Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008491.1 Hibiscus syriacus cultivar Beakdansim tig00111333_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: 44953
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:1483 original size:49 final size:50
Alignment explanation
Indices: 1423--1635 Score: 305
Period size: 49 Copynumber: 4.4 Consensus size: 50
1413 AAGTAGTGAG
1423 TTTT-AATAAAATATTTTTTTTA-TAAAATTTATCAAATCGAGATAAAAA
1 TTTTGAATAAAATATTTTTTTTATTAAAATTTATCAAATCGAGATAAAAA
*
1471 TTTTGAATAAAATA---TTTTTATTAAAATTTATCAAATTGAGATAAAAA
1 TTTTGAATAAAATATTTTTTTTATTAAAATTTATCAAATCGAGATAAAAA
* * *
1518 ATTTGAATAAAA-ATATTTTTTATTAAAATTTATCAAATTGAGATAAAAA
1 TTTTGAATAAAATATTTTTTTTATTAAAATTTATCAAATCGAGATAAAAA
* * *
1567 ATTTGAATAAAA-ATATTTTTTATTAAAATTTATCAAATCGAGACAAAAA
1 TTTTGAATAAAATATTTTTTTTATTAAAATTTATCAAATCGAGATAAAAA
1616 TTTTGAATAAAAATATTTTT
1 TTTTGAAT-AAAATATTTTT
1636 ATTAGAACTC
Statistics
Matches: 152, Mismatches: 6, Indels: 11
0.90 0.04 0.07
Matches are distributed among these distances:
46 7 0.05
47 36 0.24
48 4 0.03
49 96 0.63
50 4 0.03
51 5 0.03
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.42
Consensus pattern (50 bp):
TTTTGAATAAAATATTTTTTTTATTAAAATTTATCAAATCGAGATAAAAA
Found at i:5627 original size:21 final size:21
Alignment explanation
Indices: 5588--5627 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5578 TTTTCAGAAA
*
5588 TTTAATTTATATAATTTTAAT
1 TTTAATTTATAAAATTTTAAT
5609 TTTAATTT-TAAAATATTTA
1 TTTAATTTATAAAAT-TTTA
5628 TATTCATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTAATTTATAAAATTTTAAT
Found at i:8113 original size:31 final size:31
Alignment explanation
Indices: 8075--8153 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
8065 TTAGGCAGTA
*
8075 CTCGACTCGTGCACTTTAAAAAAAATTATTG
1 CTCGACTCGTGCACGTTAAAAAAAATTATTG
* *
8106 CTCGACTCGTACTCGTTAAAAAAAATTATTG
1 CTCGACTCGTGCACGTTAAAAAAAATTATTG
*
8137 CTCGACTCGTGCTCGTT
1 CTCGACTCGTGCACGTT
8154 GCTCGTTAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (31 bp):
CTCGACTCGTGCACGTTAAAAAAAATTATTG
Found at i:8373 original size:24 final size:24
Alignment explanation
Indices: 8346--8403 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
8336 ATATTAAAAG
* *
8346 CAAAGTAACAATCCATAAATTCAC
1 CAAAGTAACAATCCACAAATACAC
*
8370 CAAAGTAACAATCCACAAATACAT
1 CAAAGTAACAATCCACAAATACAC
*
8394 CAAACTAACA
1 CAAAGTAACA
8404 TATTAAAAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.53, C:0.26, G:0.03, T:0.17
Consensus pattern (24 bp):
CAAAGTAACAATCCACAAATACAC
Found at i:11864 original size:14 final size:14
Alignment explanation
Indices: 11841--11886 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
11831 AGAGATGAAA
*
11841 TTGTGATTTGTGAT
1 TTGTGTTTTGTGAT
11855 TTGTGTTTTGTGAT
1 TTGTGTTTTGTGAT
*
11869 TTGTGATTTTGAGAT
1 TTGTG-TTTTGTGAT
11884 TTG
1 TTG
11887 AGAGGAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
14 18 0.62
15 11 0.38
ACGTcount: A:0.13, C:0.00, G:0.28, T:0.59
Consensus pattern (14 bp):
TTGTGTTTTGTGAT
Found at i:11889 original size:7 final size:7
Alignment explanation
Indices: 11841--11877 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
11831 AGAGATGAAA
11841 TTGTGAT
1 TTGTGAT
11848 TTGTGAT
1 TTGTGAT
*
11855 TTGTGTT
1 TTGTGAT
11862 TTGTGAT
1 TTGTGAT
11869 TTGTGAT
1 TTGTGAT
11876 TT
1 TT
11878 TGAGATTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.11, C:0.00, G:0.27, T:0.62
Consensus pattern (7 bp):
TTGTGAT
Found at i:14352 original size:44 final size:43
Alignment explanation
Indices: 14304--14402 Score: 144
Period size: 44 Copynumber: 2.3 Consensus size: 43
14294 AGAAAAGACA
* *
14304 AATAAATAAATAAAATACACTAAAATTAAAAGAGAAAAAAAATG
1 AATAACTAAATAAAAAACACTAAAATTAAAA-AGAAAAAAAATG
* *
14348 AATAACTAAAATAAAAAATACTAAAATTAAAAAGGAAAAAAATG
1 AATAACT-AAATAAAAAACACTAAAATTAAAAAGAAAAAAAATG
14392 AATAACTAAAT
1 AATAACTAAAT
