Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold169
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: 2015121
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 45543 characters in sequence are not A, C, G, or T
File 7 of 14
Found at i:1032969 original size:14 final size:14
Alignment explanation
Indices: 1032944--1032978 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1032934 TAATATTTAT
*
1032944 ATATTTTATAATTA
1 ATATTATATAATTA
*
1032958 ATTTTATATAATTA
1 ATATTATATAATTA
1032972 ATATTAT
1 ATATTAT
1032979 TTTTATTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
ATATTATATAATTA
Found at i:1032980 original size:19 final size:19
Alignment explanation
Indices: 1032939--1033000 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
1032929 TATTTTAATA
* *
1032939 TTTATATATTTTATAATTAAT
1 TTTATATAATTAAT-ATT-AT
1032960 TTTATATAATTAATATTAT
1 TTTATATAATTAATATTAT
* *
1032979 TTT-TATTATTAAATAATAT
1 TTTATATAATT-AATATTAT
1032998 TTT
1 TTT
1033001 TAATCTAATC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 6 0.17
19 15 0.42
20 3 0.08
21 12 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTATATAATTAATATTAT
Found at i:1033552 original size:25 final size:26
Alignment explanation
Indices: 1033517--1033567 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
1033507 TATATGGGTG
* * *
1033517 AAATAATAAAAATTTTCTGATTATTT
1 AAATAATAAAAAATTTATAATTATTT
1033543 AAAT-ATAAAAAATTTATAATTATTT
1 AAATAATAAAAAATTTATAATTATTT
1033568 TATAATATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (26 bp):
AAATAATAAAAAATTTATAATTATTT
Found at i:1033885 original size:13 final size:12
Alignment explanation
Indices: 1033869--1033915 Score: 60
Period size: 13 Copynumber: 3.8 Consensus size: 12
1033859 TCAATACGAT
1033869 TATATAATATAAA
1 TATA-AATATAAA
1033882 TATAAAATATAAA
1 TAT-AAATATAAA
1033895 TATAAATAT-AA
1 TATAAATATAAA
*
1033906 TTTAAATATA
1 TATAAATATA
1033916 TAAATATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
11 10 0.32
12 6 0.19
13 14 0.45
14 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TATAAATATAAA
Found at i:1033886 original size:11 final size:11
Alignment explanation
Indices: 1033870--1033915 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 11
1033860 CAATACGATT
1033870 ATATAATATAA
1 ATATAATATAA
*
1033881 ATATAA-A-AT
1 ATATAATATAA
1033890 ATA-AATATAA
1 ATATAATATAA
*
1033900 ATATAATTTAA
1 ATATAATATAA
1033911 ATATA
1 ATATA
1033916 TAAATATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
8 2 0.07
9 5 0.17
10 5 0.17
11 17 0.59
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
ATATAATATAA
Found at i:1033913 original size:17 final size:17
Alignment explanation
Indices: 1033874--1033928 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 17
1033864 ACGATTATAT
*
1033874 AATATAAATATAAAATATA
1 AATATAAATAT--AATTTA
1033893 AATATAAATATAATTTA
1 AATATAAATATAATTTA
*
1033910 AATATATAA-ATATTTTA
1 AATATA-AATATAATTTA
1033927 AA
1 AA
1033929 ATTATTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 20 0.61
18 2 0.06
19 11 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AATATAAATATAATTTA
Found at i:1033922 original size:6 final size:6
Alignment explanation
Indices: 1033869--1033915 Score: 60
Period size: 6 Copynumber: 7.7 Consensus size: 6
1033859 TCAATACGAT
*
1033869 TATATAA TATAAA TATAAAA TATAAA TATAAA TAT-AA TTTAAA TATA
1 TATA-AA TATAAA TAT-AAA TATAAA TATAAA TATAAA TATAAA TATA
1033916 TAAATATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
5 4 0.11
6 22 0.61
7 10 0.28
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
TATAAA
Found at i:1034427 original size:30 final size:30
Alignment explanation
Indices: 1034366--1034427 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
1034356 ACCTCCTACT
* * *
1034366 CCACCTTATGAGTATAAGTCGCCTCCGCCA
1 CCACCTTATGAGTATAAATCGCCACCACCA
* *
1034396 CCACCTTATGTGTATAAATCTCCACCACCA
1 CCACCTTATGAGTATAAATCGCCACCACCA
1034426 CC
1 CC
1034428 TTCGCCTTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.26, C:0.39, G:0.11, T:0.24
Consensus pattern (30 bp):
CCACCTTATGAGTATAAATCGCCACCACCA
Found at i:1034547 original size:15 final size:15
Alignment explanation
Indices: 1034512--1034541 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1034502 ATTACTATAA
1034512 ATCTCCACCACCACC
1 ATCTCCACCACCACC
*
1034527 ATCTCCATCACCACC
1 ATCTCCACCACCACC
1034542 TCCTCCGTAT
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:0.27, C:0.57, G:0.00, T:0.17
Consensus pattern (15 bp):
ATCTCCACCACCACC
Found at i:1034584 original size:42 final size:42
Alignment explanation
Indices: 1034522--1034612 Score: 119
Period size: 42 Copynumber: 2.2 Consensus size: 42
1034512 ATCTCCACCA
* * * * * *
1034522 CCACCATCTCCATCACCACCTCCTCCGTATTATTATAAGTCT
1 CCACCACCACCATCACCACCTCCTCCATACTACTACAAGTCT
*
1034564 CCTCCACCACCATCACCACCTCCTCCATACTACTACAAGTCT
1 CCACCACCACCATCACCACCTCCTCCATACTACTACAAGTCT
1034606 CCACCAC
1 CCACCAC
1034613 ATCCTCCGTA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.25, C:0.47, G:0.03, T:0.24
Consensus pattern (42 bp):
CCACCACCACCATCACCACCTCCTCCATACTACTACAAGTCT
Found at i:1034612 original size:30 final size:30
Alignment explanation
Indices: 1034577--1034646 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
1034567 CCACCACCAT
*
1034577 CACCACCTCCTCCATACTACTACAAGTCTC
1 CACCACCTCCTCCATACTACTACAAGTCCC
* * *
1034607 CACCACATCCTCCGTACTACTATAAGTCCC
1 CACCACCTCCTCCATACTACTACAAGTCCC
1034637 CACCACCTCC
1 CACCACCTCC
1034647 ATCTCCATCC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.26, C:0.49, G:0.04, T:0.21
Consensus pattern (30 bp):
CACCACCTCCTCCATACTACTACAAGTCCC
Found at i:1034618 original size:72 final size:74
Alignment explanation
Indices: 1034535--1034690 Score: 181
Period size: 78 Copynumber: 2.1 Consensus size: 74
1034525 CCATCTCCAT
* * * * *
1034535 CACCACCTCCTCCGTATTATTATAAGTCTCCTCCA-CCA-CCATCACCACCTCCTCCATACTACT
1 CACCACATCCTCCGTACTACTATAAGTCCCCACCACCCATCCATCACCACCTCCTCCATACTACT
1034598 ACAAGTCTC
66 ACAAGTCTC
* * *
1034607 CACCACATCCTCCGTACTACTATAAGTCCCCACCACCTCCATCTCCATCCCCACCTCCTCCGTAT
1 CACCACATCCTCCGTACTACTATAAGTCCCCACCA-C-CCA--TCCATCACCACCTCCTCCATAC
*
1034672 TACTACCAGTCTC
62 TACTACAAGTCTC
1034685 CACCAC
1 CACCAC
1034691 CGCCCCCAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
72 30 0.43
75 3 0.04
78 36 0.52
ACGTcount: A:0.24, C:0.47, G:0.04, T:0.24
Consensus pattern (74 bp):
CACCACATCCTCCGTACTACTATAAGTCCCCACCACCCATCCATCACCACCTCCTCCATACTACT
ACAAGTCTC
Found at i:1034790 original size:48 final size:47
Alignment explanation
Indices: 1034720--1035030 Score: 284
Period size: 48 Copynumber: 6.5 Consensus size: 47
1034710 AAAGCCCCCG
* * *
1034720 TACTACTACAAGTCTCCTCCACCACCATCTCCCTCCCCACCTCCTCCA
1 TACTACTACAA-TCTCCACCACCTCCATCTCCCTCACCACCTCCTCCA
1034768 TACTACTACGAATCTCCACCACCTCCATCTCCCTC-CCGACCTCCTCCA
1 TACTACTAC-AATCTCCACCACCTCCATCTCCCTCACC-ACCTCCTCCA
* * *
1034816 TACTATTACAAATCCCCACCACCTCCATCTCCCTCCCCACCTCCTCCA
1 TACTACTAC-AATCTCCACCACCTCCATCTCCCTCACCACCTCCTCCA
* *** * * ** *** *
1034864 TACTACTACAAGTCTCCACCACCACCA-AAACATGAAGAGAAACCCCCA
1 TACTACTACAA-TCTCCACCACCTCCATCTCCCTCACCA-CCTCCTCCA
* * *
1034912 TACTACTACAAATCTCCTCCACCTCCCTCTCCATCACCACCTCCTCCA
1 TACTACTAC-AATCTCCACCACCTCCATCTCCCTCACCACCTCCTCCA
* * * * *
1034960 TACTACTACAAGTATCCACCACCTCCATCACCCTCACCACCACCACCT
1 TACTACTACAA-TCTCCACCACCTCCATCTCCCTCACCACCTCCTCCA
*
1035008 TACTACTACAAATCCCCACCACC
1 TACTACTAC-AATCTCCACCACC
1035031 ATATTATTAC
Statistics
Matches: 211, Mismatches: 43, Indels: 18
0.78 0.16 0.07
Matches are distributed among these distances:
47 9 0.04
48 189 0.90
49 13 0.06
ACGTcount: A:0.27, C:0.50, G:0.03, T:0.21
Consensus pattern (47 bp):
TACTACTACAATCTCCACCACCTCCATCTCCCTCACCACCTCCTCCA
Found at i:1034845 original size:96 final size:96
Alignment explanation
Indices: 1034621--1035030 Score: 358
Period size: 96 Copynumber: 4.2 Consensus size: 96
1034611 ACATCCTCCG
* * * * * *
1034621 TACTACTATAAGTCCCCACCACCTCCATCTCCATCCCCACCTCCTCCGTATTACTACCAGTCTCC
1 TACTACTACAAATCCCCACCACCTCCATCTCCCTCCCCACCTCCTCCATACTACTACAAGTCTCC
* ** * * *** ** * *
1034686 ACCACCGCCCCCAAAACATGAAGAAAAGCCCCCG
66 ACCACCTCCATC--ACCCTCCCGACCA-CCACCA
* * * *
1034720 TACTACTACAAGTCTCCTCCACCACCATCTCCCTCCCCACCTCCTCCATACTACTACGAA-TCTC
1 TACTACTACAAATCCCCACCACCTCCATCTCCCTCCCCACCTCCTCCATACTACTAC-AAGTCTC
* * *
1034784 CACCACCTCCATCTCCCTCCCGACCTCCTCCA
65 CACCACCTCCATCACCCTCCCGACCACCACCA
*
1034816 TACTATTACAAATCCCCACCACCTCCATCTCCCTCCCCACCTCCTCCATACTACTACAAGTCTCC
1 TACTACTACAAATCCCCACCACCTCCATCTCCCTCCCCACCTCCTCCATACTACTACAAGTCTCC
