Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016130.1 Corchorus capsularis cultivar CVL-1 contig16151, 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: 75166
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:4304 original size:22 final size:22
Alignment explanation
Indices: 4279--4320 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
4269 GACAAACACA
*
4279 TAACCCGAATGACCCGAGAAGT
1 TAACCCAAATGACCCGAGAAGT
*
4301 TAACCCAAATGATCCGAGAA
1 TAACCCAAATGACCCGAGAA
4321 TATTATAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.26, G:0.19, T:0.14
Consensus pattern (22 bp):
TAACCCAAATGACCCGAGAAGT
Found at i:5018 original size:31 final size:31
Alignment explanation
Indices: 4983--5051 Score: 129
Period size: 31 Copynumber: 2.2 Consensus size: 31
4973 AAAAAACTGT
4983 AAAAGTTAAATAAGGATATAATAGGCATTTC
1 AAAAGTTAAATAAGGATATAATAGGCATTTC
*
5014 AAAAGTTAAATAAGGATATAATAGGCGTTTC
1 AAAAGTTAAATAAGGATATAATAGGCATTTC
5045 AAAAGTT
1 AAAAGTT
5052 TTACAAAACT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.48, C:0.06, G:0.17, T:0.29
Consensus pattern (31 bp):
AAAAGTTAAATAAGGATATAATAGGCATTTC
Found at i:6007 original size:109 final size:109
Alignment explanation
Indices: 5851--6145 Score: 448
Period size: 109 Copynumber: 2.7 Consensus size: 109
5841 TAAATTAAAA
** * *
5851 TGGTAAAAATAAAAAAATTATATAAAATATT-GAATTTAATTAAATGAAAATAGAATTTTTAGTA
1 TGGTAAAAATAAAGTAATTATA-AAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGTA
*
5915 GAATAAAATTGTATATTAGAAAAAATTTTAATATATCCAATTTTTT
64 GAATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
5961 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
1 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
*
6026 ATAAAATTGTATATTAGAAAAAATTTTAGTATATCCAAATTTTT
66 ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
* *
6070 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTA
1 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAA-TT-A---AATGAAAATAGAGTTTTTA
6135 GTAGAATAAAA
61 GTAGAATAAAA
6146 CTATAATAGT
Statistics
Matches: 171, Mismatches: 8, Indels: 8
0.91 0.04 0.04
Matches are distributed among these distances:
109 119 0.70
110 23 0.13
111 1 0.01
114 28 0.16
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.38
Consensus pattern (109 bp):
TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
Found at i:6256 original size:13 final size:13
Alignment explanation
Indices: 6238--6278 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
6228 TCGTACTTTT
6238 ATATATAGTATAG
1 ATATATAGTATAG
6251 ATATATAGTATAG
1 ATATATAGTATAG
6264 ATA-A-AG-ATAG
1 ATATATAGTATAG
6274 ATATA
1 ATATA
6279 GTTATTATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 7 0.26
11 3 0.11
12 1 0.04
13 16 0.59
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.34
Consensus pattern (13 bp):
