Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A01
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 115637255
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5450143 characters in sequence are not A, C, G, or T
File 44 of 349
Found at i:12422114 original size:15 final size:15
Alignment explanation
Indices: 12422094--12422127 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
12422084 AGAATTTATA
*
12422094 TTTATATTTGTATTT
1 TTTATATTTGTAATT
*
12422109 TTTATATTTTTAATT
1 TTTATATTTGTAATT
12422124 TTTA
1 TTTA
12422128 AAATTTAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (15 bp):
TTTATATTTGTAATT
Found at i:12423543 original size:16 final size:16
Alignment explanation
Indices: 12423522--12423589 Score: 109
Period size: 16 Copynumber: 4.2 Consensus size: 16
12423512 TTTGGTTCGC
*
12423522 TGTATTGGATTAAAGG
1 TGTATTGGATTAGAGG
12423538 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
12423554 TGTAATGGATTAGAGG
1 TGTATTGGATTAGAGG
*
12423570 TGTATTGGAATAGAGG
1 TGTATTGGATTAGAGG
12423586 TGTA
1 TGTA
12423590 ATAGCAAATC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.29, C:0.00, G:0.35, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:12423846 original size:18 final size:17
Alignment explanation
Indices: 12423825--12423859 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12423815 TTATTATTAA
*
12423825 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
12423843 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
12423860 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:12423912 original size:157 final size:157
Alignment explanation
Indices: 12423719--12424025 Score: 578
Period size: 157 Copynumber: 2.0 Consensus size: 157
12423709 CCCTTATCAT
*
12423719 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTATTATCAA
1 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
*
12423784 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAA
66 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
12423849 TTTAATAAAATTCTTAATAATTAGCAG
131 TTTAATAAAATTCTTAATAATTAGCAG
* *
12423876 AAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAATTTTTAATAAGATTATTAATATCAA
1 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
12423941 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
66 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
12424006 TTTAATAAAATTCTTAATAA
131 TTTAATAAAATTCTTAATAA
12424026 CTAATATTCT
Statistics
Matches: 146, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 146 1.00
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.48
Consensus pattern (157 bp):
AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
TTTAATAAAATTCTTAATAATTAGCAG
Found at i:12423999 original size:16 final size:16
Alignment explanation
Indices: 12423962--12424003 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
12423952 TTAATCATAT
*
12423962 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
12423978 TT-AAATATATTATAA
1 TTAAAATATATTATAA
12423993 TTAAAATATAT
1 TTAAAATATAT
12424004 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:12424010 original size:14 final size:15
Alignment explanation
Indices: 12423971--12424012 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
12423961 TTTAAACATA
*
12423971 ATTATTATTAAATAT
1 ATTATAATTAAATAT
12423986 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
12424000 A-TATAATTTAATA
1 ATTATAATTAAATA
12424013 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:12431667 original size:15 final size:14
Alignment explanation
Indices: 12431619--12431677 Score: 59
Period size: 14 Copynumber: 4.3 Consensus size: 14
12431609 TTTTCTTCTG
*
12431619 ATTATATTTTAGTT
1 ATTATATTTTAATT
* *
12431633 ATTTATATTTAAAAT
1 A-TTATATTTTAATT
12431648 ATTATATTTTAATT
1 ATTATATTTTAATT
*
12431662 AGT-TATTTT-ATT
1 ATTATATTTTAATT
12431674 ATTA
1 ATTA
12431678 AGTTTTGTTA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
12 5 0.14
13 6 0.17
14 14 0.39
15 11 0.31
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (14 bp):
ATTATATTTTAATT
Found at i:12434972 original size:38 final size:38
Alignment explanation
Indices: 12434912--12434984 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 38
12434902 CTGAGCACAC
*
12434912 GCCCGTGTCGATATCGCTCCAGGTTTTCCAAATACGCG
1 GCCCATGTCGATATCGCTCCAGGTTTTCCAAATACGCG
* *
12434950 GCCCATGTGGATATTGCTCCAGGTTTTCCAAATAC
1 GCCCATGTCGATATCGCTCCAGGTTTTCCAAATAC
12434985 ACAGAAAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.29
Consensus pattern (38 bp):
GCCCATGTCGATATCGCTCCAGGTTTTCCAAATACGCG
Found at i:12436367 original size:16 final size:15
Alignment explanation
Indices: 12436337--12436366 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
12436327 GGATGGTGGG
12436337 GGGAATTCATTTTTT
1 GGGAATTCATTTTTT
12436352 GGGAATTCATTTTTT
1 GGGAATTCATTTTTT
12436367 TTTTCATCTT
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:0.20, C:0.07, G:0.20, T:0.53
Consensus pattern (15 bp):
GGGAATTCATTTTTT
Found at i:12439743 original size:17 final size:17
Alignment explanation
Indices: 12439720--12439761 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
12439710 GAGGCCTTAG
*
12439720 TATTGATT-TATTTATA
1 TATTGATTATATATATA
12439736 TGATTGATTATATATATA
1 T-ATTGATTATATATATA
12439754 TATTGATT
1 TATTGATT
12439762 GTAACTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 1 0.04
17 14 0.61
18 8 0.35
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (17 bp):
TATTGATTATATATATA
Found at i:12441235 original size:27 final size:27
Alignment explanation
Indices: 12441197--12441250 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
12441187 GCTTTGTGTA
12441197 GTCTAACCAAAACAATATATAATCTAC
1 GTCTAACCAAAACAATATATAATCTAC
12441224 GTCTAACCAAAACAATATATAATCTAC
1 GTCTAACCAAAACAATATATAATCTAC
12441251 TTATTTGCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.22, G:0.04, T:0.26
Consensus pattern (27 bp):
GTCTAACCAAAACAATATATAATCTAC
Found at i:12443799 original size:26 final size:24
Alignment explanation
Indices: 12443765--12443813 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
12443755 TAAATACAAA
* *
12443765 ATTTTAAAATATAATAAATCAAATAC
1 ATTTAAAAACATAA-AAA-CAAATAC
12443791 ATTTAAAAACATAAAAACAAATA
1 ATTTAAAAACATAAAAACAAATA
12443814 TTAAAACAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.29
25 3 0.14
26 12 0.57
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (24 bp):
ATTTAAAAACATAAAAACAAATAC
Found at i:12443879 original size:41 final size:40
Alignment explanation
Indices: 12443804--12443888 Score: 98
Period size: 41 Copynumber: 2.1 Consensus size: 40
12443794 TAAAAACATA
*
12443804 AAAACAAATATTAAAACAAGAAACAAATAAAAAATGATACT
1 AAAACAAATATTAAAACAAGAAACAAATAAAAAAT-ATAAT
* * * * **
12443845 AAAACAATTCTTAAAACAATACACAAATTGAAAATATAAT
1 AAAACAAATATTAAAACAAGAAACAAATAAAAAATATAAT
12443885 AAAA
1 AAAA
12443889 AGTGGTCATA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
40 8 0.22
41 29 0.78
ACGTcount: A:0.66, C:0.11, G:0.04, T:0.20
Consensus pattern (40 bp):
AAAACAAATATTAAAACAAGAAACAAATAAAAAATATAAT
Found at i:12449470 original size:31 final size:30
Alignment explanation
Indices: 12449435--12449492 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
12449425 AATAATACTT
*
12449435 ATAAATTAT-TGAAATTATATTTATATTTTTA
1 ATAAAATATGTGAAATT-TATTT-TATTTTTA
*
12449466 ATAAAATATGTTAAATTTATTTTATTT
1 ATAAAATATGTGAAATTTATTTTATTT
12449493 AAATAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 5 0.21
31 13 0.54
32 6 0.25
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (30 bp):
ATAAAATATGTGAAATTTATTTTATTTTTA
Found at i:12449500 original size:27 final size:26
Alignment explanation
Indices: 12449447--12449508 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
12449437 AAATTATTGA
*
12449447 AATTATATTTATATTTTTAATAAAAT
1 AATTAAATTTATATTTTTAATAAAAT
* * *
12449473 ATGTTAAATTTATTTTATTTAA-ATAAT
1 A-ATTAAATTTATATT-TTTAATAAAAT
12449500 AATTAAATT
1 AATTAAATT
12449509 ACATGTATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
26 8 0.28
27 16 0.55
28 5 0.17
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
AATTAAATTTATATTTTTAATAAAAT
Found at i:12450089 original size:42 final size:42
Alignment explanation
Indices: 12450037--12450120 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
12450027 TATCTAAAAT
* * *
12450037 AATATAAAATATTATATTACTAAGATTCAAATTAGAAATAAA
1 AATATAAAATATTATATTAATAAGATTAAAATTAAAAATAAA
*
12450079 AATATAAAATATTATATTAATAAGGTTAAAATTAAAAATAAA
1 AATATAAAATATTATATTAATAAGATTAAAATTAAAAATAAA
12450121 TAATCTTTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (42 bp):
AATATAAAATATTATATTAATAAGATTAAAATTAAAAATAAA
Found at i:12450234 original size:16 final size:15
Alignment explanation
Indices: 12450213--12450257 Score: 65
Period size: 14 Copynumber: 3.0 Consensus size: 15
12450203 TTTTTAATAT
12450213 AAATTTAGTACTTATA
1 AAATTTAGTACTTA-A
*
12450229 AAATTTAGCAC-TAA
1 AAATTTAGTACTTAA
12450243 AAATTTAGTACTTAA
1 AAATTTAGTACTTAA
12450258 TTTTTTCAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 11 0.42
15 5 0.19
16 10 0.38
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.38
Consensus pattern (15 bp):
AAATTTAGTACTTAA
Found at i:12452170 original size:9 final size:7
Alignment explanation
Indices: 12452143--12452169 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
12452133 TTTATCTCAT
12452143 ATATATC
1 ATATATC
12452150 ATATATC
1 ATATATC
12452157 ATATATC
1 ATATATC
12452164 ATATAT
1 ATATAT
