACGGTTTTAT
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
21 11 0.22
22 2 0.04
23 13 0.26
24 20 0.40
25 4 0.08
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (24 bp):
ATATTATTTATTTAAATCTATTAT
Found at i:20212913 original size:39 final size:37
Alignment explanation
Indices: 20212853--20212948 Score: 104
Period size: 38 Copynumber: 2.5 Consensus size: 37
20212843 TATCTTTCAA
*
20212853 ATTTTTATATATATATTT-TTTAAAACGGTTTTATATGTT
1 ATTTTT-TATAT-TATTTATTTTAAACGGTTTTAT-TGTT
**
20212892 ATTTTTTATATTATTTATTTTAAATTGTTTTATTGTT
1 ATTTTTTATATTATTTATTTTAAACGGTTTTATTGTT
*
20212929 ATTTATTTTTAGTTATTTAT
1 ATTT-TTTATA-TTATTTAT
20212949 ATTTTGTTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
37 13 0.26
38 23 0.46
39 14 0.28
ACGTcount: A:0.27, C:0.01, G:0.06, T:0.66
Consensus pattern (37 bp):
ATTTTTTATATTATTTATTTTAAACGGTTTTATTGTT
Found at i:20213244 original size:11 final size:11
Alignment explanation
Indices: 20213230--20213281 Score: 77
Period size: 11 Copynumber: 4.7 Consensus size: 11
20213220 ATTTCATTCA
20213230 AATTTCCTCTC
1 AATTTCCTCTC
*
20213241 AATTTCCTCTA
1 AATTTCCTCTC
20213252 AATTTCCTCTC
1 AATTTCCTCTC
*
20213263 AATTTTCTCTC
1 AATTTCCTCTC
*
20213274 AAATTCCT
1 AATTTCCT
20213282 TCCAAATTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 36 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (11 bp):
AATTTCCTCTC
Found at i:20213257 original size:33 final size:34
Alignment explanation
Indices: 20213227--20213299 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 34
20213217 CACATTTCAT
* *
20213227 TCAAATTTCCTCTCAATTTCC-TCTAAATTTCCTC
1 TCAAATTTCCTCTCAAATTCCTTCCAAATTT-CTC
*
20213261 TC-AATTTTCTCTCAAATTCCTTCCAAATTTCTC
1 TCAAATTTCCTCTCAAATTCCTTCCAAATTTCTC
20213294 TCAAAT
1 TCAAAT
20213300 CCATATTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 21 0.62
34 13 0.38
ACGTcount: A:0.26, C:0.30, G:0.00, T:0.44
Consensus pattern (34 bp):
TCAAATTTCCTCTCAAATTCCTTCCAAATTTCTC
Found at i:20213280 original size:22 final size:23
Alignment explanation
Indices: 20213227--20213299 Score: 98
Period size: 22 Copynumber: 3.3 Consensus size: 23
20213217 CACATTTCAT
*
20213227 TCAAATTTCCTCTCAATTTCCTC
1 TCAAATTTCCTCTCAATTTTCTC
20213250 T-AAATTTCCTCTCAATTTTCTC
1 TCAAATTTCCTCTCAATTTTCTC
*
20213272 TCAAA-TTCCT-TCCAAATTTCTC
1 TCAAATTTCCTCT-CAATTTTCTC
20213294 TCAAAT
1 TCAAAT
20213300 CCATATTTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
21 1 0.02
22 40 0.89
23 4 0.09
ACGTcount: A:0.26, C:0.30, G:0.00, T:0.44
Consensus pattern (23 bp):
TCAAATTTCCTCTCAATTTTCTC
Found at i:20213298 original size:11 final size:11
Alignment explanation
Indices: 20213227--20213299 Score: 71
Period size: 11 Copynumber: 6.5 Consensus size: 11
20213217 CACATTTCAT
20213227 TCAAATTTCCTC
1 TCAAATTT-CTC
20213239 TC-AATTTC-C
1 TCAAATTTCTC
20213248 TCTAAATTTCCTC
1 TC-AAATTT-CTC
*
20213261 TCAATTTTCTC
1 TCAAATTTCTC
*
20213272 TCAAATTCCT-
1 TCAAATTTCTC
20213282 TCCAAATTTCTC
1 T-CAAATTTCTC
20213294 TCAAAT
1 TCAAAT
20213300 CCATATTTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
9 3 0.06
10 2 0.04
11 34 0.67
12 9 0.18
13 3 0.06
ACGTcount: A:0.26, C:0.30, G:0.00, T:0.44
Consensus pattern (11 bp):
TCAAATTTCTC
Found at i:20214511 original size:7 final size:7
Alignment explanation
Indices: 20214499--20214524 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
20214489 TAGTCGATTG
20214499 GTATTTA
1 GTATTTA
20214506 GTATTTA
1 GTATTTA
20214513 GTATTTA
1 GTATTTA
20214520 GTATT
1 GTATT
20214525 ATGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:20215700 original size:25 final size:25
