Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold365
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: 425848
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.31
Warning! 31381 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:300273 original size:6 final size:6
Alignment explanation
Indices: 300262--300287 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
300252 GTGTGTCGAA
300262 TACTGT TACTGT TACTGT TACTGT TA
1 TACTGT TACTGT TACTGT TACTGT TA
300288 TCGATTCGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.15, G:0.15, T:0.50
Consensus pattern (6 bp):
TACTGT
Found at i:300283 original size:45 final size:45
Alignment explanation
Indices: 300189--300383 Score: 214
Period size: 45 Copynumber: 4.2 Consensus size: 45
300179 ATTTGCCGGC
* * * *
300189 TTACTGATTAGACAC-TTATGTGTCGACTACTGTTACTGTTACTAA
1 TTACTGATTCGACACTTTGTGTGTCGAATACTGTTACTGTTACT-G
300234 TTACTGATTCGACACTTTGTGTGTCGAATACTGTTACTGTTACTG
1 TTACTGATTCGACACTTTGTGTGTCGAATACTGTTACTGTTACTG
* * *
300279 TTACTGTTATCGATTCGGCGCTTTGTGTGTCGAATACTGTTACTATTACTG
1 TTAC-----T-GATTCGACACTTTGTGTGTCGAATACTGTTACTGTTACTG
* **
300330 TTACAGATTC-AGCACTTTGTGTGTTTAATACTGTTACTGTTACTG
1 TTACTGATTCGA-CACTTTGTGTGTCGAATACTGTTACTGTTACTG
300375 TTACTGATT
1 TTACTGATT
300384 ACTGTTTACT
Statistics
Matches: 128, Mismatches: 14, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
45 60 0.47
46 26 0.20
50 1 0.01
51 41 0.32
ACGTcount: A:0.22, C:0.17, G:0.18, T:0.43
Consensus pattern (45 bp):
TTACTGATTCGACACTTTGTGTGTCGAATACTGTTACTGTTACTG
Found at i:300308 original size:51 final size:50
Alignment explanation
Indices: 300216--300385 Score: 206
Period size: 51 Copynumber: 3.4 Consensus size: 50
300206 ATGTGTCGAC
* *
300216 TACTGTTACTGTTACTAATTACTGATTCGACACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACT-GTTAC-GATTCGGCACTTTGTGTGTCGAATACTGT
*
300268 TACTGTTACTGTTACTGTTATCGATTCGGCGCTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACTGTTA-CGATTCGGCACTTTGTGTGTCGAATACTGT
* * **
300319 TACTATTACTGTTAC----A-GATTCAGCACTTTGTGTGTTTAATACTGT
1 TACTGTTACTGTTACTGTTACGATTCGGCACTTTGTGTGTCGAATACTGT
300364 TACTGTTACTGTTACTGATTAC
1 TACTGTTACTGTTACTG-TTAC
300386 TGTTTACTGG
Statistics
Matches: 102, Mismatches: 9, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
45 39 0.38
47 1 0.01
50 1 0.01
51 44 0.43
52 17 0.17
ACGTcount: A:0.21, C:0.17, G:0.18, T:0.44
Consensus pattern (50 bp):
TACTGTTACTGTTACTGTTACGATTCGGCACTTTGTGTGTCGAATACTGT
Found at i:300387 original size:7 final size:6
Alignment explanation
Indices: 300358--300394 Score: 56
Period size: 6 Copynumber: 5.8 Consensus size: 6
300348 GTGTGTTTAA
300358 TACTGT TACTGT TACTGT TACTGAT TACTGTT TACTG
1 TACTGT TACTGT TACTGT TACTG-T TACTG-T TACTG
300395 GTGTGTTTGG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
6 17 0.59
7 12 0.41
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.49
Consensus pattern (6 bp):
TACTGT
Found at i:300617 original size:13 final size:15
Alignment explanation
Indices: 300599--300630 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
300589 TATATGAAAT
300599 AATGATT-TT-ATGA
1 AATGATTATTGATGA
300612 AATGATTATTGATGA
1 AATGATTATTGATGA
300627 AATG
1 AATG
300631 CATGAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 2 0.12
15 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (15 bp):
AATGATTATTGATGA
Found at i:303884 original size:25 final size:24
Alignment explanation
Indices: 303855--303921 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
303845 ACTCACCACA
*
303855 GCTCTTATGAGCGTCTCGTTATATG
1 GCTCTTATGAGCTTCTCGTT-TATG
*
303880 GCTCTCT-TGAGCTTCTAGTTTATG
1 GCTCT-TATGAGCTTCTCGTTTATG
* *
303904 GCTCGTATTAGCTTCTCG
1 GCTCTTATGAGCTTCTCG
303922 ATAATTGGCT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
23 1 0.03
24 17 0.49
25 16 0.46
26 1 0.03
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.42
Consensus pattern (24 bp):
GCTCTTATGAGCTTCTCGTTTATG
Found at i:303941 original size:25 final size:26
Alignment explanation
Indices: 303913--304017 Score: 82
Period size: 25 Copynumber: 4.2 Consensus size: 26
303903 GGCTCGTATT
303913 AGCTTCT-CGA-TAATTGGCTCTCACG
1 AGCTTCTCCGATTAA-TGGCTCTCACG
*
303938 AGCTT-TCCGATTAATAGCTCTTCA-G
1 AGCTTCTCCGATTAATGGCTC-TCACG
* * * *
303963 AGCTTCT-TGA-TATTGGCTCGCATG
1 AGCTTCTCCGATTAATGGCTCTCACG
303987 AGCTT-TCCGATTAATGGCTCTC-CAG
1 AGCTTCTCCGATTAATGGCTCTCAC-G
304012 AGCTTC
1 AGCTTC
304018 CCGTTTATAG
Statistics
Matches: 62, Mismatches: 9, Indels: 17
0.70 0.10 0.19
Matches are distributed among these distances:
23 3 0.05
24 16 0.26
25 36 0.58
26 7 0.11
ACGTcount: A:0.20, C:0.26, G:0.20, T:0.34
Consensus pattern (26 bp):
AGCTTCTCCGATTAATGGCTCTCACG
Found at i:303978 original size:49 final size:50
Alignment explanation
Indices: 303913--304017 Score: 158
Period size: 49 Copynumber: 2.1 Consensus size: 50
303903 GGCTCGTATT
* *
303913 AGCTTCTCGATAATTGGCTCTCACGAGCTTTCCGATTAATAGCTCTTCAG
1 AGCTTCTCGATAATTGGCTCGCACGAGCTTTCCGATTAATAGCTCTCCAG
* * *
303963 AGCTTCTTGAT-ATTGGCTCGCATGAGCTTTCCGATTAATGGCTCTCCAG
1 AGCTTCTCGATAATTGGCTCGCACGAGCTTTCCGATTAATAGCTCTCCAG
304012 AGCTTC
1 AGCTTC
304018 CCGTTTATAG
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
49 40 0.80
50 10 0.20
ACGTcount: A:0.20, C:0.26, G:0.20, T:0.34
Consensus pattern (50 bp):
AGCTTCTCGATAATTGGCTCGCACGAGCTTTCCGATTAATAGCTCTCCAG
Found at i:304039 original size:49 final size:49
Alignment explanation
Indices: 303937--304048 Score: 118
Period size: 49 Copynumber: 2.3 Consensus size: 49
303927 TGGCTCTCAC
* ** * ** *
303937 GAGCTTTCCGATTAATAGCTCTTCAGAGCTTCTTGATATTGGCTCGCAT
1 GAGCTTTCCGATTAATAGCTCTCCAGAGCTTCCCGATATTAGCTCAAAA
* *
303986 GAGCTTTCCGATTAATGGCTCTCCAGAGCTTCCCG-TTTATAGCTCAAAA
1 GAGCTTTCCGATTAATAGCTCTCCAGAGCTTCCCGATAT-TAGCTCAAAA
*
304035 GAGCTTCCCGATTA
1 GAGCTTTCCGATTA
304049 CATGCTCCTA
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
48 2 0.04
49 50 0.96
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (49 bp):
GAGCTTTCCGATTAATAGCTCTCCAGAGCTTCCCGATATTAGCTCAAAA
Found at i:304801 original size:17 final size:17
Alignment explanation
Indices: 304781--305100 Score: 211
Period size: 17 Copynumber: 18.2 Consensus size: 17
304771 ATAATTATTT
304781 TTTTGAAAACACGAAAA
1 TTTTGAAAACACGAAAA
* *
304798 TTTTTTAAAACACGACAA
1 -TTTTGAAAACACGAAAA
*
304816 TTTT-AGAGACACGAAAA
1 TTTTGA-AAACACGAAAA
* *
304833 TTCATAAAAACACGAAAA
1 TT-TTGAAAACACGAAAA
*
304851 TTTTTGAAAACACGGAAA
1 -TTTTGAAAACACGAAAA
* * * *
304869 TTTTTAAAACAGGGAAT
1 TTTTGAAAACACGAAAA
*
304886 TTTTGAAAACATGAAAA
1 TTTTGAAAACACGAAAA
*
304903 TTTTTG-AAACACGAAATT
1 -TTTTGAAAACACGAAA-A
304921 TTTTGGAAAACACGAAAAAAAA
1 TTTT-GAAAACACG----AAAA
** * *
304943 TTTTGATCATA-GAAAT
1 TTTTGAAAACACGAAAA
*
304959 TTTTGAAAACACGAAAG
1 TTTTGAAAACACGAAAA
* *
304976 TTTTTAAAACACCGAAAT
1 TTTTGAAAACA-CGAAAA
* *
304994 TTTTGAAAACACGAGGAT
1 TTTTGAAAACACGA-AAA
305012 TTTTGAAAACACGAAAA
1 TTTTGAAAACACGAAAA
* *
305029 TTTTCAAAACACTG-GAA
1 TTTTGAAAACAC-GAAAA
*
305046 TTTTGAAAACACGAAGAT
1 TTTTGAAAACACGAA-AA
* *
305064 TTTTG-AAACATGAGAAT
1 TTTTGAAAACACGA-AAA
*
305081 TTTTGAAGACACG-AAA
1 TTTTGAAAACACGAAAA
305097 TTTT
1 TTTT
305101 TTTTTTTGAA
Statistics
Matches: 240, Mismatches: 42, Indels: 42
0.74 0.13 0.13
Matches are distributed among these distances:
16 19 0.08
17 111 0.46
18 88 0.37
19 10 0.04
20 1 0.00
21 4 0.02
22 4 0.02
23 3 0.01
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.29
Consensus pattern (17 bp):
TTTTGAAAACACGAAAA
Found at i:304801 original size:18 final size:18
Alignment explanation
Indices: 304780--305167 Score: 284
Period size: 18 Copynumber: 21.5 Consensus size: 18
304770 AATAATTATT
304780 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
* *
304798 TTTTTTAAAACACGACAA
1 TTTTTGAAAACACGAAAA
* *
304816 TTTTAG-AGACACGAAAA
1 TTTTTGAAAACACGAAAA
** *
304833 TTCATAAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
304851 TTTTTGAAAACACGGAAA
1 TTTTTGAAAACACGAAAA
**
304869 TTTTT-AAAACA-GGGAA
1 TTTTTGAAAACACGAAAA
*
304885 TTTTTGAAAACATGAAAA
1 TTTTTGAAAACACGAAAA
*
304903 TTTTTG-AAACACGAAAT
1 TTTTTGAAAACACGAAAA
304920 TTTTTGGAAAACACGAAAAAAA
1 TTTTT-GAAAACACG---AAAA
* ** *
304942 ATTTTGATCATA-G-AAA
1 TTTTTGAAAACACGAAAA
*
304958 TTTTTGAAAACACGAAAG
1 TTTTTGAAAACACGAAAA
304976 TTTTT-AAAACACCG-AAA
1 TTTTTGAAAACA-CGAAAA
**
304993 TTTTTGAAAACACGAGGA
1 TTTTTGAAAACACGAAAA
305011 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
* *
305029 -TTTTCAAAACACTG-GAA
1 TTTTTGAAAACAC-GAAAA
*
305046 -TTTTGAAAACACGAAGA
1 TTTTTGAAAACACGAAAA
* *
305063 TTTTTG-AAACATGAGAA
1 TTTTTGAAAACACGAAAA
* *
305080 TTTTTGAAGACACGAAATTTTTT
1 TTTTTGAAAACACGAAA-----A
305103 TTTTTGAAAACA--AAGAA
1 TTTTTGAAAACACGAA-AA
*
305120 TTTTTGAAATACGA-GAAATT
1 TTTTTGAAA-AC-ACGAAA-A
305140 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
305158 TTTTTTGAAA
1 -TTTTTGAAA
305168 CAGGATTTTT
Statistics
Matches: 290, Mismatches: 51, Indels: 57
0.73 0.13 0.14
Matches are distributed among these distances:
16 21 0.07
17 101 0.35
18 107 0.37
19 24 0.08
20 12 0.04
21 6 0.02
22 8 0.03
23 11 0.04
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.31
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:304828 original size:35 final size:34
Alignment explanation
Indices: 304780--305101 Score: 274
Period size: 35 Copynumber: 9.1 Consensus size: 34
304770 AATAATTATT
304780 TTTTTGAAAACACGAAAATTTTTTAAAACACGACAA
1 TTTTTGAAAACACGAAAA-TTTTTAAAACACGA-AA
* * * *
304816 TTTTAG-AGACACGAAAATTCATAAAAACACGAAAA
1 TTTTTGAAAACACGAAAATT-TTTAAAACACG-AAA
* * *
304851 TTTTTGAAAACACGGAAATTTTTAAAACAGGGAA
1 TTTTTGAAAACACGAAAATTTTTAAAACACGAAA
* *
304885 TTTTTGAAAACATGAAAATTTTTGAAACACGAAA
1 TTTTTGAAAACACGAAAATTTTTAAAACACGAAA
* * * *
304919 TTTTTTGGAAAACACGAAAAAAAATTTT-GATCATAGAAA
1 -TTTTT-GAAAACACG---AAAATTTTTAAAACA-CGAAA
*
304958 TTTTTGAAAACACGAAAGTTTTTAAAACACCGAAA
1 TTTTTGAAAACACGAAAATTTTTAAAACA-CGAAA
**
304993 TTTTTGAAAACACGAGGATTTTTGAAAACACGAAA
1 TTTTTGAAAACACGAAAATTTTT-AAAACACGAAA
* * * *
305028 ATTTTCAAAACACTG-GAATTTTGAAAACACGAAGA
1 TTTTTGAAAACAC-GAAAATTTTTAAAACACGAA-A
* * *
305063 TTTTTG-AAACATGAGAATTTTTGAAGACACGAAA
1 TTTTTGAAAACACGAAAATTTTT-AAAACACGAAA
305097 TTTTT
1 TTTTT
305102 TTTTTTGAAA
Statistics
