Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024011.1 Corchorus olitorius cultivar O-4 contig24044, 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: 111358
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Found at i:1873 original size:35 final size:34
Alignment explanation
Indices: 1803--1891 Score: 98
Period size: 34 Copynumber: 2.7 Consensus size: 34
1793 TAAGAAAATA
* * *
1803 TTTTTTTTTCTAAAATCGCAGGAACAAGAAATTT
1 TTTTTTTTTCTAAAAACGCAGAAACAACAAATTT
*
1837 TTTTTTTTTTTAGAAAACGCA-AAACAACAAA--T
1 TTTTTTTTTCTA-AAAACGCAGAAACAACAAATTT
1869 TTTTTTTTTC-AAAAACGCA-AAAC
1 TTTTTTTTTCTAAAAACGCAGAAAC
1892 TAAAAACGCA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
30 12 0.24
31 1 0.02
32 10 0.20
34 19 0.39
35 7 0.14
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.39
Consensus pattern (34 bp):
TTTTTTTTTCTAAAAACGCAGAAACAACAAATTT
Found at i:2031 original size:29 final size:30
Alignment explanation
Indices: 1990--2062 Score: 121
Period size: 30 Copynumber: 2.4 Consensus size: 30
1980 AGTCTATTTT
1990 CCTTCCCCTGGCAAAAACCAGAAAAAGTT-C
1 CCTTCCCC-GGCAAAAACCAGAAAAAGTTAC
*
2020 CCTTCCCCGGCAAATACCAGAAAAAGTTAC
1 CCTTCCCCGGCAAAAACCAGAAAAAGTTAC
2050 CCTTCCCCGGCAA
1 CCTTCCCCGGCAA
2063 CGGCGCCAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 19 0.46
30 22 0.54
ACGTcount: A:0.33, C:0.37, G:0.14, T:0.16
Consensus pattern (30 bp):
CCTTCCCCGGCAAAAACCAGAAAAAGTTAC
Found at i:2261 original size:15 final size:16
Alignment explanation
Indices: 2238--2276 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
2228 GAGATTGACG
*
2238 GAAAGCAATTAAAC-A
1 GAAAACAATTAAACTA
2253 GAAAACAATTAAACTA
1 GAAAACAATTAAACTA
2269 GAAAACAA
1 GAAAACAA
2277 AGCAAAGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.64, C:0.13, G:0.10, T:0.13
Consensus pattern (16 bp):
GAAAACAATTAAACTA
Found at i:3053 original size:11 final size:11
Alignment explanation
Indices: 3037--3062 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3027 CCATTGTCTA
3037 AAAACTAGAAG
1 AAAACTAGAAG
3048 AAAACTAGAAG
1 AAAACTAGAAG
3059 AAAA
1 AAAA
3063 AAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:17783 original size:1 final size:1
Alignment explanation
Indices: 17777--17803 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
17767 AAGTCCAAAT
17777 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
17804 CCTCAAAAGT
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:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:19707 original size:30 final size:30
Alignment explanation
Indices: 19665--19741 Score: 102
Period size: 30 Copynumber: 2.6 Consensus size: 30
19655 ACTACTTGTT
*
19665 AAAACTTTAATTTGCTTTTGGCCC-AAAAC
1 AAAACCTTAATTTGCTTTTGGCCCAAAAAC
* *
19694 GAAAAGCTTAATTTGCATTTGGCCCAAAAAC
1 -AAAACCTTAATTTGCTTTTGGCCCAAAAAC
*
19725 AAAACCATAATTTGCTT
1 AAAACCTTAATTTGCTT
19742 AGAAATTCTA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
30 35 0.88
31 5 0.12
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (30 bp):
AAAACCTTAATTTGCTTTTGGCCCAAAAAC
Found at i:21708 original size:2 final size:2
Alignment explanation
Indices: 21701--21745 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
21691 TTTATGTGGG
*
21701 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA -A GA GT
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
21742 GA GA
1 GA GA
21746 CCTATGCACA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.02
Consensus pattern (2 bp):
GA
Found at i:24754 original size:5 final size:5
Alignment explanation
Indices: 24744--24796 Score: 53
Period size: 5 Copynumber: 11.6 Consensus size: 5
24734 AAAGACAACC
* *
24744 AAATA AAATA AAATA AAATA AAATT TAA-A AAA-A AAATA AAA-A AAA-A
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA
24790 AAA-A AAA
1 AAATA AAA
24797 AAACTTAGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
4 18 0.42
5 25 0.58
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (5 bp):
AAATA
Found at i:24776 original size:1 final size:1
Alignment explanation
Indices: 24770--24799 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
24760 AATAAAATTT
*
24770 AAAAAAAAAATAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
24800 CTTAGAAACC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.97, C:0.00, G:0.00, T:0.03
Consensus pattern (1 bp):
A
Found at i:24779 original size:13 final size:11
Alignment explanation
Indices: 24744--24799 Score: 62
Period size: 11 Copynumber: 5.2 Consensus size: 11
24734 AAAGACAACC
*
24744 AAAT-AAAATA
1 AAATAAAAAAA
24754 AAATAAAATAAA
1 AAATAAAA-AAA
**
24766 ATTTAAAAAAA
1 AAATAAAAAAA
