Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 188 of 204
Found at i:55467716 original size:5 final size:5
Alignment explanation
Indices: 55467706--55467730 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
55467696 ATTTAGAGCA
55467706 TTTTC TTTTC TTTTC TTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC
55467731 CCTTTACGAA
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:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:55480148 original size:34 final size:34
Alignment explanation
Indices: 55480107--55480177 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
55480097 TTTTATATTT
55480107 AATTACGTGTTTCGTTTTTTTTTTAAAGAAATTC
1 AATTACGTGTTTCGTTTTTTTTTTAAAGAAATTC
55480141 AATTACGTGTTTCGTTTTTTTTTTAAAGAAATTC
1 AATTACGTGTTTCGTTTTTTTTTTAAAGAAATTC
55480175 AAT
1 AAT
55480178 CACATTAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.28, C:0.08, G:0.11, T:0.52
Consensus pattern (34 bp):
AATTACGTGTTTCGTTTTTTTTTTAAAGAAATTC
Found at i:55486281 original size:31 final size:31
Alignment explanation
Indices: 55486246--55486307 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
55486236 CATGGATTTT
*
55486246 CTATTTTTCCAATTTTCTTTTT-TTATCGAAA
1 CTATTTTTCCAATTTTATTTTTGTT-TCGAAA
* *
55486277 CTATTTTTCGATTTTTATTTTTGTTTCGAAA
1 CTATTTTTCCAATTTTATTTTTGTTTCGAAA
55486308 TACTAGGGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 25 0.93
32 2 0.07
ACGTcount: A:0.21, C:0.13, G:0.06, T:0.60
Consensus pattern (31 bp):
CTATTTTTCCAATTTTATTTTTGTTTCGAAA
Found at i:55487046 original size:21 final size:20
Alignment explanation
Indices: 55487020--55487063 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
55487010 AAAAATCAAT
*
55487020 AAAAATTATTAAATTTTAATA
1 AAAAATTATAAAATTTT-ATA
55487041 AAAAATTATAAAATTTTATA
1 AAAAATTATAAAATTTTATA
55487061 AAA
1 AAA
55487064 GACCCTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAAATTATAAAATTTTATA
Found at i:55487305 original size:18 final size:17
Alignment explanation
Indices: 55487284--55487326 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
55487274 TATTATAATT
*
55487284 TTTTTATACTTTTTACGA
1 TTTTTATAATTTTTA-GA
*
55487302 TTTTTAATAATTTTTATA
1 TTTTT-ATAATTTTTAGA
55487320 TTTTTAT
1 TTTTTAT
55487327 TAAAATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 11 0.50
19 9 0.41
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTTTATAATTTTTAGA
Found at i:55487598 original size:89 final size:87
Alignment explanation
Indices: 55487440--55487609 Score: 243
Period size: 89 Copynumber: 1.9 Consensus size: 87
55487430 ACTAGGGATG
* * * *
55487440 GTTCAAGTACCCAATTGAGTGTAAAAAAAGTAAGGGCTTAATTATTTTTTTGAAAAAATTTGAGG
1 GTTCAAATACCCAATTGAGTGTAAAAAAAGTAAGAGCTTAATTATTTTTTTGAAAAAAATTGAGA
55487505 GTCTTTTTGATGCATTTTGAAA
66 GTCTTTTTGATGCATTTTGAAA
* *
55487527 GTTCAAATACCCAATTGAGTGTAAAACAAAAGTAA-AGTTTAATTGCTTTTTTTGAAAAAAATTG
1 GTTCAAATACCCAATTGAGTGT-AAA-AAAAGTAAGAGCTTAATT-ATTTTTTTGAAAAAAATTG
*
55487591 AGAGTCTTTTTTATGCATT
63 AGAGTCTTTTTGATGCATT
55487610 GTAAAAATTG
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
87 21 0.29
88 10 0.14
89 42 0.58
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (87 bp):
GTTCAAATACCCAATTGAGTGTAAAAAAAGTAAGAGCTTAATTATTTTTTTGAAAAAAATTGAGA
GTCTTTTTGATGCATTTTGAAA
Found at i:55489212 original size:19 final size:18
Alignment explanation
Indices: 55489166--55489216 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
55489156 ATATTAGTCG
55489166 TTTCATTTTTTTTT-ATT
1 TTTCATTTTTTTTTAATT
*
55489183 TTT--TTTATTTTTAATT
1 TTTCATTTTTTTTTAATT
55489199 TTTCATTATTTTTTTAAT
1 TTTCATT-TTTTTTTAAT
55489217 ATAAATGTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
15 8 0.29
16 6 0.21
17 3 0.11
18 2 0.07
19 9 0.32
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTCATTTTTTTTTAATT
Found at i:55498597 original size:29 final size:31
Alignment explanation
Indices: 55498546--55498612 Score: 86
Period size: 29 Copynumber: 2.2 Consensus size: 31
55498536 AGTCTAATTA
*
55498546 AAAATTTTAAAATTTTTATGAG-AT-TAATG
1 AAAATTTTAAAATTTTGATGAGAATCTAATG
*
55498575 AAAATTTTCAAAATTTTGA-GAGAATCTAATT
1 AAAATTTT-AAAATTTTGATGAGAATCTAATG
55498606 AAAATTT
1 AAAATTT
55498613 AAAGAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 11 0.33
30 11 0.33
31 11 0.33
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.42
Consensus pattern (31 bp):
AAAATTTTAAAATTTTGATGAGAATCTAATG
Found at i:55506290 original size:13 final size:13
Alignment explanation
Indices: 55506274--55506326 Score: 61
Period size: 13 Copynumber: 4.1 Consensus size: 13
55506264 TTTAAACCAA
*
55506274 ACTTTTCAAAAAC
1 ACTTTTCAAAAGC
* *
55506287 ACTTCTCAAAAGT
1 ACTTTTCAAAAGC
* *
55506300 ACTTTTCCATAGC
1 ACTTTTCAAAAGC
55506313 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
55506326 A
1 A
55506327 TTGCCAAACT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.32
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:55511644 original size:19 final size:20
Alignment explanation
Indices: 55511611--55511648 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
55511601 TTCATAAAAT
55511611 TAAATAATAAATATATTTAC
1 TAAATAATAAATATATTTAC
*
55511631 TAAA-AATAATTATATTTA
1 TAAATAATAAATATATTTA
55511649 TAATAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAATAATAAATATATTTAC
Found at i:55512170 original size:18 final size:18
Alignment explanation
Indices: 55512137--55512187 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
55512127 ATCCTATCAC
* *
55512137 AATTATGTTGTTATTGTCT
1 AATTTTGTTATTATTGT-T
55512156 AATTTTGTT-TTATTGTT
1 AATTTTGTTATTATTGTT
55512173 AATTTTGTTATTATT
1 AATTTTGTTATTATT
55512188 TTAGAGGCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 10 0.33
18 12 0.40
19 8 0.27
ACGTcount: A:0.22, C:0.02, G:0.12, T:0.65
Consensus pattern (18 bp):
AATTTTGTTATTATTGTT
Found at i:55512572 original size:7 final size:7
Alignment explanation
Indices: 55512560--55512589 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
55512550 CGAATTATCC
55512560 CTCTAAG
1 CTCTAAG
55512567 CTCTAAG
1 CTCTAAG
55512574 CTCTAAG
1 CTCTAAG
55512581 CTCTAAG
1 CTCTAAG
55512588 CT
1 CT
55512590 GCAATATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.27, C:0.30, G:0.13, T:0.30
Consensus pattern (7 bp):
CTCTAAG
Found at i:55518376 original size:3 final size:3
Alignment explanation
Indices: 55518368--55518406 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
55518358 ATATGTATAG
*
55518368 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
55518407 ATATTTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:55520288 original size:44 final size:43
Alignment explanation
Indices: 55520240--55520363 Score: 126
Period size: 45 Copynumber: 2.8 Consensus size: 43
55520230 TGTTGTATTT
* *
55520240 GATCTACTTCACGCCGATACATGAAGACAAGATCTGTTTTCTTC
1 GATCTACTTCACGCC-ATACATGAAGACAAGATCTGGTATCTTC
* * *
55520284 GATCTACTT--TGCCATCAGTATGGGAAGACAAGATCTGGTATCTTT
1 GATCTACTTCACGCCAT-A-CAT--GAAGACAAGATCTGGTATCTTC
*
55520329 GATCTACTTCACGCTAGTACATGAAGACAAGATCT
1 GATCTACTTCACGCCA-TACATGAAGACAAGATCT
55520364 ACTCCACCAC
Statistics
Matches: 65, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
41 2 0.03
42 4 0.06
43 2 0.03
44 22 0.34
45 28 0.43
46 2 0.03
47 4 0.06
48 1 0.02
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.31
Consensus pattern (43 bp):
GATCTACTTCACGCCATACATGAAGACAAGATCTGGTATCTTC
Found at i:55520332 original size:89 final size:88
Alignment explanation
Indices: 55520180--55520363 Score: 228
Period size: 89 Copynumber: 2.1 Consensus size: 88
55520170 TTAGGGAGAT
* * * *
55520180 AAGATCTGTAATCTTCACTCTACTTGCCGCCAGTATGGGAAGATAAAATATGTTGTATTTGATCT
1 AAGATCTGTAATCTTCACTCTACTTGCCACCAGTATGGGAAGACAAAATATGGTATATTTGATCT
55520245 ACTTCACGCCGA-TACATGAAGAC
66 ACTTCACG-CGAGTACATGAAGAC
** * * * *
55520268 AAGATCTGTTTTCTTCGA-TCTACTTTGCCATCAGTATGGGAAGACAAGATCTGGTATCTTTGAT
1 AAGATCTGTAATCTTC-ACTCTAC-TTGCCACCAGTATGGGAAGACAAAATATGGTATATTTGAT
*
55520332 CTACTTCACGCTAGTACATGAAGAC
64 CTACTTCACGCGAGTACATGAAGAC
55520357 AAGATCT
1 AAGATCT
55520364 ACTCCACCAC
Statistics
Matches: 82, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
88 21 0.26
89 61 0.74
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (88 bp):
AAGATCTGTAATCTTCACTCTACTTGCCACCAGTATGGGAAGACAAAATATGGTATATTTGATCT
ACTTCACGCGAGTACATGAAGAC
Found at i:55520476 original size:44 final size:44
Alignment explanation
Indices: 55520426--55520570 Score: 159
Period size: 44 Copynumber: 3.3 Consensus size: 44
55520416 ACCGATATAG
* *
55520426 GAAGACAGGACCTACTATCTTTGATCTACTTCACGCCAGTACAT
1 GAAGACAAGATCTACTATCTTTGATCTACTTCACGCCAGTACAT
* * * * * *
55520470 GAAGACAAGATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGA-
1 GAAGACAAGATCTACTATCTTTGATCTACTTC-ACGCCAGTA-CAT
* *
55520515 GAAGGCAAGATCTGA-TATCTCTGATCTACTTCACGCCAGTACAT
1 GAAGACAAGATCT-ACTATCTTTGATCTACTTCACGCCAGTACAT
55520559 GAAGACAAGATC
1 GAAGACAAGATC
55520571 CGTTATCTTT
Statistics
Matches: 80, Mismatches: 17, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
43 1 0.01
44 45 0.56
45 33 0.41
46 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.27
Consensus pattern (44 bp):
GAAGACAAGATCTACTATCTTTGATCTACTTCACGCCAGTACAT
Found at i:55520578 original size:44 final size:44
Alignment explanation
Indices: 55520441--55520580 Score: 167
Period size: 44 Copynumber: 3.2 Consensus size: 44
55520431 CAGGACCTAC
55520441 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCT
1 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTG-T
* * * * * *
55520486 T-TCTTTGATCTGCTTCGCCACCAGTATGA-GAAGGCAAGATCTGA
1 TATCTTTGATCTACTTC-ACGCCAGTA-CATGAAGACAAGATCTGT
* *
55520530 TATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCCGT
1 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGT
55520574 TATCTTT
1 TATCTTT
55520581 CAACCTACTC
Statistics
Matches: 76, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
43 1 0.01
44 40 0.53
45 34 0.45
46 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.31
Consensus pattern (44 bp):
TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGT
Found at i:55532664 original size:3 final size:3
Alignment explanation
Indices: 55532656--55532710 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
55532646 ATATGTATAG
