Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold372
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: 395264
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.32
Warning! 23199 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:2225 original size:40 final size:40
Alignment explanation
Indices: 2174--2252 Score: 158
Period size: 40 Copynumber: 2.0 Consensus size: 40
2164 AATTAGTTTA
2174 TTATTTTCCTTCAATTTCTTTGTTTTTCATTTCTTATTTC
1 TTATTTTCCTTCAATTTCTTTGTTTTTCATTTCTTATTTC
2214 TTATTTTCCTTCAATTTCTTTGTTTTTCATTTCTTATTT
1 TTATTTTCCTTCAATTTCTTTGTTTTTCATTTCTTATTT
2253 GCTATATTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.13, C:0.16, G:0.03, T:0.68
Consensus pattern (40 bp):
TTATTTTCCTTCAATTTCTTTGTTTTTCATTTCTTATTTC
Found at i:6708 original size:20 final size:18
Alignment explanation
Indices: 6685--6722 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 18
6675 GTTTTTTTAC
6685 AAAAATATTACAAAAAAATA
1 AAAAATA-T-CAAAAAAATA
6705 AAAAATATCAAAAAAATA
1 AAAAATATCAAAAAAATA
6723 TTAATATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.56
19 1 0.06
20 7 0.39
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.18
Consensus pattern (18 bp):
AAAAATATCAAAAAAATA
Found at i:17928 original size:72 final size:71
Alignment explanation
Indices: 17811--17951 Score: 239
Period size: 72 Copynumber: 2.0 Consensus size: 71
17801 ATAAGCAAAT
*
17811 AATCATTGCAATATATGTAAAACTAATTTAAAATATAAAAATTTATTAATATATATTATGTAAAA
1 AATCATTGCAATATATGCAAAACTAATTTAAAATATAAAAATTTATTAATATATA-TATGTAAAA
17876 ACAACAA
65 ACAACAA
*
17883 AATCATTGCAATATATGCACAAAC-AATTTAAAATATAAAAATTTATTAATATATATATGTAAAC
1 AATCATTGCAATATATGCA-AAACTAATTTAAAATATAAAAATTTATTAATATATATATGTAAAA
17947 ACAAC
65 ACAAC
17952 TTTTCTGGAA
Statistics
Matches: 66, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
71 13 0.20
72 49 0.74
73 4 0.06
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.33
Consensus pattern (71 bp):
AATCATTGCAATATATGCAAAACTAATTTAAAATATAAAAATTTATTAATATATATATGTAAAAA
CAACAA
Found at i:18043 original size:14 final size:15
Alignment explanation
Indices: 18021--18057 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
18011 CATCCAAACA
18021 CCAGAAAA-TATTTT
1 CCAGAAAATTATTTT
*
18035 CCAGTAAATTATTTT
1 CCAGAAAATTATTTT
18050 CCAGAAAA
1 CCAGAAAA
18058 GTAAATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.32
Consensus pattern (15 bp):
CCAGAAAATTATTTT
Found at i:18082 original size:14 final size:15
Alignment explanation
Indices: 18060--18097 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
18050 CCAGAAAAGT
*
18060 AAATTATTTTTCA-A
1 AAATCATTTTTCAGA
18074 AAATCATTTTTCAGA
1 AAATCATTTTTCAGA
18089 AAA-CATTTT
1 AAATCATTTT
18098 AGTGCCAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 18 0.82
15 4 0.18
ACGTcount: A:0.42, C:0.11, G:0.03, T:0.45
Consensus pattern (15 bp):
AAATCATTTTTCAGA
Found at i:22512 original size:88 final size:90
Alignment explanation
Indices: 22363--22566 Score: 256
Period size: 88 Copynumber: 2.3 Consensus size: 90
22353 AATTTTTTTA
* *
22363 AAAAAAAGTAATTAA--CCCTTCCATTTTTTTTTTGCACTCAATAGAGCACTTGAACTTTCAAAA
1 AAAAAAAGCAATTAAGCCCCTT-C-TTTTTATTTTGCACTCAATAGAGCACTTGAACTTTCAAAA
* * **
22426 TGCATCAAAAAGCCCTTAAGCTTCTTC
64 TGCATAAAAAAACCCTTAAAATTCTTC
* *
22453 AAAAAAAGCAATTAAGCCCCTTCTTTTTATTTT-CACTCAAT-GGGTACTTGAACTTTCAAAATG
1 AAAAAAAGCAATTAAGCCCCTTCTTTTTATTTTGCACTCAATAGAGCACTTGAACTTTCAAAATG
* *
22516 CATAAAAAAACCTTTAAAATTTTTC
66 CATAAAAAAACCCTTAAAATTCTTC
*
22541 -AAAAAAGCAATTAAGCCCCTGCTTTT
1 AAAAAAAGCAATTAAGCCCCTTCTTTT
22567 ATTAGAAAAT
Statistics
Matches: 101, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
87 25 0.25
88 39 0.39
89 8 0.08
90 23 0.23
91 1 0.01
92 5 0.05
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.33
Consensus pattern (90 bp):
AAAAAAAGCAATTAAGCCCCTTCTTTTTATTTTGCACTCAATAGAGCACTTGAACTTTCAAAATG
CATAAAAAAACCCTTAAAATTCTTC
Found at i:22638 original size:27 final size:28
Alignment explanation
Indices: 22584--22638 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
22574 AATTATTAAA
*
22584 TTTTTAAAAATATATAAAAATTAGAATT
1 TTTTTAAAAATATATAAAAATTAAAATT
22612 TTTTTAAAAATAGTA-AAAAA-TAAAATT
1 TTTTTAAAAATA-TATAAAAATTAAAATT
22639 GTAAAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 6 0.24
28 17 0.68
29 2 0.08
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (28 bp):
TTTTTAAAAATATATAAAAATTAAAATT
Found at i:24348 original size:16 final size:17
Alignment explanation
Indices: 24320--24360 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
24310 TCTCAAGTTT
24320 TTTTATCTT-CGAAACTA
1 TTTTAT-TTCCGAAACTA
24337 -TTTATTTCCGAAACTA
1 TTTTATTTCCGAAACTA
24353 TTTTATTT
1 TTTTATTT
24361 TTACTTGTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 2 0.09
16 13 0.59
17 7 0.32
ACGTcount: A:0.27, C:0.15, G:0.05, T:0.54
Consensus pattern (17 bp):
TTTTATTTCCGAAACTA
Found at i:30256 original size:18 final size:18
Alignment explanation
Indices: 30233--30269 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
30223 TGATTTTTCG
*
30233 AATTCGAATAACTTGAAT
1 AATTCGAATAAATTGAAT
30251 AATTCGAATAAATTGAAT
1 AATTCGAATAAATTGAAT
30269 A
1 A
30270 TCAAACTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.32
Consensus pattern (18 bp):
AATTCGAATAAATTGAAT
Found at i:30498 original size:19 final size:21
Alignment explanation
Indices: 30465--30504 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
30455 TTACTCCTCA
*
30465 AAACTTTTTATTTTTC-CCCT
1 AAACTTTTTACTTTTCACCCT
30485 AAAC-TTTTACTTTTCACCCT
1 AAACTTTTTACTTTTCACCCT
30505 TTACTCCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.23, C:0.28, G:0.00, T:0.50
Consensus pattern (21 bp):
AAACTTTTTACTTTTCACCCT
Found at i:42816 original size:25 final size:25
Alignment explanation
Indices: 42758--42817 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
42748 AGCTCTAGAT
* *
42758 AGCCATATACCGAGAAGTTCAAGCG
1 AGCCATATATCGAGAAGTCCAAGCG
*
42783 AGCCA-ATATCTAGAAGCTCCAAG-G
1 AGCCATATATCGAGAAG-TCCAAGCG
42807 AGCCATATATC
1 AGCCATATATC
42818 AGGACGCTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 15 0.50
25 15 0.50
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (25 bp):
AGCCATATATCGAGAAGTCCAAGCG
Found at i:52490 original size:27 final size:26
Alignment explanation
Indices: 52447--52499 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 26
52437 CACCAATGAT
*
52447 TCAGGGAATCAGTACTTAGCAACCCC
1 TCAGGGAATCAGCACTTAGCAACCCC
52473 TCAGGGAAATCAGCACTTAGCAACCCC
1 TCAGGG-AATCAGCACTTAGCAACCCC
52500 CTTCACATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 6 0.24
27 19 0.76
ACGTcount: A:0.32, C:0.32, G:0.19, T:0.17
Consensus pattern (26 bp):
TCAGGGAATCAGCACTTAGCAACCCC
Found at i:52494 original size:102 final size:102
Alignment explanation
Indices: 52378--52573 Score: 338
Period size: 102 Copynumber: 1.9 Consensus size: 102
52368 TGAGTCGGGG
* *
52378 AATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGGGATCAGCACTTAGCAACCACCAA
1 AATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCACCAA
* *
52443 TGATTCAGGGAATCAGTACTTAGCAACCCCTCAGGGA
66 TGAGTCAGGGAATCAGCACTTAGCAACCCCTCAGGGA
52480 AATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCACCAA
1 AATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCACCAA
* *
52545 TGAGTCGGGGAGTCAGCACTTAGCAACCC
66 TGAGTCAGGGAATCAGCACTTAGCAACCC
52574 TTTTCACATT
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 88 1.00
ACGTcount: A:0.32, C:0.29, G:0.19, T:0.20
Consensus pattern (102 bp):
AATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCACCAA
TGAGTCAGGGAATCAGCACTTAGCAACCCCTCAGGGA
Found at i:52539 original size:42 final size:42
Alignment explanation
Indices: 52480--52614 Score: 162
Period size: 42 Copynumber: 3.4 Consensus size: 42
52470 CCCTCAGGGA
*
52480 AATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGG
1 AATCAGCACTTAGCAACCCACTTCACATTTAAGATACGGTGG
*
52522 AATCAGCACTTAGCAA-CCAC--CA-A--TGAG-T-CGG-GG
1 AATCAGCACTTAGCAACCCACTTCACATTTAAGATACGGTGG
* **
52555 AGTCAGCACTTAGCAACCCTTTTCACATTTAAGATACGGTGG
1 AATCAGCACTTAGCAACCCACTTCACATTTAAGATACGGTGG
52597 AATCAGCACTTAGCAACC
1 AATCAGCACTTAGCAACC
52615 ACCAATGAAT
Statistics
Matches: 77, Mismatches: 7, Indels: 18
0.75 0.07 0.18
Matches are distributed among these distances:
33 17 0.22
34 5 0.06
35 1 0.01
36 5 0.06
37 1 0.01
38 1 0.01
39 5 0.06
40 1 0.01
41 6 0.08
42 35 0.45
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (42 bp):
AATCAGCACTTAGCAACCCACTTCACATTTAAGATACGGTGG
Found at i:52566 original size:33 final size:33
Alignment explanation
Indices: 52520--52674 Score: 126
Period size: 33 Copynumber: 4.6 Consensus size: 33
52510 AAGATACGGT
52520 GGAATCAGCACTTAGCAACCACCAATGAGTCGG
1 GGAATCAGCACTTAGCAACCACCAATGAGTCGG
* *
52553 GGAGTCAGCACTTAGCAACC-CTTTTCACATTTAAGATACGG
1 GGAATCAGCACTTAGCAACCAC----CA-A--TGAG-T-CGG
*
52594 TGGAATCAGCACTTAGCAACCACCAATGAATCGG
1 -GGAATCAGCACTTAGCAACCACCAATGAGTCGG
* *
52628 GGAATCAGCACTTAGAAACC-CC--T---TGGG
1 GGAATCAGCACTTAGCAACCACCAATGAGTCGG
52655 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
52675 CCCCTTTATA
Statistics
Matches: 103, Mismatches: 8, Indels: 28
0.74 0.06 0.20
Matches are distributed among these distances:
27 22 0.21
30 1 0.01
32 3 0.03
33 38 0.37
34 3 0.03
35 1 0.01
36 4 0.04
37 1 0.01
38 1 0.01
39 5 0.05
40 1 0.01
41 3 0.03
42 19 0.18
43 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.19
