Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168270.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_5, 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: 27802247
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 124000 characters in sequence are not A, C, G, or T
File 105 of 147
Found at i:19290331 original size:3 final size:3
Alignment explanation
Indices: 19290323--19290354 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
19290313 TTGAAATTAA
19290323 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
19290355 AAAAGAAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:19291260 original size:26 final size:26
Alignment explanation
Indices: 19291228--19291287 Score: 102
Period size: 26 Copynumber: 2.3 Consensus size: 26
19291218 TCCAAAAATA
* *
19291228 TTTAATTTCAATTCCATTTCCAAGCT
1 TTTAATTTCAATTCCACTTCCAAACT
19291254 TTTAATTTCAATTCCACTTCCAAACT
1 TTTAATTTCAATTCCACTTCCAAACT
19291280 TTTAATTT
1 TTTAATTT
19291288 GGCATCTCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.28, C:0.22, G:0.02, T:0.48
Consensus pattern (26 bp):
TTTAATTTCAATTCCACTTCCAAACT
Found at i:19299321 original size:15 final size:15
Alignment explanation
Indices: 19299280--19299326 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
19299270 GAATTCACAT
19299280 ATATATAAAAATTAA
1 ATATATAAAAATTAA
19299295 A-A-ATAAAAATTAA
1 ATATATAAAAATTAA
*
19299308 ATATATATAAATTAA
1 ATATATAAAAATTAA
19299323 ATAT
1 ATAT
19299327 GAAATCATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 12 0.41
14 2 0.07
15 15 0.52
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
ATATATAAAAATTAA
Found at i:19299323 original size:22 final size:22
Alignment explanation
Indices: 19299292--19299351 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
19299282 ATATAAAAAT
*
19299292 TAAAAATAAAAATTAAAT-ATA
1 TAAAAATAAAAATGAAATCATA
* *
19299313 TATAAATTAAATATGAAATCATA
1 TA-AAAATAAAAATGAAATCATA
19299336 TAAAAATAAAAATGAA
1 TAAAAATAAAAATGAA
19299352 GTTTAATAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
21 2 0.06
22 25 0.78
23 5 0.16
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (22 bp):
TAAAAATAAAAATGAAATCATA
Found at i:19299857 original size:20 final size:22
Alignment explanation
Indices: 19299832--19299872 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
19299822 TTGTTTTAAA
*
19299832 AGAAAAA-GAGAT-ATATTTTT
1 AGAAAAACAAGATAATATTTTT
19299852 AGAAAAACAAGATAATATTTT
1 AGAAAAACAAGATAATATTTT
19299873 AAGTAAACGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 4 0.22
22 7 0.39
ACGTcount: A:0.54, C:0.02, G:0.12, T:0.32
Consensus pattern (22 bp):
AGAAAAACAAGATAATATTTTT
Found at i:19303892 original size:3 final size:3
Alignment explanation
Indices: 19303886--19303914 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
19303876 AGAATTATTA
19303886 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
19303915 AATTTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:19304390 original size:26 final size:25
Alignment explanation
Indices: 19304356--19304406 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
19304346 CCTATTTTAA
* *
19304356 AATAATAAATTAAATAAAGAATAAAT
1 AATAATAAAATAAA-AAAGAAAAAAT
19304382 AATAATAAAATAAAAAAGAAAAAAT
1 AATAATAAAATAAAAAAGAAAAAAT
19304407 CAAATTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.22
Consensus pattern (25 bp):
AATAATAAAATAAAAAAGAAAAAAT
Found at i:19305718 original size:6 final size:6
Alignment explanation
Indices: 19305696--19305796 Score: 66
Period size: 6 Copynumber: 16.7 Consensus size: 6
19305686 TTTCATCTTG
* *
19305696 TTTTCTA TTTTGA -TTTTA TTTTT- TTTTCTA -TTTTA TTTTCA -TTTTA
1 TTTT-TA TTTTTA TTTTTA TTTTTA TTTT-TA TTTTTA TTTTTA TTTTTA
* * * * *
19305742 TTTTTGA TTTTTA TTTTTA CTTATTA TTATTA TTTTCA TCTTTAA TTATTA
1 TTTTT-A TTTTTA TTTTTA -TTTTTA TTTTTA TTTTTA T-TTTTA TTTTTA
19305793 TTTT
1 TTTT
19305797 ACTCAGTACT
Statistics
Matches: 75, Mismatches: 11, Indels: 17
0.73 0.11 0.17
Matches are distributed among these distances:
5 14 0.19
6 41 0.55
7 20 0.27
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.73
Consensus pattern (6 bp):
TTTTTA
Found at i:19305722 original size:23 final size:24
Alignment explanation
Indices: 19305696--19305746 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 24
19305686 TTTCATCTTG
19305696 TTTTCTATTTTGATTTT-ATTTT-T
1 TTTTCTATTTT-ATTTTCATTTTAT
19305719 TTTTCTATTTTATTTTCATTTTAT
1 TTTTCTATTTTATTTTCATTTTAT
19305743 TTTT
1 TTTT
19305747 GATTTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 5 0.19
23 16 0.62
24 5 0.19
ACGTcount: A:0.14, C:0.06, G:0.02, T:0.78
Consensus pattern (24 bp):
TTTTCTATTTTATTTTCATTTTAT
Found at i:19305759 original size:19 final size:18
Alignment explanation
Indices: 19305696--19305796 Score: 66
Period size: 19 Copynumber: 5.6 Consensus size: 18
19305686 TTTCATCTTG
*
19305696 TTTTCTATTTTGA-TTTTA
1 TTTT-TATTTTTATTTTTA
19305714 TTTTT-TTTTCTA-TTTTA
1 TTTTTATTTT-TATTTTTA
*
19305731 TTTTCA-TTTTATTTTTGA
1 TTTTTATTTTTATTTTT-A
*
19305749 TTTTTATTTTTACTTATTA
1 TTTTTATTTTTA-TTTTTA
* * *
19305768 TTATTATTTTCATCTTTAA
1 TTTTTATTTTTAT-TTTTA
*
19305787 TTATTATTTT
1 TTTTTATTTT
19305797 ACTCAGTACT
Statistics
Matches: 68, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
16 6 0.09
17 18 0.26
18 11 0.16
19 29 0.43
20 4 0.06
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.73
Consensus pattern (18 bp):
TTTTTATTTTTATTTTTA
Found at i:19305768 original size:13 final size:12
Alignment explanation
Indices: 19305709--19305796 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
19305699 TCTATTTTGA
*
19305709 TTTTATT-TTTT
1 TTTTATTATTAT
19305720 TTTCTATT-TTAT
1 TTT-TATTATTAT
*
19305732 TTTCATT-TTAT
1 TTTTATTATTAT
*
19305743 TTTTGATTTTTAT
1 TTTT-ATTATTAT
19305756 TTTTACTTATTAT
1 TTTTA-TTATTAT
*
19305769 TATTATT-TTCAT
1 TTTTATTATT-AT
*
19305781 CTTTAATTATTAT
1 -TTTTATTATTAT
19305794 TTT
1 TTT
19305797 ACTCAGTACT
Statistics
Matches: 63, Mismatches: 7, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
11 15 0.24
12 21 0.33
13 25 0.40
14 2 0.03
ACGTcount: A:0.19, C:0.06, G:0.01, T:0.74
Consensus pattern (12 bp):
TTTTATTATTAT
Found at i:19305776 original size:25 final size:25
Alignment explanation
Indices: 19305726--19305794 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 25
19305716 TTTTTTTCTA
* *
19305726 TTTTATTTTCATT-TTATTTTTGAT
1 TTTTATTTTTATTATTATTATTGAT
19305750 TTTTATTTTTACTTATTATTATT-AT
1 TTTTATTTTTA-TTATTATTATTGAT
* *
19305775 TTTCATCTTTAATTATTATT
1 TTTTAT-TTTTATTATTATT
19305795 TTACTCAGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
24 10 0.26
25 17 0.45
26 11 0.29
ACGTcount: A:0.22, C:0.06, G:0.01, T:0.71
Consensus pattern (25 bp):
TTTTATTTTTATTATTATTATTGAT
Found at i:19309737 original size:11 final size:10
Alignment explanation
Indices: 19309704--19309736 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
19309694 AATAATGATG
*
19309704 AAAGAAATAA
1 AAAGAAAAAA
19309714 AAAGAAAAAA
1 AAAGAAAAAA
19309724 AAAGAAAAAA
1 AAAGAAAAAA
19309734 AAA
1 AAA
19309737 ATGAAGGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.88, C:0.00, G:0.09, T:0.03
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:19311122 original size:44 final size:44
Alignment explanation
Indices: 19311072--19311209 Score: 127
Period size: 45 Copynumber: 3.1 Consensus size: 44
19311062 CAAATAAGAT
* ***
19311072 TTTTTAAATTTTGATGAGAAACCCCAAAATTTTTTGAATGCGCA
1 TTTTTAAATTTTGATGTGAAACCCCAAAATTTTTTGAATGAAAA
* *
19311116 TTTTTAAAATTTCGAATGTG-AATCCCAAAA-TTTTTGAATGAAAA
1 TTTTT-AAATTTTG-ATGTGAAACCCCAAAATTTTTTGAATGAAAA
* * * * **
19311160 TCTTTAAGTTTTAGATGTGAGACCCTAAAATTTTTTGAACAAAAA
1 TTTTTAAATTTT-GATGTGAAACCCCAAAATTTTTTGAATGAAAA
19311205 TTTTT
1 TTTTT
19311210 GAACCTCAAA
Statistics
Matches: 74, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
43 10 0.14
44 28 0.38
45 32 0.43
46 4 0.05
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.41
Consensus pattern (44 bp):
TTTTTAAATTTTGATGTGAAACCCCAAAATTTTTTGAATGAAAA
Found at i:19311342 original size:19 final size:19
Alignment explanation
Indices: 19311314--19311360 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
19311304 AACCTAAATC
*
19311314 TCTTATGAATCTTTGAAGT
1 TCTTACGAATCTTTGAAGT
*
19311333 TCTTACGAATCTTTGAATT
1 TCTTACGAATCTTTGAAGT
*
19311352 TCTTGCGAA
1 TCTTACGAA
19311361 CCTAAATTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.45
Consensus pattern (19 bp):
TCTTACGAATCTTTGAAGT
Found at i:19311370 original size:17 final size:17
Alignment explanation
