Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 176 of 213
Found at i:53057368 original size:60 final size:60
Alignment explanation
Indices: 53057304--53057423 Score: 224
Period size: 60 Copynumber: 2.0 Consensus size: 60
53057294 AGAAGCCATG
53057304 CCCTCCCCTTCCTAAGCTACCTCCTCTTCCC-AAGATTCCTCCCAAGTATTTCCACCACCA
1 CCCTCCCCTTCCTAAGCTACCTCCTC-TCCCTAAGATTCCTCCCAAGTATTTCCACCACCA
53057364 CCCTCCCCTTCCTAAGCTACCTCCTCTCCCTAAGATTCCTCCCAAGTATTTCCACCACCA
1 CCCTCCCCTTCCTAAGCTACCTCCTCTCCCTAAGATTCCTCCCAAGTATTTCCACCACCA
53057424 TCCCAAGTTC
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
59 4 0.07
60 55 0.93
ACGTcount: A:0.20, C:0.48, G:0.05, T:0.27
Consensus pattern (60 bp):
CCCTCCCCTTCCTAAGCTACCTCCTCTCCCTAAGATTCCTCCCAAGTATTTCCACCACCA
Found at i:53062614 original size:29 final size:29
Alignment explanation
Indices: 53062531--53062618 Score: 97
Period size: 29 Copynumber: 3.0 Consensus size: 29
53062521 GTTTAGAGGG
** *
53062531 TCTGAAAAAATAA-TTTGTACAAGATGGAT
1 TCTGAAAAAATAATTTTG-AGGAGATGGGT
* *
53062560 TCTGAAAAAATAGTTTTGAGGGGATGGGT
1 TCTGAAAAAATAATTTTGAGGAGATGGGT
* *
53062589 TCTGAAGAAATAATTTTGATGAGATGGGT
1 TCTGAAAAAATAATTTTGAGGAGATGGGT
53062618 T
1 T
53062619 GAGTTTTGTA
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
29 45 0.92
30 4 0.08
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.33
Consensus pattern (29 bp):
TCTGAAAAAATAATTTTGAGGAGATGGGT
Found at i:53073253 original size:26 final size:28
Alignment explanation
Indices: 53073224--53073280 Score: 91
Period size: 26 Copynumber: 2.1 Consensus size: 28
53073214 TTGAGCTTTG
53073224 ACTATTAGCATAGCAACTAACT-AC-TA
1 ACTATTAGCATAGCAACTAACTGACTTA
*
53073250 ACTATTAGCATAGCAGCTAACTGACTTA
1 ACTATTAGCATAGCAACTAACTGACTTA
53073278 ACT
1 ACT
53073281 GACTTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
26 21 0.75
27 2 0.07
28 5 0.18
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.28
Consensus pattern (28 bp):
ACTATTAGCATAGCAACTAACTGACTTA
Found at i:53081485 original size:5 final size:5
Alignment explanation
Indices: 53081477--53081526 Score: 73
Period size: 5 Copynumber: 10.0 Consensus size: 5
53081467 TTCTTTTTAG
* * *
53081477 AATTT AATTT AATTT AATTT AATTT AATTT AATTT GATTT GATTT GATTT
1 AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATTT
53081527 TCTTTTACTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (5 bp):
AATTT
Found at i:53083066 original size:16 final size:18
Alignment explanation
Indices: 53083037--53083069 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
53083027 AGTTAAATTT
53083037 ATTATCATACTAATTAAA
1 ATTATCATACTAATTAAA
53083055 ATTAT-ATA-TAATTAA
1 ATTATCATACTAATTAA
53083070 TGAAAGGCCG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTATCATACTAATTAAA
Found at i:53085795 original size:19 final size:19
Alignment explanation
Indices: 53085763--53085815 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
53085753 ACCATTGTTC
*
53085763 TTTTTT-TCATTTTTGAGT
1 TTTTTTATCAATTTTGAGT
*
53085781 TTTTTTATCAATTTT-TGT
1 TTTTTTATCAATTTTGAGT
*
53085799 TTTTTTAATCTATTTTG
1 TTTTTT-ATCAATTTTG
53085816 TCTAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 14 0.48
19 15 0.52
ACGTcount: A:0.15, C:0.06, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTTTATCAATTTTGAGT
Found at i:53085816 original size:18 final size:18
Alignment explanation
Indices: 53085757--53085805 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 18
53085747 CTATTAACCA
*
53085757 TTGTTCTTTTTTTC-ATTT
1 TTGTT-TTTTTATCAATTT
53085775 TTGAGTTTTTTTATCAATTT
1 TT--GTTTTTTTATCAATTT
53085795 TTGTTTTTTTA
1 TTGTTTTTTTA
53085806 ATCTATTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 11 0.41
19 7 0.26
20 9 0.33
ACGTcount: A:0.12, C:0.06, G:0.08, T:0.73
Consensus pattern (18 bp):
TTGTTTTTTTATCAATTT
Found at i:53091773 original size:63 final size:63
Alignment explanation
Indices: 53091693--53091816 Score: 185
Period size: 63 Copynumber: 2.0 Consensus size: 63
53091683 TTACAACTCT
* * *
53091693 ATTCTATTATAGCTTTATTCCATTCCAGTAAACCAAACATACCGTTAGAGAATGAATCCACAC
1 ATTCTATTACAGCTTTATTCCATTCCAGTAAACCAAACATACCATTAGAGAATGAAGCCACAC
* * * *
53091756 ATTCTATTACAGTTTTATTTCATTCCAGTGAACCAAACATGCCATTAGAGAATGAAGCCAC
1 ATTCTATTACAGCTTTATTCCATTCCAGTAAACCAAACATACCATTAGAGAATGAAGCCAC
53091817 GCACCCCATC
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
63 54 1.00
ACGTcount: A:0.35, C:0.23, G:0.11, T:0.31
Consensus pattern (63 bp):
ATTCTATTACAGCTTTATTCCATTCCAGTAAACCAAACATACCATTAGAGAATGAAGCCACAC
Found at i:53096842 original size:44 final size:45
Alignment explanation
Indices: 53096754--53096851 Score: 144
Period size: 44 Copynumber: 2.2 Consensus size: 45
53096744 AAGACTTGTA
* **
53096754 TCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTT
1 TCTTCGATCTACTTCACCACCAATACAGGAAGACAAGATCTGCTT
* *
53096799 TCTTCGATCTACTTCA-CGCCAATACATGAAGACAAGATCTGCTT
1 TCTTCGATCTACTTCACCACCAATACAGGAAGACAAGATCTGCTT
53096843 TCTTCGATC
1 TCTTCGATC
53096852 AATTCTACTG
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 32 0.67
45 16 0.33
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.31
Consensus pattern (45 bp):
TCTTCGATCTACTTCACCACCAATACAGGAAGACAAGATCTGCTT
Found at i:53097148 original size:45 final size:44
Alignment explanation
Indices: 53097096--53097523 Score: 195
Period size: 45 Copynumber: 9.6 Consensus size: 44
53097086 TACATGAAAA
*
53097096 CAAGATCTGCTTTCTTTGATTTGCTTCGCCACGAATATGGGTAGG
1 CAAGATCTGCTTTCTTTGATCTGCTTCGCCAC-AATATGGGTAGG
* * * * * *** * *
53097141 CAAGATCTGGTATCTCTGATCTACTTCACGC-CAATACATGAAGA
1 CAAGATCTGCTTTCTTTGATCTGCTTCGC-CACAATATGGGTAGG
* * *
53097185 CAATATCTGCTTTCTTTGATCTGCTCCGCCACCAGTATGGGTAGG
1 CAAGATCTGCTTTCTTTGATCTGCTTCGCCA-CAATATGGGTAGG
* * * * *** * *
53097230 CAAGATCTAG-TATCTCTGATCTACTTCACGC-CAATACATGAAGA
1 CAAGATCT-GCTTTCTTTGATCTGCTTCGC-CACAATATGGGTAGG
* * * *
53097274 CAAGATTTGCTTTCTTTGATCTGCTCCGCCACCAGTATGGGAAGG
1 CAAGATCTGCTTTCTTTGATCTGCTTCGCCA-CAATATGGGTAGG
* * * * * * *
53097319 CAAGATCTGGTATCTCTGATCTACTTTACGCCA-ATACAT--GAAGA
1 CAAGATCTGCTTTCTTTGATCTGC-TT-CGCCACA-ATATGGGTAGG
* * * *
53097363 CAAGATCTGCTTTCTTTGATCTACTCCGCCACCAGTATGGGAAGG
1 CAAGATCTGCTTTCTTTGATCTGCTTCGCCA-CAATATGGGTAGG
* * * * * *** * **
53097408 CAAGATCTGGTATCTCTGATCTACTTCACGC-CAATACATGAAAA
1 CAAGATCTGCTTTCTTTGATCTGCTTCGC-CACAATATGGGTAGG
* * *
53097452 CAAGATCTGCTTTCTTTGATCTGCTCCGCCACCAGTATGGGAAGG
1 CAAGATCTGCTTTCTTTGATCTGCTTCGCCA-CAATATGGGTAGG
* * * *
53097497 CAAGATCTGGTATCTATGATCTACTTC
1 CAAGATCTGCTTTCTTTGATCTGCTTC
53097524 ACGCCAGTAC
Statistics
Matches: 274, Mismatches: 91, Indels: 36
0.68 0.23 0.09
Matches are distributed among these distances:
42 5 0.02
43 7 0.03
44 113 0.41
45 137 0.50
46 7 0.03
47 5 0.02
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (44 bp):
CAAGATCTGCTTTCTTTGATCTGCTTCGCCACAATATGGGTAGG
Found at i:53097215 original size:89 final size:89
Alignment explanation
Indices: 53097086--53097557 Score: 784
Period size: 89 Copynumber: 5.3 Consensus size: 89
53097076 TTCACACCGG
* * * * * *
53097086 TACATGAAAACAAGATCTGCTTTCTTTGATTTGCTTCGCCACGAATATGGGTAGGCAAGATCTGG
1 TACATGAAGACAAGATCTGCTTTCTTTGATCTGCTCCGCCACCAGTATGGGAAGGCAAGATCTGG
53097151 TATCTCTGATCTACTTCACGCCAA
66 TATCTCTGATCTACTTCACGCCAA
* * *
53097175 TACATGAAGACAATATCTGCTTTCTTTGATCTGCTCCGCCACCAGTATGGGTAGGCAAGATCTAG
1 TACATGAAGACAAGATCTGCTTTCTTTGATCTGCTCCGCCACCAGTATGGGAAGGCAAGATCTGG
53097240 TATCTCTGATCTACTTCACGCCAA
66 TATCTCTGATCTACTTCACGCCAA
*
53097264 TACATGAAGACAAGATTTGCTTTCTTTGATCTGCTCCGCCACCAGTATGGGAAGGCAAGATCTGG
1 TACATGAAGACAAGATCTGCTTTCTTTGATCTGCTCCGCCACCAGTATGGGAAGGCAAGATCTGG
*
53097329 TATCTCTGATCTACTTTACGCCAA
66 TATCTCTGATCTACTTCACGCCAA
*
53097353 TACATGAAGACAAGATCTGCTTTCTTTGATCTACTCCGCCACCAGTATGGGAAGGCAAGATCTGG
1 TACATGAAGACAAGATCTGCTTTCTTTGATCTGCTCCGCCACCAGTATGGGAAGGCAAGATCTGG
53097418 TATCTCTGATCTACTTCACGCCAA
66 TATCTCTGATCTACTTCACGCCAA
*
53097442 TACATGAAAACAAGATCTGCTTTCTTTGATCTGCTCCGCCACCAGTATGGGAAGGCAAGATCTGG
1 TACATGAAGACAAGATCTGCTTTCTTTGATCTGCTCCGCCACCAGTATGGGAAGGCAAGATCTGG
* *
53097507 TATCTATGATCTACTTCACGCCAG
66 TATCTCTGATCTACTTCACGCCAA
*
53097531 TACATGAAGACATGATCTG-TTATCTTT
1 TACATGAAGACAAGATCTGCTT-TCTTT
53097558 CAACCTGCTC
Statistics
Matches: 361, Mismatches: 21, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
88 2 0.01
89 359 0.99
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (89 bp):
TACATGAAGACAAGATCTGCTTTCTTTGATCTGCTCCGCCACCAGTATGGGAAGGCAAGATCTGG
TATCTCTGATCTACTTCACGCCAA
Found at i:53107018 original size:20 final size:20
Alignment explanation
Indices: 53106993--53107031 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
53106983 TACTTTCTTC
53106993 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
53107013 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
53107032 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:53113902 original size:20 final size:21
Alignment explanation
Indices: 53113860--53113903 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
53113850 AACATCTTTC
**
53113860 TTTTATCTTTTATTTACTTAA
1 TTTTATCTTTTATTTACCAAA
53113881 TTTT-TCTTTTATTTACCAAA
1 TTTTATCTTTTATTTACCAAA
53113901 TTT
1 TTT
53113904 CTACTTTAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.23, C:0.11, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTATCTTTTATTTACCAAA
Found at i:53119811 original size:26 final size:26
Alignment explanation
Indices: 53119781--53119838 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
53119771 AGCTCATCAA
53119781 ACCAAACATAAAATTCAAAAGCACAT
1 ACCAAACATAAAATTCAAAAGCACAT
53119807 ACCAAACATAAAATTCAAAAGCACAT
1 ACCAAACATAAAATTCAAAAGCACAT
53119833 ACCAAA
1 ACCAAA
53119839 TCAACCATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.59, C:0.24, G:0.03, T:0.14
Consensus pattern (26 bp):
ACCAAACATAAAATTCAAAAGCACAT
Found at i:53120939 original size:19 final size:20
Alignment explanation
Indices: 53120902--53120939 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
53120892 CTTTCTTTTA
53120902 TCTTTTATATACTTAAATTT
1 TCTTTTATATACTTAAATTT
*
53120922 TCTTTTATTTAC-TAAATT
1 TCTTTTATATACTTAAATT
53120940 ACTACTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.61
Consensus pattern (20 bp):
TCTTTTATATACTTAAATTT
Found at i:53128080 original size:25 final size:24
Alignment explanation
Indices: 53128023--53128085 Score: 72
Period size: 26 Copynumber: 2.5 Consensus size: 24
53128013 TCTGAGCGTG
53128023 CCGTATATAGCTCTTTGTGAGCTTA
1 CCGT-TATAGCTCTTTGTGAGCTTA
* *
53128048 TCGATTATAGCCTCTTTGTGAGCTTC
1 CCG-TTATAG-CTCTTTGTGAGCTTA
*
53128074 CCGTTATTGCTC
1 CCGTTATAGCTC
53128086 ACTTGAACTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
24 3 0.09
25 12 0.38
26 17 0.53
ACGTcount: A:0.16, C:0.24, G:0.19, T:0.41
Consensus pattern (24 bp):
CCGTTATAGCTCTTTGTGAGCTTA
Found at i:53130411 original size:28 final size:28
Alignment explanation
Indices: 53130358--53130411 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
53130348 CTCTTTCCTT
* *
53130358 TTGTCCTAGCGGACTTACATTGTGTTTA
1 TTGTCCCAGCGGACTTACATTCTGTTTA
53130386 TTGTCCCAGCGGACTT-CATCTCTGTT
1 TTGTCCCAGCGGACTTACAT-TCTGTT
53130412 CCGTTTTTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 3 0.13
28 20 0.87
ACGTcount: A:0.15, C:0.24, G:0.20, T:0.41
Consensus pattern (28 bp):
TTGTCCCAGCGGACTTACATTCTGTTTA
Found at i:53149103 original size:34 final size:34
Alignment explanation
Indices: 53149015--53149111 Score: 108
Period size: 34 Copynumber: 2.9 Consensus size: 34
53149005 GGACCTCTCG
* * *
53149015 TGTTTATTGTCCCGACAGACTTA-CTTTATTCCG
1 TGTTTATTGTCCTGACAGACTTATCTCTATTCCA
* * *
53149048 TATTTATTATCCTTGA-GGACTTATCTCTATTCCA
1 TGTTTATTGTCC-TGACAGACTTATCTCTATTCCA
*
53149082 TGTTTACTGTCCTGACAGACTTATCTCTAT
1 TGTTTATTGTCCTGACAGACTTATCTCTAT
53149112 GGATGCTATG
Statistics
Matches: 51, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
33 19 0.37
34 32 0.63
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.44
Consensus pattern (34 bp):
TGTTTATTGTCCTGACAGACTTATCTCTATTCCA
Found at i:53152133 original size:33 final size:32
Alignment explanation
Indices: 53152096--53152178 Score: 96
Period size: 33 Copynumber: 2.5 Consensus size: 32
53152086 ATTGTCATGG
* *
53152096 CCCAGCCATGGTCTTACATTCGTACA-GCCATAA
1 CCCAGCTATGGTCTTACATTAG-A-ATGCCATAA
*
53152129 CCCAGTTATGGTCTTATCATTAGAATGCCATAA
1 CCCAGCTATGGTCTTA-CATTAGAATGCCATAA
*
53152162 CCCAGCTATAGTCTTAC
1 CCCAGCTATGGTCTTAC
53152179 TTATAAATAC
