Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168381.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_6, 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: 26551601
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 64000 characters in sequence are not A, C, G, or T
File 87 of 130
Found at i:17143568 original size:20 final size:20
Alignment explanation
Indices: 17143530--17143567 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17143520 GATTGTGTTA
*
17143530 TATATTAATTTATAATTTTG
1 TATATGAATTTATAATTTTG
17143550 TATATGAATTT-TAATTTT
1 TATATGAATTTATAATTTT
17143568 TTTTGTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (20 bp):
TATATGAATTTATAATTTTG
Found at i:17143819 original size:26 final size:26
Alignment explanation
Indices: 17143791--17143839 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
17143781 TAAAAAATAA
*
17143791 AAAATATAGGTTTGAAAA-TTTTATT
1 AAAATATAAGTTTGAAAACTTTTATT
17143816 AAAATATAAGTTTGAAAACTTTTA
1 AAAATATAAGTTTGAAAACTTTTA
17143840 ATTTTTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.41
Consensus pattern (26 bp):
AAAATATAAGTTTGAAAACTTTTATT
Found at i:17147262 original size:6 final size:6
Alignment explanation
Indices: 17147253--17147288 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
17147243 TTTAAGTCCA
* *
17147253 GATGAT GATGGT GATGGA GATGGT GATGGT GATGGT
1 GATGGT GATGGT GATGGT GATGGT GATGGT GATGGT
17147289 ACGAATTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.22, C:0.00, G:0.47, T:0.31
Consensus pattern (6 bp):
GATGGT
Found at i:17147279 original size:18 final size:18
Alignment explanation
Indices: 17147252--17147287 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
17147242 GTTTAAGTCC
17147252 AGATGATGATGGTGATGG
1 AGATGATGATGGTGATGG
*
17147270 AGATGGTGATGGTGATGG
1 AGATGATGATGGTGATGG
17147288 TACGAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.47, T:0.28
Consensus pattern (18 bp):
AGATGATGATGGTGATGG
Found at i:17147655 original size:18 final size:18
Alignment explanation
Indices: 17147632--17147689 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
17147622 TATAGTTATT
17147632 ATCCACCTCTAATGTATC
1 ATCCACCTCTAATGTATC
*
17147650 ATCCACCTCCTCAAATATATC
1 ATCCACCT-CT--AATGTATC
* *
17147671 ATCCACTTCAAATGTATC
1 ATCCACCTCTAATGTATC
17147689 A
1 A
17147690 GTTACCACAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 16 0.48
19 2 0.06
20 1 0.03
21 14 0.42
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.31
Consensus pattern (18 bp):
ATCCACCTCTAATGTATC
Found at i:17147670 original size:21 final size:21
Alignment explanation
Indices: 17147637--17147676 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
17147627 TTATTATCCA
* *
17147637 CCTCTAATGTATCATCCACCT
1 CCTCAAATATATCATCCACCT
17147658 CCTCAAATATATCATCCAC
1 CCTCAAATATATCATCCAC
17147677 TTCAAATGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.38, G:0.03, T:0.30
Consensus pattern (21 bp):
CCTCAAATATATCATCCACCT
Found at i:17150592 original size:3 final size:3
Alignment explanation
Indices: 17150584--17150624 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
17150574 CTTCAAATGC
17150584 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
17150625 TTTTGAAGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:17154439 original size:23 final size:22
Alignment explanation
Indices: 17154399--17154441 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
17154389 TAATTTTAAG
* *
17154399 TTTAATTTATTAATTTTAAAAA
1 TTTAATTGATTAAATTTAAAAA
17154421 TTTAATTAGATTAAATTTAAA
1 TTTAATT-GATTAAATTTAAA
17154442 TAAATTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TTTAATTGATTAAATTTAAAAA
Found at i:17154823 original size:12 final size:12
Alignment explanation
Indices: 17154790--17154875 Score: 58
Period size: 12 Copynumber: 7.5 Consensus size: 12
17154780 CTTTGGTTAA
17154790 AAATTA-TTA-T
1 AAATTATTTATT
17154800 AATATT-TTTATT
1 AA-ATTATTTATT
*
17154812 CAATTATTTATT
1 AAATTATTTATT
* **
17154824 AAATTAATTACA
1 AAATTATTTATT
17154836 AAATTA-TTA-T
1 AAATTATTTATT
17154846 AATATT-TTTATT
1 AA-ATTATTTATT
**
17154858 AAATTACATATT
1 AAATTATTTATT
17154870 AAATTA
1 AAATTA
17154876 ATTACATAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
10 4 0.07
11 21 0.35
12 35 0.58
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.51
Consensus pattern (12 bp):
AAATTATTTATT
Found at i:17154839 original size:46 final size:46
Alignment explanation
Indices: 17154789--17154881 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
17154779 ACTTTGGTTA
* **
17154789 AAAATTATTATAATATTTTTATTCAATTATTTATTAAATTAATTAC
1 AAAATTATTATAATATTTTTATTAAATTACATATTAAATTAATTAC
17154835 AAAATTATTATAATATTTTTATTAAATTACATATTAAATTAATTAC
1 AAAATTATTATAATATTTTTATTAAATTACATATTAAATTAATTAC
17154881 A
1 A
17154882 TAAAACTTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.49
Consensus pattern (46 bp):
AAAATTATTATAATATTTTTATTAAATTACATATTAAATTAATTAC
Found at i:17154880 original size:16 final size:16
Alignment explanation
Indices: 17154859--17154906 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
17154849 ATTTTTATTA
17154859 AATTACATATTAAATT
1 AATTACATATTAAATT
17154875 AATTACATA--AAACTT
1 AATTACATATTAAA-TT
**
17154890 AATTATGTATTAAATT
1 AATTACATATTAAATT
17154906 A
1 A
17154907 TTATAATATC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 3 0.11
15 9 0.33
16 12 0.44
17 3 0.11
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (16 bp):
AATTACATATTAAATT
Found at i:17157139 original size:12 final size:12
Alignment explanation
Indices: 17157108--17157141 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
17157098 TATATTTATT
*
17157108 TAATCAACTAAA
1 TAATCAATTAAA
*
17157120 TAATCAATTGAA
1 TAATCAATTAAA
17157132 TAATCAATTA
1 TAATCAATTA
17157142 TTATATAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.32
Consensus pattern (12 bp):
TAATCAATTAAA
Found at i:17157171 original size:18 final size:18
Alignment explanation
Indices: 17157130--17157177 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 18
17157120 TAATCAATTG
*
17157130 AATAATCAATTATTATAT
1 AATAATCAATTATGATAT
17157148 AATAATCAATTATGATTATTT
1 AATAATCAATTATGA-TA--T
17157169 AATAATCAA
1 AATAATCAA
17157178 CTAATAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 14 0.54
19 2 0.08
21 10 0.38
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (18 bp):
AATAATCAATTATGATAT
Found at i:17158108 original size:119 final size:119
Alignment explanation
Indices: 17157878--17158118 Score: 315
Period size: 119 Copynumber: 2.0 Consensus size: 119
17157868 CCAAAAATAA
* * *
17157878 TTAAATTGTTTCCATGCATTCAAGTTAGAATAGATACTTTATCGTGTAGTACATATAGATGAGAT
1 TTAAATTGTTTCCATACATTCAAGTTAGAATAGATACTTGATCATGTAGTACATATAGATGAGAT
* * *
17157943 AAAGGAGAAAGGTAAGAATTAAAGCCTGAACTTTGACTTTGATTTTTTGGTTAT
66 AAAGGAGAAAGGTAAGAATCAAAGCCTAAACTTTGACTTTCATTTTTTGGTTAT
* * *
17157997 TTAAATTGTGTT-CATATATTCAAGTTAGAATAGGTACTTGATCATGTAGTACATATAGATGAGC
1 TTAAATTGT-TTCCATACATTCAAGTTAGAATAGATACTTGATCATGTAGTACATATAGATGAGA
* * * * * **
17158061 TACAGGAG-CAGGTAGGAATCGAAGCCTAAACTTTGACTTTCCTTTTTTATTTAT
65 TAAAGGAGAAAGGTAAGAATCAAAGCCTAAACTTTGACTTTCATTTTTTGGTTAT
17158115 TTAA
1 TTAA
17158119 TCTGGCACAA
Statistics
Matches: 105, Mismatches: 16, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
118 41 0.39
119 62 0.59
120 2 0.02
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (119 bp):
TTAAATTGTTTCCATACATTCAAGTTAGAATAGATACTTGATCATGTAGTACATATAGATGAGAT
AAAGGAGAAAGGTAAGAATCAAAGCCTAAACTTTGACTTTCATTTTTTGGTTAT
Found at i:17158629 original size:17 final size:17
Alignment explanation
Indices: 17158605--17158638 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
17158595 AAATTTATTT
17158605 TTAATAAAATT-TTAAA
1 TTAATAAAATTATTAAA
17158621 TTAACTAAAATTATTAAA
1 TTAA-TAAAATTATTAAA
17158639 AAAATAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 7 0.44
18 5 0.31
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAATAAAATTATTAAA
Found at i:17159800 original size:19 final size:18
Alignment explanation
Indices: 17159776--17159822 Score: 62
Period size: 16 Copynumber: 2.7 Consensus size: 18
17159766 CTCATTTTAT
*
17159776 TTTATTTTTATTTTATTAA
1 TTTATTATTA-TTTATTAA
17159795 TTTATTATTATTTATT-A
1 TTTATTATTATTTATTAA
17159812 -TTATTATTATT
1 TTTATTATTATT
17159823 ACTATTAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 11 0.41
17 1 0.04
18 6 0.22
19 9 0.33
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTATTATTTATTAA
Found at i:17159804 original size:3 final size:3
Alignment explanation
Indices: 17159772--17159829 Score: 59
Period size: 3 Copynumber: 20.0 Consensus size: 3
17159762 TCCTCTCATT
* *
17159772 TTA TT- TTA TTT TTA TT- TTA TTA AT- TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
*
17159815 TTA TTA TTA CTA TTA
1 TTA TTA TTA TTA TTA
17159830 AACAAAAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
2 5 0.11
3 37 0.82
4 3 0.07
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:17159823 original size:19 final size:19
