Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 184 of 221
Found at i:54637837 original size:22 final size:21
Alignment explanation
Indices: 54637812--54637856 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
54637802 GTATTACTAT
*
54637812 TATTATAATTATGTATAGTGTA
1 TATTATAATTACGTAT-GTGTA
* *
54637834 TATTTTTATTACGTATGTGTA
1 TATTATAATTACGTATGTGTA
54637855 TA
1 TA
54637857 CACATATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.31, C:0.02, G:0.13, T:0.53
Consensus pattern (21 bp):
TATTATAATTACGTATGTGTA
Found at i:54637953 original size:3 final size:3
Alignment explanation
Indices: 54637945--54637976 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
54637935 TATTCCAATG
54637945 TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
54637977 GTTTATGCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:54650724 original size:132 final size:132
Alignment explanation
Indices: 54649921--54650704 Score: 1469
Period size: 132 Copynumber: 5.9 Consensus size: 132
54649911 CGTAAATAGG
*
54649921 TCCTATCTTCCTATATTGGTAGGAAGTGGATCAAAGATGCAGATCTTGTCTTCCCATATTGGTGG
1 TCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGG
54649986 CGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCA
66 CGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCA
54650051 GA
131 GA
54650053 TCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGG
1 TCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGG
54650118 CGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCA
66 CGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCA
54650183 GA
131 GA
54650185 TCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGG
1 TCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGG
*
54650250 CGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCT
66 CGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCA
54650315 GA
131 GA
54650317 TCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGG
1 TCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGG
*
54650382 CGAAGTAGATCGCAGAAAGCAGATCTTATCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCA
66 CGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCA
54650447 GA
131 GA
54650449 TCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGG
1 TCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGG
* *
54650514 CAAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCA
66 CGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCA
*
54650579 GG
131 GA
* * *
54650581 TCCTGTCTTCCTATATTGGTAGGAAGTGGATCGACGATGCAGATCTTGTCTTCCCATACTGGTGG
1 TCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGG
* *
54650646 CGAAGTAGATCGAAGAAAGCAGATCTTATCTTCATGTATTGGCGTGAAGTAGATCGAAG
66 CGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAG
54650705 ATTGTAGATC
Statistics
Matches: 638, Mismatches: 14, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
132 638 1.00
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.30
Consensus pattern (132 bp):
TCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGG
CGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCA
GA
Found at i:54650906 original size:97 final size:95
Alignment explanation
Indices: 54650742--54650930 Score: 324
Period size: 97 Copynumber: 2.0 Consensus size: 95
54650732 GCAGCGAAGC
* *
54650742 AGATCGAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGGAGCCGATAACTCTAT
1 AGATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTAT
*
54650807 CTCCCTGTATTTGGCAGTGGAATAGATTGA
66 CTCCCTGTATTTGACAGTGGAATAGATTGA
*
54650837 AGATCAAAGATGGCAGATTTTACCTCCCTGTGACTACAGTGGAGTACATTGAAGCTGATAACTCT
1 AGATCAAAGATGGCAGATTTTACCTCCC--TGACTACAGTGGAGTACATTGAAGCCGATAACTCT
54650902 ATCTCCCTGTATTTGACAGTGGAATAGAT
64 ATCTCCCTGTATTTGACAGTGGAATAGAT
54650931 CGGAGATTAC
Statistics
Matches: 88, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
95 27 0.31
97 61 0.69
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.29
Consensus pattern (95 bp):
AGATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTAT
CTCCCTGTATTTGACAGTGGAATAGATTGA
Found at i:54656560 original size:18 final size:18
Alignment explanation
Indices: 54656527--54656561 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
54656517 TATAACTTTA
**
54656527 AAAGTAAAACTTAAAAAT
1 AAAGTAAAACGAAAAAAT
54656545 AAAGTAAAACGAAAAAA
1 AAAGTAAAACGAAAAAA
54656562 AAGAATGAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.71, C:0.06, G:0.09, T:0.14
Consensus pattern (18 bp):
AAAGTAAAACGAAAAAAT
Found at i:54656644 original size:15 final size:16
Alignment explanation
Indices: 54656626--54656667 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
54656616 CAACATCTAA
54656626 TTTTAAAATATTAT-T
1 TTTTAAAATATTATAT
*
54656641 TTTTAAAA-ATTTTCAT
1 TTTTAAAATATTAT-AT
54656657 TTTTAAAATAT
1 TTTTAAAATAT
54656668 GCTACATAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 4 0.17
15 8 0.35
16 9 0.39
17 2 0.09
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTTAAAATATTATAT
Found at i:54657758 original size:18 final size:18
Alignment explanation
Indices: 54657735--54657769 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
54657725 TTAAACAAAA
* *
54657735 AAGAAAGAGAAAGAGAAG
1 AAGAAAAAGAAAAAGAAG
54657753 AAGAAAAAGAAAAAGAA
1 AAGAAAAAGAAAAAGAA
54657770 AGCATGAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (18 bp):
AAGAAAAAGAAAAAGAAG
Found at i:54661277 original size:32 final size:32
Alignment explanation
Indices: 54661241--54661305 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
54661231 AAAGTGTTAA
54661241 AGGGGATCTTAGGTAGCCTAATCACCTATACT
1 AGGGGATCTTAGGTAGCCTAATCACCTATACT
54661273 AGGGGATCTTAGGTAGCCTAATCACCTATACT
1 AGGGGATCTTAGGTAGCCTAATCACCTATACT
54661305 A
1 A
54661306 AGTTCCATGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.28
Consensus pattern (32 bp):
AGGGGATCTTAGGTAGCCTAATCACCTATACT
Found at i:54668542 original size:3 final size:3
Alignment explanation
Indices: 54668534--54668569 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
54668524 AACGTGCATG
54668534 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
54668570 GCAAATAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:54674632 original size:50 final size:50
Alignment explanation
Indices: 54674518--54674855 Score: 326
Period size: 50 Copynumber: 6.8 Consensus size: 50
54674508 TATGGTCTTG
* * * * *
54674518 CACATAATCACAAATCAATGCCATAGCCCAACTAT-GTCTTACATGGAAT
1 CACATAATCACATACCGATGTCATAGCCCAGCTATGGTCTTACATGGAAT
* *
54674567 CACATAATCACATACCGATGTCGTAGCCTAGCTATGGTCTTACACT-GAAT
1 CACATAATCACATACCGATGTCATAGCCCAGCTATGGTCTTACA-TGGAAT
* * * * **
54674617 CACGTAACCATATACCGATGCCATAGCCCAGCTATGGTCTTACACAGAAT
1 CACATAATCACATACCGATGTCATAGCCCAGCTATGGTCTTACATGGAAT
* * *
54674667 CACATAATCACATACCGATGCCATAACCCAGCTATGATCTTACATGGAAT
1 CACATAATCACATACCGATGTCATAGCCCAGCTATGGTCTTACATGGAAT
* * * * * * * *
54674717 TACGTAACCATATAACGAT-TCCATAGCCCATCTATAGTCTTACATAGAAT
1 CACATAATCACATACCGATGT-CATAGCCCAGCTATGGTCTTACATGGAAT
* *
54674767 CACATAATCACATACCGATGTCATAGCTCAGCTATGGTCTTACA-CGAAT
1 CACATAATCACATACCGATGTCATAGCCCAGCTATGGTCTTACATGGAAT
* * * * * *
54674816 CGCACT-ATCACATATCGGTGCCATATCCCAACTATGGTCT
1 CACA-TAATCACATACCGATGTCATAGCCCAGCTATGGTCT
54674856 CAAACGAAAT
Statistics
Matches: 235, Mismatches: 48, Indels: 12
0.80 0.16 0.04
Matches are distributed among these distances:
49 63 0.27
50 170 0.72
51 2 0.01
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (50 bp):
CACATAATCACATACCGATGTCATAGCCCAGCTATGGTCTTACATGGAAT
Found at i:54674708 original size:100 final size:99
Alignment explanation
Indices: 54674535--54674816 Score: 406
Period size: 100 Copynumber: 2.8 Consensus size: 99
54674525 TCACAAATCA
* * *
54674535 ATGCCATAGCCCAACTATGTCTTACATGGAATCACATAATCACATACCGATGTCGTAGCCTAGCT
1 ATGCCATAGCCCAACTATGTCTTACATAGAATCACATAATCACATACCGATGTCATAGCCCAGCT
*
54674600 ATGGTCTTACACTGAATCACGTAACCATATACCG
66 ATGGTCTTACACTGAATCACGTAACCATATAACG
* * * *
54674634 ATGCCATAGCCCAGCTATGGTCTTACACAGAATCACATAATCACATACCGATGCCATAACCCAGC
1 ATGCCATAGCCCAACTAT-GTCTTACATAGAATCACATAATCACATACCGATGTCATAGCCCAGC
* *
54674699 TATGATCTTACA-TGGAATTACGTAACCATATAACG
65 TATGGTCTTACACT-GAATCACGTAACCATATAACG
* * *
54674734 ATTCCATAGCCCATCTATAGTCTTACATAGAATCACATAATCACATACCGATGTCATAGCTCAGC
1 ATGCCATAGCCCAACTAT-GTCTTACATAGAATCACATAATCACATACCGATGTCATAGCCCAGC
54674799 TATGGTCTTACAC-GAATC
65 TATGGTCTTACACTGAATC
54674817 GCACTATCAC
Statistics
Matches: 161, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
99 22 0.14
100 139 0.86
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.26
Consensus pattern (99 bp):
ATGCCATAGCCCAACTATGTCTTACATAGAATCACATAATCACATACCGATGTCATAGCCCAGCT
ATGGTCTTACACTGAATCACGTAACCATATAACG
Found at i:54674792 original size:150 final size:148
Alignment explanation
Indices: 54674518--54674851 Score: 404
Period size: 150 Copynumber: 2.2 Consensus size: 148
54674508 TATGGTCTTG
* * * * *
54674518 CACATAATCACAAATCAATGCCATAGCCCAACTATGTCTTACATGGAATCACATAATCACATACC
1 CACATAATCACATATCGATGCCATAACCCAACTATGTCTTACATGGAATCACATAACCACATAAC
* * * * *
54674583 GATGTCGTAGCCTAGCTATGGTCTTACACTGAATCACGTAACCATATACCGATGCCATAGCCCAG
66 GATGTCATAGCCCAGCTATAGTCTTACACTGAATCACATAACCACATACCGATGCCATAGCCCAG
54674648 CTATGGTCTTACACAGAAT
131 CTATGGTCTTACAC-GAAT
* * * * *
54674667 CACATAATCACATACCGATGCCATAACCCAGCTATGATCTTACATGGAATTACGTAACCATATAA
1 CACATAATCACATATCGATGCCATAACCCAACTATG-TCTTACATGGAATCACATAACCACATAA
* * * *
54674732 CGAT-TCCATAGCCCATCTATAGTCTTACA-TAGAATCACATAATCACATACCGATGTCATAGCT
65 CGATGT-CATAGCCCAGCTATAGTCTTACACT-GAATCACATAACCACATACCGATGCCATAGCC
54674795 CAGCTATGGTCTTACACGAAT
128 CAGCTATGGTCTTACACGAAT
* * *
54674816 CGCACT-ATCACATATCGGTGCCATATCCCAACTATG
1 CACA-TAATCACATATCGATGCCATAACCCAACTATG
54674852 GTCTCAAACG
Statistics
Matches: 157, Mismatches: 24, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
149 66 0.42
150 91 0.58
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.26
Consensus pattern (148 bp):
CACATAATCACATATCGATGCCATAACCCAACTATGTCTTACATGGAATCACATAACCACATAAC
GATGTCATAGCCCAGCTATAGTCTTACACTGAATCACATAACCACATACCGATGCCATAGCCCAG
CTATGGTCTTACACGAAT
Found at i:54680518 original size:43 final size:42
Alignment explanation
Indices: 54680457--54680613 Score: 187
Period size: 43 Copynumber: 3.7 Consensus size: 42
54680447 TATATGTTAT
* *
54680457 CGTGTAAGACCACGTCTGGGACGTCGGCATCGACTTGTGTTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGA-TTGTGATTA
* *
54680500 CGTGTAAGACCATGTCTGGGACATTGGCATCGTATT-TGATT-
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCG-ATTGTGATTA
54680541 CGTGTAAGACC-CTGTCTGGGACAG-TGGCATCGATATGTGATTA
1 CGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGAT-TGTGATTA
* *
54680584 CATGTAAGACCACGTTTGGGACGTTGGCAT
1 CGTGTAAGACCACGTCTGGGACGTTGGCAT
54680614 TGTACGAGTC
Statistics
Matches: 98, Mismatches: 8, Indels: 16
0.80 0.07 0.13
Matches are distributed among these distances:
40 2 0.02
41 29 0.30
42 10 0.10
43 55 0.56
44 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (42 bp):
CGTGTAAGACCACGTCTGGGACGTTGGCATCGATTGTGATTA
Found at i:54680604 original size:84 final size:84
Alignment explanation
Indices: 54680456--54680613 Score: 223