Matches: 232, Mismatches: 39, Indels: 32
0.77 0.13 0.11
Matches are distributed among these distances:
33 1 0.00
34 68 0.29
35 102 0.44
36 32 0.14
37 9 0.04
38 8 0.03
39 12 0.05
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (34 bp):
TTTTTGAAAACACGAAAATTTTTAAAACACGAAA
Found at i:305102 original size:35 final size:35
Alignment explanation
Indices: 304780--305167 Score: 269
Period size: 35 Copynumber: 10.8 Consensus size: 35
304770 AATAATTATT
* *
304780 TTTTTGAAAACACGAAAATTTTTTAAAACACGACAA
1 TTTTTGAAAACACGAGAATTTTTGAAAACACGA-AA
* * * ** *
304816 TTTTAG-AGACACGAAAATTCATAAAAACACGAAAA
1 TTTTTGAAAACACGAGAATTTTTGAAAACACG-AAA
* *
304851 TTTTTGAAAACACG-GAAATTTTT-AAAACAGGGAA
1 TTTTTGAAAACACGAG-AATTTTTGAAAACACGAAA
* *
304885 TTTTTGAAAACATGAAAATTTTTG-AAACACGAAA
1 TTTTTGAAAACACGAGAATTTTTGAAAACACGAAA
* * ** *
304919 TTTTTTGGAAAACACGAAAAAAAATTTTGATCATA-GAAA
1 -TTTTT-GAAAACACG---AGAATTTTTGAAAACACGAAA
304958 TTTTTGAAAACACGA-AAGTTTTT-AAAACACCGAAA
1 TTTTTGAAAACACGAGAA-TTTTTGAAAACA-CGAAA
*
304993 TTTTTGAAAACACGAGGATTTTTGAAAACACGAAA
1 TTTTTGAAAACACGAGAATTTTTGAAAACACGAAA
* *
305028 ATTTTCAAAACACTG-GAA-TTTTGAAAACACGAAGA
1 TTTTTGAAAACAC-GAGAATTTTTGAAAACACGAA-A
* *
305063 TTTTTG-AAACATGAGAATTTTTGAAGACACGAAA
1 TTTTTGAAAACACGAGAATTTTTGAAAACACGAAA
*
305097 TTTTTTTTTTTGAAAACA-AAGAATTTTTGAAATACGA-GAAA
1 ------TTTTTGAAAACACGAGAATTTTTGAAA-AC-ACGAAA
*
305138 TTTTTTTGAAAACACGAAAATTTTTTGAAA
1 --TTTTTGAAAACACGAGAA-TTTTTGAAA
305168 CAGGATTTTT
Statistics
Matches: 284, Mismatches: 37, Indels: 59
0.75 0.10 0.16
Matches are distributed among these distances:
33 6 0.02
34 59 0.21
35 101 0.36
36 33 0.12
37 23 0.08
38 8 0.03
39 22 0.08
40 20 0.07
41 11 0.04
42 1 0.00
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.31
Consensus pattern (35 bp):
TTTTTGAAAACACGAGAATTTTTGAAAACACGAAA
Found at i:305120 original size:40 final size:40
Alignment explanation
Indices: 305063--305144 Score: 105
Period size: 40 Copynumber: 2.0 Consensus size: 40
305053 AACACGAAGA
* *
305063 TTTTTGAAACATGAGAATTTTTGAAGACACGA-AATTTTTT
1 TTTTTGAAACATAAGAATTTTTGAA-ACACGAGAAATTTTT
*
305103 TTTTTGAAAACA-AAGAATTTTTGAAATACGAGAAATTTTT
1 TTTTTG-AAACATAAGAATTTTTGAAACACGAGAAATTTTT
305143 TT
1 TT
305145 GAAAACACGA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
39 5 0.14
40 27 0.73
41 5 0.14
ACGTcount: A:0.38, C:0.06, G:0.13, T:0.43
Consensus pattern (40 bp):
TTTTTGAAACATAAGAATTTTTGAAACACGAGAAATTTTT
Found at i:305179 original size:37 final size:37
Alignment explanation
Indices: 305063--305180 Score: 100
Period size: 37 Copynumber: 3.1 Consensus size: 37
305053 AACACGAAGA
* *
305063 TTTTTG-AAACATGAGAATTTTTGAAGACACGAAATTTTTT
1 TTTTTGAAAACA-AAGAATTTTTGAA-ACACGAGA--TTTT
* **
305103 TTTTTGAAAACAAAGAATTTTTGAAATACGAGAAATT
1 TTTTTGAAAACAAAGAATTTTTGAAACACGAGATTTT
305140 TTTTTGAAAACACGAA-AATTTTTTGAAACA-G-GATTTT
1 TTTTTGAAAACA--AAGAA-TTTTTGAAACACGAGATTTT
305177 TTTT
1 TTTT
305181 AAGAAGTACC
Statistics
Matches: 66, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
37 22 0.33
38 3 0.05
39 18 0.27
40 18 0.27
41 5 0.08
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.42
Consensus pattern (37 bp):
TTTTTGAAAACAAAGAATTTTTGAAACACGAGATTTT
Found at i:305306 original size:15 final size:16
Alignment explanation
Indices: 305290--305321 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
305280 TGATTCTATT
305290 AAAACACGAGAATTTAA
1 AAAACACGAGAATTT-A
305307 AAAACACGAGAATTT
1 AAAACACGAGAATTT
305322 TAGAATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.19
Consensus pattern (16 bp):
AAAACACGAGAATTTA
Found at i:305478 original size:21 final size:20
Alignment explanation
Indices: 305439--305481 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
305429 CCTTATTTAT
*
305439 TAAAATTATTTAAAATAAAA
1 TAAAATTAATTAAAATAAAA
*
305459 TAAAATTGAATTAAATTAAAA
1 TAAAATT-AATTAAAATAAAA
305480 TA
1 TA
305482 TAGATACAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (20 bp):
TAAAATTAATTAAAATAAAA
Found at i:305665 original size:9 final size:9
Alignment explanation
Indices: 305648--305678 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
305638 TTTTTTTCTG
305648 TTCTCTTTT
1 TTCTCTTTT
*
305657 TTCTTTTTT
1 TTCTCTTTT
305666 TTCTCTTTT
1 TTCTCTTTT
305675 TTCT
1 TTCT
305679 TCTCTCTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (9 bp):
TTCTCTTTT
Found at i:305669 original size:18 final size:18
Alignment explanation
Indices: 305633--305679 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
305623 CAAATTGAAC
305633 CTCTTTTTT-TTTCTGTT
1 CTCTTTTTTCTTTCTGTT
* *
305650 CTCTTTTTTCTTTTTTTT
1 CTCTTTTTTCTTTCTGTT
305668 CTCTTTTTTCTT
1 CTCTTTTTTCTT
305680 CTCTCTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 9 0.33
18 18 0.67
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (18 bp):
CTCTTTTTTCTTTCTGTT
Found at i:305692 original size:18 final size:17
Alignment explanation
Indices: 305636--305694 Score: 61
Period size: 18 Copynumber: 3.5 Consensus size: 17
305626 ATTGAACCTC
305636 TTTTTTTTTCTGTTCTCT
1 TTTTTTTTTCT-TTCTCT
*
305654 TTTTTCTTTTTTTTCTC-
1 TTTTT-TTTTCTTTCTCT
*
305671 TTTTTTCTTC--TCTCT
1 TTTTTTTTTCTTTCTCT
305686 TTTTTTTTT
1 TTTTTTTTT
305695 GACCTGCTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
14 4 0.11
15 8 0.23
16 3 0.09
17 5 0.14
18 10 0.29
19 5 0.14
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (17 bp):
TTTTTTTTTCTTTCTCT
Found at i:305991 original size:4 final size:4
Alignment explanation
Indices: 305982--306052 Score: 72
Period size: 4 Copynumber: 17.0 Consensus size: 4
305972 TTTTTATTTT
* *
305982 TTTC TTTC TTTT TCTTC -TTC ATTC TTTC TTTC TTTC TTTC TTCTC TTTTC
1 TTTC TTTC TTTC T-TTC TTTC TTTC TTTC TTTC TTTC TTTC TT-TC -TTTC
*
306032 TTTC TCTTT TTTC TTTC TTTC
1 TTTC T-TTC TTTC TTTC TTTC
306053 CCGATCAGCC
Statistics
Matches: 57, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
3 3 0.05
4 43 0.75
5 9 0.16
6 2 0.04
ACGTcount: A:0.01, C:0.25, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTC
Found at i:306178 original size:13 final size:13
Alignment explanation
Indices: 306153--306191 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
306143 CTTTCCCTCA
306153 TCTTTCTTCTTTTC
1 TCTTTC-TCTTTTC
*
306167 TCTTTCTCTTTTT
1 TCTTTCTCTTTTC
*
306180 TTTTTCTCTTTT
1 TCTTTCTCTTTT
306192 GCTTGTTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 17 0.74
14 6 0.26
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TCTTTCTCTTTTC
Found at i:306220 original size:37 final size:35
Alignment explanation
Indices: 306167--306235 Score: 95
Period size: 37 Copynumber: 1.9 Consensus size: 35
306157 TCTTCTTTTC
306167 TCTTTCTCTTTTTTTTTT-CTCTTTTGCTTGTTGTT
1 TCTTTCTCTTTTTTTTTTGCT-TTTTGCTTGTTGTT
*
306202 TCTTTCTCTTTTTTTTTTTTGCTTTTTGGTTGTT
1 TCTTTCTC--TTTTTTTTTTGCTTTTTGCTTGTT
306236 TTGCTAGTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
35 8 0.27
37 20 0.67
38 2 0.07
ACGTcount: A:0.00, C:0.14, G:0.10, T:0.75
Consensus pattern (35 bp):
TCTTTCTCTTTTTTTTTTGCTTTTTGCTTGTTGTT
Found at i:306334 original size:11 final size:11
Alignment explanation
Indices: 306305--306339 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
306295 GGCGGTATGC
306305 CTTTTTTTGCT
1 CTTTTTTTGCT
*
306316 ACTGTTTTTGCT
1 -CTTTTTTTGCT
306328 CTTTTTTTGCT
1 CTTTTTTTGCT
306339 C
1 C
306340 AAAATTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.03, C:0.20, G:0.11, T:0.66
Consensus pattern (11 bp):
CTTTTTTTGCT
Found at i:306655 original size:59 final size:60
Alignment explanation
Indices: 306587--306701 Score: 162
Period size: 59 Copynumber: 1.9 Consensus size: 60
306577 GAAATGGCCA
* * *
306587 AAATGTAATTTAT-AGAAAGTTTAGGGGCCCAAATGTAA-TTTAGAAAAGTTTAGGGGTAG
1 AAATGTAATTT-TGAAAAAGTTTAGGGGCCAAAATGCAATTTTAGAAAAGTTTAGGGGTAG
* *
306646 AAATGTAATTTTGAAAAATTTTAGGGGTCAAAATGCAATTTTAGAAAAGTTTAGGG
1 AAATGTAATTTTGAAAAAGTTTAGGGGCCAAAATGCAATTTTAGAAAAGTTTAGGG
306702 TCAAAATGCA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
58 1 0.02
59 31 0.63
60 17 0.35
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.32
Consensus pattern (60 bp):
AAATGTAATTTTGAAAAAGTTTAGGGGCCAAAATGCAATTTTAGAAAAGTTTAGGGGTAG
Found at i:306712 original size:29 final size:30
Alignment explanation
Indices: 306585--306709 Score: 152
Period size: 30 Copynumber: 4.2 Consensus size: 30
306575 AGGAAATGGC
*
306585 CAAAATGTAATTTATAG-AAAGTTTAGGGGC
1 CAAAATGTAATTT-TAGAAAAGTTTAGGGGT
*
306615 CCAAATGTAA-TTTAGAAAAGTTTAGGGGT
1 CAAAATGTAATTTTAGAAAAGTTTAGGGGT
*
306644 -AGAAATGTAATTTT-GAAAAATTTTAGGGGT
1 CA-AAATGTAATTTTAG-AAAAGTTTAGGGGT
*
306674 CAAAATGCAATTTTAGAAAAGTTTA-GGGT
1 CAAAATGTAATTTTAGAAAAGTTTAGGGGT
306703 CAAAATG
1 CAAAATG
306710 CAAAAATAAA
Statistics
Matches: 83, Mismatches: 6, Indels: 13
0.81 0.06 0.13
Matches are distributed among these distances:
28 3 0.04
29 34 0.41
30 44 0.53
31 2 0.02
ACGTcount: A:0.41, C:0.06, G:0.22, T:0.31
Consensus pattern (30 bp):
CAAAATGTAATTTTAGAAAAGTTTAGGGGT
Found at i:306721 original size:7 final size:7
Alignment explanation
Indices: 306711--306745 Score: 52
Period size: 7 Copynumber: 4.7 Consensus size: 7
306701 GTCAAAATGC
306711 AAAAATAA
1 AAAAAT-A
306719 AAATAATA
1 AAA-AATA
306727 AAAAATA
1 AAAAATA
306734 AAAAATA
1 AAAAATA
306741 AAAAA
1 AAAAA
306746 ATTCTTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 16 0.62
8 7 0.27
9 3 0.12
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAAATA
Found at i:306737 original size:17 final size:15
Alignment explanation
Indices: 306711--306746 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
306701 GTCAAAATGC
306711 AAAAATAAAAATAATA
1 AAAAATAAAAATAA-A
306727 AAAAATAAAAAATAAA
1 AAAAAT-AAAAATAAA
306743 AAAA
1 AAAA
306747 TTCTTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (15 bp):
AAAAATAAAAATAAA
Found at i:307121 original size:76 final size:76
Alignment explanation
Indices: 307040--307685 Score: 894
Period size: 76 Copynumber: 8.4 Consensus size: 76
307030 ATGAGTTATT
* *
307040 TTTTTGAAAAAAATAGAAATTTAAAAATACCTCAACGTGACCCGAGGCTCAACTCACCTCTCGTA
1 TTTTTGAAAAAAACAGAAATTTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGTA
*
307105 TTATTAGTTGA
66 TTATGAGTTGA
** *
307116 TTTTTGAAAAAAACAGAAATAAAAAAATACCTCAGCGTGACCCGAGGCTCAACTTACCTCTCGTA
