Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr12
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: 39383930
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.32
Warning! 780790 characters in sequence are not A, C, G, or T
File 38 of 126
Found at i:11206449 original size:27 final size:29
Alignment explanation
Indices: 11206394--11206453 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
11206384 TGAATCTCAA
11206394 AATTATATATAAATTTTAATTTAATGTGT
1 AATTATATATAAATTTTAATTTAATGTGT
11206423 AATTATATATAAATTTTAATTT-A-GTGT
1 AATTATATATAAATTTTAATTTAATGTGT
11206450 AATT
1 AATT
11206454 GGACACGTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 8 0.26
28 1 0.03
29 22 0.71
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.52
Consensus pattern (29 bp):
AATTATATATAAATTTTAATTTAATGTGT
Found at i:11215656 original size:13 final size:12
Alignment explanation
Indices: 11215640--11215673 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
11215630 CTCATGTACC
11215640 AATTTAAACATTA
1 AATTTAAAC-TTA
11215653 AATTTAAACTTA
1 AATTTAAACTTA
11215665 AATATTAAA
1 AAT-TTAAA
11215674 TGGTATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (12 bp):
AATTTAAACTTA
Found at i:11215752 original size:15 final size:15
Alignment explanation
Indices: 11215732--11215764 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
11215722 TAATTATAAT
*
11215732 TTAATATTTTTATTA
1 TTAATATGTTTATTA
11215747 TTAATATGTTTATTA
1 TTAATATGTTTATTA
11215762 TTA
1 TTA
11215765 CAAAGAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (15 bp):
TTAATATGTTTATTA
Found at i:11218543 original size:6 final size:6
Alignment explanation
Indices: 11218532--11218562 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
11218522 AATCCATCAG
11218532 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A
11218563 AATTTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATTTAA
Found at i:11223694 original size:19 final size:18
Alignment explanation
Indices: 11223669--11223712 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
11223659 AATTAAAATT
11223669 ATAAAAATA-TTAAATAAA
1 ATAAAAATAGTTAAA-AAA
11223687 ATTAAAAA-AGTTAAAAAA
1 A-TAAAAATAGTTAAAAAA
11223705 ATAAAAAT
1 ATAAAAAT
11223713 CATTTAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 6 0.26
18 6 0.26
19 11 0.48
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (18 bp):
ATAAAAATAGTTAAAAAA
Found at i:11223721 original size:19 final size:17
Alignment explanation
Indices: 11223656--11223712 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
11223646 AATTTGAAAG
**
11223656 AAAA-ATTAAAATTATA
1 AAAATATTAAAAAAATA
11223672 AAAATATTAAATAAAATTA
1 AAAATATTAAA-AAAA-TA
11223691 AAAA-AGTTAAAAAAATA
1 AAAATA-TTAAAAAAATA
11223708 AAAAT
1 AAAAT
11223713 CATTTAAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
16 4 0.12
17 12 0.35
18 7 0.21
19 11 0.32
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (17 bp):
AAAATATTAAAAAAATA
Found at i:11224375 original size:15 final size:14
Alignment explanation
Indices: 11224351--11224390 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
11224341 TTATTAATTT
*
11224351 TTTTACAAAATTATA
1 TTTTATAAAATTA-A
11224366 TTTTATAAAATTAA
1 TTTTATAAAATTAA
*
11224380 TTTTTTAAAAT
1 TTTTATAAAAT
11224391 ATGTATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (14 bp):
TTTTATAAAATTAA
Found at i:11232753 original size:20 final size:19
Alignment explanation
Indices: 11232730--11232768 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
11232720 AAAAAATAAA
11232730 ATAATAAAATTTAAAAATTT
1 ATAATAAAA-TTAAAAATTT
* *
11232750 ATAATTATATTAAAAATTT
1 ATAATAAAATTAAAAATTT
11232769 TATCACATGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATAATAAAATTAAAAATTT
Found at i:11240639 original size:131 final size:131
Alignment explanation
Indices: 11240501--11240777 Score: 547
Period size: 131 Copynumber: 2.1 Consensus size: 131
11240491 GTACAAATGT
11240501 AATTTTATCATTTTAATATATCTTTATAATTTTAAATAATTAAATAAAAATTTTATCATTTTTAG
1 AATTTTATCATTTTAATATATCTTTATAATTTTAAATAATTAAATAAAAATTTTATCATTTTTAG
11240566 GGGGCAAAACACAATTTTACCTTTACTAATTTAAAATTTTAAAAATTTTAAAAGACCTGAATTGA
66 GGGGCAAAACACAATTTTACCTTTACTAATTTAAAATTTTAAAAATTTTAAAAGACCTGAATTGA
11240631 A
131 A
11240632 AATTTTATCATTTTAATATATCTTTATAATTTTAAATAATTAAATAAAAATTTTATCATTTTTAG
1 AATTTTATCATTTTAATATATCTTTATAATTTTAAATAATTAAATAAAAATTTTATCATTTTTAG
11240697 GGGGCAAAACACAATTTTACCTTTACTAATTTAAAATTTTAAAAATTTTAAAAGACCTGAATTGA
66 GGGGCAAAACACAATTTTACCTTTACTAATTTAAAATTTTAAAAATTTTAAAAGACCTGAATTGA
11240762 A
131 A
11240763 AATTTT-TCATTTTAA
1 AATTTTATCATTTTAA
11240778 GAGGAGCCGG
Statistics
Matches: 146, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
130 9 0.06
131 137 0.94
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (131 bp):
AATTTTATCATTTTAATATATCTTTATAATTTTAAATAATTAAATAAAAATTTTATCATTTTTAG
GGGGCAAAACACAATTTTACCTTTACTAATTTAAAATTTTAAAAATTTTAAAAGACCTGAATTGA
A
Found at i:11251834 original size:29 final size:29
Alignment explanation
Indices: 11251779--11251874 Score: 113
Period size: 29 Copynumber: 3.2 Consensus size: 29
11251769 ATACAAAAAA
11251779 AAAATTATATTTTGATCCCTTAACTTTTCT
1 AAAATTATATTTTGA-CCCTTAACTTTTCT
* *
11251809 AAAATTAT-TTTTGACCCTTTAGCTTTTTT
1 AAAATTATATTTTGACCC-TTAACTTTTCT
* **
11251838 AAAATTATATTTTGACCCCTAAAATTTCT
1 AAAATTATATTTTGACCCTTAACTTTTCT
11251867 CAAAATTA
1 -AAAATTA
11251875 CACTTGGCCT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
28 3 0.05
29 29 0.52
30 24 0.43
ACGTcount: A:0.33, C:0.16, G:0.04, T:0.47
Consensus pattern (29 bp):
AAAATTATATTTTGACCCTTAACTTTTCT
Found at i:11252439 original size:4 final size:4
Alignment explanation
Indices: 11252427--11252484 Score: 54
Period size: 4 Copynumber: 15.5 Consensus size: 4
11252417 AAGGAAGAAG
* *
11252427 AAGA GAAGA AAGA AAGA AA-A AA-A AAGA AAAA AAGA AAGG AA-A AAGA
1 AAGA -AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
11252473 AA-A AA-A AAGA AA
1 AAGA AAGA AAGA AA
11252485 AAAATTAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
3 14 0.30
4 28 0.61
5 4 0.09
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:11252444 original size:11 final size:10
Alignment explanation
Indices: 11252424--11252488 Score: 60
Period size: 10 Copynumber: 6.1 Consensus size: 10
11252414 GGGAAGGAAG
11252424 AAGAAGAGAAGA
1 AAGAA-AGAA-A
11252436 AAGAAAGAAA
1 AAGAAAGAAA
*
11252446 AAAAAAGAAAAA
1 AAGAAAG--AAA
11252458 AAGAAAGGAAA
1 AAGAAA-GAAA
*
11252469 AAGAAAAAAA
1 AAGAAAGAAA
11252479 AAGAAA-AAA
1 AAGAAAGAAA
11252488 A
1 A
11252489 TTAAAAAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
9 4 0.09
10 16 0.34
11 13 0.28
12 13 0.28
13 1 0.02
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (10 bp):
AAGAAAGAAA
Found at i:11252453 original size:26 final size:28
Alignment explanation
Indices: 11252432--11252488 Score: 91
Period size: 29 Copynumber: 2.1 Consensus size: 28
11252422 AGAAGAAGAG
11252432 AAGAAA-G-AAAGAAAAAAAAAGAAAAA
1 AAGAAAGGAAAAGAAAAAAAAAGAAAAA
11252458 AAGAAAGGAAAAAGAAAAAAAAAGAAAAA
1 AAGAAAGG-AAAAGAAAAAAAAAGAAAAA
11252487 AA
1 AA
11252489 TTAAAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 6 0.21
27 1 0.04
29 21 0.75
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (28 bp):
AAGAAAGGAAAAGAAAAAAAAAGAAAAA
Found at i:11252454 original size:10 final size:10
Alignment explanation
Indices: 11252439--11252488 Score: 68
Period size: 10 Copynumber: 5.1 Consensus size: 10
11252429 GAGAAGAAAG
11252439 AAAGAAAAAA
1 AAAGAAAAAA
11252449 AAAG--AAAA
1 AAAGAAAAAA
*
11252457 AAAGAAAGGAA
1 AAAGAAA-AAA
11252468 AAAGAAAAAA
1 AAAGAAAAAA
11252478 AAAGAAAAAA
1 AAAGAAAAAA
11252488 A
1 A
11252489 TTAAAAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
8 8 0.23
10 18 0.51
11 9 0.26
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:11252488 original size:18 final size:18
Alignment explanation
Indices: 11252432--11252488 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
11252422 AGAAGAAGAG
*
11252432 AAGAAAGAAAGAAAAAAA
1 AAGAAAAAAAGAAAAAAA
*
11252450 AAGAAAAAAAGAAAGGAAA
1 AAGAAAAAAAGAAA-AAAA
11252469 AAGAAAAAAA-AAGAAAAA
1 AAGAAAAAAAGAA-AAAAA
11252487 AA
1 AA
11252489 TTAAAAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 20 0.59
19 14 0.41
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (18 bp):
AAGAAAAAAAGAAAAAAA
Found at i:11252853 original size:8 final size:8
Alignment explanation
Indices: 11252840--11252884 Score: 56
Period size: 8 Copynumber: 5.5 Consensus size: 8
11252830 CAGGCCAGCC
11252840 AAAAAAGG
1 AAAAAAGG
11252848 AAAAAA-G
1 AAAAAAGG
11252855 AAAAAAGAG
1 AAAAAAG-G
*
11252864 AAAAGAAGA
1 AAAA-AAGG
11252873 AAAAAAGG
1 AAAAAAGG
11252881 AAAA
1 AAAA
11252885 GACCCAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
7 7 0.22
8 13 0.41
9 9 0.28
10 3 0.09
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (8 bp):
AAAAAAGG
Found at i:11252872 original size:17 final size:17
Alignment explanation
Indices: 11252840--11252886 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
11252830 CAGGCCAGCC
11252840 AAAAAAG-GAAAA-AAG
1 AAAAAAGAGAAAAGAAG
11252855 AAAAAAGAGAAAAGAAG
1 AAAAAAGAGAAAAGAAG
11252872 AAAAAA-AGGAAAAGA
1 AAAAAAGA-GAAAAGA
11252887 CCCAAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.24
16 6 0.21
17 16 0.55
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (17 bp):
AAAAAAGAGAAAAGAAG
Found at i:11253388 original size:18 final size:18
Alignment explanation
Indices: 11253338--11253388 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
11253328 AAAAAGAAAG
*
11253338 ATCGTGTTTTCAAAAGTTT
1 ATCGTG-TTTCAAAAATTT
* *
11253357 -TCATGTTTCCAAAATTT
1 ATCGTGTTTCAAAAATTT
11253374 ATCGTGTTTCAAAAA
1 ATCGTGTTTCAAAAA
11253389 ATAATAATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 10 0.38
18 16 0.62
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (18 bp):
ATCGTGTTTCAAAAATTT
Found at i:11253536 original size:18 final size:18
Alignment explanation
Indices: 11253515--11253647 Score: 68
Period size: 17 Copynumber: 7.6 Consensus size: 18
11253505 ACTTTTCGCT
11253515 TTTTCAAAAATTTTCCTG
1 TTTTCAAAAATTTTCCTG
*
11253533 TTTTC-AAAATTTCTCGTG
1 TTTTCAAAAATTT-TCCTG
* *
11253551 TTTTTC--GACTTTT-CTCG
1 -TTTTCAAAAATTTTCCT-G
*
11253568 TTTTCAAAAATTTTCGTG
1 TTTTCAAAAATTTTCCTG
*
11253586 TTTT-AGAAATTTT-CT-
1 TTTTCAAAAATTTTCCTG
* *
11253601 TATTTCTAAAATTCT-C-G
1 T-TTTCAAAAATTTTCCTG
*
11253618 TATTTCAAAAAATTTCCGTG
