Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008340.1 Hibiscus syriacus cultivar Beakdansim tig00111064_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 409852
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 1 of 2
Found at i:17701 original size:18 final size:19
Alignment explanation
Indices: 17666--17702 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
17656 CACGGAATGT
17666 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
17686 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
17703 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:17884 original size:37 final size:37
Alignment explanation
Indices: 17850--17919 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
17840 TACAAATTGT
*
17850 AAAATA-TT-TATATATTTTCTTTAAAAAATTAAATTC
1 AAAATAGTTATATAAATTTT-TTTAAAAAATTAAATTC
* *
17886 ATAATAGTTATATAAATTTTTTTACAAAATTAAA
1 AAAATAGTTATATAAATTTTTTTAAAAAATTAAA
17920 AATATAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
36 5 0.17
37 15 0.52
38 9 0.31
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (37 bp):
AAAATAGTTATATAAATTTTTTTAAAAAATTAAATTC
Found at i:21954 original size:4 final size:4
Alignment explanation
Indices: 21940--21972 Score: 57
Period size: 4 Copynumber: 8.0 Consensus size: 4
21930 TCTAAATTAG
21940 TTTA TTTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA
21973 AAATGTATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:31102 original size:27 final size:27
Alignment explanation
Indices: 31072--31125 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
31062 CTTCTATTGC
31072 TGGTCTTTTCGGCTTTAGCAACTTTGA
1 TGGTCTTTTCGGCTTTAGCAACTTTGA
31099 TGGTCTTTTCGGCTTTAGCAACTTTGA
1 TGGTCTTTTCGGCTTTAGCAACTTTGA
31126 AATGATGGTA
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:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (27 bp):
TGGTCTTTTCGGCTTTAGCAACTTTGA
Found at i:51937 original size:2 final size:2
Alignment explanation
Indices: 51930--51955 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
51920 TTTTATCATA
51930 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
51956 TTGTTTTTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52711 original size:30 final size:29
Alignment explanation
Indices: 52671--52732 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 29
52661 GTAGGGATAG
*
52671 GTTCAGCTTCAAAAAGACGATGATGAACAT
1 GTTCAACTTCAAAAAGACGATGATGAAC-T
52701 GTTCAACTTCAAAAAGACGATGATGAACT
1 GTTCAACTTCAAAAAGACGATGATGAACT
52730 GTT
1 GTT
52733 GAAATATCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 4 0.13
30 27 0.87
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (29 bp):
GTTCAACTTCAAAAAGACGATGATGAACT
Found at i:62257 original size:29 final size:29
Alignment explanation
Indices: 62215--62273 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
62205 GAAAATCATG
62215 TGACTTTCACACTTATCATTATCTTCAAA
1 TGACTTTCACACTTATCATTATCTTCAAA
62244 TGACTTTCACACTTATCATTATCTTCAAA
1 TGACTTTCACACTTATCATTATCTTCAAA
62273 T
1 T
62274 AATTTTTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.42
Consensus pattern (29 bp):
TGACTTTCACACTTATCATTATCTTCAAA
Found at i:62737 original size:2 final size:2
Alignment explanation
Indices: 62730--62765 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
62720 TTTATACTCG
62730 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
62766 TATCTCAACG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:68595 original size:21 final size:20
Alignment explanation
Indices: 68565--68617 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
68555 CGGTTCAACC
*
68565 TAAATGTTTTTAGTTTTTTAT
1 TAAAT-TTTTTAGTATTTTAT
*
68586 TAAATATTTTTGGTATTTTAT
1 TAAAT-TTTTTAGTATTTTAT
*
68607 TTAATTTTTTA
1 TAAATTTTTTA
68618 AATAATTATG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 5 0.19
21 22 0.81
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.66
Consensus pattern (20 bp):
TAAATTTTTTAGTATTTTAT
Found at i:74385 original size:16 final size:16
Alignment explanation
Indices: 74364--74395 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
74354 GTTTGTGAGG
74364 TAGTAGATTCATATTC
1 TAGTAGATTCATATTC
74380 TAGTAGATTCATATTC
1 TAGTAGATTCATATTC
74396 AAGCATGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.44
Consensus pattern (16 bp):
TAGTAGATTCATATTC
Found at i:75591 original size:33 final size:33
Alignment explanation
Indices: 75549--75615 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
75539 CCTAGTACAG
75549 ATGGTGGACACGACCTTATGTGTCATACGGATT
1 ATGGTGGACACGACCTTATGTGTCATACGGATT
*
75582 ATGGTGGACACGGCCTTATGTGTCATACGGATT
1 ATGGTGGACACGACCTTATGTGTCATACGGATT
75615 A
1 A
75616 GCACTACAGT
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:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (33 bp):
ATGGTGGACACGACCTTATGTGTCATACGGATT
Found at i:75611 original size:17 final size:17
Alignment explanation
Indices: 75562--75611 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 17
75552 GTGGACACGA
75562 CCTTATGTGTCATACGG
1 CCTTATGTGTCATACGG
* * *
75579 -ATTATG-GTGGACACGG
1 CCTTATGTGT-CATACGG
75595 CCTTATGTGTCATACGG
1 CCTTATGTGTCATACGG
75612 ATTAGCACTA
Statistics
Matches: 24, Mismatches: 6, Indels: 6
0.67 0.17 0.17
Matches are distributed among these distances:
15 2 0.08
16 10 0.42
17 10 0.42
18 2 0.08
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.32
Consensus pattern (17 bp):
CCTTATGTGTCATACGG
Found at i:75712 original size:20 final size:20
Alignment explanation
Indices: 75672--75713 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
75662 TTGTATATTG
* *
75672 GGCTATTGTCTATTGTTTAT
1 GGCTATTGTCTATGGTATAT
75692 GGCTATTGTCTATGGTATAT
1 GGCTATTGTCTATGGTATAT
75712 GG
1 GG
75714 TTATGGAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.10, G:0.26, T:0.48
Consensus pattern (20 bp):
GGCTATTGTCTATGGTATAT
Found at i:75782 original size:44 final size:44
Alignment explanation
Indices: 75714--75851 Score: 206
Period size: 44 Copynumber: 3.1 Consensus size: 44
75704 TGGTATATGG
* *
75714 TTATGGA-ATAATGGCAAGTGTATTGGTAAAATAAGCTTACGAGC
1 TTATGGATA-AATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
*
75758 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGT
1 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
* *
75802 TTATAGATAAATAGTAAGTATATTGGTAAAATAAGCTTACGAGC
1 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
*
75846 TAATGG
1 TTATGG
75852 TATTAAAAGG
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
44 84 0.99
45 1 0.01
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.32
Consensus pattern (44 bp):
TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
Found at i:77268 original size:15 final size:15
Alignment explanation
Indices: 77248--77279 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
77238 ATCAGTATGA
77248 ATATACGATGAATCC
1 ATATACGATGAATCC
77263 ATATACGATGAATCC
1 ATATACGATGAATCC
77278 AT
1 AT
77280 GAACTTGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (15 bp):
ATATACGATGAATCC
Found at i:77504 original size:115 final size:115
Alignment explanation
Indices: 77302--77532 Score: 426
Period size: 115 Copynumber: 2.0 Consensus size: 115
77292 TTGATGAGTT
77302 GTGTATGTTGTTGTCATTCGATATCCCACATCGCTTTTAACTCTCAATCATCGCATGCTTTAAAT
1 GTGTATGTTGTTGTCATTCGATATCCCACATCGCTTTTAACTCTCAATCATCGCATGCTTTAAAT
77367 GGAAAATGAGTACTATATTTTGCTCTTGTTGTGGTCATTCAAAATCCTTA
66 GGAAAATGAGTACTATATTTTGCTCTTGTTGTGGTCATTCAAAATCCTTA
* *
77417 GTGTATGTTTTTGTCATTCGATATCCCACATCGCTTTTAACTCTCAATCATCTCATGCTTTAAAT
1 GTGTATGTTGTTGTCATTCGATATCCCACATCGCTTTTAACTCTCAATCATCGCATGCTTTAAAT
* *
77482 GGCAAATGAGTACTATATTTTGCTCTTGTTGTGGTCATTCAAAATTCTTA
66 GGAAAATGAGTACTATATTTTGCTCTTGTTGTGGTCATTCAAAATCCTTA
77532 G
1 G
77533 GAGGAGGAGG
Statistics
Matches: 112, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
115 112 1.00
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.41
Consensus pattern (115 bp):
GTGTATGTTGTTGTCATTCGATATCCCACATCGCTTTTAACTCTCAATCATCGCATGCTTTAAAT
GGAAAATGAGTACTATATTTTGCTCTTGTTGTGGTCATTCAAAATCCTTA
Found at i:77890 original size:14 final size:14
Alignment explanation
Indices: 77871--77912 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 14
77861 GTCTCTTAAC
*
77871 CGTCAATTTCCATT
1 CGTCAACTTCCATT
77885 CGTCAACTTCCATT
1 CGTCAACTTCCATT
77899 CGTCAACTTCCATT
1 CGTCAACTTCCATT
77913 AACCGAAGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.21, C:0.33, G:0.07, T:0.38
Consensus pattern (14 bp):
CGTCAACTTCCATT
Found at i:79229 original size:12 final size:12
Alignment explanation
Indices: 79208--79237 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
79198 GAAATCTTAT
*
79208 TCTTAAAAATAA
1 TCTTATAAATAA
79220 TCTTATAAATAA
1 TCTTATAAATAA
79232 TCTTAT
1 TCTTAT
79238 TTTTCATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (12 bp):
TCTTATAAATAA
Found at i:80006 original size:181 final size:183
