Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 129432109
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: 129432109
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 20 of 425
Found at i:5304882 original size:14 final size:14
Alignment explanation
Indices: 5304847--5304889 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
5304837 CAAGACATAT
5304847 AAATAA-AATACAT-
1 AAATAATAATA-ATA
5304860 AAATAAATAATAATA
1 AAAT-AATAATAATA
5304875 AAATAATAATAATA
1 AAATAATAATAATA
5304889 A
1 A
5304890 CAACGAGACA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 4 0.15
14 15 0.56
15 8 0.30
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATAATAATAATA
Found at i:5308122 original size:22 final size:22
Alignment explanation
Indices: 5308076--5308117 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
5308066 CTAAAGTATA
*
5308076 AAATTATATAAGAGAAATCAAT
1 AAATTATATAAGACAAATCAAT
5308098 AAATTATAT-A-ACAAATCAAT
1 AAATTATATAAGACAAATCAAT
5308118 GTAAAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 1 0.05
22 9 0.47
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.29
Consensus pattern (22 bp):
AAATTATATAAGACAAATCAAT
Found at i:5310050 original size:20 final size:21
Alignment explanation
Indices: 5310020--5310069 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
5310010 TACTTCTCTA
*
5310020 TTTTGTTCTTTCTT-TTATTTC
1 TTTTATTCTTT-TTATTATTTC
5310041 -TTTATTCTTTTTATTATTTC
1 TTTTATTCTTTTTATTATTTC
5310061 TTTTATTCT
1 TTTTATTCT
5310070 ACTTTATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 2 0.08
20 16 0.62
21 8 0.31
ACGTcount: A:0.10, C:0.12, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTTATTCTTTTTATTATTTC
Found at i:5310079 original size:21 final size:19
Alignment explanation
Indices: 5310030--5310079 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 19
5310020 TTTTGTTCTT
5310030 TCTTT-TATTTCTTTATTC
1 TCTTTATATTTCTTTATTC
*
5310048 TTTTTATTATTTCTTTTATTC
1 TCTTTA-TATTTC-TTTATTC
5310069 TACTTTATATT
1 T-CTTTATATT
5310080 ATTATATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 4 0.15
20 6 0.23
21 12 0.46
22 4 0.15
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (19 bp):
TCTTTATATTTCTTTATTC
Found at i:5310087 original size:29 final size:29
Alignment explanation
Indices: 5310028--5310084 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
5310018 TATTTTGTTC
* *
5310028 TTTCTTTTATTTCTTTATTCTTTTTATTA
1 TTTCTTTTATTTCTTTATTATTATTATTA
5310057 TTTCTTTTATTCTACTTTA-TATTATTAT
1 TTTCTTTTATT-T-CTTTATTATTATTAT
5310085 ATTATATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 11 0.46
30 8 0.33
31 5 0.21
ACGTcount: A:0.18, C:0.11, G:0.00, T:0.72
Consensus pattern (29 bp):
TTTCTTTTATTTCTTTATTATTATTATTA
Found at i:5310091 original size:13 final size:13
Alignment explanation
Indices: 5310073--5310110 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
5310063 TTATTCTACT
5310073 TTATATTATTATA
1 TTATATTATTATA
*
5310086 TTATATTTTTA-A
1 TTATATTATTATA
5310098 TTATAATTATTAT
1 TTAT-ATTATTAT
5310111 TTCTTAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 5 0.24
13 16 0.76
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTATATTATTATA
Found at i:5311061 original size:14 final size:14
Alignment explanation
Indices: 5311038--5311072 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
5311028 ATTATTGGCT
5311038 TTGGGCTAGTGTAA
1 TTGGGCTAGTGTAA
* *
5311052 TTGGGTTAGTGTAG
1 TTGGGCTAGTGTAA
5311066 TTGGGCT
1 TTGGGCT
5311073 GAGGATTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.14, C:0.06, G:0.40, T:0.40
Consensus pattern (14 bp):
TTGGGCTAGTGTAA
Found at i:5312053 original size:13 final size:12
Alignment explanation
Indices: 5312035--5312106 Score: 73
Period size: 12 Copynumber: 6.3 Consensus size: 12
5312025 TTTAAAATTT
5312035 AAAAATTATTTAA
1 AAAAATTA-TTAA
* *
5312048 AAAAATCATAAA
1 AAAAATTATTAA
5312060 AAAAATTATTAA
1 AAAAATTATTAA
*
5312072 AAAAGTTA-T--
1 AAAAATTATTAA
5312081 -AAAATTATT-A
1 AAAAATTATTAA
5312091 AAAAATTATTAA
1 AAAAATTATTAA
5312103 AAAA
1 AAAA
5312107 TAATAATGCC
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
8 6 0.12
9 1 0.02
11 10 0.20
12 25 0.51
13 7 0.14
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (12 bp):
AAAAATTATTAA
Found at i:5312080 original size:12 final size:11
Alignment explanation
Indices: 5312035--5312107 Score: 71
Period size: 11 Copynumber: 6.5 Consensus size: 11
5312025 TTTAAAATTT
5312035 AAAAATTATTTAA
1 AAAAATTA-TT-A
* *
5312048 AAAAATCATAAA
1 AAAAATTAT-TA
5312060 AAAAATTATTA
1 AAAAATTATTA
5312071 AAAAAGTTA-T-
1 AAAAA-TTATTA
5312081 -AAAATTATTA
1 AAAAATTATTA
5312091 AAAAATTATTA
1 AAAAATTATTA
5312102 AAAAAT
1 AAAAAT
5312108 AATAATGCCG
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
8 3 0.06
9 5 0.10
11 23 0.45
12 13 0.25
13 7 0.14
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (11 bp):
AAAAATTATTA
Found at i:5312086 original size:20 final size:20
Alignment explanation
Indices: 5312061--5312104 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
5312051 AATCATAAAA
5312061 AAAATTATTAAAAAAGTTA-T
1 AAAATTATTAAAAAA-TTATT
5312081 AAAATTATTAAAAAATTATT
1 AAAATTATTAAAAAATTATT
5312101 AAAA
1 AAAA
5312105 AATAATAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (20 bp):
AAAATTATTAAAAAATTATT
Found at i:5313047 original size:19 final size:19
Alignment explanation
Indices: 5313023--5313113 Score: 134
Period size: 19 Copynumber: 4.9 Consensus size: 19
5313013 AATCATATCT
*
5313023 TCTAAGATTGTATATCATA
1 TCTAAGATTGCATATCATA
5313042 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
5313060 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
* *
5313077 TCTAAGATTACATATCACA
1 TCTAAGATTGCATATCATA
5313096 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
5313114 TGAAGATTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
17 15 0.23
18 16 0.25
19 33 0.52
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:5313081 original size:35 final size:37
Alignment explanation
Indices: 5313023--5313113 Score: 132
Period size: 35 Copynumber: 2.5 Consensus size: 37
5313013 AATCATATCT
* *
5313023 TCTAAGATTGTATATCATATCTAAGATTGCA-ATCATA
1 TCTAAGATTG-ATATCATATCTAAGATTACATATCACA
5313060 TCTAAGATTG-TATCATATCTAAGATTACATATCACA
1 TCTAAGATTGATATCATATCTAAGATTACATATCACA
5313096 TCTAAGATTGCATATCAT
1 TCTAAGATTG-ATATCAT
5313114 TGAAGATTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
35 18 0.37
36 15 0.31
37 10 0.20
38 6 0.12
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.37
Consensus pattern (37 bp):
TCTAAGATTGATATCATATCTAAGATTACATATCACA
Found at i:5313961 original size:207 final size:207
Alignment explanation
Indices: 5313504--5314297 Score: 1275
Period size: 207 Copynumber: 3.8 Consensus size: 207
5313494 AAATCTGCTT
* * * * * *
5313504 CTTCAATTTATTCCCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAACAT
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACGTAAACAC
* * * *
5313569 GCGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGTACAAGGATACCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
* * ** * **
5313634 GGATC-TGCTTCAGTCTAATCATCTGAAGGTTAGATCTGCTATATGTCTATCCTCTGTCGAATAT
131 GGATCTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTGCCCTCTGTCGAATAT
5313698 GGAGACGCCAAA
196 GGAGACGCCAAA
* *
5313710 CTTTGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAATGTAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACGTAAACAC
5313775 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
*
5313840 GGATCTTGCTTCAGTATAAACATCTGAAGGCCATATCTGCTATGTGTCTGCCCTCTGTCGAATAT
131 GGATCTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTGCCCTCTGTCGAATAT
5313905 GGAGACGCCAAA
196 GGAGACGCCAAA
*
5313917 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACATAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACGTAAACAC
*
5313982 GTGAAAACCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
* * *
5314047 GGATCTTGCTTCAGTATAAACATCTAAAGGCTAGATCTGCTATGTGTCTGCCCTCCGTCGAATAT
131 GGATCTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTGCCCTCTGTCGAATAT
5314112 GGAGACGCCAAA
196 GGAGACGCCAAA
* *
5314124 CTTCGATTTGTTCTCTAATAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACGTAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACGTAAACAC
* * *
5314189 GTGAAAGCCAAATCAGCTATGTCTTCAATTCGTTCATTGTAAGCACAAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
* * * *
5314254 GGATCTTACTTCAGTATAAACATCTGAAAGCCAAATCTGTTATG
131 GGATCTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATG
5314298 CTTTAACCTG
Statistics
Matches: 546, Mismatches: 41, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
206 123 0.23
207 423 0.77
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (207 bp):
CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACGTAAACAC
GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
GGATCTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTGCCCTCTGTCGAATAT
GGAGACGCCAAA
Found at i:5314472 original size:87 final size:83
Alignment explanation
Indices: 5314303--5314589 Score: 380
Period size: 87 Copynumber: 3.4 Consensus size: 83
5314293 TTATGCTTTA
* * *
5314303 ACCTGTTACCCTACTGCTTAGGGGGTTAAGGCGCA-TCTTCAATCTGCTCCACTACTGCTTAGGG
1 ACCTGTTACCCTACTGCTTAGGGGATTAAGGCG-AGTCTTCGATCTACTCCACTACTGCTTAGGG
*
5314367 AGATAAGATCCGCAATTTT
65 AGATAAGATCTGCAATTTT
* * * *
5314386 GACCTGTTACCCTATTGCTTAGGGGATTAAGGCGAGTCGTCGTTGATCTATTTCACTACTGCTTA
1 -ACCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTC-T--TCGATCTACTCCACTACTGCTTA
*
5314451 GGGAGATAAGATCTGTAATTTT
62 GGGAGATAAGATCTGCAATTTT
* *
5314473 AGCCTGTTACCCTACTACTTAGGGG-TTAAGGCGAGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 A-CCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTCTTCGATCTACTCCACTACTGCTTAGGG
* *
5314537 AGATAAGATCTACAAATTTA
65 AGATAAGATCTGC-AATTTT
5314557 ACCTGTTACCCTACTGCTTAGGGGATTAAGGCG
1 ACCTGTTACCCTACTGCTTAGGGGATTAAGGCG
5314590 CTGAATTTTG
Statistics
Matches: 177, Mismatches: 19, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
83 56 0.32
84 47 0.27
85 2 0.01
86 13 0.07
87 59 0.33
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (83 bp):
ACCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTCTTCGATCTACTCCACTACTGCTTAGGGA