14403 TGAAATAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
43 4 0.08
44 24 0.48
45 22 0.44
ACGTcount: A:0.70, C:0.05, G:0.06, T:0.19
Consensus pattern (43 bp):
AATAACTAAATAAAAAACACTAAAATTAAAAAGAAAAAAAATG
Found at i:14358 original size:40 final size:40
Alignment explanation
Indices: 14293--14401 Score: 112
Period size: 44 Copynumber: 2.6 Consensus size: 40
14283 AAATAAAAAT
* *
14293 AAGAAAAGACAAATAAATAAATAAAAT-ACACTAAAATTAAA
1 AAGAAAA-A-AAATGAATAACTAAAATAACACTAAAATTAAA
*
14334 AGAGAAAAAAAATGAATAACTAAAATAAAAAATACTAAAATTAAA
1 A-AGAAAAAAAATGAATAACTAAAAT----AACACTAAAATTAAA
*
14379 AAGGAAAAAAATGAATAACTAAA
1 AAGAAAAAAAATGAATAACTAAA
14402 TTGAAATAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 9
0.82 0.06 0.13
Matches are distributed among these distances:
40 15 0.26
41 2 0.03
42 6 0.10
44 21 0.36
45 14 0.24
ACGTcount: A:0.71, C:0.06, G:0.07, T:0.17
Consensus pattern (40 bp):
AAGAAAAAAAATGAATAACTAAAATAACACTAAAATTAAA
Found at i:14371 original size:45 final size:44
Alignment explanation
Indices: 14311--14401 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 44
14301 ACAAATAAAT
*
14311 AAATAAAATACACTAAAATTAAAAGAGAAAAAAAATGAATAACTA
1 AAATAAAAAACACTAAAATTAAAA-AGAAAAAAAATGAATAACTA
* *
14356 AAATAAAAAATACTAAAATTAAAAAGGAAAAAAATGAATAACTA
1 AAATAAAAAACACTAAAATTAAAAAGAAAAAAAATGAATAACTA
14400 AA
1 AA
14402 TTGAAATAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
44 21 0.49
45 22 0.51
ACGTcount: A:0.70, C:0.05, G:0.07, T:0.18
Consensus pattern (44 bp):
AAATAAAAAACACTAAAATTAAAAAGAAAAAAAATGAATAACTA
Found at i:14407 original size:22 final size:22
Alignment explanation
Indices: 14339--14412 Score: 64
Period size: 22 Copynumber: 3.4 Consensus size: 22
14329 TTAAAAGAGA
14339 AAAAAAATGAATAACTAAAAT-
1 AAAAAAATGAATAACTAAAATG
* *
14360 AAAAAATACT-AA-AATTAAAAAGG
1 AAAAAA-A-TGAATAACT-AAAATG
*
14383 AAAAAAATGAATAACTAAATTG
1 AAAAAAATGAATAACTAAAATG
*
14405 AAATAAAT
1 AAAAAAAT
14413 TAAAATTGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
21 10 0.24
22 21 0.51
23 10 0.24
ACGTcount: A:0.69, C:0.04, G:0.07, T:0.20
Consensus pattern (22 bp):
AAAAAAATGAATAACTAAAATG
Found at i:14417 original size:44 final size:44
Alignment explanation
Indices: 14324--14419 Score: 133
Period size: 44 Copynumber: 2.2 Consensus size: 44
14314 TAAAATACAC
14324 TAAAATTAAAAGAGAAAAAAAATGAATAACTAAAATAAAAAATA
1 TAAAATTAAAAGAGAAAAAAAATGAATAACTAAAATAAAAAATA
* *
14368 CTAAAATTAAAA-AGGAAAAAAATGAATAACTAAATTGAAATAAAT-
1 -TAAAATTAAAAGAGAAAAAAAATGAATAACTAAAAT-AAA-AAATA
14413 TAAAATT
1 TAAAATT
14420 GATGGATTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
44 29 0.62
45 14 0.30
46 4 0.09
ACGTcount: A:0.68, C:0.03, G:0.07, T:0.22
Consensus pattern (44 bp):
TAAAATTAAAAGAGAAAAAAAATGAATAACTAAAATAAAAAATA
Found at i:16827 original size:106 final size:106
Alignment explanation
Indices: 16642--17737 Score: 1535
Period size: 106 Copynumber: 10.6 Consensus size: 106
16632 TATTGTTCCA
* * * * * *
16642 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAAC
16707 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
16748 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAAC
* *
16813 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGCCTCG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
16854 AGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAGATTGAGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAAC
*
16919 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * * *
16960 AATCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCAGAAATTGGGAAATTATTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAAC
17025 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
17066 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAAC
* *
17131 CAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
17172 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAAC
* **
