Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014593.1 Corchorus olitorius cultivar O-4 contig14626, 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: 70847
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:1848 original size:4 final size:4
Alignment explanation
Indices: 1841--1867 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1831 AAAAAAAAAA
1841 AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAA
1868 TTGGATTGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:1952 original size:14 final size:13
Alignment explanation
Indices: 1905--1970 Score: 82
Period size: 13 Copynumber: 4.9 Consensus size: 13
1895 AGATTTTCAG
1905 GATTTTCAAAAAT
1 GATTTTCAAAAAT
1918 GATTTTCAAGAAACT
1 GATTTTCAA-AAA-T
1933 --TTTTCAAGAAAT
1 GATTTTCAA-AAAT
1945 GATTTTCAAAAAT
1 GATTTTCAAAAAT
1958 GAGTTTTCAAAAA
1 GA-TTTTCAAAAA
1971 GGTTTTAAGT
Statistics
Matches: 48, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
12 1 0.02
13 26 0.54
14 20 0.42
15 1 0.02
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (13 bp):
GATTTTCAAAAAT
Found at i:2624 original size:11 final size:11
Alignment explanation
Indices: 2608--2653 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
2598 GAAGCAATCT
2608 AAAGAAAAAAA
1 AAAGAAAAAAA
*
2619 AAAGAAAAGGAA
1 AAAGAAAA-AAA
*
2631 AAAGCAAAGAAA
1 AAAG-AAAAAAA
2643 AAAGAAAAAAA
1 AAAGAAAAAAA
2654 GGGAAAAGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
11 14 0.48
12 12 0.41
13 3 0.10
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAAA
Found at i:2634 original size:12 final size:12
Alignment explanation
Indices: 2608--2650 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
2598 GAAGCAATCT
2608 AAAGAAAA-AAA
1 AAAGAAAAGAAA
*
2619 AAAGAAAAGGAA
1 AAAGAAAAGAAA
*
2631 AAAGCAAAGAAA
1 AAAGAAAAGAAA
2643 AAAGAAAA
1 AAAGAAAA
2651 AAAGGGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
11 8 0.30
12 19 0.70
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAGAAAAGAAA
Found at i:2924 original size:87 final size:87
Alignment explanation
Indices: 2778--2944 Score: 271
Period size: 87 Copynumber: 1.9 Consensus size: 87
2768 ATATTTGAAC
*
2778 ATTTCTTGAGATGAGAAACTGATCCAGAAACATCAATTAAGTTGGGAATATCAATGCATGATCAA
1 ATTTCTTAAGATGAGAAACTGATCCAGAAACATCAATTAAGTTGGGAATATCAATGCATGATCAA
2843 ATTGGAGGAAGATTTGGGAAAT
66 ATTGGAGGAAGATTTGGGAAAT
* * * * * *
2865 ATTTCTTAAGGTGGGAAGCTGATCCAGAACCATTAATTGAGTTGGGAATATCAATGCATGATCAA
1 ATTTCTTAAGATGAGAAACTGATCCAGAAACATCAATTAAGTTGGGAATATCAATGCATGATCAA
2930 ATTGGAGGAAGATTT
66 ATTGGAGGAAGATTT
2945 AGGGGCATCA
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 73 1.00
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.29
Consensus pattern (87 bp):
ATTTCTTAAGATGAGAAACTGATCCAGAAACATCAATTAAGTTGGGAATATCAATGCATGATCAA
ATTGGAGGAAGATTTGGGAAAT
Found at i:4186 original size:37 final size:37
Alignment explanation
Indices: 3721--4179 Score: 444
Period size: 37 Copynumber: 12.4 Consensus size: 37
3711 TTCAAGATTT
*
3721 CTGTTTAGGTGTCTTATCAAATTCTTATTTAAGGTCC
1 CTGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCC
* * * * *
3758 CTGTTTAGGTGT-TTCATAAAAAT-CTTGTTCAAGATTC
1 CTGTTTAGGTGTCTT-AT-CAAATCCTTATTTAAGGTCC
* *
3795 TTGTTTAGGTGTCTTATCAAATCCTTGTTTAAGGTCC
1 CTGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCC
* * *
3832 CTGTTTAGGTGTTTTATTAAATCCTTACTTAAGGTCC
1 CTGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCC
3869 CTGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCC
1 CTGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCC
* * ** * *
3906 TTGTTTAGGTGTCTCATCGAAAT-CTGGTTCAAGATCC
1 CTGTTTAGGTGTCTTATC-AAATCCTTATTTAAGGTCC