55532656 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
55532704 TAA TAA T
1 TAA TAA T
55532711 GATGATGATA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:55534012 original size:24 final size:24
Alignment explanation
Indices: 55533961--55534013 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
55533951 ATATTTTTTC
*
55533961 CAATTTTTTTAAAAATTAATTATA
1 CAATATTTTTAAAAATTAATTATA
*
55533985 -AATATTTTTAAATATTAATT-TAA
1 CAATATTTTTAAAAATTAATTAT-A
55534008 CAATAT
1 CAATAT
55534014 GAAGAAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 1 0.04
23 19 0.76
24 5 0.20
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (24 bp):
CAATATTTTTAAAAATTAATTATA
Found at i:55534470 original size:22 final size:22
Alignment explanation
Indices: 55534421--55534470 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
55534411 TCAGAATCAG
*
55534421 ATTTTCCCGATTTCATTTCCCC
1 ATTTTCCCAATTTCATTTCCCC
*
55534443 AATTTCCCAATTTC-TTTCCGCC
1 ATTTTCCCAATTTCATTTCC-CC
*
55534465 GTTTTC
1 ATTTTC
55534471 TTCACATCTG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.14, C:0.34, G:0.06, T:0.46
Consensus pattern (22 bp):
ATTTTCCCAATTTCATTTCCCC
Found at i:55536955 original size:23 final size:22
Alignment explanation
Indices: 55536912--55536959 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
55536902 GTTTTTTTCC
*
55536912 AATTTTTTTAAAAAATTAATTAT
1 AATTTTTTTAAAAAATCAATT-T
*
55536935 AATTATTTTT-AAATATCAATTT
1 AATT-TTTTTAAAAAATCAATTT
55536957 AAT
1 AAT
55536960 AATATGATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 4 0.18
23 13 0.59
24 5 0.23
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
AATTTTTTTAAAAAATCAATTT
Found at i:55537427 original size:21 final size:20
Alignment explanation
Indices: 55537382--55537427 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 20
55537372 CTTTTAGAAA
*
55537382 GTTTAGTTTAAGATTTAACT
1 GTTTAGTTTAAGATTTAAAT
55537402 GTTTAGTTTAAGATTTATAAT
1 GTTTAGTTTAAGATTTA-AAT
55537423 GTTTA
1 GTTTA
55537428 AATTAGTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.30, C:0.02, G:0.15, T:0.52
Consensus pattern (20 bp):
GTTTAGTTTAAGATTTAAAT
Found at i:55539165 original size:60 final size:60
Alignment explanation
Indices: 55539072--55539195 Score: 248
Period size: 60 Copynumber: 2.1 Consensus size: 60
55539062 AGATGCTGAC
55539072 ATAAGAGGTAAAATTTTCTTAATTAGGTAAAGTTGAATACTCTTATTCCTTTTATGGAAA
1 ATAAGAGGTAAAATTTTCTTAATTAGGTAAAGTTGAATACTCTTATTCCTTTTATGGAAA
55539132 ATAAGAGGTAAAATTTTCTTAATTAGGTAAAGTTGAATACTCTTATTCCTTTTATGGAAA
1 ATAAGAGGTAAAATTTTCTTAATTAGGTAAAGTTGAATACTCTTATTCCTTTTATGGAAA
55539192 ATAA
1 ATAA
55539196 CTATGTATAT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 64 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.40
Consensus pattern (60 bp):
ATAAGAGGTAAAATTTTCTTAATTAGGTAAAGTTGAATACTCTTATTCCTTTTATGGAAA
Found at i:55539709 original size:17 final size:18
Alignment explanation
Indices: 55539678--55539711 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
55539668 AATTTAACTT
55539678 TAATTAAATTATTTAAAA
1 TAATTAAATTATTTAAAA
*
55539696 TAATT-AATTTTTTAAA
1 TAATTAAATTATTTAAA
55539712 TTATAAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATTAAATTATTTAAAA
Found at i:55545843 original size:2 final size:2
Alignment explanation
Indices: 55545836--55545867 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
55545826 TAATTGTTTG
*
55545836 AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55545868 TTGAATATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:55545875 original size:18 final size:18
Alignment explanation
Indices: 55545832--55545875 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
55545822 AATATAATTG
55545832 TTTG-ATATATATATATA
1 TTTGAATATATATATATA
55545849 TTT-ATATATATATATATA
1 TTTGA-ATATATATATATA
55545867 TTTGAATAT
1 TTTGAATAT
55545876 GGATACACGA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 3 0.12
18 20 0.83
19 1 0.04
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (18 bp):
TTTGAATATATATATATA
Found at i:55555647 original size:21 final size:19
Alignment explanation
Indices: 55555623--55555661 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
55555613 ATTTGCCTCC
55555623 CTATCTAAGACCATGTTTCCT
1 CTATCTAAG-CCAT-TTTCCT
55555644 CTATCTAAGCCATTTTCC
1 CTATCTAAGCCATTTTCC
55555662 GGAGGATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 4 0.22
21 9 0.50
ACGTcount: A:0.23, C:0.31, G:0.08, T:0.38
Consensus pattern (19 bp):
CTATCTAAGCCATTTTCCT
Found at i:55560036 original size:155 final size:153
Alignment explanation
Indices: 55559768--55560294 Score: 669
Period size: 155 Copynumber: 3.4 Consensus size: 153
55559758 TCGCATACGC
* * * * *
55559768 TGTTTATATTCATTTTTTTTGCTCCACAAGCAATCCGAAACCATAAACAAAGG-A-GTACTTTTT
1 TGTTTATATTCACTTTTCTTGCTACACAAGCAAGCCGAAACCATAAACAAAGGCATGCA-TTTTT
* * * *
55559831 TGCCTTTTTTAAATGGTTTTCTTGTTTCTTT-TCCGCTTTTCAAATTCTTCATTCAATTCAAGTT
65 TTCCTTTTTTAAATGGTTTTCTTGTTTCTTTGT-TGTTTTTAAAATTCTTCATTCAATTCAAGTT
55559895 CAAGAAACCATACTAAATATATATATA
129 CAAGAAACCATACT-AA-ATATATATA
* *
55559922 TGTTTATATTCGCTTTTCTTGCTACACAAGCAAGCCAAAACCATAAACAAAGGCATGCATTTTAT
1 TGTTTATATTCACTTTTCTTGCTACACAAGCAAGCCGAAACCATAAACAAAGGCATGCATTTT-T
*
55559987 TTCCTTTTTT-AATGGTTTTCTTGATTCTTTGTTGTTTTTAAAATTCTTCATTCAATTCAAGTTC
65 TTCCTTTTTTAAATGGTTTTCTTGTTTCTTTGTTGTTTTTAAAATTCTTCATTCAATTCAAGTTC
55560051 AAGAAACCATACTAAA-ATATATA
130 AAGAAACCATACTAAATATATATA
* * * *
55560074 --TTTATATTCGCTTTTTTTGCTACACAAGCAAGCTGAAACCATAAACAAAGGCATACA-TTTTT
1 TGTTTATATTCACTTTTCTTGCTACACAAGCAAGCCGAAACCATAAACAAAGGCATGCATTTTTT
* * * *
55560136 TCCTTTTTTAAATGCATTTTTTTTTTTGTTTCTTTGTTGTTTTTTAGATTCTTCATTCAATTCAA
66 TCCTTTTTTAAATG-----GTTTTCTTGTTTCTTTGTTGTTTTTAAAATTCTTCATTCAATTCAA
*
55560201 GTTCAAGAAATCATACT-AAT-TATATA
126 GTTCAAGAAACCATACTAAATATATATA
* * * *
55560227 TGTTTATATTCACTTTTCTTGCTACATAAGCAAGCCGAAACTATAAACAAAGGCATACCTTTTTT
1 TGTTTATATTCACTTTTCTTGCTACACAAGCAAGCCGAAACCATAAACAAAGGCATGCATTTTTT
55560292 TCC
66 TCC
55560295 CCTTTTTATC
Statistics
Matches: 331, Mismatches: 28, Indels: 26
0.86 0.07 0.07
Matches are distributed among these distances:
148 11 0.03
149 7 0.02
150 53 0.16
152 7 0.02
153 9 0.03
154 106 0.32
155 117 0.35
156 21 0.06
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.43
Consensus pattern (153 bp):
TGTTTATATTCACTTTTCTTGCTACACAAGCAAGCCGAAACCATAAACAAAGGCATGCATTTTTT
TCCTTTTTTAAATGGTTTTCTTGTTTCTTTGTTGTTTTTAAAATTCTTCATTCAATTCAAGTTCA
AGAAACCATACTAAATATATATA
Found at i:55560369 original size:16 final size:16
Alignment explanation
Indices: 55560348--55560378 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
55560338 TTTAAGAAAT
55560348 CATACTATATATATAC
1 CATACTATATATATAC
55560364 CATACTATATATATA
1 CATACTATATATATA
55560379 TATATGTTTA
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:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (16 bp):
CATACTATATATATAC
Found at i:55560378 original size:305 final size:307
Alignment explanation
Indices: 55559769--55560476 Score: 731
Period size: 305 Copynumber: 2.3 Consensus size: 307
55559759 CGCATACGCT
* * *
55559769 GTTTATATTCATTTTTTTTGCTCCACAAGCAATCCGAAACCATAAACAAAGG-AGTAC-TTTTTT
1 GTTTATATTCACTTTTTTTGCTACACAAGCAA-CTGAAACCATAAACAAAGGCA-TACATTTTTT
* *
55559832 GCCTTTTTTAAATG----GTTTTCTTGTTTCTTTTCCGCTTTTCAAATTCTTCATTCAATTCAAG
64 -CCTTTTTTAAATGATTTTTTTTTTTGTTTCTTTTCCGCTTTTCAAATTCTTCATTCAATTCAAG
*
55559893 TTCAAGAAACCATACTAAATATATATATATGTTTATATTCGCTTTTCTTGCTACACAAGCAAGCC
128 TTCAAGAAACCATACT-AATATATATATATGTTTATATTCACTTTTCTTGCTACACAAGCAAGCC
* * * *
55559958 AAAACCATAAACAAAGGCATGCATTTTATTTCCTTTTTTAATGGTTTTCTTGATTCTTTGTTGTT
192 AAAACCATAAACAAAGGCATACATTTTATTTCCCTTTTTAAT-GCTTGCTTGATTCTTTGTTGTT
* * *
55560023 TTTAAAATTCTTCATTCAATTCAAGTTCAAGAAACCATAC-TAAAATATATA
256 TTTAAAATTCTTCATACAAATCAACTTCAAGAAACCATACATAAAATATATA
*
55560074 -TTTATATTCGCTTTTTTTGCTACACAAGCAAGCTGAAACCATAAACAAAGGCATACATTTTTTC
1 GTTTATATTCACTTTTTTTGCTACACAAGCAA-CTGAAACCATAAACAAAGGCATACATTTTTTC
* * * *
55560138 CTTTTTTAAATGCATTTTTTTTTTTGTTTCTTTGT-TGTTTTTTAGATTCTTCATTCAATTCAAG
65 CTTTTTTAAATG-ATTTTTTTTTTTGTTTCTTT-TCCGCTTTTCAAATTCTTCATTCAATTCAAG
* * *
55560202 TTCAAGAAATCATACT-A-AT-TATATATGTTTATATTCACTTTTCTTGCTACATAAGCAAGCCG
128 TTCAAGAAACCATACTAATATATATATATGTTTATATTCACTTTTCTTGCTACACAAGCAAGCCA
* * *
55560264 AAACTATAAACAAAGGCATACCTTTT-TTTCCCCTTTTT-AT-CTTGC-TGCTT-TTTAGATT-T
193 AAACCATAAACAAAGGCATACATTTTATTT-CCCTTTTTAATGCTTGCTTGATTCTTT-G-TTGT
* * * * * *
55560323 TTCATT-CAATTCAAGTTTA-AGAAATCATACTAT-ATATATACCATACTATATATATATATA
255 TT--TTAAAATTC---TTCATACAAATCA-ACT-TCA-AGAAACCATAC-ATA-AAATATATA
* *
55560383 TGTTTATATTCACTTTTCTTGCTACACAAGTCAACTGAAACCATAAACAAAGGCATA-ACTTTTT
1 -GTTTATATTCACTTTTTTTGCTACACAAG-CAACTGAAACCATAAACAAAGGCATACATTTTTT
55560447 CGCTTTTTTTAAAATGATTTTTTTTCTTTG
64 C-C-TTTTTT-AAATGATTTTTTTT-TTTG
55560477 CTACTTTTTT
Statistics
Matches: 340, Mismatches: 34, Indels: 50
0.80 0.08 0.12
Matches are distributed among these distances:
300 3 0.01
301 8 0.02
302 10 0.03
303 2 0.01
304 72 0.21
305 83 0.24
306 12 0.04
307 1 0.00
308 2 0.01
309 62 0.18
310 8 0.02
311 50 0.15
312 18 0.05
313 9 0.03
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.44
Consensus pattern (307 bp):
GTTTATATTCACTTTTTTTGCTACACAAGCAACTGAAACCATAAACAAAGGCATACATTTTTTCC
TTTTTTAAATGATTTTTTTTTTTGTTTCTTTTCCGCTTTTCAAATTCTTCATTCAATTCAAGTTC
AAGAAACCATACTAATATATATATATGTTTATATTCACTTTTCTTGCTACACAAGCAAGCCAAAA
CCATAAACAAAGGCATACATTTTATTTCCCTTTTTAATGCTTGCTTGATTCTTTGTTGTTTTTAA
AATTCTTCATACAAATCAACTTCAAGAAACCATACATAAAATATATA
Found at i:55561914 original size:20 final size:21
Alignment explanation
Indices: 55561875--55561917 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
55561865 TTATAAAACT
*
55561875 TAATTTTATTTTAATAATTATA
1 TAATATTATTTT-ATAATTATA
55561897 TAATATTATTTT-TAATTATA
1 TAATATTATTTTATAATTATA
55561917 T
1 T
55561918 CATCTGATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
22 11 0.55
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TAATATTATTTTATAATTATA
Found at i:55563105 original size:37 final size:36
Alignment explanation
Indices: 55563062--55563167 Score: 122
Period size: 37 Copynumber: 2.8 Consensus size: 36
55563052 AGGAACATGG
* * *
55563062 CTTTCTTGTTAGTATTCTCATTCTTTTTTTAACATAC
1 CTTTCTTGTT-GTATTCTCATTCTATTATGAACATAC
