Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 12 of 345
Found at i:4140540 original size:75 final size:75
Alignment explanation
Indices: 4140421--4140591 Score: 221
Period size: 75 Copynumber: 2.4 Consensus size: 75
4140411 CATGGCAAAG
** *
4140421 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
*
4140480 CCATACTGAGC
65 CCATACCGAGC
4140491 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
4140556 CATACCGAGT
66 CATACCGAGC
**
4140566 TGAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
4140592 TGAGGAAAAC
Statistics
Matches: 88, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
70 18 0.20
73 4 0.05
74 5 0.06
75 61 0.69
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:4147945 original size:35 final size:35
Alignment explanation
Indices: 4147918--4148083 Score: 172
Period size: 35 Copynumber: 4.6 Consensus size: 35
4147908 CATGGCAAAG
*
4147918 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
4147953 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
4147988 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGC
** * * * *
4148028 TAAGAAATGTAGGTATGGCAT-TTCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATCAT-CCATACTGAGC
**
4148063 TGAAAAATGTAGGTATGGTAT
1 TGTGAAATGTAGGTATGGTAT
4148084 TTCAATGAGG
Statistics
Matches: 113, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
34 1 0.01
35 79 0.70
37 2 0.02
38 3 0.03
40 28 0.25
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
Found at i:4148037 original size:75 final size:75
Alignment explanation
Indices: 4147918--4148088 Score: 221
Period size: 75 Copynumber: 2.4 Consensus size: 75
4147908 CATGGCAAAG
** *
4147918 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
*
4147977 CCATACTGAGC
65 CCATACCGAGC
4147988 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
4148053 CATACCGAGT
66 CATACCGAGC
**
4148063 TGAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
4148089 TGAGGAAAAC
Statistics
Matches: 88, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
70 18 0.20
73 4 0.05
74 5 0.06
75 61 0.69
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:4154188 original size:12 final size:11
Alignment explanation
Indices: 4154149--4154184 Score: 56
Period size: 12 Copynumber: 3.3 Consensus size: 11
4154139 ATGACTAATG
4154149 ATAT-TAAAAT
1 ATATATAAAAT
4154159 ATATATAATAAT
1 ATATATAA-AAT
4154171 ATATATAAAAT
1 ATATATAAAAT
4154182 ATA
1 ATA
4154185 ATATTAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.17
11 9 0.38
12 11 0.46
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
ATATATAAAAT
Found at i:4154401 original size:13 final size:13
Alignment explanation
Indices: 4154383--4154407 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4154373 ATGTACGAAT
4154383 ATATACATATATA
1 ATATACATATATA
4154396 ATATACATATAT
1 ATATACATATAT
4154408 TATTATTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATACATATATA
Found at i:4154513 original size:12 final size:12
Alignment explanation
Indices: 4154475--4154514 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
4154465 TGAAAATAAT
4154475 TAAT-ATATTAA
1 TAATAATATTAA
* *
4154486 TAAAAATACTAA
1 TAATAATATTAA
4154498 TAATAATATTAA
1 TAATAATATTAA
4154510 TAATA
1 TAATA
4154515 TGTAAAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
11 3 0.12
12 21 0.88
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (12 bp):
TAATAATATTAA
Found at i:4155649 original size:16 final size:16
Alignment explanation
Indices: 4155628--4155659 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4155618 TTTTGTGTAA
*
4155628 TGGGCTGTTAGTTTAG
1 TGGGCTGGTAGTTTAG
4155644 TGGGCTGGTAGTTTAG
1 TGGGCTGGTAGTTTAG
4155660 GTTATTGGGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.06, G:0.41, T:0.41
Consensus pattern (16 bp):
TGGGCTGGTAGTTTAG
Found at i:4156645 original size:71 final size:71
Alignment explanation
Indices: 4156554--4156945 Score: 507
Period size: 74 Copynumber: 5.5 Consensus size: 71
4156544 ATTAAAAGGT
* * *
4156554 TCAACCCACCTCTCGTAATATGAGTTGATTTTTGAAACATAAATTGAAATTACCTCAACGTGTCT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAACATAAATTGAAATTACCTCAACGTGTCC
4156619 TGAGGC
66 TGAGGC
** ** * * * *
4156625 TCAACTCACCTCTCGCAATATGAGTTGATGAACTAAAAAGCAGAAATTGAAAATACCTCAGCGTA
1 TCAACTCACCTCTCGCAATATGAGTTGAT--TTTTGAAA-CATAAATTGAAATTACCTCAACGTG
*
4156690 CCCTGAGGC
63 TCCTGAGGC
* *
4156699 TCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAACATAAATTGAAATTACCTCAACGTGTCT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAACATAAATTGAAATTACCTCAACGTGTCC
4156764 TGAGGC
66 TGAGGC
** ** * * *
4156770 TCAACTCACCTCTCGCAATATGAGTTGATGAACTAAAAAGCAGAAATTGAAAATACCTCAGCGTG
1 TCAACTCACCTCTCGCAATATGAGTTGAT--TTTTGAAA-CATAAATTGAAATTACCTCAACGTG
*
4156835 CCCTGAGGC
63 TCCTGAGGC
*
4156844 TCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAACATAAATTGAAATTACCTCAACGTGT-C
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAACATAAATTGAAATTACCTCAACGTGTCC
4156908 TGAGGC
66 TGAGGC
*
4156914 TCAACTCACCTCTCGCAATATGAGCTGATTTT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTT
4156946 CTTGGAAAAC
Statistics
Matches: 271, Mismatches: 44, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
70 37 0.14
71 105 0.39
72 8 0.03
73 8 0.03
74 113 0.42
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.29
Consensus pattern (71 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAACATAAATTGAAATTACCTCAACGTGTCC
TGAGGC
Found at i:4156700 original size:74 final size:71
Alignment explanation
Indices: 4156554--4157101 Score: 513
Period size: 71 Copynumber: 7.4 Consensus size: 71
4156544 ATTAAAAGGT
* * ** ** * * *
4156554 TCAACCCACCTCTCGTAATATGAGTTGATTTTTGAAACATAAATTGAAATTACCTCAACGTGTCT
1 TCAACTCACCTCTCGCAATATGAGTTGATACTAAAAACAGAAATTGAAATTACCTCAACGTGCCC
4156619 TGAGGC
66 TGAGGC
* * *
4156625 TCAACTCACCTCTCGCAATATGAGTTGATGAACTAAAAAGCAGAAATTGAAAATACCTCAGCGTA
1 TCAACTCACCTCTCGCAATATGAGTTGAT--ACTAAAAA-CAGAAATTGAAATTACCTCAACGTG
4156690 CCCTGAGGC
63 CCCTGAGGC
* ** ** * * *
4156699 TCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAACATAAATTGAAATTACCTCAACGTGTCT
1 TCAACTCACCTCTCGCAATATGAGTTGATACTAAAAACAGAAATTGAAATTACCTCAACGTGCCC
4156764 TGAGGC
66 TGAGGC
* *
4156770 TCAACTCACCTCTCGCAATATGAGTTGATGAACTAAAAAGCAGAAATTGAAAATACCTCAGCGTG
1 TCAACTCACCTCTCGCAATATGAGTTGAT--ACTAAAAA-CAGAAATTGAAATTACCTCAACGTG
4156835 CCCTGAGGC
63 CCCTGAGGC
* ** ** * *
4156844 TCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAACATAAATTGAAATTACCTCAACGTG-TC
1 TCAACTCACCTCTCGCAATATGAGTTGATACTAAAAACAGAAATTGAAATTACCTCAACGTGCCC
4156908 TGAGGC
66 TGAGGC
*
4156914 TCAACTCACCTCTCGCAATATGAGCTGATTTTCTTGGAAAACATGAATTAAAAGCAGAAATTGAA
1 TCAACTCACCTCTCGCAATATGA---G------TT-G-ATAC-T--A--AAAA-CAGAAATTGAA
* *
4156979 AATACCTCAGCGTGCCCTGAGGC
49 ATTACCTCAACGTGCCCTGAGGC
* ** ** * * *
4157002 TCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAACATAAATTGAAATTACCTCAACGTGTCT
1 TCAACTCACCTCTCGCAATATGAGTTGATACTAAAAACAGAAATTGAAATTACCTCAACGTGCCC
4157067 TGAGGC
66 TGAGGC
*
4157073 TCAACTCACCTCTCGCAATATGAGCTGAT
1 TCAACTCACCTCTCGCAATATGAGTTGAT
4157102 TTTCTTGGAA
Statistics
Matches: 388, Mismatches: 65, Indels: 48
0.77 0.13 0.10
Matches are distributed among these distances:
70 29 0.07
71 161 0.41
72 11 0.03
73 9 0.02
74 113 0.29
76 1 0.00
77 1 0.00
78 1 0.00
79 4 0.01
80 1 0.00
81 1 0.00
82 1 0.00
85 1 0.00
86 3 0.01
87 22 0.06
88 29 0.07
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (71 bp):
TCAACTCACCTCTCGCAATATGAGTTGATACTAAAAACAGAAATTGAAATTACCTCAACGTGCCC
TGAGGC
Found at i:4156817 original size:145 final size:151
Alignment explanation
Indices: 4156554--4157193 Score: 975
Period size: 145 Copynumber: 4.2 Consensus size: 151
4156544 ATTAAAAGGT
* * *
4156554 TCAACCCACCTCTCGTAATATGAGTTGATTTTTGAAACATAAATTGAAATTACCTCAACGTGTCT
1 TCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAACATAAATTGAAATTACCTCAACGTGTCT
*
4156619 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-T-G-AAC-T-A-AAAAGCAGAAATTGAAAA
66 TGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTGGAAACATAATAAAAGCAGAAATTGAAAA
*
4156678 TACCTCAGCGTACCCTGAGGC
131 TACCTCAGCGTGCCCTGAGGC
