Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 183 of 213
Found at i:55162798 original size:90 final size:90
Alignment explanation
Indices: 55162636--55162919 Score: 313
Period size: 90 Copynumber: 3.2 Consensus size: 90
55162626 ACTATTATTC
* * ** * * ** *
55162636 AAAATGTTCGTATTATTCTTGTATCCATAAATCAATTTTAGCCCGTATTATTTGTTGGTCG-ATT
1 AAAATGTTCGTATTATTTTTGGATCTGTAAATAAAATTTATTCGGTATTATTTGTTGGTCGAATT
55162700 TTTATATTTTCGTATATCAGTTTTGT
66 TTT-TATTTTCGTATATCAGTTTTGT
* * * * * *
55162726 AAAATGTTTGTTTTATTTTTGGATCTGTAAA-AATATCTTAGTT-TGTATTATTTGTCGATCGAA
1 AAAATGTTCGTATTATTTTTGGATCTGTAAATAAAAT-TTA-TTCGGTATTATTTGTTGGTCGAA
* *
55162789 TTTTTTATTTTCGTATATCAATTTTCT
64 TTTTTTATTTTCGTATATCAGTTTTGT
* *
55162816 AAAATGTTCGTATTATTTTTGTATCTGTAAATAAAATTTATTCGGTATTATTTGTTGGTTGAATT
1 AAAATGTTCGTATTATTTTTGGATCTGTAAATAAAATTTATTCGGTATTATTTGTTGGTCGAATT
* * *
55162881 ATATATTTTCGTATATTAGTTTTGT
66 TTTTATTTTCGTATATCAGTTTTGT
*
55162906 AGAATGTTCGTATT
1 AAAATGTTCGTATT
55162920 TTCTTATATA
Statistics
Matches: 159, Mismatches: 30, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
89 4 0.03
90 145 0.91
91 10 0.06
ACGTcount: A:0.26, C:0.08, G:0.14, T:0.52
Consensus pattern (90 bp):
AAAATGTTCGTATTATTTTTGGATCTGTAAATAAAATTTATTCGGTATTATTTGTTGGTCGAATT
TTTTATTTTCGTATATCAGTTTTGT
Found at i:55162988 original size:15 final size:15
Alignment explanation
Indices: 55162968--55162996 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
55162958 TTGTTCGAAT
55162968 TATTTTTTTACTTAA
1 TATTTTTTTACTTAA
55162983 TATTTTTTTACTTA
1 TATTTTTTTACTTA
55162997 TCTATGCCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (15 bp):
TATTTTTTTACTTAA
Found at i:55165668 original size:29 final size:30
Alignment explanation
Indices: 55165636--55165725 Score: 81
Period size: 30 Copynumber: 3.3 Consensus size: 30
55165626 TTTTTATTCC
55165636 TTTTTAATTAAAATCTATCTATTCAATTA-
1 TTTTTAATTAAAATCTATCTATTCAATTAT
* *
55165665 TTTTT-ATT----TATA-CT-TT-AAATAT
1 TTTTTAATTAAAATCTATCTATTCAATTAT
* *
55165687 TTTTTAATTAAAATCGATCTATTCGATTAT
1 TTTTTAATTAAAATCTATCTATTCAATTAT
55165717 TTTTTAATT
1 TTTTTAATT
55165726 TATACTTTGA
Statistics
Matches: 46, Mismatches: 6, Indels: 17
0.67 0.09 0.25
Matches are distributed among these distances:
21 4 0.09
22 7 0.15
23 5 0.11
24 3 0.07
27 2 0.04
28 5 0.11
29 7 0.15
30 13 0.28
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.57
Consensus pattern (30 bp):
TTTTTAATTAAAATCTATCTATTCAATTAT
Found at i:55165813 original size:30 final size:30
Alignment explanation
Indices: 55165779--55165996 Score: 116
Period size: 30 Copynumber: 7.2 Consensus size: 30
55165769 ATCTATTCAA
55165779 TTATTTTTTATTTATACTTAAATTAATTTT
1 TTATTTTTTATTTATACTTAAATTAATTTT
* *
55165809 TTATTCTTTT-TTTA-A-TAAAAATATATCTATTCGT
1 TTATT-TTTTATTTATACT-TAAAT-TA---ATT-TT
* *
55165843 TTATTTTTTAATTTATACTTTAATTGATTTT
1 TTATTTTTT-ATTTATACTTAAATTAATTTT
*
55165874 TTA-TTATTATTTA-A-TTAAAATCTATATATTTT
1 TTATTTTTTATTTATACTT-AAA--T-TA-ATTTT
* *
55165906 ATTATTTTTAATTTATACTTTAATTAATTTT
1 -TTATTTTTTATTTATACTTAAATTAATTTT
* ** * *
55165937 TTA-TTTTTAATTA-AAATATATTAA---A
1 TTATTTTTTATTTATACTTAAATTAATTTT
*
55165962 TTATTTTTTATTTATACTTTAATTAATTTT
1 TTATTTTTTATTTATACTTAAATTAATTTT
55165992 TTATT
1 TTATT
55165997 CATTTTTAAT
Statistics
Matches: 138, Mismatches: 25, Indels: 50
0.65 0.12 0.23
Matches are distributed among these distances:
25 3 0.02
26 9 0.07
27 9 0.07
28 11 0.08
29 18 0.13
30 24 0.17
31 14 0.10
32 10 0.07
33 11 0.08
34 14 0.10
35 8 0.06
36 6 0.04
37 1 0.01
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.63
Consensus pattern (30 bp):
TTATTTTTTATTTATACTTAAATTAATTTT
Found at i:55165818 original size:64 final size:63
Alignment explanation
Indices: 55165686--55166121 Score: 530
Period size: 64 Copynumber: 6.9 Consensus size: 63
55165676 ACTTTAAATA
* * *
55165686 TTTTTTAATTAAAATCGATCTATTCGATTATTTTTTAATTTATACTTTGATTAAATTTTTTATTC
1 TTTTTTAATTAAAATCTATCTATTCAATTATTTTTT-ATTTATACTTTAATT-AATTTTTTATTC
* *
55165751 TTTTTTTAA-TACAAATATATCTATTCAATTATTTTTTATTTATACTTAAATTAATTTTTTATTC
1 -TTTTTTAATTA-AAATCTATCTATTCAATTATTTTTTATTTATACTTTAATTAATTTTTTATTC
* * ** * *
55165815 TTTTTTTAATAAAAATATATCTATTCGTTTATTTTTTAATTTATACTTTAATTGATTTTTTATTA
1 -TTTTTTAATTAAAATCTATCTATTCAATTATTTTTT-ATTTATACTTTAATTAATTTTTTATTC
* * ** *
55165880 TTATTTAATTAAAATCTATATATTTTATTATTTTTAATTTATACTTTAATTAATTTTTTA---
1 TTTTTTAATTAAAATCTATCTATTCAATTATTTTTTATTTATACTTTAATTAATTTTTTATTC
*
55165940 -TTTTTAATTAAAA--TA--TATTAAATTATTTTTTATTTATACTTTAATTAATTTTTTATTC
1 TTTTTTAATTAAAATCTATCTATTCAATTATTTTTTATTTATACTTTAATTAATTTTTTATTC
* * *
55165998 ATTTTTAATTAAAATCTATCTATTCAATTATTTTTAATATATACTTTAATTAATTTTTTTATTC
1 TTTTTTAATTAAAATCTATCTATTCAATTATTTTTTATTTATACTTTAATTAA-TTTTTTATTC
* * *
55166062 TTTTTTAATTAAAATCTATCTATTCCATTATTTTTTGGTTTATACTTTAAATAATTTTTT
1 TTTTTTAATTAAAATCTATCTATTCAATTATTTTTT-ATTTATACTTTAATTAATTTTTT
55166122 TATTTATGCT
Statistics
Matches: 324, Mismatches: 33, Indels: 28
0.84 0.09 0.07
Matches are distributed among these distances:
55 37 0.11
57 2 0.01
59 25 0.08
61 2 0.01
63 53 0.16
64 121 0.37
65 54 0.17
66 30 0.09
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (63 bp):
TTTTTTAATTAAAATCTATCTATTCAATTATTTTTTATTTATACTTTAATTAATTTTTTATTC
Found at i:55165846 original size:34 final size:33
Alignment explanation
Indices: 55165744--55165851 Score: 84
Period size: 34 Copynumber: 3.3 Consensus size: 33
55165734 GATTAAATTT
*
55165744 TTTATTCTTTTTTTAATACAAATATATCTATTCA
1 TTTATT-TTTTTTTAATAAAAATATATCTATTCA
* * *
55165778 ATTATTTTTTATTT-ATACTTAAAT-TA---ATT-T
1 TTTATTTTTT-TTTAATA--AAAATATATCTATTCA
*
55165808 TTTATTCTTTTTTTAATAAAAATATATCTATTCG
1 TTTATT-TTTTTTTAATAAAAATATATCTATTCA
55165842 TTTATTTTTT
1 TTTATTTTTT
55165852 AATTTATACT
Statistics
Matches: 58, Mismatches: 6, Indels: 21
0.68 0.07 0.25
Matches are distributed among these distances:
29 4 0.07
30 10 0.17
31 10 0.17
33 14 0.24
34 16 0.28
35 4 0.07
ACGTcount: A:0.31, C:0.07, G:0.01, T:0.61
Consensus pattern (33 bp):
TTTATTTTTTTTTAATAAAAATATATCTATTCA
Found at i:55165873 original size:23 final size:22
Alignment explanation
Indices: 55165847--55165942 Score: 67
Period size: 22 Copynumber: 4.5 Consensus size: 22
55165837 ATTCGTTTAT
*
55165847 TTTTTAATTTATACTTTAATTGA
1 TTTTTAATTTATA-TTTAATTAA
*
55165870 TTTTTTA-TTATTATTTAATTAA
1 TTTTTAATTTA-TATTTAATTAA
** * *
55165892 AATCT-A--TATATTTTATT-A
1 TTTTTAATTTATATTTAATTAA
55165910 TTTTTAATTTATACTTTAATTAA
1 TTTTTAATTTATA-TTTAATTAA
*
55165933 TTTTTTATTT
1 TTTTTAATTT
55165943 TTAATTAAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
18 3 0.05
19 9 0.16
20 2 0.04
21 5 0.09
22 19 0.34
23 18 0.32
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (22 bp):
TTTTTAATTTATATTTAATTAA
Found at i:55165906 original size:118 final size:124
Alignment explanation
Indices: 55165686--55166121 Score: 439
Period size: 118 Copynumber: 3.5 Consensus size: 124
55165676 ACTTTAAATA
** * *
55165686 TTTTTTAATTAAAATCGATCTATTCGATTATTTTTTAATTTATACTTTGATTAAATTTTTTATTC
1 TTTTTTAATTAAAATATATCTATTCAATTATTTTTT-ATTTATACTTTAATT-AATTTTTTATTC
* *
55165751 TTTTTTTAATACAAATATATCTATTCAATTATTTTTTATTTATACTTAAATTAA-TTTTTTATTC
64 -ATTTTTAAT-TAAA-ATATCTATT-AATTA-TTTTTATTTATACTTAAATTAACTTTTTTATTC
55165815 T
124 T
* ** *
55165816 TTTTTTAATAAAAATATATCTATTCGTTTATTTTTTAATTTATACTTTAATTGATTTTTTATT-A
1 TTTTTTAATTAAAATATATCTATTCAATTATTTTTT-ATTTATACTTTAATTAATTTTTTATTCA
* * *
55165880 TTATTTAATTAAAATCTATATATTTTATTATTTTTAATTTATACTTTAATTAA-TTTTTTA----
65 TT-TTTAATTAAAA--TATCTA-TTAATTATTTTT-ATTTATACTTAAATTAACTTTTTTATTCT
55165940 -TTTTTAATTAAAATATAT-TA---AATTATTTTTTATTTATACTTTAATTAATTTTTTATTCAT
1 TTTTTTAATTAAAATATATCTATTCAATTATTTTTTATTTATACTTTAATTAATTTTTTATTCAT
* * *
55166000 TTTTAATTAAAATCTATCTATTCAATTATTTTTAATATATACTTTAATTAATTTTTTTATTC-
66 TTTTAATTAAAA--TATCTATT-AATTATTTTT-ATTTATACTTAAATTAACTTTTTTATTCT
* * * *
55166062 TTTTTTAATTAAAATCTATCTATTCCATTATTTTTTGGTTTATACTTTAAATAATTTTTT
1 TTTTTTAATTAAAATATATCTATTCAATTATTTTTT-ATTTATACTTTAATTAATTTTTT
55166122 TATTTATGCT
Statistics
Matches: 267, Mismatches: 22, Indels: 36
0.82 0.07 0.11
Matches are distributed among these distances:
117 2 0.01
118 69 0.26
119 19 0.07
122 2 0.01
123 34 0.13
124 2 0.01
126 1 0.00
127 20 0.07
128 59 0.22
129 12 0.04
130 47 0.18
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (124 bp):
TTTTTTAATTAAAATATATCTATTCAATTATTTTTTATTTATACTTTAATTAATTTTTTATTCAT
TTTTAATTAAAATATCTATTAATTATTTTTATTTATACTTAAATTAACTTTTTTATTCT
Found at i:55165991 original size:22 final size:22
Alignment explanation
Indices: 55165960--55166055 Score: 58
Period size: 22 Copynumber: 4.5 Consensus size: 22
55165950 AAATATATTA
*
55165960 AATTATTTTTTATTTATACTTT
1 AATTAATTTTTATTTATACTTT
* *
55165982 AATTAATTTTTTATTCAT-TTTT
1 AATTAA-TTTTTATTTATACTTT
** * * *
55166004 AATTAAAATCTA--TCTA-TTC
1 AATTAATTTTTATTTATACTTT
*
55166023 AATT-ATTTTTAATATATACTTT
1 AATTAATTTTT-ATTTATACTTT
55166045 AATTAATTTTT
1 AATTAATTTTT
55166056 TTATTCTTTT
Statistics
Matches: 53, Mismatches: 14, Indels: 13
0.66 0.17 0.16
Matches are distributed among these distances:
18 3 0.06
19 8 0.15
21 6 0.11
22 20 0.38
23 16 0.30
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.60
Consensus pattern (22 bp):
AATTAATTTTTATTTATACTTT
Found at i:55166043 original size:246 final size:245
Alignment explanation
Indices: 55165638--55166121 Score: 645
Period size: 246 Copynumber: 2.0 Consensus size: 245
55165628 TTTATTCCTT
* **
55165638 TTTAATTAAAATCTATCTATTCAATTATTTTTATTTATACTTTAAATATTTTTTAATTAAAATCG
1 TTTAATTAAAATCTATATATTCAATTATTTTTATTTATACTTTAAATATTTTTTAATTAAAATAA
* ** * *
55165703 ATCTATTCGATTATTTTTTAATTTATACTTTGATTAAATTTTTTATTCTTTTTTTAATACAAATA
66 ATATATTAAATTATTTTTTAATTTATACTTTAATTAAATTTTTTATTCTATTTTTAATACAAATA
* *
55165768 TATCTATTCAATTATTTTTTATTTATACTTAAATTAA-TTTTTTATTCTTTTTTTAATAAAAATA
131 TATCTATTCAATTATTTTTAATATATACTTAAATTAATTTTTTTATTC-TTTTTTAATAAAAATA
** * *
55165832 TATCTATTCGTTTATTTTTTAATTTATACTTTAATTGATTTTTTATTATTA
195 TATCTATTCCATTATTTTTTAATTTATACTTTAAATAATTTTTTATTATTA
** * * * *
55165883 TTTAATTAAAATCTATATATTTTATTATTTTTAATTTATACTTTAATTAATTTTTTATTTTTAAT
1 TTTAATTAAAATCTATATATTCAATTATTTTT-ATTTATACTTTAAAT-ATTTTTTA-ATTAAAA
55165948 TAAAATATATTAAATTATTTTTT-ATTTATACTTTAATT-AATTTTTTATTC-ATTTTTAATTA-
63 T-AAATATATTAAATTATTTTTTAATTTATACTTTAATTAAATTTTTTATTCTATTTTTAA-TAC
* * *
55166009 AAATCTATCTATTCAATTATTTTTAATATATACTTTAATTAATTTTTTTATTCTTTTTTAATTAA
126 AAATATATCTATTCAATTATTTTTAATATATACTTAAATTAATTTTTTTATTCTTTTTTAATAAA
* **
55166074 AATCTATCTATTCCATTATTTTTTGGTTTATACTTTAAATAATTTTTT
191 AATATATCTATTCCATTATTTTTTAATTTATACTTTAAATAATTTTTT
55166122 TATTTATGCT
Statistics
Matches: 207, Mismatches: 26, Indels: 11
0.85 0.11 0.05
Matches are distributed among these distances:
245 29 0.14
246 111 0.54
247 32 0.15
248 19 0.09
249 16 0.08
ACGTcount: A:0.33, C:0.06, G:0.01, T:0.60
Consensus pattern (245 bp):
TTTAATTAAAATCTATATATTCAATTATTTTTATTTATACTTTAAATATTTTTTAATTAAAATAA
ATATATTAAATTATTTTTTAATTTATACTTTAATTAAATTTTTTATTCTATTTTTAATACAAATA
TATCTATTCAATTATTTTTAATATATACTTAAATTAATTTTTTTATTCTTTTTTAATAAAAATAT
ATCTATTCCATTATTTTTTAATTTATACTTTAAATAATTTTTTATTATTA
Found at i:55166127 original size:24 final size:24
Alignment explanation
Indices: 55166091--55166146 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
55166081 CTATTCCATT
**
55166091 ATTTTTTGGTTTATACTTTAAATA
1 ATTTTTTTATTTATACTTTAAATA
* **
55166115 ATTTTTTTATTTATGCTTTACTTA
