Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A04
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: 81554553
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2322942 characters in sequence are not A, C, G, or T
File 2 of 253
Found at i:316020 original size:4 final size:4
Alignment explanation
Indices: 316013--316065 Score: 97
Period size: 4 Copynumber: 13.2 Consensus size: 4
316003 TATCATATAT
*
316013 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAT ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
316061 ATAC A
1 ATAC A
316066 AATATTAAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:317861 original size:16 final size:16
Alignment explanation
Indices: 317836--317866 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
317826 AAAATTTTTT
*
317836 TAACTTGAACTCAAAC
1 TAACTCGAACTCAAAC
317852 TAACTCGAACTCAAA
1 TAACTCGAACTCAAA
317867 ATAATGAAAT
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:0.45, C:0.26, G:0.06, T:0.23
Consensus pattern (16 bp):
TAACTCGAACTCAAAC
Found at i:318200 original size:24 final size:24
Alignment explanation
Indices: 318173--318250 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
318163 TAATATTTTT
*
318173 ATTTCTAACTGTTAATGCTATTAA
1 ATTTCCAACTGTTAATGCTATTAA
* * * ** *
318197 ATTTCCAAATTTTTATTATAGGTTAG
1 ATTTCCAACTGTTAATGCTA--TTAA
318223 A-TTCCAACTGTTAATGCTATTAA
1 ATTTCCAACTGTTAATGCTATTAA
318246 ATTTC
1 ATTTC
318251 TTTTTTTTAA
Statistics
Matches: 38, Mismatches: 13, Indels: 6
0.67 0.23 0.11
Matches are distributed among these distances:
23 4 0.11
24 17 0.45
25 13 0.34
26 4 0.11
ACGTcount: A:0.32, C:0.13, G:0.09, T:0.46
Consensus pattern (24 bp):
ATTTCCAACTGTTAATGCTATTAA
Found at i:320719 original size:16 final size:16
Alignment explanation
Indices: 320698--320728 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
320688 ACTATGAGGG
*
320698 ACTAAATTATAATTTT
1 ACTAAATTAAAATTTT
320714 ACTAAATTAAAATTT
1 ACTAAATTAAAATTT
320729 AGACTCAAGG
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:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (16 bp):
ACTAAATTAAAATTTT
Found at i:320858 original size:20 final size:21
Alignment explanation
Indices: 320824--320877 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
320814 TGATGATATT
*
320824 TTATGATTA-TTTAATTAGATA
1 TTAT-ATTATTTTAATGAGATA
320845 -TATATTATTTTAATGAGATA
1 TTATATTATTTTAATGAGATA
*
320865 TTTTATTATTTTA
1 TTATATTATTTTA
320878 TTATTATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.14
20 14 0.48
21 11 0.38
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (21 bp):
TTATATTATTTTAATGAGATA
Found at i:320883 original size:11 final size:11
Alignment explanation
Indices: 320867--320894 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
320857 ATGAGATATT
320867 TTATTATTTTA
1 TTATTATTTTA
320878 TTATTATTTTA
1 TTATTATTTTA
320889 TTATTA
1 TTATTA
320895 ATTATTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:323085 original size:46 final size:46
Alignment explanation
Indices: 323034--323265 Score: 313
Period size: 46 Copynumber: 5.0 Consensus size: 46
323024 GTGTGCTCTC
* *
323034 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
* * *
323080 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATAGTAACA
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
* *
323126 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
* * *
323172 TGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
* * * * *
323218 TGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCA
1 TGATATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
323264 TG
1 TG
323266 TCAAAGATAA
Statistics
Matches: 168, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
45 1 0.01
46 167 0.99
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (46 bp):
TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
Found at i:326129 original size:45 final size:45
Alignment explanation
Indices: 326065--326155 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
326055 ACAATATTTT
326065 TGCGGTAGTTTGATATCTCGCCTTTTTCTGTCTCAGGCTAACTTA
1 TGCGGTAGTTTGATATCTCGCCTTTTTCTGTCTCAGGCTAACTTA
326110 TGCGGTAGTTTGATATCTCGCCTTTTTCTGTCTCAGGCTAACTTA
1 TGCGGTAGTTTGATATCTCGCCTTTTTCTGTCTCAGGCTAACTTA
326155 T
1 T
326156 AATCTTAAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (45 bp):
TGCGGTAGTTTGATATCTCGCCTTTTTCTGTCTCAGGCTAACTTA
Found at i:326519 original size:9 final size:9
Alignment explanation
Indices: 326482--326511 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
326472 TGTAAGAATG
326482 AGAGAGAAAA
1 AGAG-GAAAA
326492 AGAGGAAAA
1 AGAGGAAAA
326501 AGAGGAAAA
1 AGAGGAAAA
326510 AG
1 AG
326512 GAGAAAAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 16 0.80
10 4 0.20
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (9 bp):
AGAGGAAAA
Found at i:335229 original size:126 final size:126
Alignment explanation
Indices: 335087--335320 Score: 330
Period size: 126 Copynumber: 1.9 Consensus size: 126
335077 TATTTAAAAT
**
335087 TAATAATAACACATATGTAATTTGTATGAAATTAAAATTAA-AAAATAGTTTAAA-TAGTAAGTA
1 TAATAATAACACATATGTAATACGTATGAAATTAAAA-TAATAAAATAGTTTAAATTA-TAAGTA
* *
335150 AAAT-GAATTTTAAATAGGTAAATACATTAAATAAAGAATATTAAACGTAAGGTTTGGAACTAA
64 AAATAGAA-TTTAAATAGGTAAAAACATCAAATAAAGAATATTAAACGTAAGGTTTGGAACTAA
* *
335213 TAATAATAACATATATGTAATACGTATGAAATTAAAATAATAAAATAGTTTAAATTATGAGTAAA
1 TAATAATAACACATATGTAATACGTATGAAATTAAAATAATAAAATAGTTTAAATTATAAGTAAA
* * * *
335278 ATAGAATTTAAATATGTAAAAATATCATATGAAGAATATTAAA
66 ATAGAATTTAAATAGGTAAAAACATCAAATAAAGAATATTAAA
335321 TGCACTTTGA
Statistics
Matches: 95, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
125 3 0.03
126 87 0.92
127 5 0.05
ACGTcount: A:0.53, C:0.03, G:0.11, T:0.33
Consensus pattern (126 bp):
TAATAATAACACATATGTAATACGTATGAAATTAAAATAATAAAATAGTTTAAATTATAAGTAAA
ATAGAATTTAAATAGGTAAAAACATCAAATAAAGAATATTAAACGTAAGGTTTGGAACTAA
Found at i:336521 original size:23 final size:24
Alignment explanation
Indices: 336486--336535 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
336476 TTAAACTATG
336486 TTTTACATAATTTT-ATAAAAATTA
1 TTTTACATAATTTTGA-AAAAATTA
*
336510 TTTT-CATAATTTTGAATAAATTA
1 TTTTACATAATTTTGAAAAAATTA
336533 TTT
1 TTT
336536 GACTAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 19 0.79
24 5 0.21
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (24 bp):
TTTTACATAATTTTGAAAAAATTA
Found at i:340576 original size:2 final size:2
Alignment explanation
Indices: 340569--340596 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
340559 TTGAGAGCAG
340569 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
340597 TATATGTCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:342707 original size:27 final size:28
Alignment explanation
Indices: 342677--342734 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
342667 CCAATCATGG
*
342677 ATAATTATACATTTAATAAA-AA-TAAAA
1 ATAATTACACATTTAA-AAATAATTAAAA
*
342704 ATAATTACATATTTAAAAATAATTAAAA
1 ATAATTACACATTTAAAAATAATTAAAA
342732 ATA
1 ATA
342735 TTAATTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 3 0.11
27 16 0.59
28 8 0.30
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (28 bp):
ATAATTACACATTTAAAAATAATTAAAA
Found at i:342737 original size:27 final size:25
Alignment explanation
Indices: 342687--342751 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 25
342677 ATAATTATAC
342687 ATTTAATAAA-AA-TAAAAATAATTACA
1 ATTTAA-AAATAATTAAAAATAATT--A
342713 TATTTAAAAATAATTAAAAAT-ATTA
1 -ATTTAAAAATAATTAAAAATAATTA
342738 A-TTAAAAATAATTA
1 ATTTAAAAATAATTA
342752 GAATTTAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
23 13 0.36
24 1 0.03
25 1 0.03
26 3 0.08
27 11 0.31
28 7 0.19
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (25 bp):
ATTTAAAAATAATTAAAAATAATTA
Found at i:342741 original size:13 final size:13
Alignment explanation
Indices: 342723--342747 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
342713 TATTTAAAAA
342723 TAATTAAAAATAT
1 TAATTAAAAATAT
342736 TAATTAAAAATA
1 TAATTAAAAATA
342748 ATTAGAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TAATTAAAAATAT
Found at i:347059 original size:13 final size:13
Alignment explanation
Indices: 347039--347079 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
347029 ACTCTTCAAC
347039 AAAAAAAAA-AA-
1 AAAAAAAAACAAG
347050 AAAGAAAAAACAAG
1 AAA-AAAAAACAAG
*
347064 AAAAAAGAACAAG
1 AAAAAAAAACAAG
347077 AAA
1 AAA
347080 GAACAAATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 3 0.12
