Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005718.1 Hibiscus syriacus cultivar Beakdansim tig00013370_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: 146329
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:2176 original size:18 final size:19
Alignment explanation
Indices: 2149--2184 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2139 GCTATGTTAA
*
2149 AAATACTTTTAAAGTTATT
1 AAATACTTTTAAAATTATT
2168 AAATA-TTTTAAAATTAT
1 AAATACTTTTAAAATTAT
2185 AAAACTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (19 bp):
AAATACTTTTAAAATTATT
Found at i:20813 original size:38 final size:38
Alignment explanation
Indices: 20762--20840 Score: 140
Period size: 38 Copynumber: 2.1 Consensus size: 38
20752 TTTATGGACA
* *
20762 TTACGGTGTATGCACCTAAAAGTATAACATTAGAAATG
1 TTACGGTGTATGCACCTAAAAGTATAACATTAAAAACG
20800 TTACGGTGTATGCACCTAAAAGTATAACATTAAAAACG
1 TTACGGTGTATGCACCTAAAAGTATAACATTAAAAACG
20838 TTA
1 TTA
20841 GACACCGAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (38 bp):
TTACGGTGTATGCACCTAAAAGTATAACATTAAAAACG
Found at i:21328 original size:17 final size:17
Alignment explanation
Indices: 21306--21345 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
21296 AAATTACTTT
21306 ATTTAAATTCATTT-TAA
1 ATTTAAATT-ATTTATAA
*
21323 ATTTAAATTATTTATGA
1 ATTTAAATTATTTATAA
21340 ATTTAA
1 ATTTAA
21346 TACACAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTAAATTATTTATAA
Found at i:21650 original size:12 final size:12
Alignment explanation
Indices: 21633--21657 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
21623 TGATTATAGA
21633 GTCAAATGGAAG
1 GTCAAATGGAAG
21645 GTCAAATGGAAG
1 GTCAAATGGAAG
21657 G
1 G
21658 ATCCGAAGGC
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:0.40, C:0.08, G:0.36, T:0.16
Consensus pattern (12 bp):
GTCAAATGGAAG
Found at i:33966 original size:21 final size:21
Alignment explanation
Indices: 33922--33966 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
33912 GATTTCTGGG
* * *
33922 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCACT
*
33943 CAAGGGGAACCGATACCCCCT
1 CAAGGGGAACCGATACCCACT
33964 CAA
1 CAA
33967 ACGAACCAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.13
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCACT
Found at i:35591 original size:23 final size:23
Alignment explanation
Indices: 35560--35619 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
35550 CATTTTATAT
*
35560 GGCAATTCGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
*
35583 GGCACTTCGGTGCAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
*
35606 AGCACTTCGGTGCA
1 GGCACTTCGGTGCA
35620 TTTATACGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:49529 original size:15 final size:15
Alignment explanation
Indices: 49509--49543 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
49499 GTTAGATTCT
49509 AATTATTTAAATAAA
1 AATTATTTAAATAAA
*
49524 AATTATTTATATAAA
1 AATTATTTAAATAAA
49539 AATTA
1 AATTA
49544 GATTCAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATTATTTAAATAAA
Found at i:49669 original size:27 final size:27
Alignment explanation
Indices: 49630--49683 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
49620 TGAACAAGTT
*
49630 AAGCACGACTCAACTAACTAACGACTC
1 AAGCACAACTCAACTAACTAACGACTC
*
49657 AAGCACAATTCAACTAACTAACGACTC
1 AAGCACAACTCAACTAACTAACGACTC
49684 GCTAGATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.43, C:0.31, G:0.09, T:0.17
Consensus pattern (27 bp):
AAGCACAACTCAACTAACTAACGACTC
Found at i:49790 original size:26 final size:27
Alignment explanation
Indices: 49761--49811 Score: 95
Period size: 26 Copynumber: 1.9 Consensus size: 27
49751 ACACATGCAC
49761 AACTTTGATATAA-ATCACAAGGACCT
1 AACTTTGATATAAGATCACAAGGACCT
49787 AACTTTGATATAAGATCACAAGGAC
1 AACTTTGATATAAGATCACAAGGAC
49812 TCGCATCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (27 bp):
AACTTTGATATAAGATCACAAGGACCT
Found at i:52629 original size:20 final size:20
Alignment explanation
Indices: 52585--52993 Score: 374
Period size: 20 Copynumber: 20.2 Consensus size: 20
52575 AATGACCAAC
*
52585 AAAATCGCAACGCGAAAT-A-
1 AAAATCGCAACGCG-ATTCAG
*
52604 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTCAG
* **
52624 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTCAG
52644 AAAATCGCAACGCGATATTCCA-
1 AAAATCGCAACGCG--ATT-CAG
* * *
52666 AGAATCGCAATGCGATTAAG
1 AAAATCGCAACGCGATTCAG
* *
52686 AGAATCGCAACGCGAAAT-A-
1 AAAATCGCAACGCG-ATTCAG
*
52705 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTCAG
* **
52725 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTCAG
52745 AAAATCGCAACGCGATATTCCA-
1 AAAATCGCAACGCG--ATT-CAG
* * *
52767 AGAATCGCAATGCGATTAAG
1 AAAATCGCAACGCGATTCAG
*
52787 AGAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
*
52809 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
52829 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
52849 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
52869 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
52889 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
52909 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
52929 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
* *
52949 AGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
*
52969 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
52989 AAAAT
1 AAAAT
52994 GAGTAAATTC
Statistics
Matches: 330, Mismatches: 33, Indels: 53
0.79 0.08 0.13
Matches are distributed among these distances:
18 4 0.01
19 40 0.12
20 228 0.69
21 14 0.04
22 41 0.12
23 3 0.01
ACGTcount: A:0.42, C:0.23, G:0.20, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTCAG
Found at i:52705 original size:101 final size:102
Alignment explanation
Indices: 52587--52940 Score: 472
Period size: 101 Copynumber: 3.5 Consensus size: 102
52577 TGACCAACAA
*
52587 AATCGCAACGCGAAAT-AAAAATCGCAACGCGATTTAGAAAATCGCAACGTTGAAAAGAAAATCG
1 AATCGCAACGCGAAATCAAAAATCGCAACGCGATTCAGAAAATCGCAACGTTGAAAAGAAAATCG
52651 CAACGCGATATTCCAAGAATCGCAATGCGATTAAGAG
66 CAACGCGATATTCCAAGAATCGCAATGCGATTAAGAG
*
52688 AATCGCAACGCGAAAT-AAAAATCGCAACGCGATTTAGAAAATCGCAACGTTGAAAAGAAAATCG
1 AATCGCAACGCGAAATCAAAAATCGCAACGCGATTCAGAAAATCGCAACGTTGAAAAGAAAATCG
52752 CAACGCGATATTCCAAGAATCGCAATGCGATTAAGAG
66 CAACGCGATATTCCAAGAATCGCAATGCGATTAAGAG
** * * ****
52789 AATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACG-CGATTCCAAGAA
1 AATCGCAACGCGA-AAT-CAAAAATCGCAACGCGATTCAGAAAATCGCAACGTTGAAAAGAA-AA
* * *
52853 TCGCAACGCG--ATT-CAGAAAATCGCAACGCGATTCCA-AG
63 TCGCAACGCGATATTCCA-AGAATCGCAATGCGATT-AAGAG
*
52891 AATCGCAACGCG-ATTCAGAAAATCGCAACGCGATTCAGAAAATCGCAACG
1 AATCGCAACGCGAAATCA-AAAATCGCAACGCGATTCAGAAAATCGCAACG
52941 CGATTCCAAG
Statistics
Matches: 232, Mismatches: 14, Indels: 15
0.89 0.05 0.06
Matches are distributed among these distances:
99 2 0.01
100 33 0.14
101 116 0.50
102 33 0.14
103 5 0.02
104 43 0.19
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.16
Consensus pattern (102 bp):
AATCGCAACGCGAAATCAAAAATCGCAACGCGATTCAGAAAATCGCAACGTTGAAAAGAAAATCG
CAACGCGATATTCCAAGAATCGCAATGCGATTAAGAG
Found at i:53075 original size:6 final size:6
Alignment explanation
Indices: 53064--53150 Score: 174
Period size: 6 Copynumber: 14.5 Consensus size: 6
