Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168159.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_4, 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: 33012953
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 65000 characters in sequence are not A, C, G, or T
File 63 of 160
Found at i:13134135 original size:21 final size:20
Alignment explanation
Indices: 13134097--13134135 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
13134087 TAGCTCAGGT
*
13134097 TTAAATAATTTAAAAATTTG
1 TTAAATAACTTAAAAATTTG
*
13134117 TTAAATTAACTTAAGAATT
1 TTAAA-TAACTTAAAAATT
13134136 GAGATTGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.44
Consensus pattern (20 bp):
TTAAATAACTTAAAAATTTG
Found at i:13136530 original size:143 final size:143
Alignment explanation
Indices: 13136272--13136562 Score: 582
Period size: 143 Copynumber: 2.0 Consensus size: 143
13136262 CTAATCTTGT
13136272 TAGTACTTTACTTACAAAATATATTGGCCTTTATTTTCTTTCTTCTTTGTAGACACCTATTTATG
1 TAGTACTTTACTTACAAAATATATTGGCCTTTATTTTCTTTCTTCTTTGTAGACACCTATTTATG
13136337 TCCAGGACCAATCAAGATCAATTTTATTTGTTATTAGTATTTTTATAGTATAATATGTTATAATA
66 TCCAGGACCAATCAAGATCAATTTTATTTGTTATTAGTATTTTTATAGTATAATATGTTATAATA
13136402 TAATATTATAGTA
131 TAATATTATAGTA
13136415 TAGTACTTTACTTACAAAATATATTGGCCTTTATTTTCTTTCTTCTTTGTAGACACCTATTTATG
1 TAGTACTTTACTTACAAAATATATTGGCCTTTATTTTCTTTCTTCTTTGTAGACACCTATTTATG
13136480 TCCAGGACCAATCAAGATCAATTTTATTTGTTATTAGTATTTTTATAGTATAATATGTTATAATA
66 TCCAGGACCAATCAAGATCAATTTTATTTGTTATTAGTATTTTTATAGTATAATATGTTATAATA
13136545 TAATATTATAGTA
131 TAATATTATAGTA
13136558 TAGTA
1 TAGTA
13136563 TTATTATTAG
Statistics
Matches: 148, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
143 148 1.00
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.47
Consensus pattern (143 bp):
TAGTACTTTACTTACAAAATATATTGGCCTTTATTTTCTTTCTTCTTTGTAGACACCTATTTATG
TCCAGGACCAATCAAGATCAATTTTATTTGTTATTAGTATTTTTATAGTATAATATGTTATAATA
TAATATTATAGTA
Found at i:13136569 original size:3 final size:3
Alignment explanation
Indices: 13136561--13136701 Score: 71
Period size: 3 Copynumber: 47.7 Consensus size: 3
13136551 TATAGTATAG
* * * *
13136561 TAT TAT TAT TAG TAT TAT TA- TAGT AAT TAT ATAG TA- CAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT -TAT TAT TAT TAT TAT
* * * *
13136605 TAT TAA TAT TAT TCA- TAT TAT TAT CAT TA- TAC TA- CATT TAT TA-
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
* * * * *
13136648 TAC TAT AAT ATAT CAA TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
13136694 TAT TAT TA
1 TAT TAT TA
13136702 ATTTTGTCTT
Statistics
Matches: 105, Mismatches: 21, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
2 11 0.10
3 87 0.83
4 7 0.07
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (3 bp):
TAT
Found at i:13136579 original size:28 final size:28
Alignment explanation
Indices: 13136510--13136585 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 28
13136500 ATTTTATTTG
*
13136510 TTATTAGTATTTTTATAGTATAATATGT
1 TTATTAGTATTATTATAGTATAATATGT
* * *
13136538 TATAATA-TAATATTATAGTATAGTAT-T
1 T-TATTAGTATTATTATAGTATAATATGT
13136565 ATTATTAGTATTATTATAGTA
1 -TTATTAGTATTATTATAGTA
13136586 ATTATATAGT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
27 5 0.13
28 30 0.77
29 4 0.10
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (28 bp):
TTATTAGTATTATTATAGTATAATATGT
Found at i:13137108 original size:20 final size:19
Alignment explanation
Indices: 13137085--13137132 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
13137075 TTTGGAATTT
13137085 TGGGTTTGATTTGACGTTTC
1 TGGGTTTGATTT-ACGTTTC
* *
13137105 TGGGTTAGATTTAGGTTTC
1 TGGGTTTGATTTACGTTTC
13137124 TGGAGTTTG
1 TGG-GTTTG
13137133 GATTAGAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.12, C:0.06, G:0.33, T:0.48
Consensus pattern (19 bp):
TGGGTTTGATTTACGTTTC
Found at i:13137628 original size:18 final size:17
Alignment explanation
Indices: 13137601--13137671 Score: 72
Period size: 18 Copynumber: 4.0 Consensus size: 17
13137591 TAGGTTTTCC
13137601 TTTTTCTATTTTCATTTTA
1 TTTTT-TATTTT-ATTTTA
13137620 TTTTTTA-TTTATTTTAA
1 TTTTTTATTTTATTTT-A
*
13137637 GTTTTTATTTTATTTTTA
1 TTTTTTATTTTA-TTTTA
* *
13137655 ATTTTTATTTAATTTTA
1 TTTTTTATTTTATTTTA
13137672 CTAGTTTTAT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
16 5 0.11
17 15 0.33
18 17 0.37
19 9 0.20
ACGTcount: A:0.21, C:0.03, G:0.01, T:0.75
Consensus pattern (17 bp):
TTTTTTATTTTATTTTA
Found at i:13137643 original size:17 final size:16
Alignment explanation
Indices: 13137614--13137671 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 16
13137604 TTCTATTTTC
*
13137614 ATTTTATTTTTTATTT
1 ATTTTAATTTTTATTT
13137630 ATTTTAAGTTTTTATTTT
1 ATTTTAA-TTTTTA-TTT
13137648 ATTTTTAATTTTTATTT
1 A-TTTTAATTTTTATTT
13137665 AATTTTA
1 -ATTTTA
13137672 CTAGTTTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
16 6 0.16
17 14 0.38
18 11 0.30
19 6 0.16
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (16 bp):
ATTTTAATTTTTATTT
Found at i:13147056 original size:22 final size:22
Alignment explanation
Indices: 13147019--13147092 Score: 76
Period size: 22 Copynumber: 3.4 Consensus size: 22
13147009 TTATACCTAG
* * *
13147019 ATGTATATAACTTATAAGTACT
1 ATGTATATATCCTATAAGTAAT
* *
13147041 ATGCATATATTCTATAAGTAAT
1 ATGTATATATCCTATAAGTAAT
* * *
13147063 ATGTACATATCCCATAAGTATT
1 ATGTATATATCCTATAAGTAAT
13147085 ATGTATAT
1 ATGTATAT
13147093 CTTATAAAAA
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (22 bp):
ATGTATATATCCTATAAGTAAT
Found at i:13147356 original size:22 final size:22
Alignment explanation
Indices: 13147328--13147383 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
13147318 TATTTTTATG
*
13147328 AGATGTACATATAGTTATACAT
1 AGATGTACATATAATTATACAT
* *
13147350 AGATGTATATATAATTATACCT
1 AGATGTACATATAATTATACAT
* *
13147372 AAATATACATAT
1 AGATGTACATAT
13147384 CTTATAAGTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.38
Consensus pattern (22 bp):
AGATGTACATATAATTATACAT
Found at i:13152716 original size:28 final size:28
Alignment explanation
Indices: 13152676--13152731 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
13152666 CTAGAAAGCT
13152676 TAGACTATATTTTCAATCTCATATAATG
1 TAGACTATATTTTCAATCTCATATAATG
13152704 TAGACTATATTTTCAATCTCATATAATG
1 TAGACTATATTTTCAATCTCATATAATG
13152732 CATGTGATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (28 bp):
TAGACTATATTTTCAATCTCATATAATG
Found at i:13161172 original size:94 final size:95
Alignment explanation
Indices: 13161059--13161255 Score: 333
Period size: 94 Copynumber: 2.1 Consensus size: 95
13161049 TAAATTAAGG
* * * *
13161059 TAAACAACTTCAAATAAGAATTCTTATTAACAAATGGTGTAAAGCTAAATGTATTTGTAAATCAA
1 TAAAGAACTTCAAATAAGAATTCTCATTAACAAATGGTATAAAGCTAAATGTATATGTAAATCAA
13161124 AATATATACCTCTAATTACCACAATACTTT
66 AATATATACCTCTAATTACCACAATACTTT
*
13161154 TAAAGAACTTCAAA-AAGAATTCTCATTAACAAATGGTATAAAGCTAATTGTATATGTAAATCAA
1 TAAAGAACTTCAAATAAGAATTCTCATTAACAAATGGTATAAAGCTAAATGTATATGTAAATCAA
*
13161218 AATATATACCTCTAATTACCTCAATACTTT
66 AATATATACCTCTAATTACCACAATACTTT
13161248 TAAAGAAC
1 TAAAGAAC
13161256 AATAGCTATA
Statistics
Matches: 96, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
94 83 0.86
95 13 0.14
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.32
Consensus pattern (95 bp):
TAAAGAACTTCAAATAAGAATTCTCATTAACAAATGGTATAAAGCTAAATGTATATGTAAATCAA
AATATATACCTCTAATTACCACAATACTTT
Found at i:13167829 original size:19 final size:18
Alignment explanation
Indices: 13167805--13167898 Score: 72
Period size: 19 Copynumber: 5.1 Consensus size: 18
13167795 CATGCAAAAG
13167805 TATCATGCAAAAATATAAA
1 TATCATG-AAAAATATAAA
13167824 TATCATGTAAATAA-AT-AA
1 TATCATG-AAA-AATATAAA
13167842 TGAATCATG-AAAATATAAA
1 T--ATCATGAAAAATATAAA
*
13167861 TACTCAT-ACAAATATAAA
1 TA-TCATGAAAAATATAAA
13167879 TAAATCATG-AAAATATAAA
1 T--ATCATGAAAAATATAAA
13167898 T
1 T
13167899 CATGCTCAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 20
0.73 0.04 0.24
Matches are distributed among these distances:
17 3 0.05
18 21 0.34
19 29 0.47
20 9 0.15
ACGTcount: A:0.57, C:0.09, G:0.05, T:0.29
Consensus pattern (18 bp):
TATCATGAAAAATATAAA
Found at i:13167856 original size:37 final size:37
Alignment explanation
Indices: 13167814--13167898 Score: 118
Period size: 37 Copynumber: 2.3 Consensus size: 37
13167804 GTATCATGCA
** *
13167814 AAAATATAAATA-TCATGTAAATAAATAATGAATCATG
1 AAAATATAAATACTCATACAAATAAA-AATAAATCATG
*
13167851 AAAATATAAATACTCATACAAATATAAATAAATCATG
1 AAAATATAAATACTCATACAAATAAAAATAAATCATG
13167888 AAAATATAAAT
1 AAAATATAAAT
13167899 CATGCTCAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
37 33 0.77
38 10 0.23
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.28
Consensus pattern (37 bp):
AAAATATAAATACTCATACAAATAAAAATAAATCATG
Found at i:13167867 original size:18 final size:19
Alignment explanation
Indices: 13167814--13167898 Score: 88
Period size: 18 Copynumber: 4.6 Consensus size: 19
13167804 GTATCATGCA
13167814 AAAATATAAAT--ATCATG
1 AAAATATAAATAAATCATG
* * *
13167831 TAAATAAATAATGAATCATG
1 AAAATATA-AATAAATCATG
*
13167851 AAAATATAAAT-ACTCAT-
1 AAAATATAAATAAATCATG
13167868 ACAAATATAAATAAATCATG
1 A-AAATATAAATAAATCATG
13167888 AAAATATAAAT
1 AAAATATAAAT
13167899 CATGCTCAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
17 7 0.12
18 18 0.32
19 18 0.32
20 13 0.23
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.28
Consensus pattern (19 bp):
AAAATATAAATAAATCATG
Found at i:13169292 original size:7 final size:7
Alignment explanation
Indices: 13169280--13169321 Score: 59
Period size: 7 Copynumber: 6.1 Consensus size: 7