1 T-TTTCAAAAATTTTCC-TG
*
11253638 TTCTCAAAAA
1 TTTTCAAAAA
11253648 AATTATTATC
Statistics
Matches: 87, Mismatches: 16, Indels: 23
0.69 0.13 0.18
Matches are distributed among these distances:
15 1 0.01
16 10 0.11
17 36 0.41
18 24 0.28
19 14 0.16
20 2 0.02
ACGTcount: A:0.27, C:0.16, G:0.08, T:0.49
Consensus pattern (18 bp):
TTTTCAAAAATTTTCCTG
Found at i:11253599 original size:35 final size:37
Alignment explanation
Indices: 11253522--11253600 Score: 96
Period size: 35 Copynumber: 2.2 Consensus size: 37
11253512 GCTTTTTCAA
*
11253522 AAATTTTC-CTGTTTTCAAAATTTCTCGTGTTTTTCG
1 AAATTTTCTCTGTTTTCAAAATTTCTCGTGTTTTTAG
*
11253558 -ACTTTTCTC-GTTTTCAAAAATTT-TCGTG-TTTTAG
1 AAATTTTCTCTGTTTTC-AAAATTTCTCGTGTTTTTAG
11253592 AAATTTTCT
1 AAATTTTCT
11253601 TATTTCTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
34 5 0.14
35 24 0.65
36 8 0.22
ACGTcount: A:0.22, C:0.15, G:0.10, T:0.53
Consensus pattern (37 bp):
AAATTTTCTCTGTTTTCAAAATTTCTCGTGTTTTTAG
Found at i:11253612 original size:17 final size:17
Alignment explanation
Indices: 11253565--11253647 Score: 69
Period size: 17 Copynumber: 4.8 Consensus size: 17
11253555 TCGACTTTTC
11253565 TCGT-TTTCAAAAATTT
1 TCGTATTTCAAAAATTT
* * *
11253581 TCGTGTTTTAGAAATTT
1 TCGTATTTCAAAAATTT
* * *
11253598 TCTTATTTCTAAAATTC
1 TCGTATTTCAAAAATTT
11253615 TCGTATTTCAAAAAATTT
1 TCGTATTTC-AAAAATTT
* *
11253633 CCGTGTTCTCAAAAA
1 TCGTATT-TCAAAAA
11253648 AATTATTATC
Statistics
Matches: 51, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
16 4 0.08
17 29 0.57
18 16 0.31
19 2 0.04
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.46
Consensus pattern (17 bp):
TCGTATTTCAAAAATTT
Found at i:11260711 original size:78 final size:77
Alignment explanation
Indices: 11259877--11261247 Score: 1678
Period size: 78 Copynumber: 17.8 Consensus size: 77
11259867 AGAATTATAG
* * *
11259877 TTTTCAATTTCTATTTTTC--AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTTAGGCCG
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC-TCGG--G
*
11259940 T-ACGCC-GAGGTA-
63 TCACACCTGAGGTAT
** * * **
11259952 TTTTCAATTTCAATTTTTCAAAAAAATCAACTCAGAATGCGAGAAATGAGTTGAGCCTCGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
* *
11260017 C-GCTGAGATAT
66 CACCTGAGGTAT
* * * * *
11260028 TTTT-AATTTCTATTTTTCAAAAAAATCAGCTCATAATGCGAGAAGTGGGTTGAGCCTCGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
* *
11260092 C-GCTGATGTAT
66 CACCTGAGGTAT
* * *
11260103 TTTT-AATTTCTATTTTTC-AAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
11260166 C-GCTGAGGTA-
66 CACCTGAGGTAT
*** *
11260176 TTTTCAATTTCTGTTTTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGT
1 TTTTCAATTTCTG--TTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
*
11260241 CAC-GCTGAGGTA-
64 CACACCTGAGGTAT
* *** * *
11260253 TTTTCAATTTCTTTTTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTC-GGAC
1 TTTTCAATTTC-TGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
*
11260317 ACACGCCGAGGTAT
65 ACAC-CTGAGGTAT
** * *
11260331 TTTTCAATTTAAGTTTTTC-GAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
11260395 CATCCTGAGGTAT
66 CA-CCTGAGGTAT
* *
11260408 TTTTCAATTTATGTTTTTC-AAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
* *
11260472 CATCTTTAGGTAT
66 CA-CCTGAGGTAT
11260485 TTTTCAATTTCTGTTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
1 TTTTCAATTTCTGTTTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
*
11260550 ACATCTTGAGGTAT
65 ACA-CCTGAGGTAT
* * *
11260564 TTTTCAATTTTTTGCTTTTCAAAAAAATGAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
1 TTTTCAA-TTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
11260629 ACATCCTGAGGTAT
65 ACA-CCTGAGGTAT
* *
11260643 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTTA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
11260708 CATCATGAGGTAT
66 CA-CCTGAGGTAT
* *
11260721 TTTTCAATTTCTGTTCTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
11260786 CACGCTGAGGTAT
66 CAC-CTGAGGTAT
* *
11260799 TTTTCAATTAT-TGCTTTTCGAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
1 TTTTCAATT-TCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
11260863 ACACCCTGAGGTAT
65 ACA-CCTGAGGTAT
* * *
11260877 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCAAGATGTGAGTTGAGCCTTGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
11260942 CACGCTGAGGTAT
66 CAC-CTGAGGTAT
* *
11260955 TTTTCAATTTTTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
11261020 CACGCTGAGGTAT
66 CAC-CTGAGGTAT
* *
11261033 TTTTCAATTTCTGTTTTT--AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCG
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
11261096 CATGCTGAGGTAT
66 CA-CCTGAGGTAT
* * * *
11261109 TTTTCAATTTCTGTTGTTCAAAAAAAATCAAATCATATTACGATG-GGTGAGTTGAGCCTCAGG-
1 TTTTCAATTTCTGTTTTTC-AAAAAAATCAACTCATATTGCGA-GAGGTGAGTTGAGCCTCGGGT
*
11261172 CACATGCC-AAGGTA-
64 CACA--CCTGAGGTAT
* * * * * * *
11261186 TTTTCGATTTTTGTTTTTC--GAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCTTCGGGTC
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
11261248 GCATGCTCGG
Statistics
Matches: 1168, Mismatches: 97, Indels: 62
0.88 0.07 0.05
Matches are distributed among these distances:
73 5 0.00
74 94 0.08
75 113 0.10
76 164 0.14
77 229 0.20
78 384 0.33
79 168 0.14
80 11 0.01
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.35
Consensus pattern (77 bp):
TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
CACCTGAGGTAT
Found at i:11261538 original size:30 final size:29
Alignment explanation
Indices: 11261419--11261543 Score: 133
Period size: 29 Copynumber: 4.2 Consensus size: 29
11261409 CAAAAATAAA
* *
11261419 AAAATTATATTTTAACCCCTTAATTTTTT
1 AAAATTATATTTTGACCCCTAAATTTTTT
* * * *
11261448 CAAATTTTGTTTTGACCCCTTAGATTTTTT
1 AAAATTATATTTTGACCCC-TAAATTTTTT
* * * * *
11261478 CAATTTATATTTTGACCCCTCAACTTCTT
1 AAAATTATATTTTGACCCCTAAATTTTTT
11261507 AAAATTATATTTTGACCCCTAAATTTTCTT
1 AAAATTATATTTTGACCCCTAAATTTT-TT
11261537 AAAATTA
1 AAAATTA
11261544 CACTTGGCCC
Statistics
Matches: 76, Mismatches: 18, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
29 43 0.57
30 33 0.43
ACGTcount: A:0.30, C:0.18, G:0.04, T:0.48
Consensus pattern (29 bp):
AAAATTATATTTTGACCCCTAAATTTTTT
Found at i:11261554 original size:29 final size:31
Alignment explanation
Indices: 11261502--11261563 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 31
11261492 ACCCCTCAAC
* * *
11261502 TTCTTAAAATTATATTTTGACCCCTAAA-TT
1 TTCTTAAAATTACATCTTGACCCCAAAAGTT
*
11261532 TTCTTAAAATTACA-CTTGGCCCCAAAAGTT
1 TTCTTAAAATTACATCTTGACCCCAAAAGTT
11261562 TT
1 TT
11261564 GTTGCATTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.32, C:0.19, G:0.06, T:0.42
Consensus pattern (31 bp):
TTCTTAAAATTACATCTTGACCCCAAAAGTT
Found at i:11261939 original size:22 final size:22
Alignment explanation
Indices: 11261914--11261957 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
11261904 GAAAAGCTTC
11261914 GAAAAAAG-AGAGAAAAAGGAAG
1 GAAAAAAGAAGAG-AAAAGGAAG
* *
11261936 GAAATAAGAAGAGAGAAGGAAG
1 GAAAAAAGAAGAGAAAAGGAAG
11261958 AGAGGAGGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (22 bp):
GAAAAAAGAAGAGAAAAGGAAG
Found at i:11262126 original size:11 final size:11
Alignment explanation
Indices: 11262068--11262139 Score: 72
Period size: 11 Copynumber: 6.2 Consensus size: 11
11262058 GGGAAGGAAG
*
11262068 AAGAAGAGAAGA
1 AAGAA-AGAAAA
11262080 AAGAAAGAAAAAA
1 AAGAAAG--AAAA
*
11262093 AAGAAAAAAAA
1 AAGAAAGAAAA
*
11262104 AAGAAAGGAAA
1 AAGAAAGAAAA
11262115 AAGAAAGAAAA
1 AAGAAAGAAAA
*
11262126 ATAAAAAGAAAA
1 A-AGAAAGAAAA
11262138 AA
1 AA
11262140 ATTAAACAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
11 27 0.53
12 15 0.29
13 9 0.18
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (11 bp):
AAGAAAGAAAA
Found at i:11262145 original size:15 final size:15
Alignment explanation
Indices: 11262083--11262140 Score: 73
Period size: 16 Copynumber: 3.7 Consensus size: 15
11262073 GAGAAGAAAG
11262083 AAAGAAAAAAAAGAA
1 AAAGAAAAAAAAGAA
11262098 AAA-AAAAAGAAAGGAA
1 AAAGAAAAA-AAA-GAA
*
11262114 AAAGAAAGAAAAATAA
1 AAAGAAA-AAAAAGAA
11262130 AAAGAAAAAAA
1 AAAGAAAAAAA
11262141 TTAAACAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
14 5 0.13
15 10 0.26
16 15 0.39
17 6 0.16
18 2 0.05
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (15 bp):
AAAGAAAAAAAAGAA
Found at i:11262401 original size:17 final size:18
Alignment explanation
Indices: 11262378--11262432 Score: 58
Period size: 17 Copynumber: 3.0 Consensus size: 18
11262368 GGCCCAGCGT
11262378 CTAGCAGCCAGCAGCCCA
1 CTAGCAGCCAGCAGCCCA
* *
11262396 CT-GCAGTCAGCAGGCCA
1 CTAGCAGCCAGCAGCCCA
*
11262413 GTAGCAGCCCAGCAGGCCCA
1 CTAGCAG-CCAGCA-GCCCA
11262433 ATCCGCCCAG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
17 14 0.48
18 6 0.21
19 5 0.17
20 4 0.14
ACGTcount: A:0.25, C:0.40, G:0.27, T:0.07
Consensus pattern (18 bp):
CTAGCAGCCAGCAGCCCA
Found at i:11263053 original size:21 final size:21
Alignment explanation
Indices: 11263028--11263069 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
11263018 TAAAATTTCC
11263028 CGTG-TTTCAAAAAAATATATT
1 CGTGTTTTCAAAAAAAT-TATT
*
11263049 CGTGTTTTTAAAAAAATTATT
1 CGTGTTTTCAAAAAAATTATT
11263070 TCCGTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (21 bp):
CGTGTTTTCAAAAAAATTATT
Found at i:11263079 original size:23 final size:22
Alignment explanation
Indices: 11263036--11263080 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
11263026 CCCGTGTTTC
*
11263036 AAAAAAATATATTCGTGTTTTT
1 AAAAAAATATATTCGTATTTTT
11263058 AAAAAAAT-TATTTCCGTATTTTT
1 AAAAAAATATA-TT-CGTATTTTT
11263081 TTTTTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 2 0.10
22 10 0.50
23 8 0.40
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (22 bp):
AAAAAAATATATTCGTATTTTT
Found at i:11263156 original size:61 final size:60
Alignment explanation
Indices: 11263082--11263223 Score: 171
Period size: 61 Copynumber: 2.3 Consensus size: 60
11263072 CGTATTTTTT
* *
11263082 TTTTAAAAATTTCTCTTGTTTAAAAAAAATTT-GACTTTTCGCTTTTTCAAAAATGTTCGTG
1 TTTT-AAAATTTCTCGTGTTT-AAAAAAATTTCGACTTTTCGCGTTTTCAAAAATGTTCGTG
* * * * *
11263143 TTTTCAAAATTTCTCGTGTTTTAAATATTTTCGACTTTTCTCGTTTTCAAAAATTTTCGTG
1 TTTT-AAAATTTCTCGTGTTTAAAAAAATTTCGACTTTTCGCGTTTTCAAAAATGTTCGTG
11263204 TTTTAGAAATTT-TCGTGTTT
1 TTTTA-AAATTTCTCGTGTTT
11263224 CTAAAATTCT
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
60 16 0.23
61 55 0.77