GATAAGATCTGCAATTTT
Found at i:5314562 original size:83 final size:84
Alignment explanation
Indices: 5314299--5314589 Score: 406
Period size: 83 Copynumber: 3.4 Consensus size: 84
5314289 TCTGTTATGC
* *
5314299 TTTAACCTGTTACCCTACTGCTTAGGGGGTTAAGGCGCA-TCTTCAATCTGCTCCACTACTGCTT
1 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCG-AGTCTTCGATCTGCTCCACTACTGCTT
*
5314363 AGGGAGATAAGATCCGCAAT
65 AGGGAGATAAGATCTGCAAT
* * * ** *
5314383 TTTGACCTGTTACCCTATTGCTTAGGGGATTAAGGCGAGTCGTCGTTGATCTATTTCACTACTGC
1 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTC-T--TCGATCTGCTCCACTACTGC
*
5314448 TTAGGGAGATAAGATCTGTAAT
63 TTAGGGAGATAAGATCTGCAAT
* *
5314470 TTTAGCCTGTTACCCTACTACTTAGGGG-TTAAGGCGAGTCTTCGATCTGCTCCACTACTGCTTA
1 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTCTTCGATCTGCTCCACTACTGCTTA
* *
5314534 GGGAGATAAGATCTACAAA
66 GGGAGATAAGATCTGCAAT
5314553 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCG
1 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCG
5314590 CTGAATTTTG
Statistics
Matches: 179, Mismatches: 23, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
83 62 0.35
84 44 0.25
85 2 0.01
86 12 0.07
87 59 0.33
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.32
Consensus pattern (84 bp):
TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTCTTCGATCTGCTCCACTACTGCTTA
GGGAGATAAGATCTGCAAT
Found at i:5315546 original size:1 final size:1
Alignment explanation
Indices: 5315536--5315625 Score: 81
Period size: 1 Copynumber: 90.0 Consensus size: 1
5315526 GGCCTCTCCA
* * * * * * *
5315536 TTTTTATTTTTCTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTCTTTTTTCTTTTCTTTTTTTCTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * **
5315601 TTTTCTTTTCTTTTTCCTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
5315626 GAAATAGAAG
Statistics
Matches: 69, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 69 1.00
ACGTcount: A:0.01, C:0.11, G:0.00, T:0.88
Consensus pattern (1 bp):
T
Found at i:5315557 original size:12 final size:12
Alignment explanation
Indices: 5315536--5315615 Score: 97
Period size: 12 Copynumber: 6.4 Consensus size: 12
5315526 GGCCTCTCCA
*
5315536 TTTTTATTTTTC
1 TTTTTTTTTTTC
*
5315548 TTTTTTTTTTTT
1 TTTTTTTTTTTC
*
5315560 TTTTTTTCTTTTT
1 TTTTTTT-TTTTC
5315573 TTTTTCTTTTTTC
1 TTTTT-TTTTTTC
5315586 TTTTCTTTTTTTC
1 TTTT-TTTTTTTC
*
5315599 TTTTTTCTTTTC
1 TTTTTTTTTTTC
5315611 TTTTT
1 TTTTT
5315616 CCTTTTTTTT
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
12 29 0.48
13 29 0.48
14 3 0.05
ACGTcount: A:0.01, C:0.10, G:0.00, T:0.89
Consensus pattern (12 bp):
TTTTTTTTTTTC
Found at i:5315565 original size:20 final size:20
Alignment explanation
Indices: 5315536--5315625 Score: 108
Period size: 20 Copynumber: 4.2 Consensus size: 20
5315526 GGCCTCTCCA
*
5315536 TTTTTATTTTTCTTTTTTTT
1 TTTTTTTTTTTCTTTTTTTT
5315556 TTTTTTTTTTTCTTTTTTTTT
1 TTTTTTTTTTTC-TTTTTTTT
*
5315577 TCTTTTTTCTTTTCTTTTTTTC
1 T-TTTTTT-TTTTCTTTTTTTT
*
5315599 TTTTTTCTTTTCTTTTTCCTTT
1 TTTTTTTTTTTCTTTTT--TTT
5315621 TTTTT
1 TTTTT
5315626 GAAATAGAAG
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
20 21 0.34
21 14 0.23
22 21 0.34
23 5 0.08
ACGTcount: A:0.01, C:0.11, G:0.00, T:0.88
Consensus pattern (20 bp):
TTTTTTTTTTTCTTTTTTTT
Found at i:5315589 original size:38 final size:39
Alignment explanation
Indices: 5315542--5315623 Score: 130
Period size: 38 Copynumber: 2.1 Consensus size: 39
5315532 TCCATTTTTA
* * *
5315542 TTTTTCTTTTTTTTTTTTTTTTTTTCTTTT-TTTTTTCT
1 TTTTTCTTTTCTTTTTTTCTTTTTTCTTTTCTTTTTCCT
5315580 TTTTTCTTTTCTTTTTTTCTTTTTTCTTTTCTTTTTCCT
1 TTTTTCTTTTCTTTTTTTCTTTTTTCTTTTCTTTTTCCT
5315619 TTTTT
1 TTTTT
5315624 TTGAAATAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
38 28 0.70
39 12 0.30
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (39 bp):
TTTTTCTTTTCTTTTTTTCTTTTTTCTTTTCTTTTTCCT
Found at i:5325595 original size:2 final size:2
Alignment explanation
Indices: 5325588--5325619 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5325578 TTGAAGACTC
5325588 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
5325620 TTACACTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5326591 original size:44 final size:42
Alignment explanation
Indices: 5326525--5326610 Score: 102
Period size: 44 Copynumber: 2.0 Consensus size: 42
5326515 CCATTAAGAA
* *
5326525 AAACTTCAGAAACAAGAGAGCTTTAAAGCAACCAGACTAAGTTT
1 AAACTTCAGAAACAAGAAAGCTTT-AAGAAACCAGA-TAAGTTT
* *
5326569 AAACTTGAGAAGA-AAGAAAGCTTTAAGAAATCAGATAAGTTT
1 AAACTTCAGAA-ACAAGAAAGCTTTAAGAAACCAGATAAGTTT
5326611 CTAGTTCTCG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
42 7 0.19
43 9 0.24
44 20 0.54
45 1 0.03
ACGTcount: A:0.48, C:0.13, G:0.17, T:0.22
Consensus pattern (42 bp):
AAACTTCAGAAACAAGAAAGCTTTAAGAAACCAGATAAGTTT
Found at i:5328309 original size:44 final size:43
Alignment explanation
Indices: 5328252--5328410 Score: 140
Period size: 44 Copynumber: 3.6 Consensus size: 43
5328242 CTTATCTTTT
*
5328252 TGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
1 TGAAGTTGCAGTGGAGCAGACTGAAGCCACCAGCCTTATCTCC
* *** * * * *
5328295 TCGAAGTTGTAGTGGAGCAGACTGAATATAGCGAATCC-CATTTCC
1 T-GAAGTTGCAGTGGAGCAGACTGAAGCCA-C-CAGCCTTATCTCC
* * *
5328340 ATAAAGTTGCAGTGGAGAAGATTGAAGCCACCAGCCTTATCTCC
1 -TGAAGTTGCAGTGGAGCAGACTGAAGCCACCAGCCTTATCTCC
**
5328384 TTGAAGTTGCAGTAAAGCAGACTGAAG
1 -TGAAGTTGCAGTGGAGCAGACTGAAG
5328411 ATAGCGAATC
Statistics
Matches: 85, Mismatches: 26, Indels: 9
0.71 0.22 0.08
Matches are distributed among these distances:
43 4 0.05
44 50 0.59
45 27 0.32
46 4 0.05
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (43 bp):
TGAAGTTGCAGTGGAGCAGACTGAAGCCACCAGCCTTATCTCC
Found at i:5328405 original size:89 final size:90
Alignment explanation
Indices: 5328254--5328451 Score: 303
Period size: 89 Copynumber: 2.2 Consensus size: 90
5328244 TATCTTTTTG
* **
5328254 AAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCTCGAAGTTGTAGTGGAGCAGACTG
1 AAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCTCGAAGTTGCAGTAAAGCAGACTG
*
5328319 AATATAGCGAATCCCATTTC-CAT-A
66 AAGATAGCGAATCCCATTTCTC-TGA
* *
5328343 AAGTTGCAGTGGAGAAGATTGAAGCCACCAGCCTTATCTCCTTGAAGTTGCAGTAAAGCAGACTG
1 AAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCTCGAAGTTGCAGTAAAGCAGACTG
*
5328408 AAGATAGCGAATCTCATTTCTCTGA
66 AAGATAGCGAATCCCATTTCTCTGA
5328433 AA-TTGCAGTGGAGCAGATT
1 AAGTTGCAGTGGAGCAGATT
5328452 AAAACTACAA
Statistics
Matches: 99, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
89 95 0.96
90 4 0.04
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.25
Consensus pattern (90 bp):
AAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCTCGAAGTTGCAGTAAAGCAGACTG
AAGATAGCGAATCCCATTTCTCTGA
Found at i:5328448 original size:45 final size:45
Alignment explanation
Indices: 5328305--5328449 Score: 116
Period size: 45 Copynumber: 3.2 Consensus size: 45
5328295 TCGAAGTTGT
* *
5328305 AGTGGAGCAGACTGAATATAGCGAATCCCATTTCCAT-AAAGTTGC
1 AGTGGAGCAGACTGAAGATAGCGAATCTCATTTCCATGAAA-TTGC
* * ** * ** * * * *
5328350 AGTGGAGAAGATTGAAGCCA-CCAGCCTTATCTCCTTGAAGTTGC
1 AGTGGAGCAGACTGAAGATAGCGAATCTCATTTCCATGAAATTGC
**
5328394 AGTAAAGCAGACTGAAGATAGCGAATCTCATTTCTC-TGAAATTGC
1 AGTGGAGCAGACTGAAGATAGCGAATCTCATTTC-CATGAAATTGC
5328439 AGTGGAGCAGA
1 AGTGGAGCAGA
5328450 TTAAAACTAC
Statistics
Matches: 70, Mismatches: 27, Indels: 6
0.68 0.26 0.06
Matches are distributed among these distances:
44 27 0.39
45 42 0.60
46 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.24
Consensus pattern (45 bp):
AGTGGAGCAGACTGAAGATAGCGAATCTCATTTCCATGAAATTGC
Found at i:5328560 original size:44 final size:46
Alignment explanation
Indices: 5328506--5328623 Score: 132
Period size: 46 Copynumber: 2.6 Consensus size: 46
5328496 GATAGCAGAT
* * * ** * *
5328506 CTTATATCCCTGAAGTTGCATTGGAGC-GGAT-CGAAGCCACAATC
1 CTTATCTCCCTGAAGTTGCAATGGAGCAAGATAAAAAGACACAAAC
*
5328550 CTTATCTCCCTGAAGTTGCAATGGAGCAAGATAAAAATACACAAAC
1 CTTATCTCCCTGAAGTTGCAATGGAGCAAGATAAAAAGACACAAAC
* *
5328596 CTTATCTCCCTGAAGCTGCAGTGGAGCA
1 CTTATCTCCCTGAAGTTGCAATGGAGCA
5328624 GGTTAAAATT
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
44 25 0.40
45 3 0.05
46 34 0.55
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (46 bp):
CTTATCTCCCTGAAGTTGCAATGGAGCAAGATAAAAAGACACAAAC
Found at i:5328655 original size:45 final size:46
Alignment explanation
Indices: 5328543--5328668 Score: 155
Period size: 46 Copynumber: 2.8 Consensus size: 46
5328533 GGATCGAAGC
*
5328543 CACAATCCTTATCTCCCTGAAGTTGCAATGGAGCAAGATAAAAATA
1 CACAATCCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATAAAAATA
* * * * *
5328589 CACAAACCTTATCTCCCTGAAGCTGCAGTGGAGCAGGTTAAAATTA
1 CACAATCCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATAAAAATA
* * * *
5328635 C-CAATTCTTATATCCTTGAAGTTACAGTGGAGCA
1 CACAATCCTTATCTCCCTGAAGTTGCAGTGGAGCA
5328669 CCAATTCCTA
Statistics
Matches: 68, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
45 27 0.40
46 41 0.60
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.26
Consensus pattern (46 bp):
CACAATCCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATAAAAATA
Found at i:5330102 original size:23 final size:24
Alignment explanation
Indices: 5330047--5330103 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
5330037 TTCAACCCTT
* *
5330047 TTTATGTTTAAAATTTATTTATTTA
1 TTTATCTTT-AAATTTATATATTTA
*
5330072 TCT-TCTTTAAATTTATATA-TTA
1 TTTATCTTTAAATTTATATATTTA
5330094 TTTATCTTTA
1 TTTATCTTTA
5330104 CTATTATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
22 5 0.19
23 16 0.59
24 4 0.15
25 2 0.07
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (24 bp):
TTTATCTTTAAATTTATATATTTA
Found at i:5330111 original size:3 final size:3
Alignment explanation
Indices: 5330105--5330138 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
5330095 TTATCTTTAC
5330105 TAT TAT TAT TAT TAT TAT T-T TAT CTAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT T
5330139 TATTTATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.83
4 3 0.10
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:5330123 original size:15 final size:15
Alignment explanation
Indices: 5330089--5330139 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
