Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 46 of 316
Found at i:13212485 original size:16 final size:16
Alignment explanation
Indices: 13212464--13212531 Score: 109
Period size: 16 Copynumber: 4.2 Consensus size: 16
13212454 TTTGGTTCGC
*
13212464 TGTATTGGATTAAAGG
1 TGTATTGGATTAGAGG
13212480 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
13212496 TGTAATGGATTAGAGG
1 TGTATTGGATTAGAGG
*
13212512 TGTATTGGAATAGAGG
1 TGTATTGGATTAGAGG
13212528 TGTA
1 TGTA
13212532 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:13212788 original size:18 final size:17
Alignment explanation
Indices: 13212767--13212801 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
13212757 TTATTATTAA
*
13212767 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
13212785 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
13212802 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:13212854 original size:157 final size:157
Alignment explanation
Indices: 13212661--13212967 Score: 578
Period size: 157 Copynumber: 2.0 Consensus size: 157
13212651 CCCTTATCAT
*
13212661 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTATTATCAA
1 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
*
13212726 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAA
66 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
13212791 TTTAATAAAATTCTTAATAATTAGCAG
131 TTTAATAAAATTCTTAATAATTAGCAG
* *
13212818 AAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAATTTTTAATAAGATTATTAATATCAA
1 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
13212883 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
66 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
13212948 TTTAATAAAATTCTTAATAA
131 TTTAATAAAATTCTTAATAA
13212968 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:13212941 original size:16 final size:16
Alignment explanation
Indices: 13212904--13212945 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
13212894 TTAATCATAT
*
13212904 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
13212920 TT-AAATATATTATAA
1 TTAAAATATATTATAA
13212935 TTAAAATATAT
1 TTAAAATATAT
13212946 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:13212952 original size:14 final size:15
Alignment explanation
Indices: 13212913--13212954 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
13212903 TTTAAACATA
*
13212913 ATTATTATTAAATAT
1 ATTATAATTAAATAT
13212928 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
13212942 A-TATAATTTAATA
1 ATTATAATTAAATA
13212955 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:13214471 original size:16 final size:16
Alignment explanation
Indices: 13214450--13214484 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
13214440 CCCCCCCCCC
*
13214450 AAAAAAAAAAAAAAGA
1 AAAAAAAAAAAAAACA
*
13214466 AAAAAAAAACAAAACA
1 AAAAAAAAAAAAAACA
13214482 AAA
1 AAA
13214485 TCGCCTCATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.91, C:0.06, G:0.03, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAACA
Found at i:13220610 original size:15 final size:14
Alignment explanation
Indices: 13220562--13220620 Score: 59
Period size: 14 Copynumber: 4.3 Consensus size: 14
13220552 TTTTCTTCTG
*
13220562 ATTATATTTTAGTT
1 ATTATATTTTAATT
* *
13220576 ATTTATATTTAAAAT
1 A-TTATATTTTAATT
13220591 ATTATATTTTAATT
1 ATTATATTTTAATT
*
13220605 AGT-TATTTT-ATT
1 ATTATATTTTAATT
13220617 ATTA
1 ATTA
13220621 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:13223915 original size:38 final size:38
Alignment explanation
Indices: 13223855--13223927 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 38
13223845 CTGAGCACAC
*
13223855 GCCCGTGTCGATATCGCTCCAGGTTTTCCAAATACGCG
1 GCCCATGTCGATATCGCTCCAGGTTTTCCAAATACGCG
* *
13223893 GCCCATGTGGATATTGCTCCAGGTTTTCCAAATAC
1 GCCCATGTCGATATCGCTCCAGGTTTTCCAAATAC
13223928 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:13225310 original size:16 final size:15
Alignment explanation
Indices: 13225280--13225309 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
13225270 GGATGGTGGG
13225280 GGGAATTCATTTTTT
1 GGGAATTCATTTTTT
13225295 GGGAATTCATTTTTT
1 GGGAATTCATTTTTT
13225310 TTTCATCTTC
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:13228678 original size:17 final size:17
Alignment explanation
Indices: 13228655--13228696 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
13228645 GAGGCCTTAG
*
13228655 TATTGATT-TATTTATA
1 TATTGATTATATATATA
13228671 TGATTGATTATATATATA
1 T-ATTGATTATATATATA
13228689 TATTGATT
1 TATTGATT
13228697 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:13230170 original size:27 final size:27
Alignment explanation
Indices: 13230132--13230185 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
13230122 GCTTTGTGTA
13230132 GTCTAACCAAAACAATATATAATCTAC
1 GTCTAACCAAAACAATATATAATCTAC
13230159 GTCTAACCAAAACAATATATAATCTAC
1 GTCTAACCAAAACAATATATAATCTAC
13230186 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:13232733 original size:26 final size:24
Alignment explanation
Indices: 13232699--13232747 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
13232689 TAAATACAAA
* *
13232699 ATTTTAAAATATAATAAATCAAATAC
1 ATTTAAAAACATAA-AAA-CAAATAC
13232725 ATTTAAAAACATAAAAACAAATA
1 ATTTAAAAACATAAAAACAAATA
13232748 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:13232813 original size:41 final size:40
Alignment explanation
Indices: 13232738--13232822 Score: 98
Period size: 41 Copynumber: 2.1 Consensus size: 40
13232728 TAAAAACATA
*
13232738 AAAACAAATATTAAAACAAGAAACAAATAAAAAATGATACT
1 AAAACAAATATTAAAACAAGAAACAAATAAAAAAT-ATAAT
* * * * **
13232779 AAAACAATTCTTAAAACAATACACAAATTGAAAATATAAT
1 AAAACAAATATTAAAACAAGAAACAAATAAAAAATATAAT
13232819 AAAA
1 AAAA
13232823 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:13238406 original size:31 final size:30
Alignment explanation
Indices: 13238371--13238428 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
13238361 AATAATACTT
*
13238371 ATAAATTAT-TGAAATTATATTTATATTTTTA
1 ATAAAATATGTGAAATT-TATTT-TATTTTTA
*
13238402 ATAAAATATGTTAAATTTATTTTATTT
1 ATAAAATATGTGAAATTTATTTTATTT
13238429 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:13238436 original size:27 final size:26
Alignment explanation
Indices: 13238383--13238444 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
13238373 AAATTATTGA
*
13238383 AATTATATTTATATTTTTAATAAAAT
1 AATTAAATTTATATTTTTAATAAAAT
* * *
13238409 ATGTTAAATTTATTTTATTTAA-ATAAT
1 A-ATTAAATTTATATT-TTTAATAAAAT
13238436 AATTAAATT
1 AATTAAATT
13238445 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:13239021 original size:42 final size:42
Alignment explanation
Indices: 13238969--13239052 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
13238959 TATCTAAAAT
* * *
13238969 AATATAAAATATTATATTACTAAGATTCAAATTAGAAATAAA
1 AATATAAAATATTATATTAATAAGATTAAAATTAAAAATAAA
*
13239011 AATATAAAATATTATATTAATAAGGTTAAAATTAAAAATAAA
1 AATATAAAATATTATATTAATAAGATTAAAATTAAAAATAAA
13239053 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:13239166 original size:16 final size:15
Alignment explanation
Indices: 13239145--13239189 Score: 65
Period size: 14 Copynumber: 3.0 Consensus size: 15
13239135 TTTTTAATAT
13239145 AAATTTAGTACTTATA
1 AAATTTAGTACTTA-A
*
13239161 AAATTTAGCAC-TAA
1 AAATTTAGTACTTAA
13239175 AAATTTAGTACTTAA
1 AAATTTAGTACTTAA
13239190 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:13240423 original size:28 final size:28
Alignment explanation
Indices: 13240391--13240447 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 28
13240381 TGTTCCCCTG
13240391 ATTTCAACATTAATTTTTTTTA-AAT-GTA
1 ATTTC-ACA-TAATTTTTTTTATAATAGTA
*
13240419 ATTTCACATGATTTTTTTTATAATAGTA
1 ATTTCACATAATTTTTTTTATAATAGTA
13240447 A
1 A
13240448 GCATCCTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 11 0.42
27 6 0.23
28 9 0.35