24777 AAATAAAAAAA
1 AAATAAAAAAA
24788 AAA-AAAAAAA
1 AAATAAAAAAA
24798 AA
1 AA
24800 CTTAGAAACC
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
10 13 0.33
11 18 0.46
12 8 0.21
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (11 bp):
AAATAAAAAAA
Found at i:25109 original size:3 final size:3
Alignment explanation
Indices: 25095--25146 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
25085 AAACCCAAAA
*
25095 AAT AAA AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
25143 AAT A
1 AAT A
25147 GTACTAACAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:34724 original size:17 final size:17
Alignment explanation
Indices: 34690--34733 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
34680 CGTCTTTTTA
**
34690 TTTTCTGATTTTTCTCT
1 TTTTCTGATTTTGATCT
*
34707 TTTTTTGATTTTGATCT
1 TTTTCTGATTTTGATCT
34724 TTTTCT-ATTT
1 TTTTCTGATTT
34734 CTAGATTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.09, C:0.11, G:0.07, T:0.73
Consensus pattern (17 bp):
TTTTCTGATTTTGATCT
Found at i:38540 original size:27 final size:27
Alignment explanation
Indices: 38483--38547 Score: 105
Period size: 26 Copynumber: 2.4 Consensus size: 27
38473 ATTGATTACC
38483 CTTACTCTTTTTACTGATTACCATTCT
1 CTTACTCTTTTTACTGATTACCATTCT
* *
38510 -TTACTCTTTTTACTTATTACCATTTT
1 CTTACTCTTTTTACTGATTACCATTCT
38536 CTTACTCTTTTT
1 CTTACTCTTTTT
38548 TTTACTGGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
26 24 0.69
27 11 0.31
ACGTcount: A:0.17, C:0.23, G:0.02, T:0.58
Consensus pattern (27 bp):
CTTACTCTTTTTACTGATTACCATTCT
Found at i:38706 original size:35 final size:34
Alignment explanation
Indices: 38666--38748 Score: 112
Period size: 35 Copynumber: 2.4 Consensus size: 34
38656 AATACTCCCA
*
38666 TTTACTCTTTACTGATTACTATTATCACTTCATTG
1 TTTACTCTTTACTAATTACTATTA-CACTTCATTG
* *
38701 TTTACTCTTTTACTAATTACTATTACTCTTCCTTG
1 TTTACTC-TTTACTAATTACTATTACACTTCATTG
*
38736 ATTACTCTTTACT
1 TTTACTCTTTACT
38749 CTTTACTGGC
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
34 6 0.14
35 21 0.49
36 16 0.37
ACGTcount: A:0.22, C:0.22, G:0.04, T:0.53
Consensus pattern (34 bp):
TTTACTCTTTACTAATTACTATTACACTTCATTG
Found at i:38797 original size:22 final size:22
Alignment explanation
Indices: 38794--38953 Score: 130
Period size: 21 Copynumber: 7.8 Consensus size: 22
38784 CTTTTACGGA
*
38794 TTACTCTTTTACGGATTACTCT
1 TTACTCTTTTACTGATTACTCT
*
38816 TTACTC-TTTACTGATTACT-A
1 TTACTCTTTTACTGATTACTCT
*
38836 TTACTCTTTTCCTGATTACTCT
1 TTACTCTTTTACTGATTACTCT
*
38858 TTACTCTTTTACTGATTACTATT
1 TTACTCTTTTACTGATTACT-CT
** **
38881 TTACT-AATTACTCTTTACTCT
1 TTACTCTTTTACTGATTACTCT
**
38902 TTACT-GATTACT-ATTACTCT
1 TTACTCTTTTACTGATTACTCT
38922 TT--TC-----CTGATTACTCT
1 TTACTCTTTTACTGATTACTCT
38937 TTACT-TTTTACTGATTA
1 TTACTCTTTTACTGATTA
38954 TTATTTTACT
Statistics
Matches: 113, Mismatches: 13, Indels: 25
0.75 0.09 0.17
Matches are distributed among these distances:
14 2 0.02
15 10 0.09
17 1 0.01
18 1 0.01
20 15 0.13
21 43 0.38
22 35 0.31
23 6 0.05
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.53
Consensus pattern (22 bp):
TTACTCTTTTACTGATTACTCT
Found at i:38838 original size:72 final size:75
Alignment explanation
Indices: 38666--38997 Score: 347
Period size: 79 Copynumber: 4.3 Consensus size: 75
38656 AATACTCCCA
* * *
38666 TTTACTCTTTACTGATTACTATTATCACTTC-A-T--TGTTTACTCTTTTACTAATTACTATTAC
1 TTTACTCTTTACTGATTACTATTA-CTCTTCTATTACTCTTTACTCTTTTACTGATTACTA-T--
*
38727 TCTTCCTTGATTACTC
62 T-TTAC-TGATTACTC
** * * *
38743 TTTACTCTTTACTGGCTATTATTACTC-T-T-TTACTCTTTACTCTTTTACGGATTACTCTTTTA
1 TTTACTCTTTACTGATTACTATTACTCTTCTATTACTCTTTACTCTTTTACTGATTACTATTTTA
*
38805 CGGATTACTC
66 CTGATTACTC
38815 TTTACTCTTTACTGATTACTATTACTCTTTTCCTGATTACTCTTTACTCTTTTACTGATTACTAT
1 TTTACTCTTTACTGATTACTATTACTC--TT-CT-ATTACTCTTTACTCTTTTACTGATTACTAT
*
38880 TTTACTAATTACTC
62 TTTACTGATTACTC
*
38894 TTTACTCTTTACTGATTACTATTACTCTTTTCCTGATTACTCTTTACT-TTTTACTGATTATTAT
1 TTTACTCTTTACTGATTACTATTACTC--TT-CT-ATTACTCTTTACTCTTTTACTGATTACTAT
*
38958 TTTACTGATTGCTC
62 TTTACTGATTACTC
*
38972 TCTTATTCTTTACTGATTACTATTAC
1 T-TTACTCTTTACTGATTACTATTAC
38998 CATTGTGCTG
Statistics
Matches: 222, Mismatches: 21, Indels: 22
0.84 0.08 0.08
Matches are distributed among these distances:
72 32 0.14
73 3 0.01
74 1 0.00
75 3 0.01
76 3 0.01
77 42 0.19
78 28 0.13
79 110 0.50
ACGTcount: A:0.20, C:0.21, G:0.05, T:0.53
Consensus pattern (75 bp):
TTTACTCTTTACTGATTACTATTACTCTTCTATTACTCTTTACTCTTTTACTGATTACTATTTTA
CTGATTACTC
Found at i:38855 original size:79 final size:79
Alignment explanation
Indices: 38772--39024 Score: 384
