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 350 of 378
Found at i:105309890 original size:35 final size:36
Alignment explanation
Indices: 105309827--105309963 Score: 190
Period size: 35 Copynumber: 3.8 Consensus size: 36
105309817 CAATGATATG
*
105309827 CAATCTTAAATATGATATGCAATCTTAGATATGATA
1 CAATCTTAGATATGATATGCAATCTTAGATATGATA
105309863 CAATCTTAGATATGAT-TGCAATCTTAGATATGATA
1 CAATCTTAGATATGATATGCAATCTTAGATATGATA
* * *
105309898 TGTAATCTTAGATATGATAT--AATCTTAGATATAATTG
1 --CAATCTTAGATATGATATGCAATCTTAGATATGA-TA
105309935 CAATCTTAGATATGATATGCAATCTTAGA
1 CAATCTTAGATATGATATGCAATCTTAGA
105309964 AGATATGATT
Statistics
Matches: 90, Mismatches: 5, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
35 36 0.40
36 28 0.31
37 25 0.28
38 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (36 bp):
CAATCTTAGATATGATATGCAATCTTAGATATGATA
Found at i:105309913 original size:14 final size:15
Alignment explanation
Indices: 105309847--105309951 Score: 75
Period size: 17 Copynumber: 6.1 Consensus size: 15
105309837 TATGATATGC
105309847 AATCTTAGATATGAT
1 AATCTTAGATATGAT
105309862 ACAATCTTAGATATGATT
1 --AATCTTAGATATGA-T
105309880 GCAATCTTAGATATGATATGT
1 --AATCTTAGATATG--A--T
105309901 AATCTTAGATATGATAT
1 AATCTTAGATATG--AT
*
105309918 AATCTTAGATATAATT
1 AATCTTAGATATGA-T
105309934 GCAATCTTAGATATGAT
1 --AATCTTAGATATGAT
105309951 A
1 A
105309952 TGCAATCTTA
Statistics
Matches: 77, Mismatches: 4, Indels: 16
0.79 0.04 0.16
Matches are distributed among these distances:
15 2 0.03
16 1 0.01
17 28 0.36
18 28 0.36
19 16 0.21
20 1 0.01
21 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (15 bp):
AATCTTAGATATGAT
Found at i:105309956 original size:73 final size:73
Alignment explanation
Indices: 105309819--105309986 Score: 223
Period size: 73 Copynumber: 2.2 Consensus size: 73
105309809 ATAATCTTCA
* * *
105309819 ATGATATGCAATCTTAAATATGATATGCAATCTTAGATATGATACAATCTTAGATATGATTGCAA
1 ATGATATGTAATCTTAGATATGATAT-CAATCTTAGATATAATACAATCTTAGATATGATTGCAA
105309884 TCTT-AGAT
65 TCTTAAGAT
*
105309892 ATGATATGTAATCTTAGATATGATAT-AATCTTAGATATAATTGCAATCTTAGATATGATATGCA
1 ATGATATGTAATCTTAGATATGATATCAATCTTAGATATAA-TACAATCTTAGATATGAT-TGCA
105309956 ATCTTAGAAGAT
64 ATCTT--AAGAT
*
105309968 ATGATTTTGTAATCTTAGA
1 ATGA-TATGTAATCTTAGA
105309987 GATTTAATTT
Statistics
Matches: 84, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
71 13 0.15
72 17 0.20
73 33 0.39
76 8 0.10
77 13 0.15
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (73 bp):
ATGATATGTAATCTTAGATATGATATCAATCTTAGATATAATACAATCTTAGATATGATTGCAAT
CTTAAGAT
Found at i:105309989 original size:22 final size:22
Alignment explanation
Indices: 105309819--105309986 Score: 102
Period size: 19 Copynumber: 8.8 Consensus size: 22
105309809 ATAATCTTCA
105309819 ATGATATGCAATCTT--AA-AT
1 ATGATATGCAATCTTAGAAGAT
105309838 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
105309857 ATGATA--CAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
105309874 ATGAT-TGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
*
105309892 ATGATATGTAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
105309911 ATGATAT--AATCTTAG---AT
1 ATGATATGCAATCTTAGAAGAT
*
105309928 ATAAT-TGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
105309946 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
105309968 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
105309987 GATTTAATTT
Statistics
Matches: 129, Mismatches: 5, Indels: 26
0.81 0.03 0.16
Matches are distributed among these distances:
16 1 0.01
17 28 0.22
18 29 0.22
19 51 0.40
22 8 0.06
23 12 0.09
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:105310277 original size:18 final size:19
Alignment explanation
Indices: 105310254--105310289 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
105310244 GTTTCCCTGT
*
105310254 TTTTTTTATAT-ATTTTAA
1 TTTTTTTAAATAATTTTAA
105310272 TTTTTTTAAATAATTTTA
1 TTTTTTTAAATAATTTTA
105310290 GTATTATATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTTTTAAATAATTTTAA
Found at i:105311529 original size:22 final size:23
Alignment explanation
Indices: 105311481--105311529 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
105311471 GTAGCTTTTT
*
105311481 TATTTCTTTTAGGTTTGTCTTAC
1 TATTTCTTTTAGGTTTGCCTTAC
*
105311504 TATTT-TTTTAGTTTTAGCCTTA-
1 TATTTCTTTTAGGTTT-GCCTTAC
105311526 TATT
1 TATT
105311530 ATGCTGAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.16, C:0.10, G:0.10, T:0.63
Consensus pattern (23 bp):
TATTTCTTTTAGGTTTGCCTTAC
Found at i:105314104 original size:20 final size:20
Alignment explanation
Indices: 105314079--105314118 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
105314069 TAAATTTAGG
105314079 ATTTATATT-TATTTATCTTT
1 ATTTAT-TTGTATTTATCTTT
105314099 ATTTATTTGTATTTATCTTT
1 ATTTATTTGTATTTATCTTT
105314119 TAGAATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.70
Consensus pattern (20 bp):
ATTTATTTGTATTTATCTTT
Found at i:105316588 original size:12 final size:12
Alignment explanation
Indices: 105316573--105316602 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
105316563 ATCTTGGCCG
*
105316573 AGAAAACGCCTA
1 AGAAAACGCCCA
105316585 AGAAAACGCCCA
1 AGAAAACGCCCA
105316597 AGAAAA
1 AGAAAA
105316603 TCCTGAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.57, C:0.23, G:0.17, T:0.03
Consensus pattern (12 bp):
AGAAAACGCCCA
Found at i:105319491 original size:10 final size:10
Alignment explanation
Indices: 105319476--105319524 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
105319466 TAAATTTAGG
*
105319476 ATTTATATTT
1 ATTTATCTTT
105319486 ATTTATCTTT
1 ATTTATCTTT
*
105319496 AATTATCTTT
1 ATTTATCTTT
105319506 A-TTAT-TTGT
1 ATTTATCTT-T
105319515 ATTTATCTTT
1 ATTTATCTTT
105319525 TAGAATTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
8 2 0.06
9 6 0.18
10 24 0.71
11 2 0.06
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.67
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:105343484 original size:44 final size:44
Alignment explanation
Indices: 105343416--105343506 Score: 130
Period size: 44 Copynumber: 2.1 Consensus size: 44
105343406 AACTCTGTTT
* *
105343416 TTAGTTTCCCACTTAAACTTTAATTCA-TGTAGGTTATTTTAATA
1 TTAGTTTCCCACTTAAACTCTAATT-AGTATAGGTTATTTTAATA
* *
105343460 TTAGTTTCCTATTTAAACTCTAATTAGTATAGGTTATTTTAATA
1 TTAGTTTCCCACTTAAACTCTAATTAGTATAGGTTATTTTAATA
105343504 TTA
1 TTA
105343507 TTTGACCTAC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
43 1 0.02
44 41 0.98
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.49
Consensus pattern (44 bp):
TTAGTTTCCCACTTAAACTCTAATTAGTATAGGTTATTTTAATA
Found at i:105346540 original size:46 final size:44
Alignment explanation
Indices: 105346436--105346543 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
105346426 TGTCTTTGAC
** * * *
105346436 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
105346480 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
105346526 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
105346544 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:105352668 original size:46 final size:44
Alignment explanation
Indices: 105352564--105352671 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
105352554 TGTCTTTGAC
** * * *
105352564 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
105352608 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
105352654 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
105352672 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:105357715 original size:28 final size:27
Alignment explanation
Indices: 105357669--105357730 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
105357659 TGATATTATA
105357669 TAGATCAAGAAAAACAAAGT-TTGGATC
1 TAGATCAAGAAAAACAAAGTATTGGA-C
* *
105357696 TAGATCGAGGAAAAATAAAGTATTGGAC
1 TAGATC-AAGAAAAACAAAGTATTGGAC
105357724 TAG-TCAA
1 TAGATCAA
105357731 AACATTTCGT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
26 1 0.03
27 8 0.27
28 16 0.53
29 5 0.17
ACGTcount: A:0.47, C:0.10, G:0.21, T:0.23
Consensus pattern (27 bp):
TAGATCAAGAAAAACAAAGTATTGGAC
Found at i:105359482 original size:4 final size:4
Alignment explanation
Indices: 105359473--105359531 Score: 118
Period size: 4 Copynumber: 14.8 Consensus size: 4
105359463 GTGTGAAACA
105359473 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
105359521 TATG TATG TAT
1 TATG TATG TAT
105359532 CAATTCAGGG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 55 1.00
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:105360075 original size:6 final size:6
Alignment explanation
Indices: 105360059--105360094 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
105360049 AATAAGAGAT
105360059 AAAAT- AAAATA AAAATA AAAATA AAAATA AAAATA A
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA A
105360095 TAGTAAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:105360087 original size:18 final size:17
Alignment explanation
Indices: 105360042--105360104 Score: 67
Period size: 17 Copynumber: 3.7 Consensus size: 17
105360032 ATAAGTCTTC
*
105360042 AAAAAT-AAATAAGAGAT
1 AAAAATAAAATAA-AAAT
105360059 -AAAATAAAATAAAAAT
1 AAAAATAAAATAAAAAT
105360075 AAAAATAAAAATAAAAAT
1 AAAAAT-AAAATAAAAAT
* *
105360093 AATAGTAAAATA
1 AAAAATAAAATA
105360105 TAGGAACTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
16 8 0.20
17 17 0.43
18 15 0.38
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (17 bp):
AAAAATAAAATAAAAAT
Found at i:105361733 original size:20 final size:20
Alignment explanation
Indices: 105361687--105361733 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
105361677 ACTCCAAATC
* *
105361687 AAAATAATAAACATAAATGA
1 AAAAAAATAAACAAAAATGA
*
105361707 AAGAAAATAAACAAAAAT-A
1 AAAAAAATAAACAAAAATGA
105361726 AATAAAAA
1 AA-AAAAA
105361734 ACAAAATAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.15
Consensus pattern (20 bp):
AAAAAAATAAACAAAAATGA
Found at i:105361737 original size:17 final size:18
Alignment explanation
Indices: 105361688--105361749 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
105361678 CTCCAAATCA
*
105361688 AAATAATAAACATAAAT-G
1 AAATAAAAAACA-AAATAG
* *
105361706 AAAGAAAATAAACAAAA-AT
1 AAA-TAAA-AAACAAAATAG
105361725 AAATAAAAAACAAAATAG
1 AAATAAAAAACAAAATAG
