Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 68 of 135
Found at i:20317329 original size:55 final size:55
Alignment explanation
Indices: 20317245--20317421 Score: 164
Period size: 55 Copynumber: 3.2 Consensus size: 55
20317235 CAACGCTCCT
* * * * *
20317245 CTCGAGCTGA-AATGGCTTTACGCTCTAACCAAGATGTAACCAAACTAAAGCTTTA
1 CTCGAGCT-ATAATAGCTTTACGCTCTAACCAAGACGTAACCAAACCAAAACTCTA
* * * **
20317300 CTCGAGCTATAATAGCTTTACACTCTAACCGAGACGTAAGCAGTCCAAAACTCTA
1 CTCGAGCTATAATAGCTTTACGCTCTAACCAAGACGTAACCAAACCAAAACTCTA
* ** *
20317355 C-CTGAGCTATAATAGCTTTATGCTCTAACTGAGACGTAAGCC-AACCAAAATTCTA
1 CTC-GAGCTATAATAGCTTTACGCTCTAACCAAGACGTAA-CCAAACCAAAACTCTA
20317410 C-CTGAGCTATAA
1 CTC-GAGCTATAA
20317422 ACAGGTCAAA
Statistics
Matches: 102, Mismatches: 17, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
54 2 0.02
55 99 0.97
56 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.25
Consensus pattern (55 bp):
CTCGAGCTATAATAGCTTTACGCTCTAACCAAGACGTAACCAAACCAAAACTCTA
Found at i:20317494 original size:27 final size:28
Alignment explanation
Indices: 20317406--20317503 Score: 110
Period size: 28 Copynumber: 3.5 Consensus size: 28
20317396 CAACCAAAAT
* * * *
20317406 TCTACCTGAGCTATAAACAGGTCAAACC
1 TCTACCCGAACTATAAACAGATCAAAGC
*
20317434 TCTACCC-AAGCTATAAACAGATCAAGGC
1 TCTACCCGAA-CTATAAACAGATCAAAGC
20317462 TCTACCCGAACTAT-AACAGATCAAAGC
1 TCTACCCGAACTATAAACAGATCAAAGC
* *
20317489 TTTACCCGAGCTATA
1 TCTACCCGAACTATA
20317504 TTAGAGTATT
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
27 25 0.42
28 32 0.54
29 2 0.03
ACGTcount: A:0.37, C:0.29, G:0.13, T:0.21
Consensus pattern (28 bp):
TCTACCCGAACTATAAACAGATCAAAGC
Found at i:20318859 original size:71 final size:71
Alignment explanation
Indices: 20318743--20318884 Score: 284
Period size: 71 Copynumber: 2.0 Consensus size: 71
20318733 GCCGAATATG
20318743 CTTCCTTGTTTCTCTTAGGATTTCAGCTTTGGAAGATGAAGAAGAAGAAAAGTAATGAAATTTTC
1 CTTCCTTGTTTCTCTTAGGATTTCAGCTTTGGAAGATGAAGAAGAAGAAAAGTAATGAAATTTTC
20318808 ACCCTT
66 ACCCTT
20318814 CTTCCTTGTTTCTCTTAGGATTTCAGCTTTGGAAGATGAAGAAGAAGAAAAGTAATGAAATTTTC
1 CTTCCTTGTTTCTCTTAGGATTTCAGCTTTGGAAGATGAAGAAGAAGAAAAGTAATGAAATTTTC
20318879 ACCCTT
66 ACCCTT
20318885 TTGTTTAATT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.35
Consensus pattern (71 bp):
CTTCCTTGTTTCTCTTAGGATTTCAGCTTTGGAAGATGAAGAAGAAGAAAAGTAATGAAATTTTC
ACCCTT
Found at i:20324724 original size:141 final size:136
Alignment explanation
Indices: 20324472--20324874 Score: 481
Period size: 126 Copynumber: 3.0 Consensus size: 136
20324462 AGTCCTAAGA
* * * * *
20324472 CGACATTTTTGGGGTGACACTTTTCTAAGTGTTAGATAGATTTTCCAACATACGCTTTGGCCAAC
1 CGACA-TTTTGGGGTGACACTTTCCTAAGTGTTGGATAGAATTGCCAACATACGCTTTTGCCAAC
*
20324537 TCTTTGTATAAGGGTTGGGATATGCATGCCTAA-GACAACGCTTAAATAAGAGTTGGCTTTGTTC
65 TCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGA-AACGCTTAAATAAGAGTTGGCTTTGTCC
20324601 AACACTAT
129 AACACTAT
* *
20324609 GCCGACACTTTTGGGGTGACACTTTCCTAAGTATTGGCATAGACTTGCCAACATACGCTTTTGCC
1 --CGACA-TTTTGGGGTGACACTTTCCTAAGTGTTGG-ATAGAATTGCCAACATACGCTTTTGCC
* * *
20324674 TACTCTTTTGTGTAAGGGTTGGGATATGCATGCCTAAGGAAACGCTTAAATAAGAGTCGGCTTTG
62 AACTC-TTTGTATAAGGGTTGGGATATGCATGCCTAAGGAAACGCTTAAATAAGAGTTGGCTTTG
20324739 TCCAACACTAT
126 TCCAACACTAT
* **
20324750 ----A-------GCGACACTTTCCTAAGTGTTAGGATAGAATTGCCGGCATACGC-TTTGACCAA
1 CGACATTTTGGGGTGACACTTTCCTAAGTGTT-GGATAGAATTGCCAACATACGCTTTTG-CCAA
** *
20324803 CTCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCCACGCTTAAATAAGAGTTGGCTTTATCC
64 CTCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGAAACGCTTAAATAAGAGTTGGCTTTGTCC
20324868 AACACTA
129 AACACTA
20324875 CGCCAACCTT
Statistics
Matches: 237, Mismatches: 22, Indels: 23
0.84 0.08 0.08
Matches are distributed among these distances:
126 68 0.29
127 41 0.17
128 2 0.01
135 1 0.00
139 31 0.13
140 28 0.12
141 64 0.27
142 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.32
Consensus pattern (136 bp):
CGACATTTTGGGGTGACACTTTCCTAAGTGTTGGATAGAATTGCCAACATACGCTTTTGCCAACT
CTTTGTATAAGGGTTGGGATATGCATGCCTAAGGAAACGCTTAAATAAGAGTTGGCTTTGTCCAA
CACTAT
Found at i:20324956 original size:74 final size:72
Alignment explanation
Indices: 20324877--20325178 Score: 392
Period size: 74 Copynumber: 4.1 Consensus size: 72
20324867 CAACACTACG
*
20324877 CCAACCTTTTTAAGGTTGCCTTAGAGAAGGTCTATCCCAACCTTTTTAAAAGGTTGCCTTAGACA
1 CCAACCTTTTTAAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTT-AAAGGTTGCCTTAGAC-
*
20324942 AAATCTATC
64 AAGTCTATC
* * * *
20324951 CCAACCATTTTAAAGTTGCCTTAGACAAGGTCTATCCCAACCTTCTTTAAAGGTTGCCTCAAACA
1 CCAACCTTTTTAAGGTTGCCTTAGACAAGGTCTATCCCAACCTT-TTTAAAGGTTGCCTTAGACA
20325016 AGGTCTATC
65 A-GTCTATC
* * **
20325025 CCAACCATTTTAAGGTTGCCTTAGAC-AGGTCTATCCTAATATTTTTTAAAGGTTGCCTTAGACA
1 CCAACCTTTTTAAGGTTGCCTTAGACAAGGTCTATCCCAA-CCTTTTTAAAGGTTGCCTTAGACA
*
20325089 GGTCTATC
65 AGTCTATC
* * *
20325097 CCAACCTTTTTTAAAGGTTGCCTTAGACAATGCCTATCTCAACCTTTTTAAA-GTTGCCTTAGAC
1 CCAACC-TTTTT-AAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTAAAGGTTGCCTTAGAC
*
20325161 GAGTCTATC
64 AAGTCTATC
20325170 CCAACCTTT
1 CCAACCTTT
20325179 CAATAAAGTT
Statistics
Matches: 200, Mismatches: 22, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
72 16 0.08
73 61 0.31
74 111 0.56
75 12 0.06
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (72 bp):
CCAACCTTTTTAAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTAAAGGTTGCCTTAGACAA
GTCTATC
Found at i:20325072 original size:110 final size:108
Alignment explanation
Indices: 20324877--20325175 Score: 381
Period size: 110 Copynumber: 2.7 Consensus size: 108
20324867 CAACACTACG
*
20324877 CCAACCTTTTT-AAGGTTGCCTTAGAGAAGGTCTATCCCAACCTTTTTAAAAGGTTGCCTTAGAC
1 CCAACCTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTT--AAGGTTGCCTTAGAC
**
20324941 AAAATCTATCCCAACCATTTTAAA-GTTGCCTTAGACAAGGTCTATC
64 -AGGTCTATCCCAACCATTTTAAAGGTTGCCTTAGAC-AGGTCTATC
* * *
20324987 CCAACCTTCTTTAAAGGTTGCCTCAAACAAGGTCTATCCCAACCATTTTAAGGTTGCCTTAGACA
1 CCAACCTT-TTTAAAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTAAGGTTGCCTTAGACA
* *
20325052 GGTCTATCCTAA-TATTTTTTAAAGGTTGCCTTAGACAGGTCTATC
65 GGTCTATCCCAACCA--TTTTAAAGGTTGCCTTAGACAGGTCTATC
* * * *
20325097 CCAACCTTTTTTAAAGGTTGCCTTAGACAATGCCTATCTCAACCTTTTTAAAGTTGCCTTAGAC-
1 CCAACC-TTTTTAAAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTAAGGTTGCCTTAGACA
20325161 GAGTCTATCCCAACC
65 G-GTCTATCCCAACC
20325176 TTTCAATAAA
Statistics
Matches: 164, Mismatches: 17, Indels: 15
0.84 0.09 0.08
Matches are distributed among these distances:
108 1 0.01
109 11 0.07
110 103 0.63
111 17 0.10
112 32 0.20
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (108 bp):
CCAACCTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTAAGGTTGCCTTAGACAG
GTCTATCCCAACCATTTTAAAGGTTGCCTTAGACAGGTCTATC
Found at i:20327036 original size:17 final size:17
Alignment explanation
Indices: 20327016--20327048 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
20327006 TTTAAGGACC
20327016 TTTTAATTTTA-TTTAAG
1 TTTT-ATTTTAGTTTAAG
20327033 TTTTATTTTAGTTTAA
1 TTTTATTTTAGTTTAA
20327049 TAAGTGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTTATTTTAGTTTAAG
Found at i:20328592 original size:19 final size:19
Alignment explanation
Indices: 20328568--20328624 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
20328558 TATTTTGTGT
*
20328568 TTCGAAAAACTGAAAAAAA
1 TTCGAAAAAATGAAAAAAA
*
20328587 TTCGAAAAAAAGAAAAAAAA
1 TTCGAAAAAATG-AAAAAAA
* *
20328607 TT-GAAATATTGAAAAAAA
1 TTCGAAAAAATGAAAAAAA
20328625 GAAAAAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
18 7 0.22
19 16 0.50
20 9 0.28
ACGTcount: A:0.67, C:0.05, G:0.11, T:0.18
Consensus pattern (19 bp):
TTCGAAAAAATGAAAAAAA
Found at i:20328620 original size:27 final size:27
Alignment explanation
Indices: 20328590--20328651 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
20328580 AAAAAAATTC
20328590 GAAAAAAAGAAAAAAAATTGAAA-TATT
1 GAAAAAAAGAAAAAAAATTGAAACT-TT
*
20328617 GAAAAAAAGAAAAAAAATTTAAACTTT
1 GAAAAAAAGAAAAAAAATTGAAACTTT
20328644 GAAAAAAA
1 GAAAAAAA
20328652 TTCGAATTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
27 32 0.97
28 1 0.03
ACGTcount: A:0.71, C:0.02, G:0.10, T:0.18
Consensus pattern (27 bp):
GAAAAAAAGAAAAAAAATTGAAACTTT
Found at i:20329703 original size:19 final size:18
Alignment explanation
Indices: 20329660--20329704 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
20329650 AGAGTGTGAG
*
20329660 AAAAGAGATCGAAATTGA
1 AAAAGAAATCGAAATTGA
20329678 AAAAGAAATCGAGAA-TGA
1 AAAAGAAATCGA-AATTGA
20329696 AGAAAGAAA
1 A-AAAGAAA
20329705 AGAAAGAGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.62, C:0.04, G:0.22, T:0.11
Consensus pattern (18 bp):
AAAAGAAATCGAAATTGA
Found at i:20331115 original size:17 final size:17
Alignment explanation
Indices: 20331095--20331127 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
20331085 TTTAAGGACT
20331095 TTTTAATTTTA-TTTAAG
1 TTTT-ATTTTAGTTTAAG
20331112 TTTTATTTTAGTTTAA
1 TTTTATTTTAGTTTAA
20331128 TAAGTGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTTATTTTAGTTTAAG
Found at i:20331403 original size:50 final size:50
Alignment explanation
Indices: 20331345--20331442 Score: 135
Period size: 50 Copynumber: 2.0 Consensus size: 50
20331335 CAATTAAGTT
*
20331345 TGCATCATAAATAATGA-CATGCATTAAGTAACTTACATGTTAGTTAAATA
1 TGCATCATAAATAAT-ATCATGCATTAAGTAACTCACATGTTAGTTAAATA
** * *
20331395 TGCATCATAAATCCTATCATGCATTATGTAACTCCCATGTTAGTTAAA
1 TGCATCATAAATAATATCATGCATTAAGTAACTCACATGTTAGTTAAA
20331443 GTTTTCATCA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
49 1 0.02
50 41 0.98
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (50 bp):
TGCATCATAAATAATATCATGCATTAAGTAACTCACATGTTAGTTAAATA