* * * * *** ** *
1034881 ACCACCACCA-AAACATGAAGAGAAACCCCCA
66 ACCACCTCCATCACCCTCCCGA-CCACCACCA
* * * * * *
1034912 TACTACTACAAATCTCCTCCACCTCCCTCTCCATCACCACCTCCTCCATACTACTACAAGTATCC
1 TACTACTACAAATCCCCACCACCTCCATCTCCCTCCCCACCTCCTCCATACTACTACAAGTCTCC
*
1034977 ACCACCTCCATCACCCTCACC-ACCACCACCT
66 ACCACCTCCATCACCCTC-CCGACCACCACCA
1035008 TACTACTACAAATCCCCACCACC
1 TACTACTACAAATCCCCACCACC
1035031 ATATTATTAC
Statistics
Matches: 247, Mismatches: 59, Indels: 13
0.77 0.18 0.04
Matches are distributed among these distances:
95 6 0.02
96 168 0.68
97 8 0.03
99 64 0.26
100 1 0.00
ACGTcount: A:0.27, C:0.49, G:0.04, T:0.20
Consensus pattern (96 bp):
TACTACTACAAATCCCCACCACCTCCATCTCCCTCCCCACCTCCTCCATACTACTACAAGTCTCC
ACCACCTCCATCACCCTCCCGACCACCACCA
Found at i:1034886 original size:144 final size:144
Alignment explanation
Indices: 1034765--1035031 Score: 365
Period size: 144 Copynumber: 1.9 Consensus size: 144
1034755 CCCACCTCCT
* * *
1034765 CCATACTACTACGAATCTCCACCACCTCCATCTCCCTC-CCGACCTCCTCCATACTATTACAAAT
1 CCATACTACTACAAATCTCCACCACCTCCATCTCCATCACC-ACCTCCTCCATACTACTACAAAT
* * * * *
1034829 CCCCACCACCTCCATCTCCCTCCCCACCTCCTCCATACTACTACAAGTCTCCACCACCACCAAAA
65 ACCCACCACCTCCATCACCCTCACCACCACCACCATACTACTACAAGTCTCCACCACCACCAAAA
* *
1034894 CATGAAGAGAAACCC
130 CATCAACAGAAACCC
* * *
1034909 CCATACTACTACAAATCTCCTCCACCTCCCTCTCCATCACCACCTCCTCCATACTACTACAAGTA
1 CCATACTACTACAAATCTCCACCACCTCCATCTCCATCACCACCTCCTCCATACTACTACAAATA
* * * *
1034974 TCCACCACCTCCATCACCCTCACCACCACCACCTTACTACTACAAATCCCCACCACCA
66 CCCACCACCTCCATCACCCTCACCACCACCACCATACTACTACAAGTCTCCACCACCA
1035032 TATTATTACA
Statistics
Matches: 107, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
144 105 0.98
145 2 0.02
ACGTcount: A:0.28, C:0.49, G:0.03, T:0.20
Consensus pattern (144 bp):
CCATACTACTACAAATCTCCACCACCTCCATCTCCATCACCACCTCCTCCATACTACTACAAATA
CCCACCACCTCCATCACCCTCACCACCACCACCATACTACTACAAGTCTCCACCACCACCAAAAC
ATCAACAGAAACCC
Found at i:1035041 original size:24 final size:25
Alignment explanation
Indices: 1034999--1035055 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 25
1034989 ACCCTCACCA
*
1034999 CCACCACCTTACTACTACAAATC-C
1 CCACCACCATACTACTACAAATCTC
* * *
1035023 CCACCACCATATTATTACAAGTCTC
1 CCACCACCATACTACTACAAATCTC
1035048 CC-CCACCA
1 CCACCACCA
1035056 CCTTCCCCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 25 0.89
25 3 0.11
ACGTcount: A:0.32, C:0.46, G:0.02, T:0.21
Consensus pattern (25 bp):
CCACCACCATACTACTACAAATCTC
Found at i:1035042 original size:72 final size:72
Alignment explanation
Indices: 1034957--1035103 Score: 179
Period size: 72 Copynumber: 2.0 Consensus size: 72
1034947 ACCACCTCCT
*
1034957 CCATACTACTACAAGTATCCACCACCTCCATCACCC-TCACCACCACCACCTTACTACTACAAAT
1 CCATACTACTACAAGTATCCACCACCACCATC-CCCTTCACCACCACCACCTTACTACTACAAAT
1035021 CCCCACCA
65 CCCCACCA
* * * * * * * * *
1035029 CCATATTATTACAAGTCTCCCCCACCACCTTCCCCTTCACCACCCCCACCTTACTATTATAAGTC
1 CCATACTACTACAAGTATCCACCACCACCATCCCCTTCACCACCACCACCTTACTACTACAAATC
*
1035094 TCCACCA
66 CCCACCA
1035101 CCA
1 CCA
1035104 CCTTCACCAT
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
71 3 0.05
72 60 0.95
ACGTcount: A:0.29, C:0.48, G:0.02, T:0.22
Consensus pattern (72 bp):
CCATACTACTACAAGTATCCACCACCACCATCCCCTTCACCACCACCACCTTACTACTACAAATC
CCCACCA
Found at i:1035054 original size:120 final size:120
Alignment explanation
Indices: 1034909--1035151 Score: 290
Period size: 120 Copynumber: 2.0 Consensus size: 120
1034899 AGAGAAACCC
* * * * *
1034909 CCATACTACTACAAATCTCCTCCACCTCCCTCTCCATCACCACCTCCTCCATACTACTACAAGTA
1 CCATACTACTACAAATCTCCCCCACCACCCTCCCCATCACCACCCCCACCATACTACTACAAGTA
* * *
1034974 TCCACCACCTCCATCACCCTCACCACCACCACCTTACTACTACAAATCC-CCACCA
66 TCCACCACCACCATCACCATCACAACCACCACCTTACTACTACAAA-CCTCCACCA
* * * * * * * * *
1035029 CCATATTATTACAAGTCTCCCCCACCACCTTCCCCTTCACCACCCCCACCTTACTATTATAAGTC
1 CCATACTACTACAAATCTCCCCCACCACCCTCCCCATCACCACCCCCACCATACTACTACAAGTA
* * *
1035094 TCCACCACCACCTTCACCATCTCAACCACCTCCTTACTACTACAAACCTCCACCA
66 TCCACCACCACCATCACCATCACAACCACCACCTTACTACTACAAACCTCCACCA
1035149 CCA
1 CCA
1035152 CCTTCATCAT
Statistics
Matches: 102, Mismatches: 20, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
119 2 0.02
120 100 0.98
ACGTcount: A:0.28, C:0.49, G:0.01, T:0.22
Consensus pattern (120 bp):
CCATACTACTACAAATCTCCCCCACCACCCTCCCCATCACCACCCCCACCATACTACTACAAGTA
TCCACCACCACCATCACCATCACAACCACCACCTTACTACTACAAACCTCCACCA
Found at i:1035116 original size:21 final size:21
Alignment explanation
Indices: 1035092--1035175 Score: 78
Period size: 21 Copynumber: 3.7 Consensus size: 21
1035082 CTATTATAAG
1035092 TCTCCACCACCACCTTCACCA
1 TCTCCACCACCACCTTCACCA
* *
1035113 TCTCAACCACCTCCTTACTACTACAAA
1 TCTCCACCACCACCTT-C-AC--C--A
* *
1035140 CCTCCACCACCACCTTCATCA
1 TCTCCACCACCACCTTCACCA
1035161 TCTCCACCACCACCT
1 TCTCCACCACCACCT
1035176 CCTTACTACT
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
21 29 0.58
22 1 0.02
23 3 0.06
25 2 0.04
26 1 0.02
27 14 0.28
ACGTcount: A:0.26, C:0.52, G:0.00, T:0.21
Consensus pattern (21 bp):
TCTCCACCACCACCTTCACCA
Found at i:1035122 original size:51 final size:49
Alignment explanation
Indices: 1035038--1035204 Score: 180
Period size: 48 Copynumber: 3.4 Consensus size: 49
1035028 ACCATATTAT
* * * *
1035038 TACAAGTCTCCCCCACCACCTTC-CCCT-TCACCACCCCCACCTTACTAT
1 TACAAATCTCCACCACCACCTTCACCATCTCACCA-CCCCACCTTACTAC
* * *
1035086 TATAAGTCTCCACCACCACCTTCACCATCTCA--ACCACCTCCTTACTAC
1 TACAAATCTCCACCACCACCTTCACCATCTCACCACC-CCACCTTACTAC
* * *
1035134 TACAAACCTCCACCACCACCTTCATCATCTCCACCACCACCTCCTTACTAC
1 TACAAATCTCCACCACCACCTTCACCATCT-CACCACC-CCACCTTACTAC
1035185 TACAAATCTCCACCACCACC
1 TACAAATCTCCACCACCACC
1035205 AGCTAAATCC
Statistics
Matches: 103, Mismatches: 10, Indels: 9
0.84 0.08 0.07
Matches are distributed among these distances:
47 2 0.02
48 58 0.56
49 5 0.05
50 3 0.03
51 35 0.34
ACGTcount: A:0.26, C:0.50, G:0.01, T:0.22
Consensus pattern (49 bp):
TACAAATCTCCACCACCACCTTCACCATCTCACCACCCCACCTTACTAC
Found at i:1035153 original size:30 final size:30
Alignment explanation
Indices: 1035118--1035204 Score: 102
Period size: 30 Copynumber: 3.2 Consensus size: 30
1035108 CACCATCTCA
*
1035118 ACCACCTCCTTACTACTACAAACCTCCACC
1 ACCACCTCCTTACTACTACAAATCTCCACC
1035148 ACCA---CCTT-C-A-T-C--ATCTCCACC
1 ACCACCTCCTTACTACTACAAATCTCCACC
1035169 ACCACCTCCTTACTACTACAAATCTCCACC
1 ACCACCTCCTTACTACTACAAATCTCCACC
1035199 ACCACC
1 ACCACC
1035205 AGCTAAATCC
Statistics
Matches: 47, Mismatches: 1, Indels: 18
0.71 0.02 0.27
Matches are distributed among these distances:
21 12 0.26
23 1 0.02
24 5 0.11
25 2 0.04
26 2 0.04
27 5 0.11
28 1 0.02
30 19 0.40
ACGTcount: A:0.29, C:0.51, G:0.00, T:0.21
Consensus pattern (30 bp):
ACCACCTCCTTACTACTACAAATCTCCACC
Found at i:1035220 original size:42 final size:42
Alignment explanation
Indices: 1035173--1035289 Score: 216
Period size: 42 Copynumber: 2.8 Consensus size: 42
1035163 TCCACCACCA
**
1035173 CCTCCTTACTACTACAAATCTCCACCACCACCAGCTAAATCC
1 CCTCCTTACTACTACACTTCTCCACCACCACCAGCTAAATCC
1035215 CCTCCTTACTACTACACTTCTCCACCACCACCAGCTAAATCC
1 CCTCCTTACTACTACACTTCTCCACCACCACCAGCTAAATCC
1035257 CCTCCTTACTACTACACTTCTCCACCACCACCA
1 CCTCCTTACTACTACACTTCTCCACCACCACCA
1035290 ACTCCTTATT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 73 1.00
ACGTcount: A:0.27, C:0.48, G:0.02, T:0.23
Consensus pattern (42 bp):
CCTCCTTACTACTACACTTCTCCACCACCACCAGCTAAATCC
Found at i:1036891 original size:21 final size:21
Alignment explanation
Indices: 1036867--1036923 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
1036857 GACTGAGCCA
*
1036867 TACAAGCCACCACCATACTAC
1 TACAAGTCACCACCATACTAC
*
1036888 TACAAGTCACCACCATACTAT
1 TACAAGTCACCACCATACTAC
1036909 TACAAGTCACCACCA
1 TACAAGTCACCACCA
1036924 CCACCATCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.39, C:0.39, G:0.05, T:0.18
Consensus pattern (21 bp):
TACAAGTCACCACCATACTAC
Found at i:1036961 original size:6 final size:6
Alignment explanation
Indices: 1036952--1036979 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1036942 ATCTACAAGT
1036952 CACCTC CACCTC CACCTC CACCTC CACC
1 CACCTC CACCTC CACCTC CACCTC CACC
1036980 ATACTACTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.68, G:0.00, T:0.14
Consensus pattern (6 bp):
CACCTC
Found at i:1037035 original size:27 final size:27
Alignment explanation
Indices: 1036969--1037035 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 27
1036959 ACCTCCACCT
1036969 CCACCTCCACCATACTACTACAAATCA
1 CCACCTCCACCATACTACTACAAATCA
* * *
1036996 CCACCACCTCCATACTACTACAAATCC