105361743 AAATAAA
1 AAATAAA
105361750 GTGAAAAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
17 8 0.23
18 14 0.40
19 8 0.23
20 5 0.14
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.15
Consensus pattern (18 bp):
AAATAAAAAACAAAATAG
Found at i:105361748 original size:22 final size:23
Alignment explanation
Indices: 105361721--105361763 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
105361711 AAATAAACAA
105361721 AAATAAA-TAAAAAACAAAATAG
1 AAATAAAGTAAAAAACAAAATAG
* *
105361743 AAATAAAGTGAAAAATAAAAT
1 AAATAAAGTAAAAAACAAAAT
105361764 TTAAGAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.16
Consensus pattern (23 bp):
AAATAAAGTAAAAAACAAAATAG
Found at i:105375972 original size:28 final size:28
Alignment explanation
Indices: 105375932--105375986 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
105375922 TGAGCTCCTT
105375932 GAGCTCAGTGTGAGATCAAAACTATCTC
1 GAGCTCAGTGTGAGATCAAAACTATCTC
105375960 GAGCTCAGTGTGAGATCAAAACTATCT
1 GAGCTCAGTGTGAGATCAAAACTATCT
105375987 AACTACAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (28 bp):
GAGCTCAGTGTGAGATCAAAACTATCTC
Found at i:105378050 original size:16 final size:16
Alignment explanation
Indices: 105378031--105378065 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
105378021 CATGGAAAAG
105378031 AAAAGAAAAAATAATA
1 AAAAGAAAAAATAATA
* *
105378047 AAAATAAAATATAATA
1 AAAAGAAAAAATAATA
105378063 AAA
1 AAA
105378066 TAAATTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (16 bp):
AAAAGAAAAAATAATA
Found at i:105393460 original size:31 final size:31
Alignment explanation
Indices: 105393422--105393485 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
105393412 TTGCACACAT
105393422 GGGCGTGGGAGAAGCGAACGAAGCTAGACAC
1 GGGCGTGGGAGAAGCGAACGAAGCTAGACAC
*
105393453 GGGCGTGGGAGAAGTGAACGAAGCTAGACAC
1 GGGCGTGGGAGAAGCGAACGAAGCTAGACAC
105393484 GG
1 GG
105393486 TTGTGCGGCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.31, C:0.17, G:0.44, T:0.08
Consensus pattern (31 bp):
GGGCGTGGGAGAAGCGAACGAAGCTAGACAC
Found at i:105397468 original size:13 final size:13
Alignment explanation
Indices: 105397450--105397475 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
105397440 AAGTAATAAT
105397450 ACACGGGCGTGTC
1 ACACGGGCGTGTC
105397463 ACACGGGCGTGTC
1 ACACGGGCGTGTC
105397476 CCTGCCGAGC
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:0.15, C:0.31, G:0.38, T:0.15
Consensus pattern (13 bp):
ACACGGGCGTGTC
Found at i:105397721 original size:25 final size:26
Alignment explanation
Indices: 105397693--105397741 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
105397683 TCTCATCCCA
105397693 ATTTTA-CCCTAATAAAATTTTGACG
1 ATTTTATCCCTAATAAAATTTTGACG
**
105397718 ATTTTATCCCTGGTAAAATTTTGA
1 ATTTTATCCCTAATAAAATTTTGA
105397742 GAAAGTTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (26 bp):
ATTTTATCCCTAATAAAATTTTGACG
Found at i:105402120 original size:16 final size:16
Alignment explanation
Indices: 105402099--105402129 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
105402089 GTACCCAACG
105402099 GAAGAAAATATAAGGT
1 GAAGAAAATATAAGGT
*
105402115 GAAGAAAATGTAAGG
1 GAAGAAAATATAAGG
105402130 ATCATACCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.29, T:0.16
Consensus pattern (16 bp):
GAAGAAAATATAAGGT
Found at i:105403884 original size:24 final size:25
Alignment explanation
Indices: 105403852--105403912 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 25
105403842 CACCACAACT
105403852 CTTACGAGCATCCCATTATAAGG-C
1 CTTACGAGCATCCCATTATAAGGTC
* * *
105403876 CTTACGAGCTTCCTATTATATGGTTC
1 CTTACGAGCATCCCATTATAAGG-TC
105403902 C-TACGAGCATC
1 CTTACGAGCATC
105403913 TTGATCGGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
24 20 0.65
25 9 0.29
26 2 0.06
ACGTcount: A:0.25, C:0.28, G:0.16, T:0.31
Consensus pattern (25 bp):
CTTACGAGCATCCCATTATAAGGTC
Found at i:105404241 original size:26 final size:26
Alignment explanation
Indices: 105404176--105404241 Score: 61
Period size: 26 Copynumber: 2.7 Consensus size: 26
105404166 AGCCCAGATA
105404176 AGCTTCCTG--ATA-GGCTTTTTGTG
1 AGCTTCCTGTTATATGGCTTTTTGTG
* *
105404199 AGCTACCCGATTA-ATGGCTCTTTT-TG
1 AGCTTCCTG-TTATATGGCT-TTTTGTG
105404225 AGCTTCCTGTTATATGG
1 AGCTTCCTGTTATATGG
105404242 TTGAGAGAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
23 7 0.21
25 4 0.12
26 18 0.55
27 4 0.12
ACGTcount: A:0.17, C:0.20, G:0.23, T:0.41
Consensus pattern (26 bp):
AGCTTCCTGTTATATGGCTTTTTGTG
Found at i:105406521 original size:38 final size:38
Alignment explanation
Indices: 105406470--105406549 Score: 160
Period size: 38 Copynumber: 2.1 Consensus size: 38
105406460 ACATAAGCAC
105406470 CAAGTAAGCATAGATGAGCTCATCATACTATATTCTTT
1 CAAGTAAGCATAGATGAGCTCATCATACTATATTCTTT
105406508 CAAGTAAGCATAGATGAGCTCATCATACTATATTCTTT
1 CAAGTAAGCATAGATGAGCTCATCATACTATATTCTTT
105406546 CAAG
1 CAAG
105406550 ACATCATTCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (38 bp):
CAAGTAAGCATAGATGAGCTCATCATACTATATTCTTT
Found at i:105424275 original size:17 final size:18
Alignment explanation
Indices: 105424255--105424289 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
105424245 TTCTTTTCAT
105424255 TTTGGT-TTTGCATGAGC
1 TTTGGTATTTGCATGAGC
105424272 TTTGGTAATTTGCATGAG
1 TTTGGT-ATTTGCATGAG
105424290 GTCGTGCAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
19 10 0.62
ACGTcount: A:0.17, C:0.09, G:0.29, T:0.46
Consensus pattern (18 bp):
TTTGGTATTTGCATGAGC
Found at i:105428071 original size:48 final size:48
Alignment explanation
Indices: 105427991--105428266 Score: 295
Period size: 48 Copynumber: 5.8 Consensus size: 48
105427981 TTTGGGTGAT
* * *
105427991 ATGAGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACAAC
1 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGAC
* * *
105428039 ATGAAAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGG-CATTGAT
1 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCA-CGAC
* * ***
105428087 ATGTGCA-CTAGTGTAAGACCATGTCTGAGACATGGCATCGGCCACCTT
1 ATGAG-AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGAC
* * * ** * *
105428135 ATGAGAGCCAATGTAAGACCATGTCTGGGACATGACATCGGTAATGAG
1 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGAC
* * *
105428183 ACGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCGAC
1 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGAC
* * * *
105428231 ATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGC
1 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGC
105428267 TTTGGCAATT
Statistics
Matches: 186, Mismatches: 38, Indels: 8
0.80 0.16 0.03
Matches are distributed among these distances:
47 3 0.02
48 180 0.97
49 3 0.02
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (48 bp):
ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGAC
Found at i:105428151 original size:96 final size:96
Alignment explanation
Indices: 105428000--105428275 Score: 347
Period size: 96 Copynumber: 2.9 Consensus size: 96
105427990 TATGAGTGCC
* *
105428000 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACAACATGAAAGCTAGTGTAAGACCATGTCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACAACATGAGAGCCAGTGTAAGACCATGTCT
* * * *
105428065 GGGACATGGCATCGGCATTGATATGTGCA-CT
66 GGGACATGGCATCGGCAATGAGACGAG-AGCT
* *** *
105428096 AGTGTAAGACCATGTCTGAGACATGGCATCGGCCACCTTATGAGAGCCAATGTAAGACCATGTCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACAACATGAGAGCCAGTGTAAGACCATGTCT
* *
105428161 GGGACATGACATCGGTAATGAGACGAGAGCT
66 GGGACATGGCATCGGCAATGAGACGAGAGCT
* * * * *
105428192 AGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCGACATGTGAGCCAGTGTAAGACCATGTTT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACAACATGAGAGCCAGTGTAAGACCATGTCT
* * *
105428257 GGAACATGGCTTTGGCAAT
66 GGGACATGGCATCGGCAAT
105428276 TCACCCTCTT
Statistics
Matches: 152, Mismatches: 27, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
95 1 0.01
96 151 0.99
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (96 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACAACATGAGAGCCAGTGTAAGACCATGTCT
GGGACATGGCATCGGCAATGAGACGAGAGCT
Found at i:105428266 original size:144 final size:144
Alignment explanation
Indices: 105427990--105428254 Score: 379
Period size: 144 Copynumber: 1.8 Consensus size: 144
105427980 ATTTGGGTGA
* * * * *
105427990 TATGAGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACAACATGAAAGCTAGTGTAA
1 TATGAGAGCCAATGTAAGACCATGTCTGGGACATGACATCGGCAACAACACGAAAGCTAGTGTAA
* * * *
105428055 GACCATGTCTGGGACATGGCATCGGCATTGATATGTGCACTAGTGTAAGACCATGTCTGAGACAT
66 GACCATGTCTGGGACATGGCATCAGCATCGACATGTGCACCAGTGTAAGACCATGTCTGAGACAT
105428120 GGCATCGGCCACCT
131 GGCATCGGCCACCT
* ** * *
105428134 TATGAGAGCCAATGTAAGACCATGTCTGGGACATGACATCGGTAATGAGACGAGAGCTAGTGTAA
1 TATGAGAGCCAATGTAAGACCATGTCTGGGACATGACATCGGCAACAACACGAAAGCTAGTGTAA
*
105428199 GACCATGTCTGGGACATGGCATCAGCCTCGACATGTG-AGCCAGTGTAAGACCATGT
66 GACCATGTCTGGGACATGGCATCAGCATCGACATGTGCA-CCAGTGTAAGACCATGT
105428255 TTGGAACATG
Statistics
Matches: 105, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
143 1 0.01
144 104 0.99
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.22
Consensus pattern (144 bp):
TATGAGAGCCAATGTAAGACCATGTCTGGGACATGACATCGGCAACAACACGAAAGCTAGTGTAA
GACCATGTCTGGGACATGGCATCAGCATCGACATGTGCACCAGTGTAAGACCATGTCTGAGACAT
GGCATCGGCCACCT
Found at i:105429711 original size:55 final size:55
Alignment explanation
Indices: 105429627--105429733 Score: 205
Period size: 55 Copynumber: 1.9 Consensus size: 55
105429617 TTATAGATTT
*
105429627 CAAATTAATTATTCATGAGCACTATTCAAATTAAAAGTGATGATTTATCATCTTG
1 CAAATTAATTATTCATAAGCACTATTCAAATTAAAAGTGATGATTTATCATCTTG
105429682 CAAATTAATTATTCATAAGCACTATTCAAATTAAAAGTGATGATTTATCATC
1 CAAATTAATTATTCATAAGCACTATTCAAATTAAAAGTGATGATTTATCATC
105429734 CAATGGATAC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.37
Consensus pattern (55 bp):
CAAATTAATTATTCATAAGCACTATTCAAATTAAAAGTGATGATTTATCATCTTG
Found at i:105429715 original size:26 final size:26
Alignment explanation
Indices: 105429625--105429715 Score: 69
Period size: 26 Copynumber: 3.4 Consensus size: 26
105429615 AATTATAGAT
*
105429625 TTCAAATTAATTATTCATGAGCACTA
1 TTCAAATTAATTATTCATAAGCACTA
* * * *
105429651 TTCAAATTAA-AAGTGATGATTTATCATCT-