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (28 bp):
ATTTCACATAATTTTTTTTATAATAGTA
Found at i:13241141 original size:9 final size:7
Alignment explanation
Indices: 13241114--13241140 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
13241104 TTTATCTCAT
13241114 ATATATC
1 ATATATC
13241121 ATATATC
1 ATATATC
13241128 ATATATC
1 ATATATC
13241135 ATATAT
1 ATATAT
13241141 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:13244552 original size:20 final size:20
Alignment explanation
Indices: 13244527--13244564 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
13244517 TTAAAATTGA
13244527 CAAAAATAAAAAAATGTTTT
1 CAAAAATAAAAAAATGTTTT
* *
13244547 CAAAAATTAAAAATTGTT
1 CAAAAATAAAAAAATGTT
13244565 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:13252377 original size:24 final size:24
Alignment explanation
Indices: 13252345--13252394 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
13252335 CTACAGAAGA
* *
13252345 AAATAACAAAGATTTTATGCTAAT
1 AAATAACAAAGATATTATACTAAT
*
13252369 AAATAACAAATATATTATACTAAT
1 AAATAACAAAGATATTATACTAAT
13252393 AA
1 AA
13252395 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:13262895 original size:18 final size:19
Alignment explanation
Indices: 13262868--13262905 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
13262858 TAAATAAATA
*
13262868 ATTATATATTTTTAAAGAC
1 ATTATATATTTTGAAAGAC
13262887 ATTAT-TATTTTGAAAGAC
1 ATTATATATTTTGAAAGAC
13262905 A
1 A
13262906 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:13265021 original size:17 final size:18
Alignment explanation
Indices: 13264995--13265039 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
13264985 TTTCTTGAAG
*
13264995 TTTTTGTTTTCTGT-T-T
1 TTTTTCTTTTCTGTGTAT
13265011 TTATTTCTTTTCTGTGTAT
1 TT-TTTCTTTTCTGTGTAT
13265030 TTTTTCTTTT
1 TTTTTCTTTT
13265040 TTAAAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 2 0.08
17 11 0.44
18 9 0.36
19 3 0.12
ACGTcount: A:0.04, C:0.09, G:0.09, T:0.78
Consensus pattern (18 bp):
TTTTTCTTTTCTGTGTAT
Found at i:13265860 original size:92 final size:92
Alignment explanation
Indices: 13265702--13265903 Score: 314
Period size: 92 Copynumber: 2.2 Consensus size: 92
13265692 TCCAACCCAT
* * * * * *
13265702 TGCAACTTCGGGTAGATATTTGTCTCTTCAACCTATTTCACTGCAACTTCAGGGAGATAAGATCT
1 TGCAACTTTGGGGAGATATTCGTATCCTCAACCTATTCCACTGCAACTTCAGGGAGATAAGATCT
13265767 GTAGCTTATAGCTTTAGTTTATTCCAC
66 GTAGCTTATAGCTTTAGTTTATTCCAC
*
13265794 TGCAACTTTGGGGAGATATTCGTATCCTCAACCTATTCCACTGCAACTTCAGGGAGATAAGGTCT
1 TGCAACTTTGGGGAGATATTCGTATCCTCAACCTATTCCACTGCAACTTCAGGGAGATAAGATCT
*
13265859 GTAGCTTGTAGCTTTAGTTTATTCCAC
66 GTAGCTTATAGCTTTAGTTTATTCCAC
* *
13265886 TGTAACTTTAGGGAGATA
1 TGCAACTTTGGGGAGATA
13265904 AGACTTGCTG
Statistics
Matches: 100, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
92 100 1.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (92 bp):
TGCAACTTTGGGGAGATATTCGTATCCTCAACCTATTCCACTGCAACTTCAGGGAGATAAGATCT
GTAGCTTATAGCTTTAGTTTATTCCAC
Found at i:13266065 original size:89 final size:89
Alignment explanation
Indices: 13265964--13266220 Score: 270
Period size: 89 Copynumber: 2.9 Consensus size: 89
13265954 GGACTTGTCG
* * *
13265964 CTTCAATCTGCTCCACTCCAACTTCAAGGAGATAAGATTTGTAATCTTCAATCTGCTCCACTATA
1 CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTAT-AGCTTCAATCTGCTCCACTATA
** ***
13266029 ACT-TCA-AGTAGATAAGTTTTGTGA-
65 ACTAT-AGAG-AGATAAAATTTACCAT
* * * *
13266053 CTTCAA-CTTGCTCCATTGCAACTTCAAGGAGATAAGGTTTATAGCTTTAATCTGCTCCACTGTA
1 CTTCAATC-TGCTCCACTGCAACTTCAAGGAGATAAGATTTATAGCTTCAATCTGCTCCACTATA
13266117 ACTATAGAGAGATAAAATTTACCAT
65 ACTATAGAGAGATAAAATTTACCAT
* * * * * **
13266142 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTATGGCTTCAACCTACTCCATTGCAA
1 CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTATAGCTTCAATCTGCTCCACTATAA
*
13266207 CTTTAGAGAGATAA
66 CTATAGAGAGATAA
13266221 GGTTTATAAC
Statistics
Matches: 141, Mismatches: 22, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
88 34 0.24
89 106 0.75
90 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (89 bp):
CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTATAGCTTCAATCTGCTCCACTATAA
CTATAGAGAGATAAAATTTACCAT
Found at i:13266076 original size:44 final size:45
Alignment explanation
Indices: 13265964--13266181 Score: 203
Period size: 45 Copynumber: 4.9 Consensus size: 45
13265954 GGACTTGTCG
*
13265964 CTTCAATCTGCTCCACTCCAACTTCAAGGAGATAAGATTTGTAAT
1 CTTCAATCTGCTCCACTACAACTTCAAGGAGATAAGATTTGTAAT
* * * *
13266009 CTTCAATCTGCTCCACTATAACTTCAAGTAGATAAGTTTTGTGA-
1 CTTCAATCTGCTCCACTACAACTTCAAGGAGATAAGATTTGTAAT
* * * * *
13266053 CTTCAA-CTTGCTCCATTGCAACTTCAAGGAGATAAGGTTTAT-AG
1 CTTCAATC-TGCTCCACTACAACTTCAAGGAGATAAGATTTGTAAT
* ** * ***
13266097 CTTTAATCTGCTCCACTGTAAC-T-ATAGAGAGATAAAATTTACCAT
1 CTTCAATCTGCTCCACTACAACTTCA-AG-GAGATAAGATTTGTAAT
* *
13266142 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTT
1 CTTCAATCTGCTCCACTACAACTTCAAGGAGATAAGATTT
13266182 ATGGCTTCAA
Statistics
Matches: 143, Mismatches: 22, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
42 1 0.01
43 5 0.03
44 62 0.43
45 72 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:13266206 original size:44 final size:44
Alignment explanation
Indices: 13265963--13266228 Score: 236
Period size: 44 Copynumber: 6.0 Consensus size: 44
13265953 AGGACTTGTC
* *
13265963 GCTTCAATCTGCTCCACTCCAACTTCAAGGAGATAAGATTTGTAA
1 GCTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTAT-A
* ** * * *
13266008 TCTTCAATCTGCTCCACTATAACTTCAAGTAGATAAGTTTTGT-
1 GCTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTATA
* *
13266051 GACTTCAA-CTTGCTCCATTGCAACTTCAAGGAGATAAGGTTTATA
1 G-CTTCAATC-TGCTCCACTGCAACTTCAAGGAGATAAGATTTATA
* * * *
13266096 GCTTTAATCTGCTCCACTGTAAC-T-ATAGAGAGATAAAATTTACCA
1 GCTTCAATCTGCTCCACTGCAACTTCA-AG-GAGATAAGATTTA-TA
* * *
13266141 TCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTATG
1 GCTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTATA
* * * * *
13266185 GCTTCAACCTACTCCATTGCAACTT-TAGAGAGATAAGGTTTATA
1 GCTTCAATCTGCTCCACTGCAACTTCAAG-GAGATAAGATTTATA
13266229 ACTTGTAGCT
Statistics
Matches: 178, Mismatches: 33, Indels: 21
0.77 0.14 0.09
Matches are distributed among these distances:
42 1 0.01
43 5 0.03
44 96 0.54
45 73 0.41
46 2 0.01
47 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.32
Consensus pattern (44 bp):
GCTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTATA
Found at i:13269669 original size:50 final size:50
Alignment explanation
Indices: 13269545--13269793 Score: 275
Period size: 50 Copynumber: 4.8 Consensus size: 50
13269535 GATAATAACA
* * ** * *
13269545 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* * *
13269596 TGCCCATACCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
13269646 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
13269696 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
13269751 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
13269794 TTACCCAAAT
Statistics
Matches: 168, Mismatches: 23, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.54
51 32 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:13269724 original size:100 final size:104
Alignment explanation
Indices: 13269544--13269793 Score: 348
Period size: 100 Copynumber: 2.4 Consensus size: 104
13269534 TGATAATAAC
**
13269544 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATACCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATACCATG
* *
13269609 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* * *
13269646 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATACCATG
13269709 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
13269751 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
13269794 TTACCCAAAT
Statistics
Matches: 132, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
99 1 0.01