12 6 0.23
13 14 0.54
14 3 0.12
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAAAAACAAG
Found at i:347082 original size:17 final size:17
Alignment explanation
Indices: 347039--347072 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
347029 ACTCTTCAAC
347039 AAAAAA-AA-AAAAAAG
1 AAAAAACAAGAAAAAAG
347054 AAAAAACAAGAAAAAAG
1 AAAAAACAAGAAAAAAG
347071 AA
1 AA
347073 CAAGAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 2 0.12
17 9 0.53
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (17 bp):
AAAAAACAAGAAAAAAG
Found at i:353071 original size:14 final size:14
Alignment explanation
Indices: 353052--353086 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
353042 TGTTTCATTA
*
353052 AAAATGATTTCTAG
1 AAAATGATTTATAG
*
353066 AAAATGATTTATGG
1 AAAATGATTTATAG
353080 AAAATGA
1 AAAATGA
353087 CTTACTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.49, C:0.03, G:0.17, T:0.31
Consensus pattern (14 bp):
AAAATGATTTATAG
Found at i:353817 original size:3 final size:3
Alignment explanation
Indices: 353809--353833 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
353799 TTTTTATTTA
353809 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
353834 AATTGCTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:356905 original size:13 final size:13
Alignment explanation
Indices: 356887--356911 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
356877 CCACTGTGCG
356887 CGGTGGCCGGCGA
1 CGGTGGCCGGCGA
356900 CGGTGGCCGGCG
1 CGGTGGCCGGCG
356912 GCGACGGACG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.04, C:0.32, G:0.56, T:0.08
Consensus pattern (13 bp):
CGGTGGCCGGCGA
Found at i:357684 original size:24 final size:24
Alignment explanation
Indices: 357628--357684 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
357618 TATTTTCATG
* *
357628 ATTATTATTGTGTTTATTTTTACT
1 ATTATTATTGTATTTATTATTACT
* *
357652 ACTATTATTGTATTTATTATTAGT
1 ATTATTATTGTATTTATTATTACT
*
357676 ATTAGTATT
1 ATTATTATT
357685 ATAATTACTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.61
Consensus pattern (24 bp):
ATTATTATTGTATTTATTATTACT
Found at i:357911 original size:11 final size:11
Alignment explanation
Indices: 357895--357946 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
357885 TTTTTAATAC
357895 TATATTATGTA
1 TATATTATGTA
*
357906 TATATTATATTA
1 TATATTAT-GTA
357918 TATATTTAT-TA
1 TATA-TTATGTA
*
357929 TATTTTTATGTA
1 TA-TATTATGTA
357941 TATATT
1 TATATT
357947 TTTAATATCA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
11 19 0.56
12 11 0.32
13 4 0.12
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (11 bp):
TATATTATGTA
Found at i:357914 original size:16 final size:16
Alignment explanation
Indices: 357895--357946 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
357885 TTTTTAATAC
357895 TATATTATGTATATAT
1 TATATTATGTATATAT
* *
357911 TATATTATATATTTAT
1 TATATTATGTATATAT
357927 TATATTTTTATGTATATAT
1 TATA---TTATGTATATAT
357946 T
1 T
357947 TTTAATATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 18 0.62
19 11 0.38
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (16 bp):
TATATTATGTATATAT
Found at i:357921 original size:23 final size:22
Alignment explanation
Indices: 357853--357946 Score: 61
Period size: 23 Copynumber: 4.2 Consensus size: 22
357843 GTAACATTAT
* *
357853 TATTATTAT-TTCTAATGTGTATG
1 TATTATTATATT-T-ATATGTATA
* *
357876 TATTA-TATATTTTTA-ATACTA
1 TATTATTATATTTATATGTA-TA
357897 TATTATGTATATATTATAT-TATA
1 TATTAT-TATAT-TTATATGTATA
*
357920 TATTTATTATATTTTTATGTATA
1 TA-TTATTATATTTATATGTATA
357943 TATT
1 TATT
357947 TTTAATATCA
Statistics
Matches: 57, Mismatches: 6, Indels: 17
0.71 0.08 0.21
Matches are distributed among these distances:
20 2 0.04
21 7 0.12
22 11 0.19
23 27 0.47
24 10 0.18
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (22 bp):
TATTATTATATTTATATGTATA
Found at i:357938 original size:35 final size:37
Alignment explanation
Indices: 357876--357946 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 37
357866 AATGTGTATG
357876 TATTATATATTTTTAATACTATATTATGTATATATTA
1 TATTATATATTTTTAATACTATATTATGTATATATTA
*
357913 TATTATATATTTATT-ATA-T-TTTTATGTATATATT
1 TATTATATATTT-TTAATACTATATTATGTATATATT
357947 TTTAATATCA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
35 14 0.44
36 1 0.03
37 15 0.47
38 2 0.06
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (37 bp):
TATTATATATTTTTAATACTATATTATGTATATATTA
Found at i:357947 original size:23 final size:23
Alignment explanation
Indices: 357881--357947 Score: 75
Period size: 23 Copynumber: 2.9 Consensus size: 23
357871 GTATGTATTA
*
357881 TATATTTTTAATACTATA-TTATG
1 TATATTTTTATTA-TATATTTATG
*
357904 TATATATTATATTATATATTTAT-
1 TATAT-TTTTATTATATATTTATG
357927 TATATTTTTATGTATATATTT
1 TATATTTTTAT-TATATATTT
357948 TTAATATCAC
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
22 5 0.13
23 23 0.61
24 10 0.26
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.61
Consensus pattern (23 bp):
TATATTTTTATTATATATTTATG
Found at i:358130 original size:3 final size:3
Alignment explanation
Indices: 358122--358192 Score: 63
Period size: 3 Copynumber: 23.0 Consensus size: 3
358112 TTAATTCATA
* * * *
358122 TAT TAT TAT CAT TAT TTT CTACGT TAT -AT TCT TAT TCT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT -TA--T TAT TAT TAT TAT TAT TAT TAT TAT
*
358169 TAT TGT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT
358193 CATTGTCATT
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
2 2 0.04
3 48 0.89
4 1 0.02
5 2 0.04
6 1 0.02
ACGTcount: A:0.27, C:0.07, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:368561 original size:1 final size:1
Alignment explanation
Indices: 368555--368589 Score: 61
Period size: 1 Copynumber: 35.0 Consensus size: 1
368545 ACTCTTCAAC
*
368555 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
368590 GAAAGAACAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:380465 original size:13 final size:13
Alignment explanation
Indices: 380447--380510 Score: 87
Period size: 13 Copynumber: 4.9 Consensus size: 13
380437 TGTTTGGCAA
380447 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
380460 TGCTTTT-AAGAAG
1 TGCTTTTGAA-AAG
380473 TGCTTTTGAGAAA-
1 TGCTTTTGA-AAAG
*
380486 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
380499 TGCTTTTGAAAA
1 TGCTTTTGAAAA
380511 TTTTAGGTGT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
12 4 0.09
13 37 0.82
14 3 0.07
15 1 0.02
ACGTcount: A:0.30, C:0.08, G:0.23, T:0.39
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:380489 original size:26 final size:25
Alignment explanation
Indices: 380447--380511 Score: 103
Period size: 26 Copynumber: 2.5 Consensus size: 25
380437 TGTTTGGCAA
380447 TGCTTTTGAAAAGTGCTTTTAAGAAG
1 TGCTTTTGAAAA-TGCTTTTAAGAAG
*
380473 TGCTTTTGAGAAATGCTTTTGAGAAG
1 TGCTTTTGA-AAATGCTTTTAAGAAG
380499 TGCTTTTGAAAAT
1 TGCTTTTGAAAAT
380512 TTTAGGTGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
25 4 0.11
26 30 0.81
27 3 0.08
ACGTcount: A:0.29, C:0.08, G:0.23, T:0.40
Consensus pattern (25 bp):
TGCTTTTGAAAATGCTTTTAAGAAG
Found at i:381079 original size:19 final size:19
Alignment explanation
Indices: 381055--381102 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
381045 CAGTTCAGGC
**
381055 CCACATGCTTGTGTGGGGA
1 CCACATGCCCGTGTGGGGA
*
381074 CCACATGCCCGTGTGGGGT
1 CCACATGCCCGTGTGGGGA
*
381093 CTACATGCCC
1 CCACATGCCC
381103 TCATGGGATC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.15, C:0.31, G:0.31, T:0.23
Consensus pattern (19 bp):
CCACATGCCCGTGTGGGGA
Found at i:382098 original size:21 final size:21
Alignment explanation
Indices: 382065--382112 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
382055 GAAATTGAAA
* *
382065 TTAATGTGCTTTAGTCTCACT
1 TTAATTTGCTTTAATCTCACT
* *
382086 TTAATTTGTTTTAATTTCACT
1 TTAATTTGCTTTAATCTCACT
382107 TTAATT
1 TTAATT
382113 ACAAAATTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.08, T:0.56
Consensus pattern (21 bp):
TTAATTTGCTTTAATCTCACT
Found at i:382999 original size:13 final size:13
Alignment explanation
Indices: 382966--382999 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
382956 AATATATATA
*
382966 AACCCAAGTACCC
1 AACCCAATTACCC
*
382979 AACCCAATTACTC
1 AACCCAATTACCC
382992 AACCCAAT
1 AACCCAAT
383000 CATAAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.41, C:0.41, G:0.03, T:0.15
Consensus pattern (13 bp):
AACCCAATTACCC
Found at i:383056 original size:20 final size:21
