Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 112 of 171
Found at i:35827233 original size:20 final size:20
Alignment explanation
Indices: 35827208--35827265 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
35827198 TGTTTAGCAT
*
35827208 TTTTTTACCAATGTTTTCCA
1 TTTTTTACCAATGTTTTCAA
*
35827228 TTTTTTACCAATGTTTACAA
1 TTTTTTACCAATGTTTTCAA
* *
35827248 TTTTTGACCAATATTTTC
1 TTTTTTACCAATGTTTTC
35827266 TATTCCTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.24, C:0.17, G:0.05, T:0.53
Consensus pattern (20 bp):
TTTTTTACCAATGTTTTCAA
Found at i:35838094 original size:18 final size:18
Alignment explanation
Indices: 35838045--35838094 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
35838035 TGTCATATTT
*
35838045 ATTTTATTTTGAAAACAA
1 ATTTTATTTCGAAAACAA
*
35838063 ATTTTGTTTCCGAAAA-AA
1 ATTTTATTT-CGAAAACAA
35838081 ATCTTTATTTCGAA
1 AT-TTTATTTCGAA
35838095 TTAATCGAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 16 0.59
19 11 0.41
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (18 bp):
ATTTTATTTCGAAAACAA
Found at i:35838322 original size:15 final size:15
Alignment explanation
Indices: 35838302--35838330 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
35838292 TATTAAAACA
35838302 ATTTGAGTATTTTTT
1 ATTTGAGTATTTTTT
35838317 ATTTGAGTATTTTT
1 ATTTGAGTATTTTT
35838331 AAAAAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.14, T:0.66
Consensus pattern (15 bp):
ATTTGAGTATTTTTT
Found at i:35838426 original size:18 final size:16
Alignment explanation
Indices: 35838382--35838428 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 16
35838372 ATTTACAGGT
35838382 ATAAATAATAAAAACA
1 ATAAATAATAAAAACA
*
35838398 ATATATAAATAAAATACA
1 ATAAAT-AATAAAA-ACA
35838416 ATAAAATAATAAA
1 AT-AAATAATAAA
35838429 TTAAGTAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 5 0.19
17 7 0.27
18 11 0.42
19 3 0.12
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.23
Consensus pattern (16 bp):
ATAAATAATAAAAACA
Found at i:35838635 original size:30 final size:29
Alignment explanation
Indices: 35838601--35838812 Score: 181
Period size: 30 Copynumber: 7.1 Consensus size: 29
35838591 AATTGGCTCA
35838601 AAATTTGAATTTTTGGAAAGTTCAAGGGTC
1 AAATTTGAATTTTTGGAAAGTT-AAGGGTC
* **
35838631 AAATTTGAATTTTTAGAAAGTTCAAGCTTC
1 AAATTTGAATTTTTGGAAAGTT-AAGGGTC
* * **
35838661 AAATTGGAATTATTGGAAAGTTTGGGGTC
1 AAATTTGAATTTTTGGAAAGTTAAGGGTC
* * *
35838690 AAATTTAAATTTTTGGAAAGTTTAGGGGTT
1 AAATTTGAATTTTTGGAAAG-TTAAGGGTC
** * *
35838720 AAATTCAAATTTTTAGAAAGTTTAGAGGTC
1 AAATTTGAATTTTTGGAAAGTTAAG-GGTC
* * *
35838750 AAATTGGAATTTTTGAAAAGTTTGAGGGTC
1 AAATTTGAATTTTTGGAAAG-TTAAGGGTC
* * * *
35838780 AAATTTAAATTTTTAGACAATTTAGGGGTC
1 AAATTTGAATTTTTGGA-AAGTTAAGGGTC
35838810 AAA
1 AAA
35838813 ACATAATTTT
Statistics
Matches: 146, Mismatches: 32, Indels: 8
0.78 0.17 0.04
Matches are distributed among these distances:
29 23 0.16
30 117 0.80
31 6 0.04
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (29 bp):
AAATTTGAATTTTTGGAAAGTTAAGGGTC
Found at i:35838731 original size:89 final size:90
Alignment explanation
Indices: 35838601--35838812 Score: 286
Period size: 89 Copynumber: 2.4 Consensus size: 90
35838591 AATTGGCTCA
* * * ** *
35838601 AAATTTGAATTTTTGGAAAGTTCAAGGGTCAAATTTGAATTTTTAGAAAGTTCA-AGCTTCAAAT
1 AAATTTAAATTTTTGGAAAGTTTAGGGGTCAAATTCAAATTTTTAGAAAGTTCAGAG-GTCAAAT
*
35838665 TGGAATTATTGGAAAGTTTG-GGGTC
65 TGGAATTATTGAAAAGTTTGAGGGTC
* *
35838690 AAATTTAAATTTTTGGAAAGTTTAGGGGTTAAATTCAAATTTTTAGAAAGTTTAGAGGTCAAATT
1 AAATTTAAATTTTTGGAAAGTTTAGGGGTCAAATTCAAATTTTTAGAAAGTTCAGAGGTCAAATT
*
35838755 GGAATTTTTGAAAAGTTTGAGGGTC
66 GGAATTATTGAAAAGTTTGAGGGTC
*
35838780 AAATTTAAATTTTTAGACAA-TTTAGGGGTCAAA
1 AAATTTAAATTTTTGGA-AAGTTTAGGGGTCAAA
35838813 ACATAATTTT
Statistics
Matches: 108, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
89 71 0.66
90 35 0.32
91 2 0.02
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (90 bp):
AAATTTAAATTTTTGGAAAGTTTAGGGGTCAAATTCAAATTTTTAGAAAGTTCAGAGGTCAAATT
GGAATTATTGAAAAGTTTGAGGGTC
Found at i:35839795 original size:17 final size:17
Alignment explanation
Indices: 35839764--35839815 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
35839754 TGGGTATATG
* *
35839764 TATTTGTTTAATTTTAT
1 TATTTATTTATTTTTAT
35839781 TATTTATTTATTTTTCAT
1 TATTTATTTATTTTT-AT
* *
35839799 T-TGTATTTATTTATAT
1 TATTTATTTATTTTTAT
35839815 T
1 T
35839816 TATAAAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 3 0.10
17 24 0.80
18 3 0.10
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.71
Consensus pattern (17 bp):
TATTTATTTATTTTTAT
Found at i:35839815 original size:10 final size:10
Alignment explanation
Indices: 35839776--35839818 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
35839766 TTTGTTTAAT
35839776 TTTATTATTTA
1 TTTA-TATTTA
*
35839787 TTTATTTTTCA
1 TTTATATTT-A
*
35839798 TTTGTATTTA
1 TTTATATTTA
35839808 TTTATATTTA
1 TTTATATTTA
35839818 T
1 T
35839819 AAAAAATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 15 0.56
11 12 0.44
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (10 bp):
TTTATATTTA
Found at i:35839847 original size:20 final size:19
Alignment explanation
Indices: 35839817--35839855 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
35839807 ATTTATATTT
35839817 ATAAAAAATAAAAATAAAA
1 ATAAAAAATAAAAATAAAA
*
35839836 ATAAATAAATAAAATTAAAA
1 ATAAA-AAATAAAAATAAAA
35839856 CGGAATTGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (19 bp):
ATAAAAAATAAAAATAAAA
Found at i:35839849 original size:19 final size:20
Alignment explanation
Indices: 35839817--35839855 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
35839807 ATTTATATTT
35839817 ATAAAAAATAAAAA-TAAAA
1 ATAAAAAATAAAAATTAAAA
35839836 ATAAATAAAT-AAAATTAAAA
1 ATAAA-AAATAAAAATTAAAA
35839856 CGGAATTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (20 bp):
ATAAAAAATAAAAATTAAAA
Found at i:35840825 original size:40 final size:40
Alignment explanation
Indices: 35840701--35840837 Score: 134
Period size: 40 Copynumber: 3.5 Consensus size: 40
35840691 TATAGCTTTA
* *
35840701 GGGGTAAAAGATTGGATTG-CTTCAATCTGTCTCATGGTC
1 GGGGTAAAAGATTGGATGGTCTTCAATCTGCCTCATGGTC
* * * * * *
35840740 GGGGTAAGAGATTGGATGATCTTTAATCTGCC-CTTTGATT
1 GGGGTAAAAGATTGGATGGTCTTCAATCTGCCTC-ATGGTC
* * *
35840780 AGGGTAAAAGATTGGATGGTATTCAATTTGCCTCATGGTC
1 GGGGTAAAAGATTGGATGGTCTTCAATCTGCCTCATGGTC
* *
35840820 GGGGTAAGAGATTAGATG
1 GGGGTAAAAGATTGGATG
35840838 TGGTGACTTT
Statistics
Matches: 75, Mismatches: 20, Indels: 5
0.75 0.20 0.05
Matches are distributed among these distances:
39 17 0.23
40 57 0.76
41 1 0.01
ACGTcount: A:0.26, C:0.12, G:0.30, T:0.33
Consensus pattern (40 bp):
GGGGTAAAAGATTGGATGGTCTTCAATCTGCCTCATGGTC
Found at i:35852812 original size:30 final size:30
Alignment explanation
Indices: 35852766--35852883 Score: 146
Period size: 30 Copynumber: 3.9 Consensus size: 30
35852756 AATTAAAATC
*
35852766 GGGTCAAAATTTAAATTTTTGGAAAGTTCAA
1 GGGTC-AAATTTAAATTTTTGGAAAGTTCGA
* * * *
35852797 GGGTCAAATTCAAATTTTTGAAAAGTTTGG
1 GGGTCAAATTTAAATTTTTGGAAAGTTCGA
* *
35852827 GGGTCAAATTTGAATTTTTGGAAAATTCGA
1 GGGTCAAATTTAAATTTTTGGAAAGTTCGA
* *
35852857 GGGTCAAATTTAACTTTTTGGACAGTT
1 GGGTCAAATTTAAATTTTTGGAAAGTT
35852884 TATGGGTTAA
Statistics
Matches: 72, Mismatches: 15, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
30 67 0.93
31 5 0.07
ACGTcount: A:0.33, C:0.08, G:0.22, T:0.37
Consensus pattern (30 bp):
GGGTCAAATTTAAATTTTTGGAAAGTTCGA
Found at i:35852903 original size:60 final size:60
Alignment explanation
Indices: 35852779--35852904 Score: 137
Period size: 60 Copynumber: 2.1 Consensus size: 60
35852769 TCAAAATTTA
* * **
35852779 AATTTTTGGAAAGTTCAAGGGTCAAATTCAAATTTTTGAAAAGTTTGGGGGTCAAATTTG
1 AATTTTTGGAAAATTCAAGGGTCAAATTCAAATTTTTGAAAAGTTTGGGGGTAAAACATG
* * * * * * *
35852839 AATTTTTGGAAAATTCGAGGGTCAAATTTAACTTTTTGGACAGTTTATGGGTTAAAACAT-
1 AATTTTTGGAAAATTCAAGGGTCAAATTCAAATTTTTGAAAAGTTT-GGGGGTAAAACATG
35852899 AATTTT
1 AATTTT
35852905 AAAATAAAGT
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
60 46 0.85
61 8 0.15
ACGTcount: A:0.33, C:0.07, G:0.21, T:0.39
Consensus pattern (60 bp):
AATTTTTGGAAAATTCAAGGGTCAAATTCAAATTTTTGAAAAGTTTGGGGGTAAAACATG
Found at i:35853850 original size:17 final size:15
Alignment explanation
Indices: 35853828--35853876 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
35853818 TGGGTATGTG
*
35853828 TATTTGTTTAATTTTAT
1 TATTTGTTT-ATTAT-T
35853845 TATTTGTTTATTATT
1 TATTTGTTTATTATT
*
35853860 TATTTGTAT-TTATT
1 TATTTGTTTATTATT
35853874 TAT
1 TAT
35853877 ATTTATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
14 8 0.27
15 9 0.30
16 4 0.13
17 9 0.30
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.71
Consensus pattern (15 bp):
TATTTGTTTATTATT
Found at i:35853871 original size:10 final size:10
Alignment explanation
Indices: 35853840--35853882 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
35853830 TTTGTTTAAT
*
35853840 TTTATTATTTG
1 TTTA-TATTTA
35853851 TTTATTATTTA
1 TTTA-TATTTA
*
35853862 TTTGTATTTA
1 TTTATATTTA
35853872 TTTATATTTA
1 TTTATATTTA
35853882 T
1 T
35853883 AAAAAAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
10 16 0.55
11 13 0.45
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (10 bp):
TTTATATTTA
Found at i:35858526 original size:80 final size:80
Alignment explanation
Indices: 35858429--35858780 Score: 419
Period size: 80 Copynumber: 4.4 Consensus size: 80
35858419 GGGCACACAA
* *
35858429 TTGTGGTTTATCCGCTAGGCACTGAGTACCAGGATTTGACGGATATTTGTTGGTTAATCCAACTA
1 TTGTGGTTTATCTGCTAGGCACTGAGTGCCAGGATTTGACGGATATTTGTTGGTTAATCCAACTA
35858494 GAGCTAGGCTCACTT
66 GAGCTAGGCTCACTT
* * * *
35858509 TTATGGTTTATCTGCTAGGCACAGGGTGCTAGGATTTGACGGATATTTGTTGGTTAATCCAACTA
1 TTGTGGTTTATCTGCTAGGCACTGAGTGCCAGGATTTGACGGATATTTGTTGGTTAATCCAACTA
*
35858574 GAG-TTGAGCTCACTT
66 GAGCTAG-GCTCACTT
** * * * * * *
35858589 TTGCAGTTTAATCCGCTAGGCATTGGGTGTCAGGATTTGACGAACATTTGTTGGTTAATCCAACT
1 TTGTGGTTT-ATCTGCTAGGCACTGAGTGCCAGGATTTGACGGATATTTGTTGGTTAATCCAACT
*
35858654 AGAGCAAGGCTCACTT
65 AGAGCTAGGCTCACTT
* * *
35858670 CTGTGGTTTAT-TCGCTAGGCACT-AGGTG-TAGGATTTGATGGATATTTGTTGGTTAATCCAAC
1 TTGTGGTTTATCT-GCTAGGCACTGA-GTGCCAGGATTTGACGGATATTTGTTGGTTAATCCAAC
35858732 TAGAGCT-GGCCTCACTT
64 TAGAGCTAGG-CTCACTT
* *
35858749 TTGCGATTTATCTGCTAGGCACT-AGGTGCCAG
1 TTGTGGTTTATCTGCTAGGCACTGA-GTGCCAG
35858781 AATCATCGGT
Statistics
Matches: 230, Mismatches: 34, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
78 2 0.01
79 68 0.30
80 93 0.40
81 66 0.29
82 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (80 bp):
TTGTGGTTTATCTGCTAGGCACTGAGTGCCAGGATTTGACGGATATTTGTTGGTTAATCCAACTA
GAGCTAGGCTCACTT
Found at i:35858970 original size:82 final size:82
Alignment explanation
Indices: 35858818--35858972 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 82
35858808 GGCGCAAAAC