Found at i:20336318 original size:24 final size:26
Alignment explanation
Indices: 20336280--20336379 Score: 123
Period size: 26 Copynumber: 3.9 Consensus size: 26
20336270 GATAAGAGTG
*
20336280 TATTCTGTCTAAGCTCGTAAGAGCAT
1 TATTCTGTCTGAGCTCGTAAGAGCAT
*
20336306 TA-T-TGTCTGAGCTTGTAAGAGCAT
1 TATTCTGTCTGAGCTCGTAAGAGCAT
* * * *
20336330 TATTCTATATGAGGTTGTAAGAGCAT
1 TATTCTGTCTGAGCTCGTAAGAGCAT
*
20336356 TATTCTGTCTGGGCTCGTAAGAGC
1 TATTCTGTCTGAGCTCGTAAGAGC
20336380 TAAACTTTGT
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
24 21 0.34
25 2 0.03
26 39 0.63
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (26 bp):
TATTCTGTCTGAGCTCGTAAGAGCAT
Found at i:20339255 original size:25 final size:26
Alignment explanation
Indices: 20339210--20339428 Score: 258
Period size: 25 Copynumber: 8.7 Consensus size: 26
20339200 TTTAGCTCAA
20339210 ACGAGCCTAGA-CAGAATATCGCTCTT
1 ACGAGCC-AGATCAGAATATCGCTCTT
*
20339236 ACGAGCCA-ATCAGAATATCGCTTTT
1 ACGAGCCAGATCAGAATATCGCTCTT
* * *
20339261 ACAAACCAGA-CTGAATATCGCTCTT
1 ACGAGCCAGATCAGAATATCGCTCTT
* *
20339286 CCGAGCCA-ATCAGAATATCACTCTT
1 ACGAGCCAGATCAGAATATCGCTCTT
*
20339311 ACGAGCCA-ATTAGAATATCGCTCTT
1 ACGAGCCAGATCAGAATATCGCTCTT
* * *
20339336 ACGAGCTAGAT-AGAATATCACTCGT
1 ACGAGCCAGATCAGAATATCGCTCTT
*
20339361 ATGAGCCAGA-CAGAATATCGCTCTT
1 ACGAGCCAGATCAGAATATCGCTCTT
*
20339386 ACGAGCCAGA-CAAAATATCGCTCTT
1 ACGAGCCAGATCAGAATATCGCTCTT
20339411 ACGAGCCAGA-CAGAATAT
1 ACGAGCCAGATCAGAATAT
20339429 TTGCTCTATC
Statistics
Matches: 165, Mismatches: 23, Indels: 11
0.83 0.12 0.06
Matches are distributed among these distances:
24 2 0.01
25 153 0.93
26 10 0.06
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (26 bp):
ACGAGCCAGATCAGAATATCGCTCTT
Found at i:20342799 original size:51 final size:51
Alignment explanation
Indices: 20342738--20342875 Score: 149
Period size: 50 Copynumber: 2.7 Consensus size: 51
20342728 TGCATGACTT
*
20342738 GATTTAATGATGCAAACTTTAACTAACATGGGAGTTACATAATGCATGAT-AG
1 GATTT-ATGATGCAAACTTTAACTAACATGAGAGTTACATAATGCATG-TCAG
* * *
20342790 GATTTATGATGCATA-TTTAACTAACATGTA-AGTTACTTAATGCATGTCAT
1 GATTTATGATGCAAACTTTAACTAACATG-AGAGTTACATAATGCATGTCAG
* **
20342840 TATTTAAAATGCAAAC-TTAACTAATCATGAGAGTTA
1 GATTTATGATGCAAACTTTAACTAA-CATGAGAGTTA
20342876 ATGGATGTTA
Statistics
Matches: 73, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
49 1 0.01
50 49 0.67
51 18 0.25
52 5 0.07
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (51 bp):
GATTTATGATGCAAACTTTAACTAACATGAGAGTTACATAATGCATGTCAG
Found at i:20343101 original size:17 final size:17
Alignment explanation
Indices: 20343070--20343102 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
20343060 CAAACACTTA
20343070 TTAAACTAAAATAAAAC
1 TTAAACTAAAATAAAAC
20343087 TTAAA-TAAAATTAAAA
1 TTAAACTAAAA-TAAAA
20343103 AGTCCTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (17 bp):
TTAAACTAAAATAAAAC
Found at i:20352190 original size:30 final size:28
Alignment explanation
Indices: 20352168--20352241 Score: 112
Period size: 30 Copynumber: 2.5 Consensus size: 28
20352158 AGATTCGATT
20352168 TCTTGATTTTCTTTAAAACAAGAAAGTGAA
1 TCTTGATTTTCTTTAAAACAAG--AGTGAA
20352198 TCTTGATTTTCTTTAAAACAAGAAAGTGAA
1 TCTTGATTTTCTTTAAAACAAG--AGTGAA
20352228 TCTTGATTTTCTTT
1 TCTTGATTTTCTTT
20352242 TTCGATCATG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.43
Consensus pattern (28 bp):
TCTTGATTTTCTTTAAAACAAGAGTGAA
Found at i:20365905 original size:21 final size:21
Alignment explanation
Indices: 20365881--20365921 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
20365871 CTGAAGGAAT
20365881 AAGAAGAAGAA-GAAGAGAAGA
1 AAGAAG-AGAATGAAGAGAAGA
*
20365902 AAGATGAGAATGAAGAGAAG
1 AAGAAGAGAATGAAGAGAAG
20365922 GACCTTGCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.61, C:0.00, G:0.34, T:0.05
Consensus pattern (21 bp):
AAGAAGAGAATGAAGAGAAGA
Found at i:20371027 original size:16 final size:17
Alignment explanation
Indices: 20371008--20371043 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
20370998 ACCTAATGGC
*
20371008 TATAAATA-CTAACCAT
1 TATAAATATCTAAACAT
20371024 TATAAATATCTAAACAT
1 TATAAATATCTAAACAT
20371041 TAT
1 TAT
20371044 TCTAACTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (17 bp):
TATAAATATCTAAACAT
Found at i:20371114 original size:21 final size:21
Alignment explanation
Indices: 20371090--20371129 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
20371080 CCTAGAAATC
* *
20371090 CTTTCCTTTTTCTAGTTTTCT
1 CTTTACTTTTTCAAGTTTTCT
20371111 CTTTACTTTTTCAAGTTTT
1 CTTTACTTTTTCAAGTTTT
20371130 GAAGCAAGTG
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:0.10, C:0.20, G:0.05, T:0.65
Consensus pattern (21 bp):
CTTTACTTTTTCAAGTTTTCT
Found at i:20385075 original size:21 final size:19
Alignment explanation
Indices: 20385048--20385099 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 19
20385038 AGGCACAATT
20385048 GAGAAGGAGAAACTTGAGG-A
1 GAGAAGGAGAAA--TGAGGAA
20385068 GAAGAAGGA-AAATGAGGAA
1 G-AGAAGGAGAAATGAGGAA
20385087 GAGAAGGAAGAAA
1 GAGAAGG-AGAAA
20385100 AGGAGAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
18 11 0.39
19 3 0.11
20 7 0.25
21 7 0.25
ACGTcount: A:0.54, C:0.02, G:0.38, T:0.06
Consensus pattern (19 bp):
GAGAAGGAGAAATGAGGAA
Found at i:20385083 original size:18 final size:19
Alignment explanation
Indices: 20385062--20385115 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
20385052 AGGAGAAACT
20385062 TGAGGAGAAGAAGGAA-AA
1 TGAGGAGAAGAAGGAAGAA
20385080 TGAGGA-AGAGAAGGAAGAA
1 TGAGGAGA-AGAAGGAAGAA
* *
20385099 -AAGGAGAAGAATGAAGA
1 TGAGGAGAAGAAGGAAGA
20385116 GAAGGAAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
17 1 0.03
18 27 0.87
19 3 0.10
ACGTcount: A:0.56, C:0.00, G:0.39, T:0.06
Consensus pattern (19 bp):
TGAGGAGAAGAAGGAAGAA
Found at i:20385094 original size:9 final size:9
Alignment explanation
Indices: 20385082--20385124 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
20385072 AAGGAAAATG
20385082 AGGAAGAGA
1 AGGAAGAGA
*
20385091 AGGAAGAAA
1 AGGAAGAGA
20385100 AGG-AGAAGA
1 AGGAAG-AGA
*
20385109 ATGAAGAGA
1 AGGAAGAGA
20385118 AGGAAGA
1 AGGAAGA
20385125 TGCCCCGACA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
8 2 0.07
9 24 0.86
10 2 0.07
ACGTcount: A:0.58, C:0.00, G:0.40, T:0.02
Consensus pattern (9 bp):
AGGAAGAGA
Found at i:20385100 original size:21 final size:20
Alignment explanation
Indices: 20385066--20385108 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
20385056 GAAACTTGAG
*
20385066 GAGAAGAAGGAAAATGAGGAA
1 GAGAAGAAGGAAAAGGA-GAA
20385087 GAGAAGGAA-GAAAAGGAGAA
1 GAGAA-GAAGGAAAAGGAGAA
20385107 GA
1 GA
20385109 ATGAAGAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
21 12 0.60
22 3 0.15
ACGTcount: A:0.58, C:0.00, G:0.40, T:0.02
Consensus pattern (20 bp):
GAGAAGAAGGAAAAGGAGAA
Found at i:20385102 original size:27 final size:28
Alignment explanation
Indices: 20385067--20385124 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
20385057 AAACTTGAGG
20385067 AGAAGAAGGAAAATG-AGGAAGAGAAGGA
1 AGAAGAAGGAAAA-GAAGGAAGAGAAGGA
* *
20385095 AGAA-AAGGAGAAGAATGAAGAGAAGGA
1 AGAAGAAGGAAAAGAAGGAAGAGAAGGA
20385122 AGA
1 AGA
20385125 TGCCCCGACA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 1 0.04
27 22 0.81
28 4 0.15
ACGTcount: A:0.59, C:0.00, G:0.38, T:0.03
Consensus pattern (28 bp):
AGAAGAAGGAAAAGAAGGAAGAGAAGGA
Found at i:20385440 original size:3 final size:3
Alignment explanation
Indices: 20385432--20385457 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
20385422 GGAGCGCCCA
20385432 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
20385458 AGCCAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:20385579 original size:17 final size:18
Alignment explanation
Indices: 20385540--20385583 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
20385530 ATGCATAGCA
* *
20385540 TTTAGTTGTCATTGCATT
1 TTTATTTGTCACTGCATT
20385558 TTTATTTGTCACTGCA-T
1 TTTATTTGTCACTGCATT
20385575 TTTATTTGT
1 TTTATTTGT
20385584 TAGTACATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.16, C:0.11, G:0.14, T:0.59
Consensus pattern (18 bp):
TTTATTTGTCACTGCATT
Found at i:20388843 original size:30 final size:29
Alignment explanation
Indices: 20388786--20388849 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 29
20388776 AAAACTTCAA
*
20388786 ACAAAACT-CAAATTAGTCCCTAAACTTT
1 ACAAAAATACAAATTAGTCCCTAAACTTT
20388814 ACTAAAAATACAAATTAGTCCCTAAACTTT
1 AC-AAAAATACAAATTAGTCCCTAAACTTT
20388844 ACAAAA
1 ACAAAA
20388850 TCTCTAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 2 0.06
29 9 0.27
30 22 0.67
ACGTcount: A:0.48, C:0.22, G:0.03, T:0.27
Consensus pattern (29 bp):
ACAAAAATACAAATTAGTCCCTAAACTTT
Found at i:20388862 original size:30 final size:29
Alignment explanation
Indices: 20388786--20388864 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 29
20388776 AAAACTTCAA
20388786 ACAAAA-CTCAAATTAGTCCCTAAACTTT
1 ACAAAATCTCAAATTAGTCCCTAAACTTT
*
20388814 ACTAAAAAT-ACAAATTAGTCCCTAAACTTT
1 AC--AAAATCTCAAATTAGTCCCTAAACTTT
*
20388844 ACAAAATCTCTAATTTAGTCC
1 ACAAAATCTC-AAATTAGTCC
20388865 ATTAACAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
28 7 0.16
29 1 0.02
30 35 0.81
ACGTcount: A:0.43, C:0.23, G:0.04, T:0.30
Consensus pattern (29 bp):
ACAAAATCTCAAATTAGTCCCTAAACTTT
Found at i:20390400 original size:30 final size:30
Alignment explanation
Indices: 20390364--20390433 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
20390354 ATTGTTACTC
20390364 AAATTAGTCCCTAAACTTTACTAAAAT-TAT
1 AAATTAGTCCCTAAACTTTAC-AAAATCTAT
* * *
20390394 AAATTAGACCTTAAACTTTACAAAATCTCT
1 AAATTAGTCCCTAAACTTTACAAAATCTAT
*
20390424 AATTTAGTCC
1 AAATTAGTCC
20390434 ATTAAAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 5 0.15