Alignment explanation
Indices: 17159772--17159823 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
17159762 TCCTCTCATT
*
17159772 TTATTTTATTTTTATTTTA
1 TTATTTTATTATTATTTTA
*
17159791 TTAATTTATTATTA-TTTA
1 TTATTTTATTATTATTTTA
17159809 TTATTATTATTATTA
1 TTATT-TTATTATTA
17159824 CTATTAAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 8 0.28
19 21 0.72
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TTATTTTATTATTATTTTA
Found at i:17162084 original size:46 final size:46
Alignment explanation
Indices: 17161910--17162244 Score: 225
Period size: 46 Copynumber: 7.1 Consensus size: 46
17161900 AACAAGGTTT
* * * * *
17161910 CACAACTTTTGAAAATAAAGTTACAAA-TTCTTTTAAGTAAA-GCTTT
1 CACAATTTTTGAAAATAAATTTA-AAAGTTCCTTTAAGCAAAGGC-TC
* * * *
17161956 AACAACTTTTGAAAACAAATTTTTAAAA-CTCCTTTAAGCAAAGGCT-
1 CACAATTTTTGAAAATAAA--TTTAAAAGTTCCTTTAAGCAAAGGCTC
*
17162002 TAGCAATTTTTGAAATTGAAAGTAAATTTAAAAGTTCCTTTAAGCAAAGGCTC
1 CA-CAATTTTTG--A---AAA-TAAATTTAAAAGTTCCTTTAAGCAAAGGCTC
* * *
17162055 CATAATTTTTGAAAATAAATTTAAAAGTTCTTTTAAACAAAGGCTC
1 CACAATTTTTGAAAATAAATTTAAAAGTTCCTTTAAGCAAAGGCTC
* * * * *
17162101 CACAATTTTTTTAAAAATTAATATAAAAGTTCCTCTAAGCAAAAGCTC
1 CACAA--TTTTTGAAAATAAATTTAAAAGTTCCTTTAAGCAAAGGCTC
* ** *
17162149 CACAACTTTT-AAAAGTAAATTTAAAA-ACCCTTTTAAGCAAAGGCTT
1 CACAATTTTTGAAAA-TAAATTTAAAAGTTCC-TTTAAGCAAAGGCTC
* * * * * *
17162195 CATAA-CTTTGAAAATATATTTAAAAGCTCATTTAAGCAAAGACTC
1 CACAATTTTTGAAAATAAATTTAAAAGTTCCTTTAAGCAAAGGCTC
*
17162240 AACAA
1 CACAA
17162245 CTTTAAAAAT
Statistics
Matches: 231, Mismatches: 40, Indels: 37
0.75 0.13 0.12
Matches are distributed among these distances:
45 35 0.15
46 85 0.37
47 26 0.11
48 44 0.19
49 1 0.00
50 1 0.00
51 7 0.03
52 28 0.12
53 4 0.02
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.33
Consensus pattern (46 bp):
CACAATTTTTGAAAATAAATTTAAAAGTTCCTTTAAGCAAAGGCTC
Found at i:17162280 original size:48 final size:48
Alignment explanation
Indices: 17162216--17162307 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
17162206 AAATATATTT
*
17162216 AAAAGCTCATTTAAGCAAAGACTCAACAACTTTAAAAATTTCATCCCA
1 AAAAGCTCATTTAAGCAAAGACTCAACAACTTTAAAAATCTCATCCCA
* **
17162264 AAAAGCT-ACTTTAAGCAAAGGCTCAATGACTTTAAAAATCTCAT
1 AAAAGCTCA-TTTAAGCAAAGACTCAACAACTTTAAAAATCTCAT
17162308 ATTTGAAAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
47 1 0.03
48 38 0.97
ACGTcount: A:0.45, C:0.21, G:0.09, T:0.26
Consensus pattern (48 bp):
AAAAGCTCATTTAAGCAAAGACTCAACAACTTTAAAAATCTCATCCCA
Found at i:17162296 original size:139 final size:138
Alignment explanation
Indices: 17162020--17162301 Score: 293
Period size: 139 Copynumber: 2.0 Consensus size: 138
17162010 TTTGAAATTG
** * *
17162020 AAAGTAAATTTAAAAGTTCCTTTAAGCAAAGGCTCCATAATTTTTGAAAATAAATTTAAAAGTTC
1 AAAGTAAATTTAAAAGACCCTTTAAGCAAAGGCTCCATAATCTTTGAAAATAAATTTAAAAGCTC
* * * * * * *
17162085 TTTTAAACAAAGGCTCCACAATTTTTTTAAAAATTAATATAAAAGTTCCTCTAAGCAAAAGCTCC
66 ATTTAAACAAAGACTCAACAA--TCTTTAAAAATTAATATAAAAGCTACTCTAAGCAAAAGCTCA
*
17162150 ACAACTTTTA
129 ACAACTTTAA
* *
17162160 AAAGTAAATTTAAAA-ACCCTTTTAAGCAAAGGCTTCATAA-CTTTGAAAATATATTTAAAAGCT
1 AAAGTAAATTTAAAAGACCC-TTTAAGCAAAGGCTCCATAATCTTTGAAAATAAATTTAAAAGCT
* * * *
17162223 CATTTAAGCAAAGACTCAACAA-CTTTAAAAATTTCATCCCA-AAAAGCTACTTTAAGCAAAGGC
65 CATTTAAACAAAGACTCAACAATCTTTAAAAA-TTAAT---ATAAAAGCTACTCTAAGCAAAAGC
**
17162286 TCAATGACTTTAA
126 TCAACAACTTTAA
17162299 AAA
1 AAA
17162302 TCTCATATTT
Statistics
Matches: 117, Mismatches: 20, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
136 8 0.07
137 4 0.03
139 70 0.60
140 35 0.30
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (138 bp):
AAAGTAAATTTAAAAGACCCTTTAAGCAAAGGCTCCATAATCTTTGAAAATAAATTTAAAAGCTC
ATTTAAACAAAGACTCAACAATCTTTAAAAATTAATATAAAAGCTACTCTAAGCAAAAGCTCAAC
AACTTTAA
Found at i:17163520 original size:13 final size:13
Alignment explanation
Indices: 17163482--17163523 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
17163472 AGTCTTTCCT
17163482 TTTTCTTTCTTTC
1 TTTTCTTTCTTTC
* *
17163495 TTTTTTTTTTTTC
1 TTTTCTTTCTTTC
*
17163508 TTTTCTTACTTTC
1 TTTTCTTTCTTTC
17163521 TTT
1 TTT
17163524 AAACTTTTCC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTCTTTCTTTC
Found at i:17164830 original size:23 final size:24
Alignment explanation
Indices: 17164796--17164847 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
17164786 CATTATATAT
17164796 ATTT-TTTAAGTTGATTCAAATAA
1 ATTTATTTAAGTTGATTCAAATAA
**
17164819 ATTTATTT-AGTTGATTTTAATAA
1 ATTTATTTAAGTTGATTCAAATAA
17164842 ATTTAT
1 ATTTAT
17164848 AAAAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 23 0.88
24 3 0.12
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.54
Consensus pattern (24 bp):
ATTTATTTAAGTTGATTCAAATAA
Found at i:17165726 original size:16 final size:16
Alignment explanation
Indices: 17165695--17165738 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
17165685 TATATTTTTT
17165695 ATTAT-AATTA-AATA
1 ATTATAAATTATAATA
17165709 ATTATAAATTATAATA
1 ATTATAAATTATAATA
* *
17165725 ATAAAAAATTATAA
1 ATTATAAATTATAA
17165739 ATGATATACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 5 0.19
15 5 0.19
16 16 0.62
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTATAAATTATAATA
Found at i:17165734 original size:23 final size:24
Alignment explanation
Indices: 17165693--17165740 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
17165683 TATATATTTT
* *
17165693 TTATTATAATTAAATAATTATAAA
1 TTATAATAATTAAAAAATTATAAA
17165717 TTATAATAA-TAAAAAATTATAAA
1 TTATAATAATTAAAAAATTATAAA
17165740 T
1 T
17165741 GATATACTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
TTATAATAATTAAAAAATTATAAA
Found at i:17166023 original size:115 final size:114
Alignment explanation
Indices: 17165822--17166050 Score: 449
Period size: 115 Copynumber: 2.0 Consensus size: 114
17165812 CAATTGCGGC
17165822 CTCCCCACTTTCCTCCACCTTTGACAAAAATATTGTAACCGTCAAAACCCACACTGACCATCTAA
1 CTCCCCACTTTCCTCCACCTTTGACAAAAATATTGTAACCGTCAAAACCCACACTGACCATCTAA
17165887 CCTACCCCTAGAGTCTCCCAACTTAAGGGGCGGGTTACTGAATATATAT
66 CCTACCCCTAGAGTCTCCCAACTTAAGGGGCGGGTTACTGAATATATAT
17165936 CTCCCCACTTTCCTCCACCTTTGACAAAAAATATTGTAACCGTCAAAACCCACACTGACCATCTA
1 CTCCCCACTTTCCTCCACCTTTGAC-AAAAATATTGTAACCGTCAAAACCCACACTGACCATCTA
17166001 ACCTACCCCTAGAGTCTCCCAACTTAAGGGGCGGGTTACTGAATATATAT
65 ACCTACCCCTAGAGTCTCCCAACTTAAGGGGCGGGTTACTGAATATATAT
17166051 ATATATATAT
Statistics
Matches: 114, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
114 25 0.22
115 89 0.78
ACGTcount: A:0.30, C:0.32, G:0.12, T:0.25
Consensus pattern (114 bp):
CTCCCCACTTTCCTCCACCTTTGACAAAAATATTGTAACCGTCAAAACCCACACTGACCATCTAA
CCTACCCCTAGAGTCTCCCAACTTAAGGGGCGGGTTACTGAATATATAT
Found at i:17166050 original size:2 final size:2
Alignment explanation
Indices: 17166043--17166087 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
17166033 GGGTTACTGA
*
17166043 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17166085 AT A
1 AT A
17166088 GGTACTTTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:17177169 original size:31 final size:31
Alignment explanation
Indices: 17177129--17177204 Score: 116
Period size: 31 Copynumber: 2.5 Consensus size: 31
17177119 GAAAAAAGTT
17177129 GGTGAGAGGTGGAGATTAAGTATATAGAGCC
1 GGTGAGAGGTGGAGATTAAGTATATAGAGCC
* * * *
17177160 GGTGGGAGGTAGAGATTAAGTATGTAGAGTC
1 GGTGAGAGGTGGAGATTAAGTATATAGAGCC
17177191 GGTGAGAGGTGGAG
1 GGTGAGAGGTGGAG
17177205 GTAAAGAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.29, C:0.04, G:0.45, T:0.22
Consensus pattern (31 bp):
GGTGAGAGGTGGAGATTAAGTATATAGAGCC
Found at i:17178552 original size:62 final size:64
Alignment explanation
Indices: 17178486--17178631 Score: 170
Period size: 64 Copynumber: 2.3 Consensus size: 64
17178476 ATTTCTAGCT
* * * *
17178486 AAAAACACCTTCAATAATCTC-CTGTAAAA-ATTTTGAATAAATTATTGAAGGCATTTTTGGTC
1 AAAAACACCTTTAATAATCTCTCTCTAAAATATTTTGAATAAATTATTGAAAGCATTTTTGGCC
* * * * * ** *
17178548 AAAAACGCTTTTAATAATCCCTCTCTAAAATTTTTTGAATGAATTATTGAAAGTGTTTTTTGCC
1 AAAAACACCTTTAATAATCTCTCTCTAAAATATTTTGAATAAATTATTGAAAGCATTTTTGGCC
17178612 AAAAACACCTTTAATAATCT
1 AAAAACACCTTTAATAATCT
17178632 TATTCAATTT
Statistics
Matches: 67, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
62 17 0.25
63 7 0.10
64 43 0.64
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (64 bp):
AAAAACACCTTTAATAATCTCTCTCTAAAATATTTTGAATAAATTATTGAAAGCATTTTTGGCC
Found at i:17179000 original size:64 final size:63
Alignment explanation
Indices: 17178859--17179006 Score: 151
Period size: 64 Copynumber: 2.3 Consensus size: 63
17178849 ACTATCAGTA
* * * * *
17178859 AATAATC-CATACAAAATTTTTTGTATGGATTATTGAAGGCATTTTTGGCTAAAAATGCCTTC
1 AATAATCTCATTCAAATTTTTTTGAATAGATTATTGAAGGCATTTTTGGCTAAAAACGCCTTC
** *
17178921 AATAATCTTTC-TTCAAATTTTTTTGAATAGATTATTGAAGGTGTTTTTTTGTCT-AAAACGCCT
1 AATAATC--TCATTCAAATTTTTTTGAATAGATTATTGAA-G-GCATTTTTGGCTAAAAACGCCT
*
17178984 TT
62 TC
17178986 AATAATCTCATTC-AATTTTTT
1 AATAATCTCATTCAAATTTTTT
