Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold156
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1175753
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.30
Warning! 90626 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:409060 original size:2 final size:2
Alignment explanation
Indices: 409055--409113 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
409045 AATCATCTAC
409055 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
409097 GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA G
409114 CTGGGTTGGA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:409605 original size:161 final size:160
Alignment explanation
Indices: 409338--410315 Score: 1442
Period size: 161 Copynumber: 6.1 Consensus size: 160
409328 GAATCATCCA
* * * *
409338 CAAAGAAAATGAACGTAAACTGCAAATAACTGGAATTTTCCTAAGTCCAAGGGCCATAACTCTTT
1 CAAAGAAAATGAGCGTAAACTGCAAATAACTGGAATTTTTCTATGTCCAAGGGCCATAACTCTGT
* *
409403 TGAAAATTGCTCGATCGTACCCAA-AGTCAAACCTGACCTAGATATTATCATGATAAACCTGTAT
66 CGAAAATTGCTCGATCGTACCCAATA-TCAAACTTGACCTAGATATTATCATGATAAACCTGTAT
* * * *
409467 ACCAAATGTCATATCAATATGTGCACCCTCAG
130 ACCAAATTTCAT-TCAATATGTTCATCCTCTG
** * * *
409499 TGAAGAAAATGAGCGTAAACTGCAAATAACTGGAATTTTTCTATGTCCAAGGGCCTTAGCTCTAT
1 CAAAGAAAATGAGCGTAAACTGCAAATAACTGGAATTTTTCTATGTCCAAGGGCCATAACTCTGT
409564 CGAAAATTGCTCGATCGTACCCAATATCAAACTTGACCTAGATATTATCATGATAAACCTGTATA
66 CGAAAATTGCTCGATCGTACCCAATATCAAACTTGACCTAGATATTATCATGATAAACCTGTATA
* *
409629 CCAAATTTCAGTTCAATTTGTTCATCTTCTG
131 CCAAATTTCA-TTCAATATGTTCATCCTCTG
* * * * *
409660 CAAAGAAAATGAGCGTAAACTGCAAATAACTGGAATTTTCCTAAGTCAAAGTGCCATAACTCTCT
1 CAAAGAAAATGAGCGTAAACTGCAAATAACTGGAATTTTTCTATGTCCAAGGGCCATAACTCTGT
* * * *
409725 CGAAAATTGCTCGATCGTACCCAA-AGTCAAAATTGAACTAGATATTATCATGATGAACATGTAT
66 CGAAAATTGCTCGATCGTACCCAATA-TCAAACTTGACCTAGATATTATCATGATAAACCTGTAT
* *
409789 ACCAAATTTAATTTCAAAATGTTCATCCTCTG
130 ACCAAATTTCA-TTCAATATGTTCATCCTCTG
* *
409821 CAAAGAAAATGAGCGTATACTGCAAATAACTGGAATTTTTCTATGTCCAAAGGCCATAA--CTGT
1 CAAAGAAAATGAGCGTAAACTGCAAATAACTGGAATTTTTCTATGTCCAAGGGCCATAACTCTGT
* *
409884 CGAAAATTGCTCGATCATACCCAATATCAAACTTGACTTAGATATTATCATGATAAACCTGTATA
66 CGAAAATTGCTCGATCGTACCCAATATCAAACTTGACCTAGATATTATCATGATAAACCTGTATA
**
409949 AGAAATTTCATTTCAATATGTTCATCCTCTG
131 CCAAATTTCA-TTCAATATGTTCATCCTCTG
* * *
409980 CGAAGAAAATGAGTGTAAACTGCAAAAAACTGGAATTTTTCTATGTCCAAGGGCCATAACTCTGT
1 CAAAGAAAATGAGCGTAAACTGCAAATAACTGGAATTTTTCTATGTCCAAGGGCCATAACTCTGT
* * * *
410045 CGAAAATTGCTTGATCGTACCCAGTATTAAACTTGACCTAGATATTATCATGATAAACCTGCATG
66 CGAAAATTGCTCGATCGTACCCAATATCAAACTTGACCTAGATATTATCATGATAAACCTG--TA
410110 TACCAAATTTCATTCCAATATGTTCATCCTCTG
129 TACCAAATTTCATT-CAATATGTTCATCCTCTG
*
410143 CAAAGAAAATGAGCGTAAACTGCAAATAACTGGAATTTTTCTACGTCCAAGGGCCATAACTCTGT
1 CAAAGAAAATGAGCGTAAACTGCAAATAACTGGAATTTTTCTATGTCCAAGGGCCATAACTCTGT
*
410208 CGAAAATTGCTCGATCATACCCAATATCAAACTTGACCTAGATATTATCATGATAAACCTGTATA
66 CGAAAATTGCTCGATCGTACCCAATATCAAACTTGACCTAGATATTATCATGATAAACCTGTATA
410273 CCAAATTTCATTCCAATATGTTCATCCTCTG
131 CCAAATTTCATT-CAATATGTTCATCCTCTG
*
410304 CGAAGAAAATGA
1 CAAAGAAAATGA
410316 ACGGAAATTG
Statistics
Matches: 734, Mismatches: 74, Indels: 18
0.89 0.09 0.02
Matches are distributed among these distances:
159 141 0.19
160 2 0.00
161 440 0.60
162 4 0.01
163 147 0.20
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.29
Consensus pattern (160 bp):
CAAAGAAAATGAGCGTAAACTGCAAATAACTGGAATTTTTCTATGTCCAAGGGCCATAACTCTGT
CGAAAATTGCTCGATCGTACCCAATATCAAACTTGACCTAGATATTATCATGATAAACCTGTATA
CCAAATTTCATTCAATATGTTCATCCTCTG
Found at i:422698 original size:35 final size:38
Alignment explanation
Indices: 422656--422747 Score: 120
Period size: 39 Copynumber: 2.5 Consensus size: 38
422646 CTCCACACCT
*
422656 AGAATGTACCAGGATACAC-AAGAG-T-TT-AACACTAG
1 AGAATGTACCAGGATACACTAA-AGTTATTAAACACTAA
422691 AGAATGTACCAGGATACACTAAAGTTTATTAAACACTAA
1 AGAATGTACCAGGATACACTAAAG-TTATTAAACACTAA
*
422730 AGAATGTACCATGATACA
1 AGAATGTACCAGGATACA
422748 TGGTGTTAGT
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
35 21 0.42
36 2 0.04
37 1 0.02
38 2 0.04
39 24 0.48
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.23
Consensus pattern (38 bp):
AGAATGTACCAGGATACACTAAAGTTATTAAACACTAA
Found at i:424828 original size:49 final size:49
Alignment explanation
Indices: 424755--424966 Score: 352
Period size: 49 Copynumber: 4.3 Consensus size: 49
424745 GTGACCCTGG
* *
424755 CCTATTACCACATTATCACCATGTGGTGTTCCCTATCACTGCATGGTGAC
1 CCTATCACCACA-TATCACCATGTGGTGTTCCCTATCACTGCAAGGTGAC
*
424805 CCTATCACCACATATCACCATGTGGTGTTCCCCATCACTGCAAGGTGAC
1 CCTATCACCACATATCACCATGTGGTGTTCCCTATCACTGCAAGGTGAC
424854 CCTATCACCACATATCACCATGTGGTGTTCCCTATCACTGCAAGGTGAC
1 CCTATCACCACATATCACCATGTGGTGTTCCCTATCACTGCAAGGTGAC
* * *
424903 CCTATCACCACATATCACCATGTGGTGTTCTCTATCATTGCATGGTGAC
1 CCTATCACCACATATCACCATGTGGTGTTCCCTATCACTGCAAGGTGAC
*
424952 CCTTTCACCACATAT
1 CCTATCACCACATAT
424967 GACCCTCACC
Statistics
Matches: 154, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
49 143 0.93
50 11 0.07
ACGTcount: A:0.24, C:0.32, G:0.15, T:0.29
Consensus pattern (49 bp):
CCTATCACCACATATCACCATGTGGTGTTCCCTATCACTGCAAGGTGAC
Found at i:425714 original size:69 final size:67
Alignment explanation
Indices: 425567--425736 Score: 211
Period size: 69 Copynumber: 2.5 Consensus size: 67
425557 ATTTACTAAA
* *
425567 TCTATTACCTGTATCAGGTAGC--AATATTTTACTTCCATTACCTGTATCAGATAGTTGAAAACT
1 TCTATTACCTGTATCAGGTAGCTGAA-ATTCTACTTCCATTACCTGTATCAGATAGGTGAAAACT
425630 ACT
65 ACT
* * *
425633 T-TCATTACCTGTATCAAGTAGCTGAAATTCTACTTCCATTCACCTGTATCAGGTAGGTGATATA
1 TCT-ATTACCTGTATCAGGTAGCTGAAATTCTACTTCCATT-ACCTGTATCAGATAGGTGA-AAA
425697 CTACT
63 CTACT
* * *
425702 TCTATTACCTGTATCAGGTAGGTGATATACTACTT
1 TCTATTACCTGTATCAGGTAGCTGAAATTCTACTT
425737 ATGTAGCTGA
Statistics
Matches: 89, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
65 1 0.01
66 19 0.21
67 13 0.15
68 19 0.21
69 36 0.40
70 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (67 bp):
TCTATTACCTGTATCAGGTAGCTGAAATTCTACTTCCATTACCTGTATCAGATAGGTGAAAACTA
CT
Found at i:425717 original size:34 final size:34
Alignment explanation
Indices: 425567--425736 Score: 184
Period size: 33 Copynumber: 5.0 Consensus size: 34
425557 ATTTACTAAA
** **
425567 TCTATTACCTGTATCAGGTA-GCAATATTTTACT
1 TCTATTACCTGTATCAGGTAGGTGATATACTACT
* * * *
425600 TCCATTACCTGTATCAGATAGTTGA-AAACTACT
1 TCTATTACCTGTATCAGGTAGGTGATATACTACT
* * * *
425633 T-TCATTACCTGTATCAAGTAGCTGAAATTCTACT
1 TCT-ATTACCTGTATCAGGTAGGTGATATACTACT
*
425667 TCCATTCACCTGTATCAGGTAGGTGATATACTACT
1 TCTATT-ACCTGTATCAGGTAGGTGATATACTACT
425702 TCTATTACCTGTATCAGGTAGGTGATATACTACT
1 TCTATTACCTGTATCAGGTAGGTGATATACTACT
425736 T
1 T
425737 ATGTAGCTGA
Statistics
Matches: 112, Mismatches: 20, Indels: 9
0.79 0.14 0.06
Matches are distributed among these distances:
33 43 0.38
34 40 0.36
35 29 0.26
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (34 bp):
TCTATTACCTGTATCAGGTAGGTGATATACTACT
Found at i:425800 original size:88 final size:89
Alignment explanation
Indices: 425650--425823 Score: 280
Period size: 88 Copynumber: 2.0 Consensus size: 89
425640 CCTGTATCAA
* * *
425650 GTAGCTGAAATTCTACTTCCATTCACCTGTATCAGGTAGGTGATATACTACTTCTATTACCTGTA
1 GTAGCTGAAATACTACTTCCATTCACCTGTATCAGGTAGGTAATATACTACTTCTATCACCTGTA
425715 TCAGGTAGGTGATATACTACTTAT
66 TCAGGTAGGTGATATACTACTTAT
*
425739 GTAGCTGAAATACTTCTTCCATT-ACCTGTATCAGGTAGGTAATATTA-TACTTCTATCACCTGT
1 GTAGCTGAAATACTACTTCCATTCACCTGTATCAGGTAGGTAATA-TACTACTTCTATCACCTGT
*
425802 ATCAGGTAGGTGATATTCTACT
65 ATCAGGTAGGTGATATACTACT
425824 GTTATTACCT
Statistics
Matches: 79, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
88 56 0.71
89 23 0.29
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (89 bp):
GTAGCTGAAATACTACTTCCATTCACCTGTATCAGGTAGGTAATATACTACTTCTATCACCTGTA
TCAGGTAGGTGATATACTACTTAT
Found at i:425839 original size:122 final size:122
Alignment explanation
Indices: 425622--425850 Score: 338
Period size: 122 Copynumber: 1.9 Consensus size: 122
425612 ATCAGATAGT
* *
425622 TGAAAACTACTTTCATTACCTGTATCAAGTAGCTGAAATTCTACTTCCATTCACCTGTATCAGGT
1 TGAAAACTACTTCCATTACCTGTATCAAGTAGCTGAAATTATACTTCCATTCACCTGTATCAGGT
*
425687 AGGTGATATACTACTTCTATTACCTGTATCAGGTAGGTGATATACTACTTATGTAGC
66 AGGTGATATACTACTTCTATTACCTGTATCAGGTAGCTGATATACTACTTATGTAGC
* * * *
425744 TGAAATACTTCTTCCATTACCTGTATCAGGTAGGT-AATATTATACTTCTA-TCACCTGTATCAG
1 TGAAA-ACTACTTCCATTACCTGTATCAAGTAGCTGAA-ATTATACTTCCATTCACCTGTATCAG
*
425807 GTAGGTGATATTCTACTGT-TATTACCTGTATCAGGTAGCTGATA
64 GTAGGTGATATACTACT-TCTATTACCTGTATCAGGTAGCTGATA
425851 CTCCACCTCC
Statistics
Matches: 96, Mismatches: 8, Indels: 6
0.87 0.07 0.05
Matches are distributed among these distances:
122 60 0.62
123 36 0.38
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (122 bp):
TGAAAACTACTTCCATTACCTGTATCAAGTAGCTGAAATTATACTTCCATTCACCTGTATCAGGT
AGGTGATATACTACTTCTATTACCTGTATCAGGTAGCTGATATACTACTTATGTAGC
Found at i:425850 original size:34 final size:34
Alignment explanation
Indices: 425754--425850 Score: 133
Period size: 34 Copynumber: 2.9 Consensus size: 34
425744 TGAAATACTT
* *
425754 CTTCCATTACCTGTATCAGGTAGGTAATATTATA
1 CTTCTATTACCTGTATCAGGTAGGTGATATTATA
* *
425788 CTTCTATCACCTGTATCAGGTAGGTGATATTCTA
1 CTTCTATTACCTGTATCAGGTAGGTGATATTATA
*
425822 CTGT-TATTACCTGTATCAGGTAGCTGATA
1 CT-TCTATTACCTGTATCAGGTAGGTGATA
425851 CTCCACCTCC
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
34 55 0.98
35 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.38
Consensus pattern (34 bp):
CTTCTATTACCTGTATCAGGTAGGTGATATTATA
Found at i:427927 original size:1 final size:1
Alignment explanation
Indices: 427923--427947 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
427913 TTAAGGGGTT
427923 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
427948 TGGAGGTAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:431485 original size:2 final size:2
Alignment explanation
Indices: 431480--431537 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
431470 ATATATACAT
431480 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
*
431522 AA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA
431538 CGCAGTTCAG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:432269 original size:14 final size:15
Alignment explanation
Indices: 432245--432274 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
432235 CATTAATGCA
432245 AGTTCTTGTACATGT
1 AGTTCTTGTACATGT
432260 AGTT-TTGTACATGT
1 AGTTCTTGTACATGT
432274 A
1 A
432275 TACGGAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.23, C:0.10, G:0.20, T:0.47
Consensus pattern (15 bp):
