Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 178 of 198
Found at i:55807574 original size:2 final size:2
Alignment explanation
Indices: 55807567--55807593 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
55807557 TTAGATTGGT
55807567 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
55807594 TAAGATTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:55817659 original size:2 final size:2
Alignment explanation
Indices: 55817652--55817676 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
55817642 AAAATAGCAA
55817652 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
55817677 ACATCAAATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:55824883 original size:17 final size:18
Alignment explanation
Indices: 55824852--55824902 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 18
55824842 CAGTAAATTA
55824852 AATAATTA-AATTAA-TGT
1 AATAATTATAA-TAATTGT
*
55824869 CATAATTATAATAATTGT
1 AATAATTATAATAATTGT
55824887 AATAAATTTATAATAA
1 AAT-AA-TTATAATAA
55824903 ATAATGAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 10 0.36
18 7 0.25
19 2 0.07
20 9 0.32
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (18 bp):
AATAATTATAATAATTGT
Found at i:55833628 original size:3 final size:3
Alignment explanation
Indices: 55833622--55833682 Score: 113
Period size: 3 Copynumber: 20.3 Consensus size: 3
55833612 TTATTTAAGT
55833622 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
55833670 TTA CTA TTA TTA T
1 TTA TTA TTA TTA T
55833683 ACTAATATAA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:55838089 original size:6 final size:6
Alignment explanation
Indices: 55838080--55838139 Score: 65
Period size: 6 Copynumber: 10.7 Consensus size: 6
55838070 AAGAAAAAGA
* * *
55838080 AAAATC AAAATC AAAATC AAAGTC AAAATG AAAAT- GAAA-- AAAATC
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
55838125 AAAATC AAAAT- AAAA
1 AAAATC AAAATC AAAA
55838140 AAAACAAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
4 3 0.06
5 7 0.15
6 37 0.79
ACGTcount: A:0.70, C:0.10, G:0.05, T:0.15
Consensus pattern (6 bp):
AAAATC
Found at i:55838128 original size:15 final size:15
Alignment explanation
Indices: 55838086--55838134 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
55838076 AAGAAAAATC
55838086 AAAATCAAAATCAAA
1 AAAATCAAAATCAAA
* *
55838101 GTCAAAATGAAAATGAAA
1 ---AAAATCAAAATCAAA
55838119 AAAATCAAAATCAAA
1 AAAATCAAAATCAAA
55838134 A
1 A
55838135 TAAAAAAAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 14 0.52
18 13 0.48
ACGTcount: A:0.69, C:0.10, G:0.06, T:0.14
Consensus pattern (15 bp):
AAAATCAAAATCAAA
Found at i:55838128 original size:21 final size:21
Alignment explanation
Indices: 55838102--55838173 Score: 74
Period size: 20 Copynumber: 3.3 Consensus size: 21
55838092 AAAATCAAAG
55838102 TCAAAATGAAAATGAAAAAAA
1 TCAAAATGAAAATGAAAAAAA
*
55838123 TCAAAATCAAAAT-AAAAAAA
1 TCAAAATGAAAATGAAAAAAA
* * *
55838143 ACAAAAAGAAGAAAGAAGAAAAAA
1 TCAAAATGAA-AATG-A-AAAAAA
55838167 TCAAAAT
1 TCAAAAT
55838174 CAAGATCAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
20 14 0.35
21 14 0.35
23 1 0.03
24 11 0.28
ACGTcount: A:0.74, C:0.07, G:0.08, T:0.11
Consensus pattern (21 bp):
TCAAAATGAAAATGAAAAAAA
Found at i:55838148 original size:27 final size:27
Alignment explanation
Indices: 55838092--55838149 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
55838082 AATCAAAATC
* **
55838092 AAAATCAAAGTCAAAATGAAAATGAAA
1 AAAATCAAAATCAAAATGAAAAAAAAA
55838119 AAAATCAAAATCAAAAT-AAAAAAAACA
1 AAAATCAAAATCAAAATGAAAAAAAA-A
55838146 AAAA
1 AAAA
55838150 GAAGAAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 6 0.22
27 21 0.78
ACGTcount: A:0.74, C:0.09, G:0.05, T:0.12
Consensus pattern (27 bp):
AAAATCAAAATCAAAATGAAAAAAAAA
Found at i:55838182 original size:50 final size:51
Alignment explanation
Indices: 55838119--55838217 Score: 130
Period size: 50 Copynumber: 2.0 Consensus size: 51
55838109 GAAAATGAAA
*
55838119 AAAATCAAAATCAAAATAAAAAAAACAAAAAG-AAGAAAGAA-GAAAAAATC
1 AAAATCAAAATCAAAACAAAAAAAACAAAAAGAAAG-AAGAATGAAAAAATC
* ** *
55838169 AAAATCAAGATCAAAACAAAAATGAGAAAAAGAAAGAAGAATGAAAAAA
1 AAAATCAAAATCAAAACAAAAAAAACAAAAAGAAAGAAGAATGAAAAAA
55838218 GAGAAACCTA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
50 32 0.76
51 10 0.24
ACGTcount: A:0.74, C:0.07, G:0.11, T:0.08
Consensus pattern (51 bp):
AAAATCAAAATCAAAACAAAAAAAACAAAAAGAAAGAAGAATGAAAAAATC
Found at i:55840542 original size:44 final size:43
Alignment explanation
Indices: 55840386--55840846 Score: 188
Period size: 46 Copynumber: 10.7 Consensus size: 43
55840376 ATTATACAGG
* * * * *
55840386 TCTTATTTCCCTGAGATTACAGTAGAACAGACCGAAGA-ATTTCAGG
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGACA----AGA
* * *
55840432 TCTTACCTCCCTGAGATTACAGTGGAGTAGACCGAAGAATTTCAA-A
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAG-A---CAAGA
* * *
55840478 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGACA-AGA
* * * **
55840522 TTTTATCTCCCTGAGATTACAGCGGAGTAGATCGAAGACACTA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGACAAGA
* * * *
55840565 TCCTATCTCTCTGAGATTACAGTGGAGC-GAAT--TA-A-AGGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAG-ATCGAAGACAAGA
* * * ** * * *
55840604 TCTTATCTCTCTGA-AGTTATAGTAGAGTGGATCGTA-TC-AGG
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATCGAAGACAAGA
*
55840645 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGA-ATTGCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGACA----AGA
* ** * *
55840691 TCTTATCTCCCTGATATTACAGCAGAGCAGAT-TAA-AAATAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGACA-AG--A
* * * *
55840735 TCCTATCTCCCTGAGATTACAGTGGAGCGGAT--TA-A-AGGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGACAAGA
* * * * * * *
55840774 TCTTATCTCTCT-AAAGTTACAGTAGAGTAGATCGTA-TC-AGG
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATCGAAGACAAGA
* *
55840815 TCTTATTTCCCTGAGATTACAGTGGAACAGAT
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGAT
55840847 TGAATTTAAG
Statistics
Matches: 315, Mismatches: 72, Indels: 61
0.70 0.16 0.14
Matches are distributed among these distances:
38 3 0.01
39 50 0.16
40 2 0.01
41 58 0.18
42 9 0.03
43 29 0.09
44 64 0.20
45 3 0.01
46 94 0.30
47 2 0.01
51 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.29
Consensus pattern (43 bp):
TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGACAAGA
Found at i:55840660 original size:80 final size:80
Alignment explanation
Indices: 55840568--55840840 Score: 271
Period size: 80 Copynumber: 3.3 Consensus size: 80
55840558 GACACTATCC
* * *
55840568 TATCTCTCTGAGATTACAGTGGAGCGAATTAAAGGATCTTATCTCTCTGAAGTTATAGTAGAGTG
1 TATCTCCCTGAGATTACAGTGGAGCGAATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTA
55840633 GATCGTATCAGGTCT
66 GATCGTATCAGGTCT
** * *
55840648 TATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTGCAGATCTTATCTCCCTGATA-TTACA
1 TATCTCCCTGAGATTACAGTGGAGC-GA---ATTAA-AG--GATCTTATCTCTCTGA-AGTTACA
* * *** * *
55840712 GCAGAGCAGATTAAAAAT-AGTAATCC
58 GTAGAGTAGA-T-CGTATCAG--GTCT
* *
55840738 TATCTCCCTGAGATTACAGTGGAGCGGATTAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTA
1 TATCTCCCTGAGATTACAGTGGAGCGAATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTA
55840803 GATCGTATCAGGTCT
66 GATCGTATCAGGTCT
*
55840818 TATTTCCCTGAGATTACAGTGGA
1 TATCTCCCTGAGATTACAGTGGA
55840841 ACAGATTGAA
Statistics
Matches: 151, Mismatches: 28, Indels: 28
0.73 0.14 0.14
Matches are distributed among these distances:
80 48 0.32
81 4 0.03
82 4 0.03
83 27 0.18
84 3 0.02
85 2 0.01
86 3 0.02
87 26 0.17
88 4 0.03
89 3 0.02
90 27 0.18
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (80 bp):
TATCTCCCTGAGATTACAGTGGAGCGAATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTA
GATCGTATCAGGTCT
Found at i:55840771 original size:170 final size:167
Alignment explanation
Indices: 55840478--55840845 Score: 513
Period size: 170 Copynumber: 2.2 Consensus size: 167
55840468 GAATTTCAAA
* ** * *
55840478 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATTTTATCTCCCTGAGATTACA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGCAAGAGATCTTATCTCCCTGAGATTACA
* * * * *
55840543 GCGGAGTAGATCGAAGACACTATCCTATCTCTCTGAGATTACAGTGGAGCGAATTAAAGGATCTT
66 GCAGAGCAGATCAAAAACACTATCCTATCTCCCTGAGATTACAGTGGAGCGAATTAAAGGATCTT
* * *
55840608 ATCTCTCTGAAGTTATAGTAGAGTGGATCGTATCAGG
131 ATCTCTCTAAAGTTACAGTAGAGTAGATCGTATCAGG
*
55840645 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAG-AATTGCAGATCTTATCTCCCTGATATT
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGCAA--G-AGATCTTATCTCCCTGAGATT
* * * *
55840709 ACAGCAGAGCAGATTAAAAATAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAGGA
63 ACAGCAGAGCAGATCAAAAACACT-ATCCTATCTCCCTGAGATTACAGTGGAGCGAATTAAAGGA
55840774 TCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGTATCAGG
127 TCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGTATCAGG
* *
55840815 TCTTATTTCCCTGAGATTACAGTGGAACAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGA
55840846 TTGAATTTAA
Statistics
Matches: 177, Mismatches: 20, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
166 1 0.01
167 34 0.19
168 1 0.01
169 36 0.20
170 105 0.59
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (167 bp):
TCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGCAAGAGATCTTATCTCCCTGAGATTACA
GCAGAGCAGATCAAAAACACTATCCTATCTCCCTGAGATTACAGTGGAGCGAATTAAAGGATCTT
ATCTCTCTAAAGTTACAGTAGAGTAGATCGTATCAGG
Found at i:55840916 original size:44 final size:44
Alignment explanation
Indices: 55840867--55841067 Score: 144
Period size: 44 Copynumber: 4.7 Consensus size: 44
55840857 CTAGTAATCC
* *
55840867 TATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATTGTAGATCT
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATTCTAGATCT
* * *
55840911 TATCTCCCTAAGTAGTAGTGGAGCAGATCG--CA-TCAAG-TCT
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATTCTAGATCT
* * * * ** * *
55840951 TATCTCCCTAAGTAGTAGCGGAGCA-AACAAAAGAAACCA-ATCC
1 TATCTCCCTAAGCAGTAGTGGAGCAGATC-GAAGATTCTAGATCT
* * * * * *
55840994 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCT
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATTCTAGATCT
* * **
55841038 TATCTCTCTAAGCAATAGTAAAGCAGATCG
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCG
55841068 CATCCAGTCT
Statistics
Matches: 115, Mismatches: 35, Indels: 14
0.70 0.21 0.09
Matches are distributed among these distances:
39 2 0.02
40 27 0.23
41 3 0.03
42 2 0.02
43 29 0.25
44 52 0.45
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.25
Consensus pattern (44 bp):
TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATTCTAGATCT
Found at i:55841001 original size:127 final size:128
Alignment explanation
Indices: 55840862--55841091 Score: 363
Period size: 127 Copynumber: 1.8 Consensus size: 128
55840852 TTAAGCTAGT
* * *
55840862 AATCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATTGTAGATCTTATCTCCCTAAGTAGT
1 AATCCTATCTCCCTAAGCAGCAGTGGAGCAGGTCGAAGATTGTAGATCTTATCTCCCTAAGCAAT
**
55840927 AGTGGAGCAGATCGCATCAAGTCTTATCTCCCT-AAGTAGTAGCGGAGCAAACAAAAGAAACC