* * * * * *
3943 TTGTTTAGGTGTCTCATCAAAAT-CTTGTTCAAGATTC
1 CTGTTTAGGTGTCTTATC-AAATCCTTATTTAAGGTCC
* * * *
3980 ATGTTTAGGTTTCTTATTAAATCTTTATTTAAGGTCC
1 CTGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCC
* * * *
4017 CTATTTAGGTGTCTCATCAAAAT-CTTGTTTAAGATCC
1 CTGTTTAGGTGTCTTATC-AAATCCTTATTTAAGGTCC
**
4054 CTGTTTAGGTGTCTTATCAAATCCTTATTTAAGGAGC
1 CTGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCC
* ** * *
4091 CTGTTTAGGAT-TCTTGTCAAAATTTTTGTTTAAGATCC
1 CTGTTTAGG-TGTCTTATC-AAATCCTTATTTAAGGTCC
* *
4129 CTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTAC
1 CTGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCC
*
4166 CTATTTAGGTGTCT
1 CTGTTTAGGTGTCT
4180 CTTCAAAATC
Statistics
Matches: 346, Mismatches: 65, Indels: 22
0.80 0.15 0.05
Matches are distributed among these distances:
36 14 0.04
37 289 0.84
38 43 0.12
ACGTcount: A:0.23, C:0.16, G:0.17, T:0.44
Consensus pattern (37 bp):
CTGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCC
Found at i:4201 original size:62 final size:62
Alignment explanation
Indices: 4125--4273 Score: 253
Period size: 62 Copynumber: 2.4 Consensus size: 62
4115 TTTGTTTAAG
*
4125 ATCCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTACCTATTTAGGTGTCTCTTCAAA
1 ATCCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTACCTATTTAAGTGTCTCTTCAAA
* *
4187 ATCCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTACCTGTTTAATTGTCTCTTCAAA
1 ATCCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTACCTATTTAAGTGTCTCTTCAAA
**
4249 ATCCCAATTTAGGTTTCTTATCAAA
1 ATCCCTGTTTAGGTTTCTTATCAAA
4274 ATTTTGTTCA
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 82 1.00
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.44
Consensus pattern (62 bp):
ATCCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTACCTATTTAAGTGTCTCTTCAAA
Found at i:4221 original size:24 final size:25
Alignment explanation
Indices: 4165--4221 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
4155 ATTTAAGGTA
4165 CCTATTTAGGTGTCTCTTCAAAATC
1 CCTATTTAGGTGTCTCTTCAAAATC
* *
4190 CCTGTTTAGGTTTCT-TATC-AAATC
1 CCTATTTAGGTGTCTCT-TCAAAATC
*
4214 CTTATTTA
1 CCTATTTA
4222 AGGTACCTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.46
Consensus pattern (25 bp):
CCTATTTAGGTGTCTCTTCAAAATC
Found at i:4430 original size:54 final size:54
Alignment explanation
Indices: 4348--4595 Score: 256
Period size: 54 Copynumber: 4.6 Consensus size: 54
4338 TCTCTCTAGA
4348 AAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
1 AAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
* *
4402 AAGTTGATCTTAAGATGACCCGGTGTGGTCTTTCATAGAAGCTTTT-AGAGGTCT
1 AAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAG-TTTTCAGAGATCT
* * * * * *
4456 AAGTTGATCTTTAA-ACGACCCTGTGTGGTCTTCCATAGAAGTTTTCAAAAAACT
1 AAGTTGATC-TTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
* * * * *
4510 AAGTTGATCTTAAAGTTGATCTAGTGTGGTCATTCCA-AGAAGTTTAC-GATGATC-
1 AAGTTGATCTT-AAGATGACCCAGTGTGGTC-TTTCATAGAAGTTTTCAGA-GATCT
*
4564 AGAGTTGATCTCTAA-ACTGACCCAGTGCGGTC
1 A-AGTTGATCT-TAAGA-TGACCCAGTGTGGTC
4596 ATTCCAAGAA
Statistics
Matches: 162, Mismatches: 22, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
53 6 0.04
54 97 0.60
55 53 0.33
56 6 0.04
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (54 bp):
AAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
Found at i:4644 original size:55 final size:55
Alignment explanation
Indices: 4532--4647 Score: 130
Period size: 55 Copynumber: 2.1 Consensus size: 55
4522 AAGTTGATCT
* * * *
4532 AGTGTGGTCATTCCAAGAAGTTTACGATGATCAGAGTTGATCTCTAAACTGACCC