1 TTTTTGAAAAAAACAGAAATTTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGTA
307181 TTATGAGTTGA
66 TTATGAGTTGA
* *
307192 TTTTTG--AAAAACAGAAATTTAAAAGAAATACCTCGGCGTGACCCAAGGCTCAACTCACCTCTC
1 TTTTTGAAAAAAACAGAAATTT--AA-AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTC
307255 GTATTATGAGTTGA
63 GTATTATGAGTTGA
* *
307269 TTTTTGAAAAAAAACAGAAATTTAAAAGAAATACCTTAGCGTGACCCAAGGCTCAACTCACCTCT
1 TTTTTG-AAAAAAACAGAAATTT--AA-AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT
307334 CGTATTATGAGTTGA
62 CGTATTATGAGTTGA
307349 TTTTTGAAAAAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTC
1 TTTTTG--AAAAAAACAGAAATTT--AA-AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTC
307414 TCGTATTATGAGTTGA
61 TCGTATTATGAGTTGA
* * * *
307430 --TTTAAAAAAAGACAGAAA-TTAAAAATGCTTCAGCGTGACCCGATGCTCAACTCACCTCTCGT
1 TTTTTGAAAAAA-ACAGAAATTTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGT
307492 ATTATGAGTTGA
65 ATTATGAGTTGA
* * *
307504 -TTTTAAAAAAAGACAGAAA-TTAAAAATACCTCAGCGTGACCTGAAGCTCAACTCACCTCTCGT
1 TTTTTGAAAAAA-ACAGAAATTTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGT
307567 ATTATGAGTTGA
65 ATTATGAGTTGA
* *
307579 TTTTTGAAAAAAAATAGAAA-TTAAAAATACCTTAGCGTGACCCGAGGCTCAACTCACCTCTCGT
1 TTTTTG-AAAAAAACAGAAATTTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGT
307643 ATTATGAGTTGA
65 ATTATGAGTTGA
* *
307655 TTTTTGAAAAAAAAACAGTAATTGAAAAATA
1 TTTTTG--AAAAAAACAGAAATTTAAAAATA
307686 TTTCTTGAAA
Statistics
Matches: 526, Mismatches: 31, Indels: 24
0.91 0.05 0.04
Matches are distributed among these distances:
74 61 0.12
75 72 0.14
76 147 0.28
77 81 0.15
78 15 0.03
79 3 0.01
80 75 0.14
81 72 0.14
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (76 bp):
TTTTTGAAAAAAACAGAAATTTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGTA
TTATGAGTTGA
Found at i:319598 original size:17 final size:16
Alignment explanation
Indices: 319550--319802 Score: 103
Period size: 18 Copynumber: 14.2 Consensus size: 16
319540 ATAATTATTT
319550 TTTTGAAAACACGAAAAAA
1 TTTT-AAAACACG--AAAA
*
319569 TTTTAAAACACGAGAA
1 TTTTAAAACACGAAAA
*
319585 TTTTAGAGACACGAAAA
1 TTTTA-AAACACGAAAA
*
319602 TTCATAAAAACACGAAAA
1 TT--TTAAAACACGAAAA
*
319620 TTTTTGAAAACACGGAAAT
1 -TTTT-AAAACAC-GAAAA
* * *
319639 TTTTAAAACAGGGAAT
1 TTTTAAAACACGAAAA
*
319655 TTTTGAAAACATGAAAA
1 TTTT-AAAACACGAAAA
* *
319672 TTTTTGAAACACGAAATT
1 -TTTTAAAACACGAAA-A
319690 TTTTGAAAAACACGAAATA
1 TTTT--AAAACACGAAA-A
** * *
319709 TTTTTTTGATCATCGAAAT
1 --TTTTAAAACA-CGAAAA
*
319728 TTTTGAAAACACGAAAGT
1 TTTT-AAAACACGAAA-A
*
319746 TTTTAAAACACCTG-AAT
1 TTTTAAAACA-C-GAAAA
* *
319763 TTTTGAAAACACGAGGAT
1 TTTT-AAAACACGA-AAA
319781 TTTTGAAAACACGAAAAA
1 TTTT-AAAACACG-AAAA
319799 TTTT
1 TTTT
319803 CTTTTTTTTT
Statistics
Matches: 185, Mismatches: 27, Indels: 45
0.72 0.11 0.18
Matches are distributed among these distances:
16 17 0.09
17 61 0.33
18 70 0.38
19 28 0.15
20 5 0.03
21 4 0.02
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (16 bp):
TTTTAAAACACGAAAA
Found at i:319647 original size:35 final size:35
Alignment explanation
Indices: 319549--319802 Score: 226
Period size: 35 Copynumber: 7.1 Consensus size: 35
319539 AATAATTATT
* *
319549 TTTTTGAAAACACGAAAAAATTTTAAAACACGAGAA
1 TTTTTGAAAACACG-AAAATTTTTAAAACACGAAAA
* * * *
319585 TTTTAG-AGACACGAAAATTCATAAAAACACGAAAA
1 TTTTTGAAAACACGAAAATT-TTTAAAACACGAAAA
* **
319620 TTTTTGAAAACACGGAAATTTTTAAAACA-GGGAA
1 TTTTTGAAAACACGAAAATTTTTAAAACACGAAAA
* * *
319654 TTTTTGAAAACATGAAAATTTTTGAAACACGAAAT
1 TTTTTGAAAACACGAAAATTTTTAAAACACGAAAA
** *
319689 TTTTTGAAAAACACGAAATATTTTTTTGATCATCG-AAA
1 TTTTTG-AAAACACGAAA-A-TTTTTAAAACA-CGAAAA
* ***
319727 TTTTTGAAAACACGAAAGTTTTTAAAACACCTGAA
1 TTTTTGAAAACACGAAAATTTTTAAAACACGAAAA
**
319762 TTTTTGAAAACACGAGGATTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAATTTTT-AAAACACGAAAA
*
319798 ATTTT
1 TTTTT
319803 CTTTTTTTTT
Statistics
Matches: 172, Mismatches: 37, Indels: 18
0.76 0.16 0.08
Matches are distributed among these distances:
34 35 0.20
35 68 0.40
36 39 0.23
37 12 0.07
38 16 0.09
39 2 0.01
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.31
Consensus pattern (35 bp):
TTTTTGAAAACACGAAAATTTTTAAAACACGAAAA
Found at i:319865 original size:34 final size:34
Alignment explanation
Indices: 319816--319900 Score: 111
Period size: 34 Copynumber: 2.5 Consensus size: 34
319806 TTTTTTTTAA
*
319816 AAAACACAAAAATTTTTGAAACATTG-GAA-TTTTG
1 AAAACAC-GAAATTTTTGAAACA-TGAGAATTTTTG
319850 AAAACACGAAGATTTTTGAAACATGAGAATTTTTG
1 AAAACACGAA-ATTTTTGAAACATGAGAATTTTTG
*
319885 AAGACACGAAATTTTT
1 AAAACACGAAATTTTT
319901 TTTTTGAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
33 4 0.09
34 28 0.61
35 14 0.30
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.32
Consensus pattern (34 bp):
AAAACACGAAATTTTTGAAACATGAGAATTTTTG
Found at i:319905 original size:22 final size:22
Alignment explanation
Indices: 319879--319922 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
319869 AACATGAGAA
* *
319879 TTTTTGAAGACACGAAATTTTT
1 TTTTTGAAAACAAGAAATTTTT
*
319901 TTTTTGAAAACAAGGAATTTTT
1 TTTTTGAAAACAAGAAATTTTT
319923 GAAATACGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.45
Consensus pattern (22 bp):
TTTTTGAAAACAAGAAATTTTT
Found at i:319919 original size:39 final size:38
Alignment explanation
Indices: 319862--319970 Score: 116
Period size: 39 Copynumber: 2.8 Consensus size: 38
319852 AACACGAAGA
* *
319862 TTTTTG-AAACATGAGAATTTTTGAAGACACGA-AATTTTT
1 TTTTTGAAAACAAGAGAATTTTTGAA-ACACGAGAA--ATT
*
319901 TTTTTGAAAACAAG-GAATTTTTGAAATACGAGAAATT
1 TTTTTGAAAACAAGAGAATTTTTGAAACACGAGAAATT
* *
319938 TTTTTGAAAACACGAAAATTTTTTGAAACACGA
1 TTTTTGAAAACAAGAGAA-TTTTTGAAACACGA
319971 TTTTTTTAAG
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
37 15 0.25
38 7 0.12
39 32 0.53
40 6 0.10
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (38 bp):
TTTTTGAAAACAAGAGAATTTTTGAAACACGAGAAATT
Found at i:319921 original size:19 final size:19
Alignment explanation
Indices: 319899--319965 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
319889 CACGAAATTT
*
319899 TTTTTTTGAAAACAAGGAA
1 TTTTTTTGAAAACAAGAAA
*
319918 --TTTTTGAAATACGAGAAA
1 TTTTTTTGAAA-ACAAGAAA
*
319936 TTTTTTTGAAAACACGAAA
1 TTTTTTTGAAAACAAGAAA
*
319955 ATTTTTTGAAA
1 TTTTTTTGAAA
319966 CACGATTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
17 9 0.22
18 6 0.15
19 16 0.40
20 9 0.22
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39
Consensus pattern (19 bp):
TTTTTTTGAAAACAAGAAA
Found at i:319966 original size:18 final size:17
Alignment explanation
Indices: 319817--319970 Score: 82
Period size: 17 Copynumber: 8.5 Consensus size: 17
319807 TTTTTTTAAA
*
319817 AAACACAAAAATTTTTG
1 AAACACGAAAATTTTTG
* *
319834 AAACATTG-GAA-TTTTG
1 AAACA-CGAAAATTTTTG
*
319850 AAAACACGAAGATTTTTG
1 -AAACACGAAAATTTTTG
* *
319868 AAACATGAGAATTTTTG
1 AAACACGAAAATTTTTG
*
319885 AAGACACGAAATTTTTTTTTTG
1 AA-ACACGAAA----ATTTTTG
319907 AAA-AC-AAGGAATTTTTG
1 AAACACGAA--AATTTTTG
*
319924 AAATACGAGAAATTTTTTTG
1 AAACACGA-AAA--TTTTTG
319944 AAAACACGAAAATTTTTTG
1 -AAACACGAAAA-TTTTTG
319963 AAACACGA
1 AAACACGA
319971 TTTTTTTAAG
Statistics
Matches: 106, Mismatches: 14, Indels: 33
0.69 0.09 0.22
Matches are distributed among these distances:
16 6 0.06
17 38 0.36
18 23 0.22
19 10 0.09
20 12 0.11
21 9 0.08
22 8 0.08
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (17 bp):
AAACACGAAAATTTTTG
Found at i:319977 original size:18 final size:19
Alignment explanation
Indices: 319845--319970 Score: 81
Period size: 18 Copynumber: 6.7 Consensus size: 19
319835 AACATTGGAA
319845 TTTTGAAAACACGAAGA--T
1 TTTTGAAAACACGAA-ATTT
*
319863 TTTTG-AAACATGAGAA--T
1 TTTTGAAAACACGA-AATTT
*
319880 TTTTGAAGACACGAAATTTTTT
1 TTTTGAAAACACGAAA---TTT
* *
319902 TTTTGAAAACAAGGAA--T
1 TTTTGAAAACACGAAATTT
319919 TTTTGAAATACGA-GAAATTT
1 TTTTGAAA-AC-ACGAAATTT
*
319939 TTTTGAAAACACGAAAATT
1 TTTTGAAAACACGAAATTT
319958 TTTTG-AAACACGA
1 TTTTGAAAACACGA
319971 TTTTTTTAAG
Statistics
Matches: 88, Mismatches: 8, Indels: 24
0.73 0.07 0.20
Matches are distributed among these distances:
17 25 0.28
18 26 0.30
19 14 0.16
20 9 0.10
22 14 0.16
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (19 bp):
TTTTGAAAACACGAAATTT
Found at i:320103 original size:15 final size:16
Alignment explanation
Indices: 320087--320118 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
320077 TGATTCTATT
320087 AAAACACGAGAATTTAA
1 AAAACACGAGAATTT-A
320104 AAAACACGAGAATTT
1 AAAACACGAGAATTT
320119 TAGAATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.19
Consensus pattern (16 bp):
AAAACACGAGAATTTA
Found at i:320275 original size:16 final size:16
Alignment explanation
Indices: 320254--320293 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
320244 TTAAAATTAT
320254 TTAAAATAAAATAAAA
1 TTAAAATAAAATAAAA
** *
320270 TTAAAATTGAATTAAA
1 TTAAAATAAAATAAAA
320286 TTAAAATA
1 TTAAAATA
320294 TAGATACAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (16 bp):
TTAAAATAAAATAAAA
Found at i:320467 original size:13 final size:12
Alignment explanation
Indices: 320449--320508 Score: 59
Period size: 13 Copynumber: 4.8 Consensus size: 12
320439 TTGAACCTCT
320449 TTTTTTTGTTCTC
1 TTTTTTT-TTCTC
*
320462 TTTTTTCTTT-TT
1 TTTTTT-TTTCTC
320474 TCTTTTTTTTCTC
1 T-TTTTTTTTCTC
*
320487 TGTTTTTCTTCTC
1 T-TTTTTTTTCTC
320500 TTTTTTTTT
1 TTTTTTTTT
320509 TTCTGGCCTG
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
12 12 0.31
13 26 0.67
14 1 0.03
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (12 bp):
TTTTTTTTTCTC
Found at i:320485 original size:25 final size:27
Alignment explanation
Indices: 320445--320512 Score: 97
Period size: 25 Copynumber: 2.6 Consensus size: 27
320435 CAAATTGAAC
*
320445 CTCTTTTTTTTGTTCTCT-TTTTTCTT
1 CTCTTTTTTTTTTTCTCTGTTTTTCTT
320471 -T-TTTCTTTTTTTTCTCTGTTTTTCTT
1 CTCTTT-TTTTTTTTCTCTGTTTTTCTT
320497 CTCTTTTTTTTTTTCT
1 CTCTTTTTTTTTTTCT
320513 GGCCTGCTTC
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
24 3 0.08
25 12 0.32
26 8 0.22
27 11 0.30
28 3 0.08
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (27 bp):
CTCTTTTTTTTTTTCTCTGTTTTTCTT
Found at i:320513 original size:25 final size:26
Alignment explanation
Indices: 320445--320513 Score: 90
Period size: 26 Copynumber: 2.7 Consensus size: 26