4156699 TCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAACATAAATTGAAATTACCTCAACGTGTCT
1 TCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAACATAAATTGAAATTACCTCAACGTGTCT
*
4156764 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-T-G-AAC-T-A-AAAAGCAGAAATTGAAAA
66 TGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTGGAAACATAATAAAAGCAGAAATTGAAAA
4156823 TACCTCAGCGTGCCCTGAGGC
131 TACCTCAGCGTGCCCTGAGGC
4156844 TCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAACATAAATTGAAATTACCTCAACGTGTC-
1 TCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAACATAAATTGAAATTACCTCAACGTGTCT
4156908 TGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTCTTGGAAAACATGAATTAAAAGCAGAA
66 TGAGGCTCAACTCACCTCTCGCAATATGAGCTGA-----TTGG-AAACAT-AA-TAAAAGCAGAA
4156973 ATTGAAAATACCTCAGCGTGCCCTGAGGC
123 ATTGAAAATACCTCAGCGTGCCCTGAGGC
4157002 TCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAACATAAATTGAAATTACCTCAACGTGTCT
1 TCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAACATAAATTGAAATTACCTCAACGTGTCT
4157067 TGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTCTTGGAAAACATGAATTAAAAGCAGAA
66 TGAGGCTCAACTCACCTCTCGCAATATGAGCTGA-----TTGG-AAACAT-AA-TAAAAGCAGAA
4157132 ATTGAAAATACCTCAGCGTGCCCTGAGGC
123 ATTGAAAATACCTCAGCGTGCCCTGAGGC
*
4157161 TCAACTCACTTCT-GCGATATGAGTTGATTTTTG
1 TCAACTCACTTCTCGCAATATGAGTTGATTTTTG
4157194 GAAAAAACAA
Statistics
Matches: 474, Mismatches: 6, Indels: 17
0.95 0.01 0.03
Matches are distributed among these distances:
144 33 0.07
145 205 0.43
150 1 0.00
151 1 0.00
153 3 0.01
154 1 0.00
156 1 0.00
158 122 0.26
159 107 0.23
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.29
Consensus pattern (151 bp):
TCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAACATAAATTGAAATTACCTCAACGTGTCT
TGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTGGAAACATAATAAAAGCAGAAATTGAAAA
TACCTCAGCGTGCCCTGAGGC
Found at i:4157181 original size:158 final size:158
Alignment explanation
Indices: 4156805--4157193 Score: 753
Period size: 158 Copynumber: 2.5 Consensus size: 158
4156795 TGATGAACTA
4156805 AAAAGCAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGAGTT
1 AAAAGCAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGAGTT
4156870 GATTTTTGAAACATAAATTGAAATTACCTCAACGTGTCTGAGGCTCAACTCACCTCTCGCAATAT
66 GATTTTTGAAACATAAATTGAAATTACCTCAACGTGTCTGAGGCTCAACTCACCTCTCGCAATAT
4156935 GAGCTGATTTTCTTGGAAAACATGAATT
131 GAGCTGATTTTCTTGGAAAACATGAATT
4156963 AAAAGCAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGAGTT
1 AAAAGCAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGAGTT
4157028 GATTTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATA
66 GATTTTTGAAACATAAATTGAAATTACCTCAACGTGTC-TGAGGCTCAACTCACCTCTCGCAATA
4157093 TGAGCTGATTTTCTTGGAAAACATGAATT
130 TGAGCTGATTTTCTTGGAAAACATGAATT
*
4157122 AAAAGCAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCT-GCGATATGAGTT
1 AAAAGCAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGAGTT
4157186 GATTTTTG
66 GATTTTTG
4157194 GAAAAAACAA
Statistics
Matches: 229, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
158 122 0.53
159 107 0.47
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (158 bp):
AAAAGCAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGAGTT
GATTTTTGAAACATAAATTGAAATTACCTCAACGTGTCTGAGGCTCAACTCACCTCTCGCAATAT
GAGCTGATTTTCTTGGAAAACATGAATT
Found at i:4169662 original size:2 final size:2
Alignment explanation
Indices: 4169655--4169689 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
4169645 ATAATGTTAG
* *
4169655 AT AT AT AT AT AT AT AT AG AT AT AT AT CT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4169690 ATAGTATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:4169757 original size:12 final size:11
Alignment explanation
Indices: 4169718--4169753 Score: 56
Period size: 12 Copynumber: 3.3 Consensus size: 11
4169708 ATGACTAATG
4169718 ATAT-TAAAAT
1 ATATATAAAAT
4169728 ATATATAATAAT
1 ATATATAA-AAT
4169740 ATATATAAAAT
1 ATATATAAAAT
4169751 ATA
1 ATA
4169754 ATATTAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.17
11 9 0.38
12 11 0.46
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
ATATATAAAAT
Found at i:4169970 original size:13 final size:13
Alignment explanation
Indices: 4169952--4169976 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4169942 ATGTACGAAT
4169952 ATATACATATATA
1 ATATACATATATA
4169965 ATATACATATAT
1 ATATACATATAT
4169977 TATTATTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATACATATATA
Found at i:4170082 original size:12 final size:12
Alignment explanation
Indices: 4170044--4170083 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
4170034 TGAAAATAAT
4170044 TAAT-ATATTAA
1 TAATAATATTAA
* *
4170055 TAAAAATACTAA
1 TAATAATATTAA
4170067 TAATAATATTAA
1 TAATAATATTAA
4170079 TAATA
1 TAATA
4170084 TGTAAAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
11 3 0.12
12 21 0.88
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (12 bp):
TAATAATATTAA
Found at i:4171223 original size:16 final size:16
Alignment explanation
Indices: 4171202--4171233 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4171192 TTTTATGTAA
*
4171202 TGGGCTGTTAGTTTAG
1 TGGGCTGGTAGTTTAG
4171218 TGGGCTGGTAGTTTAG
1 TGGGCTGGTAGTTTAG
4171234 GTTATTGGGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.06, G:0.41, T:0.41
Consensus pattern (16 bp):
TGGGCTGGTAGTTTAG
Found at i:4172143 original size:17 final size:17
Alignment explanation
Indices: 4172121--4172158 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
4172111 TATTTATATA
* *
4172121 TTAATATATTTGTTATC
1 TTAATAGATTTCTTATC
4172138 TTAATAGATTTCTTATC
1 TTAATAGATTTCTTATC
4172155 TTAA
1 TTAA
4172159 AATACTTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.55
Consensus pattern (17 bp):
TTAATAGATTTCTTATC
Found at i:4172679 original size:130 final size:130
Alignment explanation
Indices: 4172513--4172884 Score: 449
Period size: 130 Copynumber: 2.9 Consensus size: 130
4172503 AAAATTCTTC
4172513 AAAACGAAGACGAAATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
1 AAAACGAAGACGAAATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
* * * * *
4172578 TTTCGCATTTGCTCAAAATAATTGAATTTCCCTTCGAAATTCCATTCATATCTTTTAAAATCCCT
66 TTTCGCATTTGCTCAAAATAATCGAATATCACTTCAAAATTCCACTCATATCTTTTAAAATCCCT
* * * * *
4172643 TAAACGAAGATGAGATTTGATGTTTGGTAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCGA
1 AAAACGAAGACGAAATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
* * * * *
4172708 TTTCGCATTTGCTCAAAATAATCGAATATCACTTTAAAATTTCGCTCGTGTCTTTTAAAATCCCT
66 TTTCGCATTTGCTCAAAATAATCGAATATCACTTCAAAATTCCACTCATATCTTTTAAAATCCCT
* * * * * * * * *
4172773 AAAACGAAGGCGATATCTGGTATTTGGCAATTCGTGGGATCGTGCCCTAATGTGTTGGGTAGCAA
1 AAAACGAAGACGAAATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
* * * * * * *
4172838 TTTCTCGA-TTGTTTAAAATAATCAAATACCCCTTCAAAATTTCACTC
66 TTTCGC-ATTTGCTCAAAATAATCGAATATCACTTCAAAATTCCACTC
4172885 GGCTCTTCTA
Statistics
Matches: 205, Mismatches: 36, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
130 204 1.00
131 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (130 bp):
AAAACGAAGACGAAATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
TTTCGCATTTGCTCAAAATAATCGAATATCACTTCAAAATTCCACTCATATCTTTTAAAATCCCT
Found at i:4172973 original size:131 final size:130
Alignment explanation
Indices: 4172540--4172991 Score: 335
Period size: 130 Copynumber: 3.5 Consensus size: 130
4172530 TGATGTTTGG
* * * * *
4172540 CAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAATTTCGC-ATTTGCTCAAAATAATTGAA
1 CAATTCGCGGAATCGTGCCCTATCGTGTTGGGTTGCGATTTCTCGA-TTGTTCAAAATAA-TCAA
* * * * * * * * * *** * * * * *
4172604 TTTCC-CTTCGAAATTCCATTCATATCTTTTAAAATCCCTTAAACGAAGATGAGATTTGATGTTT
64 ATACCACTTCAAAATTTCACTCGTGTCTTTAAAAATCCCTAAAACGAAGGCAATATCTGGTATTC
*
4172668 GG
129 GA
* * * * *
4172670 TAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCGATTTCGC-ATTTGCTCAAAATAATCGAA
1 CAATTCGCGGAATCGTGCCCTATCGTGTTGGGTTGCGATTTCTCGA-TTGTTCAAAATAATCAAA
* * * * * *
4172734 TATCACTTTAAAATTTCGCTCGTGTCTTTTAAAATCCCTAAAACGAAGGCGATATCTGGTATTTG
65 TACCACTTCAAAATTTCACTCGTGTCTTTAAAAATCCCTAAAACGAAGGCAATATCTGGTATTCG
*
4172799 G
