Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 50 of 378
Found at i:12486782 original size:27 final size:27
Alignment explanation
Indices: 12486718--12486802 Score: 82
Period size: 27 Copynumber: 3.1 Consensus size: 27
12486708 GGAGGAAAAT
12486718 ACCACTGGTGCCACCTATCAGATAGGC
1 ACCACTGGTGCCACCTATCAGATAGGC
** * *
12486745 ACCACCAGTGCTACCTATCAGATAGGG
1 ACCACTGGTGCCACCTATCAGATAGGC
** * *
12486772 GTCACTGGTGCCGCCTAT-GGTATAGGC
1 ACCACTGGTGCCACCTATCAG-ATAGGC
12486799 ACCA
1 ACCA
12486803 TACCCCTATA
Statistics
Matches: 43, Mismatches: 14, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
26 1 0.02
27 42 0.98
ACGTcount: A:0.25, C:0.31, G:0.25, T:0.20
Consensus pattern (27 bp):
ACCACTGGTGCCACCTATCAGATAGGC
Found at i:12493948 original size:40 final size:40
Alignment explanation
Indices: 12493883--12494057 Score: 251
Period size: 40 Copynumber: 4.4 Consensus size: 40
12493873 CGGATGTAAC
* * *
12493883 AACCAGCACGAATGCCTTCGAGACTTAACCCGGTAATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
* ** *
12493923 AACTCGCAAAAATGCCTTCGGGACTTAGCCCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
* **
12493963 AACCCGCACGAATGCCTTCGTGACTTGGCCCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
*
12494003 AACCCGCACGAATGACTTCGGGACTTAACCCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
12494043 AACCCGCACGAATGC
1 AACCCGCACGAATGC
12494058 TGTGCACATA
Statistics
Matches: 118, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 118 1.00
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.22
Consensus pattern (40 bp):
AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
Found at i:12501624 original size:40 final size:40
Alignment explanation
Indices: 12501552--12501726 Score: 219
Period size: 40 Copynumber: 4.4 Consensus size: 40
12501542 CGGATGTAAC
* *
12501552 AACCAGCACGAATGCCTTC-GAGACTTAACCCGGTAATAAT
1 AACCTGCACGAATGCCTTCGGA-ACTTAACCCGGTTATAAT
* * *
12501592 AA-CTCGCACAAATGCCTTCGGAATTTAGCCCGGTTATAAT
1 AACCT-GCACGAATGCCTTCGGAACTTAACCCGGTTATAAT
* * * *
12501632 AACCTGAATGAATGCCTTCGGGACTTAGCCCGGTTATAAT
1 AACCTGCACGAATGCCTTCGGAACTTAACCCGGTTATAAT
*
12501672 AACCTGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCTGCACGAATGCCTTCGGAACTTAACCCGGTTATAAT
*
12501712 AACCCGCACGAATGC
1 AACCTGCACGAATGC
12501727 TGTGCACATA
Statistics
Matches: 118, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
39 1 0.01
40 113 0.96
41 4 0.03
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.23
Consensus pattern (40 bp):
AACCTGCACGAATGCCTTCGGAACTTAACCCGGTTATAAT
Found at i:12504130 original size:21 final size:21
Alignment explanation
Indices: 12504104--12504144 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
12504094 AGACGAGCGA
* *
12504104 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
12504125 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
12504145 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:12506086 original size:16 final size:16
Alignment explanation
Indices: 12506053--12506086 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12506043 GGAGATTGTT
* *
12506053 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
12506069 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
12506085 AA
1 AA
12506087 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:12511811 original size:27 final size:27
Alignment explanation
Indices: 12511781--12511834 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
12511771 TAAAGAACAC
12511781 AGTGCGTAAAGAAAACTTTGTGCATGT
1 AGTGCGTAAAGAAAACTTTGTGCATGT
12511808 AGTGCGTAAAGAAAACTTTGTGCATGT
1 AGTGCGTAAAGAAAACTTTGTGCATGT
12511835 CTAATTATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (27 bp):
AGTGCGTAAAGAAAACTTTGTGCATGT
Found at i:12516044 original size:22 final size:23
Alignment explanation
Indices: 12516005--12516050 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
12515995 TATAATTTGA
12516005 TTATTGAATTATTCGAA-TATTT
1 TTATTGAATTATTCGAATTATTT
*
12516027 TTATTTAAGTTATT-GAATTATTT
1 TTATTGAA-TTATTCGAATTATTT
12516050 T
1 T
12516051 AAAAGAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.59
Consensus pattern (23 bp):
TTATTGAATTATTCGAATTATTT
Found at i:12516649 original size:2 final size:2
Alignment explanation
Indices: 12516642--12516666 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12516632 ATATTACTAT
12516642 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
12516667 CAATGATAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12520272 original size:2 final size:2
Alignment explanation
Indices: 12520261--12520291 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
12520251 TTGATTTAAA
12520261 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12520292 TAATATTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:12523996 original size:46 final size:44
Alignment explanation
Indices: 12523937--12524051 Score: 140
Period size: 44 Copynumber: 2.6 Consensus size: 44
12523927 ACAGGACAGA
* *
12523937 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* * *
12523983 GCAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
12524027 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
12524052 GTCAAAGACA
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 34 0.58
46 25 0.42
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:12524032 original size:44 final size:45
Alignment explanation
Indices: 12523937--12524070 Score: 144
Period size: 46 Copynumber: 3.0 Consensus size: 45
12523927 ACAGGACAGA
* *
12523937 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* * *
12523983 GCAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
12524027 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
12524071 CAGGATATTG
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
44 35 0.49
45 1 0.01
46 36 0.50
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:12526292 original size:42 final size:42
Alignment explanation
Indices: 12526229--12526341 Score: 156
Period size: 42 Copynumber: 2.7 Consensus size: 42
12526219 CTTCGTTTTC
** * *
12526229 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACAT-A
* *
12526272 T-GATGCCATAGCCCAGCTATGGTATTACACATATTCATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
12526313 TCGATGCCATAGCCCAGCTATGGTCTTAC
1 TCGATGCCATAGCCCAGCTATGGTCTTAC
12526342 GCGAATCACA
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
41 2 0.03
42 59 0.95
43 1 0.02
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
Found at i:12526381 original size:46 final size:47
Alignment explanation
Indices: 12526314--12526433 Score: 143
Period size: 47 Copynumber: 2.6 Consensus size: 47
12526304 ATTCATATAT
* * * * *
12526314 CGATGCCATAGCCCAGCTATGGTCTTACGC-GAATCACATATCTCAC
1 CGATGCCATATCCCAGATATGGTCTTACACAGAAGCACATATCACAC
* * * *
12526360 TGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTACACAGAAGCACATATCACAC
*
12526407 CGATACCATATCCCAGATATGGTCTTA
1 CGATGCCATATCCCAGATATGGTCTTA
12526434 TACGGAAATT
Statistics
Matches: 62, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
46 25 0.40
47 37 0.60
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.28
Consensus pattern (47 bp):
CGATGCCATATCCCAGATATGGTCTTACACAGAAGCACATATCACAC
Found at i:12526498 original size:31 final size:32
Alignment explanation
Indices: 12526455--12526572 Score: 154
Period size: 31 Copynumber: 3.8 Consensus size: 32
12526445 CTTGTCACTT
*
12526455 GTAGCC-GAAGCTACCACTATTCACTGATCAG
1 GTAGCCAGAAGCTACCACTTTTCACTGATCAG
* *
12526486 GTAGCCAG-AGCTACCATTTTTCACTAATCAG
1 GTAGCCAGAAGCTACCACTTTTCACTGATCAG
*
12526517 GTAGCC-GGAGCTACCACTTTTCACTGATCAG
1 GTAGCCAGAAGCTACCACTTTTCACTGATCAG
* *
12526548 GTAG-CAGAAGCTACTATTTTTCACT
1 GTAGCCAGAAGCTACCACTTTTCACT
12526573 TGTCATTTGT
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
30 2 0.03
31 73 0.96
32 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (32 bp):
GTAGCCAGAAGCTACCACTTTTCACTGATCAG
Found at i:12526552 original size:62 final size:62
Alignment explanation
Indices: 12526455--12526572 Score: 193
Period size: 62 Copynumber: 1.9 Consensus size: 62
12526445 CTTGTCACTT
12526455 GTAGCCGAAGCTACCACTATTCACTGATCAGGTAGCCAG-AGCTACCATTTTTCACTAATCAG
1 GTAGCCGAAGCTACCACTATTCACTGATCAGGTAG-CAGAAGCTACCATTTTTCACTAATCAG
* * *
12526517 GTAGCCGGAGCTACCACTTTTCACTGATCAGGTAGCAGAAGCTACTATTTTTCACT
1 GTAGCCGAAGCTACCACTATTCACTGATCAGGTAGCAGAAGCTACCATTTTTCACT
12526573 TGTCATTTGT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
61 3 0.06
62 49 0.94
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (62 bp):
GTAGCCGAAGCTACCACTATTCACTGATCAGGTAGCAGAAGCTACCATTTTTCACTAATCAG
Found at i:12526652 original size:50 final size:50
Alignment explanation
Indices: 12526568--12526724 Score: 244