320435 CAAATTGAAC
320445 CTCTTTTTTTTGTTCTCT-TTTTTCTT
1 CTCTTTTTTTT-TTCTCTGTTTTTCTT
*
320471 -TTTTCTTTTTTTTCTCTGTTTTTCTT
1 CTCTT-TTTTTTTTCTCTGTTTTTCTT
320497 CTCTTTTTTTTTT-TCTG
1 CTCTTTTTTTTTTCTCTG
320514 GCCTGCTTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
25 13 0.34
26 22 0.58
27 3 0.08
ACGTcount: A:0.00, C:0.17, G:0.04, T:0.78
Consensus pattern (26 bp):
CTCTTTTTTTTTTCTCTGTTTTTCTT
Found at i:320797 original size:4 final size:4
Alignment explanation
Indices: 320788--320872 Score: 74
Period size: 4 Copynumber: 22.0 Consensus size: 4
320778 TTTTTATTTT
* *
320788 TTTC TTTC TTTT TCTTC -TTC CTTC -TTC TTTC -TT- TTTC TTT- TTTC
1 TTTC TTTC TTTC T-TTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
*
320832 TTTC TTTC TTTC TTCTC TTTTC TCTC TTT- TTTC TTTC TTTC
1 TTTC TTTC TTTC TT-TC -TTTC TTTC TTTC TTTC TTTC TTTC
320873 CCAATCAGCC
Statistics
Matches: 68, Mismatches: 4, Indels: 18
0.76 0.04 0.20
Matches are distributed among these distances:
3 16 0.24
4 44 0.65
5 6 0.09
6 2 0.03
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTC
Found at i:320818 original size:17 final size:17
Alignment explanation
Indices: 320793--320851 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
320783 ATTTTTTTCT
320793 TTCTT-TTTCTTCTTCC
1 TTCTTCTTTCTTCTTCC
* *
320809 TTCTTCTTTCTTTTTCT
1 TTCTTCTTTCTTCTTCC
* *
320826 TTTTTCTTTCTTTCTTTC
1 TTCTTCTTTC-TTCTTCC
320844 TTC-TCTTT
1 TTCTTCTTT
320852 TCTCTCTTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
16 5 0.15
17 23 0.68
18 6 0.18
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (17 bp):
TTCTTCTTTCTTCTTCC
Found at i:320829 original size:7 final size:7
Alignment explanation
Indices: 320785--320872 Score: 63
Period size: 7 Copynumber: 12.0 Consensus size: 7
320775 AATTTTTTAT
320785 TTTTTTC
1 TTTTTTC
*
320792 TTTCTT-
1 TTTTTTC
*
320798 TTTCTTC
1 TTTTTTC
**
320805 TTCCTTC
1 TTTTTTC
*
320812 TTCTTTC
1 TTTTTTC
320819 -TTTTTC
1 TTTTTTC
320825 TTTTTTC
1 TTTTTTC
320832 TTTCTTTC
1 TTT-TTTC
320840 TTTCTTCTC
1 TTT-TT-TC
320849 TTTTCTCTC
1 TTTT-T-TC
320858 TTTTTTC
1 TTTTTTC
320865 TTTCTTTC
1 TTT-TTTC
320873 CCAATCAGCC
Statistics
Matches: 71, Mismatches: 4, Indels: 11
0.83 0.05 0.13
Matches are distributed among these distances:
6 11 0.15
7 31 0.44
8 16 0.23
9 13 0.18
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTTTC
Found at i:320852 original size:29 final size:28
Alignment explanation
Indices: 320816--320872 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
320806 TCCTTCTTCT
*
320816 TTCTTTTTCT-TTTTTCTTTCTTTCTTTC
1 TTCTTTTTCTCTCTTT-TTTCTTTCTTTC
320844 TTCTCTTTTCTCTCTTTTTTCTTTCTTTC
1 TTCT-TTTTCTCTCTTTTTTCTTTCTTTC
320873 CCAATCAGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 4 0.15
29 18 0.69
30 4 0.15
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (28 bp):
TTCTTTTTCTCTCTTTTTTCTTTCTTTC
Found at i:321006 original size:21 final size:20
Alignment explanation
Indices: 320971--321010 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
320961 TCTTTCCCCA
320971 TCTTTCTTCTTTTCTCTTTC
1 TCTTTCTTCTTTTCTCTTTC
*
320991 TCTTTCTCTTTTTTCTCTTT
1 TCTTTCT-TCTTTTCTCTTT
321011 TGCTTGTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (20 bp):
TCTTTCTTCTTTTCTCTTTC
Found at i:321007 original size:15 final size:15
Alignment explanation
Indices: 320987--321035 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 15
320977 TTCTTTTCTC
320987 TTTCTCTTTCTCTTT
1 TTTCTCTTTCTCTTT
321002 TTTCTCTTT-TGCTTGT
1 TTTCTCTTTCT-CTT-T
321018 TGTT-TCTTTCTCTTT
1 T-TTCTCTTTCTCTTT
321033 TTT
1 TTT
321036 TTTGCTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
14 3 0.10
15 14 0.47
16 10 0.33
17 3 0.10
ACGTcount: A:0.00, C:0.20, G:0.06, T:0.73
Consensus pattern (15 bp):
TTTCTCTTTCTCTTT
Found at i:321051 original size:31 final size:30
Alignment explanation
Indices: 320991--321053 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 30
320981 TTTCTCTTTC
*
320991 TCTTTCTCTTTTTTCTCTTTTGCTTGTTGTT
1 TCTTTCTCTTTTTTCTCTTTT-CTGGTTGTT
*
321022 TCTTTCTCTTTTTTTTTGCTTTT-TGGTTGTT
1 TCTTTCTC-TTTTTTCT-CTTTTCTGGTTGTT
321053 T
1 T
321054 TGCTAGTTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 16 0.57
32 7 0.25
33 5 0.18
ACGTcount: A:0.00, C:0.16, G:0.11, T:0.73
Consensus pattern (30 bp):
TCTTTCTCTTTTTTCTCTTTTCTGGTTGTT
Found at i:321153 original size:12 final size:12
Alignment explanation
Indices: 321122--321177 Score: 53
Period size: 12 Copynumber: 4.6 Consensus size: 12
321112 GGCGGTATGC
321122 CTTTTTTTTGCT
1 CTTTTTTTTGCT
*
321134 GC-TGTTTTTGCT
1 -CTTTTTTTTGCT
321146 CTTTTTTTTGCT
1 CTTTTTTTTGCT
*
321158 CAATTTTTTTT-TT
1 C--TTTTTTTTGCT
321171 CTTTTTT
1 CTTTTTT
321178 GCTTCTTGCT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
11 7 0.19
12 19 0.51
13 3 0.08
14 8 0.22
ACGTcount: A:0.04, C:0.14, G:0.09, T:0.73
Consensus pattern (12 bp):
CTTTTTTTTGCT
Found at i:321437 original size:30 final size:29
Alignment explanation
Indices: 321398--321525 Score: 125
Period size: 30 Copynumber: 4.3 Consensus size: 29
321388 TTTAAGAAAT
321398 GGCCAAAATGTAATTTATAGAAAGTTTAAG
1 GGCCAAAATGTAATTT-TAGAAAGTTTAAG
* * *
321428 GGCCCAAATGTAA-TTTAGAAAATTTTAG
1 GGCCAAAATGTAATTTTAGAAAGTTTAAG
**
321456 GGGTAGAAATGTAATTTTGAGAAAGTTT-AG
1 GGCCA-AAATGTAATTTT-AGAAAGTTTAAG
** *
321486 GGGTAAAATGTAATTTTAGAAAAGTTTAGG
1 GGCCAAAATGTAATTTTAG-AAAGTTTAAG
*
321516 GGTCAAAATG
1 GGCCAAAATG
321526 CAAAAATAAA
Statistics
Matches: 83, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
28 15 0.18
29 29 0.35
30 31 0.37
31 8 0.10
ACGTcount: A:0.40, C:0.05, G:0.24, T:0.31
Consensus pattern (29 bp):
GGCCAAAATGTAATTTTAGAAAGTTTAAG
Found at i:321466 original size:29 final size:28
Alignment explanation
Indices: 321402--321525 Score: 140
Period size: 29 Copynumber: 4.2 Consensus size: 28
321392 AGAAATGGCC
* **
321402 AAAATGTAATTTATAGAAAGTTTAAGGGCC
1 AAAATGTAATTTAGA-AAAGTTT-AGGGGT
* *
321432 CAAATGTAATTTAGAAAATTTTAGGGGT
1 AAAATGTAATTTAGAAAAGTTTAGGGGT
*
321460 AGAAATGTAATTTTGAGAAAGTTTAGGGGT
1 A-AAATGTAATTTAGA-AAAGTTTAGGGGT
321490 AAAATGTAATTTTAGAAAAGTTTAGGGGT
1 AAAATGTAA-TTTAGAAAAGTTTAGGGGT
321519 CAAAATG
1 -AAAATG
321526 CAAAAATAAA
Statistics
Matches: 81, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
28 4 0.05
29 40 0.49
30 37 0.46
ACGTcount: A:0.41, C:0.03, G:0.23, T:0.32
Consensus pattern (28 bp):
AAAATGTAATTTAGAAAAGTTTAGGGGT
Found at i:321525 original size:59 final size:59
Alignment explanation
Indices: 321401--321525 Score: 166
Period size: 59 Copynumber: 2.1 Consensus size: 59
321391 AAGAAATGGC
* *
321401 CAAAATGTAATTTATAGAAAGTTTAAGGGCCCAAATGTAATTTAGAAAATTTTAGGGGT
1 CAAAATGTAATTTATAGAAAGTTTAAGGGCCAAAATGTAATTTAGAAAAGTTTAGGGGT
**
321460 -AGAAATGTAATTT-TGAGAAAGTTT-AGGGGTAAAATGTAATTTTAGAAAAGTTTAGGGGT
1 CA-AAATGTAATTTAT-AGAAAGTTTAAGGGCCAAAATGTAA-TTTAGAAAAGTTTAGGGGT
321519 CAAAATG
1 CAAAATG
321526 CAAAAATAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
58 14 0.24
59 43 0.74
60 1 0.02
ACGTcount: A:0.41, C:0.04, G:0.23, T:0.32
Consensus pattern (59 bp):
CAAAATGTAATTTATAGAAAGTTTAAGGGCCAAAATGTAATTTAGAAAAGTTTAGGGGT
Found at i:321537 original size:29 final size:29
Alignment explanation
Indices: 321477--321537 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
321467 TAATTTTGAG
* ***
321477 AAAGTTTAGGGGTAAAATGTAATTTTAGA
1 AAAGTTTAGGGGTAAAATGCAAAAATAGA
321506 AAAGTTTAGGGGTCAAAATGCAAAAATA-A
1 AAAGTTTAGGGGT-AAAATGCAAAAATAGA
321535 AAA
1 AAA
321538 TAAAAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 17 0.63
30 10 0.37
ACGTcount: A:0.49, C:0.03, G:0.21, T:0.26
Consensus pattern (29 bp):
AAAGTTTAGGGGTAAAATGCAAAAATAGA
Found at i:327478 original size:53 final size:53
Alignment explanation
Indices: 327379--327494 Score: 160
Period size: 53 Copynumber: 2.2 Consensus size: 53
327369 TGATTGTGTG
* ** * *
327379 TCTTACAAATAATACATAATTAAACGATTTTGTTCAAGGTCGACAACATTTTA
1 TCTTACAAATAAAACATAATTAAACGATTTTGTTCAAGACCAACAACATTGTA
* * *
327432 TCTTACAGATAAAATATAATTAAACGATTTTGTTCAAGACCAACAACATTGTG
1 TCTTACAAATAAAACATAATTAAACGATTTTGTTCAAGACCAACAACATTGTA
327485 TCTTACAAAT
1 TCTTACAAAT
327495 TGAAAAATAC
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (53 bp):
TCTTACAAATAAAACATAATTAAACGATTTTGTTCAAGACCAACAACATTGTA
Found at i:329750 original size:38 final size:38
Alignment explanation
Indices: 329664--329752 Score: 108
Period size: 38 Copynumber: 2.3 Consensus size: 38
329654 TTTTGCATAC
* * *
329664 TTATAATTTTTATAATTTTCAAAAATAAATTATAGTTT
1 TTATAATTTTTATAATTTTCAAAAAAAAATTAGAGCTT
* * *
329702 TTTTAGTTTTTATAATTTTCTAAAAAAAAATTGGA-CTT
1 TTATAATTTTTATAATTTTC-AAAAAAAAATTAGAGCTT
329740 TTATAATTTTTAT
1 TTATAATTTTTAT
329753 TTTAATAATT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
38 31 0.74
39 11 0.26
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.54
Consensus pattern (38 bp):
TTATAATTTTTATAATTTTCAAAAAAAAATTAGAGCTT
Found at i:338194 original size:236 final size:237
Alignment explanation
Indices: 337769--338244 Score: 936
Period size: 236 Copynumber: 2.0 Consensus size: 237
337759 ACATTTAAAG
337769 TTTGAATTAATTTAATAAACATATATTTTAATTATATTATATATTATATTATTTTTTATAATTTT
1 TTTGAATTAA-TTAATAAACATATATTTTAATTATATTATATATTATATTATTTTTTATAATTTT
337834 GCATCACATAAAAATTAAATAATTTTCTTTTTTAAAAAAAGCAAATATTTTGATAGAATAAAAGG
65 GCATCACATAAAAATTAAATAATTTTCTTTTTTAAAAAAAGCAAATATTTTGATAGAATAAAAGG
337899 CAAAAATTACCAGAATCAATAATGGTGCCAGCACCGGTGGTAGGATTGAAAGCAATGGCAGATGG
130 CAAAAATTACCAGAATCAATAATGGTGCCAGCACCGGTGGTAGGATTGAAAGCAATGGCAGATGG
337964 TGGGATATCAACAACTTTGTTTCCAACCCTAATTCCAATCAAA
195 TGGGATATCAACAACTTTGTTTCCAACCCTAATTCCAATCAAA
338007 TTTGAATTAA-TAATAAACATATATTTTAATTATATTATATATTATATTATTTTTTATAATTTTG
1 TTTGAATTAATTAATAAACATATATTTTAATTATATTATATATTATATTATTTTTTATAATTTTG
338071 CATCACATAAAAATTAAATAATTTTCTTTTTTAAAAAAAGCAAATATTTTGATAGAATAAAAGGC
66 CATCACATAAAAATTAAATAATTTTCTTTTTTAAAAAAAGCAAATATTTTGATAGAATAAAAGGC
338136 AAAAATTACCAGAATCAATAATGGTGCCAGCACCGGTGGTAGGATTGAAAGCAATGGCAGATGGT
131 AAAAATTACCAGAATCAATAATGGTGCCAGCACCGGTGGTAGGATTGAAAGCAATGGCAGATGGT
338201 GGGATATCAACAACTTTGTTTCCAACCCTAATTCCAATCAAA
196 GGGATATCAACAACTTTGTTTCCAACCCTAATTCCAATCAAA
338243 TT
1 TT
338245 CACAAAGTAA
Statistics
Matches: 238, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