13169270 GAGCAATATA
13169280 TAAAAAT
1 TAAAAAT
13169287 TAAAAAT
1 TAAAAAT
13169294 T-AAAAT
1 TAAAAAT
13169300 TAAAAAT
1 TAAAAAT
**
13169307 CCAAAAT
1 TAAAAAT
13169314 TAAAAAT
1 TAAAAAT
13169321 T
1 T
13169322 TTGGGCTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 6 0.20
7 24 0.80
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.29
Consensus pattern (7 bp):
TAAAAAT
Found at i:13169305 original size:14 final size:14
Alignment explanation
Indices: 13169282--13169320 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
13169272 GCAATATATA
*
13169282 AAAATTAAAAAT-T
1 AAAATTAAAAATCC
13169295 AAAATTAAAAATCC
1 AAAATTAAAAATCC
13169309 AAAATTAAAAAT
1 AAAATTAAAAAT
13169321 TTTGGGCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAATTAAAAATCC
Found at i:13169305 original size:20 final size:20
Alignment explanation
Indices: 13169280--13169318 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
13169270 GAGCAATATA
*
13169280 TAAAAATTAAAAATTAAAAT
1 TAAAAATCAAAAATTAAAAT
*
13169300 TAAAAATCCAAAATTAAAA
1 TAAAAATCAAAAATTAAAA
13169319 ATTTTGGGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (20 bp):
TAAAAATCAAAAATTAAAAT
Found at i:13170178 original size:22 final size:22
Alignment explanation
Indices: 13170153--13170442 Score: 62
Period size: 22 Copynumber: 13.2 Consensus size: 22
13170143 GTTACAACTC
**
13170153 ATGCTCAAAGGTCTTGGGGATT
1 ATGCTCAAAGGTCTTGAAGATT
* * *
13170175 ATGCTTAGAGGTTTTGAAGATT
1 ATGCTCAAAGGTCTTGAAGATT
* *
13170197 ATG-TCTAAAGGTCTT-ACAAATC
1 ATGCTC-AAAGGTCTTGA-AGATT
* *
13170219 ATGCTTGAAA-TTCTTGAAGATT
1 ATGC-TCAAAGGTCTTGAAGATT
** * * *
13170241 ATGC-CTGGAGGTC-TCACAAATC
1 ATGCTC-AAAGGTCTTGA-AGATT
*
13170263 ATGCCCAAAGGTCTT-AGAGATT
1 ATGCTCAAAGGTCTTGA-AGATT
*
13170285 ATGC-CTGAAGGTCTTGAAGATT
1 ATGCTC-AAAGGTCTTGAAGATT
* * *
13170307 ATG-TCTGAAGGTCTT-ACAAATC
1 ATGCTC-AAAGGTCTTGA-AGATT
* * * *
13170329 ACGCTTAGTA-GTCTTAAAGATT
1 ATGCTCA-AAGGTCTTGAAGATT
*** *
13170351 ATGCTTGGAGGTGTTGAAGATT
1 ATGCTCAAAGGTCTTGAAGATT
* * * *
13170373 ATACTCAGAGGTCTT-ACAAATC
1 ATGCTCAAAGGTCTTGA-AGATT
* * * *
13170395 ATGCCCAAAGATATTGGAGATT
1 ATGCTCAAAGGTCTTGAAGATT
* * *
13170417 ATGTTCAAAGGTTTTAAAGATT
1 ATGCTCAAAGGTCTTGAAGATT
13170439 ATGC
1 ATGC
13170443 CCGGAGGTCT
Statistics
Matches: 187, Mismatches: 61, Indels: 40
0.65 0.21 0.14
Matches are distributed among these distances:
21 9 0.05
22 167 0.89
23 10 0.05
24 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (22 bp):
ATGCTCAAAGGTCTTGAAGATT
Found at i:13170319 original size:110 final size:110
Alignment explanation
Indices: 13170126--13170362 Score: 300
Period size: 110 Copynumber: 2.2 Consensus size: 110
13170116 GTTTTTTCAG
* * * * * * * *
13170126 AGATTATG-CTCGGAGGTGTTACAACTCATGCTCAAAGGTCTTGGGGATTATGCTTAGAGGTTTT
1 AGATTATGCCT-GGAGGTCTCACAAATCATGCCCAAAGGTCTTAGAGATTATGCTGAGAGGTCTT
* * *
13170190 GAAGATTATGTCTAAAGGTCTTACAAATCATGCTT-GAAATTCTTGA
65 GAAGATTATGTCTAAAGGTCTTACAAATCACGCTTAG-AAGTCTTAA
13170236 AGATTATGCCTGGAGGTCTCACAAATCATGCCCAAAGGTCTTAGAGATTATGCCTGA-AGGTCTT
1 AGATTATGCCTGGAGGTCTCACAAATCATGCCCAAAGGTCTTAGAGATTATG-CTGAGAGGTCTT
* *
13170300 GAAGATTATGTCTGAAGGTCTTACAAATCACGCTTAGTAGTCTTAA
65 GAAGATTATGTCTAAAGGTCTTACAAATCACGCTTAGAAGTCTTAA
*
13170346 AGATTATGCTTGGAGGT
1 AGATTATGCCTGGAGGT
13170363 GTTGAAGATT
Statistics
Matches: 110, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
110 104 0.95
111 6 0.05
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (110 bp):
AGATTATGCCTGGAGGTCTCACAAATCATGCCCAAAGGTCTTAGAGATTATGCTGAGAGGTCTTG
AAGATTATGTCTAAAGGTCTTACAAATCACGCTTAGAAGTCTTAA
Found at i:13170343 original size:66 final size:66
Alignment explanation
Indices: 13170203--13170404 Score: 194
Period size: 66 Copynumber: 3.1 Consensus size: 66
13170193 GATTATGTCT
* * ** * * * *
13170203 AAAGGTCTTACAA-ATCATGCTTGAAATTCTTGAAGATTATGCCTGGAGGTCTCACAAATCATGC
1 AAAGGTCTTA-AAGATTATGCCTGAAGGTCTTGAAGATTATGACTGAAGGTCTTACAAATCACGC
13170267 CC
65 CC
* * *
13170269 AAAGGTCTTAGAGATTATGCCTGAAGGTCTTGAAGATTATGTCTGAAGGTCTTACAAATCACGCT
1 AAAGGTCTTAAAGATTATGCCTGAAGGTCTTGAAGATTATGACTGAAGGTCTTACAAATCACGCC
*
13170334 T
66 C
* * * * * *
13170335 AGTA-GTCTTAAAGATTATGCTTGGAGGTGTTGAAGATTAT-ACTCAGAGGTCTTACAAATCATG
1 A-AAGGTCTTAAAGATTATGCCTGAAGGTCTTGAAGATTATGACTGA-AGGTCTTACAAATCACG
13170398 CCC
64 CCC
13170401 AAAG
1 AAAG
13170405 ATATTGGAGA
Statistics
Matches: 110, Mismatches: 22, Indels: 8
0.79 0.16 0.06
Matches are distributed among these distances:
65 5 0.05
66 104 0.95
67 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (66 bp):
AAAGGTCTTAAAGATTATGCCTGAAGGTCTTGAAGATTATGACTGAAGGTCTTACAAATCACGCC
C
Found at i:13170416 original size:66 final size:64
Alignment explanation
Indices: 13170230--13170554 Score: 188
Period size: 66 Copynumber: 4.8 Consensus size: 64
13170220 TGCTTGAAAT
* *
13170230 TCTTGAAGATTATGC-CTGGAGGTCTCACAAATCATGCCCAAAGGTCTTAGAGATTATGCCTGAA
1 TCTTGAAGATTAT-CTC-AGAGGTCTTACAAATCATGCCCAAA-GTCTTAGAGATTATGCCTGAA
13170294 GG
63 GG
* * * ** * * * *
13170296 TCTTGAAGATTATGTCTGAAGGTCTTACAAATCACGCTTAGTAGTCTTAAAGATTATGCTTGGAG
1 TCTTGAAGATTATCTCAG-AGGTCTTACAAATCATGCCCA-AAGTCTTAGAGATTATGCCTGAAG
13170361 G
64 G
* * * * *
13170362 TGTTGAAGATTATACTCAGAGGTCTTACAAATCATGCCCAAAGATATTGGAGATTATG-TTCAAA
1 TCTTGAAGATTAT-CTCAGAGGTCTTACAAATCATGCCCAAAG-TCTTAGAGATTATGCCT-GAA
13170426 GG
63 GG
* * * * * * * * * *
13170428 TTTTAAAGATTATGCCCGGAGGTC-TAGTCTTGAGGATTATGCCCAAAGATCTTACAAATCATAC
1 TCTTGAAGATTAT-CTCAGAGGTCTTA--C---A-AATCATGCCCAAAG-TCTTAGAGATTATGC
*
13170492 CTAAAGG
58 CTGAAGG
* * * *
13170499 TTTTAAAGATTATACTCAGAGGTCTTACAAATCATGCCTAAATGCCTTAGAGATTA
1 TCTTGAAGATTAT-CTCAGAGGTCTTACAAATCATGCCCAAA-GTCTTAGAGATTA
13170555 AACTCAAATG
Statistics
Matches: 198, Mismatches: 46, Indels: 30
0.72 0.17 0.11
Matches are distributed among these distances:
65 7 0.04
66 132 0.67
67 7 0.04
70 2 0.01
71 47 0.24
72 3 0.02
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (64 bp):
TCTTGAAGATTATCTCAGAGGTCTTACAAATCATGCCCAAAGTCTTAGAGATTATGCCTGAAGG
Found at i:13170497 original size:22 final size:22
Alignment explanation
Indices: 13170472--13170540 Score: 61
Period size: 22 Copynumber: 3.1 Consensus size: 22
13170462 GATTATGCCC
*
13170472 AAAGATCTTACAAATCATACCT
1 AAAGGTCTTACAAATCATACCT
* *
13170494 AAAGGTTTTA-AAGATTATA-CT
1 AAAGGTCTTACAA-ATCATACCT
* *
13170515 CAGAGGTCTTACAAATCATGCCT
1 -AAAGGTCTTACAAATCATACCT
13170538 AAA
1 AAA
13170541 TGCCTTAGAG
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
21 4 0.11
22 27 0.77
23 4 0.11
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (22 bp):
AAAGGTCTTACAAATCATACCT
Found at i:13170553 original size:44 final size:44
Alignment explanation
Indices: 13170471--13170601 Score: 140
Period size: 44 Copynumber: 3.0 Consensus size: 44
13170461 GGATTATGCC
* * ** * *
13170471 CAAAGATCTTACAAATCATACCTAAAGGTTTTAAAGATTATACT
1 CAAAGGTCTTACAAATCATGCCTAAAGGCCTTAGAGATTAAACT
* *
13170515 CAGAGGTCTTACAAATCATGCCTAAATGCCTTAGAGATTAAACT
1 CAAAGGTCTTACAAATCATGCCTAAAGGCCTTAGAGATTAAACT
* *
13170559 CAAATGTC-TAGTAAATCATG-CTCAAAGGCCTTAGAGATTAAAC
1 CAAAGGTCTTA-CAAATCATGCCT-AAAGGCCTTAGAGATTAAAC
13170602 CTGGAGGTAT
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
43 4 0.05
44 69 0.95
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (44 bp):
CAAAGGTCTTACAAATCATGCCTAAAGGCCTTAGAGATTAAACT
Found at i:13170563 original size:22 final size:22
Alignment explanation
Indices: 13170538--13170601 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
13170528 AATCATGCCT
13170538 AAATGCCTTAGAGATTAAACTC
1 AAATGCCTTAGAGATTAAACTC
* * * **
13170560 AAATGTC-TAGTAAATCATGCTC
1 AAATGCCTTAG-AGATTAAACTC
*
13170582 AAAGGCCTTAGAGATTAAAC
1 AAATGCCTTAGAGATTAAAC
13170602 CTGGAGGTAT
Statistics
Matches: 29, Mismatches: 11, Indels: 4
0.66 0.25 0.09
Matches are distributed among these distances:
21 3 0.10
22 23 0.79
23 3 0.10
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.27
Consensus pattern (22 bp):
AAATGCCTTAGAGATTAAACTC
Found at i:13172065 original size:33 final size:30
Alignment explanation
Indices: 13172028--13172089 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 30
13172018 CTTTTCACAT
*
13172028 TTTTTCATCTTTTTTTTCTTTTCATTTCTTTCC
1 TTTTTCAT-TTTTTTTTCCTTT--TTTCTTTCC
*
13172061 TTTTTCCTTTTTTTTTCCTTTTTTCTTTC
1 TTTTTCATTTTTTTTTCCTTTTTTCTTTC
13172090 TTGGTTCCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 8 0.30
32 12 0.44
33 7 0.26
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (30 bp):
TTTTTCATTTTTTTTTCCTTTTTTCTTTCC
Found at i:13172531 original size:18 final size:18
Alignment explanation
Indices: 13172504--13172543 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
13172494 AAATGTAGGG
13172504 TTTTAATTTTCTTTTTAT
1 TTTTAATTTTCTTTTTAT
* *
13172522 TTTTAGTTTTCTTTTTGT
1 TTTTAATTTTCTTTTTAT
13172540 TTTT
1 TTTT
13172544 TTCTAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.10, C:0.05, G:0.05, T:0.80
Consensus pattern (18 bp):
TTTTAATTTTCTTTTTAT
Found at i:13173330 original size:114 final size:114
Alignment explanation
Indices: 13173130--13173360 Score: 408
Period size: 114 Copynumber: 2.0 Consensus size: 114
13173120 ACCATCACTA
* *
13173130 ACACCTATTAACTATCACCAAATACACATTAGTAGCACCACCCTTTTTACAATCTGTAAACCTAC
1 ACACCTATTAACTATCACCAAATACACATTAGTAGCACCACCCCTTTTACAATCTGCAAACCTAC
*
13173195 CATCTTAAAACTAAGATATCATGCAATAAACACATAGAGAAAAACTAGT
66 CATCTTAAAACTAAGATATCATGCAATAAACACATACAGAAAAACTAGT
*
13173244 ACACCTATTGACTATCACCAAATACACATTAGTAGCACCACCCCTTTTACAATCTGCAAACCTAC
1 ACACCTATTAACTATCACCAAATACACATTAGTAGCACCACCCCTTTTACAATCTGCAAACCTAC
* *
