Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168492.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_9, whole genome shotgun sequence
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: 25814696
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 122000 characters in sequence are not A, C, G, or T
File 25 of 126
Found at i:5498797 original size:13 final size:12
Alignment explanation
Indices: 5498768--5499005 Score: 114
Period size: 13 Copynumber: 18.8 Consensus size: 12
5498758 ATTTTCCATA
5498768 AAACCTCAAACCCT
1 AAACCT-AAA-CCT
5498782 AAACCTCAAACCT
1 AAACCT-AAACCT
*
5498795 AAAACCTAACCCT
1 -AAACCTAAACCT
5498808 AAACCTAAACCT
1 AAACCTAAACCT
*
5498820 AAGCCTTAAATCCT
1 AAACC-TAAA-CCT
5498834 AAATCCTAAATCCT
1 AAA-CCTAAA-CCT
5498848 AAACC-AAATCCT
1 AAACCTAAA-CCT
5498860 -AACCTAAACCTT
1 AAACCTAAACC-T
** *
5498872 AAACCCCAACATT
1 AAACCTAAAC-CT
* *
5498885 GAACCCCAAATCCT
1 -AAACCTAAA-CCT
5498899 AAACCTAAACCT
1 AAACCTAAACCT
*
5498911 TAACCATAAACCT
1 AAACC-TAAACCT
* *
5498924 AAACTTAAATCT
1 AAACCTAAACCT
*
5498936 CAAACCCT-AACCA
1 -AAA-CCTAAACCT
5498949 AAACCTTAAA-CT
1 AAACC-TAAACCT
*
5498961 -AACTTTAAACCT
1 AAAC-CTAAACCT
*
5498973 AAACTTTAAACC-
1 AAAC-CTAAACCT
*
5498985 -AACCCAAATCCT
1 AAACCTAAA-CCT
5498997 AAACC-AAAC
1 AAACCTAAAC
5499006 TCCATACCCT
Statistics
Matches: 180, Mismatches: 23, Indels: 45
0.73 0.09 0.18
Matches are distributed among these distances:
10 3 0.02
11 21 0.12
12 49 0.27
13 62 0.34
14 42 0.23
15 3 0.02
ACGTcount: A:0.46, C:0.34, G:0.01, T:0.20
Consensus pattern (12 bp):
AAACCTAAACCT
Found at i:5498811 original size:12 final size:13
Alignment explanation
Indices: 5498768--5498876 Score: 93
Period size: 14 Copynumber: 8.4 Consensus size: 13
5498758 ATTTTCCATA
5498768 AAACCTCAAACCCT
1 AAACCT-AAACCCT
5498782 AAACCTCAAA-CCT
1 AAACCT-AAACCCT
5498795 AAAACCT-AACCCT
1 -AAACCTAAACCCT
5498808 AAACCTAAA-CCT
1 AAACCTAAACCCT
* *
5498820 AAGCCTTAAATCCT
1 AAACC-TAAACCCT
*
5498834 AAATCCTAAATCCT
1 AAA-CCTAAACCCT
*
5498848 AAACC-AAATCCT
1 AAACCTAAACCCT
*
5498860 -AACCTAAACCTT
1 AAACCTAAACCCT
5498872 AAACC
1 AAACC
5498877 CCAACATTGA
Statistics
Matches: 83, Mismatches: 4, Indels: 17
0.80 0.04 0.16
Matches are distributed among these distances:
11 4 0.05
12 27 0.33
13 18 0.22
14 32 0.39
15 2 0.02
ACGTcount: A:0.45, C:0.35, G:0.01, T:0.19
Consensus pattern (13 bp):
AAACCTAAACCCT
Found at i:5498814 original size:6 final size:6
Alignment explanation
Indices: 5498768--5499005 Score: 114
Period size: 6 Copynumber: 37.7 Consensus size: 6
5498758 ATTTTCCATA
*
5498768 AAACCT CAAACCCT AAACCT CAAACCT AAAACCT AACCCT AAACCT AAACCT
1 AAACCT -AAA-CCT AAACCT -AAACCT -AAACCT AAACCT AAACCT AAACCT
*
5498820 AAGCCTT AAATCCT AAATCCT AAATCCT AAACC- AAATCCT -AACCT AAACCTT
1 AAACC-T AAA-CCT AAA-CCT AAA-CCT AAACCT AAA-CCT AAACCT AAACC-T
* * * * * *
5498872 AAACCC CAACATT GAACCCC AAATCCT AAACCT AAACCT TAACCAT AAACCT
1 AAACCT AAAC-CT -AAACCT AAA-CCT AAACCT AAACCT AAACC-T AAACCT
* * * *
5498924 AAACTT AAATCT CAAACCCT -AACCA AAACCTT AAA-CT -AACTTT AAACCT
1 AAACCT AAACCT -AAA-CCT AAACCT AAACC-T AAACCT AAAC-CT AAACCT
* *
5498973 AAACTTT AAACC- -AACCC AAATCCT AAACC- AAAC
1 AAAC-CT AAACCT AAACCT AAA-CCT AAACCT AAAC
5499006 TCCATACCCT
Statistics
Matches: 180, Mismatches: 28, Indels: 48
0.70 0.11 0.19
Matches are distributed among these distances:
4 6 0.03
5 13 0.07
6 78 0.43
7 74 0.41
8 9 0.05
ACGTcount: A:0.46, C:0.34, G:0.01, T:0.20
Consensus pattern (6 bp):
AAACCT
Found at i:5499121 original size:18 final size:18
Alignment explanation
Indices: 5499098--5499157 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
5499088 TTTGTTATTA
5499098 CATGCATTCTTAAATTGT
1 CATGCATTCTTAAATTGT
* **
5499116 CATGCATTCATACTTTGT
1 CATGCATTCTTAAATTGT
* * *
5499134 CATTCA-TATTCAATTGT
1 CATGCATTCTTAAATTGT
5499151 CATGCAT
1 CATGCAT
5499158 CCATATTATT
Statistics
Matches: 31, Mismatches: 10, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
17 11 0.35
18 20 0.65
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.43
Consensus pattern (18 bp):
CATGCATTCTTAAATTGT
Found at i:5499569 original size:22 final size:21
Alignment explanation
Indices: 5499544--5499591 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
5499534 CTAAACATTA
5499544 AAAATACGATCACTTTTTTATC
1 AAAATACGATCA-TTTTTTATC
**
5499566 AAAATTTGATCATTTTTTATC
1 AAAATACGATCATTTTTTATC
5499587 AAAAT
1 AAAAT
5499592 TTAAGGATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.40, C:0.12, G:0.04, T:0.44
Consensus pattern (21 bp):
AAAATACGATCATTTTTTATC
Found at i:5499583 original size:21 final size:22
Alignment explanation
Indices: 5499551--5499593 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 22
5499541 TTAAAAATAC
5499551 GATCACTTTTTTATCAAAATTT
1 GATCACTTTTTTATCAAAATTT
5499573 GATCA-TTTTTTATCAAAATTT
1 GATCACTTTTTTATCAAAATTT
5499594 AAGGATAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.51
Consensus pattern (22 bp):
GATCACTTTTTTATCAAAATTT
Found at i:5500040 original size:9 final size:8
Alignment explanation
Indices: 5500028--5500061 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
5500018 AAAATTTGAA
5500028 AAAAAAAT
1 AAAAAAAT
*
5500036 CAAAAAAT
1 AAAAAAAT
5500044 AAAAAAAAT
1 -AAAAAAAT
5500053 AAAAAAAT
1 AAAAAAAT
5500061 A
1 A
5500062 TTTTTGACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAAAAT
Found at i:5500047 original size:17 final size:17
Alignment explanation
Indices: 5500027--5500061 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
5500017 GAAAATTTGA
*
5500027 AAAAAAAATCAAAAAAT
1 AAAAAAAATAAAAAAAT
5500044 AAAAAAAATAAAAAAAT
1 AAAAAAAATAAAAAAAT
5500061 A
1 A
5500062 TTTTTGACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.86, C:0.03, G:0.00, T:0.11
Consensus pattern (17 bp):
AAAAAAAATAAAAAAAT
Found at i:5501146 original size:38 final size:37
Alignment explanation
Indices: 5501104--5501218 Score: 115
Period size: 38 Copynumber: 3.1 Consensus size: 37
5501094 TAGATAGTAT
5501104 ATGCATTCTATTTCATCCACATTATAATAAGATAACAC
1 ATGCATTCTATTTCATCCACATT-TAATAAGATAACAC
* ** * **
5501142 ATGCACTCTATTTCATGTACATCTTAAT-ATATAGTAC
1 ATGCATTCTATTTCATCCACAT-TTAATAAGATAACAC
* * *
5501179 ATGTATTCCATTTCATCCACATCGTAATAAGATAACAC
1 ATGCATTCTATTTCATCCACAT-TTAATAAGATAACAC
5501217 AT
1 AT
5501219 ACACTCCATC
Statistics
Matches: 60, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
37 28 0.47
38 31 0.52
39 1 0.02
ACGTcount: A:0.37, C:0.21, G:0.07, T:0.36
Consensus pattern (37 bp):
ATGCATTCTATTTCATCCACATTTAATAAGATAACAC
Found at i:5501176 original size:75 final size:76
Alignment explanation
Indices: 5501065--5501288 Score: 229
Period size: 75 Copynumber: 3.0 Consensus size: 76
5501055 ATAGGATAGT
* * * * * * *
5501065 ACATACATTACATCTCATGCATATCCTAGTA-GATAGTATATGCATTCTATTTCATCCACATTAT
1 ACATACACTCCATCTCATGCACATCATAATAGGATAGTATATGCATTCCATTTCATCCACATCAT
5501129 AATAAGATAAC
66 AATAAGATAAC
* * * * * * * * *
5501140 ACATGCACTCTATTTCATGTACATCTTAATA-TATAGTACATGTATTCCATTTCATCCACATCGT
1 ACATACACTCCATCTCATGCACATCATAATAGGATAGTATATGCATTCCATTTCATCCACATCAT
5501204 AATAAGATAAC
66 AATAAGATAAC
* * * * *
5501215 ACATACACTCCATCTCATGCACATCATGATAGGATAGTATATGCACGT-GATCTCATGCACATCA
1 ACATACACTCCATCTCATGCACATCATAATAGGATAGTATATGCA-TTCCATTTCATCCACATCA
5501279 TAATAAGATA
65 TAATAAGATA
5501289 GATAGTACAG
Statistics
Matches: 118, Mismatches: 29, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
75 85 0.72
76 32 0.27
77 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (76 bp):
ACATACACTCCATCTCATGCACATCATAATAGGATAGTATATGCATTCCATTTCATCCACATCAT
AATAAGATAAC
Found at i:5501201 original size:37 final size:37
Alignment explanation
Indices: 5501053--5501212 Score: 117
Period size: 37 Copynumber: 4.2 Consensus size: 37
5501043 ATGTTGGAAA
* * * * *
5501053 TAATAGGATAGTACATACATTAC-ATCTCATGCATATCC
1 TAATA-GATAGTACATGCATT-CTATTTCATCCACATCT
* *
5501091 TAGTAGATAGTATATGCATTCTATTTCATCCACAT-T
1 TAATAGATAGTACATGCATTCTATTTCATCCACATCT
** * **
5501127 ATAATAAGATAACACATGCACTCTATTTCATGTACATCT
1 -TAAT-AGATAGTACATGCATTCTATTTCATCCACATCT
* * * *
5501166 TAATATATAGTACATGTATTCCATTTCATCCACATCG
1 TAATAGATAGTACATGCATTCTATTTCATCCACATCT
5501203 TAATAAGATA
1 TAAT-AGATA
5501213 ACACATACAC
Statistics
Matches: 93, Mismatches: 24, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
36 1 0.01
37 54 0.58
38 37 0.40
39 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (37 bp):
TAATAGATAGTACATGCATTCTATTTCATCCACATCT
Found at i:5501238 original size:38 final size:38
Alignment explanation
Indices: 5501116--5501288 Score: 134
Period size: 38 Copynumber: 4.6 Consensus size: 38
5501106 GCATTCTATT
* * * *
5501116 TCATCCACATTATAATAAGATAACACATGCACTCTATT
1 TCATGCACATCATAATAAGATAACACATGCACTCCATC
* * * ** * * *
5501154 TCATGTACATCTTAAT-ATATAGTACATGTATTCCATT
1 TCATGCACATCATAATAAGATAACACATGCACTCCATC
* * *
5501191 TCATCCACATCGTAATAAGATAACACATACACTCCATC
1 TCATGCACATCATAATAAGATAACACATGCACTCCATC
* * ** * *
5501229 TCATGCACATCATGATAGGATAGTATATGCACGT-GATC
1 TCATGCACATCATAATAAGATAACACATGCAC-TCCATC
5501267 TCATGCACATCATAATAAGATA
1 TCATGCACATCATAATAAGATA
5501289 GATAGTACAG
Statistics
Matches: 102, Mismatches: 31, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
37 28 0.27
38 73 0.72
39 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.31
Consensus pattern (38 bp):
TCATGCACATCATAATAAGATAACACATGCACTCCATC
Found at i:5504010 original size:24 final size:25
Alignment explanation
Indices: 5503969--5504035 Score: 89
Period size: 25 Copynumber: 2.6 Consensus size: 25
5503959 CATAAAAATT
* **
5503969 TAAAAAATTAAAATATTTTTATTAAA
1 TAAAATATTAAAAT-TTTGGATTAAA
*
5503995 TAAAATGTTAAAATTTTGGATTAAA
1 TAAAATATTAAAATTTTGGATTAAA
5504020 TAAAATATTAAAATTT
1 TAAAATATTAAAATTT
5504036 CATAAAAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
25 24 0.67
26 12 0.33
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (25 bp):
TAAAATATTAAAATTTTGGATTAAA
Found at i:5504045 original size:19 final size:18
Alignment explanation
Indices: 5504021--5504084 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 18
5504011 TGGATTAAAT
5504021 AAAATATTAAAATTTCATA
1 AAAATA-TAAAATTTCATA
*
5504040 AAAATATAGAAATTTTATA
1 AAAATATA-AAATTTCATA
*
5504059 GAAAATAAAAAATTCATCATA
1 -AAAATATAAAATT--TCATA
5504080 AAAAT
1 AAAAT
5504085 TCCAAAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
18 2 0.05
19 20 0.53
20 12 0.32
21 4 0.11
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.31
Consensus pattern (18 bp):
AAAATATAAAATTTCATA
Found at i:5517210 original size:25 final size:23
Alignment explanation
Indices: 5517161--5517216 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 23
5517151 TTTTTAAAAA
*