236 228 0.96
238 10 0.04
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (237 bp):
TTTGAATTAATTAATAAACATATATTTTAATTATATTATATATTATATTATTTTTTATAATTTTG
CATCACATAAAAATTAAATAATTTTCTTTTTTAAAAAAAGCAAATATTTTGATAGAATAAAAGGC
AAAAATTACCAGAATCAATAATGGTGCCAGCACCGGTGGTAGGATTGAAAGCAATGGCAGATGGT
GGGATATCAACAACTTTGTTTCCAACCCTAATTCCAATCAAA
Found at i:338977 original size:29 final size:28
Alignment explanation
Indices: 338943--339028 Score: 77
Period size: 29 Copynumber: 3.0 Consensus size: 28
338933 GAATTGAAAG
338943 TAATTTAATTTTTATATTTTATTTTAAT
1 TAATTTAATTTTTATATTTTATTTTAAT
** * *
338971 TAAATTTAATTCATATA-TTTGTTTGAAT
1 T-AATTTAATTTTTATATTTTATTTTAAT
* *
338999 T-ATTTAATTTTAATGTATTTTTTTTTAAT
1 TAATTTAATTTT--TATATTTTATTTTAAT
339028 T
1 T
339029 TTACTCTAGA
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
26 8 0.18
28 14 0.31
29 23 0.51
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.64
Consensus pattern (28 bp):
TAATTTAATTTTTATATTTTATTTTAAT
Found at i:343186 original size:68 final size:68
Alignment explanation
Indices: 343107--343333 Score: 454
Period size: 68 Copynumber: 3.3 Consensus size: 68
343097 AAGCACAGAT
343107 TTGTACACTGCCAAATCAAAACTGAGTCAAATCTGTGCTTAAAAACTGGAAGACTTCTAGCCTTC
1 TTGTACACTGCCAAATCAAAACTGAGTCAAATCTGTGCTTAAAAACTGGAAGACTTCTAGCCTTC
343172 GAC
66 GAC
343175 TTGTACACTGCCAAATCAAAACTGAGTCAAATCTGTGCTTAAAAACTGGAAGACTTCTAGCCTTC
1 TTGTACACTGCCAAATCAAAACTGAGTCAAATCTGTGCTTAAAAACTGGAAGACTTCTAGCCTTC
343240 GAC
66 GAC
343243 TTGTACACTGCCAAATCAAAACTGAGTCAAATCTGTGCTTAAAAACTGGAAGACTTCTAGCCTTC
1 TTGTACACTGCCAAATCAAAACTGAGTCAAATCTGTGCTTAAAAACTGGAAGACTTCTAGCCTTC
343308 GAC
66 GAC
343311 TTGTACACTGCCAAATCAAAACT
1 TTGTACACTGCCAAATCAAAACT
343334 AACCCGGGTC
Statistics
Matches: 159, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 159 1.00
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.26
Consensus pattern (68 bp):
TTGTACACTGCCAAATCAAAACTGAGTCAAATCTGTGCTTAAAAACTGGAAGACTTCTAGCCTTC
GAC
Found at i:344795 original size:19 final size:19
Alignment explanation
Indices: 344771--344811 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
344761 TCCTAATGTG
*
344771 CATGCTAGAATTAAATTTA
1 CATGCTAGAATCAAATTTA
*
344790 CATGCTAGAATCATATTTA
1 CATGCTAGAATCAAATTTA
344809 CAT
1 CAT
344812 TAATAGAGGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.37
Consensus pattern (19 bp):
CATGCTAGAATCAAATTTA
Found at i:347781 original size:43 final size:41
Alignment explanation
Indices: 347711--347827 Score: 128
Period size: 41 Copynumber: 2.8 Consensus size: 41
347701 GGAAGGCTCG
* ** *
347711 TACAATGCCAAC-GTCCCAGACGTGGTCTTACATGTAATCACA
1 TACAATGCC-ACTGTCCCAGACATGGTCTTACA-CAAATCAAA
* *
347753 TATCGATGCCACTGTCCCAGACAAGGTCTTACACAAATCAAA
1 TA-CAATGCCACTGTCCCAGACATGGTCTTACACAAATCAAA
* *
347795 TACAATGTCAATGTCCCAGACATGGTCTTACAC
1 TACAATGCCACTGTCCCAGACATGGTCTTACAC
347828 GTATACACAA
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
41 27 0.43
42 12 0.19
43 24 0.38
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.24
Consensus pattern (41 bp):
TACAATGCCACTGTCCCAGACATGGTCTTACACAAATCAAA
Found at i:347854 original size:84 final size:84
Alignment explanation
Indices: 347711--347870 Score: 202
Period size: 84 Copynumber: 1.9 Consensus size: 84
347701 GGAAGGCTCG
* * *
347711 TACAATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCGATGCCACTGTCCCAGACA
1 TACAATGCCAACGTCCCAGACATGGTCTTACACGTAATCACATATCGATGCAACTGTCCCAGA-A
347776 -AGGTCTTACACAAATCAAA
65 GAGGTCTTACACAAATCAAA
* *
347795 TACAATGTCAATGTCCCAGACATGGTCTTACACGT-ATACACA-AGTCGATGTCAAC-GTCCCAG
1 TACAATGCCAACGTCCCAGACATGGTCTTACACGTAAT-CACATA-TCGATG-CAACTGTCCCAG
*
347857 AAGTGGTCTTACAC
63 AAGAGGTCTTACAC
347871 GAAAATACAT
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
83 4 0.06
84 59 0.89
85 3 0.05
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.24
Consensus pattern (84 bp):
TACAATGCCAACGTCCCAGACATGGTCTTACACGTAATCACATATCGATGCAACTGTCCCAGAAG
AGGTCTTACACAAATCAAA
Found at i:347857 original size:43 final size:42
Alignment explanation
Indices: 347719--347871 Score: 145
Period size: 43 Copynumber: 3.6 Consensus size: 42
347709 CGTACAATGC
* *
347719 CAACGTCCCAGACGTGGTCTTACATGTA-ATCACATATCGATG-
1 CAACGTCCCAGACATGGTCTTACACGTATA-CACA-ATCGATGT
* * ** *
347761 CCACTGTCCCAGACAAGGTCTTACACAAAT-CA-AATACAATGT
1 CAAC-GTCCCAGACATGGTCTTACACGTATACACAAT-CGATGT
*
347803 CAATGTCCCAGACATGGTCTTACACGTATACACAAGTCGATGT
1 CAACGTCCCAGACATGGTCTTACACGTATACACAA-TCGATGT
347846 CAACGTCCCAGA-AGTGGTCTTACACG
1 CAACGTCCCAGACA-TGGTCTTACACG
347872 AAAATACATA
Statistics
Matches: 89, Mismatches: 14, Indels: 15
0.75 0.12 0.13
Matches are distributed among these distances:
40 2 0.02
41 27 0.30
42 10 0.11
43 49 0.55
44 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (42 bp):
CAACGTCCCAGACATGGTCTTACACGTATACACAATCGATGT
Found at i:350131 original size:17 final size:17
Alignment explanation
Indices: 350109--350141 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
350099 TTTTTATTTT
350109 AATTTAA-ATTCTAAAAA
1 AATTTAACATT-TAAAAA
350126 AATTTAACATTTAAAA
1 AATTTAACATTTAAAA
350142 TTTACAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (17 bp):
AATTTAACATTTAAAAA
Found at i:352248 original size:25 final size:27
Alignment explanation
Indices: 352219--352269 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
352209 AATTACATCT
*
352219 AAATTTAA-TT-TAAATTTTTTTATTC
1 AAATTTAAGTTATAAATTTTTATATTC
352244 AAATTTAAGTTATAAATTTTTATATT
1 AAATTTAAGTTATAAATTTTTATATT
352270 ATATACATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 8 0.35
26 2 0.09
27 13 0.57
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (27 bp):
AAATTTAAGTTATAAATTTTTATATTC
Found at i:353127 original size:19 final size:19
Alignment explanation
Indices: 353087--353128 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
353077 CTTTGTCCTA
*
353087 TTTTTCAATTATGTATATTT
1 TTTTTCAATTATG-ATACTT
353107 TTTTTCATATTATG-TACTT
1 TTTTTCA-ATTATGATACTT
353126 TTT
1 TTT
353129 ATGGATTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 7 0.35
20 7 0.35
21 6 0.30
ACGTcount: A:0.21, C:0.07, G:0.05, T:0.67
Consensus pattern (19 bp):
TTTTTCAATTATGATACTT
Found at i:353568 original size:24 final size:24
Alignment explanation
Indices: 353518--353575 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
353508 TTCAAACGAG
*
353518 AATAATAAAATAACATACAATTAAA
1 AATAA-AAAATAAAATACAATTAAA
* *
353543 AATTAAAAATAAAATAC-ATTCTAA
1 AATAAAAAATAAAATACAATT-AAA
353567 AATAAAAAA
1 AATAAAAAA
353576 ATTTATTGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
23 3 0.11
24 21 0.75
25 4 0.14
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (24 bp):
AATAAAAAATAAAATACAATTAAA
Found at i:354884 original size:13 final size:14
Alignment explanation
Indices: 354866--354894 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
354856 AAGCTCCAGG
354866 TTATTCAAA-GGAC
1 TTATTCAAAGGGAC
354879 TTATTCAAAGGGAC
1 TTATTCAAAGGGAC
354893 TT
1 TT
354895 GGATGCTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (14 bp):
TTATTCAAAGGGAC
Found at i:365215 original size:21 final size:21
Alignment explanation
Indices: 365173--365215 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
365163 ACATGTTCGA
*
365173 TCAATTAAAACTAGAATAAAT
1 TCAATTAAAACTACAATAAAT
*
365194 TCAATATAAAA-TACAATGAAT
1 TCAAT-TAAAACTACAATAAAT
365215 T
1 T
365216 GAAAATTGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.56, C:0.09, G:0.05, T:0.30
Consensus pattern (21 bp):
TCAATTAAAACTACAATAAAT
Found at i:366581 original size:31 final size:30
Alignment explanation
Indices: 366511--366584 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 30
366501 TATAACGGTA
* *
366511 GAGTGATTAAAATTGATAATGTATTAACTG
1 GAGTGACTAAAATTGACAATGTATTAACTG
*
366541 GAGTAACTAAAATTGACAACT-TATCTAA-TAG
1 GAGTGACTAAAATTGACAA-TGTAT-TAACT-G
366572 GAGTGACTAAAAT
1 GAGTGACTAAAAT
366585 AATAATTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 20 0.54
31 17 0.46
ACGTcount: A:0.43, C:0.08, G:0.18, T:0.31
Consensus pattern (30 bp):
GAGTGACTAAAATTGACAATGTATTAACTG
Found at i:369620 original size:33 final size:33
Alignment explanation
Indices: 369578--369644 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
369568 TGGTGGTCGC
369578 GTTGTTTCAAGATGAAACTAAATTTTAGGATGT
1 GTTGTTTCAAGATGAAACTAAATTTTAGGATGT
*
369611 GTTGTTTCAAGATGAAATTAAATTTTAGGATGT
1 GTTGTTTCAAGATGAAACTAAATTTTAGGATGT
369644 G
1 G
369645 ATGTATATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.04, G:0.22, T:0.40
Consensus pattern (33 bp):
GTTGTTTCAAGATGAAACTAAATTTTAGGATGT
Found at i:370892 original size:43 final size:43
Alignment explanation
Indices: 370510--370907 Score: 353
Period size: 43 Copynumber: 9.3 Consensus size: 43
370500 TGTTGGTCTA
* * ** *
370510 TAGCGGCGC-TTCTCGCACAAACGCCACTGAAGACCAAGACCTT
1 TAGCGGCGCTTTCTC-CACAAACGCCGCTAAAGACCATTATCTT
* * * ***
370553 TAGCGGCGC-TTCACAACAAACGCCGCTAAAGATCAGGGTCTT
1 TAGCGGCGCTTTCTCCACAAACGCCGCTAAAGACCATTATCTT
* * * * * ***
370595 TAGCGGCGTTTTCGT-TA-AAGCACCGCTAAAGATCAGGGTCTT
1 TAGCGGCGCTTTC-TCCACAAACGCCGCTAAAGACCATTATCTT
* * * *
370637 TAGCGGCGCTTT-TCCCACAAACGCCGCAAAAGACCCTGATCTA
1 TAGCGGCGCTTTCT-CCACAAACGCCGCTAAAGACCATTATCTT
* * * *
370680 TAGCGGCGCTTCCACCACAAACGCCACTAAAGAACC-TGATCTT
1 TAGCGGCGCTTTCTCCACAAACGCCGCTAAAG-ACCATTATCTT
* * *
370723 TTGCGGCGCTTTCTCCACAAACGTCGCTAAAGACCCTTATCTT
1 TAGCGGCGCTTTCTCCACAAACGCCGCTAAAGACCATTATCTT
* *
370766 TAGCGGCGCTTTATCCACAAACGCCGCGAAAGACCATTATCTT
1 TAGCGGCGCTTTCTCCACAAACGCCGCTAAAGACCATTATCTT
*
370809 TAGCGGCACTTTCTCCACAAACGCCGCTAAAGACCATTATCTT
1 TAGCGGCGCTTTCTCCACAAACGCCGCTAAAGACCATTATCTT
* *
370852 TAGCGGCGCTTTCTCTACAGACGCCGCTAAATG-CTC-TTATCTTT
1 TAGCGGCGCTTTCTCCACAAACGCCGCTAAA-GAC-CATTATC-TT
*
370896 TAGCGACGCTTT
1 TAGCGGCGCTTT
370908 TTGTCGAAAA
Statistics
Matches: 298, Mismatches: 46, Indels: 21
0.82 0.13 0.06
Matches are distributed among these distances:
40 1 0.00
42 67 0.22
43 212 0.71
44 18 0.06
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (43 bp):
TAGCGGCGCTTTCTCCACAAACGCCGCTAAAGACCATTATCTT
Found at i:377479 original size:16 final size:16
Alignment explanation
Indices: 377460--377598 Score: 69
Period size: 16 Copynumber: 8.7 Consensus size: 16
377450 TAATATTAAT