* * * *
35858818 CGTTGGTTAATCCAACTAGATTTGAGCTCATTTATTGCGGTTTATCCGCTAGGCACTAGGTGTCA
1 CGTTGGTTAATCCAACTAGACTAGAGCTCACTTATTGCGGTTTATCCGCTAGGCACTAGGTGCCA
35858883 GGAATTGATAGAATTAT
66 GGAATTGATAGAATTAT
*
35858900 CGTTTGTTAATCCAACTAGAGCTAG-GCTCACTTATTGCGGTTTATCCGCTAGGCA-TAGGGTGC
1 CGTTGGTTAATCCAACTAGA-CTAGAGCTCACTTATTGCGGTTTATCCGCTAGGCACTA-GGTGC
*
35858963 CATGAATTGA
64 CAGGAATTGA
35858973 CGAAAATATA
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
81 2 0.03
82 61 0.94
83 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.34
Consensus pattern (82 bp):
CGTTGGTTAATCCAACTAGACTAGAGCTCACTTATTGCGGTTTATCCGCTAGGCACTAGGTGCCA
GGAATTGATAGAATTAT
Found at i:35887279 original size:276 final size:275
Alignment explanation
Indices: 35886787--35887313 Score: 903
Period size: 276 Copynumber: 1.9 Consensus size: 275
35886777 CCATTTGAAT
*
35886787 TTTGACTTTTAGTACTAATTGCAACTTTTCTCTCAATCTTTTTTATTTGTCCTTTCCCCTTAACC
1 TTTGACTTTTAGTACTAATGGCAACTTTTCTCTCAATCTTTTTTATTTGTCCTTTCCCCTTAACC
35886852 TCCTCACAAAATTTCATCATTTTAATTAATCTTTATACATGTCATTGGGATTCAAAGGGGCTAGA
66 TCCTCACAAAATTTCATCATTTTAATTAATCTTTATACATGTCATTGGGATTCAAAGGGGCTAGA
* *
35886917 GTAAATTTCTTCCCTTTAAAGATAAGGGAATATCGATTTTGTTTGCCATGGTGTATGACATCATG
131 GTAAATTTCTTCCCTTTAAAGATAAGGGAATATCAATTTTGTTTGCCATGATGTATGACATCATG
* *
35886982 ATCAAATTTTCACAGCCTTCCAAGAAATAACTGTGTGGCATGCATGAGGACAACATTGAACCATA
196 ATCAAATTTTCACAGCCTTCCAAGAAATAAATGCGTGGCATGCATGAGGACAACATTGAACCATA
35887047 CCTCATAATTGTCTA
261 CCTCATAATTGTCTA
* *
35887062 TTTGACTTTTAGTACTAATGGCCACTTTTCTCTCAGTCTTTTTTATTT-TCCTTTCCCCTTAACC
1 TTTGACTTTTAGTACTAATGGCAACTTTTCTCTCAATCTTTTTTATTTGTCCTTTCCCCTTAACC
* * *
35887126 TCCTCACAGAATTTCATCATTTTTAGTTAATCTTTATGCATGTCATTGGGATTCAAAAGGGGCTA
66 TCCTCACAAAATTTCATCA-TTTTAATTAATCTTTATACATGTCATTGGGATTC-AAAGGGGCTA
*
35887191 GAGTAAATTTCTTCCCTTTAAAGATACGGGAATATCAATTTTGTTTGCCATGATGTATGACATCA
129 GAGTAAATTTCTTCCCTTTAAAGATAAGGGAATATCAATTTTGTTTGCCATGATGTATGACATCA
* * *
35887256 TGATCAAATTTTCACGGCCTTCCAAGAAGTAAATGCGTGGCATGCATGAGGTCAACAT
194 TGATCAAATTTTCACAGCCTTCCAAGAAATAAATGCGTGGCATGCATGAGGACAACAT
35887314 CAAACTATAC
Statistics
Matches: 236, Mismatches: 14, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
274 34 0.14
275 77 0.33
276 125 0.53
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.38
Consensus pattern (275 bp):
TTTGACTTTTAGTACTAATGGCAACTTTTCTCTCAATCTTTTTTATTTGTCCTTTCCCCTTAACC
TCCTCACAAAATTTCATCATTTTAATTAATCTTTATACATGTCATTGGGATTCAAAGGGGCTAGA
GTAAATTTCTTCCCTTTAAAGATAAGGGAATATCAATTTTGTTTGCCATGATGTATGACATCATG
ATCAAATTTTCACAGCCTTCCAAGAAATAAATGCGTGGCATGCATGAGGACAACATTGAACCATA
CCTCATAATTGTCTA
Found at i:35894131 original size:13 final size:13
Alignment explanation
Indices: 35894113--35894139 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35894103 TACTAAACGT
35894113 TTTAATAAATAAA
1 TTTAATAAATAAA
35894126 TTTAATAAATAAA
1 TTTAATAAATAAA
35894139 T
1 T
35894140 AATAAATGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TTTAATAAATAAA
Found at i:35894169 original size:17 final size:17
Alignment explanation
Indices: 35894116--35894169 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
35894106 TAAACGTTTT
35894116 AATAAATAA-ATTTAATA
1 AATAAATAATA-TTAATA
35894133 AATAAATAATA--AAT-
1 AATAAATAATATTAATA
**
35894147 GTTAAATAATATTAATA
1 AATAAATAATATTAATA
35894164 AATAAA
1 AATAAA
35894170 ATAAAAAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
14 9 0.31
15 3 0.10
16 3 0.10
17 13 0.45
18 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
AATAAATAATATTAATA
Found at i:35895285 original size:30 final size:30
Alignment explanation
Indices: 35895249--35895677 Score: 337
Period size: 30 Copynumber: 14.5 Consensus size: 30
35895239 GAATTTTCTA
* **
35895249 AAAATTATATTTTGACCCTCAAACTTTTTT
1 AAAATTACATTTTGACCCTCAAACTTTTCC
* * * *
35895279 ATAATTACATTTTAACCCCCAAACTCTTCC
1 AAAATTACATTTTGACCCTCAAACTTTTCC
* *
35895309 AAAATTACATTTTGACCCTTAAACTTTTCA
1 AAAATTACATTTTGACCCTCAAACTTTTCC
*
35895339 AAAATTACATTTTGATCCCT-AAGCTTTTCC
1 AAAATTACATTTTGA-CCCTCAAACTTTTCC
35895369 AAAATTACATTTTGACCCT-AAAC--TTCC
1 AAAATTACATTTTGACCCTCAAACTTTTCC
35895396 TAAAATTACATTTTGACCC-CTAAACTTTTCC
1 -AAAATTACATTTTGACCCTC-AAACTTTTCC
* * * *
35895427 AATATTACATTTTAACCCTTAAAATTTTCC
1 AAAATTACATTTTGACCCTCAAACTTTTCC
* * * *
35895457 AAAATTGCATTTTAACCC-CTAAACTTCTCT
1 AAAATTACATTTTGACCCTC-AAACTTTTCC
* *
35895487 AAAATTACATTTTGACCCT-AAACTTCTCT
1 AAAATTACATTTTGACCCTCAAACTTTTCC
* * * ** *
35895516 AAAATCACGTTTTGACTC-CAAACTACTCT
1 AAAATTACATTTTGACCCTCAAACTTTTCC
* * * * *
35895545 AAAATCACATTTTAACTTCCT-AAACCTTGCT
1 AAAATTACATTTTGAC--CCTCAAACTTTTCC
* * *
35895576 AAAA-TCCTATTTT-AACCTCAAACTTCTCC
1 AAAATTAC-ATTTTGACCCTCAAACTTTTCC
* *
35895605 AAAATCACATTTTGACCCT--AACTTTCCC
1 AAAATTACATTTTGACCCTCAAACTTTTCC
* *
35895633 AAAATTACATTTTTACCCCTTAAACTTTT-C
1 AAAATTACATTTTGA-CCCTCAAACTTTTCC
*
35895663 AAATTTACATTTTGA
1 AAAATTACATTTTGA
35895678 TCCCGTATTT
Statistics
Matches: 323, Mismatches: 56, Indels: 40
0.77 0.13 0.10
Matches are distributed among these distances:
27 4 0.01
28 41 0.13
29 78 0.24
30 170 0.53
31 30 0.09
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (30 bp):
AAAATTACATTTTGACCCTCAAACTTTTCC
Found at i:35895314 original size:60 final size:59
Alignment explanation
Indices: 35895249--35895677 Score: 411
Period size: 60 Copynumber: 7.3 Consensus size: 59
35895239 GAATTTTCTA
* * * * *
35895249 AAAATTATATTTTGACCCTCAAACTTTTTTATAATTACATTTTAACCCCCAAACTCTTCC
1 AAAATTACATTTTGACCCT-AAACTTTTCTAAAATTACATTTTAACCCCTAAACTTTTCC
* * * *
35895309 AAAATTACATTTTGACCCTTAAACTTTTCAAAAATTACATTTTGATCCCTAAGCTTTTCC
1 AAAATTACATTTTGACCC-TAAACTTTTCTAAAATTACATTTTAACCCCTAAACTTTTCC
* *
35895369 AAAATTACATTTTGACCCTAAAC-TTCCTAAAATTACATTTTGACCCCTAAACTTTTCC
1 AAAATTACATTTTGACCCTAAACTTTTCTAAAATTACATTTTAACCCCTAAACTTTTCC
* * * * * * *
35895427 AATATTACATTTTAACCCTTAAAATTTTCCAAAATTGCATTTTAACCCCTAAACTTCTCT
1 AAAATTACATTTTGACCC-TAAACTTTTCTAAAATTACATTTTAACCCCTAAACTTTTCC
* * * * * ** *
35895487 AAAATTACATTTTGACCCTAAACTTCTCTAAAATCACGTTTTGACTCC-AAACTACTCT
1 AAAATTACATTTTGACCCTAAACTTTTCTAAAATTACATTTTAACCCCTAAACTTTTCC
* * * * * * *
35895545 AAAATCACATTTTAACTTCCTAAACCTTGCTAAAA-TCCTATTTTAACCTC-AAACTTCTCC
1 AAAATTACATTTTGAC--CCTAAACTTTTCTAAAATTAC-ATTTTAACCCCTAAACTTTTCC
* * * *
35895605 AAAATCACATTTTGACCCT-AACTTTCCCAAAATTACATTTTTACCCCTTAAACTTTT-C
1 AAAATTACATTTTGACCCTAAACTTTTCTAAAATTACATTTTAACCCC-TAAACTTTTCC
*
35895663 AAATTTACATTTTGA
1 AAAATTACATTTTGA
35895678 TCCCGTATTT
Statistics
Matches: 304, Mismatches: 56, Indels: 20
0.80 0.15 0.05
Matches are distributed among these distances:
57 19 0.06
58 89 0.29
59 39 0.13
60 156 0.51
61 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (59 bp):
AAAATTACATTTTGACCCTAAACTTTTCTAAAATTACATTTTAACCCCTAAACTTTTCC
Found at i:35895445 original size:118 final size:117
Alignment explanation
Indices: 35895249--35895675 Score: 427
Period size: 118 Copynumber: 3.6 Consensus size: 117
35895239 GAATTTTCTA
* ** * * * *
35895249 AAAATTATATTTTGACCCTCAAACTTTTTTATAATTACATTTTAACCCCCAAACTCTTCCAAAAT
1 AAAATTACATTTTGACCCT-AAACTTTCCTAAAATTACATTTTGACCCCTAAACTTTTCCAAAAT
* * *
35895314 TACATTTTGACCCTTAAACTTTTCAAAAATTACATTTTGATCCCTAAGCTTTTCC
65 TACATTTTAACCCTTAAACTTTTCAAAAATTACATTTT-A-CCCTAAACTTCTCC
*
35895369 AAAATTACATTTTGACCCTAAAC-TTCCTAAAATTACATTTTGACCCCTAAACTTTTCCAATATT
1 AAAATTACATTTTGACCCTAAACTTTCCTAAAATTACATTTTGACCCCTAAACTTTTCCAAAATT
* * * *
35895433 ACATTTTAACCCTTAAAATTTTCCAAAATTGCATTTTAACCCCTAAACTTCTCT
66 ACATTTTAACCCTTAAACTTTTCAAAAATTACATTTT-A-CCCTAAACTTCTCC
* * * ** *
35895487 AAAATTACATTTTGACCCTAAAC-TTCTCTAAAATCACGTTTTGACTCC-AAACTACTCTAAAAT
1 AAAATTACATTTTGACCCTAAACTTTC-CTAAAATTACATTTTGACCCCTAAACTTTTCCAAAAT
* * * * * *
35895550 CACATTTTAACTTCC-TAAACCTTGCTAAAA-TCCTATTTTAACCTCAAACTTCTCC
65 TACATTTTAAC--CCTTAAACTTTTCAAAAATTAC-ATTTTACCCT-AAACTTCTCC
* * * *
35895605 AAAATCACATTTTGACCCT-AACTTTCCCAAAATTACATTTTTACCCCTTAAACTTTT-CAAATT
1 AAAATTACATTTTGACCCTAAACTTTCCTAAAATTACATTTTGACCCC-TAAACTTTTCCAAAAT
35895668 TACATTTT
65 TACATTTT
35895676 GATCCCGTAT
Statistics
Matches: 256, Mismatches: 43, Indels: 18
0.81 0.14 0.06
Matches are distributed among these distances:
117 22 0.09
118 170 0.66
119 44 0.17
120 20 0.08
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (117 bp):
AAAATTACATTTTGACCCTAAACTTTCCTAAAATTACATTTTGACCCCTAAACTTTTCCAAAATT
ACATTTTAACCCTTAAACTTTTCAAAAATTACATTTTACCCTAAACTTCTCC
Found at i:35910808 original size:21 final size:22
Alignment explanation
Indices: 35910782--35910832 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
35910772 CCATTCCTTG
*
35910782 ACCTAAACA-ATCAATATATAC
1 ACCTAAACATATCAAAATATAC
* *
35910803 ACCTAAAACATGTCAAAATATTC
1 ACCT-AAACATATCAAAATATAC
35910826 ACCTAAA
1 ACCTAAA
35910833 TTTCTAACCA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 4 0.16
22 8 0.32
23 13 0.52
ACGTcount: A:0.51, C:0.24, G:0.02, T:0.24
Consensus pattern (22 bp):
ACCTAAACATATCAAAATATAC
Found at i:35911475 original size:20 final size:20
Alignment explanation
Indices: 35911450--35911550 Score: 78
Period size: 20 Copynumber: 5.1 Consensus size: 20
35911440 ATGCAAAACT
35911450 GGGGCACCAAAGTGCATTCA
1 GGGGCACCAAAGTGCATTCA
** ** *
35911470 GGGGCATGAGTGTTCATTCA
1 GGGGCACCAAAGTGCATTCA
** *
35911490 -GGGCATTAGAGTGCATTCA
1 GGGGCACCAAAGTGCATTCA
* * *
35911509 GAGGCACCGAAGTGCAATCA
1 GGGGCACCAAAGTGCATTCA
* *
35911529 GGGGCACCGAAGTGCATACA
1 GGGGCACCAAAGTGCATTCA
35911549 GG
1 GG
35911551 AGCATAGTAG
Statistics
Matches: 63, Mismatches: 17, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
19 16 0.25
20 47 0.75
ACGTcount: A:0.28, C:0.21, G:0.34, T:0.18
Consensus pattern (20 bp):
GGGGCACCAAAGTGCATTCA
Found at i:35911495 original size:19 final size:19
Alignment explanation
Indices: 35911460--35911514 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
35911450 GGGGCACCAA
35911460 AGTGCATTCAGGGGCATGAG
1 AGTGCATTCA-GGGCATGAG
* * *
35911480 TGTTCATTCAGGGCATTAG
1 AGTGCATTCAGGGCATGAG
35911499 AGTGCATTCAGAGGCA
1 AGTGCATTCAG-GGCA
35911515 CCGAAGTGCA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.25, C:0.16, G:0.33, T:0.25
Consensus pattern (19 bp):
AGTGCATTCAGGGCATGAG
Found at i:35914016 original size:21 final size:20
Alignment explanation
Indices: 35913957--35914027 Score: 79
Period size: 20 Copynumber: 3.4 Consensus size: 20
35913947 AAAATTATTT
* *
35913957 AATAATTTTATTATTTCAAAAA
1 AATAATTTTAATATTT--TAAA
*
35913979 AATAATTTTAATTTTTTAAA
1 AATAATTTTAATATTTTAAA
35913999 AATAATTTTAATAATTTTAAA
1 AATAATTTTAAT-ATTTTAAA
*
35914020 AATCATTT
1 AATAATTT
35914028 GTTGAAATGG
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
20 15 0.35
21 14 0.33
22 14 0.33
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
AATAATTTTAATATTTTAAA
Found at i:35914704 original size:26 final size:26
Alignment explanation