13173309 CATCTTAAGACTAAGATATCATGCAATAAACACATACAGGAAAACTAGT
66 CATCTTAAAACTAAGATATCATGCAATAAACACATACAGAAAAACTAGT
13173358 ACA
1 ACA
13173361 AGCCAAAAGA
Statistics
Matches: 111, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 111 1.00
ACGTcount: A:0.42, C:0.26, G:0.08, T:0.24
Consensus pattern (114 bp):
ACACCTATTAACTATCACCAAATACACATTAGTAGCACCACCCCTTTTACAATCTGCAAACCTAC
CATCTTAAAACTAAGATATCATGCAATAAACACATACAGAAAAACTAGT
Found at i:13178918 original size:22 final size:22
Alignment explanation
Indices: 13178890--13178976 Score: 68
Period size: 22 Copynumber: 3.9 Consensus size: 22
13178880 TGAGTTTCAA
*
13178890 ATGTGAATCTGTGAAATTTTAG
1 ATGTGAATCTCTGAAATTTTAG
* * *
13178912 ATGTGAACCTCTAAAATGTTTCAA
1 ATGTGAATCTCTGAAAT-TTT-AG
** * *
13178936 ATGAAAATCTTTGAAATTTTGG
1 ATGTGAATCTCTGAAATTTTAG
*
13178958 ATGTGAACCTCT-AAATTTT
1 ATGTGAATCTCTGAAATTTT
13178977 TCAAATGTGA
Statistics
Matches: 48, Mismatches: 15, Indels: 5
0.71 0.22 0.07
Matches are distributed among these distances:
21 7 0.15
22 22 0.46
23 6 0.12
24 13 0.27
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.39
Consensus pattern (22 bp):
ATGTGAATCTCTGAAATTTTAG
Found at i:13178994 original size:45 final size:46
Alignment explanation
Indices: 13178883--13179002 Score: 165
Period size: 46 Copynumber: 2.7 Consensus size: 46
13178873 AGAACTTTGA
*
13178883 GTTTCAAATGTGAATCTGTGAAATTTTAGATGTGAACCTCTAAAAT
1 GTTTCAAATGTGAATCTTTGAAATTTTAGATGTGAACCTCTAAAAT
** *
13178929 GTTTCAAATGAAAATCTTTGAAATTTTGGATGTGAACCTCT-AAAT
1 GTTTCAAATGTGAATCTTTGAAATTTTAGATGTGAACCTCTAAAAT
* *
13178974 TTTTCAAATGTGAACCTTTG-AA-TTTAGAT
1 GTTTCAAATGTGAATCTTTGAAATTTTAGAT
13179003 TCTTTGAATT
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
43 6 0.09
44 2 0.03
45 20 0.31
46 37 0.57
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (46 bp):
GTTTCAAATGTGAATCTTTGAAATTTTAGATGTGAACCTCTAAAAT
Found at i:13179047 original size:24 final size:24
Alignment explanation
Indices: 13179019--13179097 Score: 81
Period size: 24 Copynumber: 3.4 Consensus size: 24
13179009 AATTTCAATA
*
13179019 TGAATCTCTAAAATTTATCGAATG
1 TGAATCTCTAAAATTTATCAAATG
** **
13179043 TGAATCT-TTGAATTT-TTTAATG
1 TGAATCTCTAAAATTTATCAAATG
* *
13179065 TGAATATTTAAAATTTATCAAATG
1 TGAATCTCTAAAATTTATCAAATG
13179089 TGAATCTCT
1 TGAATCTCT
13179098 GAATTTTTTG
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
22 11 0.26
23 12 0.29
24 19 0.45
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.44
Consensus pattern (24 bp):
TGAATCTCTAAAATTTATCAAATG
Found at i:13179067 original size:22 final size:22
Alignment explanation
Indices: 13179039--13179106 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
13179029 AAATTTATCG
13179039 AATGTGAATCTTTGAATTTTTT
1 AATGTGAATCTTTGAATTTTTT
* * **
13179061 AATGTGAATATTTAAAATTTATCA
1 AATGTGAATCTTT-GAATTT-TTT
*
13179085 AATGTGAATCTCTGAATTTTTT
1 AATGTGAATCTTTGAATTTTTT
13179107 GACGTAAACC
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
22 13 0.37
23 10 0.29
24 12 0.34
ACGTcount: A:0.34, C:0.06, G:0.12, T:0.49
Consensus pattern (22 bp):
AATGTGAATCTTTGAATTTTTT
Found at i:13179123 original size:46 final size:46
Alignment explanation
Indices: 13179027--13179146 Score: 150
Period size: 46 Copynumber: 2.6 Consensus size: 46
13179017 TATGAATCTC
* * * * *
13179027 TAAAATTTATCGAATGTGAATCTTTGAATTTTTTAATGTGAATATT
1 TAAAATTTATCAAATGTGAATCTTTGAATTTTTTAACGTAAACATA
* * *
13179073 TAAAATTTATCAAATGTGAATCTCTGAATTTTTTGACGTAAACCTA
1 TAAAATTTATCAAATGTGAATCTTTGAATTTTTTAACGTAAACATA
* *
13179119 TAAAATTCATTAAATGTGAATCTTTGAA
1 TAAAATTTATCAAATGTGAATCTTTGAA
13179147 CTCAAATGTA
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
46 63 1.00
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (46 bp):
TAAAATTTATCAAATGTGAATCTTTGAATTTTTTAACGTAAACATA
Found at i:13179254 original size:24 final size:23
Alignment explanation
Indices: 13179226--13179292 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 23
13179216 TGAACCTCTA
13179226 AAATTTTTCAAATGAGAATCTT-T
1 AAATTTTTCAAATGAGAAT-TTCT
*
13179249 GAAA-TTTT-AGATGAGAATTTCT
1 -AAATTTTTCAAATGAGAATTTCT
*
13179271 AAATTTTTTCGAATGAGAATTT
1 AAA-TTTTTCAAATGAGAATTT
13179293 TTTAAAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
21 5 0.14
22 10 0.28
23 8 0.22
24 13 0.36
ACGTcount: A:0.37, C:0.06, G:0.13, T:0.43
Consensus pattern (23 bp):
AAATTTTTCAAATGAGAATTTCT
Found at i:13179256 original size:46 final size:46
Alignment explanation
Indices: 13179196--13179290 Score: 120
Period size: 46 Copynumber: 2.1 Consensus size: 46
13179186 ATTAAATGCA
*
13179196 AATCTATGAAATTTT-GTATGTGAACCTCTAAAATTTTTCAAATGAG
1 AATCTATGAAATTTTAG-ATGAGAACCTCTAAAATTTTTCAAATGAG
* ** * *
13179242 AATCTTTGAAATTTTAGATGAGAATTTCTAAATTTTTTCGAATGAG
1 AATCTATGAAATTTTAGATGAGAACCTCTAAAATTTTTCAAATGAG
13179288 AAT
1 AAT
13179291 TTTTTAAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
46 41 0.98
47 1 0.02
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41
Consensus pattern (46 bp):
AATCTATGAAATTTTAGATGAGAACCTCTAAAATTTTTCAAATGAG
Found at i:13179788 original size:17 final size:17
Alignment explanation
Indices: 13179758--13179854 Score: 72
Period size: 18 Copynumber: 5.5 Consensus size: 17
13179748 TTTAATATGG
13179758 AAATTCTTGCTAAA-CTGA
1 AAATTCTTG-TAAATCT-A
13179776 AAATTCTTGTAAATCTA
1 AAATTCTTGTAAATCTA
* * * *
13179793 AAATTTTTGTGAATATC
1 AAATTCTTGTAAATCTA
* *
13179810 AAATTCTTATGAAATCAA
1 AAATTCTTGT-AAATCTA
*
13179828 AAATTCTTG-AGAATTTGA
1 AAATTCTTGTA-AATCT-A
13179846 AAATTCTTG
1 AAATTCTTG
13179855 AGAATTTGAA
Statistics
Matches: 62, Mismatches: 13, Indels: 8
0.75 0.16 0.10
Matches are distributed among these distances:
16 1 0.02
17 29 0.47
18 32 0.52
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.39
Consensus pattern (17 bp):
AAATTCTTGTAAATCTA
Found at i:13179825 original size:35 final size:34
Alignment explanation
Indices: 13179776--13179841 Score: 87
Period size: 35 Copynumber: 1.9 Consensus size: 34
13179766 GCTAAACTGA
* * * *
13179776 AAATTCTTGTAAATCTAAAATTTTTGTGAATATC
1 AAATTCTTATAAATCAAAAATTCTTGAGAATATC
13179810 AAATTCTTATGAAATCAAAAATTCTTGAGAAT
1 AAATTCTTAT-AAATCAAAAATTCTTGAGAAT
13179842 TTGAAAATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
34 9 0.33
35 18 0.67
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.39
Consensus pattern (34 bp):
AAATTCTTATAAATCAAAAATTCTTGAGAATATC
Found at i:13179855 original size:18 final size:18
Alignment explanation
Indices: 13179827--13179941 Score: 96
Period size: 18 Copynumber: 6.5 Consensus size: 18
13179817 TATGAAATCA
13179827 AAAATTCTTGAGAATTTG
1 AAAATTCTTGAGAATTTG
13179845 AAAATTCTTGAGAATTTG
1 AAAATTCTTGAGAATTTG
*
13179863 AAAATTCTT-ACGAACTTG
1 AAAATTCTTGA-GAATTTG
* * *
13179881 AGAGTTCTT-ACGAATAT-
1 AAAATTCTTGA-GAATTTG
* * * *
13179898 CAAATTATTGTGAAATTG
1 AAAATTCTTGAGAATTTG
13179916 AAAA-TCTTGTA-AATTTG
1 AAAATTCTTG-AGAATTTG
13179933 AAAATTCTT
1 AAAATTCTT
13179942 ACGAAACTAA
Statistics
Matches: 76, Mismatches: 16, Indels: 10
0.75 0.16 0.10
Matches are distributed among these distances:
17 23 0.30
18 53 0.70
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (18 bp):
AAAATTCTTGAGAATTTG
Found at i:13179959 original size:35 final size:35
Alignment explanation
Indices: 13179916--13180144 Score: 112
Period size: 35 Copynumber: 6.5 Consensus size: 35
13179906 TGTGAAATTG
13179916 AAAA-TCTTGTAAATTTGAAAATTCTTACGAAACT
1 AAAATTCTTGTAAATTTGAAAATTCTTACGAAACT
*
13179950 AAAATTCTTGTAAAACTTAATTTGAAAATTCTTACAAAACT
1 AAAATTCTTGT---A---AATTTGAAAATTCTTACGAAACT
* * *
13179991 AAAAATTTTTGCAAATATG-AAATT-TT-CGTAAATCT
1 -AAAATTCTTGTAAATTTGAAAATTCTTACG-AAA-CT
* * * *
13180026 -GAGTTCTTGTAAATCT-CAAATTCTTACGAAACT
1 AAAATTCTTGTAAATTTGAAAATTCTTACGAAACT
** * * * **
13180059 GAAAATTCTTACAAATTTGAAAGTTCTTGCTAATTT
1 -AAAATTCTTGTAAATTTGAAAATTCTTACGAAACT
* * * * * *
13180095 CAAACTCTTGTAAAGTTG-AAACTCTTGCGAAATT
1 AAAATTCTTGTAAATTTGAAAATTCTTACGAAACT
* *
13180129 GAAATTCTTGTGAATT
1 AAAATTCTTGTAAATT
13180145 GAATCTAAAA
Statistics
Matches: 145, Mismatches: 34, Indels: 32
0.69 0.16 0.15
Matches are distributed among these distances:
33 19 0.13
34 38 0.26
35 39 0.27
36 16 0.11
38 1 0.01
39 1 0.01
41 22 0.15
42 9 0.06
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (35 bp):
AAAATTCTTGTAAATTTGAAAATTCTTACGAAACT
Found at i:13180094 original size:18 final size:18
Alignment explanation
Indices: 13180043--13180086 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
13180033 TGTAAATCTC
*
13180043 AAATTCTTACGAAA-CTGA
1 AAATTCTTAC-AAATTTGA
13180061 AAATTCTTACAAATTTGA
1 AAATTCTTACAAATTTGA
*
13180079 AAGTTCTT
1 AAATTCTT
13180087 GCTAATTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (18 bp):
AAATTCTTACAAATTTGA
Found at i:13180146 original size:16 final size:16
Alignment explanation
Indices: 13180096--13180147 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
13180086 TGCTAATTTC
*
13180096 AAACTCTTGTAAAGTTG
1 AAACTCTTGTGAA-TTG
*
13180113 AAACTCTTGCGAAATTG
1 AAACTCTTGTG-AATTG
*
13180130 AAATTCTTGTGAATTG
1 AAACTCTTGTGAATTG
13180146 AA
1 AA
13180148 TCTAAAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 7 0.23
17 21 0.70
18 2 0.07
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.35
Consensus pattern (16 bp):
AAACTCTTGTGAATTG
Found at i:13180963 original size:14 final size:14
Alignment explanation
Indices: 13180946--13180978 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
13180936 AACCAATAAG
*
13180946 GAACAAACATAGAA
1 GAACAAACAAAGAA
13180960 GAACAAACAAAGAA
1 GAACAAACAAAGAA
13180974 -AACAA
1 GAACAA
13180979 CCATTAGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.70, C:0.15, G:0.12, T:0.03