30 29 0.85
ACGTcount: A:0.41, C:0.19, G:0.04, T:0.36
Consensus pattern (30 bp):
AAATTAGTCCCTAAACTTTACAAAATCTAT
Found at i:20407118 original size:30 final size:32
Alignment explanation
Indices: 20407082--20407151 Score: 108
Period size: 30 Copynumber: 2.2 Consensus size: 32
20407072 ATCGGCAAAT
*
20407082 GAAGAGAAGAGGAGAAAAG-G-GAGAAAAAGA
1 GAAGAGAAGAGGAGAAAAGAGAGAAAAAAAGA
*
20407112 GAAGAGAATAGGAGAAAAGAGAGAAAAAAAGA
1 GAAGAGAAGAGGAGAAAAGAGAGAAAAAAAGA
20407144 GAAGAGAA
1 GAAGAGAA
20407152 AAAGGGTTCC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 18 0.50
31 1 0.03
32 17 0.47
ACGTcount: A:0.63, C:0.00, G:0.36, T:0.01
Consensus pattern (32 bp):
GAAGAGAAGAGGAGAAAAGAGAGAAAAAAAGA
Found at i:20407149 original size:15 final size:15
Alignment explanation
Indices: 20407105--20407154 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
20407095 GAAAAGGGAG
20407105 AAAAAGAGAAGAGAA
1 AAAAAGAGAAGAGAA
20407120 TAGGAGAAA-AG-AGAGAA
1 -A--A-AAAGAGAAGAGAA
20407137 AAAAAGAGAAGAGAA
1 AAAAAGAGAAGAGAA
20407152 AAA
1 AAA
20407155 GGGTTCCCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 11
0.73 0.00 0.28
Matches are distributed among these distances:
13 3 0.10
14 3 0.10
15 9 0.31
16 2 0.07
17 6 0.21
18 3 0.10
19 3 0.10
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (15 bp):
AAAAAGAGAAGAGAA
Found at i:20410996 original size:19 final size:18
Alignment explanation
Indices: 20410974--20411009 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
20410964 TCAAAAACTT
20410974 GAGAAAAAAATAAAAATAC
1 GAGAAAAAAA-AAAAATAC
*
20410993 GAGAAAAATAAAAAATA
1 GAGAAAAAAAAAAAATA
20411010 AAAAAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.75, C:0.03, G:0.11, T:0.11
Consensus pattern (18 bp):
GAGAAAAAAAAAAAATAC
Found at i:20416020 original size:13 final size:13
Alignment explanation
Indices: 20415983--20416027 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
20415973 AACATAGATA
20415983 TTTTTTTCTTCTT
1 TTTTTTTCTTCTT
**
20415996 TTCACTTT-TTCTT
1 TT-TTTTTCTTCTT
20416009 TTTTTTTCTTCTT
1 TTTTTTTCTTCTT
20416022 TTTTTT
1 TTTTTT
20416028 ATATGTGACT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 3 0.12
13 20 0.77
14 3 0.12
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTTTTCTTCTT
Found at i:20416630 original size:17 final size:17
Alignment explanation
Indices: 20416591--20416636 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
20416581 TGATATGTGG
**
20416591 AAATGCAATGACAATGT
1 AAATGCAATGACAATCA
* *
20416608 AGATGCAGTGACAATCA
1 AAATGCAATGACAATCA
20416625 AAATGCAATGAC
1 AAATGCAATGAC
20416637 GAAGGAAACG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.46, C:0.15, G:0.20, T:0.20
Consensus pattern (17 bp):
AAATGCAATGACAATCA
Found at i:20418621 original size:255 final size:254
Alignment explanation
Indices: 20418165--20418672 Score: 881
Period size: 255 Copynumber: 2.0 Consensus size: 254
20418155 TTCACAAACA
*
20418165 AAGACGAACTCTTGTTCGTTATTAGTCAGGTTTTCGTAGAACACTTTCACAAGAGATGGTGAATA
1 AAGACGAACTCTTGTTCGTTATTAGTCAGGTTTACGTAGAACACTTTCACAAGAGATGGTGAATA
* *
20418230 GCCCCTATGATGGGTGCAAAAGGTTTCCCAACCCATTCTCGTAATAGTTTTATTGACTTGCTTCC
66 GCCCCTAGGATGGGTGCAAAAGGTTTCCCAACCCATTCTCGTAATAGTTTTATTAACTTGCTTCC
* * *
20418295 CCAGGTCTTGATGCTTCGATAGCTGAAAACCCTGCTCAGGATGACAATTGCACTTCAACATGTTA
131 CCAGGCCTTGATGCTTCGACAGCTGAAAACCCTGCTCAGGATGACAATTGCACTTCAAAATGTTA
* *
20418360 TCTTGGAAGCGGTCCTTTGCAGCCTTGGTCAAAAACACCACTGGTTTCTCTAGATGGGTG
196 TCTTGGAAGCGATCCTTTGCAGCCTTAGTCAAAAACACCACTGG-TTCTCTAGATGGGTG
20418420 AAGACGAACTCTTGTTCGTTATTAGTCAGGTTTACGTAGAACACTTTCACAAGAGATGGTGAATA
1 AAGACGAACTCTTGTTCGTTATTAGTCAGGTTTACGTAGAACACTTTCACAAGAGATGGTGAATA
*
20418485 GCCCCTAGGATGGGTGTAAAAGGTTTCCCAACCCATTCTCGTAATAGTTTTATTAACTTGCTTCC
66 GCCCCTAGGATGGGTGCAAAAGGTTTCCCAACCCATTCTCGTAATAGTTTTATTAACTTGCTTCC
* * * * *
20418550 CTAGGCCTTGATGCTTTGACAGCTGAAAACCCTGCTCAGGATGATAATTGCACTTTAAAATGTTG
131 CCAGGCCTTGATGCTTCGACAGCTGAAAACCCTGCTCAGGATGACAATTGCACTTCAAAATGTTA
20418615 TCTTGGAAGCGATCCTTTGCAGCCTTAGTCAAAAACACCACTGGTTCTCTAGATGGGT
196 TCTTGGAAGCGATCCTTTGCAGCCTTAGTCAAAAACACCACTGGTTCTCTAGATGGGT
20418673 AATGCTCTAT
Statistics
Matches: 239, Mismatches: 14, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
254 14 0.06
255 225 0.94
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (254 bp):
AAGACGAACTCTTGTTCGTTATTAGTCAGGTTTACGTAGAACACTTTCACAAGAGATGGTGAATA
GCCCCTAGGATGGGTGCAAAAGGTTTCCCAACCCATTCTCGTAATAGTTTTATTAACTTGCTTCC
CCAGGCCTTGATGCTTCGACAGCTGAAAACCCTGCTCAGGATGACAATTGCACTTCAAAATGTTA
TCTTGGAAGCGATCCTTTGCAGCCTTAGTCAAAAACACCACTGGTTCTCTAGATGGGTG
Found at i:20419300 original size:23 final size:23
Alignment explanation
Indices: 20419270--20419335 Score: 123
Period size: 23 Copynumber: 2.9 Consensus size: 23
20419260 AGTCGTTAGT
20419270 CATTCACCTTAAATTTGTGCTGC
1 CATTCACCTTAAATTTGTGCTGC
*
20419293 CATTCACCTTAAATTTGTTCTGC
1 CATTCACCTTAAATTTGTGCTGC
20419316 CATTCACCTTAAATTTGTGC
1 CATTCACCTTAAATTTGTGC
20419336 CCATCATTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.23, C:0.26, G:0.11, T:0.41
Consensus pattern (23 bp):
CATTCACCTTAAATTTGTGCTGC
Found at i:20426717 original size:18 final size:18
Alignment explanation
Indices: 20426696--20426731 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
20426686 AAAGCCTTGA
*
20426696 GTGAGCTTGCAGTTTTGG
1 GTGAGCTCGCAGTTTTGG
*
20426714 GTGAGCTCGCATTTTTGG
1 GTGAGCTCGCAGTTTTGG
20426732 AGGGTTCACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.14, G:0.36, T:0.39
Consensus pattern (18 bp):
GTGAGCTCGCAGTTTTGG
Found at i:20438373 original size:19 final size:19
Alignment explanation
Indices: 20438334--20438374 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
20438324 TGTCCAAGTG
** *
20438334 CATAATTAGTATTACATCA
1 CATAATTAGTACAACACCA
20438353 CATAATTAGTACAACACCA
1 CATAATTAGTACAACACCA
20438372 CAT
1 CAT
20438375 TAAAGCATCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.44, C:0.22, G:0.05, T:0.29
Consensus pattern (19 bp):
CATAATTAGTACAACACCA
Found at i:20439542 original size:138 final size:138
Alignment explanation
Indices: 20439294--20439578 Score: 473
Period size: 138 Copynumber: 2.1 Consensus size: 138
20439284 TAGAAAAATG
20439294 AATTATATTATTTCTAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACTAAAATTAATTAA
1 AATTATATTATTTCTAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACTAAAATTAATTAA
*
20439359 TATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTATATGAATCAAATT
66 TATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTCATATGAATCAAATT
20439424 CATATATT
131 CATATATT
* * * *
20439432 AATTATATTCTTTCTAACAGAATATTAATTTTCATGTCTTTTATATTTTGA-TCGAAATTAATTA
1 AATTATATTATTTCTAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACT-AAAATTAATTA
* * * *
20439496 ATATAATTGTTTATATTAATAAATTCGGTAAAATATATATAATTAATATTTCGTATGAATCAATT
65 ATATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTCATATGAATCAAAT
20439561 TCATATATT
130 TCATATATT
20439570 AATTATATT
1 AATTATATT
20439579 TGATTGCCTC
Statistics
Matches: 137, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
137 1 0.01
138 136 0.99
ACGTcount: A:0.40, C:0.07, G:0.06, T:0.47
Consensus pattern (138 bp):
AATTATATTATTTCTAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACTAAAATTAATTAA
TATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTCATATGAATCAAATT
CATATATT
Found at i:20442770 original size:26 final size:26
Alignment explanation
Indices: 20442734--20442793 Score: 120
Period size: 26 Copynumber: 2.3 Consensus size: 26
20442724 ACTCGGGAAA
20442734 TGCTCACACGAGCTATGAAATGGGTC
1 TGCTCACACGAGCTATGAAATGGGTC
20442760 TGCTCACACGAGCTATGAAATGGGTC
1 TGCTCACACGAGCTATGAAATGGGTC
20442786 TGCTCACA
1 TGCTCACA
20442794 TGAACTGTGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (26 bp):
TGCTCACACGAGCTATGAAATGGGTC
Found at i:20445515 original size:16 final size:16
Alignment explanation
Indices: 20445484--20445530 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
20445474 TCGTTCGGCC
**
20445484 CAAAATAAAACCAAAA
1 CAAAATAAAAATAAAA
20445500 CAAAATAAAAATAAAA
1 CAAAATAAAAATAAAA
**
20445516 -AAACCAAAAATAAAA
1 CAAAATAAAAATAAAA
20445531 AATAAAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
15 13 0.48
16 14 0.52
ACGTcount: A:0.79, C:0.13, G:0.00, T:0.09
Consensus pattern (16 bp):
CAAAATAAAAATAAAA
Found at i:20447506 original size:51 final size:51
Alignment explanation
Indices: 20447425--20447617 Score: 287
Period size: 51 Copynumber: 3.8 Consensus size: 51
20447415 GCTATAAACG
20447425 AAAGAGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAG-GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * *
20447477 AAAGGTCCGATCACTAACTGTCATCGTGAGTAAATGAATCGTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * * *
20447528 AAACGTCCGATGACTAAGTGTCATTGTGAGTAAATGAATCCGTGACGAATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* *
20447579 AAAGGTCCGATGACTCAGTGTCATCGTGAGTATATGAAT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAAT
20447618 TTCTATACAG
Statistics
Matches: 126, Mismatches: 15, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
51 122 0.97
52 4 0.03
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.28
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:20448261 original size:21 final size:23
Alignment explanation
Indices: 20448235--20448291 Score: 82
Period size: 21 Copynumber: 2.5 Consensus size: 23
20448225 GACTTGAGTT
20448235 GTATCGATAGTTAAAT-TAT-AA
1 GTATCGATAGTTAAATGTATAAA
*
20448256 GTATCGATAGTTATATGTATAGAA
1 GTATCGATAGTTAAATGTATA-AA
20448280 GTATCGATAGTT
1 GTATCGATAGTT
20448292 TGCATGCTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 15 0.47
22 3 0.09
24 14 0.44