ATATATAGTATAG
Found at i:7110 original size:32 final size:33
Alignment explanation
Indices: 7060--7132 Score: 105
Period size: 32 Copynumber: 2.3 Consensus size: 33
7050 CGGGCTTAAG
*
7060 TCGGGTTC-AGGTTAAATTTGGGTCGGGTTGAT
1 TCGGGTTCGAGGTTAAATTTGGGTCGGATTGAT
* *
7092 TCGGGTTCGA-GTTTAATTTGGGTTGGATTGAT
1 TCGGGTTCGAGGTTAAATTTGGGTCGGATTGAT
7124 TCGGGTTCG
1 TCGGGTTCG
7133 GGTCAATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 36 0.97
33 1 0.03
ACGTcount: A:0.14, C:0.10, G:0.37, T:0.40
Consensus pattern (33 bp):
TCGGGTTCGAGGTTAAATTTGGGTCGGATTGAT
Found at i:7342 original size:20 final size:20
Alignment explanation
Indices: 7309--7347 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
7299 CATAAATGAA
*
7309 ATTTTCAGAAATTATTATTT
1 ATTTTCAGAAATTAGTATTT
7329 ATTTTCA-AATATTAGTATT
1 ATTTTCAGAA-ATTAGTATT
7348 GAATTCAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (20 bp):
ATTTTCAGAAATTAGTATTT
Found at i:7376 original size:16 final size:16
Alignment explanation
Indices: 7355--7463 Score: 92
Period size: 16 Copynumber: 6.8 Consensus size: 16
7345 ATTGAATTCA
*
7355 GGTTTTTTCAGGTTCG
1 GGTTTTTTCGGGTTCG
7371 GGTTTTTTCGGGTTCG
1 GGTTTTTTCGGGTTCG
**
7387 GGTTTTTTCGGGTTTT
1 GGTTTTTTCGGGTTCG
* * * *
7403 AGATTTTTCGGATTCT
1 GGTTTTTTCGGGTTCG
* *
7419 GATTTTTTCGGGTTTG
1 GGTTTTTTCGGGTTCG
* ** *
7435 AGCATTTTCAGGTTCG
1 GGTTTTTTCGGGTTCG
*
7451 GGTTTTTTTGGGT
1 GGTTTTTTCGGGT
7464 GCGGTTTCGA
Statistics
Matches: 69, Mismatches: 24, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 69 1.00
ACGTcount: A:0.07, C:0.10, G:0.30, T:0.52
Consensus pattern (16 bp):
GGTTTTTTCGGGTTCG
Found at i:7410 original size:32 final size:33
Alignment explanation
Indices: 7374--7463 Score: 112
Period size: 32 Copynumber: 2.8 Consensus size: 33
7364 AGGTTCGGGT
*
7374 TTTTTCGGGTTCGGGTTTTTTCGGGTTTTAG-A
1 TTTTTCGGGTTCGGGTTTTTTCGGGTTTGAGCA
* * *
7406 TTTTTCGGATTCTGATTTTTTCGGGTTTGAGCA
1 TTTTTCGGGTTCGGGTTTTTTCGGGTTTGAGCA
* *
7439 -TTTTCAGGTTCGGGTTTTTTTGGGT
1 TTTTTCGGGTTCGGGTTTTTTCGGGT
7464 GCGGTTTCGA
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
32 47 0.98
33 1 0.02
ACGTcount: A:0.08, C:0.10, G:0.29, T:0.53
Consensus pattern (33 bp):
TTTTTCGGGTTCGGGTTTTTTCGGGTTTGAGCA
Found at i:7794 original size:16 final size:15
Alignment explanation
Indices: 7773--7902 Score: 102
Period size: 16 Copynumber: 8.3 Consensus size: 15
7763 AGTTTTCTCT
7773 GGTCATTCGGGTTACG
1 GGTCATTCGGGTT-CG
*
7789 GGTCA-TCTAGGTTCG
1 GGTCATTC-GGGTTCG
* *
7804 GATTATTCGGGTTCCG
1 GGTCATTCGGGTT-CG
*
7820 GGTCATTCGGGTCTTG
1 GGTCATTCGGGT-TCG
*
7836 GGTCATACGGGTTTCG
1 GGTCATTCGGG-TTCG
*
7852 GGTCATTCGGG-TCTA
1 GGTCATTCGGGTTC-G
*
7867 GGTCAATCGGGTTCCG
1 GGTCATTCGGGTT-CG
*
7883 GGTCATTTGGGTCTCG
1 GGTCATTCGGGT-TCG
7899 GGTC
1 GGTC
7903 TACCGGGTCT
Statistics