* *
55563099 CTTTCTTGCTTGTGTTCTCATTCTATTATGAATATAC
1 CTTTCTTG-TTGTATTCTCATTCTATTATGAACATAC
*
55563136 CTTTCTTGTTCGTATTCTCGTTCTATTGATGA
1 CTTTCTTGTT-GTATTCTCATTCTATT-ATGA
55563168 TTAATGTTGC
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
36 2 0.03
37 51 0.86
38 6 0.10
ACGTcount: A:0.17, C:0.19, G:0.10, T:0.54
Consensus pattern (36 bp):
CTTTCTTGTTGTATTCTCATTCTATTATGAACATAC
Found at i:55564874 original size:17 final size:18
Alignment explanation
Indices: 55564843--55564876 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
55564833 AATTTAACTT
55564843 TAATTAAATTATTTAAAA
1 TAATTAAATTATTTAAAA
*
55564861 TAATT-AATTTTTTAAA
1 TAATTAAATTATTTAAA
55564877 TTATAGACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATTAAATTATTTAAAA
Found at i:55566828 original size:64 final size:63
Alignment explanation
Indices: 55566723--55566841 Score: 202
Period size: 64 Copynumber: 1.9 Consensus size: 63
55566713 GAACGGGAAC
* * *
55566723 TGTTGGAAATTGCCAATCATTCTGCTGTTACATTTTTTGGTTGAAGTGCATGCAGAAAAAAAA
1 TGTTAGAAATTGCCAACCATGCTGCTGTTACATTTTTTGGTTGAAGTGCATGCAGAAAAAAAA
55566786 TGTTAGAAATTTGCCAACCATGCTGCTGTTACATTTTTTGGTTGAAGTGCATGCAG
1 TGTTAGAAA-TTGCCAACCATGCTGCTGTTACATTTTTTGGTTGAAGTGCATGCAG
55566842 CTTGATGACA
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
63 8 0.15
64 44 0.85
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (63 bp):
TGTTAGAAATTGCCAACCATGCTGCTGTTACATTTTTTGGTTGAAGTGCATGCAGAAAAAAAA
Found at i:55568880 original size:21 final size:19
Alignment explanation
Indices: 55568856--55568894 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
55568846 ATTTGCCTCC
55568856 CTATCTAAGACCATGTTTCCT
1 CTATCTAAG-CCAT-TTTCCT
55568877 CTATCTAAGCCATTTTCC
1 CTATCTAAGCCATTTTCC
55568895 GGAGGATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 4 0.22
21 9 0.50
ACGTcount: A:0.23, C:0.31, G:0.08, T:0.38
Consensus pattern (19 bp):
CTATCTAAGCCATTTTCCT
Found at i:55572724 original size:2 final size:2
Alignment explanation
Indices: 55572717--55572742 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
55572707 NNNNNNNNNT
55572717 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
55572743 CAGACACACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55580749 original size:9 final size:9
Alignment explanation
Indices: 55580735--55580760 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
55580725 TTCCATAAAA
55580735 TTTTCAAAG
1 TTTTCAAAG
55580744 TTTTCAAAG
1 TTTTCAAAG
55580753 TTTTCAAA
1 TTTTCAAA
55580761 TAGATTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.46
Consensus pattern (9 bp):
TTTTCAAAG
Found at i:55581215 original size:20 final size:19
Alignment explanation
Indices: 55581179--55581220 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
55581169 ATGATTTGCC
55581179 TCCTTATCTAAGACCATGTT
1 TCCTTATCTAAGACCAT-TT
55581199 TCCTCTATCTAAG-CCATTT
1 TCCT-TATCTAAGACCATTT
55581218 TCC
1 TCC
55581221 GGAGGATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.24
20 8 0.38
21 8 0.38
ACGTcount: A:0.21, C:0.31, G:0.07, T:0.40
Consensus pattern (19 bp):
TCCTTATCTAAGACCATTT
Found at i:55591345 original size:5 final size:5
Alignment explanation
Indices: 55591335--55591368 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
55591325 TTACCTTTTA
55591335 TATAT TATAT TATAT TATA- TATAT TATA- TATAT T
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT T
55591369 TTTTAGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 8 0.30
5 19 0.70
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:55591359 original size:9 final size:9
Alignment explanation
Indices: 55591333--55591368 Score: 63
Period size: 9 Copynumber: 3.9 Consensus size: 9
55591323 CATTACCTTT
55591333 TATATATTA
1 TATATATTA
55591342 TATTATATTA
1 TA-TATATTA
55591352 TATATATTA
1 TATATATTA
55591361 TATATATT
1 TATATATT
55591369 TTTTAGTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 17 0.65
10 9 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
TATATATTA
Found at i:55591469 original size:3 final size:3
Alignment explanation
Indices: 55591461--55591519 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
55591451 TGTTTTCTAA
55591461 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
55591509 ATT ATT ATT AT
1 ATT ATT ATT AT
55591520 GTTTATACTC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:55591606 original size:5 final size:5
Alignment explanation
Indices: 55591598--55591623 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
55591588 TATATGTACA
55591598 TATTT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT T
55591624 GTGTGTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:55594555 original size:29 final size:29
Alignment explanation
Indices: 55594513--55594573 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
55594503 AACAAGTAAC
55594513 AGAATTAAGTGAGTATACTAATATAGTCT
1 AGAATTAAGTGAGTATACTAATATAGTCT
55594542 AGAATTAAGTGAGTATACTAATATAGTCT
1 AGAATTAAGTGAGTATACTAATATAGTCT
55594571 AGA
1 AGA
55594574 TTTATAATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.43, C:0.07, G:0.18, T:0.33
Consensus pattern (29 bp):
AGAATTAAGTGAGTATACTAATATAGTCT
Found at i:55594588 original size:29 final size:29
Alignment explanation
Indices: 55594513--55594588 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
55594503 AACAAGTAAC
* *
55594513 AGAATTAAGTGAGTATACTAATATAGTCT
1 AGAATTAAATGAGAATACTAATATAGTCT
* *
55594542 AGAATTAAGTGAGTATACTAATATAGTCT
1 AGAATTAAATGAGAATACTAATATAGTCT
*
55594571 AGATTTATAATGA-AATAC
1 AGAATTA-AATGAGAATAC
55594589 AAAAATATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 39 0.91
30 4 0.09
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.34
Consensus pattern (29 bp):
AGAATTAAATGAGAATACTAATATAGTCT
Found at i:55595580 original size:39 final size:39
Alignment explanation
Indices: 55595526--55595601 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
55595516 TATTTTGATC
55595526 ACTTTCCCATTAATTGTCATTAGATAAGTGAGGAAAATT
1 ACTTTCCCATTAATTGTCATTAGATAAGTGAGGAAAATT
*
55595565 ACTTTCTCATTAATTGTCATTAGATAAGTGAGGAAAA
1 ACTTTCCCATTAATTGTCATTAGATAAGTGAGGAAAA
55595602 GCTAACACAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.36
Consensus pattern (39 bp):
ACTTTCCCATTAATTGTCATTAGATAAGTGAGGAAAATT
Found at i:55595686 original size:30 final size:31
Alignment explanation
Indices: 55595625--55595692 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
55595615 TGTTTTATTG
*
55595625 TTCAAATTAATCCTTATATATTAAATAAAAA
1 TTCAAATTAATCCTTAGATATTAAATAAAAA
*
55595656 TTCAATTTAATCCTT-GA-ATTAAACTAAAAA
1 TTCAAATTAATCCTTAGATATTAAA-TAAAAA
55595686 TTCAAAT
1 TTCAAAT
55595693 AAACTCAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 6 0.18
30 13 0.39
31 14 0.42
ACGTcount: A:0.49, C:0.12, G:0.01, T:0.38
Consensus pattern (31 bp):
TTCAAATTAATCCTTAGATATTAAATAAAAA
Found at i:55599596 original size:143 final size:144
Alignment explanation
Indices: 55599334--55599754 Score: 709
Period size: 143 Copynumber: 2.9 Consensus size: 144
55599324 AGTATAAAGA
* *
55599334 TTAGTATTAGATAAAGTGGAAGTGAGTTGATTAAGTCCTCCACTCATTTACCTACGTACTCTTCC
1 TTAGTGTTAGATAAAGTGGAAGTGAGTTGATTAAGTCCTCCACTCATTT---T-CCTACTCTTCC
* *
55599399 TTTTTTCTAATTAAATAAGACTGATTAGATACTTTTAAATAAAATACTTTCCTAGTCTTCCTTTT
62 TTTTTTCTAATTAAATAAGACTGACTATATACTTTTAAATAAAATACTTTCCTAGTCTTCCTTTT
55599464 TTTTTT-CCCACTTTTAT
127 TTTTTTCCCCACTTTTAT
55599481 TTAGTGTTAGATAAAGTGGAAGTGAGTTGATTAAGTCCTCCACTCATTTTCCTACTCTTCCTTTT
1 TTAGTGTTAGATAAAGTGGAAGTGAGTTGATTAAGTCCTCCACTCATTTTCCTACTCTTCCTTTT
*
55599546 TTCTAATTAAATAAGACTGACTCTATACTTTTAAATAAAATACTTTCCTAGTCTTCCTTTTTTTT
66 TTCTAATTAAATAAGACTGACTATATACTTTTAAATAAAATACTTTCCTAGTCTTCCTTTTTTTT
55599611 TTCCCCACTTTTAT
131 TTCCCCACTTTTAT
*
55599625 TTAGTGTTAGATAAAGTGGAACTGAGTTGATTAAGTCCTCCACTCATTTTCCTACTCTTCCTTTT
1 TTAGTGTTAGATAAAGTGGAAGTGAGTTGATTAAGTCCTCCACTCATTTTCCTACTCTTCC--TT
* *
55599690 TTTTCTAATTAAGTAAGACTGACTATATACTTTTAAATAAAATACTTTCCTAGCCTTCCTTTTTT
64 TTTTCTAATTAAATAAGACTGACTATATACTTTTAAATAAAATACTTTCCTAGTCTTCCTTTTTT
55599755 CCAATTTTAT
Statistics
Matches: 262, Mismatches: 9, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
143 78 0.30
144 72 0.27
146 64 0.24
147 48 0.18
ACGTcount: A:0.27, C:0.19, G:0.10, T:0.44
Consensus pattern (144 bp):
TTAGTGTTAGATAAAGTGGAAGTGAGTTGATTAAGTCCTCCACTCATTTTCCTACTCTTCCTTTT
TTCTAATTAAATAAGACTGACTATATACTTTTAAATAAAATACTTTCCTAGTCTTCCTTTTTTTT
TTCCCCACTTTTAT
Found at i:55602410 original size:20 final size:21
Alignment explanation
Indices: 55602385--55602432 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
55602375 CCAAAACTCC
55602385 GAACCTTGAA-CTCGAACCCT
1 GAACCTTGAATCTCGAACCCT
* *
55602405 GAACC-TAAATCTTGAACCCT
1 GAACCTTGAATCTCGAACCCT
*
55602425 GAATCTTG
1 GAACCTTG
55602433 CAGTTAAAGG
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
19 3 0.14
20 18 0.82
21 1 0.05
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.25
Consensus pattern (21 bp):
GAACCTTGAATCTCGAACCCT
Found at i:55606179 original size:21 final size:19
Alignment explanation
Indices: 55606155--55606193 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
55606145 ATTTGCCTCC
55606155 CTATCTAAGACCATGTTTCCT
1 CTATCTAAG-CCAT-TTTCCT
55606176 CTATCTAAGCCATTTTCC
1 CTATCTAAGCCATTTTCC
55606194 GGAGGATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 4 0.22
21 9 0.50
ACGTcount: A:0.23, C:0.31, G:0.08, T:0.38
Consensus pattern (19 bp):
CTATCTAAGCCATTTTCCT
Found at i:55612723 original size:19 final size:21
Alignment explanation
Indices: 55612694--55612747 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 21
55612684 TGTTTAATTT
55612694 TTTTAATTTAACTCGA-ATAAA
1 TTTT-ATTTAACTCGACATAAA
*
55612715 -TTTATTTAACTCGACTTAAA
1 TTTTATTTAACTCGACATAAA
*
55612735 TTTTATTTTACTC
1 TTTTATTTAACTC
55612748 AACTTGATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 11 0.38
20 7 0.24
21 11 0.38
ACGTcount: A:0.33, C:0.13, G:0.04, T:0.50
Consensus pattern (21 bp):
TTTTATTTAACTCGACATAAA
Found at i:55612741 original size:21 final size:21
Alignment explanation
Indices: 55612694--55612752 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
55612684 TGTTTAATTT
*
55612694 TTTTAATTTAACTCGA-ATAAA
1 TTTT-ATTTAACTCGACTTAAA
55612715 -TTTATTTAACTCGACTTAAA
1 TTTTATTTAACTCGACTTAAA