66 AGTAAAGCAGATCGCATCAAGTCTTATCTCCCTGAAGTAGTAGCGGAGCAAACAAAAGAAACC
* * * *
55840989 AATCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCTCTAAGCAAT
1 AATCCTATCTCCCTAAGCAGCAGTGGAGCAGGTCGAAGATTGTAGATCTTATCTCCCTAAGCAAT
*
55841054 AGTAAAGCAGATCGCATCCAGTCTTATCTCCCTGAAGT
66 AGTAAAGCAGATCGCATCAAGTCTTATCTCCCTGAAGT
55841092 TACAGTGGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
127 88 0.96
128 4 0.04
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.26
Consensus pattern (128 bp):
AATCCTATCTCCCTAAGCAGCAGTGGAGCAGGTCGAAGATTGTAGATCTTATCTCCCTAAGCAAT
AGTAAAGCAGATCGCATCAAGTCTTATCTCCCTGAAGTAGTAGCGGAGCAAACAAAAGAAACC
Found at i:55842569 original size:3 final size:3
Alignment explanation
Indices: 55842563--55842611 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
55842553 TTATTTAAGT
*
55842563 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
55842611 T
1 T
55842612 ACTAATATAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:55842768 original size:2 final size:2
Alignment explanation
Indices: 55842761--55842790 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
55842751 ATTTGTCATA
55842761 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55842791 TTACATATCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55847956 original size:16 final size:16
Alignment explanation
Indices: 55847901--55847956 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
55847891 AAAAGTTAAC
*
55847901 AACCCATACCCAAAAT
1 AACCCAAACCCAAAAT
** *
55847917 AACCTGAACCTGAAAA-
1 AACCCAAACC-CAAAAT
*
55847933 AACACAAACCCAAAAT
1 AACCCAAACCCAAAAT
55847949 AACCCAAA
1 AACCCAAA
55847957 GAGGTAATCC
Statistics
Matches: 29, Mismatches: 9, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
15 4 0.14
16 21 0.72
17 4 0.14
ACGTcount: A:0.55, C:0.32, G:0.04, T:0.09
Consensus pattern (16 bp):
AACCCAAACCCAAAAT
Found at i:55855357 original size:21 final size:22
Alignment explanation
Indices: 55855327--55855371 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
55855317 GAACAAATTG
55855327 TTGATTCTATTTCTTTCTTG-AT
1 TTGATTCTA-TTCTTTCTTGTAT
*
55855349 TTGA-TCTATTCTTTTTTGTAT
1 TTGATTCTATTCTTTCTTGTAT
55855370 TT
1 TT
55855372 CTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 8 0.38
22 4 0.19
ACGTcount: A:0.13, C:0.11, G:0.09, T:0.67
Consensus pattern (22 bp):
TTGATTCTATTCTTTCTTGTAT
Found at i:55862382 original size:35 final size:34
Alignment explanation
Indices: 55862336--55862532 Score: 286
Period size: 35 Copynumber: 5.7 Consensus size: 34
55862326 AAATGATACA
55862336 TGAACAGGAGAGATTCCCTGCAACAACATAATGCG
1 TGAACAGGAGAGATTCCCTGCAACAA-ATAATGCG
55862371 TGAACAGGAGAGATTCCCTGCAACAAAATAATGCG
1 TGAACAGGAGAGATTCCCTGCAAC-AAATAATGCG
* * *
55862406 TGAACAGGAGAGATTCCCTGCAAGAAATGATGTG
1 TGAACAGGAGAGATTCCCTGCAACAAATAATGCG
55862440 TGAACAGGAGAAGATTCCCTGCAACAAAATAATGCG
1 TGAACAGGAG-AGATTCCCTGCAAC-AAATAATGCG
* * * *
55862476 TGAACATGAGAGATTCCCTGCAAGAAATGATGTG
1 TGAACAGGAGAGATTCCCTGCAACAAATAATGCG
*
55862510 TGAACATGAGAGATTCCCTGCAA
1 TGAACAGGAGAGATTCCCTGCAA
55862533 TGCGTGAACA
Statistics
Matches: 149, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
34 49 0.33
35 81 0.54
36 19 0.13
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.19
Consensus pattern (34 bp):
TGAACAGGAGAGATTCCCTGCAACAAATAATGCG
Found at i:55862455 original size:70 final size:69
Alignment explanation
Indices: 55862336--55862532 Score: 331
Period size: 70 Copynumber: 2.8 Consensus size: 69
55862326 AAATGATACA
* * *
55862336 TGAACAGGAGAGATTCCCTGCAACAACATAATGCGTGAACAGGAGAGATTCCCTGCAACAAAATA
1 TGAACAGGAGAGATTCCCTGCAAGAA-ATGATGTGTGAACAGGAGAGATTCCCTGCAACAAAATA
55862401 ATGCG
65 ATGCG
55862406 TGAACAGGAGAGATTCCCTGCAAGAAATGATGTGTGAACAGGAGAAGATTCCCTGCAACAAAATA
1 TGAACAGGAGAGATTCCCTGCAAGAAATGATGTGTGAACAGGAG-AGATTCCCTGCAACAAAATA
55862471 ATGCG
65 ATGCG
* *
55862476 TGAACATGAGAGATTCCCTGCAAGAAATGATGTGTGAACATGAGAGATTCCCTGCAA
1 TGAACAGGAGAGATTCCCTGCAAGAAATGATGTGTGAACAGGAGAGATTCCCTGCAA
55862533 TGCGTGAACA
Statistics
Matches: 121, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
69 29 0.24
70 92 0.76
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.19
Consensus pattern (69 bp):
TGAACAGGAGAGATTCCCTGCAAGAAATGATGTGTGAACAGGAGAGATTCCCTGCAACAAAATAA
TGCG
Found at i:55862848 original size:14 final size:13
Alignment explanation
Indices: 55862821--55862858 Score: 67
Period size: 14 Copynumber: 2.8 Consensus size: 13
55862811 AGTTTCCAAA
55862821 TTTTCAAATTAAG
1 TTTTCAAATTAAG
55862834 TTTTCAAACTTAAG
1 TTTTCAAA-TTAAG
55862848 TTTTCAAATTA
1 TTTTCAAATTA
55862859 CAAATGTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (13 bp):
TTTTCAAATTAAG
Found at i:55867524 original size:15 final size:15
Alignment explanation
Indices: 55867506--55867540 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
55867496 AAAATTCAAA
55867506 AAAAAT-AATAAAATC
1 AAAAATCAA-AAAATC
55867521 AAAAATCAAAAAATC
1 AAAAATCAAAAAATC
55867536 AAAAA
1 AAAAA
55867541 ATACATTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 17 0.89
16 2 0.11
ACGTcount: A:0.77, C:0.09, G:0.00, T:0.14
Consensus pattern (15 bp):
AAAAATCAAAAAATC
Found at i:55867532 original size:8 final size:8
Alignment explanation
Indices: 55867505--55867542 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
55867495 AAAAATTCAA
55867505 AAAAAAT-
1 AAAAAATC
55867512 AATAAAATC
1 AA-AAAATC
55867521 -AAAAATC
1 AAAAAATC
55867528 AAAAAATC
1 AAAAAATC
55867536 AAAAAAT
1 AAAAAAT
55867543 ACATTTTGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
7 8 0.29
8 20 0.71
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (8 bp):
AAAAAATC
Found at i:55867580 original size:29 final size:29
Alignment explanation
Indices: 55867545--55867612 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
55867535 CAAAAAATAC
*
55867545 ATTTTGACCC-CTGAACTTTTTGAAATTAA
1 ATTTTGACCCAC-CAACTTTTTGAAATTAA
*
55867574 ATTTTGACCCACCAACTTTTTGAAATTAC
1 ATTTTGACCCACCAACTTTTTGAAATTAA
*
55867603 CTTTTGACCC
1 ATTTTGACCC
55867613 TAAAGTTTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 34 0.97
30 1 0.03
ACGTcount: A:0.28, C:0.24, G:0.09, T:0.40
Consensus pattern (29 bp):
ATTTTGACCCACCAACTTTTTGAAATTAA
Found at i:55867883 original size:10 final size:10
Alignment explanation
Indices: 55867868--55867912 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
55867858 TTTTTCGAAA
55867868 AAAAGAGAAG
1 AAAAGAGAAG
*
55867878 AAAAGAGGAG
1 AAAAGAGAAG
55867888 AAAAGAGAA-
1 AAAAGAGAAG
* *
55867897 AGAGGAGAAG
1 AAAAGAGAAG
55867907 AAAAGA
1 AAAAGA
55867913 AGGAGTACCG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
9 7 0.25
10 21 0.75
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (10 bp):
AAAAGAGAAG
Found at i:55867900 original size:16 final size:15
Alignment explanation
Indices: 55867875--55867917 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
55867865 AAAAAAAGAG
55867875 AAGAAAAGAGGAGAA
1 AAGAAAAGAGGAGAA
55867890 AAGAGAAAGAGGAG--
1 AAGA-AAAGAGGAGAA
55867904 AAGAAAAGAAGGAG
1 AAGAAAAG-AGGAG
55867918 TACCGACGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 4 0.15
14 9 0.35
15 4 0.15
16 9 0.35
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (15 bp):
AAGAAAAGAGGAGAA
Found at i:55868012 original size:12 final size:12
Alignment explanation
Indices: 55867984--55868025 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
55867974 AAGGTTTTGT
55867984 GAAGAGG-A-AA
1 GAAGAGGAAGAA
*
55867994 GAGGAGGAAGAA
1 GAAGAGGAAGAA
55868006 GAAGAGGAAGAA
1 GAAGAGGAAGAA
55868018 GAA-AGGAA
1 GAAGAGGAA
55868026 AAAAAAGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 6 0.21
11 6 0.21
12 16 0.57
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (12 bp):
GAAGAGGAAGAA
Found at i:55868880 original size:17 final size:18
Alignment explanation
Indices: 55868852--55869025 Score: 198
Period size: 18 Copynumber: 9.8 Consensus size: 18
55868842 AGAAAATTTT
55868852 TCGTGTTTTCAAAAATTC
1 TCGTGTTTTCAAAAATTC
*
55868870 TCGTG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAATTC
*
55868887 TCATGTTTTCAAAAATTC
1 TCGTGTTTTCAAAAATTC
55868905 TCGTGTTTTCAAAAAATTC
1 TCGTGTTTTC-AAAAATTC
**
55868924 -C-AATTTTCAAAAATTC
1 TCGTGTTTTCAAAAATTC
*
55868940 TCATGTTTTCAGAAAATTC
1 TCGTGTTTTCA-AAAATTC
* *
55868959 CCGTG-TTTCAAAAATCC
1 TCGTGTTTTCAAAAATTC
55868976 TCGTGTTTTCAAAAATT-
1 TCGTGTTTTCAAAAATTC
* *
55868993 TCGGTGTTTT-GAAAATTT
1 TC-GTGTTTTCAAAAATTC
55869011 TCGTGTTTTCAAAAA
1 TCGTGTTTTCAAAAA
55869026 AAAATCTCGT
Statistics
Matches: 132, Mismatches: 15, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
16 8 0.06
17 46 0.35
18 60 0.45
19 18 0.14
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.43
Consensus pattern (18 bp):
TCGTGTTTTCAAAAATTC
Found at i:55868894 original size:35 final size:36
Alignment explanation
Indices: 55868844--55869025 Score: 203
Period size: 35 Copynumber: 5.1 Consensus size: 36
55868834 AAAAAATCAG
*
55868844 AAAATTTTTCGTGTTTTCAAAAATTCTCGTG-TTTC
1 AAAAATTTTCGTGTTTTCAAAAATTCTCGTGTTTTC
*
55868879 AAAAATTTTCATGTTTTCAAAAATTCTCGTGTTTTC
1 AAAAATTTTCGTGTTTTCAAAAATTCTCGTGTTTTC
* *** *
55868915 AAAAA-ATTCCAATTTTCAAAAATTCTCATGTTTTC
1 AAAAATTTTCGTGTTTTCAAAAATTCTCGTGTTTTC
** *
55868950 AGAAAATTCCCGTG-TTTCAAAAATCCTCGTGTTTTC
1 A-AAAATTTTCGTGTTTTCAAAAATTCTCGTGTTTTC
* *
55868986 AAAAA-TTTCGGTGTTTT-GAAAATTTTCGTGTTTTC
1 AAAAATTTTC-GTGTTTTCAAAAATTCTCGTGTTTTC
55869021 AAAAA
1 AAAAA
55869026 AAAATCTCGT
Statistics
Matches: 122, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
34 2 0.02
35 82 0.67
36 37 0.30
37 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (36 bp):
AAAAATTTTCGTGTTTTCAAAAATTCTCGTGTTTTC
Found at i:55869327 original size:13 final size:14
Alignment explanation
Indices: 55869298--55869328 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
55869288 TTTAGAAAAA
55869298 TTTAAAAATAAGTT
1 TTTAAAAATAAGTT
55869312 TTTAAAAATAAGTT
1 TTTAAAAATAAGTT
55869326 TTT
1 TTT
55869329 CTTCTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (14 bp):
TTTAAAAATAAGTT
Found at i:55872574 original size:15 final size:15
Alignment explanation
Indices: 55872554--55872605 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
55872544 AACATTCAGT
55872554 ATTCATTAGTCGTTC
1 ATTCATTAGTCGTTC
*
55872569 ATTCATTCATTCAG-T-
1 ATTCATT-AGTC-GTTC
*
55872584 ATTCATTAGTCATTC
1 ATTCATTAGTCGTTC
55872599 ATTCATT
1 ATTCATT
55872606 CATTGTATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
14 4 0.13
15 21 0.70
16 4 0.13
17 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.08, T:0.48
Consensus pattern (15 bp):
ATTCATTAGTCGTTC
Found at i:55872575 original size:4 final size:4
Alignment explanation
Indices: 55872566--55872609 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
55872556 TCATTAGTCG
* *
55872566 TTCA TTCA TTCA TTCA GT-A TTCA TT-A GTCA TTCA TTCA TTCA TT
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TT
55872610 GTATGTACAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
3 4 0.12
4 30 0.88
ACGTcount: A:0.25, C:0.20, G:0.05, T:0.50
Consensus pattern (4 bp):
TTCA
Found at i:55872582 original size:30 final size:30