12452170 ACTATTACAA
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:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (7 bp):
ATATATC
Found at i:12455612 original size:20 final size:20
Alignment explanation
Indices: 12455587--12455624 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12455577 TTAAAATTGA
12455587 CAAAAATAAAAAAATGTTTT
1 CAAAAATAAAAAAATGTTTT
* *
12455607 CAAAAATTAAAAATTGTT
1 CAAAAATAAAAAAATGTT
12455625 AAAATTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (20 bp):
CAAAAATAAAAAAATGTTTT
Found at i:12463422 original size:24 final size:24
Alignment explanation
Indices: 12463390--12463439 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
12463380 CTACAGAAGA
* *
12463390 AAATAACAAAGATTTTATGCTAAT
1 AAATAACAAAGATATTATACTAAT
*
12463414 AAATAACAAATATATTATACTAAT
1 AAATAACAAAGATATTATACTAAT
12463438 AA
1 AA
12463440 TTTTTAAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.32
Consensus pattern (24 bp):
AAATAACAAAGATATTATACTAAT
Found at i:12473933 original size:18 final size:19
Alignment explanation
Indices: 12473906--12473943 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
12473896 TAAATAAATA
*
12473906 ATTATATATTTTTAAAGAC
1 ATTATATATTTTGAAAGAC
12473925 ATTAT-TATTTTGAAAGAC
1 ATTATATATTTTGAAAGAC
12473943 A
1 A
12473944 CCTATTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (19 bp):
ATTATATATTTTGAAAGAC
Found at i:12476892 original size:92 final size:92
Alignment explanation
Indices: 12476734--12476935 Score: 305
Period size: 92 Copynumber: 2.2 Consensus size: 92
12476724 TCCAACCCAT
* * ** * * *
12476734 TGCAACTTCGGGTAGATATTTTTCTCTTCAACCTATTTCACTGCAACTTCAGGGAGATAAGATCT
1 TGCAACTTTGGGGAGATATTCGTATCCTCAACCTATTCCACTGCAACTTCAGGGAGATAAGATCT
12476799 GTAGCTTATAGCTTTAGTTTATTCCAC
66 GTAGCTTATAGCTTTAGTTTATTCCAC
*
12476826 TGCAACTTTGGGGAGATATTCGTATCCTCAACCTATTCCACTGCAACTTCAGGGAGATAAGGTCT
1 TGCAACTTTGGGGAGATATTCGTATCCTCAACCTATTCCACTGCAACTTCAGGGAGATAAGATCT
*
12476891 GTAGCTTGTAGCTTTAGTTTATTCCAC
66 GTAGCTTATAGCTTTAGTTTATTCCAC
* *
12476918 TGTAACTTTAGGGAGATA
1 TGCAACTTTGGGGAGATA
12476936 AGACTTGCTG
Statistics
Matches: 99, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
92 99 1.00
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (92 bp):
TGCAACTTTGGGGAGATATTCGTATCCTCAACCTATTCCACTGCAACTTCAGGGAGATAAGATCT
GTAGCTTATAGCTTTAGTTTATTCCAC
Found at i:12477097 original size:89 final size:89
Alignment explanation
Indices: 12476996--12477252 Score: 279
Period size: 89 Copynumber: 2.9 Consensus size: 89
12476986 GGACTTGTCG
* *
12476996 CTTCAATCTGCTCCACTCCAACTTCAAGGAGATAAGATTTGTAATCTTCAATCTGCTCCACTATA
1 CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGT-AGCTTCAATCTGCTCCACTATA
** ***
12477061 ACT-TCA-AGTAGATAAGTTTTGTGA-
65 ACTAT-AGAG-AGATAAAATTTACCAT
* * * *
12477085 CTTCAA-CTTGCTCCATTGCAACTTCAAGGAGATAAGGTTTATAGCTTTAATCTGCTCCACTATA
1 CTTCAATC-TGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAGCTTCAATCTGCTCCACTATA
12477149 ACTATAGAGAGATAAAATTTACCAT
65 ACTATAGAGAGATAAAATTTACCAT
* * * * * **
12477174 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTGGCTTCAACCTACTCCATTGCAA
1 CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAGCTTCAATCTGCTCCACTATAA
*
12477239 CTTTAGAGAGATAA
66 CTATAGAGAGATAA
12477253 GGTTTATAAC
Statistics
Matches: 140, Mismatches: 23, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
88 35 0.25
89 104 0.74
90 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (89 bp):
CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAGCTTCAATCTGCTCCACTATAA
CTATAGAGAGATAAAATTTACCAT
Found at i:12477108 original size:44 final size:45
Alignment explanation
Indices: 12476996--12477215 Score: 216
Period size: 45 Copynumber: 4.9 Consensus size: 45
12476986 GGACTTGTCG
*
12476996 CTTCAATCTGCTCCACTCCAACTTCAAGGAGATAAGATTTGTAAT
1 CTTCAATCTGCTCCACTACAACTTCAAGGAGATAAGATTTGTAAT
* * * *
12477041 CTTCAATCTGCTCCACTATAACTTCAAGTAGATAAGTTTTGTGA-
1 CTTCAATCTGCTCCACTACAACTTCAAGGAGATAAGATTTGTAAT
* * * * *
12477085 CTTCAA-CTTGCTCCATTGCAACTTCAAGGAGATAAGGTTTAT-AG
1 CTTCAATC-TGCTCCACTACAACTTCAAGGAGATAAGATTTGTAAT
* * * ***
12477129 CTTTAATCTGCTCCACTATAAC-T-ATAGAGAGATAAAATTTACCAT
1 CTTCAATCTGCTCCACTACAACTTCA-AG-GAGATAAGATTTGTAAT
* *
12477174 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGT
1 CTTCAATCTGCTCCACTACAACTTCAAGGAGATAAGATTTGT
12477216 GGCTTCAACC
Statistics
Matches: 141, Mismatches: 26, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
42 1 0.01
43 5 0.04
44 61 0.43
45 71 0.50
46 2 0.01
47 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.33
Consensus pattern (45 bp):
CTTCAATCTGCTCCACTACAACTTCAAGGAGATAAGATTTGTAAT
Found at i:12477250 original size:44 final size:44
Alignment explanation
Indices: 12476964--12477307 Score: 225
Period size: 44 Copynumber: 7.6 Consensus size: 44
12476954 TTAATCCGAC
* * * *
12476964 CCACTGCAACTTTAGAG-GTATAGGACTTGTCGCTTCAATCTGCT
1 CCACTGCAACTTCAGAGAG-ATAAGATTTGTAGCTTCAATCTGCT
* *
12477008 CCACTCCAACTTCA-AGGAGATAAGATTTGTAATCTTCAATCTGCT
1 CCACTGCAACTTCAGA-GAGATAAGATTTGT-AGCTTCAATCTGCT
** *
12477053 CCACTATAACTTCA-AGTAGATAAGTTTTGT-GACTTCAA-CTTGCT
1 CCACTGCAACTTCAGAG-AGATAAGATTTGTAG-CTTCAATC-TGCT
* * * *
12477097 CCATTGCAACTTCA-AGGAGATAAGGTTTATAGCTTTAATCTGCT
1 CCACTGCAACTTCAGA-GAGATAAGATTTGTAGCTTCAATCTGCT
** * ** *
12477141 CCACTATAACTAT-AGAGAGATAAAATTTACCATCTTCAATCTGCT
1 CCACTGCAACT-TCAGAGAGATAAGATTT-GTAGCTTCAATCTGCT
* * * *
12477186 CCACTGCAACTTCAGGGAGATAAGATTTGTGGCTTCAACCTACT
1 CCACTGCAACTTCAGAGAGATAAGATTTGTAGCTTCAATCTGCT
* * * *
12477230 CCATTGCAACTTTAGAGAGATAAGGTTTATAACTTGTAGCTTTAATCTACT
1 CCACTGCAACTTCAGAGAGATAA-G---AT---TTGTAGCTTCAATCTGCT
* * *
12477281 CCACTACAACTTCGGGGAGATAAGATT
1 CCACTGCAACTTCAGAGAGATAAGATT
12477308 CACCAAGATG
Statistics
Matches: 234, Mismatches: 46, Indels: 40
0.73 0.14 0.12
Matches are distributed among these distances:
43 2 0.01
44 116 0.50
45 78 0.33
47 2 0.01
48 2 0.01
50 1 0.00
51 33 0.14
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (44 bp):
CCACTGCAACTTCAGAGAGATAAGATTTGTAGCTTCAATCTGCT
Found at i:12489732 original size:29 final size:29
Alignment explanation
Indices: 12489686--12489744 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
12489676 TTTTATTATC
*
12489686 TAACATCTATCTTCGTACATTGAGGGCAA
1 TAACATCTATCTTCGTACATTGACGGCAA
*
12489715 TAACATCTATCTTTGTACATTGACGGCAA
1 TAACATCTATCTTCGTACATTGACGGCAA
12489744 T
1 T
12489745 GTACATCTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (29 bp):
TAACATCTATCTTCGTACATTGACGGCAA
Found at i:12499874 original size:18 final size:18
Alignment explanation
Indices: 12499851--12499888 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
12499841 TTAATTAATT
*
12499851 TTTTTAAATTTTTAAAAA
1 TTTTTAAAATTTTAAAAA
*
12499869 TTTTTAAAATTTTAATAA
1 TTTTTAAAATTTTAAAAA
12499887 TT
1 TT
12499889 CTAATTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTTAAAATTTTAAAAA
Found at i:12502194 original size:21 final size:20
Alignment explanation
Indices: 12502145--12502202 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
12502135 TTAAATAATT
12502145 ATGTTTATTTTATTTAAATTTA
1 ATGTTTATTTT-TTT-AATTTA
*
12502167 A-ATTTATTTTTTTAATTTA
1 ATGTTTATTTTTTTAATTTA
12502186 ATGTATTATTTATTTTA
1 ATGT-TTATTT-TTTTA
12502203 TTATTTTCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 7 0.23
20 4 0.13
21 14 0.45
22 6 0.19
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (20 bp):
ATGTTTATTTTTTTAATTTA
Found at i:12507341 original size:2 final size:2
Alignment explanation
Indices: 12507334--12507360 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12507324 TCACATTAAC
12507334 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
12507361 TCTGCTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12522577 original size:57 final size:58
Alignment explanation
Indices: 12522489--12522601 Score: 192
Period size: 57 Copynumber: 2.0 Consensus size: 58
12522479 TCATTGCAAC
**
12522489 AAGTAATTGGATACCTTACCATTTAACATACACGTAATTTTGTGGGT-TTTTTTTTAT
1 AAGTAATTGGATACCTTACCATTTAACATACAAATAATTTTGTGGGTGTTTTTTTTAT
*
12522546 AAGTAATTGGATACCTTACCATTTAACATACAAATGATTTTGTGGGTGTTTTTTTT
1 AAGTAATTGGATACCTTACCATTTAACATACAAATAATTTTGTGGGTGTTTTTTTT
12522602 TTTTTTTGGA
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
57 44 0.85
58 8 0.15
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (58 bp):
AAGTAATTGGATACCTTACCATTTAACATACAAATAATTTTGTGGGTGTTTTTTTTAT
Found at i:12531014 original size:31 final size:31
Alignment explanation
Indices: 12530979--12531038 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 31
12530969 CAATCCAGTG
12530979 ACTTAAAT-AAAAGTTTTCA-AATAGTTTAGCT
1 ACTTAAATGAAAA-TTTT-AGAATAGTTTAGCT
12531010 ACTTAAATGAAAATTTTAGAATAGTTTAG
1 ACTTAAATGAAAATTTTAGAATAGTTTAG
12531039 TGACAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 1 0.04
31 22 0.81
32 4 0.15
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (31 bp):
ACTTAAATGAAAATTTTAGAATAGTTTAGCT
Found at i:12534433 original size:144 final size:143
Alignment explanation
Indices: 12534173--12534457 Score: 498
Period size: 144 Copynumber: 2.0 Consensus size: 143
12534163 TTTGTTTACC
12534173 AACATTACAAATTTTCATGTGAATGGTCATTAGCAATCCCTTTGGAATGAGGTTCTTCCGCCAAA
1 AACATTACAAATTTTCATGTGAATGGTCATTAGCAATCCCTTTGGAATGAGGTTCTTCCGCCAAA
* *
12534238 GATTAAAGAATTTTTATAAAGATTATTATGTGGTTTTGTGGATTGTATTAGTCAATTTTTAACTC
66 GATTAAAGAATTTTTATAAAGATTATTATGTGGTTTTATGCATTGTATTAGTCAATTTTTAA-TC
12534303 ATGGGGTGAATACT
130 ATGGGGTGAATACT
