Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 13 of 93
Found at i:6382304 original size:3 final size:3
Alignment explanation
Indices: 6382298--6382328 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
6382288 TTCTTTTTCT
*
6382298 TTA TTA TTA TTA TGA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
6382329 AAGCTCTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:6389508 original size:31 final size:30
Alignment explanation
Indices: 6389470--6389553 Score: 93
Period size: 31 Copynumber: 2.7 Consensus size: 30
6389460 TGGAGGAGAT
6389470 AAAATTATAAAATTTATTAAAAAATAAGAA
1 AAAATTATAAAATTTATTAAAAAATAAGAA
*
6389500 CAAAATTATAAATATTTA-AAACCAAAATAAGAA
1 -AAAATTATAAA-ATTTATTAA--AAAATAAGAA
6389533 AAATATTAT-AAATTT-TTAAAA
1 AAA-ATTATAAAATTTATTAAAA
6389554 CTTTGGAGGT
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
29 2 0.04
31 19 0.41
32 10 0.22
33 15 0.33
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (30 bp):
AAAATTATAAAATTTATTAAAAAATAAGAA
Found at i:6389532 original size:33 final size:31
Alignment explanation
Indices: 6389470--6389554 Score: 102
Period size: 33 Copynumber: 2.7 Consensus size: 31
6389460 TGGAGGAGAT
*
6389470 AAAATTATAAA-ATTTATTAA-AAAATAAGAA
1 AAAATTATAAATATTTA-AAACAAAATAAGAA
6389500 CAAAATTATAAATATTTAAAACCAAAATAAGAA
1 -AAAATTATAAATATTTAAAA-CAAAATAAGAA
*
6389533 AAATATTATAAATTTTTAAAAC
1 AAA-ATTATAAATATTTAAAAC
6389555 TTTGGAGGTG
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
31 13 0.27
32 9 0.19
33 26 0.54
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (31 bp):
AAAATTATAAATATTTAAAACAAAATAAGAA
Found at i:6390593 original size:240 final size:249
Alignment explanation
Indices: 6390016--6390685 Score: 780
Period size: 250 Copynumber: 2.7 Consensus size: 249
6390006 TTAATTTAAT
** * * * *
6390016 AAAAAAATCTAATTTTTGTGAAAAACAAACA-TTATATTTATATTCTCAAGTTAAAAGTATTTAA
1 AAAAAAATCTAATTTTAATG-AAATCAAACATTTAAATTTATATTTTCAAGATAAAAGTATTTAA
* * *
6390080 CGATTTAC-AATTTTAATTTAAAAATAAAAAATAATAAAGATAAAAATAATTATTGTTAGAA-GT
65 CGATTTACAAATTTTAATTTAAAAATAAATAATAATAAGGATAAAAATAATTATTGTTAAAATGT
* * ** ** *
6390143 CGTCATTGAAAAAATTAAACATAAAACTGTAAGAATTAACATAAAAACTCATACAGGTAGAACAA
130 -GCCATTGAAAAGATTTGACATAAAGTTGTAAGAATTAACATAAAAACTCACACAGGTAGAACAA
* *
6390208 ACAAATTTAAAATACTAATGTAAATGTGTGACAATTAACGTAATAGATCAATTAAGTT
194 ACAAATTTAAAATACTAACGTAAATGTGTGACAATTAAC-TAATAGA-CAATTAAGTC
* *
6390266 ACAAAAATCTAATTTTAATAAAAAAT-AAACATTTAAATTTATATTTTCAA-ACTAAAAGTATTT
1 AAAAAAATCTAATTTTAAT--GAAATCAAACATTTAAATTTATATTTTCAAGA-TAAAAGTATTT
* * *
6390329 AACGATTTATAAATTTTAATTTAAAAATAAATAATAGTAAGGAT-AAAATAATTATAGTTAAAAT
63 AACGATTTACAAATTTTAATTTAAAAATAAATAATAATAAGGATAAAAATAATTATTGTTAAAAT
* * * * *
6390393 GTGCCATTGAAAAGCTTTGAC-GAAAGTTGTAAAAATTAACGTAAAAACTCACA-AGGGTAGAAT
128 GTGCCATTGAAAAGATTTGACATAAAGTTGTAAGAATTAACATAAAAACTCACACA-GGTAGAAC
* *
6390456 AAATATATTTAAAAT-CTTAACGTAAATGTGTGACAATTAA-T-ATAG-C-A-T-A-TC
192 AAACAAATTTAAAATAC-TAACGTAAATGTGTGACAATTAACTAATAGACAATTAAGTC
* *
6390507 AAAAAAATCCAATTTTAATGAAATCAAACATTTAAATTTATATTTTCAAGATAAAAGTATTTAAT
1 AAAAAAATCTAATTTTAATGAAATCAAACATTTAAATTTATATTTTCAAGATAAAAGTATTTAAC
* *
6390572 GATTTACAAATTTTAATTTAAAAATAAGTAATAATAAGGATAAAAACAATTATTGTTAAAAAT-T
66 GATTTACAAATTTTAATTTAAAAATAAATAATAATAAGGATAAAAATAATTATTGTT-AAAATGT
* * * * *
6390636 ACCATTTAAAAGTTTTGACATAAAGTTGTAAGAATTGACATAGAAACTCA
130 GCCATTGAAAAGATTTGACATAAAGTTGTAAGAATTAACATAAAAACTCA
6390686 TAAAAGTGAA
Statistics
Matches: 360, Mismatches: 47, Indels: 34
0.82 0.11 0.08
Matches are distributed among these distances:
239 4 0.01
240 75 0.21
241 49 0.14
242 31 0.09
243 1 0.00
244 1 0.00
245 1 0.00
247 4 0.01
248 1 0.00
249 2 0.01
250 89 0.25
251 70 0.19
252 32 0.09
ACGTcount: A:0.50, C:0.08, G:0.09, T:0.33
Consensus pattern (249 bp):
AAAAAAATCTAATTTTAATGAAATCAAACATTTAAATTTATATTTTCAAGATAAAAGTATTTAAC
GATTTACAAATTTTAATTTAAAAATAAATAATAATAAGGATAAAAATAATTATTGTTAAAATGTG
CCATTGAAAAGATTTGACATAAAGTTGTAAGAATTAACATAAAAACTCACACAGGTAGAACAAAC
AAATTTAAAATACTAACGTAAATGTGTGACAATTAACTAATAGACAATTAAGTC
Found at i:6390765 original size:240 final size:238
Alignment explanation
Indices: 6390042--6390728 Score: 625
Period size: 240 Copynumber: 2.8 Consensus size: 238
6390032 TGTGAAAAAC
* * **
6390042 AAACA-TTATATTTATATTCTCAAGTTAAAAGTATTTAACGATTTAC-AATTTTAATTTAAAAAT
1 AAACATTTAAATTTATATTTTCAAACTAAAAGTATTTAACGATTTACAAATTTTAATTTAAAAAT
* * * * * ** ** *
6390105 AAAAAATAATAAAGATAAAAATAATTATTGTTAGAA-GT-CGTCATTGAAAAAATTAAACATAAA
66 AAATAATAATAAGGAT-AAAACAATTATAGTTAAAATGTAC--CATTGAAAAGCTTTGAC-GAAA
** * * * * * * * * * *
6390168 ACTGTAAGAATTAACATAAAAACTCATACAGGTAGAACAAACAAATTTAAAATACTAATGTAAAT
127 GTTGTAAAAATTAACATAAAAACTCACAAAAGTAGAATAAATATATTCAAAATATTAACGTAAAT
* * * *
6390233 GTGTGACAATTAACGTAATAGATCAATTAAGTTACAAAAATCTAATTTTAATAAAAAAT
192 ATGTGACAATTAAC---ATA-A-C-A-T-A-TCAAAAAAATC-AATTTTAAT--GAAAT
*
6390292 AAACATTTAAATTTATATTTTCAAACTAAAAGTATTTAACGATTTATAAATTTTAATTTAAAAAT
1 AAACATTTAAATTTATATTTTCAAACTAAAAGTATTTAACGATTTACAAATTTTAATTTAAAAAT
* * *
6390357 AAATAATAGTAAGGATAAAATAATTATAGTTAAAATGTGCCATTGAAAAGCTTTGACGAAAGTTG
66 AAATAATAATAAGGATAAAACAATTATAGTTAAAATGTACCATTGAAAAGCTTTGACGAAAGTTG
* ** * * *
6390422 TAAAAATTAACGTAAAAACTCACAAGGGTAGAATAAATATATTTAAAATCTTAACGTAAATGTGT
131 TAAAAATTAACATAAAAACTCACAAAAGTAGAATAAATATATTCAAAATATTAACGTAAATATGT
* *
6390487 GACAATTAATATAGCATATCAAAAAAATCCAATTTTAATGAAAT
196 GACAATTAACATAACATATCAAAAAAAT-CAATTTTAATGAAAT
*
6390531 CAAACATTTAAATTTATATTTTCAAGA-TAAAAGTATTTAATGATTTACAAATTTTAATTTAAAA
1 -AAACATTTAAATTTATATTTTCAA-ACTAAAAGTATTTAACGATTTACAAATTTTAATTTAAAA
* * * * *
6390595 ATAAGTAATAATAAGGATAAAAACAATTATTGTTAAAAAT-TACCATTTAAAAGTTTTGACATAA
64 ATAAATAATAATAAGGAT-AAAACAATTATAGTT-AAAATGTACCATTGAAAAGCTTTGAC-GAA
* * * * *
6390659 AGTTGTAAGAATTGACATAGAAACTCATAAAAGT-GAAATAAGTAT-TATCAAAATATTAACGTA
126 AGTTGTAAAAATTAACATAAAAACTCACAAAAGTAG-AATAAATATAT-TCAAAATATTAACGTA
6390722 AATATGT
189 AATATGT
6390729 ATGATTTAAC
Statistics
Matches: 371, Mismatches: 54, Indels: 32
0.81 0.12 0.07
Matches are distributed among these distances:
239 4 0.01
240 75 0.20
241 50 0.13
242 64 0.17
243 1 0.00
244 1 0.00
245 1 0.00
247 3 0.01
250 73 0.20
251 66 0.18
252 32 0.09
253 1 0.00
ACGTcount: A:0.50, C:0.08, G:0.09, T:0.33
Consensus pattern (238 bp):
AAACATTTAAATTTATATTTTCAAACTAAAAGTATTTAACGATTTACAAATTTTAATTTAAAAAT
AAATAATAATAAGGATAAAACAATTATAGTTAAAATGTACCATTGAAAAGCTTTGACGAAAGTTG
TAAAAATTAACATAAAAACTCACAAAAGTAGAATAAATATATTCAAAATATTAACGTAAATATGT
GACAATTAACATAACATATCAAAAAAATCAATTTTAATGAAAT
Found at i:6390871 original size:17 final size:17
Alignment explanation
Indices: 6390829--6390874 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
6390819 ATTTTAAGGT
6390829 AATAAAATAAAAATTAAA
1 AATAAAAT-AAAATTAAA
* * *
6390847 AATTAAATAACATTTAA
1 AATAAAATAAAATTAAA
6390864 AATAAAATAAA
1 AATAAAATAAA
6390875 TACATTTTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (17 bp):
AATAAAATAAAATTAAA
Found at i:6390876 original size:21 final size:22
Alignment explanation
Indices: 6390845--6390886 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
6390835 ATAAAAATTA
6390845 AAAATTAAATAACA-TTTAAAAT
1 AAAATTAAAT-ACATTTTAAAAT
6390867 AAAA-TAAATACATTTTAAAA
1 AAAATTAAATACATTTTAAAA
6390887 ATTACTTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.16
21 12 0.63
22 4 0.21
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (22 bp):
AAAATTAAATACATTTTAAAAT
Found at i:6403987 original size:16 final size:16
Alignment explanation
Indices: 6403943--6403993 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
6403933 TTTTTTTTAA
*
6403943 TTATTATTATTATATATT
1 TTATTA-TATT-TTTATT
6403961 TT-TTATA-TTTTATT
1 TTATTATATTTTTATT
6403975 TTATTATATTTTTATT
1 TTATTATATTTTTATT
6403991 TTA
1 TTA
6403994 GAGGTGTCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
14 7 0.23
15 6 0.20
16 12 0.40
17 3 0.10
18 2 0.07
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTATTATATTTTTATT
Found at i:6403989 original size:23 final size:25
Alignment explanation
Indices: 6403935--6403987 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
6403925 CATTCCCTTT
6403935 TTTTTTA-ATTATTATTATTATATA
1 TTTTTTATATTATTATTATTATATA
6403959 TTTTTTATATT-TTATT-TTATTATA
1 TTTTTTATATTATTATTATTA-TATA
6403983 TTTTT
1 TTTTT
6403988 ATTTTAGAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
23 3 0.11
24 21 0.78
25 3 0.11
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (25 bp):
TTTTTTATATTATTATTATTATATA
Found at i:6404748 original size:16 final size:16
Alignment explanation
Indices: 6404692--6404749 Score: 66
Period size: 16 Copynumber: 3.7 Consensus size: 16
6404682 TTTATTTTTT
**
6404692 ATTAATTAATATAAAA
1 ATTAATTAATATATTA
*
6404708 ATT-ATTAATTTATTA
1 ATTAATTAATATATTA
6404723 ATTCAA-TAATATATTA
1 ATT-AATTAATATATTA
6404739 ATTAATTAATA
1 ATTAATTAATA
6404750 AATTTTCATA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
15 14 0.40
16 20 0.57
17 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTAATTAATATATTA
Found at i:6406042 original size:31 final size:29
Alignment explanation
Indices: 6406004--6406111 Score: 119
Period size: 31 Copynumber: 3.6 Consensus size: 29
6405994 ATAATACATA
6406004 GACTAAATTGAACAAAATTAAAATGTTAAGG
1 GACTAAATTGAA-AAAATTAAAATGTT-AGG
* * *
6406035 GATTAAATTGAAAAAATATATAAT-ATAGG
1 GACTAAATTGAAAAAAT-TAAAATGTTAGG
* *
6406064 GACTAAATTGAACAAAATTGAGATGTTGAGG
1 GACTAAATTGAA-AAAATTAAAATGTT-AGG
6406095 GACTAAATTGAAAAAAT
1 GACTAAATTGAAAAAAT
6406112 ATTTAAAAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
29 17 0.26
30 17 0.26
31 31 0.48
ACGTcount: A:0.51, C:0.05, G:0.18, T:0.27
Consensus pattern (29 bp):
GACTAAATTGAAAAAATTAAAATGTTAGG
Found at i:6406069 original size:60 final size:60
Alignment explanation
Indices: 6405970--6406113 Score: 207
Period size: 60 Copynumber: 2.4 Consensus size: 60
6405960 ACCACGTCAT
*
6405970 AGGGATTAAATTGAATAAAAATATATAATACATAGACTAAATTGAACAAAATTAAAATGTTA
1 AGGGATTAAATTG-A-AAAAATATATAATACAGAGACTAAATTGAACAAAATTAAAATGTTA
* * * * *
6406032 AGGGATTAAATTGAAAAAATATATAATATAGGGACTAAATTGAACAAAATTGAGATGTTG
1 AGGGATTAAATTGAAAAAATATATAATACAGAGACTAAATTGAACAAAATTAAAATGTTA
*
6406092 AGGGACTAAATTGAAAAAATAT
1 AGGGATTAAATTGAAAAAATAT
6406114 TTAAAAAATA
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
60 61 0.81
61 1 0.01