Alignment explanation
Indices: 55872546--55872609 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
55872536 ACATAACTAA
*
55872546 CATTCAGTATTCATTAGTCGTTCATTCATT
1 CATTCAGTATTCATTAGTCATTCATTCATT
55872576 CATTCAGTATTCATTAGTCATTCATTCATT
1 CATTCAGTATTCATTAGTCATTCATTCATT
55872606 CATT
1 CATT
55872610 GTATGTACAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.25, C:0.20, G:0.08, T:0.47
Consensus pattern (30 bp):
CATTCAGTATTCATTAGTCATTCATTCATT
Found at i:55872587 original size:11 final size:11
Alignment explanation
Indices: 55872546--55872603 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
55872536 ACATAACTAA
55872546 CATTCAGTATT
1 CATTCAGTATT
*
55872557 CATT-AGTCGTT
1 CATTCAGT-ATT
55872568 CATTC---ATT
1 CATTCAGTATT
55872576 CATTCAGTATT
1 CATTCAGTATT
55872587 CATT-AGTCATT
1 CATTCAGT-ATT
55872598 CATTCA
1 CATTCA
55872604 TTCATTGTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 13
0.72 0.04 0.25
Matches are distributed among these distances:
8 7 0.18
10 6 0.16
11 24 0.63
12 1 0.03
ACGTcount: A:0.26, C:0.21, G:0.09, T:0.45
Consensus pattern (11 bp):
CATTCAGTATT
Found at i:55876408 original size:13 final size:13
Alignment explanation
Indices: 55876390--55876425 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
55876380 TTTGTAAGAG
55876390 CTTATATTTGCTC
1 CTTATATTTGCTC
55876403 CTTATATTTGCTC
1 CTTATATTTGCTC
*
55876416 TTTATCATTT
1 CTTAT-ATTT
55876426 CAATGATCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 17 0.81
14 4 0.19
ACGTcount: A:0.17, C:0.19, G:0.06, T:0.58
Consensus pattern (13 bp):
CTTATATTTGCTC
Found at i:55880093 original size:17 final size:17
Alignment explanation
Indices: 55880070--55880111 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
55880060 TATTATGCTT
*
55880070 AAAA-AAAAACAAAA-A
1 AAAAGAAAAAGAAAAGA
*
55880085 AACAGAAAAAGAAAAGA
1 AAAAGAAAAAGAAAAGA
55880102 AAAAGAAAAA
1 AAAAGAAAAA
55880112 TCAAGATGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 3 0.14
16 9 0.41
17 10 0.45
ACGTcount: A:0.86, C:0.05, G:0.10, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAAGAAAAGA
Found at i:55880094 original size:11 final size:11
Alignment explanation
Indices: 55880070--55880110 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
55880060 TATTATGCTT
*
55880070 AAAAA-AAAAC
1 AAAAAGAAAAG
*
55880080 AAAAA-AACAG
1 AAAAAGAAAAG
55880090 AAAAAGAAAAG
1 AAAAAGAAAAG
55880101 AAAAAGAAAA
1 AAAAAGAAAA
55880111 ATCAAGATGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 13 0.48
11 14 0.52
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:55881505 original size:16 final size:15
Alignment explanation
Indices: 55881484--55881521 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
55881474 TATATTTAAA
55881484 AAAAAATCAGAAAAAT-
1 AAAAAATC--AAAAATC
55881500 AAAAAATCAAAAATC
1 AAAAAATCAAAAATC
55881515 AAAAAAT
1 AAAAAAT
55881522 ACATTTTGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.29
15 7 0.33
16 8 0.38
ACGTcount: A:0.76, C:0.08, G:0.03, T:0.13
Consensus pattern (15 bp):
AAAAAATCAAAAATC
Found at i:55881559 original size:29 final size:29
Alignment explanation
Indices: 55881521--55881600 Score: 110
Period size: 29 Copynumber: 2.8 Consensus size: 29
55881511 AATCAAAAAA
55881521 TACATTTTGACCCCTAAACTTTTTGAAAT
1 TACATTTTGACCCCTAAACTTTTTGAAAT
*
55881550 TACATTTTGACCCAC-CAACTTTTTGAAAT
1 TACATTTTGACCC-CTAAACTTTTTGAAAT
* *
55881579 TACATTTTAACCCTTAAA-TTTT
1 TACATTTTGACCCCTAAACTTTT
55881601 CTCAAAATTC
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
28 4 0.09
29 40 0.89
30 1 0.02
ACGTcount: A:0.31, C:0.21, G:0.05, T:0.42
Consensus pattern (29 bp):
TACATTTTGACCCCTAAACTTTTTGAAAT
Found at i:55882106 original size:20 final size:20
Alignment explanation
Indices: 55882077--55882127 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
55882067 CAGCCCAAAA
* *
55882077 CAAAAACAAAAAGAAAATGG
1 CAAAAACAAAAAAAAAAAGG
*
55882097 CAAAAGCAAAAAAAAAAAGG
1 CAAAAACAAAAAAAAAAAGG
55882117 CAGAAAA-AAAA
1 CA-AAAACAAAA
55882128 CAGCCCATAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 23 0.88
21 3 0.12
ACGTcount: A:0.75, C:0.10, G:0.14, T:0.02
Consensus pattern (20 bp):
CAAAAACAAAAAAAAAAAGG
Found at i:55882278 original size:15 final size:14
Alignment explanation
Indices: 55882260--55882323 Score: 58
Period size: 15 Copynumber: 4.5 Consensus size: 14
55882250 GCAGCAGGCC
55882260 AAAAAAAAAGAAGAG
1 AAAAAAAAAGAA-AG
*
55882275 AAAAAAAGAGAAAG
1 AAAAAAAAAGAAAG
* *
55882289 AAAAAATAA-AAAT
1 AAAAAAAAAGAAAG
* *
55882302 AAAAAATAAAAAAAT
1 AAAAAA-AAAGAAAG
55882317 AAAAAAA
1 AAAAAAA
55882324 TAAAAAAAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
13 9 0.21
14 12 0.29
15 21 0.50
ACGTcount: A:0.84, C:0.00, G:0.09, T:0.06
Consensus pattern (14 bp):
AAAAAAAAAGAAAG
Found at i:55882306 original size:7 final size:7
Alignment explanation
Indices: 55882289--55882330 Score: 59
Period size: 8 Copynumber: 5.9 Consensus size: 7
55882279 AAAGAGAAAG
55882289 AAAAAAT
1 AAAAAAT
55882296 -AAAAAT
1 AAAAAAT
55882302 AAAAAAT
1 AAAAAAT
55882309 AAAAAAAT
1 -AAAAAAT
55882317 AAAAAAAT
1 -AAAAAAT
55882325 AAAAAA
1 AAAAAA
55882331 AAGGGAAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.18
7 12 0.36
8 15 0.45
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:55882307 original size:8 final size:8
Alignment explanation
Indices: 55882296--55882331 Score: 65
Period size: 8 Copynumber: 4.6 Consensus size: 8
55882286 AAGAAAAAAT
55882296 AAAAAT-A
1 AAAAATAA
55882303 AAAAATAA
1 AAAAATAA
55882311 AAAAATAA
1 AAAAATAA
55882319 AAAAATAA
1 AAAAATAA
55882327 AAAAA
1 AAAAA
55882332 AGGGAAAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAAATAA
Found at i:55882744 original size:21 final size:20
Alignment explanation
Indices: 55882712--55882753 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
55882702 TCGGGTTTCG
55882712 AAATTTTCGTGTCTTCAAAA
1 AAATTTTCGTGTCTTCAAAA
*
55882732 AAATTTCTCGTGTTTTCAAAA
1 AAATTT-TCGTGTCTTCAAAA
55882753 A
1 A
55882754 TAAGGTAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
AAATTTTCGTGTCTTCAAAA
Found at i:55882754 original size:19 final size:19
Alignment explanation
Indices: 55882712--55882753 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
55882702 TCGGGTTTCG
55882712 AAATTTTCGTGTCTTCAAAA
1 AAATTTTCGTGTCTTC-AAA
*
55882732 AAATTTCTCGTGTTTTCAAA
1 AAATTT-TCGTGTCTTCAAA
55882752 AA
1 AA
55882754 TAAGGTAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (19 bp):
AAATTTTCGTGTCTTCAAA
Found at i:55882889 original size:17 final size:18
Alignment explanation
Indices: 55882858--55883021 Score: 158
Period size: 18 Copynumber: 9.2 Consensus size: 18
55882848 AAAAAATCAG
55882858 AAAATTTTCCGTG-TTTCA
1 AAAATTTT-CGTGTTTTCA
*
55882876 AAAATTTTCATGTTTTCA
1 AAAATTTTCGTGTTTTCA
*
55882894 AAAATTCTCGTGTTTTCA
1 AAAATTTTCGTGTTTTCA
* ***
55882912 AAAA-ATTCCAATTTTCA
1 AAAATTTTCGTGTTTTCA
*
55882929 AAAATTTTCATGTTTTCA
1 AAAATTTTCGTGTTTTCA
**
55882947 GAAAATTCCCGTG-TTTCA
1 -AAAATTTTCGTGTTTTCA
**
55882965 AAAATCCTCGTGTTTTCA
1 AAAATTTTCGTGTTTTCA
*
55882983 AAAA-TTTCAGTGTTTT-G
1 AAAATTTTC-GTGTTTTCA
55883000 AAAATTTTCGTGTTTTCA
1 AAAATTTTCGTGTTTTCA
55883018 AAAA
1 AAAA
55883022 AACATCTCGT
Statistics
Matches: 118, Mismatches: 21, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
17 38 0.32
18 71 0.60
19 9 0.08
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (18 bp):
AAAATTTTCGTGTTTTCA
Found at i:55882907 original size:35 final size:36
Alignment explanation
Indices: 55882858--55883021 Score: 176
Period size: 35 Copynumber: 4.6 Consensus size: 36
55882848 AAAAAATCAG
*
55882858 AAAATTTTCCGTG-TTTCAAAAATTTTCATGTTTTCA
1 AAAATTTT-CGTGTTTTCAAAAATTTCCATGTTTTCA
* * *
55882894 AAAATTCTCGTGTTTTCAAAAAATTCCA-ATTTTCA
1 AAAATTTTCGTGTTTTCAAAAATTTCCATGTTTTCA
* * *
55882929 AAAATTTTCATGTTTTCAGAAAATTCCCGTG-TTTCA
1 AAAATTTTCGTGTTTTCA-AAAATTTCCATGTTTTCA
** *
55882965 AAAATCCTCGTGTTTTCAAAAATTT-CAGTGTTTT-G
1 AAAATTTTCGTGTTTTCAAAAATTTCCA-TGTTTTCA
55883000 AAAATTTTCGTGTTTTCAAAAA
1 AAAATTTTCGTGTTTTCAAAAA
55883022 AACATCTCGT
Statistics
Matches: 105, Mismatches: 18, Indels: 11
0.78 0.13 0.08
Matches are distributed among these distances:
34 1 0.01
35 54 0.51
36 50 0.48
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (36 bp):
AAAATTTTCGTGTTTTCAAAAATTTCCATGTTTTCA
Found at i:55884371 original size:3 final size:3
Alignment explanation
Indices: 55884363--55884432 Score: 56
Period size: 3 Copynumber: 23.7 Consensus size: 3
55884353 CGCTACATAG
* * *
55884363 TTA TTA TTA TTA TTA TTA TTA TTG TCT- TTA CTA TTA TT- TTT TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
* *
55884407 -TA TTCA TTA ATA TTA TTG TTA TTA TT
1 TTA TT-A TTA TTA TTA TTA TTA TTA TT
55884433 GTTAGGTTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
2 5 0.09
3 45 0.83
4 4 0.07
ACGTcount: A:0.27, C:0.04, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:55887278 original size:38 final size:39
Alignment explanation
Indices: 55887225--55887327 Score: 127
Period size: 38 Copynumber: 2.6 Consensus size: 39
55887215 TTTTAAATAC
*
55887225 AATAATTTTAGAAACACGAAACTTTTGTTTAAAAAACACG
1 AATAATTTT-GAAACACGAAATTTTTGTTTAAAAAACACG
* * **
55887265 AA-AATTTTGAAACACGAGATTTTTTTTTTGAAAACACG
1 AATAATTTTGAAACACGAAATTTTTGTTTAAAAAACACG
**
55887303 AATTTTTTTGAAACACGAAATTTTT
1 AATAATTTTGAAACACGAAATTTTT
55887328 TGAAAAGACG
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
38 27 0.50
39 25 0.46
40 2 0.04
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (39 bp):
AATAATTTTGAAACACGAAATTTTTGTTTAAAAAACACG
Found at i:55887302 original size:22 final size:20
Alignment explanation
Indices: 55887269--55887328 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 20
55887259 AACACGAAAA
55887269 TTTTGAAACACGAGATTTTTT
1 TTTTGAAACACGA-ATTTTTT
55887290 TTTTGAAAACACGAA---TTT
1 TTTTG-AAACACGAATTTTTT
55887308 TTTTGAAACACGAAATTTTTT
1 TTTTGAAACACG-AATTTTTT
55887329 GAAAAGACGT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
17 7 0.21
18 10 0.29
21 9 0.26
22 8 0.24
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (20 bp):
TTTTGAAACACGAATTTTTT
Found at i:55887308 original size:17 final size:19
Alignment explanation
Indices: 55887287--55887333 Score: 73
Period size: 17 Copynumber: 2.6 Consensus size: 19
55887277 CACGAGATTT
55887287 TTTTTTTGAAAACACG-AA
1 TTTTTTTGAAAACACGAAA
55887305 TTTTTTTG-AAACACGAAA
1 TTTTTTTGAAAACACGAAA
55887323 -TTTTTTGAAAA
1 TTTTTTTGAAAA
55887334 GACGTATCGT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 14 0.52
18 13 0.48
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.43
Consensus pattern (19 bp):
TTTTTTTGAAAACACGAAA
Found at i:55887328 original size:39 final size:38
Alignment explanation
Indices: 55887197--55887328 Score: 121
Period size: 38 Copynumber: 3.5 Consensus size: 38
55887187 TTTTTCTTTC
*
55887197 TTTGAAAACACG-AA-TTTTTTTT-AAATACA--ATAATT
1 TTTG-AAACACGAAATTTTTTTTTAAAAAACACGA-AATT
* * * *
55887232 TTAGAAACACGAAACTTTTGTTTAAAAAACACGAAAAT
1 TTTGAAACACGAAATTTTTTTTTAAAAAACACGAAATT
* ** *
55887270 TTTGAAACACGAGATTTTTTTTTTGAAAACACGAATTTT