* * *
12534317 AACATTACAGATTTTCATGTGAATGGTCATTAGTAATCCCTTTGGAATGAGGTTTTTCCGCCAAA
1 AACATTACAAATTTTCATGTGAATGGTCATTAGCAATCCCTTTGGAATGAGGTTCTTCCGCCAAA
* *
12534382 GATTAAAGAATTTTTATAGAGATTATTATGTGGTTTTATGCATTGTATTAGTCAATTTTTGATCA
66 GATTAAAGAATTTTTATAAAGATTATTATGTGGTTTTATGCATTGTATTAGTCAATTTTTAATCA
12534447 TGGGGTGAATA
131 TGGGGTGAATA
12534458 TTGACCCTTA
Statistics
Matches: 134, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
143 14 0.10
144 120 0.90
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.40
Consensus pattern (143 bp):
AACATTACAAATTTTCATGTGAATGGTCATTAGCAATCCCTTTGGAATGAGGTTCTTCCGCCAAA
GATTAAAGAATTTTTATAAAGATTATTATGTGGTTTTATGCATTGTATTAGTCAATTTTTAATCA
TGGGGTGAATACT
Found at i:12535358 original size:25 final size:25
Alignment explanation
Indices: 12535321--12535370 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
12535311 GTGGGGAGTT
*
12535321 AGGATTTGGGTGTATTAGGTAAGTC
1 AGGACTTGGGTGTATTAGGTAAGTC
*
12535346 AGGACTTGTGTGTATTAGGTAAGTC
1 AGGACTTGGGTGTATTAGGTAAGTC
12535371 TTATGGCTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.24, C:0.06, G:0.34, T:0.36
Consensus pattern (25 bp):
AGGACTTGGGTGTATTAGGTAAGTC
Found at i:12536198 original size:29 final size:29
Alignment explanation
Indices: 12536165--12536220 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
12536155 TTTGGTCTTT
*
12536165 ATATTTGTATAATGTTATTAATTAGTTTA
1 ATATTTGTATAATGTAATTAATTAGTTTA
* *
12536194 ATATTTTTGTAATGTAATTAATTAGTT
1 ATATTTGTATAATGTAATTAATTAGTT
12536221 AAACTAGTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (29 bp):
ATATTTGTATAATGTAATTAATTAGTTTA
Found at i:12537345 original size:29 final size:30
Alignment explanation
Indices: 12537311--12537369 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
12537301 CTTGGTTTGA
12537311 TGTGTAATTTTATACA-AAAATTTTGATTT
1 TGTGTAATTTTATACATAAAATTTTGATTT
*
12537340 TGTGTAATTTTATATATAAAATTTTGATTT
1 TGTGTAATTTTATACATAAAATTTTGATTT
12537370 GATTTTATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 15 0.54
30 13 0.46
ACGTcount: A:0.34, C:0.02, G:0.10, T:0.54
Consensus pattern (30 bp):
TGTGTAATTTTATACATAAAATTTTGATTT
Found at i:12543586 original size:42 final size:42
Alignment explanation
Indices: 12543535--12543628 Score: 143
Period size: 42 Copynumber: 2.2 Consensus size: 42
12543525 AAGGCCTGAG
* *
12543535 ACACGGGTGTGTCTAGAGCCGTGTGAGGCACACGGCCTGTTC
1 ACACGGGTGTGTCTAGAACCGAGTGAGGCACACGGCCTGTTC
* * *
12543577 ACATGGGTGTGTTTGGAACCGAGTGAGGCACACGGCCTGTTC
1 ACACGGGTGTGTCTAGAACCGAGTGAGGCACACGGCCTGTTC
12543619 ACACGGGTGT
1 ACACGGGTGT
12543629 TTGACCCCTG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.18, C:0.23, G:0.36, T:0.22
Consensus pattern (42 bp):
ACACGGGTGTGTCTAGAACCGAGTGAGGCACACGGCCTGTTC
Found at i:12545784 original size:5 final size:5
Alignment explanation
Indices: 12545774--12545810 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
12545764 GTTATCTAAA
12545774 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TT
12545811 TCTCTCTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:12550385 original size:16 final size:16
Alignment explanation
Indices: 12550364--12550411 Score: 78
Period size: 16 Copynumber: 3.0 Consensus size: 16
12550354 GCTAATGGGA
12550364 ATATATCAATATATAT
1 ATATATCAATATATAT
12550380 ATATATCAATATATAT
1 ATATATCAATATATAT
* *
12550396 ATATATAAATACATAT
1 ATATATCAATATATAT
12550412 GAAAGTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATATCAATATATAT
Found at i:12552394 original size:79 final size:81
Alignment explanation
Indices: 12552289--12552452 Score: 226
Period size: 79 Copynumber: 2.0 Consensus size: 81
12552279 TTTTTATCAT
* * * * *
12552289 TTTTGGGGAGAAAATTATAATTTTACCATTATTAATTTAAAATTTTATAAATTATAAAAG-GCTT
1 TTTTGGGGAGAAAACTACAATTTTACCATAACTAATTTAAAATTTTATAAATTATAAAAGATC-T
*
12552353 AAATTAAAAATTTATTA
65 AAATTAAAAATTTACTA
*
12552370 TTTTGGGG-G-AAACTACAATTTTACCATAACTAATTTAAAATTTTATAGATTATAAAAGATCTA
1 TTTTGGGGAGAAAACTACAATTTTACCATAACTAATTTAAAATTTTATAAATTATAAAAGATCTA
*
12552433 AATTGAAAATTTACTA
66 AATTAAAAATTTACTA
12552449 TTTT
1 TTTT
12552453 AAAGGAGATG
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
79 64 0.86
80 2 0.03
81 8 0.11
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.42
Consensus pattern (81 bp):
TTTTGGGGAGAAAACTACAATTTTACCATAACTAATTTAAAATTTTATAAATTATAAAAGATCTA
AATTAAAAATTTACTA
Found at i:12555335 original size:31 final size:29
Alignment explanation
Indices: 12555290--12555384 Score: 97
Period size: 31 Copynumber: 3.2 Consensus size: 29
12555280 TTCTTTAAAT
* *
12555290 ATGTATAATTGAATCAAAATTAAAGTTTC
1 ATGTATAATTGAATCAAAATCAAAGGTTC
12555319 ATGTATATATTTGAATCAAAATCAAAGGTTC
1 ATGTATA-A-TTGAATCAAAATCAAAGGTTC
*
12555350 ATATGTATAATT-ACA-CCAAATCAAA-GTTC
1 --ATGTATAATTGA-ATCAAAATCAAAGGTTC
12555379 ATGTAT
1 ATGTAT
12555385 GATTTTGAGA
Statistics
Matches: 58, Mismatches: 3, Indels: 12
0.79 0.04 0.16
Matches are distributed among these distances:
27 6 0.10
29 11 0.19
30 11 0.19
31 22 0.38
32 1 0.02
33 7 0.12
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.36
Consensus pattern (29 bp):
ATGTATAATTGAATCAAAATCAAAGGTTC
Found at i:12557815 original size:19 final size:20
Alignment explanation
Indices: 12557770--12557822 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
12557760 ATAAACTTAA
12557770 AAATTATAAAAAAAATCTAAT
1 AAATTAT-AAAAAAATCTAAT
*
12557791 ATATTATAAAAAAAT-T-AT
1 AAATTATAAAAAAATCTAAT
12557809 CAAATTAATAAAAA
1 -AAATT-ATAAAAA
12557823 CATATTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 2 0.07
19 5 0.18
20 15 0.54
21 6 0.21
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (20 bp):
AAATTATAAAAAAATCTAAT
Found at i:12561929 original size:9 final size:9
Alignment explanation
Indices: 12561837--12561929 Score: 71
Period size: 10 Copynumber: 9.8 Consensus size: 9
12561827 ATTCATAACA
12561837 ATAAAAATAT
1 ATAAAAAT-T
*
12561847 ATTAAAATT
1 ATAAAAATT
*
12561856 CTTAAAAACTT
1 -ATAAAAA-TT
*
12561867 ATAAAAATC
1 ATAAAAATT
12561876 ATATAAAATT
1 ATA-AAAATT
*
12561886 AT-TAAATT
1 ATAAAAATT
*
12561894 AAAAAAATT
1 ATAAAAATT
*
12561903 AATATAAACTT
1 -ATA-AAAATT
12561914 ATAAAAATT
1 ATAAAAATT
12561923 ATAAAAA
1 ATAAAAA
12561930 AAACATAAAA
Statistics
Matches: 65, Mismatches: 12, Indels: 13
0.72 0.13 0.14
Matches are distributed among these distances:
8 6 0.09
9 22 0.34
10 30 0.46
11 7 0.11
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (9 bp):
ATAAAAATT
Found at i:12561937 original size:28 final size:28
Alignment explanation
Indices: 12561839--12561939 Score: 80
Period size: 28 Copynumber: 3.5 Consensus size: 28
12561829 TCATAACAAT
* *
12561839 AAAAATATATTAAAATTCTTAAAAACTTATA
1 AAAAAAATA-TAAAATT-ATAAAAA-TTATA
** *
12561870 AAAATCATATAAAATTAT-TAAATTA-A
1 AAAAAAATATAAAATTATAAAAATTATA
*
12561896 AAAAATTAATATAAACTTATAAAAATTATA
1 AAAAA--AATATAAAATTATAAAAATTATA
*
12561926 AAAAAAACATAAAA
1 AAAAAAATATAAAA
12561940 ACTTGAATTG
Statistics
Matches: 56, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
26 5 0.09
27 3 0.05
28 21 0.38
29 7 0.12
30 13 0.23
31 7 0.12
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (28 bp):
AAAAAAATATAAAATTATAAAAATTATA
Found at i:12562370 original size:9 final size:9
Alignment explanation
Indices: 12562358--12562559 Score: 58
Period size: 9 Copynumber: 21.4 Consensus size: 9
12562348 TTTATGTTTT
12562358 TTTTAATAA
1 TTTTAATAA
*
12562367 TTTTTATAA
1 TTTTAATAA
*
12562376 GTTTATATCAA
1 TTTTA-AT-AA
12562387 TTTTAAT--
1 TTTTAATAA
*
12562394 TTTTTATAA
1 TTTTAATAA
*
12562403 GTTTTTAAGAA
1 --TTTTAATAA
12562414 TTTTAATACA
1 TTTTAATA-A
*
12562424 TTTTTATAAAA
1 -TTTTA-ATAA
*
12562435 TTTTAAATATG
1 TTTT-AATA-A
*
12562446 TTTTATTAA
1 TTTTAATAA
12562455 TTTT-ATAAA
1 TTTTAAT-AA
12562464 TTTT-ATAAA
1 TTTTAAT-AA
*
12562473 ATTT-ATAA
1 TTTTAATAA
** *
12562481 GTTTTTTTCA
1 -TTTTAATAA
*
12562491 TTTTATTATA
1 TTTTAATA-A
12562501 TTTTAATAA
1 TTTTAATAA
*
12562510 GTTTATATAA
1 TTTTA-ATAA
* * *
12562520 GTTTATTAT
1 TTTTAATAA
*
12562529 TTTTAAAATA
1 TTTTAATA-A
12562539 TATTTAAT--
1 T-TTTAATAA
12562547 TTTTAATAA
1 TTTTAATAA
12562556 TTTT
1 TTTT
12562560 TATACTTTTT
Statistics
Matches: 144, Mismatches: 29, Indels: 40
0.68 0.14 0.19
Matches are distributed among these distances:
7 12 0.08
8 4 0.03
9 63 0.44
10 34 0.24
11 29 0.20
12 2 0.01
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.58
Consensus pattern (9 bp):
TTTTAATAA
Found at i:12562405 original size:27 final size:28
Alignment explanation
Indices: 12562358--12562432 Score: 89
Period size: 27 Copynumber: 2.6 Consensus size: 28
12562348 TTTATGTTTT
*
12562358 TTTTAATAATTTTTATAAGTTTATATCAA
1 TTTTAAT-ATTTTTATAAGTTTATAACAA
* *
12562387 TTTTAAT-TTTTTATAAGTTTTTAAGAA
1 TTTTAATATTTTTATAAGTTTATAACAA
12562414 TTTTAATACATTTTTATAA
1 TTTTAAT--ATTTTTATAA
12562433 AATTTTAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
27 24 0.60
29 7 0.17
30 9 0.22
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.57
Consensus pattern (28 bp):
TTTTAATATTTTTATAAGTTTATAACAA
Found at i:12562469 original size:18 final size:18
Alignment explanation
Indices: 12562446--12562537 Score: 69
Period size: 18 Copynumber: 5.1 Consensus size: 18
12562436 TTTAAATATG
12562446 TTTTATTAATTTTATAAA
1 TTTTATTAATTTTATAAA
* * *
12562464 TTTTATAAAATTTATAAG
1 TTTTATTAATTTTATAAA
* * *
12562482 TTTTTTTCATTTTATTATA
1 TTTTATTAATTTTA-TAAA
* *
12562501 TTTTAATAAGTTTATATAA
1 TTTTATTAATTTTATA-AA
* *
12562520 GTTTATTATTTTTA-AAA
1 TTTTATTAATTTTATAAA
