Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007842.1 Hibiscus syriacus cultivar Beakdansim tig00110196_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: 183801
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:9251 original size:10 final size:10
Alignment explanation
Indices: 9226--9259 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
9216 AACGTTAGTA
*
9226 AAATAGAAAT
1 AAATAAAAAT
*
9236 AGATAAAAAT
1 AAATAAAAAT
9246 AAATAAAAAT
1 AAATAAAAAT
9256 AAAT
1 AAAT
9260 GGTAAATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:10250 original size:22 final size:22
Alignment explanation
Indices: 10222--10275 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
10212 TAAGGAAGCA
10222 ATAAAATAAAGATAAACAGTGT
1 ATAAAATAAAGATAAACAGTGT
*
10244 ATAAAATGAAGATAAACAGTGT
1 ATAAAATAAAGATAAACAGTGT
*
10266 ACAAAATAAA
1 ATAAAATAAA
10276 AATGAAGCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.61, C:0.06, G:0.13, T:0.20
Consensus pattern (22 bp):
ATAAAATAAAGATAAACAGTGT
Found at i:12658 original size:20 final size:20
Alignment explanation
Indices: 12633--12707 Score: 62
Period size: 20 Copynumber: 3.7 Consensus size: 20
12623 ATATGATAAT
*
12633 CAAAATTAATCAAATTATTA
1 CAAAATTTATCAAATTATTA
* * *
12653 CAAAATATCATAAAATTTATCA
1 CAAAAT-TTATCAAA-TTATTA
*
12675 -AAAATTTATCAAATAATTA
1 CAAAATTTATCAAATTATTA
**
12694 TTAAATTTATCAAA
1 CAAAATTTATCAAA
12708 CTTTTATAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
19 4 0.09
20 24 0.55
21 11 0.25
22 5 0.11
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (20 bp):
CAAAATTTATCAAATTATTA
Found at i:12692 original size:12 final size:11
Alignment explanation
Indices: 12658--12692 Score: 52
Period size: 11 Copynumber: 3.0 Consensus size: 11
12648 TATTACAAAA
12658 TATCATAAAATT
1 TATCA-AAAATT
12670 TATCAAAAATT
1 TATCAAAAATT
12681 TATCAAATAATT
1 TATCAAA-AATT
12693 ATTAAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 13 0.59
12 9 0.41
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (11 bp):
TATCAAAAATT
Found at i:15732 original size:2 final size:2
Alignment explanation
Indices: 15725--15750 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
15715 TTAAAATTCG
15725 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
15751 GTATTAATAT
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:17470 original size:26 final size:25
Alignment explanation
Indices: 17441--17489 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
17431 CGAGCTATTA
17441 TTTATATAAAAAAATTTAAAAATACT
1 TTTATAT-AAAAAATTTAAAAATACT
* *
17467 TTTATATAACATATTTAAAAATA
1 TTTATATAAAAAATTTAAAAATA
17490 ATATGATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (25 bp):
TTTATATAAAAAATTTAAAAATACT
Found at i:17580 original size:23 final size:23
Alignment explanation
Indices: 17536--17580 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
17526 TTATTAATTT
* *
17536 ATCATATAAATTATTATATAAAA
1 ATCATAAAAATTATGATATAAAA
17559 ATCATAAAAATTAATGAT-TAAA
1 ATCATAAAAATT-ATGATATAAA
17581 TTATCGTTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (23 bp):
ATCATAAAAATTATGATATAAAA
Found at i:30781 original size:30 final size:30
Alignment explanation
Indices: 30756--30850 Score: 104
Period size: 30 Copynumber: 3.2 Consensus size: 30
30746 ATCTCCTTTA
30756 CCATCGCCATCGTATTCACCATCTCCATCT
1 CCATCGCCATCGTATTCACCATCTCCATCT
* *
30786 CCATCGCCATCGTATTCATCATCCCCGA-CT
1 CCATCGCCATCGTATTCACCATCTCC-ATCT
* * * *
30816 CCATCTCCATCAGAAGT-ACCATCTCCATCG
1 CCATCGCCATC-GTATTCACCATCTCCATCT
30846 CCATC
1 CCATC
30851 AGTAGCACCT
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
29 1 0.02
30 49 0.91
31 4 0.07
ACGTcount: A:0.22, C:0.43, G:0.08, T:0.26
Consensus pattern (30 bp):
CCATCGCCATCGTATTCACCATCTCCATCT
Found at i:30841 original size:24 final size:24
Alignment explanation
Indices: 30814--30874 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
30804 TCATCCCCGA
*
30814 CTCCATCTCCATCAGAAGTACCAT
1 CTCCATCTCCATCAGAAGCACCAT
* * *
30838 CTCCATCGCCATCAGTAGCACCTT
1 CTCCATCTCCATCAGAAGCACCAT
*
30862 CACCATCTCCATC
1 CTCCATCTCCATC
30875 GCCATCAGTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.25, C:0.43, G:0.08, T:0.25
Consensus pattern (24 bp):
CTCCATCTCCATCAGAAGCACCAT
Found at i:30867 original size:30 final size:30
Alignment explanation
Indices: 30833--30904 Score: 144
Period size: 30 Copynumber: 2.4 Consensus size: 30
30823 CATCAGAAGT
30833 ACCATCTCCATCGCCATCAGTAGCACCTTC
1 ACCATCTCCATCGCCATCAGTAGCACCTTC
30863 ACCATCTCCATCGCCATCAGTAGCACCTTC
1 ACCATCTCCATCGCCATCAGTAGCACCTTC
30893 ACCATCTCCATC
1 ACCATCTCCATC
30905 AATTCCAGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.24, C:0.44, G:0.08, T:0.24
Consensus pattern (30 bp):
ACCATCTCCATCGCCATCAGTAGCACCTTC
Found at i:30872 original size:54 final size:55
Alignment explanation
Indices: 30780--30905 Score: 132
Period size: 54 Copynumber: 2.3 Consensus size: 55
30770 TTCACCATCT
* * * * *
30780 CCATCTCCATCGCCATC-GTATTCATCATCCCCGACTCCATCTCCATCAGAAGTA
1 CCATCTCCATCGCCATCAGTATGCACCATCACCGACTCCATCGCCATCAGAAGCA
* *
30834 CCATCTCCATCGCCATCAGTA-GCACCTTCACC-ATCTCCATCGCCATCAGTAGCA
1 CCATCTCCATCGCCATCAGTATGCACCATCACCGA-CTCCATCGCCATCAGAAGCA
* * *
30888 CCTTCACCATCTCCATCA
1 CCATCTCCATCGCCATCA
30906 ATTCCAGAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
53 1 0.02
54 56 0.93
55 3 0.05
ACGTcount: A:0.24, C:0.43, G:0.09, T:0.25
Consensus pattern (55 bp):
CCATCTCCATCGCCATCAGTATGCACCATCACCGACTCCATCGCCATCAGAAGCA
Found at i:30889 original size:24 final size:24
Alignment explanation
Indices: 30814--30905 Score: 76
Period size: 24 Copynumber: 3.6 Consensus size: 24
30804 TCATCCCCGA
* * *
30814 CTCCATCTCCATCAGAAGTACCAT
1 CTCCATCGCCATCAGTAGCACCAT
30838 CTCCATCGCCATCAGTAGCACCTTCACCAT
1 CTCCATCGCCATCAGTAG------CACCAT
*
30868 CTCCATCGCCATCAGTAGCACCTT
1 CTCCATCGCCATCAGTAGCACCAT
* *
30892 CACCATCTCCATCA
1 CTCCATCGCCATCA
30906 ATTCCAGAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
24 33 0.59
30 23 0.41
ACGTcount: A:0.25, C:0.42, G:0.09, T:0.24
Consensus pattern (24 bp):
CTCCATCGCCATCAGTAGCACCAT
Found at i:33489 original size:24 final size:24
Alignment explanation
Indices: 33462--33517 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
33452 CCTTCACCAA
*
33462 CGCCATCATATTCACTATCACCGT
1 CGCCATCATATTCACCATCACCGT
** *
33486 CGCCATTGTATTCCCCATCACCGT
1 CGCCATCATATTCACCATCACCGT
*
33510 CACCATCA
1 CGCCATCA
33518 CTGTCGCTAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.23, C:0.41, G:0.09, T:0.27
Consensus pattern (24 bp):
CGCCATCATATTCACCATCACCGT
Found at i:41615 original size:20 final size:18
Alignment explanation
Indices: 41590--41634 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 18
41580 TTTGGTTTAC
*
41590 GGAATATAAGATTATCAGTG
1 GGAATAAAAGATTAT-AG-G
41610 GGAATAAAAAGATTATAGG
1 GGAAT-AAAAGATTATAGG
41629 GGAATA
1 GGAATA
41635 GGATTACTCG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 1 0.04
19 6 0.26
20 7 0.30
21 9 0.39
ACGTcount: A:0.47, C:0.02, G:0.27, T:0.24
Consensus pattern (18 bp):
GGAATAAAAGATTATAGG
Found at i:44323 original size:24 final size:24
Alignment explanation
Indices: 44295--44368 Score: 75
Period size: 23 Copynumber: 3.2 Consensus size: 24
44285 AAACGAGCAC