1 TTTGAAACACGAAATTTTTTTTTAAAAAACACGAA-ATT
55887309 TTTGAAACACGAAATTTTTT
1 TTTGAAACACGAAATTTTTT
55887329 GAAAAGACGT
Statistics
Matches: 78, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
34 7 0.09
35 5 0.06
36 7 0.09
37 6 0.08
38 32 0.41
39 21 0.27
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.39
Consensus pattern (38 bp):
TTTGAAACACGAAATTTTTTTTTAAAAAACACGAAATT
Found at i:55887675 original size:13 final size:14
Alignment explanation
Indices: 55887653--55887687 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
55887643 AATTGAAATT
55887653 AAAT-TAAATA-AA
1 AAATATAAATACAA
55887665 AAATATAAATACAA
1 AAATATAAATACAA
55887679 AAATATAAA
1 AAATATAAA
55887688 ATGCATAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 4 0.19
13 6 0.29
14 11 0.52
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (14 bp):
AAATATAAATACAA
Found at i:55887838 original size:7 final size:7
Alignment explanation
Indices: 55887820--55887858 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
55887810 AAATTGAACC
55887820 TCTTTTT
1 TCTTTTT
55887827 T-TTTTT
1 TCTTTTT
55887833 TCTTTTT
1 TCTTTTT
*
55887840 TCTCTTT
1 TCTTTTT
55887847 TCTTTTT
1 TCTTTTT
55887854 T-TTTT
1 TCTTTT
55887859 GCTGGGTTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
6 10 0.34
7 19 0.66
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (7 bp):
TCTTTTT
Found at i:55888167 original size:7 final size:7
Alignment explanation
Indices: 55888139--55888225 Score: 61
Period size: 7 Copynumber: 11.9 Consensus size: 7
55888129 TATTTATTTA
55888139 TTTCTTCT
1 TTTCTT-T
55888147 TTT-TTT
1 TTTCTTT
55888153 TTTCCTTT
1 TTT-CTTT
55888161 TTTCTTT
1 TTTCTTT
*
55888168 CCCTTTCTTC
1 ---TTTCTTT
55888178 TTTCTTCT
1 TTTCTT-T
55888186 TTT-TTT
1 TTTCTTT
55888192 TTTCTTT
1 TTTCTTT
*
55888199 TTTCTTC
1 TTTCTTT
*
55888206 CTTCTTT
1 TTTCTTT
*
55888213 CTTCTTT
1 TTTCTTT
*
55888220 CTTCTT
1 TTTCTT
55888226 CCTTCCCTTG
Statistics
Matches: 67, Mismatches: 5, Indels: 15
0.77 0.06 0.17
Matches are distributed among these distances:
6 8 0.12
7 41 0.61
8 12 0.18
10 6 0.09
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTCTTT
Found at i:55888173 original size:25 final size:24
Alignment explanation
Indices: 55888145--55888215 Score: 58
Period size: 27 Copynumber: 2.9 Consensus size: 24
55888135 TTTATTTCTT
55888145 CTTTTTTTTTTCCTTTTTTCTTTCC
1 CTTTTTTTTTTCCTTTTTTCTTT-C
*
55888170 CTTTCTTCTTTCTT-CTTTTTT-TTTT
1 CTTT-TT-TTT-TTCCTTTTTTCTTTC
* *
55888195 C-TTTTTTCTTCCTTCTTTCTT
1 CTTTTTTTTTTCCTTTTTTCTT
55888216 CTTTCTTCTT
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
21 2 0.05
22 8 0.21
23 4 0.11
24 2 0.05
25 5 0.13
26 5 0.13
27 10 0.26
28 2 0.05
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (24 bp):
CTTTTTTTTTTCCTTTTTTCTTTC
Found at i:55888190 original size:39 final size:38
Alignment explanation
Indices: 55888139--55888225 Score: 140
Period size: 39 Copynumber: 2.2 Consensus size: 38
55888129 TATTTATTTA
55888139 TTTCTTCTTTTTTTTTTCCTTTTTTCTTTCC-CTTTCTTC
1 TTTCTTCTTTTTTTTTT-CTTTTTTC-TTCCTCTTTCTTC
55888178 TTTCTTCTTTTTTTTTTCTTTTTTCTTCCTTCTTTCTTC
1 TTTCTTCTTTTTTTTTTCTTTTTTCTTCC-TCTTTCTTC
55888217 TTTCTTCTT
1 TTTCTTCTT
55888226 CCTTCCCTTG
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
37 4 0.09
38 8 0.17
39 34 0.74
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (38 bp):
TTTCTTCTTTTTTTTTTCTTTTTTCTTCCTCTTTCTTC
Found at i:55888230 original size:14 final size:14
Alignment explanation
Indices: 55888139--55888230 Score: 81
Period size: 14 Copynumber: 7.0 Consensus size: 14
55888129 TATTTATTTA
55888139 TTTCTTCTTT-TT-
1 TTTCTTCTTTCTTC
*
55888151 TTT-TTCCTTTTTTC
1 TTTCTT-CTTTCTTC
*
55888165 TTTC-CCTTTCTTC
1 TTTCTTCTTTCTTC
55888178 TTTCTTCTTT-TT-
1 TTTCTTCTTTCTTC
*
55888190 TTT-TTCTTTTTTC
1 TTTCTTCTTTCTTC
*
55888203 TTCCTTCTTTCTTC
1 TTTCTTCTTTCTTC
*
55888217 TTTCTTCTTCCTTC
1 TTTCTTCTTTCTTC
55888231 CCTTGGACCT
Statistics
Matches: 65, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
11 8 0.12
12 12 0.18
13 17 0.26
14 28 0.43
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTCTTCTTTCTTC
Found at i:55888448 original size:20 final size:20
Alignment explanation
Indices: 55888423--55888475 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
55888413 TTTGATGGTT
*
55888423 ACGGTGGTGGTGGTTGTGCG
1 ACGGTGGTGGTGGTTGCGCG
55888443 ACGGTGGTGGTGGTTGCGCG
1 ACGGTGGTGGTGGTTGCGCG
55888463 ACGGTGGTGGTGG
1 ACGGTGGTGGTGG
55888476 AGGCTTTGCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.06, C:0.11, G:0.57, T:0.26
Consensus pattern (20 bp):
ACGGTGGTGGTGGTTGCGCG
Found at i:55888776 original size:30 final size:29
Alignment explanation
Indices: 55888742--55888839 Score: 81
Period size: 30 Copynumber: 3.3 Consensus size: 29
55888732 GGGGCCAAGC
*
55888742 ATAATTTTGAGAAAATTTAGGGGTCAAAAT
1 ATAATTTT-AGAAAGTTTAGGGGTCAAAAT
* * * *
55888772 ATAATTTCA-AGAAGTTGACGGGCCAAAAAT
1 ATAATTTTAGA-AAGTTTAGGGGTC-AAAAT
* *
55888802 GTAATTTTAGGAAAGTTTAGGGGTTAAAAT
1 ATAATTTTA-GAAAGTTTAGGGGTCAAAAT
*
55888832 GTAATTTT
1 ATAATTTT
55888840 TATTTTTGTT
Statistics
Matches: 53, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
28 1 0.02
29 10 0.19
30 32 0.60
31 9 0.17
32 1 0.02
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.34
Consensus pattern (29 bp):
ATAATTTTAGAAAGTTTAGGGGTCAAAAT
Found at i:55892780 original size:89 final size:89
Alignment explanation
Indices: 55892627--55893110 Score: 689
Period size: 89 Copynumber: 5.4 Consensus size: 89
55892617 TATTTGAATT
* * *
55892627 AGATCTTGTCTTCTTGTATTGGCAGCGAAGTAGATCGAAGATACCAGCCTTGCCTCACTGAGTTT
1 AGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGACACCAGCCTTGCCTCCCTGAGTTT
* *
55892692 ACAGCGGAGCAGACTAAAAATAGC
66 GCAGCGGAGCAGACTGAAAATAGC
* * *
55892716 AGATCTTATCTTCCTGTATTGGCAGCGAAGTAGATCGAAGACACCAGCCTTACCTCCCTAAGTTT
1 AGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGACACCAGCCTTGCCTCCCTGAGTTT
* *
55892781 GTAGCGGAGCAGACTGAAAGTAGC
66 GCAGCGGAGCAGACTGAAAATAGC
* * *
55892805 AGATCTTGTCTTCCTGTATTGACAGCGAAGTAGATCGAAGACACCAACCTTGCCTCCATGAGTTT
1 AGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGACACCAGCCTTGCCTCCCTGAGTTT
*
55892870 GCAGCAGAGCAGACTGAAAATAGC
66 GCAGCGGAGCAGACTGAAAATAGC
* *
55892894 AGATCTTATCTTCCTGTATTGGCAGCGAAGTAGATCGAAGACACCAGCCTTACCTCCCTGAGTTT
1 AGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGACACCAGCCTTGCCTCCCTGAGTTT
* * * *
55892959 GTAGCGGACCAGACTGAAAGTAAC
66 GCAGCGGAGCAGACTGAAAATAGC
* * * *
55892983 AGATCTTGTCTTCTTGTATTGACAGCGAAATAGATCGAAGACACCAACCTTGCCTCCCTGAGTTT
1 AGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGACACCAGCCTTGCCTCCCTGAGTTT
* ** * *
55893048 GCAACGGAATAGACTGAAAACAAC
66 GCAGCGGAGCAGACTGAAAATAGC
* *
55893072 AGATCTTGTCTTCCTGTATTGGCAGTGATGTAGATCGAA
1 AGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAA
55893111 ATAACAAACC
Statistics
Matches: 349, Mismatches: 46, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
89 349 1.00
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (89 bp):
AGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGACACCAGCCTTGCCTCCCTGAGTTT
GCAGCGGAGCAGACTGAAAATAGC
Found at i:55893132 original size:178 final size:178
Alignment explanation
Indices: 55892627--55893110 Score: 779
Period size: 178 Copynumber: 2.7 Consensus size: 178
55892617 TATTTGAATT
* * * *
55892627 AGATCTTGTCTTCTTGTATTGGCAGCGAAGTAGATCGAAGATACCAGCCTTGCCTCACTGAGTTT
1 AGATCTTGTCTTCTTGTATTGACAGCGAAGTAGATCGAAGACACCAACCTTGCCTCCCTGAGTTT
* *
55892692 ACAGCGGAGCAGACTAAAAATAGCAGATCTTATCTTCCTGTATTGGCAGCGAAGTAGATCGAAGA
66 GCAGCGGAGCAGACTGAAAATAGCAGATCTTATCTTCCTGTATTGGCAGCGAAGTAGATCGAAGA
* * *
55892757 CACCAGCCTTACCTCCCTAAGTTTGTAGCGGAGCAGACTGAAAGTAGC
131 CACCAGCCTTACCTCCCTGAGTTTGTAGCGGACCAGACTGAAAGTAAC
* *
55892805 AGATCTTGTCTTCCTGTATTGACAGCGAAGTAGATCGAAGACACCAACCTTGCCTCCATGAGTTT
1 AGATCTTGTCTTCTTGTATTGACAGCGAAGTAGATCGAAGACACCAACCTTGCCTCCCTGAGTTT
*
55892870 GCAGCAGAGCAGACTGAAAATAGCAGATCTTATCTTCCTGTATTGGCAGCGAAGTAGATCGAAGA
66 GCAGCGGAGCAGACTGAAAATAGCAGATCTTATCTTCCTGTATTGGCAGCGAAGTAGATCGAAGA
55892935 CACCAGCCTTACCTCCCTGAGTTTGTAGCGGACCAGACTGAAAGTAAC
131 CACCAGCCTTACCTCCCTGAGTTTGTAGCGGACCAGACTGAAAGTAAC
*
55892983 AGATCTTGTCTTCTTGTATTGACAGCGAAATAGATCGAAGACACCAACCTTGCCTCCCTGAGTTT
1 AGATCTTGTCTTCTTGTATTGACAGCGAAGTAGATCGAAGACACCAACCTTGCCTCCCTGAGTTT
* ** * * * * *
55893048 GCAACGGAATAGACTGAAAACAACAGATCTTGTCTTCCTGTATTGGCAGTGATGTAGATCGAA
66 GCAGCGGAGCAGACTGAAAATAGCAGATCTTATCTTCCTGTATTGGCAGCGAAGTAGATCGAA
55893111 ATAACAAACC
Statistics
Matches: 282, Mismatches: 24, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
178 282 1.00
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (178 bp):
AGATCTTGTCTTCTTGTATTGACAGCGAAGTAGATCGAAGACACCAACCTTGCCTCCCTGAGTTT
GCAGCGGAGCAGACTGAAAATAGCAGATCTTATCTTCCTGTATTGGCAGCGAAGTAGATCGAAGA
CACCAGCCTTACCTCCCTGAGTTTGTAGCGGACCAGACTGAAAGTAAC
Found at i:55893436 original size:21 final size:21
Alignment explanation
Indices: 55893410--55893453 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
55893400 CTGTCGTTGT
*
55893410 AGTGGAATAGATTAAAGCTGA
1 AGTGGAACAGATTAAAGCTGA
* *
55893431 AGTGGAGCGGATTAAAGCTGA
1 AGTGGAACAGATTAAAGCTGA
55893452 AG
1 AG
55893454 GCAACAAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.07, G:0.34, T:0.20
Consensus pattern (21 bp):
AGTGGAACAGATTAAAGCTGA
Found at i:55893975 original size:348 final size:349
Alignment explanation
Indices: 55893338--55894030 Score: 1237
Period size: 348 Copynumber: 2.0 Consensus size: 349
55893328 GAAGACAGCA
*
55893338 AATTTTATTACCTTGGCGCTATAGTGGAACAGATAAAGCTAAGAGTAGCGAATCTTGTTTCCCTG
1 AATTTTATTACCCTGGCGCTATAGTGGAACAGATAAAGCTAAGAGTAGCGAATCTTGTTTCCCTG
* * *
55893403 TCGTTGTAGTGGAATAGATTAAAGCTGAAGTGGAGCGGATTAAAGCTGAAGGCAACAAATCCTAT
66 GCGTTGTAGTGGAATAGATTAAAGCTGAAGTGGAGCGGATTAAAACTAAAGGCAACAAATCCTAT
* * *
55893468 CTCATTGGCGTTGAAGTAGAATAGATTAAAACTAAAGGTAGCAAACCTTGTTTCCCAAGCGTTGT
131 CTAATTGGCGTTGAAGTAGAACAGATTAAAACTAAAGGTAGCAAACCTTATTTCCCAAGCGTTGT
55893533 AGCGGAGCAGATTAAAGCTGAAGGCAGTAAATCTTTTCTTCCTAGCGTTAAGACTGAATGCAGCT
196 AGCGGAGCAGATTAAAGCTGAAGGCAGTAAATCTTTTCTTCCTAGCGTTAAGACTGAATGCAGCT
55893598 AATCTTATTTCTCTGAAGTTGCAGTAGAACAGATTGAAGCTATAAATTACAAAT-TTATCTCCTT
261 AATCTTATTTCTCTGAAGTTGCAGTAGAACAGATTGAAGCTATAAATTACAAATCTTATCTCCTT
*
55893662 AAAGTTGCAGTGGAGCAGACAACG
326 AAAGTTGCAGCGGAGCAGACAACG
*
55893686 AATTTTATTACCCTGGCGCTATAGTGGAACAGATAAAGCTAAGGGTAGCGAATCTTGTTTCCCTG
1 AATTTTATTACCCTGGCGCTATAGTGGAACAGATAAAGCTAAGAGTAGCGAATCTTGTTTCCCTG
* *
55893751 GCGTTGTAGTGGAATAGATTAAAGCTGAAGTGGAGTGGATTAAAACTAAAGGCAGCAAATCCTAT
66 GCGTTGTAGTGGAATAGATTAAAGCTGAAGTGGAGCGGATTAAAACTAAAGGCAACAAATCCTAT
*
55893816 CTAATTGGCGTTGCAGTAGAACAGATTAAAACTAAAGGTAGCAAACCTTATTTCCCAAGCGTTGT
131 CTAATTGGCGTTGAAGTAGAACAGATTAAAACTAAAGGTAGCAAACCTTATTTCCCAAGCGTTGT
*
55893881 AGCGGAGCAGATTAAAGCTGAAGGCAGTGAATCTTTTCTTCCTAGCGTTAAGACTGAA-GACAGC
196 AGCGGAGCAGATTAAAGCTGAAGGCAGTAAATCTTTTCTTCCTAGCGTTAAGACTGAATG-CAGC
*
55893945 TAATCTTATTTCTTTGAAGTTGCAGTAGAACAGATTGAAGCTATAAATTACAAATCTTATCTCCT
260 TAATCTTATTTCTCTGAAGTTGCAGTAGAACAGATTGAAGCTATAAATTACAAATCTTATCTCCT