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
32 2 0.05
33 36 0.84
34 5 0.12
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (32 bp):
CCCAGCTATGGTCTTACATTAGAATGCCATAA
Found at i:53152269 original size:101 final size:101
Alignment explanation
Indices: 53152088--53152313 Score: 254
Period size: 101 Copynumber: 2.2 Consensus size: 101
53152078 ACACATGCAT
* * * ** ** * * * *
53152088 TGTCATGGCCCAGCCATGGTCTTACATTCGTACAGCCATAACCCAGTTATGGTCTTATCATTAGA
1 TGTCATGGTCCAACCATGGTCTTACGTTCAAAGTGTCATAACCCAATTATGCTCTTATCATTAAA
* *
53152153 ATGCCATAACCCAGCTATAGTCTTACTTATAAATAC
66 ATGCCATAACCCAGCTATAGTCTTACATATAAACAC
* * * *
53152189 TGTCATGGTCCAACCATTGTCTTACGTTCAAAGTGTCATAATCCAATTATGCTCTTTTTATTAAA
1 TGTCATGGTCCAACCATGGTCTTACGTTCAAAGTGTCATAACCCAATTATGCTCTTATCATTAAA
* * * * *
53152254 ATGTCATATCCCAGCTATGGTTTTACATATAAACAT
66 ATGCCATAACCCAGCTATAGTCTTACATATAAACAC
53152290 TGTCATGGTCCAACCATGGTCTTA
1 TGTCATGGTCCAACCATGGTCTTA
53152314 TTCGTCAATT
Statistics
Matches: 102, Mismatches: 23, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
101 102 1.00
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (101 bp):
TGTCATGGTCCAACCATGGTCTTACGTTCAAAGTGTCATAACCCAATTATGCTCTTATCATTAAA
ATGCCATAACCCAGCTATAGTCTTACATATAAACAC
Found at i:53159693 original size:33 final size:33
Alignment explanation
Indices: 53159656--53159797 Score: 90
Period size: 33 Copynumber: 4.2 Consensus size: 33
53159646 AACCTAGTTG
*
53159656 TGGTCTTATCATCAAAATGTCATAGCCCAACTA
1 TGGTCTTATCATCAAAATGCCATAGCCCAACTA
* ** * *
53159689 TGGTCTTACTTAT-AAATACTATCATAGTCCAACCA
1 TGGTCTTA-TCATCAAA-A-TGCCATAGCCCAACTA
* * * **
53159724 TGGTCTTA-CATTCAAAGTGCCATAACTCAGTTA
1 TGGTCTTATCA-TCAAAATGCCATAGCCCAACTA
* * * **
53159757 TGGTCTTTTCATTAAAATGCCACAGCCCAGGTA
1 TGGTCTTATCATCAAAATGCCATAGCCCAACTA
53159790 TGGTCTTA
1 TGGTCTTA
53159798 CATATAGACA
Statistics
Matches: 81, Mismatches: 22, Indels: 12
0.70 0.19 0.10
Matches are distributed among these distances:
33 50 0.62
34 7 0.09
35 24 0.30
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (33 bp):
TGGTCTTATCATCAAAATGCCATAGCCCAACTA
Found at i:53159761 original size:101 final size:101
Alignment explanation
Indices: 53159622--53159832 Score: 255
Period size: 101 Copynumber: 2.1 Consensus size: 101
53159612 TCGCTCAAAG
** * * * *
53159622 ATGGTCTTACATTCGTAGTGTCATAACCTAGTTGTGGTCTTATCATCAAAATGTCATAGCCCAAC
1 ATGGTCTTACATTCAAAGTGCCATAACCTAGTTATGGTCTTATCATCAAAATGCCACAGCCCAAC
* *
53159687 TATGGTCTTACTTATAAATACTATC-ATAGTCCAACC
66 TATGGTCTTACATATAAACA-TATCTATAGTCCAACC
* * *
53159723 ATGGTCTTACATTCAAAGTGCCATAA-CTCAGTTATGGTCTTTTCATTAAAATGCCACAGCCCAG
1 ATGGTCTTACATTCAAAGTGCCATAACCT-AGTTATGGTCTTATCATCAAAATGCCACAGCCCAA
* * * *
53159787 GTATGGTCTTACATATAGACATTTCTATGGTCCAACC
65 CTATGGTCTTACATATAAACATATCTATAGTCCAACC
53159824 ATGGTCTTA
1 ATGGTCTTA
53159833 TCCGTCAATT
Statistics
Matches: 93, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
100 5 0.05
101 88 0.95
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (101 bp):
ATGGTCTTACATTCAAAGTGCCATAACCTAGTTATGGTCTTATCATCAAAATGCCACAGCCCAAC
TATGGTCTTACATATAAACATATCTATAGTCCAACC
Found at i:53160545 original size:17 final size:18
Alignment explanation
Indices: 53160523--53160563 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
53160513 ACCTAGTTGT
*
53160523 AAAAATCTCAA-AAATAA
1 AAAAATATCAAGAAATAA
53160540 AAAAATATCAAGAAATAA
1 AAAAATATCAAGAAATAA
53160558 ACAAAA
1 A-AAAA
53160564 ATTGAACTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.48
18 7 0.33
19 4 0.19
ACGTcount: A:0.73, C:0.10, G:0.02, T:0.15
Consensus pattern (18 bp):
AAAAATATCAAGAAATAA
Found at i:53170449 original size:142 final size:142
Alignment explanation
Indices: 53170193--53170472 Score: 497
Period size: 142 Copynumber: 2.0 Consensus size: 142
53170183 TTTTGGGTGG
* * *
53170193 AAGATATCTGCAAGTTTATGAATGATTTTTATTTGGACAATTTTACGGAGCAATAAAAACTACAC
1 AAGATATCTGCAAGTTTATGAATGATTTTTATTCGAACAATTTTACAGAGCAATAAAAACTACAC
* * * *
53170258 ATGAAGATTCAATTGGAGTTTTTTCAACTTGATGCTTATCAAAGCACAGAGTTGTAGAAAGCTAC
66 ATGAAGATTCAATTGGAGTATTTTCAACTTGATGATCATCAAAGCACAGAGTTGCAGAAAGCTAC
53170323 TACAGTTGCAGA
131 TACAGTTGCAGA
53170335 AAGATATCTGCAAGTTTATGAATGATTTTTATTCGAACAATTTTACAGAGCAATAAAAACTACAC
1 AAGATATCTGCAAGTTTATGAATGATTTTTATTCGAACAATTTTACAGAGCAATAAAAACTACAC
53170400 ATGAAGATTCAATTGGAGTATTTTCAACTTGATGATCATCAAAGCACAGAGTTGCAGAAAGCTAC
66 ATGAAGATTCAATTGGAGTATTTTCAACTTGATGATCATCAAAGCACAGAGTTGCAGAAAGCTAC
53170465 TACAGTTG
131 TACAGTTG
53170473 TTGAGTTGTG
Statistics
Matches: 131, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
142 131 1.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.31
Consensus pattern (142 bp):
AAGATATCTGCAAGTTTATGAATGATTTTTATTCGAACAATTTTACAGAGCAATAAAAACTACAC
ATGAAGATTCAATTGGAGTATTTTCAACTTGATGATCATCAAAGCACAGAGTTGCAGAAAGCTAC
TACAGTTGCAGA
Found at i:53170742 original size:40 final size:40
Alignment explanation
Indices: 53170646--53170843 Score: 202
Period size: 40 Copynumber: 5.0 Consensus size: 40
53170636 GAGCTATGAC
* * * * *
53170646 AAAAACGCCGCAAAAGGTCAAGCATTAGTGGCG-TTTCTG
1 AAAAACGCCGCTATAGATCAAGCATTAGCGGCGCTTTTTG
* * * *
53170685 AAACAAACGTCGCTATAGGTCGAGCATTAGCGGCACTTTTTG
1 -AA-AAACGCCGCTATAGATCAAGCATTAGCGGCGCTTTTTG
**
53170727 AAAAACGCCGCTATAGATTGAGCATTAGCGGCGCTTTTTG
1 AAAAACGCCGCTATAGATCAAGCATTAGCGGCGCTTTTTG
* * * * *
53170767 AAAAACGTCGCTATAGATCAAGCATTAACGACGCTTCTCG
1 AAAAACGCCGCTATAGATCAAGCATTAGCGGCGCTTTTTG
* *
53170807 AAAAATGCCACTATAGATCAAGCATTAGC-GCGCTTTT
1 AAAAACGCCGCTATAGATCAAGCATTAGCGGCGCTTTT
53170844 CAAAAAGCAC
Statistics
Matches: 132, Mismatches: 24, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
39 6 0.05
40 94 0.71
41 27 0.20
42 5 0.04
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.25
Consensus pattern (40 bp):
AAAAACGCCGCTATAGATCAAGCATTAGCGGCGCTTTTTG
Found at i:53170998 original size:41 final size:40
Alignment explanation
Indices: 53170894--53171002 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 40
53170884 AGCTTTAGTG
* ** *
53170894 GCATTAGCGGCGCTTTTTTAAAAAACGCTGCAATAGATCGA
1 GCATTAGCGGCGC-TTTTTGAAAAACGCCACAATAGATCAA
* *
53170935 GCATTAGCGGCGCTATTTGAAAAACGCCACTATAGATCAA
1 GCATTAGCGGCGCTTTTTGAAAAACGCCACAATAGATCAA
* * *
53170975 GCATTAGAGGCACTTTTTGGAAAACGCC
1 GCATTAGCGGCGCTTTTTGAAAAACGCC
53171003 GCAAAAAAGT
Statistics
Matches: 58, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
40 45 0.78
41 13 0.22
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (40 bp):
GCATTAGCGGCGCTTTTTGAAAAACGCCACAATAGATCAA
Found at i:53171079 original size:149 final size:145
Alignment explanation
Indices: 53170748--53171112 Score: 471
Period size: 149 Copynumber: 2.5 Consensus size: 145
53170738 TATAGATTGA
* * * * *
53170748 GCATTAGCGGCGCTTTTTGAAAAACGTCGCTATAGATCAAGCATTAACGACGCTTCTCGAAAAAT
1 GCATTAGCGGCGCTTTTTGAAAAACGCCGCTATAGATCAAGCATTAGCGGCGCTT-TTGAAAAAC
* *
53170813 GCCACTATAGATCAAGCATTAGCGCGCTTTTCAAAAAGCACCGTAAAAAAGTTGAGCAAAACACG
65 GCCACTATAGATCAAGCATTAGCGCACTTTTCAAAAAGCACCGCAAAAAAGTTGAGCAAAACACG
53170878 TTGTTGAGCTTTAGTG
130 TTGTTGAGCTTTAGTG
* * * *
53170894 GCATTAGCGGCGCTTTTTTAAAAAACGCTGCAATAGATCGAGCATTAGCGGCGCTATTTGAAAAA
1 GCATTAGCGGCGC-TTTTTGAAAAACGCCGCTATAGATCAAGCATTAGCGGCGCT-TTTGAAAAA
* ** *
53170959 CGCCACTATAGATCAAGCATTAGAGGCACTTTTTGGAAAA-CGCCGCAAAAAAGTTGAGCAAAAC
64 CGCCACTATAGATCAAGCATTAG-CGCAC-TTTTCAAAAAGCACCGCAAAAAAGTTGAGCAAAAC
*
53171023 GATGTTGTTGAGCTTTAGTG
127 -ACGTTGTTGAGCTTTAGTG
* * *
53171043 GCATTAGCGGCGCTTTTTCGAAAAATGCCGCTATAGATCTAGAATTAGCGGCGCTTTTTGGAAAA
1 GCATTAGCGGCGCTTTTT-GAAAAACGCCGCTATAGATCAAGCATTAGCGGCGC-TTTT-GAAAA
53171108 ACGCC
63 ACGCC
53171113 GCAAAAAAGT
Statistics
Matches: 189, Mismatches: 22, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
146 13 0.07
147 63 0.33
148 31 0.16
149 71 0.38
150 11 0.06
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (145 bp):
GCATTAGCGGCGCTTTTTGAAAAACGCCGCTATAGATCAAGCATTAGCGGCGCTTTTGAAAAACG
CCACTATAGATCAAGCATTAGCGCACTTTTCAAAAAGCACCGCAAAAAAGTTGAGCAAAACACGT
TGTTGAGCTTTAGTG
Found at i:53171177 original size:104 final size:105
Alignment explanation
Indices: 53170935--53171211 Score: 325
Period size: 104 Copynumber: 2.6 Consensus size: 105
53170925 AATAGATCGA
* * * *
53170935 GCATTAGCGGCGCTATTTG-AAAAACGCCACTATAGATCAAGCATTAGAGGCACTTTTTGG-AAA
1 GCATTAGCGGCGCT-TTTGTAAAAACGCCGCTATAGATCAAGAATTAGCGGCGCTTTTTGGAAAA
*
53170998 ACGCCGCAAAAAAGTTGAGCAAAACGATGTTGTTGAGCTTTAGTG
65 ACGCCGCAAAAAAGTTGAGCAAAACGA---T-TTGAGCTTTAGAG
* *
53171043 GCATTAGCGGCGCTTTT-TCGAAAAATGCCGCTATAGATCTAGAATTAGCGGCGCTTTTTGGAAA
1 GCATTAGCGGCGCTTTTGT--AAAAACGCCGCTATAGATCAAGAATTAGCGGCGCTTTTTGGAAA
*
53171107 AACGCCGCAAAAAAGTTGAGCAAAGC-A-TTGAGCTTTAGAG
64 AACGCCGCAAAAAAGTTGAGCAAAACGATTTGAGCTTTAGAG
* * * *
53171147 GCATTAGCGGCGCTTTTGTAAAAAACGCCGCAATAGATCGAGAATTAGCAGCG-TTGTT-GAAAA
1 GCATTAGCGGCGCTTTTGT-AAAAACGCCGCTATAGATCAAGAATTAGCGGCGCTTTTTGGAAAA
53171210 AC
65 AC
53171212 ACGCTATAGA
Statistics
Matches: 150, Mismatches: 14, Indels: 16
0.83 0.08 0.09
Matches are distributed among these distances:
102 7 0.05
103 4 0.03
104 58 0.39
105 1 0.01
107 3 0.02
108 14 0.09
109 36 0.24
110 27 0.18
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.25
Consensus pattern (105 bp):
GCATTAGCGGCGCTTTTGTAAAAACGCCGCTATAGATCAAGAATTAGCGGCGCTTTTTGGAAAAA
CGCCGCAAAAAAGTTGAGCAAAACGATTTGAGCTTTAGAG
Found at i:53171475 original size:21 final size:21
Alignment explanation
Indices: 53171426--53171476 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
53171416 TGTTTATTAT
53171426 TTTGGGG-TTAGAGTTTAGAG
1 TTTGGGGTTTAGAGTTTAGAG
**
53171446 TTTATGGTTTATG-GTTTAGAG
1 TTTGGGGTTTA-GAGTTTAGAG
53171467 TTTGGGGTTT
1 TTTGGGGTTT
53171477 GGGATTTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 5 0.20
21 19 0.76
22 1 0.04
ACGTcount: A:0.16, C:0.00, G:0.35, T:0.49
Consensus pattern (21 bp):
TTTGGGGTTTAGAGTTTAGAG
Found at i:53171484 original size:21 final size:20
Alignment explanation
Indices: 53171426--53171484 Score: 55
Period size: 21 Copynumber: 2.9 Consensus size: 20
53171416 TGTTTATTAT
* *
53171426 TTTGGGGTTAGAGTTTAGAG
1 TTTGGGGTTTGGGTTTAGAG
** *
53171446 TTTATGGTTTATGGTTTAGAG
1 TTTGGGGTTT-GGGTTTAGAG
53171467 TTTGGGGTTTGGGATTTA
1 TTTGGGGTTTGGG-TTTA
53171485 TTATTTTATA
Statistics
Matches: 29, Mismatches: 8, Indels: 3
0.73 0.20 0.08
Matches are distributed among these distances:
20 9 0.31
21 20 0.69
ACGTcount: A:0.17, C:0.00, G:0.36, T:0.47
Consensus pattern (20 bp):
TTTGGGGTTTGGGTTTAGAG
Found at i:53171692 original size:14 final size:14
Alignment explanation
Indices: 53171675--53171839 Score: 68
Period size: 14 Copynumber: 11.6 Consensus size: 14
53171665 TAAGTTTATA
53171675 GTTTAGGGTTTAAG
1 GTTTAGGGTTTAAG
* *
53171689 GTTTAAGGTTTATG
1 GTTTAGGGTTTAAG
* * *
53171703 ATTTAGTGTTTATG
1 GTTTAGGGTTTAAG
* *
53171717 ATTTAGGGTGT-AG
1 GTTTAGGGTTTAAG
*
53171730 GTTTATGGTTT-AG
1 GTTTAGGGTTTAAG
*** *
53171743 TGTTTATAATTTATGG
1 -GTTTAGGGTTTA-AG
* *
53171759 GTTATGGGGCTTAAG
1 GTT-TAGGGTTTAAG
*
53171774 GTTTAGGGTTTAAA
1 GTTTAGGGTTTAAG
** *
53171788 GTTTATAGTTTAGG
1 GTTTAGGGTTTAAG
*
53171802 GTTTAAGAGTTT-AG
1 GTTT-AGGGTTTAAG
*
53171816 GATTTATGGTTT-AG
1 G-TTTAGGGTTTAAG
53171830 TGTTTAGGGT
1 -GTTTAGGGT
53171840 CTAATTTTAA
Statistics
Matches: 112, Mismatches: 32, Indels: 14
0.71 0.20 0.09
Matches are distributed among these distances:
13 11 0.10
14 79 0.71
15 17 0.15
16 5 0.04
ACGTcount: A:0.22, C:0.01, G:0.30, T:0.47
Consensus pattern (14 bp):
GTTTAGGGTTTAAG
Found at i:53171732 original size:34 final size:35
Alignment explanation
Indices: 53171694--53171760 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
53171684 TTAAGGTTTA
*
53171694 AGGTTTATGATTTAGTGTTTATGATTTA-GGGTGT
1 AGGTTTATGATTTAGTGTTTATAATTTATGGGTGT
*
53171728 AGGTTTATGGTTTAGTGTTTATAATTTATGGGT
1 AGGTTTATGATTTAGTGTTTATAATTTATGGGT
53171761 TATGGGGCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 26 0.87
35 4 0.13
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.51
Consensus pattern (35 bp):
AGGTTTATGATTTAGTGTTTATAATTTATGGGTGT
Found at i:53171783 original size:7 final size:7
Alignment explanation
Indices: 53171773--53171839 Score: 53
Period size: 7 Copynumber: 9.4 Consensus size: 7
53171763 TGGGGCTTAA
53171773 GGTTTAG
1 GGTTTAG
*
53171780 GGTTTAA
1 GGTTTAG
* *
53171787 AGTTTAT
1 GGTTTAG
*
53171794 AGTTTAG
1 GGTTTAG
53171801 GGTTTAAG
1 GGTTT-AG
*
53171809 AGTTTAG
1 GGTTTAG
* *
53171816 GATTTAT
1 GGTTTAG
53171823 GGTTTAG
1 GGTTTAG
*
53171830 TGTTTAG