Indices: 19311348--19311383 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
19311338 CGAATCTTTG
*
19311348 AATTTCTTGCGAACCTA
1 AATTTCTTGCGAAACTA
19311365 AATTTCTTGCGAAACTA
1 AATTTCTTGCGAAACTA
19311382 AA
1 AA
19311384 GCTCTTAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.33
Consensus pattern (17 bp):
AATTTCTTGCGAAACTA
Found at i:19311407 original size:53 final size:53
Alignment explanation
Indices: 19311283--19311462 Score: 184
Period size: 53 Copynumber: 3.4 Consensus size: 53
19311273 CTTTTCAATG
** * * * * *
19311283 CGAATCTTTGAATTT-TTGGTGAACCTAAATCTCTTATGAATCTTTGAAGTTCTTA
1 CGAATCTTTGAATTTCTT-GCAAACCTAAATTTCTTACGAAAC--TAAAGCTCTTA
* *
19311338 CGAATCTTTGAATTTCTTGCGAACCTAAATTTCTTGCGAAACTAAAGCTCTTA
1 CGAATCTTTGAATTTCTTGCAAACCTAAATTTCTTACGAAACTAAAGCTCTTA
* * * *
19311391 AGAATCTTT-AAGTTTCTTACAAACCTGAATTTCTTATGAAACTAAAGCTCTTA
1 CGAATCTTTGAA-TTTCTTGCAAACCTAAATTTCTTACGAAACTAAAGCTCTTA
*
19311444 CGAATATTTGAATTTCTTG
1 CGAATCTTTGAATTTCTTG
19311463 TGAATATTTG
Statistics
Matches: 106, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
52 2 0.02
53 66 0.62
54 2 0.02
55 34 0.32
56 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.40
Consensus pattern (53 bp):
CGAATCTTTGAATTTCTTGCAAACCTAAATTTCTTACGAAACTAAAGCTCTTA
Found at i:19311456 original size:36 final size:36
Alignment explanation
Indices: 19311418--19311533 Score: 112
Period size: 36 Copynumber: 3.2 Consensus size: 36
19311408 TACAAACCTG
* *
19311418 AATTTCTTATGAAACTAAAGCTCTTACGAATATTTG
1 AATTTCTTATGAAACTAAAGCTCTTATGAATATTTA
* * * **
19311454 AATTTCTTGTGAATATTTGAA-CTTCTTATG-A-ATCCA
1 AATTTCTTATGAA-A-CTAAAGC-TCTTATGAATATTTA
*
19311490 AATTTCTTATGAAACTAAAGCTCTTATGAATTTTTA
1 AATTTCTTATGAAACTAAAGCTCTTATGAATATTTA
19311526 AATTTCTT
1 AATTTCTT
19311534 GTAAACTTGA
Statistics
Matches: 61, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
34 10 0.16
35 3 0.05
36 36 0.59
37 3 0.05
38 9 0.15
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.44
Consensus pattern (36 bp):
AATTTCTTATGAAACTAAAGCTCTTATGAATATTTA
Found at i:19311467 original size:19 final size:19
Alignment explanation
Indices: 19311445--19311758 Score: 166
Period size: 19 Copynumber: 17.2 Consensus size: 19
19311435 AAGCTCTTAC
19311445 GAATATTTGAATTTCTTGT
1 GAATATTTGAATTTCTTGT
* *
19311464 GAATATTTGAACTTCTTAT
1 GAATATTTGAATTTCTTGT
*** *
19311483 G-A-ATCCAAATTTCTTAT
1 GAATATTTGAATTTCTTGT
* * ** *
19311500 GAA-A-CTAAAGCTCTTAT
1 GAATATTTGAATTTCTTGT
* *
19311517 GAATTTTTAAATTTCTTGT
1 GAATATTTGAATTTCTTGT
* *
19311536 -AA-ACTTGAATTTCTTAT
1 GAATATTTGAATTTCTTGT
* *
19311553 GAA-A-TTGAAGTTCTTGC
1 GAATATTTGAATTTCTTGT
* *
19311570 GAATTTTTGAAGTTCTTGT
1 GAATATTTGAATTTCTTGT
* * *
19311589 GAATCTTTGAAGTTCTTGC
1 GAATATTTGAATTTCTTGT
*
19311608 GAATTTTTGAATTTCTTGT
1 GAATATTTGAATTTCTTGT
*
19311627 GAATCTTTGAATTTCTTGT
1 GAATATTTGAATTTCTTGT
** * *
19311646 G-A-ACCTAAATTTCTTAT
1 GAATATTTGAATTTCTTGT
* * *
19311663 GAA-A-CTGAAGTTCTTGC
1 GAATATTTGAATTTCTTGT
* * *
19311680 AAATCTTTGAAGTTCTTGT
1 GAATATTTGAATTTCTTGT
* * *
19311699 GAATCTTTGAAGTTCTTGC
1 GAATATTTGAATTTCTTGT
* * *
19311718 AAATTTTTGAATTTCTTAT
1 GAATATTTGAATTTCTTGT
* *
19311737 GAATCTTTGAATTTCTTAT
1 GAATATTTGAATTTCTTGT
19311756 GAA
1 GAA
19311759 CCTAAATATC
Statistics
Matches: 235, Mismatches: 51, Indels: 18
0.77 0.17 0.06
Matches are distributed among these distances:
17 71 0.30
18 11 0.05
19 153 0.65
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.46
Consensus pattern (19 bp):
GAATATTTGAATTTCTTGT
Found at i:19311498 original size:72 final size:70
Alignment explanation
Indices: 19311418--19311555 Score: 213
Period size: 72 Copynumber: 1.9 Consensus size: 70
19311408 TACAAACCTG
* *
19311418 AATTTCTTATGAAACTAAAGCTCTTACGAATATTTGAATTTCTTGTGAATATTTGAACTTCTTAT
1 AATTTCTTATGAAACTAAAGCTCTTACGAATATTTAAATTTCTTGT-AA-ACTTGAACTTCTTAT
19311483 GAATCCA
64 GAATCCA
* * *
19311490 AATTTCTTATGAAACTAAAGCTCTTATGAATTTTTAAATTTCTTGTAAACTTGAATTTCTTATGA
1 AATTTCTTATGAAACTAAAGCTCTTACGAATATTTAAATTTCTTGTAAACTTGAACTTCTTATGA
19311555 A
66 A
19311556 ATTGAAGTTC
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
70 16 0.26
71 2 0.03
72 43 0.70
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.43
Consensus pattern (70 bp):
AATTTCTTATGAAACTAAAGCTCTTACGAATATTTAAATTTCTTGTAAACTTGAACTTCTTATGA
ATCCA
Found at i:19311513 original size:125 final size:125
Alignment explanation
Indices: 19311302--19311610 Score: 368
Period size: 125 Copynumber: 2.5 Consensus size: 125
19311292 GAATTTTTGG
* * * * ** * *
19311302 TGAACCTAAATCTCTTATGAATCTTTGAAGTTCTTACGAATCTTTGAATTTCTTGCGAACCTAAA
1 TGAAACTAAAGCTCTTACGAATATTTGAAGTTCTTGTGAATCTTTGAACTTCTTACGAACCTAAA
* *
19311367 TTTCTTGCGAAACTAAAGCTCTTAAGAATCTTTAAGTTTCTTACAAACCTGAATTTCTTA
66 TTTCTTACGAAACTAAAGCTCTTAAGAATCTTTAAATTTCTTACAAACCTGAATTTCTTA
* * *
19311427 TGAAACTAAAGCTCTTACGAATATTTGAATTTCTTGTGAATATTTGAACTTCTTATGAATCC-AA
1 TGAAACTAAAGCTCTTACGAATATTTGAAGTTCTTGTGAATCTTTGAACTTCTTACGAA-CCTAA
* * * ** *
19311491 ATTTCTTATGAAACTAAAGCTCTTATGAATTTTTAAATTTCTTGTAAACTTGAATTTCTTA
65 ATTTCTTACGAAACTAAAGCTCTTAAGAATCTTTAAATTTCTTACAAACCTGAATTTCTTA
* * * * * * *
19311552 TGAAATTGAAGTTCTTGCGAATTTTTGAAGTTCTTGTGAATCTTTGAAGTTCTTGCGAA
1 TGAAACTAAAGCTCTTACGAATATTTGAAGTTCTTGTGAATCTTTGAACTTCTTACGAA
19311611 TTTTTGAATT
Statistics
Matches: 154, Mismatches: 29, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
125 152 0.99
126 2 0.01
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (125 bp):
TGAAACTAAAGCTCTTACGAATATTTGAAGTTCTTGTGAATCTTTGAACTTCTTACGAACCTAAA
TTTCTTACGAAACTAAAGCTCTTAAGAATCTTTAAATTTCTTACAAACCTGAATTTCTTA
Found at i:19311604 original size:38 final size:38
Alignment explanation
Indices: 19311540--19311753 Score: 242
Period size: 38 Copynumber: 5.8 Consensus size: 38
19311530 TCTTGTAAAC
* *
19311540 TTGAATTTCTTATGAA--ATTGAAGTTCTTGCGAATTT
1 TTGAATTTCTTGTGAATCTTTGAAGTTCTTGCGAATTT
*
19311576 TTGAAGTTCTTGTGAATCTTTGAAGTTCTTGCGAATTT
1 TTGAATTTCTTGTGAATCTTTGAAGTTCTTGCGAATTT
* * *
19311614 TTGAATTTCTTGTGAATCTTTGAATTTCTTGTGAA--C
1 TTGAATTTCTTGTGAATCTTTGAAGTTCTTGCGAATTT
* * * * * *
19311650 CTAAATTTCTTATGAAAC--TGAAGTTCTTGCAAATCT
1 TTGAATTTCTTGTGAATCTTTGAAGTTCTTGCGAATTT
* *
19311686 TTGAAGTTCTTGTGAATCTTTGAAGTTCTTGCAAATTT
1 TTGAATTTCTTGTGAATCTTTGAAGTTCTTGCGAATTT
* *
19311724 TTGAATTTCTTATGAATCTTTGAATTTCTT
1 TTGAATTTCTTGTGAATCTTTGAAGTTCTT
19311754 ATGAACCTAA
Statistics
Matches: 148, Mismatches: 24, Indels: 10
0.81 0.13 0.05
Matches are distributed among these distances:
34 12 0.08
36 41 0.28
38 95 0.64
ACGTcount: A:0.25, C:0.11, G:0.16, T:0.48
Consensus pattern (38 bp):
TTGAATTTCTTGTGAATCTTTGAAGTTCTTGCGAATTT
Found at i:19311784 original size:91 final size:91
Alignment explanation
Indices: 19311450--19311800 Score: 240
Period size: 91 Copynumber: 3.9 Consensus size: 91
19311440 CTTACGAATA
* * * *
19311450 TTTGAATTTCTTGTGAATATTTGAACTTCTTATGAATCC--AAATTTCTTATGAAAC-TAAAGCT
1 TTTGAATTTCTTATGAA-CTTTGAATTTCTTATGAATCCTGAAA-TTCTTATGAAACTTAAAGTT
** * *
19311512 CTTATGAATTTTTAAATTTCTTGTAAA-
64 CTTGCGAATCTTTGAATTTCTTGTAAAT
* * * ** ** * * * *
19311539 CTTGAATTTCTTATGAA-ATTGAAGTTCTTGCGAATTTTTGAAGTTCTTGTGAATCTTTGAAGTT
1 TTTGAATTTCTTATGAACTTTGAATTTCTTATGAA-TCCTGAAATTCTTATGAAAC-TTAAAGTT
* *
19311603 CTTGCGAATTTTTGAATTTCTTGTGAAT
64 CTTGCGAATCTTTGAATTTCTTGTAAAT
* * * * * *
19311631 CTTTGAATTTCTTGTGAAC-CTAAATTTCTTATGAA-ACTGAAGTTC-T-TGCAAATCTTTGAAG
1 -TTTGAATTTCTTATGAACTTTGAATTTCTTATGAATCCTGAAATTCTTATG-AAA-C-TTAAAG
* * *
19311692 TTCTTGTGAATCTTTGAAGTTCTTGCAAATT
62 TTCTTGCGAATCTTTGAATTTCTTGTAAA-T
19311723 TTTGAATTTCTTATGAATCTTTGAATTTCTTATGAA-CCT-AAATATCTTATGAAAC-TAAAGTT
1 TTTGAATTTCTTATGAA-CTTTGAATTTCTTATGAATCCTGAAAT-TCTTATGAAACTTAAAGTT
*
19311785 CTTGCAAATCTTTGAA
64 CTTGCGAATCTTTGAA
19311801 ATTTTTACAA
Statistics
Matches: 206, Mismatches: 40, Indels: 30
0.75 0.14 0.11
Matches are distributed among these distances:
87 13 0.06
88 1 0.00
89 27 0.13
90 5 0.02
91 104 0.50
92 5 0.02
93 45 0.22
94 4 0.02
95 2 0.01
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (91 bp):
TTTGAATTTCTTATGAACTTTGAATTTCTTATGAATCCTGAAATTCTTATGAAACTTAAAGTTCT
TGCGAATCTTTGAATTTCTTGTAAAT
Found at i:19311787 original size:17 final size:16
Alignment explanation
Indices: 19311749--19311787 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
19311739 ATCTTTGAAT
*
19311749 TTCTTATGAACCTAAA
1 TTCTTATGAAACTAAA
19311765 TATCTTATGAAACTAAA
1 T-TCTTATGAAACTAAA
19311782 GTTCTT
1 -TTCTT
19311788 GCAAATCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 18 0.90