5330079 TAAATTTATA
5330089 TATTA-TTTATCT-T
1 TATTATTTTATCTAT
*
5330102 TACTATTATTAT-TAT
1 TATTATT-TTATCTAT
5330117 TATTATTTTATCTAT
1 TATTATTTTATCTAT
5330132 TATTATTT
1 TATTATTT
5330140 ATTTATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 4 0.12
14 6 0.19
15 22 0.69
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTATTTTATCTAT
Found at i:5330131 original size:24 final size:25
Alignment explanation
Indices: 5330084--5330145 Score: 78
Period size: 24 Copynumber: 2.6 Consensus size: 25
5330074 TTCTTTAAAT
5330084 TTATATATTATTTATCTTTACTATTA
1 TTAT-TATTATTTATCTTTACTATTA
5330110 TTATTATTA-TTAT-TTTATCTATTA
1 TTATTATTATTTATCTTTA-CTATTA
5330134 TTA-T-TTATTTAT
1 TTATTATTATTTAT
5330146 ATATGCTTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
22 3 0.09
23 9 0.26
24 13 0.38
25 5 0.15
26 4 0.12
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (25 bp):
TTATTATTATTTATCTTTACTATTA
Found at i:5330132 original size:18 final size:18
Alignment explanation
Indices: 5330107--5330143 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5330097 ATCTTTACTA
5330107 TTATTATTATTA-TTATT
1 TTATTATTATTATTTATT
5330124 TTATCTATTATTATTTATT
1 TTAT-TATTATTATTTATT
5330143 T
1 T
5330144 ATATATGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 8 0.44
19 6 0.33
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (18 bp):
TTATTATTATTATTTATT
Found at i:5333525 original size:22 final size:22
Alignment explanation
Indices: 5333497--5333541 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
5333487 GTTATGAGAG
5333497 TAAATGTCACTTTTAGGTGGGT
1 TAAATGTCACTTTTAGGTGGGT
5333519 TAAATGTCACTTTTAGGTGGGT
1 TAAATGTCACTTTTAGGTGGGT
5333541 T
1 T
5333542 CGACTTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.09, G:0.27, T:0.42
Consensus pattern (22 bp):
TAAATGTCACTTTTAGGTGGGT
Found at i:5335022 original size:24 final size:24
Alignment explanation
Indices: 5334995--5335043 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
5334985 TTTGAAATTT
5334995 AAAAATTATTTAAAAAATCATAAA
1 AAAAATTATTTAAAAAATCATAAA
* * *
5335019 AAAATTTATTTAAAAAGTTATAAA
1 AAAAATTATTTAAAAAATCATAAA
5335043 A
1 A
5335044 TTATAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (24 bp):
AAAAATTATTTAAAAAATCATAAA
Found at i:5343124 original size:21 final size:22
Alignment explanation
Indices: 5343090--5343130 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
5343080 TGAAAGGTCA
5343090 AAAATTTGTCTAACTTTTTCCT
1 AAAATTTGTCTAACTTTTTCCT
5343112 AAAATTT-TCTAACTTTTTC
1 AAAATTTGTCTAACTTTTTC
5343131 TAATTGACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.29, C:0.17, G:0.02, T:0.51
Consensus pattern (22 bp):
AAAATTTGTCTAACTTTTTCCT
Found at i:5361456 original size:2 final size:2
Alignment explanation
Indices: 5361420--5361448 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5361410 ATTTAATACT
5361420 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5361449 GTTATATAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5361464 original size:15 final size:15
Alignment explanation
Indices: 5361419--5361456 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
5361409 TATTTAATAC
*
5361419 TTATATATATATATA
1 TTATATATATATATG
5361434 TATATATATATATATG
1 T-TATATATATATATG
5361450 TTATATA
1 TTATATA
5361457 GTATTATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
TTATATATATATATG
Found at i:5361630 original size:15 final size:13
Alignment explanation
Indices: 5361603--5361637 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
5361593 TTCTTTTCAA
5361603 ATATTATATATGT
1 ATATTATATATGT
5361616 ATATATATATAATGT
1 ATAT-TATAT-ATGT
5361631 ATATTAT
1 ATATTAT
5361638 GTATATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 4 0.20
14 8 0.40
15 8 0.40
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (13 bp):
ATATTATATATGT
Found at i:5361654 original size:21 final size:22
Alignment explanation
Indices: 5361607--5361669 Score: 76
Period size: 21 Copynumber: 2.9 Consensus size: 22
5361597 TTTCAAATAT
*
5361607 TATA-TATGTATATATATATAATG
1 TATATTATGTATATAT-TTTAA-G
5361630 TATATTATGTATATATTTTAA-
1 TATATTATGTATATATTTTAAG
*
5361651 TATATTATGTGTATATTTT
1 TATATTATGTATATATTTT
5361670 GTTTTGTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.49
23 8 0.22
24 11 0.30
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.56
Consensus pattern (22 bp):
TATATTATGTATATATTTTAAG
Found at i:5374503 original size:45 final size:45
Alignment explanation
Indices: 5374364--5374777 Score: 232
Period size: 44 Copynumber: 9.4 Consensus size: 45
5374354 GACGAAGGAC
* * *
5374364 CTTAACCCCCTAAACAGTAGGGTAACAGGTTG-A-ATTCACAGAT
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAGATTGACAGAT
** * * ** * * *
5374407 CTTAATACCCTAAACAGTAGGGAAACA-AATCAA-AGGTGACA-AGC
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAGA-TTGACAGA-T
* *
5374451 CTTAACCCCCTAAGTAGTAGGGTAATAGGCTGAAGATTGACAGAT
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAGATTGACAGAT
* * * * * ** ** *
5374496 CTTAACCCCCTAAGCAATAGGGAAACA-GATCAAAAGCGATGGCT
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAGATTGACAGAT
* *
5374540 -TTAAACCCTTAAGCAGTAGGGTAACAGGCTGAAGATTGACAGAT
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAGATTGACAGAT
* * * **
5374584 CTTAACCCCCTAAGCAGTAGGGAAACA-GATCGAAG-GTGA-AGGGC
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCT-GAAGATTGACA-GAT
* * * *
5374628 CTTAAACCCCTAAGCAGTAGGGTAATAGACTG-A-ATTTACAGAT
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAGATTGACAGAT
* * * * * * **
5374671 CTCATCACCCTAAGCAGTAGGGGAACA-GATCGAAG-GTGA-AGGGC
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCT-GAAGATTGACA-GAT
* *
5374715 CTTAAACCCCTAAGCAGTAGGGTAACAGGCT-AA-ATTTACAGAT
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAGATTGACAGAT
* *
5374758 CTTATCTCCCTAAGCAGTAG
1 CTTAACCCCCTAAGCAGTAG
5374778 TGGAGCAGAT
Statistics
Matches: 266, Mismatches: 85, Indels: 40
0.68 0.22 0.10
Matches are distributed among these distances:
42 2 0.01
43 99 0.37
44 102 0.38
45 61 0.23
46 2 0.01
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.20
Consensus pattern (45 bp):
CTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAGATTGACAGAT
Found at i:5374649 original size:264 final size:260
Alignment explanation
Indices: 5374189--5374791 Score: 702
Period size: 264 Copynumber: 2.3 Consensus size: 260
5374179 GAATCCACAG
*
5374189 GCCTTAAACCCCTAAGTAGTAGGGTAATAGGCTG-AATTTACAGATCTTATCTCCAC-AAGCAGT
1 GCCTTAAACCCCTAAGTAGTAGGGTAATAGGCTGAAATTTACAGATCTTATC-CCCCTAAGCAGT
* * * * *
5374252 AGTGGAGTAGATCGAATACTGTGGGCTTTAACCCCCTAAGCAGTAGGGTGACAAGCCGAATTATA
65 AGTGGAGCAGATC-AAAACTGTGGGCTTTAAACCCCTAAGCAGTAGGGTAACAAGCCGAATTACA
** * * *
5374317 GATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGAAGGACCTTAACCCCCTAAACAGT
129 GATCTTAACCCCCTAAGCAGTAGTGGAACAGATCAAAGACGAAGGACCTTAAACCCCTAAACAGT
**
5374382 AGGGTAACAGGTTGAATTCACAGATCTTAAT-ACCCTAAACAGTAGGGAAACAAATCAAAGGTGA
194 AGGGTAACAGACTGAATTCACAGATC-TAATCACCCTAAACAGTAGGGAAACAAATCAAAGGTGA
5374446 CA-A
258 -AGA
* * * *
5374449 GCCTTAACCCCCTAAGTAGTAGGGTAATAGGCTGAAGATTGACAGATCTTAACCCCCTAAGCAAT
1 GCCTTAAACCCCTAAGTAGTAGGGTAATAGGCTGAA-ATTTACAGATCTTATCCCCCTAAGCAGT
* * * *
5374514 AG-GGAAACAGATCAAAAGC-GAT-GGCTTTAAACCCTTAAGCAGTAGGGTAACAGGCTGAAGAT
65 AGTGG-AGCAGATCAAAA-CTG-TGGGCTTTAAACCCCTAAGCAGTAGGGTAACAAGCCG-A-AT
* ** *
5374576 TGACAGATCTTAACCCCCTAAGCAGTAG-GGAAACAGATCGAAGGTGAAGGGCCTTAAACCCCTA
125 T-ACAGATCTTAACCCCCTAAGCAGTAGTGG-AACAGATCAAAGACGAAGGACCTTAAACCCCTA
* * * * * * * *
5374640 AGCAGTAGGGTAATAGACTGAATTTACAGATCTCATCACCCTAAGCAGTAGGGGAACAGATCGAA
188 AACAGTAGGGTAACAGACTGAATTCACAGATCTAATCACCCTAAACAGTAGGGAAACAAATCAAA
*
5374705 GGTGAAGG
253 GGTGAAGA
* * *
5374713 GCCTTAAACCCCTAAGCAGTAGGGTAACAGGCT-AAATTTACAGATCTTATCTCCCTAAGCAGTA
1 GCCTTAAACCCCTAAGTAGTAGGGTAATAGGCTGAAATTTACAGATCTTATCCCCCTAAGCAGTA
5374777 GTGGAGCAGATCAAA
66 GTGGAGCAGATCAAA
5374792 GACGATGAGC
Statistics
Matches: 288, Mismatches: 42, Indels: 24
0.81 0.12 0.07
Matches are distributed among these distances:
260 33 0.11
261 40 0.14
262 67 0.23
263 13 0.05
264 135 0.47
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (260 bp):
GCCTTAAACCCCTAAGTAGTAGGGTAATAGGCTGAAATTTACAGATCTTATCCCCCTAAGCAGTA
GTGGAGCAGATCAAAACTGTGGGCTTTAAACCCCTAAGCAGTAGGGTAACAAGCCGAATTACAGA
TCTTAACCCCCTAAGCAGTAGTGGAACAGATCAAAGACGAAGGACCTTAAACCCCTAAACAGTAG
GGTAACAGACTGAATTCACAGATCTAATCACCCTAAACAGTAGGGAAACAAATCAAAGGTGAAGA
Found at i:5374804 original size:87 final size:86
Alignment explanation
Indices: 5374188--5374815 Score: 570
Period size: 87 Copynumber: 7.2 Consensus size: 86
5374178 TGAATCCACA
* *
5374188 GGCCTTAAACCCCTAAGTAGTAGGGTAATAGGCTGAATTTACAGATCTTATCTCCAC-AAGCAGT
1 GGCCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTATCTCC-CTAAGCAGT
** * * *
5374252 AGTGGAGTAGATCGAATACTG-TG
65 AG-GGAACAGATCAAAGAC-GAAG
* * * * * * *
5374275 GGCTTTAACCCCCTAAGCAGTAGGGTGACAAGCCGAA-TTATAGATCTTGTCTCCCTAAGCAGTA
1 GGCCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTATCTCCCTAAGCAGTA
*
5374339 GTGGAGCAGATCAAAGACGAAG
66 G-GGAACAGATCAAAGACGAAG
* * * * * * *
5374361 GACCTTAACCCCCTAAACAGTAGGGTAACAGGTTGAATTCACAGATCTTAAT-ACCCTAAACAGT
1 GGCCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTT-ATCTCCCTAAGCAGT
* **
5374425 AGGGAAACAAATCAAAGGTGACA-
65 AGGG-AACAGATCAAAGACGA-AG
* * * * * * * *
5374448 AGCCTTAACCCCCTAAGTAGTAGGGTAATAGGCTGAAGATTGACAGATCTTAACCCCCTAAGCAA
1 GGCCTTAAACCCCTAAGCAGTAGGGTAACAGGCTG-A-ATTTACAGATCTTATCTCCCTAAGCAG
*
5374513 TAGGGAAACAGATCAAA-AGCG-AT
64 TAGGG-AACAGATCAAAGA-CGAAG
* * * * *
5374536 GGCTTTAAACCCTTAAGCAGTAGGGTAACAGGCTGAAGATTGACAGATCTTAACCCCCTAAGCAG
1 GGCCTTAAACCCCTAAGCAGTAGGGTAACAGGCTG-A-ATTTACAGATCTTATCTCCCTAAGCAG
* **
5374601 TAGGGAAACAGATCGAAGGTGAAG
64 TAGGG-AACAGATCAAAGACGAAG
* * * *
5374625 GGCCTTAAACCCCTAAGCAGTAGGGTAATAGACTGAATTTACAGATCTCATCACCCTAAGCAGTA
1 GGCCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTATCTCCCTAAGCAGTA
* **
5374690 GGGGAACAGATCGAAGGTGAAG
66 -GGGAACAGATCAAAGACGAAG
*
5374712 GGCCTTAAACCCCTAAGCAGTAGGGTAACAGGCTAAATTTACAGATCTTATCTCCCTAAGCAGTA
1 GGCCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTATCTCCCTAAGCAGTA
* *
5374777 GTGGAGCAGATCAAAGACGATG
66 G-GGAACAGATCAAAGACGAAG
* *