Period size: 50 Copynumber: 3.1 Consensus size: 50
12526558 CTACTATTTT
* * *
12526568 TCACTTGTCATTTGTCCCTGATCAGATAGGTGTAGCCGAAGCTATCACTGA
1 TCACTT-TCATTTGTCCTTGATCAGATAAGTGTAGCCGAAGCTATCACTTA
* *
12526619 TCACTTTCACTTGTCCTTGATCAGATAACTGTAGCCGAAGCTA-CTACTTA
1 TCACTTTCATTTGTCCTTGATCAGATAAGTGTAGCCGAAGCTATC-ACTTA
12526669 TCACTTTCATTTGTCCTTGATCAGATAAGTGTAGCCGAAGCTATCACTTA
1 TCACTTTCATTTGTCCTTGATCAGATAAGTGTAGCCGAAGCTATCACTTA
12526719 TCACTT
1 TCACTT
12526725 GTTGCCATGG
Statistics
Matches: 97, Mismatches: 7, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
49 1 0.01
50 89 0.92
51 7 0.07
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (50 bp):
TCACTTTCATTTGTCCTTGATCAGATAAGTGTAGCCGAAGCTATCACTTA
Found at i:12529072 original size:13 final size:13
Alignment explanation
Indices: 12529056--12529096 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 13
12529046 TTATTTTATT
12529056 TTATTTAGTTTTA
1 TTATTTAGTTTTA
12529069 TTATTT-G-TTT-
1 TTATTTAGTTTTA
12529079 TTATTTA-TTTTA
1 TTATTTAGTTTTA
12529091 TTATTT
1 TTATTT
12529097 TAGGATTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
10 6 0.24
11 6 0.24
12 7 0.28
13 6 0.24
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.76
Consensus pattern (13 bp):
TTATTTAGTTTTA
Found at i:12529073 original size:23 final size:22
Alignment explanation
Indices: 12529044--12529098 Score: 85
Period size: 23 Copynumber: 2.5 Consensus size: 22
12529034 AAATAGAAGA
12529044 TATTATTTTATTTTATTTAGTTT
1 TATTATTTTATTTTATTTA-TTT
12529067 TATTATTTGT-TTTTATTTATTT
1 TATTATTT-TATTTTATTTATTT
12529089 TATTATTTTA
1 TATTATTTTA
12529099 GGATTAAGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
21 1 0.03
22 11 0.37
23 17 0.57
24 1 0.03
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.75
Consensus pattern (22 bp):
TATTATTTTATTTTATTTATTT
Found at i:12530544 original size:17 final size:17
Alignment explanation
Indices: 12530519--12530552 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
12530509 GTACTTGTGT
12530519 AAAACATTAAAATAATA
1 AAAACATTAAAATAATA
*
12530536 AAAATATTAAAATAATA
1 AAAACATTAAAATAATA
12530553 CTTTAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAACATTAAAATAATA
Found at i:12542602 original size:19 final size:20
Alignment explanation
Indices: 12542578--12542618 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
12542568 TAGAGGCTAT
12542578 TTTATAGATATGTTT-TGAA
1 TTTATAGATATGTTTATGAA
* *
12542597 TTTATATATATTTTTATGAA
1 TTTATAGATATGTTTATGAA
12542617 TT
1 TT
12542619 AAATCTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.59
Consensus pattern (20 bp):
TTTATAGATATGTTTATGAA
Found at i:12542970 original size:29 final size:29
Alignment explanation
Indices: 12542938--12543003 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
12542928 AAATATTTAT
* * *
12542938 AAAAATAGAAAAAAATAATTAAATTTAAA
1 AAAAATACAAAAAAACAATCAAATTTAAA
**
12542967 AAAAATTACAAAAAAACCCTCAAATTTAAA
1 AAAAA-TACAAAAAAACAATCAAATTTAAA
12542997 AAAAATA
1 AAAAATA
12543004 TATTCTTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 7 0.23
30 24 0.77
ACGTcount: A:0.70, C:0.08, G:0.02, T:0.21
Consensus pattern (29 bp):
AAAAATACAAAAAAACAATCAAATTTAAA
Found at i:12543117 original size:19 final size:19
Alignment explanation
Indices: 12543093--12543129 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12543083 ATAGACTCGT
*
12543093 AATTAAAAAAATTGAAAAA
1 AATTAAAAAAATTCAAAAA
*
12543112 AATTAAAAGAATTCAAAA
1 AATTAAAAAAATTCAAAA
12543130 TAATAGACCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.22
Consensus pattern (19 bp):
AATTAAAAAAATTCAAAAA
Found at i:12543143 original size:49 final size:48
Alignment explanation
Indices: 12543069--12543165 Score: 176
Period size: 49 Copynumber: 2.0 Consensus size: 48
12543059 AAAGCATTCT
*
12543069 AAGAATTCAAAATAATAGACTCGTAATTAAAAAAATTGAAAAAAATTAA
1 AAGAATTCAAAATAATAGACCCGTAATT-AAAAAATTGAAAAAAATTAA
12543118 AAGAATTCAAAATAATAGACCCGTAATTAAAAAATTGAAAAAAATTAA
1 AAGAATTCAAAATAATAGACCCGTAATTAAAAAATTGAAAAAAATTAA
12543166 CTTCGGAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 20 0.43
49 27 0.57
ACGTcount: A:0.61, C:0.07, G:0.08, T:0.24
Consensus pattern (48 bp):
AAGAATTCAAAATAATAGACCCGTAATTAAAAAATTGAAAAAAATTAA
Found at i:12543667 original size:18 final size:18
Alignment explanation
Indices: 12543636--12543670 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
12543626 TTTAAAAAAT
12543636 AAAATTAAAGTATTTTAA
1 AAAATTAAAGTATTTTAA
12543654 AAAATATAAA-TATTTTA
1 AAAAT-TAAAGTATTTTA
12543671 TATTATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (18 bp):
AAAATTAAAGTATTTTAA
Found at i:12546065 original size:2 final size:2
Alignment explanation
Indices: 12546058--12546083 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12546048 GTACATTTAA
12546058 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
12546084 CACGCAAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12547474 original size:19 final size:19
Alignment explanation
Indices: 12547434--12547480 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
12547424 CAATCATAAA
* *
12547434 AATTGATTTAAACTTGTGT
1 AATTTATTTAAAATTGTGT
12547453 AATTTATTTAAAATT-TGAT
1 AATTTATTTAAAATTGTG-T
*
12547472 AATGTATTT
1 AATTTATTT
12547481 TTTTATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 2 0.08
19 22 0.92
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.51
Consensus pattern (19 bp):
AATTTATTTAAAATTGTGT
Found at i:12551657 original size:10 final size:10
Alignment explanation
Indices: 12551625--12551683 Score: 68
Period size: 10 Copynumber: 5.9 Consensus size: 10
12551615 TTAAATTCTA
12551625 AAAGATAAAT
1 AAAGATAAAT
*
12551635 ACAA-TTAAAT
1 A-AAGATAAAT
*
12551645 AAAGATAATT
1 AAAGATAAAT
12551655 AAAGATAAAT
1 AAAGATAAAT
12551665 -AAGAATAAAT
1 AAAG-ATAAAT
12551675 AAAGATAAA
1 AAAGATAAA
12551684 AGCTAAAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
9 5 0.12
10 31 0.76
11 5 0.12
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:12551659 original size:30 final size:30
Alignment explanation
Indices: 12551625--12551682 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
12551615 TTAAATTCTA
*
12551625 AAAGATAAATACA-ATTAAATAAAGATAATT
1 AAAGATAAATA-AGAATAAATAAAGATAATT
12551655 AAAGATAAATAAGAATAAATAAAGATAA
1 AAAGATAAATAAGAATAAATAAAGATAA
12551683 AAGCTAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.67, C:0.02, G:0.09, T:0.22
Consensus pattern (30 bp):
AAAGATAAATAAGAATAAATAAAGATAATT
Found at i:12563493 original size:46 final size:46
Alignment explanation
Indices: 12563441--12563666 Score: 289
Period size: 46 Copynumber: 4.9 Consensus size: 46
12563431 TGTGCTCTCT
* * *
12563441 GATATGAAATGTGTAAGACTATGGTTGAAAGATACCATGACAACTA
1 GATATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAACTA
* *
12563487 GATATGAAATGTTTAAGACCATGGTTGAAAGATACTATGGCAACCT-
1 GATATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAA-CTA
*
12563533 GATATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAACTT
1 GATATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAACTA
*
12563579 GATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC-A
1 GATATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAACTA
* * * *
12563624 TGACA-GAAAATG-AGTAAGACCATAGTTGAAAGACACTATGGCA
1 -GATATG-AAATGTA-TAAGACCATGGTTGAAAGATACCATGGCA
12563667 TCATGTCAAA
Statistics
Matches: 163, Mismatches: 12, Indels: 10
0.88 0.06 0.05
Matches are distributed among these distances:
45 4 0.02
46 157 0.96
47 2 0.01
ACGTcount: A:0.41, C:0.13, G:0.22, T:0.24
Consensus pattern (46 bp):
GATATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAACTA
Found at i:12563973 original size:16 final size:17
Alignment explanation
Indices: 12563952--12563984 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
12563942 ATGATGGTGC
12563952 ATGAAAT-ATTGATATA
1 ATGAAATAATTGATATA
12563968 ATGAAATAATTGATATA
1 ATGAAATAATTGATATA
12563985 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (17 bp):
ATGAAATAATTGATATA
Found at i:12565595 original size:15 final size:15
Alignment explanation
Indices: 12565577--12565620 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 15
12565567 AGAAAATTGG
12565577 AAAGATGAAAAATTA
1 AAAGATGAAAAATTA
12565592 AAAGGATG-AAAATTA
1 AAA-GATGAAAAATTA
12565607 AGAAGATAGAAAAA
1 A-AAGAT-GAAAAA
12565621 ATAATTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 14 0.56
16 7 0.28
17 4 0.16
ACGTcount: A:0.66, C:0.00, G:0.18, T:0.16
Consensus pattern (15 bp):
AAAGATGAAAAATTA
Found at i:12569067 original size:26 final size:26
Alignment explanation
Indices: 12569037--12569102 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
12569027 TTTAAACCAA
* *