AGTTCTTGTACATGT
Found at i:434990 original size:2 final size:2
Alignment explanation
Indices: 434983--435053 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
434973 GTGCACGAAC
434983 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
435025 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
435054 TTTAACGCGT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:437820 original size:2 final size:2
Alignment explanation
Indices: 437813--437843 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
437803 TAAATCTAAA
437813 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
437844 GACAGGTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:440751 original size:2 final size:2
Alignment explanation
Indices: 440744--440785 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
440734 AAAAATGATA
440744 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
440786 GATATATCAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:441687 original size:14 final size:14
Alignment explanation
Indices: 441668--441695 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
441658 CCATCTGAAA
441668 ATATATTTTTATGC
1 ATATATTTTTATGC
441682 ATATATTTTTATGC
1 ATATATTTTTATGC
441696 TTCATCATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (14 bp):
ATATATTTTTATGC
Found at i:450407 original size:2 final size:2
Alignment explanation
Indices: 450400--450452 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
450390 AAGAACAATG
450400 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
450442 GA GA GA GA GA G
1 GA GA GA GA GA G
450453 GATTACAACT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:462951 original size:1 final size:1
Alignment explanation
Indices: 462945--462987 Score: 77
Period size: 1 Copynumber: 43.0 Consensus size: 1
462935 TCTCATCTCT
*
462945 CCCCCCCCCCCCCCCCCCCCCCCCCTCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
462988 ACTTCGAATG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.00, C:0.98, G:0.00, T:0.02
Consensus pattern (1 bp):
C
Found at i:463039 original size:11 final size:11
Alignment explanation
Indices: 463023--463047 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
463013 TCCACGCGGT
463023 ATTAATTGCTC
1 ATTAATTGCTC
463034 ATTAATTGCTC
1 ATTAATTGCTC
463045 ATT
1 ATT
463048 TAGTACAGTT
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:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (11 bp):
ATTAATTGCTC
Found at i:467088 original size:2 final size:2
Alignment explanation
Indices: 467081--467152 Score: 123
Period size: 2 Copynumber: 37.5 Consensus size: 2
467071 CATTGTGCAT
467081 GA GA GA GA GA GA GA GA GA GA GA GA GA G- GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
467122 G- GA GA GA GA GA G- GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
467153 CGTTCGTTAA
Statistics
Matches: 67, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
1 3 0.04
2 64 0.96
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:468102 original size:5 final size:5
Alignment explanation
Indices: 468092--468116 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
468082 CAACGTTTAC
468092 CAATT CAATT CAATT CAATT CAATT
1 CAATT CAATT CAATT CAATT CAATT
468117 TCTTTATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
CAATT
Found at i:468193 original size:18 final size:18
Alignment explanation
Indices: 468166--468206 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
468156 AAGACTGTTG
* *
468166 ACATACAACATCCAATGA
1 ACATAAAACATCCAATAA
*
468184 ACATAAAACATTCAATAA
1 ACATAAAACATCCAATAA
468202 ACATA
1 ACATA
468207 CATGTATACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.56, C:0.22, G:0.02, T:0.20
Consensus pattern (18 bp):
ACATAAAACATCCAATAA
Found at i:468302 original size:10 final size:12
Alignment explanation
Indices: 468273--468305 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
468263 AATTAAATAG
468273 TATATATGTATA
1 TATATATGTATA
468285 TATATATGTATA
1 TATATATGTATA
468297 -AT-TATGTAT
1 TATATATGTAT
468306 GTTTCCATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 7 0.33
11 2 0.10
12 12 0.57
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (12 bp):
TATATATGTATA
Found at i:469924 original size:25 final size:25
Alignment explanation
Indices: 469871--470023 Score: 126
Period size: 23 Copynumber: 6.4 Consensus size: 25
469861 CATATGTCAA
* *
469871 CAATGTACATG--TAGTTACACACT
1 CAATGTACATGTATAGTTACATATT
* *
469894 CGATGTACATGTATAGTCACATATT
1 CAATGTACATGTATAGTTACATATT
*
469919 CAATGTACATGTA-ATTATACATATT
1 CAATGTACATGTATAGT-TACATATT
**
469944 CAATACACATG--TAGTTACATATT
1 CAATGTACATGTATAGTTACATATT
*
469967 CAATGTACACG-A-AGTTACATATT
1 CAATGTACATGTATAGTTACATATT
* *
469990 CAATATAC-T-TATAGGTTACATTTT
1 CAATGTACATGTATA-GTTACATATT
*
470014 CAGTGTACAT
1 CAATGTACAT
470024 ATAGACATAT
Statistics
Matches: 103, Mismatches: 18, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
22 1 0.01
23 45 0.44
24 19 0.18
25 38 0.37
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (25 bp):
CAATGTACATGTATAGTTACATATT
Found at i:469964 original size:48 final size:46
Alignment explanation
Indices: 469905--470023 Score: 139
Period size: 48 Copynumber: 2.5 Consensus size: 46
469895 GATGTACATG
* *
469905 TATAGTCACATATTCAATGTACATGTAATTATACATATTCAATACACA
1 TATAGTTACATATTCAATGTACATG-AAGT-TACATATTCAATACACA
* * * *
469953 TGTAGTTACATATTCAATGTACACGAAGTTACATATTCAATATACT
1 TATAGTTACATATTCAATGTACATGAAGTTACATATTCAATACACA
* *
469999 TATAGGTTACATTTTCAGTGTACAT
1 TATA-GTTACATATTCAATGTACAT
470024 ATAGACATAT
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
46 18 0.30
47 20 0.33
48 22 0.37
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (46 bp):
TATAGTTACATATTCAATGTACATGAAGTTACATATTCAATACACA
Found at i:470349 original size:24 final size:24
Alignment explanation
Indices: 470317--470455 Score: 150
Period size: 24 Copynumber: 6.1 Consensus size: 24
470307 TGAAACCACA
*
470317 GTTGGTTACATATTCAATGTACAT
1 GTTGTTTACATATTCAATGTACAT
* *
470341 GTTGTTTACGTATTCAGTGTACAT
1 GTTGTTTACATATTCAATGTACAT
* *
470365 ATAG-TTAC--A-T--AT-TACAT
1 GTTGTTTACATATTCAATGTACAT
470382 GTTGTTTACATA-TCAAGTGTACAT
1 GTTGTTTACATATTCAA-TGTACAT
* *
470406 GTAGGTTACATATTCAATGTACAT
1 GTTGTTTACATATTCAATGTACAT
470430 GTTGTTTACATATTCAATGTACAT
1 GTTGTTTACATATTCAATGTACAT
470454 GT
1 GT
470456 AGGTTATAAT
Statistics
Matches: 95, Mismatches: 12, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
17 7 0.07
18 5 0.05
20 3 0.03
21 1 0.01
22 1 0.01
23 5 0.05
24 69 0.73
25 4 0.04
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.42
Consensus pattern (24 bp):
GTTGTTTACATATTCAATGTACAT
Found at i:470427 original size:65 final size:66
Alignment explanation
Indices: 470317--470443 Score: 168
Period size: 65 Copynumber: 1.9 Consensus size: 66
470307 TGAAACCACA
* * * *
470317 GTTGGTTACATATTCAATGTACATGTTGTTTACGTATTCAGTGTACATATAG-TTACATATTACA
1 GTTGGTTACATATTCAATGTACATGTAGGTTACATATTCAATGTACATATAGTTTACATATTACA
470381 T
66 T
* * *
470382 GTTGTTTACATA-TCAAGTGTACATGTAGGTTACATATTCAATGTACATGTTGTTTACATATT
1 GTTGGTTACATATTCAA-TGTACATGTAGGTTACATATTCAATGTACATATAGTTTACATATT
470444 CAATGTACAT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
64 4 0.08
65 40 0.75
66 9 0.17
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.43
Consensus pattern (66 bp):
GTTGGTTACATATTCAATGTACATGTAGGTTACATATTCAATGTACATATAGTTTACATATTACA
T
Found at i:470436 original size:48 final size:47
Alignment explanation
Indices: 470320--470471 Score: 192
Period size: 48 Copynumber: 3.3 Consensus size: 47
470310 AACCACAGTT
* * *
470320 GGTTACATATTCAATGTACATGTTGTTTACGTATTCAGTGTACATATA
1 GGTTACA-ATTCAATGTACATGTTGTTTACATATTCAATGTACATGTA
470368 -GTTAC-A-T--AT-TACATGTTGTTTACATA-TCAAGTGTACATGTA
1 GGTTACAATTCAATGTACATGTTGTTTACATATTCAA-TGTACATGTA
470409 GGTTACATATTCAATGTACATGTTGTTTACATATTCAATGTACATGTA
1 GGTTACA-ATTCAATGTACATGTTGTTTACATATTCAATGTACATGTA
*
470457 GGTTATAATTCAATG
1 GGTTACAATTCAATG
470472 CATGTACATG
Statistics
Matches: 91, Mismatches: 4, Indels: 19
0.80 0.04 0.17
Matches are distributed among these distances:
40 3 0.03
41 25 0.27
42 7 0.08
44 2 0.02
45 2 0.02
47 15 0.16
48 33 0.36
49 4 0.04
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (47 bp):
GGTTACAATTCAATGTACATGTTGTTTACATATTCAATGTACATGTA
Found at i:471913 original size:3 final size:3
Alignment explanation
Indices: 471907--471941 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
471897 TGACGAAGAA
* *
471907 GAT GAT GAT GAG GAT GAT GAT GGT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
471942 AGAGGAGGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.31, C:0.00, G:0.40, T:0.29
Consensus pattern (3 bp):
GAT
Found at i:485923 original size:2 final size:2
Alignment explanation
Indices: 485916--485967 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
485906 TGCATCAAAT
485916 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
485958 GA GA GA GA GA
1 GA GA GA GA GA
485968 CATGCAAACA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:486327 original size:26 final size:26
Alignment explanation
Indices: 486297--486347 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
486287 TAAATCTAAG
*
486297 AGAAGTATATAGGAAATGGGAAATAA
1 AGAAGTACATAGGAAATGGGAAATAA
*
486323 AGAAGTACATGGGAAATGGGAAATA
1 AGAAGTACATAGGAAATGGGAAATA
486348 TCTGCACCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.51, C:0.02, G:0.29, T:0.18
Consensus pattern (26 bp):
AGAAGTACATAGGAAATGGGAAATAA
Found at i:493661 original size:2 final size:2
Alignment explanation
Indices: 493656--493695 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
493646 CATGTTAATG
493656 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
493696 AACTATAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:497286 original size:14 final size:14
Alignment explanation
Indices: 497267--497310 Score: 61
Period size: 14 Copynumber: 3.0 Consensus size: 14
497257 TGTATTTATT
497267 TATATATACATGTA
1 TATATATACATGTA
497281 TATATATACATGTA
1 TATATATACATGTA
*
497295 TACAATACTACATGTA
1 TA-TATA-TACATGTA
497311 ATAGTACACC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 16 0.59
15 3 0.11
16 8 0.30
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (14 bp):
TATATATACATGTA
Found at i:507439 original size:164 final size:164
Alignment explanation
Indices: 507079--507493 Score: 575
Period size: 164 Copynumber: 2.5 Consensus size: 164
507069 CATAATACAT
* * *
507079 ACTTTGTATCTACACTACCTGAGGATGCTTTCACACAAGTTTCAGCTTTCCTGGCTGATAAGTTT
1 ACTTTGTATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGC-CATTAGTTT
* * * * * *