1 ATTTTTTTATTTATACTTTAAATA
55166139 ATTTTTTT
1 ATTTTTTT
55166147 TGTTTTTTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.66
Consensus pattern (24 bp):
ATTTTTTTATTTATACTTTAAATA
Found at i:55168746 original size:14 final size:14
Alignment explanation
Indices: 55168724--55168759 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
55168714 ATCTCAAAAC
55168724 AATATAAATTTAGAA
1 AATATAAATTTA-AA
55168739 AA-ATAAATTTAAA
1 AATATAAATTTAAA
55168752 AATATAAA
1 AATATAAA
55168760 CTGATAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 4 0.20
14 14 0.70
15 2 0.10
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (14 bp):
AATATAAATTTAAA
Found at i:55174889 original size:17 final size:18
Alignment explanation
Indices: 55174857--55174894 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
55174847 TAATTTAATT
55174857 TTAATTAAATTATTTAAA
1 TTAATTAAATTATTTAAA
*
55174875 TTAATT-AATTTTTTAAA
1 TTAATTAAATTATTTAAA
55174892 TTA
1 TTA
55174895 TAAACAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTAATTAAATTATTTAAA
Found at i:55184412 original size:24 final size:25
Alignment explanation
Indices: 55184383--55184442 Score: 104
Period size: 24 Copynumber: 2.4 Consensus size: 25
55184373 AAATATATAT
*
55184383 AAAATATATATTTGATTAAAAAT-A
1 AAAATATATATTTAATTAAAAATAA
55184407 AAAATATATATTTAATTAAAAATAA
1 AAAATATATATTTAATTAAAAATAA
55184432 AAAATATATAT
1 AAAATATATAT
55184443 ATTTAATATG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 22 0.65
25 12 0.35
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (25 bp):
AAAATATATATTTAATTAAAAATAA
Found at i:55185768 original size:29 final size:28
Alignment explanation
Indices: 55185735--55185806 Score: 81
Period size: 30 Copynumber: 2.5 Consensus size: 28
55185725 ACTATCATTT
*
55185735 GATAAAAACTAAAATTTTAAAATTCAAAA
1 GATAAAAACTAAAATTATAAAATT-AAAA
* *
55185764 GATAAAAAACTAAAAATTATCAAATTTAAA
1 GAT-AAAAACT-AAAATTATAAAATTAAAA
*
55185794 TATAAAAACTAAA
1 GATAAAAACTAAA
55185807 TTTACAACTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 3 0.08
29 10 0.27
30 12 0.32
31 12 0.32
ACGTcount: A:0.64, C:0.07, G:0.03, T:0.26
Consensus pattern (28 bp):
GATAAAAACTAAAATTATAAAATTAAAA
Found at i:55185799 original size:30 final size:30
Alignment explanation
Indices: 55185735--55185806 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
55185725 ACTATCATTT
*
55185735 GATAAAAACT-AAAATTTTAAAATTCAAAA
1 GATAAAAACTAAAAATTATAAAATTCAAAA
* *
55185764 GATAAAAAACTAAAAATTATCAAATT-TAAA
1 GAT-AAAAACTAAAAATTATAAAATTCAAAA
*
55185794 TATAAAAACTAAA
1 GATAAAAACTAAA
55185807 TTTACAACTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 13 0.35
30 12 0.32
31 12 0.32
ACGTcount: A:0.64, C:0.07, G:0.03, T:0.26
Consensus pattern (30 bp):
GATAAAAACTAAAAATTATAAAATTCAAAA
Found at i:55188174 original size:24 final size:22
Alignment explanation
Indices: 55188143--55188186 Score: 70
Period size: 24 Copynumber: 1.9 Consensus size: 22
55188133 TATTTTTATA
55188143 TTTTAAAAATATTATTCCATTTTT
1 TTTTAAAAATA-T-TTCCATTTTT
55188167 TTTTAAAAATATTTCCATTT
1 TTTTAAAAATATTTCCATTT
55188187 GCCATTTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.40
23 1 0.05
24 11 0.55
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTAAAAATATTTCCATTTTT
Found at i:55204004 original size:4 final size:4
Alignment explanation
Indices: 55203995--55204043 Score: 98
Period size: 4 Copynumber: 12.2 Consensus size: 4
55203985 CACCATGAAA
55203995 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
55204043 A
1 A
55204044 CACACACACA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:55204048 original size:2 final size:2
Alignment explanation
Indices: 55204041--55204065 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
55204031 ATACATACAT
55204041 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
55204066 TGTATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:55205294 original size:16 final size:17
Alignment explanation
Indices: 55205261--55205300 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
55205251 CATAAAATAG
55205261 TTTAAATAAATAAATTT
1 TTTAAATAAATAAATTT
*
55205278 TTTAATTAAAT-AATTT
1 TTTAAATAAATAAATTT
*
55205294 TCTAAAT
1 TTTAAAT
55205301 CTGATTCTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTAAATAAATAAATTT
Found at i:55215632 original size:39 final size:38
Alignment explanation
Indices: 55215589--55215662 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 38
55215579 TATTAATATT
*
55215589 TTTTCAAAATTTAGT-AGTTTGTAATTTTTTTAAAATTGC
1 TTTTCAAAATTTA-TCACTTTGTAA-TTTTTTAAAATTGC
* *
55215628 TTTTCAGAATTTATCACTTTTTAATTTTTTAAAAT
1 TTTTCAAAATTTATCACTTTGTAATTTTTTAAAAT
55215663 ATTGATTCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
38 12 0.39
39 19 0.61
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.55
Consensus pattern (38 bp):
TTTTCAAAATTTATCACTTTGTAATTTTTTAAAATTGC
Found at i:55217331 original size:25 final size:25
Alignment explanation
Indices: 55217303--55217418 Score: 83
Period size: 25 Copynumber: 4.6 Consensus size: 25
55217293 TTTCGGAAAT
55217303 GCTCATAAGAGCACATA-AACGAGAA
1 GCTCATAAGAGC-CATATAACGAGAA
* ** *
55217328 GCTCTTTCGAGCCATATAACGGGAA
1 GCTCATAAGAGCCATATAACGAGAA
** * *
55217353 GCTCATTTGAGCTATGTAAC-AGGAA
1 GCTCATAAGAGCCATATAACGA-GAA
** * **
55217378 GCTCATTCGAACTGTATAACGAGAA
1 GCTCATAAGAGCCATATAACGAGAA
55217403 GCTCATAAGAGCCATA
1 GCTCATAAGAGCCATA
55217419 AGCAAGAAGT
Statistics
Matches: 70, Mismatches: 18, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
24 4 0.06
25 65 0.93
26 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.22
Consensus pattern (25 bp):
GCTCATAAGAGCCATATAACGAGAA
Found at i:55219973 original size:42 final size:41
Alignment explanation
Indices: 55219922--55220008 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 41
55219912 GCATATCAAT
*
55219922 AAAAAATT-AATT-TTTTAAAGTTCAAATAAAAAATTAATATA
1 AAAAAATTAAATTCCTTT-AAGTTCAAA-AAAAAATTAATATA
* *
55219963 AAAAATATTAAATTCCTTTAAGTTCGAAAAAAAATTAATATC
1 AAAAA-ATTAAATTCCTTTAAGTTCAAAAAAAAATTAATATA
55220005 AAAA
1 AAAA
55220009 TTTGAAAGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
41 5 0.12
42 20 0.50
43 12 0.30
44 3 0.08
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.33
Consensus pattern (41 bp):
AAAAAATTAAATTCCTTTAAGTTCAAAAAAAAATTAATATA
Found at i:55220132 original size:61 final size:59
Alignment explanation
Indices: 55219982--55220312 Score: 411
Period size: 61 Copynumber: 5.5 Consensus size: 59
55219972 AAATTCCTTT
* * * *
55219982 AAGTTCGAA-AAAAAATTAATATCAAAATTTGAAAGTTGGAAGAAAAAAAAGTTTTTTA
1 AAGTTCGAATAAAAAATTAATATCAAAATTTGTAAGTTAGAAGAAAACAAAGTTTTTAA
* * *
55220040 AAGTTCGAATAAAAAATTAATGTCAAAATTTGTTAGTAAGAAGAAAACCAAAGTTTTTAA
1 AAGTTCGAATAAAAAATTAATATCAAAATTTGTAAGTTAGAAGAAAA-CAAAGTTTTTAA
* *
55220100 AAGTTTGAATTAAAAAATTAATATAAAAATTTGTAAGTTAGAAGAAAAACAAAGTTTTTAA
1 AAGTTCGAA-TAAAAAATTAATATCAAAATTTGTAAGTTAGAAG-AAAACAAAGTTTTTAA
* * *
55220161 AAGTTCGAATAAAAAATTAACATCAAAATTCGAAAGTTAGAAGAAAA-ATAATGTGTTTATAA
1 AAGTTCGAATAAAAAATTAATATCAAAATTTGTAAGTTAGAAGAAAACA-AA-GT-TTT-TAA
* *
55220223 AATGTT--AATAAAAAATTAATATCAAAATTTGTAAGTCAGAAGAAATACAAAGTTTTTTA
1 AA-GTTCGAATAAAAAATTAATATCAAAATTTGTAAGTTAGAAGAAA-ACAAAGTTTTTAA
55220282 AAGTTCGAATAAAGAAA-TAATATCAAAATTT
1 AAGTTCGAATAAA-AAATTAATATCAAAATTT
55220313 ATAACTGAAA
Statistics
Matches: 237, Mismatches: 22, Indels: 26
0.83 0.08 0.09
Matches are distributed among these distances:
58 13 0.05
59 42 0.18
60 73 0.31
61 93 0.39
62 12 0.05
63 4 0.02
ACGTcount: A:0.53, C:0.05, G:0.12, T:0.31
Consensus pattern (59 bp):
AAGTTCGAATAAAAAATTAATATCAAAATTTGTAAGTTAGAAGAAAACAAAGTTTTTAA
Found at i:55220204 original size:121 final size:121
Alignment explanation
Indices: 55219991--55220311 Score: 436
Period size: 121 Copynumber: 2.7 Consensus size: 121
55219981 TAAGTTCGAA
* *
55219991 AAAAAATTAATATCAAAATTTGAAAGTTGGAAGAAAAA-AAAGTTTTTTAAAGTTCGAATAAAAA
1 AAAAAATTAATATCAAAATTTGTAAGTTAGAAGAAAAACAAAGTTTTTTAAAGTTCGAATAAAAA
* * ** *
55220055 ATTAATGTCAAAATTTGTTAGTAAGAAGAAAACCAAAGT-TTT-TAAAA-GTTTGAATT
66 ATTAATATCAAAATTCGAAAGTAAGAAGAAAAACAAAGTGTTTATAAAATG-TT-AA-T
* *
55220111 AAAAAATTAATATAAAAATTTGTAAGTTAGAAGAAAAACAAAGTTTTTAAAAGTTCGAATAAAAA
1 AAAAAATTAATATCAAAATTTGTAAGTTAGAAGAAAAACAAAGTTTTTTAAAGTTCGAATAAAAA
* * * *
55220176 ATTAACATCAAAATTCGAAAGTTAGAAGAAAAATAATGTGTTTATAAAATGTTAAT
66 ATTAATATCAAAATTCGAAAGTAAGAAGAAAAACAAAGTGTTTATAAAATGTTAAT
* *
55220232 AAAAAATTAATATCAAAATTTGTAAGTCAGAAGAAATACAAAGTTTTTTAAAGTTCGAATAAAGA
1 AAAAAATTAATATCAAAATTTGTAAGTTAGAAGAAAAACAAAGTTTTTTAAAGTTCGAATAAA-A
55220297 AA-TAATATCAAAATT
65 AATTAATATCAAAATT
55220312 TATAACTGAA
Statistics
Matches: 178, Mismatches: 18, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
120 35 0.20
121 127 0.71
122 8 0.04
123 7 0.04
124 1 0.01
ACGTcount: A:0.53, C:0.05, G:0.12, T:0.31
Consensus pattern (121 bp):
AAAAAATTAATATCAAAATTTGTAAGTTAGAAGAAAAACAAAGTTTTTTAAAGTTCGAATAAAAA
ATTAATATCAAAATTCGAAAGTAAGAAGAAAAACAAAGTGTTTATAAAATGTTAAT
Found at i:55220769 original size:21 final size:21
Alignment explanation
Indices: 55220743--55220785 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
55220733 AGACAAAAGG
55220743 TGTAAGTTATTTTATTATATT
1 TGTAAGTTATTTTATTATATT
55220764 TGTAAGTTATTTTATTATATT
1 TGTAAGTTATTTTATTATATT
55220785 T
1 T
55220786 TTAATATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (21 bp):
TGTAAGTTATTTTATTATATT
Found at i:55221611 original size:171 final size:171
Alignment explanation
Indices: 55221326--55221666 Score: 576
Period size: 171 Copynumber: 2.0 Consensus size: 171
55221316 ACAACGAAGC
* * * *
55221326 AGATGAGTACTTCGAGGATCGTACCCAGGGGAGGTGAGCACTAAATTAACCCTAACCTAAGCACA
1 AGATGAGTACTTCGAAGATCATACCCAAGGGAGGCGAGCACTAAATTAACCCTAACCTAAGCACA
*
55221391 AATAGAGCTATTTAGTACTTTAAATAAATTCTATTATGAATCAACATAAAGAAAGATTTTTTGGT
66 AATAGAGCTATTTAGTACTTTAAATAAATTCTATTATGAATAAACATAAAGAAAGATTTTTTGGT
55221456 ATTTTTGTAAATAAAGAATAAAATAATATAAAGAAAAAGAA
131 ATTTTTGTAAATAAAGAATAAAATAATATAAAGAAAAAGAA
* *
55221497 AGATGAGTGCTTCGAAGATCATACCTAAGGGAGGCGAGCACTAAATTAACCCTAACCTAAGCACA
1 AGATGAGTACTTCGAAGATCATACCCAAGGGAGGCGAGCACTAAATTAACCCTAACCTAAGCACA
*
55221562 AATAGAGCTCA-TTAGTACTTTAAATAAATTCTATTATGAATAAACATAAAGAAAGATTTTTTTG
66 AATAGAGCT-ATTTAGTACTTTAAATAAATTCTATTATGAATAAACATAAAGAAAGATTTTTTGG
* *
55221626 TATTTTTTTAAATAAAGAATAAATTAATATAAAGAAAAAGA
130 TATTTTTGTAAATAAAGAATAAAATAATATAAAGAAAAAGA
55221667 CTTTGGGAAA
Statistics
Matches: 159, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
171 158 0.99
172 1 0.01
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (171 bp):
AGATGAGTACTTCGAAGATCATACCCAAGGGAGGCGAGCACTAAATTAACCCTAACCTAAGCACA
AATAGAGCTATTTAGTACTTTAAATAAATTCTATTATGAATAAACATAAAGAAAGATTTTTTGGT
ATTTTTGTAAATAAAGAATAAAATAATATAAAGAAAAAGAA
Found at i:55228809 original size:15 final size:13
Alignment explanation
Indices: 55228765--55228815 Score: 50
Period size: 15 Copynumber: 3.7 Consensus size: 13
55228755 GTGTGCCAAT
55228765 TTTTAATTATTTTTA
1 TTTTAATTA--TTTA
55228780 TTTTAATTA-TTA
1 TTTTAATTATTTA
55228792 TTTTAATTTATTTAA
1 TTTTAA-TTATTT-A
*
55228807 TTTTCATTA
1 TTTTAATTA
55228816 GATACCTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
12 9 0.28
13 3 0.09
14 5 0.16
15 15 0.47
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTAATTATTTA
Found at i:55234035 original size:19 final size:19
Alignment explanation