44295 TAAACGAACATGTTCGTGAACATA
1 TAAACGAACATGTTCGTGAACATA
*
44319 TAAACGAACATCTTCGCT-AACAT-
1 TAAACGAACATGTTCG-TGAACATA
**
44342 TAAATAAACATGTTC-TCGAACA-A
1 TAAACGAACATGTTCGT-GAACATA
44365 TAAA
1 TAAA
44369 TTAACGAACA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
21 1 0.02
23 20 0.48
24 20 0.48
25 1 0.02
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.26
Consensus pattern (24 bp):
TAAACGAACATGTTCGTGAACATA
Found at i:44363 original size:85 final size:85
Alignment explanation
Indices: 44198--44379 Score: 195
Period size: 85 Copynumber: 2.1 Consensus size: 85
44188 AATTGAACAT
* * * * * *
44198 ATAAACTAACACTAAATGAATATATTCGTGAACATATAAACAAACAAGTTTACGAACAGTAAATG
1 ATAAACGAACACTAAACGAACATATTCGTGAACATATAAACAAACAACTTCACGAACAGTAAATA
*
44263 AACATATTTGAGAACAATAG
66 AACATATTTGAGAACAATAA
* * * * * * *
44283 ATAAACGAGCACTAAACGAACATGTTCGTGAACATATAAACGAACATCTTCGCTAACATTAAATA
1 ATAAACGAACACTAAACGAACATATTCGTGAACATATAAACAAACAACTTCACGAACAGTAAATA
* *
44348 AACATGTTCT-CGAACAATAA
66 AACATATT-TGAGAACAATAA
*
44368 ATTAACGAACAC
1 ATAAACGAACAC
44380 GAACACAATT
Statistics
Matches: 78, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
85 77 0.99
86 1 0.01
ACGTcount: A:0.48, C:0.17, G:0.12, T:0.24
Consensus pattern (85 bp):
ATAAACGAACACTAAACGAACATATTCGTGAACATATAAACAAACAACTTCACGAACAGTAAATA
AACATATTTGAGAACAATAA
Found at i:48382 original size:10 final size:10
Alignment explanation
Indices: 48369--48422 Score: 54
Period size: 10 Copynumber: 5.1 Consensus size: 10
48359 TTGTTTATTG
48369 TGTTCGTTTA
1 TGTTCGTTTA
*
48379 TGTTCGTTTT
1 TGTTCGTTTA
*
48389 TGTTCATTTATTA
1 TGTTC--GT-TTA
*
48402 TGTTCGTTTG
1 TGTTCGTTTA
48412 TGTTCGTTTA
1 TGTTCGTTTA
48422 T
1 T
48423 CATTTAAATG
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
10 26 0.74
11 1 0.03
12 1 0.03
13 7 0.20
ACGTcount: A:0.09, C:0.09, G:0.19, T:0.63
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:48387 original size:23 final size:22
Alignment explanation
Indices: 48346--48399 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
48336 TTTTTTGTGT
*
48346 TGTTCATTTATATTTGTTTATTG
1 TGTTCATTTATATTCGTTT-TTG
* *
48369 TGTTCGTTTATGTTCG-TTTT-
1 TGTTCATTTATATTCGTTTTTG
48389 TGTTCATTTAT
1 TGTTCATTTAT
48400 TATGTTCGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 10 0.37
21 2 0.07
22 2 0.07
23 13 0.48
ACGTcount: A:0.13, C:0.07, G:0.15, T:0.65
Consensus pattern (22 bp):
TGTTCATTTATATTCGTTTTTG
Found at i:48402 original size:23 final size:23
Alignment explanation
Indices: 48376--48422 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
48366 TTGTGTTCGT
*
48376 TTATGTTCGTTTTTGTTCATTTA
1 TTATGTTCGTTTGTGTTCATTTA
*
48399 TTATGTTCGTTTGTGTTCGTTTA
1 TTATGTTCGTTTGTGTTCATTTA
48422 T
1 T
48423 CATTTAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.11, C:0.09, G:0.17, T:0.64
Consensus pattern (23 bp):
TTATGTTCGTTTGTGTTCATTTA
Found at i:60050 original size:228 final size:230
Alignment explanation
Indices: 59415--60271 Score: 1153
Period size: 231 Copynumber: 3.8 Consensus size: 230
59405 AACATCATCC
* * * *
59415 TCATTATCATCTCTGTCACCTATATGTATTTTTTTCAAATCCATAATTCATATAAATTTAAAATG
1 TCATTATCATCTCTGTCACCTATATGTATTTTTTTCAAACCCATAATTCACATAAATTTCAAATA
* ** *
59480 ATTTAAAAGCATAAATAAC---CAATACTAAAATATTAAG--TGAAAAATTAAAGATTGAGATAA
66 ATTT-AAAGCATAAATAACTAATAATACTAAAATATTAAGAAAAAAAAATCAAAGATTGAGATAA
59540 ACATACCACAAAAAGGAGAATCGGGAAACTGAGAGTCAAATTCATCTTCAATTGGAACATTGTTA
130 ACATACCACAAAAAGGAGAATCGGGAAACTGAGAGTCAAATTCATCTTCAATTGGAACATTGTTA
*
59605 TCATCTACA-GAACCGTATCTTGTAGAAAGTTTAAT
195 TCATCCACAGGAACCGTATCTTGTAGAAAGTTTAAT
* * * * *
59640 TCATTGTCATCTCTGTCACCTACATGAATTTTTTTCAAACTCACAATTCACATAAATTTCAAATA
1 TCATTATCATCTCTGTCACCTATATGTATTTTTTTCAAACCCATAATTCACATAAATTTCAAATA
59705 ATTTAAAGCATAAATAACTAATAATACTAAAATATTAAGTGAAAAAAAAATCAAAGATTGAGATA
66 ATTTAAAGCATAAATAACTAATAATACTAAAATATTAA--GAAAAAAAAATCAAAGATTGAGATA
** *
59770 AACATACCACAAAAAGGAGAATCGGGAAACTCTGAGTCAAATTCATCTTCAATTGGAACATCGTT
129 AACATACCACAAAAAGGAGAATCGGGAAACTGAGAGTCAAATTCATCTTCAATTGGAACATTGTT
59835 ATCATCCACAGGAACCGTATCTTGTAGAAAGTTTAAT
194 ATCATCCACAGGAACCGTATCTTGTAGAAAGTTTAAT
* * * **
59872 TCATTATCATC-C-GACACCTATATGTA-TTTTTTCAAACCCTTTATTCACATAAATTTCAAACG
1 TCATTATCATCTCTGTCACCTATATGTATTTTTTTCAAACCCATAATTCACATAAATTTCAAATA
* * * *
59934 ATTTAAAGCATAAATAACTAATAATACCAAAATAATAAGCCAAAAAAAATCAAAGATTGCGATAA
66 ATTTAAAGCATAAATAACTAATAATACTAAAATATTAAG-AAAAAAAAATCAAAGATTGAGATAA
* * * * *
59999 ACATACCACGACATGGAAAATCGGGAAACTGAGAGTCAAATTCATCTTCAATTGGAACTTTGTTA
130 ACATACCACAAAAAGGAGAATCGGGAAACTGAGAGTCAAATTCATCTTCAATTGGAACATTGTTA
* *
60064 TCATCCACAGGAACTGTATCTAGTAGAAAGTTTAAT
195 TCATCCACAGGAACCGTATCTTGTAGAAAGTTTAAT
* * * * * *
60100 TCATTATCA-CACCCGTCACCTATGTGTATTTTTTTAAAACTCGA-AATTCACATAATTTTCAAA
1 TCATTATCATC-TCTGTCACCTATATGTATTTTTTTCAAAC-CCATAATTCACATAAATTTCAAA
* * *
60163 TAATTTAAAGCATAAATAACAAAT-ATGCTAAAATATTAAGAAAAAAAAATCAGAGATTGAGATA
64 TAATTTAAAGCATAAATAACTAATAATACTAAAATATTAAGAAAAAAAAATCAAAGATTGAGATA
** * * *
60227 AACATACCAGGAAAAGGAGAATGGGGAAACTGGGAATCAAATTCA
129 AACATACCACAAAAAGGAGAATCGGGAAACTGAGAGTCAAATTCA
60272 GAGGGCTGGG
Statistics
Matches: 554, Mismatches: 64, Indels: 24
0.86 0.10 0.04
Matches are distributed among these distances:
224 14 0.03
225 60 0.11
227 18 0.03
228 123 0.22
229 127 0.23
230 36 0.06
231 139 0.25
232 37 0.07
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.29
Consensus pattern (230 bp):
TCATTATCATCTCTGTCACCTATATGTATTTTTTTCAAACCCATAATTCACATAAATTTCAAATA
ATTTAAAGCATAAATAACTAATAATACTAAAATATTAAGAAAAAAAAATCAAAGATTGAGATAAA
CATACCACAAAAAGGAGAATCGGGAAACTGAGAGTCAAATTCATCTTCAATTGGAACATTGTTAT
CATCCACAGGAACCGTATCTTGTAGAAAGTTTAAT
Found at i:74610 original size:76 final size:76
Alignment explanation
Indices: 74479--74636 Score: 273
Period size: 76 Copynumber: 2.1 Consensus size: 76
74469 GGCTAAGGCC
* *
74479 CTACCTGCCCCATTTAGATTCCCCCTTCGAGCTCATACCCATTTTGATTTAGTAAACAATGATGC
1 CTACTTGCCCCATTTAGATTCCCCCTTAGAGCTCATACCCATTTTGATTTAGTAAACAATGATG-
*
74544 A-ATTTTGTCAT
65 ATATTTGGTCAT
74555 CTACTTGCCCCATTTAGATTCCCCCTTAGAGCTCATACCCATTTTGATTTAGTAAACAATGATGA
1 CTACTTGCCCCATTTAGATTCCCCCTTAGAGCTCATACCCATTTTGATTTAGTAAACAATGATGA
74620 TATTTGGTCAT
66 TATTTGGTCAT
74631 CTACTT
1 CTACTT
74637 CTATGATTTA
Statistics
Matches: 78, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
75 1 0.01
76 77 0.99
ACGTcount: A:0.25, C:0.26, G:0.12, T:0.37
Consensus pattern (76 bp):
CTACTTGCCCCATTTAGATTCCCCCTTAGAGCTCATACCCATTTTGATTTAGTAAACAATGATGA
TATTTGGTCAT
Found at i:74735 original size:12 final size:12
Alignment explanation
Indices: 74720--74744 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
74710 ATATTTTTGA
74720 TAAAATATTATT
1 TAAAATATTATT
74732 TAAAATATTATT
1 TAAAATATTATT
74744 T
1 T
74745 TTTACTGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAAAATATTATT
Found at i:74972 original size:18 final size:18
Alignment explanation
Indices: 74949--74985 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
74939 ATCAGAAATA
74949 TTAAAAAATATTAATATT
1 TTAAAAAATATTAATATT
74967 TTAAAAAATATTAATATT
1 TTAAAAAATATTAATATT
74985 T
1 T
74986 CTGATAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTAAAAAATATTAATATT
Found at i:75689 original size:18 final size:18