62 13 0.17
ACGTcount: A:0.52, C:0.04, G:0.16, T:0.28
Consensus pattern (60 bp):
AGGGATTAAATTGAAAAAATATATAATACAGAGACTAAATTGAACAAAATTAAAATGTTA
Found at i:6406509 original size:106 final size:108
Alignment explanation
Indices: 6406377--6406584 Score: 359
Period size: 106 Copynumber: 1.9 Consensus size: 108
6406367 TAAAATGACT
*
6406377 AAATATGTTGATTTAGTTACAACTTTCACAATTTATAAATACACATTCTTT-TGAAATTATTCAA
1 AAATATGTTGATTTAGTTACAACTTTCACAATTTACAAATACACATT-TTTATGAAATTATTCAA
6406441 CTCTTA-CCAATTTA-CTTTTATTTAAATTTACTCAAATTAGCA
65 CTCTTACCCAATTTACCTTTTATTTAAATTTACTCAAATTAGCA
* *
6406483 AAATATGTTGATTTAGTTACAACTTTCATAATTTACAGATACACATTTTTATGAAATTATTCAAC
1 AAATATGTTGATTTAGTTACAACTTTCACAATTTACAAATACACATTTTTATGAAATTATTCAAC
6406548 TCTTACCCAATTTACCTTTTATTTAAATTTACTCAAA
66 TCTTACCCAATTTACCTTTTATTTAAATTTACTCAAA
6406585 AATTCTTATA
Statistics
Matches: 96, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
105 3 0.03
106 63 0.66
107 8 0.08
108 22 0.23
ACGTcount: A:0.37, C:0.15, G:0.05, T:0.43
Consensus pattern (108 bp):
AAATATGTTGATTTAGTTACAACTTTCACAATTTACAAATACACATTTTTATGAAATTATTCAAC
TCTTACCCAATTTACCTTTTATTTAAATTTACTCAAATTAGCA
Found at i:6407244 original size:2 final size:2
Alignment explanation
Indices: 6407239--6407265 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6407229 GTAAAAAAAT
6407239 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
6407266 TTTTTTTTTA
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:6414944 original size:39 final size:39
Alignment explanation
Indices: 6414901--6415029 Score: 122
Period size: 39 Copynumber: 3.3 Consensus size: 39
6414891 GGAAAAGGAA
* *
6414901 AGGGAGAGAGAGAGGAGAGATAGGGATAAGGAGAA-AGAG
1 AGGGAGAGAGAGAGGAGAGAGAGGGAAAAGGA-AAGAGAG
* *
6414940 AGGGATAGGGAGAGGAGAGAGAGGGAAAAGGAAAGAGAG
1 AGGGAGAGAGAGAGGAGAGAGAGGGAAAAGGAAAGAGAG
* * * * *
6414979 A-GGAGGGAAAG-GGAGAAAGAGAAGGAAAGGGAGAGAGAG
1 AGGGAGAGAGAGAGGAG--AGAGAGGGAAAAGGAAAGAGAG
6415018 A-GGAGAGAGAGA
1 AGGGAGAGAGAGA
6415030 AGCAGTAGTC
Statistics
Matches: 73, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
37 4 0.05
38 8 0.11
39 61 0.84
ACGTcount: A:0.47, C:0.00, G:0.50, T:0.02
Consensus pattern (39 bp):
AGGGAGAGAGAGAGGAGAGAGAGGGAAAAGGAAAGAGAG
Found at i:6414945 original size:18 final size:17
Alignment explanation
Indices: 6414922--6415020 Score: 63
Period size: 18 Copynumber: 5.2 Consensus size: 17
6414912 GAGGAGAGAT
6414922 AGGGATAAGGAGAAAGAG
1 AGGGA-AAGGAGAAAGAG
*
6414940 AGGGATAGGGAGAGGAGAGAG
1 AGGGA-AAGGAGA--A-AGAG
*
6414961 AGGGAAAAGGAAAGAGAGAGG
1 AGGG-AAAGG--AGAAAGA-G
6414982 AGGGAAAGGGAGAAAGAG
1 AGGGAAA-GGAGAAAGAG
* *
6415000 AAGGAAAGGGAGAGAGAG
1 AGGGAAA-GGAGAAAGAG
6415018 AGG
1 AGG
6415021 AGAGAGAGAA
Statistics
Matches: 66, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
18 31 0.47
19 6 0.09
20 7 0.11
21 18 0.27
22 1 0.02
23 3 0.05
ACGTcount: A:0.47, C:0.00, G:0.51, T:0.02
Consensus pattern (17 bp):
AGGGAAAGGAGAAAGAG
Found at i:6414967 original size:66 final size:65
Alignment explanation
Indices: 6414823--6415028 Score: 181
Period size: 66 Copynumber: 3.1 Consensus size: 65
6414813 CAGCCGCGAC
* *
6414823 AGAGAAAGGGAAAGGGAGAGAGAGAGGGACAGAGATAGGGATTTAGAG--AG-GAGGAGTAGTAG
1 AGAGAGAGGGAAAGGGAGAGAGAGA-GG--AGAGATAGGGA-TAAGAGAAAGAGAGG-G-A-TAG
6414885 AGAGAGG
59 AGAGAGG
* *
6414892 -GA-A-AAGGAAAGGGAGAGAGAGAGGAGAGATAGGGATAAGGAGAAAGAGAGGGATAGGGAGAG
1 AGAGAGAGGGAAAGGGAGAGAGAGAGGAGAGATAGGGATAA-GAGAAAGAGAGGGATAGAGAGAG
6414954 G
65 G
* * * * * * * *
6414955 AGAGAGAGGGAAAAGGAAAGAGAGAGGAGGGAAAGGGAGAAAGAGAAGGAAAGGGAGAGAGAGAG
1 AGAGAGAGGGAAAGGGAGAGAGAGAGGAGAGATAGGGA-TAAGAGAAAGAGAGGGATAGAGAGAG
6415020 G
65 G
6415021 AGAGAGAG
1 AGAGAGAG
6415029 AAGCAGTAGT
Statistics
Matches: 116, Mismatches: 13, Indels: 19
0.78 0.09 0.13
Matches are distributed among these distances:
62 2 0.02
63 23 0.20
64 3 0.03
65 6 0.05
66 77 0.66
67 3 0.03
68 2 0.02
ACGTcount: A:0.46, C:0.00, G:0.49, T:0.04
Consensus pattern (65 bp):
AGAGAGAGGGAAAGGGAGAGAGAGAGGAGAGATAGGGATAAGAGAAAGAGAGGGATAGAGAGAGG
Found at i:6434439 original size:16 final size:16
Alignment explanation
Indices: 6434413--6434454 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
6434403 AAATTATAAA
6434413 TAAAA-ATTAATATTT
1 TAAAATATTAATATTT
*
6434428 TAAAATATTAATTTTT
1 TAAAATATTAATATTT
* *
6434444 TTAATTATTAA
1 TAAAATATTAA
6434455 GTGAAATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 5 0.22
16 18 0.78
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAAAATATTAATATTT
Found at i:6434440 original size:20 final size:20
Alignment explanation
Indices: 6434381--6434440 Score: 52
Period size: 20 Copynumber: 3.0 Consensus size: 20
6434371 TAATATTTCC
6434381 ATATTTTAATAATATTATATTTA
1 ATATTTTAA-AATATTA-A-TTA
* **
6434404 A-ATTAT-AAATAAAAATTA
1 ATATTTTAAAATATTAATTA
6434422 ATATTTTAAAATATTAATT
1 ATATTTTAAAATATTAATT
6434441 TTTTTAATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 7
0.69 0.14 0.17
Matches are distributed among these distances:
18 4 0.14
19 5 0.17
20 14 0.48
21 1 0.03
22 4 0.14
23 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
ATATTTTAAAATATTAATTA
Found at i:6435199 original size:42 final size:42
Alignment explanation
Indices: 6435153--6435260 Score: 198
Period size: 42 Copynumber: 2.6 Consensus size: 42
6435143 TAACATTTAA
* *
6435153 ATTATAAATAAAATATTAGTATTTTTTAATATTAATGATTAG
1 ATTATAAACAAAATATTAATATTTTTTAATATTAATGATTAG
6435195 ATTATAAACAAAATATTAATATTTTTTAATATTAATGATTAG
1 ATTATAAACAAAATATTAATATTTTTTAATATTAATGATTAG
6435237 ATTATAAACAAAATATTAATATTT
1 ATTATAAACAAAATATTAATATTT
6435261 AAAAATAAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (42 bp):
ATTATAAACAAAATATTAATATTTTTTAATATTAATGATTAG
Found at i:6469860 original size:2 final size:2
Alignment explanation
Indices: 6469853--6469892 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
6469843 TTAGATTAAT
* * *
6469853 TA TA TA TA TA TA TA TA TA TA TT TA TA TA TC TA TA TC TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6469893 CATCTGCATA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:6470846 original size:12 final size:13
Alignment explanation
Indices: 6470802--6470884 Score: 55
Period size: 12 Copynumber: 6.2 Consensus size: 13
6470792 TTTTTTGTCA
6470802 TTTATTATTATTT
1 TTTATTATTATTT
* *
6470815 AATTATCATT-TTCAT
1 -TTTATTATTATT--T
6470830 TTTATT-TTATTT
1 TTTATTATTATTT
6470842 TTTATTATCATATTT
1 TTTATTAT--TATTT
*
6470857 TCTATT-TTATTT
1 TTTATTATTATTT
* *
6470869 CTAATTATTATTT
1 TTTATTATTATTT
6470882 TTT
1 TTT
6470885 CATACTTTAC
Statistics
Matches: 52, Mismatches: 10, Indels: 15
0.68 0.13 0.19
Matches are distributed among these distances:
12 15 0.29
13 12 0.23
14 14 0.27
15 11 0.21
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTATTATTATTT
Found at i:6470857 original size:20 final size:18
Alignment explanation
Indices: 6470823--6470884 Score: 54
Period size: 20 Copynumber: 3.3 Consensus size: 18
6470813 TTAATTATCA
*
6470823 TTTTCATTT-TATTTTAT
1 TTTTTATTTCTATTTTAT
*
6470840 TTTTTATTATCATATTTTCT
1 TTTTTATT-TC-TATTTTAT
*
6470860 ATTTTATTTCTAATTATTAT
1 TTTTTATTTCT-ATT-TTAT
6470880 TTTTT
1 TTTTT
6470885 CATACTTTAC
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
17 7 0.20
18 2 0.06
19 5 0.14
20 21 0.60
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTTATTTCTATTTTAT
Found at i:6470862 original size:27 final size:28
Alignment explanation
Indices: 6470832--6470904 Score: 76
Period size: 27 Copynumber: 2.6 Consensus size: 28
6470822 ATTTTCATTT
6470832 TATTTTATTTTTTATTATCATATTTTC-
1 TATTTTATTTTTTATTATCATATTTTCA
* * * *
6470859 TATTTTATTTCTAATTATTATTTTTTCA
1 TATTTTATTTTTTATTATCATATTTTCA
*
6470887 TACTTTACATTTTTTATT
1 TA-TTT-TATTTTTTATT
6470905 CTAAGTTACT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
27 23 0.64
28 2 0.06
29 3 0.08
30 8 0.22
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.68
Consensus pattern (28 bp):
TATTTTATTTTTTATTATCATATTTTCA
Found at i:6471005 original size:17 final size:18
Alignment explanation
Indices: 6470983--6471047 Score: 55
Period size: 19 Copynumber: 3.5 Consensus size: 18
6470973 ACAAAAATTT
6470983 TATTTTTTTTATTATA-C
1 TATTTTTTTTATTATATC
*
6471000 TATTTTTATTTTTTATATC
1 TATTTTT-TTTATTATATC
6471019 T-TTATATTTTTATTATTAT-
1 TATT-T-TTTTTATTA-TATC
6471038 TATATTTTTT
1 TAT-TTTTTT
6471048 CATAAGCAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
17 7 0.18
18 10 0.26
19 14 0.36
20 7 0.18
21 1 0.03
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (18 bp):
TATTTTTTTTATTATATC
Found at i:6471006 original size:23 final size:23
Alignment explanation
Indices: 6470980--6471042 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
6470970 TGAACAAAAA
*
6470980 TTTTATTTTTTTTAT-TATACTAT
1 TTTTATTTTTTATATCTATA-TAT
*
6471003 TTTTATTTTTTATATCTTTATAT
1 TTTTATTTTTTATATCTATATAT
6471026 TTTTATTATTATTATAT
1 TTTTATT-TT-TTATAT
6471043 TTTTTCATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 24 0.69
24 5 0.14
25 6 0.17
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTTATTTTTTATATCTATATAT
Found at i:6474924 original size:52 final size:52
Alignment explanation
Indices: 6474846--6474950 Score: 174
Period size: 52 Copynumber: 2.0 Consensus size: 52
6474836 GAGAAAAATT
* * *
6474846 TGTTGTGGTTTATTGTGAGGTTTATATGTTGTCTTGGCACAATTAGATGGTA
1 TGTTGTGGTTTATTGTGAGGTTTATATGCTATCTTGGCACAATTAGAAGGTA
*
6474898 TGTTGTGGTTTATTGTGTGGTTTATATGCTATCTTGGCACAATTAGAAGGTA
1 TGTTGTGGTTTATTGTGAGGTTTATATGCTATCTTGGCACAATTAGAAGGTA
6474950 T
1 T
6474951 ACTTGTTTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.20, C:0.07, G:0.28, T:0.46
Consensus pattern (52 bp):
TGTTGTGGTTTATTGTGAGGTTTATATGCTATCTTGGCACAATTAGAAGGTA
Found at i:6475116 original size:35 final size:34
Alignment explanation
Indices: 6475029--6475126 Score: 142
Period size: 34 Copynumber: 2.9 Consensus size: 34
6475019 AAGTGGCTTT
* *
6475029 TTTTTTGTAATTGGCAAATATTGTACAGGTGCCA
1 TTTTTTGTAATTGACATATATTGTACAGGTGCCA
* *
6475063 TTTTTTGTAATTGACATATATTGTATAGGTGCCT
1 TTTTTTGTAATTGACATATATTGTACAGGTGCCA
*
6475097 TTCTTTTGTAATTGCCATATATTGTACAGG
1 TT-TTTTGTAATTGACATATATTGTACAGG
6475127 GGCTTTATTG
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
34 32 0.56
35 25 0.44
ACGTcount: A:0.24, C:0.11, G:0.18, T:0.46
Consensus pattern (34 bp):
TTTTTTGTAATTGACATATATTGTACAGGTGCCA