1 TTCAAATTAATTA-T--TCA-TAAGCA-CTA
*
105429680 TGCAAATTAATTATTCATAAGCACTA
1 TTCAAATTAATTATTCATAAGCACTA
105429706 TTCAAATTAA
1 TTCAAATTAA
105429716 AAGTGATGAT
Statistics
Matches: 48, Mismatches: 10, Indels: 14
0.67 0.14 0.19
Matches are distributed among these distances:
25 3 0.06
26 24 0.50
27 2 0.04
28 2 0.04
29 14 0.29
30 3 0.06
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.38
Consensus pattern (26 bp):
TTCAAATTAATTATTCATAAGCACTA
Found at i:105433080 original size:16 final size:17
Alignment explanation
Indices: 105433040--105433080 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
105433030 AAACCGGATG
*
105433040 ATCTGATTGTTTGACAT
1 ATCTGATTGTTGGACAT
105433057 ATCTGATTGTTGGACAT
1 ATCTGATTGTTGGACAT
105433074 A-CTGATT
1 ATCTGATT
105433081 TGATTAGGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 6 0.26
17 17 0.74
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.44
Consensus pattern (17 bp):
ATCTGATTGTTGGACAT
Found at i:105439716 original size:8 final size:8
Alignment explanation
Indices: 105439703--105439739 Score: 65
Period size: 8 Copynumber: 4.6 Consensus size: 8
105439693 GAAATACCGA
*
105439703 CTTTTCGG
1 CTTTTCAG
105439711 CTTTTCAG
1 CTTTTCAG
105439719 CTTTTCAG
1 CTTTTCAG
105439727 CTTTTCAG
1 CTTTTCAG
105439735 CTTTT
1 CTTTT
105439740 GTCGATCTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.08, C:0.24, G:0.14, T:0.54
Consensus pattern (8 bp):
CTTTTCAG
Found at i:105449534 original size:17 final size:18
Alignment explanation
Indices: 105449508--105449576 Score: 74
Period size: 17 Copynumber: 4.1 Consensus size: 18
105449498 TCGCAGAGAG
*
105449508 TAACAGTTCATATGAA-A
1 TAACAGTTCATATCAATA
*
105449525 TAATAGTTCATA-CAATA
1 TAACAGTTCATATCAATA
*
105449542 TAACAGTTCATAT-AACA
1 TAACAGTTCATATCAATA
*
105449559 TAACATTTCATA-CAATA
1 TAACAGTTCATATCAATA
105449576 T
1 T
105449577 CATAACTCAT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
16 2 0.05
17 41 0.95
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.33
Consensus pattern (18 bp):
TAACAGTTCATATCAATA
Found at i:105449551 original size:34 final size:34
Alignment explanation
Indices: 105449508--105449576 Score: 104
Period size: 34 Copynumber: 2.0 Consensus size: 34
105449498 TCGCAGAGAG
*
105449508 TAACAGTTCATATGAA-ATAATAGTTCATACAATA
1 TAACAGTTCATAT-AACATAACAGTTCATACAATA
*
105449542 TAACAGTTCATATAACATAACATTTCATACAATA
1 TAACAGTTCATATAACATAACAGTTCATACAATA
105449576 T
1 T
105449577 CATAACTCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 2 0.06
34 30 0.94
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.33
Consensus pattern (34 bp):
TAACAGTTCATATAACATAACAGTTCATACAATA
Found at i:105449995 original size:14 final size:14
Alignment explanation
Indices: 105449978--105450021 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
105449968 GCATAATTTG
*
105449978 CAATTCATAATTCA
1 CAATTCATAGTTCA
*
105449992 CAATATCACAGTTCA
1 CAAT-TCATAGTTCA
105450007 CAATTCATAGTTCA
1 CAATTCATAGTTCA
105450021 C
1 C
105450022 CTTAGCACAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.39, C:0.25, G:0.05, T:0.32
Consensus pattern (14 bp):
CAATTCATAGTTCA
Found at i:105450030 original size:29 final size:29
Alignment explanation
Indices: 105449978--105450040 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 29
105449968 GCATAATTTG
* *
105449978 CAATTCATAATTCACAATATCACAGTTCA
1 CAATTCATAATTCACAATAGCACAATTCA
* ** *
105450007 CAATTCATAGTTCACCTTAGCACAATTCT
1 CAATTCATAATTCACAATAGCACAATTCA
105450036 CAATT
1 CAATT
105450041 TAACAAAATT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (29 bp):
CAATTCATAATTCACAATAGCACAATTCA
Found at i:105450311 original size:17 final size:17
Alignment explanation
Indices: 105450288--105450333 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
105450278 ATAGTTCGTC
*
105450288 ATATAACACAATTCACA
1 ATATAACACAATACACA
* * *
105450305 GTATAACACAGTACATA
1 ATATAACACAATACACA
105450322 ATATAACACAAT
1 ATATAACACAAT
105450334 GTAGTTTGCA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.52, C:0.20, G:0.04, T:0.24
Consensus pattern (17 bp):
ATATAACACAATACACA
Found at i:105450454 original size:17 final size:17
Alignment explanation
Indices: 105450401--105450484 Score: 69
Period size: 17 Copynumber: 4.8 Consensus size: 17
105450391 TCGCACACTA
105450401 GTAAGGTTCGCACTATG
1 GTAAGGTTCGCACTATG
* * * * *
105450418 GTATGGCTGGCACAACG
1 GTAAGGTTCGCACTATG
*
105450435 GTAAGGTTCACACTATG
1 GTAAGGTTCGCACTATG
* *
105450452 GTAGGGGTTAGCACTATAG
1 GTA-AGGTTCGCACTAT-G
*
105450471 GTAGGGTTCGCACT
1 GTAAGGTTCGCACT
105450485 TTAGGTAGGA
Statistics
Matches: 50, Mismatches: 15, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
17 26 0.52
18 20 0.40
19 4 0.08
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (17 bp):
GTAAGGTTCGCACTATG
Found at i:105450475 original size:19 final size:19
Alignment explanation
Indices: 105450445--105450493 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 19
105450435 GTAAGGTTCA
105450445 CACTAT-GGTAGGGGTTAG
1 CACTATAGGTAGGGGTTAG
*
105450463 CACTATAGGTA-GGGTTCG
1 CACTATAGGTAGGGGTTAG
*
105450481 CACTTTAGGTAGG
1 CACTATAGGTAGG
105450494 AGTTTGCACA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 22 0.81
19 5 0.19
ACGTcount: A:0.22, C:0.14, G:0.35, T:0.29
Consensus pattern (19 bp):
CACTATAGGTAGGGGTTAG
Found at i:105450785 original size:22 final size:22
Alignment explanation
Indices: 105450755--105450867 Score: 145
Period size: 22 Copynumber: 5.0 Consensus size: 22
105450745 AACATACAAA
*
105450755 GTTCGCATATCATTCAACATAG
1 GTTCACATATCATTCAACATAG
*
105450777 GTTCACATATCATTCAATATAG
1 GTTCACATATCATTCAACATAG
** * *
105450799 CATGTTCGTATATAATTCAACATAA
1 ---GTTCACATATCATTCAACATAG
105450824 GTTCACATATCATTCAACATAG
1 GTTCACATATCATTCAACATAG
105450846 GTTCACATATCATTCAACATAG
1 GTTCACATATCATTCAACATAG
105450868 CATGTTCGTA
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
22 60 0.78
25 17 0.22
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.34
Consensus pattern (22 bp):
GTTCACATATCATTCAACATAG
Found at i:105450817 original size:47 final size:47
Alignment explanation
Indices: 105450755--105450866 Score: 149
Period size: 47 Copynumber: 2.4 Consensus size: 47
105450745 AACATACAAA
* * *
105450755 GTTCGCATATCATTCAACATAGGTTCACATATCATTCAATATAGCAT
1 GTTCGCATATAATTCAACATAAGTTCACATATCATTCAACATAGCAT
*
105450802 GTTCGTATATAATTCAACATAAGTTCACATATCATTCAACATAG---
1 GTTCGCATATAATTCAACATAAGTTCACATATCATTCAACATAGCAT
* *
105450846 GTTCACATATCATTCAACATA
1 GTTCGCATATAATTCAACATA
105450867 GCATGTTCGT
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
44 18 0.31
47 40 0.69
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.34
Consensus pattern (47 bp):
GTTCGCATATAATTCAACATAAGTTCACATATCATTCAACATAGCAT
Found at i:105455491 original size:3 final size:3
Alignment explanation
Indices: 105455483--105455533 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
105455473 TCAAGTCATC
105455483 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
105455531 AAT
1 AAT
105455534 GTTGTAATAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:105456302 original size:22 final size:22
Alignment explanation
Indices: 105456258--105456310 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
105456248 AAACAATAAA
* * * *
105456258 AACAAAATAATAGTAATATAAT
1 AACAAAATGATAGCAAAACAAT
105456280 AACAAAATGATAGCAAAACAAT
1 AACAAAATGATAGCAAAACAAT
*
105456302 ATCAAAATG
1 AACAAAATG
105456311 GCAGCAAACA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.62, C:0.09, G:0.08, T:0.21
Consensus pattern (22 bp):
AACAAAATGATAGCAAAACAAT
Found at i:105456316 original size:22 final size:22
Alignment explanation
Indices: 105456277--105456318 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
105456267 ATAGTAATAT
*
105456277 AATAACAAAATGATAGCAAAAC
1 AATAACAAAATGACAGCAAAAC
* *
105456299 AATATCAAAATGGCAGCAAA
1 AATAACAAAATGACAGCAAA
105456319 CAGCAGCTAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.60, C:0.14, G:0.12, T:0.14
Consensus pattern (22 bp):
AATAACAAAATGACAGCAAAAC
Found at i:105457046 original size:13 final size:13
Alignment explanation
Indices: 105457030--105457054 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
105457020 AAATCTATTA
105457030 GAAAAAAAAGTTT
1 GAAAAAAAAGTTT
105457043 GAAAAAAAAGTT
1 GAAAAAAAAGTT
105457055 AATAATAAAA
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:0.64, C:0.00, G:0.16, T:0.20
Consensus pattern (13 bp):
GAAAAAAAAGTTT
Found at i:105465775 original size:24 final size:24
Alignment explanation
Indices: 105465747--105465826 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 24
105465737 GTACATGTAT
105465747 GCTCATAGGAGCTGTAAACGAGAA
1 GCTCATAGGAGCTGTAAACGAGAA
* * * *
105465771 TCTCAT-GTGAGCTGGATAATGGGAA
1 GCTCATAG-GAGCTGTA-AACGAGAA
*
105465796 GCTCATACGAGCTGTAAATCG-GAAA
1 GCTCATAGGAGCTGTAAA-CGAG-AA
105465821 GCTCAT
1 GCTCAT
105465827 GCAATCTTAA
Statistics
Matches: 43, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
23 1 0.02
24 15 0.35
25 27 0.63
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.23
Consensus pattern (24 bp):
GCTCATAGGAGCTGTAAACGAGAA
Found at i:105468773 original size:96 final size:96
Alignment explanation
Indices: 105468571--105469034 Score: 738
Period size: 96 Copynumber: 4.9 Consensus size: 96
105468561 ACAAGATATG
105468571 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAGGTGTATG--TATGTGATAAGGCC
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAGGTGTATGTATATGTGATAAGGCC
*
105468634 GAATGACCAATGTGATGAATGTGAAAGTATATA
66 GAATGGCCAATGTGATGAATGTGAAAG--TATA
* *
105468667 TATATATGATAAGGCCGAATGGCCAATGTGATGAATATGAAGGTGTATGTATATGTGATAAGGCC
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAGGTGTATGTATATGTGATAAGGCC
* *
105468732 GAATGGCCAATGTGATGAATGTGAAGGTGTA
66 GAATGGCCAATGTGATGAATGTGAAAGTATA
*
105468763 TGTATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAGGTGTATGTATATGTGATAAGGCC
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAGGTGTATGTATATGTGATAAGGCC
105468828 GAATGGCCAATGTGATGAATGTGAAAGTATA
66 GAATGGCCAATGTGATGAATGTGAAAGTATA
* *
105468859 TATATATGATAAGGCCGAATGACCAATGTGATGAATGTGAAGGTGTATGTATATGTGATAAGGCC
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAGGTGTATGTATATGTGATAAGGCC
* *
