Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr6
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: 44797108
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 921406 characters in sequence are not A, C, G, or T
File 57 of 144
Found at i:17576024 original size:19 final size:19
Alignment explanation
Indices: 17576000--17576055 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
17575990 GTCATCAATT
17576000 TTTTATGATTTTTATAAAA
1 TTTTATGATTTTTATAAAA
* *
17576019 TTTTAT-AATTTTAT-AAT
1 TTTTATGATTTTTATAAAA
*
17576036 TTTTAATGATATTTATAAAA
1 TTTT-ATGATTTTTATAAAA
17576056 AATATAATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
17 6 0.21
18 9 0.31
19 12 0.41
20 2 0.07
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (19 bp):
TTTTATGATTTTTATAAAA
Found at i:17576037 original size:37 final size:35
Alignment explanation
Indices: 17575996--17576078 Score: 103
Period size: 37 Copynumber: 2.3 Consensus size: 35
17575986 AGGGGTCATC
* **
17575996 AATTTTTTATGATTTTTATAAAATTTTATAATTTTAT
1 AATTTTTTATGATATTTATAAAA-AATATAATTTT-T
*
17576033 AATTTTTAATGATATTTATAAAAAATATAATTTTT
1 AATTTTTTATGATATTTATAAAAAATATAATTTTT
17576068 AATATTTTTAT
1 AAT-TTTTTAT
17576079 TAAAAATTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
35 4 0.10
36 15 0.38
37 21 0.52
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (35 bp):
AATTTTTTATGATATTTATAAAAAATATAATTTTT
Found at i:17576049 original size:28 final size:28
Alignment explanation
Indices: 17576000--17576129 Score: 67
Period size: 28 Copynumber: 4.6 Consensus size: 28
17575990 GTCATCAATT
* *
17576000 TTTTATGATTTTT-ATAAAATTTTAT-AA
1 TTTTATAATTTTTAAT-ATATTTTATAAA
17576027 TTTTATAATTTTTAATGATA-TTTATAAA
1 TTTTATAATTTTTAAT-ATATTTTATAAA
***
17576055 AAATATAATTTTTAATAT-TTTTATTAAAA
1 TTTTATAATTTTTAATATATTTTA-T-AAA
* * *
17576084 ATTAATATTTTTCTAA-A-A-TTTATTAATA
1 TTTTATAATTTT-TAATATATTTTA-TAA-A
17576112 TTTTTATAATTTTTAATA
1 -TTTTATAATTTTTAATA
17576130 AGAGTAAGGG
Statistics
Matches: 80, Mismatches: 13, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
27 25 0.31
28 30 0.38
29 22 0.28
30 3 0.04
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.57
Consensus pattern (28 bp):
TTTTATAATTTTTAATATATTTTATAAA
Found at i:17576066 original size:27 final size:27
Alignment explanation
Indices: 17576030--17576094 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
17576020 TTTATAATTT
17576030 TATAATTTTTAATGATATTTATAAAAAA
1 TATAATTTTTAAT-ATATTTATAAAAAA
* *
17576058 TATAATTTTTAATATTTTTATTAAAAA
1 TATAATTTTTAATATATTTATAAAAAA
17576085 T-TAATATTTT
1 TATAAT-TTTT
17576095 TCTAAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 4 0.12
27 17 0.50
28 13 0.38
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (27 bp):
TATAATTTTTAATATATTTATAAAAAA
Found at i:17576126 original size:21 final size:21
Alignment explanation
Indices: 17576061--17576120 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
17576051 TAAAAAATAT
17576061 AATTT-TTAATATTTTTATTAA
1 AATTTATTAATATTTTTA-TAA
*
17576082 AA---ATTAATATTTTTCTAA
1 AATTTATTAATATTTTTATAA
17576100 AATTTATTAATATTTTTATAA
1 AATTTATTAATATTTTTATAA
17576121 TTTTTAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
18 5 0.15
19 11 0.33
21 17 0.52
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
AATTTATTAATATTTTTATAA
Found at i:17576233 original size:84 final size:85
Alignment explanation
Indices: 17576139--17576305 Score: 212
Period size: 87 Copynumber: 2.0 Consensus size: 85
17576129 AAGAGTAAGG
** * * **
17576139 GCTTAATTGCTTTTTTGAAAAAT-TTTGAGGGTCTTTTT-GGTGCATTTTGAAAATTCAAGTATT
1 GCTTAATTGCTTTTTAAAAAAATATTTAAGGGCCTTTTTAACTG-ATTTTGAAAATTCAAGTATT
* *
17576202 CAATTGAGTGGAAAAAAAAGA
65 CAAATGAGTGCAAAAAAAAGA
*
17576223 GCTTAATTGCTTTTTAAAAAAATAAGTTTAAGGGCCTTTTTAACTGATTTTGAAAGTTCAAGTAT
1 GCTTAATTGCTTTTTAAAAAAAT-A-TTTAAGGGCCTTTTTAACTGATTTTGAAAATTCAAGTAT
17576288 TCAAATGAGTGCAAAAAA
64 TCAAATGAGTGCAAAAAA
17576306 TGGGGCTTTT
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
84 21 0.30
87 47 0.67
88 2 0.03
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (85 bp):
GCTTAATTGCTTTTTAAAAAAATATTTAAGGGCCTTTTTAACTGATTTTGAAAATTCAAGTATTC
AAATGAGTGCAAAAAAAAGA
Found at i:17578315 original size:28 final size:28
Alignment explanation
Indices: 17578266--17578324 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
17578256 TTTCTTTTTA
*
17578266 AAAATACATAAAAATCTAAAAATTAAAT
1 AAAATACATAAAAATCTAAAAAATAAAT
* * * * *
17578294 AAAATAGATAAAATTTTCAAAAATAGAT
1 AAAATACATAAAAATCTAAAAAATAAAT
17578322 AAA
1 AAA
17578325 GTTTTTATAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.25
Consensus pattern (28 bp):
AAAATACATAAAAATCTAAAAAATAAAT
Found at i:17578406 original size:17 final size:17
Alignment explanation
Indices: 17578384--17578425 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
17578374 GGCTCAATTG
17578384 AATAAATTATTTTTAAA
1 AATAAATTATTTTTAAA
*
17578401 AATAAAAATATTTTTAAA
1 AAT-AAATTATTTTTAAA
*
17578419 AGTAAAT
1 AATAAAT
17578426 GACATCAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
AATAAATTATTTTTAAA
Found at i:17580738 original size:18 final size:19
Alignment explanation
Indices: 17580704--17580740 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
17580694 TTTCATTTTC
*
17580704 TTTTAAAAATATTTTTATT
1 TTTTAAAAATATATTTATT
17580723 TTTTAAAAATA-ATTTATT
1 TTTTAAAAATATATTTATT
17580741 CAATTGAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTAAAAATATATTTATT
Found at i:17583155 original size:27 final size:29
Alignment explanation
Indices: 17583091--17583159 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 29
17583081 ATATTAATTC
17583091 ATATATATTAAATCAAATTATAATATGATA
1 ATATA-ATTAAATCAAATTATAATATGATA
17583121 AT-TAAATTAAAT-AAATTATACA-AT-ATA
1 ATAT-AATTAAATCAAATTATA-ATATGATA
17583148 ATATAATTAAAT
1 ATATAATTAAAT
17583160 TAAGTTAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
27 13 0.36
28 11 0.31
29 9 0.25
30 3 0.08
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (29 bp):
ATATAATTAAATCAAATTATAATATGATA
Found at i:17583729 original size:21 final size:21
Alignment explanation
Indices: 17583705--17583745 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
17583695 TTAAAATTTA
17583705 AAATT-TTAAAAATTATTAAAT
1 AAATTATT-AAAATTATTAAAT
*
17583726 AAATTATTAACATTATTAAA
1 AAATTATTAAAATTATTAAA
17583746 AAGTATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
AAATTATTAAAATTATTAAAT
Found at i:17589157 original size:20 final size:19
Alignment explanation
Indices: 17589133--17589176 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
17589123 ATTTTATTTA
17589133 AATTTAATTATAAAAAAAT
1 AATTTAATTATAAAAAAAT
* *
17589152 ATATTTAATTGTTAAAAAAT
1 A-ATTTAATTATAAAAAAAT
17589172 AATTT
1 AATTT
17589177 CACATCTCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
AATTTAATTATAAAAAAAT
Found at i:17592600 original size:47 final size:48
Alignment explanation
Indices: 17592547--17592672 Score: 130
Period size: 47 Copynumber: 2.6 Consensus size: 48
17592537 GTGGGAACAA
* * *
17592547 AGGAATTGGATAACGGTAGGTTTAATATTTACTTTAGCCCTCAAAG-G
1 AGGAATTGGATAAAGGTAGGTTTAATGTTTACATTAGCCCTCAAAGAG
* * ** *
17592594 AGGAATTGCG-TAAAAGTAGGTTTAATGTTTACATTAGGCCTTTAAGAT
1 AGGAATTG-GATAAAGGTAGGTTTAATGTTTACATTAGCCCTCAAAGAG
* * *
17592642 AAGAATTGGATAAGGGTAGGTTCAATGTTTA
1 AGGAATTGGATAAAGGTAGGTTTAATGTTTA
17592673 ATACATTAGG
Statistics
Matches: 64, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
47 38 0.59
48 26 0.41
ACGTcount: A:0.33, C:0.09, G:0.25, T:0.33
Consensus pattern (48 bp):
AGGAATTGGATAAAGGTAGGTTTAATGTTTACATTAGCCCTCAAAGAG
Found at i:17593282 original size:16 final size:15
Alignment explanation
Indices: 17593261--17593294 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
17593251 TTGTGATAGG
17593261 TTTTATTTTATATGTT
1 TTTTATTTTATAT-TT
*
17593277 TTTTATTTTTTATTT
1 TTTTATTTTATATTT
17593292 TTT
1 TTT
17593295 AGTCTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (15 bp):
TTTTATTTTATATTT
Found at i:17598604 original size:12 final size:12
Alignment explanation
Indices: 17598564--17598605 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 12
17598554 TTAATATAAA
17598564 ATTAAAAA-A-T
1 ATTAAAAATATT
17598574 ATTAAAAATATTAT
1 ATTAAAAATA-T-T
17598588 ATTAAAAATATT
1 ATTAAAAATATT
17598600 ATTAAA
1 ATTAAA
17598606 TTATTTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 8 0.29
11 1 0.04
12 7 0.25
13 1 0.04
14 11 0.39
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
ATTAAAAATATT
Found at i:17598608 original size:17 final size:14
Alignment explanation
Indices: 17598572--17598601 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
17598562 AAATTAAAAA
17598572 ATATTAAAAATATT
1 ATATTAAAAATATT
17598586 ATATTAAAAATATT
1 ATATTAAAAATATT
17598600 AT
1 AT
17598602 TAAATTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATATTAAAAATATT
Found at i:17598614 original size:15 final size:14
Alignment explanation
Indices: 17598596--17598638 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
17598586 ATATTAAAAA
17598596 TATTATTAAATTATT
1 TATTATT-AATTATT
*
17598611 TATTATTTATTAATT
1 TATTATTAATT-ATT
*
17598626 TATTTTTAATTAT
1 TATTATTAATTAT
17598639 GATCCTATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 5 0.21
15 19 0.79
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TATTATTAATTATT
Found at i:17602939 original size:35 final size:35
Alignment explanation
Indices: 17602873--17602940 Score: 95
Period size: 35 Copynumber: 1.9 Consensus size: 35
17602863 GTTATGGGCC
*
17602873 CACATGCCCGTGTGGACCCTTACGCTTGTGTCGCT
1 CACATGCCCGTGTGGACCCATACGCTTGTGTCGCT
17602908 CACATGCCCGTGTAGG-CCCATACG-TTCGTGTCG
1 CACATGCCCGTGT-GGACCCATACGCTT-GTGTCG
17602941 TCCACACGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 2 0.07
35 26 0.87
36 2 0.07
ACGTcount: A:0.13, C:0.34, G:0.26, T:0.26
Consensus pattern (35 bp):
CACATGCCCGTGTGGACCCATACGCTTGTGTCGCT
Found at i:17608032 original size:30 final size:32
Alignment explanation
Indices: 17607965--17608035 Score: 85
Period size: 30 Copynumber: 2.3 Consensus size: 32
17607955 TTCACCCTTA
* *
17607965 AAATATTTACACAATTAATCCTTCAAAATTTT
1 AAATATTTACACAATTAACCCCTCAAAATTTT
* *
17607997 -CATATTTACAC-TTTAACCCCTC-AAATTTT
1 AAATATTTACACAATTAACCCCTCAAAATTTT
17608026 AAATATTTAC
1 AAATATTTAC
17608036 TCTTGGGCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
29 7 0.21
30 16 0.48
31 10 0.30
ACGTcount: A:0.39, C:0.20, G:0.00, T:0.41
Consensus pattern (32 bp):
AAATATTTACACAATTAACCCCTCAAAATTTT
Found at i:17612164 original size:19 final size:21
Alignment explanation
Indices: 17612124--17612168 Score: 67
Period size: 19 Copynumber: 2.2 Consensus size: 21