Found at i:6475176 original size:19 final size:19
Alignment explanation
Indices: 6475144--6475180 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
6475134 TTGGTCAAAG
6475144 TATTGGTACCTTACAAGCT
1 TATTGGTACCTTACAAGCT
* *
6475163 TATTGTTACTTTACAAGC
1 TATTGGTACCTTACAAGC
6475181 CTCTTGTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.41
Consensus pattern (19 bp):
TATTGGTACCTTACAAGCT
Found at i:6479108 original size:17 final size:17
Alignment explanation
Indices: 6479084--6479131 Score: 57
Period size: 15 Copynumber: 3.0 Consensus size: 17
6479074 GCTTTCTTTA
6479084 AGTATATATATTATAAT
1 AGTATATATATTATAAT
*
6479101 A-T-TATATA-AATAAT
1 AGTATATATATTATAAT
*
6479115 GGTATATATATTATAAT
1 AGTATATATATTATAAT
6479132 TAATAATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
14 5 0.20
15 7 0.28
16 7 0.28
17 6 0.24
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (17 bp):
AGTATATATATTATAAT
Found at i:6479136 original size:24 final size:22
Alignment explanation
Indices: 6479095--6479138 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
6479085 GTATATATAT
6479095 TATAATATTATATAAATAATGG
1 TATAATATTATATAAATAATGG
*
6479117 TATATATATTATAATTAATAAT
1 TATA-ATATTAT-ATAAATAAT
6479139 TTTATAAGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 7 0.37
24 8 0.42
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (22 bp):
TATAATATTATATAAATAATGG
Found at i:6479144 original size:24 final size:22
Alignment explanation
Indices: 6479094--6479145 Score: 59
Period size: 24 Copynumber: 2.3 Consensus size: 22
6479084 AGTATATATA
6479094 TTATAATATTATATAAATAATG
1 TTATAATATTATATAAATAATG
* * *
6479116 GTATATATATTATAATTAATAATT
1 TTATA-ATATTAT-ATAAATAATG
6479140 TTATAA
1 TTATAA
6479146 GTCATAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
22 4 0.17
23 8 0.33
24 12 0.50
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (22 bp):
TTATAATATTATATAAATAATG
Found at i:6481677 original size:26 final size:26
Alignment explanation
Indices: 6481648--6481726 Score: 131
Period size: 26 Copynumber: 3.0 Consensus size: 26
6481638 TTACGGTATT
*
6481648 CATCTACTTCTGGTGGTAAAATTATC
1 CATCTACTTCTGGTGGCAAAATTATC
*
6481674 CATCTACTTTTGGTGGCAAAATTATC
1 CATCTACTTCTGGTGGCAAAATTATC
*
6481700 CATCTACTTCTGGTGACAAAATTATC
1 CATCTACTTCTGGTGGCAAAATTATC
6481726 C
1 C
6481727 TTAGATTCTA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 49 1.00
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.37
Consensus pattern (26 bp):
CATCTACTTCTGGTGGCAAAATTATC
Found at i:6481769 original size:25 final size:25
Alignment explanation
Indices: 6481741--6481824 Score: 89
Period size: 25 Copynumber: 3.4 Consensus size: 25
6481731 ATTCTAATAG
6481741 TAAAATTATTATCCACTTCTGATGA
1 TAAAATTATTATCCACTTCTGATGA
* * * *
6481766 TAAAAGTATTCT-TAGATTCTGATGA
1 TAAAATTATTATCCA-CTTCTGATGA
* * *
6481791 AAAAATTATTATCCACTTATGATGG
1 TAAAATTATTATCCACTTCTGATGA
6481816 TAAAATTAT
1 TAAAATTAT
6481825 AATTAGAATT
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
24 1 0.02
25 43 0.96
26 1 0.02
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (25 bp):
TAAAATTATTATCCACTTCTGATGA
Found at i:6481780 original size:50 final size:50
Alignment explanation
Indices: 6481691--6481820 Score: 145
Period size: 50 Copynumber: 2.6 Consensus size: 50
6481681 TTTTGGTGGC
* * * * * *
6481691 AAAATTATCCATCTACTTCTGGTGACAAAATTATCCTTAGATTCTAAT-AGT
1 AAAATTAT-TATCCACTTCTGATGATAAAAGTATCCTTAGATTCTAATGA-A
* *
6481742 AAAATTATTATCCACTTCTGATGATAAAAGTATTCTTAGATTCTGATGAA
1 AAAATTATTATCCACTTCTGATGATAAAAGTATCCTTAGATTCTAATGAA
* *
6481792 AAAATTATTATCCACTTATGATGGTAAAA
1 AAAATTATTATCCACTTCTGATGATAAAA
6481821 TTATAATTAG
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
50 59 0.87
51 9 0.13
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (50 bp):
AAAATTATTATCCACTTCTGATGATAAAAGTATCCTTAGATTCTAATGAA
Found at i:6487461 original size:48 final size:49
Alignment explanation
Indices: 6487399--6487495 Score: 160
Period size: 48 Copynumber: 2.0 Consensus size: 49
6487389 GAAAAATCTT
* *
6487399 CTTTTGTTAAAATAAGATCGAAGAACAATTTCTT-GAAAATCTTAAAGC
1 CTTTTGTTAAAATAAGATCGAAGAACAACTTCTTAAAAAATCTTAAAGC
*
6487447 CTTTTGTTAGAATAAGATCGAAGAACAACTTCTTAAAAAATCTTAAAGC
1 CTTTTGTTAAAATAAGATCGAAGAACAACTTCTTAAAAAATCTTAAAGC
6487496 TTAAATATCA
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
48 32 0.71
49 13 0.29
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.32
Consensus pattern (49 bp):
CTTTTGTTAAAATAAGATCGAAGAACAACTTCTTAAAAAATCTTAAAGC
Found at i:6487854 original size:77 final size:79
Alignment explanation
Indices: 6487721--6487890 Score: 182
Period size: 77 Copynumber: 2.2 Consensus size: 79
6487711 GACTCCATCG
* * * * ** * *
6487721 AATTTTGATTGAGCCAAATTTAGGTTTTATTTCTAAATTATTTTGATTTATTTAGAGATAAAATG
1 AATTTTGATT-AGCCAAAGTTAGGATTTATCTCTAAATTATCTAAATCTATATAGAGATAAAATG
*
6487786 AATGACTTATAGGTC
65 AATGACTCATAGGTC
* * *
6487801 AATTTTGATTAGCC-AAGTT-GGATTTATCTCTAAATTATCTAAATCTATATAGAGATATATTGG
1 AATTTTGATTAGCCAAAGTTAGGATTTATCTCTAAATTATCTAAATCTATATAGAGATAAAATGA
*
6487864 ATGACTCATAGGTG
66 ATGACTCATAGGTC
* *
6487878 TATTTTGCTTAGC
1 AATTTTGATTAGC
6487891 AAAATTATTT
Statistics
Matches: 75, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
77 57 0.76
78 4 0.05
79 4 0.05
80 10 0.13
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (79 bp):
AATTTTGATTAGCCAAAGTTAGGATTTATCTCTAAATTATCTAAATCTATATAGAGATAAAATGA
ATGACTCATAGGTC
Found at i:6496793 original size:82 final size:80
Alignment explanation
Indices: 6496691--6496884 Score: 298
Period size: 82 Copynumber: 2.4 Consensus size: 80
6496681 AAAATAAACG
*
6496691 TTATATTTAACAATTGATTCATATTTATCATACACAAAGTTTTAATTCAATCTAATATTTTATTG
1 TTATATTTAACAACTGATTCATATTTATCATACACAAAGTTTTAATTCAATCTAATATTTTATTG
* **
6496756 ACTATTATTAATTTTTT
66 AATATTATTAA--AATT
* * *
6496773 TTATATTTAACAACTGATTCATACTTATCATATACAAAGTTTTAATTTAATCTAATATTTTATTG
1 TTATATTTAACAACTGATTCATATTTATCATACACAAAGTTTTAATTCAATCTAATATTTTATTG
6496838 AATATTATTAAAATT
66 AATATTATTAAAATT
*
6496853 TTATATTTAACAACTGATCCATATTTATCATA
1 TTATATTTAACAACTGATTCATATTTATCATA
6496885 TAATAAAAAT
Statistics
Matches: 103, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
80 32 0.31
82 71 0.69
ACGTcount: A:0.38, C:0.10, G:0.04, T:0.48
Consensus pattern (80 bp):
TTATATTTAACAACTGATTCATATTTATCATACACAAAGTTTTAATTCAATCTAATATTTTATTG
AATATTATTAAAATT
Found at i:6506114 original size:19 final size:19
Alignment explanation
Indices: 6506073--6506121 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
6506063 AAAAAAAATG
*
6506073 AATTAAAAAAATATAATAAA
1 AATT-AAAAAATATAAGAAA
6506093 AATTAAAAAATA-AAGAAGA
1 AATTAAAAAATATAAGAA-A
*
6506112 AATGAAAAAA
1 AATTAAAAAA
6506122 AGGGGAGAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 4 0.15
19 18 0.69
20 4 0.15
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (19 bp):
AATTAAAAAATATAAGAAA
Found at i:6507793 original size:8 final size:8
Alignment explanation
Indices: 6507782--6507839 Score: 89
Period size: 8 Copynumber: 7.1 Consensus size: 8
6507772 TACAATAATA
6507782 ATAAAAAT
1 ATAAAAAT
6507790 ATAAAAAT
1 ATAAAAAT
6507798 ATAAAAAT
1 ATAAAAAT
6507806 ATAAAAAT
1 ATAAAAAT
*
6507814 ATAAAGAT
1 ATAAAAAT
*
6507822 ATAAAAAA
1 ATAAAAAT
6507830 ATAATAAAT
1 ATAA-AAAT
6507839 A
1 A
6507840 GTATAATAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
8 41 0.91
9 4 0.09
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (8 bp):
ATAAAAAT
Found at i:6507809 original size:24 final size:24
Alignment explanation
Indices: 6507781--6507865 Score: 97
Period size: 24 Copynumber: 3.6 Consensus size: 24
6507771 ATACAATAAT
6507781 AATAAAAATATAAAAATATAAAAA
1 AATAAAAATATAAAAATATAAAAA
* *
6507805 TATAAAAATATAAAGATATAAAAA
1 AATAAAAATATAAAAATATAAAAA
*
6507829 AATAATAAATAGT-ATAATA-AAAAA
1 AATAA-AAATA-TAAAAATATAAAAA
6507853 AAT--AAATATAAAA
1 AATAAAAATATAAAA
6507866 TTTTTATTCA
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
20 1 0.02
21 7 0.13
24 34 0.65
25 9 0.17
26 1 0.02
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (24 bp):
AATAAAAATATAAAAATATAAAAA
Found at i:6507850 original size:21 final size:20
Alignment explanation
Indices: 6507778--6507862 Score: 80
Period size: 16 Copynumber: 4.7 Consensus size: 20
6507768 TAAATACAAT
6507778 AATAATAAA-A-AT-ATAAA
1 AATAATAAATATATAATAAA
6507795 AAT-ATAAA-A-AT-ATAAA
1 AATAATAAATATATAATAAA
*
6507811 AAT-ATAAAGATATAA-AAA
1 AATAATAAATATATAATAAA
6507829 AATAATAAATAGTATAATAAA
1 AATAATAAATA-TATAATAAA
*
6507850 AAAAATAAATATA
1 AATAATAAATATA
6507863 AAATTTTTAT
Statistics
Matches: 60, Mismatches: 2, Indels: 9
0.85 0.03 0.13
Matches are distributed among these distances:
16 21 0.35
17 4 0.07
18 8 0.13
19 7 0.12
20 7 0.12
21 13 0.22
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (20 bp):
AATAATAAATATATAATAAA
Found at i:6520098 original size:37 final size:37
Alignment explanation
Indices: 6519982--6520340 Score: 478
Period size: 37 Copynumber: 9.7 Consensus size: 37
6519972 AAAAAGGTTG
*
6519982 CGTTGCCTCAGTTTTGAGGAGTTCA-TTTTAAAGTCT
1 CGTTGCCTCAATTTTGAGGAGTTCATTTTTAAAGTCT
6520018 CGTTGCCTCAATTTTGAGGAGTTCA-TTTTAAAGTCT
1 CGTTGCCTCAATTTTGAGGAGTTCATTTTTAAAGTCT
*
6520054 CGTTGCCTCAATTTTAAGGAGTTCATTTTTAAAGTCT
1 CGTTGCCTCAATTTTGAGGAGTTCATTTTTAAAGTCT
* * *
6520091 TGGTGCCTCAACTTTGAGGAGTTCA-TTTTAAAGTCT
1 CGTTGCCTCAATTTTGAGGAGTTCATTTTTAAAGTCT
*
6520127 CGTTGCCTCAATTTTGAGGAGTTCATTTTAAAAGGT-T
1 CGTTGCCTCAATTTTGAGGAGTTCATTTTTAAA-GTCT
* *
6520164 ACGCTGCCTCAGTTTTGAGGAGTTCATTTTTAAAGTCT
1 -CGTTGCCTCAATTTTGAGGAGTTCATTTTTAAAGTCT
*
6520202 CGTTGCCTCAATTTTGAGGAGTTCATTTTAAAAGTCT
1 CGTTGCCTCAATTTTGAGGAGTTCATTTTTAAAGTCT
* * *
6520239 CATTGCCTCAGTTTTGAGGAGTTCATTTTAAAAGTCT
1 CGTTGCCTCAATTTTGAGGAGTTCATTTTTAAAGTCT
* *
6520276 CGTGGCCTCAGTTTTGAGGAGTTCATTTTTTAAAAG--T
1 CGTTGCCTCAATTTTGAGGAGTTCA-TTTTT-AAAGTCT
* *
6520313 CGTAATGCCTCAGTTTTGAGGAATTCAT
1 CGT--TGCCTCAATTTTGAGGAGTTCAT
6520341 GTAAAAAAAA
Statistics
Matches: 291, Mismatches: 23, Indels: 16
0.88 0.07 0.05
Matches are distributed among these distances:
36 92 0.32
37 137 0.47
38 38 0.13
39 24 0.08
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (37 bp):
CGTTGCCTCAATTTTGAGGAGTTCATTTTTAAAGTCT
Found at i:6520511 original size:19 final size:19
Alignment explanation
Indices: 6520470--6520518 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