Period size: 84 Copynumber: 1.9 Consensus size: 84
54680446 ATATATGTTA
* * *
54680456 TCGTGTAAGACCACGTCTGGGACGTCGGCATCGACTTGTGTTTACGTGTAAGACCATGTCTGGGA
1 TCGTGTAAGACCACGTCTGGGACGTCGGCATCGACTTGTGATTACATGTAAGACCACGTCTGGGA
54680521 CATTGGCATCGTATTTGAT
66 CATTGGCATCGTATTTGAT
*
54680540 TCGTGTAAGACC-CTGTCTGGGACAGT-GGCATCGA-TATGTGATTACATGTAAGACCACGTTTG
1 TCGTGTAAGACCAC-GTCTGGGAC-GTCGGCATCGACT-TGTGATTACATGTAAGACCACGTCTG
*
54680602 GGACGTTGGCAT
63 GGACATTGGCAT
54680614 TGTACGAGTC
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
83 2 0.03
84 62 0.94
85 2 0.03
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (84 bp):
TCGTGTAAGACCACGTCTGGGACGTCGGCATCGACTTGTGATTACATGTAAGACCACGTCTGGGA
CATTGGCATCGTATTTGAT
Found at i:54680803 original size:16 final size:17
Alignment explanation
Indices: 54680774--54680805 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
54680764 TGAATTGATG
54680774 ATATGAAGTTATGTGAA
1 ATATGAAGTTATGTGAA
54680791 ATATGAA-TTATGTGA
1 ATATGAAGTTATGTGA
54680806 TTGTATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.38
Consensus pattern (17 bp):
ATATGAAGTTATGTGAA
Found at i:54691014 original size:7 final size:7
Alignment explanation
Indices: 54691002--54691026 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
54690992 AGTCGATTGA
54691002 TATTTAG
1 TATTTAG
54691009 TATTTAG
1 TATTTAG
54691016 TATTTAG
1 TATTTAG
54691023 TATT
1 TATT
54691027 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:54691696 original size:18 final size:18
Alignment explanation
Indices: 54691669--54691708 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
54691659 CAGGTGCGTT
*
54691669 TCCTAGCCCTTATATATA
1 TCCTAACCCTTATATATA
*
54691687 TCCTAACCCTTATATGTA
1 TCCTAACCCTTATATATA
54691705 TCCT
1 TCCT
54691709 TTTCCGAGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.25, C:0.30, G:0.05, T:0.40
Consensus pattern (18 bp):
TCCTAACCCTTATATATA
Found at i:54691988 original size:21 final size:21
Alignment explanation
Indices: 54691964--54692012 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
54691954 AGATGCCGTA
54691964 CCGGAAGAACCAA-AATCC-CCG
1 CCGGAAGAA-CAACAA-CCGCCG
54691985 CCGGAAGAACAACAACCGCCG
1 CCGGAAGAACAACAACCGCCG
54692006 CCGGAAG
1 CCGGAAG
54692013 CTAGAGAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 5 0.19
21 21 0.81
ACGTcount: A:0.37, C:0.37, G:0.24, T:0.02
Consensus pattern (21 bp):
CCGGAAGAACAACAACCGCCG
Found at i:54692168 original size:25 final size:25
Alignment explanation
Indices: 54692134--54692256 Score: 141
Period size: 25 Copynumber: 5.1 Consensus size: 25
54692124 GAGTATTTTA
54692134 AAGTTTATTTGATGTAATAAAATAG
1 AAGTTTATTTGATGTAATAAAATAG
54692159 AAGTTTATTTGATGTAATAAAAATAG
1 AAGTTTATTTGATGTAAT-AAAATAG
* * ** *
54692185 AAATTTTTTTGA-GT--T-ATTTTG
1 AAGTTTATTTGATGTAATAAAATAG
54692206 -A-TATTATTTGATGTAATAAAATAG
1 AAGT-TTATTTGATGTAATAAAATAG
54692230 AAGTTTATTTGATGTAATAAAATAG
1 AAGTTTATTTGATGTAATAAAATAG
54692255 AA
1 AA
54692257 ATTTTTGAAT
Statistics
Matches: 81, Mismatches: 9, Indels: 16
0.76 0.08 0.15
Matches are distributed among these distances:
19 1 0.01
20 8 0.10
21 5 0.06
23 2 0.02
24 3 0.04
25 44 0.54
26 18 0.22
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.43
Consensus pattern (25 bp):
AAGTTTATTTGATGTAATAAAATAG
Found at i:54692213 original size:71 final size:67
Alignment explanation
Indices: 54692138--54692283 Score: 247
Period size: 71 Copynumber: 2.1 Consensus size: 67
54692128 ATTTTAAAGT
*
54692138 TTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAAATAGAAATTTTTTTGAGTTATT
1 TTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAAT-AAAATAGAAA--TTTTTGA-ATATT
54692203 TTGATA
62 TTGATA
54692209 TTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAAATTTTTGAATATTTTGA
1 TTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAAATTTTTGAATATTTTGA
54692274 TA
66 TA
54692276 TTATTTGA
1 TTATTTGA
54692284 GAATTCTACT
Statistics
Matches: 74, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
67 18 0.24
68 7 0.09
70 10 0.14
71 39 0.53
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (67 bp):
TTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAAATTTTTGAATATTTTGA
TA
Found at i:54692323 original size:28 final size:24
Alignment explanation
Indices: 54692292--54692938 Score: 673
Period size: 23 Copynumber: 26.2 Consensus size: 24
54692282 GAGAATTCTA
54692292 CTAACCTAATTAAATTGAAAAGAAAACC
1 CTAACCTAATTAAATT----AGAAAACC
*
54692320 CTAATCTAATTAAATT-GAAAACC
1 CTAACCTAATTAAATTAGAAAACC
*
54692343 CTAACCTAATTAAATTA-AAAACT
1 CTAACCTAATTAAATTAGAAAACC
* *
54692366 CTAACCTAGTTAAATT-GAAAACT
1 CTAACCTAATTAAATTAGAAAACC
*
54692389 CTAACCTAATTAAATTGAAAAGAAAACT
1 CTAACCTAATTAAATT----AGAAAACC
54692417 CTAACCTAATTAAATTGAAAAGAAAACC
1 CTAACCTAATTAAATT----AGAAAACC
54692445 CTAACCTAATT-AATTGAAAAGAAAACC
1 CTAACCTAATTAAATT----AGAAAACC
*
54692472 CTAACCTAATTAAATTGAAAAAAAACC
1 CTAACCTAATTAAATT---AGAAAACC
54692499 CTAACCTAATTAAATTA-AAAACC
1 CTAACCTAATTAAATTAGAAAACC
* *
54692522 CTAACCTAATTAAATTGAAAAAAAACT
1 CTAACCTAATTAAATT---AGAAAACC
*
54692549 CTAACCTAATTAAATT-TAAAACC
1 CTAACCTAATTAAATTAGAAAACC
54692572 CTAACCTAATTAAATTA-AAAACC
1 CTAACCTAATTAAATTAGAAAACC
54692595 CTAACCTAATTAAATT-GAAAACC
1 CTAACCTAATTAAATTAGAAAACC
*
54692618 CTAACCTAGTTAAATT-GAAAACC
1 CTAACCTAATTAAATTAGAAAACC
54692641 CTAACCTAATTAAATTA-AAAACC
1 CTAACCTAATTAAATTAGAAAACC
54692664 CTAACCTAATTAAATTGAAAAGAAAACC
1 CTAACCTAATTAAATT----AGAAAACC
54692692 CTAACCTAATTAAATTGAAAAGAAAACC
1 CTAACCTAATTAAATT----AGAAAACC
*
54692720 TTAACCTAATTAAATT-GAAAACC
1 CTAACCTAATTAAATTAGAAAACC
* *
54692743 CTAACCTAGTTAAATT-GAAAACT
1 CTAACCTAATTAAATTAGAAAACC
*
54692766 CTAACCTAATTAAATTGAAAAAAAAAACC
1 CTAACCTAATTAAATT-----AGAAAACC
54692795 CTAACCTAATTAAATT-GAAAACC
1 CTAACCTAATTAAATTAGAAAACC
54692818 CTAACCTAATTAAATTA-AAAACC
1 CTAACCTAATTAAATTAGAAAACC
*
54692841 CTAACCTAATTAAA-AAGAAAACC
1 CTAACCTAATTAAATTAGAAAACC
***
54692864 CTAACCTAATTAAA-TCCTAAACC
1 CTAACCTAATTAAATTAGAAAACC
54692887 CTAACCTAATTAAATT-GAAAACC
1 CTAACCTAATTAAATTAGAAAACC
* *
54692910 CTAACTTAATTAAATT-GAAAACT
1 CTAACCTAATTAAATTAGAAAACC
54692933 CTAACC
1 CTAACC
54692939 CTTAACATTC
Statistics
Matches: 559, Mismatches: 31, Indels: 63
0.86 0.05 0.10
Matches are distributed among these distances:
22 1 0.00
23 347 0.62
24 2 0.00
26 1 0.00
27 74 0.13
28 113 0.20
29 21 0.04
ACGTcount: A:0.51, C:0.19, G:0.04, T:0.26
Consensus pattern (24 bp):
CTAACCTAATTAAATTAGAAAACC
Found at i:54696205 original size:125 final size:125
Alignment explanation
Indices: 54695982--54696347 Score: 590
Period size: 124 Copynumber: 2.9 Consensus size: 125
54695972 CCCAAACATG
* *
54695982 CTACTGTAGCTAAAGCGCGTCCACAAGGGCGCGATTTTCACAAATTCTTCTCAAATAGCATCCTG
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTT-ACAAATTCTTCTCAAATAGCATCCTG
54696047 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCATCCATGAC
65 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCATCCATGAC
* *
54696108 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCAATTTTACAAATTATTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCCTGC
*
54696173 TAGAAGCGATTTTATATTATTTGCTCAGAAACGTC-AAAAAAAATTATTTCATCCATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCATCCATGAC
* * * *
54696232 CTACTGTAGCAAAAGCGAGTCCACGACGGCGCGATTTCACAAATTCTTCTCAAATAGCATCTTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCCTGC
* * ***
54696297 TAGAAGCGGTTTTATACTATTTGATCAGAAACGTCAACTCAAAATTATTTC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTC
54696348 TTGCCGAACC
Statistics
Matches: 222, Mismatches: 17, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
124 115 0.52
125 72 0.32
126 35 0.16
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCATCCATGAC
Found at i:54706661 original size:58 final size:59
Alignment explanation
Indices: 54706589--54706700 Score: 181
Period size: 59 Copynumber: 1.9 Consensus size: 59
54706579 AACATAAATA
*
54706589 CCAACTATAACTTTCAATAGAGAAAAT-ATAAAGCATGCATATAAGCAAAAACCAAAAG
1 CCAACTATAACTTTCAATAGAGAAAATAAAAAAGCATGCATATAAGCAAAAACCAAAAG
* * *
54706647 CCAACTATAGCTTTCAGTAGGGAAAATAAAAAAGCATGCATATAAGCAAAAACC
1 CCAACTATAACTTTCAATAGAGAAAATAAAAAAGCATGCATATAAGCAAAAACC
54706701 CTAAACCAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
58 24 0.49
59 25 0.51
ACGTcount: A:0.51, C:0.18, G:0.12, T:0.19
Consensus pattern (59 bp):
CCAACTATAACTTTCAATAGAGAAAATAAAAAAGCATGCATATAAGCAAAAACCAAAAG
Found at i:54719443 original size:60 final size:60
Alignment explanation
Indices: 54719310--54719445 Score: 152
Period size: 60 Copynumber: 2.3 Consensus size: 60
54719300 AAAATTTTAA
* *
54719310 AAAGTACAAGAACTAAAAA-AGACCAAATTAAAGTTCAATGACTAAATCCACAATATTAGT
1 AAAGTACAAGGACTAAAAATA-ATCAAATTAAAGTTCAATGACTAAATCCACAATATTAGT
* * * *
54719370 AGAGTACAAGGACTAAAAATAATCAAATTAAA-TTACATTGACTAAATTCACAACT-TTCGT
1 AAAGTACAAGGACTAAAAATAATCAAATTAAAGTT-CAATGACTAAATCCACAA-TATTAGT
* *
54719430 AAAGTGCAGGGACTAA
1 AAAGTACAAGGACTAA
54719446 TAGCAGAGTT
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
59 2 0.03
60 60 0.94
61 2 0.03
ACGTcount: A:0.49, C:0.15, G:0.12, T:0.24
Consensus pattern (60 bp):
AAAGTACAAGGACTAAAAATAATCAAATTAAAGTTCAATGACTAAATCCACAATATTAGT
Found at i:54721220 original size:114 final size:114
Alignment explanation
Indices: 54721039--54721817 Score: 1108
Period size: 114 Copynumber: 6.9 Consensus size: 114
54721029 CGTTTTCCAA
* * *
54721039 AAAGCGCCGC--AAAAAACTAAGCCCAAAGGCGTCGTTTTC-AGAGCTTTCGAGGATTTAGCGGC
1 AAAGCGCCGCAAAAAAAACTAAGCCCAACGGCGCCGTTTTCTA-AGCTTTCGGGGATTTAGCGGC
54721101 GTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGG
65 GTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGG
* * * * * *
54721151 AAAGCGCCGCAAAAAAAACTAAGCCCAATGACGCCGTTTTGTAAGCTTTCAGAGATTTAGTGGCG
1 AAAGCGCCGCAAAAAAAACTAAGCCCAACGGCGCCGTTTTCTAAGCTTTCGGGGATTTAGCGGCG
* * *
54721216 TTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTCGTGGCGTTTTTGGA
66 TTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGG
* * * * * *
54721265 AAAGTGCCGC-AAAAAAACTATGCCCAATGGCGCCG-TTTCTGAGCTTTCGGGGATTTAGAGGTG
1 AAAGCGCCGCAAAAAAAACTAAGCCCAACGGCGCCGTTTTCTAAGCTTTCGGGGATTTAGCGGCG
* * *
54721328 CTTTTAAGAAAGCGCCGCTAATGCTCAAGGCTTTAGCGGCGTTCTTGGG
66 TTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGG
* * *
54721377 AAAGCGCCGC-AAAAAAACTAAGCCCAACGGCGCCGTTTTCTGAGCTTTTGGGGATTTAGCGACG
1 AAAGCGCCGCAAAAAAAACTAAGCCCAACGGCGCCGTTTTCTAAGCTTTCGGGGATTTAGCGGCG
*
54721441 TTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGAGGCGTTTTTGGG
66 TTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGG
* * * *
54721490 GAAGTGCCGCAAAAAAAACTAAGCCCAACGGTGCCGTTTTCTGAA-CTTTCAGGGATTTAGCGGC
1 AAAGCGCCGCAAAAAAAACTAAGCCCAACGGCGCCGTTTTCT-AAGCTTTCGGGGATTTAGCGGC
* * *
54721554 GTTTTTATGAAAGCGCCACTAATGCTCAGGGCTTTAGCGACGTTTTTTGGG
65 GTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCG-TTTTTGGG
* * *
54721605 -AAGCGCCGCAAAAAAGACTAAGCCCAACGGCGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCA
1 AAAGCGCCGCAAAAAAAACTAAGCCCAACGGCGCCGTTTTCTAAGCTTTCGGGGATTTAGCGGCG
*
54721669 TTTTTATGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGG
66 TTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGG
*