55894010 TAAAGTTGCAGCGGAGCAGAC
325 TAAAGTTGCAGCGGAGCAGAC
55894031 TGAAGATAAA
Statistics
Matches: 329, Mismatches: 14, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
347 1 0.00
348 299 0.91
349 29 0.09
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (349 bp):
AATTTTATTACCCTGGCGCTATAGTGGAACAGATAAAGCTAAGAGTAGCGAATCTTGTTTCCCTG
GCGTTGTAGTGGAATAGATTAAAGCTGAAGTGGAGCGGATTAAAACTAAAGGCAACAAATCCTAT
CTAATTGGCGTTGAAGTAGAACAGATTAAAACTAAAGGTAGCAAACCTTATTTCCCAAGCGTTGT
AGCGGAGCAGATTAAAGCTGAAGGCAGTAAATCTTTTCTTCCTAGCGTTAAGACTGAATGCAGCT
AATCTTATTTCTCTGAAGTTGCAGTAGAACAGATTGAAGCTATAAATTACAAATCTTATCTCCTT
AAAGTTGCAGCGGAGCAGACAACG
Found at i:55894061 original size:45 final size:44
Alignment explanation
Indices: 55894000--55894107 Score: 135
Period size: 45 Copynumber: 2.4 Consensus size: 44
55893990 AATTACAAAT
* *
55894000 CTTATCTCCTTAAAGTTGCAGCGGAGCAGACTGAAGATAAAAAAC
1 CTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGAT-AAAAAC
* ** ** *
55894045 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACCAAT
1 CTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGATAAAAAC
55894089 CTTATCTCCCTGAAGTTGC
1 CTTATCTCCCTGAAGTTGC
55894108 GATGGAGAAG
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 22 0.40
45 33 0.60
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGATAAAAAC
Found at i:55894114 original size:44 final size:44
Alignment explanation
Indices: 55893997--55894157 Score: 162
Period size: 44 Copynumber: 3.6 Consensus size: 44
55893987 ATAAATTACA
* * * * * **
55893997 AATCTTATCTCCTTAAAGTTGCAGCGGAGCAGACTGAAGATAAAA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTGAAGAT-ACC
* * *
55894042 AACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTGAAGATACC
* **
55894086 AATCTTATCTCCCTGAAGTTGC-GATGGAGAAGATTGAAGCTATT
1 AATCTTATCTCCCTGAAGTTGCAG-TGGAGAAGATTGAAGATACC
* *
55894130 AATCCTATCACCCTGAAGTTGCAGTGGA
1 AATCTTATCTCCCTGAAGTTGCAGTGGA
55894158 ACAGATTAAA
Statistics
Matches: 98, Mismatches: 16, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
43 1 0.01
44 61 0.62
45 36 0.37
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTGAAGATACC
Found at i:55895806 original size:24 final size:22
Alignment explanation
Indices: 55895756--55895806 Score: 59
Period size: 24 Copynumber: 2.3 Consensus size: 22
55895746 ATATGCATGC
55895756 ATACA-TTTTTATAATATACGT
1 ATACATTTTTTATAATATACGT
* *
55895777 ACACATTTTTTATAATTTATATGT
1 ATACATTTTTTATAA--TATACGT
55895801 ATACAT
1 ATACAT
55895807 AGTTATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 4 0.17
22 9 0.38
24 11 0.46
ACGTcount: A:0.37, C:0.10, G:0.04, T:0.49
Consensus pattern (22 bp):
ATACATTTTTTATAATATACGT
Found at i:55896871 original size:23 final size:25
Alignment explanation
Indices: 55896837--55896891 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
55896827 GATGTTTTTA
55896837 TATATATATTTTT-GGTGAAAATGTT
1 TATATAT-TTTTTAGGTGAAAATGTT
* * *
55896862 TATATCTTTTTTAGGTGAAATTTTT
1 TATATATTTTTTAGGTGAAAATGTT
55896887 TATAT
1 TATAT
55896892 GATGAACATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 5 0.19
25 21 0.81
ACGTcount: A:0.29, C:0.02, G:0.13, T:0.56
Consensus pattern (25 bp):
TATATATTTTTTAGGTGAAAATGTT
Found at i:55904283 original size:18 final size:18
Alignment explanation
Indices: 55904261--55904394 Score: 123
Period size: 17 Copynumber: 7.7 Consensus size: 18
55904251 TGAAATTCGA
55904261 AAAATTTTTGAAAACACG
1 AAAATTTTTGAAAACACG
* * * *
55904279 GAAATCTTTG-CAATACG
1 AAAATTTTTGAAAACACG
* *
55904296 AGAA-TTTTAAAAACACG
1 AAAATTTTTGAAAACACG
* *
55904313 AAAATTTCT-AAAACATG
1 AAAATTTTTGAAAACACG
55904330 AAAATTTTTGAAAACACG
1 AAAATTTTTGAAAACACG
* *
55904348 AGATTTTTTG-AAACACG
1 AAAATTTTTGAAAACACG
* * *
55904365 AAAATATTTGGAAATACG
1 AAAATTTTTGAAAACACG
55904383 AAAATTTTTGAA
1 AAAATTTTTGAA
55904395 GCACGAAGTT
Statistics
Matches: 89, Mismatches: 23, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
16 3 0.03
17 44 0.49
18 42 0.47
ACGTcount: A:0.47, C:0.10, G:0.13, T:0.30
Consensus pattern (18 bp):
AAAATTTTTGAAAACACG
Found at i:55904346 original size:35 final size:34
Alignment explanation
Indices: 55904246--55904401 Score: 125
Period size: 35 Copynumber: 4.5 Consensus size: 34
55904236 AAAAAATGAG
** *
55904246 AATTTTGAAATTCGAAAAATTTTTGAAAACACGGA
1 AATTTTGAAACACG-AAAATTTTTGAAAACACGAA
* * * *
55904281 AATCTTTGCAATACGAGAA-TTTTAAAAACACGAA
1 AAT-TTTGAAACACGAAAATTTTTGAAAACACGAA
* *
55904315 AATTTCTAAAACATGAAAATTTTTGAAAACACGAGA
1 AATTT-TGAAACACGAAAATTTTTGAAAACACGA-A
** * * *
55904351 TTTTTTGAAACACGAAAATATTTGGAAATACGAA
1 AATTTTGAAACACGAAAATTTTTGAAAACACGAA
*
55904385 AATTTTTGAAGCACGAA
1 AA-TTTTGAAACACGAA
55904402 GTTTTTTTTA
Statistics
Matches: 95, Mismatches: 21, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
33 2 0.02
34 25 0.26
35 55 0.58
36 13 0.14
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.29
Consensus pattern (34 bp):
AATTTTGAAACACGAAAATTTTTGAAAACACGAA
Found at i:55904472 original size:17 final size:17
Alignment explanation
Indices: 55904449--55904497 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
55904439 TTATTATTAT
55904449 TTTTTGAAACACGAGAAA
1 TTTTTGAAACACGA-AAA
*
55904467 -TTTTGAAAACATGAAAA
1 TTTTTG-AAACACGAAAA
*
55904484 TTTTTTAAACACGA
1 TTTTTGAAACACGA
55904498 TTATTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (17 bp):
TTTTTGAAACACGAAAA
Found at i:55905017 original size:15 final size:16
Alignment explanation
Indices: 55904981--55905019 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
55904971 TTGGGCCCCC
55904981 CTTTTTTC-TTTTCTT
1 CTTTTTTCTTTTTCTT
*
55904996 CTCTTTTCTTTTTCTT
1 CTTTTTTCTTTTTCTT
55905012 -TTTTTTCT
1 CTTTTTTCT
55905020 ACTGGGCTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (16 bp):
CTTTTTTCTTTTTCTT
Found at i:55905265 original size:12 final size:12
Alignment explanation
Indices: 55905248--55905329 Score: 59
Period size: 12 Copynumber: 7.2 Consensus size: 12
55905238 TTATTTTTTA
55905248 TTTTTTTCTCTC
1 TTTTTTTCTCTC
* *
55905260 TTTTTTTCTTTT
1 TTTTTTTCTCTC
55905272 TTCTTTTTCT-TC
1 TT-TTTTTCTCTC
*
55905284 TTCTTTT-TCT-
1 TTTTTTTCTCTC
*
55905294 TTATTTT-TCT-
1 TTTTTTTCTCTC
* *
55905304 TTTTCTTCTTTC
1 TTTTTTTCTCTC
55905316 TTTTTTTCT-TC
1 TTTTTTTCTCTC
55905327 TTT
1 TTT
55905330 CTTCTTCCTC
Statistics
Matches: 57, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
10 15 0.26
11 12 0.21
12 23 0.40
13 7 0.12
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTTTTCTCTC
Found at i:55905265 original size:19 final size:17
Alignment explanation
Indices: 55905241--55905320 Score: 74
Period size: 19 Copynumber: 4.5 Consensus size: 17
55905231 CCGTCTGTTA
*
55905241 TTTTTTATT-TTTTTCTC
1 TTTTTT-TTCTTTTTTTC
55905258 TCTTTTTTTC-TTTTTTC
1 T-TTTTTTTCTTTTTTTC
*
55905275 TTTTTCTTCTTCTTTTTC
1 TTTTTTTTCTT-TTTTTC
55905293 TTTATTTTTCTTTTTCTTC
1 TTT-TTTTTCTTTTT-TTC
55905312 TTTCTTTTT
1 TTT-TTTTT
55905321 TTCTTCTTTC
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
16 7 0.13
17 11 0.21
18 17 0.32
19 18 0.34
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTTTTTCTTTTTTTC
Found at i:55905271 original size:6 final size:6
Alignment explanation
Indices: 55905262--55905335 Score: 73
Period size: 6 Copynumber: 12.3 Consensus size: 6
55905252 TTTCTCTCTT
* *
55905262 TTTTTC TTTTTTC TTTTTC TTCTTC TTTTTC --TTTA TTTTTC TTTTTC
1 TTTTTC -TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
*
55905309 TTCTTTC TTTTT- TTCTTC TTTCTTC TT
1 TT-TTTC TTTTTC TTTTTC TTT-TTC TT
55905336 CCTCCTTCTC
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
4 3 0.05
5 4 0.07
6 32 0.57
7 17 0.30
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:55905284 original size:28 final size:27
Alignment explanation
Indices: 55905241--55905332 Score: 116
Period size: 28 Copynumber: 3.3 Consensus size: 27
55905231 CCGTCTGTTA
*
55905241 TTTTTTATTTTT-TTCTCTCTTTTTTTC
1 TTTTTTCTTTTTCTTCT-TCTTTTTTTC
55905268 TTTTTTCTTTTTCTTCTTCTTTTTCTT-
1 TTTTTTCTTTTTCTTCTTCTTTTT-TTC
55905295 TATTTTTCTTTTTCTTCTTTCTTTTTTTC
1 T-TTTTTCTTTTTCTTC-TTCTTTTTTTC
*
55905324 TTCTTTCTT
1 TTTTTTCTT
55905333 CTTCCTCCTT
Statistics
Matches: 58, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
27 19 0.33
28 30 0.52
29 9 0.16
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.80
Consensus pattern (27 bp):
TTTTTTCTTTTTCTTCTTCTTTTTTTC
Found at i:55905331 original size:19 final size:19
Alignment explanation
Indices: 55905252--55905332 Score: 78
Period size: 19 Copynumber: 4.3 Consensus size: 19
55905242 TTTTTATTTT
* *
55905252 TTTCTCTCTTTTTTTCTTT
1 TTTCTTTCTTTTTTTCTTC
*
55905271 TTTCTTT-TTCTTCTTCTT-
1 TTTCTTTCTT-TTTTTCTTC
* *
55905289 TTTCTTTATTTTTCTTTTTC
1 TTTCTTTCTTTTT-TTCTTC
55905309 -TTCTTTCTTTTTTTCTTC
1 TTTCTTTCTTTTTTTCTTC
55905327 TTTCTT
1 TTTCTT
55905333 CTTCCTCCTT
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
18 16 0.31
19 35 0.69
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTCTTTCTTTTTTTCTTC
Found at i:55905334 original size:25 final size:23
Alignment explanation
Indices: 55905248--55905336 Score: 94
Period size: 22 Copynumber: 3.8 Consensus size: 23
55905238 TTATTTTTTA
55905248 TTTTTTTCTCTCTTTTT-TTCTTT-
1 TTTTTTT-T-TCTTTTTCTTCTTTC
* *
55905271 TTTCTTTTTCTTCTTCTT-TTTC
1 TTTTTTTTTCTTTTTCTTCTTTC
*
55905293 TTTATTTTTCTTTTTCTTCTTTC
1 TTTTTTTTTCTTTTTCTTCTTTC
55905316 TTTTTTTCTTCTTTCTTCTTC
1 TTTTTTT-TTCTTT-TTCTTC
55905337 CTCCTTCTCT
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
21 9 0.16
22 19 0.34
23 16 0.29
24 6 0.11
25 6 0.11
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (23 bp):
TTTTTTTTTCTTTTTCTTCTTTC
Found at i:55905344 original size:28 final size:25
Alignment explanation
Indices: 55905248--55905336 Score: 95
Period size: 23 Copynumber: 3.8 Consensus size: 25
55905238 TTATTTTTTA
55905248 TTTTTTTCTCTCTTT-TT-TTCTTT-
1 TTTTTTTCT-TCTTTCTTCTTCTTTC
*
55905271 TTTCTTT-TTC-TTCTTCTT-TTTC
1 TTTTTTTCTTCTTTCTTCTTCTTTC
*
55905293 TTTATTT-TTCTTT-TTCTTCTTTC
1 TTTTTTTCTTCTTTCTTCTTCTTTC
55905316 TTTTTTTCTTCTTTCTTCTTC
1 TTTTTTTCTTCTTTCTTCTTC
55905337 CTCCTTCTCT
Statistics
Matches: 56, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
20 2 0.04
21 7 0.12
22 17 0.30
23 18 0.32
24 6 0.11
25 6 0.11
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (25 bp):
TTTTTTTCTTCTTTCTTCTTCTTTC
Found at i:55905650 original size:24 final size:25
Alignment explanation
Indices: 55905605--55905655 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 25
55905595 GAGGCTTTGG
*
55905605 GCTGTTGTTTCTTGAATGTTTTGCT
1 GCTGTTGTTTCTTCAATGTTTTGCT
* * *
55905630 GCTGTT-TTTTTTCAATTTTTTTCT
1 GCTGTTGTTTCTTCAATGTTTTGCT
55905654 GC
1 GC
55905656 AAAAACCCCA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.08, C:0.14, G:0.18, T:0.61
Consensus pattern (25 bp):
GCTGTTGTTTCTTCAATGTTTTGCT
Found at i:55905904 original size:30 final size:29
Alignment explanation
Indices: 55905867--55905987 Score: 93
Period size: 30 Copynumber: 4.1 Consensus size: 29
55905857 CAAGTGTAAT
* *
55905867 TTTGAGAAAATTTAGGGGTTAAAATATAA
1 TTTGAGAAAATTAAGGGGTCAAAATATAA
** * *
55905896 TTTCGAGAAGTTTATA--GGTTAAAATGTAA