507144 CTGAGGATAAGATTTTTAAAGATTTACTCTATATATTCATGTGTTTAACTTCGACCCCTCATTGT
65 CTGAGAAGAAGATTTTTGAAGATATACTCTATATATTCA-GTGTTTAAATTCGACCCCCCATTGT
507209 GGCCCCACCCTACACCCGGGGGTCATGATTTTCACA
129 GGCCCCACCCTACACCCGGGGGTCATGATTTTCACA
* * * *
507245 ACTTTGAATCTACATTACCTGAGGATGCTTCCATACAAGTGTCAGCTTTCCTGGCCAATTAGTTT
1 ACTTTGTATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCC-ATTAGTTT
507310 CTGAGAAGAAGATTTTTGAAGATATACTCTATATATTCA-TG-TTAAATTGCGACCCCCCATTGT
65 CTGAGAAGAAGATTTTTGAAGATATACTCTATATATTCAGTGTTTAAATT-CGACCCCCCATTGT
* *
507373 GGCCCCACCCTACCCCCGGGGGTCATTATTTTCACA
129 GGCCCCACCCTACACCCGGGGGTCATGATTTTCACA
* * * * *
507409 ATTTTGTATCTACACTACCAGAGGATGCTTCCACACCAGTTTCAGCTTTCCTGGTC-TTATGGTT
1 ACTTTGTATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCCATTA-GTTT
507473 CATGAGAAGAAGATTTTTGAA
65 C-TGAGAAGAAGATTTTTGAA
507494 AATTTCTCGA
Statistics
Matches: 221, Mismatches: 24, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
162 3 0.01
163 10 0.05
164 116 0.52
166 92 0.42
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (164 bp):
ACTTTGTATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCCATTAGTTTC
TGAGAAGAAGATTTTTGAAGATATACTCTATATATTCAGTGTTTAAATTCGACCCCCCATTGTGG
CCCCACCCTACACCCGGGGGTCATGATTTTCACA
Found at i:508217 original size:2 final size:2
Alignment explanation
Indices: 508210--508270 Score: 104
Period size: 2 Copynumber: 30.5 Consensus size: 2
508200 TATTCTTGTT
*
508210 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC CC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
*
508252 AC AC AC AC CC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC A
508271 ATACTACATG
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:513097 original size:29 final size:29
Alignment explanation
Indices: 513055--513114 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
513045 TCTACCTGTG
513055 ATCCATTACAGTAAAACAAATCATCTTTA
1 ATCCATTACAGTAAAACAAATCATCTTTA
513084 ATCCATTACAGTAAAACAAATCATCTTTA
1 ATCCATTACAGTAAAACAAATCATCTTTA
513113 AT
1 AT
513115 TTGTTTGCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.32
Consensus pattern (29 bp):
ATCCATTACAGTAAAACAAATCATCTTTA
Found at i:514441 original size:146 final size:146
Alignment explanation
Indices: 514210--514895 Score: 1232
Period size: 146 Copynumber: 4.7 Consensus size: 146
514200 CTTTCTCAAT
* *
514210 TGACTTTGGGTCAAGGTCATGACACACCCTTTA-ATCATAAGCAATCTTTGTGTGAAGTAAGAAC
1 TGACCTTGGGTCAAGGTCATGACACACCC-TTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAAC
* * *
514274 TTCCAATGTTTCCCCATAAGAAAGATATGGACCGAACACGAATTTTGCATTTTTTCTGCCAGTGA
65 TTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTTGCACTTTTTCTGCCAGTGA
*
514339 CCTTGACCTTGCCCAAA
130 CCTTGACCTTGCCCGAA
514356 TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACT
1 TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACT
*
514421 TCCAATGTTTCCCCATAAGAAAGATATGGACCGGACACGAATTTTGCACTTTTTCTGCCAGTGAC
66 TCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTTGCACTTTTTCTGCCAGTGAC
*
514486 CTTGACCTTGTCCGAA
131 CTTGACCTTGCCCGAA
*
514502 TGACCTTGGGTCAAGGTCATGATACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACT
1 TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACT
514567 TCCAATGTTTCTCCATAAGAAAGATATGGACCGGACA-GAAATTTTGCACTTTTTCTGCCAGTGA
66 TCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACG-AATTTTGCACTTTTTCTGCCAGTGA
514631 CCTTGACCTTGCCCGAA
130 CCTTGACCTTGCCCGAA
514648 TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACT
1 TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACT
*
514713 TCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGCATTTTGCACTTTTTCTGCCAGTGAC
66 TCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTTGCACTTTTTCTGCCAGTGAC
*
514778 CTTGACCTTGCCCGAT
131 CTTGACCTTGCCCGAA
*
514794 TGACCTTGGGTCAAGGTAATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACT
1 TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACT
514859 TCCAATGTTTCTCCATAAGAAAGATATGGACCGGACA
66 TCCAATGTTTCTCCATAAGAAAGATATGGACCGGACA
514896 TGATTGCACA
Statistics
Matches: 524, Mismatches: 13, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
145 4 0.01
146 519 0.99
147 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.29
Consensus pattern (146 bp):
TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACT
TCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTTGCACTTTTTCTGCCAGTGAC
CTTGACCTTGCCCGAA
Found at i:514915 original size:4 final size:4
Alignment explanation
Indices: 514906--514940 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
514896 TGATTGCACA
* *
514906 GACG GACG GACA GACG GACA GACG GACG GACG GAC
1 GACG GACG GACG GACG GACG GACG GACG GACG GAC
514941 AAGGTGATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.31, C:0.26, G:0.43, T:0.00
Consensus pattern (4 bp):
GACG
Found at i:514920 original size:12 final size:12
Alignment explanation
Indices: 514903--514941 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
514893 ACATGATTGC
514903 ACAGACGGACGG
1 ACAGACGGACGG
*
514915 ACAGACGGACAG
1 ACAGACGGACGG
*
514927 ACGGACGGACGG
1 ACAGACGGACGG
514939 ACA
1 ACA
514942 AGGTGATTCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.36, C:0.26, G:0.38, T:0.00
Consensus pattern (12 bp):
ACAGACGGACGG
Found at i:520383 original size:18 final size:18
Alignment explanation
Indices: 520360--520394 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
520350 CAACAGAGAC
520360 AGAAAGACAGATGGACAA
1 AGAAAGACAGATGGACAA
*
520378 AGAAAGATAGATGGACA
1 AGAAAGACAGATGGACA
520395 GACAAACTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.09, G:0.29, T:0.09
Consensus pattern (18 bp):
AGAAAGACAGATGGACAA
Found at i:525090 original size:11 final size:11
Alignment explanation
Indices: 525074--525099 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
525064 TCTTTATTGA
525074 ATGTAGATCTG
1 ATGTAGATCTG
525085 ATGTAGATCTG
1 ATGTAGATCTG
525096 ATGT
1 ATGT
525100 GGTAAATTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.08, G:0.27, T:0.38
Consensus pattern (11 bp):
ATGTAGATCTG
Found at i:525936 original size:14 final size:14
Alignment explanation
Indices: 525919--525965 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
525909 TTCATTGTTA
*
525919 ACAGTCCATTA-TT
1 ACAGTCCATAAGTT
525932 CACAGTCCATAAGTT
1 -ACAGTCCATAAGTT
525947 ACAGTCCATAAGTT
1 ACAGTCCATAAGTT
525961 ACAGT
1 ACAGT
525966 TCACATCTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 29 0.94
15 2 0.06
ACGTcount: A:0.34, C:0.23, G:0.13, T:0.30
Consensus pattern (14 bp):
ACAGTCCATAAGTT
Found at i:534166 original size:2 final size:2
Alignment explanation
Indices: 534159--534189 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
534149 TATTATCTCC
534159 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
534190 NNNNNNNNNN
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:538478 original size:20 final size:20
Alignment explanation
Indices: 538455--538518 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
538445 CGACGTTAAT
538455 CTATATTTCACATCTGTAAA
1 CTATATTTCACATCTGTAAA
* * * * *
538475 CTATAGTTAAC-GCGGTAAT
1 CTATATTTCACATCTGTAAA
*
538494 CTATGTTTCACATCTGTAAA
1 CTATATTTCACATCTGTAAA
538514 CTATA
1 CTATA
538519 GTTAACAATC
Statistics
Matches: 31, Mismatches: 12, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
19 13 0.42
20 18 0.58
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.38
Consensus pattern (20 bp):
CTATATTTCACATCTGTAAA
Found at i:538504 original size:39 final size:40
Alignment explanation
Indices: 538430--538524 Score: 156
Period size: 39 Copynumber: 2.4 Consensus size: 40
538420 TTTACGGATC
* *
538430 GTAAACTATAGTTACCGACGTTAATCTATATTTCACATCT
1 GTAAACTATAGTTAACGACGGTAATCTATATTTCACATCT
*
538470 GTAAACTATAGTTAACG-CGGTAATCTATGTTTCACATCT
1 GTAAACTATAGTTAACGACGGTAATCTATATTTCACATCT
538509 GTAAACTATAGTTAAC
1 GTAAACTATAGTTAAC
538525 AATCATTTGC
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 36 0.69
40 16 0.31
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.36
Consensus pattern (40 bp):
GTAAACTATAGTTAACGACGGTAATCTATATTTCACATCT
Found at i:539166 original size:39 final size:40
Alignment explanation
Indices: 539123--539212 Score: 130
Period size: 39 Copynumber: 2.3 Consensus size: 40
539113 TGTTTTCAGT
* *
539123 GTTAACTATAGTTTACAGATGTGAAACATATATTATA-G-C
1 GTTAACTATAGTTTACAGACGTGAAACATAGATT-TACGTC
*
539162 GTTAACTATAGTTTACAGACGTGAAATATAGATTTACGTC
1 GTTAACTATAGTTTACAGACGTGAAACATAGATTTACGTC
539202 GTTAACTATAG
1 GTTAACTATAG
539213 CTTTCGATCC
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
38 2 0.04
39 32 0.70
40 12 0.26
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.36
Consensus pattern (40 bp):
GTTAACTATAGTTTACAGACGTGAAACATAGATTTACGTC
Found at i:539211 original size:20 final size:20
Alignment explanation
Indices: 539123--539212 Score: 71
Period size: 20 Copynumber: 4.5 Consensus size: 20
539113 TGTTTTCAGT
*
539123 GTTAACTATAGTTTACAGAT
1 GTTAACTATAGTTTACAGAC
* *
539143 GTGAAAC-ATA-TATTATAG-C
1 GT-TAACTATAGT-TTACAGAC
539162 GTTAACTATAGTTTACAGAC
1 GTTAACTATAGTTTACAGAC
* * *
539182 GTGAAATATAGATTTAC-GTC
1 GTTAACTATAG-TTTACAGAC
539202 GTTAACTATAG
1 GTTAACTATAG
539213 CTTTCGATCC
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
18 3 0.06
19 11 0.20
20 32 0.59
21 8 0.15
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.36
Consensus pattern (20 bp):
GTTAACTATAGTTTACAGAC
Found at i:539461 original size:20 final size:20
Alignment explanation
Indices: 539436--539485 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
539426 TACAGATATA
539436 TAAACTAT-GATTATCATTCG
1 TAAACTATAGATTA-CATTCG
*
539456 TAAACTATAGTTTACATTCG
1 TAAACTATAGATTACATTCG
539476 TGAAA-TATAG
1 T-AAACTATAG
539486 TTTCACAGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 20 0.74
21 7 0.26
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (20 bp):
TAAACTATAGATTACATTCG
Found at i:539486 original size:20 final size:20
Alignment explanation
Indices: 539436--539531 Score: 81
Period size: 21 Copynumber: 4.7 Consensus size: 20
539426 TACAGATATA
*
539436 TAAACTAT-GATTATCATTCG
1 TAAACTATAGTTTA-CATTCG
539456 TAAACTATAGTTTACATTCG
1 TAAACTATAGTTTACATTCG
*
539476 TGAAA-TATAGTTTCACAGAT-G
1 T-AAACTATAGTTT-ACA-TTCG
* *
539497 TAAACTATAGTTAACGAATCG
1 TAAACTATAGTTTAC-ATTCG
*
539518 TTAACTATAGTTTA
1 TAAACTATAGTTTA
539532 GGATCCAAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
20 30 0.47
21 33 0.52
22 1 0.02
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (20 bp):
TAAACTATAGTTTACATTCG
Found at i:541257 original size:19 final size:20
Alignment explanation