17237 CAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCAAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
17278 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAAC
17342 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
**
17383 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AA--G----TTGACAGT
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAAC
* *** *
17441 CAGCGGTCCCTTCGTCTTGAAGTTGAACTTGTACTGTCTTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
17482 AGTCCAATATCCTTCGTTGTGAAGTTGAAATT-G----G----T---AAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAAC
17535 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * **
17576 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGATCTGAAATTAAG-AA--G----TTGACAGT
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAAC
* * *** *
17634 CAGCAGTCCCTTCGTCTTGAAGTTGAACTTGTACTGTCTTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
17675 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAGTTGTTTGTTGACA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACA
17738 GACAACTTTT
Statistics
Matches: 892, Mismatches: 72, Indels: 52
0.88 0.07 0.05
Matches are distributed among these distances:
88 2 0.00
90 2 0.00
94 75 0.08
95 1 0.00
98 1 0.00
99 160 0.18
100 1 0.00
102 2 0.00
103 2 0.00
104 1 0.00
105 97 0.11
106 548 0.61
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:17663 original size:193 final size:192
Alignment explanation
Indices: 17315--17707 Score: 723
Period size: 193 Copynumber: 2.0 Consensus size: 192
17305 AAATTGGCTC
* *
17315 TGAAATTGGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1 TGAAATTGGGAAATTGTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
* *
17380 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGACAGTCAGC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGATCTGAAATTAAGAAGTTGACAGTCAGC
*
17445 GGTCCCTTCGTCTTGAAGTTGAACTTGTACTGTCTTGAGTCCAATATCCTTCGTTGTGAAGT
131 AGTCCCTTCGTCTTGAAGTTGAACTTGTACTGTCTTGAGTCCAATATCCTTCGTTGTGAAGT
*
17507 TGAAATTGGTAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTG-TTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
17572 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGATCTGAAATTAAGAAGTTGACAGTCAG
65 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGATCTGAAATTAAGAAGTTGACAGTCAG
17637 CAGTCCCTTCGTCTTGAAGTTGAACTTGTACTGTCTTGAGTCCAATATCCTTCGTTGTGAAGT
130 CAGTCCCTTCGTCTTGAAGTTGAACTTGTACTGTCTTGAGTCCAATATCCTTCGTTGTGAAGT
17700 TGAAATTG
1 TGAAATTG
17708 ACTCTGAAAT
Statistics
Matches: 194, Mismatches: 6, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
192 14 0.07
193 180 0.93
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (192 bp):
TGAAATTGGGAAATTGTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGATCTGAAATTAAGAAGTTGACAGTCAGC
AGTCCCTTCGTCTTGAAGTTGAACTTGTACTGTCTTGAGTCCAATATCCTTCGTTGTGAAGT
Found at i:17752 original size:99 final size:99
Alignment explanation
Indices: 17351--17727 Score: 460
Period size: 99 Copynumber: 3.9 Consensus size: 99
17341 CCAGCGGTCC
* **
17351 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
1 CTTCGTCTTGAAGTTGAACTTGCACTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
* * * * *
17416 GCTCTGAAATTGAGAAGTTGACAGTCAGCGGTCC
66 GATCTGAAATTAAGAAGTTGACAGTCAGCAGACA
* *
17450 CTTCGTCTTGAAGTTGAACTTGTACTGTCTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
1 CTTCGTCTTGAAGTTGAACTTGCACTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
**** ** * * *
17515 G---T-AAATTGTTTA-TTGACAACCAGCGGTCC
66 GATCTGAAATTAAGAAGTTGACAGTCAGCAGACA
* **
17544 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
1 CTTCGTCTTGAAGTTGAACTTGCACTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
* *
17609 GATCTGAAATTAAGAAGTTGACAGTCAGCAGTCC
66 GATCTGAAATTAAGAAGTTGACAGTCAGCAGACA
* *
17643 CTTCGTCTTGAAGTTGAACTTGTACTGTCTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT-