105468924 AAATGGCCAATGTGATGAATGTGAAAGTGTA
66 GAATGGCCAATGTGATGAATGTGAAAGTATA
* * * * *
105468955 TGTATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA--AGTATATATTTATGATAAGGCC
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAGGTGTATGTATATGTGATAAGGCC
*
105469018 GAATGGTCAATGTGATG
66 GAATGGCCAATGTGATG
105469035 GAACTGGAAG
Statistics
Matches: 342, Mismatches: 24, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
94 33 0.10
96 270 0.79
98 39 0.11
ACGTcount: A:0.34, C:0.08, G:0.30, T:0.28
Consensus pattern (96 bp):
TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAGGTGTATGTATATGTGATAAGGCC
GAATGGCCAATGTGATGAATGTGAAAGTATA
Found at i:105469059 original size:47 final size:47
Alignment explanation
Indices: 105468571--105469061 Score: 691
Period size: 47 Copynumber: 10.3 Consensus size: 47
105468561 ACAAGATATG
105468571 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAGGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAGGTGTA
* * * *
105468618 TGTATGTGATAAGGCCGAATGACCAATGTGATGAATGTGAAAGTATATA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTG-AAG-GTGTA
* *
105468667 TATATATGATAAGGCCGAATGGCCAATGTGATGAATATGAAGGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAGGTGTA
105468714 TGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAGGTGTA
1 --TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAGGTGTA
*
105468763 TGTATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAGGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAGGTGTA
* *
105468810 TGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTATA
1 --TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAGGTGTA
* *
105468859 TATATATGATAAGGCCGAATGACCAATGTGATGAATGTGAAGGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAGGTGTA
* *
105468906 TGTATATGTGATAAGGCCAAATGGCCAATGTGATGAATGTGAAAGTGTA
1 --TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAGGTGTA
* * *
105468955 TGTATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTATA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAGGTGTA
* * *
105469002 TATTTATGATAAGGCCGAATGGTCAATGTGATGGAACTG-GAA-GTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGAT-GAA-TGTGAAGGTGTA
105469049 TA-ACTGTGATAAG
1 TATA-TGTGATAAG
105469062 TCCCGAAGGA
Statistics
Matches: 399, Mismatches: 34, Indels: 22
0.88 0.07 0.05
Matches are distributed among these distances:
47 215 0.54
48 12 0.03
49 172 0.43
ACGTcount: A:0.34, C:0.08, G:0.30, T:0.28
Consensus pattern (47 bp):
TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAGGTGTA
Found at i:105480516 original size:27 final size:27
Alignment explanation
Indices: 105480485--105480538 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
105480475 TAAAAATGTA
*
105480485 AAAAAATTATATATAATATATAATTTTT
1 AAAAAATTATA-AAAATATATAATTTTT
*
105480513 AAAAAATTTTAAAAATATATAATTTT
1 AAAAAATTATAAAAATATATAATTTT
105480539 AAATTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 14 0.58
28 10 0.42
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
AAAAAATTATAAAAATATATAATTTTT
Found at i:105480587 original size:20 final size:18
Alignment explanation
Indices: 105480544--105480605 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 18
105480534 ATTTTAAATT
105480544 TTAAAAATCAAAATAATA
1 TTAAAAATCAAAATAATA
*
105480562 TATAAAAATTCAAAAATATTA
1 T-TAAAAA-TC-AAAATAATA
105480583 TT-AAAAT-AAATTATAATA
1 TTAAAAATCAAA--ATAATA
105480601 TTAAA
1 TTAAA
105480606 TATTTAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
16 3 0.08
18 9 0.25
19 12 0.33
20 3 0.08
21 9 0.25
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
TTAAAAATCAAAATAATA
Found at i:105480616 original size:233 final size:239
Alignment explanation
Indices: 105480357--105480835 Score: 613
Period size: 232 Copynumber: 2.0 Consensus size: 239
105480347 TAAAAATAGA
*
105480357 AAATTATAATATTAAATATTTAAATATTAAAA-A-AAATGATTTTGACTAATCAAT-TCCGGCCA
1 AAATTATAATATTAAATATTTAAATATTAAAACACAAATGATTTTGACAAATCAATGT-CGGCCA
* * *
105480419 CATGGTGTTATTGTCTTTTTTTTTATTTTTTTTAGTATTATATATATTATATTAATTAAAAATGT
65 CATGGCGCTATTGTC--CTTTTTTA--TTTTTTAGTATTATATATATTATATTAATTAAAAATGT
* *
105480484 AAAAAAATTATATATAATATAT-A-A-TTTT-T-AA-AAAAT-TTTA-AAAATATATAATTTTAA
126 -AAAAAATCATATATAATATATAATATTTTTATAAATAAAATATTTATAAAATATATAATTTAAA
* *
105480541 ATTTTAAAAA-TCAAAATAATATATAAAAATTCAAAAATATTATTAAAAT
190 ATTTTAAAAAGTCAAAATAATATATAAAAATTAAAAAATATTATAAAAAT
*** *
105480590 AAATTATAATATTAAATATTTAAATATTAAAACACTTTTGATTTTGACAAATCAATGGTTGGCCA
1 AAATTATAATATTAAATATTTAAATATTAAAACACAAATGATTTTGACAAATCAAT-GTCGGCCA
* *
105480655 CGTGGCGCTATTGTCCTTTTTTATTTTTTAGTATTATATATATTATATTGATTAAAAATGTAAAA
65 CATGGCGCTATTGTCCTTTTTTATTTTTTAGTATTATATATATTATATTAATTAAAAATGTAAAA
*
105480720 TATCATATATAATATATAATATTTTTAAAAAATAAAAATAAAATATTTATAAAATATATAATTTA
130 AATCATATATAATATATAATATTTTT-----AT--AAATAAAATATTTATAAAATATATAATTTA
105480785 AAATTTTAAAAAGTCAAAATAATATATAAAAATTAAAAAATATTATAAAAA
188 AAATTTTAAAAAGTCAAAATAATATATAAAAATTAAAAAATATTATAAAAA
105480836 AGTAATTAAA
Statistics
Matches: 211, Mismatches: 15, Indels: 26
0.84 0.06 0.10
Matches are distributed among these distances:
231 19 0.09
232 38 0.18
233 33 0.16
234 12 0.06
235 17 0.08
236 17 0.08
237 1 0.00
240 1 0.00
243 2 0.01
244 5 0.02
245 4 0.02
246 26 0.12
247 36 0.17
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (239 bp):
AAATTATAATATTAAATATTTAAATATTAAAACACAAATGATTTTGACAAATCAATGTCGGCCAC
ATGGCGCTATTGTCCTTTTTTATTTTTTAGTATTATATATATTATATTAATTAAAAATGTAAAAA
ATCATATATAATATATAATATTTTTATAAATAAAATATTTATAAAATATATAATTTAAAATTTTA
AAAAGTCAAAATAATATATAAAAATTAAAAAATATTATAAAAAT
Found at i:105480792 original size:24 final size:24
Alignment explanation
Indices: 105480724--105480796 Score: 62
Period size: 24 Copynumber: 3.0 Consensus size: 24
105480714 GTAAAATATC
*
105480724 ATATATAATATATAATATTTT-TAAA
1 ATATATAAT-T-TAAAATTTTATAAA
* **
105480749 AAATA-AAAATAAAATATTTATAAA
1 ATATATAATTTAAAAT-TTTATAAA
105480773 ATATATAATTTAAAATTTTA-AAA
1 ATATATAATTTAAAATTTTATAAA
105480796 A
1 A
105480797 GTCAAAATAA
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
22 5 0.13
23 7 0.18
24 14 0.37
25 12 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
ATATATAATTTAAAATTTTATAAA
Found at i:105480816 original size:20 final size:19
Alignment explanation
Indices: 105480791--105480835 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
105480781 TTTAAAATTT
105480791 TAAAAAGTCAAAATAATA-TA
1 TAAAAA-TCAAAA-AATATTA
*
105480811 TAAAAATTAAAAAATATTA
1 TAAAAATCAAAAAATATTA
105480830 TAAAAA
1 TAAAAA
105480836 AGTAATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 13 0.57
20 6 0.26
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (19 bp):
TAAAAATCAAAAAATATTA
Found at i:105480952 original size:27 final size:30
Alignment explanation
Indices: 105480902--105480968 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 30
105480892 GAATTATGTA
*
105480902 TTTTAGAATTTTATATAAAAA-TTTA-ATT
1 TTTTATAATTTTATATAAAAATTTTATATT
105480930 TTTTATAATTTT-TA-AAAATATTTTATATT
1 TTTTATAATTTTATATAAAA-ATTTTATATT
105480959 TTTTAATAAT
1 TTTT-ATAAT
105480969 ATTGTTAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
26 4 0.12
27 3 0.09
28 15 0.44
29 7 0.21
30 5 0.15
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (30 bp):
TTTTATAATTTTATATAAAAATTTTATATT
Found at i:105480980 original size:19 final size:20
Alignment explanation
Indices: 105480933--105480980 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
105480923 TTTAATTTTT
* *
105480933 TATAATTTTTAAAAATATTT
1 TATAGTTTTTAAAAATATTG
* *
105480953 TATATTTTTTAATAATATTG
1 TATAGTTTTTAAAAATATTG
105480973 T-TAGTTTT
1 TATAGTTTT
105480981 AACTAATTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.60
Consensus pattern (20 bp):
TATAGTTTTTAAAAATATTG
Found at i:105480980 original size:20 final size:20
Alignment explanation
Indices: 105480930--105480971 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
105480920 AAATTTAATT
*
105480930 TTTTATAATTTTTAAAAATA
1 TTTTATATTTTTTAAAAATA
*
105480950 TTTTATATTTTTTAATAATA
1 TTTTATATTTTTTAAAAATA
105480970 TT
1 TT
105480972 GTTAGTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTATATTTTTTAAAAATA
Found at i:105481084 original size:19 final size:19
Alignment explanation
Indices: 105481060--105481096 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
105481050 TTATATATAT
105481060 TTTTATTTTTATACATTTA
1 TTTTATTTTTATACATTTA
*
105481079 TTTTATTTTTATATATTT
1 TTTTATTTTTATACATTT
105481097 TAATGTGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTATTTTTATACATTTA
Found at i:105481113 original size:37 final size:36
Alignment explanation
Indices: 105481045--105481115 Score: 90
Period size: 35 Copynumber: 1.9 Consensus size: 36
105481035 TATAAAAAAA
* * *
105481045 TTATTTTATATATATTTTTATTTTTATACATTTATT
1 TTATTTTATATATATTTTAATTTATAAACATTTATT
105481081 TTATTTT-TATATATTTTAATGTGTATAAACATTTA
1 TTATTTTATATATATTTTAAT-T-TATAAACATTTA
105481116 ATAAAAGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
35 12 0.40
36 8 0.27
37 10 0.33
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (36 bp):
TTATTTTATATATATTTTAATTTATAAACATTTATT
Found at i:105484903 original size:18 final size:18
Alignment explanation
Indices: 105484880--105484917 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
105484870 GCTTACACAT
105484880 ATATTT-CTTCATTTTCCA
1 ATATTTACTTC-TTTTCCA
*
105484898 ATATTTATTTCTTTTCCA
1 ATATTTACTTCTTTTCCA
105484916 AT
1 AT
105484918 TACCAAGCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.24, C:0.18, G:0.00, T:0.58
Consensus pattern (18 bp):
ATATTTACTTCTTTTCCA
Found at i:105488136 original size:48 final size:48
Alignment explanation
Indices: 105488072--105488345 Score: 229
Period size: 48 Copynumber: 5.7 Consensus size: 48
105488062 TGATATGTAT
* *
105488072 GCTAGTGTAAGACCATGTTTGGAACATGGAATCGGCCATATTATGAGA
1 GCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCATATTATGAGA
* * * * ** *
105488120 GCAAGTGCAAGACCATGTCTGGGATATGGCATCGGCGTTGA-TATGTA-C
1 GCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCAT-ATTATG-AGA
** * *
105488168 GCTAGTGTAAGACCATGTTTGGGACATGGTGTCGGCCACAATATGAGA
1 GCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCATATTATGAGA
* * * * *