5517161 TAAAATTTT-AAAATATTGAATT
1 TAAAATTTTCCAAATATTGAATT
*
5517183 TAAAACTTTTCCAAATATTTGATTT
1 TAAAA-TTTTCCAAATA-TTGAATT
5517208 TAAAATTTT
1 TAAAATTTT
5517217 AGTTCTAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 5 0.17
23 4 0.14
24 9 0.31
25 11 0.38
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (23 bp):
TAAAATTTTCCAAATATTGAATT
Found at i:5520061 original size:13 final size:13
Alignment explanation
Indices: 5520043--5520067 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5520033 ATAAGATTGT
5520043 TTGAGTAAAAATA
1 TTGAGTAAAAATA
5520056 TTGAGTAAAAAT
1 TTGAGTAAAAAT
5520068 CACAACGTTA
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:0.00, G:0.16, T:0.32
Consensus pattern (13 bp):
TTGAGTAAAAATA
Found at i:5520579 original size:18 final size:17
Alignment explanation
Indices: 5520556--5520608 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 17
5520546 TATATTAAAA
*
5520556 TTAAATTCATAATTTTAT
1 TTAAATTAATAATTTT-T
5520574 TTAAATTAAATAATATTTT
1 TTAAATT-AATAAT-TTTT
*
5520593 TAAAATTAATAATTTT
1 TTAAATTAATAATTTT
5520609 GACATAAGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 3 0.10
18 13 0.42
19 12 0.39
20 3 0.10
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAAATTAATAATTTTT
Found at i:5520743 original size:19 final size:18
Alignment explanation
Indices: 5520700--5520744 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
5520690 TTATTGAATC
*
5520700 AAAATTA-TTTAATTTAA
1 AAAATTATTTTAATTCAA
5520717 AAATATTATTTTAATTCAA
1 AAA-ATTATTTTAATTCAA
5520736 ATAAATTAT
1 A-AAATTAT
5520745 AAATTTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 3 0.12
18 4 0.17
19 15 0.62
20 2 0.08
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
AAAATTATTTTAATTCAA
Found at i:5520929 original size:2 final size:2
Alignment explanation
Indices: 5520922--5520961 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
5520912 TTCTTTCTTT
*
5520922 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5520962 ACCCTCCTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:5521104 original size:20 final size:21
Alignment explanation
Indices: 5521063--5521106 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
5521053 CCCTTTCAAA
*
5521063 AATATATTTCATATAAAATTTT
1 AATAAATTTCATAT-AAATTTT
*
5521085 AATAAATTTCATATAATTTTT
1 AATAAATTTCATATAAATTTT
5521106 A
1 A
5521107 TTTATAGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (21 bp):
AATAAATTTCATATAAATTTT
Found at i:5521643 original size:6 final size:6
Alignment explanation
Indices: 5521632--5521718 Score: 63
Period size: 6 Copynumber: 14.2 Consensus size: 6
5521622 TTATTTTTTA
* * *
5521632 AATTAT AATTAT AATTAT AATTAT AATTAA ATATTAT ATTTAT -ATAATT
1 AATTAT AATTAT AATTAT AATTAT AATTAT A-ATTAT AATTAT AATTA-T
* *
5521681 AATTA- AATAAT CAATTATT ATATCAT AATTA- AATTAT A
1 AATTAT AATTAT -AATTA-T A-ATTAT AATTAT AATTAT A
5521719 CTCACTAAAT
Statistics
Matches: 63, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
5 11 0.17
6 33 0.52
7 15 0.24
8 4 0.06
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (6 bp):
AATTAT
Found at i:5521667 original size:25 final size:25
Alignment explanation
Indices: 5521639--5521714 Score: 68
Period size: 25 Copynumber: 3.0 Consensus size: 25
5521629 TTAAATTATA
*
5521639 ATTATAATTATAATTATAATTAAAT
1 ATTATAATTATAATAATAATTAAAT
*
5521664 ATTATATTTAT-ATAATTAATTAAAT
1 ATTATAATTATAATAA-TAATTAAAT
*
5521689 A--ATCAATTATTATATCATAATTAAAT
1 ATTAT-AATTA-TA-ATAATAATTAAAT
5521715 TATACTCACT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
23 2 0.05
24 7 0.17
25 21 0.50
26 9 0.21
27 3 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (25 bp):
ATTATAATTATAATAATAATTAAAT
Found at i:5522552 original size:2 final size:2
Alignment explanation
Indices: 5522545--5522569 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5522535 ACTCAACTAC
5522545 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
5522570 AAAGGTGTGT
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:5531778 original size:3 final size:3
Alignment explanation
Indices: 5531772--5531838 Score: 71
Period size: 3 Copynumber: 22.3 Consensus size: 3
5531762 ATGATAATAA
* * * * * *
5531772 TAT TAT TAT TCT TAT TAT TAT TAT TAA TAT TAA TAA TAA TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
5531820 TAT TAT TAT TAT TAC TAT T
1 TAT TAT TAT TAT TAT TAT T
5531839 TTTGCATGAA
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:5534290 original size:66 final size:65
Alignment explanation
Indices: 5534188--5534366 Score: 168
Period size: 66 Copynumber: 2.8 Consensus size: 65
5534178 AGGACTAAAT
* * * * *
5534188 CGCAAGTTACGAAATGAAAATGA-CTGGGTTTAAACCATGAGTCAAAAATTATGA-TCGGGATTG
1 CGCAAGTTAAGAAATGAAAATGATC-GGATTTGAACCATGAGTCAAAAATTATGACT-AGAATTG
5534251 AA
64 AA
* * * *
5534253 CTGCAAGTTAAGAAATGAAAATGATCGAATTTGAACCATAAGCCAAAAA-TATTACTAGAATTGA
1 C-GCAAGTTAAGAAATGAAAATGATCGGATTTGAACCATGAGTCAAAAATTATGACTAGAATTGA
*
5534317 G
65 A
* * * *
5534318 CACAAGTTAATAAATGAAAATGATTGGGA-TTGAACTATGAGTCAAAAAT
1 CGCAAGTTAAGAAATGAAAATGA-TCGGATTTGAACCATGAGTCAAAAAT
5534367 AACTAGGATT
Statistics
Matches: 92, Mismatches: 17, Indels: 10
0.77 0.14 0.08
Matches are distributed among these distances:
64 36 0.39
65 15 0.16
66 40 0.43
67 1 0.01
ACGTcount: A:0.44, C:0.11, G:0.20, T:0.25
Consensus pattern (65 bp):
CGCAAGTTAAGAAATGAAAATGATCGGATTTGAACCATGAGTCAAAAATTATGACTAGAATTGAA
Found at i:5534351 original size:64 final size:62
Alignment explanation
Indices: 5534256--5534379 Score: 151
Period size: 64 Copynumber: 2.0 Consensus size: 62
5534246 GATTGAACTG
5534256 CAAGTTAAGAAATGAAAATGATCGAATTTGAACCATAAGCCAAAAATATTACTAGAATTGAGCA
1 CAAGTTAAGAAATGAAAATGATCGAATTTGAACCATAAGCCAAAAATA--ACTAGAATTGAGCA
* * * * * * *
5534320 CAAGTTAATAAATGAAAATGATTGGGA-TTGAACTATGAGTCAAAAATAACTAGGATTGAG
1 CAAGTTAAGAAATGAAAATGA-TCGAATTTGAACCATAAGCCAAAAATAACTAGAATTGAG
5534380 TCATAAGTCG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 11 0.21
64 38 0.73
65 3 0.06
ACGTcount: A:0.47, C:0.10, G:0.19, T:0.25
Consensus pattern (62 bp):
CAAGTTAAGAAATGAAAATGATCGAATTTGAACCATAAGCCAAAAATAACTAGAATTGAGCA
Found at i:5534797 original size:35 final size:36
Alignment explanation
Indices: 5534758--5535065 Score: 182
Period size: 35 Copynumber: 8.8 Consensus size: 36
5534748 CTGAATCGCG
* * * *
5534758 AGTCAAAGAAT-AAAGATGACCAGGATTGAACTGTA
1 AGTCAAAAAATGAAAAATGACCAGGACTGAACTATA
** * * * *
5534793 AGTCAAAAAATGAAAAATGACTGGGATTAAACCATG
1 AGTCAAAAAATGAAAAATGACCAGGACTGAACTATA
* * * *** **
5534829 AGTTAAAGAATAAAAAATGATTGGGACTGAACCGTA
1 AGTCAAAAAATGAAAAATGACCAGGACTGAACTATA
* *
5534865 AATC-AAAAATG-AAAATGACCAGGACTGAACTACA
1 AGTCAAAAAATGAAAAATGACCAGGACTGAACTATA
* * * * * **
5534899 AGTCGAGAAAT-AAAAATAACCAAGATTGAACTGCA
1 AGTCAAAAAATGAAAAATGACCAGGACTGAACTATA
*** *
5534934 AGTCAAAAAATG-AAAATGGTTAGGACTGAACCATA
1 AGTCAAAAAATGAAAAATGACCAGGACTGAACTATA
* * * * *
5534969 AGTCAAAAAAT-AAAGATGACCAAGATTGAATTATG
1 AGTCAAAAAATGAAAAATGACCAGGACTGAACTATA
* * * *
5535004 AGTCGAATAATG-AAAATGACAAGGACTGAACTACA
1 AGTCAAAAAATGAAAAATGACCAGGACTGAACTATA
* *
5535039 AGTTAAAAAAT-AAAAATGACCAAGACT
1 AGTCAAAAAATGAAAAATGACCAGGACT
5535066 AAATCGTAAG
Statistics
Matches: 200, Mismatches: 66, Indels: 14
0.71 0.24 0.05
Matches are distributed among these distances:
34 20 0.10
35 133 0.67
36 47 0.23
ACGTcount: A:0.50, C:0.12, G:0.19, T:0.19
Consensus pattern (36 bp):
AGTCAAAAAATGAAAAATGACCAGGACTGAACTATA
Found at i:5535008 original size:105 final size:105
Alignment explanation
Indices: 5534547--5535092 Score: 375
Period size: 105 Copynumber: 5.2 Consensus size: 105
5534537 ATTAAGCTAC
* * *
5534547 AAGTCAAAAAATAAAGATGACCAGGTTTGAA-TCATGAGT-TAAAGAATAAATATGACTAAGATT
1 AAGTCAAAAAATAAAGATGACCAGGATTGAACT-ATGAGTCGAAA-AATAAAAATGACTAAGATT
* * * * * * * ** *
5534610 GAACTGCGAGTCAAGAAATGAAAATAATCAGGA-TCAAATGGC
64 GAACTACAAGTCAAAAAATAAAAATGATTAGGACT-GAACCGT
* * * * * * * ** *
5534652 AAGTCCAAAAATAAATATGACAAGGATTGAACCATGAGTTGAGAAATGAAAACAACTGAGATTGA
1 AAGTCAAAAAATAAAGATGACCAGGATTGAACTATGAGTCGAAAAATAAAAATGACTAAGATTGA
* * * * * * * *
5534717 ACCATAAATCAGAAAATAAAAATAATTAAGACTGAATCGC
66 ACTACAAGTCAAAAAATAAAAATGATTAGGACTGAACCGT
* * * * * ** *
5534757 GAGTCAAAGAATAAAGATGACCAGGATTGAACTGTAAGTCAAAAAATGAAAAATGACTGGGATTA
1 AAGTCAAAAAATAAAGATGACCAGGATTGAACTATGAGTCGAAAAAT-AAAAATGACTAAGATTG
* ** * * *
5534822 AACCATGAGTTAAAGAATAAAAAATGATTGGGACTGAACCGT
65 AACTACAAGTCAAAAAAT-AAAAATGATTAGGACTGAACCGT
* * ** * * *
5534864 AAATC-AAAAATGAAA-ATGACCAGGACTGAACTACAAGTCGAGAAATAAAAATAACCAAGATTG
1 AAGTCAAAAAAT-AAAGATGACCAGGATTGAACTATGAGTCGAAAAATAAAAATGACTAAGATTG
* * * *
5534927 AACTGCAAGTCAAAAAATGAAAATGGTTAGGACTGAACCAT
65 AACTACAAGTCAAAAAATAAAAATGATTAGGACTGAACCGT
* * * * *
5534968 AAGTCAAAAAATAAAGATGACCAAGATTGAATTATGAGTCGAATAATGAAAATGAC-AAGGACTG
1 AAGTCAAAAAATAAAGATGACCAGGATTGAACTATGAGTCGAAAAATAAAAATGACTAA-GATTG
* ** * * *
5535032 AACTACAAGTTAAAAAATAAAAATGACCAAGACTAAATCGT
65 AACTACAAGTCAAAAAATAAAAATGATTAGGACTGAACCGT
*
5535073 AAGTCAAAGAATAAAGATGA
1 AAGTCAAAAAATAAAGATGA
5535093 TTAGGACTAA
Statistics
Matches: 337, Mismatches: 95, Indels: 18
0.75 0.21 0.04
Matches are distributed among these distances:
104 28 0.08
105 226 0.67
106 59 0.18
107 24 0.07
ACGTcount: A:0.50, C:0.12, G:0.18, T:0.20
Consensus pattern (105 bp):
AAGTCAAAAAATAAAGATGACCAGGATTGAACTATGAGTCGAAAAATAAAAATGACTAAGATTGA
ACTACAAGTCAAAAAATAAAAATGATTAGGACTGAACCGT
Found at i:5535086 original size:35 final size:35
Alignment explanation
Indices: 5535037--5535125 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 35
5535027 GACTGAACTA
* * *
5535037 CAAGTTAAAAAATAAAAATGACCAAGACTAAATCG
1 CAAGTCAAAGAATAAAAATGACCAAGACTAAACCG
* * ** * *
5535072 TAAGTCAAAGAATAAAGATGATTAGGACTAAGCCG
1 CAAGTCAAAGAATAAAAATGACCAAGACTAAACCG
*
5535107 CAAGTCACAGAATAAAAAT
1 CAAGTCAAAGAATAAAAAT
5535126 AAAAGGGACT
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.53, C:0.13, G:0.16, T:0.18
Consensus pattern (35 bp):
CAAGTCAAAGAATAAAAATGACCAAGACTAAACCG
Found at i:5535099 original size:70 final size:70
Alignment explanation
Indices: 5534758--5535100 Score: 253
Period size: 70 Copynumber: 4.9 Consensus size: 70
5534748 CTGAATCGCG
* * * * * * *
5534758 AGTCAAAGAATAAAGATGACCAGGATTGAA-CTGTAAGTCAAAAAATGAAAAATGACTGGGATTA
1 AGTCAAAAAATAAAAATGACCAAGATTGAATC-GTAAGTCAAAAAATG-AAAATGATTAGGACTG
* **
5534822 AACCATG
64 AACTACA
* * **** * * * **
5534829 AGTTAAAGAATAAAAAATGATTGGGACTGAACCGTAAATC-AAAAATGAAAATGACCAGGACTGA
1 AGTCAAAAAAT-AAAAATGACCAAGATTGAATCGTAAGTCAAAAAATGAAAATGATTAGGACTGA
5534893 ACTACA
65 ACTACA
* * * * *
5534899 AGTCGAGAAATAAAAATAACCAAGATTGAA-CTGCAAGTCAAAAAATGAAAATGGTTAGGACTGA
1 AGTCAAAAAATAAAAATGACCAAGATTGAATC-GTAAGTCAAAAAATGAAAATGATTAGGACTGA