130 A
* * * * *
4172800 CAATTCGTGGGATCGTGCCCTAAT-GTGTTGGGTAGCAATTTCTCGATTGTTTAAAATAATCAAA
1 CAATTCGCGGAATCGTGCCCT-ATCGTGTTGGGTTGCGATTTCTCGATTGTTCAAAATAATCAAA
* * * *
4172864 TACCCCTTCAAAATTTCACTCG-GCTCTTCTAAAAATCCTTTAAAACGAGGGCAATA-CTCGGTG
65 TACCACTTCAAAATTTCACTCGTG-TCTT-TAAAAATCC-CTAAAACGAAGGCAATATCT-GGTA
4172927 TTCGA
126 TTCGA
* * * *
4172932 CAATTCG-GGAATCATG-CCTGATCGTGTTGGGTTGTGATTTCTCGTTTGTTCAAAACAATC
1 CAATTCGCGGAATCGTGCCCT-ATCGTGTTGGGTTGCGATTTCTCGATTGTTCAAAATAATC
4172992 GAGTATTCCT
Statistics
Matches: 263, Mismatches: 51, Indels: 15
0.80 0.16 0.05
Matches are distributed among these distances:
129 5 0.02
130 181 0.69
131 50 0.19
132 27 0.10
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (130 bp):
CAATTCGCGGAATCGTGCCCTATCGTGTTGGGTTGCGATTTCTCGATTGTTCAAAATAATCAAAT
ACCACTTCAAAATTTCACTCGTGTCTTTAAAAATCCCTAAAACGAAGGCAATATCTGGTATTCGA
Found at i:4185541 original size:22 final size:22
Alignment explanation
Indices: 4185499--4185539 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
4185489 ATTGAATTGA
*
4185499 GACTCGATTAATAGATGATATC
1 GACTCAATTAATAGATGATATC
4185521 GACTCAATTAA-AGAT-ATAT
1 GACTCAATTAATAGATGATAT
4185540 ATAAATCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 4 0.22
22 10 0.56
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (22 bp):
GACTCAATTAATAGATGATATC
Found at i:4190204 original size:5 final size:6
Alignment explanation
Indices: 4190179--4190203 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4190169 TTTCTTCACT
4190179 CCACCC CCACCC CCACCC CCACCC C
1 CCACCC CCACCC CCACCC CCACCC C
4190204 AAACAATTAT
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:0.16, C:0.84, G:0.00, T:0.00
Consensus pattern (6 bp):
CCACCC
Found at i:4193159 original size:55 final size:55
Alignment explanation
Indices: 4193078--4193188 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
4193068 AAACCGATAA
4193078 AACTTTAATACTGATCCCTTTTTCCCCTGGTTTGCAGCTCAGGAGGTGTTGTGAT
1 AACTTTAATACTGATCCCTTTTTCCCCTGGTTTGCAGCTCAGGAGGTGTTGTGAT
4193133 AACTTTAATACTGATCCCTTTTTCCCCTGGTTTGCAGCTCAGGAGGTGTTGTGAT
1 AACTTTAATACTGATCCCTTTTTCCCCTGGTTTGCAGCTCAGGAGGTGTTGTGAT
4193188 A
1 A
4193189 GCATCTCGAG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.38
Consensus pattern (55 bp):
AACTTTAATACTGATCCCTTTTTCCCCTGGTTTGCAGCTCAGGAGGTGTTGTGAT
Found at i:4199224 original size:15 final size:15
Alignment explanation
Indices: 4199204--4199253 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
4199194 AGATCACTTA
4199204 GGGTAACCAGATGGT
1 GGGTAACCAGATGGT
* *
4199219 GGGTAACCAGGTGCT
1 GGGTAACCAGATGGT
* * *
4199234 GGATAACCAGCTGGA
1 GGGTAACCAGATGGT
4199249 GGGTA
1 GGGTA
4199254 CTGATGAGGA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.26, C:0.16, G:0.40, T:0.18
Consensus pattern (15 bp):
GGGTAACCAGATGGT
Found at i:4201455 original size:6 final size:6
Alignment explanation
Indices: 4201444--4201479 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
4201434 GTCAATGGCA
* *
4201444 GGCTTT GGCTTT GGCTTT GGCGTT GGCGTT GGCTTT
1 GGCTTT GGCTTT GGCTTT GGCTTT GGCTTT GGCTTT
4201480 TTGTTTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.17, G:0.39, T:0.44
Consensus pattern (6 bp):
GGCTTT
Found at i:4202310 original size:20 final size:20
Alignment explanation
Indices: 4202269--4202311 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
4202259 ATAAAAACCT
* *
4202269 TTACTTTAAATCACATTTAA
1 TTACTTTAAATCAAATTAAA
4202289 TTACTTT-AATGCAAATTAAA
1 TTACTTTAAAT-CAAATTAAA
4202309 TTA
1 TTA
4202312 GTAAATACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.42, C:0.12, G:0.02, T:0.44
Consensus pattern (20 bp):
TTACTTTAAATCAAATTAAA
Found at i:4203472 original size:17 final size:18
Alignment explanation
Indices: 4203450--4203484 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
4203440 AAAGCTTCTT
4203450 TTTTTAATTTT-TTATAC
1 TTTTTAATTTTATTATAC
4203467 TTTTTAATTTTATTATAC
1 TTTTTAATTTTATTATAC
4203485 ACACTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTTAATTTTATTATAC
Found at i:4215443 original size:30 final size:30
Alignment explanation
Indices: 4215409--4215471 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
4215399 ACTTAACAAG
*
4215409 CAAATATCTCTAAAGTAATAACAAAATTAA
1 CAAATATCTCTAAAATAATAACAAAATTAA
* *
4215439 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATATCTCTAAAATAATAACAAAATTAA
4215469 CAA
1 CAA
4215472 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.57, C:0.13, G:0.03, T:0.27
Consensus pattern (30 bp):
CAAATATCTCTAAAATAATAACAAAATTAA
Found at i:4215556 original size:22 final size:22
Alignment explanation
Indices: 4215509--4215556 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
4215499 CAATAACAAC
* *
4215509 AAAATAGTAGCAACATAATAGT
1 AAAATAGTAGCAAAATAAGAGT
*
4215531 AAAATGGTAGCAAAATAGAGAG-
1 AAAATAGTAGCAAAATA-AGAGT
4215553 AAAA
1 AAAA
4215557 CAACAAGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.58, C:0.06, G:0.19, T:0.17
Consensus pattern (22 bp):
AAAATAGTAGCAAAATAAGAGT
Found at i:4216265 original size:2 final size:2
Alignment explanation
Indices: 4216258--4216296 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
4216248 GTTCTAAATT
*
4216258 TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4216297 GAATAATGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4216273 original size:12 final size:12
Alignment explanation
Indices: 4216252--4216296 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
4216242 ATTTATGTTC
*
4216252 TAAATTTATATA
1 TAAATATATATA
4216264 TAAATATATATA
1 TAAATATATATA
*
4216276 TATATATATATA
1 TAAATATATATA
*
4216288 TATATATAT
1 TAAATATAT
4216297 GAATAATGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
TAAATATATATA
Found at i:4230464 original size:21 final size:21
Alignment explanation
Indices: 4230415--4230466 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
4230405 AAAATATTTA
*
4230415 AAAATTAT--AAAAAATTTAT
1 AAAATTATAGAAAAAAATTAT
* **
4230434 TAAACAATAGAAAAAAATTAT
1 AAAATTATAGAAAAAAATTAT
4230455 AAAATTATAGAA
1 AAAATTATAGAA
4230467 TTGCAAAAAA
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
19 5 0.21
21 19 0.79
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (21 bp):
AAAATTATAGAAAAAAATTAT
Found at i:4231597 original size:12 final size:12
Alignment explanation
Indices: 4231580--4231605 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4231570 AGATTGGATT
4231580 AAATTAATTTTA
1 AAATTAATTTTA
4231592 AAATTAATTTTA
1 AAATTAATTTTA
4231604 AA
1 AA
4231606 TGAATAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
AAATTAATTTTA
Found at i:4233864 original size:46 final size:44
Alignment explanation
Indices: 4233721--4233864 Score: 98
Period size: 46 Copynumber: 3.1 Consensus size: 44
4233711 CCCGCCCATA
* * *
4233721 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCAGATGCCCA---A-ATC-CT
* * * *
4233770 --CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGC--ATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTC--AGATGCCCAAATCC-T
4233813 AAGTGAACTCGGACTCAACTCAACGAGTTCAGATGCCCAAATATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCAGATGCCC-AA-ATCCT
4233860 AGTGA
1 AGTGA
4233865 CATGTCACTT
Statistics
Matches: 74, Mismatches: 11, Indels: 23
0.69 0.10 0.21
Matches are distributed among these distances:
42 1 0.01
43 4 0.05
44 5 0.07
46 31 0.42
47 26 0.35
48 4 0.05
49 3 0.04
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.22
Consensus pattern (44 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCAGATGCCCAAATCCT
Found at i:4235767 original size:18 final size:18
Alignment explanation
Indices: 4235744--4235786 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
4235734 AAATAGGTTT
4235744 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
4235762 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
4235780 TTAATTA
1 TTAATTA
4235787 CACTTTAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:4236865 original size:5 final size:5
Alignment explanation
Indices: 4236857--4236889 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
4236847 ATATAATCTT
*
4236857 AAATG AAATA AAATA AAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAA
4236890 AACCATTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:4250561 original size:28 final size:28
Alignment explanation
Indices: 4250508--4250561 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
4250498 TTTTTAGTTG
* * *
4250508 AATAAGATTTTTTTTGTTTGTTAAATTA
1 AATAAGATTTTTTTTCTATGTAAAATTA
4250536 AATAAGATTTTTTTTCTAAT-TAAAAT
1 AATAAGATTTTTTTTCT-ATGTAAAAT
4250562 GGAAACTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
28 21 0.95
29 1 0.05
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (28 bp):
AATAAGATTTTTTTTCTATGTAAAATTA
Found at i:4257650 original size:18 final size:16
Alignment explanation
Indices: 4257609--4257648 Score: 71
Period size: 16 Copynumber: 2.4 Consensus size: 16
4257599 GAAGTATCGT
4257609 ATTTATTTATATATTTA
1 ATTT-TTTATATATTTA
4257626 ATTTTTTATATATTTA
1 ATTTTTTATATATTTA
4257642 ATTTTTT
1 ATTTTTT
4257649 TTTAAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 19 0.83
17 4 0.17
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
ATTTTTTATATATTTA
Found at i:4258103 original size:31 final size:31
Alignment explanation
Indices: 4258017--4258104 Score: 85
Period size: 31 Copynumber: 2.8 Consensus size: 31
4258007 CATTCCCATT
* *
4258017 ACTTAAATA-AAAACTTTTA-AATGATTTAATA
1 ACTTAAA-AGAAAA-TTTTAGAATAATTCAATA
*
4258048 ACTTAAAAGAAAATTTTCGAATAATTCAATA
1 ACTTAAAAGAAAATTTTAGAATAATTCAATA
4258079 AC-TAAAACGAAAA-TTTAGACATAATT
1 ACTTAAAA-GAAAATTTTAGA-ATAATT
4258105 TATTGAGTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
30 15 0.31
31 34 0.69
ACGTcount: A:0.52, C:0.09, G:0.06, T:0.33
Consensus pattern (31 bp):
ACTTAAAAGAAAATTTTAGAATAATTCAATA
Found at i:4258237 original size:41 final size:42
Alignment explanation
Indices: 4258192--4258281 Score: 105
Period size: 41 Copynumber: 2.2 Consensus size: 42
4258182 TTATAAACAT
* * * *
4258192 ATGAAAT-TTATAGCAGCACTTATGATAATTATCACCATTAA
1 ATGAAATAATATAGCAGCACTTACGATAATAATCACAATTAA
* *
4258233 ATG-AATAATATAGTAGCACTTGCGATAATAATCACAATTAA
1 ATGAAATAATATAGCAGCACTTACGATAATAATCACAATTAA
4258274 AT-AAATAA
1 ATGAAATAA
4258282 GACAAACTAG
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
40 3 0.07
41 38 0.93
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.31
Consensus pattern (42 bp):
ATGAAATAATATAGCAGCACTTACGATAATAATCACAATTAA
Found at i:4266750 original size:2 final size:2
Alignment explanation
Indices: 4266743--4266767 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4266733 TGGCACGGTG
4266743 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4266768 CAAATGGTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4268397 original size:27 final size:27
Alignment explanation
Indices: 4268338--4268397 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
4268328 GAATCTTGGA
* *
4268338 TTTTTTTTATATTTTAAAATTTATTTT
1 TTTTTTTTATATTTTAAAAATTATATT
*
4268365 TATTTTTTTAT-TTTTAAAAATTATAAT
1 T-TTTTTTTATATTTTAAAAATTATATT
4268392 TTTTTT
1 TTTTTT
4268398 AATTTGTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 5 0.17
27 15 0.52
28 9 0.31
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (27 bp):
TTTTTTTTATATTTTAAAAATTATATT
Found at i:4271253 original size:31 final size:28
Alignment explanation
Indices: 4271204--4271274 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 28
4271194 TATATTAATT
*
4271204 TATAATTTCATTATTTTAAAAGGACTAAATA
1 TATAATTTTA-TATTTT-AAAGGACTAAA-A
**
4271235 TAATAATTTTATATTTTAAAGGGTTAAAA
1 T-ATAATTTTATATTTTAAAGGACTAAAA
4271264 TATAATTTTAT
1 TATAATTTTAT
4271275 CATAAATTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 10 0.28
29 2 0.06
30 9 0.25
31 7 0.19
32 8 0.22
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (28 bp):
TATAATTTTATATTTTAAAGGACTAAAA
Found at i:4271611 original size:5 final size:5
Alignment explanation
Indices: 4271601--4271627 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
4271591 TTTAAAAAAA
4271601 TATTT TATTT TATTT TATTT TATTT TA
1 TATTT TATTT TATTT TATTT TATTT TA
4271628 ATAGGTAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
TATTT
Found at i:4272364 original size:14 final size:14
Alignment explanation
Indices: 4272345--4272371 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4272335 AAATTTAAGA
4272345 TTTAATTTTTTTAT
1 TTTAATTTTTTTAT
4272359 TTTAATTTTTTTA
1 TTTAATTTTTTTA
4272372 CATAATTTAG
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:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTAATTTTTTTAT
Found at i:4279644 original size:15 final size:15
Alignment explanation
Indices: 4279626--4279662 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
4279616 TTCTATAAAC
4279626 ATTTTTATAAAAATA
1 ATTTTTATAAAAATA
*
4279641 A-TTTTAAAAAAATA
1 ATTTTTATAAAAATA
4279655 ATTTTTAT
1 ATTTTTAT
4279663 TCTACATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTTTTATAAAAATA
Found at i:4283119 original size:20 final size:20
Alignment explanation
Indices: 4283094--4283135 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
4283084 AAACATTAGA
4283094 CACTACTATAGGGGTAACAC
1 CACTACTATAGGGGTAACAC
4283114 CACTACTATAGGGGTAACAC
1 CACTACTATAGGGGTAACAC
4283134 CA
1 CA
4283136 AAACTTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (20 bp):
CACTACTATAGGGGTAACAC
Found at i:4283365 original size:13 final size:15
Alignment explanation
Indices: 4283320--4283365 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
4283310 AAAATGAATA
* *
4283320 ATACATAGGAGTAAT
1 ATACATAGTAATAAT
*
4283335 ATACATAGTAAAAAT
1 ATACATAGTAATAAT
4283350 ATACAT-GT-ATAAT
1 ATACATAGTAATAAT
4283363 ATA
1 ATA
4283366 TGAAATGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 7 0.26
14 2 0.07
15 18 0.67
ACGTcount: A:0.52, C:0.07, G:0.11, T:0.30
Consensus pattern (15 bp):
ATACATAGTAATAAT
Found at i:4299111 original size:20 final size:19
Alignment explanation
Indices: 4299059--4299112 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
4299049 ACAATATAAT
*
4299059 TCAAGTAATTATAACATGAA
1 TCAA-TAATTAAAACATGAA
*
4299079 TCAACAATATAAAACATCGAA
1 TCAATAAT-TAAAACAT-GAA
*
4299100 TTAATAATTAAAA
1 TCAATAATTAAAA
4299113 TATACCTAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.11
20 16 0.57
21 9 0.32
ACGTcount: A:0.56, C:0.11, G:0.06, T:0.28
Consensus pattern (19 bp):
TCAATAATTAAAACATGAA
Found at i:4300973 original size:19 final size:18
Alignment explanation
Indices: 4300946--4300981 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
4300936 TATAAATATA
4300946 AATATTAAAAATCAAAAT
1 AATATTAAAAATCAAAAT
*
4300964 AATATATAAAAATTAAAA
1 AATAT-TAAAAATCAAAA
4300982 AAAAGTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (18 bp):
AATATTAAAAATCAAAAT
Found at i:4304880 original size:34 final size:34
Alignment explanation
Indices: 4304839--4304905 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
4304829 TTATCTTGTC
*
4304839 TCTTAGTTAATACTCAATTTATTACTAACTGGTT
1 TCTTAGTTAATACTCAATATATTACTAACTGGTT
* *
4304873 TCTTAGTTAATGCTCAATATGTTACTAACTGGT
1 TCTTAGTTAATACTCAATATATTACTAACTGGT
4304906 CTTTTCTTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.45
Consensus pattern (34 bp):
TCTTAGTTAATACTCAATATATTACTAACTGGTT
Found at i:4319122 original size:19 final size:18
Alignment explanation
Indices: 4319097--4319152 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
4319087 TTCAATTTTT
4319097 TTTTAAAATTATATAACA
1 TTTTAAAATTATATAACA
*
4319115 TGTTTAAAACTAATTATAACA
1 T-TTTAAAA-TTA-TATAACA
*
4319136 TTTTCAAAATTTTATAA
1 TTTT-AAAATTATATAA
4319153 ACTTCATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 1 0.03
19 12 0.39
20 6 0.19
21 12 0.39
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (18 bp):
TTTTAAAATTATATAACA
Found at i:4319330 original size:21 final size:21
Alignment explanation
Indices: 4319292--4319332 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4319282 ATATTTAGTT
**
4319292 AAATTTTAAAAATTGAATTTA
1 AAATTTTAAAAACAGAATTTA
4319313 AAATTTTAAAAACAGAATTT
1 AAATTTTAAAAACAGAATTT
4319333 GATTAGTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (21 bp):
AAATTTTAAAAACAGAATTTA
Found at i:4319567 original size:18 final size:19
Alignment explanation
Indices: 4319531--4319568 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