Alignment explanation
Indices: 79692--80057 Score: 612
Period size: 181 Copynumber: 2.0 Consensus size: 183
79682 TAAATAACTC
*
79692 ATACAACGTTTATGATACTCCAGTAATTAATCATAAGAAAAACTATATACATATACATTAAAAAA
1 ATACAACGTTTATGATACTCCAATAATTAATCATAAGAAAAACTATATACATATACATTAAAAAA
79757 ACAACGGAAAAAACAAATCAAAATATTAAACCACATATAAATATAATAATTAAATTAAAAAAGGT
66 ACAACGGAAAAAACAAATCAAAATATTAAACCACATATAAATATAATAATTAAATTAAAAAAGGT
** *
79822 AAAGTAACAAATACCGAAGTTGTCTCCTTCC-GGAAAATATTCAATCTTTGAT
131 AAAGTAACAAATACCGAAGTTGTCTCCTTCCAAAAAAATATTCAATATTTGAT
* *
79874 ATACAGCGTTTATGATACTCCAATAATTAATTATAAGAAAAACTATATACATATACATTAAAAAA
1 ATACAACGTTTATGATACTCCAATAATTAATCATAAGAAAAACTATATACATATACATTAAAAAA
**
79939 AC-A-GGAAAAAAACAAATCAAAATATTAAACCATGTATAAATATAATAATTAAATTAAAAAAGG
66 ACAACGG-AAAAAACAAATCAAAATATTAAACCACATATAAATATAATAATTAAATTAAAAAAGG
* *
80002 TAAAGTAACAATTACCGAAGTTGTCTCCTTCCAAAAAAATATTTAATATTTGAT
130 TAAAGTAACAAATACCGAAGTTGTCTCCTTCCAAAAAAATATTCAATATTTGAT
80056 AT
1 AT
80058 GTACCAAAAA
Statistics
Matches: 172, Mismatches: 10, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
180 2 0.01
181 87 0.51
182 83 0.48
ACGTcount: A:0.51, C:0.13, G:0.08, T:0.28
Consensus pattern (183 bp):
ATACAACGTTTATGATACTCCAATAATTAATCATAAGAAAAACTATATACATATACATTAAAAAA
ACAACGGAAAAAACAAATCAAAATATTAAACCACATATAAATATAATAATTAAATTAAAAAAGGT
AAAGTAACAAATACCGAAGTTGTCTCCTTCCAAAAAAATATTCAATATTTGAT
Found at i:82461 original size:69 final size:70
Alignment explanation
Indices: 82329--82469 Score: 257
Period size: 69 Copynumber: 2.0 Consensus size: 70
82319 GCACATTCTG
*
82329 TGGCTTCATTACTTGGTATATGATACGAACATAGTCTTCCATAATGATGCTCAACTCTTCTTTCT
1 TGGCTTCATTACTTGGTATATGATACGAACA-AGTCTTCCAAAATGATGCTCAACTCTTCTTTCT
82394 TCTATT
65 TCTATT
82400 TGGCTTCATTACTTGGTATATGATACGAAC-AGTCTTCCAAAATGATGCTCAACTCTTCTTTCTT
1 TGGCTTCATTACTTGGTATATGATACGAACAAGTCTTCCAAAATGATGCTCAACTCTTCTTTCTT
82464 CTATT
66 CTATT
82469 T
1 T
82470 ACCATTTGCT
Statistics
Matches: 69, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
69 39 0.57
71 30 0.43
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (70 bp):
TGGCTTCATTACTTGGTATATGATACGAACAAGTCTTCCAAAATGATGCTCAACTCTTCTTTCTT
CTATT
Found at i:83822 original size:25 final size:25
Alignment explanation
Indices: 83776--83846 Score: 126
Period size: 25 Copynumber: 2.9 Consensus size: 25
83766 ACCGTCCGTC
*
83776 ACTCCCCTT-TAATTACCACCTATT
1 ACTCCCCTTATAAATACCACCTATT
83800 ACTCCCCTTATAAATACCACCTATT
1 ACTCCCCTTATAAATACCACCTATT
83825 ACTCCCCTTATAAATACCACCT
1 ACTCCCCTTATAAATACCACCT
83847 CATACAACTC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
24 9 0.20
25 36 0.80
ACGTcount: A:0.30, C:0.38, G:0.00, T:0.32
Consensus pattern (25 bp):
ACTCCCCTTATAAATACCACCTATT
Found at i:90581 original size:21 final size:22
Alignment explanation
Indices: 90557--90602 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
90547 TTTTGTTGAA
*
90557 TTTTATT-CACTTTTAATTCTT
1 TTTTATTACACTTTTAATTATT
* *
90578 TTTTATTACATTTTTATTTATT
1 TTTTATTACACTTTTAATTATT
90600 TTT
1 TTT
90603 AAAAAATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTTATTACACTTTTAATTATT
Found at i:91216 original size:19 final size:18
Alignment explanation
Indices: 91175--91217 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
91165 TTTATTTGCG
*
91175 AAAATTTAAATTTAAATT
1 AAAATTTAAAATTAAATT
*
91193 AAAATTTAAAAATTCAATT
1 AAAATTT-AAAATTAAATT
*
91212 CAAATT
1 AAAATT
91218 ACTCACATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAATTTAAAATTAAATT
Found at i:91354 original size:39 final size:40
Alignment explanation
Indices: 91300--91375 Score: 102
Period size: 39 Copynumber: 1.9 Consensus size: 40
91290 ATAAAGAAAT
91300 ATTAAATGAAAAAAAT-AACAAATCAAAAAAAAAGGAAAAA
1 ATTAAATGAAAAAAATAAACAAAT-AAAAAAAAAGGAAAAA
* * *
91340 ATTAAAT-AAGAAAATAAATAAATAAATAAAAAGGAA
1 ATTAAATGAAAAAAATAAACAAATAAAAAAAAAGGAA
91376 TAGAAAATGA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
39 19 0.59
40 13 0.41
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.16
Consensus pattern (40 bp):
ATTAAATGAAAAAAATAAACAAATAAAAAAAAAGGAAAAA
Found at i:92723 original size:3 final size:3
Alignment explanation
Indices: 92717--92779 Score: 51
Period size: 3 Copynumber: 20.7 Consensus size: 3
92707 AAAATAAATA
* *
92717 AAT AAT AA- AAT AAA AAT AAGGT AAAT AAT AAT AAT AAT AAT AAT AGT
1 AAT AAT AAT AAT AAT AAT AA--T -AAT AAT AAT AAT AAT AAT AAT AAT
92764 AA- ATAT AAT -AT AAT AA
1 AAT A-AT AAT AAT AAT AA
92780 AAAACATTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
2 5 0.10
3 39 0.80
4 2 0.04
5 1 0.02
6 2 0.04
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:92729 original size:12 final size:12
Alignment explanation
Indices: 92712--92759 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
92702 GGAAAAAAAT
92712 AAATAAATAATA
1 AAATAAATAATA
92724 AAATAAA-AATA
1 AAATAAATAATA
**
92735 AGGTAAATAATA
1 AAATAAATAATA
92747 ATAAT-AATAATA
1 A-AATAAATAATA
92759 A
1 A
92760 TAGTAAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
11 9 0.30
12 20 0.67
13 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (12 bp):
AAATAAATAATA
Found at i:92844 original size:16 final size:15
Alignment explanation
Indices: 92805--92849 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
92795 ACTATATAAT
92805 ATATATGTTT-AAAAA
1 ATATAT-TTTCAAAAA
92820 ATA-ATTTTCAAAACA
1 ATATATTTTCAAAA-A
92835 ATATATTTTCAAAAA
1 ATATATTTTCAAAAA
92850 TTGTTTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 3 0.11
14 6 0.22
15 8 0.30
16 10 0.37
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (15 bp):
ATATATTTTCAAAAA
Found at i:92861 original size:29 final size:30
Alignment explanation
Indices: 92805--92862 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
92795 ACTATATAAT
*
92805 ATATATGTTTAAAAAATAATTTTCAAAACA
1 ATATATGTTTAAAAAATAATTTTAAAAACA
* **
92835 ATATAT-TTTCAAAAATTGTTTTAAAAAC
1 ATATATGTTTAAAAAATAATTTTAAAAAC
92863 TTATGTATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (30 bp):
ATATATGTTTAAAAAATAATTTTAAAAACA
Found at i:92914 original size:74 final size:72
Alignment explanation
Indices: 92834--93142 Score: 332
Period size: 74 Copynumber: 4.0 Consensus size: 72
92824 TTTTCAAAAC
*
92834 AATATATTTTCAAAAATTGTTTTAAAAACTTATGTATTATATATATATTTTCAAAAACGTTTTAA
1 AATATATTTTCAAAAA-TGTTTTAAAAAC-TA--TA-TATATATATATTTTC-AAAATGTTTTAA
*
92899 AAATTATATAATATAT
60 AAA-CATAT-A-ATAT
*** *
92915 ATATATATGTTTTTTAAATGTTTTAAAAACTATATAATATATATGTTTTCAAAATGTTTTAAAAA
1 A-ATATAT-TTTCAAAAATGTTTTAAAAACTATAT-ATATATATATTTTCAAAATGTTTTAAAAA
92980 CTATATAATAT
63 C-ATATAATAT
*
92991 ATATATATTTTC-AAAATGTTTTAAAAACTATATATTATACATATTTTCAAAATGTTTTAAAAAC
1 A-ATATATTTTCAAAAATGTTTTAAAAACTATATA-TATATATATTTTCAAAATGTTTTAAAAAC
93055 TATATAATAT
64 -ATATAATAT
*
93065 ATATATATGTTTTCAAAAATGTTTTAAAAATTATATATCATATATATTTTCAAAATGTTTTCAAA
1 A-ATATA--TTTTCAAAAATGTTTTAAAAACTATATAT-ATATATATTTTCAAAATGTTTT-AAA
**
93130 ATTATATAATAT
61 AACATATAATAT
93142 A
1 A
93143 TACTTATATA
Statistics
Matches: 204, Mismatches: 14, Indels: 24
0.84 0.06 0.10
Matches are distributed among these distances:
73 1 0.00
74 64 0.31
75 3 0.01
76 18 0.09
77 53 0.26
78 23 0.11
79 15 0.07
81 3 0.01
82 18 0.09
83 6 0.03
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (72 bp):
AATATATTTTCAAAAATGTTTTAAAAACTATATATATATATATTTTCAAAATGTTTTAAAAACAT
ATAATAT
Found at i:92962 original size:36 final size:36
Alignment explanation
Indices: 92909--93144 Score: 303
Period size: 36 Copynumber: 6.3 Consensus size: 36
92899 AAATTATATA
* **
92909 ATATATATATATATGTTTTTTAAATGTTTTAAAAACT
1 ATATA-ATATATATATTTTCAAAATGTTTTAAAAACT
*
92946 ATATAATATATATGTTTTCAAAATGTTTTAAAAACT
1 ATATAATATATATATTTTCAAAATGTTTTAAAAACT
92982 ATATAATATATATATATTTTCAAAATGTTTTAAAAACT
1 ATAT-A-ATATATATATTTTCAAAATGTTTTAAAAACT
* *
93020 ATATATTATACATATTTTCAAAATGTTTTAAAAACT
1 ATATAATATATATATTTTCAAAATGTTTTAAAAACT
*
93056 ATATAATATATATATATGTTTTCAAAAATGTTTTAAAAATT
1 ATAT-A-ATATATATA--TTTTC-AAAATGTTTTAAAAACT
* *
93097 ATAT-ATCATATATATTTTCAAAATGTTTTCAAAATT
1 ATATAAT-ATATATATTTTCAAAATGTTTTAAAAACT
93133 ATATAATATATA
1 ATATAATATATA
93145 CTTATATATT
Statistics
Matches: 181, Mismatches: 9, Indels: 19
0.87 0.04 0.09
Matches are distributed among these distances:
36 91 0.50
37 15 0.08
38 43 0.24
39 7 0.04
40 5 0.03
41 20 0.11
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (36 bp):
ATATAATATATATATTTTCAAAATGTTTTAAAAACT
Found at i:94545 original size:39 final size:39
Alignment explanation
Indices: 94497--94791 Score: 292
Period size: 39 Copynumber: 7.7 Consensus size: 39
94487 CCACCACCAG
* * *
94497 CCAAGGCACCTCCCAAGCCACCAACTTATGCTCCTCCGC
1 CCAAGGCACCACCCAAGCCACCAACTTATCCTCCTCCAC
* *
94536 CCAAAGCACCACCCAAGCCACCCACTTATCCTCCTCCAC
1 CCAAGGCACCACCCAAGCCACCAACTTATCCTCCTCCAC
* * *
94575 CCAAGGCACCTCCCAAGCCACCAACTTATGCTCCTCCGC
1 CCAAGGCACCACCCAAGCCACCAACTTATCCTCCTCCAC
* *
94614 CCAAAGCACCACCCAAGCCATCC-ACTTATCCTCCTCCAA