105488216 GCCAGTGTATGATCATGTTTGGAACATGGCATC-G--ATATTAAGACGAGA
1 GCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCATATT---ATGAGA
**
105488264 GCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCC-TAGACATGTA-A
1 GCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCATA-TTATG-AGA
* * *
105488312 GCCAGTGTAAGACCATGTCTGAGACATGGCATCG
1 GCTAGTGTAAGACCATGTTTGGGACATGGCATCG
105488346 ATAATTTACT
Statistics
Matches: 176, Mismatches: 38, Indels: 24
0.74 0.16 0.10
Matches are distributed among these distances:
45 3 0.02
47 3 0.02
48 164 0.93
49 4 0.02
50 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (48 bp):
GCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCATATTATGAGA
Found at i:105488233 original size:96 final size:95
Alignment explanation
Indices: 105488062--105488346 Score: 304
Period size: 96 Copynumber: 3.0 Consensus size: 95
105488052 GGCATTTGAG
* * * *
105488062 TGATATGTATGCTAGTGTAAGACCATGTTTGGAACATGGAATCGGCCATATTATGAGAGCAAGTG
1 TGATATGTAAGCTAGTGTAAGACCATGTTTGGGACATGGAATCGGCCA-AATATGAGAGCCAGTG
* * * *
105488127 CAAGACCATGTCTGGGATATGGCATCGGCGT
65 TAAGACCATGTCTGGGACATGGCATCGACAT
* **
105488158 TGATATGTACGCTAGTGTAAGACCATGTTTGGGACATGGTGTCGGCCACAATATGAGAGCCAGTG
1 TGATATGTAAGCTAGTGTAAGACCATGTTTGGGACATGGAATCGGCCA-AATATGAGAGCCAGTG
* * * * *
105488223 TATGATCATGTTTGGAACATGGCATCGATAT
65 TAAGACCATGTCTGGGACATGGCATCGACAT
* * * * * *
105488254 TAAGACG-AGAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTAGACATGTA-AGCCAG
1 TGATATGTA-AGCTAGTGTAAGACCATGTTTGGGACATGGAATCGGCC-AAATATG-AGAGCCAG
*
105488317 TGTAAGACCATGTCTGAGACATGGCATCGA
63 TGTAAGACCATGTCTGGGACATGGCATCGA
105488347 TAATTTACTC
Statistics
Matches: 157, Mismatches: 29, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
95 1 0.01
96 154 0.98
97 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (95 bp):
TGATATGTAAGCTAGTGTAAGACCATGTTTGGGACATGGAATCGGCCAAATATGAGAGCCAGTGT
AAGACCATGTCTGGGACATGGCATCGACAT
Found at i:105497255 original size:48 final size:48
Alignment explanation
Indices: 105497197--105497363 Score: 237
Period size: 48 Copynumber: 3.5 Consensus size: 48
105497187 AGAGACAGTT
* * *
105497197 TAAGATCATGT-TGAGGACAAGGCATTGGTGTTGATATGTGCGCTAGTG
1 TAAGACCATGTCTG-GGACATGGCATTGGCGTTGATATGTGCGCTAGTG
* * * *
105497245 TAAGACCATGTCTAGGACATGGCATTTGCGTTGATATGAGCGCCAGTG
1 TAAGACCATGTCTGGGACATGGCATTGGCGTTGATATGTGCGCTAGTG
* *
105497293 TAAGACCATGTCTGGGACATGGCATCGGCATTGATATGTGCGCTAGTG
1 TAAGACCATGTCTGGGACATGGCATTGGCGTTGATATGTGCGCTAGTG
105497341 TAAGACCATGTCTGGGACATGGC
1 TAAGACCATGTCTGGGACATGGC
105497364 GTCAGCCACA
Statistics
Matches: 105, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
48 104 0.99
49 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.28
Consensus pattern (48 bp):
TAAGACCATGTCTGGGACATGGCATTGGCGTTGATATGTGCGCTAGTG
Found at i:105497378 original size:48 final size:47
Alignment explanation
Indices: 105497228--105497462 Score: 220
Period size: 48 Copynumber: 4.9 Consensus size: 47
105497218 GCATTGGTGT
* * * * **
105497228 TGATATGTGCGCTAGTGTAAGACCATGTCTAGGACATGGCATTTGCGT
1 TGATATGAGCGCCAGTGTAAGACCATGTCTGGGACATGGCA-TCGCCA
*
105497276 TGATATGAGCGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
1 TGATATGAGCGCCAGTGTAAGACCATGTCTGGGACATGGCATCGCCA
* * *
105497323 TTGATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCGTCAGCCA
1 -TGATATGAGCGCCAGTGTAAGACCATGTCTGGGACATGGCATC-GCCA
** * * * * *
105497372 CAATATGAGAGCCAGTGTAAGACCAT-TTTGGAACATGACATCGACA
1 TGATATGAGCGCCAGTGTAAGACCATGTCTGGGACATGGCATCGCCA
* * * * **
105497418 TTGAGACGAGAGCTAGTGTAAGACCATGTCTGGGGTATGGCATCG
1 -TGATATGAGCGCCAGTGTAAGACCATGTCTGGGACATGGCATCG
105497463 GTAATTTACT
Statistics
Matches: 152, Mismatches: 31, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
46 3 0.02
47 35 0.23
48 111 0.73
49 3 0.02
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (47 bp):
TGATATGAGCGCCAGTGTAAGACCATGTCTGGGACATGGCATCGCCA
Found at i:105497449 original size:95 final size:96
Alignment explanation
Indices: 105497142--105497461 Score: 275
Period size: 96 Copynumber: 3.3 Consensus size: 96
105497132 TGATATGTGT
* * * * * * * *
105497142 GCTAGTGTAAGACCATGTTTGGAACATGACATCGGCCACATTATGAGAGACAGTTTAAGATCATG
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCACAATATGAGAGCCAGTGTAAGACCATG
* * * * *** * * * *
105497207 T-TGAGGACAAGGCATTGGTGTTGATATGTGC
66 TCTG-GAACATGACATCGACATTGAGACGAGA
* ** **** *
105497238 GCTAGTGTAAGACCATGTCTAGGACATGGCATTTGCGTTGATATGAGCGCCAGTGTAAGACCATG
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCACAATATGAGAGCCAGTGTAAGACCATG
* * * * * * *
105497303 TCTGGGACATGGCATCGGCATTGATATGTGC
66 TCTGGAACATGACATCGACATTGAGACGAGA
*
105497334 GCTAGTGTAAGACCATGTCTGGGACATGGCGTCAGCCACAATATGAGAGCCAGTGTAAGACCAT-
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCACAATATGAGAGCCAGTGTAAGACCATG
*
105497398 TTTGGAACATGACATCGACATTGAGACGAGA
66 TCTGGAACATGACATCGACATTGAGACGAGA
**
105497429 GCTAGTGTAAGACCATGTCTGGGGTATGGCATC
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATC
105497462 GGTAATTTAC
Statistics
Matches: 184, Mismatches: 39, Indels: 3
0.81 0.17 0.01
Matches are distributed among these distances:
95 53 0.29
96 129 0.70
97 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.26
Consensus pattern (96 bp):
GCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCACAATATGAGAGCCAGTGTAAGACCATG
TCTGGAACATGACATCGACATTGAGACGAGA
Found at i:105499638 original size:35 final size:35
Alignment explanation
Indices: 105499598--105499667 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
105499588 ACAACCCACA
*
105499598 CCACCCAATTATTCTTTGAGAGAGAATAAAGATGG
1 CCACCCAATTATTCTTTGAAAGAGAATAAAGATGG
105499633 CCACCCAATTATTCTTTGAAAGAGAATAAAGATGG
1 CCACCCAATTATTCTTTGAAAGAGAATAAAGATGG
105499668 TATTCTCTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.26
Consensus pattern (35 bp):
CCACCCAATTATTCTTTGAAAGAGAATAAAGATGG
Found at i:105499740 original size:28 final size:29
Alignment explanation
Indices: 105499708--105499770 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 29
105499698 TAAACGTAAA
* * *
105499708 GAAAAGACATTAAGACA-TAAAATGCATG
1 GAAAAAACATTAAAACATTAAAATGCAAG
*
105499736 GAAAAAACATTAAAACATTTAAATGCAAG
1 GAAAAAACATTAAAACATTAAAATGCAAG
105499765 GAAAAA
1 GAAAAA
105499771 GCTATTGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 15 0.50
29 15 0.50
ACGTcount: A:0.59, C:0.10, G:0.14, T:0.17
Consensus pattern (29 bp):
GAAAAAACATTAAAACATTAAAATGCAAG
Found at i:105499836 original size:16 final size:16
Alignment explanation
Indices: 105499801--105499840 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
105499791 TCACAAACCA
105499801 ATTTTTTTTTTTCACT
1 ATTTTTTTTTTTCACT
**
105499817 -TTTTTTTTTTTTGCT
1 ATTTTTTTTTTTCACT
105499832 ATTTTTTTT
1 ATTTTTTTT
105499841 CACTTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.07, C:0.07, G:0.03, T:0.82
Consensus pattern (16 bp):
ATTTTTTTTTTTCACT
Found at i:105500961 original size:66 final size:66
Alignment explanation
Indices: 105500870--105501002 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
105500860 AGAGTGTAAT
105500870 ATACTGATAGGTATTTTAGATCCGTCTATAAAAAGTCCATCTTATATTAAAGGAATATACACATC
1 ATACTGATAGGTATTTTAGATCCGTCTATAAAAAGTCCATCTTATATTAAAGGAATATACACATC
105500935 C
66 C
105500936 ATACTGATAGGTATTTTAGATCCGTCTATAAAAAGTCCATCTTATATTAAAGGAATATACACATC
1 ATACTGATAGGTATTTTAGATCCGTCTATAAAAAGTCCATCTTATATTAAAGGAATATACACATC
105501001 C
66 C
105501002 A
1 A
105501003 GCAGTAAAGT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (66 bp):
ATACTGATAGGTATTTTAGATCCGTCTATAAAAAGTCCATCTTATATTAAAGGAATATACACATC
C
Found at i:105502703 original size:7 final size:7
Alignment explanation
Indices: 105502682--105502720 Score: 62
Period size: 7 Copynumber: 5.6 Consensus size: 7
105502672 TATAGCTTCA
105502682 TATTACTT
1 TATTA-TT
105502690 T-TTATT
1 TATTATT
105502696 TATTATT
1 TATTATT
105502703 TATTATT
1 TATTATT
105502710 TATTATT
1 TATTATT
105502717 TATT
1 TATT
105502721 GTTACTCACG
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 3 0.10
7 26 0.87
8 1 0.03
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (7 bp):
TATTATT
Found at i:105503090 original size:22 final size:21
Alignment explanation
Indices: 105503046--105503107 Score: 90
Period size: 21 Copynumber: 2.9 Consensus size: 21
105503036 ATAAAATTTC
105503046 TAATTATGAATATA-AGTTTTA
1 TAATTATGAATATACA-TTTTA
*
105503067 TAATTATGAAAGATACATTTTA
1 TAATTATG-AATATACATTTTA
105503089 TAATTATGAATATACATTT
1 TAATTATGAATATACATTT
105503108 CTATTCAAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.49
22 18 0.49
23 1 0.03
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (21 bp):
TAATTATGAATATACATTTTA
Found at i:105505395 original size:24 final size:25
Alignment explanation
Indices: 105505350--105505396 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
105505340 TATTTTTGAG
* *
105505350 TCTTTTTTTGCCATCAATTTTTTGT
1 TCTTTTTTTGCAATCAACTTTTTGT
*
105505375 TCTTTTTTT-CAATCTACTTTTT
1 TCTTTTTTTGCAATCAACTTTTT
105505397 CTAACAGATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 10 0.53
25 9 0.47
ACGTcount: A:0.13, C:0.17, G:0.04, T:0.66
Consensus pattern (25 bp):
TCTTTTTTTGCAATCAACTTTTTGT
Found at i:105505583 original size:19 final size:19
Alignment explanation
Indices: 105505559--105505613 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
105505549 TTAGATTAAA
105505559 AAATAACTCATAATTATCT
1 AAATAACTCATAATTATCT
105505578 AAAT-A---A-AATTA---
1 AAATAACTCATAATTATCT
105505589 AAATAACTCATAATTATCT
1 AAATAACTCATAATTATCT
105505608 AAATAA
1 AAATAA
105505614 ATTAACTCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 16
0.64 0.00 0.36
Matches are distributed among these distances:
11 4 0.14
12 1 0.04
14 5 0.18
15 2 0.07
16 5 0.18
18 1 0.04
19 10 0.36
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATAACTCATAATTATCT
Found at i:105505594 original size:30 final size:29
Alignment explanation
Indices: 105505558--105505618 Score: 113
Period size: 30 Copynumber: 2.1 Consensus size: 29
105505548 ATTAGATTAA
105505558 AAAATAACTCATAATTATCTAAATAAAATT
1 AAAATAACTCATAATTATCTAAAT-AAATT
105505588 AAAATAACTCATAATTATCTAAATAAATT
1 AAAATAACTCATAATTATCTAAATAAATT
105505617 AA
1 AA
105505619 CTCAGTAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 7 0.23