ACGTcount: A:0.26, C:0.12, G:0.11, T:0.51
Consensus pattern (60 bp):
TTTTAAAATTTCTCGTGTTTAAAAAAATTTCGACTTTTCGCGTTTTCAAAAATGTTCGTG
Found at i:11263172 original size:18 final size:18
Alignment explanation
Indices: 11263125--11263164 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
11263115 ACTTTTCGCT
*
11263125 TTTTCAAAAATGT-TCGTG
1 TTTTC-AAAATTTCTCGTG
11263143 TTTTCAAAATTTCTCGTG
1 TTTTCAAAATTTCTCGTG
11263161 TTTT
1 TTTT
11263165 AAATATTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.53
Consensus pattern (18 bp):
TTTTCAAAATTTCTCGTG
Found at i:11263173 original size:27 final size:26
Alignment explanation
Indices: 11263143--11263200 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
11263133 AATGTTCGTG
* *
11263143 TTTTCAAAATTTCTCGTGTTTTAAATA
1 TTTTCAAAATTTCTCGT-TTTCAAAAA
* **
11263170 TTTTCGACTTTTCTCGTTTTCAAAAA
1 TTTTCAAAATTTCTCGTTTTCAAAAA
11263196 TTTTC
1 TTTTC
11263201 GTGTTTTAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 12 0.46
27 14 0.54
ACGTcount: A:0.24, C:0.16, G:0.07, T:0.53
Consensus pattern (26 bp):
TTTTCAAAATTTCTCGTTTTCAAAAA
Found at i:11263206 original size:18 final size:18
Alignment explanation
Indices: 11263185--11263265 Score: 71
Period size: 17 Copynumber: 4.6 Consensus size: 18
11263175 GACTTTTCTC
11263185 GTTTTCAAAAATTTTCGT
1 GTTTTCAAAAATTTTCGT
*
11263203 GTTTT-AGAAATTTTCGT
1 GTTTTCAAAAATTTTCGT
*
11263220 G-TTTCTAAAATTCTT-GT
1 GTTTTCAAAAATT-TTCGT
* *
11263237 -ATTTCAAAAAATTTCCGT
1 GTTTTC-AAAAATTTTCGT
*
11263255 GTTCTCAAAAA
1 GTTTTCAAAAA
11263266 AATTATTATC
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
16 3 0.06
17 24 0.48
18 20 0.40
19 3 0.06
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.46
Consensus pattern (18 bp):
GTTTTCAAAAATTTTCGT
Found at i:11263720 original size:29 final size:28
Alignment explanation
Indices: 11263687--11263751 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 28
11263677 TGAATCTCAA
11263687 AATTATAT-ATGAACTTTAATTTAATGTGT
1 AATTATATAATGAACTTTAATTT-A-GTGT
11263716 AATTATATACATGAACTTTAATTTAGTGT
1 AATTATATA-ATGAACTTTAATTTAGTGT
11263745 AATTATA
1 AATTATA
11263752 CACGTGAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
29 19 0.56
30 1 0.03
31 14 0.41
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (28 bp):
AATTATATAATGAACTTTAATTTAGTGT
Found at i:11263759 original size:29 final size:31
Alignment explanation
Indices: 11263695--11263759 Score: 98
Period size: 29 Copynumber: 2.2 Consensus size: 31
11263685 AAAATTATAT
*
11263695 ATGAACTTTAATTTAATGTGTAATTATATAC
1 ATGAACTTTAATTTAATGTGTAATTATACAC
11263726 ATGAACTTTAATTT-A-GTGTAATTATACAC
1 ATGAACTTTAATTTAATGTGTAATTATACAC
*
11263755 GTGAA
1 ATGAA
11263760 ATTCTGTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 17 0.53
30 1 0.03
31 14 0.44
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (31 bp):
ATGAACTTTAATTTAATGTGTAATTATACAC
Found at i:11266067 original size:20 final size:19
Alignment explanation
Indices: 11266028--11266254 Score: 79
Period size: 19 Copynumber: 11.9 Consensus size: 19
11266018 TACAATAATA
*
11266028 TTTTTTGAAAACACGGAAT
1 TTTTTTGAAAACACGAAAT
11266047 TTTTTTGAAAACACTGAAA-
1 TTTTTTGAAAACAC-GAAAT
* * *
11266066 -TTTTCG-ATACATGAGAAT
1 TTTTTTGAAAACACGA-AAT
11266084 TTTTTTG---ACACGAAA-
1 TTTTTTGAAAACACGAAAT
**
11266099 AATTTTGAAAACACGAAA-
1 TTTTTTGAAAACACGAAAT
* *
11266117 ATTTTT-AAAACATGAATAT
1 TTTTTTGAAAACACGAA-AT
*
11266136 TTTTTT-TAAACACG-AAT
1 TTTTTTGAAAACACGAAAT
* *
11266153 TTTTTTAAAAAAAAACATGAGAA-
1 TTTTTT----GAAAACACGA-AAT
11266176 TTTTTTGAAAACACGAACACAT
1 TTTTTTGAAAACACG-A-A-AT
**
11266198 GAAAATTTTGAAAACACGAAA-
1 ---TTTTTTGAAAACACGAAAT
* *
11266219 ATTTTTG-AAACACGGGAA-
1 TTTTTTGAAAACAC-GAAAT
11266237 TTTTTTGAAAACACGAAA
1 TTTTTTGAAAACACGAAA
11266255 ACACGAAAAT
Statistics
Matches: 160, Mismatches: 24, Indels: 49
0.69 0.10 0.21
Matches are distributed among these distances:
15 5 0.03
16 4 0.03
17 34 0.21
18 38 0.24
19 43 0.27
20 5 0.03
21 1 0.01
22 7 0.04
23 7 0.04
24 3 0.02
25 13 0.08
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (19 bp):
TTTTTTGAAAACACGAAAT
Found at i:11266069 original size:18 final size:18
Alignment explanation
Indices: 11266029--11266139 Score: 56
Period size: 17 Copynumber: 6.3 Consensus size: 18
11266019 ACAATAATAT
* *
11266029 TTTTTGAAAACACGGAATT
1 TTTTTGAAAACACTGAA-A
11266048 TTTTTGAAAACACTGAAA
1 TTTTTGAAAACACTGAAA
* *
11266066 TTTTCG-ATACA-TGAGAA
1 TTTTTGAAAACACTGA-AA
***
11266083 TTTTT-TTGACAC-GAAAA
1 TTTTTGAAAACACTG-AAA
*
11266100 ATTTTGAAAACAC-GAAAA
1 TTTTTGAAAACACTG-AAA
11266118 TTTTT-AAAACA-TGAATA
1 TTTTTGAAAACACTGAA-A
11266135 TTTTT
1 TTTTT
11266140 TTTAAACACG
Statistics
Matches: 73, Mismatches: 12, Indels: 16
0.72 0.12 0.16
Matches are distributed among these distances:
16 5 0.07
17 33 0.45
18 19 0.26
19 16 0.22
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.38
Consensus pattern (18 bp):
TTTTTGAAAACACTGAAA
Found at i:11266069 original size:19 final size:18
Alignment explanation
Indices: 11266027--11266254 Score: 101
Period size: 18 Copynumber: 12.1 Consensus size: 18
11266017 ATACAATAAT
11266027 ATTTTTTGAAAACACGGAA
1 ATTTTTTGAAAACAC-GAA
*
11266046 TTTTTTTGAAAACACTGAA
1 ATTTTTTGAAAACAC-GAA
* * *
11266065 A-TTTTCG-ATACATGAGA
1 ATTTTTTGAAAACACGA-A
11266082 ATTTTTTTG---ACACGAA
1 A-TTTTTTGAAAACACGAA
**
11266098 AAATTTTGAAAACACGAA
1 ATTTTTTGAAAACACGAA
* *
11266116 AATTTTT-AAAACATGAA
1 ATTTTTTGAAAACACGAA
**
11266133 TATTTTTTTTAAACACGAA
1 -ATTTTTTGAAAACACGAA
* * *
11266152 TTTTTTTAAAAAAAAACATGAGA
1 ATTTTTT----GAAAACACGA-A
11266175 ATTTTTTGAAAACACGAACA
1 ATTTTTTGAAAACACG-A-A
*
11266195 CATGAAAATTTTGAAAACACGAA
1 -AT----TTTTTGAAAACACGAA
* *
11266218 AATTTTTG-AAACACGGGA
1 ATTTTTTGAAAACAC-GAA
11266236 ATTTTTTGAAAACACGAA
1 ATTTTTTGAAAACACGAA
11266254 A
1 A
11266255 ACACGAAAAT
Statistics
Matches: 159, Mismatches: 29, Indels: 43
0.69 0.13 0.19
Matches are distributed among these distances:
15 5 0.03
16 4 0.03
17 26 0.16
18 47 0.30
19 43 0.27
20 2 0.01
21 2 0.01
22 8 0.05
23 8 0.05
24 1 0.01
25 13 0.08
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (18 bp):
ATTTTTTGAAAACACGAA
Found at i:11266117 original size:17 final size:17
Alignment explanation
Indices: 11266091--11266138 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
11266081 AATTTTTTTG
11266091 ACACGAAAAATTTTGAAA
1 ACACG-AAAATTTTGAAA
*
11266109 ACACGAAAATTTTTAAA
1 ACACGAAAATTTTGAAA
* *
11266126 ACATGAATATTTT
1 ACACGAAAATTTT
11266139 TTTTAAACAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 22 0.81
18 5 0.19
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.31
Consensus pattern (17 bp):
ACACGAAAATTTTGAAA
Found at i:11266139 original size:17 final size:17
Alignment explanation
Indices: 11266100--11266162 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
11266090 GACACGAAAA
* *
11266100 ATTTTGAAAACACGAAA
1 ATTTTTAAAACACGAAT
*
11266117 ATTTTTAAAACATGAAT
1 ATTTTTAAAACACGAAT
*
11266134 ATTTTTTTTAAACACGAAT
1 A--TTTTTAAAACACGAAT
*
11266153 TTTTTTAAAA
1 ATTTTTAAAA
11266163 AAAAACATGA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
17 23 0.62
19 14 0.38
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.41
Consensus pattern (17 bp):
ATTTTTAAAACACGAAT
Found at i:11266194 original size:25 final size:25
Alignment explanation
Indices: 11266149--11266217 Score: 63
Period size: 24 Copynumber: 2.8 Consensus size: 25
11266139 TTTTAAACAC
* **
11266149 GAATTTTTTTAAAA-AAAAACATGA
1 GAATTTTTTGAAAACACGAACATGA
11266173 GAATTTTTTGAAAACACGAACACATGA
1 GAATTTTTTGAAAACACG-A-ACATGA
*
11266200 -AA-ATTTTGAAAACACGAA
1 GAATTTTTTGAAAACACGAA
11266218 AATTTTTGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
23 1 0.03
24 14 0.37
25 14 0.37
26 3 0.08
27 6 0.16
ACGTcount: A:0.51, C:0.10, G:0.12, T:0.28
Consensus pattern (25 bp):
GAATTTTTTGAAAACACGAACATGA
Found at i:11266220 original size:17 final size:17
Alignment explanation
Indices: 11266198--11266255 Score: 64
Period size: 17 Copynumber: 3.3 Consensus size: 17
11266188 ACGAACACAT
11266198 GAAAATTTTGAAAACAC
1 GAAAATTTTGAAAACAC
11266215 GAAAATTTTTG-AAACAC
1 GAAAA-TTTTGAAAACAC
**
11266232 GGGAATTTTTTGAAAACAC
1 --GAAAATTTTGAAAACAC
11266251 GAAAA
1 GAAAA
11266256 CACGAAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
17 14 0.42
18 10 0.30
19 9 0.27
ACGTcount: A:0.48, C:0.10, G:0.16, T:0.26
Consensus pattern (17 bp):
GAAAATTTTGAAAACAC
Found at i:11266342 original size:20 final size:22
Alignment explanation
Indices: 11266317--11266370 Score: 71
Period size: 20 Copynumber: 2.6 Consensus size: 22
11266307 AAAAAATATT
*
11266317 CACGAG-AGTTTTTTTTG-AAA
1 CACGAGAAATTTTTTTTGAAAA
11266337 CACGAGAAATTTTTTTTGAAAA
1 CACGAGAAATTTTTTTTGAAAA
11266359 CAC--GAAATTTTT
1 CACGAGAAATTTTT
11266371 CAAACACGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 15 0.48
21 10 0.32
22 6 0.19
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (22 bp):
CACGAGAAATTTTTTTTGAAAA
Found at i:11266375 original size:16 final size:17
Alignment explanation
Indices: 11266349--11266397 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
11266339 CGAGAAATTT
*
11266349 TTTTTGAAAACACGAAA
1 TTTTTAAAAACACGAAA
* *
11266366 TTTTT-CAAACACGGAAG
1 TTTTTAAAAACAC-GAAA
11266383 TTTTTAAAAACACGA
1 TTTTTAAAAACACGA
11266398 TAACATCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 6 0.22
17 15 0.56
18 6 0.22
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (17 bp):
TTTTTAAAAACACGAAA
Found at i:11266440 original size:19 final size:21
Alignment explanation
Indices: 11266416--11266460 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
11266406 AAAAAATATT
11266416 CACGAG-AGTTTTTTTG-AAA
1 CACGAGAAGTTTTTTTGAAAA
*
11266435 CACGAGAATTTTTTTTGAAAA
1 CACGAGAAGTTTTTTTGAAAA
11266456 CACGA
1 CACGA
11266461 AAACATGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.26
20 9 0.39
21 8 0.35
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (21 bp):
CACGAGAAGTTTTTTTGAAAA
Found at i:11266498 original size:18 final size:17
Alignment explanation
Indices: 11266467--11266501 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
11266457 ACGAAAACAT
*
11266467 GAAATTTTTCAAACACG
1 GAAATTTTTAAAACACG
11266484 GAAATTTTTAAAAACACG
1 GAAATTTTT-AAAACACG
11266502 ATAACATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.29
Consensus pattern (17 bp):
GAAATTTTTAAAACACG
Found at i:11266507 original size:105 final size:103
Alignment explanation