4319521 GTTTAAAAGT
**
4319531 TAAAATAAATATATTTTTA
1 TAAAATAAATATAAATTTA
4319550 TAAAAT-AATATAAATTTA
1 TAAAATAAATATAAATTTA
4319568 T
1 T
4319569 TTTTCACAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TAAAATAAATATAAATTTA
Found at i:4326794 original size:42 final size:42
Alignment explanation
Indices: 4326746--4326826 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
4326736 AACAGAAGAG
*
4326746 ATTAATAAAAGAGAGGAAATGAACAGTTTCTTAGTTAAGAAA
1 ATTAATAAAAGAGAGGAAATGAACAATTTCTTAGTTAAGAAA
*
4326788 ATTAATAAAAGAGAGGAAATGAACAATTTTTTAGTTAAG
1 ATTAATAAAAGAGAGGAAATGAACAATTTCTTAGTTAAG
4326827 GTTTAAGGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.49, C:0.04, G:0.19, T:0.28
Consensus pattern (42 bp):
ATTAATAAAAGAGAGGAAATGAACAATTTCTTAGTTAAGAAA
Found at i:4329570 original size:22 final size:22
Alignment explanation
Indices: 4329508--4329575 Score: 61
Period size: 22 Copynumber: 3.1 Consensus size: 22
4329498 TAGAATTTAC
4329508 AAGTAAAATAAAATATAATTATA
1 AAGTAAAATAAAAT-TAATTATA
* *
4329531 AA-TATATATTTAAA-TAATTATA
1 AAGTA-A-AATAAAATTAATTATA
*
4329553 AAGTAAAATCAAATTAA-TATA
1 AAGTAAAATAAAATTAATTATA
4329574 AA
1 AA
4329576 ACATAAAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
21 11 0.30
22 16 0.43
23 5 0.14
24 5 0.14
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (22 bp):
AAGTAAAATAAAATTAATTATA
Found at i:4347162 original size:2 final size:2
Alignment explanation
Indices: 4347151--4347186 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
4347141 GTATTTCTAT
4347151 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4347187 TTGTCTTTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4352772 original size:75 final size:75
Alignment explanation
Indices: 4352674--4352821 Score: 271
Period size: 75 Copynumber: 2.0 Consensus size: 75
4352664 CTAAATGTTA
4352674 GGGCTACAGCAGTTAGTGTAACTAC-CGCGTCCTAGAATGGAAATACGAGCAACAAAATTATATT
1 GGGCTACAGCAGTTAGTGTAACTACAC-CGTCCTAGAATGGAAATACGAGCAACAAAATTATATT
4352738 ATAACATTCCT
65 ATAACATTCCT
*
4352749 GGGCTACAGCAGTTAGTGTAACTACACTGTCCTAGAATGGAAATACGAGCAACAAAATTATATTA
1 GGGCTACAGCAGTTAGTGTAACTACACCGTCCTAGAATGGAAATACGAGCAACAAAATTATATTA
4352814 TAACATTC
66 TAACATTC
4352822 TTGGCGAGCA
Statistics
Matches: 71, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
75 70 0.99
76 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (75 bp):
GGGCTACAGCAGTTAGTGTAACTACACCGTCCTAGAATGGAAATACGAGCAACAAAATTATATTA
TAACATTCCT
Found at i:4357873 original size:2 final size:2
Alignment explanation
Indices: 4357866--4357894 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4357856 TTATTGAAAT
4357866 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4357895 TTTTTATGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4358059 original size:17 final size:18
Alignment explanation
Indices: 4358029--4358064 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
4358019 AATAAATTAT
*
4358029 TAAAAATTTATAAAAAAA
1 TAAAAATATATAAAAAAA
4358047 TAAAAATAT-TAAAAAAA
1 TAAAAATATATAAAAAAA
4358064 T
1 T
4358065 CAGTTCAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
TAAAAATATATAAAAAAA
Found at i:4359505 original size:15 final size:15
Alignment explanation
Indices: 4359455--4359507 Score: 51
Period size: 15 Copynumber: 3.8 Consensus size: 15
4359445 TAATTTTTAA
*
4359455 ATTTATTTTAAATAT
1 ATTTATTTTGAATAT
* *
4359470 ATTTATATT---TAC
1 ATTTATTTTGAATAT
4359482 A-TTATTTTGAATAT
1 ATTTATTTTGAATAT
4359496 ATTTATTTTGAA
1 ATTTATTTTGAA
4359508 AGAACAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
11 6 0.20
12 3 0.10
14 3 0.10
15 18 0.60
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (15 bp):
ATTTATTTTGAATAT
Found at i:4369031 original size:53 final size:53
Alignment explanation
Indices: 4368950--4369100 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
4368940 CTTACACGGT
* *
4368950 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
4369005 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
4369058 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
4369101 GCACACTTGT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:4378737 original size:53 final size:53
Alignment explanation
Indices: 4378671--4378863 Score: 298
Period size: 53 Copynumber: 3.6 Consensus size: 53
4378661 ATAAGTGCGC
*
4378671 CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGATAATATGACT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGATAATATGACT
4378724 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGATAATATGACT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGATAATATGACT
* ** * *
4378777 CCGTATAAGACCATAGCTGGGCTACGGCATCGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGATAATATGACT
* *
4378830 CCGTATAAGACCAT-GTCTGGGATATGGCTTCGGT
1 CCGTATAAGACCATAG-CTGGGCTATGGCATCGGT
4378864 ATGATATGTG
Statistics
Matches: 130, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
52 1 0.01
53 129 0.99
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (53 bp):
CCGTATAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGATAATATGACT
Found at i:4380294 original size:47 final size:47
Alignment explanation
Indices: 4380185--4380295 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
4380175 CCGGGATAAG
*
4380185 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
4380232 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
4380279 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
4380296 ACTCAATGTC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
46 1 0.02
47 53 0.95
48 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.25
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:4381065 original size:4 final size:4
Alignment explanation
Indices: 4381051--4381084 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
4381041 AAATTTCCCT
*
4381051 TTTC TTTTC TTTC TTTC TTTC CTTC TTTC TTTC T
1 TTTC -TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
4381085 CACGTTTGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTC
Found at i:4387548 original size:47 final size:47
Alignment explanation
Indices: 4387439--4387549 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
4387429 CCGGGATAAG
*
4387439 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
4387486 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
4387533 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
4387550 ACTCAATGTC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
46 1 0.02
47 53 0.95
48 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.25
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:4390797 original size:15 final size:15
Alignment explanation
Indices: 4390768--4390817 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
4390758 CAAAGATAAC
*
4390768 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
4390782 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
4390797 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
4390812 AAGAAA
1 AAGAAA
4390818 CCCAAGATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 8 0.26
15 23 0.74
ACGTcount: A:0.60, C:0.12, G:0.18, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:4390826 original size:15 final size:15
Alignment explanation
Indices: 4390779--4390826 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
4390769 AGAAAACCGA
4390779 ATAAAGAAATCC-AG
1 ATAAAGAAATCCAAG
* *
4390793 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
4390809 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
4390824 ATA
1 ATA
4390827 CGATACTATG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 26 0.96
16 1 0.04
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:4395083 original size:2 final size:2
Alignment explanation
Indices: 4395076--4395110 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4395066 ATAAGTAAAC
4395076 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 A
4395111 AATTTAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4398592 original size:14 final size:14
Alignment explanation
Indices: 4398573--4398605 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
4398563 GGCTTTCTAA
4398573 CACTTTTCCTCTGT
1 CACTTTTCCTCTGT
4398587 CACTTTTCCTCTGT