12569037 ATTTTTCAAAAGCACTTCTTAAAAGT
1 ATTTTTCAAAAGCACTTCTCAAAAGC
*
12569063 ATTTTTGC-ACAGCACTTCTCAAAAGC
1 ATTTTT-CAAAAGCACTTCTCAAAAGC
* *
12569089 ACTTTTAAAAAGCA
1 ATTTTTCAAAAGCA
12569103 TTGCCAAACT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
26 31 0.97
27 1 0.03
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (26 bp):
ATTTTTCAAAAGCACTTCTCAAAAGC
Found at i:12580528 original size:20 final size:21
Alignment explanation
Indices: 12580492--12580543 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
12580482 TTGCAAATAA
* *
12580492 AAAATATATAAACATAT-GAT
1 AAAATATATAATCATATAAAT
*
12580512 AAAATATATAATTATATAAAT
1 AAAATATATAATCATATAAAT
12580533 AAAATA-ATAAT
1 AAAATATATAAT
12580544 AAATAGAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 20 0.71
21 8 0.29
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (21 bp):
AAAATATATAATCATATAAAT
Found at i:12580608 original size:11 final size:12
Alignment explanation
Indices: 12580587--12580624 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
12580577 TTTGAAACAT
12580587 TATATAAAATAA
1 TATATAAAATAA
12580599 TATA-AAAATAA
1 TATATAAAATAA
*
12580610 TATTTAATAATAA
1 TATATAA-AATAA
12580623 TA
1 TA
12580625 AAAGTACTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 10 0.43
12 6 0.26
13 7 0.30
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
TATATAAAATAA
Found at i:12585647 original size:60 final size:60
Alignment explanation
Indices: 12585568--12585692 Score: 164
Period size: 60 Copynumber: 2.1 Consensus size: 60
12585558 TTTTCTTTTA
* * * * *
12585568 AATTTTTAGAATTAGAACTAAATTAACATATTTTGTAAATGTTGAA-ACTTAAATTTATTG
1 AATTTATAGAATTAGAACTAAAATAACAAATTTTGTAAATATTAAAGAC-TAAATTTATTG
*
12585628 AATTTATAGAATTCA-AACTAAAATAATAAATTTTGTAAATATTAAAGACTAAATTTATTG
1 AATTTATAGAATT-AGAACTAAAATAACAAATTTTGTAAATATTAAAGACTAAATTTATTG
12585688 AATTT
1 AATTT
12585693 TTTTATTAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
60 54 0.95
61 3 0.05
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.42
Consensus pattern (60 bp):
AATTTATAGAATTAGAACTAAAATAACAAATTTTGTAAATATTAAAGACTAAATTTATTG
Found at i:12586407 original size:14 final size:15
Alignment explanation
Indices: 12586388--12586417 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12586378 GACCCATAAA
12586388 CCTTGAA-CCCAAAC
1 CCTTGAAGCCCAAAC
12586402 CCTTGAAGCCCAAAC
1 CCTTGAAGCCCAAAC
12586417 C
1 C
12586418 TAAACCTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.33, C:0.43, G:0.10, T:0.13
Consensus pattern (15 bp):
CCTTGAAGCCCAAAC
Found at i:12586437 original size:20 final size:20
Alignment explanation
Indices: 12586392--12586471 Score: 72
Period size: 20 Copynumber: 3.9 Consensus size: 20
12586382 CATAAACCTT
*
12586392 GAACCCAAACCCTTGAAGCCC
1 GAACCCAAA-CCTTGAACCCC
* *
12586413 AAACCTAAACCTTGAACCCC
1 GAACCCAAACCTTGAACCCC
* * *
12586433 GAACCCTCAACCTT-ACATCTC
1 GAACCC-AAACCTTGA-ACCCC
12586454 GAACCCAAACCTTGAACC
1 GAACCCAAACCTTGAACC
12586472 ACAAGTTCGG
Statistics
Matches: 46, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
20 23 0.50
21 23 0.50
ACGTcount: A:0.35, C:0.41, G:0.09, T:0.15
Consensus pattern (20 bp):
GAACCCAAACCTTGAACCCC
Found at i:12588664 original size:4 final size:4
Alignment explanation
Indices: 12588655--12588682 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
12588645 CCTCTGTTTA
12588655 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
12588683 TTAAAAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:12588832 original size:27 final size:26
Alignment explanation
Indices: 12588783--12588835 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
12588773 TACGTCTTAT
12588783 ATATTTTAAATTATTATAAATTTTAA
1 ATATTTTAAATTATTATAAATTTTAA
* **
12588809 ATATTTTACATATATTATTTATTTTAA
1 ATATTTTAAAT-TATTATAAATTTTAA
12588836 CTACTATACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (26 bp):
ATATTTTAAATTATTATAAATTTTAA
Found at i:12588992 original size:24 final size:22
Alignment explanation
Indices: 12588944--12588989 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
12588934 GTTATACTAT
12588944 TTTATATGTAAATTATTTTATTA
1 TTTAT-TGTAAATTATTTTATTA
*
12588967 TTTATTGTAAACT-TTTTATTA
1 TTTATTGTAAATTATTTTATTA
12588988 TT
1 TT
12588990 ATTAATTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.45
22 7 0.32
23 5 0.23
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.63
Consensus pattern (22 bp):
TTTATTGTAAATTATTTTATTA
Found at i:12603784 original size:46 final size:47
Alignment explanation
Indices: 12603637--12603895 Score: 182
Period size: 46 Copynumber: 5.6 Consensus size: 47
12603627 TTATTTGTGT
* **
12603637 GCCAGTGTAAGA-CATGTCTGGGACATGCATCAGCCACATTATG-AGA
1 GCCAGTGTAAGACCATGTCTGGGACATGCATCAGCCTCAAGATGTA-A
* * * * * *
12603683 GCCAGTGTAAGACCATATCTGGGGCGTGGCATCGGCATTGAA-ATG-AGA
1 GCCAGTGTAAGACCATGTCTGGGACAT-GCATCAGC-CTCAAGATGTA-A
*
12603731 GCTAGTGTAAGA-CATGTCTGGGACATGCATCAGCCTCAAGATGTAA
1 GCCAGTGTAAGACCATGTCTGGGACATGCATCAGCCTCAAGATGTAA
* * * * *
12603777 GCCAGTGTGAGA-CATGTTTGGGACATGCAT-TGGCTATAAGATGT--
1 GCCAGTGTAAGACCATGTCTGGGACATGCATCAGCCT-CAAGATGTAA
* * * * *
12603821 GTCAGTGTAAGACCATGTCTGGGACATGGCAT-TGACTTGATGCATGT--
1 GCCAGTGTAAGACCATGTCTGGGACAT-GCATCAG-CCTCAAG-ATGTAA
12603868 GCCAGTGTAAGACCATGTCTGGGACATG
1 GCCAGTGTAAGACCATGTCTGGGACATG
12603896 GAATCGGCAT
Statistics
Matches: 174, Mismatches: 29, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
44 10 0.06
45 19 0.11
46 66 0.38
47 54 0.31
48 24 0.14
49 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.25
Consensus pattern (47 bp):
GCCAGTGTAAGACCATGTCTGGGACATGCATCAGCCTCAAGATGTAA
Found at i:12606643 original size:6 final size:5
Alignment explanation
Indices: 12606633--12606701 Score: 58
Period size: 5 Copynumber: 14.0 Consensus size: 5
12606623 TAAGTTTTGT
12606633 TTTTA TCTTTA TTTTA -TTTA -TTTA TTTTA -TTTA -TTTA TTTTA TTTTA
1 TTTTA T-TTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
*
12606680 -CTTA TTTTTA TTATTAA TTTTA
1 TTTTA -TTTTA TT-TT-A TTTTA
12606702 AAAATTTAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
4 19 0.35
5 21 0.38
6 12 0.22
7 3 0.05
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:12606654 original size:9 final size:9
Alignment explanation
Indices: 12606634--12606687 Score: 58
Period size: 9 Copynumber: 5.9 Consensus size: 9
12606624 AAGTTTTGTT
12606634 TTTATCTTTA
1 TTTAT-TTTA
12606644 TTT-TATTTA
1 TTTAT-TTTA
12606653 TTTATTTTA
1 TTTATTTTA
12606662 TTTA-TTTA
1 TTTATTTTA
12606670 TTTTATTTTA
1 -TTTATTTTA
*
12606680 CTTATTTT
1 TTTATTTT
12606688 TATTATTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
8 4 0.10
9 27 0.69
10 8 0.21
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTATTTTA
Found at i:12606656 original size:13 final size:13
Alignment explanation
Indices: 12606640--12606701 Score: 81
Period size: 13 Copynumber: 4.7 Consensus size: 13
12606630 TGTTTTTATC
12606640 TTTATTTTATTTA
1 TTTATTTTATTTA
12606653 TTTATTTTATTTA
1 TTTATTTTATTTA
12606666 TTTATTTTATTTTA
1 TTTATTTTA-TTTA
*
12606680 CTTATTTT-TATTA
1 TTTATTTTAT-TTA
*
12606693 TTAATTTTA
1 TTTATTTTA
12606702 AAAATTTAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
12 1 0.02
13 31 0.72
14 11 0.26
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:12606678 original size:31 final size:32
Alignment explanation
Indices: 12606634--12606699 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 32
12606624 AAGTTTTGTT
* *
12606634 TTTATCTTTATTTTATTTATTTATT-TTATTTA
1 TTTATCTTTATTTTACTTATTT-TTATTATTAA
12606666 TTTAT-TTTATTTTACTTATTTTTATTATTAA
1 TTTATCTTTATTTTACTTATTTTTATTATTAA
12606697 TTT
1 TTT
12606700 TAAAAATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 2 0.06
31 24 0.77
32 5 0.16
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (32 bp):
TTTATCTTTATTTTACTTATTTTTATTATTAA
Found at i:12606693 original size:18 final size:18
Alignment explanation
Indices: 12606649--12606694 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
12606639 CTTTATTTTA
*
12606649 TTTATTTATTTTATTTATT
1 TTTA-TTATTTTACTTATT
12606668 TATT-TTATTTTACTTATT
1 T-TTATTATTTTACTTATT
12606686 TTTATTATT
1 TTTATTATT
12606695 AATTTTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 2 0.08
18 19 0.79
19 1 0.04
20 2 0.08
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTATTATTTTACTTATT
Found at i:12606742 original size:23 final size:23
Alignment explanation
Indices: 12606719--12606777 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
12606709 AAAATGAATA
12606719 TTTGAAATATTTTATAATATATAT
1 TTTGAAATATTTTA-AATATATAT
**
12606743 TTTTTAA-ATTTTAAATATA-AT
1 TTTGAAATATTTTAAATATATAT
12606764 TTTGAAATTATTTT
1 TTTGAAA-TATTTT
12606778 TAAAATTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