377460 TAAGTTGTGTATTATG
1 TAAGTTGTGTATTATG
*
377476 TAAGTTATGTAAGTTATGTATT
1 TAAG-T-TGT--G-TAT-TATG
*
377498 TAAG-TGTGTGTTATG
1 TAAGTTGTGTATTATG
*
377513 TAAGTTGTGTATAATG
1 TAAGTTGTGTATTATG
* *
377529 T---TAGT-TATCA--
1 TAAGTTGTGTATTATG
*
377539 -AAGTTATGTATTATG
1 TAAGTTGTGTATTATG
* *
377554 TAAGTTATTTAAGTTATG
1 TAAGTTGTGT-A-TTATG
377572 TAAGTTGTGTATTATG
1 TAAGTTGTGTATTATG
*
377588 TAAGTTATGTA
1 TAAGTTGTGTA
377599 GGCTATGTAT
Statistics
Matches: 93, Mismatches: 14, Indels: 32
0.67 0.10 0.23
Matches are distributed among these distances:
12 6 0.06
13 7 0.08
15 7 0.08
16 39 0.42
17 4 0.04
18 16 0.17
19 3 0.03
20 1 0.01
21 3 0.03
22 7 0.08
ACGTcount: A:0.29, C:0.01, G:0.22, T:0.48
Consensus pattern (16 bp):
TAAGTTGTGTATTATG
Found at i:377485 original size:9 final size:9
Alignment explanation
Indices: 377471--377647 Score: 113
Period size: 9 Copynumber: 20.2 Consensus size: 9
377461 AAGTTGTGTA
377471 TTATGTAAG
1 TTATGTAAG
377480 TTATGTAAG
1 TTATGTAAG
*
377489 TTATGT-AT
1 TTATGTAAG
**
377497 TTAAGTGTGTG
1 TT-A-TGTAAG
377508 TTATGTAAG
1 TTATGTAAG
*
377517 TTGTGT-A-
1 TTATGTAAG
* *
377524 TAATGTTAG
1 TTATGTAAG
**
377533 TTATCAAAG
1 TTATGTAAG
377542 TTATGT-A-
1 TTATGTAAG
377549 TTATGTAAG
1 TTATGTAAG
*
377558 TTATTTAAG
1 TTATGTAAG
377567 TTATGTAAG
1 TTATGTAAG
*
377576 TTGTGT-A-
1 TTATGTAAG
377583 TTATGTAAG
1 TTATGTAAG
*
377592 TTATGTAGG
1 TTATGTAAG
*
377601 CTATGT-A-
1 TTATGTAAG
377608 TTATGTAAG
1 TTATGTAAG
*
377617 TTAT-TATG
1 TTATGTAAG
377625 TTATTATGTAAG
1 ---TTATGTAAG
*
377637 TTATGCAAG
1 TTATGTAAG
377646 TT
1 TT
377648 TATATATAAG
Statistics
Matches: 128, Mismatches: 25, Indels: 30
0.70 0.14 0.16
Matches are distributed among these distances:
7 20 0.16
8 13 0.10
9 82 0.64
10 4 0.03
11 6 0.05
12 3 0.02
ACGTcount: A:0.29, C:0.02, G:0.21, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:377495 original size:25 final size:25
Alignment explanation
Indices: 377460--377647 Score: 141
Period size: 25 Copynumber: 7.2 Consensus size: 25
377450 TAATATTAAT
*
377460 TAAGTTGTGTATTATGTAAGTTATG
1 TAAGTTATGTATTATGTAAGTTATG
**
377485 TAAGTTATGTATTTAAGTGTGTGTTATG
1 TAAGTTATGTA-TT-A-TGTAAGTTATG
* * * *
377513 TAAGTTGTGTATAATGTTAGTTATC
1 TAAGTTATGTATTATGTAAGTTATG
* *
377538 AAAGTTATGTATTATGTAAGTTATT
1 TAAGTTATGTATTATGTAAGTTATG
*
377563 TAAGTTATGTAAGTTGTGT-A-TTATG
1 TAAGTTATGT-A-TTATGTAAGTTATG
*
377588 TAAGTTATGTAGGCTATGT-A-TTATG
1 TAAGTTATGTA--TTATGTAAGTTATG
377613 TAAGTTATTATGTTATTATGTAAGTTATG
1 TAAG---TTATG-TATTATGTAAGTTATG
*
377642 CAAGTT
1 TAAGTT
377648 TATATATAAG
Statistics
Matches: 131, Mismatches: 20, Indels: 23
0.75 0.11 0.13
Matches are distributed among these distances:
24 1 0.01
25 76 0.58
26 7 0.05
27 12 0.09
28 25 0.19
29 10 0.08
ACGTcount: A:0.29, C:0.02, G:0.21, T:0.48
Consensus pattern (25 bp):
TAAGTTATGTATTATGTAAGTTATG
Found at i:377569 original size:34 final size:34
Alignment explanation
Indices: 377531--377595 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
377521 GTATAATGTT
377531 AGTTATCAAAGTTATGTATTATGTAAGTTATTTA
1 AGTTATCAAAGTTATGTATTATGTAAGTTATTTA
** *
377565 AGTTATGTAAGTTGTGTATTATGTAAGTTAT
1 AGTTATCAAAGTTATGTATTATGTAAGTTAT
377596 GTAGGCTATG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.32, C:0.02, G:0.18, T:0.48
Consensus pattern (34 bp):
AGTTATCAAAGTTATGTATTATGTAAGTTATTTA
Found at i:377606 original size:34 final size:34
Alignment explanation
Indices: 377539--377614 Score: 102
Period size: 34 Copynumber: 2.3 Consensus size: 34
377529 TTAGTTATCA
* *
377539 AAGTTATGTATTATGTAAGTTATTTAAGTTATGT
1 AAGTTATGTATTATGTAAGTTATGTAAGCTATGT
* *
377573 AAGTTGTGTATTATGTAAGTTATGTAGGCTATGT
1 AAGTTATGTATTATGTAAGTTATGTAAGCTATGT
377607 -A-TTATGTA
1 AAGTTATGTA
377615 AGTTATTATG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 6 0.16
33 1 0.03
34 30 0.81
ACGTcount: A:0.30, C:0.01, G:0.21, T:0.47
Consensus pattern (34 bp):
AAGTTATGTATTATGTAAGTTATGTAAGCTATGT
Found at i:378869 original size:7 final size:7
Alignment explanation
Indices: 378857--378881 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
378847 AACTATTTGC
378857 AAAACAG
1 AAAACAG
378864 AAAACAG
1 AAAACAG
378871 AAAACAG
1 AAAACAG
378878 AAAA
1 AAAA
378882 TCTCGCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.12, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAACAG
Found at i:378905 original size:12 final size:12
Alignment explanation
Indices: 378888--378921 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
378878 AAAATCTCGC
*
378888 AAAACAGACTAG
1 AAAACAAACTAG
378900 AAAACAAACTAG
1 AAAACAAACTAG
378912 AAAACCAAAC
1 AAAA-CAAAC
378922 CCAATAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.65, C:0.21, G:0.09, T:0.06
Consensus pattern (12 bp):
AAAACAAACTAG
Found at i:380099 original size:83 final size:82
Alignment explanation
Indices: 379929--380148 Score: 194
Period size: 83 Copynumber: 2.7 Consensus size: 82
379919 GAAACAGCAC
* * * * * * *
379929 CGTTTTAAGAACCTTAAATATATATTTGCGGCGTTTTAGCAAAAACGCCACTAAAAATTAACTTA
1 CGTTTTAAGAAACTTTAATACATAGTTCCGGCGTTTTACCAAAAACGCCACTAAAAATTAACGTA
* * *
379994 TTGAATACAAACGGTGC
66 TTGAAGACAAACAGTGA
* * *
380011 CGTTTTAAGAAACTTTAATCCATAGTTCCGGCGTTTTCCCGAAAAACGCCACTAAAATTTTAA-G
1 CGTTTTAAGAAACTTTAATACATAGTTCCGGCGTTTTACC-AAAAACGCCACTAAAA-ATTAACG
* *
380075 TCTTGAAGAGAAACAGTGA
64 TATTGAAGACAAACAGTGA
* ** * *
380094 CGTTTTGAA-AAACATTAATACATCA-TTGTGGCGTTTTTAGCATAAACGCCACTAA
1 CGTTTT-AAGAAACTTTAATACAT-AGTTCCGGCG-TTTTACCAAAAACGCCACTAA
380149 TAGATTACAC
Statistics
Matches: 111, Mismatches: 22, Indels: 9
0.78 0.15 0.06
Matches are distributed among these distances:
82 32 0.29
83 67 0.60
84 12 0.11
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.30
Consensus pattern (82 bp):
CGTTTTAAGAAACTTTAATACATAGTTCCGGCGTTTTACCAAAAACGCCACTAAAAATTAACGTA
TTGAAGACAAACAGTGA
Found at i:380740 original size:450 final size:450
Alignment explanation
Indices: 379898--381169 Score: 2158
Period size: 451 Copynumber: 2.8 Consensus size: 450
379888 ATTGCTTCCA
*
379898 TAATTGCCAAAATTAAATTCTGAAACAGCACCGTTTTAAGAACCTTAAATATATATTTGCGGCGT
1 TAATTGCCAAAATTAAATTCTGAAACAGCACCGTTTTAAGAACCTTCAATATATATTTGCGGCGT
* *
379963 TTTAGCAAAAACGCCACTAAAAATTAACTTATTGAATACAAACGGTGCCGTTTTAAGAAACTTTA
66 TTTAGCAAAAACGCCACTAAAAATTAACTTACTGAATAGAAACGGTGCCGTTTTAAGAAACTTTA
* *
380028 ATCCATAGTTCCGGCGTTTTCCCGAAAAACGCCACTAAAATTTTAAGTCTTGAAGAGAAACAGTG
131 ATCCATAGTTCCGGCGTTTTCCCGAAAAACGCCACTAAAATTTCAAGTCCTGAAGAGAAACAGTG
*
380093 ACGTTTTGAAAAACATTAATACATCATTGTGGCGTTTTTAGCATAAACGCCACTAATAGATTACA
196 ACGTTTTGAAAAACATTAATACATCATTGCGGCGTTTTTAGCATAAACGCCACTAATAGATTACA
380158 CTCCTCTTCTGAAACGGTGCCGTTTTGAGAAATTATAATACATATTTATGGCATTTTCCCAGAAA
261 CTCCTCTTCTGAAACGGTGCCGTTTTGAGAAATTATAATACATATTTATGGCATTTTCCCAGAAA
380223 ACGCCACAAATTAAATTAAATTTCTAAATGGATACGACGCCGTTTTGAAAAAAATGGGAAAATAG
326 ACGCCACAAATTAAATTAAATTTCTAAATGGATACGACGCCGTTTTGAAAAAAATGGGAAAATAG
* *
380288 TTGCGGCATTTTTTCCCAAACGCCGCTAATGTTTTTT-TTCCTTATAA-TGTGGTCCTACG
391 TTGCGGCATTTCTACCCAAACGCCGCTAATGTTTTTTATTCCTTATAACTGTGGTCCT-CG
* *
380347 TAATTGCCAAAATTAAATTCTAAAACAGCACCGTTTTAAGAACCTTCAATATATATTTACGGCGT
1 TAATTGCCAAAATTAAATTCTGAAACAGCACCGTTTTAAGAACCTTCAATATATATTTGCGGCGT
* *
380412 TTTACGCAAAAACGCCACTAAGAATTAACTTACTGAATAGAAACGGTGTCGTTTTAAGAAACTTT
66 TTTA-GCAAAAACGCCACTAAAAATTAACTTACTGAATAGAAACGGTGCCGTTTTAAGAAACTTT
*
380477 AATCCATAGTTCCGGTGTTTTCCCGAAAAACGCCACTAAAATTTCAAGTCCTGAAGAGAAACAGT
130 AATCCATAGTTCCGGCGTTTTCCCGAAAAACGCCACTAAAATTTCAAGTCCTGAAGAGAAACAGT
* * *
380542 GACGTTTTGAAAAACATTAATACATCAATGCGGCGTTTTTAGCTTAAACGCCACTAATATATTAC
195 GACGTTTTGAAAAACATTAATACATCATTGCGGCGTTTTTAGCATAAACGCCACTAATAGATTAC
* *
380607 ACTCCTCTTCTGAAACGGTGCCGTTTTGAGAAATTATAATACATATTTATGGCGTTTTCCCAAAA
260 ACTCCTCTTCTGAAACGGTGCCGTTTTGAGAAATTATAATACATATTTATGGCATTTTCCCAGAA
* * *
380672 AACGCCACAAATTAAATTAAATTTCTAAATGGATACGACGTCGTTTTGAAAAAAATGGGTACATA
325 AACGCCACAAATTAAATTAAATTTCTAAATGGATACGACGCCGTTTTGAAAAAAATGGGAAAATA
* * *
380737 GTTGCGGCGTTTCTACCCAAACGCCGCTAATGTTTTTTATTTCTTATAACTGTGGTCCTGG
390 GTTGCGGCATTTCTACCCAAACGCCGCTAATGTTTTTTATTCCTTATAACTGTGGTCCTCG
* *
380798 TAATTGCCAAAATTAAATTCTGAAACAGCACCGTTTTAAGAACCTTCAATATATAGTTGCAGCGT
1 TAATTGCCAAAATTAAATTCTGAAACAGCACCGTTTTAAGAACCTTCAATATATATTTGCGGCG-
* *
380863 TTTTAGCAAAAACACCACTAAAAATTAACTTACTGAA-AGGAAACGATGCCGTTTTAAGAAACTT
65 TTTTAGCAAAAACGCCACTAAAAATTAACTTACTGAATA-GAAACGGTGCCGTTTTAAGAAACTT
* * *
380927 TAATCCATATTTCCGGCGTTTT-CCGAAAAAACGCCACTAAAATGTCAAGTCCTGAAGTGAAAC-
129 TAATCCATAGTTCCGGCGTTTTCCCG-AAAAACGCCACTAAAATTTCAAGTCCTGAAGAGAAACA
* *
380990 GTTGACGTTTTGAAAAACATTAATACATCCTTGCGGCGTTTCTAGCATAAACGCCACTAATAGAT
193 G-TGACGTTTTGAAAAACATTAATACATCATTGCGGCGTTTTTAGCATAAACGCCACTAATAGAT
381055 TACACTCCTCTTCTGAAACGGTGCCGTTTTGAGAAATTATAATACATATTTATGGCATTTTCCCA
257 TACACTCCTCTTCTGAAACGGTGCCGTTTTGAGAAATTATAATACATATTTATGGCATTTTCCCA
381120 GAAAACGCCACAAATTAAATTAAATTTCTAAATGGATACGACGCCGTTTT
322 GAAAACGCCACAAATTAAATTAAATTTCTAAATGGATACGACGCCGTTTT
381170 NNNNNNNNNN
Statistics
Matches: 772, Mismatches: 44, Indels: 12
0.93 0.05 0.01
Matches are distributed among these distances:
449 66 0.09
450 344 0.45
451 348 0.45
452 14 0.02
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (450 bp):
TAATTGCCAAAATTAAATTCTGAAACAGCACCGTTTTAAGAACCTTCAATATATATTTGCGGCGT
TTTAGCAAAAACGCCACTAAAAATTAACTTACTGAATAGAAACGGTGCCGTTTTAAGAAACTTTA
ATCCATAGTTCCGGCGTTTTCCCGAAAAACGCCACTAAAATTTCAAGTCCTGAAGAGAAACAGTG
ACGTTTTGAAAAACATTAATACATCATTGCGGCGTTTTTAGCATAAACGCCACTAATAGATTACA
CTCCTCTTCTGAAACGGTGCCGTTTTGAGAAATTATAATACATATTTATGGCATTTTCCCAGAAA
ACGCCACAAATTAAATTAAATTTCTAAATGGATACGACGCCGTTTTGAAAAAAATGGGAAAATAG
TTGCGGCATTTCTACCCAAACGCCGCTAATGTTTTTTATTCCTTATAACTGTGGTCCTCG
Found at i:382183 original size:42 final size:39
Alignment explanation
Indices: 382124--382322 Score: 209
Period size: 42 Copynumber: 4.8 Consensus size: 39
382114 TAAAATGTCC
382124 TTAGCGGCGCTTTTCCAGAAAACGCCGCTAAAGACCCCAGCA
1 TTAGCGGCGCTTTT-CA-AAAACGCCGCTAAAG-CCCCAGCA
* **
382166 TTAGCGGTGCTTTTCCAGAAAACGCCGCTAAAGGCCAAAGCA
1 TTAGCGGCGCTTTT-CA-AAAACGCCGCTAAA-GCCCCAGCA
* * *
382208 TTAGCGGCGCTTTTACAAAAACACCGCTAAAGCCCATAGAA
1 TTAGCGGCGCTTTT-CAAAAACGCCGCTAAAGCCC-CAGCA
*
382249 TTAGCGGCGCTTATTCAAAAACGCCGCTAAAGCCTACAGCA
1 TTAGCGGCGCTT-TTCAAAAACGCCGCTAAAGCC-CCAGCA