5374799 AGCCTT-GACCCCTAAGC
1 GGCCTTAAACCCCTAAGC
5374816 TGTAACGCCC
Statistics
Matches: 452, Mismatches: 74, Indels: 31
0.81 0.13 0.06
Matches are distributed among these distances:
85 2 0.00
86 82 0.18
87 216 0.48
88 83 0.18
89 69 0.15
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.21
Consensus pattern (86 bp):
GGCCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTATCTCCCTAAGCAGTA
GGGAACAGATCAAAGACGAAG
Found at i:5379291 original size:22 final size:23
Alignment explanation
Indices: 5379265--5379309 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
5379255 ACCTGATCAG
5379265 AATACGACACAT-AAGTGCCTGA
1 AATACGACACATAAAGTGCCTGA
*
5379287 AATACGACATATAAAGTGCCTGA
1 AATACGACACATAAAGTGCCTGA
5379310 TCAGTAAAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (23 bp):
AATACGACACATAAAGTGCCTGA
Found at i:5379526 original size:23 final size:24
Alignment explanation
Indices: 5379500--5379594 Score: 93
Period size: 28 Copynumber: 3.6 Consensus size: 24
5379490 AAATGTCCAA
5379500 CCAAAACACACCAG-TATAATCCT
1 CCAAAACACACCAGATATAATCCT
5379523 CCAAAACACACCAGTATCATATAATCCT
1 CCAAAACACACCAG----ATATAATCCT
*
5379551 CCCAAACACACCAGAATAATATAATCCAT
1 CCAAAACACACCAG----ATATAATCC-T
5379580 CCAAAACACACCAGA
1 CCAAAACACACCAGA
5379595 ATAGCACAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
23 14 0.23
25 1 0.02
28 33 0.53
29 14 0.23
ACGTcount: A:0.46, C:0.34, G:0.04, T:0.16
Consensus pattern (24 bp):
CCAAAACACACCAGATATAATCCT
Found at i:5379596 original size:29 final size:28
Alignment explanation
Indices: 5379514--5379597 Score: 132
Period size: 28 Copynumber: 3.0 Consensus size: 28
5379504 AACACACCAG
* *
5379514 TATAATCCTCCAAAACACACCAGTATCA
1 TATAATCCTCCAAAACACACCAGAATAA
*
5379542 TATAATCCTCCCAAACACACCAGAATAA
1 TATAATCCTCCAAAACACACCAGAATAA
5379570 TATAATCCATCCAAAACACACCAGAATA
1 TATAATCC-TCCAAAACACACCAGAATA
5379598 GCACAAAGTG
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 33 0.65
29 18 0.35
ACGTcount: A:0.46, C:0.31, G:0.04, T:0.19
Consensus pattern (28 bp):
TATAATCCTCCAAAACACACCAGAATAA
Found at i:5383748 original size:26 final size:26
Alignment explanation
Indices: 5383720--5383827 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
5383710 TGGTACAAAT
*
5383720 TGATAATGGGTTAGGTAAATGTTCCT
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
5383746 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
5383772 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
5383798 TGATAATGGTTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
5383824 TGAT
1 TGAT
5383828 GGGCATTTCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.31, C:0.06, G:0.24, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:5385502 original size:54 final size:54
Alignment explanation
Indices: 5385420--5385581 Score: 238
Period size: 54 Copynumber: 3.0 Consensus size: 54
5385410 TGGAGGAAGC
*
5385420 GTCCTGGTGGCTATGCCACAATTATCTGATTTGGTGGCTTTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTTTGCCACATATATCT
*
5385474 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTTTGCCACATATATCT
* * * * *
5385528 GTTCTGGTGGCTCTGCCACAA-TATCTGTATCTGGTGACTTCGTCACA-ATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTG-ATCTGGTGGCTTTGCCACATATATCT
5385581 G
1 G
5385582 GCAACCTCGC
Statistics
Matches: 99, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
53 13 0.13
54 86 0.87
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (54 bp):
GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTTTGCCACATATATCT
Found at i:5385574 original size:27 final size:27
Alignment explanation
Indices: 5385423--5385581 Score: 175
Period size: 27 Copynumber: 5.9 Consensus size: 27
5385413 AGGAAGCGTC
*
5385423 CTGGTGGCTATGCCACAATTATCTG-AT
1 CTGGTGGCTCTGCCACAA-TATCTGTAT
* * *
5385450 TTGGTGGCTTTGCCACATATATCTGT-C
1 CTGGTGGCTCTGCCACA-ATATCTGTAT
*
5385477 CTGGTGGCTATGCCACAATTATCTG-AT
1 CTGGTGGCTCTGCCACAA-TATCTGTAT
5385504 CTGGTGGCTCTGCCACATATATCTGT-T
1 CTGGTGGCTCTGCCACA-ATATCTGTAT
5385531 CTGGTGGCTCTGCCACAATATCTGTAT
1 CTGGTGGCTCTGCCACAATATCTGTAT
* *
5385558 CTGGTGACT-TCGTCACAATATCTG
1 CTGGTGGCTCT-GCCACAATATCTG
5385582 GCAACCTCGC
Statistics
Matches: 115, Mismatches: 9, Indels: 16
0.82 0.06 0.11
Matches are distributed among these distances:
26 10 0.09
27 103 0.90
28 2 0.02
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATATCTGTAT
Found at i:5385575 original size:81 final size:80
Alignment explanation
Indices: 5385423--5385581 Score: 200
Period size: 81 Copynumber: 2.0 Consensus size: 80
5385413 AGGAAGCGTC
* *
5385423 CTGGTGGCTATGCCACAATTATCTGATTTGGTGGCTTTGCCACATATATCTGTCCTGGTGGCTAT
1 CTGGTGGCTATGCCACAATTATCTGATTTGGTGGCTCTGCCACATATATCTGTCCTGGTGACTAT
5385488 GCCACAATTATCTGAT
66 GCCACAA-TATCTGAT
* *
5385504 CTGGTGGCTCTGCCAC-ATATATCTG-TTCTGGTGGCTCTGCCACA-ATATCTGTATCTGGTGAC
1 CTGGTGGCTATGCCACAAT-TATCTGATT-TGGTGGCTCTGCCACATATATCTGT-CCTGGTGAC
*
5385566 T-TCGTCACAATATCTG
63 TAT-GCCACAATATCTG
5385582 GCAACCTCGC
Statistics
Matches: 69, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
80 19 0.28
81 50 0.72
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (80 bp):
CTGGTGGCTATGCCACAATTATCTGATTTGGTGGCTCTGCCACATATATCTGTCCTGGTGACTAT
GCCACAATATCTGAT
Found at i:5386932 original size:39 final size:39
Alignment explanation
Indices: 5386888--5386968 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
5386878 CGCAATTAAG
5386888 TTTTTTCAATTTTAATCTTACCCAGGAATTTGTCCTGCT
1 TTTTTTCAATTTTAATCTTACCCAGGAATTTGTCCTGCT
5386927 TTTTTTCAATTTTAATCTTACCCAGGAATTTGTCCTGCT
1 TTTTTTCAATTTTAATCTTACCCAGGAATTTGTCCTGCT
5386966 TTT
1 TTT
5386969 CAACTTGGTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.20, C:0.20, G:0.10, T:0.51
Consensus pattern (39 bp):
TTTTTTCAATTTTAATCTTACCCAGGAATTTGTCCTGCT
Found at i:5387293 original size:2 final size:2
Alignment explanation
Indices: 5387259--5387285 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5387249 ATTTAATACT
5387259 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5387286 GTTATATAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5387301 original size:15 final size:15
Alignment explanation
Indices: 5387258--5387293 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
5387248 TATTTAATAC
5387258 TTATATATATATAT-
1 TTATATATATATATG
*
5387272 ATATATATATATATG
1 TTATATATATATATG
5387287 TTATATA
1 TTATATA
5387294 GTATTATGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
TTATATATATATATG
Found at i:5387467 original size:15 final size:13
Alignment explanation
Indices: 5387440--5387474 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
5387430 TTCTTTTCAA
5387440 ATATTATATATGT
1 ATATTATATATGT
5387453 ATATATATATAATGT
1 ATAT-TATAT-ATGT
5387468 ATATTAT
1 ATATTAT
5387475 GTATATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 4 0.20
14 8 0.40
15 8 0.40
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (13 bp):
ATATTATATATGT
Found at i:5387491 original size:21 final size:22
Alignment explanation
Indices: 5387444--5387506 Score: 76
Period size: 21 Copynumber: 2.9 Consensus size: 22
5387434 TTTCAAATAT
*
5387444 TATA-TATGTATATATATATAATG
1 TATATTATGTATATAT-TTTAA-G
5387467 TATATTATGTATATATTTTAA-
1 TATATTATGTATATATTTTAAG
*
5387488 TATATTATGTGTATATTTT
1 TATATTATGTATATATTTT
5387507 GTTTTGTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.49
23 8 0.22
24 11 0.30
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.56
Consensus pattern (22 bp):
TATATTATGTATATATTTTAAG
Found at i:5387705 original size:2 final size:2
Alignment explanation
Indices: 5387698--5387725 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5387688 AACTAATTTA
5387698 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
5387726 TAGCGTACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5392302 original size:16 final size:17
Alignment explanation
Indices: 5392272--5392304 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5392262 AATAGAAAAA
*
5392272 AAGATAAAAATACAAAG
1 AAGAGAAAAATACAAAG
5392289 AAGAGAAAAA-ACAAAG
1 AAGAGAAAAATACAAAG
5392305 TTCAAAGCGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.73, C:0.06, G:0.15, T:0.06
Consensus pattern (17 bp):
AAGAGAAAAATACAAAG
Found at i:5392385 original size:2 final size:2
Alignment explanation
Indices: 5392378--5392403 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5392368 CTGTTTATGC
5392378 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
5392404 TCTTTATTTT
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):
AT
Found at i:5395324 original size:26 final size:26
Alignment explanation
Indices: 5395288--5395394 Score: 157
Period size: 26 Copynumber: 4.2 Consensus size: 26
5395278 CATGAAATTC
5395288 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
5395314 TTATCATGAAACATTTACCTAACCC-
1 TTATCATGAAACATTTACCTAACCCA
* *
5395339 --ATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* *
5395363 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
5395389 TTATCA
1 TTATCA
5395395 ATTTGTATCA
Statistics
Matches: 76, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
23 21 0.28
26 55 0.72
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:5395366 original size:49 final size:49
Alignment explanation
Indices: 5395290--5395386 Score: 167
Period size: 49 Copynumber: 2.0 Consensus size: 49
5395280 TGAAATTCTT
5395290 ATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCC
1 ATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCC
* * *
5395339 ATCATGGAACATTTACCTAACCTATTATCATGGAACATTTACCTAACC
1 ATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACC
5395387 TATTATCAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (49 bp):
ATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCC
Found at i:5401141 original size:26 final size:26
Alignment explanation
Indices: 5401105--5401211 Score: 157
Period size: 26 Copynumber: 4.2 Consensus size: 26
5401095 CATGAAATTC
5401105 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
5401131 TTATCATGAAACATTTACCTAACCC-
1 TTATCATGAAACATTTACCTAACCCA
* *
5401156 --ATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* *
5401180 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
5401206 TTATCA
1 TTATCA
5401212 ATTTGTATCA
Statistics