1 CACTTTTCCTCTGT
4398601 CACTT
1 CACTT
4398606 CACCTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.09, C:0.36, G:0.06, T:0.48
Consensus pattern (14 bp):
CACTTTTCCTCTGT
Found at i:4399701 original size:2 final size:2
Alignment explanation
Indices: 4399694--4399720 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4399684 ATCATTCGAT
4399694 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4399721 CATTCTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4399908 original size:6 final size:6
Alignment explanation
Indices: 4399897--4399927 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
4399887 TCGAAGCCGG
4399897 AACAGT AACAGT AACAGT AACAGT AACAGT A
1 AACAGT AACAGT AACAGT AACAGT AACAGT A
4399928 CGGTACACAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (6 bp):
AACAGT
Found at i:4399973 original size:6 final size:6
Alignment explanation
Indices: 4399962--4399998 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
4399952 ACAAATATGA
*
4399962 AACAGT AACAGT AACAGT AACAGT AACGGT AACAGT A
1 AACAGT AACAGT AACAGT AACAGT AACAGT AACAGT A
4399999 TTCGACACAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.49, C:0.16, G:0.19, T:0.16
Consensus pattern (6 bp):
AACAGT
Found at i:4401138 original size:5 final size:5
Alignment explanation
Indices: 4401128--4401182 Score: 110
Period size: 5 Copynumber: 11.0 Consensus size: 5
4401118 TTTCTTTTAT
4401128 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
4401178 ATATA
1 ATATA
4401183 CTTAATTATT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 50 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:4405158 original size:30 final size:30
Alignment explanation
Indices: 4405123--4405182 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
4405113 CTTTAATATG
* *
4405123 AACTTTGGCAAAATTATATTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
* *
4405153 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
4405183 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.40
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTGCCCCTA
Found at i:4407902 original size:40 final size:40
Alignment explanation
Indices: 4407846--4407952 Score: 169
Period size: 40 Copynumber: 2.7 Consensus size: 40
4407836 ATGAGACACT
4407846 TCGAATTATCCTATGAGGCATTGGGTGTCAATTTACTACG
1 TCGAATTATCCTATGAGGCATTGGGTGTCAATTTACTACG
* * * * *
4407886 TCGAATTATCCCATGAGACACTAGGTGTCAATTTACTATG
1 TCGAATTATCCTATGAGGCATTGGGTGTCAATTTACTACG
4407926 TCGAATTATCCTATGAGGCATTGGGTG
1 TCGAATTATCCTATGAGGCATTGGGTG
4407953 CCAAGCTAGT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 58 1.00
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (40 bp):
TCGAATTATCCTATGAGGCATTGGGTGTCAATTTACTACG
Found at i:4408192 original size:16 final size:16
Alignment explanation
Indices: 4408142--4408193 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
4408132 TTATATACTT
* *
4408142 ATGAATTGAGTATGGT
1 ATGAATTGAGTATTGC
*
4408158 ATGAAATGATGTATT-C
1 ATGAATTGA-GTATTGC
4408174 ATGAATTGAGTATTGC
1 ATGAATTGAGTATTGC
4408190 ATGA
1 ATGA
4408194 CTAATGCCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 5 0.17
16 21 0.70
17 4 0.13
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.37
Consensus pattern (16 bp):
ATGAATTGAGTATTGC
Found at i:4438337 original size:23 final size:23
Alignment explanation
Indices: 4438307--4438352 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
4438297 AACAATGGAT
4438307 CGTACCGATTGATACACCAACCA
1 CGTACCGATTGATACACCAACCA
4438330 CGTACCGATTGATACACCAACCA
1 CGTACCGATTGATACACCAACCA
4438353 ATTGAATAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.13, T:0.17
Consensus pattern (23 bp):
CGTACCGATTGATACACCAACCA
Found at i:4438651 original size:21 final size:20
Alignment explanation
Indices: 4438628--4438712 Score: 57
Period size: 21 Copynumber: 3.9 Consensus size: 20
4438618 TTGTTTTAGT
4438628 ATTATTTTTATTTATTTTAA
1 ATTATTTTTATTTATTTTAA
* *
4438648 TATTTGTTTTTATAT-TTTTAA
1 -A-TTATTTTTATTTATTTTAA
4438669 ATATATTTGATTTATTATATTTTTAA
1 AT-TA-TT--TTTATT-TA-TTTTAA
4438695 ATT-TTTTTATTTAATTTT
1 ATTATTTTTATTT-ATTTT
4438713 TTTATTTAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 19
0.69 0.05 0.26
Matches are distributed among these distances:
19 1 0.02
20 7 0.14
21 16 0.31
22 10 0.20
23 7 0.14
24 1 0.02
25 1 0.02
26 8 0.16
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.69
Consensus pattern (20 bp):
ATTATTTTTATTTATTTTAA
Found at i:4438674 original size:24 final size:26
Alignment explanation
Indices: 4438647--4438696 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
4438637 ATTTATTTTA
4438647 ATATTTG-TTT-TTATATTTTTAAAT
1 ATATTTGATTTATTATATTTTTAAAT
4438671 ATATTTGATTTATTATATTTTTAAAT
1 ATATTTGATTTATTATATTTTTAAAT
4438697 TTTTTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 7 0.29
25 3 0.12
26 14 0.58
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (26 bp):
ATATTTGATTTATTATATTTTTAAAT
Found at i:4438707 original size:14 final size:14
Alignment explanation
Indices: 4438690--4438721 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
4438680 TTATTATATT
4438690 TTTAAATTTTTTTA
1 TTTAAATTTTTTTA
4438704 TTT-AATTTTTTTA
1 TTTAAATTTTTTTA
4438717 TTTAA
1 TTTAA
4438722 TGAAATAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTAAATTTTTTTA
Found at i:4438712 original size:13 final size:13
Alignment explanation
Indices: 4438694--4438722 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
4438684 TATATTTTTA
4438694 AATTTTTTTATTT
1 AATTTTTTTATTT
4438707 AATTTTTTTATTT
1 AATTTTTTTATTT
4438720 AAT
1 AAT
4438723 GAAATAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
AATTTTTTTATTT
Found at i:4442311 original size:2 final size:2
Alignment explanation
Indices: 4442304--4442340 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
4442294 AAGATAATAG
*
4442304 TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4442341 CCCAAAACAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4445352 original size:21 final size:21
Alignment explanation
Indices: 4445327--4445395 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
4445317 TATAATGATT
4445327 ATTATTATGGTTTTATATTAA
1 ATTATTATGGTTTTATATTAA
**
4445348 ATTATTATAATTATTA-ATT-A
1 ATTATTATGGTT-TTATATTAA
* *
4445368 A-CATTATGGTTTTATATTAG
1 ATTATTATGGTTTTATATTAA
4445388 ATTATTAT
1 ATTATTAT
4445396 TATTAGCATT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
18 3 0.08
19 10 0.27
20 3 0.08
21 18 0.49
22 3 0.08
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.55
Consensus pattern (21 bp):
ATTATTATGGTTTTATATTAA
Found at i:4449428 original size:21 final size:21
Alignment explanation
Indices: 4449395--4449452 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
4449385 GGGACCTGCT
*
4449395 AAAG-AAGAGAAGAAAGATGA
1 AAAGAAAGACAAGAAAGATGA
4449415 CAAA-AAAGACAAGAAAGATGA
1 -AAAGAAAGACAAGAAAGATGA
4449436 AAAGAAAGACAA-AAAGA
1 AAAGAAAGACAAGAAAGA
4449453 AGGGTGAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
20 8 0.24
21 26 0.76
ACGTcount: A:0.69, C:0.05, G:0.22, T:0.03
Consensus pattern (21 bp):
AAAGAAAGACAAGAAAGATGA
Found at i:4449429 original size:24 final size:21
Alignment explanation
Indices: 4449404--4449467 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 21
4449394 TAAAGAAGAG
4449404 AAGAAAGATGACAAAAAAGAC-
1 AAGAAAGATGA-AAAAAAGACA
4449425 AAGAAAGATGAAAAGAAAGACAAA
1 AAGAAAGATGAAAA-AAAGAC--A
* *
4449449 AAGAAGGGTGAAAAAAAGA
1 AAGAAAGATGAAAAAAAGA
4449468 AATGATTATA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
20 3 0.08
21 17 0.46
23 5 0.14
24 12 0.32
ACGTcount: A:0.67, C:0.05, G:0.23, T:0.05
Consensus pattern (21 bp):
AAGAAAGATGAAAAAAAGACA
Found at i:4450101 original size:16 final size:16
Alignment explanation
Indices: 4450080--4450111 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
4450070 TTGGAAAATA
4450080 ATTTTAAAAATAATTT
1 ATTTTAAAAATAATTT
4450096 ATTTTAAAAATAATTT
1 ATTTTAAAAATAATTT
4450112 TTAAACCCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTTAAAAATAATTT
Found at i:4454625 original size:7 final size:7
Alignment explanation
Indices: 4454613--4454638 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