Indices: 35914653--35914705 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
35914643 GCTATTTAAA
* *
35914653 ATATATTTAAATATTTAGATTAATTT
1 ATATATTTAAATATTTAAAATAATTT
*
35914679 ATATA-TTAATTATTTAAAATATATTT
1 ATATATTTAAATATTTAAAATA-ATTT
35914705 A
1 A
35914706 AAATTTAGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
ATATATTTAAATATTTAAAATAATTT
Found at i:35914711 original size:18 final size:18
Alignment explanation
Indices: 35914646--35914712 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 18
35914636 TATTTTAGCT
35914646 ATTTAAAATATATTTAAA
1 ATTTAAAATATATTTAAA
*
35914664 TATTTAGATTAATTTATATATTAATT
1 -ATTTA-A--AA--TATAT-TTAA-A
35914690 ATTTAAAATATATTTAAA
1 ATTTAAAATATATTTAAA
35914708 ATTTA
1 ATTTA
35914713 GATTAATTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 15
0.70 0.04 0.27
Matches are distributed among these distances:
18 5 0.13
19 9 0.23
20 6 0.15
22 4 0.10
24 6 0.15
25 9 0.23
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (18 bp):
ATTTAAAATATATTTAAA
Found at i:35916028 original size:26 final size:26
Alignment explanation
Indices: 35915999--35916057 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
35915989 GAGAGTGTGT
*
35915999 GAAAGCGTTTTTTGCATAGTTGTCAA
1 GAAAGCGTTTTCTGCATAGTTGTCAA
*
35916025 GAAAGCGTTTTCTGTATAGTTGTCAA
1 GAAAGCGTTTTCTGCATAGTTGTCAA
35916051 GAAAGCG
1 GAAAGCG
35916058 CTTCTAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34
Consensus pattern (26 bp):
GAAAGCGTTTTCTGCATAGTTGTCAA
Found at i:35916662 original size:30 final size:28
Alignment explanation
Indices: 35916601--35916664 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 28
35916591 AAATTAAGAG
*
35916601 TTATTTTTTTATTTTCATGTATTATTTTT
1 TTATTTTTTTATTTTCATGTA-TATTATT
35916630 TTATTTTTTTATTTTTCACATGTA-ATTATT
1 TTATTTTTTTA-TTTT--CATGTATATTATT
35916660 TTATT
1 TTATT
35916665 GGGATATCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
29 11 0.35
30 14 0.45
32 6 0.19
ACGTcount: A:0.20, C:0.05, G:0.03, T:0.72
Consensus pattern (28 bp):
TTATTTTTTTATTTTCATGTATATTATT
Found at i:35917574 original size:22 final size:20
Alignment explanation
Indices: 35917525--35917581 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 20
35917515 ATGATTATTG
35917525 ATAATTATTTTATTTAATTT
1 ATAATTATTTTATTTAATTT
*
35917545 AAATATTATTATGT-TTTAATTT
1 ATA-ATTATT-T-TATTTAATTT
*
35917567 CATAATTATATTATT
1 -ATAATTATTTTATT
35917582 AGTGAATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 9
0.71 0.07 0.22
Matches are distributed among these distances:
20 3 0.10
21 9 0.31
22 14 0.48
23 3 0.10
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (20 bp):
ATAATTATTTTATTTAATTT
Found at i:35923874 original size:27 final size:27
Alignment explanation
Indices: 35923799--35923874 Score: 71
Period size: 27 Copynumber: 2.8 Consensus size: 27
35923789 CTCAGTTCTT
*
35923799 CACATACACTAGCAAACACCAGCTTGC
1 CACATACACTAGCAAACACCAGCTCGC
* * * * ** *
35923826 CAAACACATTGGGGAACCCCAGCTCGC
1 CACATACACTAGCAAACACCAGCTCGC
*
35923853 CACATACACTAACAAACACCAG
1 CACATACACTAGCAAACACCAG
35923875 TTCGTCAAAC
Statistics
Matches: 33, Mismatches: 16, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.38, C:0.37, G:0.13, T:0.12
Consensus pattern (27 bp):
CACATACACTAGCAAACACCAGCTCGC
Found at i:35925370 original size:51 final size:49
Alignment explanation
Indices: 35925286--35925387 Score: 127
Period size: 50 Copynumber: 2.0 Consensus size: 49
35925276 AAGAAAAAGG
35925286 AATCATTTGGAAATGATTAAAGTTTTTCCAAAATGAAAATGGAGAAATGA
1 AATCATTTGGAAATGATTAAAGTTTTTCCAAAATGAAAATGGA-AAATGA
* * *
35925336 AATCATTTGGAAATGAATGT-GA-TTTTCTCTAAAATGAAAATGGAAATTGA
1 AATCATTTGGAAATG-AT-TAAAGTTTT-TCCAAAATGAAAATGGAAAATGA
35925386 AA
1 AA
35925388 ATGACCTTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
50 26 0.57
51 19 0.41
52 1 0.02
ACGTcount: A:0.45, C:0.06, G:0.18, T:0.31
Consensus pattern (49 bp):
AATCATTTGGAAATGATTAAAGTTTTTCCAAAATGAAAATGGAAAATGA
Found at i:35925934 original size:19 final size:19
Alignment explanation
Indices: 35925896--35925950 Score: 67
Period size: 19 Copynumber: 2.7 Consensus size: 19
35925886 AATACTTATG
35925896 TATTAGATTAAATTTAATTTAA
1 TATTAGATT-AA--TAATTTAA
35925918 TATTAAGA-TAATAATTTAA
1 TATT-AGATTAATAATTTAA
35925937 TATTAGATTAATAA
1 TATTAGATTAATAA
35925951 AATACTATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
18 3 0.10
19 18 0.58
21 2 0.06
22 5 0.16
23 3 0.10
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.45
Consensus pattern (19 bp):
TATTAGATTAATAATTTAA
Found at i:35926003 original size:20 final size:17
Alignment explanation
Indices: 35925968--35926009 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 17
35925958 TCAAGATAAT
35925968 TATTAAATTAATATTAA
1 TATTAAATTAATATTAA
35925985 TATTAAATTTAATAAATTAA
1 TATTAAA-TTAAT--ATTAA
35926005 TATTA
1 TATTA
35926010 TTTTTGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 7 0.32
18 5 0.23
20 10 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TATTAAATTAATATTAA
Found at i:35926509 original size:11 final size:11
Alignment explanation
Indices: 35926493--35926518 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
35926483 TTGATTTTAG
35926493 CACAGATTAAA
1 CACAGATTAAA
35926504 CACAGATTAAA
1 CACAGATTAAA
35926515 CACA
1 CACA
35926519 ATTCACAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.23, G:0.08, T:0.15
Consensus pattern (11 bp):
CACAGATTAAA
Found at i:35936312 original size:9 final size:9
Alignment explanation
Indices: 35936298--35936338 Score: 82
Period size: 9 Copynumber: 4.6 Consensus size: 9
35936288 CAAAATCCAA
35936298 AATAATTAT
1 AATAATTAT
35936307 AATAATTAT
1 AATAATTAT
35936316 AATAATTAT
1 AATAATTAT
35936325 AATAATTAT
1 AATAATTAT
35936334 AATAA
1 AATAA
35936339 ATAATAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
AATAATTAT
Found at i:35936320 original size:3 final size:3
Alignment explanation
Indices: 35936298--35936354 Score: 55
Period size: 3 Copynumber: 19.3 Consensus size: 3
35936288 CAAAATCCAA
* * * *
35936298 AAT AAT TAT AAT AAT TAT AAT AAT TAT AAT AAT TAT AAT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
35936344 AA- AAT AA- AAT A
1 AAT AAT AAT AAT A
35936355 TTGTAAATTT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
2 4 0.09
3 36 0.84
4 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:35937987 original size:22 final size:22
Alignment explanation
Indices: 35937962--35938034 Score: 85
Period size: 22 Copynumber: 3.2 Consensus size: 22
35937952 AAGAGTGATT
35937962 AAAAGAGAAAGAAATAGAAAAG
1 AAAAGAGAAAGAAATAGAAAAG
*
35937984 AAAAGAGAAAGAAATAAGAAAGG
1 AAAAGAGAAAGAAAT-AGAAAAG
*
35938007 AATGAGAGAAAGAAA-AGAGAAAGG
1 AA-AAGAGAAAGAAATAGA-AAA-G
35938031 AAAA
1 AAAA
35938035 ATAAGAGGCT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
22 18 0.42
23 11 0.26
24 14 0.33
ACGTcount: A:0.70, C:0.00, G:0.26, T:0.04
Consensus pattern (22 bp):
AAAAGAGAAAGAAATAGAAAAG
Found at i:35938005 original size:11 final size:12
Alignment explanation
Indices: 35937965--35938029 Score: 84
Period size: 11 Copynumber: 5.7 Consensus size: 12
35937955 AGTGATTAAA
35937965 AGAGAAAGAAAT
1 AGAGAAAGAAAT
35937977 AGA-AAAGAAA-
1 AGAGAAAGAAAT
35937987 AGAGAAAGAAAT
1 AGAGAAAGAAAT
*
35937999 A-AGAAAGGAAT
1 AGAGAAAGAAAT
35938010 GAGAGAAAGAAA-
1 -AGAGAAAGAAAT
35938022 AGAGAAAG
1 AGAGAAAG
35938030 GAAAAATAAG
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
10 3 0.06
11 31 0.66
12 5 0.11
13 8 0.17
ACGTcount: A:0.68, C:0.00, G:0.28, T:0.05
Consensus pattern (12 bp):
AGAGAAAGAAAT
Found at i:35938019 original size:24 final size:23
Alignment explanation
Indices: 35937962--35938034 Score: 96
Period size: 24 Copynumber: 3.2 Consensus size: 23
35937952 AAGAGTGATT
*
35937962 AAAAGAGAAAGAAAT-AGAAAAG
1 AAAAGAGAAAGAAATAAGAAAGG
35937984 AAAAGAGAAAGAAATAAGAAAGG
1 AAAAGAGAAAGAAATAAGAAAGG
*
35938007 AATGAGAGAAAGAAA-AGAGAAAGG
1 AA-AAGAGAAAGAAATA-AGAAAGG
35938031 AAAA
1 AAAA
35938035 ATAAGAGGCT
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
22 15 0.33
23 10 0.22
24 20 0.44
ACGTcount: A:0.70, C:0.00, G:0.26, T:0.04
Consensus pattern (23 bp):
AAAAGAGAAAGAAATAAGAAAGG
Found at i:35939484 original size:61 final size:59
Alignment explanation
Indices: 35939337--35939508 Score: 161
Period size: 61 Copynumber: 2.8 Consensus size: 59
35939327 TAACACGTTC
* ** *
35939337 TCTTAATTTGGTACTTAAATATTTTTTTGATTCAATTTGATATCTGAGTTTGATAATTTTT
1 TCTTAATTTGGTACCT-AA-ATTTTTTTGACCCAATTTGATATCTGAATTTGATAATTTTT
* *
35939398 T-TTAATTTGGTAACTAAATCTTTTTTGAACCCAATTTGATA-CTTGAATTT-AGTATTTTTT
1 TCTTAATTTGGTACCTAAAT-TTTTTTG-ACCCAATTTGATATC-TGAATTTGA-TAATTTTT
** * *
35939458 TCTTAATTTGGTACCTAAACTTTTTTTAGATTCAATTTGGTATCTAAATTT
1 TCTTAATTTGGTACCTAAA-TTTTTTT-GACCCAATTTGATATCTGAATTT
35939509 ATTAAATGTT
Statistics
Matches: 92, Mismatches: 11, Indels: 16
0.77 0.09 0.13
Matches are distributed among these distances:
58 2 0.02
59 11 0.12
60 37 0.40
61 39 0.42
62 3 0.03
ACGTcount: A:0.27, C:0.09, G:0.10, T:0.53
Consensus pattern (59 bp):
TCTTAATTTGGTACCTAAATTTTTTTGACCCAATTTGATATCTGAATTTGATAATTTTT
Found at i:35939509 original size:61 final size:62
Alignment explanation
Indices: 35939337--35939509 Score: 187
Period size: 60 Copynumber: 2.8 Consensus size: 62
35939327 TAACACGTTC
* * *
35939337 TCTTAATTTGGTACTTAAA-TATTTTTTTGATTCAATTTGATATCTGAGTTT-GATAATTTTT
1 TCTTAATTTGGTACCTAAACT-TTTTTTAGATTCAATTTGATATCTGAATTTAGATAATTTTT
* * ** *
35939398 T-TTAATTTGGTAACTAAATCTTTTTTGA-ACCCAATTTGATA-CTTGAATTTAG-TATTTTTT
1 TCTTAATTTGGTACCTAAA-CTTTTTTTAGATTCAATTTGATATC-TGAATTTAGATAATTTTT
* *
35939458 TCTTAATTTGGTACCTAAACTTTTTTTAGATTCAATTTGGTATCTAAATTTA
1 TCTTAATTTGGTACCTAAACTTTTTTTAGATTCAATTTGATATCTGAATTTA
35939510 TTAAATGTTA
Statistics
Matches: 91, Mismatches: 14, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
59 1 0.01
60 48 0.53
61 40 0.44
62 2 0.02
ACGTcount: A:0.28, C:0.09, G:0.10, T:0.53
Consensus pattern (62 bp):
TCTTAATTTGGTACCTAAACTTTTTTTAGATTCAATTTGATATCTGAATTTAGATAATTTTT
Found at i:35939742 original size:30 final size:29
Alignment explanation
Indices: 35939707--35939818 Score: 106
Period size: 30 Copynumber: 3.9 Consensus size: 29
35939697 GGACCCCAAA
*
35939707 AAATTTAAATACCAACTT-AAAAAATAAGTC
1 AAATTTAAATACCAAATTAAAAAAAT-A-TC
*
35939737 AAATTTAGATACCAAATTTAAAAAAATATC
1 AAATTTAAATACCAAA-TTAAAAAAATATC
* *
35939767 TAATTTTAATACCAAATTAAATAAAA-A--
1 AAATTTAAATACCAAATTAAA-AAAATATC
**
35939794 AAATTTAAATATTAAATTAAAAAAA
1 AAATTTAAATACCAAATTAAAAAAA
35939819 GTTAAATTCA
Statistics
Matches: 70, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
26 4 0.06
27 17 0.24
29 6 0.09
30 33 0.47
31 3 0.04
32 7 0.10
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.30
Consensus pattern (29 bp):
AAATTTAAATACCAAATTAAAAAAATATC
Found at i:35939808 original size:22 final size:22
Alignment explanation
Indices: 35939782--35939825 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