* *
5534963 ACCATA
65 ACTACA
* ** * * * **
5534969 AGTCAAAAAATAAAGATGACCAAGATTGAATTATGAGTCGAATAATGAAAATGACAAGGACTGAA
1 AGTCAAAAAATAAAAATGACCAAGATTGAATCGTAAGTCAAAAAATGAAAATGATTAGGACTGAA
5535034 CTACA
66 CTACA
* * * *
5535039 AGTTAAAAAATAAAAATGACCAAGACTAAATCGTAAGTCAAAGAAT-AAAGATGATTAGGACT
1 AGTCAAAAAATAAAAATGACCAAGATTGAATCGTAAGTCAAAAAATGAAA-ATGATTAGGACT
5535101 AAGCCGCAAG
Statistics
Matches: 209, Mismatches: 57, Indels: 13
0.75 0.20 0.05
Matches are distributed among these distances:
68 1 0.00
69 21 0.10
70 149 0.71
71 17 0.08
72 20 0.10
73 1 0.00
ACGTcount: A:0.50, C:0.12, G:0.19, T:0.20
Consensus pattern (70 bp):
AGTCAAAAAATAAAAATGACCAAGATTGAATCGTAAGTCAAAAAATGAAAATGATTAGGACTGAA
CTACA
Found at i:5536081 original size:11 final size:10
Alignment explanation
Indices: 5536066--5536092 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
5536056 TCTTTTTTTT
5536066 CTTTTTTGAC
1 CTTTTTTGAC
5536076 CTTTTTTGAC
1 CTTTTTTGAC
5536086 CTTTTTT
1 CTTTTTT
5536093 ATTATTACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.07, C:0.19, G:0.07, T:0.67
Consensus pattern (10 bp):
CTTTTTTGAC
Found at i:5544109 original size:22 final size:24
Alignment explanation
Indices: 5544065--5544109 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
5544055 TCAATACATT
*
5544065 TTATGGGCTCTTAAAGTGGGCTTC
1 TTATGGGCTCTCAAAGTGGGCTTC
5544089 TTATGGGCT-TCAAA-TGGGCTT
1 TTATGGGCTCTCAAAGTGGGCTT
5544110 TGTTAAGGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
23 4 0.20
24 9 0.45
ACGTcount: A:0.18, C:0.16, G:0.29, T:0.38
Consensus pattern (24 bp):
TTATGGGCTCTCAAAGTGGGCTTC
Found at i:5545150 original size:17 final size:16
Alignment explanation
Indices: 5545130--5545163 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5545120 GGTTTTTGCA
*
5545130 TAATTTAAGTTTTAGTT
1 TAATTTAA-TTTAAGTT
5545147 TAATTTAATTTAAGTT
1 TAATTTAATTTAAGTT
5545163 T
1 T
5545164 TTTGCATCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (16 bp):
TAATTTAATTTAAGTT
Found at i:5552260 original size:22 final size:22
Alignment explanation
Indices: 5552235--5552277 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
5552225 CTTAAAACTC
5552235 ATTCGTTTATTGTTCATTTATT
1 ATTCGTTTATTGTTCATTTATT
*
5552257 ATTCGTTTGTTGTTCATTTAT
1 ATTCGTTTATTGTTCATTTAT
5552278 AATAATACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.16, C:0.09, G:0.12, T:0.63
Consensus pattern (22 bp):
ATTCGTTTATTGTTCATTTATT
Found at i:5556699 original size:61 final size:59
Alignment explanation
Indices: 5556491--5556821 Score: 272
Period size: 60 Copynumber: 5.5 Consensus size: 59
5556481 GCATTTTTGG
* *
5556491 TTTTTGGCCAAAAATGCCTTCAATAATCTCTTTC-ATTTTTTTTATGGATTATTCAAGGTA
1 TTTTTGGCCAAAAATGCCTTGAATAATCT-TTTCAATTTTTTTTA-GGATTATTCAAGGCA
* * ** ** *** * * *
5556551 TTTTTGGCCAAAAAATGCTTTGAATAATCCCTTGAAAAATTGAATGGGGTTATTTAAGGCA
1 TTTTTGGCC-AAAAATGCCTTGAATAAT-CTTTTCAATTTTTTTTAGGATTATTCAAGGCA
* * * **
5556612 TTTTTAGCCAAAAAACGCCTTGAATAATCTTATTTCAATTTTTTTTAAGATTATTCAAGGTG
1 TTTTTGGCC-AAAAATGCCTTGAATAATC-T-TTTCAATTTTTTTTAGGATTATTCAAGGCA
* * * * *
5556674 TTTTTGGCCAAAAATGTCTTCAATAATCTCTTTTAATTTTTTTTAAGATTATTCAAGGCG
1 TTTTTGGCCAAAAATGCCTTGAATAATCT-TTTCAATTTTTTTTAGGATTATTCAAGGCA
* *
5556734 TTTCTGGCCAAAACA-GCCTTGAATAATCCTTTTCCA-TTTTTTTAGGGATTATTCAAGGCA
1 TTTTTGGCCAAAA-ATGCCTTGAATAAT-CTTTTCAATTTTTTTTA-GGATTATTCAAGGCA
* **
5556794 TTTTTGGCTAGAAAATATCTTGAATAAT
1 TTTTTGGCCA-AAAATGCCTTGAATAAT
5556822 TTCTTACAAA
Statistics
Matches: 212, Mismatches: 49, Indels: 19
0.76 0.17 0.07
Matches are distributed among these distances:
59 8 0.04
60 87 0.41
61 87 0.41
62 30 0.14
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (59 bp):
TTTTTGGCCAAAAATGCCTTGAATAATCTTTTCAATTTTTTTTAGGATTATTCAAGGCA
Found at i:5556728 original size:60 final size:60
Alignment explanation
Indices: 5556491--5556826 Score: 286
Period size: 61 Copynumber: 5.5 Consensus size: 60
5556481 GCATTTTTGG
* * *
5556491 TTTTTGGCCAAAAATGCCTTCAATAATCTC-TTTCATTTTTTTTATGGATTATTCAAGGTA
1 TTTTTGGCCAAAAATGCCTTGAATAATCTCTTTTAATTTTTTTTA-GGATTATTCAAGGCA
* * ** ** *** * * *
5556551 TTTTTGGCCAAAAAATGCTTTGAATAATCCCTTGAAAAATTGAATGGGGTTATTTAAGGCA
1 TTTTTGGCC-AAAAATGCCTTGAATAATCTCTTTTAATTTTTTTTAGGATTATTCAAGGCA
* * * **
5556612 TTTTTAGCCAAAAAACGCCTTGAATAATCT-TATTTCAATTTTTTTTAAGATTATTCAAGGTG
1 TTTTTGGCC-AAAAATGCCTTGAATAATCTCT-TTT-AATTTTTTTTAGGATTATTCAAGGCA
* * * *
5556674 TTTTTGGCCAAAAATGTCTTCAATAATCTCTTTTAATTTTTTTTAAGATTATTCAAGGCG
1 TTTTTGGCCAAAAATGCCTTGAATAATCTCTTTTAATTTTTTTTAGGATTATTCAAGGCA
* *
5556734 TTTCTGGCCAAAACA-GCCTTGAATAATC-CTTTTCCA-TTTTTTTAGGGATTATTCAAGGCA
1 TTTTTGGCCAAAA-ATGCCTTGAATAATCTCTTTT-AATTTTTTTTA-GGATTATTCAAGGCA
* ** *
5556794 TTTTTGGCTAGAAAATATCTTGAATAATTTCTT
1 TTTTTGGCCA-AAAATGCCTTGAATAATCTCTT
5556827 ACAAAAAATT
Statistics
Matches: 217, Mismatches: 48, Indels: 20
0.76 0.17 0.07
Matches are distributed among these distances:
59 13 0.06
60 81 0.37
61 91 0.42
62 32 0.15
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.43
Consensus pattern (60 bp):
TTTTTGGCCAAAAATGCCTTGAATAATCTCTTTTAATTTTTTTTAGGATTATTCAAGGCA
Found at i:5557322 original size:125 final size:125
Alignment explanation
Indices: 5557083--5557410 Score: 307
Period size: 128 Copynumber: 2.6 Consensus size: 125
5557073 CAAAAAAGGG
* ** *
5557083 ATTATTCAAGGCATTTTTGGCCAAAAAATGCCTTGAATAATCCCCTTCCATTTTCTTTTGAGATT
1 ATTATTCAAAGCATTTTTGGCCAAAAAACACCTTGAATAATCCCCTTCCA-TTTCTTTTGAAATT
* *
5557148 ATTCAAGGTGTTTTTGAACAAAAAATGCTTTGAATAATCCCTTAGAAAAAATTGAAAGGGATT
65 ATTCAAGGTATTTTTGAACAAAAAAT-CATTGAATAATCCCTTA-AAAAAATTGAAAGGGATT
* * * *
5557211 ATTATTCAAAGCATTTTTTGCCTAAAAACACTTTGAATAATCTCCTAT-C-TTT-TTTTGAAATT
1 ATTATTCAAAGCATTTTTGGCCAAAAAACACCTTGAATAATCCCCT-TCCATTTCTTTTGAAATT
* *
5557273 ATTCAAGGTATTTTTG-TCTAAAAACAT-ATTGAATAATCCCTTACAAAAAATTGAATGGG---
65 ATTCAAGGTATTTTTGAAC-AAAAA-ATCATTGAATAATCCCTTA-AAAAAATTGAAAGGGATT
* * * * * * * **
5557332 GTTATTCAAGGTATTTCTGACC-AAAAACACCTTGAATAAT-CCCTTTCATTTTTTATTGGGGAT
1 ATTATTCAAAGCATTTTTGGCCAAAAAACACCTTGAATAATCCCCTTCCATTTCTT-TT-GAAAT
*
5557395 TATTCAAGGTGTTTTT
64 TATTCAAGGTATTTTT
5557411 AGCCAAAAAT
Statistics
Matches: 168, Mismatches: 24, Indels: 21
0.79 0.11 0.10
Matches are distributed among these distances:
118 1 0.01
119 4 0.02
120 20 0.12
121 18 0.11
122 2 0.01
123 18 0.11
124 30 0.18
125 29 0.17
126 5 0.03
128 40 0.24
129 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (125 bp):
ATTATTCAAAGCATTTTTGGCCAAAAAACACCTTGAATAATCCCCTTCCATTTCTTTTGAAATTA
TTCAAGGTATTTTTGAACAAAAAATCATTGAATAATCCCTTAAAAAAATTGAAAGGGATT
Found at i:5559775 original size:17 final size:17
Alignment explanation
Indices: 5559743--5559790 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
5559733 GAATAATATA
* * *
5559743 AAAAAGAAAATGAAATT
1 AAAAATAAAATAAAAAT
*
5559760 AAAAA-ATAATAAAAAT
1 AAAAATAAAATAAAAAT
5559776 AAAAATAAAATAAAA
1 AAAAATAAAATAAAA
5559791 TGTGGGCGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 13 0.50
17 13 0.50
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (17 bp):
AAAAATAAAATAAAAAT
Found at i:5559789 original size:27 final size:30
Alignment explanation
Indices: 5559734--5559790 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 30
5559724 TTATTTTCTG
*
5559734 AATAATATAAAAAAGAAAATGAAATTAAAA
1 AATAATATAAAAAAGAAAATGAAAATAAAA
*
5559764 AATAATA-AAAATA-AAAAT-AAAATAAAA
1 AATAATATAAAAAAGAAAATGAAAATAAAA
5559791 TGTGGGCGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 8 0.32
28 5 0.20
29 5 0.20
30 7 0.28
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (30 bp):
AATAATATAAAAAAGAAAATGAAAATAAAA
Found at i:5563628 original size:307 final size:307
Alignment explanation
Indices: 5563038--5563642 Score: 955
Period size: 307 Copynumber: 2.0 Consensus size: 307
5563028 TTAAGCATGT
* * * *
5563038 AATTATTCAAATTTGTCAAGTATATGCTTAATCATAGAATTATTTAAAACATGCATGATCTTATA
1 AATTATTCAAATTTGTCAACTATATGCTTAATCATAAAATTATTCAAAACATGCATAATCTTATA
* *
5563103 GGTTCATGCAATATAAATAGCATGTTAGAACAATATCGTTTATAAATATTATAGCAAACAATAAC
66 GGTTCATGCAATATAAATAGCATGCTAGAACAATATCCTTTATAAATATTATAGCAAACAATAAC
* *
5563168 TATAAATTTTAACATGCCTACTCATACATTGTCATTTTTCAAAGCATTTTCTATTTTAAGACAAA
131 GATAAATTTTAACATGCCTACTCATACATAGTCATTTTTC-AAGCATTTTCTATTTTAAGACAAA
*
5563233 ATAACTTTGTGTTTGTCTCTAATACAATCTTGAAGAAAAATATAGTAACCAATCTATAAAACATA
195 ATAACTTTGTCTTTGTCTCTAATACAATCTTGAAGAAAAATATAGTAACCAATCTATAAAACATA
*
5563298 AATTTATAGTGCTTTGCCTTTTTTATATTTGTTGGAATACATTGTGTA
260 AATCTATAGTGCTTTGCCTTTTTTATATTTGTTGGAATACATTGTGTA
*
5563346 AATTATTCAAATTTGTCAACTGTCATGCTTAATCATAAAATTATTCAAAACATGCATAATCTTAT
1 AATTATTCAAATTTGTCAACTAT-ATGCTTAATCATAAAATTATTCAAAACATGCATAATCTTAT
*
5563411 AGGTTCATGCAATATAAATAGCTTGCTAGAACAA-ATCCTTTATAAATATTATAGCAAACAATAA
65 AGGTTCATGCAATATAAATAGCATGCTAGAACAATATCCTTTATAAATATTATAGCAAACAATAA
* * *
5563475 CGGTAAATTTTAACATGCCCT-CTCATACATAGTCATTTTTTC-AGTATTTTTTATTTTAAGACA
130 CGATAAATTTTAACATG-CCTACTCATACATAGTCA-TTTTTCAAGCATTTTCTATTTTAAGACA
** * * * **
5563538 AAATAACTTTGTCTTTGTCTCTAATACAATCTTGAAGCGAAATTTATTAAGCAATCTATAAAATG
193 AAATAACTTTGTCTTTGTCTCTAATACAATCTTGAAGAAAAATATAGTAACCAATCTATAAAACA
5563603 TAAATCTATAGTGCTTTGCCTTTTTTATATTTGTTGGAAT
258 TAAATCTATAGTGCTTTGCCTTTTTTATATTTGTTGGAAT
5563643 GCTTTGCATA
Statistics
Matches: 272, Mismatches: 22, Indels: 7
0.90 0.07 0.02
Matches are distributed among these distances:
307 115 0.42
308 78 0.29
309 79 0.29
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (307 bp):
AATTATTCAAATTTGTCAACTATATGCTTAATCATAAAATTATTCAAAACATGCATAATCTTATA
GGTTCATGCAATATAAATAGCATGCTAGAACAATATCCTTTATAAATATTATAGCAAACAATAAC
GATAAATTTTAACATGCCTACTCATACATAGTCATTTTTCAAGCATTTTCTATTTTAAGACAAAA
TAACTTTGTCTTTGTCTCTAATACAATCTTGAAGAAAAATATAGTAACCAATCTATAAAACATAA
ATCTATAGTGCTTTGCCTTTTTTATATTTGTTGGAATACATTGTGTA
Found at i:5564319 original size:34 final size:34
Alignment explanation
Indices: 5564280--5564349 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 34
5564270 TTTGAAGTTT
*
5564280 TATAATTTTATGAAAATAAATTT-TCGAAAATTTA
1 TATAATTTTATGAAAATAAATTTAT-GAAAAATTA
*
5564314 TATAATTTTTTGAAAATAAATTTATGAAAAATTA
1 TATAATTTTATGAAAATAAATTTATGAAAAATTA
5564348 TA
1 TA
5564350 AACCTTTTCG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 32 0.97
35 1 0.03
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (34 bp):
TATAATTTTATGAAAATAAATTTATGAAAAATTA
Found at i:5564363 original size:34 final size:34
Alignment explanation
Indices: 5564291--5564379 Score: 92
Period size: 34 Copynumber: 2.6 Consensus size: 34
5564281 ATAATTTTAT
* * *
5564291 GAAAATAAATTT-TCGAAAATTTATATAATTTTTT
1 GAAAATAAATTTAT-GAAAAATTATATAACTTTTC
5564325 GAAAATAAATTTATGAAAAATTATA-AACCTTTTC
1 GAAAATAAATTTATGAAAAATTATATAA-CTTTTC
*
5564359 GAAAATTTAACTTTATGAAAA