Consensus pattern (14 bp):
GAACAAACAAAGAA
Found at i:13185808 original size:12 final size:12
Alignment explanation
Indices: 13185791--13185857 Score: 50
Period size: 12 Copynumber: 5.5 Consensus size: 12
13185781 AAATCATACT
13185791 ATGCAAAAAATC
1 ATGCAAAAAATC
*
13185803 ATGCAATAAAT-
1 ATGCAAAAAATC
*
13185814 AT--AAAATCATACC
1 ATGCAAAA--A-ATC
*
13185827 ATGCAATAAATC
1 ATGCAAAAAATC
13185839 ATGCAAAAATATC
1 ATGCAAAAA-ATC
13185852 ATGCAA
1 ATGCAA
13185858 CAATATAAGA
Statistics
Matches: 42, Mismatches: 6, Indels: 13
0.69 0.10 0.21
Matches are distributed among these distances:
9 3 0.07
11 3 0.07
12 21 0.50
13 12 0.29
15 3 0.07
ACGTcount: A:0.54, C:0.16, G:0.07, T:0.22
Consensus pattern (12 bp):
ATGCAAAAAATC
Found at i:13185824 original size:36 final size:35
Alignment explanation
Indices: 13185777--13185850 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 35
13185767 TGTTTAAGGT
*
13185777 TATAAAATCATACTATGCAAAAAATCATGCAATAAA
1 TATAAAATCATACCATGCAAAAAATCATGCAA-AAA
*
13185813 TATAAAATCATACCATGCAATAAATCATGCAAAAA
1 TATAAAATCATACCATGCAAAAAATCATGCAAAAA
13185848 TAT
1 TAT
13185851 CATGCAACAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 6 0.17
36 30 0.83
ACGTcount: A:0.54, C:0.15, G:0.05, T:0.26
Consensus pattern (35 bp):
TATAAAATCATACCATGCAAAAAATCATGCAAAAA
Found at i:13185854 original size:13 final size:13
Alignment explanation
Indices: 13185826--13185863 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
13185816 AAAATCATAC
*
13185826 CATGCAATAA-AT
1 CATGCAAAAATAT
13185838 CATGCAAAAATAT
1 CATGCAAAAATAT
*
13185851 CATGCAACAATAT
1 CATGCAAAAATAT
13185864 AAGATATCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 9 0.39
13 14 0.61
ACGTcount: A:0.50, C:0.18, G:0.08, T:0.24
Consensus pattern (13 bp):
CATGCAAAAATAT
Found at i:13185922 original size:40 final size:41
Alignment explanation
Indices: 13185878--13185964 Score: 104
Period size: 40 Copynumber: 2.1 Consensus size: 41
13185868 TATCATGTAA
* * *
13185878 ATAAATTATTAATCATGCAAATATAAAT-ACTCATACAAAT
1 ATAAATTAATAATCATACAAATATAAATAAATCATACAAAT
* * * *
13185918 ATAAATTAATAATTATACAAGTATAAATAAATCATGCAACT
1 ATAAATTAATAATCATACAAATATAAATAAATCATACAAAT
13185959 ATAAAT
1 ATAAAT
13185965 AATGCTAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 24 0.62
41 15 0.38
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.32
Consensus pattern (41 bp):
ATAAATTAATAATCATACAAATATAAATAAATCATACAAAT
Found at i:13185928 original size:22 final size:22
Alignment explanation
Indices: 13185878--13185945 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 22
13185868 TATCATGTAA
* *
13185878 ATAAATTATTAATCATGCAAAT
1 ATAAATTAATAATCATACAAAT
*
13185900 AT--A--AATACTCATACAAAT
1 ATAAATTAATAATCATACAAAT
* *
13185918 ATAAATTAATAATTATACAAGT
1 ATAAATTAATAATCATACAAAT
13185940 ATAAAT
1 ATAAAT
13185946 AAATCATGCA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
18 14 0.39
20 2 0.06
22 20 0.56
ACGTcount: A:0.54, C:0.09, G:0.03, T:0.34
Consensus pattern (22 bp):
ATAAATTAATAATCATACAAAT
Found at i:13188027 original size:23 final size:24
Alignment explanation
Indices: 13187995--13188044 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
13187985 ATAGAGAAAG
* *
13187995 AAAAAGTAAATAG-AAAAGAAATA
1 AAAAAGTAAAAAGAAAAAAAAATA
*
13188018 AAAAATTAAAAAGAAAAAAAAATA
1 AAAAAGTAAAAAGAAAAAAAAATA
13188042 AAA
1 AAA
13188045 TAAAATGACT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (24 bp):
AAAAAGTAAAAAGAAAAAAAAATA
Found at i:13188028 original size:17 final size:16
Alignment explanation
Indices: 13187991--13188044 Score: 63
Period size: 18 Copynumber: 3.1 Consensus size: 16
13187981 AAATATAGAG
*
13187991 AAAGAAAAAGTAAATAGA
1 AAAGAAAAA-AAAATA-A
13188009 AAAGAAATAAAAAATTAA
1 AAAGAAA-AAAAAA-TAA
13188027 AAAGAAAAAAAAATAA
1 AAAGAAAAAAAAATAA
13188043 AA
1 AA
13188045 TAAAATGACT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
16 5 0.15
17 6 0.18
18 18 0.55
19 4 0.12
ACGTcount: A:0.80, C:0.00, G:0.09, T:0.11
Consensus pattern (16 bp):
AAAGAAAAAAAAATAA
Found at i:13188999 original size:3 final size:3
Alignment explanation
Indices: 13188986--13189020 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
13188976 TGCAAAGATG
*
13188986 ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
13189021 GAAAAAGAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:13198185 original size:10 final size:10
Alignment explanation
Indices: 13198172--13198205 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
13198162 AAATCTTAAA
13198172 GATTCTTGAT
1 GATTCTTGAT
13198182 GATTCTTGAT
1 GATTCTTGAT
* *
13198192 CAATCTTGAT
1 GATTCTTGAT
13198202 GATT
1 GATT
13198206 TTTTATGCAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.24, C:0.12, G:0.18, T:0.47
Consensus pattern (10 bp):
GATTCTTGAT
Found at i:13199618 original size:51 final size:51
Alignment explanation
Indices: 13199563--13199669 Score: 144
Period size: 51 Copynumber: 2.1 Consensus size: 51
13199553 AGTTGCATGA
*
13199563 TTAGTGCATGTT-GTTTCGGTTTAATTATTTTATGTTCCAAAACAATTTTTG
1 TTAGTGCAT-TTAGTTTCAGTTTAATTATTTTATGTTCCAAAACAATTTTTG
** * * *
13199614 TTAGTTTATTTAGTTTTAGTTTAATTATTTTATGTTCTAAAACTATTTTTG
1 TTAGTGCATTTAGTTTCAGTTTAATTATTTTATGTTCCAAAACAATTTTTG
13199665 TTAGT
1 TTAGT
13199670 TTATTTAGAA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
50 2 0.04
51 47 0.96
ACGTcount: A:0.24, C:0.07, G:0.13, T:0.56
Consensus pattern (51 bp):
TTAGTGCATTTAGTTTCAGTTTAATTATTTTATGTTCCAAAACAATTTTTG
Found at i:13199670 original size:51 final size:51
Alignment explanation
Indices: 13199581--13199677 Score: 176
Period size: 51 Copynumber: 1.9 Consensus size: 51
13199571 TGTTGTTTCG
13199581 GTTTAATTATTTTATGTTCCAAAACAATTTTTGTTAGTTTATTTAGTTTTA
1 GTTTAATTATTTTATGTTCCAAAACAATTTTTGTTAGTTTATTTAGTTTTA
* *
13199632 GTTTAATTATTTTATGTTCTAAAACTATTTTTGTTAGTTTATTTAG
1 GTTTAATTATTTTATGTTCCAAAACAATTTTTGTTAGTTTATTTAG
13199678 AATTGATTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.27, C:0.05, G:0.10, T:0.58
Consensus pattern (51 bp):
GTTTAATTATTTTATGTTCCAAAACAATTTTTGTTAGTTTATTTAGTTTTA
Found at i:13200080 original size:31 final size:31
Alignment explanation
Indices: 13200040--13200108 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
13200030 TTTTGCATGT
*
13200040 TATTAGTTTCGATTCATGTTAATTAGGGTTCA
1 TATTAGTTTCGATTCATGCT-ATTAGGGTTCA
* * *
13200072 TATT-GTTTCGGTTTATGCTATTAGGGTTTA
1 TATTAGTTTCGATTCATGCTATTAGGGTTCA
13200102 TA-TAGTT
1 TATTAGTT
13200109 GTGGTTTAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 1 0.03
30 15 0.47
31 12 0.38
32 4 0.12
ACGTcount: A:0.22, C:0.07, G:0.20, T:0.51
Consensus pattern (31 bp):
TATTAGTTTCGATTCATGCTATTAGGGTTCA
Found at i:13200304 original size:19 final size:20
Alignment explanation
Indices: 13200264--13200304 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
13200254 ATGCTTTAGG
*
13200264 TTTTGGTTTGCATATTTATA
1 TTTTGGTTTACATATTTATA
*
13200284 TTTTGTTTTACATATTT-TA
1 TTTTGGTTTACATATTTATA
13200303 TT
1 TT
13200305 GAATTTTCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.20, C:0.05, G:0.10, T:0.66
Consensus pattern (20 bp):
TTTTGGTTTACATATTTATA
Found at i:13205096 original size:145 final size:143
Alignment explanation
Indices: 13204833--13205247 Score: 413
Period size: 145 Copynumber: 2.9 Consensus size: 143
13204823 GGGAAAATAC
* * * * * * *
13204833 AAAATTACTAAAATACCC-TTTAAGGAGTCTTTTCATAAATTAGCTTTCCCTAGCTCAAATTTTC
1 AAAATTACTAAAATACCCATATAAGG-GTATTCTCATAATTTAGCATTCCCGAGCTC-AATTTTT
* *
13204897 ATGAAACTTTTTAGATTTTAATTTCATAATATTTCATAATTTTTAGTGTATTTGAAATCACAGCA
64 ATGAAACTTTTTAGATCTTAATTTCATAATATTTCATGATTTTTAGTGT-TTTGAAATCACAGCA
* ** *
13204962 ATATCCTGAGAAGTAT
128 ATACCCCAAAAAGTAT
* * * * *
13204978 AAAATTA-TCAAAATACCCTTATAAGGTTATTCTCGTAATTTATCATTCCCGAGCTTGAATTTTT
1 AAAATTACT-AAAATACCCATATAAGGGTATTCTCATAATTTAGCATTCCCGAGC-TCAATTTTT
* * *
13205042 ATGAAACTTTTTAGATCTTAATTTCATAATATTTCATGATTTTTGGTGTGTTTGAAATTACAGCT
64 ATGAAACTTTTTAGATCTTAATTTCATAATATTTCATGATTTTTAGTGT-TTTGAAATCACAGCA
* *
13205107 GTACCCCAAAAAGTGT
128 ATACCCCAAAAAGTAT
* * * * * **
13205123 GAAATTACTAAAATATCCATATAAGGGTATTTTTATAATTTAGCCTTTTCGAGCTCAGATTTTCT
1 AAAATTACTAAAATACCCATATAAGGGTATTCTCATAATTTAGCATTCCCGAGCTCA-ATTTT-T
* * * * * *
13205188 -TGAAACTTTCTAGATCTCAATTTTATAATATTTCTTGATTTTTTGTGTTTTAAAATCACA
64 ATGAAACTTTTTAGATCTTAATTTCATAATATTTCATGATTTTTAGTGTTTTGAAATCACA
13205248 AAAATGAGCA
Statistics
Matches: 222, Mismatches: 42, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
144 13 0.06
145 200 0.90
146 9 0.04
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (143 bp):
AAAATTACTAAAATACCCATATAAGGGTATTCTCATAATTTAGCATTCCCGAGCTCAATTTTTAT
GAAACTTTTTAGATCTTAATTTCATAATATTTCATGATTTTTAGTGTTTTGAAATCACAGCAATA
CCCCAAAAAGTAT
Found at i:13217856 original size:11 final size:11
Alignment explanation
Indices: 13217832--13217878 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
13217822 GATAAAAAAC
*
13217832 AAAAAAA-AAG
1 AAAAAAATAAT
13217842 AAAAAAATAAT
1 AAAAAAATAAT
*
13217853 AAAATAATAAT
1 AAAAAAATAAT
13217864 AAAAAGAATAA-
1 AAAAA-AATAAT
13217875 AAAA
1 AAAA
13217879 TGAAAGAGGA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
10 7 0.22
11 20 0.62
12 5 0.16
ACGTcount: A:0.83, C:0.00, G:0.04, T:0.13
Consensus pattern (11 bp):
AAAAAAATAAT
Found at i:13218872 original size:37 final size:37
Alignment explanation
Indices: 13218813--13218895 Score: 103
Period size: 37 Copynumber: 2.2 Consensus size: 37
13218803 GAAAAACAAG
* * * ** *
13218813 ATTTTTAAAGTTTTAAAGCCTTTATTTAGGGGGAGCC
1 ATTTTCAAAGTTTCAAAACCTTTATTTAGAAGGAGCA
*