Matches: 90, Mismatches: 15, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
14 2 0.02
15 21 0.23
16 63 0.70
17 4 0.04
ACGTcount: A:0.11, C:0.20, G:0.36, T:0.33
Consensus pattern (15 bp):
GGTCATTCGGGTTCG
Found at i:7830 original size:9 final size:9
Alignment explanation
Indices: 7818--7864 Score: 57
Period size: 9 Copynumber: 5.7 Consensus size: 9
7808 ATTCGGGTTC
7818 CGGGTCATT
1 CGGGTCATT
7827 CGGGTC-TT
1 CGGGTCATT
*
7835 -GGGTCATA
1 CGGGTCATT
7843 CGGGT--TT
1 CGGGTCATT
7850 CGGGTCATT
1 CGGGTCATT
7859 CGGGTC
1 CGGGTC
7865 TAGGTCAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
7 11 0.34
8 3 0.09
9 18 0.56
ACGTcount: A:0.09, C:0.21, G:0.38, T:0.32
Consensus pattern (9 bp):
CGGGTCATT
Found at i:7840 original size:63 final size:63
Alignment explanation
Indices: 7768--7910 Score: 157
Period size: 63 Copynumber: 2.3 Consensus size: 63
7758 CAGATAGTTT
* * * * *
7768 TCTCTGGTCATTCGGGTTACGGGTCA-TCTAGGT-TCGGATTATTCGGGTTCCGGGTCATTCGGG
1 TCTCGGGTCATACGGGTTACGGGTCATTC-AGGTCTAGG-TCAATCGGGTTCCGGGTCATTCGGG
* * * *
7831 TCTTGGGTCATACGGGTTTCGGGTCATTCGGGTCTAGGTCAATCGGGTTCCGGGTCATTTGGG
1 TCTCGGGTCATACGGGTTACGGGTCATTCAGGTCTAGGTCAATCGGGTTCCGGGTCATTCGGG
7894 TCTCGGGTC-TACCGGGT
1 TCTCGGGTCATA-CGGGT
7911 CTCAGGTTGG
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
62 2 0.03
63 60 0.90
64 5 0.07
ACGTcount: A:0.10, C:0.21, G:0.35, T:0.34
Consensus pattern (63 bp):
TCTCGGGTCATACGGGTTACGGGTCATTCAGGTCTAGGTCAATCGGGTTCCGGGTCATTCGGG
Found at i:7854 original size:32 final size:33
Alignment explanation
Indices: 7811--7910 Score: 127
Period size: 32 Copynumber: 3.2 Consensus size: 33
7801 TCGGATTATT
7811 CGGGTTCCGGGTCATTCGGGTCTTGGGTCATA-
1 CGGGTTCCGGGTCATTCGGGTCTTGGGTCATAC
* * *
7843 CGGGTTTCGGGTCATTCGGGTC-TAGGTCA-AT
1 CGGGTTCCGGGTCATTCGGGTCTTGGGTCATAC
* *
7874 CGGGTTCCGGGTCATTTGGGTCTCGGGTC-TAC
1 CGGGTTCCGGGTCATTCGGGTCTTGGGTCATAC
7906 CGGGT
1 CGGGT
7911 CTCAGGTTGG
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
30 1 0.02
31 26 0.45
32 31 0.53
ACGTcount: A:0.09, C:0.22, G:0.38, T:0.31
Consensus pattern (33 bp):
CGGGTTCCGGGTCATTCGGGTCTTGGGTCATAC
Found at i:7878 original size:31 final size:30
Alignment explanation
Indices: 7810--7896 Score: 120
Period size: 31 Copynumber: 2.8 Consensus size: 30
7800 TTCGGATTAT
*
7810 TCGGGTTCCGGGTCATTCGGGTCTTGGGTCA
1 TCGGGTTCCGGGTCATTCGGGTC-TAGGTCA
*
7841 TACGGGTTTCGGGTCATTCGGGTCTAGGTCAA
1 T-CGGGTTCCGGGTCATTCGGGTCTAGGTC-A
*
7873 TCGGGTTCCGGGTCATTTGGGTCT
1 TCGGGTTCCGGGTCATTCGGGTCT
7897 CGGGTCTACC
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
31 27 0.54
32 23 0.46
ACGTcount: A:0.09, C:0.21, G:0.37, T:0.33
Consensus pattern (30 bp):
TCGGGTTCCGGGTCATTCGGGTCTAGGTCA
Found at i:8666 original size:54 final size:54
Alignment explanation
Indices: 8607--8740 Score: 241
Period size: 54 Copynumber: 2.5 Consensus size: 54