1 GGTTTAG
53171837 GGT
1 GGT
53171840 CTAATTTTAA
Statistics
Matches: 46, Mismatches: 13, Indels: 2
0.75 0.21 0.03
Matches are distributed among these distances:
7 40 0.87
8 6 0.13
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.46
Consensus pattern (7 bp):
GGTTTAG
Found at i:53171814 original size:15 final size:15
Alignment explanation
Indices: 53171794--53171835 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
53171784 TAAAGTTTAT
53171794 AGTTTAGGGTTTAAG
1 AGTTTAGGGTTTAAG
* *
53171809 AGTTTAGGATTTATG
1 AGTTTAGGGTTTAAG
*
53171824 -GTTTAGTGTTTA
1 AGTTTAGGGTTTA
53171836 GGGTCTAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.48
Consensus pattern (15 bp):
AGTTTAGGGTTTAAG
Found at i:53171836 original size:21 final size:20
Alignment explanation
Indices: 53171668--53171837 Score: 97
Period size: 21 Copynumber: 8.1 Consensus size: 20
53171658 TAGGATGTAA
*
53171668 GTTTATAGTTTAGGGTTTAAG
1 GTTTATGGTTTAGGGTTT-AG
* * *
53171689 GTTTAAGGTTTATGATTTAG
1 GTTTATGGTTTAGGGTTTAG
* *
53171709 TGTTTATGATTTAGGGTGTAG
1 -GTTTATGGTTTAGGGTTTAG
* *
53171730 GTTTATGGTTTAGTGTTTATA
1 GTTTATGGTTTAGGGTTTA-G
* * *
53171751 ATTTATGGGTTATGGGGCTTAAG
1 GTTTAT-GGTT-TAGGG-TTTAG
* ** *
53171774 GTTTAGGGTTTAAAGTTTATA
1 GTTTATGGTTTAGGGTTTA-G
* *
53171795 GTTTAGGGTTTAAGAGTTTAG
1 GTTTATGGTTT-AGGGTTTAG
*
53171816 GATTTATGGTTTAGTGTTTAG
1 G-TTTATGGTTTAGGGTTTAG
53171837 G
1 G
53171838 GTCTAATTTT
Statistics
Matches: 112, Mismatches: 29, Indels: 16
0.71 0.18 0.10
Matches are distributed among these distances:
20 21 0.19
21 57 0.51
22 24 0.21
23 7 0.06
24 3 0.03
ACGTcount: A:0.22, C:0.01, G:0.29, T:0.48
Consensus pattern (20 bp):
GTTTATGGTTTAGGGTTTAG
Found at i:53174358 original size:9 final size:9
Alignment explanation
Indices: 53174346--53174401 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 9
53174336 AAATATATAT
53174346 CATAACTTA
1 CATAACTTA
53174355 CATAACTTA
1 CATAACTTA
*
53174364 CATAA-ATA
1 CATAACTTA
* * *
53174372 TATATCATA
1 CATAACTTA
*
53174381 TCAAAACTTA
1 -CATAACTTA
53174391 CATAACTTA
1 CATAACTTA
53174400 CA
1 CA
53174402 GAATTTTAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
8 5 0.14
9 27 0.73
10 5 0.14
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (9 bp):
CATAACTTA
Found at i:53174467 original size:21 final size:21
Alignment explanation
Indices: 53174443--53174569 Score: 92
Period size: 21 Copynumber: 6.4 Consensus size: 21
53174433 TCTTAACTTA
53174443 ATAACTTATATATATCATATC
1 ATAACTTATATATATCATATC
53174464 ATAACTTATATA-A-C-TCA-C
1 ATAACTTATATATATCAT-ATC
* * *
53174482 ATAAC--ATACATAAC-T-TA
1 ATAACTTATATATATCATATC
*
53174499 ATAACTTATATATATCATAAC
1 ATAACTTATATATATCATATC
* * * * *
53174520 ATAACTCACATA-ACTTACATG
1 ATAACTTATATATA-TCATATC
53174541 ATAACTTATATATATCATATC
1 ATAACTTATATATATCATATC
53174562 ATAACTTA
1 ATAACTTA
53174570 CATAACTCAC
Statistics
Matches: 79, Mismatches: 17, Indels: 20
0.68 0.15 0.17
Matches are distributed among these distances:
16 4 0.05
17 6 0.08
18 9 0.11
19 9 0.11
20 3 0.04
21 47 0.59
22 1 0.01
ACGTcount: A:0.46, C:0.17, G:0.01, T:0.36
Consensus pattern (21 bp):
ATAACTTATATATATCATATC
Found at i:53174476 original size:9 final size:9
Alignment explanation
Indices: 53174463--53174630 Score: 101
Period size: 9 Copynumber: 18.0 Consensus size: 9
53174453 TATATCATAT
53174463 CATAACTTA
1 CATAACTTA
* *
53174472 TATAACTCA
1 CATAACTTA
*
53174481 CATAACATA
1 CATAACTTA
53174490 CATAACTTA
1 CATAACTTA
53174499 -ATAACTTA
1 CATAACTTA
* *
53174507 TATATATCATAA
1 CATA-A-C-TTA
*
53174519 CATAACTCA
1 CATAACTTA
53174528 CATAACTTA
1 CATAACTTA
53174537 CATGATAACTTA
1 C---ATAACTTA
* *
53174549 TATATATCATA
1 CATA-A-CTTA
53174560 TCATAACTTA
1 -CATAACTTA
*
53174570 CATAACTCA
1 CATAACTTA
53174579 CATAACTTA
1 CATAACTTA
53174588 CATAA--TA
1 CATAACTTA
*
53174595 CATAA-ATA
1 CATAACTTA
* * *
53174603 TATATCATA
1 CATAACTTA
53174612 TCATAACTTA
1 -CATAACTTA
53174622 CATAACTTA
1 CATAACTTA
53174631 ATTATACTTA
Statistics
Matches: 125, Mismatches: 21, Indels: 26
0.73 0.12 0.15
Matches are distributed among these distances:
7 7 0.06
8 13 0.10
9 71 0.57
10 12 0.10
11 6 0.05
12 16 0.13
ACGTcount: A:0.46, C:0.19, G:0.01, T:0.34
Consensus pattern (9 bp):
CATAACTTA
Found at i:53174529 original size:47 final size:46
Alignment explanation
Indices: 53174473--53174628 Score: 167
Period size: 42 Copynumber: 3.3 Consensus size: 46
53174463 CATAACTTAT
*
53174473 ATAACTCACATAACATACATAACTTAATAACTTATATATATCATAAC
1 ATAACTCACATAAC-TACATAACTTAATAACTTATATATATCATATC
* *
53174520 ATAACTCACATAACT---T-ACATGATAACTTATATATATCATATC
1 ATAACTCACATAACTACATAACTTAATAACTTATATATATCATATC
* *
53174562 ATAACTTACATAACTCACATAACTTACATAATACATAAATATATATCATATC
1 ATAACTCACATAACT-ACATAACTTA-AT-A-AC-T-TATATATATCATATC
*
53174614 ATAACTTACATAACT
1 ATAACTCACATAACT
53174629 TAATTATACT
Statistics
Matches: 92, Mismatches: 7, Indels: 15
0.81 0.06 0.13
Matches are distributed among these distances:
42 37 0.40
43 1 0.01
46 2 0.02
47 17 0.18
48 2 0.02
49 1 0.01
50 2 0.02
51 1 0.01
52 29 0.32
ACGTcount: A:0.47, C:0.19, G:0.01, T:0.33
Consensus pattern (46 bp):
ATAACTCACATAACTACATAACTTAATAACTTATATATATCATATC
Found at i:53174551 original size:98 final size:93
Alignment explanation
Indices: 53174443--53174642 Score: 287
Period size: 98 Copynumber: 2.1 Consensus size: 93
53174433 TCTTAACTTA
*
53174443 ATAACTTATATATATCATATCATAACTTATATAACTCACATAACATACATAACTTA-ATAACTTA
1 ATAACTTATATATATCATATCATAACTTACATAACTCACATAACATACATAA--TACATAA---A
53174507 TATATATCATAACATAACTCACATAACTTACATG
61 TATATATCATAACATAACTCACATAACTTA-ATG
*
53174541 ATAACTTATATATATCATATCATAACTTACATAACTCACATAACTTACATAATACATAAATATAT
1 ATAACTTATATATATCATATCATAACTTACATAACTCACATAACATACATAATACATAAATATAT
* * *
53174606 ATCATATCATAACTTACATAACTTAATT
66 ATCATAACATAACTCACATAACTTAATG
53174634 AT-ACTTATA
1 ATAACTTATA
53174643 AATAAACAAC
Statistics
Matches: 96, Mismatches: 5, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
92 7 0.07
93 4 0.04
94 29 0.30
96 2 0.02
97 4 0.04
98 50 0.52
ACGTcount: A:0.46, C:0.17, G:0.01, T:0.36
Consensus pattern (93 bp):
ATAACTTATATATATCATATCATAACTTACATAACTCACATAACATACATAATACATAAATATAT
ATCATAACATAACTCACATAACTTAATG
Found at i:53174820 original size:14 final size:14
Alignment explanation
Indices: 53174801--53174831 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
53174791 CCAAGAGAAT
53174801 ATGATTCTTTGCCC
1 ATGATTCTTTGCCC
53174815 ATGATTCTTTGCCC
1 ATGATTCTTTGCCC
53174829 ATG
1 ATG
53174832 TAAGAAGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.16, C:0.26, G:0.16, T:0.42
Consensus pattern (14 bp):
ATGATTCTTTGCCC
Found at i:53176142 original size:13 final size:14
Alignment explanation
Indices: 53176126--53176154 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
53176116 TTTTAAATAT
53176126 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
53176139 TTATAATGGTTTAA
1 TTATAATGGTTTAA
53176153 TT
1 TT
53176155 CGTCGTTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:53177013 original size:43 final size:43
Alignment explanation
Indices: 53176966--53177122 Score: 148
Period size: 43 Copynumber: 3.8 Consensus size: 43
53176956 TTTAGCGACG
* * *
53176966 TTTGTGATAAAAGCGCCGTTAAAGATCATGTTCTTTAACGGTA
1 TTTGTGATAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGTA
* * * *
53177009 TTTGTG---AAA---TCGCTAAAAGTCAT-TCTCTATAGCGGCA
1 TTTGTGATAAAAGCGCCGCTAAAGGTCATGT-TCTTTAGCGGTA
* * *
53177046 TTTGTGATAAAAGCGTCGCTAAAGGTCATGTTCTTTAGCGATG
1 TTTGTGATAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGTA
**
53177089 TTTGTGATAAAAGTACCGCTAAAGGTCATGTTCT
1 TTTGTGATAAAAGCGCCGCTAAAGGTCATGTTCT
53177123 ATAATGGCAT
Statistics
Matches: 91, Mismatches: 15, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
36 1 0.01
37 25 0.27
40 6 0.07
43 58 0.64
44 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (43 bp):
TTTGTGATAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGTA
Found at i:53177841 original size:5 final size:5
Alignment explanation
Indices: 53177831--53177859 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
53177821 TTGGTGTGAA
53177831 ATTTT ATTTT ATTTT ATTTT ATTTT ATTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTT
53177860 AAAAAATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
ATTTT
Found at i:53186958 original size:11 final size:11
Alignment explanation
Indices: 53186942--53186969 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
53186932 CAAAAATATA
53186942 ATAATTATTAT
1 ATAATTATTAT
53186953 ATAATTATTAT
1 ATAATTATTAT
53186964 ATAATT
1 ATAATT
53186970 TTCCCTCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
ATAATTATTAT
Found at i:53188869 original size:27 final size:27
Alignment explanation
Indices: 53188800--53189007 Score: 229
Period size: 27 Copynumber: 7.7 Consensus size: 27
53188790 AGATATGTCA
* * *
53188800 GAAATGAAAGCCTTTATGGTGAACCAT
1 GAAAAGAAAGCCTTTGTGGCGAACCAT
* * *
53188827 GAAGAGAGAGCATTTGTGGCGAACCAT
1 GAAAAGAAAGCCTTTGTGGCGAACCAT
*
53188854 GAAAAGAAAGCCTTTGTGGTGAACCAT
1 GAAAAGAAAGCCTTTGTGGCGAACCAT
* *
53188881 GAAATA-AGAGCCTTGGTGGCGAACCAT
1 GAAA-AGAAAGCCTTTGTGGCGAACCAT
**
53188908 GAAAAGAAAGCCTTTGTGGAAAACCAT
1 GAAAAGAAAGCCTTTGTGGCGAACCAT
* * *
53188935 GAAAAGAAAGTCTTTATGGTGAACCAT
1 GAAAAGAAAGCCTTTGTGGCGAACCAT
* * *
53188962 GAAAAGAAATCCTTTGTGGCAAACAAT
1 GAAAAGAAAGCCTTTGTGGCGAACCAT
* *
53188989 GAAATGAAAACCTTTGTGG
1 GAAAAGAAAGCCTTTGTGG
53189008 AAAATCCTGG
Statistics
Matches: 150, Mismatches: 29, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
26 1 0.01
27 148 0.99
28 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.22
Consensus pattern (27 bp):
GAAAAGAAAGCCTTTGTGGCGAACCAT
Found at i:53188981 original size:81 final size:81
Alignment explanation
Indices: 53188800--53189011 Score: 255
Period size: 81 Copynumber: 2.6 Consensus size: 81
53188790 AGATATGTCA
* * * * * * **
53188800 GAAATGAAAGCCTTTATGGTGAACCATGAAGAGAGAGCATTTGTGGCGAACCATGAAAAGAAAGC
1 GAAAAGAAAGCCTTTGTGGCGAACCATGAAAAGAAAGCCTTTGTGGAAAACCATGAAAAGAAAGC
*
53188865 CTTTGTGGTGAACCAT
66 CTTTATGGTGAACCAT
* *
53188881 GAAATA-AGAGCCTTGGTGGCGAACCATGAAAAGAAAGCCTTTGTGGAAAACCATGAAAAGAAAG
1 GAAA-AGAAAGCCTTTGTGGCGAACCATGAAAAGAAAGCCTTTGTGGAAAACCATGAAAAGAAAG
*
53188945 TCTTTATGGTGAACCAT
65 CCTTTATGGTGAACCAT
* * * * *
53188962 GAAAAGAAATCCTTTGTGGCAAACAATGAAATGAAAACCTTTGTGGAAAA
1 GAAAAGAAAGCCTTTGTGGCGAACCATGAAAAGAAAGCCTTTGTGGAAAA
53189012 TCCTGGAAGG
Statistics
Matches: 110, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
80 1 0.01
81 109 0.99
ACGTcount: A:0.40, C:0.14, G:0.25, T:0.22
Consensus pattern (81 bp):
GAAAAGAAAGCCTTTGTGGCGAACCATGAAAAGAAAGCCTTTGTGGAAAACCATGAAAAGAAAGC
CTTTATGGTGAACCAT
Found at i:53189166 original size:27 final size:27
Alignment explanation
Indices: 53189136--53189187 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
53189126 AAAGGAACAA
* * *
53189136 TACTCATGGTGAACTTTAAAAGAATGG
1 TACTCATAGCGAACTCTAAAAGAATGG
*
53189163 TACTCATAGCGAACTCTAAAGGAAT
1 TACTCATAGCGAACTCTAAAAGAAT
53189188 TGTATACATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.27
Consensus pattern (27 bp):
TACTCATAGCGAACTCTAAAAGAATGG
Found at i:53190989 original size:5 final size:5
Alignment explanation
Indices: 53190976--53191013 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
53190966 AAATGAATTG
*
53190976 TATGG TATGA TATGA TATGA TATGA TATGA TATGA TAT
1 TATGA TATGA TATGA TATGA TATGA TATGA TATGA TAT
53191014 AGTGGATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.37, C:0.00, G:0.21, T:0.42
Consensus pattern (5 bp):
TATGA
Found at i:53191312 original size:36 final size:37
Alignment explanation
Indices: 53191269--53191361 Score: 118
Period size: 36 Copynumber: 2.6 Consensus size: 37
53191259 AACCTATTAA
*
53191269 GGCGTGTTATTGGTTGGATTGGCCCTTATAAACATTT
1 GGCGTGTTATTGGTTGGATTAGCCCTTATAAACATTT
* * * *
53191306 GG-GTGTTATTGGTTGTATTAGCTCTTATGAGCATTT
1 GGCGTGTTATTGGTTGGATTAGCCCTTATAAACATTT
*
53191342 GGCGTGTT-TCGGTTGGATTA
1 GGCGTGTTATTGGTTGGATTA
53191362 CTTGTGTACT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
36 41 0.85
37 7 0.15
ACGTcount: A:0.16, C:0.11, G:0.30, T:0.43
Consensus pattern (37 bp):
GGCGTGTTATTGGTTGGATTAGCCCTTATAAACATTT
Found at i:53197631 original size:50 final size:50
Alignment explanation
Indices: 53197572--53197671 Score: 137
Period size: 50 Copynumber: 2.0 Consensus size: 50
53197562 AAATAAAAAA
* * *
53197572 CCGGCCAGCATGCAAAATTGAAAAGATGTGGTGCCAAATATATAAAGTGT