Indices: 55234011--55234049 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
55234001 CAATTGAGGG
*
55234011 TAATTAGCGATTTAATTGA
1 TAATTAGAGATTTAATTGA
*
55234030 TAATTAGATATTTAATTGA
1 TAATTAGAGATTTAATTGA
55234049 T
1 T
55234050 CATAGGCCGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.13, T:0.46
Consensus pattern (19 bp):
TAATTAGAGATTTAATTGA
Found at i:55239482 original size:23 final size:23
Alignment explanation
Indices: 55239422--55239487 Score: 57
Period size: 23 Copynumber: 3.0 Consensus size: 23
55239412 AATTAAATTG
* **
55239422 TATATTTTTATAATAGTA-AAAT
1 TATATATTTATAATTTTATAAAT
* *
55239444 TGTA-ATTTCATCATTTTATAAAT
1 TATATATTT-ATAATTTTATAAAT
55239467 TATATATTTATAATTTT-TAAA
1 TATATATTTATAATTTTATAAA
55239488 GGATTATCAC
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
21 3 0.09
22 13 0.38
23 14 0.41
24 4 0.12
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (23 bp):
TATATATTTATAATTTTATAAAT
Found at i:55242406 original size:24 final size:24
Alignment explanation
Indices: 55242370--55242416 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
55242360 ATAAACTAAG
* * *
55242370 GACAATTGGATGGTGATGATAATA
1 GACAAGTGGATGGTAATAATAATA
*
55242394 GACAAGTGTATGGTAATAATAAT
1 GACAAGTGGATGGTAATAATAAT
55242417 TACATGTGTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.40, C:0.04, G:0.26, T:0.30
Consensus pattern (24 bp):
GACAAGTGGATGGTAATAATAATA
Found at i:55242564 original size:13 final size:14
Alignment explanation
Indices: 55242538--55242570 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
55242528 AAAATAAATG
55242538 AAAGAAAAAGAAAC
1 AAAGAAAAAGAAAC
55242552 AAAGAAAAA-AAAC
1 AAAGAAAAAGAAAC
*
55242565 AGAGAA
1 AAAGAA
55242571 CGAAATAGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (14 bp):
AAAGAAAAAGAAAC
Found at i:55242604 original size:18 final size:18
Alignment explanation
Indices: 55242581--55242617 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
55242571 CGAAATAGGG
55242581 AGAAAAGAAAGGAAAGAA
1 AGAAAAGAAAGGAAAGAA
* *
55242599 AGAAAATAAATGAAAGAA
1 AGAAAAGAAAGGAAAGAA
55242617 A
1 A
55242618 AAGAAACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.22, T:0.05
Consensus pattern (18 bp):
AGAAAAGAAAGGAAAGAA
Found at i:55242629 original size:73 final size:72
Alignment explanation
Indices: 55242516--55242676 Score: 252
Period size: 73 Copynumber: 2.2 Consensus size: 72
55242506 AATAATAACT
* *
55242516 AAAAG-AATAAACAAAATAAATGAAAGAAAAAGAAACAAAGAAAAAAAACAGAGAACGAAATAGG
1 AAAAGAAAGAAACAAAATAAATGAAAGAAAAAGAAACAAAGAAAAAAAACAGAG-ACGAAACAGG
55242580 GAGAAAAG
65 GAGAAAAG
* * * *
55242588 AAAGGAAAGAAAGAAAATAAATGAAAGAAAAAGAAACAAAGAAACAAAACAGAGATGAAACAGGG
1 AAAAGAAAGAAACAAAATAAATGAAAGAAAAAGAAACAAAGAAAAAAAACAGAGACGAAACAGGG
55242653 AGAAAAG
66 AGAAAAG
55242660 AAAAGAAAGAAACAAAA
1 AAAAGAAAGAAACAAAA
55242677 GAAACAAAAG
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
72 35 0.44
73 45 0.56
ACGTcount: A:0.71, C:0.06, G:0.19, T:0.04
Consensus pattern (72 bp):
AAAAGAAAGAAACAAAATAAATGAAAGAAAAAGAAACAAAGAAAAAAAACAGAGACGAAACAGGG
AGAAAAG
Found at i:55242729 original size:5 final size:6
Alignment explanation
Indices: 55242712--55242736 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
55242702 AGGGGAAAGG
55242712 AGAAAA AGAAAA AGAAAA AGAAAA A
1 AGAAAA AGAAAA AGAAAA AGAAAA A
55242737 CTAGAGTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:55243126 original size:17 final size:18
Alignment explanation
Indices: 55243104--55243137 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
55243094 TAAATGAGTT
55243104 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
55243121 AATTAGGGTATAAATTG
1 AATTAGGATATAAATTG
55243138 AAAAGAAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:55244911 original size:27 final size:26
Alignment explanation
Indices: 55244873--55245099 Score: 242
Period size: 27 Copynumber: 8.5 Consensus size: 26
55244863 ACCTTAAAAT
* *
55244873 AGGTGAAATGACCAAAATAGCCCCATA
1 AGGTAAAATGACCGAAATA-CCCCATA
* *
55244900 AGGTAGAATGACTGAAATACCCCATA
1 AGGTAAAATGACCGAAATACCCCATA
* *
55244926 GGGTAAAATGATCGAAATACCCTCAT-
1 AGGTAAAATGACCGAAATACCC-CATA
*
55244952 AGGATAAAATGACTGAAATACCCCCATA
1 AGG-TAAAATGACCGAAATA-CCCCATA
*
55244980 AGGTAAAATGATCGAAATAGCCCCATA
1 AGGTAAAATGACCGAAATA-CCCCATA
*
55245007 AGGTAAAATGATCGAAATACCCC-TA
1 AGGTAAAATGACCGAAATACCCCATA
*
55245032 TAGGATAGAATGACCGAAATACCCTCATA
1 -AGG-TAAAATGACCGAAATACCC-CATA
* *
55245061 GGGTAGAATGACCGAAATACCCCCATA
1 AGGTAAAATGACCGAAATA-CCCCATA
*
55245088 GGGTAAAATGAC
1 AGGTAAAATGAC
55245100 TGTTATACCC
Statistics
Matches: 173, Mismatches: 18, Indels: 18
0.83 0.09 0.09
Matches are distributed among these distances:
25 2 0.01
26 34 0.20
27 123 0.71
28 12 0.07
29 2 0.01
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.19
Consensus pattern (26 bp):
AGGTAAAATGACCGAAATACCCCATA
Found at i:55245099 original size:54 final size:54
Alignment explanation
Indices: 55244878--55245099 Score: 272
Period size: 54 Copynumber: 4.1 Consensus size: 54
55244868 AAAATAGGTG
* * *
55244878 AAATGACCAAAATAGCCCCATAAGGTAGAATGACTGAAATA-CCCCATAGGGTA
1 AAATGACCGAAATAGCCCCATAAGGTAAAATGACCGAAATACCCCCATAGGGTA
* * *
55244931 AAATGATCGAAATA-CCCTCAT-AGGATAAAATGACTGAAATACCCCCATAAGGTA
1 AAATGACCGAAATAGCCC-CATAAGG-TAAAATGACCGAAATACCCCCATAGGGTA
* * * *
55244985 AAATGATCGAAATAGCCCCATAAGGTAAAATGATCGAAATACCCCTATAGGATA
1 AAATGACCGAAATAGCCCCATAAGGTAAAATGACCGAAATACCCCCATAGGGTA
* * *
55245039 GAATGACCGAAATA-CCCTCATAGGGTAGAATGACCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATAGCCC-CATAAGGTAAAATGACCGAAATACCCCCATAGGGTA
55245093 AAATGAC
1 AAATGAC
55245100 TGTTATACCC
Statistics
Matches: 146, Mismatches: 17, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
52 6 0.04
53 33 0.23
54 101 0.69
55 6 0.04
ACGTcount: A:0.43, C:0.21, G:0.18, T:0.18
Consensus pattern (54 bp):
AAATGACCGAAATAGCCCCATAAGGTAAAATGACCGAAATACCCCCATAGGGTA
Found at i:55245112 original size:81 final size:79
Alignment explanation
Indices: 55244878--55245098 Score: 309
Period size: 81 Copynumber: 2.7 Consensus size: 79
55244868 AAAATAGGTG
* *
55244878 AAATGACCAAAATAGCCCCATAAGGTAGAATGACTGAAATACCCCATAGGGTAAAATGATCGAAA
1 AAATGACCGAAATA-CCCCATAAGGTAGAATGACCGAAATACCCCATAGGGTAAAATGATCGAAA
55244943 TA-CCCTCATAGGATA
65 TACCCCT-ATAGGATA
* * * *
55244958 AAATGACTGAAATACCCCCATAAGGTAAAATGATCGAAATAGCCCCATAAGGTAAAATGATCGAA
1 AAATGACCGAAATA-CCCCATAAGGTAGAATGACCGAAATA-CCCCATAGGGTAAAATGATCGAA
55245023 ATACCCCTATAGGATA
64 ATACCCCTATAGGATA
* *
55245039 GAATGACCGAAATACCCTCATAGGGTAGAATGACCGAAATACCCCCATAGGGTAAAATGA
1 AAATGACCGAAATACCC-CATAAGGTAGAATGACCGAAATA-CCCCATAGGGTAAAATGA
55245099 CTGTTATACC
Statistics
Matches: 124, Mismatches: 14, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
80 38 0.31
81 82 0.66
82 4 0.03
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.19
Consensus pattern (79 bp):
AAATGACCGAAATACCCCATAAGGTAGAATGACCGAAATACCCCATAGGGTAAAATGATCGAAAT
ACCCCTATAGGATA
Found at i:55245125 original size:81 final size:78
Alignment explanation
Indices: 55244876--55245126 Score: 283
Period size: 81 Copynumber: 3.1 Consensus size: 78
55244866 TTAAAATAGG
* *
55244876 TGAAATGACCAAAATAGCCCCATAAGGTAGAATGACTGAAATACCCCATAGGGTAAAATGATCGA
1 TGAAATGACCGAAATA-CCCCATAAGGTAGAATGACCGAAATACCCCATAGGGTAAAATGATCGA
55244941 AATACCCTCATAG-GA
65 AATACCC-C-TAGAGA
* * * * *
55244956 TAAAATGACTGAAATACCCCCATAAGGTAAAATGATCGAAATAGCCCCATAAGGTAAAATGATCG
1 TGAAATGACCGAAATA-CCCCATAAGGTAGAATGACCGAAATA-CCCCATAGGGTAAAATGATCG
*
55245021 AAATACCCCTATAGGA
64 AAATACCCCTAGA-GA
*
55245037 T-AGAATGACCGAAATACCCTCATAGGGTAGAATGACCGAAATACCCCCATAGGGTAAAATGA-C
1 TGA-AATGACCGAAATACCC-CATAAGGTAGAATGACCGAAATA-CCCCATAGGGTAAAATGATC
**
55245100 TGTTATACCCCTAGGAGA
63 -GAAATACCCCTA-GAGA
55245118 TGAAATGAC
1 TGAAATGAC
55245127 TGTTATGGCC
Statistics
Matches: 145, Mismatches: 18, Indels: 15
0.81 0.10 0.08
Matches are distributed among these distances:
79 2 0.01
80 42 0.29
81 99 0.68
82 2 0.01
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (78 bp):
TGAAATGACCGAAATACCCCATAAGGTAGAATGACCGAAATACCCCATAGGGTAAAATGATCGAA
ATACCCCTAGAGA
Found at i:55250981 original size:21 final size:21
Alignment explanation
Indices: 55250957--55251007 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
55250947 ATGGAAACCT
*
55250957 ATAAAGGTTG-ACCGAAAGCTC
1 ATAAAGGTTGAACAGAAA-CTC
*
55250978 AT-AAGAGCTGAACAGAAACTC
1 ATAAAG-GTTGAACAGAAACTC
55250999 ATAAAGGTT
1 ATAAAGGTT
55251008 AAACTGAAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
20 3 0.12
21 12 0.50
22 9 0.38
ACGTcount: A:0.43, C:0.16, G:0.22, T:0.20
Consensus pattern (21 bp):
ATAAAGGTTGAACAGAAACTC
Found at i:55251018 original size:42 final size:42
Alignment explanation
Indices: 55250945--55251053 Score: 105
Period size: 42 Copynumber: 2.6 Consensus size: 42
55250935 CACAAGTGCT
* * * * *
55250945 AAATGGAAACCTATAAAGGTT-GACCGAAAGCTCATAAGAGCTG
1 AAAT-GAAACCCATAAAGGTTAAACTG-AAGCTCAAAAAAGCTG
*
55250988 AACA-GAAACTCATAAAGGTTAAACTGAAGCTCAAAAAAGCTG
1 AA-ATGAAACCCATAAAGGTTAAACTGAAGCTCAAAAAAGCTG
* *
55251030 AAATGAAACCCATTAGGGTTAAAC
1 AAATGAAACCCATAAAGGTTAAAC
55251054 GGAAACTTAT
Statistics
Matches: 54, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
41 1 0.02
42 47 0.87
43 5 0.09
44 1 0.02
ACGTcount: A:0.46, C:0.17, G:0.19, T:0.18
Consensus pattern (42 bp):
AAATGAAACCCATAAAGGTTAAACTGAAGCTCAAAAAAGCTG
Found at i:55252651 original size:29 final size:28
Alignment explanation
Indices: 55252588--55252668 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 28
55252578 CAATATAGTC
* *
55252588 CTTTAATTAATTTATTTTTATTGTTTGT
1 CTTTAATTTATTTATTTTTATTATTTGT
* *
55252616 CTGTTAATTTATTTATTTTTCTTTATTTTT
1 CT-TTAATTTATTTATTTTT-ATTATTTGT
*
55252646 CTTTAAGTTATTTTTATTTTTAT
1 CTTTAA-TT-TATTTATTTTTAT
55252669 ATCCACTATT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
28 2 0.05
29 20 0.47
30 11 0.26
31 10 0.23
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.70
Consensus pattern (28 bp):
CTTTAATTTATTTATTTTTATTATTTGT
Found at i:55256977 original size:27 final size:26
Alignment explanation
Indices: 55256931--55257006 Score: 82
Period size: 27 Copynumber: 2.9 Consensus size: 26
55256921 TTTTCTTATC
* * *
55256931 ACAATTTCACTCC-AGTAAAATTTTG
1 ACAATTTTACCCCTAGTAAAATTTTA
55256956 ACAATTTTACCCCTTAGTAAAATTTTA
1 ACAATTTTACCCC-TAGTAAAATTTTA
* * *
55256983 ACGATTTTTCCCCTGGTAAAATTT
1 ACAATTTTACCCCTAGTAAAATTT
55257007 CAAGAAATTC
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
25 11 0.26
26 10 0.23
27 22 0.51
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (26 bp):
ACAATTTTACCCCTAGTAAAATTTTA
Found at i:55257171 original size:18 final size:17
Alignment explanation
Indices: 55257148--55257181 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
55257138 AGCACTGCAA
55257148 ATTTCCAATTTCAATTTC
1 ATTTCC-ATTTCAATTTC
*
55257166 ATTTCCATTTCCATTT
1 ATTTCCATTTCAATTT
55257182 TTGGAAACCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTCCATTTCAATTTC
Found at i:55266255 original size:136 final size:136
Alignment explanation
Indices: 55266068--55266335 Score: 482
Period size: 136 Copynumber: 2.0 Consensus size: 136
55266058 GTCACACTTG
55266068 AATTTATTACTCGTCTCAACTTACATAATTTCCATGAATCAACATATCAAGATATTGATATATAT
1 AATTTATTACTCGTCTCAACTTACATAATTTCCATGAATCAACATATCAAGATATTGATATATAT
* *
55266133 ATACATTTCATGATACATATCATTCTTTTACCATTTCTTCATATACATATATCATCCACGACAAC
66 ATACATTTCATGATACATATCATTCTTTTACCATTTCTTCAAATACATATATCATCCAAGACAAC