Alignment explanation
Indices: 383027--383076 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
383017 ATTTAATAAA
*
383027 TAAAAATAAAAATCTAAA-AC
1 TAAAAGTAAAAATCTAAACAC
* *
383047 TAAAAGTAAAAGTCTAAACTC
1 TAAAAGTAAAAATCTAAACAC
383068 TAAAAGTAA
1 TAAAAGTAA
383077 CAGACGACAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.62, C:0.10, G:0.06, T:0.22
Consensus pattern (21 bp):
TAAAAGTAAAAATCTAAACAC
Found at i:384042 original size:15 final size:15
Alignment explanation
Indices: 384022--384050 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
384012 TAAATAAAGG
384022 AAAGAAACAGAATGA
1 AAAGAAACAGAATGA
384037 AAAGAAACAGAATG
1 AAAGAAACAGAATG
384051 TGGAAATGAA
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:0.66, C:0.07, G:0.21, T:0.07
Consensus pattern (15 bp):
AAAGAAACAGAATGA
Found at i:384061 original size:18 final size:15
Alignment explanation
Indices: 384020--384065 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
384010 AGTAAATAAA
384020 GGAAAGAAACAGAAT
1 GGAAAGAAACAGAAT
*
384035 GAAAAGAAACAGAATGT
1 GGAAAGAAACAGAA--T
384052 GGAAATGAAACAGA
1 GGAAA-GAAACAGA
384066 GAAGAAACAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 13 0.50
17 5 0.19
18 8 0.31
ACGTcount: A:0.59, C:0.07, G:0.26, T:0.09
Consensus pattern (15 bp):
GGAAAGAAACAGAAT
Found at i:384478 original size:23 final size:21
Alignment explanation
Indices: 384431--384471 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
384421 TTTGGTTAAA
384431 AATTGAATAGAAATGAAGTATG
1 AATTGAATAGAAA-GAAGTATG
384453 AATTGAGATAGAAA-AAGTA
1 AATTGA-ATAGAAAGAAGTA
384472 AGTGAATCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 6 0.33
23 7 0.39
ACGTcount: A:0.54, C:0.00, G:0.22, T:0.24
Consensus pattern (21 bp):
AATTGAATAGAAAGAAGTATG
Found at i:384838 original size:15 final size:15
Alignment explanation
Indices: 384790--384839 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
384780 TTTATCAAAT
384790 TTATATTGATTGAAA
1 TTATATTGATTGAAA
* * *
384805 TCATTTTGATTGAAT
1 TTATATTGATTGAAA
384820 TTATATTGATTGAAA
1 TTATATTGATTGAAA
384835 TTATA
1 TTATA
384840 ATATATATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (15 bp):
TTATATTGATTGAAA
Found at i:385498 original size:18 final size:19
Alignment explanation
Indices: 385477--385517 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
385467 AATGAAATGA
385477 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
385495 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
385514 GAAA
1 GAAA
385518 ATATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:388154 original size:20 final size:20
Alignment explanation
Indices: 388129--388175 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
388119 CGGTTGATTT
388129 GGTTAATGGTATTTCGGGTC
1 GGTTAATGGTATTTCGGGTC
388149 GGTTAATGGTATTTCGGGTC
1 GGTTAATGGTATTTCGGGTC
388169 GGTTAAT
1 GGTTAAT
388176 CGACTGAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.17, C:0.09, G:0.34, T:0.40
Consensus pattern (20 bp):
GGTTAATGGTATTTCGGGTC
Found at i:408702 original size:17 final size:17
Alignment explanation
Indices: 408643--408702 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
408633 TAATAAATTT
408643 AAAATATAATATATAATAA
1 AAAATATAAT-TAT-ATAA
408662 AAAATAT-ATT-TAT-A
1 AAAATATAATTATATAA
*
408676 AGAATAATAATTATATAA
1 AAAAT-ATAATTATATAA
408694 AAAATATAA
1 AAAATATAA
408703 AATATATTGG
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 5 0.14
15 4 0.11
16 4 0.11
17 8 0.23
18 7 0.20
19 7 0.20
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
AAAATATAATTATATAA
Found at i:409216 original size:19 final size:19
Alignment explanation
Indices: 409188--409295 Score: 154
Period size: 17 Copynumber: 5.9 Consensus size: 19
409178 AATCATATCT
*
409188 TCTAAGATTGTATATCATA
1 TCTAAGATTGCATATCATA
*
409207 TCTAATATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
409225 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
409242 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
*
409259 TCTAAGATTGCATATCACA
1 TCTAAGATTGCATATCATA
409278 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
409296 TGAAGATTAT
Statistics
Matches: 81, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
17 33 0.41
18 15 0.19
19 33 0.41
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:426581 original size:23 final size:23
Alignment explanation
Indices: 426537--426581 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
426527 ATGCAGCAAA
* *
426537 AGACCAGCAGCAATTCAGCATGG
1 AGACAAGCAGCAATTCAACATGG
426560 AGACAAGCAGC-ATCTCAACATG
1 AGACAAGCAGCAAT-TCAACATG
426582 AAGATCAGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.38, C:0.27, G:0.22, T:0.13
Consensus pattern (23 bp):
AGACAAGCAGCAATTCAACATGG
Found at i:427491 original size:27 final size:27
Alignment explanation
Indices: 427461--427531 Score: 83
Period size: 27 Copynumber: 2.6 Consensus size: 27
427451 CCAATCATGG
*
427461 ATAATTATACATTTAATAAA-AA-TAAAA
1 ATAATTACA-ATTTAA-AAATAATTAAAA
427488 ATAATTACATATTTAAAAATAATTAAAA
1 ATAATTACA-ATTTAAAAATAATTAAAA
*
427516 ATAATTAGAATTTAAA
1 ATAATTACAATTTAAA
427532 TAGAGCTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
26 3 0.08
27 23 0.59
28 13 0.33
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (27 bp):
ATAATTACAATTTAAAAATAATTAAAA
Found at i:443051 original size:21 final size:21
Alignment explanation
Indices: 443027--443078 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
443017 ATTATTACTA
*
443027 TTTTTATTATCAT-TTTTTATT
1 TTTTTATT-TAATATTTTTATT
443048 TTTTTATTTAATATTTTTATT
1 TTTTTATTTAATATTTTTATT
*
443069 CTTTTATTTA
1 TTTTTATTTA
443079 TTTGCTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 3 0.11
21 25 0.89
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTTTATTTAATATTTTTATT
Found at i:448037 original size:14 final size:15
Alignment explanation
Indices: 448010--448042 Score: 50
Period size: 14 Copynumber: 2.2 Consensus size: 15
448000 TTAGATTTAC
448010 AAATAAAATTTTAAAA
1 AAATAAAA-TTTAAAA
448026 AAATAAAA-TTAAAA
1 AAATAAAATTTAAAA
448040 AAA
1 AAA
448043 AAAGTGTACG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
16 8 0.47
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAATAAAATTTAAAA
Found at i:448041 original size:16 final size:16
Alignment explanation
Indices: 448010--448044 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
448000 TTAGATTTAC
**
448010 AAATAAAATTTTAAAA
1 AAATAAAATTAAAAAA
448026 AAATAAAATTAAAAAA
1 AAATAAAATTAAAAAA
448042 AAA
1 AAA
448045 AGTGTACGGT
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
AAATAAAATTAAAAAA
Found at i:448042 original size:15 final size:16
Alignment explanation
Indices: 448010--448043 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
448000 TTAGATTTAC
*
448010 AAATAAAATTTTAAAA
1 AAATAAAATTTAAAAA
448026 AAATAAAA-TTAAAAA
1 AAATAAAATTTAAAAA
448041 AAA
1 AAA
448044 AAGTGTACGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAATAAAATTTAAAAA
Found at i:451000 original size:14 final size:14
Alignment explanation
Indices: 450981--451011 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
450971 TAATTGATTT
450981 TTTAATTAAATAAA
1 TTTAATTAAATAAA
*
450995 TTTAATTAATTAAA
1 TTTAATTAAATAAA
451009 TTT
1 TTT
451012 TCTAAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTAATTAAATAAA
Found at i:466173 original size:197 final size:197
Alignment explanation
Indices: 465838--466230 Score: 761
Period size: 197 Copynumber: 2.0 Consensus size: 197
465828 TGACTTTTTT
465838 CTTATCACTTGTTGAAAGAACATAAGAAGACTTCATGTAAGCTAGGAACAATAAAGAGAGAGGCA
1 CTTATCACTTGTTGAAAGAACATAAGAAGACTTCATGTAAGCTAGGAACAATAAAGAGAGAGGCA
465903 GATGAACAGTATCAAGCAATCTGCAGATTTCAGGATATCAAGGGAAAGACCAAAAGAAAACAACT
66 GATGAACAGTATCAAGCAATCTGCAGATTTCAGGATATCAAGGGAAAGACCAAAAGAAAACAACT
465968 CACCTCATGGATTATTTGCTTCACCGACTTTTTAAAGGGAACAACTAAATCCACATGTTGTTCTT
131 CACCTCATGGATTATTTGCTTCACCGACTTTTTAAAGGGAACAACTAAATCCACATGTTGTTCTT
466033 TG
196 TG
466035 CTTATCACTTGTTGAAAGAACATAAGAAGACTTCATGTAAGCTAGGAACAATAAAGAGTA-AGGC
1 CTTATCACTTGTTGAAAGAACATAAGAAGACTTCATGTAAGCTAGGAACAATAAAGAG-AGAGGC
*
466099 AGCTGAACAGTATCAAGCAATCTGCAGATTTCAGGATATCAAGGGAAAGACCAAAAGAAAACAAC
65 AGATGAACAGTATCAAGCAATCTGCAGATTTCAGGATATCAAGGGAAAGACCAAAAGAAAACAAC
466164 TCACCTCATGGATTATTTGCTTCACCGACTTTTTAAAGGGAACAACTAAATCCACATGTTGTTCT
130 TCACCTCATGGATTATTTGCTTCACCGACTTTTTAAAGGGAACAACTAAATCCACATGTTGTTCT
466229 TT
195 TT
466231 AGTGTCCTGC
Statistics
Matches: 194, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