6520460 CAAAAAAATG
*
6520470 AATTAAAAAAATATAATAAA
1 AATT-AAAAAATATAAGAAA
6520490 AATTAAAAAATA-AAGAAGA
1 AATTAAAAAATATAAGAA-A
*
6520509 AATGAAAAAA
1 AATTAAAAAA
6520519 GAAGGGAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 4 0.15
19 18 0.69
20 4 0.15
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (19 bp):
AATTAAAAAATATAAGAAA
Found at i:6525337 original size:18 final size:18
Alignment explanation
Indices: 6525316--6525351 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
6525306 TTTAAATTGT
6525316 TAATGAAATTTTATTTTA
1 TAATGAAATTTTATTTTA
**
6525334 TAATTTAATTTTATTTTA
1 TAATGAAATTTTATTTTA
6525352 AAAGTGATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
TAATGAAATTTTATTTTA
Found at i:6527023 original size:80 final size:80
Alignment explanation
Indices: 6526924--6527108 Score: 257
Period size: 80 Copynumber: 2.3 Consensus size: 80
6526914 TACCAAGAGT
* *
6526924 AGAAATGACATTAAGGTATGTTCTTGGGTTCTATCTCTTGCCATATCG-TCATATTGTTGTCT-A
1 AGAAATGACATTAAGGTATGTTCTTGGATTCCATCTCTTGCCATATCGCT-ATATTGTTGT-TAA
* *
6526987 TTTAGAAATCAAAAAGC
64 TTTACAAACCAAAAAGC
* * *
6527004 AGAAATGACATCAAGGTATGTTCTTGGATTCCATCTCTTGCCATCTTGCTATATTGTTGTTAATT
1 AGAAATGACATTAAGGTATGTTCTTGGATTCCATCTCTTGCCATATCGCTATATTGTTGTTAATT
*
6527069 TACAAACCAAAGAGC
66 TACAAACCAAAAAGC
*
6527084 AGATATGACATTAAGGTATGTTCTT
1 AGAAATGACATTAAGGTATGTTCTT
6527109 AAATTTATTG
Statistics
Matches: 93, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
79 1 0.01
80 91 0.98
81 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (80 bp):
AGAAATGACATTAAGGTATGTTCTTGGATTCCATCTCTTGCCATATCGCTATATTGTTGTTAATT
TACAAACCAAAAAGC
Found at i:6527461 original size:88 final size:88
Alignment explanation
Indices: 6527352--6527530 Score: 216
Period size: 88 Copynumber: 2.0 Consensus size: 88
6527342 AAATATTGTC
* * * * *
6527352 ACACGTCATGCGTAATAACTAAATTATTACACGTTATGTTTAAAAATCCTTGGTTGCTACACGCC
1 ACACGTCATGCGTAATAACTAAATTATTACACATCATGTCTAAAAATCATTAGTTGCTACACGCC
* *
6527417 ATGCTTAAAAATTCTTAATTGCT
66 ATGCCTAAAAATTATTAATTGCT
* * * * * *
6527440 ACACGTCATGAC-TAATGACTAAGTTGTTATACATCATGTCTAAAAATTATTAGTTGCTACATGC
1 ACACGTCATG-CGTAATAACTAAATTATTACACATCATGTCTAAAAATCATTAGTTGCTACACGC
*
6527504 CATGCCTAAAAATTATTAGTTGCT
65 CATGCCTAAAAATTATTAATTGCT
6527528 ACA
1 ACA
6527531 TGCCATGCTT
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
88 75 0.99
89 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (88 bp):
ACACGTCATGCGTAATAACTAAATTATTACACATCATGTCTAAAAATCATTAGTTGCTACACGCC
ATGCCTAAAAATTATTAATTGCT
Found at i:6527602 original size:92 final size:92
Alignment explanation
Indices: 6527408--6527630 Score: 244
Period size: 92 Copynumber: 2.5 Consensus size: 92
6527398 TCCTTGGTTG
* * * *
6527408 CTACACGCCATGCTTAAAAATTCTTAA-TTGCTACACGTCATG----ACTAATGACTAAGTTGTT
1 CTACATGCCATGCCTAAAAA-TCATAAGTTGCTACACGCCATGCTTAACTAATGACTAAGTTGTT
* * ** *
6527468 ATACATCATGTCTAAAAATTATTAGTTG
65 ACACATCATGCCTAAAAATTATTAAATA
* * *
6527496 CTACATGCCATGCCTAAAAATTATTAGTTGCTACATGCCATGCTTAACTAATGGACTAAGTTGTT
1 CTACATGCCATGCCTAAAAATCATAAGTTGCTACACGCCATGCTTAACTAAT-GACTAAGTTGTT
6527561 ACACATCATGCCT-AAAATT-TCTAAATA
65 ACACATCATGCCTAAAAATTAT-TAAATA
* *
6527588 CTACATGTCATGCCTAAAAATCCTAAGTTGCTACACGCCATGC
1 CTACATGCCATGCCTAAAAATCATAAGTTGCTACACGCCATGC
6527631 ATCATCCTAA
Statistics
Matches: 111, Mismatches: 17, Indels: 10
0.80 0.12 0.07
Matches are distributed among these distances:
87 3 0.03
88 31 0.28
91 1 0.01
92 53 0.48
93 23 0.21
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.32
Consensus pattern (92 bp):
CTACATGCCATGCCTAAAAATCATAAGTTGCTACACGCCATGCTTAACTAATGACTAAGTTGTTA
CACATCATGCCTAAAAATTATTAAATA
Found at i:6527622 original size:30 final size:30
Alignment explanation
Indices: 6527392--6527676 Score: 127
Period size: 30 Copynumber: 9.6 Consensus size: 30
6527382 ACGTTATGTT
** * *
6527392 TAAAAATCCTTGGTTGCTACACGCCATGCT
1 TAAAAATCCTAAGTTGCTACACGTCATGCC
* *
6527422 TAAAAATTCTTAA-TTGCTACACGTCATGAC
1 TAAAAA-TCCTAAGTTGCTACACGTCATGCC
** * * * *
6527452 TAATGA--CTAAGTTGTTATACATCATGTC
1 TAAAAATCCTAAGTTGCTACACGTCATGCC
** * * *
6527480 TAAAAATTATTAGTTGCTACATGCCATGCC
1 TAAAAATCCTAAGTTGCTACACGTCATGCC
** * * * *
6527510 TAAAAATTATTAGTTGCTACATGCCATGCT
1 TAAAAATCCTAAGTTGCTACACGTCATGCC
* * * *
6527540 TAACTAATGGACTAAGTTGTTACACATCATGCC
1 TAA-AAAT--CCTAAGTTGCTACACGTCATGCC
* * * * *
6527573 TAAAATTTCTAA-ATACTACATGTCATGCC
1 TAAAAATCCTAAGTTGCTACACGTCATGCC
*
6527602 TAAAAATCCTAAGTTGCTACACGCCATG-C
1 TAAAAATCCTAAGTTGCTACACGTCATGCC
** **
6527631 --ATCATCCTAAGTTGCTACACACCATGCC
1 TAAAAATCCTAAGTTGCTACACGTCATGCC
* *
6527659 TAACAAT-CTAAGTCGCTA
1 TAAAAATCCTAAGTTGCTA
6527677 TACACCATGT
Statistics
Matches: 191, Mismatches: 53, Indels: 23
0.72 0.20 0.09
Matches are distributed among these distances:
27 26 0.14
28 18 0.09
29 33 0.17
30 88 0.46
31 6 0.03
32 2 0.01
33 18 0.09
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32
Consensus pattern (30 bp):
TAAAAATCCTAAGTTGCTACACGTCATGCC
Found at i:6535646 original size:23 final size:23
Alignment explanation
Indices: 6535620--6535665 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
6535610 CAAGATGGAA
6535620 AGACTATGATACCTATTGGTCTT
1 AGACTATGATACCTATTGGTCTT
6535643 AGACTATGATACCTATTGGTCTT
1 AGACTATGATACCTATTGGTCTT
6535666 CCCTTGCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.39
Consensus pattern (23 bp):
AGACTATGATACCTATTGGTCTT
Found at i:6551428 original size:26 final size:24
Alignment explanation
Indices: 6551370--6551428 Score: 57
Period size: 26 Copynumber: 2.4 Consensus size: 24
6551360 TATTTTTTTA
*
6551370 ACAAATTATAATATTAAAATTTAT
1 ACAAATTATAATATTAAAATATAT
* *
6551394 A-AACTTTATCAATAATTATAATATAT
1 ACAA-ATTAT-AAT-ATTAAAATATAT
6551420 ACAAATTAT
1 ACAAATTAT
6551429 GTATAAATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
23 2 0.07
24 5 0.19
25 3 0.11
26 15 0.56
27 2 0.07
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.41
Consensus pattern (24 bp):
ACAAATTATAATATTAAAATATAT
Found at i:6551822 original size:212 final size:211
Alignment explanation
Indices: 6551424--6551876 Score: 578
Period size: 212 Copynumber: 2.1 Consensus size: 211
6551414 ATATATACAA
*
6551424 ATTATGTATAAATTAAATATAGGTATATATAATATATTACTTTATTATATATATGAAATTAATTA
1 ATTATGTATAAATTAAATATA--TATATATAATATATTACTTTATTATATATATGAAATTAATAA
* **
6551489 CACAATTTATATATTATAATATTTTAATTTTTATATCAAAGTTTGTATAAATAATAATTAATTAT
64 CACAACTTATATATTATAATA--TTAATTTTTATATCAAAGTTTGTATAAATAATAACCAATTAT
* * * *
6551554 AAACGATATGTTATAAAAATTAAGACAATAATTAAAAAAATTATTAAGTATAATCATATAAATAA
127 AAACAATATATTATAAAAATCAAGACAATAATTAAAAAAATCATTAAGTATAATCATATAAATAA
6551619 AGTCGATTATAAGTTACAGTAAT
192 A-T--ATTATAAGTTACAGTAAT
*
6551642 ACTTATATATAAATTAAATATATATATAT-ATAATATTACTTTATTATGTATATATGAAATTAAT
1 A-TTATGTATAAATTAAATATATATATATAAT-ATATTACTTTATTA--TATATATGAAATTAAT
*
6551706 AACACAACTTATATGTTAT-A-A-T-A-TTTTATATCAAAGTTTGTATAAATAATAACCAATTAT
62 AACACAACTTATATATTATAATATTAATTTTTATATCAAAGTTTGTATAAATAATAACCAATTAT
* * ** * * *
6551766 AAATAATATATTATAAAAACTCGAG-TGATAATTAATAAGATCATTAAGTGTAATCATATAAATA
127 AAACAATATATTATAAAAA-TCAAGACAATAATTAAAAAAATCATTAAGTATAATCATATAAATA
*
6551830 AATATTATAAGTTATAGTAAT
191 AATATTATAAGTTACAGTAAT
6551851 ATCTATGTATAAATTAAATATATATA
1 AT-TATGTATAAATTAAATATATATA
6551877 ATGTTTATAC
Statistics
Matches: 210, Mismatches: 19, Indels: 21
0.84 0.08 0.08
Matches are distributed among these distances:
208 1 0.00
209 40 0.19
211 1 0.00
212 86 0.41
213 4 0.02
214 1 0.00
216 2 0.01
217 22 0.10
218 2 0.01
219 51 0.24
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.41
Consensus pattern (211 bp):
ATTATGTATAAATTAAATATATATATATAATATATTACTTTATTATATATATGAAATTAATAACA
CAACTTATATATTATAATATTAATTTTTATATCAAAGTTTGTATAAATAATAACCAATTATAAAC
AATATATTATAAAAATCAAGACAATAATTAAAAAAATCATTAAGTATAATCATATAAATAAATAT
TATAAGTTACAGTAAT
Found at i:6552074 original size:212 final size:214
Alignment explanation
Indices: 6551832--6552235 Score: 550
Period size: 216 Copynumber: 1.9 Consensus size: 214
6551822 TATAAATAAA
** *
6551832 TATTATAAGTTATAGTAATATCTATGTATAAATTAAATATATAT-A-ATGTTTATACAA-T-TAG
1 TATTATAAGTTATAAAAATATCTATGTATAAATTAAATATATATAATATATTTATACAATTATAG
* * ** **
6551893 ATATATTTAAAACATTTTATATTATGAAACATTACTAAGGTGTAATAACTATAATGTATTAATAT
66 ATATATTTAAAACATTTTATATTACGAAACATTAATAAGACGTAATAACTATAACATATTAATAT
* *
6551958 ATAAAATATTTACTATCACATATTATAATATTAACATATTAA-TTATATCATTTCAAATATATAC
131 ATAAAACATTTACTATCA-ATATTATAATATTAACATA-TAAGTTATATCATTTAAAATATATAC
6552022 TTGNATTATATAAATAAAGTTT
194 TTG-ATTATATAAATAAAGTTT
*
6552044 TATTATAAGTTATAAAAATA-CTTTTGTATAAATTAAATATATATAATATATTTATACAATTATA
1 TATTATAAGTTATAAAAATATC-TATGTATAAATTAAATATATATAATATATTTATACAATTATA
* * * *
6552108 TATATATTTATAACATTTTATATTACGAAACATTAATATGACGTAATAATTATAACATATTAATA
65 GATATATTTAAAACATTTTATATTACGAAACATTAATAAGACGTAATAACTATAACATATTAATA
* * * *
6552173 TGTAAGACATTTACTATCATTATTATAATATTAACATATAAGTTATATTATTTAAAATATATA
130 TATAAAACATTTACTATCAATATTATAATATTAACATATAAGTTATATCATTTAAAATATATA
6552236 ACTTATAATT
Statistics
Matches: 166, Mismatches: 20, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
211 1 0.01
212 39 0.23
213 1 0.01
214 14 0.08
215 38 0.23
216 73 0.44
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.43
Consensus pattern (214 bp):
TATTATAAGTTATAAAAATATCTATGTATAAATTAAATATATATAATATATTTATACAATTATAG
ATATATTTAAAACATTTTATATTACGAAACATTAATAAGACGTAATAACTATAACATATTAATAT
ATAAAACATTTACTATCAATATTATAATATTAACATATAAGTTATATCATTTAAAATATATACTT
GATTATATAAATAAAGTTT
Found at i:6552232 original size:21 final size:20
Alignment explanation
Indices: 6552195--6552233 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
6552185 ACTATCATTA
*
6552195 TTATAATATTAACATATAAG
1 TTATAATATTAAAATATAAG
*
6552215 TTATATTATTTAAAATATA
1 TTATAATA-TTAAAATATA
6552234 TAACTTATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (20 bp):
TTATAATATTAAAATATAAG
Found at i:6552500 original size:23 final size:24
Alignment explanation
Indices: 6552474--6552521 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
6552464 ACCGATCAAA
6552474 AAATCAATTGA-ACCAAAT-ATTTT
1 AAATCAATT-ACACCAAATCATTTT
*
6552497 AAATTAATTACACCAAATCATTTT
1 AAATCAATTACACCAAATCATTTT
6552521 A
1 A
6552522 TTCAAATCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 1 0.05
23 15 0.68
24 6 0.27