1 AGTGCGGTCATTCCAAGAAGTTTACCATGATCAGAGTTGAACTCTAAACTAACCC
* *
4587 AGTGCGGTCATTCCAAGAAAGGTTT-CCATGATCA-AGGTTGAACTCTTAA-TAATCC
1 AGTGCGGTCATTCCAAG-AA-GTTTACCATGATCAGA-GTTGAACTCTAAACTAACCC
4642 AGTGCG
1 AGTGCG
4648 CTTAATTAAG
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
55 27 0.52
56 21 0.40
57 4 0.08
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.28
Consensus pattern (55 bp):
AGTGCGGTCATTCCAAGAAGTTTACCATGATCAGAGTTGAACTCTAAACTAACCC
Found at i:4700 original size:33 final size:33
Alignment explanation
Indices: 4658--4735 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
4648 CTTAATTAAG
* * * *
4658 AAGTTCAAAATTTGCATTTCATTTCAAAATTCA
1 AAGTTCAAAATCTGCATATCATATCAAAACTCA
4691 AAGTTCAAAATCTGCATATCATATCAAAACTCA
1 AAGTTCAAAATCTGCATATCATATCAAAACTCA
4724 AAGTTCAAAATC
1 AAGTTCAAAATC
4736 CACAGTTTCT
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:0.44, C:0.18, G:0.06, T:0.32
Consensus pattern (33 bp):
AAGTTCAAAATCTGCATATCATATCAAAACTCA
Found at i:4885 original size:7 final size:7
Alignment explanation
Indices: 4871--4915 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
4861 ATTTCATTGC
4871 TCAAAAT
1 TCAAAAT
*
4878 TTAAAAT
1 TCAAAAT
4885 TCAAAAT
1 TCAAAAT
*
4892 TCAAAAC
1 TCAAAAT
*
4899 TCAAAAC
1 TCAAAAT
4906 TCAAAAT
1 TCAAAAT
4913 TCA
1 TCA
4916 TGTCTCAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.56, C:0.18, G:0.00, T:0.27
Consensus pattern (7 bp):
TCAAAAT
Found at i:4895 original size:21 final size:21
Alignment explanation
Indices: 4871--5103 Score: 121
Period size: 21 Copynumber: 11.0 Consensus size: 21
4861 ATTTCATTGC
* * *
4871 TCAAAATTTAAAATTCAAAAT
1 TCAAAACTCAAAACTCAAAAT
4892 TCAAAACTCAAAACTCAAAAT
1 TCAAAACTCAAAACTCAAAAT
*** * *
4913 TCATGTCTCAAAAATCAAATT
1 TCAAAACTCAAAACTCAAAAT
** * *
4934 TCAAAACATGC--ATTTCAGCATT
1 TCAAAAC-T-CAAAACTCA-AAAT
** * *
4956 TC-ATTCTTCAAAAGTCAAAAG
1 TCAAAAC-TCAAAACTCAAAAT
* * *
4977 TCAAAAGTCAAAAGTCAAAAG
1 TCAAAACTCAAAACTCAAAAT
* * *
4998 TCAAAAGTCAAAAGTCAAAAG
1 TCAAAACTCAAAACTCAAAAT
* * *
5019 TCAAAAGTCAAAAGTCAAAAG
1 TCAAAACTCAAAACTCAAAAT
* * *
5040 TCAAAAGTCAAAAGTCAAAAG
1 TCAAAACTCAAAACTCAAAAT
* *
5061 TCAAAAGTCAAAATTCAAAAT
1 TCAAAACTCAAAACTCAAAAT
* *
5082 TCAAAATTCAAAATTCAAAAT
1 TCAAAACTCAAAACTCAAAAT
5103 T
1 T
5104 TGCATTTTTT
Statistics
Matches: 178, Mismatches: 28, Indels: 12
0.82 0.13 0.06
Matches are distributed among these distances:
20 1 0.01
21 165 0.93
22 11 0.06
23 1 0.01
ACGTcount: A:0.52, C:0.16, G:0.08, T:0.24
Consensus pattern (21 bp):
TCAAAACTCAAAACTCAAAAT
Found at i:4937 original size:14 final size:14
Alignment explanation
Indices: 4874--5100 Score: 66
Period size: 14 Copynumber: 16.2 Consensus size: 14
4864 TCATTGCTCA
4874 AAATTT-AAAATTC
1 AAATTTCAAAATTC
* *
4887 AAAATTCAAAACTC
1 AAATTTCAAAATTC
**
4901 AAAACTCAAAATTC
1 AAATTTCAAAATTC
** * *
4915 ATGTCTCAAAAATC
1 AAATTTCAAAATTC
4929 AAATTTCAAAA--C
1 AAATTTCAAAATTC
* * *
4941 ATGCATTTCAGCATTTC
1 A--AATTTCA-AAATTC
* *
4958 -ATTCTTCAAAAGTC
1 AAAT-TTCAAAATTC
** *
4972 AAAAGTCAAAAGTC
1 AAATTTCAAAATTC
** *
4986 AAAAGTCAAAAGTC
1 AAATTTCAAAATTC
** *
5000 AAAAGTCAAAAGTC
1 AAATTTCAAAATTC
** *
5014 AAAAGTCAAAAGTC
1 AAATTTCAAAATTC
** *
5028 AAAAGTCAAAAGTC
1 AAATTTCAAAATTC
** *
5042 AAAAGTCAAAAGTC
1 AAATTTCAAAATTC
** *
5056 AAAAGTCAAAAGTC
1 AAATTTCAAAATTC
*
5070 AAAATTCAAAATTC
1 AAATTTCAAAATTC
*
5084 AAAATTCAAAATTC
1 AAATTTCAAAATTC
5098 AAA
1 AAA
5101 ATTTGCATTT
Statistics
Matches: 182, Mismatches: 24, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
12 2 0.01
13 5 0.03
14 168 0.92
15 6 0.03
17 1 0.01
ACGTcount: A:0.53, C:0.16, G:0.08, T:0.23
Consensus pattern (14 bp):
AAATTTCAAAATTC