* *
55612735 TTTTATTTTACTCAACTT
1 TTTTATTTAACTCGACTT
55612753 GATTAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 11 0.33
20 7 0.21
21 15 0.45
ACGTcount: A:0.34, C:0.14, G:0.03, T:0.49
Consensus pattern (21 bp):
TTTTATTTAACTCGACTTAAA
Found at i:55615259 original size:153 final size:151
Alignment explanation
Indices: 55614810--55615340 Score: 636
Period size: 159 Copynumber: 3.5 Consensus size: 151
55614800 ACGTTCATTG
* * *
55614810 TTTATATTCA-TTTTTTTTGCTCCACAAGCAATCCAAAACCATAAACAAAGGAATACTTTTTTTC
1 TTTATATTCACTTTTTTTTGCTACACAAGCAAGCCAAAACCATAAACAAAGGCATACTTTTTTTC
* *
55614874 GCCTTTTTAAATGGTTTTCTTGTTTCTTT-TTCGCTTTTTAAATTCTTCATTCAATTCAAGTTCA
66 -CTTTTTTAAATGGTTTTCTTGTTTCTTTGTT-GTTTTTTAAATTCTTCATTCAATTCAAGTTCA
55614938 AGAAACCATACTAAATATATATA
129 AGAAACCATACTAAATATATATA
* * * **
55614961 TTTATATTTATATTCACTTTTCTTGCTACACAAGCAAGCCAAAATCATAAACAAAGGCACGCTTT
1 TTTATATTCA-CTT---TTTT-TTGCTACACAAGCAAGCCAAAACCATAAACAAAGGCATAC--T
* * * *
55615026 TTTTTTCCCTTTTTTTAATGATTTTCTTGATTCTTTGTTGTTTTTAAAATTCTTCATTCAATTCA
59 TTTTTT-CCTTTTTTAAATGGTTTTCTTGTTTCTTTGTTGTTTTTTAAATTCTTCATTCAATTCA
* *
55615091 AGTTCAATAAACCATATTAAATATATATA
123 AGTTCAAGAAACCATACTAAATATATATA
** *
55615120 TTTATATTCACTTTTTTTTGCTACACAAGCAAGCTGAAACCATAAACAAAGGCATACATTTTTCT
1 TTTATATTCACTTTTTTTTGCTACACAAGCAAGCCAAAACCATAAACAAAGGCATAC-TTTTTTT
* * ***
55615185 CCTTTTTTAAATGGCTTTCTTGTTTCTTTGTTGTTGTTTTTAATTCTTTGCTCAATTCAAGTTCA
65 CCTTTTTTAAATGGTTTTCTTGTTTCTTTGTTGTT-TTTTAAATTCTTCATTCAATTCAAGTTCA
* * *
55615250 AGAATCCATACTAAATATATGTG
129 AGAAACCATACTAAATATATATA
* * * ** *
55615273 TTTATATTCAC-TTTTCTTGCTACATAAGTAAGCTGAAACCATAAACAAAGGCATACTTGTTTTC
1 TTTATATTCACTTTTTTTTGCTACACAAGCAAGCCAAAACCATAAACAAAGGCATACTTTTTTTC
55615337 CTTT
66 CTTT
55615341 CTTACCGTTG
Statistics
Matches: 326, Mismatches: 43, Indels: 22
0.83 0.11 0.06
Matches are distributed among these distances:
151 19 0.06
152 73 0.22
153 61 0.19
154 35 0.11
155 4 0.01
156 4 0.01
157 34 0.10
158 2 0.01
159 91 0.28
160 3 0.01
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.44
Consensus pattern (151 bp):
TTTATATTCACTTTTTTTTGCTACACAAGCAAGCCAAAACCATAAACAAAGGCATACTTTTTTTC
CTTTTTTAAATGGTTTTCTTGTTTCTTTGTTGTTTTTTAAATTCTTCATTCAATTCAAGTTCAAG
AAACCATACTAAATATATATA
Found at i:55615322 original size:152 final size:150
Alignment explanation
Indices: 55614810--55615340 Score: 632
Period size: 153 Copynumber: 3.5 Consensus size: 150
55614800 ACGTTCATTG
* * * * *
55614810 TTTATATTCATTTTTTTTGCTCCACAAGCAATCCAAAACCATAAACAAAGGAATACTTTTTTTCG
1 TTTATATTCACTTTTCTTGCTACACAAGCAAGCCAAAACCATAAACAAAGGCATACTTTTTTTC-
* *
55614875 CCTTTTTAAATGGTTTTCTTGTTTCTTT-TTCGCTTTTTAAATTCTTCATTCAATTCAAGTTCAA
65 CTTTTTTAAATGGTTTTCTTGTTTCTTTGTT-GTTTTTTAAATTCTTCATTCAATTCAAGTTCAA
55614939 GAAACCATACTAAATATATATATTTATA
129 GAAACCATACT--A-A-ATATA--TATA
* **
55614967 TTTATATTCACTTTTCTTGCTACACAAGCAAGCCAAAATCATAAACAAAGGCACGCTTTTTTTTT
1 TTTATATTCACTTTTCTTGCTACACAAGCAAGCCAAAACCATAAACAAAGGCATAC--TTTTTTT
* * * *
55615032 CCCTTTTTTTAATGATTTTCTTGATTCTTTGTTGTTTTTAAAATTCTTCATTCAATTCAAGTTCA
64 -CCTTTTTTAAATGGTTTTCTTGTTTCTTTGTTGTTTTTTAAATTCTTCATTCAATTCAAGTTCA
* *
55615097 ATAAACCATATTAAATATATATA
128 AGAAACCATACTAAATATATATA
* ** *
55615120 TTTATATTCACTTTTTTTTGCTACACAAGCAAGCTGAAACCATAAACAAAGGCATACATTTTTCT
1 TTTATATTCAC-TTTTCTTGCTACACAAGCAAGCCAAAACCATAAACAAAGGCATAC-TTTTTTT
* * ***
55615185 CCTTTTTTAAATGGCTTTCTTGTTTCTTTGTTGTTGTTTTTAATTCTTTGCTCAATTCAAGTTCA
64 CCTTTTTTAAATGGTTTTCTTGTTTCTTTGTTGTT-TTTTAAATTCTTCATTCAATTCAAGTTCA
* * *
55615250 AGAATCCATACTAAATATATGTG
128 AGAAACCATACTAAATATATATA
* * ** *
55615273 TTTATATTCACTTTTCTTGCTACATAAGTAAGCTGAAACCATAAACAAAGGCATACTTGTTTTCC
1 TTTATATTCACTTTTCTTGCTACACAAGCAAGCCAAAACCATAAACAAAGGCATACTTTTTTTCC
55615338 TTT
66 TTT
55615341 CTTACCGTTG
Statistics
Matches: 325, Mismatches: 43, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
151 10 0.03
152 73 0.22
153 74 0.23
154 39 0.12
155 5 0.02
156 1 0.00
157 49 0.15
159 71 0.22
160 3 0.01
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.44
Consensus pattern (150 bp):
TTTATATTCACTTTTCTTGCTACACAAGCAAGCCAAAACCATAAACAAAGGCATACTTTTTTTCC
TTTTTTAAATGGTTTTCTTGTTTCTTTGTTGTTTTTTAAATTCTTCATTCAATTCAAGTTCAAGA
AACCATACTAAATATATATA
Found at i:55615546 original size:2 final size:2
Alignment explanation
Indices: 55615541--55615574 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
55615531 ACCCTACTAA
55615541 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55615575 TAAGAGAGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55615754 original size:26 final size:25
Alignment explanation
Indices: 55615705--55615754 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
55615695 TTAGTTGAGA
*
55615705 GTTTAATGAAACGATACGTTTTGAT
1 GTTTAATGAAACGATACGTATTGAT
* *
55615730 GTTTAATGAAAACGGTGCGTATTGA
1 GTTTAATG-AAACGATACGTATTGA
55615755 AAGTTTGATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (25 bp):
GTTTAATGAAACGATACGTATTGAT
Found at i:55617499 original size:18 final size:19
Alignment explanation
Indices: 55617456--55617500 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
55617446 CATCTCACAA
*
55617456 CCAAATTTCTCCGTCTTTG
1 CCAAATTTCTCCGTCATTG
*
55617475 CCTAATTTCT-CGTCATTG
1 CCAAATTTCTCCGTCATTG
*
55617493 TCAAATTT
1 CCAAATTT
55617501 TAATAGAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.20, C:0.27, G:0.09, T:0.44
Consensus pattern (19 bp):
CCAAATTTCTCCGTCATTG
Found at i:55618204 original size:37 final size:37
Alignment explanation
Indices: 55618154--55618304 Score: 194
Period size: 37 Copynumber: 4.1 Consensus size: 37
55618144 TAATTCATAG
* **
55618154 GAATATAGCTTTCTTGTTTGTATTCTCATTCGGTTAT
1 GAATATACCTTTCTTGTTTGTATTCTCATTCTATTAT
* * *
55618191 GAATATAGCTTTCTTGTTAGTATTCTCATTCTATTTT
1 GAATATACCTTTCTTGTTTGTATTCTCATTCTATTAT
* * *
55618228 GAACATACCTTTCTTGCTTGTTTTCTCATTCTATTAT
1 GAATATACCTTTCTTGTTTGTATTCTCATTCTATTAT
* *
55618265 GAATATACCTTTCTTGTTCGTATTCTCGTTCTATTGAT
1 GAATATACCTTTCTTGTTTGTATTCTCATTCTATT-AT
55618303 GA
1 GA
55618305 TTAATGTTGC
Statistics
Matches: 98, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
37 94 0.96
38 4 0.04
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.51
Consensus pattern (37 bp):
GAATATACCTTTCTTGTTTGTATTCTCATTCTATTAT
Found at i:55619264 original size:33 final size:33
Alignment explanation
Indices: 55619222--55619289 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
55619212 TCAAATGTCA
*
55619222 AGGATAGGAAGAAAAGAGATGAAGAATTAGCAG
1 AGGATAGGAAGAAAAGAGATCAAGAATTAGCAG
55619255 AGGATAGGAAGAAAAGAGATCAAGAATTAGCAG
1 AGGATAGGAAGAAAAGAGATCAAGAATTAGCAG
55619288 AG
1 AG
55619290 AAGTTGTGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.51, C:0.04, G:0.32, T:0.12
Consensus pattern (33 bp):
AGGATAGGAAGAAAAGAGATCAAGAATTAGCAG
Found at i:55620455 original size:17 final size:17
Alignment explanation
Indices: 55620433--55620467 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
55620423 CAATGACATG
55620433 GAAAAAATTGTTGAAAT
1 GAAAAAATTGTTGAAAT
55620450 GAAAAAATTGTTGAAAT
1 GAAAAAATTGTTGAAAT
55620467 G
1 G
55620468 TTATTACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.20, T:0.29
Consensus pattern (17 bp):
GAAAAAATTGTTGAAAT
Found at i:55624117 original size:20 final size:19
Alignment explanation
Indices: 55624081--55624122 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
55624071 ATGATTTGCC
55624081 TCCTTATCTAAGACCATGTT
1 TCCTTATCTAAGACCAT-TT
55624101 TCCTCTATCTAAG-CCATTT
1 TCCT-TATCTAAGACCATTT
55624120 TCC
1 TCC
55624123 GGAGGATTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.24
20 8 0.38
21 8 0.38
ACGTcount: A:0.21, C:0.31, G:0.07, T:0.40
Consensus pattern (19 bp):
TCCTTATCTAAGACCATTT
Found at i:55626226 original size:33 final size:33
Alignment explanation
Indices: 55626189--55626254 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
55626179 GTTTGCGGTG
*
55626189 ACCATTCTTATATTTATTTGTTAGCTTTGCTTT
1 ACCATTCCTATATTTATTTGTTAGCTTTGCTTT
55626222 ACCATTCCTATATTTATTTGTTAGCTTTGCTTT
1 ACCATTCCTATATTTATTTGTTAGCTTTGCTTT
55626255 CTCTTTCTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.18, C:0.17, G:0.09, T:0.56
Consensus pattern (33 bp):
ACCATTCCTATATTTATTTGTTAGCTTTGCTTT
Found at i:55652818 original size:17 final size:20
Alignment explanation
Indices: 55652779--55652819 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
55652769 TTCACTATTA
*
55652779 TGTTGTTATTGTATAACTCT
1 TGTTGTTATTGTATAAATCT
55652799 TGTT-TTATTGT-TAAAT-T
1 TGTTGTTATTGTATAAATCT
55652816 TGTT
1 TGTT
55652820 ACTATTTTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 5 0.25
18 4 0.20
19 7 0.35
20 4 0.20
ACGTcount: A:0.20, C:0.05, G:0.15, T:0.61
Consensus pattern (20 bp):
TGTTGTTATTGTATAAATCT
Found at i:55656330 original size:109 final size:109
Alignment explanation
Indices: 55656131--55656455 Score: 442
Period size: 109 Copynumber: 3.0 Consensus size: 109
55656121 ATTGAAATTC
* * * * * * *
55656131 AAAAGGATATTTGGCAATTTGGTTAAACGAG--AAATCGAAACCCAACACGTTAGGGCACG-TTC
1 AAAAGGATATTTAGCCATTTGATTGAACGAGAAAAATCGACACCCAACACCTTAGGGCACGTTTT
* * *
55656193 CTCGAATTTCCAAACGCAAAACATTGCCTTACTTTGAAATTTTT
66 CTCGAATTTCCAAACGCAAAATATTGCCTTACTTTAAAAATTTT
* *
55656237 AAAAAGG-TATTTAGTCATTTGATTGAATGAGAAAAATCGACACCCAACACCTTAGGGCACGTTT
1 -AAAAGGATATTTAGCCATTTGATTGAACGAGAAAAATCGACACCCAACACCTTAGGGCACGTTT
*
55656301 TCTCGAATTTCCAAACGCAAAATATTGCCTTATTTTAAAAATTTT
65 TCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTAAAAATTTT
* * *
55656346 AAAAGGATATTTAGCCATTTGATTGAACGAGAAAAATCGACACCTAGCACCTTAGGGCATGTTTT
1 AAAAGGATATTTAGCCATTTGATTGAACGAGAAAAATCGACACCCAACACCTTAGGGCACGTTTT
* *
55656411 CTCGAATTTCCCAAACGCAAAATATTACCTTATTTTAAAAATTTT
66 CTCGAATTT-CCAAACGCAAAATATTGCCTTACTTTAAAAATTTT
55656456 CCTTTTTTGA
Statistics
Matches: 194, Mismatches: 19, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
106 18 0.09
107 6 0.03
108 32 0.16
109 104 0.54
110 34 0.18
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (109 bp):
AAAAGGATATTTAGCCATTTGATTGAACGAGAAAAATCGACACCCAACACCTTAGGGCACGTTTT
CTCGAATTTCCAAACGCAAAATATTGCCTTACTTTAAAAATTTT
Found at i:55657209 original size:3 final size:3
Alignment explanation
Indices: 55657201--55657275 Score: 111
Period size: 3 Copynumber: 25.7 Consensus size: 3