1 CTTCGTCTTGAAGTTGAACTTGCACTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
*
17707 GACTCTGAAATTGAGAAGTTG
66 GA-TCTGAAATTAAGAAGTTG
17728 TTTGTTGACA
Statistics
Matches: 244, Mismatches: 28, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
94 76 0.31
95 7 0.03
96 1 0.00
97 1 0.00
98 8 0.03
99 151 0.62
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (99 bp):
CTTCGTCTTGAAGTTGAACTTGCACTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
GATCTGAAATTAAGAAGTTGACAGTCAGCAGACA
Found at i:21039 original size:21 final size:21
Alignment explanation
Indices: 21013--21057 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
21003 GATTTCTGGG
* *
21013 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
21034 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
21055 CAA
1 CAA
21058 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:22811 original size:23 final size:22
Alignment explanation
Indices: 22752--22818 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
22742 TATGGACATC
*
22752 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
22774 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
22796 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
22819 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:24943 original size:44 final size:44
Alignment explanation
Indices: 24894--25001 Score: 148
Period size: 44 Copynumber: 2.5 Consensus size: 44
24884 ACAAATAAAT
*
24894 AAATAAAATACACTAAAATT-AAAAGAGAAAAAAATGAATAACTA
1 AAATAAAATAAACTAAAATTAAAAAG-GAAAAAAATGAATAACTA
24938 AAATAAAA-AATACTAAAATTAAAAAGGAAAAAAATGAATAACTA
1 AAATAAAATAA-ACTAAAATTAAAAAGGAAAAAAATGAATAACTA
* * *
24982 AATTGAAATAAATTAAAATT
1 AAATAAAATAAACTAAAATT
25002 GATGGATTAA
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
43 1 0.02
44 49 0.86
45 7 0.12
ACGTcount: A:0.68, C:0.05, G:0.06, T:0.21
Consensus pattern (44 bp):
AAATAAAATAAACTAAAATTAAAAAGGAAAAAAATGAATAACTA
Found at i:24989 original size:22 final size:22
Alignment explanation
Indices: 24920--24994 Score: 66
Period size: 22 Copynumber: 3.4 Consensus size: 22
24910 AATTAAAAGA
24920 GAAAAAAATGAATAACTAAAAT
1 GAAAAAAATGAATAACTAAAAT
* *
24942 -AAAAAATACT-AA-AATTAAAAAG
1 GAAAAAA-A-TGAATAACT-AAAAT
*
24964 GAAAAAAATGAATAACTAAATT
1 GAAAAAAATGAATAACTAAAAT
*
24986 GAAATAAAT
1 GAAAAAAAT
24995 TAAAATTGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
21 10 0.24
22 21 0.51
23 10 0.24
ACGTcount: A:0.68, C:0.04, G:0.08, T:0.20
Consensus pattern (22 bp):
GAAAAAAATGAATAACTAAAAT
Found at i:27672 original size:24 final size:24
Alignment explanation
Indices: 27645--27705 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
27635 TTGAAAATAT
* *
27645 TATTATTATTTAAATGTGATGTAC
1 TATTATTATTTAAATATGATGTAA
* * *
27669 TATTGTTGTTTTAATATGATGTAA
1 TATTATTATTTAAATATGATGTAA
*
27693 TTTTAATTATTTA
1 TATT-ATTATTTA
27706 CTTTGATAAT
Statistics
Matches: 27, Mismatches: 9, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
24 22 0.81
25 5 0.19
ACGTcount: A:0.31, C:0.02, G:0.11, T:0.56
Consensus pattern (24 bp):
TATTATTATTTAAATATGATGTAA
Found at i:31028 original size:6 final size:6
Alignment explanation
Indices: 31017--31041 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
31007 GCGCACGTCT
31017 CCATCC CCATCC CCATCC CCATCC C
1 CCATCC CCATCC CCATCC CCATCC C
31042 TTGTGTTCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.68, G:0.00, T:0.16
Consensus pattern (6 bp):
CCATCC
Found at i:35042 original size:20 final size:20
Alignment explanation
Indices: 35017--35109 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
35007 TTTTCCCAAT
35017 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
35037 TCGCAACGCGAATCGGGAAA
1 TCGCAATGCGAATAAGTAAA
35057 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
35078 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
35099 TCGCAATGCGA
1 TCGCAATGCGA