ACGTcount: A:0.48, C:0.15, G:0.02, T:0.35
Consensus pattern (24 bp):
AAATCAATTACACCAAATCATTTT
Found at i:6561982 original size:19 final size:18
Alignment explanation
Indices: 6561960--6562005 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
6561950 TTCACTATAC
6561960 TTCTTTCTCTCTCTTCTTT
1 TTCTTT-TCTCTCTTCTTT
*
6561979 TTCTCTTTCTCTTTTCTTT
1 TTCT-TTTCTCTCTTCTTT
6561998 TGTCTTTT
1 T-TCTTTT
6562006 TATTTTTTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.00, C:0.26, G:0.02, T:0.72
Consensus pattern (18 bp):
TTCTTTTCTCTCTTCTTT
Found at i:6563212 original size:30 final size:29
Alignment explanation
Indices: 6563155--6563216 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 29
6563145 CAATCAAATT
* * *
6563155 TTTATATTTTTATTTGCAATTAGATAAGTC
1 TTTATATTTTTATTTGAAATCAAATAAG-C
*
6563185 TTTATATTTTTATTTTAAATCAAATAAGC
1 TTTATATTTTTATTTGAAATCAAATAAGC
6563214 TTT
1 TTT
6563217 TACAACTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 4 0.14
30 24 0.86
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.55
Consensus pattern (29 bp):
TTTATATTTTTATTTGAAATCAAATAAGC
Found at i:6563489 original size:43 final size:43
Alignment explanation
Indices: 6563436--6563522 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 43
6563426 AATAAAGACT
* *
6563436 TTTTTAATTTTTTTTCATAATTTAAAGACTTATTTGAGTATTA
1 TTTTAAATTTTTTTACATAATTTAAAGACTTATTTGAGTATTA
* *
6563479 TTTTAAATTTTTTTACATAATTTAAGGATTTATTTGAGTATTA
1 TTTTAAATTTTTTTACATAATTTAAAGACTTATTTGAGTATTA
6563522 T
1 T
6563523 GTAAAAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.57
Consensus pattern (43 bp):
TTTTAAATTTTTTTACATAATTTAAAGACTTATTTGAGTATTA
Found at i:6567281 original size:2 final size:2
Alignment explanation
Indices: 6567274--6567318 Score: 65
Period size: 2 Copynumber: 22.5 Consensus size: 2
6567264 CCTTTTTATT
*
6567274 TA TA TA TA TA TA TA TA CA CTA TA TA TA TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
6567316 TA T
1 TA T
6567319 TCATTTTGTC
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 1 0.03
2 37 0.95
3 1 0.03
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:6567298 original size:15 final size:14
Alignment explanation
Indices: 6567277--6567317 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
6567267 TTTTATTTAT
6567277 ATATATATATATAC
1 ATATATATATATAC
*
6567291 ACTATATATATAT-T
1 A-TATATATATATAC
6567305 ATATATATATATA
1 ATATATATATATA
6567318 TTCATTTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 11 0.46
14 2 0.08
15 11 0.46
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (14 bp):
ATATATATATATAC
Found at i:6567318 original size:15 final size:15
Alignment explanation
Indices: 6567273--6567319 Score: 69
Period size: 15 Copynumber: 3.1 Consensus size: 15
6567263 TCCTTTTTAT
6567273 TTATATATATATATA
1 TTATATATATATATA
*
6567288 -TACACTATATATATA
1 TTATA-TATATATATA
6567303 TTATATATATATATA
1 TTATATATATATATA
6567318 TT
1 TT
6567320 CATTTTGTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 3 0.11
15 22 0.79
16 3 0.11
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (15 bp):
TTATATATATATATA
Found at i:6570829 original size:43 final size:43
Alignment explanation
Indices: 6570776--6570862 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 43
6570766 AATAAAGACT
* *
6570776 TTTTTAATTTTTTTTCATAATTTAAAGACTTATTTGAGTATTA
1 TTTTAAATTTTTTTACATAATTTAAAGACTTATTTGAGTATTA
* *
6570819 TTTTAAATTTTTTTACATAATTTAAGGATTTATTTGAGTATTA
1 TTTTAAATTTTTTTACATAATTTAAAGACTTATTTGAGTATTA
6570862 T
1 T
6570863 GTAAAAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.57
Consensus pattern (43 bp):
TTTTAAATTTTTTTACATAATTTAAAGACTTATTTGAGTATTA
Found at i:6574636 original size:2 final size:2
Alignment explanation
Indices: 6574631--6574668 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
6574621 AAAAAAAAAA
*
6574631 AT AT AT AT AT AC AT AT AT AT -T AT A- AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6574669 TCATTTTGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6579471 original size:23 final size:22
Alignment explanation
Indices: 6579428--6579471 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
6579418 AAATACAAAC
* **
6579428 ATATTTTTATTATAATTTAATA
1 ATATTTTTATTAGAAGATAATA
6579450 ATATTTTGTATTAGAAGATAAT
1 ATATTTT-TATTAGAAGATAAT
6579472 TAAACCTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (22 bp):
ATATTTTTATTAGAAGATAATA
Found at i:6587396 original size:79 final size:79
Alignment explanation
Indices: 6587265--6587423 Score: 282
Period size: 79 Copynumber: 2.0 Consensus size: 79
6587255 GTTCCTCCCT
*
6587265 TCTCTACCAGCGTTGATCTGACCTTACCCACTAGCTTCAACAGCCTCCGTCGGTCGACTTCCCAA
1 TCTCTACCAGCGTCGATCTGACCTTACCCACTAGCTTCAACAGCCTCCGTCGGTCGACTTCCCAA
6587330 GACCAAATACCCCC
66 GACCAAATACCCCC
* *
6587344 TCTCTACCGGCGTCGATCTGACCTTACCCACTAGCTTCAACAGCCTCCGTCGGTCGGCTTCCCAA
1 TCTCTACCAGCGTCGATCTGACCTTACCCACTAGCTTCAACAGCCTCCGTCGGTCGACTTCCCAA
*
6587409 GACCAAATAGCCCC
66 GACCAAATACCCCC
6587423 T
1 T
6587424 TATTTACCGG
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
79 76 1.00
ACGTcount: A:0.21, C:0.40, G:0.16, T:0.23
Consensus pattern (79 bp):
TCTCTACCAGCGTCGATCTGACCTTACCCACTAGCTTCAACAGCCTCCGTCGGTCGACTTCCCAA
GACCAAATACCCCC
Found at i:6587953 original size:11 final size:11
Alignment explanation
Indices: 6587936--6588021 Score: 55
Period size: 12 Copynumber: 7.0 Consensus size: 11
6587926 TTCATTCATC
6587936 ATTTTTTTTATT
1 ATTTTTTTT-TT
*
6587948 TTTTTTATTTTT
1 ATTTTT-TTTTT
6587960 ATTTGTTTCTTATT
1 ATTT-TTT-TT-TT
6587974 AATTTTTTATTTTT
1 -A-TTTTT-TTTTT
** *
6587988 AAGTTCTTTTT
1 ATTTTTTTTTT
6587999 ATTTTTTATTTT
1 ATTTTTT-TTTT
6588011 ATTTTTTTTTT
1 ATTTTTTTTTT
6588022 GTAAGTAGGT
Statistics
Matches: 58, Mismatches: 8, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
11 13 0.22
12 24 0.41
13 8 0.14
14 4 0.07
15 5 0.09
16 4 0.07
ACGTcount: A:0.15, C:0.02, G:0.02, T:0.80
Consensus pattern (11 bp):
ATTTTTTTTTT
Found at i:6588015 original size:17 final size:16
Alignment explanation
Indices: 6587937--6588021 Score: 52
Period size: 16 Copynumber: 5.2 Consensus size: 16
6587927 TCATTCATCA
6587937 TTTT-TTTTATTTTTT
1 TTTTATTTTATTTTTT
*
6587952 TTAT-TTTTATTTGTTT
1 TTTTATTTTATTT-TTT
* *
6587968 CTTATTAATTT-TTTATT
1 -TT-TTATTTTATTTTTT
* *
6587985 TTTAAGTTCTT-TTTATT
1 TTTTA-TT-TTATTTTTT
6588002 TTTTATTTTATTTTTT
1 TTTTATTTTATTTTTT
6588018 TTTT
1 TTTT
6588022 GTAAGTAGGT
Statistics
Matches: 55, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
15 15 0.27
16 17 0.31
17 16 0.29
18 4 0.07
19 3 0.05
ACGTcount: A:0.14, C:0.02, G:0.02, T:0.81
Consensus pattern (16 bp):
TTTTATTTTATTTTTT
Found at i:6588015 original size:36 final size:39
Alignment explanation
Indices: 6587939--6588027 Score: 100
Period size: 37 Copynumber: 2.4 Consensus size: 39
6587929 ATTCATCATT
* *
6587939 TTTTTTATTTTT--TTTATTTTTATTTGTTTCTTATTAA
1 TTTTTTATTTTTAAGTTATTTTTATTTGTTTATTATTAA
*
6587976 TTTTTTATTTTTAAGTTCTTTTTATTT-TTTATT-TT-A
1 TTTTTTATTTTTAAGTTATTTTTATTTGTTTATTATTAA
6588012 TTTTTT-TTTTGTAAGT
1 TTTTTTATTTT-TAAGT
6588028 AGGTGTCTAC
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
35 4 0.09
36 12 0.26
37 14 0.30
38 5 0.11
39 11 0.24
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.78
Consensus pattern (39 bp):
TTTTTTATTTTTAAGTTATTTTTATTTGTTTATTATTAA
Found at i:6588871 original size:24 final size:24
Alignment explanation
Indices: 6588823--6588953 Score: 165
Period size: 24 Copynumber: 5.5 Consensus size: 24
6588813 CAGTCTCTGA
* *
6588823 TGATGCTTGTTTCACTGGCTCCAC
1 TGATTCTTGTTTCACAGGCTCCAC
* * *
6588847 CGATTCTAGTTCCACAGGCTCCAC
1 TGATTCTTGTTTCACAGGCTCCAC
*
6588871 CGATTC-TGTTTGCACAGGCTCCAC
1 TGATTCTTGTTT-CACAGGCTCCAC
*
6588895 TGATTCTTGTTTCACTGGCTCCAC
1 TGATTCTTGTTTCACAGGCTCCAC
* *
6588919 TGGTTCTTGTTTCACGGGCTCCAC
1 TGATTCTTGTTTCACAGGCTCCAC
6588943 TGATTCTTGTT
1 TGATTCTTGTT
6588954 GCACTAGTTC
Statistics
Matches: 93, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
23 3 0.03
24 85 0.91
25 5 0.05
ACGTcount: A:0.14, C:0.30, G:0.20, T:0.37
Consensus pattern (24 bp):
TGATTCTTGTTTCACAGGCTCCAC
Found at i:6588909 original size:72 final size:72
Alignment explanation
Indices: 6588823--6588957 Score: 191
Period size: 72 Copynumber: 1.9 Consensus size: 72
6588813 CAGTCTCTGA
6588823 TGATGCTTGTTTCACTGGCTCCACCGATTCTAGTTCCACAGGCTCCACCGATTC-TGTTTGCACA
1 TGATGCTTGTTTCACTGGCTCCACCGATTCTAGTTCCACAGGCTCCACCGATTCTTG-TTGCACA
6588887 GGCTCCAC
65 GGCTCCAC
* * * * * * *
6588895 TGATTCTTGTTTCACTGGCTCCACTGGTTCTTGTTTCACGGGCTCCACTGATTCTTGTTGCAC
1 TGATGCTTGTTTCACTGGCTCCACCGATTCTAGTTCCACAGGCTCCACCGATTCTTGTTGCAC
6588958 TAGTTCCGGT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
72 53 0.96
73 2 0.04
ACGTcount: A:0.14, C:0.30, G:0.20, T:0.36
Consensus pattern (72 bp):
TGATGCTTGTTTCACTGGCTCCACCGATTCTAGTTCCACAGGCTCCACCGATTCTTGTTGCACAG
GCTCCAC
Found at i:6588976 original size:48 final size:49
Alignment explanation
Indices: 6588823--6588977 Score: 138
Period size: 48 Copynumber: 3.2 Consensus size: 49
6588813 CAGTCTCTGA
* * * * *
6588823 TGATGCTTGTTT-CACTGGCTCCACCGATTCTAGTTCCAC-AGGCTCCAC
1 TGATACTTGTTTGCACAGGCTCCACTGATTCTTGTTGCACTA-GCTCCAC
* * * *
6588871 CGATTC-TGTTTGCACAGGCTCCACTGATTCTTGTTTCACTGGCTCCAC
1 TGATACTTGTTTGCACAGGCTCCACTGATTCTTGTTGCACTAGCTCCAC
* * * * **
6588919 TGGTTCTTGTTT-CACGGGCTCCACTGATTCTTGTTGCACTAGTTCCGG
1 TGATACTTGTTTGCACAGGCTCCACTGATTCTTGTTGCACTAGCTCCAC
6588967 TGATACTTGTT
1 TGATACTTGTT
6588978 CCGCTACCTC
Statistics
Matches: 87, Mismatches: 17, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
47 5 0.06
48 77 0.89
49 5 0.06
ACGTcount: A:0.14, C:0.28, G:0.21, T:0.37
Consensus pattern (49 bp):
TGATACTTGTTTGCACAGGCTCCACTGATTCTTGTTGCACTAGCTCCAC
Found at i:6594272 original size:167 final size:166
Alignment explanation
Indices: 6593950--6594282 Score: 557
Period size: 166 Copynumber: 2.0 Consensus size: 166
6593940 TATGCTTATA
*
6593950 TATGTTGAATGCTATGGGTGAGTTTTGGGGTTAGTTTGGATTTTTTTTTTTTTCAGTTGGGGGAA
1 TATGTTGAATGCTATGGGTGAGTTTTGGGGATAGTTTGGATTTTTTTTTTTTTCAGTTGGGGGAA
* * *
6594015 CTGAATAGCTTTGGATAGCGTATTTGAAATTGCAAGTTCATGAATTTGTGAAAGAAGGATTGGTG
66 CTGAAAAGCTTTGGATAGCGTATTTGAAATTGCAAGCTCATGAATTTGTGAAAGAAGGATTGATG
6594080 TCATTTCTTCAATGAAAAAAAAAGAGAGTAAATCTTG
131 TCATTTCTTCAATGAAAAAAAAA-AGAGTAAATCTTG