1 TTT-GAGAAAATTA-AGGGGTCAAAATATAA
* * *
55905925 TTTTAGGAAAGTTAAGGGGTCAAAACATAA
1 TTTGA-GAAAATTAAGGGGTCAAAATATAA
* *
55905955 TTTTAAAAAAGTTAAGGGGTCAAAATATAA
1 TTTGAGAAAA-TTAAGGGGTCAAAATATAA
55905985 TTT
1 TTT
55905988 TTTATTTTTG
Statistics
Matches: 73, Mismatches: 13, Indels: 11
0.75 0.13 0.11
Matches are distributed among these distances:
28 2 0.03
29 27 0.37
30 43 0.59
31 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.20, T:0.34
Consensus pattern (29 bp):
TTTGAGAAAATTAAGGGGTCAAAATATAA
Found at i:55905988 original size:30 final size:30
Alignment explanation
Indices: 55905916--55905988 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
55905906 TTTATAGGTT
* **
55905916 AAAATGTAATTTTAGGAAAGTTAAGGGGTC
1 AAAATATAATTTTAAAAAAGTTAAGGGGTC
*
55905946 AAAACATAATTTTAAAAAAGTTAAGGGGTC
1 AAAATATAATTTTAAAAAAGTTAAGGGGTC
55905976 AAAATATAATTTT
1 AAAATATAATTTT
55905989 TTATTTTTGT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.47, C:0.04, G:0.18, T:0.32
Consensus pattern (30 bp):
AAAATATAATTTTAAAAAAGTTAAGGGGTC
Found at i:55906341 original size:78 final size:76
Alignment explanation
Indices: 55906254--55907137 Score: 974
Period size: 77 Copynumber: 11.5 Consensus size: 76
55906244 CATGTGCCTA
*
55906254 AGGCTCAACTCACC-CATCGCAATATGAGTTGATTTTTTTTAACAACAGAAATTGAAAAATACCT
1 AGGCTCAACTCACCTC-TCGCAATATGAGTTGATTTTTTTTAAAAACAGAAATTGAAAAATACCT
55906318 CAGCGTGCGACCCG
65 CAGCGT--GACCCG
* *
55906332 AGGCTCAACTCACCTCTCGCAATATGAGTTGAGTTTTTTGAAAAACAGAAATTGAAAAATACCTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAAACAGAAATTGAAAAATACCTC
55906397 AGCGTGTACCCG
66 AGCGTG-ACCCG
*
55906409 AGGCTCAACTCAACTCTCGCAATATGAGTTGATTTTTTTTTGAAAAACAGAAATTG-AAAATACC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTT-AAAAACAGAAATTGAAAAATACC
* *
55906473 TCAGCGTAACCTG
64 TCAGCGTGACCCG
* * **
55906486 AGGCTTAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAAACAGAAATT-AAAAATACCTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAAACAGAAATTGAAAAATACCTC
*
55906550 AGCGTAACCCG
66 AGCGTGACCCG
55906561 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAAACAGAAATTGAAAAATACC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTT-AAAAACAGAAATTGAAAAATACC
*
55906626 TCTG-GATGACCCG
64 TCAGCG-TGACCCG
* * * * *
55906639 AGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTT-GAAACAGAAACTG-AAATTACTTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAAACAGAAATTGAAAAATACCTC
55906702 AG-GATGACCCG
66 AGCG-TGACCCG
* * ** *
55906713 AGGCTCAACTCAGCTCTCGCATTATGAGTTGATTCTTGATTTGATTTTTTTAAA-AGAAATTAAA
1 AGGCTCAACTCACCTCTCGCA--AT-A--TGA--GTTGATTT--TTTTTAAAAACAGAAATTGAA
* *
55906777 AAATACCTCGGCTTGCAGCCCG
57 AAATACCTCAGCGTG-A-CCCG
* *
55906799 AGGCTCAACTCACTTCTCGCAATATGAGTTGA--TTTTTGAAAAACAGAAATTG-AAAATACCTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAAACAGAAATTGAAAAATACCTC
55906861 AGCGTGACCCG
66 AGCGTGACCCG
* * * * * *
55906872 AAGCTCAACTCACTTCTCGCATTATGAGTTGA--TTTTTGAAAAATAGGAATTG-AAAATACCTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAAACAGAAATTGAAAAATACCTC
*
55906934 AACGTGACCCG
66 AGCGTGACCCG
* * ** *
55906945 AGGCTCAACTCACCTCTCACATTATGAGTTGA-TTTTTTGGAAAATAGAAATT-AAAATATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAAACAGAAATTGAAAA-ATACCT
*
55907008 CGGCGTGTGACCCG
65 CAGC--GTGACCCG
* * * *
55907022 AAGCTCAACTCACCTCTCGCAATATAAGTTGA-TTTTTTTAAAAACAGAAATTTAAAAGAAATGC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAAACAGAAA-TT-GAA-AAATAC
* *
55907086 CTCGGCATGTGACCTG
63 CTCAGC--GTGACCCG
*
55907102 AAGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
55907138 AAAAGACAAA
Statistics
Matches: 704, Mismatches: 68, Indels: 65
0.84 0.08 0.08
Matches are distributed among these distances:
73 101 0.14
74 59 0.08
75 103 0.15
76 21 0.03
77 144 0.20
78 137 0.19
79 22 0.03
80 50 0.07
81 15 0.02
83 12 0.02
84 16 0.02
85 1 0.00
86 23 0.03
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (76 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAAACAGAAATTGAAAAATACCTC
AGCGTGACCCG
Found at i:55906344 original size:152 final size:152
Alignment explanation
Indices: 55906134--55907137 Score: 930
Period size: 152 Copynumber: 6.5 Consensus size: 152
55906124 TTTATTCTTT
* * * * *
55906134 ATTTTTTATTAAAAA-AGAAA-TCAAAAATAGCC-CGGCATGCGACCCGAAGCTCAACTCACCTC
1 ATTTTTTTTTAAAAACAGAAATTGAAAAATA-CCTCAGCGTG-GACCCGAGGCTCAACTCACCTC
* * * * * * ** * * *
55906196 TTGAATTATGTGTTGA-TCTTCGAAAAACAAAAATCGAAAATACCTTGGCATGTGCCTAAGGCTC
64 TCGAATTATGAGTTGATTTTTTGAAAAACAGAAATTGAAAATACCTCAGCGTGTACCCAAGGCTC
55906260 AACTCACCCATCGCAATATGAGTTG
129 AACTCACCC-TCGCAATATGAGTTG
*
55906285 A-TTTTTTTTAACAACAGAAATTGAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCT
1 ATTTTTTTTTAAAAACAGAAATTGAAAAATACCTCAGCGTG-GACCCGAGGCTCAACTCACCTCT
*
55906349 CGCAA-TATGAGTTGAGTTTTTTGAAAAACAGAAATTGAAAAATACCTCAGCGTGTACCCGAGGC
65 CG-AATTATGAGTTGA-TTTTTTGAAAAACAGAAATTG-AAAATACCTCAGCGTGTACCCAAGGC
*
55906413 TCAACTCAACTCTCGCAATATGAGTTG
127 TCAACTC-ACCCTCGCAATATGAGTTG
* * *
55906440 ATTTTTTTTTGAAAAACAGAAATTG-AAAATACCTCAGCGT-AACCTGAGGCTTAACTCACCTCT
1 ATTTTTTTTT-AAAAACAGAAATTGAAAAATACCTCAGCGTGGACCCGAGGCTCAACTCACCTCT
* * * *
55906503 CGCATTATGAGTTGATTTTTTGAAAAAACAGAAATTAAAAATACCTCAGCGT-AACCCGAGGCTC
65 CGAATTATGAGTTGATTTTTTG-AAAAACAGAAATTGAAAATACCTCAGCGTGTACCCAAGGCTC
55906567 AACTCACCTCTCGCAATATGAGTTG
129 AACTCACC-CTCGCAATATGAGTTG
*
55906592 ATTTTTTTTTGAAAAACAGAAATTGAAAAATACCTCTG-GAT-GACCCGAGGCTCAACTCACCTC
1 ATTTTTTTTT-AAAAACAGAAATTGAAAAATACCTCAGCG-TGGACCCGAGGCTCAACTCACCTC
* *** * * * *
55906655 TCGCATTATGAGTTGATTTTTTTTGAAACAGAAACTGAAATTACTTCAG-GATG-ACCCGAGGCT
64 TCGAATTATGAGTTGATTTTTTGAAAAACAGAAATTGAAAATACCTCAGCG-TGTACCCAAGGCT
* *
55906718 CAACTCAGCTCTCGCATTATGAGTTG
128 CAACTCA-CCCTCGCAATATGAGTTG
** * * * *
55906744 ATTCTTGATTTGATTTTTTTAAA-AGAAATTAAAAAATACCTCGGCTTGCAGCCCGAGGCTCAAC
1 A----T--TTT--TTTTTAAAAACAGAAATTGAAAAATACCTCAGCGTGGA-CCCGAGGCTCAAC
*
55906808 TCACTTCTCGCAA-TATGAGTTGA-TTTTTGAAAAACAGAAATTGAAAATACCTCAGCGTG-ACC
57 TCACCTCTCG-AATTATGAGTTGATTTTTTGAAAAACAGAAATTGAAAATACCTCAGCGTGTACC
* *
55906870 CGAA-GCTCAACTCACTTCTCGCATTATGAGTTG
121 C-AAGGCTCAACTCAC-CCTCGCAATATGAGTTG
* * * *
55906903 A---TTTTTGAAAAATAGGAATTG-AAAATACCTCAACGT-GACCCGAGGCTCAACTCACCTCTC
1 ATTTTTTTTTAAAAACAGAAATTGAAAAATACCTCAGCGTGGACCCGAGGCTCAACTCACCTCTC
* * * *
55906963 -ACATTATGAGTTGATTTTTTGGAAAATAGAAATTAAAATATACCTCGGCGTGTGACCCGAA-GC
66 GA-ATTATGAGTTGATTTTTTGAAAAACAGAAATTGAAA-ATACCTCAGCGTGT-ACCC-AAGGC
*
55907026 TCAACTCACCTCTCGCAATATAAGTTG
127 TCAACTCACC-CTCGCAATATGAGTTG
* * * * * *
55907053 A--TTTTTTTAAAAACAGAAATTTAAAAGAAATGCCTCGGCATGTGACCTGAAGCTCAACTCACC
1 ATTTTTTTTTAAAAACAGAAA-TT-GAA-AAATACCTCAGCGTG-GACCCGAGGCTCAACTCACC
55907116 TCTCGCAA-TATGAGTTGATTTT
62 TCTCG-AATTATGAGTTGATTTT
55907138 AAAAGACAAA
Statistics
Matches: 721, Mismatches: 82, Indels: 94
0.80 0.09 0.10
Matches are distributed among these distances:
144 1 0.00
145 1 0.00
146 31 0.04
147 21 0.03
148 31 0.04
149 6 0.01
150 45 0.06
151 25 0.03
152 160 0.22
153 79 0.11
154 62 0.09
155 53 0.07
156 27 0.04
157 49 0.07
158 25 0.03
159 65 0.09
160 39 0.05
161 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (152 bp):
ATTTTTTTTTAAAAACAGAAATTGAAAAATACCTCAGCGTGGACCCGAGGCTCAACTCACCTCTC
GAATTATGAGTTGATTTTTTGAAAAACAGAAATTGAAAATACCTCAGCGTGTACCCAAGGCTCAA
CTCACCCTCGCAATATGAGTTG
Found at i:55906426 original size:77 final size:75
Alignment explanation
Indices: 55906174--55907159 Score: 1002
Period size: 78 Copynumber: 12.9 Consensus size: 75
55906164 CCCGGCATGC
* * * * * * *
55906174 GACCCGAAGCTCAACTCACCTCTTG-AATTATGTGTTGA-TCTTCGAAAAACAAAAATCG-AAAA
1 GACCCGAGGCTCAACTCACCTCTCGCAA-TATGAGTTGATTTTTTGAAAAACAGAAATTGAAAAA
**
55906236 TACCTTGGCATGT
65 TACCTCAGC--GT
** * *
55906249 G-CCTAAGGCTCAACTCACC-CATCGCAATATGAGTTGATTTTTTTTAACAACAGAAATTGAAAA
1 GACCCGAGGCTCAACTCACCTC-TCGCAATATGAGTTGA-TTTTTTGAAAAACAGAAATTGAAAA
55906312 ATACCTCAGCGT
64 ATACCTCAGCGT
55906324 GCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAGTTTTTTGAAAAACAGAAATTGAAA
1 --GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAAACAGAAATTGAAA
55906389 AATACCTCAGCGT
63 AATACCTCAGCGT
*
55906402 GTACCCGAGGCTCAACTCAACTCTCGCAATATGAGTTGATTTTTTTTTGAAAAACAGAAATTG-A
1 G-ACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTTGAAAAACAGAAATTGAA
55906466 AAATACCTCAGCGT
62 AAATACCTCAGCGT
* * * *
55906480 AACCTGAGGCTTAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAAACAGAAATT-AAAAA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTG-AAAAACAGAAATTGAAAAA
55906544 TACCTCAGCGT
65 TACCTCAGCGT
*
55906555 AACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAAACAGAAATTGAAA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTTGAAAAACAGAAATTGAAA
*
55906620 AATACCTCTG-GAT
63 AATACCTCAGCG-T
* *** * *
55906633 GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTTGAAACAGAAACTG-AAATT
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAAAT
*
55906697 ACTTCAG-GAT
66 ACCTCAGCG-T
* * *
55906707 GACCCGAGGCTCAACTCAGCTCTCGCATTATGAGTTGATTCTTGATTTGATTTTTTTAAA-AGAA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-T-TT--TTTGA------AAAACAGAA
* * *
55906771 ATTAAAAAATACCTCGGCTT
56 ATTGAAAAATACCTCAGCGT
*
55906791 GCAGCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTG-AAA
1 G-A-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAA
55906854 ATACCTCAGCGT
64 ATACCTCAGCGT
* * * * *
55906866 GACCCGAAGCTCAACTCACTTCTCGCATTATGAGTTGA-TTTTTGAAAAATAGGAATTG-AAAAT
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAAAT
*
55906929 ACCTCAACGT
66 ACCTCAGCGT
* * * *
55906939 GACCCGAGGCTCAACTCACCTCTCACATTATGAGTTGATTTTTTGGAAAATAGAAATT-AAAATA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAA-A
*
55907003 TACCTCGGCGTGT
65 TACCTCAGC--GT
* * * *
55907016 GACCCGAAGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTAAAAACAGAAATTTAAAAGA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAA-TT-GAA-A
* *
55907081 AATGCCTCGGCATGT
63 AATACCTCAGC--GT
* * *
55907096 GACCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTT-AAAAGACAAAAATTGAAAAA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAA-ACAGAAATTGAAAAA
55907158 TA
65 TA
55907160 TAATTCTTGA
Statistics
Matches: 786, Mismatches: 81, Indels: 88
0.82 0.08 0.09
Matches are distributed among these distances:
73 102 0.13
74 103 0.13
75 115 0.15
76 26 0.03
77 152 0.19
78 153 0.19
79 22 0.03
80 50 0.06
81 7 0.01
83 8 0.01
84 14 0.02
85 1 0.00
86 33 0.04
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.28
Consensus pattern (75 bp):
GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAAAT
ACCTCAGCGT
Found at i:55906878 original size:73 final size:73
Alignment explanation
Indices: 55906767--55907159 Score: 430
Period size: 73 Copynumber: 5.2 Consensus size: 73
55906757 TTTTTTTAAA
* * *
55906767 AGAAATTAAAAAATACCTCGGCTTGCAGCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGAT
1 AGAAATT-AAAAATACCTCGGCGTG-A-CCCGAAGCTCAACTCACCTCTCGCAATATGAGTTGAT
55906832 TTTTGAAAAAC
63 TTTTGAAAAAC
* * * *
55906843 AGAAATTGAAAATACCTCAGCGTGACCCGAAGCTCAACTCACTTCTCGCATTATGAGTTGATTTT