54721718 AACA-CGCCGCAAAAAAAACTAAGCCCAACGGCGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGC
1 AA-AGCGCCGCAAAAAAAACTAAGCCCAACGGCGCCGTTTTCTAAGCTTTCGGGGATTTAGCGGC
* *
54721782 GTTTGTAAGAAAGCGCCGCTAATGCTCAGGGATTTA
65 GTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTA
54721818 AAATAATTTA
Statistics
Matches: 596, Mismatches: 61, Indels: 18
0.88 0.09 0.03
Matches are distributed among these distances:
112 107 0.18
113 109 0.18
114 369 0.62
115 11 0.02
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (114 bp):
AAAGCGCCGCAAAAAAAACTAAGCCCAACGGCGCCGTTTTCTAAGCTTTCGGGGATTTAGCGGCG
TTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGG
Found at i:54722126 original size:21 final size:22
Alignment explanation
Indices: 54722075--54722119 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
54722065 GTTCTATGCT
*
54722075 TTAGGGGTTATGGGATTTAGGG
1 TTAGAGGTTATGGGATTTAGGG
*
54722097 TTAGAGGTTA-GGGATTTGGGG
1 TTAGAGGTTATGGGATTTAGGG
54722118 TT
1 TT
54722120 TAAGGTTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.18, C:0.00, G:0.44, T:0.38
Consensus pattern (22 bp):
TTAGAGGTTATGGGATTTAGGG
Found at i:54722671 original size:43 final size:43
Alignment explanation
Indices: 54722610--54722765 Score: 276
Period size: 43 Copynumber: 3.6 Consensus size: 43
54722600 ACGTAAAATT
54722610 TAAAGGTCTTGTTCTTTAGCGGCGTTTGTGGTAGAAGCGCCGC
1 TAAAGGTCTTGTTCTTTAGCGGCGTTTGTGGTAGAAGCGCCGC
*
54722653 TAAAGGTCTTGTTCTTTAGCGGCGTTTGTGGTGGAAGCGCCGC
1 TAAAGGTCTTGTTCTTTAGCGGCGTTTGTGGTAGAAGCGCCGC
* * *
54722696 TAAAGGTCATGATCTTTAACGGCGTTTGTGGTAGAAGCGCCGC
1 TAAAGGTCTTGTTCTTTAGCGGCGTTTGTGGTAGAAGCGCCGC
54722739 TAAAGGTCTTGTTCTTTAGCGGCGTTT
1 TAAAGGTCTTGTTCTTTAGCGGCGTTT
54722766 ATTTTTAAAA
Statistics
Matches: 105, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 105 1.00
ACGTcount: A:0.17, C:0.18, G:0.31, T:0.33
Consensus pattern (43 bp):
TAAAGGTCTTGTTCTTTAGCGGCGTTTGTGGTAGAAGCGCCGC
Found at i:54722879 original size:22 final size:23
Alignment explanation
Indices: 54722847--54722889 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
54722837 TAGCGGCGTT
*
54722847 AAAAAGCGCCGCTAAAGGCCTAA
1 AAAAAGCGCCGCTAAAAGCCTAA
54722870 AAAAAG-GCCGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
54722890 GTTTTGGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.44, C:0.26, G:0.21, T:0.09
Consensus pattern (23 bp):
AAAAAGCGCCGCTAAAAGCCTAA
Found at i:54727326 original size:11 final size:11
Alignment explanation
Indices: 54727310--54727334 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
54727300 AAATCCTTTT
54727310 AACAAAAAAAA
1 AACAAAAAAAA
54727321 AACAAAAAAAA
1 AACAAAAAAAA
54727332 AAC
1 AAC
54727335 TTAAGTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (11 bp):
AACAAAAAAAA
Found at i:54729561 original size:25 final size:25
Alignment explanation
Indices: 54729509--54729561 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
54729499 TATGCTTTTA
* *
54729509 TATATATATATTATAAATTATAGAT
1 TATAGATATATTATAAATTAAAGAT
* * *
54729534 TATAGATATATTGTAGATTAAAGTT
1 TATAGATATATTATAAATTAAAGAT
54729559 TAT
1 TAT
54729562 GAAAAGTGTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.47
Consensus pattern (25 bp):
TATAGATATATTATAAATTAAAGAT
Found at i:54734555 original size:7 final size:7
Alignment explanation
Indices: 54734543--54734567 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
54734533 TAAATTCTTA
54734543 AAAATTT
1 AAAATTT
54734550 AAAATTT
1 AAAATTT
54734557 AAAATTT
1 AAAATTT
54734564 AAAA
1 AAAA
54734568 AGTAAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (7 bp):
AAAATTT
Found at i:54735092 original size:72 final size:71
Alignment explanation
Indices: 54735016--54735148 Score: 223
Period size: 72 Copynumber: 1.9 Consensus size: 71
54735006 TTTTGAATTG
*
54735016 TTTATTATT-TATTTTATAATATTTTAATTGTTTTATAATATTTGTTTATTCAAACATGTTTTTT
1 TTTATTATTAT-TTTTATAATATTTTAAATGTTTTATAATATTTGTTTATTCAAACAT-TTTTTT
54735080 TTAATTTT
64 TTAATTTT
*
54735088 TTTATTATTATTTTTATAATATTTTAAATGTTTTATAATATTTTTTTATTCAAACATTTTT
1 TTTATTATTATTTTTATAATATTTTAAATGTTTTATAATATTTGTTTATTCAAACATTTTT
54735149 AAAATATATA
Statistics
Matches: 58, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
71 4 0.07
72 53 0.91
73 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (71 bp):
TTTATTATTATTTTTATAATATTTTAAATGTTTTATAATATTTGTTTATTCAAACATTTTTTTTT
AATTTT
Found at i:54735121 original size:9 final size:10
Alignment explanation
Indices: 54735099--54735131 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
54735089 TTATTATTAT
54735099 TTTTATAATA
1 TTTTATAATA
*
54735109 TTTTA-AATG
1 TTTTATAATA
54735118 TTTTATAATA
1 TTTTATAATA
54735128 TTTT
1 TTTT
54735132 TTTATTCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (10 bp):
TTTTATAATA
Found at i:54735435 original size:13 final size:13
Alignment explanation
Indices: 54735419--54735444 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54735409 ATATTATAAA
54735419 ACATTTAAAATAT
1 ACATTTAAAATAT
54735432 ACATTTAAAATAT
1 ACATTTAAAATAT
54735445 TATAATACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
ACATTTAAAATAT
Found at i:54736103 original size:22 final size:22
Alignment explanation
Indices: 54736078--54736122 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
54736068 AAAATTTAAA
54736078 AAAGAAAATATAAAAATATTTT
1 AAAGAAAATATAAAAATATTTT
* * * *
54736100 AAAGATATTATGAATATATTTT
1 AAAGAAAATATAAAAATATTTT
54736122 A
1 A
54736123 TAATTTTTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.38
Consensus pattern (22 bp):
AAAGAAAATATAAAAATATTTT
Found at i:54743355 original size:42 final size:42
Alignment explanation
Indices: 54743276--54743356 Score: 103
Period size: 42 Copynumber: 1.9 Consensus size: 42
54743266 AAACAATGAG
* *
54743276 TCACACGGCCTAGCCACTCGCTCGTGTCCTTGCCCGTGTGGC
1 TCACACGGCCTAGACACTCGCTCGTGTCATTGCCCGTGTGGC
*
54743318 TCACACGGCCT-GACACTCGC-CTGTGTCATCTGGCCGTGT
1 TCACACGGCCTAGACACTCGCTC-GTGTCAT-TGCCCGTGT
54743357 AGGTCTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
40 1 0.03
41 14 0.41
42 19 0.56
ACGTcount: A:0.11, C:0.38, G:0.26, T:0.25
Consensus pattern (42 bp):
TCACACGGCCTAGACACTCGCTCGTGTCATTGCCCGTGTGGC
Found at i:54743380 original size:104 final size:104
Alignment explanation
Indices: 54743202--54743449 Score: 252
Period size: 104 Copynumber: 2.4 Consensus size: 104
54743192 CCCGTATGCA
* * * * *
54743202 TGCCCGTATGGCTTACACGGCCTAACACACGCCCGTGTCGTCTGCTTGTGTGGTTCAAAATCGTA
1 TGCCCGTGTGGCTCACACGGCCTGACACACGCCCGTGTCATCTGCTCGTGTGGTTCAAAATCGTA
*
54743267 AACAATGAGTCACACGGCCTAGCCAC-TCG-CTCGTGTCCT
66 AACAATGAGTCACACGGCCTAGACACAT-GTC-CGTGTCCT
* * * *
54743306 TGCCCGTGTGGCTCACACGGCCTGACACTCGCCTGTGTCATCTGGC-CGTGTAGG-TCTAAATCT
1 TGCCCGTGTGGCTCACACGGCCTGACACACGCCCGTGTCATCT-GCTCGTGT-GGTTCAAAATCG
* * * * *
54743369 TAATCACTGAGTCACATGGCTTGGACACATGTCCGTGTCCT
64 TAAACAATGAGTCACACGGCCTAGACACATGTCCGTGTCCT
* * * *
54743410 TGCCCATGTGACTCACACAGCCTGGGCACACGCCCGTGTC
1 TGCCCGTGTGGCTCACACGGCCT-GACACACGCCCGTGTC
54743450 CCTGGCCTGT
Statistics
Matches: 118, Mismatches: 21, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
104 99 0.84
105 19 0.16
ACGTcount: A:0.19, C:0.32, G:0.24, T:0.25
Consensus pattern (104 bp):
TGCCCGTGTGGCTCACACGGCCTGACACACGCCCGTGTCATCTGCTCGTGTGGTTCAAAATCGTA
AACAATGAGTCACACGGCCTAGACACATGTCCGTGTCCT
Found at i:54744077 original size:5 final size:5
Alignment explanation
Indices: 54744069--54744096 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
54744059 ATAGAAAGGA
54744069 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
54744097 GATGATGACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:54744218 original size:38 final size:38
Alignment explanation
Indices: 54744167--54744242 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
54744157 GAATGTTCCC
54744167 TATCGCATACTCCGGGATTCAATCACAGGACCAAATAG
1 TATCGCATACTCCGGGATTCAATCACAGGACCAAATAG
*
54744205 TATCGTATACTCCGGGATTCAATCACAGGACCAAATAG
1 TATCGCATACTCCGGGATTCAATCACAGGACCAAATAG
54744243 AATACTGACA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (38 bp):
TATCGCATACTCCGGGATTCAATCACAGGACCAAATAG
Found at i:54745154 original size:16 final size:17
Alignment explanation
Indices: 54745128--54745167 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
54745118 GTGATGTAAT
*
54745128 TATTTTCCTTTTCTTTC
1 TATTTTTCTTTTCTTTC
*
54745145 -ATTTTTCTTTTTTTTC
1 TATTTTTCTTTTCTTTC
54745161 TATTTTT
1 TATTTTT
54745168 TACCCTTCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (17 bp):
TATTTTTCTTTTCTTTC
Found at i:54745156 original size:17 final size:17
Alignment explanation
Indices: 54745130--54745167 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
54745120 GATGTAATTA
54745130 TTTTCCTTTTCTTTC-AT
1 TTTTCCTTTT-TTTCTAT
*
54745147 TTTTCTTTTTTTTCTAT
1 TTTTCCTTTTTTTCTAT
54745164 TTTT
1 TTTT
54745168 TACCCTTCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTCCTTTTTTTCTAT
Found at i:54745295 original size:6 final size:6
Alignment explanation
Indices: 54745281--54745324 Score: 70
Period size: 6 Copynumber: 7.3 Consensus size: 6
54745271 GTATGAGCAA
* *
54745281 TCACCG TCACTG TCACCG TCACCG TCACCG TCACCG TCGCCG TC
1 TCACCG TCACCG TCACCG TCACCG TCACCG TCACCG TCACCG TC
54745325 TTCTTTTCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.14, C:0.48, G:0.18, T:0.20
Consensus pattern (6 bp):
TCACCG
Found at i:54747277 original size:17 final size:18
Alignment explanation
Indices: 54747257--54747290 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
54747247 GTTTTGTTCT
*
54747257 TTTTTTCTTTTT-ATTTG
1 TTTTTCCTTTTTCATTTG
54747274 TTTTTCCTTTTTCATTT
1 TTTTTCCTTTTTCATTT
54747291 TCTATTTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.06, C:0.12, G:0.03, T:0.79
Consensus pattern (18 bp):
TTTTTCCTTTTTCATTTG
Found at i:54748003 original size:15 final size:14
Alignment explanation
Indices: 54747946--54748031 Score: 67
Period size: 15 Copynumber: 6.3 Consensus size: 14
54747936 GTATATCTAT
54747946 TTATATTTTATACTA
1 TTATATTTTATA-TA
*
54747961 TTCATACTTT-T-T-
1 TT-ATATTTTATATA
54747973 TTATATTTTATATA
1 TTATATTTTATATA
*
54747987 TTATATGTTTGTATA
1 TTATAT-TTTATATA
54748002 -T-T-TTTTATATA
1 TTATATTTTATATA
*
54748013 TTATTCTTTTATATA
1 TTA-TATTTTATATA
54748028 TTAT
1 TTAT
54748032 TCTTTTATTT
Statistics
Matches: 58, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 13 0.22
12 5 0.09
13 3 0.05
14 9 0.16
15 22 0.38
16 6 0.10
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (14 bp):
TTATATTTTATATA
Found at i:54748025 original size:24 final size:24
Alignment explanation
Indices: 54747947--54748050 Score: 88
Period size: 26 Copynumber: 4.2 Consensus size: 24
54747937 TATATCTATT
* *
54747947 TATATTTTATACTATTCATACTTTTTT
1 TATATTTTATA-TATT-ATTC-TTTTA
*
54747974 TATATTTTATATATTATATGTTTGTA
1 TATATTTTATATATTAT-TCTTT-TA
*
54748000 TATTTTTTATATATTATTCTTTTA
1 TATATTTTATATATTATTCTTTTA
*
54748024 TATATTATTCT-T-TTATT-TTTTA
1 TATATT-TTATATATTATTCTTTTA
54748046 TATAT
1 TATAT
54748051 GTATAATATA
Statistics
Matches: 67, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
22 10 0.15
23 5 0.07
24 8 0.12
25 12 0.18
26 21 0.31
27 11 0.16
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (24 bp):