Alignment explanation
Indices: 75647--75706 Score: 84
Period size: 18 Copynumber: 3.2 Consensus size: 18
75637 TTAAGGTATA
*
75647 AAACATTACTTTTTCAAAAT
1 AAACATTAC-TTTT-AAAGT
75667 AAACATTACTTTTAAAGT
1 AAACATTACTTTTAAAGT
*
75685 AAACATTACTTTTAAGGT
1 AAACATTACTTTTAAAGT
75703 AAAC
1 AAAC
75707 GTAAGTTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
18 25 0.66
19 4 0.11
20 9 0.24
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.37
Consensus pattern (18 bp):
AAACATTACTTTTAAAGT
Found at i:76476 original size:31 final size:31
Alignment explanation
Indices: 76441--76537 Score: 86
Period size: 31 Copynumber: 3.1 Consensus size: 31
76431 AGTAATGAAT
* *
76441 TTTGATAAGTTTAAGGACCATTTTTTAATAA
1 TTTGATAAGTTTAAAGACCATTTTATAATAA
* ** * *
76472 TTTGATAAGCTTAAAGATAATTTTCTAACAA
1 TTTGATAAGTTTAAAGACCATTTTATAATAA
* * * *
76503 TTTAATAAATGTTAATGACCATTTTATAATCA
1 TTTGATAAGT-TTAAAGACCATTTTATAATAA
76535 TTT
1 TTT
76538 AAAAAATTAA
Statistics
Matches: 50, Mismatches: 15, Indels: 1
0.76 0.23 0.02
Matches are distributed among these distances:
31 32 0.64
32 18 0.36
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.44
Consensus pattern (31 bp):
TTTGATAAGTTTAAAGACCATTTTATAATAA
Found at i:76932 original size:109 final size:109
Alignment explanation
Indices: 76797--77016 Score: 404
Period size: 109 Copynumber: 2.0 Consensus size: 109
76787 TCCTTAGTGG
*
76797 TTTTATAATTTATGAGGACTCGATCAATATGTGTATAGTTATCATTTTCAAATTTTAGAATCCTT
1 TTTTATAATTTATGAGGACTCAATCAATATGTGTATAGTTATCATTTTCAAATTTTAGAATCCTT
*
76862 TTTCGATATAAGATTAATGTTGTATACCTCTCCAAGACGTGACA
66 TTTCGATATAAGATTAATGTCGTATACCTCTCCAAGACGTGACA
*
76906 TTTTATAATTTATGAGGACTCAATCAATATGTGTATAGTTATCATTTTCAAATTTTAGAATTCTT
1 TTTTATAATTTATGAGGACTCAATCAATATGTGTATAGTTATCATTTTCAAATTTTAGAATCCTT
*
76971 TTTCGATATAAGATTAATGTCGTATACCTCTCTAAGACGTGACA
66 TTTCGATATAAGATTAATGTCGTATACCTCTCCAAGACGTGACA
77015 TT
1 TT
77017 CACCACTATA
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
109 107 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.42
Consensus pattern (109 bp):
TTTTATAATTTATGAGGACTCAATCAATATGTGTATAGTTATCATTTTCAAATTTTAGAATCCTT
TTTCGATATAAGATTAATGTCGTATACCTCTCCAAGACGTGACA
Found at i:81983 original size:33 final size:31
Alignment explanation
Indices: 81935--81997 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 31
81925 GTTTGAACAT
81935 TTTATATTTATTAATG-TGATATAATGTTCTA
1 TTTATATTTATTAATGATGAT-TAATGTTCTA
*
81966 TTTATATTAATATTAATGATGATTAATTTTCT
1 TTTATATT--TATTAATGATGATTAATGTTCT
81998 CTCATTGGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 8 0.29
33 16 0.57
34 4 0.14
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.56
Consensus pattern (31 bp):
TTTATATTTATTAATGATGATTAATGTTCTA
Found at i:84580 original size:2 final size:2
Alignment explanation
Indices: 84573--84630 Score: 61
Period size: 2 Copynumber: 31.0 Consensus size: 2
84563 TTGTTTGTAT
* * *
84573 TA TA TA TA -A T- TA -A TA TA -A AA TA TA TA AA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
84611 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
84631 ATCGGGGCGG
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
1 4 0.09
2 43 0.91
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:85600 original size:22 final size:22
Alignment explanation
Indices: 85573--85627 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
85563 GGTTAAACAA
85573 AAGATAAAACTATCTACAAAAT
1 AAGATAAAACTATCTACAAAAT
85595 AAGATAAAACTATCTACAAAAT
1 AAGATAAAACTATCTACAAAAT
85617 AA-AT-AAACTAT
1 AAGATAAAACTAT
85628 TGAAGGACCA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 7 0.21
21 2 0.06
22 24 0.73
ACGTcount: A:0.60, C:0.13, G:0.04, T:0.24
Consensus pattern (22 bp):
AAGATAAAACTATCTACAAAAT
Found at i:89875 original size:57 final size:61
Alignment explanation
Indices: 89813--89953 Score: 159
Period size: 61 Copynumber: 2.4 Consensus size: 61
89803 CCTACATTGA
* *
89813 AAAAATATGTTATACTTTAAGTAT-TATTTTAATAAAAAATAT-TG-TAA-TAT-TAAGATG
1 AAAAATATGATATACTTTAAGTATCTATTTTAAAAAAAAATATATGTTAAGTATCT-AGATG
** * *
89870 AAAAATATGATATA-TTTTGGATATCTGTTTTAAAAAAAAATATATGTTAAGTATCTATATG
1 AAAAATATGATATACTTTAAG-TATCTATTTTAAAAAAAAATATATGTTAAGTATCTAGATG
*
89931 AAAAATATGATAAACTTTAAGTA
1 AAAAATATGATATACTTTAAGTA
89954 CTTAGATAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
56 4 0.06
57 16 0.24
58 16 0.24
59 2 0.03
60 3 0.04
61 22 0.32
62 5 0.07
ACGTcount: A:0.48, C:0.03, G:0.10, T:0.40
Consensus pattern (61 bp):
AAAAATATGATATACTTTAAGTATCTATTTTAAAAAAAAATATATGTTAAGTATCTAGATG
Found at i:92934 original size:26 final size:26
Alignment explanation
Indices: 92905--92961 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
92895 AGGATACACC
92905 CTAATTATACTTAAAAAAGTTATATA
1 CTAATTATACTTAAAAAAGTTATATA
92931 CTAATTATACTTAAAAAAGTTATATA
1 CTAATTATACTTAAAAAAGTTATATA
92957 CTAAT
1 CTAAT
92962 GAAGTTAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.39
Consensus pattern (26 bp):
CTAATTATACTTAAAAAAGTTATATA
Found at i:92981 original size:25 final size:26
Alignment explanation
Indices: 92905--92971 Score: 100
Period size: 26 Copynumber: 2.6 Consensus size: 26
92895 AGGATACACC
*
92905 CTAATTATACTTAAAAAAGTTATATA
1 CTAATGATACTTAAAAAAGTTATATA
*
92931 CTAATTATACTTAAAAAAGTTATATA
1 CTAATGATACTTAAAAAAGTTATATA
*
92957 CTAATGA-AGTTAAAA
1 CTAATGATACTTAAAA
92972 TAATTGTATA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
25 7 0.18
26 32 0.82
ACGTcount: A:0.51, C:0.07, G:0.06, T:0.36
Consensus pattern (26 bp):
CTAATGATACTTAAAAAAGTTATATA
Found at i:95158 original size:169 final size:169
Alignment explanation
Indices: 94878--95211 Score: 465
Period size: 169 Copynumber: 2.0 Consensus size: 169
94868 CAAAGATCTG
* * * *
94878 TTAGACTCGATTACGAGTGTCGGACACGGATAATGTTACATATCCGGACAATCTTCTGATGATTA
1 TTAGACTCGATTACGAGGGTCAGACACGGATAATGTTACATATCCGGACAATCTTCAGAGGATTA
* * * * *
94943 TATTCATGTACTTAGGTCTGCATATGTGTCGAACACTTGTACATCATCATCAATGAACTAAACTC
66 TATTCATGTACTCAGGTCCGCATATGTGTCAAACACTTGAACATCATCATCAAGGAACTAAACTC
*
95008 TATCAACTACTTCATAATTTCTTCTACATATATATGAAC
131 CATCAACTACTTCATAATTTCTTCTACATATATATGAAC
* * * * * *
95047 TTAGACTCGATTTCTAGGGTCAGACACGGATATTTTTACATAATTC-GACAATGTTCAGAGGATT
1 TTAGACTCGATTACGAGGGTCAGACACGGATAATGTTACAT-ATCCGGACAATCTTCAGAGGATT
* *
95111 ATA-TCAATGTACTCATGTCCGGATATGTGTCAAACACTTGAACATCATCATCAAGGAACTAAAC
65 ATATTC-ATGTACTCAGGTCCGCATATGTGTCAAACACTTGAACATCATCATCAAGGAACTAAAC
*
95175 TCCATCAATTACTTCATAATTTCTTCTACATATATAT
129 TCCATCAACTACTTCATAATTTCTTCTACATATATAT
95212 ATATATATAT
Statistics
Matches: 144, Mismatches: 19, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
168 2 0.01
169 139 0.97
170 3 0.02
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (169 bp):
TTAGACTCGATTACGAGGGTCAGACACGGATAATGTTACATATCCGGACAATCTTCAGAGGATTA
TATTCATGTACTCAGGTCCGCATATGTGTCAAACACTTGAACATCATCATCAAGGAACTAAACTC
CATCAACTACTTCATAATTTCTTCTACATATATATGAAC
Found at i:102677 original size:21 final size:21
Alignment explanation
Indices: 102628--102669 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
102618 AACTTTAAGG
102628 TAAAATTTGTAAATATGTGGA
1 TAAAATTTGTAAATATGTGGA
102649 TAAAATTTGTAAATATGTGGA
1 TAAAATTTGTAAATATGTGGA
102670 AAGCATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.19, T:0.38