Indices: 11266220--11266567 Score: 487
Period size: 105 Copynumber: 3.4 Consensus size: 103
11266210 AACACGAAAA
* * * *
11266220 TTTTTGAAACACGGGAA-TTTTTTGAAAACACGAAAACACGAAAATTTGTCAAATACGGAATTTT
1 TTTTTGAAACACGAGAATTTTTTTGAAAACACGAAAACA-G-AAATTTTTCAAACACGGAA---A
**
11266284 TTTTTTGAAACACGATAACATCAAAAAAATATTCACGAGAGTTT
61 TTTTTAAAAACACGATAACATCAAAAAAATATTCACGAGAG-TT
*
11266328 TTTTTGAAACACGAGAAATTTTTTTTG-AAA-AC----AC-GAAATTTTTCAAACACGGAAGTTT
1 TTTTTGAAACACGAG-AA-TTTTTTTGAAAACACGAAAACAGAAATTTTTCAAACACGGAAATTT
11266386 TTAAAAACACGATAACATCAAAAAAATATTCACGAGAGTT
64 TTAAAAACACGATAACATCAAAAAAATATTCACGAGAGTT
11266426 TTTTTGAAACACGAGAATTTTTTTTGAAAACACGAAAACATGAAATTTTTCAAACACGGAAATTT
1 TTTTTGAAACACGAGAA-TTTTTTTGAAAACACGAAAACA-GAAATTTTTCAAACACGGAAATTT
11266491 TTAAAAACACGATAACATCAAAAAAATATTCACGAGAGTT
64 TTAAAAACACGATAACATCAAAAAAATATTCACGAGAGTT
11266531 TTTTTGAAACACGAGAATTTTTTTGAAAACACGAAAA
1 TTTTTGAAACACGAGAATTTTTTTGAAAACACGAAAA
11266568 TTTTCAAACA
Statistics
Matches: 222, Mismatches: 7, Indels: 26
0.87 0.03 0.10
Matches are distributed among these distances:
97 11 0.05
98 20 0.09
99 41 0.18
102 17 0.08
103 3 0.01
104 20 0.09
105 82 0.37
108 14 0.06
109 4 0.02
110 3 0.01
111 7 0.03
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.31
Consensus pattern (103 bp):
TTTTTGAAACACGAGAATTTTTTTGAAAACACGAAAACAGAAATTTTTCAAACACGGAAATTTTT
AAAAACACGATAACATCAAAAAAATATTCACGAGAGTT
Found at i:11266578 original size:16 final size:17
Alignment explanation
Indices: 11266551--11266677 Score: 69
Period size: 17 Copynumber: 7.2 Consensus size: 17
11266541 ACGAGAATTT
11266551 TTTTGAAAACACGAAAA
1 TTTTGAAAACACGAAAA
* * *
11266568 TTTT-CAAACACGGGAAT
1 TTTTGAAAACAC-GAAAA
11266585 TTTTGAAAACACGAAAA
1 TTTTGAAAACACGAAAA
** ** *
11266602 TTTTTTATTCACGAGAAT
1 TTTTGAAAACACGA-AAA
* *
11266620 TTTTG-AAACATGAAGATT
1 TTTTGAAAACACGAA-A-A
* *
11266638 TTTTGAAAACATGGAAATT
1 TTTTGAAAACA-CGAAA-A
*
11266657 TTTTGAAAACACGGAAA
1 TTTTGAAAACACGAAAA
11266674 TTTT
1 TTTT
11266678 ATTATTATTT
Statistics
Matches: 84, Mismatches: 19, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
16 7 0.08
17 34 0.40
18 21 0.25
19 19 0.23
20 3 0.04
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (17 bp):
TTTTGAAAACACGAAAA
Found at i:11266672 original size:19 final size:19
Alignment explanation
Indices: 11266530--11266677 Score: 111
Period size: 19 Copynumber: 8.2 Consensus size: 19
11266520 TCACGAGAGT
*
11266530 TTTTTTG-AAACACGAGAAT
1 TTTTTTGAAAACACG-GAAA
11266549 TTTTTTGAAAACAC-GAAA
1 TTTTTTGAAAACACGGAAA
* * *
11266567 -ATTTT-CAAACACGGGAA
1 TTTTTTGAAAACACGGAAA
*
11266584 -TTTTTGAAAACACGAAAA
1 TTTTTTGAAAACACGGAAA
**
11266602 TTTTTT--ATTCAC-GAGAA
1 TTTTTTGAAAACACGGA-AA
*
11266619 -TTTTTG-AAACA-TGAAGA
1 TTTTTTGAAAACACGGAA-A
*
11266636 TTTTTTGAAAACATGGAAA
1 TTTTTTGAAAACACGGAAA
11266655 TTTTTTGAAAACACGGAAA
1 TTTTTTGAAAACACGGAAA
11266674 TTTT
1 TTTT
11266678 ATTATTATTT
Statistics
Matches: 103, Mismatches: 15, Indels: 22
0.74 0.11 0.16
Matches are distributed among these distances:
16 13 0.13
17 23 0.22
18 18 0.17
19 40 0.39
20 9 0.09
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (19 bp):
TTTTTTGAAAACACGGAAA
Found at i:11267287 original size:15 final size:15
Alignment explanation
Indices: 11267269--11267297 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
11267259 GGCGTTGGGC
11267269 TGGGCAGTGGCCTGT
1 TGGGCAGTGGCCTGT
11267284 TGGGCAGTGGCCTG
1 TGGGCAGTGGCCTG
11267298 CTGCGGGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.21, G:0.48, T:0.24
Consensus pattern (15 bp):
TGGGCAGTGGCCTGT
Found at i:11267414 original size:11 final size:12
Alignment explanation
Indices: 11267398--11267453 Score: 57
Period size: 11 Copynumber: 4.9 Consensus size: 12
11267388 TGTTTTTTTC
11267398 TTTTTC-TTCTA
1 TTTTTCTTTCTA
* *
11267409 TTTTTCTTTTTC
1 TTTTTCTTTCTA
11267421 TTTCTT-TTTCT-
1 TTT-TTCTTTCTA
11267432 TTTTTCTTTCTA
1 TTTTTCTTTCTA
11267444 -TTTTCTTTCT
1 TTTTTCTTTCT
11267454 TCTCCTTCCT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
10 2 0.05
11 24 0.63
12 10 0.26
13 2 0.05
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTTCTTTCTA
Found at i:11267418 original size:23 final size:23
Alignment explanation
Indices: 11267383--11267440 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
11267373 CTATTTTTTA
*
11267383 TTCTTTGTT-TTTTTCTTT-TTC
1 TTCTTTTTTCTTTTTCTTTCTTC
*
11267404 TTCTATTTTTCTTTTTCTTTCTTT
1 TTCT-TTTTTCTTTTTCTTTCTTC
11267428 TTCTTTTTTCTTT
1 TTCTTTTTTCTTT
11267441 CTATTTTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 4 0.12
22 4 0.12
23 18 0.56
24 6 0.19
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.81
Consensus pattern (23 bp):
TTCTTTTTTCTTTTTCTTTCTTC
Found at i:11267429 original size:35 final size:35
Alignment explanation
Indices: 11267392--11267456 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
11267382 ATTCTTTGTT
11267392 TTTTTC-TTTTTC-TTCTATTTTTCTTT-TTCTTTC
1 TTTTTCTTTTTTCTTTCTA-TTTTCTTTCTTCTTTC
11267425 TTTTTCTTTTTTCTTTCTATTTTCTTTCTTCT
1 TTTTTCTTTTTTCTTTCTATTTTCTTTCTTCT
11267457 CCTTCCTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 6 0.21
34 14 0.48
35 9 0.31
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.78
Consensus pattern (35 bp):
TTTTTCTTTTTTCTTTCTATTTTCTTTCTTCTTTC
Found at i:11267432 original size:27 final size:28
Alignment explanation
Indices: 11267390--11267454 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 28
11267380 TTATTCTTTG
11267390 TTTT-TTTCTTTTTCTTCTATT-TTTCT-
1 TTTTCTTTCTTTTTCTT-TATTCTTTCTA
*
11267416 TTTTCTTTCTTTTTCTTTTTTCTTTCTA
1 TTTTCTTTCTTTTTCTTTATTCTTTCTA
11267444 TTTTCTTTCTT
1 TTTTCTTTCTT
11267455 CTCCTTCCTC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
26 7 0.20
27 17 0.49
28 11 0.31
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (28 bp):
TTTTCTTTCTTTTTCTTTATTCTTTCTA
Found at i:11267448 original size:18 final size:18
Alignment explanation
Indices: 11267393--11267456 Score: 82
Period size: 17 Copynumber: 3.7 Consensus size: 18
11267383 TTCTTTGTTT
11267393 TTTTC-TTTTTC-TTCTA
1 TTTTCTTTTTTCTTTCTA
11267409 TTTT-TCTTTTTCTTTCT-
1 TTTTCT-TTTTTCTTTCTA
11267426 TTTTCTTTTTTCTTTCTA
1 TTTTCTTTTTTCTTTCTA
*
11267444 TTTTCTTTCTTCT
1 TTTTCTTTTTTCT
11267457 CCTTCCTCTT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
16 4 0.10
17 21 0.50
18 17 0.40
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTCTTTTTTCTTTCTA
Found at i:11267704 original size:17 final size:17
Alignment explanation
Indices: 11267682--11267723 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
11267672 TGTAGGGGCG
*
11267682 ACGGTGGTGGTGGCG-CC
1 ACGGTGGTGGT-GCGACA
*
11267699 ACGGTGGCGGTGCGACA
1 ACGGTGGTGGTGCGACA
11267716 ACGGTGGT
1 ACGGTGGT
11267724 TGCGGGAGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.12, C:0.21, G:0.50, T:0.17
Consensus pattern (17 bp):
ACGGTGGTGGTGCGACA
Found at i:11267778 original size:22 final size:22
Alignment explanation
Indices: 11267752--11267799 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
11267742 ATGAGGGCCC
* * *
11267752 TTTTGCTGCTTTTTTTTTGATT
1 TTTTGCTGCTGTTTTCTTAATT
11267774 TTTTGCTGCTGTTTTCTTAATT
1 TTTTGCTGCTGTTTTCTTAATT
11267796 TTTT
1 TTTT
11267800 TCTTTTTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.06, C:0.10, G:0.12, T:0.71
Consensus pattern (22 bp):
TTTTGCTGCTGTTTTCTTAATT
Found at i:11268126 original size:30 final size:30
Alignment explanation
Indices: 11268082--11268165 Score: 107
Period size: 30 Copynumber: 2.8 Consensus size: 30
11268072 GTAATTTCTT
11268082 AAAATTTAAGGGGTTAAAATGTAATTTAAAG
1 AAAATTTAA-GGGTTAAAATGTAATTTAAAG
** *
11268113 AAAATTTAAGGGTTTGAATGTAATTTATAG
1 AAAATTTAAGGGTTAAAATGTAATTTAAAG
*
11268143 AAAAGTTT-AGGGTCAAAATGTAA
1 AAAA-TTTAAGGGTTAAAATGTAA
11268166 ATTTCAAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
30 34 0.74
31 12 0.26
ACGTcount: A:0.45, C:0.01, G:0.20, T:0.33
Consensus pattern (30 bp):
AAAATTTAAGGGTTAAAATGTAATTTAAAG
Found at i:11268233 original size:19 final size:19
Alignment explanation
Indices: 11268196--11268236 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
11268186 TAAAATGTAA
*
11268196 TTTATATTTTTTTGTATTT
1 TTTATATTTTTTTGGATTT
11268215 TTTAT-TTTTTTTGAGATTT
1 TTTATATTTTTTTG-GATTT
11268234 TTT
1 TTT
11268237 TACTACTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (19 bp):
TTTATATTTTTTTGGATTT
Found at i:11269147 original size:163 final size:163
Alignment explanation
Indices: 11268582--11269227 Score: 984
Period size: 163 Copynumber: 4.0 Consensus size: 163
11268572 TAGAAATTGA
* * * ***
11268582 AAATACCTCAGCGT--AACCCGAGGCTCAACTCACTTCTAGCATTATGAGTTGATTTTTTT-TTT
1 AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAA
* * * *
11268644 GA-A-A-AAACAGAAATTGAAATTACCTCAGCGTGACCCGAGGCTCAAAC-CATCTCTCGCATTA
66 AACAGAGAAACATAAATTGAAAATACCTCAGCGTGACCCGAGGCTC-AACTCACCTCTCGCATTA
11268705 TGAGTTGATTTTTTTTGAAAAAAGAAATTTAAAAG
130 TGAGTTGA-TTTTTTTGAAAAAAGAAATTTAAAAG
11268740 AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAA
1 AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAA
*
11268805 AACAGAGAAACATAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCACATTAT
66 AACAGAGAAACATAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTAT
*
11268870 GAGTTGA-TTTTTTGAAAAGAGAAATTTAAAAG
131 GAGTTGATTTTTTTGAAAAAAGAAATTTAAAAG
* *
11268902 GAATACCTCAGCGTGCGACCCGGGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAA
1 AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAA
* *
11268967 AACAGAGAAACATAAATTGAAAACACCTCAGCGTGACCCGAGGTTCAACTCACCTCTCGCATTAT
66 AACAGAGAAACATAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTAT
11269032 GAGTTGATTTTTTTGAAAAAAGAAATTTAAAAG
131 GAGTTGATTTTTTTGAAAAAAGAAATTTAAAAG
* * * *
11269065 AAATACCTCAGCGTGGGACCCGAGGCTCGACTCACGTCTCGCAAGATGAGTTGATTTTTTTGAAA
1 AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAA
** * *
11269130 AACAGAGAAACATAAATTGAAAATACCTCAGCGTGATTCGAGACTCAACTCACCTTTCGCATTAT
66 AACAGAGAAACATAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTAT
*
11269195 GAGTTGATTTTTTTGAAAAACAGAAATTGAAAA
131 GAGTTGATTTTTTTGAAAAA-AGAAATTTAAAA
11269228 ATATTTCTTA
Statistics
Matches: 448, Mismatches: 31, Indels: 12
0.91 0.06 0.02
Matches are distributed among these distances:
158 14 0.03
160 42 0.09
161 1 0.00
162 157 0.35
163 166 0.37
164 68 0.15
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.28
Consensus pattern (163 bp):
AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAA
AACAGAGAAACATAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTAT
GAGTTGATTTTTTTGAAAAAAGAAATTTAAAAG
Found at i:11270119 original size:15 final size:15
Alignment explanation
Indices: 11270104--11270140 Score: 60
Period size: 13 Copynumber: 2.6 Consensus size: 15
11270094 CTTTGTTTTG
11270104 TGTTTTTTTTTG--T
1 TGTTTTTTTTTGCTT
11270117 TGTTTTTTTTTGCTT
1 TGTTTTTTTTTGCTT
11270132 TGTTTTTTT
1 TGTTTTTTT
11270141 CAGGCATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 12 0.55
15 10 0.45
ACGTcount: A:0.00, C:0.03, G:0.14, T:0.84
Consensus pattern (15 bp):
TGTTTTTTTTTGCTT
Found at i:11270122 original size:13 final size:13
Alignment explanation
Indices: 11270099--11270140 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
11270089 TTTTTCTTTG
11270099 TTTTG-TGTTTTT
1 TTTTGTTGTTTTT
11270111 TTTTGTTGTTTTT
1 TTTTGTTGTTTTT
11270124 TTTTGCTTTGTTTTT
1 TTTTG--TTGTTTTT
11270139 TT
1 TT
11270141 CAGGCATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 5 0.19
13 12 0.44
15 10 0.37
ACGTcount: A:0.00, C:0.02, G:0.14, T:0.83
Consensus pattern (13 bp):
TTTTGTTGTTTTT
Found at i:11283444 original size:20 final size:19
Alignment explanation
Indices: 11283406--11283567 Score: 85
Period size: 19 Copynumber: 8.8 Consensus size: 19
11283396 ACAATAATAA
*
11283406 TTTTTGAAAACACGGAATT
1 TTTTTGAAAACACGAAATT
11283425 TTTTTGAAAACACTGAAA--
1 TTTTTGAAAACAC-GAAATT
* * *
11283443 TTTTCG-ATACATGAGAATT
1 TTTTTGAAAACACGA-AATT
*
11283462 TTTTTG---ACACGAAA-A
1 TTTTTGAAAACACGAAATT
*
11283477 ATTTTGAAAACACGAAA--
1 TTTTTGAAAACACGAAATT
* *
11283494 ATTTTGAAAACATGAATATT
1 TTTTTGAAAACACGAA-ATT
* * *
11283514 TTTTT-TAAACACGGATTT
1 TTTTTGAAAACACGAAATT
* *
11283532 TTTTTAAAAAACATGAGAA-T
1 TTTTT-GAAAACACGA-AATT
11283552 TTTTTGAAAACACGAA
1 TTTTTGAAAACACGAA
11283568 CACATGAAAA
Statistics
Matches: 110, Mismatches: 20, Indels: 27
0.70 0.13 0.17
Matches are distributed among these distances:
15 5 0.05
16 4 0.04
17 26 0.24
18 22 0.20
19 33 0.30
20 19 0.17
21 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.36
Consensus pattern (19 bp):
TTTTTGAAAACACGAAATT
Found at i:11283446 original size:17 final size:18
Alignment explanation
Indices: 11283376--11283505 Score: 51
Period size: 17 Copynumber: 7.3 Consensus size: 18
11283366 TTTTGTTTTT
11283376 AAACAC-GAGAATTTTGA
1 AAACACTGAGAATTTTGA
* * *
11283393 AATACAATAATAATTTTTGA
1 AA-ACACTGAGAA-TTTTGA
11283413 AAACAC-G-GAATTTTTTTGA
1 AAACACTGAGAA---TTTTGA
11283432 AAACACTGA-AATTTTCG-
1 AAACACTGAGAATTTT-GA
* **
11283449 ATACA-TGAGAATTTTTT
1 AAACACTGAGAATTTTGA
** *
11283466 TGACAC-GAAAAATTTTGA
1 AAACACTG-AGAATTTTGA
*
11283484 AAACAC-GAAAATTTTGA
1 AAACACTGAGAATTTTGA
11283501 AAACA
1 AAACA
11283506 TGAATATTTT
Statistics
Matches: 86, Mismatches: 15, Indels: 24
0.69 0.12 0.19
Matches are distributed among these distances:
16 3 0.03
17 37 0.43
18 16 0.19
19 19 0.22
20 11 0.13
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (18 bp):
AAACACTGAGAATTTTGA
Found at i:11283446 original size:18 final size:18
Alignment explanation
Indices: 11283404--11283516 Score: 67
Period size: 17 Copynumber: 6.4 Consensus size: 18
11283394 ATACAATAAT
*
11283404 AATTTTTGAAAACACGGA
1 AATTTTTGAAAACACTGA
*
11283422 ATTTTTTTGAAAACACTGA
1 A-ATTTTTGAAAACACTGA
* *
11283441 AATTTTCG-ATACA-TGA
1 AATTTTTGAAAACACTGA
***
11283457 GAATTTTT-TTGACAC-GAA
1 -AATTTTTGAAAACACTG-A
*
11283475 AAATTTTGAAAACAC-GA
1 AATTTTTGAAAACACTGA
*
11283492 AAATTTTGAAAACA-TGA
1 AATTTTTGAAAACACTGA
11283509 ATATTTTT
1 A-ATTTTT
11283517 TTTAAACACG
Statistics
Matches: 74, Mismatches: 13, Indels: 16
0.72 0.13 0.16
Matches are distributed among these distances:
16 3 0.04
17 38 0.51
18 17 0.23
19 16 0.22
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (18 bp):
AATTTTTGAAAACACTGA
Found at i:11283514 original size:17 final size:17
Alignment explanation
Indices: 11283468--11283515 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
11283458 AATTTTTTTG
11283468 ACACGAAAAATTTTGAAA
1 ACACG-AAAATTTTGAAA
11283486 ACACGAAAATTTTGAAA
1 ACACGAAAATTTTGAAA
* *
11283503 ACATGAATATTTT
1 ACACGAAAATTTT
11283516 TTTTAAACAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
17 23 0.82
18 5 0.18
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.29
Consensus pattern (17 bp):
ACACGAAAATTTTGAAA
Found at i:11283601 original size:18 final size:18
Alignment explanation
Indices: 11283569--11283630 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 18
11283559 AAACACGAAC
11283569 ACATGAAAA-TTTTGAAA
1 ACATGAAAATTTTTGAAA
11283586 ACATGAAAATTTTTG-AA
1 ACATGAAAATTTTTGAAA
* * *
11283603 ACACGGGAATTTTTTGAAA
1 ACA-TGAAAATTTTTGAAA
*
11283622 ACACGAAAA
1 ACATGAAAA
11283631 CACGAAAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
17 14 0.39
18 17 0.47
19 5 0.14
ACGTcount: A:0.48, C:0.10, G:0.15, T:0.27
Consensus pattern (18 bp):
ACATGAAAATTTTTGAAA
Found at i:11283630 original size:44 final size:45
Alignment explanation
Indices: 11283582--11283776 Score: 148
Period size: 44 Copynumber: 4.3 Consensus size: 45
11283572 TGAAAATTTT
*
11283582 GAAAACATGAAAATTTTTGAAACACGGGAA-TTTTTTGAAAACAC
1 GAAAACATGAAAATTTTTCAAACACGGGAATTTTTTTGAAAACAC
* * * *
11283626 GAAAACACGAAAATTTGTCAAATACGGGAATTTTTTTG-AAACAG
1 GAAAACATGAAAATTTTTCAAACACGGGAATTTTTTTGAAAACAC
* * * * *
11283670 GATAACATCAAAAAAATATTCAAGAAAACACGAGAATTTTTTTTGAAAACAC
1 GAAAACAT--GAAAATTTTTC----AAACACGGGAA-TTTTTTTGAAAACAC
* * * *
11283722 GATAACATTAAAA-TTTTCAAACAC-GGAA-ATTTTTAAAAACAC
1 GAAAACATGAAAATTTTTCAAACACGGGAATTTTTTTGAAAACAC
* *
11283764 GATAACATCAAAA
1 GAAAACATGAAAA
11283777 AAATATTCAC
Statistics
Matches: 122, Mismatches: 20, Indels: 20
0.75 0.12 0.12
Matches are distributed among these distances:
42 24 0.20
44 40 0.33
45 13 0.11
46 7 0.06
49 4 0.03
50 13 0.11
51 8 0.07
52 13 0.11
ACGTcount: A:0.49, C:0.13, G:0.12, T:0.26
Consensus pattern (45 bp):
GAAAACATGAAAATTTTTCAAACACGGGAATTTTTTTGAAAACAC
Found at i:11283723 original size:96 final size:94
Alignment explanation
Indices: 11283612--11283785 Score: 258
Period size: 94 Copynumber: 1.8 Consensus size: 94
11283602 AACACGGGAA
* * ** *
11283612 TTTTTTGAAAACACGAAAACACGAAAATTTGTCAAATACGGGAATTTTTTTGAAACAGGATAACA
1 TTTTTTGAAAACACGAAAACACGAAAATTT-TCAAACAC-GGAAATTTTTAAAAACACGATAACA
11283677 TCAAAAAAATATTCAAGAAAACACGAGAATT
64 TCAAAAAAATATTCAAGAAAACACGAGAATT
* **
11283708 TTTTTTGAAAACACGATAACATTAAAATTTTCAAACACGGAAATTTTTAAAAACACGATAACATC
1 TTTTTTGAAAACACGAAAACACGAAAATTTTCAAACACGGAAATTTTTAAAAACACGATAACATC
11283773 AAAAAAATATTCA
66 AAAAAAATATTCA
11283786 CGAGAGTTTT
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
94 36 0.51
95 7 0.10
96 27 0.39
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.28
Consensus pattern (94 bp):
TTTTTTGAAAACACGAAAACACGAAAATTTTCAAACACGGAAATTTTTAAAAACACGATAACATC
AAAAAAATATTCAAGAAAACACGAGAATT
Found at i:11283808 original size:19 final size:19
Alignment explanation
Indices: 11283784--11283820 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
11283774 AAAAAATATT
*
11283784 CACGAGAGTTTTTTTGAAG
1 CACGAGAATTTTTTTGAAG
11283803 CACGAGAATTTTTTTGAA
1 CACGAGAATTTTTTTGAA
11283821 AACATGGAAA
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:0.30, C:0.11, G:0.22, T:0.38
Consensus pattern (19 bp):
CACGAGAATTTTTTTGAAG
Found at i:11283847 original size:16 final size:17
Alignment explanation
Indices: 11283828--11283859 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
11283818 GAAAACATGG
11283828 AAACAT-GAAATTTTTC
1 AAACATGGAAATTTTTC
11283844 AAACATGGAAATTTTT
1 AAACATGGAAATTTTT
11283860 AAAAACACGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (17 bp):
AAACATGGAAATTTTTC
Found at i:11283912 original size:19 final size:21
Alignment explanation
Indices: 11283888--11283932 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
11283878 AAAAAATATT
11283888 CACGAG-AGTTTTTTTG-AAA
1 CACGAGAAGTTTTTTTGAAAA
*
11283907 CACGAGAATTTTTTTTGAAAA
1 CACGAGAAGTTTTTTTGAAAA
11283928 CACGA
1 CACGA
11283933 AAACACGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.26
20 9 0.39
21 8 0.35
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (21 bp):
CACGAGAAGTTTTTTTGAAAA
Found at i:11283962 original size:105 final size:105
Alignment explanation
Indices: 11283695--11283972 Score: 459
Period size: 104 Copynumber: 2.7 Consensus size: 105
11283685 ATATTCAAGA
* *
11283695 AAACACGAGAATTTTTTTTGAAAACACGATAACATTAAAATTTTCAAACACGGAAATTTTTAAAA
1 AAACACGAGAATTTTTTTTGAAAACACGAAAACATGAAAATTTTCAAACACGGAAATTTTTAAAA
11283760 ACACGATAACATCAAAAAAATATTCACGAGAGTTTTTTTG
66 ACACGATAACATCAAAAAAATATTCACGAGAGTTTTTTTG
* * * * *
11283800 AAGCACGAGAA-TTTTTTTGAAAACATGGAAACATGAAATTTTTCAAACATGGAAATTTTTAAAA
1 AAACACGAGAATTTTTTTTGAAAACACGAAAACATGAAAATTTTCAAACACGGAAATTTTTAAAA
11283864 ACACGATAACATCAAAAAAATATTCACGAGAGTTTTTTTG
66 ACACGATAACATCAAAAAAATATTCACGAGAGTTTTTTTG
* * *
11283904 AAACACGAGAATTTTTTTTGAAAACACGAAAACACGAAAATTTTCAAACACGGGAATTTTTGAAA
1 AAACACGAGAATTTTTTTTGAAAACACGAAAACATGAAAATTTTCAAACACGGAAATTTTTAAAA
11283969 ACAC
66 ACAC
11283973 CAAAATTTTT
Statistics
Matches: 157, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
104 97 0.62
105 60 0.38
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.29
Consensus pattern (105 bp):
AAACACGAGAATTTTTTTTGAAAACACGAAAACATGAAAATTTTCAAACACGGAAATTTTTAAAA
ACACGATAACATCAAAAAAATATTCACGAGAGTTTTTTTG
Found at i:11283972 original size:18 final size:18
Alignment explanation
Indices: 11283931--11284053 Score: 92
Period size: 18 Copynumber: 6.9 Consensus size: 18
11283921 TTGAAAACAC
11283931 GAAAACACGAAAA-TTTT
1 GAAAACACGAAAATTTTT
* **
11283948 -CAAACACGGGAATTTTT
1 GAAAACACGAAAATTTTT
*
11283965 GAAAACACCAAAATTTTT
1 GAAAACACGAAAATTTTT
* ** * *
11283983 -TATTCGCGAGAATTTTT
1 GAAAACACGAAAATTTTT
*
11284000 G-AAACACGAAGATTTTTT
1 GAAAACACGAA-AATTTTT
*
11284018 GAAAACACGGAAATTTTTT
1 GAAAACAC-GAAAATTTTT
*
11284037 GAAAACACGGAAATTTT
1 GAAAACACGAAAATTTT
11284054 ATTATTATTT
Statistics
Matches: 80, Mismatches: 20, Indels: 11
0.72 0.18 0.10
Matches are distributed among these distances:
16 9 0.11
17 20 0.25
18 27 0.34
19 21 0.26
20 3 0.04
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (18 bp):
GAAAACACGAAAATTTTT
Found at i:11284023 original size:19 final size:18
Alignment explanation
Indices: 11283995--11284053 Score: 84
Period size: 19 Copynumber: 3.2 Consensus size: 18
11283985 TTCGCGAGAA