17179007 GCAAGCCAAC
Statistics
Matches: 71, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
62 7 0.10
63 10 0.14
64 27 0.38
65 18 0.25
66 9 0.13
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.45
Consensus pattern (63 bp):
AATAATCTCATTCAAATTTTTTTGAATAGATTATTGAAGGCATTTTTGGCTAAAAACGCCTTC
Found at i:17180590 original size:14 final size:15
Alignment explanation
Indices: 17180538--17180591 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 15
17180528 AAAAATAAAA
17180538 AAAAT-AAAAATGAG
1 AAAATGAAAAATGAG
*
17180552 AAGAAAGAAAAATGAG
1 AA-AATGAAAAATGAG
* *
17180568 AAGA-CAAAAATG-G
1 AAAATGAAAAATGAG
17180581 AAAATGAAAAA
1 AAAATGAAAAA
17180592 AAGAAAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
13 4 0.12
14 14 0.44
15 3 0.09
16 11 0.34
ACGTcount: A:0.70, C:0.02, G:0.19, T:0.09
Consensus pattern (15 bp):
AAAATGAAAAATGAG
Found at i:17180701 original size:21 final size:21
Alignment explanation
Indices: 17180662--17180701 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
17180652 AGTTAAGAGT
* **
17180662 TAAATTTATTTTTTTAAAATG
1 TAAATTGATTTTTCAAAAATG
17180683 TAAATTGATTTTTCAAAAA
1 TAAATTGATTTTTCAAAAA
17180702 ACTATTTTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (21 bp):
TAAATTGATTTTTCAAAAATG
Found at i:17180769 original size:9 final size:9
Alignment explanation
Indices: 17180740--17180811 Score: 63
Period size: 9 Copynumber: 7.7 Consensus size: 9
17180730 ATTTATTCAA
17180740 AAAAAAAAG
1 AAAAAAAAG
* *
17180749 AAAATAAGG
1 AAAAAAAAG
17180758 AAAAAAAAG
1 AAAAAAAAG
*
17180767 AAAAATTAAAA
1 AAAAA--AAAG
17180778 AAAGAAAAAG
1 AAA-AAAAAG
* *
17180788 AATAAATAG
1 AAAAAAAAG
*
17180797 AAAAAAAGG
1 AAAAAAAAG
17180806 AAAAAA
1 AAAAAA
17180812 TAAAATAAAA
Statistics
Matches: 49, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
9 36 0.73
10 5 0.10
11 6 0.12
12 2 0.04
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.07
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:17180779 original size:18 final size:17
Alignment explanation
Indices: 17180738--17180822 Score: 64
Period size: 18 Copynumber: 4.5 Consensus size: 17
17180728 TTATTTATTC
17180738 AAAAAAAAAAG-AAAAT
1 AAAAAAAAAAGAAAAAT
17180754 AAGGAAAAAAAAGAAAAATT
1 AA--AAAAAAAAGAAAAA-T
17180774 AAAAAAAGAAAAAGAATAAAT
1 --AAAAA-AAAAAGAA-AAAT
* *
17180795 AGAAAAAAAGGAAAAAAT
1 AAAAAAAAAAG-AAAAAT
17180813 AAAATAAAAA
1 AAAA-AAAAA
17180823 TAATTTAGAT
Statistics
Matches: 56, Mismatches: 3, Indels: 17
0.74 0.04 0.22
Matches are distributed among these distances:
16 2 0.04
18 21 0.38
19 15 0.27
20 4 0.07
21 9 0.16
22 5 0.09
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.08
Consensus pattern (17 bp):
AAAAAAAAAAGAAAAAT
Found at i:17180822 original size:22 final size:23
Alignment explanation
Indices: 17180761--17180822 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
17180751 AATAAGGAAA
*
17180761 AAAAAG-A-AAAATTAAAAAAAG
1 AAAAAGAATAAAATAAAAAAAAG
17180782 AAAAAGAAT-AAATAGAAAAAAAG
1 AAAAAGAATAAAATA-AAAAAAAG
*
17180805 GAAAA-AATAAAATAAAAA
1 AAAAAGAATAAAATAAAAA
17180823 TAATTTAGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
21 6 0.17
22 12 0.34
23 17 0.49
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.10
Consensus pattern (23 bp):
AAAAAGAATAAAATAAAAAAAAG
Found at i:17180932 original size:22 final size:20
Alignment explanation
Indices: 17180907--17180958 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
17180897 TTAAAAATAA
17180907 AATAAATAATTTATAAATATTT
1 AATAAATAATTTATAAA-A-TT
**
17180929 AATATCTAATTTTATAAAATT
1 AATAAATAA-TTTATAAAATT
17180950 AA-AAATAAT
1 AATAAATAAT
17180959 CCTCGTCTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
19 1 0.04
20 4 0.16
21 4 0.16
22 8 0.32
23 8 0.32
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
AATAAATAATTTATAAAATT
Found at i:17181263 original size:21 final size:22
Alignment explanation
Indices: 17181234--17181279 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
17181224 TAAAAATATA
*
17181234 AAATATATTTTTA-ATTTTATT
1 AAATATATTTATATATTTTATT
* *
17181255 AAATTTATTTATATTTTTTATT
1 AAATATATTTATATATTTTATT
17181277 AAA
1 AAA
17181280 ATTTTAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
AAATATATTTATATATTTTATT
Found at i:17181388 original size:20 final size:20
Alignment explanation
Indices: 17181363--17181402 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
17181353 AAACTTAAAT
*
17181363 GAAAGGATTAAGATAAGATA
1 GAAAGGATAAAGATAAGATA
17181383 GAAAGGATAAAGATAAGATA
1 GAAAGGATAAAGATAAGATA
17181403 CTAAGATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.25, T:0.17
Consensus pattern (20 bp):
GAAAGGATAAAGATAAGATA
Found at i:17190631 original size:20 final size:22
Alignment explanation
Indices: 17190597--17190637 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
17190587 TAAATTAAAA
*
17190597 TTTTTATATATTATTTTAATAT
1 TTTTTATATATTATTTAAATAT
17190619 TTTTTA-ATA-TATTTAAATA
1 TTTTTATATATTATTTAAATA
17190638 AATTTAAGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 3 0.17
22 6 0.33
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTTTATATATTATTTAAATAT
Found at i:17191143 original size:1 final size:1
Alignment explanation
Indices: 17191137--17191164 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
17191127 AATGTAGACG
17191137 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
17191165 GGGGGTGTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:17191606 original size:22 final size:22
Alignment explanation
Indices: 17191578--17191621 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
17191568 TGCATTTCAG
17191578 ATACCCCAATTCTAATAAACGA
1 ATACCCCAATTCTAATAAACGA
17191600 ATACCCCAATTCTAATAAACGA
1 ATACCCCAATTCTAATAAACGA
17191622 TTTAAGGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.27, G:0.05, T:0.23
Consensus pattern (22 bp):
ATACCCCAATTCTAATAAACGA
Found at i:17198441 original size:12 final size:12
Alignment explanation
Indices: 17198434--17198458 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17198424 TTTATAATTG
17198434 TTTATATATATT
1 TTTATATATATT
17198446 TTTATATATATT
1 TTTATATATATT
17198458 T
1 T
17198459 AATTTTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTATATATATT
Found at i:17202952 original size:2 final size:2
Alignment explanation
Indices: 17202945--17202980 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
17202935 TTTTATAACT
*
17202945 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17202981 ATACGACTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:17210154 original size:76 final size:76
Alignment explanation
Indices: 17210026--17210174 Score: 183
Period size: 76 Copynumber: 2.0 Consensus size: 76
17210016 CATTATCCGA
* * * ** * * *
17210026 TAAATTTACTGGTATTTTTTTTGTGTTTTTGCTAGTATTTGTTTCTTAATATTT-TCTTGGTGTG
1 TAAATTTACTGATATTTCTTTAGTGTTTTTGCTAAAATTTATCTCTTAATATTTCT-TTGGTATG
17210090 ATTGTAGGCTAG
65 ATTGTAGGCTAG
* * *
17210102 TAAATTTATTGATATTTCTTTAGTGTTTTTGCTAAAATTTATCTGTTGATATTTCTTTGGTATGA
1 TAAATTTACTGATATTTCTTTAGTGTTTTTGCTAAAATTTATCTCTTAATATTTCTTTGGTATGA
17210167 TTGTAGGC
66 TTGTAGGC
17210175 ACTGTTTGTG
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
76 60 0.98
77 1 0.02
ACGTcount: A:0.20, C:0.07, G:0.18, T:0.55
Consensus pattern (76 bp):
TAAATTTACTGATATTTCTTTAGTGTTTTTGCTAAAATTTATCTCTTAATATTTCTTTGGTATGA
TTGTAGGCTAG
Found at i:17211500 original size:36 final size:36
Alignment explanation
Indices: 17211446--17211531 Score: 93
Period size: 36 Copynumber: 2.4 Consensus size: 36
17211436 GTATTGATTG
*** *
17211446 GATTTGAAACTTTTGTTGAAACTAAAAT-AAAACATG
1 GATTTGAAACTAGAGTTGAAACTAAAATGAAAAC-TA
* **
17211482 GATTTGAAGCTAGAGTTGAAACTGGAATGAAAACTA
1 GATTTGAAACTAGAGTTGAAACTAAAATGAAAACTA
17211518 GATTTGAAACTAGA
1 GATTTGAAACTAGA
17211532 TTTGTTGAAG
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
36 36 0.88
37 5 0.12
ACGTcount: A:0.43, C:0.08, G:0.20, T:0.29
Consensus pattern (36 bp):
GATTTGAAACTAGAGTTGAAACTAAAATGAAAACTA
Found at i:17211507 original size:24 final size:24
Alignment explanation
Indices: 17211475--17211554 Score: 72
Period size: 24 Copynumber: 3.2 Consensus size: 24
17211465 AACTAAAATA
*
17211475 AAACATGGATTTGAAGCTAGAGTTG
1 AAAC-TGGATTTGAAGCTAGATTTG
* *
17211500 AAACTGGA-ATGAAAACTAGATTTG
1 AAACTGGATTTG-AAGCTAGATTTG
*
17211524 AAACTAGATTTGTTGAAGCTAGATTTG
1 AAACTGGA--T-TTGAAGCTAGATTTG
17211551 AAAC
1 AAAC
17211555 CAGATTTAAG
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
23 2 0.05
24 21 0.48
25 4 0.09
27 15 0.34
28 2 0.05
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.29
Consensus pattern (24 bp):
AAACTGGATTTGAAGCTAGATTTG
Found at i:17211527 original size:12 final size:12
Alignment explanation
Indices: 17211482--17211561 Score: 63
Period size: 12 Copynumber: 6.4 Consensus size: 12
17211472 ATAAAACATG
*
17211482 GATTTGAAGCTA
1 GATTTGAAACTA
* *
17211494 GAGTTGAAACTG
1 GATTTGAAACTA
*
17211506 GA-ATGAAAACTA
1 GATTTG-AAACTA
17211518 GATTTGAAACTA
1 GATTTGAAACTA
*
17211530 GATTTGTTGAAGCTA
