Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 2 of 444
Found at i:388508 original size:30 final size:31
Alignment explanation
Indices: 388447--388527 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 31
388437 ATTTTAAAAA
*
388447 TATTTATAATATTAATATATAATATTATAAT
1 TATTTATATTATTAATATATAATATTATAAT
388478 T-TTTAATATTATTAA-ATATAAATATT-TAAT
1 TATTT-ATATTATTAATATAT-AATATTATAAT
*
388508 TATTTATATTAAATAATATA
1 TATTTATATT-ATTAATATA
388528 ACAAATTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
30 17 0.40
31 23 0.53
32 3 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (31 bp):
TATTTATATTATTAATATATAATATTATAAT
Found at i:388528 original size:30 final size:30
Alignment explanation
Indices: 388448--388528 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
388438 TTTTAAAAAT
*
388448 ATTTATAATATTAAT-ATAT-AATATTATA
1 ATTTTTAATATTAATAATATAAATATTATA
*
388476 ATTTTTAATATTATTAAATATAAATATT-TA
1 ATTTTTAATATTAAT-AATATAAATATTATA
388506 ATTATTT-ATATTAAATAATATAA
1 ATT-TTTAATATT-AATAATATAA
388529 CAAATTATTA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
28 13 0.29
30 21 0.47
31 11 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (30 bp):
ATTTTTAATATTAATAATATAAATATTATA
Found at i:388699 original size:15 final size:15
Alignment explanation
Indices: 388648--388701 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
388638 TATTTATATT
*
388648 AATATTTTAATAATA
1 AATATATTAATAATA
*
388663 AATATATACTATAAATATA
1 AATATAT--TA-ATA-ATA
388682 AATATATTAATAATA
1 AATATATTAATAATA
388697 AATAT
1 AATAT
388702 TTTATACCGT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 14 0.44
16 2 0.06
17 4 0.12
18 2 0.06
19 10 0.31
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (15 bp):
AATATATTAATAATA
Found at i:389609 original size:32 final size:31
Alignment explanation
Indices: 389568--389631 Score: 101
Period size: 31 Copynumber: 2.0 Consensus size: 31
389558 AACATTTCAA
* *
389568 TTTTTTTAAAAAAGTTGATGATTAAATTTAAT
1 TTTTTTTAAAAAA-TTGAAGACTAAATTTAAT
389600 TTTTTTTAAAAAATTGAAGACTAAATTTAAT
1 TTTTTTTAAAAAATTGAAGACTAAATTTAAT
389631 T
1 T
389632 AAAAATAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 17 0.57
32 13 0.43
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (31 bp):
TTTTTTTAAAAAATTGAAGACTAAATTTAAT
Found at i:393306 original size:2 final size:2
Alignment explanation
Indices: 393299--393323 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
393289 TTTTATTATT
393299 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
393324 TAATCTATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:394605 original size:12 final size:14
Alignment explanation
Indices: 394576--394612 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
394566 TCAAGATAGG
394576 AAAATTGACACTAA
1 AAAATTGACACTAA
*
394590 AAAATTGACATTAA
1 AAAATTGACACTAA
394604 AAAATTGAC
1 AAAATTGAC
394613 CTTTCTTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.57, C:0.11, G:0.08, T:0.24
Consensus pattern (14 bp):
AAAATTGACACTAA
Found at i:395615 original size:30 final size:30
Alignment explanation
Indices: 395581--395641 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
395571 TAATACTCAC
395581 TTTTATTACTCAATTAGAATCGACATACAA
1 TTTTATTACTCAATTAGAATCGACATACAA
*
395611 TTTTATTATTCAATTAGAATCGACATACAA
1 TTTTATTACTCAATTAGAATCGACATACAA
395641 T
1 T
395642 GAGGGTTTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTATTACTCAATTAGAATCGACATACAA
Found at i:395915 original size:14 final size:16
Alignment explanation
Indices: 395884--395915 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
395874 TAGAAAAGAT
395884 TCAAATATTTATTATG
1 TCAAATATTTATTATG
395900 TCAAA-ATTTA-TATG
1 TCAAATATTTATTATG
395914 TC
1 TC
395916 TATAATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 5 0.31
16 5 0.31
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (16 bp):
TCAAATATTTATTATG
Found at i:399984 original size:26 final size:26
Alignment explanation
Indices: 399955--400008 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
399945 TGATACCTAC
399955 AAATTATTTATTAATTGAAATTGTTG
1 AAATTATTTATTAATTGAAATTGTTG
399981 AAATTATTTATTAATTGAAATTGTTG
1 AAATTATTTATTAATTGAAATTGTTG
400007 AA
1 AA
400009 GAGATTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (26 bp):
AAATTATTTATTAATTGAAATTGTTG
Found at i:400015 original size:26 final size:26
Alignment explanation
Indices: 399955--400016 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
399945 TGATACCTAC
*
399955 AAATTATTTATTAATTGAAATTGTTG
1 AAATGATTTATTAATTGAAATTGTTG
*
399981 AAATTATTTATTAATTGAAATTGTTG
1 AAATGATTTATTAATTGAAATTGTTG
400007 AAGA-GATTTA
1 AA-ATGATTTA
400017 AATACCAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
26 33 0.97
27 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (26 bp):
AAATGATTTATTAATTGAAATTGTTG
Found at i:409711 original size:17 final size:16
Alignment explanation
Indices: 409670--409712 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
409660 ATTTAGAGGT
*
409670 TCGATTTTAAATTTAT
1 TCGATTTTAAATTTAA
*
409686 TCTATTTTAAATTTAA
1 TCGATTTTAAATTTAA
409702 TCGGATTTTAA
1 TC-GATTTTAA
409713 TATAATAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 16 0.70
17 7 0.30
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (16 bp):
TCGATTTTAAATTTAA
Found at i:411940 original size:17 final size:17
Alignment explanation
Indices: 411918--411951 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
411908 CCATTAAAAT
411918 GAAAAGAACAA-AAAAGA
1 GAAAAGAA-AAGAAAAGA
411935 GAAAAGAAAAGAAAAGA
1 GAAAAGAAAAGAAAAGA
411952 AAATATAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 14 0.88
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (17 bp):
GAAAAGAAAAGAAAAGA
Found at i:425392 original size:2 final size:2
Alignment explanation
Indices: 425385--425409 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
425375 CAATTTTCTT
425385 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
425410 CCTTCTAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:428087 original size:30 final size:30
Alignment explanation
Indices: 428053--428115 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
428043 ATCACCTTAC
428053 AAATACAACCGAAGCAAAACAAAACCAACA
1 AAATACAACCGAAGCAAAACAAAACCAACA
* *
428083 AAATACAACTGAGGCAAAACAAAACCAACA
1 AAATACAACCGAAGCAAAACAAAACCAACA
428113 AAA
1 AAA
428116 AGAAAATGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.63, C:0.24, G:0.08, T:0.05
Consensus pattern (30 bp):
AAATACAACCGAAGCAAAACAAAACCAACA
Found at i:436565 original size:27 final size:25
Alignment explanation
Indices: 436535--436886 Score: 133
Period size: 27 Copynumber: 14.7 Consensus size: 25
436525 CACATTAAAA
*
436535 TTAAATTAAAATGGAAACAAAGATAAT
1 TTAAATTGAAATGGAAA-AAA-ATAAT
436562 TTAAA-TGAAATGAGAAAAAAATAA-
1 TTAAATTGAAATG-GAAAAAAATAAT
*
436586 TT---TT-AAATGTAAAAAAAATAAT
1 TTAAATTGAAATG-GAAAAAAATAAT
436608 TTAAA-TGAAATGAGAAAAAAATTAAAT
1 TTAAATTGAAATG-GAAAAAAA-T-AAT
*
436635 TTAAA-TGAAAT-G-AGAAAA-AA-
1 TTAAATTGAAATGGAAAAAAATAAT
* *
436655 TTAAATTAAAATGGATACAAAGATAAT
1 TTAAATTGAAATGGA-A-AAAAATAAT
*
436682 TTAAA-TGAAATGAGGAAAAAATTAATT
1 TTAAATTGAAAT--GGAAAAAAATAA-T
* * *
436709 TTAAA-TGTAA--CAAAAAGATAAT
1 TTAAATTGAAATGGAAAAAAATAAT
436731 TTAAA-TGAAATGAGAAGAAAAATAAAT
1 TTAAATTGAAATG-GAA-AAAAAT-AAT
*
436758 TTAAA-TGTAAA---AAAATAATAAT
1 TTAAATTG-AAATGGAAAAAAATAAT
* *
436780 ATAAA-TGAAAT-GACAAAAATAAAT
1 TTAAATTGAAATGGAAAAAAAT-AAT
* * *
436804 TTAAAATG----GGAAGATAAATAAA
1 TTAAATTGAAATGGAA-AAAAATAAT
*
436826 TTAAA-TGAAAT-G-AGAAAA-AA-
1 TTAAATTGAAATGGAAAAAAATAAT
*
436846 TTAAATTTAAAT-GAAAAAATATAAT
1 TTAAATTGAAATGGAAAAAA-ATAAT
*
436871 TTTAA-TGAAATGGAAA
1 TTAAATTGAAATGGAAA
436887 TGGAAATGAA
Statistics
Matches: 251, Mismatches: 33, Indels: 84
0.68 0.09 0.23
Matches are distributed among these distances:
20 10 0.04
21 35 0.14
22 39 0.16
23 26 0.10
24 26 0.10
25 32 0.13
26 28 0.11
27 49 0.20
28 6 0.02
ACGTcount: A:0.61, C:0.01, G:0.11, T:0.27
Consensus pattern (25 bp):
TTAAATTGAAATGGAAAAAAATAAT
Found at i:436601 original size:20 final size:20
Alignment explanation
Indices: 436576--436614 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
436566 ATGAAATGAG
436576 AAAAAAATAATTTTAAATGTA
1 AAAAAAATAA-TTTAAATGTA
436597 AAAAAAATAATTTAAATG
1 AAAAAAATAATTTAAATG
436615 AAATGAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (20 bp):
AAAAAAATAATTTAAATGTA
Found at i:436630 original size:22 final size:22
Alignment explanation
Indices: 436559--436990 Score: 117
Period size: 22 Copynumber: 18.6 Consensus size: 22
436549 AAACAAAGAT
436559 AATTTAAATGAAATGAGAAAAAAA