17612114 TTGAGCATTT
17612124 TTTTCTTTTATGTTCTTTTAA
1 TTTTCTTTTATGTTCTTTTAA
*
17612145 TTTTCTTTT-TTTTC-TTTAA
1 TTTTCTTTTATGTTCTTTTAA
17612164 TTTTC
1 TTTTC
17612169 ATTCTATTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.43
20 4 0.17
21 9 0.39
ACGTcount: A:0.11, C:0.11, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTTCTTTTATGTTCTTTTAA
Found at i:17612178 original size:19 final size:19
Alignment explanation
Indices: 17612140--17612178 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
17612130 TTTATGTTCT
* * *
17612140 TTTAATTTTCTTTTTTTTC
1 TTTAATTTTCATTCTATTC
17612159 TTTAATTTTCATTCTATTC
1 TTTAATTTTCATTCTATTC
17612178 T
1 T
17612179 ACTTCTCCCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTAATTTTCATTCTATTC
Found at i:17621332 original size:13 final size:15
Alignment explanation
Indices: 17621314--17621346 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
17621304 TTAGGTTTAC
17621314 ATAAATTT-TT-TTT
1 ATAAATTTGTTATTT
17621327 ATAAATTTGTTATTT
1 ATAAATTTGTTATTT
17621342 ATAAA
1 ATAAA
17621347 GACAGTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.44
14 2 0.11
15 8 0.44
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (15 bp):
ATAAATTTGTTATTT
Found at i:17624251 original size:98 final size:98
Alignment explanation
Indices: 17624128--17624518 Score: 746
Period size: 98 Copynumber: 4.0 Consensus size: 98
17624118 AAAAATCATG
* * *
17624128 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTCTT
1 AAGGAAATATTCCGAGTTTGGGATTCTAAAGGGATTGTGCCCTAATGTATTGGGTGTGATTTCTT
17624193 AAATCTTGGATAAGTGGATGTTCTTTTAAAGTA
66 AAATCTTGGATAAGTGGATGTTCTTTTAAAGTA
17624226 AAGGAAATATTCCGAGTTTGGGATTCTAAAGGGATTGTGCCCTAATGTATTGGGTGTGATTTCTT
1 AAGGAAATATTCCGAGTTTGGGATTCTAAAGGGATTGTGCCCTAATGTATTGGGTGTGATTTCTT
17624291 AAATCTTGGATAAGTGGATGTTCTTTTAAAGTA
66 AAATCTTGGATAAGTGGATGTTCTTTTAAAGTA
17624324 AAGGAAATATTCCGAGTTTGGGATTCTAAAGGGATTGTGCCCTAATGTATTGGGTGTGATTTCTT
1 AAGGAAATATTCCGAGTTTGGGATTCTAAAGGGATTGTGCCCTAATGTATTGGGTGTGATTTCTT
17624389 AAATCTTGGATAAGTGGATGTTCTTTTAAAGTA
66 AAATCTTGGATAAGTGGATGTTCTTTTAAAGTA
17624422 AAGGAAATATTCCGAGTTTGGGATTCTAAAGGGATTGTGCCCTAATGTATTGGGTGTGATTTCTT
1 AAGGAAATATTCCGAGTTTGGGATTCTAAAGGGATTGTGCCCTAATGTATTGGGTGTGATTTCTT
*
17624487 AAATCTTGGATGAGTGGATGTTCTTTTAAAGT
66 AAATCTTGGATAAGTGGATGTTCTTTTAAAGT
17624519 TTTATTGTAT
Statistics
Matches: 289, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
98 289 1.00
ACGTcount: A:0.28, C:0.09, G:0.25, T:0.38
Consensus pattern (98 bp):
AAGGAAATATTCCGAGTTTGGGATTCTAAAGGGATTGTGCCCTAATGTATTGGGTGTGATTTCTT
AAATCTTGGATAAGTGGATGTTCTTTTAAAGTA
Found at i:17636150 original size:44 final size:44
Alignment explanation
Indices: 17635998--17636598 Score: 314
Period size: 45 Copynumber: 13.7 Consensus size: 44
17635988 TCGCATCTAG
* * * ** *
17635998 TCTTATCTCTCTGAAGTTGCAGTGAAGCAGACTAAA-CAAAGCGAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGA-C-AA
* ** ** *
17636043 TTTTATC-CTCCTGAAGTTGCAGT-GAGGCAGGCTAAAGATGGCAAA
1 TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGATTAAAGCCGAC-AA
* *
17636088 TCTTATCTCCCTAAAGTTACAGTGGAGCAGATTAAAGCCGACAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAA
* * ** * *
17636132 TCCTATCTCCCTGAAGTTACAGTGGAGTGGATTAAAACC-TCAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACA-A
* * *
17636176 TCTTATCTCCCTGAAGTTGCA---GAG-A-A-TAGA-TCGCATCTAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCG-A-C-AA
* * * * **
17636216 TGTTATCTCCCTAAAGTTGCAGTGAAGCAGACT-AAGCAAAGCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGA-CAA
* * ** *
17636260 GTCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGCAAA
1 -TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGATTAAAGCCGAC-AA
* *
17636306 TCTTATCTCCCTGAAGTTACAGTGGAGCAAATTAAAGCCGACAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAA
* * * * ** * *
17636350 TCCTATCTCCCTAAAGTTACAGTAGAGTGGATTAAAACC-TCAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACA-A
* * * * *
17636394 TCTTAACTCCCTGAAGTTGCAG-AGAGTAGA-T--CG-C-ATCTAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGA-C-AA
* **
17636434 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGCAAAACAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC-CGAC-AA
* * ** *
17636479 TCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGCAAA
1 TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGATTAAAGCCGAC-AA
17636524 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAA
*
17636568 TCCTATCTCCCTGAAGTTGCAGTGGAGCAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
17636599 CTGGTAGATC
Statistics
Matches: 430, Mismatches: 88, Indels: 77
0.72 0.15 0.13
Matches are distributed among these distances:
37 1 0.00
38 3 0.01
39 2 0.00
40 42 0.10
41 11 0.03
42 2 0.00
43 14 0.03
44 150 0.35
45 186 0.43
46 19 0.04
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAA
Found at i:17636301 original size:218 final size:218
Alignment explanation
Indices: 17635914--17636594 Score: 1146
Period size: 218 Copynumber: 3.1 Consensus size: 218
17635904 ATAAATTGAG
* * *
17635914 TCCTATCTCCTTAAAGTTACAGTGGAGCGGATTAAAACCTCAGATCTTATCTCTCTGAAGTTGCA
1 TCCTATCTCCCTAAAGTTACAGTGGAGTGGATTAAAACCTCAGATCTTATCTCCCTGAAGTTGCA
* * * *
17635979 GAGAGCAGATCGCATCTAGTCTTATCTCTCTGAAGTTGCAGTGAAGCAGACTAAACAAAGCGAGT
66 GAGAGTAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGAAGCAGACTAAGCAAAGCAAGT
* * * *
17636044 TTTATCCTCCTGAAGTTGCAGTGAGGCAGGCTAAAGATGGCAAATCTTATCTCCCTAAAGTTACA
131 CTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTACA
17636109 GTGGAGCAGATTAAAGCCGACAA
196 GTGGAGCAGATTAAAGCCGACAA
*
17636132 TCCTATCTCCCTGAAGTTACAGTGGAGTGGATTAAAACCTCAGATCTTATCTCCCTGAAGTTGCA
1 TCCTATCTCCCTAAAGTTACAGTGGAGTGGATTAAAACCTCAGATCTTATCTCCCTGAAGTTGCA
* * *
17636197 GAGAATAGATCGCATCTAGTGTTATCTCCCTAAAGTTGCAGTGAAGCAGACTAAGCAAAGCAAGT
66 GAGAGTAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGAAGCAGACTAAGCAAAGCAAGT
17636262 CTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTACA
131 CTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTACA
*
17636327 GTGGAGCAAATTAAAGCCGACAA
196 GTGGAGCAGATTAAAGCCGACAA
* *
17636350 TCCTATCTCCCTAAAGTTACAGTAGAGTGGATTAAAACCTCAGATCTTAACTCCCTGAAGTTGCA
1 TCCTATCTCCCTAAAGTTACAGTGGAGTGGATTAAAACCTCAGATCTTATCTCCCTGAAGTTGCA
* * *
17636415 GAGAGTAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAAACAAAT
66 GAGAGTAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGAAGCAGACTAAGCAAAGCAAGT
*
17636480 CTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCA
131 CTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTACA
17636545 GTGGAGCAGATTAAAGCCGACAA
196 GTGGAGCAGATTAAAGCCGACAA
* *
17636568 TCCTATCTCCCTGAAGTTGCAGTGGAG
1 TCCTATCTCCCTAAAGTTACAGTGGAG
17636595 CAGACTGGTA
Statistics
Matches: 433, Mismatches: 30, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
218 433 1.00
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (218 bp):
TCCTATCTCCCTAAAGTTACAGTGGAGTGGATTAAAACCTCAGATCTTATCTCCCTGAAGTTGCA
GAGAGTAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGAAGCAGACTAAGCAAAGCAAGT
CTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTACA
GTGGAGCAGATTAAAGCCGACAA
Found at i:17638679 original size:98 final size:98
Alignment explanation
Indices: 17638556--17638750 Score: 347
Period size: 98 Copynumber: 2.0 Consensus size: 98
17638546 AAAAATCATG
*
17638556 AAGGAAATATTCCGAGTTTGAGATTCTAAA-GGAATTGTGCCCTAACGTATTGGGTGTGATTTCT
1 AAGGAAATATTCCGAGTTTGAGATTCTAAATGG-ATCGTGCCCTAACGTATTGGGTGTGATTTCT
17638620 TAAATCTTGGATAAGTGGATGTTCTTTTAAAGTA
65 TAAATCTTGGATAAGTGGATGTTCTTTTAAAGTA
*
17638654 AAGGAAATATTCCGAGTTTGGGATTCTAAATGGATCGTGCCCTAACGTATTGGGTGTGATTTCTT
1 AAGGAAATATTCCGAGTTTGAGATTCTAAATGGATCGTGCCCTAACGTATTGGGTGTGATTTCTT
*
17638719 AAATCTTGGATGAGTGGATGTTCTTTTAAAGT
66 AAATCTTGGATAAGTGGATGTTCTTTTAAAGT
17638751 TTTATTGTAT
Statistics
Matches: 93, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
98 91 0.98
99 2 0.02
ACGTcount: A:0.28, C:0.11, G:0.25, T:0.37
Consensus pattern (98 bp):
AAGGAAATATTCCGAGTTTGAGATTCTAAATGGATCGTGCCCTAACGTATTGGGTGTGATTTCTT
AAATCTTGGATAAGTGGATGTTCTTTTAAAGTA
Found at i:17651867 original size:25 final size:24
Alignment explanation
Indices: 17651821--17651866 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
17651811 ATCTTCTTCA
*
17651821 TTTTTCTTCTTTCTTTTATTTTCT
1 TTTTTCTTCTTTCTTTGATTTTCT
17651845 TTTTTCCTTC-TTCTTTGATTTT
1 TTTTT-CTTCTTTCTTTGATTTT
17651867 TATTTGCTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.76
Consensus pattern (24 bp):
TTTTTCTTCTTTCTTTGATTTTCT
Found at i:17656757 original size:14 final size:14
Alignment explanation
Indices: 17656738--17656777 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
17656728 TTCCTATTGT
17656738 AAAATTGTATTTCA
1 AAAATTGTATTTCA
*
17656752 AAAATTGAATATTCA
1 AAAATTGTAT-TTCA
*
17656767 AAATTTGTATT
1 AAAATTGTATT
17656778 ATTGAATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.42
Consensus pattern (14 bp):
AAAATTGTATTTCA
Found at i:17658327 original size:88 final size:88
Alignment explanation
Indices: 17658160--17658329 Score: 198
Period size: 88 Copynumber: 1.9 Consensus size: 88
17658150 GACTCCGCCG
* * * * * **
17658160 TTCCTAGCATTGACATTCCGTGCGGACTTCAGGCATGCTAGACACGTGTTTCACTCTGAGTTGTC
1 TTCCTAGCATTGACATTCCGTACGGACTTCAAGCATACTAGACACATATTTCACTCTGAGTTACC
17658225 TGCAGAGCACGCGGTCCTTTCTA
66 TGCAGAGCACGCGGTCCTTTCTA
* * * * * *
17658248 TTCCTAGTATTGACATTCCGTACGGGCTTTAAGCCTACTAGACACATATTTCACTTTGGGTTACC
1 TTCCTAGCATTGACATTCCGTACGGACTTCAAGCATACTAGACACATATTTCACTCTGAGTTACC
*
17658313 TGC-GAAGCATGCGGTCC
66 TGCAG-AGCACGCGGTCC
17658330 CCCTTCTGTG
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
87 1 0.01
88 66 0.99
ACGTcount: A:0.20, C:0.26, G:0.22, T:0.31
Consensus pattern (88 bp):
TTCCTAGCATTGACATTCCGTACGGACTTCAAGCATACTAGACACATATTTCACTCTGAGTTACC
TGCAGAGCACGCGGTCCTTTCTA
Found at i:17669348 original size:3 final size:3
Alignment explanation
Indices: 17669340--17669387 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
17669330 CCCACCTCCT
17669340 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
17669388 CCCTCTATTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:17669420 original size:4 final size:4
Alignment explanation
Indices: 17669411--17669436 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
17669401 AAAATTGGGT
17669411 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
17669437 CTCTCCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:17671698 original size:10 final size:10
Alignment explanation
Indices: 17671683--17671716 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
17671673 GTAAATAAGT
17671683 TTTTTTGAAA