4454603 TCCACCATGA
4454613 TCAAGCC
1 TCAAGCC
4454620 TCAAGCC
1 TCAAGCC
4454627 TCAAGCC
1 TCAAGCC
4454634 TCAAG
1 TCAAG
4454639 ATTTCAATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.38, G:0.15, T:0.15
Consensus pattern (7 bp):
TCAAGCC
Found at i:4455885 original size:35 final size:35
Alignment explanation
Indices: 4455839--4455908 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
4455829 TCAGAAAGTA
4455839 AAAGTGGTAAACCATTAGCAACAAGAGAACGCATT
1 AAAGTGGTAAACCATTAGCAACAAGAGAACGCATT
4455874 AAAGTGGTAAACCATTAGCAACAAGAGAACGCATT
1 AAAGTGGTAAACCATTAGCAACAAGAGAACGCATT
4455909 CTGTCTATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (35 bp):
AAAGTGGTAAACCATTAGCAACAAGAGAACGCATT
Found at i:4457463 original size:20 final size:20
Alignment explanation
Indices: 4457440--4457496 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 20
4457430 ATTCCCTAAA
4457440 TCCATGATTGATTCAGCATT
1 TCCATGATTGATTCAGCATT
* *
4457460 TCCAT-ATGGGA---GGCATT
1 TCCATGAT-TGATTCAGCATT
4457477 TCCATGATTGATTCAGCATT
1 TCCATGATTGATTCAGCATT
4457497 CCCTAAATCC
Statistics
Matches: 28, Mismatches: 4, Indels: 10
0.67 0.10 0.24
Matches are distributed among these distances:
17 12 0.43
18 2 0.07
19 2 0.07
20 12 0.43
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (20 bp):
TCCATGATTGATTCAGCATT
Found at i:4462680 original size:24 final size:24
Alignment explanation
Indices: 4462644--4462718 Score: 89
Period size: 24 Copynumber: 3.1 Consensus size: 24
4462634 GGGACCTGCT
* *
4462644 AAAGAAGAGAAGAAAGATGACAAA-
1 AAAGACGAAAAGAAAGATGA-AAAG
* *
4462668 AAAGACGATAAGAAAGGTGAAAAG
1 AAAGACGAAAAGAAAGATGAAAAG
*
4462692 AAAGACGAAAAGAAGGATGAAAAG
1 AAAGACGAAAAGAAAGATGAAAAG
4462716 AAA
1 AAA
4462719 TGATTATCAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
23 3 0.07
24 41 0.93
ACGTcount: A:0.64, C:0.04, G:0.27, T:0.05
Consensus pattern (24 bp):
AAAGACGAAAAGAAAGATGAAAAG
Found at i:4462683 original size:12 final size:12
Alignment explanation
Indices: 4462653--4462718 Score: 62
Period size: 12 Copynumber: 5.5 Consensus size: 12
4462643 TAAAGAAGAG
*
4462653 AAGAAAGATGACA
1 AAGAAAGACGA-A
*
4462666 AA-AAAGACGAT
1 AAGAAAGACGAA
**
4462677 AAGAAAGGTGAA
1 AAGAAAGACGAA
4462689 AAGAAAGACGAA
1 AAGAAAGACGAA
* *
4462701 AAGAAGGATGAA
1 AAGAAAGACGAA
4462713 AAGAAA
1 AAGAAA
4462719 TGATTATCAA
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
11 2 0.05
12 38 0.90
13 2 0.05
ACGTcount: A:0.64, C:0.05, G:0.26, T:0.06
Consensus pattern (12 bp):
AAGAAAGACGAA
Found at i:4464500 original size:22 final size:22
Alignment explanation
Indices: 4464472--4464516 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
4464462 AGCATAAAAC
4464472 ACGGTCCATAAATATCGAATTA
1 ACGGTCCATAAATATCGAATTA
4464494 ACGGTCCATAAATATCGAATTA
1 ACGGTCCATAAATATCGAATTA
4464516 A
1 A
4464517 AAGTTAGGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (22 bp):
ACGGTCCATAAATATCGAATTA
Found at i:4466319 original size:21 final size:21
Alignment explanation
Indices: 4466293--4466353 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
4466283 GGCTTTACTG
4466293 ATCAGGCACTTTATGTGTCGT
1 ATCAGGCACTTTATGTGTCGT
* **
4466314 ATCAGGCACGTCGTGTGTCGT
1 ATCAGGCACTTTATGTGTCGT
* *
4466335 TTTAGGCACTTTATGTGTC
1 ATCAGGCACTTTATGTGTC
4466354 ATATACTGAT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.16, C:0.20, G:0.26, T:0.38
Consensus pattern (21 bp):
ATCAGGCACTTTATGTGTCGT
Found at i:4471238 original size:13 final size:13
Alignment explanation
Indices: 4471220--4471248 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
4471210 TTGTTGATCG
4471220 GCTTACAAAATCA
1 GCTTACAAAATCA
4471233 GCTTACAAAATCA
1 GCTTACAAAATCA
4471246 GCT
1 GCT
4471249 CACTTTATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.24, G:0.10, T:0.24
Consensus pattern (13 bp):
GCTTACAAAATCA
Found at i:4474521 original size:21 final size:20
Alignment explanation
Indices: 4474497--4474555 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
4474487 CAAATAATTC
* *
4474497 TAAAAGTTATAAAATTTTATT
1 TAAAAATTATAAAA-ATTATT
*
4474518 TAAAATTTATAAGAAATTATT
1 TAAAAATTATAA-AAATTATT
4474539 TAAAAATTATTAAAAAT
1 TAAAAATTA-TAAAAAT
4474556 AATATTCATT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 28 0.85
22 5 0.15
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.42
Consensus pattern (20 bp):
TAAAAATTATAAAAATTATT
Found at i:4479892 original size:18 final size:18
Alignment explanation
Indices: 4479851--4479893 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
4479841 CTCATTCTTC
*
4479851 TAGAGGAAGAGGTAGAAG
1 TAGAGGAAGAGGAAGAAG
* * *
4479869 TTGAGGAAGGGGAAGAGG
1 TAGAGGAAGAGGAAGAAG
4479887 TAGAGGA
1 TAGAGGA
4479894 GACAGTTGGA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.49, T:0.12
Consensus pattern (18 bp):
TAGAGGAAGAGGAAGAAG
Found at i:4481001 original size:39 final size:39
Alignment explanation
Indices: 4480947--4481024 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
4480937 GAGAATATTG
*
4480947 CTCCAAGGAATTTGGAGCATTTTGTGATAGCCATGGCAT
1 CTCCAAGGAATTTGGACCATTTTGTGATAGCCATGGCAT
*
4480986 CTCCAAGGAATTTGGACCATTTTGTGATAGTCATGGCAT
1 CTCCAAGGAATTTGGACCATTTTGTGATAGCCATGGCAT
4481025 TTGGAAAGAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (39 bp):
CTCCAAGGAATTTGGACCATTTTGTGATAGCCATGGCAT
Found at i:4486715 original size:18 final size:19
Alignment explanation
Indices: 4486692--4486729 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
4486682 CCGAAGATTG
4486692 TAATTCATG-TCTT-TCTCA
1 TAATTCA-GCTCTTGTCTCA
4486710 TAATTCAGCTCTTGTCTCA
1 TAATTCAGCTCTTGTCTCA
4486729 T
1 T
4486730 TTCTTCAACG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.06
18 11 0.61
19 6 0.33
ACGTcount: A:0.21, C:0.24, G:0.08, T:0.47
Consensus pattern (19 bp):
TAATTCAGCTCTTGTCTCA
Found at i:4492491 original size:32 final size:32
Alignment explanation
Indices: 4492453--4492516 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
4492443 ATATATTGAT
4492453 GTAAATCTTTGATCAACATATATATGACTGAA
1 GTAAATCTTTGATCAACATATATATGACTGAA
4492485 GTAAATCTTTGATCAACATATATATGACTGAA
1 GTAAATCTTTGATCAACATATATATGACTGAA
4492517 AATAGTTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (32 bp):
GTAAATCTTTGATCAACATATATATGACTGAA
Found at i:4494919 original size:13 final size:13
Alignment explanation
Indices: 4494903--4494945 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
4494893 TAATATATGT
*
4494903 AAAATGAATATAA
1 AAAATGTATATAA
* *
4494916 AAAATTTCTATAA
1 AAAATGTATATAA
4494929 AAAA-GTATATAA
1 AAAATGTATATAA
4494941 AAAAT
1 AAAAT
4494946 ATAAATTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (13 bp):
AAAATGTATATAA
Found at i:4498159 original size:26 final size:26
Alignment explanation
Indices: 4498130--4498210 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
4498120 ATTTATCTCG
4498130 TTATGGACAGGTGTTGAGTAACTCTT
1 TTATGGACAGGTGTTGAGTAACTCTT
* * * *
4498156 TTATGTACA--T-TTACGATTTA-TCTCG
1 TTATGGACAGGTGTT--GAGTAACTCT-T
4498181 TTATGGACAGGTGTTGAGTAACTCTT
1 TTATGGACAGGTGTTGAGTAACTCTT
4498207 TTAT
1 TTAT
4498211 ATAAAGTATA
Statistics
Matches: 40, Mismatches: 8, Indels: 14
0.65 0.13 0.23
Matches are distributed among these distances:
23 2 0.05
24 4 0.10
25 12 0.30
26 16 0.40
27 4 0.10
28 2 0.05
ACGTcount: A:0.23, C:0.12, G:0.21, T:0.43
Consensus pattern (26 bp):
TTATGGACAGGTGTTGAGTAACTCTT
Found at i:4498185 original size:25 final size:25
Alignment explanation
Indices: 4498109--4498185 Score: 61
Period size: 25 Copynumber: 3.0 Consensus size: 25
4498099 TGAACACATG
4498109 GTACATTTACGATTTATCTCGTTAT
1 GTACATTTACGATTTATCTCGTTAT
* * * *
4498134 GGACAGGTGTT--GA-GTAACTCTTTTAT
1 GTACA--T-TTACGATTTATCTC-GTTAT
4498160 GTACATTTACGATTTATCTCGTTAT
1 GTACATTTACGATTTATCTCGTTAT
4498185 G
1 G
4498186 GACAGGTGTT
Statistics
Matches: 37, Mismatches: 8, Indels: 14
0.63 0.14 0.24
Matches are distributed among these distances:
23 2 0.05
24 1 0.03
25 16 0.43
26 15 0.41
27 1 0.03
28 2 0.05
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.44
Consensus pattern (25 bp):
GTACATTTACGATTTATCTCGTTAT
Found at i:4498185 original size:51 final size:51
Alignment explanation