55657191 AAGAGCAACT
55657201 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA ATGA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
*
55657249 AGA A-A A-A ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
55657276 GCTAAAAAGG
Statistics
Matches: 68, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
2 6 0.09
3 60 0.88
4 2 0.03
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:55658796 original size:22 final size:22
Alignment explanation
Indices: 55658766--55658812 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
55658756 TATATATTCC
55658766 AATT-TTTTTAAAAATTAATTAT
1 AATTATTTTTAAAAATTAATT-T
*
55658788 AATTATTTTTAAATATTAATTT
1 AATTATTTTTAAAAATTAATTT
55658810 AAT
1 AAT
55658813 AATATGACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
AATTATTTTTAAAAATTAATTT
Found at i:55659245 original size:36 final size:36
Alignment explanation
Indices: 55659204--55659284 Score: 121
Period size: 36 Copynumber: 2.3 Consensus size: 36
55659194 ATTTCCTTAG
*
55659204 TTTTCCCCAAGTCAGAATCAGA-TTTCCTCGATTTCA
1 TTTTCCCCAAGTCAAAATCAGATTTTCC-CGATTTCA
*
55659240 TTTTCCCTAAGTCAAAATCAGATTTTCCCGATTTCA
1 TTTTCCCCAAGTCAAAATCAGATTTTCCCGATTTCA
55659276 -TTTCCCCAA
1 TTTTCCCCAA
55659285 TTTCCCAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
35 8 0.20
36 28 0.68
37 5 0.12
ACGTcount: A:0.26, C:0.28, G:0.09, T:0.37
Consensus pattern (36 bp):
TTTTCCCCAAGTCAAAATCAGATTTTCCCGATTTCA
Found at i:55659310 original size:22 final size:22
Alignment explanation
Indices: 55659261--55659310 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
55659251 TCAAAATCAG
*
55659261 ATTTTCCCGATTTCATTTCCCC
1 ATTTTCCCAATTTCATTTCCCC
*
55659283 AATTTCCCAATTTC-TTTCCGCC
1 ATTTTCCCAATTTCATTTCC-CC
*
55659305 GTTTTC
1 ATTTTC
55659311 TTCACATCTG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.14, C:0.34, G:0.06, T:0.46
Consensus pattern (22 bp):
ATTTTCCCAATTTCATTTCCCC
Found at i:55661754 original size:23 final size:23
Alignment explanation
Indices: 55661723--55661769 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
55661713 GAGGAAATCT
*
55661723 GATTTTGACTTGGGGAAAACTAA
1 GATTCTGACTTGGGGAAAACTAA
55661746 GATTCTGACTTGGGGAAAACTAA
1 GATTCTGACTTGGGGAAAACTAA
55661769 G
1 G
55661770 GAAATTTGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.34, C:0.11, G:0.28, T:0.28
Consensus pattern (23 bp):
GATTCTGACTTGGGGAAAACTAA
Found at i:55662123 original size:15 final size:15
Alignment explanation
Indices: 55662103--55662132 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
55662093 CTCAGTTTAC
*
55662103 TTTTAAATAAAAAAA
1 TTTTAAACAAAAAAA
55662118 TTTTAAACAAAAAAA
1 TTTTAAACAAAAAAA
55662133 CATTACTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
TTTTAAACAAAAAAA
Found at i:55663008 original size:18 final size:18
Alignment explanation
Indices: 55662948--55663016 Score: 54
Period size: 18 Copynumber: 3.9 Consensus size: 18
55662938 ACGACCGTTT
* *
55662948 ACGATACTATTTACGTAT
1 ACGATACTATTTACATAC
*
55662966 ACGATA-T-TGTT-CATCC
1 ACGATACTAT-TTACATAC
* *
55662982 ACGACACTATTTACATAG
1 ACGATACTATTTACATAC
*
55663000 ACGATACTATTCACATA
1 ACGATACTATTTACATA
55663017 TACAGTAGTT
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
16 8 0.21
17 6 0.15
18 25 0.64
ACGTcount: A:0.35, C:0.22, G:0.10, T:0.33
Consensus pattern (18 bp):
ACGATACTATTTACATAC
Found at i:55672046 original size:22 final size:23
Alignment explanation
Indices: 55672004--55672046 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
55671994 TTTCCAAAAT
*
55672004 TTTTAAAAAATTAATTATAATTA
1 TTTTAAAAAATCAATTATAATTA
*
55672027 TTTTAAAATATCAATT-TAAT
1 TTTTAAAAAATCAATTATAAT
55672047 AATATGATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TTTTAAAAAATCAATTATAATTA
Found at i:55672481 original size:143 final size:143
Alignment explanation
Indices: 55672210--55672482 Score: 467
Period size: 143 Copynumber: 1.9 Consensus size: 143
55672200 AGTATAAAGA
*
55672210 TTAGTATTAGATAAAGTGGAAGTGAGTTGATTAAGTCCTCCATTCATTTACCTACTCTTCCTTTT
1 TTAGTATTAGATAAAGTGGAAGTGAGTTGATTAAGTCCTCCACTCATTTACCTACTCTTCCTTTT
55672275 TTCTAATTAAATAAGACTGACTATATACTTTTAAATAAAATACTTTCCTAGGTCTTCCTTTTTTT
66 TTCTAATTAAATAAGACTGACTATATACTTTTAAATAAAATACTTTCCTAGGTCTTCCTTTTTTT
55672340 TTCCCACTTTTAT
131 TTCCCACTTTTAT
* *
55672353 TTAGTGTTAGATAAAGTGGAAGTGAGTTGATTAAGTCCTCCACTCATTTTCCTACTCTTCCTTTT
1 TTAGTATTAGATAAAGTGGAAGTGAGTTGATTAAGTCCTCCACTCATTTACCTACTCTTCC--TT
* * *
55672418 TTTTCTAATTAAGTAAGACTGACTATATACTTTTAAATAGAATACTTTCGTA-GTCTTCCTTTTT
64 TTTTCTAATTAAATAAGACTGACTATATACTTTTAAATAAAATACTTTCCTAGGTCTTCCTTTTT
55672482 T
129 T
55672483 CCAATTTTAT
Statistics
Matches: 122, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
143 58 0.48
144 13 0.11
145 51 0.42
ACGTcount: A:0.27, C:0.17, G:0.11, T:0.45
Consensus pattern (143 bp):
TTAGTATTAGATAAAGTGGAAGTGAGTTGATTAAGTCCTCCACTCATTTACCTACTCTTCCTTTT
TTCTAATTAAATAAGACTGACTATATACTTTTAAATAAAATACTTTCCTAGGTCTTCCTTTTTTT
TTCCCACTTTTAT
Found at i:55674922 original size:22 final size:22
Alignment explanation
Indices: 55674881--55674922 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
55674871 TTCCCAAAAT
*
55674881 TTTTAAAAATTAATTATAATTA
1 TTTTAAAAATCAATTATAATTA
55674903 TTTTAAAATATCAATT-TAAT
1 TTTTAAAA-ATCAATTATAAT
55674923 AATATGATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTTAAAAATCAATTATAATTA
Found at i:55682329 original size:21 final size:19
Alignment explanation
Indices: 55682305--55682343 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
55682295 ATTTGCCTCC
55682305 CTATCTAAGACCATGTTTCCT
1 CTATCTAAG-CCAT-TTTCCT
55682326 CTATCTAAGCCATTTTCC
1 CTATCTAAGCCATTTTCC
55682344 AGAGGATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 4 0.22
21 9 0.50
ACGTcount: A:0.23, C:0.31, G:0.08, T:0.38
Consensus pattern (19 bp):
CTATCTAAGCCATTTTCCT
Found at i:55687752 original size:22 final size:22
Alignment explanation
Indices: 55687727--55687803 Score: 68
Period size: 22 Copynumber: 3.4 Consensus size: 22
55687717 CCAAAATATT
55687727 ATCTCCTAAACTTTAGCATCTA
1 ATCTCCTAAACTTTAGCATCTA
* * * *
55687749 ATCTCCT-AA-TTAAACCAAAATATT
1 ATCTCCTAAACTT-TAGC---ATCTA
55687773 ATCTCCTAAACTTTAGCATCTA
1 ATCTCCTAAACTTTAGCATCTA
55687795 ATCTCCTAA
1 ATCTCCTAA
55687804 TTAAAAGAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
20 2 0.05
21 4 0.10
22 19 0.46
24 10 0.24
25 4 0.10
26 2 0.05
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (22 bp):
ATCTCCTAAACTTTAGCATCTA
Found at i:55687766 original size:46 final size:46
Alignment explanation
Indices: 55687714--55687808 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
55687704 ACAAAGATAG
55687714 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
55687760 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
55687806 AAA
1 AAA
55687809 AGAAAATAGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.41, C:0.23, G:0.02, T:0.34
Consensus pattern (46 bp):
AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
Found at i:55689142 original size:29 final size:28
Alignment explanation
Indices: 55689109--55689170 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 28
55689099 AAAGCCGTTT
55689109 TTTTTTCAAAATTTACCGAAATGGGCCAA
1 TTTTTTCAAAATTTACCGAAATGGGCC-A
* ** * *
55689138 TTTTTTGATTATTTACCGGAATGGTCCA
1 TTTTTTCAAAATTTACCGAAATGGGCCA
55689166 TTTTT
1 TTTTT
55689171 CGGAAAATCG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 6 0.21
29 22 0.79
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.45
Consensus pattern (28 bp):
TTTTTTCAAAATTTACCGAAATGGGCCA
Found at i:55689904 original size:7 final size:7
Alignment explanation
Indices: 55689892--55689916 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
55689882 AGTCGATTGA
55689892 TATTTAG
1 TATTTAG
55689899 TATTTAG
1 TATTTAG
55689906 TATTTAG
1 TATTTAG
55689913 TATT
1 TATT
55689917 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:55691033 original size:25 final size:25
Alignment explanation
Indices: 55691004--55691114 Score: 83
Period size: 25 Copynumber: 4.6 Consensus size: 25
55690994 TTTAAATTTA
55691004 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
** *
55691029 TTATTTGATGTAATACGCATAGAAAT
1 TTATTTGATGTAATA-AAATAGAAGT
** *
55691055 TT-TTTCGA-GT--T-ATTTTG-A-T
1 TTATTT-GATGTAATAAAATAGAAGT
55691074 ATTATTTGATGTAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATAGAAGT
*
55691100 TTATTTGATATAATA
1 TTATTTGATGTAATA
55691115 GGCATAGAAA
Statistics
Matches: 65, Mismatches: 11, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
19 1 0.02
20 5 0.08
21 7 0.11
23 2 0.03
24 3 0.05
25 35 0.54
26 12 0.18
ACGTcount: A:0.38, C:0.03, G:0.14, T:0.45
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:55691090 original size:71 final size:71
Alignment explanation
Indices: 55691002--55691186 Score: 316
Period size: 71 Copynumber: 2.6 Consensus size: 71
55690992 TATTTAAATT
*
55691002 TATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATACGCATAGAAATTTTTTCGAGTTA
1 TATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATACGCATAGAAATTTTTTCGAGCTA
55691067 TTTTGA
66 TTTTGA
* * *
55691073 TATTATTTGATGTAATAAAATAGAAGTTTATTTGATATAATAGGCATAGAAATTTTTTCTAGCTA
1 TATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATACGCATAGAAATTTTTTCGAGCTA
55691138 TTTTGA
66 TTTTGA
*
55691144 TATTATTTGATATAATAAAATAGAAGTTCTATTTGATGTAATA
1 TATTATTTGATGTAATAAAATAGAAGTT-TATTTGATGTAATA
55691187 AAAACCCTAA
Statistics
Matches: 107, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
71 94 0.88
72 13 0.12
ACGTcount: A:0.37, C:0.04, G:0.14, T:0.45
Consensus pattern (71 bp):
TATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATACGCATAGAAATTTTTTCGAGCTA
TTTTGA
Found at i:55691208 original size:18 final size:18
Alignment explanation
Indices: 55691185--55691237 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 18
55691175 TTTGATGTAA
55691185 TAAAAACCCTAATTTAAT
1 TAAAAACCCTAATTTAAT
55691203 TAAAAACCCTAACCTAATTTAAT
1 TAAAAA--C---CCTAATTTAAT
55691226 TAAAAACCCTAA
1 TAAAAACCCTAA
55691238 CCCTAACCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
18 11 0.37
20 1 0.03
21 1 0.03
23 17 0.57
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.28
Consensus pattern (18 bp):
TAAAAACCCTAATTTAAT
Found at i:55691218 original size:23 final size:23