Matches: 76, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
23 21 0.28
26 55 0.72
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:5401183 original size:49 final size:49
Alignment explanation
Indices: 5401107--5401203 Score: 167
Period size: 49 Copynumber: 2.0 Consensus size: 49
5401097 TGAAATTCTT
5401107 ATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCC
1 ATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCC
* * *
5401156 ATCATGGAACATTTACCTAACCTATTATCATGGAACATTTACCTAACC
1 ATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACC
5401204 TATTATCAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (49 bp):
ATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCC
Found at i:5402026 original size:3 final size:3
Alignment explanation
Indices: 5402018--5402067 Score: 64
Period size: 3 Copynumber: 16.0 Consensus size: 3
5402008 TCATTATTGC
* *
5402018 TAT TAT TAT TAT TAT TAT TATT TAC TAT TAT TATT TAT TAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TA-T TAT TAT TAT TAT
5402065 TAT
1 TAT
5402068 CATTTCTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
3 35 0.85
4 6 0.15
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:5402048 original size:13 final size:13
Alignment explanation
Indices: 5402017--5402065 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
5402007 TTCATTATTG
5402017 CTATTATTA-TTA
1 CTATTATTATTTA
*
5402029 TTATTATTATTTA
1 CTATTATTATTTA
5402042 CTATTATTATTTA
1 CTATTATTATTTA
* *
5402055 TTATCATTATT
1 CTATTATTATT
5402066 ATCATTTCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
12 8 0.25
13 24 0.75
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (13 bp):
CTATTATTATTTA
Found at i:5402063 original size:16 final size:16
Alignment explanation
Indices: 5402020--5402067 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
5402010 ATTATTGCTA
*
5402020 TTATTATTATTATTA-
1 TTATTATCATTATTAT
5402035 TTATT-TACTATTATTAT
1 TTATTAT-C-ATTATTAT
5402052 TTATTATCATTATTAT
1 TTATTATCATTATTAT
5402068 CATTTCTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 1 0.04
15 5 0.18
16 15 0.54
17 6 0.21
18 1 0.04
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATTATCATTATTAT
Found at i:5402065 original size:19 final size:18
Alignment explanation
Indices: 5402018--5402077 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 18
5402008 TCATTATTGC
5402018 TATTATTATTATTATTA-T
1 TATTA-TATTATTATTATT
*
5402036 TATT-TACTATTATTATT
1 TATTATATTATTATTATT
*
5402053 TATTATCATTATTATCATT
1 TATTAT-ATTATTATTATT
*
5402072 TCTTAT
1 TATTAT
5402078 TTTGTTTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
16 10 0.29
17 5 0.14
18 5 0.14
19 15 0.43
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (18 bp):
TATTATATTATTATTATT
Found at i:5402284 original size:3 final size:3
Alignment explanation
Indices: 5402269--5402331 Score: 72
Period size: 3 Copynumber: 20.7 Consensus size: 3
5402259 CACTTGACTG
* * *
5402269 TTA TTA CTA TTA TTA TTA TTA TTA TTA TTTA TTG TTA TTA TTA TCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
* *
5402315 TTG TTA TTA TTG TTA TT
1 TTA TTA TTA TTA TTA TT
5402332 TGTTGATGGT
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.27, C:0.03, G:0.05, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:5407091 original size:20 final size:20
Alignment explanation
Indices: 5407058--5407098 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5407048 AGAGGTGATT
**
5407058 TCATTTTTTTATTTTCTTTC
1 TCATTTTTCAATTTTCTTTC
*
5407078 TCATTTTTCAATTTTTTTTC
1 TCATTTTTCAATTTTCTTTC
5407098 T
1 T
5407099 TTTATAATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (20 bp):
TCATTTTTCAATTTTCTTTC
Found at i:5407108 original size:3 final size:3
Alignment explanation
Indices: 5407102--5407159 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
5407092 TTTTTCTTTT
5407102 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5407150 ATA ATA ATA A
1 ATA ATA ATA A
5407160 AGAGGCTTAC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5407787 original size:3 final size:3
Alignment explanation
Indices: 5407779--5408115 Score: 308
Period size: 3 Copynumber: 111.7 Consensus size: 3
5407769 ATTAATTAAA
* *
5407779 ATT ATT ATT ATT -TCT ACT ATT ATTT ATT ATC ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT AT-T ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT
* * * *
5407825 ATT ACT ATT ATT ATT GTT -TT -TT ACT ATT ATT ATTT ATT ATC ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT
* * *
5407869 ATT AAT ATT ATT ACT ATT ATT ATT ATT ATT ATT ACT ATT ATT ATT -TT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * *
5407916 TTT ACT ATT ATT ATT ATT TTT ACT ATT ACT ATT ATT TTCT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT
* * * *
5407962 ATA ATT ATT ATT ACT ATC ATT ATT ATT ATT ACT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
5408010 ATT ATT ATT -TT ACT ATT ATT ATT -TCGT ATC ATT ATT GTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT--T ATT ATT ATT ATT ATT ATT
* * * * *
5408055 ACT ATT ATT ATT ATTT ACT ATT ATT ATTT ATT ATT ATT GTT GTT GTT
1 ATT ATT ATT ATT A-TT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT
*
5408102 ATT ATT ATC ATT AT
1 ATT ATT ATT ATT AT
5408116 CTGTTCAATT
Statistics
Matches: 271, Mismatches: 50, Indels: 26
0.78 0.14 0.07
Matches are distributed among these distances:
2 10 0.04
3 245 0.90
4 15 0.06
5 1 0.00
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:5408221 original size:18 final size:18
Alignment explanation
Indices: 5408183--5408221 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5408173 TATTTGCTTA
* *
5408183 TTTATTTATTCTTTTAGT
1 TTTATTTATTATTTTACT
*
5408201 TTTATTTATTATTTTTCT
1 TTTATTTATTATTTTACT
5408219 TTT
1 TTT
5408222 TACTAGCTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.77
Consensus pattern (18 bp):
TTTATTTATTATTTTACT
Found at i:5410389 original size:5 final size:5
Alignment explanation
Indices: 5410379--5410424 Score: 58
Period size: 5 Copynumber: 9.4 Consensus size: 5
5410369 TTCATGCATC
* * *
5410379 TACAT TACAT TGCAT TACAT TACAT TACAT CACA- TACAT CACAT TA
1 TACAT TACAT TACAT TACAT TACAT TACAT TACAT TACAT TACAT TA
5410425 ATCAAAAGAG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
4 3 0.09
5 31 0.91
ACGTcount: A:0.39, C:0.24, G:0.02, T:0.35
Consensus pattern (5 bp):
TACAT
Found at i:5410399 original size:15 final size:15
Alignment explanation
Indices: 5410373--5410417 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
5410363 TATGAATTCA
5410373 TGCATCTACATTACAT
1 TGCAT-TACATTACAT
5410389 TGCATTACATTACAT
1 TGCATTACATTACAT
* *
5410404 TACATCACA-TACAT
1 TGCATTACATTACAT
5410418 CACATTAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 5 0.19
15 17 0.63
16 5 0.19
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (15 bp):
TGCATTACATTACAT
Found at i:5410428 original size:9 final size:10
Alignment explanation
Indices: 5410375--5410428 Score: 58
Period size: 10 Copynumber: 5.5 Consensus size: 10
5410365 TGAATTCATG
5410375 CATCTACATTA
1 CATC-ACATTA
**
5410386 CATTGCATTA
1 CATCACATTA
*
5410396 CATTACATTA
1 CATCACATTA
5410406 CATCACA-TA
1 CATCACATTA
5410415 CATCACATTA
1 CATCACATTA
5410425 -ATCA
1 CATCA
5410429 AAAGAGTTAG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
9 13 0.34
10 22 0.58
11 3 0.08
ACGTcount: A:0.39, C:0.26, G:0.02, T:0.33
Consensus pattern (10 bp):
CATCACATTA
Found at i:5412865 original size:93 final size:93
Alignment explanation
Indices: 5412757--5412930 Score: 278
Period size: 93 Copynumber: 1.9 Consensus size: 93
5412747 CTGCCCATAA
* * *
5412757 ACGAACTCGGACTCAACTCAATGAGCTCAGG-CGTTTGCATCCATAAGTGAACTCGGACTCAACT
1 ACGAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACT
*
5412821 CAACGAGCTCGGATGCCTAGTTACATCTC
65 CAACGAGATCGGATGCCTAGTTACATCTC
* *
5412850 ACGAACTTGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCTGACTCAACTC
1 ACGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
5412915 AACGAGATCGGATGCC
66 AACGAGATCGGATGCC
5412931 CAAATATCCT
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
92 2 0.03
93 72 0.97
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.21
Consensus pattern (93 bp):
ACGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
AACGAGATCGGATGCCTAGTTACATCTC
Found at i:5412926 original size:46 final size:45
Alignment explanation
Indices: 5412759--5412926 Score: 164
Period size: 46 Copynumber: 3.6 Consensus size: 45
5412749 GCCCATAAAC
* *
5412759 GAACTCGGACTCAACTCAATGAGCTCAGG-CGTTTGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGCTC-GGAC-ATTGCATCCATAAGT
* * *
5412805 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACAT-C-TCA-C
1 GAACTCGGACTCAACTCAACGAGCTCGGA---C-A-TTGCATCCATAAGT
*
5412852 GAACTTGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGCTCGGACATT-GCATCCATAAGT
* *
5412898 GAACTCTGACTCAACTCAACGAGATCGGA
1 GAACTCGGACTCAACTCAACGAGCTCGGA
5412927 TGCCCAAATA
Statistics
Matches: 100, Mismatches: 13, Indels: 18
0.76 0.10 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 4 0.04
46 51 0.51
47 28 0.28
48 2 0.02
49 2 0.02
50 5 0.05
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (45 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTGCATCCATAAGT
Found at i:5414804 original size:21 final size:21
Alignment explanation
Indices: 5414778--5414817 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
5414768 AATCAACTCT
*
5414778 GTAAATCTGGGTTTTTTTTCC
1 GTAAATCTAGGTTTTTTTTCC
5414799 GTAAATCTAGGTTTTTTTT
1 GTAAATCTAGGTTTTTTTT
5414818 AGTTTGGTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.10, G:0.17, T:0.55
Consensus pattern (21 bp):
GTAAATCTAGGTTTTTTTTCC
Found at i:5420409 original size:20 final size:19
Alignment explanation
Indices: 5420375--5420412 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
5420365 TGACTAGTTA
5420375 CAACTAACGAACTCGGACT
1 CAACTAACGAACTCGGACT
*
5420394 CAACTCAACGAGCTCGGAC
1 CAACT-AACGAACTCGGAC
5420413 ATTCGCATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.34, C:0.34, G:0.18, T:0.13
Consensus pattern (19 bp):
CAACTAACGAACTCGGACT
Found at i:5428224 original size:17 final size:19
Alignment explanation
Indices: 5428197--5428234 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