13218850 ATTTTCAAAGTTTCAAAACCTTTGTTTAGAAGGAGCA
1 ATTTTCAAAGTTTCAAAACCTTTATTTAGAAGGAGCA
13218887 ATTTTCAAA
1 ATTTTCAAA
13218896 CAAGATTTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.39
Consensus pattern (37 bp):
ATTTTCAAAGTTTCAAAACCTTTATTTAGAAGGAGCA
Found at i:13218982 original size:37 final size:36
Alignment explanation
Indices: 13218930--13219023 Score: 98
Period size: 37 Copynumber: 2.6 Consensus size: 36
13218920 AAGCCTTTGT
* * *
13218930 TTAGGAGGAGTCATTTTCAAAGTTTCAAAGCCTCTA
1 TTAGGGGGAGCCATTTTCAAAGTTTCAAAGCATCTA
* * * * *
13218966 TTCATGGGGAGCCATTTTTAATGTTTCAAAGCATTTG
1 TT-AGGGGGAGCCATTTTCAAAGTTTCAAAGCATCTA
*
13219003 TTAGGGGGAGCAATTTTCAAA
1 TTAGGGGGAGCCATTTTCAAA
13219024 CAAGATTTTT
Statistics
Matches: 45, Mismatches: 12, Indels: 2
0.76 0.20 0.03
Matches are distributed among these distances:
36 17 0.38
37 28 0.62
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (36 bp):
TTAGGGGGAGCCATTTTCAAAGTTTCAAAGCATCTA
Found at i:13219076 original size:52 final size:50
Alignment explanation
Indices: 13218979--13219125 Score: 170
Period size: 52 Copynumber: 2.9 Consensus size: 50
13218969 ATGGGGAGCC
* * *
13218979 ATTTTTAATGTTTCAAAGCATTTG-TTAGGGGGAGCAATTTTCAAACAAG
1 ATTTTTAATGTTTCAAAGCCTCTGTTTAGGGGGAGCAATTTTCAAACAAA
* *
13219028 ATTTTTAAAGTTTCAAAGCCTCTGTTTAGGGGGGGAGCCATTTTCAAACAAA
1 ATTTTTAATGTTTCAAAGCCTCTGTTTA--GGGGGAGCAATTTTCAAACAAA
* * ** * *
13219080 ATTTTTAATGTGTCATAGCCTCTGTTTAAAGGGAGCCATCTTCAAA
1 ATTTTTAATGTTTCAAAGCCTCTGTTTAGGGGGAGCAATTTTCAAA
13219126 TAAGGCTTTT
Statistics
Matches: 84, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
49 21 0.25
50 18 0.21
52 45 0.54
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (50 bp):
ATTTTTAATGTTTCAAAGCCTCTGTTTAGGGGGAGCAATTTTCAAACAAA
Found at i:13219391 original size:22 final size:22
Alignment explanation
Indices: 13219366--13219408 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
13219356 TTGAGATTTA
13219366 TAAGACCT-TTAGGCATAATCTC
1 TAAGACCTCTTA-GCATAATCTC
13219388 TAAGACCTCTTAGCATAATCT
1 TAAGACCTCTTAGCATAATCT
13219409 AATCCAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.33
Consensus pattern (22 bp):
TAAGACCTCTTAGCATAATCTC
Found at i:13221584 original size:59 final size:59
Alignment explanation
Indices: 13221512--13221628 Score: 207
Period size: 59 Copynumber: 2.0 Consensus size: 59
13221502 AAATCATATA
*
13221512 AAACTAAATGGATACAAGTTGTAAATTAGAAGAACACTCAATGAACATCATAAGATTTT
1 AAACTAAATGGATACAAGTTGAAAATTAGAAGAACACTCAATGAACATCATAAGATTTT
* *
13221571 AAACTAAATGGATACAAGTTGAAAATTGGAAGAACACTCGATGAACATCATAAGATTT
1 AAACTAAATGGATACAAGTTGAAAATTAGAAGAACACTCAATGAACATCATAAGATTT
13221629 AAATTGAAGA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.26
Consensus pattern (59 bp):
AAACTAAATGGATACAAGTTGAAAATTAGAAGAACACTCAATGAACATCATAAGATTTT
Found at i:13223497 original size:19 final size:19
Alignment explanation
Indices: 13223470--13223519 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
13223460 AGGATCAATA
*
13223470 AAGTATGCTTATGTTCCAT
1 AAGTTTGCTTATGTTCCAT
13223489 AAGTTTGCTTATGTTCCAT
1 AAGTTTGCTTATGTTCCAT
13223508 AAGTTTGCTTAT
1 AAGTTTGCTTAT
13223520 CACATCTCTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.16, T:0.46
Consensus pattern (19 bp):
AAGTTTGCTTATGTTCCAT
Found at i:13223812 original size:16 final size:16
Alignment explanation
Indices: 13223793--13223827 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
13223783 TTATTTTTGC
13223793 TTTTTTTTCCTTTTCT
1 TTTTTTTTCCTTTTCT
*
13223809 TTTTTTTTCTTTTTCT
1 TTTTTTTTCCTTTTCT
13223825 TTT
1 TTT
13223828 GCAAGCTAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (16 bp):
TTTTTTTTCCTTTTCT
Found at i:13223816 original size:10 final size:11
Alignment explanation
Indices: 13223786--13223827 Score: 52
Period size: 10 Copynumber: 3.9 Consensus size: 11
13223776 CACTTCATTA
13223786 TTTTTGCTTTT-
1 TTTTT-CTTTTC
*
13223797 TTTTCCTTTTC
1 TTTTTCTTTTC
13223808 TTTTT-TTTTC
1 TTTTTCTTTTC
13223818 TTTTTCTTTT
1 TTTTTCTTTT
13223828 GCAAGCTAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 15 0.56
11 12 0.44
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.83
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:13224960 original size:18 final size:18
Alignment explanation
Indices: 13224937--13224971 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
13224927 AAATCAATTA
* *
13224937 ATAAATGATAAATAATAT
1 ATAAATAATAAAAAATAT
13224955 ATAAATAATAAAAAATA
1 ATAAATAATAAAAAATA
13224972 AATATAAAAA
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:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (18 bp):
ATAAATAATAAAAAATAT
Found at i:13230930 original size:77 final size:77
Alignment explanation
Indices: 13230839--13230993 Score: 310
Period size: 77 Copynumber: 2.0 Consensus size: 77
13230829 CAAACAATCT
13230839 AGCCTTCTAGTTCTTTACCTAAAAAATTGTCCATGTCGGTATCTTAGGGCACATAGATCAAAAAG
1 AGCCTTCTAGTTCTTTACCTAAAAAATTGTCCATGTCGGTATCTTAGGGCACATAGATCAAAAAG
13230904 AAGGACATGATC
66 AAGGACATGATC
13230916 AGCCTTCTAGTTCTTTACCTAAAAAATTGTCCATGTCGGTATCTTAGGGCACATAGATCAAAAAG
1 AGCCTTCTAGTTCTTTACCTAAAAAATTGTCCATGTCGGTATCTTAGGGCACATAGATCAAAAAG
13230981 AAGGACATGATC
66 AAGGACATGATC
13230993 A
1 A
13230994 CTCTCTTGAA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.28
Consensus pattern (77 bp):
AGCCTTCTAGTTCTTTACCTAAAAAATTGTCCATGTCGGTATCTTAGGGCACATAGATCAAAAAG
AAGGACATGATC
Found at i:13231178 original size:9 final size:9
Alignment explanation
Indices: 13231160--13231223 Score: 60
Period size: 9 Copynumber: 6.9 Consensus size: 9
13231150 GGGGAATGCC
13231160 AAAAAAAA-
1 AAAAAAAAG
13231168 AAAAGAAAA-
1 AAAA-AAAAG
*
13231177 AAATGAAAAG
1 AAA-AAAAAG
13231187 AAAAAAAAGG
1 AAAAAAAA-G
*
13231197 AAAAGAAAG
1 AAAAAAAAG
13231206 AAAAAAAAG
1 AAAAAAAAG
13231215 AAGAAAAAA
1 AA-AAAAAA
13231224 TCTTTGATTG
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
8 4 0.09
9 26 0.55
10 17 0.36
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:13231185 original size:15 final size:14
Alignment explanation
Indices: 13231160--13231222 Score: 60
Period size: 14 Copynumber: 4.5 Consensus size: 14
13231150 GGGGAATGCC
13231160 AAAAAAA-AAAAAG
1 AAAAAAAGAAAAAG
13231173 AAAAAAATG-AAAAG
1 AAAAAAA-GAAAAAG
*
13231187 AAAAAAAAGGAAAAG
1 -AAAAAAAGAAAAAG
*
13231202 AAAGAAA-AAAAAG
1 AAAAAAAGAAAAAG
13231215 AAGAAAAA
1 AA-AAAAA
13231223 ATCTTTGATT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
13 14 0.33
14 16 0.38
15 12 0.29
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (14 bp):
AAAAAAAGAAAAAG
Found at i:13231190 original size:24 final size:23
Alignment explanation
Indices: 13231160--13231213 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 23
13231150 GGGGAATGCC
13231160 AAAAAAAAAAAAGAAAA-AAATGA
1 AAAAAAAAAAAAGAAAAGAAA-GA
*
13231183 AAAGAAAAAAAAGGAAAAGAAAGA
1 AAA-AAAAAAAAAGAAAAGAAAGA
13231207 AAAAAAA
1 AAAAAAA
13231214 GAAGAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 7 0.25
24 18 0.64
25 3 0.11
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (23 bp):
AAAAAAAAAAAAGAAAAGAAAGA
Found at i:13231749 original size:19 final size:19
Alignment explanation
Indices: 13231727--13231797 Score: 65
Period size: 18 Copynumber: 3.7 Consensus size: 19
13231717 AAAAAGTGAA
*
13231727 GAAAAAGAGAAAAAAAAGG
1 GAAAAAGAGAAAAAAAAAG
*
13231746 GAAAAAGTGAAAGAAAGAAAAG
1 GAAAAAGAG-AA-AAA-AAAAG
* *
13231768 CAAACAGA-AAAAAAAAAG
1 GAAAAAGAGAAAAAAAAAG
13231786 GAAAAA-AGAAAA
1 GAAAAAGAGAAAA
13231798 GAGAAGAAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
17 1 0.02
18 13 0.32
19 11 0.27
20 4 0.10
21 3 0.07
22 9 0.22
ACGTcount: A:0.75, C:0.03, G:0.21, T:0.01
Consensus pattern (19 bp):
GAAAAAGAGAAAAAAAAAG
Found at i:13232192 original size:16 final size:15
Alignment explanation
Indices: 13232160--13232195 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
13232150 AACAACGAGA
13232160 AAAGAAAAAAAAAAG
1 AAAGAAAAAAAAAAG
*
13232175 AAAGAAAAAAGAAGAG
1 AAAGAAAAAA-AAAAG
13232191 AAAGA
1 AAAGA
13232196 GATGAATGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAAAAAAG
Found at i:13233660 original size:23 final size:23
Alignment explanation
Indices: 13233630--13233674 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
13233620 AGATAAGATG
13233630 TTTTGAAA-CAAAGAGTGAAAATT
1 TTTTGAAATCAAA-AGTGAAAATT
*
13233653 TTTTGAAATGAAAAGTGAAAAT
1 TTTTGAAATCAAAAGTGAAAAT
13233675 GTTGAAGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.49, C:0.02, G:0.18, T:0.31
Consensus pattern (23 bp):
TTTTGAAATCAAAAGTGAAAATT
Found at i:13233782 original size:40 final size:40
Alignment explanation
Indices: 13233738--13233827 Score: 103
Period size: 41 Copynumber: 2.2 Consensus size: 40
13233728 TACGTGATCT
* *
13233738 CCAAGACCTT-GAGCAAAATTTTAGAATTTTGAATGATTTC
1 CCAAGACCTTGGA-CAAAATTTTACAATTTTGAATGAATTC
* *
13233778 CCAAGGCCTTTGGACAAAATTTTACATTTTTGAATGAATTC
1 CCAAGACC-TTGGACAAAATTTTACAATTTTGAATGAATTC
13233819 CACAA-ACCT
1 C-CAAGACCT
13233828 CAGGGCAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
40 8 0.19
41 29 0.69
42 5 0.12
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.33
Consensus pattern (40 bp):
CCAAGACCTTGGACAAAATTTTACAATTTTGAATGAATTC
Found at i:13233837 original size:41 final size:41
Alignment explanation
Indices: 13233750--13233838 Score: 99
Period size: 41 Copynumber: 2.2 Consensus size: 41
13233740 AAGACCTTGA
* * * **
13233750 GCAAAATTTTAGAATTTTGAATGATTTCCCAAGGCCTTTGG
1 GCAAAATTTTACAATTTTGAATGAATTCCCAAGACCTCAGG
* *
13233791 ACAAAATTTTACATTTTTGAATGAATTCCACAA-ACCTCAGG
1 GCAAAATTTTACAATTTTGAATGAATTCC-CAAGACCTCAGG
13233832 GCAAAAT