1 AATTTAAATGAAATGAG--AAAAA
*
436583 TAATTTTAAATGTAAA--A-AAAAT
1 -AA-TTTAAATG-AAATGAGAAAAA
436605 AATTTAAATGAAATGAGAAAAAAATTA
1 AATTTAAATGAAATGAG---AAAA--A
436632 AATTTAAATGAAATGAG-AAAA
1 AATTTAAATGAAATGAGAAAAA
* *
436653 AA-TTAAATTAAAATGGATACAAAGA
1 AATTTAAA-TGAAAT-GAGA-AAA-A
436678 TAATTTAAATGAAATGAGGAAAAAA
1 -AATTTAAATGAAATGA-G-AAAAA
* *
436703 TTAATTTTAAATGTAA-CA-AAAAGA
1 --AA-TTTAAATGAAATGAGAAAA-A
436727 TAATTTAAATGAAATGAGAAGAAA
1 -AATTTAAATGAAATGAGAA-AAA
* *
436751 AA--TAAATTTAAATGTAAAAAAA
1 AATTTAAA-TGAAATG-AGAAAAA
*
436773 TAATAATATAAATGAAATGACAAAAATA
1 -AAT--T-TAAATGAAATGA-GAAAA-A
* * *
436801 AATTTAAAATGGGAA-GATAAATA
1 AATTT-AAAT-GAAATGAGAAAAA
436824 AA-TTAAATGAAATGAG-AAAA
1 AATTTAAATGAAATGAGAAAAA
* *
436844 AA-TTAAATTTAAATGAAAAAATA
1 AATTTAAA-TGAAATGAGAAAA-A
* *
436867 TAATTTTAATGAAATG-GAAATGGA
1 -AATTTAAATGAAATGAGAAA--AA
* **
436891 AA-TGAAATGAAATGA-AATGA
1 AATTTAAATGAAATGAGAAAAA
* *
436911 AATTCAAATGAAATGA-AATAGA
1 AATTTAAATGAAATGAGAA-AAA
* * **
436933 AATTCAAATTAAAT-AGAACTGA
1 AATTTAAATGAAATGAGAA-AAA
** *
436955 AATAGAAATGAAATGAAAAAAA
1 AATTTAAATGAAATGAGAAAAA
*
436977 AAGTTGAAATGAAA
1 AA-TTTAAATGAAA
436991 AAAATTAATG
Statistics
Matches: 316, Mismatches: 40, Indels: 104
0.69 0.09 0.23
Matches are distributed among these distances:
19 3 0.01
20 30 0.09
21 43 0.14
22 75 0.24
23 40 0.13
24 20 0.06
25 24 0.08
26 26 0.08
27 50 0.16
28 5 0.02
ACGTcount: A:0.61, C:0.01, G:0.12, T:0.25
Consensus pattern (22 bp):
AATTTAAATGAAATGAGAAAAA
Found at i:436638 original size:47 final size:48
Alignment explanation
Indices: 436531--436641 Score: 172
Period size: 46 Copynumber: 2.4 Consensus size: 48
436521 AAAACACATT
* *
436531 AAAATTAAATTAAAATGGAAACAAAGATAATTTAAATGAAATGAGAAA
1 AAAATTAAATTTAAATGGAAACAAAAATAATTTAAATGAAATGAGAAA
* *
436579 AAAA-TAATTTTAAATGTAAA-AAAAATAATTTAAATGAAATGAGAAA
1 AAAATTAAATTTAAATGGAAACAAAAATAATTTAAATGAAATGAGAAA
436625 AAAATTAAATTTAAATG
1 AAAATTAAATTTAAATG
436642 AAATGAGAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
46 29 0.51
47 24 0.42
48 4 0.07
ACGTcount: A:0.62, C:0.01, G:0.10, T:0.27
Consensus pattern (48 bp):
AAAATTAAATTTAAATGGAAACAAAAATAATTTAAATGAAATGAGAAA
Found at i:436660 original size:120 final size:123
Alignment explanation
Indices: 436531--436764 Score: 413
Period size: 120 Copynumber: 1.9 Consensus size: 123
436521 AAAACACATT
436531 AAAATTAAATTAAAATGGAAACAAAGATAATTTAAATGAAATGA-GAAAAAAATAATTTTAAATG
1 AAAATTAAATTAAAATGGAAACAAAGATAATTTAAATGAAATGAGGAAAAAAATAATTTTAAATG
436595 TAA-AAAAA-ATAATTTAAATGAAATGAGAA-AAAAATTAAATTTAAATGAAATGAGAA
66 TAACAAAAAGATAATTTAAATGAAATGAGAAGAAAAA-TAAATTTAAATGAAATGAGAA
* *
436651 AAAATTAAATTAAAATGGATACAAAGATAATTTAAATGAAATGAGGAAAAAATTAATTTTAAATG
1 AAAATTAAATTAAAATGGAAACAAAGATAATTTAAATGAAATGAGGAAAAAAATAATTTTAAATG
436716 TAACAAAAAGATAATTTAAATGAAATGAGAAGAAAAATAAATTTAAATG
66 TAACAAAAAGATAATTTAAATGAAATGAGAAGAAAAATAAATTTAAATG
436765 TAAAAAAATA
Statistics
Matches: 108, Mismatches: 2, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
120 43 0.40
121 22 0.20
122 5 0.05
123 33 0.31
124 5 0.05
ACGTcount: A:0.61, C:0.01, G:0.12, T:0.26
Consensus pattern (123 bp):
AAAATTAAATTAAAATGGAAACAAAGATAATTTAAATGAAATGAGGAAAAAAATAATTTTAAATG
TAACAAAAAGATAATTTAAATGAAATGAGAAGAAAAATAAATTTAAATGAAATGAGAA
Found at i:436692 original size:26 final size:23
Alignment explanation
Indices: 436543--436886 Score: 170
Period size: 26 Copynumber: 14.4 Consensus size: 23
436533 AATTAAATTA
436543 AAATGGAAACAAAGATAATTTAAATG
1 AAATGG-AA-AAA-ATAATTTAAATG
436569 AAATGAGAAAAAAATAATTTTAAATG
1 AAATG-G-AAAAAATAA-TTTAAATG
*
436595 TAA---AAAAAATAATTTAAATG
1 AAATGGAAAAAATAATTTAAATG
436615 AAATGAGAAAAAAATTAAATTTAAATG
1 AAATG-G-AAAAAA-T-AATTTAAATG
* *
436642 AAAT-GAGAAAA-AA-TTAAATTA
1 AAATGGAAAAAATAATTTAAA-TG
436663 AAATGGATACAAAGATAATTTAAATG
1 AAATGGA-A-AAA-ATAATTTAAATG
436689 AAATGAGGAAAAAATTAATTTTAAATG
1 AAAT--GGAAAAAA-TAA-TTTAAATG
* *
436716 TAA--CAAAAAGATAATTTAAATG
1 AAATGGAAAAA-ATAATTTAAATG
436738 AAATGAGAAGAAAAATAAATTTAAATG
1 AAATG-G-A-AAAAAT-AATTTAAATG
*
436765 TAAA---AAAATAATAATATAAATG
1 -AAATGGAAAA-AATAATTTAAATG
436787 AAAT-GACAAAAATAAATTT--A--
1 AAATGGA-AAAAAT-AATTTAAATG
*
436807 AAATGGGAAGATAAATAAATTAAATG
1 AAAT-GGAA-A-AAATAATTTAAATG
436833 AAATGAGAAAAAATTAAATTTAAATG
1 AAATG-GAAAAAA-T-AATTTAAATG
* *
436859 -AA---AAAATATAATTTTAATG
1 AAATGGAAAAAATAATTTAAATG
436878 AAATGGAAA
1 AAATGGAAA
436887 TGGAAATGAA
Statistics
Matches: 254, Mismatches: 16, Indels: 99
0.69 0.04 0.27
Matches are distributed among these distances:
19 9 0.04
20 22 0.09
21 25 0.10
22 32 0.13
23 23 0.09
24 20 0.08
25 18 0.07
26 51 0.20
27 48 0.19
28 6 0.02
ACGTcount: A:0.61, C:0.01, G:0.12, T:0.26
Consensus pattern (23 bp):
AAATGGAAAAAATAATTTAAATG
Found at i:436726 original size:49 final size:47
Alignment explanation
Indices: 436615--436886 Score: 279
Period size: 49 Copynumber: 5.8 Consensus size: 47
436605 AATTTAAATG
* *
436615 AAATGAGAAAAAAA-TTAAATTTAAATGAAATGAGAAAAAATTAAATTA
1 AAATG-GAAAAAAAGAT-AATTTAAATGAAATGAGAAAAAATTAAATTT
* * *
436663 AAATGGATACAAAGATAATTTAAATGAAATGAGGAAAAAATTAATTTT
1 AAATGGAAAAAAAGATAATTTAAATGAAATGA-GAAAAAATTAAATTT
* *
436711 AAATGTAACAAAAAGATAATTTAAATGAAATGAGAAGAAAAATAAATTT
1 AAATGGAA-AAAAAGATAATTTAAATGAAATGAGAA-AAAATTAAATTT
* * * *
436760 AAATGTAAAAAAATAATAATATAAATGAAATGA-CAAAAA-TAAATTT
1 AAATGGAAAAAAA-GATAATTTAAATGAAATGAGAAAAAATTAAATTT
* * *
436806 AAAATGGGAAGATAA-ATAAATTAAATGAAATGAGAAAAAATTAAATTT
1 -AAAT-GGAAAAAAAGATAATTTAAATGAAATGAGAAAAAATTAAATTT
* *
436854 AAAT-G-AAAAAATATAATTTTAATGAAATG-GAAA
1 AAATGGAAAAAAAGATAATTTAAATGAAATGAGAAA
436887 TGGAAATGAA
Statistics
Matches: 191, Mismatches: 23, Indels: 24
0.80 0.10 0.10
Matches are distributed among these distances:
44 8 0.04
45 16 0.08
46 23 0.12
47 39 0.20
48 47 0.25
49 58 0.30
ACGTcount: A:0.61, C:0.01, G:0.12, T:0.26
Consensus pattern (47 bp):
AAATGGAAAAAAAGATAATTTAAATGAAATGAGAAAAAATTAAATTT
Found at i:436829 original size:123 final size:119
Alignment explanation
Indices: 436531--436808 Score: 370
Period size: 120 Copynumber: 2.3 Consensus size: 119
436521 AAAACACATT
* *
436531 AAAATTAAATTAAAATGGAAACAAAGATAATTTAAATGAAATGA-GAAAAAAATAATTTTAAATG
1 AAAATTAAATTAAAATGG-AACAAAAATAATTTAAATGAAATGAGGAAAAAATTAATTTTAAATG
*
436595 TAAAAAAAATAATTTAAATGAAATGAGAAAAAAATTAAATTTAAATGAAATGAGAA
65 TAAAAAAAATAATTTAAATGAAATGAGAAAAAAATTAAATTTAAATGAAA-GAAAA
*
436651 AAAATTAAATTAAAATGGATACAAAGATAATTTAAATGAAATGAGGAAAAAATTAATTTTAAATG
1 AAAATTAAATTAAAATGGA-ACAAAAATAATTTAAATGAAATGAGGAAAAAATTAATTTTAAATG
436716 TAACAAAAAGATAATTTAAATGAAATGAGAAGAAAAA-TAAATTTAAATGTAAA-AAAA
65 TAA-AAAAA-ATAATTTAAATGAAATGAGAA-AAAAATTAAATTTAAATG-AAAGAAAA
*
436773 TAATAATATAAA-TGAAAT-G-ACAAAAATAAATTTAAA
1 -AA-AAT-TAAATTAAAATGGAACAAAAAT-AATTTAAA
436809 ATGGGAAGAT
Statistics
Matches: 144, Mismatches: 4, Indels: 18
0.87 0.02 0.11
Matches are distributed among these distances:
119 1 0.01
120 42 0.29
121 29 0.20
122 16 0.11
123 36 0.25
124 16 0.11
125 4 0.03
ACGTcount: A:0.62, C:0.01, G:0.10, T:0.26
Consensus pattern (119 bp):
AAAATTAAATTAAAATGGAACAAAAATAATTTAAATGAAATGAGGAAAAAATTAATTTTAAATGT
AAAAAAAATAATTTAAATGAAATGAGAAAAAAATTAAATTTAAATGAAAGAAAA
Found at i:436863 original size:19 final size:19
Alignment explanation
Indices: 436839--436880 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
436829 AATGAAATGA
436839 GAAAAAAT-TAAATTTAAAT
1 GAAAAAATAT-AATTTAAAT
*
436858 GAAAAAATATAATTTTAAT
1 GAAAAAATATAATTTAAAT
436877 GAAA
1 GAAA
436881 TGGAAATGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 20 0.95
20 1 0.05
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (19 bp):
GAAAAAATATAATTTAAAT
Found at i:436897 original size:5 final size:5
Alignment explanation
Indices: 436874--437116 Score: 139
Period size: 5 Copynumber: 44.2 Consensus size: 5
436864 ATATAATTTT
*
436874 AATGA AATGGA AATGGA AATGA AATGA AATGA AATGA AATTCA AATGA
1 AATGA AAT-GA AAT-GA AATGA AATGA AATGA AATGA AA-TGA AATGA
* * *
436922 AATGA AATAGA AATTCA AATTA AATAGA ACTGA AATAGA AATGA AATGAA
1 AATGA AAT-GA AA-TGA AATGA AAT-GA AATGA AAT-GA AATGA AATG-A
** * *
436972 AAAAA AAGTTGA AATGA AA-AA AAT-T AATGA AATGA AATGATA AATGAA
1 AATGA AA--TGA AATGA AATGA AATGA AATGA AATGA AATG--A AATG-A
* * *
437020 ATATGA ATATGA AATGA AATGTA ATTTGT AATGA ATATGA AACGA AATGA
1 A-ATGA A-ATGA AATGA AATG-A A-ATGA AATGA A-ATGA AATGA AATGA
* *
437070 AATGTGA AATGA ATATAA AATGA AATGA TATTATGA AATGG AATGA A
1 AA--TGA AATGA A-ATGA AATGA AATGA -A--ATGA AATGA AATGA A
437117 TGTTTAAATG
Statistics
Matches: 190, Mismatches: 25, Indels: 46
0.73 0.10 0.18
Matches are distributed among these distances:
4 6 0.03
5 104 0.55
6 56 0.29
7 20 0.11
8 4 0.02
ACGTcount: A:0.57, C:0.02, G:0.17, T:0.24
Consensus pattern (5 bp):
AATGA
Found at i:436897 original size:11 final size:10
Alignment explanation
Indices: 436874--437116 Score: 139
Period size: 11 Copynumber: 22.1 Consensus size: 10
436864 ATATAATTTT
436874 AATGAAATGGA
1 AATGAAAT-GA
436885 AATGGAAATGA
1 AAT-GAAATGA
436896 AATGAAATGA
1 AATGAAATGA
*
436906 AATGAAATTCA
1 AATGAAA-TGA
436917 AATGAAATGA
1 AATGAAATGA
*
436927 AATAGAAATTCA
1 AAT-GAAA-TGA
*
436939 AATTAAATAGA
1 AATGAAAT-GA
*
436950 ACTGAAATAGA
1 AATGAAAT-GA
436961 AATGAAATGAA
1 AATGAAATG-A
**
436972 AAAAAAAGTTGA
1 AATGAAA--TGA
*
436984 AATGAAA-AA
1 AATGAAATGA
*
436993 AAT-TAATGA
1 AATGAAATGA
437002 AATGAAATGATA
1 AATGAAATG--A
437014 AATGAAATATGA
1 AATG-AA-ATGA
437026 ATATGAAATGA
1 A-ATGAAATGA
* *
437037 AATGTAATTTGT
1 AATG-AA-ATGA
437049 AATGAATATGA
1 AATGAA-ATGA
*
437060 AACGAAATGA
1 AATGAAATGA
437070 AATGTGAAATGA
1 AA--TGAAATGA
*
437082 ATATAAAATGA
1 A-ATGAAATGA
437093 AATGATATTATGA
1 AATGA-A--ATGA
*
437106 AATGGAATGA
1 AATGAAATGA
437116 A
1 A
437117 TGTTTAAATG
Statistics
Matches: 184, Mismatches: 25, Indels: 47
0.72 0.10 0.18
Matches are distributed among these distances:
8 2 0.01
9 8 0.04
10 42 0.23
11 73 0.40
12 40 0.22
13 16 0.09
14 3 0.02
ACGTcount: A:0.57, C:0.02, G:0.17, T:0.24
Consensus pattern (10 bp):
AATGAAATGA
Found at i:437002 original size:18 final size:16
Alignment explanation
Indices: 436960--437008 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 16
436950 ACTGAAATAG
436960 AAATGAAATGAAAAAA
1 AAATGAAATGAAAAAA
436976 AAAGTTGAAATGAAAAAA
1 AAA--TGAAATGAAAAAA
436994 ATTAATGAAATGAAA
1 A--AATGAAATGAAA
437009 TGATAAATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
16 3 0.10
18 24 0.83
20 2 0.07
ACGTcount: A:0.67, C:0.00, G:0.14, T:0.18
Consensus pattern (16 bp):
AAATGAAATGAAAAAA
Found at i:437018 original size:12 final size:13
Alignment explanation
Indices: 436998--437098 Score: 58
Period size: 12 Copynumber: 8.2 Consensus size: 13
436988 AAAAAAATTA
436998 ATGAAATGAAATG
1 ATGAAATGAAATG
437011 AT-AAATGAAAT-
1 ATGAAATGAAATG
437022 ATGAATATG-AA--
1 ATGAA-ATGAAATG
*
437033 ATGAAATGTAAT-
1 ATGAAATGAAATG
* *
437045 TTGTAATGAATATG
1 ATGAAATGAA-ATG
*
437059 AAACGAAATGAAATG
1 --ATGAAATGAAATG
437074 -TGAAATG-AAT-
1 ATGAAATGAAATG
*
437084 ATAAAATGAAATG
1 ATGAAATGAAATG
437097 AT
1 AT
437099 ATTATGAAAT
Statistics
Matches: 69, Mismatches: 8, Indels: 22
0.70 0.08 0.22
Matches are distributed among these distances:
10 3 0.04
11 18 0.26
12 29 0.42
13 9 0.13
15 3 0.04
16 7 0.10
ACGTcount: A:0.53, C:0.01, G:0.18, T:0.28
Consensus pattern (13 bp):
ATGAAATGAAATG
Found at i:437066 original size:28 final size:28
Alignment explanation
Indices: 436998--437097 Score: 112
Period size: 28 Copynumber: 3.5 Consensus size: 28
436988 AAAAAAATTA
*
436998 ATGAAATGAAATGATAAATG-AAATATGAAT
1 ATGAAATGAAATG--AAATGTGAA-ATGAAT
* * *
437028 ATGAAATGAAATGTAATTTGTAATGAAT
1 ATGAAATGAAATGAAATGTGAAATGAAT
*
437056 ATGAAACGAAATGAAATGTGAAATGAAT
1 ATGAAATGAAATGAAATGTGAAATGAAT
*
437084 ATAAAATGAAATGA
1 ATGAAATGAAATGA
437098 TATTATGAAA
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
28 45 0.76
29 1 0.02
30 13 0.22
ACGTcount: A:0.54, C:0.01, G:0.18, T:0.27
Consensus pattern (28 bp):
ATGAAATGAAATGAAATGTGAAATGAAT
Found at i:437184 original size:21 final size:20
Alignment explanation
Indices: 437132--437227 Score: 78
Period size: 20 Copynumber: 4.8 Consensus size: 20
437122 AAATGAAAAC
*
437132 AAATATTGAAATGAAAATAT
1 AAATTTTGAAATGAAAATAT
437152 AAATTTTGAAATGAGAAATAATT
1 AAATTTTGAAATGA-AAAT-A-T
437175 AAA-TTT-AAAT--AAA-A-
1 AAATTTTGAAATGAAAATAT
*
437189 AAATATTGAAATGAAAATAT
1 AAATTTTGAAATGAAAATAT
*
437209 AAATGTAATGAAATGAAAA
1 AAAT-T-TTGAAATGAAAA
437228 AAAAAAAAAG
Statistics
Matches: 61, Mismatches: 4, Indels: 20
0.72 0.05 0.24
Matches are distributed among these distances:
14 3 0.05
15 2 0.03
16 5 0.08
18 6 0.10
19 1 0.02
20 17 0.28
21 8 0.13
22 15 0.25
23 4 0.07
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.29
Consensus pattern (20 bp):
AAATTTTGAAATGAAAATAT
Found at i:437206 original size:22 final size:22
Alignment explanation
Indices: 437167--437235 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 22
437157 TTGAAATGAG
* **
437167 AAATAATTAAATTTAAATAAAA
1 AAATAATGAAATGAAAATAAAA
* *
437189 AAATATTGAAATGAAAATATAA
1 AAATAATGAAATGAAAATAAAA
** *
437211 ATGTAATGAAATGAAAAAAAAA
1 AAATAATGAAATGAAAATAAAA
437233 AAA
1 AAA
437236 AGGTGAAAGG
Statistics
Matches: 35, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (22 bp):
AAATAATGAAATGAAAATAAAA
Found at i:437452 original size:16 final size:16
Alignment explanation
Indices: 437431--437465 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
437421 ACCAAAATTT
*
437431 TATTTTTAAATATTAG
1 TATTTTTAAATACTAG
*
437447 TATTTTTATATACTAG
1 TATTTTTAAATACTAG
437463 TAT
1 TAT
437466 GATACGATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.57
Consensus pattern (16 bp):
TATTTTTAAATACTAG
Found at i:460066 original size:18 final size:18
Alignment explanation
Indices: 460043--460079 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
460033 AAACCACCGG
* *
460043 TGCGATTGGTTTAATCAA
1 TGCGATTAGTATAATCAA
460061 TGCGATTAGTATAATCAA
1 TGCGATTAGTATAATCAA
460079 T
1 T
460080 TTAACCCGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (18 bp):
TGCGATTAGTATAATCAA
Found at i:460707 original size:18 final size:19
Alignment explanation
Indices: 460680--460719 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
460670 TGCATCATCC
*
460680 ATAATTAAATT-TAAAAAA
1 ATAATGAAATTATAAAAAA
*
460698 ATAATGAAATTATAAATAA
1 ATAATGAAATTATAAAAAA
460717 ATA
1 ATA
460720 TTAATAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (19 bp):
ATAATGAAATTATAAAAAA
Found at i:461415 original size:3 final size:3
Alignment explanation
Indices: 461407--461464 Score: 53
Period size: 3 Copynumber: 19.3 Consensus size: 3
461397 CTCTCATGTT
* * * * *
461407 TGA TGA TGA TGA TGA TGA TGA TGG TGA CGA CGA TGA CGA TGA CGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
* *
461455 CGA AGA TGA T
1 TGA TGA TGA T
461465 AATGGTGGTG
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.33, C:0.09, G:0.34, T:0.24
Consensus pattern (3 bp):
TGA
Found at i:463376 original size:9 final size:9
Alignment explanation
Indices: 463357--463392 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
463347 TAGTACTTAT
463357 TTTTTTCTTC
1 TTTTTT-TTC
463367 TTTTTTTTC
1 TTTTTTTTC
*
463376 TTTTTTTTA
1 TTTTTTTTC
463385 TTTTTTTT
1 TTTTTTTT
463393 AAATTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 19 0.76
10 6 0.24
ACGTcount: A:0.03, C:0.08, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:464609 original size:6 final size:6
Alignment explanation
Indices: 464593--464649 Score: 59
Period size: 6 Copynumber: 9.7 Consensus size: 6
464583 ATATTTAACT
464593 AAAAT- AAAATA AAAATAA AAAATA AATAATA AAAGA-A AAAAT- -AAATA
1 AAAATA AAAATA AAAAT-A AAAATA AA-AATA AAA-ATA AAAATA AAAATA
464640 AAAATA AAAA
1 AAAATA AAAA
464650 GAAAGATTGG
Statistics
Matches: 45, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
4 4 0.09
5 6 0.13
6 22 0.49
7 13 0.29
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:464609 original size:11 final size:11
Alignment explanation
Indices: 464593--464648 Score: 60
Period size: 11 Copynumber: 4.8 Consensus size: 11
464583 ATATTTAACT
464593 AAAATAAAATA
1 AAAATAAAATA
464604 AAAATAAAAAATA
1 AAAAT--AAAATA
*
464617 AATAATAAAAGA
1 AA-AATAAAATA
464629 AAAA-ATAAATA
1 AAAATA-AAATA
464640 AAAATAAAA
1 AAAATAAAA
464649 AGAAAGATTG
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
10 1 0.03
11 18 0.47
12 8 0.21
13 8 0.21
14 3 0.08
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:464615 original size:7 final size:7
Alignment explanation
Indices: 464598--464649 Score: 54
Period size: 7 Copynumber: 7.4 Consensus size: 7
464588 TAACTAAAAT
464598 AAAAT-A
1 AAAATAA
464604 AAAATAA
1 AAAATAA
464611 AAAATAA
1 AAAATAA
*
464618 ATAATAA
1 AAAATAA
*
464625 AAGAAAAA
1 AA-AATAA
464633 ATAAAT-A
1 A-AAATAA
464640 AAAATAA
1 AAAATAA
464647 AAA
1 AAA
464650 GAAAGATTGG
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
6 9 0.24
7 21 0.55
8 7 0.18
9 1 0.03
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.15
Consensus pattern (7 bp):
AAAATAA
Found at i:464625 original size:25 final size:25
Alignment explanation
Indices: 464595--464653 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
464585 ATTTAACTAA
*
464595 AATAAAA-TAAAAATAAAAAATAAAT