6594117 TATGTTGAATGCTATGGGTGAG-TTTGGGGATAGTTTGGATTTTTCTTTTTTTT-AGTT-GGGGA
1 TATGTTGAATGCTATGGGTGAGTTTTGGGGATAGTTTGGATTTTT-TTTTTTTTCAGTTGGGGGA
*
6594179 AGCTGAAAAGCTTTGGATAGTGTATTTGAAATTGCAAGCTCATGAATTTGT-ATAAGAAGGATTG
65 A-CTGAAAAGCTTTGGATAGCGTATTTGAAATTGCAAGCTCATGAATTTGTGA-AAGAAGGATTG
6594243 ATGTCATTTCTTCAATGAAAAAAAAAAGAGTAAATCTTG
128 ATGTCATTTCTTCAATGAAAAAAAAAAGAGTAAATCTTG
6594282 T
1 T
6594283 TTTCTGAATG
Statistics
Matches: 158, Mismatches: 5, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
165 21 0.13
166 107 0.68
167 30 0.19
ACGTcount: A:0.29, C:0.07, G:0.26, T:0.39
Consensus pattern (166 bp):
TATGTTGAATGCTATGGGTGAGTTTTGGGGATAGTTTGGATTTTTTTTTTTTTCAGTTGGGGGAA
CTGAAAAGCTTTGGATAGCGTATTTGAAATTGCAAGCTCATGAATTTGTGAAAGAAGGATTGATG
TCATTTCTTCAATGAAAAAAAAAAGAGTAAATCTTG
Found at i:6603849 original size:16 final size:17
Alignment explanation
Indices: 6603809--6603852 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
6603799 AATATTTAGT
6603809 AGATAAAAATA-AGAAA
1 AGATAAAAATATAGAAA
6603825 AGA-ATAAAATATA-AAA
1 AGATA-AAAATATAGAAA
6603841 AGATAAAAATAT
1 AGATAAAAATAT
6603853 TTTTTATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 1 0.04
16 22 0.88
17 2 0.08
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (17 bp):
AGATAAAAATATAGAAA
Found at i:6604113 original size:13 final size:13
Alignment explanation
Indices: 6604091--6604124 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
6604081 CAATTTTTAA
6604091 ATTTAAAATATAT
1 ATTTAAAATATAT
* *
6604104 TTTTATAATATAT
1 ATTTAAAATATAT
6604117 ATTTAAAA
1 ATTTAAAA
6604125 ATTTAAACTT
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATTTAAAATATAT
Found at i:6604200 original size:42 final size:42
Alignment explanation
Indices: 6604154--6604252 Score: 103
Period size: 42 Copynumber: 2.4 Consensus size: 42
6604144 TATAATAACA
* * *
6604154 TTAATAATTGATCATT-T-AAATATTAATATTTTTTTTTATAAT
1 TTAATAATT-AACATTGTAAAATATGAATA-TTTTATTTATAAT
* *
6604196 TTAATCATTAAGATTGTAAAATATGAATATTTTATTTATAAT
1 TTAATAATTAACATTGTAAAATATGAATATTTTATTTATAAT
**
6604238 TTAACCATTAACATT
1 TTAATAATTAACATT
6604253 TTAATATTTA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.08
42 34 0.71
43 10 0.21
ACGTcount: A:0.40, C:0.05, G:0.04, T:0.51
Consensus pattern (42 bp):
TTAATAATTAACATTGTAAAATATGAATATTTTATTTATAAT
Found at i:6604272 original size:42 final size:41
Alignment explanation
Indices: 6604166--6604272 Score: 101
Period size: 42 Copynumber: 2.6 Consensus size: 41
6604156 AATAATTGAT
* *
6604166 CATTTAAATATTAATATTTTTT-TTTATAATTTAATCATTAA
1 CATTTTAATATTAAT-TTTTTTATTTATAATTTAACCATTAA
* * * *
6604207 GATTGTAAAATATGAA-TATTTTATTTATAATTTAACCATTAA
1 CATT-T-TAATATTAATTTTTTTATTTATAATTTAACCATTAA
*
6604249 CATTTTAATATTTATTTTATTTAT
1 CATTTTAATATTAATTTT-TTTAT
6604273 AGTTGAAATG
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
40 6 0.12
41 11 0.21
42 27 0.52
43 8 0.15
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (41 bp):
CATTTTAATATTAATTTTTTTATTTATAATTTAACCATTAA
Found at i:6610481 original size:10 final size:10
Alignment explanation
Indices: 6610466--6610506 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
6610456 TTATGTTACG
*
6610466 TATGTATGTA
1 TATGTATATA
6610476 TATGTATATA
1 TATGTATATA
*
6610486 TGTGTATATA
1 TATGTATATA
*
6610496 TATATATATA
1 TATGTATATA
6610506 T
1 T
6610507 CAAATAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (10 bp):
TATGTATATA
Found at i:6610493 original size:16 final size:16
Alignment explanation
Indices: 6610472--6610502 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6610462 TACGTATGTA
*
6610472 TGTATATGTATATATG
1 TGTATATATATATATG
6610488 TGTATATATATATAT
1 TGTATATATATATAT
6610503 ATATCAAATA
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:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (16 bp):
TGTATATATATATATG
Found at i:6627005 original size:99 final size:99
Alignment explanation
Indices: 6626810--6626993 Score: 314
Period size: 99 Copynumber: 1.9 Consensus size: 99
6626800 TCATCAAGGC
** *
6626810 TAGAAGCATAGTTGATTTACAACCTCTTTGAAAGATGATCTCCAGTAGTCTTGGCTTGAGGTAGT
1 TAGAAGCATAGTTGATTTACAACCTCTTCAAAAGATGATCTCCAATAGTCTTGGCTTGAGGTAGT
* *
6626875 ATACTAAATGAAAAACAACACTGTCGACAGAATT
66 ATACCAAATAAAAAACAACACTGTCGACAGAATT
*
6626909 TAGAAGCATAGTTGATTTACAACCTCTTCAAAAGATGATCTCCAATAGTTTTGGCTTGAGGTAGT
1 TAGAAGCATAGTTGATTTACAACCTCTTCAAAAGATGATCTCCAATAGTCTTGGCTTGAGGTAGT
6626974 ATACCAAATAAAAAACAACA
66 ATACCAAATAAAAAACAACA
6626994 TTGTTGGCAG
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
99 79 1.00
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (99 bp):
TAGAAGCATAGTTGATTTACAACCTCTTCAAAAGATGATCTCCAATAGTCTTGGCTTGAGGTAGT
ATACCAAATAAAAAACAACACTGTCGACAGAATT
Found at i:6628644 original size:15 final size:15
Alignment explanation
Indices: 6628624--6628682 Score: 75
Period size: 15 Copynumber: 3.9 Consensus size: 15
6628614 CAACAAACTC
6628624 CCTCTCCTTCTCCAT
1 CCTCTCCTTCTCCAT
6628639 CCTCTCCTTCTCC-T
1 CCTCTCCTTCTCCAT
* *
6628653 CTCTCTCCCTCTCCCT
1 C-CTCTCCTTCTCCAT
*
6628669 CCTCTCCTCCTCCA
1 CCTCTCCTTCTCCA
6628683 CCACATCCTC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
14 2 0.05
15 34 0.89
16 2 0.05
ACGTcount: A:0.03, C:0.59, G:0.00, T:0.37
Consensus pattern (15 bp):
CCTCTCCTTCTCCAT
Found at i:6628659 original size:30 final size:30
Alignment explanation
Indices: 6628625--6628681 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
6628615 AACAAACTCC
* *
6628625 CTCTCCTTCTCCATCCTCTCCTTCTCCTCT
1 CTCTCCCTCTCCATCCTCTCCTCCTCCTCT
*
6628655 CTCTCCCTCTCCCTCCTCTCCTCCTCC
1 CTCTCCCTCTCCATCCTCTCCTCCTCC
6628682 ACCACATCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.02, C:0.60, G:0.00, T:0.39
Consensus pattern (30 bp):
CTCTCCCTCTCCATCCTCTCCTCCTCCTCT
Found at i:6628670 original size:4 final size:5
Alignment explanation
Indices: 6628624--6628677 Score: 51
Period size: 5 Copynumber: 10.8 Consensus size: 5
6628614 CAACAAACTC
*
6628624 CCTCT CCTTCT CC-AT CCTCT CCTTCT CCTCT -CTCT CCCTCT CC-CT
1 CCTCT CC-TCT CCTCT CCTCT CC-TCT CCTCT CCTCT -CCTCT CCTCT
6628669 CCTCT CCTC
1 CCTCT CCTC
6628678 CTCCACCACA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
4 11 0.27
5 16 0.39
6 14 0.34
ACGTcount: A:0.02, C:0.59, G:0.00, T:0.39
Consensus pattern (5 bp):
CCTCT
Found at i:6630426 original size:30 final size:30
Alignment explanation
Indices: 6630366--6630439 Score: 75
Period size: 30 Copynumber: 2.5 Consensus size: 30
6630356 AATTATTAGT
*
6630366 TATAAAAACTTATTTGATTCAAAATAAAAA
1 TATAAAAACTTATTTGACTCAAAATAAAAA
*
6630396 TATAAAAACTTGA-TTGACT-ATAATAGAAAA
1 TATAAAAACTT-ATTTGACTCAAAATA-AAAA
6630426 TA-AACAAA-TTATTT
1 TATAA-AAACTTATTT
6630440 AAATATTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
28 1 0.03
29 11 0.29
30 25 0.66
31 1 0.03
ACGTcount: A:0.54, C:0.07, G:0.05, T:0.34
Consensus pattern (30 bp):
TATAAAAACTTATTTGACTCAAAATAAAAA
Found at i:6630458 original size:19 final size:19
Alignment explanation
Indices: 6630431--6630468 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
6630421 GAAAATAAAC
* *
6630431 AAATTATTTAAATATTTTT
1 AAATAATTTAAAGATTTTT
6630450 AAATAATTTAAAGATTTTT
1 AAATAATTTAAAGATTTTT
6630469 TAAAATATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (19 bp):
AAATAATTTAAAGATTTTT
Found at i:6652772 original size:22 final size:21
Alignment explanation
Indices: 6652747--6652835 Score: 51
Period size: 21 Copynumber: 4.2 Consensus size: 21
6652737 TTAGGTATAT
6652747 TTAATAAACTTTTAATTAATTA
1 TTAATAAACTTTTAATT-ATTA
*
6652769 TTAA-ACCAA-TTATAATTATT-
1 TTAATA--AACTTTTAATTATTA
* ** * *
6652789 TAAATATTCTATTAAGTA-TA
1 TTAATAAACTTTTAATTATTA
6652809 TTTAATAAACTTTTAATTAATTA
1 -TTAATAAACTTTTAATT-ATTA
6652832 TTAA
1 TTAA
6652836 ACCAATTATA
Statistics
Matches: 47, Mismatches: 12, Indels: 16
0.63 0.16 0.21
Matches are distributed among these distances:
19 1 0.02
20 9 0.19
21 17 0.36
22 16 0.34
23 4 0.09
ACGTcount: A:0.45, C:0.06, G:0.01, T:0.48
Consensus pattern (21 bp):
TTAATAAACTTTTAATTATTA
Found at i:6652811 original size:63 final size:63
Alignment explanation
Indices: 6652732--6652917 Score: 336
Period size: 63 Copynumber: 3.0 Consensus size: 63
6652722 GTGATTTATT
6652732 TTCTATTAGGTATATTTAATAAACTTTTAATTAATTATTAAACCAATTATAATTATTTAAATA
1 TTCTATTAGGTATATTTAATAAACTTTTAATTAATTATTAAACCAATTATAATTATTTAAATA
*
6652795 TTCTATTAAGTATATTTAATAAACTTTTAATTAATTATTAAACCAATTATAATTATTTAAATA
1 TTCTATTAGGTATATTTAATAAACTTTTAATTAATTATTAAACCAATTATAATTATTTAAATA
* * *
6652858 TTCAATTAGGTATATTTAATAGACTTTTAATTAATTATTAAACCAATGATAATTATTTAA
1 TTCTATTAGGTATATTTAATAAACTTTTAATTAATTATTAAACCAATTATAATTATTTAA
6652918 TTCCCATTGA
Statistics
Matches: 118, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 118 1.00
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (63 bp):
TTCTATTAGGTATATTTAATAAACTTTTAATTAATTATTAAACCAATTATAATTATTTAAATA
Found at i:6652847 original size:22 final size:22
Alignment explanation
Indices: 6652759--6652849 Score: 59
Period size: 22 Copynumber: 4.3 Consensus size: 22
6652749 AATAAACTTT
6652759 TAATTAATTATTAAACCAATTA
1 TAATTAATTATTAAACCAATTA
* *
6652781 TAATT-A-T-TTAAA--TATTC
1 TAATTAATTATTAAACCAATTA
* ** *
6652798 T-ATTAAGTATATTTAATAAACTTT
1 TAATTAA-T-TATTAAACCAA-TTA
6652822 TAATTAATTATTAAACCAATTA
1 TAATTAATTATTAAACCAATTA
6652844 TAATTA
1 TAATTA
6652850 TTTAAATATT
Statistics
Matches: 51, Mismatches: 9, Indels: 18
0.65 0.12 0.23
Matches are distributed among these distances:
16 3 0.06
17 5 0.10
19 5 0.10
20 2 0.04
21 5 0.10
22 13 0.25
23 9 0.18
24 4 0.08
25 5 0.10
ACGTcount: A:0.46, C:0.07, G:0.01, T:0.46
Consensus pattern (22 bp):
TAATTAATTATTAAACCAATTA
Found at i:6653007 original size:23 final size:23
Alignment explanation
Indices: 6652981--6653027 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
6652971 ACTACCAATA
6652981 TAGTAAGAACAACTAAAGATCAC
1 TAGTAAGAACAACTAAAGATCAC
**
6653004 TAGTAAGAATGACTAAAGATCAC
1 TAGTAAGAACAACTAAAGATCAC
6653027 T
1 T
6653028 CTTTAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.49, C:0.15, G:0.15, T:0.21
Consensus pattern (23 bp):
TAGTAAGAACAACTAAAGATCAC
Found at i:6660127 original size:8 final size:8
Alignment explanation
Indices: 6660114--6660163 Score: 59
Period size: 8 Copynumber: 6.2 Consensus size: 8
6660104 TTTTTTAGGT
6660114 GGGGGGG-
1 GGGGGGGA
6660121 GGGGGGG-
1 GGGGGGGA
*
6660128 GGGTAGGGA