11283995 TTTTTG-AAACACGAAGAT
1 TTTTTGAAAACACGAA-AT
11284013 TTTTTGAAAACACGGAAAT
1 TTTTTGAAAACAC-GAAAT
11284032 TTTTTGAAAACACGGAAAT
1 TTTTTGAAAACAC-GAAAT
11284051 TTT
1 TTT
11284054 ATTATTATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
18 6 0.15
19 30 0.77
20 3 0.08
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAT
Found at i:11284664 original size:15 final size:15
Alignment explanation
Indices: 11284646--11284674 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
11284636 GGCGTTGGGC
11284646 TGGGCAGTGGCCTGT
1 TGGGCAGTGGCCTGT
11284661 TGGGCAGTGGCCTG
1 TGGGCAGTGGCCTG
11284675 CTGCGGGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.21, G:0.48, T:0.24
Consensus pattern (15 bp):
TGGGCAGTGGCCTGT
Found at i:11284791 original size:11 final size:12
Alignment explanation
Indices: 11284775--11284830 Score: 57
Period size: 11 Copynumber: 4.9 Consensus size: 12
11284765 TGTTTTTTTC
11284775 TTTTTC-TTCTA
1 TTTTTCTTTCTA
* *
11284786 TTTTTCTTTTTC
1 TTTTTCTTTCTA
11284798 TTTCTT-TTTCT-
1 TTT-TTCTTTCTA
11284809 TTTTTCTTTCTA
1 TTTTTCTTTCTA
11284821 -TTTTCTTTCT
1 TTTTTCTTTCT
11284831 TCTCCTTCCT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
10 2 0.05
11 24 0.63
12 10 0.26
13 2 0.05
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTTCTTTCTA
Found at i:11284795 original size:23 final size:23
Alignment explanation
Indices: 11284760--11284817 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
11284750 CTATTTTTTA
*
11284760 TTCTTTGTT-TTTTTCTTT-TTC
1 TTCTTTTTTCTTTTTCTTTCTTC
*
11284781 TTCTATTTTTCTTTTTCTTTCTTT
1 TTCT-TTTTTCTTTTTCTTTCTTC
11284805 TTCTTTTTTCTTT
1 TTCTTTTTTCTTT
11284818 CTATTTTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 4 0.12
22 4 0.12
23 18 0.56
24 6 0.19
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.81
Consensus pattern (23 bp):
TTCTTTTTTCTTTTTCTTTCTTC
Found at i:11284806 original size:35 final size:35
Alignment explanation
Indices: 11284769--11284833 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
11284759 ATTCTTTGTT
11284769 TTTTTC-TTTTTC-TTCTATTTTTCTTT-TTCTTTC
1 TTTTTCTTTTTTCTTTCTA-TTTTCTTTCTTCTTTC
11284802 TTTTTCTTTTTTCTTTCTATTTTCTTTCTTCT
1 TTTTTCTTTTTTCTTTCTATTTTCTTTCTTCT
11284834 CCTTCCTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 6 0.21
34 14 0.48
35 9 0.31
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.78
Consensus pattern (35 bp):
TTTTTCTTTTTTCTTTCTATTTTCTTTCTTCTTTC
Found at i:11284809 original size:27 final size:28
Alignment explanation
Indices: 11284767--11284831 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 28
11284757 TTATTCTTTG
11284767 TTTT-TTTCTTTTTCTTCTATT-TTTCT-
1 TTTTCTTTCTTTTTCTT-TATTCTTTCTA
*
11284793 TTTTCTTTCTTTTTCTTTTTTCTTTCTA
1 TTTTCTTTCTTTTTCTTTATTCTTTCTA
11284821 TTTTCTTTCTT
1 TTTTCTTTCTT
11284832 CTCCTTCCTC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
26 7 0.20
27 17 0.49
28 11 0.31
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (28 bp):
TTTTCTTTCTTTTTCTTTATTCTTTCTA
Found at i:11284825 original size:18 final size:18
Alignment explanation
Indices: 11284770--11284833 Score: 82
Period size: 17 Copynumber: 3.7 Consensus size: 18
11284760 TTCTTTGTTT
11284770 TTTTC-TTTTTC-TTCTA
1 TTTTCTTTTTTCTTTCTA
11284786 TTTT-TCTTTTTCTTTCT-
1 TTTTCT-TTTTTCTTTCTA
11284803 TTTTCTTTTTTCTTTCTA
1 TTTTCTTTTTTCTTTCTA
*
11284821 TTTTCTTTCTTCT
1 TTTTCTTTTTTCT
11284834 CCTTCCTCTT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
16 4 0.10
17 21 0.50
18 17 0.40
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTCTTTTTTCTTTCTA
Found at i:11285081 original size:17 final size:17
Alignment explanation
Indices: 11285059--11285100 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
11285049 TGTAGGGGCG
11285059 ACGGTGGTGGTGGCG-CC
1 ACGGTGGTGGT-GCGACC
* *
11285076 ACGGTGGCGGTGCGACG
1 ACGGTGGTGGTGCGACC
11285093 ACGGTGGT
1 ACGGTGGT
11285101 TGCGGGAGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.10, C:0.21, G:0.52, T:0.17
Consensus pattern (17 bp):
ACGGTGGTGGTGCGACC
Found at i:11285512 original size:30 final size:30
Alignment explanation
Indices: 11285477--11285579 Score: 102
Period size: 30 Copynumber: 3.4 Consensus size: 30
11285467 TTAAGCTGTC
11285477 AAAATGTAATTTAAAGAAAATTTAGGGGTT
1 AAAATGTAATTTAAAGAAAATTTAGGGGTT
* * *
11285507 TAAATGTAATTTATAGAAAAGTTT-GGGGTC
1 AAAATGTAATTTAAAGAAAA-TTTAGGGGTT
* * * * *
11285537 AAAATATAAATTTCAA-AAAGTATAGGGGCT
1 AAAATGT-AATTTAAAGAAAATTTAGGGGTT
11285567 AAAATGTAATTTA
1 AAAATGTAATTTA
11285580 TATTTTTTGT
Statistics
Matches: 57, Mismatches: 13, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
29 7 0.12
30 41 0.72
31 9 0.16
ACGTcount: A:0.46, C:0.03, G:0.18, T:0.33
Consensus pattern (30 bp):
AAAATGTAATTTAAAGAAAATTTAGGGGTT
Found at i:11289963 original size:304 final size:304
Alignment explanation
Indices: 11289414--11290019 Score: 980
Period size: 304 Copynumber: 2.0 Consensus size: 304
11289404 TTTCTCGTTG
*
11289414 AAACAAAAATCAGAAGTTGCTGGTGTCTTCTGGAAATTCAAAGCCAGAGTTGAGAATGAAAGTGG
1 AAACAAAAATCAAAAGTTGCTGGTGTCTTCTGGAAATTCAAAGCCAGAGTTGAGAATGAAAGTGG
* * * *
11289479 ATGCATGATTTAGATTTTAAGATCTAATAATGGTAAGGAGTACAATTCAAAAACCTTTAATAGGT
66 ATGCATGAATCAGATTTTAAGATCTAATAATGGCAAGGAGTACAATTCAAAAACCTTCAATAGGT
* * * *
11289544 TTTGTGAAGAGGATGAAATTGAGCATCAGTTGATGGTGCCATACACTCCACAATAAAATGGAGTC
131 TTTATGAAGAGGATGAAATTGAACATCAGTTGACGGTGCCATACACTCCACAACAAAATGGAGTC
11289609 AGTGAAAGGAGGAACAGATTCATAATAGAGATGACTCGATGTATGCTTCATGAGAAGAATC-TTC
196 AGTGAAAGGAGGAACAGATTCATAATAGAGATGACTCGATGTATGCTTCATGAGAAGAATCTTTC
* * *
11289673 CAAAAAGCTTTTGGGGAGAAGCTGCAAACACTGCTGTGTTCTTGT
261 C-AAAAGATTTTGGGAAGAAGCTGCAAACACTACTGTGTTCTTGT
* * * * *
11289718 AAACAAAAATTAAAATTTGTTGGTGTGTTTTGGAAATTCAAAGCCAGAGTTGAGAATGAAAGTGG
1 AAACAAAAATCAAAAGTTGCTGGTGTCTTCTGGAAATTCAAAGCCAGAGTTGAGAATGAAAGTGG
* * *
11289783 ATGCATGAATCAGATTTTAAGATCTGATAATGGCAAGGAGTACACTTCAGAAACCTTCAATAGGT
66 ATGCATGAATCAGATTTTAAGATCTAATAATGGCAAGGAGTACAATTCAAAAACCTTCAATAGGT
* * *
11289848 TTTATGAAGAGGTTGGAATTGAACGTCAGTTGACGGTGCCATACACTCCACAACAAAATGGAGTC
131 TTTATGAAGAGGATGAAATTGAACATCAGTTGACGGTGCCATACACTCCACAACAAAATGGAGTC
*
11289913 AGTGAAAGGAGGAACAGATTCATAATGGAGATGACTCGATGTATGCTTCATGAGAAGAATCTTTC
196 AGTGAAAGGAGGAACAGATTCATAATAGAGATGACTCGATGTATGCTTCATGAGAAGAATCTTTC
11289978 CAAAAGATTTTGGGAAGAAGCTGCAAACACTACTGTGTTCTT
261 CAAAAGATTTTGGGAAGAAGCTGCAAACACTACTGTGTTCTT
11290020 ACAAAATCAG
Statistics
Matches: 277, Mismatches: 24, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
304 273 0.99
305 4 0.01
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (304 bp):
AAACAAAAATCAAAAGTTGCTGGTGTCTTCTGGAAATTCAAAGCCAGAGTTGAGAATGAAAGTGG
ATGCATGAATCAGATTTTAAGATCTAATAATGGCAAGGAGTACAATTCAAAAACCTTCAATAGGT
TTTATGAAGAGGATGAAATTGAACATCAGTTGACGGTGCCATACACTCCACAACAAAATGGAGTC
AGTGAAAGGAGGAACAGATTCATAATAGAGATGACTCGATGTATGCTTCATGAGAAGAATCTTTC
CAAAAGATTTTGGGAAGAAGCTGCAAACACTACTGTGTTCTTGT
Found at i:11294864 original size:16 final size:17
Alignment explanation
Indices: 11294845--11294878 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
11294835 GACTCAAATT
11294845 TAATAACTCATAT-TAA
1 TAATAACTCATATGTAA
*
11294861 TAATAATTCATATGTAA
1 TAATAACTCATATGTAA
11294878 T
1 T
11294879 TAATTTAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (17 bp):
TAATAACTCATATGTAA
Found at i:11295833 original size:152 final size:152
Alignment explanation
Indices: 11295552--11296009 Score: 846
Period size: 152 Copynumber: 3.0 Consensus size: 152
11295542 CCCATGTTGG
*
11295552 ATGGATCCAATTAGGAATATTGAAAGACAAAGATGAAGACTTTTATAAAATCAATCGATG-ACAA
1 ATGGATCCAATTAGGAATATTGAAAGACAAAGATGAAGACTTTTATAAAATCAATCGATGAAAAA
* * * * *
11295616 GACTCGCCGTGCACTTCTCATTGGAAGGGAACCTCTTGCAAGTTGCAACCAATGTCAAGGGTTTG
66 GACTCGGCGTGCAATTCTCATTGGAAGGGAACCTCTTGCAAGTTGTAACCAATTTCAAGGCTTTG
*
11295681 AATGGCATTTTGTGGAAGAAAA
131 AATGCCATTTTGTGGAAGAAAA
11295703 ATGGATCCAATTAGGAATATTGAAAGACAAAGATGAAGACTTTTATAAAATCAATCGATGAAAAA
1 ATGGATCCAATTAGGAATATTGAAAGACAAAGATGAAGACTTTTATAAAATCAATCGATGAAAAA
11295768 GACTCGGCGTGCAATTCTCATTGGAAGGGAACCTCTTGCAAGTTGTAACCAATTTCAAGGCTTTG
66 GACTCGGCGTGCAATTCTCATTGGAAGGGAACCTCTTGCAAGTTGTAACCAATTTCAAGGCTTTG
11295833 AATGCCATTTTGTGGAAGAAAA
131 AATGCCATTTTGTGGAAGAAAA
11295855 ATGGATCCAATTAGGAATATTGAAAGACAAAGATGAAGACTTTTATAAAATCAATCGATGAAAAA
1 ATGGATCCAATTAGGAATATTGAAAGACAAAGATGAAGACTTTTATAAAATCAATCGATGAAAAA
11295920 GACTCGGCGTGCAATTCTCATTGGAAGGGAACCTCTTGCAAGTTGTAACCAATTTCAAGGCTTTG
66 GACTCGGCGTGCAATTCTCATTGGAAGGGAACCTCTTGCAAGTTGTAACCAATTTCAAGGCTTTG
11295985 AATGCCATTTTGTGGAAGAAAA
131 AATGCCATTTTGTGGAAGAAAA
11296007 ATG
1 ATG
11296010 TGATATTCTT
Statistics
Matches: 299, Mismatches: 7, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
151 60 0.20
152 239 0.80
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.27
Consensus pattern (152 bp):
ATGGATCCAATTAGGAATATTGAAAGACAAAGATGAAGACTTTTATAAAATCAATCGATGAAAAA
GACTCGGCGTGCAATTCTCATTGGAAGGGAACCTCTTGCAAGTTGTAACCAATTTCAAGGCTTTG
AATGCCATTTTGTGGAAGAAAA
Found at i:11297229 original size:19 final size:19
Alignment explanation
Indices: 11297186--11297231 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
11297176 ATTTTTATTT
*
11297186 AATTAT-TTAAAATTATAA
1 AATTATATTAAAATGATAA
11297204 AGA-TATATTAAAATGATAA
1 A-ATTATATTAAAATGATAA
11297223 AATTATATT
1 AATTATATT
11297232 TTTAGTATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (19 bp):
AATTATATTAAAATGATAA
Found at i:11298216 original size:16 final size:16
Alignment explanation
Indices: 11298170--11298219 Score: 75
Period size: 16 Copynumber: 3.1 Consensus size: 16
11298160 AAGCCAAATT
11298170 AAAATAAGAGGAA-ATG
1 AAAATAAGAGGAAGA-G
11298186 AAAATAGAGAGGAAGAG
1 AAAATA-AGAGGAAGAG
11298203 AAAATAAGAGGAAGAG
1 AAAATAAGAGGAAGAG
11298219 A
1 A
11298220 GTGTACCATG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
16 17 0.53
17 14 0.44
18 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.30, T:0.08
Consensus pattern (16 bp):
AAAATAAGAGGAAGAG
Found at i:11305534 original size:19 final size:19
Alignment explanation
Indices: 11305490--11305560 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 19
11305480 TATTTTGATA
*
11305490 TTAACTTGTTTTGAAACAGTT
1 TTAACTTG-ATTGAAACA-TT
11305511 TTAACTTGATTGAAA-ATGT
1 TTAACTTGATTGAAACAT-T
**
11305530 TTAACTCAATTGAAACCATT
1 TTAACTTGATTGAAA-CATT
11305550 TTAACTTGATT
1 TTAACTTGATT
11305561 TTATCATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