1 GCAAAAT
13233839 CTCATATTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 36 0.92
42 3 0.08
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.33
Consensus pattern (41 bp):
GCAAAATTTTACAATTTTGAATGAATTCCCAAGACCTCAGG
Found at i:13234038 original size:40 final size:40
Alignment explanation
Indices: 13233732--13234250 Score: 199
Period size: 40 Copynumber: 12.8 Consensus size: 40
13233722 AATGAGTACG
* * *
13233732 TGATCTCCAAGACCT-TGAGCAAAATTTTAGAAT-TTTGAA
1 TGATTTCCAAGACCTCTGGGCAAAATCTTA-AATCTTTGAA
* * * * * *
13233771 TGATTTCCCAAGGCCTTTGGACAAAATTTTACATTTTTGAA
1 TGATTT-CCAAGACCTCTGGGCAAAATCTTAAATCTTTGAA
* * * * * *
13233812 TGAATTCCACAAACCTCAGGGCAAAATCTCATAT-TTTAAA
1 TGATTTCCA-AGACCTCTGGGCAAAATCTTAAATCTTTGAA
* * *** *
13233852 TGGTTTCAAAAGACCTAAAGG-AAAATTCTTAAAACTTTGAA
1 TGATTTC-CAAGACCTCTGGGCAAAA-TCTTAAATCTTTGAA
* ** * * * *
13233893 TGATCTCTGAGACCTCTAGGCAAAAGCTTAGATTTTTGAA
1 TGATTTCCAAGACCTCTGGGCAAAATCTTAAATCTTTGAA
** * * * * *
13233933 TGATTTTTAAAACCTCTGAGTAAAAGT-TTAAATTTTTAAA
1 TGATTTCCAAGACCTCTGGGCAAAA-TCTTAAATCTTTGAA
* * *
13233973 TGATTTCTAAGACCTCTAGGTAAAATCTTAAATCTTTGAA
1 TGATTTCCAAGACCTCTGGGCAAAATCTTAAATCTTTGAA
* * *
13234013 TGATCTCCAAGACCTCTGGGCAAAATTTTAAA-CTTTTAAA
1 TGATTTCCAAGACCTCTGGGCAAAATCTTAAATC-TTTGAA
* * * * * ** *
13234053 AGATTTTCAAAGAACTCCGAGTGAAAT-TTGAAAAT-TTTAAA
1 TGA-TTTCCAAGACCTCTGGGCAAAATCTT--AAATCTTTGAA
* * * * *
13234094 GGATTTTCAAAGACTTCTAGGCAAAGTCTTAAATCTTTGAA
1 TGA-TTTCCAAGACCTCTGGGCAAAATCTTAAATCTTTGAA
* * * ** *
13234135 AGATCTCCAAGACATCTGGATAAAATTTTAAATCTTTGAA
1 TGATTTCCAAGACCTCTGGGCAAAATCTTAAATCTTTGAA
* ** * * * * * * *
13234175 AGATTTTTAAAGACCTTTAGACAAAATTTTTAGATGTTTAAA
1 TGA-TTTCCAAGACCTCTGGGCAAAA-TCTTAAATCTTTGAA
* **
13234217 TGATTTTCAAAGACCTCTAAGCAAAATCTTAAAT
1 TGA-TTTCCAAGACCTCTGGGCAAAATCTTAAAT
13234251 TACTAAAGGA
Statistics
Matches: 360, Mismatches: 101, Indels: 36
0.72 0.20 0.07
Matches are distributed among these distances:
39 11 0.03
40 189 0.52
41 122 0.34
42 38 0.11
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (40 bp):
TGATTTCCAAGACCTCTGGGCAAAATCTTAAATCTTTGAA
Found at i:13234140 original size:122 final size:120
Alignment explanation
Indices: 13233844--13234250 Score: 374
Period size: 122 Copynumber: 3.3 Consensus size: 120
13233834 AAAATCTCAT
** * **
13233844 ATTTTAAATGG-TTTCAAAAGACCTAAAGG-AAAATTCTTAAAACTTTGAATGATCTCTGAGACC
1 ATTTTAAA-GGATTTC-AAAGACCTCTAGGCAAAA-TCTTAAATCTTTGAATGATCTCCAAGACC
* ** * * * *
13233907 TCTAGGCAAAAGCTTAGATTTTTGAATGATTTTTAAA-ACCTCTGAGTAAAAGTTTAAA
63 TCTGGGCAAAATTTTA-AATTTTGAAAGATTTTTAAAGAACTCCGAGTAAAAGTTTAAA
* * * *
13233965 TTTTTAAATGATTTCTAAGACCTCTAGGTAAAATCTTAAATCTTTGAATGATCTCCAAGACCTCT
1 ATTTTAAAGGATTTCAAAGACCTCTAGGCAAAATCTTAAATCTTTGAATGATCTCCAAGACCTCT
* * *
13234030 GGGCAAAATTTTAAACTTTTAAAAGATTTTCAAAGAACTCCGAGTGAAA-TTTGAAA
66 GGGCAAAATTTTAAA-TTTTGAAAGATTTTTAAAGAACTCCGAGTAAAAGTTT-AAA
* * * *
13234086 ATTTTAAAGGATTTTCAAAGACTTCTAGGCAAAGTCTTAAATCTTTGAAAGATCTCCAAGACATC
1 ATTTTAAAGGA-TTTCAAAGACCTCTAGGCAAAATCTTAAATCTTTGAATGATCTCCAAGACCTC
** * ** * * * *
13234151 TGGATAAAATTTTAAATCTTTGAAAGATTTTTAAAGACCT-TTAGACAAAATTTTTAG
65 TGGGCAAAATTTTAAAT-TTTGAAAGATTTTTAAAGAACTCCGAG-TAAAAGTTTAAA
* *
13234208 ATGTTTAAATGATTTTCAAAGACCTCTAAGCAAAATCTTAAAT
1 AT-TTTAAAGGA-TTTCAAAGACCTCTAGGCAAAATCTTAAAT
13234251 TACTAAAGGA
Statistics
Matches: 235, Mismatches: 41, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
119 1 0.00
120 68 0.29
121 41 0.17
122 86 0.37
123 39 0.17
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (120 bp):
ATTTTAAAGGATTTCAAAGACCTCTAGGCAAAATCTTAAATCTTTGAATGATCTCCAAGACCTCT
GGGCAAAATTTTAAATTTTGAAAGATTTTTAAAGAACTCCGAGTAAAAGTTTAAA
Found at i:13234303 original size:40 final size:38
Alignment explanation
Indices: 13234162--13234303 Score: 106
Period size: 42 Copynumber: 3.5 Consensus size: 38
13234152 GGATAAAATT
* *
13234162 TTAAATCTTTGAAA-GATTTTTAAAGACCTTTAGACAAAATTT
1 TTAAAT-TTT-AAATGATTTTT-AAGACCTTTAGGCAAAA--C
* * * *
13234204 TTAGATGTTTAAATGATTTTCAAAGACCTCTAAGCAAAATC
1 TTAAAT-TTTAAATGATTTT-TAAGACCTTTAGGCAAAA-C
* *
13234245 TTAAATTACTAAAGGATTTTTAAGACCTTTAGGCAAAAC
1 TTAAATT-TTAAATGATTTTTAAGACCTTTAGGCAAAAC
13234284 TTCAAAATTTTAAATGATTT
1 TT--AAATTTTAAATGATTT
13234304 CCCAAAACCT
Statistics
Matches: 80, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
39 3 0.04
40 25 0.31
41 24 0.30
42 28 0.35
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (38 bp):
TTAAATTTTAAATGATTTTTAAGACCTTTAGGCAAAAC
Found at i:13234672 original size:22 final size:21
Alignment explanation
Indices: 13234647--13234701 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
13234637 TAAGTCTTTT
13234647 AAATATTCAAAACAA-AACAACA
1 AAATATT-AAAACAAGAACAA-A
*
13234669 AAAT-TTAAAAAAAGAACAAA
1 AAATATTAAAACAAGAACAAA
*
13234689 AAAAATTAAAACA
1 AAATATTAAAACA
13234702 TAAAAATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 10 0.36
21 14 0.50
22 4 0.14
ACGTcount: A:0.73, C:0.11, G:0.02, T:0.15
Consensus pattern (21 bp):
AAATATTAAAACAAGAACAAA
Found at i:13235010 original size:20 final size:21
Alignment explanation
Indices: 13234968--13235008 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
13234958 CTCATTGCAT
*
13234968 TAGCCTAAATAATACCCAAAA
1 TAGCCTAAATAAAACCCAAAA
13234989 TAGCCT-AATAAAAGCCCAAA
1 TAGCCTAAATAAAA-CCCAAA
13235009 TAATGGCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.51, C:0.24, G:0.07, T:0.17
Consensus pattern (21 bp):
TAGCCTAAATAAAACCCAAAA
Found at i:13235085 original size:22 final size:20
Alignment explanation
Indices: 13235035--13235087 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
13235025 CCACTAACTA
*
13235035 AAAAATTAAATAATATATAAT
1 AAAAA-TAAATAATAAATAAT
*
13235056 ATATAATAAATAAATAAATAAT
1 A-AAAATAAAT-AATAAATAAT
13235078 GAAAAATAAA
1 -AAAAATAAA
13235088 CAAGCTTAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 6 0.23
22 19 0.73
23 1 0.04
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (20 bp):
AAAAATAAATAATAAATAAT
Found at i:13236678 original size:21 final size:21
Alignment explanation
Indices: 13236653--13236714 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 21
13236643 GTTGGGGAAT
13236653 TAATAAATATTAAAATAAAAA
1 TAATAAATATTAAAATAAAAA
**
13236674 TAATAAAT-TTTTAATAAAAA
1 TAATAAATATTAAAATAAAAA
13236694 T-A-AAATATTTAAAATATAAAA
1 TAATAAATA-TTAAAATA-AAAA
13236715 ATTATTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 4 0.12
19 1 0.03
20 17 0.50
21 12 0.35
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
TAATAAATATTAAAATAAAAA
Found at i:13236704 original size:18 final size:20
Alignment explanation
Indices: 13236653--13236705 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
13236643 GTTGGGGAAT
*
13236653 TAATAAATATTAAAATAAAAA
1 TAATAAATATT-TAATAAAAA
*
13236674 TAATAAATTTTTAATAAAAA
1 TAATAAATATTTAATAAAAA
13236694 T-A-AAATATTTAA
1 TAATAAATATTTAA
13236706 AATATAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 9 0.31
19 1 0.03
20 9 0.31
21 10 0.34
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TAATAAATATTTAATAAAAA
Found at i:13236823 original size:13 final size:13
Alignment explanation
Indices: 13236805--13236852 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
13236795 TAAATTCCTA
*
13236805 AAATCCCAAAGTG
1 AAATCCTAAAGTG
**
13236818 AAATCCTAAAACG
1 AAATCCTAAAGTG
13236831 AAATCCTAAAGTG
1 AAATCCTAAAGTG
*
13236844 AAAACCTAA
1 AAATCCTAA
13236853 GCCTTAAAGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.52, C:0.21, G:0.10, T:0.17
Consensus pattern (13 bp):
AAATCCTAAAGTG
Found at i:13245170 original size:10 final size:10
Alignment explanation
Indices: 13245133--13245166 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
13245123 AGAAAAGATC
13245133 AAAACAAATA
1 AAAACAAATA
*
13245143 AAAGCAAATA
1 AAAACAAATA
*
13245153 AAAATAAATA
1 AAAACAAATA
13245163 AAAA
1 AAAA
13245167 TAAAAGTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.79, C:0.06, G:0.03, T:0.12
Consensus pattern (10 bp):
AAAACAAATA
Found at i:13245789 original size:27 final size:26
Alignment explanation
Indices: 13245759--13245876 Score: 86
Period size: 27 Copynumber: 4.6 Consensus size: 26
13245749 AGAGTGATTG
13245759 TATTGAAAAGAATTTAAAGAACAATTA
1 TATTGAAAA-AATTTAAAGAACAATTA
*
13245786 TATTG-AAAAATTTAGAA-AAAAACTTAA
1 TATTGAAAAAATTTA-AAGAACAA-TT-A
* * *** *
13245813 TCTTG--AAAA-TAAAAGAGTGATTG
1 TATTGAAAAAATTTAAAGAACAATTA
13245836 TATTGAAAAGAATTTAAAGAACAATTA
1 TATTGAAAA-AATTTAAAGAACAATTA
13245863 TATTG-AAAAATTTA
1 TATTGAAAAAATTTA
13245877 GAAAATAATT
Statistics
Matches: 70, Mismatches: 13, Indels: 18
0.69 0.13 0.18
Matches are distributed among these distances:
23 4 0.06
24 4 0.06
25 22 0.31
26 16 0.23
27 24 0.34
ACGTcount: A:0.53, C:0.03, G:0.12, T:0.31
Consensus pattern (26 bp):
TATTGAAAAAATTTAAAGAACAATTA
Found at i:13245811 original size:77 final size:77
Alignment explanation
Indices: 13245724--13245881 Score: 316
Period size: 77 Copynumber: 2.1 Consensus size: 77
13245714 GAAAGCTTAT
13245724 AAAAAAACTTAATCTTGAAAATAAAAGAGTGATTGTATTGAAAAGAATTTAAAGAACAATTATAT
1 AAAAAAACTTAATCTTGAAAATAAAAGAGTGATTGTATTGAAAAGAATTTAAAGAACAATTATAT
13245789 TGAAAAATTTAG
66 TGAAAAATTTAG
13245801 AAAAAAACTTAATCTTGAAAATAAAAGAGTGATTGTATTGAAAAGAATTTAAAGAACAATTATAT
1 AAAAAAACTTAATCTTGAAAATAAAAGAGTGATTGTATTGAAAAGAATTTAAAGAACAATTATAT
13245866 TGAAAAATTTAG
66 TGAAAAATTTAG
13245878 AAAA
1 AAAA
13245882 TAATTTTTAT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 81 1.00
ACGTcount: A:0.54, C:0.04, G:0.13, T:0.29
Consensus pattern (77 bp):
AAAAAAACTTAATCTTGAAAATAAAAGAGTGATTGTATTGAAAAGAATTTAAAGAACAATTATAT
TGAAAAATTTAG