35939772 TTAATACCAA
*
35939782 ATTAAATAAAAAAAATTTAAAT
1 ATTAAATAAAAAAAAGTTAAAT
*
35939804 ATTAAATTAAAAAAAGTTAAAT
1 ATTAAATAAAAAAAAGTTAAAT
35939826 TCAGTTACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (22 bp):
ATTAAATAAAAAAAAGTTAAAT
Found at i:35941872 original size:19 final size:19
Alignment explanation
Indices: 35941850--35941889 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
35941840 ATTGTATTAC
35941850 CTCTTT-GTATTGATATTTT
1 CTCTTTAGT-TTGATATTTT
*
35941869 CTCTTTAGTTTGTTATTTT
1 CTCTTTAGTTTGATATTTT
35941888 CT
1 CT
35941890 TTCATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 17 0.89
20 2 0.11
ACGTcount: A:0.12, C:0.12, G:0.10, T:0.65
Consensus pattern (19 bp):
CTCTTTAGTTTGATATTTT
Found at i:35947411 original size:19 final size:19
Alignment explanation
Indices: 35947389--35947426 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
35947379 ATTGTATTAC
35947389 CTCTTT-GTATTGATATTTT
1 CTCTTTAGT-TTGATATTTT
*
35947408 CTCTTTAGTTTGTTATTTT
1 CTCTTTAGTTTGATATTTT
35947427 TTTTTCTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.13, C:0.11, G:0.11, T:0.66
Consensus pattern (19 bp):
CTCTTTAGTTTGATATTTT
Found at i:35952488 original size:14 final size:15
Alignment explanation
Indices: 35952469--35952506 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
35952459 CTATTATTTG
*
35952469 TATCAAGATT-AAAA
1 TATCAAAATTCAAAA
35952483 TATCAAAATTCAAAA
1 TATCAAAATTCAAAA
35952498 TATACAAAA
1 TAT-CAAAA
35952507 ACTAAAATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.43
15 7 0.33
16 5 0.24
ACGTcount: A:0.61, C:0.11, G:0.03, T:0.26
Consensus pattern (15 bp):
TATCAAAATTCAAAA
Found at i:35952497 original size:15 final size:14
Alignment explanation
Indices: 35952469--35952535 Score: 57
Period size: 15 Copynumber: 4.6 Consensus size: 14
35952459 CTATTATTTG
*
35952469 TATCAAGATTAAAA
1 TATCAAAATTAAAA
35952483 TATCAAAATTCAAAA
1 TATCAAAATT-AAAA
*
35952498 TATACAAAAACTAAAA
1 TAT-C-AAAATTAAAA
35952514 TTGATCAAAA-TAAAA
1 -T-ATCAAAATTAAAA
35952529 TAT-AAAA
1 TATCAAAA
35952536 ACCCACAACT
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
12 4 0.09
13 2 0.04
14 10 0.22
15 12 0.26
16 9 0.20
17 7 0.15
18 2 0.04
ACGTcount: A:0.63, C:0.09, G:0.03, T:0.25
Consensus pattern (14 bp):
TATCAAAATTAAAA
Found at i:35957396 original size:127 final size:127
Alignment explanation
Indices: 35957165--35957425 Score: 468
Period size: 127 Copynumber: 2.1 Consensus size: 127
35957155 CCTTTAAACT
35957165 AAGTTTTTAGCCATTAAAACGCAAGCTTTGAATAAAAACCGAAAATAGGTTCTTTAATGGTGAAA
1 AAGTTTTTAGCCATTAAAACGCAAGCTTTGAATAAAAACCGAAAATAGGTTCTTTAATGGTGAAA
* *
35957230 TTCAGGTTTGTGTATAAAAACTTGATATTAAAGTGTTTTTCAACTTGTTTTAACATGTTTAG
66 TTCAGGTTTGTGTATAAAAACTTGATATTAAAGTATTTTTCAACTTGTTTTAACATGATTAG
* *
35957292 AAGTTTTTAGCCATTAAAACGCAAGCTTTGAATAAAAGCTGAAAATAGGTTCTTTAATGGTGAAA
1 AAGTTTTTAGCCATTAAAACGCAAGCTTTGAATAAAAACCGAAAATAGGTTCTTTAATGGTGAAA
* *
35957357 TTCGGGTTTGTGTATGAAAACTTGATATTAAAGTATTTTTCAACTTGTTTTAACATGATTAG
66 TTCAGGTTTGTGTATAAAAACTTGATATTAAAGTATTTTTCAACTTGTTTTAACATGATTAG
35957419 AAGTTTT
1 AAGTTTT
35957426 CTAAAATTAC
Statistics
Matches: 128, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
127 128 1.00
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (127 bp):
AAGTTTTTAGCCATTAAAACGCAAGCTTTGAATAAAAACCGAAAATAGGTTCTTTAATGGTGAAA
TTCAGGTTTGTGTATAAAAACTTGATATTAAAGTATTTTTCAACTTGTTTTAACATGATTAG
Found at i:35959257 original size:30 final size:30
Alignment explanation
Indices: 35959199--35959257 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
35959189 TACCACCTAA
* * *
35959199 GATACCTTTTCGGTCTCACCTAGGTAGATG
1 GATACCCTTTCGATCTCACCTAGCTAGATG
35959229 GATACCCTTTCGATCTCACCT-GTCTAGAT
1 GATACCCTTTCGATCTCACCTAG-CTAGAT
35959258 ATTCTATTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.04
30 24 0.96
ACGTcount: A:0.20, C:0.27, G:0.19, T:0.34
Consensus pattern (30 bp):
GATACCCTTTCGATCTCACCTAGCTAGATG
Found at i:35977695 original size:26 final size:26
Alignment explanation
Indices: 35977666--35977716 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
35977656 AATCAAATAT
*
35977666 AACATACATACAATAAAATGCAAAGC
1 AACATACATAAAATAAAATGCAAAGC
*
35977692 AACATATATAAAATAAAATGCAAAG
1 AACATACATAAAATAAAATGCAAAG
35977717 GATCACAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.61, C:0.14, G:0.08, T:0.18
Consensus pattern (26 bp):
AACATACATAAAATAAAATGCAAAGC
Found at i:35977731 original size:26 final size:26
Alignment explanation
Indices: 35977677--35977736 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
35977667 ACATACATAC
* *
35977677 AATAAAATGCAAAGCAACATATATAA
1 AATAAAATGCAAAGCAACACAAATAA
* * *
35977703 AATAAAATGCAAAGGATCACAAATTA
1 AATAAAATGCAAAGCAACACAAATAA
*
35977729 AATTAAAT
1 AATAAAAT
35977737 CGAATTTTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.60, C:0.10, G:0.08, T:0.22
Consensus pattern (26 bp):
AATAAAATGCAAAGCAACACAAATAA
Found at i:35979500 original size:20 final size:20
Alignment explanation
Indices: 35979477--35979527 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
35979467 CAATCTCATT
*
35979477 AAAAAATTCTCCTCTGAACA
1 AAAAAATCCTCCTCTGAACA
* * *
35979497 AAAAAATCCTTCTTTGAATA
1 AAAAAATCCTCCTCTGAACA
35979517 AAAAAATCCTC
1 AAAAAATCCTC
35979528 TCAATCTTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.47, C:0.22, G:0.04, T:0.27
Consensus pattern (20 bp):
AAAAAATCCTCCTCTGAACA
Found at i:35982306 original size:53 final size:53
Alignment explanation
Indices: 35982199--35982476 Score: 258
Period size: 53 Copynumber: 5.2 Consensus size: 53
35982189 TTTAGAGGAG
* * * * *
35982199 CATGGGCATGTGTTAGGGTGTGTGTGTATTTTGTTTGGGGGCACACGGGCTGACA
1 CATGGGCGTGTGTCAGGGTGTGTGTATATTTT-TCT-GGGGCACATGGGCTGACA
* * *
35982254 CATGAGCGTGTGTC-GAGGTGTGTGTATATTTTTCTGAGGCACATGGGTTGACA
1 CATGGGCGTGTGTCAG-GGTGTGTGTATATTTTTCTGGGGCACATGGGCTGACA
* * * * * * *
35982307 AATGGGCATGTGTCAAGGTGTGTGTATACTATTCTTGGGCACATGAGCTGACA
1 CATGGGCGTGTGTCAGGGTGTGTGTATATTTTTCTGGGGCACATGGGCTGACA
* * *
35982360 CATGGGCGTGTGTCAGGGTGTGTGTATATTATTT-T-TGGCACA-AGGCTAACA
1 CATGGGCGTGTGTCAGGGTGTGTGTATATT-TTTCTGGGGCACATGGGCTGACA
* * * * **
35982411 CATGGGCGTGTTTCAGGGTGTGTGTATACTGTTCTGGGGAACATGGTTTGACA
1 CATGGGCGTGTGTCAGGGTGTGTGTATATTTTTCTGGGGCACATGGGCTGACA
* *
35982464 CATTGGTGTGTGT
1 CATGGGCGTGTGT
35982477 ACATTATTTT
Statistics
Matches: 178, Mismatches: 39, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
50 2 0.01
51 35 0.20
52 11 0.06
53 99 0.56
54 5 0.03
55 26 0.15
ACGTcount: A:0.19, C:0.13, G:0.35, T:0.33
Consensus pattern (53 bp):
CATGGGCGTGTGTCAGGGTGTGTGTATATTTTTCTGGGGCACATGGGCTGACA
Found at i:35982475 original size:104 final size:103
Alignment explanation
Indices: 35982412--35982621 Score: 305
Period size: 104 Copynumber: 2.0 Consensus size: 103
35982402 AGGCTAACAC
35982412 ATGGGCGTGTTTCAGGGTGTGTGTATACTGTTCTGGGGAACATGGTTTGACACATTGGTGTGTGT
1 ATGGGCGTGTTTCAGGGTGTGTGTATACTGTTCTGGGGAACATGG-TTGACACATTGGTGTGTGT
** * * *
35982477 ACATTATTTTGAGACACATGGCCTGTAGTAAGCTATAAA
65 ACAGGATTGTGAGACACATGGCCTGCAGCAAGCTATAAA
35982516 ATGGGCGTGTTTCAGGGTGTGTGTATACTGTTCTGGGGAACATGGGTTGACACATTGGTGTGTGT
1 ATGGGCGTGTTTCAGGGTGTGTGTATACTGTTCTGGGGAACAT-GGTTGACACATTGGTGTGTGT
* * * *
35982581 ACATTG-TTTTGAGACACATGGCCTGTAGTAAGCTATAAA
65 ACA-GGATTGTGAGACACATGGCCTGCAGCAAGCTATAAA
35982620 AT
1 AT
35982622 CGATATTTGT
Statistics
Matches: 103, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
104 100 0.97
105 3 0.03
ACGTcount: A:0.23, C:0.12, G:0.30, T:0.34
Consensus pattern (103 bp):
ATGGGCGTGTTTCAGGGTGTGTGTATACTGTTCTGGGGAACATGGTTGACACATTGGTGTGTGTA
CAGGATTGTGAGACACATGGCCTGCAGCAAGCTATAAA
Found at i:35991423 original size:59 final size:59
Alignment explanation
Indices: 35991323--35991434 Score: 206
Period size: 59 Copynumber: 1.9 Consensus size: 59
35991313 CATCAATGTC
35991323 AACGCAATTTTACATGATGAAATTACTGAAGCCACGAGTAAACAGACAGGTATAATGCA
1 AACGCAATTTTACATGATGAAATTACTGAAGCCACGAGTAAACAGACAGGTATAATGCA
* *
35991382 AACGTAATTTTACATGATGAAATTACTGAAGCCACGGGTAAACAGACAGGTAT
1 AACGCAATTTTACATGATGAAATTACTGAAGCCACGAGTAAACAGACAGGTAT
35991435 CTTACCTTTC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 51 1.00
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (59 bp):
AACGCAATTTTACATGATGAAATTACTGAAGCCACGAGTAAACAGACAGGTATAATGCA
Found at i:35995119 original size:29 final size:29
Alignment explanation
Indices: 35995077--35995223 Score: 154
Period size: 29 Copynumber: 5.1 Consensus size: 29
35995067 ACGGATGGGG
* * *
35995077 GTATAATGTCTGCATCTGTAATTGTATAT
1 GTATCATGTCTGCATCTGTAACTGTATCT
* *
35995106 GTATCATGTCTGCAACTGTAACTATATCT
1 GTATCATGTCTGCATCTGTAACTGTATCT
* *
35995135 GTATCATGTCTACATCCGTAACTGTATCT
1 GTATCATGTCTGCATCTGTAACTGTATCT
* *
35995164 GTATCATGTC-ACATCCGTAACTGTATCT
1 GTATCATGTCTGCATCTGTAACTGTATCT
* * * *
35995192 GTGA-CATGACTGTATCTGTATCTGTATTT
1 GT-ATCATGTCTGCATCTGTAACTGTATCT
35995221 GTA
1 GTA
35995224 GTGTGACTGT
Statistics
Matches: 101, Mismatches: 15, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
28 26 0.26
29 75 0.74
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.40
Consensus pattern (29 bp):
GTATCATGTCTGCATCTGTAACTGTATCT
Found at i:35998018 original size:29 final size:31
Alignment explanation
Indices: 35997985--35998046 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 31
35997975 TTTAAAAGTC
35997985 AATAAAATTTTTTG-ACCT-TTAAAAATTAA
1 AATAAAATTTTTTGAACCTCTTAAAAATTAA
* **
35998014 AATAAATTTTTTTGAATGTCTTAAAAATTAA
1 AATAAAATTTTTTGAACCTCTTAAAAATTAA
35998045 AA
1 AA
35998047 AAAGTTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 13 0.46
30 2 0.07
31 13 0.46
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (31 bp):
AATAAAATTTTTTGAACCTCTTAAAAATTAA
Found at i:35998773 original size:17 final size:17
Alignment explanation
Indices: 35998748--35998844 Score: 86
Period size: 17 Copynumber: 5.6 Consensus size: 17
35998738 CTAGCTTTTA
* * *
35998748 ATTTAAAATTTTAATTC
1 ATTTTAAATTTGAATTT
35998765 ATTTTAAATTTGAATTT
1 ATTTTAAATTTGAATTT
* * *
35998782 ATTTTAAAATTGAAATC
1 ATTTTAAATTTGAATTT
*** *
35998799 ATTTTGGGTTTTAAATTT
1 ATTTT-AAATTTGAATTT
35998817 ATTTTAAATTTGAATTT
1 ATTTTAAATTTGAATTT
*
35998834 ATTTTGAATTT
1 ATTTTAAATTT
35998845 AAAATTAATT
Statistics
Matches: 61, Mismatches: 18, Indels: 2
0.75 0.22 0.02
Matches are distributed among these distances:
17 51 0.84
18 10 0.16
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.56
Consensus pattern (17 bp):
ATTTTAAATTTGAATTT
Found at i:35998850 original size:35 final size:34
Alignment explanation
Indices: 35998748--35998856 Score: 110
Period size: 34 Copynumber: 3.2 Consensus size: 34
35998738 CTAGCTTTTA
* * * *
35998748 ATTTAAAATTTTAATTCATTTTAAATTTGAATTT
1 ATTTTAAATTTGAATTCATTTTGAATTTAAATTT
* * **
35998782 ATTTTAAAATTGAAATCATTTTGGGTTTTAAATTT
1 ATTTTAAATTTGAATTCATTTT-GAATTTAAATTT