1 TTTTTTGAAA
17671693 TTTTTTGAAA
1 TTTTTTGAAA
* *
17671703 TTTGTTGAAC
1 TTTTTTGAAA
17671713 TTTT
1 TTTT
17671717 AAATACTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.24, C:0.03, G:0.12, T:0.62
Consensus pattern (10 bp):
TTTTTTGAAA
Found at i:17674758 original size:2 final size:2
Alignment explanation
Indices: 17674751--17674775 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17674741 CTTAATTTTC
17674751 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 T
17674776 TTCTTTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17677619 original size:19 final size:19
Alignment explanation
Indices: 17677583--17677621 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
17677573 AAACCGGTTG
*
17677583 ATTTATAAATTATCTATTC
1 ATTTAAAAATTATCTATTC
17677602 ATTTAAAAACTTAT-TATTC
1 ATTTAAAAA-TTATCTATTC
17677621 A
1 A
17677622 ACAATGCAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTAAAAATTATCTATTC
Found at i:17679810 original size:24 final size:26
Alignment explanation
Indices: 17679754--17679816 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 26
17679744 AATCGAATTC
* *
17679754 TATTTTTTATTTAATATATAATTAATT
1 TATTTTTTA-TTAATATATAAATAATA
17679781 TAATTTTTTATT-ATATATAAATAA-A
1 T-ATTTTTTATTAATATATAAATAATA
*
17679806 TATTTTATATT
1 TATTTTTTATT
17679817 TAAAATAGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
24 9 0.28
25 1 0.03
26 11 0.34
27 3 0.09
28 8 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
TATTTTTTATTAATATATAAATAATA
Found at i:17685367 original size:20 final size:20
Alignment explanation
Indices: 17685325--17685369 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
17685315 AAAAATATAA
* *
17685325 ATTTTGAAATTTTTATAAAT
1 ATTTTAAAATTTTGATAAAT
17685345 ATTTTAAAATTTTGA-AAATT
1 ATTTTAAAATTTTGATAAA-T
17685365 ATTTT
1 ATTTT
17685370 GATTTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (20 bp):
ATTTTAAAATTTTGATAAAT
Found at i:17687518 original size:3 final size:3
Alignment explanation
Indices: 17687512--17687559 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
17687502 CTTTTAATAA
* * *
17687512 TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT CAT TAT CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
17687560 AATTGCCCTT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:17687607 original size:19 final size:19
Alignment explanation
Indices: 17687568--17687617 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
17687558 ATAATTGCCC
* * *
17687568 TTATATATATACGTTTTTT
1 TTATATATATACATATATT
17687587 TTATATATATACATATATT
1 TTATATATATACATATATT
* *
17687606 TTTTGTATATAC
1 TTATATATATAC
17687618 TTACACACAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.58
Consensus pattern (19 bp):
TTATATATATACATATATT
Found at i:17687956 original size:18 final size:17
Alignment explanation
Indices: 17687933--17687968 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
17687923 TTTAATTTTA
*
17687933 TATTTGTTTATTTACTTT
1 TATTTGTTGATTT-CTTT
17687951 TATTTGTTGATTTCTTT
1 TATTTGTTGATTTCTTT
17687968 T
1 T
17687969 CATTATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.14, C:0.06, G:0.08, T:0.72
Consensus pattern (17 bp):
TATTTGTTGATTTCTTT
Found at i:17688280 original size:111 final size:110
Alignment explanation
Indices: 17688076--17688293 Score: 373
Period size: 111 Copynumber: 2.0 Consensus size: 110
17688066 TATCAAAAAC
* *
17688076 AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
1 AAAAATTTTCAAATAAGGCAATGTTTTGCATTTGAGAAATTCGAGAAAACGTGCCCTAAGGTGCT
* *
17688141 GGGTGTCGATTTTTCTCGTTCAACCAAATGGCTAAATATCCTTTT
66 GGGTGTCGATTTTTCTCGTTCAACCAAATAGCCAAATATCCTTTT
*
17688186 AAAAATTTTCGAAATAAGGCAATGTTTTGCATTTGAGAAATTTGAGAAAACGTGCCCTAAGGTGC
1 AAAAATTTTC-AAATAAGGCAATGTTTTGCATTTGAGAAATTCGAGAAAACGTGCCCTAAGGTGC
*
17688251 TGGGTGTCGATTTTTCTCGTTTAACCAAATAGCCAAATATCCT
65 TGGGTGTCGATTTTTCTCGTTCAACCAAATAGCCAAATATCCT
17688294 CTCGAATTTC
Statistics
Matches: 101, Mismatches: 6, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
110 10 0.10
111 91 0.90
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (110 bp):
AAAAATTTTCAAATAAGGCAATGTTTTGCATTTGAGAAATTCGAGAAAACGTGCCCTAAGGTGCT
GGGTGTCGATTTTTCTCGTTCAACCAAATAGCCAAATATCCTTTT
Found at i:17690324 original size:18 final size:20
Alignment explanation
Indices: 17690287--17690329 Score: 72
Period size: 18 Copynumber: 2.2 Consensus size: 20
17690277 ACATGTATAA
17690287 GTATGTGTATTAATTAAAAT
1 GTATGTGTATTAATTAAAAT
17690307 GTATGTGTATT-A-TAAAAT
1 GTATGTGTATTAATTAAAAT
17690325 GTATG
1 GTATG
17690330 CATGTATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 11 0.48
19 1 0.04
20 11 0.48
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.44
Consensus pattern (20 bp):
GTATGTGTATTAATTAAAAT
Found at i:17692139 original size:44 final size:43
Alignment explanation
Indices: 17691945--17692269 Score: 116
Period size: 44 Copynumber: 7.6 Consensus size: 43
17691935 GATGTGATCT
* * * **
17691945 GCTCTACT-CAACTTCAGAGAGATAAGATCCATCATTTTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGAT-CTTGGTTTTAATCC
* * * * *
17691988 GCTTCACTGCAACTTCAGGAAGATAGGA--TTGGTTTCTTCAGCC
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTTGG-TT-TTAATCC
** * * * * * *
17692031 TGCTCTGCTGCAACTTCAGGAAGATAAG-GCTT-GATATGATCT
1 -GCTCCACTGCAACTTCAGGGAGATAAGATCTTGGTTTTAATCC
* **
17692073 GCTCCACTACTGCTT-AGGGAGATAAGATCTATGGTTTTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGATCT-TGGTTTTAATCC
* **
17692116 GCTCCACTGCAACTTCAGGGAGATAGGA--TTGGTTTTTTTTCTGTC
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTTGG-TTTTAATC---C
* ** * *** **
17692161 TGCTCCACTACTGCTT-AGGGAGATAAGA-C-TGGATGCGATTT
1 -GCTCCACTGCAACTTCAGGGAGATAAGATCTTGGTTTTAATCC
* * **
17692202 GCTCCTCTACTGCTT-AGGGAGATAAGATCTGTGGTTTTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGATCT-TGGTTTTAATCC
* *
17692245 ACTCCATTGCAACTTCAGGGAGATA
1 GCTCCACTGCAACTTCAGGGAGATA
17692270 GGATTGGTTT
Statistics
Matches: 202, Mismatches: 60, Indels: 39
0.67 0.20 0.13
Matches are distributed among these distances:
40 36 0.18
41 17 0.08
42 13 0.06
43 45 0.22
44 62 0.31
45 17 0.08
46 12 0.06
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.32
Consensus pattern (43 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATCTTGGTTTTAATCC
Found at i:17692325 original size:22 final size:22
Alignment explanation
Indices: 17692300--17692346 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
17692290 GCTCCACTAC
*
17692300 TGCTTAGGGAGATAACACTGGA
1 TGCTTAGAGAGATAACACTGGA
*
17692322 TGCTTAGAGAGATAAGACTGGA
1 TGCTTAGAGAGATAACACTGGA
17692344 TGC
1 TGC
17692347 GATCTGCTCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.32, C:0.13, G:0.32, T:0.23
Consensus pattern (22 bp):
TGCTTAGAGAGATAACACTGGA
Found at i:17692443 original size:150 final size:150
Alignment explanation
Indices: 17692172--17692474 Score: 534
Period size: 150 Copynumber: 2.0 Consensus size: 150
17692162 GCTCCACTAC
* * * *
17692172 TGCTTAGGGAGATAAGACTGGATGCGATTTGCTCCTCTACTGCTTAGGGAGATAAGATCTGTGGT
1 TGCTTAGAGAGATAAGACTGGATGCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTGGT
* *
17692237 TTTAATCCACTCCATTGCAACTTCAGGGAGATAGGATTGGTTTTTTTTCGTTTGCTCCACTACTG
66 TTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGGTTTTTTTTCGTCTGCTCCACTACTG
17692302 CTTAGGGAGATAACACTGGA
131 CTTAGGGAGATAACACTGGA
17692322 TGCTTAGAGAGATAAGACTGGATGCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTGGT
1 TGCTTAGAGAGATAAGACTGGATGCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTGGT
*
17692387 TTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGGTTTTTTTTCGTCTGCTCCGCTACTG
66 TTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGGTTTTTTTTCGTCTGCTCCACTACTG
*
17692452 CTTAGGGAGATAAGACTGGA
131 CTTAGGGAGATAACACTGGA
17692472 TGC
1 TGC
17692475 GATCTGCTCC
Statistics
Matches: 145, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
150 145 1.00
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (150 bp):
TGCTTAGAGAGATAAGACTGGATGCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTGGT
TTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGGTTTTTTTTCGTCTGCTCCACTACTG
CTTAGGGAGATAACACTGGA
Found at i:17692490 original size:40 final size:40
Alignment explanation
Indices: 17692322--17692885 Score: 290
Period size: 40 Copynumber: 13.4 Consensus size: 40
17692312 TAACACTGGA
* * *
17692322 TGCTTAGAGAGATAAGACTGGATGCGATCTGCTCCACTAC
1 TGCTTAGGGAGATAAGACTGGTTTCGATCTGCTCCACTAC
* ** ** *
17692362 TACTTAGGGAGATAAGATCTGTGGTTTTAATCCACTCCACTGC
1 TGCTTAGGGAGATAAGA-C--TGGTTTCGATCTGCTCCACTAC
** * * *
17692405 AACTTCAGGGAGATAGGATTGGTTTTTTTTCG-TCTGCTCCGCTAC
1 TGCTT-AGGGAGATAAGACTGG-----TTTCGATCTGCTCCACTAC
* *
17692450 TGCTTAGGGAGATAAGACTGGATGCGATCTGCTCCACTAC
1 TGCTTAGGGAGATAAGACTGGTTTCGATCTGCTCCACTAC
** ** *
17692490 TGCTTAGGGAGATAAGATCTGTGGTTTTAATCCACTCCACTGC
1 TGCTTAGGGAGATAAGA-C--TGGTTTCGATCTGCTCCACTAC
** * * *
17692533 AACTTCAGGGAGATAGGATTGGTTTTTTTCG-TCTGCTCAACTAC
1 TGCTT-AGGGAGATAAGACTGG----TTTCGATCTGCTCCACTAC
* * *
17692577 TGCTTAGGGAGATAAGACTAGATGCGATCTGCTCCACTAC
1 TGCTTAGGGAGATAAGACTGGTTTCGATCTGCTCCACTAC
** ** *
17692617 TGCTTAGGGAGATAAGATCTGTGGTTTTAATCCACTCCACTGC
1 TGCTTAGGGAGATAAGA-C--TGGTTTCGATCTGCTCCACTAC
** * *
17692660 AACTTCAGGGAGATAGGATTGGTTTTTTTCG-TCTGCTCCACTAC
1 TGCTT-AGGGAGATAAGACTGG----TTTCGATCTGCTCCACTAC
* * * *
17692704 TGCTTAGGGAGATAAAACTAGATGCGATCTGCTCCACTAC
1 TGCTTAGGGAGATAAGACTGGTTTCGATCTGCTCCACTAC
* ** ** *
17692744 TACTTAGGGAGATAAGATCTGTGGTTTTAATCCACTCCACTGC
1 TGCTTAGGGAGATAAGA-C--TGGTTTCGATCTGCTCCACTAC
** * *
17692787 AACTTTAGGGAGATAGGATTGGTTTTTTTCG-TCTGCTCCACTAC
1 TGC-TTAGGGAGATAAGACTGG----TTTCGATCTGCTCCACTAC
* *** *
17692831 TGCTTAGGAAGATAAGACTGGAAGCGATCGGCTCCACTAC
1 TGCTTAGGGAGATAAGACTGGTTTCGATCTGCTCCACTAC
17692871 TGCTTAGGGAGATAA
1 TGCTTAGGGAGATAA
17692886 TATCTGTTAT
Statistics
Matches: 384, Mismatches: 103, Indels: 74
0.68 0.18 0.13
Matches are distributed among these distances:
39 11 0.03
40 127 0.33
41 16 0.04
43 110 0.29
44 96 0.25
45 21 0.05
46 3 0.01
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.31
Consensus pattern (40 bp):
TGCTTAGGGAGATAAGACTGGTTTCGATCTGCTCCACTAC
Found at i:17692576 original size:87 final size:87
Alignment explanation
Indices: 17692477--17692847 Score: 275
Period size: 87 Copynumber: 4.3 Consensus size: 87
17692467 CTGGATGCGA
17692477 TCTGCTCCACTACTGCTTAGGGAGATAAGATCT-GTGGTTTTAATCCACTCCACTGCAACTTCAG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTAGTGGTTTTAATCCACTCCACTGCAACTT-AG
*
17692541 GGAGATAGGATTGGTTTTTTTCG
65 GGAGATAAGATTGGTTTTTTTCG
* * * **
17692564 TCTGCTCAACTACTGCTTAGGGAGATAAGA-CTAGATGCGATCTGCTCCACT--ACTG---CTTA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTAG-TG-GTTTTAATCCACTCCACTGCAACTTA