Indices: 541204--541255 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
541194 AAAAACTGTT
541204 ATCAACAGTTTTTGTAAATA
1 ATCAACAGTTTTTGTAAATA
*
541224 ATTAACAGTTTTTGTAAATA
1 ATCAACAGTTTTTGTAAATA
541244 ATCAACAGTTTT
1 ATCAACAGTTTT
541256 GTCACCATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (20 bp):
ATCAACAGTTTTTGTAAATA
Found at i:542055 original size:29 final size:29
Alignment explanation
Indices: 542008--542078 Score: 126
Period size: 29 Copynumber: 2.5 Consensus size: 29
541998 GGTAAATTAA
*
542008 AAAGCAAATT-CCTCACAGTCTTGCTCGC
1 AAAGTAAATTGCCTCACAGTCTTGCTCGC
542036 AAAGTAAATTGCCTCACAGTCTTGCTCGC
1 AAAGTAAATTGCCTCACAGTCTTGCTCGC
542065 AAAGTAAATTGCCT
1 AAAGTAAATTGCCT
542079 TAAACGACTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
28 9 0.22
29 32 0.78
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (29 bp):
AAAGTAAATTGCCTCACAGTCTTGCTCGC
Found at i:544763 original size:200 final size:200
Alignment explanation
Indices: 544420--544822 Score: 806
Period size: 200 Copynumber: 2.0 Consensus size: 200
544410 TAGCTTGCGA
544420 CAATTTTAAGATCATCTCAGATTCAATTCGGTTATTATACTATACATGTTTTATATAACTATATA
1 CAATTTTAAGATCATCTCAGATTCAATTCGGTTATTATACTATACATGTTTTATATAACTATATA
544485 GAGCATTCTCTGTGTTTTTATCTCCAGATACATCGTGTACAACTTCAGAGGCGTGTGTGAAGACG
66 GAGCATTCTCTGTGTTTTTATCTCCAGATACATCGTGTACAACTTCAGAGGCGTGTGTGAAGACG
544550 GAGACAAAAGTTGGTATGATAAAGAAGTTGACATGATGGTTATAAATCTGGCTAAATCTGATGAT
131 GAGACAAAAGTTGGTATGATAAAGAAGTTGACATGATGGTTATAAATCTGGCTAAATCTGATGAT
544615 AAACC
196 AAACC
544620 CAATTTTAAGATCATCTCAGATTCAATTCGGTTATTATACTATACATGTTTTATATAACTATATA
1 CAATTTTAAGATCATCTCAGATTCAATTCGGTTATTATACTATACATGTTTTATATAACTATATA
544685 GAGCATTCTCTGTGTTTTTATCTCCAGATACATCGTGTACAACTTCAGAGGCGTGTGTGAAGACG
66 GAGCATTCTCTGTGTTTTTATCTCCAGATACATCGTGTACAACTTCAGAGGCGTGTGTGAAGACG
544750 GAGACAAAAGTTGGTATGATAAAGAAGTTGACATGATGGTTATAAATCTGGCTAAATCTGATGAT
131 GAGACAAAAGTTGGTATGATAAAGAAGTTGACATGATGGTTATAAATCTGGCTAAATCTGATGAT
544815 AAACC
196 AAACC
544820 CAA
1 CAA
544823 AATATTCAGC
Statistics
Matches: 203, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
200 203 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (200 bp):
CAATTTTAAGATCATCTCAGATTCAATTCGGTTATTATACTATACATGTTTTATATAACTATATA
GAGCATTCTCTGTGTTTTTATCTCCAGATACATCGTGTACAACTTCAGAGGCGTGTGTGAAGACG
GAGACAAAAGTTGGTATGATAAAGAAGTTGACATGATGGTTATAAATCTGGCTAAATCTGATGAT
AAACC
Found at i:546224 original size:14 final size:15
Alignment explanation
Indices: 546203--546237 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
546193 CATGTGCAGA
*
546203 TAAAAAAAATTACTT
1 TAAAAAAATTTACTT
546218 TAAAAAAATTTACTT
1 TAAAAAAATTTACTT
546233 TAAAA
1 TAAAA
546238 CTTGCAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (15 bp):
TAAAAAAATTTACTT
Found at i:551589 original size:28 final size:28
Alignment explanation
Indices: 551570--551912 Score: 315
Period size: 28 Copynumber: 12.2 Consensus size: 28
551560 ACTTGAAATA
* *
551570 TTCCTGGGTCTCTGACCTACCTGAGATT
1 TTCCTGGTTCTGTGACCTACCTGAGATT
551598 TTCCTGGTTCTGTGACCTACCTGAGATT
1 TTCCTGGTTCTGTGACCTACCTGAGATT
551626 TTCCTGGTTCTGTGA-CTAACCTGAGATT
1 TTCCTGGTTCTGTGACCT-ACCTGAGATT
** * * *
551654 TTTTTGGATCTTTGACCTACCTGGGATT
1 TTCCTGGTTCTGTGACCTACCTGAGATT
* * * *
551682 TTCTTGGGTT-TGTGGCTTACC-CAGATT
1 TTCCT-GGTTCTGTGACCTACCTGAGATT
* *
551709 TTCCTGGCTCTGTGACCTACCTGAGGTT
1 TTCCTGGTTCTGTGACCTACCTGAGATT
* *
551737 TTCCTGTTTCTGTGACCTACCTGAAATT
1 TTCCTGGTTCTGTGACCTACCTGAGATT
* * *
551765 TTCCTAGGTT-TGTGACCAGTACTTGAAATA
1 TTCCT-GGTTCTGTGACC--TACCTGAGATT
* * *
551795 TTCCTGAG-TCTATGACTTACCTAAGATT
1 TTCCTG-GTTCTGTGACCTACCTGAGATT
* * *
551823 CT-CTGGTTCTGTGATCTACC-AAGGATT
1 TTCCTGGTTCTGTGACCTACCTGA-GATT
*
551850 TTCCTGGTTCTGT-AGCCAACCTGAGATT
1 TTCCTGGTTCTGTGA-CCTACCTGAGATT
* *
551878 TCCCTGGTTCCGTGACCTACCTGAGATT
1 TTCCTGGTTCTGTGACCTACCTGAGATT
551906 TTCCTGG
1 TTCCTGG
551913 GTTTGTTGGA
Statistics
Matches: 254, Mismatches: 45, Indels: 32
0.77 0.14 0.10
Matches are distributed among these distances:
26 6 0.02
27 38 0.15
28 178 0.70
29 12 0.05
30 20 0.08
ACGTcount: A:0.17, C:0.24, G:0.21, T:0.39
Consensus pattern (28 bp):
TTCCTGGTTCTGTGACCTACCTGAGATT
Found at i:551630 original size:56 final size:56
Alignment explanation
Indices: 551518--551914 Score: 322
Period size: 56 Copynumber: 7.1 Consensus size: 56
551508 TGGATCTACT
* * * * ** * * *
551518 TGGGTTTGTGACCTTCCTAAGATTTTCCTGAGAT-TGTGTTCTACTTGAAATATTCC
1 TGGGTCTGTGACCTACCTGAGATTTTCCTG-GTTCTGTGACCTACCTGAGATTTTCC
*
551574 TGGGTCTCTGACCTACCTGAGATTTTCCTGGTTCTGTGACCTACCTGAGATTTTCC
1 TGGGTCTGTGACCTACCTGAGATTTTCCTGGTTCTGTGACCTACCTGAGATTTTCC
* ** * * * *
551630 TGGTTCTGTGA-CTAACCTGAGATTTTTTTGGATCTTTGACCTACCTGGGATTTTCT
1 TGGGTCTGTGACCT-ACCTGAGATTTTCCTGGTTCTGTGACCTACCTGAGATTTTCC
* * * * * *
551686 TGGGTTTGTGGCTTACC-CAGATTTTCCTGGCTCTGTGACCTACCTGAGGTTTTCC
1 TGGGTCTGTGACCTACCTGAGATTTTCCTGGTTCTGTGACCTACCTGAGATTTTCC
** * * * *
551741 TGTTTCTGTGACCTACCTGAAATTTTCCTAGGTT-TGTGACCAGTACTTGAAATATTCC
1 TGGGTCTGTGACCTACCTGAGATTTTCCT-GGTTCTGTGACC--TACCTGAGATTTTCC
* * * * * * *
551799 TGAGTCTATGACTTACCTAAGATTCT-CTGGTTCTGTGATCTACC-AAGGATTTTCC
1 TGGGTCTGTGACCTACCTGAGATTTTCCTGGTTCTGTGACCTACCTGA-GATTTTCC
* * * *
551854 TGGTTCTGT-AGCCAACCTGAGATTTCCCTGGTTCCGTGACCTACCTGAGATTTTCC
1 TGGGTCTGTGA-CCTACCTGAGATTTTCCTGGTTCTGTGACCTACCTGAGATTTTCC
551910 TGGGT
1 TGGGT
551915 TTGTTGGATG
Statistics
Matches: 263, Mismatches: 66, Indels: 24
0.75 0.19 0.07
Matches are distributed among these distances:
54 2 0.01
55 71 0.27
56 147 0.56
57 13 0.05
58 30 0.11
ACGTcount: A:0.17, C:0.22, G:0.21, T:0.39
Consensus pattern (56 bp):
TGGGTCTGTGACCTACCTGAGATTTTCCTGGTTCTGTGACCTACCTGAGATTTTCC
Found at i:551753 original size:83 final size:83
Alignment explanation
Indices: 551520--551912 Score: 264
Period size: 83 Copynumber: 4.7 Consensus size: 83
551510 GATCTACTTG
* * * * * * * * *
551520 GGTTTGTGACCTTCCTAAGATTTTCCTGAGAT-TGTGTTCT-ACTTGAAATATTCCTGGGTCTCT
1 GGTTTGTGACCTACCTCAGATTTTCCTG-GCTCTGTG-ACTAACCTGAGATTTTCCTGGATCTGT
551583 GACCTACCTGAGATTTTCCT
64 GACCTACCTGAGATTTTCCT
* * ** *
551603 GGTTCTGTGACCTACCTGAGATTTTCCTGGTTCTGTGACTAACCTGAGATTTTTTTGGATCTTTG
1 GGTT-TGTGACCTACCTCAGATTTTCCTGGCTCTGTGACTAACCTGAGATTTTCCTGGATCTGTG
* *
551668 ACCTACCTGGGATTTTCTT
65 ACCTACCTGAGATTTTCCT
* * * **
551687 GGGTTTGTGGCTTACC-CAGATTTTCCTGGCTCTGTGACCT-ACCTGAGGTTTTCCTGTTTCTGT
1 -GGTTTGTGACCTACCTCAGATTTTCCTGGCTCTGTGA-CTAACCTGAGATTTTCCTGGATCTGT
*
551750 GACCTACCTGAAATTTTCCT
64 GACCTACCTGAGATTTTCCT
* * * * * * * * *
551770 AGGTTTGTGACCAGTACTTGAAATATTCCTGAG-TCTATGACTTACCTAAGATTCT-CTGGTTCT
1 -GGTTTGTGACC--TACCTCAGATTTTCCTG-GCTCTGTGACTAACCTGAGATTTTCCTGGATCT
* *
551833 GTGATCTACC-AAGGATTTTCCT
62 GTGACCTACCTGA-GATTTTCCT
* * * * *
551855 GGTTCTGT-AGCCAACCTGAGATTTCCCTGGTTCCGTGACCT-ACCTGAGATTTTCCTGG
1 GGTT-TGTGA-CCTACCTCAGATTTTCCTGGCTCTGTGA-CTAACCTGAGATTTTCCTGG
551913 GTTTGTTGGA
Statistics
Matches: 244, Mismatches: 50, Indels: 31
0.75 0.15 0.10
Matches are distributed among these distances:
82 1 0.00
83 97 0.40
84 83 0.34
85 38 0.16
86 24 0.10
87 1 0.00
ACGTcount: A:0.17, C:0.23, G:0.21, T:0.39
Consensus pattern (83 bp):
GGTTTGTGACCTACCTCAGATTTTCCTGGCTCTGTGACTAACCTGAGATTTTCCTGGATCTGTGA
CCTACCTGAGATTTTCCT
Found at i:555300 original size:60 final size:56
Alignment explanation
Indices: 555200--555371 Score: 231
Period size: 56 Copynumber: 3.0 Consensus size: 56
555190 TGCTTAATTT
*
555200 TCACTACTTGCTATTAAG-ACTCAAA-TTCCATGGTTTTAATTTCTGGTAATAGTAAA
1 TCACTACTTGCTATTAAGAAC-CAAAGTT-GATGGTTTTAATTTCTGGTAATAGTAAA
* *
555256 TCACTACTTGCTTTTTAAAAAGAACCAAAGTTGATGGTTTTAATTTCTGGCAATAGTAAA
1 TCACTACTTGC-TATT---AAGAACCAAAGTTGATGGTTTTAATTTCTGGTAATAGTAAA
* *
555316 TCACTACTTGCTATTAAGAACCAAATTTGATGGTTTTAATTTCTGGTAATCGTAAA
1 TCACTACTTGCTATTAAGAACCAAAGTTGATGGTTTTAATTTCTGGTAATAGTAAA
555372 AATCCACTTT
Statistics
Matches: 103, Mismatches: 7, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
56 49 0.48
57 3 0.03
59 3 0.03
60 44 0.43
61 4 0.04
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (56 bp):
TCACTACTTGCTATTAAGAACCAAAGTTGATGGTTTTAATTTCTGGTAATAGTAAA
Found at i:555924 original size:21 final size:22
Alignment explanation
Indices: 555900--555955 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
555890 AAGCCTCTTT
*
555900 TGCAAAATCAACA-GA-CATCGA
1 TGCAAAA-CAACATGATCACCGA
555921 TGCAAAACAA-ATGATCACCGA
1 TGCAAAACAACATGATCACCGA
555942 TGCAAAACCAACAT
1 TGCAAAA-CAACAT
555956 TCATGCACTG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
19 1 0.03
20 5 0.17
21 19 0.63
22 3 0.10
23 2 0.07
ACGTcount: A:0.48, C:0.25, G:0.12, T:0.14
Consensus pattern (22 bp):
TGCAAAACAACATGATCACCGA
Found at i:556946 original size:21 final size:21
Alignment explanation
Indices: 556890--556949 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
556880 AATTCAGTGC
556890 ATGA-CTGTTGGTTTTGCATCG
1 ATGATCTGTT-GTTTTGCATCG
556911 ATGATCAT-TTGTTTTGCATCG
1 ATGATC-TGTTGTTTTGCATCG
*
556932 GTG-TCTGTTGATTTTGCA
1 ATGATCTGTTG-TTTTGCA
556950 AAAGAGGCTG
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
19 1 0.03
20 5 0.15
21 24 0.71
22 3 0.09
23 1 0.03
ACGTcount: A:0.15, C:0.13, G:0.25, T:0.47
Consensus pattern (21 bp):
ATGATCTGTTGTTTTGCATCG
Found at i:558411 original size:1 final size:1
Alignment explanation
Indices: 558405--558429 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
558395 AGTACGCCAG
558405 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
558430 TTTAGGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:559830 original size:44 final size:46
Alignment explanation
Indices: 559737--559836 Score: 125
Period size: 44 Copynumber: 2.2 Consensus size: 46
559727 GTTTTTTATA
*
559737 TTTCATGTTACATGCATATGTGTATTACCATTGTTTGCTTTTTTCAG
1 TTTCATGTTACATGCA-ATGTGTATTACCATTGTTTGCTTTTTCCAG
* *
559784 TTTCATGTTACATGC-CT-TGTATTATCATTGTTT-CTTTTTCCTAG
1 TTTCATGTTACATGCAATGTGTATTACCATTGTTTGCTTTTTCC-AG
*
559828 TTTTATGTT
1 TTTCATGTT
559837 TTATGTATTA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
43 7 0.15
44 25 0.52
45 1 0.02
47 15 0.31
ACGTcount: A:0.17, C:0.15, G:0.13, T:0.55
Consensus pattern (46 bp):
TTTCATGTTACATGCAATGTGTATTACCATTGTTTGCTTTTTCCAG
Found at i:571256 original size:62 final size:62
Alignment explanation
Indices: 571203--571433 Score: 374
Period size: 62 Copynumber: 3.7 Consensus size: 62
571193 CAAACTTACT
*
571203 AGCCCTCTATGACAGTGATATCCAGATTGACAGAATCACTCTTCATCTGGATCACACCTGCC
1 AGCCCTCTATGACAGTGATATCCAGATTGACAGAATCACTCTTCATCTGGATCACACCTACC
* * *
571265 AGCCCTGTATGACAGAGATATCCAGATTGACAGAATCACTCTTCATCTGGATCACACCTGCC
1 AGCCCTCTATGACAGTGATATCCAGATTGACAGAATCACTCTTCATCTGGATCACACCTACC
* * *