21 7 0.24
22 6 0.21
23 11 0.38
24 5 0.17
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (23 bp):
TTTGAAATATTTTAAATATATAT
Found at i:12606760 original size:32 final size:30
Alignment explanation
Indices: 12606718--12606793 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 30
12606708 TAAAATGAAT
* *
12606718 ATTTGAAATATTTTAT-AATATATATTTTTTAA
1 ATTTTAAATATTTT-TGAA-AT-TATTTTTAAA
12606750 ATTTTAAATATAATTTTGAAATTATTTTTAAA
1 ATTTTAAATAT--TTTTGAAATTATTTTTAAA
12606782 ATTTTAAATATT
1 ATTTTAAATATT
12606794 ATTTTTAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
30 1 0.03
32 30 0.77
33 3 0.08
34 5 0.13
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (30 bp):
ATTTTAAATATTTTTGAAATTATTTTTAAA
Found at i:12606766 original size:20 final size:19
Alignment explanation
Indices: 12606761--12606819 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 19
12606751 TTTTAAATAT
12606761 AATTTTGAAAT-TATTTTTAA
1 AATTTT-AAATATATTTTT-A
12606781 AATTTTAAATATTATTTTTA
1 AATTTTAAATA-TATTTTTA
*
12606801 AATATTAAATATATATTTT
1 AATTTTAAATATAT-TTTT
12606820 TAATAATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
19 7 0.20
20 21 0.60
21 7 0.20
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
AATTTTAAATATATTTTTA
Found at i:12606796 original size:21 final size:21
Alignment explanation
Indices: 12606770--12606836 Score: 91
Period size: 21 Copynumber: 3.1 Consensus size: 21
12606760 TAATTTTGAA
*
12606770 ATTATTTTTAAAATTTTAAAT
1 ATTATTTTTAAAATATTAAAT
12606791 ATTATTTTT-AAATATTAAAT
1 ATTATTTTTAAAATATTAAAT
*
12606811 ATATATTTTTAATAATATAAAAT
1 AT-TATTTTTAA-AATATTAAAT
12606834 ATT
1 ATT
12606837 TAAATATTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
20 12 0.29
21 16 0.39
22 2 0.05
23 11 0.27
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTATTTTTAAAATATTAAAT
Found at i:12606798 original size:32 final size:32
Alignment explanation
Indices: 12606740--12606803 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
12606730 TTATAATATA
*
12606740 TATTTTTTAAATTTTAAATATAATTTTGAAAT
1 TATTTTTAAAATTTTAAATATAATTTTGAAAT
* *
12606772 TATTTTTAAAATTTTAAATATTATTTTTAAAT
1 TATTTTTAAAATTTTAAATATAATTTTGAAAT
12606804 ATTAAATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (32 bp):
TATTTTTAAAATTTTAAATATAATTTTGAAAT
Found at i:12606801 original size:13 final size:13
Alignment explanation
Indices: 12606783--12606807 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12606773 ATTTTTAAAA
12606783 TTTTAAATATTAT
1 TTTTAAATATTAT
12606796 TTTTAAATATTA
1 TTTTAAATATTA
12606808 AATATATATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTTAAATATTAT
Found at i:12606926 original size:21 final size:21
Alignment explanation
Indices: 12606887--12606927 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
12606877 GTTTATAATA
*
12606887 TTTTAAATATTATTTAATTAG
1 TTTTAAATATTATTAAATTAG
12606908 TTTTATAATATT-TTAAATTA
1 TTTTA-AATATTATTAAATTA
12606928 TGATTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTAAATATTATTAAATTAG
Found at i:12607253 original size:19 final size:20
Alignment explanation
Indices: 12607231--12607273 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
12607221 TAAAAAAAAG
12607231 ATTTGTTAAAAAAAG-ATTT
1 ATTTGTTAAAAAAAGAATTT
*
12607250 ATTTGTTAAAAAATGAATTT
1 ATTTGTTAAAAAAAGAATTT
12607270 ATTT
1 ATTT
12607274 AAAAATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (20 bp):
ATTTGTTAAAAAAAGAATTT
Found at i:12607786 original size:20 final size:20
Alignment explanation
Indices: 12607763--12607827 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
12607753 ATAATTTTTT
12607763 AATTTTAGTACACATTTATA
1 AATTTTAGTACACATTTATA
* * ** * *
12607783 AATTAATATTTTA-ATTTTTT
1 AATT-TTAGTACACATTTATA
*
12607803 AATTTTAGTACACATTCATA
1 AATTTTAGTACACATTTATA
12607823 AATTT
1 AATTT
12607828 ATGTACTTAA
Statistics
Matches: 30, Mismatches: 13, Indels: 4
0.64 0.28 0.09
Matches are distributed among these distances:
19 4 0.13
20 22 0.73
21 4 0.13
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (20 bp):
AATTTTAGTACACATTTATA
Found at i:12607849 original size:40 final size:40
Alignment explanation
Indices: 12607762--12607849 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 40
12607752 TATAATTTTT
* * * *
12607762 TAATTTTAGTACACATTTATAAATTAATATTTTAATTTTT
1 TAATTTTAGTACACATTCATAAATTAATATCTTAATTATA
* *
12607802 TAATTTTAGTACACATTCATAAATTTATGTACTTAA-TATA
1 TAATTTTAGTACACATTCATAAATTAATAT-CTTAATTATA
*
12607842 TATTTTTA
1 TAATTTTA
12607850 ATAGGTAAAG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
40 36 0.90
41 4 0.10
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.52
Consensus pattern (40 bp):
TAATTTTAGTACACATTCATAAATTAATATCTTAATTATA
Found at i:12607929 original size:18 final size:18
Alignment explanation
Indices: 12607902--12607937 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
12607892 TTTTAAAAAC
*
12607902 TTAAAGAAATTAAATATA
1 TTAAAAAAATTAAATATA
*
12607920 TTAAAAAAATTAAGTATA
1 TTAAAAAAATTAAATATA
12607938 GCCAATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (18 bp):
TTAAAAAAATTAAATATA
Found at i:12607984 original size:17 final size:19
Alignment explanation
Indices: 12607950--12607988 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
12607940 CAATTTTAAA
*
12607950 ATTTTAATATATTTAATAT
1 ATTTTAATATATTAAATAT
12607969 ATTTTAA-A-ATTAAATAT
1 ATTTTAATATATTAAATAT
12607986 ATT
1 ATT
12607989 AAAAAATGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 11 0.58
18 1 0.05
19 7 0.37
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTTTAATATATTAAATAT
Found at i:12608002 original size:68 final size:67
Alignment explanation
Indices: 12607908--12608041 Score: 207
Period size: 68 Copynumber: 2.0 Consensus size: 67
12607898 AAACTTAAAG
* *
12607908 AAATTAAATATATTAAAAAAATTAAGTATAGCCAATTTTAAAATTTTAATATATTTAATATATTT
1 AAATTAAATATATTAAAAAAATTAAGTATAACCAATTTTAAAATTTTAATATATTCAATATATTT
12607973 TA
66 TA
* *
12607975 AAATTAAATATATT-AAAAAATGCTAAGTATAATCAATTTTAAAATTTTAATATATTCAATTTAT
1 AAATTAAATATATTAAAAAAAT--TAAGTATAACCAATTTTAAAATTTTAATATATTCAATATAT
12608039 TTT
64 TTT
12608042 TTAAAAATAT
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
66 7 0.11
67 14 0.23
68 40 0.66
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (67 bp):
AAATTAAATATATTAAAAAAATTAAGTATAACCAATTTTAAAATTTTAATATATTCAATATATTT
TA
Found at i:12608059 original size:68 final size:64
Alignment explanation
Indices: 12607913--12608060 Score: 172
Period size: 68 Copynumber: 2.2 Consensus size: 64
12607903 TAAAGAAATT
* * *
12607913 AAATATA-TTAAAAAAATTAAGTATAGCCAATTTTAAAATTTTAATATATTTAATATATTTTAA
1 AAATATATTTTAAAAAATTAAGTATAACCAATTTTAAAATTTTAATATATTCAATATATTTTAA
* * * *
12607976 AATTAAATATATTAAAAAATGCTAAGTATAATCAATTTTAAAATTTTAATATATTCAATTTATTT
1 AA--ATATATTTTAAAAAAT--TAAGTATAACCAATTTTAAAATTTTAATATATTCAA--TATAT
12608041 TTTAA
60 TTTAA
12608046 AAATATATTTTAAAA
1 AAATATATTTTAAAA
12608061 TGTTAATATA
Statistics
Matches: 69, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
63 2 0.03
65 4 0.06
66 8 0.12
68 44 0.64
70 11 0.16
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (64 bp):
AAATATATTTTAAAAAATTAAGTATAACCAATTTTAAAATTTTAATATATTCAATATATTTTAA
Found at i:12608302 original size:77 final size:79
Alignment explanation
Indices: 12608143--12608288 Score: 181
Period size: 77 Copynumber: 1.9 Consensus size: 79
12608133 ATGTAAAAAA
* * * * * *
12608143 ATTTAAATATATTAAAATTTAAATATGTTTAAAGGAAAATGTTGAGTATAACCAATTATCAATTT
1 ATTTAAATATATTAAAATTTAAACATGATTAAA-GAAAATATTAAGTATAACCAATTATAAAATT
12608208 TTAATAACTGAATAT
65 TTAATAACTGAATAT
* *
12608223 ATTTAAATATATTAAAATTTTGAACAT-ATTAAA-AAAA-ATTAAGTATAACCAATTTTAAAATT
1 ATTTAAATATATTAAAA-TTTAAACATGATTAAAGAAAATATTAAGTATAACCAATTATAAAATT
12608285 TTAA
65 TTAA
12608289 AATTTTAATA
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
77 24 0.42
78 4 0.07
80 22 0.39
81 7 0.12
ACGTcount: A:0.49, C:0.05, G:0.06, T:0.40
Consensus pattern (79 bp):
ATTTAAATATATTAAAATTTAAACATGATTAAAGAAAATATTAAGTATAACCAATTATAAAATTT
TAATAACTGAATAT
Found at i:12610517 original size:30 final size:30
Alignment explanation
Indices: 12610481--12610546 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
12610471 GTCACAGAGC
* * * * *
12610481 AGTTCATATTACTCAGATATTGGCGGTTCA
1 AGTTCATATCACCCAGACATAGGCGGCTCA
*
12610511 AGTTCATATCACCCAGACATAGGCGGCTCG
1 AGTTCATATCACCCAGACATAGGCGGCTCA
12610541 AGTTCA
1 AGTTCA
12610547 GAGCGACCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (30 bp):
AGTTCATATCACCCAGACATAGGCGGCTCA
Found at i:12612775 original size:19 final size:19
Alignment explanation
Indices: 12612751--12612794 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