5428187 TAGAAGTGAA
*
5428197 TGGATAGGTTT-GAATAAG
1 TGGATAGGTTTCAAATAAG
5428215 TGGA-AGGTTTCAAATAAG
1 TGGATAGGTTTCAAATAAG
5428233 TG
1 TG
5428235 TAAGAATAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.34, C:0.03, G:0.32, T:0.32
Consensus pattern (19 bp):
TGGATAGGTTTCAAATAAG
Found at i:5431974 original size:143 final size:142
Alignment explanation
Indices: 5431708--5432175 Score: 634
Period size: 143 Copynumber: 3.3 Consensus size: 142
5431698 ATATAGCAAA
* * ** * * *
5431708 CCTTATCTTCCTGAAGTTGCGGCAGAGCAGACTAAAGACAGCGAATCTTATTTCCCTGATGTTGC
1 CCTTATCTCCCTAAAGTTGCAACAGAGCAGACTGAAGACAACGAATCTTATTTCCCTGAAGTTGC
* * *
5431773 AGTGGAACGGATTGAAGCTACAAATTATGGCAAATATTATCTTCCTAAAGTTGTAGTGGAGCAGA
66 AGTGGAACGGATTGAAGCTACAAATTATGGCGAATCTTATCTTCCT-AAGTTGCAGTGGAGCAGA
5431838 TTGAAGCCACCAG
130 TTGAAGCCACCAG
* **
5431851 CCTTATCTCCCTAAAGTTGCAGCAGAGCAGACTGAAGACATTGAATCTTATTTCCCTGAAGTTGC
1 CCTTATCTCCCTAAAGTTGCAACAGAGCAGACTGAAGACAACGAATCTTATTTCCCTGAAGTTGC
* ** *
5431916 AATGGAATAGATTAAAGCTACAAATTATGGCGAATCTTATCTTCCTAAGGTTGCAGTGGAGCAGA
66 AGTGGAACGGATTGAAGCTACAAATTATGGCGAATCTTATCTTCCTAA-GTTGCAGTGGAGCAGA
5431981 TTGAAGCCACCAG
130 TTGAAGCCACCAG
** * *
5431994 TGTTATCTCCCTAAAGTTGCAACGGAGCAGACTGAAGACAACAAATCTTATTTCCCT-AACGTTG
1 CCTTATCTCCCTAAAGTTGCAACAGAGCAGACTGAAGACAACGAATCTTATTTCCCTGAA-GTTG
* *
5432058 TAGTGGAACGGATTGAAGATACAAATTATGGCGAATCTTATCTTCCTGAAGTTGCAGTGGAGCAG
65 CAGTGGAACGGATTGAAGCTACAAATTATGGCGAATCTTATCTTCCT-AAGTTGCAGTGGAGCAG
*
5432123 ATTGAAGCCATCAG
129 ATTGAAGCCACCAG
* *
5432137 TCTTATCTCCC-AGAAGTTGCAATAGGAGCAGACTGAAGA
1 CCTTATCTCCCTA-AAGTTGCAACA-GAGCAGACTGAAGA
5432176 TAGCAGACCC
Statistics
Matches: 289, Mismatches: 31, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
142 5 0.02
143 268 0.93
144 16 0.06
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (142 bp):
CCTTATCTCCCTAAAGTTGCAACAGAGCAGACTGAAGACAACGAATCTTATTTCCCTGAAGTTGC
AGTGGAACGGATTGAAGCTACAAATTATGGCGAATCTTATCTTCCTAAGTTGCAGTGGAGCAGAT
TGAAGCCACCAG
Found at i:5433649 original size:3 final size:3
Alignment explanation
Indices: 5433643--5433673 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5433633 TTATTTATTG
5433643 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
5433674 TATTATTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:5433678 original size:3 final size:3
Alignment explanation
Indices: 5433672--5433835 Score: 161
Period size: 3 Copynumber: 54.7 Consensus size: 3
5433662 CATCATCATC
* * **
5433672 ATT ATT ATT ATT ATT ATT ATT ATT TTT ATT ACT ATT ACC ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * *
5433720 ATT ACT ATT ACT ATT ATT TTCT ATT ATT ATA ATT ATT ATT AGT ATC
1 ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT
* *
5433766 ATT ATT ATT ATT ACT ATT ATT ATT -TT -TT ACT ATT ATTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT
* * *
5433810 ATT GTT GTT ATT ATT ATT ATC ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
5433836 CTTTTAATTT
Statistics
Matches: 130, Mismatches: 28, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
2 4 0.03
3 121 0.93
4 5 0.04
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:5433943 original size:18 final size:18
Alignment explanation
Indices: 5433905--5433943 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5433895 TATTTGCTTG
* *
5433905 TTTATTTATTCTTTTAGT
1 TTTATTTATTATTTTACT
*
5433923 TTTATTTATTATTTTTCT
1 TTTATTTATTATTTTACT
5433941 TTT
1 TTT
5433944 TACCAGCTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.77
Consensus pattern (18 bp):
TTTATTTATTATTTTACT
Found at i:5440539 original size:142 final size:145
Alignment explanation
Indices: 5440268--5440562 Score: 443
Period size: 142 Copynumber: 2.0 Consensus size: 145
5440258 TCATATAAGT
* *
5440268 AAAGAGATCTATTCATTGATAAGAAAAACAAAAAACATGAGTAGTGATTGGATTGATGATAAAAT
1 AAAGAGATCTATTCATTGAT---AAAAACAAAAAACATGAGTAGTAATTGGATTGATAATAAAAT
* * * *
5440333 AAAACCTTGAATCACGAATAGTGATTCGATTAATGATAAAGAAATAAAATTTTTTATTCTGTTTT
63 AAAACCTTGAATCACGAACAGTGATTCGATTAATGATAAAGAAATAAAATTCTTGATTCAGTTTT
5440398 CCACCTTAACAA-AAAAA
128 CCACCTTAACAACAAAAA
*
5440415 AAAGAGATCTATTCATTGAT-AAAA-AAAAAACGTGAGTAGTAATTGGATTGATAATAAAATAAA
1 AAAGAGATCTATTCATTGATAAAAACAAAAAACATGAGTAGTAATTGGATTGATAATAAAATAAA
* *
5440478 ATCTTGGATCACGAACAGTGATTCGATTAATGATAAAGAAATAAAATTCTTGATTCAGTTTTCCA
66 ACCTTGAATCACGAACAGTGATTCGATTAATGATAAAGAAATAAAATTCTTGATTCAGTTTTCCA
* *
5440543 CTTTAACAACAGAAA
131 CCTTAACAACAAAAA
5440558 AAAGA
1 AAAGA
5440563 ATTGATCAAA
Statistics
Matches: 136, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
142 103 0.76
143 13 0.10
147 20 0.15
ACGTcount: A:0.46, C:0.10, G:0.14, T:0.29
Consensus pattern (145 bp):
AAAGAGATCTATTCATTGATAAAAACAAAAAACATGAGTAGTAATTGGATTGATAATAAAATAAA
ACCTTGAATCACGAACAGTGATTCGATTAATGATAAAGAAATAAAATTCTTGATTCAGTTTTCCA
CCTTAACAACAAAAA
Found at i:5444247 original size:18 final size:18
Alignment explanation
Indices: 5444189--5444253 Score: 53
Period size: 20 Copynumber: 3.5 Consensus size: 18
5444179 AAATATAAAT
5444189 TATTCTATTTATATTT-TA
1 TATT-TATTTATATTTATA
* **
5444207 T-TTTATATATATAAATAA
1 TATTTATTTATATTTAT-A
5444225 TTATTTATTTATATTTATA
1 -TATTTATTTATATTTATA
5444244 TATTTTATTT
1 TA-TTTATTT
5444254 GCTAACGTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 9
0.71 0.12 0.18
Matches are distributed among these distances:
16 8 0.22
17 3 0.08
18 4 0.11
19 9 0.25
20 12 0.33
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
TATTTATTTATATTTATA
Found at i:5449075 original size:17 final size:17
Alignment explanation
Indices: 5449049--5449081 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5449039 GGCTTAGCCA
*
5449049 TGTGATCCACACGGGCG
1 TGTGACCCACACGGGCG
5449066 TGTGACCCACACGGGC
1 TGTGACCCACACGGGC
5449082 AGGCCACATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.33, G:0.33, T:0.15
Consensus pattern (17 bp):
TGTGACCCACACGGGCG
Found at i:5451534 original size:14 final size:13
Alignment explanation
Indices: 5451515--5451545 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
5451505 GTATTTTCAT
5451515 TATATATATGTATA
1 TATATATATGT-TA
5451529 TATATATATGTTA
1 TATATATATGTTA
5451542 TATA
1 TATA
5451546 GCATTATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (13 bp):
TATATATATGTTA
Found at i:5456148 original size:30 final size:28
Alignment explanation
Indices: 5456113--5456180 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 28
5456103 ACCTTATTTT
5456113 TATATTAT-ATATTATAAAATTATTTTATTA
1 TATATTATCATATTAT--AATTA-TTTATTA
*
5456143 TATATTATTTCATATTATTATTATTTATTA
1 TATATTA--TCATATTATAATTATTTATTA
5456173 TATATTAT
1 TATATTAT
5456181 TTTTCACAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
28 1 0.03
30 21 0.62
31 4 0.12
32 1 0.03
33 7 0.21
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (28 bp):
TATATTATCATATTATAATTATTTATTA
Found at i:5456157 original size:10 final size:10
Alignment explanation
Indices: 5456137--5456181 Score: 58
Period size: 10 Copynumber: 4.5 Consensus size: 10
5456127 TAAAATTATT
5456137 TTATTATATA
1 TTATTATATA
5456147 TTATT-TCATA
1 TTATTAT-ATA
5456157 TTATTAT-TA
1 TTATTATATA
5456166 TTTATTATATA
1 -TTATTATATA
5456177 TTATT
1 TTATT
5456182 TTTCACAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
9 3 0.10
10 25 0.81
11 3 0.10
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (10 bp):
TTATTATATA
Found at i:5456181 original size:23 final size:23
Alignment explanation
Indices: 5456107--5456181 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
5456097 TTTTTAACCT
*
5456107 TATTTTTA-TATTATATATTATAA
1 TATTATTATTATTATATATTAT-A
* *
5456130 AATTATT-TTATTATATATTATT
1 TATTATTATTATTATATATTATA
*
5456152 TCA-TATTATTATTATTTATTATA
1 T-ATTATTATTATTATATATTATA
5456175 TATTATT
1 TATTATT
5456182 TTTCACAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
22 5 0.12
23 37 0.88
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (23 bp):
TATTATTATTATTATATATTATA
Found at i:5456551 original size:21 final size:23
Alignment explanation
Indices: 5456506--5456551 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
5456496 ATTAATTACT
* *
5456506 TATTTTATACTTATATTTATATA
1 TATTATATAATTATATTTATATA
5456529 TATTATATAATTAT-TTTAT-TA
1 TATTATATAATTATATTTATATA
5456550 TA
1 TA
5456552 AATATAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 5 0.24
23 12 0.57
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (23 bp):
TATTATATAATTATATTTATATA
Found at i:5460386 original size:14 final size:16
Alignment explanation
Indices: 5460367--5460399 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
5460357 CGATATCCTT
5460367 TTTGCAT-TCAT-GCA
1 TTTGCATCTCATAGCA
5460381 TTTGCATCTCATAGCA
1 TTTGCATCTCATAGCA
5460397 TTT
1 TTT
5460400 TATCATATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 4 0.24
16 6 0.35
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.45
Consensus pattern (16 bp):
TTTGCATCTCATAGCA
Found at i:5468812 original size:210 final size:210
Alignment explanation
Indices: 5468450--5469119 Score: 919
Period size: 210 Copynumber: 3.2 Consensus size: 210
5468440 GCAGCATAGT
* * *
5468450 AGATCTCACCTTCAGATGTTTACGTTGAAGCAGATCCAAGATGACAAATCTTATCTCTCTGTATT
1 AGATCTCACCTTCAGATGATTACGCTGAAGCAGATCCAAGATGACAGATCTTATCTCTCTGTATT
*
5468515 CGGCAGGGAGCAAATCGAAGATATAGCTAATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTA
66 CGGCAGGGAGCAAATCGAAGATATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTA
* *
5468580 AGATGATTTGTCGTCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATTTCCACTTTGATGGA
131 AGATGATTTGTCGTCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCACTTTAATGGA
* *
5468645 -AGGCAGACACATAGC
196 GA-GCAGATACACAGC
*
5468660 AGATCTCACCTTCAGATGTTTACGCTGAAGCAGATCCAAGATGACAGATCTTATCTCTCTGTATT
1 AGATCTCACCTTCAGATGATTACGCTGAAGCAGATCCAAGATGACAGATCTTATCTCTCTGTATT
* * *
5468725 CGGCGGGGAGCAAATCGAAGATATAGCTGATTTGACTTTTACGTGTTTACGATGAAGCAAATCTA
66 CGGCAGGGAGCAAATCGAAGATATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTA
* * *
5468790 AGATGATTTATCGTCTCTGTATTGTCAGAGAACAAATTGAAGTCTGGCATCTCCACTTCAATGGA
131 AGATGATTTGTCGTCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCACTTTAATGGA
*
5468855 GAGTAGATACACAGC
196 GAGCAGATACACAGC