1 GGG-GGGGA
6660137 GGGGGGGA
1 GGGGGGGA
6660145 GGGGGGGA
1 GGGGGGGA
6660153 GGGGAGGGA
1 GGGG-GGGA
6660162 GG
1 GG
6660164 TAGGGTTGGA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
7 10 0.26
8 19 0.50
9 9 0.24
ACGTcount: A:0.12, C:0.00, G:0.86, T:0.02
Consensus pattern (8 bp):
GGGGGGGA
Found at i:6660140 original size:13 final size:12
Alignment explanation
Indices: 6660114--6660163 Score: 59
Period size: 13 Copynumber: 4.2 Consensus size: 12
6660104 TTTTTTAGGT
6660114 GGGGGGG-GGG-
1 GGGGGGGAGGGA
6660124 GGGGGGGTAGGGA
1 GGGGGGG-AGGGA
*
6660137 GGGGGGGAGGGG
1 GGGGGGGAGGGA
6660149 GGGAGGGGAGGGA
1 GGG-GGGGAGGGA
6660162 GG
1 GG
6660164 TAGGGTTGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
10 7 0.21
12 10 0.29
13 17 0.50
ACGTcount: A:0.12, C:0.00, G:0.86, T:0.02
Consensus pattern (12 bp):
GGGGGGGAGGGA
Found at i:6660140 original size:21 final size:21
Alignment explanation
Indices: 6660116--6660160 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
6660106 TTTTAGGTGG
*
6660116 GGGGGGGGGGGGGGGTA-GGGA
1 GGGGGGGAGGGGGGG-AGGGGA
6660137 GGGGGGGAGGGGGGGAGGGGA
1 GGGGGGGAGGGGGGGAGGGGA
6660158 GGG
1 GGG
6660161 AGGTAGGGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.11, C:0.00, G:0.87, T:0.02
Consensus pattern (21 bp):
GGGGGGGAGGGGGGGAGGGGA
Found at i:6660148 original size:25 final size:24
Alignment explanation
Indices: 6660114--6660163 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
6660104 TTTTTTAGGT
*
6660114 GGGGGGGGGGGGGG-GGGTAGGGA
1 GGGGGGGGGGGGGGAGGGGAGGGA
6660137 GGGGGGGAGGGGGGGAGGGGAGGGA
1 GGGGGGG-GGGGGGGAGGGGAGGGA
6660162 GG
1 GG
6660164 TAGGGTTGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 7 0.29
24 7 0.29
25 10 0.42
ACGTcount: A:0.12, C:0.00, G:0.86, T:0.02
Consensus pattern (24 bp):
GGGGGGGGGGGGGGAGGGGAGGGA
Found at i:6660168 original size:21 final size:21
Alignment explanation
Indices: 6660124--6660168 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
6660114 GGGGGGGGGG
*
6660124 GGGGGGGTAGGGAGGGGGGGA
1 GGGGGGGTAGGGAGGGAGGGA
*
6660145 GGGGGGG-AGGGGAGGGAGGTA
1 GGGGGGGTA-GGGAGGGAGGGA
6660166 GGG
1 GGG
6660169 TTGGACTGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.16, C:0.00, G:0.80, T:0.04
Consensus pattern (21 bp):
GGGGGGGTAGGGAGGGAGGGA
Found at i:6670064 original size:20 final size:19
Alignment explanation
Indices: 6670039--6670123 Score: 56
Period size: 20 Copynumber: 4.5 Consensus size: 19
6670029 TTTTGTCATT
6670039 TTTTTATTATTTAATTATTA
1 TTTTTATTATTTAATT-TTA
6670059 TTTTTA-T-TTT-ATTTTA
1 TTTTTATTATTTAATTTTA
* *
6670075 TTCTTTATTA-TCATATTTTC
1 TT-TTTATTATTTA-ATTTTA
*
6670095 TATTTTATT-TCTAATTATTA
1 T-TTTTATTATTTAATT-TTA
6670115 TTTTT-TTAT
1 TTTTTATTAT
6670124 ACCTTACATT
Statistics
Matches: 51, Mismatches: 5, Indels: 19
0.68 0.07 0.25
Matches are distributed among these distances:
16 5 0.10
17 7 0.14
18 7 0.14
19 9 0.18
20 22 0.43
21 1 0.02
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTTATTATTTAATTTTA
Found at i:6670075 original size:27 final size:26
Alignment explanation
Indices: 6670036--6670123 Score: 70
Period size: 30 Copynumber: 3.1 Consensus size: 26
6670026 NNNTTTTGTC
*
6670036 ATTTTTTTATTATTTAATTATTATTTTT
1 ATTTTATT-TTATTT-ATTATTATTTTT
6670064 ATTTTATTTTATTCTTTATTATCATATTTTCT
1 ATTTTATTTTA---TTTATTAT--TATTTT-T
*
6670096 ATTTTATTTCTAATTATTATT-TTTTT
1 ATTTTATTT-TATTTATTATTATTTTT
6670122 AT
1 AT
6670124 ACCTTACATT
Statistics
Matches: 51, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
26 3 0.06
27 7 0.14
28 8 0.16
29 5 0.10
30 10 0.20
31 6 0.12
32 10 0.20
33 2 0.04
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.72
Consensus pattern (26 bp):
ATTTTATTTTATTTATTATTATTTTT
Found at i:6670248 original size:4 final size:4
Alignment explanation
Indices: 6670230--6670303 Score: 53
Period size: 4 Copynumber: 17.5 Consensus size: 4
6670220 GTTGTCTTAG
* *
6670230 ATTT TTTT A-TT ATTT ATTT ATTT ACTTT ATTT AATTT AATTT ATAT ATTTT
1 ATTT ATTT ATTT ATTT ATTT ATTT A-TTT ATTT -ATTT -ATTT ATTT A-TTT
*
6670281 ATATT ATTT -TTT TTTT AATTT AT
1 AT-TT ATTT ATTT ATTT -ATTT AT
6670304 GTGTCTACAG
Statistics
Matches: 58, Mismatches: 5, Indels: 14
0.75 0.06 0.18
Matches are distributed among these distances:
3 6 0.10
4 29 0.50
5 23 0.40
ACGTcount: A:0.27, C:0.01, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:6670260 original size:9 final size:8
Alignment explanation
Indices: 6670230--6670303 Score: 53
Period size: 9 Copynumber: 8.8 Consensus size: 8
6670220 GTTGTCTTAG
*
6670230 ATTTTTTT
1 ATTTATTT
6670238 A-TTATTT
1 ATTTATTT
6670245 ATTTATTT
1 ATTTATTT
6670253 ACTTTATTT
1 A-TTTATTT
6670262 AATTTAATTT
1 -ATTT-ATTT
*
6670272 ATATATTTT
1 ATTTA-TTT
6670281 ATATTATTT
1 AT-TTATTT
*
6670290 -TTTTTTT
1 ATTTATTT
6670297 AATTTAT
1 -ATTTAT
6670304 GTGTCTACAG
Statistics
Matches: 53, Mismatches: 5, Indels: 15
0.73 0.07 0.21
Matches are distributed among these distances:
7 11 0.21
8 10 0.19
9 25 0.47
10 7 0.13
ACGTcount: A:0.27, C:0.01, G:0.00, T:0.72
Consensus pattern (8 bp):
ATTTATTT
Found at i:6670281 original size:14 final size:13
Alignment explanation
Indices: 6670241--6670289 Score: 53
Period size: 14 Copynumber: 3.6 Consensus size: 13
6670231 TTTTTTTATT
6670241 ATTTATTTATTTA
1 ATTTATTTATTTA
*
6670254 CTTTATTTAATTTA
1 ATTTATTT-ATTTA
* *
6670268 ATTTATATATTTT
1 ATTTATTTATTTA
6670281 ATATTATTT
1 AT-TTATTT
6670290 TTTTTTTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
13 13 0.45
14 16 0.55
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (13 bp):
ATTTATTTATTTA
Found at i:6670289 original size:23 final size:22
Alignment explanation
Indices: 6670232--6670289 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
6670222 TGTCTTAGAT
* *
6670232 TTTTTTATTATTTATTTATTTA
1 TTTTATATTATTTATTTATATA
*
6670254 CTTTAT-TTAATTTAATTTATATA
1 TTTTATATT-ATTT-ATTTATATA
6670277 TTTTATATTATTT
1 TTTTATATTATTT
6670290 TTTTTTTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
21 2 0.07
22 8 0.28
23 17 0.59
24 2 0.07
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTATATTATTTATTTATATA
Found at i:6672814 original size:35 final size:35
Alignment explanation
Indices: 6672760--6672879 Score: 132
Period size: 35 Copynumber: 3.4 Consensus size: 35
6672750 AGAGAACAAT
* * *
6672760 TAGAACAAGTGAAGTGCTACTTCACGTAGAATAAC
1 TAGAATAAGTGAAGCGCTACTTCACGCAGAATAAC
*
6672795 TGGAATAAGTGAAGCGCTACTTCACGCAGAATAAC
1 TAGAATAAGTGAAGCGCTACTTCACGCAGAATAAC
*** * * * *
6672830 TAGAATAAGTGAAGTATTACTTAAAGCAGAACAAT
1 TAGAATAAGTGAAGCGCTACTTCACGCAGAATAAC
*
6672865 TAGAATAAGTAAAGC
1 TAGAATAAGTGAAGC
6672880 ATTACTCCAT
Statistics
Matches: 71, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 71 1.00
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.23
Consensus pattern (35 bp):
TAGAATAAGTGAAGCGCTACTTCACGCAGAATAAC
Found at i:6673198 original size:28 final size:28
Alignment explanation
Indices: 6673108--6673188 Score: 108
Period size: 29 Copynumber: 2.9 Consensus size: 28
6673098 TCTTACCTTG
* * *
6673108 TTTTCGTGTACCTATTCATGTACATCTT
1 TTTTCTTGTACCTATTCTTGTACAGCTT
* *
6673136 TTTCTCTTGTACCTATTCTTCTATAGCTT
1 TTT-TCTTGTACCTATTCTTGTACAGCTT
6673165 TTTTCTTGTACCTATTCTTGTACA
1 TTTTCTTGTACCTATTCTTGTACA
6673189 CATCTTTTCT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 22 0.49
29 23 0.51
ACGTcount: A:0.16, C:0.22, G:0.09, T:0.53
Consensus pattern (28 bp):
TTTTCTTGTACCTATTCTTGTACAGCTT
Found at i:6678744 original size:22 final size:23
Alignment explanation
Indices: 6678718--6678785 Score: 68
Period size: 27 Copynumber: 2.8 Consensus size: 23
6678708 TTATTAGATT
6678718 TTTTAAATATTAATAATCT-AGAA
1 TTTTAAATATTAATAAT-TAAGAA
*
6678741 TTTAATTAAAATATTAATAATTAATAA
1 -TT--TT-AAATATTAATAATTAAGAA
6678768 -TTTAAATATTAATAATTA
1 TTTTAAATATTAATAATTA
6678786 TTTNNNNNNN
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
22 15 0.38
23 2 0.05
24 2 0.05
25 1 0.03
26 3 0.08
27 16 0.41
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (23 bp):
TTTTAAATATTAATAATTAAGAA
Found at i:6678772 original size:15 final size:15
Alignment explanation
Indices: 6678743--6678784 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
6678733 ATCTAGAATT
6678743 TAATTAA-AATATTAA
1 TAATTAATAAT-TTAA
6678758 TAATTAATAATTTAA
1 TAATTAATAATTTAA
6678773 -ATATTAATAATT
1 TA-ATTAATAATT
6678785 ATTTNNNNNN
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 1 0.04
15 21 0.84
16 3 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TAATTAATAATTTAA
Found at i:6679252 original size:19 final size:19
Alignment explanation
Indices: 6679230--6679292 Score: 74
Period size: 19 Copynumber: 3.2 Consensus size: 19
6679220 ATAATTGATA
6679230 ATTTAAATATTAATATTTT
1 ATTTAAATATTAATATTTT
*
6679249 ATTTATAAT-TTAATATTAAT
1 ATTTA-AATATTAATATT-TT
6679269 ATTTTAAAATATTAATATTTT
1 A-TTT-AAATATTAATATTTT
6679290 ATT
1 ATT
6679293 AAAAATTGGA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
19 13 0.35
20 7 0.19
21 8 0.22
22 9 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTAAATATTAATATTTT
Found at i:6679281 original size:16 final size:16
Alignment explanation
Indices: 6679260--6679290 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
6679250 TTTATAATTT
6679260 AATATTAATATTTTAA
1 AATATTAATATTTTAA
6679276 AATATTAATATTTTA
1 AATATTAATATTTTA
6679291 TTAAAAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATATTAATATTTTAA
Found at i:6690261 original size:27 final size:28
Alignment explanation
Indices: 6690205--6690262 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
6690195 TGAACGATGA
*
6690205 GAATGTTGGAAATTAAACTTGAATTCAT
1 GAATATTGGAAATTAAACTTGAATTCAT
*
6690233 GAATATTGGGAATTAAA-TTGAATTCAT
1 GAATATTGGAAATTAAACTTGAATTCAT
6690260 GAA
1 GAA
6690263 ATCATGAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
27 13 0.46
28 15 0.54
ACGTcount: A:0.41, C:0.05, G:0.19, T:0.34
Consensus pattern (28 bp):
GAATATTGGAAATTAAACTTGAATTCAT
Found at i:6690923 original size:4 final size:4
Alignment explanation
Indices: 6690908--6690988 Score: 55
Period size: 4 Copynumber: 21.0 Consensus size: 4
6690898 GACTTTGATA
* *
6690908 AATT AATT --TT AATT AATT AATGT -ATA AATT AATA AATT -ATT AATT
1 AATT AATT AATT AATT AATT AAT-T AATT AATT AATT AATT AATT AATT
* * * *
6690953 TATT AATT AAAT AA-T ATTTT AATT AATT AATA AATT