12612741 GTGTAGGTTT
12612751 GACAACCTTGTAATCAATC
1 GACAACCTTGTAATCAATC
12612770 GACAACCTTGTAATCAATC
1 GACAACCTTGTAATCAATC
12612789 GACAAC
1 GACAAC
12612795 TTCATGCTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.39, C:0.27, G:0.11, T:0.23
Consensus pattern (19 bp):
GACAACCTTGTAATCAATC
Found at i:12614007 original size:13 final size:13
Alignment explanation
Indices: 12613989--12614014 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12613979 AAATTTTAAA
12613989 ATATTTAAAATAT
1 ATATTTAAAATAT
12614002 ATATTTAAAATAT
1 ATATTTAAAATAT
12614015 TATAAAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATTTAAAATAT
Found at i:12614015 original size:9 final size:9
Alignment explanation
Indices: 12613972--12614001 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
12613962 TATAAAAATT
12613972 ATATTTAAA
1 ATATTTAAA
12613981 AT-TTTAAA
1 ATATTTAAA
12613989 ATATTTAAA
1 ATATTTAAA
12613998 ATAT
1 ATAT
12614002 ATATTTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
ATATTTAAA
Found at i:12614032 original size:22 final size:22
Alignment explanation
Indices: 12613985--12614032 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
12613975 TTTAAAATTT
* * *
12613985 TAAAATATTTAAAATATATATT
1 TAAAATATTTAAAACAAATATA
12614007 TAAAATATTATAAAACAAATA-A
1 TAAAATATT-TAAAACAAATATA
12614029 TAAA
1 TAAA
12614033 TTTGAAAGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
TAAAATATTTAAAACAAATATA
Found at i:12614077 original size:24 final size:22
Alignment explanation
Indices: 12614049--12614152 Score: 74
Period size: 24 Copynumber: 4.6 Consensus size: 22
12614039 AGGTCGTATC
*
12614049 TTTAAAATAATATATTTTAAATAA
1 TTTAAAATAATA-ATTTAAAAT-A
*
12614073 TTTAAAAATCATAATTTAAAATA
1 TTT-AAAATAATAATTTAAAATA
*
12614096 TTATAAAAT-A-CATTT-AAA-A
1 TT-TAAAATAATAATTTAAAATA
12614115 TTTAAAAT-ATACATTTAAAATA
1 TTTAAAATAATA-ATTTAAAATA
*
12614137 TTATAAAGCTAATAAT
1 TT-TAAA-ATAATAAT
12614153 AAATTTGAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
18 7 0.11
19 3 0.05
20 7 0.11
21 7 0.11
22 4 0.06
23 12 0.18
24 15 0.23
25 11 0.17
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (22 bp):
TTTAAAATAATAATTTAAAATA
Found at i:12614128 original size:20 final size:20
Alignment explanation
Indices: 12614071--12614135 Score: 80
Period size: 20 Copynumber: 3.1 Consensus size: 20
12614061 TATTTTAAAT
12614071 AATTTAAAAATCATA-ATTTAA
1 AATTT-AAAAT-ATACATTTAA
12614092 AATATTATAAA-ATACATTTAA
1 AAT-TTA-AAATATACATTTAA
12614113 AATTTAAAATATACATTTAA
1 AATTTAAAATATACATTTAA
12614133 AAT
1 AAT
12614136 ATTATAAAGC
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
19 3 0.08
20 19 0.47
21 13 0.32
22 5 0.12
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
AATTTAAAATATACATTTAA
Found at i:12614157 original size:41 final size:42
Alignment explanation
Indices: 12613991--12614180 Score: 114
Period size: 41 Copynumber: 4.6 Consensus size: 42
12613981 ATTTTAAAAT
* *
12613991 ATTT-AAAAT-ATATATTTAAAATATTATAAAACAAATAATAA
1 ATTTAAAAATCATACATTTAAAATATTAT-AAACTAATAATAA
** * * ** *
12614032 ATTTGAAAGGTCGTATC-TTTAAAATAATAT-ATTTTA-AAT-A
1 ATTT-AAAAATCATA-CATTTAAAATATTATAAACTAATAATAA
* *
12614072 ATTTAAAAATCATA-ATTTAAAATATTATAAAATACAT-TTAAA
1 ATTTAAAAATCATACATTTAAAATATTATAAACTA-ATAAT-AA
12614114 ATTT-AAAAT-ATACATTTAAAATATTATAAAGCTAATAATAA
1 ATTTAAAAATCATACATTTAAAATATTATAAA-CTAATAATAA
**
12614155 ATTTGAAAGGTCATATC-TTTAAAATA
1 ATTT-AAAAATCATA-CATTTAAAATA
12614181 CTTAAATATT
Statistics
Matches: 111, Mismatches: 21, Indels: 31
0.68 0.13 0.19
Matches are distributed among these distances:
38 12 0.11
39 9 0.08
40 10 0.09
41 37 0.33
42 10 0.09
43 6 0.05
44 26 0.23
45 1 0.01
ACGTcount: A:0.53, C:0.05, G:0.04, T:0.38
Consensus pattern (42 bp):
ATTTAAAAATCATACATTTAAAATATTATAAACTAATAATAA
Found at i:12614219 original size:123 final size:121
Alignment explanation
Indices: 12613991--12614225 Score: 332
Period size: 123 Copynumber: 1.9 Consensus size: 121
12613981 ATTTTAAAAT
* *
12613991 ATTTAAAATATATATTTAAAATATTATAAAACAAATAATAAATTTGAAAGGTCGTATCTTTAAAA
1 ATTTAAAATATACATTTAAAATATTATAAAACAAATAATAAATTTGAAAGGTCATATCTTTAAAA
*
12614056 TAATATATTTTAAATAATTTAAAAATCATAATTTAAAATATTATAAAATACATTTAAA
66 TAAAATATTTTAAATAATTTAAAAATCATAATTT-AAATATT-TAAAATACATTTAAA
* *
12614114 ATTTAAAATATACATTTAAAATATTATAAAGCTAATAATAAATTTGAAAGGTCATATCTTTAAAA
1 ATTTAAAATATACATTTAAAATATTATAAAACAAATAATAAATTTGAAAGGTCATATCTTTAAAA
* *
12614179 TACTTAAATATTTTATATTA-TTAAAAAT-ATATATTT-AATATTTAAAA
66 TA---AAATATTTTAAATAATTTAAAAATCATA-ATTTAAATATTTAAAA
12614226 AACTAATATT
Statistics
Matches: 101, Mismatches: 7, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
122 5 0.05
123 69 0.68
124 3 0.03
125 12 0.12
126 12 0.12
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.40
Consensus pattern (121 bp):
ATTTAAAATATACATTTAAAATATTATAAAACAAATAATAAATTTGAAAGGTCATATCTTTAAAA
TAAAATATTTTAAATAATTTAAAAATCATAATTTAAATATTTAAAATACATTTAAA
Found at i:12614226 original size:22 final size:23
Alignment explanation
Indices: 12614185--12614238 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
12614175 AAAATACTTA
* *
12614185 AATATTTTATATTATTAAAAA-T
1 AATATTTAATATTATAAAAAACT
12614207 ATATATTTAATATT-TAAAAAACT
1 A-ATATTTAATATTATAAAAAACT
12614230 AATATTTAA
1 AATATTTAA
12614239 AAAATAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 15 0.54
23 13 0.46
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
AATATTTAATATTATAAAAAACT
Found at i:12614249 original size:36 final size:36
Alignment explanation
Indices: 12614201--12614312 Score: 131
Period size: 34 Copynumber: 3.1 Consensus size: 36
12614191 TTATATTATT
*
12614201 AAAAATATATATTTAATATTTAAAAAACTAATATTTA
1 AAAAATATATATTTAAAATTTAAAAAA-TAATATTTA
* *
12614238 AAAAATA-ATATTCAAAATTTTAAAAAAT-A-ATTTC
1 AAAAATATATATTTAAAA-TTTAAAAAATAATATTTA
*
12614272 AAATATATATATTTAAAATTTAAAAAATATATATTATA
1 AAAAATATATATTTAAAATTTAAAAAATA-ATATT-TA
12614310 AAA
1 AAA
12614313 TATTTCAAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 11
0.79 0.08 0.14
Matches are distributed among these distances:
34 20 0.32
35 10 0.16
36 10 0.16
37 19 0.30
38 4 0.06
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (36 bp):
AAAAATATATATTTAAAATTTAAAAAATAATATTTA
Found at i:12614254 original size:13 final size:15
Alignment explanation
Indices: 12614214--12614254 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
12614204 AATATATATT
12614214 TAATATTTAAAAAAC
1 TAATATTTAAAAAAC
12614229 TAATATTTAAAAAA-
1 TAATATTTAAAAAAC
*
12614243 TAATATTCAAAA
1 TAATATTTAAAA
12614255 TTTTAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (15 bp):
TAATATTTAAAAAAC
Found at i:12614259 original size:22 final size:21
Alignment explanation
Indices: 12614234--12614274 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
12614224 AAAACTAATA
12614234 TTTAAAAAATAATATTCAAAAT
1 TTTAAAAAATAAT-TTCAAAAT
12614256 TTTAAAAAATAATTTCAAA
1 TTTAAAAAATAATTTCAAA
12614275 TATATATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (21 bp):
TTTAAAAAATAATTTCAAAAT
Found at i:12614262 original size:21 final size:21
Alignment explanation
Indices: 12614233--12614274 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12614223 AAAAACTAAT
12614233 ATTT-AAAAAATAATATTCAAA
1 ATTTAAAAAAATAAT-TTCAAA
*
12614254 ATTTTAAAAAATAATTTCAAA
1 ATTTAAAAAAATAATTTCAAA
12614275 TATATATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (21 bp):
ATTTAAAAAAATAATTTCAAA
Found at i:12614301 original size:22 final size:23
Alignment explanation
Indices: 12614266--12614313 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
12614256 TTTAAAAAAT
* *
12614266 AATTTCAAATATATATATT-TAA
1 AATTTAAAAAATATATATTATAA
12614288 AATTTAAAAAATATATATTATAA
1 AATTTAAAAAATATATATTATAA
12614311 AAT
1 AAT
12614314 ATTTCAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
AATTTAAAAAATATATATTATAA
Found at i:12614359 original size:46 final size:47
Alignment explanation
Indices: 12614258--12614360 Score: 111
Period size: 47 Copynumber: 2.2 Consensus size: 47
12614248 TTCAAAATTT
* * *
12614258 TAAAAAATAATTTCAAATATATATATTTAAAATTTAAAAAATATATAT
1 TAAAAAAT-ATTTCAAATAGACATATTTAAAATTTAAAAAATATATAA
* * * *
12614306 TATAAAATATTTCAAATAGACAT-TTTAAATTTCTTAAAATTA-ATAA
1 TAAAAAATATTTCAAATAGACATATTTAAAATT-TAAAAAATATATAA
12614352 TAAAAAATA
1 TAAAAAATA
12614361 AGTAAAATAA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
46 19 0.41
47 20 0.43
48 7 0.15
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (47 bp):
TAAAAAATATTTCAAATAGACATATTTAAAATTTAAAAAATATATAA
Found at i:12614366 original size:23 final size:23
Alignment explanation
Indices: 12614340--12614384 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
12614330 TTAAATTTCT
*