Consensus pattern (21 bp):
TAAAATTTGTAAATATGTGGA
Found at i:104562 original size:16 final size:16
Alignment explanation
Indices: 104534--104578 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
104524 ACCCGACCTA
*
104534 TTTTCAACCTGACATG
1 TTTTTAACCTGACATG
*
104550 TTTTTAACTTGACATG
1 TTTTTAACCTGACATG
104566 TTTTTAACCTGAC
1 TTTTTAACCTGAC
104579 CTGTAAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.44
Consensus pattern (16 bp):
TTTTTAACCTGACATG
Found at i:104889 original size:23 final size:24
Alignment explanation
Indices: 104851--104896 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
104841 ATGCAAAGGA
*
104851 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAATTTAATTTATAT
104875 AAATT-ATATAATTTAATTTATA
1 AAATTAATATAATTTAATTTATA
104897 AAAAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
AAATTAATATAATTTAATTTATAT
Found at i:104906 original size:23 final size:23
Alignment explanation
Indices: 104856--104906 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
104846 AAGGAAAATT
* * *
104856 AATATAGTTTAATTTATATAAAT
1 AATATAATTTAATTTATAAAAAA
*
104879 TATATAATTTAATTTATAAAAAA
1 AATATAATTTAATTTATAAAAAA
104902 AATAT
1 AATAT
104907 TATATAAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
AATATAATTTAATTTATAAAAAA
Found at i:110415 original size:17 final size:17
Alignment explanation
Indices: 110386--110419 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
110376 TAAGCTCATG
110386 TGAAAATTGAATTATAA
1 TGAAAATTGAATTATAA
110403 TGAATAATT-AATTATAA
1 TGAA-AATTGAATTATAA
110420 ATTTACATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (17 bp):
TGAAAATTGAATTATAA
Found at i:111024 original size:20 final size:20
Alignment explanation
Indices: 110984--111024 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
110974 TTTGATCATG
*
110984 ATATTTCCATATGCATGTAT
1 ATATTTCCATATGCATATAT
111004 ATATTT-CATATGACATATAT
1 ATATTTCCATATG-CATATAT
111024 A
1 A
111025 ATCATATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (20 bp):
ATATTTCCATATGCATATAT
Found at i:112860 original size:19 final size:20
Alignment explanation
Indices: 112828--112872 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
112818 AAATTTTGTT
* *
112828 AATTTATAATTTAACTATTA
1 AATTTATAAATTAAATATTA
112848 AATTT-TAAATTAAATATT-
1 AATTTATAAATTAAATATTA
112866 AATTTAT
1 AATTTAT
112873 TTATGGATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 5 0.23
19 12 0.55
20 5 0.23
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
AATTTATAAATTAAATATTA
Found at i:115675 original size:21 final size:21
Alignment explanation
Indices: 115645--115692 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
115635 TAATTTTCAA
*
115645 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
115666 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
115687 ACATTG
1 ACATTG
115693 CAATATTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:119746 original size:75 final size:74
Alignment explanation
Indices: 119655--119827 Score: 256
Period size: 75 Copynumber: 2.3 Consensus size: 74
119645 CCCCCTGGGG
* ** *
119655 GGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACAAAAATGTTTAGGGGGGAATCGG
1 GGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAACAAAAACATTCA-GGGGGAATCGG
119720 TTCCTCCTAT
65 TTCCTCCTAT
* * * *
119730 GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGCCAAACCATTCAGGGGGAATCGGT
1 GGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAACAAAAACATTCAGGGGGAATCGGT
119795 TCCTCCTAT
66 TCCTCCTAT
*
119804 GGGGGAATCGGTTCCCTCTGAGCA
1 GGGGGAATCGGTTCCCTCCGAGCA
119828 ATCTGTAATT
Statistics
Matches: 89, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
74 44 0.49
75 45 0.51
ACGTcount: A:0.22, C:0.24, G:0.30, T:0.24
Consensus pattern (74 bp):
GGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAACAAAAACATTCAGGGGGAATCGGT
TCCTCCTAT
Found at i:119827 original size:74 final size:75
Alignment explanation
Indices: 119655--119832 Score: 259
Period size: 74 Copynumber: 2.4 Consensus size: 75
119645 CCCCCTGGGG
* * ** *
119655 GGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACAAAAATGTTTAGGGGGGAATCGG
1 GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAACAAAAACATTCAGGGGGGAATCGG
119720 TTCCTCCTAT
66 TTCCTCCTAT
* * *
119730 GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGCCAAACCATTCA-GGGGGAATCGG
1 GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAACAAAAACATTCAGGGGGGAATCGG
119794 TTCCTCCTAT
66 TTCCTCCTAT
* *
119804 GGGGGAATCGGTTCCCTCTGAGCAATCTG
1 GGGGGAATCGGTTCCCTCCGAGCATTCTG
119833 TAATTTTTGG
Statistics
Matches: 93, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
74 48 0.52
75 45 0.48
ACGTcount: A:0.22, C:0.24, G:0.30, T:0.24
Consensus pattern (75 bp):
GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAACAAAAACATTCAGGGGGGAATCGG
TTCCTCCTAT
Found at i:122505 original size:20 final size:21
Alignment explanation
Indices: 122451--122513 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
122441 GATTCCCCTG
122451 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
122475 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
122495 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
122514 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:127507 original size:106 final size:106
Alignment explanation
Indices: 127322--127787 Score: 731
Period size: 106 Copynumber: 4.4 Consensus size: 106
127312 GTATTGTTCC
* ** * * *
127322 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTGGAACTG-GAAAATTGTTTATTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AAGTTGTTTATTGACA
* *
127386 ACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG-CATG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
127428 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
127493 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
127534 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
127599 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
127640 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATT-AGGAAGTTGTTTTTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA-GAAGTTGTTTATTGACA
*
127704 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
127746 GAGTCCAATATCTTTCGTTGTGAAGTTGAAATAGACTCTGAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAA
127788 TGAAATTGGA
Statistics
Matches: 337, Mismatches: 20, Indels: 6
0.93 0.06 0.02
Matches are distributed among these distances:
105 1 0.00
106 334 0.99
107 2 0.01
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:131750 original size:8 final size:8
Alignment explanation
Indices: 131722--131790 Score: 50
Period size: 8 Copynumber: 8.4 Consensus size: 8
131712 TTAAGTAAAT
*
131722 AAATAACA
1 AAATAATA
*
131730 AAACAATA
1 AAATAATA
*
131738 GAATAATA
1 AAATAATA
131746 AAATAATA
1 AAATAATA
*
131754 AAATAA-G
1 AAATAATA
*
131761 AAATCAAAA
1 AAAT-AATA
*
131770 CAAATAAAA
1 -AAATAATA
131779 ATAATAATA
1 A-AATAATA
131788 AAA
1 AAA
131791 AGATGAAATT
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
7 4 0.08
8 30 0.61
9 11 0.22
10 4 0.08
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.17
Consensus pattern (8 bp):
AAATAATA
Found at i:132126 original size:19 final size:19