1 GAAAA--TAAATTTATGAAAA
5564380 TGAATTTACG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
33 2 0.04
34 31 0.66
35 1 0.02
36 13 0.28
ACGTcount: A:0.48, C:0.06, G:0.07, T:0.39
Consensus pattern (34 bp):
GAAAATAAATTTATGAAAAATTATATAACTTTTC
Found at i:5564462 original size:35 final size:33
Alignment explanation
Indices: 5564396--5564495 Score: 119
Period size: 34 Copynumber: 2.9 Consensus size: 33
5564386 TACGAAGAGG
* * *
5564396 TTTATAATATTTTAAAATTTTATTTTTAAAAAA
1 TTTATAATTTTTTAAAAATTTATTTTAAAAAAA
*
5564429 TTATATAATTTTTTAAAAATTTATTTTCAAAAAAG
1 TT-TATAATTTTTTAAAAATTTATTTT-AAAAAAA
* *
5564464 TTTATAATTTTTCATAAATTTATTTCTAAAAA
1 TTTATAATTTTTTAAAAATTTATTT-TAAAAA
5564496 TTTATGTGAA
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
33 2 0.03
34 48 0.83
35 8 0.14
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (33 bp):
TTTATAATTTTTTAAAAATTTATTTTAAAAAAA
Found at i:5565630 original size:2 final size:2
Alignment explanation
Indices: 5565623--5565653 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5565613 TCACGCAAAG
5565623 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 A
5565654 GAGAGAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5565658 original size:2 final size:2
Alignment explanation
Indices: 5565653--5565683 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5565643 ATATATATAT
5565653 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
5565684 AAACAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5567228 original size:2 final size:2
Alignment explanation
Indices: 5567223--5567253 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5567213 TACACACACA
5567223 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 A
5567254 GCCATTTACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5571570 original size:36 final size:38
Alignment explanation
Indices: 5571502--5571572 Score: 101
Period size: 36 Copynumber: 1.9 Consensus size: 38
5571492 CAAGAAGCAA
* *
5571502 TCTTTATCTTTTTTAGGCTCAAGATAGTAACCTCTCAC
1 TCTTTATCTTTTCTAGGCTCAAGATAGCAACCTCTCAC
*
5571540 TCTTTATC-TTTCTAGTCT-AAGATAGCAACCTCT
1 TCTTTATCTTTTCTAGGCTCAAGATAGCAACCTCT
5571573 AGTATTACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 14 0.47
37 8 0.27
38 8 0.27
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.42
Consensus pattern (38 bp):
TCTTTATCTTTTCTAGGCTCAAGATAGCAACCTCTCAC
Found at i:5572573 original size:13 final size:13
Alignment explanation
Indices: 5572552--5572600 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
5572542 ATTTTAGAGT
5572552 TTTTCAAAAACCA
1 TTTTCAAAAACCA
*
5572565 TTTT-GAAAACCA
1 TTTTCAAAAACCA
*
5572577 TTTTCAAAAATCA
1 TTTTCAAAAACCA
*
5572590 TTTTGAAAAAC
1 TTTTCAAAAAC
5572601 TCCACCTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.45, C:0.16, G:0.04, T:0.35
Consensus pattern (13 bp):
TTTTCAAAAACCA
Found at i:5572575 original size:12 final size:12
Alignment explanation
Indices: 5572558--5572598 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
5572548 GAGTTTTTCA
5572558 AAAACCATTTTG
1 AAAACCATTTTG
*
5572570 AAAACCATTTTCA
1 AAAACCATTTT-G
*
5572583 AAAATCATTTTG
1 AAAACCATTTTG
5572595 AAAA
1 AAAA
5572599 ACTCCACCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 15 0.60
13 10 0.40
ACGTcount: A:0.49, C:0.15, G:0.05, T:0.32
Consensus pattern (12 bp):
AAAACCATTTTG
Found at i:5576097 original size:303 final size:307
Alignment explanation
Indices: 5575534--5576146 Score: 820
Period size: 303 Copynumber: 2.0 Consensus size: 307
5575524 TGAACCATTT
* * *
5575534 CAACAAATTTCAAATGACAAAACAAAGTTGTTTAAGTGGTCATTTGGCCTTAGAAACAAAGAAAT
1 CAACAAATTTCAAATGACAAAACAAAGTTATTCAAGTGGTCATTTGACCTTAGAAACAAAGAAAT
* *
5575599 AAAAAAGTCAACTTTGAAACCCCACATTTCCTTGTAAAAGGCTTTTAAGATGGGCAAATACATTT
66 AAAAAAGTCAACTTTGAAACCCCACATTTCCTTGTAAAAGGCTTTTAAGATAGACAAATACATTT
* *
5575664 AAACTCAAATTTAAGCTTTTTAAACCATTTAGAAAAGTTTTATATCACAATTTGGAATTGTCCTC
131 AAACTC--ATTTAAGCTATTTAAA-CA--TAGAAAAGTTTTATATCACAATTTGGAATTGTCCTA
* * *
5575729 ATGGCTTTTATGTCCATATATGCTCAAAAACAAGATTTGATCTTTTAAGTTTCAAAATCTTTTAT
191 ATGGCTTTTATGCCCAAATATGCTCAAAAACAAGATTTGATCTTTTAAGTTTCAAAATATTTTAT
5575794 AACTTGCATGTAACACTATGAAAAATTAAAA-CTATTGCAAGTTAATCAAGTTTTC
256 AACTTGCATGTAACACTATG---AATTAAAATC-ATTGCAAGTTAATCAAGTTTTC
* *
5575849 CAACAAATTTCAAATGACTAAACAAAGTTATTCAAGTGGTCATTTGACCTTAGAAACAAGGAAAT
1 CAACAAATTTCAAATGACAAAACAAAGTTATTCAAGTGGTCATTTGACCTTAGAAACAAAGAAAT
* * *
5575914 -AAAAAGTCAACTCTT-AAACCCTATATTTCCTTG-AAGAAGGCTTTTACGATAGACAAATACAT
66 AAAAAAGTCAACT-TTGAAACCCCACATTTCCTTGTAA-AAGGCTTTTAAGATAGACAAATACAT
* * *
5575976 TTAAGCTC-TTTAA-ATCATTT-AA-A-A-AAAA-TTTTATATCACAATTTGGATTTGT-CTAAA
129 TTAAACTCATTTAAGCT-ATTTAAACATAGAAAAGTTTTATATCACAATTTGGAATTGTCCT-AA
*
5576033 TGGTTTTTATGCCCAAATATGCTCAAAAACAAGATTTGATCTTTTCAA-TTTCAAAATATTTTAT
192 TGGCTTTTATGCCCAAATATGCTCAAAAACAAGATTTGATCTTTT-AAGTTTCAAAATATTTTAT
* *
5576097 AACTTGCTTGTAACACTATGAATTAAAATCATTGTAAGTTAATCAAGTTT
256 AACTTGCATGTAACACTATGAATTAAAATCATTGCAAGTTAATCAAGTTT
5576147 CTTTGTTTGT
Statistics
Matches: 271, Mismatches: 21, Indels: 27
0.85 0.07 0.08
Matches are distributed among these distances:
300 27 0.10
301 1 0.00
302 2 0.01
303 100 0.37
304 6 0.02
305 1 0.00
308 1 0.00
310 3 0.01
311 8 0.03
313 2 0.01
314 58 0.21
315 62 0.23
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (307 bp):
CAACAAATTTCAAATGACAAAACAAAGTTATTCAAGTGGTCATTTGACCTTAGAAACAAAGAAAT
AAAAAAGTCAACTTTGAAACCCCACATTTCCTTGTAAAAGGCTTTTAAGATAGACAAATACATTT
AAACTCATTTAAGCTATTTAAACATAGAAAAGTTTTATATCACAATTTGGAATTGTCCTAATGGC
TTTTATGCCCAAATATGCTCAAAAACAAGATTTGATCTTTTAAGTTTCAAAATATTTTATAACTT
GCATGTAACACTATGAATTAAAATCATTGCAAGTTAATCAAGTTTTC
Found at i:5576453 original size:31 final size:31
Alignment explanation
Indices: 5576418--5576481 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
5576408 CACAAATTCT
* *
5576418 CAAATAAATCTCAAAAATTAATTTCAACTAA
1 CAAATAAATCTCAAAAATCAATTTCAACAAA
*
5576449 CAAATATATCTCAAAAATCAATTTCAACAAA
1 CAAATAAATCTCAAAAATCAATTTCAACAAA
5576480 CA
1 CA
5576482 TTACCATCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.55, C:0.19, G:0.00, T:0.27
Consensus pattern (31 bp):
CAAATAAATCTCAAAAATCAATTTCAACAAA
Found at i:5577083 original size:18 final size:17
Alignment explanation
Indices: 5577056--5577088 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5577046 TAACTCATCA
5577056 AATTTCTTTTTCAAATC
1 AATTTCTTTTTCAAATC
*
5577073 AATTTTTTTTTCAAAT
1 AATTTCTTTTTCAAAT
5577089 TTTCTCTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.12, G:0.00, T:0.58
Consensus pattern (17 bp):
AATTTCTTTTTCAAATC
Found at i:5583801 original size:17 final size:17
Alignment explanation
Indices: 5583779--5583813 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
5583769 TTGTGCACAA
5583779 GGCTACGTGCATTTGCC
1 GGCTACGTGCATTTGCC
5583796 GGCTACGTGCATTTGCC
1 GGCTACGTGCATTTGCC
5583813 G
1 G
5583814 TCCAACTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.29, G:0.31, T:0.29
Consensus pattern (17 bp):
GGCTACGTGCATTTGCC
Found at i:5584275 original size:5 final size:5
Alignment explanation
Indices: 5584265--5584289 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
5584255 AACTTTCAAC
5584265 CATTT CATTT CATTT CATTT CATTT
1 CATTT CATTT CATTT CATTT CATTT
5584290 AAAAAACCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (5 bp):
CATTT
Found at i:5588395 original size:17 final size:17
Alignment explanation
Indices: 5588370--5588409 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
5588360 TTACAAATGG
*
5588370 AGATTTAAGTCCATTGT
1 AGATATAAGTCCATTGT
5588387 AGATATAAGTCCATTGT
1 AGATATAAGTCCATTGT
5588404 AGATAT
1 AGATAT
5588410 CTAATTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (17 bp):
AGATATAAGTCCATTGT
Found at i:5589198 original size:31 final size:30
Alignment explanation
Indices: 5589142--5589201 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
5589132 AGCAGAAGAA
* *
5589142 AGTAAAAGAAAATAAAAGCTAAGAAAAAAT
1 AGTAAAAAAAAATAAAAACTAAGAAAAAAT
5589172 AGTAAAAAAAATATAAAAAACT-AGAAAAAA
1 AGTAAAAAAAA-AT-AAAAACTAAGAAAAAA
5589202 AGAATACCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 10 0.38
31 10 0.38
32 6 0.23
ACGTcount: A:0.73, C:0.03, G:0.10, T:0.13
Consensus pattern (30 bp):
AGTAAAAAAAAATAAAAACTAAGAAAAAAT
Found at i:5595170 original size:112 final size:117
Alignment explanation
Indices: 5594986--5595197 Score: 317
Period size: 121 Copynumber: 1.8 Consensus size: 117
5594976 TAAGTTTGAC
*
5594986 ACTTGTAGTTTTAAGGGCTATTGCATTTGTCATTTTTCCCTTGTCTTTATTTTTTTTGTTGGCCT
1 ACTTGTAGTTTTAAGGGCTATTACATTTGTCATTTTTCCCTTGTC--TA-TTTTTTTGTT-GCCT
*
5595051 AGTTTAAAATGGAATAGAGGGGGTGCGACATTATACAGTTAGAGCATGGGCATGAT
62 AGTTTAAAATGGAATAGAGGGGGTGCGACACTATACAGTTAGAGCATGGGCATGAT
5595107 ACTTGTAGTTTTAAGGGCTATTACATTTGTCATTTTT-CCTTGTC-A-TTTTTT-TT-CCTAGTT
1 ACTTGTAGTTTTAAGGGCTATTACATTTGTCATTTTTCCCTTGTCTATTTTTTTGTTGCCTAGTT
* *
5595167 TAAAATGGAATAGAGTGGGTGGGACACTATA
66 TAAAATGGAATAGAGGGGGTGCGACACTATA
5595198 TAGGTAAGAT
Statistics
Matches: 87, Mismatches: 4, Indels: 9
0.87 0.04 0.09
Matches are distributed among these distances:
112 35 0.40
114 2 0.02
115 6 0.07
117 1 0.01
120 7 0.08
121 36 0.41
ACGTcount: A:0.23, C:0.12, G:0.22, T:0.42
Consensus pattern (117 bp):
ACTTGTAGTTTTAAGGGCTATTACATTTGTCATTTTTCCCTTGTCTATTTTTTTGTTGCCTAGTT
TAAAATGGAATAGAGGGGGTGCGACACTATACAGTTAGAGCATGGGCATGAT
Found at i:5595367 original size:3 final size:3
Alignment explanation
Indices: 5595361--5595406 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
5595351 TTGTTGGTTA
5595361 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5595407 GAAATTAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5596472 original size:77 final size:77
Alignment explanation
Indices: 5596388--5596668 Score: 248
Period size: 78 Copynumber: 3.6 Consensus size: 77
5596378 TCATTTTCTT
* * * *
5596388 TTACATTAAGGCATATGAGTTAACACAATCTTCACTTCCTGCTGACATGCCCAATATGCCCCTAG
1 TTACATTAAGGCATATGAGTTAACACAGTCTCCACTTCCTACTGACATGCCCAATGTGCCCCTAG
5596453 CACCTTTATCTA
66 CACCTTTATCTA
* * * * * * * *
5596465 TTGCATTAAGGCATATAAGTTAACATAGTC-CTCATTTTTCTACTAACATGTCCAATGTGCCCTT
1 TTACATTAAGGCATATGAGTTAACACAGTCTC-CA-CTTCCTACTGACATGCCCAATGTGCCCCT
5596529 A-CACCTTTTATCTA
64 AGCACC-TTTATCTA
** * * * ** ** *
5596543 TTATGTTAAGGTATATGGGTTAACATAGT-TCCCACTTCCTACTGACATGCTTAATGCACCCACA
1 TTACATTAAGGCATATGAGTTAACACAGTCT-CCACTTCCTACTGACATGCCCAATGTGCCC-CT
*
5596607 AGCA-ATTT-TCTA
64 AGCACCTTTATCTA
* * *
5596619 TTACATTAAGGCATATGTGTTAACACAGTCTCCACTTCCCATTGACATGC
1 TTACATTAAGGCATATGAGTTAACACAGTCTCCACTTCCTACTGACATGC
5596669 TAAATACGTC
Statistics
Matches: 160, Mismatches: 36, Indels: 17
0.75 0.17 0.08
Matches are distributed among these distances:
76 45 0.28
77 55 0.34
78 57 0.36
79 3 0.02
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.34
Consensus pattern (77 bp):
TTACATTAAGGCATATGAGTTAACACAGTCTCCACTTCCTACTGACATGCCCAATGTGCCCCTAG
CACCTTTATCTA
Found at i:5596635 original size:76 final size:77
Alignment explanation
Indices: 5596539--5596732 Score: 205
Period size: 76 Copynumber: 2.6 Consensus size: 77
5596529 ACACCTTTTA
** * * * *
5596539 TCTATTATGTTAAGGTATATGGGTTAACATAGTTC-CCACTTCCTACTGACATGCTTAATGCACC
1 TCTATTACATTAAGGCATATGGGTTAACATAGTTCTCCACTTCCCACTGACATGCTAAATACACC
5596603 CACAAGCAATTT
66 CACAAGCAATTT
* * * **
5596615 TCTATTACATTAAGGCATATGTGTTAACACAG-TCTCCACTTCCCATTGACATGCTAAATACGTC
1 TCTATTACATTAAGGCATATGGGTTAACATAGTTCTCCACTTCCCACTGACATGCTAAATACACC
** *
5596679 CACGTGCCATTT
66 CACAAGCAATTT
* * * *
5596691 TCTATTGCATTAAGGCACACGGGTTAACATAG-TCTCTACTTC
1 TCTATTACATTAAGGCATATGGGTTAACATAGTTCTCCACTTC
5596733 TTATTGACAA
Statistics
Matches: 97, Mismatches: 20, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
75 2 0.02
76 95 0.98
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (77 bp):
TCTATTACATTAAGGCATATGGGTTAACATAGTTCTCCACTTCCCACTGACATGCTAAATACACC
CACAAGCAATTT
Found at i:5596766 original size:76 final size:75
Alignment explanation
Indices: 5596611--5596783 Score: 168
Period size: 76 Copynumber: 2.3 Consensus size: 75
5596601 CCCACAAGCA
* * * * * *
5596611 ATTTTCTATTACATTAAGGCATATGTGTTAACACAGTCTCCACTTCCCATTGACATGCTAAATAC
1 ATTTTCTATTGCATTAAGGCACACGGGTTAACACAGTCTCCACTTCCCATTGACAAGCTAAACAC
* *
5596676 GTCCACGTGCC
66 CTCCACAT-CC
* * **
5596687 ATTTTCTATTGCATTAAGGCACACGGGTTAACATAGTCTCTACTTCTTATTGACAAGCTAAAGCA
1 ATTTTCTATTGCATTAAGGCACACGGGTTAACACAGTCTCCACTTCCCATTGACAAGCTAAA-CA
*
5596752 CCTAGCACAT-C
65 CCT-CCACATCC
* **
5596763 ATTTTTTATTGTGTTAAGGCA
1 ATTTTCTATTGCATTAAGGCA
5596784 TATAGGTTAA
Statistics
Matches: 79, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
76 72 0.91
77 3 0.04
78 4 0.05
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (75 bp):
ATTTTCTATTGCATTAAGGCACACGGGTTAACACAGTCTCCACTTCCCATTGACAAGCTAAACAC
CTCCACATCC
Found at i:5597068 original size:52 final size:52
Alignment explanation
Indices: 5596974--5597075 Score: 136
Period size: 52 Copynumber: 2.0 Consensus size: 52
5596964 TTTATCAGTG
* *
5596974 TATTAAGGCTCTACACTAACATGCCCAATGTGCCGCTGACACCTTCATCTAT
1 TATTAAGGCTCTACACTAACATGCCCAATGTACCGCTAACACCTTCATCTAT
* *
5597026 TATTAAGGC-CTCACACTAACATGCCTAATGTACTC-TTAACACCTTCATCT
1 TATTAAGGCTCT-ACACTAACATGCCCAATGTAC-CGCTAACACCTTCATCT
5597076 TTTGTGTTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
51 2 0.05
52 41 0.93
53 1 0.02
ACGTcount: A:0.28, C:0.30, G:0.11, T:0.30
Consensus pattern (52 bp):
TATTAAGGCTCTACACTAACATGCCCAATGTACCGCTAACACCTTCATCTAT
Found at i:5600138 original size:5 final size:5
Alignment explanation
Indices: 5600121--5600223 Score: 61
Period size: 5 Copynumber: 20.6 Consensus size: 5
5600111 TATAGTCTGG
* **
5600121 TATAT TATTT TATA- T-TAT TATAT TATGG TATGAT TATA- T-TAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TAT-AT TATAT TATAT TATAT
* * * * * *
5600168 TATGT TATAT TTTAT TGTAA TATAT TATAT TGTTAT CATAT TATTAT TATTAT
1 TATAT TATAT TATAT TATAT TATAT TATAT T-ATAT TATAT TA-TAT TA-TAT
5600221 TAT
1 TAT
5600224 TATCATCTTT
Statistics
Matches: 74, Mismatches: 17, Indels: 14
0.70 0.16 0.13
Matches are distributed among these distances:
3 4 0.05
4 4 0.05
5 49 0.66
6 17 0.23
ACGTcount: A:0.33, C:0.01, G:0.06, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:5600139 original size:3 final size:3
Alignment explanation
Indices: 5600123--5600239 Score: 58
Period size: 3 Copynumber: 41.3 Consensus size: 3
5600113 TAGTCTGGTA
*
5600123 TAT TAT T-T TA- TAT TAT TA- TAT TAT GGTAT GAT TA- TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT --TAT TAT TAT TAT TAT TAT
* * * * *
5600165 TAT TA- TGT TA- TAT T-T TAT TGT AAT ATAT TA- TAT TGT TAT CA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT
*
5600206 TAT TAT TAT TAT TAT TAT TAT CAT CT-T TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT T
5600240 TTTTTTTCAA
Statistics
Matches: 85, Mismatches: 14, Indels: 30
0.66 0.11 0.23
Matches are distributed among these distances:
2 19 0.22
3 61 0.72
4 2 0.02
5 3 0.04
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:5600143 original size:8 final size:8
Alignment explanation
Indices: 5600126--5600223 Score: 69
Period size: 8 Copynumber: 12.1 Consensus size: 8
5600116 TCTGGTATAT
5600126 TATT-TTA
1 TATTATTA
5600133 TATTATTA
1 TATTATTA
**
5600141 TATTATGG
1 TATTATTA
*
5600149 TATGATTA
1 TATTATTA
5600157 TATTATTA
1 TATTATTA
5600165 TATTATGTTA
1 TATTA--TTA
5600175 TATT-TTA
1 TATTATTA
*
5600182 T-TGTAATA
1 TAT-TATTA
5600190 TATTA-TA
1 TATTATTA
* *
5600197 TTGTTATCA
1 -TATTATTA
5600206 TATTATTA
1 TATTATTA
5600214 TTATTATTA
1 -TATTATTA
5600223 T
1 T
5600224 TATCATCTTT
Statistics
Matches: 71, Mismatches: 11, Indels: 17
0.72 0.11 0.17
Matches are distributed among these distances:
6 1 0.01
7 11 0.15
8 42 0.59
9 10 0.14
10 7 0.10
ACGTcount: A:0.33, C:0.01, G:0.06, T:0.60
Consensus pattern (8 bp):
TATTATTA
Found at i:5600610 original size:22 final size:21
Alignment explanation
Indices: 5600577--5600618 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
5600567 TTTAGGTTGC
*
5600577 TAGGATTTTGGGTTCAATTTT
1 TAGGATTCTGGGTTCAATTTT
*
5600598 TAGGCATTCTGGGTTTAATTT
1 TAGG-ATTCTGGGTTCAATTT
5600619 AAAGTTTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.19, C:0.07, G:0.24, T:0.50
Consensus pattern (21 bp):
TAGGATTCTGGGTTCAATTTT
Found at i:5601077 original size:19 final size:19
Alignment explanation
Indices: 5601053--5601117 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 19
5601043 CCAGGTTTTC
5601053 TTTTTTATTTTTATTTTAT
1 TTTTTTATTTTTATTTTAT
*
5601072 TTTTTTATTTGATTTTTTTAT
1 TTTTTTATTT--TTATTTTAT
5601093 TTATATTTGATTTTTAGTTTTAT
1 TT-T-TTT-ATTTTTA-TTTTAT
5601116 TT
1 TT
5601118 ATTTCATTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
19 10 0.26
21 10 0.26
22 3 0.08
23 11 0.29
24 4 0.11
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.78
Consensus pattern (19 bp):
TTTTTTATTTTTATTTTAT
Found at i:5601106 original size:17 final size:16
Alignment explanation
Indices: 5601056--5601121 Score: 56
Period size: 13 Copynumber: 4.4 Consensus size: 16
5601046 GGTTTTCTTT
5601056 TTTATTTTTA-TTTTA
1 TTTATTTTTAGTTTTA
*
5601071 -TT-TTTTTA-TTTGA
1 TTTATTTTTAGTTTTA
5601084 -TT-TTTTTA-TTTATA
1 TTTATTTTTAGTTT-TA
5601098 TTTGATTTTTAGTTTTA
1 TTT-ATTTTTAGTTTTA
5601115 TTTATTT
1 TTTATTT
5601122 CATTTCACTG
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
13 21 0.48
14 3 0.07
15 2 0.05
16 4 0.09
17 11 0.25
18 3 0.07
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.77
Consensus pattern (16 bp):
TTTATTTTTAGTTTTA
Found at i:5601108 original size:13 final size:12
Alignment explanation
Indices: 5601056--5601096 Score: 57
Period size: 13 Copynumber: 3.4 Consensus size: 12
5601046 GGTTTTCTTT
*
5601056 TTTATTTTTAT-
1 TTTATTTTTTTA
5601067 TTTATTTTTTTA
1 TTTATTTTTTTA
5601079 TTTGATTTTTTTA
1 TTT-ATTTTTTTA
5601092 TTTAT
1 TTTAT
5601097 ATTTGATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 10 0.37
12 5 0.19
13 12 0.44
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.80
Consensus pattern (12 bp):
TTTATTTTTTTA
Found at i:5601166 original size:18 final size:17
Alignment explanation
Indices: 5601132--5601166 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
5601122 CATTTCACTG
*
5601132 ATTTTTATTAGTTATTT
1 ATTTTTATTAGTGATTT
5601149 ATTTTTATTGAGTGATTT
1 ATTTTTATT-AGTGATTT
5601167 GTCATTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.23, C:0.00, G:0.11, T:0.66
Consensus pattern (17 bp):
ATTTTTATTAGTGATTT
Found at i:5606006 original size:14 final size:14
Alignment explanation
Indices: 5605989--5606030 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
5605979 AAAAAAATTA
*
5605989 CAAAAAAATAAAAG
1 CAAAAAAAAAAAAG
5606003 CAAAAAAAAAAAAG
1 CAAAAAAAAAAAAG
* *
5606017 CAAGAAGAAAAAAG
1 CAAAAAAAAAAAAG
5606031 GAAGACTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.79, C:0.07, G:0.12, T:0.02
Consensus pattern (14 bp):
CAAAAAAAAAAAAG
Found at i:5607286 original size:121 final size:119
Alignment explanation
Indices: 5606896--5607427 Score: 417
Period size: 121 Copynumber: 4.4 Consensus size: 119
5606886 CAGTTTAATT
* ** * * ** *
5606896 TTGGTCATTCATTTTTTACCTCGACTCGATCTTGGTTGCTTTATCTTTTAGACTCACGATTTTAT
1 TTGGTCATTAATTTTAAACCTCGACTCGATCCTGATCACTTTATCTTTTAGACTCAC-AATTTAT
* * * *
5606961 C-CTGGTCATTCACTCTC-AGCTCAGTCCAGATCATTTTCTTGACTTGTAATTTTATT
65 CTC-GGTCATTCA-TCTCGA-CTCAGTCCAGATCATTTTTTTGACTTGTGATTTCATC
* * ** *
5607017 TTGGTCATTTATTTTAAACCTCGACTTGATCCTGATTGCTTTATCTTTTAGACTCACAATTTGTC
1 TTGGTCATTAATTTTAAACCTCGACTCGATCCTGATCACTTTATCTTTTAGACTCACAATTTATC
* * * * * * * *
5607082 TTGGTCATTCAATCTCGGCTCAATCCAAATCA-TTTTCTAACTCGTGGTTTCATC
66 TCGGTCATTC-ATCTCGACTCAGTCCAGATCATTTTTTTGACTTGTGATTTCATC
* * * *
5607136 TTGGTCATTAATTTTCAACCTCAACTCGATCCCGATCACTTTATCTTTTAGACTAACAATTTCAT
1 TTGGTCATTAATTTTAAACCTCGACTCGATCCTGATCACTTTATCTTTTAGACTCACAATTT-AT
* **
5607201 CTCGGTCATTCGATCTCGATTCAGTCCAGATCATTTTTTTGACTTACGATTTCATC
65 CTCGGTCATTC-ATCTCGACTCAGTCCAGATCATTTTTTTGACTTGTGATTTCATC
*** * * * * *** *
5607257 TCAATTATTCATTTTAAACCTTGACTCGATCCTGATCGA-TTTATCTTTTAGATTCATGGCTTTG
1 TTGGTCATTAATTTTAAACCTCGACTCGATCCTGATC-ACTTTATCTTTTAGACTCA-CAATTTA
* * * * * *
5607321 TC-CTAGTCATTCAATCTTGACTCAGTCCAAATCATTTTCTTAACTTGTGGTTTCATC
64 TCTC-GGTCATTC-ATCTCGACTCAGTCCAGATCATTTTTTTGACTTGTGATTTCATC
* * * ** * * *
5607378 TTAGTCATTCATCTTCGATCTTGACTCGATCCTGATCGCTTTATCTTTTA
1 TTGGTCATTAATTTTAAACCTCGACTCGATCCTGATCACTTTATCTTTTA
5607428 AATTTACTGT
Statistics
Matches: 328, Mismatches: 74, Indels: 18
0.78 0.18 0.04
Matches are distributed among these distances:
119 68 0.21
120 59 0.18
121 197 0.60
122 4 0.01
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.44
Consensus pattern (119 bp):
TTGGTCATTAATTTTAAACCTCGACTCGATCCTGATCACTTTATCTTTTAGACTCACAATTTATC
TCGGTCATTCATCTCGACTCAGTCCAGATCATTTTTTTGACTTGTGATTTCATC
Found at i:5607629 original size:3 final size:3
Alignment explanation
Indices: 5607621--5607732 Score: 51
Period size: 3 Copynumber: 38.3 Consensus size: 3
5607611 TAGTCTAGTA
*
5607621 TAT TAT TAT ATAT TAT TA- TAT TAT GGTAT GAT TAT ATAT TA- TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT --TAT TAT TAT -TAT TAT TAT TAT
* * * * *
5607668 TAT TA- TAT TA- TGT TA- TAT T-T TCT TGT AAT ATAT TA- TAT TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
* *
5607709 TAT CA- TAT TAT TAT TCT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
5607733 TTCTTTATTT
Statistics