571327 AGCCCTGTATGACAGCGATATCCAGATTGACAGAATCAAC-CTTCATCTGGATCACACTTACC
1 AGCCCTCTATGACAGTGATATCCAGATTGACAGAATC-ACTCTTCATCTGGATCACACCTACC
*
571389 AGCCCTCTATGACAGTGATATCCAGATTAACAGAATCACTCTTCA
1 AGCCCTCTATGACAGTGATATCCAGATTGACAGAATCACTCTTCA
571434 CATGCACTAA
Statistics
Matches: 159, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
61 2 0.01
62 155 0.97
63 2 0.01
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (62 bp):
AGCCCTCTATGACAGTGATATCCAGATTGACAGAATCACTCTTCATCTGGATCACACCTACC
Found at i:587242 original size:13 final size:13
Alignment explanation
Indices: 587224--587258 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
587214 AGAAACTTTT
587224 TATAATAATACAA
1 TATAATAATACAA
*
587237 TATAATAATATAA
1 TATAATAATACAA
587250 TATAATAAT
1 TATAATAAT
587259 GCATTACAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (13 bp):
TATAATAATACAA
Found at i:589801 original size:25 final size:25
Alignment explanation
Indices: 589773--589824 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
589763 TGGTTAAAAA
589773 AGATGCAATGAAGACTTTTGAATCT
1 AGATGCAATGAAGACTTTTGAATCT
589798 AGATGCAATGAAGACTTTTGAATCT
1 AGATGCAATGAAGACTTTTGAATCT
589823 AG
1 AG
589825 GGTAATAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.31
Consensus pattern (25 bp):
AGATGCAATGAAGACTTTTGAATCT
Found at i:590912 original size:13 final size:13
Alignment explanation
Indices: 590894--590919 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
590884 CTTATGAAAC
590894 GACAATGCCCATT
1 GACAATGCCCATT
590907 GACAATGCCCATT
1 GACAATGCCCATT
590920 TTAGAGAAAA
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:0.31, C:0.31, G:0.15, T:0.23
Consensus pattern (13 bp):
GACAATGCCCATT
Found at i:599918 original size:28 final size:28
Alignment explanation
Indices: 599875--599931 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
599865 AATTCACATG
*
599875 AATATTGTGTTCGAGAAGGATTTCGGAC
1 AATATTGTGTTCGAGAAAGATTTCGGAC
*
599903 AATATTGTGTTTGAGAAAGATTTCGGAC
1 AATATTGTGTTCGAGAAAGATTTCGGAC
599931 A
1 A
599932 GATTGTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.33
Consensus pattern (28 bp):
AATATTGTGTTCGAGAAAGATTTCGGAC
Found at i:610770 original size:107 final size:107
Alignment explanation
Indices: 610585--610894 Score: 428
Period size: 107 Copynumber: 2.9 Consensus size: 107
610575 AGCCTAATCG
* * * * *
610585 GTGAACACTACTCACTGAGCT-AGGATGGCTGAATTATCATAGTTCCCGATGCCTTCCGATTGTG
1 GTGAACACTAATCACTGAGCTAAGGACGACTGAATCACCATAGTTCCCGATGCCTTCCGATTGTG
*
610649 TTAGCACATCGGAAGTCCTCGGGACCAATGTGTGCTTGATCA
66 TTAGCACATCGGAAGTCCTCGGGACCAATGTGTGCTGGATCA
* * *
610691 GTGAACACTAATCACTGGGCTAAGGACGACTG-ATCCACCGTAGTTCCCGATGCGTTCCGATTGC
1 GTGAACACTAATCACTGAGCTAAGGACGACTGAAT-CACCATAGTTCCCGATGCCTTCCGATTG-
* * *
610755 T-TAAGCACATCGGAAGTCCTCGGGACCCATGGGTGCTGGATCA
64 TGTTAGCACATCGGAAGTCCTCGGGACCAATGTGTGCTGGATCA
* * *
610798 GTGAACACTAATCACTGAGCTAAGGACGACTGAATTATCATAGTTCCAGATGCCTTCCGATTGTG
1 GTGAACACTAATCACTGAGCTAAGGACGACTGAATCACCATAGTTCCCGATGCCTTCCGATTGTG
*
610863 TTAGCACATCGGATGTCCTCGGGAACCAATGT
66 TTAGCACATCGGAAGTCCTCGGG-ACCAATGT
610895 AAGTGAACAA
Statistics
Matches: 176, Mismatches: 22, Indels: 10
0.85 0.11 0.05
Matches are distributed among these distances:
106 22 0.12
107 145 0.82
108 9 0.05
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.26
Consensus pattern (107 bp):
GTGAACACTAATCACTGAGCTAAGGACGACTGAATCACCATAGTTCCCGATGCCTTCCGATTGTG
TTAGCACATCGGAAGTCCTCGGGACCAATGTGTGCTGGATCA
Found at i:612051 original size:2 final size:2
Alignment explanation
Indices: 612044--612119 Score: 134
Period size: 2 Copynumber: 38.0 Consensus size: 2
612034 TACTTTATAT
* *
612044 GA GA GA GA GA GA GA GA GA GA GA GT TA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
612086 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
612120 NAATCGGTGA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.03
Consensus pattern (2 bp):
GA
Found at i:613631 original size:2 final size:2
Alignment explanation
Indices: 613624--613665 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
613614 TACTTTATAT
613624 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
613666 CTCAATCATC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:617100 original size:2 final size:2
Alignment explanation
Indices: 617093--617125 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
617083 TTGTGACGTG
617093 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
617126 CAGTTCTGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:632606 original size:1 final size:1
Alignment explanation
Indices: 632600--632624 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
632590 ACCTCAACAA
632600 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
632625 TCCTCCCTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:633253 original size:12 final size:12
Alignment explanation
Indices: 633233--633299 Score: 62
Period size: 12 Copynumber: 5.6 Consensus size: 12
633223 TCCCTTTATA
*
633233 CATCATCGTGGT
1 CATCATCGTCGT
*
633245 CATCGTCGTCGT
1 CATCATCGTCGT
* *
633257 CATCATCATCAT
1 CATCATCGTCGT
* *
633269 CATCATCATCAT
1 CATCATCGTCGT
* *
633281 CATCATCATCAT
1 CATCATCGTCGT
633293 CATCATC
1 CATCATC
633300 ATCATTATTA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 50 1.00
ACGTcount: A:0.25, C:0.33, G:0.09, T:0.33
Consensus pattern (12 bp):
CATCATCGTCGT
Found at i:633262 original size:3 final size:3
Alignment explanation
Indices: 633256--633304 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
633246 ATCGTCGTCG
633256 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
633304 T
1 T
633305 TATTAACCAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:634015 original size:4 final size:4
Alignment explanation
Indices: 634006--634059 Score: 108
Period size: 4 Copynumber: 13.5 Consensus size: 4
633996 ACAGAAAGCC
634006 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
634054 AATA AA
1 AATA AA
634060 CTGATCAATA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 50 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:634176 original size:2 final size:2
Alignment explanation
Indices: 634171--634219 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
634161 AACTGTGAAT
* * * *
634171 GA GA GA GA GA GA GA AA GA TA GA CA GA GA AA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
634213 GA GA GA G
1 GA GA GA G
634220 TTACGTCAGA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.53, C:0.02, G:0.43, T:0.02
Consensus pattern (2 bp):
GA
Found at i:639673 original size:2 final size:2
Alignment explanation
Indices: 639668--639722 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
639658 ACACTGTTGA
639668 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
639710 AG AG AT AG AG AG A
1 AG AG AG AG AG AG A
639723 TAGATTAATA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.47, T:0.02
Consensus pattern (2 bp):
AG
Found at i:642885 original size:35 final size:35
Alignment explanation
Indices: 642839--642909 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
642829 CTTATATATA
*
642839 TATATATTTCAAAGTGATCGGGTGGATAACAGGGC
1 TATATATTTCAAAGTGATCGGGTGAATAACAGGGC
642874 TATATATTTCAAAGTGATCGGGTGAATAACAGGGC
1 TATATATTTCAAAGTGATCGGGTGAATAACAGGGC
642909 T
1 T
642910 GGGAACATAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.32, C:0.11, G:0.27, T:0.30
Consensus pattern (35 bp):
TATATATTTCAAAGTGATCGGGTGAATAACAGGGC
Found at i:643045 original size:35 final size:35
Alignment explanation
Indices: 642999--643067 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
642989 TCTGACGACT
*
642999 ATTTCTGATCATGTACAACATAATGTCTGTGGGCG
1 ATTTCTGATCATGTACAACATAATGTCCGTGGGCG
*
643034 ATTTCTGATCATTTACAACATAATGTCCGTGGGC
1 ATTTCTGATCATGTACAACATAATGTCCGTGGGC
643068 AATATTGCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (35 bp):
ATTTCTGATCATGTACAACATAATGTCCGTGGGCG
Found at i:649452 original size:2 final size:2
Alignment explanation
Indices: 649445--649490 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
649435 GCACTACTCT
649445 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
649487 GA GA
1 GA GA
649491 AATATCATGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:655809 original size:2 final size:2
Alignment explanation
Indices: 655802--655840 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
655792 AAATGCATGT
655802 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
655841 CTGTTCAGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:656750 original size:180 final size:180
Alignment explanation
Indices: 656448--657168 Score: 1327
Period size: 180 Copynumber: 4.0 Consensus size: 180
656438 ACCCTACATG
* * *
656448 TATATGCAACATTTTGCCAAAAAATGACTAAGTTCAAAAGCTAGTATTTTTTTC-ATAAATTATC
1 TATATGCAATATTTTGACAAAAAATGACTAAGTTCAAAAGCTGGTA-TTTTTTCGATAAATTATC
* *
656512 GGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACATTTGATCTGCAAAAGAACAA
65 AGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAA
656577 CTTCCTATCTGGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
130 CTTCCTATCTGGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
656628 TATATGCAATATTTTGACAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCA
1 TATATGCAATATTTTGACAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCA
*
656693 GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAT
66 GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC
* *
656758 TTCCTATCTGGAGAACTGTAGGAGGATTTAACCGTACAATGAGGGTACCC
131 TTCCTATCTGGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
656808 TATATGCAATATTTTGACAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCA
1 TATATGCAATATTTTGACAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCA
*
656873 GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACATTTGATCTGCAAAAGAACAAC
66 GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC
656938 TTCCTATCTGGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
131 TTCCTATCTGGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
656988 TATATGCAATATTTTGACAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCA
1 TATATGCAATATTTTGACAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCA
657053 GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC
66 GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC
* *
657118 TTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
131 TTCCTATCTGGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
657168 T
1 T
657169 TTTGGCAGCC
Statistics
Matches: 525, Mismatches: 15, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
179 7 0.01
180 518 0.99
