Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009072.1 Hibiscus syriacus cultivar Beakdansim tig00112503_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2600608
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 13
Found at i:11719 original size:2 final size:2
Alignment explanation
Indices: 11712--11747 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
11702 TGTATTTGGC
11712 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11748 CAGCGGCACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16320 original size:13 final size:13
Alignment explanation
Indices: 16298--16331 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
16288 CTATTTTGAA
16298 TTTTAAATTTAAT
1 TTTTAAATTTAAT
*
16311 TTTTATATTTAAT
1 TTTTAAATTTAAT
16324 TTTTAAAT
1 TTTTAAAT
16332 CAAGTTTTTA
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TTTTAAATTTAAT
Found at i:17516 original size:7 final size:7
Alignment explanation
Indices: 17504--17533 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
17494 ATTTATTTAT
17504 TTTAAAA
1 TTTAAAA
17511 TTTAAAA
1 TTTAAAA
17518 TTTAAAA
1 TTTAAAA
17525 TTTAAAA
1 TTTAAAA
17532 TT
1 TT
17534 ATCTCATTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
TTTAAAA
Found at i:19347 original size:31 final size:29
Alignment explanation
Indices: 19312--19414 Score: 77
Period size: 32 Copynumber: 3.4 Consensus size: 29
19302 CTCATCATAT
19312 TTTTAGATATTTTTATAATTTTTAACAATA
1 TTTTAGATATTTTTATAATTTTTAA-AATA
* * *
19342 GTTTTAAAATATTATAATAATTCTTT-AAATA
1 -TTTT-AGATATTTTTATAATT-TTTAAAATA
* * *
19373 TTTTA-ATAATTCTATAATATTTAAAATAA
1 TTTTAGATATTTTTATAATTTTTAAAAT-A
19402 TTTT-GAATATTTT
1 TTTTAG-ATATTTT
19415 AGGATTTTTT
Statistics
Matches: 56, Mismatches: 10, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
27 3 0.05
28 13 0.23
29 6 0.11
30 9 0.16
31 8 0.14
32 14 0.25
33 3 0.05
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (29 bp):
TTTTAGATATTTTTATAATTTTTAAAATA
Found at i:19437 original size:10 final size:10
Alignment explanation
Indices: 19310--19452 Score: 65
Period size: 10 Copynumber: 14.6 Consensus size: 10
19300 GTCTCATCAT
19310 ATTTTTAGAT-
1 ATTTTTA-ATA
19320 ATTTTT-ATA
1 ATTTTTAATA
*
19329 ATTTTTAACA
1 ATTTTTAATA
19339 ATAGTTTTAA-A
1 AT--TTTTAATA
*
19350 ATATTATAATA
1 AT-TTTTAATA
19361 ATTCTTT-A-A
1 ATT-TTTAATA
19370 ATATTTTAATA
1 AT-TTTTAATA
*
19381 ATTCTATAAT-
1 ATT-TTTAATA
**
19391 ATTTAAAATA
1 ATTTTTAATA
*
19401 ATTTTGAAT-
1 ATTTTTAATA
**
19410 A-TTTT-AGG
1 ATTTTTAATA
19418 ATTTTT--TA
1 ATTTTTAATA
19426 ATTTTTAATA
1 ATTTTTAATA
19436 ATTTTTTAATA
1 A-TTTTTAATA
19447 ATTTTT
1 ATTTTT
19453 TTAGCAAATG
Statistics
Matches: 105, Mismatches: 12, Indels: 32
0.70 0.08 0.21
Matches are distributed among these distances:
7 1 0.01
8 12 0.11
9 22 0.21
10 38 0.36
11 26 0.25
12 6 0.06
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.56
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:19443 original size:11 final size:11
Alignment explanation
Indices: 19427--19453 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
19417 GATTTTTTAA
19427 TTTTTAATAAT
1 TTTTTAATAAT
19438 TTTTTAATAAT
1 TTTTTAATAAT
19449 TTTTT
1 TTTTT
19454 TAGCAAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTTTAATAAT
Found at i:22874 original size:6 final size:6
Alignment explanation
Indices: 22863--22887 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
22853 TATTTCCTGC
22863 AAAGAA AAAGAA AAAGAA AAAGAA A
1 AAAGAA AAAGAA AAAGAA AAAGAA A
22888 GAATGGATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:23773 original size:18 final size:19
Alignment explanation
Indices: 23737--23775 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
23727 CAGTTTGGAG
*
23737 GAAAGACAGAGAGCTGAAAA
1 GAAAAACAGAGAGC-GAAAA
23757 GAAAAACAGAGAG-GAAAA
1 GAAAAACAGAGAGCGAAAA
23775 G
1 G
23776 GGCCATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
20 12 0.67
ACGTcount: A:0.59, C:0.08, G:0.31, T:0.03
Consensus pattern (19 bp):
GAAAAACAGAGAGCGAAAA
Found at i:27830 original size:42 final size:42
Alignment explanation
Indices: 27771--27852 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
27761 TTAAGAATGT
27771 TTTTAATATGTTAGTTTGATT-TA-TTGATGGATTGTTATTTGA
1 TTTTAATATGTTAGTTTG-TTATATTTG-TGGATTGTTATTTGA
27813 TTTTAATATGTTAGTTTGTTATATTTGTGGATTGTTATTT
1 TTTTAATATGTTAGTTTGTTATATTTGTGGATTGTTATTT
27853 TCGAGTTTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
41 2 0.05
42 33 0.87
43 3 0.08
ACGTcount: A:0.22, C:0.00, G:0.18, T:0.60
Consensus pattern (42 bp):
TTTTAATATGTTAGTTTGTTATATTTGTGGATTGTTATTTGA
Found at i:28886 original size:2 final size:2
Alignment explanation
Indices: 28879--28912 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
28869 TGCTTCCACC
28879 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28913 GATTTCCTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35766 original size:20 final size:20
Alignment explanation
Indices: 35741--35782 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
35731 GATGTAATTA
35741 TGGGTTATTGTGGGCATGGT
1 TGGGTTATTGTGGGCATGGT
35761 TGGGTTATTGTGGGCATGGT
1 TGGGTTATTGTGGGCATGGT
35781 TG
1 TG
35783 CAGGGTAGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.10, C:0.05, G:0.45, T:0.40
Consensus pattern (20 bp):
TGGGTTATTGTGGGCATGGT
Found at i:40495 original size:12 final size:12
Alignment explanation
Indices: 40478--40504 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
40468 CATCATCTAC
40478 TTTATACCATGA
1 TTTATACCATGA
40490 TTTATACCATGA
1 TTTATACCATGA
40502 TTT
1 TTT
40505 TTAGAACCGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.48
Consensus pattern (12 bp):
TTTATACCATGA
Found at i:45982 original size:51 final size:51
Alignment explanation
Indices: 45761--46226 Score: 493
Period size: 51 Copynumber: 8.9 Consensus size: 51
45751 TGGCGGGTCT
* ** *
45761 GCTCCCTATTCTTTCATG-GAGTATAAGACTCGAACAATCTTCAGTAAACGTGTCT
1 GCTCCCTATTCCTTCA-GAGAGTATAAGACT----CAATCTTCAACAAACGTGTCC
* * ** **
45816 GCTCCCTATTCATTCAGGGAGTATAAGACTCGAATAATCTTCAGTAAACGTGTTT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTC----AATCTTCAACAAACGTGTCC
* * * * * * *
45871 TCTCTCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCAAAAAATGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACT----CAATCTTCAACAAACGTGTCC
* * * * *
45926 GCTCCCTTTTCCTTTAGAGAGTATAAGACTCGATCTTCAATAAACGTGTTC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAACAAACGTGTCC
* * *
45977 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAACAAACGTGTCC
* * *
46028 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAACAAACGTGTCC
* * *
46079 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAACAAACGTGTCC
* * *
46130 GCTCCCTATTCCTTCAGAGAGTATATGACTCAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAACAAACGTGTCC
*
46181 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACG
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAACAAACG
46227 AGTTTGCTTC
Statistics
Matches: 368, Mismatches: 34, Indels: 22
0.87 0.08 0.05
Matches are distributed among these distances:
51 255 0.69
54 1 0.00
55 111 0.30
59 1 0.00
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (51 bp):
GCTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAACAAACGTGTCC
Found at i:47547 original size:13 final size:13
Alignment explanation
Indices: 47531--47555 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47521 TTCTCTTTTT
47531 TTTCATTTTTCTC
1 TTTCATTTTTCTC
47544 TTTCATTTTTCT
1 TTTCATTTTTCT
47556 TCCATTTTCC
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:0.08, C:0.20, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTCATTTTTCTC
Found at i:47618 original size:8 final size:8
Alignment explanation
Indices: 47605--47638 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
47595 ATTATTATTA
47605 TTTTTTCT
1 TTTTTTCT
47613 TTTTTTCT
1 TTTTTTCT
*
47621 TTTTCTCT
1 TTTTTTCT
47629 TTTATTTCT
1 TTT-TTTCT
47638 T
1 T
47639 CTTCAAGCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 18 0.78
9 5 0.22
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTTCT
Found at i:57171 original size:45 final size:47
Alignment explanation
Indices: 57104--57202 Score: 130
Period size: 45 Copynumber: 2.1 Consensus size: 47
57094 TGTTATCCAC
* * *
57104 AAAAAGAAATCCTAACCTCATGATATCTAATTCGCATGC-TTATTCA
1 AAAAATAAATCCTAACCGCATGATATCTAATTCGCAAGCATTATTCA
* *
57150 AAAAATAAA-CCTAACCGCATGATATCTAGTTCGCAAGCATTTATTCG
1 AAAAATAAATCCTAACCGCATGATATCTAATTCGCAAGCA-TTATTCA
57197 AAAAAT
1 AAAAAT