Matches: 82, Mismatches: 14, Indels: 26
0.67 0.11 0.21
Matches are distributed among these distances:
2 14 0.17
3 57 0.70
4 8 0.10
5 3 0.04
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:5607640 original size:8 final size:8
Alignment explanation
Indices: 5607590--5607683 Score: 54
Period size: 8 Copynumber: 11.8 Consensus size: 8
5607580 TGCCATTTGT
5607590 TATTATT-
1 TATTATTA
*
5607597 T-TTATCA
1 TATTATTA
5607604 TATTA-TA
1 TATTATTA
*
5607611 TAGTCTAGTA
1 TA-T-TATTA
5607621 TATTATTATA
1 TATTA-T-TA
5607631 TATTATTA
1 TATTATTA
**
5607639 TATTATGG
1 TATTATTA
*
5607647 TATGATTA
1 TATTATTA
5607655 TA-TATTA
1 TATTATTA
5607662 TATTATTA
1 TATTATTA
5607670 T-TATATTA
1 TAT-TATTA
*
5607678 TGTTAT
1 TATTAT
5607684 ATTTTCTTGT
Statistics
Matches: 68, Mismatches: 9, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
6 4 0.06
7 12 0.18
8 36 0.53
9 5 0.07
10 11 0.16
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.57
Consensus pattern (8 bp):
TATTATTA
Found at i:5607640 original size:18 final size:18
Alignment explanation
Indices: 5607604--5607678 Score: 75
Period size: 18 Copynumber: 4.2 Consensus size: 18
5607594 ATTTTTATCA
*
5607604 TATTATATAGTCTAGTATAT
1 TATTATATA-T-TATTATAT
5607624 TATTATATATTATTATAT
1 TATTATATATTATTATAT
**
5607642 TATGGTATGATTA-TATAT
1 TATTATAT-ATTATTATAT
5607660 TA-TAT-TATTATTATAT
1 TATTATATATTATTATAT
5607676 TAT
1 TAT
5607679 GTTATATTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
15 4 0.09
16 8 0.17
17 1 0.02
18 20 0.43
19 5 0.11
20 9 0.19
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.56
Consensus pattern (18 bp):
TATTATATATTATTATAT
Found at i:5607644 original size:5 final size:5
Alignment explanation
Indices: 5607624--5607706 Score: 51
Period size: 5 Copynumber: 15.8 Consensus size: 5
5607614 TCTAGTATAT
**
5607624 TATTA TA-TA TTATTA TATTA TGGTA TGATTATA TATTA TATTA TTATTA
1 TATTA TATTA -TATTA TATTA TATTA T-A-T-TA TATTA TATTA -TATTA
* * * * *
5607673 TATTA TGTTA TATTT TCTTG TAATA TATTA TATT
1 TATTA TATTA TATTA TATTA TATTA TATTA TATT
5607707 GTTATCATAT
Statistics
Matches: 59, Mismatches: 13, Indels: 12
0.70 0.15 0.14
Matches are distributed among these distances:
4 2 0.03
5 45 0.76
6 8 0.14
7 1 0.02
8 3 0.05
ACGTcount: A:0.34, C:0.01, G:0.06, T:0.59
Consensus pattern (5 bp):
TATTA
Found at i:5607664 original size:41 final size:38
Alignment explanation
Indices: 5607619--5607722 Score: 109
Period size: 41 Copynumber: 2.6 Consensus size: 38
5607609 TATAGTCTAG
* *
5607619 TATATTATTATATATTATTATATTATGGTATGATTATATAT
1 TATATTATTATATATTATTATATT-TGCT-TG-TAATATAT
*
5607660 TATATTATTATTATATTATGTTATATTTTCTTGTAATATAT
1 TATATTATTA-TATATTA--TTATATTTGCTTGTAATATAT
*
5607701 TATATTGTTATCATATTATTAT
1 TATATTATTAT-ATATTATTAT
5607723 TCTTATTATT
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
39 4 0.07
40 1 0.02
41 32 0.58
42 9 0.16
43 2 0.04
44 7 0.13
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.59
Consensus pattern (38 bp):
TATATTATTATATATTATTATATTTGCTTGTAATATAT
Found at i:5607686 original size:18 final size:17
Alignment explanation
Indices: 5607619--5607686 Score: 68
Period size: 18 Copynumber: 3.9 Consensus size: 17
5607609 TATAGTCTAG
5607619 TATATTATTATATATTAT
1 TATATTATT-TATATTAT
*
5607637 TATATTATGGTATGATTA-
1 TATATTAT-TTAT-ATTAT
*
5607655 TATATTATAT-TATTAT
1 TATATTATTTATATTAT
5607671 TATATTATGTTATATT
1 TATATTAT-TTATATT
5607687 TTCTTGTAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
15 4 0.10
16 9 0.21
17 2 0.05
18 23 0.55
19 4 0.10
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (17 bp):
TATATTATTTATATTAT
Found at i:5608174 original size:20 final size:20
Alignment explanation
Indices: 5608129--5608179 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
5608119 GTTTGATTTA
5608129 AAGTTTCT-GGATTTAGACTT
1 AAGTTTCTAGG-TTTAGACTT
* **
5608149 AGGTTTCTAGGTTTAGGGTT
1 AAGTTTCTAGGTTTAGACTT
5608169 AAGTTTC-AGGT
1 AAGTTTCTAGGT
5608180 GTAGTTTTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 4 0.15
20 20 0.77
21 2 0.08
ACGTcount: A:0.22, C:0.08, G:0.27, T:0.43
Consensus pattern (20 bp):
AAGTTTCTAGGTTTAGACTT
Found at i:5608559 original size:18 final size:18
Alignment explanation
Indices: 5608526--5608560 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5608516 AGGTTTTCTT
*
5608526 TTTTCTAATTTAATTTTA
1 TTTTCTAATATAATTTTA
*
5608544 TTTTCTAATATGATTTT
1 TTTTCTAATATAATTTT
5608561 TTATTTATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.66
Consensus pattern (18 bp):
TTTTCTAATATAATTTTA
Found at i:5608576 original size:24 final size:24
Alignment explanation
Indices: 5608538--5608594 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
5608528 TTCTAATTTA
*
5608538 ATTTTATTTTCTAATATGATTTTT
1 ATTTTATTTTATAATATGATTTTT
*
5608562 -TATTTATTTTATAATTTGATTTTT
1 AT-TTTATTTTATAATATGATTTTT
5608586 ATTTTATTT
1 ATTTTATTT
5608595 ATTTCATTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 1 0.03
24 27 0.93
25 1 0.03
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.70
Consensus pattern (24 bp):
ATTTTATTTTATAATATGATTTTT
Found at i:5608643 original size:18 final size:17
Alignment explanation
Indices: 5608609--5608643 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
5608599 CATTTCACTA
*
5608609 ATTTTTATTAGTTATTT
1 ATTTTTATTAGTGATTT
5608626 ATTTTTATTAAGTGATTT
1 ATTTTTATT-AGTGATTT
5608644 GTCATTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.66
Consensus pattern (17 bp):
ATTTTTATTAGTGATTT
Found at i:5610845 original size:29 final size:29
Alignment explanation
Indices: 5610813--5610886 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
5610803 CATTTTTTTA
5610813 AAATAAACTTTTATATTTTTAT-TGTA-CTC
1 AAATAAACTTTTAT-TTTTTATATGTATC-C
* *
5610842 AAAT-AAGTCTTTATTTTTTTTATGTATCC
1 AAATAAACT-TTTATTTTTTATATGTATCC
5610871 AAATAAACTTTTATTT
1 AAATAAACTTTTATTT
5610887 CGAATAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
28 9 0.24
29 25 0.66
30 4 0.11
ACGTcount: A:0.34, C:0.09, G:0.04, T:0.53
Consensus pattern (29 bp):
AAATAAACTTTTATTTTTTATATGTATCC
Found at i:5612014 original size:16 final size:17
Alignment explanation
Indices: 5611993--5612066 Score: 66
Period size: 16 Copynumber: 4.5 Consensus size: 17
5611983 GCCCAATTCA
5611993 ATTTTTATTT-TGTATT
1 ATTTTTATTTATGTATT
5612009 ATTTTTATTT-T-TATT
1 ATTTTTATTTATGTATT
*
5612024 CTTTTGTATTTTATGTATT
1 ATTTT-TA-TTTATGTATT
* *
5612043 -TTATTATTTATTTATT
1 ATTTTTATTTATGTATT
*
5612059 ATTATTAT
1 ATTTTTAT
5612067 GTATTAATAT
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
15 8 0.16
16 22 0.44
17 12 0.24
18 4 0.08
19 4 0.08
ACGTcount: A:0.22, C:0.01, G:0.04, T:0.73
Consensus pattern (17 bp):
ATTTTTATTTATGTATT
Found at i:5612057 original size:41 final size:41
Alignment explanation
Indices: 5612005--5612131 Score: 109
Period size: 41 Copynumber: 3.1 Consensus size: 41
5611995 TTTTATTTTG
5612005 TATTA-TT-TTTATTTTTATTCT-TTTGTATTTTATGTATTT
1 TATTATTTATTTATTTTTATTCTATTT-TATTTTATGTATTT
* * * * * * *
5612044 TATTATTTATTTATTATTATTATGTATTAATATATGTATATC
1 TATTATTTATTTATTTTTATTCTATTTTATTTTATGTAT-TT
* *
5612086 T-TTATTTATTTATTTTTTTTCTATTAATATTTATATGTATTT
1 TATTATTTATTTATTTTTATTCTATT-TTATTT-TATGTATTT
5612128 TATT
1 TATT
5612132 TATATGGTTA
Statistics
Matches: 66, Mismatches: 15, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
39 5 0.08
40 2 0.03
41 41 0.62
42 9 0.14
43 9 0.14
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (41 bp):
TATTATTTATTTATTTTTATTCTATTTTATTTTATGTATTT
Found at i:5612152 original size:26 final size:26
Alignment explanation
Indices: 5612123--5612186 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
5612113 TATTTATATG
*
5612123 TATT-TTATTTATATGGTTATATTTAT
1 TATTATTATTTATATGATTATA-TTAT
*
5612149 TATTATTA-TTATATTATTATATTAT
1 TATTATTATTTATATGATTATATTAT
*
5612174 TATTATTTTTTAT
1 TATTATTATTTAT
5612187 CTTGTAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 11 0.33
26 19 0.58
27 3 0.09
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (26 bp):
TATTATTATTTATATGATTATATTAT
Found at i:5612153 original size:3 final size:3
Alignment explanation
Indices: 5612145--5612180 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
5612135 ATGGTTATAT
5612145 TTA TTA TTA TTA TTA -TA TTA TTA -TA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5612181 TTTTATCTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5612163 original size:8 final size:8
Alignment explanation
Indices: 5612139--5612176 Score: 58
Period size: 8 Copynumber: 4.5 Consensus size: 8
5612129 ATTTATATGG
5612139 TTATATTTA
1 TTATA-TTA
5612148 TTATTATTA
1 TTA-TATTA
5612157 TTATATTA
1 TTATATTA
5612165 TTATATTA
1 TTATATTA
5612173 TTAT
1 TTAT
5612177 TATTTTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 17 0.61
9 9 0.32
10 2 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
TTATATTA
Found at i:5613109 original size:12 final size:12
Alignment explanation
Indices: 5613092--5613122 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
5613082 CCTTGAGTCG
5613092 AGCCGAGCCGAT
1 AGCCGAGCCGAT
*
5613104 AGCCGAGCTGAT
1 AGCCGAGCCGAT
5613116 AGCCGAG
1 AGCCGAG
5613123 TCGCTCCTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.26, C:0.29, G:0.35, T:0.10
Consensus pattern (12 bp):
AGCCGAGCCGAT
Found at i:5613166 original size:13 final size:12
Alignment explanation
Indices: 5613146--5613177 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
5613136 TTTTTTTTGA
5613146 ATTTTTTTATTT
1 ATTTTTTTATTT
5613158 ATTTGTTTTATTT
1 ATTT-TTTTATTT
5613171 ATTTTTT
1 ATTTTTT
5613178 CCTTTATTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (12 bp):
ATTTTTTTATTT
Found at i:5613378 original size:58 final size:57
Alignment explanation
Indices: 5613222--5613471 Score: 299
Period size: 58 Copynumber: 4.4 Consensus size: 57
5613212 TCTTTATCTA
* * *
5613222 TTTCCTT-TAAATAAAG-ATCAAGAAATACTTTTTGGG-AAAAGTTGAAAGTATCAAT
1 TTTCCTTAAAAATAAAGTTTCAAAAAATA-TTTTTGGGAAAAAGTTGAAAGTATCAAT
* *
5613277 TTTTCTTAAAAATAAATTTTCAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAAT
1 TTTCCTTAAAAATAAAGTTTCAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAAT
* * *
5613334 TTTCCTTGAGAATCAAAGTTTCCAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAAT
1 TTTCCTTAAAAAT-AAAGTTTCAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAAT
* ** **
5613392 TTTCCTTAAAAATAAAATTTCAAAAAAGGGGTTTTTGAAAAAAAGTTGAAAGTATCAAT
1 TTTCCTTAAAAATAAAGTTTCAAAAAA--TATTTTTGGGAAAAAGTTGAAAGTATCAAT
* *
5613451 TTTCCTTGAGAATCAAAGTTT
1 TTTCCTTAAAAAT-AAAGTTT
5613472 TTTAAACACC
Statistics
Matches: 167, Mismatches: 21, Indels: 9
0.85 0.11 0.05
Matches are distributed among these distances:
55 6 0.04
56 15 0.09
57 50 0.30
58 53 0.32