* *
35998817 ATTTTAAATTTGAATTTATTTTGAATTTAAAATT
1 ATTTTAAATTTGAATTCATTTTGAATTTAAATTT
*
35998851 AATTTA
1 ATTTTA
35998857 TTAAAAATCC
Statistics
Matches: 59, Mismatches: 15, Indels: 2
0.78 0.20 0.03
Matches are distributed among these distances:
34 32 0.54
35 27 0.46
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (34 bp):
ATTTTAAATTTGAATTCATTTTGAATTTAAATTT
Found at i:36000853 original size:31 final size:30
Alignment explanation
Indices: 36000768--36000866 Score: 96
Period size: 30 Copynumber: 3.3 Consensus size: 30
36000758 AAAGTAGTGC
*
36000768 TTTAACTCC-AAAACTTTCTCAAAATTACAT
1 TTTAAC-CCTAAAACTTTCTAAAAATTACAT
* *
36000798 TTTAACCCCT-AAAC-TTCTTTAAAATTATAT
1 TTTAA-CCCTAAAACTTTC-TAAAAATTACAT
*
36000828 TTTAACCCTAAAAACTTTCTAAAAATTAGAT
1 TTTAACCCT-AAAACTTTCTAAAAATTACAT
*
36000859 TTTGACCC
1 TTTAACCC
36000867 CCAAGTTTTA
Statistics
Matches: 58, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
29 7 0.12
30 26 0.45
31 22 0.38
32 3 0.05
ACGTcount: A:0.38, C:0.21, G:0.02, T:0.38
Consensus pattern (30 bp):
TTTAACCCTAAAACTTTCTAAAAATTACAT
Found at i:36000889 original size:29 final size:29
Alignment explanation
Indices: 36000857--36001272 Score: 163
Period size: 29 Copynumber: 14.4 Consensus size: 29
36000847 TAAAAATTAG
36000857 ATTTTGACCCCCAAGTTTTA-CAAAATTCC
1 ATTTTGACCCCCAA-TTTTACCAAAATTCC
** * *
36000886 ATTTTTG-CCTTCAATTTCACCAAAATTAC
1 A-TTTTGACCCCCAATTTTACCAAAATTCC
* *
36000915 ATTTCGATCCCCAAGTTTTA--AGAAATTCC
1 ATTTTGACCCCCAA-TTTTACCA-AAATTCC
* * *
36000944 ATTTAG-CCCCCGATTATACCAAAATTACC
1 ATTTTGACCCCCAATTTTACCAAAATT-CC
* * *
36000973 ATTTT-ACCCCCGAACTTT-CTAAAATCCC
1 ATTTTGACCCCC-AATTTTACCAAAATTCC
* *
36001001 ATTTTTG-CCCCCGATTTCACCAAAATTACC
1 A-TTTTGACCCCCAATTTTACCAAAATT-CC
* * *
36001031 ATTTT-ACTCCCGAACTTT-CTAAAATTCC
1 ATTTTGAC-CCCCAATTTTACCAAAATTCC
* ** * *
36001059 ATTTTTACGACCGATTTCACCAAAATTACC
1 ATTTTGACCCCCAATTTTACCAAAATT-CC
**
36001089 ATTTT-ACCCTTGAATTTT-CCAAAATTCC
1 ATTTTGACCC-CCAATTTTACCAAAATTCC
* * *
36001117 ATTTT-AACCCCGATTTTACCAAAATCACC
1 ATTTTGACCCCCAATTTTACCAAAAT-TCC
* * * *
36001146 ATTTT-ACCTCCGAACTTT-CTAAAATTCT
1 ATTTTGACC-CCCAATTTTACCAAAATTCC
** *
36001174 ATTTTTGA-CCCTGATTTTATCAAAAATTACC
1 A-TTTTGACCCCCAATTTTA-CCAAAATT-CC
* * *
36001205 ATTTT-ACCCCAAAACTTT-CCAAAATCCCC
1 ATTTTGACCCC-CAATTTTACCAAAAT-TCC
*
36001234 TTTTTGA--CCCAATTTTAACCAAAATTACC
1 ATTTTGACCCCCAATTTT-ACCAAAATT-CC
36001263 ATTTTG-CCCC
1 ATTTTGACCCC
36001273 TAGGTATCCA
Statistics
Matches: 280, Mismatches: 70, Indels: 73
0.66 0.17 0.17
Matches are distributed among these distances:
27 14 0.05
28 63 0.22
29 141 0.50
30 56 0.20
31 6 0.02
ACGTcount: A:0.31, C:0.28, G:0.05, T:0.36
Consensus pattern (29 bp):
ATTTTGACCCCCAATTTTACCAAAATTCC
Found at i:36000976 original size:58 final size:57
Alignment explanation
Indices: 36000859--36001214 Score: 260
Period size: 58 Copynumber: 6.2 Consensus size: 57
36000849 AAAATTAGAT
** *
36000859 TTTGACCCCCAAGTTTTACAAAATTCCATTTTTGCCTTCAATTTCACCAAAATTA-CA
1 TTTGACCCCCAAGTTTTA-AAAATTCCATTTTTGCCCCCGATTTCACCAAAATTACCA
* *
36000916 TTTCGATCCCCAAGTTTTAAGAAATTCCA-TTTAGCCCCCGATTAT-ACCAAAATTACCA
1 TTT-GACCCCCAAGTTTTAA-AAATTCCATTTTTGCCCCCGATT-TCACCAAAATTACCA
* * *
36000974 TTTTACCCCCGAACTTTCT-AAAATCCCATTTTTGCCCCCGATTTCACCAAAATTACCA
1 TTTGACCCCC-AAGTTT-TAAAAATTCCATTTTTGCCCCCGATTTCACCAAAATTACCA
* * * * **
36001032 TTTTACTCCCGAACTTTCT-AAAATTCCATTTTTACGACCGATTTCACCAAAATTACCA
1 TTTGAC-CCCCAAGTTT-TAAAAATTCCATTTTTGCCCCCGATTTCACCAAAATTACCA
* ** * ** * *
36001090 TTTTACCCTTGAA-TTTTCCAAAATTCCA-TTTTAACCCCGATTTTACCAAAATCACCA
1 TTTGACCC-CCAAGTTTT-AAAAATTCCATTTTTGCCCCCGATTTCACCAAAATTACCA
* * * * * * * *
36001147 TTTTACCTCCGAACTTTCT-AAAATTCTATTTTTGACCCTGATTTTATCAAAAATTACCA
1 TTTGACC-CCCAAGTTT-TAAAAATTCCATTTTTGCCCCCGATTTCA-CCAAAATTACCA
*
36001206 TTTTACCCC
1 TTTGACCCC
36001215 AAAACTTTCC
Statistics
Matches: 255, Mismatches: 27, Indels: 33
0.81 0.09 0.10
Matches are distributed among these distances:
56 1 0.00
57 84 0.33
58 148 0.58
59 22 0.09
ACGTcount: A:0.30, C:0.28, G:0.05, T:0.36
Consensus pattern (57 bp):
TTTGACCCCCAAGTTTTAAAAATTCCATTTTTGCCCCCGATTTCACCAAAATTACCA
Found at i:36008019 original size:6 final size:6
Alignment explanation
Indices: 36008008--36008087 Score: 69
Period size: 6 Copynumber: 13.5 Consensus size: 6
36007998 TTCAATGAAT
* * *
36008008 AAAAGA AAAAGA AGAAGA AAAACA AAAAGA AAAATA AAAA-A CAAAA-A
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA -AAAAGA
*
36008055 AACAACA AACAA-A AAAAGA AAAAG- AAAAGA AAA
1 AA-AAGA AA-AAGA AAAAGA AAAAGA AAAAGA AAA
36008088 GGAGAGGTCG
Statistics
Matches: 64, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
5 10 0.16
6 48 0.75
7 6 0.09
ACGTcount: A:0.82, C:0.06, G:0.10, T:0.01
Consensus pattern (6 bp):
AAAAGA
Found at i:36008055 original size:15 final size:15
Alignment explanation
Indices: 36008037--36008077 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
36008027 AAACAAAAAG
*
36008037 AAAAATAAAAAACAA
1 AAAAACAAAAAACAA
*
36008052 AAAAACAACAAACAA
1 AAAAACAAAAAACAA
*
36008067 AAAAAGAAAAA
1 AAAAACAAAAA
36008078 GAAAAGAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.85, C:0.10, G:0.02, T:0.02
Consensus pattern (15 bp):
AAAAACAAAAAACAA
Found at i:36009106 original size:50 final size:49
Alignment explanation
Indices: 36008976--36009306 Score: 233
Period size: 50 Copynumber: 6.7 Consensus size: 49
36008966 TTTGGCAGGG
* * *
36008976 AAAGATCTAAGACCACAACGGCAGATCCAGTACCACGAAGACAAGAA-AA
1 AAAGATCTAAG-CCGCAACGGCGGATCCAGTACCACGAAGACAAGAAGGA
* * * ** * * *
36009025 GAAAGATTTAAGCCGCAACGACGAATTTAGTATCATGAAGACATGAAGGA
1 -AAAGATCTAAGCCGCAACGGCGGATCCAGTACCACGAAGACAAGAAGGA
* * *
36009075 AAAGATCTAAGACCGCAACGGCGGATCTAGTACCACAAAGATACAA-AAGGG
1 AAAGATCTAAG-CCGCAACGGCGGATCCAGTACCACGAAG--ACAAGAAGGA
* * * * * *
36009126 AAAGGTCTAAGTCGTAACGGCAGAT-CATGTACCTCAGAAGACAAGAAGGG
1 AAAGATCTAAGCCGCAACGGCGGATCCA-GTACCAC-GAAGACAAGAAGGA
* * * *
36009176 AAAGATCTAAGCTGCAACGGCGGATCCAATA-CAGCGAAGAC-ATAAGGG
1 AAAGATCTAAGCCGCAACGGCGGATCCAGTACCA-CGAAGACAAGAAGGA
* * * * * * *
36009224 AAGGATCTAAGCCGTAACGGCGGAACTAGTACCACAAAGACACG-ACGA
1 AAAGATCTAAGCCGCAACGGCGGATCCAGTACCACGAAGACAAGAAGGA
**
36009272 GAAAGATCTAAGAATGCAACGGCGGATCCAGTACC
1 -AAAGATCTAAG-CCGCAACGGCGGATCCAGTACC
36009307 GCAAAAAGAC
Statistics
Matches: 216, Mismatches: 52, Indels: 26
0.73 0.18 0.09
Matches are distributed among these distances:
48 39 0.18
49 60 0.28
50 95 0.44
51 19 0.09
52 3 0.01
ACGTcount: A:0.41, C:0.21, G:0.24, T:0.13
Consensus pattern (49 bp):
AAAGATCTAAGCCGCAACGGCGGATCCAGTACCACGAAGACAAGAAGGA
Found at i:36009256 original size:98 final size:100
Alignment explanation
Indices: 36008972--36009331 Score: 288
Period size: 100 Copynumber: 3.6 Consensus size: 100
36008962 CAGGTTTGGC
** * * * ** * *
36008972 AGGGAAAGATCTAAGACCACAACGGCAGATCCAGTACCACGAAG-ACAAGAAAAGAAAGATTTAA
1 AGGGAAAGATCTAAGACTGCAACGGCGGATCCAATACCACAAAGAACAA-AAGGGAAAGGTCTAA
* * ** * * *
36009036 GCCGCAACGAC-GAATTTAGTATCA-TGAAGACATGA
65 GCCGTAACGGCAGAACAT-GTACCACAGAAGACAAGA
* * * *
36009071 AGGAAAAGATCTAAGACCGCAACGGCGGATCTAGTACCACAAAGATACAAAAGGGAAAGGTCTAA
1 AGGGAAAGATCTAAGACTGCAACGGCGGATCCAATACCACAAAGA-ACAAAAGGGAAAGGTCTAA
* * *
36009136 GTCGTAACGGCAGATCATGTACCTCAGAAGACAAGA
65 GCCGTAACGGCAGAACATGTACCACAGAAGACAAGA
* *
36009172 AGGGAAAGATCTAAG-CTGCAACGGCGGATCCAATA-CAGCGAAG-ACATAAGGG-AAGGATCTA
1 AGGGAAAGATCTAAGACTGCAACGGCGGATCCAATACCA-CAAAGAACAAAAGGGAAAGG-TCTA
* *
36009233 AGCCGTAACGGCGGAAC-TAGTACCACA-AAGACACGA
64 AGCCGTAACGGCAGAACAT-GTACCACAGAAGACAAGA
* * * * * * *
36009269 CGAGAAAGATCTAAGAATGCAACGGCGGATCCAGTACCGCAAAAAGACAAAAGGGAAAAGTCT
1 AGGGAAAGATCTAAGACTGCAACGGCGGATCCAATACCACAAAGA-ACAAAAGGGAAAGGTCT
36009332 TTATCTCTCT
Statistics
Matches: 210, Mismatches: 39, Indels: 23
0.77 0.14 0.08
Matches are distributed among these distances:
97 26 0.12
98 54 0.26
99 42 0.20
100 55 0.26
101 33 0.16
ACGTcount: A:0.42, C:0.20, G:0.25, T:0.13
Consensus pattern (100 bp):
AGGGAAAGATCTAAGACTGCAACGGCGGATCCAATACCACAAAGAACAAAAGGGAAAGGTCTAAG
CCGTAACGGCAGAACATGTACCACAGAAGACAAGA
Found at i:36009487 original size:92 final size:92
Alignment explanation
Indices: 36009330--36010150 Score: 1351
Period size: 92 Copynumber: 8.9 Consensus size: 92
36009320 AGGGAAAAGT
* * ** * *
36009330 CTTTATCTCTCTGAAGTTGTAGTAAGAGTAAGATGAAGCTTCAAACACCCATTCCTATCCTCTTG
1 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTG
*
36009395 AAGTTACAGTAAAGTTGGATAACGAAC
66 AAGTTATAGTAAAGTTGGATAACGAAC
*
36009422 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATAAAGCTTCAAACGTCAATTCTTATCCTCTTG
1 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTG
*
36009487 AAGTTATAGTAAAGTTGGACAACGAAC
66 AAGTTATAGTAAAGTTGGATAACGAAC
* * *
36009514 CCTTATCTCTCTAAAGTTATAGTAAGAGCAAGATGAAGCTTTAAACGTCAATTCTTATCCTCTTG
1 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTG
*
36009579 AAGTTATAGTAAATTTAGG-TAACGAAC
66 AAGTTATAGTAAAGTT-GGATAACGAAC
*
36009606 CTTTATCTCTCTGAAGTTATAGTAAGAGCAATATGAAGCTTCAAACGTCAATTCTTATCCTCTTG
1 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTG
36009671 AAGTTATAGTAAAGTTGGATAACGAAC
66 AAGTTATAGTAAAGTTGGATAACGAAC
*
36009698 CTTTATCTCTTTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTG
1 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTG
36009763 AAGTTATAGTAAAGTTGGATAACGAAC
66 AAGTTATAGTAAAGTTGGATAACGAAC
* * *
36009790 CCTTATCTCTCTAAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCTTATCCTCTTG
1 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTG
*
36009855 AAGTTATAGTAAAGTTGGATAATGAAC
66 AAGTTATAGTAAAGTTGGATAACGAAC
36009882 CTTTATCTCTCTGAAGTTATAGTAAGAGCCAA-ATGAAGCTTCAAACGTCAATTCTTATCCTCTT
1 CTTTATCTCTCTGAAGTTATAGTAAGAG-CAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTT
* *
36009946 AAAGTTATAGTAAAGTTGGATAACAAAC
65 GAAGTTATAGTAAAGTTGGATAACGAAC
36009974 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTG
1 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTG
*
36010039 AAGTTATAGTAAAGTTGGATAATGAAC
66 AAGTTATAGTAAAGTTGGATAACGAAC
* * *
36010066 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATAAAGCTTCAAACATCAATTCCTA-CCTTCTT
1 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCC-TCTT
**
36010130 GAAGTTGCAGTAAAGTTGGAT
65 GAAGTTATAGTAAAGTTGGAT
36010151 TAAAAACAAA
Statistics
Matches: 683, Mismatches: 41, Indels: 10
0.93 0.06 0.01
Matches are distributed among these distances:
91 7 0.01
92 671 0.98
93 5 0.01
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (92 bp):
CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTG
AAGTTATAGTAAAGTTGGATAACGAAC
Found at i:36009715 original size:40 final size:40
Alignment explanation
Indices: 36009660--36010090 Score: 145
Period size: 40 Copynumber: 9.6 Consensus size: 40
36009650 ACGTCAATTC
36009660 TTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAACCT
1 TTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAACCT
*** *
36009700 TTAT-CTCTTTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATT
1 TTATCCTC-TTGAAGTTATAGTAA-AGTTGGAT-AA----CGAAC--C---T
*
36009751 CTTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAACCC
1 -TTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAACCT
* *** *
36009792 TTAT-CTCTCTAAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACATCAATT
1 TTATCCTCT-TGAAGTTATAGTAA-AGTTGGAT-AA----CGAAC--C---T
*
36009843 CTTATCCTCTTGAAGTTATAGTAAAGTTGGATAATGAACCT
1 -TTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAACCT
* * *
36009884 TTAT-CTCTCTGAAGTTATAGTAAGAGCCAAATGAAGCTTCAAACGTCAA-TT
1 TTATCCTCT-TGAAGTTATAGTAA-AG----TTG--G-AT--AACG--AACCT
* *
36009935 CTTATCCTCTTAAAGTTATAGTAAAGTTGGATAACAAACCT
1 -TTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAACCT
*** *
36009976 TTAT-CTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATT
1 TTATCCTCT-TGAAGTTATAGTAA-AGTTGGAT-AA----CGAAC--C---T
*
36010027 CTTATCCTCTTGAAGTTATAGTAAAGTTGGATAATGAACCT
1 -TTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAACCT
36010068 TTAT-CTCTCTGAAGTTATAGTAA
1 TTATCCTCT-TGAAGTTATAGTAA
36010091 GAGCAAGATA
Statistics
Matches: 293, Mismatches: 39, Indels: 118
0.65 0.09 0.26
Matches are distributed among these distances:
39 19 0.06
40 91 0.31
41 20 0.07
42 9 0.03
44 4 0.01
45 3 0.01
46 23 0.08
47 3 0.01
48 4 0.01
50 9 0.03
51 20 0.07
52 73 0.25
53 15 0.05
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (40 bp):
TTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAACCT
Found at i:36010725 original size:17 final size:17
Alignment explanation
Indices: 36010700--36010738 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
36010690 CCAACTTTTA
* *
36010700 ATTTAAAATTTGAACTC
1 ATTTTAAATTTGAAATC
36010717 ATTTTAAATTTGAAATC
1 ATTTTAAATTTGAAATC
36010734 ATTTT
1 ATTTT
36010739 GGGTTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (17 bp):
ATTTTAAATTTGAAATC
Found at i:36010767 original size:17 final size:17
Alignment explanation
Indices: 36010700--36010778 Score: 59
Period size: 17 Copynumber: 4.6 Consensus size: 17
36010690 CCAACTTTTA
* *
36010700 ATTTAAAATTTGAACTC
1 ATTTTAAATTTGAATTC
*
36010717 ATTTTAAATTTGAAATC
1 ATTTTAAATTTGAATTC
*** * *
36010734 ATTTTGGGTTTTAAATTT
1 ATTTT-AAATTTGAATTC
*
36010752 ATTTTAAATTTGAATTT
1 ATTTTAAATTTGAATTC
*
36010769 ATTTTGAATT
1 ATTTTAAATT
36010779 GAAAATTAAT
Statistics
Matches: 48, Mismatches: 13, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
17 37 0.77
18 11 0.23
ACGTcount: A:0.34, C:0.04, G:0.09, T:0.53
Consensus pattern (17 bp):
ATTTTAAATTTGAATTC
Found at i:36010785 original size:35 final size:35
Alignment explanation
Indices: 36010717--36010790 Score: 85
Period size: 35 Copynumber: 2.1 Consensus size: 35
36010707 ATTTGAACTC
** ** *
36010717 ATTTTAAATTTGAAATCATTTTGGGTTTTAAATTT
1 ATTTTAAATTTGAAATCATTTTGAATTGAAAATTA
* *
36010752 ATTTTAAATTTGAATTTATTTTGAATTGAAAATTA
1 ATTTTAAATTTGAAATCATTTTGAATTGAAAATTA
36010787 ATTT
1 ATTT
36010791 ATTAAAAGTC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.35, C:0.01, G:0.09, T:0.54
Consensus pattern (35 bp):
ATTTTAAATTTGAAATCATTTTGAATTGAAAATTA
Found at i:36010837 original size:18 final size:19
Alignment explanation
Indices: 36010803--36010841 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
36010793 TAAAAGTCCA
*
36010803 AAATACAAGTCCAAAGCCC
1 AAATACAAATCCAAAGCCC
36010822 AAATACAAAT-CAAAGCCC
1 AAATACAAATCCAAAGCCC
36010840 AA
1 AA
36010842 TTGGGCCCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.54, C:0.28, G:0.08, T:0.10
Consensus pattern (19 bp):
AAATACAAATCCAAAGCCC
Found at i:36012768 original size:30 final size:30
Alignment explanation
Indices: 36012734--36012830 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
36012724 AAAAGTAGTG
* *
36012734 TTTTGACCCTTGAACTTCTTCAAAATTATA
1 TTTTGACCCTTAAACTTCTTAAAAATTATA
* * *
36012764 TTTTGACCCTAAAAATT-TCTAAAAATTACA
1 TTTTGACCCTTAAACTTCT-TAAAAATTATA
* * *
36012794 TTTTAACCCCTAAACTTCTTTAAAATTATA
1 TTTTGACCCTTAAACTTCTTAAAAATTATA
36012824 TTTTGAC
1 TTTTGAC
36012831 TCCAAAAGTT
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
29 1 0.02
30 51 0.96
31 1 0.02
ACGTcount: A:0.35, C:0.19, G:0.04, T:0.42
Consensus pattern (30 bp):
TTTTGACCCTTAAACTTCTTAAAAATTATA
Found at i:36012820 original size:60 final size:60
Alignment explanation
Indices: 36012746--36012862 Score: 173
Period size: 60 Copynumber: 1.9 Consensus size: 60
36012736 TTGACCCTTG
36012746 AACTTCTTCAAAATTATATTTTGAC-CCTAAAAATTTCTAAAAATTACATTTTAACCCCTA
1 AACTTCTTCAAAATTATATTTTGACTCC-AAAAATTTCTAAAAATTACATTTTAACCCCTA
* * * * *
36012806 AACTTCTTTAAAATTATATTTTGACTCCAAAAGTTTTTGAAAATTACATTTTTACCC
1 AACTTCTTCAAAATTATATTTTGACTCCAAAAATTTCTAAAAATTACATTTTAACCC
36012863 TCAAGTTTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
60 49 0.96
61 2 0.04
ACGTcount: A:0.38, C:0.18, G:0.03, T:0.41
Consensus pattern (60 bp):
AACTTCTTCAAAATTATATTTTGACTCCAAAAATTTCTAAAAATTACATTTTAACCCCTA
Found at i:36012849 original size:30 final size:28
Alignment explanation
Indices: 36012755--36012862 Score: 90
Period size: 30 Copynumber: 3.6 Consensus size: 28
36012745 GAACTTCTTC
* *
36012755 AAAATTATATTTTGACCCTAAAAATTTCTA
1 AAAATTACATTTTGACCC-AAAAATTT-TT
* * *
36012785 AAAATTACATTTTAACCCCTAAACTTCTTT
1 AAAATTACATTTTGA-CCCAAAAATT-TTT
* *
36012815 AAAATTATATTTTGACTCCAAAAGTTTTT
1 AAAATTACATTTTGAC-CCAAAAATTTTT
*
36012844 GAAAATTACATTTTTACCC
1 -AAAATTACATTTTGACCC
36012863 TCAAGTTTTA
Statistics
Matches: 63, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
29 6 0.10
30 53 0.84
31 4 0.06
ACGTcount: A:0.39, C:0.17, G:0.04, T:0.41
Consensus pattern (28 bp):
AAAATTACATTTTGACCCAAAAATTTTT
Found at i:36012936 original size:58 final size:58
Alignment explanation
Indices: 36012845--36013096 Score: 325
Period size: 58 Copynumber: 4.4 Consensus size: 58
36012835 AAAGTTTTTG
* * *
36012845 AAAATTA-CATTTTTACCCTC-AAGTTT-TACAAAATTCCATTTTTACCCCCGATTATACC
1 AAAATTACCA-TTTTACCCTCGAACTTTCT--AAAATTCCATTTTTAACCCCGATTTTACC
*
36012903 AAAATTACCATTTTACCCCCGAACTTTCTAAAATTCCATTTTT-ACCCTCGATTTTACC
1 AAAATTACCATTTTACCCTCGAACTTTCTAAAATTCCATTTTTAACCC-CGATTTTACC
* * *
36012961 AAAATTACCATTTTACCCTCAAACTTTCTAAAATTCTATTTTTAACCCCGATTTTACG
1 AAAATTACCATTTTACCCTCGAACTTTCTAAAATTCCATTTTTAACCCCGATTTTACC
* * * *
36013019 AAAATTACCATTTTACCCTCGAATTTTCCAAAATTCCA-TTTTAACCTCGATTTTACT
1 AAAATTACCATTTTACCCTCGAACTTTCTAAAATTCCATTTTTAACCCCGATTTTACC
*
36013076 AAAATTACCATTTTGCCCTCG
1 AAAATTACCATTTTACCCTCG
36013097 GGTATCCAAA
Statistics
Matches: 174, Mismatches: 15, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
57 40 0.23
58 122 0.70
59 11 0.06
60 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.04, T:0.38
Consensus pattern (58 bp):
AAAATTACCATTTTACCCTCGAACTTTCTAAAATTCCATTTTTAACCCCGATTTTACC
Found at i:36013096 original size:29 final size:29
Alignment explanation
Indices: 36012845--36013096 Score: 227
Period size: 29 Copynumber: 8.7 Consensus size: 29
36012835 AAAGTTTTTG
*
36012845 AAAATTA-CATTTTTACCCTCAAGTTTTA-C
1 AAAATTACCA-TTTTACCCTCGA-TTTTACC
* *
36012874 AAAATT-CCATTTTTACCCCCGATTATACC
1 AAAATTACCA-TTTTACCCTCGATTTTACC
* * *
36012903 AAAATTACCATTTTACCCCCGAACTTT-CT
1 AAAATTACCATTTTACCCTCG-ATTTTACC
36012932 AAAATT-CCATTTTTACCCTCGATTTTACC
1 AAAATTACCA-TTTTACCCTCGATTTTACC
* * *
36012961 AAAATTACCATTTTACCCTCAAACTTT-CT
1 AAAATTACCATTTTACCCTC-GATTTTACC
* *
36012990 AAAATT-CTATTTTTAACCC-CGATTTTACG
1 AAAATTACCA-TTTT-ACCCTCGATTTTACC
36013019 AAAATTACCATTTTACCCTCGAATTTT-CC
1 AAAATTACCATTTTACCCTCG-ATTTTACC
* *
36013048 AAAATT-CCATTTTAACCTCGATTTTACT
1 AAAATTACCATTTTACCCTCGATTTTACC
*
36013076 AAAATTACCATTTTGCCCTCG
1 AAAATTACCATTTTACCCTCG
36013097 GGTATCCAAA
Statistics
Matches: 185, Mismatches: 22, Indels: 32
0.77 0.09 0.13
Matches are distributed among these distances:
27 5 0.03
28 41 0.22
29 115 0.62
30 24 0.13
ACGTcount: A:0.31, C:0.26, G:0.04, T:0.38
Consensus pattern (29 bp):
AAAATTACCATTTTACCCTCGATTTTACC
Found at i:36014993 original size:14 final size:14
Alignment explanation
Indices: 36014974--36015011 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
36014964 TCTAATCCTT
36014974 AAAAACAATTTAAA
1 AAAAACAATTTAAA
36014988 AAAAACAATTTAAA
1 AAAAACAATTTAAA
36015002 AAAAACAATT
1 AAAAACAATT
36015012 ATTAAGAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.71, C:0.08, G:0.00, T:0.21
Consensus pattern (14 bp):
AAAAACAATTTAAA
Found at i:36023067 original size:49 final size:50
Alignment explanation
Indices: 36022975--36023089 Score: 162
Period size: 49 Copynumber: 2.3 Consensus size: 50
36022965 TAAATATAAA
*
36022975 ATATTTATATAAAATACAAGATATGAATAAAACAATATAAATAAATATTT
1 ATATTTATATAAAACACAAGATATGAATAAAACAATATAAATAAATATTT
* * *
36023025 ATATTTATATAAAACACCAA-AT-TTAATAAAATAATTTAAATAAATATTT
1 ATATTTATATAAAACA-CAAGATATGAATAAAACAATATAAATAAATATTT
*
36023074 ATATTTATTTAAAACA
1 ATATTTATATAAAACA
36023090 TCATATCTGA
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
49 39 0.66
50 17 0.29
51 3 0.05
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (50 bp):
ATATTTATATAAAACACAAGATATGAATAAAACAATATAAATAAATATTT
Found at i:36027395 original size:77 final size:77
Alignment explanation
Indices: 36027309--36027641 Score: 243
Period size: 82 Copynumber: 4.2 Consensus size: 77
36027299 TAAAATTTTG
* * * * *
36027309 AAACAAAATCAAAATCAATTCTATTGAATGGTAAGAATAAATCCTGAAACAAAATTATTTAATTA
1 AAACAAAATCAAAATCAATTCTATTAAACGGCAAGAAAAAATCCCGAAACAAAATTATTTAATTA
* *
36027374 GTTTTTGTTAGA
66 ATTCTTGTTAGA
* * * *
36027386 AAACAAAATCAAAATTAATTCTATTAAACGGCAGGAAAAAATCCCGAAATAGAATTATTTAATTA
1 AAACAAAATCAAAATCAATTCTATTAAACGGCAAGAAAAAATCCCGAAACAAAATTATTTAATTA
* *
36027451 ATTCTTGTTTGG
66 ATTCTTGTTAGA
* * * * ** * * * *
36027463 AAACAAAATCAAAATAGAATAAAATTTGTTGAACGGCGGGAATAAATCTCGAAACAGAATTATTC
1 AAACAAAATCAAAAT-CAAT----TCTATTAAACGGCAAGAAAAAATCCCGAAACAAAATTATTT
* * *
36027528 AATCAATTCTTGTTCGG
61 AATTAATTCTTGTTAGA
* * * ** * * * *
36027545 AAACAAAATCAAAATAGAATAAAATCTATTGAACAGCGGGAATAAATCTCGAAACAGAATTATTC
1 AAACAAAATCAAAAT-CAAT----TCTATTAAACGGCAAGAAAAAATCCCGAAACAAAATTATTT
* *
36027610 AATTAATTCTTGTTTGG
61 AATTAATTCTTGTTAGA
36027627 AAACAAAATCAAAAT
1 AAACAAAATCAAAAT
36027642 AAAATAAAAT
Statistics
Matches: 222, Mismatches: 29, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
77 79 0.36
78 3 0.01
82 140 0.63
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (77 bp):
AAACAAAATCAAAATCAATTCTATTAAACGGCAAGAAAAAATCCCGAAACAAAATTATTTAATTA
ATTCTTGTTAGA
Found at i:36027536 original size:82 final size:82
Alignment explanation
Indices: 36027343--36027695 Score: 439
Period size: 82 Copynumber: 4.4 Consensus size: 82
36027333 TGAATGGTAA
* * * * * * *
36027343 GAATAAATCCTGAAACAAAATTATTTAATTAGTTTTTGTTAGAAAACAAAATCAAAAT----T--
1 GAATAAATCCCGAAACAGAATTATTCAATTAATTCTTGTTTGGAAACAAAATCAAAATAGAATAA