1 CCAAGGCACCACCCAAGCCA-CCAACTTATCCTCCTCCAC
*
94653 CCAAGGCACCAACCAAGCCACCAACTTATCCTCCT----
1 CCAAGGCACCACCCAAGCCACCAACTTATCCTCCTCCAC
**
94688 -C----CA--A-CCAAGCCACCAACTTACGCTCCTCCAC
1 CCAAGGCACCACCCAAGCCACCAACTTATCCTCCTCCAC
* * *
94719 CCAAGGCACCACCGACGAAGCCACCGACTTACCCTCCTACAC
1 CCAAGGCACCACC--C-AAGCCACCAACTTATCCTCCTCCAC
94761 CCAAGGCACCACCGACCAAGCCACCAACTTA
1 CCAAGGCACCA-C--CCAAGCCACCAACTTA
94792 CCCACCACCG
Statistics
Matches: 213, Mismatches: 23, Indels: 37
0.78 0.08 0.14
Matches are distributed among these distances:
27 21 0.10
28 1 0.00
30 2 0.01
32 1 0.00
34 1 0.00
36 2 0.01
38 3 0.01
39 130 0.61
40 2 0.01
41 1 0.00
42 46 0.22
43 2 0.01
45 1 0.00
ACGTcount: A:0.28, C:0.49, G:0.10, T:0.13
Consensus pattern (39 bp):
CCAAGGCACCACCCAAGCCACCAACTTATCCTCCTCCAC
Found at i:94696 original size:66 final size:67
Alignment explanation
Indices: 94626--94771 Score: 172
Period size: 69 Copynumber: 2.2 Consensus size: 67
94616 AAAGCACCAC
*
94626 CCAAGCCATCC-ACTTATC-CTCCTCCAACCAAGGCACCA-ACCAAGCCACCAACTTATCCTCCT
1 CCAAGCCA-CCAACTTA-CGCTCCTCCAACCAAGGCACCACACCAAGCCACCAACTTACCCTCCT
*
94688 CCAA
64 ACAA
* * *
94692 CCAAGCCACCAACTTACGCTCCTCCACCCAAGGCACCACCGACGAAGCCACCGACTTACCCTCCT
1 CCAAGCCACCAACTTACGCTCCTCCAACCAAGGCACCA-C-ACCAAGCCACCAACTTACCCTCCT
*
94757 ACAC
64 ACAA
*
94761 CCAAGGCACCA
1 CCAAGCCACCA
94772 CCGACCAAGC
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
65 3 0.04
66 32 0.47
69 33 0.49
ACGTcount: A:0.29, C:0.48, G:0.10, T:0.13
Consensus pattern (67 bp):
CCAAGCCACCAACTTACGCTCCTCCAACCAAGGCACCACACCAAGCCACCAACTTACCCTCCTAC
AA
Found at i:94702 original size:78 final size:78
Alignment explanation
Indices: 94497--94689 Score: 341
Period size: 78 Copynumber: 2.5 Consensus size: 78
94487 CCACCACCAG
94497 CCAAGGCACCTCCCAAGCCACCAACTTATGCTCCTCCGCCCAAAGCACCACCCAAGCCACCCACT
1 CCAAGGCACCTCCCAAGCCACCAACTTATGCTCCTCCGCCCAAAGCACCACCCAAGCCACCCACT
*
94562 TATCCTCCTCCAC
66 TATCCTCCTCCAA
*
94575 CCAAGGCACCTCCCAAGCCACCAACTTATGCTCCTCCGCCCAAAGCACCACCCAAGCCATCCACT
1 CCAAGGCACCTCCCAAGCCACCAACTTATGCTCCTCCGCCCAAAGCACCACCCAAGCCACCCACT
94640 TATCCTCCTCCAA
66 TATCCTCCTCCAA
** *
94653 CCAAGGCACCAACCAAGCCACCAACTTATCCTCCTCC
1 CCAAGGCACCTCCCAAGCCACCAACTTATGCTCCTCC
94690 AACCAAGCCA
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 110 1.00
ACGTcount: A:0.27, C:0.50, G:0.09, T:0.15
Consensus pattern (78 bp):
CCAAGGCACCTCCCAAGCCACCAACTTATGCTCCTCCGCCCAAAGCACCACCCAAGCCACCCACT
TATCCTCCTCCAA
Found at i:94731 original size:30 final size:27
Alignment explanation
Indices: 94661--94729 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 27
94651 AACCAAGGCA
94661 CCAACCAAGCCACCAACTTATCCTCCT
1 CCAACCAAGCCACCAACTTATCCTCCT
94688 CCAACCAAGCCACCAACTTA-CGCTCCT
1 CCAACCAAGCCACCAACTTATC-CTCCT
* *
94715 CCACCCAAGGCACCA
1 CCAACCAAGCCACCA
94730 CCGACGAAGC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
26 1 0.03
27 38 0.97
ACGTcount: A:0.30, C:0.49, G:0.07, T:0.13
Consensus pattern (27 bp):
CCAACCAAGCCACCAACTTATCCTCCT
Found at i:94742 original size:42 final size:42
Alignment explanation
Indices: 94691--94794 Score: 172
Period size: 42 Copynumber: 2.5 Consensus size: 42
94681 TCCTCCTCCA
* *
94691 ACCAAGCCACCAACTTACGCTCCTCCACCCAAGGCACCACCG
1 ACCAAGCCACCAACTTACCCTCCTACACCCAAGGCACCACCG
* *
94733 ACGAAGCCACCGACTTACCCTCCTACACCCAAGGCACCACCG
1 ACCAAGCCACCAACTTACCCTCCTACACCCAAGGCACCACCG
94775 ACCAAGCCACCAACTTACCC
1 ACCAAGCCACCAACTTACCC
94795 ACCACCGTCA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.30, C:0.49, G:0.12, T:0.10
Consensus pattern (42 bp):
ACCAAGCCACCAACTTACCCTCCTACACCCAAGGCACCACCG
Found at i:96590 original size:22 final size:21
Alignment explanation
Indices: 96555--96595 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
96545 TCCAAATTTC
96555 TTTATAATTAAATTTTCATAAT
1 TTTATAATTAAA-TTTCATAAT
* *
96577 TTTATTATTTAATTTCATA
1 TTTATAATTAAATTTCATA
96596 TTTCTTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTATAATTAAATTTCATAAT
Found at i:96619 original size:26 final size:26
Alignment explanation
Indices: 96586--96678 Score: 177
Period size: 26 Copynumber: 3.6 Consensus size: 26
96576 TTTTATTATT
*
96586 TAATTTCATATTTCTTAAAAATTTTA
1 TAATTTCATATTTCTAAAAAATTTTA
96612 TAATTTCATATTTCTAAAAAATTTTA
1 TAATTTCATATTTCTAAAAAATTTTA
96638 TAATTTCATATTTCTAAAAAATTTTA
1 TAATTTCATATTTCTAAAAAATTTTA
96664 TAATTTCATATTTCT
1 TAATTTCATATTTCT
96679 TAAATTTTTA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
26 66 1.00
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.53
Consensus pattern (26 bp):
TAATTTCATATTTCTAAAAAATTTTA
Found at i:97514 original size:14 final size:14
Alignment explanation
Indices: 97495--97526 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
97485 GTGGAATTCT
97495 AAATATTTAAATAA
1 AAATATTTAAATAA
*
97509 AAATATTTATATAA
1 AAATATTTAAATAA
97523 AAAT
1 AAAT
97527 TCATCGAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATATTTAAATAA
Found at i:97586 original size:25 final size:24
Alignment explanation
Indices: 97558--97607 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
97548 ATTCTTTTTA
97558 ATATATATACTTTTTAATAAAATTT
1 ATATATA-ACTTTTTAATAAAATTT
* *
97583 ATATATAATTTTTTTATAAAATTT
1 ATATATAACTTTTTAATAAAATTT
97607 A
1 A
97608 AAAGATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
ATATATAACTTTTTAATAAAATTT
Found at i:97615 original size:25 final size:24
Alignment explanation
Indices: 97568--97615 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
97558 ATATATATAC
* *
97568 TTTTTAATAAAATTTATATATAAT
1 TTTTTAATAAAATTTAAAGATAAT
*
97592 TTTTTTATAAAATTTAAAAGATAA
1 TTTTTAATAAAATTT-AAAGATAA
97616 ATGGGTAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
TTTTTAATAAAATTTAAAGATAAT
Found at i:97687 original size:18 final size:17
Alignment explanation
Indices: 97656--97689 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
97646 GTATTATTTT
*
97656 AATTTTAATTAATATTA
1 AATTTTAATCAATATTA
97673 AATTTTACATCAATATT
1 AATTTTA-ATCAATATT
97690 TAACTAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
AATTTTAATCAATATTA
Found at i:106416 original size:3 final size:3
Alignment explanation
Indices: 106408--106452 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
106398 ACTCCTCACT
* * *
106408 ATC ATC ATC ATC ACC ATT ATC ATC ATC ATC ATC ATC GTC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
106453 GTCGTCGTCA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.31, C:0.33, G:0.02, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:106448 original size:12 final size:12
Alignment explanation
Indices: 106409--106471 Score: 63
Period size: 12 Copynumber: 5.2 Consensus size: 12
106399 CTCCTCACTA
*
106409 TCATCATCATCA
1 TCATCATCATCG
* * *
106421 CCATTATCATCA
1 TCATCATCATCG
106433 TCATCATCATCG
1 TCATCATCATCG
*
106445 TCATCATCGTCG
1 TCATCATCATCG
* *
106457 TCGTCATCGTCG
1 TCATCATCATCG
106469 TCA
1 TCA
106472 GGAGCAGATA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 43 1.00
ACGTcount: A:0.24, C:0.33, G:0.10, T:0.33
Consensus pattern (12 bp):
TCATCATCATCG
Found at i:108505 original size:13 final size:13
Alignment explanation
Indices: 108484--108521 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
108474 CTTCCATTTT
*
108484 ATAACTAAAAAAA
1 ATAATTAAAAAAA
108497 ATAATTAAATAAAA
1 ATAATTAAA-AAAA
108511 AT-ATTAAAAAA
1 ATAATTAAAAAA
108522 TTTAAATAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 3 0.13
13 14 0.61
14 6 0.26
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (13 bp):
ATAATTAAAAAAA
Found at i:108550 original size:29 final size:29
Alignment explanation
Indices: 108495--108601 Score: 116
Period size: 29 Copynumber: 3.7 Consensus size: 29
108485 TAACTAAAAA
*
108495 AAATAATTAAATAAAAATATTAAAAAATTT
1 AAATAA-TAAATAAAAATACTAAAAAATTT
108525 AAATAACTAAAT-AAAATACTAAAAAATATT
1 AAATAA-TAAATAAAAATACTAAAAAAT-TT
108555 AAAT-AT-AATAAAATATACTAAAAAATTAT
1 AAATAATAAATAAAA-ATACTAAAAAATT-T
108584 AAAT-AT-AATAAAATATAC
1 AAATAATAAATAAAA-ATAC
108602 CATATCACCC
Statistics
Matches: 71, Mismatches: 2, Indels: 9
0.87 0.02 0.11
Matches are distributed among these distances:
27 3 0.04
28 5 0.07
29 46 0.65
30 17 0.24
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (29 bp):
AAATAATAAATAAAAATACTAAAAAATTT
Found at i:108587 original size:19 final size:19
Alignment explanation
Indices: 108505--108596 Score: 57
Period size: 19 Copynumber: 4.8 Consensus size: 19
108495 AAATAATTAA
* *
108505 ATAAAAATATTAAAAAATT
1 ATAAATATACTAAAAAATT
*
108524 -TAAATA-ACTAAATAAAAT
1 ATAAATATACTAAA-AAATT
* *
108542 ACTAAAAAATATTAAATATAA-T
1 A-T-AAATATACTAAA-A-AATT
108564 A-AAATATACTAAAAAATT
1 ATAAATATACTAAAAAATT
*
108582 ATAAATATAATAAAA
1 ATAAATATACTAAAA
108597 TATACCATAT
Statistics
Matches: 57, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
17 7 0.12
18 12 0.21
19 22 0.39
20 1 0.02
21 4 0.07
22 9 0.16
23 2 0.04