1 CCGGCCAGCATGCAAAATAGAAAAGATATGGTGCCAAATATACAAAGTGT
* * **
53197622 CCGGTCAGCATGCGAAATAGGGAAGATATGGTGCCAAATATACAAAGTGT
1 CCGGCCAGCATGCAAAATAGAAAAGATATGGTGCCAAATATACAAAGTGT
53197672 GGAAGACTTG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (50 bp):
CCGGCCAGCATGCAAAATAGAAAAGATATGGTGCCAAATATACAAAGTGT
Found at i:53223942 original size:71 final size:71
Alignment explanation
Indices: 53223856--53223997 Score: 266
Period size: 71 Copynumber: 2.0 Consensus size: 71
53223846 GAGTTCTTTT
*
53223856 TATTTGGGTTATGACTAGTTTCTTTATAATAAGGAACTAACTTTTTGTTGACATATTTTCTAGGT
1 TATTTGGGTTATGACTAGTTTCTTTATAATAAGAAACTAACTTTTTGTTGACATATTTTCTAGGT
53223921 TGAAAA
66 TGAAAA
*
53223927 TATTTGGGTTATGACTGGTTTCTTTATAATAAGAAACTAACTTTTTGTTGACATATTTTCTAGGT
1 TATTTGGGTTATGACTAGTTTCTTTATAATAAGAAACTAACTTTTTGTTGACATATTTTCTAGGT
53223992 TGAAAA
66 TGAAAA
53223998 AGGAAGGGCA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.30, C:0.08, G:0.17, T:0.45
Consensus pattern (71 bp):
TATTTGGGTTATGACTAGTTTCTTTATAATAAGAAACTAACTTTTTGTTGACATATTTTCTAGGT
TGAAAA
Found at i:53224656 original size:39 final size:39
Alignment explanation
Indices: 53224591--53224741 Score: 151
Period size: 39 Copynumber: 3.7 Consensus size: 39
53224581 ACGTTGTTTG
* * *
53224591 AAATTATA-TTTAAGTCTTTAAATAAATTATATTAAGTT
1 AAATTATATTTTAAGCCTCTAATTAAATTATATTAAGTT
* * *
53224629 AAATTATATTTTAAACCTCTAAGTAAATTATGTTAAGTT
1 AAATTATATTTTAAGCCTCTAATTAAATTATATTAAGTT
* *
53224668 AACAATTAAATTATGTTGAACCCTCTAATTAAATTATATTAAGTT
1 -A-AATT--A-TAT-TTTAAGCCTCTAATTAAATTATATTAAGTT
* *
53224713 ACATTATATTTTAAGTCTCTAATTAAATT
1 AAATTATATTTTAAGCCTCTAATTAAATT
53224742 TGTGTGATGA
Statistics
Matches: 93, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
38 8 0.09
39 42 0.45
40 4 0.04
41 5 0.05
43 4 0.04
44 4 0.04
45 26 0.28
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (39 bp):
AAATTATATTTTAAGCCTCTAATTAAATTATATTAAGTT
Found at i:53240083 original size:7 final size:7
Alignment explanation
Indices: 53240072--53240105 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
53240062 GTTTTGTTAT
*
53240072 AAAATTT
1 AAAATTC
53240079 AAAATTC
1 AAAATTC
53240086 AAAATTC
1 AAAATTC
53240093 AAAATTC
1 AAAATTC
53240100 AAAATT
1 AAAATT
53240106 TTTTTGTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.32
Consensus pattern (7 bp):
AAAATTC
Found at i:53244524 original size:18 final size:16
Alignment explanation
Indices: 53244495--53244617 Score: 56
Period size: 17 Copynumber: 7.2 Consensus size: 16
53244485 TCCCATATCC
53244495 TTTAATTAAATTCTATT
1 TTTAATTAAATT-TATT
53244512 TTTAATATAAATTTATT
1 TTTAAT-TAAATTTATT
* *
53244529 ACTTTAAATATAA-TTATCC
1 --TTTAATTA-AATTTAT-T
*
53244548 TATAATT-AA-TTA-T
1 TTTAATTAAATTTATT
*
53244561 TTTAATTTTAATTTATT
1 TTTAA-TTAAATTTATT
* *
53244578 GCTTTAAATATAATTTATCA
1 --TTTAATTA-AATTTAT-T
53244598 TTTAATTAAATTCTATT
1 TTTAATTAAATT-TATT
53244615 TTT
1 TTT
53244618 TATTTTAAAT
Statistics
Matches: 81, Mismatches: 11, Indels: 28
0.68 0.09 0.23
Matches are distributed among these distances:
13 4 0.05
14 2 0.02
15 7 0.09
16 3 0.04
17 23 0.28
18 23 0.28
19 19 0.23
ACGTcount: A:0.37, C:0.06, G:0.01, T:0.56
Consensus pattern (16 bp):
TTTAATTAAATTTATT
Found at i:53244543 original size:19 final size:18
Alignment explanation
Indices: 53244494--53244595 Score: 60
Period size: 19 Copynumber: 5.9 Consensus size: 18
53244484 GTCCCATATC
*
53244494 CTTTAATTA-AATTCTATT
1 CTTTAAATATAATT-TATT
53244512 -TTT-AATATAAATTTATT
1 CTTTAAATAT-AATTTATT
*
53244529 ACTTTAAATATAA-TTATC
1 -CTTTAAATATAATTTATT
*
53244547 CTAT-AAT-TAA-TTA-T
1 CTTTAAATATAATTTATT
* *
53244561 -TTTAATTTTAATTTATT
1 CTTTAAATATAATTTATT
53244578 GCTTTAAATATAATTTAT
1 -CTTTAAATATAATTTAT
53244596 CATTTAATTA
Statistics
Matches: 65, Mismatches: 8, Indels: 21
0.69 0.09 0.22
Matches are distributed among these distances:
13 2 0.03
14 2 0.03
15 9 0.14
16 9 0.14
17 11 0.17
18 8 0.12
19 19 0.29
20 5 0.08
ACGTcount: A:0.38, C:0.06, G:0.01, T:0.55
Consensus pattern (18 bp):
CTTTAAATATAATTTATT
Found at i:53244619 original size:55 final size:53
Alignment explanation
Indices: 53244490--53244642 Score: 188
Period size: 49 Copynumber: 2.9 Consensus size: 53
53244480 GCCCGTCCCA
* * *
53244490 TATCCTTTAATTAAATTCTATTTTTAATATAAATTTATTACTTTAAATATAAT
1 TATCCTTTAATTAAATTCTATTTTTAATTTTAATTTATTGCTTTAAATATAAT
*
53244543 TATCCTATAATT-AA-T-TA-TTTTAATTTTAATTTATTGCTTTAAATATAATT
1 TATCCTTTAATTAAATTCTATTTTTAATTTTAATTTATTGCTTTAAATATAA-T
* * * *
53244593 TATCATTTAATTAAATTCTATTTTTTATTTTAAATTTCTTGTTTTAAATA
1 TATCCTTTAATTAAATTCTATTTTTAATTTT-AATTTATTGCTTTAAATA
53244643 ATTTTTTAAT
Statistics
Matches: 85, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
49 28 0.33
50 13 0.15
51 3 0.04
52 3 0.04
53 13 0.15
54 9 0.11
55 16 0.19
ACGTcount: A:0.36, C:0.07, G:0.01, T:0.56
Consensus pattern (53 bp):
TATCCTTTAATTAAATTCTATTTTTAATTTTAATTTATTGCTTTAAATATAAT
Found at i:53246312 original size:11 final size:11
Alignment explanation
Indices: 53246296--53246347 Score: 61
Period size: 11 Copynumber: 4.7 Consensus size: 11
53246286 TATCTTTAAT
53246296 AATAATAATAC
1 AATAATAATAC
53246307 AATAATAATAC
1 AATAATAATAC
* **
53246318 TTATAAT-ATTT
1 -AATAATAATAC
53246329 AATAATAATAC
1 AATAATAATAC
53246340 AATAATAA
1 AATAATAA
53246348 AAATATGTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 5 0.15
11 23 0.70
12 5 0.15
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.35
Consensus pattern (11 bp):
AATAATAATAC
Found at i:53246337 original size:33 final size:34
Alignment explanation
Indices: 53246272--53246347 Score: 111
Period size: 33 Copynumber: 2.2 Consensus size: 34
53246262 AAATATATTG
*
53246272 AATAATAATACTTATATCTTTAATAATAATAATAC
1 AATAATAATACTTATATCATT-ATAATAATAATAC
53246307 AATAATAATACTTATAAT-ATT-TAATAATAATAC
1 AATAATAATACTTAT-ATCATTATAATAATAATAC
53246340 AATAATAA
1 AATAATAA
53246348 AAATATGTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
33 20 0.51
35 17 0.44
36 2 0.05
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (34 bp):
AATAATAATACTTATATCATTATAATAATAATAC
Found at i:53247124 original size:14 final size:14
Alignment explanation
Indices: 53247105--53247132 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
53247095 ACGAAATCCC
53247105 ATATGTTCTTGCAT
1 ATATGTTCTTGCAT
53247119 ATATGTTCTTGCAT
1 ATATGTTCTTGCAT
53247133 TCGACCAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.50
Consensus pattern (14 bp):
ATATGTTCTTGCAT
Found at i:53250888 original size:22 final size:22
Alignment explanation
Indices: 53250858--53250905 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
53250848 TTTATTTTAT
*
53250858 TTTTTTTCCATTATTAGTGTTA
1 TTTTATTCCATTATTAGTGTTA
53250880 TTTTATTCCATTATTAGTGTTA
1 TTTTATTCCATTATTAGTGTTA
53250902 TTTT
1 TTTT
53250906 TTTTAAATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.19, C:0.08, G:0.08, T:0.65
Consensus pattern (22 bp):
TTTTATTCCATTATTAGTGTTA
Found at i:53261546 original size:143 final size:142
Alignment explanation
Indices: 53261227--53261692 Score: 596
Period size: 143 Copynumber: 3.3 Consensus size: 142
53261217 ACTACGGTGA
* * *
53261227 ATCTTATC-TCCTTGAAGTTGCAGTGGAGCAGATTTAAGCCACCAGCCTTATCTTCCTGAAGTCG
1 ATCTTATCTTCC-TGAAGTTGCAGTAGAGCAGATTGAAGCCACCAGCCTTATC-TCCTGAAGTTG
* * * *
53261291 CAGCAGAGCAGACTGAAGGTAATGAATCTTATTTCCCTGACGTTGTAGT-GAACAGATTAAAGCT
64 CAGCGGAGCAGACTGAAGATAACGAATCTTATTTCCCTGGCGTTGTAGTGGAACAGATTAAAGCT
**
53261355 ACAAATTATGATGG
129 ACAAATTATGGCGG
*
53261369 ATCTTATCTTCCTGAAGTTGCAGTAGAGTAGATTGAAGCCACCAGCCTTATCTCCGTGAAGTTGC
1 ATCTTATCTTCCTGAAGTTGCAGTAGAGCAGATTGAAGCCACCAGCCTTATCTCC-TGAAGTTGC
* * * * *
53261434 AGCGGAGCAGACTAAAGATAGCGAATCTTATTTCCCTGGCATTGCAGTGGAACATATTAAAGCTA
65 AGCGGAGCAGACTGAAGATAACGAATCTTATTTCCCTGGCGTTGTAGTGGAACAGATTAAAGCTA
53261499 CAAATTATGGCGG
130 CAAATTATGGCGG
* * * ** *
53261512 ATCTTATC-TCCTTGAAGTTGTAATAGAGCAGATTGATGTTACCAGCCTTATCTCCCTGAAATTG
1 ATCTTATCTTCC-TGAAGTTGCAGTAGAGCAGATTGAAGCCACCAGCCTTATCT-CCTGAAGTTG
* * * *
53261576 CAGCGGAGCAGACTGAAGACATCAAATCTTATTTCCCTGGCGTTGTAGTGGAATAGATTAAAGCT
64 CAGCGGAGCAGACTGAAGATAACGAATCTTATTTCCCTGGCGTTGTAGTGGAACAGATTAAAGCT
53261641 ACAAATTATGGCGG
129 ACAAATTATGGCGG
* * ** *
53261655 ACCTTATCTTCCTGAAGTTACAGCGGAGCAGACTGAAG
1 ATCTTATCTTCCTGAAGTTGCAGTAGAGCAGATTGAAG
53261693 ACAACGAATC
Statistics
Matches: 280, Mismatches: 38, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
141 3 0.01
142 96 0.34
143 176 0.63
144 5 0.02
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.28
Consensus pattern (142 bp):
ATCTTATCTTCCTGAAGTTGCAGTAGAGCAGATTGAAGCCACCAGCCTTATCTCCTGAAGTTGCA
GCGGAGCAGACTGAAGATAACGAATCTTATTTCCCTGGCGTTGTAGTGGAACAGATTAAAGCTAC
AAATTATGGCGG
Found at i:53261687 original size:99 final size:99
Alignment explanation
Indices: 53261557--53261785 Score: 350
Period size: 99 Copynumber: 2.3 Consensus size: 99
53261547 ATGTTACCAG
* * * *
53261557 CCTTATCTCCCTGAAATTGCAGCGGAGCAGACTGAAGACATCAAATCTTATTTCCCTGGCGTTGT
1 CCTTATCTTCCTGAAGTTGCAGCGGAGCAGACTGAAGACAACAAATCTTATTTCCCTGGCATTGT
*
53261622 AGTGGAATAGATTAAAGCTACAAATTATGGCGGA
66 AATGGAATAGATTAAAGCTACAAATTATGGCGGA
* * *
53261656 CCTTATCTTCCTGAAGTTACAGCGGAGCAGACTGAAGACAACGAATCTTATTTCCCTGGTATTGT
1 CCTTATCTTCCTGAAGTTGCAGCGGAGCAGACTGAAGACAACAAATCTTATTTCCCTGGCATTGT
*
53261721 AATGGAATAGATTAAAGCTACAAATTATGGTGGA
66 AATGGAATAGATTAAAGCTACAAATTATGGCGGA
* * *
53261755 TCTTATCTTCCTAAAGTTGCAGTGGAGCAGA
1 CCTTATCTTCCTGAAGTTGCAGCGGAGCAGA
53261786 TCGAAACCAC
Statistics
Matches: 117, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
99 117 1.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.29
Consensus pattern (99 bp):
CCTTATCTTCCTGAAGTTGCAGCGGAGCAGACTGAAGACAACAAATCTTATTTCCCTGGCATTGT
AATGGAATAGATTAAAGCTACAAATTATGGCGGA
Found at i:53261819 original size:44 final size:45
Alignment explanation
Indices: 53261756--53261861 Score: 142
Period size: 44 Copynumber: 2.4 Consensus size: 45
53261746 TATGGTGGAT
* *
53261756 CTTATCTTCCTAAAGTTGCAGTGGAGCAGATCGAAACCAC-AATC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAACCACTAATC
* * **
53261800 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAATTACTAATC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAACCACTAATC
*
53261845 CTTATCTCCTTGAAGTT
1 CTTATCTCCCTGAAGTT
53261862 ATAGCGGAGT
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 34 0.63
45 20 0.37
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (45 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAACCACTAATC
Found at i:53261884 original size:242 final size:242
Alignment explanation
Indices: 53261414--53261886 Score: 549
Period size: 242 Copynumber: 2.0 Consensus size: 242
53261404 AAGCCACCAG
* * *
53261414 CCTTATCTCCGTGAAGTTGCAGCGGAGCAGACTAAAGATAGCGAATCTTATTTCCCTGGCATTGC
1 CCTTATCTCCGTGAAGTTACAGCGGAGCAGACTAAAGACAACGAATCTTATTTCCCTGGCATTGC
* * * *
53261479 AGTGGAACATATTAAAGCTACAAATTATGGCGGATCTTATCTCCTTGAAGTTGTAATAGAGCAGA
66 AATGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTCCTTAAAGTTGCAATAGAGCAGA
* **** * *
53261544 TTGATGTTACCAGCCTTATCTCCCTGAAATTGCAGCGGAGCAGACTGAAGACATCAAATCTTATT
131 TCGAAACCACAAGCCTTATCTCCCTGAAATTGCAGCGGAGCAGACTGAAGACATCAAATCTTATC
** * * *
53261609 TCCCTGGCGTTGTAGTGGAATAGATTAAAGCTACAAATTATGGCGGA
196 TCCCTGAAGTTATAGCGGAATAGATCAAAGCTACAAATTATGGCGGA
* *
53261656 CCTTATCTTCC-TGAAGTTACAGCGGAGCAGACTGAAGACAACGAATCTTATTTCCCTGGTATTG
1 CCTTATC-TCCGTGAAGTTACAGCGGAGCAGACTAAAGACAACGAATCTTATTTCCCTGGCATTG
* * * * *
53261720 TAATGGAATAGATTAAAGCTACAAATTATGGTGGATCTTATCTTCC-TAAAGTTGCAGTGGAGCA
65 CAATGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATC-TCCTTAAAGTTGCAATAGAGCA
* * * ** * *
53261784 GATCGAAACCACAATCCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAA-A-TTACTAATCCT
129 GATCGAAACCACAAGCCTTATCTCCCTGAAATTGCAGCGGAGCAGACTGAAGACAT-CAAAT-CT
* * * *
53261847 TATCTCCTTGAAGTTATAGCGGAGTGGATCGAAGCTACAA
192 TATCTCCCTGAAGTTATAGCGGAATAGATCAAAGCTACAA
53261887 GTCTCTTTTC
Statistics
Matches: 190, Mismatches: 37, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
240 1 0.01
241 5 0.03
242 178 0.94
243 6 0.03
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (242 bp):
CCTTATCTCCGTGAAGTTACAGCGGAGCAGACTAAAGACAACGAATCTTATTTCCCTGGCATTGC
AATGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTCCTTAAAGTTGCAATAGAGCAGA
TCGAAACCACAAGCCTTATCTCCCTGAAATTGCAGCGGAGCAGACTGAAGACATCAAATCTTATC
TCCCTGAAGTTATAGCGGAATAGATCAAAGCTACAAATTATGGCGGA
Found at i:53263351 original size:21 final size:22
Alignment explanation