57203 GAAAATAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
45 26 0.57
46 8 0.17
47 12 0.26
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.28
Consensus pattern (47 bp):
AAAAATAAATCCTAACCGCATGATATCTAATTCGCAAGCATTATTCA
Found at i:61894 original size:21 final size:22
Alignment explanation
Indices: 61856--61901 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
61846 TTATAACACG
* *
61856 TTTATTTTTATATTTTGGTACA
1 TTTATTTATATATTTTGGCACA
61878 TTTATTTATAT-TTTTGGCACA
1 TTTATTTATATATTTTGGCACA
61899 TTT
1 TTT
61902 TTCGATTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.22, C:0.07, G:0.09, T:0.63
Consensus pattern (22 bp):
TTTATTTATATATTTTGGCACA
Found at i:63068 original size:18 final size:18
Alignment explanation
Indices: 63045--63102 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
63035 GTCAAATCAA
63045 ACTTACATCGATTCATTC
1 ACTTACATCGATTCATTC
* *
63063 ACTTACGT-G--TCATTAA
1 ACTTACATCGATTCATT-C
63079 ACTTACATCGATTCATTC
1 ACTTACATCGATTCATTC
63097 ACTTAC
1 ACTTAC
63103 GTGTCATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
15 5 0.16
16 7 0.22
17 2 0.06
18 13 0.41
19 5 0.16
ACGTcount: A:0.29, C:0.26, G:0.07, T:0.38
Consensus pattern (18 bp):
ACTTACATCGATTCATTC
Found at i:63081 original size:34 final size:34
Alignment explanation
Indices: 63043--63119 Score: 154
Period size: 34 Copynumber: 2.3 Consensus size: 34
63033 TAGTCAAATC
63043 AAACTTACATCGATTCATTCACTTACGTGTCATT
1 AAACTTACATCGATTCATTCACTTACGTGTCATT
63077 AAACTTACATCGATTCATTCACTTACGTGTCATT
1 AAACTTACATCGATTCATTCACTTACGTGTCATT
63111 AAACTTACA
1 AAACTTACA
63120 GTGGATACAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.32, C:0.23, G:0.08, T:0.36
Consensus pattern (34 bp):
AAACTTACATCGATTCATTCACTTACGTGTCATT
Found at i:63084 original size:16 final size:16
Alignment explanation
Indices: 63063--63118 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
63053 CGATTCATTC
63063 ACTTACGTGTCATTAA
1 ACTTACGTGTCATTAA
* *
63079 ACTTACATCGATTCATT-C
1 ACTTACGT-G--TCATTAA
63097 ACTTACGTGTCATTAA
1 ACTTACGTGTCATTAA
63113 ACTTAC
1 ACTTAC
63119 AGTGGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
15 5 0.16
16 13 0.41
17 2 0.06
18 7 0.22
19 5 0.16
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.38
Consensus pattern (16 bp):
ACTTACGTGTCATTAA
Found at i:63365 original size:32 final size:30
Alignment explanation
Indices: 63318--63405 Score: 90
Period size: 32 Copynumber: 2.9 Consensus size: 30
63308 AAACACAACC
*
63318 TCAATATT-CTAAGCTTTGCTAAGCTTT-AC
1 TCAA-ATTCCTAAGCTTTGCTAAGCTTTCAA
*
63347 TCAAATTCTCTCATAGCTTTTCTAAGCTTTCAA
1 TCAAATTC-CT-A-AGCTTTGCTAAGCTTTCAA
* *
63380 TCATATTCCTAAGCTTCGCTAAGCTT
1 TCAAATTCCTAAGCTTTGCTAAGCTT
63406 CACCCTCTCT
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
28 3 0.06
29 4 0.08
30 15 0.31
31 2 0.04
32 17 0.35
33 8 0.16
ACGTcount: A:0.26, C:0.24, G:0.09, T:0.41
Consensus pattern (30 bp):
TCAAATTCCTAAGCTTTGCTAAGCTTTCAA
Found at i:64573 original size:32 final size:30
Alignment explanation
Indices: 64534--64612 Score: 97
Period size: 32 Copynumber: 2.6 Consensus size: 30
64524 CCTCAGTATT
*
64534 CTAAGCTTTGCTAAGCTTT-ACTCAAATTC
1 CTAAGCTTTGCTAAGCTTTCAATCAAATTC
* *
64563 TCTCATAGCTTTTCTAAGCTTTCAATCATATTC
1 -CT-A-AGCTTTGCTAAGCTTTCAATCAAATTC
64596 CTAAGCTTTGCTAAGCT
1 CTAAGCTTTGCTAAGCT
64613 CTACCCTCTC
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
30 15 0.36
31 2 0.05
32 17 0.40
33 8 0.19
ACGTcount: A:0.25, C:0.24, G:0.10, T:0.41
Consensus pattern (30 bp):
CTAAGCTTTGCTAAGCTTTCAATCAAATTC
Found at i:68444 original size:162 final size:163
Alignment explanation
Indices: 68177--68502 Score: 645
Period size: 162 Copynumber: 2.0 Consensus size: 163
68167 GAAGGGTCAC
68177 TTTAAAAGAGATTGCCGAGCACTGAAGAAAAATACCGGCGCACGGGAATCTGCCAACGTGACATA
1 TTTAAAAGAGATTGCCGAGCACTGAAGAAAAATACCGGCGCACGGGAATCTGCCAACGTGACATA
68242 GGAGACAGGTGATGCCATGATTCTAAGCGTAAACAGTCCGACTGAATCATTGATCTTGGATTCAG
66 GGAGACAGGTGATGCCATGATTCTAAGCGTAAACAGTCCGACTGAATCATTGATCTTGGATTCAG
68307 GGGCATC-TTCCACTCCACCCCATGCCGAGAAA
131 GGGCATCTTTCCACTCCACCCCATGCCGAGAAA
68339 TTTAAAAGAGATTGCCGAGCACTGAAGAAAAATACCGGCGCACGGGAATCTGCCAACGTGACATA
1 TTTAAAAGAGATTGCCGAGCACTGAAGAAAAATACCGGCGCACGGGAATCTGCCAACGTGACATA
68404 GGAGACAGGTGATGCCATGATTCTAAGCGTAAACAGTCCGACTGAATCATTGATCTTGGATTCAG
66 GGAGACAGGTGATGCCATGATTCTAAGCGTAAACAGTCCGACTGAATCATTGATCTTGGATTCAG
68469 GGGCATCTTTCCACTCCACCCCATGCCGAGAAA
131 GGGCATCTTTCCACTCCACCCCATGCCGAGAAA
68502 T
1 T
68503 CATGGAGAAC
Statistics
Matches: 163, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
162 137 0.84
163 26 0.16
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21
Consensus pattern (163 bp):
TTTAAAAGAGATTGCCGAGCACTGAAGAAAAATACCGGCGCACGGGAATCTGCCAACGTGACATA
GGAGACAGGTGATGCCATGATTCTAAGCGTAAACAGTCCGACTGAATCATTGATCTTGGATTCAG
GGGCATCTTTCCACTCCACCCCATGCCGAGAAA
Found at i:76262 original size:9 final size:9
Alignment explanation
Indices: 76248--76274 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
76238 ATATAAAGCT
76248 GAAACACAA
1 GAAACACAA
76257 GAAACACAA
1 GAAACACAA
76266 GAAACACAA
1 GAAACACAA
76275 AGTGAATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.22, G:0.11, T:0.00
Consensus pattern (9 bp):
GAAACACAA
Found at i:80168 original size:32 final size:32
Alignment explanation
Indices: 80123--80212 Score: 119
Period size: 32 Copynumber: 2.8 Consensus size: 32
80113 TGTGGCTGAT
*
80123 TATTCATTATACCCATTGTTTAATTGGCGGAC
1 TATTCATTCTACCCATTGTTTAATTGGCGGAC
* * ** *
80155 TCTTCATTCTACCCATTGTTTAACTGGTTGAT
1 TATTCATTCTACCCATTGTTTAATTGGCGGAC
80187 TATTCATTCTACCCATTG-TTAATTGG
1 TATTCATTCTACCCATTGTTTAATTGG
80213 ATGATTTTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
31 7 0.14
32 43 0.86
ACGTcount: A:0.22, C:0.20, G:0.13, T:0.44
Consensus pattern (32 bp):
TATTCATTCTACCCATTGTTTAATTGGCGGAC
Found at i:80230 original size:31 final size:32
Alignment explanation
Indices: 80163--80240 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 32
80153 ACTCTTCATT
* * *
80163 CTACCCATTGTTTAACTGGTTGATTATTCATT
1 CTACCCATTGTTTAACTGGATGATTATTAATC
* *
80195 CTACCCATTG-TTAATTGGATGATTTTTAATC
1 CTACCCATTGTTTAACTGGATGATTATTAATC
**
80226 CTACCTGTTGTTTAA
1 CTACCCATTGTTTAA
80241 TCGGCTGATC
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.46
Consensus pattern (32 bp):
CTACCCATTGTTTAACTGGATGATTATTAATC
Found at i:81799 original size:31 final size:33
Alignment explanation
Indices: 81756--81818 Score: 78
Period size: 31 Copynumber: 2.0 Consensus size: 33
81746 CGACCCGACC
**
81756 TGAATATATATAATTTTA-CCT-TATATATTTA
1 TGAATATATATAATAATACCCTCTATATATTTA
81787 TGAATA-ATTATAATAATACCCTCTATATATTT
1 TGAATATA-TATAATAATACCCTCTATATATTT
81819 TTTTTCTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 1 0.04
31 14 0.52
32 3 0.11
33 9 0.33
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.48
Consensus pattern (33 bp):
TGAATATATATAATAATACCCTCTATATATTTA
Found at i:82186 original size:258 final size:257
Alignment explanation
Indices: 81619--82197 Score: 925
Period size: 257 Copynumber: 2.3 Consensus size: 257
81609 GGGTCGGGTT
* *
81619 GGGTCGGGTTTCTAATTCATATATTCGTATCAGGTCGGGTGAAACTTTATTTTTGGTCGGGTCGG
1 GGGTCGGGTTTCTAATTCATATATTCGGATCGGGTCGGGTGAAACTTTATTTTTGGTCGGGTCGG
* ** *
81684 GTCAGTTTTTTTAAGTGTGATATTTGGGTCGGGTCGATTTCGGGTTTAGGGTGAAAAATACCCGA
66 ATCAGTTTTTTTAAGTGTGATATTCAGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGA
** * * *
81749 CCCGACCTGAATATATATAATTTTACCTTATATATTTATGAATAATTATAATAATACCCTCTATA
131 CCCGACCAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCTCTATA
81814 TATTTTTTTTCTCAATTAAGTCACTATTTTTATTGAAAAATAATAATTTTTATTATTATTTC
196 TATTTTTTTTCTCAATTAAGTCACTATTTTTATTGAAAAATAATAATTTTTATTATTATTTC
*
81876 GGGTCGGGTTTCTAATTCATATATTCGGATCGGGTCGGGTGAAACTTTATTTTTTGTCGGGTCGG
1 GGGTCGGGTTTCTAATTCATATATTCGGATCGGGTCGGGTGAAACTTTATTTTTGGTCGGGTCGG
* *
81941 ATCAG-TTTTTTAAGTGTGATATTCAGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAATACTCGA
66 ATCAGTTTTTTTAAGTGTGATATTCAGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGA
82005 CCCGACCCAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCTCTCTA
131 CCCGA-CCAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACC-CTCTA
82070 TATATAATTTTTTT-TCAATTAAGTCACTATTTTTATTGAATAAA-AATAATTTTT-TTATTATT
194 TATAT--TTTTTTTCTCAATTAAGTCACTATTTTTATTGAA-AAATAATAATTTTTATTATTATT
82132 TC
256 TC
* * *
82134 GGGTCGGGTTTCTAATTCATATATTCGGGTGGGGTAGGGTGAAACTTTA-TTTTGGTCGGGTCGG
1 GGGTCGGGTTTCTAATTCATATATTCGGATCGGGTCGGGTGAAACTTTATTTTTGGTCGGGTCGG