Period size: 79 Copynumber: 3.2 Consensus size: 79
38762 TATTACTCTT
* * *
38772 TTACTCTTTACTCTTTTACGGATTACTCTTTTACGGATTACTCTTTACTCTTTACTGATTACTAT
1 TTACTCTTTACTCTTTTACTGATTACTATTTTACTGATTACTCTTTACTCTTTACTGATTACTAT
38837 TACTCTTTTCCTGA
66 TACTCTTTTCCTGA
*
38851 TTACTCTTTACTCTTTTACTGATTACTATTTTACTAATTACTCTTTACTCTTTACTGATTACTAT
1 TTACTCTTTACTCTTTTACTGATTACTATTTTACTGATTACTCTTTACTCTTTACTGATTACTAT
38916 TACTCTTTTCCTGA
66 TACTCTTTTCCTGA
* * *
38930 TTACTCTTTACT-TTTTACTGATTATTATTTTACTGATTGCTCTCTTATTCTTTACTGATTACTA
1 TTACTCTTTACTCTTTTACTGATTACTATTTTACTGATTACTCT-TTACTCTTTACTGATTACTA
* *
38994 TTAC-CATTGTGCTGA
65 TTACTC-TTTTCCTGA
*
39009 TTACTCTTCACTCTTT
1 TTACTCTTTACTCTTT
39025 GAATTTTAAT
Statistics
Matches: 160, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
78 29 0.18
79 128 0.80
80 3 0.02
ACGTcount: A:0.20, C:0.21, G:0.06, T:0.53
Consensus pattern (79 bp):
TTACTCTTTACTCTTTTACTGATTACTATTTTACTGATTACTCTTTACTCTTTACTGATTACTAT
TACTCTTTTCCTGA
Found at i:38870 original size:8 final size:7
Alignment explanation
Indices: 38737--38948 Score: 85
Period size: 7 Copynumber: 29.7 Consensus size: 7
38727 TCTTCCTTGA
38737 TTACTCT
1 TTACTCT
38744 TTACTCT
1 TTACTCT
**
38751 TTACTGG
1 TTACTCT
*
38758 CTA-T-T
1 TTACTCT
38763 ATTACTCTT
1 -TTACTC-T
38772 TTACTCT
1 TTACTCT
38779 TTACTCTT
1 TTACTC-T
***
38787 TTACGGA
1 TTACTCT
38794 TTACTCTT
1 TTACTC-T
***
38802 TTACGGA
1 TTACTCT
38809 TTACTCT
1 TTACTCT
38816 TTACTCT
1 TTACTCT
**
38823 TTACTGA
1 TTACTCT
*
38830 TTACT-A
1 TTACTCT
38836 TTACTCT
1 TTACTCT
*
38843 TTTC-CT
1 TTACTCT
38849 GATTACTCT
1 --TTACTCT
38858 TTACTCTT
1 TTACTC-T
**
38866 TTACTGA
1 TTACTCT
*
38873 TTACTATT
1 TTACT-CT
**
38881 TTACTAA
1 TTACTCT
38888 TTACTCT
1 TTACTCT
38895 TTACTCT
1 TTACTCT
**
38902 TTACTGA
1 TTACTCT
*
38909 TTACT-A
1 TTACTCT
38915 TTACTCT
1 TTACTCT
*
38922 TTTC-CT
1 TTACTCT
38928 GATTACTCT
1 --TTACTCT
*
38937 TTACTTT
1 TTACTCT
38944 TTACT
1 TTACT
38949 GATTATTATT
Statistics
Matches: 153, Mismatches: 36, Indels: 32
0.69 0.16 0.14
Matches are distributed among these distances:
6 19 0.12
7 97 0.63
8 32 0.21
9 5 0.03
ACGTcount: A:0.19, C:0.22, G:0.05, T:0.53
Consensus pattern (7 bp):
TTACTCT
Found at i:38934 original size:15 final size:14
Alignment explanation
Indices: 38762--38938 Score: 88
Period size: 15 Copynumber: 12.8 Consensus size: 14
38752 TACTGGCTAT
38762 TATTACTCTTTTAC
1 TATTACTCTTTTAC
*
38776 TCTTTACTCTTTTAC
1 T-ATTACTCTTTTAC
*
38791 GGATTACTCTTTTAC
1 -TATTACTCTTTTAC
*
38806 GGATTACTC-TTTAC
1 -TATTACTCTTTTAC
* **
38820 TCTTTACT-GATTAC
1 T-ATTACTCTTTTAC
*
38834 TATTACTCTTTTCC
1 TATTACTCTTTTAC
38848 TGATTA--C---T-C
1 T-ATTACTCTTTTAC
38857 T-TTACTCTTTTAC
1 TATTACTCTTTTAC
*
38870 TGATTACTATTTTAC
1 T-ATTACTCTTTTAC
38885 TAATTACTC-TTTAC
1 T-ATTACTCTTTTAC
* **
38899 TCTTTACT-GATTAC
1 T-ATTACTCTTTTAC
*
38913 TATTACTCTTTTCC
1 TATTACTCTTTTAC
38927 TGATTACTCTTT
1 T-ATTACTCTTT
38939 ACTTTTTACT
Statistics
Matches: 126, Mismatches: 20, Indels: 33
0.70 0.11 0.18
Matches are distributed among these distances:
7 3 0.02
9 3 0.02
10 1 0.01
12 1 0.01
13 13 0.10
14 40 0.32
15 65 0.52
ACGTcount: A:0.20, C:0.22, G:0.05, T:0.53
Consensus pattern (14 bp):
TATTACTCTTTTAC
Found at i:43160 original size:60 final size:60
Alignment explanation
Indices: 43034--43190 Score: 194
Period size: 60 Copynumber: 2.6 Consensus size: 60
43024 TCAACCTTAA
* * * *
43034 AAACTAAGAAAGACTTGTCTGAGGT-TCGAAACTGAAAGAAGACCAGTCCGTCGTCCATATT
1 AAACTGAGAAAGACCTGTCTGAGGTCT-GAAATTGAAA-AAGACCAGTCCGTCGTCCAAATT
* * * *
43095 AAACTGAGAATGACCTGTCTGAGGTCTGAAATTGAAAAAGACCAGTCTGTGGTCTAAATT
1 AAACTGAGAAAGACCTGTCTGAGGTCTGAAATTGAAAAAGACCAGTCCGTCGTCCAAATT
*
43155 AAACTGAGAAAGACCTATCTGAGGTC-GAAATT-AAAA
1 AAACTGAGAAAGACCTGTCTGAGGTCTGAAATTGAAAA
43191 CTGAGAAAGA
Statistics
Matches: 85, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
58 4 0.05
59 6 0.07
60 43 0.51
61 31 0.36
62 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.24
Consensus pattern (60 bp):
AAACTGAGAAAGACCTGTCTGAGGTCTGAAATTGAAAAAGACCAGTCCGTCGTCCAAATT
Found at i:43197 original size:33 final size:32
Alignment explanation
Indices: 43092--43213 Score: 112
Period size: 33 Copynumber: 3.9 Consensus size: 32
43082 CGTCGTCCAT
* *
43092 ATTAAACTGAGAATGACCTGTCTGAGGTCTGAA
1 ATTAAACTGAGAAAGACCTATCTGAGGTC-GAA
* * *
43125 A-T----TGAAAAAGACC-AGTCTGTGGTCTAA
1 ATTAAACTGAGAAAGACCTA-TCTGAGGTCGAA
43152 ATTAAACTGAGAAAGACCTATCTGAGGTCGAA
1 ATTAAACTGAGAAAGACCTATCTGAGGTCGAA
* *
43184 ATTAAAACTGAGAAAGACCTGTCTAAGGTC
1 ATT-AAACTGAGAAAGACCTATCTGAGGTC
43214 TTAAACTGAA
Statistics
Matches: 71, Mismatches: 10, Indels: 16