18 1 0.05
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (16 bp):
TTCTTATGAAACTAAA
Found at i:19311817 original size:110 final size:110
Alignment explanation
Indices: 19311511--19311800 Score: 463
Period size: 110 Copynumber: 2.6 Consensus size: 110
19311501 AAACTAAAGC
* * * * * * * *
19311511 TCTTATGAATTTTTAAATTTCTTGTAAACTTGAATTTCTTATGAAATTGAAGTTCTTGCGAATTT
1 TCTTATGAATCTTTGAATTTCTTGTGAACCTAAATTTCTTATGAAACTGAAGTTCTTGCAAATCT
*
19311576 TTGAAGTTCTTGTGAATCTTTGAAGTTCTTGCGAATTTTTGAATT
66 TTGAAGTTCTTGTGAATCTTTGAAGTTCTTGCAAATTTTTGAATT
*
19311621 TCTTGTGAATCTTTGAATTTCTTGTGAACCTAAATTTCTTATGAAACTGAAGTTCTTGCAAATCT
1 TCTTATGAATCTTTGAATTTCTTGTGAACCTAAATTTCTTATGAAACTGAAGTTCTTGCAAATCT
19311686 TTGAAGTTCTTGTGAATCTTTGAAGTTCTTGCAAATTTTTGAATT
66 TTGAAGTTCTTGTGAATCTTTGAAGTTCTTGCAAATTTTTGAATT
* * *
19311731 TCTTATGAATCTTTGAATTTCTTATGAACCTAAATATCTTATGAAACTAAAGTTCTTGCAAATCT
1 TCTTATGAATCTTTGAATTTCTTGTGAACCTAAATTTCTTATGAAACTGAAGTTCTTGCAAATCT
19311796 TTGAA
66 TTGAA
19311801 ATTTTTACAA
Statistics
Matches: 166, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
110 166 1.00
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.46
Consensus pattern (110 bp):
TCTTATGAATCTTTGAATTTCTTGTGAACCTAAATTTCTTATGAAACTGAAGTTCTTGCAAATCT
TTGAAGTTCTTGTGAATCTTTGAAGTTCTTGCAAATTTTTGAATT
Found at i:19313070 original size:15 final size:15
Alignment explanation
Indices: 19313046--19313075 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19313036 TGAAACACTT
*
19313046 CCACTTAAATTGAAC
1 CCACTCAAATTGAAC
19313061 CCACTCAAATTGAAC
1 CCACTCAAATTGAAC
19313076 ATTATGTGAA
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:0.40, C:0.30, G:0.07, T:0.23
Consensus pattern (15 bp):
CCACTCAAATTGAAC
Found at i:19319207 original size:12 final size:12
Alignment explanation
Indices: 19319190--19319215 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
19319180 AGGGTCATGA
19319190 TATTGATATGTT
1 TATTGATATGTT
19319202 TATTGATATGTT
1 TATTGATATGTT
19319214 TA
1 TA
19319216 AACACATTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (12 bp):
TATTGATATGTT
Found at i:19322900 original size:17 final size:17
Alignment explanation
Indices: 19322856--19322909 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
19322846 ATTGTTTAAT
19322856 TTTCTATTTTTAGCAAC
1 TTTCTATTTTTAGCAAC
* *
19322873 TTTTTATTTTTAGTAA-
1 TTTCTATTTTTAGCAAC
19322889 TTTCTATATTTT-GCAAGC
1 TTTCTAT-TTTTAGCAA-C
19322907 TTT
1 TTT
19322910 AGTTAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
16 9 0.30
17 18 0.60
18 3 0.10
ACGTcount: A:0.22, C:0.11, G:0.07, T:0.59
Consensus pattern (17 bp):
TTTCTATTTTTAGCAAC
Found at i:19328393 original size:45 final size:45
Alignment explanation
Indices: 19328340--19328437 Score: 126
Period size: 45 Copynumber: 2.2 Consensus size: 45
19328330 GGCCAATATG
* * *
19328340 TGCCAATGGTGATCAAGGTAAGTGCCTA-TACCAAAGGCCAGCTTA
1 TGCCAATGGTGATCAAGGTAAATG-CTAGTACCAAAGACCAACTTA
* * *
19328385 TGCCAATGGTGGTCGAGGTAAATGCTAGTACCAAAGACTAACTTA
1 TGCCAATGGTGATCAAGGTAAATGCTAGTACCAAAGACCAACTTA
19328430 TGCCAATG
1 TGCCAATG
19328438 ATGGTTGAGG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 3 0.07
45 43 0.93
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.23
Consensus pattern (45 bp):
TGCCAATGGTGATCAAGGTAAATGCTAGTACCAAAGACCAACTTA
Found at i:19334819 original size:21 final size:21
Alignment explanation
Indices: 19334775--19334819 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
19334765 GCCCCAGATG
* * *
19334775 GACCAAGCCTTGGTGCAAGTA
1 GACCAAGCCATAGTGCAAGCA
*
19334796 GACCAAGCCATAGTGTAAGCA
1 GACCAAGCCATAGTGCAAGCA
19334817 GAC
1 GAC
19334820 TAGGCCTAGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.24, G:0.27, T:0.16
Consensus pattern (21 bp):
GACCAAGCCATAGTGCAAGCA
Found at i:19337476 original size:144 final size:143
Alignment explanation
Indices: 19337127--19337520 Score: 490
Period size: 144 Copynumber: 2.7 Consensus size: 143
19337117 GGGAATTACA
* * * * * * * *
19337127 AAATTACTAAAATGCCT-TTTAGGAGTATCTTTGTAATTTAGACTTCCTGAGTTCAGATTTTCAT
1 AAATTACTAAAATACCTCTTAAGG-GTATTTTTGTAATTTGGCCTTCCTAAGCTCGGATTTTCAT
* * * *
19337191 GAAACTTTTCAGATCTTAATTTCAAAATA-TTCATGATTTTTTGTGCATTTGAAATCACAACAAT
65 GAAACTTTTCAAATCTTAATTTCATAATATTTCATGATTTTTGGTGCATTTAAAATCACAACAAT
19337255 ACCTAAAAAGTGTG
130 ACCTAAAAAGTGTG
* * ** *
19337269 AAATTA-TCAAAATACCCCTTAAAGGTATTTTCATAATTTGGCCTTTCC-AAGCTTGGAATTTTC
1 AAATTACT-AAAATACCTCTTAAGGGTATTTTTGTAATTTGGCC-TTCCTAAGCTCGG-ATTTTC
* **
19337332 ATGAAACTTTTCAAATCTTAATTTCATAATATTTCATGATTTTTGGTGCATTTAAAATCATAGTA
63 ATGAAACTTTTCAAATCTTAATTTCATAATATTTCATGATTTTTGGTGCATTTAAAATCACAACA
* *
19337397 GTACCTCAAAAGGTGTG
128 ATACCT-AAAAAGTGTG
* *
19337414 AAGTTACTAAAATACCTCTTCAGGGTATTTTTGTAATTTGGCCTTCCTAAGCTCGGATTTTCATG
1 AAATTACTAAAATACCTCTTAAGGGTATTTTTGTAATTTGGCCTTCCTAAGCTCGGATTTTCATG
*
19337479 AAACTTTTCAAATCTTAATTTTATAATATTTCATGATTTTTG
66 AAACTTTTCAAATCTTAATTTCATAATATTTCATGATTTTTG
19337521 ATATTTTAAA
Statistics
Matches: 214, Mismatches: 30, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
141 1 0.00
142 31 0.14
143 43 0.20
144 87 0.41
145 51 0.24
146 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (143 bp):
AAATTACTAAAATACCTCTTAAGGGTATTTTTGTAATTTGGCCTTCCTAAGCTCGGATTTTCATG
AAACTTTTCAAATCTTAATTTCATAATATTTCATGATTTTTGGTGCATTTAAAATCACAACAATA
CCTAAAAAGTGTG
Found at i:19338075 original size:3 final size:3
Alignment explanation
Indices: 19338063--19338092 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
19338053 TTTATTTTTC
19338063 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
19338093 AAGATGTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:19347966 original size:17 final size:17
Alignment explanation
Indices: 19347944--19347985 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
19347934 GACTCCCCTC
*
19347944 AAATCACCTATAAACCA
1 AAATCACCTAAAAACCA
19347961 AAATCATCC-AAAAACCA
1 AAATCA-CCTAAAAACCA
19347978 AAA-CACCT
1 AAATCACCT
19347986 CATTTTCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
15 2 0.09
16 2 0.09
17 16 0.73
18 2 0.09
ACGTcount: A:0.55, C:0.31, G:0.00, T:0.14
Consensus pattern (17 bp):
AAATCACCTAAAAACCA
Found at i:19348265 original size:7 final size:7
Alignment explanation
Indices: 19348253--19348288 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
19348243 GGTGGGTTTT
19348253 GATGATG
1 GATGATG
19348260 GATGATG
1 GATGATG
19348267 GATGATG
1 GATGATG
19348274 GATGATG
1 GATGATG
19348281 GATGATG
1 GATGATG
19348288 G
1 G
19348289 CGTTGGTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.44, T:0.28
Consensus pattern (7 bp):
GATGATG
Found at i:19348892 original size:21 final size:21
Alignment explanation
Indices: 19348868--19348908 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
19348858 TTTATTTTTT
* *
19348868 ATATTTAAATTCGATTTGATA
1 ATATATAAATTAGATTTGATA
*
19348889 ATATATAAATTATATTTGAT
1 ATATATAAATTAGATTTGAT
19348909 TTAATTTGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (21 bp):
ATATATAAATTAGATTTGATA
Found at i:19348957 original size:14 final size:14
Alignment explanation
Indices: 19348940--19348978 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
19348930 ATTATTTTTA
19348940 AAATATAAATATTT
1 AAATATAAATATTT
19348954 AAATATATAAT-TTT
1 AAATATA-AATATTT
*
19348968 ATATATAAATA
1 AAATATAAATA
19348979 AATAATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 3 0.14
14 16 0.73
15 3 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AAATATAAATATTT
Found at i:19348971 original size:20 final size:20
Alignment explanation
Indices: 19348948--19348985 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
19348938 TAAAATATAA
* *
19348948 ATATTTAAATATATAATTTT
1 ATATATAAATAAATAATTTT
19348968 ATATATAAATAAATAATT
1 ATATATAAATAAATAATT
19348986 AAAAAATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATATATAAATAAATAATTTT
Found at i:19349438 original size:22 final size:21
Alignment explanation
Indices: 19349397--19349438 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 21
19349387 AATTGTCTAT
*
19349397 TTTGATCTCTCTCTTTTTTTC
1 TTTGATCTCTCTCTTGTTTTC
19349418 TTTG-TCTCTCTCAATTGTTTT
1 TTTGATCTCTCTC--TTGTTTT
19349439 TAGCAAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 8 0.44
21 4 0.22
22 6 0.33
ACGTcount: A:0.07, C:0.21, G:0.07, T:0.64
Consensus pattern (21 bp):
TTTGATCTCTCTCTTGTTTTC
Found at i:19350028 original size:2 final size:2
Alignment explanation
Indices: 19350015--19350050 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
19350005 ATACGTTCAA
*