1 CCACCTCCACCATACTACTACAAATCA
* *
1037023 CCTCCTCCCCCAT
1 CCACCTCCACCAT
1037036 TGCCATCTCC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.30, C:0.51, G:0.00, T:0.19
Consensus pattern (27 bp):
CCACCTCCACCATACTACTACAAATCA
Found at i:1037124 original size:48 final size:48
Alignment explanation
Indices: 1037053--1037267 Score: 209
Period size: 48 Copynumber: 4.5 Consensus size: 48
1037043 TCCTCCTCCT
* * * *
1037053 TACTATTACAAGTTCCCACCACCACCGGTTCACTCACCACCA-AAGCCA
1 TACTATTACAAATCCCCACCACCACCAGTCCACTCACCACCACAA-CCA
* * * *
1037101 TACTACTACAAATCCCCACCACCACCAATCCACTCTCCACCACCACCA
1 TACTATTACAAATCCCCACCACCACCAGTCCACTCACCACCACAACCA
* * * * * * * *
1037149 TACTACTACAAGTCTCCACCCCCACCA-TCCCCTTCAGCACCCCCACCA
1 TACTATTACAAATCCCCACCACCACCAGTCCAC-TCACCACCACAACCA
* * * *
1037197 TACTATTACAAATCCCCCCCACCACCAGTCCAGTCCCCTCCACAACCA
1 TACTATTACAAATCCCCACCACCACCAGTCCACTCACCACCACAACCA
*
1037245 TACTATTACAAATCACCACCACC
1 TACTATTACAAATCCCCACCACC
1037268 TCCGGTAAAG
Statistics
Matches: 135, Mismatches: 29, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
47 4 0.03
48 127 0.94
49 4 0.03
ACGTcount: A:0.31, C:0.48, G:0.04, T:0.17
Consensus pattern (48 bp):
TACTATTACAAATCCCCACCACCACCAGTCCACTCACCACCACAACCA
Found at i:1037164 original size:27 final size:27
Alignment explanation
Indices: 1037098--1037176 Score: 80
Period size: 27 Copynumber: 3.1 Consensus size: 27
1037088 ACCACCAAAG
*
1037098 CCATACTACTACAAATCCCCACCACCA
1 CCATACTACTACAAATCTCCACCACCA
*
1037125 CCA-A-T-C--C-ACTCTCCACCACCA
1 CCATACTACTACAAATCTCCACCACCA
* *
1037146 CCATACTACTACAAGTCTCCACCCCCA
1 CCATACTACTACAAATCTCCACCACCA
1037173 CCAT
1 CCAT
1037177 CCCCTTCAGC
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
21 15 0.36
22 2 0.05
23 1 0.02
24 2 0.05
25 1 0.02
26 2 0.05
27 19 0.45
ACGTcount: A:0.32, C:0.51, G:0.01, T:0.16
Consensus pattern (27 bp):
CCATACTACTACAAATCTCCACCACCA
Found at i:1037198 original size:96 final size:96
Alignment explanation
Indices: 1037098--1037493 Score: 291
Period size: 96 Copynumber: 4.1 Consensus size: 96
1037088 ACCACCAAAG
* *
1037098 CCATACTACTACAAATCCCCACCACCACCAATCCACTCTCCACCACCACCATACTACTACAAGTC
1 CCATACTACTACAAATCCCCACCACCACCAGTCCACTCTCCACCACCACCATACTACTACAAATC
* *
1037163 TCCACCCCCACCATCCCCTTCAGCACCCCCA
66 TCCACCACCTCCATCCCCTTCAGCACCCCCA
* * * * * * *
1037194 CCATACTATTACAAATCCCCCCCACCACCAGTCCAGTCCCCTCCACAACCATACTATTACAAATC
1 CCATACTACTACAAATCCCCACCACCACCAGTCCACTCTCCACCACCACCATACTACTACAAATC
* **** *
1037259 ACCACCACCTCCGGTAAAGGCTACAGCA--CCCA
66 TCCACCACCTCC---ATCCCCTTCAGCACCCCCA
* * ** * * * * * * *
1037291 -CTTACCACTACAGCTCCCCTCCTCCACC--TTCACCATCTCCTCCTCCTCCCTACTACTACAAA
1 CCATACTACTACAAATCCCCACCACCACCAGTCCA-C-TCTCCACCACCACCATACTACTACAAA
* * * * **
1037353 TCTCCACCATCTCCATCTCCATCACCACCAACA
64 TCTCCACCACCTCCATCCCCTTCAGCACCCCCA
* * * * * * *
1037386 CCTTACTATTACAAGTCCCCACCACCACCAGTCCACTGTCCACCACCACCCTATTACTACAAGTC
1 CCATACTACTACAAATCCCCACCACCACCAGTCCACTCTCCACCACCACCATACTACTACAAATC
* * * *
1037451 CCCACCTCCTCCATCCCCTTCATC-CCCTCCC
66 TCCACCACCTCCATCCCCTTCAGCACCC-CCA
1037482 CCATACTACTAC
1 CCATACTACTAC
1037494 CACTCACGTC
Statistics
Matches: 222, Mismatches: 67, Indels: 22
0.71 0.22 0.07
Matches are distributed among these distances:
93 6 0.03
94 3 0.01
95 4 0.02
96 193 0.87
97 5 0.02
98 3 0.01
99 8 0.04
ACGTcount: A:0.27, C:0.50, G:0.04, T:0.20
Consensus pattern (96 bp):
CCATACTACTACAAATCCCCACCACCACCAGTCCACTCTCCACCACCACCATACTACTACAAATC
TCCACCACCTCCATCCCCTTCAGCACCCCCA
Found at i:1038215 original size:19 final size:20
Alignment explanation
Indices: 1038191--1038229 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1038181 TATATTTTGA
*
1038191 TTTTTTAAT-TATTTTAAAT
1 TTTTTTAATATATCTTAAAT
1038210 TTTTTTAATATATCTTAAAT
1 TTTTTTAATATATCTTAAAT
1038230 GGTACGTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTTTAATATATCTTAAAT
Found at i:1038440 original size:2 final size:2
Alignment explanation
Indices: 1038433--1038473 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
1038423 GATCCCTTTG
* * *
1038433 TA TA TA TA TA TA TA TA TG TG TG TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1038474 TGTAAATGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1039536 original size:16 final size:16
Alignment explanation
Indices: 1039498--1039547 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
1039488 TCTGTAATCA
*
1039498 AGTTTTAAGTTATTTC
1 AGTTTTAAGTTATTTT
**
1039514 AAATTTAAGTTATTTT
1 AGTTTTAAGTTATTTT
1039530 AGTTTTATA-TTATTTT
1 AGTTTTA-AGTTATTTT
1039546 AG
1 AG
1039548 GTTTGGCTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
16 27 0.96
17 1 0.04
ACGTcount: A:0.30, C:0.02, G:0.10, T:0.58
Consensus pattern (16 bp):
AGTTTTAAGTTATTTT
Found at i:1040242 original size:34 final size:33
Alignment explanation
Indices: 1040187--1040252 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 33
1040177 AGTTTAATTC
**
1040187 ATTTAAAATTATTATTTAAATA-ATAAAATATTT
1 ATTTAAAATTATTATAAAAATATAT-AAATATTT
*
1040220 ATTTAAATTTAATTATAAAAATATATAAATATT
1 ATTTAAAATT-ATTATAAAAATATATAAATATT
1040253 AAATAAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 9 0.32
34 17 0.61
35 2 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (33 bp):
ATTTAAAATTATTATAAAAATATATAAATATTT
Found at i:1040266 original size:33 final size:35
Alignment explanation
Indices: 1040223--1040295 Score: 87
Period size: 33 Copynumber: 2.1 Consensus size: 35
1040213 AATATTTATT
* *
1040223 TAAATTTAATTATAAAAATATA-TAAAT-ATTAAA
1 TAAATATAATTATAAAAATATATTAAATAATAAAA
* **
1040256 TAAATATAATTTTTTAAATATATTAAATAATAAAA
1 TAAATATAATTATAAAAATATATTAAATAATAAAA
1040291 TAAAT
1 TAAAT
1040296 TTTTTAATCA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
33 18 0.55
34 5 0.15
35 10 0.30
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (35 bp):
TAAATATAATTATAAAAATATATTAAATAATAAAA
Found at i:1043831 original size:187 final size:172
Alignment explanation
Indices: 1043606--1044051 Score: 588
Period size: 173 Copynumber: 2.5 Consensus size: 172
1043596 CCTCAAAGAA
* * * * *
1043606 AAGGCGCGAAAAAAACTTAATTTTCCTAAGCCACCAAATTGAGCATTAAAGTAAATAACGTTTAG
1 AAGGCGCG-AAAAAACTTAGTTTTCCCAAACCACCAAATTGTGCATTAAAGTAAATAACTTTTAG
* *
1043671 ATTGATTATGGTAATATCATTATTGAACAGAGATATTAAAAAAAAAAGAACATGTTCTCAGTGTT
65 ATTGATTATGGTAATATCATTATTGAACAGAG--A-T--AAAAAAAAGAACATGCTCTAAGTGTT
**
1043736 TTTAACGGTGCAAGGCGCACTCTAGTGTAGGTGCTAGAATCCTTATATTG-TTAGGCGC
125 TTTAACGGT---A-GCGC-CT-TA----A-GCACTAGAATCCTTATATTGCTTAGGCGC
1043794 AAGGCGCGAAAAAACTTAGTTTTCCCAAACCACCAAATTGTGCATTAAAGTAAATAACTTTTAGA
1 AAGGCGCGAAAAAACTTAGTTTTCCCAAACCACCAAATTGTGCATTAAAGTAAATAACTTTTAGA
* *
1043859 TTGATTATGGTAATATCATTATTGAACAGAGATAAAAACAAGAACATGCTGTAAGTGTTTTTAAC
66 TTGATTATGGTAATATCATTATTGAACAGAGATAAAAAAAAGAACATGCTCTAAGTGTTTTTAAC
**
1043924 GGTATTGCCTTAAGCACTAGAATCCTTATATTGCCTTAGGCGC
131 GGTAGCGCCTTAAGCACTAGAATCCTTATATTG-CTTAGGCGC
**
1043967 AAGGCATGAAAAAACTTAGTTTTCCCAAACCACCAAATTGTGCATTAAAGTAAATAACTTTTAGA
1 AAGGCGCGAAAAAACTTAGTTTTCCCAAACCACCAAATTGTGCATTAAAGTAAATAACTTTTAGA
1044032 TTGATTATGGTAATATCATT
66 TTGATTATGGTAATATCATT
1044052 GTATAAAAAA
Statistics
Matches: 241, Mismatches: 15, Indels: 19
0.88 0.05 0.07
Matches are distributed among these distances:
171 18 0.07
172 1 0.00
173 91 0.38
176 2 0.01
177 2 0.01
178 2 0.01
179 1 0.00
182 31 0.13
184 1 0.00
185 1 0.00
187 83 0.34
188 8 0.03
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (172 bp):
AAGGCGCGAAAAAACTTAGTTTTCCCAAACCACCAAATTGTGCATTAAAGTAAATAACTTTTAGA
TTGATTATGGTAATATCATTATTGAACAGAGATAAAAAAAAGAACATGCTCTAAGTGTTTTTAAC
GGTAGCGCCTTAAGCACTAGAATCCTTATATTGCTTAGGCGC
Found at i:1047482 original size:2 final size:2
Alignment explanation
Indices: 1047475--1047513 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1047465 GAAAGATGAA
1047475 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1047514 AAGAAAAAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1053702 original size:7 final size:8
Alignment explanation
Indices: 1053686--1053710 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1053676 TCTATAGCTG
1053686 TTTTATTT
1 TTTTATTT
1053694 TTTTATTT
1 TTTTATTT
1053702 TTTTATTT
1 TTTTATTT
1053710 T
1 T
1053711 ATATCAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTATTT
Found at i:1063010 original size:32 final size:32
Alignment explanation
Indices: 1062974--1063038 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 32
1062964 CAGATTTATT
*
1062974 TATGAATGCAATCTT-TTGGTATCAAAATTTAA
1 TATGAATGCAAT-TTGTTGATATCAAAATTTAA
1063006 TATGAATGCAATTTGTTGATATCAAAATTTAA