Consensus pattern (33 bp):
GGAATCAGCACTTAGCAACCACCAATGAGTCGG
Found at i:52580 original size:75 final size:75
Alignment explanation
Indices: 52480--52649 Score: 295
Period size: 75 Copynumber: 2.3 Consensus size: 75
52470 CCCTCAGGGA
52480 AATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCACCAA
1 AATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCACCAA
*
52545 TGAGTCGGGG
66 TGAATCGGGG
* **
52555 AGTCAGCACTTAGCAACCCTTTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCACCAA
1 AATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCACCAA
52620 TGAATCGGGG
66 TGAATCGGGG
*
52630 AATCAGCACTTAGAAACCCC
1 AATCAGCACTTAGCAACCCC
52650 TTGGGGGAAT
Statistics
Matches: 88, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 88 1.00
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.21
Consensus pattern (75 bp):
AATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCACCAA
TGAATCGGGG
Found at i:52635 original size:177 final size:177
Alignment explanation
Indices: 52339--52677 Score: 561
Period size: 177 Copynumber: 1.9 Consensus size: 177
52329 TATCCGTTAT
* *
52339 CGGTGGATTCAACATTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
1 CGGTGGAATCAACACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
* * * *
52404 ATTTAAGATACGGTGGGATCAGCACTTAGCAACCACCAATGATTCAGGGAATCAGTACTTAGCAA
66 ATTTAAGATACGGTGGAATCAGCACTTAGCAACCACCAATGAATCAGGGAATCAGCACTTAGAAA
52469 CCCCTCAGGGAAATCAGCACTTAGCAACCCCCTTCACATTTAAGATA
131 CCCCTCAGGGAAATCAGCACTTAGCAACCCCCTTCACATTTAAGATA
* * *
52516 CGGTGGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAGTCAGCACTTAGCAACCCTTTTCAC
1 CGGTGGAATCAACACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
*
52581 ATTTAAGATACGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGAAA
66 ATTTAAGATACGGTGGAATCAGCACTTAGCAACCACCAATGAATCAGGGAATCAGCACTTAGAAA
** *
52646 CCCCTTGGGGGAATCAGCACTTAGCAACCCCC
131 CCCCTCAGGGAAATCAGCACTTAGCAACCCCC
52678 CTTTATATTC
Statistics
Matches: 149, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
177 149 1.00
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.21
Consensus pattern (177 bp):
CGGTGGAATCAACACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
ATTTAAGATACGGTGGAATCAGCACTTAGCAACCACCAATGAATCAGGGAATCAGCACTTAGAAA
CCCCTCAGGGAAATCAGCACTTAGCAACCCCCTTCACATTTAAGATA
Found at i:56966 original size:21 final size:21
Alignment explanation
Indices: 56942--57013 Score: 54
Period size: 21 Copynumber: 3.4 Consensus size: 21
56932 ACATAAATGC
56942 TAAACAGAAACCCATAAGGGT
1 TAAACAGAAACCCATAAGGGT
** * * * * *
56963 TAAATGGTAGCTCATAAGAGC
1 TAAACAGAAACCCATAAGGGT
* * *
56984 TGAACGGAAACCTATAAGGGT
1 TAAACAGAAACCCATAAGGGT
57005 TAAACAGAA
1 TAAACAGAA
57014 GCTCAATAGA
Statistics
Matches: 34, Mismatches: 17, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.18
Consensus pattern (21 bp):
TAAACAGAAACCCATAAGGGT
Found at i:56995 original size:42 final size:42
Alignment explanation
Indices: 56948--57060 Score: 138
Period size: 42 Copynumber: 2.7 Consensus size: 42
56938 ATGCTAAACA
** *
56948 GAAACCCATAAGGGTTAAATGGTAGCTC-ATAAGAGCTGAACG
1 GAAACCCATAAGGGTTAAACAGAAGCTCAAT-AGAGCTGAACG
*
56990 GAAACCTATAAGGGTTAAACAGAAGCTCAATAGAGCTGAACG
1 GAAACCCATAAGGGTTAAACAGAAGCTCAATAGAGCTGAACG
* * * *
57032 GAAACTCATATGAGTTAAACAAAAGCTCA
1 GAAACCCATAAGGGTTAAACAGAAGCTCA
57061 TGGGAGCTAA
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
42 59 0.97
43 2 0.03
ACGTcount: A:0.42, C:0.17, G:0.22, T:0.19
Consensus pattern (42 bp):
GAAACCCATAAGGGTTAAACAGAAGCTCAATAGAGCTGAACG
Found at i:64003 original size:20 final size:21
Alignment explanation
Indices: 63961--64003 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
63951 TCGAAGACTG
*
63961 AATAGAAGCACATAAGTGCTA
1 AATAGAAGCACATAAGGGCTA
* *
63982 AATAGAA-CCCATAAGGGTTA
1 AATAGAAGCACATAAGGGCTA
64002 AA
1 AA
64004 CGGAAGCTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.49, C:0.14, G:0.19, T:0.19
Consensus pattern (21 bp):
AATAGAAGCACATAAGGGCTA
Found at i:66407 original size:27 final size:27
Alignment explanation
Indices: 66369--66422 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
66359 AGAACCACCG
66369 CTTGAGTTAGTAAAAATTTGATTTCAT
1 CTTGAGTTAGTAAAAATTTGATTTCAT
66396 CTTGAGTTAGTAAAAATTTGATTTCAT
1 CTTGAGTTAGTAAAAATTTGATTTCAT
66423 GATATTCTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.44
Consensus pattern (27 bp):
CTTGAGTTAGTAAAAATTTGATTTCAT
Found at i:71347 original size:47 final size:49
Alignment explanation
Indices: 71254--71348 Score: 122
Period size: 47 Copynumber: 2.0 Consensus size: 49
71244 TCTATTGATA
* *
71254 AATGAATGTCCATAACCCCCTCAAATTTATCCTATTGTAACCCCTAAAG
1 AATGAATGTCCATAACCCCCTCAAATTCATCATATTGTAACCCCTAAAG
* * * *
71303 AATGAATGTCTATAA-CCCCT-AAATTCATTATCTTGTAACGCCTAAA
1 AATGAATGTCCATAACCCCCTCAAATTCATCATATTGTAACCCCTAAA
71349 TCATTTATAG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
47 21 0.52
48 5 0.12
49 14 0.35
ACGTcount: A:0.36, C:0.25, G:0.08, T:0.31
Consensus pattern (49 bp):
AATGAATGTCCATAACCCCCTCAAATTCATCATATTGTAACCCCTAAAG
Found at i:75525 original size:19 final size:19
Alignment explanation
Indices: 75473--75537 Score: 85
Period size: 19 Copynumber: 3.3 Consensus size: 19
75463 GCGCCAATGG
*
75473 GTAATTTTGTATGTATATT
1 GTAATTTTGTATGAATATT
*
75492 GTAACTTTTTATATGAATATT
1 GTAA--TTTTGTATGAATATT
*
75513 ATAATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
75532 GTAATT
1 GTAATT
75538 ATTTTATAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
19 23 0.59
21 16 0.41
ACGTcount: A:0.32, C:0.02, G:0.12, T:0.54
Consensus pattern (19 bp):
GTAATTTTGTATGAATATT
Found at i:75588 original size:61 final size:61
Alignment explanation
Indices: 75516--75659 Score: 270
Period size: 61 Copynumber: 2.4 Consensus size: 61
75506 GAATATTATA
*
75516 ATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTATATTTATAGTTTTTGATTAGT
1 ATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTATATTTATAGTTTTGGATTAGT
*
75577 ATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGATTAGT
1 ATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTATATTTATAGTTTTGGATTAGT
75638 ATTTTGTATGAATATTGTAATT
1 ATTTTGTATGAATATTGTAATT
75660 TTGTAATTTT
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 81 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.58
Consensus pattern (61 bp):
ATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTATATTTATAGTTTTGGATTAGT
Found at i:75668 original size:27 final size:27
Alignment explanation
Indices: 75638--75690 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
75628 TTGGATTAGT
*
75638 ATTTTGTATGAATATTGTAATTTTGTA
1 ATTTTGTATGAATATTGTAATATTGTA
75665 ATTTTGTATGAATATTGTAATATTGT
1 ATTTTGTATGAATATTGTAATATTGT
75691 TACAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (27 bp):
ATTTTGTATGAATATTGTAATATTGTA
Found at i:76874 original size:23 final size:22
Alignment explanation
Indices: 76840--76898 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 22
76830 CCCGGCCCGT
76840 TTTTTAATTAAAATTAAAATTATA
1 TTTTTAA-TAAAATTAAAATTA-A
76864 TTTTTAATAAAATTAAAATTAA
1 TTTTTAATAAAATTAAAATTAA
* *
76886 TTGTTATTAAAAT
1 TTTTTAATAAAAT
76899 AAATTGTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
22 12 0.36
23 14 0.42
24 7 0.21
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TTTTTAATAAAATTAAAATTAA
Found at i:76896 original size:16 final size:16
Alignment explanation
Indices: 76875--76930 Score: 94
Period size: 16 Copynumber: 3.5 Consensus size: 16
76865 TTTTAATAAA
*
76875 ATTAAAATTAATTGTT
1 ATTAAAATAAATTGTT
76891 ATTAAAATAAATTGTT
1 ATTAAAATAAATTGTT
*
76907 ATCAAAATAAATTGTT
1 ATTAAAATAAATTGTT
76923 ATTAAAAT
1 ATTAAAAT
76931 TGTATCAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (16 bp):
ATTAAAATAAATTGTT
Found at i:77002 original size:19 final size:19
Alignment explanation
Indices: 76978--77028 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 19
76968 ATCTAACATT
76978 TTGTTAATAAAATTATTAA
1 TTGTTAATAAAATTATTAA
76997 TTGTTAAT----TGTATTAA
1 TTGTTAATAAAAT-TATTAA
*
77013 TTGTTACTAAAATTAT
1 TTGTTAATAAAATTAT
77029 CAAATTATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 10
0.70 0.03 0.27
Matches are distributed among these distances:
15 1 0.04
16 13 0.50
19 11 0.42
20 1 0.04
ACGTcount: A:0.39, C:0.02, G:0.08, T:0.51
Consensus pattern (19 bp):
TTGTTAATAAAATTATTAA
Found at i:79775 original size:20 final size:20
Alignment explanation
Indices: 79750--79789 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
79740 AAAAATAATC
79750 TTATTTATAACTCGGTTATT
1 TTATTTATAACTCGGTTATT
*
79770 TTATTTATAACTCTGTTATT
1 TTATTTATAACTCGGTTATT
79790 GAATATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.25, C:0.10, G:0.07, T:0.57
Consensus pattern (20 bp):
TTATTTATAACTCGGTTATT
Found at i:79798 original size:20 final size:20
Alignment explanation
Indices: 79755--79798 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
79745 TAATCTTATT
** *
79755 TATAACTCGGTTATTTTATT
1 TATAACTCGGTTATTGAATA
*
79775 TATAACTCTGTTATTGAATA
1 TATAACTCGGTTATTGAATA
79795 TATA
1 TATA
79799 TATACAAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.50
Consensus pattern (20 bp):
TATAACTCGGTTATTGAATA
Found at i:81440 original size:10 final size:10
Alignment explanation
Indices: 81425--81456 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
81415 GCCTAAAATT
81425 ATATATAATG
1 ATATATAATG
*