Found at i:13250470 original size:21 final size:21
Alignment explanation
Indices: 13250428--13250473 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
13250418 AATGAGGAAT
*
13250428 TTTGGAAAATTTTTTATACAA
1 TTTGGAAAATTTTTGATACAA
* * *
13250449 TTTGGAAGATTTTTGGTGCAA
1 TTTGGAAAATTTTTGATACAA
13250470 TTTG
1 TTTG
13250474 TGCTAATGGC
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:0.28, C:0.04, G:0.20, T:0.48
Consensus pattern (21 bp):
TTTGGAAAATTTTTGATACAA
Found at i:13251063 original size:15 final size:15
Alignment explanation
Indices: 13251030--13251081 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
13251020 TAGCTTAGGA
**
13251030 TTTAAATTTTTTGTTC
1 TTTAAA-TTTTTGCAC
13251046 TTTAAATTTTTGCAC
1 TTTAAATTTTTGCAC
*
13251061 TTTACATTTTCTTGCAC
1 TTTA-AATTT-TTGCAC
13251078 TTTA
1 TTTA
13251082 CTTTCTTGCA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
15 11 0.35
16 10 0.32
17 10 0.32
ACGTcount: A:0.21, C:0.13, G:0.06, T:0.60
Consensus pattern (15 bp):
TTTAAATTTTTGCAC
Found at i:13251075 original size:17 final size:15
Alignment explanation
Indices: 13251055--13251091 Score: 56
Period size: 17 Copynumber: 2.3 Consensus size: 15
13251045 CTTTAAATTT
13251055 TTGCACTTTACATTTTC
1 TTGCACTTTAC--TTTC
13251072 TTGCACTTTACTTTC
1 TTGCACTTTACTTTC
13251087 TTGCA
1 TTGCA
13251092 TTTTCATACT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 9 0.45
17 11 0.55
ACGTcount: A:0.16, C:0.24, G:0.08, T:0.51
Consensus pattern (15 bp):
TTGCACTTTACTTTC
Found at i:13251086 original size:15 final size:16
Alignment explanation
Indices: 13251045--13251091 Score: 62
Period size: 15 Copynumber: 3.0 Consensus size: 16
13251035 ATTTTTTGTT
*
13251045 CTTTAAATTT-TTGCA
1 CTTTACATTTCTTGCA
13251060 CTTTACATTTTCTTGCA
1 CTTTACA-TTTCTTGCA
13251077 CTTTAC-TTTCTTGCA
1 CTTTACATTTCTTGCA
13251092 TTTTCATACT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 15 0.52
16 3 0.10
17 11 0.38
ACGTcount: A:0.19, C:0.21, G:0.06, T:0.53
Consensus pattern (16 bp):
CTTTACATTTCTTGCA
Found at i:13254219 original size:17 final size:18
Alignment explanation
Indices: 13254199--13254232 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
13254189 GGTATAGTTC
13254199 AGAAGG-GGATAAGAGTA
1 AGAAGGTGGATAAGAGTA
13254216 AGAAGGTGGATAAGAGT
1 AGAAGGTGGATAAGAGT
13254233 GTAGTTCCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.44, C:0.00, G:0.41, T:0.15
Consensus pattern (18 bp):
AGAAGGTGGATAAGAGTA
Found at i:13258119 original size:21 final size:22
Alignment explanation
Indices: 13258095--13258135 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
13258085 ATGAATTTTG
13258095 CAAATT-CTTATG-TTTCTTGCT
1 CAAATTCCTT-TGATTTCTTGCT
13258116 CAAATTCCTTTGATTTCTTG
1 CAAATTCCTTTGATTTCTTG
13258136 TTGATATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.20, C:0.20, G:0.10, T:0.51
Consensus pattern (22 bp):
CAAATTCCTTTGATTTCTTGCT
Found at i:13260284 original size:12 final size:12
Alignment explanation
Indices: 13260267--13260291 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13260257 TTTCGAGACT
13260267 AACCTTGTAATA
1 AACCTTGTAATA
13260279 AACCTTGTAATA
1 AACCTTGTAATA
13260291 A
1 A
13260292 TCCAGATGAT
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:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (12 bp):
AACCTTGTAATA
Found at i:13273593 original size:17 final size:17
Alignment explanation
Indices: 13273554--13273593 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
13273544 AAAAAAAAAC
*
13273554 ATAAATATAAAAATTAT
1 ATAAATATAAAAATAAT
13273571 ATAAATAATAAAAATAAT
1 ATAAAT-ATAAAAATAAT
13273589 A-AAAT
1 ATAAAT
13273594 TTGTAAGCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
ATAAATATAAAAATAAT
Found at i:13274134 original size:10 final size:11
Alignment explanation
Indices: 13274105--13274134 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
13274095 ATTTAGTAGC
13274105 AAAAAAAAGTA
1 AAAAAAAAGTA
13274116 AAAAAAAAG-A
1 AAAAAAAAGTA
13274126 AAAAAAAAG
1 AAAAAAAAG
13274135 CTGGAATGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (11 bp):
AAAAAAAAGTA
Found at i:13275964 original size:14 final size:14
Alignment explanation
Indices: 13275920--13275964 Score: 67
Period size: 13 Copynumber: 3.4 Consensus size: 14
13275910 ATAAAATCTA
*
13275920 AAACCCTAAAGTG-
1 AAACCCTAAAATGT
13275933 AAACCCTAAAAT-T
1 AAACCCTAAAATGT
13275946 AAACCCTAAAATGT
1 AAACCCTAAAATGT
13275960 AAACC
1 AAACC
13275965 AAAAACAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 23 0.79
14 6 0.21
ACGTcount: A:0.51, C:0.24, G:0.07, T:0.18
Consensus pattern (14 bp):
AAACCCTAAAATGT
Found at i:13276155 original size:16 final size:16
Alignment explanation
Indices: 13276134--13276167 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
13276124 ATAACTCTTT
13276134 AATTAAAAT-AATAATA
1 AATT-AAATCAATAATA
13276150 AATTAAATCAATAATA
1 AATTAAATCAATAATA
13276166 AA
1 AA
13276168 AAATGAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
AATTAAATCAATAATA
Found at i:13276930 original size:12 final size:13
Alignment explanation
Indices: 13276903--13276961 Score: 59
Period size: 14 Copynumber: 4.5 Consensus size: 13
13276893 TAGGGCCTTG
13276903 GGGTTTTACGATTTA
1 GGGTTTT-C-ATTTA
13276918 -GGTTTTCATTTA
1 GGGTTTTCATTTA
*
13276930 GGGTTTT-TTTTA
1 GGGTTTTCATTTA
*
13276942 GGGTTTACATTTTA
1 GGGTTTTCA-TTTA
13276956 GGGTTT
1 GGGTTT
13276962 AATTTTAAGG
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
12 15 0.39
13 7 0.18
14 16 0.42
ACGTcount: A:0.15, C:0.05, G:0.25, T:0.54
Consensus pattern (13 bp):
GGGTTTTCATTTA
Found at i:13276961 original size:26 final size:25
Alignment explanation
Indices: 13276914--13276981 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 25
13276904 GGTTTTACGA
*
13276914 TTTAGGTTTTCA-TTTAGGGTTT-TT
1 TTTAGG-TTTCATTTTAGGGTTTAAT
13276938 TTTAGGGTTTACATTTTAGGGTTTAAT
1 TTTA-GGTTT-CATTTTAGGGTTTAAT
13276965 TTTAAGGTTTCATTTTA
1 TTT-AGGTTTCATTTTA
13276982 AGGTCTCAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
24 7 0.18
25 4 0.11
26 17 0.45
27 9 0.24
28 1 0.03
ACGTcount: A:0.19, C:0.04, G:0.19, T:0.57
Consensus pattern (25 bp):
TTTAGGTTTCATTTTAGGGTTTAAT
Found at i:13276968 original size:13 final size:13
Alignment explanation
Indices: 13276926--13276981 Score: 69
Period size: 13 Copynumber: 4.3 Consensus size: 13
13276916 TAGGTTTTCA
*
13276926 TTTAGGGTTT-TT
1 TTTAGGGTTTAAT
13276938 TTTAGGGTTTACAT
1 TTTAGGGTTTA-AT
13276952 TTTAGGGTTTAAT
1 TTTAGGGTTTAAT
* *
13276965 TTTAAGGTTTCAT
1 TTTAGGGTTTAAT
13276978 TTTA
1 TTTA
13276982 AGGTCTCAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
12 10 0.26
13 17 0.44
14 12 0.31
ACGTcount: A:0.20, C:0.04, G:0.20, T:0.57
Consensus pattern (13 bp):
TTTAGGGTTTAAT
Found at i:13277245 original size:14 final size:13
Alignment explanation
Indices: 13277231--13277264 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
13277221 TTATTAATAT
13277231 TTATTTATCTTTA
1 TTATTTATCTTTA
*
13277244 TTATATTATTTTTA
1 TTAT-TTATCTTTA
13277258 TTATTTA
1 TTATTTA
13277265 ATAATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (13 bp):
TTATTTATCTTTA
Found at i:13280219 original size:62 final size:61
Alignment explanation
Indices: 13279993--13280219 Score: 208
Period size: 62 Copynumber: 3.7 Consensus size: 61
13279983 AAAAGGGAAC
* * * * *
13279993 GGATTATTGAAGGTGTTTTTGGCAAAAAATGCCTTCAATAATCTCATATA-AAAAATTGAAAG
1 GGATTATTCAAGGTGTTTTTGGC-AAAAACGCCTTCAATAATC-CATTTATAAAAATTCAAGG
** * ** * * * *
13280055 GGATTATTCAAGGCATTTTTGGCCAAAAATGAGTTCAATAATCCACTCATAAAGATTCAAGA
1 GGATTATTCAAGGTGTTTTTGG-CAAAAACGCCTTCAATAATCCATTTATAAAAATTCAAGG
* *
13280117 GGATTATTCAAGGTATTTTTCAGGCAAAAAC-CCTTCAATAATCCATTTATAAAAATTTAAGG
1 GGATTATTCAAGGTGTTTTT--GGCAAAAACGCCTTCAATAATCCATTTATAAAAATTCAAGG
* *
13280179 GGATTATTCAAGGTGTTTTCT-GCTAGAAACGCCTTTAATAA
1 GGATTATTCAAGGTGTTTT-TGGC-AAAAACGCCTTCAATAA
13280220 CCCCCTTCAA
Statistics
Matches: 134, Mismatches: 24, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
60 2 0.01
61 8 0.06
62 114 0.85
63 8 0.06
64 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (61 bp):
GGATTATTCAAGGTGTTTTTGGCAAAAACGCCTTCAATAATCCATTTATAAAAATTCAAGG
Found at i:13282522 original size:19 final size:19
Alignment explanation
Indices: 13282498--13282539 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
13282488 TTACATACTA
13282498 TTTAGATTATATAAAATTG
1 TTTAGATTATATAAAATTG
*
13282517 TTTAGATTATATATAATTG
1 TTTAGATTATATAAAATTG
13282536 TTTA
1 TTTA
13282540 TTGTTTGGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (19 bp):
TTTAGATTATATAAAATTG
Found at i:13287550 original size:22 final size:24
Alignment explanation
Indices: 13287525--13287570 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
13287515 AATATTATGC
13287525 AATTACATTT-TTTA-ATG-AATTT
1 AATTAC-TTTCTTTATATGTAATTT
13287547 AATTACTTTCTTTATATGTAATTT
1 AATTACTTTCTTTATATGTAATTT
13287571 TTCTATGTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 3 0.14
22 10 0.48
23 3 0.14
24 5 0.24
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.57
Consensus pattern (24 bp):
AATTACTTTCTTTATATGTAATTT
Found at i:13290704 original size:52 final size:53
Alignment explanation
Indices: 13290594--13290714 Score: 151
Period size: 52 Copynumber: 2.3 Consensus size: 53
13290584 TTAATTATTA
*
13290594 GTATAGGTAAGAAAATAAAAAATACAATTTTATACTGACAGTCTCTAACTATCG
1 GTATAGGTAAGAAAATAAAAAATACAA-TTTATACTGACAGTCGCTAACTATCG
13290648 GTATAGGTAAGAAAATGAAAAAATACAA-TT-TACTGACAGAT-GCTAAGC-ATCG
1 GTATAGGTAAGAAAAT-AAAAAATACAATTTATACTGACAG-TCGCTAA-CTATCG
**
13290700 GTATACATAAGAAAA
1 GTATAGGTAAGAAAA
13290715 ATTATAAGTC