TATATTTTATATATTATTCTTTTA
Found at i:54748046 original size:15 final size:15
Alignment explanation
Indices: 54748000--54748039 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
54747990 TATGTTTGTA
54748000 TATT-TTTTATATAT
1 TATTCTTTTATATAT
54748014 TATTCTTTTATATAT
1 TATTCTTTTATATAT
54748029 TATTCTTTTAT
1 TATTCTTTTAT
54748040 TTTTTATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 4 0.16
15 21 0.84
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTCTTTTATATAT
Found at i:54748063 original size:37 final size:36
Alignment explanation
Indices: 54747968--54748069 Score: 90
Period size: 37 Copynumber: 2.9 Consensus size: 36
54747958 CTATTCATAC
54747968 TTTTTT-TATATT-TT-ATATAT-TATATGT-TTGTATA
1 TTTTTTATATATTATTAATATATATATAT-TCTT-T-TA
** *
54748002 TTTTTTATATATTATTCTTTTATATATTATTCTTTTA
1 TTTTTTATATATTATTAATATATATA-TATTCTTTTA
54748039 TTTTTTATATATGTA-TAATATATATATATTC
1 TTTTTTATATAT-TATTAATATATATATATTC
54748070 ATACCCCATT
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
34 6 0.11
35 6 0.11
36 7 0.12
37 26 0.46
38 6 0.11
39 5 0.09
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (36 bp):
TTTTTTATATATTATTAATATATATATATTCTTTTA
Found at i:54750383 original size:15 final size:15
Alignment explanation
Indices: 54750360--54750389 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
54750350 GGGCAACATG
54750360 GCCTCGGAAGGTTGC
1 GCCTCGGAAGGTTGC
*
54750375 GCCTTGGAAGGTTGC
1 GCCTCGGAAGGTTGC
54750390 TAGTTCGTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.23, G:0.40, T:0.23
Consensus pattern (15 bp):
GCCTCGGAAGGTTGC
Found at i:54754945 original size:11 final size:11
Alignment explanation
Indices: 54754931--54754955 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
54754921 TTTTCTTTCA
54754931 TTTTTCTATTT
1 TTTTTCTATTT
54754942 TTTTTCTATTT
1 TTTTTCTATTT
54754953 TTT
1 TTT
54754956 ACCCTTCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTCTATTT
Found at i:54759816 original size:50 final size:50
Alignment explanation
Indices: 54759688--54759874 Score: 203
Period size: 50 Copynumber: 3.6 Consensus size: 50
54759678 AAAGAGATCA
* *
54759688 CATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGACTATGAAAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAGGTCC
*
54759744 CATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
** * * * **
54759794 CCCGTAAGACCATGTCTAGGACATGGCATGGGCACCGATATGAGAACTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
* * *
54759844 CATGTAAGACCATATCTGAGATATGGCATTG
1 CATGTAAGACCATGTCTGGGACATGGCATTG
54759875 ACAGTATAGA
Statistics
Matches: 113, Mismatches: 18, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
50 76 0.67
53 3 0.03
55 1 0.01
56 33 0.29
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (50 bp):
CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
Found at i:54766575 original size:25 final size:25
Alignment explanation
Indices: 54766546--54766595 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
54766536 AACAATTTGA
*
54766546 GAACAATCCTGGGTCCTTTTGAAAC
1 GAACAATCCAGGGTCCTTTTGAAAC
54766571 GAACAATCCAGGGTCCTTTTGAAAC
1 GAACAATCCAGGGTCCTTTTGAAAC
54766596 AAAATGGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (25 bp):
GAACAATCCAGGGTCCTTTTGAAAC
Found at i:54769007 original size:28 final size:31
Alignment explanation
Indices: 54768972--54769029 Score: 86
Period size: 28 Copynumber: 2.0 Consensus size: 31
54768962 TGAAATTTGA
*
54768972 AATTTAATTTTT-TA-TTTT-TATTTTAAAT
1 AATTTAATTTTTATACTTTTAAATTTTAAAT
54769000 AATTTAATTTTTATACTTTTAAATTTTAAA
1 AATTTAATTTTTATACTTTTAAATTTTAAA
54769030 ATTACAATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 12 0.46
29 2 0.08
30 4 0.15
31 8 0.31
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (31 bp):
AATTTAATTTTTATACTTTTAAATTTTAAAT
Found at i:54769753 original size:29 final size:24
Alignment explanation
Indices: 54769721--54769791 Score: 79
Period size: 24 Copynumber: 2.7 Consensus size: 24
54769711 ATATGTTATG
54769721 ATAATTTTAAATATAATTAAATAATTAAA
1 ATAATTTTAAA-A-AATTAAATAA-T--A
54769750 ATAAAATTTTAAAAAATTAAATAATA
1 AT--AATTTTAAAAAATTAAATAATA
54769776 ATAATTTTAAAAAATT
1 ATAATTTTAAAAAATT
54769792 CTATTGATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
24 14 0.35
26 3 0.08
28 1 0.03
29 12 0.30
30 1 0.03
31 9 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
ATAATTTTAAAAAATTAAATAATA
Found at i:54769767 original size:21 final size:24
Alignment explanation
Indices: 54769737--54769791 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
54769727 TTAAATATAA
*
54769737 TTAAATAATT-AA-AATAA-AATT
1 TTAAAAAATTAAATAATAATAATT
54769758 TTAAAAAATTAAATAATAATAATT
1 TTAAAAAATTAAATAATAATAATT
54769782 TTAAAAAATT
1 TTAAAAAATT
54769792 CTATTGATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 9 0.30
22 2 0.07
23 5 0.17
24 14 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
TTAAAAAATTAAATAATAATAATT
Found at i:54769864 original size:17 final size:18
Alignment explanation
Indices: 54769842--54769878 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
54769832 ATCTTTATGA
54769842 ATATTATATTTA-ATTTT
1 ATATTATATTTATATTTT
54769859 ATATTATATTTATATTTT
1 ATATTATATTTATATTTT
54769877 AT
1 AT
54769879 TATATTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATATTATATTTATATTTT
Found at i:54774003 original size:25 final size:25
Alignment explanation
Indices: 54773969--54774016 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
54773959 ACTTTTATTG
54773969 ATGACTTTTCCAGAAAAGTGTGGGC
1 ATGACTTTTCCAGAAAAGTGTGGGC
*
54773994 ATGATTTTTCCAGAAAAGTGTGG
1 ATGACTTTTCCAGAAAAGTGTGG
54774017 ACGTTCTTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.31
Consensus pattern (25 bp):
ATGACTTTTCCAGAAAAGTGTGGGC
Found at i:54775437 original size:3 final size:3
Alignment explanation
Indices: 54775423--54775473 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
54775413 ACACTAGTAC
* * * * *
54775423 ATA ATT ATA ATA ATA GTA ATA CTA ATA ATA CTA ATA AT- ATA AAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
54775470 ATA A
1 ATA A
54775474 GGATATTTGA
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:54777305 original size:132 final size:132
Alignment explanation
Indices: 54777188--54778366 Score: 2243
Period size: 132 Copynumber: 8.9 Consensus size: 132
54777178 GATCTACAAT
* * *
54777188 CTTCGATCTACTTCACGCCAATACATGAAGATAAGATCTGCTTTCTTCGATCTACTTCGCCACCA
1 CTTCGATCTACTTCACGCCGATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCA
* * * * *
54777253 GTATGGAAAGACAAGATCTGCATCGTCGATCCACTTCCTACCAATATAGGAAGACAGGACCTGCT
66 ATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCT
*
54777318 AT
131 AC
* *
54777320 CTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTTGCCACCA
1 CTTCGATCTACTTCACGCCGATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCA
54777385 ATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCT
66 ATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCT
54777450 AC
131 AC
54777452 CTTCGATCTACTTCACGCCGATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCA
1 CTTCGATCTACTTCACGCCGATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCA
54777517 ATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCT
66 ATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCT
54777582 AC
131 AC
54777584 CTTCGATCTACTTCACGCCGATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCA
1 CTTCGATCTACTTCACGCCGATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCA
54777649 ATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCT
66 ATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCT
54777714 AC
131 AC
54777716 CTTCGATCTACTTCACGCCGATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCA
1 CTTCGATCTACTTCACGCCGATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCA
54777781 ATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCT
66 ATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCT
54777846 AC
131 AC
54777848 CTTCGATCTACTTCACGCCGATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCA
1 CTTCGATCTACTTCACGCCGATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCA
*
54777913 ATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAAGATCTGCT
66 ATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCT
54777978 AC
131 AC
54777980 CTTCGATCTACTTCACGCC-ATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCA
1 CTTCGATCTACTTCACGCCGATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCA
54778044 ATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCT
66 ATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCT
54778109 AC
131 AC
54778111 CTTCGATCTACTTCACGCCGATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCA
1 CTTCGATCTACTTCACGCCGATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCA
54778176 ATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCT
66 ATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCT
54778241 AC
131 AC
54778243 CTTCGATCTACTTCACGCCGATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCA
1 CTTCGATCTACTTCACGCCGATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCA
54778308 ATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGA
66 ATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGA
54778367 CCTATTTACG
Statistics
Matches: 1033, Mismatches: 13, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
131 130 0.13
132 903 0.87
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (132 bp):
CTTCGATCTACTTCACGCCGATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCA
ATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCT
AC
Found at i:54790502 original size:3 final size:3
Alignment explanation
Indices: 54790488--54790538 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
54790478 ACACTAGTAC
* * * * *
54790488 ATA ATT ATA ATA ATA GTA ATA CTA ATA ATA CTA ATA AT- ATA AAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
54790535 ATA A
1 ATA A
54790539 GGATATTTGA
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:54793203 original size:15 final size:15
Alignment explanation
Indices: 54793183--54793217 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
54793173 ACCAATGAGG
54793183 ATCCATTAATGAGTA
1 ATCCATTAATGAGTA
54793198 ATCCATTAATGAGTA
1 ATCCATTAATGAGTA
54793213 ATCCA
1 ATCCA
54793218 ACGAGTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.31
Consensus pattern (15 bp):
ATCCATTAATGAGTA
Found at i:54794368 original size:30 final size:29
Alignment explanation
Indices: 54794334--54794391 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
54794324 AGAGGTGGGA
*
54794334 TGGGAAGAGAATAAAAGTTTTAGGGGAAAG
1 TGGG-AGAGAATAAAAATTTTAGGGGAAAG
* * *
54794364 TGGGAGGGAGTAAAAATTTTGGGGGAAA
1 TGGGAGAGAATAAAAATTTTAGGGGAAA
54794392 ATAAAAGGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.21
Consensus pattern (29 bp):
TGGGAGAGAATAAAAATTTTAGGGGAAAG
Found at i:54795013 original size:3 final size:3
Alignment explanation
Indices: 54795005--54795037 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
54794995 TAAAGTGGTA
54795005 TTC TTC TTC TTC TTC TTC TTC TTC TTC -TC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