82198 GTCTCGGATG
Statistics
Matches: 299, Mismatches: 18, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
256 59 0.20
257 128 0.43
258 66 0.22
259 36 0.12
260 10 0.03
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (257 bp):
GGGTCGGGTTTCTAATTCATATATTCGGATCGGGTCGGGTGAAACTTTATTTTTGGTCGGGTCGG
ATCAGTTTTTTTAAGTGTGATATTCAGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGA
CCCGACCAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCTCTATA
TATTTTTTTTCTCAATTAAGTCACTATTTTTATTGAAAAATAATAATTTTTATTATTATTTC
Found at i:82594 original size:17 final size:17
Alignment explanation
Indices: 82568--82628 Score: 104
Period size: 17 Copynumber: 3.6 Consensus size: 17
82558 TATAGAATTG
*
82568 GATTCCAATTTCTGATA
1 GATTCTAATTTCTGATA
82585 GATTCTAATTTCTGATA
1 GATTCTAATTTCTGATA
82602 GATTCTAATTTCTGATA
1 GATTCTAATTTCTGATA
*
82619 GATTTTAATT
1 GATTCTAATT
82629 CCTTCACATA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 42 1.00
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.48
Consensus pattern (17 bp):
GATTCTAATTTCTGATA
Found at i:82792 original size:3 final size:3
Alignment explanation
Indices: 82786--82813 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
82776 CTTATTATTA
82786 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
82814 CACGATATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:85066 original size:21 final size:21
Alignment explanation
Indices: 85042--85103 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
85032 GTTAGACAGA
85042 GGGGAATCGGTACCCCCTGGG
1 GGGGAATCGGTACCCCCTGGG
* * * *
85063 GGGGAATCTGTTCCCTCTGTG
1 GGGGAATCGGTACCCCCTGGG
*
85084 GGGGAATTGGTACCCCCTGG
1 GGGGAATCGGTACCCCCTGG
85104 ACATTCTGTT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.13, C:0.26, G:0.39, T:0.23
Consensus pattern (21 bp):
GGGGAATCGGTACCCCCTGGG
Found at i:88597 original size:20 final size:20
Alignment explanation
Indices: 88553--88632 Score: 99
Period size: 21 Copynumber: 3.9 Consensus size: 20
88543 TTAGACAGGC
*
88553 GGAATCGGTACCCCCTGGGG
1 GGAATCTGTACCCCCTGGGG
*
88573 AGGAATCTGTTCCCCCTGGGG
1 -GGAATCTGTACCCCCTGGGG
*
88594 GGAATC-GATACCCTCTAGGGG
1 GGAATCTG-TACCCCCT-GGGG
88615 GGAATCTGTACCCCCTGG
1 GGAATCTGTACCCCCTGG
88633 ACATTCTGTT
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
19 1 0.02
20 14 0.27
21 35 0.69
22 1 0.02
ACGTcount: A:0.17, C:0.29, G:0.34, T:0.20
Consensus pattern (20 bp):
GGAATCTGTACCCCCTGGGG
Found at i:88619 original size:41 final size:41
Alignment explanation
Indices: 88553--88632 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 41
88543 TTAGACAGGC
* *
88553 GGAATCGGTACCCCCTGGGGAGGAATCTGTTCCCCCTGGGG
1 GGAATCGATACCCCCTGGGGAGGAATCTGTACCCCCTGGGG
*
88594 GGAATCGATACCCTCTAGGGG-GGAATCTGTACCCCCTGG
1 GGAATCGATACCCCCT-GGGGAGGAATCTGTACCCCCTGG
88633 ACATTCTGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
41 31 0.89
42 4 0.11
ACGTcount: A:0.17, C:0.29, G:0.34, T:0.20
Consensus pattern (41 bp):
GGAATCGATACCCCCTGGGGAGGAATCTGTACCCCCTGGGG
Found at i:89115 original size:23 final size:23
Alignment explanation
Indices: 89048--89108 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
89038 CACCACAGCT
89048 CGTATAAATGCACCGAAGTGCCA
1 CGTATAAATGCACCGAAGTGCCA
* *
89071 CGTATAATTGCACCGAAGTGCCG
1 CGTATAAATGCACCGAAGTGCCA
*
89094 CGTAGAAATGCACCG
1 CGTATAAATGCACCG
89109 TCGTGCCATA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.31, C:0.26, G:0.25, T:0.18
Consensus pattern (23 bp):
CGTATAAATGCACCGAAGTGCCA
Found at i:89780 original size:65 final size:66
Alignment explanation
Indices: 89710--89866 Score: 169
Period size: 65 Copynumber: 2.4 Consensus size: 66
89700 CAATATTTCA
* ** * * *
89710 TTTTTCCTTTAAG-GGGTATCAATACACCCCTTGAGGTATCGGTACCCTTACTGCATTCTGCT-A
1 TTTTTCCTTTAAGAGGGTATCGATACACAAC-TGAGGTATCAGTACCCTCACTACATTCTG-TGA
89773 TT-
64 TTC
* * *
89775 TTTTT-CTTTCAAGAAGGTATCGGTACACAACTGAGGTATCAGTACCCTCATTACATTCTGTGAT
1 TTTTTCCTTT-AAGAGGGTATCGATACACAACTGAGGTATCAGTACCCTCACTACATTCTGTGAT
89839 TC
65 TC
*
89841 TTTTTCGTTTAAGAGGGTATCGATAC
1 TTTTTCCTTTAAGAGGGTATCGATAC
89867 CTGTTGAATG
Statistics
Matches: 75, Mismatches: 12, Indels: 9
0.78 0.12 0.09
Matches are distributed among these distances:
64 5 0.07
65 36 0.48
66 31 0.41
67 3 0.04
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (66 bp):
TTTTTCCTTTAAGAGGGTATCGATACACAACTGAGGTATCAGTACCCTCACTACATTCTGTGATT
C
Found at i:93164 original size:22 final size:22
Alignment explanation
Indices: 93139--93191 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
93129 GTGGGTATCG
93139 GTACCATCCAAGAGGGGTACCA
1 GTACCATCCAAGAGGGGTACCA
*
93161 GTACCATCCAAGAGGGGTACCG
1 GTACCATCCAAGAGGGGTACCA
93183 GTACCATCC
1 GTACCATCC
93192 GGGCAATATG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.15
Consensus pattern (22 bp):
GTACCATCCAAGAGGGGTACCA
Found at i:96946 original size:66 final size:66
Alignment explanation
Indices: 96810--96946 Score: 168
Period size: 65 Copynumber: 2.1 Consensus size: 66
96800 CCTTTAGGGG
** * * *
96810 GTATCGATACACCCCTTGAGGTATCGATACCCTTACTGCATTCTGTTATTTTTTTCGTTCAATAG
1 GTATCGATACACAACTTGAGGTATCGATACCCTTACTACATTCTGTGATTTTTTTCGTTCAAGAG
*
96875 G
66 A
* * * *
96876 GTATCGATACACAAC-TGGGGTATCGGTACCCTTACTACATTCTGTGATTCTTTTTTGTTTAAGA
1 GTATCGATACACAACTTGAGGTATCGATACCCTTACTACATTCTGTGATT-TTTTTCGTTCAAGA
96940 GA
65 GA
96942 GTATC
1 GTATC
96947 AGTACCTGTT
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
65 30 0.50
66 30 0.50
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (66 bp):
GTATCGATACACAACTTGAGGTATCGATACCCTTACTACATTCTGTGATTTTTTTCGTTCAAGAG
A
Found at i:102242 original size:254 final size:247
Alignment explanation
Indices: 101750--102247 Score: 729
Period size: 254 Copynumber: 2.0 Consensus size: 247
101740 ACATGCAAAC
*
101750 TTTTTCTACATAAATATTAATATTCATCAACAATCAAATTAACTATAATAGATATTTTAAAATTA
1 TTTTTCTACATAAATATTAATATTCATCAACAATCAAATTAACTATAATAGATATTTAAAAATTA
*
101815 AAAACAAAATTAATGATATAATATTACTTAATTAAAAATTAAAATATACATATACTTACTAATGT
66 AAAAC-AAA-TAAT-ATATAATATTACTTAATTAAAAATTAAAATATACATATACTTACTAATAT
* *
101880 TTTCTCCTTCTTCTTATTGTTCTTCTTTTACAATTTTGTATTATTCTCAAATTACATGCATAATA
128 TTTCTCCTTCTTCTTATTGTTCTCCTTTTACAATTTTGTATTATTCTCAAACTACATGCATAATA
101945 TTAAAATTATATTAACAGTTCTCAACAATCAAACTAACTATATAATATAGTAAAT
193 TTAAAATTATATTAACAGTTCTCAACAATCAAACTAACTATATAATATAGTAAAT
102000 TTTTTCTACATAAATATTAATATTCATCAACAATCAAATTAACTA-AATAGATAATTTAAAAATT
1 TTTTTCTACATAAATATTAATATTCATCAACAATCAAATTAACTATAATAGAT-ATTTAAAAATT
*
102064 AAAAAC-AA-AAT-T-T-ATATTACTTAATTAAAAATTAAAATATACATCTACTTACTAATATTT
65 AAAAACAAATAATATATAATATTACTTAATTAAAAATTAAAATATACATATACTTACTAATATTT
* *
102124 TCTCATTCTTCCTTCTTCATTCTTCTGCTTCTCCTTTTACAATTTTTTCATTCTTCTCAAACTAC
130 TCTC---CTT-CTTCTT-A----T-TG-TTCTCCTTTTACAATTTTGT-ATTATTCTCAAACTAC
* *
102189 ATGCATAATATTAAAATTATATTAACATTTCTCAACAATCAAACTAGCTATATAATATA
183 ATGCATAATATTAAAATTATATTAACAGTTCTCAACAATCAAACTAACTATATAATATA
102248 TCATTTAAAA
Statistics
Matches: 226, Mismatches: 9, Indels: 22
0.88 0.04 0.09
Matches are distributed among these distances:
242 49 0.22
243 1 0.00
244 1 0.00
245 3 0.01
246 9 0.04
247 1 0.00
248 2 0.01
249 7 0.03
250 61 0.27
251 1 0.00
252 2 0.01
253 18 0.08
254 71 0.31
ACGTcount: A:0.42, C:0.14, G:0.02, T:0.42
Consensus pattern (247 bp):
TTTTTCTACATAAATATTAATATTCATCAACAATCAAATTAACTATAATAGATATTTAAAAATTA
AAAACAAATAATATATAATATTACTTAATTAAAAATTAAAATATACATATACTTACTAATATTTT
CTCCTTCTTCTTATTGTTCTCCTTTTACAATTTTGTATTATTCTCAAACTACATGCATAATATTA
AAATTATATTAACAGTTCTCAACAATCAAACTAACTATATAATATAGTAAAT
Found at i:102354 original size:3 final size:3
Alignment explanation
Indices: 102340--102394 Score: 65
Period size: 3 Copynumber: 17.7 Consensus size: 3
102330 AAATTTCTAA
* * *
102340 TTC TTCC TTC TTC TTCC TTC TCC TTT TTC TTC TTC TTC TTG TTC TTC
1 TTC TT-C TTC TTC TT-C TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
102387 TTC TTC TT
1 TTC TTC TT
102395 TTACAATATT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
3 38 0.86
4 6 0.14
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:114323 original size:21 final size:21
Alignment explanation
Indices: 114294--114346 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
114284 ATTCTGACTA
114294 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
114315 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
114336 TCGCAATGCGA
1 TCGCATTGCGA
114347 ATACATAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:114361 original size:20 final size:20