19350015 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19350051 TAGCAAATGA
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):
AT
Found at i:19350396 original size:23 final size:25
Alignment explanation
Indices: 19350361--19350407 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
19350351 CAATCATTGA
*
19350361 ATAATCAATTAAT-AAAT-TACAAC
1 ATAATCAAATAATCAAATCTACAAC
*
19350384 ATAATTAAATAATCAAATCTACAA
1 ATAATCAAATAATCAAATCTACAA
19350408 ATATTGAGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 11 0.55
24 4 0.20
25 5 0.25
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (25 bp):
ATAATCAAATAATCAAATCTACAAC
Found at i:19356454 original size:2 final size:2
Alignment explanation
Indices: 19356443--19356475 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
19356433 AGTATTCACT
*
19356443 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19356476 AAACTGTCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19357792 original size:5 final size:5
Alignment explanation
Indices: 19357782--19357811 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
19357772 TAAAAGACAA
19357782 ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT
19357812 TAAAATATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:19357893 original size:15 final size:16
Alignment explanation
Indices: 19357873--19357906 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
19357863 TTAATTTAAA
19357873 AATATAAAA-AATTAT
1 AATATAAAATAATTAT
19357888 AATATAAAATAATTAT
1 AATATAAAATAATTAT
19357904 AAT
1 AAT
19357907 TTTAAGATGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AATATAAAATAATTAT
Found at i:19359433 original size:22 final size:22
Alignment explanation
Indices: 19359408--19359450 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
19359398 ATGATAGAAT
19359408 ATGGATGCAATTGAAGGCACAC
1 ATGGATGCAATTGAAGGCACAC
19359430 ATGGATGCAATTGAAGGCACA
1 ATGGATGCAATTGAAGGCACA
19359451 TTTCTTGCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.16, G:0.28, T:0.19
Consensus pattern (22 bp):
ATGGATGCAATTGAAGGCACAC
Found at i:19359950 original size:30 final size:30
Alignment explanation
Indices: 19359914--19359973 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
19359904 AAAACTGTTA
19359914 AATATAAATTTTAAAAATAATTACATAAAT
1 AATATAAATTTTAAAAATAATTACATAAAT
*
19359944 AATATAATTTTTAAAAATAATTACATAAAT
1 AATATAAATTTTAAAAATAATTACATAAAT
19359974 CAACTCATCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (30 bp):
AATATAAATTTTAAAAATAATTACATAAAT
Found at i:19363539 original size:25 final size:25
Alignment explanation
Indices: 19363511--19363560 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
19363501 TTAAAGCAAC
19363511 AAAGATTTTCATATTCTAAAGACTA
1 AAAGATTTTCATATTCTAAAGACTA
19363536 AAAGATTTTCATATTCTAAAGACTA
1 AAAGATTTTCATATTCTAAAGACTA
19363561 CATAATGAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.36
Consensus pattern (25 bp):
AAAGATTTTCATATTCTAAAGACTA
Found at i:19365299 original size:5 final size:6
Alignment explanation
Indices: 19365281--19365306 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
19365271 AATTCTTTAT
19365281 AATAAA AATAAA AATAAA AATAAA AA
1 AATAAA AATAAA AATAAA AATAAA AA
19365307 ACAAATTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AATAAA
Found at i:19365621 original size:21 final size:21
Alignment explanation
Indices: 19365597--19365641 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
19365587 TCATACTTAA
*
19365597 AATTGTCAAATATT-AAATTTT
1 AATTATCAAA-ATTAAAATTTT
*
19365618 AATTATTAAAATTAAAATTTT
1 AATTATCAAAATTAAAATTTT
19365639 AAT
1 AAT
19365642 ATTTTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (21 bp):
AATTATCAAAATTAAAATTTT
Found at i:19365656 original size:21 final size:20
Alignment explanation
Indices: 19365605--19365661 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
19365595 AAAATTGTCA
19365605 AATATTAAATTTTAATTATT
1 AATATTAAATTTTAATTATT
* *
19365625 AAAATTAAAATTTTAATATTTT
1 AATATT-AAATTTTAAT-TATT
*
19365647 ATTATTAAATTTTAA
1 AATATTAAATTTTAA
19365662 CGTATCGATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 5 0.16
21 19 0.61
22 7 0.23
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AATATTAAATTTTAATTATT
Found at i:19368401 original size:22 final size:22
Alignment explanation
Indices: 19368371--19368420 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
19368361 AAATTACATA
*
19368371 AAAAGACATTATGGTTTGGGTC
1 AAAACACATTATGGTTTGGGTC
*
19368393 AAAACACATTGTGGTTTGGGTC
1 AAAACACATTATGGTTTGGGTC
19368415 AAAACA
1 AAAACA
19368421 AATCTACCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (22 bp):
AAAACACATTATGGTTTGGGTC
Found at i:19368542 original size:21 final size:21
Alignment explanation
Indices: 19368518--19368557 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
19368508 GCAGCTTTTT
*
19368518 TTTTCATTTTATTTTTTCTCG
1 TTTTCATTTTATTTCTTCTCG
*
19368539 TTTTCTTTTTATTTCTTCT
1 TTTTCATTTTATTTCTTCT
19368558 TTAGCTTCCA
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:0.07, C:0.15, G:0.03, T:0.75
Consensus pattern (21 bp):
TTTTCATTTTATTTCTTCTCG
Found at i:19369056 original size:102 final size:102
Alignment explanation
Indices: 19368876--19369176 Score: 416
Period size: 99 Copynumber: 3.0 Consensus size: 102
19368866 ATTGGGATTA
* * * *
19368876 CCTTATTTTTCAAAATAGGATTGAGTCAGATTGGTT-TTTAGGTTTCAATGCGACTTGGGTCTTA
1 CCTTGTTTTTCAAAATAGGACTGAGTCAGATTGGTTGTTAAGGTTTCAATGTGACTTGGGTCTTA
*
19368940 AGTTTGGTTGTTATGGAAGGTCATTTTGAGGAAATTG
66 AGTTTAGTTGTTATGGAAGGTCATTTTGAGGAAATTG
* * *
19368977 CCTTGTTTTTCAAAATAGAACTAAGTTAGATTGGTTGTTAAGGTTTCAATGTGACTTGGGTCTTA
1 CCTTGTTTTTCAAAATAGGACTGAGTCAGATTGGTTGTTAAGGTTTCAATGTGACTTGGGTCTTA
** *
19369042 AGTTTAGTTGTTAT-G--GGTC-TTAAGATTGG-GATTG
66 AGTTTAGTTGTTATGGAAGGTCATTTTGA--GGAAATTG
*
19369076 CCTTGTTTTTCACAATAGGACTGAGTCAGATTGGTTGTTAAGGTTTCAATGTGACTTGGGTCTTA
1 CCTTGTTTTTCAAAATAGGACTGAGTCAGATTGGTTGTTAAGGTTTCAATGTGACTTGGGTCTTA
* *
19369141 AGTTTTGTTGTTATGAAAGGTCATTTTGAGGAAATT
66 AGTTTAGTTGTTATGGAAGGTCATTTTGAGGAAATT
19369177 ACTTTGATTT
Statistics
Matches: 172, Mismatches: 20, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
98 4 0.02
99 82 0.48
100 2 0.01
101 34 0.20
102 46 0.27
103 4 0.02
ACGTcount: A:0.24, C:0.09, G:0.25, T:0.42
Consensus pattern (102 bp):
CCTTGTTTTTCAAAATAGGACTGAGTCAGATTGGTTGTTAAGGTTTCAATGTGACTTGGGTCTTA
AGTTTAGTTGTTATGGAAGGTCATTTTGAGGAAATTG
Found at i:19371226 original size:24 final size:24
Alignment explanation
Indices: 19371199--19371248 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
19371189 AAAAACTATA
*
19371199 TAAATTTTGCATTCTTAATAAATT
1 TAAATTTTACATTCTTAATAAATT
* * *
19371223 TAAATTTTATATTTTTAATGAATT
1 TAAATTTTACATTCTTAATAAATT
19371247 TA
1 TA
19371249 TTTACATATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (24 bp):
TAAATTTTACATTCTTAATAAATT
Found at i:19371971 original size:16 final size:16
Alignment explanation
Indices: 19371950--19372012 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
19371940 GTTATTCACT
19371950 TGTCACATGTTATAAA
1 TGTCACATGTTATAAA
* * *
19371966 TGTCACTTTTTTTTAACA
1 TGTCAC-ATGTTATAA-A
* *
19371984 TGTCACTTGTTATGAA
1 TGTCACATGTTATAAA
19372000 TGTCACATGTTAT
1 TGTCACATGTTAT
19372013 TCATGAATCA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
16 19 0.50
17 12 0.32
18 7 0.18
ACGTcount: A:0.27, C:0.14, G:0.13, T:0.46
Consensus pattern (16 bp):
TGTCACATGTTATAAA
Found at i:19372670 original size:20 final size:19
Alignment explanation
Indices: 19372623--19372662 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 19
19372613 ATTATCATTT
19372623 AAAAATAATCCTAAATAATA
1 AAAAAT-ATCCTAAATAATA
19372643 AATAAATATCCTAAGATAAT
1 AA-AAATATCCTAA-ATAAT
19372663 CCAAAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.60, C:0.10, G:0.03, T:0.28
Consensus pattern (19 bp):
AAAAATATCCTAAATAATA
Found at i:19374840 original size:27 final size:27
Alignment explanation
Indices: 19374809--19374860 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
19374799 TGTATGAATA
* *
19374809 TATGCAATAAGCATTAAGCACTTATGT
1 TATGCAACAAGCAATAAGCACTTATGT
* *
19374836 TATGCAACAGGCAATAAGCATTTAT
1 TATGCAACAAGCAATAAGCACTTAT
19374861 ATCTATGTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (27 bp):
TATGCAACAAGCAATAAGCACTTATGT
Found at i:19378078 original size:42 final size:42
Alignment explanation
Indices: 19377993--19378080 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 42
19377983 CACTTAATAA
* * * *
19377993 ATAATCTTAAATGATAAATAATAAATAACTAAATATCCCAAG