197 193 0.99
198 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.25
Consensus pattern (197 bp):
CTTATCACTTGTTGAAAGAACATAAGAAGACTTCATGTAAGCTAGGAACAATAAAGAGAGAGGCA
GATGAACAGTATCAAGCAATCTGCAGATTTCAGGATATCAAGGGAAAGACCAAAAGAAAACAACT
CACCTCATGGATTATTTGCTTCACCGACTTTTTAAAGGGAACAACTAAATCCACATGTTGTTCTT
TG
Found at i:471154 original size:16 final size:16
Alignment explanation
Indices: 471133--471164 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
471123 TTTTTATTTG
471133 AAAATATTGGTCCTTC
1 AAAATATTGGTCCTTC
471149 AAAATATTGGTCCTTC
1 AAAATATTGGTCCTTC
471165 TGTTTTACCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (16 bp):
AAAATATTGGTCCTTC
Found at i:472039 original size:32 final size:31
Alignment explanation
Indices: 472003--472067 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 31
471993 AAAAAGTAAT
*
472003 TTAAAAAATATAAAATATT-TAGAAATTAAAAA
1 TTAAAAAATA-AAAACATTATA-AAATTAAAAA
472035 TTAAAAAATAAAAACATTCATAAAATTAAAAA
1 TTAAAAAATAAAAACATT-ATAAAATTAAAAA
472067 T
1 T
472068 ATATATAGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 7 0.23
32 21 0.70
33 2 0.07
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (31 bp):
TTAAAAAATAAAAACATTATAAAATTAAAAA
Found at i:477428 original size:21 final size:21
Alignment explanation
Indices: 477402--477443 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
477392 TTTTAAATAT
477402 AAAATCAAATCAGATCAAAAC
1 AAAATCAAATCAGATCAAAAC
477423 AAAATCAAATCAGATCAAAAC
1 AAAATCAAATCAGATCAAAAC
477444 GAGACGAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.62, C:0.19, G:0.05, T:0.14
Consensus pattern (21 bp):
AAAATCAAATCAGATCAAAAC
Found at i:478953 original size:82 final size:81
Alignment explanation
Indices: 478852--479014 Score: 281
Period size: 82 Copynumber: 2.0 Consensus size: 81
478842 TTGTGTTAAC
* * *
478852 CCGATGATAAAGAGTGTTCATCGTTTCAAATGATTTAAATTTGAGGTCATGCTATTTATTTTTAT
1 CCGATGATAAAGAGTGTTCATCGTTTCAAATGATTTAAATTTGA-GTCATGATAATTATTCTTAT
478917 AATTCACTAAAAATATT
65 AATTCACTAAAAATATT
*
478934 CCGATGATAAAGGGTGTTCATCGTTTCAAATGATTTAAATTTGAGTCATGATAATTATTCTTATA
1 CCGATGATAAAGAGTGTTCATCGTTTCAAATGATTTAAATTTGAGTCATGATAATTATTCTTATA
478999 ATTCACTAAAAATATT
66 ATTCACTAAAAATATT
479015 ATACATTTTT
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
81 34 0.44
82 43 0.56
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.40
Consensus pattern (81 bp):
CCGATGATAAAGAGTGTTCATCGTTTCAAATGATTTAAATTTGAGTCATGATAATTATTCTTATA
ATTCACTAAAAATATT
Found at i:488026 original size:28 final size:29
Alignment explanation
Indices: 487994--488054 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
487984 ACTTATGCGA
** *
487994 CAAACATATCATAACCCGAA-CAAAAAAT
1 CAAACATAAAATAACCCAAATCAAAAAAT
*
488022 CAAACTTAAAATAACCCAAATTCAAAAAAT
1 CAAACATAAAATAACCCAAA-TCAAAAAAT
488052 CAA
1 CAA
488055 TTTTATAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 16 0.59
30 11 0.41
ACGTcount: A:0.59, C:0.23, G:0.02, T:0.16
Consensus pattern (29 bp):
CAAACATAAAATAACCCAAATCAAAAAAT
Found at i:491252 original size:12 final size:12
Alignment explanation
Indices: 491235--491264 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
491225 TATTGCATTT
491235 ATACATATATAC
1 ATACATATATAC
*
491247 ATACATATATAT
1 ATACATATATAC
491259 ATACAT
1 ATACAT
491265 GAACATGGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (12 bp):
ATACATATATAC
Found at i:493730 original size:23 final size:25
Alignment explanation
Indices: 493700--493750 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
493690 AGCTTGAATC
493700 TTTTTTTTAT-T-TGTATAATACGA
1 TTTTTTTTATATGTGTATAATACGA
493723 TTTTTTTTATATGTGTATAATACGA
1 TTTTTTTTATATGTGTATAATACGA
493748 TTT
1 TTT
493751 ATGTTCGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 10 0.38
24 1 0.04
25 15 0.58
ACGTcount: A:0.25, C:0.04, G:0.10, T:0.61
Consensus pattern (25 bp):
TTTTTTTTATATGTGTATAATACGA
Found at i:493823 original size:15 final size:15
Alignment explanation
Indices: 493803--493833 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
493793 ATAACACAAA
*
493803 TTTTTTTATTTTAAT
1 TTTTTTTAATTTAAT
493818 TTTTTTTAATTTAAT
1 TTTTTTTAATTTAAT
493833 T
1 T
493834 ATAAAGTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTTTAATTTAAT
Found at i:501591 original size:2 final size:2
Alignment explanation
Indices: 501584--501616 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
501574 GGTTTATGCC
*
501584 AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
501617 TAACGAGGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:502257 original size:13 final size:13
Alignment explanation
Indices: 502235--502264 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
502225 CGCCAAATTA
*
502235 AAATTTATATATT
1 AAATTGATATATT
502248 AAATTGATATATT
1 AAATTGATATATT
502261 AAAT
1 AAAT
502265 CAAAGTTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (13 bp):
AAATTGATATATT
Found at i:506583 original size:13 final size:13
Alignment explanation
Indices: 506565--506589 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
506555 AATTTTTAAA
506565 AAAAGAAAAAAAG
1 AAAAGAAAAAAAG
506578 AAAAGAAAAAAA
1 AAAAGAAAAAAA
506590 CCCATGCTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAAAG
Found at i:508748 original size:7 final size:7
Alignment explanation
Indices: 508736--508771 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
508726 CACATACGAT
508736 GTAAGAG
1 GTAAGAG
508743 GTAAGAG
1 GTAAGAG
508750 GTAAGAG
1 GTAAGAG
508757 GTAAGAG
1 GTAAGAG
508764 GTAAGAG
1 GTAAGAG
508771 G
1 G
508772 ATGACTGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.42, C:0.00, G:0.44, T:0.14
Consensus pattern (7 bp):
GTAAGAG
Found at i:509808 original size:40 final size:39
Alignment explanation
Indices: 509753--509833 Score: 153
Period size: 40 Copynumber: 2.1 Consensus size: 39
509743 ACTCAACTTT
509753 AAGCTCGATTAATTCAATAGACAATGACTAAATTAGAAAC
1 AAGCTCGATTAATTCAATAGACAATGACT-AATTAGAAAC
509793 AAGCTCGATTAATTCAATAGACAATGACTAATTAGAAAC
1 AAGCTCGATTAATTCAATAGACAATGACTAATTAGAAAC
509832 AA
1 AA
509834 AAACAAAAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 12 0.29
40 29 0.71
ACGTcount: A:0.48, C:0.15, G:0.12, T:0.25
Consensus pattern (39 bp):
AAGCTCGATTAATTCAATAGACAATGACTAATTAGAAAC
Found at i:509903 original size:17 final size:18
Alignment explanation
Indices: 509881--509917 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
509871 ATGATATTGA
*
509881 ATTTTT-GAATGTTTTTT
1 ATTTTTGGAATATTTTTT
509898 ATTTTTGGAATATTTTTT
1 ATTTTTGGAATATTTTTT
509916 AT
1 AT
509918 CACATTTAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.22, C:0.00, G:0.11, T:0.68
Consensus pattern (18 bp):
ATTTTTGGAATATTTTTT
Found at i:515582 original size:26 final size:26
Alignment explanation
Indices: 515545--515628 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
515535 TGATACAAAT
*
515545 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
515571 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
515597 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
515623 TGATAA
1 TGATAA
515629 GAATTTCATG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:517290 original size:27 final size:26
Alignment explanation
Indices: 517250--517361 Score: 143
Period size: 27 Copynumber: 4.2 Consensus size: 26
517240 AGGAAGCGTC
*
517250 CTGGTGGCTATGCCACGATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
517277 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
517304 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTG-AT
* * *
517332 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGAT
517358 CTGG
1 CTGG
517362 CAGCCATGCT
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
26 7 0.09
27 52 0.68
28 17 0.22
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:517354 original size:54 final size:54
Alignment explanation
Indices: 517250--517361 Score: 181
Period size: 54 Copynumber: 2.1 Consensus size: 54
517240 AGGAAGCGTC
*
517250 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACGATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
* *
517304 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACGATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
517358 CTGG
1 CTGG
517362 CAGCCATGCT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
54 36 0.67
55 18 0.33
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (54 bp):
CTGGTGGCTATGCCACGATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:517447 original size:19 final size:22