Alignment explanation
Indices: 55691192--55691239 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
55691182 TAATAAAAAC
55691192 CCTAATTTAATTAAAAACCCTAA
1 CCTAATTTAATTAAAAACCCTAA
55691215 CCTAATTTAATTAAAAACCCTAA
1 CCTAATTTAATTAAAAACCCTAA
55691238 CC
1 CC
55691240 CTAACCTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.29
Consensus pattern (23 bp):
CCTAATTTAATTAAAAACCCTAA
Found at i:55691240 original size:29 final size:29
Alignment explanation
Indices: 55691207--55691482 Score: 419
Period size: 29 Copynumber: 9.6 Consensus size: 29
55691197 TTTAATTAAA
55691207 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
* *
55691236 AACCCTAACCTAATTCAAATAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
* * *
55691265 AACCCTAACCTACTTCAAATAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
55691294 AACCATAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
* *
55691323 AACCCTAACCTAACTTAATTAAAACCCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
* *
55691352 AACCCTAACCTAATTCAAATAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
55691381 AA-CCTAACCTAACTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
* *
55691409 AACCCTAACCTAATTCAAATAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
55691438 AACTCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
55691467 AACCCTAACCTAATTT
1 AACCCTAACCTAATTT
55691483 TACATAATTT
Statistics
Matches: 222, Mismatches: 24, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
28 25 0.11
29 197 0.89
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.25
Consensus pattern (29 bp):
AACCCTAACCTAATTTAATTAAAAACCCT
Found at i:55691543 original size:55 final size:56
Alignment explanation
Indices: 55691477--55691715 Score: 394
Period size: 55 Copynumber: 4.3 Consensus size: 56
55691467 AACCCTAACC
*
55691477 TAATTTTACATAATTTGATAATTTTACTAGCCATTAACACAA-TTTTTGGACTTAA
1 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTTGGACTTAA
55691532 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAA-TTTTTGGACTTAA
1 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTTGGACTTAA
* ** *
55691587 TAATTTTACATAATTTGATAATTTTACTAACCATTAACAAAATTTTTTATACCATAA
1 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTTGGA-CTTAA
55691644 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTTTGG-CTTAA
1 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAA-TTTTTTGGACTTAA
55691700 TAATTTTACATAATTT
1 TAATTTTACATAATTT
55691716 TACATAATTT
Statistics
Matches: 172, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
55 95 0.55
56 26 0.15
57 45 0.26
58 6 0.03
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (56 bp):
TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTTGGACTTAA
Found at i:55691685 original size:112 final size:110
Alignment explanation
Indices: 55691477--55691715 Score: 390
Period size: 112 Copynumber: 2.1 Consensus size: 110
55691467 AACCCTAACC
* * * *
55691477 TAATTTTACATAATTTGATAATTTTACTAGCCATTAACACAATTTTTGGACTTAATAATTTTACA
1 TAATTTTACATAATTTGATAATTTTACTAACCATTAACAAAATTTTTAGACATAATAATTTTACA
55691542 TAATTTGATAATTTTACTAACCATTAACACAA-TTTTTGGACTTAA
66 TAATTTGATAATTTTACTAACCATTAACACAATTTTTTGG-CTTAA
*
55691587 TAATTTTACATAATTTGATAATTTTACTAACCATTAACAAAATTTTTTATACCATAATAATTTTA
1 TAATTTTACATAATTTGATAATTTTACTAACCATTAACAAAA-TTTTTAGA-CATAATAATTTTA
55691652 CATAATTTGATAATTTTACTAACCATTAACACAATTTTTTTGGCTTAA
64 CATAATTTGATAATTTTACTAACCATTAACACAA-TTTTTTGGCTTAA
55691700 TAATTTTACATAATTT
1 TAATTTTACATAATTT
55691716 TACATAATTT
Statistics
Matches: 120, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
110 40 0.33
111 6 0.05
112 46 0.38
113 21 0.17
114 7 0.06
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (110 bp):
TAATTTTACATAATTTGATAATTTTACTAACCATTAACAAAATTTTTAGACATAATAATTTTACA
TAATTTGATAATTTTACTAACCATTAACACAATTTTTTGGCTTAA
Found at i:55691714 original size:10 final size:10
Alignment explanation
Indices: 55691699--55691725 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
55691689 TTTTGGCTTA
55691699 ATAATTTTAC
1 ATAATTTTAC
55691709 ATAATTTTAC
1 ATAATTTTAC
55691719 ATAATTT
1 ATAATTT
55691726 GATAATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (10 bp):
ATAATTTTAC
Found at i:55691715 original size:66 final size:66
Alignment explanation
Indices: 55691643--55691789 Score: 260
Period size: 66 Copynumber: 2.2 Consensus size: 66
55691633 TTATACCATA
55691643 ATAATTTTACATAATTTGATAATTTTACTAACCATTAACACA-ATTTTTTTGGCTTAATAATTTT
1 ATAATTTTACATAATTTGATAATTTTACTAACCATTAACA-ATATTTTTTTGGCTTAATAATTTT
55691707 AC
65 AC
* *
55691709 ATAATTTTACATAATTTGATAATTTTATTAACCATTAACAATATTTTTTTGGCTTAATAGTTTTA
1 ATAATTTTACATAATTTGATAATTTTACTAACCATTAACAATATTTTTTTGGCTTAATAATTTTA
55691774 C
66 C
55691775 ATAATTTTACATAAT
1 ATAATTTTACATAAT
55691790 GTTAGATTTG
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
65 1 0.01
66 77 0.99
ACGTcount: A:0.37, C:0.10, G:0.05, T:0.48
Consensus pattern (66 bp):
ATAATTTTACATAATTTGATAATTTTACTAACCATTAACAATATTTTTTTGGCTTAATAATTTTA
C
Found at i:55695124 original size:124 final size:124
Alignment explanation
Indices: 55694901--55695248 Score: 567
Period size: 124 Copynumber: 2.8 Consensus size: 124
55694891 CCAAACTTGT
* *
55694901 TACTGTAGCAAAATCGCGTCCACGAGGGTGCGATTTCACAATTTCTTCTCAAATAGCATCCTGGT
1 TACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTTAAATAGCATCCTGGT
*
55694966 AGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACC
66 AGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATAACC
* * * * *
55695025 TATTGTAGCAAAATCCCGTCCACGAGGGCCCGATTTCATAATTTCTTCTTAAATAGCATCTTGGT
1 TACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTTAAATAGCATCCTGGT
*
55695090 ACAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATAACC
66 AGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATAACC
*
55695149 TACTGTAGCAGAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTT-TTCAAATAGCATCCTGG
1 TACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTT-AAATAGCATCCTGG
55695213 TAGAAGCGATTTTATACTATTTGAC-CAGAAA-GTCAA
65 TAGAAGCGATTTTATACTATTTG-CTCAGAAACGTCAA
55695249 CTCGAAATAA
Statistics
Matches: 206, Mismatches: 16, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
123 7 0.03
124 198 0.96
125 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (124 bp):
TACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTTAAATAGCATCCTGGT
AGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATAACC
Found at i:55696420 original size:39 final size:39
Alignment explanation
Indices: 55696302--55696437 Score: 143
Period size: 39 Copynumber: 3.4 Consensus size: 39
55696292 TTTAAGAATT
*
55696302 TCAAATAATATTATTAATTTAATATATACATTCTTCATA
1 TCAAATAATATTATTAATTTAATATATACAATCTTCATA
* * * *
55696341 TTAAATTTAATATGTATT-TTTTTATA-ATTAAAAATCTTCATA
1 TCAAA--TAATAT-TATTAATTTAATATA-T-ACAATCTTCATA
55696383 TCAAATAATATTATTAATTTAATATATACAATCTTCATA
1 TCAAATAATATTATTAATTTAATATATACAATCTTCATA
* *
55696422 TTAAAT-ATATAATTAA
1 TCAAATAATATTATTAA
55696438 AAACCTAATT
Statistics
Matches: 79, Mismatches: 11, Indels: 15
0.75 0.10 0.14
Matches are distributed among these distances:
38 9 0.11
39 24 0.30
40 14 0.18
41 14 0.18
42 18 0.23
ACGTcount: A:0.45, C:0.07, G:0.01, T:0.47
Consensus pattern (39 bp):
TCAAATAATATTATTAATTTAATATATACAATCTTCATA
Found at i:55699211 original size:37 final size:37
Alignment explanation
Indices: 55699161--55699274 Score: 156
Period size: 37 Copynumber: 3.1 Consensus size: 37
55699151 TAGTTCATAG
* * *
55699161 GAATATAGCTTTCTTGTTTGTATTCTCATTCGATTAT
1 GAATATACCTTTCTTGTTTGTTTTCTCATTCTATTAT
* *
55699198 GAATATACCTTTCTTGTTAGTTTTCTCATTCTATTTT
1 GAATATACCTTTCTTGTTTGTTTTCTCATTCTATTAT
* *
55699235 GAACATACCTTTCTTGCTTGTTTTCTCATTCTATTGAT
1 GAATATACCTTTCTTGTTTGTTTTCTCATTCTATT-AT
55699273 GA
1 GA
55699275 TTAATGCTGC
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
37 64 0.96
38 3 0.04
ACGTcount: A:0.20, C:0.17, G:0.11, T:0.52
Consensus pattern (37 bp):
GAATATACCTTTCTTGTTTGTTTTCTCATTCTATTAT
Found at i:55700774 original size:17 final size:18
Alignment explanation
Indices: 55700743--55700776 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
55700733 ATTTTAACTT
55700743 TAATTAAATTATTTAAAA
1 TAATTAAATTATTTAAAA
*
55700761 TAATT-AATTTTTTAAA
1 TAATTAAATTATTTAAA
55700777 TTATAAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATTAAATTATTTAAAA
Found at i:55700973 original size:20 final size:20
Alignment explanation
Indices: 55700948--55700998 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
55700938 CCCAAAACCC
*
55700948 CGAACCCCGAACCTTGAAC-T
1 CGAACCCCGAA-CTTAAACTT
*
55700968 CGAACCCTGAACTTAAACTT
1 CGAACCCCGAACTTAAACTT
*
55700988 TGAACCCCGAA
1 CGAACCCCGAA
55700999 TCTCGCAGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 6 0.23
20 20 0.77
ACGTcount: A:0.33, C:0.35, G:0.14, T:0.18
Consensus pattern (20 bp):
CGAACCCCGAACTTAAACTT
Found at i:55702377 original size:21 final size:19
Alignment explanation
Indices: 55702353--55702391 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
55702343 ATTTGCCTCC
55702353 CTATCTAAGACCATGTTTCCT
1 CTATCTAAG-CCAT-TTTCCT
55702374 CTATCTAAGCCATTTTCC
1 CTATCTAAGCCATTTTCC
55702392 GGAGGATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 4 0.22
21 9 0.50
ACGTcount: A:0.23, C:0.31, G:0.08, T:0.38
Consensus pattern (19 bp):
CTATCTAAGCCATTTTCCT
Found at i:55705980 original size:15 final size:15
Alignment explanation
Indices: 55705960--55705989 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
55705950 CAGTATGATA
55705960 AGAAATTAAATTAAG
1 AGAAATTAAATTAAG
55705975 AGAAATTAAATTAAG
1 AGAAATTAAATTAAG
55705990 GATTTTCTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.13, T:0.27
Consensus pattern (15 bp):
AGAAATTAAATTAAG
Found at i:55713190 original size:21 final size:21
Alignment explanation
Indices: 55713166--55713206 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
55713156 GAGATTTAGG
*
55713166 GTTTAAGGTTAAGGGTTTATA
1 GTTTAAGGTTAAGGATTTATA
* *
55713187 GTTTAGGGTTTAGGATTTAT
1 GTTTAAGGTTAAGGATTTAT
55713207 GATTAATTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.46
Consensus pattern (21 bp):
GTTTAAGGTTAAGGATTTATA
Found at i:55713376 original size:15 final size:16
Alignment explanation
Indices: 55713344--55713382 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