* *
382290 TTAGCGGCGCTTCTTAATAAAACGCTGCTAAAG
1 TTAGCGGCGCTT-TTCA-AAAACGCCGCTAAAG
382323 ACCCGAAAGG
Statistics
Matches: 136, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
40 3 0.02
41 64 0.47
42 68 0.50
43 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.21, T:0.20
Consensus pattern (39 bp):
TTAGCGGCGCTTTTCAAAAACGCCGCTAAAGCCCCAGCA
Found at i:382252 original size:41 final size:42
Alignment explanation
Indices: 382124--382301 Score: 238
Period size: 41 Copynumber: 4.3 Consensus size: 42
382114 TAAAATGTCC
382124 TTAGCGGCGCTTTTCCAGAAAACGCCGCTAAAGACCC-CAGCA
1 TTAGCGGCGCTTTTCCAGAAAACGCCGCTAAAG-CCCACAGCA
* * *
382166 TTAGCGGTGCTTTTCCAGAAAACGCCGCTAAAGGCCAAAGCA
1 TTAGCGGCGCTTTTCCAGAAAACGCCGCTAAAGCCCACAGCA
* * * *
382208 TTAGCGGCGCTTTTACA-AAAACACCGCTAAAGCCCATAGAA
1 TTAGCGGCGCTTTTCCAGAAAACGCCGCTAAAGCCCACAGCA
*
382249 TTAGCGGCGCTTATT-CA-AAAACGCCGCTAAAGCCTACAGCA
1 TTAGCGGCGCTT-TTCCAGAAAACGCCGCTAAAGCCCACAGCA
382290 TTAGCGGCGCTT
1 TTAGCGGCGCTT
382302 CTTAATAAAA
Statistics
Matches: 121, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
41 68 0.56
42 53 0.44
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.20
Consensus pattern (42 bp):
TTAGCGGCGCTTTTCCAGAAAACGCCGCTAAAGCCCACAGCA
Found at i:382292 original size:82 final size:84
Alignment explanation
Indices: 382124--382326 Score: 247
Period size: 83 Copynumber: 2.4 Consensus size: 84
382114 TAAAATGTCC
* * * *
382124 TTAGCGGCGCTTTTCCAGAAAACGCCGCTAAAGACCCCAGCATTAGCGGTGCTTTTCCAGAAAAC
1 TTAGCGGCGCTTTTACAGAAAACACCGCTAAAGACCCCAGAATTAGCGGCGCTTTTCCAGAAAAC
382189 GCCGCTAAAGGCCAAAGCA
66 GCCGCTAAAGGCCAAAGCA
*
382208 TTAGCGGCGCTTTTACA-AAAACACCGCTAAAG-CCCATAGAATTAGCGGCGCTTATT-CA-AAA
1 TTAGCGGCGCTTTTACAGAAAACACCGCTAAAGACCC-CAGAATTAGCGGCGCTT-TTCCAGAAA
*
382269 ACGCCGCTAAA-GCCTACAGCA
64 ACGCCGCTAAAGGCC-AAAGCA
* * *
382290 TTAGCGGCGCTTCTTA-ATAAAACGCTGCTAAAGACCC
1 TTAGCGGCGCTT-TTACAGAAAACACCGCTAAAGACCC
382327 GAAAGGTAGG
Statistics
Matches: 105, Mismatches: 8, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
81 3 0.03
82 35 0.33
83 46 0.44
84 21 0.20
ACGTcount: A:0.32, C:0.29, G:0.20, T:0.20
Consensus pattern (84 bp):
TTAGCGGCGCTTTTACAGAAAACACCGCTAAAGACCCCAGAATTAGCGGCGCTTTTCCAGAAAAC
GCCGCTAAAGGCCAAAGCA
Found at i:382485 original size:40 final size:41
Alignment explanation
Indices: 382400--382485 Score: 95
Period size: 40 Copynumber: 2.1 Consensus size: 41
382390 CTAATGGTTC
* * * * *
382400 TTTTTAGCAAAAACGCCGCTAATGCTCCTATTTTAGCGGCG
1 TTTTTAACAAAAACGCCGCGAATGCTCCGATTTTAGCGACA
*
382441 TTTTTAAC-AAAACGCCGCGAATGCT-CGATTTTTGCCGACA
1 TTTTTAACAAAAACGCCGCGAATGCTCCGATTTTAG-CGACA
382481 TTTTT
1 TTTTT
382486 TATGAAAACG
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
39 7 0.18
40 24 0.63
41 7 0.18
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.35
Consensus pattern (41 bp):
TTTTTAACAAAAACGCCGCGAATGCTCCGATTTTAGCGACA
Found at i:391580 original size:33 final size:32
Alignment explanation
Indices: 391528--391623 Score: 120
Period size: 33 Copynumber: 2.9 Consensus size: 32
391518 ATTACATCCA
*
391528 TATTTTGTATATCTGTTAATATGATTGCATCTG
1 TATTTTGTATATCTATTAATATGATTGCATC-G
* * *
391561 TATTATGTGTATCTATTAATATGATTACAATCG
1 TATTTTGTATATCTATTAATATGATTGC-ATCG
* *
391594 TATTTTGTATATATACTAATATGATTGCAT
1 TATTTTGTATATCTATTAATATGATTGCAT
391624 GCATTTGGGT
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
32 2 0.04
33 48 0.91
34 3 0.06
ACGTcount: A:0.30, C:0.08, G:0.12, T:0.49
Consensus pattern (32 bp):
TATTTTGTATATCTATTAATATGATTGCATCG
Found at i:392969 original size:16 final size:16
Alignment explanation
Indices: 392948--392981 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
392938 ATATTCTCAC
392948 TATAATTAATAAA-AAA
1 TATAATTAA-AAATAAA
392964 TATAATTAAAAATAAA
1 TATAATTAAAAATAAA
392980 TA
1 TA
392982 ATGAAGCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.18
16 14 0.82
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
TATAATTAAAAATAAA
Found at i:397216 original size:12 final size:12
Alignment explanation
Indices: 397199--397230 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
397189 TGCATGAATT
397199 AAGAATAATTAA
1 AAGAATAATTAA
397211 AAGAATAATTAA
1 AAGAATAATTAA
*
397223 AAGTATAA
1 AAGAATAA
397231 AGGGTGAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.25
Consensus pattern (12 bp):
AAGAATAATTAA
Found at i:398413 original size:41 final size:40
Alignment explanation
Indices: 398368--398479 Score: 122
Period size: 37 Copynumber: 2.9 Consensus size: 40
398358 CGACTTCAAG
* *
398368 TCGATGAGACACTGCGTGTCAATTTATTACTTCGGATTTAT
1 TCGATGAGACACTGGGTGTCAATTTATTACTTCGG-TTTAA
* * *
398409 TCGATGTGGCACTGGGTGCCAA--T-TTACTTCGGTTTAA
1 TCGATGAGACACTGGGTGTCAATTTATTACTTCGGTTTAA
* * *
398446 CCGATAAGACACTGGGTGTCAATTTAATACTTCG
1 TCGATGAGACACTGGGTGTCAATTTATTACTTCG
398480 AATTATCTAA
Statistics
Matches: 57, Mismatches: 11, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
37 21 0.37
38 9 0.16
39 2 0.04
40 7 0.12
41 18 0.32
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (40 bp):
TCGATGAGACACTGGGTGTCAATTTATTACTTCGGTTTAA
Found at i:401169 original size:3 final size:3
Alignment explanation
Indices: 401161--401198 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
401151 GTGTGAAAAT
401161 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
401199 ATAACAAAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:403070 original size:37 final size:39
Alignment explanation
Indices: 402980--403079 Score: 123
Period size: 37 Copynumber: 2.6 Consensus size: 39
402970 GACTTCGAGT
* **
402980 CGATGAGACACTGGGTGTCAATTTATTACTTCGGATTTATT
1 CGATGAGACACTGGGTGCCAA--TATTACTTCGGATTTAAC
* *
403021 CGGTGAGGCACTGGGTGCCAAT-TTACTTC-GATTTAAC
1 CGATGAGACACTGGGTGCCAATATTACTTCGGATTTAAC
403058 CGATGAGACACTGGGTGCCAAT
1 CGATGAGACACTGGGTGCCAAT
403080 CTGGTGTGTT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
37 26 0.50
38 7 0.13
39 1 0.02
41 18 0.35
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (39 bp):
CGATGAGACACTGGGTGCCAATATTACTTCGGATTTAAC
Found at i:414164 original size:3 final size:3
Alignment explanation
Indices: 414156--414180 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
414146 TACATTTTAG
414156 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
414181 AGGCCTGAGA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:416134 original size:7 final size:7
Alignment explanation
Indices: 416122--416153 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
416112 TAAAAACAAT
416122 AATTTTA
1 AATTTTA
416129 AATTTTA
1 AATTTTA
416136 AATTTTA
1 AATTTTA
416143 AATTTTA
1 AATTTTA
416150 AATT
1 AATT
416154 ATCATAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
AATTTTA
Found at i:416187 original size:99 final size:99
Alignment explanation
Indices: 416071--416286 Score: 405
Period size: 99 Copynumber: 2.2 Consensus size: 99
416061 TGAGAATTAG
*
416071 AAAATATTTTTTCTTTAAAATGTTCCGTACTTGAAAAAGGTTAAAAACAATAATTTTAAATTTTA
1 AAAATA-TTATTCTTTAAAATGTTCCGTACTTGAAAAAGGTTAAAAACAATAATTTTAAATTTTA
416136 AATTTTAAATTTTAAATTATCATAATTTAAACTCA
65 AATTTTAAATTTTAAATTATCATAATTTAAACTCA
416171 AAAATATTATTCTTTAAAATGTTCCGTACTTGAAAAAGGTTAAAAACAATAATTTTAAATTTTAA
1 AAAATATTATTCTTTAAAATGTTCCGTACTTGAAAAAGGTTAAAAACAATAATTTTAAATTTTAA
416236 ATTTTAAATTTTAAATTATCATAATTTAAACTCA
66 ATTTTAAATTTTAAATTATCATAATTTAAACTCA
*
416270 AAAATATTATTTTTTAA
1 AAAATATTATTCTTTAA
416287 CAATTTTTAT
Statistics
Matches: 114, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
99 108 0.95
100 6 0.05
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (99 bp):
AAAATATTATTCTTTAAAATGTTCCGTACTTGAAAAAGGTTAAAAACAATAATTTTAAATTTTAA
ATTTTAAATTTTAAATTATCATAATTTAAACTCA
Found at i:416233 original size:7 final size:7
Alignment explanation
Indices: 416221--416252 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
416211 TAAAAACAAT
416221 AATTTTA
1 AATTTTA
416228 AATTTTA
1 AATTTTA
416235 AATTTTA
1 AATTTTA
416242 AATTTTA
1 AATTTTA
416249 AATT
1 AATT
416253 ATCATAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
AATTTTA
Found at i:421266 original size:116 final size:117
Alignment explanation
Indices: 421124--421357 Score: 461
Period size: 116 Copynumber: 2.0 Consensus size: 117
421114 ATAAACATAA
421124 AATGATGCTATATCAATAATTGTGTTAATCATTTATTAGAATTAGATCGAATCAAAATTTTATAT
1 AATGATGCTATATCAATAATTGTGTTAATCATTTATTAGAATTAGATCGAATCAAAATTTTATAT
421189 ATAAAATTGCACATTAAACATTAATATTGGATAAAGTAATATATATGTATAT
66 ATAAAATTGCACATTAAACATTAATATTGGATAAAGTAATATATATGTATAT
421241 AATGATGCTA-ATCAATAATTGTGTTAATCATTTATTAGAATTAGATCGAATCAAAATTTTATAT
1 AATGATGCTATATCAATAATTGTGTTAATCATTTATTAGAATTAGATCGAATCAAAATTTTATAT
421305 ATAAAATTGCACATTAAACATTAATATTGGATAAAGTAATATATATGTATAT
66 ATAAAATTGCACATTAAACATTAATATTGGATAAAGTAATATATATGTATAT
421357 A
1 A
421358 TACTATTATC
Statistics
Matches: 117, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
116 107 0.91
117 10 0.09
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.39
Consensus pattern (117 bp):
AATGATGCTATATCAATAATTGTGTTAATCATTTATTAGAATTAGATCGAATCAAAATTTTATAT
ATAAAATTGCACATTAAACATTAATATTGGATAAAGTAATATATATGTATAT
Found at i:422061 original size:84 final size:84
Alignment explanation
Indices: 421973--422334 Score: 382
Period size: 84 Copynumber: 4.2 Consensus size: 84
421963 CCACTAAACT
* * *
421973 CGCCCTCTGAACCAAAACCACAGCCACCACCAGTGCCTGAACCAAAACCGCAACCACAACCACCA
1 CGCCCTCTGAACCAAAACCACAACCACCACCAGTGCCTAAACCAAATCCGCAACCACAACCACCA
* *
422038 CCGGT-AGCTAAACCGAACC
66 CCAGTGA-CTAAACCTAACC
* *
422057 CGCCCTCTGAACCAAAACCACAACCACCACC-GATTCCTAAACCAAATCCGCAGCCACAACCACC
1 CGCCCTCTGAACCAAAACCACAACCACCACCAG-TGCCTAAACCAAATCCGCAACCACAACCACC
*
422121 AACAGTGACTAAACCTAACC
65 ACCAGTGACTAAACCTAACC
* * *
422141 CGCCCTCTGAACCAAAACCACAACCACCACCAATGCCTAAACCTAACCCGCCTTCTGAACCAAAA
1 CGCCCTCTGAACCAAAACCACAACCACCACCAGTGCCTAAACCAAATCCG----C--AACC---A
*
422206 CCGCAACCACCACCAGTGACAAAACCTAACC
57 ---CAACCACCACCAGTGACTAAACCTAACC
* * * *
422237 CGCCTTCTGAACCAAAACCGCAGCCACCACCAGTGCCTAAACCAAAT------CCACAACCAGCA
1 CGCCCTCTGAACCAAAACCACAACCACCACCAGTGCCTAAACCAAATCCGCAACCACAACCACCA
422296 CCAGTGACTAAACCTAACC
66 CCAGTGACTAAACCTAACC
422315 CG-CCTCCTGAACCAAAACCA
1 CGCCCT-CTGAACCAAAACCA
422335 ATACCTCAAC
Statistics
Matches: 237, Mismatches: 25, Indels: 38