30 24 0.77
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (29 bp):
AAAATAACTCATAATTATCTAAATAAATT
Found at i:105508430 original size:51 final size:51
Alignment explanation
Indices: 105508354--105508507 Score: 187
Period size: 51 Copynumber: 3.2 Consensus size: 51
105508344 CTGATCACAT
*
105508354 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAAATAAGTGTAGCTAAAGCTACCACTTATCAC
* *
105508405 TTATCATTTGTCACTGATTAAATAAGTGTAGCTAAAGCT---AC----CAC
1 TTATCACTTGTCACTGATCAAATAAGTGTAGCTAAAGCTACCACTTATCAC
* * * *
105508449 TTATCACTTGTCACTGATCAGATAAGTGTAGCTGAGGCTACCACTTATTAC
1 TTATCACTTGTCACTGATCAAATAAGTGTAGCTAAAGCTACCACTTATCAC
*
105508500 TTGTCACT
1 TTATCACT
105508508 GATCAGAAGT
Statistics
Matches: 86, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
44 37 0.43
47 2 0.02
48 2 0.02
51 45 0.52
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (51 bp):
TTATCACTTGTCACTGATCAAATAAGTGTAGCTAAAGCTACCACTTATCAC
Found at i:105508513 original size:44 final size:44
Alignment explanation
Indices: 105508354--105508514 Score: 214
Period size: 44 Copynumber: 3.5 Consensus size: 44
105508344 CTGATCACAT
105508354 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
* *
105508398 TTATCACTTATCATTTGTCACTGATTAAATAAGTGTAGCTAAAGCTACCAC
1 TTAT--C--A-C--TTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
* *
105508449 TTATCACTTGTCACTGATCAGATAAGTGTAGCTGAGGCTACCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
*
105508493 TTATTACTTGTCACTGATCAGA
1 TTATCACTTGTCACTGATCAGA
105508515 AGTACTCAAA
Statistics
Matches: 103, Mismatches: 7, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
44 58 0.56
46 2 0.02
47 1 0.01
48 1 0.01
49 2 0.02
51 39 0.38
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (44 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
Found at i:105516086 original size:37 final size:37
Alignment explanation
Indices: 105516036--105516120 Score: 161
Period size: 37 Copynumber: 2.3 Consensus size: 37
105516026 TCACATTTAT
*
105516036 CACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTGATCAGATAAGTGTAGCTAAAGCTAC
105516073 CACTTATCACTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTGATCAGATAAGTGTAGCTAAAGCTAC
105516110 CACTTATCACT
1 CACTTATCACT
105516121 TGTCACTTGT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (37 bp):
CACTTATCACTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:105516139 original size:58 final size:58
Alignment explanation
Indices: 105516073--105516185 Score: 208
Period size: 58 Copynumber: 1.9 Consensus size: 58
105516063 CTAAAGCTAC
105516073 CACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTGT
1 CACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTGT
* *
105516131 CACTTATCACTGATCAGATAAGTGTAGCTGAGGCTACCACTTATCACTTGTCACT
1 CACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACT
105516186 GATCAGAAGT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (58 bp):
CACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTGT
Found at i:105522233 original size:29 final size:30
Alignment explanation
Indices: 105522199--105522269 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
105522189 TATTATAGAG
* *
105522199 AATGAATCAAATTAG-TCTTTTTATTATT-A
1 AATGAATCAAATTAGTTC-TTATACTATTAA
*
105522228 AATGAATCAATTTAGTTCTTATACTATTAA
1 AATGAATCAAATTAGTTCTTATACTATTAA
*
105522258 AAAGAATCAAAT
1 AATGAATCAAAT
105522270 ATGTTCAAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 22 0.63
30 13 0.37
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.41
Consensus pattern (30 bp):
AATGAATCAAATTAGTTCTTATACTATTAA
Found at i:105522798 original size:30 final size:30
Alignment explanation
Indices: 105522764--105522825 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
105522754 CTTAACAAGT
*
105522764 AAATGCCTCTAAAATAAAAATAAAATTAAC
1 AAATGCCTCTAAAATAAAAACAAAATTAAC
* * *
105522794 AAATGTCTTTAAAATAATAACAAAATTAAC
1 AAATGCCTCTAAAATAAAAACAAAATTAAC
105522824 AA
1 AA
105522826 TAAAATAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.60, C:0.11, G:0.03, T:0.26
Consensus pattern (30 bp):
AAATGCCTCTAAAATAAAAACAAAATTAAC
Found at i:105522884 original size:11 final size:11
Alignment explanation
Indices: 105522863--105522932 Score: 52
Period size: 11 Copynumber: 6.4 Consensus size: 11
105522853 CAATAACAAC
*
105522863 AAAATAGTAGT
1 AAAATAATAGT
*
105522874 AACATAATAGT
1 AAAATAATAGT
*
105522885 AAAATGATAGT
1 AAAATAATAGT
**
105522896 AAAATAGGGAG-
1 AAAATA-ATAGT
**
105522907 AAAATAATAAA
1 AAAATAATAGT
*
105522918 AAAATAATATT
1 AAAATAATAGT
105522929 AAAA
1 AAAA
105522933 AACAAAAAAA
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
10 1 0.02
11 42 0.93
12 2 0.04
ACGTcount: A:0.63, C:0.01, G:0.13, T:0.23
Consensus pattern (11 bp):
AAAATAATAGT
Found at i:105525396 original size:23 final size:23
Alignment explanation
Indices: 105525370--105525413 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
105525360 TAATTAGAAA
*
105525370 AATTAATTAA-ATTTATTTTAATT
1 AATTAAATAATATTT-TTTTAATT
105525393 AATTAAATAATATTTTTTTAA
1 AATTAAATAATATTTTTTTAA
105525414 ATAGAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
AATTAAATAATATTTTTTTAATT
Found at i:105525413 original size:19 final size:19
Alignment explanation
Indices: 105525370--105525408 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
105525360 TAATTAGAAA
*
105525370 AATTAATTAAATTTATTTT
1 AATTAATTAAATATATTTT
105525389 AATTAATTAAATAATATTTT
1 AATTAATTAAAT-ATATTTT
105525409 TTTAAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
AATTAATTAAATATATTTT
Found at i:105527121 original size:116 final size:116
Alignment explanation
Indices: 105526917--105527146 Score: 442
Period size: 116 Copynumber: 2.0 Consensus size: 116
105526907 TTAAGGATCG
*
105526917 ACTTTTCGAATCTCAAAATACGAGATATTGCTTGTTTAAAACAACATTTTAGTGTGTCGGGTAAA
1 ACTTTTCGAATCTCAAAAGACGAGATATTGCTTGTTTAAAACAACATTTTAGTGTGTCGGGTAAA
*
105526982 ATGTAACACTATTTCGTAGTAAAATGGAAAATGGATTACGGTACCGATAAT
66 ATGTAACACTATTTCGTAGTAAAATGGAAAATGGATTACGGTAACGATAAT
105527033 ACTTTTCGAATCTCAAAAGACGAGATATTGCTTGTTTAAAACAACATTTTAGTGTGTCGGGTAAA
1 ACTTTTCGAATCTCAAAAGACGAGATATTGCTTGTTTAAAACAACATTTTAGTGTGTCGGGTAAA
105527098 ATGTAACACTATTTCGTAGTAAAATGGAAAATGGATTACGGTAACGATA
66 ATGTAACACTATTTCGTAGTAAAATGGAAAATGGATTACGGTAACGATA
105527147 TGCATAATCA
Statistics
Matches: 112, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
116 112 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.32
Consensus pattern (116 bp):
ACTTTTCGAATCTCAAAAGACGAGATATTGCTTGTTTAAAACAACATTTTAGTGTGTCGGGTAAA
ATGTAACACTATTTCGTAGTAAAATGGAAAATGGATTACGGTAACGATAAT
Found at i:105527622 original size:3 final size:3
Alignment explanation
Indices: 105527303--105527603 Score: 204
Period size: 3 Copynumber: 99.3 Consensus size: 3
105527293 AAAAATGATG
* * * *
105527303 ATA ATA ATA ATG ATA ATA ATA CTA ATA ATA GTA ATA ATA ATA GAAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
* * * * * *
105527349 ATA ATA ATG GTA AAA AGTA ATA ATA ATA GTA ATA A-A A-A AAA ACA
1 ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA
** * * * * *
105527393 GCA ATG ATA ATA ATA ATA TTG ATA ATAA ATA ATA ATA GTA A-A AAA
1 ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA
* * *
105527438 ATA GTA ATA ATA GAAA ATA ATA ATA ATA A-A ATGA AGA ATA ATA ATA
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA
* * *
105527484 ATA CATTA ATA ATA A-A ATA AGGA ATA ATA ATA ACA ACA ATA AT- ATAA
1 ATA -A-TA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA AT-A
*
105527531 ATA ATA ATA ATA ATA ATA ATA AT- ATA ATAA ATA ATA ATA ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA
* * *
105527576 ATA GTGA A-A ATA ATA ATA GTG ATA ATA A
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA A
105527604 ATTAATTAAT
Statistics
Matches: 233, Mismatches: 47, Indels: 36
0.74 0.15 0.11
Matches are distributed among these distances:
2 16 0.07
3 194 0.83
4 21 0.09
5 2 0.01
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:105527847 original size:20 final size:21
Alignment explanation
Indices: 105527824--105527862 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
105527814 AATGGGCGAA
105527824 AATTT-AAAAAAATAAAAACT
1 AATTTCAAAAAAATAAAAACT
*
105527844 AATTTCAAAACAATAAAAA
1 AATTTCAAAAAAATAAAAA
105527863 AGCGGAAGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (21 bp):
AATTTCAAAAAAATAAAAACT
Found at i:105529560 original size:143 final size:143
Alignment explanation
Indices: 105529379--105529662 Score: 460
Period size: 143 Copynumber: 2.0 Consensus size: 143
105529369 GGATTGTGAC
* *
105529379 TTGTAGCTTCAATCTGTTCTACTACAACTTCAGGGAAATGAGATTCGCTATCTTCAGTCTGCTTC
1 TTGTAGCTTCAATCTGTTCAACTACAACTTCAGGGAAATGAGATTCGCTATCTTCAGTCTGCTCC
* * *
105529444 GCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTACTCCACTGCAACTTTAGGAAGATAA
66 GCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTACTCCACTCCAACTTCAGAAAGATAA
*
105529509 GATTTGCCATAAT
131 GATCTGCCATAAT
* * * * *
105529522 TTGTAGCTTCAATCTGTTCAATTGCAACTTTAGGGAAATGAGATTCGTTATTTTCAGTCTGCTCC
1 TTGTAGCTTCAATCTGTTCAACTACAACTTCAGGGAAATGAGATTCGCTATCTTCAGTCTGCTCC
*
105529587 GCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTCCAACTTCAGAAAGATAA
66 GCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTACTCCACTCCAACTTCAGAAAGATAA
105529652 GATCTGCCATA
131 GATCTGCCATA
105529663 CTAGATCTAC
Statistics
Matches: 129, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
143 129 1.00
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.31
Consensus pattern (143 bp):
TTGTAGCTTCAATCTGTTCAACTACAACTTCAGGGAAATGAGATTCGCTATCTTCAGTCTGCTCC
GCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTACTCCACTCCAACTTCAGAAAGATAA
GATCTGCCATAAT
Found at i:105530190 original size:46 final size:46
Alignment explanation
Indices: 105530060--105530194 Score: 119
Period size: 46 Copynumber: 2.9 Consensus size: 46
105530050 CTGGTTTGCT
** ** * * *
105530060 CCACTGCAACTTCAAGGAAATAAAATTTTTAGTTTCTTCCATCCATC
1 CCACTGCAAC-TCAAGGGTATAGGATTTGTAGCTTCTTCAATCCATC
* * * *
105530107 CTACTGTAACTCAAGGGTATAGGATTTGTATCATCTTCAATCCATC
1 CCACTGCAACTCAAGGGTATAGGATTTGTAGCTTCTTCAATCCATC
* * *
105530153 CCACTGCATCTC-AGGAGTATTGGATTTGTGGCTTCTTCAATC
1 CCACTGCAACTCAAGG-GTATAGGATTTGTAGCTTCTTCAATC