1 AATAAAAGAAAAAATAAAAAA-AAAT
*
464620 AATAAAAGAAAAAATAAATAAAAAT
1 AATAAAAGAAAAAATAAAAAAAAAT
464645 -A-AAAAGAAA
1 AATAAAAGAAA
464654 GATTGGGTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 8 0.26
24 1 0.03
25 11 0.35
26 11 0.35
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.15
Consensus pattern (25 bp):
AATAAAAGAAAAAATAAAAAAAAAT
Found at i:464631 original size:19 final size:19
Alignment explanation
Indices: 464604--464640 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
464594 AAATAAAATA
*
464604 AAAATAAAAAATAAATAAT
1 AAAAGAAAAAATAAATAAT
464623 AAAAGAAAAAATAAATAA
1 AAAAGAAAAAATAAATAA
464641 AAATAAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (19 bp):
AAAAGAAAAAATAAATAAT
Found at i:471639 original size:26 final size:24
Alignment explanation
Indices: 471601--471648 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
471591 ATAAAAAGAT
**
471601 TTTAAAATTATAATAAATTAAATACA
1 TTTAAAAACATAA-AAA-TAAATACA
471627 TTTAAAAACATAAAAATAAATA
1 TTTAAAAACATAAAAATAAATA
471649 TTAAACAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 3 0.15
26 11 0.55
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (24 bp):
TTTAAAAACATAAAAATAAATACA
Found at i:471660 original size:21 final size:20
Alignment explanation
Indices: 471620--471663 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
471610 ATAATAAATT
*
471620 AAATACATTTAAAAACATAA
1 AAATAAATTTAAAAACATAA
471640 AAATAAATATTAAACAA-ATAA
1 AAATAAAT-TTAAA-AACATAA
471661 AAA
1 AAA
471664 ATGATATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 7 0.33
21 12 0.57
22 2 0.10
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (20 bp):
AAATAAATTTAAAAACATAA
Found at i:473466 original size:81 final size:81
Alignment explanation
Indices: 473328--473480 Score: 218
Period size: 81 Copynumber: 1.9 Consensus size: 81
473318 ATCGAAGTTC
* * *
473328 AGAGAAAAATCAAGTTATTAGGCAAGGAGTGCTGGTATAATCTGGAACCAGACCAACCTACAGGC
1 AGAGAAAAATCAAGTTATTAGGCAAGGAGTGCTGGTATAATCTGGAACCAGAACAACCAACAGAC
473393 GCAACAGCACAAGATA
66 GCAACAGCACAAGATA
** * **
473409 AGAGAAAAATCCTGTTATTTGGCAAGGAGTGC-GGCTATTTTCTGGAACCAGAACAACCAACAGA
1 AGAGAAAAATCAAGTTATTAGGCAAGGAGTGCTGG-TATAATCTGGAACCAGAACAACCAACAGA
473473 CGCAACAG
65 CGCAACAG
473481 GAGAAGTTAT
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
80 2 0.03
81 61 0.97
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.18
Consensus pattern (81 bp):
AGAGAAAAATCAAGTTATTAGGCAAGGAGTGCTGGTATAATCTGGAACCAGAACAACCAACAGAC
GCAACAGCACAAGATA
Found at i:474219 original size:11 final size:12
Alignment explanation
Indices: 474197--474222 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
474187 AGCTCGATTG
474197 TTAAGTTTTTTT
1 TTAAGTTTTTTT
474209 TTAAGTTTTTTT
1 TTAAGTTTTTTT
474221 TT
1 TT
474223 TAAAGTTTAG
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:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (12 bp):
TTAAGTTTTTTT
Found at i:474220 original size:13 final size:13
Alignment explanation
Indices: 474197--474230 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
474187 AGCTCGATTG
474197 TTAAG-TTTTTTT
1 TTAAGTTTTTTTT
474209 TTAAGTTTTTTTT
1 TTAAGTTTTTTTT
474222 TTAAAGTTT
1 TT-AAGTTT
474231 AGTTAGTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 5 0.25
13 9 0.45
14 6 0.30
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.71
Consensus pattern (13 bp):
TTAAGTTTTTTTT
Found at i:476463 original size:44 final size:45
Alignment explanation
Indices: 476381--476465 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 45
476371 AATCTAGAAG
* *
476381 TTAAGCGATAGTGGTTAAATTAGCTGGACGTTGAAAATATTAGTC
1 TTAAGCAATAGTGGTTAAATTAGCTGGACGTCGAAAATATTAGTC
** *
476426 TTAAGCAATAGTGGTT-TGTTAGCTGGCCGTCGAAAATATT
1 TTAAGCAATAGTGGTTAAATTAGCTGGACGTCGAAAATATT
476466 GAAATGATTC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
44 20 0.57
45 15 0.43
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.34
Consensus pattern (45 bp):
TTAAGCAATAGTGGTTAAATTAGCTGGACGTCGAAAATATTAGTC
Found at i:483480 original size:32 final size:32
Alignment explanation
Indices: 483406--483470 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
483396 TAATCGAGCA
483406 TTGAAAATATTGCAATTCTTTTATACTAAACC
1 TTGAAAATATTGCAATTCTTTTATACTAAACC
483438 TTGAAAATATTGCAATTCTTTTATACTAAACC
1 TTGAAAATATTGCAATTCTTTTATACTAAACC
483470 T
1 T
483471 CTATGATATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.42
Consensus pattern (32 bp):
TTGAAAATATTGCAATTCTTTTATACTAAACC
Found at i:493131 original size:16 final size:16
Alignment explanation
Indices: 493092--493133 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
493082 AATTTGGTTT
493092 TTATATTATTTTTACAA
1 TTAT-TTATTTTTACAA
*
493109 TTTTTTATTTTTA-ATA
1 TTATTTATTTTTACA-A
493125 TTATTTATT
1 TTATTTATT
493134 ATTATATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 1 0.05
16 18 0.82
17 3 0.14
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (16 bp):
TTATTTATTTTTACAA
Found at i:493135 original size:3 final size:3
Alignment explanation
Indices: 493113--493187 Score: 55
Period size: 3 Copynumber: 25.0 Consensus size: 3
493103 TTACAATTTT
* * * *
493113 TTA TTT TTA ATA TTA TTTA TTA TTA -TA TTTA CTA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
* * *
493159 TTA TTA TTA GTA -TA TTT TTA CTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
493188 GAATTATTTT
Statistics
Matches: 55, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
2 4 0.07
3 46 0.84
4 5 0.09
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:493185 original size:20 final size:21
Alignment explanation
Indices: 493160--493198 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
493150 TCATTATTAT
*
493160 TATTATTAGTA-TATTTTTAC
1 TATTATTAGAATTATTTTTAC
493180 TATTATTAGAATTATTTTT
1 TATTATTAGAATTATTTTT
493199 TTAGTTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.62
Consensus pattern (21 bp):
TATTATTAGAATTATTTTTAC
Found at i:493618 original size:64 final size:58
Alignment explanation
Indices: 493534--493666 Score: 135
Period size: 64 Copynumber: 2.2 Consensus size: 58
493524 CTTTTAACAC
* * *
493534 TATA-TTATGTATATATTTTTACAT-GTATTATGTACATATTTTCAATAACTATATCATATGTA
1 TATATTTATGTACATACTTTTA-ATAGTATTATGTACATATTTT---TAA-TATA-AATATGTA
* **
493596 TATATTTTATGTACATACTTTTAATATTATTATGTATTTATTTTTAATATAAATATGTA
1 TATA-TTTATGTACATACTTTTAATAGTATTATGTACATATTTTTAATATAAATATGTA
493655 TATATTTATGTA
1 TATATTTATGTA
493667 GTATTATTAA
Statistics
Matches: 62, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
58 8 0.13
59 11 0.18
60 4 0.06
61 3 0.05
62 4 0.06
63 2 0.03
64 30 0.48
ACGTcount: A:0.35, C:0.05, G:0.06, T:0.53
Consensus pattern (58 bp):
TATATTTATGTACATACTTTTAATAGTATTATGTACATATTTTTAATATAAATATGTA
Found at i:493629 original size:23 final size:23
Alignment explanation
Indices: 493597--493654 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
493587 TCATATGTAT
493597 ATATT-TTATGTACATACTTTTA
1 ATATTATTATGTACATACTTTTA
** *
493619 ATATTATTATGTATTTATTTTTA
1 ATATTATTATGTACATACTTTTA
* *
493642 ATATAAATATGTA
1 ATATTATTATGTA
493655 TATATTTATG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 5 0.17
23 25 0.83
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.55
Consensus pattern (23 bp):
ATATTATTATGTACATACTTTTA
Found at i:493655 original size:23 final size:23
Alignment explanation
Indices: 493603--493661 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
493593 GTATATATTT
* * * *
493603 TATGTACATACTTTTAATATTAT
1 TATGTATATATTTTTAATATAAA
*
493626 TATGTATTTATTTTTAATATAAA
1 TATGTATATATTTTTAATATAAA
493649 TATGTATATATTT
1 TATGTATATATTT
493662 ATGTAGTATT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (23 bp):
TATGTATATATTTTTAATATAAA
Found at i:493740 original size:24 final size:24
Alignment explanation
Indices: 493697--493759 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
493687 TTTTAATATG
*
493697 TATATACTATGTA-A-ATATTTTAA
1 TATATATTATGTATACAT-TTTTAA
*
493720 TACTATATTATGTATACATTTTTTA
1 TA-TATATTATGTATACATTTTTAA
*
493745 TATATATTACGTATA
1 TATATATTATGTATA
493760 TATATCTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
23 2 0.06
24 22 0.65
25 8 0.24
26 2 0.06
ACGTcount: A:0.38, C:0.06, G:0.05, T:0.51
Consensus pattern (24 bp):
TATATATTATGTATACATTTTTAA
Found at i:493912 original size:25 final size:25
Alignment explanation
Indices: 493822--493912 Score: 92
Period size: 25 Copynumber: 3.5 Consensus size: 25
493812 CTATATTACG
* *
493822 TTTTTACATATTATCTTATGTATATA
1 TTTTTA-ATACTATATTATGTATATA
*
493848 TTTTTTAATAACTATATTATGTATGTA
1 -TTTTTAAT-ACTATATTATGTATATA
** *
493875 TTTTTAACGCTATATTATGTACATA