** **
17692623 GGGAGATAAGATCT-GTGGTTTTAA
64 GGGAGATAAGAT-TGGTTTTTTTCG
** * ** * * ** ** ** * **
17692647 TCCACTCCACTGCAACTTCAGGGAGATAGGAT-TGGTTTTTTTCGTCTGCTCCACTACTGCTTAG
1 TCTGCTCCACTACTGCTT-AGGGAGATAAGATCTAGTGGTTTTAATCCACTCCACTGCAACTTAG
* * * * *
17692711 GGAGATAAAACTAG----ATGCG
65 GGAGATAAGATTGGTTTTTTTCG
*
17692730 ATCTGCTCCACTACTACTTAGGGAGATAAGATCT-GTGGTTTTAATCCACTCCACTGCAACTTTA
1 -TCTGCTCCACTACTGCTTAGGGAGATAAGATCTAGTGGTTTTAATCCACTCCACTGCAAC-TTA
*
17692794 GGGAGATAGGATTGGTTTTTTTCG
64 GGGAGATAAGATTGGTTTTTTTCG
*
17692818 TCTGCTCCACTACTGCTTAGGAAGATAAGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA
17692848 CTGGAAGCGA
Statistics
Matches: 210, Mismatches: 55, Indels: 38
0.69 0.18 0.13
Matches are distributed among these distances:
82 6 0.03
83 61 0.29
84 49 0.23
86 3 0.01
87 77 0.37
88 5 0.02
89 9 0.04
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.32
Consensus pattern (87 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGATCTAGTGGTTTTAATCCACTCCACTGCAACTTAGG
GAGATAAGATTGGTTTTTTTCG
Found at i:17692900 original size:127 final size:127
Alignment explanation
Indices: 17692322--17692892 Score: 1016
Period size: 127 Copynumber: 4.5 Consensus size: 127
17692312 TAACACTGGA
* *
17692322 TGCTTAGAGAGATAAGACTGGATGCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTGGT
1 TGCTTAGGGAGATAAGACTGGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGT
*
17692387 TTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGGTTTTTTTTCGTCTGCTCCGCTAC
66 TTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGG-TTTTTTTCGTCTGCTCCACTAC
17692450 TGCTTAGGGAGATAAGACTGGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGT
1 TGCTTAGGGAGATAAGACTGGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGT
*
17692515 TTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGGTTTTTTTCGTCTGCTCAACTAC
66 TTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGGTTTTTTTCGTCTGCTCCACTAC
*
17692577 TGCTTAGGGAGATAAGACTAGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGT
1 TGCTTAGGGAGATAAGACTGGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGT
17692642 TTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGGTTTTTTTCGTCTGCTCCACTAC
66 TTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGGTTTTTTTCGTCTGCTCCACTAC
* * *
17692704 TGCTTAGGGAGATAAAACTAGATGCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTGGT
1 TGCTTAGGGAGATAAGACTGGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGT
*
17692769 TTTAATCCACTCCACTGCAACTTTAGGGAGATAGGATTGGTTTTTTTCGTCTGCTCCACTAC
66 TTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGGTTTTTTTCGTCTGCTCCACTAC
* * * *
17692831 TGCTTAGGAAGATAAGACTGGAAGCGATCGGCTCCACTACTGCTTAGGGAGATAATATCTGT
1 TGCTTAGGGAGATAAGACTGGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
17692893 TATTTTAAGT
Statistics
Matches: 427, Mismatches: 16, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
127 324 0.76
128 103 0.24
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (127 bp):
TGCTTAGGGAGATAAGACTGGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGT
TTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGGTTTTTTTCGTCTGCTCCACTAC
Found at i:17693085 original size:100 final size:100
Alignment explanation
Indices: 17692912--17693375 Score: 581
Period size: 100 Copynumber: 4.7 Consensus size: 100
17692902 TCTGATTAAC
* **** * * ** *
17692912 TGCAATGTCGGGGAAACAAGATTTGTTGTTGTAGCTTTAATCAGTTCTGCTGCACCACCAAGGAA
1 TGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTTAATCTGCTCCACTGCACCACCAGGGAA
*
17692977 GTAAGATTCACCGTTCCGGCTTCAATCTTTTAAAT
66 GTAAGATTCACCGTTGCGGCTTCAATCTTTTAAAT
* * * *
17693012 TGCAATGTCGGGGAAGCAAGATTCGCCGTCGTAGTTTTAATCTGCTCCACTGCATCACCAGGGAA
1 TGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTTAATCTGCTCCACTGCACCACCAGGGAA
* * *
17693077 GTAAGATTCACCTTTGCAGCTTCAATCTTTTTAAT
66 GTAAGATTCACCGTTGCGGCTTCAATCTTTTAAAT
* * * * * *
17693112 TGCAATGTC-GGGAA-CAAAATTTACCGTTGTAGCTTCAATCTGATCCACTGTACCGCCAGGGAA
1 TGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTTAATCTGCTCCACTGCACCACCAGGGAA
* * *
17693175 GTAAGATTCGCCATTGCGGCTTCAATCTTTTTAAT
66 GTAAGATTCACCGTTGCGGCTTCAATCTTTTAAAT
* * * *
17693210 TGCAATATCGGGGAAGCAAGATTCACCGTTGTAGCTTTAATCTGCTCCACTGCATCGCCATGGAA
1 TGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTTAATCTGCTCCACTGCACCACCAGGGAA
**
17693275 GTAAGATTCGTCGTTGCGGCTTCAATCTTTTAAAT
66 GTAAGATTCACCGTTGCGGCTTCAATCTTTTAAAT
* * **
17693310 TACAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTTAATCTGCTCCACTGCACTGCCAGGGAA
1 TGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTTAATCTGCTCCACTGCACCACCAGGGAA
17693375 G
66 G
17693376 GTAACTTCAT
Statistics
Matches: 316, Mismatches: 46, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
98 79 0.25
99 10 0.03
100 227 0.72
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (100 bp):
TGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTTAATCTGCTCCACTGCACCACCAGGGAA
GTAAGATTCACCGTTGCGGCTTCAATCTTTTAAAT
Found at i:17693277 original size:198 final size:200
Alignment explanation
Indices: 17692961--17693375 Score: 600
Period size: 198 Copynumber: 2.1 Consensus size: 200
17692951 ATCAGTTCTG
* * * *
17692961 CTGCACCACCAAGGAAGTAAGATTCACCGTTCCGGCTTCAATCTTTTAAATTGCAATGTCGGGGA
1 CTGCACCGCCAGGGAAGTAAGATTCACCATTCCGGCTTCAATCTTTTAAATTGCAATATCGGGGA
* * *
17693026 AGCAAGATTCGCCGTCGTAGTTTTAATCTGCTCCACTGCATCACCAGGGAAGTAAGATTCACCTT
66 AGCAAGATTCACCGTCGTAGCTTTAATCTGCTCCACTGCATCACCAGGGAAGTAAGATTCACCGT
* * *
17693091 TGCAGCTTCAATCTTTTTAATTGCAATGTC-GGGAA-CAAAATTTACCGTTGTAGCTTCAATCTG
131 TGCAGCTTCAATCTTTTAAATTACAATGTCAGGGAAGCAAAATTCACCGTTGTAGCTTCAATCTG
17693154 ATCCA
196 ATCCA
* * * *
17693159 CTGTACCGCCAGGGAAGTAAGATTCGCCATTGCGGCTTCAATCTTTTTAATTGCAATATCGGGGA
1 CTGCACCGCCAGGGAAGTAAGATTCACCATTCCGGCTTCAATCTTTTAAATTGCAATATCGGGGA
* * * **
17693224 AGCAAGATTCACCGTTGTAGCTTTAATCTGCTCCACTGCATCGCCATGGAAGTAAGATTCGTCGT
66 AGCAAGATTCACCGTCGTAGCTTTAATCTGCTCCACTGCATCACCAGGGAAGTAAGATTCACCGT
* * *
17693289 TGCGGCTTCAATCTTTTAAATTACAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTTAATCTG
131 TGCAGCTTCAATCTTTTAAATTACAATGTCAGGGAAGCAAAATTCACCGTTGTAGCTTCAATCTG
*
17693354 CTCCA
196 ATCCA
*
17693359 CTGCACTGCCAGGGAAG
1 CTGCACCGCCAGGGAAG
17693376 GTAACTTCAT
Statistics
Matches: 190, Mismatches: 25, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
198 141 0.74
199 5 0.03
200 44 0.23
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.29
Consensus pattern (200 bp):
CTGCACCGCCAGGGAAGTAAGATTCACCATTCCGGCTTCAATCTTTTAAATTGCAATATCGGGGA
AGCAAGATTCACCGTCGTAGCTTTAATCTGCTCCACTGCATCACCAGGGAAGTAAGATTCACCGT
TGCAGCTTCAATCTTTTAAATTACAATGTCAGGGAAGCAAAATTCACCGTTGTAGCTTCAATCTG
ATCCA
Found at i:17693352 original size:50 final size:50
Alignment explanation
Indices: 17692973--17693352 Score: 237
Period size: 50 Copynumber: 7.6 Consensus size: 50
17692963 GCACCACCAA
* * * * *
17692973 GGAAGTAAGATTCACCGTTCCGGCTTCAATCTTTTAAATTGCAATGTCGG
1 GGAAGCAAGATTCACCGTTGCAGCTTCAATCTTTTCAATTGCAATGTCAG
* * * * * ** * * **
17693023 GGAAGCAAGATTCGCCGTCGTAGTTTTAATCTGCTCCACTGC-ATCACCAG
1 GGAAGCAAGATTCACCGTTGCAGCTTCAATCTTTTCAATTGCAAT-GTCAG
* * *
17693073 GGAAGTAAGATTCACCTTTGCAGCTTCAATCTTTTTAATTGCAATGTC-G
1 GGAAGCAAGATTCACCGTTGCAGCTTCAATCTTTTCAATTGCAATGTCAG
* * * ** * * * ** *
17693122 GGAA-CAAAATTTACCGTTGTAGCTTCAATCTGATCCACTGTACCGCCAG
1 GGAAGCAAGATTCACCGTTGCAGCTTCAATCTTTTCAATTGCAATGTCAG
* * * * * * *
17693171 GGAAGTAAGATTCGCCATTGCGGCTTCAATCTTTTTAATTGCAATATCGG
1 GGAAGCAAGATTCACCGTTGCAGCTTCAATCTTTTCAATTGCAATGTCAG
* * ** * * * *
17693221 GGAAGCAAGATTCACCGTTGTAGCTTTAATCTGCTCCACTGC-ATCGCCAT
1 GGAAGCAAGATTCACCGTTGCAGCTTCAATCTTTTCAATTGCAAT-GTCAG
* ** * * *
17693271 GGAAGTAAGATTCGTCGTTGCGGCTTCAATCTTTTAAATTACAATGTCAG
1 GGAAGCAAGATTCACCGTTGCAGCTTCAATCTTTTCAATTGCAATGTCAG
* *
17693321 GGAAGCAAGATTCACCGTTGTAGCTTTAATCT
1 GGAAGCAAGATTCACCGTTGCAGCTTCAATCT
17693353 GCTCCACTGC
Statistics
Matches: 227, Mismatches: 97, Indels: 12
0.68 0.29 0.04
Matches are distributed among these distances:
48 29 0.13
49 14 0.06
50 180 0.79
51 4 0.02
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (50 bp):
GGAAGCAAGATTCACCGTTGCAGCTTCAATCTTTTCAATTGCAATGTCAG
Found at i:17693712 original size:24 final size:24
Alignment explanation
Indices: 17693655--17693712 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
17693645 CCGGACTGCC
17693655 CCACTGTAATCTTCAAAGTTCAAT
1 CCACTGTAATCTTCAAAGTTCAAT
* * *
17693679 CCACTATAATCTTCAAGGTTCAGT
1 CCACTGTAATCTTCAAAGTTCAAT
*
17693703 CTACTGTAAT
1 CCACTGTAAT
17693713 TTAGGGACAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.34
Consensus pattern (24 bp):
CCACTGTAATCTTCAAAGTTCAAT
Found at i:17697761 original size:19 final size:20
Alignment explanation
Indices: 17697732--17697781 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
17697722 CCTTTTGTGA
*
17697732 AAATCTAATGCATATG-ATG
1 AAATGTAATGCATATGTATG
*
17697751 CAATGTAATGCATATGTATG
1 AAATGTAATGCATATGTATG
17697771 AAATG-AATGCA
1 AAATGTAATGCA
17697782 AAAAGAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 20 0.74
20 7 0.26
ACGTcount: A:0.42, C:0.10, G:0.18, T:0.30
Consensus pattern (20 bp):
AAATGTAATGCATATGTATG
Found at i:17700114 original size:18 final size:20
Alignment explanation
Indices: 17700077--17700119 Score: 72
Period size: 18 Copynumber: 2.2 Consensus size: 20
17700067 ACATGTATAA
17700077 GTATGTGTATTAATTAAAAT
1 GTATGTGTATTAATTAAAAT
17700097 GTATGTGTATT-A-TAAAAT
1 GTATGTGTATTAATTAAAAT
17700115 GTATG
1 GTATG
17700120 CATGTATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 11 0.48
19 1 0.04
20 11 0.48
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.44
Consensus pattern (20 bp):
GTATGTGTATTAATTAAAAT
Found at i:17706868 original size:18 final size:18
Alignment explanation
Indices: 17706841--17706875 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
17706831 TGGAAAGATG
17706841 GAAAAATATATA-ATTTT
1 GAAAAATATATATATTTT
17706858 GAAATAATATATATATTT
1 GAAA-AATATATATATTT
17706876 CTCAATTCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 8 0.50
19 4 0.25
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (18 bp):
GAAAAATATATATATTTT
Found at i:17707561 original size:21 final size:21
Alignment explanation
Indices: 17707535--17707576 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
17707525 TTTATTAAAA
17707535 TTTAAATATATACAATATATT
1 TTTAAATATATACAATATATT
* *
17707556 TTTAAATATTTACATTATATT
1 TTTAAATATATACAATATATT
17707577 GTATATATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTAAATATATACAATATATT
Found at i:17712888 original size:26 final size:26