81435 ATATATAATA
1 ATATATAATG
81445 ATATATAATG
1 ATATATAATG
81455 AT
1 AT
81457 GGGGACGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (10 bp):
ATATATAATG
Found at i:82375 original size:18 final size:18
Alignment explanation
Indices: 82352--82396 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
82342 ATATTTCGGG
82352 CGGGCCGTCGGGTCAGAC
1 CGGGCCGTCGGGTCAGAC
82370 CGGGCCGTCGGGTCAGAC
1 CGGGCCGTCGGGTCAGAC
82388 CGGGCCGTC
1 CGGGCCGTC
82397 CGGCCCATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.09, C:0.36, G:0.44, T:0.11
Consensus pattern (18 bp):
CGGGCCGTCGGGTCAGAC
Found at i:83313 original size:29 final size:29
Alignment explanation
Indices: 83267--83339 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
83257 GATTTTTATG
*
83267 TTATGTATATTATTTTAT-TATATAATATA
1 TTATGTATATTATATTATAT-TATAATATA
*
83296 TTATGTTATATTA-ATTATATTATATTATA
1 TTATG-TATATTATATTATATTATAATATA
83325 TTAT-TATA-TATATTA
1 TTATGTATATTATATTA
83340 ATAAAGTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
26 2 0.05
27 8 0.21
29 21 0.54
30 8 0.21
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (29 bp):
TTATGTATATTATATTATATTATAATATA
Found at i:83317 original size:5 final size:5
Alignment explanation
Indices: 83272--83339 Score: 70
Period size: 5 Copynumber: 13.4 Consensus size: 5
83262 TTATGTTATG
*
83272 TATAT TAT-T T-TAT TATAT AATATAT TATGT TATAT TA-AT TATAT TATAT
1 TATAT TATAT TATAT TATAT --TATAT TATAT TATAT TATAT TATAT TATAT
83321 TATAT TATTAT ATATAT TA
1 TATAT TA-TAT -TATAT TA
83340 ATAAAGTAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
3 1 0.02
4 8 0.15
5 32 0.59
6 6 0.11
7 7 0.13
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:86229 original size:19 final size:19
Alignment explanation
Indices: 86189--86229 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
86179 TTTATTTTTT
***
86189 AAATGAAGATAATTATTTA
1 AAATGAAGATAATTAAACA
86208 AAATGAAGATAATTAAACA
1 AAATGAAGATAATTAAACA
86227 AAA
1 AAA
86230 CCATTTAGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.61, C:0.02, G:0.10, T:0.27
Consensus pattern (19 bp):
AAATGAAGATAATTAAACA
Found at i:90466 original size:36 final size:36
Alignment explanation
Indices: 90426--90497 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
90416 AATATTGCCG
90426 TTACTGTTACCGATTC-AGCACTTTGTGTGTCGAATA
1 TTACTGTTACCGATTCGA-CACTTTGTGTGTCGAATA
*
90462 TTACTGTTATCGATTCGACACTTTGTGTGTCGAATA
1 TTACTGTTACCGATTCGACACTTTGTGTGTCGAATA
90498 CTGTTACCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 33 0.97
37 1 0.03
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.40
Consensus pattern (36 bp):
TTACTGTTACCGATTCGACACTTTGTGTGTCGAATA
Found at i:90651 original size:45 final size:45
Alignment explanation
Indices: 90462--90656 Score: 248
Period size: 45 Copynumber: 4.3 Consensus size: 45
90452 GTGTCGAATA
*
90462 TTACTGTTA-TCGATTCGACACTTTGTGTGTCGAATACTGTTACCA
1 TTACTGTTACT-GATTCGACACTTTGTGTGTCGAATACTGTTACCG
* * *
90507 TTATTGTTACTGATTTGACACTTTGTGTGTCGAATATTGTTACCG
1 TTACTGTTACTGATTCGACACTTTGTGTGTCGAATACTGTTACCG
* * *
90552 TTACTGTTACTAATTCGGCACTTTGTGTGTCGAATACTGTTACTG
1 TTACTGTTACTGATTCGACACTTTGTGTGTCGAATACTGTTACCG
* * * * *
90597 TTATTGTTACCGATTCGACACTTTATGTGTTGAATACTGTTACTG
1 TTACTGTTACTGATTCGACACTTTGTGTGTCGAATACTGTTACCG
* *
90642 CTACCGTTACTGATT
1 TTACTGTTACTGATT
90657 ACTGATAGGT
Statistics
Matches: 129, Mismatches: 20, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
45 128 0.99
46 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.18, T:0.43
Consensus pattern (45 bp):
TTACTGTTACTGATTCGACACTTTGTGTGTCGAATACTGTTACCG
Found at i:95932 original size:16 final size:17
Alignment explanation
Indices: 95901--95933 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
95891 TTAGCTGGAA
95901 AAAAATATAAATATGTAC
1 AAAAATAT-AATATGTAC
95919 AAAAATAT-ATATGTA
1 AAAAATATAATATGTA
95934 TATAGATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.30
Consensus pattern (17 bp):
AAAAATATAATATGTAC
Found at i:97558 original size:45 final size:44
Alignment explanation
Indices: 97501--97621 Score: 156
Period size: 44 Copynumber: 2.7 Consensus size: 44
97491 CGGCTTTAAC
**
97501 CTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTCAT-CTTTAGT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-CATAC-TTAGT
* * *
97546 CTGCCCCACTGCAACTTCA-GAAGGATAAGACTTGCTTACTTAGT
1 CTGCTCCACTGCAACTTCAGGGA-GATAAGACTTGCATACTTAGT
97590 CTGCTCCACTGCAACTTCAGGGAGATAAGACT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACT
97622 AGATGCGATC
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
44 36 0.55
45 30 0.45
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (44 bp):
CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCATACTTAGT
Found at i:97604 original size:44 final size:45
Alignment explanation
Indices: 97501--97700 Score: 150
Period size: 44 Copynumber: 4.6 Consensus size: 45
97491 CGGCTTTAAC
* **
97501 CTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTCATCTTTAGT
1 CTGCTCCACTGCAACTTCAGAGAGATAAGACTTGTCATCTTTAGT
* *
97546 CTGCCCCACTGCAACTTCAGA-AGGATAAGACTTG-CTTAC-TTAGT
1 CTGCTCCACTGCAACTTCAGAGA-GATAAGACTTGTCAT-CTTTAGT
* * *
97590 CTGCTCCACTGCAACTTCAGGGAGATAAGACTAG--ATGC--GA-T
1 CTGCTCCACTGCAACTTCAGAGAGATAAGACTTGTCAT-CTTTAGT
* * * ** *
97631 CTGCT-CTCTGTAACTTCAGAGAGATAAGATTTGTGGT-TTTAAT
1 CTGCTCCACTGCAACTTCAGAGAGATAAGACTTGTCATCTTTAGT
* * *
97674 CCGCTCCACTACAACTTCAGGGAGATA
1 CTGCTCCACTGCAACTTCAGAGAGATA
97701 GGATCATTGG
Statistics
Matches: 123, Mismatches: 23, Indels: 19
0.75 0.14 0.12
Matches are distributed among these distances:
40 23 0.19
41 6 0.05
42 3 0.02
43 7 0.06
44 54 0.44
45 30 0.24
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (45 bp):
CTGCTCCACTGCAACTTCAGAGAGATAAGACTTGTCATCTTTAGT
Found at i:124656 original size:16 final size:17
Alignment explanation
Indices: 124625--124657 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
124615 TTAGCTGGAA
124625 AAAAATATAAATATGTAC
1 AAAAATAT-AATATGTAC
124643 AAAAATAT-ATATGTA
1 AAAAATATAATATGTA
124658 TATAGATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.30
Consensus pattern (17 bp):
AAAAATATAATATGTAC
Found at i:125599 original size:32 final size:32
Alignment explanation
Indices: 125563--125624 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
125553 CCCTAACGGC
125563 ATTTCAGAAGCATCCAAAGTATCAACCTTTGT
1 ATTTCAGAAGCATCCAAAGTATCAACCTTTGT
125595 ATTTCAGAAGCATCCAAAGTATCAACCTTT
1 ATTTCAGAAGCATCCAAAGTATCAACCTTT
125625 AAATGACTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.23, G:0.11, T:0.31
Consensus pattern (32 bp):
ATTTCAGAAGCATCCAAAGTATCAACCTTTGT
Found at i:128207 original size:130 final size:130
Alignment explanation
Indices: 127999--128248 Score: 333
Period size: 130 Copynumber: 1.9 Consensus size: 130
127989 AATAGTAATC
* * * * *
127999 AAGTCATTCATCACAAAGACGAACGACCCGTTACCACATTTACTTTTCCTCAACCATGTAATGGC
1 AAGTCATTCATCACAAAGAAGAACGACCCATGACCACATTTACTTTTCATCAACCATGCAATGGC
* * * *
128064 AATAAAGGGATATCATTTACCTGTATTTTAGGCTATGAATTCTACTATTCTGAATGTCAATCCAA
66 AATAAAGGAATATCATTTACCAGTATTTTAGGCTATGAATACCACTATTCTGAATGTCAATCCAA
*
128129 AAGTCATTCATCATAAAGAAGAACGACCCATGACCACATTTACTTTTCATCAACCATGCAAT-GC
1 AAGTCATTCATCACAAAGAAGAACGACCCATGACCACATTTACTTTTCATCAACCATGCAATGGC
* * * * *
128193 TAAT-GAGAGAATATCATTTAGCAGTGTTTTAGGTTATGAATACCACTATTGTGAAT
66 -AATAAAG-GAATATCATTTACCAGTATTTTAGGCTATGAATACCACTATTCTGAAT
128249 TACGCTACAT
Statistics
Matches: 103, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
129 4 0.04
130 99 0.96
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.31
Consensus pattern (130 bp):
AAGTCATTCATCACAAAGAAGAACGACCCATGACCACATTTACTTTTCATCAACCATGCAATGGC
AATAAAGGAATATCATTTACCAGTATTTTAGGCTATGAATACCACTATTCTGAATGTCAATCCAA
Found at i:129612 original size:25 final size:25
Alignment explanation
Indices: 129557--129627 Score: 81
Period size: 25 Copynumber: 2.9 Consensus size: 25
129547 AGCCCTCTCT
* *
129557 CAAGCCATATGATGAGAAGCTCATG
1 CAAGCCATATAATGGGAAGCTCATG
*
129582 TAAGCCATATAATGGGAAGCTCATG
1 CAAGCCATATAATGGGAAGCTCATG
* * *
129607 CGAGCCA-ATAACGGGTAGCTC
1 CAAGCCATATAATGGGAAGCTC
129628 CGAAGAGCCA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
24 12 0.31
25 27 0.69
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.20
Consensus pattern (25 bp):
CAAGCCATATAATGGGAAGCTCATG
Found at i:129653 original size:25 final size:26
Alignment explanation
Indices: 129623--129751 Score: 87
Period size: 25 Copynumber: 5.2 Consensus size: 26
129613 AATAACGGGT
129623 AGCTCCGAAGAGCCATTA-ATCGAGA
1 AGCTCCGAAGAGCCATTATATCGAGA
* *
129648 AGCTCCGGATAGCCA-TATATC-AGAA
1 AGCTCCGAAGAGCCATTATATCGAG-A
* *
129673 AG-TTC-AAGTG--AGTTATATCGAGA
1 AGCTCCGAAGAGCCA-TTATATCGAGA
* *
129696 AGCTCCGGAGAGCCATTA-ATCAAGA
1 AGCTCCGAAGAGCCATTATATCGAGA
* *
129721 AGCTCACGAAGGGTCA-TATATCGAGA
1 AGCTC-CGAAGAGCCATTATATCGAGA
*
129747 CGCTC
1 AGCTC
129752 ATAAGAGTTG
Statistics
Matches: 78, Mismatches: 15, Indels: 21
0.68 0.13 0.18
Matches are distributed among these distances:
21 1 0.01
23 11 0.14
24 10 0.13
25 35 0.45
26 20 0.26
27 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.20
Consensus pattern (26 bp):
AGCTCCGAAGAGCCATTATATCGAGA
Found at i:137409 original size:25 final size:25
Alignment explanation
Indices: 137380--137441 Score: 97
Period size: 25 Copynumber: 2.5 Consensus size: 25
137370 GCCCCCTCTC
*
137380 GAGCCATATAACGGGAAGATCATGT