53054 GACACGTATT
53064 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
53112 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
53151 CGAGACGAGA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 81 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:53662 original size:6 final size:6
Alignment explanation
Indices: 53651--53689 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
53641 TCTCGTCTCG
53651 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
53690 AATACGTGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.00, C:0.15, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:53840 original size:40 final size:40
Alignment explanation
Indices: 53785--54272 Score: 624
Period size: 40 Copynumber: 12.1 Consensus size: 40
53775 GAATTTACTC
53785 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
53825 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
53865 ATTTTCTTAATCGCGTTGCGATTTTCTT--AATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGA--TTCTTGGAATCGCGTTGCG
53905 A--TTCTTGGAATCGCGTTGCGATTTTCTT--AATCGCGTTGCG
1 ATTTTCTT--AATCGCGTTGCGA--TTCTTGGAATCGCGTTGCG
*
53945 ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
53985 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
54025 ATTTTCTTAATCGCGTTGCGATTTTCTT--AATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGA--TTCTTGGAATCGCGTTGCG
*
54065 ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
54105 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
* *
54147 ATTCTCTTAATCGCATTGCGATTCTTGGAATATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
* **** *
54189 ATTTTCTT--TTGACCGTTGCGATT-TTCTTTTCAACGTTGCG
1 ATTTTCTTAATCG--CGTTGCGATTCTTGGAATC-GCGTTGCG
* * *
54229 ATTTTCTAAATCGCGTTGCGATT-TT-TATTTCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGA-ATCGCGTTGCG
54268 ATTTT
1 ATTTT
54273 GTTGGTCATT
Statistics
Matches: 409, Mismatches: 19, Indels: 41
0.87 0.04 0.09
Matches are distributed among these distances:
38 15 0.04
39 15 0.04
40 294 0.72
41 3 0.01
42 82 0.20
ACGTcount: A:0.15, C:0.20, G:0.23, T:0.42
Consensus pattern (40 bp):
ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
Found at i:54245 original size:20 final size:20
Alignment explanation
Indices: 53785--54272 Score: 542
Period size: 20 Copynumber: 24.2 Consensus size: 20
53775 GAATTTACTC
53785 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
53805 A--TTCTTGGAATCGCGTTGCG
1 ATTTTCTT--AATCGCGTTGCG
53825 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
53845 A--TTCTTGGAATCGCGTTGCG
1 ATTTTCTT--AATCGCGTTGCG
53865 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
53885 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
53905 A--TTCTTGGAATCGCGTTGCG
1 ATTTTCTT--AATCGCGTTGCG
53925 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
*
53945 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
53965 A--TTCTTGGAATCGCGTTGCG
1 ATTTTCTT--AATCGCGTTGCG
53985 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
54005 A--TTCTTGGAATCGCGTTGCG
1 ATTTTCTT--AATCGCGTTGCG
54025 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
54045 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
*
54065 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
54085 A--TTCTTGGAATCGCGTTGCG
1 ATTTTCTT--AATCGCGTTGCG
54105 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
***
54125 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCG
* *
54147 ATTCTCTTAATCGCATTGCG
1 ATTTTCTTAATCGCGTTGCG
***
54167 ATTCTTGGAATATCGCGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCG
*
54189 ATTTTCTT--TTGACCGTTGCG
1 ATTTTCTTAATCG--CGTTGCG
* *
54209 ATTTTCTT-TTCAACGTTGCG
1 ATTTTCTTAATC-GCGTTGCG
*
54229 ATTTTCTAAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
*
54249 A-TTT-TTATTTCGCGTTGCG
1 ATTTTCTTA-ATCGCGTTGCG
54268 ATTTT
1 ATTTT
54273 GTTGGTCATT
Statistics
Matches: 405, Mismatches: 28, Indels: 70
0.81 0.06 0.14
Matches are distributed among these distances:
18 32 0.08
19 14 0.03
20 290 0.72
21 12 0.03
22 57 0.14
ACGTcount: A:0.15, C:0.20, G:0.23, T:0.42
Consensus pattern (20 bp):
ATTTTCTTAATCGCGTTGCG
Found at i:56816 original size:23 final size:23
Alignment explanation
Indices: 56786--56844 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
56776 TACAACTACC
56786 TATTACATTATATAAACGATACA
1 TATTACATTATATAAACGATACA
* * *
56809 TATTACATTATATAAGCGCTACC
1 TATTACATTATATAAACGATACA
*
56832 TATTACATCATAT
1 TATTACATTATAT
56845 TTTTACCTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (23 bp):
TATTACATTATATAAACGATACA
Found at i:57292 original size:23 final size:23
Alignment explanation
Indices: 57262--57324 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
57252 ACTTTACAAC
57262 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
57285 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
57308 TACCTATTACATCATAT
1 TACCTATTACATTATAT
57325 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:57768 original size:23 final size:23
Alignment explanation
Indices: 57738--57800 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
57728 ACTTTACAAC
*
57738 TACCTATTACATTATATAAATGA
1 TACCTATTACATTATATAAACGA
* *
57761 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
57784 TACCTATTACATCATAT
1 TACCTATTACATTATAT
57801 TTTACCTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:58241 original size:23 final size:23
Alignment explanation
Indices: 58211--58273 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
58201 ACTTTACAAC
*
58211 TACCTATTACATTATATAAATGA
1 TACCTATTACATTATATAAACGA
* *
58234 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
58257 TACCTATTACATCATAT
1 TACCTATTACATTATAT
58274 TTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:58754 original size:23 final size:23
Alignment explanation
Indices: 58691--58746 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
58681 TACTTTACAA
58691 CTACCTATTACATTATATAAACG
1 CTACCTATTACATTATATAAACG
* *
58714 ATACCTATTACATTATATAAGCG
1 CTACCTATTACATTATATAAACG
58737 CTACCTATTA
1 CTACCTATTA
58747 TATCATATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (23 bp):
CTACCTATTACATTATATAAACG
Found at i:58756 original size:481 final size:481
Alignment explanation
Indices: 56377--58987 Score: 4772
Period size: 481 Copynumber: 5.5 Consensus size: 481
56367 TTATAATATG
*
56377 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATAATTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
* *
56442 TCAATTTTTTTTAATAGTGTTTCATGTTTTTCACCTACAATATTAATTTAATAATTTCATTTGCA
66 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
56507 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
131 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
* *
56572 TAACCAAAGATAATAATAAATATGTAATATATATTTTTATTATTTTTAATTTAATAATAATATAT
196 TAACCAAAGATAATAATAAATATGT-ATATATATATTTATTGTTTTTAATTTAATAATAATATAT
*
56637 ATCCTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
260 ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
*
56702 CAAAAGATAACCTTAAATTAATGTTTTCCACAATGAAAAAAGTATGGACACTTTTATAAAAATGA
325 CAAAAGATAACCTTAAATTAATGTTTTCCACAATGAAAAAAGTATGGACACTTTTATAAAAAGGA
*
56767 TAGATACTTTACAACTACCTATTACATTATATAAACGATACATATTACATTATATAAGCGCTACC