18 1 0.02
19 15 0.36
20 16 0.38
21 10 0.24
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.44
Consensus pattern (19 bp):
TTAACTTGATTGAAACATT
Found at i:11315917 original size:27 final size:29
Alignment explanation
Indices: 11315887--11315943 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
11315877 TAAGAATTGA
*
11315887 ATTAAAT-A-AATTAAAATTCATATACAC
1 ATTAAATCATAATTAAAATCCATATACAC
*
11315914 ATTAAATCATATTTAAAATCCATATACAC
1 ATTAAATCATAATTAAAATCCATATACAC
11315943 A
1 A
11315944 AAATTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 7 0.27
28 1 0.04
29 18 0.69
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (29 bp):
ATTAAATCATAATTAAAATCCATATACAC
Found at i:11318686 original size:30 final size:30
Alignment explanation
Indices: 11318655--11318780 Score: 141
Period size: 30 Copynumber: 4.2 Consensus size: 30
11318645 TTTTATTTTG
*
11318655 CATTTTGACCCCTAAACTTTTCTAAAATTG
1 CATTTTGACCCCTAAACTTTTCTAAAATTA
11318685 CATTTTGACCCCTAAACTTTT-TCAAAATTA
1 CATTTTGACCCCTAAACTTTTCT-AAAATTA
* * *
11318715 TATTTAT-ACACCTGAACTTTTCT-AAATTA
1 CATTT-TGACCCCTAAACTTTTCTAAAATTA
* * * *
11318744 CATTTGGGCCCCTAAACTTTCCAAAAATTA
1 CATTTTGACCCCTAAACTTTTCTAAAATTA
11318774 CATTTTG
1 CATTTTG
11318781 GCCTCATATT
Statistics
Matches: 79, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
29 22 0.28
30 55 0.70
31 2 0.03
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.40
Consensus pattern (30 bp):
CATTTTGACCCCTAAACTTTTCTAAAATTA
Found at i:11319145 original size:25 final size:25
Alignment explanation
Indices: 11319129--11319177 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
11319119 AACAAGCATA
11319129 AACAAAAAAACAGCAAACAAGAAAC
1 AACAAAAAAACAGCAAACAAGAAAC
* *
11319154 AACAAAAAAATAGCAAAGAAGAAA
1 AACAAAAAAACAGCAAACAAGAAA
11319178 AAGGAGAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.73, C:0.14, G:0.10, T:0.02
Consensus pattern (25 bp):
AACAAAAAAACAGCAAACAAGAAAC
Found at i:11319326 original size:17 final size:17
Alignment explanation
Indices: 11319304--11319370 Score: 50
Period size: 17 Copynumber: 4.1 Consensus size: 17
11319294 AACGAAGAAG
11319304 AAAAGAAAAAAGAAAAA
1 AAAAGAAAAAAGAAAAA
** **
11319321 AAAAG---AGGGAAGGA
1 AAAAGAAAAAAGAAAAA
* *
11319335 AAAAGAAAAAGGAAAGA
1 AAAAGAAAAAAGAAAAA
*
11319352 AAAAGAAAGAAGAAAAA
1 AAAAGAAAAAAGAAAAA
11319369 AA
1 AA
11319371 TTTAAAACAG
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
14 10 0.26
17 28 0.74
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAAAGAAAAA
Found at i:11319338 original size:18 final size:17
Alignment explanation
Indices: 11319312--11319370 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
11319302 AGAAAAGAAA
11319312 AAAGAAAAAAAAAGAGGG
1 AAAGAAAAAAAAAGA-GG
*
11319330 AAGGAAAAAGAAAA-AGG
1 AAAGAAAAA-AAAAGAGG
* *
11319347 AAAGAAAAAGAAAGAAG
1 AAAGAAAAAAAAAGAGG
11319364 AAA-AAAA
1 AAAGAAAA
11319371 TTTAAAACAG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
16 7 0.20
17 15 0.43
18 9 0.26
19 4 0.11
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAAAAAGAGG
Found at i:11319369 original size:31 final size:31
Alignment explanation
Indices: 11319297--11319369 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
11319287 GGGGCCGAAC
**
11319297 GAAGAAGAAAAGAAAAAAGAAAAAAAAAGAGG
1 GAAGAA-AAAAGAAAAAAGAAAAAAAAAGAAA
* * *
11319329 GAAGGAAAAAGAAAAAGGAAAGAAAAAGAAA
1 GAAGAAAAAAGAAAAAAGAAAAAAAAAGAAA
11319360 GAAGAAAAAA
1 GAAGAAAAAA
11319370 ATTTAAAACA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
31 30 0.86
32 5 0.14
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (31 bp):
GAAGAAAAAAGAAAAAAGAAAAAAAAAGAAA
Found at i:11319853 original size:18 final size:17
Alignment explanation
Indices: 11319827--11319878 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 17
11319817 ATCGCATATT
*
11319827 TTTAAGTTTTTTTTTGTA
1 TTTAAGTTTTTATTT-TA
*
11319845 TTTATGTTTTTATTTTA
1 TTTAAGTTTTTATTTTA
*
11319862 TTTTA--TTTTATTTTA
1 TTTAAGTTTTTATTTTA
11319877 TT
1 TT
11319879 CGTTAAAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 12 0.40
17 5 0.17
18 13 0.43
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (17 bp):
TTTAAGTTTTTATTTTA
Found at i:11319860 original size:5 final size:5
Alignment explanation
Indices: 11319852--11319878 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
11319842 GTATTTATGT
11319852 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
11319879 CGTTAAAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:11320202 original size:18 final size:18
Alignment explanation
Indices: 11320179--11320224 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
11320169 AAACTAATTG
11320179 TGTTTCAAAAATTT-TCA
1 TGTTTCAAAAATTTCTCA
*
11320196 TGTTTTC-AAAATTTCTCC
1 TG-TTTCAAAAATTTCTCA
11320214 TGTTTCAAAAA
1 TGTTTCAAAAA
11320225 AATAATACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.46
Consensus pattern (18 bp):
TGTTTCAAAAATTTCTCA
Found at i:11320284 original size:17 final size:17
Alignment explanation
Indices: 11320264--11320325 Score: 72
Period size: 18 Copynumber: 3.6 Consensus size: 17
11320254 TTCGTTTAAA
*
11320264 AAAAAACTTCGTGTTTC
1 AAAAAATTTCGTGTTTC
*
11320281 -AAAAATTTCCGTGTTTT
1 AAAAAATTT-CGTGTTTC
*
11320298 AAAAATTTTCGTGTTTTC
1 AAAAAATTTCGTG-TTTC
11320316 AAAAAATTTC
1 AAAAAATTTC
11320326 CCGTGTTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
16 7 0.19
17 11 0.30
18 19 0.51
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (17 bp):
AAAAAATTTCGTGTTTC
Found at i:11320331 original size:54 final size:54
Alignment explanation
Indices: 11320263--11320412 Score: 146
Period size: 54 Copynumber: 2.8 Consensus size: 54
11320253 ATTCGTTTAA
* *
11320263 AAAAAAACTT-CGTGTTTCAAAAATTTCCGTGTTTTAAAAATTTTCGTGTTTTC
1 AAAAAAATTTCCGTGTTTTAAAAATTTCCGTGTTTTAAAAATTTTCGTGTTTTC
* ** *
11320316 -AAAAAATTTCCCGTGTTTTTAAAAA-TTCTCGTATTTT-GTAATTTTCTTGTTTTC
1 AAAAAAATTT-CCGTG-TTTTAAAAATTTC-CGTGTTTTAAAAATTTTCGTGTTTTC
* * *
11320370 AGAAAAAATTTCCATGTTTTATAAATTTTCGTGTTTTCAAAAA
1 A-AAAAAATTTCCGTGTTTTAAAAATTTCCGTGTTTT-AAAAA
11320413 AATTCCTGTC
Statistics
Matches: 76, Mismatches: 12, Indels: 15
0.74 0.12 0.15
Matches are distributed among these distances:
52 8 0.11
54 36 0.47
55 21 0.28
56 11 0.14
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.46
Consensus pattern (54 bp):
AAAAAAATTTCCGTGTTTTAAAAATTTCCGTGTTTTAAAAATTTTCGTGTTTTC
Found at i:11320404 original size:17 final size:17
Alignment explanation
Indices: 11320271--11320449 Score: 99
Period size: 17 Copynumber: 9.9 Consensus size: 17
11320261 AAAAAAAAAC
*
11320271 TTCGTGTTTCAAAAATT
1 TTCGTGTTTTAAAAATT
*
11320288 TCCGTGTTTTAAAAATT
1 TTCGTGTTTTAAAAATT
11320305 TTCGTGTTTTCAAAAAATT
1 TTCGTGTTTT--AAAAATT
*
11320324 TCCCGTGTTTTTAAAAATT
1 T-TCGTG-TTTTAAAAATT
* * **
11320343 CTCGTATTTT-GTAATT
1 TTCGTGTTTTAAAAATT
*
11320359 TTCTTGTTTTCAGAAAAAATT
1 TTCGTGTTTT----AAAAATT
* * *
11320380 TCCATGTTTTATAAATT
1 TTCGTGTTTTAAAAATT
*
11320397 TTCGTGTTTTCAAAAAAAT
1 TTCGTGTTTT--AAAAATT
* * *
11320416 TCCTGTCTTTTAAAATTT
1 TTC-GTGTTTTAAAAATT
*
11320434 TTTGTGTTTTCAAAAA
1 TTCGTGTTTT-AAAAA
11320450 AATTGACCGT
Statistics
Matches: 120, Mismatches: 29, Indels: 25
0.69 0.17 0.14
Matches are distributed among these distances:
16 11 0.09
17 48 0.40
18 13 0.11
19 22 0.18
20 10 0.08
21 16 0.13
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.49
Consensus pattern (17 bp):
TTCGTGTTTTAAAAATT
Found at i:11320497 original size:36 final size:37
Alignment explanation
Indices: 11320363--11320504 Score: 134
Period size: 37 Copynumber: 3.8 Consensus size: 37
11320353 GTAATTTTCT
* * *
11320363 TGTTTTCAGAAAAAATTTC-CATGTTTTATAAATTTTCG
1 TGTTTTCA-AAAAAATTCCTCGTGTTTCATAAATTTT-G
* *
11320401 TGTTTTCAAAAAAATTCCT-GTCTTTTA-AAATTTTTTG
1 TGTTTTCAAAAAAATTCCTCGTGTTTCATAAA--TTTTG
*
11320438 TGTTTTCAAAAAAATTGAC-CGTGTTTCATAAATTTCTG
1 TGTTTTCAAAAAAATT-CCTCGTGTTTCATAAATTT-TG
11320476 TG-TTTCAAAAAAA-TCCTCGTGTTTCATAA
1 TGTTTTCAAAAAAATTCCTCGTGTTTCATAA
11320505 TTTATCAAAA
Statistics
Matches: 89, Mismatches: 7, Indels: 18
0.78 0.06 0.16
Matches are distributed among these distances:
35 1 0.01
36 16 0.18
37 46 0.52
38 23 0.26
39 3 0.03
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.45
Consensus pattern (37 bp):
TGTTTTCAAAAAAATTCCTCGTGTTTCATAAATTTTG
Found at i:11320507 original size:74 final size:74
Alignment explanation
Indices: 11320336--11320507 Score: 190
Period size: 74 Copynumber: 2.3 Consensus size: 74
11320326 CCGTGTTTTT
* * * *
11320336 AAAAATTCTCGTATTTTGTAATTTTCTTGTTTTCAGAAAAAATTTCCATGTTTTATAAATTTTCG
1 AAAAATCCTCGTATTTTATAATTTTCTTGTTTTCAGAAAAAATTACCATGTTTCATAAATTTTCG
11320401 TGTTTTCAA
66 TGTTTTCAA
* * * *
11320410 AAAAATTCCT-GTCTTTTAAAATTTTTTGTGTTTTCA-AAAAAATTGACCGTGTTTCATAAA-TT
1 AAAAA-TCCTCGTATTTTATAATTTTCT-TGTTTTCAGAAAAAATT-ACCATGTTTCATAAATTT
11320472 TC-TGTGTTTCAA
63 TCGTGT-TTTCAA
* *
11320484 AAAAATCCTCGTGTTTCATAATTT
1 AAAAATCCTCGTATTTTATAATTT
11320508 ATCAAAATTT
Statistics
Matches: 82, Mismatches: 11, Indels: 10
0.80 0.11 0.10
Matches are distributed among these distances:
73 7 0.09
74 52 0.63
75 23 0.28
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.47
Consensus pattern (74 bp):
AAAAATCCTCGTATTTTATAATTTTCTTGTTTTCAGAAAAAATTACCATGTTTCATAAATTTTCG
TGTTTTCAA
Found at i:11320574 original size:20 final size:21
Alignment explanation
Indices: 11320511--11320575 Score: 64
Period size: 22 Copynumber: 3.2 Consensus size: 21
11320501 ATAATTTATC
* * *
11320511 AAAATTTTTGTGTTCTCAAAA
1 AAAATTATCGTGTTTTCAAAA
*
11320532 TAAAATTATTGTGTTTT--AAA
1 -AAAATTATCGTGTTTTCAAAA
11320552 AAAATT-TCGTGTTTTCAAAA
1 AAAATTATCGTGTTTTCAAAA
11320572 AAAA
1 AAAA
11320576 AGTTGTGCTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
18 8 0.21
19 6 0.16
20 10 0.26
22 14 0.37
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.42
Consensus pattern (21 bp):
AAAATTATCGTGTTTTCAAAA
Found at i:11327994 original size:14 final size:14
Alignment explanation
Indices: 11327977--11328003 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11327967 CTTTTAAGAA
11327977 TTATATTTTTCAAT
1 TTATATTTTTCAAT
11327991 TTATATTTTTCAA
1 TTATATTTTTCAA
11328004 AAAAATCAAC
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:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (14 bp):
TTATATTTTTCAAT
Found at i:11328115 original size:75 final size:74
Alignment explanation
Indices: 11328006--11328578 Score: 680