1 GAGCCATGTAACGGGAAGATCATGT
* *
137405 GAGCCATGTAATGGGAAGCTCATGT
1 GAGCCATGTAACGGGAAGATCATGT
137430 GAGCCATGTAAC
1 GAGCCATGTAAC
137442 TAAAAGCTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (25 bp):
GAGCCATGTAACGGGAAGATCATGT
Found at i:137448 original size:25 final size:25
Alignment explanation
Indices: 137399--137449 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
137389 AACGGGAAGA
**
137399 TCATGTGAGCCATGTAATGGGAAGC
1 TCATGTGAGCCATGTAATGAAAAGC
137424 TCATGTGAGCCATGTAACT-AAAAGC
1 TCATGTGAGCCATGTAA-TGAAAAGC
137449 T
1 T
137450 TATCCATGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 22 0.96
26 1 0.04
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.25
Consensus pattern (25 bp):
TCATGTGAGCCATGTAATGAAAAGC
Found at i:137560 original size:26 final size:26
Alignment explanation
Indices: 137504--137582 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 26
137494 AAGCTCATGC
* *
137504 GAGCCA-ATAACGAGTAGCTC-CGAA
1 GAGCCATATAACGAGAAGCTCTTGAA
137528 GAGCCAT-TAATCGAGAAGCTCTTGAA
1 GAGCCATATAA-CGAGAAGCTCTTGAA
* * *
137554 GGGCCATATAACGAGATGCTCAT-AA
1 GAGCCATATAACGAGAAGCTCTTGAA
137579 GAGC
1 GAGC
137583 TGCAGTGTGT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
24 9 0.20
25 14 0.31
26 19 0.42
27 3 0.07
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18
Consensus pattern (26 bp):
GAGCCATATAACGAGAAGCTCTTGAA
Found at i:137581 original size:51 final size:48
Alignment explanation
Indices: 137462--137582 Score: 129
Period size: 48 Copynumber: 2.5 Consensus size: 48
137452 TCCATGCTGT
* *
137462 ATAACGGGTAGCTCATAAGAGCCATAATCAGGAAGCTCATGCGAGCCA
1 ATAACGAGTAGCTCATAAGAGCCATAATCAGGAAGCTCATGAGAGCCA
** * *
137510 ATAACGAGTAGCTCCGAAGAGCCATTAATC-GAGAAGCTCTTGAAGGGCCA
1 ATAACGAGTAGCTCATAAGAGCCA-TAATCAG-GAAGCTCATG-AGAGCCA
137560 TATAACGAG-ATGCTCATAAGAGC
1 -ATAACGAGTA-GCTCATAAGAGC
137583 TGCAGTGTGT
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
48 22 0.37
49 14 0.23
50 6 0.10
51 18 0.30
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.18
Consensus pattern (48 bp):
ATAACGAGTAGCTCATAAGAGCCATAATCAGGAAGCTCATGAGAGCCA
Found at i:138327 original size:17 final size:18
Alignment explanation
Indices: 138299--138332 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
138289 ATCTTACCAA
*
138299 ACATTCATACACTATTAT
1 ACATTCATACACCATTAT
138317 ACATT-ATACACCATTA
1 ACATTCATACACCATTA
138333 CTAAGTTTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.35
Consensus pattern (18 bp):
ACATTCATACACCATTAT
Found at i:138637 original size:44 final size:44
Alignment explanation
Indices: 138572--138777 Score: 313
Period size: 44 Copynumber: 4.5 Consensus size: 44
138562 ACACGGATCA
* **
138572 CACTTATCACTTGTCATTGATCAGATAAGCGTAGCTAAAGCTAC
1 CACTTATCACTTGTCACTGATCAGATAAGTATAGCTAAAGCTAC
138616 CACTTATCACTTGTCACTGATCAGATAAGTATAGCTAAAGCTAC
1 CACTTATCACTTGTCACTGATCAGATAAGTATAGCTAAAGCTAC
138660 CACTTATCACTTGTCACTGATCAGATAAGTATAGCTAAAGCTAC
1 CACTTATCACTTGTCACTGATCAGATAAGTATAGCTAAAGCTAC
*
138704 CACTTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTAC
1 CAC-T-T-A----TCACTTGTCACTGATCAGATAAGTATAGCTAAAGCTAC
138755 CACTTATCACTTGTCACTGATCA
1 CACTTATCACTTGTCACTGATCA
138778 AAAGTACTCA
Statistics
Matches: 151, Mismatches: 4, Indels: 14
0.89 0.02 0.08
Matches are distributed among these distances:
44 105 0.70
45 1 0.01
46 1 0.01
47 1 0.01
48 1 0.01
49 1 0.01
50 1 0.01
51 40 0.26
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.31
Consensus pattern (44 bp):
CACTTATCACTTGTCACTGATCAGATAAGTATAGCTAAAGCTAC
Found at i:138671 original size:51 final size:51
Alignment explanation
Indices: 138616--138772 Score: 238
Period size: 51 Copynumber: 3.2 Consensus size: 51
138606 CTAAAGCTAC
138616 CACTTATCACTTGTCACTGATCAGATAAGTATAGCTAAAGCT---AC----
1 CACTTATCACTTGTCACTGATCAGATAAGTATAGCTAAAGCTACCACTTAT
138660 CACTTATCACTTGTCACTGATCAGATAAGTATAGCTAAAGCTACCACTTAT
1 CACTTATCACTTGTCACTGATCAGATAAGTATAGCTAAAGCTACCACTTAT
* *
138711 CACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CACTTATCACTTGTCACTGATCAGATAAGTATAGCTAAAGCTACCACTTAT
*
138762 CACTTGTCACT
1 CACTTATCACT
138773 GATCAAAAGT
Statistics
Matches: 104, Mismatches: 2, Indels: 7
0.92 0.02 0.06
Matches are distributed among these distances:
44 42 0.40
47 2 0.02
51 60 0.58
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.31
Consensus pattern (51 bp):
CACTTATCACTTGTCACTGATCAGATAAGTATAGCTAAAGCTACCACTTAT
Found at i:138737 original size:95 final size:88
Alignment explanation
Indices: 138572--138777 Score: 313
Period size: 95 Copynumber: 2.3 Consensus size: 88
138562 ACACGGATCA
* *
138572 CACTTATCACTTGTCATTGATCAGATAAGCGTAGCTAAAGCTACCACTTATCACTTGTCACTGAT
1 CACTTATCACTTGTCACTGATCAGATAAGCATAGCTAAAGCTACCACTTATCACTTGTCACTGAT
138637 CAGATAAGTATAGCTAAAGCTAC
66 CAGATAAGTATAGCTAAAGCTAC
*
138660 CACTTATCACTTGTCACTGATCAGATAAGTATAGCTAAAGCTACCACTTATCACTTGTCACTTGT
1 CACTTATCACTTGTCACTGATCAGATAAGCATAGCTAAAGCTACCAC-T-T-A----TCACTTGT
*
138725 CACTGATCAGATAAGTGTAGCTAAAGCTAC
59 CACTGATCAGATAAGTATAGCTAAAGCTAC
138755 CACTTATCACTTGTCACTGATCA
1 CACTTATCACTTGTCACTGATCA
138778 AAAGTACTCA
Statistics
Matches: 107, Mismatches: 4, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
88 44 0.41
89 1 0.01
90 1 0.01
91 1 0.01
95 60 0.56
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.31
Consensus pattern (88 bp):
CACTTATCACTTGTCACTGATCAGATAAGCATAGCTAAAGCTACCACTTATCACTTGTCACTGAT
CAGATAAGTATAGCTAAAGCTAC
Found at i:141071 original size:5 final size:5
Alignment explanation
Indices: 141047--141080 Score: 50
Period size: 5 Copynumber: 6.4 Consensus size: 5
141037 TAATTTAATA
141047 CAATT CATATT CATATT CAATT CAATT CAATT CA
1 CAATT CA-ATT CA-ATT CAATT CAATT CAATT CA
141081 CATCTTAGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 17 0.61
6 11 0.39
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (5 bp):
CAATT
Found at i:143625 original size:26 final size:26
Alignment explanation
Indices: 143568--143625 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
143558 GTTGAGAAAA
* *
143568 TTATTTAATTGATAAATTGATTTAGT
1 TTATTTAATTAATAAATTAATTTAGT
* *
143594 TAATTTAATTAATTAATTAATTATA-T
1 TTATTTAATTAATAAATTAATT-TAGT
143620 TTATTT
1 TTATTT
143626 TGGTAAATAG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 24 0.92
27 2 0.08
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (26 bp):
TTATTTAATTAATAAATTAATTTAGT
Found at i:145739 original size:40 final size:40
Alignment explanation
Indices: 145684--145765 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
145674 AAGCCCCTAC
* *
145684 CAGTCCCCTAGATTCACCTATATCTGTATGTAATTACAAG
1 CAGTCCCCTAAATTCACCTAGATCTGTATGTAATTACAAG
145724 CAGTCCCCTAAATTCACCTAGATCTGTATGTAATTACAAG
1 CAGTCCCCTAAATTCACCTAGATCTGTATGTAATTACAAG
145764 CA
1 CA
145766 ATTACAACTG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.30
Consensus pattern (40 bp):
CAGTCCCCTAAATTCACCTAGATCTGTATGTAATTACAAG
Found at i:152461 original size:43 final size:43
Alignment explanation
Indices: 152363--152520 Score: 192
Period size: 42 Copynumber: 3.7 Consensus size: 43
152353 ATGTTCCAAT
* * ** *
152363 ATCGATTTGAGATCTCGTATAAGACCATATATGGGATATT-GC
1 ATCGATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGC
* *
152405 ATCAATTTGAGATTTTGTGTAAGACCATAGCTGGGCTATTGGC
1 ATCGATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGC
152448 ATCGATTTGAGATTTCGTGTAAGACCATAGCTGGGGCTATTGGC
1 ATCGATTTGAGATTTCGTGTAAGACCATAGCT-GGGCTATTGGC
* ** *
152492 ATCAATACGAGATTTCCATGTAAGACCAT
1 ATCGATTTGAGATTT-CGTGTAAGACCAT
152521 GTTTGTAACA
Statistics
Matches: 100, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
42 33 0.33
43 32 0.32
44 23 0.23
45 12 0.12
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.32
Consensus pattern (43 bp):
ATCGATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGC
Found at i:152504 original size:44 final size:43
Alignment explanation
Indices: 152367--152520 Score: 193
Period size: 43 Copynumber: 3.6 Consensus size: 43
152357 TCCAATATCG
* * ** *
152367 ATTTGAGATCTCGTATAAGACCATATATGGGATATT-GCATCA
1 ATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCA
* *
152409 ATTTGAGATTTTGTGTAAGACCATAGCTGGGCTATTGGCATCG
1 ATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCA
152452 ATTTGAGATTTCGTGTAAGACCATAGCTGGGGCTATTGGCATCA
1 ATTTGAGATTTCGTGTAAGACCATAGCT-GGGCTATTGGCATCA
** *
152496 ATACGAGATTTCCATGTAAGACCAT
1 ATTTGAGATTT-CGTGTAAGACCAT
152521 GTTTGTAACA
Statistics
Matches: 97, Mismatches: 12, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
42 30 0.31
43 32 0.33
44 23 0.24
45 12 0.12
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (43 bp):
ATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCA
Found at i:153102 original size:43 final size:45
Alignment explanation
Indices: 153041--153140 Score: 150
Period size: 44 Copynumber: 2.3 Consensus size: 45
153031 AGTTTTGGAT
* **
153041 GTGTAAGACCATAGCT-GGGCTATTGGCATCGATTTGAGATTT-C
1 GTGTAAGACCATAGCTGGGGCTATTGGCATCAATACGAGATTTCC
153084 GTGTAAGACCATAGCTGGGGCTATTGGCATCAATACGAGATTTCC
1 GTGTAAGACCATAGCTGGGGCTATTGGCATCAATACGAGATTTCC
*
153129 ATGTAAGACCAT
1 GTGTAAGACCAT
153141 GTTTGTAACA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
43 16 0.31
44 23 0.45
45 12 0.24
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (45 bp):
GTGTAAGACCATAGCTGGGGCTATTGGCATCAATACGAGATTTCC
Found at i:156498 original size:16 final size:17