100 49 0.37
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATACCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:13269909 original size:13 final size:13
Alignment explanation
Indices: 13269888--13269919 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
13269878 GCTTGGATCA
*
13269888 TCATCAAATAAAT
1 TCATAAAATAAAT
13269901 TCATAAAATAAAT
1 TCATAAAATAAAT
13269914 TCATAA
1 TCATAA
13269920 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:13270163 original size:29 final size:30
Alignment explanation
Indices: 13270131--13270187 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
13270121 CCTCGACTCT
*
13270131 AACTTTT-CAAAATTATAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
13270160 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
13270188 AGGGCTCGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 7 0.29
30 17 0.71
ACGTcount: A:0.32, C:0.23, G:0.04, T:0.42
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:13281453 original size:29 final size:29
Alignment explanation
Indices: 13281407--13281465 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
13281397 TTTTATTATC
*
13281407 TAACATCTATCTTCGTACATTGAGGGCAA
1 TAACATCTATCTTCGTACATTGACGGCAA
*
13281436 TAACATCTATCTTTGTACATTGACGGCAA
1 TAACATCTATCTTCGTACATTGACGGCAA
13281465 T
1 T
13281466 GTACATATTA
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:13291608 original size:10 final size:10
Alignment explanation
Indices: 13291593--13291627 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
13291583 TCATTTAATT
*
13291593 AATTTTTTTA
1 AATTTTTTAA
13291603 AA-TTTTTAA
1 AATTTTTTAA
13291612 AATTTTTTAA
1 AATTTTTTAA
13291622 AATTTT
1 AATTTT
13291628 AATAATTCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
AATTTTTTAA
Found at i:13291634 original size:19 final size:19
Alignment explanation
Indices: 13291586--13291634 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 19
13291576 CATATTATCA
*
13291586 TTTAATTAATTTTTTTAAATT
1 TTTAA-TAA-TTTTTTAAAAT
13291607 TTTAA-AATTTTTTAAAAT
1 TTTAATAATTTTTTAAAAT
13291625 TTTAATAATT
1 TTTAATAATT
13291635 CTAATTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 15 0.58
19 6 0.23
21 5 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTAATAATTTTTTAAAAT
Found at i:13314370 original size:58 final size:59
Alignment explanation
Indices: 13314272--13314386 Score: 196
Period size: 58 Copynumber: 2.0 Consensus size: 59
13314262 TCATTGCAAC
**
13314272 AAGTAATTGGATACCTTACCATTTAACATACACGTAATTTTGTGGGT-TTTTTTTTTAT
1 AAGTAATTGGATACCTTACCATTTAACATACAAATAATTTTGTGGGTGTTTTTTTTTAT
*
13314330 AAGTAATTGGATACCTTACCATTTAACATACAAATGATTTTGTGGGTGTTTTTTTTT
1 AAGTAATTGGATACCTTACCATTTAACATACAAATAATTTTGTGGGTGTTTTTTTTT
13314387 TTGATAAATT
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
58 44 0.83
59 9 0.17
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.46
Consensus pattern (59 bp):
AAGTAATTGGATACCTTACCATTTAACATACAAATAATTTTGTGGGTGTTTTTTTTTAT
Found at i:13323073 original size:21 final size:21
Alignment explanation
Indices: 13323047--13323087 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
13323037 ATCTGCTCAA
* *
13323047 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
13323068 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
13323088 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:13328116 original size:31 final size:31
Alignment explanation
Indices: 13328081--13328140 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 31
13328071 CAATCCAGTG
13328081 ACTTAAAT-AAAAGTTTTCA-AATAGTTTAGCT
1 ACTTAAATGAAAA-TTTT-AGAATAGTTTAGCT
13328112 ACTTAAATGAAAATTTTAGAATAGTTTAG
1 ACTTAAATGAAAATTTTAGAATAGTTTAG
13328141 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:13331535 original size:144 final size:143
Alignment explanation
Indices: 13331275--13331559 Score: 489
Period size: 144 Copynumber: 2.0 Consensus size: 143
13331265 TTTGTTTACC
*
13331275 AACATTATAAATTTTCACGTGAATGGTCATTAGCAATCCCTTTGGAATGAGGTTCTTCCGCCAAA
1 AACATTACAAATTTTCACGTGAATGGTCATTAGCAATCCCTTTGGAATGAGGTTCTTCCGCCAAA
* *
13331340 GATTAAAGAATTTTTATAAAGATTATTATGTGGTTTTGTGGATTGTATTAGTCAATTTTTAACTC
66 GATTAAAGAATTTTTATAAAGATTATTATGTGGTTTTATGCATTGTATTAGTCAATTTTTAA-TC
13331405 ATGGGGTGAATACT
130 ATGGGGTGAATACT
* * *
13331419 AACATTACAGATTTTCATGTGAATGGTCATTAGCAATCCCTTTGGAATGAGGTTTTTCCGCCAAA
1 AACATTACAAATTTTCACGTGAATGGTCATTAGCAATCCCTTTGGAATGAGGTTCTTCCGCCAAA
* *
13331484 GATTAAAGAATTTTTATAGAGATTATTATGTGGTTTTATGCATTGTATTAGTCAATTTTTGATCA
66 GATTAAAGAATTTTTATAAAGATTATTATGTGGTTTTATGCATTGTATTAGTCAATTTTTAATCA
13331549 TGGGGTGAATA
131 TGGGGTGAATA
13331560 TTGACCCTTA
Statistics
Matches: 133, Mismatches: 8, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
143 14 0.11
144 119 0.89
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.39
Consensus pattern (143 bp):
AACATTACAAATTTTCACGTGAATGGTCATTAGCAATCCCTTTGGAATGAGGTTCTTCCGCCAAA
GATTAAAGAATTTTTATAAAGATTATTATGTGGTTTTATGCATTGTATTAGTCAATTTTTAATCA
TGGGGTGAATACT
Found at i:13332460 original size:25 final size:25
Alignment explanation
Indices: 13332423--13332472 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
13332413 GTGGGGAGTT
*
13332423 AGGATTTGGGTGTATTAGGTAAGTC
1 AGGACTTGGGTGTATTAGGTAAGTC
*
13332448 AGGACTTGTGTGTATTAGGTAAGTC
1 AGGACTTGGGTGTATTAGGTAAGTC
13332473 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:13333305 original size:29 final size:29
Alignment explanation
Indices: 13333272--13333327 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
13333262 TTTGGTCTTT
*
13333272 ATATTTGTATAATGTTATTAATTAGTTTA
1 ATATTTGTATAATGTAATTAATTAGTTTA
* *
13333301 ATATTTTTGTAATGTAATTAATTAGTT
1 ATATTTGTATAATGTAATTAATTAGTT
13333328 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:13334475 original size:29 final size:30
Alignment explanation
Indices: 13334441--13334499 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
13334431 CTTGGTTTGA
13334441 TGTGTAATTTTATACA-AAAATTTTGATTT
1 TGTGTAATTTTATACATAAAATTTTGATTT
*
13334470 TGTGTAATTTTATATATAAAATTTTGATTT
1 TGTGTAATTTTATACATAAAATTTTGATTT
13334500 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:13340716 original size:42 final size:42
Alignment explanation
Indices: 13340665--13340758 Score: 134
Period size: 42 Copynumber: 2.2 Consensus size: 42
13340655 AAGGCCTGAG
* *
13340665 ACACGGGTGTGTCTAGAGCCGTGTGAGGCACACGGCCTGTTC
1 ACACGGGTGTGTCTAGAACCGAGTGAGGCACACGGCCTGTTC
* * * *
13340707 ACATGGGTGTGTTTGGAATCGAGTGAGGCACACGGCCTGTTC
1 ACACGGGTGTGTCTAGAACCGAGTGAGGCACACGGCCTGTTC
13340749 ACACGGGTGT
1 ACACGGGTGT
13340759 TTGACCCCTG
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.18, C:0.22, G:0.36, T:0.23
Consensus pattern (42 bp):
ACACGGGTGTGTCTAGAACCGAGTGAGGCACACGGCCTGTTC
Found at i:13342917 original size:5 final size:5
Alignment explanation
Indices: 13342907--13342933 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
13342897 GTTATCTAAA
13342907 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
13342934 TCTCTCTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:13343943 original size:16 final size:16
Alignment explanation
Indices: 13343922--13343954 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
13343912 CATATGAGAA
13343922 GGAAGTTTTTTGTATG
1 GGAAGTTTTTTGTATG
13343938 GGAAGTTTTTTGTATG
1 GGAAGTTTTTTGTATG
13343954 G
1 G
13343955 CGATCATCGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.00, G:0.33, T:0.48
Consensus pattern (16 bp):
GGAAGTTTTTTGTATG
Found at i:13347517 original size:12 final size:12
Alignment explanation
Indices: 13347500--13347539 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
13347490 GCTAATGGGA
*
13347500 ATATATCAATAT
1 ATATATAAATAT
13347512 ATATATAAATAT
1 ATATATAAATAT
*
13347524 ATATATAAATAC
1 ATATATAAATAT
13347536 ATAT
1 ATAT
13347540 GAAAGTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (12 bp):