59 37 0.22
60 6 0.04
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (57 bp):
TTTCCTTAAAAATAAAGTTTCAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAAT
Found at i:5613386 original size:115 final size:116
Alignment explanation
Indices: 5613244--5613471 Score: 370
Period size: 115 Copynumber: 2.0 Consensus size: 116
5613234 AAAGATCAAG
* * *
5613244 AAATACTTTTTGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAAA-TATT
1 AAATACTTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAGGATT
**
5613308 TTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTGAGAATCAAAGTTTCCAA
66 TTTGAAAAAAAGTTGAAAGTATCAATTTTCCTTGAGAATCAAAGTTTCCAA
*
5613359 AAATA-TTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAGGGG
1 AAATACTTTTTGGG-AAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAA-GGA
5613423 TTTTTGAAAAAAAGTTGAAAGTATCAATTTTCCTTGAGAATCAAAGTTT
64 TTTTTGAAAAAAAGTTGAAAGTATCAATTTTCCTTGAGAATCAAAGTTT
5613472 TTTAAACACC
Statistics
Matches: 104, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
114 8 0.08
115 49 0.47
117 47 0.45
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.36
Consensus pattern (116 bp):
AAATACTTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAGGATT
TTTGAAAAAAAGTTGAAAGTATCAATTTTCCTTGAGAATCAAAGTTTCCAA
Found at i:5613560 original size:16 final size:15
Alignment explanation
Indices: 5613539--5613618 Score: 56
Period size: 16 Copynumber: 5.1 Consensus size: 15
5613529 GCCCAATTCA
5613539 ATTTTTATTCTGTATT
1 ATTTTTATT-TGTATT
*
5613555 ATTTTTATTTTTATT
1 ATTTTTATTTGTATT
*
5613570 CTTTTGTATTT-TATGT
1 ATTTT-TATTTGTAT-T
*
5613586 A-TTTTATTATTTATTT
1 ATTTTTATT-TGTA-TT
*
5613602 ATTATTATTATGTATT
1 ATTTTTATT-TGTATT
5613618 A
1 A
5613619 ATATATGTAT
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
14 4 0.08
15 16 0.30
16 22 0.42
17 11 0.21
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.70
Consensus pattern (15 bp):
ATTTTTATTTGTATT
Found at i:5613703 original size:23 final size:24
Alignment explanation
Indices: 5613654--5613697 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
5613644 TTGGTAATAT
5613654 TTATATTTATT-TTATTTATATAG
1 TTATATTTATTATTATTTATATAG
5613677 TTATATTTATTATTA-TTATAT
1 TTATATTTATTATTATTTATAT
5613698 TATTATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (24 bp):
TTATATTTATTATTATTTATATAG
Found at i:5614346 original size:9 final size:9
Alignment explanation
Indices: 5614334--5614380 Score: 51
Period size: 9 Copynumber: 5.0 Consensus size: 9
5614324 TTCATCTTTT
5614334 AGAGAGAAG
1 AGAGAGAAG
*
5614343 AGAGAGAAA
1 AGAGAGAAG
5614352 AGAGAAGGAAG
1 AGAG-A-GAAG
5614363 AGAGAGAAG
1 AGAGAGAAG
5614372 -GAGGAGAAG
1 AGA-GAGAAG
5614381 GTTTCTGCCA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
8 2 0.06
9 22 0.67
10 2 0.06
11 7 0.21
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (9 bp):
AGAGAGAAG
Found at i:5614661 original size:13 final size:13
Alignment explanation
Indices: 5614631--5614677 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
5614621 CCGCTCAAGG
*
5614631 TTTTTTTTTTTTGAA
1 TTTTTTTTATTT--A
5614646 TTTTTTTTATTTA
1 TTTTTTTTATTTA
*
5614659 TTTGTTTTATTTA
1 TTTTTTTTATTTA
5614672 TTTTTT
1 TTTTTT
5614678 CCTTTATTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 18 0.62
15 11 0.38
ACGTcount: A:0.13, C:0.00, G:0.04, T:0.83
Consensus pattern (13 bp):
TTTTTTTTATTTA
Found at i:5614728 original size:17 final size:16
Alignment explanation
Indices: 5614706--5614771 Score: 59
Period size: 17 Copynumber: 4.2 Consensus size: 16
5614696 TATTTAATAT
5614706 TTTTTATCTTTATCTTA
1 TTTTTATCTTTAT-TTA
* *
5614723 TTTTTATTTTTGTTTTA
1 TTTTTATCTTT-ATTTA
*
5614740 CTTTT-T-TTTA-TT-
1 TTTTTATCTTTATTTA
5614752 TTTTTATCTTTATTTA
1 TTTTTATCTTTATTTA
5614768 TTTT
1 TTTT
5614772 CACTTTTATT
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
12 4 0.10
13 3 0.08
14 4 0.10
15 5 0.13
16 5 0.13
17 17 0.44
18 1 0.03
ACGTcount: A:0.14, C:0.06, G:0.02, T:0.79
Consensus pattern (16 bp):
TTTTTATCTTTATTTA
Found at i:5614748 original size:21 final size:22
Alignment explanation
Indices: 5614714--5614754 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
5614704 ATTTTTTATC
5614714 TTTATCTTATTTTTATTTTTGT
1 TTTATCTTATTTTTATTTTTGT
*
5614736 TTTA-CTTTTTTTTATTTTT
1 TTTATCTTATTTTTATTTTT
5614755 TTATCTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.12, C:0.05, G:0.02, T:0.80
Consensus pattern (22 bp):
TTTATCTTATTTTTATTTTTGT
Found at i:5614887 original size:57 final size:57
Alignment explanation
Indices: 5614807--5614967 Score: 232
Period size: 57 Copynumber: 2.8 Consensus size: 57
5614797 TAAATAAAGA
* *
5614807 TCAAAAAATATTTTTTGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTT
1 TCAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATT
* *
5614864 TCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATT
1 TCAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATT
** * *
5614921 TCAAAAAAGGGGTTTTTGGAAAAAAGTTGAAAGTATTAATTTTCCTT
1 TCAAAAAA--TATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTT
5614968 GAGAATCAAA
Statistics
Matches: 92, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
57 61 0.66
59 31 0.34
ACGTcount: A:0.43, C:0.06, G:0.13, T:0.37
Consensus pattern (57 bp):
TCAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATT
Found at i:5615070 original size:16 final size:17
Alignment explanation
Indices: 5615049--5615122 Score: 66
Period size: 16 Copynumber: 4.5 Consensus size: 17
5615039 GCCCAATTAA
5615049 ATTTTTATTT-TGTATT
1 ATTTTTATTTATGTATT
5615065 ATTTTTATTT-T-TATT
1 ATTTTTATTTATGTATT
*
5615080 CTTTTGTATTTTATGTATT
1 ATTTT-TA-TTTATGTATT
* *
5615099 -TTATTATTTATTTATT
1 ATTTTTATTTATGTATT
*
5615115 ATTATTAT
1 ATTTTTAT
5615123 GTATTAATAT
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
15 8 0.16
16 22 0.44
17 12 0.24
18 4 0.08
19 4 0.08
ACGTcount: A:0.22, C:0.01, G:0.04, T:0.73
Consensus pattern (17 bp):
ATTTTTATTTATGTATT
Found at i:5615661 original size:25 final size:24
Alignment explanation
Indices: 5615626--5615672 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
5615616 TCGAAAATAA
*
5615626 TTTTTTAAAAATTTTTGGTGAAAAT
1 TTTTTTAAAAATTTCTGG-GAAAAT
*
5615651 TTTTTTGAAAATTTCTGGGAAA
1 TTTTTTAAAAATTTCTGGGAAA
5615673 TTTCCAGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.34, C:0.02, G:0.15, T:0.49
Consensus pattern (24 bp):
TTTTTTAAAAATTTCTGGGAAAAT
Found at i:5616226 original size:17 final size:16
Alignment explanation
Indices: 5616204--5616269 Score: 59
Period size: 17 Copynumber: 4.2 Consensus size: 16
5616194 TATTTAATAT
5616204 TTTTTATCTTTATCTTA
1 TTTTTATCTTTAT-TTA
* *
5616221 TTTTTATTTTTGTTTTA
1 TTTTTATCTTT-ATTTA
*
5616238 CTTTT-T-TTTA-TT-
1 TTTTTATCTTTATTTA
5616250 TTTTTATCTTTATTTA
1 TTTTTATCTTTATTTA
5616266 TTTT
1 TTTT
5616270 CACTTTTATT
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
12 4 0.10
13 3 0.08
14 4 0.10
15 5 0.13
16 5 0.13
17 17 0.44
18 1 0.03
ACGTcount: A:0.14, C:0.06, G:0.02, T:0.79
Consensus pattern (16 bp):
TTTTTATCTTTATTTA
Found at i:5616247 original size:21 final size:22
Alignment explanation
Indices: 5616212--5616252 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
5616202 ATTTTTTATC
5616212 TTTATCTTATTTTTATTTTTGT
1 TTTATCTTATTTTTATTTTTGT
*
5616234 TTTA-CTTTTTTTTATTTTT
1 TTTATCTTATTTTTATTTTT
5616253 TTATCTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.12, C:0.05, G:0.02, T:0.80
Consensus pattern (22 bp):
TTTATCTTATTTTTATTTTTGT
Found at i:5616456 original size:59 final size:57
Alignment explanation
Indices: 5616305--5616581 Score: 394
Period size: 59 Copynumber: 4.8 Consensus size: 57
5616295 TAAATAAAGA
* * *
5616305 TCAAAAAATATTTTTTGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTT
1 TCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATT
*
5616362 TCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATT
1 TCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATT
*
5616419 TCAAAAAA-AGGGTTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATTAAAATTT
1 TCAAAAAATA---TTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT-AAAAATAAAA-TT
* ** *
5616480 TCAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTCGAAAATCAAAGTT
1 TCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAAATT
*
5616538 TCCAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCC
1 T-CAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
5616582 CTGCACAAAA
Statistics
Matches: 199, Mismatches: 13, Indels: 14
0.88 0.06 0.06
Matches are distributed among these distances:
56 1 0.01
57 61 0.31
58 7 0.04
59 110 0.55
60 9 0.05
61 10 0.05
62 1 0.01
ACGTcount: A:0.43, C:0.08, G:0.13, T:0.35
Consensus pattern (57 bp):
TCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATT
Found at i:5617765 original size:20 final size:21
Alignment explanation
Indices: 5617715--5617759 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
5617705 TTCATACTAG
*
5617715 ATTTCATTT-TAAAAATGTAC
1 ATTTCATTTAGAAAAATGTAC
5617735 ATTTCATTTAGAAAAATGTAC
1 ATTTCATTTAGAAAAATGTAC
5617756 ATTT
1 ATTT
5617760 TATTAGTGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (21 bp):
ATTTCATTTAGAAAAATGTAC
Found at i:5618927 original size:27 final size:27
Alignment explanation
Indices: 5618843--5618929 Score: 72
Period size: 27 Copynumber: 3.1 Consensus size: 27
5618833 TATGTATATC
5618843 TTTATTTATTTATTTTTT-TC-TGTTAATA
1 TTTA-TTATTT-TTTTTTATCTTG-TAATA
* * *
5618871 TTTA-TATGTATTTTATTTATATAGTTATA
1 TTTATTAT-T-TTTT-TTTATCTTGTAATA
5618900 TTTATTATTTTTTTTTATCTTGTAATA
1 TTTATTATTTTTTTTTATCTTGTAATA
5618927 TTT
1 TTT
5618930 TGTGGATTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
26 3 0.06
27 18 0.38
28 12 0.26
29 10 0.21
30 4 0.09
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.69
Consensus pattern (27 bp):
TTTATTATTTTTTTTTATCTTGTAATA
Found at i:5619907 original size:13 final size:12
Alignment explanation
Indices: 5619882--5619920 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
5619872 TCTAAGTTTT
*
5619882 TTTTTTTAATTA
1 TTTTTTTATTTA
5619894 TTTGTTTTATTTA
1 TTT-TTTTATTTA
*
5619907 TTTTTTTCTTTA
1 TTTTTTTATTTA
5619919 TT
1 TT
5619921 AGATTAGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 13 0.54
13 11 0.46
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (12 bp):
TTTTTTTATTTA
Found at i:5620146 original size:73 final size:74
Alignment explanation
Indices: 5620064--5620211 Score: 235
Period size: 73 Copynumber: 2.0 Consensus size: 74
5620054 TTTTGAGAAA
* *
5620064 AGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAAA-TATTTTTGGAGAAAAGATGAA
1 AGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCAAAAAAGGATTTTTGGAGAAAAGATGAA
5620128 AGTATCAAT
66 AGTATCAAT