390 TAGATACTTTACAACTACCTATTACATTATATAAACGATACCTATTACATTATATAAGCGCTACC
56832 TATTACATCATATTTTTACCTATTATA
455 TATTACATCATATTTTTACCTATTATA
* * *
56859 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCAACATTTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATA-CTTTTTTTAAAGTTATGTAATTTATGT
*
56924 TTCAA-TTTTTTTAATAGTGTTTTATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTAC
65 TTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTAC
56988 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
130 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
*
57053 TTAACCAAAGATAATAATAAATATGTA-ATATATGTTTATTGTTTTTAATTTAATAATAATATAT
195 TTAACCAAAGATAATAATAAATATGTATATATATATTTATTGTTTTTAATTTAATAATAATATAT
*
57117 ATCGTAACGTAAAAAATAAATTATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
260 ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
57182 CAAAAGATAACCTTAAATTAATGTTTTCCACAATGAAAAAAGTATGGACACTTTTATAAAAAGGA
325 CAAAAGATAACCTTAAATTAATGTTTTCCACAATGAAAAAAGTATGGACACTTTTATAAAAAGGA
*
57247 TAGACACTTTACAACTACCTATTACATTATATAAACGATACCTATTACATTATATAAGCGCTACC
390 TAGATACTTTACAACTACCTATTACATTATATAAACGATACCTATTACATTATATAAGCGCTACC
57312 TATTACATCATATTTTTACCTATTATA
455 TATTACATCATATTTTTACCTATTATA
*
57339 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGACACTTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATAC-TTTTTTTAAAGTTATGTAATTTATGT
*
57404 TTCAATTTTTTTTAATAGTGTTTTATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTAC
65 TTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTAC
57469 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
130 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
57534 TTAACCAAAGATAATAATAAATATGTA-ATATATA-TTATTG-TTTTAATTTAATAATAATATAT
195 TTAACCAAAGATAATAATAAATATGTATATATATATTTATTGTTTTTAATTTAATAATAATATAT
*
57596 ATCGTAATGT-AAAAA-AAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
260 ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
*
57659 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTG-AAAAAGTATGGACACTTTTATAAAAAGGA
325 CAAAAGATAACCTTAAATTAATGTTTTCCACAATGAAAAAAGTATGGACACTTTTATAAAAAGGA
*
57723 TAGATACTTTACAACTACCTATTACATTATATAAATGATACCTATTACATTATATAAGCGCTACC
390 TAGATACTTTACAACTACCTATTACATTATATAAACGATACCTATTACATTATATAAGCGCTACC
57788 TATTACATCATA-TTTTACCTATTATA
455 TATTACATCATATTTTTACCTATTATA
*
57814 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGACACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
*
57879 TCAA-TTTTTTTAATAGTGTTTTATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
66 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
57943 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
131 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
58008 TAACCAAAGATAATAATAAATATG--TA-ATATA--TATTGTTTTTAATTTAAT-ATAATATATA
196 TAACCAAAGATAATAATAAATATGTATATATATATTTATTGTTTTTAATTTAATAATAATATATA
*
58067 TCGTAATGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
261 TCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
*
58132 AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGAT
326 AAAAGATAACCTTAAATTAATGTTTTCCACAATGAAAAAAGTATGGACACTTTTATAAAAAGGAT
*
58197 AGATACTTTACAACTACCTATTACATTATATAAATGATACCTATTACATTATATAAGCGCTACCT
391 AGATACTTTACAACTACCTATTACATTATATAAACGATACCTATTACATTATATAAGCGCTACCT
58262 ATTACATCATATTTTTACCTATTATA
456 ATTACATCATATTTTTACCTATTATA
58288 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATAC-TTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
58352 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
66 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
58417 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
131 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
*
58482 TAACCAAAGATAATAATAAATATGTAATATATATATTTATTGTTTTTAATATAATAATAATATAT
196 TAACCAAAGATAATAATAAATATGT-ATATATATATTTATTGTTTTTAATTTAATAATAATATAT
58547 ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
260 ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
58612 CAAAAGATAACCTTAAATTAATGTTTTCCACAATGAAAAAAGTATGGACACTTTTATAAAAAGGA
325 CAAAAGATAACCTTAAATTAATGTTTTCCACAATGAAAAAAGTATGGACACTTTTATAAAAAGGA
58677 TAGATACTTTACAACTACCTATTACATTATATAAACGATACCTATTACATTATATAAGCGCTACC
390 TAGATACTTTACAACTACCTATTACATTATATAAACGATACCTATTACATTATATAAGCGCTACC
*
58742 TATTATATCATATTTTTACCTATTATA
455 TATTACATCATATTTTTACCTATTATA
**
58769 TTGAAAGTGTCCATACTTTTTATAAAAATAATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
*
58834 TCAATTTTTTTTAATAGTATTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
66 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
* *
58899 CAAAAAATTATTTGATT-ATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATAT
131 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
58963 TAACCAAAGATAATAATAAATATGT
196 TAACCAAAGATAATAATAAATATGT
58988 TTTCCACAGT
Statistics
Matches: 2078, Mismatches: 33, Indels: 37
0.97 0.02 0.02
Matches are distributed among these distances:
470 24 0.01
471 22 0.01
472 84 0.04
473 285 0.14
474 230 0.11
475 52 0.03
476 104 0.05
477 83 0.04
478 10 0.00
479 31 0.01
480 342 0.16
481 491 0.24
482 289 0.14
483 31 0.01
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (481 bp):
TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
TAACCAAAGATAATAATAAATATGTATATATATATTTATTGTTTTTAATTTAATAATAATATATA
TCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
AAAAGATAACCTTAAATTAATGTTTTCCACAATGAAAAAAGTATGGACACTTTTATAAAAAGGAT
AGATACTTTACAACTACCTATTACATTATATAAACGATACCTATTACATTATATAAGCGCTACCT
ATTACATCATATTTTTACCTATTATA
Found at i:59184 original size:228 final size:229
Alignment explanation
Indices: 58786--59723 Score: 1702
Period size: 228 Copynumber: 4.1 Consensus size: 229
58776 TGTCCATACT
* ** *
58786 TTTTATAAAAATAATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAG
1 TTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATATTTTTTAATAG
*
58851 TATTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATT
66 TGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATT
58916 ATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATA
131 ATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATA
58981 AATATGTTTTCCACAGTGAAATAAGTATGGACAC
196 AATATGTTTTCCACAGTGAAATAAGTATGGACAC
59015 TTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAA-ATTTTTTAATAG
1 TTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATATTTTTTAATAG
59079 TGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATT
66 TGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATT
*
59144 TTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATA
131 ATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATA
59209 AATATGTTTTCCACAGTGAAATAAGTATGGACAC
196 AATATGTTTTCCACAGTGAAATAAGTATGGACAC
59243 TTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAA-ATTTTTTAATAG
1 TTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATATTTTTTAATAG
59307 TGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATT
66 TGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATT
* *
59372 ATTTGATATTTTATAAAATATTATTTAGAATTTATATTTAACAATATTAACCAAAAATAATAATA
131 ATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATA
**
59437 AATATGTTTTCCACAGTGAAATAAGTATAAACAC
196 AATATGTTTTCCACAGTGAAATAAGTATGGACAC
*