Alignment explanation
Indices: 517423--517462 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 22
517413 CTCCCCACAC
517423 GGTGTA-A-GGTTGG-TATGGG
1 GGTGTATACGGTTGGATATGGG
517442 GGTGTATACGGTTGGATATGG
1 GGTGTATACGGTTGGATATGG
517463 TTGGGTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 6 0.33
22 5 0.28
ACGTcount: A:0.17, C:0.03, G:0.47, T:0.33
Consensus pattern (22 bp):
GGTGTATACGGTTGGATATGGG
Found at i:518733 original size:24 final size:24
Alignment explanation
Indices: 518704--518757 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
518694 TAGAAAATGG
518704 TTTAAACTAC-ATGATATATGAA-AA
1 TTTAAACT-CTATGATATAT-AAGAA
*
518728 TTTAAAGTCTATGATATATAAGAA
1 TTTAAACTCTATGATATATAAGAA
518752 TTTAAA
1 TTTAAA
518758 ATAAATAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 3 0.11
24 24 0.89
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.37
Consensus pattern (24 bp):
TTTAAACTCTATGATATATAAGAA
Found at i:521875 original size:93 final size:93
Alignment explanation
Indices: 521768--521938 Score: 263
Period size: 93 Copynumber: 1.8 Consensus size: 93
521758 GCCCCTAATT
* * * *
521768 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGTATCCATAAGTGAACTC-AGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGA-ACTCAACTCA
*
521832 ATGAGTTCGGATGCCTAGTTACGTTTCAC
65 ACGAGTTCGGATGCCTAGTTACGTTTCAC
* *
521861 GAACTCGGACTCAACTCAACGAGTTTGGACATTCGCATCCATAAATGAACTCGAACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGAACTCAACTCAA
521926 CGAGTTCGGATGC
66 CGAGTTCGGATGC
521939 TCAACTATCC
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
93 69 0.99
94 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGAACTCAACTCAA
CGAGTTCGGATGCCTAGTTACGTTTCAC
Found at i:522390 original size:30 final size:30
Alignment explanation
Indices: 522356--522416 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
522346 ATTTAATACG
522356 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
522386 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
522416 A
1 A
522417 TCTCGGGAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.36
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:547483 original size:49 final size:48
Alignment explanation
Indices: 547405--547500 Score: 174
Period size: 49 Copynumber: 2.0 Consensus size: 48
547395 NNNTTTTGAA
*
547405 AACAGAAATTGAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTTG
1 AACAGAAATTGAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTTG
547453 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTT
1 AACAGAAATTGAAA-TACCTCAACGTGTCTTGAGGCTCAACTCATTTT
547501 CGCAATATGA
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 14 0.30
49 32 0.70
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (48 bp):
AACAGAAATTGAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTTG
Found at i:547635 original size:74 final size:73
Alignment explanation
Indices: 547448--547662 Score: 291
Period size: 68 Copynumber: 3.0 Consensus size: 73
547438 GCTCAACTCA
547448 TTTTG-AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT-TCGCAATATGA
1 TTTTGAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGA
*
547511 -TTGA--A
66 GTTGATTT
*
547516 TTTTGAAA-ACAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGA
1 TTTTGAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGA
547580 GTTGATTT
66 GTTGATTT
* * * **
547588 TTTTGAAACAGAAATTGAAAATACCTCAGCATGTGAC-TGAGGCTCAACTCACCTCTCGCAATAT
1 TTTTGAAACAGAAATTGAAATTACCTCA--ACGTGTCTTGAGGCTCAACTCATTTCTCGCAATAT
*
547652 GAGCTGATTT
64 GAGTTGATTT
547662 T
1 T
547663 GAAAAAGTAG
Statistics
Matches: 130, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
68 48 0.37
69 13 0.10
70 4 0.03
72 8 0.06
73 17 0.13
74 35 0.27
75 5 0.04
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (73 bp):
TTTTGAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGA
GTTGATTT
Found at i:547739 original size:13 final size:13
Alignment explanation
Indices: 547712--547745 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
547702 GAGTTGATTC
*
547712 TTGAACAACATAAA
1 TTGAA-AACAGAAA
547726 TTGAAAACAGAAA
1 TTGAAAACAGAAA
547739 TTGAAAA
1 TTGAAAA
547746 TACCTCAGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.59, C:0.09, G:0.12, T:0.21
Consensus pattern (13 bp):
TTGAAAACAGAAA
Found at i:547778 original size:136 final size:137
Alignment explanation
Indices: 547593--548202 Score: 1058
Period size: 136 Copynumber: 4.4 Consensus size: 137
547583 GATTTTTTTG
547593 AAACAGAAATTGAAAATACCTCAGCATGTGA-CTGAGGCTCAACTCACCTCTCGCAATATGAGCT
1 AAACAGAAATTGAAAATACCTCAGC--GTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGCT
547657 GATTTTGAAAAAGTAGAAATTAAAAGGTTCAA-C-CCTCTCGCAAT-TGAGTTGATTCTTGAACA
64 GATTTTG-AAAAGTAGAAATT-AAAGGTTCAACCACCTCTCGCAATATGAGTTGATTCTTGAACA
*
547719 ACATAAATTGA
127 ACGTAAATTGA
547730 AAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGA
1 AAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGA
547795 TTTTGAAAAGTAGAAATTAAAGGTTCAACC-CACTCTCGCAATATGAGTTGATTCTTGAACAACG
66 TTTTGAAAAGTAGAAATTAAAGGTTCAACCAC-CTCTCGCAATATGAGTTGATTCTTGAACAACG
547859 -AAATTGA
130 TAAATTGA
547866 AAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGA
1 AAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGA
547931 TTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGAAACA
66 TTTTG-AAAAGTAGAAATT-AAAGGTTCAA-CCACCTCTCGCAATATGAGTTGATTCTTG-AACA
547996 ACGTAAATTGA
127 ACGTAAATTGA
548007 AAA-AGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGA
1 AAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGA
548071 TTTTTGAAAAGTAGAAATTAAAGGTTCAACCACCTCTCGCAATATGAGTTGATTCTTGAAC-A-G
66 -TTTTGAAAAGTAGAAATTAAAGGTTCAACCACCTCTCGCAATATGAGTTGATTCTTGAACAACG
548134 TAAATTGA
130 TAAATTGA
548142 AAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 AAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
548203 TTGAAATTAA
Statistics
Matches: 460, Mismatches: 1, Indels: 25
0.95 0.00 0.05
Matches are distributed among these distances:
134 10 0.02
135 31 0.07
136 185 0.40
137 61 0.13
138 39 0.08
139 37 0.08
140 82 0.18
141 15 0.03
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.25
Consensus pattern (137 bp):
AAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGA
TTTTGAAAAGTAGAAATTAAAGGTTCAACCACCTCTCGCAATATGAGTTGATTCTTGAACAACGT
AAATTGA
Found at i:548054 original size:276 final size:272
Alignment explanation
Indices: 547593--548202 Score: 1086
Period size: 276 Copynumber: 2.2 Consensus size: 272
547583 GATTTTTTTG
547593 AAACAGAAATTGAAAATACCTCAGCATGTGA-CTGAGGCTCAACTCACCTCTCGCAATATGAGCT
1 AAACAGAAATTGAAAATACCTCAGC--GTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGCT
547657 GATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCTCTCGCAATTGAGTTGATTCTTGAACAACA
64 GATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCTCTCGCAATTGAGTTGATTCTTGAACAACA
547722 TAAATTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATA
129 TAAATTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATA
547787 TGAGCTGA-TTTTGAAAAGTAGAAATTAAAGGTTCAACC-CACTCTCGCAATATGAGTTGATTCT
194 TGAGCTGATTTTTGAAAAGTAGAAATTAAAGGTTCAACCAC-CTCTCGCAATATGAGTTGATTCT
547850 TGAACAACG-AAATTGA
258 TGAAC-A-GTAAATTGA
547866 AAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGA
1 AAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGA
547931 TTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGAAACA
66 TTTTGAAAAAGTAGAAATTAAAAGGTTCAA--C-CCTCTCGCAAT-TGAGTTGATTCTTG-AACA
*
547996 ACGTAAATTGAAAA-AGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCA
126 ACATAAATTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCA
548060 ATATGAGCTGATTTTTGAAAAGTAGAAATTAAAGGTTCAACCACCTCTCGCAATATGAGTTGATT
191 ATATGAGCTGATTTTTGAAAAGTAGAAATTAAAGGTTCAACCACCTCTCGCAATATGAGTTGATT
548125 CTTGAACAGTAAATTGA
256 CTTGAACAGTAAATTGA
548142 AAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 AAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
548203 TTGAAATTAA
Statistics
Matches: 327, Mismatches: 1, Indels: 15
0.95 0.00 0.04
Matches are distributed among these distances:
271 4 0.01
272 65 0.20
273 25 0.08
274 1 0.00
275 12 0.04
276 144 0.44
277 75 0.23
278 1 0.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.25
Consensus pattern (272 bp):
AAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGA
TTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCTCTCGCAATTGAGTTGATTCTTGAACAACATA
AATTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATG
AGCTGATTTTTGAAAAGTAGAAATTAAAGGTTCAACCACCTCTCGCAATATGAGTTGATTCTTGA
ACAGTAAATTGA
Found at i:548153 original size:13 final size:14
Alignment explanation
Indices: 548129--548157 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
548119 TTGATTCTTG
548129 AACAGTAAATTGAA
1 AACAGTAAATTGAA
548143 AACAG-AAATTGAA
1 AACAGTAAATTGAA
548156 AA
1 AA
548158 TACCTCAGCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.62, C:0.07, G:0.14, T:0.17
Consensus pattern (14 bp):
AACAGTAAATTGAA
Found at i:548260 original size:71 final size:71
Alignment explanation
Indices: 548135--548299 Score: 235
Period size: 71 Copynumber: 2.3 Consensus size: 71
548125 CTTGAACAGT
* * * *
548135 AAATTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATAT
1 AAATTAAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATAT
548200 GAGTTG
66 GAGTTG
*
548206 AAATTAAAACACAAAAATTGAAAATACCTCAGCGT-CCCCGAGGCTCAACTCACCTCTAGCAATA
1 AAATTAAAA-ACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATA
548270 TGAGTTG
65 TGAGTTG
**
548277 ATTTTGAAAAACAAAAATT-AAAA
1 AAATT-AAAAACAAAAATTGAAAA
548300 GGCTTAACTC
Statistics
Matches: 85, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
70 4 0.05
71 53 0.62
72 28 0.33
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.22
Consensus pattern (71 bp):
AAATTAAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATAT
GAGTTG
Found at i:548394 original size:122 final size:122
Alignment explanation
Indices: 548175--548419 Score: 379
Period size: 122 Copynumber: 2.0 Consensus size: 122
548165 GCGTGACCTG
* *
548175 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAACTAAAAATACCTCAGCG
548240 TCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
66 TCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGA-TTTG-AAAACAAAAATTAAA
* * * *
548299 AGGCTTAACTCACCTCTCGCAATATGAG-T-CAATTTAAA-ACATAAACTAAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAACTAAAAATACCTCAGCG
*
548361 TGCCCCGAGGCTCAACTCACTTCTAGCAATATGAGTTGATTTGAAAACAAAAATTAAA
66 T-CCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTGAAAACAAAAATTAAA
548419 A
1 A
548420 ATACCTCAAC
Statistics
Matches: 113, Mismatches: 7, Indels: 6
0.90 0.06 0.05
Matches are distributed among these distances:
120 16 0.14
121 26 0.23
122 43 0.38
123 1 0.01
124 27 0.24
ACGTcount: A:0.40, C:0.22, G:0.13, T:0.24
Consensus pattern (122 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAACTAAAAATACCTCAGCG
TCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTGAAAACAAAAATTAAA
Found at i:548441 original size:70 final size:69
Alignment explanation
Indices: 548299--548472 Score: 224
Period size: 70 Copynumber: 2.5 Consensus size: 69
548289 AAAAATTAAA
* * ** * *
548299 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCAGCGTGC
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTAAAACAAAAACTAAAAATACCTCAACGTGC
548364 CCCG
66 CCCG
* *
548368 AGGCTCAACTCACTTCTAGCAATATGAGTTGATTTGAAAACAAAAATTAAAAATACCTCAACGTG
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTT-AAAACAAAAACTAAAAATACCTCAACGTG
* **
548433 TCTTG
65 CCCCG
548438 AGGCTCAACTCA-TCTCTCGCAATATGAGTTGATTT
1 AGGCTCAACTCACT-TCTCGCAATATGAGTTGATTT
548473 CCTTGAAAAG
Statistics
Matches: 91, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
69 31 0.34
70 60 0.66
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (69 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTAAAACAAAAACTAAAAATACCTCAACGTGC
CCCG
Found at i:558871 original size:10 final size:10
Alignment explanation
Indices: 558858--558888 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
558848 CGCCCGTCGT
558858 CGGCCACCGC
1 CGGCCACCGC
558868 CGGCCACCGC
1 CGGCCACCGC
558878 CGGCCACCGC
1 CGGCCACCGC
558888 C
1 C
558889 CACGGTGGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.10, C:0.61, G:0.29, T:0.00
Consensus pattern (10 bp):
CGGCCACCGC
Found at i:559510 original size:12 final size:12
Alignment explanation
Indices: 559485--559533 Score: 55
Period size: 12 Copynumber: 4.0 Consensus size: 12
559475 CTACAGTATA
*
559485 TTTTTCATCATCT
1 TTTTTC-TCTTCT
559498 TTTTTCTCTTCT
1 TTTTTCTCTTCT
*
559510 TTCTTCTCTTCT
1 TTTTTCTCTTCT
559522 TTTATT-TCTTCT
1 TTT-TTCTCTTCT
559534 ATGGTCAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
12 24 0.75
13 8 0.25
ACGTcount: A:0.06, C:0.24, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTTCTCTTCT
Found at i:561435 original size:23 final size:23
Alignment explanation
Indices: 561405--561452 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
561395 GATTTCATAC
561405 TTAAGCTTTATTCACCAAAGTAT
1 TTAAGCTTTATTCACCAAAGTAT
561428 TTAAGCTTTATTCACCAAAGTAT
1 TTAAGCTTTATTCACCAAAGTAT
561451 TT
1 TT
561453 GAAATATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (23 bp):
TTAAGCTTTATTCACCAAAGTAT
Found at i:562144 original size:42 final size:42
Alignment explanation
Indices: 562096--562205 Score: 150
Period size: 42 Copynumber: 2.6 Consensus size: 42
562086 TCATTTTCTC
** *
562096 GATGCCATAGTTCAACTATGGTCTTACACATCTTCAGATAAT
1 GATGCCATAGCCCAACTATGGTCTTACACATATTCAGATAAT
* * *
562138 GATGCCATAGCCCAGCTATGGTCTTACACATATTCATATATT
1 GATGCCATAGCCCAACTATGGTCTTACACATATTCAGATAAT
562180 GATGCCATAGCCCAGA-TATGGTCTTA
1 GATGCCATAGCCCA-ACTATGGTCTTA
562206 TACGGAAATC
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
42 60 1.00
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (42 bp):
GATGCCATAGCCCAACTATGGTCTTACACATATTCAGATAAT
Found at i:562262 original size:31 final size:31
Alignment explanation
Indices: 562227--562375 Score: 255
Period size: 31 Copynumber: 4.8 Consensus size: 31
562217 CTTGTCACTT
*
562227 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
562258 GTAGCC-AGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGA-AGCTACCACTTTTCACTGATCAG
*
562289 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
562320 GTAGCAGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
562351 GTAGCCGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
562376 TGTTATTTGT
Statistics
Matches: 111, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
30 1 0.01
31 110 0.99
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:562457 original size:50 final size:50
Alignment explanation
Indices: 562351--562527 Score: 282
Period size: 50 Copynumber: 3.5 Consensus size: 50
562341 CACTGATCAG
* * * *
562351 GTAGCCGAAGCTACCACTTTTCACTTGTTATTTGTCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTT-TCATTTGTCCTTGATCAGATAAGT
* *
562402 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGGTAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
*
562452 GTAGCCGAAGCTATTACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
562502 GTAGCCGAAGCTATCACTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
562528 GTTGCCATGG
Statistics
Matches: 116, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 92 0.79
51 24 0.21
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
Found at i:566801 original size:19 final size:18
Alignment explanation
Indices: 566777--566875 Score: 65
Period size: 19 Copynumber: 5.3 Consensus size: 18
566767 TTTTAGATTT
566777 TTTTTTGAAATTTTTATAA
1 TTTTTT-AAATTTTTATAA
***
566796 TTTTTTAAA-AAATATAA
1 TTTTTTAAATTTTTATAA
**
566813 AATTTTAAATTTTTATAAA
1 TTTTTTAAATTTTTAT-AA
* * *
566832 TATTTTAAATTTTAAAAA
1 TTTTTTAAATTTTTATAA
*
566850 TTATTTTGAATTATTTTATAA
1 TT-TTTT-AAAT-TTTTATAA
566871 TTTTT
1 TTTTT
566876 ATTGAGAGAG
Statistics
Matches: 60, Mismatches: 15, Indels: 9
0.71 0.18 0.11
Matches are distributed among these distances:
17 12 0.20
18 9 0.15
19 25 0.42
20 6 0.10
21 8 0.13
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (18 bp):
TTTTTTAAATTTTTATAA
Found at i:566829 original size:18 final size:19
Alignment explanation
Indices: 566808--566844 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
566798 TTTTAAAAAA
566808 TATAAA-ATTTTAAATTTT
1 TATAAATATTTTAAATTTT
566826 TATAAATATTTTAAATTTT
1 TATAAATATTTTAAATTTT
566845 AAAAATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATAAATATTTTAAATTTT
Found at i:567489 original size:27 final size:29
Alignment explanation
Indices: 567454--567508 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
567444 AAATATAATA
**
567454 TTATATAA-T-AAATATATTTATAAAAAT
1 TTATATAATTAAAATATAAATATAAAAAT
567481 TTATATAATTAAAATATAAATATAAAAA
1 TTATATAATTAAAATATAAATATAAAAA
567509 AATTAGAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 8 0.33
28 1 0.04
29 15 0.62