Indices: 53263327--53263367 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
53263317 TTAAGTTAAT
53263327 ATTATTT-TTATTTTTATATCC
1 ATTATTTATTATTTTTATATCC
*
53263348 ATTATTTATTTTTTTTATAT
1 ATTATTTATTATTTTTATAT
53263368 ATCTAAATCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (22 bp):
ATTATTTATTATTTTTATATCC
Found at i:53263602 original size:18 final size:17
Alignment explanation
Indices: 53263572--53263605 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
53263562 TAAATCTATC
53263572 TTATATTAGTTTTTATT
1 TTATATTAGTTTTTATT
*
53263589 TTATCATTATTTTTTAT
1 TTAT-ATTAGTTTTTAT
53263606 ATTGGCTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (17 bp):
TTATATTAGTTTTTATT
Found at i:53265233 original size:41 final size:41
Alignment explanation
Indices: 53265188--53265281 Score: 107
Period size: 41 Copynumber: 2.3 Consensus size: 41
53265178 CATTAGTGGT
* * * *
53265188 GTTTTTTCTATAAACGCTGTAAAAGGTAAAACAATAACGGC
1 GTTTTTCCTATAAAAGCAGCAAAAGGTAAAACAATAACGGC
* * **
53265229 GTTTTACCTATAAAAGCAGCAAAAGTTAAAGTAATAACGGC
1 GTTTTTCCTATAAAAGCAGCAAAAGGTAAAACAATAACGGC
*
53265270 GTTTTTCATATA
1 GTTTTTCCTATA
53265282 GCGCGAATTT
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (41 bp):
GTTTTTCCTATAAAAGCAGCAAAAGGTAAAACAATAACGGC
Found at i:53269395 original size:90 final size:90
Alignment explanation
Indices: 53269293--53269478 Score: 363
Period size: 90 Copynumber: 2.1 Consensus size: 90
53269283 CGAAATGGAT
53269293 AAGAATTGGATGGATTTGTCAAGGGTAAGCAACTACTATCGAAATGGAGTACAAACTTTTCTAAA
1 AAGAATTGGATGGATTTGTCAAGGGTAAGCAACTACTATCGAAATGGAGTACAAACTTTTCTAAA
53269358 TTTTGCATTTCAAAATGCAAGCCAA
66 TTTTGCATTTCAAAATGCAAGCCAA
53269383 AAGAATTGGATGGATTTGTCAAGGGTAAGCAACTACTATCGAAATGGAGTACAAACTTTTCTAAA
1 AAGAATTGGATGGATTTGTCAAGGGTAAGCAACTACTATCGAAATGGAGTACAAACTTTTCTAAA
53269448 TTTTGCATTTCAAAATGCAAGCCAA
66 TTTTGCATTTCAAAATGCAAGCCAA
*
53269473 GAGAAT
1 AAGAAT
53269479 ATGATTCTTT
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 95 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.28
Consensus pattern (90 bp):
AAGAATTGGATGGATTTGTCAAGGGTAAGCAACTACTATCGAAATGGAGTACAAACTTTTCTAAA
TTTTGCATTTCAAAATGCAAGCCAA
Found at i:53272417 original size:23 final size:23
Alignment explanation
Indices: 53272398--53272482 Score: 98
Period size: 23 Copynumber: 3.7 Consensus size: 23
53272388 TATTTTAGTT
*
53272398 TTATCATGTATTTTTATTTAAAG
1 TTATCATGTATTATTATTTAAAG
* *
53272421 TTATCATGTATTATTATTTTGAAT
1 TTATCATGTATTATTA-TTTAAAG
* * * *
53272445 TTATCATCTATGATCATTTAAAT
1 TTATCATGTATTATTATTTAAAG
53272468 TTATCATGTATTATT
1 TTATCATGTATTATT
53272483 TTATGCATCC
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
23 33 0.65
24 18 0.35
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.55
Consensus pattern (23 bp):
TTATCATGTATTATTATTTAAAG
Found at i:53272463 original size:24 final size:23
Alignment explanation
Indices: 53272413--53272474 Score: 70
Period size: 24 Copynumber: 2.7 Consensus size: 23
53272403 ATGTATTTTT
* * * *
53272413 ATTTAAAGTTATCATGTATTATT
1 ATTTAAATTTATCATCTATGATC
*
53272436 ATTTTGAATTTATCATCTATGATC
1 A-TTTAAATTTATCATCTATGATC
53272460 ATTTAAATTTATCAT
1 ATTTAAATTTATCAT
53272475 GTATTATTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 14 0.44
24 18 0.56
ACGTcount: A:0.34, C:0.08, G:0.06, T:0.52
Consensus pattern (23 bp):
ATTTAAATTTATCATCTATGATC
Found at i:53272475 original size:47 final size:47
Alignment explanation
Indices: 53272370--53272482 Score: 131
Period size: 47 Copynumber: 2.4 Consensus size: 47
53272360 TATATTATTC
** * * ** *
53272370 TAAATTTATCAT-TAACATTATTTTAGTTTTATCATGTATTTTTATT
1 TAAATTTATCATGTATTATTATTTTAGATTTATCATCTATGATCATT
*
53272416 TAAAGTTATCATGTATTATTATTTT-GAATTTATCATCTATGATCATT
1 TAAATTTATCATGTATTATTATTTTAG-ATTTATCATCTATGATCATT
53272463 TAAATTTATCATGTATTATT
1 TAAATTTATCATGTATTATT
53272483 TTATGCATCC
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
46 12 0.21
47 44 0.79
ACGTcount: A:0.32, C:0.07, G:0.06, T:0.55
Consensus pattern (47 bp):
TAAATTTATCATGTATTATTATTTTAGATTTATCATCTATGATCATT
Found at i:53276685 original size:43 final size:44
Alignment explanation
Indices: 53276624--53276719 Score: 131
Period size: 43 Copynumber: 2.2 Consensus size: 44
53276614 GCATTTTCCC
* * * * *
53276624 ACAAACACTGCTATAGAACATGATCTTTAGCGGCACTTTTA-CT
1 ACAAACGCCGCTAAAGAACATGATCTTTAGCGGCAATTCTAGCT
*
53276667 ACAAACGCCGCTAAAGAACATGATCTTTTGCGGCAATTCTAGCT
1 ACAAACGCCGCTAAAGAACATGATCTTTAGCGGCAATTCTAGCT
53276711 ACAAACGCC
1 ACAAACGCC
53276720 ACAACATGCT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
43 35 0.76
44 11 0.24
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (44 bp):
ACAAACGCCGCTAAAGAACATGATCTTTAGCGGCAATTCTAGCT
Found at i:53280301 original size:35 final size:35
Alignment explanation
Indices: 53280262--53280333 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
53280252 GAGAGAAAGA
53280262 AAATCAACACAAGTTTGTTAACACAGTTTGAATTT
1 AAATCAACACAAGTTTGTTAACACAGTTTGAATTT
53280297 AAATCAACACAAGTTTGTTAACACAGTTTGAATTT
1 AAATCAACACAAGTTTGTTAACACAGTTTGAATTT
53280332 AA
1 AA
53280334 TAATCATATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (35 bp):
AAATCAACACAAGTTTGTTAACACAGTTTGAATTT
Found at i:53281055 original size:31 final size:30
Alignment explanation
Indices: 53280998--53281056 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
53280988 GTAAATACTC
* *
53280998 AAAATTTGAAGGGTTAAAATGTAAATATGA
1 AAAATTTGAAGGATCAAAATGTAAATATGA
*
53281028 AAAATTTGAAGGATCAATAGTGTAAATAT
1 AAAATTTGAAGGATCAA-AATGTAAATAT
53281057 TTTAAGGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.49, C:0.02, G:0.19, T:0.31
Consensus pattern (30 bp):
AAAATTTGAAGGATCAAAATGTAAATATGA
Found at i:53282647 original size:26 final size:26
Alignment explanation
Indices: 53282611--53282667 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
53282601 GCATGAAATG
*
53282611 AATAGCTTGTTGTGAGTAAATAAGTA
1 AATAGCTTGTTGTAAGTAAATAAGTA
53282637 AATAGCTTGTTGTAAGTAAATAAGTA
1 AATAGCTTGTTGTAAGTAAATAAGTA
53282663 AATAG
1 AATAG
53282668 TGGTAATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.42, C:0.04, G:0.21, T:0.33
Consensus pattern (26 bp):
AATAGCTTGTTGTAAGTAAATAAGTA
Found at i:53282826 original size:249 final size:250
Alignment explanation
Indices: 53282380--53282862 Score: 878
Period size: 249 Copynumber: 1.9 Consensus size: 250
53282370 ACCATGACTG
* * *
53282380 AAGTGAATAGCTTGTTGTGAGTAAATAAGTTAATAGTGGTAATATATATATCAAGGATGTGGAAT
1 AAGTAAATAGCTTGTTGTAAGTAAATAAGTAAATAGTGGTAATATATATATCAAGGATGTGGAAT
53282445 GGAGTGGAGGAGGAGGAAAAATAATATATGTGAATATTCAGCTAATATGAGTTTAATTTAAAATA
66 GGAGT-G-GGAGGAGGAAAAATAATATATGTGAATATTCAGCTAATATGAGTTTAATTTAAAATA
*
53282510 GCTAATTTACATGTTTTAGGTTCAGGGACTAAATTGAATAAAATTAAAATTTTAAGGGTAATTTT
129 GCTAATTTACATGTTTTAGGTTCAGGGACTAAATTGAATAAAAGTAAAATTTTAAGGGTAATTTT
53282575 GTAAAAATGTCAAAAATGGCCAAATTGCATGAAATGAATAGCTTGTTGTGAGTAAAT
194 GTAAAAATGTCAAAAATGGCCAAATTGCATGAAATGAATAGCTTGTTGTGAGTAAAT
53282632 AAGTAAATAGCTTGTTGTAAGTAAATAAGTAAATAGTGGTAATATATATATCAAGGATGTGGAAT
1 AAGTAAATAGCTTGTTGTAAGTAAATAAGTAAATAGTGGTAATATATATATCAAGGATGTGGAAT
* *
53282697 GGAGT-GGAGGAGGAAAAATAATATATGTGAATATTCAGCTAATATGAGTTTATTTTACAATAGC
66 GGAGTGGGAGGAGGAAAAATAATATATGTGAATATTCAGCTAATATGAGTTTAATTTAAAATAGC
*
53282761 TAATTTACATGTTTTTGGTTCAGGGACTAAATTGAATAAAAGTAAAATTTTAAGGGTAATTTTGT
131 TAATTTACATGTTTTAGGTTCAGGGACTAAATTGAATAAAAGTAAAATTTTAAGGGTAATTTTGT
53282826 AAAAATGTCAAAAATGGCCAAATTGCATGAAATGAAT
196 AAAAATGTCAAAAATGGCCAAATTGCATGAAATGAAT
53282863 TGTTTTATCA
Statistics
Matches: 224, Mismatches: 7, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
249 157 0.70
252 67 0.30
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.33
Consensus pattern (250 bp):
AAGTAAATAGCTTGTTGTAAGTAAATAAGTAAATAGTGGTAATATATATATCAAGGATGTGGAAT
GGAGTGGGAGGAGGAAAAATAATATATGTGAATATTCAGCTAATATGAGTTTAATTTAAAATAGC
TAATTTACATGTTTTAGGTTCAGGGACTAAATTGAATAAAAGTAAAATTTTAAGGGTAATTTTGT
AAAAATGTCAAAAATGGCCAAATTGCATGAAATGAATAGCTTGTTGTGAGTAAAT
Found at i:53283246 original size:57 final size:57
Alignment explanation
Indices: 53283170--53283278 Score: 175
Period size: 57 Copynumber: 1.9 Consensus size: 57
53283160 GATCCTATCC
*
53283170 TGATATAGCCCTCCCGAAGAATATGTGTGAAAA-GGATATAGCCCGGACGGGTGATCT
1 TGATATAGCCCTCCCGAAGAATATGT-AGAAAATGGATATAGCCCGGACGGGTGATCT
* *
53283227 TGATATAGCCCTCCCGAAGAATATGTAGAAAATGGATTTAGCCCGGATGGGT
1 TGATATAGCCCTCCCGAAGAATATGTAGAAAATGGATATAGCCCGGACGGGT
53283279 AATCCGAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
56 5 0.10
57 43 0.90
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.24
Consensus pattern (57 bp):
TGATATAGCCCTCCCGAAGAATATGTAGAAAATGGATATAGCCCGGACGGGTGATCT
Found at i:53283412 original size:67 final size:67
Alignment explanation
Indices: 53283298--53283423 Score: 227
Period size: 67 Copynumber: 1.9 Consensus size: 67
53283288 TAGGGTCTGA
*
53283298 ATTTAGCCTGGACTGGTAATCCCTCTGTAAGAAATGAGGTTCACGGGAGTGTGCTCTCTTGCAGG
1 ATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCACGGGAGTGTGCTCTCTTGCAGG
53283363 GG
66 GG
53283365 ATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTT-AGCGGGAGTGTGCTCTCT
1 ATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCA-CGGGAGTGTGCTCTCT
53283424 GAATTGGGAA
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
66 1 0.02
67 56 0.98
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.29
Consensus pattern (67 bp):
ATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCACGGGAGTGTGCTCTCTTGCAGG
GG
Found at i:53283594 original size:26 final size:26
Alignment explanation
Indices: 53283536--53283594 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
53283526 ATAAAAATAG
53283536 AAAATGATAAGTACTTGAAATACATA
1 AAAATGATAAGTACTTGAAATACATA
* * * *
53283562 GAAATGATAATTATTTGATATAC-TA
1 AAAATGATAAGTACTTGAAATACATA
53283587 AAATATGA
1 AAA-ATGA
53283595 CATGGAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
25 4 0.15
26 23 0.85
ACGTcount: A:0.51, C:0.05, G:0.12, T:0.32
Consensus pattern (26 bp):
AAAATGATAAGTACTTGAAATACATA
Found at i:53285087 original size:49 final size:49
Alignment explanation
Indices: 53285026--53285152 Score: 182
Period size: 49 Copynumber: 2.6 Consensus size: 49
53285016 TGTGATTTTT
* *
53285026 GTGTAAGGCCATAGCTGGACTATGGCATCAGTAAGTGATATGTGATTCC
1 GTGTAAGACCATAGCTGGACTATGGCATCAGTAAGTGATATGTGATTAC
** ** *
53285075 GTGTAAGACCATAGCTGGGTTATGGCATTGGTATGTGATATGTGATTAC
1 GTGTAAGACCATAGCTGGACTATGGCATCAGTAAGTGATATGTGATTAC
*
53285124 GTGTAAGACCATAGTTGGACTATGGCATC
1 GTGTAAGACCATAGCTGGACTATGGCATC
53285153 GAGAAAATAA
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
49 67 1.00
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (49 bp):
GTGTAAGACCATAGCTGGACTATGGCATCAGTAAGTGATATGTGATTAC
Found at i:53288838 original size:67 final size:67
Alignment explanation
Indices: 53288730--53288856 Score: 218
Period size: 67 Copynumber: 1.9 Consensus size: 67
53288720 TTTATATTAC
* * *
53288730 AGGGGATTTAGCCTGGACTGGTAATCCTGCTGTAAGAAATGAGGTTTGCGGGAGTATGCTCTCTT
1 AGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCAGGAGTATGCTCTCTT
53288795 GT
66 GT
*
53288797 AGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCAGGAGTGTGCT
1 AGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCAGGAGTATGCT
53288857 ATCTGAATTG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 56 1.00
ACGTcount: A:0.22, C:0.16, G:0.34, T:0.28
Consensus pattern (67 bp):
AGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCAGGAGTATGCTCTCTT
GT
Found at i:53290081 original size:28 final size:30
Alignment explanation
Indices: 53290027--53290082 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
53290017 GGTATTGACT
*
53290027 AAATTATAAATATATGAAAAGTTTAAGGTC
1 AAATTATAAATATATCAAAAGTTTAAGGTC
*
53290057 AAATTGTAAATAT-TCAAAAG-TTAAGG
1 AAATTATAAATATATCAAAAGTTTAAGG
53290083 GATTGAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 6 0.25
29 6 0.25
30 12 0.50
ACGTcount: A:0.50, C:0.04, G:0.14, T:0.32
Consensus pattern (30 bp):
AAATTATAAATATATCAAAAGTTTAAGGTC
Found at i:53297395 original size:13 final size:15
Alignment explanation
Indices: 53297369--53297400 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
53297359 TTGGTTATTT
53297369 TGTGTTTTGTTTTTA
1 TGTGTTTTGTTTTTA
53297384 TGTG-TTTG-TTTTA
1 TGTGTTTTGTTTTTA
53297397 TGTG
1 TGTG
53297401 CAGCGAGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 4 0.24
15 4 0.24
ACGTcount: A:0.06, C:0.00, G:0.25, T:0.69