Found at i:5103 original size:7 final size:7
Alignment explanation
Indices: 4963--5101 Score: 242
Period size: 7 Copynumber: 19.9 Consensus size: 7
4953 ATTTCATTCT
4963 TCAAAAG
1 TCAAAAG
4970 TCAAAAG
1 TCAAAAG
4977 TCAAAAG
1 TCAAAAG
4984 TCAAAAG
1 TCAAAAG
4991 TCAAAAG
1 TCAAAAG
4998 TCAAAAG
1 TCAAAAG
5005 TCAAAAG
1 TCAAAAG
5012 TCAAAAG
1 TCAAAAG
5019 TCAAAAG
1 TCAAAAG
5026 TCAAAAG
1 TCAAAAG
5033 TCAAAAG
1 TCAAAAG
5040 TCAAAAG
1 TCAAAAG
5047 TCAAAAG
1 TCAAAAG
5054 TCAAAAG
1 TCAAAAG
5061 TCAAAAG
1 TCAAAAG
*
5068 TCAAAAT
1 TCAAAAG
*
5075 TCAAAAT
1 TCAAAAG
*
5082 TCAAAAT
1 TCAAAAG
*
5089 TCAAAAT
1 TCAAAAG
5096 TCAAAA
1 TCAAAA
5102 TTTGCATTTT
Statistics
Matches: 131, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
7 131 1.00
ACGTcount: A:0.58, C:0.14, G:0.11, T:0.17
Consensus pattern (7 bp):
TCAAAAG
Found at i:10632 original size:24 final size:25
Alignment explanation
Indices: 10605--10656 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
10595 TTTATTTTTA
10605 ATTTATTATTTGTAT-TTAAAATAT
1 ATTTATTATTTGTATATTAAAATAT
* *
10629 ATTTATTATTTGTTTATTAATATAT
1 ATTTATTATTTGTATATTAAAATAT
10654 ATT
1 ATT
10657 ATATCTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 14 0.56
25 11 0.44
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (25 bp):
ATTTATTATTTGTATATTAAAATAT
Found at i:15762 original size:32 final size:32
Alignment explanation
Indices: 15726--15822 Score: 124
Period size: 32 Copynumber: 3.0 Consensus size: 32
15716 CCGCCCGACT
* *
15726 CGAATGACCCGCAACCCAGATGAACCGAGACC
1 CGAATGACCCGTAACCCAGATGACCCGAGACC
* *
15758 CGAATGACCCATAACCCAGATGACCCGAAACC
1 CGAATGACCCGTAACCCAGATGACCCGAGACC
**
15790 TAAATGACCCGTAACCC-GAGTGACCCGAGACC
1 CGAATGACCCGTAACCCAGA-TGACCCGAGACC
15822 C
1 C
15823 ATATGAGCCG
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
31 2 0.04
32 53 0.96
ACGTcount: A:0.34, C:0.37, G:0.20, T:0.09
Consensus pattern (32 bp):
CGAATGACCCGTAACCCAGATGACCCGAGACC
Found at i:15838 original size:32 final size:32
Alignment explanation
Indices: 15728--15851 Score: 110
Period size: 32 Copynumber: 3.9 Consensus size: 32
15718 GCCCGACTCG
* * *
15728 AATGACCCGCAACCC-AGATGAACCGAGACCCG
1 AATGACCCGAAACCCGAG-TGACCCGAGACCCA
* *
15760 AATGACCC-ATAACCC-AGATGACCCGAAACCTA
1 AATGACCCGA-AACCCGAG-TGACCCGAGACCCA
*
15792 AATGACCCGTAACCCGAGTGACCCGAGACCCA
1 AATGACCCGAAACCCGAGTGACCCGAGACCCA
* * * *
15824 TATGAGCCGAAACCCGAATAACCCGAGA
1 AATGACCCGAAACCCGAGTGACCCGAGA
15852 AGTTAACCCA
Statistics
Matches: 76, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
32 74 0.97
33 2 0.03
ACGTcount: A:0.36, C:0.35, G:0.19, T:0.10
Consensus pattern (32 bp):
AATGACCCGAAACCCGAGTGACCCGAGACCCA
Found at i:15849 original size:16 final size:16
Alignment explanation
Indices: 15726--15849 Score: 94
Period size: 16 Copynumber: 7.8 Consensus size: 16
15716 CCGCCCGACT
*
15726 CGAATGACCCGCAACC
1 CGAATGACCCGAAACC
* *
15742 C-AGATGAACCGAGACC
1 CGA-ATGACCCGAAACC
15758 CGAATGACCC-ATAACC
1 CGAATGACCCGA-AACC
15774 C-AGATGACCCGAAACC
1 CGA-ATGACCCGAAACC
** *
15790 TAAATGACCCGTAACC
1 CGAATGACCCGAAACC
* *
15806 CGAGTGACCCGAGACC
1 CGAATGACCCGAAACC
*
15822 C-ATATGAGCCGAAACC
1 CGA-ATGACCCGAAACC
*
15838 CGAATAACCCGA
1 CGAATGACCCGA
15850 GAAGTTAACC
Statistics
Matches: 83, Mismatches: 17, Indels: 16
0.72 0.15 0.14
Matches are distributed among these distances:
15 4 0.05
16 75 0.90
17 4 0.05
ACGTcount: A:0.35, C:0.35, G:0.19, T:0.10
Consensus pattern (16 bp):
CGAATGACCCGAAACC
Found at i:16443 original size:42 final size:42
Alignment explanation
Indices: 16380--16461 Score: 155
Period size: 42 Copynumber: 2.0 Consensus size: 42