* * ** *
5468870 AGAT-TCGACCTTTAGACGATTA-GACTGAAGCAAGATCCAAGATGATTTG-GC--ATC-CT-TG
1 AGATCTC-ACCTTCAGATGATTACG-CTGAAGC-AGATCCAAGATGA-CAGATCTTATCTCTCTG
* * * * * *
5468928 TACTT--ACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACATGTTTACGATAAAGCAA
62 TA-TTCGGCAGGGAGCAAATCGAAGATATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAA
* * *
5468991 ATCTAAGATGATTTGTCATCTCTGTATTGTCAGATAACAAATCGAAGTTTGGCATCTCCACTTTA
126 ATCTAAGATGATTTGTCGTCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCACTTTA
5469056 ATGGAGAGCAGATACACAGC
191 ATGGAGAGCAGATACACAGC
* * *
5469076 ATATCTCACCTTCAGATGATTATGCTGAAGCAAATCCAAGATGA
1 AGATCTCACCTTCAGATGATTACGCTGAAGCAGATCCAAGATGA
5469120 TTTGGCATTC
Statistics
Matches: 412, Mismatches: 40, Indels: 21
0.87 0.08 0.04
Matches are distributed among these distances:
205 12 0.03
206 150 0.36
207 7 0.02
208 4 0.01
209 6 0.01
210 217 0.53
211 15 0.04
212 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.29
Consensus pattern (210 bp):
AGATCTCACCTTCAGATGATTACGCTGAAGCAGATCCAAGATGACAGATCTTATCTCTCTGTATT
CGGCAGGGAGCAAATCGAAGATATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTA
AGATGATTTGTCGTCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCACTTTAATGGA
GAGCAGATACACAGC
Found at i:5469016 original size:206 final size:206
Alignment explanation
Indices: 5468525--5469160 Score: 827
Period size: 206 Copynumber: 3.1 Consensus size: 206
5468515 CGGCAGGGAG
* *
5468525 CAAATCGAAGATATAGCTAATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTG
1 CAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTG
* * *
5468590 TCGTCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATTTCCACTTTGATGGA-AGGCAGACA
66 TCGTCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCACTTTAATGGAGA-GCAGATA
* * ** *
5468654 CATAGCAGATCTCACCTTCAGATGTTTACGCTGAAGC-AGATCCAAGATGA-CAGATCTTATCTC
130 CACAGCAGATCTCACCTTCAGATGATTACGCTGAAGCAAGATCCAAGATGATTTG-GC--ATC-C
* ** *
5468717 TCTGTA-TTCGGCGGGGAG
191 T-TGTACTT--ACAAGGAA
* * * *
5468735 CAAATCGAAGATATAGCTGATTTGACTTTTACGTGTTTACGATGAAGCAAATCTAAGATGATTTA
1 CAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTG
* * *
5468800 TCGTCTCTGTATTGTCAGAGAACAAATTGAAGTCTGGCATCTCCACTTCAATGGAGAGTAGATAC
66 TCGTCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCACTTTAATGGAGAGCAGATAC
* *
5468865 ACAGCAGAT-TCGACCTTTAGACGATTA-GACTGAAGCAAGATCCAAGATGATTTGGCATCCTTG
131 ACAGCAGATCTC-ACCTTCAGATGATTACG-CTGAAGCAAGATCCAAGATGATTTGGCATCCTTG
5468928 TACTTACAAGGAA
194 TACTTACAAGGAA
* *
5468941 CAAATCGAAGACATAGCTGATTTGGCTTTCACATGTTTACGATAAAGCAAATCTAAGATGATTTG
1 CAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTG
* * *
5469006 TCATCTCTGTATTGTCAGATAACAAATCGAAGTTTGGCATCTCCACTTTAATGGAGAGCAGATAC
66 TCGTCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCACTTTAATGGAGAGCAGATAC
* * * *
5469071 ACAGCATATCTCACCTTCAGATGATTATGCTGAAGCAA-ATCCAAGATGATTTGGCATTCTTGTT
131 ACAGCAGATCTCACCTTCAGATGATTACGCTGAAGCAAGATCCAAGATGATTTGGCATCCTTGTA
*
5469135 CTTACAAGAAA
196 CTTACAAGGAA
*
5469146 CAAATCAAAGACATA
1 CAAATCGAAGACATA
5469161 ACTAAAGTGG
Statistics
Matches: 378, Mismatches: 40, Indels: 21
0.86 0.09 0.05
Matches are distributed among these distances:
205 48 0.13
206 152 0.40
207 7 0.02
208 4 0.01
209 6 0.02
210 145 0.38
211 15 0.04
212 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (206 bp):
CAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTG
TCGTCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCACTTTAATGGAGAGCAGATAC
ACAGCAGATCTCACCTTCAGATGATTACGCTGAAGCAAGATCCAAGATGATTTGGCATCCTTGTA
CTTACAAGGAA
Found at i:5470422 original size:30 final size:28
Alignment explanation
Indices: 5470387--5470454 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 28
5470377 ACCTTATTTT
5470387 TATATTAT-ATATTATAAAATTATTTTATTA
1 TATATTATCATATTAT--AATTA-TTTATTA
*
5470417 TATATTATTTCATATTATTATTATTTATTA
1 TATATTA--TCATATTATAATTATTTATTA
5470447 TATATTAT
1 TATATTAT
5470455 TTTTCACAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
28 1 0.03
30 21 0.62
31 4 0.12
32 1 0.03
33 7 0.21
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (28 bp):
TATATTATCATATTATAATTATTTATTA
Found at i:5470431 original size:10 final size:10
Alignment explanation
Indices: 5470411--5470455 Score: 58
Period size: 10 Copynumber: 4.5 Consensus size: 10
5470401 TAAAATTATT
5470411 TTATTATATA
1 TTATTATATA
5470421 TTATT-TCATA
1 TTATTAT-ATA
5470431 TTATTAT-TA
1 TTATTATATA
5470440 TTTATTATATA
1 -TTATTATATA
5470451 TTATT
1 TTATT
5470456 TTTCACAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
9 3 0.10
10 25 0.81
11 3 0.10
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (10 bp):
TTATTATATA
Found at i:5470455 original size:23 final size:23
Alignment explanation
Indices: 5470381--5470455 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
5470371 TTTTTAACCT
*
5470381 TATTTTTA-TATTATATATTATAA
1 TATTATTATTATTATATATTAT-A
* *
5470404 AATTATT-TTATTATATATTATT
1 TATTATTATTATTATATATTATA
*
5470426 TCA-TATTATTATTATTTATTATA
1 T-ATTATTATTATTATATATTATA
5470449 TATTATT
1 TATTATT
5470456 TTTCACAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
22 5 0.12
23 37 0.88
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (23 bp):
TATTATTATTATTATATATTATA
Found at i:5470808 original size:25 final size:23
Alignment explanation
Indices: 5470780--5470843 Score: 60
Period size: 25 Copynumber: 2.8 Consensus size: 23
5470770 ATTAATTACT
* *
5470780 TATTTTATACTTATATTTATATATA
1 TATTATATAATTAT-TTTAT-TATA
5470805 TATTATATAATTATTTTATTATA
1 TATTATATAATTATTTTATTATA
* *
5470828 -AATATA-AATTTTTTTA
1 TATTATATAATTATTTTA
5470844 CATATTTGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
21 9 0.26
22 5 0.14
23 4 0.11
24 5 0.14
25 12 0.34
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
TATTATATAATTATTTTATTATA
Found at i:5470900 original size:17 final size:17
Alignment explanation
Indices: 5470880--5470936 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
5470870 TTCTAAACCA
*
5470880 ATATATTTTTTATTTTT
1 ATATAATTTTTATTTTT
*
5470897 ATATAATTATTATCCTTTT
1 ATATAATTTTTAT--TTTT
* *
5470916 ATA-AATTTTTGTTATT
1 ATATAATTTTTATTTTT
5470932 ATATA
1 ATATA
5470937 TTATATATTG
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 6 0.19
17 12 0.38
18 7 0.22
19 7 0.22
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.63
Consensus pattern (17 bp):
ATATAATTTTTATTTTT
Found at i:5474100 original size:2 final size:2
Alignment explanation
Indices: 5474093--5474122 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5474083 CTCCGCATTA
5474093 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
5474123 TTCCTCCATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5474929 original size:39 final size:39
Alignment explanation
Indices: 5474886--5474961 Score: 93
Period size: 41 Copynumber: 1.9 Consensus size: 39
5474876 TTATCTTAAC
* *
5474886 ATTTTTA-ATG-ATATATTATAGTAGTATATAATAAATTTA
1 ATTTTTATATGTATAAATTATA-TAATATATAA-AAATTTA
5474925 ATTTTTATATGTTATAAATTATATAATATATAAAAAT
1 ATTTTTATATG-TATAAATTATATAATATATAAAAAT
5474962 AACATAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
39 7 0.22
40 7 0.22
41 9 0.28
42 9 0.28
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (39 bp):
ATTTTTATATGTATAAATTATATAATATATAAAAATTTA
Found at i:5476091 original size:53 final size:53
Alignment explanation
Indices: 5476029--5476135 Score: 198
Period size: 53 Copynumber: 2.0 Consensus size: 53
5476019 TATTATTAAC
5476029 TATTGAAATAAAATATTTGAAAGAAGTTTTATTAGTAT-TTTTTTTTCAAATCG
1 TATTGAAATAAAATATTTGAAAGAAGTTTTATTAGTATATTTTTTTT-AAATCG
5476082 TATTGAAATAAAATATTTGAAAGAAGTTTTATTAGTATATTTTTTTTAAATCG
1 TATTGAAATAAAATATTTGAAAGAAGTTTTATTAGTATATTTTTTTTAAATCG
5476135 T
1 T
5476136 CAAAATTAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
53 45 0.85
54 8 0.15
ACGTcount: A:0.38, C:0.03, G:0.11, T:0.48
Consensus pattern (53 bp):
TATTGAAATAAAATATTTGAAAGAAGTTTTATTAGTATATTTTTTTTAAATCG
Found at i:5477956 original size:24 final size:24
Alignment explanation
Indices: 5477901--5477948 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
5477891 CAATTCTTGG
5477901 GAAACAACTTAACTAAAAGACTGT
1 GAAACAACTTAACTAAAAGACTGT
5477925 GAAACAACTTAACTAAAAGACTGT
1 GAAACAACTTAACTAAAAGACTGT
5477949 AAGTCAACAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
GAAACAACTTAACTAAAAGACTGT
Found at i:5477979 original size:81 final size:81
Alignment explanation
Indices: 5477844--5478005 Score: 324
Period size: 81 Copynumber: 2.0 Consensus size: 81
5477834 CAATTCTTGG
5477844 GAAACAACTTAACTAAAAGACTGTAAGTCAACAGTCTCATTACTTTTCAATTCTTGGGAAACAAC
1 GAAACAACTTAACTAAAAGACTGTAAGTCAACAGTCTCATTACTTTTCAATTCTTGGGAAACAAC
5477909 TTAACTAAAAGACTGT
66 TTAACTAAAAGACTGT
5477925 GAAACAACTTAACTAAAAGACTGTAAGTCAACAGTCTCATTACTTTTCAATTCTTGGGAAACAAC
1 GAAACAACTTAACTAAAAGACTGTAAGTCAACAGTCTCATTACTTTTCAATTCTTGGGAAACAAC
5477990 TTAACTAAAAGACTGT
66 TTAACTAAAAGACTGT
5478006 AAGTCAACAG
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (81 bp):
GAAACAACTTAACTAAAAGACTGTAAGTCAACAGTCTCATTACTTTTCAATTCTTGGGAAACAAC
TTAACTAAAAGACTGT
Found at i:5480549 original size:30 final size:30
Alignment explanation
Indices: 5480515--5480580 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
5480505 GTTATTTTAG
5480515 TTTATAGTTCAAATATTTTAATTATAAAAA
1 TTTATAGTTCAAATATTTTAATTATAAAAA
5480545 TTTATAGTTCAAATATTTTAATTATAAAAA
1 TTTATAGTTCAAATATTTTAATTATAAAAA
*
5480575 GTTATA
1 TTTATA
5480581 TAAATTTAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (30 bp):
TTTATAGTTCAAATATTTTAATTATAAAAA
Found at i:5480562 original size:15 final size:15
Alignment explanation
Indices: 5480515--5480562 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
5480505 GTTATTTTAG
5480515 TTTATAGTTCAAATA
1 TTTATAGTTCAAATA
* * *
5480530 TTT-TAATTATAAAAA
1 TTTATAGTT-CAAATA
5480545 TTTATAGTTCAAATA
1 TTTATAGTTCAAATA
5480560 TTT
1 TTT
5480563 TAATTATAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
14 4 0.16
15 17 0.68
16 4 0.16
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (15 bp):
TTTATAGTTCAAATA
Found at i:5482404 original size:29 final size:29
Alignment explanation
Indices: 5482371--5482428 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
5482361 TGATTTCGTA
*