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.39
Consensus pattern (23 bp):
GTATCGATAGTTAAATGTATAAA
Found at i:20450784 original size:111 final size:108
Alignment explanation
Indices: 20450586--20450802 Score: 292
Period size: 111 Copynumber: 2.0 Consensus size: 108
20450576 AAAATCGAGG
* * * *
20450586 CAATGTTCTTTATTTAGGGAATTCGAGAAATTGTGCCATAACGTGTTGGGTATAGTTTTTTCTTT
1 CAATGTTCTTTATTTAGGGAACTCGAAAAATTGTGCCATAACGTGCTAGGTATAGTTTTTTCTTT
**
20450651 GAACCTAAATAATTGAGTATCCTATTTAAAATCGATAAATGCT
66 GAACCTAAATAATTGAACATCCTATTTAAAATCGATAAATGCT
* * *
20450694 CAATGTTCTGTTATTTTAGGGGACTCGAAAAATTGTGCCCTAATGTGCTAGGTAT-GTTTTTTTT
1 CAATGTTCT-TTA-TTTAGGGAACTCGAAAAATTGTGCCATAACGTGCTAGGTATAG--TTTTTT
* *
20450758 CTTTGAACCTAAGTAATTGAACATCCTATTTAAAATCGATGAATG
62 CTTTGAACCTAAATAATTGAACATCCTATTTAAAATCGATAAATG
20450803 TTTTTTGTTT
Statistics
Matches: 94, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
108 9 0.10
109 4 0.04
110 34 0.36
111 47 0.50
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (108 bp):
CAATGTTCTTTATTTAGGGAACTCGAAAAATTGTGCCATAACGTGCTAGGTATAGTTTTTTCTTT
GAACCTAAATAATTGAACATCCTATTTAAAATCGATAAATGCT
Found at i:20453282 original size:51 final size:51
Alignment explanation
Indices: 20453206--20453444 Score: 282
Period size: 51 Copynumber: 4.6 Consensus size: 51
20453196 GCTATAAATG
20453206 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
*
20453257 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * * * *
20453308 AAAGGTCCGATAATTAAGTATCATCGTGAGTAAATGAATCCATGACGAATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
** * * * ** **
20453359 AAAGGTCCGATGACCCAGTGTAATCGTGAGTATATAAATTCCTACACGGAAC
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTACGGATT
*
20453411 AAAGGGGTCCGATGACTATA-TGTCTTCGTGAGTA
1 AAA--GGTCCGATGACTA-AGTGTCATCGTGAGTA
20453445 TTAAATGAAA
Statistics
Matches: 158, Mismatches: 26, Indels: 5
0.84 0.14 0.03
Matches are distributed among these distances:
51 124 0.78
52 10 0.06
54 23 0.15
55 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:20460618 original size:51 final size:51
Alignment explanation
Indices: 20460431--20460615 Score: 262
Period size: 51 Copynumber: 3.6 Consensus size: 51
20460421 GCTATAAACG
* *
20460431 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGAATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
20460482 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * * * * * *
20460533 AAAGGTCTGATGACTAAATATCATCATGAGTATATGAATCCATGAGGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* *
20460584 AAAGGTCTGATGACTCAGTGTCATCGTGAGTA
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTA
20460616 TATAATTTCC
Statistics
Matches: 120, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 120 1.00
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:20464594 original size:26 final size:26
Alignment explanation
Indices: 20464560--20464617 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
20464550 CACCCACGAA
*
20464560 TGTCACTGCATGAACATGTCCAGAAT
1 TGTCGCTGCATGAACATGTCCAGAAT
*
20464586 TGTCGCTGCATGAACGTGTCCAGAAT
1 TGTCGCTGCATGAACATGTCCAGAAT
20464612 TG-CGCT
1 TGTCGCT
20464618 CAGAATTATC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 4 0.13
26 26 0.87
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (26 bp):
TGTCGCTGCATGAACATGTCCAGAAT
Found at i:20468361 original size:5 final size:5
Alignment explanation
Indices: 20468351--20468386 Score: 54
Period size: 5 Copynumber: 6.8 Consensus size: 5
20468341 TCAGTCACAT
20468351 AAAAG AAAAG AAGAAG AAAAG AAAAG AAAAAG AAAA
1 AAAAG AAAAG AA-AAG AAAAG AAAAG -AAAAG AAAA
20468387 ATATTTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 19 0.66
6 10 0.34
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:20468369 original size:11 final size:10
Alignment explanation
Indices: 20468351--20468386 Score: 54
Period size: 11 Copynumber: 3.4 Consensus size: 10
20468341 TCAGTCACAT
20468351 AAAAGAAAAG
1 AAAAGAAAAG
20468361 AAGAAGAAAAG
1 AA-AAGAAAAG
20468372 AAAAGAAAAAG
1 AAAAG-AAAAG
20468383 AAAA
1 AAAA
20468387 ATATTTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 5 0.21
11 19 0.79
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAG
Found at i:20468372 original size:16 final size:16
Alignment explanation
Indices: 20468351--20468386 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
20468341 TCAGTCACAT
*
20468351 AAAAGAAAAGAAGAAG
1 AAAAGAAAAGAAAAAG
20468367 AAAAGAAAAGAAAAAG
1 AAAAGAAAAGAAAAAG
20468383 AAAA
1 AAAA
20468387 ATATTTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAGAAAAAG
Found at i:20469038 original size:26 final size:25
Alignment explanation
Indices: 20469003--20469063 Score: 86
Period size: 26 Copynumber: 2.4 Consensus size: 25
20468993 TTGCACACAG
20469003 GAATTTCGCTGCATGAACATGTCCA
1 GAATTTCGCTGCATGAACATGTCCA
*
20469028 GAATTGTCGCTGCATGAACGTGTCCA
1 GAATT-TCGCTGCATGAACATGTCCA
* *
20469054 AAATTACGCT
1 GAATTTCGCT
20469064 CAGAATTGTC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
25 9 0.28
26 23 0.72
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (25 bp):
GAATTTCGCTGCATGAACATGTCCA
Found at i:20482691 original size:49 final size:48
Alignment explanation
Indices: 20482615--20482746 Score: 203
Period size: 49 Copynumber: 2.8 Consensus size: 48
20482605 TATTTATGCT
*
20482615 TCATTAAGTGTTTT-TTTGTTAAATGCATCTTTGTTTAATAATCTGCA
1 TCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTACA
*
20482662 TCATTAAGTGTTTTAGTTTGTTAAATGCATCTTTGTTTAGTAATCTACA
1 TCATTAAGTGTTTT-GTTTGTTAAATGCATCTTTGTTTAATAATCTACA
* * *
20482711 TTATTAATTGTTTTGTTTGTTAAACGCATCTTTGTT
1 TCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTT
20482747 AAATGCCTTG
Statistics
Matches: 78, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
47 14 0.18
48 21 0.27
49 43 0.55
ACGTcount: A:0.24, C:0.10, G:0.14, T:0.52
Consensus pattern (48 bp):
TCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTACA
Found at i:20482761 original size:48 final size:46
Alignment explanation
Indices: 20482617--20482761 Score: 152
Period size: 49 Copynumber: 3.0 Consensus size: 46
20482607 TTTATGCTTC
*
20482617 ATTAAGTGTTTT-TTTGTTAAATGCATCTTTGTTTAATAATC-TGCATC
1 ATTAAGTGTTTTGTTTGTTAAATGCATCTTTG-TT-A-AATCTTGCATT
*
20482664 ATTAAGTGTTTTAGTTTGTTAAATGCATCTTTGTTTAGTAATC-TACATT
1 ATTAAGTGTTTT-GTTTGTTAAATGCATCTTTG-TTA--AATCTTGCATT
* *
20482713 ATTAATTGTTTTGTTTGTTAAACGCATCTTTGTTAAATGCCTTGCATT
1 ATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTAAAT--CTTGCATT
20482761 A
1 A
20482762 ATGCATCATC
Statistics
Matches: 87, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
45 3 0.03
47 16 0.18
48 26 0.30
49 42 0.48
ACGTcount: A:0.26, C:0.10, G:0.14, T:0.50
Consensus pattern (46 bp):
ATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTAAATCTTGCATT
Found at i:20501275 original size:10 final size:10
Alignment explanation
Indices: 20501260--20501284 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
20501250 GACCATCCAA
20501260 GACTTGAAAT
1 GACTTGAAAT
20501270 GACTTGAAAT
1 GACTTGAAAT
20501280 GACTT
1 GACTT
20501285 TTTGTATGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (10 bp):
GACTTGAAAT
Found at i:20513624 original size:26 final size:26
Alignment explanation
Indices: 20513555--20513620 Score: 89
Period size: 26 Copynumber: 2.6 Consensus size: 26
20513545 CAGCTATCAG
*
20513555 ATGCGACGACAATTCTGGACACGTTC
1 ATGCAACGACAATTCTGGACACGTTC
* * *
20513581 ATGCAATGATAATTCTGGACATGTTC
1 ATGCAACGACAATTCTGGACACGTTC
20513607 ATGCAACGA-AATTC
1 ATGCAACGACAATTC
20513621 CTGGGTGGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
25 5 0.14
26 30 0.86
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (26 bp):
ATGCAACGACAATTCTGGACACGTTC
Found at i:20513670 original size:37 final size:37
Alignment explanation
Indices: 20513619--20513703 Score: 116
Period size: 37 Copynumber: 2.3 Consensus size: 37
20513609 GCAACGAAAT
* * * *
20513619 TCCTGGGTGGAATTGAAGAATACTTATGTAGCGATAG
1 TCCTGGATGCAATTGAAGAATACTTATGCAGCGACAG
*
20513656 TCCTGGATGCAATTGAAGAATACTTATGCAGTGACAG
1 TCCTGGATGCAATTGAAGAATACTTATGCAGCGACAG
*
20513693 TCTTGGATGCA
1 TCCTGGATGCA
20513704 TTCTGGAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.29
Consensus pattern (37 bp):
TCCTGGATGCAATTGAAGAATACTTATGCAGCGACAG
Found at i:20513765 original size:36 final size:38
Alignment explanation
Indices: 20513716--20513795 Score: 110
Period size: 37 Copynumber: 2.2 Consensus size: 38
20513706 CTGGAAATAT
* **
20513716 TCATGCGGGGACAG-TTTTGGGTGCAATCT-GGAGTGC
1 TCATGCGGGGACAGTTTTTGGGCGCAATCTAAAAGTGC
*
20513752 TCATGCGGTGACAGTTTTTGGGCGCAATCTAAAAGTGC
1 TCATGCGGGGACAGTTTTTGGGCGCAATCTAAAAGTGC
20513790 TCATGC
1 TCATGC
20513796 TGCGACATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
36 13 0.34
37 14 0.37
38 11 0.29
ACGTcount: A:0.20, C:0.19, G:0.33, T:0.29
Consensus pattern (38 bp):
TCATGCGGGGACAGTTTTTGGGCGCAATCTAAAAGTGC
Found at i:20514178 original size:4 final size:4
Alignment explanation
Indices: 20514161--20514194 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
20514151 TTTACTTAAA
* *
20514161 TTAT TTAT TCAT TTAT TTAT TTAC TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
20514195 TCATGCATCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:20520076 original size:66 final size:66
Alignment explanation
Indices: 20520001--20520135 Score: 148
Period size: 66 Copynumber: 2.0 Consensus size: 66
20519991 GGTCGTGGCA
* * *
20520001 GTTGACCATA-AGGATTAACGCTTGACTGTGC-AGATTGCCCATATGCATTAGAACTTGGCTGCC
1 GTTGACCATACAGG-TTAACACTTGACAGTGCAAG-TTGACCATATGCATTAGAACTTGGCTGCC
20520064 TAG
64 TAG
* * * * * * *
20520067 GTTGGCCATACAGGTTAGCACTTGGCAGTGCAAGTTGACCATATGGATTAGCACTTGGTTGCGTA