1 TATGAATGCAATTTGTTGATATCAAAATTTAA
1063038 T
1 T
1063039 TTAAAAGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 2 0.06
32 29 0.94
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (32 bp):
TATGAATGCAATTTGTTGATATCAAAATTTAA
Found at i:1063173 original size:28 final size:28
Alignment explanation
Indices: 1063141--1063208 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
1063131 CTCATCTAAG
1063141 TTTAAAAAATTATTT-TTAAAATTTAAAA
1 TTTAAAAAATT-TTTATTAAAATTTAAAA
* **
1063169 TTTAATAAATTTTTATTAAGTTTTAAAA
1 TTTAAAAAATTTTTATTAAAATTTAAAA
* *
1063197 TATAAATAATTT
1 TTTAAAAAATTT
1063209 AATATTTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
27 3 0.09
28 30 0.91
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (28 bp):
TTTAAAAAATTTTTATTAAAATTTAAAA
Found at i:1063193 original size:35 final size:37
Alignment explanation
Indices: 1063154--1063222 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
1063144 AAAAAATTAT
*
1063154 TTTTAAAAT-TTAA-AATTTAATAAATTTTTATTAAG
1 TTTTAAAATATAAATAATTTAATAAATTTTTATTAAG
**
1063189 TTTTAAAATATAAATAATTTAATATTTTTTTATT
1 TTTTAAAATATAAATAATTTAATAAATTTTTATT
1063223 TATATTATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 9 0.31
36 3 0.10
37 17 0.59
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (37 bp):
TTTTAAAATATAAATAATTTAATAAATTTTTATTAAG
Found at i:1063227 original size:28 final size:28
Alignment explanation
Indices: 1063196--1063254 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
1063186 AAGTTTTAAA
*
1063196 ATATAAATAAT-TTA-ATATTTTTTTATTT
1 ATAT-AATAATATTATATATTTATTT-TTT
*
1063224 ATATTATAATATTATATATTTATTTTTT
1 ATATAATAATATTATATATTTATTTTTT
1063252 ATA
1 ATA
1063255 AGATAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 5 0.19
28 13 0.48
29 9 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (28 bp):
ATATAATAATATTATATATTTATTTTTT
Found at i:1063232 original size:27 final size:28
Alignment explanation
Indices: 1063202--1063254 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
1063192 TAAAATATAA
*
1063202 ATAAT-TTA-ATATTTTTTTATTTATATT
1 ATAATATTATATATTTATTT-TTTATATT
1063229 ATAATATTATATATTTATTTTTTATA
1 ATAATATTATATATTTATTTTTTATA
1063255 AGATAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 5 0.22
28 9 0.39
29 9 0.39
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (28 bp):
ATAATATTATATATTTATTTTTTATATT
Found at i:1063401 original size:19 final size:18
Alignment explanation
Indices: 1063353--1063404 Score: 72
Period size: 17 Copynumber: 2.9 Consensus size: 18
1063343 TTAATATCAA
*
1063353 TTATTTTTTAA-TGAATT
1 TTATTTTTTAATTTAATT
1063370 TTATTTTTT-ATTTAATT
1 TTATTTTTTAATTTAATT
1063387 TTATTTTTTGAATTTAAT
1 TTATTTTTT-AATTTAAT
1063405 ATTTTTATCA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 1 0.03
17 23 0.74
19 7 0.23
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (18 bp):
TTATTTTTTAATTTAATT
Found at i:1063787 original size:17 final size:17
Alignment explanation
Indices: 1063767--1063800 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1063757 CATTGTTTGC
*
1063767 TTTTTAGTTAATCAATT
1 TTTTTAATTAATCAATT
*
1063784 TTTTTAATTTATCAATT
1 TTTTTAATTAATCAATT
1063801 GAATTATTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (17 bp):
TTTTTAATTAATCAATT
Found at i:1064664 original size:20 final size:22
Alignment explanation
Indices: 1064631--1064697 Score: 61
Period size: 22 Copynumber: 3.1 Consensus size: 22
1064621 AAAATTTACA
1064631 TTTTTATAATATAATT-ATAT-AT
1 TTTTTAT-A-ATAATTGATATAAT
*
1064653 TTTTTATAATAATTGTTATAAT
1 TTTTTATAATAATTGATATAAT
*
1064675 TTTATTATACTAATTG-T-TAAT
1 TTT-TTATAATAATTGATATAAT
1064696 TT
1 TT
1064698 ATTAAGATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
20 6 0.15
21 10 0.25
22 13 0.32
23 11 0.28
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (22 bp):
TTTTTATAATAATTGATATAAT
Found at i:1064671 original size:23 final size:22
Alignment explanation
Indices: 1064631--1064693 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
1064621 AAAATTTACA
**
1064631 TTTTTATAAT-ATAATTATATAT
1 TTTTTATAATAATTGTTATA-AT
1064653 TTTTTATAATAATTGTTATAAT
1 TTTTTATAATAATTGTTATAAT
*
1064675 TTTATTATACTAATTGTTA
1 TTT-TTATAATAATTGTTA
1064694 ATTTATTAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
22 15 0.42
23 21 0.58
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.59
Consensus pattern (22 bp):
TTTTTATAATAATTGTTATAAT
Found at i:1064698 original size:20 final size:22
Alignment explanation
Indices: 1064645--1064701 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
1064635 TATAATATAA
*
1064645 TTATATATTTTTTATAATAATTG
1 TTATA-ATTTATTATAATAATTG
*
1064668 TTATAATTTTATTATACTAATTG
1 TTATAA-TTTATTATAATAATTG
1064691 -T-TAATTTATTA
1 TTATAATTTATTA
1064702 AGATATTTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 7 0.23
21 3 0.10
22 2 0.06
23 19 0.61
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.60
Consensus pattern (22 bp):
TTATAATTTATTATAATAATTG
Found at i:1065481 original size:12 final size:14
Alignment explanation
Indices: 1065456--1065486 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1065446 TTTAAGTGAC
1065456 ATATATTTTATAAA
1 ATATATTTTATAAA
*
1065470 ATATATTTTAAAAA
1 ATATATTTTATAAA
1065484 ATA
1 ATA
1065487 AAAATTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATATATTTTATAAA
Found at i:1066142 original size:2 final size:2
Alignment explanation
Indices: 1066135--1066168 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1066125 ACTCCTTCAG
1066135 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1066169 GTATGGCGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1066452 original size:107 final size:109
Alignment explanation
Indices: 1066307--1066507 Score: 275
Period size: 112 Copynumber: 1.8 Consensus size: 109
1066297 ATAGATTTTC
*
1066307 TTTTGTCAATATTTTAGTTACCCATTTTTATTTTCATGTTTTAAAGC-AA-AC-TCTTTTTGGTT
1 TTTTGTAAATATTTTAGTTACCCATTTTTATTTTCATGTTTTAAAGCTAACACTTCTTTTTGGTT
*
1066369 ATTTGTAATTTTCAATTTCCAATTTGCAGTGGAAAGCATGGATT
66 ATTTGTAATTTTCAATGTCCAATTTGCAGTGGAAAGCATGGATT
* * *
1066413 TTTTGTAAATTTTTTGAG-TACCCATTTTATATTTTCATGTTTTAAAGCTAACCCTTTTTTTTTT
1 TTTTGTAAATATTTT-AGTTACCCATTTT-TATTTTCATGTTTTAAAGCTAACAC--TTCTTTTT
* *
1066477 GGTTATTTGTGATTTTCAATGTCTAATTTGC
62 GGTTATTTGTAATTTTCAATGTCCAATTTGC
1066508 TGTAGAAACC
Statistics
Matches: 81, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
106 23 0.28
107 21 0.26
108 2 0.02
109 1 0.01
112 34 0.42
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.52
Consensus pattern (109 bp):
TTTTGTAAATATTTTAGTTACCCATTTTTATTTTCATGTTTTAAAGCTAACACTTCTTTTTGGTT
ATTTGTAATTTTCAATGTCCAATTTGCAGTGGAAAGCATGGATT
Found at i:1079086 original size:69 final size:69
Alignment explanation
Indices: 1078970--1079107 Score: 249
Period size: 69 Copynumber: 2.0 Consensus size: 69
1078960 ATCATAGTTA
* * *
1078970 TGCATAAGTCGGTCGATATATAAAACTTTTTTCATTTGTTAACTTGACTACTTTAGCTTGACTTG
1 TGCATAAGTCAGTCGATATATAAAACTTTTTTCATTTGTTAAATTGACTACTCTAGCTTGACTTG
1079035 CAGG
66 CAGG
1079039 TGCATAAGTCAGTCGATATATAAAACTTTTTTCATTTGTTAAATTGACTACTCTAGCTTGACTTG
1 TGCATAAGTCAGTCGATATATAAAACTTTTTTCATTTGTTAAATTGACTACTCTAGCTTGACTTG
1079104 CAGG
66 CAGG
1079108 CTATGTCTGA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.40
Consensus pattern (69 bp):
TGCATAAGTCAGTCGATATATAAAACTTTTTTCATTTGTTAAATTGACTACTCTAGCTTGACTTG
CAGG
Found at i:1079987 original size:14 final size:14
Alignment explanation
Indices: 1079950--1079991 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
1079940 CATTTATAAA
1079950 ATATT-TAAAATAT
1 ATATTGTAAAATAT
1079963 -TA-TGT-AAATAT
1 ATATTGTAAAATAT
1079974 ATATTGTAAAATAT
1 ATATTGTAAAATAT
1079988 ATAT
1 ATAT
1079992 AATATATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
11 7 0.28
12 5 0.20
13 3 0.12
14 10 0.40
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (14 bp):
ATATTGTAAAATAT
Found at i:1080031 original size:25 final size:25
Alignment explanation
Indices: 1079944--1080033 Score: 85
Period size: 27 Copynumber: 3.5 Consensus size: 25
1079934 ATATAACATT
*
1079944 TATAAAATATTTAAAATATTATGTAAA
1 TATAAAATA-TTAAAAT-TTATATAAA
* *
1079971 TAT-ATAT-TGTAAAATATATATAATA
1 TATAAAATAT-TAAAATTTATATAA-A
*
1079996 TATTAATATATTAAAATTTATATAAA
1 TA-TAAAATATTAAAATTTATATAAA
1080022 TATAAAATATTA
1 TATAAAATATTA
1080034 TTATGACATA
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
24 7 0.13
25 18 0.34
26 7 0.13
27 20 0.38
28 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (25 bp):
TATAAAATATTAAAATTTATATAAA
Found at i:1081024 original size:25 final size:26