55266198 TCTCGA
131 TCTCGA
* *
55266204 AATTTATTACTCGTCTTAACTTACATGATTTCCATGAATCAACATATCAAGATATTGATATATAT
1 AATTTATTACTCGTCTCAACTTACATAATTTCCATGAATCAACATATCAAGATATTGATATATAT
**
55266269 ATACATTTCATGATACATATCATTCTTTTACTGTTTCTTCAAATACATATATCATCCAAGACAAC
66 ATACATTTCATGATACATATCATTCTTTTACCATTTCTTCAAATACATATATCATCCAAGACAAC
55266334 TC
131 TC
55266336 CCGATAACTT
Statistics
Matches: 126, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
136 126 1.00
ACGTcount: A:0.35, C:0.20, G:0.06, T:0.39
Consensus pattern (136 bp):
AATTTATTACTCGTCTCAACTTACATAATTTCCATGAATCAACATATCAAGATATTGATATATAT
ATACATTTCATGATACATATCATTCTTTTACCATTTCTTCAAATACATATATCATCCAAGACAAC
TCTCGA
Found at i:55266464 original size:21 final size:21
Alignment explanation
Indices: 55266440--55266528 Score: 63
Period size: 21 Copynumber: 4.2 Consensus size: 21
55266430 TCGTAGGAGC
*
55266440 TAAACGGAAACCCATAAGGGT
1 TAAACGGAAACCCATAAGAGT
* * * *
55266461 TAAACAGAAGCTCA-ATAGAGC
1 TAAACGGAAACCCATA-AGAGT
* * *
55266482 TGAACGGAAACCCATTAGGGT
1 TAAACGGAAACCCATAAGAGT
* * *
55266503 TGAACGGAAACTCATATGAGT
1 TAAACGGAAACCCATAAGAGT
55266524 TAAAC
1 TAAAC
55266529 AGAAGCTCGT
Statistics
Matches: 49, Mismatches: 17, Indels: 4
0.70 0.24 0.06
Matches are distributed among these distances:
20 1 0.02
21 48 0.98
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (21 bp):
TAAACGGAAACCCATAAGAGT
Found at i:55266471 original size:42 final size:42
Alignment explanation
Indices: 55266383--55266503 Score: 129
Period size: 42 Copynumber: 2.9 Consensus size: 42
55266373 ATATGTATAT
** * * **
55266383 GAAGCTC-ATGAGAGCTAAACAAAAACTCATAAGGGTTGAATG
1 GAAGCTCAAT-AGAGCTAAACGGAAACCCATAAGGGTTAAACA
*
55266425 GAAGCTC-GTAGGAGCTAAACGGAAACCCATAAGGGTTAAACA
1 GAAGCTCAATA-GAGCTAAACGGAAACCCATAAGGGTTAAACA
* *
55266467 GAAGCTCAATAGAGCTGAACGGAAACCCATTAGGGTT
1 GAAGCTCAATAGAGCTAAACGGAAACCCATAAGGGTT
55266504 GAACGGAAAC
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
41 1 0.01
42 64 0.96
43 2 0.03
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.17
Consensus pattern (42 bp):
GAAGCTCAATAGAGCTAAACGGAAACCCATAAGGGTTAAACA
Found at i:55270598 original size:25 final size:24
Alignment explanation
Indices: 55270556--55270632 Score: 84
Period size: 25 Copynumber: 3.1 Consensus size: 24
55270546 ACATACCACA
* *
55270556 GCTCTTTATGAGCATCCTGATATAG
1 GCTCTTT-TGAACTTCCTGATATAG
55270581 GCTCTTTGTGAACTTCCTGATAT-G
1 GCTCTTT-TGAACTTCCTGATATAG
* *
55270605 GCTCATTTGAACTTCCTGTTATATG
1 GCTCTTTTGAACTTCCTGATATA-G
55270630 GCT
1 GCT
55270633 ATCAGGAGCT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
23 14 0.31
24 7 0.16
25 24 0.53
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.40
Consensus pattern (24 bp):
GCTCTTTTGAACTTCCTGATATAG
Found at i:55276329 original size:2 final size:2
Alignment explanation
Indices: 55276322--55276350 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
55276312 AAAGAATAAC
55276322 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
55276351 TGTTCATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:55286350 original size:19 final size:18
Alignment explanation
Indices: 55286305--55286358 Score: 67
Period size: 19 Copynumber: 3.1 Consensus size: 18
55286295 TGATGAATAA
55286305 AATAAAATAA-AATAATT
1 AATAAAATAATAATAATT
* *
55286322 -TTAAAATAATAATTATT
1 AATAAAATAATAATAATT
55286339 AATAAAATTAATAATAATT
1 AATAAAA-TAATAATAATT
55286358 A
1 A
55286359 TTTAAAAACT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
16 8 0.27
17 6 0.20
18 5 0.17
19 11 0.37
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AATAAAATAATAATAATT
Found at i:55288201 original size:20 final size:21
Alignment explanation
Indices: 55288154--55288201 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
55288144 ATATAAAATA
*
55288154 ATTAATTTTATAATAATATTT
1 ATTAATTTTATAAAAATATTT
55288175 ATT-ATTTTA-AAAAATAATTT
1 ATTAATTTTATAAAAAT-ATTT
55288195 -TTAATTT
1 ATTAATTT
55288202 ATTTATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 7 0.29
20 14 0.58
21 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTAATTTTATAAAAATATTT
Found at i:55289422 original size:3 final size:3
Alignment explanation
Indices: 55289414--55289442 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
55289404 TCAACTCTAC
55289414 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
55289443 GATAAGGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:55289842 original size:88 final size:88
Alignment explanation
Indices: 55289693--55289856 Score: 256
Period size: 88 Copynumber: 1.9 Consensus size: 88
55289683 TGATTCCACC
* * * *
55289693 GTTCCTAGTACTAACATTCCGTGCGGACTTCAGGCCTGCTGGACATGTGTTTCATTCTAGGTTGC
1 GTTCCTAGTACTAACATTCCGTGCGGACTTCAAGCATGCTGGACACGTGTTTCACTCTAGGTTGC
*
55289758 CTGCGGAGCACGCGGTCCTTTCT
66 CTACGGAGCACGCGGTCCTTTCT
** *
55289781 GTTCCTAGTACTAACATTTTGTGTGGACTTCAAGCATGCTGGACACGTGTTTCACTCTAGGTTGC
1 GTTCCTAGTACTAACATTCCGTGCGGACTTCAAGCATGCTGGACACGTGTTTCACTCTAGGTTGC
55289846 CTACGGAGCAC
66 CTACGGAGCAC
55289857 AAGGCCCCCC
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
88 68 1.00
ACGTcount: A:0.18, C:0.26, G:0.25, T:0.32
Consensus pattern (88 bp):
GTTCCTAGTACTAACATTCCGTGCGGACTTCAAGCATGCTGGACACGTGTTTCACTCTAGGTTGC
CTACGGAGCACGCGGTCCTTTCT
Found at i:55290941 original size:105 final size:101
Alignment explanation
Indices: 55290768--55290964 Score: 261
Period size: 105 Copynumber: 1.9 Consensus size: 101
55290758 ACACTCGTAA
* ** * *
55290768 TGCCATAACCCAGTTATGGTCTTATCATCAGGATGCCATAGCCCAGCTATGGTCTTACACGTATA
1 TGCCATAACCCAGTTATGGTATTATCATCAAAATGCCATAGCCCAACTATGGTCTTACACGTAAA
55290833 CATTTACTGCCATGGTCCAACCATGGTCTTACGTTTAAGG
66 CA--T--TGCCATGGTCCAACCATGGTCTTACGTTTAAGG
* * * *
55290873 TGCCATAACCCAGTTATGGTATTTTCATTAAAATGCCATAGCCCAACTATGGTCTTATA-TTCAA
1 TGCCATAACCCAGTTATGGTATTATCATCAAAATGCCATAGCCCAACTATGGTCTTACACGT-AA
55290937 ACATTGCCATGGTCCAACCATGGTCTTA
65 ACATTGCCATGGTCCAACCATGGTCTTA
55290965 TCCGTCAATT
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
101 24 0.29
103 1 0.01
104 1 0.01
105 56 0.68
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (101 bp):
TGCCATAACCCAGTTATGGTATTATCATCAAAATGCCATAGCCCAACTATGGTCTTACACGTAAA
CATTGCCATGGTCCAACCATGGTCTTACGTTTAAGG
Found at i:55297262 original size:42 final size:42
Alignment explanation
Indices: 55297210--55297333 Score: 142
Period size: 42 Copynumber: 3.0 Consensus size: 42
55297200 AGGCTGCACA
* * *
55297210 GAAGCACATAAGTA-CTAAACAAAAACCCGTAATGGTTAAACG
1 GAAGCTCATAAG-AGCTAAACAAAAACCCATAAGGGTTAAACG
* *
55297252 GAAGCTCATAAGAGCTAAACGAAAACCCATAAGGGTTAAACT
1 GAAGCTCATAAGAGCTAAACAAAAACCCATAAGGGTTAAACG
* * ** *
55297294 GAAGCTCAAAAGAGCTGAACTGAAACCCAGAAGGGTTAAA
1 GAAGCTCATAAGAGCTAAACAAAAACCCATAAGGGTTAAA
55297334 TTGAAACTCA
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
41 1 0.01
42 70 0.99
ACGTcount: A:0.46, C:0.19, G:0.20, T:0.15
Consensus pattern (42 bp):
GAAGCTCATAAGAGCTAAACAAAAACCCATAAGGGTTAAACG
Found at i:55297270 original size:21 final size:21
Alignment explanation
Indices: 55297246--55297309 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
55297236 CCGTAATGGT
55297246 TAAACGGAAGCTCATAAGAGC
1 TAAACGGAAGCTCATAAGAGC
* * * * *
55297267 TAAACGAAAACCCATAAGGGT
1 TAAACGGAAGCTCATAAGAGC
* *
55297288 TAAACTGAAGCTCAAAAGAGC
1 TAAACGGAAGCTCATAAGAGC
55297309 T
1 T
55297310 GAACTGAAAC
Statistics
Matches: 31, Mismatches: 12, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.45, C:0.19, G:0.20, T:0.16
Consensus pattern (21 bp):
TAAACGGAAGCTCATAAGAGC
Found at i:55297352 original size:21 final size:21
Alignment explanation
Indices: 55297256--55297380 Score: 74
Period size: 21 Copynumber: 6.0 Consensus size: 21
55297246 TAAACGGAAG
* *
55297256 CTCATAAGAGCTAAA-CGAAAA
1 CTCATAAGAGTTAAATTG-AAA
* * * *
55297277 CCCATAAGGGTTAAACTGAAG
1 CTCATAAGAGTTAAATTGAAA
* * * *
55297298 CTCAAAAGAGCTGAACTGAAA
1 CTCATAAGAGTTAAATTGAAA
* * *
55297319 CCCAGAAGGGTTAAATTGAAA
1 CTCATAAGAGTTAAATTGAAA
* *
55297340 CTCATATGAGTT-AATTGAAG
1 CTCATAAGAGTTAAATTGAAA
* *
55297360 CTCATAAGAGCTAAACTGAAA
1 CTCATAAGAGTTAAATTGAAA
55297381 GAAAACACGG
Statistics
Matches: 76, Mismatches: 26, Indels: 4
0.72 0.25 0.04
Matches are distributed among these distances:
20 17 0.22
21 58 0.76
22 1 0.01
ACGTcount: A:0.44, C:0.17, G:0.19, T:0.20
Consensus pattern (21 bp):
CTCATAAGAGTTAAATTGAAA
Found at i:55306455 original size:36 final size:35
Alignment explanation
Indices: 55306404--55306531 Score: 96
Period size: 36 Copynumber: 3.5 Consensus size: 35
55306394 ATATTAATTG
* *
55306404 TGTGCCCAGGACTAGTTGAATAAATCGACAAAGATT
1 TGTGCCTAGCACTAGTTGAATAAAT-GACAAAGATT
* * * *
55306440 TGTGCCTAGCCCTAGTCAGATTAACTGACGATATTA-ATT
1 TGTGCCTAGCACTAGT-TGAATAAATGAC-A-A--AGATT
* *
55306479 GTGTGCCTAACACTAGTTGAATAAATTGACAAAGACT
1 -TGTGCCTAGCACTAGTTGAATAAA-TGACAAAGATT
*
55306516 TGCGCCTAGCACTAGT
1 TGTGCCTAGCACTAGT
55306532 CGGATAAACT
Statistics
Matches: 70, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
36 31 0.44
37 9 0.13
38 2 0.03
39 9 0.13
40 19 0.27
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (35 bp):
TGTGCCTAGCACTAGTTGAATAAATGACAAAGATT
Found at i:55306484 original size:40 final size:40
Alignment explanation
Indices: 55306373--55306495 Score: 123
Period size: 40 Copynumber: 3.2 Consensus size: 40
55306363 TTTCACCCAA
*
55306373 CACTAGTCAGATTAACTGACGATATTAATTGTGTGCCCAG
1 CACTAGTCAGATTAACTGACGATATTAATTGTGTGCCTAG
* * * *
55306413 GACTAGT-TGAATAAATCGAC-A-A--AGATT-TGTGCCTAG
1 CACTAGTCAGATTAACT-GACGATATTA-ATTGTGTGCCTAG
* *
55306449 CCCTAGTCAGATTAACTGACGATATTAATTGTGTGCCTAA
1 CACTAGTCAGATTAACTGACGATATTAATTGTGTGCCTAG
55306489 CACTAGT
1 CACTAGT
55306496 TGAATAAATT
Statistics
Matches: 63, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
36 17 0.27
37 10 0.16
38 2 0.03
39 10 0.16
40 24 0.38
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30
Consensus pattern (40 bp):
CACTAGTCAGATTAACTGACGATATTAATTGTGTGCCTAG
Found at i:55306523 original size:76 final size:76
Alignment explanation
Indices: 55306328--55306543 Score: 288
Period size: 76 Copynumber: 2.8 Consensus size: 76
55306318 CGATAGTAGA
** * * * * *
55306328 TGTGCCCTGCACTAGTCGAATAAATTGACAAAGATTTTCACCCAACACTAGTCAGATTAACTGAC
1 TGTGCCCAACACTAGTTGAATAAATTGACAAAGATTTGCGCCTAGCACTAGTCAGATTAACTGAC
55306393 GATATTAATTG
66 GATATTAATTG
** * * *
55306404 TGTGCCCAGGACTAGTTGAATAAATCGACAAAGATTTGTGCCTAGCCCTAGTCAGATTAACTGAC
1 TGTGCCCAACACTAGTTGAATAAATTGACAAAGATTTGCGCCTAGCACTAGTCAGATTAACTGAC
55306469 GATATTAATTG
66 GATATTAATTG
* * * *
55306480 TGTGCCTAACACTAGTTGAATAAATTGACAAAGACTTGCGCCTAGCACTAGTCGGATAAACTGA
1 TGTGCCCAACACTAGTTGAATAAATTGACAAAGATTTGCGCCTAGCACTAGTCAGATTAACTGA
55306544 TGATCACATA
Statistics
Matches: 121, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
76 121 1.00
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (76 bp):
TGTGCCCAACACTAGTTGAATAAATTGACAAAGATTTGCGCCTAGCACTAGTCAGATTAACTGAC
GATATTAATTG
Found at i:55321950 original size:21 final size:21
Alignment explanation
Indices: 55321924--55321965 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
55321914 TATAATAATT
55321924 TAAAAATTACT-AAAATAAAAA
1 TAAAAA-TACTAAAAATAAAAA
*
55321945 TAAAAATATTAAAAATAAAAA
1 TAAAAATACTAAAAATAAAAA
55321966 ATTAAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (21 bp):
TAAAAATACTAAAAATAAAAA
Found at i:55321957 original size:15 final size:15
Alignment explanation