55713334 GATATTCTAG
55713344 ATTAATATAAATGAAA
1 ATTAATATAAATGAAA
55713360 A-TAATATAAAT-ATAA
1 ATTAATATAAATGA-AA
55713375 ATTAATAT
1 ATTAATAT
55713383 TTTAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 1 0.05
15 13 0.62
16 7 0.33
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
ATTAATATAAATGAAA
Found at i:55714087 original size:17 final size:19
Alignment explanation
Indices: 55714067--55714109 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 19
55714057 CTGTCATCTC
55714067 CCCCAAATCCCTAA-A-TT
1 CCCCAAATCCCTAACAGTT
*
55714084 CCCCTAATCCCTAACAGTT
1 CCCCAAATCCCTAACAGTT
55714103 CCCCAAA
1 CCCCAAA
55714110 CCCGACGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 13 0.59
18 1 0.05
19 8 0.36
ACGTcount: A:0.33, C:0.44, G:0.02, T:0.21
Consensus pattern (19 bp):
CCCCAAATCCCTAACAGTT
Found at i:55715386 original size:17 final size:17
Alignment explanation
Indices: 55715360--55715397 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
55715350 CGTTATTACT
55715360 TTTTCAAAGT-TTTAATA
1 TTTTCAAAGTATTTAA-A
*
55715377 TTTTCTAAGTATTTAAA
1 TTTTCAAAGTATTTAAA
55715394 TTTT
1 TTTT
55715398 TCAGTAACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (17 bp):
TTTTCAAAGTATTTAAA
Found at i:55716955 original size:144 final size:144
Alignment explanation
Indices: 55716695--55716984 Score: 580
Period size: 144 Copynumber: 2.0 Consensus size: 144
55716685 TAAAATTTCT
55716695 TAACTTTTGTAAATGGTATTAACTTGCTTAATATAAATTAAACTTATATAATATTAAGATCAAAT
1 TAACTTTTGTAAATGGTATTAACTTGCTTAATATAAATTAAACTTATATAATATTAAGATCAAAT
55716760 TTCAAGACTTGCAAAATCTTTGGATCAGATTTCATAATTTATGTATTTTATGTAACTTACATAAT
66 TTCAAGACTTGCAAAATCTTTGGATCAGATTTCATAATTTATGTATTTTATGTAACTTACATAAT
55716825 ATATAACATGCATA
131 ATATAACATGCATA
55716839 TAACTTTTGTAAATGGTATTAACTTGCTTAATATAAATTAAACTTATATAATATTAAGATCAAAT
1 TAACTTTTGTAAATGGTATTAACTTGCTTAATATAAATTAAACTTATATAATATTAAGATCAAAT
55716904 TTCAAGACTTGCAAAATCTTTGGATCAGATTTCATAATTTATGTATTTTATGTAACTTACATAAT
66 TTCAAGACTTGCAAAATCTTTGGATCAGATTTCATAATTTATGTATTTTATGTAACTTACATAAT
55716969 ATATAACATGCATA
131 ATATAACATGCATA
55716983 TA
1 TA
55716985 GCTTAAGTAA
Statistics
Matches: 146, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
144 146 1.00
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.41
Consensus pattern (144 bp):
TAACTTTTGTAAATGGTATTAACTTGCTTAATATAAATTAAACTTATATAATATTAAGATCAAAT
TTCAAGACTTGCAAAATCTTTGGATCAGATTTCATAATTTATGTATTTTATGTAACTTACATAAT
ATATAACATGCATA
Found at i:55717131 original size:20 final size:20
Alignment explanation
Indices: 55717103--55717154 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
55717093 TGGAAATAAA
* *
55717103 ATAAAATTAATATAACTTAT
1 ATAATATTAAGATAACTTAT
*
55717123 ATAATATTAAGATTACTTAT
1 ATAATATTAAGATAACTTAT
*
55717143 ATAGTATTAAGA
1 ATAATATTAAGA
55717155 CAAAATTTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.40
Consensus pattern (20 bp):
ATAATATTAAGATAACTTAT
Found at i:55717181 original size:9 final size:9
Alignment explanation
Indices: 55717167--55717405 Score: 175
Period size: 9 Copynumber: 27.9 Consensus size: 9
55717157 AAATTTCTAA
55717167 TTACATAAC
1 TTACATAAC
*
55717176 TTACATAAA
1 TTACATAAC
*
55717185 TTAAATAAC
1 TTACATAAC
55717194 TTACATAAC
1 TTACATAAC
*
55717203 TTACATAAA
1 TTACATAAC
*
55717212 TTAAATAAC
1 TTACATAAC
55717221 TTACATAAC
1 TTACATAAC
*
55717230 TTACATAAA
1 TTACATAAC
*
55717239 TTAAATAAC
1 TTACATAAC
*
55717248 TTTCATAAC
1 TTACATAAC
*
55717257 TTACATTA-
1 TTACATAAC
55717265 -TACATAACC
1 TTACATAA-C
*
55717274 TT-CTTAAC
1 TTACATAAC
*
55717282 TTACATTA-
1 TTACATAAC
**
55717290 -TACACGAC
1 TTACATAAC
*
55717298 TCACATAA-
1 TTACATAAC
*
55717306 TTA-AT-AT
1 TTACATAAC
*
55717313 TATACACAAC
1 T-TACATAAC
*
55717323 TTTCATAA-
1 TTACATAAC
*
55717331 -TACATTAC
1 TTACATAAC
55717339 TTACATAAC
1 TTACATAAC
* *
55717348 GTACATTAC
1 TTACATAAC
55717357 TTACAGT-AC
1 TTACA-TAAC
55717366 TTACATAA-
1 TTACATAAC
55717374 -TACATAA-
1 TTACATAAC
55717381 -TACATAAC
1 TTACATAAC
55717389 TTACATAAC
1 TTACATAAC
55717398 TTACATAA
1 TTACATAA
55717406 TAAATAAAAA
Statistics
Matches: 179, Mismatches: 35, Indels: 32
0.73 0.14 0.13
Matches are distributed among these distances:
6 1 0.01
7 33 0.18
8 8 0.04
9 133 0.74
10 4 0.02
ACGTcount: A:0.45, C:0.19, G:0.01, T:0.35
Consensus pattern (9 bp):
TTACATAAC
Found at i:55717391 original size:32 final size:33
Alignment explanation
Indices: 55717340--55717412 Score: 96
Period size: 32 Copynumber: 2.2 Consensus size: 33
55717330 ATACATTACT
*
55717340 TACATAACGTACATTACTTACAGT-ACTTACATAA
1 TACATAAC-TACATAACTTACA-TAACTTACATAA
55717374 TACATAA-TACATAACTTACATAACTTACATAA
1 TACATAACTACATAACTTACATAACTTACATAA
*
55717406 TAAATAA
1 TACATAA
55717413 AAATATATCA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
31 1 0.03
32 28 0.78
34 7 0.19
ACGTcount: A:0.48, C:0.18, G:0.03, T:0.32
Consensus pattern (33 bp):
TACATAACTACATAACTTACATAACTTACATAA
Found at i:55722431 original size:21 final size:21
Alignment explanation
Indices: 55722395--55722465 Score: 106
Period size: 21 Copynumber: 3.4 Consensus size: 21
55722385 CTACAACTTA
*
55722395 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* *
55722416 AAGTAGCGGCTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
*
55722437 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGGG
55722458 AAGCAGAG
1 AAGCAGAG
55722466 CAGAGCAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.31, C:0.18, G:0.46, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:55722857 original size:42 final size:42
Alignment explanation
Indices: 55722787--55723068 Score: 377
Period size: 42 Copynumber: 6.7 Consensus size: 42
55722777 GTATAAAAGT
** *
55722787 GCCGCTAAAGATAATGTTCTTTTA-CGGCGCTTACAAAAAAAC
1 GCCGCTAAAGACCATGTTC-TTTAGCGGCGCTTAGAAAAAAAC
* * * *
55722829 ACCGTTAAAGACCATGTTCTTCAGCGGCGCTTAGAAAGAAAC
1 GCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAAC
* * * *
55722871 GCCGCTAAAGACAATGTTCTTTAGAGGCACTTAGAAAGAAAC
1 GCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAAC
55722913 GCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAAC
1 GCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAAC
*
55722955 GCCGCTAAAGACCATGTTCTTTAGCAGCGCTTAGAAAATAAAC
1 GCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAA-AAAC
* ** *
55722998 GCCGCTAAAGAGCATGTTCTTTAGCGGCGCTTAGAAAGGAAT
1 GCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAAC
* *
55723040 GCCGCCAAAGACCATGTTCTTTAGAGGCG
1 GCCGCTAAAGACCATGTTCTTTAGCGGCG
55723069 TTTTTTTTAA
Statistics
Matches: 212, Mismatches: 26, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
41 3 0.01
42 170 0.80
43 39 0.18
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.23
Consensus pattern (42 bp):
GCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAAC
Found at i:55723125 original size:127 final size:127
Alignment explanation
Indices: 55722812--55723105 Score: 333
Period size: 126 Copynumber: 2.3 Consensus size: 127
55722802 GTTCTTTTAC
* * * * * * * * *
55722812 GGCGCTTACAAAAAAACACCGTTAAAGACCATGTTCTTCAGCGGCGCTTAG-AAAGAAACGCCGC
1 GGCGCTTAGAAAAAAACGCCGCTAAAAAACATGGTCTTTAGCAGCGCTTAGAAAATAAACGCCGC
* *
55722876 TAAAGACAATGTTCTTTAGAGGCACTTAGAAAGAAACGCCGCTAAAGACCATGTTCTTTAGC
66 TAAAGACAATGTTCTTTAGAGGCACTTAGAAAGAAACGCCGCCAAAGACCATGTTCTTTAGA
* * *
55722938 GGCGCTTAGAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCAGCGCTTAGAAAATAAACGCCGC
1 GGCGCTTAGAAAAAAACGCCGCTAAAAAACATGGTCTTTAGCAGCGCTTAGAAAATAAACGCCGC
* * * *
55723003 TAAAGAGC-ATGTTCTTTAGCGGCGCTTAGAAAGGAATGCCGCCAAAGACCATGTTCTTTAGA
66 TAAAGA-CAATGTTCTTTAGAGGCACTTAGAAAGAAACGCCGCCAAAGACCATGTTCTTTAGA
****** *
55723065 GGCG-TTTTTTTTAAGCGCCGCTAAAAAACATGGTCTTTAGC
1 GGCGCTTAGAAAAAAACGCCGCTAAAAAACATGGTCTTTAGC
55723106 GGCGTTTCTG
Statistics
Matches: 144, Mismatches: 22, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
126 73 0.51
127 70 0.49
128 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.23
Consensus pattern (127 bp):
GGCGCTTAGAAAAAAACGCCGCTAAAAAACATGGTCTTTAGCAGCGCTTAGAAAATAAACGCCGC
TAAAGACAATGTTCTTTAGAGGCACTTAGAAAGAAACGCCGCCAAAGACCATGTTCTTTAGA
Found at i:55724472 original size:21 final size:20
Alignment explanation
Indices: 55724430--55724483 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 20
55724420 AATTTTTTGA
55724430 ATTTAACTCGAA--TAAATTT
1 ATTTAACTC-AACTTAAATTT
55724449 ATTTAACTCAACTTAAATTTT
1 ATTTAACTCAACTTAAA-TTT
*
55724470 ATTTCACTCAACTT
1 ATTTAACTCAACTT
55724484 GATTAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 2 0.06
19 9 0.29
20 4 0.13
21 16 0.52
ACGTcount: A:0.37, C:0.17, G:0.02, T:0.44
Consensus pattern (20 bp):
ATTTAACTCAACTTAAATTT
Found at i:55726282 original size:2 final size:2
Alignment explanation
Indices: 55726277--55726310 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
55726267 ACCATACTAA
55726277 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55726311 GTTTATATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55726865 original size:2 final size:2
Alignment explanation
Indices: 55726858--55726899 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
55726848 CAAAAACCCT
55726858 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
55726900 ATAGAGNNNN
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55728809 original size:19 final size:18
Alignment explanation
Indices: 55728787--55728822 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
55728777 TTAGTAAAAA
*
55728787 AAAAGTTAAAACTTAAATT
1 AAAACTTAAAAC-TAAATT
55728806 AAAACTTAAAACTAAAT
1 AAAACTTAAAACTAAAT
55728823 GTTAGTAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.61, C:0.08, G:0.03, T:0.28
Consensus pattern (18 bp):
AAAACTTAAAACTAAATT
Found at i:55728866 original size:8 final size:7
Alignment explanation
Indices: 55728845--55728888 Score: 52
Period size: 7 Copynumber: 5.9 Consensus size: 7
55728835 CATTTAAAAA
55728845 TAATTTT
1 TAATTTT
55728852 TAATTTT
1 TAATTTT
55728859 TAATTTT
1 TAATTTT
55728866 TAATATAATT
1 TAAT-T--TT
*
55728876 TAATATT
1 TAATTTT
55728883 TAATTT
1 TAATTT
55728889 AAGCCTATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
7 25 0.78
8 1 0.03
10 6 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
TAATTTT
Found at i:55730179 original size:42 final size:42