12562537 T
1 T
12562538 ATATTTAATT
Statistics
Matches: 53, Mismatches: 19, Indels: 5
0.69 0.25 0.06
Matches are distributed among these distances:
17 2 0.04
18 28 0.53
19 23 0.43
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (18 bp):
TTTTATTAATTTTATAAA
Found at i:12563568 original size:20 final size:21
Alignment explanation
Indices: 12563525--12563569 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
12563515 ACTTTAATTA
*
12563525 TAAAAAAAAATAAACTTAATT
1 TAAAAAAAAATAAACTTAAGT
* *
12563546 TAAAAAAATATATAC-TAAGT
1 TAAAAAAAAATAAACTTAAGT
12563566 TAAA
1 TAAA
12563570 TCTATTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.29
Consensus pattern (21 bp):
TAAAAAAAAATAAACTTAAGT
Found at i:12575279 original size:28 final size:27
Alignment explanation
Indices: 12575247--12575299 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
12575237 TATTAACCCT
* *
12575247 TATAAAAATACATATATTATATAATAAA
1 TATAAAAATAAACATATTATA-AATAAA
12575275 TATAAAAATAAACATATTATAAATA
1 TATAAAAATAAACATATTATAAATA
12575300 TTATTATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (27 bp):
TATAAAAATAAACATATTATAAATAAA
Found at i:12576940 original size:4 final size:4
Alignment explanation
Indices: 12576926--12576957 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
12576916 CTATTACCAT
12576926 AAAC AAAAC AAAC AAAC AAAC AAAC AAAC AAA
1 AAAC -AAAC AAAC AAAC AAAC AAAC AAAC AAA
12576958 TCGAATCTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:12579401 original size:2 final size:2
Alignment explanation
Indices: 12579394--12579418 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12579384 ATGATGAACA
12579394 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
12579419 ATATACCATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12583904 original size:30 final size:30
Alignment explanation
Indices: 12583865--12583925 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
12583855 ACTAACAAAG
*
12583865 TGTATGATATATCATCAAATTCTACATTTT
1 TGTAGGATATATCATCAAATTCTACATTTT
12583895 TGTAGGATATATCATCAAATTCTACATTTT
1 TGTAGGATATATCATCAAATTCTACATTTT
12583925 T
1 T
12583926 TGTTTTGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (30 bp):
TGTAGGATATATCATCAAATTCTACATTTT
Found at i:12584936 original size:39 final size:39
Alignment explanation
Indices: 12584884--12584961 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
12584874 TTGCTCATCA
12584884 AAACCCAAAGTACTAAGCTGTACTTTTTTAGTTTTTTTC
1 AAACCCAAAGTACTAAGCTGTACTTTTTTAGTTTTTTTC
*
12584923 AAACCCAAAGTACTAAGCTTTACTTTTTTAGTTTTTTTC
1 AAACCCAAAGTACTAAGCTGTACTTTTTTAGTTTTTTTC
12584962 TTAGTGACCA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.28, C:0.18, G:0.09, T:0.45
Consensus pattern (39 bp):
AAACCCAAAGTACTAAGCTGTACTTTTTTAGTTTTTTTC
Found at i:12585789 original size:23 final size:24
Alignment explanation
Indices: 12585763--12585813 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
12585753 TTATGGTTTT
12585763 AAGGCAAAA-AAAAAAGA-AAAAAA
1 AAGG-AAAATAAAAAAGAGAAAAAA
**
12585786 AAGGAAAATAGTAAAGAGAAAAAA
1 AAGGAAAATAAAAAAGAGAAAAAA
12585810 AAGG
1 AAGG
12585814 GTTTCTAGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 4 0.17
23 10 0.42
24 10 0.42
ACGTcount: A:0.75, C:0.02, G:0.20, T:0.04
Consensus pattern (24 bp):
AAGGAAAATAAAAAAGAGAAAAAA
Found at i:12590330 original size:5 final size:5
Alignment explanation
Indices: 12590320--12590357 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
12590310 AATAATTAAG
12590320 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TAT
12590358 TATATATAAA
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:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:12591452 original size:12 final size:12
Alignment explanation
Indices: 12591435--12591459 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12591425 GCCGACTACT
12591435 GTTACTGTTACC
1 GTTACTGTTACC
12591447 GTTACTGTTACC
1 GTTACTGTTACC
12591459 G
1 G
12591460 ATTCGACACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (12 bp):
GTTACTGTTACC
Found at i:12591490 original size:45 final size:45
Alignment explanation
Indices: 12591437--12591543 Score: 162
Period size: 45 Copynumber: 2.4 Consensus size: 45
12591427 CGACTACTGT
*
12591437 TACTGTTACCGTTACTGTTACCGATTC-GACACTTTGTGTGTCGAA
1 TACTGTTACCGTTACTGTTACAGATTCAG-CACTTTGTGTGTCGAA
* *
12591482 TATTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAA
1 TACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAA
*
12591527 TACTGTTACTGTTACTG
1 TACTGTTACCGTTACTG
12591544 CTACTGCTAC
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
45 55 0.98
46 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.41
Consensus pattern (45 bp):
TACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAA
Found at i:12591558 original size:18 final size:18
Alignment explanation
Indices: 12591527--12591561 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12591517 GTGTGTTGAA
* *
12591527 TACTGTTACTGTTACTGC
1 TACTGCTACCGTTACTGC
12591545 TACTGCTACCGTTACTG
1 TACTGCTACCGTTACTG
12591562 ATTACTGATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.40
Consensus pattern (18 bp):
TACTGCTACCGTTACTGC
Found at i:12594464 original size:34 final size:34
Alignment explanation
Indices: 12594425--12594499 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
12594415 AAACAAGTTT
*
12594425 ATTGCTACTACAATGATCCATTATAAGCAT-ATTA
1 ATTGCTACCACAATGATCCATTATAAGCATGA-TA
*** *
12594459 ATTGCTACCATGTTGATCTATTATAAGCATGATA
1 ATTGCTACCACAATGATCCATTATAAGCATGATA
12594493 ATTGCTA
1 ATTGCTA
12594500 TTGTATCGAC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 34 0.97
35 1 0.03
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (34 bp):
ATTGCTACCACAATGATCCATTATAAGCATGATA
Found at i:12594550 original size:33 final size:33
Alignment explanation
Indices: 12594444--12594553 Score: 103
Period size: 34 Copynumber: 3.3 Consensus size: 33
12594434 ACAATGATCC
* * * *
12594444 ATTATAAGCATATTAATTGCTACCATGTTGATCT
1 ATTATAAGCATGTT-ATTGCTACCGTATTGATTT
* ** * *
12594478 ATTATAAGCATGATAATTGCTATTGTATCGACTT
1 ATTATAAGCATG-TTATTGCTACCGTATTGATTT
*
12594512 ATTATAAGCATGTTATTGCTACCGTATTGGTTT
1 ATTATAAGCATGTTATTGCTACCGTATTGATTT
*
12594545 GTTATAAGC
1 ATTATAAGC
12594554 GTGTCATGTT
Statistics
Matches: 59, Mismatches: 16, Indels: 3
0.76 0.21 0.04
Matches are distributed among these distances:
33 23 0.39
34 35 0.59
35 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (33 bp):
ATTATAAGCATGTTATTGCTACCGTATTGATTT
Found at i:12596486 original size:30 final size:30
Alignment explanation
Indices: 12596447--12596508 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
12596437 TGTATGAGTA
* *
12596447 TGGGTAAAATTCAGCCTAACATGGGTATAT
1 TGGGGAAAATTCAGCCCAACATGGGTATAT
*
12596477 TGGGGAAAATTCGGCCCAACATGGGTATAT
1 TGGGGAAAATTCAGCCCAACATGGGTATAT
12596507 TG
1 TG
12596509 AAATTATGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (30 bp):
TGGGGAAAATTCAGCCCAACATGGGTATAT
Found at i:12596533 original size:38 final size:38
Alignment explanation
Indices: 12596477--12596551 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
12596467 ATGGGTATAT
12596477 TGGGGAAAATTCGGCCCAACATGGGTATATTGAAATTA
1 TGGGGAAAATTCGGCCCAACATGGGTATATTGAAATTA
* *
12596515 TGGGTAAAATTTGGCCCAACATGGGTATATTGAAATT
1 TGGGGAAAATTCGGCCCAACATGGGTATATTGAAATT
12596552 TTGCATATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.29
Consensus pattern (38 bp):
TGGGGAAAATTCGGCCCAACATGGGTATATTGAAATTA
Found at i:12597233 original size:56 final size:56
Alignment explanation
Indices: 12597160--12597303 Score: 216
Period size: 56 Copynumber: 2.6 Consensus size: 56
12597150 ACATGGAAGT
*
12597160 ATATGCGATTCTGATATATGTGTACGAGTAAGACCACGTTTTATACGTTGGCATCG
1 ATATGCGATTCCGATATATGTGTACGAGTAAGACCACGTTTTATACGTTGGCATCG
* * *
12597216 ATTTGCGACTCCGATATATGTGTGCGAGTAAGACCACGTTTTATACGTTGGCATCG
1 ATATGCGATTCCGATATATGTGTACGAGTAAGACCACGTTTTATACGTTGGCATCG
* ** *
12597272 ATATGTGATTCCGATATGCGTTTACGAGTAAG
1 ATATGCGATTCCGATATATGTGTACGAGTAAG
12597304 GCCCTATCTG
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 77 1.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (56 bp):
ATATGCGATTCCGATATATGTGTACGAGTAAGACCACGTTTTATACGTTGGCATCG
Found at i:12601402 original size:14 final size:14
Alignment explanation
Indices: 12601385--12601420 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
12601375 ATAAATATAT
* *
12601385 AATATAAATACAAA
1 AATAAAAATAAAAA
12601399 AATAAAAATAAAAA
1 AATAAAAATAAAAA
12601413 AATAAAAA
1 AATAAAAA
12601421 AAGAGAGCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.17
Consensus pattern (14 bp):
AATAAAAATAAAAA
Found at i:12602021 original size:3 final size:3
Alignment explanation
Indices: 12602013--12602038 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
12602003 TTATTCTACT
12602013 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
12602039 GTGTGTTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:12602141 original size:12 final size:13
Alignment explanation
Indices: 12602124--12602153 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
12602114 CTAATGTGTC
12602124 TATATTATGTAT-
1 TATATTATGTATA
12602136 TATATTATGTATA
1 TATATTATGTATA
12602149 TATAT
1 TATAT
12602154 ATTTATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (13 bp):
TATATTATGTATA
Found at i:12602463 original size:15 final size:15
Alignment explanation
Indices: 12602443--12602492 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