Indices: 55321939--55321990 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 15
55321929 ATTACTAAAA
55321939 TAAAAATAAAAATAT
1 TAAAAATAAAAATAT
55321954 TAAAAATAAAAA-AT
1 TAAAAATAAAAATAT
55321968 TAAATAATATATAAATAT
1 TAAA-AATA-A-AAATAT
55321986 ATAAA
1 -TAAA
55321991 TTTATTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
14 6 0.19
15 16 0.50
16 1 0.03
17 3 0.09
18 2 0.06
19 4 0.12
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
TAAAAATAAAAATAT
Found at i:55323619 original size:27 final size:28
Alignment explanation
Indices: 55323576--55323637 Score: 65
Period size: 27 Copynumber: 2.2 Consensus size: 28
55323566 AAACACTATT
* *
55323576 AAAA-ATAATAGAAAATACAA-AATTTA
1 AAAATATAATAGAAAATAAAATAATATA
* *
55323602 AAAATATAATATATAATAAAATAATATA
1 AAAATATAATAGAAAATAAAATAATATA
55323630 AATAATAT
1 AA-AATAT
55323638 TTTTGAAGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 4 0.14
27 13 0.45
28 7 0.24
29 5 0.17
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (28 bp):
AAAATATAATAGAAAATAAAATAATATA
Found at i:55326065 original size:33 final size:33
Alignment explanation
Indices: 55326023--55326090 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
55326013 GTATACAAGT
*
55326023 TGAGACCGTGGCCATCCCTAGGTTCTTGGGAGC
1 TGAGACCGTGGCCATCCCTAGGTTCTTGCGAGC
*
55326056 TGAGACCGTGGCCATCCCTGGGTTCTTGCGAGC
1 TGAGACCGTGGCCATCCCTAGGTTCTTGCGAGC
55326089 TG
1 TG
55326091 GATCTGCAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.13, C:0.28, G:0.34, T:0.25
Consensus pattern (33 bp):
TGAGACCGTGGCCATCCCTAGGTTCTTGCGAGC
Found at i:55329147 original size:57 final size:57
Alignment explanation
Indices: 55329016--55329155 Score: 138
Period size: 57 Copynumber: 2.5 Consensus size: 57
55329006 CCACGAGCCG
* * * * *
55329016 TTTTAGGCTTAAGAAATTTTCTAAAATAATCGGCTGGAAATATCAATCTGCAAACTG
1 TTTTAGACTTGAGAAATTTTCTAAAATAATCAGCTGGAAATATCAATCAGCAAACTA
* * * * ** *
55329073 TTTTAGATTTG-GAAAATTTTCTAAAATAATCAGCTGGGAGTATTAATCAGTGAGCTA
1 TTTTAGACTTGAG-AAATTTTCTAAAATAATCAGCTGGAAATATCAATCAGCAAACTA
* *
55329130 TTTTATACTTGAGAAATTTTCAAAAA
1 TTTTAGACTTGAGAAATTTTCTAAAA
55329156 AAAATTGACT
Statistics
Matches: 66, Mismatches: 15, Indels: 4
0.78 0.18 0.05
Matches are distributed among these distances:
56 1 0.02
57 64 0.97
58 1 0.02
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (57 bp):
TTTTAGACTTGAGAAATTTTCTAAAATAATCAGCTGGAAATATCAATCAGCAAACTA
Found at i:55329494 original size:138 final size:138
Alignment explanation
Indices: 55329246--55329920 Score: 629
Period size: 138 Copynumber: 4.9 Consensus size: 138
55329236 GAGTTTGTAA
* * * *
55329246 CTCTCACTAACTATGTTGAAGGCTAC-GATTTTAATCCCT-CGAGCCTTATTATGATAGCTGGGA
1 CTCTCACTAACTATGTTGGAGGCTACAG-TTTTAAT-CCTGCGAGCCTTAGTATGACAGTTGGGA
* * * * *
55329309 GCTTTGCTCTTGCTAACTGTGTTGGAGGATACAGTTTTAATCTTGCAAGCCTTAGTATGAAAACT
64 GCTTTGCTCTTGCTAACTGTGTTGGAGGTTACGGTTTTAATCCTACAAGCCTTAGTATGATAACT
**
55329374 AAGAGCATTT-
129 GGGAGC-TTTG
* *
55329384 CTCTCGCTAACTATGTTGGAGGCTACAGTTTTAATCCTGCAAGCCTTAGTATGACAGTTGGGAGC
1 CTCTCACTAACTATGTTGGAGGCTACAGTTTTAATCCTGCGAGCCTTAGTATGACAGTTGGGAGC
* * ** * * **
55329449 TTTGCTCTCGCTAACTGTGTTAGAGGTTGTGGTTTTAATCCTGCAAGTCTTTA-TATGATAGTTG
66 TTTGCTCTTGCTAACTGTGTTGGAGGTTACGGTTTTAATCCTACAAG-CCTTAGTATGATAACTG
55329513 GGAGCTTTG
130 GGAGCTTTG
* * *** * * *
55329522 CTCTCCCTAACTATGTTGAAGGCTTTGGTTTTAATCCTGTGAGCCTTAGTATGGCAGCTGGGAGC
1 CTCTCACTAACTATGTTGGAGGCTACAGTTTTAATCCTGCGAGCCTTAGTATGACAGTTGGGAGC
** * * * * ** * * *
55329587 TTTGCTCTTGCTAACCATATTGGAGGTTATGAATTTTTATCCTACAAATCTTATTATGACAATTG
66 TTTGCTCTTGCTAACTGTGTTGGAGGTTACG-GTTTTAATCCTACAAGCCTTAGTATGATAACTG
55329652 GGAGCTTTG
130 GGAGCTTTG
** ** ** * * *
55329661 CTCTCACTAACTATGTTGGAGGCTGGAACTTTAATCCTATGTGCCTTAGTATGATAATTGGGAGC
1 CTCTCACTAACTATGTTGGAGGCTACAGTTTTAATCCTGCGAGCCTTAGTATGACAGTTGGGAGC
* * * * * * * * * * * *
55329726 TTTGCACTCGCTGACTATGTTGGAGGCTCCGATTTTAATCTTACGAGTCTTAATATGATAGCTGG
66 TTTGCTCTTGCTAACTGTGTTGGAGGTTACGGTTTTAATCCTACAAGCCTTAGTATGATAACTGG
55329791 GAGCTTTG
131 GAGCTTTG
* * * * * *
55329799 CTCTCGCTAACTGTGTTGGAGGCTGCTGTTTTAATCCTGCAAGCCTTAGTATGACAGTTGGGAAC
1 CTCTCACTAACTATGTTGGAGGCTACAGTTTTAATCCTGCGAGCCTTAGTATGACAGTTGGGAGC
* * * *
55329864 TTTACTCTTGCTAACTGTGTTGGAGGTTGCGGTTTTTAATCCTACGATCCTTAGTAT
66 TTTGCTCTTGCTAACTGTGTTGGAGGTTACGG-TTTTAATCCTACAAGCCTTAGTAT
55329921 TCACAGAATA
Statistics
Matches: 434, Mismatches: 96, Indels: 13
0.80 0.18 0.02
Matches are distributed among these distances:
137 6 0.01
138 298 0.69
139 130 0.30
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (138 bp):
CTCTCACTAACTATGTTGGAGGCTACAGTTTTAATCCTGCGAGCCTTAGTATGACAGTTGGGAGC
TTTGCTCTTGCTAACTGTGTTGGAGGTTACGGTTTTAATCCTACAAGCCTTAGTATGATAACTGG
GAGCTTTG
Found at i:55329889 original size:277 final size:275
Alignment explanation
Indices: 55329246--55329920 Score: 735
Period size: 277 Copynumber: 2.4 Consensus size: 275
55329236 GAGTTTGTAA
* *
55329246 CTCTCACTAACTATGTTGAAGGCTAC-GATTTTAATCCCT-CGAGCCTTATTATGATAGCTGGGA
1 CTCTCACTAACTATGTTGAAGGCT-CTG-TTTTAAT-CCTGCGAGCCTTAGTATGACAGCTGGGA
* * * * *
55329309 GCTTTGCTCTTGCTAACTGTGTTGGAGGATACAGTTTTAATCTTGCAAGCCTTAGTATGAAAACT
63 GCTTTGCTCTTGCTAACTGTGTTGGAGGTTACAATTTTAATCCTACAAACCTTAGTATGAAAACT
* ** *
55329374 AAGAGCATTTCTCTCGCTAACTATGTTGGAGGCTACAGTTTTAATCCTGCAAGCCTTAGTATGAC
128 AAGAGCATTTCTCTCACTAACTATGTTGGAGGCTACAACTTTAATCCTACAAGCCTTAGTATGAC
* * * * ** * * *
55329439 AGTTGGGAGCTTTGCTCTCGCTAACTGTGTTAGAGGTTGTGGTTTTAATCCTGCAAGTCTTTATA
193 AATTGGGAGCTTTGCACTCGCTAACTATGTTAGAGGCTCCGATTTTAATCCTACAAGTCTTAATA
*
55329504 TGATAGTTGGGAGCTTTG
258 TGATAGCTGGGAGCTTTG
* * * *
55329522 CTCTCCCTAACTATGTTGAAGGCTTTGGTTTTAATCCTGTGAGCCTTAGTATGGCAGCTGGGAGC
1 CTCTCACTAACTATGTTGAAGGCTCT-GTTTTAATCCTGCGAGCCTTAGTATGACAGCTGGGAGC
** * * * * * * * *
55329587 TTTGCTCTTGCTAACCATATTGGAGGTTATGAATTTTTATCCTACAAATCTTATTATGACAATTG
65 TTTGCTCTTGCTAACTGTGTTGGAGGTTA-CAATTTTAATCCTACAAACCTTAGTATGAAAACTA
* ** *** *
55329652 GGAGC-TTTGCTCTCACTAACTATGTTGGAGGCTGGAACTTTAATCCTATGTGCCTTAGTATGAT
129 AGAGCATTT-CTCTCACTAACTATGTTGGAGGCTACAACTTTAATCCTACAAGCCTTAGTATGAC
* * * *
55329716 AATTGGGAGCTTTGCACTCGCTGACTATGTTGGAGGCTCCGATTTTAATCTTACGAGTCTTAATA
193 AATTGGGAGCTTTGCACTCGCTAACTATGTTAGAGGCTCCGATTTTAATCCTACAAGTCTTAATA
55329781 TGATAGCTGGGAGCTTTG
258 TGATAGCTGGGAGCTTTG
* * * * * *
55329799 CTCTCGCTAACTGTGTTGGAGGCTGCTGTTTTAATCCTGCAAGCCTTAGTATGACAGTTGGGAAC
1 CTCTCACTAACTATGTTGAAGGCT-CTGTTTTAATCCTGCGAGCCTTAGTATGACAGCTGGGAGC
* * ** * *
55329864 TTTACTCTTGCTAACTGTGTTGGAGGTTGCGGTTTTTAATCCTACGATCCTTAGTAT
65 TTTGCTCTTGCTAACTGTGTTGGAGGTTAC-AATTTTAATCCTACAAACCTTAGTAT
55329921 TCACAGAATA
Statistics
Matches: 324, Mismatches: 68, Indels: 13
0.80 0.17 0.03
Matches are distributed among these distances:
275 3 0.01
276 80 0.25
277 240 0.74
278 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (275 bp):
CTCTCACTAACTATGTTGAAGGCTCTGTTTTAATCCTGCGAGCCTTAGTATGACAGCTGGGAGCT
TTGCTCTTGCTAACTGTGTTGGAGGTTACAATTTTAATCCTACAAACCTTAGTATGAAAACTAAG
AGCATTTCTCTCACTAACTATGTTGGAGGCTACAACTTTAATCCTACAAGCCTTAGTATGACAAT
TGGGAGCTTTGCACTCGCTAACTATGTTAGAGGCTCCGATTTTAATCCTACAAGTCTTAATATGA
TAGCTGGGAGCTTTG
Found at i:55329899 original size:69 final size:69
Alignment explanation
Indices: 55329246--55329920 Score: 566
Period size: 69 Copynumber: 9.8 Consensus size: 69
55329236 GAGTTTGTAA
* * * * * * * *
55329246 CTCTCACTAACTATGTTGAAGGCTACGATTTTAATCCCT-CGAGCCTTATTATGATAGCTGGGAG
1 CTCTCGCTAACTATGTTGGAGGCTGCGGTTTTAAT-CCTGCAAGCCTTAGTATGACAGTTGGGAG
55329310 CTTTG
65 CTTTG
* * * * * * * ** **
55329315 CTCTTGCTAACTGTGTTGGAGGATACAGTTTTAATCTTGCAAGCCTTAGTATGAAAACTAAGAGC
1 CTCTCGCTAACTATGTTGGAGGCTGCGGTTTTAATCCTGCAAGCCTTAGTATGACAGTTGGGAGC
55329380 ATTT-
66 -TTTG
* *
55329384 CTCTCGCTAACTATGTTGGAGGCTACAGTTTTAATCCTGCAAGCCTTAGTATGACAGTTGGGAGC
1 CTCTCGCTAACTATGTTGGAGGCTGCGGTTTTAATCCTGCAAGCCTTAGTATGACAGTTGGGAGC
55329449 TTTG
66 TTTG
* * * * * *
55329453 CTCTCGCTAACTGTGTTAGAGGTTGTGGTTTTAATCCTGCAAGTCTTTA-TATGATAGTTGGGAG
1 CTCTCGCTAACTATGTTGGAGGCTGCGGTTTTAATCCTGCAAG-CCTTAGTATGACAGTTGGGAG
55329517 CTTTG
65 CTTTG
* * ** ** * *
55329522 CTCTCCCTAACTATGTTGAAGGCTTTGGTTTTAATCCTGTGAGCCTTAGTATGGCAGCTGGGAGC
1 CTCTCGCTAACTATGTTGGAGGCTGCGGTTTTAATCCTGCAAGCCTTAGTATGACAGTTGGGAGC
55329587 TTTG
66 TTTG
* * * * ** * * * ** * *
55329591 CTCTTGCTAACCATATTGGAGGTTATGAATTTTTATCCTACAAATCTTATTATGACAATTGGGAG
1 CTCTCGCTAACTATGTTGGAGGCTGCG-GTTTTAATCCTGCAAGCCTTAGTATGACAGTTGGGAG
55329656 CTTTG
65 CTTTG
* ** **** * *
55329661 CTCTCACTAACTATGTTGGAGGCTG-GAACTTTAATCCTATGTGCCTTAGTATGATAATTGGGAG
1 CTCTCGCTAACTATGTTGGAGGCTGCG-GTTTTAATCCTGCAAGCCTTAGTATGACAGTTGGGAG
55329725 CTTTG
65 CTTTG
* * * * * * * * * * *
55329730 CACTCGCTGACTATGTTGGAGGCTCCGATTTTAATCTTACGAGTCTTAATATGATAGCTGGGAGC
1 CTCTCGCTAACTATGTTGGAGGCTGCGGTTTTAATCCTGCAAGCCTTAGTATGACAGTTGGGAGC
55329795 TTTG
66 TTTG
* * *
55329799 CTCTCGCTAACTGTGTTGGAGGCTGCTGTTTTAATCCTGCAAGCCTTAGTATGACAGTTGGGAAC
1 CTCTCGCTAACTATGTTGGAGGCTGCGGTTTTAATCCTGCAAGCCTTAGTATGACAGTTGGGAGC
*
55329864 TTTA
66 TTTG
* * * * * *
55329868 CTCTTGCTAACTGTGTTGGAGGTTGCGGTTTTTAATCCTACGATCCTTAGTAT
1 CTCTCGCTAACTATGTTGGAGGCTGCGG-TTTTAATCCTGCAAGCCTTAGTAT
55329921 TCACAGAATA
Statistics
Matches: 489, Mismatches: 109, Indels: 15
0.80 0.18 0.02
Matches are distributed among these distances:
68 9 0.02
69 401 0.82
70 79 0.16
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (69 bp):
CTCTCGCTAACTATGTTGGAGGCTGCGGTTTTAATCCTGCAAGCCTTAGTATGACAGTTGGGAGC
TTTG
Found at i:55337215 original size:38 final size:38
Alignment explanation
Indices: 55337094--55337208 Score: 194
Period size: 38 Copynumber: 3.0 Consensus size: 38
55337084 TCCCTATCCA
*
55337094 TACTTCAAATCTGTCTTATTTTTTAGACTTAATATTTT
1 TACTTCAAATCTGTCTCATTTTTTAGACTTAATATTTT
*
55337132 TACTTTAAATCTGTCTCATTTTTTAGACTTAATATTTT
1 TACTTCAAATCTGTCTCATTTTTTAGACTTAATATTTT
* *
55337170 TACTTCAAATCTGTCTCATTTTTTAAATTTAATATTTT
1 TACTTCAAATCTGTCTCATTTTTTAGACTTAATATTTT
55337208 T
1 T
55337209 TGTTCAAGCC
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 72 1.00
ACGTcount: A:0.27, C:0.13, G:0.04, T:0.56
Consensus pattern (38 bp):
TACTTCAAATCTGTCTCATTTTTTAGACTTAATATTTT
Found at i:55342061 original size:18 final size:18
Alignment explanation
Indices: 55342040--55342074 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
55342030 TAATATTATA
55342040 AAATA-AAATAATTATTTC
1 AAATATAAAT-ATTATTTC
55342058 AAATATAAATATTATTT
1 AAATATAAATATTATTT
55342075 TTATATGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATATAAATATTATTTC
Found at i:55345132 original size:25 final size:26
Alignment explanation
Indices: 55345084--55345133 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
55345074 ATACGAGTAT
* * *
55345084 GTAAATGGGAAGCTCTTTCGAGCCAC
1 GTAAATGGGAAGCTCATACAAGCCAC
55345110 GTAAA-GGGAAGCTCATACAAGCCA
1 GTAAATGGGAAGCTCATACAAGCCA
55345134 TAAACGAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.34, C:0.22, G:0.26, T:0.18
Consensus pattern (26 bp):
GTAAATGGGAAGCTCATACAAGCCAC
Found at i:55345189 original size:25 final size:25
Alignment explanation
Indices: 55345161--55345273 Score: 122
Period size: 25 Copynumber: 4.5 Consensus size: 25
55345151 AGAGTCATTA
* *
55345161 ATCGGGAAACTCATAAGAGCCAATT
1 ATCGGGAAGCTCATGAGAGCCAATT
*
55345186 ATCGAGAAGCTCCA-GAGAGCC-ATT
1 ATCGGGAAGCT-CATGAGAGCCAATT
*
55345210 AATCAGGAAGCTCATGAGAGCCAATT
1 -ATCGGGAAGCTCATGAGAGCCAATT
* * *
55345236 ATTGGGAAGCTCGTGAGAGCCAAAT
1 ATCGGGAAGCTCATGAGAGCCAATT