1 TTTTTAATACTATATTATGTATATA
*
493900 TTTTTAGTACTAT
1 TTTTTAATACTAT
493913 GTATCCTTTT
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
25 24 0.45
26 9 0.17
27 20 0.38
ACGTcount: A:0.31, C:0.08, G:0.07, T:0.55
Consensus pattern (25 bp):
TTTTTAATACTATATTATGTATATA
Found at i:500862 original size:8 final size:8
Alignment explanation
Indices: 500849--500881 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
500839 TCACCAACAA
500849 AGCTAGGG
1 AGCTAGGG
500857 AGCTAGGG
1 AGCTAGGG
500865 AGCTAGGG
1 AGCTAGGG
500873 AGCTAGGG
1 AGCTAGGG
500881 A
1 A
500882 CAGTAAACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.27, C:0.12, G:0.48, T:0.12
Consensus pattern (8 bp):
AGCTAGGG
Found at i:505408 original size:15 final size:15
Alignment explanation
Indices: 505388--505433 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
505378 ACAAAATAAT
505388 AACATAAGTGACTAA
1 AACATAAGTGACTAA
* *
505403 AACATAA-T-ATTTCA
1 AACATAAGTGA-CTAA
505417 AACATAAGTGACTAA
1 AACATAAGTGACTAA
505432 AA
1 AA
505434 TGTAACCTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 6
0.71 0.12 0.18
Matches are distributed among these distances:
13 1 0.04
14 10 0.42
15 12 0.50
16 1 0.04
ACGTcount: A:0.54, C:0.13, G:0.09, T:0.24
Consensus pattern (15 bp):
AACATAAGTGACTAA
Found at i:510302 original size:35 final size:35
Alignment explanation
Indices: 510258--510424 Score: 192
Period size: 35 Copynumber: 4.6 Consensus size: 35
510248 TCCTCATTGA
** *
510258 AATACCATACCTACATTTTTCAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* **
510293 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
* *
510333 AATACCATACCTACATTTCACAGCTCAATATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
510368 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
510403 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
510425 CTTTACCATG
Statistics
Matches: 115, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
35 86 0.75
39 3 0.03
40 26 0.23
ACGTcount: A:0.34, C:0.25, G:0.10, T:0.31
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:510341 original size:75 final size:73
Alignment explanation
Indices: 510253--510424 Score: 217
Period size: 75 Copynumber: 2.4 Consensus size: 73
510243 GGTTTTCCTC
** ** * **
510253 ATTGAAATACCATACCTACATTTTTCAACTCGGTATGGGA-AATGCCATACCTACATTTCTTAAC
1 ATTGAAATACCATACCTACATTTCACAACTCAATAT-GGATAATACCATACCTACATTTCACAAC
510317 TCAGTATGG
65 TCAGTATGG
*
510326 ATTTGATAATACCATACCTACATTTCACAGCTCAATATGGATAATACCATACCTACATTTCACAA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAATATGGATAATACCATACCTACATTTCACAA
510391 CTCAGTATGG
64 CTCAGTATGG
510401 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
510425 CTTTACCATG
Statistics
Matches: 88, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
70 21 0.24
73 3 0.03
74 7 0.08
75 57 0.65
ACGTcount: A:0.34, C:0.24, G:0.10, T:0.31
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAATATGGATAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:512912 original size:28 final size:28
Alignment explanation
Indices: 512875--512981 Score: 160
Period size: 28 Copynumber: 3.8 Consensus size: 28
512865 GCAATCAAAT
*
512875 ATGGTACTTAGTGTACGAAATATTGAGA
1 ATGGCACTTAGTGTACGAAATATTGAGA
512903 ATGGCACTTAGTGTACGAAATATTGAGA
1 ATGGCACTTAGTGTACGAAATATTGAGA
* *
512931 ATGGCACTTAGTGTGCGAGATATTGAGA
1 ATGGCACTTAGTGTACGAAATATTGAGA
* * *
512959 ATGACACTTAGTGTGCAAAATAT
1 ATGGCACTTAGTGTACGAAATAT
512982 CGAATGATTC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 73 1.00
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (28 bp):
ATGGCACTTAGTGTACGAAATATTGAGA
Found at i:517969 original size:30 final size:30
Alignment explanation
Indices: 517933--517990 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
517923 AACAAAAAAG
*
517933 CCATAGGAGGTCTGGAAAAAGTTGGTTTCT
1 CCATAGGAGGTCTGGAAAAAGCTGGTTTCT
517963 CCATAGGAGGTCTGGAAAAAGCTGGTTT
1 CCATAGGAGGTCTGGAAAAAGCTGGTTT
517991 TCATATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.28, C:0.14, G:0.31, T:0.28
Consensus pattern (30 bp):
CCATAGGAGGTCTGGAAAAAGCTGGTTTCT
Found at i:518820 original size:35 final size:35
Alignment explanation
Indices: 518774--518898 Score: 162
Period size: 35 Copynumber: 3.6 Consensus size: 35
518764 ATCCACGACA
* *
518774 AGTTATGATACGTAGGTATGGCATCGCCCATACCG
1 AGTTATGATACGTAGGTATGGCATCGTCCATACTG
* **
518809 AGTTATGATACGTAGGTATGACATTATCCATACTG
1 AGTTATGATACGTAGGTATGGCATCGTCCATACTG
*
518844 AGTTATGATACATAGGTATGGCATCGTCCATACTG
1 AGTTATGATACGTAGGTATGGCATCGTCCATACTG
* * *
518879 AGTGAT-AAATGTAGGTATGG
1 AGTTATGATACGTAGGTATGG
518899 TATTTCAACG
Statistics
Matches: 77, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
34 11 0.14
35 66 0.86
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (35 bp):
AGTTATGATACGTAGGTATGGCATCGTCCATACTG
Found at i:519913 original size:22 final size:20
Alignment explanation
Indices: 519874--519913 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
519864 CACAACCGAC
*
519874 CCACACGGGTGTGTCCCTAT
1 CCACACGGGTGTGGCCCTAT
519894 CCACACGGGCATGTGGCCCT
1 CCACACGGG--TGTGGCCCT
519914 GTTTCAGAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
22 8 0.47
ACGTcount: A:0.15, C:0.38, G:0.28, T:0.20
Consensus pattern (20 bp):
CCACACGGGTGTGGCCCTAT
Found at i:536949 original size:2 final size:2
Alignment explanation
Indices: 536942--536966 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
536932 GGTAACAATT
536942 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
536967 TATTATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:540373 original size:2 final size:2
Alignment explanation
Indices: 540366--540392 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
540356 TAATAAAGTC
540366 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
540393 AACAATTGAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:545219 original size:18 final size:18
Alignment explanation
Indices: 545196--545231 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
545186 ACCTTGATGG
545196 CGGACCGCTGTTCGAACC
1 CGGACCGCTGTTCGAACC
*
545214 CGGACCGCTGTTTGAACC
1 CGGACCGCTGTTCGAACC
545232 GGCTCGAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.36, G:0.28, T:0.19
Consensus pattern (18 bp):
CGGACCGCTGTTCGAACC
Found at i:547806 original size:86 final size:85
Alignment explanation
Indices: 547647--547810 Score: 242
Period size: 85 Copynumber: 1.9 Consensus size: 85
547637 TTCTCAATTT
* *
547647 ATATTAAATAACTTTAAATTTGAAATTTGAAACTCACAAAGAATATTTCTTTTTCTATACTTTAT
1 ATATTAAATAACTTTAAATTTGAAATTTGAAACCCACAAAGAATATTTCTTTTTCTATACTTTAA
*
547712 ATACTTTTTTTTTTCAAATA
66 AAACTTTTTTTTTTCAAATA
* *
547732 ATATTAAATAACTTTAAAATTTGAAATTTGAAACCCAC-AAGAATATTTTTTTTTCTTTTA-TTT
1 ATATTAAATAACTTT-AAATTTGAAATTTGAAACCCACAAAGAATATTTCTTTTTC-TATACTTT
*
547795 AAAAACATTTTTTTTT
64 AAAAACTTTTTTTTTT
547811 GCCTTTTTTT
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
85 47 0.66
86 24 0.34
ACGTcount: A:0.38, C:0.10, G:0.04, T:0.49
Consensus pattern (85 bp):
ATATTAAATAACTTTAAATTTGAAATTTGAAACCCACAAAGAATATTTCTTTTTCTATACTTTAA
AAACTTTTTTTTTTCAAATA
Found at i:547849 original size:5 final size:6
Alignment explanation
Indices: 547832--547856 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
547822 AGATGCTCAG
547832 ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA A
547857 GCCAAACACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:555911 original size:93 final size:93
Alignment explanation
Indices: 555799--555970 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
555789 TACCCATAAG
* *
555799 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
555864 ACGAGCTCGGATGCCTAGTTACATTTCA
66 ACGAGCTCGGATGCCTAGTTACATTTCA
* *
555892 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATATGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
555957 ACGAGTTCGGATGC
66 ACGAGCTCGGATGC
555971 TCAACCATCC
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATTTCA
Found at i:555967 original size:46 final size:46
Alignment explanation
Indices: 555800--555967 Score: 189
Period size: 46 Copynumber: 3.6 Consensus size: 46
555790 ACCCATAAGC
* * *
555800 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATATGT
* * * **
555846 GAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTTACATTTCAC
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--TCCATAT-GT
*
555893 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATATGT
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATATGT
*
555939 GAACTCGGACTCAACTCAACGAGTTCGGA
1 GAACTCGGACTCAACTCAACGAGCTCGGA
555968 TGCTCAACCA
Statistics