12602433 ATTGCTAATG
12602443 TATATG-TATATATCA
1 TATATGTTATATAT-A
*
12602458 TATATGTTTTATATA
1 TATATGTTATATATA
* *
12602473 TATATATTATGTATA
1 TATATGTTATATATA
12602488 TATAT
1 TATAT
12602493 TTTCAATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 24 0.80
16 6 0.20
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (15 bp):
TATATGTTATATATA
Found at i:12602482 original size:13 final size:13
Alignment explanation
Indices: 12602443--12602493 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
12602433 ATTGCTAATG
*
12602443 TATATGTATATAT
1 TATATATATATAT
* *
12602456 CATATATGT-T-T
1 TATATATATATAT
12602467 TATATATATATAT
1 TATATATATATAT
*
12602480 TATGTATATATAT
1 TATATATATATAT
12602493 T
1 T
12602494 TTCAATATTA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
11 8 0.27
12 2 0.07
13 20 0.67
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (13 bp):
TATATATATATAT
Found at i:12602501 original size:24 final size:26
Alignment explanation
Indices: 12602472--12602581 Score: 74
Period size: 26 Copynumber: 4.5 Consensus size: 26
12602462 TGTTTTATAT
12602472 ATATA-TATTATGTATATATATTTTC
1 ATATACTATTATGTATATATATTTTC
*
12602497 A-ATATTATTA-GT-TATAT-TTTT-
1 ATATACTATTATGTATATATATTTTC
* * * * *
12602518 ATATACTATTCTATGTACATATTTCC
1 ATATACTATTATGTATATATATTTTC
*
12602544 ATAT-CATCTTATGTATATATATTCTT-
1 ATATAC-TATTATGTATATATATT-TTC
*
12602570 AAATACTATTAT
1 ATATACTATTAT
12602582 ATGTATATGT
Statistics
Matches: 63, Mismatches: 13, Indels: 17
0.68 0.14 0.18
Matches are distributed among these distances:
21 1 0.02
22 11 0.17
23 6 0.10
24 9 0.14
25 10 0.16
26 24 0.38
27 2 0.03
ACGTcount: A:0.35, C:0.09, G:0.04, T:0.53
Consensus pattern (26 bp):
ATATACTATTATGTATATATATTTTC
Found at i:12603651 original size:27 final size:28
Alignment explanation
Indices: 12603621--12603677 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
12603611 TAATGATAAA
*
12603621 AATTTAA-ATAATATTTATCTTAATGAT
1 AATTTAACATAATATTTATATTAATGAT
*
12603648 AA-TTAACATAATATTTATATTTATGAT
1 AATTTAACATAATATTTATATTAATGAT
12603675 AAT
1 AAT
12603678 ATTATTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 4 0.15
27 22 0.85
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (28 bp):
AATTTAACATAATATTTATATTAATGAT
Found at i:12603685 original size:21 final size:21
Alignment explanation
Indices: 12603659--12603713 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
12603649 ATTAACATAA
12603659 TATTTATATTTATGATAATAT
1 TATTTATATTTATGATAATAT
*
12603680 TATTTATATTTATGATAATTT
1 TATTTATATTTATGATAATAT
* *
12603701 TATATATTTTTAT
1 TATTTATATTTAT
12603714 TTTTTTAGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (21 bp):
TATTTATATTTATGATAATAT
Found at i:12603764 original size:20 final size:20
Alignment explanation
Indices: 12603741--12603778 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
12603731 TTACGTAAAA
12603741 TTTTCAAAATTTATTTAACC
1 TTTTCAAAATTTATTTAACC
*
12603761 TTTTCAAATTTTATTTAA
1 TTTTCAAAATTTATTTAA
12603779 ATGTGTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTTCAAAATTTATTTAACC
Found at i:12604426 original size:18 final size:18
Alignment explanation
Indices: 12604377--12604435 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 18
12604367 AAAAATATAT
* **
12604377 AAAATATATTTTTAATAA
1 AAAATAGATTTTTTTTAA
12604395 TAAAATAGGAATTTTTTTTAA
1 -AAAATA-G-ATTTTTTTTAA
12604416 AAAATAGATTTTTTTTAA
1 AAAATAGATTTTTTTTAA
12604434 AA
1 AA
12604436 CACTTTTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 13 0.37
19 7 0.20
20 6 0.17
21 9 0.26
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (18 bp):
AAAATAGATTTTTTTTAA
Found at i:12609701 original size:21 final size:22
Alignment explanation
Indices: 12609649--12609703 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
12609639 AAAAAAATTA
* *
12609649 AAATATTATTTTGTTAAATAAT
1 AAATATTATATTGTTAAACAAT
* **
12609671 AATTGGTATATT-TTAAACAAT
1 AAATATTATATTGTTAAACAAT
12609692 AAATATTATATT
1 AAATATTATATT
12609704 CATTCAAATT
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.47
Consensus pattern (22 bp):
AAATATTATATTGTTAAACAAT
Found at i:12610161 original size:29 final size:31
Alignment explanation
Indices: 12610105--12610164 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 31
12610095 AACCTGAAAT
* *
12610105 TTGAAATCTAAAAAGTAGAAGGACTAAATTC
1 TTGAAATCTAAAAAGTACAAAGACTAAATTC
*
12610136 TTGAAAT-TAAAAA-TACAAAGATTAAATTC
1 TTGAAATCTAAAAAGTACAAAGACTAAATTC
12610165 CTAATTTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 13 0.50
30 6 0.23
31 7 0.27
ACGTcount: A:0.52, C:0.08, G:0.12, T:0.28
Consensus pattern (31 bp):
TTGAAATCTAAAAAGTACAAAGACTAAATTC
Found at i:12610229 original size:18 final size:17
Alignment explanation
Indices: 12610197--12610230 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
12610187 ACCTATGGCA
12610197 TATTTTAGCATTTTTTG
1 TATTTTAGCATTTTTTG
*
12610214 TATTTATAGTATTTTTT
1 TATTT-TAGCATTTTTT
12610231 TAAAAAGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.21, C:0.03, G:0.09, T:0.68
Consensus pattern (17 bp):
TATTTTAGCATTTTTTG
Found at i:12611355 original size:11 final size:10
Alignment explanation
Indices: 12611318--12611360 Score: 54
Period size: 11 Copynumber: 4.3 Consensus size: 10
12611308 TTTCTAAAAT
12611318 TTTATATTTA
1 TTTATATTTA
12611328 TTTGA-ATTT-
1 TTT-ATATTTA
12611337 TTTATATTTA
1 TTTATATTTA
12611347 TTATATATTTA
1 TT-TATATTTA
12611358 TTT
1 TTT
12611361 CAATTTTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
8 1 0.03
9 7 0.24
10 10 0.34
11 11 0.38
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (10 bp):
TTTATATTTA
Found at i:12614888 original size:15 final size:15
Alignment explanation
Indices: 12614865--12614895 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12614855 CAAATATTAG
*
12614865 CATCTTCTTCTTCTT
1 CATCATCTTCTTCTT
12614880 CATCATCTTCTTCTT
1 CATCATCTTCTTCTT
12614895 C
1 C
12614896 GGCTGTTGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.10, C:0.35, G:0.00, T:0.55
Consensus pattern (15 bp):
CATCATCTTCTTCTT
Found at i:12618912 original size:4 final size:4
Alignment explanation
Indices: 12618903--12618934 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
12618893 TTTTTCTACA
12618903 TATG TATG TATG TATG TATG TAATG TATG TAT
1 TATG TATG TATG TATG TATG T-ATG TATG TAT
12618935 TAGTTTCCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:12632085 original size:1 final size:1
Alignment explanation
Indices: 12632079--12632110 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
12632069 TTTGCTTCCT
12632079 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
12632111 GACTTTGGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:12633510 original size:86 final size:88
Alignment explanation
Indices: 12633315--12633569 Score: 313
Period size: 86 Copynumber: 2.9 Consensus size: 88
12633305 CAGATCAATG
* * *
12633315 AAGACAAAGGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAA-CCTTGCCTC
1 AAGACAAAAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAA-ACACAAAGCCTTGCCTC
** * * * *
12633379 TTTCGGTTG-TGATAGAGCTGGTTG
65 CATCGGTTGCAG-TGGAGCTAGTTA
* *
12633403 AAGACAAAAGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAA-ACAAAGCCTTGCATCC
1 AAGACAAAAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAACACAAAGCCTTGCCTCC
*
12633467 ATCGATTGCAGTGGAGCTAGTTA
66 ATCGGTTGCAGTGGAGCTAGTTA
** *
12633490 AAGA-AGTAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATC-AAAGACAAAGCCTTGCCTCC
1 AAGACAAAAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAACACAAAGCCTTGCCTCC
*
12633553 ATCGGTTGCATTGGAGC
66 ATCGGTTGCAGTGGAGC
12633570 AGATTGAAGC
Statistics
Matches: 146, Mismatches: 18, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
85 3 0.02
86 71 0.49
87 28 0.19
88 44 0.30
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (88 bp):
AAGACAAAAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAACACAAAGCCTTGCCTCC
ATCGGTTGCAGTGGAGCTAGTTA
Found at i:12633587 original size:86 final size:84
Alignment explanation
Indices: 12633324--12633623 Score: 300
Period size: 86 Copynumber: 3.5 Consensus size: 84
12633314 GAAGACAAAG
* * * * **
12633324 GATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTGT
1 GATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCAAAGACA-AAGCCTTGCCTCCATCGGTTG-
* * * *
12633389 GATAGAGCTGGTTGAAGACAAAA
64 CATGGAGC-AGTTGAAG-CAAGA
* * *
12633412 GATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAA-ACAAAGCCTTGCATCCATCGATTGC
1 GATCTTGCCTTCCTGCATTAACAGCGAAGCAGATC-AAAGACAAAGCCTTGCCTCCATCGGTTGC
*
12633476 AGTGGAGCTAGTTAAAG-AAGTA
65 A-TGGAGC-AGTTGAAGCAAG-A
12633498 GATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCAAAGACAAAGCCTTGCCTCCATCGGTTGCA
1 GATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCAAAGACAAAGCCTTGCCTCCATCGGTTGCA
*
12633563 TTGGAGCAGATTGAAGCCAGA
66 -TGGAGCAG-TTGAAGCAAGA
** * * *
12633584 GATCTTATCTCCCTGAGATT-ACAGCGGAGCAGATCAAAGA
1 GATCTTGCCTTCCTG-CATTAACAGCGAAGCAGATCAAAGA
12633624 TAGTAATCCT
Statistics
Matches: 180, Mismatches: 25, Indels: 16
0.81 0.11 0.07
Matches are distributed among these distances:
85 7 0.04
86 103 0.57
87 33 0.18
88 35 0.19
89 2 0.01
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.24
Consensus pattern (84 bp):
GATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCAAAGACAAAGCCTTGCCTCCATCGGTTGCA
TGGAGCAGTTGAAGCAAGA
Found at i:12633777 original size:46 final size:46
Alignment explanation