1 GTTGACCATACAGGTTAACACTTGACAGTGCAAGTTGACCATATGCATTAGAACTTGGCTGCCTA
20520132 G
66 G
20520133 GTT
1 GTT
20520136 AGTTGTATTG
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
66 52 0.91
67 5 0.09
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (66 bp):
GTTGACCATACAGGTTAACACTTGACAGTGCAAGTTGACCATATGCATTAGAACTTGGCTGCCTA
G
Found at i:20521354 original size:18 final size:17
Alignment explanation
Indices: 20521322--20521355 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
20521312 CACTAGTCGA
*
20521322 AGCAGTTGGGGGGCAGG
1 AGCAGTTGAGGGGCAGG
20521339 AGCAGTTGTAGGGGCAG
1 AGCAGTTG-AGGGGCAG
20521356 CTATAACAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.21, C:0.12, G:0.53, T:0.15
Consensus pattern (17 bp):
AGCAGTTGAGGGGCAGG
Found at i:20526596 original size:18 final size:18
Alignment explanation
Indices: 20526573--20526609 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
20526563 ATTATCAATC
20526573 ATATCAGCAGACTACTCA
1 ATATCAGCAGACTACTCA
*
20526591 ATATCAGTAGACTACTCA
1 ATATCAGCAGACTACTCA
20526609 A
1 A
20526610 CACCAGCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.24, G:0.11, T:0.24
Consensus pattern (18 bp):
ATATCAGCAGACTACTCA
Found at i:20537831 original size:19 final size:20
Alignment explanation
Indices: 20537786--20537829 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
20537776 GAAAAGAATT
20537786 AAAGAATTTGAGAGAAGAAGA
1 AAAG-ATTTGAGAGAAGAAGA
20537807 AGAAGATTTGTAGAGAA-AAGA
1 A-AAGATTTG-AGAGAAGAAGA
20537828 AA
1 AA
20537830 GACTCAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
20 1 0.05
21 11 0.52
22 9 0.43
ACGTcount: A:0.57, C:0.00, G:0.27, T:0.16
Consensus pattern (20 bp):
AAAGATTTGAGAGAAGAAGA
Found at i:20537831 original size:22 final size:21
Alignment explanation
Indices: 20537765--20537831 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 21
20537755 ATGAGGATTG
20537765 AGATTTGAGAAGAAAAGAATTA-A
1 AGATTTGAG-AGAAAAGAA--AGA
20537788 AGAATTTGAGAGAAGAAG-AAGA
1 AG-ATTTGAGAGAA-AAGAAAGA
20537810 AGATTTGTAGAGAAAAGAAAGA
1 AGATTTG-AGAGAAAAGAAAGA
20537832 CTCAAATTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
21 9 0.23
22 13 0.33
23 7 0.18
24 10 0.26
ACGTcount: A:0.55, C:0.00, G:0.27, T:0.18
Consensus pattern (21 bp):
AGATTTGAGAGAAAAGAAAGA
Found at i:20538510 original size:24 final size:23
Alignment explanation
Indices: 20538483--20538541 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 23
20538473 TTTCTAGAAG
*
20538483 ATTTAGTATTTATTAGCATAATAT
1 ATTTA-TATTTATTAGCATAAAAT
*
20538507 ATTTTATATTTATTAGTATAAAAT
1 A-TTTATATTTATTAGCATAAAAT
*
20538531 CTTTACTATTT
1 ATTTA-TATTT
20538542 CTTTTTATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 4 0.13
24 22 0.73
25 4 0.13
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (23 bp):
ATTTATATTTATTAGCATAAAAT
Found at i:20544341 original size:15 final size:15
Alignment explanation
Indices: 20544321--20544354 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
20544311 TTTAATTTTC
*
20544321 TTTTATTGCATGTGA
1 TTTTATTGCAGGTGA
*
20544336 TTTTATTTCAGGTGA
1 TTTTATTGCAGGTGA
20544351 TTTT
1 TTTT
20544355 TTTCTTTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.06, G:0.18, T:0.59
Consensus pattern (15 bp):
TTTTATTGCAGGTGA
Found at i:20549520 original size:2 final size:2
Alignment explanation
Indices: 20549513--20549542 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
20549503 TTATGGAGAA
20549513 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
20549543 GATTATGGAA
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:20550252 original size:80 final size:80
Alignment explanation
Indices: 20550095--20550253 Score: 221
Period size: 80 Copynumber: 2.0 Consensus size: 80
20550085 AAAAACGTTA
* * *
20550095 GTTAATCCAACTAGAGGTGGACTCACTTATTGCGGTTTATCCACTAGGCACTAGGTGCCAGGAAT
1 GTTAATCCAACTAGAGCTGGACTCACTTATCGCGGTTTATCCACTAGGCACCAGGTGCCAGGAAT
*
20550160 TGATGGACTTTGTTG
66 TGAAGGACTTTGTTG
* * * * *
20550175 GTTAATCCAACTAGATCTGGGCTCACTTATCGCGGTTTATCCGCTAGGCACCAGGTGCCATGATT
1 GTTAATCCAACTAGAGCTGGACTCACTTATCGCGGTTTATCCACTAGGCACCAGGTGCCAGGAAT
20550240 TGACAGGA-TTTGTT
66 TGA-AGGACTTTGTT
20550254 AATGACAAAG
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
80 66 0.96
81 3 0.04
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.31
Consensus pattern (80 bp):
GTTAATCCAACTAGAGCTGGACTCACTTATCGCGGTTTATCCACTAGGCACCAGGTGCCAGGAAT
TGAAGGACTTTGTTG
Found at i:20556919 original size:80 final size:80
Alignment explanation
Indices: 20556764--20556984 Score: 302
Period size: 80 Copynumber: 2.8 Consensus size: 80
20556754 TGCAAAACCA
* * ** *
20556764 TTGGTTATTCCAACTAAAGCTGGGCTCACTTATTGC-CATTATCTGATAGGCACTAGGTGCCAAG
1 TTGGTTAATCCAACTAGAGCTGGGCTCACTTATTGCGGTTTATCTGCTAGGCACTAGGTGCCAAG
20556828 AATTGACGGACTTTG
66 AATTGACGGACTTTG
* * * *
20556843 TTGGTTAATCCAACCAGAGCTGGGCTCACTTATTGCGGTTTATCTGCTAGGCACTGGGTGCTAGG
1 TTGGTTAATCCAACTAGAGCTGGGCTCACTTATTGCGGTTTATCTGCTAGGCACTAGGTGCCAAG
*
20556908 AATTGATGGACTTTG
66 AATTGACGGACTTTG
* * * *
20556923 TTGGTTAATCCAACTAGAGCTGGGCTTACTT-CTGCGGTTTATCTACTTGGCACTAGGTGCCA
1 TTGGTTAATCCAACTAGAGCTGGGCTCACTTATTGCGGTTTATCTGCTAGGCACTAGGTGCCA
20556985 TGATCATCGG
Statistics
Matches: 124, Mismatches: 17, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
79 59 0.48
80 65 0.52
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (80 bp):
TTGGTTAATCCAACTAGAGCTGGGCTCACTTATTGCGGTTTATCTGCTAGGCACTAGGTGCCAAG
AATTGACGGACTTTG
Found at i:20557051 original size:261 final size:262
Alignment explanation
Indices: 20556582--20557137 Score: 830
Period size: 261 Copynumber: 2.1 Consensus size: 262
20556572 GTGCAAAATC
* *
20556582 GTTGGTTAATCCAACTAGAGCTGGACTCACTT-TTGCAGTTTATCCGCTAAAAATTGGGTGCCAA
1 GTTGGTTAATCCAACTAGAGCTGGGCTCACTTATTGCAGTTTATCCGCTAAAAACTGGGTGCCAA
*
20556646 GAATTGACGGACTTTGTTGGTTAATCCAACTAGAACTGGGCTTACTTCTGCGGTTTATCCGCTAG
66 GAATTGACGGACTTTGTTGGTTAATCCAACTAGAACTGGGCTTACTTCTGCGGTTTATCCACTAG
* * *
20556711 GCACTAGGTGCCATGATCGTCGGTTTATCCAACTAGAGCTGGGTGCAAAACCATTGGTTATTCCA
131 GCACTAGGTGCCATGATCATCGGTTTATCCAACTAGAGCTGGGTGCAAAACCATTAGTTAATCCA
* *
20556776 ACTAAAGCTGGGCTCACTTATTGC-CATTATCTGATAGGCACTAGGTGCCAAGAATTGACGGACT
196 ACTAAAGCTGGGCTCACTTATTACGCATTATCTGATAGGCACTAGGTGCCAAGAATTGACGAACT
20556840 TT
261 TT
* * * *** * *
20556842 GTTGGTTAATCCAACCAGAGCTGGGCTCACTTATTGCGGTTTATCTGCTAGGCACTGGGTGCTAG
1 GTTGGTTAATCCAACTAGAGCTGGGCTCACTTATTGCAGTTTATCCGCTAAAAACTGGGTGCCAA
* * * *
20556907 GAATTGATGGACTTTGTTGGTTAATCCAACTAGAGCTGGGCTTACTTCTGCGGTTTATCTACTTG
66 GAATTGACGGACTTTGTTGGTTAATCCAACTAGAACTGGGCTTACTTCTGCGGTTTATCCACTAG
20556972 GCACTAGGTGCCATGATCATCGGTTTATCCAACTAGCA-CTGGGTGCAAAACCATTAGTTAATCC
131 GCACTAGGTGCCATGATCATCGGTTTATCCAACTAG-AGCTGGGTGCAAAACCATTAGTTAATCC
* * * ** * * *
20557036 AATTAGAGTTGGGCTCACTTATTACGGTTTATCTGCTAGGCACTAGGTGCCAGGAATTGATGAAC
195 AACTAAAGCTGGGCTCACTTATTACGCATTATCTGATAGGCACTAGGTGCCAAGAATTGACGAAC
20557101 TTT
260 TTT
20557104 GTTGGTTAATCCAACTAGAGCTGGGCTCACTTAT
1 GTTGGTTAATCCAACTAGAGCTGGGCTCACTTAT
20557138 CACGATTTAT
Statistics
Matches: 264, Mismatches: 29, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
260 30 0.11
261 164 0.62
262 70 0.27
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (262 bp):
GTTGGTTAATCCAACTAGAGCTGGGCTCACTTATTGCAGTTTATCCGCTAAAAACTGGGTGCCAA
GAATTGACGGACTTTGTTGGTTAATCCAACTAGAACTGGGCTTACTTCTGCGGTTTATCCACTAG
GCACTAGGTGCCATGATCATCGGTTTATCCAACTAGAGCTGGGTGCAAAACCATTAGTTAATCCA
ACTAAAGCTGGGCTCACTTATTACGCATTATCTGATAGGCACTAGGTGCCAAGAATTGACGAACT
TT
Found at i:20563604 original size:37 final size:37
Alignment explanation
Indices: 20563548--20563803 Score: 305
Period size: 37 Copynumber: 6.9 Consensus size: 37
20563538 ATTTAAACAA
* *
20563548 TCAGCCTTTGTGCCTAGTAGGCTTCGTGTTGGTGTTT
1 TCAGGCTTTGTGCCTAGTAGGCTTCGTGCTGGTGTTT
* *
20563585 TCAGGTTTTGTGCCTAGTAGGCTTCGTGCCGGTGTTT
1 TCAGGCTTTGTGCCTAGTAGGCTTCGTGCTGGTGTTT
* * *
20563622 TCAGGCTTTGTGCCTAGTGGGCTTCGTGCCGATGTTT
1 TCAGGCTTTGTGCCTAGTAGGCTTCGTGCTGGTGTTT
* * * *
20563659 TCAGGCTTTATGCTTATTAGGCTTCGTGCTGATGTTT
1 TCAGGCTTTGTGCCTAGTAGGCTTCGTGCTGGTGTTT
* *
20563696 TCAGGTTTTGTGCCTAGTAGGCTTCGTGCTGGTATTT
1 TCAGGCTTTGTGCCTAGTAGGCTTCGTGCTGGTGTTT
* * ** *
20563733 TCAAGCTTTATGCCTAGTAGGCTTCGTGCCAGTGTAT
1 TCAGGCTTTGTGCCTAGTAGGCTTCGTGCTGGTGTTT
* * * * *
20563770 TCGGGCTATGTGCCTTGTAGGCTTTGTGCCGGTG
1 TCAGGCTTTGTGCCTAGTAGGCTTCGTGCTGGTG
20563804 ATCCAAGAAC
Statistics
Matches: 187, Mismatches: 32, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 187 1.00
ACGTcount: A:0.11, C:0.19, G:0.30, T:0.40
Consensus pattern (37 bp):
TCAGGCTTTGTGCCTAGTAGGCTTCGTGCTGGTGTTT
Found at i:20564507 original size:21 final size:21
Alignment explanation
Indices: 20564483--20564531 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
20564473 TTAGTACCGA
*
20564483 TAGAACTAATTTAGGTATCGG
1 TAGAACTAATCTAGGTATCGG
* **
20564504 TAGAAGTTGTCTAGGTATCGG
1 TAGAACTAATCTAGGTATCGG
20564525 TAGAACT
1 TAGAACT
20564532 TTTATAGTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.31, C:0.10, G:0.27, T:0.33
Consensus pattern (21 bp):
TAGAACTAATCTAGGTATCGG
Found at i:20565150 original size:24 final size:24
Alignment explanation
Indices: 20565118--20565166 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
20565108 TGCATACTTC
20565118 AAGGTAAAAGCATCAAACCAACCT
1 AAGGTAAAAGCATCAAACCAACCT
20565142 AAGGTAAAAGCATCAAACCAACCT
1 AAGGTAAAAGCATCAAACCAACCT
20565166 A
1 A
20565167 CTTTTTCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.51, C:0.24, G:0.12, T:0.12
Consensus pattern (24 bp):
AAGGTAAAAGCATCAAACCAACCT
Found at i:20570833 original size:37 final size:37
Alignment explanation
Indices: 20570783--20570984 Score: 316
Period size: 37 Copynumber: 5.5 Consensus size: 37
20570773 ATTTAAACAA