59471 TTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAG
1 TTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATATTTTTTAATAG
*
59536 TGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACACAAAATTATTTGATT
66 TGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATT
*
59601 GTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAAT
131 -ATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAAT
*
59666 AAATATATTTT-CACAGTGAAATAAGTATGGACAC
195 AAATATGTTTTCCACAGTGAAATAAGTATGGACAC
* *
59700 TTTTATAAAAAGGATAGATACTTT
1 TTTTATAAAAATGATATATACTTT
59724 ACAATATAAC
Statistics
Matches: 686, Mismatches: 21, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
228 448 0.65
229 167 0.24
230 71 0.10
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.45
Consensus pattern (229 bp):
TTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATATTTTTTAATAG
TGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATT
ATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATA
AATATGTTTTCCACAGTGAAATAAGTATGGACAC
Found at i:62447 original size:7 final size:7
Alignment explanation
Indices: 62383--62445 Score: 117
Period size: 7 Copynumber: 9.0 Consensus size: 7
62373 TATGGTTACC
62383 GGTTGAG
1 GGTTGAG
62390 GGTTGAG
1 GGTTGAG
62397 GGTTGAG
1 GGTTGAG
62404 GGTTGAG
1 GGTTGAG
62411 GGTTGAG
1 GGTTGAG
62418 GGTTGAG
1 GGTTGAG
62425 GGTTGAG
1 GGTTGAG
62432 GGTTGAG
1 GGTTGAG
*
62439 AGTTGAG
1 GGTTGAG
62446 AGAGGGGGTG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
7 55 1.00
ACGTcount: A:0.16, C:0.00, G:0.56, T:0.29
Consensus pattern (7 bp):
GGTTGAG
Found at i:63304 original size:11 final size:14
Alignment explanation
Indices: 63268--63294 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
63258 ATATTAAATA
63268 ATAAATATAATTAT
1 ATAAATATAATTAT
63282 ATAAATATAATTA
1 ATAAATATAATTA
63295 AAAAATAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAAATATAATTAT
Found at i:67196 original size:81 final size:81
Alignment explanation
Indices: 67100--67258 Score: 309
Period size: 81 Copynumber: 2.0 Consensus size: 81
67090 AATGAGGGCG
*
67100 ATTACAATATAATATTTATTATAAATATTCTTAATTATTTGATAATGAAAATTCAAATATTTTTA
1 ATTACAATATAATATTTATTATAAATATTCTTAATTATTTGATAATGAAAATTCAAACATTTTTA
67165 TAGTCTCTATTCTCTC
66 TAGTCTCTATTCTCTC
67181 ATTACAATATAATATTTATTATAAATATTCTTAATTATTTGATAATGAAAATTCAAACATTTTTA
1 ATTACAATATAATATTTATTATAAATATTCTTAATTATTTGATAATGAAAATTCAAACATTTTTA
67246 TAGTCTCTATTCT
66 TAGTCTCTATTCT
67259 TCAAACTTAA
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 77 1.00
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.48
Consensus pattern (81 bp):
ATTACAATATAATATTTATTATAAATATTCTTAATTATTTGATAATGAAAATTCAAACATTTTTA
TAGTCTCTATTCTCTC
Found at i:70667 original size:13 final size:15
Alignment explanation
Indices: 70638--70669 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
70628 ATATATATAC
70638 ATATATTATATATGT
1 ATATATTATATATGT
70653 ATATATTAT-TA-GT
1 ATATATTATATATGT
70666 ATAT
1 ATAT
70670 GTCAAGTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.35
14 2 0.12
15 9 0.53
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (15 bp):
ATATATTATATATGT
Found at i:79046 original size:3 final size:3
Alignment explanation
Indices: 79035--79095 Score: 56
Period size: 3 Copynumber: 21.0 Consensus size: 3
79025 TTTTTTATCG
** * *
79035 TTA TT- TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTG TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
79080 TTA TTA TTTA TTA TTA
1 TTA TTA -TTA TTA TTA
79096 CATATTTTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
2 5 0.11
3 39 0.83
4 3 0.06
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:80910 original size:20 final size:21
Alignment explanation
Indices: 80881--80919 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
80871 ATTATTTGGT
80881 TGTTTGTAGT-ATGTAAATGA
1 TGTTTGTAGTAATGTAAATGA
*
80901 TGTTTTTAGTAATGTAAAT
1 TGTTTGTAGTAATGTAAAT
80920 ATTTTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.49
Consensus pattern (21 bp):
TGTTTGTAGTAATGTAAATGA
Found at i:81120 original size:17 final size:18
Alignment explanation
Indices: 81098--81131 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
81088 AAGTCGATTA
*
81098 TATTTTACTAAT-TAATT
1 TATTTTAATAATGTAATT
81115 TATTTTAATAATGTAAT
1 TATTTTAATAATGTAAT
81132 GTGTGTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (18 bp):
TATTTTAATAATGTAATT
Found at i:86851 original size:36 final size:35
Alignment explanation
Indices: 86794--86897 Score: 115
Period size: 36 Copynumber: 3.0 Consensus size: 35
86784 CTTGAGATCG
86794 TTTCTC-AAAAACAAACTTTGTCTCGCTTGAGACAA
1 TTTCTCTAAAAACAAA-TTTGTCTCGCTTGAGACAA
** *
86829 TTTCTCTAAAAACAAATGTTGTCTCATTTGAGACTA
1 TTTCTCTAAAAACAAAT-TTGTCTCGCTTGAGACAA
* *
86865 TATCT-T-AAAGCAAATTTCGTCTCGCTTGAGACA
1 TTTCTCTAAAAACAAATTT-GTCTCGCTTGAGACA
86898 TCATTTTCTC
Statistics
Matches: 58, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
33 2 0.03
34 20 0.34
35 8 0.14
36 28 0.48
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (35 bp):
TTTCTCTAAAAACAAATTTGTCTCGCTTGAGACAA
Found at i:87189 original size:28 final size:27
Alignment explanation
Indices: 87149--87243 Score: 113
Period size: 28 Copynumber: 3.5 Consensus size: 27
87139 TTCTCTTGAA
87149 AAAATCTTTGAGTTAGTTCCTTTTAAAT
1 AAAATCTTTGAGTT-GTTCCTTTTAAAT
* *
87177 AAAATCTTGGAGTTTGTTCCTTTTGAAT
1 AAAATCTTTGAG-TTGTTCCTTTTAAAT
* *
87205 AAATATCTTTGAGTTGTTTCTTTT-GA-
1 AAA-ATCTTTGAGTTGTTCCTTTTAAAT
87231 AAAATCTTTGAGT
1 AAAATCTTTGAGT
87244 CTATTTATTT
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
25 10 0.17
26 3 0.05
27 1 0.02
28 36 0.60
29 10 0.17
ACGTcount: A:0.28, C:0.09, G:0.15, T:0.47
Consensus pattern (27 bp):
AAAATCTTTGAGTTGTTCCTTTTAAAT
Found at i:87255 original size:54 final size:55
Alignment explanation
Indices: 87144--87258 Score: 128
Period size: 54 Copynumber: 2.1 Consensus size: 55
87134 ACAGTTTCTC
* * *
87144 TTGAAAAAATCTTTGAGTTAGTTCCTTTTAAATAAAATCTTGGAGTTTGTTCCTT
1 TTGAAAAAATCTTTGAGTTAGTTCCTTTTAAATAAAATCTTGGAGTCTATTCATT
* * * *
87199 TTGAATAAATATCTTTGAGTT-GTTTCTTTT-GA-AAAATCTTTGAGTCTATTTATT
1 TTGAA-AAA-ATCTTTGAGTTAGTTCCTTTTAAATAAAATCTTGGAGTCTATTCATT
87253 TTGAAA
1 TTGAAA
87259 CAAAGTTTTG
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
53 1 0.02
54 22 0.43
55 6 0.12
56 11 0.22
57 11 0.22
ACGTcount: A:0.30, C:0.09, G:0.14, T:0.48
Consensus pattern (55 bp):
TTGAAAAAATCTTTGAGTTAGTTCCTTTTAAATAAAATCTTGGAGTCTATTCATT
Found at i:87412 original size:28 final size:27
Alignment explanation
Indices: 87339--87402 Score: 94
Period size: 27 Copynumber: 2.3 Consensus size: 27
87329 CTTTAGACAA
87339 TTTTGTGAAAAAATCTTTGAGATTGTTC
1 TTTTG-GAAAAAATCTTTGAGATTGTTC
*
87367 TTTTGGAAAAAATCTTTGAGTTTGTT-
1 TTTTGGAAAAAATCTTTGAGATTGTTC
87393 TCTTTGGAAA
1 T-TTTGGAAA
87403 CAAAATTTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
26 1 0.03
27 28 0.82
28 5 0.15
ACGTcount: A:0.28, C:0.06, G:0.19, T:0.47
Consensus pattern (27 bp):
TTTTGGAAAAAATCTTTGAGATTGTTC
Found at i:87440 original size:37 final size:37
Alignment explanation
Indices: 87390--87516 Score: 119
Period size: 37 Copynumber: 3.6 Consensus size: 37
87380 CTTTGAGTTT
87390 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