5482371 TTATTT-TCTATATATATTTCCTTTTAAAT
1 TTATTTATATATATATATTT-CTTTTAAAT
* *
5482400 TTATTTATATTTATATATTTTTTTTAAAT
1 TTATTTATATATATATATTTCTTTTAAAT
5482429 CTATATGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (29 bp):
TTATTTATATATATATATTTCTTTTAAAT
Found at i:5484199 original size:19 final size:20
Alignment explanation
Indices: 5484164--5484209 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
5484154 AATAAAAATA
*
5484164 AATAAAATTTATTAAATTTT
1 AATAAAATATATTAAATTTT
5484184 AATAAAATAT-TTAAATTTT
1 AATAAAATATATTAAATTTT
*
5484203 ATTAAAA
1 AATAAAA
5484210 AATAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AATAAAATATATTAAATTTT
Found at i:5484767 original size:19 final size:19
Alignment explanation
Indices: 5484739--5484783 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
5484729 TTTTTGATAT
*
5484739 ATTTTATATATTTTTTTACA
1 ATTTT-TATAATTTTTTACA
*
5484759 ATTTTTATAATTTTTTACG
1 ATTTTTATAATTTTTTACA
5484778 ATTTTT
1 ATTTTT
5484784 TTTTCTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (19 bp):
ATTTTTATAATTTTTTACA
Found at i:5485379 original size:5 final size:5
Alignment explanation
Indices: 5485369--5485395 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
5485359 TTGTTTCTAG
5485369 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
5485396 TCCTCTTGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:5488927 original size:21 final size:21
Alignment explanation
Indices: 5488839--5488937 Score: 65
Period size: 21 Copynumber: 4.7 Consensus size: 21
5488829 GTAGGGGTCT
** * *
5488839 ACACGCCTATGTGGAGGCCAC
1 ACACGCCCGTGTGAAGGCCCC
* *
5488860 ACACACTCGTGTGAAGGCCCC
1 ACACGCCCGTGTGAAGGCCCC
** * * **
5488881 ACATACCCTTGTAGATGG-GGC
1 ACACGCCCGTGT-GAAGGCCCC
5488902 ACACGCCCGTGTGAAGGCCCC
1 ACACGCCCGTGTGAAGGCCCC
*
5488923 ACACGCCCGTATGAA
1 ACACGCCCGTGTGAA
5488938 CAACCTGTGT
Statistics
Matches: 57, Mismatches: 19, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
20 4 0.07
21 49 0.86
22 4 0.07
ACGTcount: A:0.24, C:0.34, G:0.26, T:0.15
Consensus pattern (21 bp):
ACACGCCCGTGTGAAGGCCCC
Found at i:5489488 original size:25 final size:25
Alignment explanation
Indices: 5489460--5489537 Score: 79
Period size: 24 Copynumber: 3.2 Consensus size: 25
5489450 CAGTTTAACA
5489460 GTAAAAGAAAAAAAAGAAATTCTAT
1 GTAAAAGAAAAAAAAGAAATTCTAT
*** * * *
5489485 GT-AAACCCAAAAATGAAACT-TAC
1 GTAAAAGAAAAAAAAGAAATTCTAT
*
5489508 CTAAAAGAAAAAAAAGAAATTCTAT
1 GTAAAAGAAAAAAAAGAAATTCTAT
5489533 GTAAA
1 GTAAA
5489538 CCCAAAAATG
Statistics
Matches: 37, Mismatches: 14, Indels: 4
0.67 0.25 0.07
Matches are distributed among these distances:
23 3 0.08
24 26 0.70
25 8 0.22
ACGTcount: A:0.60, C:0.10, G:0.10, T:0.19
Consensus pattern (25 bp):
GTAAAAGAAAAAAAAGAAATTCTAT
Found at i:5489502 original size:24 final size:24
Alignment explanation
Indices: 5489469--5489550 Score: 76
Period size: 24 Copynumber: 3.4 Consensus size: 24
5489459 AGTAAAAGAA
5489469 AAAAAAGAAATTCTATGTAAACCC
1 AAAAAAGAAATTCTATGTAAACCC
* * ** ***
5489493 AAAAATGAAACT-TACCTAAAAGAA
1 AAAAAAGAAATTCTATGT-AAACCC
5489517 AAAAAAGAAATTCTATGTAAACCC
1 AAAAAAGAAATTCTATGTAAACCC
*
5489541 AAAAATGAAA
1 AAAAAAGAAA
5489551 CTTACCTCTT
Statistics
Matches: 41, Mismatches: 15, Indels: 4
0.68 0.25 0.07
Matches are distributed among these distances:
23 3 0.07
24 35 0.85
25 3 0.07
ACGTcount: A:0.60, C:0.13, G:0.09, T:0.18
Consensus pattern (24 bp):
AAAAAAGAAATTCTATGTAAACCC
Found at i:5489517 original size:48 final size:48
Alignment explanation
Indices: 5489461--5489557 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
5489451 AGTTTAACAG
5489461 TAAAAGAAAAAAAAGAAATTCTATGTAAACCCAAAAATGAAACTTACC
1 TAAAAGAAAAAAAAGAAATTCTATGTAAACCCAAAAATGAAACTTACC
5489509 TAAAAGAAAAAAAAGAAATTCTATGTAAACCCAAAAATGAAACTTACC
1 TAAAAGAAAAAAAAGAAATTCTATGTAAACCCAAAAATGAAACTTACC
5489557 T
1 T
5489558 CTTCAACTTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.58, C:0.14, G:0.08, T:0.20
Consensus pattern (48 bp):
TAAAAGAAAAAAAAGAAATTCTATGTAAACCCAAAAATGAAACTTACC
Found at i:5491157 original size:136 final size:136
Alignment explanation
Indices: 5490913--5491333 Score: 752
Period size: 136 Copynumber: 3.1 Consensus size: 136
5490903 CATTGGGCCT
** * * *
5490913 AAGCCCATTCAGGTAACAGTGGTATTGGGCCAGAGCCCTTTTCGGATTACAATAAACTGGGTCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAAAGCCCTTTTCAGATTACAATAAACTGGGTCTT
5490978 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
5491043 ATATGC
131 ATATGC
*
5491049 AAGCCCATTTGGGTAATAGTGGTACTGGGCCAAAGCCCTTTTCAGATTACAATAAACTGGGTCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAAAGCCCTTTTCAGATTACAATAAACTGGGTCTT
5491114 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
5491179 ATATGC
131 ATATGC
*
5491185 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAAAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAAAGCCCTTTTCAGATTACAATAAACTGGGTCTT
* * *
5491250 AGCCCCTTATTCAGATAACAATATGGCCCATAGGCCCATTTTAAAATACATGCAACATAAATAAC
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
5491315 ATATGC
131 ATATGC
5491321 AAGCCCATTTGGG
1 AAGCCCATTTGGG
5491334 GAGACTACTC
Statistics
Matches: 274, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
136 274 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (136 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGGCCAAAGCCCTTTTCAGATTACAATAAACTGGGTCTT
AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
ATATGC
Found at i:5491244 original size:32 final size:34
Alignment explanation
Indices: 5491208--5491272 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
5491198 TAACAGTGGT
*
5491208 ACTGGGCCAAAG-CCCTT-TTCAGATTACAATAA
1 ACTGGGCCAAAGCCCCTTATTCAGATAACAATAA
**
5491240 ACTGGGCCTTAGCCCCTTATTCAGATAACAATA
1 ACTGGGCCAAAGCCCCTTATTCAGATAACAATA
5491273 TGGCCCATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 10 0.36
33 5 0.18
34 13 0.46
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.26
Consensus pattern (34 bp):
ACTGGGCCAAAGCCCCTTATTCAGATAACAATAA
Found at i:5493092 original size:26 final size:26
Alignment explanation
Indices: 5493056--5493191 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
5493046 CATGAAATTC
*
5493056 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
*
5493082 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
*
5493108 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
5493134 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
5493160 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
5493186 TTATCA
1 TTATCA
5493192 ATTTGTATCA
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 107 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCTA
Found at i:5497177 original size:135 final size:135
Alignment explanation
Indices: 5496935--5497353 Score: 784
Period size: 135 Copynumber: 3.1 Consensus size: 135
5496925 CATTGGGCCT
** *
5496935 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCTTA
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAAAGCCCTTTTCAGATTACAATAAACTGGGCTTA
5497000 GCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAACA
66 GCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAACA
5497065 TATGC
131 TATGC
5497070 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAAAGCCCTTTTCAGATTACAATAAACTGGGCTTA
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAAAGCCCTTTTCAGATTACAATAAACTGGGCTTA
5497135 GCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAACA
66 GCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAACA
5497200 TATGC
131 TATGC
5497205 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAAAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAAAGCCCTTTTCAGATTACAATAAACTGGG-CTT
* *
5497270 AGCCCCTTATTCAGATAACAATATGGCCCATAGGCCCATTTTAAAATACATGCAACATCAATAAC
65 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
5497335 ATATGC
130 ATATGC
5497341 AAGCCCATTTGGG
1 AAGCCCATTTGGG
5497354 GAGACTACTC
Statistics
Matches: 278, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
135 193 0.69
136 85 0.31
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (135 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGGCCAAAGCCCTTTTCAGATTACAATAAACTGGGCTTA
GCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAACA
TATGC
Found at i:5497264 original size:32 final size:34
Alignment explanation
Indices: 5497228--5497292 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
5497218 TAACAGTGGT
*
5497228 ACTGGGCCAAAG-CCCTT-TTCAGATTACAATAA
1 ACTGGGCCAAAGCCCCTTATTCAGATAACAATAA
**
5497260 ACTGGGCCTTAGCCCCTTATTCAGATAACAATA
1 ACTGGGCCAAAGCCCCTTATTCAGATAACAATA
5497293 TGGCCCATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 10 0.36
33 5 0.18
34 13 0.46
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.26
Consensus pattern (34 bp):
ACTGGGCCAAAGCCCCTTATTCAGATAACAATAA
Found at i:5499107 original size:26 final size:26
Alignment explanation
Indices: 5499071--5499206 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
5499061 CATGAAATTC
*
5499071 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
*
5499097 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
*
5499123 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
5499149 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
5499175 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
5499201 TTATCA
1 TTATCA
5499207 ATTTGTATCA
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 107 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCTA
Found at i:5501156 original size:21 final size:21
Alignment explanation
Indices: 5501127--5501173 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
5501117 GAACACCAAA
* *
5501127 TTGAAGATCTCACCGCGTGAC
1 TTGACGATCCCACCGCGTGAC
5501148 TTGACGATCCCACCGCGTGAC
1 TTGACGATCCCACCGCGTGAC
5501169 TTGAC
1 TTGAC
5501174 ACAGAAGTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.32, G:0.23, T:0.23
Consensus pattern (21 bp):
TTGACGATCCCACCGCGTGAC
Found at i:5501798 original size:2 final size:2
Alignment explanation
Indices: 5501791--5501816 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5501781 AAGAATAAAG
5501791 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
5501817 TAACTAGTTT
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):
AT
Done.