ATATATAAATAT
Found at i:13349506 original size:79 final size:81
Alignment explanation
Indices: 13349391--13349554 Score: 226
Period size: 79 Copynumber: 2.0 Consensus size: 81
13349381 TTTTTATCAT
* * * * *
13349391 TTTTGGGGGGAAAATTATAATTTTACCATTATTAATTTAAAATTTTATAAATTATAAAAG-GCTT
1 TTTTGGGGGGAAAACTACAATTTTACCATAACTAATTTAAAATTTTATAAATTATAAAAGATC-T
*
13349455 AAATTAAAAATTTATTA
65 AAATTAAAAATTTACTA
*
13349472 TTTT-GGGGG-AAACTACAATTTTACCATAACTAATTTAAAATTTTATAGATTATAAAAGATCTA
1 TTTTGGGGGGAAAACTACAATTTTACCATAACTAATTTAAAATTTTATAAATTATAAAAGATCTA
*
13349535 AATTGAAAATTTACTA
66 AATTAAAAATTTACTA
13349551 TTTT
1 TTTT
13349555 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 6 0.08
81 4 0.05
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (81 bp):
TTTTGGGGGGAAAACTACAATTTTACCATAACTAATTTAAAATTTTATAAATTATAAAAGATCTA
AATTAAAAATTTACTA
Found at i:13352448 original size:31 final size:29
Alignment explanation
Indices: 13352403--13352497 Score: 97
Period size: 31 Copynumber: 3.2 Consensus size: 29
13352393 TTCTTTAAAT
* *
13352403 ATGTATAATTGAATCAAAATTAAAGTTTC
1 ATGTATAATTGAATCAAAATCAAAGGTTC
13352432 ATGTATATATTTGAATCAAAATCAAAGGTTC
1 ATGTATA-A-TTGAATCAAAATCAAAGGTTC
*
13352463 ATATGTATAATT-ACA-CCAAATCAAA-GTTC
1 --ATGTATAATTGA-ATCAAAATCAAAGGTTC
13352492 ATGTAT
1 ATGTAT
13352498 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:13354970 original size:18 final size:21
Alignment explanation
Indices: 13354934--13354977 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
13354924 AAAATTATAA
13354934 AAAAAATTATAATATATT-AT
1 AAAAAATTATAATATATTAAT
*
13354954 AAAAAATTATCA-A-ATTAAT
1 AAAAAATTATAATATATTAAT
13354973 AAAAA
1 AAAAA
13354978 CATATTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 8 0.36
20 11 0.50
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (21 bp):
AAAAAATTATAATATATTAAT
Found at i:13360060 original size:9 final size:9
Alignment explanation
Indices: 13359968--13360060 Score: 71
Period size: 10 Copynumber: 9.8 Consensus size: 9
13359958 ATTCATAACA
13359968 ATAAAAATAT
1 ATAAAAAT-T
*
13359978 ATTAAAATT
1 ATAAAAATT
*
13359987 CTTAAAAACTT
1 -ATAAAAA-TT
*
13359998 ATAAAAATC
1 ATAAAAATT
13360007 ATATAAAATT
1 ATA-AAAATT
*
13360017 AT-TAAATT
1 ATAAAAATT
*
13360025 AAAAAAATT
1 ATAAAAATT
*
13360034 AATATAAACTT
1 -ATA-AAAATT
13360045 ATAAAAATT
1 ATAAAAATT
13360054 ATAAAAA
1 ATAAAAA
13360061 AACATAAAAA
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:13360499 original size:9 final size:9
Alignment explanation
Indices: 13360487--13360688 Score: 58
Period size: 9 Copynumber: 21.4 Consensus size: 9
13360477 TTTTATGTTT
13360487 TTTTAATAA
1 TTTTAATAA
*
13360496 TTTTTATAA
1 TTTTAATAA
*
13360505 GTTTATATCAA
1 TTTTA-AT-AA
13360516 TTTTAAT--
1 TTTTAATAA
*
13360523 TTTTTATAA
1 TTTTAATAA
*
13360532 GTTTTTAAGAA
1 --TTTTAATAA
13360543 TTTTAATACA
1 TTTTAATA-A
*
13360553 TTTTTATAAAA
1 -TTTTA-ATAA
*
13360564 TTTTAAATATG
1 TTTT-AATA-A
*
13360575 TTTTATTAA
1 TTTTAATAA
13360584 TTTT-ATAAA
1 TTTTAAT-AA
13360593 TTTT-ATAAA
1 TTTTAAT-AA
*
13360602 ATTT-ATAA
1 TTTTAATAA
** *
13360610 GTTTTTTTCA
1 -TTTTAATAA
*
13360620 TTTTATTATA
1 TTTTAATA-A
13360630 TTTTAATAA
1 TTTTAATAA
*
13360639 GTTTATATAA
1 TTTTA-ATAA
* * *
13360649 GTTTATTAT
1 TTTTAATAA
*
13360658 TTTTAAAATA
1 TTTTAATA-A
13360668 TATTTAAT--
1 T-TTTAATAA
13360676 TTTTAATAA
1 TTTTAATAA
13360685 TTTT
1 TTTT
13360689 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:13360534 original size:27 final size:28
Alignment explanation
Indices: 13360487--13360561 Score: 89
Period size: 27 Copynumber: 2.6 Consensus size: 28
13360477 TTTTATGTTT
*
13360487 TTTTAATAATTTTTATAAGTTTATATCAA
1 TTTTAAT-ATTTTTATAAGTTTATAACAA
* *
13360516 TTTTAAT-TTTTTATAAGTTTTTAAGAA
1 TTTTAATATTTTTATAAGTTTATAACAA
13360543 TTTTAATACATTTTTATAA
1 TTTTAAT--ATTTTTATAA
13360562 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:13360598 original size:18 final size:18
Alignment explanation
Indices: 13360575--13360666 Score: 69
Period size: 18 Copynumber: 5.1 Consensus size: 18
13360565 TTTAAATATG
13360575 TTTTATTAATTTTATAAA
1 TTTTATTAATTTTATAAA
* * *
13360593 TTTTATAAAATTTATAAG
1 TTTTATTAATTTTATAAA
* * *
13360611 TTTTTTTCATTTTATTATA
1 TTTTATTAATTTTA-TAAA
* *
13360630 TTTTAATAAGTTTATATAA
1 TTTTATTAATTTTATA-AA
* *
13360649 GTTTATTATTTTTA-AAA
1 TTTTATTAATTTTATAAA
13360666 T
1 T
13360667 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:13361752 original size:14 final size:15
Alignment explanation
Indices: 13361733--13361770 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
13361723 AAGTAAAAAA
13361733 ATAATATAAA-TTTT
1 ATAATATAAACTTTT
13361747 ATAATATATAACTTTT
1 ATAATATA-AACTTTT
13361763 ATAA-ATAA
1 ATAATATAA
13361771 TGTTTTATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 9 0.41
15 5 0.23
16 8 0.36
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAATATAAACTTTT
Found at i:13361755 original size:16 final size:16
Alignment explanation
Indices: 13361736--13361766 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13361726 TAAAAAAATA
13361736 ATATAAATTTTATAAT
1 ATATAAATTTTATAAT
*
13361752 ATATAACTTTTATAA
1 ATATAAATTTTATAA
13361767 ATAATGTTTT
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:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATAAATTTTATAAT
Found at i:13375031 original size:4 final size:4
Alignment explanation
Indices: 13375017--13375048 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
13375007 CTATTACCAT
13375017 AAAC AAAAC AAAC AAAC AAAC AAAC AAAC AAA
1 AAAC -AAAC AAAC AAAC AAAC AAAC AAAC AAA
13375049 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:13382000 original size:30 final size:30
Alignment explanation
Indices: 13381961--13382021 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
13381951 ACTAACAAAG
*
13381961 TGTATGATATATCATCAAATTCTACATTTT
1 TGTAGGATATATCATCAAATTCTACATTTT
13381991 TGTAGGATATATCATCAAATTCTACATTTT
1 TGTAGGATATATCATCAAATTCTACATTTT
13382021 T
1 T
13382022 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:13383032 original size:39 final size:39
Alignment explanation
Indices: 13382980--13383057 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
13382970 TTGCTCATCA
13382980 AAACCCAAAGTACTAAGCTGTACTTTTTTAGTTTTTTTC
1 AAACCCAAAGTACTAAGCTGTACTTTTTTAGTTTTTTTC
*
13383019 AAACCCAAAGTACTAAGCTTTACTTTTTTAGTTTTTTTC
1 AAACCCAAAGTACTAAGCTGTACTTTTTTAGTTTTTTTC
13383058 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:13383885 original size:23 final size:24
Alignment explanation
Indices: 13383859--13383909 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
13383849 TTATGGTTTT
13383859 AAGGCAAAA-AAAAAAGA-AAAAAA
1 AAGG-AAAATAAAAAAGAGAAAAAA
**
13383882 AAGGAAAATAGTAAAGAGAAAAAA
1 AAGGAAAATAAAAAAGAGAAAAAA
13383906 AAGG
1 AAGG
13383910 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:13388406 original size:5 final size:5
Alignment explanation
Indices: 13388396--13388483 Score: 162
Period size: 5 Copynumber: 18.0 Consensus size: 5
13388386 AATAATTAAG
13388396 TATAT TATA- T-TAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
13388444 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
13388484 AAAAGAAACA
Statistics
Matches: 81, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
3 2 0.02
4 2 0.02
5 77 0.95
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:13389311 original size:40 final size:40
Alignment explanation
Indices: 13389264--13389344 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
13389254 AATTATGGGA
* ** *
13389264 TACTGAATATTGTTTTGAATACTGAATTGAACTGTGAAAT
1 TACTGAATAATGTTACGAATACTGAATTGAACTGTAAAAT
* * *
13389304 TACTGAATAATGTTACGTATATTGCATTGAACTGTAAAAT
1 TACTGAATAATGTTACGAATACTGAATTGAACTGTAAAAT
13389344 T
1 T
13389345 TCTAATGAAG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.40
Consensus pattern (40 bp):
TACTGAATAATGTTACGAATACTGAATTGAACTGTAAAAT