* * *
5620137 AGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCAAAAAAGGGGTTTTTGGGGAAAAGTTGA
1 AGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCAAAAAA-GGATTTTTGGAGAAAAGATGA
5620202 AAGTATCAAT
65 AAGTATCAAT
5620212 TTTCCTTGAG
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
73 42 0.62
75 26 0.38
ACGTcount: A:0.45, C:0.05, G:0.16, T:0.34
Consensus pattern (74 bp):
AGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCAAAAAAGGATTTTTGGAGAAAAGATGAA
AGTATCAAT
Found at i:5620202 original size:59 final size:57
Alignment explanation
Indices: 5620137--5620508 Score: 460
Period size: 58 Copynumber: 6.4 Consensus size: 57
5620127 AAGTATCAAT
* **
5620137 AGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCAAAAAAGGGGTTTTTGGGGAAA
1 AGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAA--TATTTTTGGGGAAA
* * * * *
5620196 AGTTGAAAGTATCAATTTTCCTTGAGAATCAAAGTTTCCAAAAATATTTTTGGGAAAA
1 AGTTGAAAGTATCAATTTTCCTTAAAAAT-AAAATTTCAAAAAATATTTTTGGGGAAA
* * *
5620254 AGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCAAAAAAGGAGTTTTTGAGGAAA
1 AGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAA-TA-TTTTTGGGGAAA
* *
5620313 AGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAA-AGGTTTTTGAGGAAA
1 AGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAATA--TTTTTGGGGAAA
** * *
5620371 AGTTGAAAGTATCAATTTTCCTCGAAAATCAAAGTTTTCAAAAAATATTTTTGGGAAAA
1 AGTTGAAAGTATCAATTTTCCTTAAAAAT-AAA-ATTTCAAAAAATATTTTTGGGGAAA
* *
5620430 AATTGAAAATATCAATTTTCCTTAAAAAT-AAATTTCCAAAAAAATATTTTTGGGGAAA
1 AGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTT-C-AAAAAATATTTTTGGGGAAA
5620488 AGTTGAAAGTATCAATTTTCC
1 AGTTGAAAGTATCAATTTTCC
5620509 CTGCACAAAA
Statistics
Matches: 274, Mismatches: 30, Indels: 19
0.85 0.09 0.06
Matches are distributed among these distances:
56 3 0.01
57 16 0.06
58 116 0.42
59 115 0.42
60 23 0.08
61 1 0.00
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.34
Consensus pattern (57 bp):
AGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAATATTTTTGGGGAAA
Found at i:5620272 original size:117 final size:114
Alignment explanation
Indices: 5620137--5620506 Score: 501
Period size: 117 Copynumber: 3.2 Consensus size: 114
5620127 AAGTATCAAT
*
5620137 AGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCAAAAAAGGGGTTTTTGGGGAAAAGTTGA
1 AGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCAAAAAAGGAGTTTTTGGGGAAAAGTTGA
* *
5620202 AAGTATCAATTTTCCTTGAGAATCAAAGTTTCCAAAAATATTTTTGGGAAAA
66 AAGTATCAATTTTCCTTAAAAAT-AAA-TTTCCAAAAATATTTTTGGG-AAA
*
5620254 AGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCAAAAAAGGAGTTTTTGAGGAAAAGTTGA
1 AGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCAAAAAAGGAGTTTTTGGGGAAAAGTTGA
* *
5620319 AAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAGGTTTTTGAGGAAA
66 AAGTATCAATTTTCCTTAAAAATAAATTTCCAAAAATA--TTTTTG-GGAAA
* ** * * * *
5620371 AGTTGAAAGTATCAATTTTCCTCGAAAATCAAAGTTTTCAAAAAA-TA-TTTTTGGGAAAAAATT
1 AGTTGAAAGTATCAATTTTTCTTAAAAAT-AAA-ATTTCAAAAAAGGAGTTTTTGGGGAAAAGTT
*
5620434 GAAAATATCAATTTTCCTTAAAAATAAATTTCCAAAAAAATATTTTTGGGGAAA
64 GAAAGTATCAATTTTCCTTAAAAATAAATTTCC--AAAAATATTTTT-GGGAAA
5620488 AGTTGAAAGTATCAATTTT
1 AGTTGAAAGTATCAATTTT
5620507 CCCTGCACAA
Statistics
Matches: 228, Mismatches: 17, Indels: 16
0.87 0.07 0.06
Matches are distributed among these distances:
115 10 0.04
116 3 0.01
117 192 0.84
118 7 0.03
119 16 0.07
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.35
Consensus pattern (114 bp):
AGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCAAAAAAGGAGTTTTTGGGGAAAAGTTGA
AAGTATCAATTTTCCTTAAAAATAAATTTCCAAAAATATTTTTGGGAAA
Found at i:5623786 original size:13 final size:12
Alignment explanation
Indices: 5623759--5623793 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
5623749 GGGTTGTTTT
5623759 ATTTTAAAAAAA
1 ATTTTAAAAAAA
*
5623771 ATTTGAAAACAAA
1 ATTTTAAAA-AAA
5623784 ATTTTAAAAA
1 ATTTTAAAAA
5623794 TTGTTGGAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (12 bp):
ATTTTAAAAAAA
Found at i:5630350 original size:2 final size:2
Alignment explanation
Indices: 5630343--5630410 Score: 91
Period size: 2 Copynumber: 34.0 Consensus size: 2
5630333 TCATAGGTAT
* *
5630343 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TG TG
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * *
5630385 TC TC TG TC TC TC TC CC TC TC CC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
5630411 CGTCTTTGCT
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.00, C:0.49, G:0.04, T:0.47
Consensus pattern (2 bp):
TC
Found at i:5638925 original size:19 final size:19
Alignment explanation
Indices: 5638887--5638926 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
5638877 TTTTAAATAA
*
5638887 AATTTATAAGTATTATATT
1 AATTTATAAATATTATATT
5638906 AATTTATAAAT-TTATAATT
1 AATTTATAAATATTAT-ATT
5638925 AA
1 AA
5638927 ATATTAGACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
AATTTATAAATATTATATT
Found at i:5645433 original size:15 final size:15
Alignment explanation
Indices: 5645413--5645443 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5645403 ACTAAAGTGA
*
5645413 TTATTCAAGGCGTTT
1 TTATTCAAGGCATTT
5645428 TTATTCAAGGCATTT
1 TTATTCAAGGCATTT
5645443 T
1 T
5645444 GTGACAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.13, G:0.16, T:0.48
Consensus pattern (15 bp):
TTATTCAAGGCATTT
Found at i:5645937 original size:233 final size:233
Alignment explanation
Indices: 5645526--5645980 Score: 597
Period size: 233 Copynumber: 2.0 Consensus size: 233
5645516 AATTGGAGAT
* * *
5645526 GATTATTGAAGGCGTTTTTAGTCAAAAAAACCTTTAATAATCTAAGAATTATTCAATGCATTTTT
1 GATTATTGAAGGCGTTTTTAGTCAAAAAAACCTTCAATAATCCAAGAATTATTCAAGGCATTTTT
* * * * * *
5645591 TGCCCAAAATGCCTTCAATAACCCCATTCAATATTATGTTAAGGATTATGCAAGGTATTTTCTGG
66 GGCCAAAAATACCTTCAATAACCCCATTCAATATTATGTTAAGGATTATGCAAAGCATTTTCTAG
* * * *
5645656 GCAAAAACACCTTCAATAATCTCTTTATAAATGCCTGAAGGAGATTATTCAAGGCGTTTTATCAC
131 GCAAAAACACCTTCAACAATCTCTCTATAAACGCCTAAAGGAGATTATTCAAGGCGTTTTATCAC
5645721 AAAAACACCTTGAATAATCCCAAAAAAAAAAGGGAAGG
196 AAAAACACCTTGAATAATCCCAAAAAAAAAAGGGAAGG
* * ** * *
5645759 GATTATTGAAGGTGTTTTTGGTCAAAAATGCCTTCAATAATCCATGATTTATTCAAGGCATTTTT
1 GATTATTGAAGGCGTTTTTAGTCAAAAAAACCTTCAATAATCCAAGAATTATTCAAGGCATTTTT
* * * * *
5645824 GGCCAAAAATATCTTCAATAACCCCATTTAATATTTTGTTAGGGATTATTCAAAGCATTTTCTAG
66 GGCCAAAAATACCTTCAATAACCCCATTCAATATTATGTTAAGGATTATGCAAAGCATTTTCTAG
* * * * *
5645889 GCAAAAACATCTTCAACAATCTCCTCT-TAAACGTCTAAAGGGGATTATTTAAGGTGTTTTATCA
131 GCAAAAACACCTTCAACAATCT-CTCTATAAACGCCTAAAGGAGATTATTCAAGGCGTTTTATCA
** * *
5645953 CAAAAATGCCTTGAATGATTCCAAAAAA
195 CAAAAACACCTTGAATAATCCCAAAAAA
5645981 GTAAGAAGGA
Statistics
Matches: 188, Mismatches: 33, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
233 185 0.98
234 3 0.02
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.33
Consensus pattern (233 bp):
GATTATTGAAGGCGTTTTTAGTCAAAAAAACCTTCAATAATCCAAGAATTATTCAAGGCATTTTT
GGCCAAAAATACCTTCAATAACCCCATTCAATATTATGTTAAGGATTATGCAAAGCATTTTCTAG
GCAAAAACACCTTCAACAATCTCTCTATAAACGCCTAAAGGAGATTATTCAAGGCGTTTTATCAC
AAAAACACCTTGAATAATCCCAAAAAAAAAAGGGAAGG
Found at i:5646080 original size:62 final size:64
Alignment explanation
Indices: 5645974--5646134 Score: 154
Period size: 62 Copynumber: 2.6 Consensus size: 64
5645964 TGAATGATTC
* * * * *
5645974 CAAAAAAGTAAGAAGGAATTA-TCGAAGGCATTTTT--TACAGAAAACGCCTCGACTAATCCCTT
1 CAAAAAAATATGAAGGGATTATTC-AAGGCATTTTTGGTACAGAAAACGCCTCGAATAATCCATT
** * *
5646036 TTAAAAAAT-TGGAAGGGATTATTCAAGGCATTTTTGGT-CA-AAAACGCCTTGAATAATCTATT
1 CAAAAAAATAT-GAAGGGATTATTCAAGGCATTTTTGGTACAGAAAACGCCTCGAATAATCCATT
* **
5646098 CAAAAAAATATAAAATGATTATTCAAGGCATTTTTGG
1 CAAAAAAATATGAAGGGATTATTCAAGGCATTTTTGG
5646135 CTAGAAATGC
Statistics
Matches: 80, Mismatches: 14, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
62 74 0.93
63 5 0.06
64 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (64 bp):
CAAAAAAATATGAAGGGATTATTCAAGGCATTTTTGGTACAGAAAACGCCTCGAATAATCCATT
Found at i:5646211 original size:125 final size:125
Alignment explanation
Indices: 5646052--5646278 Score: 269
Period size: 125 Copynumber: 1.8 Consensus size: 125
5646042 AATTGGAAGG
* * * * * *
5646052 GATTATTCAAGGCATTTTTGGTCAAAAACGCCTTGAATAATCTATTCA-AAAAAATATAAAATGA
1 GATTATGCAAGGCATTTTTGGGCAAAAACACCTTGAATAATCCACTCATAAAAAATA-AAAAGGA
* *
5646116 TTATTCAAGGCATTTTTGGCTAGAA-ATGCCTTTAATAACCCTATTCAATTTTTTTGTAAAA
65 TTATTCAAGGCATTTTTGGC-AAAATATGCCTTCAATAACCCTATTCAATTTTTTTGTAAAA
* * * * * * * *
5646177 GATTATGCAAGGTATTTTTGGGCTAAAATACCTTGATTAGTCCCCTCATAAAAAATAGAGAGGAT
1 GATTATGCAAGGCATTTTTGGGCAAAAACACCTTGAATAATCCACTCATAAAAAATAAAAAGGAT
*
5646242 TATTGAAGGCATTTTTGGCAAAATATGCCTTCAATAA
66 TATTCAAGGCATTTTTGGCAAAATATGCCTTCAATAA
5646279 TCTCCTATAA
Statistics
Matches: 83, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
124 3 0.04
125 72 0.87
126 8 0.10
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.35
Consensus pattern (125 bp):
GATTATGCAAGGCATTTTTGGGCAAAAACACCTTGAATAATCCACTCATAAAAAATAAAAAGGAT
TATTCAAGGCATTTTTGGCAAAATATGCCTTCAATAACCCTATTCAATTTTTTTGTAAAA
Found at i:5654151 original size:54 final size:55
Alignment explanation
Indices: 5654090--5654226 Score: 177
Period size: 55 Copynumber: 2.5 Consensus size: 55
5654080 AAATATAAAA
* * *
5654090 AAAATTAAAACATATAAGTCT-TATTGATAATCTCTAATCATCGATAAAGGTAAG
1 AAAATTAAAACATACAAGTCTATACTGACAATCTCTAATCATCGATAAAGGTAAG
* * * * * *
5654144 AAAATTAAAGCATACAATTCTATACTGACAGTCTCTAATCATTGGTATAGGTAAG
1 AAAATTAAAACATACAAGTCTATACTGACAATCTCTAATCATCGATAAAGGTAAG
*
5654199 AAAATTAAAAAATACAAGTCTATACTGA
1 AAAATTAAAACATACAAGTCTATACTGA
5654227 TGGATGCTTA
Statistics
Matches: 70, Mismatches: 12, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
54 18 0.26
55 52 0.74
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.30
Consensus pattern (55 bp):
AAAATTAAAACATACAAGTCTATACTGACAATCTCTAATCATCGATAAAGGTAAG
Found at i:5665562 original size:19 final size:19
Alignment explanation
Indices: 5665540--5665581 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
5665530 TGAAAAACAG
5665540 AAAATGAATGAAAAA-GAAA
1 AAAATGAAT-AAAAAGGAAA
5665559 AAAATGAATAAAAAGGAAA
1 AAAATGAATAAAAAGGAAA
5665578 AAAA
1 AAAA
5665582 AAAACAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (19 bp):
AAAATGAATAAAAAGGAAA
Found at i:5665613 original size:16 final size:15
Alignment explanation
Indices: 5665589--5665623 Score: 61
Period size: 16 Copynumber: 2.3 Consensus size: 15
5665579 AAAAAAACAA
5665589 AAAAGAAGATAAAAG
1 AAAAGAAGATAAAAG
5665604 AAAAGAAAGATAAAAG
1 AAAAG-AAGATAAAAG
5665620 AAAA
1 AAAA
5665624 AATAATGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (15 bp):
AAAAGAAGATAAAAG
Done.