1 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
* * * *
87427 GTTTCTTTTGAAACAAAA------ATCT-TTGAG-TCT
1 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT-A
87457 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
1 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
* *
87494 ATTTCTTTTGAAA-AAAATCTTTG
1 GTTTCTTTGGAAACAAAAT-TTTG
87517 AATCTGTTTT
Statistics
Matches: 70, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
29 1 0.01
30 21 0.30
31 3 0.04
36 8 0.11
37 36 0.51
38 1 0.01
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.44
Consensus pattern (37 bp):
GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
Found at i:87563 original size:64 final size:65
Alignment explanation
Indices: 87364--87588 Score: 276
Period size: 67 Copynumber: 3.4 Consensus size: 65
87354 TTTGAGATTG
* * *
87364 TTCTTTTGGAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAGT
1 TTCTTTTGAAAAAAATCTTTGAATCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAGT
*
87429 TTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
1 TTCTTTTG-AA-AAAAATCTTTGAATCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
*
87494 AT
64 GT
* * * *
87496 TTCTTTTGAAAAAAATCTTTGAATCTGTTT-TTCT-TAAA-ATAAATTTTGTATCTCTTGAGACA
1 TTCTTTTGAAAAAAATCTTTGAATCTGTTTCTT-TGGAAACA-AAATTTTGTCTCTCTTAAGATA
87558 GT
64 GT
* ** *
87560 TTCTCTTGAAGTAAATCTTTGAATATGTT
1 TTCTTTTGAAAAAAATCTTTGAATCTGTT
87589 CATTTTGAAA
Statistics
Matches: 143, Mismatches: 13, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
63 1 0.01
64 50 0.35
65 28 0.20
66 3 0.02
67 61 0.43
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.46
Consensus pattern (65 bp):
TTCTTTTGAAAAAAATCTTTGAATCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAGT
Found at i:87764 original size:63 final size:62
Alignment explanation
Indices: 87666--87783 Score: 159
Period size: 63 Copynumber: 1.9 Consensus size: 62
87656 GAAACAAAAC
*
87666 AAACATCTTTGAGATCATTTCCCTTTAAACGAATTTTGTCTCATTCGAGACAGTTTTCCTTT
1 AAACATCTTTGAGATCATTTCCCTTTAAACAAATTTTGTCTCATTCGAGACAGTTTTCCTTT
* * *
87728 AAACAATCTTTGAG-TCATTT-TCTTTGAAACAAAATTTTGTCTCTTTTGAGACAGTT
1 AAAC-ATCTTTGAGATCATTTCCCTTT-AAAC-AAATTTTGTCTCATTCGAGACAGTT
87784 GCTTTTGAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
61 4 0.08
62 14 0.29
63 31 0.63
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.42
Consensus pattern (62 bp):
AAACATCTTTGAGATCATTTCCCTTTAAACAAATTTTGTCTCATTCGAGACAGTTTTCCTTT
Found at i:87973 original size:43 final size:45
Alignment explanation
Indices: 87920--88033 Score: 151
Period size: 46 Copynumber: 2.6 Consensus size: 45
87910 AGACCAGATC
*
87920 TCCTCATCACGTAGGAGCCGTGTCA-ACC-ATAGATAACCAGCCG
1 TCCTCATCACGTAGGAACCGTGTCACACCTATAGATAACCAGCCG
* * **
87963 TCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGCCG
1 TCCTCATCACGTAGGAACCGTGTCA-CACCTATAGATAACCAGCCG
*
88009 TCCTCATCATGTAGGAACCGTGTCA
1 TCCTCATCACGTAGGAACCGTGTCA
88034 TCCCCAGACC
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
43 23 0.38
45 3 0.05
46 35 0.57
ACGTcount: A:0.25, C:0.31, G:0.21, T:0.24
Consensus pattern (45 bp):
TCCTCATCACGTAGGAACCGTGTCACACCTATAGATAACCAGCCG
Found at i:88097 original size:43 final size:43
Alignment explanation
Indices: 87864--88198 Score: 219
Period size: 43 Copynumber: 7.9 Consensus size: 43
87854 CATAACTCCT
* *
87864 TTAGATGACCAGATCTCCTCGTCACGTATGAGCCGTGTCATTCCC
1 TTAGATGACCAGACCTCCTCATCACGTATGAGCCGTGTCA--CCC
* * * *
87909 ---CA-GACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACC
1 TTAGATGACCAGACCTCCTCATCACGTATGAGCCGTGTCACCC
* * * * *
87948 ATAGATAACCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCT
1 TTAGATGACCAGACC-TCCTCATCACGTATGAGCCGTG---TCACCC
* * * *
87994 TTAGATGGCCAG-CCGTCCTCATCATGTAGGAACCGTGTCATCCC
1 TTAGATGACCAGACC-TCCTCATCACGTATGAGCCGTGTCA-CCC
* * *
88038 ---CA-GACCAGATCTCTTCATCACGTATGAGCCGTGTCACCC
1 TTAGATGACCAGACCTCCTCATCACGTATGAGCCGTGTCACCC
* ** *
88077 TTAGATGACCAGACCTCTTCATTGCGTATGAGTCGTGTCA---
1 TTAGATGACCAGACCTCCTCATCACGTATGAGCCGTGTCACCC
**** * *
88117 TTTCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCACCC
1 TTAGATGACCAGACCTCCTCATCACGTATGAGCCGTGTCACCC
* ** *
88160 TTAGATGACCAGACCTCTTCATTGCGTATGAGCAGTGTC
1 TTAGATGACCAGACCTCCTCATCACGTATGAGCCGTGTC
88199 GTCCCCACCA
Statistics
Matches: 230, Mismatches: 43, Indels: 36
0.74 0.14 0.12
Matches are distributed among these distances:
39 5 0.02
40 58 0.25
41 34 0.15
42 4 0.02
43 90 0.39
44 2 0.01
46 37 0.16
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (43 bp):
TTAGATGACCAGACCTCCTCATCACGTATGAGCCGTGTCACCC
Found at i:88127 original size:83 final size:83
Alignment explanation
Indices: 88027--88205 Score: 308
Period size: 83 Copynumber: 2.2 Consensus size: 83
88017 ATGTAGGAAC
88027 CGTGTCATCCCCAGACCAGATCTCTTCATCACGTATGAGCCGTGTCACCCTTAGATGACCAGACC
1 CGTGTCATCCCCAGACCAGATCTCTTCATCACGTATGAGCCGTGTCACCCTTAGATGACCAGACC
88092 TCTTCATTGCGTATGAGT
66 TCTTCATTGCGTATGAGT
*
88110 CGTGTCATTTCCC-GACCAGATCTCTTCATCACGTATGAGCCGTGTCACCCTTAGATGACCAGAC
1 CGTGTCA-TCCCCAGACCAGATCTCTTCATCACGTATGAGCCGTGTCACCCTTAGATGACCAGAC
88174 CTCTTCATTGCGTATGAG-
65 CTCTTCATTGCGTATGAGT
*
88192 CAGTGTCGTCCCCA
1 C-GTGTCATCCCCA
88206 CCAACAGAAC
Statistics
Matches: 90, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
82 5 0.06
83 81 0.90
84 4 0.04
ACGTcount: A:0.21, C:0.32, G:0.20, T:0.28
Consensus pattern (83 bp):
CGTGTCATCCCCAGACCAGATCTCTTCATCACGTATGAGCCGTGTCACCCTTAGATGACCAGACC
TCTTCATTGCGTATGAGT
Found at i:88366 original size:3 final size:3
Alignment explanation
Indices: 88355--88415 Score: 56
Period size: 3 Copynumber: 21.0 Consensus size: 3
88345 TTTTTTATCG
** * *
88355 TTA TT- TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTG TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
88400 TTA TTA TTTA TTA TTA
1 TTA TTA -TTA TTA TTA
88416 CATATTTTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
2 5 0.11
3 39 0.83
4 3 0.06
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:90447 original size:17 final size:18
Alignment explanation
Indices: 90425--90458 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
90415 AAGTCGATTA
*
90425 TATTTTACTAAT-TAATT
1 TATTTTAATAATGTAATT
90442 TATTTTAATAATGTAAT
1 TATTTTAATAATGTAAT
90459 GTGTGTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (18 bp):
TATTTTAATAATGTAATT
Found at i:91921 original size:32 final size:31
Alignment explanation
Indices: 91883--91959 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
91873 CGGGGTCGTG
*
91883 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAACA-ATCTCAGGGCCGCA
** *
91915 GGGCCTACCCGAGAATAATCTCAGGGCCGCA
1 GGGCCTACCTAAGAACAATCTCAGGGCCGCA
*
91946 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
91960 GTCACATTAG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAACAATCTCAGGGCCGCA
Found at i:92841 original size:7 final size:7
Alignment explanation
Indices: 92829--92866 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
92819 GTCAAAGAAA
92829 GTCAACG
1 GTCAACG
92836 GTCAACG
1 GTCAACG
92843 GTCAACG
1 GTCAACG
92850 GTCAACG
1 GTCAACG
92857 GTCAACG
1 GTCAACG
92864 GTC
1 GTC
92867 GGGTCGGGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:92873 original size:5 final size:5
Alignment explanation