Alignment explanation
Indices: 132104--132159 Score: 112
Period size: 19 Copynumber: 2.9 Consensus size: 19
132094 TTAATTTCAC
132104 GCGCCCCTTGCGATATCGA
1 GCGCCCCTTGCGATATCGA
132123 GCGCCCCTTGCGATATCGA
1 GCGCCCCTTGCGATATCGA
132142 GCGCCCCTTGCGATATCG
1 GCGCCCCTTGCGATATCG
132160 CGAGAGAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.14, C:0.38, G:0.27, T:0.21
Consensus pattern (19 bp):
GCGCCCCTTGCGATATCGA
Found at i:132249 original size:38 final size:32
Alignment explanation
Indices: 132164--132250 Score: 84
Period size: 33 Copynumber: 2.5 Consensus size: 32
132154 ATATCGCGAG
132164 AGAAAAAGGCGGTTTTGCTCCCCTTTATAGGAA
1 AGAAAAAGG-GGTTTTGCTCCCCTTTATAGGAA
**
132197 AGTAAAGGGGGGTTTTGCTCCCCTTTACGATATGAGGAA
1 AG-AAAAAGGGGTTTTGCTCCCC-TT----TAT-AGGAA
132236 AGAAAAAGGGGTTTT
1 AGAAAAAGGGGTTTT
132251 TGCTAAACAT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
33 15 0.35
34 7 0.16
38 14 0.33
39 7 0.16
ACGTcount: A:0.30, C:0.14, G:0.29, T:0.28
Consensus pattern (32 bp):
AGAAAAAGGGGTTTTGCTCCCCTTTATAGGAA
Found at i:143923 original size:13 final size:13
Alignment explanation
Indices: 143904--143933 Score: 51
Period size: 13 Copynumber: 2.2 Consensus size: 13
143894 ACAAATAAGC
143904 AAAAAAAGAAACAG
1 AAAAAAA-AAACAG
143918 AAAAAAAAAACAG
1 AAAAAAAAAACAG
143931 AAA
1 AAA
143934 CTTTCTCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.83, C:0.07, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAACAG
Found at i:147844 original size:31 final size:32
Alignment explanation
Indices: 147802--147887 Score: 106
Period size: 31 Copynumber: 2.8 Consensus size: 32
147792 TTAAATAATG
*
147802 ATAA-ATTTTGATAAGTTTAATGATT-ATTTT
1 ATAATATTTTGATAAATTTAATGATTCATTTT
*
147832 ATAATATTTTGATAATTTTAATG-TTCATTTT
1 ATAATATTTTGATAAATTTAATGATTCATTTT
* *
147863 ATACTAATTTGATAGAATTTAATGA
1 ATAATATTTTGATA-AATTTAATGA
147888 CGATTTTGTA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
30 6 0.12
31 34 0.71
32 8 0.17
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.51
Consensus pattern (32 bp):
ATAATATTTTGATAAATTTAATGATTCATTTT
Found at i:147894 original size:32 final size:30
Alignment explanation
Indices: 147808--147929 Score: 86
Period size: 31 Copynumber: 3.9 Consensus size: 30
147798 AATGATAAAT
* * *
147808 TTTGATAAGTTTAATGATTATTTTATAATAT
1 TTTGATAAATTTAATGA-CATTTTATAATAA
* * *
147839 TTTGATAATTTTAATGTTCATTTTATACTAA
1 TTTGATAAATTTAATG-ACATTTTATAATAA
* *
147870 TTTGATAGAATTTAATGACGATTTTGTAATCA
1 TTTGATA-AATTTAATGAC-ATTTTATAATAA
* *
147902 -TTGAGAACA-ATAATGACCATTTTATAAT
1 TTTGATAA-ATTTAATGA-CATTTTATAAT
147930 TTTTAAAAAT
Statistics
Matches: 73, Mismatches: 13, Indels: 11
0.75 0.13 0.11
Matches are distributed among these distances:
30 16 0.22
31 40 0.55
32 17 0.23
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.48
Consensus pattern (30 bp):
TTTGATAAATTTAATGACATTTTATAATAA
Found at i:161748 original size:17 final size:18
Alignment explanation
Indices: 161715--161748 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
161705 TTAATCAGGA
161715 TAAAATAGTTAACATTAT
1 TAAAATAGTTAACATTAT
*
161733 TAAAAT-GTTCACATTA
1 TAAAATAGTTAACATTA
161749 GTTTAATGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (18 bp):
TAAAATAGTTAACATTAT
Found at i:164074 original size:54 final size:54
Alignment explanation
Indices: 164010--164186 Score: 191
Period size: 54 Copynumber: 3.3 Consensus size: 54
164000 AGCGCTCACA
* * *
164010 TAAGGCGTGGGCACGACTTTTTCATCCAGACCTAACGAAGAAGAAGTCTTCAGT
1 TAAGGCGTGGGCACGACTTATTCATCCAGAACTAACGCAGAAGAAGTCTTCAGT
* * *
164064 TAAGGCGTGGGCACAACTTATCCAT-CATGAGA-T-ACTGCAGAAGAAGTCTCCAGT
1 TAAGGCGTGGGCACGACTTATTCATCCA-GA-ACTAAC-GCAGAAGAAGTCTTCAGT
* * * *
164118 TAAGGCGTAGGCACGGCTTATTCATCCAAAACTACCGCAGAAGAA-TCCTTCAGT
1 TAAGGCGTGGGCACGACTTATTCATCCAGAACTAACGCAGAAGAAGT-CTTCAGT
*
164172 TAAGGCGTGAGCACG
1 TAAGGCGTGGGCACG
164187 CCATCTATTG
Statistics
Matches: 101, Mismatches: 15, Indels: 14
0.78 0.12 0.11
Matches are distributed among these distances:
53 6 0.06
54 92 0.91
55 3 0.03
ACGTcount: A:0.31, C:0.23, G:0.24, T:0.22
Consensus pattern (54 bp):
TAAGGCGTGGGCACGACTTATTCATCCAGAACTAACGCAGAAGAAGTCTTCAGT
Found at i:165182 original size:21 final size:20
Alignment explanation
Indices: 165156--165214 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 20
165146 AAAAGGCAAC
*
165156 CTTCTTCATTTTGTTCTTCTT
1 CTTCTTC-TTTTCTTCTTCTT
*
165177 CTTCTTCTCTTTCTTCTTTTT
1 CTTCTTCT-TTTCTTCTTCTT
165198 CTTCTTCTTTTTCTTCT
1 CTTCTTC-TTTTCTTCT
165215 GTTTTGGTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.03
21 32 0.94
22 1 0.03
ACGTcount: A:0.02, C:0.27, G:0.02, T:0.69
Consensus pattern (20 bp):
CTTCTTCTTTTCTTCTTCTT
Found at i:165183 original size:9 final size:9
Alignment explanation
Indices: 165156--165214 Score: 59
Period size: 9 Copynumber: 6.6 Consensus size: 9
165146 AAAAGGCAAC
165156 CTTCTTCATT
1 CTTCTTC-TT
*
165166 -TTGTTCTT
1 CTTCTTCTT
165174 CTTCTTCTT
1 CTTCTTCTT
165183 C-TCTTTCTT
1 CTTC-TTCTT
*
165192 CTTTTTCTT
1 CTTCTTCTT
*
165201 CTTCTTTTT
1 CTTCTTCTT
165210 CTTCT
1 CTTCT
165215 GTTTTGGTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
8 4 0.10
9 36 0.88
10 1 0.02
ACGTcount: A:0.02, C:0.27, G:0.02, T:0.69
Consensus pattern (9 bp):
CTTCTTCTT
Found at i:165184 original size:12 final size:12
Alignment explanation
Indices: 165156--165214 Score: 59
Period size: 12 Copynumber: 4.9 Consensus size: 12
165146 AAAAGGCAAC
165156 CTTCTTCATT-TT
1 CTTCTTC-TTCTT
*
165168 GTTCTTCTTCTT
1 CTTCTTCTTCTT
165180 CTTC-TCTTTCTT
1 CTTCTTC-TTCTT
*
165192 CTTTTTCTTCTT
1 CTTCTTCTTCTT
*
165204 CTTTTTCTTCT
1 CTTCTTCTTCT
165215 GTTTTGGTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
11 4 0.10
12 35 0.85
13 2 0.05
ACGTcount: A:0.02, C:0.27, G:0.02, T:0.69
Consensus pattern (12 bp):
CTTCTTCTTCTT
Found at i:167248 original size:14 final size:14
Alignment explanation
Indices: 167220--167261 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
167210 TGGACAATTA
*
167220 AAATGAAAATAAAAT
1 AAATAAAAAT-AAAT
*
167235 TAATAAAAATAAAT
1 AAATAAAAATAAAT
167249 AAATAAAAATAAA
1 AAATAAAAATAAA
167262 CAACAACGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.21
Consensus pattern (14 bp):
AAATAAAAATAAAT
Found at i:167351 original size:36 final size:37
Alignment explanation
Indices: 167304--167380 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
167294 TTCTACAAAC
* *
167304 TATATAATATATA-TTTTCAAAA-GTATTTTAAAATTA
1 TATATAATATATATTTTTAAAAACGT-TTTCAAAATTA
*
167340 TATATTATATATATTTTTAAAAACGTTTTCAAAATTA
1 TATATAATATATATTTTTAAAAACGTTTTCAAAATTA
167377 TATA
1 TATA
167381 GTTTTCAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 12 0.33
37 22 0.61
38 2 0.06
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (37 bp):
TATATAATATATATTTTTAAAAACGTTTTCAAAATTA
Found at i:167561 original size:35 final size:36
Alignment explanation
Indices: 167484--167597 Score: 104
Period size: 36 Copynumber: 3.1 Consensus size: 36
167474 TTTAAAAAAT
* * * **
167484 TATATTTATTTTAAAAATGTTTTTTTAAAACCGTATAA
1 TATATTTATCTTAAAAACG--TTTTAAAAACTATATAA
*
167522 TATATTT-TCTTAAAAACGTTTTAAAAACTATATAT
1 TATATTTATCTTAAAAACGTTTTAAAAACTATATAA
* * ** *
167557 TATATTTATTTTCAAAGTGTTTTAAAAACTATAAAA
1 TATATTTATCTTAAAAACGTTTTAAAAACTATATAA