16370 TGTTGACACA
*
16380 TACCTCACCTGATAATTAATTATGTATTTAATATTCAAAACC
1 TACCTCACCTGATAATCAATTATGTATTTAATATTCAAAACC
16422 TACCTCACCTGATAATCAATTATGTATTTAATATTCAAAA
1 TACCTCACCTGATAATCAATTATGTATTTAATATTCAAAA
16462 TTAATATCTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.39, C:0.18, G:0.05, T:0.38
Consensus pattern (42 bp):
TACCTCACCTGATAATCAATTATGTATTTAATATTCAAAACC
Found at i:17009 original size:16 final size:16
Alignment explanation
Indices: 16988--17063 Score: 100
Period size: 16 Copynumber: 4.8 Consensus size: 16
16978 AACCCGCCCA
*
16988 ACCCGAGACCTGGTA-G
1 ACCCGAGACC-CGTATG
*
17004 ACCCGAGACCCGAATG
1 ACCCGAGACCCGTATG
17020 ACCCGAGACCCGTATG
1 ACCCGAGACCCGTATG
*
17036 ACCCGAGACCCGAATG
1 ACCCGAGACCCGTATG
*
17052 ACCCGAAACCCG
1 ACCCGAGACCCG
17064 AACCCAAATG
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
15 2 0.04
16 52 0.96
ACGTcount: A:0.29, C:0.38, G:0.25, T:0.08
Consensus pattern (16 bp):
ACCCGAGACCCGTATG
Found at i:17014 original size:7 final size:7
Alignment explanation
Indices: 16988--17068 Score: 65
Period size: 7 Copynumber: 10.6 Consensus size: 7
16978 AACCCGCCCA
16988 ACCCGAG
1 ACCCGAG
*
16995 ACCTGGTAG
1 ACC-CG-AG
17004 ACCCGAG
1 ACCCGAG
17011 ACCCGAATG
1 ACCCG-A-G
17020 ACCCGAG
1 ACCCGAG
17027 ACCCGTATG
1 ACCCG-A-G
17036 ACCCGAG
1 ACCCGAG
17043 ACCCGAATG
1 ACCCG-A-G
*
17052 ACCCGAA
1 ACCCGAG
17059 ACCCGA-
1 ACCCGAG
17065 ACCC
1 ACCC
17069 AAATGATCTG
Statistics
Matches: 63, Mismatches: 3, Indels: 17
0.76 0.04 0.20
Matches are distributed among these distances:
6 4 0.06
7 28 0.44
8 8 0.13
9 23 0.37
ACGTcount: A:0.30, C:0.40, G:0.23, T:0.07
Consensus pattern (7 bp):
ACCCGAG
Found at i:17022 original size:9 final size:9
Alignment explanation
Indices: 17010--17058 Score: 61
Period size: 9 Copynumber: 5.9 Consensus size: 9
17000 GTAGACCCGA
17010 GACCCGAAT
1 GACCCGAAT
17019 GACCCG-A-
1 GACCCGAAT
*
17026 GACCCGTAT
1 GACCCGAAT
17035 GACCCG-A-
1 GACCCGAAT
17042 GACCCGAAT
1 GACCCGAAT
17051 GACCCGAA
1 GACCCGAA
17059 ACCCGAACCC
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
7 12 0.33
8 4 0.11
9 20 0.56
ACGTcount: A:0.31, C:0.37, G:0.24, T:0.08
Consensus pattern (9 bp):
GACCCGAAT
Found at i:17024 original size:32 final size:32
Alignment explanation
Indices: 16988--17063 Score: 118
Period size: 32 Copynumber: 2.4 Consensus size: 32
16978 AACCCGCCCA
*
16988 ACCCGAGACCTGGTA-GACCCGAGACCCGAATG
1 ACCCGAGACC-CGTATGACCCGAGACCCGAATG
17020 ACCCGAGACCCGTATGACCCGAGACCCGAATG
1 ACCCGAGACCCGTATGACCCGAGACCCGAATG
*
17052 ACCCGAAACCCG
1 ACCCGAGACCCG
17064 AACCCAAATG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
31 3 0.07
32 38 0.93
ACGTcount: A:0.29, C:0.38, G:0.25, T:0.08
Consensus pattern (32 bp):
ACCCGAGACCCGTATGACCCGAGACCCGAATG
Found at i:17064 original size:16 final size:16
Alignment explanation
Indices: 17003--17065 Score: 108
Period size: 16 Copynumber: 3.9 Consensus size: 16
16993 AGACCTGGTA
17003 GACCCGAGACCCGAAT
1 GACCCGAGACCCGAAT
*
17019 GACCCGAGACCCGTAT
1 GACCCGAGACCCGAAT
17035 GACCCGAGACCCGAAT
1 GACCCGAGACCCGAAT
*
17051 GACCCGAAACCCGAA
1 GACCCGAGACCCGAA
17066 CCCAAATGAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.32, C:0.38, G:0.24, T:0.06
Consensus pattern (16 bp):
GACCCGAGACCCGAAT
Found at i:17073 original size:22 final size:22
Alignment explanation
Indices: 17036--17087 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
17026 GACCCGTATG
*
17036 ACCCGAGACCCGAATGACCCGAA
1 ACCCGA-ACCCAAATGACCCGAA
* *
17059 ACCCGAACCCAAATGATCTGAA
1 ACCCGAACCCAAATGACCCGAA
17081 ACCCGAA
1 ACCCGAA
17088 TGATCCGAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 20 0.77