Indices: 92863--92903 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
92853 AACGGTCAAC
*
92863 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC
92904 AGACCGGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 28 0.88
7 4 0.12
ACGTcount: A:0.05, C:0.22, G:0.54, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:92884 original size:22 final size:22
Alignment explanation
Indices: 92856--92904 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
92846 AACGGTCAAC
92856 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
92878 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
92900 GGTCA
1 GGTCA
92905 GACCGGTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.10, C:0.22, G:0.49, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:92918 original size:9 final size:9
Alignment explanation
Indices: 92900--92998 Score: 81
Period size: 9 Copynumber: 10.3 Consensus size: 9
92890 GGTCGGGTCG
*
92900 GGTCAGACC
1 GGTCAAACC
92909 GGTCAAACC
1 GGTCAAACC
* *
92918 GTCTCAGACC
1 G-GTCAAACC
92928 GGTCAAACC
1 GGTCAAACC
*
92937 GGTTCGAACC
1 GG-TCAAACC
*
92947 GGTTGAAACC
1 GG-TCAAACC
92957 GGTCAAACC
1 GGTCAAACC
92966 GGTCAGAACC
1 GGTCA-AACC
*
92976 GGTTGAAAACC
1 GG-T-CAAACC
*
92987 GGTTAAACC
1 GGTCAAACC
92996 GGT
1 GGT
92999 TTCCAGCAGC
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
9 36 0.49
10 30 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.27, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:92947 original size:19 final size:19
Alignment explanation
Indices: 92906--92999 Score: 79
Period size: 19 Copynumber: 4.8 Consensus size: 19
92896 GTCGGGTCAG
92906 ACCGGTCAAACC-GTCTC-A
1 ACCGGTCAAACCGGT-TCGA
92924 GACCGGTCAAACCGGTTCGA
1 -ACCGGTCAAACCGGTTCGA
* *
92944 ACCGGTTGAAACCGG-TCAA
1 ACCGG-TCAAACCGGTTCGA
92963 ACCGGTCAGAACCGGTT-GAAA
1 ACCGGTCA-AACCGGTTCG--A
*
92984 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
93000 TCCAGCAGCC
Statistics
Matches: 63, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
18 2 0.03
19 33 0.52
20 20 0.32
21 8 0.13
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.17
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCGA
Found at i:92957 original size:29 final size:31
Alignment explanation
Indices: 92925--92999 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
92915 ACCGTCTCAG
92925 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
92954 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
92984 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
93000 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 15 0.36
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:99217 original size:31 final size:30
Alignment explanation
Indices: 99182--99271 Score: 110
Period size: 31 Copynumber: 2.9 Consensus size: 30
99172 CTAAGGGAAC
99182 ATCTTAGGGCCTG-AGAGCCTACCCAAGATA
1 ATCTTAGGGCC-GCAGAGCCTACCCAAGATA
* *
99212 GATCTTAGGGCCGCAGGGCCTACCCGAGAATA
1 -ATCTTAGGGCCGCAGAGCCTACCCAAG-ATA
* *
99244 ATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ATCTTAGGGCCGCAGAGCCTACCCAAGA
99272 GTCACATTAG
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
30 2 0.04
31 46 0.90
32 3 0.06
ACGTcount: A:0.28, C:0.29, G:0.27, T:0.17
Consensus pattern (30 bp):
ATCTTAGGGCCGCAGAGCCTACCCAAGATA
Found at i:100153 original size:7 final size:7
Alignment explanation
Indices: 100141--100178 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
100131 GTCAAAGAAA
100141 GTCAACG
1 GTCAACG
100148 GTCAACG
1 GTCAACG
100155 GTCAACG
1 GTCAACG
100162 GTCAACG
1 GTCAACG
100169 GTCAACG
1 GTCAACG
100176 GTC
1 GTC
100179 GGGTCGGGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:100185 original size:5 final size:5
Alignment explanation
Indices: 100175--100215 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
100165 AACGGTCAAC
*
100175 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC
100216 AGACCGGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 28 0.88
7 4 0.12
ACGTcount: A:0.05, C:0.22, G:0.54, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:100196 original size:22 final size:22
Alignment explanation
Indices: 100168--100216 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
100158 AACGGTCAAC
100168 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
100190 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
100212 GGTCA
1 GGTCA
100217 GACCGGTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.10, C:0.22, G:0.49, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:100236 original size:19 final size:19
Alignment explanation
Indices: 100214--100268 Score: 92
Period size: 19 Copynumber: 2.9 Consensus size: 19
100204 TCGGGTCGGG
*
100214 TCAGACCGGTCAAACCGTC
1 TCAGACCGGTCAAACCGAC
*
100233 TCAGACCGGTCAAACCGAG
1 TCAGACCGGTCAAACCGAC
100252 TCAGACCGGTCAAACCG
1 TCAGACCGGTCAAACCG
100269 GTTCGAACCG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.29, C:0.35, G:0.24, T:0.13
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGAC
Found at i:100264 original size:38 final size:37
Alignment explanation
Indices: 100212--100329 Score: 118
Period size: 38 Copynumber: 3.1 Consensus size: 37
100202 GGTCGGGTCG
100212 GGTCAGACCGGTCAAACCGTCTC-AGACCGG-TCAAACC
1 GGTCAGACCGGTCAAACCGT-TCGA-ACCGGTTCAAACC
*
100249 GAGTCAGACCGGTCAAACCGGTTCGAACCGGTTGAAACC
1 G-GTCAGACCGGTCAAACC-GTTCGAACCGGTTCAAACC
*
100288 GGTCAAACCGGTCAGAACCGGTT-GAAAACCGGTT-AAACC
1 GGTCAGACCGGTCA-AACC-GTTCG--AACCGGTTCAAACC
100327 GGT
1 GGT
100330 TTCCAGCAGC
Statistics
Matches: 72, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
37 1 0.01
38 37 0.51
39 26 0.36
40 8 0.11
ACGTcount: A:0.29, C:0.29, G:0.27, T:0.15
Consensus pattern (37 bp):
GGTCAGACCGGTCAAACCGTTCGAACCGGTTCAAACC
Found at i:100278 original size:19 final size:18
Alignment explanation
Indices: 100218--100330 Score: 88
Period size: 19 Copynumber: 5.9 Consensus size: 18
100208 GTCGGGTCAG
100218 ACCGGTCAAACC-GTCTCA
1 ACCGGTCAAACCGGT-TCA
100236 GACCGGTCAAACCGAG-TCA
1 -ACCGGTCAAACCG-GTTCA
100255 GACCGGTCAAACCGGTTCGA
1 -ACCGGTCAAACCGGTTC-A
*
100275 ACCGGTTGAAACCGG-TCAA
1 ACCGG-TCAAACCGGTTC-A
*
100294 ACCGGTCAGAACCGGTTGAAA
1 ACCGGTCA-AACCGGTT--CA
*
100315 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
100331 TCCAGCAGCC
Statistics
Matches: 80, Mismatches: 5, Indels: 17
0.78 0.05 0.17
Matches are distributed among these distances:
18 3 0.04
19 50 0.62
20 18 0.22
21 9 0.11
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.16
Consensus pattern (18 bp):
ACCGGTCAAACCGGTTCA
Found at i:100308 original size:29 final size:29
Alignment explanation
Indices: 100256--100329 Score: 114
Period size: 29 Copynumber: 2.5 Consensus size: 29
100246 ACCGAGTCAG
100256 ACCGGTCAAACCGGTTCGAACCGGTTG-AA
1 ACCGGTCAAACCGG-TCGAACCGGTTGAAA
100285 ACCGGTCAAACCGGTCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTC-GAACCGGTTGAAA
*
100315 ACCGGTTAAACCGGT
1 ACCGGTCAAACCGGT
100330 TTCCAGCAGC
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 16 0.38
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (29 bp):
ACCGGTCAAACCGGTCGAACCGGTTGAAA
Found at i:100330 original size:9 final size:9
Alignment explanation
Indices: 100212--100329 Score: 101
Period size: 9 Copynumber: 12.3 Consensus size: 9