Alignment explanation
Indices: 55730074--55730368 Score: 360
Period size: 42 Copynumber: 7.0 Consensus size: 42
55730064 AGCGTTTACA
* *
55730074 GAAAAAAACGCCGCTAAAGGTCATGTCCTTTAGCGGCGCTTAG
1 GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT-G
* *
55730117 GAAAAAAACACCGCTAATGATCATGTTCTTTAGCGGCGCTTG
1 GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTG
* * * *
55730159 GGAAAAAACGTCGCTGATGATCATGTTCTTTAGCGGCGCTTG
1 GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTG
* * *
55730201 GGAAAAAACGCCGCTAAAGGA-CATGATCTTTAGCGGCACTTAG
1 GAAAAAAACGCCGCTAAA-GATCATGTTCTTTAGCGGCGCTT-G
* *
55730244 GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTA
1 GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTG
* * * * *
55730286 CAAAAAAACGCCGCTAAA-ACTAATGTTCTATAGCAGCGTTTG
1 GAAAAAAACGCCGCTAAAGA-TCATGTTCTTTAGCGGCGCTTG
* *
55730328 GTAAAAAACACCGCTAAAGATCATGTTCTTTAGCGGCGCTT
1 GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
55730369 CATCTACAAA
Statistics
Matches: 217, Mismatches: 30, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
41 1 0.00
42 141 0.65
43 75 0.35
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (42 bp):
GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTG
Found at i:55730183 original size:85 final size:84
Alignment explanation
Indices: 55730074--55730368 Score: 353
Period size: 85 Copynumber: 3.5 Consensus size: 84
55730064 AGCGTTTACA
* * *
55730074 GAAAAAAACGCCGCTAAAGGTCATGTCCTTTAGCGGCGCTTAGGAAAAAAACACCGCTAATGATC
1 GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAA-GATC
55730139 ATGTTCTTTAGCGGCGCTTG
65 ATGTTCTTTAGCGGCGCTTG
* * * * *
55730159 GGAAAAAACGTCGCTGATGATCATGTTCTTTAGCGGCGCTT-GGGAAAAAACGCCGCTAAAGGA-
1 GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAAACGCCGCT-AA-GAT
* *
55730222 CATGATCTTTAGCGGCACTTAG
64 CATGTTCTTTAGCGGCGCTT-G
* * * *
55730244 GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTA-CAAAAAAACGCCGCTAAAACTA
1 GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAGA-TC
* * *
55730308 ATGTTCTATAGCAGCGTTTG
65 ATGTTCTTTAGCGGCGCTTG
* *
55730328 GTAAAAAACACCGCTAAAGATCATGTTCTTTAGCGGCGCTT
1 GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
55730369 CATCTACAAA
Statistics
Matches: 177, Mismatches: 28, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
83 1 0.01
84 73 0.41
85 103 0.58
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (84 bp):
GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAGATCA
TGTTCTTTAGCGGCGCTTG
Found at i:55730404 original size:127 final size:127
Alignment explanation
Indices: 55730076--55730368 Score: 383
Period size: 127 Copynumber: 2.3 Consensus size: 127
55730066 CGTTTACAGA
* * *
55730076 AAAAAACGCCGCTAAAGGTCATGTCCTTTAGCGGCGCTTAGGAAAAAAACACCGCTAATGATCAT
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAAACACCGCTAAAGATCAT
*** * ** * * *
55730141 GTTCTTTAGCGGCGCTTGGGAAAAAACGTCGCTGATGATCATGTTCTTTAGCGGCGCTTGGG
66 GTTCTTTAGCGGCGCTTACAAAAAAACGCCGCTGAAAATAATGTTCTATAGCAGCGCTTGGG
* * *
55730203 AAAAAACGCCGCTAAAGGA-CATGATCTTTAGCGGCACTTAGGAAAAAAACGCCGCTAAAGATCA
1 AAAAAACGCCGCTAAA-GATCATGTTCTTTAGCGGCGCTTAGGAAAAAAACACCGCTAAAGATCA
* * *
55730267 TGTTCTTTAGCGGCGTTTACAAAAAAACGCCGCT-AAAACTAATGTTCTATAGCAGCGTTTGGT
65 TGTTCTTTAGCGGCGCTTACAAAAAAACGCCGCTGAAAA-TAATGTTCTATAGCAGCGCTTGGG
*
55730330 AAAAAACACCGCTAAAGATCATGTTCTTTAGCGGCGCTT
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
55730369 CATCTACAAA
Statistics
Matches: 142, Mismatches: 21, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
126 4 0.03
127 137 0.96
128 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.25
Consensus pattern (127 bp):
AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAAACACCGCTAAAGATCAT
GTTCTTTAGCGGCGCTTACAAAAAAACGCCGCTGAAAATAATGTTCTATAGCAGCGCTTGGG
Found at i:55734958 original size:21 final size:19
Alignment explanation
Indices: 55734934--55734972 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
55734924 ATTTGCCTCC
55734934 CTATCTAAGACCATGTTTCCT
1 CTATCTAAG-CCAT-TTTCCT
55734955 CTATCTAAGCCATTTTCC
1 CTATCTAAGCCATTTTCC
55734973 GGAGGATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 4 0.22
21 9 0.50
ACGTcount: A:0.23, C:0.31, G:0.08, T:0.38
Consensus pattern (19 bp):
CTATCTAAGCCATTTTCCT
Found at i:55768670 original size:37 final size:37
Alignment explanation
Indices: 55768620--55768733 Score: 156
Period size: 37 Copynumber: 3.1 Consensus size: 37
55768610 TAATTCATAG
* *
55768620 GAATATAGCTTTCTTGTTTGTATTCTCATTCGATTAT
1 GAATATACCTTTCTTGTTTGTATTCTCATTCTATTAT
* *
55768657 GAATATACCTTTCTTGTTAGTATTCTCATTCTATTTT
1 GAATATACCTTTCTTGTTTGTATTCTCATTCTATTAT
* * *
55768694 GAACATACCTTTCTTGCTTGTTTTCTCATTCTATTGAT
1 GAATATACCTTTCTTGTTTGTATTCTCATTCTATT-AT
55768732 GA
1 GA
55768734 TTAATGCTGC
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
37 64 0.96
38 3 0.04
ACGTcount: A:0.21, C:0.17, G:0.11, T:0.51
Consensus pattern (37 bp):
GAATATACCTTTCTTGTTTGTATTCTCATTCTATTAT
Found at i:55775275 original size:19 final size:21
Alignment explanation
Indices: 55775251--55775299 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 21
55775241 AATTTTCTTA
55775251 ATTTAACTCGA-ATAAA-TTT
1 ATTTAACTCGACATAAATTTT
*
55775270 ATTTAACTCGACTTAAATTTT
1 ATTTAACTCGACATAAATTTT
*
55775291 ATTTCACTC
1 ATTTAACTC
55775300 AACTTGATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 11 0.42
20 4 0.15
21 11 0.42
ACGTcount: A:0.35, C:0.16, G:0.04, T:0.45
Consensus pattern (21 bp):
ATTTAACTCGACATAAATTTT
Found at i:55775293 original size:21 final size:20
Alignment explanation
Indices: 55775251--55775304 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
55775241 AATTTTCTTA
*
55775251 ATTTAACTCGA-ATAAATTT
1 ATTTAACTCGACTTAAATTT
55775270 ATTTAACTCGACTTAAATTTT
1 ATTTAACTCGACTTAAA-TTT
* *
55775291 ATTTCACTCAACTT
1 ATTTAACTCGACTT
55775305 GATTAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 11 0.37
20 4 0.13
21 15 0.50
ACGTcount: A:0.35, C:0.17, G:0.04, T:0.44
Consensus pattern (20 bp):
ATTTAACTCGACTTAAATTT
Found at i:55777699 original size:154 final size:151
Alignment explanation
Indices: 55777415--55778156 Score: 756
Period size: 153 Copynumber: 5.0 Consensus size: 151
55777405 ACGCTGTTCG
* * * * * * *
55777415 TATTTACTTTTTTTGCTCCACAAGCAATCCAAAACCATAAACAAAGGAATACTTTTTTCGCCTTT
1 TATTCACTTTTCTTGCTACACAAGCAAGCCGAAACCATAAACAAAGGCATACTTTTTTCTCCTTT
*
55777480 TTTAAATGGTTTTCTTGTTTCTTTTCCGCTTTTTCAATTCTTCATTCAATTCAAGTTCAAGAAAC
66 TTTAAATGGTTTTCTTGTTTCTTTT-CG-TTTTTAAATTCTTCATTCAATTCAAGTTCAAGAAAC
55777545 CATACTAAATATATATATGTTTA
129 CATACTAAATATATATATGTTTA
* * *
55777568 TATTCACTTTTCTTGCTACACAAGCAAGCCAAAACCATAAACAAAGGCATGCCTTTTTTTTTCCT
1 TATTCACTTTTCTTGCTACACAAGCAAGCCGAAACCATAAACAAAGGCAT-AC-TTTTTTCTCCT
* * *
55777633 TTTTT-AATGGTTTTCTTGATTCTTTGTTGTTTTTAAAATTCTTCATTCAATTCAAGTTGAAGAA
64 TTTTTAAATGGTTTTCTTGTTTCTTT-TCGTTTTT-AAATTCTTCATTCAATTCAAGTTCAAGAA
*
55777697 ACCATACTAAATATAT-T-TATTTA
127 ACCATACTAAATATATATATGTTTA
* * * *
55777720 TATTCACTTTTTTTTTGCTATACAAGCAAGCTGAAACCATAAACAAAGGCATACATTTTTCTCCT
1 TATTCAC--TTTTCTTGCTACACAAGCAAGCCGAAACCATAAACAAAGGCATACTTTTTTCTCCT
** * * * *
55777785 TTTTTAAATGACTTTCTTGTTTCTTTGTTGTTTTTTAGATTCTTCGTTCAGTTCAAGTTCAAGAA
64 TTTTTAAATGGTTTTCTTGTTTCTTT-TCG-TTTTTAAATTCTTCATTCAATTCAAGTTCAAGAA
* *
55777850 ACCATA-TTAA-ATATATGTGTTTA
127 ACCATACTAAATATATATATGTTTA
* * * *
55777873 TATTCACTTTTCTTGCTACATAAGCAAGCCGCAACCATAAACAAAGGCATACCTTTTTCTTCTTT
1 TATTCACTTTTCTTGCTACACAAGCAAGCCGAAACCATAAACAAAGGCATACTTTTTTCTCCTTT
** * * *
55777938 TTT---T--TTCCCTT-TTTAC----C-TTTTTAGATTCCTCATTCAATTTAAGTTCAAGAAACC
66 TTTAAATGGTTTTCTTGTTT-CTTTTCGTTTTTAAATTCTTCATTCAATTCAAGTTCAAGAAACC
*
55777992 ATACTATATATATATATGTTTA
130 ATACTAAATATATATATGTTTA
* *
55778014 TATTCACTTTTCTTGCTACACAAGTCAA-CCGAAACCATAAACAAAGGCATAAC-TTTTTCGCTT
1 TATTCACTTTTCTTGCTACACAAG-CAAGCCGAAACCATAAACAAAGGCAT-ACTTTTTTCTCCT
** * * * * *
55778077 TTTTTAAAAAG--AT-TT-TTTCTTTGCTGCTTTTTAAATT-TTTATTCAATTTAAGTTCAAAAA
64 TTTTTAAATGGTTTTCTTGTTTCTTTTC-G-TTTTTAAATTCTTCATTCAATTCAAGTTCAAGAA
* *
55778137 ACCCTACTATATATATATAT
127 ACCATACTAAATATATATAT
55778157 ATATTAAGAG
Statistics
Matches: 502, Mismatches: 60, Indels: 59
0.81 0.10 0.10
Matches are distributed among these distances:
139 36 0.07
140 2 0.00
141 68 0.14
142 6 0.01
143 5 0.01
145 3 0.01
146 6 0.01
148 40 0.08
149 9 0.02
151 58 0.12
152 30 0.06
153 116 0.23
154 108 0.22
155 15 0.03
ACGTcount: A:0.30, C:0.18, G:0.08, T:0.43
Consensus pattern (151 bp):
TATTCACTTTTCTTGCTACACAAGCAAGCCGAAACCATAAACAAAGGCATACTTTTTTCTCCTTT
TTTAAATGGTTTTCTTGTTTCTTTTCGTTTTTAAATTCTTCATTCAATTCAAGTTCAAGAAACCA
TACTAAATATATATATGTTTA
Found at i:55777987 original size:139 final size:140
Alignment explanation
Indices: 55777816--55778081 Score: 403
Period size: 141 Copynumber: 1.9 Consensus size: 140
55777806 TCTTTGTTGT
* * * *
55777816 TTTTTAGATTCTTCGTTCAGTTCAAGTTCAAGAAACCATA-T-TAAATATATGTGTTTATATTCA
1 TTTTTAGATTCCTCATTCAATTCAAGTTCAAGAAACCATACTATAAATATATATGTTTATATTCA
* * * *
55777879 CTTTTCTTGCTACATAAG-CAAGCCGCAACCATAAACAAAGGCATACCTTTTTCTTCTTTTTTTT
66 CTTTTCTTGCTACACAAGTCAA-CCGAAACCATAAACAAAGGCATAACTTTTTC-GCTTTTTTTT
55777943 TCCCTTTTTACC
129 TCCCTTTTTACC
* *
55777955 TTTTTAGATTCCTCATTCAATTTAAGTTCAAGAAACCATACTATATATATATATGTTTATATTCA
1 TTTTTAGATTCCTCATTCAATTCAAGTTCAAGAAACCATACTATAAATATATATGTTTATATTCA
55778020 CTTTTCTTGCTACACAAGTCAACCGAAACCATAAACAAAGGCATAACTTTTTCGCTTTTTTT
66 CTTTTCTTGCTACACAAGTCAACCGAAACCATAAACAAAGGCATAACTTTTTCGCTTTTTTT
55778082 AAAAAGATTT
Statistics
Matches: 114, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
139 36 0.32
140 9 0.08
141 66 0.58
142 3 0.03
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (140 bp):
TTTTTAGATTCCTCATTCAATTCAAGTTCAAGAAACCATACTATAAATATATATGTTTATATTCA
CTTTTCTTGCTACACAAGTCAACCGAAACCATAAACAAAGGCATAACTTTTTCGCTTTTTTTTTC
CCTTTTTACC
Found at i:55778909 original size:16 final size:16
Alignment explanation
Indices: 55778888--55778924 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
55778878 TTTTTGTTGG
55778888 ACATATGATAAAAAGT
1 ACATATGATAAAAAGT
55778904 ACATATGATAAAAAGT
1 ACATATGATAAAAAGT
55778920 ACATA
1 ACATA
55778925 ATTAATAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.57, C:0.08, G:0.11, T:0.24
Consensus pattern (16 bp):
ACATATGATAAAAAGT
Done.