1 GA--T-TTGAAACTA
*
17211545 GATTTGAAACCA
1 GATTTGAAACTA
17211557 GATTT
1 GATTT
17211562 AAGGTTTGTG
Statistics
Matches: 54, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
11 2 0.04
12 38 0.70
13 3 0.06
14 1 0.02
15 10 0.19
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.31
Consensus pattern (12 bp):
GATTTGAAACTA
Found at i:17211545 original size:15 final size:15
Alignment explanation
Indices: 17211521--17211550 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17211511 AAAACTAGAT
17211521 TTGAAACTAGATTTG
1 TTGAAACTAGATTTG
*
17211536 TTGAAGCTAGATTTG
1 TTGAAACTAGATTTG
17211551 AAACCAGATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.40
Consensus pattern (15 bp):
TTGAAACTAGATTTG
Found at i:17213721 original size:23 final size:22
Alignment explanation
Indices: 17213694--17213757 Score: 58
Period size: 22 Copynumber: 2.8 Consensus size: 22
17213684 TTTAGAGGAT
*
17213694 AAAAAATTTATTTTTGTTTATTTG
1 AAAACATTT-TTTTT-TTTATTTG
*
17213718 AAAACTATTTTTATTTTTA-TTG
1 AAAAC-ATTTTTTTTTTTATTTG
*
17213740 AAAAGATTTTTTTATTTT
1 AAAACATTTTTTT-TTTT
17213758 TTATTTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 7 0.21
22 11 0.32
23 4 0.12
24 8 0.24
25 4 0.12
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.59
Consensus pattern (22 bp):
AAAACATTTTTTTTTTTATTTG
Found at i:17213726 original size:21 final size:22
Alignment explanation
Indices: 17213702--17213743 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
17213692 ATAAAAAATT
*
17213702 TATTTTTGTTTAT-TTGAAAAC
1 TATTTTTATTTATATTGAAAAC
*
17213723 TATTTTTATTTTTATTGAAAA
1 TATTTTTATTTATATTGAAAA
17213744 GATTTTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.60
Consensus pattern (22 bp):
TATTTTTATTTATATTGAAAAC
Found at i:17214271 original size:9 final size:9
Alignment explanation
Indices: 17214257--17214290 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
17214247 CATGTTTTTC
17214257 CCCAAAAAA
1 CCCAAAAAA
17214266 CCCAAAAAAA
1 CCC-AAAAAA
*
17214276 TCCAAAAAA
1 CCCAAAAAA
17214285 CCCAAA
1 CCCAAA
17214291 TTTCTTTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.65, C:0.32, G:0.00, T:0.03
Consensus pattern (9 bp):
CCCAAAAAA
Found at i:17215273 original size:89 final size:89
Alignment explanation
Indices: 17215161--17215513 Score: 353
Period size: 89 Copynumber: 4.0 Consensus size: 89
17215151 CACATGATCG
* * * *
17215161 GGATGAAACCACGAGTCAAAATAAAGTGACTAAGATCAAGTCGAGGTTAAAAATAAATGATCAGA
1 GGATGAAACCA-AAGTCAAAATAAAGTGACCAAGATCAAGTCGAGATCAAAAATAAATGATCAGA
* *
17215226 -ATGAAATCATGAATCATTTGACCA
65 GATGAAACCATGAATCATGTGACCA
* * * * * * *
17215250 GGATGAAAACCACAGTTAAAATAAAATGACCAAGACCAAATTGAGATCGAAAATAAATGATC-GA
1 GGATG-AAACCAAAGTCAAAATAAAGTGACCAAGATCAAGTCGAGATCAAAAATAAATGATCAGA
*
17215314 GATGAAACCATGAATCATGTGACGA
65 GATGAAACCATGAATCATGTGACCA
* * *
17215339 TGATGAAACCAAAAGTTAAAATAAAGTGACC-AGA-CTGAGTCGAGATCAAAAATAAATGATCA-
1 GGATGAAACC-AAAGTCAAAATAAAGTGACCAAGATC-AAGTCGAGATCAAAAATAAATGATCAG
* * * *
17215401 AGATGAAACCATAAATCCTATGATC-
64 AGATGAAACCATGAATCATGTGACCA
* * * * *
17215426 GAGATTAAATCATAAGTCAAAATAAAGTGACCAAGACTGAA-TCGAGGTTAAAAATAAATGATCA
1 G-GATGAAACCA-AAGTCAAAATAAAGTGACCAAGA-TCAAGTCGAGATCAAAAATAAATGATCA
17215490 G-GATGAAACCATGAATCATGTGAC
63 GAGATGAAACCATGAATCATGTGAC
17215514 TTGGACAAAA
Statistics
Matches: 216, Mismatches: 37, Indels: 22
0.79 0.13 0.08
Matches are distributed among these distances:
87 2 0.01
88 76 0.35
89 131 0.61
90 7 0.03
ACGTcount: A:0.47, C:0.14, G:0.18, T:0.20
Consensus pattern (89 bp):
GGATGAAACCAAAGTCAAAATAAAGTGACCAAGATCAAGTCGAGATCAAAAATAAATGATCAGAG
ATGAAACCATGAATCATGTGACCA
Found at i:17226832 original size:22 final size:21
Alignment explanation
Indices: 17226803--17226845 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
17226793 GGATAAAAAG
17226803 ATTATTTT-TGTTTATTTGAAA
1 ATTATTTTATGTTTA-TTGAAA
*
17226824 ATTATTTTTATTTTTATTGAAA
1 ATTA-TTTTATGTTTATTGAAA
17226846 GGATTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 4 0.21
22 10 0.53
23 5 0.26
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (21 bp):
ATTATTTTATGTTTATTGAAA
Found at i:17226957 original size:11 final size:10
Alignment explanation
Indices: 17226922--17227023 Score: 62
Period size: 11 Copynumber: 9.5 Consensus size: 10
17226912 ACTCTTTTTT
17226922 TAAAAAAAAA
1 TAAAAAAAAA
*
17226932 -AAAACAAAA
1 TAAAAAAAAA
** *
17226941 CCAAAAATAA
1 TAAAAAAAAA
*
17226951 TAAAAAAATAGGT
1 TAAAAAAA-A--A
17226964 TAAAAATAAAA
1 TAAAAA-AAAA
*
17226975 TAAAATAAAA
1 TAAAAAAAAA
17226985 TAAAACCAAAAA
1 TAAAA--AAAAA
17226997 TAAAAATAAAA
1 TAAAAA-AAAA
17227008 TAAAATAAAAA
1 TAAAA-AAAAA
*
17227019 GAAAA
1 TAAAA
17227024 CTTGAGATCT
Statistics
Matches: 71, Mismatches: 12, Indels: 17
0.71 0.12 0.17
Matches are distributed among these distances:
9 8 0.11
10 21 0.30
11 23 0.32
12 10 0.14
13 7 0.10
14 2 0.03
ACGTcount: A:0.78, C:0.05, G:0.03, T:0.14
Consensus pattern (10 bp):
TAAAAAAAAA
Found at i:17226976 original size:5 final size:5
Alignment explanation
Indices: 17226966--17227017 Score: 68
Period size: 5 Copynumber: 9.8 Consensus size: 5
17226956 AAATAGGTTA
*
17226966 AAAAT AAAAT AAAAT AAAAT AAAACCA AAAAT AAAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAA--T AAAAT -AAAAT AAAAT AAAAT
17227014 AAAA
1 AAAA
17227018 AGAAAACTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
5 33 0.79
6 5 0.12
7 4 0.10
ACGTcount: A:0.81, C:0.04, G:0.00, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:17227017 original size:49 final size:48
Alignment explanation
Indices: 17226922--17227023 Score: 125
Period size: 49 Copynumber: 2.1 Consensus size: 48
17226912 ACTCTTTTTT
***
17226922 TAAAAAAAAAAAAACAAAACCAAAAATAATAAAAAAATAGGTTAAAAA
1 TAAAAAAAAAAAAACAAAACCAAAAATAATAAAAAAATAAAATAAAAA
* *
17226970 TAAAATAAAATAAAATAAAACCAAAAATAA-AAATAAAATAAAATAAAAA
1 TAAAA-AAAAAAAAACAAAACCAAAAATAATAAA-AAAATAAAATAAAAA
*
17227019 GAAAA
1 TAAAA
17227024 CTTGAGATCT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
48 8 0.17
49 38 0.83
ACGTcount: A:0.78, C:0.05, G:0.03, T:0.14
Consensus pattern (48 bp):
TAAAAAAAAAAAAACAAAACCAAAAATAATAAAAAAATAAAATAAAAA
Found at i:17227018 original size:23 final size:22
Alignment explanation
Indices: 17226971--17227018 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
17226961 GGTTAAAAAT
*
17226971 AAAATAAAATAAAATAAAACCA
1 AAAATAAAATAAAATAAAACAA
*
17226993 AAAATAAAAATAAAATAAAATAA
1 AAAAT-AAAATAAAATAAAACAA
17227016 AAA
1 AAA
17227019 GAAAACTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.81, C:0.04, G:0.00, T:0.15
Consensus pattern (22 bp):
AAAATAAAATAAAATAAAACAA
Found at i:17227023 original size:28 final size:27
Alignment explanation
Indices: 17226965--17227023 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 27
17226955 AAAATAGGTT
*
17226965 AAAAATAAAATAAAATAAAATAAAACC
1 AAAAATAAAATAAAATAAAATAAAAAC
*
17226992 AAAAATAAAAATAAAATAAAATAAAAAG
1 AAAAAT-AAAATAAAATAAAATAAAAAC
17227020 AAAA
1 AAAA
17227024 CTTGAGATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 6 0.21
28 23 0.79
ACGTcount: A:0.81, C:0.03, G:0.02, T:0.14
Consensus pattern (27 bp):
AAAAATAAAATAAAATAAAATAAAAAC
Found at i:17227441 original size:21 final size:21
Alignment explanation
Indices: 17227415--17227454 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
17227405 ACTCAAAAAA
* *
17227415 CCTAGATTTTTTTTAATTTTC
1 CCTAGATTTCTTTAAATTTTC
17227436 CCTAGATTTCTTTAAATTT
1 CCTAGATTTCTTTAAATTT
17227455 CACCCAGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.15, G:0.05, T:0.57
Consensus pattern (21 bp):
CCTAGATTTCTTTAAATTTTC
Found at i:17227455 original size:20 final size:21
Alignment explanation
Indices: 17227415--17227464 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
17227405 ACTCAAAAAA
* *
17227415 CCTAGATTTTTTTTAATTTTC
1 CCTAGATTTTCTTTAAATTTC
17227436 CCTAGA-TTTCTTTAAATTTC
1 CCTAGATTTTCTTTAAATTTC
*
17227456 ACCCAGATT
1 -CCTAGATT
17227465 ACTCTTAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 12 0.50
21 11 0.46
22 1 0.04
ACGTcount: A:0.24, C:0.20, G:0.06, T:0.50
Consensus pattern (21 bp):
CCTAGATTTTCTTTAAATTTC
Found at i:17227874 original size:22 final size:21
Alignment explanation
Indices: 17227847--17227892 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
17227837 AGATTGAAAC
* * * *
17227847 AAAAAAGGAAAGCAGTAAAGG
1 AAAAAAAGAAAACAGAAAAAG
17227868 AAAAAAAGAAAACAGAAAAAG
1 AAAAAAAGAAAACAGAAAAAG
17227889 AAAA
1 AAAA
17227893 CAAAAATAAA
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:0.74, C:0.04, G:0.20, T:0.02
Consensus pattern (21 bp):
AAAAAAAGAAAACAGAAAAAG
Found at i:17227886 original size:13 final size:12
Alignment explanation
Indices: 17227869--17227898 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
17227859 CAGTAAAGGA
17227869 AAAAAAGAAAAC
1 AAAAAAGAAAAC
17227881 AGAAAAAGAAAAC
1 A-AAAAAGAAAAC
17227894 AAAAA
1 AAAAA
17227899 TAAAAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.83, C:0.07, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAC
Found at i:17240715 original size:20 final size:20
Alignment explanation
Indices: 17240690--17240738 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
17240680 AAATATTTTG
*
17240690 AATAAATTTGATTATTCATT
1 AATAAATTTAATTATTCATT
* *
17240710 AATAAAATTAATTATTTATT
1 AATAAATTTAATTATTCATT
*
17240730 AATATATTT
1 AATAAATTT
17240739 TATAAATATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (20 bp):
AATAAATTTAATTATTCATT
Found at i:17245715 original size:6 final size:6
Alignment explanation
Indices: 17245704--17245731 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
17245694 AACAGGCCTT
17245704 GGCGTC GGCGTC GGCGTC GGCGTC GGCG
1 GGCGTC GGCGTC GGCGTC GGCGTC GGCG
17245732 ATGGAATGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.54, T:0.14
Consensus pattern (6 bp):
GGCGTC
Found at i:17246193 original size:38 final size:38
Alignment explanation
Indices: 17246142--17246214 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
17246132 AACAAAACAG
17246142 TTCTTTTCTAAGGATTACT-AGCCTGGTGATGTGATTAC
1 TTCTTTTCTAAGGATTACTAAGCC-GGTGATGTGATTAC
*
17246180 TTCTTTTCTAAGGATTACTAATCCGGTGATGTGAT
1 TTCTTTTCTAAGGATTACTAAGCCGGTGATGTGAT
17246215 GGTAAGATGG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
38 30 0.91
39 3 0.09
ACGTcount: A:0.22, C:0.15, G:0.21, T:0.42
Consensus pattern (38 bp):
TTCTTTTCTAAGGATTACTAAGCCGGTGATGTGATTAC
Found at i:17246993 original size:11 final size:10
Alignment explanation
Indices: 17246953--17247010 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
17246943 ATAAACTTTC
17246953 AAAAAATTTCT
1 AAAAAATTT-T
*
17246964 AAAAGAATTAT
1 AAAA-AATTTT
* *
17246975 AAATATTTTT
1 AAAAAATTTT
17246985 AAAAAATTTT
1 AAAAAATTTT
*
17246995 -AAAAATTAT
1 AAAAAATTTT
17247004 AAAAAAT
1 AAAAAAT
17247011 AAAAAATTGA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
9 8 0.21
10 18 0.47
11 8 0.21
12 4 0.11
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (10 bp):
AAAAAATTTT
Found at i:17247028 original size:34 final size:35
Alignment explanation
Indices: 17246984--17247064 Score: 103
Period size: 34 Copynumber: 2.4 Consensus size: 35
17246974 TAAATATTTT
*
17246984 TAAAAAATTTTAAAAATTATA-AAAAATAAAAAAT
1 TAAAAAATTTTAAAAATTATATAAAAATAAAAAAA
* * * *
17247018 TGAAATATTTT-AAAATTCTATAAAATTAAAAAAA
1 TAAAAAATTTTAAAAATTATATAAAAATAAAAAAA
17247052 TAAAAAATTTTAA
1 TAAAAAATTTTAA
17247065 TAAAAATCCA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
33 8 0.21
34 29 0.76
35 1 0.03
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (35 bp):
TAAAAAATTTTAAAAATTATATAAAAATAAAAAAA
Found at i:17247253 original size:21 final size:22
Alignment explanation
Indices: 17247222--17247264 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
17247212 AAATTTGTAC
17247222 AAATTCTTCATTT-TTTAATTTA
1 AAATTCTTCATTTATTT-ATTTA
17247244 AAATT-TTCATTTATTTATTTA
1 AAATTCTTCATTTATTTATTTA
17247265 TTTTTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (22 bp):
AAATTCTTCATTTATTTATTTA
Found at i:17247613 original size:18 final size:18
Alignment explanation
Indices: 17247590--17247691 Score: 106
Period size: 18 Copynumber: 5.7 Consensus size: 18
17247580 AGATTTTTTG
17247590 AATTTTT-AAATTTTCAT
1 AATTTTTAAAATTTTCAT
*
17247607 AATTTTTTAAA-TTTCTAT
1 AATTTTTAAAATTTTC-AT
17247625 AATTTTTAAAAAATTTT-AT
1 AATTTTT--AAAATTTTCAT
*
17247644 -ATTTTTAAAATTTT-TT
1 AATTTTTAAAATTTTCAT
*
17247660 AAATTTTAAAATATTTCAT
1 AATTTTTAAAAT-TTTCAT
17247679 AATTTTTAAAATT
1 AATTTTTAAAATT
17247692 AAAAAAAAAT
Statistics
Matches: 72, Mismatches: 5, Indels: 15
0.78 0.05 0.16
Matches are distributed among these distances:
16 9 0.12
17 21 0.29
18 22 0.31
19 14 0.19
20 3 0.04
21 3 0.04
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
AATTTTTAAAATTTTCAT
Found at i:17247614 original size:35 final size:34
Alignment explanation
Indices: 17247539--17247691 Score: 112
Period size: 36 Copynumber: 4.3 Consensus size: 34
17247529 TTTTTTGGAA
* * ** * *
17247539 TTTTTATATTTTTTAACTTTTGGATTTTTATTAAAA
1 TTTTTAAATTTTTTAATTTTTAAATTTTCA-T-AAT
*
17247575 TTTTTAGATTTTTTGAATTTTTAAATTTTCATAAT
1 TTTTTAAATTTTTT-AATTTTTAAATTTTCATAAT
*
17247610 TTTTTAAATTTCTATAATTTTTAAAAAATTTT-AT-AT
1 TTTTTAAATTT-TTTAATTTTT---AAATTTTCATAAT
* *
17247646 TTTTAAAATTTTTTAAATTTTAAAATATTTCATAAT
1 TTTTTAAATTTTTT-AATTTTTAAAT-TTTCATAAT
*
17247682 TTTTAAAATT
1 TTTTTAAATT
17247692 AAAAAAAAAT
Statistics
Matches: 97, Mismatches: 11, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
33 4 0.04
34 3 0.03
35 23 0.24
36 46 0.47
37 14 0.14
38 7 0.07
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (34 bp):
TTTTTAAATTTTTTAATTTTTAAATTTTCATAAT
Found at i:17247655 original size:36 final size:36
Alignment explanation
Indices: 17247597--17247691 Score: 120
Period size: 36 Copynumber: 2.6 Consensus size: 36
17247587 TTGAATTTTT
* *
17247597 AAATTTTCATAATTTTTTAAATTTCTATAATTTTTAAA
1 AAATTTT-ATAATTTTTAAAATTT-TATAAATTTTAAA
*
17247635 AAATTTTAT-ATTTTTAAAATTTTTTAAATTTTAAA
1 AAATTTTATAATTTTTAAAATTTTATAAATTTTAAA
* *
17247670 ATATTTCATAATTTTTAAAATT
1 AAATTTTATAATTTTTAAAATT
17247692 AAAAAAAAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
35 18 0.35
36 24 0.47
37 2 0.04
38 7 0.14
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (36 bp):
AAATTTTATAATTTTTAAAATTTTATAAATTTTAAA
Found at i:17247658 original size:9 final size:9
Alignment explanation
Indices: 17247569--17247733 Score: 86
Period size: 9 Copynumber: 18.2 Consensus size: 9
17247559 TGGATTTTTA
17247569 TTAAAATTT
1 TTAAAATTT
*
17247578 TT-AGATTT
1 TTAAAATTT
**
17247586 TTTGAATTT
1 TTAAAATTT
17247595 TT-AAATTT
1 TTAAAATTT
* *
17247603 TCATAATTT
1 TTAAAATTT
*
17247612 TTTAAATTT
1 TTAAAATTT
* *
17247621 CTATAATTT
1 TTAAAATTT
*
17247630 TTAAAAAATT
1 TT-AAAATTT
*
17247640 TT-ATATTT
1 TTAAAATTT
17247648 TTAAAATTT
1 TTAAAATTT
*
17247657 TTTAAA-TT
1 TTAAAATTT
17247665 TTAAAATATT
1 TTAAAAT-TT
* *
17247675 TCATAATTT
1 TTAAAATTT
*
17247684 TTAAAATTA
1 TTAAAATTT
** **
17247693 AAAAAAAAT
1 TTAAAATTT
*
17247702 TAAAAATTTCT
1 TTAAAA-TT-T
17247713 TTAAAATTTT
1 TTAAAA-TTT
17247723 TTAAAATTT
1 TTAAAATTT
17247732 TT
1 TT
17247734 TGACATTGAT
Statistics
Matches: 114, Mismatches: 34, Indels: 16
0.70 0.21 0.10
Matches are distributed among these distances:
8 26 0.23
9 58 0.51
10 21 0.18
11 9 0.08
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (9 bp):
TTAAAATTT
Found at i:17247725 original size:10 final size:10
Alignment explanation
Indices: 17247704--17247734 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
17247694 AAAAAAATTA
17247704 AAAATTTCTTT
1 AAAATTT-TTT
17247715 AAAATTTTTT
1 AAAATTTTTT
17247725 AAAATTTTTT
1 AAAATTTTTT
17247735 GACATTGATG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 13 0.65
11 7 0.35
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (10 bp):
AAAATTTTTT
Found at i:17249398 original size:25 final size:24
Alignment explanation
Indices: 17249360--17249408 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
17249350 ATAAAAAACT
*
17249360 TAAAAAGATAAAAATAAAAGTAAAA
1 TAAAAAGATAAAAAAAAAAG-AAAA
17249385 TAAAAA-ATACAAAAAAAAAGAAAA
1 TAAAAAGATA-AAAAAAAAAGAAAA
17249409 CATACCTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.80, C:0.02, G:0.06, T:0.12
Consensus pattern (24 bp):
TAAAAAGATAAAAAAAAAAGAAAA
Found at i:17250960 original size:40 final size:40
Alignment explanation
Indices: 17250861--17251018 Score: 176
Period size: 40 Copynumber: 3.9 Consensus size: 40
17250851 ACCAGAGGCA
*
17250861 CAATAACTTTTAAAAATTTAAACGGCTCATCTAAGCAAAGGCT
1 CAATAACTTTTAAAAATTTAAACGGCTCCTCTAAGC-AA--CT
* *
17250904 TAATAACTTTTGAAAATTTTAAA-GGCTCCTCTAAGCAACT
1 CAATAACTTTT-AAAAATTTAAACGGCTCCTCTAAGCAACT
* * *
17250944 CAATAACTTTTAAAAATTTTAAA-AGCTTCTCTAAGCAATT
1 CAATAACTTTTAAAAA-TTTAAACGGCTCCTCTAAGCAACT
* * *
17250984 CGATAACTTTTAAAAATTTAAATGGCTCTTCTAAG
1 CAATAACTTTTAAAAATTTAAACGGCTCCTCTAAG
17251019 AAAATGCTCG
Statistics
Matches: 100, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
39 10 0.10
40 56 0.56
42 2 0.02
43 22 0.22
44 10 0.10
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.34
Consensus pattern (40 bp):
CAATAACTTTTAAAAATTTAAACGGCTCCTCTAAGCAACT
Found at i:17251168 original size:44 final size:43
Alignment explanation
Indices: 17251071--17251168 Score: 97
Period size: 44 Copynumber: 2.2 Consensus size: 43
17251061 GTAGAGGCTC
* * * * * *
17251071 AACAACTTTTTGAAATTTTAAATGGCTCCTCTAGGCATAGGTTT
1 AACAAC-TTTTGAAACTTTAAATGACTCCTCTAAGCAAAAGCTT
* * *
17251115 GACATCTTTTGAAAACTTTAAATGACTCCTCTAAGTAAAAGCTT
1 AACAACTTTTG-AAACTTTAAATGACTCCTCTAAGCAAAAGCTT
17251159 AACAACTTTT
1 AACAACTTTT
17251169 AAATATTTAA
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
43 5 0.12
44 37 0.88
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (43 bp):
AACAACTTTTGAAACTTTAAATGACTCCTCTAAGCAAAAGCTT
Found at i:17255376 original size:29 final size:30
Alignment explanation
Indices: 17255332--17255396 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 30