100202 GGTCGGGTCG
*
100212 GGTCAGACC
1 GGTCAAACC
100221 GGTCAAACC
1 GGTCAAACC
* *
100230 GTCTCAGACC
1 G-GTCAAACC
100240 GGTCAAACC
1 GGTCAAACC
*
100249 GAGTCAGACC
1 G-GTCAAACC
100259 GGTCAAACC
1 GGTCAAACC
*
100268 GGTTCGAACC
1 GG-TCAAACC
*
100278 GGTTGAAACC
1 GG-TCAAACC
100288 GGTCAAACC
1 GGTCAAACC
100297 GGTCAGAACC
1 GGTCA-AACC
*
100307 GGTTGAAAACC
1 GG-T-CAAACC
*
100318 GGTTAAACC
1 GGTCAAACC
100327 GGT
1 GGT
100330 TTCCAGCAGC
Statistics
Matches: 90, Mismatches: 13, Indels: 12
0.78 0.11 0.10
Matches are distributed among these distances:
9 44 0.49
10 38 0.42
11 7 0.08
12 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.27, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:102478 original size:31 final size:30
Alignment explanation
Indices: 102450--102513 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
102440 AAATATTACG
* * *
102450 TTTTGGTTATTTATGTTATCTATTTATTAAA
1 TTTTGGTCACTTATGTTATCGA-TTATTAAA
*
102481 TTTTGGTCACTTATGTTATCGATTATTATA
1 TTTTGGTCACTTATGTTATCGATTATTAAA
102511 TTT
1 TTT
102514 CAGTCACTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 10 0.34
31 19 0.66
ACGTcount: A:0.23, C:0.06, G:0.11, T:0.59
Consensus pattern (30 bp):
TTTTGGTCACTTATGTTATCGATTATTAAA
Found at i:102520 original size:30 final size:31
Alignment explanation
Indices: 102460--102521 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
102450 TTTTGGTTAT
* **
102460 TTATGTTATCTATTTATTAAATTTTGGTCAC
1 TTATGTTATCGATTTATTAAATTTCAGTCAC
*
102491 TTATGTTATCGA-TTATTATATTTCAGTCAC
1 TTATGTTATCGATTTATTAAATTTCAGTCAC
102521 T
1 T
102522 AAATCATTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 16 0.59
31 11 0.41
ACGTcount: A:0.26, C:0.11, G:0.10, T:0.53
Consensus pattern (31 bp):
TTATGTTATCGATTTATTAAATTTCAGTCAC
Found at i:102665 original size:13 final size:13
Alignment explanation
Indices: 102649--102684 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
102639 ATAATAAATC
*
102649 AATTTGACCTTTA
1 AATTTGACCATTA
102662 AATTTGACCATTA
1 AATTTGACCATTA
102675 AATTTGACCA
1 AATTTGACCA
102685 ATGTCTCTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.39
Consensus pattern (13 bp):
AATTTGACCATTA
Found at i:110647 original size:34 final size:36
Alignment explanation
Indices: 110603--110702 Score: 150
Period size: 34 Copynumber: 2.8 Consensus size: 36
110593 TTTCATCCTA
* *
110603 CTAGGATTCAAACTCTTAAAAATAGGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
*
110638 -TAGGATTCAAACTCCTAAAAATATGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
110673 GCTAGGATTCAAACTCCTAAAAATAGGATA
1 -CTAGGATTCAAACTCCTAAAAATAGGATA
110703 TAGTTCTACT
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
34 28 0.48
35 3 0.05
37 27 0.47
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
Found at i:114588 original size:23 final size:22
Alignment explanation
Indices: 114529--114590 Score: 79
Period size: 24 Copynumber: 2.7 Consensus size: 22
114519 TAAAAAGGGC
*
114529 AAAAAGAAAAAAAAACAAAAAA
1 AAAAAGAAAAAAGAACAAAAAA
*
114551 CAAAAGCAAAAAAAGAACAAAAAGA
1 AAAAAG--AAAAAAGAACAAAAA-A
114576 AAAAAGAAAAAAGAA
1 AAAAAGAAAAAAGAA
114591 AAAGGGACAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 5 0.15
23 9 0.26
24 14 0.41
25 6 0.18
ACGTcount: A:0.84, C:0.06, G:0.10, T:0.00
Consensus pattern (22 bp):
AAAAAGAAAAAAGAACAAAAAA
Found at i:114593 original size:31 final size:31
Alignment explanation
Indices: 114529--114593 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 31
114519 TAAAAAGGGC
114529 AAAAAGAAAAAAAAACAAAAAACAAAAGCAA
1 AAAAAGAAAAAAAAACAAAAAACAAAAGCAA
114560 AAAAAGAACAAAAAGAA-AAAAGAA-AAAAG-AA
1 AAAAAGAA-AAAAA-AACAAAA-AACAAAAGCAA
114591 AAA
1 AAA
114594 GGGACAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
31 13 0.42
32 14 0.45
33 4 0.13
ACGTcount: A:0.85, C:0.06, G:0.09, T:0.00
Consensus pattern (31 bp):
AAAAAGAAAAAAAAACAAAAAACAAAAGCAA
Found at i:115220 original size:22 final size:22
Alignment explanation
Indices: 115192--115235 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
115182 AGCTACCCCA
115192 TCAAACC-TTTGAGCATCAAATG
1 TCAAACCATTT-AGCATCAAATG
115214 TCAAACCATTTAGCATCAAATG
1 TCAAACCATTTAGCATCAAATG
115236 AACAAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (22 bp):
TCAAACCATTTAGCATCAAATG
Found at i:115694 original size:18 final size:18
Alignment explanation
Indices: 115671--115706 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
115661 TGAACATCAA
*
115671 ATATTGGGGCATTTTTGG
1 ATATTGGGGCATCTTTGG
115689 ATATTGGGGCATCTTTGG
1 ATATTGGGGCATCTTTGG
115707 GGATTCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.08, G:0.33, T:0.42
Consensus pattern (18 bp):
ATATTGGGGCATCTTTGG
Found at i:116232 original size:36 final size:36
Alignment explanation
Indices: 116189--116296 Score: 216
Period size: 36 Copynumber: 3.0 Consensus size: 36
116179 ACTAGAAGAG
116189 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAA
116225 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAA
116261 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAA
116297 ATATTTAAAT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 72 1.00
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAA
Found at i:117236 original size:105 final size:105
Alignment explanation
Indices: 117051--117680 Score: 869
Period size: 105 Copynumber: 6.0 Consensus size: 105
117041 ATATCGTGAC
* * ** * *
117051 ACTCGAGACAACACAAGTTCAACTTCATAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTC
*
117116 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 AATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
117157 ACTCCAGATAACGCAAGTTCAACTTCACGAGGAAGGGACCGCTGCTTGTAAACAACAACTTCTCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
* *
117222 ATTTCAGAGCCAATTTTAACTTCACAACGAAGGATATTGG
66 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
** * *
117262 ACTTTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAGCAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
117327 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
117367 ACTCCAGACAATGCAAGTTCAACTTCACGACGAATGGACCACTGCTTGTCAACAACAACTT-TCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCT-C
117431 AATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 AATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
117472 ACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
** *
117533 A-CTCAGATTCAATTTCAACTTTACAACGAAGGATATTGG
66 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
** * * * * *
117572 ACTTGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTC
** * *
117637 GGT-TCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
65 AATCT-CAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
117678 ACT
1 ACT
117681 TGGAATAATT
Statistics
Matches: 471, Mismatches: 45, Indels: 16
0.89 0.08 0.03
Matches are distributed among these distances:
100 82 0.17
101 3 0.01
102 3 0.01
103 5 0.01
104 4 0.01
105 296 0.63
106 78 0.17
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:118271 original size:34 final size:36
Alignment explanation
Indices: 118227--118326 Score: 159
Period size: 34 Copynumber: 2.8 Consensus size: 36
118217 TTTCATCCTA
*
118227 CTAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
*