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.29
Consensus pattern (19 bp):
ATAAATATACTAAAAAATT
Found at i:108597 original size:10 final size:10
Alignment explanation
Indices: 108534--108600 Score: 63
Period size: 10 Copynumber: 7.1 Consensus size: 10
108524 TAAATAACTA
108534 AATAAAATACT
1 AATAAAATA-T
108545 AA-AAAATAT
1 AATAAAATAT
108554 --T-AAATAT
1 AATAAAATAT
108561 AATAAAATAT
1 AATAAAATAT
* *
108571 ACTAAAAAAT
1 AATAAAATAT
*
108581 TAT-AAATAT
1 AATAAAATAT
108590 AATAAAATAT
1 AATAAAATAT
108600 A
1 A
108601 CCATATCACC
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
7 6 0.13
9 9 0.20
10 28 0.62
11 2 0.04
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (10 bp):
AATAAAATAT
Found at i:109082 original size:2 final size:2
Alignment explanation
Indices: 109070--109105 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
109060 TAAACAATTC
109070 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
109106 ATACAAGGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:111077 original size:12 final size:12
Alignment explanation
Indices: 111060--111086 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
111050 TTAATTGTGA
111060 AAATTGAAATTT
1 AAATTGAAATTT
111072 AAATTGAAATTT
1 AAATTGAAATTT
111084 AAA
1 AAA
111087 ACATTCAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (12 bp):
AAATTGAAATTT
Found at i:111199 original size:3 final size:3
Alignment explanation
Indices: 111191--111226 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
111181 AAAGAACGAA
111191 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
111227 TCAAAGGGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:111364 original size:16 final size:15
Alignment explanation
Indices: 111344--111387 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
111334 ATGAAATAGG
111344 ATAAAAATAAAAAAA
1 ATAAAAATAAAAAAA
*
111359 ATTAAACAT-AAAAAA
1 A-TAAAAATAAAAAAA
111374 ATAAAAATATAAAA
1 ATAAAAATA-AAAA
111388 GGGATTAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
14 6 0.25
15 8 0.33
16 10 0.42
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.18
Consensus pattern (15 bp):
ATAAAAATAAAAAAA
Found at i:113440 original size:84 final size:83
Alignment explanation
Indices: 113080--113485 Score: 315
Period size: 84 Copynumber: 4.8 Consensus size: 83
113070 GACAAATAGC
* * * * * * * *
113080 CCTTCTTGCCTTGAGCTATGCTGTAAATTTGATTTGTCTCTG-AGCGGAATGTAGTCAAACTCGA
1 CCTTCTAGCCTTGAGTTATGCTGCAAA--TGATGTGCCTC-GAAGCTGAGTGTAGTCGAACTCGA
* *
113144 AGGTCTTTTGTTGACAGATAA
63 AGGTCTTTGGTTGGCAGATAA
* * * * * *
113165 CCTATCTAGCCTTGAGTTATGTTGTAAATGATGCAT-CTTTG-AGCTGATTATAGTCGAACTCGA
1 CCT-TCTAGCCTTGAGTTATGCTGCAAATGATG--TGCCTCGAAGCTGAGTGTAGTCGAACTCGA
* * *
113228 AGGTCTTTTGTTGGTAGGTAA
63 AGGTCTTTGGTTGGCAGATAA
* * * * * * *
113249 CCCTTCTAGCCTTGAGTTATGTTACAAATGATGTACCCTCGAAGCTAAGTGTAATCAAACTCGAG
1 -CCTTCTAGCCTTGAGTTATGCTGCAAATGATGT-GCCTCGAAGCTGAGTGTAGTCGAACTCGAA
113314 GGTCTTTGG-T---AGATAGA
64 GGTCTTTGGTTGGCAGATA-A
* * * * * *
113331 CCTTCTCA-ACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCGAACTAGAAG
1 CCTTCT-AGCCTTGAGTTATGCTGCAAATGATGTGCCTCGAAGCTGAGTGTAGTCGAACTCGAAG
*
113395 GTCTTTGGTTGGCGGATAA
65 GTCTTTGGTTGGCAGATAA
* * *
113414 CCCTTCTAGTCTTGAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGTATAGTCGAACTCGAA
1 -CCTTCTAGCCTTGAGTTATGCTGCAAATGATGTG-CCTCGAAGCTGAGTGTAGTCGAACTCGAA
*
113479 GGCCTTT
64 GGTCTTT
113486 ATGTTTCAAG
Statistics
Matches: 256, Mismatches: 49, Indels: 32
0.76 0.15 0.09
Matches are distributed among these distances:
80 31 0.12
81 31 0.12
82 3 0.01
83 2 0.01
84 104 0.41
85 63 0.25
86 22 0.09
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (83 bp):
CCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTCGAAGCTGAGTGTAGTCGAACTCGAAGG
TCTTTGGTTGGCAGATAA
Found at i:113619 original size:67 final size:68
Alignment explanation
Indices: 113487--113627 Score: 187
Period size: 67 Copynumber: 2.1 Consensus size: 68
113477 AAGGCCTTTA
* * * ** *
113487 TGTTTCAAGAGAAACATTTCAAAGGTTTTTTGTGTTTCAAGAGAAACTGTCTCCAGGGAGGCAAA
1 TGTTTCAAGAGAAACATTTCAAAGG-TATTGGTGTTTCAAGAGAAACTGTCTCAAAAGAGACAAA
*
113552 ATTT
65 ACTT
113556 TGTTTCAAGAGAAACATATTCAAA-G-ATTGGTGTTTCAAGAGAAACTGTCTCAAAAGAGACAAA
1 TGTTTCAAGAGAAACAT-TTCAAAGGTATTGGTGTTTCAAGAGAAACTGTCTCAAAAGAGACAAA
113619 ACTT
65 ACTT
113623 TGTTT
1 TGTTT
113628 TAAAGGGAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
67 40 0.62
69 18 0.28
70 6 0.09
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (68 bp):
TGTTTCAAGAGAAACATTTCAAAGGTATTGGTGTTTCAAGAGAAACTGTCTCAAAAGAGACAAAA
CTT
Found at i:113638 original size:38 final size:36
Alignment explanation
Indices: 113586--113882 Score: 168
Period size: 36 Copynumber: 8.4 Consensus size: 36
113576 CAAAGATTGG
* *
113586 TGTTTCAAGAGAAACTGTCTCAAAAGAGACAAAACTT
1 TGTTTAAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * *
113623 TGTTTTAAAGGGAAACTCTCTGAAGAGAGACAAAATT
1 TG-TTTAAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * * *
113660 TGTTTCAAGAGAAGCTGTCTCAAGATAGACAAAGCTT
1 TGTTTAAAGAGAAACTGTCTCAAGAGAGACAAA-ATT
* * * * *
113697 AGTTCCAAA-AGAAATTATCTCAAGGGAGAC-AAATT
1 TGTT-TAAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * * * *
113732 CGTTTCAAG-GAAAATATATTC-A-A-AG-----ATT
1 TGTTTAAAGAGAAACTGT-CTCAAGAGAGACAAAATT
* * * *
113760 GTTTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 -TGTTTAAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * * * *
113797 TGTTTTAAGGGAAACTGTCTCAACATATAC-AAATT
1 TGTTTAAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
113832 TTTTTTAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTAAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
113868 TGTTTCAAGAGAAAC
1 TGTTTAAAGAGAAAC
113883 AAAACTTTGT
Statistics
Matches: 200, Mismatches: 44, Indels: 33
0.72 0.16 0.12
Matches are distributed among these distances:
28 3 0.01
29 9 0.05
30 8 0.04
31 1 0.00
32 4 0.02
34 10 0.05
35 38 0.19
36 68 0.34
37 30 0.15
38 29 0.14
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.28
Consensus pattern (36 bp):
TGTTTAAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:113877 original size:21 final size:22
Alignment explanation
Indices: 113851--113894 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
113841 GGAAACTGTC
*
113851 TCAAGAGAGACAAAA-TTTGTT
1 TCAAGAGAAACAAAACTTTGTT
113872 TCAAGAGAAACAAAACTTTGTT
1 TCAAGAGAAACAAAACTTTGTT
113894 T
1 T
113895 TGAGTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (22 bp):
TCAAGAGAAACAAAACTTTGTT
Found at i:115413 original size:95 final size:94
Alignment explanation
Indices: 115249--115432 Score: 271
Period size: 95 Copynumber: 1.9 Consensus size: 94
115239 ATGTAAACAT
** * * * * *
115249 CTTTATCAGGTTAGCTGAATCTTATCCATAAAGCTGGGGCGTTTAACCAATTATTTTAGAGGGAC
1 CTTTATCAGGCAAGCTGAATATTATCCATAAAGCTGAGGCGTTTAACCAATTACTCTAGAGGGAA
115314 AACTCAAGCTTTATTGTATAGTATAATCAC
66 AACTCAAGCTTTATTGTATA-TATAATCAC
*
115344 CTTTATCAGGCAAGCTGAATATTATCCATAAAG-TCGAGGCGTTTAACCAATTGCTCTAGAGGGA
1 CTTTATCAGGCAAGCTGAATATTATCCATAAAGCT-GAGGCGTTTAACCAATTACTCTAGAGGGA
115408 AAACTCAAGCTTTATTGTATATATA
65 AAACTCAAGCTTTATTGTATATATA
115433 TAATATTATA
Statistics
Matches: 80, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
94 5 0.06
95 75 0.94
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (94 bp):
CTTTATCAGGCAAGCTGAATATTATCCATAAAGCTGAGGCGTTTAACCAATTACTCTAGAGGGAA
AACTCAAGCTTTATTGTATATATAATCAC
Found at i:118192 original size:15 final size:16
Alignment explanation
Indices: 118168--118200 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
118158 TGCAAGTAAT
*
118168 GAAAATAAAAT-AAAA
1 GAAAACAAAATGAAAA
118183 GAAAACAAAATGAAAA
1 GAAAACAAAATGAAAA
118199 GA
1 GA
118201 GTTAGTGAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.76, C:0.03, G:0.12, T:0.09
Consensus pattern (16 bp):
GAAAACAAAATGAAAA
Found at i:119286 original size:23 final size:23
Alignment explanation
Indices: 119237--119283 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
119227 AAAAGGTTAG
*
119237 ATAAAAAAGAAAAAAAATATTAA
1 ATAAAAAAGAAAAAAAATAATAA
* *
119260 ATAAAAGAGAGAAAATAATAATAA
1 ATAAAAAAGA-AAAAAAATAATAA
119284 TAATAATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (23 bp):
ATAAAAAAGAAAAAAAATAATAA
Found at i:130810 original size:31 final size:31
Alignment explanation
Indices: 130775--130834 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
130765 AAGGACATGT
*
130775 TCCCTGTGACCATGATAATGACAATGTGATC
1 TCCCTATGACCATGATAATGACAATGTGATC
130806 TCCCTATGACCATGATAATGACAATGTGA
1 TCCCTATGACCATGATAATGACAATGTGA
130835 GCATTTTGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (31 bp):
TCCCTATGACCATGATAATGACAATGTGATC
Found at i:130964 original size:23 final size:22
Alignment explanation
Indices: 130917--130965 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
130907 TTTTACATCA
*
130917 AAATTTTCTTTTTCAATACTTT