0.73 0.10 0.16
Matches are distributed among these distances:
27 3 0.04
28 18 0.25
32 24 0.34
33 26 0.37
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.25
Consensus pattern (32 bp):
ATTAAACTGAGAAAGACCTATCTGAGGTCGAA
Found at i:43285 original size:29 final size:30
Alignment explanation
Indices: 43196--43394 Score: 294
Period size: 30 Copynumber: 6.6 Consensus size: 30
43186 TAAAACTGAG
*
43196 AAAGACCTGTCTAAGGTCTTAAACTGAAAA
1 AAAGACCTGTCTGAGGTCTTAAACTGAAAA
*
43226 AAAGACCTGACTGAGGTCTTAAACTGAAAA
1 AAAGACCTGTCTGAGGTCTTAAACTGAAAA
* *
43256 AAAGACATGTTTGAGGTCTTAAACTG-AAA
1 AAAGACCTGTCTGAGGTCTTAAACTGAAAA
* *
43285 AAAGACCTGTTTGAGGTGTTAAACTGAAAA
1 AAAGACCTGTCTGAGGTCTTAAACTGAAAA
43315 AAAGACCTGTCTGAGGTCTTAAACTG-AAA
1 AAAGACCTGTCTGAGGTCTTAAACTGAAAA
*
43344 AAAGACCAGTCTGAGGTCTTAAACTGAAAAA
1 AAAGACCTGTCTGAGGTCTTAAACTG-AAAA
*
43375 TAAAGACCTGTTTGAGGTCT
1 -AAAGACCTGTCTGAGGTCT
43395 GAAATTAAAA
Statistics
Matches: 153, Mismatches: 12, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
29 55 0.36
30 78 0.51
31 3 0.02
32 17 0.11
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.25
Consensus pattern (30 bp):
AAAGACCTGTCTGAGGTCTTAAACTGAAAA
Found at i:43300 original size:59 final size:59
Alignment explanation
Indices: 43196--43394 Score: 299
Period size: 59 Copynumber: 3.3 Consensus size: 59
43186 TAAAACTGAG
* * *
43196 AAAGACCTGTCTAAGGTCTTAAACTGAAAAAAAGACCTGACTGAGGTCTTAAACTGAAAA
1 AAAGACCTGTTTGAGGTCTTAAACTG-AAAAAAGACCTGTCTGAGGTCTTAAACTGAAAA
* * *
43256 AAAGACATGTTTGAGGTCTTAAACTGAAAAAAGACCTGTTTGAGGTGTTAAACTGAAAA
1 AAAGACCTGTTTGAGGTCTTAAACTGAAAAAAGACCTGTCTGAGGTCTTAAACTGAAAA
* *
43315 AAAGACCTGTCTGAGGTCTTAAACTGAAAAAAGACCAGTCTGAGGTCTTAAACTGAAAAA
1 AAAGACCTGTTTGAGGTCTTAAACTGAAAAAAGACCTGTCTGAGGTCTTAAACTG-AAAA
43375 TAAAGACCTGTTTGAGGTCT
1 -AAAGACCTGTTTGAGGTCT
43395 GAAATTAAAA
Statistics
Matches: 125, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
59 80 0.64
60 27 0.22
61 18 0.14
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.25
Consensus pattern (59 bp):
AAAGACCTGTTTGAGGTCTTAAACTGAAAAAAGACCTGTCTGAGGTCTTAAACTGAAAA
Found at i:43755 original size:50 final size:50
Alignment explanation
Indices: 43474--43759 Score: 220
Period size: 51 Copynumber: 5.5 Consensus size: 50
43464 GATTGCACCA
43474 GATCACTTGAAGATAAACTTAAACCACCTAG-AAACTTTCTTGATTGACCGCACTG
1 GATCACTTGAAGATAAACTTAAACCA-CT-GTAAA----CTTGATTGACCGCACTG
* * * ** * *
43529 GATCACTTGAAGATAAACTTGAACCACTATAATCTTTCTGACCGACCGCATTT
1 GATCACTTGAAGATAAACTTAAACCACTGTAAAC--T-TGATTGACCGCACTG
* * * * *
43582 TATCTCTTG-AGAATAAACTTAAACCACTGTAAGCTTGATTGATCGCACTA
1 GATCACTTGAAG-ATAAACTTAAACCACTGTAAACTTGATTGACCGCACTG
* * * * * ***
43632 GATCCCTTTGATGATGAACTTAAACCATTGGAAACTTTCTGGCGGACCGCACTG
1 GATCAC-TTGAAGATAAACTTAAACCACTGTAAAC--T-TGATTGACCGCACTG
*
43686 GAT--CTTGAAGATAAACTTAAACCACTGTAAACTTGATTGATCGCACTG
1 GATCACTTGAAGATAAACTTAAACCACTGTAAACTTGATTGACCGCACTG
*
43734 GATCCCTTGAAGATAAACTTAAACCA
1 GATCACTTGAAGATAAACTTAAACCA
43760 TTTGAAAGTT
Statistics
Matches: 182, Mismatches: 37, Indels: 29
0.73 0.15 0.12
Matches are distributed among these distances:
48 14 0.08
49 1 0.01
50 36 0.20
51 46 0.25
52 5 0.03
53 38 0.21
54 17 0.09
55 25 0.14
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (50 bp):
GATCACTTGAAGATAAACTTAAACCACTGTAAACTTGATTGACCGCACTG
Found at i:43846 original size:24 final size:24
Alignment explanation
Indices: 43819--43911 Score: 114
Period size: 24 Copynumber: 3.9 Consensus size: 24
43809 ATTGGAGAAT
*
43819 TGAAGCTTTGAATACTTGAAAAAC
1 TGAAGCTTTGAATAATTGAAAAAC
* * *
43843 TGAAGCTTTAAATACTTGAAAAAT
1 TGAAGCTTTGAATAATTGAAAAAC
* *
43867 TGAAGTTTTGAATAATTGAAGAAC
1 TGAAGCTTTGAATAATTGAAAAAC
* *
43891 TGAAGCATTGAAGAATTGAAA
1 TGAAGCTTTGAATAATTGAAA
43912 TTGAAGCATT
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 58 1.00
ACGTcount: A:0.44, C:0.08, G:0.18, T:0.30
Consensus pattern (24 bp):
TGAAGCTTTGAATAATTGAAAAAC
Found at i:43885 original size:8 final size:8
Alignment explanation
Indices: 43858--43941 Score: 61
Period size: 8 Copynumber: 11.0 Consensus size: 8
43848 CTTTAAATAC
*
43858 TTGAAAAA
1 TTGAAGAA
**
43866 TTGAAGTT
1 TTGAAGAA
*
43874 TTGAATAA
1 TTGAAGAA
43882 TTGAAGAA
1 TTGAAGAA
* *
43890 CTGAAGCA
1 TTGAAGAA
43898 TTGAAGAA
1 TTGAAGAA
43906 TTG-A-AA
1 TTGAAGAA
*
43912 TTGAAGCA
1 TTGAAGAA
43920 TTGAA-ATA
1 TTGAAGA-A
43928 TTG-A-AA
1 TTGAAGAA
43934 TTGAAGAA
1 TTGAAGAA
43942 AGGCCACCCC
Statistics
Matches: 58, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
6 9 0.16
7 5 0.09
8 44 0.76
ACGTcount: A:0.46, C:0.04, G:0.20, T:0.30
Consensus pattern (8 bp):