118262 -TAGGATTCAAACTCCTAAAAATATGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
118297 GCTAGGATTCAAACTCCTAAAAATAGGATA
1 -CTAGGATTCAAACTCCTAAAAATAGGATA
118327 TAGTTCTACT
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
34 29 0.49
35 3 0.05
37 27 0.46
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.29
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
Found at i:118745 original size:32 final size:34
Alignment explanation
Indices: 118709--118782 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
118699 ATTATTCTTG
*
118709 TTATATATGCATAT-T-ACTTTCTATTAGTTTTA
1 TTATATATGCATATATGACTTTCTATTAGTGTTA
* ** *
118741 TTATATATGTATATATGTTTTTTTATTAGTGTTA
1 TTATATATGCATATATGACTTTCTATTAGTGTTA
118775 TTATATAT
1 TTATATAT
118783 ATATATATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
32 13 0.37
33 1 0.03
34 21 0.60
ACGTcount: A:0.28, C:0.04, G:0.08, T:0.59
Consensus pattern (34 bp):
TTATATATGCATATATGACTTTCTATTAGTGTTA
Found at i:118934 original size:16 final size:18
Alignment explanation
Indices: 118913--118947 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
118903 TTTACTCATT
118913 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
118929 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
118947 T
1 T
118948 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:127405 original size:57 final size:57
Alignment explanation
Indices: 127332--127496 Score: 249
Period size: 57 Copynumber: 2.9 Consensus size: 57
127322 TGAGCTTGCG
* * *
127332 TCGAGCAATGGGTTAAATGTAGACAGTGTTAGCAGTTCAAGAAGGCAAAGTCTTGTA
1 TCGAGCAATGGGTTAAATGCAGACAGTGTAAGCAGTTCAAGAAGACAAAGTCTTGTA
* * * *
127389 TCGCGCAATGTGTTAAATGCAAACAGTGTAAGCAGTTCAAGAAGTCAAAGTCTTGTA
1 TCGAGCAATGGGTTAAATGCAGACAGTGTAAGCAGTTCAAGAAGACAAAGTCTTGTA
* *
127446 TTGAGCAATGGGTTAAATGCAGACAGAGTAAGCAGTTCAAGAAGACAAAGT
1 TCGAGCAATGGGTTAAATGCAGACAGTGTAAGCAGTTCAAGAAGACAAAGT
127497 TTGAGATCAA
Statistics
Matches: 96, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 96 1.00
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.24
Consensus pattern (57 bp):
TCGAGCAATGGGTTAAATGCAGACAGTGTAAGCAGTTCAAGAAGACAAAGTCTTGTA
Found at i:129352 original size:2 final size:2
Alignment explanation
Indices: 129345--129381 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
129335 ACTTTTGAAT
*
129345 TA TA TA TA TA TT TA -A 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
129382 GGAAACTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:129609 original size:39 final size:39
Alignment explanation
Indices: 129566--129668 Score: 133
Period size: 39 Copynumber: 2.6 Consensus size: 39
129556 TTTAAAAAAA
*
129566 TTAGAATGTTAATGTGAAATAATTTAAGAAATTA-AGAAT
1 TTAGAATGTTAATGTGAAATAATTTAAGAAATTAGA-AAC
129605 TTAGAATGTT-ATGATGACAA-AATTTAAGAAATTAGAAAC
1 TTAGAATGTTAATG-TGA-AATAATTTAAGAAATTAGAAAC
129644 TTAGAATGTTAGA-GTGAAATAATTT
1 TTAGAATGTTA-ATGTGAAATAATTT
129669 CTAAATTATG
Statistics
Matches: 57, Mismatches: 1, Indels: 12
0.81 0.01 0.17
Matches are distributed among these distances:
38 5 0.09
39 47 0.82
40 4 0.07
41 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.17, T:0.35
Consensus pattern (39 bp):
TTAGAATGTTAATGTGAAATAATTTAAGAAATTAGAAAC
Found at i:135774 original size:114 final size:114
Alignment explanation
Indices: 135574--135802 Score: 406
Period size: 114 Copynumber: 2.0 Consensus size: 114
135564 ATGAAGCAAC
* * *
135574 TGTTAACATTTGAACCTGATAAACCATGGAACATACATCTCATGCAATTAAGATTTTGCAAAGCT
1 TGTTAACATTTGAACCTAATAAACCATGGAACATACATCTCACGCAATTAAGATTTTGCAAAGCC
135639 AGAAATTCACCACTCACCAATACTTTCATGGGGATTAACTCCCAAAATA
66 AGAAATTCACCACTCACCAATACTTTCATGGGGATTAACTCCCAAAATA
135688 TGTTAACATTTGAACCTAATAAACCATGGAACATACATCTCACGCAATGT-AGATTTTGCAAAGC
1 TGTTAACATTTGAACCTAATAAACCATGGAACATACATCTCACGCAAT-TAAGATTTTGCAAAGC
*
135752 CAGAAATTCACCACTCACCAATACTTTCATGGGGATTAACTCTCAAAATA
65 CAGAAATTCACCACTCACCAATACTTTCATGGGGATTAACTCCCAAAATA
135802 T
1 T
135803 AAAACTATGA
Statistics
Matches: 110, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
114 109 0.99
115 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (114 bp):
TGTTAACATTTGAACCTAATAAACCATGGAACATACATCTCACGCAATTAAGATTTTGCAAAGCC
AGAAATTCACCACTCACCAATACTTTCATGGGGATTAACTCCCAAAATA
Found at i:138293 original size:15 final size:15
Alignment explanation
Indices: 138273--138303 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
138263 TGATGGAAAG
138273 ATTATTATATATATT
1 ATTATTATATATATT
*
138288 ATTATTATTTATATT
1 ATTATTATATATATT
138303 A
1 A
138304 GGGTAAAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTATTATATATATT
Found at i:138964 original size:34 final size:36
Alignment explanation
Indices: 138926--138999 Score: 84
Period size: 34 Copynumber: 2.1 Consensus size: 36
138916 TTCATGTTCA
* *
138926 AAATTTC-AAAACACCTT-AATTTCATTCTAAACC-T
1 AAATTTCTAAAACA-ATTCAATTACATTCTAAACCTT
*
138960 AAA-TTCTAAAATAATTCAATTACATTCTAAACCTT
1 AAATTTCTAAAACAATTCAATTACATTCTAAACCTT
138995 AAATT
1 AAATT
139000 GAAGTATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
33 5 0.15
34 23 0.70
35 4 0.12
36 1 0.03
ACGTcount: A:0.45, C:0.19, G:0.00, T:0.36
Consensus pattern (36 bp):
AAATTTCTAAAACAATTCAATTACATTCTAAACCTT
Found at i:139066 original size:33 final size:35
Alignment explanation
Indices: 138995--139102 Score: 134
Period size: 33 Copynumber: 3.2 Consensus size: 35
138985 TCTAAACCTT
* * * *
138995 AAATTGAAGTATTTTAGAATTTGGGGTTTA-AAT-
1 AAATTGAATTACTTTGGAATTTAGGGTTTAGAATG
*
139028 TAATTGAATTA-TTTGGAATTTAGGG-TTAGAATG
1 AAATTGAATTACTTTGGAATTTAGGGTTTAGAATG
*
139061 AAATTGAATTACTTTGGAAATTAGGGTTTAGAATG
1 AAATTGAATTACTTTGGAATTTAGGGTTTAGAATG
139096 AAATTGA
1 AAATTGA
139103 GGATTGTTTA
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
31 3 0.05
32 15 0.23
33 19 0.29
34 13 0.20
35 15 0.23
ACGTcount: A:0.37, C:0.01, G:0.22, T:0.40
Consensus pattern (35 bp):
AAATTGAATTACTTTGGAATTTAGGGTTTAGAATG
Found at i:139284 original size:29 final size:29
Alignment explanation
Indices: 139227--139284 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
139217 CGGAATAAAT
* * * * *
139227 GTTGGGGGACTATATTGCAAGTTTTAAAA
1 GTTGGGGGACCAAAATGCAAGCTTCAAAA
139256 GTTGGGGGACCAAAATGCAAGCTTCAAAA
1 GTTGGGGGACCAAAATGCAAGCTTCAAAA
139285 ATATTCAGTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.26
Consensus pattern (29 bp):
GTTGGGGGACCAAAATGCAAGCTTCAAAA
Found at i:139731 original size:22 final size:20
Alignment explanation
Indices: 139700--139761 Score: 52
Period size: 22 Copynumber: 2.9 Consensus size: 20
139690 AAATAAGTCC
*
139700 TTAAGTTATTATATATTTTT
1 TTAATTTATTATATATTTTT
*
139720 ATTAATTTTATTTTGAATATTTTT
1 -TTAA-TTTATTAT--ATATTTTT
*
139744 TTGATTTATTAATATATT
1 TTAATTTATT-ATATATT
139762 AGAGTTTAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
21 9 0.27
22 12 0.36
23 4 0.12
24 8 0.24
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.65
Consensus pattern (20 bp):
TTAATTTATTATATATTTTT
Found at i:143642 original size:6 final size:6
Alignment explanation
Indices: 143631--143657 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
143621 CGGGAATTTT
143631 TTTTCC TTTTCC TTTTCC TTTTCC TTT
1 TTTTCC TTTTCC TTTTCC TTTTCC TTT
143658 CAGTATACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTTCC
Done.