Alignment explanation
Indices: 17712852--17712919 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 26
17712842 AACCTTTGAA
* **
17712852 AAAAGATTTTTTAATTTTAAAAATAG
1 AAAATATTTTTTAAGATTAAAAATAG
*
17712878 AAAATATTTTTTGAAGATTAAAAATAT
1 AAAATATTTTTT-AAGATTAAAAATAG
17712905 AAAATATTTTCTTAA
1 AAAATATTTT-TTAA
17712920 ACCAATTAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 11 0.31
27 23 0.64
28 2 0.06
ACGTcount: A:0.50, C:0.01, G:0.06, T:0.43
Consensus pattern (26 bp):
AAAATATTTTTTAAGATTAAAAATAG
Found at i:17719407 original size:24 final size:24
Alignment explanation
Indices: 17719369--17719432 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 24
17719359 GAGAGAGAGA
17719369 AAAAAAAGTTGAAATAAC-ATAAAAC
1 AAAAAAA-TTGAAATAACTA-AAAAC
*
17719394 AGAAAAAATT-AAATTACTAAAAAC
1 A-AAAAAATTGAAATAACTAAAAAC
17719418 AAAAAAATATGAAAT
1 AAAAAAAT-TGAAAT
17719433 CCAATTGTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
23 7 0.21
24 13 0.38
25 8 0.24
26 6 0.18
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (24 bp):
AAAAAAATTGAAATAACTAAAAAC
Found at i:17727268 original size:40 final size:39
Alignment explanation
Indices: 17727185--17727276 Score: 105
Period size: 40 Copynumber: 2.3 Consensus size: 39
17727175 GGAACGTGTT
* *
17727185 AGCAAATCGCGTCCATGTCAGCGCGATTTGCTGACGTGGC
1 AGCAAATCGCGTCCACGTAAGCGCGATTTGCTGACGT-GC
* *
17727225 AGCAAATCGCGTCCACGTAAGCGCGGTTTGTGTCGACGT-C
1 AGCAAATCGCGTCCACGTAAGCGCGATTTG-CT-GACGTGC
*
17727265 AGCAAAGCGCGT
1 AGCAAATCGCGT
17727277 TGACGTTGAC
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
40 39 0.87
41 1 0.02
42 5 0.11
ACGTcount: A:0.22, C:0.27, G:0.30, T:0.21
Consensus pattern (39 bp):
AGCAAATCGCGTCCACGTAAGCGCGATTTGCTGACGTGC
Found at i:17727364 original size:9 final size:9
Alignment explanation
Indices: 17727350--17727380 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
17727340 CACATTATGA
17727350 TTTTTAGGG
1 TTTTTAGGG
*
17727359 TTTTTAGGA
1 TTTTTAGGG
17727368 TTTTTAGGG
1 TTTTTAGGG
17727377 TTTT
1 TTTT
17727381 AGAAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.13, C:0.00, G:0.26, T:0.61
Consensus pattern (9 bp):
TTTTTAGGG
Found at i:17727774 original size:127 final size:126
Alignment explanation
Indices: 17727494--17728062 Score: 716
Period size: 126 Copynumber: 4.5 Consensus size: 126
17727484 GATAAAATCA
* * * * * * * * *
17727494 AAGCAGGATGATTTATCAGAAGGATTTTTGAAGTTGCGCCCACATGTACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGTGCCCACGTGGACGCGCTTTTGCTACAGT
** *
17727559 AGGTCTTGGAAAAATAATTTCAAGTTGACGTTTCTGAGCAAATAGT-TTAAAAAACGCTTC
66 AGGTCTTGGAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAAAAACGCTTC
* * *
17727619 AAGCAAGATGCTTTATGAGAAGAATTTGTGAAATCGTGCCCTCGTGGACGCGCTTTTGTTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGTGCCCACGTGGACGCGCTTTTGCTACAGT
* * *
17727684 TGGTCTTGGAAGAAATAATTTTGAGTTGAGGTTTCTGAGCAAATAGTTTAAAAAAACGCTTC
66 AGGTCTTGGAA-AAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAAAAACGCTTC
* *
17727746 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATTGCT-CCCACGTGGACGCACTTTTGCTACAG
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCG-TGCCCACGTGGACGCGCTTTTGCTACAG
* ** * * *
17727810 TAGGTCCTAAAAAAATAATTTTGAGTTGACATTTCTGAGCAAATAGTATAAAACAACGCTGC
65 TAGGTCTTGGAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAAAAACGCTTC
* * * *
17727872 AAGCAAGATGCTATT-TGAGAATAATTTGTGAAATCGTGCCCTCGTGGACGCGTTTTTGCTACAG
1 AAGCAGGATGCT-TTATGAGAAGAATTTGTGAAATCGTGCCCACGTGGACGCGCTTTTGCTACAG
* * * * *
17727936 TAGATCTTGGAAAAATAATTTTGACTTGACGTTTTTGAGCAAATA--ATATAAAACCGCTTC
65 TAGGTCTTGGAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAAAAACGCTTC
* * * **
17727996 TAGTAGGATGCTTTATGAGAATAATTTGTGAAATCAAGCCCACGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGTGCCCACGTGGACGCGCTTTTGCTACAGT
17728061 AG
66 AG
17728063 CATGTTTGGG
Statistics
Matches: 383, Mismatches: 55, Indels: 13
0.85 0.12 0.03
Matches are distributed among these distances:
123 2 0.01
124 68 0.18
125 64 0.17
126 168 0.44
127 80 0.21
128 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.31
Consensus pattern (126 bp):
AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGTGCCCACGTGGACGCGCTTTTGCTACAGT
AGGTCTTGGAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAAAAACGCTTC
Found at i:17731324 original size:22 final size:21
Alignment explanation
Indices: 17731243--17731698 Score: 511
Period size: 22 Copynumber: 21.2 Consensus size: 21
17731233 TTATATTTAA
*
17731243 GTTAGGGTTTTTAAGTTAAGT
1 GTTAGGGTTTTTAAGTTAAGG
*
17731264 GTTAGGGTTTTT-ATTTAAGG
1 GTTAGGGTTTTTAAGTTAAGG
* *
17731284 GTTATGGTTTTAAAGTTAAGG
1 GTTAGGGTTTTTAAGTTAAGG
* *
17731305 GTTTAGGGTTTTTAATTTAAAG
1 G-TTAGGGTTTTTAAGTTAAGG
* * * *
17731327 GTTACGATTTTAAAATTAAGG
1 GTTAGGGTTTTTAAGTTAAGG
* *
17731348 GATTAGGATTTTAAAGTTAAGG
1 G-TTAGGGTTTTTAAGTTAAGG
17731370 GTTAGGGTTTTTAAGTTAAAGG
1 GTTAGGGTTTTTAAGTT-AAGG
* * *
17731392 CTTAGGGTTTTTAATTTATGG
1 GTTAGGGTTTTTAAGTTAAGG
* *
17731413 GTTTAAGGTTTTTAATTTAAGG
1 G-TTAGGGTTTTTAAGTTAAGG
*
17731435 GTTTAGGGTTTTTAATTTAAAGG
1 G-TTAGGGTTTTTAAGTT-AAGG
*
17731458 GTTAGAGTTTTTAAGTTAAGG
1 GTTAGGGTTTTTAAGTTAAGG
17731479 GTTAGGGTTTTTAAGTTAAGG
1 GTTAGGGTTTTTAAGTTAAGG
* *
17731500 GTTTATGGTTTTTAATTTAAGGG
1 G-TTAGGGTTTTTAAGTTAA-GG
*
17731523 GTTAGGGTTTTAAAGTTAAGG
1 GTTAGGGTTTTTAAGTTAAGG
*
17731544 GTTTAGGGTTTTTAAGTTAATG
1 G-TTAGGGTTTTTAAGTTAAGG
* *
17731566 GTTAAGGTTTTTAAGTTAAATG
1 GTTAGGGTTTTTAAGTT-AAGG
* *
17731588 TTTAGCGTTTTTAAGTTAAGGG
1 GTTAGGGTTTTTAAGTTAA-GG
17731610 GTTAGGGTTTTTAAGTTAAGG
1 GTTAGGGTTTTTAAGTTAAGG
*
17731631 GTTA-TGTTTTTAAGGTTAAGG
1 GTTAGGGTTTTTAA-GTTAAGG
*
17731652 GTTTAGGGTTTTTAATTTAAGG
1 G-TTAGGGTTTTTAAGTTAAGG
*
17731674 GTTAGGGGTTTTAAGTTAAGG
1 GTTAGGGTTTTTAAGTTAAGG
17731695 GTTA
1 GTTA
17731699 AAGTTAGGGT
Statistics
Matches: 374, Mismatches: 47, Indels: 28
0.83 0.10 0.06
Matches are distributed among these distances:
20 24 0.06
21 134 0.36
22 200 0.53
23 16 0.04
ACGTcount: A:0.26, C:0.01, G:0.28, T:0.45
Consensus pattern (21 bp):
GTTAGGGTTTTTAAGTTAAGG
Found at i:17731338 original size:43 final size:43
Alignment explanation
Indices: 17731243--17731697 Score: 515
Period size: 43 Copynumber: 10.6 Consensus size: 43
17731233 TTATATTTAA
* *
17731243 GTTAGGGTTTTTAAGTTAAGTG-TTAGGGTTTTT-ATTTAAGG
1 GTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGG
* * * *
17731284 GTTATGGTTTTAAAGTTAAGGGTTTAGGGTTTTTAATTTAAAG
1 GTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGG
* * * * * * *
17731327 GTTACGATTTTAAAATTAAGGGATTAGGATTTTAAAGTTAAGG
1 GTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGG
* * * *
17731370 GTTAGGGTTTTTAAGTTAAAGGCTTAGGGTTTTTAATTTATGG
1 GTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGG
* * *
17731413 GTTTAAGGTTTTTAATTTAAGGGTTTAGGGTTTTTAATTTAAAGG
1 G-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTT-AAGG
*
17731458 GTTAGAGTTTTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGG
1 GTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGG
* * * *
17731500 GTTTATGGTTTTTAATTTAAGGGGTTAGGGTTTTAAAGTTAAGG
1 G-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGG
* * *
17731544 GTTTAGGGTTTTTAAGTTAATGG-TTAAGGTTTTTAAGTTAAATG
1 G-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTT-AAGG
* * *
17731588 TTTAGCGTTTTTAAGTTAAGGGGTTAGGGTTTTTAAGTTAAGG
1 GTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGG
* *
17731631 GTTA-TGTTTTTAAGGTTAAGGGTTTAGGGTTTTTAATTTAAGG
1 GTTAGGGTTTTTAA-GTTAAGGGTTTAGGGTTTTTAAGTTAAGG
*
17731674 GTTAGGGGTTTTAAGTTAAGGGTT
1 GTTAGGGTTTTTAAGTTAAGGGTT
17731698 AAAGTTAGGG
Statistics
Matches: 352, Mismatches: 52, Indels: 18
0.83 0.12 0.04
Matches are distributed among these distances:
41 19 0.05
42 24 0.07
43 189 0.54
44 116 0.33
45 4 0.01
ACGTcount: A:0.26, C:0.01, G:0.28, T:0.45
Consensus pattern (43 bp):
GTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGG
Found at i:17731368 original size:65 final size:64
Alignment explanation
Indices: 17731244--17731697 Score: 515
Period size: 65 Copynumber: 7.0 Consensus size: 64
17731234 TATATTTAAG
* * *
17731244 TTAGGGTTTTTAAGTT-AAGTGTTAGGGTTTTT-ATTTAAGGGTTATGGTTTTAAAGTTAAGGGT
1 TTAGGGTTTTTAAGTTAAAG-GTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGT
* * * * * * *
17731307 TTAGGGTTTTTAATTTAAAGGTTACGATTTTAAAATTAAGGGATTAGGATTTTAAAGTTAAGGG-
1 TTAGGGTTTTTAAGTTAAAGGTTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGT
* * * *
17731371 TTAGGGTTTTTAAGTTAAAGGCTTAGGGTTTTTAATTTATGGGTTTAAGGTTTTTAATTTAAGGG
1 TTAGGGTTTTTAAGTTAAAGG-TTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGG
17731436 T
64 T
* *
17731437 TTAGGGTTTTTAATTTAAAGGGTTAGAGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGT
1 TTAGGGTTTTTAAGTTAAA-GGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGT
* * * * *
17731502 TTATGGTTTTTAATTTAAGGGGTTAGGGTTTTAAAGTTAAGGGTTTAGGGTTTTTAAGTTAATGG
1 TTAGGGTTTTTAAGTTAA-AGGTTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGG
17731567 -
64 T
* * *
17731567 TTAAGGTTTTTAAGTTAAATGTTTAGCGTTTTTAAGTTAAGGGGTTAGGGTTTTTAAGTTAAGGG
1 TTAGGGTTTTTAAGTTAAA-GGTTAGGGTTTTTAAGTTAA-GGGTTAGGGTTTTTAAGTTAAGGG
17731632 -
64 T
* * * *
17731632 TTA-TGTTTTTAAGGTTAAGGGTTTAGGGTTTTTAATTTAAGGGTTAGGGGTTTTAAGTTAAGGG
1 TTAGGGTTTTTAA-GTTAAAGG-TTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGG
17731696 T
64 T
17731697 T
1 T
17731698 AAAGTTAGGG
Statistics
Matches: 336, Mismatches: 42, Indels: 24
0.84 0.10 0.06
Matches are distributed among these distances:
63 24 0.07
64 63 0.19
65 188 0.56
66 59 0.18
67 2 0.01
ACGTcount: A:0.26, C:0.01, G:0.28, T:0.46
Consensus pattern (64 bp):
TTAGGGTTTTTAAGTTAAAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGT
Found at i:17733193 original size:20 final size:20
Alignment explanation
Indices: 17733156--17733193 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
17733146 TTTATTTTTA
*
17733156 AAAATCTACATAATAATTAT
1 AAAATCTACATAAAAATTAT
17733176 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
17733194 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTAT
Found at i:17734111 original size:13 final size:13
Alignment explanation
Indices: 17734087--17734125 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
17734077 ATTTTTACGG
17734087 TTTAAAAA-AATT
1 TTTAAAAATAATT
17734099 TTTAAAAATAATT
1 TTTAAAAATAATT
*
17734112 TTTAAAAATTATT
1 TTTAAAAATAATT
17734125 T
1 T
17734126 AAAAATAGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 8 0.32
13 17 0.68
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TTTAAAAATAATT
Found at i:17734172 original size:51 final size:51
Alignment explanation
Indices: 17734128--17734227 Score: 139