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (180 bp):
TATATGCAATATTTTGACAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCA
GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC
TTCCTATCTGGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
Found at i:659241 original size:2 final size:2
Alignment explanation
Indices: 659234--659266 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
659224 TTGAAACTAA
659234 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
659267 CAAATTGAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:667740 original size:66 final size:68
Alignment explanation
Indices: 667609--667747 Score: 228
Period size: 66 Copynumber: 2.1 Consensus size: 68
667599 AGACTTTCCT
*
667609 ATTTATCTTACAAGACAGGATTTGATCCTTCTATTTCATATAATATTCCTACATTTCTACATGTA
1 ATTTATCTTACAAGACAGGATTTGATCCTCCTA-TTCATATAATATTCCTACATTTCTACATGTA
667674 AACA
65 AACA
* *
667678 ATTTATCTTACAAGGCAGGATTTTATCCTCCTA-TCA-ATAATATTCCTACATTTCTACATGTAA
1 ATTTATCTTACAAGACAGGATTTGATCCTCCTATTCATATAATATTCCTACATTTCTACATGTAA
667741 ACA
66 ACA
667744 ATTT
1 ATTT
667748 CTTAATGATA
Statistics
Matches: 67, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
66 34 0.51
67 3 0.04
69 30 0.45
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.40
Consensus pattern (68 bp):
ATTTATCTTACAAGACAGGATTTGATCCTCCTATTCATATAATATTCCTACATTTCTACATGTAA
ACA
Found at i:675847 original size:11 final size:11
Alignment explanation
Indices: 675831--675855 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
675821 ACCAATTATT
675831 TTAAAAAAGTC
1 TTAAAAAAGTC
675842 TTAAAAAAGTC
1 TTAAAAAAGTC
675853 TTA
1 TTA
675856 CATGTAACAT
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:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (11 bp):
TTAAAAAAGTC
Found at i:680245 original size:47 final size:47
Alignment explanation
Indices: 680176--680594 Score: 608
Period size: 47 Copynumber: 8.8 Consensus size: 47
680166 TGTAAGATTA
* * *
680176 AAAAAAGTCAGACATTATTACATCTGACCATTTTGAGGTCTGTAGAT
1 AAAAAAGTCATAAATTAATACATCTGACCATTTTGAGGTCTGTAGAT
*
680223 AAAAAAGTCATAAATTAATACATGTGACCATTTTGAGGTCTGTAGAT
1 AAAAAAGTCATAAATTAATACATCTGACCATTTTGAGGTCTGTAGAT
* * *
680270 AAACAAGTCATAAATTAATAAATGTGACCATTTTGAGGTCTGTAGAT
1 AAAAAAGTCATAAATTAATACATCTGACCATTTTGAGGTCTGTAGAT
* * *
680317 AAAAAAAAGTCATACATTATTTCATCTGACCATTTTGAGGTCTGTAGAT
1 --AAAAAAGTCATAAATTAATACATCTGACCATTTTGAGGTCTGTAGAT
680366 AAAAAAGTCATAAATTAATACATCTGACCATTTTGAGGTCTGTAGAT
1 AAAAAAGTCATAAATTAATACATCTGACCATTTTGAGGTCTGTAGAT
680413 AAAAAAGTCATAAATTAATACATCTGACCATTTTGAGGTCTGTAGAT
1 AAAAAAGTCATAAATTAATACATCTGACCATTTTGAGGTCTGTAGAT
* * *
680460 AAACAAGTCATAAATTAATAAATGTGACCATTTTGAGGTCTGTAGAT
1 AAAAAAGTCATAAATTAATACATCTGACCATTTTGAGGTCTGTAGAT
* * *
680507 AAAAAAAAGTCATACATTATTTCATCTGACCATTTTGAGGTCTGTAGAT
1 --AAAAAAGTCATAAATTAATACATCTGACCATTTTGAGGTCTGTAGAT
* *
680556 AAAAAGGTCA-AACATT-ATAACATCTGACCATTTGGAGGT
1 AAAAAAGTCATAA-ATTAAT-ACATCTGACCATTTTGAGGT
680595 GAGAAAACAG
Statistics
Matches: 337, Mismatches: 29, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
46 2 0.01
47 253 0.75
49 82 0.24
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (47 bp):
AAAAAAGTCATAAATTAATACATCTGACCATTTTGAGGTCTGTAGAT
Found at i:680334 original size:143 final size:141
Alignment explanation
Indices: 680164--680594 Score: 625
Period size: 143 Copynumber: 3.0 Consensus size: 141
680154 CCTCCAGACC
*
680164 TCTGTAAGATTAAAAAAAGTCAGACATTATTACATCTGACCATTTTGAGGTCTGTAGATAAAAAA
1 TCTGT-AGA-TAAAAAAAGTCATACATTATTACATCTGACCATTTTGAGGTCTGTAGATAAAAAA
* *
680229 GTCATAAATTAATACATGTGACCATTTTGAGGTCTGTAGATAAACAAGTCATAAATTAATAAATG
64 GTCATAAATTAATACATCTGACCATTTTGAGGTCTGTAGATAAA-AAGTCATAAATTAATAAATC
680294 TGACCATTTTGAGG
128 TGACCATTTTGAGG
*
680308 TCTGTAGATAAAAAAAAGTCATACATTATTTCATCTGACCATTTTGAGGTCTGTAGATAAAAAAG
1 TCTGTAGAT-AAAAAAAGTCATACATTATTACATCTGACCATTTTGAGGTCTGTAGATAAAAAAG
*
680373 TCATAAATTAATACATCTGACCATTTTGAGGTCTGTAGATAAAAAAGTCATAAATTAATACATCT
65 TCATAAATTAATACATCTGACCATTTTGAGGTCTGTAGAT-AAAAAGTCATAAATTAATAAATCT
680438 GACCATTTTGAGG
129 GACCATTTTGAGG
* * * * *
680451 TCTGTAGAT-AAACAAGTCATAAATTAATAAATGTGACCATTTTGAGGTCTGTAGATAAAAAAAA
1 TCTGTAGATAAAAAAAGTCATACATTATTACATCTGACCATTTTGAGGTCTGTAGAT--AAAAAA
* * *
680515 GTCATACATTATTTCATCTGACCATTTTGAGGTCTGTAGATAAAAAGGTCA-AACATT-ATAACA
64 GTCATAAATTAATACATCTGACCATTTTGAGGTCTGTAGATAAAAA-GTCATAA-ATTAATAA-A
*
680578 TCTGACCATTTGGAGG
126 TCTGACCATTTTGAGG
680594 T
1 T
680595 GAGAAAACAG
Statistics
Matches: 264, Mismatches: 16, Indels: 15
0.89 0.05 0.05
Matches are distributed among these distances:
141 41 0.16
142 11 0.04
143 204 0.77
144 8 0.03
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (141 bp):
TCTGTAGATAAAAAAAGTCATACATTATTACATCTGACCATTTTGAGGTCTGTAGATAAAAAAGT
CATAAATTAATACATCTGACCATTTTGAGGTCTGTAGATAAAAAGTCATAAATTAATAAATCTGA
CCATTTTGAGG
Found at i:680499 original size:190 final size:189
Alignment explanation
Indices: 680176--680594 Score: 750
Period size: 190 Copynumber: 2.2 Consensus size: 189
680166 TGTAAGATTA
* *
680176 AAAAAAGTCAGACATTATTACATCTGACCATTTTGAGGTCTGTAGATAAAAAAGTCATAAATTAA
1 AAAAAAGTCA-AAATTAATACATCTGACCATTTTGAGGTCTGTAGATAAAAAAGTCATAAATTAA
*
680241 TACATGTGACCATTTTGAGGTCTGTAGATAAACAAGTCATAAATTAATAAATGTGACCATTTTGA
65 TACATCTGACCATTTTGAGGTCTGTAGATAAACAAGTCATAAATTAATAAATGTGACCATTTTGA
680306 GGTCTGTAGATAAAAAAAAGTCATACATTATTTCATCTGACCATTTTGAGGTCTGTAGAT
130 GGTCTGTAGATAAAAAAAAGTCATACATTATTTCATCTGACCATTTTGAGGTCTGTAGAT
680366 AAAAAAGTCATAAATTAATACATCTGACCATTTTGAGGTCTGTAGATAAAAAAGTCATAAATTAA
1 AAAAAAGTCA-AAATTAATACATCTGACCATTTTGAGGTCTGTAGATAAAAAAGTCATAAATTAA
680431 TACATCTGACCATTTTGAGGTCTGTAGATAAACAAGTCATAAATTAATAAATGTGACCATTTTGA
65 TACATCTGACCATTTTGAGGTCTGTAGATAAACAAGTCATAAATTAATAAATGTGACCATTTTGA
680496 GGTCTGTAGATAAAAAAAAGTCATACATTATTTCATCTGACCATTTTGAGGTCTGTAGAT
130 GGTCTGTAGATAAAAAAAAGTCATACATTATTTCATCTGACCATTTTGAGGTCTGTAGAT
* *
680556 AAAAAGGTCAAACATT-ATAACATCTGACCATTTGGAGGT
1 AAAAAAGTCAAA-ATTAAT-ACATCTGACCATTTTGAGGT
680595 GAGAAAACAG
Statistics
Matches: 221, Mismatches: 6, Indels: 4
0.96 0.03 0.02
Matches are distributed among these distances:
189 4 0.02
190 217 0.98
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (189 bp):
AAAAAAGTCAAAATTAATACATCTGACCATTTTGAGGTCTGTAGATAAAAAAGTCATAAATTAAT
ACATCTGACCATTTTGAGGTCTGTAGATAAACAAGTCATAAATTAATAAATGTGACCATTTTGAG
GTCTGTAGATAAAAAAAAGTCATACATTATTTCATCTGACCATTTTGAGGTCTGTAGAT
Found at i:690292 original size:298 final size:296
Alignment explanation
Indices: 689740--690777 Score: 1735
Period size: 298 Copynumber: 3.6 Consensus size: 296
689730 ATCTAAAATG
689740 AATTGCACAAAATACTATGTTTACCCATTAAAGGTCCTTCCTGACAGTGATGAGCTGATTCCGTT
1 AATTGCACAAAATACTATGTTTACCCATTAAAGGTCCTTCCTGACAGTGATGAGCTGATTCCGTT
689805 GCAGCTAACTGTGGCATGTCCATCTTACAGCCTTGACCCACATGGCCTGCAGTGTCACCTA-AAA
66 GCAGCTAACTGTGGCATGTCCATCTTACAGCCTTGACCCACATGGCCTGCAGTGTCACCTAGAAA
* * *
689869 AAAACCGATTGTCTCATTCAAAAATTTGCTATTTTCACATCCTTCAGAGACATATACATGCATCC
131 AAAA-CAACTGTCTCATTCAAAAATTTGCTATTTTCACATCC-TCCGAGACATATACATGCATCC
689934 ATGCTTAAATAATTCAGCTAATTCAATTAATTTATGGCAGTTTTTTAAATGCAGTCATGTGTCAT
194 ATGCTTAAATAATTCAGCTAATTCAATTAATTTATGGCAGTTTTTTAAATGCAGTCATGTGTCAT
689999 ATATGGATCTGAAATGACAAGAATTAAGGCAATTTATC
259 ATATGGATCTGAAATGACAAGAATTAAGGCAATTTATC
690037 AATTGCACAAAATACTATGTTTACCCATTAAAGGTCCTTCCTGACAGTGATGAGCTGATTCCGTT
1 AATTGCACAAAATACTATGTTTACCCATTAAAGGTCCTTCCTGACAGTGATGAGCTGATTCCGTT
690102 GCAGCTAACTGTGGCATGTCCATCTTACAGCCTTGACCCACATGGCCTGCAGTGTCACCTAGAAA
66 GCAGCTAACTGTGGCATGTCCATCTTACAGCCTTGACCCACATGGCCTGCAGTGTCACCTAGAAA
* *
690167 AAAACCGATTGTCTCATTCAAAAATTTGCTATTTTCACATCCTGCCGAGACATATACATGCATCC
131 AAAA-CAACTGTCTCATTCAAAAATTTGCTATTTTCACATCCT-CCGAGACATATACATGCATCC
690232 ATGCTTAAATAATTCAGCTAATTCAATTAATTTATGGCAGTTTTTTAAATGCAGTCATGTGTCAT
194 ATGCTTAAATAATTCAGCTAATTCAATTAATTTATGGCAGTTTTTTAAATGCAGTCATGTGTCAT
690297 ATATGGATCTGAAATGACAAGAATTAAGGCAATTTATC
259 ATATGGATCTGAAATGACAAGAATTAAGGCAATTTATC
690335 AATTGCACAAAATACTATGTTTACCCATTAAAGGTCCTTCCTGACAGTGATGAGCTGATTCCGTT
1 AATTGCACAAAATACTATGTTTACCCATTAAAGGTCCTTCCTGACAGTGATGAGCTGATTCCGTT
690400 GCAGCTAACTGTGGCATGTCCATCTTACAGCCTTGACCCACATGGCCTGCAGTGTCACCTAGAAA
66 GCAGCTAACTGTGGCATGTCCATCTTACAGCCTTGACCCACATGGCCTGCAGTGTCACCTAGAAA
*
690465 AAAACAACTGTCTCATTCAAATATTTGCTATTTTCACATCCTCCAGAGACATATACATGCATCCA
131 AAAACAACTGTCTCATTCAAAAATTTGCTATTTTCACATCCTCC-GAGACATATACATGCATCCA
690530 TGCTTAAATAATTCAGCTAATTCAATTAATTTATGGCAGTTTTTTAAATGCAGTCATGTGTCATA
195 TGCTTAAATAATTCAGCTAATTCAATTAATTTATGGCAGTTTTTTAAATGCAGTCATGTGTCATA
690595 TATGGATC-----T---AA-AA-T---G--A---AT-
260 TATGGATCTGAAATGACAAGAATTAAGGCAATTTATC
* *
690613 --TT-CACAAAATACTATGTTTACCCATTAAAGGTCCTTCCTGACAGTGATCAGCTGATTCTGTT
1 AATTGCACAAAATACTATGTTTACCCATTAAAGGTCCTTCCTGACAGTGATGAGCTGATTCCGTT
* ** * *
690675 GCAGCTAACTGTGGCGTGTCTGTCTTACAGCCTAGACCAACATGGCCTGCAGTGTCACCTAGAAA
66 GCAGCTAACTGTGGCATGTCCATCTTACAGCCTTGACCCACATGGCCTGCAGTGTCACCTAGAAA
* *
690740 AAAACAACTGTCTTATTCAAATATTTGCTATTTTCACA
131 AAAACAACTGTCTCATTCAAAAATTTGCTATTTTCACA
690778 CACTCCACAT
Statistics
Matches: 726, Mismatches: 12, Indels: 28
0.95 0.02 0.04
Matches are distributed among these distances:
275 155 0.21
276 2 0.00
279 2 0.00
282 1 0.00
284 1 0.00
287 1 0.00
288 2 0.00
289 2 0.00
292 1 0.00
296 2 0.00
297 255 0.35
298 302 0.42
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.32
Consensus pattern (296 bp):
AATTGCACAAAATACTATGTTTACCCATTAAAGGTCCTTCCTGACAGTGATGAGCTGATTCCGTT
GCAGCTAACTGTGGCATGTCCATCTTACAGCCTTGACCCACATGGCCTGCAGTGTCACCTAGAAA
AAAACAACTGTCTCATTCAAAAATTTGCTATTTTCACATCCTCCGAGACATATACATGCATCCAT
GCTTAAATAATTCAGCTAATTCAATTAATTTATGGCAGTTTTTTAAATGCAGTCATGTGTCATAT
ATGGATCTGAAATGACAAGAATTAAGGCAATTTATC
Found at i:705826 original size:11 final size:11
Alignment explanation
Indices: 705810--705839 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
705800 GTCCAAACTT
*
705810 CTTTAAGTCAC
1 CTTTAAGCCAC
705821 CTTTAAGCCAC
1 CTTTAAGCCAC
705832 CTTTAAGC
1 CTTTAAGC
705840 ATCTCTAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.27, C:0.30, G:0.10, T:0.33
Consensus pattern (11 bp):
CTTTAAGCCAC
Found at i:706217 original size:2 final size:2
Alignment explanation
Indices: 706210--706254 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
706200 TAATCGGTGA
706210 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
706252 TC T
1 TC T
706255 GTTCATCCGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:706666 original size:111 final size:112
Alignment explanation
Indices: 706471--706697 Score: 402
Period size: 111 Copynumber: 2.0 Consensus size: 112
706461 TAGTTTTGTT
* *