Period size: 75 Copynumber: 7.6 Consensus size: 74
11327996 TTTTTCAAAA
* * *
11328006 AAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCATGCTAAGGTATTTCTTTTAAATT
1 AAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT-TTTTAAATT
11328071 TCTGTTTTTT
65 TCTGTTTTTT
* *
11328081 AAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCATGCTAAGGTATTTCTTTTAAATT
1 AAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT-TTTTAAATT
11328146 TCTGTTTTTT
65 TCTGTTTTTT
11328156 AAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTA---TTTTAAAT
1 AAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGT--CACGCTGAGGTATTTTTTTAAAT
*
11328218 TTCTGTTTTTCAA
64 TTCTGTTTTT--T
* *
11328231 AAATCAACTCATAATAC-AGAGGTGAGTTGAGCATTGGGTCACGCTGAGGTA--TTTTT-AATTT
1 AAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTAAATTT
* *
11328292 ATATCTTTTT
66 CTGT-TTTTT
11328302 AAAAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA---TTTTA
1 -----AAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTA
*
11328364 AATTTCTGTTTTTCAA
61 AATTTCTGTTTTT--T
11328380 AAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTCTTTTAAATT
1 AAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT-TTTTAAATT
*
11328445 TCTATTTTTTTT
65 TC--TGTTTTTT
* * * **
11328457 CAAAAAAACAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCACGCTGAGGTATTTTTTTTA
1 ----AAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA-TTTTTTTA
*
11328522 AATTTCTGTTTTTCAA
61 AATTTCTGTTTTT--T
* *
11328538 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
1 AAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTC
11328579 GCAAGCCGAG
Statistics
Matches: 444, Mismatches: 26, Indels: 54
0.85 0.05 0.10
Matches are distributed among these distances:
72 19 0.04
73 78 0.18
74 20 0.05
75 131 0.30
76 25 0.06
77 98 0.22
79 12 0.03
81 58 0.13
82 3 0.01
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (74 bp):
AAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTAAATTT
CTGTTTTTT
Found at i:11328805 original size:30 final size:30
Alignment explanation
Indices: 11328774--11328899 Score: 134
Period size: 30 Copynumber: 4.2 Consensus size: 30
11328764 TTTATTTTTG
*
11328774 CATTTTGACCCCTAAACTTTTCTAAAATTG
1 CATTTTGACCCCTAAACTTTTCTAAAATTA
*
11328804 CATTTTGACCCTTAAAC-TTTCTTAAAATTA
1 CATTTTGACCCCTAAACTTTTC-TAAAATTA
11328834 CATTTAT-ACCCCTAAACTTTTCT-AAATTA
1 CATTT-TGACCCCTAAACTTTTCTAAAATTA
* * * * *
11328863 CATCTGGGCCCTTAAAC-TTTCCAAAATTTA
1 CATTTTGACCCCTAAACTTTTCTAAAA-TTA
11328893 CATTTTG
1 CATTTTG
11328900 GCCTCATATT
Statistics
Matches: 80, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
28 4 0.05
29 25 0.31
30 46 0.57
31 5 0.06
ACGTcount: A:0.31, C:0.23, G:0.06, T:0.40
Consensus pattern (30 bp):
CATTTTGACCCCTAAACTTTTCTAAAATTA
Found at i:11328894 original size:59 final size:60
Alignment explanation
Indices: 11328781--11328897 Score: 166
Period size: 59 Copynumber: 2.0 Consensus size: 60
11328771 TTGCATTTTG
* * * *
11328781 ACCCCTAAACTTTTCTAAAATTGCATTTTGACCCTTAAACTTTCTTAAAATTACATTTAT
1 ACCCCTAAACTTTTCTAAAATTACATCTGGACCCTTAAACTTTCTCAAAATTACATTTAT
*
11328841 ACCCCTAAACTTTTCT-AAATTACATCTGGGCCCTTAAACTTTC-CAAAATTTACATTT
1 ACCCCTAAACTTTTCTAAAATTACATCTGGACCCTTAAACTTTCTCAAAA-TTACATTT
11328898 TGGCCTCATA
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
58 4 0.08
59 31 0.61
60 16 0.31
ACGTcount: A:0.32, C:0.24, G:0.04, T:0.39
Consensus pattern (60 bp):
ACCCCTAAACTTTTCTAAAATTACATCTGGACCCTTAAACTTTCTCAAAATTACATTTAT
Found at i:11329295 original size:24 final size:24
Alignment explanation
Indices: 11329261--11329311 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
11329251 AAGCAAGCAT
11329261 AAACAAAAAAAAACAGCAAACAAG
1 AAACAAAAAAAAACAGCAAACAAG
* *
11329285 AAACAACAAAAAACAGCAAAGAAG
1 AAACAAAAAAAAACAGCAAACAAG
11329309 AAA
1 AAA
11329312 AAGGAGAGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.75, C:0.16, G:0.10, T:0.00
Consensus pattern (24 bp):
AAACAAAAAAAAACAGCAAACAAG
Found at i:11330124 original size:18 final size:18
Alignment explanation
Indices: 11330101--11330146 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
11330091 AAACTAATTG
11330101 TGTTTCAAAAATTT-TCA
1 TGTTTCAAAAATTTCTCA
*
11330118 TGTTTTC-AAAATTTCTCG
1 TG-TTTCAAAAATTTCTCA
11330136 TGTTTCAAAAA
1 TGTTTCAAAAA
11330147 AATAATACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.46
Consensus pattern (18 bp):
TGTTTCAAAAATTTCTCA
Found at i:11330205 original size:17 final size:17
Alignment explanation
Indices: 11330176--11330261 Score: 77
Period size: 18 Copynumber: 4.9 Consensus size: 17
11330166 GTGTTTTATA
* *
11330176 TTCG-GTTTAAAAAAAC
1 TTCGTGTTTCAAAAAAT
11330192 TTCGTGTTTC-AAAAAT
1 TTCGTGTTTCAAAAAAT
* *
11330208 TTCCGTGTTTTAAAAATT
1 TT-CGTGTTTCAAAAAAT
11330226 TTCGTGTTTTCAAAAAAT
1 TTCGTG-TTTCAAAAAAT
11330244 TTCCCGTGTTTTCAAAAA
1 TT--CGTG-TTTCAAAAA
11330262 TTCTCGTATT
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
16 11 0.19
17 15 0.26
18 18 0.31
20 14 0.24
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.42
Consensus pattern (17 bp):
TTCGTGTTTCAAAAAAT
Found at i:11330252 original size:54 final size:54
Alignment explanation
Indices: 11330186--11330332 Score: 149
Period size: 54 Copynumber: 2.7 Consensus size: 54
11330176 TTCGGTTTAA
*
11330186 AAAAACTT-CGTGTTTCAAAAATTTCCGTGTTTTAAAAATTTTCGTGTTTTCA-
1 AAAAATTTCCGTGTTTCAAAAATTTCCGTGTTTTAAAAATTTTCGTGTTTTCAG
* *** *
11330238 AAAAATTTCCCGTGTTTTCAAAAA-TTCTCGT-ATTTCGTAATTTTCTTGTTTTCAG
1 AAAAATTT-CCGTG-TTTCAAAAATTTC-CGTGTTTTAAAAATTTTCGTGTTTTCAG
* * *
11330293 AAAAATTTCCATGTTTTATAAATTTCCGTGTTTTCAAAAA
1 AAAAATTTCCGTGTTTCAAAAATTTCCGTGTTTT-AAAAA
11330333 AATTCTTGTC
Statistics
Matches: 74, Mismatches: 13, Indels: 13
0.74 0.13 0.13
Matches are distributed among these distances:
52 7 0.09
53 10 0.14
54 35 0.47
55 22 0.30
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (54 bp):
AAAAATTTCCGTGTTTCAAAAATTTCCGTGTTTTAAAAATTTTCGTGTTTTCAG
Found at i:11330417 original size:36 final size:37
Alignment explanation
Indices: 11330184--11330424 Score: 180
Period size: 37 Copynumber: 6.6 Consensus size: 37
11330174 TATTCGGTTT
* *
11330184 AAAAAAACT-TCGTGTTTCAAAAATTTCCGTGTTTT-
1 AAAAAAATTCTCGTGTTTCATAAATTTCCGTGTTTTC
* *
11330219 --AAAAATTTTCGTGTTTTCAAAAAATTTCCCGTGTTTTC
1 AAAAAAATTCTCGTG-TTTC-ATAAATTT-CCGTGTTTTC
* * * *
11330257 --AAAAATTCTCGTATTTCGT-AATTTTCTTGTTTTC
1 AAAAAAATTCTCGTGTTTCATAAATTTCCGTGTTTTC
* * *
11330291 AGAAAAATT-TCCATGTTTTATAAATTTCCGTGTTTTC
1 AAAAAAATTCT-CGTGTTTCATAAATTTCCGTGTTTTC
* * * ** *
11330328 AAAAAAATTCTTGTCTTTTA-AAATTTTTTGTGTTTTA
1 AAAAAAATTCTCGTGTTTCATAAA-TTTCCGTGTTTTC
11330365 AAAAAAATTGAC-CGTGTTTCATAAATTTCCGTG-TTTC
1 AAAAAAATT--CTCGTGTTTCATAAATTTCCGTGTTTTC
*
11330402 AAAAAAATCCTCGTGTTTCATAA
1 AAAAAAATTCTCGTGTTTCATAA
11330425 TTTATCAAAA
Statistics
Matches: 164, Mismatches: 27, Indels: 29
0.75 0.12 0.13
Matches are distributed among these distances:
33 6 0.04
34 13 0.08
35 11 0.07
36 36 0.22
37 70 0.43
38 24 0.15
39 4 0.02
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (37 bp):
AAAAAAATTCTCGTGTTTCATAAATTTCCGTGTTTTC
Found at i:11330476 original size:20 final size:19
Alignment explanation
Indices: 11330464--11330530 Score: 59
Period size: 19 Copynumber: 3.7 Consensus size: 19
11330454 AAATTTTGTA
11330464 TTTTAAAAAAAAATCGTGT
1 TTTTAAAAAAAAATCGTGT
** *
11330483 TTTT--AAAATTATTGTG-
1 TTTTAAAAAAAAATCGTGT
**
11330499 TTTTAAAAAAATTTCGTGT
1 TTTTAAAAAAAAATCGTGT
*
11330518 TTTCAAAAAAAAA
1 TTTTAAAAAAAAA
11330531 AGTTGTGTTT
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
16 4 0.11
17 9 0.25
18 9 0.25
19 14 0.39
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.42
Consensus pattern (19 bp):
TTTTAAAAAAAAATCGTGT
Found at i:11330516 original size:35 final size:34
Alignment explanation
Indices: 11330452--11330525 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 34
11330442 GTTCTCAAAA
11330452 TAAAATTTTGTATTTTAAAAAAAAATCGTGTTTT
1 TAAAATTTTGTATTTTAAAAAAAAATCGTGTTTT
* **
11330486 TAAAATTATTGTGTTTTAAAAAAATTTCGTGTTTT
1 TAAAATT-TTGTATTTTAAAAAAAAATCGTGTTTT
*
11330521 CAAAA
1 TAAAA
11330526 AAAAAAGTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
34 7 0.20
35 28 0.80
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (34 bp):
TAAAATTTTGTATTTTAAAAAAAAATCGTGTTTT
Found at i:11330541 original size:20 final size:22
Alignment explanation
Indices: 11330503--11330545 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
11330493 ATTGTGTTTT
*
11330503 AAAAAAATTTCGTGTTTTCAAA
1 AAAAAAAGTTCGTGTTTTCAAA
11330525 AAAAAAAGTT-GTG-TTTCAAA
1 AAAAAAAGTTCGTGTTTTCAAA
11330545 A
1 A
11330546 TTATCGTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 3 0.15
22 9 0.45
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.33
Consensus pattern (22 bp):
AAAAAAAGTTCGTGTTTTCAAA
Found at i:11331210 original size:21 final size:20
Alignment explanation
Indices: 11331181--11331219 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
11331171 AATGATAAAG
* *
11331181 TAAATAAACATAATAAAAGAA
1 TAAAGAAAC-TAAAAAAAGAA
11331202 TAAAGAAACTAAAAAAAG
1 TAAAGAAACTAAAAAAAG
11331220 TTAAAAGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.72, C:0.05, G:0.08, T:0.15
Consensus pattern (20 bp):
TAAAGAAACTAAAAAAAGAA
Found at i:11332285 original size:28 final size:29
Alignment explanation
Indices: 11332240--11332296 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 29
11332230 ACTACTATTA
11332240 CTGTTACCGATTCAGCACTTTGTGTGTCG
1 CTGTTACCGATTCAGCACTTTGTGTGTCG
*
11332269 CTGTTA-CGATTCGGCACTTTGTGTGTCG
1 CTGTTACCGATTCAGCACTTTGTGTGTCG
11332297 AATACTGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 21 0.78
29 6 0.22
ACGTcount: A:0.12, C:0.23, G:0.26, T:0.39
Consensus pattern (29 bp):
CTGTTACCGATTCAGCACTTTGTGTGTCG
Found at i:11332332 original size:45 final size:44
Alignment explanation
Indices: 11332269--11332364 Score: 138
Period size: 45 Copynumber: 2.2 Consensus size: 44
11332259 TTGTGTGTCG
**
11332269 CTGTTACGATTCGGCACTTTGTGTGTCGAATACTGTTACCGTTA
1 CTGTTACGATTCAACACTTTGTGTGTCGAATACTGTTACCGTTA
* *
11332313 CTGTTACAGATTCAACACTTTGTGTGTTGAATACTGTTACTGTTA
1 CTGTTAC-GATTCAACACTTTGTGTGTCGAATACTGTTACCGTTA
*
11332358 TTGTTAC
1 CTGTTAC
11332365 TGCTACCGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 7 0.15
45 39 0.85
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.42
Consensus pattern (44 bp):
CTGTTACGATTCAACACTTTGTGTGTCGAATACTGTTACCGTTA
Done.