Found at i:13389571 original size:12 final size:12
Alignment explanation
Indices: 13389554--13389578 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13389544 GCCGACTACT
13389554 GTTACTGTTACC
1 GTTACTGTTACC
13389566 GTTACTGTTACC
1 GTTACTGTTACC
13389578 G
1 G
13389579 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:13389609 original size:45 final size:45
Alignment explanation
Indices: 13389556--13389662 Score: 162
Period size: 45 Copynumber: 2.4 Consensus size: 45
13389546 CGACTACTGT
*
13389556 TACTGTTACCGTTACTGTTACCGATTC-GACACTTTGTGTGTCGAA
1 TACTGTTACCGTTACTGTTACAGATTCAG-CACTTTGTGTGTCGAA
* *
13389601 TATTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAA
1 TACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAA
*
13389646 TACTGTTACTGTTACTG
1 TACTGTTACCGTTACTG
13389663 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:13389657 original size:6 final size:6
Alignment explanation
Indices: 13389646--13389687 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
13389636 GTGTGTTGAA
* *
13389646 TACTGT TACTGT TACTGC TACTGC TACTGT TACTGAT TACTG
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTG
13389688 ATTAGGTACT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
6 27 0.82
7 6 0.18
ACGTcount: A:0.19, C:0.21, G:0.17, T:0.43
Consensus pattern (6 bp):
TACTGT
Found at i:13394604 original size:30 final size:30
Alignment explanation
Indices: 13394565--13394626 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
13394555 TGTATGAGTA
* *
13394565 TGGGTAAAATTCAGCCTAACATGGGTATAT
1 TGGGGAAAATTCAGCCCAACATGGGTATAT
*
13394595 TGGGGAAAATTCGGCCCAACATGGGTATAT
1 TGGGGAAAATTCAGCCCAACATGGGTATAT
13394625 TG
1 TG
13394627 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:13394651 original size:38 final size:38
Alignment explanation
Indices: 13394595--13394669 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
13394585 ATGGGTATAT
13394595 TGGGGAAAATTCGGCCCAACATGGGTATATTGAAATTA
1 TGGGGAAAATTCGGCCCAACATGGGTATATTGAAATTA
* *
13394633 TGGGTAAAATTTGGCCCAACATGGGTATATTGAAATT
1 TGGGGAAAATTCGGCCCAACATGGGTATATTGAAATT
13394670 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:13395347 original size:56 final size:56
Alignment explanation
Indices: 13395277--13395420 Score: 225
Period size: 56 Copynumber: 2.6 Consensus size: 56
13395267 ACCTGGAAGT
13395277 ATATGCGATTCCGATATATGTGTACGAGTAAGACCACGTTTTATACGTTGGCATCG
1 ATATGCGATTCCGATATATGTGTACGAGTAAGACCACGTTTTATACGTTGGCATCG
* * *
13395333 ATTTGCGACTCCGATATATGTGTGCGAGTAAGACCACGTTTTATACGTTGGCATCG
1 ATATGCGATTCCGATATATGTGTACGAGTAAGACCACGTTTTATACGTTGGCATCG
* ** *
13395389 ATATGTGATTCCGATATGCGTTTACGAGTAAG
1 ATATGCGATTCCGATATATGTGTACGAGTAAG
13395421 GCCCTATCTG
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
56 78 1.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (56 bp):
ATATGCGATTCCGATATATGTGTACGAGTAAGACCACGTTTTATACGTTGGCATCG
Found at i:13399517 original size:14 final size:14
Alignment explanation
Indices: 13399500--13399535 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
13399490 ATAAATATAT
* *
13399500 AATATAAATACAAA
1 AATAAAAATAAAAA
13399514 AATAAAAATAAAAA
1 AATAAAAATAAAAA
13399528 AATAAAAA
1 AATAAAAA
13399536 AGAGAGCTTT
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:13400133 original size:3 final size:3
Alignment explanation
Indices: 13400125--13400171 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
13400115 TTATTCTACT
13400125 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
13400172 GTGTGTTGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:13400319 original size:18 final size:17
Alignment explanation
Indices: 13400283--13400322 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
13400273 TTATGTTATA
*
13400283 TATATATATTTATACAT
1 TATATATATTTAAACAT
*
13400300 TATATATACTTTAAATAT
1 TATATATA-TTTAAACAT
13400318 TATAT
1 TATAT
13400323 CTTATATACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATATATTTAAACAT
Found at i:13400459 original size:20 final size:20
Alignment explanation
Indices: 13400436--13400484 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
13400426 TTAATACTAC
***
13400436 ATTATATATATATTTTTTAT
1 ATTATATATATATTTCAAAT
**
13400456 ATTATGCATATATTTCAAAT
1 ATTATATATATATTTCAAAT
13400476 ATTATATAT
1 ATTATATAT
13400485 TAAGTATTTC
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (20 bp):
ATTATATATATATTTCAAAT
Found at i:13400601 original size:15 final size:15
Alignment explanation
Indices: 13400581--13400630 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
13400571 ATTGCTAATG
13400581 TATATG-TATATATCA
1 TATATGTTATATAT-A
*
13400596 TATATGTTTTATATA
1 TATATGTTATATATA
* *
13400611 TATATATTATGTATA
1 TATATGTTATATATA
13400626 TATAT
1 TATAT
13400631 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:13400620 original size:13 final size:13
Alignment explanation
Indices: 13400581--13400631 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
13400571 ATTGCTAATG
*
13400581 TATATGTATATAT
1 TATATATATATAT
* *
13400594 CATATATGT-T-T
1 TATATATATATAT
13400605 TATATATATATAT
1 TATATATATATAT
*
13400618 TATGTATATATAT
1 TATATATATATAT
13400631 T
1 T
13400632 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:13400639 original size:24 final size:26
Alignment explanation
Indices: 13400610--13400719 Score: 74
Period size: 26 Copynumber: 4.5 Consensus size: 26
13400600 TGTTTTATAT
13400610 ATATA-TATTATGTATATATATTTTC
1 ATATACTATTATGTATATATATTTTC
*
13400635 A-ATATTATTA-GT-TATAT-TTTT-
1 ATATACTATTATGTATATATATTTTC
* * * * *
13400656 ATATACTATTCTATGTACATATTTCC
1 ATATACTATTATGTATATATATTTTC
*
13400682 ATAT-CATCTTATGTATATATATTCTT-
1 ATATAC-TATTATGTATATATATT-TTC
*
13400708 AAATACTATTAT
1 ATATACTATTAT
13400720 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:13401791 original size:27 final size:28
Alignment explanation
Indices: 13401761--13401819 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 28
13401751 TAATGATAAA
*
13401761 AATTTAA-ATAATATTTATCTTAATGAT
1 AATTTAACATAATATTTATATTAATGAT
*
13401788 AA-TTAACATAATATTTATATTTATGAT
1 AATTTAACATAATATTTATATTAATGAT
13401815 AATTT
1 AATTT
13401820 TATATATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 4 0.14
27 22 0.79
28 2 0.07
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (28 bp):
AATTTAACATAATATTTATATTAATGAT
Found at i:13401883 original size:20 final size:20
Alignment explanation
Indices: 13401860--13401897 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
13401850 TTACGTAAAA
13401860 TTTTCAAAATTTATTTAACC
1 TTTTCAAAATTTATTTAACC
*
13401880 TTTTCAAATTTTATTTAA
1 TTTTCAAAATTTATTTAA
13401898 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:13402538 original size:19 final size:19
Alignment explanation
Indices: 13402516--13402555 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
13402506 TTTTAATAAT
13402516 AAAATAGGAATTTTTTT-AA
1 AAAATA-GAATTTTTTTGAA
*
13402535 AAAATAGATTTTTTTTGAA
1 AAAATAGAATTTTTTTGAA
13402554 AA
1 AA
13402556 CACTTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.42
Consensus pattern (19 bp):
AAAATAGAATTTTTTTGAA
Found at i:13402734 original size:13 final size:13
Alignment explanation
Indices: 13402716--13402745 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
13402706 ATATAATTAT
13402716 TTTAAAATTTAAA
1 TTTAAAATTTAAA
*
13402729 TTTAAAATTTATA
1 TTTAAAATTTAAA
13402742 TTTA
1 TTTA
13402746 TCAAATACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TTTAAAATTTAAA
Found at i:13403780 original size:24 final size:24
Alignment explanation
Indices: 13403753--13403804 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
13403743 TTAGTAAGTC
*
13403753 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
13403777 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
13403801 AAAT
1 AAAT