20570783 TCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTGTTT
1 TCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTGTTT
*
20570820 TCAGGCTTTGTGCCTAGTAGGCTTCATGCCGGTGTTT
1 TCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTGTTT
* * * *
20570857 TCAGGATTTGTGCCTAGTGGGCTTCGTGTCGGTGATT
1 TCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTGTTT
* *
20570894 TCAGGCTTTATGCCTATTAGGCTTCGTGCCGGTGTTT
1 TCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTGTTT
* *
20570931 TCAGGTTTTGTGCCTAGTAGGCTTCGTGTCGGTGTTT
1 TCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTGTTT
20570968 TCAGGCTTTGTG-CTAGT
1 TCAGGCTTTGTGCCTAGT
20570985 GTTTTCAAGC
Statistics
Matches: 148, Mismatches: 17, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
36 5 0.03
37 143 0.97
ACGTcount: A:0.10, C:0.19, G:0.31, T:0.40
Consensus pattern (37 bp):
TCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTGTTT
Found at i:20570986 original size:21 final size:22
Alignment explanation
Indices: 20570962--20571006 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
20570952 CTTCGTGTCG
*
20570962 GTGTTTTCAGGCTTTGTG-CTA
1 GTGTTTTCAAGCTTTGTGCCTA
20570983 GTGTTTTCAAGCTTTGTGCCTA
1 GTGTTTTCAAGCTTTGTGCCTA
20571005 GT
1 GT
20571007 AAGCTTCGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.11, C:0.16, G:0.27, T:0.47
Consensus pattern (22 bp):
GTGTTTTCAAGCTTTGTGCCTA
Found at i:20571793 original size:21 final size:21
Alignment explanation
Indices: 20571769--20571819 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
20571759 TTTTAGTACT
*
20571769 GGTAGAACTAATTTAGGTATC
1 GGTAGAACTAATCTAGGTATC
* **
20571790 GGTAGAAGTTGTCTAGGTATC
1 GGTAGAACTAATCTAGGTATC
20571811 GGTAGAACT
1 GGTAGAACT
20571820 TTTATAGTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.29, C:0.10, G:0.29, T:0.31
Consensus pattern (21 bp):
GGTAGAACTAATCTAGGTATC
Found at i:20577805 original size:11 final size:11
Alignment explanation
Indices: 20577789--20577813 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20577779 TATTTTCAAA
20577789 AAATCTTTTAT
1 AAATCTTTTAT
20577800 AAATCTTTTAT
1 AAATCTTTTAT
20577811 AAA
1 AAA
20577814 AACCAACATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (11 bp):
AAATCTTTTAT
Found at i:20582075 original size:86 final size:86
Alignment explanation
Indices: 20581956--20582153 Score: 233
Period size: 86 Copynumber: 2.3 Consensus size: 86
20581946 TATTCTTTAT
* * * * * *
20581956 CGAGGCATAAGTCTTCCTTTCAAACATAATCTCACGCTCATTCTGAGACATGATTCTTCCTTTAA
1 CGAGACATGAGTCTTCCTTTTAAACATAATCTCACGCTCATTCCGAGACACGAGTCTTCCTTTAA
**
20582021 A-TATAGTCTCATTCTCA-ACC
66 ACT-TAGTCTCAAGCTCATACC
* * *
20582041 CGAGACATGAGTCTTCCTTTTTAAACATATTCTCATGCTCATTCCGAGTCACGAGTCTTCCTTTA
1 CGAGACATGAGTCTTCC-TTTTAAACATAATCTCACGCTCATTCCGAGACACGAGTCTTCCTTTA
* *
20582106 AACTTATTCTCAAGCTCATTCC
65 AACTTAGTCTCAAGCTCATACC
20582128 C-AGACATGAGTCTTCC-TTTAAACATA
1 CGAGACATGAGTCTTCCTTTTAAACATA
20582154 CGAACTTACC
Statistics
Matches: 97, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
84 10 0.10
85 15 0.15
86 68 0.70
87 4 0.04
ACGTcount: A:0.27, C:0.27, G:0.11, T:0.35
Consensus pattern (86 bp):
CGAGACATGAGTCTTCCTTTTAAACATAATCTCACGCTCATTCCGAGACACGAGTCTTCCTTTAA
ACTTAGTCTCAAGCTCATACC
Found at i:20582150 original size:42 final size:42
Alignment explanation
Indices: 20581965--20582153 Score: 209
Period size: 42 Copynumber: 4.4 Consensus size: 42
20581955 TCGAGGCATA
* * **
20581965 AGTCTTCCTTTCAAACATAATCTCACGCTCATTCTGAGACATG
1 AGTCTTCCTTT-AAACATATTCTCATGCTCATTCCCAGACATG
* * * * *
20582008 ATTCTTCCTTTAAATATAGTCTCATTCTCA-ACCCGAGACATG
1 AGTCTTCCTTTAAACATATTCTCATGCTCATTCCC-AGACATG
* * *
20582050 AGTCTTCCTTTTTAAACATATTCTCATGCTCATTCCGAGTCACG
1 AGTCTTCC--TTTAAACATATTCTCATGCTCATTCCCAGACATG
* *
20582094 AGTCTTCCTTTAAACTTATTCTCAAGCTCATTCCCAGACATG
1 AGTCTTCCTTTAAACATATTCTCATGCTCATTCCCAGACATG
20582136 AGTCTTCCTTTAAACATA
1 AGTCTTCCTTTAAACATA
20582154 CGAACTTACC
Statistics
Matches: 120, Mismatches: 22, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
41 1 0.01
42 75 0.62
43 10 0.08
44 32 0.27
45 2 0.02
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.36
Consensus pattern (42 bp):
AGTCTTCCTTTAAACATATTCTCATGCTCATTCCCAGACATG
Found at i:20597131 original size:16 final size:16
Alignment explanation
Indices: 20597110--20597156 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
20597100 ATTAAACCAA
20597110 GTACTGAAAATAAAAG
1 GTACTGAAAATAAAAG
20597126 GTACTGAAAATAAAAG
1 GTACTGAAAATAAAAG
*
20597142 ATACTGAAAAGTAAA
1 GTACTGAAAA-TAAA
20597157 TAATAAAGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 25 0.86
17 4 0.14
ACGTcount: A:0.57, C:0.06, G:0.17, T:0.19
Consensus pattern (16 bp):
GTACTGAAAATAAAAG
Found at i:20598889 original size:11 final size:11
Alignment explanation
Indices: 20598873--20598898 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
20598863 TATGAATGCT
20598873 AGGAGTGGGAA
1 AGGAGTGGGAA
20598884 AGGAGTGGGAA
1 AGGAGTGGGAA
20598895 AGGA
1 AGGA
20598899 AAAGAGAATG
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:0.38, C:0.00, G:0.54, T:0.08
Consensus pattern (11 bp):
AGGAGTGGGAA
Found at i:20604776 original size:12 final size:12
Alignment explanation
Indices: 20604755--20604784 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
20604745 TGTAAATGGA
*
20604755 GAGAACATAGGT
1 GAGAAAATAGGT
20604767 GAGAAAATAGGT
1 GAGAAAATAGGT
20604779 GAGAAA
1 GAGAAA
20604785 TGAAGTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.33, T:0.13
Consensus pattern (12 bp):
GAGAAAATAGGT
Found at i:20608861 original size:118 final size:118
Alignment explanation
Indices: 20608653--20608889 Score: 438
Period size: 118 Copynumber: 2.0 Consensus size: 118
20608643 AGGAAAATAA
20608653 TACAAAGTATTAAAGTAATTCATGAATAATTTTATTAACAAATCTATTTGAAAAATTACAGTGTT
1 TACAAAGTATTAAAGTAATTCATGAATAATTTTATTAACAAATCTATTTGAAAAATTACAGTGTT
*
20608718 CTTAAACAAAAATACTACACTTAGGGCACCAGATCCAACATTATTAACTAAGG
66 CTTAAACAAAAATACTACACTTAGGGCACCAGATCCAACAGTATTAACTAAGG
* *
20608771 TACAAAGTATTAAAGTAATTCATGAATAATTTTATTAACAAATCTATTTGAAAATTTATAGTGTT
1 TACAAAGTATTAAAGTAATTCATGAATAATTTTATTAACAAATCTATTTGAAAAATTACAGTGTT
*
20608836 CTTAAACGAAAATACTACACTTAGGGCACCAGATCCAACAGTATTAACTAAGG
66 CTTAAACAAAAATACTACACTTAGGGCACCAGATCCAACAGTATTAACTAAGG
20608889 T
1 T
20608890 GTGTGACCCA
Statistics
Matches: 115, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
118 115 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (118 bp):
TACAAAGTATTAAAGTAATTCATGAATAATTTTATTAACAAATCTATTTGAAAAATTACAGTGTT
CTTAAACAAAAATACTACACTTAGGGCACCAGATCCAACAGTATTAACTAAGG
Found at i:20609012 original size:22 final size:22
Alignment explanation
Indices: 20608987--20609030 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
20608977 TCCTATCTCT
20608987 CCCTCCAAATCGATGGCACCGA
1 CCCTCCAAATCGATGGCACCGA
*
20609009 CCCTCCAAATTGATGGCACCGA
1 CCCTCCAAATCGATGGCACCGA
20609031 TTGATCTAAA
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:0.27, C:0.39, G:0.18, T:0.16
Consensus pattern (22 bp):
CCCTCCAAATCGATGGCACCGA
Found at i:20610542 original size:27 final size:26
Alignment explanation
Indices: 20610512--20610587 Score: 89
Period size: 28 Copynumber: 2.8 Consensus size: 26
20610502 TTAGAATGCG
*
20610512 CCACGAAGGCATTCTTTTCATAGATCA
1 CCACAAAGGC-TTCTTTTCATAGATCA
* *
20610539 CCACAAAGGCTTTCTTTACCAGAGATCA
1 CCACAAAGGC-TTCTTT-TCATAGATCA
20610567 CCACAAAGGCTTCCTTTTCAT
1 CCACAAAGGCTT-CTTTTCAT
20610588 TCAAAGCTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
27 19 0.46
28 22 0.54
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.29
Consensus pattern (26 bp):
CCACAAAGGCTTCTTTTCATAGATCA
Found at i:20611981 original size:17 final size:16
Alignment explanation
Indices: 20611959--20611995 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
20611949 TGTGAAAGCA
20611959 TAAAAATAAAAAAAAGG
1 TAAAAATAAAAAAAA-G
*
20611976 TAAAAATAAAATAAAG
1 TAAAAATAAAAAAAAG
20611992 TAAA
1 TAAA
20611996 TAAGAGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (16 bp):
TAAAAATAAAAAAAAG
Found at i:20613450 original size:10 final size:10
Alignment explanation
Indices: 20613435--20613464 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
20613425 CATAGAGTTG
*
20613435 GTTAAGTACA
1 GTTAAGCACA
20613445 GTTAAGCACA
1 GTTAAGCACA
20613455 GTTAAGCACA
1 GTTAAGCACA
20613465 CAAAAATGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (10 bp):
GTTAAGCACA
Found at i:20613726 original size:23 final size:22
Alignment explanation
Indices: 20613688--20613747 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 22
20613678 CACACTTTTC
20613688 TTACTC-TTTTCTTTTTGTAT-TT
1 TTACTCATTTT-TTTTTGT-TCTT
20613710 TTACTCATTTTTGTTTTGTTCTT
1 TTACTCATTTTT-TTTTGTTCTT
*
20613733 TTCACTTATTTTTTT
1 TT-ACTCATTTTTTT
20613748 CCTTTCTTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
22 8 0.24
23 16 0.48
24 9 0.27
ACGTcount: A:0.10, C:0.13, G:0.05, T:0.72
Consensus pattern (22 bp):
TTACTCATTTTTTTTTGTTCTT
Found at i:20616398 original size:13 final size:13
Alignment explanation
Indices: 20616380--20616404 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20616370 TATGTTAGTG
20616380 ATTAAAAATTAAA
1 ATTAAAAATTAAA
20616393 ATTAAAAATTAA
1 ATTAAAAATTAA
20616405 GGGTTAGTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAAAAATTAAA
Found at i:20617850 original size:17 final size:17
Alignment explanation
Indices: 20617830--20617871 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
20617820 AAGTTGTGTG
20617830 AAAGCATAAAAATAAAA-
1 AAAG-ATAAAAATAAAAT
*
20617847 AAAGGTAAAAATAAAAT
1 AAAGATAAAAATAAAAT
20617864 AAAG-TAAA
1 AAAGATAAA
20617872 TAAGACAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.74, C:0.02, G:0.10, T:0.14