Alignment explanation
Indices: 114336--114429 Score: 100
Period size: 20 Copynumber: 4.7 Consensus size: 20
114326 TTTTCCTAAT
114336 TCGCAATGCGAATACATAAA
1 TCGCAATGCGAATACATAAA
* **
114356 TCGCAACGCGAATTTGGA-AAA
1 TCGCAATGCGAA--TACATAAA
* *
114377 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACATAAA
*
114397 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACATAAA
*
114417 CCGCAATGCGAAT
1 TCGCAATGCGAAT
114430 CTGACTATCG
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
19 1 0.02
20 45 0.74
21 13 0.21
22 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACATAAA
Found at i:114409 original size:61 final size:60
Alignment explanation
Indices: 114336--114449 Score: 165
Period size: 61 Copynumber: 1.9 Consensus size: 60
114326 TTTTCCTAAT
* *
114336 TCGCAATGCGAATACATAAATCGCAACGCGAATTTGGAAAATCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACATAAACCGCAACGCGAATCT-GAAAATCGCAATGCGATTACGTAAA
* * **
114397 TCGCAATGCGAATACGTAAACCGCAATGCGAATCTGACTATCGCAATGCGATT
1 TCGCAATGCGAATACATAAACCGCAACGCGAATCTGAAAATCGCAATGCGATT
114450 TACATAGCGC
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
60 16 0.34
61 31 0.66
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (60 bp):
TCGCAATGCGAATACATAAACCGCAACGCGAATCTGAAAATCGCAATGCGATTACGTAAA
Found at i:115066 original size:20 final size:20
Alignment explanation
Indices: 115019--115067 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
115009 CAACGAGTGA
*
115019 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
**
115039 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
115059 ATCGCAATG
1 ATCGCAATG
115068 AGAGAATCGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.22
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:115134 original size:20 final size:20
Alignment explanation
Indices: 115109--115158 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
115099 TGCGATTCTT
115109 GCGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTC
**
115129 GCGTTGCGATAGTCATTTTC
1 GCGTTGCGATAGTCAAATTC
*
115149 GTGTTGCGAT
1 GCGTTGCGAT
115159 TTTCATTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.18, C:0.18, G:0.28, T:0.36
Consensus pattern (20 bp):
GCGTTGCGATAGTCAAATTC
Found at i:115164 original size:20 final size:20
Alignment explanation
Indices: 115126--115180 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
115116 GATAGTCAAA
* **
115126 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
115146 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
115166 TTCGTGTTGCGATTT
1 TTCGTGTTGCGATTT
115181 AAAGTTTCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.16, G:0.24, T:0.49
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:115188 original size:20 final size:20
Alignment explanation
Indices: 115145--115188 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
115135 CGATAGTCAT
** *
115145 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
115165 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
115185 TTTC
1 TTTC
115189 ATAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:120793 original size:21 final size:21
Alignment explanation
Indices: 120767--120848 Score: 67
Period size: 20 Copynumber: 3.9 Consensus size: 21
120757 CAGAACCCCA
* *
120767 GGGGGGTATCGATTCCCTTGT
1 GGGGGGAATCGATTCCCTTAT
* *
120788 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGATT-CCCTT-AT
* * *
120811 AGGGGGAATCGGTTCCCTCAT
1 GGGGGGAATCGATTCCCTTAT
*
120832 -GGGGGTATCGATTCCCT
1 GGGGGGAATCGATTCCCT
120849 CTGCACCAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
20 15 0.30
21 13 0.26
22 9 0.18
23 13 0.26
ACGTcount: A:0.15, C:0.23, G:0.35, T:0.27
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCTTAT
Found at i:124691 original size:22 final size:21
Alignment explanation
Indices: 124649--124688 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
124639 GAGTTTATTT
*
124649 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
124670 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
124689 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:132510 original size:138 final size:138
Alignment explanation
Indices: 132262--132517 Score: 512
Period size: 138 Copynumber: 1.9 Consensus size: 138
132252 AACTTTAACA
132262 AATCTCCACCTTGACACAAATTTTGAAAATGAAAAGGTTTCGAGACAAAACACTCAAATTCAATG
1 AATCTCCACCTTGACACAAATTTTGAAAATGAAAAGGTTTCGAGACAAAACACTCAAATTCAATG
132327 TGACACACAAACTCAACAAAAAAAAATTCTTCACTTCAATGAACAATTCTCCAAATAAGTAGAAA
66 TGACACACAAACTCAACAAAAAAAAATTCTTCACTTCAATGAACAATTCTCCAAATAAGTAGAAA
132392 TCTACTTT
131 TCTACTTT
132400 AATCTCCACCTTGACACAAATTTTGAAAATGAAAAGGTTTCGAGACAAAACACTCAAATTCAATG
1 AATCTCCACCTTGACACAAATTTTGAAAATGAAAAGGTTTCGAGACAAAACACTCAAATTCAATG
132465 TGACACACAAACTCAACAAAAAAAAATTCTTCACTTCAATGAACAATTCTCCA
66 TGACACACAAACTCAACAAAAAAAAATTCTTCACTTCAATGAACAATTCTCCA
132518 CCTCTTCCAC
Statistics
Matches: 118, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
138 118 1.00
ACGTcount: A:0.45, C:0.22, G:0.09, T:0.25
Consensus pattern (138 bp):
AATCTCCACCTTGACACAAATTTTGAAAATGAAAAGGTTTCGAGACAAAACACTCAAATTCAATG
TGACACACAAACTCAACAAAAAAAAATTCTTCACTTCAATGAACAATTCTCCAAATAAGTAGAAA
TCTACTTT
Found at i:136318 original size:14 final size:14
Alignment explanation
Indices: 136301--136381 Score: 73
Period size: 14 Copynumber: 6.1 Consensus size: 14
136291 GATTGGGTTA
* *
136301 AACATAAATGAATG
1 AACATAAACGAACG
136315 AACATAAACGAACG
1 AACATAAACGAACG
136329 AACAT--A--AACG
1 AACATAAACGAACG
*
136339 AACATAACCGAACG
1 AACATAAACGAACG
*
136353 AACATAACCGAACG
1 AACATAAACGAACG
*
136367 TAA-ATGAACGAACG
1 -AACATAAACGAACG
136381 A
1 A
136382 GACCTATGCT
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
10 9 0.16
12 1 0.02
13 1 0.02
14 44 0.77
15 2 0.04
ACGTcount: A:0.54, C:0.20, G:0.15, T:0.11
Consensus pattern (14 bp):
AACATAAACGAACG
Found at i:136350 original size:24 final size:24
Alignment explanation
Indices: 136314--136379 Score: 96
Period size: 24 Copynumber: 2.8 Consensus size: 24
136304 ATAAATGAAT
136314 GAACATAAACGAACGAACATAAAC
1 GAACATAAACGAACGAACATAAAC
* *
136338 GAACATAACCGAACGAACATAACC
1 GAACATAAACGAACGAACATAAAC
* *
136362 GAACGTAAATGAACGAAC
1 GAACATAAACGAACGAAC
136380 GAGACCTATG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.53, C:0.23, G:0.15, T:0.09
Consensus pattern (24 bp):
GAACATAAACGAACGAACATAAAC
Found at i:137547 original size:15 final size:15
Alignment explanation
Indices: 137529--137559 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
137519 TATATTTTCT
137529 TTAAAAAAATTTATA
1 TTAAAAAAATTTATA
*
137544 TTAATAAAATTTATA
1 TTAAAAAAATTTATA
137559 T
1 T
137560 AATTTTTTTA
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAAAAAAATTTATA
Found at i:138530 original size:21 final size:21
Alignment explanation
Indices: 138506--138570 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
138496 AAGGAAAATT
138506 GTGCATCGATGTACTGCTACA
1 GTGCATCGATGTACTGCTACA
138527 GTGCATCGATGTACTGCTACA
1 GTGCATCGATGTACTGCTACA
* *
138548 GTGCATCGATGCACTGATACA
1 GTGCATCGATGTACTGCTACA
138569 GT
1 GT
138571 ACTACTACAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.28
Consensus pattern (21 bp):
GTGCATCGATGTACTGCTACA
Found at i:147995 original size:18 final size:18
Alignment explanation
Indices: 147972--148018 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
147962 TTGATCGGTT
147972 TTGACCCGACCAGACCCG
1 TTGACCCGACCAGACCCG
* *
147990 TTGACCCGACCCGACTCG
1 TTGACCCGACCAGACCCG
*
148008 TTGACCTGACC
1 TTGACCCGACC
148019 GTTGACCCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.19, C:0.43, G:0.21, T:0.17
Consensus pattern (18 bp):
TTGACCCGACCAGACCCG
Found at i:148097 original size:29 final size:29
Alignment explanation
Indices: 148051--148125 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
148041 CCCGTTGATC
148051 GGGTGCTATTTTAGTAATTATTTCTAAAA
1 GGGTGCTATTTTAGTAATTATTTCTAAAA
* *
148080 GGGTGTTATTTTCA-TAATTATTTTTAAAA
1 GGGTGCTATTTT-AGTAATTATTTCTAAAA
* *
148109 GGGTGCTACTTTCGTAA
1 GGGTGCTATTTTAGTAA
148126 AATGGTTGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
29 38 0.97
30 1 0.03
ACGTcount: A:0.28, C:0.08, G:0.19, T:0.45
Consensus pattern (29 bp):
GGGTGCTATTTTAGTAATTATTTCTAAAA
Found at i:148887 original size:24 final size:24
Alignment explanation
Indices: 148835--148892 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
148825 ATTTTTGACG
* *
148835 GGATTTTGATATGATACTTGACCT
1 GGATTTTGATATGATACATGACAT
* *
148859 AGATTTTTATATGATACATGACAT
1 GGATTTTGATATGATACATGACAT