13403805 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:13405009 original size:19 final size:20
Alignment explanation
Indices: 13404973--13405020 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
13404963 ATATGTAATT
*
13404973 TTTTTAATTTTTATAAAT-A
1 TTTTAAATTTTTATAAATAA
13404992 TTTTAAATTTTTGA-AAATAA
1 TTTTAAATTTTT-ATAAATAA
*
13405012 TTTTGAATT
1 TTTTAAATT
13405021 ATTTTGTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (20 bp):
TTTTAAATTTTTATAAATAA
Found at i:13405506 original size:21 final size:22
Alignment explanation
Indices: 13405454--13405508 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
13405444 AAAAAATTTA
* *
13405454 AAATATTATTTTGTTAAATAAT
1 AAATATTATATTGTTAAACAAT
* **
13405476 AATTGGTATATT-TTAAACAAT
1 AAATATTATATTGTTAAACAAT
13405497 AAATATTATATT
1 AAATATTATATT
13405509 CATTGAAATT
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:13405965 original size:29 final size:31
Alignment explanation
Indices: 13405909--13405968 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 31
13405899 AACCTGAAAT
* *
13405909 TTGAAATCTAAAAAGTAGAAGGACTAAATTC
1 TTGAAATCTAAAAAGTACAAAGACTAAATTC
*
13405940 TTGAAAT-TAAAAA-TACAAAGATTAAATTC
1 TTGAAATCTAAAAAGTACAAAGACTAAATTC
13405969 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:13406033 original size:18 final size:17
Alignment explanation
Indices: 13406001--13406034 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
13405991 ACCTATGGCA
13406001 TATTTTAGCATTTTTTG
1 TATTTTAGCATTTTTTG
*
13406018 TATTTATAGTATTTTTT
1 TATTT-TAGCATTTTTT
13406035 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:13407160 original size:11 final size:10
Alignment explanation
Indices: 13407123--13407165 Score: 54
Period size: 11 Copynumber: 4.3 Consensus size: 10
13407113 TTTCTAAAAT
13407123 TTTATATTTA
1 TTTATATTTA
13407133 TTTGA-ATTT-
1 TTT-ATATTTA
13407142 TTTATATTTA
1 TTTATATTTA
13407152 TTATATATTTA
1 TT-TATATTTA
13407163 TTT
1 TTT
13407166 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:13410709 original size:15 final size:15
Alignment explanation
Indices: 13410686--13410716 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
13410676 CAAATATTAG
*
13410686 CATCTTCTTCTTCTT
1 CATCATCTTCTTCTT
13410701 CATCATCTTCTTCTT
1 CATCATCTTCTTCTT
13410716 C
1 C
13410717 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:13414731 original size:4 final size:4
Alignment explanation
Indices: 13414722--13414753 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
13414712 TTTTTCTACA
13414722 TATG TATG TATG TATG TATG TAATG TATG TAT
1 TATG TATG TATG TATG TATG T-ATG TATG TAT
13414754 TAGTTTACCA
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:13432553 original size:25 final size:25
Alignment explanation
Indices: 13432524--13432618 Score: 154
Period size: 25 Copynumber: 3.8 Consensus size: 25
13432514 CTGTACATGT
*
13432524 ATGCTCACATGAGCTGTAAATCAGA
1 ATGCTCACATGAGCTGTGAATCAGA
13432549 ATGCTCACATGAGCTGTGAATCAGA
1 ATGCTCACATGAGCTGTGAATCAGA
* *
13432574 ATGCTCACACGAGCTGTGAATTAGA
1 ATGCTCACATGAGCTGTGAATCAGA
*
13432599 ATGCTTACATGAGCTGTGAA
1 ATGCTCACATGAGCTGTGAA
13432619 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:13432639 original size:27 final size:25
Alignment explanation
Indices: 13432524--13432642 Score: 121
Period size: 25 Copynumber: 4.7 Consensus size: 25
13432514 CTGTACATGT
* * *
13432524 ATGCTCACATGAGCTGTAAATCAGA
1 ATGCTCACACGAGCTGTGAATGAGA
* *
13432549 ATGCTCACATGAGCTGTGAATCAGA
1 ATGCTCACACGAGCTGTGAATGAGA
*
13432574 ATGCTCACACGAGCTGTGAATTAGA
1 ATGCTCACACGAGCTGTGAATGAGA
* * * *
13432599 ATGCTTACATGAGCTGTGAAAATGGGT
1 ATGCTCACACGAGCTGTG--AATGAGA
*
13432626 CTGCTCACACGAGCTGT
1 ATGCTCACACGAGCTGT
13432643 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:13453257 original size:29 final size:29
Alignment explanation
Indices: 13453211--13453269 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
13453201 AAATTGAATC
*
13453211 AAATCAAAACGTTATATATAAAATTGCACA
1 AAATCAAAAC-TTATATATAAAATTACACA
*
13453241 AAATCAAAA-TTCATATATAACATTACACA
1 AAATCAAAACTT-ATATATAAAATTACACA
13453270 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:13457923 original size:24 final size:22
Alignment explanation
Indices: 13457868--13457926 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 22
13457858 TATACATAAT
13457868 ATATATA-ATAAATATTGAAAA
1 ATATATACATAAATATTGAAAA
*
13457889 ATGTATGTACATAACATATATGAAAA
1 A--TATATACATAA-ATAT-TGAAAA
13457915 ATATATACATAA
1 ATATATACATAA
13457927 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:13457929 original size:27 final size:24
Alignment explanation
Indices: 13457865--13457986 Score: 72
Period size: 26 Copynumber: 4.8 Consensus size: 24
13457855 ATATATACAT
13457865 AATATAT-ATAATAAATATTGAAA
1 AATATATAATAATAAATATTGAAA
* *
13457888 AATGTAT-GTACATAACATATATGAAA
1 AATATATAATA-ATAA-ATAT-TGAAA
*
13457914 AATATATACATAAT-AATATTTAAA
1 AATATATA-ATAATAAATATTGAAA
* *
13457938 AA-AAATAATAAGTGATAATAGTGAAAA
1 AATATATAATAA-T-A-AATATTG-AAA
13457965 TAATAGGTATAATAATAAATAT
1 -AATA--TATAATAATAAATAT
13457987 AATGATGTAT
Statistics
Matches: 75, Mismatches: 10, Indels: 23
0.69 0.09 0.21
Matches are distributed among these distances:
22 4 0.05
23 13 0.17
24 10 0.13
25 8 0.11
26 17 0.23
27 5 0.07
28 8 0.11
29 2 0.03
30 1 0.01
31 7 0.09
ACGTcount: A:0.57, C:0.02, G:0.08, T:0.32
Consensus pattern (24 bp):
AATATATAATAATAAATATTGAAA
Found at i:13458441 original size:3 final size:3
Alignment explanation
Indices: 13458414--13458494 Score: 50
Period size: 3 Copynumber: 28.3 Consensus size: 3
13458404 AGCTAGAACA
* * *
13458414 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
*
13458456 AAT AA- AGAT AA- AGA- AAT AAT AGT AAT AAT AAT AAT AAT A
1 AAT AAT A-AT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT A
13458495 GAAAAGATTG
Statistics
Matches: 61, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
2 11 0.18
3 47 0.77
4 3 0.05
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:13458492 original size:26 final size:25
Alignment explanation
Indices: 13458420--13458498 Score: 74
Period size: 26 Copynumber: 3.1 Consensus size: 25
13458410 AACAAATACT
*
13458420 AATAATAGTAAAAACTAATAATATA-A
1 AATAATAGT-AAAA-TAATAATAAAGA
*
13458446 TATAATA-TAAAATAA-AGATAAAGA
1 AATAATAGTAAAATAATA-ATAAAGA
13458470 AATAATAGTAATAATAATAATAATAGA
1 AATAATAGTAA-AATAATAATAA-AGA
13458497 AA
1 AA
13458499 AGATTGGTAC
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
22 1 0.02
23 7 0.16
24 11 0.25
25 4 0.09
26 15 0.34
27 6 0.14
ACGTcount: A:0.66, C:0.01, G:0.06, T:0.27
Consensus pattern (25 bp):
AATAATAGTAAAATAATAATAAAGA
Found at i:13460375 original size:14 final size:14
Alignment explanation
Indices: 13460331--13460366 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
13460321 ATTCTTTAAA
*
13460331 AAAAACAGACATT-
1 AAAAACAGAAATTG
13460344 AAAAACAGAAATTG
1 AAAAACAGAAATTG
13460358 AAAAACAGA
1 AAAAACAGA
13460367 TTTTGAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.67, C:0.11, G:0.11, T:0.11
Consensus pattern (14 bp):
AAAAACAGAAATTG
Found at i:13460603 original size:76 final size:76
Alignment explanation
Indices: 13460394--13460595 Score: 298
Period size: 76 Copynumber: 2.7 Consensus size: 76
13460384 CATGTAACGA
* *
13460394 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAATAGAAACTAAAAATACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAAACATAAACTAAAAATACCTCA
* *
13460459 GCGTGTGACCCG
65 ACGTATGACCCG
* *
13460471 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTAAAAAACATCAACTAAAAATACCTCAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACATAAACTAAAAATACCTCAA
13460536 CGTATGACCCG
66 CGTATGACCCG
* ** *
13460547 AGGCTCAGCTCACCTCTAACAATATGAATTGA-TTTTTGAAAAACATAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACATAAA
13460596 TTGAAAAAAA
Statistics
Matches: 113, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