Indices: 12633705--12633959 Score: 201
Period size: 46 Copynumber: 5.8 Consensus size: 46
12633695 GAAGATCACA
* * * *
12633705 TCAGGTCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATT
1 TCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAATT
* * *
12633751 TCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAG-ATA
1 TCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAATT
* * * **
12633796 T-A-ATCCTATCTCCCTGAAGTTACAGTGGAGCGGA-TTAA-AA-T
1 TCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAATT
** * * * * * *
12633837 AAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATC---GCA--
1 TCA-GATCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAATT
* * *
12633879 TCAGGTCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGAATT
1 TCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAATT
*
12633925 GCAGATCTTATC-CCCTGAGGTTACAGTGGAGCAGA
1 TCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGA
12633960 TTGAAGCCAG
Statistics
Matches: 165, Mismatches: 33, Indels: 23
0.75 0.15 0.10
Matches are distributed among these distances:
41 31 0.19
42 5 0.03
43 29 0.18
44 30 0.18
45 24 0.15
46 46 0.28
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (46 bp):
TCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAATT
Found at i:12633858 original size:44 final size:44
Alignment explanation
Indices: 12633662--12633999 Score: 194
Period size: 41 Copynumber: 7.8 Consensus size: 44
12633652 TGGAGCGGAT
* * * *
12633662 TAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATC--ACA
1 TAAA-GATCTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAAA
* * * * *
12633705 T-CAGGTCTTATCTCCCTG-AGATTACAGTGGAACAGACCAAAGAA
1 TAAAGATCTTATCTCCCTGAAG-TTACAGTGGAGCAGATCGAA-AA
** * * *
12633749 TTTCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGA
1 -TAAAGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAAA
* * * *
12633794 TATA-ATCCTATCTCCCTGAAGTTACAGTGGAGCGGAT-TAAAA
1 TAAAGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAAA
* * * *
12633836 TAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCG--CA
1 TAAA-GATCTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAAA
* * * * * *
12633879 T-CAGGTCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGAA
1 TAAAGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAA-AA
** * * **
12633923 TTGCAGATCTTATC-CCCTGAGGTTACAGTGGAGCAGATTGAAGC
1 -TAAAGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAAA
* * *
12633967 CAGAGGTCTTATCTCCCTGATA-TTACAGTGGAG
1 TAAAGATCTTATCTCCCTGA-AGTTACAGTGGAG
12634000 TAGACTTAAA
Statistics
Matches: 229, Mismatches: 49, Indels: 33
0.74 0.16 0.11
Matches are distributed among these distances:
40 2 0.01
41 58 0.25
42 8 0.03
43 42 0.18
44 49 0.21
45 27 0.12
46 42 0.18
47 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (44 bp):
TAAAGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAAA
Found at i:12633932 original size:87 final size:87
Alignment explanation
Indices: 12633667--12634004 Score: 292
Period size: 87 Copynumber: 3.9 Consensus size: 87
12633657 CGGATTAAAG
* * *
12633667 GATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCTTATCTCCCTGAGATTACAG
1 GATCTTATCTCCCTGAAGTTACAGTAGAGCAGATCGCATCAGGTCTTATCTCCCTGAGATTACAG
* *
12633732 TGGAACAGACCAAAGAATTTCA
66 TGGAGCAGACCAAAGAATTACA
* ** * ** *
12633754 GATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGAT-ATAATCCTATCTCCCTGA-AGTT
1 GATCTTATCTCCCTGAAGTTACAGTAGAGCAGATCG--CATCA-GGTCTTATCTCCCTGAGA-TT
* ** *
12633817 ACAGTGGAGCGGA-TTAA-AA-TAAA
62 ACAGTGGAGCAGACCAAAGAATTACA
* * * *
12633840 GGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCTCTGAGGTTACA
1 -GATCTTATCTCCCTGAAGTTACAGTAGAGCAGATCGCATCAGGTCTTATCTCCCTGAGATTACA
* * *
12633905 GTGGAGTAGACCGAAGAATTGCA
65 GTGGAGCAGACCAAAGAATTACA
* * * * * *
12633928 GATCTTATC-CCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGGTCTTATCTCCCTGATATTA
1 GATCTTATCTCCCTGAAGTTACAGTAGAGCAGATCGCA-TC--AGGTCTTATCTCCCTGAGATTA
*
12633992 CAGTGGAGTAGAC
63 CAGTGGAGCAGAC
12634005 TTAAACCTAA
Statistics
Matches: 195, Mismatches: 43, Indels: 24
0.74 0.16 0.09
Matches are distributed among these distances:
85 27 0.14
86 27 0.14
87 75 0.38
88 6 0.03
89 60 0.31
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (87 bp):
GATCTTATCTCCCTGAAGTTACAGTAGAGCAGATCGCATCAGGTCTTATCTCCCTGAGATTACAG
TGGAGCAGACCAAAGAATTACA
Found at i:12633980 original size:130 final size:128
Alignment explanation
Indices: 12633751--12634003 Score: 298
Period size: 130 Copynumber: 2.0 Consensus size: 128
12633741 CCAAAGAATT
*
12633751 TCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGATATAATCCTATCTCCCTGAAGT
1 TCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGACCGAAGATATAATCCTATCTCCCTGAAGT
* * *
12633816 TACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGCA
66 TACAGTGGAGCAGATTAAAACAAAGGATCTTATCTCCCTGATA-TTACAGTAGAGTAGATCGCA
* * * * *
12633879 TCAGGTCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGA-ATTGCAGATCTTATC-CCCTG
1 TCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGACCGAAGATA-T--A-ATCCTATCTCCCTG
* ** * *
12633942 AGGTTACAGTGGAGCAGATTGAAGCCAGAGG-TCTTATCTCCCTGATATTACAGTGGAGTAGA
62 AAGTTACAGTGGAGCAGATT-AAAACAAAGGATCTTATCTCCCTGATATTACAGTAGAGTAGA
12634004 CTTAAACCTA
Statistics
Matches: 105, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
127 1 0.01
128 39 0.37
130 51 0.49
131 14 0.13
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (128 bp):
TCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGACCGAAGATATAATCCTATCTCCCTGAAGT
TACAGTGGAGCAGATTAAAACAAAGGATCTTATCTCCCTGATATTACAGTAGAGTAGATCGCA
Found at i:12633982 original size:174 final size:174
Alignment explanation
Indices: 12633583--12633999 Score: 569
Period size: 174 Copynumber: 2.4 Consensus size: 174
12633573 TTGAAGCCAG
* * * * *
12633583 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATT
1 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACAG-AATCCTATCTCCCTGATATT
*
12633648 ACAATGGAGCGGA-T----TAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCA
65 ACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCA
*
12633708 GGTCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTC
130 GGTCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTGC
* *
12633753 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGATATAATCCTATCTCCCTGA-AGTT
1 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACAGAATCCTATCTCCCTGATA-TT
* *
12633817 ACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCA
65 ACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCA
* * ** *
12633882 GGTCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGAATTGC
130 GGTCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTGC
* * * * *
12633927 AGATCTTATC-CCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGGTCTTATCTCCCTGATATT
1 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACAGA-ATCCTATCTCCCTGATATT
12633991 ACAGTGGAG
65 ACAGTGGAG
12634000 TAGACTTAAA
Statistics
Matches: 219, Mismatches: 20, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
168 1 0.00
169 29 0.13
170 42 0.19
173 29 0.13
174 117 0.53
175 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (174 bp):
AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACAGAATCCTATCTCCCTGATATTA
CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAG
GTCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTGC
Found at i:12634046 original size:174 final size:173
Alignment explanation
Indices: 12633583--12634048 Score: 500
Period size: 174 Copynumber: 2.7 Consensus size: 173
12633573 TTGAAGCCAG
* * * *
12633583 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTG-AGAT
1 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACAG-AATCCTATCTCCCTGAAG-T
* * * * * *
12633647 TACAATGGAGCGGATT---A-AAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCA
64 TACAGTGGAGCAGATTAAAATAAAGACCTTATCTCTCTGAAGTTACAGCAGAGTAGATCACATCA
*
12633708 GGTCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTC
129 GGTCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTGC
* *
12633753 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGATATAATCCTATCTCCCTGAAGTTA
1 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACAGAATCCTATCTCCCTGAAGTTA
* * * *
12633818 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
66 CAGTGGAGCAGATTAAAATAAA-GACCTTATCTCTCTGAAGTTACAGCAGAGTAGATCACATCAG
* * ** *
12633883 GTCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGAATTGC
130 GTCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTGC
* * * * *
12633927 AGATCTTATC-CCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGGTCTTATCTCCCTGATA-T
1 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACAGA-ATCCTATCTCCCTGA-AGT
* * * ***
12633990 TACAGTGGAGTAGACTTAAACCTAAA-ACCTTGTC-CTTCTGAAGTTGTGGCAGAGTAGAT
64 TACAGTGGAGCAGA-TTAAA-ATAAAGACCTTATCTC-TCTGAAGTTACAGCAGAGTAGAT
12634049 TGAAGCTACA
Statistics
Matches: 255, Mismatches: 30, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
169 30 0.12
170 43 0.17
172 1 0.00
173 32 0.13
174 139 0.55
175 6 0.02
176 4 0.02
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (173 bp):
AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACAGAATCCTATCTCCCTGAAGTTA
CAGTGGAGCAGATTAAAATAAAGACCTTATCTCTCTGAAGTTACAGCAGAGTAGATCACATCAGG
TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTGC
Found at i:12634316 original size:15 final size:15
Alignment explanation