Period size: 51 Copynumber: 2.0 Consensus size: 51
17734118 AATTATTTAA
*
17734128 AAATAGGGATTTAAGAGAAATTTA-AGAGGAACTTGAGAGCAAATTGAGATT
1 AAATAGGGATTTAAGAGAAATTTAGA-AGGAACTAGAGAGCAAATTGAGATT
* * * *
17734179 AAATATGGATTTGAGAGAAATTTGGAAGGAAGTAGAGAGCAAATTGAGA
1 AAATAGGGATTTAAGAGAAATTTAGAAGGAACTAGAGAGCAAATTGAGA
17734228 GGAAATTTAG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
51 42 0.98
52 1 0.02
ACGTcount: A:0.45, C:0.03, G:0.28, T:0.24
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAGAAGGAACTAGAGAGCAAATTGAGATT
Found at i:17734255 original size:14 final size:12
Alignment explanation
Indices: 17734187--17734251 Score: 59
Period size: 11 Copynumber: 5.8 Consensus size: 12
17734177 TTAAATATGG
17734187 ATTTGAGA-GAA
1 ATTTGAGAGGAA
17734198 ATTTG-GAAGG-A
1 ATTTGAG-AGGAA
* * *
17734209 AGTAGAGAGCAA
1 ATTTGAGAGGAA
17734221 A-TTGAGAGGAA
1 ATTTGAGAGGAA
17734232 ATTT-AGAGGAA
1 ATTTGAGAGGAA
17734243 ATTTGAGAG
1 ATTTGAGAG
17734252 AGGATTAGTT
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
10 1 0.02
11 32 0.74
12 10 0.23
ACGTcount: A:0.43, C:0.02, G:0.32, T:0.23
Consensus pattern (12 bp):
ATTTGAGAGGAA
Found at i:17736622 original size:14 final size:14
Alignment explanation
Indices: 17736597--17736623 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17736587 AAAATATAAA
17736597 AAATAAAATATTTG
1 AAATAAAATATTTG
17736611 AAATAAAATATTT
1 AAATAAAATATTT
17736624 TAATATATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (14 bp):
AAATAAAATATTTG
Found at i:17737365 original size:40 final size:40
Alignment explanation
Indices: 17737320--17737395 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
17737310 GGAAAAATAA
* *
17737320 AATTTTTAAAATTTCTATTTATCTGATTAAACATTTTTCT
1 AATTTTTAAAATTTATATTTATCTAATTAAACATTTTTCT
* * *
17737360 AATTTTTAAATTTTATGTTTATCTAATTAAATATTT
1 AATTTTTAAAATTTATATTTATCTAATTAAACATTT
17737396 ATTTTAAACA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.57
Consensus pattern (40 bp):
AATTTTTAAAATTTATATTTATCTAATTAAACATTTTTCT
Found at i:17745357 original size:35 final size:35
Alignment explanation
Indices: 17745298--17745429 Score: 176
Period size: 35 Copynumber: 3.7 Consensus size: 35
17745288 ACAATCCAAT
**
17745298 CGAAACACACCATATGCTCATAAGAG-TCAATCTATC
1 CGAAACACACCA-ATGCTCATAAGAGCT-AATCCCTC
* *
17745334 TGAAACACACCAATGCTCGTAAGAGCTAATCCCTC
1 CGAAACACACCAATGCTCATAAGAGCTAATCCCTC
*
17745369 CGAAACACACCAATGCTCGTAAGAGCTAATCCCTC
1 CGAAACACACCAATGCTCATAAGAGCTAATCCCTC
* *
17745404 CGAAATACACTAATGCTCATAAGAGC
1 CGAAACACACCAATGCTCATAAGAGC
17745430 AACTCCAATC
Statistics
Matches: 87, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
35 75 0.86
36 12 0.14
ACGTcount: A:0.37, C:0.30, G:0.14, T:0.20
Consensus pattern (35 bp):
CGAAACACACCAATGCTCATAAGAGCTAATCCCTC
Found at i:17748632 original size:27 final size:24
Alignment explanation
Indices: 17748578--17748636 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 24
17748568 GCGTGCTCAG
* **
17748578 TTTTGTGAATTTTAAAAATAGAGT
1 TTTTGTTAATTTTAAAAATAGACA
17748602 TTTTGTTAATTTTAATAAATATGCACA
1 TTTTGTTAATTTTAA-AAATA-G-ACA
17748629 TTTTGTTA
1 TTTTGTTA
17748637 TGTTATTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 14 0.48
25 5 0.17
26 1 0.03
27 9 0.31
ACGTcount: A:0.34, C:0.03, G:0.12, T:0.51
Consensus pattern (24 bp):
TTTTGTTAATTTTAAAAATAGACA
Found at i:17760188 original size:24 final size:23
Alignment explanation
Indices: 17760161--17760205 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
17760151 CCAATTGAAC
* *
17760161 TAAATTTTTAATATTTTTATTTTT
1 TAAAATTTTAATA-ATTTATTTTT
17760185 TAAAATTTTAATAATTTATTT
1 TAAAATTTTAATAATTTATTT
17760206 AATCAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TAAAATTTTAATAATTTATTTTT
Found at i:17764508 original size:18 final size:17
Alignment explanation
Indices: 17764473--17764507 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
17764463 AAGAACTTAT
*
17764473 ATTTTTAAATAAATAAA
1 ATTTTTAAAAAAATAAA
17764490 ATTTTTAAAAAAATAAA
1 ATTTTTAAAAAAATAAA
17764507 A
1 A
17764508 AATTTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
ATTTTTAAAAAAATAAA
Found at i:17764513 original size:17 final size:17
Alignment explanation
Indices: 17764476--17764515 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
17764466 AACTTATATT
* **
17764476 TTTAAATAAATAAAATT
1 TTTAAAAAAATAAAAAA
17764493 TTTAAAAAAATAAAAAA
1 TTTAAAAAAATAAAAAA
17764510 TTTAAA
1 TTTAAA
17764516 TTTAAATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TTTAAAAAAATAAAAAA
Found at i:17764516 original size:6 final size:6
Alignment explanation
Indices: 17764507--17764531 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
17764497 AAAAAATAAA
17764507 AAATTT AAATTT AAATTT AAATTT A
1 AAATTT AAATTT AAATTT AAATTT A
17764532 TAGAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AAATTT
Found at i:17764954 original size:20 final size:23
Alignment explanation
Indices: 17764913--17764955 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
17764903 TTTTTAAAAA
17764913 TTTAAAAATATATAATAATTATT
1 TTTAAAAATATATAATAATTATT
17764936 TTTAAAAAT-TA-AA-AATTATT
1 TTTAAAAATATATAATAATTATT
17764956 AAAAAAAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 7 0.35
21 2 0.10
22 2 0.10
23 9 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TTTAAAAATATATAATAATTATT
Found at i:17764962 original size:20 final size:20
Alignment explanation
Indices: 17764939--17764982 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
17764929 AATTATTTTT
17764939 AAAAATTA-AAAATTAT-TAA
1 AAAAATTATAAAATT-TGTAA
*
17764958 AAAAAGTATAAAATTTGTAA
1 AAAAATTATAAAATTTGTAA
17764978 AAAAA
1 AAAAA
17764983 ATATTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (20 bp):
AAAAATTATAAAATTTGTAA
Found at i:17774545 original size:4 final size:4
Alignment explanation
Indices: 17774536--17774588 Score: 106
Period size: 4 Copynumber: 13.2 Consensus size: 4
17774526 GAATTAAGGA
17774536 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
17774584 TATG T
1 TATG T
17774589 GTTTTCTTTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 49 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:17774895 original size:21 final size:21
Alignment explanation
Indices: 17774871--17774946 Score: 99
Period size: 21 Copynumber: 3.8 Consensus size: 21
17774861 ATTATAAAAA
17774871 TAATTAAAAATAAAAATACAT
1 TAATTAAAAATAAAAATACAT
17774892 TAATTAAAAATAAAAATA-AT
1 TAATTAAAAATAAAAATACAT
17774912 T-A--AAAAATCAACAAAT-CAT
1 TAATTAAAAAT-AA-AAATACAT
17774931 TAATTAAAAATAAAAA
1 TAATTAAAAATAAAAA
17774947 ATTTGAAACA
Statistics
Matches: 49, Mismatches: 0, Indels: 13
0.79 0.00 0.21
Matches are distributed among these distances:
17 6 0.12
18 2 0.04
19 8 0.16
20 7 0.14
21 20 0.41
22 6 0.12
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (21 bp):
TAATTAAAAATAAAAATACAT
Found at i:17774899 original size:15 final size:16
Alignment explanation
Indices: 17774864--17774917 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 16
17774854 TAATATGATT
17774864 ATAAAAATAATTAAAA
1 ATAAAAATAATTAAAA
17774880 ATAAAAATACATTAATTAAAA
1 AT--AAA-A-A-TAATTAAAA
17774901 ATAAAAATAATTAAAA
1 ATAAAAATAATTAAAA
17774917 A
1 A
17774918 ATCAACAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
16 12 0.36
17 1 0.03
18 4 0.12
19 4 0.12
20 1 0.03
21 11 0.33
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (16 bp):
ATAAAAATAATTAAAA
Found at i:17774943 original size:39 final size:37
Alignment explanation
Indices: 17774864--17774946 Score: 132
Period size: 39 Copynumber: 2.2 Consensus size: 37
17774854 TAATATGATT
17774864 ATAAAAATAATTAAAAATAAAAATACATTAATTAAAA
1 ATAAAAATAATTAAAAATAAAAATACATTAATTAAAA
17774901 ATAAAAATAATTAAAAAATCAACAAAT-CATTAATTAAAA
1 ATAAAAATAATT-AAAAAT-AA-AAATACATTAATTAAAA
17774940 ATAAAAA
1 ATAAAAA
17774947 ATTTGAAACA
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
37 12 0.28
38 6 0.14
39 21 0.49
40 4 0.09
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (37 bp):
ATAAAAATAATTAAAAATAAAAATACATTAATTAAAA
Found at i:17775290 original size:133 final size:130
Alignment explanation
Indices: 17775006--17775305 Score: 320
Period size: 133 Copynumber: 2.3 Consensus size: 130
17774996 ATGGAACCTC
* * * ** *
17775006 AGACTCAATGATGTAATCGCAATTATCTAACCATCTAACGAAAGGAGCTAATATGTTAAAAATAT
1 AGACTCAAAGATGTAATTGCAACTATCTAACCATCTAACGAAAAAAACTAATATGTTAAAAATAT
* ** *
17775071 TAATTAAAAAAAACTTGAAGCAACGTGAAATAAAAAATACAAATGCAAGTAGTAGAAGAGTCAAA
66 TAATTAAAAAAAACTTGAAGCAACATGAAATAAAAAAT---AATG-AAGTAAAAGAAGAATCAAA
*
17775136 CTCG
127 CTCA
* * *
17775140 AGACTCAAGGATGTAATTACAACTATCTAACCATCTAAC-AAAAAAACTAATATGTTTAAAATCA
1 AGACTCAAAGATGTAATTGCAACTATCTAACCATCTAACGAAAAAAACTAATATGTTAAAAAT-A
*
17775204 TTAATTAAAAATTTAAAAAGCTTGAAGCAACATGAAA-AAAAAAT-ATG-AGTAAAAGAGGAATC
65 TTAATT--AAA---AAAAA-CTTGAAGCAACATGAAATAAAAAATAATGAAGTAAAAGAAGAATC
*
17775266 AAACTTA
124 AAACTCA
*
17775273 AGATTCAAAGATGTAATTGCAACTATCTAACCA
1 AGACTCAAAGATGTAATTGCAACTATCTAACCA
17775306 AATAACTAAT
Statistics
Matches: 141, Mismatches: 18, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
133 65 0.46
134 42 0.30
135 3 0.02
136 3 0.02
139 12 0.09
140 16 0.11
ACGTcount: A:0.50, C:0.13, G:0.13, T:0.24
Consensus pattern (130 bp):
AGACTCAAAGATGTAATTGCAACTATCTAACCATCTAACGAAAAAAACTAATATGTTAAAAATAT
TAATTAAAAAAAACTTGAAGCAACATGAAATAAAAAATAATGAAGTAAAAGAAGAATCAAACTCA
Found at i:17776619 original size:71 final size:71
Alignment explanation
Indices: 17776487--17776622 Score: 177
Period size: 71 Copynumber: 1.9 Consensus size: 71
17776477 GAGTGTGCCT
* * * *
17776487 AGCACTAGTCGGTATAACTGACAATAAATGCGCCCTACACTGGTCGGTAGAACCAACAAATATGT
1 AGCACTAGTCGGTATAACCGACAATAAATGCGCCCTACACTAGTCGATAAAACCAACAAATATGT
17776552 CTGTCC
66 CTGTCC
* * *
17776558 AGCACT-GATCGGTATAACCGACAATAGATGCGCTCTACGCTAGTCGATAAAACCGAA-AAATAT
1 AGCACTAG-TCGGTATAACCGACAATAAATGCGCCCTACACTAGTCGATAAAACC-AACAAATAT
17776621 GT
64 GT
17776623 ATGAAATCAT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
70 1 0.02
71 53 0.95
72 2 0.04
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.22
Consensus pattern (71 bp):
AGCACTAGTCGGTATAACCGACAATAAATGCGCCCTACACTAGTCGATAAAACCAACAAATATGT
CTGTCC
Found at i:17780650 original size:147 final size:144
Alignment explanation
Indices: 17780371--17780650 Score: 337
Period size: 147 Copynumber: 1.9 Consensus size: 144
17780361 GTTACGTACC
* * * * * * *
17780371 ATTAATATAAAATGTACATTATAATATCATAATTGTATATAAGTTACATATTATTAATAATCTAT
1 ATTAATATAAAACGTACATTATAATAACATAATTATATATAAGATACATATAATTAATAATCGAC
* * * * * * **
17780436 CTTAATTATATACTGCTGATTGTTTATATTATTATCTACAATAAAGTTAGTAATACATTTAGGGT