17255322 GGCCCAAAAA
* *
17255332 TTTTAATTATGATTTTGGTTTTAATTATGG
1 TTTTTATTATGATTTTGGTTTTAATTATAG
*
17255362 TTTTTATT-TGATTTTGGTTTTAATTTTAG
1 TTTTTATTATGATTTTGGTTTTAATTATAG
17255391 TTTTTA
1 TTTTTA
17255397 ATATTTTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 25 0.78
30 7 0.22
ACGTcount: A:0.20, C:0.00, G:0.14, T:0.66
Consensus pattern (30 bp):
TTTTTATTATGATTTTGGTTTTAATTATAG
Found at i:17256330 original size:11 final size:11
Alignment explanation
Indices: 17256314--17256410 Score: 62
Period size: 10 Copynumber: 9.2 Consensus size: 11
17256304 TAGGTTTTCT
17256314 TTTTTTTATTA
1 TTTTTTTATTA
17256325 -TTTTTTATT-
1 TTTTTTTATTA
** *
17256334 TGATTTGATT-
1 TTTTTTTATTA
* *
17256344 TTTGTTT-TGA
1 TTTTTTTATTA
17256354 TTTTTTTATTA
1 TTTTTTTATTA
*
17256365 TTTTATT-TTA
1 TTTTTTTATTA
*
17256375 TTTTTTTCTTA
1 TTTTTTTATTA
17256386 TTTTTTTCATT-
1 TTTTTTT-ATTA
*
17256397 TTTTGCTTATTA
1 TTTT-TTTATTA
17256409 TT
1 TT
17256411 CTAATTGAGT
Statistics
Matches: 65, Mismatches: 14, Indels: 13
0.71 0.15 0.14
Matches are distributed among these distances:
9 1 0.02
10 33 0.51
11 25 0.38
12 6 0.09
ACGTcount: A:0.14, C:0.03, G:0.05, T:0.77
Consensus pattern (11 bp):
TTTTTTTATTA
Found at i:17256330 original size:12 final size:12
Alignment explanation
Indices: 17256313--17256392 Score: 51
Period size: 11 Copynumber: 6.4 Consensus size: 12
17256303 GTAGGTTTTC
17256313 TTTTTTTTATTA
1 TTTTTTTTATTA
17256325 TTTTTTATTTGATTTGA
1 -TTTTT-TTT-A-TT-A
*
17256342 TTTTTGTTT-TGA
1 TTTTT-TTTATTA
17256354 -TTTTTTTATTA
1 TTTTTTTTATTA
17256365 TTTTATTTTATT-
1 TTTT-TTTTATTA
*
17256377 TTTTTCTTATT-
1 TTTTTTTTATTA
17256388 TTTTT
1 TTTTT
17256393 CATTTTTTGC
Statistics
Matches: 56, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
10 3 0.05
11 17 0.30
12 8 0.14
13 13 0.23
14 3 0.05
15 1 0.02
16 10 0.18
17 1 0.02
ACGTcount: A:0.14, C:0.01, G:0.05, T:0.80
Consensus pattern (12 bp):
TTTTTTTTATTA
Found at i:17256344 original size:17 final size:16
Alignment explanation
Indices: 17256322--17256380 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 16
17256312 CTTTTTTTTA
17256322 TTATTTTTTATTTGAT
1 TTATTTTTTATTTGAT
17256338 TTGATTTTTGT-TTTGAT
1 TT-ATTTTT-TATTTGAT
*
17256355 TT-TTTTATTATTTTATT
1 TTATTTT-TTATTTGA-T
17256372 TTATTTTTT
1 TTATTTTTT
17256381 TCTTATTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
15 5 0.14
16 7 0.19
17 19 0.53
18 5 0.14
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (16 bp):
TTATTTTTTATTTGAT
Found at i:17256370 original size:5 final size:5
Alignment explanation
Indices: 17256308--17256398 Score: 53
Period size: 5 Copynumber: 17.8 Consensus size: 5
17256298 TCAGTGTAGG
* * * *
17256308 TTTTC TTTT- TTTTA TTATT- TTTTA TTTGA TTTGA TTTTTG TTTTGA
1 TTTTA TTTTA TTTTA TT-TTA TTTTA TTTTA TTTTA -TTTTA TTTT-A
* * *
17256354 TTTTT TTATTA TTTTA TTTTA TTTTT TTCTTA TTTT- TTTCA TTTT
1 TTTTA TT-TTA TTTTA TTTTA TTTTA TT-TTA TTTTA TTTTA TTTT
17256399 TTGCTTATTA
Statistics
Matches: 68, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
4 9 0.13
5 42 0.62
6 17 0.25
ACGTcount: A:0.13, C:0.03, G:0.04, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:17256379 original size:21 final size:20
Alignment explanation
Indices: 17256313--17256400 Score: 81
Period size: 21 Copynumber: 4.2 Consensus size: 20
17256303 GTAGGTTTTC
17256313 TTTTTT-TTATTATTTTTTAT
1 TTTTTTATTATT-TTTTTTAT
* *
17256333 TTGATTTGATT-TTTGTTTTGAT
1 TT--TTTTATTATTT-TTTTTAT
17256355 TTTTTTATTATTTTATTTTAT
1 TTTTTTATTATTTT-TTTTAT
* *
17256376 TTTTTTCTTATTTTTTTCAT
1 TTTTTTATTATTTTTTTTAT
17256396 TTTTT
1 TTTTT
17256401 GCTTATTATT
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
20 19 0.34
21 22 0.39
22 13 0.23
23 2 0.04
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.80
Consensus pattern (20 bp):
TTTTTTATTATTTTTTTTAT
Found at i:17256381 original size:8 final size:8
Alignment explanation
Indices: 17256348--17256400 Score: 54
Period size: 8 Copynumber: 6.5 Consensus size: 8
17256338 TTGATTTTTG
*
17256348 TTTTGATT
1 TTTTTATT
17256356 TTTTTATT
1 TTTTTATT
*
17256364 ATTTTATT
1 TTTTTATT
17256372 TTATTT-TT
1 TT-TTTATT
*
17256380 TTCTTATT
1 TTTTTATT
17256388 TTTTTCATT
1 TTTTT-ATT
17256397 TTTT
1 TTTT
17256401 GCTTATTATT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
7 2 0.05
8 25 0.68
9 10 0.27
ACGTcount: A:0.13, C:0.04, G:0.02, T:0.81
Consensus pattern (8 bp):
TTTTTATT
Found at i:17256405 original size:20 final size:20
Alignment explanation
Indices: 17256348--17256407 Score: 75
Period size: 21 Copynumber: 3.0 Consensus size: 20
17256338 TTGATTTTTG
* *
17256348 TTTTGATTTTTTTATTATTT
1 TTTTCATTTTTTTCTTATTT
*
17256368 TATTTTATTTTTTTCTTATTT
1 T-TTTCATTTTTTTCTTATTT
*
17256389 TTTTCATTTTTTGCTTATT
1 TTTTCATTTTTTTCTTATT
17256408 ATTCTAATTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 17 0.49
21 18 0.51
ACGTcount: A:0.13, C:0.05, G:0.03, T:0.78
Consensus pattern (20 bp):
TTTTCATTTTTTTCTTATTT
Found at i:17256538 original size:21 final size:21
Alignment explanation
Indices: 17256510--17256576 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
17256500 GGTTATTAAT
* *
17256510 TATT-ATTGCATGGTATTTTA
1 TATTAATTGCATGATAGTTTA
* *
17256530 TCTTAATTGTATGATAGTTTA
1 TATTAATTGCATGATAGTTTA
* *
17256551 TATTTATTGCATAATA-TATTA
1 TATTAATTGCATGATAGT-TTA
17256572 TATTA
1 TATTA
17256577 TTATTAAATG
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
20 4 0.11
21 32 0.89
ACGTcount: A:0.31, C:0.04, G:0.10, T:0.54
Consensus pattern (21 bp):
TATTAATTGCATGATAGTTTA
Found at i:17256590 original size:23 final size:23
Alignment explanation
Indices: 17256564--17256624 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
17256554 TTATTGCATA
17256564 ATATATTATATTATTATTAAATG
1 ATATATTATATTATTATTAAATG
**
17256587 ATATATTATATTATTATTGCATG
1 ATATATTATATTATTATTAAATG
*
17256610 ACATATTATATTATT
1 ATATATTATATTATT
17256625 CAATGATACT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.52
Consensus pattern (23 bp):
ATATATTATATTATTATTAAATG
Found at i:17256600 original size:20 final size:20
Alignment explanation
Indices: 17256575--17256637 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 20
17256565 TATATTATAT
17256575 TATTATTAAATGATATATTA
1 TATTATTAAATGATATATTA
* *
17256595 TATTATTATTGCATGACATATTA
1 TATTATTA---AATGATATATTA
*
17256618 TATTATTCAATGATACTATT
1 TATTATTAAATGATA-TATT
17256638 TTGCATGACA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
20 13 0.38
21 4 0.12
23 17 0.50
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.49
Consensus pattern (20 bp):
TATTATTAAATGATATATTA
Found at i:17256958 original size:38 final size:37
Alignment explanation
Indices: 17256883--17256958 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
17256873 ATAAAATTTC
*
17256883 AATCTTACCAATAGATTGAAGATAATTCTTGACATAA
1 AATCTTACCAATAGATTGAAGATAATTCTTGAAATAA
* * *
17256920 AATCTTATCAATATATTGAAAGATATTTC-TGAGAATAA
1 AATCTTACCAATAGATTG-AAGATAATTCTTGA-AATAA
17256958 A
1 A
17256959 TTATTTTTAC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
37 19 0.58
38 14 0.42
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.34
Consensus pattern (37 bp):
AATCTTACCAATAGATTGAAGATAATTCTTGAAATAA
Found at i:17257997 original size:21 final size:21
Alignment explanation
Indices: 17257971--17258011 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
17257961 GTTTGCATTA
17257971 TTTTTTGTATATATTATGTTG
1 TTTTTTGTATATATTATGTTG
17257992 TTTTTTGTATATATTATGTT
1 TTTTTTGTATATATTATGTT
17258012 TACCAACCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (21 bp):
TTTTTTGTATATATTATGTTG
Found at i:17261653 original size:19 final size:20
Alignment explanation
Indices: 17261611--17261654 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
17261601 TAGGGCATGT
*
17261611 ATTTGCATCATGTATAGAAC
1 ATTTGAATCATGTATAGAAC
17261631 ATTTGAATCATAGTAT-G-AC
1 ATTTGAATCAT-GTATAGAAC
17261650 ATTTG
1 ATTTG
17261655 CATTATTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 7 0.32
20 11 0.50
21 4 0.18
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (20 bp):
ATTTGAATCATGTATAGAAC
Found at i:17262024 original size:24 final size:22
Alignment explanation
Indices: 17261994--17262180 Score: 90
Period size: 24 Copynumber: 8.1 Consensus size: 22
17261984 ATTGGATGAT
*
17261994 AATCTTTAAAACTTTTCAAATGTG
1 AATCTTTAAAA-TTTT-AGATGTG
* *
17262018 AATCTTTGAAATTTTAGATATG
1 AATCTTTAAAATTTTAGATGTG
* *
17262040 AAATCTTAAAAATTTTTTGGATGAT-
1 -AATCTTTAAAA--TTTTAGATG-TG
* *
17262065 AA-CTTTTGAAATTTTGGATGTG
1 AATC-TTTAAAATTTTAGATGTG
* *
17262087 AATCTCTAAAATTTTTCAAATGTG
1 AATCTTTAAAA-TTTT-AGATGTG
* * *
17262111 AATATTTGAAATTTTGGATGTG
1 AATCTTTAAAATTTTAGATGTG
* * * *
17262133 AAACTCTAAAATTTTTCAAATGAG
1 AATCTTTAAAA-TTTT-AGATGTG
* * *
17262157 AATCTTTGAAATTTTGGTTGTG
1 AATCTTTAAAATTTTAGATGTG
17262179 AA
1 AA
17262181 ATATTAATGT
Statistics
Matches: 120, Mismatches: 32, Indels: 24
0.68 0.18 0.14
Matches are distributed among these distances:
21 1 0.01
22 38 0.32