54795038 ACATCATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:54797797 original size:32 final size:31
Alignment explanation
Indices: 54797748--54797833 Score: 100
Period size: 32 Copynumber: 2.7 Consensus size: 31
54797738 TGAAATATTT
54797748 AAAAGTTTTCATTTAAGTAACTAAACCATTC
1 AAAAGTTTTCATTTAAGTAACTAAACCATTC
* * * *
54797779 AAGAGTTTTCAATTTAAGTTATTAAACTATTC
1 AAAAGTTTTC-ATTTAAGTAACTAAACCATTC
* * *
54797811 AAAAGTTTTTATATAAGTCACTA
1 AAAAGTTTTCATTTAAGTAACTA
54797834 GGTTGCTAAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
31 19 0.42
32 26 0.58
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.40
Consensus pattern (31 bp):
AAAAGTTTTCATTTAAGTAACTAAACCATTC
Found at i:54798312 original size:16 final size:16
Alignment explanation
Indices: 54798275--54798314 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
54798265 TTGATAAAAT
* *
54798275 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
54798291 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
54798307 TAAAATTA
1 TAAAATTA
54798315 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:54798373 original size:66 final size:68
Alignment explanation
Indices: 54798303--54798448 Score: 197
Period size: 75 Copynumber: 2.1 Consensus size: 68
54798293 AAATTAATTG
* *
54798303 TTAGTAAAATTATCAAATTATTAATTG-TTAATTG-TATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAAATTATCAAATTATTAATTGATTAATTGTTATTAATTGTTATAACAAAATCTAACATT
54798366 TGA
66 TGA
54798369 TTAGTAAAATTATCAAATTATTAATTGTATTAATTGTTAATTATATTAATTGTTATAACAAAATC
1 TTAGTAAAATTATCAAATTATTAATTG-ATTAATTG-----T-TATTAATTGTTATAACAAAATC
54798434 TAACATTTGA
59 TAACATTTGA
54798444 TTAGT
1 TTAGT
54798449 TTACATTTTT
Statistics
Matches: 69, Mismatches: 2, Indels: 9
0.86 0.03 0.11
Matches are distributed among these distances:
66 27 0.39
68 7 0.10
75 35 0.51
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (68 bp):
TTAGTAAAATTATCAAATTATTAATTGATTAATTGTTATTAATTGTTATAACAAAATCTAACATT
TGA
Found at i:54798408 original size:16 final size:16
Alignment explanation
Indices: 54798384--54798423 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
54798374 AAAATTATCA
* *
54798384 AATTATTAATTGTATT
1 AATTGTTAATTATATT
54798400 AATTGTTAATTATATT
1 AATTGTTAATTATATT
54798416 AATTGTTA
1 AATTGTTA
54798424 TAACAAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (16 bp):
AATTGTTAATTATATT
Found at i:54798616 original size:19 final size:19
Alignment explanation
Indices: 54798589--54798634 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
54798579 TCTGTCGGGG
*
54798589 AAATGAAATTGAAAACTAA
1 AAATAAAATTGAAAACTAA
*
54798608 AAATAAAATTGAAAACTTA
1 AAATAAAATTGAAAACTAA
*
54798627 AACTAAAA
1 AAATAAAA
54798635 AATTAAACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.65, C:0.07, G:0.07, T:0.22
Consensus pattern (19 bp):
AAATAAAATTGAAAACTAA
Found at i:54798719 original size:20 final size:20
Alignment explanation
Indices: 54798691--54798731 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
54798681 AATGTCGGGG
*
54798691 AAATGAAATTGAAAACATAA
1 AAATAAAATTGAAAACATAA
*
54798711 AAATAAAATTGAAAACTTAA
1 AAATAAAATTGAAAACATAA
54798731 A
1 A
54798732 CTGTCAGGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.66, C:0.05, G:0.07, T:0.22
Consensus pattern (20 bp):
AAATAAAATTGAAAACATAA
Found at i:54798783 original size:27 final size:28
Alignment explanation
Indices: 54798753--54798826 Score: 73
Period size: 27 Copynumber: 2.6 Consensus size: 28
54798743 AATGAAATTG
54798753 AAAACTAAAACTAAAAATTTAAACAT-A
1 AAAACTAAAACTAAAAATTTAAACATAA
* *
54798780 AAAA-TAAATA-TATATATTTTAAACATAA
1 AAAACTAAA-ACTA-AAAATTTAAACATAA
54798808 AAAACTTAAAACATAAAAA
1 AAAAC-TAAAAC-TAAAAA
54798827 ACTTAATATA
Statistics
Matches: 36, Mismatches: 4, Indels: 11
0.71 0.08 0.22
Matches are distributed among these distances:
26 6 0.17
27 16 0.44
28 5 0.14
29 1 0.03
30 6 0.17
31 2 0.06
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (28 bp):
AAAACTAAAACTAAAAATTTAAACATAA
Found at i:54798821 original size:16 final size:16
Alignment explanation
Indices: 54798800--54798832 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
54798790 TATATATTTT
54798800 AAACATAAAAAACTTA
1 AAACATAAAAAACTTA
54798816 AAACATAAAAAACTTA
1 AAACATAAAAAACTTA
54798832 A
1 A
54798833 TATATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.70, C:0.12, G:0.00, T:0.18
Consensus pattern (16 bp):
AAACATAAAAAACTTA
Found at i:54800989 original size:32 final size:32
Alignment explanation
Indices: 54800941--54801011 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 32
54800931 TCACCAATTT
*
54800941 TATT-TTTTAATTTTTAAAAATATTTATAT-TA
1 TATTATTTTAATATTTAAAAAT-TTTATATATA
*
54800972 TATTATTTTAATATTTAATAATTTTATATATA
1 TATTATTTTAATATTTAAAAATTTTATATATA
*
54801004 TTTTATTT
1 TATTATTT
54801012 ATTGAAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
31 11 0.31
32 24 0.69
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (32 bp):
TATTATTTTAATATTTAAAAATTTTATATATA
Found at i:54803814 original size:3 final size:3
Alignment explanation
Indices: 54803808--54803882 Score: 105
Period size: 3 Copynumber: 24.7 Consensus size: 3
54803798 GTATAAATGT
* * * *
54803808 ATA ATA ATG GTA ATA ATAA ATC ATA ATA ATA ATA ATA ATA ATA GTA
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA
54803854 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
54803883 TACTATTCTA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
3 60 0.95
4 3 0.05
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:54805707 original size:44 final size:44
Alignment explanation
Indices: 54805412--54805713 Score: 261
Period size: 44 Copynumber: 6.9 Consensus size: 44
54805402 TCTTTTCCAA
* * * * *
54805412 GTAGCTTCATTCTAATCCACTACAGCTTCA--GATGTATAGGATTT
1 GTAGCTTCAATCTACTCCACTGCAACTTCAGGGA-G-ATAAGATTT
* *
54805456 GTTGCTTCAATCTACTCCACTGCAACTTCA--GATGTATAGGATTT
1 GTAGCTTCAATCTACTCCACTGCAACTTCAGGGA-G-ATAAGATTT
* * * * * * * * *
54805500 GTTGTTTTAATCTACTACACTACAACTTTAGAGAGATTAGACTT
1 GTAGCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTT
* * * * * * * *
54805544 GTAGCTTTAATTTGCTGCACTACAACTTCAGGGAGATGAGACTC
1 GTAGCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTT
* * * *
54805588 GTATCTTCAATCTGCTCCACTGCAACCTCAGGGAGATAAAATTT
1 GTAGCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTT
* *
54805632 GTAACTTCAATCTACTCCACTGCATCTTCAGGGAGATAAGATTT
1 GTAGCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTT
*
54805676 GTAACTTCAATCTACTCCACTGCAACTTCAGGGAGATA
1 GTAGCTTCAATCTACTCCACTGCAACTTCAGGGAGATA
54805714 TTACTCAAAG
Statistics
Matches: 218, Mismatches: 38, Indels: 4
0.84 0.15 0.02
Matches are distributed among these distances:
44 215 0.99
45 1 0.00
46 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.33
Consensus pattern (44 bp):
GTAGCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTT
Found at i:54807528 original size:41 final size:41
Alignment explanation
Indices: 54807483--54807597 Score: 176
Period size: 41 Copynumber: 2.8 Consensus size: 41
54807473 ACTGGCACTT
* * * *
54807483 AGCCTACTAGACATAAAGTCTTAAATGTTTCACAGGCGTCA
1 AGCCTGCTAGACGTAAAGTCTGAAATGTTTCACAGGCATCA
*
54807524 AGCCTGCTAGACGTAAAGTCTGAAATGTTTCACCGGCATCA
1 AGCCTGCTAGACGTAAAGTCTGAAATGTTTCACAGGCATCA
*
54807565 AGCCTGCTAGACGTAAATTCTGAAATGTTTCAC
1 AGCCTGCTAGACGTAAAGTCTGAAATGTTTCAC
54807598 TAGCAATAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 68 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (41 bp):
AGCCTGCTAGACGTAAAGTCTGAAATGTTTCACAGGCATCA
Found at i:54814409 original size:17 final size:17
Alignment explanation
Indices: 54814387--54814424 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
54814377 TGGCTATATG
54814387 AAGATGAAAATCTCACA
1 AAGATGAAAATCTCACA
54814404 AAGATGAAAATCTCACA
1 AAGATGAAAATCTCACA
54814421 AAGA
1 AAGA
54814425 CATACGAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.55, C:0.16, G:0.13, T:0.16
Consensus pattern (17 bp):
AAGATGAAAATCTCACA
Found at i:54815803 original size:4 final size:4
Alignment explanation
Indices: 54815789--54815836 Score: 60
Period size: 4 Copynumber: 12.0 Consensus size: 4
54815779 CACAAAAAAT
* * * *
54815789 TAAA GAAA TAAA TAAA TGAA TGAA TATA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
54815837 AACATAACAT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:54817761 original size:19 final size:21
Alignment explanation
Indices: 54817737--54817776 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
54817727 GTAAATCATG
54817737 CCATTG-CATGTG-TTGAATA
1 CCATTGACATGTGTTTGAATA
*
54817756 CCATTGATATGTGTTTGAATA
1 CCATTGACATGTGTTTGAATA
54817777 TGTGAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 5 0.28
21 7 0.39
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (21 bp):
CCATTGACATGTGTTTGAATA
Found at i:54817864 original size:14 final size:14
Alignment explanation
Indices: 54817845--54817873 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
54817835 TTATGTTCAT
54817845 AACATTGCTTATGC
1 AACATTGCTTATGC
54817859 AACATTGCTTATGC
1 AACATTGCTTATGC
54817873 A
1 A
54817874 TTTTTACATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (14 bp):
AACATTGCTTATGC
Found at i:54819916 original size:3 final size:3
Alignment explanation
Indices: 54819910--54819941 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
54819900 ACTAATTAGG
*
54819910 TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
54819942 TGTTTCTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:54819959 original size:21 final size:19
Alignment explanation
Indices: 54819910--54819980 Score: 63
Period size: 21 Copynumber: 3.5 Consensus size: 19
54819900 ACTAATTAGG
54819910 TTATTATTATTAT-TATTATT
1 TTATTATTATT-TCT-TTATT
* *
54819930 GTTATTATTATTTGTTTCTT
1 -TTATTATTATTTCTTTATT
*
54819950 TATATATATTGTTTCTTTATT
1 T-TAT-TATTATTTCTTTATT
54819971 TTATTATTAT
1 TTATTATTAT
54819981 ATTTTAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
19 6 0.14
20 11 0.26
21 25 0.60
ACGTcount: A:0.24, C:0.03, G:0.04, T:0.69
Consensus pattern (19 bp):
TTATTATTATTTCTTTATT
Found at i:54820045 original size:3 final size:3
Alignment explanation
Indices: 54820037--54820074 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
54820027 CAAAGTTTAA
*
54820037 ATT ATT ATT ATT ATT ATT ATT AATT ATT ATT ATC ATT A
1 ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT A
54820075 GCTTTTATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:54820287 original size:3 final size:3
Alignment explanation
Indices: 54820233--54820270 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
54820223 ATTTTCAAAA
54820233 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
54820271 AGTTCCCCTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:54820515 original size:19 final size:18
Alignment explanation
Indices: 54820491--54820526 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
54820481 GTTTGCTGTT
*
54820491 ATTATTATTATTTATCGTC
1 ATTATTAATATTT-TCGTC
54820510 ATTATTAATATTTTCGT
1 ATTATTAATATTTTCGT
54820527 TTCTAAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.28, C:0.08, G:0.06, T:0.58
Consensus pattern (18 bp):
ATTATTAATATTTTCGTC
Found at i:54834761 original size:72 final size:72