23 6 0.23
ACGTcount: A:0.38, C:0.37, G:0.17, T:0.08
Consensus pattern (22 bp):
ACCCGAACCCAAATGACCCGAA
Found at i:28650 original size:2 final size:2
Alignment explanation
Indices: 28611--28640 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
28601 CTTTATTTAC
28611 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28641 ATGGTATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28882 original size:29 final size:30
Alignment explanation
Indices: 28835--28951 Score: 121
Period size: 31 Copynumber: 3.9 Consensus size: 30
28825 AAAAATGACA
* *
28835 CATGACATGTGTC-TTTTTTGTGTAC-GAGG
1 CATGACACGTGTCACTTTTTG-GTACAGAGG
* *
28864 CATGCCACGTGTCACTTTTTGGTACATGTGG
1 CATGACACGTGTCACTTTTTGGTACA-GAGG
* *
28895 CGTGACACGTGTCACTTTTTGGTACATGTGG
1 CATGACACGTGTCACTTTTTGGTACA-GAGG
* *
28926 CATGACACATGTCGCTTTTTGGTACA
1 CATGACACGTGTCACTTTTTGGTACA
28952 TGTGGTGTGC
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
29 15 0.20
30 6 0.08
31 55 0.72
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.37
Consensus pattern (30 bp):
CATGACACGTGTCACTTTTTGGTACAGAGG
Found at i:28904 original size:31 final size:31
Alignment explanation
Indices: 28873--28987 Score: 167
Period size: 31 Copynumber: 3.7 Consensus size: 31
28863 GCATGCCACG
*
28873 TGTCACTTTTTGGTACATGTGGCGTGACACG
1 TGTCACTTTTTGGTACATGTGGCGTGACACA
*
28904 TGTCACTTTTTGGTACATGTGGCATGACACA
1 TGTCACTTTTTGGTACATGTGGCGTGACACA
* * *
28935 TGTCGCTTTTTGGTACATGTGGTGTGCCACA
1 TGTCACTTTTTGGTACATGTGGCGTGACACA
* *
28966 TGTCGCTTTTTGGTACACGTGG
1 TGTCACTTTTTGGTACATGTGG
28988 TATACCACAT
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 77 1.00
ACGTcount: A:0.16, C:0.19, G:0.28, T:0.37
Consensus pattern (31 bp):
TGTCACTTTTTGGTACATGTGGCGTGACACA
Found at i:28988 original size:31 final size:31
Alignment explanation
Indices: 28862--28997 Score: 164
Period size: 31 Copynumber: 4.4 Consensus size: 31
28852 TTGTGTACGA
*
28862 GGCATGCCACGTGTCACTTTTTGGTACATGT
1 GGCATGCCACATGTCACTTTTTGGTACATGT
* * *
28893 GGCGTGACACGTGTCACTTTTTGGTACATGT
1 GGCATGCCACATGTCACTTTTTGGTACATGT
* *
28924 GGCATGACACATGTCGCTTTTTGGTACATGT
1 GGCATGCCACATGTCACTTTTTGGTACATGT
** * *
28955 GGTGTGCCACATGTCGCTTTTTGGTACACGT
1 GGCATGCCACATGTCACTTTTTGGTACATGT
* *
28986 GGTATACCACAT
1 GGCATGCCACAT
28998 TGGACACTGT
Statistics
Matches: 94, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 94 1.00
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.35
Consensus pattern (31 bp):
GGCATGCCACATGTCACTTTTTGGTACATGT
Found at i:31532 original size:1 final size:1
Alignment explanation
Indices: 31528--31564 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
31518 CCTTTTTTTT
31528 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
31565 GATCAGAATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:32893 original size:11 final size:11
Alignment explanation
Indices: 32879--32916 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
32869 ATTCATAACA
32879 AATTTATAATT
1 AATTTATAATT
32890 AATTTATAATT
1 AATTTATAATT
32901 -ATTTGATAATT
1 AATTT-ATAATT
*
32912 TATTT
1 AATTT
32917 TATATAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:33086 original size:2 final size:2
Alignment explanation
Indices: 33079--33119 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
33069 AGTAGGTTTA
*
33079 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
33120 AATTTAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:33133 original size:20 final size:20
Alignment explanation
Indices: 33087--33144 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
33077 TAATATATAT
* *
33087 ATATATATATATATATTTAT
1 ATATATATATATAAATTTAA