*
148883 GGATTCTGAT
1 GGATTTTGAT
148893 CTGCTACTTG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.41
Consensus pattern (24 bp):
GGATTTTGATATGATACATGACAT
Found at i:149514 original size:2 final size:2
Alignment explanation
Indices: 149501--149583 Score: 157
Period size: 2 Copynumber: 41.5 Consensus size: 2
149491 CGCTCATAAC
*
149501 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
149543 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
149584 AATTTAAAAC
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:149647 original size:24 final size:24
Alignment explanation
Indices: 149620--149672 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
149610 AGAAGATCAG
* *
149620 AATCCATGTCATGTATCATATAAA
1 AATCCAGGTCAAGTATCATATAAA
*
149644 AATCCAGGTCAAGTATCATATCAA
1 AATCCAGGTCAAGTATCATATAAA
149668 AATCC
1 AATCC
149673 CGTCAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (24 bp):
AATCCAGGTCAAGTATCATATAAA
Found at i:149684 original size:23 final size:24
Alignment explanation
Indices: 149634--149690 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
149624 CATGTCATGT
* **
149634 ATCATATAAAAATCCAGGTCAAGT
1 ATCATATAAAAATCCACGTCAAAA
*
149658 ATCATATCAAAATCC-CGTCAAAA
1 ATCATATAAAAATCCACGTCAAAA
*
149681 ATCAGATAAA
1 ATCATATAAA
149691 CTATTCATAT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 13 0.48
24 14 0.52
ACGTcount: A:0.49, C:0.19, G:0.09, T:0.23
Consensus pattern (24 bp):
ATCATATAAAAATCCACGTCAAAA
Found at i:150420 original size:29 final size:29
Alignment explanation
Indices: 150373--150444 Score: 99
Period size: 29 Copynumber: 2.5 Consensus size: 29
150363 ATCAACCATT
* *
150373 TTACGAAAATAGCACCCTTTTAAAAATAA
1 TTACGAAAATAACAACCTTTTAAAAATAA
* *
150402 TTTCGAAAATAACAACCTTTTAGAAATAA
1 TTACGAAAATAACAACCTTTTAAAAATAA
*
150431 TTACTAAAATAACA
1 TTACGAAAATAACA
150445 TCCGGAAGGT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.50, C:0.15, G:0.06, T:0.29
Consensus pattern (29 bp):
TTACGAAAATAACAACCTTTTAAAAATAA
Found at i:150968 original size:24 final size:24
Alignment explanation
Indices: 150941--151012 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
150931 ATTTTTAATG
150941 GGATTTTGATATGATACTTGACCT
1 GGATTTTGATATGATACTTGACCT
* * **
150965 GGATTTTTATATGATACATGATAT
1 GGATTTTGATATGATACTTGACCT
* * *
150989 GGATTCTGATCTGCTACTTGACCT
1 GGATTTTGATATGATACTTGACCT
151013 AAATTATGTT
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.42
Consensus pattern (24 bp):
GGATTTTGATATGATACTTGACCT
Found at i:151204 original size:27 final size:27
Alignment explanation
Indices: 151174--151228 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
151164 ATAATATAGA
* *
151174 TATATTCAAAATGATTGCAAATACATG
1 TATATCCAAAATGATAGCAAATACATG
151201 TATATCCAAAATGATAGCAAATACATG
1 TATATCCAAAATGATAGCAAATACATG
151228 T
1 T
151229 CACCAGATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.31
Consensus pattern (27 bp):
TATATCCAAAATGATAGCAAATACATG
Found at i:151705 original size:24 final size:24
Alignment explanation
Indices: 151666--151738 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
151656 AAACATAATT
* *
151666 CAGGTCAAGTAGCATATCAGAATC
1 CAGGTCAAGTATCATATCAAAATC
* * *
151690 CATGTCATGTATCATATAAAAATC
1 CAGGTCAAGTATCATATCAAAATC
* *
151714 CAGGTTAAGTATCATATCAATATC
1 CAGGTCAAGTATCATATCAAAATC
151738 C
1 C
151739 CGTCAAAAAT
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (24 bp):
CAGGTCAAGTATCATATCAAAATC
Found at i:152403 original size:10 final size:10
Alignment explanation
Indices: 152390--152421 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
152380 TCTTTTTAAT
152390 AGCCGGTCAA
1 AGCCGGTCAA
152400 AGCCGGTCAA
1 AGCCGGTCAA
152410 AGCCGGTCAA
1 AGCCGGTCAA
152420 AG
1 AG
152422 TTCTGGTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.31, C:0.28, G:0.31, T:0.09
Consensus pattern (10 bp):
AGCCGGTCAA
Found at i:152504 original size:29 final size:29
Alignment explanation
Indices: 152463--152526 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
152453 CCATTTTATG
152463 AAAATAGCACCCTTTTAAAAATAATTACA
1 AAAATAGCACCCTTTTAAAAATAATTACA
* *
152492 AAAATAGCACCCTTTTAGAAATAATTACT
1 AAAATAGCACCCTTTTAAAAATAATTACA
152521 AAAATA
1 AAAATA
152527 ACATCCAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.52, C:0.16, G:0.05, T:0.28
Consensus pattern (29 bp):
AAAATAGCACCCTTTTAAAAATAATTACA
Found at i:153061 original size:24 final size:24
Alignment explanation
Indices: 153026--153097 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
153016 ATTTTTGACG
153026 GGATTTTGATATGATACTTGACCT
1 GGATTTTGATATGATACTTGACCT
* * *
153050 GGATTTTTATATGATACATGACAT
1 GGATTTTGATATGATACTTGACCT
* * *
153074 GGATTCTGATCTGCTACTTGACCT
1 GGATTTTGATATGATACTTGACCT
153098 AAATTATGTT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.40
Consensus pattern (24 bp):
GGATTTTGATATGATACTTGACCT
Found at i:153122 original size:2 final size:2
Alignment explanation
Indices: 153115--153157 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
153105 GTTATAAATT
153115 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
153157 T
1 T
153158 CCGTTATAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:153314 original size:27 final size:27
Alignment explanation
Indices: 153279--153333 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
153269 ATAAAATAGA
*
153279 TATAGCCAAAATGATTGCAAATACATG
1 TATAGCCAAAATGATAGCAAATACATG
*
153306 TATATCCAAAATGATAGCAAATACATG
1 TATAGCCAAAATGATAGCAAATACATG
153333 T
1 T
153334 CACCAAATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.27
Consensus pattern (27 bp):
TATAGCCAAAATGATAGCAAATACATG
Found at i:153793 original size:2 final size:2
Alignment explanation
Indices: 153786--153824 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
153776 TCCGCTCATA
153786 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
153825 ATTTAAAACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:153870 original size:24 final size:24
Alignment explanation
Indices: 153840--153912 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
153830 AAACAGAATT
* * *
153840 CAGGTCAAGTAGCAGATCAGAATC
1 CAGGTCAAGTATCATATCAAAATC
* * *
153864 CATGTCATGTATCATATAAAAATC
1 CAGGTCAAGTATCATATCAAAATC
153888 CAGGTCAAGTATCATATCAAAATC
1 CAGGTCAAGTATCATATCAAAATC
153912 C
1 C
153913 CATCAAAAAT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.25
Consensus pattern (24 bp):
CAGGTCAAGTATCATATCAAAATC
Found at i:154664 original size:29 final size:29
Alignment explanation
Indices: 154622--154696 Score: 123
Period size: 29 Copynumber: 2.6 Consensus size: 29
154612 ATCAACCATT
*
154622 TTACGAAAATAGCACCCTTTTAAAAATAA
1 TTACAAAAATAGCACCCTTTTAAAAATAA
*
154651 TTACAAAAATAGCACCCTTTTAGAAATAA
1 TTACAAAAATAGCACCCTTTTAAAAATAA
*
154680 TTACTAAAATAGCACCC
1 TTACAAAAATAGCACCC
154697 GAAAGGTCAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.27
Consensus pattern (29 bp):
TTACAAAAATAGCACCCTTTTAAAAATAA
Found at i:155225 original size:24 final size:24
Alignment explanation
Indices: 155196--155259 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
155186 ACGAGATTTA
* *
155196 TGATATGATACTTGACTTGGATTT
1 TGATATGATACTTGACATGGATTC
* *
155220 TTATATGATACATGACATGGATTC
1 TGATATGATACTTGACATGGATTC
*
155244 TGATATGCTACTTGAC
1 TGATATGATACTTGAC
155260 CTAAATTATG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (24 bp):
TGATATGATACTTGACATGGATTC
Found at i:161472 original size:29 final size:29
Alignment explanation
Indices: 161439--161513 Score: 114
Period size: 29 Copynumber: 2.6 Consensus size: 29
161429 CCCGTTGATC
161439 GGGTGCTATTTTAGTAATTATTTCTAAAA
1 GGGTGCTATTTTAGTAATTATTTCTAAAA
* *
161468 GGGTGCTATTTTTGTAATTATTTTTAAAA
1 GGGTGCTATTTTAGTAATTATTTCTAAAA
* *
161497 GGGTGTTATTTTCGTAA
1 GGGTGCTATTTTAGTAA
161514 AATGGTTGAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.27, C:0.05, G:0.20, T:0.48
Consensus pattern (29 bp):
GGGTGCTATTTTAGTAATTATTTCTAAAA
Found at i:162260 original size:24 final size:24
Alignment explanation
Indices: 162225--162297 Score: 85
Period size: 24 Copynumber: 3.0 Consensus size: 24
162215 ATTTTTGACG
162225 GGATTTTGATATGATACTTGACCT
1 GGATTTTGATATGATACTTGACCT
* *
162249 GGATTTTTATATGATA-TATGACAT
1 GGATTTTGATATGATACT-TGACCT
* * *
162273 GGATTCTGATCTGCTACTTGACCT
1 GGATTTTGATATGATACTTGACCT
162297 G
1 G
162298 AATTATGTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
23 1 0.03
24 38 0.95
25 1 0.03
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.41
Consensus pattern (24 bp):