Alignment explanation
Indices: 54834644--54834786 Score: 259
Period size: 72 Copynumber: 2.0 Consensus size: 72
54834634 TCTCGGATTT
* * *
54834644 AAAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTTTTCTTAATTCCCGAGATCGTTTAAAA
1 AAAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCAAGATCATTTAAAA
54834709 CTTGAGA
66 CTTGAGA
54834716 AAAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCAAGATCATTTAAAA
1 AAAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCAAGATCATTTAAAA
54834781 CTTGAG
66 CTTGAG
54834787 TTTGAAGAGA
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (72 bp):
AAAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCAAGATCATTTAAAA
CTTGAGA
Found at i:54835544 original size:18 final size:20
Alignment explanation
Indices: 54835523--54835596 Score: 71
Period size: 23 Copynumber: 3.6 Consensus size: 20
54835513 ATAATTTTAG
54835523 AATAATA-ATACATAT-TAA
1 AATAATATATACATATATAA
54835541 AATAATATATACATATATAA
1 AATAATATATACATATATAA
* * * *
54835561 AGATAAAAGATATATAAAGATAA
1 A-AT--AATATATACATATATAA
54835584 AATAATATATACA
1 AATAATATATACA
54835597 GGAGTAATAA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
18 7 0.16
19 8 0.18
20 12 0.27
21 2 0.04
22 2 0.04
23 14 0.31
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (20 bp):
AATAATATATACATATATAA
Found at i:54835547 original size:21 final size:21
Alignment explanation
Indices: 54835524--54835566 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
54835514 TAATTTTAGA
54835524 ATAATA-ATACATAT-TAAA-
1 ATAATATATACATATATAAAG
54835542 ATAATATATACATATATAAAG
1 ATAATATATACATATATAAAG
54835563 ATAA
1 ATAA
54835567 AAGATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.27
19 8 0.36
20 4 0.18
21 4 0.18
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (21 bp):
ATAATATATACATATATAAAG
Found at i:54835575 original size:17 final size:17
Alignment explanation
Indices: 54835553--54835585 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
54835543 TAATATATAC
54835553 ATATATAAAGATAAAAG
1 ATATATAAAGATAAAAG
54835570 ATATATAAAGATAAAA
1 ATATATAAAGATAAAA
54835586 TAATATATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (17 bp):
ATATATAAAGATAAAAG
Found at i:54837202 original size:44 final size:44
Alignment explanation
Indices: 54837165--54837304 Score: 137
Period size: 44 Copynumber: 3.2 Consensus size: 44
54837155 CTGCGACCTA
*
54837165 AGAGAGATAAGGTTTG-TATCTTCAACCTGC-CACACTGCAACTTC
1 AGAGAGATAAGGTTTGTTA-CTTCAACCTACTC-CACTGCAACTTC
* * * *
54837209 AGGGGGATAAGGTTTGTTACTTTAACCTACTCTACTGCAACTTC
1 AGAGAGATAAGGTTTGTTACTTCAACCTACTCCACTGCAACTTC
* * * * *
54837253 AGAGAGATAAGGTTTGATA--T-GATCTGCTCTACTGCAACTTC
1 AGAGAGATAAGGTTTGTTACTTCAACCTACTCCACTGCAACTTC
54837294 AGAGAGATAAG
1 AGAGAGATAAG
54837305 ATCTGCAATT
Statistics
Matches: 83, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
41 29 0.35
42 1 0.01
44 50 0.60
45 3 0.04
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.29
Consensus pattern (44 bp):
AGAGAGATAAGGTTTGTTACTTCAACCTACTCCACTGCAACTTC
Found at i:54837815 original size:220 final size:220
Alignment explanation
Indices: 54837401--54837941 Score: 699
Period size: 220 Copynumber: 2.5 Consensus size: 220
54837391 GGAGACAGGG
* * * ** *
54837401 TCTAAAATCTTTAACCTATTCTGCTGCAACTCAGGGAGATAGGACTGGTGGCTTAAATCTT-CTT
1 TCTACAATCTTCAACCTACTCCACTGCTACTCAGGGAGATAGGACTGGTGGCTTAAAT-TTGCTT
* * * * *
54837465 CCCTACTACATTGGGAAGATAAGATTCGCCATCTTTAATCTGCTCCACTAGTGCTTAGGGAGACA
65 CCCTACTACCTTGGGAAGATAAGATTCGCCATCTTCAATCTGCTCCACTACTGCTTAAGGACACA
* *** * * **
54837530 GGATCTACAATCTTCAACCTACTCTACTGCTATTTAAAGAGATAAGGCTGGTGCTTTTTATCTGC
130 GGATCTACAATCTTCAACCTACTCCACTGCTACCCAAAGAGATAAGGATAGTGCTTTCAATCTGC
*
54837595 TTCACTGCTGGTACAGGAAGACAAAA
195 TTCACTGCTAGTACAGGAAGACAAAA
* * * *
54837621 TCTACAATCTTCAACTTACTCTACTGCTATTCAGGGAGATAGCACTGGTGGCTTAAATTTGCTTC
1 TCTACAATCTTCAACCTACTCCACTGCTACTCAGGGAGATAGGACTGGTGGCTTAAATTTGCTTC
* *
54837686 CCTACTACCTTGGGAAGATAAGATTCGCCCTCTTCAATCTGCTCCACTACTGCTTAAGGACACAT
66 CCTACTACCTTGGGAAGATAAGATTCGCCATCTTCAATCTGCTCCACTACTGCTTAAGGACACAG
* * *
54837751 GATCTGCAATCTTCAACCTTCTCCACTGCTACCC-AGGAAGATAAGGATAGTGCTTTCAATCTGC
131 GATCTACAATCTTCAACCTACTCCACTGCTACCCAAAG-AGATAAGGATAGTGCTTTCAATCTGC
* *
54837815 TTCACTGCTAGTACAGGAAGACGAGA
195 TTCACTGCTAGTACAGGAAGACAAAA
* * * *
54837841 TCTACAATCTTCGACCTACTCCACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAGTCTGCTTC
1 TCTACAATCTTCAACCTACTCCACTGCTACTCAGGGAGATAGGACTGGTGGCTTAAATTTGCTTC
* ** *
54837906 CTTACTACCTTTTGAAGATAAGATTCGCCGTCTTCA
66 CCTACTACCTTGGGAAGATAAGATTCGCCATCTTCA
54837942 GCTTTAATCT
Statistics
Matches: 278, Mismatches: 41, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
219 4 0.01
220 274 0.99
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (220 bp):
TCTACAATCTTCAACCTACTCCACTGCTACTCAGGGAGATAGGACTGGTGGCTTAAATTTGCTTC
CCTACTACCTTGGGAAGATAAGATTCGCCATCTTCAATCTGCTCCACTACTGCTTAAGGACACAG
GATCTACAATCTTCAACCTACTCCACTGCTACCCAAAGAGATAAGGATAGTGCTTTCAATCTGCT
TCACTGCTAGTACAGGAAGACAAAA
Found at i:54842694 original size:19 final size:19
Alignment explanation
Indices: 54842653--54842694 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
54842643 TCTTTCTTTT
*
54842653 TGCATTCATTCCATGCATT
1 TGCATTCATTCCATGCATA
*
54842672 TGCATTACATTGCAT-CATA
1 TGCATT-CATTCCATGCATA
54842691 TGCA
1 TGCA
54842695 AAAAAGAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (19 bp):
TGCATTCATTCCATGCATA
Found at i:54844922 original size:17 final size:19
Alignment explanation
Indices: 54844878--54844953 Score: 61
Period size: 19 Copynumber: 3.9 Consensus size: 19
54844868 AAATTGTTAA
*
54844878 AAAAAAGAAGAGAAAAAAAACG
1 AAAAAAGAA-AG-AAGAAAA-G
*
54844900 AGAAAAAG-AAGGA-AAAAG
1 A-AAAAAGAAAGAAGAAAAG
54844918 AAAAAAGAAAGAAGAAAAG
1 AAAAAAGAAAGAAGAAAAG
54844937 AAAAGAA-AAAGAA-AAAA
1 AAAA-AAGAAAGAAGAAAA
54844954 AAGAGAGGCC
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
17 6 0.12
18 10 0.21
19 19 0.40
20 3 0.06
21 2 0.04
22 2 0.04
23 6 0.12
ACGTcount: A:0.79, C:0.01, G:0.20, T:0.00
Consensus pattern (19 bp):
AAAAAAGAAAGAAGAAAAG
Found at i:54844944 original size:40 final size:39
Alignment explanation
Indices: 54844878--54844957 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 39
54844868 AAATTGTTAA
* *
54844878 AAAAAAGAAGAGAAAAAAAACGAGAAAAAGAAGGAAAAAG
1 AAAAAAGAAGAGAAAAAAAACAAGAAAAAGAA-AAAAAAG
54844918 AAAAAAGAA-AGAAGAAAAGAA-AAGAAAAAGAAAAAAAAG
1 AAAAAAGAAGAGAA-AAAA-AACAAGAAAAAGAAAAAAAAG
54844957 A
1 A
54844958 GAGGCCAAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
39 11 0.31
40 23 0.64
41 2 0.06
ACGTcount: A:0.79, C:0.01, G:0.20, T:0.00
Consensus pattern (39 bp):
AAAAAAGAAGAGAAAAAAAACAAGAAAAAGAAAAAAAAG
Found at i:54845880 original size:24 final size:25
Alignment explanation
Indices: 54845853--54845911 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
54845843 ATGTCCCAAA
* *
54845853 ATTACAGTGGGTTTAACCTTT-AAG
1 ATTACAGTGGGATTAAACTTTGAAG
**
54845877 ATTACA-ACGGATTAAACTTTGAAG
1 ATTACAGTGGGATTAAACTTTGAAG
54845901 ATTACAGTGGG
1 ATTACAGTGGG
54845912 GGCAATCAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
23 10 0.37
24 15 0.56
25 2 0.07
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (25 bp):
ATTACAGTGGGATTAAACTTTGAAG
Found at i:54846364 original size:100 final size:99
Alignment explanation
Indices: 54846190--54847530 Score: 1642
Period size: 100 Copynumber: 13.4 Consensus size: 99
54846180 ATACCCTTGC
* *
54846190 CATTGCAATTAAAAAGATTGAAGCCACAACAGAAAATCTTACTTCTCTGGCGGTAG-AGCGGAAC
1 CATTGCAATTAAAAAGATTGAAGCCACAACGGCAAATCTTACTTC-CTGGCGGT-GCAGCGGAAC
* * *
54846254 TA-ATTAAAGCTACAACGGTGAATCTTGCTTCCACGA
64 -AGATTGAAGCTACAACGGCGAATCTTGCTTCCCCGA
* * *
54846290 CATTGCAATTAAAAAGATTGAAGCCACAACGGCAAATCTGATCTTCCTGGCAGTGCAGCGAAACA
1 CATTGCAATTAAAAAGATTGAAGCCACAACGGCAAATCTTA-CTTCCTGGCGGTGCAGCGGAACA
* *
54846355 AATTGAAGCTACAATGGCGAATCTTGCTTCCCCGA
65 GATTGAAGCTACAACGGCGAATCTTGCTTCCCCGA
* * * *
54846390 CATTACAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTTCATGGCGGTGCAACGGAACA
1 CATTGCAATTAAAAAGATTGAAGCCACAACGGCAAATCTTAC-TTCCTGGCGGTGCAGCGGAACA
* * *
54846455 GATTGAAGTTACAACGGTGAATCTTGCTTCCCCAA
65 GATTGAAGCTACAACGGCGAATCTTGCTTCCCCGA
* * * * * * * *
54846490 TATTGCAATTAAAAAGATTGAACCCACAACAGCGAATCTTACCTCCCTGACGGTGCAGCGAAATA
1 CATTGCAATTAAAAAGATTGAAGCCACAACGGCAAATCTTA-CTTCCTGGCGGTGCAGCGGAACA
** *
54846555 GATTGAAGCTACAACAACGAATCTTACTTCCCCGA
65 GATTGAAGCTACAACGGCGAATCTTGCTTCCCCGA
* * *
54846590 CATTGTAATTAAAAAGATTGAAGGCATAACGGCAAATCTTACTTTCCTGGCGGTGCAGCGGAACA
1 CATTGCAATTAAAAAGATTGAAGCCACAACGGCAAATCTTAC-TTCCTGGCGGTGCAGCGGAACA
* *
54846655 GATTGAAGCTACAACGGTGAATCTTGCTTTCCCGA
65 GATTGAAGCTACAACGGCGAATCTTGCTTCCCCGA
* *** * *
54846690 CATTGCAATTAAAAAGATTGAAGCCACAACGGCTAATCTTACTTTCCTAATGGTGTAGCGAAACA
1 CATTGCAATTAAAAAGATTGAAGCCACAACGGCAAATCTTAC-TTCCTGGCGGTGCAGCGGAACA
*
54846755 GATTGAAGCTACAACGGCAAATCTTGCTTCCCCGA
65 GATTGAAGCTACAACGGCGAATCTTGCTTCCCCGA
* * * *
54846790 CATTGCAATTAAAAAGATTGAAGCCACAACGGAAAATCTTATCTTCCTAGCGGTGCAACGGAATA
1 CATTGCAATTAAAAAGATTGAAGCCACAACGGCAAATCTTA-CTTCCTGGCGGTGCAGCGGAACA
* *
54846855 GATTGAAGCTACAATGGTGAATCTTGCTTCCCCGA
65 GATTGAAGCTACAACGGCGAATCTTGCTTCCCCGA
* * * *
54846890 CATTGCAATTAAAAATATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAACA
1 CATTGCAATTAAAAAGATTGAAGCCACAACGGCAAATCTTACTT-CCTGGCGGTGCAGCGGAACA
*
54846955 GATTGAAGCTACAACGGCGAATCTTGCTTCCCTGA
65 GATTGAAGCTACAACGGCGAATCTTGCTTCCCCGA
* * * * *
54846990 CATTACAATTAAAAAGATAGAAGCCACAACGGTAAATCTTACATCCCTGGCGGTACAGCGGAACA
1 CATTGCAATTAAAAAGATTGAAGCCACAACGGCAAATCTTAC-TTCCTGGCGGTGCAGCGGAACA
* **
54847055 GATTGAAGCTACAACGGTGAATCTTGCTTCCTTGA
65 GATTGAAGCTACAACGGCGAATCTTGCTTCCCCGA
* * ** * ** *
54847090 CATTGTAATTAAAAAGATTGAAGCCACAATGGTGAATCTTACCTTCTTGGCTATGCAGCGGAATA
1 CATTGCAATTAAAAAGATTGAAGCCACAACGGCAAATCTTA-CTTCCTGGCGGTGCAGCGGAACA
**
54847155 GATTGAAGCTACAACGATGAATCTTGCTTCCCCGA
65 GATTGAAGCTACAACGGCGAATCTTGCTTCCCCGA
* **
54847190 CATTGCAATTAAAAAGATTAAAGCCACAACGGTGAATCTTACTTTCCTGGCGGTGCAGCGGAACA
1 CATTGCAATTAAAAAGATTGAAGCCACAACGGCAAATCTTAC-TTCCTGGCGGTGCAGCGGAACA
* * *
54847255 GATTGAAGCTAAAACGGCAAATCTTGCTTCCCGGA
65 GATTGAAGCTACAACGGCGAATCTTGCTTCCCCGA
* * *
54847290 CATTGCAATTAAAAAGATTGAAGCCACAATGGCAAATCTTACTTCCCTGGCGGTACAGCGGAATA
1 CATTGCAATTAAAAAGATTGAAGCCACAACGGCAAATCTTACTT-CCTGGCGGTGCAGCGGAACA
54847355 GATTGAAGCTACAACGGCGAATCTTGCTTCCCCGA
65 GATTGAAGCTACAACGGCGAATCTTGCTTCCCCGA
* * *** ** * *
54847390 CATTACAATTAAAAAGATTAAAGCCACAACGATGAATCTTACCTTCCTTGGCGGTATAGTGGAGC
1 CATTGCAATTAAAAAGATTGAAGCCACAACGGCAAATCTTA-CTTCC-TGGCGGTGCAGCGGAAC
* * * ***
54847455 AGATTGAAGCCACAACAGCGAATCTTACTTCTTTGA
64 AGATTGAAGCTACAACGGCGAATCTTGCTTCCCCGA
* * * **
54847491 CATTACAATTAAACAGATTGAAGCTACAACATCAAATCTT
1 CATTGCAATTAAAAAGATTGAAGCCACAACGGCAAATCTT
54847531 GTTTTCCTGG
Statistics
Matches: 1071, Mismatches: 156, Indels: 27
0.85 0.12 0.02
Matches are distributed among these distances:
99 10 0.01
100 974 0.91
101 87 0.08
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.24
Consensus pattern (99 bp):
CATTGCAATTAAAAAGATTGAAGCCACAACGGCAAATCTTACTTCCTGGCGGTGCAGCGGAACAG
ATTGAAGCTACAACGGCGAATCTTGCTTCCCCGA
Found at i:54847632 original size:44 final size:45