1 AATT AATT AATT AATT A-ATT AATT AATT AATT AATT
6690989 TTCTTAATCA
Statistics
Matches: 59, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
2 2 0.03
3 5 0.08
4 49 0.83
5 3 0.05
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (4 bp):
AATT
Found at i:6690939 original size:16 final size:15
Alignment explanation
Indices: 6690908--6690961 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
6690898 GACTTTGATA
*
6690908 AATTAATT-TTAATT
1 AATTAATTATAAATT
6690922 AATTAATGTATAAATT
1 AATTAAT-TATAAATT
* *
6690938 AATAAATTATTAATT
1 AATTAATTATAAATT
*
6690953 TATTAATTA
1 AATTAATTA
6690962 AATAATATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
14 7 0.21
15 15 0.45
16 11 0.33
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (15 bp):
AATTAATTATAAATT
Found at i:6692051 original size:33 final size:33
Alignment explanation
Indices: 6692013--6692086 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
6692003 TTTCTTAATC
* * *
6692013 TATCACGTTAACATTATCATATCATTATGTTAA
1 TATCACGTTAACATTATCATATAATCATGTCAA
* **
6692046 TATCACATTAGTATTATCATATAATCATGTCAA
1 TATCACGTTAACATTATCATATAATCATGTCAA
*
6692079 TGTCACGT
1 TATCACGT
6692087 GATACTACCA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (33 bp):
TATCACGTTAACATTATCATATAATCATGTCAA
Found at i:6694499 original size:8 final size:8
Alignment explanation
Indices: 6694488--6694514 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
6694478 CTTGAAAACG
6694488 AAGCTCAA
1 AAGCTCAA
6694496 AAGCTCAA
1 AAGCTCAA
6694504 AAGCTCAA
1 AAGCTCAA
6694512 AAG
1 AAG
6694515 TACCAGCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.22, G:0.15, T:0.11
Consensus pattern (8 bp):
AAGCTCAA
Found at i:6703772 original size:2 final size:2
Alignment explanation
Indices: 6703765--6703843 Score: 117
Period size: 2 Copynumber: 39.5 Consensus size: 2
6703755 TCAATTGATT
*
6703765 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA NA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6703807 TA TA GTA TA TA TA TA TA TA TA -A TA TA -A TA TCA TA TA T
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA T
6703844 TAAGTTAGAT
Statistics
Matches: 71, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
1 2 0.03
2 65 0.92
3 4 0.06
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.47
Consensus pattern (2 bp):
TA
Found at i:6706849 original size:8 final size:8
Alignment explanation
Indices: 6706838--6706872 Score: 70
Period size: 8 Copynumber: 4.4 Consensus size: 8
6706828 CTTGAAAACG
6706838 AAGCTCAA
1 AAGCTCAA
6706846 AAGCTCAA
1 AAGCTCAA
6706854 AAGCTCAA
1 AAGCTCAA
6706862 AAGCTCAA
1 AAGCTCAA
6706870 AAG
1 AAG
6706873 TACCAGCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.51, C:0.23, G:0.14, T:0.11
Consensus pattern (8 bp):
AAGCTCAA
Found at i:6715256 original size:28 final size:28
Alignment explanation
Indices: 6715224--6715278 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
6715214 TAGTTGGTAG
* *
6715224 AGATTTGAAAGGTCACTTTAATGTGAAA
1 AGATTTGAAAGGCCACTTGAATGTGAAA
*
6715252 AGATTTGAAAGGCCACTTGGATGTGAA
1 AGATTTGAAAGGCCACTTGAATGTGAA
6715279 CAGAAAGGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.36, C:0.09, G:0.25, T:0.29
Consensus pattern (28 bp):
AGATTTGAAAGGCCACTTGAATGTGAAA
Found at i:6715742 original size:43 final size:43
Alignment explanation
Indices: 6715702--6715794 Score: 134
Period size: 43 Copynumber: 2.2 Consensus size: 43
6715692 GCCTAATATT
*
6715702 TAATAT-TCTTGATCTAGGGTACTATGGTTCCAAGCATAATAGA
1 TAATATCT-TTGATCTAGGATACTATGGTTCCAAGCATAATAGA
* *
6715745 TGATATCTTTGATTTAGGATACTATGGTTCCAAGCATAATAGA
1 TAATATCTTTGATCTAGGATACTATGGTTCCAAGCATAATAGA
*
6715788 TGATATC
1 TAATATC
6715795 CTTAATATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
43 45 0.98
44 1 0.02
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (43 bp):
TAATATCTTTGATCTAGGATACTATGGTTCCAAGCATAATAGA
Found at i:6716161 original size:43 final size:43
Alignment explanation
Indices: 6716099--6716382 Score: 134
Period size: 43 Copynumber: 6.6 Consensus size: 43
6716089 GCTACAATTT
* *
6716099 CAAGCATAATAAATT-ATATCCTTGATATAGGGTATTATGGTAC
1 CAAGCATAAT-ACTTGATATCCTTGATATAGGGTATTATGGTTC
* * *
6716142 CAAGCATAATACTTGATATCCTTAATCTATAGTG-A-TATAGTTC
1 CAAGCATAATACTTGATATCCTTGA--TATAGGGTATTATGGTTC
* * * * * * * ** * *
6716185 AAATCATTATGCTTGATATCTTTGAT-TTGTAGTGCTACGCTTC
1 CAAGCATAATACTTGATATCCTTGATATAG-GGTATTATGGTTC
* * * * *
6716228 CAA-AACTAATGCTTGATATCTTTGATCT-GAGGTATTACGGTTC
1 CAAGCA-TAATACTTGATATCCTTGATATAG-GGTATTATGGTTC
** * * * *
6716271 CAAGCATAATAGATGATAACCTTGATATAAGGTATTGTGGTAC
1 CAAGCATAATACTTGATATCCTTGATATAGGGTATTATGGTTC
* * *
6716314 CAAGCATAATGCTTGATATCCTTGATCTATAGTG-A-TATAGTTC
1 CAAGCATAATACTTGATATCCTTGA--TATAGGGTATTATGGTTC
* * * *
6716357 AAATCATTATGCTTGATATCCTTGAT
1 CAAGCATAATACTTGATATCCTTGAT
6716383 CTGTAATAAT
Statistics
Matches: 181, Mismatches: 48, Indels: 26
0.71 0.19 0.10
Matches are distributed among these distances:
40 2 0.01
41 3 0.02
42 4 0.02
43 157 0.87
44 4 0.02
45 11 0.06
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (43 bp):
CAAGCATAATACTTGATATCCTTGATATAGGGTATTATGGTTC
Found at i:6716243 original size:86 final size:85
Alignment explanation
Indices: 6716148--6716425 Score: 228
Period size: 86 Copynumber: 3.2 Consensus size: 85
6716138 GTACCAAGCA
* * *
6716148 TAATACTTGATATCCTTAATCTATAGTGATATAGTTCAAATCATTATGCTTGATATCTTTGATTT
1 TAATGCTTGATATCCTTGATCTATAGTGATATAGTTCAAATCATTATGCTTGATATCCTTGATTT
*
6716213 GTAGTGCTACGCTTCCAAAAC
66 GTAATG-TACGCTTCCAAAAC
* * * * * * *
6716234 TAATGCTTGATATCTTTGATCT-GAG-G-TATTACGGTTCCAAGCATAATAG-ATGATAACCTTG
1 TAATGCTTGATATCCTTGATCTATAGTGATA-TA--GTTCAAATCATTAT-GCTTGATATCCTTG
* * * * *
6716295 ATATAAGGTATTGT--GGTACC-AAGC
62 AT-T--TGTAATGTACGCTTCCAAAAC
*
6716319 ATAATGCTTGATATCCTTGATCTATAGTGATATAGTTCAAATCATTATGCTTGATATCCTTGATC
1 -TAATGCTTGATATCCTTGATCTATAGTGATATAGTTCAAATCATTATGCTTGATATCCTTGATT
* **
6716384 TGTAATAATACGCTTCCAAGCC
65 TGTAAT-GTACGCTTCCAAAAC
*
6716406 TAATGTTTGATATCCTTGAT
1 TAATGCTTGATATCCTTGAT
6716426 TTGAGATACT
Statistics
Matches: 145, Mismatches: 31, Indels: 32
0.70 0.15 0.15
Matches are distributed among these distances:
83 6 0.04
84 4 0.03
85 6 0.04
86 112 0.77
87 6 0.04
88 4 0.03
89 7 0.05
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (85 bp):
TAATGCTTGATATCCTTGATCTATAGTGATATAGTTCAAATCATTATGCTTGATATCCTTGATTT
GTAATGTACGCTTCCAAAAC
Found at i:6716296 original size:172 final size:172
Alignment explanation
Indices: 6716071--6716465 Score: 549
Period size: 172 Copynumber: 2.3 Consensus size: 172
6716061 TATTCACTAA
* * * * * *
6716071 ATATCCTTGATCT-AGGGTGCTACAATTTCAAGCATAATAAATTATATCCTTGATATAGGGTATT
1 ATATCCTTGATCTGA-GATACTACGATTCCAAGCATAATAAATGATATCCTTGATATAAGGTATT
6716135 ATGGTACCAAGCATAATACTTGATATCCTTAATCTATAGTGATATAGTTCAAATCATTATGCTTG
65 ATGGTACCAAGCATAATACTTGATATCCTTAATCTATAGTGATATAGTTCAAATCATTATGCTTG
* * * **
6716200 ATATCTTTGATTTGTAGTGCTACGCTTCCAAAACTAATGCTTG
130 ATATCCTTGATCTGTAATAATACGCTTCCAAAACTAATGCTTG
* * * * * * *
6716243 ATATCTTTGATCTGAGGTATTACGGTTCCAAGCATAATAGATGATAACCTTGATATAAGGTATTG
1 ATATCCTTGATCTGAGATACTACGATTCCAAGCATAATAAATGATATCCTTGATATAAGGTATTA
* *
6716308 TGGTACCAAGCATAATGCTTGATATCCTTGATCTATAGTGATATAGTTCAAATCATTATGCTTGA
66 TGGTACCAAGCATAATACTTGATATCCTTAATCTATAGTGATATAGTTCAAATCATTATGCTTGA
** *
6716373 TATCCTTGATCTGTAATAATACGCTTCCAAGCCTAATGTTTG
131 TATCCTTGATCTGTAATAATACGCTTCCAAAACTAATGCTTG
* *
6716415 ATATCCTTGATTTGAGATACTACGATTTCAAGCATAATAAATGATATCCTT
1 ATATCCTTGATCTGAGATACTACGATTCCAAGCATAATAAATGATATCCTT
6716466 AATACTACTT
Statistics
Matches: 193, Mismatches: 29, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
172 192 0.99
173 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (172 bp):
ATATCCTTGATCTGAGATACTACGATTCCAAGCATAATAAATGATATCCTTGATATAAGGTATTA
TGGTACCAAGCATAATACTTGATATCCTTAATCTATAGTGATATAGTTCAAATCATTATGCTTGA
TATCCTTGATCTGTAATAATACGCTTCCAAAACTAATGCTTG
Found at i:6716383 original size:43 final size:42
Alignment explanation
Indices: 6716143--6716425 Score: 159
Period size: 43 Copynumber: 6.6 Consensus size: 42
6716133 TTATGGTACC
* *
6716143 AAGCATAATACTTGATATCCTTAATCTATAGTGATATAGTTCA
1 AAGCATAATGCTTGATATCCTTGATCTATAGTG-TATAGTTCA
* * * * * *
6716186 AATCATTATGCTTGATATCTTTGATTTGTAGTGCTA-CGCTTCCA
1 AAGCATAATGCTTGATATCCTTGATCTATAGTG-TATAG-TT-CA
* * * *
6716230 AAAC-TAATGCTTGATATCTTTGATCT-GAG-GTATTACGGTTCC
1 AAGCATAATGCTTGATATCCTTGATCTATAGTGTA-TA--GTTCA
* * * * *
6716272 AAGCATAATAG-ATGATAACCTTGATATA-AG-GTATTGTGGTACC
1 AAGCATAAT-GCTTGATATCCTTGATCTATAGTGTATAGT--T-CA
6716315 AAGCATAATGCTTGATATCCTTGATCTATAGTGATATAGTTCA
1 AAGCATAATGCTTGATATCCTTGATCTATAGTG-TATAGTTCA
* * * * * *
6716358 AATCATTATGCTTGATATCCTTGATCTGTAAT-AATACGCTTCC
1 AAGCATAATGCTTGATATCCTTGATCTATAGTGTATA-G-TTCA
* *
6716401 AAGCCTAATGTTTGATATCCTTGAT
1 AAGCATAATGCTTGATATCCTTGAT
6716426 TTGAGATACT
Statistics
Matches: 186, Mismatches: 36, Indels: 36
0.72 0.14 0.14
Matches are distributed among these distances:
40 4 0.02
41 4 0.02
42 11 0.06
43 151 0.81
44 10 0.05
45 1 0.01
46 5 0.03
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (42 bp):
AAGCATAATGCTTGATATCCTTGATCTATAGTGTATAGTTCA
Found at i:6716447 original size:43 final size:43
Alignment explanation
Indices: 6716313--6716452 Score: 124
Period size: 43 Copynumber: 3.3 Consensus size: 43
6716303 TATTGTGGTA
* * *
6716313 CCAAGCATAATGCTTGATATCCTTGATCTATAGTGATATA-G-TT
1 CCAAGCATAATGTTTGATATCCTTGATCTGTAAT-A-ATACGATT
* * * * *
6716356 CAAATCATTATGCTTGATATCCTTGATCTGTAATAATACGCTT
1 CCAAGCATAATGTTTGATATCCTTGATCTGTAATAATACGATT
* * *
6716399 CCAAGCCTAATGTTTGATATCCTTGATTTG-AGATACTACGATT
1 CCAAGCATAATGTTTGATATCCTTGATCTGTA-ATAATACGATT
*
6716442 TCAAGCATAAT
1 CCAAGCATAAT
6716453 AAATGATATC
Statistics
Matches: 79, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
41 3 0.04
42 3 0.04
43 73 0.92
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (43 bp):
CCAAGCATAATGTTTGATATCCTTGATCTGTAATAATACGATT
Found at i:6717794 original size:11 final size:11
Alignment explanation
Indices: 6717778--6717811 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
6717768 AAAGTCGTTT
6717778 TAAGAAAAAAA
1 TAAGAAAAAAA
*
6717789 TAAGAAAGAAA
1 TAAGAAAAAAA
6717800 TAAAGAAAAAAA
1 T-AAGAAAAAAA
6717812 AGTAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (11 bp):
TAAGAAAAAAA
Done.