GGATTTTGATATGATACTTGACCT
Found at i:162321 original size:2 final size:2
Alignment explanation
Indices: 162314--162348 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
162304 GTTTTAAATT
162314 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
162349 CCGTTATGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:184518 original size:21 final size:25
Alignment explanation
Indices: 184461--184518 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 25
184451 TTTGCAACCA
*
184461 ATTACAACACAAGCTCTAAGCCCAG
1 ATTACAACACAAGCTCCAAGCCCAG
*
184486 ATTAC-ACTCAAGC-CCAA-CCCAG
1 ATTACAACACAAGCTCCAAGCCCAG
184508 -TTACAAC-CAAG
1 ATTACAACACAAG
184519 ATCTAACCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
21 8 0.27
22 7 0.23
23 3 0.10
24 7 0.23
25 5 0.17
ACGTcount: A:0.40, C:0.34, G:0.10, T:0.16
Consensus pattern (25 bp):
ATTACAACACAAGCTCCAAGCCCAG
Found at i:184526 original size:22 final size:23
Alignment explanation
Indices: 184461--184530 Score: 65
Period size: 22 Copynumber: 3.0 Consensus size: 23
184451 TTTGCAACCA
184461 ATTACAACACAAGCTCTAAGCCCAG
1 ATTACAACACAAG-TCTAA-CCCAG
* * *
184486 ATTAC-ACTCAAGCCCAACCCAG
1 ATTACAACACAAGTCTAACCCAG
184508 -TTACAAC-CAAGATCTAACCCAG
1 ATTACAACACAAG-TCTAACCCAG
184530 A
1 A
184531 CCTGGCTCAG
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
21 8 0.22
22 15 0.41
23 3 0.08
24 6 0.16
25 5 0.14
ACGTcount: A:0.40, C:0.34, G:0.10, T:0.16
Consensus pattern (23 bp):
ATTACAACACAAGTCTAACCCAG
Found at i:185017 original size:10 final size:10
Alignment explanation
Indices: 185002--185036 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
184992 GACTCGGGGG
185002 GAGAAAGAAA
1 GAGAAAGAAA
*
185012 GAGAAA-AAG
1 GAGAAAGAAA
185021 GAGAAAGAAA
1 GAGAAAGAAA
185031 GAGAAA
1 GAGAAA
185037 AAGGAGAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (10 bp):
GAGAAAGAAA
Found at i:185055 original size:21 final size:19
Alignment explanation
Indices: 185001--185043 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
184991 AGACTCGGGG
185001 GGAGAAAGAAAGAGAAAAA
1 GGAGAAAGAAAGAGAAAAA
185020 GGAGAAAGAAAGAGAAAAA
1 GGAGAAAGAAAGAGAAAAA
185039 GGAGA
1 GGAGA
185044 GAGGGATAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (19 bp):
GGAGAAAGAAAGAGAAAAA
Found at i:189663 original size:12 final size:12
Alignment explanation
Indices: 189646--189691 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
189636 AAGCAGAGAG
189646 AAAAACAAAGAA
1 AAAAACAAAGAA
189658 AAAAACCAAAGAA
1 AAAAA-CAAAGAA
* *
189671 AAAACCCAAGAA
1 AAAAACAAAGAA
189683 AAAAACAAA
1 AAAAACAAA
189692 TAAGAAAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
12 18 0.62
13 11 0.38
ACGTcount: A:0.78, C:0.15, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAACAAAGAA
Found at i:190955 original size:35 final size:35
Alignment explanation
Indices: 190924--191009 Score: 109
Period size: 36 Copynumber: 2.4 Consensus size: 35
190914 AATTTGTCGA
190924 GCTTGAGACAGTTTTCTAAAAACAAATTTTGTCTC
1 GCTTGAGACAGTTTTCTAAAAACAAATTTTGTCTC
* * * * *
190959 GCTTGAGACAATTTCACTCAATACAAGTTTTGTCTC
1 GCTTGAGACAGTTT-TCTAAAAACAAATTTTGTCTC
*
190995 TCTTGAGACAGTTTT
1 GCTTGAGACAGTTTT
191010 TCTTGAAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
35 13 0.31
36 29 0.69
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (35 bp):
GCTTGAGACAGTTTTCTAAAAACAAATTTTGTCTC
Found at i:191102 original size:30 final size:30
Alignment explanation
Indices: 191068--191314 Score: 98
Period size: 30 Copynumber: 7.6 Consensus size: 30
191058 GCTTGAGAAA
191068 GTTTCTCTTGAAACAAAAATCTTTGAGTCT
1 GTTTCTCTTGAAACAAAAATCTTTGAGTCT
* * *** * *
191098 GTTTCCCTAGAAACAACTTTTGTTTCTCTTGAGACA
1 GTTTCTCTTGAAACAA-----AAATCT-TTGAGTCT
** * *
191134 GTTTCTCTTGAAACACCAGTCTTTAAGTCT
1 GTTTCTCTTGAAACAAAAATCTTTGAGTCT
* * *
191164 GTTTCTCTTGAAACAAAGTTTAGTCTCTCTTGAGACA
1 GTTTCTCTTGAAACAAA----A--ATCT-TTGAGTCT
* ** *
191201 CTTTCTCTTGAAACACCAATCTTTTAGTCT
1 GTTTCTCTTGAAACAAAAATCTTTGAGTCT
** * *
191231 GTTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACA
1 GTTTCTCTTGAAACAAA------AATCT-TTGAGTCT
* *
191268 GTTTCTCTTGAAACAAAAGTCTTTGAGTAT
1 GTTTCTCTTGAAACAAAAATCTTTGAGTCT
191298 GTTTCTCTTGAAACAAA
1 GTTTCTCTTGAAACAAA
191315 GTTTCGTCTC
Statistics
Matches: 155, Mismatches: 42, Indels: 40
0.65 0.18 0.17
Matches are distributed among these distances:
30 75 0.48
31 9 0.06
33 1 0.01
34 1 0.01
35 3 0.02
36 25 0.16
37 41 0.26
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.40
Consensus pattern (30 bp):
GTTTCTCTTGAAACAAAAATCTTTGAGTCT
Found at i:191214 original size:67 final size:67
Alignment explanation
Indices: 190983--191530 Score: 630
Period size: 66 Copynumber: 8.3 Consensus size: 67
190973 CACTCAATAC
* * *
190983 AAGTTTTGTCTCTCTTGAGACAGTTTTTCTTG--A-AAAAATCTTTGAGTATCTTTCCCTTGAAA
1 AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAAATCTTTGAGTCTGTTTCCCTTGAAA
191045 C-
66 CA
* * *
191046 AAGTTTTGTCTCGCTTGAGAAAGTTTCTCTTGAAACAAAAATCTTTGAGTCTGTTTCCCTAGAAA
1 AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAAATCTTTGAGTCTGTTTCCCTTGAAA
191111 C-
66 CA
* * ** * * *
191112 AACTTTTGTTTCTCTTGAGACAGTTTCTCTTGAAACACCAGTCTTTAAGTCTGTTTCTCTTGAAA
1 AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAAATCTTTGAGTCTGTTTCCCTTGAAA
191177 CA
66 CA
* * ** * *
191179 AAGTTTAGTCTCTCTTGAGACACTTTCTCTTGAAACACCAATCTTTTAGTCTGTTTCTCTTGAAA
1 AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAAATCTTTGAGTCTGTTTCCCTTGAAA
191244 CA
66 CA
* * *
191246 AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAAGTCTTTGAGTATGTTTCTCTTGAAA
1 AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAAATCTTTGAGTCTGTTTCCCTTGAAA
191311 CA
66 CA
* * * * * * *
191313 AAGTTTCGTCTCTCTTGAGACATTTTTTATTGAAA-AGAAAATCTTTGATTTTATTTCCCTTGAA
1 AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA-AAAATCTTTGAGTCTGTTTCCCTTGAA
191377 AC-
65 ACA
* * ** *
191379 AAGTTTTGTCTCGCTTGAGATAGTTTCTCTTGAAACACCAATCTTTGAAATC-GTTTCCCTTGAA
1 AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAAATCTTTG-AGTCTGTTTCCCTTGAA
*
191443 ACG
65 ACA
* * * ** *
191446 AA-TTTTGTCTCCCTTGAGACAGTTTATATTGAAACATGAATATTTGAGTCTGTTTCCCTTGAAA
1 AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAAATCTTTGAGTCTGTTTCCCTTGAAA
191510 CA
66 CA
*
191512 AA-TTTTATCTCTCTTGAGA
1 AAGTTTTGTCTCTCTTGAGA
191531 AATTATCCCT
Statistics
Matches: 416, Mismatches: 60, Indels: 15
0.85 0.12 0.03
Matches are distributed among these distances:
63 29 0.07
65 4 0.01
66 202 0.49
67 181 0.44
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (67 bp):
AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAAATCTTTGAGTCTGTTTCCCTTGAAA
CA
Found at i:191785 original size:131 final size:131
Alignment explanation
Indices: 191535--191894 Score: 355
Period size: 131 Copynumber: 2.7 Consensus size: 131
191525 TTGAGAAATT
* * * * * *
191535 ATCCCTAAAGATGACATGTCTTCCTCATCACGAATGAACTGTGTCATCCACTGACCAGACCTCTT
1 ATCCCTAAAGATG-CATATCATCCTCATCACGTATGAATTGTGTCATCCACCGACCAGACCTCCT
* * * *
191600 CATCACGTATGAGTCGCGTCACCCTTAGATAACCAGCCATCTTCATAACATAGGAAATGTGTTAT
65 CATCACGTAGGAGCCGCGTCACCCTTAGATAACCAGCCACCCTCATAACATAGGAAATGTGTTAT
191665 -C
130 AC
*
191666 ATCCCTAAAGATAGCATATCATCCTCATCACGTAGGAATTGTGTCATCCACCGACCAGACCTCCT
1 ATCCCTAAAGAT-GCATATCATCCTCATCACGTATGAATTGTGTCATCCACCGACCAGACCTCCT
* * * **** *
191731 CATCACGTAGGAGCCGCGTCATCCC-TAGATAACTAGTCACCCTCGTCGTGTAGGAACTGTGTTA
65 CATCACGTAGGAGCCGCGTCA-CCCTTAGATAACCAGCCACCCTCATAACATAGGAAATGTGTTA
191795 TCAAC
129 T--AC
* * * * * * * * *
191800 ATTCCATAAAGATGGCCTACCATCTTCATCGCATATGAATCGTGTCATCCACCGACCAGATCTTC
1 A-TCCCTAAAGAT-GCATATCATCCTCATCACGTATGAATTGTGTCATCCACCGACCAGACCTCC
* ** *
191865 TCATCACGTAAGAGTTGTGTCACCCTTAGA
64 TCATCACGTAGGAGCCGCGTCACCCTTAGA
191895 CGACCAGAAC
Statistics
Matches: 188, Mismatches: 34, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
131 105 0.56
132 4 0.02
134 5 0.03
135 74 0.39
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (131 bp):
ATCCCTAAAGATGCATATCATCCTCATCACGTATGAATTGTGTCATCCACCGACCAGACCTCCTC
ATCACGTAGGAGCCGCGTCACCCTTAGATAACCAGCCACCCTCATAACATAGGAAATGTGTTATA
C
Found at i:192090 original size:3 final size:3
Alignment explanation
Indices: 192082--192129 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
192072 GGTCTCAAAA
192082 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
192129 T
1 T
192130 TACATTATTT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:193817 original size:22 final size:22
Alignment explanation