1 ATAATCTTAAATAATAAACAATAAATAACAAAAAATCCCAAG
*
19378035 ATAATCTTAAATAATAGATACAAT-AATAA-AAAAAATCCTAAG
1 ATAATCTTAAATAATA-A-ACAATAAATAACAAAAAATCCCAAG
19378077 ATAA
1 ATAA
19378081 AATACTAAGA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
42 29 0.74
43 6 0.15
44 4 0.10
ACGTcount: A:0.58, C:0.10, G:0.05, T:0.27
Consensus pattern (42 bp):
ATAATCTTAAATAATAAACAATAAATAACAAAAAATCCCAAG
Found at i:19387539 original size:27 final size:27
Alignment explanation
Indices: 19387509--19387562 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
19387499 TATCGGTGGT
19387509 GCTTTTGAAAGAACAACATAATCTAGA
1 GCTTTTGAAAGAACAACATAATCTAGA
19387536 GCTTTTGAAAGAACAACATAATCTAGA
1 GCTTTTGAAAGAACAACATAATCTAGA
19387563 AAAGCCATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (27 bp):
GCTTTTGAAAGAACAACATAATCTAGA
Found at i:19391577 original size:20 final size:21
Alignment explanation
Indices: 19391547--19391585 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
19391537 CAATGTTTGA
19391547 AAATCCCATCTCTCAAAAAAC
1 AAATCCCATCTCTCAAAAAAC
*
19391568 AAAT-CCATCTTTCAAAAA
1 AAATCCCATCTCTCAAAAA
19391586 GGATGATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.49, C:0.28, G:0.00, T:0.23
Consensus pattern (21 bp):
AAATCCCATCTCTCAAAAAAC
Found at i:19394204 original size:22 final size:22
Alignment explanation
Indices: 19394178--19394222 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
19394168 GTTCTATCAG
19394178 ACCTTTGTTGAGCAATTCTAAA
1 ACCTTTGTTGAGCAATTCTAAA
19394200 ACCTTTGTTGAGCAATTCTAAA
1 ACCTTTGTTGAGCAATTCTAAA
19394222 A
1 A
19394223 TTTGTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (22 bp):
ACCTTTGTTGAGCAATTCTAAA
Found at i:19398963 original size:33 final size:32
Alignment explanation
Indices: 19398884--19398963 Score: 92
Period size: 33 Copynumber: 2.5 Consensus size: 32
19398874 TTTTTATAAA
* *
19398884 ATAAAAA-TAATAATTTTATATTAAAATCTAT
1 ATAAAAATTAAAAATTTTATATTAAAATATAT
*
19398915 TTAAATACATT-AAAATTTTATATTAAAATAATAT
1 ATAAA-A-ATTAAAAATTTTATATTAAAAT-ATAT
19398949 ATAAAAATTAAAAAT
1 ATAAAAATTAAAAAT
19398964 CGATAAATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
31 4 0.10
32 4 0.10
33 24 0.60
34 8 0.20
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (32 bp):
ATAAAAATTAAAAATTTTATATTAAAATATAT
Found at i:19399954 original size:33 final size:33
Alignment explanation
Indices: 19399894--19399959 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
19399884 TACCAAACCA
* * *
19399894 AGCTGAAGAAAATACATGAAGAGTGACACTGTT
1 AGCTGAAGAAAATACATGAAAAATGACAATGTT
*
19399927 AGCTGAAGAAAATGCATGAAAAATGACAATGTT
1 AGCTGAAGAAAATACATGAAAAATGACAATGTT
19399960 GGCAGTGTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.45, C:0.11, G:0.23, T:0.21
Consensus pattern (33 bp):
AGCTGAAGAAAATACATGAAAAATGACAATGTT
Found at i:19400179 original size:11 final size:11
Alignment explanation
Indices: 19400163--19400188 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
19400153 GGCTAAAATG
19400163 TTTTCTTTTCT
1 TTTTCTTTTCT
19400174 TTTTCTTTTCT
1 TTTTCTTTTCT
19400185 TTTT
1 TTTT
19400189 TTTGTACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTCTTTTCT
Found at i:19400657 original size:3 final size:3
Alignment explanation
Indices: 19400649--19400683 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
19400639 GGAAAAAGAA
*
19400649 AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
19400684 AAGAAGACAA
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:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:19401601 original size:29 final size:30
Alignment explanation
Indices: 19401539--19401611 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
19401529 CATCAATATT
**
19401539 TTTAAATTATAACAAAATATTTAATATGACA
1 TTTAAATTATAA-AAAATATTTAATACAACA
* *
19401570 TTTAAATT-TAAAAAATTTTTAATACAATA
1 TTTAAATTATAAAAAATATTTAATACAACA
*
19401599 TTTGAATTATAAA
1 TTTAAATTATAAA
19401612 TCTATTAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 21 0.58
30 7 0.19
31 8 0.22
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (30 bp):
TTTAAATTATAAAAAATATTTAATACAACA
Found at i:19403749 original size:16 final size:16
Alignment explanation
Indices: 19403724--19403763 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
19403714 ATCTTTAAAA
*
19403724 ATCATTATAAACCATC
1 ATCATCATAAACCATC
*
19403740 ATCATCATAAATCATC
1 ATCATCATAAACCATC
*
19403756 ATTATCAT
1 ATCATCAT
19403764 TTGTTTATAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (16 bp):
ATCATCATAAACCATC
Found at i:19403884 original size:23 final size:24
Alignment explanation
Indices: 19403858--19403907 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
19403848 TTATAACCCG
*
19403858 CTAACTAGGG-CTAATGCTAACTA
1 CTAACTAGGGCCTAATACTAACTA
*
19403881 CTAACTAGGGCCTAATACTAATTA
1 CTAACTAGGGCCTAATACTAACTA
19403905 CTA
1 CTA
19403908 TAACTTGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (24 bp):
CTAACTAGGGCCTAATACTAACTA
Found at i:19405590 original size:59 final size:60
Alignment explanation
Indices: 19405468--19405615 Score: 160
Period size: 60 Copynumber: 2.5 Consensus size: 60
19405458 GCTTAGATGA
* *
19405468 AAAATTACCTTCATAAAAGCTTAGTTTGACAAATTGCTTTTATAAAGGGTCAACTTGGCT
1 AAAATTACCTTCATAAAAGCTTAGCTCGACAAATTGCTTTTATAAAGGGTCAACTTGGCT
* * * *
19405528 AAAA-TACCTTCATAAAGGCTTAGCTCGACCAAATTG-TTTTCATATAGGTTC-AGTTCGG-T
1 AAAATTACCTTCATAAAAGCTTAGCTCGA-CAAATTGCTTTT-ATAAAGGGTCAACTT-GGCT
* * *
19405587 AAAATTCCCTTCAAAAAAGCTCAGCTCGA
1 AAAATTACCTTCATAAAAGCTTAGCTCGA
19405616 TAAAATTACC
Statistics
Matches: 74, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
59 33 0.45
60 41 0.55
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (60 bp):
AAAATTACCTTCATAAAAGCTTAGCTCGACAAATTGCTTTTATAAAGGGTCAACTTGGCT
Found at i:19405620 original size:30 final size:30
Alignment explanation
Indices: 19405577--19405637 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
19405567 TCATATAGGT
* * * *
19405577 TCAGTTCGGTAAAATTCCCTTCAAAAAAGC
1 TCAGCTCGATAAAATTACCTGCAAAAAAGC
*
19405607 TCAGCTCGATAAAATTACCTGCAAAATAGC
1 TCAGCTCGATAAAATTACCTGCAAAAAAGC
19405637 T
1 T
19405638 TAACTCAGCC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (30 bp):
TCAGCTCGATAAAATTACCTGCAAAAAAGC
Found at i:19405855 original size:60 final size:60
Alignment explanation
Indices: 19405768--19405890 Score: 165
Period size: 60 Copynumber: 2.0 Consensus size: 60
19405758 CAGCTCGATA
* * * *
19405768 AAATTACCTTCAAAAGTGCTTAACTCGATCAAATTACTTTTATAAAGGCTCAGCTTAGCC
1 AAATTACCTTAAAAAATGCTTAACTCGATCAAATTACCTTCATAAAGGCTCAGCTTAGCC
* * * * *
19405828 AAATTACCTTAAAAAATGTTTATCTCGATGAAATTTCCTTCATAAAGGCTTAGCTTAGCC
1 AAATTACCTTAAAAAATGCTTAACTCGATCAAATTACCTTCATAAAGGCTCAGCTTAGCC
19405888 AAA
1 AAA
19405891 ATGCTTTCAT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.33
Consensus pattern (60 bp):
AAATTACCTTAAAAAATGCTTAACTCGATCAAATTACCTTCATAAAGGCTCAGCTTAGCC
Found at i:19405902 original size:30 final size:30
Alignment explanation
Indices: 19405866--19405932 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
19405856 TGAAATTTCC
* *
19405866 TTCATAAAGGCTTAGCTTAGCCAAAA-TGCT
1 TTCATAAAGACTTAG-TTAGCCAAAATTGCA
* *
19405896 TTCATAAAGACTTAGTTTGGCAAAATTGCA
1 TTCATAAAGACTTAGTTAGCCAAAATTGCA
19405926 TTCATAA
1 TTCATAA
19405933 TCATAAAGGC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 8 0.25
30 24 0.75
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (30 bp):
TTCATAAAGACTTAGTTAGCCAAAATTGCA
Found at i:19406319 original size:15 final size:16
Alignment explanation
Indices: 19406299--19406328 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19406289 CACTTTATCA
19406299 TAAAT-CATCTTAGTC
1 TAAATCCATCTTAGTC
19406314 TAAATCCATCTTAGT
1 TAAATCCATCTTAGT
19406329 ATAAGAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (16 bp):
TAAATCCATCTTAGTC
Found at i:19407288 original size:31 final size:31
Alignment explanation
Indices: 19407253--19407319 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
19407243 TACTTTGGTA
* * *
19407253 TAAATCATCTCAATACGAATTCATCTTGATG
1 TAAATCACCTCAATACAAATTCATCTGGATG
* *
19407284 TAAATCACCTCGATACAAATTTATCTGGATG
1 TAAATCACCTCAATACAAATTCATCTGGATG
19407315 TAAAT
1 TAAAT
19407320 TAACTCTGCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.34
Consensus pattern (31 bp):
TAAATCACCTCAATACAAATTCATCTGGATG
Found at i:19408451 original size:11 final size:12
Alignment explanation
Indices: 19408425--19408462 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
19408415 ATTTTTTTGT
19408425 TTTTTATATATTA
1 TTTTTATATA-TA