105530195 AATTGATCTT
Statistics
Matches: 69, Mismatches: 18, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
45 3 0.04
46 58 0.84
47 8 0.12
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.35
Consensus pattern (46 bp):
CCACTGCAACTCAAGGGTATAGGATTTGTAGCTTCTTCAATCCATC
Found at i:105533971 original size:28 final size:28
Alignment explanation
Indices: 105533940--105534018 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
105533930 GCAATCAAAT
*
105533940 ATGGTACTCAGTGTACGAAATATTGAGA
1 ATGGCACTCAGTGTACGAAATATTGAGA
* * *
105533968 ATGGCACTTAGTGTGCGAGATATTGAGA
1 ATGGCACTCAGTGTACGAAATATTGAGA
* * * *
105533996 ATGACACTTAGTGTGCAAAATAT
1 ATGGCACTCAGTGTACGAAATAT
105534019 CGAATGATTC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.29
Consensus pattern (28 bp):
ATGGCACTCAGTGTACGAAATATTGAGA
Found at i:105539910 original size:32 final size:33
Alignment explanation
Indices: 105539869--105539990 Score: 97
Period size: 32 Copynumber: 3.7 Consensus size: 33
105539859 CTAATAATAG
105539869 TAATAATAAT-AGAAAATAATAATGGTAAAAAA
1 TAATAATAATAAGAAAATAATAATGGTAAAAAA
* *
105539901 TAATAATAAT-AG-TAATAATAATAGTAATAAAA
1 TAATAATAATAAGAAAATAATAATGGTAA-AAAA
* ** * * * * *
105539933 GAATAGCAATGATAATAATAATATTGATAATAAA
1 TAATAATAATAAGAA-AATAATAATGGTAAAAAA
* *
105539967 TAATAATAGTAAAAAAATAATAAT
1 TAATAATAATAAGAAAATAATAAT
105539991 AAAATGAAGA
Statistics
Matches: 68, Mismatches: 18, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
31 13 0.19
32 23 0.34
33 9 0.13
34 12 0.18
35 11 0.16
ACGTcount: A:0.62, C:0.01, G:0.08, T:0.29
Consensus pattern (33 bp):
TAATAATAATAAGAAAATAATAATGGTAAAAAA
Found at i:105539948 original size:44 final size:46
Alignment explanation
Indices: 105539855--105540103 Score: 131
Period size: 44 Copynumber: 5.7 Consensus size: 46
105539845 TAATGATAAG
* * *
105539855 AATACTAATAATAGTAATAATAATAG-AA-AATAATAATGGTAAAA
1 AATAATAATAATAGTAATAATAATAGTAATAATAAGAATAGTAAAA
* *
105539899 AATAATAATAATAGTAATAATAATAGTAATAA-AAGAATAG-CAAT
1 AATAATAATAATAGTAATAATAATAGTAATAATAAGAATAGTAAAA
* * *
105539943 GATAATAATAATATTGATAATAA-A-TAATAAT-AG--TA--AAAA
1 AATAATAATAATAGTAATAATAATAGTAATAATAAGAATAGTAAAA
* * * *
105539982 AATAATAATAA-AATGAAGAATAATAATACATTAATAATAATA--AAATA
1 AATAATAATAATAGT-AATAATAATAGTA-A-TAATAAGAATAGTAAA-A
** * *
105540029 GGGAATAATAATAATAACAACAATAATA-T-A-AATAATAAT-GT-AAA
1 ---AATAATAATAATAGTAATAATAATAGTAATAATAAGAATAGTAAAA
* * *
105540073 AATAATAATAGTAATAATAATAATAATAATA
1 AATAATAATAATAGTAATAATAATAGTAATA
105540104 GTGATAATAA
Statistics
Matches: 164, Mismatches: 20, Indels: 42
0.73 0.09 0.19
Matches are distributed among these distances:
38 2 0.01
39 18 0.11
40 3 0.02
41 24 0.15
42 10 0.06
43 6 0.04
44 50 0.30
45 19 0.12
46 7 0.04
47 2 0.01
49 1 0.01
50 20 0.12
51 2 0.01
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.28
Consensus pattern (46 bp):
AATAATAATAATAGTAATAATAATAGTAATAATAAGAATAGTAAAA
Found at i:105540021 original size:35 final size:36
Alignment explanation
Indices: 105539835--105540103 Score: 173
Period size: 35 Copynumber: 7.5 Consensus size: 36
105539825 AAAAATGATG
* * * *
105539835 ATAATAATAATAATGATAA-GAATACTAATAATAGTA
1 ATAATAATAATAATAATAATGAAAAATAATAATA-CA
* *
105539871 ATAATAATAGAAAATAATAATGGTAAAA-AATAAT--A
1 ATAATAATA-ATAATAATAAT-GAAAAATAATAATACA
* * * *
105539906 ATAATAGTAATAATAATAGT-AATAA-AAGAATAGCA
1 ATAATAATAATAATAATAATGAAAAATAATAATA-CA
* * * *
105539941 ATGATAATAATAATATTGAT-AATAAATAATAATAGTA
1 ATAATAATAATAATAATAATGAA-AAATAATAATA-CA
* *
105539978 A-AAAAATAATAATAA-AATGAAGAATAATAATACA
1 ATAATAATAATAATAATAATGAAAAATAATAATACA
* ** *
105540012 TTAATAATAATAA-AATAGGGAATAATAATAATAACA
1 ATAATAATAATAATAATAATGAAAAATAATAAT-ACA
* *
105540048 ACAATAAT-ATAAATAATAATGTAAAAATAATAATAGTA
1 ATAATAATAAT-AATAATAATG-AAAAATAATAATA-CA
105540086 ATAATAATAATAATAATA
1 ATAATAATAATAATAATA
105540104 GTGATAATAA
Statistics
Matches: 179, Mismatches: 37, Indels: 32
0.72 0.15 0.13
Matches are distributed among these distances:
32 8 0.04
34 12 0.07
35 64 0.36
36 35 0.20
37 23 0.13
38 32 0.18
39 5 0.03
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.28
Consensus pattern (36 bp):
ATAATAATAATAATAATAATGAAAAATAATAATACA
Found at i:105540132 original size:3 final size:3
Alignment explanation
Indices: 105539835--105540113 Score: 196
Period size: 3 Copynumber: 93.3 Consensus size: 3
105539825 AAAAATGATG
* * * * *
105539835 ATA ATA ATA ATA ATG ATA AGA ATA CTA ATA ATA GTA ATA ATA ATA GAAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
* * * *
105539884 ATA ATA ATG GTA A-A A-A ATA ATA ATA ATA GTA ATA ATA ATA GTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* ** * * *
105539930 A-A AGA ATA GCA ATG ATA ATA ATA ATA TTG ATA ATAA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA
* * *
105539975 GTA A-A AAA ATA ATA ATA A-A ATGA AGA ATA ATA ATA CATTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA -A-TA ATA ATA
** * *
105540021 ATA A-A ATA GGGA ATA ATA ATA ATA ACA ACA ATA AT- ATAA ATA ATA
1 ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA
* * * * *
105540066 AT- GTA AAA ATA ATA ATA GTA ATA ATA ATA ATA ATA ATA GTG ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
105540113 A
1 A
105540114 ATTAATTAAT
Statistics
Matches: 212, Mismatches: 50, Indels: 28
0.73 0.17 0.10
Matches are distributed among these distances:
2 15 0.07
3 183 0.86
4 12 0.06
5 2 0.01
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:105546703 original size:35 final size:35
Alignment explanation
Indices: 105546664--105546734 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
105546654 TCTATGATCA
*
105546664 CATATATTTAAAGATCCCCTTCCATATTTGCCAAG
1 CATATATTTAAAGATCACCTTCCATATTTGCCAAG
* * * *
105546699 CATATCTTTGAAGATTACTTTCCATATTTGCCAAG
1 CATATATTTAAAGATCACCTTCCATATTTGCCAAG
105546734 C
1 C
105546735 TCCGGAGATG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.37
Consensus pattern (35 bp):
CATATATTTAAAGATCACCTTCCATATTTGCCAAG
Found at i:105547282 original size:11 final size:11
Alignment explanation
Indices: 105547266--105547308 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
105547256 GTAATTAGAA
105547266 AAAATAATATT
1 AAAATAATATT
105547277 AAAATAATA-T
1 AAAATAATATT
*
105547287 ATAATAATATT
1 AAAATAATATT
105547298 AAAATTAATAT
1 AAAA-TAATAT
105547309 ACAAATATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 9 0.32
11 13 0.46
12 6 0.21
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
AAAATAATATT
Found at i:105547294 original size:10 final size:10
Alignment explanation
Indices: 105547266--105547315 Score: 55
Period size: 11 Copynumber: 4.6 Consensus size: 10
105547256 GTAATTAGAA
105547266 AAAATAATATT
1 AAAATAATA-T
105547277 AAAATAATAT
1 AAAATAATAT
*
105547287 ATAATAATATT
1 AAAATAATA-T
105547298 AAAATTAATAT
1 AAAA-TAATAT
105547309 ACAAATA
1 A-AAATA
105547316 TGGAATTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 9 0.26
11 17 0.50
12 8 0.24
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (10 bp):
AAAATAATAT
Found at i:105547294 original size:21 final size:22
Alignment explanation
Indices: 105547268--105547309 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
105547258 AATTAGAAAA
105547268 AATAATATTAAAA-TAATATAT
1 AATAATATTAAAATTAATATAT
105547289 AATAATATTAAAATTAATATA
1 AATAATATTAAAATTAATATA
105547310 CAAATATGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AATAATATTAAAATTAATATAT
Found at i:105555863 original size:11 final size:11
Alignment explanation
Indices: 105555847--105555871 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
105555837 AGCCAGTAGA
105555847 CATGTATTTGC
1 CATGTATTTGC
105555858 CATGTATTTGC
1 CATGTATTTGC
105555869 CAT
1 CAT
105555872 TTTAGAGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.20, G:0.16, T:0.44
Consensus pattern (11 bp):
CATGTATTTGC
Found at i:105559245 original size:31 final size:31
Alignment explanation
Indices: 105559207--105559302 Score: 192
Period size: 31 Copynumber: 3.1 Consensus size: 31
105559197 AAAAAAGGAA
105559207 TGAAAGATAAGATCAAACGAATGTGCTTCAT
1 TGAAAGATAAGATCAAACGAATGTGCTTCAT
105559238 TGAAAGATAAGATCAAACGAATGTGCTTCAT
1 TGAAAGATAAGATCAAACGAATGTGCTTCAT
105559269 TGAAAGATAAGATCAAACGAATGTGCTTCAT
1 TGAAAGATAAGATCAAACGAATGTGCTTCAT
105559300 TGA
1 TGA
105559303 GTTAGCTTCT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 65 1.00
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26
Consensus pattern (31 bp):
TGAAAGATAAGATCAAACGAATGTGCTTCAT
Found at i:105563361 original size:6 final size:6
Alignment explanation
Indices: 105563350--105563383 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
105563340 TTACTTAAAT
105563350 TTCCTA TTCCTA TTCCTA TTCCTA TTCCT- TTCCT
1 TTCCTA TTCCTA TTCCTA TTCCTA TTCCTA TTCCT
105563384 TGCTTTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.12, C:0.35, G:0.00, T:0.53
Consensus pattern (6 bp):
TTCCTA
Found at i:105576506 original size:2 final size:2
Alignment explanation
Indices: 105576499--105576527 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
105576489 TTTAATTGTT
105576499 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
105576528 TCAGGATCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:105581097 original size:36 final size:37
Alignment explanation
Indices: 105581016--105581097 Score: 148
Period size: 37 Copynumber: 2.2 Consensus size: 37
105581006 CAAAAGAGAT
105581016 ATGCCAATGAAGTTCTTAAAAAATTCATAATGGGGGC
1 ATGCCAATGAAGTTCTTAAAAAATTCATAATGGGGGC
105581053 ATGCCAATGAAGTTCTTAAAAAATTCATAATGGGGGC
1 ATGCCAATGAAGTTCTTAAAAAATTCATAATGGGGGC
*
105581090 TTG-CAATG
1 ATGCCAATG
105581098 GAGTCAAGAA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
36 5 0.11
37 39 0.89
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (37 bp):
ATGCCAATGAAGTTCTTAAAAAATTCATAATGGGGGC
Found at i:105586034 original size:26 final size:27
Alignment explanation
Indices: 105585998--105586048 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
105585988 CACAAAATAT
105585998 ATAAATTT-AAATAAATAAACACGAGC
1 ATAAATTTAAAATAAATAAACACGAGC
* *
105586024 ATAAATTTAAAATTAATGAACACGA
1 ATAAATTTAAAATAAATAAACACGA
105586049 ACAAAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.57, C:0.10, G:0.08, T:0.25
Consensus pattern (27 bp):