Indices: 193766--193819 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
193756 CTTTAGGATA
* **
193766 ATTCTATGTGGTTCTTCGGGAC
1 ATTCTATGTGGTCCTTAAGGAC
193788 A-TCTATGTGGTCCTTAAGGAC
1 ATTCTATGTGGTCCTTAAGGAC
193809 ATTCTATGTGG
1 ATTCTATGTGG
193820 CACTTCGGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.39
Consensus pattern (22 bp):
ATTCTATGTGGTCCTTAAGGAC
Found at i:194255 original size:14 final size:15
Alignment explanation
Indices: 194236--194264 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
194226 AATTTAAGTC
194236 ATATG-TATTTTGTT
1 ATATGTTATTTTGTT
194250 ATATGTTATTTTGTT
1 ATATGTTATTTTGTT
194265 GGTATGTAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.21, C:0.00, G:0.14, T:0.66
Consensus pattern (15 bp):
ATATGTTATTTTGTT
Found at i:194587 original size:25 final size:25
Alignment explanation
Indices: 194553--194609 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
194543 AACAAAATAG
194553 TGAGAATTTCTGATCTGATAAGTAA
1 TGAGAATTTCTGATCTGATAAGTAA
194578 TGAGAATTTCTGATCTGATAAGTAA
1 TGAGAATTTCTGATCTGATAAGTAA
194603 TGAGAAT
1 TGAGAAT
194610 GATGTCTTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.37, C:0.07, G:0.21, T:0.35
Consensus pattern (25 bp):
TGAGAATTTCTGATCTGATAAGTAA
Found at i:203115 original size:12 final size:12
Alignment explanation
Indices: 203098--203139 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
203088 ATTGGGATTA
* *
203098 GGAGGTGAATAT
1 GGAGGTGAGTTT
*
203110 GGAGGTGGGTTT
1 GGAGGTGAGTTT
203122 GGAGGTGAGTTT
1 GGAGGTGAGTTT
203134 GGAGGT
1 GGAGGT
203140 CGGTTTGATC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.19, C:0.00, G:0.52, T:0.29
Consensus pattern (12 bp):
GGAGGTGAGTTT
Found at i:203125 original size:24 final size:24
Alignment explanation
Indices: 203098--203146 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
203088 ATTGGGATTA
*
203098 GGAGGTGAATATGGAGGTGGGTTT
1 GGAGGTGAATATGGAGGTCGGTTT
* *
203122 GGAGGTGAGTTTGGAGGTCGGTTT
1 GGAGGTGAATATGGAGGTCGGTTT
203146 G
1 G
203147 ATCGACTCGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.16, C:0.02, G:0.51, T:0.31
Consensus pattern (24 bp):
GGAGGTGAATATGGAGGTCGGTTT
Found at i:212065 original size:21 final size:21
Alignment explanation
Indices: 212041--212096 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
212031 ATTTGTCTCT
* *
212041 AAGGACCTTATGTATGTCCCG
1 AAGGACCTCATATATGTCCCG
212062 AAGGACCTCATATATGTCCCG
1 AAGGACCTCATATATGTCCCG
*
212083 AATGACCTCATATA
1 AAGGACCTCATATA
212097 ACCCTCGACT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (21 bp):
AAGGACCTCATATATGTCCCG
Found at i:214281 original size:30 final size:30
Alignment explanation
Indices: 214247--214317 Score: 97
Period size: 30 Copynumber: 2.4 Consensus size: 30
214237 TAAGATTGTT
* *
214247 CTGAATCACTTGAACTTTCTCTTCCACTTC
1 CTGAATCAATTGAACTTTCTCTTCAACTTC
* * *
214277 CTGAATCAATTGAACTTTTTCTTCAATTTT
1 CTGAATCAATTGAACTTTCTCTTCAACTTC
214307 CTGAATCAATT
1 CTGAATCAATT
214318 CAGGACCAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.25, C:0.24, G:0.07, T:0.44
Consensus pattern (30 bp):
CTGAATCAATTGAACTTTCTCTTCAACTTC
Found at i:215722 original size:55 final size:56
Alignment explanation
Indices: 215654--215763 Score: 195
Period size: 55 Copynumber: 2.0 Consensus size: 56
215644 GAGTCCAAGC
215654 AAATAATAAATCTTTCCTCATCAACTTAGTCAAA-GTAAAGCTATCATCGAAAAGA
1 AAATAATAAATCTTTCCTCATCAACTTAGTCAAAGGTAAAGCTATCATCGAAAAGA
* *
215709 AAATAATACATCTTTCCTCATCAACTTAGTCAAAGGTAAAGTTATCATCGAAAAG
1 AAATAATAAATCTTTCCTCATCAACTTAGTCAAAGGTAAAGCTATCATCGAAAAG
215764 TTCTTAACAA
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
55 33 0.63
56 19 0.37
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.28
Consensus pattern (56 bp):
AAATAATAAATCTTTCCTCATCAACTTAGTCAAAGGTAAAGCTATCATCGAAAAGA
Found at i:226057 original size:96 final size:98
Alignment explanation
Indices: 225893--226080 Score: 344
Period size: 96 Copynumber: 1.9 Consensus size: 98
225883 CCAACATTCT
225893 ATTTTAAGGCAAAAACCCTATTTTAGAGCACTTACAGTTTGTTAACTAATAAATTCCATCCACAT
1 ATTTTAAGGCAAAAACCCTATTTTAGAGCACTTACAGTTTGTTAACTAATAAATTCCATCCACAT
225958 A-GGGT-TTTTTTATCCCAAAATAAAAAATTAA
66 AGGGGTCTTTTTTATCCCAAAATAAAAAATTAA
* *
225989 ATTTTAAGGCAAAAATCCTATTTTAGAGCACTTACAGTTTGTTAACTAATAAATTTCATCCACAT
1 ATTTTAAGGCAAAAACCCTATTTTAGAGCACTTACAGTTTGTTAACTAATAAATTCCATCCACAT
226054 AGGGGTCTTTTTTATCCCAAAATAAAA
66 AGGGGTCTTTTTTATCCCAAAATAAAA
226081 TGTTAAGAGC
Statistics
Matches: 88, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
96 64 0.73
97 4 0.05
98 20 0.23
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.35
Consensus pattern (98 bp):
ATTTTAAGGCAAAAACCCTATTTTAGAGCACTTACAGTTTGTTAACTAATAAATTCCATCCACAT
AGGGGTCTTTTTTATCCCAAAATAAAAAATTAA
Found at i:226246 original size:17 final size:18
Alignment explanation
Indices: 226226--226267 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
226216 GCATGGTAAT
**
226226 AAAATTAA-TTGATTGAA
1 AAAATTAATTTGAAGGAA
*
226243 AAAAATAATTTGAAGGAA
1 AAAATTAATTTGAAGGAA
226261 AAAATTA
1 AAAATTA
226268 CTGCCCAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.60, C:0.00, G:0.12, T:0.29
Consensus pattern (18 bp):
AAAATTAATTTGAAGGAA
Found at i:227929 original size:2 final size:2
Alignment explanation
Indices: 227924--227958 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
227914 TAAAAATGAA
*
227924 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
227959 AAGAGGAAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:230925 original size:2 final size:2
Alignment explanation
Indices: 230918--230945 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
230908 CTATAGAATT
230918 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
230946 GCTTCAATTT
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:232344 original size:20 final size:21
Alignment explanation
Indices: 232319--232411 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
232309 TTTTCCCAAT
*
232319 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
232339 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
232360 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
232380 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
232401 TCGCAATGCGA
1 TCGCAATGCGA
232412 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:232425 original size:20 final size:19
Alignment explanation
Indices: 232400--232514 Score: 77
Period size: 20 Copynumber: 5.7 Consensus size: 19
232390 AATTGGGAAA
*
232400 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACT-ACT
* * *
232420 ATCGCAATGCGATAATACAAA
1 ATCGCAACGCGATACTAC--T
* *
232441 ATCGTAACGAGATACTTACT
1 ATCGCAACGCGATAC-TACT
*
232461 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACT-ACT
* *
232481 TTCGCAACGCGATAATACAT
1 ATCGCAACGCGATACTAC-T
*
232501 AATCGCAATGCGAT
1 -ATCGCAACGCGAT
232515 TTTCAAAGCG
Statistics
Matches: 76, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
19 5 0.07
20 46 0.61
21 22 0.29
22 3 0.04
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.24
Consensus pattern (19 bp):
ATCGCAACGCGATACTACT
Found at i:232426 original size:41 final size:41
Alignment explanation
Indices: 232319--232411 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
232309 TTTTCCCAAT
232319 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
232360 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
232401 TCGCAATGCGA
1 TCGCAATGCGA
232412 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:232442 original size:41 final size:41
Alignment explanation
Indices: 232397--232474 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
232387 GCGAATTGGG
* * *
232397 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAC
* * *
232438 AAAATCGTAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA
232475 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAC
Found at i:232710 original size:22 final size:22
Alignment explanation
Indices: 232682--232725 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
232672 CACTCTCTCA
232682 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
* *
232704 CCCATCTCTGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
232726 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:233013 original size:20 final size:20
Alignment explanation
Indices: 232988--233026 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
232978 GCGATTCTCT
232988 TGTTGCGATAGTCATTTTCG
1 TGTTGCGATAGTCATTTTCG
**
233008 TGTTGCGATTTTCATTTTC
1 TGTTGCGATAGTCATTTTC