Statistics
Matches: 61, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
52 30 0.49
53 4 0.07
54 16 0.26
55 11 0.18
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.26
Consensus pattern (53 bp):
GTATAGGTAAGAAAATAAAAAATACAATTTATACTGACAGTCGCTAACTATCG
Found at i:13290964 original size:180 final size:180
Alignment explanation
Indices: 13290662--13291025 Score: 728
Period size: 180 Copynumber: 2.0 Consensus size: 180
13290652 AGGTAAGAAA
13290662 ATGAAAAAATACAATTTACTGACAGATGCTAAGCATCGGTATACATAAGAAAAATTATAAGTCAT
1 ATGAAAAAATACAATTTACTGACAGATGCTAAGCATCGGTATACATAAGAAAAATTATAAGTCAT
13290727 ACTGATAGGCGTTAACCATCAGCATTGGTAAGAAAAATTAAAACATATAATTCTATACTGACAGA
66 ACTGATAGGCGTTAACCATCAGCATTGGTAAGAAAAATTAAAACATATAATTCTATACTGACAGA
13290792 TGCTAGCCATTGGGATAAGTAAGAAAATTAAAACATACAAATCTATACTG
131 TGCTAGCCATTGGGATAAGTAAGAAAATTAAAACATACAAATCTATACTG
13290842 ATGAAAAAATACAATTTACTGACAGATGCTAAGCATCGGTATACATAAGAAAAATTATAAGTCAT
1 ATGAAAAAATACAATTTACTGACAGATGCTAAGCATCGGTATACATAAGAAAAATTATAAGTCAT
13290907 ACTGATAGGCGTTAACCATCAGCATTGGTAAGAAAAATTAAAACATATAATTCTATACTGACAGA
66 ACTGATAGGCGTTAACCATCAGCATTGGTAAGAAAAATTAAAACATATAATTCTATACTGACAGA
13290972 TGCTAGCCATTGGGATAAGTAAGAAAATTAAAACATACAAATCTATACTG
131 TGCTAGCCATTGGGATAAGTAAGAAAATTAAAACATACAAATCTATACTG
13291022 ATGA
1 ATGA
13291026 GCTTTAAACA
Statistics
Matches: 184, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
180 184 1.00
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (180 bp):
ATGAAAAAATACAATTTACTGACAGATGCTAAGCATCGGTATACATAAGAAAAATTATAAGTCAT
ACTGATAGGCGTTAACCATCAGCATTGGTAAGAAAAATTAAAACATATAATTCTATACTGACAGA
TGCTAGCCATTGGGATAAGTAAGAAAATTAAAACATACAAATCTATACTG
Found at i:13291049 original size:55 final size:55
Alignment explanation
Indices: 13290933--13291053 Score: 129
Period size: 55 Copynumber: 2.2 Consensus size: 55
13290923 CATCAGCATT
* * ** *
13290933 GGTAAGAAAAATTAAAACATATAATTCTATACTGACAGATGCTAGCCATTGGGATA
1 GGTAAG-AAAATTAAAACATACAAATCTATACTGACAGATGCTAAACATTAGGATA
* * *
13290989 AGTAAGAAAATTAAAACATACAAATCTATACTGA-TGA-GCTTTAAACATTAGTATA
1 GGTAAGAAAATTAAAACATACAAATCTATACTGACAGATGC--TAAACATTAGGATA
13291044 GGTAAGAAAA
1 GGTAAGAAAA
13291054 AATTACAAGT
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
53 2 0.04
54 2 0.04
55 45 0.83
56 5 0.09
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.26
Consensus pattern (55 bp):
GGTAAGAAAATTAAAACATACAAATCTATACTGACAGATGCTAAACATTAGGATA
Found at i:13292002 original size:20 final size:20
Alignment explanation
Indices: 13291964--13292002 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
13291954 CATTTCTAGA
*
13291964 TTTTTTTTGTTGCTCTTCCC
1 TTTTTTTTGTTACTCTTCCC
* *
13291984 TTTTTTTTTTTACTTTTCC
1 TTTTTTTTGTTACTCTTCC
13292003 TTCCTCATAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.03, C:0.21, G:0.05, T:0.72
Consensus pattern (20 bp):
TTTTTTTTGTTACTCTTCCC
Found at i:13292408 original size:11 final size:11
Alignment explanation
Indices: 13292383--13292420 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
13292373 TTACAAATTT
13292383 TATTATTT-T-
1 TATTATTTATA
13292392 TATTATTTATA
1 TATTATTTATA
13292403 TATTATTTATA
1 TATTATTTATA
13292414 T-TTATTT
1 TATTATTT
13292421 TGTTCATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 8 0.30
10 7 0.26
11 12 0.44
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TATTATTTATA
Found at i:13292417 original size:17 final size:16
Alignment explanation
Indices: 13292381--13292419 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
13292371 TCTTACAAAT
13292381 TTTATTATTTTTATTA
1 TTTATTATTTTTATTA
13292397 TTTATATATTATTTA-TA
1 TTTAT-TATT-TTTATTA
13292414 TTTATT
1 TTTATT
13292420 TTGTTCATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 6 0.29
17 11 0.52
18 4 0.19
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTATTATTTTTATTA
Found at i:13292662 original size:18 final size:18
Alignment explanation
Indices: 13292619--13292654 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
13292609 TTTGAGGCCT
13292619 AATAAAAAAATAAACCTA
1 AATAAAAAAATAAACCTA
*
13292637 AATTAAAAAGATAAACCT
1 AA-TAAAAAAATAAACCT
13292655 GGATAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 2 0.12
19 14 0.88
ACGTcount: A:0.67, C:0.11, G:0.03, T:0.19
Consensus pattern (18 bp):
AATAAAAAAATAAACCTA
Found at i:13293410 original size:35 final size:35
Alignment explanation
Indices: 13293363--13293491 Score: 102
Period size: 35 Copynumber: 3.7 Consensus size: 35
13293353 ATTGAACTGT
*
13293363 AAGTC-AGAAAATAAAGATAACCGAGACT-AAGCCAC
1 AAGTCAAG-AAATAAAGATAACCAAGACTGAA-CCAC
* * *
13293398 AAGTCAAGAAATAAAGAATAATCAAGATTGAATCAC
1 AAGTCAAGAAATAAAG-ATAACCAAGACTGAACCAC
* * * * ** *
13293434 AAGTCAAGAAATAAAGATGATCAAAATTGAGTCGC
1 AAGTCAAGAAATAAAGATAACCAAGACTGAACCAC
13293469 AAGTCAAGAAATAAA-AGTAACCA
1 AAGTCAAGAAATAAAGA-TAACCA
13293492 GGGAAAATTT
Statistics
Matches: 80, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
34 1 0.01
35 47 0.59
36 30 0.38
37 2 0.03
ACGTcount: A:0.53, C:0.14, G:0.16, T:0.16
Consensus pattern (35 bp):
AAGTCAAGAAATAAAGATAACCAAGACTGAACCAC
Found at i:13294478 original size:10 final size:10
Alignment explanation
Indices: 13294465--13294497 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
13294455 TTTGTTTTTC
13294465 TTTTTTTCCT
1 TTTTTTTCCT
*
13294475 TTTTTTT-AT
1 TTTTTTTCCT
13294484 TTTTTTTCCT
1 TTTTTTTCCT
13294494 TTTT
1 TTTT
13294498 CTTTAAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTTCCT
Found at i:13294480 original size:18 final size:18
Alignment explanation
Indices: 13294436--13294497 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 18
13294426 TTTTTCTTTA
* **
13294436 TTTTCTTTCTCTTTTTTGT
1 TTTTTTTTCT-TTTTTTCC
13294455 TTTGTTTTTCTTTTTTTCC
1 TTT-TTTTTCTTTTTTTCC
*
13294474 TTTTTTTTATTTTTTTTCC
1 TTTTTTTT-CTTTTTTTCC
13294493 TTTTT
1 TTTTT
13294498 CTTTAAATGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 5 0.14
19 26 0.70
20 6 0.16
ACGTcount: A:0.02, C:0.13, G:0.03, T:0.82
Consensus pattern (18 bp):
TTTTTTTTCTTTTTTTCC
Found at i:13294490 original size:19 final size:20
Alignment explanation
Indices: 13294465--13294502 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
13294455 TTTGTTTTTC
13294465 TTTTTTTCCTTTTT-TTTAT
1 TTTTTTTCCTTTTTCTTTAT
13294484 TTTTTTTCCTTTTTCTTTA
1 TTTTTTTCCTTTTTCTTTA
13294503 AATGAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTTTTTCCTTTTTCTTTAT
Found at i:13301800 original size:3 final size:3
Alignment explanation
Indices: 13301794--13301849 Score: 58
Period size: 3 Copynumber: 18.7 Consensus size: 3
13301784 TTTTTTATTA
* * * * * *
13301794 TTG TTG TTG TTG TTG TTA TTA TTA TTA TTA TTG TTG TTA TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
13301842 TTG TTG TT
1 TTG TTG TT
13301850 TTATTAATTT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.11, C:0.00, G:0.21, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:13304937 original size:23 final size:25
Alignment explanation
Indices: 13304911--13304957 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
13304901 AAACCAAAAT
*
13304911 AAAGCCTA-TTTGA-AGCCCATAAG
1 AAAGCCTACTTTAAGAGCCCATAAG
13304934 AAAGCCTACTTTAAGAGCCCATAA
1 AAAGCCTACTTTAAGAGCCCATAA
13304958 AATTCATCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.38
24 4 0.19
25 9 0.43
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.21
Consensus pattern (25 bp):
AAAGCCTACTTTAAGAGCCCATAAG
Found at i:13305597 original size:143 final size:143
Alignment explanation
Indices: 13305368--13305697 Score: 411
Period size: 143 Copynumber: 2.3 Consensus size: 143
13305358 GTTTTTTTTT
* * * *
13305368 CATG-AACTTTTTAGATCTCAATTTCATAATATTTCATGATTTTTATTGCATTTGAAATCATAAT
1 CATGAAACTTTTTAGATCTCAATTTTATAATATTTCATGATTTTTAGTGCATTTGAAACCACAAT
** * *
13305432 AATACCTCAAGAGTGTTCAATTACCAAAATACCC-TTAAGAGGTATTTTCATAATTTT-GCCTTT
66 AATACCTCAAGAGTGTGAAATTACCAAAATACCCTTTAAG-GATATTTTCAT-ATTTTGGCCTTC
***
13305495 TTGAACTTGGATTTC
129 TTGAACTCAAATTTC
*
13305510 CATGAAACTTTGTAGATCTCAATTTTATAATATTTCATGATTTTTAGTGCA-TTGAAACCACAAT
1 CATGAAACTTTTTAGATCTCAATTTTATAATATTTCATGATTTTTAGTGCATTTGAAACCACAAT
* **
13305574 AGTATCCT-AAGAGGTGTGAAATTACCAAAATACCCTTTAAGGATATTTTTGTATTTTGGCCTTC
66 AATA-CCTCAAGA-GTGTGAAATTACCAAAATACCCTTTAAGGATATTTTCATATTTTGGCCTTC
* *
13305638 TTGAGCTCAAATTTT
129 TTGAACTCAAATTTC
*
13305653 CATGAAACTTTTTAGATC-CTAATTTTATAATAATTCATGATTTTT
1 CATGAAACTTTTTAGATCTC-AATTTTATAATATTTCATGATTTTT
13305698 GGTACTTTAA
Statistics
Matches: 163, Mismatches: 19, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
142 28 0.17
143 130 0.80
144 5 0.03
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.42
Consensus pattern (143 bp):
CATGAAACTTTTTAGATCTCAATTTTATAATATTTCATGATTTTTAGTGCATTTGAAACCACAAT
AATACCTCAAGAGTGTGAAATTACCAAAATACCCTTTAAGGATATTTTCATATTTTGGCCTTCTT
GAACTCAAATTTC
Found at i:13306901 original size:3 final size:3
Alignment explanation
Indices: 13306893--13306948 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
13306883 AGATTTAGGC
13306893 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
13306941 ATA ATA AT
1 ATA ATA AT
13306949 GATTTTAAAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:13310400 original size:19 final size:20
Alignment explanation
Indices: 13310376--13310413 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
13310366 TCCATGAATT
13310376 TTGCA-TAACTTTTATGTCC
1 TTGCATTAACTTTTATGTCC
*
13310395 TTGCATTACCTTTTATGTC
1 TTGCATTAACTTTTATGTC
13310414 ATTAAGGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.18, C:0.21, G:0.11, T:0.50
Consensus pattern (20 bp):
TTGCATTAACTTTTATGTCC
Done.