75 15 0.13
76 66 0.58
77 32 0.28
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (76 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACATAAACTAAAAATACCTCAA
CGTATGACCCG
Found at i:13460658 original size:87 final size:87
Alignment explanation
Indices: 13460524--13460777 Score: 350
Period size: 89 Copynumber: 2.9 Consensus size: 87
13460514 ACATCAACTA
* * * *
13460524 AAAATACCTCAACGTATGACCC-GAGGCTCAGCTCACCTCTA-ACAATATGAATTGATTTTTGAA
1 AAAATACCTCAGCG--TG-CCCTGAGGCTCAACTCACCTC-ACGCAATATGAGTTGATTTTTGAA
*
13460587 AAACATAAATTGAAAAAAAGACATTG
62 AAACAGAAATTGAAAAAAAGACATTG
13460613 AAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCACGCAATATGAGTTGATTTTTTTGAAAA
1 AAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCACGCAATATGAGTTGA--TTTTTGAAAA
* **
13460678 GCAGAAATTGAAAAGCAGACATTG
64 ACAGAAATTGAAAAAAAGACATTG
* *
13460702 AAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAAC
1 AAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCACGCAATATGAGTTGATTTTTGAAAAAC
13460767 AGAAATTGAAA
66 AGAAATTGAAA
13460778 TTACCTCAGC
Statistics
Matches: 150, Mismatches: 11, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
86 4 0.03
87 51 0.34
89 95 0.63
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (87 bp):
AAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCACGCAATATGAGTTGATTTTTGAAAAAC
AGAAATTGAAAAAAAGACATTG
Found at i:13460690 original size:14 final size:14
Alignment explanation
Indices: 13460671--13460705 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
13460661 GTTGATTTTT
13460671 TTGAAAAGCAGAAA
1 TTGAAAAGCAGAAA
*
13460685 TTGAAAAGCAGACA
1 TTGAAAAGCAGAAA
13460699 TTGAAAA
1 TTGAAAA
13460706 TACCTCAGCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.54, C:0.09, G:0.20, T:0.17
Consensus pattern (14 bp):
TTGAAAAGCAGAAA
Found at i:13460818 original size:73 final size:72
Alignment explanation
Indices: 13460685--13460844 Score: 248
Period size: 73 Copynumber: 2.2 Consensus size: 72
13460675 AAAGCAGAAA
*
13460685 TTGAAAAGCAGACATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAA-CAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
13460750 GTTGATTT
65 GTTGATTT
* * * *
13460758 TTGACAAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTTGCAATATGA
1 TTGA-AAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
13460823 GTTGATTT
65 GTTGATTT
*
13460831 TTGAAAATAGAAAT
1 TTGAAAACAGAAAT
13460845 AAACATCAAA
Statistics
Matches: 80, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
72 9 0.11
73 68 0.85
74 3 0.04
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.29
Consensus pattern (72 bp):
TTGAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAG
TTGATTT
Found at i:13470520 original size:50 final size:51
Alignment explanation
Indices: 13470466--13470564 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 51
13470456 TTTTTATTTC
13470466 ATATT-GTTTCAAATTTTTT-TATTTTTAATTAAGATTTATAATTAATAAAT
1 ATATTAGTTTCAAATTTTTTAT-TTTTTAATTAAGATTTATAATTAATAAAT
* * ** *
13470516 ATATTATTTTCAAATTTTTTATTTTTTAATTCATCTTTTTAATTAATAA
1 ATATTAGTTTCAAATTTTTTATTTTTTAATTAAGATTTATAATTAATAA
13470565 CTTTTTTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
50 5 0.12
51 36 0.86
52 1 0.02
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (51 bp):
ATATTAGTTTCAAATTTTTTATTTTTTAATTAAGATTTATAATTAATAAAT
Found at i:13471128 original size:31 final size:34
Alignment explanation
Indices: 13471083--13471154 Score: 96
Period size: 35 Copynumber: 2.2 Consensus size: 34
13471073 CATCATTGGA
*
13471083 TATTATTATAGG-A-TATTA-TAAAATACATTGT
1 TATTATCATAGGAATTATTAGTAAAATACATTGT
*
13471114 TATTATCATTGGATATTATTAGTAAAATACATTGT
1 TATTATCATAGGA-ATTATTAGTAAAATACATTGT
13471149 TATTAT
1 TATTAT
13471155 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:13471168 original size:17 final size:18
Alignment explanation
Indices: 13471096--13471171 Score: 68
Period size: 17 Copynumber: 4.3 Consensus size: 18
13471086 TATTATAGGA
13471096 TATTATAAAATACATTGT
1 TATTATAAAATACATTGT
* * ** *
13471114 TATTAT-CATTGGA-TAT
1 TATTATAAAATACATTGT
13471130 TATTAGTAAAATACATTGT
1 TATTA-TAAAATACATTGT
*
13471149 TATTATAAAA-ACATTTT
1 TATTATAAAATACATTGT
13471166 TATTAT
1 TATTAT
13471172 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:13476265 original size:19 final size:19
Alignment explanation
Indices: 13476227--13476265 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
13476217 TCATACTACA
**
13476227 AAATATTTATTATTGTAAT
1 AAATATTTATTATTAAAAT
13476246 AAATATTTATTATTAAAAT
1 AAATATTTATTATTAAAAT
13476265 A
1 A
13476266 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:13482082 original size:20 final size:20
Alignment explanation
Indices: 13482059--13482112 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
13482049 TAAATCTATT
13482059 TTAAATTTTATAA-TTATAAA
1 TTAAATTTTATAATTTA-AAA
*
13482079 TTAAATTATAGTAATTTAAAA
1 TTAAATTTTA-TAATTTAAAA
*
13482100 TT-AATTTAATAAT
1 TTAAATTTTATAAT
13482113 ATGATAGAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 4 0.14
20 14 0.48
21 8 0.28
22 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
TTAAATTTTATAATTTAAAA
Found at i:13482100 original size:21 final size:20
Alignment explanation
Indices: 13482059--13482112 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
13482049 TAAATCTATT
*
13482059 TTAAATTTTATAATTATAAA
1 TTAAATTATATAATTATAAA
13482079 TTAAATTATAGTAATT-TAAAA
1 TTAAATTATA-TAATTAT-AAA
*
13482100 TTAATTTA-ATAAT
1 TTAAATTATATAAT
13482113 ATGATAGAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 4 0.13
20 11 0.37
21 15 0.50
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
TTAAATTATATAATTATAAA
Found at i:13491371 original size:22 final size:22
Alignment explanation
Indices: 13491310--13491378 Score: 61
Period size: 22 Copynumber: 3.1 Consensus size: 22
13491300 ATGAAAAAAA
* * *
13491310 CTATTTTTTTAATATTATTTT-
1 CTATTATTTTACTACTATTTTG
*
13491331 CTTATTATTTT-CTCTCTATTTTG
1 C-TATTATTTTACT-ACTATTTTG
*
13491354 CTATTATTTTACTACTATATTG
1 CTATTATTTTACTACTATTTTG
13491376 CTA
1 CTA
13491379 CGATTTTATT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
21 2 0.05
22 33 0.87
23 3 0.08
ACGTcount: A:0.22, C:0.13, G:0.03, T:0.62
Consensus pattern (22 bp):
CTATTATTTTACTACTATTTTG
Found at i:13491639 original size:12 final size:12
Alignment explanation
Indices: 13491609--13491641 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
13491599 TATATATTTT
13491609 AAAATT-ATATA
1 AAAATTAATATA
13491620 AAAA-TAATATA
1 AAAATTAATATA
13491631 AAAATTAATAT
1 AAAATTAATAT
13491642 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:13495100 original size:96 final size:99
Alignment explanation
Indices: 13494975--13495180 Score: 262
Period size: 96 Copynumber: 2.1 Consensus size: 99
13494965 GTTTTTAAAT
* * * ** *
13494975 TTTAGGG-TTTTAAGGAAAAAAATTAAATAAATTAGGGTTTAGTGTTTGTTAATTAAATTAATTA
1 TTTAGGGTTTTTAAGGAAAAAAATAAAATAAATTAGGATTTAGGGTTACTTAAGTAAATTAATTA
*
13495039 CT-AA-TTTT-AAAAAATTAGATTATGG-TTTAGTG
66 -TAAATTTTTAAAAAAATTAGATTA-GGATTTAGGG
* *
13495071 TTTATGGTTTTTAAGG-AAAAAATAAAATAAATTAGGATTTAGGGTTACTTGAGTAAATTAATTA
1 TTTAGGGTTTTTAAGGAAAAAAATAAAATAAATTAGGATTTAGGGTTACTTAAGTAAATTAATTA
13495135 TAAATTTTTAAAAAAATTAGATTAGGATTTTAGGG
66 TAAATTTTTAAAAAAATTAGATTAGGA-TTTAGGG
13495170 TTTAGGGTTTT
1 TTTAGGGTTTT
13495181 AGGGTATTTA
Statistics
Matches: 94, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
95 1 0.01
96 49 0.52
97 14 0.15
98 14 0.15
99 16 0.17
ACGTcount: A:0.39, C:0.01, G:0.17, T:0.42
Consensus pattern (99 bp):
TTTAGGGTTTTTAAGGAAAAAAATAAAATAAATTAGGATTTAGGGTTACTTAAGTAAATTAATTA
TAAATTTTTAAAAAAATTAGATTAGGATTTAGGG
Found at i:13495180 original size:15 final size:15
Alignment explanation
Indices: 13495156--13495185 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13495146 AAAAATTAGA
13495156 TTAGGATTTTAGGGT