Alignment explanation
Indices: 1080995--1081047 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
1080985 TTAAATTTGA
*
1080995 ATTTTATTATTTA-ATAAT-TAAAAAT
1 ATTTT-TTATTTATAAAATATAAAAAT
1081020 A-TTTTTATTTATAAAATATAAAAAT
1 ATTTTTTATTTATAAAATATAAAAAT
1081045 ATT
1 ATT
1081048 AATATAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
23 7 0.29
24 7 0.29
25 9 0.38
26 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
ATTTTTTATTTATAAAATATAAAAAT
Found at i:1081030 original size:23 final size:25
Alignment explanation
Indices: 1081001--1081047 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
1080991 TTGAATTTTA
*
1081001 TTATTTA-ATAAT-TAAAAATATTT
1 TTATTTATAAAATATAAAAATATTT
1081024 TTATTTATAAAATATAAAAATATT
1 TTATTTATAAAATATAAAAATATT
1081048 AATATAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.33
24 4 0.19
25 10 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TTATTTATAAAATATAAAAATATTT
Found at i:1081220 original size:11 final size:11
Alignment explanation
Indices: 1081204--1081237 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1081194 ATGGTAAAAA
1081204 ATAATATAAAT
1 ATAATATAAAT
1081215 ATAATATAAAT
1 ATAATATAAAT
*
1081226 -TAATAAAAAT
1 ATAATATAAAT
1081236 AT
1 AT
1081238 TTAAATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:1082407 original size:18 final size:18
Alignment explanation
Indices: 1082381--1082415 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1082371 TTATATATAT
1082381 ATATATATATATCAATTG
1 ATATATATATATCAATTG
*
1082399 ATATTTATATATCAATT
1 ATATATATATATCAATT
1082416 AAAAGTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.49
Consensus pattern (18 bp):
ATATATATATATCAATTG
Found at i:1084266 original size:26 final size:24
Alignment explanation
Indices: 1084230--1084286 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 24
1084220 AATTCAAACA
*
1084230 TTATATAATTTTTACATATTAATATAT
1 TTAT-TAATTTATACA-ATT-ATATAT
1084257 TTATTAATTTATACAATTATATAT
1 TTATTAATTTATACAATTATATAT
1084281 TT-TTAA
1 TTATTAA
1084287 AATAAATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 4 0.14
24 8 0.28
25 3 0.10
26 10 0.34
27 4 0.14
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (24 bp):
TTATTAATTTATACAATTATATAT
Found at i:1084428 original size:3 final size:3
Alignment explanation
Indices: 1084422--1084480 Score: 73
Period size: 3 Copynumber: 19.3 Consensus size: 3
1084412 ATAATAATAA
* * * *
1084422 TAT TAT TAT TAT TAT TGT TAT TAT TAT TAA TAA TAT TAT TAT TAAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT
1084468 TAT TAT TAT TAT T
1 TAT TAT TAT TAT T
1084481 TTTTGTTTAC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
3 47 0.96
4 2 0.04
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:1084444 original size:15 final size:15
Alignment explanation
Indices: 1084419--1084480 Score: 88
Period size: 15 Copynumber: 4.1 Consensus size: 15
1084409 ATAATAATAA
1084419 TAATATTATTATTAT
1 TAATATTATTATTAT
* *
1084434 TATTGTTATTATTAT
1 TAATATTATTATTAT
*
1084449 TAATAATATTATTAT
1 TAATATTATTATTAT
1084464 TAAATATTATTATTAT
1 T-AATATTATTATTAT
1084480 T
1 T
1084481 TTTTGTTTAC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
15 26 0.65
16 14 0.35
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (15 bp):
TAATATTATTATTAT
Found at i:1090903 original size:32 final size:32
Alignment explanation
Indices: 1090867--1090949 Score: 114
Period size: 32 Copynumber: 2.6 Consensus size: 32
1090857 TATTTATCTT
1090867 AAAATTTATATAATATAAATTATTAATATATC
1 AAAATTTATATAATATAAATTATTAATATATC
** * *
1090899 AAAATTTATATAATACGAATTATTAATGTATT
1 AAAATTTATATAATATAAATTATTAATATATC
1090931 AAAATTTATATGAA-ATAAA
1 AAAATTTATAT-AATATAAA
1090950 AAATATCTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
32 42 0.95
33 2 0.05
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (32 bp):
AAAATTTATATAATATAAATTATTAATATATC
Found at i:1091573 original size:22 final size:23
Alignment explanation
Indices: 1091562--1091605 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1091552 TTAATATTTT
1091562 AATATAATATAA-AAATAATTAA
1 AATATAATATAATAAATAATTAA
1091584 AATATAATATAATATAA-AATTA
1 AATATAATATAATA-AATAATTA
1091606 GTACCAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 12 0.60
23 6 0.30
24 2 0.10
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (23 bp):
AATATAATATAATAAATAATTAA
Found at i:1091587 original size:17 final size:17
Alignment explanation
Indices: 1091561--1091603 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
1091551 ATTAATATTT
*
1091561 TAATATAATATA-AAAA
1 TAATATAAAATATAAAA
*
1091577 TAAT-TAAAATATAATA
1 TAATATAAAATATAAAA
1091593 TAATATAAAAT
1 TAATATAAAAT
1091604 TAGTACCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 6 0.26
16 11 0.48
17 6 0.26
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TAATATAAAATATAAAA
Found at i:1091596 original size:27 final size:28
Alignment explanation
Indices: 1091547--1091602 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
1091537 TTTTTAATTT
* *
1091547 AATAATTAATATTTTAATATAATATAAA
1 AATAATTAATAATATAATATAATATAAA
1091575 AATAATTAA-AATATAATATAATATAAA
1 AATAATTAATAATATAATATAATATAAA
1091602 A
1 A
1091603 TTAGTACCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 17 0.65
28 9 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (28 bp):
AATAATTAATAATATAATATAATATAAA
Found at i:1094339 original size:24 final size:24
Alignment explanation
Indices: 1094307--1094355 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1094297 TTCTAGATGT
1094307 CTAAGTTCTACCAAACCTTGGTCA
1 CTAAGTTCTACCAAACCTTGGTCA
1094331 CTAAGTTCTACCAAACCTTGGTCA
1 CTAAGTTCTACCAAACCTTGGTCA
1094355 C
1 C
1094356 AGTGTACTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.31, G:0.12, T:0.29
Consensus pattern (24 bp):
CTAAGTTCTACCAAACCTTGGTCA
Found at i:1100022 original size:22 final size:22
Alignment explanation
Indices: 1099997--1100041 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1099987 TTTTATTAGG
*
1099997 TTATAAACATCCAAGAAAGACT
1 TTATAAACAACCAAGAAAGACT
*
1100019 TTATAAACAACCAAGCAAGACT
1 TTATAAACAACCAAGAAAGACT
1100041 T
1 T
1100042 AAATGATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.20, G:0.09, T:0.22
Consensus pattern (22 bp):
TTATAAACAACCAAGAAAGACT
Found at i:1100769 original size:23 final size:23
Alignment explanation
Indices: 1100739--1100786 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
1100729 AGGATGTCCC
1100739 AAAACTATTAATTATATTAATTT
1 AAAACTATTAATTATATTAATTT
1100762 AAAACTATTAATTATATTAATTT
1 AAAACTATTAATTATATTAATTT
1100785 AA
1 AA
1100787 GAGTTAGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (23 bp):
AAAACTATTAATTATATTAATTT
Found at i:1101020 original size:31 final size:31
Alignment explanation
Indices: 1100985--1101056 Score: 144
Period size: 31 Copynumber: 2.3 Consensus size: 31
1100975 ATTCTCGATT
1100985 AATTTGTTCAAAATTAGGTAAACAATTGGAA
1 AATTTGTTCAAAATTAGGTAAACAATTGGAA
1101016 AATTTGTTCAAAATTAGGTAAACAATTGGAA
1 AATTTGTTCAAAATTAGGTAAACAATTGGAA
1101047 AATTTGTTCA
1 AATTTGTTCA
1101057 TTAAGCTAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.43, C:0.07, G:0.15, T:0.35
Consensus pattern (31 bp):
AATTTGTTCAAAATTAGGTAAACAATTGGAA
Found at i:1102080 original size:24 final size:21
Alignment explanation
Indices: 1102031--1102081 Score: 59
Period size: 24 Copynumber: 2.3 Consensus size: 21
1102021 ATTTGAATAA
1102031 AAAT-TATTTTTATATTAATT
1 AAATATATTTTTATATTAATT
*
1102051 ATATATATTTTTATAATTAAAATT
1 AAATATATTTTTAT-ATT--AATT
1102075 AAATATA
1 AAATATA
1102082 AATATTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 3 0.12
21 9 0.36
22 3 0.12
24 10 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
AAATATATTTTTATATTAATT
Found at i:1102101 original size:28 final size:28
Alignment explanation
Indices: 1102034--1102101 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 28
1102024 TGAATAAAAA
* * *
1102034 TTAT-TTTTATATTAATTATATATATTT
1 TTATATTTTAAATTAAATATAAATATTT
* *
1102061 TTATAATTAAAATTAAATATAAATATTT
1 TTATATTTTAAATTAAATATAAATATTT
1102089 TTATATTTTAAAT
1 TTATATTTTAAAT
1102102 AATAATTTAA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
27 4 0.12
28 29 0.88
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
TTATATTTTAAATTAAATATAAATATTT
Found at i:1102343 original size:3 final size:3
Alignment explanation
Indices: 1102335--1102377 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
1102325 TCTCTGAACC
1102335 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1102378 CAAGAAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1102551 original size:2 final size:2