Alignment explanation
Indices: 20215666--20215923 Score: 228
Period size: 25 Copynumber: 10.9 Consensus size: 25
20215656 TATTTTGATA
20215666 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
*
20215691 TTATTTGATGTAATAAAATAGAAAT
1 TTATTTGATGTAATAAAATAGAAGT
* ** *
20215716 TTTTTTGA-GT--T-ATTTTG-A-T
1 TTATTTGATGTAATAAAATAGAAGT
20215735 ATTATTTGATGTAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATAGAAGT
*
20215761 TTATTTGATGTAATAAAATAGAAAT
1 TTATTTGATGTAATAAAATAGAAGT
* ** *
20215786 TTTTTTGA-GT--T-ATTTTG-A-T
1 TTATTTGATGTAATAAAATAGAAGT
20215805 ATTATTTGATGTAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATAGAAGT
*
20215831 TTATTTGATGTAATAAAATAGAAAT
1 TTATTTGATGTAATAAAATAGAAGT
* ** *
20215856 TTTTTTGA-GT--T-ATTTTG-A-T
1 TTATTTGATGTAATAAAATAGAAGT
20215875 ATTATTTGATGTAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATAGAAGT
20215901 TTATTTGATGTAATAAAATAGAA
1 TTATTTGATGTAATAAAATAGAA
20215924 ATTGTACGAT
Statistics
Matches: 185, Mismatches: 27, Indels: 42
0.73 0.11 0.17
Matches are distributed among these distances:
19 3 0.02
20 24 0.13
21 15 0.08
22 3 0.02
23 3 0.02
24 15 0.08
25 119 0.64
26 3 0.02
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:20215737 original size:70 final size:70
Alignment explanation
Indices: 20215622--20215926 Score: 558
Period size: 70 Copynumber: 4.4 Consensus size: 70
20215612 TATTTTGATA
* ****
20215622 TTATTTTATGTAATAAAATA-AAAAAAATTTGAGTTATTTTGATATTATTTGATGTAATAAAATA
1 TTATTTGATGTAATAAAATAGAAATTTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATA
20215686 GAAGT
66 GAAGT
20215691 TTATTTGATGTAATAAAATAGAAATTTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATA
1 TTATTTGATGTAATAAAATAGAAATTTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATA
20215756 GAAGT
66 GAAGT
20215761 TTATTTGATGTAATAAAATAGAAATTTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATA
1 TTATTTGATGTAATAAAATAGAAATTTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATA
20215826 GAAGT
66 GAAGT
20215831 TTATTTGATGTAATAAAATAGAAATTTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATA
1 TTATTTGATGTAATAAAATAGAAATTTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATA
20215896 GAAGT
66 GAAGT
20215901 TTATTTGATGTAATAAAATAGAAATT
1 TTATTTGATGTAATAAAATAGAAATT
20215927 GTACGATCAC
Statistics
Matches: 230, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
69 19 0.08
70 211 0.92
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (70 bp):
TTATTTGATGTAATAAAATAGAAATTTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATA
GAAGT
Found at i:20215741 original size:45 final size:49
Alignment explanation
Indices: 20215666--20215922 Score: 211
Period size: 45 Copynumber: 5.4 Consensus size: 49
20215656 TATTTTGATA
20215666 TTATTTGATGTAATAAAATAGA-AGTTTATTTGATGTAATAAAATAGAAAT
1 TTATTTGATGT-ATAAAATAGATA-TTTATTTGATGTAATAAAATAGAAAT
* ** * *
20215716 TTTTTTGA-GT-T-ATTTTGATA-TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTATAAAATAGATATTTATTTGATGTAATAAAATAGAAAT
* * ** * *
20215761 TTATTTGATGTAATAAAATAGAAATTTTTTTGA-GT--T-ATTTTGATA-
1 TTATTTGATGT-ATAAAATAGATATTTATTTGATGTAATAAAATAGAAAT
20215806 TTATTTGATGTAATAAAATAGA-AGTTTATTTGATGTAATAAAATAGAAAT
1 TTATTTGATGT-ATAAAATAGATA-TTTATTTGATGTAATAAAATAGAAAT
* ** * *
20215856 TTTTTTGA-GT-T-ATTTTGATA-TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTATAAAATAGATATTTATTTGATGTAATAAAATAGAAAT
20215901 TTATTTGATGTAATAAAATAGA
1 TTATTTGATGT-ATAAAATAGA
20215923 AATTGTACGA
Statistics
Matches: 160, Mismatches: 30, Indels: 35
0.71 0.13 0.16
Matches are distributed among these distances:
44 1 0.01
45 92 0.57