1 AAATTTTCTTTTTCAATACTCT
*
130939 AAATTTTCATTTTTGAA-AGCTCT
1 AAATTTTC-TTTTTCAATA-CTCT
130962 AAAT
1 AAAT
130966 CCTTTTTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.33, C:0.12, G:0.04, T:0.51
Consensus pattern (22 bp):
AAATTTTCTTTTTCAATACTCT
Found at i:131005 original size:19 final size:20
Alignment explanation
Indices: 130969--131016 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
130959 TCTAAATCCT
* *
130969 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATTCCATTTTAG
130989 TTTTCAAAA-TCCATTTTAG
1 TTTTCAAAATTCCATTTTAG
131008 TTTTCAAAA
1 TTTTCAAAA
131017 GAAAATCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.50
Consensus pattern (20 bp):
TTTTCAAAATTCCATTTTAG
Found at i:142814 original size:17 final size:17
Alignment explanation
Indices: 142792--142830 Score: 71
Period size: 16 Copynumber: 2.4 Consensus size: 17
142782 TGTACAAGAG
142792 CTAATCCAAGGTTTAAT
1 CTAATCCAAGGTTTAAT
142809 CTAAT-CAAGGTTTAAT
1 CTAATCCAAGGTTTAAT
142825 CTAATC
1 CTAATC
142831 TAATCTATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (17 bp):
CTAATCCAAGGTTTAAT
Found at i:149750 original size:27 final size:27
Alignment explanation
Indices: 149711--149775 Score: 123
Period size: 27 Copynumber: 2.4 Consensus size: 27
149701 ATACTCTAAT
149711 TCATT-TAGCTTCAAAACCATCCCAAA
1 TCATTATAGCTTCAAAACCATCCCAAA
149737 TCATTATAGCTTCAAAACCATCCCAAA
1 TCATTATAGCTTCAAAACCATCCCAAA
149764 TCATTATAGCTT
1 TCATTATAGCTT
149776 TCTCCCAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 5 0.13
27 33 0.87
ACGTcount: A:0.37, C:0.28, G:0.05, T:0.31
Consensus pattern (27 bp):
TCATTATAGCTTCAAAACCATCCCAAA
Found at i:156325 original size:2 final size:2
Alignment explanation
Indices: 156318--156368 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
156308 GTGTTTTCTT
156318 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
156360 TA TA TA TA T
1 TA TA TA TA T
156369 TATTTTATTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:157658 original size:17 final size:17
Alignment explanation
Indices: 157636--157673 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
157626 TTTATTTAAT
*
157636 TTGTATTA-GTTTTATTA
1 TTGTATTATG-TTAATTA
157653 TTGTATTATGTTAATTA
1 TTGTATTATGTTAATTA
157670 TTGT
1 TTGT
157674 GAATATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 18 0.95
18 1 0.05
ACGTcount: A:0.24, C:0.00, G:0.13, T:0.63
Consensus pattern (17 bp):
TTGTATTATGTTAATTA
Found at i:170854 original size:17 final size:17
Alignment explanation
Indices: 170834--170866 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
170824 ATACCAAAAC
170834 AAATAA-AATAAATAAAT
1 AAATAATAA-AAATAAAT
170851 AAATAATAAAAATAAA
1 AAATAATAAAAATAAA
170867 ATAATATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (17 bp):
AAATAATAAAAATAAAT
Found at i:171181 original size:14 final size:15
Alignment explanation
Indices: 171146--171174 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
171136 AAATTTCAAA
171146 AATATTA-TAATTAT
1 AATATTATTAATTAT
171160 AATATTATTAATTAT
1 AATATTATTAATTAT
171175 TTATTATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
AATATTATTAATTAT
Found at i:171338 original size:13 final size:13
Alignment explanation
Indices: 171296--171341 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
171286 TTATATTTTA
*
171296 ATTATTTATT-AT
1 ATTATTAATTAAT
*
171308 ATTTAATAATTAAT
1 A-TTATTAATTAAT
171322 ATTATTAATTAAT
1 ATTATTAATTAAT
171335 ATTATTA
1 ATTATTA
171342 TTGTATTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
12 1 0.03
13 25 0.86
14 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
ATTATTAATTAAT
Found at i:171340 original size:16 final size:16
Alignment explanation
Indices: 171253--171343 Score: 50
Period size: 16 Copynumber: 5.8 Consensus size: 16
171243 ATTTTTATAA
171253 AATATCTATT-TTAATT
1 AATAT-TATTATTAATT
* *
171269 ACTATGATTA-TATATT
1 AATATTATTATTA-ATT
*
171285 ATTA-TATT-TTAATT
1 AATATTATTATTAATT
*
171299 ATTTATTA-TATTTAA-T
1 A-ATATTATTA-TTAATT
*
171315 AATTAATATTATTAATT
1 AA-TATTATTATTAATT
171332 AATATTATTATT
1 AATATTATTATT
171344 GTATTTATTT
Statistics
Matches: 58, Mismatches: 7, Indels: 20
0.68 0.08 0.24
Matches are distributed among these distances:
14 4 0.07
15 14 0.24
16 31 0.53
17 9 0.16
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (16 bp):
AATATTATTATTAATT
Found at i:171418 original size:13 final size:12
Alignment explanation
Indices: 171400--171470 Score: 64
Period size: 10 Copynumber: 6.2 Consensus size: 12
171390 ATCTATTTTA
171400 ATTATTATATTT
1 ATTATTATATTT
171412 A-TA-TATTATTT
1 ATTATTA-TATTT
171423 ATTTATTATATTT
1 A-TTATTATATTT
* *
171436 AATAAT-TA-TT
1 ATTATTATATTT
171446 ATTATTA-A-TT
1 ATTATTATATTT
171456 ATTATTATATTT
1 ATTATTATATTT
171468 ATT
1 ATT
171471 TTTAGTACAA
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
10 18 0.38
11 11 0.23
12 9 0.19
13 8 0.17
14 2 0.04
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
ATTATTATATTT
Found at i:171421 original size:16 final size:16
Alignment explanation
Indices: 171276--171576 Score: 73
Period size: 16 Copynumber: 19.7 Consensus size: 16
171266 ATTACTATGA
171276 TTATATATTATTATAT
1 TTATATATTATTATAT
171292 TT-TA-ATTATT-TA-
1 TTATATATTATTATAT
*
171304 TTATAT-TTA--ATAA
1 TTATATATTATTATAT
171317 TTA-ATATTATTA-AT
1 TTATATATTATTATAT
* *
171331 TAATATTATTATTGTAT
1 TTATA-TATTATTATAT
*
171348 TTATTTACTATATTCA-A-
1 TTATATA-T-TATT-ATAT
** *
171365 GAATATAATTATT-TTT
1 TTATAT-ATTATTATAT
* * *
171381 TTATAAAATA-TCTAT
1 TTATATATTATTATAT
171396 TT-TA-ATTATTATAT
1 TTATATATTATTATAT
171410 TTATATATTATT-TAT
1 TTATATATTATTATAT
* *
171425 TTATTATATT-TAATAA
1 TTA-TATATTATTATAT
171441 TTAT-TATTATTA-A-
1 TTATATATTATTATAT
*
171454 TTAT-TATTATATTTAT
1 TTATATATTAT-TATAT
* **
171470 TTTTAGTACAATTAT-T
1 TTATA-TATTATTATAT
* * *
171486 TTTTATA-AATATCTAT
1 TTATATATTAT-TATAT
*
171502 TT-TA-ATTACTATAT
1 TTATATATTATTATAT
171516 TT-TGATTATTTATTATAT
1 TTAT-A-TA-TTATTATAT
*
171534 TTA-ATAATTATTATTT
1 TTATAT-ATTATTATAT
171550 TTA-AGTATTATTATAT
1 TTATA-TATTATTATAT
* *
171566 TCATTTATTAT
1 TTATATATTAT
171577 ATTCATTTAA
Statistics
Matches: 212, Mismatches: 34, Indels: 78
0.65 0.10 0.24
Matches are distributed among these distances:
12 6 0.03
13 26 0.12
14 35 0.17
15 32 0.15
16 77 0.36
17 16 0.08
18 20 0.09
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (16 bp):
TTATATATTATTATAT
Found at i:171573 original size:13 final size:13
Alignment explanation
Indices: 171557--171585 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
171547 TTTTTAAGTA
171557 TTATTATATTCAT
1 TTATTATATTCAT
171570 TTATTATATTCAT
1 TTATTATATTCAT
171583 TTA
1 TTA
171586 ATTTCTACGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (13 bp):
TTATTATATTCAT
Found at i:179912 original size:5 final size:5
Alignment explanation
Indices: 179902--179927 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
179892 AAGTATGAGA
179902 AATAT AATAT AATAT AATAT AATAT A
1 AATAT AATAT AATAT AATAT AATAT A
179928 CGAATTTTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:180182 original size:51 final size:51
Alignment explanation
Indices: 180101--180199 Score: 153
Period size: 51 Copynumber: 1.9 Consensus size: 51
180091 CAATACTTAA
* *
180101 AAGTACGAGGGCGTTTAACAAAAATGTGTTTGTCTACTTTTAAAAGGATTT
1 AAGTACGAGGGCGTTTAACAAAAATATGTTTATCTACTTTTAAAAGGATTT
* * *
180152 AAGTATGAGGGTGTTTAACAAAATTATGTTTATCTACTTTTAAAAGGA
1 AAGTACGAGGGCGTTTAACAAAAATATGTTTATCTACTTTTAAAAGGA
180200 GCACAATATA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.36
Consensus pattern (51 bp):
AAGTACGAGGGCGTTTAACAAAAATATGTTTATCTACTTTTAAAAGGATTT
Found at i:183131 original size:94 final size:94
Alignment explanation
Indices: 182970--183158 Score: 378
Period size: 94 Copynumber: 2.0 Consensus size: 94
182960 AACTTTAGGA
182970 CTTTGGAGGCTCTAATTTAGTTAGGAAAAGGTAGGCTTTACCAGCTTTAAATTAGTTGTCTGTTT
1 CTTTGGAGGCTCTAATTTAGTTAGGAAAAGGTAGGCTTTACCAGCTTTAAATTAGTTGTCTGTTT
183035 ACTCTTGGTCAATCTGTCCCTGCTTGGCT
66 ACTCTTGGTCAATCTGTCCCTGCTTGGCT
183064 CTTTGGAGGCTCTAATTTAGTTAGGAAAAGGTAGGCTTTACCAGCTTTAAATTAGTTGTCTGTTT
1 CTTTGGAGGCTCTAATTTAGTTAGGAAAAGGTAGGCTTTACCAGCTTTAAATTAGTTGTCTGTTT
183129 ACTCTTGGTCAATCTGTCCCTGCTTGGCT
66 ACTCTTGGTCAATCTGTCCCTGCTTGGCT
183158 C
1 C
183159 CCACGTTTCT
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 95 1.00
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (94 bp):
CTTTGGAGGCTCTAATTTAGTTAGGAAAAGGTAGGCTTTACCAGCTTTAAATTAGTTGTCTGTTT
ACTCTTGGTCAATCTGTCCCTGCTTGGCT
Found at i:190777 original size:2 final size:2
Alignment explanation
Indices: 190770--190843 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
190760 ACCCTTAATT
190770 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
190812 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
190844 GCTTATAATT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:194649 original size:14 final size:14