1 AGAAATTAAAAATACCTCGGCGTGACCCGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
*
55906908 TGAAAAAT
66 TGAAAAAC
* * ** * * *
55906916 AGGAATTGAAAATACCTCAACGTGACCCGAGGCTCAACTCACCTCTCACATTATGAGTTGATTTT
1 AGAAATTAAAAATACCTCGGCGTGACCCGAAGCTCAACTCACCTCTCGCAATATGAGTTGA-TTT
* *
55906981 TTGGAAAAT
65 TTGAAAAAC
*
55906990 AGAAATTAAAATATACCTCGGCGTGTGACCCGAAGCTCAACTCACCTCTCGCAATATAAGTTGAT
1 AGAAATTAAAA-ATACCTCGGC--GTGACCCGAAGCTCAACTCACCTCTCGCAATATGAGTTGA-
*
55907055 TTTTTTAAAAAC
62 TTTTTGAAAAAC
* *
55907067 AGAAATTTAAAAGAAATGCCTCGGCATGTGACCTGAAGCTCAACTCACCTCTCGCAATATGAGTT
1 AGAAA-TT--AA-AAATACCTCGGC--GTGACCCGAAGCTCAACTCACCTCTCGCAATATGAGTT
55907132 GA-TTTT-AAAAGAC
60 GATTTTTGAAAA-AC
*
55907145 AAAAATTGAAAAATA
1 AGAAATT-AAAAATA
55907160 TAATTCTTGA
Statistics
Matches: 278, Mismatches: 30, Indels: 19
0.85 0.09 0.06
Matches are distributed among these distances:
73 101 0.36
74 21 0.08
75 26 0.09
76 9 0.03
77 57 0.21
78 12 0.04
80 50 0.18
81 2 0.01
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (73 bp):
AGAAATTAAAAATACCTCGGCGTGACCCGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
TGAAAAAC
Found at i:55908049 original size:27 final size:27
Alignment explanation
Indices: 55908019--55908076 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
55908009 TGATTTTTAT
*
55908019 TTTTCT-TTTCTTTCCTTTTTTGTTTTC
1 TTTTCTGTTTCTCT-CTTTTTTGTTTTC
* * *
55908046 TTTTTTGTTTCTCTGTTTTTTGTTTTT
1 TTTTCTGTTTCTCTCTTTTTTGTTTTC
55908073 TTTT
1 TTTT
55908077 GGTTTTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.81
Consensus pattern (27 bp):
TTTTCTGTTTCTCTCTTTTTTGTTTTC
Found at i:55908083 original size:12 final size:12
Alignment explanation
Indices: 55908033--55908086 Score: 58
Period size: 11 Copynumber: 4.4 Consensus size: 12
55908023 CTTTTCTTTC
55908033 CTTTTTTGTTTT
1 CTTTTTTGTTTT
55908045 CTTTTTTGTTTCT
1 CTTTTTTGTTT-T
55908058 CTGTTTTTTGTTTT
1 C--TTTTTTGTTTT
*
55908072 -TTTTTGGTTTT
1 CTTTTTTGTTTT
55908083 -TTTT
1 CTTTT
55908087 AGGCATAATA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
11 14 0.37
12 11 0.29
13 2 0.05
14 1 0.03
15 10 0.26
ACGTcount: A:0.00, C:0.07, G:0.11, T:0.81
Consensus pattern (12 bp):
CTTTTTTGTTTT
Found at i:55908938 original size:439 final size:438
Alignment explanation
Indices: 55908121--55908999 Score: 1598
Period size: 439 Copynumber: 2.0 Consensus size: 438
55908111 CTGAGTTCAC
55908121 TGGATTAGGTAATTCTTTCCCATCCATCTCAGTGAGAATCAAAGCCCCTCCCGAGAATGCCTTTT
1 TGGATTAGGTAATTCTTTCCCATCCATCTCAGTGAGAATCAAAGCCCCTCCCGAGAATGCCTTTT
*
55908186 TTACAACGTATGGCCTTTCCCAATTTGGTGACCATTTTCCTCGAAAGTCTTTTTGTATCGGGAGG
66 TTACAACGTATGGCCCTTCCCAATTTGGTGACCATTTTCCTCGAAAGTCTTTTTGTATCGGGAGG
* *
55908251 ATTTTTCTTAACACAAGTTCCCCTTCGCGGAATTCTCTTGGTCGCACCTTCTTATTATGGGCTGT
131 ATTTTTCTTAACACAAGTTCCCCTTCGCAGAATTCTCTTGGTCGCACCTTCTTATTATGGGCCGT
55908316 GATCATTCTTTTCTGATACATCTGTCCATAACAAATTGCCTTCAAGCGCTTCCCTTCAATAAGGT
196 GATCATTCTTTTCTGATACATCTGTCCATAACAAATTGCCTTCAAGCGCTTCCCTTCAATAAGGT
*
55908381 TTAGTTGATCATATCGAGCTTGAACCCATTCTGATTCTTCTAACTTTGTCTCCATTAAGACGCGC
261 TTAGTTGATCATATCGAGCTTGAACCCACTCTGATTCTTCTAACTTTGTCTCCATTAAGACGCGC
*
55908446 AGGGATAGGATCTCTACTTTGATAGGCAGAACGACTTCCATCCCGTAGACCAGAGAAAAGGGA-G
326 AGGGATAGGATCTCTACTTTGATAGGCAGAACGACTTCCATCCCGTAGACCAGAGAAAA-AGATG
* *
55908510 TTGCCCCCGTAGACGTCTGTACAGAGGTGCGATATGCGTACAAAGTGAA
390 TTGCCCCCGTAGACGTCCGTACAGAGGTGCGATATGCGTACAAAGCGAA
* * *
55908559 TGGATTAGGTAATTCTTTCTCATCCATCTCGGTGAGAATCAGAGCCCCTCCCGAGAATGCCTTTT
1 TGGATTAGGTAATTCTTTCCCATCCATCTCAGTGAGAATCAAAGCCCCTCCCGAGAATGCC-TTT
55908624 TTTACAACGTATGGCCCTTCCCAATTTGGTGACCATTTTCCTCGAAAGTCTTTTTGTATCGGGAG
65 TTTACAACGTATGGCCCTTCCCAATTTGGTGACCATTTTCCTCGAAAGTCTTTTTGTATCGGGAG
* *
55908689 GATTTTTCTTAGCACAAGTTCCCCTTCGCAGAATTCTCTTGGTCGCACCTTTTTATTATGGGCCG
130 GATTTTTCTTAACACAAGTTCCCCTTCGCAGAATTCTCTTGGTCGCACCTTCTTATTATGGGCCG
*
55908754 TGATCATTCTTTTCTGATACATCTGTCCATGACAAATTGCCTTCAAGCGCTTCCCTTCAATAAGG
195 TGATCATTCTTTTCTGATACATCTGTCCATAACAAATTGCCTTCAAGCGCTTCCCTTCAATAAGG
*
55908819 TTTAGTTGATCATATCGAGCTTGAATCCACTCTGATTCTTCTAACTTTGTCTCCATTAAGACGCG
260 TTTAGTTGATCATATCGAGCTTGAACCCACTCTGATTCTTCTAACTTTGTCTCCATTAAGACGCG
*
55908884 CAGGGATGGGATCTCTACTTTGATAGGCAGAACGACTTCCATCCCGTAGACCAGAGAAAAAGATG
325 CAGGGATAGGATCTCTACTTTGATAGGCAGAACGACTTCCATCCCGTAGACCAGAGAAAAAGATG
55908949 TTGCCCCCGTAGACGTCCGTACAGAGGTGCGATATGCGTACAAAGCGAA
390 TTGCCCCCGTAGACGTCCGTACAGAGGTGCGATATGCGTACAAAGCGAA
55908998 TG
1 TG
55909000 ATAGCTTCTC
Statistics
Matches: 424, Mismatches: 15, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
438 60 0.14
439 364 0.86
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (438 bp):
TGGATTAGGTAATTCTTTCCCATCCATCTCAGTGAGAATCAAAGCCCCTCCCGAGAATGCCTTTT
TTACAACGTATGGCCCTTCCCAATTTGGTGACCATTTTCCTCGAAAGTCTTTTTGTATCGGGAGG
ATTTTTCTTAACACAAGTTCCCCTTCGCAGAATTCTCTTGGTCGCACCTTCTTATTATGGGCCGT
GATCATTCTTTTCTGATACATCTGTCCATAACAAATTGCCTTCAAGCGCTTCCCTTCAATAAGGT
TTAGTTGATCATATCGAGCTTGAACCCACTCTGATTCTTCTAACTTTGTCTCCATTAAGACGCGC
AGGGATAGGATCTCTACTTTGATAGGCAGAACGACTTCCATCCCGTAGACCAGAGAAAAAGATGT
TGCCCCCGTAGACGTCCGTACAGAGGTGCGATATGCGTACAAAGCGAA
Found at i:55915837 original size:17 final size:18
Alignment explanation
Indices: 55915811--55915945 Score: 161
Period size: 17 Copynumber: 7.7 Consensus size: 18
55915801 TTGAAATTCG
55915811 GAAAATTTTTGAAAACAC
1 GAAAATTTTTGAAAACAC
* *
55915829 GAAAATTTTTG-CAATAC
1 GAAAATTTTTGAAAACAC
* *
55915846 GAGAA-TTTTAAAAACAC
1 GAAAATTTTTGAAAACAC
*
55915863 GAAAATTTCT-AAAACAC
1 GAAAATTTTTGAAAACAC
55915880 GAAAATTTTTGAAAACAC
1 GAAAATTTTTGAAAACAC
* *
55915898 GAGATTTTTTG-AAACAC
1 GAAAATTTTTGAAAACAC
* *
55915915 GAAAATTTTTGGAAATAC
1 GAAAATTTTTGAAAACAC
55915933 GAAAATTTTTGAA
1 GAAAATTTTTGAA
55915946 GCATGAAGTT
Statistics
Matches: 98, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
16 4 0.04
17 47 0.48
18 47 0.48
ACGTcount: A:0.47, C:0.10, G:0.13, T:0.30
Consensus pattern (18 bp):
GAAAATTTTTGAAAACAC
Found at i:55915942 original size:35 final size:35
Alignment explanation
Indices: 55915811--55915945 Score: 173
Period size: 35 Copynumber: 3.9 Consensus size: 35
55915801 TTGAAATTCG
* *
55915811 GAAAATTTTTGAAAACACGAAAATTTTTGCAATAC
1 GAAAATTTTTGAAAACACGAAAATTTTTGAAACAC
* * * *
55915846 GAGAA-TTTTAAAAACACGAAAATTTCTAAAACAC
1 GAAAATTTTTGAAAACACGAAAATTTTTGAAACAC
* *
55915880 GAAAATTTTTGAAAACACGAGATTTTTTGAAACAC
1 GAAAATTTTTGAAAACACGAAAATTTTTGAAACAC
* *
55915915 GAAAATTTTTGGAAATACGAAAATTTTTGAA
1 GAAAATTTTTGAAAACACGAAAATTTTTGAA
55915946 GCATGAAGTT
Statistics
Matches: 83, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
34 28 0.34
35 55 0.66
ACGTcount: A:0.47, C:0.10, G:0.13, T:0.30
Consensus pattern (35 bp):
GAAAATTTTTGAAAACACGAAAATTTTTGAAACAC
Found at i:55916031 original size:18 final size:17
Alignment explanation
Indices: 55916004--55916052 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 17
55915994 TTGTTATTAT
55916004 TTTTTGAAACACGAGAAA
1 TTTTTGAAACACGA-AAA
*
55916022 -TTTTGAAAACATGAAAA
1 TTTTTG-AAACACGAAAA
55916039 TTTTTGAAACACGA
1 TTTTTGAAACACGA
55916053 TTATTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (17 bp):
TTTTTGAAACACGAAAA
Found at i:55916061 original size:18 final size:17
Alignment explanation
Indices: 55916004--55916060 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
55915994 TTGTTATTAT
*
55916004 TTTTTGAAACACGAGAA
1 TTTTTGAAACACGATAA
* * *
55916021 ATTTTGAAAACATGAAAA
1 TTTTTG-AAACACGATAA
*
55916039 TTTTTGAAACACGATTA
1 TTTTTGAAACACGATAA
55916056 TTTTT
1 TTTTT
55916061 TTTTAAAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
17 18 0.56
18 14 0.44
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.39
Consensus pattern (17 bp):
TTTTTGAAACACGATAA
Found at i:55916560 original size:13 final size:13
Alignment explanation
Indices: 55916537--55916582 Score: 58
Period size: 12 Copynumber: 3.4 Consensus size: 13
55916527 TGGGCCCCCC
55916537 TTTTTTC-TTTCT
1 TTTTTTCTTTTCT
55916549 TTTTTTCTTTTCT
1 TTTTTTCTTTTCT
55916562 TCTCTTTTCTTTTTCT
1 T-T-TTTTC-TTTTCT
55916578 TTTTT
1 TTTTT
55916583 CTGCTGGGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 7 0.23
13 6 0.20
14 4 0.13
15 6 0.20
16 7 0.23
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTTCTTTTCT
Found at i:55916567 original size:10 final size:9
Alignment explanation
Indices: 55916539--55916573 Score: 54
Period size: 10 Copynumber: 3.9 Consensus size: 9
55916529 GGCCCCCCTT
55916539 TTTTCTTTC
1 TTTTCTTTC
55916548 TTTT-TTTC
1 TTTTCTTTC
55916556 TTTTCTTCTC
1 TTTTCTT-TC
55916566 TTTTCTTT
1 TTTTCTTT
55916574 TTCTTTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 8 0.33
9 7 0.29
10 9 0.38
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTCTTTC
Found at i:55916583 original size:13 final size:13
Alignment explanation
Indices: 55916536--55916584 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
55916526 TTGGGCCCCC
*
55916536 CTTTTTTCTTTCT
1 CTTTTTTCTTTTT
55916549 -TTTTTTCTTTTCTT
1 CTTTTTTC-TTT-TT
*
55916563 CTCTTTTCTTTTT
1 CTTTTTTCTTTTT
55916576 CTTTTTTCT
1 CTTTTTTCT
55916585 GCTGGGCTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
12 7 0.23
13 13 0.43
14 4 0.13
15 6 0.20
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
CTTTTTTCTTTTT
Found at i:55916670 original size:16 final size:16
Alignment explanation
Indices: 55916651--55916682 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
55916641 GGTACCAGCT
55916651 GCTGGACTGGGCCTGC
1 GCTGGACTGGGCCTGC
*
55916667 GCTGGATTGGGCCTGC
1 GCTGGACTGGGCCTGC
55916683 TGTGGCTTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.28, G:0.44, T:0.22
Consensus pattern (16 bp):
GCTGGACTGGGCCTGC
Found at i:55916835 original size:6 final size:6
Alignment explanation
Indices: 55916826--55916901 Score: 64
Period size: 6 Copynumber: 12.5 Consensus size: 6
55916816 TTTCTCTCTT
* * * * * *
55916826 TTTTTC TTTTTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC
1 TTTTTC -TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
*
55916875 TTTTTC TTCTTTC TTTTT- TTCTTC TTT
1 TTTTTC TT-TTTC TTTTTC TTTTTC TTT
55916902 CTTCCTCCTC
Statistics
Matches: 63, Mismatches: 4, Indels: 5
0.88 0.06 0.07
Matches are distributed among these distances:
5 4 0.06
6 47 0.75
7 12 0.19
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (6 bp):
TTTTTC
Found at i:55916850 original size:12 final size:12
Alignment explanation
Indices: 55916835--55916881 Score: 85
Period size: 12 Copynumber: 3.9 Consensus size: 12
55916825 TTTTTTCTTT
55916835 TTTCTATTTCTA
1 TTTCTATTTCTA
55916847 TTTCTATTTCTA
1 TTTCTATTTCTA
55916859 TTTCTATTTCTA
1 TTTCTATTTCTA
*
55916871 TTTCTTTTTCT
1 TTTCTATTTCT
55916882 TCTTTCTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTCTATTTCTA
Found at i:55916858 original size:18 final size:18
Alignment explanation
Indices: 55916835--55916881 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
55916825 TTTTTTCTTT
55916835 TTTCTATTTCTATTTCTA
1 TTTCTATTTCTATTTCTA
55916853 TTTCTATTTCTATTTCTA
1 TTTCTATTTCTATTTCTA
*
55916871 TTTCTTTTTCT
1 TTTCTATTTCT
55916882 TCTTTCTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTCTATTTCTATTTCTA
Found at i:55916891 original size:12 final size:12
Alignment explanation
Indices: 55916815--55916905 Score: 50
Period size: 12 Copynumber: 7.7 Consensus size: 12
55916805 ATTTTTTATT
55916815 TTTTCTCTCTTT-
1 TTTTCT-TCTTTC
*
55916827 TTTTCTTTTTTC
1 TTTTCTTCTTTC
*
55916839 TATTTC-TATTTC
1 T-TTTCTTCTTTC
*
55916851 TATTTC-TATTTC
1 T-TTTCTTCTTTC
*
55916863 TATTTC-TATTTC
1 T-TTTCTTCTTTC
55916875 TTTTTCTTCTTTC
1 -TTTTCTTCTTTC
*
55916888 TTTTTTTC-TTC
1 TTTTCTTCTTTC
55916899 -TTTCTTC
1 TTTTCTTC
55916906 CTCCTCCTTC
Statistics
Matches: 70, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
10 6 0.09
11 7 0.10
12 47 0.67
13 10 0.14
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTCTTCTTTC
Found at i:55916893 original size:15 final size:15
Alignment explanation
Indices: 55916875--55916904 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
55916865 TTTCTATTTC
55916875 TTTTTCTTCTTTCTT
1 TTTTTCTTCTTTCTT
55916890 TTTTTCTTCTTTCTT
1 TTTTTCTTCTTTCTT
55916905 CCTCCTCCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTCTTCTTTCTT
Found at i:55917524 original size:30 final size:29
Alignment explanation
Indices: 55917498--55917575 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
55917488 AGAAGTTCAT
*
55917498 AGGTTAAAATGTAATTTTAGAAAAGTTAA
1 AGGTTAAAATGTAATTTTAAAAAAGTTAA
* ***
55917527 AGGGTCAAAACACAATTTTAAAAAAGTTAA
1 A-GGTTAAAATGTAATTTTAAAAAAGTTAA
*
55917557 GGGGTTAAAATGTAATTTT
1 -AGGTTAAAATGTAATTTT
55917576 TTTATTTTTG
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
29 1 0.03
30 36 0.97
ACGTcount: A:0.46, C:0.04, G:0.18, T:0.32
Consensus pattern (29 bp):
AGGTTAAAATGTAATTTTAAAAAAGTTAA
Found at i:55917592 original size:17 final size:17
Alignment explanation
Indices: 55917567--55917601 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
55917557 GGGGTTAAAA
*
55917567 TGTAATTTTTTTATTTT
1 TGTAATTTTTGTATTTT
*
55917584 TGTATTTTTTGTATTTT
1 TGTAATTTTTGTATTTT
55917601 T
1 T
55917602 TTTAAAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.09, T:0.77
Consensus pattern (17 bp):
TGTAATTTTTGTATTTT
Found at i:55917603 original size:10 final size:9
Alignment explanation
Indices: 55917571--55917602 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
55917561 TTAAAATGTA
55917571 ATTTTTT-T
1 ATTTTTTGT
55917579 A-TTTTTGT
1 ATTTTTTGT
55917587 ATTTTTTGT
1 ATTTTTTGT
55917596 ATTTTTT
1 ATTTTTT
55917603 TTAAAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 5 0.23
8 3 0.14
9 14 0.64
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.81
Consensus pattern (9 bp):
ATTTTTTGT
Found at i:55918536 original size:20 final size:20
Alignment explanation
Indices: 55918499--55918536 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
55918489 TATGTTTTGT
*
55918499 TATATTAATCTACTTTTTTA
1 TATATTAATCTACATTTTTA
55918519 TATATGTAATCT-CATTTT
1 TATAT-TAATCTACATTTT
55918537 ACGATAGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.29, C:0.11, G:0.03, T:0.58
Consensus pattern (20 bp):
TATATTAATCTACATTTTTA
Found at i:55923383 original size:17 final size:18
Alignment explanation
Indices: 55923361--55923400 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
55923351 ACCCAAACCG
*
55923361 ATAAAACCCA-ACATAAA
1 ATAAAACCCAGAAATAAA
55923378 ATAAAACCCAGAAATAAA
1 ATAAAACCCAGAAATAAA
55923396 A-AAAA
1 ATAAAA
55923401 AATGGACCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.70, C:0.17, G:0.03, T:0.10
Consensus pattern (18 bp):
ATAAAACCCAGAAATAAA
Found at i:55923401 original size:18 final size:17
Alignment explanation
Indices: 55923363--55923401 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
55923353 CCAAACCGAT
* *
55923363 AAAACCCAACATAAAAT
1 AAAACCCAAAATAAAAA
55923380 AAAACCCAGAAATAAAAA
1 AAAACCCA-AAATAAAAA
55923398 AAAA
1 AAAA
55923402 ATGGACCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.72, C:0.18, G:0.03, T:0.08
Consensus pattern (17 bp):
AAAACCCAAAATAAAAA
Found at i:55925372 original size:5 final size:5
Alignment explanation
Indices: 55925364--55925396 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
55925354 TTTATTGCAA
55925364 AAAAG AAAAG AAAAG AAAAG AAAAG AAATAG AA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAA-AG AA
55925397 GGACATATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:55942973 original size:22 final size:23
Alignment explanation
Indices: 55942941--55942983 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
55942931 TATTTTTCAA
55942941 TTTCTTGTTTTACCTT-TTTCCTT
1 TTTCTTGTTTTA-CTTATTTCCTT
55942964 TTTCTT-TTTTACTTATTTCC
1 TTTCTTGTTTTACTTATTTCC
55942984 CCTCTCTCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 3 0.16
22 10 0.53
23 6 0.32
ACGTcount: A:0.07, C:0.21, G:0.02, T:0.70
Consensus pattern (23 bp):
TTTCTTGTTTTACTTATTTCCTT
Found at i:55945851 original size:15 final size:16
Alignment explanation
Indices: 55945821--55945854 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
55945811 TTTTTTAGAA
55945821 AAAACATTAACAAAAC
1 AAAACATTAACAAAAC
*
55945837 AAAACA-TAACTAAAC
1 AAAACATTAACAAAAC
55945852 AAA
1 AAA
55945855 GAAGACGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.71, C:0.18, G:0.00, T:0.12
Consensus pattern (16 bp):
AAAACATTAACAAAAC
Found at i:55945979 original size:12 final size:12
Alignment explanation
Indices: 55945964--55946006 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
55945954 CCTGCTCCTG
55945964 CTCCACCTCCAA
1 CTCCACCTCCAA
*
55945976 CTCCACCGCCAA
1 CTCCACCTCCAA
** *
55945988 CAGCACCTCCTA
1 CTCCACCTCCAA
55946000 CTCCACC
1 CTCCACC
55946007 ACCTACACCA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.23, C:0.58, G:0.05, T:0.14
Consensus pattern (12 bp):
CTCCACCTCCAA
Found at i:55946018 original size:24 final size:24
Alignment explanation
Indices: 55945966--55946018 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
55945956 TGCTCCTGCT
*
55945966 CCACCTCCAACTCCACCGCCAACA
1 CCACCTCCAACTCCACCACCAACA
* * *
55945990 GCACCTCCTACTCCACCACCTACA
1 CCACCTCCAACTCCACCACCAACA
55946014 CCACC
1 CCACC
55946019 ACCAGCACCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.26, C:0.58, G:0.04, T:0.11
Consensus pattern (24 bp):
CCACCTCCAACTCCACCACCAACA
Found at i:55946046 original size:9 final size:9
Alignment explanation
Indices: 55946034--55946149 Score: 51
Period size: 9 Copynumber: 12.9 Consensus size: 9
55946024 CACCACCAAA
*
55946034 TCCACCGAC
1 TCCACCGAG
55946043 TCCACCG-G
1 TCCACCGAG
* *
55946051 TTCCTCCAAG
1 -TCCACCGAG
* *
55946061 TCCATCGAC
1 TCCACCGAG
55946070 TCCACCG-G
1 TCCACCGAG
* *
55946078 TACCTCCAAG
1 T-CCACCGAG
*
55946088 TCCACCGAC
1 TCCACCGAG
55946097 TCCACCG-G
1 TCCACCGAG
* *
55946105 TACCTCCAAG
1 T-CCACCGAG
*
55946115 TCCACCGAC
1 TCCACCGAG
55946124 TCCACCG-G
1 TCCACCGAG
* *
55946132 TTCCTCCAAG
1 -TCCACCGAG
55946142 TCCACCGA
1 TCCACCGA
55946150 ATCCTCCGGT
Statistics
Matches: 74, Mismatches: 25, Indels: 16
0.64 0.22 0.14
Matches are distributed among these distances:
8 2 0.03
9 66 0.89
10 6 0.08
ACGTcount: A:0.21, C:0.47, G:0.15, T:0.17
Consensus pattern (9 bp):
TCCACCGAG
Found at i:55946047 original size:27 final size:27
Alignment explanation
Indices: 55946029--55946174 Score: 229
Period size: 27 Copynumber: 5.4 Consensus size: 27
55946019 ACCAGCACCA
* *
55946029 CCAAATCCACCGACTCCACCGGTTCCT
1 CCAAGTCCACCGACTCCACCGGTACCT
*
55946056 CCAAGTCCATCGACTCCACCGGTACCT
1 CCAAGTCCACCGACTCCACCGGTACCT
55946083 CCAAGTCCACCGACTCCACCGGTACCT
1 CCAAGTCCACCGACTCCACCGGTACCT
*
55946110 CCAAGTCCACCGACTCCACCGGTTCCT
1 CCAAGTCCACCGACTCCACCGGTACCT
* * *
55946137 CCAAGTCCACCGAATCCTCCGGTTCCT
1 CCAAGTCCACCGACTCCACCGGTACCT
55946164 CCAAGTCCACC
1 CCAAGTCCACC
55946175 CAAACCACCA
Statistics
Matches: 112, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 112 1.00
ACGTcount: A:0.21, C:0.47, G:0.14, T:0.18
Consensus pattern (27 bp):
CCAAGTCCACCGACTCCACCGGTACCT
Found at i:55946183 original size:81 final size:78
Alignment explanation
Indices: 55946019--55946207 Score: 243
Period size: 81 Copynumber: 2.4 Consensus size: 78
55946009 CTACACCACC
* * * *
55946019 ACCAGCACCACCAAATCCACCGACTCCACCGGTTCCTCCAAGTCCATCGACTCCACCGGTACCTC
1 ACCACCACCACCAAGTCCACCGACTCCACCGGTTCCTCCAAGTCCACCGAATCCACCGGTACCTC
* *
55946084 CAAGTCCACCGAC
66 CAAGTCCACCCAA
* * * *
55946097 TCCACCGGTACCTCCAAGTCCACCGACTCCACCGGTTCCTCCAAGTCCACCGAATCCTCCGGTTC
1 ACCACC---ACCACCAAGTCCACCGACTCCACCGGTTCCTCCAAGTCCACCGAATCCACCGGTAC
55946162 CTCCAAGTCCACCCAA
63 CTCCAAGTCCACCCAA
* *
55946178 ACCACCACCACCAAGTCCACCTACACCACC
1 ACCACCACCACCAAGTCCACCGACTCCACC
55946208 AAAGGGAGTA
Statistics
Matches: 94, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
78 25 0.27
81 69 0.73
ACGTcount: A:0.25, C:0.49, G:0.12, T:0.15
Consensus pattern (78 bp):
ACCACCACCACCAAGTCCACCGACTCCACCGGTTCCTCCAAGTCCACCGAATCCACCGGTACCTC
CAAGTCCACCCAA
Found at i:55947214 original size:15 final size:15
Alignment explanation
Indices: 55947165--55947222 Score: 50
Period size: 15 Copynumber: 4.0 Consensus size: 15
55947155 TCCACTTATA
*
55947165 TTATTATTTTAAT-T
1 TTATTAATTTAATAT
* *
55947179 TTTTTAATTGTATTA-
1 TTATTAATT-TAATAT
55947194 TT-TTAATTTAATAT
1 TTATTAATTTAATAT
*
55947208 TTATTAATTTTATAT
1 TTATTAATTTAATAT
55947223 GTTTTCTCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
13 4 0.11
14 15 0.43
15 16 0.46
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
TTATTAATTTAATAT
Found at i:55954232 original size:18 final size:18
Alignment explanation
Indices: 55954209--55954273 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
55954199 TCTAAAATTT
55954209 ACATTTAAAAAAATATAA
1 ACATTTAAAAAAATATAA
*
55954227 ACATTTTAAAAAATA-AA
1 ACATTTAAAAAAATATAA
*
55954244 A-ATTCTAAATAATATATAA
1 ACATT-TAAA-AAAATATAA
* *
55954263 AAAATTAAAAA
1 ACATTTAAAAA
55954274 TTTTCTAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
16 3 0.08
17 6 0.15
18 21 0.54
19 7 0.18
20 2 0.05
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (18 bp):
ACATTTAAAAAAATATAA
Found at i:55954252 original size:16 final size:18
Alignment explanation
Indices: 55954216--55954259 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 18
55954206 TTTACATTTA
*
55954216 AAAAAATATAAACATTTT
1 AAAAAATATAAACATTCT
55954234 AAAAAATA-AAA-ATTCT
1 AAAAAATATAAACATTCT
*
55954250 AAATAATATA
1 AAAAAATATA
55954260 TAAAAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 11 0.48
17 4 0.17
18 8 0.35
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAAAATATAAACATTCT
Found at i:55960598 original size:49 final size:49
Alignment explanation
Indices: 55960541--55960634 Score: 134
Period size: 49 Copynumber: 1.9 Consensus size: 49
55960531 TGTTTAGAAC
* * *
55960541 TACCCATAACTCTTCATCAACCCATAAATAAGAGGATAATATGCTTCAG
1 TACCCATAACTCCTCACCAACCCATAAATAAGAAGATAATATGCTTCAG
* * *
55960590 TACCCATAATTCCTCCCCAACCCATAAATAAGAATATAATATGCT
1 TACCCATAACTCCTCACCAACCCATAAATAAGAAGATAATATGCT
55960635 CCAAAAGGCT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 39 1.00
ACGTcount: A:0.39, C:0.27, G:0.07, T:0.27
Consensus pattern (49 bp):
TACCCATAACTCCTCACCAACCCATAAATAAGAAGATAATATGCTTCAG
Done.