Alignment explanation
Indices: 156479--156514 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
156469 TGTTTTTAGG
156479 TCTTTAGGAATTT-ATT
1 TCTTTAGGAATTTAATT
*
156495 TCTTTAGTAATTTAATT
1 TCTTTAGGAATTTAATT
156512 TCT
1 TCT
156515 CAAAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.25, C:0.08, G:0.08, T:0.58
Consensus pattern (17 bp):
TCTTTAGGAATTTAATT
Found at i:157647 original size:19 final size:20
Alignment explanation
Indices: 157610--157650 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
157600 TGATTGTTTG
*
157610 CTTGATTGATAGAAAATTAT
1 CTTGAATGATAGAAAATTAT
*
157630 CTTGAATGA-AGAATATTAT
1 CTTGAATGATAGAAAATTAT
157649 CT
1 CT
157651 ATGACTGTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (20 bp):
CTTGAATGATAGAAAATTAT
Found at i:166512 original size:42 final size:43
Alignment explanation
Indices: 166444--166641 Score: 305
Period size: 42 Copynumber: 4.7 Consensus size: 43
166434 AGATCCTGTA
* * * *
166444 TAAGACCATATCTAGGATA-TGACATCGATTTGAGA-TTCGTG
1 TAAGACCATAGCTGGGCTATTGGCATCGATTTGAGACTTCGTG
166485 TAAGACCATAGCTGGGCTATTGGCATCGATTTGAGACTT-GTG
1 TAAGACCATAGCTGGGCTATTGGCATCGATTTGAGACTTCGTG
166527 TAAGACCATAGCTGGGCTATTGGCATCGATTTGAGACTT-GTG
1 TAAGACCATAGCTGGGCTATTGGCATCGATTTGAGACTTCGTG
* *
166569 TAAGACCATAGCTGGGCTATTGGCATCGATTTGAGATTTCGTA
1 TAAGACCATAGCTGGGCTATTGGCATCGATTTGAGACTTCGTG
*
166612 TAAGACCATAGCTGGGCTATTGACATCGAT
1 TAAGACCATAGCTGGGCTATTGGCATCGAT
166642 ACAAGATTTC
Statistics
Matches: 147, Mismatches: 7, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
41 16 0.11
42 98 0.67
43 33 0.22
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.31
Consensus pattern (43 bp):
TAAGACCATAGCTGGGCTATTGGCATCGATTTGAGACTTCGTG
Found at i:170564 original size:32 final size:32
Alignment explanation
Indices: 170527--170594 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
170517 GGTTTAAAGT
*
170527 GCATTCATTACTAGGAGGTTGATTACGAATAA
1 GCATTCATTACTAGGAGGCTGATTACGAATAA
*
170559 GCATTCATTCCTAGGAGGCTGATTACGAATAA
1 GCATTCATTACTAGGAGGCTGATTACGAATAA
170591 -CATT
1 GCATT
170595 ATTTTGGCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
31 4 0.12
32 30 0.88
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (32 bp):
GCATTCATTACTAGGAGGCTGATTACGAATAA
Found at i:173923 original size:17 final size:19
Alignment explanation
Indices: 173887--173926 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
173877 TGTAAATTAT
*
173887 AAATATATATATAATCTAA
1 AAATATATATATAATATAA
173906 AAATA-ATATA-AATATAA
1 AAATATATATATAATATAA
173923 AAAT
1 AAAT
173927 TTATTGTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 10 0.50
18 5 0.25
19 5 0.25
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATATATATATAATATAA
Found at i:193729 original size:12 final size:12
Alignment explanation
Indices: 193712--193739 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
193702 CACACGGCCG
193712 TGTCCCAGCCCA
1 TGTCCCAGCCCA
193724 TGTCCCAGCCCA
1 TGTCCCAGCCCA
193736 TGTC
1 TGTC
193740 TTACCCATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.14, C:0.46, G:0.18, T:0.21
Consensus pattern (12 bp):
TGTCCCAGCCCA
Found at i:194791 original size:101 final size:101
Alignment explanation
Indices: 194652--194875 Score: 313
Period size: 101 Copynumber: 2.2 Consensus size: 101
194642 ACATGCATTA
* * ** *
194652 CCATGGCCCAGCCATGGTCTTACATTCTTAGTGCCATAACCCAGTTATGGTCTTATCATCAGAAT
1 CCATGGTCCAACCATGGTCTTACATTCAAAGTGCCATAACCCAGTTATGGTCTTATCATCAAAAT
*
194717 GCCATAACTTAGCTATGGTCTTACTTATAAATACTG
66 GACATAACTTAGCTATGGTCTTACTTATAAATACTG
* * * * * *
194753 TCATGGTCCAACCATGGTCTTACGTTCAAAGTGTCATAACCTAGTTATGGTCTTTTCATTAAAAT
1 CCATGGTCCAACCATGGTCTTACATTCAAAGTGCCATAACCCAGTTATGGTCTTATCATCAAAAT
** *
194818 GACATAGTTTAGCTATGGTCTTACTTATAGATACTG
66 GACATAACTTAGCTATGGTCTTACTTATAAATACTG
194854 CCATGGTCCAACCATGGTCTTA
1 CCATGGTCCAACCATGGTCTTA
194876 TCCGTCAATT
Statistics
Matches: 107, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
101 107 1.00
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (101 bp):
CCATGGTCCAACCATGGTCTTACATTCAAAGTGCCATAACCCAGTTATGGTCTTATCATCAAAAT
GACATAACTTAGCTATGGTCTTACTTATAAATACTG
Found at i:197888 original size:34 final size:34
Alignment explanation
Indices: 197842--197913 Score: 126
Period size: 34 Copynumber: 2.1 Consensus size: 34
197832 ACATTCCTTC
197842 ATCAGATACCATATAATGAGTGCAGCCATTGTCA
1 ATCAGATACCATATAATGAGTGCAGCCATTGTCA
* *
197876 ATCAGATGCCATATAATGAGTGCAGTCATTGTCA
1 ATCAGATACCATATAATGAGTGCAGCCATTGTCA
197910 ATCA
1 ATCA
197914 ACCAATCCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (34 bp):
ATCAGATACCATATAATGAGTGCAGCCATTGTCA
Found at i:201071 original size:117 final size:117
Alignment explanation
Indices: 200863--201073 Score: 341
Period size: 117 Copynumber: 1.8 Consensus size: 117
200853 TTTGATTTGT
* * *
200863 TGGTTATTTGTGATTCATTATTACAATTTCAGTGCCACAATGTAGTGTTTGTTTTGTCGATTTTT
1 TGGTTAATTGTGATTCATTATTACAATTTCAGTGCCACAATGTAGGGTTTGTTTTGTCGATTTGT
* * *
200928 GATGCTATAGTGGTCCCGATGTTGTTGATAAAATTGTTGTCAAAATTGTAGA
66 GATGCGACAGTGGTCCCGATGATGTTGATAAAATTGTTGTCAAAATTGTAGA
* * *
200980 TGGTTAATTGTGATTTATTATTGCAATTTCAGTGCCACAATGTAGGGTTTGTTTTGTTGATTTGT
1 TGGTTAATTGTGATTCATTATTACAATTTCAGTGCCACAATGTAGGGTTTGTTTTGTCGATTTGT
201045 GATGCGACAGTGGTCCCGATGATGTTGAT
66 GATGCGACAGTGGTCCCGATGATGTTGAT
201074 TTCTGTTATC
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
117 85 1.00
ACGTcount: A:0.22, C:0.10, G:0.24, T:0.44
Consensus pattern (117 bp):
TGGTTAATTGTGATTCATTATTACAATTTCAGTGCCACAATGTAGGGTTTGTTTTGTCGATTTGT
GATGCGACAGTGGTCCCGATGATGTTGATAAAATTGTTGTCAAAATTGTAGA
Found at i:201714 original size:33 final size:32
Alignment explanation
Indices: 201677--201752 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 32
201667 TGACTACTGA
* *
201677 GGAGGGTGATGTTAAAGGGGTGGAAGTTGATGG
1 GGAGGGTGATGATAAAGGGGTAGAAGTTGA-GG
* *
201710 GGAGGGTGATGATGAAGGGGTAGAATTTGAGG
1 GGAGGGTGATGATAAAGGGGTAGAAGTTGAGG
*
201742 GTGAAGGTGAT
1 G-GAGGGTGAT
201753 CTGGAAAAGG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 3 0.08
33 34 0.92
ACGTcount: A:0.26, C:0.00, G:0.50, T:0.24
Consensus pattern (32 bp):
GGAGGGTGATGATAAAGGGGTAGAAGTTGAGG
Found at i:202018 original size:50 final size:51
Alignment explanation
Indices: 201920--202021 Score: 143
Period size: 50 Copynumber: 2.0 Consensus size: 51
201910 GTGAAGTTGA
* * * * *
201920 TGCTGATGAATATGCTGGTGATTTTGTAACATCAGATGGAGTGGATAATGT
1 TGCTGATGAATATACTGATGATTTTGCAACATCAGATGGACTAGATAATGT
*
201971 TGCTGATGAATATATTGATGA-TTTGCAACATCAGATGGACTAGATAATGT
1 TGCTGATGAATATACTGATGATTTTGCAACATCAGATGGACTAGATAATGT
202021 T
1 T
202022 ACTGCTGCAC
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
50 27 0.60
51 18 0.40
ACGTcount: A:0.30, C:0.09, G:0.25, T:0.35
Consensus pattern (51 bp):
TGCTGATGAATATACTGATGATTTTGCAACATCAGATGGACTAGATAATGT
Found at i:213334 original size:17 final size:16
Alignment explanation
Indices: 213294--213335 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
213284 GAATGCTAAC
*
213294 GATTTAGGGATTTTAA
1 GATTTAGGGATTTGAA
213310 GATTTAGGGATTTGAA
1 GATTTAGGGATTTGAA
213326 GATTTTAGGG
1 GA-TTTAGGG
213336 GTTCAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 17 0.71
17 7 0.29
ACGTcount: A:0.29, C:0.00, G:0.31, T:0.40
Consensus pattern (16 bp):
GATTTAGGGATTTGAA
Found at i:216613 original size:5 final size:5
Alignment explanation
Indices: 216603--216629 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
216593 AAAATTTTTT
216603 ATTCG ATTCG ATTCG ATTCG ATTCG AT
1 ATTCG ATTCG ATTCG ATTCG ATTCG AT
216630 CGAATGCTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (5 bp):
ATTCG
Found at i:217457 original size:6 final size:7
Alignment explanation
Indices: 217440--217466 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
217430 GCTTGCTGCA
217440 TTTTTTC
1 TTTTTTC
217447 TTTTTTC
1 TTTTTTC
217454 TTTTTTC
1 TTTTTTC
217461 TTTTTT
1 TTTTTT
217467 AAGTTACCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTC
Found at i:223123 original size:36 final size:40
Alignment explanation
Indices: 223033--223137 Score: 119
Period size: 36 Copynumber: 2.7 Consensus size: 40
223023 AATTCGAAGT
* * *
223033 AGTAAATTGACACCCAGTATCTCATTGAATAAATCAGAAG
1 AGTAAATTGACACCCAGTGTCTCATCGAATAAATCACAAG
* *
223073 TAGTAAATTAACACCCAGTGTCTCATCG-TTAAA-C-CAA-
1 -AGTAAATTGACACCCAGTGTCTCATCGAATAAATCACAAG
*
223110 AGTAAATTGACACCCAGTGCCTCATCGA
1 AGTAAATTGACACCCAGTGTCTCATCGA
223138 CTCGAAGTCG
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
36 25 0.45
38 2 0.04
39 1 0.02
40 4 0.07
41 24 0.43
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (40 bp):
AGTAAATTGACACCCAGTGTCTCATCGAATAAATCACAAG
Found at i:224057 original size:21 final size:20
Alignment explanation
Indices: 224024--224062 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
224014 CTTCGTCTCA
224024 TTCTTTCTCCCTTTTCTTTCT
1 TTCTTTCTCCC-TTTCTTTCT
* *
224045 TTCTTTTTTCCTTTCTTT
1 TTCTTTCTCCCTTTCTTT
224063 TTCCTTCTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (20 bp):
TTCTTTCTCCCTTTCTTTCT
Found at i:224409 original size:13 final size:13
Alignment explanation
Indices: 224391--224425 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
224381 ACTAACTTCT
224391 TAAATATTTTTAA
1 TAAATATTTTTAA
224404 TAAATATTTTTAA
1 TAAATATTTTTAA
224417 TAAATATTT
1 TAAATATTT
224426 ATGAGTCTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TAAATATTTTTAA