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (29 bp):
TTATATAATTAAAATATAAATATAAAAAT
Found at i:569175 original size:16 final size:18
Alignment explanation
Indices: 569120--569175 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 18
569110 GAGACAAAAT
*
569120 TTATATCTCGTATTTTAAA
1 TTATAT-TCATATTTTAAA
569139 TTATATTCATAATATTATAAA
1 TTATATTCAT-AT-TT-TAAA
569160 -TATATT-ATATTTTAAA
1 TTATATTCATATTTTAAA
569176 AGATTCCTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
16 4 0.12
17 2 0.06
18 5 0.15
19 10 0.30
20 8 0.24
21 4 0.12
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (18 bp):
TTATATTCATATTTTAAA
Found at i:570820 original size:33 final size:33
Alignment explanation
Indices: 570781--570861 Score: 139
Period size: 33 Copynumber: 2.5 Consensus size: 33
570771 AAACATATTT
570781 TTATTATTGTATTATTATTAAATATTATAAGTA
1 TTATTATTGTATTATTATTAAATATTATAAGTA
*
570814 TTATTATTGTATGATTATTAAATATTATAAGTA
1 TTATTATTGTATTATTATTAAATATTATAAGTA
570847 TTATTA-T-TATTATTA
1 TTATTATTGTATTATTA
570862 AAGATAAAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
31 7 0.15
32 1 0.02
33 38 0.83
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (33 bp):
TTATTATTGTATTATTATTAAATATTATAAGTA
Found at i:570881 original size:3 final size:3
Alignment explanation
Indices: 570776--570861 Score: 50
Period size: 3 Copynumber: 28.7 Consensus size: 3
570766 TTGTTAAACA
* * * * *
570776 TAT TTT TAT TAT T-G TAT TAT TAT TAAA TAT TAT AAG TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT
* * * * *
570821 T-G TAT GAT TAT TAAA TAT TAT AAG TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TA
570862 AAGATAAAAG
Statistics
Matches: 59, Mismatches: 20, Indels: 8
0.68 0.23 0.09
Matches are distributed among these distances:
2 2 0.03
3 53 0.90
4 4 0.07
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:585471 original size:3 final size:3
Alignment explanation
Indices: 585465--585494 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
585455 TTCCACTCAA
585465 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
585495 CAATTTACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:589460 original size:21 final size:22
Alignment explanation
Indices: 589431--589476 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
589421 ATATTTTTAA
589431 TTTTAAAAATTATTTTA-AATT
1 TTTTAAAAATTATTTTATAATT
*
589452 TTTTGAAAATTATTTTATAATT
1 TTTTAAAAATTATTTTATAATT
589474 TTT
1 TTT
589477 GTTGAGAGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTTAAAAATTATTTTATAATT
Found at i:589477 original size:21 final size:21
Alignment explanation
Indices: 589422--589477 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
589412 TTTGTATAAA
*
589422 TATTTT-TAA-TTTTAAAAAT
1 TATTTTATAATTTTTGAAAAT
589441 TATTTTA-AATTTTTTGAAAAT
1 TATTTTATAA-TTTTTGAAAAT
589462 TATTTTATAATTTTTG
1 TATTTTATAATTTTTG
589478 TTGAGAGAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 8 0.25
21 22 0.69
22 2 0.06
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.61
Consensus pattern (21 bp):
TATTTTATAATTTTTGAAAAT
Found at i:591918 original size:3 final size:3
Alignment explanation
Indices: 591910--591951 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
591900 TAACAATGAT
* * *
591910 ATA ATA ATA ATA ATA ATA ATG ATA ATA GTA ACA ATA A-A ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
591952 AATTGCTAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:604946 original size:34 final size:34
Alignment explanation
Indices: 604905--604973 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
604895 GTACTAATGG
604905 AAAAAAGTTGTGATTCAAGTAGCAACTTTGTCAA
1 AAAAAAGTTGTGATTCAAGTAGCAACTTTGTCAA
604939 AAAAAAGTTGTGATTCAAGTAGCAACTTTGTCAA
1 AAAAAAGTTGTGATTCAAGTAGCAACTTTGTCAA
604973 A
1 A
604974 CTTCAATTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (34 bp):
AAAAAAGTTGTGATTCAAGTAGCAACTTTGTCAA
Found at i:607193 original size:37 final size:36
Alignment explanation
Indices: 607152--607341 Score: 105
Period size: 37 Copynumber: 5.0 Consensus size: 36
607142 ATTTCCTGTT
*
607152 GCGATTGTCATTTTTACGGTTTGCTCGATTTAAGATA
1 GCGATT-TCATTTTTACGGTTCGCTCGATTTAAGATA
* ** * * * *
607189 GCGATCTTCGATATTCTAACAATTCACTTGATTTAATATC
1 GCGAT-TTC-AT-TT-TTACGGTTCGCTCGATTTAAGATA
607229 GCGACTTTCATTTTTACGGTTCGCTCGATTTAAGATA
1 GCGA-TTTCATTTTTACGGTTCGCTCGATTTAAGATA
* * * * * *
607266 ACAATCTTCAATATTCTAACAGTTC-CTTCGATTTAAAACCA
1 GCGAT-TTC-AT-TT-TTACGGTTCGC-TCGATTTAAGA-TA
* *
607307 -CGGTTGTCATTTTTACTGTTCGCTCGATTTAAGAT
1 GCGATT-TCATTTTTACGGTTCGCTCGATTTAAGAT
607342 CACGACCTTC
Statistics
Matches: 113, Mismatches: 27, Indels: 27
0.68 0.16 0.16
Matches are distributed among these distances:
36 1 0.01
37 46 0.41
38 10 0.09
39 10 0.09
40 44 0.39
41 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.41
Consensus pattern (36 bp):
GCGATTTCATTTTTACGGTTCGCTCGATTTAAGATA
Found at i:607222 original size:40 final size:38
Alignment explanation
Indices: 607178--607301 Score: 101
Period size: 40 Copynumber: 3.2 Consensus size: 38
607168 CGGTTTGCTC
*
607178 GATTTAAGATAGCGATCTTCGATATTCTAACAATTCACTT
1 GATTTAAGATAGCGATCTTC-ATATTCTAACAGTTC-CTT
* * * * *
607218 GATTTAATATCGCGA-CTTTCAT-TT-TTACGGTTCGCTC
1 GATTTAAGATAGCGATC-TTCATATTCTAACAGTTC-CTT
* *
607255 GATTTAAGATAACAATCTTCAATATTCTAACAGTTCCTT
1 GATTTAAGATAGCGATCTTC-ATATTCTAACAGTTCCTT
607294 CGATTTAA
1 -GATTTAA
607302 AACCACGGTT
Statistics
Matches: 64, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
37 22 0.34
38 5 0.08
39 7 0.11
40 30 0.47
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.40
Consensus pattern (38 bp):
GATTTAAGATAGCGATCTTCATATTCTAACAGTTCCTT
Found at i:607397 original size:77 final size:76
Alignment explanation
Indices: 607157--607398 Score: 268
Period size: 77 Copynumber: 3.1 Consensus size: 76
607147 CTGTTGCGAT
* * *
607157 TGTCATTTTTACGGTTTGCTCGATTTAAGATAGCGATCTTCGATATTCTAACAATTCACTTGATT
1 TGTCATTTTTACGGTTCGCTCGATTTAAGATA-CGATCTTCGATATTCTAACAGTTCATTTGATT
*
607222 TAATATCGCGAC
65 TAATATCGCGGC
* * * * *
607234 TTTCATTTTTACGGTTCGCTCGATTTAAGATAACAATCTTCAATATTCTAACAGTTCCTTCGATT
1 TGTCATTTTTACGGTTCGCTCGATTTAAGAT-ACGATCTTCGATATTCTAACAGTTCATTTGATT
* * * *
607299 TAAAACCACGGT
65 TAATATCGCGGC
* * * * *
607311 TGTCATTTTTACTGTTCGCTCGATTTAAGATCACGACCTTCGATATTCTAGCAGTTCGTTTAATT
1 TGTCATTTTTACGGTTCGCTCGATTTAAGAT-ACGATCTTCGATATTCTAACAGTTCATTTGATT
* *
607376 TAATATTGTGGC
65 TAATATCGCGGC
*
607388 TGTCTTTTTTA
1 TGTCATTTTTA
607399 TGGTCCATTT
Statistics
Matches: 134, Mismatches: 30, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
77 133 0.99
78 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (76 bp):
TGTCATTTTTACGGTTCGCTCGATTTAAGATACGATCTTCGATATTCTAACAGTTCATTTGATTT
AATATCGCGGC
Found at i:612318 original size:13 final size:13
Alignment explanation
Indices: 612273--612319 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
612263 TCCAATCTCA
*
612273 TTGAACCCCGAAC
1 TTGAACCCTGAAC
*
612286 TTGAAACCTGAACC
1 TTGAACCCTGAA-C
612300 TTGAACCCTGAAC
1 TTGAACCCTGAAC
*
612313 TCGAACC
1 TTGAACC
612320 TTTTTTATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
13 17 0.59
14 12 0.41
ACGTcount: A:0.32, C:0.34, G:0.15, T:0.19
Consensus pattern (13 bp):
TTGAACCCTGAAC
Found at i:612418 original size:27 final size:27
Alignment explanation
Indices: 612362--612423 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
612352 ATTTTTTTAA
*
612362 CTTGAACCCTGAACCTAGAACCTCAGC
1 CTTGAACCCTGAACCTAGAACCTCAAC
* *
612389 CTTGAACCTTGAACCTTGAACC-CAAAC
1 CTTGAACCCTGAACCTAGAACCTC-AAC
*
612416 CTTAAACC
1 CTTGAACC
612424 AAAAGGCCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 1 0.03
27 29 0.97
ACGTcount: A:0.32, C:0.35, G:0.11, T:0.21
Consensus pattern (27 bp):
CTTGAACCCTGAACCTAGAACCTCAAC
Found at i:612423 original size:7 final size:7
Alignment explanation
Indices: 612362--612410 Score: 55
Period size: 7 Copynumber: 7.1 Consensus size: 7
612352 ATTTTTTTAA
612362 CTTGAAC
1 CTTGAAC
*
612369 CCTGAAC
1 CTTGAAC
*
612376 CTAGAAC
1 CTTGAAC
* *
612383 C-TCAGC
1 CTTGAAC
612389 CTTGAAC
1 CTTGAAC
612396 CTTGAAC
1 CTTGAAC
612403 CTTGAAC
1 CTTGAAC
612410 C
1 C
612411 CAAACCTTAA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
6 3 0.09
7 30 0.91
ACGTcount: A:0.29, C:0.35, G:0.14, T:0.22
Consensus pattern (7 bp):
CTTGAAC
Found at i:612457 original size:21 final size:19
Alignment explanation
Indices: 612433--612483 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
612423 CAAAAGGCCA
612433 AGTTTATGGTTCAAGGTTTAG