35110 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.17
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:35059 original size:41 final size:41
Alignment explanation
Indices: 35014--35109 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
35004 CGATTTTCCC
35014 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATCGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATCGGGA
*
35055 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATCGGGA
*
35096 AAATCGCAATGCGA
1 AATTCGCAATGCGA
35110 TACTGACTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.18
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATCGGGA
Found at i:35063 original size:21 final size:20
Alignment explanation
Indices: 35017--35109 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
35007 TTTTCCCAAT
*
35017 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
35037 TCGCAACGCGAATCGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
35057 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
35078 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
35099 TCGCAATGCGA
1 TCGCAATGCGA
35110 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.17
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:35122 original size:41 final size:41
Alignment explanation
Indices: 35036--35171 Score: 114
Period size: 41 Copynumber: 3.3 Consensus size: 41
35026 GAATAAGTAA
* * * *
35036 ATCGCAACGCGAATCGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
35077 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * *** * * *
35118 ATCGCAATGCGATAATAAAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
35160 TTCGCAACGCGA
1 ATCGCAACGCGA
35172 TACTGACTTT
Statistics
Matches: 78, Mismatches: 14, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
40 4 0.05
41 42 0.54
42 32 0.41
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:35123 original size:20 final size:20
Alignment explanation
Indices: 35098--35193 Score: 84
Period size: 20 Copynumber: 4.7 Consensus size: 20
35088 AATTGGGAAA
*
35098 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
35118 ATCGCAATGCGATAATAAAAAA
1 ATCGCAACGCGATACT--GACT
* *
35140 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
35160 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
35180 TTCGCAACGCGATA
1 ATCGCAACGCGATA
35194 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
20 47 0.77
22 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:35409 original size:22 final size:22
Alignment explanation
Indices: 35381--35424 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
35371 CACTCTCTCA
35381 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
35403 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
35425 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:35711 original size:20 final size:20
Alignment explanation
Indices: 35686--35723 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
35676 CGATTCTCTC
35686 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
35706 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
35724 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:37064 original size:18 final size:18
Alignment explanation
Indices: 37043--37087 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
37033 TCCACTTCGG
*
37043 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
37061 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
37079 GAGCCATCA
1 GAGCCATCA
37088 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:37583 original size:20 final size:20
Alignment explanation
Indices: 37558--37603 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
37548 TAGTTTACTT
*
37558 TCGCAACATGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
37578 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
37598 TCGCAA
1 TCGCAA
37604 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:37612 original size:19 final size:20