Alignment explanation
Indices: 1102493--1102532 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
1102483 TCACACATAC
* *
1102493 AT AT AT -T AT AT AT AT AT AT AT AT AT GT AT AT AT CT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1102533 CATACACATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1102645 original size:16 final size:16
Alignment explanation
Indices: 1102593--1102707 Score: 54
Period size: 16 Copynumber: 6.6 Consensus size: 16
1102583 TAATTATTAA
*
1102593 ATTTAATATTATAATTAT
1 ATTTAATAATAT-A-TAT
* *
1102611 ATTT-ATTATATATAG
1 ATTTAATAATATATAT
*
1102626 ATTTAATAATTTATAT
1 ATTTAATAATATATAT
*
1102642 ATTTATATTATAATTATAT
1 ATTTA-ATAAT-A-TATAT
1102661 ATTTTATCATAATATAATTAT
1 A-TTTA--ATAATAT-A-TAT
*
1102682 ATTTAA-AATATTTTAT
1 ATTTAATAATA-TATAT
1102698 ATTTATATAA
1 ATTTA-ATAA
1102708 AATTTTTTAA
Statistics
Matches: 75, Mismatches: 11, Indels: 22
0.69 0.10 0.20
Matches are distributed among these distances:
15 6 0.08
16 22 0.29
17 14 0.19
18 8 0.11
19 7 0.09
20 10 0.13
21 8 0.11
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (16 bp):
ATTTAATAATATATAT
Found at i:1102654 original size:20 final size:20
Alignment explanation
Indices: 1102587--1102673 Score: 69
Period size: 18 Copynumber: 4.5 Consensus size: 20
1102577 ATAAATTAAT
1102587 TATTA-AATTTA-ATA-TTA
1 TATTATAATTTATATATTTA
*
1102604 TAATTAT-ATTTATTATATATA
1 T-ATTATAATTTA-TATATTTA
*
1102625 GATTTAATAATTTATATATTTA
1 TA-TT-ATAATTTATATATTTA
1102647 TATTATAA-TTATATATTT-
1 TATTATAATTTATATATTTA
*
1102665 TATCATAAT
1 TATTATAAT
1102674 ATAATTATAT
Statistics
Matches: 56, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
17 1 0.02
18 16 0.29
19 10 0.18
20 8 0.14
21 6 0.11
22 10 0.18
23 5 0.09
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (20 bp):
TATTATAATTTATATATTTA
Found at i:1102676 original size:23 final size:21
Alignment explanation
Indices: 1102631--1102683 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 21
1102621 TATAGATTTA
1102631 ATAATT-TATATATTTATATT
1 ATAATTATATATATTTATATT
1102651 ATAATTATATAT-TTTATCATAAT
1 ATAATTATATATATTTAT-AT--T
1102674 ATAATTATAT
1 ATAATTATAT
1102684 TTAAAATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 11 0.38
21 7 0.24
23 11 0.38
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
ATAATTATATATATTTATATT
Found at i:1102686 original size:48 final size:49
Alignment explanation
Indices: 1102593--1102700 Score: 116
Period size: 48 Copynumber: 2.2 Consensus size: 49
1102583 TAATTATTAA
* *
1102593 ATTTAATATTATAATTATATTTATTATATATAGATTTAATAATTT-ATAT
1 ATTT-ATATTATAATTATATTTATTATATATAGAATTAATAATTTAAAAT
*
1102642 ATTTATATTATAATTATATATT-TTATCATAATATAATT-AT-ATTTAAAAT
1 ATTTATATTATAATTATAT-TTATTAT-AT-ATAGAATTAATAATTTAAAAT
1102691 ATTTTATATT
1 A-TTTATATT
1102701 TATATAAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
48 23 0.45
49 14 0.27
50 14 0.27
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.56
Consensus pattern (49 bp):
ATTTATATTATAATTATATTTATTATATATAGAATTAATAATTTAAAAT
Found at i:1102725 original size:18 final size:20
Alignment explanation
Indices: 1102673--1102725 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
1102663 TTTATCATAA
1102673 TATAATTATATTTAAAATATTT
1 TATAATTATA--TAAAATATTT
* *
1102695 TATATTTATATAAAATTTTT
1 TATAATTATATAAAATATTT
1102715 TA-AATTA-ATAA
1 TATAATTATATAA
1102726 TTCATATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 4 0.14
19 4 0.14
20 11 0.39
22 9 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TATAATTATATAAAATATTT
Found at i:1102814 original size:12 final size:14
Alignment explanation
Indices: 1102602--1102807 Score: 54
Period size: 15 Copynumber: 14.0 Consensus size: 14
1102592 AATTTAATAT
1102602 TATAATTATATTTA
1 TATAATTATATTTA
*
1102616 T-TATATATAGATTTA
1 TATA-AT-TATATTTA
1102631 -ATAATTTATATATT-
1 TATAA-TTATAT-TTA
*
1102645 TAT-ATTATAATTA
1 TATAATTATATTTA
* *
1102658 TAT-ATTTTATCATAA
1 TATAATTATAT--TTA
1102673 TATAATTATATTTAA
1 TATAATTATATTT-A
* *
1102688 AATATTTTATATTTA
1 TATA-ATTATATTTA
* *
1102703 TATAA-AAT-TTTT
1 TATAATTATATTTA
*
1102715 TA-AATTAATAATTCA
1 TATAATT-AT-ATTTA
*
1102730 TATTATATATATTTA
1 TATAAT-TATATTTA
*
1102745 -AAAATTATACTTATA
1 TATAATTATA-TT-TA
*
1102760 CCATATATTAAATATTT-
1 -TATA-ATT--ATATTTA
1102777 TATACGTATTATATTTA
1 TATA---ATTATATTTA
1102794 TATAATTATATTTA
1 TATAATTATATTTA
1102808 AAATTATTAA
Statistics
Matches: 141, Mismatches: 23, Indels: 56
0.64 0.10 0.25
Matches are distributed among these distances:
11 2 0.01
12 7 0.05
13 23 0.16
14 25 0.18
15 37 0.26
16 27 0.19
17 7 0.05
18 8 0.06
19 2 0.01
20 3 0.02
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (14 bp):
TATAATTATATTTA
Found at i:1102965 original size:15 final size:14
Alignment explanation
Indices: 1102931--1102972 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
1102921 TTACTCAAAT
*
1102931 TTAATTTAAAT-AA
1 TTAAATTAAATAAA
1102944 TTAAATTAAATAAA
1 TTAAATTAAATAAA
*
1102958 TATAAATTATATAAA
1 T-TAAATTAAATAAA
1102973 AATTATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 10 0.40
14 3 0.12
15 12 0.48
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TTAAATTAAATAAA
Found at i:1103192 original size:2 final size:2
Alignment explanation
Indices: 1103185--1103222 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1103175 GGAAGTTGTG
1103185 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1103223 TTGCAAGCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1103387 original size:20 final size:20
Alignment explanation
Indices: 1103371--1103411 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1103361 TTTTTAATTT
1103371 TAAATATATTTTATTAAATA
1 TAAATATATTTTATTAAATA
**
1103391 TATTTATATTTTATTAAATA
1 TAAATATATTTTATTAAATA
1103411 T
1 T
1103412 TTTTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TAAATATATTTTATTAAATA
Found at i:1103389 original size:14 final size:15
Alignment explanation
Indices: 1103370--1103400 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1103360 TTTTTTAATT
1103370 TTAAATATATTT-TA
1 TTAAATATATTTATA
1103384 TTAAATATATTTATA
1 TTAAATATATTTATA
1103399 TT
1 TT
1103401 TTATTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTAAATATATTTATA
Found at i:1103423 original size:11 final size:12
Alignment explanation
Indices: 1103376--1103423 Score: 52
Period size: 11 Copynumber: 4.4 Consensus size: 12
1103366 AATTTTAAAT
1103376 ATATTTTATTAA
1 ATATTTTATTAA
*
1103388 ATA---TATT-T
1 ATATTTTATTAA
1103396 ATATTTTATTAA
1 ATATTTTATTAA
1103408 ATATTTT-TTAA
1 ATATTTTATTAA
1103419 ATATT
1 ATATT
1103424 AATTTAGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
8 3 0.10
9 4 0.13
11 13 0.43
12 10 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
ATATTTTATTAA
Found at i:1104728 original size:18 final size:19
Alignment explanation
Indices: 1104701--1104742 Score: 77
Period size: 18 Copynumber: 2.3 Consensus size: 19
1104691 TATGGACTAT
1104701 AATAGAATTAAAAGTATAA
1 AATAGAATTAAAAGTATAA
1104720 AATAG-ATTAAAAGTATAA
1 AATAGAATTAAAAGTATAA
1104738 AATAG
1 AATAG
1104743 GCCATTTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.26
Consensus pattern (19 bp):
AATAGAATTAAAAGTATAA
Found at i:1106286 original size:19 final size:20
Alignment explanation
Indices: 1106254--1106303 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
1106244 ATTTTAAATA
1106254 TTTTA-TAT-TTATATA-AT
1 TTTTAGTATATTATATAGAT
1106271 TTTTAGTATATTATATAGAT
1 TTTTAGTATATTATATAGAT
*
1106291 TTTAAGATATATT
1 TTTTAG-TATATT
1106304 CGTGCCATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 5 0.18
18 3 0.11
19 7 0.25
20 7 0.25
21 6 0.21
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (20 bp):
TTTTAGTATATTATATAGAT
Found at i:1106293 original size:45 final size:46
Alignment explanation
Indices: 1106211--1106300 Score: 107
Period size: 45 Copynumber: 2.0 Consensus size: 46
1106201 TATATTCATA
* *
1106211 TTATATTTATGTATTTTATCATATTATAATCATATTTTAA-ATATT
1 TTATATTTATATATTTTATCATATTATAATCAGATTTTAAGATATT
1106256 TTATATTTATATAATTTTTAGT-ATATTAT-AT-AGATTTTAAGATAT
1 TTATATTTATAT-A-TTTTA-TCATATTATAATCAGATTTTAAGATAT
1106301 ATTCGTGCCA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
45 19 0.49
46 7 0.18
47 12 0.31
48 1 0.03
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (46 bp):
TTATATTTATATATTTTATCATATTATAATCAGATTTTAAGATATT
Found at i:1106301 original size:21 final size:19
Alignment explanation
Indices: 1106257--1106303 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
1106247 TTAAATATTT
*