* * *
36027402 AATTCTATTAAACGGCAG
66 AATT-TGTTGAACGGCGG
* * *
36027420 GAAAAAATCCCGAAATAGAATTATTTAATTAATTCTTGTTTGGAAACAAAATCAAAATAGAATAA
1 GAATAAATCCCGAAACAGAATTATTCAATTAATTCTTGTTTGGAAACAAAATCAAAATAGAATAA
36027485 AATTTGTTGAACGGCGG
66 AATTTGTTGAACGGCGG
* * *
36027502 GAATAAATCTCGAAACAGAATTATTCAATCAATTCTTGTTCGGAAACAAAATCAAAATAGAATAA
1 GAATAAATCCCGAAACAGAATTATTCAATTAATTCTTGTTTGGAAACAAAATCAAAATAGAATAA
* * *
36027567 AATCTATTGAACAGCGG
66 AATTTGTTGAACGGCGG
* *
36027584 GAATAAATCTCGAAACAGAATTATTCAATTAATTCTTGTTTGGAAACAAAATCAAAATAAAATAA
1 GAATAAATCCCGAAACAGAATTATTCAATTAATTCTTGTTTGGAAACAAAATCAAAATAGAATAA
*
36027649 AATTTGTTGAACGGCGA
66 AATTTGTTGAACGGCGG
* *
36027666 GAATAAATCCCGAAACAGATTTATTTAATT
1 GAATAAATCCCGAAACAGAATTATTCAATT
36027696 TTAATTTTTA
Statistics
Matches: 240, Mismatches: 30, Indels: 7
0.87 0.11 0.03
Matches are distributed among these distances:
77 50 0.21
81 1 0.00
82 185 0.77
83 4 0.02
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.29
Consensus pattern (82 bp):
GAATAAATCCCGAAACAGAATTATTCAATTAATTCTTGTTTGGAAACAAAATCAAAATAGAATAA
AATTTGTTGAACGGCGG
Found at i:36028226 original size:49 final size:50
Alignment explanation
Indices: 36028139--36028257 Score: 150
Period size: 49 Copynumber: 2.4 Consensus size: 50
36028129 AATATAAATA
* * * * * *
36028139 TAAAATACAAGATCTGAAAAAAATAATTTAAATAAATATTTATGTTTATG
1 TAAAACACCAGATCTGAAAAAAACAAATTAAAGAAATATTTATATTTATG
* *
36028189 TAAAACACCAGATCT-AACAAAACAAATTAAAGAAATATTTATATTTATT
1 TAAAACACCAGATCTGAAAAAAACAAATTAAAGAAATATTTATATTTATG
*
36028238 TAAAACATCAGATCTGAAAA
1 TAAAACACCAGATCTGAAAA
36028258 CAATTTAAAT
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
49 42 0.72
50 16 0.28
ACGTcount: A:0.53, C:0.09, G:0.07, T:0.31
Consensus pattern (50 bp):
TAAAACACCAGATCTGAAAAAAACAAATTAAAGAAATATTTATATTTATG
Found at i:36031772 original size:84 final size:85
Alignment explanation
Indices: 36031674--36031838 Score: 314
Period size: 85 Copynumber: 2.0 Consensus size: 85
36031664 CCAAAAATAA
*
36031674 AAAACCTTAAACTAAAAAATG-AAAAAAAACCTAGCAACTGCCCTTGGATGCTTGGTCGTCGTTG
1 AAAACCTTAAACTAAAAAATGAAAAAAAAACCTAGCAACTGCCCTTGGATGCTTGGTCGCCGTTG
36031738 CCCTTACCCGGAAATCATAT
66 CCCTTACCCGGAAATCATAT
36031758 AAAACCTTAAACTAAAAAATGAAAAAAAAACCTAGCAACTGCCCTTGGATGCTTGGTCGCCGTTG
1 AAAACCTTAAACTAAAAAATGAAAAAAAAACCTAGCAACTGCCCTTGGATGCTTGGTCGCCGTTG
36031823 CCCTTACCCGGAAATC
66 CCCTTACCCGGAAATC
36031839 TTAAAGATTT
Statistics
Matches: 79, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
84 21 0.27
85 58 0.73
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.22
Consensus pattern (85 bp):
AAAACCTTAAACTAAAAAATGAAAAAAAAACCTAGCAACTGCCCTTGGATGCTTGGTCGCCGTTG
CCCTTACCCGGAAATCATAT
Found at i:36032877 original size:19 final size:18
Alignment explanation
Indices: 36032850--36032892 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
36032840 TTTATTATGT
* *
36032850 TATTAATTTTATTTAATTG
1 TATTCATTTCATTT-ATTG
*
36032869 TATTCATTTCATTTATTT
1 TATTCATTTCATTTATTG
36032887 TATTCA
1 TATTCA
36032893 GGTATTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (18 bp):
TATTCATTTCATTTATTG
Found at i:36036481 original size:24 final size:21
Alignment explanation
Indices: 36036452--36036512 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 21
36036442 ATTAAATATC
36036452 ATAAAATAATAATAATAATAAAAT
1 ATAAAA-AATAAT-A-AATAAAAT
36036476 ATAAAAAAATAATAAATAAAAT
1 AT-AAAAAATAATAAATAAAAT
36036498 ATAAAAAATAA-AAAT
1 ATAAAAAATAATAAAT
36036513 CCTCACATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.11
21 9 0.25
22 10 0.28
23 1 0.03
24 8 0.22
25 4 0.11
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (21 bp):
ATAAAAAATAATAAATAAAAT
Found at i:36036484 original size:27 final size:29
Alignment explanation
Indices: 36036445--36036511 Score: 84
Period size: 27 Copynumber: 2.4 Consensus size: 29
36036435 TACATGCATT
* * *
36036445 AAATATCATAAAATAAT-AATAATA-ATA
1 AAATATAAAAAAATAATAAATAAAATATA
36036472 AAATATAAAAAAATAATAAATAAAATATA
1 AAATATAAAAAAATAATAAATAAAATATA
*
36036501 AAAAATAAAAA
1 AAATATAAAAA
36036512 TCCTCACATA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 15 0.44
28 6 0.18
29 13 0.38
ACGTcount: A:0.75, C:0.01, G:0.00, T:0.24
Consensus pattern (29 bp):
AAATATAAAAAAATAATAAATAAAATATA
Found at i:36036496 original size:22 final size:22
Alignment explanation
Indices: 36036452--36036512 Score: 81
Period size: 24 Copynumber: 2.8 Consensus size: 22
36036442 ATTAAATATC
*
36036452 ATAAAATAATAATAATAATAAAAT
1 ATAAAAAAATAAT-A-AATAAAAT
36036476 ATAAAAAAATAATAAATAAAAT
1 ATAAAAAAATAATAAATAAAAT
36036498 AT-AAAAAATAA-AAAT
1 ATAAAAAAATAATAAAT
36036513 CCTCACATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
20 4 0.11
21 9 0.25
22 10 0.28
23 1 0.03
24 12 0.33
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (22 bp):
ATAAAAAAATAATAAATAAAAT
Found at i:36039340 original size:21 final size:21
Alignment explanation
Indices: 36039316--36039387 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
36039306 TTTCAATATT
*
36039316 GGTAGAAGTAAGACTTGTTTC
1 GGTAGAAGTAAGACTTGTATC
*
36039337 GGTAGAAG-AGGCACTTGTATC
1 GGTAGAAGTAAG-ACTTGTATC
* **
36039358 GGTAGAACTATCACTTGTATC
1 GGTAGAAGTAAGACTTGTATC
*
36039379 GATAGAAGT
1 GGTAGAAGT
36039388 CTGCACTATT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
20 2 0.05
21 39 0.93
22 1 0.02
ACGTcount: A:0.31, C:0.12, G:0.28, T:0.29
Consensus pattern (21 bp):
GGTAGAAGTAAGACTTGTATC
Found at i:36042275 original size:50 final size:50
Alignment explanation
Indices: 36042192--36042347 Score: 156
Period size: 50 Copynumber: 3.1 Consensus size: 50
36042182 TGACATCCAT
* *
36042192 TAACTCTCATGATTAGTTAAGTTTGCATTATAAATAATGACATGCATTAAG
1 TAACTCTCATG-TTAGTTAAATTTGCATCATAAATAATGACATGCATTAAG
* ** **
36042243 TAACT-TACATGTTAGTTAAATATGCATCATAAATCCT-ATCATGCATTATC
1 TAACTCT-CATGTTAGTTAAATTTGCATCATAAATAATGA-CATGCATTAAG
* *
36042293 TAACTCTCATGTTAGTTAAAGTTTGCATCATTAAATCAA-GTCATGCATTTAG
1 TAACTCTCATGTTAGTTAAA-TTTGCATCA-TAAAT-AATGACATGCATTAAG
36042345 TAA
1 TAA
36042348 TCCATTAGTT
Statistics
Matches: 84, Mismatches: 14, Indels: 13
0.76 0.13 0.12
Matches are distributed among these distances:
49 1 0.01
50 49 0.58
51 18 0.21
52 16 0.19
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.38
Consensus pattern (50 bp):
TAACTCTCATGTTAGTTAAATTTGCATCATAAATAATGACATGCATTAAG
Found at i:36045102 original size:50 final size:49
Alignment explanation
Indices: 36044984--36045137 Score: 152
Period size: 50 Copynumber: 3.1 Consensus size: 49
36044974 GAATGAACTA
* *
36044984 ATGG-ATTACTAAATGCATGACT-TGATTTAATGATGCAAACTTTAACTATC
1 ATGGAATTACTTAATGCATGA-TATGATTT-ATGATGCAAA-TTTAACTAAC
* * *
36045034 ATGGGAATTACATAATGCATGATAGGATTTATGATGCATATTTAACTAAC
1 AT-GGAATTACTTAATGCATGATATGATTTATGATGCAAATTTAACTAAC
* * *
36045084 ATGTAAGTTACTTAATGCATG-TCATTATTTATGATGCAAACTTAACTAATC
1 ATGGAA-TTACTTAATGCATGAT-ATGATTTATGATGCAAATTTAACTAA-C
36045135 ATG
1 ATG
36045138 AGAGTTAATG
Statistics
Matches: 87, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
49 4 0.05
50 48 0.55
51 16 0.18
52 19 0.22
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (49 bp):
ATGGAATTACTTAATGCATGATATGATTTATGATGCAAATTTAACTAAC
Found at i:36050033 original size:21 final size:21
Alignment explanation
Indices: 36050007--36050079 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
36049997 GTTTTTAGTA
* *
36050007 CGGTAGAAGTAAGACTTGTTT
1 CGGTAGAAGTAACACTTGTAT
36050028 CGGTAGAAG-AGACACTTGTAT
1 CGGTAGAAGTA-ACACTTGTAT
* *
36050049 CGGTAGAACTATCACTTGTAT
1 CGGTAGAAGTAACACTTGTAT
36050070 CGGTAGAAGT
1 CGGTAGAAGT
36050080 CTGCACTATT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
20 1 0.02
21 43 0.96
22 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (21 bp):
CGGTAGAAGTAACACTTGTAT
Found at i:36051193 original size:24 final size:24
Alignment explanation
Indices: 36051125--36051196 Score: 63
Period size: 24 Copynumber: 2.9 Consensus size: 24
36051115 TCAGAGTTCT
* *
36051125 TTTTTTTGTTATTTATATTTACTTGC
1 TTTTTTTGTT-TTTTTATTTA-TTGA
* *** *
36051151 TTATTTTGGCATTTAATTTATTGA
1 TTTTTTTGTTTTTTTATTTATTGA
36051175 TTTTTTTGTTTTTTTATTTATT
1 TTTTTTTGTTTTTTTATTTATT
36051197 TGTCATTTAT
Statistics
Matches: 34, Mismatches: 12, Indels: 2
0.71 0.25 0.04
Matches are distributed among these distances:
24 20 0.59
25 7 0.21
26 7 0.21
ACGTcount: A:0.17, C:0.04, G:0.08, T:0.71
Consensus pattern (24 bp):
TTTTTTTGTTTTTTTATTTATTGA
Found at i:36051314 original size:15 final size:13
Alignment explanation
Indices: 36051276--36051318 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
36051266 AATTTTTATT
36051276 TTTA-TTTATTTA
1 TTTAGTTTATTTA
*
36051288 TTTTGTTTATTTA
1 TTTAGTTTATTTA
36051301 TTTAAGTGTTATTTA
1 TTT-AGT-TTATTTA
36051316 TTT
1 TTT
36051319 TCATGTCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 3 0.12
13 11 0.42
14 2 0.08
15 10 0.38
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (13 bp):
TTTAGTTTATTTA
Found at i:36051362 original size:16 final size:15
Alignment explanation
Indices: 36051341--36051381 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
36051331 ATTGATTCTC
36051341 TTTTATTATTATTTTA
1 TTTTATTATTA-TTTA
*
36051357 TTTTATTTTTATTTA
1 TTTTATTATTATTTA
36051372 TTGTTATTAT
1 TT-TTATTAT
36051382 CTTGTTTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (15 bp):
TTTTATTATTATTTA
Found at i:36052977 original size:58 final size:58
Alignment explanation
Indices: 36052892--36053071 Score: 242
Period size: 58 Copynumber: 3.1 Consensus size: 58
36052882 AGAAATAGTA
*
36052892 AAAATGGAGAAATGAGAAATATTTGGAAATGAAATGTGGTTTTCTCCAAAATAAAAATG
1 AAAATGGAGAAAT-AGAAACATTTGGAAATGAAATGTGGTTTTCTCCAAAATAAAAATG
*
36052951 AAAATGGAGAAATAGAAACATTTGGAAATGAAATGTGGTTTTCTCCAAAATGAAAATG
1 AAAATGGAGAAATAGAAACATTTGGAAATGAAATGTGGTTTTCTCCAAAATAAAAATG
* * * *
36053009 AAAATGGAGAAATA-AAAGCATTTGAAAAT-ATATATGG-TTTCTTCTAAAATGAAAAA-G
1 AAAATGGAGAAATAGAAA-CATTTGGAAATGAAATGTGGTTTTC-TCCAAAAT-AAAAATG
36053066 AAAATG
1 AAAATG
36053072 AAAAAAACCT
Statistics
Matches: 111, Mismatches: 7, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
56 4 0.04
57 23 0.21
58 71 0.64
59 13 0.12
ACGTcount: A:0.49, C:0.06, G:0.19, T:0.27
Consensus pattern (58 bp):
AAAATGGAGAAATAGAAACATTTGGAAATGAAATGTGGTTTTCTCCAAAATAAAAATG
Found at i:36055138 original size:47 final size:47
Alignment explanation
Indices: 36055033--36055138 Score: 113
Period size: 47 Copynumber: 2.3 Consensus size: 47
36055023 CATAGTAATG
* * * *
36055033 CAGATAAAATGCCAATAGTTAAAATTGTGAACAAGCCACAAAAATCA
1 CAGATAAACTGCCAATAATCAAAATCGTGAACAAGCCACAAAAATCA
* ** * * *
36055080 TAGATCGACTGCCAATAATCAAAATCGTGGACAAGCCACCAAAATCG
1 CAGATAAACTGCCAATAATCAAAATCGTGAACAAGCCACAAAAATCA
*
36055127 CATATAAACTGC
1 CAGATAAACTGC
36055139 TAGTAACTTT
Statistics
Matches: 45, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.45, C:0.22, G:0.14, T:0.19