23 31 0.26
24 42 0.35
25 7 0.06
26 1 0.01
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (22 bp):
AATCTTTAAAATTTTAGATGTG
Found at i:17262098 original size:22 final size:22
Alignment explanation
Indices: 17262073--17262147 Score: 78
Period size: 22 Copynumber: 3.3 Consensus size: 22
17262063 ATAACTTTTG
17262073 AAATTTTGGATGTGAATCTCTA
1 AAATTTTGGATGTGAATCTCTA
** * * *
17262095 AAATTTTTCAAATGTGAATATTTG
1 AAA-TTTT-GGATGTGAATCTCTA
*
17262119 AAATTTTGGATGTGAAACTCTA
1 AAATTTTGGATGTGAATCTCTA
17262141 AAATTTT
1 AAATTTT
17262148 TCAAATGAGA
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
22 19 0.47
23 8 0.20
24 13 0.32
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.43
Consensus pattern (22 bp):
AAATTTTGGATGTGAATCTCTA
Found at i:17262119 original size:46 final size:45
Alignment explanation
Indices: 17261985--17262272 Score: 253
Period size: 46 Copynumber: 6.3 Consensus size: 45
17261975 TCTTAAAACA
* *
17261985 TTGGATGAT-AATCTTTAAAACTTTTCAAATGTGAATCTTTGAAATT
1 TTGGATG-TGAATCTCTAAAATTTTTCAAATGTGAAT-TTTGAAATT
* * ***
17262031 TTAGATATGAAATCT-TAAAAATTTTTTGGATGAT-AACTTTTGAAATT
1 TTGGATGTG-AATCTCT-AAAATTTTTCAAATG-TGAA-TTTTGAAATT
17262078 TTGGATGTGAATCTCTAAAATTTTTCAAATGTGAATATTTGAAATT
1 TTGGATGTGAATCTCTAAAATTTTTCAAATGTGAAT-TTTGAAATT
* *
17262124 TTGGATGTGAAACTCTAAAATTTTTCAAATGAGAATCTTTGAAATT
1 TTGGATGTGAATCTCTAAAATTTTTCAAATGTGAAT-TTTGAAATT
* * ** * * **
17262170 TTGGTTGTGAAATAT-TAATGTTTTT-TAATATGAATTTTTTAATT
1 TTGGATGTG-AATCTCTAAAATTTTTCAAATGTGAATTTTGAAATT
* * * * *
17262214 TTGAATGTGAATCTCCAAAATTTTTTAAATATGAATTTTTGAAAAT
1 TTGGATGTGAATCTCTAAAATTTTTCAAATGTGAA-TTTTGAAATT
17262260 TTGGATGTGAATC
1 TTGGATGTGAATC
17262273 CTTAAGTTTT
Statistics
Matches: 195, Mismatches: 35, Indels: 24
0.77 0.14 0.09
Matches are distributed among these distances:
43 4 0.02
44 21 0.11
45 18 0.09
46 112 0.57
47 38 0.19
48 2 0.01
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.45
Consensus pattern (45 bp):
TTGGATGTGAATCTCTAAAATTTTTCAAATGTGAATTTTGAAATT
Found at i:17262268 original size:136 final size:139
Alignment explanation
Indices: 17262000--17262270 Score: 352
Period size: 136 Copynumber: 2.0 Consensus size: 139
17261990 TGATAATCTT
* * *
17262000 TAAAACTTTTCAAATGTGAATCTTTGAAATTTTAGATATGAAATCTTAAAAATTTTTTGGATGAT
1 TAAAACTTTTCAAATGAGAATCTTTGAAATTTTAGATATGAAATATTAAAAATTTTTTGAATGAT
* * * *
17262065 AACTTTTGAAATTTTGGATGTGAATCTCTAAAATTTTTCAAATGTGAATATTTGAAATTTTGGAT
66 AACTTTTGAAATTTTGAATGTGAATCTCCAAAATTTTTCAAATATGAATATTTGAAAATTTGGAT
17262130 GTGAAACTC
131 GTGAAACTC
* * * * **
17262139 TAAAATTTTTCAAATGAGAATCTTTGAAATTTTGGTTGTGAAATATT-AATGTTTTTT-AAT-AT
1 TAAAACTTTTCAAATGAGAATCTTTGAAATTTTAGATATGAAATATTAAAAATTTTTTGAATGAT
** * *
17262201 GAA-TTTTTTAATTTTGAATGTGAATCTCCAAAATTTTTTAAATATGAATTTTTGAAAATTTGGA
66 -AACTTTTGAAATTTTGAATGTGAATCTCCAAAATTTTTCAAATATGAATATTTGAAAATTTGGA
17262265 TGTGAA
130 TGTGAA
17262271 TCCTTAAGTT
Statistics
Matches: 114, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
136 61 0.54
137 4 0.04
138 8 0.07
139 41 0.36
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.45
Consensus pattern (139 bp):
TAAAACTTTTCAAATGAGAATCTTTGAAATTTTAGATATGAAATATTAAAAATTTTTTGAATGAT
AACTTTTGAAATTTTGAATGTGAATCTCCAAAATTTTTCAAATATGAATATTTGAAAATTTGGAT
GTGAAACTC
Found at i:17262306 original size:90 final size:87
Alignment explanation
Indices: 17262068--17262344 Score: 236
Period size: 90 Copynumber: 3.1 Consensus size: 87
17262058 GGATGATAAC
* * *
17262068 TTTTGAAATTTTGGATGTGAATCTCTAAAATTTTTCAAATGTGAATATTTGAAATTTTGGATGTG
1 TTTTGAAATTTTGGATGTGAATC-CTTAAGTTTTTCAAA-ATGAATATTT--AATTTT-GATGTG
* *
17262133 AAACTCTAAAATTTTTCAAATGAGAAT
61 AATCTCCAAAATTTTTCAAATGAGAAT
* * * * * *
17262160 CTTTGAAATTTTGGTTGTGAAAT-ATTAATGTTTTTTAATATGAATTTTTTAATTTTGAATGTGA
1 TTTTGAAATTTTGGATGTG-AATCCTTAA-GTTTTTCAAAATGAA-TATTTAATTTTG-ATGTGA
*
17262224 ATCTCCAAAATTTTTTAAAT-ATGAAT
62 ATCTCCAAAATTTTTCAAATGA-GAAT
* * * *
17262250 TTTTGAAAATTTGGATGTGAATCCTTAAGTTTTTGAAAAAGAATATTTAACTTTTTGGTGTGAAT
1 TTTTGAAATTTTGGATGTGAATCCTTAAGTTTTTCAAAATGAATATTTAA--TTTTGATGTGAAT
** * *
17262315 CT-CTGAATTTTTGAAATGAAAAT
64 CTCCAAAATTTTTCAAATGAGAAT
*
17262338 CTTTGAA
1 TTTTGAA
17262345 TTCTAGAGGT
Statistics
Matches: 150, Mismatches: 26, Indels: 22
0.76 0.13 0.11
Matches are distributed among these distances:
88 27 0.18
89 27 0.18
90 58 0.39
91 7 0.05
92 28 0.19
93 3 0.02
ACGTcount: A:0.34, C:0.06, G:0.15, T:0.45
Consensus pattern (87 bp):
TTTTGAAATTTTGGATGTGAATCCTTAAGTTTTTCAAAATGAATATTTAATTTTGATGTGAATCT
CCAAAATTTTTCAAATGAGAAT
Found at i:17262573 original size:17 final size:17
Alignment explanation
Indices: 17262551--17262622 Score: 83
Period size: 17 Copynumber: 4.2 Consensus size: 17
17262541 ATTAATGAAG
17262551 TTCTTGCAAACCTTAAA
1 TTCTTGCAAACCTTAAA
* *
17262568 TTCTTG-AGAGCCTGAAA
1 TTCTTGCA-AACCTTAAA
*
17262585 TTCTTGCAAGCCTTAAA
1 TTCTTGCAAACCTTAAA
* *
17262602 TTCTTGCGAACCTAAAA
1 TTCTTGCAAACCTTAAA
17262619 TTCT
1 TTCT
17262623 AAAGAACCTG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
16 1 0.02
17 45 0.96
18 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (17 bp):
TTCTTGCAAACCTTAAA
Found at i:17262599 original size:34 final size:34
Alignment explanation
Indices: 17262546--17262622 Score: 109
Period size: 34 Copynumber: 2.3 Consensus size: 34
17262536 AAGTTATTAA
* *
17262546 TGAAGTTCTTGCAAACCTTAAATTCTTGAGAGCC
1 TGAAATTCTTGCAAACCTTAAATTCTTGAGAACC
* *
17262580 TGAAATTCTTGCAAGCCTTAAATTCTTGCGAACC
1 TGAAATTCTTGCAAACCTTAAATTCTTGAGAACC
*
17262614 TAAAATTCT
1 TGAAATTCT
17262623 AAAGAACCTG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (34 bp):
TGAAATTCTTGCAAACCTTAAATTCTTGAGAACC
Found at i:17262657 original size:17 final size:17
Alignment explanation
Indices: 17262609--17262658 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
17262599 AAATTCTTGC
* *
17262609 GAACCTAAAATTCTAAA
1 GAACCTAAAGTTCTTAA
*
17262626 GAACCTGAAAG-TCTTAT
1 GAACCT-AAAGTTCTTAA
17262643 GAACCTAAAGTTCTTA
1 GAACCTAAAGTTCTTA
17262659 CAAACTGGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 4 0.14
17 21 0.75
18 3 0.11
ACGTcount: A:0.42, C:0.18, G:0.12, T:0.28
Consensus pattern (17 bp):
GAACCTAAAGTTCTTAA
Found at i:17262688 original size:17 final size:17
Alignment explanation
Indices: 17262660--17262707 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
17262650 AAGTTCTTAC
* **
17262660 AAACTGGAAATTTTTGC
1 AAACTTGAAATTTTTAA
* *
17262677 AAACTTGCAATTCTTAA
1 AAACTTGAAATTTTTAA
17262694 AAACTTGAAATTTT
1 AAACTTGAAATTTT
17262708 AGAGAACTTC
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (17 bp):
AAACTTGAAATTTTTAA
Found at i:17262792 original size:50 final size:50
Alignment explanation
Indices: 17262732--17262839 Score: 126
Period size: 50 Copynumber: 2.1 Consensus size: 50
17262722 TTTTGCGAGC
* * * * * * *
17262732 TTGAAATTCTTGCGAATTTAAAGTTCTTTCAAACCTTAAATTCTTGCAAA
1 TTGAAATTCTTACGAATATAAAATTCTTGCAAAACTTAAATCCTTACAAA
* *
17262782 TTGAAGTTCTTATGAATATAAAATTCTTGCAAAACTTAAATCCTTACAAA
1 TTGAAATTCTTACGAATATAAAATTCTTGCAAAACTTAAATCCTTACAAA
17262832 TCTGAAAT
1 T-TGAAAT
17262840 CTTTTGAATC
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
50 42 0.89
51 5 0.11
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (50 bp):
TTGAAATTCTTACGAATATAAAATTCTTGCAAAACTTAAATCCTTACAAA
Found at i:17263139 original size:18 final size:18
Alignment explanation
Indices: 17263116--17263233 Score: 69
Period size: 18 Copynumber: 6.5 Consensus size: 18
17263106 AGCCTGTGAA
17263116 AATCTTGAAATTTTTACG
1 AATCTTGAAATTTTTACG
* ** * *
17263134 AATCTTAAAACCTCTATG
1 AATCTTGAAATTTTTACG
17263152 AATCTTGAAATTTTTTAC-
1 AATCTTGAAA-TTTTTACG
*
17263170 AATCGTG-AATTATTTACG
1 AATCTTGAAATT-TTTACG
* **
17263188 AACTTTTGAAATCGTTACG
1 AA-TCTTGAAATTTTTACG
* * * **
17263207 ACTCTTGGAATTCTTGTG
1 AATCTTGAAATTTTTACG
17263225 AATCTTGAA
1 AATCTTGAA
17263234 TCTTTGTGAA
Statistics
Matches: 71, Mismatches: 24, Indels: 10
0.68 0.23 0.10
Matches are distributed among these distances:
16 2 0.03
17 7 0.10
18 47 0.66
19 12 0.17
20 3 0.04
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (18 bp):
AATCTTGAAATTTTTACG
Found at i:17263557 original size:6 final size:6
Alignment explanation
Indices: 17263546--17263613 Score: 68
Period size: 6 Copynumber: 11.2 Consensus size: 6
17263536 ATTTTTATTC
* *
17263546 TAGTTT TAGTTT TAATTT TAGGTTT TA-TTT TA-TTT TAGTTT TAATTT
1 TAGTTT TAGTTT TAGTTT TA-GTTT TAGTTT TAGTTT TAGTTT TAGTTT
*
17263593 TAGGTTT CTAATTT TAGTTT T
1 TA-GTTT -TAGTTT TAGTTT T
17263614 TATTATTTTA
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
5 10 0.19
6 29 0.56
7 11 0.21
8 2 0.04
ACGTcount: A:0.21, C:0.01, G:0.12, T:0.66
Consensus pattern (6 bp):
TAGTTT
Found at i:17263584 original size:29 final size:30
Alignment explanation
Indices: 17263538--17263613 Score: 118
Period size: 29 Copynumber: 2.5 Consensus size: 30
17263528 AGCCTAAAAT
*
17263538 TTTTATTCTAGTTTTAGTTTTAATTTTAGG
1 TTTTATTTTAGTTTTAGTTTTAATTTTAGG
17263568 TTTTATTTTA-TTTTAGTTTTAATTTTAGG