TTGAAGAA
Found at i:43916 original size:14 final size:14
Alignment explanation
Indices: 43880--43926 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
43870 AGTTTTGAAT
*
43880 AATTGAAGAACTGA
1 AATTGAAGAATTGA
43894 AGCATTGAAGAATTGA
1 A--ATTGAAGAATTGA
*
43910 AATTGAAGCATTGA
1 AATTGAAGAATTGA
43924 AAT
1 AAT
43927 ATTGAAATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 16 0.55
16 13 0.45
ACGTcount: A:0.47, C:0.06, G:0.21, T:0.26
Consensus pattern (14 bp):
AATTGAAGAATTGA
Found at i:44049 original size:96 final size:96
Alignment explanation
Indices: 43971--44251 Score: 445
Period size: 96 Copynumber: 2.9 Consensus size: 96
43961 TGAAATGAAT
* * * * * *
43971 TGAAGAAAGACCACCTTGGGTTAACTTGAAGAAAGATCGCTCTGGATCAATTGAAGTAAATTAAA
1 TGAAGAAAGACCACCCTAGGTCAACTTGAAGCAAGATCGCTCTGGATCGATTGAAGTAAACTAAA
44036 GAATGATCGCCCTGGATCAATTGAAACTAAC
66 GAATGATCGCCCTGGATCAATTGAAACTAAC
* *
44067 TGAAGAAAGATCACCCTAGGTCAACTTGAAGCAAGATCGCTCTGGATCGATTGAAGTAAACTGAA
1 TGAAGAAAGACCACCCTAGGTCAACTTGAAGCAAGATCGCTCTGGATCGATTGAAGTAAACTAAA
* * *
44132 GAATAATCGCCTTAGATCAATTGAAACTAAC
66 GAATGATCGCCCTGGATCAATTGAAACTAAC
* *
44163 TGAAGAAAGACCGCCCTAGGTCAACTTGAAGCAAGATTGCTCTGGATCGATTGAAGTAAACTAAA
1 TGAAGAAAGACCACCCTAGGTCAACTTGAAGCAAGATCGCTCTGGATCGATTGAAGTAAACTAAA
44228 GAATGATCGCCCTGGATCAATTGA
66 GAATGATCGCCCTGGATCAATTGA
44252 GCTGTTTGAA
Statistics
Matches: 167, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
96 167 1.00
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.23
Consensus pattern (96 bp):
TGAAGAAAGACCACCCTAGGTCAACTTGAAGCAAGATCGCTCTGGATCGATTGAAGTAAACTAAA
GAATGATCGCCCTGGATCAATTGAAACTAAC
Found at i:44073 original size:35 final size:34
Alignment explanation
Indices: 43992--44192 Score: 127
Period size: 35 Copynumber: 6.0 Consensus size: 34
43982 CACCTTGGGT
* *
43992 TAACTTGAAGAAAGATCGCTCTGGATCAATTGAAG
1 TAAC-TGAAGAAAGATCGCCCTGGATCAATTGAAC
* * *
44027 TAAATTAAAGAATGATCGCCCTGGATCAATTGAAAC
1 T-AACTGAAGAAAGATCGCCCTGGATCAATTG-AAC
*
44063 TAACTGAAGAAAGATCACCCTAGG-TC-----AAC
1 TAACTGAAGAAAGATCGCCCT-GGATCAATTGAAC
* * * *
44092 T---TGAAGCAAGATCGCTCTGGATCGATTGAAG
1 TAACTGAAGAAAGATCGCCCTGGATCAATTGAAC
* *
44123 TAAACTGAAGAATA-ATCGCCTTAGATCAATTGAAAC
1 T-AACTGAAGAA-AGATCGCCCTGGATCAATTG-AAC
*
44159 TAACTGAAGAAAGACCGCCCTAGG-TCAACTTGAA
1 TAACTGAAGAAAGATCGCCCT-GGATCAA-TTGAA
44193 GCAAGATTGC
Statistics
Matches: 126, Mismatches: 22, Indels: 36
0.68 0.12 0.20
Matches are distributed among these distances:
25 2 0.02
26 16 0.13
29 4 0.03
31 3 0.02
34 1 0.01
35 85 0.67
36 15 0.12
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (34 bp):
TAACTGAAGAAAGATCGCCCTGGATCAATTGAAC
Found at i:45340 original size:20 final size:19
Alignment explanation
Indices: 45298--45340 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
45288 TCCTTTGTTC
* * *
45298 TTTTTCTTTTTGATTTCTT
1 TTTTTCTTTTTAATTCCTA
45317 TTTTTCTTTTTTAATTCCTA
1 TTTTTC-TTTTTAATTCCTA
45337 TTTT
1 TTTT
45341 ATTTTACTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.09, C:0.12, G:0.02, T:0.77
Consensus pattern (19 bp):
TTTTTCTTTTTAATTCCTA
Found at i:45660 original size:15 final size:15
Alignment explanation
Indices: 45640--45670 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
45630 CATTCGAACA
45640 TAGTTCCTTGAAAGC
1 TAGTTCCTTGAAAGC
*
45655 TAGTTCCTTGCAAGC
1 TAGTTCCTTGAAAGC
45670 T
1 T
45671 TTCTACCTAA
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:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (15 bp):
TAGTTCCTTGAAAGC
Found at i:48165 original size:27 final size:28
Alignment explanation
Indices: 48103--48182 Score: 101
Period size: 27 Copynumber: 2.8 Consensus size: 28
48093 AGCGAACTTG
*
48103 AAATGACCAAAATGCCCCATATATATGTGC
1 AAATGA-CAAAATGCCCC-TAGATATGTGC
48133 AAATGACGAAAATGCCCCT-GA-ATGTGC
1 AAATGAC-AAAATGCCCCTAGATATGTGC
48160 AAATGATCAAAATGCCCCTAGAT
1 AAATGA-CAAAATGCCCCTAGAT
48183 GACCCTAATG
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
27 23 0.51
28 4 0.09
29 2 0.04
30 16 0.36
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.21
Consensus pattern (28 bp):
AAATGACAAAATGCCCCTAGATATGTGC
Found at i:48538 original size:50 final size:50
Alignment explanation
Indices: 48498--48611 Score: 133
Period size: 50 Copynumber: 2.3 Consensus size: 50
48488 TCTAACATTA
*
48498 AAAAAG-TCGTCTCCCGCTCATCCCTCGAACTGTCTTCCAATTCAATCTT
1 AAAAAGATCATCTCCCGCTCATCCCTCGAACTGTCTTCCAATTCAATCTT
* * * * * *
48547 AAAAGGATCATCTCCCGCTTATCCTTTGAACTGTCTTCCAATTGAATCCT
1 AAAAAGATCATCTCCCGCTCATCCCTCGAACTGTCTTCCAATTCAATCTT
*
48597 AAGAAA-AACATCTCC
1 AA-AAAGATCATCTCC
48612 TGATAGTCTT