Consensus pattern (47 bp):
CAGATAAACTGCCAATAATCAAAATCGTGAACAAGCCACAAAAATCA
Found at i:36062841 original size:13 final size:13
Alignment explanation
Indices: 36062825--36062853 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
36062815 CAATTTTTTC
36062825 TTTTTCTTTTCTT
1 TTTTTCTTTTCTT
36062838 TTTTTCTTTTCTT
1 TTTTTCTTTTCTT
36062851 TTT
1 TTT
36062854 CTCATTCAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTCTTTTCTT
Found at i:36063630 original size:21 final size:21
Alignment explanation
Indices: 36063605--36063644 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
36063595 TCCTACGTGT
*
36063605 GTTTCTTCTTT-TTGTCCTTGC
1 GTTTCCTCTTTCTT-TCCTTGC
36063626 GTTTCCTCTTTCTTTCCTT
1 GTTTCCTCTTTCTTTCCTT
36063645 CGTACCAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.00, C:0.28, G:0.10, T:0.62
Consensus pattern (21 bp):
GTTTCCTCTTTCTTTCCTTGC
Found at i:36075156 original size:21 final size:21
Alignment explanation
Indices: 36075130--36075169 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
36075120 GTAAGAAAAA
*
36075130 GTCAACAATTAATAGTCAATG
1 GTCAACAATCAATAGTCAATG
*
36075151 GTCAACAATCAATGGTCAA
1 GTCAACAATCAATAGTCAA
36075170 AGTCAACGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.25
Consensus pattern (21 bp):
GTCAACAATCAATAGTCAATG
Found at i:36083635 original size:24 final size:24
Alignment explanation
Indices: 36083606--36083653 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
36083596 GAGCAGGCCA
*
36083606 ATTTTCATAGCTTGTGTGACCATT
1 ATTTTCATAGCTCGTGTGACCATT
*
36083630 ATTTTCATAGCTCGTGTGAGCATT
1 ATTTTCATAGCTCGTGTGACCATT
36083654 TCTATCCCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.44
Consensus pattern (24 bp):
ATTTTCATAGCTCGTGTGACCATT
Found at i:36093093 original size:36 final size:36
Alignment explanation
Indices: 36093065--36093153 Score: 178
Period size: 36 Copynumber: 2.5 Consensus size: 36
36093055 ATAATATGTT
36093065 ACATGGCATGAAGAACATACTCACATATATTCTGTC
1 ACATGGCATGAAGAACATACTCACATATATTCTGTC
36093101 ACATGGCATGAAGAACATACTCACATATATTCTGTC
1 ACATGGCATGAAGAACATACTCACATATATTCTGTC
36093137 ACATGGCATGAAGAACA
1 ACATGGCATGAAGAACA
36093154 ATGATGGTAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 53 1.00
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.25
Consensus pattern (36 bp):
ACATGGCATGAAGAACATACTCACATATATTCTGTC
Found at i:36096297 original size:17 final size:18
Alignment explanation
Indices: 36096260--36096299 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
36096250 TAACAAAATG
36096260 ATGCAGTGACAAAATAAA
1 ATGCAGTGACAAAATAAA
* *
36096278 ATGCAGTGATAATA-AAA
1 ATGCAGTGACAAAATAAA
36096295 ATGCA
1 ATGCA
36096300 TTAAAACTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.53, C:0.10, G:0.17, T:0.20
Consensus pattern (18 bp):
ATGCAGTGACAAAATAAA
Found at i:36106148 original size:13 final size:14
Alignment explanation
Indices: 36106109--36106149 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
36106099 GTACATTGAC
* *
36106109 ATTTAACCTCTAAG
1 ATTTAACCTCTGAT
36106123 ATTTAACCTCTGAT
1 ATTTAACCTCTGAT
36106137 ATTTAA-CTCTGAT
1 ATTTAACCTCTGAT
36106150 TGCATTAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 7 0.28
14 18 0.72
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (14 bp):
ATTTAACCTCTGAT
Found at i:36114401 original size:32 final size:32
Alignment explanation
Indices: 36114365--36114459 Score: 172
Period size: 32 Copynumber: 3.0 Consensus size: 32
36114355 GTCATCCATA
* *
36114365 CATGTACCTGAAATATATTAATCAGCTAATTG
1 CATGTACCTGAAACACATTAATCAGCTAATTG
36114397 CATGTACCTGAAACACATTAATCAGCTAATTG
1 CATGTACCTGAAACACATTAATCAGCTAATTG
36114429 CATGTACCTGAAACACATTAATCAGCTAATT
1 CATGTACCTGAAACACATTAATCAGCTAATT
36114460 AATTTCAGCT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 61 1.00
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.31
Consensus pattern (32 bp):
CATGTACCTGAAACACATTAATCAGCTAATTG
Found at i:36121026 original size:32 final size:32
Alignment explanation
Indices: 36120990--36121084 Score: 163
Period size: 32 Copynumber: 3.0 Consensus size: 32
36120980 GTCATCCATA
* *
36120990 CATGTACCTGAAATATATTAATCAGCTAATTG
1 CATGTACCTGAAACACATTAATCAGCTAATTG
36121022 CATGTACCTGAAACACATTAATCAGCTAATTG
1 CATGTACCTGAAACACATTAATCAGCTAATTG
*
36121054 CATGTACCTAAAACACATTAATCAGCTAATT
1 CATGTACCTGAAACACATTAATCAGCTAATT
36121085 AATTTTAGCT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 60 1.00
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.31
Consensus pattern (32 bp):
CATGTACCTGAAACACATTAATCAGCTAATTG
Found at i:36123567 original size:13 final size:14
Alignment explanation
Indices: 36123538--36123567 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
36123528 TTCAGTACAT
36123538 TGACATTTAATCTC
1 TGACATTTAATCTC
36123552 TGACATTTAA-CTC
1 TGACATTTAATCTC
36123565 TGA
1 TGA
36123568 TTGCATTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (14 bp):
TGACATTTAATCTC
Found at i:36123920 original size:36 final size:36
Alignment explanation
Indices: 36123787--36123910 Score: 203
Period size: 36 Copynumber: 3.4 Consensus size: 36
36123777 GACGCAATCA
* *
36123787 AACATACCAACATATTTTCTGTCATATGGCATGAAG
1 AACATACCCACATATTTTCTGTCACATGGCATGAAG
* * *
36123823 AACATACCTACATATTTTCTATCACATGCCATGAAG
1 AACATACCCACATATTTTCTGTCACATGGCATGAAG
36123859 AACATACCCACATATTTTCTGTCACATGGCATGAAG
1 AACATACCCACATATTTTCTGTCACATGGCATGAAG
36123895 AACATACCCACATATT
1 AACATACCCACATATT
36123911 CACTTTCACA
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 81 1.00
ACGTcount: A:0.36, C:0.24, G:0.10, T:0.29
Consensus pattern (36 bp):
AACATACCCACATATTTTCTGTCACATGGCATGAAG
Found at i:36124017 original size:23 final size:23
Alignment explanation
Indices: 36123990--36124114 Score: 133
Period size: 23 Copynumber: 5.4 Consensus size: 23
36123980 ATCTTAATTC
*
36123990 TTTAAGCACAAATCCCATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
36124013 TTTAAGAATAAATCACACTAATA
1 TTTAAGCACAAATCACATTAATA
*
36124036 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
36124059 TTTGAGCACAAAACATATTAATA
1 TTTAAGCACAAATCACATTAATA
** * * *
36124082 TTTAATAATAAATCATAGTAATA
1 TTTAAGCACAAATCACATTAATA
36124105 TTTAAGCACA
1 TTTAAGCACA
36124115 GATATAAGAA
Statistics
Matches: 83, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 83 1.00
ACGTcount: A:0.48, C:0.14, G:0.06, T:0.33
Consensus pattern (23 bp):
TTTAAGCACAAATCACATTAATA
Found at i:36130374 original size:21 final size:24
Alignment explanation
Indices: 36130348--36130404 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
36130338 AAGTTAGAGA
36130348 AATGTG-TT-ACA-TTCGAAAATG
1 AATGTGTTTCACACTTCGAAAATG
*
36130369 AATGTGGTTTCTCACTTCGAAAATG
1 AATGT-GTTTCACACTTCGAAAATG
36130394 AATGTGGTTTC
1 AATGT-GTTTC
36130405 TCATTAAGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 5 0.16
22 1 0.03
23 2 0.06
24 2 0.06
25 21 0.68
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (24 bp):
AATGTGTTTCACACTTCGAAAATG
Found at i:36130388 original size:25 final size:25
Alignment explanation
Indices: 36130359--36130407 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
36130349 ATGTGTTACA
36130359 TTCGAAAATGAATGTGGTTTCTCAC
1 TTCGAAAATGAATGTGGTTTCTCAC
36130384 TTCGAAAATGAATGTGGTTTCTCA
1 TTCGAAAATGAATGTGGTTTCTCA
36130408 TTAAGTATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (25 bp):
TTCGAAAATGAATGTGGTTTCTCAC
Found at i:36132940 original size:21 final size:24
Alignment explanation
Indices: 36132914--36132956 Score: 65
Period size: 21 Copynumber: 1.9 Consensus size: 24
36132904 ACTCAAAAGA
36132914 AAATAAAA-A-TA-TTTTATAATT
1 AAATAAAATATTATTTTTATAATT
36132935 AAATAAAATATTATTTTTATAA
1 AAATAAAATATTATTTTTATAA
36132957 ATATTAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 1 0.05
23 2 0.11
24 8 0.42
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
AAATAAAATATTATTTTTATAATT
Found at i:36139686 original size:20 final size:22
Alignment explanation
Indices: 36139661--36139702 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
36139651 ACAAAAATGT
36139661 ATGTTT-TT-TTATTATTTGAA
1 ATGTTTATTATTATTATTTGAA
36139681 ATGTTTAGTTATTATTATTTGA
1 ATGTTTA-TTATTATTATTTGA
36139703 TATTTAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
22 2 0.11
23 11 0.58
ACGTcount: A:0.26, C:0.00, G:0.12, T:0.62
Consensus pattern (22 bp):
ATGTTTATTATTATTATTTGAA
Found at i:36139743 original size:26 final size:26
Alignment explanation
Indices: 36139689--36139743 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
36139679 AAATGTTTAG
**
36139689 TTATTATTATTTGATATTTAATTGTT
1 TTATTATTATTTGATATTTAATAATT
36139715 TTATTATTATTTGAT-TTTAATAATAT
1 TTATTATTATTTGATATTTAATAAT-T
36139741 TTA
1 TTA
36139744 CATAATTGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 7 0.27
26 19 0.73
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (26 bp):
TTATTATTATTTGATATTTAATAATT
Found at i:36144281 original size:63 final size:63
Alignment explanation
Indices: 36144182--36144308 Score: 254
Period size: 63 Copynumber: 2.0 Consensus size: 63
36144172 CAACAAAAAA
36144182 AGCTTCAGCTATTGCTTCAAGGAAGTGCTGACTAAATTAATTATTTATTACTAAATGATGGGC
1 AGCTTCAGCTATTGCTTCAAGGAAGTGCTGACTAAATTAATTATTTATTACTAAATGATGGGC
36144245 AGCTTCAGCTATTGCTTCAAGGAAGTGCTGACTAAATTAATTATTTATTACTAAATGATGGGC
1 AGCTTCAGCTATTGCTTCAAGGAAGTGCTGACTAAATTAATTATTTATTACTAAATGATGGGC
36144308 A
1 A
36144309 CTCAAGAATT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (63 bp):
AGCTTCAGCTATTGCTTCAAGGAAGTGCTGACTAAATTAATTATTTATTACTAAATGATGGGC
Found at i:36170990 original size:21 final size:21
Alignment explanation
Indices: 36170964--36171011 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
36170954 ATGACCAGCT
*
36170964 GAAGGAAAAGGAAAAAGAAGA
1 GAAGGAAAAAGAAAAAGAAGA
* *
36170985 GAAGGAAAAAGAGAATGAAGA
1 GAAGGAAAAAGAAAAAGAAGA
*
36171006 AAAGGA
1 GAAGGA
36171012 CCCTGTTAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (21 bp):
GAAGGAAAAAGAAAAAGAAGA
Found at i:36171330 original size:21 final size:21
Alignment explanation
Indices: 36171301--36171342 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
36171291 GAAGGATAAA
* * *
36171301 AAGAGGAAAATGCGCAAAGAC
1 AAGAAGAAAAAGCACAAAGAC
36171322 AAGAAGAAAAAGCACAAAGAC
1 AAGAAGAAAAAGCACAAAGAC
36171343 GAGGGTGAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.60, C:0.14, G:0.24, T:0.02
Consensus pattern (21 bp):
AAGAAGAAAAAGCACAAAGAC
Found at i:36171464 original size:17 final size:18
Alignment explanation
Indices: 36171442--36171483 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
36171432 ATAGTTTTCA
36171442 TGCATTCT-TATTGTCAC
1 TGCATTCTGTATTGTCAC
* *
36171459 TGCATTTTGTTTTGTCAC
1 TGCATTCTGTATTGTCAC
36171477 TGCATTC
1 TGCATTC
36171484 CTCTTCTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.14, C:0.21, G:0.14, T:0.50
Consensus pattern (18 bp):
TGCATTCTGTATTGTCAC
Done.