46 18 0.11
47 5 0.03
48 3 0.02
49 20 0.12
50 21 0.13
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (49 bp):
TTATTTGATGTATAAAATAGATATTTATTTGATGTAATAAAATAGAAAT
Found at i:20216924 original size:43 final size:43
Alignment explanation
Indices: 20216863--20217088 Score: 256
Period size: 43 Copynumber: 5.3 Consensus size: 43
20216853 GCTTTTTAGG
* *
20216863 CCTTTAGCGGCGCTTTTCCCACAAATGCCGCTAAAGACCAAGA
1 CCTTTAGCGGCACTTTTCCCACAAACGCCGCTAAAGACCAAGA
* * * * *
20216906 CCTTTAGCAGTACTTTTCCCATAAACGTCGCTAAAGACCATGA
1 CCTTTAGCGGCACTTTTCCCACAAACGCCGCTAAAGACCAAGA
* * * *
20216949 CCTTTAGCGGCGCTTTTTCCACAAGCGCCGCTAAAGACCAATA
1 CCTTTAGCGGCACTTTTCCCACAAACGCCGCTAAAGACCAAGA
* * *
20216992 CCTTTAGCGGCACTTTCCCCAAAAACGCCGCTAAAGAACAAGA
1 CCTTTAGCGGCACTTTTCCCACAAACGCCGCTAAAGACCAAGA
* * * * * *
20217035 CCTTTAGCGACGCTTTTTCTACAAACGCCACTAAAG-CTCATGA
1 CCTTTAGCGGCACTTTTCCCACAAACGCCGCTAAAGAC-CAAGA
20217078 CCTTTAGCGGC
1 CCTTTAGCGGC
20217089 GCCTCTATTA
Statistics
Matches: 149, Mismatches: 33, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
43 149 1.00
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.23
Consensus pattern (43 bp):
CCTTTAGCGGCACTTTTCCCACAAACGCCGCTAAAGACCAAGA
Found at i:20217018 original size:86 final size:86
Alignment explanation
Indices: 20216863--20217088 Score: 294
Period size: 86 Copynumber: 2.6 Consensus size: 86
20216853 GCTTTTTAGG
* * * * * * *
20216863 CCTTTAGCGGCGCTTTTCCCACAAATGCCGCTAAAGACCAAGACCTTTAGCAGTACTTTTCCCAT
1 CCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGACCAATACCTTTAGCGGCACTTTCCCCAA
* * *
20216928 AAACGTCGCTAAAGACCATGA
66 AAACGCCGCTAAAGAACAAGA
*
20216949 CCTTTAGCGGCGCTTTTTCCACAAGCGCCGCTAAAGACCAATACCTTTAGCGGCACTTTCCCCAA
1 CCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGACCAATACCTTTAGCGGCACTTTCCCCAA
20217014 AAACGCCGCTAAAGAACAAGA
66 AAACGCCGCTAAAGAACAAGA
* * *
20217035 CCTTTAGCGACGCTTTTTCTACAAACGCCACTAAAG-CTC-ATGACCTTTAGCGGC
1 CCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGAC-CAAT-ACCTTTAGCGGC
20217089 GCCTCTATTA
Statistics
Matches: 123, Mismatches: 15, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
85 3 0.02
86 120 0.98
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.23
Consensus pattern (86 bp):
CCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGACCAATACCTTTAGCGGCACTTTCCCCAA
AAACGCCGCTAAAGAACAAGA
Found at i:20217102 original size:86 final size:85
Alignment explanation
Indices: 20216863--20217153 Score: 270
Period size: 86 Copynumber: 3.4 Consensus size: 85
20216853 GCTTTTTAGG
* * * * * * * *
20216863 CCTTTAGCGGCGCTTTTCCCACAAATGCCGCTAAAGACCAAGACCTTTAGCAGTACTTTTC-CCA
1 CCTTTAGCGACGCTTTT-TCACAAACGCCACTAAAGACCAATACCTTTAGCGGCAC-TCTCACCA
* * *
20216927 TAAACGTCGCTAAAGACCATGA
64 AAAACGCCGCTAAAGAACATGA
* * * * *
20216949 CCTTTAGCGGCGCTTTTTCCACAAGCGCCGCTAAAGACCAATACCTTTAGCGGCACTTTCCCCAA
1 CCTTTAGCGACGCTTTTT-CACAAACGCCACTAAAGACCAATACCTTTAGCGGCACTCTCACCAA
*
20217014 AAACGCCGCTAAAGAACAAGA
65 AAACGCCGCTAAAGAACATGA
* *
20217035 CCTTTAGCGACGCTTTTTCTACAAACGCCACTAAAG-CTC-ATGACCTTTAGCGGCGC-CTCTAT
1 CCTTTAGCGACGCTTTTTC-ACAAACGCCACTAAAGAC-CAAT-ACCTTTAGCGGCACTCTC-AC
* *
20217097 TAAAAACGCCGCT--ATAACATTGA
62 CAAAAACGCCGCTAAAGAACA-TGA
*
20217120 CTTTTAGCGACGCTTTTTCACAAACGCCACTAAA
1 CCTTTAGCGACGCTTTTTCACAAACGCCACTAAA
20217154 AGCATAACTT
Statistics
Matches: 177, Mismatches: 21, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
84 20 0.11
85 30 0.17
86 127 0.72
ACGTcount: A:0.29, C:0.31, G:0.16, T:0.24
Consensus pattern (85 bp):
CCTTTAGCGACGCTTTTTCACAAACGCCACTAAAGACCAATACCTTTAGCGGCACTCTCACCAAA
AACGCCGCTAAAGAACATGA
Done.