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
49 5 0.09
50 47 0.87
51 2 0.04
ACGTcount: A:0.29, C:0.31, G:0.11, T:0.30
Consensus pattern (50 bp):
AAAAAGATCATCTCCCGCTCATCCCTCGAACTGTCTTCCAATTCAATCTT
Found at i:49580 original size:51 final size:51
Alignment explanation
Indices: 49504--49606 Score: 170
Period size: 51 Copynumber: 2.0 Consensus size: 51
49494 ACTCCGATGA
* * *
49504 CGGTTTTGTGACGTTTTCCGAAGGTTCATCGAGATTGGTTTTGATGTTGCC
1 CGGTTTTGTGACATTTGCCGAAGGTTCATCGAGATTGGTTTTAATGTTGCC
*
49555 CGGTTTTGTGACATTTGCTGAAGGTTCATCGAGATTGGTTTTAATGTTGCC
1 CGGTTTTGTGACATTTGCCGAAGGTTCATCGAGATTGGTTTTAATGTTGCC
49606 C
1 C
49607 TACCCAACTC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.16, C:0.16, G:0.28, T:0.41
Consensus pattern (51 bp):
CGGTTTTGTGACATTTGCCGAAGGTTCATCGAGATTGGTTTTAATGTTGCC
Found at i:57421 original size:11 final size:11
Alignment explanation
Indices: 57405--57430 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
57395 GTGCGTGAGC
57405 ATGCATGATGA
1 ATGCATGATGA
57416 ATGCATGATGA
1 ATGCATGATGA
57427 ATGC
1 ATGC
57431 CATGTAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.12, G:0.27, T:0.27
Consensus pattern (11 bp):
ATGCATGATGA
Found at i:60999 original size:21 final size:21
Alignment explanation
Indices: 60973--61016 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
60963 TTTTGTTTCT
*
60973 ATTTCGTTCACCGTAAGTTGC
1 ATTTCGTTCACCATAAGTTGC
*
60994 ATTTCGTTGACCATAAGTTGC
1 ATTTCGTTCACCATAAGTTGC
61015 AT
1 AT
61017 GGTATTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (21 bp):
ATTTCGTTCACCATAAGTTGC
Found at i:63678 original size:21 final size:21
Alignment explanation
Indices: 63652--63691 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
63642 TTGTTTGATG
*
63652 CAATTTGGCCCCTGCTTTATT
1 CAATTTGGCCCCTGATTTATT
63673 CAATTTGGCCCCTGATTTA
1 CAATTTGGCCCCTGATTTA
63692 GAATATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.28, G:0.15, T:0.40
Consensus pattern (21 bp):
CAATTTGGCCCCTGATTTATT
Found at i:69893 original size:68 final size:67
Alignment explanation
Indices: 69657--70127 Score: 503
Period size: 68 Copynumber: 7.1 Consensus size: 67
69647 ACAGAATTTT
* * *
69657 AGAAGTACACC-GAAGACGGTTTGCTAGAAAGACTTTTCAAAAATGGATTGGAAGACAATCTCAT
1 AGAAGTACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAGTTGATTGGAAGACAATCTCAT
69721 CA
66 CA
* * * * * *
69723 AGAAGT-GATCGGAAGACGGTTTGCTAGAAAGAATTTGCAGAAGATGATTGGAAGACAATCTCGT
1 AGAAGTACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAGTTGATTGGAAGACAATCTCAT
69787 CA
66 CA
*
69789 AGAAGTAAACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAGTTGATTGGAAGACAATCTCAT
1 AGAAGTACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAGTTGATTGGAAGACAATCTCA-
*
69854 TTA
65 TCA
*
69857 AGGAA-TACACCGGAAGACGGTTTGCTAGAAAAAATTTTCAAAAGTTGATTGGAAGACAATCTCA
1 A-GAAGTACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAGTTGATTGGAAGACAATCTCA
*
69921 TTAA
65 -TCA
* * * ** *
69925 AGAA-TACATCGGAAGACGGTTTGTTA-AGAAGAATTTTCACAGAGTAAACTGGAAGACAATCTC
1 AGAAGTACACCGGAAGACGGTTTGCTAGA-AAGAATTTTCA-AAAGTTGATTGGAAGACAATCTC
*
69988 ATTA
64 ATCA
* * * *
69992 AGGAA-TATACCGGAAGACGGTTTG-TCAGAAAGAATTTTCAAATGTTGAATTGGAAGGCGATCT
1 A-GAAGTACACCGGAAGACGGTTTGCT-AGAAAGAATTTTCAAAAGTTG-ATTGGAAGACAATCT
*
70055 TATCA
63 CATCA
* * * * * * **
70060 AGAAGTACACCAGAAGATGGTTT-CT-G-AACAATTTTCAGAAGTTGATCGGAAGACGATCTTGT
1 AGAAGTACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAGTTGATTGGAAGACAATCTCAT
70122 CA
66 CA
70124 AGAA
1 AGAA
70128 CTACGCTAGA
Statistics
Matches: 346, Mismatches: 47, Indels: 26
0.83 0.11 0.06
Matches are distributed among these distances:
64 21 0.06
65 17 0.05
66 62 0.18
67 94 0.27
68 148 0.43
69 4 0.01
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.25
Consensus pattern (67 bp):
AGAAGTACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAGTTGATTGGAAGACAATCTCAT
CA
Found at i:69938 original size:135 final size:134
Alignment explanation
Indices: 69657--70118 Score: 528
Period size: 135 Copynumber: 3.5 Consensus size: 134
69647 ACAGAATTTT
* * *
69657 AGAAGTACACC-GAAGACGGTTTGCTAGAAAGACTTTTCAAAAATGGATTGGAAGACAATCTCAT
1 AGAAGTACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAGTTGATTGGAAGACAATCTCAT
* * * * * *
69721 CAA-GAAGT-GATCGGAAGACGGTTTGCTAGAAAGAATTTGCAGAAGATGATTGGAAGACAATCT
66 TAAGGAA-TACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAGTTGATTGGAAGACAATCT
*
69784 CGTCA
130 CATCA
*
69789 AGAAGTAAACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAGTTGATTGGAAGACAATCTCAT
1 AGAAGTACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAGTTGATTGGAAGACAATCTCA-