19408438 TTTTTATATA-A
1 TTTTTATATATA
19408449 TTTTTA-ATATA
1 TTTTTATATATA
19408460 TTT
1 TTT
19408463 AAATAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 3 0.12
11 11 0.46
13 10 0.42
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTTATATATA
Found at i:19409734 original size:3 final size:3
Alignment explanation
Indices: 19409726--19409768 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
19409716 CAACTTTTGT
19409726 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
19409769 CTTTTTTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:19410499 original size:12 final size:13
Alignment explanation
Indices: 19410478--19410504 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
19410468 TAATCGTAGG
19410478 TTTTCTTTTTTTT
1 TTTTCTTTTTTTT
19410491 TTTTCTTTTTTTT
1 TTTTCTTTTTTTT
19410504 T
1 T
19410505 GTTTACATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (13 bp):
TTTTCTTTTTTTT
Found at i:19414518 original size:9 final size:9
Alignment explanation
Indices: 19414501--19414536 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
19414491 AAAAAATGAT
19414501 GAAAAAAAA
1 GAAAAAAAA
*
19414510 AAAAGAAAAA
1 GAAA-AAAAA
19414520 GAAAAAAAA
1 GAAAAAAAA
19414529 GAAAAAAA
1 GAAAAAAA
19414537 GATAATGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:19414528 original size:23 final size:23
Alignment explanation
Indices: 19414502--19414548 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
19414492 AAAAATGATG
19414502 AAAAAAAAAAAAGAAAAAGAAAA
1 AAAAAAAAAAAAGAAAAAGAAAA
* * *
19414525 AAAAGAAAAAAAGATAATGAAAA
1 AAAAAAAAAAAAGAAAAAGAAAA
19414548 A
1 A
19414549 GAAATTGATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.11, T:0.04
Consensus pattern (23 bp):
AAAAAAAAAAAAGAAAAAGAAAA
Found at i:19414552 original size:6 final size:6
Alignment explanation
Indices: 19414503--19414552 Score: 50
Period size: 6 Copynumber: 8.5 Consensus size: 6
19414493 AAAATGATGA
* * *
19414503 AAAAAA AAAAAG AAAAAG AAAAA- AAAGAA- AAAAAG ATAATG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG
19414550 AAA
1 AAA
19414553 TTGATAAGGT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
5 5 0.14
6 32 0.86
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:19415842 original size:20 final size:21
Alignment explanation
Indices: 19415817--19415855 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
19415807 AATAAGAATA
19415817 TTTG-AATTTTGGATGTGAGC
1 TTTGAAATTTTGGATGTGAGC
*
19415837 TTTGAAATTTTTGATGTGA
1 TTTGAAATTTTGGATGTGA
19415856 ATTCATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.23, C:0.03, G:0.26, T:0.49
Consensus pattern (21 bp):
TTTGAAATTTTGGATGTGAGC
Found at i:19416335 original size:31 final size:32
Alignment explanation
Indices: 19416231--19416335 Score: 97
Period size: 31 Copynumber: 3.2 Consensus size: 32
19416221 TCTTGGTCAC
** * *
19416231 TTATTTTTGATCTCGACTCAATCTAAATCATT
1 TTATTTTTGATCTCGGTTCGATCCAAATCATT
* * *
19416263 TTATTTTTTGACTCACGGTTCGATCCCAATCACCT
1 TTA-TTTTTGA-TCTCGGTTCGATCCAAATCA-TT
*
19416298 GT-TTTTT-ATCTCGGTTCGATCCAAATCATT
1 TTATTTTTGATCTCGGTTCGATCCAAATCATT
19416328 TTATTTTT
1 TTATTTTT
19416336 TTAATTTATG
Statistics
Matches: 57, Mismatches: 12, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
30 2 0.04
31 23 0.40
32 4 0.07
33 12 0.21
34 14 0.25
35 2 0.04
ACGTcount: A:0.22, C:0.21, G:0.10, T:0.48
Consensus pattern (32 bp):
TTATTTTTGATCTCGGTTCGATCCAAATCATT
Found at i:19416699 original size:133 final size:131
Alignment explanation
Indices: 19416172--19416798 Score: 424
Period size: 133 Copynumber: 4.8 Consensus size: 131
19416162 CCTCATATTC
* * * ** * ** *
19416172 GATCTCGACTTGGTCCAGATCATTTTATTTTTTTTAACTCGCGGTTTGATCTTGGTCACTTATTT
1 GATCTCGACTTAGTCCAAATCATTTTA-TTTTTTTAACTCACGGTTCAATCCTAATCACTCATTT
*
19416237 T-TGATCTCGACTCAATCTAAATCATTTTA-TTTTTTGACTCACGGTTCGATCCCAATCACCTGT
65 TCT-ATCTCGACTCAATCTAAATCATTTTATTTTTTTGACTCGCGGTTCGATCCCAATCA-CTGT
19416300 TTTT
128 TTTT
* * * * * * * * *
19416304 TATCTCG-GTTCGATCCAAATCATTTTATTTTTTTAATTTATGGTTCAATCTTGATCATTCATTT
1 GATCTCGACTTAG-TCCAAATCATTTTATTTTTTTAACTCACGGTTCAATCCTAATCACTCATTT
* * * * * * * ****
19416368 TCGATCTCGACTCAATCCAAATCA-TTTCTTTTTTGGACACGCGATTCAATTTTGATCACTCG-T
65 TCTATCTCGACTCAATCTAAATCATTTTATTTTTTTGACTCGCGGTTCGATCCCAATCACT-GTT
19416431 TTT
129 TTT
* * ** * ** * * *
19416434 GATCTCGATTTAGTTCAAATCATTTTATTTTTTTGGCTCGCATTTCAAT-CTCAGTTACTCATCT
1 GATCTCGACTTAGTCCAAATCATTTTATTTTTTTAACTCACGGTTCAATCCT-AATCACTCATTT
* * * * * * * * *
19416498 TCAATCTCGGCTCAGTCTAAATCAATTTATGTTTTCTAACTAGCAGTTTGATCCCAATCATCTGT
65 TCTATCTCGACTCAATCTAAATCATTTTAT-TTTTTTGACTCGCGGTTCGATCCCAATCA-CTGT
19416563 TTTT
128 TTTT
* * * * *
19416567 GATCTCGACTTAGTCTAGATCATTTTAGTTTTTTAATTCACGGTTCAATCCTAATAACTCATTTT
1 GATCTCGACTTAGTCCAAATCATTTTATTTTTTTAACTCACGGTTCAATCCTAATCACTCATTTT
* * *
19416632 CTATCTC-AGCTCAATCTAGATCATTTTATTTTTTCTGACTCGCGGTTCGATCCCAGTCACATAT
66 CTATCTCGA-CTCAATCTAAATCATTTTATTTTTT-TGACTCGCGGTTCGATCCCAATCAC-TGT
19416696 TTTT
128 TTTT
* * * ** * * * * * *
19416700 TATTTCGACTTGGTAAAAATTATTTTATTTTTTTGACTCACGATTTAAT-CTCGATCACTTATTT
1 GATCTCGACTTAGTCCAAATCATTTTATTTTTTTAACTCACGGTTCAATCCT-AATCACTCATTT
* * * * * *
19416764 TTTATCTTGACTCGATCCAGATCATTTTACTTTTT
65 TCTATCTCGACTCAATCTAAATCATTTTATTTTTT
19416799 AGATTTGTGG
Statistics
Matches: 372, Mismatches: 107, Indels: 31
0.73 0.21 0.06
Matches are distributed among these distances:
129 1 0.00
130 69 0.19
131 80 0.22
132 43 0.12
133 176 0.47
134 3 0.01
ACGTcount: A:0.23, C:0.20, G:0.11, T:0.46
Consensus pattern (131 bp):
GATCTCGACTTAGTCCAAATCATTTTATTTTTTTAACTCACGGTTCAATCCTAATCACTCATTTT
CTATCTCGACTCAATCTAAATCATTTTATTTTTTTGACTCGCGGTTCGATCCCAATCACTGTTTT
T
Found at i:19422073 original size:14 final size:14
Alignment explanation
Indices: 19422050--19422081 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
19422040 TAGTAAGGTG
*
19422050 GATTATAATAGGAA
1 GATTAGAATAGGAA
19422064 GATTAGAATAGGAA
1 GATTAGAATAGGAA
19422078 GATT
1 GATT
19422082 GCATTTACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.25, T:0.28
Consensus pattern (14 bp):
GATTAGAATAGGAA
Found at i:19422531 original size:16 final size:16
Alignment explanation
Indices: 19422510--19422545 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
19422500 ATTCAAATCC
19422510 TTGTGAGTTATTTTT-T
1 TTGTGAGTT-TTTTTGT
19422526 TTGTGAGTTTTTTTGT
1 TTGTGAGTTTTTTTGT
19422542 TTGT
1 TTGT
19422546 AATTAATCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.08, C:0.00, G:0.22, T:0.69
Consensus pattern (16 bp):
TTGTGAGTTTTTTTGT
Found at i:19422892 original size:66 final size:66
Alignment explanation
Indices: 19422722--19422900 Score: 164
Period size: 66 Copynumber: 2.7 Consensus size: 66
19422712 CGGTTACTTG
* * * *
19422722 TTTTCAATCTC-AGCTCAATCTAAATCATTTTATTTTTTTTAACTCGTGGTTCAATCTTGATAAC
1 TTTTCTATCTCGA-CTCGATCTAAATCATTTTA-TTTTTCTAACTCGTGGTTCAATCTCGATAAC
19422786 TCA
64 TCA
* ** * **
19422789 TTTTCTATCTCGACTCGATCTAGATTGTGTTATTTTTCTAACTCGTGGTTCAATCTCGATCGCTC
1 TTTTCTATCTCGACTCGATCTAAATCATTTTATTTTTCTAACTCGTGGTTCAATCTCGATAACTC
19422854 A
66 A
* * * * * * *
19422855 TGTTT-TATCTTGGCTTGGTCTATATCATTTTAATTTTCTGACTCGT
1 T-TTTCTATCTCGACTCGATCTAAATCATTTTATTTTTCTAACTCGT
19422901 TGCTCAGTTT
Statistics
Matches: 90, Mismatches: 20, Indels: 5
0.78 0.17 0.04
Matches are distributed among these distances:
66 62 0.69
67 27 0.30
68 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.12, T:0.47
Consensus pattern (66 bp):
TTTTCTATCTCGACTCGATCTAAATCATTTTATTTTTCTAACTCGTGGTTCAATCTCGATAACTC
A
Found at i:19423925 original size:16 final size:16
Alignment explanation
Indices: 19423897--19423931 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
19423887 TTTGTTTACA
19423897 TTTTTGACATTTTTAT
1 TTTTTGACATTTTTAT
19423913 TTTTTAGAC-TTTTTAT
1 TTTTT-GACATTTTTAT
19423929 TTT
1 TTT
19423932 ATTTTTTACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.83
17 3 0.17
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.71
Consensus pattern (16 bp):
TTTTTGACATTTTTAT
Found at i:19423955 original size:9 final size:8
Alignment explanation
Indices: 19423925--19423975 Score: 50
Period size: 9 Copynumber: 6.0 Consensus size: 8
19423915 TTTAGACTTT
19423925 TTATTTTA
1 TTATTTTA
19423933 TT-TTTTA
1 TTATTTTA
19423940 CTTATTATTA
1 -TTATT-TTA
*
19423950 TTATTATTG
1 TTATT-TTA
19423959 TTATTTTA
1 TTATTTTA
19423967 CTTATTTTA
1 -TTATTTTA
19423976 AATTAGATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
7 5 0.14
8 6 0.16
9 23 0.62
10 3 0.08
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.71