66 CTTAATTATATAATGCTCATTGTATATATTATAATCTACAATAAAATCAGT-ATACATTTAAAGT
17780501 TTAAGTTTACATATT
130 TTAAGTTTACATATT
*
17780516 ATTAATATAAAAACGTACATTATAATAACATAGTTATATATAGAGATACATATAATTAATAATCG
1 ATTAATAT-AAAACGTACATTATAATAACATAATTATATATA-AGATACATATAATTAATAATCG
* * *
17780581 ACCTTAATTATATAATGTTCATTGTATATTTTATAATCTACCATAAAATCAGT-TACATATTCAA
64 ACCTTAATTATATAATGCTCATTGTATATATTATAATCTACAATAAAATCAGTATACAT-TT-AA
17780645 AGTTTA
127 AGTTTA
17780651 GGTTGTATAT
Statistics
Matches: 112, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
145 13 0.12
146 31 0.28
147 68 0.61
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (144 bp):
ATTAATATAAAACGTACATTATAATAACATAATTATATATAAGATACATATAATTAATAATCGAC
CTTAATTATATAATGCTCATTGTATATATTATAATCTACAATAAAATCAGTATACATTTAAAGTT
TAAGTTTACATATT
Found at i:17781838 original size:16 final size:16
Alignment explanation
Indices: 17781817--17781855 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
17781807 AATTATGGAG
*
17781817 ATATATGAAAGCATGT
1 ATATATAAAAGCATGT
*
17781833 ATATATAAAAGTATGT
1 ATATATAAAAGCATGT
17781849 ATATATA
1 ATATATA
17781856 TGTATACGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.49, C:0.03, G:0.13, T:0.36
Consensus pattern (16 bp):
ATATATAAAAGCATGT
Found at i:17781841 original size:34 final size:34
Alignment explanation
Indices: 17781793--17781857 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
17781783 ATATATATAT
*
17781793 GCATATATACATAAAATTATGGAGATATATGAAA
1 GCATATATACATAAAAGTATGGAGATATATGAAA
* * * *
17781827 GCATGTATATATAAAAGTATGTATATATATG
1 GCATATATACATAAAAGTATGGAGATATATG
17781858 TATACGTTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.46, C:0.05, G:0.15, T:0.34
Consensus pattern (34 bp):
GCATATATACATAAAAGTATGGAGATATATGAAA
Found at i:17782097 original size:13 final size:13
Alignment explanation
Indices: 17782079--17782104 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17782069 GAATCATAAA
17782079 ATATAAAATACAT
1 ATATAAAATACAT
17782092 ATATAAAATACAT
1 ATATAAAATACAT
17782105 GTTTTAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (13 bp):
ATATAAAATACAT
Found at i:17782268 original size:20 final size:19
Alignment explanation
Indices: 17782215--17782269 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
17782205 AGGGTACGTG
17782215 TATATATATAT-ATATAGA
1 TATATATATATAATATAGA
* * *
17782233 TAAATCATAAAAAATATAGA
1 TATAT-ATATATAATATAGA
17782253 TATTATATATATAATAT
1 TA-TATATATATAATAT
17782270 GAAAACGCAT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
18 4 0.14
19 4 0.14
20 18 0.64
21 2 0.07
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.40
Consensus pattern (19 bp):
TATATATATATAATATAGA
Found at i:17782385 original size:5 final size:5
Alignment explanation
Indices: 17782369--17782397 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
17782359 AATAATTTTT
17782369 ATAAA A-AAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
17782398 CAATAACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
ATAAA
Found at i:17783699 original size:24 final size:24
Alignment explanation
Indices: 17783665--17783716 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
17783655 TTTCTAGAAG
* **
17783665 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAACATAATAT
*
17783689 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATGAACATAATAT
17783713 ATTT
1 ATTT
17783717 GACTTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAACATAATAT
Found at i:17785675 original size:24 final size:25
Alignment explanation
Indices: 17785648--17785694 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
17785638 CATAAGGTTT
*
17785648 TATTTATTATTAAATTAT-AAATTA
1 TATTAATTATTAAATTATGAAATTA
*
17785672 TATTAATTATTATATTATGAAAT
1 TATTAATTATTAAATTATGAAAT
17785695 AAATAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (25 bp):
TATTAATTATTAAATTATGAAATTA
Found at i:17790160 original size:17 final size:16
Alignment explanation
Indices: 17790128--17790161 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
17790118 TTGGCTATTC
*
17790128 TGTTTCTTTCTTCTTT
1 TGTTTCTTTATTCTTT
17790144 TGTTTCTTTTATTCTTT
1 TGTTTC-TTTATTCTTT
17790161 T
1 T
17790162 ATTTTAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.03, C:0.15, G:0.06, T:0.76
Consensus pattern (16 bp):
TGTTTCTTTATTCTTT
Found at i:17790209 original size:14 final size:14
Alignment explanation
Indices: 17790150--17790200 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
17790140 CTTTTGTTTC
*
17790150 TTTTA-TTCTTTTA
1 TTTTATTTCCTTTA
* *
17790163 TTTTAACTTACTTTA
1 TTTT-ATTTCCTTTA
*
17790178 CTTTATTTCCTTTA
1 TTTTATTTCCTTTA
17790192 TTTTATTTC
1 TTTTATTTC
17790201 TTTTGTTTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
13 4 0.13
14 17 0.57
15 9 0.30
ACGTcount: A:0.18, C:0.14, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTATTTCCTTTA
Found at i:17790369 original size:14 final size:17
Alignment explanation
Indices: 17790350--17790386 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
17790340 ATTTATTTCT
17790350 TAATATAA-T-ATTT-A
1 TAATATAATTAATTTAA
17790364 TAATATAATTAATTTAA
1 TAATATAATTAATTTAA
17790381 TAATAT
1 TAATAT
17790387 CCTTTATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 8 0.40
15 1 0.05
16 4 0.20
17 7 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAATATAATTAATTTAA
Found at i:17792986 original size:24 final size:24
Alignment explanation
Indices: 17792923--17792974 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
17792913 TTTCTATAAG
* * *
17792923 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
17792947 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
17792971 ATTT
1 ATTT
17792975 GACTTTGATT
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:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:17793887 original size:14 final size:14
Alignment explanation
Indices: 17793842--17793889 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
17793832 AGTGGACACC
* *
17793842 TTATAAATTTTTTT
1 TTATAAATTTTATA
*
17793856 TTATAAAAGTTATATA
1 TTAT-AAA-TTTTATA
17793872 TTATAAATTTTATA
1 TTATAAATTTTATA
17793886 TTAT
1 TTAT
17793890 TTTTATCTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 14 0.50
15 6 0.21
16 8 0.29
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (14 bp):
TTATAAATTTTATA
Found at i:17796270 original size:28 final size:28
Alignment explanation
Indices: 17796238--17796299 Score: 124
Period size: 28 Copynumber: 2.2 Consensus size: 28
17796228 AGCCTTTATA
17796238 AAAATTTTAAATTAGTATAGATAAAATT
1 AAAATTTTAAATTAGTATAGATAAAATT
17796266 AAAATTTTAAATTAGTATAGATAAAATT
1 AAAATTTTAAATTAGTATAGATAAAATT
17796294 AAAATT
1 AAAATT
17796300 ATACTTTATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (28 bp):
AAAATTTTAAATTAGTATAGATAAAATT
Found at i:17799911 original size:3 final size:3
Alignment explanation
Indices: 17799877--17799956 Score: 112
Period size: 3 Copynumber: 27.3 Consensus size: 3
17799867 GTACCATTAG
* *
17799877 AGA AG- AGA AG- AGA AGA A-A AGA ACA ATA GAGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA -AGA AGA AGA AGA AGA
17799920 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
17799957 ATTGATGCAC
Statistics
Matches: 70, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
2 6 0.09
3 62 0.89
4 2 0.03
ACGTcount: A:0.66, C:0.01, G:0.31, T:0.01
Consensus pattern (3 bp):
AGA
Found at i:17808798 original size:16 final size:16
Alignment explanation
Indices: 17808777--17808813 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
17808767 TTGGTTCGAT
*
17808777 GTAATGGAATAGATGC
1 GTAATGGAATAGAGGC
17808793 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
17808809 GTAAT
1 GTAAT
17808814 AGCAATTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.05, G:0.32, T:0.24
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:17808857 original size:45 final size:44
Alignment explanation
Indices: 17808793--17808887 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 44
17808783 GAATAGATGC
17808793 GTAATGGAATAGAGGCGTAATAGCAATTCAAT-TGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAG-AATTC-ATGTGTTTGGTTGAAT
* *
17808838 GTAATGGAATAGAGGCGTAATAGTATTCTTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGAATTCATGTGTTTGGTTGAAT
*
17808882 GGAATG
1 GTAATG
17808888 ATGCTATAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 22 0.48
45 23 0.50
ACGTcount: A:0.31, C:0.05, G:0.29, T:0.35
Consensus pattern (44 bp):
GTAATGGAATAGAGGCGTAATAGAATTCATGTGTTTGGTTGAAT
Found at i:17809056 original size:23 final size:23
Alignment explanation
Indices: 17809029--17809088 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
17809019 TAACATCATT
17809029 ATTCTTATATATAATTTAATAAA
1 ATTCTTATATATAATTTAATAAA
* *
17809052 ATTCTTATAT-GAATTTACTAAA
1 ATTCTTATATATAATTTAATAAA
*
17809074 A-TCATAATATATAAT
1 ATTC-TTATATATAAT
17809089 ACTATAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 16 0.52
23 13 0.42
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTCTTATATATAATTTAATAAA
Found at i:17809083 original size:22 final size:21
Alignment explanation
Indices: 17809037--17809122 Score: 56
Period size: 22 Copynumber: 4.2 Consensus size: 21
17809027 TTATTCTTAT
*
17809037 ATATAATTTAATAAAATTCTT
1 ATATAATTTAATAAAATTCTA
*
17809058 ATATGAATTTACTAAAA-TCATA
1 ATAT-AATTTAATAAAATTC-TA
** **
17809080 ATAT-A--TAATACTA-TAAA
1 ATATAATTTAATAAAATTCTA
17809097 ATATAATTTAATAAAATTCTTA
1 ATATAATTTAATAAAATTC-TA
17809119 ATAT
1 ATAT
17809123 TAAATGTTCT
Statistics
Matches: 47, Mismatches: 11, Indels: 13
0.66 0.15 0.18
Matches are distributed among these distances:
17 5 0.11
18 7 0.15
20 7 0.15
21 7 0.15
22 21 0.45
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.42
Consensus pattern (21 bp):
ATATAATTTAATAAAATTCTA
Found at i:17809105 original size:38 final size:39
Alignment explanation
Indices: 17809058--17809182 Score: 134
Period size: 38 Copynumber: 3.3 Consensus size: 39
17809048 TAAAATTCTT
17809058 ATATGAATTTACTAAAATCATAATATATAATACTATAAA
1 ATATGAATTTACTAAAATCATAATATATAATACTATAAA
* * * ***
17809097 ATAT-AATTTAATAAAATTCTTAATAT-TAA-A-TGTTCTG
1 ATATGAATTTACTAAAA-TCATAATATATAATACT-ATAAA
*
17809134 ATATGAATTTACTAAAATCATAATATATAATGCTATAAA
1 ATATGAATTTACTAAAATCATAATATATAATACTATAAA
17809173 ATAT-AATTTA
1 ATATGAATTTA
17809183 ACATAATTAT
Statistics
Matches: 67, Mismatches: 13, Indels: 13
0.72 0.14 0.14
Matches are distributed among these distances:
36 1 0.01
37 14 0.21
38 34 0.51
39 17 0.25
40 1 0.01
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (39 bp):
ATATGAATTTACTAAAATCATAATATATAATACTATAAA
Found at i:17811151 original size:13 final size:13
Alignment explanation
Indices: 17811133--17811162 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