*
69854 TTAAGGAATACACCGGAAGACGGTTTGCTAGAAAAAATTTTCAAAAGTTGATTGGAAGACAATCT
65 TTAAGGAATACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAGTTGATTGGAAGACAATCT
*
69919 CATTAA
130 CA-TCA
* * * ** *
69925 AGAA-TACATCGGAAGACGGTTTGTTA-AGAAGAATTTTCACAGAGTAAACTGGAAGACAATCTC
1 AGAAGTACACCGGAAGACGGTTTGCTAGA-AAGAATTTTCA-AAAGTTGATTGGAAGACAATCTC
* * * *
69988 ATTAAGGAATATACCGGAAGACGGTTTG-TCAGAAAGAATTTTCAAATGTTGAATTGGAAGGCGA
64 ATTAAGGAATACACCGGAAGACGGTTTGCT-AGAAAGAATTTTCAAAAGTTG-ATTGGAAGACAA
*
70052 TCTTATCA
127 TCTCATCA
* * * * * *
70060 AGAAGTACACCAGAAGATGGTTT-CT-G-AACAATTTTCAGAAGTTGATCGGAAGACGATCT
1 AGAAGTACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAGTTGATTGGAAGACAATCT
70119 TGTCAAGAAC
Statistics
Matches: 280, Mismatches: 39, Indels: 22
0.82 0.11 0.06
Matches are distributed among these distances:
132 25 0.09
133 59 0.21
134 6 0.02
135 135 0.48
136 55 0.20
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.25
Consensus pattern (134 bp):
AGAAGTACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAGTTGATTGGAAGACAATCTCAT
TAAGGAATACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAGTTGATTGGAAGACAATCTC
ATCA
Found at i:70125 original size:64 final size:63
Alignment explanation
Indices: 70024--70269 Score: 262
Period size: 64 Copynumber: 3.8 Consensus size: 63
70014 TGTCAGAAAG
* * * *
70024 AATTTTCA-AATGTTGAATTGGAAGGCGATCTTATCAAGAAGTACACCAGAAGATGGTTTCTGAA
1 AATTTTCAGAA-GTTG-ATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATAGTTTCTGAA
* * * * *
70088 CAATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAACTACGCTAGAAGATAGCTTCTAAAA
1 -AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATAGTTTCT-GAA
* * * *
70153 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTTAAAAAGCACACCAGAAGATAGTTCCTCGAA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATAGTTTCT-GAA
* * * *
70217 AAGGTTTCAGAAGTTGATTGGAAGACGATCTTGTTAAG-AGAAGCACCAGAAGA
1 AA-TTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTA-CACCAGAAGA
70270 CGGCTATTTA
Statistics
Matches: 154, Mismatches: 23, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
64 96 0.62
65 56 0.36
66 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (63 bp):
AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATAGTTTCTGAA
Found at i:70603 original size:50 final size:51
Alignment explanation
Indices: 70478--70610 Score: 232
Period size: 51 Copynumber: 2.6 Consensus size: 51
70468 AAAAGATGAT
70478 TTTTTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTTTTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
* * *
70529 TTTTTAAGAATGAATTGGGAGACAGTTCAAAGGATAAGCTGAAGACGGT-C
1 TTTTTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
70579 TTTTTAAGATTGAATTGGAAGACAGTTCAAAG
1 TTTTTAAGATTGAATTGGAAGACAGTTCAAAG
70611 AAGTTGATCG
Statistics
Matches: 77, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
50 31 0.40
51 46 0.60
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.28
Consensus pattern (51 bp):
TTTTTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
Found at i:71046 original size:21 final size:21
Alignment explanation
Indices: 71016--71059 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
71006 TTTTGTCTCT
*
71016 ATTTCATTGACCGTAAGTTGC
1 ATTTCATTGACCGTAAATTGC
*
71037 ATTTCGTTGACCGTAAATTGC
1 ATTTCATTGACCGTAAATTGC
71058 AT
1 AT
71060 GGTATTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (21 bp):
ATTTCATTGACCGTAAATTGC
Found at i:78517 original size:15 final size:16
Alignment explanation
Indices: 78484--78523 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
78474 TTGCTTTGTT
78484 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
78500 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
78515 TTGCTTTCT
1 TTGTTTTCT
78524 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:80791 original size:27 final size:30
Alignment explanation
Indices: 80729--80801 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 30
80719 AGTGAACTTG
*
80729 AAATGACCAAAATGCCCCATATATATGTGC
1 AAATGACCAAAATGCCCCATAGATATGTGC
80759 AAATGACCAAAATGCCCC-T-GA-ATGTGC
1 AAATGACCAAAATGCCCCATAGATATGTGC
*
80786 AAATGACGAAAATGCC
1 AAATGACCAAAATGCC
80802 TCTGGATGAC
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
27 21 0.51
28 1 0.02
29 1 0.02
30 18 0.44
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.19
Consensus pattern (30 bp):
AAATGACCAAAATGCCCCATAGATATGTGC
Found at i:84027 original size:21 final size:21
Alignment explanation
Indices: 83988--84027 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
83978 AGGAGTTGCC
*