Alignment explanation
Indices: 194630--194662 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
194620 TGATTGGGTT
194630 TTAAATATATTAAA
1 TTAAATATATTAAA
194644 TTAAATATATTAAA
1 TTAAATATATTAAA
*
194658 ATAAA
1 TTAAA
194663 ACTTATTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TTAAATATATTAAA
Found at i:195364 original size:23 final size:23
Alignment explanation
Indices: 195330--195382 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
195320 CTCGGCTTCC
195330 CTCGGATTCCCTCGCATAGCTCG
1 CTCGGATTCCCTCGCATAGCTCG
195353 CTCGG-TTGCCCTCGCATAGCTCG
1 CTCGGATT-CCCTCGCATAGCTCG
*
195376 TTCGGAT
1 CTCGGAT
195383 GGCCTTGGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 2 0.07
23 24 0.89
24 1 0.04
ACGTcount: A:0.11, C:0.36, G:0.25, T:0.28
Consensus pattern (23 bp):
CTCGGATTCCCTCGCATAGCTCG
Found at i:197047 original size:20 final size:20
Alignment explanation
Indices: 197024--197135 Score: 86
Period size: 20 Copynumber: 5.6 Consensus size: 20
197014 CACAGGTTCA
*
197024 AAAATTACAACGCGAAAGTC
1 AAAATTGCAACGCGAAAGTC
* *
197044 AAAATCGCAACTCGAAAGTC
1 AAAATTGCAACGCGAAAGTC
*
197064 -AAATTCGCAATGCGAAAGTC
1 AAAATT-GCAACGCGAAAGTC
* * * *
197084 AAAATCGTAATGCAAAAGTC
1 AAAATTGCAACGCGAAAGTC
*
197104 -AAATTCACAACGCGAATAGT-
1 AAAATT-GCAACGCGAA-AGTC
*
197124 TAAATTGCAACG
1 AAAATTGCAACG
197136 ATAATATGTA
Statistics
Matches: 72, Mismatches: 15, Indels: 10
0.74 0.15 0.10
Matches are distributed among these distances:
19 8 0.11
20 52 0.72
21 12 0.17
ACGTcount: A:0.46, C:0.20, G:0.16, T:0.19
Consensus pattern (20 bp):
AAAATTGCAACGCGAAAGTC
Found at i:197079 original size:40 final size:40
Alignment explanation
Indices: 197025--197119 Score: 131
Period size: 40 Copynumber: 2.4 Consensus size: 40
197015 ACAGGTTCAA
*
197025 AAATT-ACAACGCGAAAGTCAAAATCGCAACT-CGAAAGTC
1 AAATTCACAACGCGAAAGTCAAAATCGCAA-TGCAAAAGTC
* * *
197064 AAATTCGCAATGCGAAAGTCAAAATCGTAATGCAAAAGTC
1 AAATTCACAACGCGAAAGTCAAAATCGCAATGCAAAAGTC
197104 AAATTCACAACGCGAA
1 AAATTCACAACGCGAA
197120 TAGTTAAATT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
39 6 0.12
40 42 0.88
ACGTcount: A:0.46, C:0.21, G:0.16, T:0.17
Consensus pattern (40 bp):
AAATTCACAACGCGAAAGTCAAAATCGCAATGCAAAAGTC
Found at i:197141 original size:20 final size:20
Alignment explanation
Indices: 197124--197195 Score: 99
Period size: 20 Copynumber: 3.6 Consensus size: 20
197114 CGCGAATAGT
*
197124 TAAATTGCAACGATAATATG
1 TAAATCGCAACGATAATATG
* ** *
197144 TAATTCGCAACGCGAATAGG
1 TAAATCGCAACGATAATATG
197164 TAAATCGCAACGATAATATG
1 TAAATCGCAACGATAATATG
197184 TAAATCGCAACG
1 TAAATCGCAACG
197196 CGAATTCTCC
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.24
Consensus pattern (20 bp):
TAAATCGCAACGATAATATG
Found at i:197149 original size:40 final size:40
Alignment explanation
Indices: 197105--197200 Score: 156
Period size: 40 Copynumber: 2.4 Consensus size: 40
197095 GCAAAAGTCA
* * *
197105 AATTCACAACGCGAATAGTTAAATTGCAACGATAATATGT
1 AATTCGCAACGCGAATAGGTAAATCGCAACGATAATATGT
197145 AATTCGCAACGCGAATAGGTAAATCGCAACGATAATATGT
1 AATTCGCAACGCGAATAGGTAAATCGCAACGATAATATGT
*
197185 AAATCGCAACGCGAAT
1 AATTCGCAACGCGAAT
197201 TCTCCAAATT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.23
Consensus pattern (40 bp):
AATTCGCAACGCGAATAGGTAAATCGCAACGATAATATGT
Found at i:208456 original size:27 final size:29
Alignment explanation
Indices: 208389--208456 Score: 79
Period size: 27 Copynumber: 2.4 Consensus size: 29
208379 TGTTTAAGTT
* *
208389 ATATTTTA-TTATATTTAGTATTTTGTTA
1 ATATTTTATTTAAATTTAGAATTTTGTTA
* *
208417 GTAATTTATTTAAATTTA-AATTTT-TTA
1 ATATTTTATTTAAATTTAGAATTTTGTTA
208444 ATATTTTATTTAA
1 ATATTTTATTTAA
208457 TTAATTTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
27 14 0.42
28 11 0.33
29 8 0.24
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (29 bp):
ATATTTTATTTAAATTTAGAATTTTGTTA
Found at i:210777 original size:33 final size:32
Alignment explanation
Indices: 210715--210797 Score: 80
Period size: 33 Copynumber: 2.5 Consensus size: 32
210705 AAATACTTAC
210715 TTTATTTTGTTAATTTGGTTGATAATTTTA-AA
1 TTTATTTTGTTAATTTGGTTGAT-ATTTTATAA
* *
210747 TTTTATTTTGTTTATTTTGTTGGACT-TTTTATTAA
1 -TTTATTTTGTTAATTTGGTT-GA-TATTTTA-TAA
*
210782 TTTATTTTGATAATTT
1 TTTATTTTGTTAATTT
210798 TTTTTATTAC
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
33 23 0.55
34 16 0.38
35 3 0.07
ACGTcount: A:0.23, C:0.01, G:0.11, T:0.65
Consensus pattern (32 bp):
TTTATTTTGTTAATTTGGTTGATATTTTATAA
Found at i:213767 original size:21 final size:21
Alignment explanation
Indices: 213741--213782 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
213731 CCAGAATGGG
*
213741 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
213762 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
213783 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:213974 original size:21 final size:21
Alignment explanation
Indices: 213895--213992 Score: 95
Period size: 21 Copynumber: 5.0 Consensus size: 21
213885 AAACCATGCA
*
213895 GGGGGAATATGTACCCCCTGG
1 GGGGGAATCTGTACCCCCTGG
* *
213916 GGGAGAATCTGT--TCCC---
1 GGGGGAATCTGTACCCCCTGG
213932 -GGGGAATC-GATACCCCCT-G
1 GGGGGAATCTG-TACCCCCTGG
*
213951 GGGGGAATCTGTTCCCCCTGG
1 GGGGGAATCTGTACCCCCTGG
213972 GGGGGAATCTGTACCCCCTGG
1 GGGGGAATCTGTACCCCCTGG
213993 ACAATCTGAT
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 1 0.02
15 8 0.13
17 3 0.05
19 3 0.05
20 15 0.24
21 32 0.52
ACGTcount: A:0.16, C:0.28, G:0.36, T:0.20
Consensus pattern (21 bp):
GGGGGAATCTGTACCCCCTGG
Found at i:223258 original size:24 final size:24
Alignment explanation
Indices: 223226--223276 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
223216 TGTTCATATG
223226 GTATTGATACCAAAGGTAAGAGAA
1 GTATTGATACCAAAGGTAAGAGAA
223250 GTATTGATACCAAAGGTAAGAGAA
1 GTATTGATACCAAAGGTAAGAGAA
223274 GTA
1 GTA
223277 CAAATACTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.45, C:0.08, G:0.25, T:0.22
Consensus pattern (24 bp):
GTATTGATACCAAAGGTAAGAGAA
Found at i:223283 original size:24 final size:24
Alignment explanation
Indices: 223232--223283 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
223222 TATGGTATTG
***
223232 ATACCAAAGGTAAGAGAAGTATTG
1 ATACCAAAGGTAAGAGAAGTACAA
223256 ATACCAAAGGTAAGAGAAGTACAA
1 ATACCAAAGGTAAGAGAAGTACAA
223280 ATAC
1 ATAC
223284 TCTCTAGGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.12, G:0.21, T:0.17
Consensus pattern (24 bp):
ATACCAAAGGTAAGAGAAGTACAA
Found at i:229006 original size:20 final size:21
Alignment explanation
Indices: 228959--229017 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
228949 ACCGTTAGAC
* *
228959 AGGGGGAATCGGTACCCTCTG
1 AGGGGGAATCTGTACCCCCTG
*
228980 AGGGGGAATCTGTTCCCCCTG
1 AGGGGGAATCTGTACCCCCTG
229001 -GGGGGAATCTGTACCCC
1 AGGGGGAATCTGTACCCC
229018 TGGACAATCT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 16 0.47
21 18 0.53
ACGTcount: A:0.17, C:0.27, G:0.36, T:0.20
Consensus pattern (21 bp):
AGGGGGAATCTGTACCCCCTG
Found at i:238657 original size:33 final size:33
Alignment explanation
Indices: 238590--238660 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
238580 TTGTCTTCTT
* *
238590 TCTTCTTCCCGCTGCTTATCGCGCTGCAATCTC
1 TCTTCTTCCCGCTGCTTATCACGCTGCAACCTC
* *
238623 TCTTCTTCCCGCTGCTTCTCACG-TATCAACCTC
1 TCTTCTTCCCGCTGCTTATCACGCT-GCAACCTC
238656 TCTTC
1 TCTTC
238661 CTCCTTCCTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 1 0.03
33 32 0.97
ACGTcount: A:0.10, C:0.41, G:0.11, T:0.38
Consensus pattern (33 bp):
TCTTCTTCCCGCTGCTTATCACGCTGCAACCTC
Found at i:239400 original size:2 final size:2
Alignment explanation
Indices: 239393--239441 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
239383 CTGGATCAAC
239393 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
239435 AT AT AT A
1 AT AT AT A
239442 CCAAAGATTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:242223 original size:30 final size:30
Alignment explanation
Indices: 242189--242248 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
242179 GATTTCTAAG
* *
242189 TTTTATCCTAAA-ACTTTAGATAAAATATTA
1 TTTTAACCTAAACA-TTTAGATAAAACATTA
*
242219 TTTTAACCTTAACATTTAGATAAAACATTA
1 TTTTAACCTAAACATTTAGATAAAACATTA
242249 ATATGACCCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.43, C:0.12, G:0.03, T:0.42
Consensus pattern (30 bp):
TTTTAACCTAAACATTTAGATAAAACATTA
Found at i:242602 original size:14 final size:15
Alignment explanation
Indices: 242561--242611 Score: 68
Period size: 15 Copynumber: 3.3 Consensus size: 15
242551 CACTAAACCA
*
242561 ATAAATTTTATGTTT
1 ATAATTTTTATGTTT
242576 ATAATATTATTATG-TT
1 ATAAT-TT-TTATGTTT
242592 ATAATTTTTATGTTT
1 ATAATTTTTATGTTT
242607 ATAAT
1 ATAAT
242612 ATTAGCCGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 5 0.16
15 13 0.41
16 9 0.28
17 5 0.16
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (15 bp):
ATAATTTTTATGTTT
Found at i:242877 original size:11 final size:11