*
55345261 AGCGGGAAGCTCA
1 ATCGGGAAGCTCA
55345274 AAAGAGATGC
Statistics
Matches: 72, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
24 5 0.07
25 62 0.86
26 5 0.07
ACGTcount: A:0.35, C:0.20, G:0.27, T:0.18
Consensus pattern (25 bp):
ATCGGGAAGCTCATGAGAGCCAATT
Found at i:55345224 original size:50 final size:50
Alignment explanation
Indices: 55345116--55345257 Score: 146
Period size: 50 Copynumber: 2.9 Consensus size: 50
55345106 CCACGTAAAG
* * * * *
55345116 GGAAGCTCATACA-AGCC-ATAAACGAAAAGC-CCGAGAGAGTCATTAATCG
1 GGAAGCTCATA-AGAGCCAATTATCGAGAAGCTCC-AGAGAGCCATTAATCA
*
55345165 GGAAACTCATAAGAGCCAATTATCGAGAAGCTCCAGAGAGCCATTAATCA
1 GGAAGCTCATAAGAGCCAATTATCGAGAAGCTCCAGAGAGCCATTAATCA
* * * **
55345215 GGAAGCTCATGAGAGCCAATTATTGGGAAGCTCGTGAGAGCCA
1 GGAAGCTCATAAGAGCCAATTATCGAGAAGCTCCAGAGAGCCA
55345258 AATAGCGGGA
Statistics
Matches: 78, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
48 1 0.01
49 14 0.18
50 61 0.78
51 2 0.03
ACGTcount: A:0.37, C:0.21, G:0.25, T:0.17
Consensus pattern (50 bp):
GGAAGCTCATAAGAGCCAATTATCGAGAAGCTCCAGAGAGCCATTAATCA
Found at i:55345269 original size:50 final size:49
Alignment explanation
Indices: 55345115--55345279 Score: 140
Period size: 50 Copynumber: 3.3 Consensus size: 49
55345105 GCCACGTAAA
* * * *
55345115 GGGAAGCTCATACA-AGCC-ATAAACGAAAAGC-CCGAGAGAGTCATTAATC
1 GGGAAGCTCATA-AGAGCCAATTATCGAGAAGCTCC-AGAGAGCCA-TAATC
*
55345164 GGGAAACTCATAAGAGCCAATTATCGAGAAGCTCCAGAGAGCCATTAATC
1 GGGAAGCTCATAAGAGCCAATTATCGAGAAGCTCCAGAGAGCCA-TAATC
* * * * **
55345214 AGGAAGCTCATGAGAGCCAATTATTGGGAAGCTCGTGAGAGCCA-AATAGC
1 GGGAAGCTCATAAGAGCCAATTATCGAGAAGCTCCAGAGAGCCATAAT--C
*
55345264 GGGAAGCTCAAAAGAG
1 GGGAAGCTCATAAGAG
55345280 ATGCGGTGTG
Statistics
Matches: 96, Mismatches: 15, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
48 4 0.04
49 15 0.16
50 75 0.78
51 2 0.02
ACGTcount: A:0.38, C:0.20, G:0.26, T:0.16
Consensus pattern (49 bp):
GGGAAGCTCATAAGAGCCAATTATCGAGAAGCTCCAGAGAGCCATAATC
Found at i:55345740 original size:21 final size:22
Alignment explanation
Indices: 55345710--55345754 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
55345700 TCTCCTCACT
*
55345710 TTTTTTATTTTTAT-TTTAAAA
1 TTTTTAATTTTTATATTTAAAA
*
55345731 TTTTTAATTTTTATATTTCAAA
1 TTTTTAATTTTTATATTTAAAA
55345753 TT
1 TT
55345755 AAAAATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTTTAATTTTTATATTTAAAA
Found at i:55345799 original size:22 final size:22
Alignment explanation
Indices: 55345760--55345802 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
55345750 AAATTAAAAA
*
55345760 TTTTGAGAAACTTTGAGAAACT
1 TTTTGAGAAAATTTGAGAAACT
55345782 TTTTG-GAAAATTTGGAGAAAC
1 TTTTGAGAAAATTT-GAGAAAC
55345803 AACTCAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.37, C:0.07, G:0.21, T:0.35
Consensus pattern (22 bp):
TTTTGAGAAAATTTGAGAAACT
Found at i:55346084 original size:35 final size:34
Alignment explanation
Indices: 55345997--55346145 Score: 142
Period size: 34 Copynumber: 4.4 Consensus size: 34
55345987 CTTTTTCTTG
* * * *
55345997 TCTTTTCTTGTAGTGAATATTTCCTGTTCACACA
1 TCTTTTCTTGCAGAGAATCTTTCCTGTTCACTCA
* * *
55346031 TCATTTCTT-CAAAGGAATCTTTCCTGTTCACCTCG
1 TCTTTTCTTGCAGA-GAATCTTTCCTGTTCA-CTCA
55346066 TCTTTTCTTGCAGAGAATCTTTCCTGTTCA-TGCA
1 TCTTTTCTTGCAGAGAATCTTTCCTGTTCACT-CA
* * **
55346100 TC-ATTCTTTGCAGGGAATCTTTCCTGTTCACAAA
1 TCTTTTC-TTGCAGAGAATCTTTCCTGTTCACTCA
55346134 TCTTTTCTTGCA
1 TCTTTTCTTGCA
55346146 TCATTTCTTC
Statistics
Matches: 93, Mismatches: 15, Indels: 14
0.76 0.12 0.11
Matches are distributed among these distances:
33 5 0.05
34 56 0.60
35 29 0.31
36 3 0.03
ACGTcount: A:0.19, C:0.24, G:0.13, T:0.44
Consensus pattern (34 bp):
TCTTTTCTTGCAGAGAATCTTTCCTGTTCACTCA
Found at i:55346117 original size:69 final size:69
Alignment explanation
Indices: 55345996--55346130 Score: 184
Period size: 69 Copynumber: 2.0 Consensus size: 69
55345986 TCTTTTTCTT
* *
55345996 GTCTTTTCTTGTAGTGAATATTTCCTGTTCACACATCATTTCTTCAAAGGAATCTTTCCTGTTCA
1 GTCTTTTCTTGCAGAGAATATTTCCTGTTCACACATCATTTCTTCAAAGGAATCTTTCCTGTTCA
55346061 CCTC
66 CCTC
* ** *
55346065 GTCTTTTCTTGCAGAGAATCTTTCCTGTTCATGCATCA-TTCTTTGC-AGGGAATCTTTCCTGTT
1 GTCTTTTCTTGCAGAGAATATTTCCTGTTCACACATCATTTC-TT-CAAAGGAATCTTTCCTGTT
55346128 CAC
64 CAC
55346131 AAATCTTTTC
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
68 3 0.05
69 54 0.93
70 1 0.02
ACGTcount: A:0.19, C:0.24, G:0.14, T:0.43
Consensus pattern (69 bp):
GTCTTTTCTTGCAGAGAATATTTCCTGTTCACACATCATTTCTTCAAAGGAATCTTTCCTGTTCA
CCTC
Found at i:55348958 original size:20 final size:23
Alignment explanation
Indices: 55348923--55348967 Score: 69
Period size: 20 Copynumber: 2.1 Consensus size: 23
55348913 GAACAAATTA
55348923 TTGATTCTATTTCTTTTTTG-AT
1 TTGATTCTATTTCTTTTTTGTAT
55348945 TTGA-TCTA-TTCTTTTTTGTAT
1 TTGATTCTATTTCTTTTTTGTAT
55348966 TT
1 TT
55348968 CTCTTATTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.45
21 8 0.36
22 4 0.18
ACGTcount: A:0.13, C:0.09, G:0.09, T:0.69
Consensus pattern (23 bp):
TTGATTCTATTTCTTTTTTGTAT
Found at i:55349023 original size:21 final size:23
Alignment explanation
Indices: 55348999--55349041 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 23
55348989 TTAATTTTTT
*
55348999 AAAACATATTT-CTTCT-TTTAG
1 AAAACAGATTTGCTTCTGTTTAG
*
55349020 AAAAGAGATTTGCTTCTGTTTA
1 AAAACAGATTTGCTTCTGTTTA
55349042 TAATTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 5 0.28
23 4 0.22
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.44
Consensus pattern (23 bp):
AAAACAGATTTGCTTCTGTTTAG
Found at i:55353748 original size:14 final size:14
Alignment explanation
Indices: 55353729--55353763 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
55353719 AAATTATAAA
55353729 ATATATAAATATAT
1 ATATATAAATATAT
* *
55353743 ATATATAAGTATGT
1 ATATATAAATATAT
55353757 ATATATA
1 ATATATA
55353764 TGTTTATGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (14 bp):
ATATATAAATATAT
Found at i:55360349 original size:12 final size:12
Alignment explanation
Indices: 55360332--55360386 Score: 67
Period size: 12 Copynumber: 4.5 Consensus size: 12
55360322 TGTTCATTTA
55360332 TTCATCAAGTCT
1 TTCATCAAGTCT
*
55360344 TTCATCAAGTGTTT
1 TTCATCAA--GTCT
*
55360358 TTCATCAAGTTT
1 TTCATCAAGTCT
55360370 TTCATCAAG-CT
1 TTCATCAAGTCT
55360381 TTCATC
1 TTCATC
55360387 TTCTGAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
11 7 0.18
12 21 0.54
14 11 0.28
ACGTcount: A:0.24, C:0.22, G:0.09, T:0.45
Consensus pattern (12 bp):
TTCATCAAGTCT
Found at i:55360556 original size:54 final size:54
Alignment explanation
Indices: 55360497--55360601 Score: 210
Period size: 54 Copynumber: 1.9 Consensus size: 54
55360487 ACCTTACGTC
55360497 ACTCACATCCATCTACTTTCATTTCTTTTATTCAACCCTCTCCAAATATGCGAA
1 ACTCACATCCATCTACTTTCATTTCTTTTATTCAACCCTCTCCAAATATGCGAA
55360551 ACTCACATCCATCTACTTTCATTTCTTTTATTCAACCCTCTCCAAATATGC
1 ACTCACATCCATCTACTTTCATTTCTTTTATTCAACCCTCTCCAAATATGC
55360602 CCAACTCCAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.27, C:0.32, G:0.03, T:0.38
Consensus pattern (54 bp):
ACTCACATCCATCTACTTTCATTTCTTTTATTCAACCCTCTCCAAATATGCGAA
Found at i:55375239 original size:16 final size:16
Alignment explanation
Indices: 55375218--55375250 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
55375208 TTCGCTGTAT
55375218 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
55375234 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
55375250 T
1 T
55375251 AGCAAATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.36, T:0.21
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:55375510 original size:18 final size:17
Alignment explanation
Indices: 55375489--55375523 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
55375479 TTATTATTAA
*
55375489 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
55375507 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
55375524 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:55375630 original size:18 final size:17
Alignment explanation
Indices: 55375609--55375643 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
55375599 TTATTATTAA
*
55375609 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
55375627 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
55375644 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:55375641 original size:59 final size:57
Alignment explanation
Indices: 55375469--55375764 Score: 206
Period size: 59 Copynumber: 5.0 Consensus size: 57
55375459 TTAATCATAT
* *
55375469 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTC
1 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTA
* * * * ** * * *
55375526 TTAATAATCA-ATATTCTTATATGAATTTACTCAAATCATAATATATGATACT-ATAAAATATAA
1 TT--TAA-CATA-ATTATTAT-TAAATATATTTTAATTAAAATATATGAT-TTAATAAAAT-T-A
* *
55375589 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTC
1 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTA
* * * * ** * * *
55375646 TTAATAATCA-ATATTCTTATAAGAATTTACTAAAATCATAATATATGATACT-ATAAAATATAA
1 TT--TAA-CATA-ATTATTATTA-AATATATTTTAATTAAAATATATGAT-TTAATAAAAT-T-A
55375709 TTTGAA-ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 TTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
55375765 TAAAATAATT
Statistics
Matches: 176, Mismatches: 42, Indels: 41
0.68 0.16 0.16
Matches are distributed among these distances:
57 4 0.02
58 4 0.02
59 62 0.35
60 37 0.21
61 59 0.34
62 6 0.03
63 4 0.02
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (57 bp):
TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTA
Found at i:55375702 original size:61 final size:61
Alignment explanation
Indices: 55375517--55375704 Score: 181
Period size: 61 Copynumber: 3.1 Consensus size: 61
55375507 ATATAATTTA
* *
55375517 ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 ATAAAATTCTTAATAATCAATATTCTTATAAGAATTTACTAAAATCATAATATATGATACT
* * * * * ** * * * *
55375578 ATAAAA-T-ATAATTTAA-C-ATAATTATTATTA-AATATATTTTAATTAAAATATATAAT-TT
1 ATAAAATTCTTAA--TAATCAAT-ATTCTTATAAGAATTTACTAAAATCATAATATATGATACT
55375636 AATAAAATTCTTAATAATCAATATTCTTATAAGAATTTACTAAAATCATAATATATGATACT
1 -ATAAAATTCTTAATAATCAATATTCTTATAAGAATTTACTAAAATCATAATATATGATACT
55375698 ATAAAAT
1 ATAAAAT
55375705 ATAATTTGAA
Statistics
Matches: 94, Mismatches: 23, Indels: 20
0.69 0.17 0.15
Matches are distributed among these distances:
58 1 0.01
59 33 0.35
60 19 0.20
61 40 0.43
62 1 0.01
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (61 bp):
ATAAAATTCTTAATAATCAATATTCTTATAAGAATTTACTAAAATCATAATATATGATACT
Found at i:55375750 original size:18 final size:17
Alignment explanation
Indices: 55375727--55375763 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
55375717 AATTATTATT
55375727 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
55375743 AAATATATGATTTAATA
1 AAATATATGATTTAATA
55375760 AAAT
1 AAAT
55375764 TTAAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:55375773 original size:120 final size:120
Alignment explanation
Indices: 55375469--55375764 Score: 549
Period size: 120 Copynumber: 2.5 Consensus size: 120
55375459 TTAATCATAT
55375469 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
* *
55375534 CAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA
66 CAATATTCTTATAAGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
55375589 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
55375654 CAATATTCTTATAAGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