Consensus pattern (8 bp):
TTATTTTA
Found at i:19427408 original size:17 final size:18
Alignment explanation
Indices: 19427386--19427429 Score: 72
Period size: 17 Copynumber: 2.4 Consensus size: 18
19427376 AGGATTGTCA
19427386 TCTATTGTAGCTTAAG-T
1 TCTATTGTAGCTTAAGCT
19427403 TCTATTGTAGCTTAAGCT
1 TCTATTGTAGCTTAAGCT
19427421 TCTTATTGT
1 TC-TATTGT
19427430 TGTTGGAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 16 0.64
18 3 0.12
19 6 0.24
ACGTcount: A:0.20, C:0.14, G:0.16, T:0.50
Consensus pattern (18 bp):
TCTATTGTAGCTTAAGCT
Found at i:19442919 original size:21 final size:21
Alignment explanation
Indices: 19442894--19442945 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
19442884 CAGTGGTGGA
*
19442894 GGTGAGATTAGTTATTGTAAC
1 GGTGAGATTAGTTACTGTAAC
* *
19442915 GGTGAGATTGGTTACTGTAGC
1 GGTGAGATTAGTTACTGTAAC
*
19442936 GATGAGATTA
1 GGTGAGATTA
19442946 AAATCAATGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.06, G:0.33, T:0.35
Consensus pattern (21 bp):
GGTGAGATTAGTTACTGTAAC
Found at i:19444342 original size:22 final size:22
Alignment explanation
Indices: 19444317--19444360 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
19444307 ATTTTTTGAC
19444317 CTTAATTCTA-AGGATACAAATA
1 CTTAATTCTAGA-GATACAAATA
19444339 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
19444361 TAAATATACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:19445843 original size:22 final size:22
Alignment explanation
Indices: 19445817--19445860 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
19445807 TGTATATTTA
*
19445817 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
*
19445839 TATTTGTATCCCTAGATTTAAG
1 TATTTGTATCCCTAGAATTAAG
19445861 GACAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:19447294 original size:22 final size:22
Alignment explanation
Indices: 19447266--19447307 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
19447256 TATATTTATA
**
19447266 TTTGTATTTCTAGAATTAAGTT
1 TTTGTATCCCTAGAATTAAGTT
19447288 TTTGTATCCCTAGAATTAAG
1 TTTGTATCCCTAGAATTAAG
19447308 GACAAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.48
Consensus pattern (22 bp):
TTTGTATCCCTAGAATTAAGTT
Found at i:19447494 original size:25 final size:23
Alignment explanation
Indices: 19447450--19447499 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
19447440 AATATACATT
19447450 CAGTTTTTCTCTTAAGTTTTCACA
1 CAGTTTTTCTCTTAAGTTTTC-CA
*
19447474 CAGTTTTATTTCTT-AGTTTTTCCA
1 CAGTTTT-TCTCTTAAG-TTTTCCA
19447498 CA
1 CA
19447500 ATATTAACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.20, C:0.20, G:0.08, T:0.52
Consensus pattern (23 bp):
CAGTTTTTCTCTTAAGTTTTCCA
Found at i:19452681 original size:22 final size:22
Alignment explanation
Indices: 19452653--19452696 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
19452643 TGTATATTTA
19452653 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
19452675 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
19452697 GACAAAAAAT
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:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:19456609 original size:22 final size:22
Alignment explanation
Indices: 19456583--19456626 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
19456573 TGTATATTTA
*
19456583 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATACCTAGAATTAAG
*
19456605 TATTTGTATACTTAGAATTAAG
1 TATTTGTATACCTAGAATTAAG
19456627 GACAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (22 bp):
TATTTGTATACCTAGAATTAAG
Found at i:19459366 original size:87 final size:88
Alignment explanation
Indices: 19459230--19459394 Score: 210
Period size: 88 Copynumber: 1.9 Consensus size: 88
19459220 GACGTCGGTC
* * ** * *
19459230 TTATCTTAGATTATGCAAGGTTTGACTTTTCTATTCCTTGAGGGACATTTT-AACATTTTTGGTT
1 TTATCTTAGATTATGCAAGGTTAGACTTTTCTATTCCTTCAAAGACATTTTAAAAATTTCTGGTT
19459294 GGTGATATGCATGAGCATTCATG
66 GGTGATATGCATGAGCATTCATG
* *
19459317 TTATCTTTAGA-TATGCAAGGTTAGACTTTTTTCTGTCCTTCAAAG-CATTTTAAAAATTTCTGG
1 TTATC-TTAGATTATGCAAGGTTAGACTTTTCTAT-TCCTTCAAAGACATTTTAAAAATTTCTGG
*
19459380 TTGGTGATATTCATG
64 TTGGTGATATGCATG
19459395 GCACCTCCTT
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
87 31 0.47
88 35 0.53
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.44
Consensus pattern (88 bp):
TTATCTTAGATTATGCAAGGTTAGACTTTTCTATTCCTTCAAAGACATTTTAAAAATTTCTGGTT
GGTGATATGCATGAGCATTCATG
Found at i:19462739 original size:12 final size:13
Alignment explanation
Indices: 19462716--19462771 Score: 55
Period size: 14 Copynumber: 4.3 Consensus size: 13
19462706 ATTTTTATAA
19462716 TTTATAATATAAATT
1 TTTA-AATA-AAATT
19462731 TTTAAATAAAAATT
1 TTTAAAT-AAAATT
19462745 TTT-AATAAAA-T
1 TTTAAATAAAATT
*
19462756 ATT-AATAAAATT
1 TTTAAATAAAATT
19462768 TTTA
1 TTTA
19462772 TCATTAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
11 10 0.28
12 7 0.19
13 3 0.08
14 11 0.31
15 5 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTAAATAAAATT
Found at i:19462785 original size:28 final size:27
Alignment explanation
Indices: 19462753--19462813 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 27
19462743 TTTTTAATAA
**
19462753 AATATTAATAAAATTTTTATCATTAAAT
1 AATATTAATAAAATTTAAATCA-TAAAT
* * *
19462781 AATATTTATCAAATTTAAATTATAAAT
1 AATATTAATAAAATTTAAATCATAAAT
19462808 AATATT
1 AATATT
19462814 TTTAATAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 11 0.39
28 17 0.61
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (27 bp):
AATATTAATAAAATTTAAATCATAAAT
Found at i:19466474 original size:30 final size:30
Alignment explanation
Indices: 19466438--19466496 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
19466428 AAAACTTAAT
19466438 AAAATTGAATGTATAA-TAATAAAATTCAAC
1 AAAATTGAA-GTATAAGTAATAAAATTCAAC
19466468 AAAATTGAAGTATAAGTAATAAAATTCAA
1 AAAATTGAAGTATAAGTAATAAAATTCAA
19466497 TATTAAACCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 6 0.21
30 22 0.79
ACGTcount: A:0.58, C:0.05, G:0.08, T:0.29
Consensus pattern (30 bp):
AAAATTGAAGTATAAGTAATAAAATTCAAC
Found at i:19468735 original size:30 final size:30
Alignment explanation
Indices: 19468688--19468756 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
19468678 TTATATTTTT
19468688 AAAAAA-TTTACGAAAGATATTAAAAATTC
1 AAAAAATTTTACGAAAGATATTAAAAATTC
* * * *
19468717 AAATAATTTTACGTAAGATTTTCAAAATTC
1 AAAAAATTTTACGAAAGATATTAAAAATTC
19468747 AAAAAATTTT
1 AAAAAATTTT
19468757 TATTTTAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 5 0.15
30 29 0.85
ACGTcount: A:0.52, C:0.07, G:0.06, T:0.35
Consensus pattern (30 bp):
AAAAAATTTTACGAAAGATATTAAAAATTC
Found at i:19469096 original size:17 final size:18
Alignment explanation
Indices: 19469069--19469103 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
19469059 ATTTTTTAAA
19469069 TATATATTTTATTATTAT
1 TATATATTTTATTATTAT
*
19469087 TATA-ATTTTATTCTTAT
1 TATATATTTTATTATTAT
19469104 GAAAAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (18 bp):
TATATATTTTATTATTAT
Found at i:19474295 original size:3 final size:3
Alignment explanation
Indices: 19474287--19474334 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
19474277 CTCCATAGCT
19474287 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT- TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
19474334 T
1 T
19474335 GTTAAGCTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:19475603 original size:16 final size:16
Alignment explanation
Indices: 19475560--19475606 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
19475550 TAGTTTAGCT
19475560 TTTTTAAGTTTTCTTA
1 TTTTTAAGTTTTCTTA
*
19475576 TTCTTT-ACTTTT-TGTA
1 TT-TTTAAGTTTTCT-TA
19475592 TTTTTAAGTTTTCTT
1 TTTTTAAGTTTTCTT
19475607 TTAAGTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
15 4 0.16
16 17 0.68
17 4 0.16
ACGTcount: A:0.15, C:0.09, G:0.06, T:0.70
Consensus pattern (16 bp):
TTTTTAAGTTTTCTTA
Found at i:19475671 original size:5 final size:5
Alignment explanation
Indices: 19475661--19475685 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
19475651 TTAAATTCAA
19475661 GTTTT GTTTT GTTTT GTTTT GTTTT
1 GTTTT GTTTT GTTTT GTTTT GTTTT
19475686 TAATTTAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (5 bp):
GTTTT
Found at i:19476260 original size:78 final size:78
Alignment explanation
Indices: 19476163--19476316 Score: 299
Period size: 78 Copynumber: 2.0 Consensus size: 78
19476153 ATTTTATATA
19476163 TATATATATATATAAAATCACTCTTGTGGATAAATAAATTAAATATTGATCACTCTTTTGGATAA
1 TATATATATATATAAAATCACTCTTGTGGATAAATAAATTAAATATTGATCACTCTTTTGGATAA