1 TTAGGATTTTAGGGT
*
13495171 TTAGGGTTTTAGGGT
1 TTAGGATTTTAGGGT
13495186 ATTTAAGAAA
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:0.17, C:0.00, G:0.37, T:0.47
Consensus pattern (15 bp):
TTAGGATTTTAGGGT
Found at i:13495625 original size:126 final size:126
Alignment explanation
Indices: 13495253--13495798 Score: 801
Period size: 126 Copynumber: 4.3 Consensus size: 126
13495243 TAATCTAAAA
* * *
13495253 AAGCTTCTACGTGGATGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAAATTTGAGAAGACGTGT
1 AAGCTTCCACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTGT
*
13495318 CTGCGCAAATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTAAAAG
66 CTGCGCAAATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAG
*
13495379 AAGC-TCCAACGTGGACGCTCTTTTGCTACAGTAGTATCTG-AAAAATAATTTTGAGAAGACGTG
1 AAGCTTCC-ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTG
* * * *
13495442 ACTGTGCAAATAGTGTAAAAAATGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAG
65 TCTGCGCAAATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAG
* *
13495504 AAGCTTCCACGTAGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACATGT
1 AAGCTTCCACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTGT
* * * *
13495569 CTGCGTAAATAGTGGT-AAAAACGCTTCAAGCAGGATGCATTTTCAGCAAAATTACTGGAAG
66 CTGCGCAAATAGT-GTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAG
* * * * * *
13495630 AAGCTCCCACGTGGATGCTCTTTTGCTATAGTGGTCTCTGAAAAAATAATTTTGAAAAAACGTGT
1 AAGCTTCCACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTGT
** * *
13495695 CTGCATAAATAGTGTCAAAAACGCTTCAAGCAGGATGCATTTTCAGCAACAGTACTGAAAG
66 CTGCGCAAATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAG
* * *
13495756 AAGCTCCCACGTGGACGCTCTTTTGCTACAGTGGTTTCTGAAA
1 AAGCTTCCACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAA
13495799 TAACTTGGGC
Statistics
Matches: 381, Mismatches: 34, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
125 117 0.31
126 262 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:13497665 original size:30 final size:30
Alignment explanation
Indices: 13497608--13497673 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
13497598 GTTGAACTAT
*
13497608 TGGGCCCGGTGACTGTGTAGGTCCTGTT-A
1 TGGGCCCGGTGACTGTGTAGGGCCTGTTGA
* *
13497637 CTGGGCCGGGTGATTGTGT-GGGCGCTGTTGA
1 -TGGGCCCGGTGACTGTGTAGGGC-CTGTTGA
13497668 TGGGCC
1 TGGGCC
13497674 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:13498181 original size:7 final size:7
Alignment explanation
Indices: 13498171--13498197 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
13498161 GTTAAATAAA
13498171 AAATACT
1 AAATACT
13498178 AAATACT
1 AAATACT
13498185 AAATACT
1 AAATACT
13498192 AAATAC
1 AAATAC
13498198 GAATCCACTA
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:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (7 bp):
AAATACT
Found at i:13498182 original size:14 final size:14
Alignment explanation
Indices: 13498163--13498196 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
13498153 AAATATTAGT
13498163 TAAATAAAAAATAC
1 TAAATAAAAAATAC
**
13498177 TAAATACTAAATAC
1 TAAATAAAAAATAC
13498191 TAAATA
1 TAAATA
13498197 CGAATCCACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAATAAAAAATAC
Found at i:13499370 original size:22 final size:21
Alignment explanation
Indices: 13499344--13499392 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
13499334 TTTTTTGAAA
**
13499344 AAATTAACGAGAGTTTTGAGAGG
1 AAATTAA-GAGAAATTTGAGA-G
*
13499367 AATTTAAGAGAAATTTGAGAG
1 AAATTAAGAGAAATTTGAGAG
13499388 AAATT
1 AAATT
13499393 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:13499406 original size:11 final size:11
Alignment explanation
Indices: 13499358--13499400 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
13499348 TAACGAGAGT
*
13499358 TTTGAGAGGAA
1 TTTGAGAGAAA
*
13499369 TTTAAGAGAAA
1 TTTGAGAGAAA
13499380 TTTGAGAGAAA
1 TTTGAGAGAAA
13499391 TTTGAGAGAA
1 TTTGAGAGAA
13499401 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:13507375 original size:116 final size:116
Alignment explanation
Indices: 13507171--13507404 Score: 432
Period size: 116 Copynumber: 2.0 Consensus size: 116
13507161 AGTAACTTAA
13507171 GGAAAAGTTCTTAAGGTGGCTACACGCAACACATGTATAAAACAGAAAAGTTCTTTGCAGATGTT
1 GGAAAAGTTCTTAAGGTGGCTACACGCAACACATGTATAAAACAGAAAAGTTCTTTGCAGATGTT
* *
13507236 ACTTATTTTTTATTTAGCATCTCCTCTTTAAACCACCCAAAAACTTGGAGG
66 ACTTATTTTTTATTTAGCATCTCCTCTTTAAAACACCCAAAAACATGGAGG
* *
13507287 GGAAAAGTTCTTAAGGTGGCTACACGCAACATATGTATAAAACAGAAAAGTTCTTTGTAGATGTT
1 GGAAAAGTTCTTAAGGTGGCTACACGCAACACATGTATAAAACAGAAAAGTTCTTTGCAGATGTT
13507352 ACTTATTTTTTATTTAGCATCTCCTCTTTAAAACACCCAAAAACATGGAGG
66 ACTTATTTTTTATTTAGCATCTCCTCTTTAAAACACCCAAAAACATGGAGG
13507403 GG
1 GG
13507405 GGATCCTATT
Statistics
Matches: 114, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
116 114 1.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (116 bp):
GGAAAAGTTCTTAAGGTGGCTACACGCAACACATGTATAAAACAGAAAAGTTCTTTGCAGATGTT
ACTTATTTTTTATTTAGCATCTCCTCTTTAAAACACCCAAAAACATGGAGG
Found at i:13507701 original size:39 final size:39
Alignment explanation
Indices: 13507647--13507727 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
13507637 TAGTAGTAAC
13507647 TTAGTTCATTCTAACTCCAATAACTAAATGATTGACAAT
1 TTAGTTCATTCTAACTCCAATAACTAAATGATTGACAAT
13507686 TTAGTTCATTCTAACTCCAATAACTAAATGATTGACAAT
1 TTAGTTCATTCTAACTCCAATAACTAAATGATTGACAAT
13507725 TTA
1 TTA
13507728 ACTGTTCTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.38, C:0.17, G:0.07, T:0.37
Consensus pattern (39 bp):
TTAGTTCATTCTAACTCCAATAACTAAATGATTGACAAT
Found at i:13510182 original size:73 final size:73
Alignment explanation
Indices: 13510054--13510199 Score: 229
Period size: 73 Copynumber: 2.0 Consensus size: 73
13510044 GCATCCCTAG
*
13510054 AATTAGTCTGTTTCCTAGTATAAAGTTTCCTAAGTTAGGCTCACTAAGTACATAAATATTAATGT
1 AATTAGTCTATTTCCTAGTATAAAGTTTCCTAAGTTAGGCTCACTAAGTACATAAATATTAATGT
*
13510119 ACTTTCTT
66 AATTTCTT
* * ** *
13510127 AATTAGTCTATTTCCTAGTATAGAGTTTCCTAAGTTAGGCTCACTATGTGTATAAATATTTATGT
1 AATTAGTCTATTTCCTAGTATAAAGTTTCCTAAGTTAGGCTCACTAAGTACATAAATATTAATGT
13510192 AATTTCTT
66 AATTTCTT
13510200 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:13511940 original size:33 final size:33
Alignment explanation
Indices: 13511896--13511961 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
13511886 TTTTTTCTTG
13511896 ACATTCCAGCTCCTGT-TCAGCAACCAAACACTC
1 ACATTCCAGCTCCTGTCT-AGCAACCAAACACTC
*
13511929 ACATTCTAGCTCCTGTCTAGCAACCAAACACTC
1 ACATTCCAGCTCCTGTCTAGCAACCAAACACTC
13511962 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:13519035 original size:16 final size:16
Alignment explanation
Indices: 13519014--13519056 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
13519004 AAGGATAAGA
13519014 AATAAAAGTTTAGGGG
1 AATAAAAGTTTAGGGG
13519030 AATAAAAGTTTAGGGG
1 AATAAAAGTTTAGGGG
13519046 AATAAAAGTTT
1 AATAAAAGTTT
13519057 GAGAGAGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.47, C:0.00, G:0.26, T:0.28
Consensus pattern (16 bp):
AATAAAAGTTTAGGGG
Found at i:13519095 original size:27 final size:28
Alignment explanation
Indices: 13519042--13519095 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
13519032 TAAAAGTTTA
*
13519042 GGGGAATAAAAGTTTGAGAGAGTAAATG
1 GGGGAATAAAAGTTTGAGAGAGAAAATG
* * *
13519070 GGGGAGTAAAATTTTG-GAGGGAAAAT
1 GGGGAATAAAAGTTTGAGAGAGAAAAT
13519096 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:13522933 original size:24 final size:24
Alignment explanation
Indices: 13522874--13522935 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
13522864 TATTTTAATA
13522874 TATAAAATATAAAT-TTAAATATT
1 TATAAAATATAAATATTAAATATT
* *
13522897 TTTAAACA-ATAAATATTAATTATT
1 TATAAA-ATATAAATATTAAATATT
*
13522921 TATAAAATTTAAATA
1 TATAAAATATAAATA
13522936 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
Done.