66 CAATATTCTTATAAGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
*
55375709 TTTGAA-ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 TTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
55375765 TAAAATAATT
Statistics
Matches: 172, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
120 170 0.99
121 2 0.01
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (120 bp):
TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
CAATATTCTTATAAGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
Found at i:55375799 original size:47 final size:46
Alignment explanation
Indices: 55375746--55375985 Score: 182
Period size: 44 Copynumber: 5.3 Consensus size: 46
55375736 TTAATTAAAA
*
55375746 TATATG-ATTTAATAAAATTTAAAATAATTATTACTAATAAATTTTCT
1 TATATGAATTT-ATATAATTTAAAATAATTATTA-TAATAAATTTTCT
* *
55375793 TATATGAATTTGTATAATTTAAAATAATTATTAT--TAAATATAAT-T
1 TATATGAATTTATATAATTTAAAATAATTATTATAATAAAT-T-TTCT
* * *
55375838 TA-AT-AATAATATATAATTTCATAA-AATTCTTATAATAAATTTTCT
1 TATATGAAT-TTATATAATTT-AAAATAATTATTATAATAAATTTTCT
* *
55375883 TATATGAATTTATATAATTTAAAATAATTA--ATATTAAATATAAT-T
1 TATATGAATTTATATAATTTAAAATAATTATTATAATAAAT-T-TTCT
* * * *
55375928 TA-AT-AATGATATATAATTTCATAA-AATTCTTAATAATAAATATTCT
1 TATATGAAT-TTATATAATTT-AAAATAATTATT-ATAATAAATTTTCT
55375974 TATATGAATTTA
1 TATATGAATTTA
55375986 CTAAAATCAT
Statistics
Matches: 152, Mismatches: 20, Indels: 42
0.71 0.09 0.20
Matches are distributed among these distances:
43 6 0.04
44 49 0.32
45 22 0.14
46 27 0.18
47 41 0.27
48 7 0.05
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (46 bp):
TATATGAATTTATATAATTTAAAATAATTATTATAATAAATTTTCT
Found at i:55375886 original size:90 final size:90
Alignment explanation
Indices: 55375771--55375985 Score: 367
Period size: 90 Copynumber: 2.4 Consensus size: 90
55375761 AATTTAAAAT
* * *
55375771 AATTATTACTAATAAATTTTCTTATATGAATTTGTATAATTTAAAATAATTATTATTAAATATAA
1 AATTCTTA-TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAA
55375836 TTTAATAATAATATATAATTTCATAA
65 TTTAATAATAATATATAATTTCATAA
55375862 AATTCTTATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAAT
1 AATTCTTATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAAT
*
55375927 TTAATAATGATATATAATTTCATAA
66 TTAATAATAATATATAATTTCATAA
*
55375952 AATTCTTAATAATAAATATTCTTATATGAATTTA
1 AATTCTT-ATAATAAATTTTCTTATATGAATTTA
55375986 CTAAAATCAT
Statistics
Matches: 118, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
90 86 0.73
91 32 0.27
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (90 bp):
AATTCTTATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAAT
TTAATAATAATATATAATTTCATAA
Found at i:55380086 original size:23 final size:24
Alignment explanation
Indices: 55380026--55380088 Score: 78
Period size: 23 Copynumber: 2.7 Consensus size: 24
55380016 TCTACTCACT
55380026 AACAAATCAAGAACAATCTCCAGC
1 AACAAATCAAGAACAATCTCCAGC
* *
55380050 AGAC-TATCAA-AACAATTTCCAG-
1 A-ACAAATCAAGAACAATCTCCAGC
55380072 AACAAATCAAGAACAAT
1 AACAAATCAAGAACAAT
55380089 ATCAAAACAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
21 2 0.06
22 6 0.18
23 17 0.52
24 6 0.18
25 2 0.06
ACGTcount: A:0.52, C:0.24, G:0.08, T:0.16
Consensus pattern (24 bp):
AACAAATCAAGAACAATCTCCAGC
Found at i:55380097 original size:22 final size:22
Alignment explanation
Indices: 55380055--55380100 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
55380045 CCAGCAGACT
* *
55380055 ATCAAAACAATTTCCAGAACAA
1 ATCAAAACAATATCCAAAACAA
55380077 ATCAAGAACAATAT-CAAAACAA
1 ATCAA-AACAATATCCAAAACAA
55380099 AT
1 AT
55380101 GCAACAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.59, C:0.20, G:0.04, T:0.17
Consensus pattern (22 bp):
ATCAAAACAATATCCAAAACAA
Found at i:55380122 original size:107 final size:107
Alignment explanation
Indices: 55379999--55380459 Score: 798
Period size: 107 Copynumber: 4.3 Consensus size: 107
55379989 CTATACTTGT
*
55379999 AATTTCCAGTTTCATCTTCTACTCACTAACAAATCAAGAACAATCTCCAGCAGACTATCAAAACA
1 AATTTCCAGTTTCATCTTCTACTCACTAACAAATCAAGAACAATTTCCAGCAGACTATCAAAACA
55380064 ATTTCCAGAACAAATCAAGAACAATATCAAAACAAATGCAAC
66 ATTTCCAGAACAAATCAAGAACAATATCAAAACAAATGCAAC
* * * *
55380106 AATTTCCAGCTTCATCTTCCT-CTCACAAACAAATCAAGAACAGTTTCCAACAGACTATCAAAAC
1 AATTTCCAGTTTCATCTT-CTACTCACTAACAAATCAAGAACAATTTCCAGCAGACTATCAAAAC
55380170 AATTTCCAGAACAAATCAAGAACAATATCAAAACAAATGCAAC
65 AATTTCCAGAACAAATCAAGAACAATATCAAAACAAATGCAAC
* *
55380213 AATTTCCAATTTCATCTTCTACTCACTAACAAATCAAGAACAATTTCTAGCAGACTATCAAAACA
1 AATTTCCAGTTTCATCTTCTACTCACTAACAAATCAAGAACAATTTCCAGCAGACTATCAAAACA
* * *
55380278 ATTGCCAGAACAAATCAAGAACAATATCTAAACAAATGTAAC
66 ATTTCCAGAACAAATCAAGAACAATATCAAAACAAATGCAAC
* *
55380320 AATTTCCAGTTTCATCTTCTACTCACTAACAAATCAGGAACAATTTCCAGCAGACTATCAAAATA
1 AATTTCCAGTTTCATCTTCTACTCACTAACAAATCAAGAACAATTTCCAGCAGACTATCAAAACA
55380385 ATTTCCAGAACAAATCAAGAACAATATCAAAACAAATGCAAC
66 ATTTCCAGAACAAATCAAGAACAATATCAAAACAAATGCAAC
55380427 AATTTCCAGTTTCATCTTCTACTCACTAACAAA
1 AATTTCCAGTTTCATCTTCTACTCACTAACAAA
55380460 GAGAAACTAA
Statistics
Matches: 331, Mismatches: 21, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
106 2 0.01
107 327 0.99
108 2 0.01
ACGTcount: A:0.45, C:0.25, G:0.07, T:0.24
Consensus pattern (107 bp):
AATTTCCAGTTTCATCTTCTACTCACTAACAAATCAAGAACAATTTCCAGCAGACTATCAAAACA
ATTTCCAGAACAAATCAAGAACAATATCAAAACAAATGCAAC
Found at i:55380193 original size:23 final size:21
Alignment explanation
Indices: 55380133--55380195 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 21
55380123 TCCTCTCACA
*
55380133 AACAAATCAAGAACAGTTTCC
1 AACAAATCAAGAACAATTTCC
55380154 AACAGACTATCAA-AACAATTTCC
1 AACA-A--ATCAAGAACAATTTCC
55380177 AGAACAAATCAAGAACAAT
1 --AACAAATCAAGAACAAT
55380196 ATCAAAACAA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
21 4 0.11
22 6 0.17
23 15 0.43
24 6 0.17
25 4 0.11
ACGTcount: A:0.52, C:0.22, G:0.08, T:0.17
Consensus pattern (21 bp):
AACAAATCAAGAACAATTTCC
Found at i:55380204 original size:22 final size:22
Alignment explanation
Indices: 55380162--55380207 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
55380152 CCAACAGACT
* *
55380162 ATCAAAACAATTTCCAGAACAA
1 ATCAAAACAATATCCAAAACAA
55380184 ATCAAGAACAATAT-CAAAACAA
1 ATCAA-AACAATATCCAAAACAA
55380206 AT
1 AT
55380208 GCAACAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.59, C:0.20, G:0.04, T:0.17
Consensus pattern (22 bp):
ATCAAAACAATATCCAAAACAA
Found at i:55380300 original size:23 final size:24
Alignment explanation
Indices: 55380240--55380302 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 24
55380230 TCTACTCACT
* *
55380240 AACAAATCAAGAACAATTTCTAGC
1 AACAAATCAAGAACAATTGCCAGC
*
55380264 AGAC-TATCAA-AACAATTGCCAG-
1 A-ACAAATCAAGAACAATTGCCAGC
55380286 AACAAATCAAGAACAAT
1 AACAAATCAAGAACAAT
55380303 ATCTAAACAA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
21 2 0.06
22 6 0.19
23 16 0.50
24 6 0.19
25 2 0.06
ACGTcount: A:0.52, C:0.21, G:0.10, T:0.17
Consensus pattern (24 bp):
AACAAATCAAGAACAATTGCCAGC
Found at i:55380562 original size:19 final size:18
Alignment explanation
Indices: 55380520--55380564 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
55380510 GTAAACTCTT
* *
55380520 TCAAAAAACGGCAGATTA
1 TCAAAAAACAGCAGACTA
55380538 TCAAAAAACAGCAGACTA
1 TCAAAAAACAGCAGACTA
55380556 TCAAAAAAC
1 TCAAAAAAC
55380565 TGTCTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.56, C:0.20, G:0.11, T:0.13
Consensus pattern (18 bp):
TCAAAAAACAGCAGACTA
Found at i:55382994 original size:25 final size:25
Alignment explanation
Indices: 55382966--55383029 Score: 128
Period size: 25 Copynumber: 2.6 Consensus size: 25
55382956 TTAGCCCTCT
55382966 CGAGCTTCCCGTTATATGGTTCTTG
1 CGAGCTTCCCGTTATATGGTTCTTG
55382991 CGAGCTTCCCGTTATATGGTTCTTG
1 CGAGCTTCCCGTTATATGGTTCTTG
55383016 CGAGCTTCCCGTTA
1 CGAGCTTCCCGTTA
55383030 ATAGCTCTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.12, C:0.27, G:0.23, T:0.38
Consensus pattern (25 bp):
CGAGCTTCCCGTTATATGGTTCTTG
Found at i:55385073 original size:132 final size:132
Alignment explanation
Indices: 55384836--55385099 Score: 519
Period size: 132 Copynumber: 2.0 Consensus size: 132
55384826 AATGATATTA
55384836 AATGTCTATATCTGATCTGTAAATTCTAGTAATGCTCCATAACCTTGTTCTAGTGACAGATATGG
1 AATGTCTATATCTGATCTGTAAATTCTAGTAATGCTCCATAACCTTGTTCTAGTGACAGATATGG
55384901 GTTAGGGGTGTTACATGTGCACCTAAGGAGATACTTAACATGCTTCTCTTGCCTATATCTTTCAT
66 GTTAGGGGTGTTACATGTGCACCTAAGGAGATACTTAACATGCTTCTCTTGCCTATATCTTTCAT
55384966 TG
131 TG
*
55384968 AATGTCTATATCTGATCTGTAAATTCTAGTAATGCTCCATAACCTTGTTCTAGTGACGGATATGG
1 AATGTCTATATCTGATCTGTAAATTCTAGTAATGCTCCATAACCTTGTTCTAGTGACAGATATGG
55385033 GTTAGGGGTGTTACATGTGCACCTAAGGAGATACTTAACATGCTTCTCTTGCCTATATCTTTCAT
66 GTTAGGGGTGTTACATGTGCACCTAAGGAGATACTTAACATGCTTCTCTTGCCTATATCTTTCAT
55385098 TG
131 TG
55385100 CTTCTCCATC
Statistics
Matches: 131, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
132 131 1.00
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.37
Consensus pattern (132 bp):
AATGTCTATATCTGATCTGTAAATTCTAGTAATGCTCCATAACCTTGTTCTAGTGACAGATATGG
GTTAGGGGTGTTACATGTGCACCTAAGGAGATACTTAACATGCTTCTCTTGCCTATATCTTTCAT
TG
Found at i:55388268 original size:93 final size:93
Alignment explanation
Indices: 55388109--55388284 Score: 325
Period size: 93 Copynumber: 1.9 Consensus size: 93
55388099 AGAATCAGTA
55388109 ATTTCTTTGACAGAAGTTATAAGCAACTCGACTCATTCAATAAGTTCTGCTACACCAGAAAATGA
1 ATTTCTTTGACAGAAGTTATAAGCAACTCGACTCATTCAATAAGTTCTGCTACACCAGAAAATGA
55388174 ATGCATGAATCCTGAATCTGATTTCACG
66 ATGCATGAATCCTGAATCTGATTTCACG
* *
55388202 ATTTCTTTGACTGAAGTTATAAGCAACTCGACTCATTCGATAAGTTCTGCTACACCAGAAAATGA
1 ATTTCTTTGACAGAAGTTATAAGCAACTCGACTCATTCAATAAGTTCTGCTACACCAGAAAATGA
*
55388267 ATGCATGTATCCTGAATC
66 ATGCATGAATCCTGAATC
55388285 CGGTTTCGCT
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 80 1.00
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (93 bp):
ATTTCTTTGACAGAAGTTATAAGCAACTCGACTCATTCAATAAGTTCTGCTACACCAGAAAATGA
ATGCATGAATCCTGAATCTGATTTCACG
Found at i:55389390 original size:32 final size:31
Alignment explanation
Indices: 55389354--55389420 Score: 111
Period size: 29 Copynumber: 2.2 Consensus size: 31
55389344 CAATGGAAAC
55389354 ATGTGAGAAAACTGCTGATAACAACTTTTTGT
1 ATGTGAG-AAACTGCTGATAACAACTTTTTGT
55389386 ATGT--GAAACTGCTGATAACAACTTTTTGT
1 ATGTGAGAAACTGCTGATAACAACTTTTTGT
55389415 ATGTGA
1 ATGTGA
55389421 TTATACATAC
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
29 28 0.85
30 1 0.03
32 4 0.12
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (31 bp):
ATGTGAGAAACTGCTGATAACAACTTTTTGT
Found at i:55389396 original size:29 final size:29
Alignment explanation
Indices: 55389362--55389420 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
55389352 ACATGTGAGA
55389362 AAACTGCTGATAACAACTTTTTGTATGTG
1 AAACTGCTGATAACAACTTTTTGTATGTG
55389391 AAACTGCTGATAACAACTTTTTGTATGTG
1 AAACTGCTGATAACAACTTTTTGTATGTG
55389420 A
1 A
55389421 TTATACATAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (29 bp):
AAACTGCTGATAACAACTTTTTGTATGTG
Found at i:55397480 original size:51 final size:50
Alignment explanation
Indices: 55397419--55397605 Score: 232
Period size: 51 Copynumber: 3.7 Consensus size: 50
55397409 TGCTATCCGG
* *
55397419 TACACATAGTAGCCTACACTTAGTACTACACATGTGACCAATATCATCTGG
1 TACACATAGTAGCCTACACATAGTACTACACATGTGACCAA-ATCATCTGA
* * * *
55397470 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAAGCTATCTGA
1 TACACATAGTAGCCTACACATAGTACTACACATGTGACCAAATC-ATCTGA
* * *
55397521 TACACATAGTAGCCTGCACTTAGTACTACACATGTGACCATAAAT-ATCTTA
1 TACACATAGTAGCCTACACATAGTACTACACATGTGACC--AAATCATCTGA
* *
55397572 TACTCATAGTATCCTACACATAGTACTACACATG
1 TACACATAGTAGCCTACACATAGTACTACACATG
55397606 AGTTCACATG
Statistics
Matches: 118, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
50 2 0.02
51 113 0.96
53 3 0.03
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.27
Consensus pattern (50 bp):
TACACATAGTAGCCTACACATAGTACTACACATGTGACCAAATCATCTGA
Found at i:55397560 original size:102 final size:102
Alignment explanation
Indices: 55397401--55397603 Score: 282
Period size: 102 Copynumber: 2.0 Consensus size: 102
55397391 CACCACCCTT
* * * *
55397401 GTGATCAATGCTATCCGGTACACATAGTAGCCTACACTTAGTACTACACATGTGACCA-ATATCA
1 GTGACCAAAGCTATCCGATACACATAGTAGCCTACACTTAGTACTACACATGTGACCATAAAT-A
* * *
55397465 TCTGGTACACGTAGTAGCCTGCACATAGTACTACACAC
65 TCTGATACACATAGTAGCCTACACATAGTACTACACAC
* *
55397503 GTGACCAAAGCTATCTGATACACATAGTAGCCTGCACTTAGTACTACACATGTGACCATAAATAT
1 GTGACCAAAGCTATCCGATACACATAGTAGCCTACACTTAGTACTACACATGTGACCATAAATAT
* * *
55397568 CTTATACTCATAGTATCCTACACATAGTACTACACA
66 CTGATACACATAGTAGCCTACACATAGTACTACACA
55397604 TGAGTTCACA
Statistics
Matches: 88, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
102 85 0.97
103 3 0.03
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.27
Consensus pattern (102 bp):
GTGACCAAAGCTATCCGATACACATAGTAGCCTACACTTAGTACTACACATGTGACCATAAATAT
CTGATACACATAGTAGCCTACACATAGTACTACACAC
Found at i:55416642 original size:18 final size:18
Alignment explanation
Indices: 55416619--55416657 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
55416609 CTATTCCAAT
*
55416619 ATTTATTATTGGAATTT-A
1 ATTTATT-TTGAAATTTGA
55416637 ATTTATTTTGAAATTTGA
1 ATTTATTTTGAAATTTGA
55416655 ATT
1 ATT
55416658 CACATAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.56
Consensus pattern (18 bp):
ATTTATTTTGAAATTTGA
Found at i:55417488 original size:109 final size:106
Alignment explanation
Indices: 55417311--55417521 Score: 305
Period size: 109 Copynumber: 2.0 Consensus size: 106
55417301 CCAAATCCTA
* * * *
55417311 TACTTTGAAACTTTAGAAGGGTATTTAGCCATTTGGCTAAAAGAGAAATCGAAACCCAGCACATT
1 TACTTTGAAACTTTAAAAGGATATTTAGCCATTTGGCTAAAAGAAAAAGCGAAACCCAGCACATT
*
55417376 AGGGCACGTTTTCTCGAATTTCCAAATGCAAAATATTACCT
66 AGGGCACGTTTTCTCGAATTTCCAAACGCAAAATATTACCT
* * * *
55417417 TACTTTGAAATTTTTAAAAGGATATTTAGCTATTTGGTTGAACGAGAAAAAGCGAAACCCAGCAC
1 TACTTTGAAA-CTTTAAAAGGATATTTAGCCATTTGGCT-AA-AAGAAAAAGCGAAACCCAGCAC
*
55417482 ATTAGGGCACGTTTTCTCGAATTTCCAAACGCTAAATATT
63 ATTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAATATT
55417522 GCCTCAATTA
Statistics
Matches: 92, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
106 10 0.11
107 23 0.25
108 2 0.02
109 57 0.62
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (106 bp):
TACTTTGAAACTTTAAAAGGATATTTAGCCATTTGGCTAAAAGAAAAAGCGAAACCCAGCACATT
AGGGCACGTTTTCTCGAATTTCCAAACGCAAAATATTACCT
Found at i:55418121 original size:3 final size:3
Alignment explanation
Indices: 55418106--55418171 Score: 96
Period size: 3 Copynumber: 22.0 Consensus size: 3
55418096 AAAATAAAAT
* * * *
55418106 TAA TAA TAG TAA TAA TAA TGA TAA TAA CAC TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
55418154 TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
55418172 ACTAAATAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:55420189 original size:17 final size:16
Alignment explanation
Indices: 55420161--55420198 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
55420151 TTGAATCGAT
55420161 TTTTTTATTTTTAATATA
1 TTTTTTATTTTT-ATA-A
55420179 TTTTTTA-TTTTATAA
1 TTTTTTATTTTTATAA
55420194 TTTTT
1 TTTTT
55420199 AACAATTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 6 0.30
16 3 0.15
17 4 0.20
18 7 0.35
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTTATTTTTATAA
Found at i:55422183 original size:16 final size:17
Alignment explanation
Indices: 55422162--55422195 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
55422152 AATAATTAGG
55422162 GCAAAAGTAT-AATTTT
1 GCAAAAGTATGAATTTT
55422178 GCAAAAGTATGAATTTT
1 GCAAAAGTATGAATTTT
55422195 G
1 G
55422196 GACCGAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.35
Consensus pattern (17 bp):
GCAAAAGTATGAATTTT
Found at i:55426201 original size:24 final size:24
Alignment explanation
Indices: 55426169--55426223 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
55426159 AAATTATGGA
* *
55426169 TCACACGGCCTGGGACACGGGTTG
1 TCACACGGCCTGAGACACGGGCTG
55426193 TCACACGGCCTGAGACACGGGCTG
1 TCACACGGCCTGAGACACGGGCTG
*
55426217 CCACACG
1 TCACACG
55426224 ACCGTGTGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.35, G:0.33, T:0.13
Consensus pattern (24 bp):
TCACACGGCCTGAGACACGGGCTG
Found at i:55427793 original size:375 final size:372
Alignment explanation
Indices: 55427106--55427857 Score: 1414
Period size: 375 Copynumber: 2.0 Consensus size: 372
55427096 GGGTGAAACG
55427106 ATACTAGATGTACTTTTTATTTATTTTAAAAAAATTCTAAGTCAAATGATTTGAATGAAATGTTT
1 ATACTAGATGTACTTTTTATTTATTTTAAAAAAATTCTAAGTCAAATGATTTGAATGAAATGTTT
55427171 ATCATTTAAAACGGACTCTTAAAAGTATAAAACATTACAACTTAAATATTTGATAAAATAGACAT
66 ATCATTTAAAACGGACTCTTAAAAGTATAAAACATTACAACTTAAATATTTGATAAAATAGACAT
*
55427236 ATTCGCGACATATAATACTATTCACCATTTGAAAACATGTTCTAAAAAATGTCCCCCTGTATGCA
131 ATTCGCGACATATAATACTATTCACCATTTGAAAACATATTCTAAAAAATGTCCCCCTGTATGCA
*
55427301 TAACATCGCACTACAATCAACCATCTTGGCACATTCCTGGTTTGGTCCTTTCTAGCGAACTAGTT
196 TAACATCACACTACAATCAACCATCTTGGCACATTCCTGGTTTGGTCCTTTCTAGCGAACTAGTT
*
55427366 CAACTCAAGAACTTGTATTACAAATAAAATCCATAATTTCAATGGAACTTAATGAGTCTCAACCA
261 CAACTCAAGAACTTGTATTACAAATAAAATCCATAAGTTCAATGGAACTTAATGAGTCTCAACCA
55427431 ATTTTACCTTTAAACGATGATGTTGAACTCCTTGACTTAAGAATTCT
326 ATTTTACCTTTAAACGATGATGTTGAACTCCTTGACTTAAGAATTCT
55427478 ATACTAGATGTACTTTTTATTTATTTTAAAAAAATTCTAAGTCAAATGATTTGAATGAAATGTTT
1 ATACTAGATGTACTTTTTATTTATTTTAAAAAAATTCTAAGTCAAATGATTTGAATGAAATGTTT
55427543 ATCATTTAAAACGGACTCTTAAAAGTAGTACAAAACATTACAACTTAAATATTTGATAAAATAGA
66 ATCATTTAAAACGGACTCTTAAAAGTA-T--AAAACATTACAACTTAAATATTTGATAAAATAGA
*
55427608 CATATTCGCGACATATAATACTATTCACCATTTGAAAACATATTCTAAAAAATGTCCCCTTGTAT
128 CATATTCGCGACATATAATACTATTCACCATTTGAAAACATATTCTAAAAAATGTCCCCCTGTAT
* *
55427673 GCATAACATCACACTACGATCAACCATCTTGGCACATTCCTGGTTTGGTCCTTTCTAGCGAACTG
193 GCATAACATCACACTACAATCAACCATCTTGGCACATTCCTGGTTTGGTCCTTTCTAGCGAACTA
55427738 GTTCAACTCAAGAACTTGTATTACAAATAAAATCCATAAGTTCAATGGAACTTAATGAGTCTCAA
258 GTTCAACTCAAGAACTTGTATTACAAATAAAATCCATAAGTTCAATGGAACTTAATGAGTCTCAA
55427803 CCAATTTTACCTTTAAACGATGATGTTGAACTCCTTGACTTAAGAATTCT
323 CCAATTTTACCTTTAAACGATGATGTTGAACTCCTTGACTTAAGAATTCT
*
55427853 CTACT
1 ATACT
55427858 TCTTTTTAGA
Statistics
Matches: 370, Mismatches: 7, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
372 92 0.25
373 1 0.00
375 277 0.75
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (372 bp):
ATACTAGATGTACTTTTTATTTATTTTAAAAAAATTCTAAGTCAAATGATTTGAATGAAATGTTT
ATCATTTAAAACGGACTCTTAAAAGTATAAAACATTACAACTTAAATATTTGATAAAATAGACAT
ATTCGCGACATATAATACTATTCACCATTTGAAAACATATTCTAAAAAATGTCCCCCTGTATGCA
TAACATCACACTACAATCAACCATCTTGGCACATTCCTGGTTTGGTCCTTTCTAGCGAACTAGTT
CAACTCAAGAACTTGTATTACAAATAAAATCCATAAGTTCAATGGAACTTAATGAGTCTCAACCA
ATTTTACCTTTAAACGATGATGTTGAACTCCTTGACTTAAGAATTCT
Found at i:55428492 original size:25 final size:25
Alignment explanation
Indices: 55428431--55428493 Score: 90
Period size: 25 Copynumber: 2.5 Consensus size: 25
55428421 TACGTCATAT
*
55428431 AGGCTTTACAGGTAAACTGCCACAA
1 AGGCTTTACAAGTAAACTGCCACAA
** *
55428456 AGGCTTCCCAAGTAAATTGCCACAA
1 AGGCTTTACAAGTAAACTGCCACAA
55428481 AGGCTTTACAAGT
1 AGGCTTTACAAGT
55428494 GACTCATCAC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (25 bp):
AGGCTTTACAAGTAAACTGCCACAA
Found at i:55429388 original size:152 final size:152
Alignment explanation
Indices: 55429141--55429432 Score: 530
Period size: 152 Copynumber: 1.9 Consensus size: 152
55429131 ATCCAGTAGC
* *
55429141 AGTAACTGCGTACAAGATCACAAAATTTCTATTAGAATCTTCATTAATAGATAGTTTACTAATGT
1 AGTAACTGCGTACAAGATCACAAAATTTCTATTAGAATCTTCAGTAATAGATAGTTTACTAACGT
*
55429206 TTCAACTACATGCAACCCCTATGCAGGGCCTTTCACTCACACTCTACTTTTCTTACACGTTTCAA
66 TTCAACTACATGCAACCCCTATGCAGGGCCTTTCACTCACACTCTACTTTTCTTACACCTTTCAA
55429271 TATCCTTACTTCATTAATAGAT
131 TATCCTTACTTCATTAATAGAT
**
55429293 AGTAACTGCGTACAAGATCATGAAATTTCTATTAGAATCTTCAGTAATAGATAGTTTACTAACGT
1 AGTAACTGCGTACAAGATCACAAAATTTCTATTAGAATCTTCAGTAATAGATAGTTTACTAACGT
*
55429358 TTCAACTACATGCAACCCCTATGTAGGGCCTTTCACTCACACTCTACTTTTCTTACACCTTTCAA
66 TTCAACTACATGCAACCCCTATGCAGGGCCTTTCACTCACACTCTACTTTTCTTACACCTTTCAA
55429423 TATCCTTACT
131 TATCCTTACT
55429433 CATCAACAAT
Statistics
Matches: 134, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
152 134 1.00
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.35
Consensus pattern (152 bp):
AGTAACTGCGTACAAGATCACAAAATTTCTATTAGAATCTTCAGTAATAGATAGTTTACTAACGT
TTCAACTACATGCAACCCCTATGCAGGGCCTTTCACTCACACTCTACTTTTCTTACACCTTTCAA
TATCCTTACTTCATTAATAGAT
Found at i:55431073 original size:40 final size:40
Alignment explanation
Indices: 55430975--55431237 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
55430965 TCCTCGTTCA
* * * * *
55430975 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
55431014 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
55431054 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
55431094 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
55431134 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
55431174 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
55431214 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
55431238 CAGCATTCAC
Statistics
Matches: 200, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 37 0.19
40 155 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:55436376 original size:24 final size:23
Alignment explanation
Indices: 55436335--55436397 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 23
55436325 CTCATCTTCT
* * *
55436335 TCATCTTCACCTCGACCCTTGTAC
1 TCATCTTCATCTCCACCCTCGT-C
*
55436359 TCATCTTCATTTCCACCCTCGTC
1 TCATCTTCATCTCCACCCTCGTC
55436382 TACATCTTCATCTCCA
1 T-CATCTTCATCTCCA
55436398 GCCATTGTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
23 2 0.06
24 31 0.94
ACGTcount: A:0.17, C:0.41, G:0.05, T:0.37
Consensus pattern (23 bp):
TCATCTTCATCTCCACCCTCGTC
Found at i:55437897 original size:15 final size:15
Alignment explanation
Indices: 55437868--55437897 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
55437858 TTTTAAGAAT
*
55437868 TAAAAAATAATAAAA
1 TAAAAAATAAAAAAA
55437883 TAAAAAATAAAAAAA
1 TAAAAAATAAAAAAA
55437898 CGAAGGAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
TAAAAAATAAAAAAA
Found at i:55438223 original size:51 final size:51
Alignment explanation
Indices: 55438168--55438269 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
55438158 CCATACTTGA
55438168 GGGCAAACATGGGCTAAGTAGGGGGAATATGATAATACTCTAAAATGACAT
1 GGGCAAACATGGGCTAAGTAGGGGGAATATGATAATACTCTAAAATGACAT
55438219 GGGCAAACATGGGCTAAGTAGGGGGAATATGATAATACTCTAAAATGACAT
1 GGGCAAACATGGGCTAAGTAGGGGGAATATGATAATACTCTAAAATGACAT
55438270 ACTTATTTGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.39, C:0.12, G:0.27, T:0.22
Consensus pattern (51 bp):
GGGCAAACATGGGCTAAGTAGGGGGAATATGATAATACTCTAAAATGACAT
Done.