Alignment explanation
Indices: 242827--242885 Score: 57
Period size: 11 Copynumber: 5.4 Consensus size: 11
242817 TGCAATTTAG
*
242827 ATATTTATATT
1 ATATATATATT
*
242838 ATCTATATATTT
1 ATATATATA-TT
* *
242850 AGATATAGATT
1 ATATATATATT
*
242861 -TATATATTTT
1 ATATATATATT
242871 ATATATATATT
1 ATATATATATT
242882 ATAT
1 ATAT
242886 TTCTTTATTT
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
10 7 0.19
11 22 0.59
12 8 0.22
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (11 bp):
ATATATATATT
Found at i:242892 original size:21 final size:20
Alignment explanation
Indices: 242860--242908 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
242850 AGATATAGAT
*
242860 TTATATATTTTATATATATA
1 TTATATTTTTTATATATATA
*
242880 TTATATTTCTTTATTTATATA
1 TTATATTT-TTTATATATATA
*
242901 ATATATTT
1 TTATATTT
242909 ATTTTCTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (20 bp):
TTATATTTTTTATATATATA
Found at i:242905 original size:30 final size:26
Alignment explanation
Indices: 242868--242923 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
242858 ATTTATATAT
242868 TTTATAT-ATATA-TTATATTTCTTTA
1 TTTATATAATATATTTAT-TTTCTTTA
242893 TTTATATAATATATTTATTTTCTTTA
1 TTTATATAATATATTTATTTTCTTTA
242919 TTTAT
1 TTTAT
242924 GGGCTCAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
25 7 0.24
26 18 0.62
27 4 0.14
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (26 bp):
TTTATATAATATATTTATTTTCTTTA
Found at i:243829 original size:28 final size:28
Alignment explanation
Indices: 243809--243902 Score: 134
Period size: 28 Copynumber: 3.4 Consensus size: 28
243799 GCGGCAGGGT
*
243809 CGACCATATATCACTCAGGCGGCAGAAC
1 CGACCATATATCAATCAGGCGGCAGAAC
* *
243837 CGACCATATATCAATCAGGCGGTATAAC
1 CGACCATATATCAATCAGGCGGCAGAAC
* *
243865 CGACCATATATCAATCAGGTGGCAGAGC
1 CGACCATATATCAATCAGGCGGCAGAAC
*
243893 CGGCCATATA
1 CGACCATATA
243903 ATAGAACTAA
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 58 1.00
ACGTcount: A:0.33, C:0.28, G:0.21, T:0.18
Consensus pattern (28 bp):
CGACCATATATCAATCAGGCGGCAGAAC
Found at i:250596 original size:12 final size:12
Alignment explanation
Indices: 250576--250606 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
250566 AAAATCATTT
250576 AAATATATTTTA
1 AAATATATTTTA
*
250588 AAATTTATTTTA
1 AAATATATTTTA
250600 AAATATA
1 AAATATA
250607 GATTGATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAATATATTTTA
Found at i:250936 original size:22 final size:22
Alignment explanation
Indices: 250590--250955 Score: 489
Period size: 22 Copynumber: 16.6 Consensus size: 22
250580 ATATTTTAAA
*
250590 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
* ***
250612 ATTTATTTTAAAATATGAAAAA
1 ATTTATTTTAAAATATGGATTG
* ***
250634 AATTATTTTAAAATATGGAAAA
1 ATTTATTTTAAAATATGGATTG
*
250656 AATTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
***
250678 ATTTATTTTAAAATATGGAAAA
1 ATTTATTTTAAAATATGGATTG
*
250700 AATTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
250722 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
* ***
250744 ATTTATTTTAAAATATAGAAAA
1 ATTTATTTTAAAATATGGATTG
250766 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
250788 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
250810 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* ***
250832 ATTTATTTTAAAATATGAAAAA
1 ATTTATTTTAAAATATGGATTG
250854 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
250876 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
250898 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
250920 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
250942 ATTTATTTTTAAAA
1 ATTTA-TTTTAAAA
250956 AAATTTATTA
Statistics
Matches: 303, Mismatches: 40, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
22 295 0.97
23 8 0.03
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.47
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:251037 original size:31 final size:31
Alignment explanation
Indices: 250980--251038 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
250970 AGTTGTATGG
*
250980 ATTATTTAAATTTCAATATTATAAAACTAAA
1 ATTATTTAAATTTCAATATTACAAAACTAAA
* *
251011 ATTATTTAAATTTCAGTATTGCAAAACT
1 ATTATTTAAATTTCAATATTACAAAACT
251039 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATTTCAATATTACAAAACTAAA
Found at i:255725 original size:86 final size:86
Alignment explanation
Indices: 255600--255763 Score: 205
Period size: 86 Copynumber: 1.9 Consensus size: 86
255590 AGAACCCTTC
*
255600 ATTTTTATATGATACTTTTTTTTTTCATAATTAAATCCTTTAATTTTATTC-AAT-TTA-TTTTT
1 ATTTTTATATCATACTTTTTTTTTTCATAATTAAATCCTTTAA-TTT-TTCAAATCTTACTTTTT
255662 TATC-TTTATAATTGAGGTTCGTA
64 TA-CATTTATAATTGAGGTTCGTA
* *
255685 ATTTTTATAATCATA-TTTTTTATCTTT-ATAATTGATTCCTTTAATTTTTCAAATCTTACTTTT
1 ATTTTTAT-ATCATACTTTTTT-T-TTTCATAATTAAATCCTTTAATTTTTCAAATCTTACTTTT
255748 TTACATTTATAATTGA
63 TTACATTTATAATTGA
255764 TGATTCTAAG
Statistics
Matches: 69, Mismatches: 3, Indels: 12
0.82 0.04 0.14
Matches are distributed among these distances:
84 3 0.04
85 20 0.29
86 25 0.36
87 21 0.30
ACGTcount: A:0.28, C:0.09, G:0.04, T:0.59
Consensus pattern (86 bp):
ATTTTTATATCATACTTTTTTTTTTCATAATTAAATCCTTTAATTTTTCAAATCTTACTTTTTTA
CATTTATAATTGAGGTTCGTA
Found at i:255730 original size:43 final size:44
Alignment explanation
Indices: 255600--255764 Score: 136
Period size: 43 Copynumber: 3.8 Consensus size: 44
255590 AGAACCCTTC
* * *
255600 ATTTTTAT-ATGATACTTTTTT-T-TTTCATAATTAAATCCTTTA
1 ATTTTTATAATCATACTTTTTTATCTTT-ATAATTGATTCCTTTA
* *
255642 A-TTTTATTCAAT-TTA-TTTTTTATCTTTATAATTGAGGTT-C-GTA
1 ATTTTTA-T-AATCATACTTTTTTATCTTTATAATTGA--TTCCTTTA
255685 ATTTTTATAATCATA-TTTTTTATCTTTATAATTGATTCCTTTA
1 ATTTTTATAATCATACTTTTTTATCTTTATAATTGATTCCTTTA
*
255728 ATTTTTCA-AATCTTACTTTTTTA-CATTTATAATTGAT
1 ATTTTT-ATAATCATACTTTTTTATC-TTTATAATTGAT
255765 GATTCTAAGT
Statistics
Matches: 102, Mismatches: 7, Indels: 26
0.76 0.05 0.19
Matches are distributed among these distances:
41 7 0.07
42 12 0.12
43 51 0.50
44 31 0.30
45 1 0.01
ACGTcount: A:0.28, C:0.09, G:0.04, T:0.59
Consensus pattern (44 bp):
ATTTTTATAATCATACTTTTTTATCTTTATAATTGATTCCTTTA
Found at i:255913 original size:44 final size:44
Alignment explanation
Indices: 255784--256096 Score: 299
Period size: 44 Copynumber: 7.2 Consensus size: 44
255774 TTTTTCAATA
* * * *
255784 ACCTTCATAATTGA-GCTCCTAATTTTTTTTAATATCACTTTCT
1 ACCTTTATAATTGAGGCACCTAATTTTTTTTAATCTCACTTTTT
** *
255827 ACCTTTATAATTGAAACCCCTAA---TTTTTAATCTCACTTTTT
1 ACCTTTATAATTGAGGCACCTAATTTTTTTTAATCTCACTTTTT
255868 ACCTTTATAATTGAGGCACCTAATTTTTTTTAATCTCACTTTTT
1 ACCTTTATAATTGAGGCACCTAATTTTTTTTAATCTCACTTTTT
* * *
255912 ACCTTTATAATTGAGACACCTAA-TTTTTTTAATCCCTCTTTTT
1 ACCTTTATAATTGAGGCACCTAATTTTTTTTAATCTCACTTTTT
* * * *
255955 A-CTTATATAATTTAGGC-CCTTAATTTTTTTCAATTTCATTTTTTT
1 ACCTT-TATAATTGAGGCACC-TAATTTTTTTTAATCTCA-CTTTTT
* * * * *
256000 A-CTTTAAAATTGAGGCCCCT-A-GTTTTTTAATCGCAATTTTT
1 ACCTTTATAATTGAGGCACCTAATTTTTTTTAATCTCACTTTTT
*
256041 ACCTTTATAATTGATG-ACTCTAATTTTTTTTAATCGT-ACTTTTTT
1 ACCTTTATAATTGAGGCAC-CTAATTTTTTTTAATC-TCAC-TTTTT
*
256086 ACTTTTATAAT
1 ACCTTTATAAT
256097 CTAAACCTCT
Statistics
Matches: 223, Mismatches: 32, Indels: 28
0.79 0.11 0.10
Matches are distributed among these distances:
41 43 0.19
42 29 0.13
43 47 0.21
44 78 0.35
45 26 0.12
ACGTcount: A:0.26, C:0.18, G:0.06, T:0.50
Consensus pattern (44 bp):
ACCTTTATAATTGAGGCACCTAATTTTTTTTAATCTCACTTTTT
Found at i:255934 original size:85 final size:85
Alignment explanation
Indices: 255784--256096 Score: 332
Period size: 87 Copynumber: 3.6 Consensus size: 85
255774 TTTTTCAATA
* * * * *
255784 ACCTTCATAATTGA-GCTCCTAATTTTTTTTAATATCACTTTCTACCTTTATAATTGAAACCCCT
1 ACCTTTATAATTGAGGCACCTAATTTTTTTTAATCTCACTTTTTACCTTTATAATTGAGACCCCT
*
255848 AATTTTTAATCTCACTTTTT
66 AATTTTTAATCCCACTTTTT
*
255868 ACCTTTATAATTGAGGCACCTAATTTTTTTTAATCTCACTTTTTACCTTTATAATTGAGACACCT
1 ACCTTTATAATTGAGGCACCTAATTTTTTTTAATCTCACTTTTTACCTTTATAATTGAGACCCCT
*
255933 AATTTTTTTAATCCCTCTTTTT
66 AA--TTTTTAATCCCACTTTTT
* * * * * *
255955 A-CTTATATAATTTAGGC-CCTTAATTTTTTTCAATTTCATTTTTTTA-CTTTAAAATTGAGGCC
1 ACCTT-TATAATTGAGGCACC-TAATTTTTTTTAATCTCA-CTTTTTACCTTTATAATTGAGACC
* * *
256017 CCTAGTTTTTTAATCGCAATTTTT
63 CCTA-ATTTTTAATCCCACTTTTT
* *
256041 ACCTTTATAATTGATG-ACTCTAATTTTTTTTAATCGT-ACTTTTTTACTTTTATAAT
1 ACCTTTATAATTGAGGCAC-CTAATTTTTTTTAATC-TCAC-TTTTTACCTTTATAAT
256097 CTAAACCTCT
Statistics
Matches: 190, Mismatches: 26, Indels: 23
0.79 0.11 0.10
Matches are distributed among these distances:
84 13 0.07
85 47 0.25
86 51 0.27
87 73 0.38
88 6 0.03
ACGTcount: A:0.26, C:0.18, G:0.06, T:0.50
Consensus pattern (85 bp):
ACCTTTATAATTGAGGCACCTAATTTTTTTTAATCTCACTTTTTACCTTTATAATTGAGACCCCT
AATTTTTAATCCCACTTTTT
Found at i:263601 original size:70 final size:70
Alignment explanation
Indices: 263488--263624 Score: 161
Period size: 70 Copynumber: 2.0 Consensus size: 70