ATAAATTTAAAATAAATAAACACGAGC
Found at i:105586612 original size:16 final size:17
Alignment explanation
Indices: 105586591--105586628 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
105586581 CAATCAAGTC
*
105586591 ATTAGTT-TTTAATTTG
1 ATTAGTTATCTAATTTG
105586607 ATTAGTTGATCTAATTTG
1 ATTAGTT-ATCTAATTTG
105586625 ATTA
1 ATTA
105586629 AATAGGTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
18 12 0.63
ACGTcount: A:0.29, C:0.03, G:0.13, T:0.55
Consensus pattern (17 bp):
ATTAGTTATCTAATTTG
Found at i:105586872 original size:20 final size:20
Alignment explanation
Indices: 105586847--105586910 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
105586837 TTTTTTTTTA
105586847 CTTAATACATCATTTGGTAC
1 CTTAATACATCATTTGGTAC
** *
105586867 CTTAATTTGAT-ATTT-TTA-
1 CTTAA-TACATCATTTGGTAC
105586885 CTTAATACATCATTTGGTAC
1 CTTAATACATCATTTGGTAC
105586905 CTTAAT
1 CTTAAT
105586911 TTGATATTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
17 3 0.09
18 9 0.26
19 4 0.12
20 15 0.44
21 3 0.09
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.47
Consensus pattern (20 bp):
CTTAATACATCATTTGGTAC
Found at i:105586891 original size:38 final size:38
Alignment explanation
Indices: 105586841--105586920 Score: 160
Period size: 38 Copynumber: 2.1 Consensus size: 38
105586831 TTGATTTTTT
105586841 TTTTTACTTAATACATCATTTGGTACCTTAATTTGATA
1 TTTTTACTTAATACATCATTTGGTACCTTAATTTGATA
105586879 TTTTTACTTAATACATCATTTGGTACCTTAATTTGATA
1 TTTTTACTTAATACATCATTTGGTACCTTAATTTGATA
105586917 TTTT
1 TTTT
105586921 ATTCTAGTGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.28, C:0.12, G:0.07, T:0.53
Consensus pattern (38 bp):
TTTTTACTTAATACATCATTTGGTACCTTAATTTGATA
Found at i:105586899 original size:18 final size:18
Alignment explanation
Indices: 105586841--105586899 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
105586831 TTGATTTTTT
105586841 TTTTTACTTAATACATCA
1 TTTTTACTTAATACATCA
* **
105586859 TTTGGTACCTTAATTTGAT-A
1 TTT-TTA-CTTAA-TACATCA
105586879 TTTTTACTTAATACATCA
1 TTTTTACTTAATACATCA
105586897 TTT
1 TTT
105586900 GGTACCTTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
17 3 0.10
18 12 0.39
19 4 0.13
20 9 0.29
21 3 0.10
ACGTcount: A:0.29, C:0.14, G:0.05, T:0.53
Consensus pattern (18 bp):
TTTTTACTTAATACATCA
Found at i:105586919 original size:20 final size:20
Alignment explanation
Indices: 105586858--105586919 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
105586848 TTAATACATC
105586858 ATTTGGTACCTTAATTTGAT
1 ATTTGGTACCTTAATTTGAT
* **
105586878 ATTT-TTA-CTTAA-TACAT
1 ATTTGGTACCTTAATTTGAT
105586895 CATTTGGTACCTTAATTTGAT
1 -ATTTGGTACCTTAATTTGAT
105586916 ATTT
1 ATTT
105586920 TATTCTAGTG
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
17 3 0.09
18 9 0.28
19 4 0.12
20 13 0.41
21 3 0.09
ACGTcount: A:0.27, C:0.11, G:0.10, T:0.52
Consensus pattern (20 bp):
ATTTGGTACCTTAATTTGAT
Found at i:105591273 original size:40 final size:40
Alignment explanation
Indices: 105591217--105591309 Score: 132
Period size: 40 Copynumber: 2.3 Consensus size: 40
105591207 GGCGTTTGGA
* * * * *
105591217 TAAAAAACGCCCCTATAGGTCGAGCATTAGCGGCGCTTTT
1 TAAAAAATGCCGCTATAGATCGAGCATTAGCGACGCTTTC
105591257 TAAAAAATGCCGCTATAGATCGAGCATTAGCGACGCTTTC
1 TAAAAAATGCCGCTATAGATCGAGCATTAGCGACGCTTTC
*
105591297 TGAAAAATGCCGC
1 TAAAAAATGCCGC
105591310 AAAAAATATT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.24
Consensus pattern (40 bp):
TAAAAAATGCCGCTATAGATCGAGCATTAGCGACGCTTTC
Found at i:105591708 original size:21 final size:21
Alignment explanation
Indices: 105591640--105591873 Score: 132
Period size: 22 Copynumber: 10.9 Consensus size: 21
105591630 AACACTCCCT
* * *
105591640 TAAACCCTTAAATACAAAATCT
1 TAAACCC-TAAATCCTAAATCC
* * * *
105591662 TAAATCCTAAAACTCTAAACCT
1 TAAACCCTAAATC-CTAAATCC
105591684 TAAACCCTAAA-CCTAAATCAC
1 TAAACCCTAAATCCTAAATC-C
**
105591705 TAAACCCTTAAAT-AAAAATCC
1 TAAACCC-TAAATCCTAAATCC
* *
105591726 TAAATCCTAAATCCTAAAACTC
1 TAAACCCTAAATCCTAAATC-C
* * *
105591748 TAAACCTTAAACCCTAAACCC
1 TAAACCCTAAATCCTAAATCC
* * *
105591769 TTAAGCCCTTAAATACGAAATCC
1 -TAAACCC-TAAATCCTAAATCC
* * *
105591792 TAAATCCTAAATCATAAAACTC
1 TAAACCCTAAATCCTAAATC-C
* *
105591814 TAAACCTTAAA-CCTTAAACCC
1 TAAACCCTAAATCC-TAAATCC
* *
105591835 TAAACCCTAAATCTTAAATAC
1 TAAACCCTAAATCCTAAATCC
* *
105591856 TAAACCATAAACCCTAAA
1 TAAACCCTAAATCCTAAA
105591874 CTATAGACAC
Statistics
Matches: 160, Mismatches: 41, Indels: 23
0.71 0.18 0.10
Matches are distributed among these distances:
20 11 0.07
21 65 0.41
22 74 0.46
23 10 0.06
ACGTcount: A:0.47, C:0.28, G:0.01, T:0.24
Consensus pattern (21 bp):
TAAACCCTAAATCCTAAATCC
Found at i:105591874 original size:7 final size:7
Alignment explanation
Indices: 105591671--105591899 Score: 102
Period size: 7 Copynumber: 32.0 Consensus size: 7
105591661 TTAAATCCTA
*
105591671 AAACTCT
1 AAACCCT
*
105591678 AAACCTT
1 AAACCCT
105591685 AAACCCT
1 AAACCCT
105591692 AAA-CCT
1 AAACCCT
*
105591698 AAATCACT
1 AAA-CCCT
105591706 AAACCCTT
1 AAACCC-T
***
105591714 AAA-TAA
1 AAACCCT
*
105591720 AAATCCT
1 AAACCCT
*
105591727 AAATCCT
1 AAACCCT
*
105591734 AAATCCT
1 AAACCCT
*
105591741 AAAACTCT
1 -AAACCCT
*
105591749 AAACCTT
1 AAACCCT
105591756 AAACCCT
1 AAACCCT
105591763 AAACCCTT
1 AAACCC-T
*
105591771 AAGCCCTT
1 AAACCC-T
** *
105591779 AAATACG
1 AAACCCT
*
105591786 AAATCCT
1 AAACCCT
*
105591793 AAATCCT
1 AAACCCT
* *
105591800 AAATCAT
1 AAACCCT
*
105591807 AAAACTCT
1 -AAACCCT
*
105591815 AAACCTT
1 AAACCCT
*
105591822 AAACCTT
1 AAACCCT
105591829 AAACCCT
1 AAACCCT
105591836 AAACCCT
1 AAACCCT
* *
105591843 AAATCTT
1 AAACCCT
**
105591850 AAATACT
1 AAACCCT
*
105591857 AAACCAT
1 AAACCCT
105591864 AAACCCT
1 AAACCCT
**
105591871 AAACTAT
1 AAACCCT
* *
105591878 AGACACT
1 AAACCCT
105591885 AAACCCTT
1 AAACCC-T
105591893 AAACCCT
1 AAACCCT
105591900 TAAATACAAA
Statistics
Matches: 169, Mismatches: 45, Indels: 16
0.73 0.20 0.07
Matches are distributed among these distances:
6 9 0.05
7 124 0.73
8 36 0.21
ACGTcount: A:0.46, C:0.29, G:0.01, T:0.24
Consensus pattern (7 bp):
AAACCCT
Found at i:105591940 original size:130 final size:130
Alignment explanation
Indices: 105591614--105591940 Score: 362
Period size: 122 Copynumber: 2.6 Consensus size: 130
105591604 AATTATCCGT
105591614 AAACCCTAAACCTGTAAACACT---CCCTTAAACCCTTAAATACAAAATCTTAAATCCTAAAACT
1 AAACCCTAAACCT-TAAACACTAAACCCTTAAACCCTTAAATACAAAATCTTAAATCCTAAAACT
* * *
105591676 CTAAACCTTAAACCCTAAACCTAAATCACTAAACCCTTAAATAAAAATCCTAAATCCTAAATCCT
65 CTAAACCTAAAACCCTAAACCTAAATCACTAAACCCTTAAACAAAAATCCTAAATACTAAATCCT
105591741 A
130 A
* * * * *
105591742 AAACTCTAAACCTTAAACCCTAAACCCTTAAGCCCTTAAATACGAAATCCTAAATCCT-AAA-TC
1 AAACCCTAAACCTTAAACACTAAACCCTTAAACCCTTAAATACAAAATCTTAAATCCTAAAACTC
* ** *
105591805 ---A--TAAAACTCTAAACCTTAAA-C-CTTAAACCC-TAAACCCTAAATCTTAAATACTAAA-C
66 TAAACCTAAAACCCTAAACC-TAAATCAC-TAAACCCTTAAA-CAAAAATCCTAAATACTAAATC
105591861 C-A
128 CTA
*
105591863 TAAACCCTAAA-CTATAGACACTAAACCCTTAAACCCTTAAATACAAAATCTTAAATCCTAAAAC
1 -AAACCCTAAACCT-TAAACACTAAACCCTTAAACCCTTAAATACAAAATCTTAAATCCTAAAAC
105591927 TCTAAACCGTAAAA
64 TCTAAACC-TAAAA
105591941 ATAAAATTCA
Statistics
Matches: 165, Mismatches: 18, Indels: 30
0.77 0.08 0.14
Matches are distributed among these distances:
121 3 0.02
122 56 0.34
123 38 0.23
124 6 0.04
125 1 0.01
127 8 0.05
128 14 0.08
129 3 0.02
130 36 0.22
ACGTcount: A:0.46, C:0.28, G:0.02, T:0.24
Consensus pattern (130 bp):
AAACCCTAAACCTTAAACACTAAACCCTTAAACCCTTAAATACAAAATCTTAAATCCTAAAACTC
TAAACCTAAAACCCTAAACCTAAATCACTAAACCCTTAAACAAAAATCCTAAATACTAAATCCTA
Found at i:105592253 original size:3 final size:3
Alignment explanation
Indices: 105592245--105592303 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
105592235 CATTTTAGTA
105592245 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
105592293 AAT AAT AAT AA
1 AAT AAT AAT AA
105592304 AAGAGAAAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:105597575 original size:7 final size:7
Alignment explanation
Indices: 105597565--105597589 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
105597555 AGATAATACA
105597565 TATCAAG
1 TATCAAG
105597572 TATCAAG
1 TATCAAG
105597579 TATCAAG
1 TATCAAG
105597586 TATC
1 TATC
105597590 TAATAGGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (7 bp):
TATCAAG
Found at i:105597665 original size:9 final size:9
Alignment explanation
Indices: 105597647--105597785 Score: 120
Period size: 9 Copynumber: 15.6 Consensus size: 9
105597637 TATTTATGTA
105597647 TTATGTAAG
1 TTATGTAAG
*
105597656 TTAAGTAAG
1 TTATGTAAG
*
105597665 TTTTGTAAG
1 TTATGTAAG
105597674 TTATGTAAG
1 TTATGTAAG
*
105597683 TTTTGTAAG
1 TTATGTAAG
105597692 TTATGTAAG
1 TTATGTAAG
* *
105597701 ATATGATATG
1 TTATG-TAAG
* * *
105597711 ATATAT-AT
1 TTATGTAAG
*
105597719 TTGTGTAAG
1 TTATGTAAG
*
105597728 TGATGTAAG
1 TTATGTAAG
* *
105597737 TTATAT-AT
1 TTATGTAAG
*
105597745 TTATCTAAG
1 TTATGTAAG
*
105597754 TTATCTAAG
1 TTATGTAAG
*
105597763 TTATGTAAA
1 TTATGTAAG
105597772 TTATGTAAG
1 TTATGTAAG
105597781 TTATG
1 TTATG
105597786 ATATGATATA
Statistics
Matches: 102, Mismatches: 25, Indels: 6
0.77 0.19 0.05
Matches are distributed among these distances:
8 9 0.09
9 86 0.84
10 7 0.07
ACGTcount: A:0.34, C:0.01, G:0.19, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:105597746 original size:26 final size:26
Alignment explanation
Indices: 105597712--105597766 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
105597702 TATGATATGA
* * *
105597712 TATATATTTGTGTAAGTGATGTAAGT
1 TATATATTTATCTAAGTGATCTAAGT
*
105597738 TATATATTTATCTAAGTTATCTAAGT
1 TATATATTTATCTAAGTGATCTAAGT
105597764 TAT
1 TAT
105597767 GTAAATTATG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.33, C:0.04, G:0.15, T:0.49
Consensus pattern (26 bp):
TATATATTTATCTAAGTGATCTAAGT
Found at i:105598512 original size:23 final size:23
Alignment explanation
Indices: 105598484--105598529 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
105598474 AATTTTTATT
* *
105598484 ATTATCAAATGAATTTTCTTAAC
1 ATTATCAAATAAATTTTATTAAC
105598507 ATTATCAAATAAATTTTATTAAC
1 ATTATCAAATAAATTTTATTAAC
105598530 CAAATACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.43
Consensus pattern (23 bp):
ATTATCAAATAAATTTTATTAAC
Done.