12614340 TAAAATTAATAATAA-AAAATAAG
1 TAAAATAAATAA-AATAAAATAAG
12614363 TAAAATAAATAAAATAAAATAA
1 TAAAATAAATAAAATAAAATAA
12614385 AATAAAGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (23 bp):
TAAAATAAATAAAATAAAATAAG
Found at i:12614369 original size:9 final size:9
Alignment explanation
Indices: 12614355--12614390 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
12614345 TTAATAATAA
*
12614355 AAAATAAGT
1 AAAATAAAT
12614364 AAAATAAAT
1 AAAATAAAT
12614373 AAAATAAAAT
1 AAAAT-AAAT
12614383 AAAATAAA
1 AAAATAAA
12614391 GATAAAAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 16 0.64
10 9 0.36
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (9 bp):
AAAATAAAT
Found at i:12614417 original size:5 final size:5
Alignment explanation
Indices: 12614340--12614397 Score: 57
Period size: 5 Copynumber: 11.0 Consensus size: 5
12614330 TTAAATTTCT
12614340 TAAAA TTAATAA TAAAA -AATAA GTAAAA T-AAA TAAAA TAAAA TAAAA
1 TAAAA -TAA-AA TAAAA TAA-AA -TAAAA TAAAA TAAAA TAAAA TAAAA
12614387 TAAAGA TAAAA
1 TAAA-A TAAAA
12614398 ACAAAACTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
4 6 0.13
5 23 0.50
6 13 0.28
7 4 0.09
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.22
Consensus pattern (5 bp):
TAAAA
Found at i:12621210 original size:13 final size:13
Alignment explanation
Indices: 12621192--12621216 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12621182 ACAAACGATA
12621192 AAATTTTCACACG
1 AAATTTTCACACG
12621205 AAATTTTCACAC
1 AAATTTTCACAC
12621217 ATATCACATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:12624011 original size:29 final size:29
Alignment explanation
Indices: 12623944--12624000 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
12623934 TATTTATGGC
*
12623944 ACAAAATGTTAGGGCATGTCAACTATAAT
1 ACAAAAGGTTAGGGCATGTCAACTATAAT
12623973 ACAAAAGGTTAGGGCATGTCAACTATAA
1 ACAAAAGGTTAGGGCATGTCAACTATAA
12624001 GTCTCTTGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (29 bp):
ACAAAAGGTTAGGGCATGTCAACTATAAT
Found at i:12632200 original size:17 final size:17
Alignment explanation
Indices: 12632180--12632241 Score: 106
Period size: 17 Copynumber: 3.6 Consensus size: 17
12632170 TTTTTTAAGG
12632180 TTAGGGTTTTTGGTGGT
1 TTAGGGTTTTTGGTGGT
*
12632197 TTAGGGTTTTTGATGGT
1 TTAGGGTTTTTGGTGGT
*
12632214 TTAGGATTTTTGGTGGT
1 TTAGGGTTTTTGGTGGT
12632231 TTAGGGTTTTT
1 TTAGGGTTTTT
12632242 AAGAAAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.10, C:0.00, G:0.35, T:0.55
Consensus pattern (17 bp):
TTAGGGTTTTTGGTGGT
Found at i:12632207 original size:34 final size:35
Alignment explanation
Indices: 12632169--12632241 Score: 105
Period size: 34 Copynumber: 2.1 Consensus size: 35
12632159 TTTTGTCCTA
* *
12632169 TTTTTTTAAGG-TTAGGGTTTTTGGTGGTTTAGGG
1 TTTTTTGAAGGTTTAGGATTTTTGGTGGTTTAGGG
*
12632203 -TTTTTGATGGTTTAGGATTTTTGGTGGTTTAGGG
1 TTTTTTGAAGGTTTAGGATTTTTGGTGGTTTAGGG
12632237 TTTTT
1 TTTTT
12632242 AAGAAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 8 0.24
34 22 0.65
35 4 0.12
ACGTcount: A:0.11, C:0.00, G:0.33, T:0.56
Consensus pattern (35 bp):
TTTTTTGAAGGTTTAGGATTTTTGGTGGTTTAGGG
Found at i:12632355 original size:23 final size:24
Alignment explanation
Indices: 12632315--12632361 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
12632305 AAAAATAATT
12632315 AAATTAGGGTTTAGGATT-TTTTA
1 AAATTAGGGTTTAGGATTGTTTTA
**
12632338 AAATTAGGGTTTCTGATTGTTTTA
1 AAATTAGGGTTTAGGATTGTTTTA
12632362 GATTAAGGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.28, C:0.02, G:0.21, T:0.49
Consensus pattern (24 bp):
AAATTAGGGTTTAGGATTGTTTTA
Found at i:12632440 original size:160 final size:151
Alignment explanation
Indices: 12632230--12632643 Score: 479
Period size: 160 Copynumber: 2.7 Consensus size: 151
12632220 TTTTTGGTGG
* **
12632230 TTTAGGGTTTTTAAGAAAAAAATTAATGAACACTTAGAGTTGAGGGTTAATTAATTAAATTAACT
1 TTTAGTGTTTTTAAGGGAAAAATTAATGAACACTTAGAGTTGAGGGTTAATTAATTAAATTAACT
*
12632295 ATGAAAATAAAAAAATAATTAAATTAGGGTTTAGGATTTTTTAAAATTAGGGTTTCTGATTGTTT
66 ATGAAAATAAAAAAATAATTAAATTAGGGTTTAGG-TTTTTT--AATTAGGGTTT-T--TTG--G
*
12632360 TAGATTAAG-GTTTTAGTGGTTTAGGGTT
123 TAGATTAAGAGTTTTAGTGGTTTAAGGTT
* *
12632388 TTTAGTATTTTTTTAAGGGAAAAATTAATGAACACTTAGAGTTGATGGTTAATTAATTAAATTAA
1 TTTAG--TGTTTTTAAGGGAAAAATTAATGAACACTTAGAGTTGAGGGTTAATTAATTAAATTAA
* ** *
12632453 CTATGAAAATAAGAAAAAATCAATTAAATTAGGGCTTA-G--TGGT--TTAGGGTTTTTTGGTGG
64 CTATGAAAAT-A-AAAAAAT-AATTAAATTAGGGTTTAGGTTTTTTAATTAGGGTTTTTTGGTAG
* *
12632513 TTTAAGATTTTTAGTGGTTTAAGGTT
126 ATTAAGAGTTTTAGTGGTTTAAGGTT
** * *
12632539 TTTAGTGTTTTTAA-GGAAAAATTAATTTA-A-TTAAAGTTCAGGGTTAATTAATTAAATTAACT
1 TTTAGTGTTTTTAAGGGAAAAATTAATGAACACTTAGAGTTGAGGGTTAATTAATTAAATTAACT
12632601 ATGAAAAT-AAAAAATAATTAAATTAGGGTTTAGGGTTTTTTAA
66 ATGAAAATAAAAAAATAATTAAATTAGGGTTTA-GGTTTTTTAA
12632644 GGTTTATTAA
Statistics
Matches: 222, Mismatches: 22, Indels: 34
0.80 0.08 0.12
Matches are distributed among these distances:
142 16 0.07
143 7 0.03
144 1 0.00
146 39 0.18
147 1 0.00
148 13 0.06
149 8 0.04
150 7 0.03
151 22 0.10
152 3 0.01
154 1 0.00
155 9 0.04
158 5 0.02
159 2 0.01
160 63 0.28
161 1 0.00
162 8 0.04
163 16 0.07
ACGTcount: A:0.38, C:0.03, G:0.19, T:0.41
Consensus pattern (151 bp):
TTTAGTGTTTTTAAGGGAAAAATTAATGAACACTTAGAGTTGAGGGTTAATTAATTAAATTAACT
ATGAAAATAAAAAAATAATTAAATTAGGGTTTAGGTTTTTTAATTAGGGTTTTTTGGTAGATTAA
GAGTTTTAGTGGTTTAAGGTT
Found at i:12632529 original size:17 final size:17
Alignment explanation
Indices: 12632488--12632545 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
12632478 AAATTAGGGC
* *
12632488 TTAGTGGTTTAGGGTTTT
1 TTAGTGGTTTA-AGATTT
*
12632506 TTGGTGGTTTAAGATTT
1 TTAGTGGTTTAAGATTT
*
12632523 TTAGTGGTTTAAGGTTT
1 TTAGTGGTTTAAGATTT
12632540 TTAGTG
1 TTAGTG
12632546 TTTTTAAGGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
17 25 0.71
18 10 0.29
ACGTcount: A:0.16, C:0.00, G:0.31, T:0.53
Consensus pattern (17 bp):
TTAGTGGTTTAAGATTT
Found at i:12632898 original size:126 final size:124
Alignment explanation
Indices: 12632668--12632995 Score: 505
Period size: 126 Copynumber: 2.6 Consensus size: 124
12632658 ATTAACTATT
* *
12632668 AATTACGGAAAAAAGCTCCCACGTGGACGCTTTTTTGCTATAGTAGTATCTGATAAAATAATTTT
1 AATTACGG-AAAAAGCCCCCACGTGGACGCTTTTTT-CTACAGTAGTATCTGATAAAATAATTTT
* *
12632733 AAGAAGATGTTTCTGAACAAATAGTGTCAAAAACACTTCAAGAAGGATGCACTTTCAGCAA
64 GAGAAGATGTTTCTAAACAAATAGTGTCAAAAACACTTCAAGAAGGATGCACTTTCAGCAA
12632794 AATTACAGGAAAAAGCCCCCACGTGGACGCCTTTTTTCTACAGTAGTATCTGATAAAATAATTTT
1 AATTAC-GGAAAAAGCCCCCACGTGGACG-CTTTTTTCTACAGTAGTATCTGATAAAATAATTTT
* * *
12632859 GAGAAGATGTTTCTAAACAAATGGTGTCAAAAACGCTTCAATAAGGATGCACTTTCAGCAA
64 GAGAAGATGTTTCTAAACAAATAGTGTCAAAAACACTTCAAGAAGGATGCACTTTCAGCAA
* * *
12632920 AATTACGAGAAAAAG-CTCCACGTGGACGCTCTTTTGCTACAGTAGTATCTAATAAAATAATTTT
1 AATTACG-GAAAAAGCCCCCACGTGGACGCT-TTTTTCTACAGTAGTATCTGATAAAATAATTTT
12632984 GAGAAGATGTTT
64 GAGAAGATGTTT
12632996 AAAAGTAGTA
Statistics
Matches: 188, Mismatches: 10, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
124 2 0.01
125 56 0.30
126 121 0.64
127 9 0.05
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (124 bp):
AATTACGGAAAAAGCCCCCACGTGGACGCTTTTTTCTACAGTAGTATCTGATAAAATAATTTTGA
GAAGATGTTTCTAAACAAATAGTGTCAAAAACACTTCAAGAAGGATGCACTTTCAGCAA
Found at i:12634784 original size:25 final size:25
Alignment explanation
Indices: 12634746--12634801 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
12634736 CCTCATTAAG
12634746 GAAAAGGACAGGCTTCTGGGAGATA
1 GAAAAGGACAGGCTTCTGGGAGATA
*
12634771 GAAAAGGACTGGCTTCTGGGAGATA
1 GAAAAGGACAGGCTTCTGGGAGATA
*
12634796 AAAAAG
1 GAAAAG
12634802 TACAAAGGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.39, C:0.11, G:0.34, T:0.16
Consensus pattern (25 bp):
GAAAAGGACAGGCTTCTGGGAGATA
Found at i:12637196 original size:18 final size:18
Alignment explanation
Indices: 12637170--12637212 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
12637160 GACTGGAAAA
* *
12637170 AGGAAACATAAAAGGGTT
1 AGGATACATAAAAGGGCT
*
12637188 AGGATACATATAAGGGCT
1 AGGATACATAAAAGGGCT
12637206 AGGATAC
1 AGGATAC
12637213 GCACTTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:12638928 original size:11 final size:11
Alignment explanation
Indices: 12638884--12638929 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
12638874 CTTTAACAAA
*
12638884 AATTGAGAGA-
1 AATTTAGAGAG
12638894 AATTT-GAGAG
1 AATTTAGAGAG
* *
12638904 AATTTGGAAAG
1 AATTTAGAGAG
12638915 AATTTAGAGAG
1 AATTTAGAGAG
12638926 AATT
1 AATT
12638930 GTTGTCAGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
9 4 0.13
10 9 0.30
11 17 0.57
ACGTcount: A:0.46, C:0.00, G:0.26, T:0.28
Consensus pattern (11 bp):
AATTTAGAGAG
Found at i:12639594 original size:19 final size:20