1 TTTTATTTTAGTTTTAGTTTTAATTTTAGG
17263597 TTTCTAATTTTAGTTTT
1 TTT-T-ATTTTAGTTTT
17263614 TATTATTTTA
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
29 22 0.52
30 10 0.24
31 6 0.14
32 4 0.10
ACGTcount: A:0.20, C:0.03, G:0.11, T:0.67
Consensus pattern (30 bp):
TTTTATTTTAGTTTTAGTTTTAATTTTAGG
Found at i:17263621 original size:29 final size:29
Alignment explanation
Indices: 17263543--17263623 Score: 75
Period size: 29 Copynumber: 2.9 Consensus size: 29
17263533 AAAATTTTTA
*
17263543 TTCTAGTTTTAG-TTTTA--ATTTTAGGT
1 TTCTAATTTTAGTTTTTATTATTTTAGGT
*
17263569 TT-T-ATTTTA-TTTTAGTTTTAATTTTAGGT
1 TTCTAATTTTAGTTTT--TATT-ATTTTAGGT
17263598 TTCTAATTTTAGTTTTTATTATTTTA
1 TTCTAATTTTAGTTTTTATTATTTTA
17263624 TTTTTAGTCA
Statistics
Matches: 43, Mismatches: 3, Indels: 15
0.70 0.05 0.25
Matches are distributed among these distances:
24 8 0.19
25 1 0.02
26 3 0.07
29 17 0.40
30 4 0.09
31 6 0.14
32 4 0.09
ACGTcount: A:0.21, C:0.02, G:0.10, T:0.67
Consensus pattern (29 bp):
TTCTAATTTTAGTTTTTATTATTTTAGGT
Found at i:17263639 original size:41 final size:42
Alignment explanation
Indices: 17263554--17263640 Score: 97
Period size: 41 Copynumber: 2.1 Consensus size: 42
17263544 TCTAGTTTTA
* ***
17263554 GTTTTAATTTTAGGTTTTATTTTATTTTAGTTTTAATTTTAG
1 GTTTTAATTTTAGGTTTTATATTATTTTAGTTTTAATCAAAG
* *
17263596 GTTTCTAATTTTA-GTTTT-TATTATTTTATTTTTAGTCAAAG
1 GTTT-TAATTTTAGGTTTTATATTATTTTAGTTTTAATCAAAG
17263637 GTTT
1 GTTT
17263641 AAAAAAAAGT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
41 21 0.55
42 9 0.24
43 8 0.21
ACGTcount: A:0.22, C:0.02, G:0.11, T:0.64
Consensus pattern (42 bp):
GTTTTAATTTTAGGTTTTATATTATTTTAGTTTTAATCAAAG
Found at i:17264561 original size:6 final size:6
Alignment explanation
Indices: 17264546--17264579 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
17264536 ATAGTGCAAG
* *
17264546 TTTTCT TTTTCC TTTTCC TTTTTC TTTTCC TTTT
1 TTTTCC TTTTCC TTTTCC TTTTCC TTTTCC TTTT
17264580 GATTTGATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTTCC
Found at i:17264618 original size:17 final size:17
Alignment explanation
Indices: 17264592--17264646 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
17264582 TTTGATTTGA
*
17264592 TTTGTTTTTTTTTTTTT
1 TTTGTATTTTTTTTTTT
*
17264609 TTTGTATTTTTTGTTTT
1 TTTGTATTTTTTTTTTT
* *
17264626 ATTATATTTCTTTTTTTT
1 TTTGTATTT-TTTTTTTT
17264644 TTT
1 TTT
17264647 TCATTTTTCA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
17 22 0.71
18 9 0.29
ACGTcount: A:0.07, C:0.02, G:0.05, T:0.85
Consensus pattern (17 bp):
TTTGTATTTTTTTTTTT
Found at i:17264835 original size:23 final size:23
Alignment explanation
Indices: 17264808--17264878 Score: 106
Period size: 23 Copynumber: 3.1 Consensus size: 23
17264798 TAGTTTATAT
*
17264808 TTATTGCATGATATATTATACTC
1 TTATTGCATGATATATTATACTA
*
17264831 TTATTGCATGATATATTATATTA
1 TTATTGCATGATATATTATACTA
* *
17264854 TTATTGCATGACATATTATATTA
1 TTATTGCATGATATATTATACTA
17264877 TT
1 TT
17264879 CAATGATACT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.51
Consensus pattern (23 bp):
TTATTGCATGATATATTATACTA
Found at i:17265029 original size:13 final size:13
Alignment explanation
Indices: 17265011--17265049 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
17265001 ATTAGAAGAA
17265011 TTAAAAAATTTTC
1 TTAAAAAATTTTC
*
17265024 TTAAAAAATATTTT
1 TTAAAAAAT-TTTC
*
17265038 TTTAAAAATTTT
1 TTAAAAAATTTT
17265050 AATAACAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (13 bp):
TTAAAAAATTTTC
Found at i:17273885 original size:22 final size:22
Alignment explanation
Indices: 17273860--17273909 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
17273850 AGTTCCTTTC
*
17273860 CTTATTTT-TTTACATTTTTATT
1 CTTATTTTGGTTA-ATTTTTATT
17273882 CTTATTTTGGTTAATTTTTATT
1 CTTATTTTGGTTAATTTTTATT
*
17273904 TTTATT
1 CTTATT
17273910 AATAATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 22 0.88
23 3 0.12
ACGTcount: A:0.18, C:0.06, G:0.04, T:0.72
Consensus pattern (22 bp):
CTTATTTTGGTTAATTTTTATT
Found at i:17274265 original size:3 final size:3
Alignment explanation
Indices: 17274257--17274294 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
17274247 AACATACATA
17274257 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
17274295 ACTTAAAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:17274900 original size:9 final size:9
Alignment explanation
Indices: 17274886--17274914 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
17274876 TTTTGCTCTC
17274886 TTTTTTATT
1 TTTTTTATT
17274895 TTTTTTATT
1 TTTTTTATT
17274904 TTTTTTATT
1 TTTTTTATT
17274913 TT
1 TT
17274915 CGTTGTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTTATT
Found at i:17275390 original size:20 final size:22
Alignment explanation
Indices: 17275365--17275412 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
17275355 CATTGGCCCC
17275365 TTAATTTTTA-CTT-TTTTTTA
1 TTAATTTTTATCTTATTTTTTA
*
17275385 TTAATTTTTATTTTATTTTTTA
1 TTAATTTTTATCTTATTTTTTA
17275407 TTAATT
1 TTAATT
17275413 AGTTTATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 10 0.40
21 2 0.08
22 13 0.52
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (22 bp):
TTAATTTTTATCTTATTTTTTA
Found at i:17276967 original size:2 final size:2
Alignment explanation
Indices: 17276960--17276989 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
17276950 TCTATCTTTG
17276960 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17276990 AAAATTTCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17278219 original size:16 final size:17
Alignment explanation
Indices: 17278198--17278230 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
17278188 CTCTTTCTCT
17278198 CTTTTT-TTTTTTTTTC
1 CTTTTTATTTTTTTTTC
17278214 CTTTTTATTTTTTTTTC
1 CTTTTTATTTTTTTTTC
17278231 TCTCAAAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (17 bp):
CTTTTTATTTTTTTTTC
Found at i:17278358 original size:16 final size:17
Alignment explanation
Indices: 17278342--17278394 Score: 55
Period size: 16 Copynumber: 3.5 Consensus size: 17
17278332 AATTTTAATT
17278342 TAATTATATTATTATT-
1 TAATTATATTATTATTA
17278358 T--TTA-ATT-TTATTA
1 TAATTATATTATTATTA
*
17278371 TAATT-TAATATTATTA
1 TAATTATATTATTATTA
17278387 TAATTATA
1 TAATTATA
17278395 AAAATAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 11
0.71 0.02 0.26
Matches are distributed among these distances:
12 5 0.17
13 4 0.13
14 3 0.10
15 4 0.13
16 12 0.40
17 2 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TAATTATATTATTATTA
Found at i:17278394 original size:6 final size:6
Alignment explanation
Indices: 17278332--17278424 Score: 52
Period size: 6 Copynumber: 16.0 Consensus size: 6
17278322 AATTTAATCA
* * * *
17278332 AATTTT AATT-T AATTAT -ATTATT ATTTTT AATT-T TATTAT AATT-T
1 AATTAT AATTAT AATTAT AATTA-T AATTAT AATTAT AATTAT AATTAT
* ** * *
17278377 AA-TAT TATTAT AATTAT AAAAAT AAATTAT AAATAT ATTTAT AATTAT
1 AATTAT AATTAT AATTAT AATTAT -AATTAT AATTAT AATTAT AATTAT
17278425 TTATTATTTA
Statistics
Matches: 65, Mismatches: 15, Indels: 14
0.69 0.16 0.15
Matches are distributed among these distances:
4 1 0.02
5 18 0.28
6 40 0.62
7 6 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (6 bp):
AATTAT
Found at i:17278451 original size:19 final size:18
Alignment explanation
Indices: 17278410--17278475 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
17278400 AAATTATAAA
*
17278410 TATATTTATAAT--TATT
1 TATATTTATATTCATATT
*
17278426 TATTATTTATCTTCATATTT
1 TA-TATTTATATTCATA-TT
*
17278446 TATATTTATATTTATATT
1 TATATTTATATTCATATT
*
17278464 TATATTTCTATT
1 TATATTTATATT
17278476 TATTCTATTA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
16 2 0.05
17 8 0.20
18 13 0.32
19 14 0.34
20 4 0.10
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (18 bp):
TATATTTATATTCATATT
Found at i:17278455 original size:6 final size:6
Alignment explanation
Indices: 17278410--17278478 Score: 70
Period size: 6 Copynumber: 11.5 Consensus size: 6
17278400 AAATTATAAA
* * *
17278410 TATATT TATA-A T-TATT TATTATT TATCTT CATATTT TATATT TATATT
1 TATATT TATATT TATATT TA-TATT TATATT TATA-TT TATATT TATATT
*
17278458 TATATT TATATT TCTATT TAT
1 TATATT TATATT TATATT TAT
17278479 TCTATTATAT
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
4 2 0.04
5 2 0.04
6 36 0.71
7 11 0.22
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65
Consensus pattern (6 bp):
TATATT
Found at i:17278537 original size:11 final size:12
Alignment explanation
Indices: 17278521--17278576 Score: 53
Period size: 11 Copynumber: 4.6 Consensus size: 12
17278511 ATTTTATTTC
17278521 ATATTA-TATAT
1 ATATTAGTATAT
*
17278532 ATATTAGCATA-
1 ATATTAGTATAT
17278543 ATATTAGTATAAT
1 ATATTAGTAT-AT
*
17278556 ATATTAGGTGTAAT
1 ATATTA-GTAT-AT
17278570 ATATTAG
1 ATATTAG
17278577 GATAATATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
11 15 0.39
12 4 0.11
13 7 0.18
14 12 0.32
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.45
Consensus pattern (12 bp):
ATATTAGTATAT
Done.