Matches: 102, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 61 0.60
47 32 0.31
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATATGT
Found at i:557398 original size:17 final size:18
Alignment explanation
Indices: 557357--557399 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
557347 ATTATTTACT
557357 TATTATATAAGTAAATAA
1 TATTATATAAGTAAATAA
* *
557375 TAATATA-AAGTAAATTA
1 TATTATATAAGTAAATAA
557392 TATTATAT
1 TATTATAT
557400 TATATAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (18 bp):
TATTATATAAGTAAATAA
Found at i:565605 original size:21 final size:21
Alignment explanation
Indices: 565579--565619 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
565569 AGACAAGCGA
* *
565579 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
565600 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
565620 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:574520 original size:16 final size:16
Alignment explanation
Indices: 574496--574526 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
574486 TCAAGCAATT
*
574496 CAAATTTGAAATAACC
1 CAAAATTGAAATAACC
574512 CAAAATTGAAATAAC
1 CAAAATTGAAATAAC
574527 TAAAACCCGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.16, G:0.06, T:0.23
Consensus pattern (16 bp):
CAAAATTGAAATAACC
Found at i:577965 original size:21 final size:21
Alignment explanation
Indices: 577941--578008 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
577931 GGTGAGAATT
577941 TTTTAAGCATGCTCAAACACA
1 TTTTAAGCATGCTCAAACACA
* *
577962 TTTTAATGCA-G--AAGAACGTCGA
1 TTTTAA-GCATGCTCA-AAC-AC-A
577984 -TTTAAGCATGCTCAAACACA
1 TTTTAAGCATGCTCAAACACA
578004 TTTTA
1 TTTTA
578009 TCCTTTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 16
0.64 0.07 0.29
Matches are distributed among these distances:
19 1 0.03
20 7 0.20
21 19 0.54
22 7 0.20
23 1 0.03
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (21 bp):
TTTTAAGCATGCTCAAACACA
Found at i:579930 original size:5 final size:6
Alignment explanation
Indices: 579913--579940 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
579903 ATTATTGTTC
579913 ATAAAA ATAAAA ATAAAA ATAAAA ATAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAA
579941 TTAAATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
ATAAAA
Found at i:580992 original size:54 final size:54
Alignment explanation
Indices: 580933--581040 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
580923 CTCCAGTTTG
580933 AAGCTTTTGCCGTTTAAGTCAAGTAATTACCGATTATTATTGTTTCCTTTTGCC
1 AAGCTTTTGCCGTTTAAGTCAAGTAATTACCGATTATTATTGTTTCCTTTTGCC
580987 AAGCTTTTGCCGTTTAAGTCAAGTAATTACCGATTATTATTGTTTCCTTTTGCC
1 AAGCTTTTGCCGTTTAAGTCAAGTAATTACCGATTATTATTGTTTCCTTTTGCC
581041 TTAATTCTTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.22, C:0.19, G:0.15, T:0.44
Consensus pattern (54 bp):
AAGCTTTTGCCGTTTAAGTCAAGTAATTACCGATTATTATTGTTTCCTTTTGCC
Found at i:584941 original size:2 final size:2
Alignment explanation
Indices: 584934--584958 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
584924 CAAAGAACGC
584934 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
584959 TGTTCCTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:586954 original size:13 final size:14
Alignment explanation
Indices: 586922--586948 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
586912 AAATTCGAAT
586922 AAATTTTTAAATTC
1 AAATTTTTAAATTC
586936 AAATTTTTAAATT
1 AAATTTTTAAATT
586949 GAATTTAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (14 bp):
AAATTTTTAAATTC
Found at i:588168 original size:31 final size:30
Alignment explanation
Indices: 588133--588195 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
588123 TAATAAAGGT
*
588133 AAAATTACACTTTGATCCTTTAAAAATGATA
1 AAAATTACAC-TTAATCCTTTAAAAATGATA
** *
588164 AAAATTTGACTTAATCCTTTAAAAATTATA
1 AAAATTACACTTAATCCTTTAAAAATGATA
588194 AA
1 AA
588196 TATATATACT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 20 0.71
31 8 0.29
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.37
Consensus pattern (30 bp):
AAAATTACACTTAATCCTTTAAAAATGATA
Found at i:596119 original size:23 final size:23
Alignment explanation
Indices: 596076--596119 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
596066 ACGATGATAG
* *
596076 ATATTAATTTTAATATTATAAAT
1 ATATAAATTTTAATATGATAAAT
596099 ATATAAATTTATAA-ATGATAA
1 ATATAAATTT-TAATATGATAA
596120 TCAAAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 15 0.83
24 3 0.17
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
ATATAAATTTTAATATGATAAAT
Found at i:599079 original size:24 final size:24
Alignment explanation
Indices: 599052--599110 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
599042 CAATTAAAAC
599052 TTTATTTTTAATATTTTTATACAT
1 TTTATTTTTAATATTTTTATACAT
* *
599076 TTTAATTTTATTATTTTTATACAT
1 TTTATTTTTAATATTTTTATACAT
*
599100 TTCATTATTTA
1 TTTATT-TTTA
599111 TTTGTGTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
24 26 0.87
25 4 0.13
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (24 bp):
TTTATTTTTAATATTTTTATACAT
Found at i:600794 original size:21 final size:21
Alignment explanation
Indices: 600769--600871 Score: 93
Period size: 21 Copynumber: 4.8 Consensus size: 21
600759 ACACATATAT
*
600769 ATATAAATAATAGTATTAGAA
1 ATATAAATAATAATATTAGAA
600790 ATATACAAT-ATAATATTAGAA
1 ATATA-AATAATAATATTAGAA
* **
600811 ATATATATAATAGTATAAAAGAAAA
1 ATATAAATAATA--ATATTAG--AA
*
600836 ATATAACTAATAATATTA-AA
1 ATATAAATAATAATATTAGAA
*
600856 ATATATATAATAATAT
1 ATATAAATAATAATAT
600872 ATGTGAAATA
Statistics
Matches: 66, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
20 18 0.27
21 24 0.36
22 3 0.05
23 9 0.14
25 12 0.18
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (21 bp):
ATATAAATAATAATATTAGAA
Found at i:600794 original size:23 final size:23
Alignment explanation
Indices: 600767--600883 Score: 102
Period size: 23 Copynumber: 5.2 Consensus size: 23
600757 ACACACATAT
*
600767 ATATATAAATAATAGTATTAGAA
1 ATATATAAATAATAATATTAGAA
*
600790 ATATA-CAAT-ATAATATTAGAA
1 ATATATAAATAATAATATTAGAA
* **
600811 ATATATATAATAGT-ATAAAAGAA
1 ATATATA-AATAATAATATTAGAA
* *
600834 AAATATAACTAATAATATTA-AA
1 ATATATAAATAATAATATTAGAA
600856 ATATATATAATAAT-ATATGT-GAA
1 ATATATA-AATAATAATAT-TAGAA
600879 ATATA
1 ATATA
600884 ATATTAAAAA
Statistics
Matches: 74, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
21 16 0.22
22 19 0.26
23 38 0.51
24 1 0.01
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (23 bp):
ATATATAAATAATAATATTAGAA
Found at i:600856 original size:20 final size:20
Alignment explanation
Indices: 600833--600871 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
600823 GTATAAAAGA
600833 AAAATATA-ACTAATAATATT
1 AAAATATATA-TAATAATATT
600853 AAAATATATATAATAATAT
1 AAAATATATATAATAATAT
600872 ATGTGAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAATATATATAATAATATT
Found at i:601188 original size:18 final size:20
Alignment explanation
Indices: 601153--601194 Score: 61
Period size: 18 Copynumber: 2.1 Consensus size: 20
601143 AATAGTACCT
601153 TAAAAATAATTAGTATATTAA
1 TAAAAATAATTAG-ATATTAA
601174 TAAAAATAA-TA-ATATTAA
1 TAAAAATAATTAGATATTAA
601192 TAA
1 TAA
601195 TATGTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.48
20 2 0.10
21 9 0.43
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
TAAAAATAATTAGATATTAA
Found at i:601195 original size:21 final size:21
Alignment explanation
Indices: 601153--601196 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
601143 AATAGTACCT
* *
601153 TAAAAATAATTAGTATATTAA
1 TAAAAATAATTAATATAATAA
601174 TAAAAATAA-TAATATTAATAA
1 TAAAAATAATTAATA-TAATAA
601195 TA
1 TA
601197 TGTAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
TAAAAATAATTAATATAATAA
Found at i:601691 original size:16 final size:16
Alignment explanation
Indices: 601652--601697 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
601642 AAAAAAAAGA
* *
601652 AAAAAAGAGAAGGGAG
1 AAAAGAGAGAGGGGAG
601668 AAAAGAGAGAGGGGAG
1 AAAAGAGAGAGGGGAG
**
601684 AAGGGAGAGAGGGG
1 AAAAGAGAGAGGGG
601698 TTCTGGCGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (16 bp):
AAAAGAGAGAGGGGAG
Found at i:602234 original size:22 final size:22
Alignment explanation
Indices: 602177--602234 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
602167 TACGAGGACT
* * *
602177 GTGGAGGTATGGGACTGTTGTA
1 GTGGAGGTATGGGGCCGCTGTA
*
602199 GTGGGGGTATGGGGCCGCTGTA
1 GTGGAGGTATGGGGCCGCTGTA
602221 GTGGAGGTATGGGG
1 GTGGAGGTATGGGG
602235 TTGCTTCATG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.14, C:0.07, G:0.53, T:0.26
Consensus pattern (22 bp):
GTGGAGGTATGGGGCCGCTGTA
Found at i:606724 original size:28 final size:28