167593 TATAT
1 TATAT
167598 AGATGTTTCA
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
35 20 0.32
36 27 0.43
37 9 0.14
38 7 0.11
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.47
Consensus pattern (36 bp):
TATATTTATCTTAAAAACGTTTTAAAAACTATATAA
Found at i:167625 original size:38 final size:37
Alignment explanation
Indices: 167534--167641 Score: 128
Period size: 36 Copynumber: 2.9 Consensus size: 37
167524 TATTTTCTTA
* * *
167534 AAAACGTTTTAAAAACTATATATTATATTTAT-TTTC
1 AAAATGTTTTAAAAACTATATAATATATATATGTTTC
* * *
167570 AAAGTGTTTTAAAAACTATAAAATATATAGATGTTTC
1 AAAATGTTTTAAAAACTATATAATATATATATGTTTC
* *
167607 AAATATGTTTTCAAAACTATATTATATATATATGT
1 AAA-ATGTTTTAAAAACTATATAATATATATATGT
167642 ATATACAAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
36 26 0.44
37 7 0.12
38 26 0.44
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (37 bp):
AAAATGTTTTAAAAACTATATAATATATATATGTTTC
Found at i:168570 original size:105 final size:105
Alignment explanation
Indices: 168271--169138 Score: 1238
Period size: 105 Copynumber: 8.3 Consensus size: 105
168261 CATTGTTCCA
* * **
168271 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAATTG-TTGTTGACAA
* * * *
168335 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
64 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
** *
168377 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTGA-A-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAACC
168437 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * * *
168477 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGTTCTGGGATTGGGAAGTTGTTGTTGACAAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAACC
*
168542 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
168582 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA-A-T--GAAATT-TTATTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAACC
168642 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
168682 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATT-GGAAAGTTGTTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAA-TTGTTGTTGACAAC
*
168746 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
168787 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAACC
168852 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
168892 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGG-AAATTG-TTGTTGACAA
168957 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
64 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
168999 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTG-TTGTTGACAAC
* * * *
169064 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
169105 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
169139 CGCGGATGGC
Statistics
Matches: 697, Mismatches: 48, Indels: 31
0.90 0.06 0.04
Matches are distributed among these distances:
100 171 0.25
101 7 0.01
102 8 0.01
103 5 0.01
104 8 0.01
105 279 0.40
106 100 0.14
107 98 0.14
109 21 0.03
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAACC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:168624 original size:205 final size:207
Alignment explanation
Indices: 168271--169138 Score: 1251
Period size: 205 Copynumber: 4.1 Consensus size: 207
168261 CATTGTTCCA
* * * **
168271 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
* * ** *
168336 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
** *
168401 TTGAAATTGAATCTGAA-TGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACT
131 TTGAAATTGGCTCTGAATTGAAATTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
168465 TGCGTTGTCTGG
196 TGCGTTGTCTGG
* * ** * *
168477 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGTTCTGGGATTGGGAAGTTG-TTGTTGACAAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
*
168541 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
* *
168606 TTGAAATTGGCTCTGAA-TGAAATTTTATTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACT
131 TTGAAATTGGCTCTGAATTGAAATTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
168670 TGCGTTGTCTGG
196 TGCGTTGTCTGG
*
168682 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATT-GGAAAGTTG-TTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA-TTGTTTGTTGACAA
*
168745 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAA
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAA
*
168810 GTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
130 GTTGAAATTGGCTCTGA-ATT--GAAATT-TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
168875 GAACTTGCGTTGTCTGG
191 GAACTTGCGTTGTCTGG
* *
168892 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGG-AAATTGTTTGTTGACAA
* *
168957 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCATTGTGAA
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAA
* *
169022 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGT
130 GTTGAAATTGGCTCTG-AATTGA-AA--T-TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
* *
169087 TGAACTTGTGTTGTCTCG
190 TGAACTTGCGTTGTCTGG
* * *
169105 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
169139 CGCGGATGGC
Statistics
Matches: 603, Mismatches: 42, Indels: 24
0.90 0.06 0.04
Matches are distributed among these distances:
204 4 0.01
205 276 0.46
206 46 0.08
207 1 0.00
209 5 0.01
210 94 0.16
211 6 0.01
212 93 0.15
213 53 0.09
214 4 0.01
216 21 0.03
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (207 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
TTGAAATTGGCTCTGAATTGAAATTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
TGCGTTGTCTGG
Found at i:168833 original size:310 final size:311
Alignment explanation
Indices: 168271--169138 Score: 1309
Period size: 310 Copynumber: 2.8 Consensus size: 311
168261 CATTGTTCCA
* * *
168271 AGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCT-GAA-C-TGAAATTGTTTATTGACAA
* * * *
168335 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAA
62 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
**
168400 GTTGAAATTGAATCTGAA-TGAAA-TT-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
127 GTTGAAATTGGCTCTGAATTGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
* * *
168462 ACTTGCGTTGTCTGGAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGTTCTGGGATTGGGAAG
192 ACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAG
168527 TTGTTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
257 TTGTTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
*
168582 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAA-TGAAA-T-TTTATTGACAAGCAG
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAACTGAAATTGTTTATTGACAACCAG
168644 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
168709 AAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
131 AAATTGGCTCTGA-ATT-GAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
*
168774 TTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTT
194 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTT
* *
168839 GTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
259 GTTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
*
168892 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTG-AACT--G-AAATTGTTTATTGACAA
*
168957 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCATTGTGAA
62 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
* * *
169022 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGT
127 GTTGAAATTGGCTCTG-AATTGA-AAGTTG-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGT
* * * * *
169087 TGAACTTGTGTTGTCTCGAGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
189 TGAACTTGCGTTGTCTGGAGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
169139 CGCGGATGGC
Statistics
Matches: 511, Mismatches: 27, Indels: 28
0.90 0.05 0.05
Matches are distributed among these distances:
305 85 0.17
306 2 0.00
307 5 0.01
308 4 0.01
309 2 0.00
310 193 0.38
311 37 0.07
312 2 0.00
314 1 0.00
315 3 0.01
316 3 0.01
317 99 0.19
318 50 0.10
319 3 0.01
321 22 0.04
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (311 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAACTGAAATTGTTTATTGACAACCAG
CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
AAATTGGCTCTGAATTGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
GCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGT
TGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
Found at i:169878 original size:67 final size:66
Alignment explanation
Indices: 169743--169900 Score: 176
Period size: 68 Copynumber: 2.4 Consensus size: 66
169733 AAGATATCTG
* * **
169743 TTGTTTCATGAGAAA-TGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGA
1 TTGTTTCAAGAGAAACT-ATCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGA
169807 TTT
65 -TT
* ** * *
169810 TGTGTTTCAAGAGTAACTATCTCAAGGGCGACAAAATT-TGTTTTAGGGGAAATAAATTCAAAGG
1 T-TGTTTCAAGAGAAACTATCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGA
169874 TT
65 TT
* *
169876 TTGTTTCAAGGGAAACTGTCTCAAG
1 TTGTTTCAAGAGAAACTATCTCAAG
169901 ATAGACGAAA
Statistics
Matches: 77, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
65 21 0.27
66 3 0.04
67 23 0.30
68 29 0.38
69 1 0.01
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.33
Consensus pattern (66 bp):
TTGTTTCAAGAGAAACTATCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGAT
T
Found at i:169917 original size:65 final size:67
Alignment explanation
Indices: 169744--170207 Score: 184
Period size: 73 Copynumber: 6.7 Consensus size: 67
169734 AGATATCTGT
* * * * ** *
169744 TGTTTCATGAGAAA-TGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TGTTTCAAGAGAAACT-ATCTCAAGAGAGACAAAATT-TGTTTTAAGGGAAATAAATTCAAAGAG
169808 TTTG
64 TTTG
* * * *
169812 TGTTTCAAGAGTAACTATCTCAAGGGCGACAAAATTTGTTTTAGGGGAAATAAATTCAAAG-GTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAGTT
169876 T-
66 TG
* * * * * *
169877 TGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACT--GTCTCAAGAG
1 TGTTTCAAGAGAAACTATCTCAAGAGAGAC-AAAATTTGTTTTAAGGGAAA-TAAAT-TCAA-AG
*
169939 AGACAAAACTT-
62 AG------TTTG
* * * * * ** * * * * * *
169950 AGTTCCAAAAGAAACTGTCTCAAGGGAGACGGAATTTGTTTCAAAGAAAACATATTCAAATA-TT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAGTT
170014 T-
66 TG
* * * * *
170015 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACT--GTCTCAATAGA
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTTAAGGGAAA-TAAAT-TCAA-AGA
**
170078 CGAAAAT-
63 -G--TTTG
* * *
170085 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACT--GTCTCAAGAGA
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTTAAGGGAAA-TAAAT-TCAA-AGA
*
170148 GAAAAAAATT-
63 G------TTTG
* *
170158 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAA
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTTAAGGGAAA
170208 CTGTCTCAAG
Statistics
Matches: 316, Mismatches: 54, Indels: 47
0.76 0.13 0.11
Matches are distributed among these distances:
64 2 0.01
65 86 0.27
66 12 0.04
67 23 0.07
68 29 0.09
69 2 0.01
70 61 0.19
72 4 0.01
73 96 0.30
74 1 0.00
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (67 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAGTT
TG
Found at i:169927 original size:36 final size:36
Alignment explanation
Indices: 169875--170227 Score: 390
Period size: 36 Copynumber: 10.0 Consensus size: 36
169865 ATTCAAAGGT
* *
169875 TTTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
169912 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * **
169947 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGGAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
169984 TTTGTTTCAA-AGAAAACATAT-TC-----A-A-ATAT
1 TTTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
*
170013 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
170049 TTTATTTCAAGGGAAACTGTCTC-A-ATAGACGAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
170084 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
170119 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGAAAAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAG-ACAAAA
170156 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
170192 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGAAAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
170228 CTCTTCTAGT
Statistics
Matches: 269, Mismatches: 29, Indels: 37
0.80 0.09 0.11
Matches are distributed among these distances:
28 2 0.01
29 17 0.06
30 2 0.01
31 1 0.00
34 26 0.10
35 17 0.06
36 139 0.52
37 65 0.24
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:170109 original size:15 final size:15
Alignment explanation
Indices: 170055--170111 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
170045 AAAATTTATT
*
170055 TCAAGGGAAACTGTC
1 TCAAGAGAAACTGTC
* *
170070 TCAATAGACGAAAATTGTT
1 TC-A-AGA-G-AAACTGTC
170089 TCAAGAGAAACTGTC
1 TCAAGAGAAACTGTC
170104 TCAAGAGA
1 TCAAGAGA
170112 GACAAAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 5 0.15
18 2 0.06
19 8 0.24
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (15 bp):
TCAAGAGAAACTGTC
Found at i:170191 original size:73 final size:73
Alignment explanation
Indices: 170013--170227 Score: 366
Period size: 73 Copynumber: 3.0 Consensus size: 73
170003 ATTCAAATAT
* * *
170013 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAATAGA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
170078 CG---AAAA
66 -GAAAAAAA
170084 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
170148 GAAAAAAA
66 GAAAAAAA
170156 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
170221 GAAAAAA
66 GAAAAAA
170228 CTCTTCTAGT
Statistics
Matches: 137, Mismatches: 3, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
69 1 0.01
70 61 0.45
72 4 0.03
73 71 0.52
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.25
Consensus pattern (73 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
GAAAAAAA
Found at i:170330 original size:143 final size:142
Alignment explanation
Indices: 169879--170333 Score: 346
Period size: 143 Copynumber: 3.2 Consensus size: 142
169869 AAAGGTTTTG
* * * *
169879 TTTCAAGGGAAACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGA-GA
1 TTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAATTTATTTCAAGGGAAACTGTCTCAAGAGACGA
* * * * **
169942 CAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGGAATTTGTTTCAA-AGAAAAC--AT-
65 AAAAAC-T--TT-CAAGAGAAACGGTCTCAAGAGAGACAAAATTTGTTTCAAGA-AAAACGAATC
*** * * *
170003 ---A-TTCAAATATTTTG
125 AAGAGAGAAAAAAATTTC
* *
170017 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAATAGACGAA
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGACGAA
*** * ** **
170082 AATTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAG
66 AAAACTTTCAAGAGAAACGGTCTCAAGAGAGACAAAATTTGTTTCAAGAAAAAC-GAATCAAGAG
*
170147 AGAAAAAAATTTG
130 AGAAAAAAATTTC
*
170160 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA-GAA
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGACGAA
* * * *
170224 AAAACTCTTCTAGTGAAAACGGTCTCAAGCGAGACAAATATTAT-TTT-AAGAAAAAC-AATCAT
66 AAAACT-TTCAAGAG-AAACGGTCTCAAGAGAGACAAA-ATT-TGTTTCAAGAAAAACGAATCAA
* *
170286 GAGTGAAATAAATCTTC
127 GAGAGAAAAAAAT-TTC
* * * *
170303 TTTCGAGTA-AAACAGTCCCAAGTGAGACAAA
1 TTTCAAG-AGAAACTGTCTCAAGAGAGACAAA
170334 GTCTGTTTTA
Statistics
Matches: 258, Mismatches: 42, Indels: 29
0.78 0.13 0.09
Matches are distributed among these distances:
135 39 0.15
136 2 0.01
137 4 0.02
138 54 0.21
139 4 0.02
142 21 0.08
143 99 0.38
144 28 0.11
145 6 0.02
146 1 0.00
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.25
Consensus pattern (142 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGACGAA
AAAACTTTCAAGAGAAACGGTCTCAAGAGAGACAAAATTTGTTTCAAGAAAAACGAATCAAGAGA
GAAAAAAATTTC
Found at i:171251 original size:22 final size:22
Alignment explanation
Indices: 171152--171244 Score: 159
Period size: 22 Copynumber: 4.2 Consensus size: 22
171142 TTGTGTTTGG
* *
171152 TCAAAGGTTTGGCATTTGATAC
1 TCAAAGGTTTGACATTTGATGC
171174 TCAAAGGTTTGACATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
171196 TCAAAGGTTTGACATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
*
171218 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTTGATGC
171240 TCAAA
1 TCAAA
171245 AGATTGATGG
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 68 1.00
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (22 bp):
TCAAAGGTTTGACATTTGATGC
Found at i:171751 original size:11 final size:12
Alignment explanation
Indices: 171733--171761 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
171723 TGCTCATATG
171733 TGTTTCTCTGGA
1 TGTTTCTCTGGA
171745 T-TTTCTCTGGA
1 TGTTTCTCTGGA
171756 TGTTTC
1 TGTTTC
171762 ATGATCTTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.07, C:0.17, G:0.21, T:0.55
Consensus pattern (12 bp):
TGTTTCTCTGGA
Found at i:171913 original size:16 final size:16
Alignment explanation
Indices: 171894--171979 Score: 50
Period size: 17 Copynumber: 5.1 Consensus size: 16
171884 TCTTTTTGAT
171894 TTTTGCTCTTTTTTTC
1 TTTTGCTCTTTTTTTC
* *
171910 TTTTGTTCTTGTTTCTC
1 TTTTGCTCTT-TTTTTC
* * *
171927 TTTTTCTTTGTTTTTTTT
1 TTTTGC--TCTTTTTTTC
171945 TTTTGCT-TTTTTGCTTC
1 TTTTGCTCTTTTT--TTC
*
171962 TTTT-CTTTTTTTGTTC
1 TTTTGCTCTTTTT-TTC
171978 TT
1 TT
171980 GATTGGATCT
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
15 5 0.09
16 17 0.31
17 20 0.37
18 9 0.17
19 3 0.06
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.78
Consensus pattern (16 bp):
TTTTGCTCTTTTTTTC
Found at i:171955 original size:25 final size:25
Alignment explanation
Indices: 171882--171974 Score: 75
Period size: 25 Copynumber: 3.7 Consensus size: 25
171872 TTTGTCCCTT
** *
171882 TTTCTTTTTGATTTTTGCTCTTTT-
1 TTTCTTTTTTTTTTTTGCTTTTTTC
*
171906 TTTCTTTTGTTCTTGTTT-CTCTTTTTC
1 TTTCTTTT-TT-TTTTTTGCT-TTTTTC
*
171933 TTTGTTTTTTTTTTTTGCTTTTTTGC
1 TTTCTTTTTTTTTTTTGCTTTTTT-C
*
171959 -TTCTTTTCTTTTTTTG
1 TTTCTTTTTTTTTTTTG
171975 TTCTTGATTG
Statistics
Matches: 55, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
24 8 0.15
25 27 0.49
26 13 0.24
27 7 0.13
ACGTcount: A:0.01, C:0.13, G:0.09, T:0.77
Consensus pattern (25 bp):
TTTCTTTTTTTTTTTTGCTTTTTTC
Found at i:171973 original size:8 final size:8
Alignment explanation
Indices: 171900--171973 Score: 69
Period size: 8 Copynumber: 9.1 Consensus size: 8
171890 TGATTTTTGC
171900 TCTTTTTT
1 TCTTTTTT
*
171908 TCTTTTGT
1 TCTTTTTT
*
171916 TC-TTGTT
1 TCTTTTTT
*
171923 TCTCTTTT
1 TCTTTTTT
171931 TCTTTGTTT
1 TCTTT-TTT
*
171940 TTTTTTTT
1 TCTTTTTT
171948 TGCTTTTTT
1 T-CTTTTTT
* *
171957 GCTTCTTT
1 TCTTTTTT
171965 TCTTTTTT
1 TCTTTTTT
171973 T
1 T
171974 GTTCTTGATT
Statistics
Matches: 51, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
7 5 0.10
8 33 0.65
9 13 0.25
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.80
Consensus pattern (8 bp):
TCTTTTTT
Found at i:176229 original size:14 final size:14
Alignment explanation
Indices: 176201--176242 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
176191 TGGACAATTA
*
176201 AAATGAAAATAAAAT
1 AAATAAAAAT-AAAT
*
176216 TAATAAAAATAAAT
1 AAATAAAAATAAAT
176230 AAATAAAAATAAA
1 AAATAAAAATAAA
176243 CAACAACGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.21
Consensus pattern (14 bp):
AAATAAAAATAAAT
Found at i:176332 original size:36 final size:36
Alignment explanation
Indices: 176285--176360 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
176275 TTCTACAAAC
* *
176285 TATATAATATATATTTTCAAAA-GTATTTTAAAATTA
1 TATATAATATATATTTTAAAAACGT-TTTCAAAATTA
*
176321 TATATTATATATATTTTAAAAACGTTTTCAAAATTA
1 TATATAATATATATTTTAAAAACGTTTTCAAAATTA
176357 TATA
1 TATA
176361 GTTTTCAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 34 0.94
37 2 0.06
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (36 bp):
TATATAATATATATTTTAAAAACGTTTTCAAAATTA
Found at i:177870 original size:6 final size:6
Alignment explanation
Indices: 177835--177868 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
177825 AAGTTAAAAA
* *
177835 AACCCA AACCCT AACCCT AACCCT AACCTT AACC
1 AACCCT AACCCT AACCCT AACCCT AACCCT AACC
177869 TTGACCTGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.38, C:0.47, G:0.00, T:0.15
Consensus pattern (6 bp):
AACCCT
Found at i:180155 original size:55 final size:55
Alignment explanation
Indices: 180043--180172 Score: 154
Period size: 55 Copynumber: 2.4 Consensus size: 55
180033 AGGGAACTCA
* ** *
180043 AACTC-GGGTGGTGTCGGACACACGTATCAAACTCGATTAACAAAGCATTTCACG
1 AACTCGGGGTGGTGTCGGACACACGTATCAAACACGAGAAACAAAGCATTCCACG
* * **
180097 AACTCGGGGTGGTGTCGGACACACGTGTCAAACACGAGAAACAATGCATTCCTTG
1 AACTCGGGGTGGTGTCGGACACACGTATCAAACACGAGAAACAAAGCATTCCACG
***
180152 AACTCGATTTGGTGTCGGACA
1 AACTCGGGGTGGTGTCGGACA
180173 TACGAGTAAC
Statistics
Matches: 64, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
54 5 0.08
55 59 0.92
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.22
Consensus pattern (55 bp):
AACTCGGGGTGGTGTCGGACACACGTATCAAACACGAGAAACAAAGCATTCCACG
Found at i:182048 original size:20 final size:20
Alignment explanation
Indices: 182023--182063 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
182013 TTCGTCTGTT
*
182023 GCCCGCTGGCCGCTGCCGCC
1 GCCCGCCGGCCGCTGCCGCC
* *
182043 GCCCGCCGTCTGCTGCCGCC
1 GCCCGCCGGCCGCTGCCGCC
182063 G
1 G
182064 TCAGCCGTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.00, C:0.54, G:0.34, T:0.12
Consensus pattern (20 bp):
GCCCGCCGGCCGCTGCCGCC
Found at i:182070 original size:20 final size:20
Alignment explanation
Indices: 182034--182072 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
182024 CCCGCTGGCC
*
182034 GCTGCCGCCGCCCGCCGTCT
1 GCTGCCGCCGCCAGCCGTCT
*
182054 GCTGCCGCCGTCAGCCGTC
1 GCTGCCGCCGCCAGCCGTC
182073 CGCCGCCACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.03, C:0.51, G:0.31, T:0.15
Consensus pattern (20 bp):
GCTGCCGCCGCCAGCCGTCT
Done.