Found at i:231872 original size:23 final size:23
Alignment explanation
Indices: 231840--231883 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
231830 ACTACCATTT
231840 TCTAAATAAAATAATAATAAATA
1 TCTAAATAAAATAATAATAAATA
* *
231863 TCTAAGTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
231884 ATAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:231876 original size:13 final size:11
Alignment explanation
Indices: 231844--231886 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
231834 CCATTTTCTA
*
231844 AATAAAATAAT
1 AATAAAATATT
231855 AAT-AAATATCT
1 AATAAAATAT-T
231866 AAGTAAAATATT
1 AA-TAAAATATT
231878 AATAAAATA
1 AATAAAATA
231887 ATATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 4 0.14
13 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATATT
Found at i:238089 original size:123 final size:124
Alignment explanation
Indices: 237870--238143 Score: 480
Period size: 123 Copynumber: 2.2 Consensus size: 124
237860 TTTCGAGTTG
*
237870 ACGTTTCTG-GTCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAA
1 ACGTTTCTGAGT-AAATAGTATAAAATCACTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAA
*
237934 ATCGTGCCCTCGTGGATGCGATTTCACTACAGTTGGTCATGTAAGAAATAA-TTTTTTTA
65 ATCGTGCCCTCGTGGACGCGATTTCACTACAGTTGGTCATGTAAGAAATAATTTTTTTTA
237993 ACGTTTCTGAGTAAATAGTATAAAATCACTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAAA
1 ACGTTTCTGAGTAAATAGTATAAAATCACTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAAA
* *
238058 TCGTGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTTTTTG
66 TCGTGCCCTCGTGGACGCGATTTCACTACAGTTGGTCATGTAAGAAATAATTTTTTTTA
*
238117 ACGTTTCTGAGCAAATAGTATAAAATC
1 ACGTTTCTGAGTAAATAGTATAAAATC
238144 GTGCCCTTGT
Statistics
Matches: 144, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
123 109 0.76
124 35 0.24
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (124 bp):
ACGTTTCTGAGTAAATAGTATAAAATCACTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAAA
TCGTGCCCTCGTGGACGCGATTTCACTACAGTTGGTCATGTAAGAAATAATTTTTTTTA
Found at i:243272 original size:14 final size:14
Alignment explanation
Indices: 243255--243283 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
243245 TTATATACAT
243255 AATACTAAATACCA
1 AATACTAAATACCA
243269 AATACTAAATACCA
1 AATACTAAATACCA
243283 A
1 A
243284 TTGACTAGCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.21, G:0.00, T:0.21
Consensus pattern (14 bp):
AATACTAAATACCA
Found at i:260905 original size:28 final size:28
Alignment explanation
Indices: 260863--260932 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
260853 AGGGGTTCAG
* *
260863 CATTGGGTGCCGCCTGTCAGGTACCCTC
1 CATTGGGTGCCGCCTATCAGGAACCCTC
*
260891 CATTGGGTGCTGCCTATCAGGAACCCTC
1 CATTGGGTGCCGCCTATCAGGAACCCTC
*
260919 CACT-GGTGCCGCCT
1 CATTGGGTGCCGCCT
260933 CTCAATCATC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 9 0.24
28 28 0.76
ACGTcount: A:0.13, C:0.36, G:0.27, T:0.24
Consensus pattern (28 bp):
CATTGGGTGCCGCCTATCAGGAACCCTC
Found at i:269311 original size:28 final size:27
Alignment explanation
Indices: 269253--269313 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
269243 TTTTTTACAG
**
269253 AAATAGTATAGAAAAAAAAAAATACTG
1 AAATAGTATAGAAAAAAAAAAATACCA
*
269280 AAATAGTAT-GATAGAAAAAAAATTACCA
1 AAATAGTATAGA-A-AAAAAAAAATACCA
269308 AAATAG
1 AAATAG
269314 GTTACTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 2 0.07
27 10 0.34
28 17 0.59
ACGTcount: A:0.64, C:0.05, G:0.11, T:0.20
Consensus pattern (27 bp):
AAATAGTATAGAAAAAAAAAAATACCA
Found at i:269487 original size:13 final size:13
Alignment explanation
Indices: 269469--269514 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
269459 GTAGGCGCCA
269469 ATGGAGGAGCCTC
1 ATGGAGGAGCCTC
269482 ATGGA-GAGGCGC-C
1 ATGGAGGA-GC-CTC
269495 AATGGAGGAGCCTC
1 -ATGGAGGAGCCTC
269509 ATGGAG
1 ATGGAG
269515 AGGCGCCAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
12 2 0.07
13 15 0.54
14 9 0.32
15 2 0.07
ACGTcount: A:0.26, C:0.20, G:0.41, T:0.13
Consensus pattern (13 bp):
ATGGAGGAGCCTC
Found at i:269491 original size:27 final size:27
Alignment explanation
Indices: 269461--269526 Score: 132
Period size: 27 Copynumber: 2.4 Consensus size: 27
269451 CCTGTCTAGT
269461 AGGCGCCAATGGAGGAGCCTCATGGAG
1 AGGCGCCAATGGAGGAGCCTCATGGAG
269488 AGGCGCCAATGGAGGAGCCTCATGGAG
1 AGGCGCCAATGGAGGAGCCTCATGGAG
269515 AGGCGCCAATGG
1 AGGCGCCAATGG
269527 TGCCCTCTGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.26, C:0.23, G:0.41, T:0.11
Consensus pattern (27 bp):
AGGCGCCAATGGAGGAGCCTCATGGAG
Found at i:269918 original size:27 final size:27
Alignment explanation
Indices: 269887--269993 Score: 127
Period size: 27 Copynumber: 4.1 Consensus size: 27
269877 ATTTTTTATG
*
269887 AATATTGTAATGTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGT
*
269914 AATATTATAATTTTGTATGAATATTG-
1 AATATTGTAATTTTGTATGAATATTGT
*
269940 CA-A-T-T--TTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGT
269962 AATATTGTAATTTTTTGTATGAATATTGT
1 AATATTGTAA--TTTTGTATGAATATTGT
269991 AAT
1 AAT
269994 TNNNNNNNNN
Statistics
Matches: 68, Mismatches: 4, Indels: 14
0.79 0.05 0.16
Matches are distributed among these distances:
21 16 0.24
22 1 0.01
23 2 0.03
24 2 0.03
25 2 0.03
26 1 0.01
27 24 0.35
29 20 0.29
ACGTcount: A:0.34, C:0.01, G:0.14, T:0.51
Consensus pattern (27 bp):
AATATTGTAATTTTGTATGAATATTGT
Found at i:269973 original size:29 final size:29
Alignment explanation
Indices: 269933--269993 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
269923 ATTTTGTATG
269933 AATATTGCAATTTTTTGTATGAATATTGT
1 AATATTGCAATTTTTTGTATGAATATTGT
*
269962 AATATTGTAATTTTTTGTATGAATATTGT
1 AATATTGCAATTTTTTGTATGAATATTGT
269991 AAT
1 AAT
269994 TNNNNNNNNN
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.52
Consensus pattern (29 bp):
AATATTGCAATTTTTTGTATGAATATTGT
Found at i:269994 original size:21 final size:21
Alignment explanation
Indices: 269837--269964 Score: 129
Period size: 19 Copynumber: 6.0 Consensus size: 21
269827 TAGATTAGAA
*
269837 TTTTGTATGAATATTTTAAATT
1 TTTTGTATGAATATTGT-AATT
*
269859 TTTTGTATGAATATTATAA-T
1 TTTTGTATGAATATTGTAATT
269879 TTTT-TATGAATATTGTAA--
1 TTTTGTATGAATATTGTAATT
*
269897 TGTTGTATGAATATTGTAATATTAT
1 TTTTGTATGAATATTGT-A-A-T-T
*
269922 AATTTTGTATGAATATTGCAATT
1 --TTTTGTATGAATATTGTAATT
269945 TTTTGTATGAATATTGTAAT
1 TTTTGTATGAATATTGTAAT
269965 ATTGTAATTT
Statistics
Matches: 91, Mismatches: 6, Indels: 19
0.78 0.05 0.16
Matches are distributed among these distances:
18 3 0.03
19 25 0.27
20 6 0.07
21 22 0.24
22 16 0.18
23 1 0.01
24 1 0.01
25 1 0.01
26 1 0.01
27 15 0.16
ACGTcount: A:0.33, C:0.01, G:0.12, T:0.54
Consensus pattern (21 bp):
TTTTGTATGAATATTGTAATT
Found at i:273708 original size:22 final size:22
Alignment explanation
Indices: 273673--273736 Score: 103
Period size: 22 Copynumber: 3.0 Consensus size: 22
273663 TACCTAATTT
*
273673 TTTTCTTCT-TTTCCTTCCTTC
1 TTTTCTTCTGCTTCCTTCCTTC
273694 TTTTCTTCTGCTTCCTTCCTTC
1 TTTTCTTCTGCTTCCTTCCTTC
*
273716 TTTTCTTTTGCTTCCTTCCTT
1 TTTTCTTCTGCTTCCTTCCTT
273737 ATTCTTTCTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
21 9 0.22
22 31 0.77
ACGTcount: A:0.00, C:0.33, G:0.03, T:0.64
Consensus pattern (22 bp):
TTTTCTTCTGCTTCCTTCCTTC
Found at i:273729 original size:18 final size:18
Alignment explanation
Indices: 273678--273743 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 18
273668 AATTTTTTTC
273678 TTCTTTTCCTTCCTTCTT
1 TTCTTTTCCTTCCTTCTT
273696 TTCTTCTGCTTCCTTCCTTCTT
1 TTC-T-T--TTCCTTCCTTCTT
*
273718 TTCTTTTGCTTCCTTCCTT
1 TTCTTTTCCTTCCTT-CTT
273737 ATTCTTT
1 -TTCTTT
273744 CTTCCGTTTC
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
18 12 0.29
19 4 0.10
20 8 0.20
21 1 0.02
22 16 0.39
ACGTcount: A:0.02, C:0.32, G:0.03, T:0.64
Consensus pattern (18 bp):
TTCTTTTCCTTCCTTCTT
Found at i:273854 original size:27 final size:27
Alignment explanation
Indices: 273824--273932 Score: 182
Period size: 27 Copynumber: 4.0 Consensus size: 27
273814 ATTTCAGTAT
273824 GGCACCACCATTGGCGCCTCCCAGATA
1 GGCACCACCATTGGCGCCTCCCAGATA
*
273851 GGCACCACCATTGGTGCCTCCCAGATA
1 GGCACCACCATTGGCGCCTCCCAGATA
* *
273878 GGCACCACCATTGGTGCCTCCCAAATA
1 GGCACCACCATTGGCGCCTCCCAGATA
*
273905 GGCACCACCATTGGCGCCTTCCAGATA
1 GGCACCACCATTGGCGCCTCCCAGATA
273932 G
1 G
273933 ACGCCAATAT
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 77 1.00
ACGTcount: A:0.23, C:0.38, G:0.22, T:0.17
Consensus pattern (27 bp):
GGCACCACCATTGGCGCCTCCCAGATA
Found at i:288021 original size:36 final size:37
Alignment explanation
Indices: 287971--288051 Score: 101
Period size: 36 Copynumber: 2.2 Consensus size: 37
287961 ATATAATTAT
* * * * * *
287971 CACTTTTAAGTATTACAACTATATCATTATGCCGAAA
1 CACTTATAAGTATTACAAATACACCAATAGGCCGAAA
288008 CACTTATAA-TATTACAAATACACCAATAGGCCGAAA
1 CACTTATAAGTATTACAAATACACCAATAGGCCGAAA
288044 CACTTATA
1 CACTTATA
288052 TGTTCAATCG
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
36 30 0.79
37 8 0.21
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.30
Consensus pattern (37 bp):
CACTTATAAGTATTACAAATACACCAATAGGCCGAAA
Found at i:288322 original size:43 final size:43
Alignment explanation
Indices: 288256--288383 Score: 154
Period size: 43 Copynumber: 3.0 Consensus size: 43
288246 GGCTCGTACA
* *
288256 ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCCACTGTCCCAGACGTGGTCTTACATGTAAACACATATCG