Alignment explanation
Indices: 606688--606765 Score: 138
Period size: 28 Copynumber: 2.8 Consensus size: 28
606678 ATTTAAAATA
* *
606688 AAATTAAATGAAATTTTAAAAAGAAAAC
1 AAATCAAATCAAATTTTAAAAAGAAAAC
606716 AAATCAAATCAAATTTTAAAAAGAAAAC
1 AAATCAAATCAAATTTTAAAAAGAAAAC
606744 AAATCAAATCAAATTTTAAAAA
1 AAATCAAATCAAATTTTAAAAA
606766 ATTGATTTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.64, C:0.08, G:0.04, T:0.24
Consensus pattern (28 bp):
AAATCAAATCAAATTTTAAAAAGAAAAC
Found at i:606804 original size:12 final size:12
Alignment explanation
Indices: 606783--606821 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
606773 TTATTAATCA
606783 AAATATTAAAAAT
1 AAATA-TAAAAAT
*
606796 AAATATAAAAAC
1 AAATATAAAAAT
*
606808 AAATATGAAAAT
1 AAATATAAAAAT
606820 AA
1 AA
606822 TAATATAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 18 0.78
13 5 0.22
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (12 bp):
AAATATAAAAAT
Found at i:607844 original size:38 final size:38
Alignment explanation
Indices: 607799--607874 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
607789 AATAAATATC
607799 ACAATTTGATGCATTTAATGGGGAAATAAATTTAATGT
1 ACAATTTGATGCATTTAATGGGGAAATAAATTTAATGT
607837 ACAATTTGATGCATTTAATGGGGAAATAAATTTAATGT
1 ACAATTTGATGCATTTAATGGGGAAATAAATTTAATGT
607875 GTGGACCACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.39, C:0.05, G:0.18, T:0.37
Consensus pattern (38 bp):
ACAATTTGATGCATTTAATGGGGAAATAAATTTAATGT
Found at i:609316 original size:80 final size:80
Alignment explanation
Indices: 609193--609346 Score: 190
Period size: 80 Copynumber: 1.9 Consensus size: 80
609183 TAATTATATA
*
609193 AAAATAAAATAAATATTTTTAAATTAAAATAATTCAATATTTTAT-AATATCAATTATATAAAAT
1 AAAATAAAATAAATATTATTAAATTAAAATAATTCAATATTTTATGAATATCAATTATATAAAAT
609257 ATATAAATTCAAAGCAT
66 A-A-AAATTCAAAGCAT
* * * *
609274 AAAATATATTAAA-ATTATTAAATTAAAGA-AATTTC-ATTTTTTATGGTATATCAATTATATAA
1 AAAATAAAATAAATATTATTAAATTAAA-ATAA-TTCAATATTTTAT-GAATATCAATTATATAA
609336 AATAAAAATTC
63 AATAAAAATTC
609347 TATTTTAAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
80 29 0.45
81 16 0.25
82 19 0.30
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.40
Consensus pattern (80 bp):
AAAATAAAATAAATATTATTAAATTAAAATAATTCAATATTTTATGAATATCAATTATATAAAAT
AAAAATTCAAAGCAT
Found at i:611162 original size:37 final size:37
Alignment explanation
Indices: 611092--611162 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 37
611082 TTTGCTGCAG
* * * **
611092 AGTAAAGACAAAGATGAACAGGGATGATTCCCTGTAA
1 AGTAAAGAAAAAAATAAACAGGGATGACCCCCTGTAA
*
611129 AGTAAAGAAAAAAATAAACAGGGGTGACCCCCTG
1 AGTAAAGAAAAAAATAAACAGGGATGACCCCCTG
611163 ATTCCCTACA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 28 1.00
ACGTcount: A:0.45, C:0.15, G:0.24, T:0.15
Consensus pattern (37 bp):
AGTAAAGAAAAAAATAAACAGGGATGACCCCCTGTAA
Found at i:612047 original size:20 final size:22
Alignment explanation
Indices: 612022--612069 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
612012 TACATATTAA
612022 ATTTTATAT-AAAAT-TAAAAT
1 ATTTTATATGAAAATATAAAAT
*
612042 ATTTTA-ATGATAATATAAAAT
1 ATTTTATATGAAAATATAAAAT
*
612063 TTTTTAT
1 ATTTTAT
612070 CATTTTGATG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 2 0.09
20 10 0.43
21 11 0.48
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
ATTTTATATGAAAATATAAAAT
Found at i:614418 original size:2 final size:2
Alignment explanation
Indices: 614413--614443 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
614403 GAGTAAAGTA
614413 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
614444 AAAGAAAGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:616610 original size:67 final size:67
Alignment explanation
Indices: 616532--616661 Score: 233
Period size: 67 Copynumber: 1.9 Consensus size: 67
616522 CAATACTGGT
* * *
616532 TTTCGGATTAGTTGTTGGTTGCGACTTCTTCAATAATATTATTCTATTTTTCTTTTGTTTTTAGA
1 TTTCGGATTAGTTATTGGTTGCGACTTCTTCAAAAATATTATTCTATTTTTCTTTTATTTTTAGA
616597 AC
66 AC
616599 TTTCGGATTAGTTATTGGTTGCGACTTCTTCAAAAATATTATTCTATTTTTCTTTTATTTTTA
1 TTTCGGATTAGTTATTGGTTGCGACTTCTTCAAAAATATTATTCTATTTTTCTTTTATTTTTA
616662 AGTTCTAGCT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 60 1.00
ACGTcount: A:0.21, C:0.12, G:0.13, T:0.55
Consensus pattern (67 bp):
TTTCGGATTAGTTATTGGTTGCGACTTCTTCAAAAATATTATTCTATTTTTCTTTTATTTTTAGA
AC
Found at i:616797 original size:2 final size:2
Alignment explanation
Indices: 616790--616829 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
616780 TCGTGTTCTA
616790 AT AT AT AT AT AT 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 AT AT
616830 GAGATTTATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:626922 original size:21 final size:21
Alignment explanation
Indices: 626896--626936 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
626886 ATCTGCTCAA
* *
626896 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
626917 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
626937 TCGCTTGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:634615 original size:105 final size:102
Alignment explanation
Indices: 634486--634704 Score: 359
Period size: 105 Copynumber: 2.1 Consensus size: 102
634476 ATTACATTAA
634486 AAAAAATCACAAAACACTAAACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAACA
1 AAAAAATCACAAAACACTAAACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAACA
*
634551 AAGTAACTATAAAATTATTTTTTTAAAAAAATAAATTACT
66 AAATAACTATAAAATTATTTTTTT---AAAATAAATTACT
634591 AAAAAATCACAAAACAC-ATAACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAAC
1 AAAAAATCACAAAACACTA-AACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAAC
* **
634655 AAAATAACTATAAAATTATTTTTTTTAAATTCATTACT
65 AAAATAACTATAAAATTATTTTTTTAAAATAAATTACT
634693 AAAAAATCACAA
1 AAAAAATCACAA
634705 GTTCAAGTAG
Statistics
Matches: 109, Mismatches: 4, Indels: 5
0.92 0.03 0.04
Matches are distributed among these distances:
102 22 0.20
104 1 0.01
105 86 0.79
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (102 bp):
AAAAAATCACAAAACACTAAACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAACA
AAATAACTATAAAATTATTTTTTTAAAATAAATTACT
Found at i:641281 original size:80 final size:81
Alignment explanation
Indices: 641184--641352 Score: 277
Period size: 80 Copynumber: 2.1 Consensus size: 81
641174 CAAAGCACTA
* *
641184 AACTAAGCACTAACAATTTATATAACATAATCATAAATTACTAACAAAATAACTATAAAATTA-T
1 AACTAAACACTAACAATTCATATAACATAATCATAAATTACTAACAAAATAACTATAAAATTATT
641248 TTTTTTAAAAATACAT
66 TTTTTTAAAAATACAT
*
641264 AACTAAACACTAACAATTCATATAACCTAATCATAAATTACTAACAAAATAACTATAAAATTATT
1 AACTAAACACTAACAATTCATATAACATAATCATAAATTACTAACAAAATAACTATAAAATTA-T
*
641329 TTTTTTTAAAATTACAT
65 TTTTTTTAAAAATACAT
*
641346 TACTAAA
1 AACTAAA
641353 ATCACAAAAC
Statistics
Matches: 82, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
80 60 0.73
82 22 0.27
ACGTcount: A:0.51, C:0.14, G:0.01, T:0.34
Consensus pattern (81 bp):
AACTAAACACTAACAATTCATATAACATAATCATAAATTACTAACAAAATAACTATAAAATTATT
TTTTTTAAAAATACAT
Found at i:641835 original size:16 final size:18
Alignment explanation
Indices: 641814--641849 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
641804 ATAAAATAAT
641814 AATATTTT-AT-TAAAAA
1 AATATTTTAATATAAAAA
641830 AATATTTTAATATAAAAA
1 AATATTTTAATATAAAAA
641848 AA
1 AA
641850 GAGTTCGTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 2 0.11
18 8 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AATATTTTAATATAAAAA
Found at i:641847 original size:19 final size:18
Alignment explanation
Indices: 641804--641849 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 18
641794 TTTAATAAAA
641804 ATAAAATAATAATATTTTAT
1 ATAAAA-AA-AATATTTTAT
641824 -T-AAAAAAATATTTTAAT
1 ATAAAAAAAATATTTT-AT
641841 ATAAAAAAA
1 ATAAAAAAA
641850 GAGTTCGTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
16 8 0.35
17 4 0.17
18 4 0.17
19 7 0.30
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
ATAAAAAAAATATTTTAT
Found at i:644403 original size:22 final size:23
Alignment explanation
Indices: 644360--644405 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
644350 TTAAAATGAT
* *
644360 AAAATTATATCTTTACTATCGTA
1 AAAATTATAACTTTAATATCGTA
*
644383 AAAATTATAAC-TTAATTTCGTA
1 AAAATTATAACTTTAATATCGTA
644405 A
1 A
644406 CCTCCTAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.41
Consensus pattern (23 bp):
AAAATTATAACTTTAATATCGTA
Found at i:644969 original size:14 final size:14
Alignment explanation
Indices: 644931--644974 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
644921 TAATTTTTTT
*
644931 ATCTTAGAATATTAA