Alignment explanation
Indices: 12639544--12639597 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
12639534 ATAAATAAAT
12639544 AAAAGT-TATAAAAATATTA
1 AAAAGTATATAAAAATATTA
* *
12639563 AATATTA-ATAAAAATATTA
1 AAAAGTATATAAAAATATTA
*
12639582 AAAAGTATAAAAAAAT
1 AAAAGTATATAAAAAT
12639598 TTGTAAAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 21 0.75
20 7 0.25
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.30
Consensus pattern (20 bp):
AAAAGTATATAAAAATATTA
Found at i:12639685 original size:29 final size:29
Alignment explanation
Indices: 12639652--12639711 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
12639642 TTAACTATTA
*
12639652 ACTTAAGTCGTTGATCGTTAAAGTTAACG
1 ACTTAAGCCGTTGATCGTTAAAGTTAACG
12639681 ACTTAAGCCGTTGATCGTTAAAGTTAACG
1 ACTTAAGCCGTTGATCGTTAAAGTTAACG
12639710 AC
1 AC
12639712 CCTCAATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Consensus pattern (29 bp):
ACTTAAGCCGTTGATCGTTAAAGTTAACG
Found at i:12639922 original size:21 final size:20
Alignment explanation
Indices: 12639907--12640012 Score: 83
Period size: 21 Copynumber: 5.3 Consensus size: 20
12639897 CTTTATAAAA
* *
12639907 TTTTATATATTTTTTATATAT
1 TTTTATAAATTTTATATAT-T
* *
12639928 TTCTATATATTTTATATA-T
1 TTTTATAAATTTTATATATT
* * *
12639947 TTTTACAATTTTTTATAAATT
1 TTTTATAA-ATTTTATATATT
*
12639968 TTTTAT-GATTTTATAT-TT
1 TTTTATAAATTTTATATATT
* *
12639986 TTTTCTAAATTTTAAATATT
1 TTTTATAAATTTTATATATT
12640006 TTTTATA
1 TTTTATA
12640013 GTTTTTAAAT
Statistics
Matches: 66, Mismatches: 15, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
18 7 0.11
19 21 0.32
20 16 0.24
21 22 0.33
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (20 bp):
TTTTATAAATTTTATATATT
Found at i:12639923 original size:11 final size:10
Alignment explanation
Indices: 12639907--12640019 Score: 85
Period size: 10 Copynumber: 11.5 Consensus size: 10
12639897 CTTTATAAAA
12639907 TTTTATATATT
1 TTTTATATA-T
12639918 TTTTATATAT
1 TTTTATATAT
*
12639928 TTCTATATA-
1 TTTTATATAT
12639937 TTTTATATAT
1 TTTTATATAT
*
12639947 TTTTACA-ATT
1 TTTTATATA-T
*
12639957 TTTTATAAAT
1 TTTTATATAT
12639967 TTTT-TATGA-
1 TTTTATAT-AT
*
12639976 TTTTATATTT
1 TTTTATATAT
* *
12639986 TTTTCTA-AA
1 TTTTATATAT
*
12639995 TTTTAAATAT
1 TTTTATATAT
12640005 TTTT-TATAGT
1 TTTTATATA-T
12640015 TTTTA
1 TTTTA
12640020 AATTTTAAAA
Statistics
Matches: 80, Mismatches: 13, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
9 23 0.29
10 47 0.59
11 10 0.12
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (10 bp):
TTTTATATAT
Found at i:12639924 original size:9 final size:9
Alignment explanation
Indices: 12639906--12640025 Score: 78
Period size: 9 Copynumber: 12.6 Consensus size: 9
12639896 GCTTTATAAA
*
12639906 ATTTTATAT
1 ATTTTTTAT
12639915 ATTTTTTAT
1 ATTTTTTAT
*
12639924 ATATTTCTAT
1 AT-TTTTTAT
*
12639934 ATATTTTAT
1 ATTTTTTAT
*
12639943 ATATTTTTACA
1 AT-TTTTTA-T
12639954 ATTTTTTAT
1 ATTTTTTAT
12639963 AAATTTTTTAT
1 --ATTTTTTAT
*
12639974 GATTTTATAT
1 -ATTTTTTAT
* *
12639984 TTTTTTCTAA
1 ATTTTT-TAT
**
12639994 ATTTTAAAT
1 ATTTTTTAT
12640003 ATTTTTTAT
1 ATTTTTTAT
* *
12640012 AGTTTTTAA
1 ATTTTTTAT
12640021 ATTTT
1 ATTTT
12640026 AAAAATGTTA
Statistics
Matches: 84, Mismatches: 21, Indels: 12
0.72 0.18 0.10
Matches are distributed among these distances:
9 40 0.48
10 33 0.39
11 11 0.13
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.66
Consensus pattern (9 bp):
ATTTTTTAT
Found at i:12639940 original size:19 final size:19
Alignment explanation
Indices: 12639906--12640017 Score: 93
Period size: 19 Copynumber: 5.8 Consensus size: 19
12639896 GCTTTATAAA
*
12639906 ATTTTATATATTTTTTATAT
1 ATTTT-TATATATTTTATAT
*
12639926 ATTTCTATATATTTTATAT
1 ATTTTTATATATTTTATAT
* * *
12639945 ATTTTTACAATTTTTTATAA
1 ATTTTTA-TATATTTTATAT
12639965 ATTTTT-TATGATTTTATAT
1 ATTTTTATAT-ATTTTATAT
* * * *
12639984 TTTTTTCTAAATTTTAAAT
1 ATTTTTATATATTTTATAT
12640003 ATTTTT-TATAGTTTT
1 ATTTTTATATA-TTTT
12640018 TAAATTTTAA
Statistics
Matches: 74, Mismatches: 14, Indels: 9
0.76 0.14 0.09
Matches are distributed among these distances:
18 5 0.07
19 48 0.65
20 21 0.28
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (19 bp):
ATTTTTATATATTTTATAT
Found at i:12639963 original size:29 final size:29
Alignment explanation
Indices: 12639898--12640008 Score: 100
Period size: 29 Copynumber: 3.8 Consensus size: 29
12639888 TTCTTACGGC
*
12639898 TTTATAAAATTTTATATATTTTTTA-TATATT
1 TTTAT-AAATTTTATATA-TTTTTACAAT-TT
* *
12639929 TCTATATATTTTATATATTTTTACAATTT
1 TTTATAAATTTTATATATTTTTACAATTT
* * *
12639958 TTTATAAATTTTTTATGA-TTTTATATTTT
1 TTTATAAATTTTATAT-ATTTTTACAATTT
* *
12639987 TTTCTAAATTTTAAATATTTTT
1 TTTATAAATTTTATATATTTTT
12640009 TATAGTTTTT
Statistics
Matches: 66, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
28 1 0.02
29 47 0.71
30 14 0.21
31 4 0.06
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.65
Consensus pattern (29 bp):
TTTATAAATTTTATATATTTTTACAATTT
Found at i:12639989 original size:39 final size:39
Alignment explanation
Indices: 12639838--12639989 Score: 123
Period size: 39 Copynumber: 3.9 Consensus size: 39
12639828 AATACAATAA
* * *
12639838 TTTTTATAATTTTTTTAAGAATTTTGTAT-TTCTTTAC-AT
1 TTTTTATAAATTTTTTATG-ATTTTATATATT-TTTACAAT
* ** * * *
12639877 TTTTTAT-AATTTTCTTACGGCTTTATAAAATTTTATATAT
1 TTTTTATAAATTTT-TTATGATTTTATATATTTTTACA-AT
* *
12639917 TTTTTATATATTTCTATAT-ATTTTATATATTTTTACAAT
1 TTTTTATAAATTT-TTTATGATTTTATATATTTTTACAAT
*
12639956 TTTTTATAAATTTTTTATGATTTTATATTTTTTT
1 TTTTTATAAATTTTTTATGATTTTATATATTTTT
12639990 CTAAATTTTA
Statistics
Matches: 87, Mismatches: 19, Indels: 14
0.73 0.16 0.12
Matches are distributed among these distances:
38 18 0.21
39 40 0.46
40 22 0.25
41 6 0.07
42 1 0.01
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (39 bp):
TTTTTATAAATTTTTTATGATTTTATATATTTTTACAAT
Found at i:12642554 original size:21 final size:21
Alignment explanation
Indices: 12642528--12642569 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
12642518 ATCAACTCAA
12642528 CTAAATCCCAATTCTTATTGT
1 CTAAATCCCAATTCTTATTGT
12642549 CTAAATCCCAATTCTTATTGT
1 CTAAATCCCAATTCTTATTGT
12642570 ATACATATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.24, G:0.05, T:0.43
Consensus pattern (21 bp):
CTAAATCCCAATTCTTATTGT
Found at i:12645864 original size:19 final size:20
Alignment explanation
Indices: 12645813--12645872 Score: 63
Period size: 19 Copynumber: 3.0 Consensus size: 20
12645803 AATAATAATG
12645813 AAAATA-TTT-TTATTTTAT
1 AAAATATTTTATTATTTTAT
*
12645831 AAAATAAATTATATTATTTTA-
1 AAAAT--ATTTTATTATTTTAT
*
12645852 AAAATATTTTATTGTTTTAT
1 AAAATATTTTATTATTTTAT
12645872 A
1 A
12645873 TTTTTTTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
18 5 0.15
19 12 0.35
20 2 0.06
21 7 0.21
22 8 0.24
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
AAAATATTTTATTATTTTAT
Found at i:12651248 original size:22 final size:22
Alignment explanation
Indices: 12651223--12651268 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
12651213 ATCATTTTAG
12651223 TTAAAGCTGATTTAGTTGGACA
1 TTAAAGCTGATTTAGTTGGACA
12651245 TTAAAGCTGATTTAGTTGGACA
1 TTAAAGCTGATTTAGTTGGACA
12651267 TT
1 TT
12651269 TTCTTTCTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.39
Consensus pattern (22 bp):
TTAAAGCTGATTTAGTTGGACA
Found at i:12658210 original size:72 final size:72
Alignment explanation
Indices: 12658120--12658265 Score: 274
Period size: 72 Copynumber: 2.0 Consensus size: 72
12658110 GCCAGTAAGC
* *
12658120 TTCAGATTCAAGTATTGTTGGTTGTTGGAAGAAAAATTACGGCCTTTAAAGCTCTCCTTTGCCAT
1 TTCAGATTCAAGTATTGTTGGTCGTCGGAAGAAAAATTACGGCCTTTAAAGCTCTCCTTTGCCAT
12658185 CTCCTTA
66 CTCCTTA
12658192 TTCAGATTCAAGTATTGTTGGTCGTCGGAAGAAAAATTACGGCCTTTAAAGCTCTCCTTTGCCAT
1 TTCAGATTCAAGTATTGTTGGTCGTCGGAAGAAAAATTACGGCCTTTAAAGCTCTCCTTTGCCAT
12658257 CTCCTTA
66 CTCCTTA
12658264 TT
1 TT
12658266 TTTCTTCATC
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.37
Consensus pattern (72 bp):
TTCAGATTCAAGTATTGTTGGTCGTCGGAAGAAAAATTACGGCCTTTAAAGCTCTCCTTTGCCAT
CTCCTTA
Found at i:12660004 original size:42 final size:41
Alignment explanation
Indices: 12659928--12660006 Score: 97
Period size: 42 Copynumber: 1.9 Consensus size: 41
12659918 GAATAGCTGC
* *
12659928 TTTTACTAATTTGTTACATATAAATTATTGAATTATTGACT
1 TTTTACTAATTCGTTACATATAAATTAGTGAATTATTGACT
**
12659969 TTTTACTAATTCCGTTTTATATAAATT-GTGAAATTATT
1 TTTTACTAATT-CGTTACATATAAATTAGTG-AATTATT
12660007 AATTTTCATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
41 13 0.41
42 19 0.59
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.52
Consensus pattern (41 bp):
TTTTACTAATTCGTTACATATAAATTAGTGAATTATTGACT
Found at i:12670002 original size:39 final size:39