* *
288299 ATGCCACTGTCCTAGACAG-GGTCTTACACGTAAACACA-AGTCG
1 ATGCCACTGTCCCAGAC-GTGGTCTTACATGTAAACACATA-TCG
* *
288342 ATGCCAAC-GTCCCAAACGTGGTCTTACATGAAAACACATATC
1 ATGCC-ACTGTCCCAGACGTGGTCTTACATGTAAACACATATC
288384 AGAATCCTAT
Statistics
Matches: 72, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
42 2 0.03
43 66 0.92
44 4 0.06
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.23
Consensus pattern (43 bp):
ATGCCACTGTCCCAGACGTGGTCTTACATGTAAACACATATCG
Found at i:288776 original size:14 final size:14
Alignment explanation
Indices: 288757--288790 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
288747 AGAAAATTGC
288757 CATTTTGCCCCTGA
1 CATTTTGCCCCTGA
*
288771 CATTTTGCCCTTGA
1 CATTTTGCCCCTGA
288785 CATTTT
1 CATTTT
288791 ACACTTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.15, C:0.29, G:0.12, T:0.44
Consensus pattern (14 bp):
CATTTTGCCCCTGA
Found at i:289141 original size:23 final size:23
Alignment explanation
Indices: 289114--289159 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 23
289104 TTGTGATATA
289114 TATTAA-ACATATATTAACCTTAT
1 TATTAATAC-TATATTAACCTTAT
289137 TATTAATTTACTATATTAACCTT
1 TATTAA--TACTATATTAACCTT
289160 TACTAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 6 0.30
25 12 0.60
26 2 0.10
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (23 bp):
TATTAATACTATATTAACCTTAT
Found at i:290024 original size:23 final size:23
Alignment explanation
Indices: 289972--290016 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
289962 AATCAGTAAA
*
289972 AAATTTATTTTTCACTTAGTATT
1 AAATATATTTTTCACTTAGTATT
*
289995 AAATATATTTTTCACTTTGTAT
1 AAATATATTTTTCACTTAGTAT
290017 AATCTATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.31, C:0.09, G:0.04, T:0.56
Consensus pattern (23 bp):
AAATATATTTTTCACTTAGTATT
Found at i:293590 original size:101 final size:101
Alignment explanation
Indices: 293410--293655 Score: 384
Period size: 101 Copynumber: 2.4 Consensus size: 101
293400 AATTCATCCT
* * * *
293410 TTACATTCATAGTGCCATAACCCAGTTATGGTTTTATCATTAGAATGCCATAGCCCAGCTATGGT
1 TTACATTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAAAATGCCATAGCCCAACTATGGT
293475 CTTACATATAAACACTACCATGGTCCAACCATGGTC
66 CTTACATATAAACACTACCATGGTCCAACCATGGTC
* * * *
293511 TTACGTTCATAGTGCCACAACCCAGTTATAGTCTTATCATCAAAATGCCATGGCCCAACTATGGT
1 TTACATTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAAAATGCCATAGCCCAACTATGGT
*
293576 CTTACATATAAACACTGCCATGGTCCAACCATGGTC
66 CTTACATATAAACACTACCATGGTCCAACCATGGTC
* *
293612 TTGCATTCATAGTGCCATAAACCAGTTATGGTCTTATCCATCAA
1 TTACATTCATAGTGCCATAACCCAGTTATGGTCTTAT-CATCAA
293656 TTCATCTTTT
Statistics
Matches: 130, Mismatches: 14, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
101 124 0.95
102 6 0.05
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.30
Consensus pattern (101 bp):
TTACATTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAAAATGCCATAGCCCAACTATGGT
CTTACATATAAACACTACCATGGTCCAACCATGGTC
Found at i:293596 original size:35 final size:34
Alignment explanation
Indices: 293455--293618 Score: 109
Period size: 35 Copynumber: 4.8 Consensus size: 34
293445 ATCATTAGAA
* *
293455 TGCCATAGCCCAGCTATGGTCTTACATATAAACAC
1 TGCCATGGCCCAACTATGGTCTTACAT-TAAACAC
* * * * * * *
293490 TACCATGGTCCAACCATGGTCTTACGTT-CATAG
1 TGCCATGGCCCAACTATGGTCTTACATTAAACAC
*** ** * *
293523 TGCCACAACCCAGTTATAGTCTTATCATCAAA-A-
1 TGCCATGGCCCAACTATGGTCTTA-CATTAAACAC
293556 TGCCATGGCCCAACTATGGTCTTACATATAAACAC
1 TGCCATGGCCCAACTATGGTCTTACAT-TAAACAC
* * *
293591 TGCCATGGTCCAACCATGGTCTTGCATT
1 TGCCATGGCCCAACTATGGTCTTACATT
293619 CATAGTGCCA
Statistics
Matches: 93, Mismatches: 31, Indels: 11
0.69 0.23 0.08
Matches are distributed among these distances:
32 3 0.03
33 38 0.41
34 6 0.06
35 46 0.49
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (34 bp):
TGCCATGGCCCAACTATGGTCTTACATTAAACAC
Found at i:297732 original size:22 final size:22
Alignment explanation
Indices: 297707--297770 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
297697 TTATCATTCC
297707 GCACTTCAGTGCCTACTGTTTT
1 GCACTTCAGTGCCTACTGTTTT
* * * *
297729 GCACTTCGGTGCTTAATGATTT
1 GCACTTCAGTGCCTACTGTTTT
*
297751 GCACTTCAGTGCCCACTGTT
1 GCACTTCAGTGCCTACTGTT
297771 ATATTAGTGC
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.16, C:0.27, G:0.20, T:0.38
Consensus pattern (22 bp):
GCACTTCAGTGCCTACTGTTTT
Found at i:297755 original size:44 final size:44
Alignment explanation
Indices: 297686--297770 Score: 127
Period size: 44 Copynumber: 1.9 Consensus size: 44
297676 TACCGTTTCA
*
297686 CACTTCGGTGCTTATCATTCCGCACTTCAGTGCCTACTGTTTTG
1 CACTTCGGTGCTTATCATTCCGCACTTCAGTGCCCACTGTTTTG
* *
297730 CACTTCGGTGCTTAATGATT-TGCACTTCAGTGCCCACTGTT
1 CACTTCGGTGCTT-ATCATTCCGCACTTCAGTGCCCACTGTT
297771 ATATTAGTGC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 32 0.86
45 5 0.14
ACGTcount: A:0.15, C:0.28, G:0.19, T:0.38
Consensus pattern (44 bp):
CACTTCGGTGCTTATCATTCCGCACTTCAGTGCCCACTGTTTTG
Found at i:299859 original size:23 final size:22
Alignment explanation
Indices: 299816--299873 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
299806 AAAGGGTATC
* *
299816 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
299837 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
299860 TGCATATCATATCT
1 TACAAATCATATCT
299874 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:300157 original size:18 final size:18
Alignment explanation
Indices: 300134--300168 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
300124 TTGGGATTGT
* *
300134 TTTGAATTGGTTTTAAAC
1 TTTGAAATGGCTTTAAAC
300152 TTTGAAATGGCTTTAAA
1 TTTGAAATGGCTTTAAA
300169 ACAATGTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.46
Consensus pattern (18 bp):
TTTGAAATGGCTTTAAAC
Found at i:300250 original size:21 final size:21
Alignment explanation
Indices: 300224--300282 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
300214 AAAATTTACC
300224 TAAGGTATCGATACCTAAGGG
1 TAAGGTATCGATACCTAAGGG
*
300245 TAAGGTATCGATACTTAAGGG
1 TAAGGTATCGATACCTAAGGG
** *
300266 TAACATACCGATACCTA
1 TAAGGTATCGATACCTA
300283 GAGCTTGGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (21 bp):
TAAGGTATCGATACCTAAGGG
Found at i:301985 original size:28 final size:27
Alignment explanation
Indices: 301933--302000 Score: 75
Period size: 31 Copynumber: 2.4 Consensus size: 27
301923 ATATAATTTT
*
301933 TTAATTCTTTTTATTTTTAGGTTTTATAATA
1 TTAATTTTTTTTATTTTT--GTTTTA-AA-A
301964 TTAATTTTTTTTATTTTT-TTTTAAAA
1 TTAATTTTTTTTATTTTTGTTTTAAAA
*
301990 TTAATATTTTT
1 TTAATTTTTTT
302001 AGGATTAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 11 0.31
27 2 0.06
28 5 0.14
31 17 0.49
ACGTcount: A:0.26, C:0.01, G:0.03, T:0.69
Consensus pattern (27 bp):
TTAATTTTTTTTATTTTTGTTTTAAAA
Found at i:302179 original size:90 final size:92
Alignment explanation
Indices: 302059--302242 Score: 237
Period size: 90 Copynumber: 2.0 Consensus size: 92
302049 AATCCCCTCC
** * *
302059 TTTTTTTGCACTCAATTGAGCACTTAAACTTTCAAAATTTATCAAAAAGGCCCTCAAACTTCTTA
1 TTTTTTTGCACTCAATTGAGCACTTAAACTTTCAAAATGCATCAAAAAGACCCTCAAAATTCTTA
*
302124 AAAAAAGCATTTAAGCCCCTGCT-TTA
66 AAAAAAGCAATTAAGCCCCTGCTCTTA
* * * * * *
302150 TTTTTTT-CACTCAATTGGGTACTTGAACTTTCAAAATGCATTAAAAAGACCCTCAAAATTTTTC
1 TTTTTTTGCACTCAATTGAGCACTTAAACTTTCAAAATGCATCAAAAAGACCCTCAAAATTCTTA
* *
302214 AAAAAAGCAATTAAGTCCTTGCTCTTA
66 AAAAAAGCAATTAAGCCCCTGCTCTTA
302241 TT
1 TT
302243 AAAAATTATA
Statistics
Matches: 79, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
90 67 0.85
91 12 0.15
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.36
Consensus pattern (92 bp):
TTTTTTTGCACTCAATTGAGCACTTAAACTTTCAAAATGCATCAAAAAGACCCTCAAAATTCTTA
AAAAAAGCAATTAAGCCCCTGCTCTTA
Found at i:302676 original size:90 final size:89
Alignment explanation
Indices: 302570--302780 Score: 239
Period size: 89 Copynumber: 2.4 Consensus size: 89
302560 AATTTTAAAT
* *
302570 AAAAGCAGGGGCTTAATTGCTTTTTTTTTTAATTTTAAGGGTCTTTTTA-ATGCATTTTGAAAGT
1 AAAAGCAGGGACTTAATTG-TTTTTTTTTTAATTTTAAGGGCCTTTTTATA-GCATTTTGAAAGT
* *
302634 TCAAGTACCTAATTGAGTGCAAAAAA
64 TCAAGTACCAAAATGAGTGCAAAAAA
* ** * * *
302660 AAAAGTAGGGACTTAATTG-TTTTTTTAAAAGGTTTGAGGGCCTTTTTGTAGCATTTTGAAAGTT
1 AAAAGCAGGGACTTAATTGTTTTTTTTTTAA-TTTTAAGGGCCTTTTTATAGCATTTTGAAAGTT
* * *
302724 TAAGTATCAAAATGAGTGCAAAAGA
65 CAAGTACCAAAATGAGTGCAAAAAA
*
302749 AAAAGCA-AGAGCTTAATTGTTTTTTTTTTAAT
1 AAAAGCAGGGA-CTTAATTGTTTTTTTTTTAAT
302781 AAAAAAATTG
Statistics
Matches: 99, Mismatches: 18, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
88 11 0.11
89 61 0.62
90 27 0.27
ACGTcount: A:0.34, C:0.08, G:0.19, T:0.39
Consensus pattern (89 bp):
AAAAGCAGGGACTTAATTGTTTTTTTTTTAATTTTAAGGGCCTTTTTATAGCATTTTGAAAGTTC
AAGTACCAAAATGAGTGCAAAAAA
Found at i:307384 original size:2 final size:2
Alignment explanation
Indices: 307377--307406 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
307367 CTCTAGTTTC
307377 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
307407 ATATATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:320317 original size:16 final size:16
Alignment explanation
Indices: 320290--320324 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
320280 GGGGCAGAAG
320290 AGAAGTTTTTATTAACA
1 AGAAGTTTTTATTAA-A
320307 AGAAG-TTTTATTAAA
1 AGAAGTTTTTATTAAA
320322 AGA
1 AGA
320325 CTTAGATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 9 0.50
17 5 0.28