1 ATCTTA-AATTTTAA
*
644946 A-CTCAAATTTTAA
1 ATCTTAAATTTTAA
644959 ATCTTAAATTTTAA
1 ATCTTAAATTTTAA
644973 AT
1 AT
644975 TCGAAGGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 8 0.32
14 16 0.64
15 1 0.04
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.43
Consensus pattern (14 bp):
ATCTTAAATTTTAA
Found at i:647589 original size:6 final size:6
Alignment explanation
Indices: 647578--647633 Score: 58
Period size: 6 Copynumber: 8.7 Consensus size: 6
647568 AATCAAAATG
* *
647578 ATATAC ATATAC AGTAGATGC ATATAC ATATAC ATATAC ATATAC ACTATAT
1 ATATAC ATATAC A-T--ATAC ATATAC ATATAC ATATAC ATATAC A-TATAC
647630 ATAT
1 ATAT
647634 GTATGAACAC
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
6 32 0.74
7 6 0.14
8 1 0.02
9 4 0.09
ACGTcount: A:0.46, C:0.14, G:0.05, T:0.34
Consensus pattern (6 bp):
ATATAC
Found at i:651056 original size:43 final size:43
Alignment explanation
Indices: 651012--651149 Score: 116
Period size: 43 Copynumber: 3.2 Consensus size: 43
651002 TATGGCTGTG
*
651012 GATGCACAACATGTTAGCAGGTAAGAGCTGTCAATAGGTTGTG
1 GATGCACAACATGTTAGCAGGTAAGAGCTGTCAATAGGTTGTA
* ** * ** * * ** **
651055 GATGCACAGCAAAATAATGCAGAAAAAATCTCCCAATA-ACTGTA
1 GATGCACAAC-ATGTTA-GCAGGTAAGAGCTGTCAATAGGTTGTA
**
651099 GATGCACAACATGTTAATAGGTAAGAGCTGTCAATAGGTTGTA
1 GATGCACAACATGTTAGCAGGTAAGAGCTGTCAATAGGTTGTA
651142 GATGCACA
1 GATGCACA
651150 TCATATTTGT
Statistics
Matches: 65, Mismatches: 27, Indels: 6
0.66 0.28 0.06
Matches are distributed among these distances:
42 12 0.18
43 24 0.37
44 15 0.23
45 14 0.22
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (43 bp):
GATGCACAACATGTTAGCAGGTAAGAGCTGTCAATAGGTTGTA
Found at i:651410 original size:35 final size:34
Alignment explanation
Indices: 651371--651445 Score: 80
Period size: 34 Copynumber: 2.2 Consensus size: 34
651361 TTAATACAGT
* *
651371 AGCAAATAGTATGCTTTATAAC-ATATCAATACAAA
1 AGCAAATAATACGC-TTATAACAAT-TCAATACAAA
* * *
651406 AGCAATTAATACGCTTATAACAATTCAATATAAT
1 AGCAAATAATACGCTTATAACAATTCAATACAAA
651440 AGCAAA
1 AGCAAA
651446 AGACATGTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
34 20 0.61
35 13 0.39
ACGTcount: A:0.49, C:0.15, G:0.08, T:0.28
Consensus pattern (34 bp):
AGCAAATAATACGCTTATAACAATTCAATACAAA
Found at i:651443 original size:69 final size:68
Alignment explanation
Indices: 651313--651445 Score: 151
Period size: 69 Copynumber: 1.9 Consensus size: 68
651303 GCAATATGAC
* *** * * * *
651313 ATGCTTATAACATATCGATACGGTAGCCATTAATGCACTTATAGCAAATTAATACAGTAGCAAAT
1 ATGCTTATAACATATCAATACAAAAGCAATTAATACACTTATAACAAATTAATACAATAGCAAAT
651378 AGT
66 AGT
* *
651381 ATGCTTTATAACATATCAATACAAAAGCAATTAATACGCTTATAAC-AATTCAATATAATAGCAA
1 ATGC-TTATAACATATCAATACAAAAGCAATTAATACACTTATAACAAATT-AATACAATAGCAA
651445 A
64 A
651446 AGACATGTTT
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
68 8 0.15
69 45 0.85
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.29
Consensus pattern (68 bp):
ATGCTTATAACATATCAATACAAAAGCAATTAATACACTTATAACAAATTAATACAATAGCAAAT
AGT
Found at i:652880 original size:40 final size:35
Alignment explanation
Indices: 652814--652944 Score: 136
Period size: 35 Copynumber: 3.6 Consensus size: 35
652804 CATGGCAAAG
652814 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
*
652849 TGTGATATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGT
** * *** *
652889 TAAGAAATGTAGGTATGGCATTGCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
*
652924 TGTAAAATGTAGGTATGGTAT
1 TGTGAAATGTAGGTATGGTAT
652945 TTCAATGAGG
Statistics
Matches: 78, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
35 44 0.56
37 2 0.03
38 4 0.05
40 28 0.36
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.34
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
Found at i:655301 original size:16 final size:16
Alignment explanation
Indices: 655280--655310 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
655270 TATAATTAAC
655280 TTTTTTTAA-ATAATA
1 TTTTTTTAATATAATA
655295 TTTTTTTAATATAATA
1 TTTTTTTAATATAATA
655311 ATAATTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTTTTAATATAATA
Found at i:657123 original size:31 final size:32
Alignment explanation
Indices: 657055--657125 Score: 85
Period size: 31 Copynumber: 2.2 Consensus size: 32
657045 ACGAAATTCA
*
657055 ATATTTAATATCTATTTTTTTTATCACAAGTG
1 ATATTTAATATCTATTTTTGTTATCACAAGTG
657087 ATATTTAA-AT-TATATTTTGTTACTCA-AAGTG
1 ATATTTAATATCTAT-TTTTGTTA-TCACAAGTG
*
657118 GTATTTAA
1 ATATTTAA
657126 GTTTTAATCC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 3 0.09
31 21 0.60
32 11 0.31
ACGTcount: A:0.34, C:0.07, G:0.08, T:0.51
Consensus pattern (32 bp):
ATATTTAATATCTATTTTTGTTATCACAAGTG
Found at i:664911 original size:6 final size:6
Alignment explanation
Indices: 664893--664928 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
664883 GTTCCGTAAC
*
664893 ACCCCA ACACCA ACCCCA ACCCCA ACCCCA ACCCCA
1 ACCCCA ACCCCA ACCCCA ACCCCA ACCCCA ACCCCA
664929 TCCAACATCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.36, C:0.64, G:0.00, T:0.00
Consensus pattern (6 bp):
ACCCCA
Found at i:665714 original size:36 final size:36
Alignment explanation
Indices: 665673--665744 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
665663 TTTAGCTTTC
*
665673 ACTAGATTTAGAATTAGGATTAAATTGACATGATAT
1 ACTAGATTTAGAATTAGGATCAAATTGACATGATAT
665709 ACTAGATTTAGAATTAGGATCAAATTGACATGATAT
1 ACTAGATTTAGAATTAGGATCAAATTGACATGATAT
665745 GTAAATATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.42, C:0.07, G:0.17, T:0.35
Consensus pattern (36 bp):
ACTAGATTTAGAATTAGGATCAAATTGACATGATAT
Found at i:666212 original size:2 final size:2
Alignment explanation
Indices: 666205--666230 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
666195 TAAAGTGATA
666205 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
666231 TTTTTTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:668818 original size:21 final size:22
Alignment explanation
Indices: 668792--668833 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
668782 ATTTATTTAT
668792 TTTCAATAAA-ATATTCTATTC
1 TTTCAATAAAGATATTCTATTC
*
668813 TTTCAATAAAGATATTTTATT
1 TTTCAATAAAGATATTCTATT
668834 ACAGAATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (22 bp):
TTTCAATAAAGATATTCTATTC
Found at i:672194 original size:28 final size:28
Alignment explanation
Indices: 672154--672221 Score: 127
Period size: 28 Copynumber: 2.4 Consensus size: 28
672144 GTGTACTAGT
*
672154 TGAGAAAGTGGGGGGGGGGGGACTGACA
1 TGAGAAAGTGGGGAGGGGGGGACTGACA
672182 TGAGAAAGTGGGGAGGGGGGGACTGACA
1 TGAGAAAGTGGGGAGGGGGGGACTGACA
672210 TGAGAAAGTGGG
1 TGAGAAAGTGGG
672222 AACATGCTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.28, C:0.06, G:0.54, T:0.12
Consensus pattern (28 bp):
TGAGAAAGTGGGGAGGGGGGGACTGACA
Found at i:674891 original size:3 final size:3
Alignment explanation
Indices: 674883--674909 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
674873 AGGAAAATAA
674883 GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT
674910 ACTCACAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:677687 original size:12 final size:12
Alignment explanation
Indices: 677662--677695 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
677652 GGGGTTATGG
677662 GTAAAAAG--AT
1 GTAAAAAGATAT
677672 GTAAAAAGATAT
1 GTAAAAAGATAT
677684 GTAAAAAGATAT
1 GTAAAAAGATAT
677696 TTAATATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.36
12 14 0.64
ACGTcount: A:0.59, C:0.00, G:0.18, T:0.24
Consensus pattern (12 bp):
GTAAAAAGATAT
Found at i:678356 original size:3 final size:3
Alignment explanation
Indices: 678348--678386 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
678338 ATTTTATTTT
678348 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
678387 AATTTTAGAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:681412 original size:36 final size:36
Alignment explanation
Indices: 681362--681496 Score: 139
Period size: 36 Copynumber: 3.8 Consensus size: 36
681352 AAACTGTTCA
* *
681362 TTGATGATATAAAATGCAAGAAGTGTAGACTGTCCG
1 TTGACGATATAAAATGGAAGAAGTGTAGACTGTCCG
* * *
681398 TTGACGATACAAAATGGAAGAAGTGTAAATCAT-T-CA
1 TTGACGATATAAAATGGAAGAAGTGTAGA-C-TGTCCG
** * * * *
681434 TTGGTGATATAAAATGTAAGAAGTATAGACCGTCTG
1 TTGACGATATAAAATGGAAGAAGTGTAGACTGTCCG
681470 TTGACGATATAAAATGGAAGAAGTGTA
1 TTGACGATATAAAATGGAAGAAGTGTA
681497 AAGCATTCAT
Statistics
Matches: 77, Mismatches: 18, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
35 2 0.03
36 72 0.94
37 2 0.03
38 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.24, T:0.27
Consensus pattern (36 bp):
TTGACGATATAAAATGGAAGAAGTGTAGACTGTCCG
Done.