1106257 TATATTTATATAATTTTTAG
1 TATA-TTATATAATTTTAAG
1106277 TATATTATATAGATTTTAAG
1 TATATTATATA-ATTTTAAG
1106297 ATATATT
1 -TATATT
1106304 CGTGCCATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 7 0.29
20 11 0.46
21 6 0.25
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.55
Consensus pattern (19 bp):
TATATTATATAATTTTAAG
Found at i:1109216 original size:9 final size:9
Alignment explanation
Indices: 1109202--1109248 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
1109192 AAAATATTTT
*
1109202 TTTAATCAA
1 TTTAATTAA
1109211 TTTAATTAA
1 TTTAATTAA
* *
1109220 TTTTATAAA
1 TTTAATTAA
*
1109229 TTTATTTAA
1 TTTAATTAA
1109238 TTTAA-TAA
1 TTTAATTAA
1109246 TTT
1 TTT
1109249 TAAACCGAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
8 6 0.19
9 25 0.81
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (9 bp):
TTTAATTAA
Found at i:1109232 original size:18 final size:18
Alignment explanation
Indices: 1109202--1109251 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
1109192 AAAATATTTT
*
1109202 TTTAATCAATTTAATTAA
1 TTTAATAAATTTAATTAA
* *
1109220 TTTTATAAATTTATTTAA
1 TTTAATAAATTTAATTAA
*
1109238 TTTAATAATTTTAA
1 TTTAATAAATTTAA
1109252 ACCGAAAACC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTAATAAATTTAATTAA
Found at i:1114522 original size:42 final size:42
Alignment explanation
Indices: 1114428--1114512 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
1114418 TATTTTACAT
* * * * * *
1114428 TAATGTTATTAATTAAATTTTGATGTGATATTTAATATTTAA
1 TAATATTATTAAATAAATATTAATGTGATATTTAACATTCAA
1114470 TAATATTATTAAATAAATATTAATGTGATATTTAACATTCAA
1 TAATATTATTAAATAAATATTAATGTGATATTTAACATTCAA
1114512 T
1 T
1114513 TTGATTATTA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.48
Consensus pattern (42 bp):
TAATATTATTAAATAAATATTAATGTGATATTTAACATTCAA
Found at i:1114942 original size:16 final size:16
Alignment explanation
Indices: 1114890--1114955 Score: 59
Period size: 16 Copynumber: 4.2 Consensus size: 16
1114880 ATAAATGTTT
1114890 TAAAATTTATAT--TA
1 TAAAATTTATATAATA
1114904 TAAAA-TTAT-TAACATA
1 TAAAATTTATAT-A-ATA
1114920 TTAAAATTTATATAATA
1 -TAAAATTTATATAATA
* *
1114937 TAAAATATATAAAATA
1 TAAAATTTATATAATA
1114953 TAA
1 TAA
1114956 TTATAATATA
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
12 1 0.02
13 4 0.09
14 5 0.12
16 19 0.44
17 8 0.19
18 5 0.12
19 1 0.02
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (16 bp):
TAAAATTTATATAATA
Found at i:1114948 original size:9 final size:9
Alignment explanation
Indices: 1114934--1114984 Score: 59
Period size: 9 Copynumber: 5.4 Consensus size: 9
1114924 AATTTATATA
1114934 ATATAAAAT
1 ATATAAAAT
1114943 ATATAAAAT
1 ATATAAAAT
*
1114952 ATAATTATAAT
1 AT-A-TAAAAT
1114963 ATAATAAAAT
1 AT-ATAAAAT
1114973 ATAT-AAAT
1 ATATAAAAT
1114981 ATAT
1 ATAT
1114985 GTACAAATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
8 8 0.21
9 13 0.34
10 8 0.21
11 9 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
ATATAAAAT
Found at i:1114953 original size:21 final size:21
Alignment explanation
Indices: 1114929--1114975 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
1114919 ATTAAAATTT
1114929 ATATAATATAAAATAT-ATAAA
1 ATATAAT-TAAAATATAATAAA
*
1114950 ATATAATTATAATATAATAAA
1 ATATAATTAAAATATAATAAA
1114971 ATATA
1 ATATA
1114976 TAAATATATG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
ATATAATTAAAATATAATAAA
Found at i:1115122 original size:14 final size:14
Alignment explanation
Indices: 1115093--1115136 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
1115083 ATTAAATATG
*
1115093 ATAATAT-ATAAAT
1 ATAATATGATTAAT
1115106 ATAATATGATTAAT
1 ATAATATGATTAAT
*
1115120 ATAATATGTTTAAT
1 ATAATATGATTAAT
1115134 ATA
1 ATA
1115137 TATTTGTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
13 7 0.25
14 21 0.75
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (14 bp):
ATAATATGATTAAT
Found at i:1115337 original size:19 final size:19
Alignment explanation
Indices: 1115309--1115395 Score: 63
Period size: 19 Copynumber: 4.6 Consensus size: 19
1115299 TAGATATGCT
*
1115309 TATAACTATAA-AAAAATAA
1 TATAAATATAATAAAAAT-A
*
1115328 TATAAATATAATATAAATA
1 TATAAATATAATAAAAATA
** *
1115347 TATAAATATTTTAAAATTA
1 TATAAATATAATAAAAATA
* *
1115366 -ATTAATGT-ATAAAAATTTA
1 TATAAATATAATAAAAA--TA
1115385 TATAAATATAA
1 TATAAATATAA
1115396 AATAATTTAG
Statistics
Matches: 51, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
17 5 0.10
18 6 0.12
19 28 0.55
20 11 0.22
21 1 0.02
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (19 bp):
TATAAATATAATAAAAATA
Found at i:1115340 original size:11 final size:11
Alignment explanation
Indices: 1115324--1115348 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1115314 CTATAAAAAA
1115324 ATAATATAAAT
1 ATAATATAAAT
1115335 ATAATATAAAT
1 ATAATATAAAT
1115346 ATA
1 ATA
1115349 TAAATATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:1115367 original size:28 final size:27
Alignment explanation
Indices: 1115331--1115395 Score: 69
Period size: 26 Copynumber: 2.3 Consensus size: 27
1115321 AAAATAATAT
*
1115331 AAATATAATATAAATATATAAATATTTTA
1 AAATATAAT-T-AATATATAAAAATTTTA
*
1115360 AAAT-TAATTAATGTATAAAAATTTATA
1 AAATATAATTAATATATAAAAATTT-TA
1115387 TAAATATAA
1 -AAATATAA
1115396 AATAATTTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
26 13 0.42
27 3 0.10
28 8 0.26
29 7 0.23
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (27 bp):
AAATATAATTAATATATAAAAATTTTA
Found at i:1119931 original size:18 final size:17
Alignment explanation
Indices: 1119897--1119950 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
1119887 TGTTTAAGAT
1119897 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
1119914 ATTTTGATATGTTA-AT-A
1 ATTTT-ATAT-TTATATAA
*
1119931 A-TTTATA-TTATATAG
1 ATTTTATATTTATATAA
1119946 ATTTT
1 ATTTT
1119951 GATACATACA
Statistics
Matches: 31, Mismatches: 1, Indels: 11
0.72 0.02 0.26
Matches are distributed among these distances:
13 3 0.10
14 2 0.06
15 4 0.13
16 6 0.19
17 7 0.23
18 6 0.19
19 3 0.10
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:1120139 original size:14 final size:14
Alignment explanation
Indices: 1120120--1120146 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1120110 TTTTAATTAT
1120120 AAAAATAATATAAC
1 AAAAATAATATAAC
1120134 AAAAATAATATAA
1 AAAAATAATATAA
1120147 TACATTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAAATAATATAAC
Found at i:1121948 original size:12 final size:12
Alignment explanation
Indices: 1121933--1121963 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
1121923 TATTATTATT
1121933 ATTATTATTGGA
1 ATTATTATTGGA
1121945 ATTATTATTGGA
1 ATTATTATTGGA
1121957 ATTATTA
1 ATTATTA
1121964 GGCATTATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (12 bp):
ATTATTATTGGA
Found at i:1121953 original size:3 final size:3
Alignment explanation
Indices: 1121909--1121941 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1121899 TATCTTCACA
1121909 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1121942 GGAATTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1123501 original size:11 final size:11
Alignment explanation
Indices: 1123464--1123530 Score: 56
Period size: 11 Copynumber: 6.5 Consensus size: 11
1123454 ATTAAAATTT
1123464 ATATAAATATAA
1 ATAT-AATATAA
* *
1123476 A-ATATTTTAA
1 ATATAATATAA
1123486 ATATAAT-TATA
1 ATATAATATA-A
1123497 ATAT-A-ATAA
1 ATATAATATAA
1123506 A-AT-ATATAA
1 ATATAATATAA
1123515 ATATAATATAA
1 ATATAATATAA
1123526 ATATA
1 ATATA
1123531 CAAATTATAA
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
8 3 0.07
9 7 0.15
10 13 0.28
11 22 0.48
12 1 0.02
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
ATATAATATAA
Found at i:1123872 original size:12 final size:12
Alignment explanation
Indices: 1123855--1123879 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1123845 CTTAAAATTG
1123855 TCTTTTTTTTTT
1 TCTTTTTTTTTT
1123867 TCTTTTTTTTTT
1 TCTTTTTTTTTT
1123879 T
1 T
1123880 GAAAATTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TCTTTTTTTTTT
Found at i:1124356 original size:49 final size:50
Alignment explanation
Indices: 1124265--1124362 Score: 130
Period size: 49 Copynumber: 2.0 Consensus size: 50
1124255 AAATATAAGT
1124265 ATTTTTAAGTAAAAAAATAGTTATTTTTTTTAAAAAATAAAAA-AAGTAA
1 ATTTTTAAGTAAAAAAATAGTTATTTTTTTTAAAAAATAAAAATAAGTAA
* **
1124314 ATTTTTAAG-AAAAAAATAGGTTTTTCTTTTTTTTAAAA-AAAAATAAGTA
1 ATTTTTAAGTAAAAAAATA-GTTATT-TTTTTTAAAAAATAAAAATAAGTA
1124363 GTTAATTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
48 9 0.21
49 19 0.44
50 15 0.35
ACGTcount: A:0.51, C:0.01, G:0.07, T:0.41