233027 AGAAACTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.15, G:0.21, T:0.51
Consensus pattern (20 bp):
TGTTGCGATAGTCATTTTCG
Found at i:234368 original size:18 final size:18
Alignment explanation
Indices: 234347--234391 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
234337 TCCACTTCGG
*
234347 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
234365 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
234383 GAGCCATCA
1 GAGCCATCA
234392 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:234648 original size:13 final size:13
Alignment explanation
Indices: 234630--234656 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
234620 TGGCGTGTTG
234630 AGGTGTCTACATT
1 AGGTGTCTACATT
234643 AGGTGTCTACATT
1 AGGTGTCTACATT
234656 A
1 A
234657 CGCGGTAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (13 bp):
AGGTGTCTACATT
Found at i:234946 original size:19 final size:20
Alignment explanation
Indices: 234903--234958 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
234893 ACGAAAATGA
234903 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
234923 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
**
234942 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
234959 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:234966 original size:14 final size:14
Alignment explanation
Indices: 234947--235036 Score: 81
Period size: 14 Copynumber: 5.9 Consensus size: 14
234937 ATGCGAAATG
234947 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
234961 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
234977 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
* *
234993 AAAATCGCAATGAGAA
1 AAAATCGCAA--CGAC
235009 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
235025 AAAATCGCAACG
1 AAAATCGCAACG
235037 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
14 30 0.48
16 14 0.23
18 18 0.29
ACGTcount: A:0.49, C:0.22, G:0.18, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:234989 original size:32 final size:33
Alignment explanation
Indices: 234931--235053 Score: 214
Period size: 32 Copynumber: 3.8 Consensus size: 33
234921 GGAAATGGCT
234931 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
234964 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
234996 ATCGCAATGAGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
235028 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
235054 TGCGATTTGT
Statistics
Matches: 86, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
32 61 0.71
33 25 0.29
ACGTcount: A:0.48, C:0.21, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:235089 original size:14 final size:14
Alignment explanation
Indices: 235070--235126 Score: 69
Period size: 14 Copynumber: 3.8 Consensus size: 14
235060 TTGTGTTTCG
235070 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
235084 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
235100 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
235116 CGTTGCGATTT
1 CGTTGCGATTT
235127 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 22 0.59
16 4 0.11
18 11 0.30
ACGTcount: A:0.09, C:0.18, G:0.26, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:235104 original size:32 final size:32
Alignment explanation
Indices: 235065--235142 Score: 147
Period size: 32 Copynumber: 2.4 Consensus size: 32
235055 GCGATTTGTG
235065 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
235097 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
*
235129 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
235143 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.46
Consensus pattern (32 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
Found at i:235161 original size:20 final size:19
Alignment explanation
Indices: 235127--235181 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
235117 GTTGCGATTT
*
235127 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
235146 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
235166 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
235182 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:237091 original size:13 final size:13
Alignment explanation
Indices: 237044--237096 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
237034 TTGATTGTTT
237044 AATTGATTTGTAA
1 AATTGATTTGTAA
*
237057 AAGATGATTTGTAA
1 AA-TTGATTTGTAA
**
237071 ATATTGATTTGTTT
1 A-ATTGATTTGTAA
*
237085 AATTGATGTGTA
1 AATTGATTTGTA
237097 CATAATTTGT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
13 11 0.34
14 20 0.62
15 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (13 bp):
AATTGATTTGTAA
Found at i:237221 original size:19 final size:19
Alignment explanation
Indices: 237199--237266 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
237189 ATCGCAACGA
237199 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
237218 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
237237 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
237251 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
237267 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:237341 original size:20 final size:20
Alignment explanation
Indices: 237285--237342 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
237275 TCGCATTGCG
* *
237285 ATTTTCTCGTTGCGATTGCC
1 ATTTTCGCGTTGCGATAGCC
*
237305 ATTTTCGAGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
237325 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
237343 TCAAATGAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.40
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:238447 original size:24 final size:24
Alignment explanation
Indices: 238391--238449 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
238381 AGTCAGTATT
* *
238391 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATATTGGTCAATACA
* *
238415 CGGACTTTGATATTGGTCAATACA
1 CGAAATTTGATATTGGTCAATACA
*
238439 CGAATTTTGAT
1 CGAAATTTGAT
238450 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (24 bp):
CGAAATTTGATATTGGTCAATACA
Found at i:238641 original size:12 final size:12
Alignment explanation
Indices: 238624--238648 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
238614 ATATAATCCT
238624 GAAGAAGAAAAA
1 GAAGAAGAAAAA
238636 GAAGAAGAAAAA
1 GAAGAAGAAAAA
238648 G
1 G
238649 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:240963 original size:19 final size:19
Alignment explanation
Indices: 240941--241032 Score: 78
Period size: 19 Copynumber: 5.4 Consensus size: 19
240931 GGAAATTACT
240941 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
240960 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
240974 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
240993 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
241007 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
241026 ATCGCAA
1 ATCGCAA
241033 CGAGGGAATC
Statistics
Matches: 55, Mismatches: 8, Indels: 20
0.66 0.10 0.24
Matches are distributed among these distances:
14 18 0.33
15 2 0.04
16 4 0.07
17 4 0.07
18 2 0.04
19 25 0.45
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:240983 original size:33 final size:33
Alignment explanation
Indices: 240941--241067 Score: 184
Period size: 33 Copynumber: 3.8 Consensus size: 33
240931 GGAAATTACT
240941 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
240974 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
241006 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
241040 ATCGCAACGTGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
241068 CGAATTTAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
32 1 0.01
33 81 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:241054 original size:66 final size:66
Alignment explanation
Indices: 240942--241074 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
240932 GAAATTACTA
* *
240942 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGCGAAT
241007 T
66 T
* *
241008 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAACGTGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGCGAAT
241073 T
66 T
241074 T
1 T
241075 AATTTCGCGT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:241089 original size:19 final size:20
Alignment explanation
Indices: 241067--241109 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
241057 AAATCGCAAC
241067 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
241086 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
241106 GCGA
1 GCGA
241110 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Done.