33107 ATATATATATATAAATTTAA
1 ATATATATATATAAATTTAA
33127 A-AT-TATATTCATAAATTT
1 ATATATATA-T-ATAAATTT
33145 TGAAACACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.12
19 3 0.09
20 27 0.79
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATATATATATAAATTTAA
Found at i:34933 original size:14 final size:15
Alignment explanation
Indices: 34914--34942 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
34904 TAGTTTTTGG
34914 CATATTAAAA-AAAA
1 CATATTAAAAGAAAA
34928 CATATTAAAAGAAAA
1 CATATTAAAAGAAAA
34943 AAACTATTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.69, C:0.07, G:0.03, T:0.21
Consensus pattern (15 bp):
CATATTAAAAGAAAA
Found at i:39434 original size:22 final size:24
Alignment explanation
Indices: 39395--39439 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
39385 AAATAAAAAT
*
39395 AAAAAAATTCATATTTTTGCGTTA
1 AAAAAAATTCATATTTTTCCGTTA
*
39419 AAAAAAATT-TTA-TTTTCCGTT
1 AAAAAAATTCATATTTTTCCGTT
39440 TTTAATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
23 2 0.11
24 9 0.47
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (24 bp):
AAAAAAATTCATATTTTTCCGTTA
Found at i:44104 original size:19 final size:21
Alignment explanation
Indices: 44080--44121 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
44070 TTGAAGATTT
44080 ATTGAAGA-TA-ATTTCAAGA
1 ATTGAAGACTATATTTCAAGA
44099 ATTGAAGACTATTATTTCAAGA
1 ATTGAAGACTA-TATTTCAAGA
44121 A
1 A
44122 GCAAGAATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 8 0.40
20 2 0.10
22 10 0.50
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.33
Consensus pattern (21 bp):
ATTGAAGACTATATTTCAAGA
Found at i:45814 original size:22 final size:22
Alignment explanation
Indices: 45787--45832 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
45777 CTTGTTGATT
*
45787 ATTTTGGTATC-ACAACATTGAG
1 ATTTTGGCATCAAC-ACATTGAG
45809 ATTTTGGCATCAACACATTGAG
1 ATTTTGGCATCAACACATTGAG
45831 AT
1 AT
45833 ACGCAATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (22 bp):
ATTTTGGCATCAACACATTGAG
Found at i:46032 original size:30 final size:30
Alignment explanation
Indices: 45986--46061 Score: 91
Period size: 29 Copynumber: 2.5 Consensus size: 30
45976 TACCGTACAT
* *
45986 GTCCATCTACTTACAAAAAGGGAACAATTTG
1 GTCCCTCTACTTACAAAAA-CGAACAATTTG
* * *
46017 GTCTCTCTAC-TACAAAAACTATCAATTTG
1 GTCCCTCTACTTACAAAAACGAACAATTTG
46046 GTCCCTCTACTTACAA
1 GTCCCTCTACTTACAA
46062 TTTGGTATCA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 17 0.45
30 13 0.34
31 8 0.21
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.30
Consensus pattern (30 bp):
GTCCCTCTACTTACAAAAACGAACAATTTG
Found at i:47733 original size:65 final size:65
Alignment explanation
Indices: 47653--47814 Score: 229
Period size: 67 Copynumber: 2.5 Consensus size: 65
47643 AGACATGGAG
*
47653 TCATTAATTCAGTATTATCCCAAATATATTAGTTTGGGTGAGTGAATTAAAAATATCTTAAAATA
1 TCATTAATTCAGTATTATCCCAAATATATTACTTTGGGTGAGTGAATTAAAAATATCTTAAAATA
* * *
47718 TTATTAATTCAGTATTATTATCCC-AATATATTACTTTTGGTGAGTGAATTAAAAATATTTTAAA
1 TCATTAATTCAG---TATTATCCCAAATATATTACTTTGGGTGAGTGAATTAAAAATATCTTAAA
*
47782 ATG
63 ATA
*
47785 TCATTGATTCAGTATTAT-CCAAATATATTA
1 TCATTAATTCAGTATTATCCCAAATATATTA
47815 TTTTTTAGCA
Statistics
Matches: 86, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
63 2 0.02
64 15 0.17
65 11 0.13
67 49 0.57
68 9 0.10
ACGTcount: A:0.38, C:0.09, G:0.10, T:0.42
Consensus pattern (65 bp):
TCATTAATTCAGTATTATCCCAAATATATTACTTTGGGTGAGTGAATTAAAAATATCTTAAAATA
Found at i:47894 original size:90 final size:91
Alignment explanation
Indices: 47743--47909 Score: 255
Period size: 90 Copynumber: 1.8 Consensus size: 91