0.79 0.08 0.13
Matches are distributed among these distances:
77 2 0.01
78 41 0.17
81 1 0.00
83 1 0.00
84 119 0.50
85 1 0.00
88 1 0.00
90 3 0.01
93 1 0.00
96 67 0.28
ACGTcount: A:0.37, C:0.43, G:0.10, T:0.10
Consensus pattern (84 bp):
CGCCCTCTGAACCAAAACCACAACCACCACCAGTGCCTAAACCAAATCCGCAACCACAACCACCA
CCAGTGACTAAACCTAACC
Found at i:422076 original size:48 final size:47
Alignment explanation
Indices: 422024--422279 Score: 239
Period size: 48 Copynumber: 5.6 Consensus size: 47
422014 CCAAAACCGC
* *
422024 AACCACAACCACCACCGGTAGCTAAACCGAACCCGCCCTCTGAACCAA
1 AACCACAACCACCACCAGT-GCTAAACCTAACCCGCCCTCTGAACCAA
* * * *
422072 AACCACAACCACCACCGATTCCTAAACC-AA------ATCCG---C--
1 AACCACAACCACCACC-AGTGCTAAACCTAACCCGCCCTCTGAACCAA
* *
422108 AGCCACAACCACCAACAGTGACTAAACCTAACCCGCCCTCTGAACCAA
1 AACCACAACCACCACCAGTG-CTAAACCTAACCCGCCCTCTGAACCAA
* *
422156 AACCACAACCACCACCAATGCCTAAACCTAACCCGCCTTCTGAACCAA
1 AACCACAACCACCACCAGTG-CTAAACCTAACCCGCCCTCTGAACCAA
* * *
422204 AACCGCAACCACCACCAGTGACAAAACCTAACCCGCCTTCTGAACCAA
1 AACCACAACCACCACCAGTG-CTAAACCTAACCCGCCCTCTGAACCAA
* *
422252 AACCGCAGCCACCACCAGTGCCTAAACC
1 AACCACAACCACCACCAGTG-CTAAACC
422280 AAATCCACAA
Statistics
Matches: 171, Mismatches: 23, Indels: 28
0.77 0.10 0.13
Matches are distributed among these distances:
35 2 0.01
36 21 0.12
37 2 0.01
38 1 0.01
41 3 0.02
43 3 0.02
46 1 0.01
47 2 0.01
48 135 0.79
49 1 0.01
ACGTcount: A:0.37, C:0.43, G:0.10, T:0.10
Consensus pattern (47 bp):
AACCACAACCACCACCAGTGCTAAACCTAACCCGCCCTCTGAACCAA
Found at i:422158 original size:24 final size:24
Alignment explanation
Indices: 422131--422255 Score: 73
Period size: 24 Copynumber: 5.2 Consensus size: 24
422121 AACAGTGACT
422131 AAACCTAACCCGCCCTCTGAACCA
1 AAACCTAACCCGCCCTCTGAACCA
* ** *
422155 AAACCACAACCAC-CACCAATG--CCT
1 AAACC-TAACC-CGC-CCTCTGAACCA
*
422179 AAACCTAACCCGCCTTCTGAACCA
1 AAACCTAACCCGCCCTCTGAACCA
* **
422203 AAACCGCAACCAC-CACCAGTG-A-CA
1 AAACC-TAACC-CGC-CCTCTGAACCA
*
422227 AAACCTAACCCGCCTTCTGAACCA
1 AAACCTAACCCGCCCTCTGAACCA
422251 AAACC
1 AAACC
422256 GCAGCCACCA
Statistics
Matches: 72, Mismatches: 17, Indels: 24
0.64 0.15 0.21
Matches are distributed among these distances:
22 8 0.11
23 11 0.15
24 33 0.46
25 11 0.15
26 9 0.12
ACGTcount: A:0.38, C:0.43, G:0.08, T:0.11
Consensus pattern (24 bp):
AAACCTAACCCGCCCTCTGAACCA
Found at i:422250 original size:132 final size:125
Alignment explanation
Indices: 422024--422481 Score: 353
Period size: 132 Copynumber: 3.5 Consensus size: 125
422014 CCAAAACCGC
* * *
422024 AACCACAACCACCACCGGTAGCTAAACCGAACCCGCCCTCTGAACCAAAACCACAACCACCACC-
1 AACCACAACCACCACCAGT-GCTAAACCTAACCCGCCTTCTGAACCAAAACCACAACCACCACCA
** * * *** ** * * * *
422088 GATTCCTAAACCAAATCCGCAGCCACAACCACCAACAG-TGACTAAACCTAACCCGCCCTCTGAA
65 G-TGACTAAACCTAACCCGCCTTCTGAACCA-AAACAGCAG-C--AACC--ACCAGCCC-CTAAA
422152 CCAA
122 CCAA
* *
422156 AACCACAACCACCACCAATGCCTAAACCTAACCCGCCTTCTGAACCAAAACCGCAACCACCACCA
1 AACCACAACCACCACCAGTG-CTAAACCTAACCCGCCTTCTGAACCAAAACCACAACCACCACCA
* * * **
422221 GTGACAAAACCTAACCCGCCTTCTGAACCAAAACCGCAGCCACCACCAGTGCCTAAACCAA
65 GTGACTAAACCTAACCCGCCTTCTGAACCAAAACAGCAGCAACCACCAGCCCCTAAACCAA
* * *
422282 ATCCACAACCAGCACCAGTGACTAAACCTAACCCGCCTCCTGAACCAAAACCAATACCTCAACCA
1 AACCACAACCACCACCAGTG-CTAAACCTAACCCGCCTTCTGAACCAAAACC---A---CAACCA
* * * * **
422347 CCACCAGTGACTAAACCTAACCTGCCTTCTGAACCAAAACTGCAACCACCACCAGTGCCTAAACC
59 CCACCAGTGACTAAACCTAACCCGCCTTCTGAACCAAAACAGCAGCAACCACCAGCCCCTAAACC
422412 AA
124 AA
* * * * *
422414 ATCCACAACCATCACCACCACCAGTTGCTAAACCTAACCCTCCCTCAGAACCAAAACCGCAACCA
1 A---ACCA-CA--ACCACCACCAG-TGCTAAACCTAACCCGCCTTCTGAACCAAAACCACAACCA
422479 CCA
59 CCA
422482 TCTGAGGAGC
Statistics
Matches: 269, Mismatches: 41, Indels: 32
0.79 0.12 0.09
Matches are distributed among these distances:
126 55 0.20
127 5 0.02
129 3 0.01
131 6 0.02
132 156 0.58
133 1 0.00
135 2 0.01
136 2 0.01
138 37 0.14
139 2 0.01
ACGTcount: A:0.37, C:0.43, G:0.09, T:0.11
Consensus pattern (125 bp):
AACCACAACCACCACCAGTGCTAAACCTAACCCGCCTTCTGAACCAAAACCACAACCACCACCAG
TGACTAAACCTAACCCGCCTTCTGAACCAAAACAGCAGCAACCACCAGCCCCTAAACCAA
Found at i:422282 original size:30 final size:30
Alignment explanation
Indices: 422246--422309 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
422236 CCGCCTTCTG
* * *
422246 AACCAAAACCGCAGCCACCACCAGTGCCTA
1 AACCAAAACCACAACCACCACCAGTGACTA
* *
422276 AACCAAATCCACAACCAGCACCAGTGACTA
1 AACCAAAACCACAACCACCACCAGTGACTA
422306 AACC
1 AACC
422310 TAACCCGCCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.41, C:0.41, G:0.11, T:0.08
Consensus pattern (30 bp):
AACCAAAACCACAACCACCACCAGTGACTA
Found at i:422347 original size:180 final size:176
Alignment explanation
Indices: 422024--422403 Score: 482
Period size: 180 Copynumber: 2.1 Consensus size: 176
422014 CCAAAACCGC
* * *
422024 AACCACAACCACCACCGGT-AGCTAAACCGAACCCGCCCTCTGAACCAAAACCACAACCACCACC
1 AACCGCAACCACCACCAGTGAGCAAAACCGAACCCGCCCTCTGAACCAAAACCACAACCACCACC
*
422088 GATTCCTAAACCAAATCCGCAGCCACAACCACCAACAGTGACTAAACCTAACCCGCCCTCTGAAC
66 GATGCCTAAACCAAAT---C--CCACAACCACCAACAGTGACTAAACCTAACCCGCCCTCTGAAC
*
422153 CAAAACCACAACCACCACCAATGCCTAAACCTAACCCGCCTTCTGAACCAA
126 CAAAACCACAACCACCACCAATGACTAAACCTAACCCGCCTTCTGAACCAA
* * * *
422204 AACCGCAACCACCACCAGTGA-CAAAACCTAACCCGCCTTCTGAACCAAAACCGCAGCCACCACC
1 AACCGCAACCACCACCAGTGAGCAAAACCGAACCCGCCCTCTGAACCAAAACCACAACCACCACC
* *
422268 -AGTGCCTAAACCAAAT-CCACAACCAGCACCAGTGACTAAACCTAACCCG-CCTCCTGAACCAA
66 GA-TGCCTAAACCAAATCCCACAACCACCAACAGTGACTAAACCTAACCCGCCCT-CTGAACCAA
* *
422330 AACCAATACCTCAACCACCACCAGTGACTAAACCTAACCTGCCTTCTGAACCAA
129 AACC---A---CAACCACCACCAATGACTAAACCTAACCCGCCTTCTGAACCAA
*
422384 AACTGCAACCACCACCAGTG
1 AACCGCAACCACCACCAGTG
422404 CCTAAACCAA
Statistics
Matches: 177, Mismatches: 14, Indels: 18
0.85 0.07 0.09
Matches are distributed among these distances:
173 3 0.02
174 44 0.25
177 1 0.01
179 1 0.01
180 127 0.72
181 1 0.01
ACGTcount: A:0.37, C:0.42, G:0.10, T:0.11
Consensus pattern (176 bp):
AACCGCAACCACCACCAGTGAGCAAAACCGAACCCGCCCTCTGAACCAAAACCACAACCACCACC
GATGCCTAAACCAAATCCCACAACCACCAACAGTGACTAAACCTAACCCGCCCTCTGAACCAAAA
CCACAACCACCACCAATGACTAAACCTAACCCGCCTTCTGAACCAA
Found at i:422393 original size:48 final size:51
Alignment explanation
Indices: 422287--422411 Score: 157
Period size: 54 Copynumber: 2.5 Consensus size: 51
422277 ACCAAATCCA
* *
422287 CAACCAGCACCAGTGACTAAACCTAACCCGCCTCCTGAACCAAAACCAATACCT
1 CAACCACCACCAGTGACTAAACCTAACCCGCCTCCTGAACCAAAACC-AT--CG
* *
422341 CAACCACCACCAGTGACTAAACCTAACCTGCCTTCTGAACCAAAA-C-T-G
1 CAACCACCACCAGTGACTAAACCTAACCCGCCTCCTGAACCAAAACCATCG
*
422389 CAACCACCACCAGTGCCTAAACC
1 CAACCACCACCAGTGACTAAACC
422412 AAATCCACAA
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
48 22 0.33
51 1 0.02
53 1 0.02
54 42 0.64
ACGTcount: A:0.36, C:0.41, G:0.10, T:0.14
Consensus pattern (51 bp):
CAACCACCACCAGTGACTAAACCTAACCCGCCTCCTGAACCAAAACCATCG
Found at i:422412 original size:84 final size:84
Alignment explanation
Indices: 422324--422481 Score: 216
Period size: 84 Copynumber: 1.9 Consensus size: 84
422314 CCGCCTCCTG
* *
422324 AACCAAAACCA-ATACC-TCAACCACCACCAG-TGACTAAACCTAA-CCTGCCTTCTGAACCAAA
1 AACCAAAACCACA-ACCATC-ACCACCACCAGTTG-CTAAACCTAACCCT-CCCTCAGAACCAAA
*
422385 ACTGCAACCACCACCAGTGCCTA
62 ACCGCAACCACCACCAGTGCCTA
*
422408 AACCAAATCCACAACCATCACCACCACCAGTTGCTAAACCTAACCCTCCCTCAGAACCAAAACCG
1 AACCAAAACCACAACCATCACCACCACCAGTTGCTAAACCTAACCCTCCCTCAGAACCAAAACCG
422473 CAACCACCA
66 CAACCACCA
422482 TCTGAGGAGC
Statistics
Matches: 66, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
84 58 0.88
85 8 0.12
ACGTcount: A:0.39, C:0.42, G:0.07, T:0.13
Consensus pattern (84 bp):
AACCAAAACCACAACCATCACCACCACCAGTTGCTAAACCTAACCCTCCCTCAGAACCAAAACCG
CAACCACCACCAGTGCCTA
Found at i:425499 original size:39 final size:38
Alignment explanation
Indices: 425413--425502 Score: 92
Period size: 39 Copynumber: 2.3 Consensus size: 38
425403 AAATTCAAGA
* *
425413 ATTAGCGGCGCTTGACAGAAAACGCCGCTAAAAATGAGC
1 ATTAGCGGCG-TTAACAAAAAACGCCGCTAAAAATGAGC
* * * *
425452 TTTCGCGGCGTTAATAAAAAAGCGCCGCTGAAAAT-ATGC
1 ATTAGCGGCGTTAACAAAAAA-CGCCGCTAAAAATGA-GC
425491 ATTAGCGGCGTT
1 ATTAGCGGCGTT
425503 TTTGACAAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
38 9 0.22
39 32 0.78
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (38 bp):
ATTAGCGGCGTTAACAAAAAACGCCGCTAAAAATGAGC
Found at i:425714 original size:41 final size:39
Alignment explanation
Indices: 425669--425838 Score: 103
Period size: 41 Copynumber: 4.2 Consensus size: 39
425659 TTTAATCAAC
425669 CGCCGCTAAAGTTAAGGTATTTAGCGGCGATTTCTTTGAAG
1 CGCCGCTAAAGTTAAGGT-TTTAGCGGCG-TTTCTTTGAAG
* * *
425710 CGCCGCGAATA-TT-TGGTCTTATAGCGGCGTTT-TTATATAAG
1 CGCCGCTAA-AGTTAAGGT-TT-TAGCGGCGTTTCTT-T-GAAG
** * * * *
425751 CAACGCTAAAGTTAAGATTTTTAGTGGCGATTCTATGATAAG
1 CGCCGCTAAAGTTAAG-GTTTTAGCGGCGTTTCTTTG--AAG
* ** *
425793 CGCCGCTAATGTTGGGGTTTTAGCGGCGTTTTTGTTGAAG
1 CGCCGCTAAAGTTAAGGTTTTAGCGGCGTTTCT-TTGAAG
425833 CGCCGC
1 CGCCGC
425839 AAAAAAACAT
Statistics
Matches: 95, Mismatches: 23, Indels: 23
0.67 0.16 0.16
Matches are distributed among these distances:
39 2 0.02
40 19 0.20
41 52 0.55
42 21 0.22
43 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (39 bp):
CGCCGCTAAAGTTAAGGTTTTAGCGGCGTTTCTTTGAAG
Found at i:425758 original size:82 final size:81
Alignment explanation
Indices: 425642--425825 Score: 203
Period size: 82 Copynumber: 2.2 Consensus size: 81
425632 CTAATGGTCG
* * ** * *
425642 GGGGTTTTAGTGGCGTTTTTA-ATCAACCGCCGCTAAAGTTAAGGTATTTAGCGGCGATTTCTTT
1 GGGGTTTTAGCGGCGTTTTTATAT-AAGCAACGCTAAAGTTAAGATATTTAGCGGCGA-TTCTAT
425706 G-AAGCGCCGCGAATATT
64 GAAAGCGCCGCGAATATT
* * *
425723 -TGGTCTTATAGCGGCGTTTTTATATAAGCAACGCTAAAGTTAAGATTTTTAGTGGCGATTCTAT
1 GGGGT-TT-TAGCGGCGTTTTTATATAAGCAACGCTAAAGTTAAGATATTTAGCGGCGATTCTAT
* *
425787 GATAAGCGCCGCTAATGTT
64 GA-AAGCGCCGCGAATATT
425806 GGGGTTTTAGCGGCGTTTTT
1 GGGGTTTTAGCGGCGTTTTT
425826 GTTGAAGCGC
Statistics
Matches: 85, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
80 3 0.04
81 8 0.09
82 53 0.62
83 18 0.21
84 3 0.04
ACGTcount: A:0.22, C:0.15, G:0.27, T:0.36
Consensus pattern (81 bp):
GGGGTTTTAGCGGCGTTTTTATATAAGCAACGCTAAAGTTAAGATATTTAGCGGCGATTCTATGA
AAGCGCCGCGAATATT
Done.