Alignment explanation
Indices: 54847574--54847685 Score: 120
Period size: 45 Copynumber: 2.5 Consensus size: 45
54847564 CCATAAACCT
* * * *
54847574 TATC-CCCATGAAGTTGTAGTGGGGCAAGTTGAAGATA-CAAGTCC
1 TATCTCCC-TGAAGTTGCAGTGGAGCAAGTTAAAGATAGCAAATCC
* * **
54847618 TATCTCCCTGAAGTTGCAGTGGAGTAGGTTAAAGATAGCAAATTT
1 TATCTCCCTGAAGTTGCAGTGGAGCAAGTTAAAGATAGCAAATCC
*
54847663 TATTTCCCTGAAGTTGCAGTGGA
1 TATCTCCCTGAAGTTGCAGTGGA
54847686 ACCGATTAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
44 28 0.49
45 29 0.51
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (45 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAAGTTAAAGATAGCAAATCC
Found at i:54849718 original size:13 final size:13
Alignment explanation
Indices: 54849700--54849725 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54849690 TATACATACT
54849700 TATATATTTTATA
1 TATATATTTTATA
54849713 TATATATTTTATA
1 TATATATTTTATA
54849726 ATTTATTTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATATATTTTATA
Found at i:54849739 original size:20 final size:20
Alignment explanation
Indices: 54849689--54849746 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
54849679 ATTTATGTAC
*
54849689 ATATACATACTTATATATTTT
1 ATATACATA-TTATATAATTT
* *
54849710 ATATATATATTTTATAATTT
1 ATATACATATTATATAATTT
*
54849730 ATTTACATATCTATATA
1 ATATACATAT-TATATA
54849747 TATATCTGTA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATACATATTATATAATTT
Found at i:54851774 original size:5 final size:5
Alignment explanation
Indices: 54851766--54851804 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
54851756 TTTTTCGCTC
*
54851766 TTCTT TTCTT TTCTT TTCTTTT TTCTT TTCGT TTCTT TT
1 TTCTT TTCTT TTCTT TTC--TT TTCTT TTCTT TTCTT TT
54851805 TTTCAAGTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 25 0.83
7 5 0.17
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (5 bp):
TTCTT
Found at i:54851789 original size:17 final size:17
Alignment explanation
Indices: 54851764--54851806 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
54851754 CTTTTTTCGC
*
54851764 TCTTCTTTTCTTTTCTTT
1 TCTT-TTTTCTTTTCGTT
54851782 TCTTTTTTCTTTTCGTT
1 TCTTTTTTCTTTTCGTT
54851799 TCTTTTTT
1 TCTTTTTT
54851807 TCAAGTGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 20 0.83
18 4 0.17
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (17 bp):
TCTTTTTTCTTTTCGTT
Found at i:54852264 original size:21 final size:21
Alignment explanation
Indices: 54852239--54852300 Score: 74
Period size: 20 Copynumber: 2.9 Consensus size: 21
54852229 TCGGTAGAGG
54852239 TTTTTGTTTTTTATTTTTCATT
1 TTTTTGTTTTTTATTTTT-ATT
54852261 TTTTTG-TTTTT-TTTTTATGT
1 TTTTTGTTTTTTATTTTTAT-T
54852281 TTTTATGTTTTTTTATTTTT
1 TTTT-TG-TTTTTTATTTTT
54852301 TTTCACTGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
19 2 0.06
20 10 0.29
21 7 0.20
22 6 0.17
23 5 0.14
24 5 0.14
ACGTcount: A:0.08, C:0.02, G:0.06, T:0.84
Consensus pattern (21 bp):
TTTTTGTTTTTTATTTTTATT
Found at i:54852283 original size:28 final size:27
Alignment explanation
Indices: 54852238--54852303 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 27
54852228 CTCGGTAGAG
54852238 GTTTTTGTTTTTTATTTTTCAT-TTTTTT
1 GTTTTT-TTTTTTATTTTT-ATGTTTTTT
*
54852266 GTTTTTTTTTTATGTTTTTATGTTTTTT
1 GTTTTTTTTTT-TATTTTTATGTTTTTT
*
54852294 -TATTTTTTTT
1 GTTTTTTTTTT
54852304 CACTGTACCA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
27 16 0.47
28 18 0.53
ACGTcount: A:0.08, C:0.02, G:0.08, T:0.83
Consensus pattern (27 bp):
GTTTTTTTTTTTATTTTTATGTTTTTT
Found at i:54855234 original size:21 final size:21
Alignment explanation
Indices: 54855211--54855253 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
54855201 TAATTTTAGA
54855211 ATAATA-ATACATAT-TAAA-
1 ATAATATATACATATATAAAG
54855229 ATAATATATACATATATAAAG
1 ATAATATATACATATATAAAG
54855250 ATAA
1 ATAA
54855254 AAGATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.27
19 8 0.36
20 4 0.18
21 4 0.18
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (21 bp):
ATAATATATACATATATAAAG
Found at i:54855262 original size:17 final size:17
Alignment explanation
Indices: 54855240--54855272 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
54855230 TAATATATAC
54855240 ATATATAAAGATAAAAG
1 ATATATAAAGATAAAAG
54855257 ATATATAAAGATAAAA
1 ATATATAAAGATAAAA
54855273 TAATATATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (17 bp):
ATATATAAAGATAAAAG
Found at i:54857130 original size:12 final size:12
Alignment explanation
Indices: 54857100--54857133 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
54857090 CCGTGTGTCA
*
54857100 CACACGACCTCG
1 CACACGGCCTCG
54857112 CACACGGCCTCG
1 CACACGGCCTCG
54857124 CACACGGCCT
1 CACACGGCCT
54857134 GTTACACGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.21, C:0.50, G:0.21, T:0.09
Consensus pattern (12 bp):
CACACGGCCTCG
Found at i:54862811 original size:14 final size:14
Alignment explanation
Indices: 54862792--54862821 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
54862782 TTACTCATCT
54862792 TTTTATTTTCAAGC
1 TTTTATTTTCAAGC
54862806 TTTTATTTTCAAGC
1 TTTTATTTTCAAGC
54862820 TT
1 TT
54862822 AAATTTATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.13, G:0.07, T:0.60
Consensus pattern (14 bp):
TTTTATTTTCAAGC
Found at i:54865386 original size:9 final size:9
Alignment explanation
Indices: 54865374--54865398 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
54865364 GATGATGTAT
54865374 TTATTATTG
1 TTATTATTG
54865383 TTATTATTG
1 TTATTATTG
54865392 TTATTAT
1 TTATTAT
54865399 AGCATTTGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (9 bp):
TTATTATTG
Found at i:54865817 original size:97 final size:97
Alignment explanation
Indices: 54865689--54865870 Score: 355
Period size: 97 Copynumber: 1.9 Consensus size: 97
54865679 GGAAATATTC
54865689 CGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATA
1 CGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATA
54865754 AGTGGATGTTCTTTTAAAGTAAAAAAAAATTT
66 AGTGGATGTTCTTTTAAAGTAAAAAAAAATTT
*
54865786 CGAGTTTGGGATTTTAAAGGAATTGTTCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATA
1 CGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATA
54865851 AGTGGATGTTCTTTTAAAGT
66 AGTGGATGTTCTTTTAAAGT
54865871 TTTATTGTAC
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
97 84 1.00
ACGTcount: A:0.28, C:0.09, G:0.24, T:0.40
Consensus pattern (97 bp):
CGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATA
AGTGGATGTTCTTTTAAAGTAAAAAAAAATTT
Found at i:54871444 original size:44 final size:45
Alignment explanation
Indices: 54871264--54871722 Score: 156
Period size: 44 Copynumber: 10.4 Consensus size: 45
54871254 CCCTGGCAAC
* * * *
54871264 AGTGGAATAGATCGAAGATTTCAGATATTATCTCCCTAAG-CAGT
1 AGTGGAGTAGATTGAAGATTTCAGATCTTATCTCCCTAGGTCAGT
* * * ** * * * *
54871308 AGTGGAGCAAATCGAAGATGGCAGATTTTACCTCCCTGTGGTTA-T
1 AGTGGAGTAGATTGAAGATTTCAGATCTTATCTCCCT-AGGTCAGT
* * **
54871353 AGTGGAGTACATTGAAG---CCAGTAAT-TCTA-CTTCCCTAGG-CAAC
1 AGTGGAGTAGATTGAAGATTTCAG--ATCT-TATC-TCCCTAGGTCAGT
* *
54871396 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAG-CAGT
1 AGTGGAGTAGATTGAAGATTTCAGATCTTATCTCCCTAGGTCAGT
* * ** * * * *
54871440 AGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTA-T
1 AGTGGAGTAGATTGAAGATTTCAGATCTTATCTCCCT-AGGTCAGT
* * **
54871485 AGTGGAGTACATTGAAG---CCAGTAAT-TCTA-CTTCCCT-GGTCAAC
1 AGTGGAGTAGATTGAAGATTTCAG--ATCT-TATC-TCCCTAGGTCAGT
* *
54871528 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAG-CAGT
1 AGTGGAGTAGATTGAAGATTTCAGATCTTATCTCCCTAGGTCAGT
* * ** * * * *
54871572 AGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTATGGTTA-T
1 AGTGGAGTAGATTGAAGATTTCAGATCTTATCTCCCTA-GGTCAGT
* * ** * * *
54871617 AGTGGAGCACATTGAAG--CCCATAAT-TCTA-CTTCCCT-GGACAAT
1 AGTGGAGTAGATTGAAGATTTCA-GATCT-TATC-TCCCTAGGTCAGT
* *
54871660 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAG-CAGT
1 AGTGGAGTAGATTGAAGATTTCAGATCTTATCTCCCTAGGTCAGT
* *
54871704 AGTGGAGCAGATCGAAGAT
1 AGTGGAGTAGATTGAAGAT
54871723 GGTGAATTTT
Statistics
Matches: 305, Mismatches: 74, Indels: 72
0.68 0.16 0.16
Matches are distributed among these distances:
42 14 0.05
43 54 0.18
44 169 0.55
45 59 0.19
46 9 0.03
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.29
Consensus pattern (45 bp):
AGTGGAGTAGATTGAAGATTTCAGATCTTATCTCCCTAGGTCAGT
Found at i:54871460 original size:132 final size:132
Alignment explanation
Indices: 54871177--54871785 Score: 1039
Period size: 132 Copynumber: 4.6 Consensus size: 132
54871167 TTGCATTGAC
* *
54871177 AGTGGAGCAAATCGAAGATGGC-GAATTTTACCTCCCTGTGGTTATAGTGAAGTACATTGAAGCC
1 AGTGGAGCAGATCGAAGATGGCAG-ATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCC
* *
54871241 AGTAATTCTACTTCCCTGG-CAACAGTGGAATAGATCGAAGATTTCAGATATTATCTCCCTAAGC
65 AGTAATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGC
54871305 AGT
130 AGT
*
54871308 AGTGGAGCAAATCGAAGATGGCAGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCA
1 AGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCA
54871373 GTAATTCTACTTCCCTAGG-CAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGC
66 GTAATTCTACTTCCCT-GGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGC
54871437 AGT
130 AGT
54871440 AGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCA
1 AGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCA
*
54871505 GTAATTCTACTTCCCTGGTCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCA
66 GTAATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCA
54871570 GT
131 GT
* * *
54871572 AGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTATGGTTATAGTGGAGCACATTGAAGCCC
1 AGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAG-CC
*
54871637 A-TAATTCTACTTCCCTGGACAATAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGC
65 AGTAATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGC
54871701 AGT
130 AGT
*
54871704 AGTGGAGCAGATCGAAGATGG-TGAATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCC
1 AGTGGAGCAGATCGAAGATGGCAG-ATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCC
*
54871768 AATAATTCTACTTCCCTG
65 AGTAATTCTACTTCCCTG
54871786 AAGTTGCAGT
Statistics
Matches: 460, Mismatches: 12, Indels: 11
0.95 0.02 0.02
Matches are distributed among these distances:
131 84 0.18
132 373 0.81
133 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (132 bp):
AGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCA
GTAATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCA
GT
Found at i:54871958 original size:44 final size:44
Alignment explanation
Indices: 54871780--54872349 Score: 273
Period size: 44 Copynumber: 13.3 Consensus size: 44
54871770 TAATTCTACT
* *
54871780 TCCCTGAAGTTGCAGTGGAGCAGGTTAAAGCCGGTAATCCTATC
1 TCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGGTAATCTTATC
* * *
54871824 TCGCTGAAGTTGCAGTGG-GCGGATTAAAACCTCGG--ATCTTATC
1 TCCCTGAAGTTGCAGTGGAGCAGATT-AAAGC-CGGTAATCTTATC
* * * * *** *
54871867 TCTCTGAAGTTACAG-AGAGCAGA-T--CGCATCTACTCTTATC
1 TCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGGTAATCTTATC
*
54871907 TCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGGTAATCCTATC
1 TCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGGTAATCTTATC
* *
54871951 TCGCTGAAGTTGCAGTGG-GCAGATTAAAACC--TCAGATCTTATC
1 TCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGGT-A-ATCTTATC
** * * ** * *
54871994 TCTTTGAAGTTACAG-AGAGCAGATTGTA-TC--TAGTCTTATC
1 TCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGGTAATCTTATC
* * *
54872034 TCCCAGAAGTTGCAGTGAAGCAGACT-AA----GTAAGTCTTATC
1 TCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGGTAA-TCTTATC
* * * ** *
54872074 -CTCTTGAAGTTGCAGTGGGGCAGACTGAAA-TTGGCAAGTCTTATC
1 TC-CCTGAAGTTGCAGTGGAGCAGA-TTAAAGCCGGTAA-TCTTATC
* * * *
54872119 TCCTTGAAGTTGTAGTGGAGCAGATTAAAGCCGATAATCCTATC
1 TCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGGTAATCTTATC
* *
54872163 TCCCTGAAGTTGCAGTGGAGCGGATTAGAA-CC-TTAGATCTTATC
1 TCCCTGAAGTTGCAGTGGAGCAGATTA-AAGCCGGTA-ATCTTATC
* * * *** * *
54872207 TCTCTGAAGTTGTAG-AGAGCAGATCGCATCC---AGTCTTATC
1 TCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGGTAATCTTATC
* * *** *
54872247 TCCCTGAAGTTGCAGTAGAGCAGACTAAA-TAAGCAAGTCTTATC
1 TCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGGTAA-TCTTATC
* * ** **
54872291 -CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATAGCAAATCTTATC
1 TC-CCTGAAGTTGCAGTGGA-GCAGATTAAAG-CCGGTAATCTTATC
54872336 TCCCTGAAGTTGCA
1 TCCCTGAAGTTGCA
54872350 AAGGAGTAGA
Statistics
Matches: 405, Mismatches: 85, Indels: 71
0.72 0.15 0.13
Matches are distributed among these distances:
39 4 0.01
40 84 0.21
41 26 0.06
42 10 0.02
43 83 0.20
44 134 0.33
45 58 0.14
46 6 0.01
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.28
Consensus pattern (44 bp):
TCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGGTAATCTTATC
Found at i:54872006 original size:127 final size:127
Alignment explanation
Indices: 54871780--54872057 Score: 475
Period size: 127 Copynumber: 2.2 Consensus size: 127
54871770 TAATTCTACT
* *
54871780 TCCCTGAAGTTGCAGTGGAGCAGGTTAAAGCCGGTAATCCTATCTCGCTGAAGTTGCAGTGGGCG
1 TCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGGTAATCCTATCTCGCTGAAGTTGCAGTGGGCA
*
54871845 GATTAAAACCTCGGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCTACTCTTATC
66 GATTAAAACCTCAGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCTACTCTTATC
54871907 TCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGGTAATCCTATCTCGCTGAAGTTGCAGTGGGCA
1 TCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGGTAATCCTATCTCGCTGAAGTTGCAGTGGGCA
* * * *
54871972 GATTAAAACCTCAGATCTTATCTCTTTGAAGTTACAGAGAGCAGATTGTATCTAGTCTTATC
66 GATTAAAACCTCAGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCTACTCTTATC
* *
54872034 TCCCAGAAGTTGCAGTGAAGCAGA
1 TCCCTGAAGTTGCAGTGGAGCAGA
54872058 CTAAGTAAGT
Statistics
Matches: 142, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
127 142 1.00
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (127 bp):
TCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGGTAATCCTATCTCGCTGAAGTTGCAGTGGGCA
GATTAAAACCTCAGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCTACTCTTATC
Found at i:54872274 original size:213 final size:213
Alignment explanation
Indices: 54871900--54872349 Score: 654
Period size: 213 Copynumber: 2.1 Consensus size: 213
54871890 TCGCATCTAC
* *
54871900 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGGTAATCCTATCTCGCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCA
* * * *
54871965 GTGGGCAGATTAAAACCTCAGATCTTATCTCTTTGAAGTTACAGAGAGCAGATTGTATCTAGTCT
66 GTGGGCAGATTAAAACCTCAGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCCAGTCT
* * *
54872030 TATCTCCCAGAAGTTGCAGTGAAGCAGAC-TAAGTAAGTCTTATCCTCTTGAAGTTGCAGTGGGG
131 TATCTCCCAGAAGTTGCAGTGAAGCAGACATAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGG
* *
54872094 CAGACTGAA-ATTGGCAAG
196 CAGACTGAAGA-TAGCAAA
* *
54872112 TCTTATCTCCTTGAAGTTGTAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCA
* * * **
54872177 GTGGAGCGGATTAGAACCTTAGATCTTATCTCTCTGAAGTTGTAGAGAGCAGATCGCATCCAGTC
66 GTGG-GCAGATTAAAACCTCAGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCCAGTC
*
54872242 TTATCTCCCTGAAGTTGCAGT-AGAGCAGACTAAATAAGCAAGTCTTATCCTCCTGAAGTTGCAG
130 TTATCTCCCAGAAGTTGCAGTGA-AGCAGAC---ATAAGCAAGTCTTATCCTCCTGAAGTTGCAG
54872306 TGAGGCAGACTGAAGATAGCAAA
191 TGAGGCAGACTGAAGATAGCAAA
54872329 TCTTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCA
54872350 AAGGAGTAGA
Statistics
Matches: 210, Mismatches: 21, Indels: 9
0.88 0.09 0.04
Matches are distributed among these distances:
212 66 0.31
213 78 0.37
217 65 0.31
218 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (213 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCA
GTGGGCAGATTAAAACCTCAGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCCAGTCT
TATCTCCCAGAAGTTGCAGTGAAGCAGACATAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGG
CAGACTGAAGATAGCAAA
Found at i:54872365 original size:45 final size:45
Alignment explanation
Indices: 54872240--54872365 Score: 129
Period size: 45 Copynumber: 2.8 Consensus size: 45
54872230 TCGCATCCAG
*
54872240 TCTTATCTCCCTGAAGTTGC-AGTAGAGCAGACT-AA-ATAAGCAAG
1 TCTTATCTCCCTGAAGTTGCAAG--GAGCAGACTGAAGATAAGCAAA
54872284 TCTTATC-CTCCTGAAGTTGC-AGTGAGGCAGACTGAAGAT-AGCAAA
1 TCTTATCTC-CCTGAAGTTGCAAG-GA-GCAGACTGAAGATAAGCAAA
* *
54872329 TCTTATCTCCCTGAAGTTGCAAAGGAGTAGATTGAAG
1 TCTTATCTCCCTGAAGTTGC-AAGGAGCAGACTGAAG
54872366 CATTAGTTCC
Statistics
Matches: 71, Mismatches: 4, Indels: 13
0.81 0.05 0.15
Matches are distributed among these distances:
43 3 0.04
44 27 0.38
45 34 0.48
46 5 0.07
47 2 0.03
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (45 bp):
TCTTATCTCCCTGAAGTTGCAAGGAGCAGACTGAAGATAAGCAAA
Found at i:54872387 original size:173 final size:173
Alignment explanation
Indices: 54871784--54872388 Score: 390
Period size: 173 Copynumber: 3.5 Consensus size: 173
54871774 TCTACTTCCC
** * * * ** *
54871784 TGAAGTTGCAGTGGAGCAGGTTAAAGCCGGTAATCCTATCTCGCTGAAGTTGCAGTGG-GCGGAT
1 TGAAGTTGCAGTGGAGCAGACTAAAGCAGATAATCCTATCTCCCTGAAGTTGCAAAGGAGCAGAT
* * ** * ** * *
54871848 TAAAACCTCGGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCTACTCTTAT-CTCCCT
66 TAGAACATTAGATCCTATCTCTCTGAAGTTGTAGAGAGCAGATCGCATCCAGTCTTATCCT-CCT
* * *** * *
54871912 GAAGTTGCAGTGGAGCAGA-TTAAAGCCGGTAA-TCCTATCTCGC-
130 GAAGTTGCAGTAGAGCAGACTGAAA-TAAGCAAGTCTTATCTC-CT
* ** * ** * *
54871955 TGAAGTTGCAGTGG-GCAGATTAAA--ACCTCAGATCTTATCTCTTTGAAGTTACAGA-GAGCAG
1 TGAAGTTGCAGTGGAGCAGACTAAAGCAGAT-A-ATCCTATCTCCCTGAAGTTGCAAAGGAGCAG
* * * * * * ** *
54872016 ATT-G--TATCTAG-TCTTATCTCCCAGAAGTTGCAGTGAAGCAGA-CTAAGT-AAGTCTTATCC
64 ATTAGAACAT-TAGATCCTATCTCTCTGAAGTTGTAGAG-AGCAGATCGCA-TCCAGTCTTATCC
* * * **
54872075 TCTTGAAGTTGCAGTGGGGCAGACTGAAATTGGCAAGTCTTATCTCCT
126 TCCTGAAGTTGCAGTAGAGCAGACTGAAATAAGCAAGTCTTATCTCCT
* * * ** *
54872123 TGAAGTTGTAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGAT
1 TGAAGTTGCAGTGGAGCAGACTAAAGCAGATAATCCTATCTCCCTGAAGTTGCAAAGGAGCAGAT
* *
54872188 TAGAACCTTAGATCTTATCTCTCTGAAGTTGTAGAGAGCAGATCGCATCCAGTCTTAT-CTCCCT
66 TAGAACATTAGATCCTATCTCTCTGAAGTTGTAGAGAGCAGATCGCATCCAGTCTTATCCT-CCT
54872252 GAAGTTGCAGTAGAGCAGACT-AAATAAGCAAGTCTTATCCTCC-
130 GAAGTTGCAGTAGAGCAGACTGAAATAAGCAAGTCTTAT-CTCCT
* * * *
54872295 TGAAGTTGCAGT-GAGGCAGACTGAAGATAGCA-AATCTTATCTCCCTGAAGTTGCAAAGGAGTA
1 TGAAGTTGCAGTGGA-GCAGACTAAAG-CAG-ATAATCCTATCTCCCTGAAGTTGCAAAGGAGCA
*
54872358 GATT-GAAGCATTAGTTCCTATAC-CTCTGAAG
63 GATTAGAA-CATTAGATCCTAT-CTCTCTGAAG
54872389 ATGCAGTAGG
Statistics
Matches: 340, Mismatches: 67, Indels: 52
0.74 0.15 0.11
Matches are distributed among these distances:
167 55 0.16
168 36 0.11
169 31 0.09
170 43 0.13
171 18 0.05
172 50 0.15
173 105 0.31
174 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (173 bp):
TGAAGTTGCAGTGGAGCAGACTAAAGCAGATAATCCTATCTCCCTGAAGTTGCAAAGGAGCAGAT
TAGAACATTAGATCCTATCTCTCTGAAGTTGTAGAGAGCAGATCGCATCCAGTCTTATCCTCCTG
AAGTTGCAGTAGAGCAGACTGAAATAAGCAAGTCTTATCTCCT
Found at i:54874087 original size:9 final size:9
Alignment explanation
Indices: 54874075--54874099 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
54874065 GATGATGTAT
54874075 TTATTATTG
1 TTATTATTG
54874084 TTATTATTG
1 TTATTATTG
54874093 TTATTAT
1 TTATTAT
54874100 AGTATTTGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (9 bp):
TTATTATTG
Found at i:54874501 original size:98 final size:98
Alignment explanation
Indices: 54874376--54874572 Score: 367
Period size: 98 Copynumber: 2.0 Consensus size: 98
54874366 AAAAAAATAA
* *
54874376 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAAGAAATATTCCAAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
54874441 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
*
54874474 TAAAAGAAATATTCCAAGTTTGGGATTTTAAAGGAATTGTTCCCTAACGTATTGGGTGTGATTTC
1 TAAAAGAAATATTCCAAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
54874539 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
54874572 T
1 T
54874573 TTTATTGTAC
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 96 1.00
ACGTcount: A:0.29, C:0.09, G:0.23, T:0.39
Consensus pattern (98 bp):
TAAAAGAAATATTCCAAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:54880961 original size:25 final size:24
Alignment explanation
Indices: 54880932--54880978 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
54880922 ATACCATTAA
*
54880932 AAAGAAAGAACAGAAAAGAAAAAAT
1 AAAGAAA-AACAAAAAAGAAAAAAT
*
54880957 AAAGAAATACAAAAAAGAAAAA
1 AAAGAAAAACAAAAAAGAAAAA
54880979 GAACCACCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.79, C:0.04, G:0.13, T:0.04
Consensus pattern (24 bp):
AAAGAAAAACAAAAAAGAAAAAAT
Found at i:54884526 original size:6 final size:6
Alignment explanation
Indices: 54884506--54884538 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
54884496 TTTCCTTTAA
54884506 TTTA-T TTTA-T TTTATT TTTATT TTTATT TTTAT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTAT
54884539 AAAGAAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 9 0.33
6 18 0.67
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTATT
Found at i:54890635 original size:43 final size:42
Alignment explanation
Indices: 54890526--54890689 Score: 181
Period size: 43 Copynumber: 3.9 Consensus size: 42
54890516 TACCGTAACA
* * *
54890526 ATGCCATATCCCAGATATGGTCTTACATGTAATCTCATATCG
1 ATGCCATATCCCAGACATGGTCTTACACGGAATCTCATATCG
* * *
54890568 ATGTCAATAGCCCA-ACCGAT-GTCTTACACGGAATCACATATCG
1 ATG-CCATATCCCAGA-C-ATGGTCTTACACGGAATCTCATATCG
*
54890611 ATGCCAATATCCTAGACATGGTCTTACA-GGAAATCTCATATCG
1 ATGCC-ATATCCCAGACATGGTCTTACACGG-AATCTCATATCG
* *
54890654 ATGCCATATCCCAGATATGGTCTTACACGTAATCTC
1 ATGCCATATCCCAGACATGGTCTTACACGGAATCTC
54890690 GGTAACCCTA
Statistics
Matches: 101, Mismatches: 13, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
42 35 0.35
43 63 0.62
44 3 0.03
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (42 bp):
ATGCCATATCCCAGACATGGTCTTACACGGAATCTCATATCG
Found at i:54894462 original size:17 final size:16
Alignment explanation
Indices: 54894440--54894471 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
54894430 CTTTTTTTTT
54894440 CATTTCATTTACATTTC
1 CATTTCATTTA-ATTTC
54894457 CATTTCATTTAATTT
1 CATTTCATTTAATTT
54894472 TTTTCCATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.25, C:0.19, G:0.00, T:0.56
Consensus pattern (16 bp):
CATTTCATTTAATTTC
Done.