47733 TATTATCCCA
* * * * *
47743 ATATATTACTTTTGGTGAGTGAATTAAAAATATTTTAAAATGTCATTGATTCAGTATTATCCAAA
1 ATATATTACTTTGGGTGAGTGAATTAAAAATATTTTAAAATATCATTAATTCAATAATATCCAAA
47808 TATATTATTTTTTAGCAATTTACTAG
66 TATATTATTTTTTAGCAATTTACTAG
* * *
47834 ATATATTAGTTTGGGTGAGTGAATT-AAAATATTTTAAAATATTATTAATTCAATAATATCCCAA
1 ATATATTACTTTGGGTGAGTGAATTAAAAATATTTTAAAATATCATTAATTCAATAATATCCAAA
47898 TATATTATTTTT
66 TATATTATTTTT
47910 AAAAAATTTA
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
90 45 0.66
91 23 0.34
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.46
Consensus pattern (91 bp):
ATATATTACTTTGGGTGAGTGAATTAAAAATATTTTAAAATATCATTAATTCAATAATATCCAAA
TATATTATTTTTTAGCAATTTACTAG
Found at i:48533 original size:70 final size:71
Alignment explanation
Indices: 48450--48594 Score: 238
Period size: 71 Copynumber: 2.1 Consensus size: 71
48440 AACAAAATAG
*
48450 AAAAATGTATAAATCTAAAA-AAAATCGCTCAATTTAGAGCAAAACGTTTATGAAATTGTCAATG
1 AAAAATGTATAAATCTAAAAGAAAATCGCTCAATTTAGAGCAAAACGTTTATGAAATTATCAATG
48514 TAAGAC
66 TAAGAC
** * *
48520 AAAAATGTATAAATCTAAAAGTTAATTGCTCAATTTAGAGCAAAACGTTTTTGAAATTATCAATG
1 AAAAATGTATAAATCTAAAAGAAAATCGCTCAATTTAGAGCAAAACGTTTATGAAATTATCAATG
48585 TAAGAC
66 TAAGAC
48591 AAAA
1 AAAA
48595 TATTTACTAA
Statistics
Matches: 69, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
70 20 0.29
71 49 0.71
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.29
Consensus pattern (71 bp):
AAAAATGTATAAATCTAAAAGAAAATCGCTCAATTTAGAGCAAAACGTTTATGAAATTATCAATG
TAAGAC
Found at i:53583 original size:2 final size:2
Alignment explanation
Indices: 53578--53607 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
53568 GAAAAAACTA
53578 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53608 CAAGCCTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55609 original size:21 final size:22
Alignment explanation
Indices: 55569--55609 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
55559 AACAAACTCG
*
55569 TAACCCGAATAACCCGAGAAGA
1 TAACCCGAATAACCCAAGAAGA
*
55591 TAACCCG-ATGACCCAAGAA
1 TAACCCGAATAACCCAAGAA
55610 TATTATAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.44, C:0.29, G:0.17, T:0.10
Consensus pattern (22 bp):
TAACCCGAATAACCCAAGAAGA
Found at i:57355 original size:1 final size:1
Alignment explanation
Indices: 57349--57375 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
57339 TATACTTAGA
57349 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
57376 GTCCAGGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:57456 original size:38 final size:38
Alignment explanation
Indices: 57405--57484 Score: 160
Period size: 38 Copynumber: 2.1 Consensus size: 38
57395 ATTGGAATAT
57405 ATGAGAAAAAAGCAGAAAAAATTCTACGCAAAATACAA
1 ATGAGAAAAAAGCAGAAAAAATTCTACGCAAAATACAA
57443 ATGAGAAAAAAGCAGAAAAAATTCTACGCAAAATACAA
1 ATGAGAAAAAAGCAGAAAAAATTCTACGCAAAATACAA
57481 ATGA
1 ATGA
57485 AGCCAAGCCC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.60, C:0.12, G:0.14, T:0.14
Consensus pattern (38 bp):
ATGAGAAAAAAGCAGAAAAAATTCTACGCAAAATACAA
Found at i:61039 original size:31 final size:30
Alignment explanation
Indices: 61004--61078 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
60994 ATACCGTAAA
61004 GGTCCCTCTACTTACAAAAAAGGATCAATTT
1 GGTCCCTCTACTTACAAAAAAGG-TCAATTT
* **
61035 GGTCCCTCTAC-TATAAAAACTGTCAATTT
1 GGTCCCTCTACTTACAAAAAAGGTCAATTT
* *
61064 GATCCCTGTACTTAC
1 GGTCCCTCTACTTAC
61079 GATTTGGTGT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
29 16 0.43
30 10 0.27
31 11 0.30
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (30 bp):
GGTCCCTCTACTTACAAAAAAGGTCAATTT
Done.