ACGTcount: A:0.46, C:0.03, G:0.14, T:0.37
Consensus pattern (16 bp):
AGAAGTTTTTATTAAA
Found at i:327556 original size:19 final size:19
Alignment explanation
Indices: 327521--327577 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
327511 TTTTAATAAA
*
327521 TATAAAT-TTTAGAATTTT
1 TATAAATATTTTGAATTTT
327539 TATAAATATTTTGAA-TTT
1 TATAAATATTTTGAATTTT
327557 TA-AAATTTATTTTGAATTTT
1 TATAAA--TATTTTGAATTTT
327577 T
1 T
327578 TTGTAATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
17 3 0.09
18 12 0.35
19 15 0.44
20 4 0.12
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:339900 original size:19 final size:19
Alignment explanation
Indices: 339856--339907 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
339846 ATTACAAAAA
*
339856 AAAAATTAAAAATAATTTT
1 AAAAATTCAAAATAATTTT
* *
339875 TATAATTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
339894 AAAAATTCTAAAAT
1 AAAAATTC-AAAAT
339908 GTATATTTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 4 0.15
19 17 0.65
20 5 0.19
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:343274 original size:30 final size:30
Alignment explanation
Indices: 343238--343297 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
343228 AAAGTTAGAC
343238 TCGAATGAATATATTAGCTCGCCATACTTG
1 TCGAATGAATATATTAGCTCGCCATACTTG
343268 TCGAATGAATATATTAGCTCGCCATACTTG
1 TCGAATGAATATATTAGCTCGCCATACTTG
343298 ACGGATACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (30 bp):
TCGAATGAATATATTAGCTCGCCATACTTG
Found at i:345418 original size:46 final size:46
Alignment explanation
Indices: 345252--345418 Score: 237
Period size: 46 Copynumber: 3.6 Consensus size: 46
345242 TATGTAAGAG
*
345252 CCTATTCTTGTAATT-TCTAGTCCGCAACATATGCAAGAGCTTAGAA
1 CCTATTCTTGT-ATTCTCGAGTCCGCAACATATGCAAGAGCTTAGAA
* * *
345298 CCTATTCTTGTATTTTCGAGTCTGCAACATATGCAAGAGTTTAGAA
1 CCTATTCTTGTATTCTCGAGTCCGCAACATATGCAAGAGCTTAGAA
* * **
345344 CCTATTCCTGTATTCTCGAGTTCGCAACATATGCAAGAGCTCGGAA
1 CCTATTCTTGTATTCTCGAGTCCGCAACATATGCAAGAGCTTAGAA
*
345390 CCTATTCTTGTATTCTCGAGTCCACAACA
1 CCTATTCTTGTATTCTCGAGTCCGCAACA
345419 CATGTAGGAA
Statistics
Matches: 107, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
45 3 0.03
46 104 0.97
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (46 bp):
CCTATTCTTGTATTCTCGAGTCCGCAACATATGCAAGAGCTTAGAA
Found at i:347172 original size:23 final size:23
Alignment explanation
Indices: 347146--347210 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 23
347136 TTCATTTAAC
*
347146 TTAATCGAACATGTTTACGAACA
1 TTAATCGAACATGTTCACGAACA
* * *
347169 TTAAACGAACATATTCATGAACA
1 TTAATCGAACATGTTCACGAACA
* *
347192 TAAAATTGAACATGTTCAC
1 T-TAATCGAACATGTTCAC
347211 AGACAATGTT
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
23 20 0.62
24 12 0.38
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (23 bp):
TTAATCGAACATGTTCACGAACA
Found at i:358133 original size:25 final size:25
Alignment explanation
Indices: 358105--358153 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
358095 CAGAGAAAAT
*
358105 TTTTAGATCAATTTATATT-TTTTTC
1 TTTTAGAGCAATTTA-ATTATTTTTC
*
358130 TTTTTGAGCAATTTAATTATTTTT
1 TTTTAGAGCAATTTAATTATTTTT
358154 GAATAATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 3 0.14
25 18 0.86
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.63
Consensus pattern (25 bp):
TTTTAGAGCAATTTAATTATTTTTC
Found at i:360888 original size:32 final size:32
Alignment explanation
Indices: 360850--361303 Score: 458
Period size: 32 Copynumber: 14.2 Consensus size: 32
360840 ATATTTTATG
* *
360850 TATTGCTGAATT-AATTTGTATACGTATATATA
1 TATTGCCGAATTGAA-TTGTATATGTATATATA
* * * *
360882 TATTGCTGAATTGAATTGTATAGGTATACACA
1 TATTGCCGAATTGAATTGTATATGTATATATA
*
360914 TATTGCCTAATTGAATTGTATATGTATACT-TA
1 TATTGCCGAATTGAATTGTATATGTATA-TATA
* * **
360946 TATTGCCGAATTGAATTGTATAGGTATACACC
1 TATTGCCGAATTGAATTGTATATGTATATATA
*
360978 TATTGCCGAATTGAATTGTATATGTATACT-TG
1 TATTGCCGAATTGAATTGTATATGTATA-TATA
* * **
361010 TATTGTCGAATTGAATTGTATAGGTATATACC
1 TATTGCCGAATTGAATTGTATATGTATATATA
*
361042 TATTGCCGAATTGAATTGTATATGCATACT-TA
1 TATTGCCGAATTGAATTGTATATGTATA-TATA
* * **
361074 TATTGCCGAATTGAATTGTATAGGTATACACC
1 TATTGCCGAATTGAATTGTATATGTATATATA
*
361106 TATTGCCGAATTGAATTATATATGTATACT-TA
1 TATTGCCGAATTGAATTGTATATGTATA-TATA
* * * **
361138 TATTGCCGAATTGAATTGCATAGGTATACACC
1 TATTGCCGAATTGAATTGTATATGTATATATA
* *
361170 TATTGTCGAATTGAATTGTATA-G-ATATACA
1 TATTGCCGAATTGAATTGTATATGTATATATA
* *
361200 CCTATTGTCGAATTAAATTGTATATGTATACT-TA
1 --TATTGCCGAATTGAATTGTATATGTATA-TATA
361234 TATTGCCGAATTGAATTGTATATGTATACT-TA
1 TATTGCCGAATTGAATTGTATATGTATA-TATA
* * *
361266 TGTTGCCGAATTGATTTGTATATGTATTTATA
1 TATTGCCGAATTGAATTGTATATGTATATATA
361298 TATTGC
1 TATTGC
361304 TGATTTAATT
Statistics
Matches: 353, Mismatches: 54, Indels: 30
0.81 0.12 0.07
Matches are distributed among these distances:
30 5 0.01
31 3 0.01
32 336 0.95
33 4 0.01
34 4 0.01
35 1 0.00
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.41
Consensus pattern (32 bp):
TATTGCCGAATTGAATTGTATATGTATATATA
Found at i:361303 original size:64 final size:64
Alignment explanation
Indices: 360850--361292 Score: 622
Period size: 64 Copynumber: 6.9 Consensus size: 64
360840 ATATTTTATG
* * *
360850 TATTGCTGAATT-AATTTGTATACGTATA-TATATATTGCTGAATTGAATTGTATAGGTATACAC
1 TATTGCCGAATTGAA-TTGTATATGTATACT-TATATTGCCGAATTGAATTGTATAGGTATACAC
*
360913 A
64 C
*
360914 TATTGCCTAATTGAATTGTATATGTATACTTATATTGCCGAATTGAATTGTATAGGTATACACC
1 TATTGCCGAATTGAATTGTATATGTATACTTATATTGCCGAATTGAATTGTATAGGTATACACC
* * *
360978 TATTGCCGAATTGAATTGTATATGTATACTTGTATTGTCGAATTGAATTGTATAGGTATATACC
1 TATTGCCGAATTGAATTGTATATGTATACTTATATTGCCGAATTGAATTGTATAGGTATACACC
*
361042 TATTGCCGAATTGAATTGTATATGCATACTTATATTGCCGAATTGAATTGTATAGGTATACACC
1 TATTGCCGAATTGAATTGTATATGTATACTTATATTGCCGAATTGAATTGTATAGGTATACACC
* *
361106 TATTGCCGAATTGAATTATATATGTATACTTATATTGCCGAATTGAATTGCATAGGTATACACC
1 TATTGCCGAATTGAATTGTATATGTATACTTATATTGCCGAATTGAATTGTATAGGTATACACC
* *** * * * ***
361170 TATTGTCGAATTGAATTGTATA-GATATACACCTATTGTCGAATTAAATTGTATATGTATACTTA
1 TATTGCCGAATTGAATTGTATATG-TATACTTATATTGCCGAATTGAATTGTATAGGTATACACC
* * *
361234 TATTGCCGAATTGAATTGTATATGTATACTTATGTTGCCGAATTGATTTGTATATGTAT
1 TATTGCCGAATTGAATTGTATATGTATACTTATATTGCCGAATTGAATTGTATAGGTAT
361293 TTATATATTG
Statistics
Matches: 339, Mismatches: 36, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
63 1 0.00
64 334 0.99
65 4 0.01
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (64 bp):
TATTGCCGAATTGAATTGTATATGTATACTTATATTGCCGAATTGAATTGTATAGGTATACACC
Found at i:364285 original size:16 final size:16
Alignment explanation
Indices: 364264--364294 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
364254 ATTGGGTTAA
364264 GAAAATTATTTAATTG
1 GAAAATTATTTAATTG
364280 GAAAATTATTTAATT
1 GAAAATTATTTAATT
364295 AGTTTAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (16 bp):
GAAAATTATTTAATTG
Found at i:365739 original size:18 final size:19
Alignment explanation
Indices: 365704--365741 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
365694 ATTTTTTTTC
*
365704 TTTTTTTTTTAAATCTCAA
1 TTTTTTTTATAAATCTCAA
*
365723 TTTTTTTTATGAA-CTCAA
1 TTTTTTTTATAAATCTCAA
365741 T
1 T
365742 ATAACCCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.26, C:0.11, G:0.03, T:0.61
Consensus pattern (19 bp):
TTTTTTTTATAAATCTCAA
Found at i:372918 original size:21 final size:21
Alignment explanation
Indices: 372868--372920 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
372858 TTCATGTTTA
372868 CTTTCTGTTTAGCTCTCACGAG
1 CTTT-TGTTTAGCTCTCACGAG
* ***
372890 CTTCTGTTTAGCTCTTTTGAG
1 CTTTTGTTTAGCTCTCACGAG
372911 CTTTTGTTTA
1 CTTTTGTTTA
372921 ACCTTTATGG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.11, C:0.21, G:0.17, T:0.51
Consensus pattern (21 bp):
CTTTTGTTTAGCTCTCACGAG
Found at i:372947 original size:42 final size:42
Alignment explanation
Indices: 372899--373046 Score: 176
Period size: 42 Copynumber: 3.5 Consensus size: 42
372889 GCTTCTGTTT
** * *
372899 AGCTCTTTTGAGCTTTTGTTTAACCTTTATGGGTTTTCATTCC
1 AGCTCTTACGAGCTTCTGTTCAACCTTTATGGGTTTTCATT-C
*
372942 A-CTCTTACGAGCTTCTGTTCAACCCTTT-TGGGTTTTCGTTC
1 AGCTCTTACGAGCTTCTGTTCAA-CCTTTATGGGTTTTCATTC
* *
372983 AGCTCTTACGAGCTTCCGTTCAACCTTTATGGG-TTTCTATTT
1 AGCTCTTACGAGCTTCTGTTCAACCTTTATGGGTTTTC-ATTC
*
373025 AGCTCTTATGAGCTTCTGTTCA
1 AGCTCTTACGAGCTTCTGTTCA
373047 GCTTCCGGGC
Statistics
Matches: 91, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
41 11 0.12
42 74 0.81
43 6 0.07
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (42 bp):
AGCTCTTACGAGCTTCTGTTCAACCTTTATGGGTTTTCATTC
Found at i:373049 original size:21 final size:21
Alignment explanation
Indices: 372943--373049 Score: 65
Period size: 21 Copynumber: 5.1 Consensus size: 21
372933 TTTCATTCCA
* *
372943 CTCTTACGAGCTTCTGTTCAA
1 CTCTTATGAGCTTCTGTTCAG
* * * *
372964 CCCTTTTG-GGTTTTCGTTCAG
1 CTCTTATGAGCTTCT-GTTCAG
* * *
372985 CTCTTACGAGCTTCCGTTCAA
1 CTCTTATGAGCTTCTGTTCAG
* * * *
373006 C-CTTTATGGGTTTCTATTTAG
1 CTC-TTATGAGCTTCTGTTCAG
373027 CTCTTATGAGCTTCTGTTCAG
1 CTCTTATGAGCTTCTGTTCAG
373048 CT
1 CT
373050 TCCGGGCTTC
Statistics
Matches: 58, Mismatches: 24, Indels: 8
0.64 0.27 0.09
Matches are distributed among these distances:
20 5 0.09
21 49 0.84
22 4 0.07
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.43
Consensus pattern (21 bp):
CTCTTATGAGCTTCTGTTCAG
Done.