Alignment explanation
Indices: 12669959--12670137 Score: 250
Period size: 39 Copynumber: 4.6 Consensus size: 39
12669949 GCTTTGGTGA
12669959 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTCTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTCTGT
* * *
12669998 GCTTCAGTCAGCTTTCGGGCTTCTGTTTAGCACTTCTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTCTGT
* * *
12670037 GCTTCAGTCAGCCTTCGGGCTTCCATTTAGCACTTGTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTCTGT
* * *
12670076 GCTTCAGTTAGCCTCCAGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTCTGT
* **
12670115 GCTTCAGCTAAACTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
12670138 AGATCACGAA
Statistics
Matches: 123, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 123 1.00
ACGTcount: A:0.13, C:0.28, G:0.22, T:0.37
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTCTGT
Found at i:12671676 original size:20 final size:20
Alignment explanation
Indices: 12671631--12671696 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
12671621 AAATTTACCT
* **
12671631 AGTATCAATACCTATAAAAA
1 AGTATCAATACCTTTAATCA
*
12671651 ATTATCAATACCTTTAATCA
1 AGTATCAATACCTTTAATCA
** *
12671671 AGTATCAATAAATTTCATCA
1 AGTATCAATACCTTTAATCA
12671691 AGTATC
1 AGTATC
12671697 GATGTAAAGA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (20 bp):
AGTATCAATACCTTTAATCA
Found at i:12674124 original size:25 final size:25
Alignment explanation
Indices: 12674094--12674144 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
12674084 AACCCTTAAG
12674094 AGAAAACTCAAGAAAACTAAGGCGA
1 AGAAAACTCAAGAAAACTAAGGCGA
12674119 AGAAAACTCAAGAAAACTAAGGCGA
1 AGAAAACTCAAGAAAACTAAGGCGA
12674144 A
1 A
12674145 AACTAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.57, C:0.16, G:0.20, T:0.08
Consensus pattern (25 bp):
AGAAAACTCAAGAAAACTAAGGCGA
Found at i:12678221 original size:29 final size:30
Alignment explanation
Indices: 12678174--12678241 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
12678164 TGGCCCAAGA
* *
12678174 GTAAATACTCAAAATTTGAAGGATTAA-AGT
1 GTAAATA-TCAAAAGTTGAAGGACTAATAGT
*
12678204 GTAAATATGAAAAGTTGAAGGACTAATAGT
1 GTAAATATCAAAAGTTGAAGGACTAATAGT
*
12678234 GCAAATAT
1 GTAAATAT
12678242 TTTAAGGGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (30 bp):
GTAAATATCAAAAGTTGAAGGACTAATAGT
Found at i:12680421 original size:46 final size:46
Alignment explanation
Indices: 12680371--12680648 Score: 346
Period size: 46 Copynumber: 6.0 Consensus size: 46
12680361 GTGTGCTCTC
* * *
12680371 TGATATGAAATGTGTAAGACCATAGTTGAAAGAAACCATGGCAATC-
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAA-CA
* * *
12680417 TGATATGAAATGTGTAAGACTATGGTTGAAAGATACCATGGCAACC
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
*
12680463 TGATATGAAAT-ATGTAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGA-GTAAGACCATGGTTGAAAGATACCATGGCAACA
*
12680509 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
*** * *
12680555 TGACGGGAAATGAATAAGACCATGGTTGAAAGATACCAGGGCAACA
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
* * * * *
12680601 TGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCA
1 TGATATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
12680647 TG
1 TG
12680649 TCAAAGATAA
Statistics
Matches: 209, Mismatches: 19, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
45 2 0.01
46 206 0.99
47 1 0.00
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.22
Consensus pattern (46 bp):
TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
Found at i:12680950 original size:16 final size:17
Alignment explanation
Indices: 12680929--12680961 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
12680919 ATGATGGAGC
12680929 ATGAAAT-ATTGATATA
1 ATGAAATAATTGATATA
12680945 ATGAAATAATTGATATA
1 ATGAAATAATTGATATA
12680962 TACTTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (17 bp):
ATGAAATAATTGATATA
Found at i:12684505 original size:6 final size:6
Alignment explanation
Indices: 12684494--12684521 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
12684484 AGTGACTTTT
12684494 TTATAA TTATAA TTATAA TTATAA TTAT
1 TTATAA TTATAA TTATAA TTATAA TTAT
12684522 TATGTTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTATAA
Found at i:12684882 original size:34 final size:34
Alignment explanation
Indices: 12684844--12684912 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
12684834 AGTGGAGGGG
12684844 TTTGAATGGAGTTTAGGGAAACTTTGAGGGTTGT
1 TTTGAATGGAGTTTAGGGAAACTTTGAGGGTTGT
12684878 TTTGAATGGAGTTTAGGGAAACTTTGAGGGTTGT
1 TTTGAATGGAGTTTAGGGAAACTTTGAGGGTTGT
12684912 T
1 T
12684913 CTGCAAGCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.23, C:0.03, G:0.35, T:0.39
Consensus pattern (34 bp):
TTTGAATGGAGTTTAGGGAAACTTTGAGGGTTGT
Found at i:12686428 original size:37 final size:37
Alignment explanation
Indices: 12686387--12686465 Score: 149
Period size: 37 Copynumber: 2.1 Consensus size: 37
12686377 GGGCACCTAG
12686387 AGAAAACACACAGAGTAGGAGGCAAGGAATTACTCGA
1 AGAAAACACACAGAGTAGGAGGCAAGGAATTACTCGA
*
12686424 AGAAAACACACGGAGTAGGAGGCAAGGAATTACTCGA
1 AGAAAACACACAGAGTAGGAGGCAAGGAATTACTCGA
12686461 AGAAA
1 AGAAA
12686466 GCCGATTGAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.47, C:0.15, G:0.28, T:0.10
Consensus pattern (37 bp):
AGAAAACACACAGAGTAGGAGGCAAGGAATTACTCGA
Found at i:12689561 original size:25 final size:26
Alignment explanation
Indices: 12689533--12689586 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 26
12689523 CAATTAGTAT
*
12689533 AAAATATT-AATAATTCAATA-AATTG
1 AAAA-ATTAAATAATTAAATAGAATTG
12689558 AAAAATTAAATAATTAAATAGAATTG
1 AAAAATTAAATAATTAAATAGAATTG
12689584 AAA
1 AAA
12689587 TTTAGGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 3 0.12
25 15 0.58
26 8 0.31
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (26 bp):
AAAAATTAAATAATTAAATAGAATTG
Found at i:12690295 original size:16 final size:15
Alignment explanation
Indices: 12690270--12690303 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
12690260 AAAGTTGATA
*
12690270 ATAATTAATATACATT
1 ATAATAAATATA-ATT
12690286 ATAATAAATATAATT
1 ATAATAAATATAATT
12690301 ATA
1 ATA
12690304 TATAGTTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:12713473 original size:17 final size:17
Alignment explanation
Indices: 12713453--12713485 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
12713443 ATTAAGAATG
12713453 TTATTAAATTATATTTT
1 TTATTAAATTATATTTT
12713470 TTATTAAATTATATTT
1 TTATTAAATTATATTT
12713486 AATACTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTATTAAATTATATTTT
Found at i:12713536 original size:58 final size:54
Alignment explanation
Indices: 12713430--12713560 Score: 140
Period size: 58 Copynumber: 2.3 Consensus size: 54
12713420 TTAATTCATA
* *
12713430 TAATAATAATTATATTAAGAATGTTATTAAATTATATTTTTTATTAAATTATATT
1 TAATAATAATTATATTAAGAATATGATTAAATTATATTTTTTATTAAATTAT-TT
* *
12713485 TAATACTAATTATGTTAA-AATATGATTAAATTATTTATTATTTTTATTAAATTATTT
1 TAATAATAATTATATTAAGAATATGATTAAATTA--TA-T-TTTTTATTAAATTATTT
*
12713542 TCAATAGTAATCT-TATTAA
1 T-AATAATAAT-TATATTAA
12713561 AATTTAATAA
Statistics
Matches: 64, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
54 13 0.20
55 16 0.25
56 2 0.03
57 4 0.06
58 28 0.44
59 1 0.02
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (54 bp):
TAATAATAATTATATTAAGAATATGATTAAATTATATTTTTTATTAAATTATTT
Found at i:12718867 original size:15 final size:15
Alignment explanation
Indices: 12718847--12718882 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
12718837 TCTTCTTTTT
* *
12718847 TTCTTCATCCTCTTC
1 TTCTTCATCATCGTC
12718862 TTCTTCATCATCGTC
1 TTCTTCATCATCGTC
12718877 TTCTTC
1 TTCTTC
12718883 TTCTCCTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.08, C:0.36, G:0.03, T:0.53
Consensus pattern (15 bp):
TTCTTCATCATCGTC
Found at i:12718878 original size:18 final size:18
Alignment explanation
Indices: 12718851--12718885 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
12718841 CTTTTTTTCT
12718851 TCATCCTCTTCTTCTTCA
1 TCATCCTCTTCTTCTTCA
*
12718869 TCATCGTCTTCTTCTTC
1 TCATCCTCTTCTTCTTC
12718886 TCCTTCTGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.09, C:0.37, G:0.03, T:0.51
Consensus pattern (18 bp):
TCATCCTCTTCTTCTTCA
Found at i:12722268 original size:22 final size:21
Alignment explanation
Indices: 12722250--12722287 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12722240 TGTTTTCATA
12722250 ATATTTT-TA-AATTTATTTC
1 ATATTTTGTATAATTTATTTC
12722269 ATATTTTGTATAATTTATT
1 ATATTTTGTATAATTTATT
12722288 ATATTTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 2 0.12
21 8 0.47
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (21 bp):
ATATTTTGTATAATTTATTTC
Done.