17811123 AGTCATGTTT
*
17811133 AACAAGGAAATCA
1 AACAAGAAAATCA
17811146 AACAAGAAAATCA
1 AACAAGAAAATCA
17811159 AACA
1 AACA
17811163 TGCAATACAA
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:0.67, C:0.17, G:0.10, T:0.07
Consensus pattern (13 bp):
AACAAGAAAATCA
Found at i:17812226 original size:42 final size:42
Alignment explanation
Indices: 17812167--17812259 Score: 168
Period size: 42 Copynumber: 2.2 Consensus size: 42
17812157 TTTACAAACG
* *
17812167 AAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGTAA
1 AAAACGCCGCTAAAGACCATGTTCTTTAGAGGCGCTTAGAAA
17812209 AAAACGCCGCTAAAGACCATGTTCTTTAGAGGCGCTTAGAAA
1 AAAACGCCGCTAAAGACCATGTTCTTTAGAGGCGCTTAGAAA
17812251 AAAACGCCG
1 AAAACGCCG
17812260 TTTTTTCTTA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (42 bp):
AAAACGCCGCTAAAGACCATGTTCTTTAGAGGCGCTTAGAAA
Found at i:17812317 original size:42 final size:43
Alignment explanation
Indices: 17812260--17812433 Score: 266
Period size: 42 Copynumber: 4.1 Consensus size: 43
17812250 AAAAACGCCG
17812260 TTTTTTCTTAAGCGCCTCTAAAGAACATGTTCTTTAGCGGCGT
1 TTTTTTCTTAAGCGCCTCTAAAGAACATGTTCTTTAGCGGCGT
* * *
17812303 TTTTTTC-TAAGCGCCTCTAAAGAATATGGTCTTTAACGGCGT
1 TTTTTTCTTAAGCGCCTCTAAAGAACATGTTCTTTAGCGGCGT
17812345 TTTTTTC-TAAGCGCCTCTAAAGAACATGTTCTTTAGCGGCG-
1 TTTTTTCTTAAGCGCCTCTAAAGAACATGTTCTTTAGCGGCGT
* * *
17812386 TTTTTTCTTAAGCGCCGCTAAAGAATATG-TCTTTAGCCGCGT
1 TTTTTTCTTAAGCGCCTCTAAAGAACATGTTCTTTAGCGGCGT
17812428 TTTTTT
1 TTTTTT
17812434 ACAAAAACGC
Statistics
Matches: 120, Mismatches: 9, Indels: 5
0.90 0.07 0.04
Matches are distributed among these distances:
41 18 0.15
42 95 0.79
43 7 0.06
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.40
Consensus pattern (43 bp):
TTTTTTCTTAAGCGCCTCTAAAGAACATGTTCTTTAGCGGCGT
Found at i:17812776 original size:21 final size:21
Alignment explanation
Indices: 17812747--17812791 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
17812737 CTCTGCTCTA
*
17812747 CTTCTCTCGCTGCAGCCTCCG
1 CTTCCCTCGCTGCAGCCTCCG
* *
17812768 CTTCCCTCGCTGCCGCCTCTG
1 CTTCCCTCGCTGCAGCCTCCG
17812789 CTT
1 CTT
17812792 TAAGTTGTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.02, C:0.49, G:0.18, T:0.31
Consensus pattern (21 bp):
CTTCCCTCGCTGCAGCCTCCG
Found at i:17818273 original size:25 final size:25
Alignment explanation
Indices: 17818205--17818343 Score: 131
Period size: 25 Copynumber: 5.5 Consensus size: 25
17818195 ATTCTTTAAG
* **
17818205 AATTATGTAACTGCTGTATTATGAA
1 AATTATGTAAGTTATGTATTATGAA
17818230 GAATTATGCT-AGTTATGTATTATGAA
1 -AATTATG-TAAGTTATGTATTATGAA
* *
17818256 AATTATGTAAGCTGTGTACTGTAT--A
1 AATTATGTAAGTTATGTA-T-TATGAA
* * *
17818281 AGTTATGTAAGTTTTATATTATGAA
1 AATTATGTAAGTTATGTATTATGAA
**
17818306 AATTAAATAAGTTATGTATTATGAA
1 AATTATGTAAGTTATGTATTATGAA
17818331 AATTATGTAAGTT
1 AATTATGTAAGTT
17818344 CAATATTATG
Statistics
Matches: 91, Mismatches: 16, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
23 3 0.03
24 2 0.02
25 61 0.67
26 21 0.23
27 4 0.04
ACGTcount: A:0.37, C:0.04, G:0.17, T:0.42
Consensus pattern (25 bp):
AATTATGTAAGTTATGTATTATGAA
Found at i:17818350 original size:25 final size:24
Alignment explanation
Indices: 17818221--17818362 Score: 85
Period size: 25 Copynumber: 5.7 Consensus size: 24
17818211 GTAACTGCTG
*
17818221 TATTATGAAGAATTATGCT-AGTTATG
1 TATTATGAA-AATTATG-TAAGTTA-A
*
17818247 TATTATGAAAATTATGTAAGCTGT-G
1 TATTATGAAAATTATGTAAG-T-TAA
* *
17818272 TACTGTAT--AAGTTATGTAAGTTTTA
1 TA-T-TATGAAAATTATGTAAG-TTAA
** *
17818297 TATTATGAAAATTAAATAAGTTATG
1 TATTATGAAAATTATGTAAGTTA-A
17818322 TATTATGAAAATTATGTAAGTTCAA
1 TATTATGAAAATTATGTAAGTT-AA
* *
17818347 TATTATGTAAGTTATG
1 TATTATGAAAATTATG
17818363 AATTACGAAA
Statistics
Matches: 93, Mismatches: 13, Indels: 21
0.73 0.10 0.17
Matches are distributed among these distances:
23 3 0.03
24 5 0.05
25 69 0.74
26 12 0.13
27 4 0.04
ACGTcount: A:0.38, C:0.03, G:0.16, T:0.43
Consensus pattern (24 bp):
TATTATGAAAATTATGTAAGTTAA
Found at i:17818358 original size:41 final size:42
Alignment explanation
Indices: 17818304--17818424 Score: 154
Period size: 41 Copynumber: 2.9 Consensus size: 42
17818294 TTATATTATG
**
17818304 AAAATTAAATAAGTTATGTATTATGAAAATTATGTAAGTTC-
1 AAAATTATGTAAGTTATGTATTATGAAAATTATGTAAGTTCA
* * * *
17818345 AATATTATGTAAGTTATGAATTACGAAAATTATGCAAGTTCA
1 AAAATTATGTAAGTTATGTATTATGAAAATTATGTAAGTTCA
* * *
17818387 AAAATTATGTAAGCTATGTATTATGAAATTTAAGTAAG
1 AAAATTATGTAAGTTATGTATTATGAAAATTATGTAAG
17818425 CTGTGTATTG
Statistics
Matches: 66, Mismatches: 13, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
41 35 0.53
42 31 0.47
ACGTcount: A:0.45, C:0.04, G:0.14, T:0.37
Consensus pattern (42 bp):
AAAATTATGTAAGTTATGTATTATGAAAATTATGTAAGTTCA
Found at i:17818367 original size:16 final size:15
Alignment explanation
Indices: 17818330--17818359 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
17818320 TGTATTATGA
17818330 AAATTATGTAAGTTC
1 AAATTATGTAAGTTC
17818345 AATATTATGTAAGTT
1 AA-ATTATGTAAGTT
17818360 ATGAATTACG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 2 0.14
16 12 0.86
ACGTcount: A:0.40, C:0.03, G:0.13, T:0.43
Consensus pattern (15 bp):
AAATTATGTAAGTTC
Found at i:17819188 original size:17 final size:17
Alignment explanation
Indices: 17819168--17819203 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
17819158 GAGTCTTGAA
17819168 CATGGGTATTTATCTAG
1 CATGGGTATTTATCTAG
*
17819185 CATGTGTATTTATCTAG
1 CATGGGTATTTATCTAG
17819202 CA
1 CA
17819204 CGGTTTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.42
Consensus pattern (17 bp):
CATGGGTATTTATCTAG
Found at i:17822545 original size:14 final size:14
Alignment explanation
Indices: 17822526--17822555 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
17822516 TTATATAAAA
*
17822526 TAGTTTGATTCAAT
1 TAGTTTGATCCAAT
17822540 TAGTTTGATCCAAT
1 TAGTTTGATCCAAT
17822554 TA
1 TA
17822556 AATTATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.47
Consensus pattern (14 bp):
TAGTTTGATCCAAT
Found at i:17830541 original size:13 final size:13
Alignment explanation
Indices: 17830523--17830554 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
17830513 AAGTATTGAA
*
17830523 ATTTTAATTTTAG
1 ATTTTAATTTTAC
17830536 ATTTTAATTTTAC
1 ATTTTAATTTTAC
17830549 ATTTTA
1 ATTTTA
17830555 GAAATAATTA
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:0.31, C:0.03, G:0.03, T:0.62
Consensus pattern (13 bp):
ATTTTAATTTTAC
Found at i:17830562 original size:19 final size:19
Alignment explanation
Indices: 17830522--17830563 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
17830512 TAAGTATTGA
**
17830522 AATTTTAATTTTAGATTTT
1 AATTTTAATTTTAGATAAT
17830541 AATTTTACATTTTAGA-AAT
1 AATTTTA-ATTTTAGATAAT
17830560 AATT
1 AATT
17830564 ATATAGATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (19 bp):
AATTTTAATTTTAGATAAT
Found at i:17832776 original size:17 final size:19
Alignment explanation
Indices: 17832756--17832797 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
17832746 GATAACTAAG
*
17832756 ATAAAT-AAAA-TAGAATA
1 ATAAATAAAAATTAGAACA
17832773 ATAAATCAAAAATTAGAACA
1 ATAAAT-AAAAATTAGAACA
17832793 ATAAA
1 ATAAA
17832798 GAAGCAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 6 0.29
19 4 0.19
20 11 0.52
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.21
Consensus pattern (19 bp):
ATAAATAAAAATTAGAACA
Found at i:17836457 original size:37 final size:37
Alignment explanation
Indices: 17836416--17836603 Score: 176
Period size: 37 Copynumber: 5.1 Consensus size: 37
17836406 ATGATAATAA
17836416 TTTTTGAAAACAC-AAAATTTTTGAAACAC-AAGAATCTT
1 TTTTTGAAAACACGAAAATTTTTGAAACACGAA-AA--TT
* * *
17836454 TTTTTGAAAACACGAGATTTTTTGAAGCACGAAAATT
1 TTTTTGAAAACACGAAAATTTTTGAAACACGAAAATT
* **
17836491 TTTTTTAAAACGTGAAAATTTTTTGAAACACGAAAA-T
1 TTTTTGAAAACACGAAAA-TTTTTGAAACACGAAAATT
* *
17836528 TTTTTGAAAACGCGAAAATTTTT-AAACACGAGAATTT
1 TTTTTGAAAACACGAAAATTTTTGAAACACGA-AAATT
* *
17836565 TTTTTG-AAACATGGAAAA-TTTTAAAACACG--AATT
1 TTTTTGAAAACA-CGAAAATTTTTGAAACACGAAAATT
17836599 TTTTT
1 TTTTT
17836604 CTTTTTTTTT
Statistics
Matches: 128, Mismatches: 15, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
34 8 0.06
35 8 0.06
36 15 0.12
37 51 0.40
38 29 0.23
39 15 0.12
40 2 0.02
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (37 bp):
TTTTTGAAAACACGAAAATTTTTGAAACACGAAAATT
Found at i:17836474 original size:18 final size:18
Alignment explanation
Indices: 17836453--17836586 Score: 114
Period size: 19 Copynumber: 7.2 Consensus size: 18
17836443 ACAAGAATCT
*
17836453 TTTTTTGAAAACACG-AGA
1 TTTTTTG-AAACACGAAAA
*
17836471 TTTTTTGAAGCACGAAAA
1 TTTTTTGAAACACGAAAA
*
17836489 TTTTTTTTAAA-ACGTGAAAA
1 -TTTTTTGAAACAC--GAAAA
17836509 TTTTTTGAAACACGAAAA
1 TTTTTTGAAACACGAAAA
*
17836527 TTTTTTGAAAACGCGAAAA
1 TTTTTTG-AAACACGAAAA
*
17836546 -TTTTT-AAACACGAGAATT
1 TTTTTTGAAACACGA-AA-A
*
17836564 TTTTTTGAAACATGGAAAA
1 TTTTTTGAAACA-CGAAAA
17836583 TTTT
1 TTTT
17836587 AAAACACGAA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
16 7 0.07
17 8 0.08
18 28 0.29
19 36 0.38
20 14 0.15
21 2 0.02
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (18 bp):
TTTTTTGAAACACGAAAA
Found at i:17836474 original size:38 final size:39
Alignment explanation
Indices: 17836416--17836586 Score: 182
Period size: 38 Copynumber: 4.6 Consensus size: 39
17836406 ATGATAATAA
17836416 TTTTTGAAAACAC-AAAA-TTTTTGAAACAC-AAGAATCTT
1 TTTTTGAAAACACGAAAATTTTTTGAAACACGAA-AAT-TT
* *
17836454 TTTTTGAAAACACG-AGATTTTTTGAAGCACGAAAATTT
1 TTTTTGAAAACACGAAAATTTTTTGAAACACGAAAATTT
**
17836492 TTTTT-AAAACGTGAAAATTTTTTGAAACACGAAAA--T
1 TTTTTGAAAACACGAAAATTTTTTGAAACACGAAAATTT
* *
17836528 TTTTTGAAAACGCGAAAA-TTTTT-AAACACGAGAATTT
1 TTTTTGAAAACACGAAAATTTTTTGAAACACGAAAATTT
*
17836565 TTTTTG-AAACATGGAAAATTTT
1 TTTTTGAAAACA-CGAAAATTTT
17836587 AAAACACGAA
Statistics
Matches: 114, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
35 10 0.09
36 15 0.13
37 29 0.25
38 44 0.39
39 14 0.12
40 2 0.02
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (39 bp):
TTTTTGAAAACACGAAAATTTTTTGAAACACGAAAATTT
Found at i:17837443 original size:13 final size:13
Alignment explanation
Indices: 17837414--17837471 Score: 52
Period size: 12 Copynumber: 4.7 Consensus size: 13
17837404 TGATATATTT
*
17837414 TTTCTTTTTTTTC
1 TTTCTTTCTTTTC
17837427 -TTCTTTCTTTTC
1 TTTCTTTCTTTTC
*
17837439 TTTCTCT-TTTTC
1 TTTCTTTCTTTTC
*
17837451 -TTCTCTCTTTT-
1 TTTCTTTCTTTTC
17837462 TCTTCTTTCT
1 T-TTCTTTCT
17837472 CTTCGGGCCG
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
11 6 0.16
12 20 0.53
13 12 0.32
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTCTTTCTTTTC
Done.