263478 TGGCCAAGTA
* * ** *
263488 AGCTTGGAAATATGAAAATGAGGACTCCTCGATTTCCCGTCGGCCGGTTGTATCGAAGTACGATG
1 AGCTTGGAAATATGAAAATGAGGACTCCTCGATTTCCCGTCGGCAGATCATATCAAAGTACGATG
263553 TTTTG
66 TTTTG
* * **
263558 AGCTTGGAAATATGAAAATGGGGAGTCGC-CG-TGTTCGTGTCGGCAGATCATATCAAAGTACGA
1 AGCTTGGAAATATGAAAATGAGGACTC-CTCGAT-TTCCCGTCGGCAGATCATATCAAAGTACGA
263621 TGTT
64 TGTT
263625 AGTGCTCGTC
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
69 1 0.02
70 54 0.96
71 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (70 bp):
AGCTTGGAAATATGAAAATGAGGACTCCTCGATTTCCCGTCGGCAGATCATATCAAAGTACGATG
TTTTG
Found at i:275802 original size:20 final size:20
Alignment explanation
Indices: 275776--275821 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
275766 AGAATAACAA
* *
275776 AGTTTTTGGTTAATTTTAAG
1 AGTTTTTGGCTAATTTCAAG
*
275796 GGTTTTTGGCTAATTTCAAG
1 AGTTTTTGGCTAATTTCAAG
275816 AGTTTT
1 AGTTTT
275822 GAGTTTTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.22, C:0.04, G:0.22, T:0.52
Consensus pattern (20 bp):
AGTTTTTGGCTAATTTCAAG
Found at i:277217 original size:16 final size:16
Alignment explanation
Indices: 277172--277217 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
277162 CCAAAATTTA
* *
277172 TAAATAATATATAAAT
1 TAAATATTATATATAT
*
277188 TATATATTATATATAT
1 TAAATATTATATATAT
*
277204 TAAATATTAAATAT
1 TAAATATTATATAT
277218 TTTTTGGTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TAAATATTATATATAT
Found at i:277295 original size:2 final size:2
Alignment explanation
Indices: 277288--277317 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
277278 CTAAAGATAA
277288 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
277318 TAATAATTCC
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:279802 original size:24 final size:24
Alignment explanation
Indices: 279732--279802 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
279722 CAATCTTATA
*
279732 TGGCACTACGGTGC-ATTTCTACG
1 TGGCACTTCGGTGCAATTTCTACG
* * *
279755 CGACACTTCGGTGCAAATTCTACG
1 TGGCACTTCGGTGCAATTTCTACG
* *
279779 TGGCACTTCGGTACAATTTATACG
1 TGGCACTTCGGTGCAATTTCTACG
279803 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
23 11 0.29
24 27 0.71
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.30
Consensus pattern (24 bp):
TGGCACTTCGGTGCAATTTCTACG
Found at i:292569 original size:15 final size:16
Alignment explanation
Indices: 292544--292577 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
292534 AATATAATGA
292544 ATTATTTATATTATGT
1 ATTATTTATATTATGT
*
292560 ATTA-TTATATTTTGT
1 ATTATTTATATTATGT
292575 ATT
1 ATT
292578 TTGAACTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (16 bp):
ATTATTTATATTATGT
Found at i:302895 original size:7 final size:7
Alignment explanation
Indices: 302883--302918 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
302873 ATTAGCCAAA
302883 AATATAT
1 AATATAT
302890 AATATAT
1 AATATAT
*
302897 AATATTT
1 AATATAT
302904 AATATAT
1 AATATAT
302911 AATATAT
1 AATATAT
302918 A
1 A
302919 TTATTTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
AATATAT
Found at i:302909 original size:21 final size:21
Alignment explanation
Indices: 302883--302925 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
302873 ATTAGCCAAA
302883 AATATATAATATATAATATTT
1 AATATATAATATATAATATTT
*
302904 AATATATAATATATATTATTT
1 AATATATAATATATAATATTT
302925 A
1 A
302926 TAAAATTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AATATATAATATATAATATTT
Found at i:308981 original size:15 final size:16
Alignment explanation
Indices: 308944--308984 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
308934 TTAAATTTAC
*
308944 ATATATATTATATTCG
1 ATATATATTATATCCG
*
308960 ATGTATATTAT-TCCG
1 ATATATATTATATCCG
308975 ATATATATTA
1 ATATATATTA
308985 CTTTTCCATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (16 bp):
ATATATATTATATCCG
Found at i:310361 original size:58 final size:56
Alignment explanation
Indices: 310253--310363 Score: 143
Period size: 58 Copynumber: 1.9 Consensus size: 56
310243 ATATTAAAGA
* *
310253 AATATATATATATATATAATAATAAAATATAGTAAAAAAATAAATGAAAATAATTT
1 AATATATATATATATATAATAATAAAATATAATAAAAAAATAAATAAAAATAATTT
* **
310309 AATATATATATATATATATATACATATAATATAATAACATGAAT-AATAAAAATAA
1 AATATATATATATATATA-ATA-ATAAAATATAATAA-AAAAATAAATAAAAATAA
310364 ATGAATAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
56 18 0.38
57 3 0.06
58 22 0.47
59 4 0.09
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (56 bp):
AATATATATATATATATAATAATAAAATATAATAAAAAAATAAATAAAAATAATTT
Found at i:310826 original size:34 final size:34
Alignment explanation
Indices: 310783--310852 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
310773 TGAATCCTAG
*
310783 TAAAATTCTATCATATCTTTAGGAGTTTGAATCC
1 TAAAATTCTATCATATCTTTAGGAGTTTAAATCC
* *
310817 TAAAATTCTATCCTATTTTTAGGAGTTTAAATCC
1 TAAAATTCTATCATATCTTTAGGAGTTTAAATCC
310851 TA
1 TA
310853 GTAGGACGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (34 bp):
TAAAATTCTATCATATCTTTAGGAGTTTAAATCC
Found at i:312508 original size:175 final size:180
Alignment explanation
Indices: 312217--312571 Score: 675
Period size: 175 Copynumber: 2.0 Consensus size: 180
312207 GCCACGAGAC
312217 GGACGGCGGCGGCGGCGGCGCGCGAGAGTCCCCCTTGTTCTCTATCACTTAACAAGGAAGTGGGA
1 GGACGGCGGCGGCGGCGGCGCGCGAGAGTCCCCCTTGTTCTCTATCACTTAACAAGGAAGTGGGA
312282 AAGCCAAGCCTTAAATATCATTCCCAATAGTGTTTCCAATACTATGTGGGA-TAAGCATTACCAA
66 AAGCCAAGCCTTAAATATCATTCCCAATAGTGTTTCCAATACTATGTGGGATTAAGCATTACCAA
312346 CACTTATTT-CAATACAA-GTGA-TATTCAGGAAAC-ATTAACAATCATG
131 CACTTATTTCCAATACAATGTGATTATTCAGGAAACAATTAACAATCATG
312392 GGACGGCGGCGGCGGCGGCGCGCGAGAGTCCCCCTTGTTCTCTATCACTTAACAAGGAAGTGGGA
1 GGACGGCGGCGGCGGCGGCGCGCGAGAGTCCCCCTTGTTCTCTATCACTTAACAAGGAAGTGGGA
312457 AAGCCAAGCCTTAAATATCATTCCCAATAGTGTTTCCAATACTATGTGGGATTAAGCATTACCAA
66 AAGCCAAGCCTTAAATATCATTCCCAATAGTGTTTCCAATACTATGTGGGATTAAGCATTACCAA
312522 CACTTATTTCCAATACAATGTGATTATTCAGGAAACAATTAACAATCATG
131 CACTTATTTCCAATACAATGTGATTATTCAGGAAACAATTAACAATCATG
312572 CACCTTAAAA
Statistics
Matches: 175, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
175 116 0.66
176 22 0.13
177 8 0.05
178 4 0.02
179 12 0.07
180 13 0.07
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (180 bp):
GGACGGCGGCGGCGGCGGCGCGCGAGAGTCCCCCTTGTTCTCTATCACTTAACAAGGAAGTGGGA
AAGCCAAGCCTTAAATATCATTCCCAATAGTGTTTCCAATACTATGTGGGATTAAGCATTACCAA
CACTTATTTCCAATACAATGTGATTATTCAGGAAACAATTAACAATCATG
Found at i:312894 original size:6 final size:6
Alignment explanation
Indices: 312883--312911 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
312873 TCTCGTCTCG
312883 GGTCGT GGTCGT GGTCGT GGTCGT GGTCG
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCG
312912 ACTATCGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.17, G:0.52, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:315299 original size:36 final size:35
Alignment explanation
Indices: 315231--315357 Score: 102
Period size: 36 Copynumber: 3.6 Consensus size: 35
315221 AATACGAAAT
*
315231 AAATAAAC-AACAT-AA-AAAATAAAAAAATGATA
1 AAATAAACAAAAATAAACAAAATAAAAAAATGATA
* * * *
315263 AAGTAAAGAGAAATAAACAAAATAAATAGAATGATA
1 AAATAAACAAAAATAAACAAAATAAA-AAAATGATA
*
315299 AAATAAACAAAAATAAAACATACAA-AAAAAAATAATA
1 AAATAAACAAAAAT-AAACA-A-AATAAAAAAATGATA
* *
315336 AACAAAAAC-AAAATAAAAAAAA
1 AA-ATAAACAAAAATAAACAAAA
315358 CAAAGGAAAA
Statistics
Matches: 75, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
32 6 0.08
33 3 0.04
34 4 0.05
35 9 0.12
36 23 0.31
37 19 0.25
38 9 0.12
39 2 0.03
ACGTcount: A:0.76, C:0.06, G:0.05, T:0.13
Consensus pattern (35 bp):
AAATAAACAAAAATAAACAAAATAAAAAAATGATA
Found at i:315316 original size:15 final size:15
Alignment explanation
Indices: 315296--315357 Score: 63
Period size: 15 Copynumber: 4.1 Consensus size: 15
315286 AAATAGAATG
315296 ATAAAATAAACAAAA
1 ATAAAATAAACAAAA
* *
315311 ATAAAACATACAAAAA
1 ATAAAATAAAC-AAAA
*
315327 AAAATAATAAACAAAA
1 ATAA-AATAAACAAAA
*
315343 ACAAAATAAA-AAAA
1 ATAAAATAAACAAAA
315357 A
1 A
315358 CAAAGGAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
14 5 0.13
15 15 0.38
16 14 0.36
17 5 0.13
ACGTcount: A:0.81, C:0.08, G:0.00, T:0.11
Consensus pattern (15 bp):
ATAAAATAAACAAAA
Found at i:315512 original size:36 final size:35
Alignment explanation
Indices: 315472--315570 Score: 101
Period size: 36 Copynumber: 2.7 Consensus size: 35
315462 AAATGTATAT
315472 AAAAATATAAAAAAAACAAATAGAAAAA-CCAAAAAG
1 AAAAATATAAAAAAAA-AAATA-AAAAAGCCAAAAAG
* * * *
315508 AAAAATAGAAGAACAAATAATAAAAAAGCCAAAATG
1 AAAAATATAA-AAAAAAAAATAAAAAAGCCAAAAAG
315544 AAAAATAGTAAAATAAAAAAAATAAAA
1 AAAAATA-T-AAA-AAAAAAAATAAAA
315571 TAAAATATAT
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
35 5 0.10
36 27 0.53
37 6 0.12
38 13 0.25
ACGTcount: A:0.76, C:0.06, G:0.07, T:0.11
Consensus pattern (35 bp):
AAAAATATAAAAAAAAAAATAAAAAAGCCAAAAAG
Done.