Alignment explanation
Indices: 37569--37624 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
37559 CGCAACATGA
37569 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
37589 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
**
37608 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
37625 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:37632 original size:14 final size:14
Alignment explanation
Indices: 37613--37670 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
37603 ATGCGAAATG
37613 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
37627 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
37643 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
37659 AAAATCGCAACG
1 AAAATCGCAACG
37671 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:37655 original size:32 final size:33
Alignment explanation
Indices: 37597--37687 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
37587 GGAAATGGCT
*
37597 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
37630 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
37662 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
37688 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:37681 original size:19 final size:19
Alignment explanation
Indices: 37577--37692 Score: 83
Period size: 19 Copynumber: 6.6 Consensus size: 19
37567 GAAAATGACT
***
37577 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGAAA
*
37597 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
37616 ATCGCAA--CG--A-CAAA
1 ATCGCAACGCGAAATGAAA
37630 ATCGCAACGCGAAATG-AA
1 ATCGCAACGCGAAATGAAA
*
37648 ATCGCAA--CG--A-CAAA
1 ATCGCAACGCGAAATGAAA
37662 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
37681 ATCGCAATGCGA
1 ATCGCAACGCGA
37693 TTTGTGTTTC
Statistics
Matches: 76, Mismatches: 9, Indels: 23
0.70 0.08 0.21
Matches are distributed among these distances:
14 20 0.26
15 1 0.01
16 6 0.08
17 2 0.03
18 11 0.14
19 27 0.36
20 9 0.12
ACGTcount: A:0.43, C:0.23, G:0.22, T:0.12
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:37762 original size:19 final size:19
Alignment explanation
Indices: 37699--37821 Score: 96
Period size: 20 Copynumber: 6.7 Consensus size: 19
37689 GCGATTTGTG
37699 TTTCGCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTCA
37717 TTTCGCGTTGCGA-TTT--
1 TTTCGCGTTGCGATTTTCA
*
37733 TGT--CGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
* ***
37750 TTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGATTTTCA
**
37769 TTTCCGCGTTGCGATAGTCA
1 TTT-CGCGTTGCGATTTTCA
* *
37789 TTTCACGTTGCGATTTTAA
1 TTTCGCGTTGCGATTTTCA
*
37808 GTTTCGTGTTGCGA
1 -TTTCGCGTTGCGA
37822 AAGTAAACTA
Statistics
Matches: 84, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 16 0.19
19 25 0.30
20 28 0.33
ACGTcount: A:0.14, C:0.20, G:0.24, T:0.42
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:39829 original size:14 final size:15
Alignment explanation
Indices: 39810--39886 Score: 59
Period size: 14 Copynumber: 4.7 Consensus size: 15
39800 CGAAATGGCT
39810 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
*
39824 ATCGCAATGCGAAATGAA
1 ATCGCAA-GCGAGA--AA
39842 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCG--A-GAAA
39861 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
39875 ATCGCAATGCGA
1 ATCGCAA-GCGA
39887 TTATCATTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.35
15 1 0.02
16 7 0.13
17 2 0.04
18 13 0.25
19 9 0.17
20 1 0.02
21 1 0.02
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (15 bp):
ATCGCAAGCGAGAAA
Found at i:39842 original size:19 final size:19
Alignment explanation
Indices: 39820--39886 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
39810 ATCGCAACGA
39820 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
39839 G-AAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
39857 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