Consensus pattern (50 bp):
ATTTTTAAGTAAAAAAATAGTTATTTTTTTTAAAAAATAAAAATAAGTAA
Found at i:1124371 original size:27 final size:25
Alignment explanation
Indices: 1124266--1124373 Score: 60
Period size: 25 Copynumber: 4.2 Consensus size: 25
1124256 AATATAAGTA
** *
1124266 TTTTTAAGTAAAAAAATAGTTATTT
1 TTTTTAAAAAAAAAAATAGTTAATT
* *
1124291 TTTTTAAAAAATAAAAAAAG-TAA-A
1 TTTTTAAAAAA-AAAAATAGTTAATT
* **
1124315 TTTTT-AAGAAAAAAATAGGTTTTTCTTT
1 TTTTTAAAAAAAAAAATA-G---TTAATT
1124343 TTTTTAAAAAAAAATAAGTAGTTAATT
1 TTTTTAAAAAAAAA-AA-TAGTTAATT
1124370 TTTT
1 TTTT
1124374 AGTTTTAAGT
Statistics
Matches: 60, Mismatches: 13, Indels: 18
0.66 0.14 0.20
Matches are distributed among these distances:
22 6 0.10
23 5 0.08
24 5 0.08
25 11 0.18
26 7 0.12
27 9 0.15
28 5 0.08
29 7 0.12
30 3 0.05
31 2 0.03
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.44
Consensus pattern (25 bp):
TTTTTAAAAAAAAAAATAGTTAATT
Found at i:1124888 original size:3 final size:3
Alignment explanation
Indices: 1124880--1124906 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1124870 GCTAATAACC
1124880 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1124907 CATTATTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1125712 original size:2 final size:2
Alignment explanation
Indices: 1125705--1125733 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1125695 TAATTTTATC
1125705 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1125734 AGATCGAATG
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1126186 original size:20 final size:20
Alignment explanation
Indices: 1126137--1126188 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
1126127 ATTATTTATC
*
1126137 ATTATT-TTTAAAAATTTAA
1 ATTATTATTTAATAATTTAA
* *
1126156 ATT-TAATTTAATGATTTAA
1 ATTATTATTTAATAATTTAA
1126175 ATTATTATTTAATA
1 ATTATTATTTAATA
1126189 TAATTAATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 1 0.04
19 17 0.65
20 8 0.31
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
ATTATTATTTAATAATTTAA
Found at i:1126230 original size:20 final size:19
Alignment explanation
Indices: 1126172--1126230 Score: 56
Period size: 20 Copynumber: 3.3 Consensus size: 19
1126162 TTTAATGATT
1126172 TAAATTATTA-TTTAAT-A
1 TAAATTATTATTTTAATAA
1126189 T-AATTA--ATTTTAAATAA
1 TAAATTATTATTTT-AATAA
*
1126206 AAAATTATTATTTTAATTAA
1 TAAATTATTATTTTAA-TAA
1126226 TAAAT
1 TAAAT
1126231 AATAATTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 11
0.72 0.04 0.24
Matches are distributed among these distances:
14 1 0.03
15 3 0.09
16 8 0.24
17 2 0.06
18 5 0.15
19 2 0.06
20 12 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TAAATTATTATTTTAATAA
Found at i:1126241 original size:34 final size:34
Alignment explanation
Indices: 1126173--1126241 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
1126163 TTAATGATTT
* **
1126173 AAATTATTATTTAATATAATTAATTTTAAATAAA
1 AAATTATTATTTAATATAATAAATAATAAATAAA
*
1126207 AAATTATTATTTTAAT-TAATAAATAATAATTAAA
1 AAATTATTA-TTTAATATAATAAATAATAAATAAA
1126241 A
1 A
1126242 TATAAATTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 24 0.80
35 6 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (34 bp):
AAATTATTATTTAATATAATAAATAATAAATAAA
Found at i:1127480 original size:24 final size:24
Alignment explanation
Indices: 1127453--1127506 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1127443 TATTTTTATT
1127453 TAAATATAATTATAAATATTAATA
1 TAAATATAATTATAAATATTAATA
* * * * *
1127477 TAAAAATAATTTTTAATATTATTT
1 TAAATATAATTATAAATATTAATA
1127501 TAAATA
1 TAAATA
1127507 ATAAAACGGG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TAAATATAATTATAAATATTAATA
Found at i:1134375 original size:2 final size:2
Alignment explanation
Indices: 1134368--1134412 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1134358 ATAACAGCAA
1134368 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1134410 AT A
1 AT A
1134413 ACCAAAGTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1135379 original size:19 final size:21
Alignment explanation
Indices: 1135340--1135381 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
1135330 ATAAAATACG
*
1135340 CATAACACATATTAATTATGT
1 CATAACACATATTAATCATGT
1135361 CATAA-ACATA-TAATCATGT
1 CATAACACATATTAATCATGT
1135380 CA
1 CA
1135382 CATCTATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 10 0.50
20 5 0.25
21 5 0.25
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (21 bp):
CATAACACATATTAATCATGT
Found at i:1137259 original size:43 final size:42
Alignment explanation
Indices: 1137182--1137262 Score: 101
Period size: 43 Copynumber: 1.9 Consensus size: 42
1137172 TATATGCTAC
* *
1137182 AAAAGTCACATCAATTTTTGCTATAAAATTTGATTTTATTAT
1 AAAACTCACATCAATTTTTGCTATAAAATATGATTTTATTAT
* *
1137224 AAAACTCACATCAACTTTTT-TTAATAGAATATGATTTTA
1 AAAACTCACATCAA-TTTTTGCT-ATAAAATATGATTTTA
1137263 GTACAGCGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
42 14 0.42
43 19 0.58
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (42 bp):
AAAACTCACATCAATTTTTGCTATAAAATATGATTTTATTAT
Found at i:1137524 original size:16 final size:16
Alignment explanation
Indices: 1137503--1137569 Score: 82
Period size: 16 Copynumber: 4.2 Consensus size: 16
1137493 TGGTTTCAAG
**
1137503 TTATTTTACGTTTAAA
1 TTATTTTAAATTTAAA
*
1137519 TTATTTTAAA-TTATAG
1 TTATTTTAAATTTA-AA
*
1137535 TTATTTTAATTTTAAA
1 TTATTTTAAATTTAAA
1137551 TTATTTTAAATTTAAA
1 TTATTTTAAATTTAAA
1137567 TTA
1 TTA
1137570 ATCAAATTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
15 3 0.07
16 37 0.86
17 3 0.07
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.58
Consensus pattern (16 bp):
TTATTTTAAATTTAAA
Found at i:1137528 original size:10 final size:10
Alignment explanation
Indices: 1137513--1137562 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
1137503 TTATTTTACG
1137513 TTTAAATTAT
1 TTTAAATTAT
1137523 TTTAAATTAT
1 TTTAAATTAT
* **
1137533 AGTTATTTTAAT
1 -TTTAAATT-AT
1137545 TTTAAATTAT
1 TTTAAATTAT
1137555 TTTAAATT
1 TTTAAATT
1137563 TAAATTAATC
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
10 20 0.62
11 10 0.31
12 2 0.06
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (10 bp):
TTTAAATTAT
Found at i:1137537 original size:32 final size:32
Alignment explanation
Indices: 1137501--1137562 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
1137491 TTTGGTTTCA
*
1137501 AGTTATTTTACGTTTAAATTATTTTAAATTAT
1 AGTTATTTTAAGTTTAAATTATTTTAAATTAT
*
1137533 AGTTATTTTAATTTTAAATTATTTTAAATT
1 AGTTATTTTAAGTTTAAATTATTTTAAATT
1137563 TAAATTAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (32 bp):
AGTTATTTTAAGTTTAAATTATTTTAAATTAT
Found at i:1137578 original size:32 final size:32
Alignment explanation
Indices: 1137513--1137578 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
1137503 TTATTTTACG
* * **
1137513 TTTAAATTATTTTAAATTATAGTTATTTTAAT
1 TTTAAATTATTTTAAATTATAATTAATCAAAT
1137545 TTTAAATTATTTTAAATT-TAAATTAATCAAAT
1 TTTAAATTATTTTAAATTAT-AATTAATCAAAT
1137577 TT
1 TT
1137579 AATATTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 1 0.03
32 28 0.97
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (32 bp):
TTTAAATTATTTTAAATTATAATTAATCAAAT
Found at i:1137629 original size:16 final size:15
Alignment explanation
Indices: 1137598--1137632 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1137588 ATTAATTGAG
1137598 TTTAAGTTAATTAAT
1 TTTAAGTTAATTAAT
*
1137613 TTTAGGTTAATTTAAT
1 TTTAAGTTAA-TTAAT
1137629 TTTA
1 TTTA
1137633 TATTCAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (15 bp):
TTTAAGTTAATTAAT
Found at i:1137730 original size:15 final size:15
Alignment explanation
Indices: 1137712--1137761 Score: 64
Period size: 15 Copynumber: 3.2 Consensus size: 15
1137702 AATTCAGATA
*
1137712 ATTTAAATTAAAATT
1 ATTTAAATTTAAATT
1137727 ATTTTAAATTTTAAATT
1 A-TTTAAA-TTTAAATT
*
1137744 ATTTAATTTTAAATT
1 ATTTAAATTTAAATT
1137759 ATT
1 ATT
1137762 AACTTATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 12 0.39
16 11 0.35
17 8 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTTAAATTTAAATT
Found at i:1137734 original size:16 final size:16
Alignment explanation
Indices: 1137713--1137761 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
1137703 ATTCAGATAA
*
1137713 TTTAAATTAAAATTAT
1 TTTAAATTTAAATTAT
1137729 TTTAAATTTTAAATTA-
1 TTTAAA-TTTAAATTAT
*
1137745 TTTAATTTTAAATTAT
1 TTTAAATTTAAATTAT
1137761 T
1 T
1137762 AACTTATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 9 0.31
16 12 0.41
17 8 0.28
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTAAATTTAAATTAT
Done.