Consensus pattern (15 bp):
TGTGTTTTGTTTTTA
Found at i:53315652 original size:95 final size:94
Alignment explanation
Indices: 53315475--53315907 Score: 326
Period size: 95 Copynumber: 4.6 Consensus size: 94
53315465 CTTTACAAAT
* * * * *
53315475 TTTAGATAAGTGTCTTAAGTGGCTTAGCAGTGTATCTAG-TATTAGACTTAGCGAGCAGTTTCCT
1 TTTAGCTAAGTGCCTTAAGAGGCTTAGCAGTATATCT-GCTATTAGACTTAGTGAGCAGTTTCCT
* **
53315539 CTCAAG-TTGTCTGTTTTATAACTTCATTGA-A
65 CT-AAGAGTGTCTACTTTATAA-TT-ATTGACA
* * * *
53315570 TTTAGCTAAGTGCCCTAATAGGCTTAGCAGTATATCTGCTATTAGAATTAGTGAGTAGTTTCCTC
1 TTTAGCTAAGTGCCTTAAGAGGCTTAGCAGTATATCTGCTATTAGACTTAGTGAGCAGTTTCCTC
* * *
53315635 TAAGAGTATCTACTTTATAAATATTGACT
66 TAAGAGTGTCTACTTTATAATTATTGACA
* * * * * ** *
53315664 TTTGGCTAAGTGCCTTAAGAGGC-TAGAAGCA-ATTCTTCTATTACACTTAGTGATTAGTTTCTT
1 TTTAGCTAAGTGCCTTAAGAGGCTTAGCAGTATA-TCTGCTATTAGACTTAGTGAGCAGTTTCCT
** * * *
53315727 CTCGGTGTGTCTACTTTAAAACTTTGTTGA-A
65 CTAAGAGTGTCTACTTTATAA--TTATTGACA
* * * * *
53315758 TTTAGCTACGTGCCTTAAGAGGCTTAGCAATATA-CTTGCTGTTAGACTTAGTGAACAGTTCCCT
1 TTTAGCTAAGTGCCTTAAGAGGCTTAGCAGTATATC-TGCTATTAGACTTAGTGAGCAGTTTCCT
* * * * **
53315822 CT-TGAATTGTCTGCTCTATAGA-TATTGATT
65 CTAAG-AGTGTCTACTTTATA-ATTATTGACA
* * **
53315852 TTTGGCTAAGTGCCTTAAAAGGCTTAGCAGTATATCTGCTATTAGTTTTAGTGAGC
1 TTTAGCTAAGTGCCTTAAGAGGCTTAGCAGTATATCTGCTATTAGACTTAGTGAGC
53315908 TTGAAAGGCG
Statistics
Matches: 264, Mismatches: 61, Indels: 27
0.75 0.17 0.08
Matches are distributed among these distances:
92 1 0.00
93 57 0.22
94 94 0.36
95 110 0.42
96 2 0.01
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (94 bp):
TTTAGCTAAGTGCCTTAAGAGGCTTAGCAGTATATCTGCTATTAGACTTAGTGAGCAGTTTCCTC
TAAGAGTGTCTACTTTATAATTATTGACA
Found at i:53315953 original size:20 final size:20
Alignment explanation
Indices: 53315911--53315955 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
53315901 AGTGAGCTTG
* *
53315911 AAAGGCGATGTCGAGCATGA
1 AAAGGCAATGTCGAGCATAA
53315931 AAAGGCAATGTCGAGTC-TAA
1 AAAGGCAATGTCGAG-CATAA
53315951 AAAGG
1 AAAGG
53315956 TAGTGTCGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 21 0.95
21 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.31, T:0.16
Consensus pattern (20 bp):
AAAGGCAATGTCGAGCATAA
Found at i:53316985 original size:21 final size:21
Alignment explanation
Indices: 53316961--53317185 Score: 73
Period size: 20 Copynumber: 11.0 Consensus size: 21
53316951 GGAGATTAAT
53316961 AGTTTTCTCTAGGAGTTAAGC
1 AGTTTTCTCTAGGAGTTAAGC
* * *
53316982 AGTTTTCTTTAGGAATT-TGAC
1 AGTTTTCTCTAGGAGTTAAG-C
*
53317003 AGTCTTT-TCAAGGAGTTAAG-
1 AGT-TTTCTCTAGGAGTTAAGC
* * *
53317023 AGTTTTCCCTAGAAGTTTAGC
1 AGTTTTCTCTAGGAGTTAAGC
* * *
53317044 AATCTTTC-ATAGGAGTTAA-T
1 AGT-TTTCTCTAGGAGTTAAGC
*** * * *
53317064 AACATTCCCTAAGAGTTAA-T
1 AGTTTTCTCTAGGAGTTAAGC
* * *
53317084 AGTTTT-TCCTAGTAGTTTAGG
1 AGTTTTCT-CTAGGAGTTAAGC
*
53317105 AGTCTTC-CTTA-GATGTTAA-C
1 AGTTTTCTC-TAGGA-GTTAAGC
*
53317125 AGTTTTCTCTAAGAGTT-A-C
1 AGTTTTCTCTAGGAGTTAAGC
*
53317144 AATTTT-TCCTAGGAGTTAAGC
1 AGTTTTCT-CTAGGAGTTAAGC
* *
53317165 AGTTTTC-CCAGGAGTTTAGC
1 AGTTTTCTCTAGGAGTTAAGC
53317185 A
1 A
53317186 ATCTTCACAA
Statistics
Matches: 148, Mismatches: 38, Indels: 37
0.66 0.17 0.17
Matches are distributed among these distances:
18 1 0.01
19 21 0.14
20 62 0.42
21 56 0.38
22 8 0.05
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Consensus pattern (21 bp):
AGTTTTCTCTAGGAGTTAAGC
Found at i:53317050 original size:41 final size:42
Alignment explanation
Indices: 53316970--53317062 Score: 104
Period size: 41 Copynumber: 2.2 Consensus size: 42
53316960 TAGTTTTCTC
** *
53316970 TAGGAGTTAAGCAGTTTTCTTTAGGAATTTGACAGTCTTTTCA
1 TAGGAGTTAAGCAGTTTTCCCTAGGAATTTGACAATC-TTTCA
53317013 -AGGAGTTAAG-AGTTTTCCCTA-GAAGTTT-AGCAATCTTTCA
1 TAGGAGTTAAGCAGTTTTCCCTAGGAA-TTTGA-CAATCTTTCA
53317053 TAGGAGTTAA
1 TAGGAGTTAA
53317063 TAACATTCCC
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
40 9 0.20
41 25 0.57
42 10 0.23
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.38
Consensus pattern (42 bp):
TAGGAGTTAAGCAGTTTTCCCTAGGAATTTGACAATCTTTCA
Found at i:53330248 original size:137 final size:138
Alignment explanation
Indices: 53330001--53330303 Score: 437
Period size: 137 Copynumber: 2.2 Consensus size: 138
53329991 CACAAATAAA
* * * *
53330001 TAATATTCTTTTGGAAAGAATATAATTAATATATGAATTTGATTTATACAAAATATTGATTGTAT
1 TAATATTCTTTTGGAAAGAATATAATTAACATATGAATTTGATTCATACAAAATATTAACTGTAT
* * * *
53330066 ATATTTTACCAAATTTATTATTATAAACAATTGTATTAATTAATTTTGGTCAAAATATAAAAGAA
66 ATATTTTACCAAATTTATTAATATAAAAAATTATATTAATTAATTTCGGTCAAAATATAAAAGAA
53330131 ATAGAAAT
131 ATAGAAAT
** **
53330139 TAATATTCTTACGGAAAGAATATAATTAACATATTCA-TTGATTCATACAAAATATTAACTGTAT
1 TAATATTCTTTTGGAAAGAATATAATTAACATATGAATTTGATTCATACAAAATATTAACTGTAT
* * *
53330203 ATATTTTATCGAATTTATTAATATAAAAAATTATATTAATTAATTTCGGTCAAAATATAAAAGAC
66 ATATTTTACCAAATTTATTAATATAAAAAATTATATTAATTAATTTCGGTCAAAATATAAAAGAA
**
53330268 ATTTAAAT
131 ATAGAAAT
*
53330276 TAATATTCTTTTGGAAAGAATACAATTA
1 TAATATTCTTTTGGAAAGAATATAATTA
53330304 CTTTTTCCAA
Statistics
Matches: 145, Mismatches: 20, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
137 113 0.78
138 32 0.22
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (138 bp):
TAATATTCTTTTGGAAAGAATATAATTAACATATGAATTTGATTCATACAAAATATTAACTGTAT
ATATTTTACCAAATTTATTAATATAAAAAATTATATTAATTAATTTCGGTCAAAATATAAAAGAA
ATAGAAAT
Found at i:53330414 original size:75 final size:75
Alignment explanation
Indices: 53330278--53330424 Score: 199
Period size: 75 Copynumber: 2.0 Consensus size: 75
53330268 ATTTAAATTA
* * **
53330278 ATATTCTTTTGGAAAGAATACAATTACTTTTTCCAATTTTCCATTTGTCTTCTTTGTTAATAAGA
1 ATATTCTTTTGGAAAGAATACAATTACTTTTTCCAACTTTCCATTTGCCTTCTCAGTTAATAAGA
53330343 GAATAATCCT
66 GAATAATCCT
* *
53330353 ATATTCTTTTGGAAAGAATATAATT-CTTTTTTCTAACTTTCCATTTGCCTTCTCCAG-TAATAA
1 ATATTCTTTTGGAAAGAATACAATTAC-TTTTTCCAACTTTCCATTTGCCTTCT-CAGTTAATAA
*
53330416 GGGAATAAT
64 GAGAATAAT
53330425 AATGGTTTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
74 1 0.02
75 61 0.97
76 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (75 bp):
ATATTCTTTTGGAAAGAATACAATTACTTTTTCCAACTTTCCATTTGCCTTCTCAGTTAATAAGA
GAATAATCCT
Found at i:53357174 original size:15 final size:16
Alignment explanation
Indices: 53357147--53357176 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
53357137 AATTACAATT
53357147 AATATATATTATATAA
1 AATATATATTATATAA
53357163 AATATA-ATTATATA
1 AATATATATTATATA
53357177 TTAGTTGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATATATATTATATAA
Found at i:53388303 original size:41 final size:41
Alignment explanation
Indices: 53388239--53388334 Score: 122
Period size: 41 Copynumber: 2.3 Consensus size: 41
53388229 TCGAGTTTTT
* ** *
53388239 AGCCTAGCAGGCTTTATGCCGGTGAATTATTTCAGGCTTTA
1 AGCCTAGCAGGCTTAATGCCGGTGAACCATATCAGGCTTTA
* *
53388280 TA-CCTAGCAGGCTTAATGTCGGTGTACCATATCAGGCTTTA
1 -AGCCTAGCAGGCTTAATGCCGGTGAACCATATCAGGCTTTA
53388321 AGCCTAGCAGGCTT
1 AGCCTAGCAGGCTT
53388335 GGTGCCGATA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
40 1 0.02
41 45 0.96
42 1 0.02
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.31
Consensus pattern (41 bp):
AGCCTAGCAGGCTTAATGCCGGTGAACCATATCAGGCTTTA
Found at i:53391676 original size:17 final size:17
Alignment explanation
Indices: 53391628--53391669 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
53391618 CCTAAAGGGA
53391628 TTATGAAAGAAAAATAT
1 TTATGAAAGAAAAATAT
53391645 TTATGAAAGAAAAATAT
1 TTATGAAAGAAAAATAT
53391662 TTATGAAA
1 TTATGAAA
53391670 TGTAAATCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.57, C:0.00, G:0.12, T:0.31
Consensus pattern (17 bp):
TTATGAAAGAAAAATAT
Found at i:53394224 original size:27 final size:27
Alignment explanation
Indices: 53394169--53394231 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
53394159 CCAAAAAGGT
* *
53394169 TATTCTTTCATAATTTTCCACAAAGGC
1 TATTCTTTCATAATTATCCACAAAAGC
*
53394196 TATTCTTTCATAATTCAT-CATAAAAGC
1 TATTCTTTCATAATT-ATCCACAAAAGC
53394223 TATTCTTTC
1 TATTCTTTC
53394232 CTGTCATGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.30, C:0.21, G:0.05, T:0.44
Consensus pattern (27 bp):
TATTCTTTCATAATTATCCACAAAAGC
Found at i:53407654 original size:21 final size:21
Alignment explanation
Indices: 53407628--53407670 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
53407618 TCCGGGTGGA
53407628 TCAGCTCTTATGAGCTTCTGT
1 TCAGCTCTTATGAGCTTCTGT
*
53407649 TCAGCTTTTATGAGCTTCTGT
1 TCAGCTCTTATGAGCTTCTGT
53407670 T
1 T
53407671 GGAATGTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (21 bp):
TCAGCTCTTATGAGCTTCTGT
Found at i:53424542 original size:43 final size:43
Alignment explanation
Indices: 53424479--53424565 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
53424469 TTGCCAGATA
*
53424479 TAGAATTCGTGGTTTGTATTCTTTAACTATCGACCTAGATTCT
1 TAGAATTCGTGGTTTCTATTCTTTAACTATCGACCTAGATTCT
*
53424522 TAGAATTCGTGGTTTCTATTCTTTAACTATCGACTTAGATTCT
1 TAGAATTCGTGGTTTCTATTCTTTAACTATCGACCTAGATTCT
53424565 T
1 T
53424566 TCTTACTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.23, C:0.16, G:0.15, T:0.46
Consensus pattern (43 bp):
TAGAATTCGTGGTTTCTATTCTTTAACTATCGACCTAGATTCT
Found at i:53426099 original size:14 final size:13
Alignment explanation
Indices: 53426079--53426112 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
53426069 AATCAAGCAA
53426079 AAAAAATTAGAATT
1 AAAAAATTA-AATT
*
53426093 TAAAAATTAAATT
1 AAAAAATTAAATT
53426106 AAAAAAT
1 AAAAAAT
53426113 ATTAAAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (13 bp):
AAAAAATTAAATT
Found at i:53426116 original size:15 final size:15
Alignment explanation
Indices: 53426078--53426125 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 15
53426068 GAATCAAGCA
*
53426078 AAAAAAATTAGAATT
1 AAAAAAATTAAAATT
*
53426093 -TAAAAATT-AAATT
1 AAAAAAATTAAAATT
53426106 AAAAAATATTAAAATT
1 AAAAAA-ATTAAAATT
53426122 AAAA
1 AAAA
53426126 TTAAAATGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
13 4 0.15
14 11 0.41
15 3 0.11
16 9 0.33
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (15 bp):
AAAAAAATTAAAATT
Found at i:53427864 original size:47 final size:48
Alignment explanation
Indices: 53427754--53427870 Score: 125
Period size: 47 Copynumber: 2.5 Consensus size: 48
53427744 TTAAAAATTG
* *
53427754 ATGAT-AATTTAAAAATAATAATACGTGATAAATTCAAAATAATAATAT
1 ATGATAAATTT-AAAATAATAATACATGATAAACTCAAAATAATAATAT
* * * **
53427802 ATGTTAACTTT-AAATAAAAATACATGATAAAC-CTAAAATAATGTTA-
1 ATGATAAATTTAAAATAATAATACATGATAAACTC-AAAATAATAATAT
53427848 ATGATAAATTTAAAATAATAATA
1 ATGATAAATTTAAAATAATAATA
53427871 TATTATAATA
Statistics
Matches: 56, Mismatches: 10, Indels: 7
0.77 0.14 0.10
Matches are distributed among these distances:
46 10 0.18
47 38 0.68
48 4 0.07
49 4 0.07
ACGTcount: A:0.56, C:0.05, G:0.06, T:0.33
Consensus pattern (48 bp):
ATGATAAATTTAAAATAATAATACATGATAAACTCAAAATAATAATAT
Found at i:53427884 original size:24 final size:23
Alignment explanation
Indices: 53427724--53427888 Score: 124
Period size: 24 Copynumber: 7.2 Consensus size: 23
53427714 ATAAATTTGG
*
53427724 AATAATAATACATGATAAATTTA
1 AATAATAATACATGATAAATTAA
* *
53427747 AA-AAT--T-GATGATAATTTAAA
1 AATAATAATACATGATAAATT-AA
*
53427767 AATAATAATACGTGATAAATTCAA
1 AATAATAATACATGATAAATT-AA
* * * *
53427791 AATAATAATATATGTTAACTTTA
1 AATAATAATACATGATAAATTAA
* *
53427814 AATAAAAATACATGATAAACCTAA
1 AATAATAATACATGATAAA-TTAA
**
53427838 AATAATGTTA-ATGATAAATTTAA
1 AATAATAATACATGATAAA-TTAA
* *
53427861 AATAATAATATATTATAATATTAA
1 AATAATAATACATGATAA-ATTAA
53427885 AATA
1 AATA
53427889 GTATTGATAA
Statistics
Matches: 108, Mismatches: 26, Indels: 15
0.72 0.17 0.10
Matches are distributed among these distances:
19 9 0.08
20 4 0.04
21 3 0.03
22 3 0.03
23 38 0.35
24 50 0.46
25 1 0.01
ACGTcount: A:0.56, C:0.04, G:0.05, T:0.35
Consensus pattern (23 bp):
AATAATAATACATGATAAATTAA
Found at i:53429410 original size:45 final size:45
Alignment explanation
Indices: 53429361--53429464 Score: 111
Period size: 45 Copynumber: 2.3 Consensus size: 45
53429351 TTAATCTACT
* *
53429361 CCACTATAACTTCAAGGACATAAGA-TTCACCATCTTTAGTCTGCC
1 CCACTGTAACTTCAAGGACATAAGACTT-ACCATCTTCAGTCTGCC
* * ** * * *
53429406 CCACTGCAACTTCAGGGGGATAAGACTTGCTATCTTCAGTCTGCT
1 CCACTGTAACTTCAAGGACATAAGACTTACCATCTTCAGTCTGCC
53429451 CCACTGTAACTTCA
1 CCACTGTAACTTCA
53429465 GGGAGATAGG
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
45 46 0.96
46 2 0.04