Consensus pattern (17 bp):
AAAGATAAAAATAAAAT
Found at i:20617857 original size:16 final size:16
Alignment explanation
Indices: 20617836--20617871 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
20617826 TGTGAAAGCA
20617836 TAAAAATAAAA-AAAGG
1 TAAAAATAAAATAAA-G
20617852 TAAAAATAAAATAAAG
1 TAAAAATAAAATAAAG
20617868 TAAA
1 TAAA
20617872 TAAGACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.84
17 3 0.16
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (16 bp):
TAAAAATAAAATAAAG
Found at i:20625884 original size:50 final size:50
Alignment explanation
Indices: 20625825--20626018 Score: 212
Period size: 50 Copynumber: 3.9 Consensus size: 50
20625815 ACATATAACG
* * * *
20625825 TGTGCAAGCTGGAGAGCTTAAATGCATAAATAAGTTCACAAGTGTAAACA
1 TGTGCAAGCTGGCGAGCTTAAACGCATAAATAAGTTGACAAGCGTAAACA
* * * * *
20625875 TGTGCAAGCTGGCGAGCATAAACACATAAATAAGCTGACGAGCGTAAACG
1 TGTGCAAGCTGGCGAGCTTAAACGCATAAATAAGTTGACAAGCGTAAACA
* *
20625925 TGTGTAAGCTGGTGAG-TGTAAACGCATAAATAAGTTGACAAGCGTAAA-A
1 TGTGCAAGCTGGCGAGCT-TAAACGCATAAATAAGTTGACAAGCGTAAACA
* * * * *
20625974 TTGTGCAAGTTGGCTAGCGTAAACGCATAAATAAGCTGACGAGCG
1 -TGTGCAAGCTGGCGAGCTTAAACGCATAAATAAGTTGACAAGCG
20626019 CGAATGTGTA
Statistics
Matches: 118, Mismatches: 23, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
50 118 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (50 bp):
TGTGCAAGCTGGCGAGCTTAAACGCATAAATAAGTTGACAAGCGTAAACA
Found at i:20625997 original size:100 final size:100
Alignment explanation
Indices: 20625821--20626018 Score: 283
Period size: 100 Copynumber: 2.0 Consensus size: 100
20625811 ATGTACATAT
* *
20625821 AACGTGTGCAAGCTGGAGAGCTTAAATGCATAAATAAGTTCACAAGTGTAAACATGTGCAAGCTG
1 AACGTGTGCAAGCTGGAGAGCTTAAACGCATAAATAAGTTCACAAGCGTAAACATGTGCAAGCTG
20625886 GCGAGCATAAACACATAAATAAGCTGACGAGCGTA
66 GCGAGCATAAACACATAAATAAGCTGACGAGCGTA
* * * *
20625921 AACGTGTGTAAGCTGGTGAG-TGTAAACGCATAAATAAGTTGACAAGCGTAAA-ATTGTGCAAGT
1 AACGTGTGCAAGCTGGAGAGCT-TAAACGCATAAATAAGTTCACAAGCGTAAACA-TGTGCAAGC
* * *
20625984 TGGCTAGCGTAAACGCATAAATAAGCTGACGAGCG
64 TGGCGAGCATAAACACATAAATAAGCTGACGAGCG
20626019 CGAATGTGTA
Statistics
Matches: 87, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
99 2 0.02
100 85 0.98
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (100 bp):
AACGTGTGCAAGCTGGAGAGCTTAAACGCATAAATAAGTTCACAAGCGTAAACATGTGCAAGCTG
GCGAGCATAAACACATAAATAAGCTGACGAGCGTA
Found at i:20626034 original size:50 final size:50
Alignment explanation
Indices: 20625875--20626037 Score: 159
Period size: 50 Copynumber: 3.3 Consensus size: 50
20625865 AGTGTAAACA
* * * * * * *
20625875 TGTGCAAGCTGGCGAGCATAAACACATAAATAAGCTGACGAGCGTAAACG
1 TGTGTAAGTTGGCTAGCGTAAACGCATAAATAAGCTGACGAGCGAAAATG
* * * *
20625925 TGTGTAAGCTGG-TGAGTGTAAACGCATAAATAAGTTGACAAGCGTAAAAT-
1 TGTGTAAGTTGGCT-AGCGTAAACGCATAAATAAGCTGACGAGCG-AAAATG
* **
20625975 TGTGCAAGTTGGCTAGCGTAAACGCATAAATAAGCTGACGAGCGCGAATG
1 TGTGTAAGTTGGCTAGCGTAAACGCATAAATAAGCTGACGAGCGAAAATG
*
20626025 TGTATAAGTTGGC
1 TGTGTAAGTTGGC
20626038 AATTATAAAT
Statistics
Matches: 91, Mismatches: 18, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
49 3 0.03
50 84 0.92
51 4 0.04
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.22
Consensus pattern (50 bp):
TGTGTAAGTTGGCTAGCGTAAACGCATAAATAAGCTGACGAGCGAAAATG
Found at i:20639269 original size:41 final size:42
Alignment explanation
Indices: 20639214--20639392 Score: 157
Period size: 41 Copynumber: 4.3 Consensus size: 42
20639204 ACTTGATGTA
* * *
20639214 TAAATGGAAAACTCATGTCTTGGGATGAGCGTGAGAGTATA-T
1 TAAA-GGAAGACTCATGTCTCGGGATGAGCATGAGAGTATACT
20639256 TAAAGGAAGACTCATGTCTCGGGATGAGCATGAGAGTATACT
1 TAAAGGAAGACTCATGTCTCGGGATGAGCATGAGAGTATACT
* * ** * **
20639298 T-AAGGAAGACTTATGACTCGAAAGGAGCATGAG-GTTATGTT
1 TAAAGGAAGACTCATGTCTCGGGATGAGCATGAGAG-TATACT
* * * * * * **
20639339 TTAAGGAAGACTCGTGACTCGAGATGAGCATAAGATTATGTT
1 TAAAGGAAGACTCATGTCTCGGGATGAGCATGAGAGTATACT
20639381 TAAAGGAAGACT
1 TAAAGGAAGACT
20639393 TAAGACTCGG
Statistics
Matches: 116, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
40 1 0.01
41 65 0.56
42 50 0.43
ACGTcount: A:0.35, C:0.11, G:0.28, T:0.26
Consensus pattern (42 bp):
TAAAGGAAGACTCATGTCTCGGGATGAGCATGAGAGTATACT
Found at i:20639349 original size:42 final size:42
Alignment explanation
Indices: 20639297--20639401 Score: 138
Period size: 42 Copynumber: 2.5 Consensus size: 42
20639287 GAGAGTATAC
* *
20639297 TTAAGGAAGACTTATGACTCGAAAGGAGCATGAGGTTATGTT
1 TTAAGGAAGACTTATGACTCGAAAGGAGCATAAGATTATGTT
** * *
20639339 TTAAGGAAGACTCGTGACTCGAGATGAGCATAAGATTATGTT
1 TTAAGGAAGACTTATGACTCGAAAGGAGCATAAGATTATGTT
* *
20639381 TAAAGGAAGACTTAAGACTCG
1 TTAAGGAAGACTTATGACTCG
20639402 GTTATTACAT
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.35, C:0.11, G:0.27, T:0.27
Consensus pattern (42 bp):
TTAAGGAAGACTTATGACTCGAAAGGAGCATAAGATTATGTT
Found at i:20641159 original size:23 final size:23
Alignment explanation
Indices: 20641124--20641312 Score: 261
Period size: 23 Copynumber: 8.2 Consensus size: 23
20641114 ATCTTAATTC
20641124 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
20641147 TTTAATCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
20641170 TTTAAGCACAAATCACATTAAAA
1 TTTAAGCACAAATCACATTAATA
*
20641193 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
20641216 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
20641239 TTTAAGCATAAATCACATTAATG
1 TTTAAGCACAAATCACATTAATA
*
20641262 CTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
20641285 TTTAATCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
20641308 TTTAA
1 TTTAA
20641313 ACACGAATAT
Statistics
Matches: 143, Mismatches: 23, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 143 1.00
ACGTcount: A:0.47, C:0.14, G:0.04, T:0.35
Consensus pattern (23 bp):
TTTAAGCACAAATCACATTAATA
Found at i:20641179 original size:46 final size:46
Alignment explanation
Indices: 20641124--20641312 Score: 297
Period size: 46 Copynumber: 4.1 Consensus size: 46
20641114 ATCTTAATTC
* *
20641124 TTTAAGCACAAATCACATTAATATTTAATCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATATTTAAGCATAAATCACATTAATA
*
20641170 TTTAAGCACAAATCACATTAAAATTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATATTTAAGCATAAATCACATTAATA
* * *
20641216 TTTGAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATG
1 TTTAAGCACAAATCACATTAATATTTAAGCATAAATCACATTAATA
* * *
20641262 CTTAAGCACAAATCACATTAATATTTAATCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATATTTAAGCATAAATCACATTAATA
20641308 TTTAA
1 TTTAA
20641313 ACACGAATAT
Statistics
Matches: 129, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 129 1.00
ACGTcount: A:0.47, C:0.14, G:0.04, T:0.35
Consensus pattern (46 bp):
TTTAAGCACAAATCACATTAATATTTAAGCATAAATCACATTAATA
Found at i:20641235 original size:69 final size:69
Alignment explanation
Indices: 20641124--20641312 Score: 306
Period size: 69 Copynumber: 2.7 Consensus size: 69
20641114 ATCTTAATTC
20641124 TTTAAGCACAAATCACATTAATATTTAATCATAAATCATATTAATATTTAAGCACAAATCACATT
1 TTTAAGCACAAATCACATTAATATTTAATCATAAATCATATTAATATTTAAGCACAAATCACATT
20641189 AAAA
66 AAAA
* * * * *
20641193 TTTAAGCATAAATCACATTAATATTTGAGCACAAATCATATTAATATTTAAGCATAAATCACATT
1 TTTAAGCACAAATCACATTAATATTTAATCATAAATCATATTAATATTTAAGCACAAATCACATT
**
20641258 AATG
66 AAAA
*
20641262 CTTAAGCACAAATCACATTAATATTTAATCATAAATCATATTAATATTTAA
1 TTTAAGCACAAATCACATTAATATTTAATCATAAATCATATTAATATTTAA
20641313 ACACGAATAT
Statistics
Matches: 108, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 108 1.00
ACGTcount: A:0.47, C:0.14, G:0.04, T:0.35
Consensus pattern (69 bp):
TTTAAGCACAAATCACATTAATATTTAATCATAAATCATATTAATATTTAAGCACAAATCACATT
AAAA
Found at i:20646826 original size:26 final size:25
Alignment explanation
Indices: 20646763--20646826 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 25
20646753 AGGTGAAGAT
* *
20646763 ATCAATAACAAAATTTTAAGTATAAA
1 ATCAA-AACTAAATTTTAAATATAAA
*
20646789 ATTAAAACTAAATTTTAAATAATAATA
1 ATCAAAACTAAATTTTAAAT-ATAA-A
20646816 ATCAAAA-TAAA
1 ATCAAAACTAAA
20646827 ATCTTTAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 13 0.41
26 12 0.38
27 7 0.22
ACGTcount: A:0.61, C:0.06, G:0.02, T:0.31
Consensus pattern (25 bp):
ATCAAAACTAAATTTTAAATATAAA
Found at i:20655220 original size:195 final size:194
Alignment explanation
Indices: 20654827--20655274 Score: 539
Period size: 195 Copynumber: 2.3 Consensus size: 194
20654817 TACCAGTACT
* * * *
20654827 CGATGCTGTTCACACGAGCTATCGAGGACTCGCAACGTATGCGGTACCCCAACCATCGGTACAGT
1 CGATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTACCCCAACCATCGATACAGT
* * * *
20654892 GCCTGTCTGTACTATAAACTGTTCCCTAACGATGCTGCTCACACGAGTTGTCGAGAGTATGCATA
66 G-CTATCTGTACTATAAACTGTTCCCTAACGATGCTGCTCACACGAGCTATCGAGAATATGCATA
* * *
20654957 AAGCATAGTCCCAGCCATCGTAGGGCTTATAATCCATTTAGGATCCATATCTCTTTTCCAGGTCA
130 AAGCATAATCCCAGCCATCGTAGGGCCTATAATCCATTTAGGATCCATATCTCTTTTCCAGCTCA
* * *
20655022 CGATGCTGCTCAC-CTGAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAGCCATTGATAC-G
1 CGATGCTGCTCACAC-GAGCTGTCGAGGACTCGCAACATATGCGGTACCCCAACCATCGATACAG
* *
20655085 -G-TATCTGTGC-ATATAACTGTTCCCTAACGATGTTGCTCACACGAGCTATCGAGAATATGCAC
65 TGCTATCTGTACTATA-AACTGTTCCCTAACGATGCTGCTCACACGAGCTATCGAGAATATGCA-
* * * * * * * * *
20655147 TTATGCATAAATCTCAGCCATCGTAGGGCCTGTAATCCATTCTTGGATTCTTTTCTCATTTCTC-
128 TAAAGCAT-AATCCCAGCCATCGTAGGGCCTATAATCCATT-TAGGATCCATATCTCTTTTC-CA
20655211 GACTCA
190 G-CTCA
* *
20655217 CGATGCTGCTCACACGAGCTGTCGAGGACTCGTAACATATGCGGTACCCTAACCATCG
1 CGATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTACCCCAACCATCG
20655275 TGTCAGTTTC
Statistics
Matches: 215, Mismatches: 30, Indels: 16
0.82 0.11 0.06
Matches are distributed among these distances:
190 3 0.01
191 50 0.23
192 6 0.03
193 29 0.13
194 18 0.08
195 108 0.50
196 1 0.00
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.27
Consensus pattern (194 bp):
CGATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTACCCCAACCATCGATACAGT
GCTATCTGTACTATAAACTGTTCCCTAACGATGCTGCTCACACGAGCTATCGAGAATATGCATAA
AGCATAATCCCAGCCATCGTAGGGCCTATAATCCATTTAGGATCCATATCTCTTTTCCAGCTCA
Found at i:20659150 original size:23 final size:23
Alignment explanation
Indices: 20659120--20659166 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
20659110 CTAAAGGAAG
20659120 AAGAGACACCTTTCTCTTTCCTT
1 AAGAGACACCTTTCTCTTTCCTT
*
20659143 AAGAGACAGCTTTCTCTTTCCTT
1 AAGAGACACCTTTCTCTTTCCTT
20659166 A
1 A
20659167 TGAGTGTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.23, C:0.28, G:0.11, T:0.38
Consensus pattern (23 bp):
AAGAGACACCTTTCTCTTTCCTT
Found at i:20659510 original size:37 final size:37
Alignment explanation
Indices: 20659469--20659556 Score: 115
Period size: 37 Copynumber: 2.4 Consensus size: 37
20659459 TTCCTGCGAG
* * *
20659469 GACAGTTTTGGGTGCAATCTGGAAGTGCTCATGCGGT
1 GACAGTTTTAGGCGCAATCTAGAAGTGCTCATGCGGT
* *
20659506 GACAGTTTTAGGCGCAATCTAGAAGTGCTCATGCAGC
1 GACAGTTTTAGGCGCAATCTAGAAGTGCTCATGCGGT
20659543 GACA-TGTTTAGGCG
1 GACAGT-TTTAGGCG
20659557 TAATTCTGGA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
36 1 0.02
37 44 0.98
ACGTcount: A:0.23, C:0.18, G:0.32, T:0.27
Consensus pattern (37 bp):
GACAGTTTTAGGCGCAATCTAGAAGTGCTCATGCGGT
Found at i:20670932 original size:26 final size:27
Alignment explanation
Indices: 20670903--20670964 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 27
20670893 AGATTGATAT
20670903 TGGCTCGTAAG-AGCAATATACTACAC
1 TGGCTCGTAAGAAGCAATATACTACAC
* * **
20670929 TGGCTTGT-AGAAGCGATATACTGTAC
1 TGGCTCGTAAGAAGCAATATACTACAC
*
20670955 TAGCTCGTAA
1 TGGCTCGTAA
20670965 AAGTGATTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
25 2 0.07
26 25 0.89
27 1 0.04
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (27 bp):
TGGCTCGTAAGAAGCAATATACTACAC
Found at i:20679672 original size:18 final size:18
Alignment explanation
Indices: 20679651--20679696 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
20679641 CTTCTCTTCA
20679651 TTCTTCTCCTT-TTTTTCC
1 TTCTTCTCCTTATTTTT-C
20679669 TTC-TCTTCCTTATTTTTC
1 TTCTTC-TCCTTATTTTTC
*
20679687 GTCTTCTCCT
1 TTCTTCTCCT
20679697 CAAGTTCTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
17 2 0.08
18 15 0.62
19 7 0.29
ACGTcount: A:0.02, C:0.33, G:0.02, T:0.63
Consensus pattern (18 bp):
TTCTTCTCCTTATTTTTC
Found at i:20696416 original size:23 final size:23
Alignment explanation
Indices: 20696390--20696459 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
20696380 TTTATTTAAT
*
20696390 TTAATCGAATATGTTCACGAACA
1 TTAATCGAACATGTTCACGAACA
* * * *
20696413 TTAAACGAACATGTTAATGAATA
1 TTAATCGAACATGTTCACGAACA
*
20696436 TATAATTGAACATGTTCACGAACA
1 T-TAATCGAACATGTTCACGAACA
20696460 ATGTTAATGA
Statistics
Matches: 36, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
23 19 0.53
24 17 0.47
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.30
Consensus pattern (23 bp):
TTAATCGAACATGTTCACGAACA
Found at i:20696485 original size:11 final size:11
Alignment explanation
Indices: 20696469--20696508 Score: 53
Period size: 11 Copynumber: 3.4 Consensus size: 11
20696459 AATGTTAATG
20696469 AATAATAAATA
1 AATAATAAATA
20696480 AATAATAAATA
1 AATAATAAATA
20696491 AATACATACACATA
1 AATA-ATA-A-ATA
20696505 AATA
1 AATA
20696509 TTGTTTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 15 0.58
12 3 0.12
13 1 0.04
14 7 0.27
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (11 bp):
AATAATAAATA
Found at i:20698295 original size:24 final size:24
Alignment explanation
Indices: 20698265--20698327 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
20698255 TAAAGTAATA
20698265 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAATTGAAACAAATAAAC
* *
20698289 AGAGTTTAATTGAAACAATTAAAT
1 AGAGTTTAATTGAAACAAATAAAC
*
20698313 AGAGTTTAACTGAAA
1 AGAGTTTAATTGAAA
20698328 GATTATTTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.51, C:0.06, G:0.14, T:0.29
Consensus pattern (24 bp):
AGAGTTTAATTGAAACAAATAAAC
Found at i:20700235 original size:24 final size:24
Alignment explanation
Indices: 20700207--20700267 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
20700197 AAGTAATAAT
20700207 AGTTTAATTGAAACAAATAAACAG
1 AGTTTAATTGAAACAAATAAACAG
*
20700231 AGTTTAATTGAAACAATTAAACAG
1 AGTTTAATTGAAACAAATAAACAG
* *
20700255 AATTTAACTGAAA
1 AGTTTAATTGAAA
20700268 GATTATTTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.52, C:0.08, G:0.11, T:0.28
Consensus pattern (24 bp):
AGTTTAATTGAAACAAATAAACAG
Found at i:20702389 original size:14 final size:14
Alignment explanation
Indices: 20702370--20702398 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
20702360 ACCCAAGCTT
20702370 TGACCCAAAGTGTG
1 TGACCCAAAGTGTG
20702384 TGACCCAAAGTGTG
1 TGACCCAAAGTGTG
20702398 T
1 T
20702399 AAGCCAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (14 bp):
TGACCCAAAGTGTG
Found at i:20702405 original size:14 final size:14
Alignment explanation
Indices: 20702372--20702406 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
20702362 CCAAGCTTTG
*
20702372 ACCCAAAGTGTGTG
1 ACCCAAAGTGTGTA
20702386 ACCCAAAGTGTGTA
1 ACCCAAAGTGTGTA
*
20702400 AGCCAAA
1 ACCCAAA
20702407 TTCCCATGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (14 bp):
ACCCAAAGTGTGTA
Found at i:20702588 original size:36 final size:36
Alignment explanation
Indices: 20702538--20702623 Score: 111
Period size: 36 Copynumber: 2.4 Consensus size: 36
20702528 CCCGAACCCG
* * *
20702538 CTTTGACCTTTTGACCCGAGTTGACCGACCTGTTGA
1 CTTTAACCTGTTGACCCGAGTTGACCGACCCGTTGA
**
20702574 CTTTAACCTGTTGACCCGAGTTGATTGACCCGTTGA
1 CTTTAACCTGTTGACCCGAGTTGACCGACCCGTTGA
*
20702610 C-TTAATCTGTTGAC
1 CTTTAACCTGTTGAC
20702624 TATTGACCTT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
35 12 0.27
36 32 0.73
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.35
Consensus pattern (36 bp):
CTTTAACCTGTTGACCCGAGTTGACCGACCCGTTGA
Found at i:20705455 original size:3 final size:3
Alignment explanation
Indices: 20705449--20705477 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
20705439 TTCTTCAGGA
20705449 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
20705478 AGCTTTCTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:20706411 original size:26 final size:26
Alignment explanation
Indices: 20706355--20706410 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
20706345 TTAATTAGTC
*
20706355 TAAAATATTAACAACTTAAAATAAAT
1 TAAAATATTAACAAATTAAAATAAAT
* *
20706381 TAAAATTTTAATAAATTAAAA-AAAT
1 TAAAATATTAACAAATTAAAATAAAT
20706406 TAAAA
1 TAAAA
20706411 AATAATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 9 0.33
26 18 0.67
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (26 bp):
TAAAATATTAACAAATTAAAATAAAT
Found at i:20715563 original size:21 final size:21
Alignment explanation
Indices: 20715538--20715600 Score: 108
Period size: 21 Copynumber: 3.0 Consensus size: 21
20715528 GATACCTTAT
20715538 AAAAGGTATCGATACTTTTTG
1 AAAAGGTATCGATACTTTTTG
*
20715559 AAAAGGTATAGATACTTTTTG
1 AAAAGGTATCGATACTTTTTG
*
20715580 AAAAGGTATCAATACTTTTTG
1 AAAAGGTATCGATACTTTTTG
20715601 TCATTGTTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (21 bp):
AAAAGGTATCGATACTTTTTG
Found at i:20728314 original size:23 final size:22
Alignment explanation
Indices: 20728278--20728321 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
20728268 TAAATATTTC
*
20728278 ATTAAATAATTTGGGTTGAATTA
1 ATTAAATAAATTGGGTT-AATTA
*
20728301 ATTAATTAAATTGGGTTAATT
1 ATTAAATAAATTGGGTTAATT
20728322 TTATTTCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (22 bp):
ATTAAATAAATTGGGTTAATTA
Found at i:20728704 original size:7 final size:7
Alignment explanation
Indices: 20728692--20728736 Score: 81
Period size: 7 Copynumber: 6.4 Consensus size: 7
20728682 TATAAATAAG
20728692 ATCCCTC
1 ATCCCTC
20728699 ATCCCTC
1 ATCCCTC
20728706 ATCCCTC
1 ATCCCTC
20728713 ATCCCTC
1 ATCCCTC
*
20728720 ATCCTTC
1 ATCCCTC
20728727 ATCCCTC
1 ATCCCTC
20728734 ATC
1 ATC
20728737 TTTCTTTCCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.16, C:0.53, G:0.00, T:0.31
Consensus pattern (7 bp):
ATCCCTC
Found at i:20744219 original size:16 final size:17
Alignment explanation
Indices: 20744198--20744231 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
20744188 CTTAAAACCC
*
20744198 TAAATA-CTAACCATTA
1 TAAATATCTAAACATTA
20744214 TAAATATCTAAACATTA
1 TAAATATCTAAACATTA
20744231 T
1 T
20744232 TCTAACTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAATATCTAAACATTA
Found at i:20765028 original size:5 final size:5
Alignment explanation
Indices: 20765001--20765038 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
20764991 TTAATAACCC
20765001 AAAAT CAAAAT AATAAT -AAAT AAAAT AAAAT AAAAT AA
1 AAAAT -AAAAT AA-AAT AAAAT AAAAT AAAAT AAAAT AA
20765039 TGTAAATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
4 3 0.10
5 19 0.63
6 8 0.27
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:20766092 original size:14 final size:14
Alignment explanation
Indices: 20766059--20766107 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
20766049 TTCGAAAAAA
*
20766059 AGTCAATGGTCAA-
1 AGTCAACGGTCAAC
*
20766072 AGTCAACAGTCAAC
1 AGTCAACGGTCAAC
* *
20766086 GGTCAACGATCAAC
1 AGTCAACGGTCAAC
20766100 AGTCAACG
1 AGTCAACG
20766108 ATCAGTCAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
13 11 0.38
14 18 0.62
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.16
Consensus pattern (14 bp):
AGTCAACGGTCAAC
Done.