706471 CGTTTTTGTATATCTAATTAGAGTCTATTGTTTTTCCAACTTAAGAAAACCCCTGGAACTAACAC
1 CGTTTGTGTATATCTAATTAAAGTCTATTGTTTTTCCAACTTAAGAAAACCCCTGGAACTAACAC
* * *
706536 ATAATATACAAGATATACACAACAGTTGTGTCGTGTGCCCAGGTGCA
66 AGAATATACAAGATATACACAACAGGTGTGACGTGTGCCCAGGTGCA
706583 CGTTTGTGTATATCTAATTAAAGTCTATTGTTTTTCCAA-TTAAGAAAACCCCTGGAACTAACAC
1 CGTTTGTGTATATCTAATTAAAGTCTATTGTTTTTCCAACTTAAGAAAACCCCTGGAACTAACAC
706647 AGAATATACAAGATATACACAACAGGTGTGACGTGTGCCCAGGTGCA
66 AGAATATACAAGATATACACAACAGGTGTGACGTGTGCCCAGGTGCA
706694 CGTT
1 CGTT
706698 AGGGTTTCTA
Statistics
Matches: 110, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
111 73 0.66
112 37 0.34
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (112 bp):
CGTTTGTGTATATCTAATTAAAGTCTATTGTTTTTCCAACTTAAGAAAACCCCTGGAACTAACAC
AGAATATACAAGATATACACAACAGGTGTGACGTGTGCCCAGGTGCA
Found at i:730444 original size:5 final size:5
Alignment explanation
Indices: 730434--730500 Score: 50
Period size: 5 Copynumber: 13.4 Consensus size: 5
730424 ATACGATTGA
* * * *
730434 ATATG ATATG ATATG ATTTG ATATG ATTTT A-ATA ATAT- ATAAT- ATATTG
1 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG AT-ATG ATA-TG
730483 AATATG ATATG ATATG AT
1 -ATATG ATATG ATATG AT
730501 TTGAGATGAC
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
4 5 0.10
5 41 0.80
6 2 0.04
7 3 0.06
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (5 bp):
ATATG
Found at i:733508 original size:198 final size:199
Alignment explanation
Indices: 733150--733536 Score: 686
Period size: 198 Copynumber: 1.9 Consensus size: 199
733140 GTCGTGTCCA
733150 GCATACCAAGAGTTAATTTGCCAAAACATATGCAGCCCTCATAAGTTGTGTATGTCGGTTCTTTG
1 GCATACCAAGAGTTAATTTGCCAAAACATATGCAGCCCTCATAAGTTGTGTATGTCGGTTCTTTG
* * *
733215 TTATTTGGTGTGTAAATGGGAAAAAGTGATATTTGTTTGATCTGGTTTTACTACAGTGTAATTTT
66 TTATTTGATGTGTAAATGGGAAAAAGTGATATTTGTTCGATCTGATTTTACTACAGTGTAATTTT
*
733280 GATTCACCTGCGCTTCCCCAACTTTAACCAATTGTCCCATGCAAACATGAATATCAAAGAAATAT
131 GATTCACCTGCGCTTCCCCAACTTTAACCAATTGTCCCATGCAAACATAAATATCAAAGAAATAT
733345 CAAG
196 CAAG
* * * *
733349 GCATATCAAGAGTTAATTTGCCCAAACATATGCAGCCTTCATCAGTTGTGTATGTCGGTTCTTTG
1 GCATACCAAGAGTTAATTTGCCAAAACATATGCAGCCCTCATAAGTTGTGTATGTCGGTTCTTTG
733414 TTATTTGATGTGTAAAT-GGAAAAAGTGATATTTGTTCGATCTGATTTTACTACAGTGTAATTTT
66 TTATTTGATGTGTAAATGGGAAAAAGTGATATTTGTTCGATCTGATTTTACTACAGTGTAATTTT
*
733478 GATTCACCTGCGCTTCCCCAACTTTAACCAATTGTCCCATGCGAACATAAATATCAAAG
131 GATTCACCTGCGCTTCCCCAACTTTAACCAATTGTCCCATGCAAACATAAATATCAAAG
733537 TTGTCGTTAC
Statistics
Matches: 179, Mismatches: 9, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
198 102 0.57
199 77 0.43
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (199 bp):
GCATACCAAGAGTTAATTTGCCAAAACATATGCAGCCCTCATAAGTTGTGTATGTCGGTTCTTTG
TTATTTGATGTGTAAATGGGAAAAAGTGATATTTGTTCGATCTGATTTTACTACAGTGTAATTTT
GATTCACCTGCGCTTCCCCAACTTTAACCAATTGTCCCATGCAAACATAAATATCAAAGAAATAT
CAAG
Found at i:735780 original size:8 final size:8
Alignment explanation
Indices: 735764--735799 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
735754 ACAGATTGAT
735764 GGACAGAC
1 GGACAGAC
*
735772 GGACTGAC
1 GGACAGAC
735780 GGACAGAC
1 GGACAGAC
*
735788 GTACAGAC
1 GGACAGAC
735796 GGAC
1 GGAC
735800 TCCTGACAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.33, C:0.25, G:0.36, T:0.06
Consensus pattern (8 bp):
GGACAGAC
Found at i:739172 original size:273 final size:267
Alignment explanation
Indices: 738680--739228 Score: 956
Period size: 273 Copynumber: 2.0 Consensus size: 267
738670 GGGGTTAACT
* *
738680 AAACACTTATGATTCAATTGTCTGATCATATAGTCTAGTAAAAGCAATATTCAAACAACCAATGT
1 AAACTCTTATGATTCAATTGTCTGATCATATAGTCTAGTAAAAGCAATATTCAAAAAACCAATGT
738745 ATTAATTTATTAGATAATGTCATTATATCCATCTAATGAATTACACGTGCTAAATTATATGTACC
66 ATTAATTTATTAGATAATGTCATTATATCCATCTAATGAATTACACGTGCTAAATTATATGTACC
738810 ATCAATAACATATTCTTCTTGAAATGACTTAATAGAGCTTATAACAATAAGATCTAACAAATTCT
131 ATCAATAACATATTCTTCTTGAAATGACTTAATAGAGCTTATAACAATAAGATCTAACAAATTCT
*
738875 GAGAAAATAAATACCAAGAATTACCAATTCTATTGAATATTAAT-AAAAGTATTTCTGTTTATGT
196 GAGAAAATAAATACCAAAAATTACCAATTCTATTGAATATTAATGAAAA-TATTTCTGTTTATGT
738939 AAACCCAC
260 AAACCCAC
738947 AAACTCTTATGATTCAATTGTCTGATCATATAGTCTAGTAAAAGCAATACTAGTATTCAAAAAAC
1 AAACTCTTATGATTCAATTGTCTGATCATATAGTCTAGTAAAAGC---A--A-TATTCAAAAAAC
*
739012 CAATGTATTAATTTATTAGATAATGTCATTATATCCATCTAATGAATTACATGTGCTAAATTATA
60 CAATGTATTAATTTATTAGATAATGTCATTATATCCATCTAATGAATTACACGTGCTAAATTATA
* * *
739077 TGTACTATCGATAACATATTCTTCTTGAAATGACTTAATAGAGCTTATAACAATAAGATTTAACA
125 TGTACCATCAATAACATATTCTTCTTGAAATGACTTAATAGAGCTTATAACAATAAGATCTAACA
739142 AATTCTGAGAAAATAAATACCAAAAATTACCAATTCTATTGAATATTAATGAAAATATTTCTGTT
190 AATTCTGAGAAAATAAATACCAAAAATTACCAATTCTATTGAATATTAATGAAAATATTTCTGTT
*
739207 TATGTAAACCCAT
255 TATGTAAACCCAC
739220 AAACTCTTA
1 AAACTCTTA
739229 CTTTTCACTG
Statistics
Matches: 267, Mismatches: 8, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
267 44 0.16
270 1 0.00
272 1 0.00
273 217 0.81
274 4 0.01
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (267 bp):
AAACTCTTATGATTCAATTGTCTGATCATATAGTCTAGTAAAAGCAATATTCAAAAAACCAATGT
ATTAATTTATTAGATAATGTCATTATATCCATCTAATGAATTACACGTGCTAAATTATATGTACC
ATCAATAACATATTCTTCTTGAAATGACTTAATAGAGCTTATAACAATAAGATCTAACAAATTCT
GAGAAAATAAATACCAAAAATTACCAATTCTATTGAATATTAATGAAAATATTTCTGTTTATGTA
AACCCAC
Found at i:768037 original size:16 final size:17
Alignment explanation
Indices: 768016--768052 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
768006 AGGAAGATCC
768016 TTTATGTTTGGT-TTAT
1 TTTATGTTTGGTGTTAT
*
768032 TTTATGTTTTGTGTTAT
1 TTTATGTTTGGTGTTAT
768049 TTTA
1 TTTA
768053 ATATATTACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.14, C:0.00, G:0.16, T:0.70
Consensus pattern (17 bp):
TTTATGTTTGGTGTTAT
Found at i:769300 original size:20 final size:20
Alignment explanation
Indices: 769261--769300 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
769251 TGAATCAAAT
*
769261 TCCTACAGGAAATACCATTC
1 TCCTACAGGAAATACAATTC
*
769281 TCCTACAGGAAATATAATTC
1 TCCTACAGGAAATACAATTC
769301 CTATAGGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.25, G:0.10, T:0.28
Consensus pattern (20 bp):
TCCTACAGGAAATACAATTC
Found at i:769308 original size:18 final size:19
Alignment explanation
Indices: 769258--769308 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 19
769248 GTCTGAATCA
769258 AATTCCTACAGGAAATACC
1 AATTCCTACAGGAAATACC
* *
769277 ATTCTCCTACAGGAAATA-T
1 AAT-TCCTACAGGAAATACC
*
769296 AATTCCTATAGGA
1 AATTCCTACAGGA
769309 TTGTCAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 9 0.33
19 4 0.15
20 14 0.52
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (19 bp):
AATTCCTACAGGAAATACC
Found at i:769356 original size:21 final size:21
Alignment explanation
Indices: 769277--769374 Score: 55
Period size: 20 Copynumber: 4.9 Consensus size: 21
769267 AGGAAATACC
* *
769277 ATTCTCCTACAGGAAATAT-A
1 ATTCTCCTATAGGAATTATCA
*
769297 A-T-TCCTATAGG-ATTGTCA
1 ATTCTCCTATAGGAATTATCA
* * **
769315 ATATTTCCTGTA-GAAGGATCA
1 AT-TCTCCTATAGGAATTATCA
769336 ATTCTCCTATAGGAATTATC-
1 ATTCTCCTATAGGAATTATCA
* *
769356 ATTTTCCTATGGGATATTA
1 ATTCTCCTATAGGA-ATTA
769375 ATTTTCAAAG
Statistics
Matches: 58, Mismatches: 13, Indels: 13
0.69 0.15 0.15
Matches are distributed among these distances:
17 3 0.05
18 10 0.17
19 1 0.02
20 22 0.38
21 22 0.38
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (21 bp):
ATTCTCCTATAGGAATTATCA
Found at i:769898 original size:169 final size:170
Alignment explanation
Indices: 769592--769900 Score: 496
Period size: 169 Copynumber: 1.8 Consensus size: 170
769582 AATTAGGAGT
*
769592 AAATTTACAGGCCTAAAATTTGAATTCTAAATTTTGAATTGCGAACTGCGTTCAAGAACACAGTT
1 AAATTTACAGGCCTAAAATATGAATTCTAAATTTTGAATTGCGAACTGCGTTCAAGAACACAGTT
* * * * **
769657 CGCTTTTCCATTGCAAATAAGCCAGAATCTCAAAAAGTTGAAATGATTACTTCACCATATTTTCA
66 CACTATTCAATTGCAAATAAGCCAGAATCTCAAAAAGTAGAAATGACCACTTCACCATATTTTCA
769722 AGGTGGTAATTAATGGTATATCACCAGTAGATGACCCTGA
131 AGGTGGTAATTAATGGTATATCACCAGTAGATGACCCTGA
* *
769762 AAATTT-CAGGCC-ACAAATATGAATTCTAAATTTTGAATTGCGAACTGCGTTCTAGAACGCAGT
1 AAATTTACAGGCCTA-AAATATGAATTCTAAATTTTGAATTGCGAACTGCGTTCAAGAACACAGT
*
769825 TCACTATTCAATTGCAAATAAGCCAGAATCTCAAAAAGTAGAGATGACCACTTCACCATATTTTC
65 TCACTATTCAATTGCAAATAAGCCAGAATCTCAAAAAGTAGAAATGACCACTTCACCATATTTTC
*
769890 AGGGTGGTAAT
130 AAGGTGGTAAT
769901 GGTATACCAA
Statistics
Matches: 127, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
168 1 0.01
169 120 0.94
170 6 0.05
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (170 bp):
AAATTTACAGGCCTAAAATATGAATTCTAAATTTTGAATTGCGAACTGCGTTCAAGAACACAGTT
CACTATTCAATTGCAAATAAGCCAGAATCTCAAAAAGTAGAAATGACCACTTCACCATATTTTCA
AGGTGGTAATTAATGGTATATCACCAGTAGATGACCCTGA
Found at i:772370 original size:42 final size:43
Alignment explanation
Indices: 772289--772375 Score: 158
Period size: 42 Copynumber: 2.0 Consensus size: 43
772279 TAAAAAAAAC
772289 CCGAAAGTCAACTCGTATACAAAAAAAATTCCCGTATACCTAA
1 CCGAAAGTCAACTCGTATACAAAAAAAATTCCCGTATACCTAA
*
772332 CCGAAAGTCAACTCGTATAC-CAAAAAATTCCCGTATACCTAA
1 CCGAAAGTCAACTCGTATACAAAAAAAATTCCCGTATACCTAA
772374 CC
1 CC
772376 ATTAGCGTGT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
42 23 0.53
43 20 0.47
ACGTcount: A:0.41, C:0.29, G:0.09, T:0.21
Consensus pattern (43 bp):
CCGAAAGTCAACTCGTATACAAAAAAAATTCCCGTATACCTAA
Found at i:777003 original size:111 final size:112
Alignment explanation
Indices: 776787--777006 Score: 397
Period size: 111 Copynumber: 2.0 Consensus size: 112
776777 AACCGACGCG
* * * *
776787 AAGCGGAGTTTGACAATGGTTTTTGAGGGGTTTCATTTTCAACAGTTACCCTCCCAAACAGGCAC
1 AAGCGGAGGTTGACAATGGTTTTCGAGGGGTGTCAATTTCAACAGTTACCCTCCCAAACAGGCAC
776852 TCTTTATTTTATTATACTGAATGTCTTATTTTCAAAGAAAATTTTCA
66 TCTTTATTTTATTATACTGAATGTCTTATTTTCAAAGAAAATTTTCA
776899 AAGCGGAGGTTGACAATGGTTTTCGAGGGGTGTCAATTTCAACAGTTACCCTCCC-AACAGGCAC
1 AAGCGGAGGTTGACAATGGTTTTCGAGGGGTGTCAATTTCAACAGTTACCCTCCCAAACAGGCAC
776963 TCTTTATTTTATTATACTGAATGTCTTATTTTCAAAGAAAATTT
66 TCTTTATTTTATTATACTGAATGTCTTATTTTCAAAGAAAATTT
777007 AACTGCTTTT
Statistics
Matches: 104, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
111 53 0.51
112 51 0.49
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (112 bp):
AAGCGGAGGTTGACAATGGTTTTCGAGGGGTGTCAATTTCAACAGTTACCCTCCCAAACAGGCAC
TCTTTATTTTATTATACTGAATGTCTTATTTTCAAAGAAAATTTTCA
Found at i:787934 original size:115 final size:118
Alignment explanation
Indices: 787720--787959 Score: 353
Period size: 115 Copynumber: 2.0 Consensus size: 118
787710 TTTTCCACAA
787720 AGACTGTTAAACCAGGTCTGTTGATGCTTAGCTTATTGGATCCAATATTTTATTTTCAATAATTT