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (45 bp):
CCACTGTAACTTCAAGGACATAAGACTTACCATCTTCAGTCTGCC
Found at i:53429661 original size:51 final size:50
Alignment explanation
Indices: 53429595--53430120 Score: 518
Period size: 51 Copynumber: 10.8 Consensus size: 50
53429585 CTATTGTAAT
* * *
53429595 GCCAGGGAAACAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTACAAC
1 GCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCT-TTCCACTGCAAC
* *
53429646 GCCAAGGAAATAAGATTCGCTGTCTTCAGCTCTAATC--T--ACTGCAAC
1 GCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTTTCCACTGCAAC
* * *
53429692 GCC-AGAGAAATAAGATTTGCTGCCTTCAGCATTAATCTGTTCCACTGTAAC
1 GCCAAG-GAAATAAGATTCGCTGCCTTCAGCTTTAATCT-TTCCACTGCAAC
* * * * *
53429743 ACCAATGAAACAAGATTCGCTGCCTTTAGCTTTAATC--T--ATTGCAAC
1 GCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTTTCCACTGCAAC
* * *
53429789 GCCAGGGAAACAAG--TCACTGCCTTCAGCTTTAATCTATTCCACTGCAAC
1 GCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCT-TTCCACTGCAAC
* * * *
53429838 GGCAAGGAAATAAGATCCGTTGCCATT-AGCTTTAATC--T--ATTGCAAC
1 GCCAAGGAAATAAGATTCGCTGCC-TTCAGCTTTAATCTTTCCACTGCAAC
* * * * *
53429884 G-CAAGGGAAACAAGATTTGCTACCTTTAGCTTTAATCTGTTCCACTGCAAT
1 GCCAA-GGAAATAAGATTCGCTGCCTTCAGCTTTAATCT-TTCCACTGCAAC
*
53429935 GCCAAGGAAATAAGATTCGCTGTCTTCAGCTTTAATCTGTTCCACTGCAAC
1 GCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCT-TTCCACTGCAAC
* * *
53429986 GCCAAGGAAATAAGATTCGCTACCTTCAGCTTTAATCTATTGCACTACAAC
1 GCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCT-TTCCACTGCAAC
* *
53430037 GCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAA--TAT--ATTGCAAC
1 GCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTTTCCACTGCAAC
* * *
53430083 GCTAGGGAAACAAGATTCGCTGCCTTCAGCTTTAATCT
1 GCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCT
53430121 ATTGCAACGC
Statistics
Matches: 394, Mismatches: 56, Indels: 53
0.78 0.11 0.11
Matches are distributed among these distances:
44 19 0.05
45 7 0.02
46 124 0.31
47 1 0.00
48 5 0.01
49 21 0.05
51 211 0.54
52 6 0.02
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (50 bp):
GCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTTTCCACTGCAAC
Found at i:53429727 original size:97 final size:97
Alignment explanation
Indices: 53429576--53430120 Score: 682
Period size: 97 Copynumber: 5.6 Consensus size: 97
53429566 TGTGACTTAT
** * *
53429576 AGCTTTAGCCTATTGTAATGCCAGGGAAACAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACT
1 AGCTTTAATCTATTGCAACGCCAGGGAAACAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACT
* *
53429641 ACAACGCCAAGGAAATAAGATTCGCTGTCTTC
66 GCAACGCCAAGGAAATAAGATTCGCTGCCTTC
* * * * * *
53429673 AGCTCTAATCTACTGCAACGCCAGAGAAATAAGATTTGCTGCCTTCAGCATTAATCTGTTCCACT
1 AGCTTTAATCTATTGCAACGCCAGGGAAACAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACT
* * * * *
53429738 GTAACACCAATGAAACAAGATTCGCTGCCTTT
66 GCAACGCCAAGGAAATAAGATTCGCTGCCTTC
* *
53429770 AGCTTTAATCTATTGCAACGCCAGGGAAACAAG--TCACTGCCTTCAGCTTTAATCTATTCCACT
1 AGCTTTAATCTATTGCAACGCCAGGGAAACAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACT
* * *
53429833 GCAACGGCAAGGAAATAAGATCCGTTGCCATT-
66 GCAACGCCAAGGAAATAAGATTCGCTGCC-TTC
* * * *
53429865 AGCTTTAATCTATTGCAACGCAAGGGAAACAAGATTTGCTACCTTTAGCTTTAATCTGTTCCACT
1 AGCTTTAATCTATTGCAACGCCAGGGAAACAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACT
* *
53429930 GCAATGCCAAGGAAATAAGATTCGCTGTCTTC
66 GCAACGCCAAGGAAATAAGATTCGCTGCCTTC
* * * * *
53429962 AGCTTTAATCTGTTCCACTGCAACGCCAAGGAAATAAGATTCGCTACCTTCAGCTTTAATCTATT
1 AGCTTTAATC---T--ATTGCAACGCCAGGGAAACAAGATTCGCTGCCTTCAGCTTTAATCTGTT
* *
53430027 GCACTACAACGCCAAGGAAATAAGATTCGCTGCCTTC
61 CCACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTC
* *
53430064 AGCTTTAATATATTGCAACGCTAGGGAAACAAGATTCGCTGCCTTCAGCTTTAATCT
1 AGCTTTAATCTATTGCAACGCCAGGGAAACAAGATTCGCTGCCTTCAGCTTTAATCT
53430121 ATTGCAACGC
Statistics
Matches: 379, Mismatches: 60, Indels: 18
0.83 0.13 0.04
Matches are distributed among these distances:
95 80 0.21
96 4 0.01
97 209 0.55
99 1 0.00
100 1 0.00
102 84 0.22
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (97 bp):
AGCTTTAATCTATTGCAACGCCAGGGAAACAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACT
GCAACGCCAAGGAAATAAGATTCGCTGCCTTC
Found at i:53431880 original size:27 final size:27
Alignment explanation
Indices: 53431850--53431914 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
53431840 CCACAATGAA
* *
53431850 CATTTCTTTTAG-GTACGCCACGAAAG
1 CATTTCTTTTAGAGTACCCCACAAAAG
* *
53431876 CCA-TTCCTTCAGAGTACCCCACAAAAG
1 -CATTTCTTTTAGAGTACCCCACAAAAG
53431903 CATTTCTTTTAG
1 CATTTCTTTTAG
53431915 TTTATCGCTA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
26 9 0.30
27 21 0.70
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (27 bp):
CATTTCTTTTAGAGTACCCCACAAAAG
Found at i:53431983 original size:27 final size:27
Alignment explanation
Indices: 53431946--53432021 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
53431936 CTTTGAGAGA
* *
53431946 TCACCAAAAAGGTTATTCTTTCATAAT
1 TCACCACAAAGGCTATTCTTTCATAAT
**
53431973 TTGCCACAAAGGCTATTCTTTCATAAT
1 TCACCACAAAGGCTATTCTTTCATAAT
*
53432000 TCATCACAAAGGCTATTCTTTC
1 TCACCACAAAGGCTATTCTTTC
53432022 CTGTCATGTT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.37
Consensus pattern (27 bp):
TCACCACAAAGGCTATTCTTTCATAAT
Found at i:53434163 original size:29 final size:29
Alignment explanation
Indices: 53434121--53434176 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
53434111 TGCCCATTGA
53434121 GGTGTGCATTATGCTATTTTAGCTTTTGG
1 GGTGTGCATTATGCTATTTTAGCTTTTGG
53434150 GGTGTGCATTATGCTATTTTAGCTTTT
1 GGTGTGCATTATGCTATTTTAGCTTTT
53434177 TTTATCTCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.14, C:0.11, G:0.25, T:0.50
Consensus pattern (29 bp):
GGTGTGCATTATGCTATTTTAGCTTTTGG
Found at i:53439544 original size:26 final size:24
Alignment explanation
Indices: 53439515--53439562 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
53439505 TAAAAAGTGA
*
53439515 TGATAATTTAAAAAATTAATAATACG
1 TGATAAATT-AAAAA-TAATAATACG
*
53439541 TGATAAATTCAAAATAATAATA
1 TGATAAATTAAAAATAATAATA
53439563 TATGTTAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
25 4 0.20
26 8 0.40
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.33
Consensus pattern (24 bp):
TGATAAATTAAAAATAATAATACG
Found at i:53441229 original size:44 final size:44
Alignment explanation
Indices: 53441032--53441288 Score: 191
Period size: 44 Copynumber: 5.9 Consensus size: 44
53441022 CGTCTTGTTT
** * * * * *
53441032 CTTCAATCCACTCTACTGCAACTTCAAGGTGATAGGATTATTGG
1 CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTACTAG
* * * * *
53441076 CTTTAATCTGCTCTACTGCAACTTCAAGGACATAAGATTCACCAT
1 CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATT-ACTAG
* * * * * * *
53441121 CTTCAGTCTACCCCACTGCAACTTCAGGGGGATAAGACTTGCTAT
1 CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGA-TTACTAG
* * * * *
53441166 CTTCAGTCTGCTCCACTGCAACTTCAAGGAAATAGGATTATTGG
1 CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTACTAG
* *
53441210 CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-C--G
1 CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTACTAG
* *
53441251 CCTT-GATCTGCTCTACTGCAACTTC-AGAGAGATAAGAT
1 -CTTCAATCTGCTCCACTGCAACTTCAAG-GAGATAAGAT
53441289 CTGTGACTTA
Statistics
Matches: 170, Mismatches: 39, Indels: 11
0.77 0.18 0.05
Matches are distributed among these distances:
40 1 0.01
41 30 0.18
42 3 0.02
44 70 0.41
45 64 0.38
46 2 0.01
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.30
Consensus pattern (44 bp):
CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTACTAG
Found at i:53441272 original size:41 final size:42
Alignment explanation
Indices: 53441081--53441288 Score: 170
Period size: 45 Copynumber: 4.8 Consensus size: 42
53441071 ATTGGCTTTA
* * * *
53441081 ATCTGCTCTACTGCAACTTCAAGGACATAAGATTCACCATCTTC
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTC-GC-TCTTC
* * *
53441125 AGTCTACCCCACTGCAACTTCAGGGGGATAAGACTT-GCTATCTTC
1 A-TCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTCGC--TCTTC
* * * * *
53441170 AGTCTGCTCCACTGCAACTTCAAGGAAATAGGATTATTGGCT-TTA
1 A-TCTGCTCCACTGCAACTTCAGGGAGATA--A-GATTCGCTCTTC
*
53441215 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGC-CTTG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTCTTC
* *
53441256 ATCTGCTCTACTGCAACTTCAGAGAGATAAGAT
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
53441289 CTGTGACTTA
Statistics
Matches: 135, Mismatches: 21, Indels: 19
0.77 0.12 0.11
Matches are distributed among these distances:
41 38 0.28
42 1 0.01
44 28 0.21
45 59 0.44
46 3 0.02
47 3 0.02
48 3 0.02
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.28
Consensus pattern (42 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTCTTC
Found at i:53441350 original size:46 final size:46
Alignment explanation
Indices: 53441300--53442179 Score: 724
Period size: 46 Copynumber: 18.3 Consensus size: 46
53441290 TGTGACTTAT
* *
53441300 AGCTTTAATCTATTGCAATGCCAGGGAAACAAGATTTGCTGCCTTC
1 AGCTTTAATCTATTGCAACGCCAGGGAAACAAGATTCGCTGCCTTC
* * * * * *
53441346 AGCTTTAATCTGTTCCACTACAACGCCAAGGAAATAAGATTAGCTGTCTTC
1 AGCTTTAATC---T--ATTGCAACGCCAGGGAAACAAGATTCGCTGCCTTC
* * * * *
53441397 AGCTCTAATTTACTGCAACGCCAGGGAAATAAGATTTGCTGCCTTC
1 AGCTTTAATCTATTGCAACGCCAGGGAAACAAGATTCGCTGCCTTC
* * * * * * * *
53441443 AGCATTAATCTGTTCCACTACAACACCAAGGAAATAAGATTTGCTGTCTTC
1 AGCTTTAATC---T--ATTGCAACGCCAGGGAAACAAGATTCGCTGCCTTC
* *
53441494 AGCTTTAATCTATTGCAACGCGAGGGAAACAAGATTCACTGCCTTC
1 AGCTTTAATCTATTGCAACGCCAGGGAAACAAGATTCGCTGCCTTC
*
53441540 AGCTTCAATCTATTGCAACGCCAGGGAAACAAG--TCGCTGCCTTC
1 AGCTTTAATCTATTGCAACGCCAGGGAAACAAGATTCGCTGCCTTC
* * * * * *
53441584 AGCTTTAATCTGTTCCACTGCAACGGCAAGGAAATAAGATTCGTTGCCATC
1 AGCTTTAATC---T--ATTGCAACGCCAGGGAAACAAGATTCGCTGCCTTC
* *
53441635 AGCTTTAATCTATTGCAACGCAAGGGAAACAAGATTTGCTGCCTTC
1 AGCTTTAATCTATTGCAACGCCAGGGAAACAAGATTCGCTGCCTTC
* * * *
53441681 AGCTTTAATCTGTT-CCACTGCAACACCGAGGACATAAGATTCGCTGCCTTC
1 AGCTTTAATCTATTGCAAC-GC--CA--G-GGAAACAAGATTCGCTGCCTTC
*
53441732 AGCTTTAATCTATTGCAACGCTAGGGAAACAAGA-TCTGCTGCCTTC
1 AGCTTTAATCTATTGCAACGCCAGGGAAACAAGATTC-GCTGCCTTC
* * * * *
53441778 AGCTTTAATCTGTTCCACTACAATGCCAAGGAAATAAGATTCGCTACCTTC
1 AGCTTTAATCTATTGCA--AC---GCCAGGGAAACAAGATTCGCTGCCTTC
* * * *
53441829 AGCTTTAATCTGTTCCACTGCAACGCCAAGGAAATAAGATTCTCTGCCTTC
1 AGCTTTAATC---T--ATTGCAACGCCAGGGAAACAAGATTCGCTGCCTTC
* * * *
53441880 AGCTTTAATCTATTGCAATGCTAGGGAAACAAGATTCGCTGACTTT
1 AGCTTTAATCTATTGCAACGCCAGGGAAACAAGATTCGCTGCCTTC
* * *
53441926 AGCTTTAATCTATTGGAATGCCAGAGAAACAAGATTCGCTGCCTTC
1 AGCTTTAATCTATTGCAACGCCAGGGAAACAAGATTCGCTGCCTTC
* * * *
53441972 AGCTTTAATCTGTTCCACTGCAACGCCAAGGAAATAAGATTCACTGCCTTC
1 AGCTTTAATC---T--ATTGCAACGCCAGGGAAACAAGATTCGCTGCCTTC
* *
53442023 AACTTTAATCTATTGCAATGCCAGGGAAACAAGATTCGCTGCCTTC
1 AGCTTTAATCTATTGCAACGCCAGGGAAACAAGATTCGCTGCCTTC
* * ** * *
53442069 AGCTTTAATCTGTTCCACTACAACGCCAAAGAAATAATATTCGCTGCCTTC
1 AGCTTTAATC---T--ATTGCAACGCCAGGGAAACAAGATTCGCTGCCTTC
* * *
53442120 AGGTTTAATCTATTACAACGCCAGGGAGACAAGATTCGCTGCCTTC
1 AGCTTTAATCTATTGCAACGCCAGGGAAACAAGATTCGCTGCCTTC
* *
53442166 ATCTTTAATGTATT
1 AGCTTTAATCTATT
53442180 CCACTGCAAC
Statistics
Matches: 674, Mismatches: 114, Indels: 92
0.77 0.13 0.10
Matches are distributed among these distances:
44 19 0.03
45 5 0.01
46 336 0.50
47 2 0.00
48 9 0.01
49 23 0.03
50 1 0.00
51 268 0.40
52 5 0.01
54 3 0.00
56 3 0.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (46 bp):
AGCTTTAATCTATTGCAACGCCAGGGAAACAAGATTCGCTGCCTTC
Found at i:53441431 original size:97 final size:96
Alignment explanation
Indices: 53441313--53442206 Score: 752
Period size: 97 Copynumber: 9.2 Consensus size: 96
53441303 TTTAATCTAT
* * * *
53441313 TGCAATGCCAGGGAAACAAGATTTGCTGCCTTCAGCTTTAATCTGTTCCACTACAACGCCAAGGA
1 TGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATC--TT--ACTGCAACGCCAAGGA
* * * *
53441378 AATAAGATTAGCTGTCTTCAGCTCTAA-T-TT-AC
62 AACAAGATTCGCTGCCTTCAGCTTTAACTGTTCAC
* * * *
53441410 TGCAACGCCAGGGAAATAAGATTTGCTGCCTTCAGCATTAATCTGTTCCACTACAACACCAAGGA
1 TGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATC--TT--ACTGCAACGCCAAGGA
* * * * *
53441475 AATAAGATTTGCTGTCTTCAGCTTTAA-T-CT-AT
62 AACAAGATTCGCTGCCTTCAGCTTTAACTGTTCAC
* * * * * *
53441507 TGCAACGCGAGGGAAACAAGATTCACTGCCTTCAGCTTCAATC-TATTGCAACGCCAGGGAAACA
1 TGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTTACTGCAACGCCAAGGAAACA
53441571 AG--TCGCTGCCTTCAGCTTTAATCTGTTCCAC
66 AGATTCGCTGCCTTCAGCTTTAA-CTGTT-CAC
* * * * *
53441602 TGCAACGGCAAGGAAATAAGATTCGTTGCCATCAGCTTTAATC-TATTGCAACG-CAAGGGAAAC
1 TGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTTACTGCAACGCCAA-GGAAAC
*
53441665 AAGATTTGCTGCCTTCAGCTTTAATCTGTTCCAC
65 AAGATTCGCTGCCTTCAGCTTTAA-CTGTT-CAC
* * * * *
53441699 TGCAACACC-GAGGACATAAGATTCGCTGCCTTCAGCTTTAATC-TATTGCAACGCTAGGGAAAC
1 TGCAACGCCAG-GGAAATAAGATTCGCTGCCTTCAGCTTTAATCTTACTGCAACGCCAAGGAAAC
53441762 AAGA-TCTGCTGCCTTCAGCTTTAATCTGTTCCAC
65 AAGATTC-GCTGCCTTCAGCTTTAA-CTGTT-CAC
* * * *
53441796 TACAATGCCAAGGAAATAAGATTCGCTACCTTCAGCTTTAATCTGTTCCACTGCAACGCCAAGGA
1 TGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATC--TT--ACTGCAACGCCAAGGA
* * * *
53441861 AATAAGATTCTCTGCCTTCAGCTTTAA-T-CT-AT
62 AACAAGATTCGCTGCCTTCAGCTTTAACTGTTCAC
* * * * * * * *
53441893 TGCAATGCTAGGGAAACAAGATTCGCTGACTTTAGCTTTAATC-TATTGGAATGCC-AGAGAAAC
1 TGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTTACTGCAACGCCAAG-GAAAC
53441956 AAGATTCGCTGCCTTCAGCTTTAATCTGTTCCAC
65 AAGATTCGCTGCCTTCAGCTTTAA-CTGTT-CAC
* * * * * *
53441990 TGCAACGCCAAGGAAATAAGATTCACTGCCTTCAACTTTAATC-TATTGCAATGCCAGGGAAACA
1 TGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTTACTGCAACGCCAAGGAAACA
53442054 AGATTCGCTGCCTTCAGCTTTAATCTGTTCCAC
66 AGATTCGCTGCCTTCAGCTTTAA-CTGTT-CAC
* ** * * * * * *
53442087 TACAACGCCAAAGAAATAATATTCGCTGCCTTCAGGTTTAATC-TATTACAACGCCAGGGAGACA
1 TGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTTACTGCAACGCCAAGGAAACA
*
53442151 AGATTCGCTGCCTTCATCTTTAA-TGTATTCCAC
66 AGATTCGCTGCCTTCAGCTTTAACTG--TT-CAC
* * *
53442184 TGCAACACCCGGGAAAAAAGATT
1 TGCAACGCCAGGGAAATAAGATT
53442207 TGCCATAATG
Statistics
Matches: 674, Mismatches: 96, Indels: 54
0.82 0.12 0.07
Matches are distributed among these distances:
90 17 0.03
91 2 0.00
92 53 0.08
93 1 0.00
94 5 0.01
95 58 0.09
96 1 0.00
97 495 0.73
98 2 0.00
99 1 0.00
100 2 0.00
102 35 0.05
103 2 0.00
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (96 bp):
TGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTTACTGCAACGCCAAGGAAACA
AGATTCGCTGCCTTCAGCTTTAACTGTTCAC
Found at i:53441834 original size:194 final size:194
Alignment explanation
Indices: 53441324--53442189 Score: 883
Period size: 194 Copynumber: 4.5 Consensus size: 194
53441314 GCAATGCCAG
* * * * * * *
53441324 GGAAACAAGATTTGCTGCCTTCAGCTTTAATCTGTTCCACTACAACGCCAAGGAAATAAGATTAG
1 GGAAATAAGATTCGCTGCCTTCAGCTTTAATC---T--ATTGCAACGCCAGGGAAACAAGATTCG
* * * * *
53441389 CTGTCTTCAGCTCTAA--T-TT--ACTGCAACGCCAGGGAAATAAGATTTGCTGCCTTCAGCATT
61 CTGCCTTCAGCTTTAATCTGTTCCACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTT
* * * * * * *
53441449 AATCTGTTCCACTACAACACCAAGGAAATAAGATTTGCTGTCTTCAGCTTTAATC---T--ATTG
126 AATCTATTGCA--AC-GCA--AGGGAAACAAGATTTGCTGCCTTCAGCTTTAATCTGTTCCACTG
*
53441509 CAAC-GCGA
186 CAACACCGA
* * *
53441517 GGGAAACAAGATTCACTGCCTTCAGCTTCAATCTATTGCAACGCCAGGGAAACAAG--TCGCTGC
1 -GGAAATAAGATTCGCTGCCTTCAGCTTTAATCTATTGCAACGCCAGGGAAACAAGATTCGCTGC
* * *
53441580 CTTCAGCTTTAATCTGTTCCACTGCAACGGCAAGGAAATAAGATTCGTTGCCATCAGCTTTAATC
65 CTTCAGCTTTAATCTGTTCCACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATC
53441645 TATTGCAACGCAAGGGAAACAAGATTTGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACACCGA
130 TATTGCAACGCAAGGGAAACAAGATTTGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACACCGA
* *
53441710 GGACATAAGATTCGCTGCCTTCAGCTTTAATCTATTGCAACGCTAGGGAAACAAGA-TCTGCTGC
1 GGAAATAAGATTCGCTGCCTTCAGCTTTAATCTATTGCAACGCCAGGGAAACAAGATTC-GCTGC
* * *
53441774 CTTCAGCTTTAATCTGTTCCACTACAATGCCAAGGAAATAAGATTCGCTACCTTCAGCTTTAATC
65 CTTCAGCTTTAATCTGTTCCACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATC
* * * * *
53441839 TGTTCCACTGCAACGCCAA-GGAAATAAGATTCT-CTGCCTTCAGCTTTAATCTATTGCAATGC-
130 ---T--ATTGCAACG-CAAGGGAAACAAGATT-TGCTGCCTTCAGCTTTAATCTGTTCCACTGCA
*
53441901 -TA--G-
188 ACACCGA
* * * * * *
53441904 GGAAACAAGATTCGCTGACTTTAGCTTTAATCTATTGGAATGCCAGAGAAACAAGATTCGCTGCC
1 GGAAATAAGATTCGCTGCCTTCAGCTTTAATCTATTGCAACGCCAGGGAAACAAGATTCGCTGCC
* *
53441969 TTCAGCTTTAATCTGTTCCACTGCAACGCCAAGGAAATAAGATTCACTGCCTTCAACTTTAATCT
66 TTCAGCTTTAATCTGTTCCACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCT
* * * * * *
53442034 ATTGCAATGCCAGGGAAACAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTACAACGCCAA
131 ATTGCAACGCAAGGGAAACAAGATTTGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACACCGA
* * * * *
53442098 AGAAATAATATTCGCTGCCTTCAGGTTTAATCTATTACAACGCCAGGGAGACAAGATTCGCTGCC
1 GGAAATAAGATTCGCTGCCTTCAGCTTTAATCTATTGCAACGCCAGGGAAACAAGATTCGCTGCC
* * *
53442163 TTCATCTTTAATGTATTCCACTGCAAC
66 TTCAGCTTTAATCTGTTCCACTGCAAC
53442190 ACCCGGGAAA
Statistics
Matches: 564, Mismatches: 80, Indels: 56
0.81 0.11 0.08
Matches are distributed among these distances:
187 47 0.08
188 2 0.00
189 64 0.11
190 5 0.01
191 2 0.00
192 101 0.18
193 5 0.01
194 284 0.50
195 3 0.01
197 2 0.00
199 45 0.08
200 4 0.01
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (194 bp):
GGAAATAAGATTCGCTGCCTTCAGCTTTAATCTATTGCAACGCCAGGGAAACAAGATTCGCTGCC
TTCAGCTTTAATCTGTTCCACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCT
ATTGCAACGCAAGGGAAACAAGATTTGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACACCGA
Found at i:53443459 original size:14 final size:15
Alignment explanation
Indices: 53443435--53443470 Score: 65
Period size: 14 Copynumber: 2.5 Consensus size: 15
53443425 GCCTCTCTAT
53443435 TTTTTACTTTTTTCA
1 TTTTTACTTTTTTCA
53443450 TTTTTA-TTTTTTCA
1 TTTTTACTTTTTTCA
53443464 TTTTTAC
1 TTTTTAC
53443471 GACTCAAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTTACTTTTTTCA
Found at i:53449736 original size:13 final size:14
Alignment explanation
Indices: 53449705--53449739 Score: 54
Period size: 13 Copynumber: 2.5 Consensus size: 14
53449695 ATGAAACGAA
53449705 TTAAAATAAATCAAT
1 TTAAAA-AAATCAAT
53449720 TTAAAAAAATC-AT
1 TTAAAAAAATCAAT
53449733 TTAAAAA
1 TTAAAAA
53449740 TACATGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 9 0.45
14 5 0.25
15 6 0.30
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (14 bp):
TTAAAAAAATCAAT
Found at i:53450069 original size:18 final size:19
Alignment explanation
Indices: 53450035--53450078 Score: 63
Period size: 18 Copynumber: 2.3 Consensus size: 19
53450025 TTGGAATAAT
53450035 AATACATGATAAATTTAAAA
1 AATA-ATGATAAATTTAAAA
*
53450055 ATTAATGAT-AATTTAAAA
1 AATAATGATAAATTTAAAA
53450073 AATAAT
1 AATAAT
53450079 AATACGTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 14 0.64
19 5 0.23
20 3 0.14
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (19 bp):
AATAATGATAAATTTAAAA
Found at i:53455078 original size:24 final size:24
Alignment explanation
Indices: 53455050--53455099 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
53455040 AGGTCCTCAG
53455050 TCATTCATTCTATCGGTTCCAAAA
1 TCATTCATTCTATCGGTTCCAAAA
* *
53455074 TCATTCGTTCTATCGGTTCCCAAA
1 TCATTCATTCTATCGGTTCCAAAA
53455098 TC
1 TC
53455100 CTAACAATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.28, G:0.10, T:0.38
Consensus pattern (24 bp):
TCATTCATTCTATCGGTTCCAAAA
Found at i:53457842 original size:126 final size:129
Alignment explanation
Indices: 53457613--53457844 Score: 319
Period size: 126 Copynumber: 1.8 Consensus size: 129
53457603 TGCATTTTTT
* *** *
53457613 TTGCAATGAAGAGTGTTATTGTGAGCTATCTCATACTTCGAAAGATTTTTTTGTAAAATATTTTC
1 TTGCAATGAAGAGCGTTATTGTGAGCTATCTCATACTTCGAAAGAACATTTTGGAAAATATTTTC
*
53457678 GTATGCGAACCTTGGTTTTACAGCTTGAAGCTTCGCTCTCGTGAACTATGATGTGGCTCTTCGCA
66 -TATGCGAACCTTGGTTTTACAGCTAGAAGCTTCGCTCTCGTGAACTATGATGTGGCTCTTCGCA
* * *
53457743 TTGCAATGAAGAGCGTTGTTGTGAGCTATTTTATACTT-GAAA-AACATTTTGGAAACAT-TTTT
1 TTGCAATGAAGAGCGTTATTGTGAGCTATCTCATACTTCGAAAGAACATTTTGGAAA-ATATTTT
* *
53457805 -TATGCGAACCTTGGTTTTACAGCTAGGAGCTTTGCTCTCG
65 CTATGCGAACCTTGGTTTTACAGCTAGAAGCTTCGCTCTCG
53457845 CTAGCTGTGC
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
126 37 0.41
128 13 0.14
129 6 0.07
130 34 0.38
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (129 bp):
TTGCAATGAAGAGCGTTATTGTGAGCTATCTCATACTTCGAAAGAACATTTTGGAAAATATTTTC
TATGCGAACCTTGGTTTTACAGCTAGAAGCTTCGCTCTCGTGAACTATGATGTGGCTCTTCGCA
Found at i:53457930 original size:69 final size:69
Alignment explanation
Indices: 53457810--53458309 Score: 396
Period size: 69 Copynumber: 7.2 Consensus size: 69
53457800 TTTTTTATGC
** * * * * *
53457810 GAACCTTGGTTTTACAGCTAGGAGCTTTGCTCTCGCTAGCTGTGCTAGAGGTTGTGGCTTTTTGC
1 GAACCTTAATTTTACAGTTGGGAGCTTTGCTCTCGCTAACTGTGCTAGAGGTTGTGGCTCTTCGC
*
53457875 CTGG
66 CTGT
** * * ** * *
53457879 GGTCCTTAATTTTACAGTTGGGAGCTTTGCCCTCGCTAACTGTGTTAGAGGTCATGGCACTTCAC
1 GAACCTTAATTTTACAGTTGGGAGCTTTGCTCTCGCTAACTGTGCTAGAGGTTGTGGCTCTTCGC
*
53457944 CTGC
66 CTGT
* * * * * *
53457948 GAACCTTAGTTTTACAGATGGGAGCTTTGCTCTCACTAACTATG-TTGCAGGTCGTGGCTCTTCG
1 GAACCTTAATTTTACAGTTGGGAGCTTTGCTCTCGCTAACTGTGCTAG-AGGTTGTGGCTCTTCG
*
53458012 CCTAT
65 CCTGT
* * * * **** *
53458017 -AGACCTTAATTTTACAATTGAGAGCTTTGCTCTTGCTAACTGTGCTGGAGGTTACACCTCTTTG
1 GA-ACCTTAATTTTACAGTTGGGAGCTTTGCTCTCGCTAACTGTGCTAGAGGTTGTGGCTCTTCG
53458081 CCTGT
65 CCTGT
* * * * *
53458086 GAACCTTAATTTTACAGTTGGGAACTTTGCTCTCGCTACCTATGCTGGAGGTTGTGCCTCTTCGC
1 GAACCTTAATTTTACAGTTGGGAGCTTTGCTCTCGCTAACTGTGCTAGAGGTTGTGGCTCTTCGC
53458151 CTG-
66 CTGT
* * * * * * * ** * * *
53458154 CAACCCTTAATTTTATAGCTAGGAGATTTGTTCTCGTTAGTTGTGCTGGAGGTCGTGGCTCTTCA
1 GAA-CCTTAATTTTACAGTTGGGAGCTTTGCTCTCGCTAACTGTGCTAGAGGTTGTGGCTCTTCG
*
53458219 CCTGC
65 CCTGT
* ** * * ***
53458224 AAACCTTAATTTTACAACTGGGAGCTTTGCTCTTGCTAACTGTGCT-GAAGGTCGCAACTCTTCG
1 GAACCTTAATTTTACAGTTGGGAGCTTTGCTCTCGCTAACTGTGCTAG-AGGTTGTGGCTCTTCG
53458288 CCTGT
65 CCTGT
*
53458293 AAACCTTAATTTTACAG
1 GAACCTTAATTTTACAG
53458310 GTAACATTTT
Statistics
Matches: 340, Mismatches: 84, Indels: 14
0.78 0.19 0.03
Matches are distributed among these distances:
68 6 0.02
69 329 0.97
70 5 0.01
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (69 bp):
GAACCTTAATTTTACAGTTGGGAGCTTTGCTCTCGCTAACTGTGCTAGAGGTTGTGGCTCTTCGC
CTGT
Found at i:53458055 original size:138 final size:137
Alignment explanation
Indices: 53457807--53458309 Score: 463
Period size: 138 Copynumber: 3.6 Consensus size: 137
53457797 ACATTTTTTA
** * * * * * *
53457807 TGCGAACCTTGGTTTTACAGCTAGGAGCTTTGCTCTCGCTAGCTGTGCTAGAGGTTGTGGCTTTT
1 TGCGAACCTTAATTTTACAGATGGGAGCTTTGCTCTCGCTAACTATGCT-GAGGTCGTGGCTCTT
* ** * * * * *
53457872 TGCCTGGGGTCCTTAATTTTACAGTTGGGAGCTTTGCCCTCGCTAACTGTGTTAGAGGTCATGGC
65 CGCCTGTAGACCTTAATTTTACAGTTGAGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTCATGGC
*
53457937 ACTTCACC
130 TCTTCACC
* * *
53457945 TGCGAACCTTAGTTTTACAGATGGGAGCTTTGCTCTCACTAACTATGTTGCAGGTCGTGGCTCTT
1 TGCGAACCTTAATTTTACAGATGGGAGCTTTGCTCTCGCTAACTATGCTG-AGGTCGTGGCTCTT
* * * * ***
53458010 CGCCTATAGACCTTAATTTTACAATTGAGAGCTTTGCTCTTGCTAACTGTGCTGGAGGTTACACC
65 CGCCTGTAGACCTTAATTTTACAGTTGAGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTCATGGC
**
53458075 TCTTTGCC
130 TCTTCACC
* * * * * *
53458083 TGTGAACCTTAATTTTACAGTTGGGAACTTTGCTCTCGCTACCTATGCTGGAGGTTGTGCCTCTT
1 TGCGAACCTTAATTTTACAGATGGGAGCTTTGCTCTCGCTAACTATGCT-GAGGTCGTGGCTCTT
* * * * * * ** *
53458148 CGCCTGCA-ACCCTTAATTTTATAGCT-AGGAGATTTGTTCTCGTTAGTTGTGCTGGAGGTCGTG
65 CGCCTGTAGA-CCTTAATTTTACAGTTGA-GAGCTTTGCTCTCGCTAACTGTGCTGGAGGTCATG
53458211 GCTCTTCACC
128 GCTCTTCACC
* * * ***
53458221 TGCAAACCTTAATTTTACA-ACTGGGAGCTTTGCTCTTGCTAACTGTGCTGAAGGTCGCAACTCT
1 TGCGAACCTTAATTTTACAGA-TGGGAGCTTTGCTCTCGCTAACTATGCTG-AGGTCGTGGCTCT
*
53458285 TCGCCTGTAAACCTTAATTTTACAG
64 TCGCCTGTAGACCTTAATTTTACAG
53458310 GTAACATTTT
Statistics
Matches: 291, Mismatches: 67, Indels: 14
0.78 0.18 0.04
Matches are distributed among these distances:
137 4 0.01
138 285 0.98
139 2 0.01
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.35
Consensus pattern (137 bp):
TGCGAACCTTAATTTTACAGATGGGAGCTTTGCTCTCGCTAACTATGCTGAGGTCGTGGCTCTTC
GCCTGTAGACCTTAATTTTACAGTTGAGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTCATGGCT
CTTCACC
Found at i:53478437 original size:25 final size:24
Alignment explanation
Indices: 53478409--53478455 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
53478399 TAAAAATTGA
*
53478409 TGATAATTTAAAAAATAATAATACG
1 TGATAAATT-AAAAATAATAATACG
*
53478434 TGATAAATTCAAAATAATAATA
1 TGATAAATTAAAAATAATAATA
53478456 TATGTTAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.32
Consensus pattern (24 bp):
TGATAAATTAAAAATAATAATACG
Done.