83988 AAAGATGCCATTTGATCCATT
1 AAAGATGCCATTAGATCCATT
*
84009 AAAGATGCCATTAGGTCCA
1 AAAGATGCCATTAGATCCA
84028 ATGACAAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (21 bp):
AAAGATGCCATTAGATCCATT
Found at i:91634 original size:21 final size:21
Alignment explanation
Indices: 91608--91649 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
91598 TAAGGAAGAA
91608 GTTTCAAGCTCATCAGAGTTG
1 GTTTCAAGCTCATCAGAGTTG
*
91629 GTTTCAAGCTCATCGGAGTTG
1 GTTTCAAGCTCATCAGAGTTG
91650 CCTAAGATGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.33
Consensus pattern (21 bp):
GTTTCAAGCTCATCAGAGTTG
Found at i:92066 original size:11 final size:11
Alignment explanation
Indices: 92015--92059 Score: 90
Period size: 11 Copynumber: 4.1 Consensus size: 11
92005 AGGAGTAGGA
92015 TCCTTCCTAGC
1 TCCTTCCTAGC
92026 TCCTTCCTAGC
1 TCCTTCCTAGC
92037 TCCTTCCTAGC
1 TCCTTCCTAGC
92048 TCCTTCCTAGC
1 TCCTTCCTAGC
92059 T
1 T
92060 TTTTCCTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 34 1.00
ACGTcount: A:0.09, C:0.44, G:0.09, T:0.38
Consensus pattern (11 bp):
TCCTTCCTAGC
Found at i:94550 original size:21 final size:21
Alignment explanation
Indices: 94524--94565 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
94514 TAAGGAAGAA
94524 GTTTCAAGCTCATCAGAGTTG
1 GTTTCAAGCTCATCAGAGTTG
*
94545 GTTTCAAGCTCATCGGAGTTG
1 GTTTCAAGCTCATCAGAGTTG
94566 CCTAAGATGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.33
Consensus pattern (21 bp):
GTTTCAAGCTCATCAGAGTTG
Found at i:97587 original size:28 final size:29
Alignment explanation
Indices: 97505--97580 Score: 136
Period size: 29 Copynumber: 2.7 Consensus size: 29
97495 TGTTTGTTCA
97505 AGTGCGGGTTGTGCACTTGAGGTTAATTT
1 AGTGCGGGTTGTGCACTTGAGGTTAATTT
97534 AGTGCGGGTTGTGCACTTGAGGTTAATTT
1 AGTGCGGGTTGTGCACTTGAGGTTAATTT
*
97563 AGTGCAGGTT-TGCACTTG
1 AGTGCGGGTTGTGCACTTG
97581 TTGTTAAAGC
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
28 8 0.17
29 38 0.83
ACGTcount: A:0.17, C:0.12, G:0.34, T:0.37
Consensus pattern (29 bp):
AGTGCGGGTTGTGCACTTGAGGTTAATTT
Found at i:100514 original size:61 final size:61
Alignment explanation
Indices: 100438--100621 Score: 201
Period size: 61 Copynumber: 3.0 Consensus size: 61
100428 TTTAAAACTA
* *
100438 AGAAAGACCTATCTAAGGTCTGAAGTTGAAGAAGACTAGTCTGTGATCGATATTGAAATTG
1 AGAAAGACCTGTCTAAGGTCTGAAGTTGAAGAAGACCAGTCTGTGATCGATATTGAAATTG
* * * * * * * *
100499 AGAAAGACCTGTCTAAGGTCTGAAATGGAAGAAGACCCGTCTGTGGTTGACT-TTAAAAACTA
1 AGAAAGACCTGTCTAAGGTCTGAAGTTGAAGAAGACCAGTCTGTGATCGA-TATT-GAAATTG
* * * *
100561 AGAAAGACTTGTCTGAGGTCTAAAGTTGAAGAAGACCAGTTTGTGGA-CGATATTGAAATTG
1 AGAAAGACCTGTCTAAGGTCTGAAGTTGAAGAAGACCAGTCTGT-GATCGATATTGAAATTG
100622 GCTGGGACCT
Statistics
Matches: 97, Mismatches: 22, Indels: 8
0.76 0.17 0.06
Matches are distributed among these distances:
61 50 0.52
62 46 0.47
63 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.27
Consensus pattern (61 bp):
AGAAAGACCTGTCTAAGGTCTGAAGTTGAAGAAGACCAGTCTGTGATCGATATTGAAATTG
Found at i:100713 original size:123 final size:123
Alignment explanation
Indices: 100425--100713 Score: 332
Period size: 123 Copynumber: 2.3 Consensus size: 123
100415 TTCGTGGCCA
* * * *
100425 ACTTTTAAAACTAAGAAAGACCTATCTAAGGTCTGAAGTTGAAGAAGACTAGTCTGTGATCGATA
1 ACTTTAAAAACTAAGAAAGACCTGTCTGAGGTCTGAAGTTGAAGAAGACCAGTCTGTGATCGATA
* * ** *
100490 TTGAAATTGAGAAAGACCTGTCTAAGGTCTGAAATGGAAGAAGACCCGTCTGTGGTTG
66 TTGAAATTGAGAAAGACCTATCTAAGGTCCGAAATGGAAGAAGACCAATCTGTGGTCG
* * *
100548 ACTTTAAAAACTAAGAAAGACTTGTCTGAGGTCTAAAGTTGAAGAAGACCAGTTTGTGGA-CGAT
1 ACTTTAAAAACTAAGAAAGACCTGTCTGAGGTCTGAAGTTGAAGAAGACCAGTCTGT-GATCGAT
*** * * * *
100612 ATTGAAATTG-GCTGGGACCTATTTGAGGTCCGAAACTGG-TGAAGGCCAATCTGTGGTCG
65 ATTGAAATTGAG-AAAGACCTATCTAAGGTCCGAAA-TGGAAGAAGACCAATCTGTGGTCG
* * *
100671 ACTTTAAAAACTAAGAAAGACCTGTATGAGGCCTGAATTTGAA
1 ACTTTAAAAACTAAGAAAGACCTGTCTGAGGTCTGAAGTTGAA
100714 ACTTGAGAAG
Statistics
Matches: 139, Mismatches: 24, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
122 1 0.01
123 133 0.96
124 5 0.04
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (123 bp):
ACTTTAAAAACTAAGAAAGACCTGTCTGAGGTCTGAAGTTGAAGAAGACCAGTCTGTGATCGATA
TTGAAATTGAGAAAGACCTATCTAAGGTCCGAAATGGAAGAAGACCAATCTGTGGTCG
Found at i:109835 original size:16 final size:15
Alignment explanation
Indices: 109797--109838 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
109787 ACAGAGGTTG
109797 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
109812 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
109827 ACTAGAAAACAA
1 AC-AGAAAACAA
109839 AACAAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Done.