Indices: 12634291--12634323 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
12634281 TACCCAATTA
12634291 CAACACCCAATA-CC
1 CAACACCCAATAGCC
12634305 CAACAGCCCAATAGCC
1 CAACA-CCCAATAGCC
12634321 CAA
1 CAA
12634324 AATCATCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 7 0.41
16 5 0.29
ACGTcount: A:0.42, C:0.45, G:0.06, T:0.06
Consensus pattern (15 bp):
CAACACCCAATAGCC
Found at i:12642172 original size:25 final size:25
Alignment explanation
Indices: 12642143--12642237 Score: 154
Period size: 25 Copynumber: 3.8 Consensus size: 25
12642133 CTGTACATGT
*
12642143 ATGCTCACATGAGCTGTAAATCAGA
1 ATGCTCACATGAGCTGTGAATCAGA
12642168 ATGCTCACATGAGCTGTGAATCAGA
1 ATGCTCACATGAGCTGTGAATCAGA
* *
12642193 ATGCTCACACGAGCTGTGAATTAGA
1 ATGCTCACATGAGCTGTGAATCAGA
*
12642218 ATGCTTACATGAGCTGTGAA
1 ATGCTCACATGAGCTGTGAA
12642238 AATGGGTCTG
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 65 1.00
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (25 bp):
ATGCTCACATGAGCTGTGAATCAGA
Found at i:12642258 original size:27 final size:25
Alignment explanation
Indices: 12642143--12642261 Score: 121
Period size: 25 Copynumber: 4.7 Consensus size: 25
12642133 CTGTACATGT
* * *
12642143 ATGCTCACATGAGCTGTAAATCAGA
1 ATGCTCACACGAGCTGTGAATGAGA
* *
12642168 ATGCTCACATGAGCTGTGAATCAGA
1 ATGCTCACACGAGCTGTGAATGAGA
*
12642193 ATGCTCACACGAGCTGTGAATTAGA
1 ATGCTCACACGAGCTGTGAATGAGA
* * * *
12642218 ATGCTTACATGAGCTGTGAAAATGGGT
1 ATGCTCACACGAGCTGTG--AATGAGA
*
12642245 CTGCTCACACGAGCTGT
1 ATGCTCACACGAGCTGT
12642262 AGGTCGAAAC
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
25 63 0.78
27 18 0.22
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.25
Consensus pattern (25 bp):
ATGCTCACACGAGCTGTGAATGAGA
Found at i:12644669 original size:38 final size:38
Alignment explanation
Indices: 12644625--12644700 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
12644615 ATTATGTCAC
*
12644625 CCTATCTCTAGGCATGCAATCAACTCTGCTTAATTATG
1 CCTATCTCTAGGCATGCAATCAACTCCGCTTAATTATG
*
12644663 CCTATCTCTAGGCATGCAATTAACTCCGCTTAATTATG
1 CCTATCTCTAGGCATGCAATCAACTCCGCTTAATTATG
12644701 TTAGATCTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.34
Consensus pattern (38 bp):
CCTATCTCTAGGCATGCAATCAACTCCGCTTAATTATG
Found at i:12657823 original size:21 final size:22
Alignment explanation
Indices: 12657798--12657851 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
12657788 ATTGGGTTGA
*
12657798 AAATTTATTTAATTGAG-AAAT
1 AAATTTATTTAATTAAGTAAAT
* * *
12657819 TAATTAAATTAATTAAGTAAAT
1 AAATTTATTTAATTAAGTAAAT
12657841 AATATTTATTT
1 AA-ATTTATTT
12657852 TAGAAATAGA
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
21 13 0.54
22 5 0.21
23 6 0.25
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (22 bp):
AAATTTATTTAATTAAGTAAAT
Found at i:12662912 original size:29 final size:29
Alignment explanation
Indices: 12662866--12662924 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
12662856 AAATTGAATC
*
12662866 AAATCAAAACGTTATATATAAAATTGCACA
1 AAATCAAAAC-TTATATATAAAATTACACA
*
12662896 AAATCAAAA-TTCATATATAACATTACACA
1 AAATCAAAACTT-ATATATAAAATTACACA
12662925 TTGAACAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 2 0.08
29 15 0.58
30 9 0.35
ACGTcount: A:0.54, C:0.15, G:0.03, T:0.27
Consensus pattern (29 bp):
AAATCAAAACTTATATATAAAATTACACA
Found at i:12667587 original size:24 final size:22
Alignment explanation
Indices: 12667532--12667590 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 22
12667522 TATACATAAT
12667532 ATATATA-ATAAATATTGAAAA
1 ATATATACATAAATATTGAAAA
*
12667553 ATGTATGTACATAACATATATGAAAA
1 A--TATATACATAA-ATAT-TGAAAA
12667579 ATATATACATAA
1 ATATATACATAA
12667591 TAATATTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
21 1 0.03
23 5 0.16
24 14 0.45
25 4 0.13
26 7 0.23
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (22 bp):
ATATATACATAAATATTGAAAA
Found at i:12667593 original size:27 final size:24
Alignment explanation
Indices: 12667529--12667651 Score: 65
Period size: 23 Copynumber: 4.8 Consensus size: 24
12667519 ATATATACAT
12667529 AATATAT-ATAATAAATATTGAAA
1 AATATATAATAATAAATATTGAAA
* *
12667552 AATGTAT-GTACATAACATATATGAAA
1 AATATATAATA-ATAA-ATAT-TGAAA
*
12667578 AATATATACATAAT-AATATT-TAA
1 AATATATA-ATAATAAATATTGAAA
* *
12667601 AATAAAATAATAAGTGAAAATAGTGAAAA
1 AAT-ATATAATAA-T--AAATATTG-AAA
12667630 TAATAGGTATAATAATAAATAT
1 -AATA--TATAATAATAAATAT
12667652 AATGATGTAT
Statistics
Matches: 75, Mismatches: 10, Indels: 25
0.68 0.09 0.23
Matches are distributed among these distances:
23 17 0.23
24 10 0.13
25 8 0.11
26 12 0.16
27 7 0.09
28 7 0.09
29 3 0.04
30 4 0.05
31 7 0.09
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.32
Consensus pattern (24 bp):
AATATATAATAATAAATATTGAAA
Found at i:12668104 original size:3 final size:3
Alignment explanation
Indices: 12668077--12668163 Score: 62
Period size: 3 Copynumber: 30.3 Consensus size: 3
12668067 AGCTAGAACA
* * *
12668077 AAT ACT AAT AAT AGT AAA AACT AAT AAT -AT AAT -AT AAT -AT AA-
1 AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT
*
12668119 AAT AA- AGAT AA- AGA- AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT A-AT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
12668163 A
1 A
12668164 GAAAAGATTG
Statistics
Matches: 67, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
2 11 0.16
3 53 0.79
4 3 0.04
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:12676148 original size:31 final size:34
Alignment explanation
Indices: 12676103--12676174 Score: 96
Period size: 35 Copynumber: 2.2 Consensus size: 34
12676093 CATCATTGGA
*
12676103 TATTATTATAGG-A-TATTA-TAAAATACATTGT
1 TATTATCATAGGAATTATTAGTAAAATACATTGT
*
12676134 TATTATCATTGGATATTATTAGTAAAATACATTGT
1 TATTATCATAGGA-ATTATTAGTAAAATACATTGT
12676169 TATTAT
1 TATTAT
12676175 AAAAACATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 10 0.29
33 1 0.03
34 5 0.14
35 19 0.54
ACGTcount: A:0.39, C:0.04, G:0.10, T:0.47
Consensus pattern (34 bp):
TATTATCATAGGAATTATTAGTAAAATACATTGT
Found at i:12676188 original size:17 final size:18
Alignment explanation
Indices: 12676116--12676191 Score: 68
Period size: 17 Copynumber: 4.3 Consensus size: 18
12676106 TATTATAGGA
12676116 TATTATAAAATACATTGT
1 TATTATAAAATACATTGT
* * ** *
12676134 TATTAT-CATTGGA-TAT
1 TATTATAAAATACATTGT
12676150 TATTAGTAAAATACATTGT
1 TATTA-TAAAATACATTGT
*
12676169 TATTATAAAA-ACATTTT
1 TATTATAAAATACATTGT
12676186 TATTAT
1 TATTAT
12676192 TTATTATAGT
Statistics
Matches: 44, Mismatches: 11, Indels: 7
0.71 0.18 0.11
Matches are distributed among these distances:
16 7 0.16
17 16 0.36
18 14 0.32
19 7 0.16
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.47
Consensus pattern (18 bp):
TATTATAAAATACATTGT
Found at i:12677617 original size:32 final size:30
Alignment explanation
Indices: 12677565--12677623 Score: 75
Period size: 29 Copynumber: 1.9 Consensus size: 30
12677555 AATTGGAAAG
12677565 AAAAAAAAAATTTTAAGCCC-TTAAAAGTA
1 AAAAAAAAAATTTTAAGCCCTTTAAAAGTA
*
12677594 AAAAAAAAATATTTTTAGGGCCCTTTAAAA
1 AAAAAAAAA-A-TTTTA-AGCCCTTTAAAA
12677624 ATTGGTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 9 0.36
30 1 0.04
31 5 0.20
32 4 0.16
33 6 0.24
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.27
Consensus pattern (30 bp):
AAAAAAAAAATTTTAAGCCCTTTAAAAGTA
Found at i:12681258 original size:19 final size:19
Alignment explanation
Indices: 12681220--12681258 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
12681210 TCATACTACA
**
12681220 AAATATTTATTATTGTAAT
1 AAATATTTATTATTAAAAT
12681239 AAATATTTATTATTAAAAT
1 AAATATTTATTATTAAAAT
12681258 A
1 A
12681259 TTAATATTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
AAATATTTATTATTAAAAT
Found at i:12687089 original size:21 final size:20
Alignment explanation
Indices: 12687054--12687107 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
12687044 TAAATCTATT
*
12687054 TTAAATTTTATAA-TTATAAA
1 TTAAATTTAATAATTTA-AAA
12687074 TTAAATTATAATAATTTAAAA
1 TTAAATT-TAATAATTTAAAA
12687095 TT-AATTTAATAAT
1 TTAAATTTAATAAT
12687108 ATGATAGAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
19 7 0.23
20 11 0.35
21 10 0.32
22 3 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTAAATTTAATAATTTAAAA
Found at i:12696354 original size:11 final size:11
Alignment explanation
Indices: 12696340--12696379 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
12696330 TATTTTCTCT
12696340 CTATTTTGCTA
1 CTATTTTGCTA
*
12696351 CTATTTTACTA
1 CTATTTTGCTA
*
12696362 CTATATTGCTA
1 CTATTTTGCTA
12696373 CTATTTT
1 CTATTTT
12696380 ATTGTTATTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.23, C:0.17, G:0.05, T:0.55
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:12696633 original size:12 final size:12
Alignment explanation
Indices: 12696603--12696635 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
12696593 TATATATTTT
12696603 AAAATT-ATATA
1 AAAATTAATATA
12696614 AAAA-TAATATA
1 AAAATTAATATA
12696625 AAAATTAATAT
1 AAAATTAATAT
12696636 GGGTGGGCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:12700624 original size:126 final size:126
Alignment explanation
Indices: 12700252--12700797 Score: 774
Period size: 126 Copynumber: 4.3 Consensus size: 126
12700242 TAATCTAAAA
* * *
12700252 AAGCTTCTACGTGGATGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAAATTTGAGAAGACGTGT
1 AAGCTTCCACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTGT
*
12700317 CTGCGCAAATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTAAAAG
66 CTGCGCAAATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAG
*
12700378 AAGC-TCCAACGTGGACGCTCTTTTGCTACAGTAGTATCTG-AAAAATAATTTTGAGAAGACGTG
1 AAGCTTCC-ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTG
* ** * *
12700441 ACTATGCAAATAGTGTAAAAAATGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAG
65 TCTGCGCAAATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAG
* **
12700503 AAGCTTCCACGTAGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGATATGT
1 AAGCTTCCACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTGT
* * * *
12700568 CTGCGTAAATAGTGGT-AAAAACGCTTCAAGCAGGATGCATTTTCAGCAAAATTACTGGAAG
66 CTGCGCAAATAGT-GTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAG
* * * * * *
12700629 AAGCTCCCACGTGGATGCTCTTTTGCTATAGTGGTCTCTGAAAAAATAATTTTGAAAAAACGTGT
1 AAGCTTCCACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTGT
** * * *
12700694 CTGCATAAATAGTGTCAAAAACGCTTCAAACAGGATGCATTTTCAGCAACAGTACTGAAAG
66 CTGCGCAAATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAG
* * *
12700755 AAGCTCCCACGTGGACGCTCTTTTGCTACAGTGGTTTCTGAAA
1 AAGCTTCCACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAA
12700798 TAACTTGGGC
Statistics
Matches: 376, Mismatches: 39, Indels: 10
0.88 0.09 0.02
Matches are distributed among these distances:
125 116 0.31
126 258 0.69
127 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (126 bp):
AAGCTTCCACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTGT
CTGCGCAAATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAG
Found at i:12702661 original size:30 final size:30
Alignment explanation
Indices: 12702604--12702669 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
12702594 GTTGAACTAT
*
12702604 TGGGCCCGGTGACTGTGTAGGTCCTGTT-A
1 TGGGCCCGGTGACTGTGTAGGGCCTGTTGA
* *
12702633 CTGGGCCGGGTGATTGTGT-GGGCGCTGTTGA
1 -TGGGCCCGGTGACTGTGTAGGGC-CTGTTGA
12702664 TGGGCC
1 TGGGCC
12702670 TGCATTCTCG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 3 0.10
30 27 0.87
31 1 0.03
ACGTcount: A:0.08, C:0.20, G:0.44, T:0.29
Consensus pattern (30 bp):
TGGGCCCGGTGACTGTGTAGGGCCTGTTGA
Found at i:12704308 original size:15 final size:15
Alignment explanation
Indices: 12704285--12704320 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
12704275 AAATTTTTTT
12704285 ATTTA-AAAAAATAA
1 ATTTAGAAAAAATAA
12704299 ATTTAGAAAAAATAA
1 ATTTAGAAAAAATAA
*
12704314 AATTAGA
1 ATTTAGA
12704321 GCTTTTTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.28
Consensus pattern (15 bp):
ATTTAGAAAAAATAA
Found at i:12704359 original size:22 final size:21
Alignment explanation
Indices: 12704333--12704381 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
12704323 TTTTTTGAAA
**
12704333 AAATTAACGAGAGTTTTGAGAGG
1 AAATTAA-GAGAAATTTGAGA-G
*
12704356 AATTTAAGAGAAATTTGAGAG
1 AAATTAAGAGAAATTTGAGAG
12704377 AAATT
1 AAATT
12704382 TGAGAGAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 5 0.23
22 11 0.50
23 6 0.27
ACGTcount: A:0.45, C:0.02, G:0.24, T:0.29
Consensus pattern (21 bp):
AAATTAAGAGAAATTTGAGAG
Found at i:12704395 original size:11 final size:11
Alignment explanation
Indices: 12704347--12704389 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
12704337 TAACGAGAGT
*
12704347 TTTGAGAGGAA
1 TTTGAGAGAAA
*
12704358 TTTAAGAGAAA
1 TTTGAGAGAAA
12704369 TTTGAGAGAAA
1 TTTGAGAGAAA
12704380 TTTGAGAGAA
1 TTTGAGAGAA
12704390 TATTGAAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.44, C:0.00, G:0.28, T:0.28
Consensus pattern (11 bp):
TTTGAGAGAAA
Found at i:12712682 original size:40 final size:39
Alignment explanation
Indices: 12712628--12712709 Score: 155
Period size: 40 Copynumber: 2.1 Consensus size: 39
12712618 TAGTAGTAAC
12712628 TTAGTTCATTCTAACTCCAATAACTAAATGATTGACAAT
1 TTAGTTCATTCTAACTCCAATAACTAAATGATTGACAAT
12712667 TTAGTTTCATTCTAACTCCAATAACTAAATGATTGACAAT
1 TTAG-TTCATTCTAACTCCAATAACTAAATGATTGACAAT
12712707 TTA
1 TTA
12712710 ACTGTTCTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 4 0.10
40 38 0.90
ACGTcount: A:0.38, C:0.17, G:0.07, T:0.38
Consensus pattern (39 bp):
TTAGTTCATTCTAACTCCAATAACTAAATGATTGACAAT
Found at i:12715161 original size:73 final size:73
Alignment explanation
Indices: 12715033--12715178 Score: 229
Period size: 73 Copynumber: 2.0 Consensus size: 73
12715023 GCATCCCTAG
*
12715033 AATTAGTCTGTTTCCTAGTATAAAGTTTCCTAAGTTAGGCTCACTAAGTACATAAATATTAATGT
1 AATTAGTCTATTTCCTAGTATAAAGTTTCCTAAGTTAGGCTCACTAAGTACATAAATATTAATGT
*
12715098 ACTTTCTT
66 AATTTCTT
* * ** *
12715106 AATTAGTCTATTTCCTAGTATAGAGTTTCCTAAGTTAGGCTCACTATGTGTATAAATATTTATGT
1 AATTAGTCTATTTCCTAGTATAAAGTTTCCTAAGTTAGGCTCACTAAGTACATAAATATTAATGT
12715171 AATTTCTT
66 AATTTCTT
12715179 GTGAATATAC
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 66 1.00
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (73 bp):
AATTAGTCTATTTCCTAGTATAAAGTTTCCTAAGTTAGGCTCACTAAGTACATAAATATTAATGT
AATTTCTT
Found at i:12716924 original size:33 final size:33
Alignment explanation
Indices: 12716880--12716945 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
12716870 TTTTTTCTTG
12716880 ACATTCCAGCTCCTGT-TCAGCAACCAAACACTC
1 ACATTCCAGCTCCTGTCT-AGCAACCAAACACTC
*
12716913 ACATTCTAGCTCCTGTCTAGCAACCAAACACTC
1 ACATTCCAGCTCCTGTCTAGCAACCAAACACTC
12716946 CCACTCAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.30, C:0.38, G:0.09, T:0.23
Consensus pattern (33 bp):
ACATTCCAGCTCCTGTCTAGCAACCAAACACTC
Found at i:12723373 original size:17 final size:17
Alignment explanation
Indices: 12723351--12723384 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
12723341 ATCCACTAAT
*
12723351 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
12723368 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
12723385 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:12728011 original size:17 final size:17
Alignment explanation
Indices: 12727989--12728022 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
12727979 ATCCACTAAT
*
12727989 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
12728006 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
12728023 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:12729162 original size:27 final size:28
Alignment explanation
Indices: 12729109--12729162 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
12729099 TAAAAGTTTA
*
12729109 GGGGAATAAAAGTTTGAGAGAGTAAATG
1 GGGGAATAAAAGTTTGAGAGAGAAAATG
* * *
12729137 GGGGAGTAAAATTTTG-GAGGGAAAAT
1 GGGGAATAAAAGTTTGAGAGAGAAAAT
12729163 ATTTAAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 8 0.36
28 14 0.64
ACGTcount: A:0.41, C:0.00, G:0.37, T:0.22
Consensus pattern (28 bp):
GGGGAATAAAAGTTTGAGAGAGAAAATG
Found at i:12732997 original size:24 final size:24
Alignment explanation
Indices: 12732938--12732999 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
12732928 TATTTTAATA
12732938 TATAAAATATAAAT-TTAAATATT
1 TATAAAATATAAATATTAAATATT
* *
12732961 TTTAAACA-ATAAATATTAATTATT
1 TATAAA-ATATAAATATTAAATATT
*
12732985 TATAAAATTTAAATA
1 TATAAAATATAAATA
12733000 GAATATATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
23 12 0.38
24 20 0.62
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
TATAAAATATAAATATTAAATATT
Found at i:12736886 original size:24 final size:24
Alignment explanation
Indices: 12736846--12736896 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
12736836 ATAAACTATC
12736846 AAAAATACTAAAAATA-TCAAAAT
1 AAAAATACTAAAAATATTCAAAAT
* * *
12736869 AAAAATATCTCAACATATTGAAAAT
1 AAAAATA-CTAAAAATATTCAAAAT
12736894 AAA
1 AAA
12736897 TTTTAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 7 0.30
24 7 0.30
25 9 0.39
ACGTcount: A:0.65, C:0.10, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAAATACTAAAAATATTCAAAAT
Found at i:12737011 original size:31 final size:30
Alignment explanation
Indices: 12736950--12737013 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
12736940 ACTTAACAAG
**
12736950 CAAATGTTTCTAAAATAATAACCAAATTAA
1 CAAATGTTTCTAAAATAATAAAAAAATTAA
12736980 CAAATGTGTT-TAAAATAATAAAAAAAATTAA
1 CAAATGT-TTCTAAAATAAT-AAAAAAATTAA
12737011 CAA
1 CAA
12737014 TAAAATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 16 0.53
31 14 0.47
ACGTcount: A:0.58, C:0.09, G:0.05, T:0.28
Consensus pattern (30 bp):
CAAATGTTTCTAAAATAATAAAAAAATTAA
Found at i:12737068 original size:22 final size:22
Alignment explanation
Indices: 12737043--12737085 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
12737033 TATCCAAACA
12737043 ATAACAACAAAATAGTAGCAAC
1 ATAACAACAAAATAGTAGCAAC
* **
12737065 ATAATAGTAAAATAGTAGCAA
1 ATAACAACAAAATAGTAGCAA
12737086 AATAGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAC
Found at i:12737089 original size:11 final size:11
Alignment explanation
Indices: 12737050--12737090 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
12737040 ACAATAACAA
12737050 CAAAATAGTAG
1 CAAAATAGTAG
* *
12737061 CAACATAATAG
1 CAAAATAGTAG
*
12737072 TAAAATAGTAG
1 CAAAATAGTAG
12737083 CAAAATAG
1 CAAAATAG
12737091 GGAGAAATCA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:12738287 original size:19 final size:20
Alignment explanation
Indices: 12738245--12738288 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
12738235 CTAAAATAGA
*
12738245 AAATTATTTTTAAAGTCTTT
1 AAATTATTTTTAAAATCTTT
*
12738265 -AATTCTTTTTAAAAT-TTT
1 AAATTATTTTTAAAATCTTT
12738283 AAATTA
1 AAATTA
12738289 ATAAAAGTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.55
Consensus pattern (20 bp):
AAATTATTTTTAAAATCTTT
Done.