Indices: 4498109--4498210 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
4498099 TGAACACATG
4498109 GTACATTTACGATTTATCTCGTTATGGACAGGTGTTGAGTAACTCTTTTAT
1 GTACATTTACGATTTATCTCGTTATGGACAGGTGTTGAGTAACTCTTTTAT
4498160 GTACATTTACGATTTATCTCGTTATGGACAGGTGTTGAGTAACTCTTTTAT
1 GTACATTTACGATTTATCTCGTTATGGACAGGTGTTGAGTAACTCTTTTAT
4498211 ATAAAGTATA
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:0.24, C:0.14, G:0.20, T:0.43
Consensus pattern (51 bp):
GTACATTTACGATTTATCTCGTTATGGACAGGTGTTGAGTAACTCTTTTAT
Found at i:4500999 original size:22 final size:23
Alignment explanation
Indices: 4500956--4501000 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
4500946 AAAATATGCT
* *
4500956 AAAAATTATATTTTAACCTTTCA
1 AAAAATTATAATTTAACATTTCA
*
4500979 AAAAATTGTAATTTAA-ATTTCA
1 AAAAATTATAATTTAACATTTCA
4501001 TCATAACATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (23 bp):
AAAAATTATAATTTAACATTTCA
Found at i:4502586 original size:9 final size:9
Alignment explanation
Indices: 4502572--4502602 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
4502562 TTATTTTATT
4502572 AAAAAATTAA
1 AAAAAATT-A
4502582 AAAAAATTA
1 AAAAAATTA
4502591 AAAAAATTA
1 AAAAAATTA
4502600 AAA
1 AAA
4502603 TTAACATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 13 0.62
10 8 0.38
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAAAAATTA
Found at i:4502587 original size:10 final size:10
Alignment explanation
Indices: 4502572--4502602 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
4502562 TTATTTTATT
4502572 AAAAAATTAA
1 AAAAAATTAA
4502582 AAAAAATT-A
1 AAAAAATTAA
4502591 AAAAAATTAA
1 AAAAAATTAA
4502601 AA
1 AA
4502603 TTAACATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (10 bp):
AAAAAATTAA
Found at i:4505404 original size:17 final size:17
Alignment explanation
Indices: 4505375--4505408 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
4505365 CAAAAAAGAA
4505375 ACTGTCTTTTTTTTTTT
1 ACTGTCTTTTTTTTTTT
4505392 ACTGT-TTTCTTTTTTTT
1 ACTGTCTTT-TTTTTTTT
4505409 TCTTGCTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.06, C:0.12, G:0.06, T:0.76
Consensus pattern (17 bp):
ACTGTCTTTTTTTTTTT
Found at i:4505404 original size:20 final size:20
Alignment explanation
Indices: 4505379--4505433 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
4505369 AAAGAAACTG
*
4505379 TCTTTTTTTTTTTACTGTTT
1 TCTTTTTTTTTTTACTATTT
*
4505399 TCTTTTTTTTTCTTGCTATTT
1 TCTTTTTTTTT-TTACTATTT
4505420 TCTTATTATTTTTT
1 TCTT-TT-TTTTTT
4505434 CACTTTTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 11 0.37
21 11 0.37
22 3 0.10
23 5 0.17
ACGTcount: A:0.07, C:0.11, G:0.04, T:0.78
Consensus pattern (20 bp):
TCTTTTTTTTTTTACTATTT
Found at i:4505407 original size:21 final size:21
Alignment explanation
Indices: 4505381--4505442 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
4505371 AGAAACTGTC
*
4505381 TTTTTTTTTTTACTGTTTTCT
1 TTTTTTTTTTTACTATTTTCT
* *
4505402 TTTTTTTTCTTGCTATTTTCT
1 TTTTTTTTTTTACTATTTTCT
* * *
4505423 TATTATTTTTTCACTTTTTT
1 T-TTTTTTTTTTACTATTTT
4505443 GTTACCATTT
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
21 19 0.59
22 13 0.41
ACGTcount: A:0.08, C:0.11, G:0.03, T:0.77
Consensus pattern (21 bp):
TTTTTTTTTTTACTATTTTCT
Found at i:4505513 original size:17 final size:19
Alignment explanation
Indices: 4505477--4505523 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
4505467 TATTATTTGG
4505477 ATATTGTATAACTCTTGTT
1 ATATTGTATAACTCTTGTT
*
4505496 ATATTGT-TAA-TTTTGTT
1 ATATTGTATAACTCTTGTT
*
4505513 ACTATTTTATA
1 A-TATTGTATA
4505524 GGCATTTGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 7 0.29
18 8 0.33
19 9 0.38
ACGTcount: A:0.28, C:0.06, G:0.09, T:0.57
Consensus pattern (19 bp):
ATATTGTATAACTCTTGTT
Found at i:4506593 original size:3 final size:3
Alignment explanation
Indices: 4506587--4506621 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
4506577 AGGAGGACAT
*
4506587 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA ACA GC
1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GC
4506622 CACAGCCTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.34, C:0.34, G:0.31, T:0.00
Consensus pattern (3 bp):
GCA
Found at i:4508538 original size:41 final size:41
Alignment explanation
Indices: 4508481--4508566 Score: 172
Period size: 41 Copynumber: 2.1 Consensus size: 41
4508471 TAGAGAGTGA
4508481 TGTAGATTTTAGTATGAATATGAAGTTGCTACATGAGGAGT
1 TGTAGATTTTAGTATGAATATGAAGTTGCTACATGAGGAGT
4508522 TGTAGATTTTAGTATGAATATGAAGTTGCTACATGAGGAGT
1 TGTAGATTTTAGTATGAATATGAAGTTGCTACATGAGGAGT
4508563 TGTA
1 TGTA
4508567 CGACTTAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.31, C:0.05, G:0.27, T:0.37
Consensus pattern (41 bp):
TGTAGATTTTAGTATGAATATGAAGTTGCTACATGAGGAGT
Found at i:4510267 original size:6 final size:6
Alignment explanation
Indices: 4510218--4510259 Score: 75
Period size: 6 Copynumber: 7.0 Consensus size: 6
4510208 GATGCGAAAC
*
4510218 CAGAAG CAGAAG CAGAAG CAGAAA CAGAAG CAGAAG CAGAAG
1 CAGAAG CAGAAG CAGAAG CAGAAG CAGAAG CAGAAG CAGAAG
4510260 AAACAGAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.52, C:0.17, G:0.31, T:0.00
Consensus pattern (6 bp):
CAGAAG
Found at i:4510270 original size:12 final size:12
Alignment explanation
Indices: 4510213--4510259 Score: 67
Period size: 12 Copynumber: 3.8 Consensus size: 12
4510203 AAGATGATGC
4510213 GAAACCAGAAGCA
1 GAAA-CAGAAGCA
*
4510226 GAAGCAGAAGCA
1 GAAACAGAAGCA
4510238 GAAACAGAAGCA
1 GAAACAGAAGCA
*
4510250 GAAGCAGAAG
1 GAAACAGAAG
4510260 AAACAGAAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
12 28 0.90
13 3 0.10
ACGTcount: A:0.53, C:0.17, G:0.30, T:0.00
Consensus pattern (12 bp):
GAAACAGAAGCA
Found at i:4510280 original size:21 final size:21
Alignment explanation
Indices: 4510237--4510282 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
4510227 AAGCAGAAGC
* *
4510237 AGAAACAGAAGCAGAAGCAGA
1 AGAAACAGAAGAAAAAGCAGA
* *
4510258 AGAAACAGAAGAAAAATCTGA
1 AGAAACAGAAGAAAAAGCAGA
4510279 AGAA
1 AGAA
4510283 GCTGGTGCAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.61, C:0.11, G:0.24, T:0.04
Consensus pattern (21 bp):
AGAAACAGAAGAAAAAGCAGA
Found at i:4511845 original size:2 final size:2
Alignment explanation
Indices: 4511838--4511862 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4511828 AGAAAATTAC
4511838 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
4511863 TACAAATGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4522821 original size:6 final size:6
Alignment explanation
Indices: 4522810--4522842 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
4522800 TGAATTTCGT
*
4522810 GAAGGG GAAGGG GAAGGG GAAGGG GAATGG GAA
1 GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG GAA
4522843 AGTAGAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.61, T:0.03
Consensus pattern (6 bp):
GAAGGG
Found at i:4525046 original size:17 final size:17
Alignment explanation
Indices: 4525026--4525059 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4525016 AAATAGATTT
4525026 TTAATTAAAAATTTTAA
1 TTAATTAAAAATTTTAA
*
4525043 TTAATTAAAATTTTTAA
1 TTAATTAAAAATTTTAA
4525060 ACCTAAACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAATTAAAAATTTTAA
Found at i:4527147 original size:12 final size:13
Alignment explanation
Indices: 4527127--4527178 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
4527117 TTAAATACTT
4527127 AAAT-TTTTTTAA
1 AAATATTTTTTAA
*
4527139 AAATATTTTTTTA
1 AAATATTTTTTAA
* * *
4527152 CAATA-CTTTCAA
1 AAATATTTTTTAA
4527164 AAATATTTTTTAA
1 AAATATTTTTTAA
4527177 AA
1 AA
4527179 GCATTGTTAA
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
12 12 0.40
13 18 0.60
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (13 bp):
AAATATTTTTTAA
Found at i:4533147 original size:24 final size:24
Alignment explanation
Indices: 4533120--4533178 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
4533110 AGGATTATAT
4533120 TTGATGTATTATCAATGCATGAGC
1 TTGATGTATTATCAATGCATGAGC
* *
4533144 TTGATGTAGTATCAATGTATGAGC
1 TTGATGTATTATCAATGCATGAGC
* *
4533168 TTCATGAATTA
1 TTGATGTATTA
4533179 CACTATCAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (24 bp):
TTGATGTATTATCAATGCATGAGC
Done.