19476228 AAATTAAATTATT
66 AAATTAAATTATT
*
19476241 TATATATATATATATAATCACTCTTGTGGATAAATAAATTAAATATTGATCACTCTTTTGGATAA
1 TATATATATATATAAAATCACTCTTGTGGATAAATAAATTAAATATTGATCACTCTTTTGGATAA
19476306 AAATTAAATTA
66 AAATTAAATTA
19476317 CCCCTTAAGC
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 75 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.41
Consensus pattern (78 bp):
TATATATATATATAAAATCACTCTTGTGGATAAATAAATTAAATATTGATCACTCTTTTGGATAA
AAATTAAATTATT
Found at i:19479571 original size:2 final size:2
Alignment explanation
Indices: 19479564--19479590 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19479554 GTTTGTTGTT
19479564 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
19479591 GTATGTATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19480386 original size:12 final size:11
Alignment explanation
Indices: 19480369--19480407 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
19480359 AATATTATTT
19480369 AAAATTTTAGTA
1 AAAATTTTA-TA
19480381 AAAATTTTATA
1 AAAATTTTATA
* *
19480392 TAAATTTAATA
1 AAAATTTTATA
19480403 AAAAT
1 AAAAT
19480408 AAAAAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 15 0.62
12 9 0.38
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (11 bp):
AAAATTTTATA
Found at i:19482447 original size:14 final size:13
Alignment explanation
Indices: 19482428--19482486 Score: 54
Period size: 12 Copynumber: 4.7 Consensus size: 13
19482418 TAATGATGTA
19482428 AATTATTAAAATAT
1 AATTA-TAAAATAT
* *
19482442 AATTATGATATA-
1 AATTATAAAATAT
19482454 AATTATAAAATAT
1 AATTATAAAATAT
19482467 -ATT-T-AAATATT
1 AATTATAAAATA-T
19482478 AATTATAAA
1 AATTATAAA
19482487 CATAATATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
10 5 0.14
11 2 0.06
12 16 0.44
13 6 0.17
14 7 0.19
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (13 bp):
AATTATAAAATAT
Found at i:19482481 original size:24 final size:25
Alignment explanation
Indices: 19482426--19482486 Score: 79
Period size: 24 Copynumber: 2.4 Consensus size: 25
19482416 TATAATGATG
*
19482426 TAAATTATTAAAATATAATTATGATA
1 TAAATTA-TAAAATATAATTATAATA
*
19482452 TAAATTATAAAATATATTTA-AATA
1 TAAATTATAAAATATAATTATAATA
*
19482476 TTAATTATAAA
1 TAAATTATAAA
19482487 CATAATATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
24 13 0.41
25 12 0.38
26 7 0.22
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (25 bp):
TAAATTATAAAATATAATTATAATA
Found at i:19482605 original size:10 final size:10
Alignment explanation
Indices: 19482581--19482634 Score: 56
Period size: 10 Copynumber: 5.5 Consensus size: 10
19482571 AAACACAAAT
*
19482581 AATATGAACA
1 AATATGAATA
*
19482591 TATATGAATA
1 AATATGAATA
*
19482601 AATATG-ATT
1 AATATGAATA
19482610 AATATGAATA
1 AATATGAATA
* *
19482620 TATACGAATA
1 AATATGAATA
19482630 AATAT
1 AATAT
19482635 AATTAACGTA
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
9 8 0.24
10 26 0.76
ACGTcount: A:0.54, C:0.04, G:0.09, T:0.33
Consensus pattern (10 bp):
AATATGAATA
Found at i:19482612 original size:29 final size:29
Alignment explanation
Indices: 19482580--19482640 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
19482570 TAAACACAAA
* *
19482580 TAATATGAACATATATGAATAAATATGAT
1 TAATATGAACATATACGAATAAATATAAT
*
19482609 TAATATGAATATATACGAATAAATATAAT
1 TAATATGAACATATACGAATAAATATAAT
19482638 TAA
1 TAA
19482641 CGTAAATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.34
Consensus pattern (29 bp):
TAATATGAACATATACGAATAAATATAAT
Found at i:19482648 original size:29 final size:29
Alignment explanation
Indices: 19482590--19482652 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
19482580 TAATATGAAC
* * * *
19482590 ATATATGAATAAATATGATTAATATGAAT
1 ATATACGAATAAATATAATTAACATAAAT
*
19482619 ATATACGAATAAATATAATTAACGTAAAT
1 ATATACGAATAAATATAATTAACATAAAT
19482648 ATATA
1 ATATA
19482653 TAAAAACATG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.35
Consensus pattern (29 bp):
ATATACGAATAAATATAATTAACATAAAT
Found at i:19483019 original size:47 final size:48
Alignment explanation
Indices: 19482916--19483020 Score: 110
Period size: 47 Copynumber: 2.2 Consensus size: 48
19482906 TTTATATTAT
*
19482916 TAATATAAAATAATTTTATAATAATTATTAAATGAGTGTTATAATTAAA
1 TAAT-TAAAATAATTTTATAATAATTATTAAATGAGTCTTATAATTAAA
* * *
19482965 TATTTAAAATAATTTT-TATATGA-TATTAAAT-AG-CTTATTAATTATCA
1 TAATTAAAATAATTTTATA-ATAATTATTAAATGAGTCTTA-TAATTA-AA
19483012 TAATTAAAA
1 TAATTAAAA
19483021 GATTAAAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
45 3 0.06
46 8 0.17
47 19 0.40
48 15 0.31
49 3 0.06
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.45
Consensus pattern (48 bp):
TAATTAAAATAATTTTATAATAATTATTAAATGAGTCTTATAATTAAA
Found at i:19486193 original size:4 final size:4
Alignment explanation
Indices: 19486186--19486247 Score: 65
Period size: 4 Copynumber: 15.2 Consensus size: 4
19486176 CATACATAAC
*
19486186 AATA AATA AATA ATTA AA-A AATA AATA ATCATAA AATA AAT- AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA A--AT-A AATA AATA AATA AATA
*
19486235 ACTA AATA AATA A
1 AATA AATA AATA A
19486248 CCAAAAATTA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
3 6 0.12
4 37 0.76
5 2 0.04
6 2 0.04
7 2 0.04
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:19486200 original size:34 final size:34
Alignment explanation
Indices: 19486162--19486255 Score: 97
Period size: 34 Copynumber: 2.8 Consensus size: 34
19486152 TTTAACAAAT
*
19486162 TAATTAAACAAATACAT-A-CATAACAATAAATAAA
1 TAATTAAA-AAATAAATAATCATAA-AATAAATAAA
19486196 TAATTAAAAAATAAATAATCATAAAATAAAT-AA
1 TAATTAAAAAATAAATAATCATAAAATAAATAAA
* * *
19486229 TAAATAACTAAATAAATAACCA-AAAAT
1 TAATTAA-AAAATAAATAATCATAAAAT
19486256 TAACAATTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
33 20 0.38
34 28 0.53
35 5 0.09
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.24
Consensus pattern (34 bp):
TAATTAAAAAATAAATAATCATAAAATAAATAAA
Found at i:19486209 original size:15 final size:15
Alignment explanation
Indices: 19486189--19486243 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
19486179 ACATAACAAT
19486189 AAATAAATAATTAAA
1 AAATAAATAATTAAA
* *
19486204 AAATAAATAATCATA
1 AAATAAATAATTAAA
19486219 AAATAAATAA-TAAA
1 AAATAAATAATTAAA
*
19486233 TAACTAAATAA
1 -AAATAAATAA
19486244 ATAACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
14 2 0.06
15 32 0.94
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (15 bp):
AAATAAATAATTAAA
Found at i:19486210 original size:19 final size:20
Alignment explanation
Indices: 19486186--19486247 Score: 76
Period size: 19 Copynumber: 3.2 Consensus size: 20
19486176 CATACATAAC
19486186 AATAAATAAATAATTAAA-A
1 AATAAATAAATAATTAAATA
* *
19486205 AATAAAT-AATCATAAAATA
1 AATAAATAAATAATTAAATA
*
19486224 AAT-AATAAATAACTAAATA
1 AATAAATAAATAATTAAATA
19486243 AATAA
1 AATAA
19486248 CCAAAAATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
18 11 0.31
19 23 0.66
20 1 0.03
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (20 bp):
AATAAATAAATAATTAAATA
Found at i:19486267 original size:14 final size:14
Alignment explanation
Indices: 19486250--19486289 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
19486240 ATAAATAACC
*
19486250 AAAAATTAACAATT
1 AAAAATTAACAATG
19486264 AAAAATTTAA-AATG
1 AAAAA-TTAACAATG
19486278 AAAAATTAACAA
1 AAAAATTAACAA
19486290 AAAGGGAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 4 0.17
14 15 0.65
15 4 0.17
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.25
Consensus pattern (14 bp):
AAAAATTAACAATG
Found at i:19486494 original size:23 final size:23
Alignment explanation
Indices: 19486455--19486508 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
19486445 GCACTAACTT
*
19486455 CAAAATTAATATAAAGAGAAA-AA
1 CAAAATAAATATAAAGA-AAATAA
19486478 CAAAATAAATA-ATAAGAAAATAA
1 CAAAATAAATATA-AAGAAAATAA
*
19486501 GAAAATAA
1 CAAAATAA
19486509 GAAAAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 4 0.15
23 23 0.85
ACGTcount: A:0.72, C:0.04, G:0.07, T:0.17
Consensus pattern (23 bp):
CAAAATAAATATAAAGAAAATAA
Found at i:19486501 original size:8 final size:8
Alignment explanation
Indices: 19486479--19486513 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
19486469 AGAGAAAAAC
19486479 AAAATAA-
1 AAAATAAG
*
19486486 ATAATAAG
1 AAAATAAG
19486494 AAAATAAG
1 AAAATAAG
19486502 AAAATAAG
1 AAAATAAG
19486510 AAAA
1 AAAA
19486514 AAATTATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 6 0.24
8 19 0.76
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (8 bp):
AAAATAAG
Done.