39871 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
39887 TTATCATTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
14 11 0.25
15 1 0.02
16 2 0.05
17 2 0.05
18 18 0.41
19 10 0.23
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:39962 original size:20 final size:20
Alignment explanation
Indices: 39912--39962 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
39902 GCGATATTCT
*
39912 CGTTGCGATAACCATTTTCA
1 CGTTGCGATAGCCATTTTCA
39932 CGTTGCGATAGCCATTTTCA
1 CGTTGCGATAGCCATTTTCA
39952 CGTTGCGATAG
1 CGTTGCGATAG
39963 TCAAATGAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCA
Found at i:40325 original size:14 final size:14
Alignment explanation
Indices: 40306--40341 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
40296 ATTGTTTAAT
40306 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
40320 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
40334 TGATTTGT
1 TGATTTGT
40342 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:40467 original size:14 final size:14
Alignment explanation
Indices: 40448--40501 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
40438 CGAAATGGCT
40448 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
40462 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
40481 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
40495 ATCGCAA
1 ATCGCAA
40502 TGCGATTATC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.31
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:40519 original size:33 final size:33
Alignment explanation
Indices: 40429--40506 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
40419 AAAACAGACT
* ***
40429 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
40462 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
40495 ATCGCAATGCGA
1 ATCGCAATGCGA
40507 TTATCATTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:40582 original size:20 final size:20
Alignment explanation
Indices: 40532--40585 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
40522 GCGATATTCT
**
40532 CGTTGCGATAACCATTTTCA
1 CGTTGCGATAGTCATTTTCA
40552 CGTTGCGATAGTCATTTTCA
1 CGTTGCGATAGTCATTTTCA
40572 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
40586 AATGAATGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCA
Found at i:40843 original size:42 final size:42
Alignment explanation
Indices: 40777--40875 Score: 128
Period size: 42 Copynumber: 2.4 Consensus size: 42
40767 CGCTTTGAAA
* * *
40777 ATCGCATTGCGA-TTATGTATTATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTTTTTTATTATCGCATTGCGAAAGTAAGT
* * * *
40818 ATCTCGTTGCGATTTTTTTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTTTTATTATCGCATTGCGAAAGTAAGT
40860 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
40876 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
41 10 0.21
42 38 0.79
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.40
Consensus pattern (42 bp):
ATCGCATTGCGATTTTTTTATTATCGCATTGCGAAAGTAAGT
Found at i:40905 original size:20 final size:20
Alignment explanation
Indices: 40861--40953 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
40851 ATAGTCAGTA
* **
40861 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
40882 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
40902 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
40923 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
40943 TCGCATTGCGA
1 TCGCATTGCGA
40954 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:40906 original size:41 final size:41
Alignment explanation
Indices: 40861--40956 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
40851 ATAGTCAGTA
*
40861 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
40902 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
40943 TCGCATTGCGAATT
1 TCGCATTGCGAATT
40957 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Done.