1 AGACTGTTAAACCAGGTCTGTTGATGC-T-GC-TATTGGATCCAATATTTTATTTTCAATAATTT
*
787785 AAAATACCCCATTAACAAATTTTATTTTATTTTTTTAAATCATGATAAATA-AAGT
63 AAAATACCCCATTAACAAATTTTATTTTATTTTTTTAAATCATAATAAATAGAAGT
*
787840 AGACTGTTAAACCAGGAT-TGTTGATGC-G-TATTGGATCTAATATTTTATTTTCAATAATTTAA
1 AGACTGTTAAACCAGG-TCTGTTGATGCTGCTATTGGATCCAATATTTTATTTTCAATAATTTAA
** * *
787902 AATACCCCATTAACATCTTTCTATTTTATTTTTTTAATTTATAATAAATAGAAGT
65 AATACCCCATTAACAAATTT-TATTTTATTTTTTTAAATCATAATAAATAGAAGT
787957 AGA
1 AGA
787960 TATTTATGTG
Statistics
Matches: 111, Mismatches: 6, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
115 51 0.46
116 26 0.23
117 8 0.07
120 25 0.23
121 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (118 bp):
AGACTGTTAAACCAGGTCTGTTGATGCTGCTATTGGATCCAATATTTTATTTTCAATAATTTAAA
ATACCCCATTAACAAATTTTATTTTATTTTTTTAAATCATAATAAATAGAAGT
Found at i:790257 original size:16 final size:16
Alignment explanation
Indices: 790236--790266 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
790226 ATGGAATTAC
790236 TTCGTTATATCCGTAG
1 TTCGTTATATCCGTAG
790252 TTCGTTATATCCGTA
1 TTCGTTATATCCGTA
790267 TAACGAATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.19, G:0.16, T:0.45
Consensus pattern (16 bp):
TTCGTTATATCCGTAG
Found at i:814731 original size:29 final size:29
Alignment explanation
Indices: 814699--814767 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 29
814689 CTAGTGAGCT
* *
814699 TGAGCTTTGTGGACTCAGTACTCAGCTGG
1 TGAGCATTGTGGACTCAGTACTCACCTGG
* * *
814728 TGAGGAATGAGGACTCAGTACTCACCTGG
1 TGAGCATTGTGGACTCAGTACTCACCTGG
*
814757 TAAGCATTGTG
1 TGAGCATTGTG
814768 ATATCAGTTC
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (29 bp):
TGAGCATTGTGGACTCAGTACTCACCTGG
Found at i:814806 original size:29 final size:29
Alignment explanation
Indices: 814773--814851 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 29
814763 TTGTGATATC
* *
814773 AGTTCTAACCTGATGAGCTATGTGGACTT
1 AGTTCTAACCTGGTGAGCTATGTGAACTT
* * * *
814802 GGTTCTAAACAGGTGAGCTAAGTGAACTT
1 AGTTCTAACCTGGTGAGCTATGTGAACTT
*
814831 AGTTCTTACCTGGTGAGCTAT
1 AGTTCTAACCTGGTGAGCTAT
814852 ATAGGCTCAA
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.33
Consensus pattern (29 bp):
AGTTCTAACCTGGTGAGCTATGTGAACTT
Found at i:815049 original size:29 final size:29
Alignment explanation
Indices: 815016--816153 Score: 2168
Period size: 29 Copynumber: 39.2 Consensus size: 29
815006 CCCTGTAAGT
*
815016 TATGTGGACTTGGAGCTTACCTGGTGAGC
1 TATGTGGACTTGGTGCTTACCTGGTGAGC
815045 TATGTGGACTTGGTGCTTACCTGGTGAGC
1 TATGTGGACTTGGTGCTTACCTGGTGAGC
*
815074 TATGTAGACTTGGTGCTTACCTGGTGAGC
1 TATGTGGACTTGGTGCTTACCTGGTGAGC
815103 TATGTGGACTTGGTGCTTACCTGGTGAGC
1 TATGTGGACTTGGTGCTTACCTGGTGAGC
815132 TATGTGGACTTGGTGCTTACCTGGTGAGC
1 TATGTGGACTTGGTGCTTACCTGGTGAGC
815161 TATGTGGACTTGGTGCTTACCTGGTGAGC
1 TATGTGGACTTGGTGCTTACCTGGTGAGC
815190 TATGTGGACTTGGTGCTTACCTGGTGAGC
1 TATGTGGACTTGGTGCTTACCTGGTGAGC
815219 TATGTGGACTTGGTGCTTACCTGGTGAGC
1 TATGTGGACTTGGTGCTTACCTGGTGAGC
815248 TATGTGGACTTGGTGCTTACCTGGTGAGC
1 TATGTGGACTTGGTGCTTACCTGGTGAGC
815277 TATGTGGACTTGGTGCTTACCTGGTGAGC
1 TATGTGGACTTGGTGCTTACCTGGTGAGC
815306 TATGTGGACTTGGTGCTTACCTGGTGAGC
1 TATGTGGACTTGGTGCTTACCTGGTGAGC
815335 TATGTGGACTTGGTGCTTACCTGGTGAGC
1 TATGTGGACTTGGTGCTTACCTGGTGAGC
815364 TATGTGGACTTGGTGCTTACCTGGTGAGC
1 TATGTGGACTTGGTGCTTACCTGGTGAGC
815393 TATGTGGACTTGGTGCTTACCTGGTGAGC
1 TATGTGGACTTGGTGCTTACCTGGTGAGC
815422 TATGTGGACTTGGTGCTTACCTGGTGAGC
1 TATGTGGACTTGGTGCTTACCTGGTGAGC
815451 TATGTGGACTTGGTGCTTACCTGGTGAGC
1 TATGTGGACTTGGTGCTTACCTGGTGAGC
815480 TATGTGGACTTGGTGCTTACCTGGTGAGC
1 TATGTGGACTTGGTGCTTACCTGGTGAGC
815509 TATGTGGACTTGGTGCTTACCTGGTGAGC
1 TATGTGGACTTGGTGCTTACCTGGTGAGC
815538 TATGTGGACTTGGTGCTTACCTGGTGAGC
1 TATGTGGACTTGGTGCTTACCTGGTGAGC
815567 TATGTGGACTTGGTGCTTACCTGGTGAGC
1 TATGTGGACTTGGTGCTTACCTGGTGAGC
815596 TATGTGGACTTGGTGCTTACCTGGTGAGC
1 TATGTGGACTTGGTGCTTACCTGGTGAGC
815625 TATGTGGACTTGGTGCTTACCTGGTGAGC
1 TATGTGGACTTGGTGCTTACCTGGTGAGC
815654 TATGTGGACTTGGTGCTTACCTGGTGAGC
1 TATGTGGACTTGGTGCTTACCTGGTGAGC
815683 TATGTGGACTTGGTGCTTACCTGGTGAGC
1 TATGTGGACTTGGTGCTTACCTGGTGAGC
815712 TATGTGGACTTGGTGCTTACCTGGTGAGC
1 TATGTGGACTTGGTGCTTACCTGGTGAGC
815741 TATGTGGACTTGGTGCTTACCTGGTGAGC
1 TATGTGGACTTGGTGCTTACCTGGTGAGC
815770 TATGTGGACTTGGTGCTTACCTGGTGAGC
1 TATGTGGACTTGGTGCTTACCTGGTGAGC
815799 TATGTGGACTTGGTGCTTACCTGGTGAGC
1 TATGTGGACTTGGTGCTTACCTGGTGAGC
*
815828 TATGTAGACTTGGTGCTTACCTGGTGAGC
1 TATGTGGACTTGGTGCTTACCTGGTGAGC
815857 TATGTGGACTTGGTGCTTACCTGGTGAGC
1 TATGTGGACTTGGTGCTTACCTGGTGAGC
*
815886 TATGTGGACTTGGAGCTTACCTGGTGAGC
1 TATGTGGACTTGGTGCTTACCTGGTGAGC
* *
815915 TATGTAGACTTGGTGCTTACCTGATGAGC
1 TATGTGGACTTGGTGCTTACCTGGTGAGC
*
815944 TATGTGGACGTGGTGCTTACCTGGTGAGC
1 TATGTGGACTTGGTGCTTACCTGGTGAGC
*
815973 TTTGTGGACTTGGTGCTTACCTGGTGAGC
1 TATGTGGACTTGGTGCTTACCTGGTGAGC
816002 TATGTGGACTTGGTGCTTACCTGGTGAGC
1 TATGTGGACTTGGTGCTTACCTGGTGAGC
*
816031 TATGTGGACTTGGAGCTTACCTGGTGAGC
1 TATGTGGACTTGGTGCTTACCTGGTGAGC
*
816060 TATGTAGACTTGGTGCTTACCTGGTGAGC
1 TATGTGGACTTGGTGCTTACCTGGTGAGC
**
816089 TATGTGGACTTGGAACTTACCTGGTGAGC
1 TATGTGGACTTGGTGCTTACCTGGTGAGC
816118 TATGTGGACTTGGTGCTTACCTGGTGAGC
1 TATGTGGACTTGGTGCTTACCTGGTGAGC
816147 TATGTGG
1 TATGTGG
816154 GCGGCGGTCA
Statistics
Matches: 1086, Mismatches: 23, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 1086 1.00
ACGTcount: A:0.15, C:0.17, G:0.34, T:0.34
Consensus pattern (29 bp):
TATGTGGACTTGGTGCTTACCTGGTGAGC
Found at i:819057 original size:38 final size:38
Alignment explanation
Indices: 819010--819084 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
819000 TGTTGATGTA
*
819010 ATTTGTTAAACATAATGCAAT-AAAGATATGTGGTAAAT
1 ATTTGTTAAACACAATGCAATGAAA-ATATGTGGTAAAT
* * *
819048 ATTTTTTAAACACAGTGCAATGAAAATATTTGGTAAA
1 ATTTGTTAAACACAATGCAATGAAAATATGTGGTAAA
819085 AATAAATTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 29 0.91
39 3 0.09
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.35
Consensus pattern (38 bp):
ATTTGTTAAACACAATGCAATGAAAATATGTGGTAAAT
Found at i:823543 original size:11 final size:11
Alignment explanation
Indices: 823527--823619 Score: 62
Period size: 11 Copynumber: 7.7 Consensus size: 11
823517 ATATTGCCTT
823527 TCATATGAGAA
1 TCATATGAGAA
*
823538 TCATATGATAA
1 TCATATGAGAA
* *
823549 TCATATGTGTA
1 TCATATGAGAA
823560 TCATATGTATATTGAA
1 TCATATG---A--GAA
*
823576 TCATATGAGTA
1 TCATATGAGAA
823587 TCACATATG-GCAGA
1 T--CATATGAG-A-A
823601 TCATATGAGAA
1 TCATATGAGAA
823612 TCATATGA
1 TCATATGA
823620 ACACTCATGT
Statistics
Matches: 64, Mismatches: 8, Indels: 20
0.70 0.09 0.22
Matches are distributed among these distances:
11 37 0.58
12 8 0.12
13 8 0.12
14 2 0.03
16 9 0.14
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (11 bp):
TCATATGAGAA
Found at i:827654 original size:2 final size:2
Alignment explanation
Indices: 827647--827682 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
827637 GGTGCCAAAA
827647 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
827683 AAAGGAGAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:831230 original size:3 final size:3
Alignment explanation
Indices: 831224--831265 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
831214 ACAAGAAGAA
* *
831224 GAT GAT GAT AAT AAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
831266 AAAGCTCTCC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.38, C:0.00, G:0.29, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:852992 original size:17 final size:17
Alignment explanation
Indices: 852970--853004 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
852960 AATTATGTAA
*
852970 TTTTTAATGTTTTTTTT
1 TTTTTAATATTTTTTTT
852987 TTTTTAATATTTTTTTT
1 TTTTTAATATTTTTTTT
853004 T
1 T
853005 GCTTCTTGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (17 bp):
TTTTTAATATTTTTTTT
Found at i:860459 original size:2 final size:2
Alignment explanation
Indices: 860452--860507 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
860442 TGACTCTGAT
860452 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
860494 TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC
860508 GCGATCGTTG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:862357 original size:2 final size:2
Alignment explanation
Indices: 862350--862387 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
862340 TCATCAGGTA
*
862350 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
862388 ATCTATCTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:873289 original size:13 final size:13
Alignment explanation
Indices: 873271--873301 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
873261 GATGTATCTT
*
873271 TTTTTTTTTTTCC
1 TTTTTTTTTTACC
873284 TTTTTTTTTTACC
1 TTTTTTTTTTACC
873297 TTTTT
1 TTTTT
873302 AAATCCTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTTTTTACC
Found at i:874423 original size:1 final size:1
Alignment explanation
Indices: 874417--874443 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
874407 CTCCCACCTA
874417 CCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCC
874444 TTTAAAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:880802 original size:3 final size:3
Alignment explanation
Indices: 880787--880837 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
880777 AAGAGAGATT
* * *
880787 ATA ATA ATG ATA ATA ATA ATG ATA ATA ATA ATT ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
880835 ATA
1 ATA
880838 GTTACAAACC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:880802 original size:12 final size:12
Alignment explanation
Indices: 880787--880837 Score: 84
Period size: 12 Copynumber: 4.2 Consensus size: 12
880777 AAGAGAGATT
880787 ATAATAATGATA
1 ATAATAATGATA
880799 ATAATAATGATA
1 ATAATAATGATA
*
880811 ATAATAATTATA
1 ATAATAATGATA
*
880823 ATAATAATAATA
1 ATAATAATGATA
880835 ATA
1 ATA
880838 GTTACAAACC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (12 bp):
ATAATAATGATA
Found at i:881526 original size:2 final size:2
Alignment explanation
Indices: 881519--881580 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
881509 ACTACGAAAA
881519 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
881561 TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC
881581 CCCCCAATGA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:888434 original size:2 final size:2
Alignment explanation
Indices: 888427--888479 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
888417 TGAACGCAAT
888427 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
888469 TC TC TC TC TC T
1 TC TC TC TC TC T
888480 GGAGCTCCAG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Done.