1 AGTTTA-GGTTCAAGG-TTAG
* *
612454 AGTTTAGGATTTAAGGTTCG
1 AGTTTAGG-TTCAAGGTTAG
612474 AGTTTAGGTT
1 AGTTTAGGTT
612484 TAGGTTCAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 2 0.07
20 13 0.48
21 12 0.44
ACGTcount: A:0.24, C:0.04, G:0.29, T:0.43
Consensus pattern (19 bp):
AGTTTAGGTTCAAGGTTAG
Found at i:612478 original size:20 final size:18
Alignment explanation
Indices: 612453--612490 Score: 58
Period size: 20 Copynumber: 2.0 Consensus size: 18
612443 TCAAGGTTTA
612453 GAGTTTAGGATTTAAGGTTC
1 GAGTTTAGG-TTT-AGGTTC
612473 GAGTTTAGGTTTAGGTTC
1 GAGTTTAGGTTTAGGTTC
612491 AAGGTTCGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 3 0.17
20 9 0.50
ACGTcount: A:0.21, C:0.05, G:0.32, T:0.42
Consensus pattern (18 bp):
GAGTTTAGGTTTAGGTTC
Found at i:612497 original size:25 final size:27
Alignment explanation
Indices: 612448--612499 Score: 81
Period size: 25 Copynumber: 2.0 Consensus size: 27
612438 ATGGTTCAAG
*
612448 GTTTAGAGTTTAGGATTTAAGGTTCGA
1 GTTTAGAGTTTAGGATTCAAGGTTCGA
612475 GTTTAG-GTTTAGG-TTCAAGGTTCGA
1 GTTTAGAGTTTAGGATTCAAGGTTCGA
612500 ATTCTGGGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 11 0.46
26 7 0.29
27 6 0.25
ACGTcount: A:0.23, C:0.06, G:0.31, T:0.40
Consensus pattern (27 bp):
GTTTAGAGTTTAGGATTCAAGGTTCGA
Found at i:614853 original size:23 final size:23
Alignment explanation
Indices: 614825--614911 Score: 97
Period size: 23 Copynumber: 3.9 Consensus size: 23
614815 TTTATCGATT
* * *
614825 AGGCACTTTATGTGTCGTATTTT
1 AGGCACCTCATGTGTCGTATTTC
*
614848 AGGCACCTCGTGTGTCGTATTTC
1 AGGCACCTCATGTGTCGTATTTC
*
614871 AGGCACCTCGTGTGTCGTA--TC
1 AGGCACCTCATGTGTCGTATTTC
* *
614892 AGGCACTTTATGTGTCGTAT
1 AGGCACCTCATGTGTCGTAT
614912 ACTGATCAGG
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
21 18 0.32
23 38 0.68
ACGTcount: A:0.16, C:0.21, G:0.25, T:0.38
Consensus pattern (23 bp):
AGGCACCTCATGTGTCGTATTTC
Found at i:614893 original size:21 final size:21
Alignment explanation
Indices: 614848--614911 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
614838 GTCGTATTTT
614848 AGGCACCTCGTGTGTCGTATTTC
1 AGGCACCTCGTGTGTCGTA--TC
614871 AGGCACCTCGTGTGTCGTATC
1 AGGCACCTCGTGTGTCGTATC
* **
614892 AGGCACTTTATGTGTCGTAT
1 AGGCACCTCGTGTGTCGTAT
614912 ACTGATCAGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 19 0.50
23 19 0.50
ACGTcount: A:0.16, C:0.23, G:0.27, T:0.34
Consensus pattern (21 bp):
AGGCACCTCGTGTGTCGTATC
Found at i:616842 original size:18 final size:18
Alignment explanation
Indices: 616809--616902 Score: 122
Period size: 18 Copynumber: 5.4 Consensus size: 18
616799 AAGGTTTTCT
616809 TATTGATGATA-T--CGA
1 TATTGATGATAGTGACGA
616824 TATTGATGATAGTGACGA
1 TATTGATGATAGTGACGA
*
616842 TATTGATGCTAGTGACGA
1 TATTGATGATAGTGACGA
* *
616860 TATTGATGCTAGTGACGC
1 TATTGATGATAGTGACGA
* *
616878 TATTGATGATAGTGGCGC
1 TATTGATGATAGTGACGA
616896 TATTGAT
1 TATTGAT
616903 CGTGACCTTG
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
15 11 0.15
16 1 0.01
18 60 0.83
ACGTcount: A:0.28, C:0.10, G:0.27, T:0.36
Consensus pattern (18 bp):
TATTGATGATAGTGACGA
Found at i:617895 original size:42 final size:42
Alignment explanation
Indices: 617836--617919 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
617826 ATCCCACAAC
617836 AAGAAAATTCCCACTAGAAATTTCTTACTTTCTTTTAATAAT
1 AAGAAAATTCCCACTAGAAATTTCTTACTTTCTTTTAATAAT
*
617878 AAGAAAATTTCCACTAGAAATTTCTTACTTTCTTTTAATAAT
1 AAGAAAATTCCCACTAGAAATTTCTTACTTTCTTTTAATAAT
617920 TTTATTAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (42 bp):
AAGAAAATTCCCACTAGAAATTTCTTACTTTCTTTTAATAAT
Found at i:619937 original size:3 final size:3
Alignment explanation
Indices: 619929--619958 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
619919 AGATGAAATC
619929 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
619959 CATTTCCTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:620665 original size:71 final size:71
Alignment explanation
Indices: 620555--620695 Score: 264
Period size: 71 Copynumber: 2.0 Consensus size: 71
620545 AGTCACCCAG
620555 TTATTAGCGTGTTTCTGTTTTGGTCACCCTGATTTAAAAAAATTTATTTTAATCATTAACGTTAT
1 TTATTAGCGTGTTTCTGTTTTGGTCACCCTGATTTAAAAAAATTTATTTTAATCATTAACGTTAT
620620 TGACAA
66 TGACAA
* *
620626 TTATTAGCGTGTTTTTGTTTTGGTCACCCTGATTTAAAAAATTTTATTTTAATCATTAACGTTAT
1 TTATTAGCGTGTTTCTGTTTTGGTCACCCTGATTTAAAAAAATTTATTTTAATCATTAACGTTAT
620691 TGACA
66 TGACA
620696 TTTGATATTT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.47
Consensus pattern (71 bp):
TTATTAGCGTGTTTCTGTTTTGGTCACCCTGATTTAAAAAAATTTATTTTAATCATTAACGTTAT
TGACAA
Found at i:622055 original size:32 final size:32
Alignment explanation
Indices: 622019--622079 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
622009 AAAAATATAC
622019 ATTAAATGTTGAGCTTGTTAGAAATTTTCAAT
1 ATTAAATGTTGAGCTTGTTAGAAATTTTCAAT
*
622051 ATTAAATGTTGAGCTTGTTAGAATTTTTC
1 ATTAAATGTTGAGCTTGTTAGAAATTTTC
622080 TAACATTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.31, C:0.07, G:0.16, T:0.46
Consensus pattern (32 bp):
ATTAAATGTTGAGCTTGTTAGAAATTTTCAAT
Found at i:627698 original size:18 final size:18
Alignment explanation
Indices: 627675--627717 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
627665 GAATAGGTTT
627675 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
627693 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
627711 TTAATTA
1 TTAATTA
627718 CACCTTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:636797 original size:22 final size:22
Alignment explanation
Indices: 636772--636816 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
636762 AACGATCAAT
636772 CTTACACTGAAACAACACCTAG
1 CTTACACTGAAACAACACCTAG
636794 CTTACACTGAAACAACACCTAG
1 CTTACACTGAAACAACACCTAG
636816 C
1 C
636817 GAGAGTGCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.33, G:0.09, T:0.18
Consensus pattern (22 bp):
CTTACACTGAAACAACACCTAG
Found at i:638796 original size:34 final size:35
Alignment explanation
Indices: 638752--638818 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
638742 CAGTAAAATA
*
638752 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* * *
638786 TTTTCTGTAAAATTATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
638819 CTGGTGTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:639394 original size:18 final size:18
Alignment explanation
Indices: 639371--639406 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
639361 AAGCTGCTTG
639371 AGCTATTAAGCAAGTCGA
1 AGCTATTAAGCAAGTCGA
639389 AGCTATTAAGCAAGTCGA
1 AGCTATTAAGCAAGTCGA
639407 CTTTTAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (18 bp):
AGCTATTAAGCAAGTCGA
Found at i:639769 original size:143 final size:143
Alignment explanation
Indices: 639510--639769 Score: 301
Period size: 143 Copynumber: 1.8 Consensus size: 143
639500 TGAAATTTCG
* *
639510 GGTTAAATTTTGCTATTAGTCTTTACACTTTACATAAATTATAGATTTAGTCCATATACTTTAAT
1 GGTTAAATTTTGCTATTAGTCTTTACACTATACATAAATTATAGATTTAGTCCATACACTTTAAT
* * * * * * * *
639575 TTGGTCAATTTTAGACTCTATATTTTTTAAATTTTGTAATTTCAGTCTTGACCCGAATGGTAGTA
66 TAGATCAATTTTAGACCCTATACTTCTCAAATTTTGAAATTTCAATCTTGACCCGAATGGTAGTA
639640 GTTAAATATGCTT
131 GTTAAATATGCTT
* ** * * *
639653 GGTTAAATTTTGCTATTAGTC-TTATACTATGTATAAAGTTTTAGATTTAGTTCATACATTTTAA
1 GGTTAAATTTTGCTATTAGTCTTTACACTATACATAAA-TTATAGATTTAGTCCATACACTTTAA
* * *
639717 TTAGATC-ATTCTTAGCCCCTGTACTTCTCAAA-TTTGAAAATTTCAATTTTGAC
65 TTAGATCAATT-TTAGACCCTATACTTCTCAAATTTTG-AAATTTCAATCTTGAC
639770 ATAAATGATA
Statistics
Matches: 95, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
142 19 0.20
143 76 0.80
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.46
Consensus pattern (143 bp):
GGTTAAATTTTGCTATTAGTCTTTACACTATACATAAATTATAGATTTAGTCCATACACTTTAAT
TAGATCAATTTTAGACCCTATACTTCTCAAATTTTGAAATTTCAATCTTGACCCGAATGGTAGTA
GTTAAATATGCTT
Found at i:640874 original size:2 final size:2
Alignment explanation
Indices: 640867--640895 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
640857 AGCTAAAAGA
640867 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 A
640896 GTGTTTGATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:642963 original size:6 final size:6
Alignment explanation
Indices: 642917--642950 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
642907 CAGTTGTCAG
*
642917 ATATCT ATATCT ATATCT ATTTCT ATATCT ATAT
1 ATATCT ATATCT ATATCT ATATCT ATATCT ATAT
642951 ATAATATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.32, C:0.15, G:0.00, T:0.53
Consensus pattern (6 bp):
ATATCT
Done.