8597 CAAATTTAAC
8607 ATGATTTATAATAGGTAAAATTATAACAATAATATTAATTGTATTGAATAAATG
1 ATGATTTATAATAGGTAAAATTATAACAATAATATTAATTGTATTGAATAAATG
8661 ATGATTTATAATAGGTAAAATTATAACAATAATATTAATTGTATTGAATAAATG
1 ATGATTTATAATAGGTAAAATTATAACAATAATATTAATTGTATTGAATAAATG
* **
8715 ATGATTTAGAATAAATAAAATTATAA
1 ATGATTTATAATAGGTAAAATTATAA
8741 ATTTTATTGA
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 77 1.00
ACGTcount: A:0.50, C:0.01, G:0.10, T:0.38
Consensus pattern (54 bp):
ATGATTTATAATAGGTAAAATTATAACAATAATATTAATTGTATTGAATAAATG
Found at i:8862 original size:16 final size:15
Alignment explanation
Indices: 8817--8943 Score: 51
Period size: 16 Copynumber: 8.1 Consensus size: 15
8807 TTATTTGGGT
*
8817 TTCGGGTCATACGGG
1 TTCGGGTCATCCGGG
* * *
8832 TCTCGGATTACCCGGG
1 T-TCGGGTCATCCGGG
8848 TTACGGGTCATCCGGG
1 TT-CGGGTCATCCGGG
** **
8864 TTTCAAAGTCATCTAGG
1 -TTC-GGGTCATCCGGG
**
8881 TTACGGGTCATTTGGG
1 TT-CGGGTCATCCGGG
8897 TCTCGGGTC-T-CGGG
1 T-TCGGGTCATCCGGG
*
8911 TCTCGGGTCATCTGGG
1 T-TCGGGTCATCCGGG
* *
8927 TTGTGGGTCATTCGGG
1 TT-CGGGTCATCCGGG
8943 T
1 T
8944 CGCGGATTGG
Statistics
Matches: 83, Mismatches: 20, Indels: 17
0.69 0.17 0.14
Matches are distributed among these distances:
14 12 0.14
15 5 0.06
16 54 0.65
17 12 0.14
ACGTcount: A:0.12, C:0.21, G:0.35, T:0.31
Consensus pattern (15 bp):
TTCGGGTCATCCGGG
Found at i:8906 original size:7 final size:7
Alignment explanation
Indices: 8894--8919 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
8884 CGGGTCATTT
8894 GGGTCTC
1 GGGTCTC
8901 GGGTCTC
1 GGGTCTC
8908 GGGTCTC
1 GGGTCTC
8915 GGGTC
1 GGGTC
8920 ATCTGGGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.27, G:0.46, T:0.27
Consensus pattern (7 bp):
GGGTCTC
Found at i:8935 original size:30 final size:31
Alignment explanation
Indices: 8884--8944 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 31
8874 ATCTAGGTTA
*
8884 CGGGTCATTTGGGTCTCGGGTC-TCGGGTCT
1 CGGGTCATCTGGGTCTCGGGTCATCGGGTCT
*
8914 CGGGTCATCTGGGT-TGTGGGTCATTCGGGTC
1 CGGGTCATCTGGGTCT-CGGGTCA-TCGGGTC
8945 GCGGATTGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
29 1 0.04
30 18 0.69
32 7 0.27
ACGTcount: A:0.05, C:0.21, G:0.41, T:0.33
Consensus pattern (31 bp):
CGGGTCATCTGGGTCTCGGGTCATCGGGTCT
Found at i:10039 original size:131 final size:132
Alignment explanation
Indices: 9861--10129 Score: 470
Period size: 131 Copynumber: 2.1 Consensus size: 132
9851 AGTTTAGTAG
* * *
9861 ACTA-CACATGCTGGGTCTAAGGGTTGACATGTGTACTTTATGGAATAGTTTTGAATTTTAAAAA
1 ACTATCACATGCTGGATCTAAGGGTTGACATGTGTACTTTAGGGAATAGTTTTAAATTTTAAAAA
* *
9925 CAAAATTAATTAAAAAAAAGGTACTATGTGTCAACTCCTCAGCCCGCTTGTGGAGTCCAAAATTT
66 CAAAATTAATTAAAAAAAAGGTAATATGTGTCAACTCCCCAGCCCGCTTGTGGAGTCCAAAATTT
9990 AC
131 AC
9992 ACTATCACATGCTGGATCT-AGGGTTGACATGTGTACTTTAGGGAATAGTTTTAAATTTTAAAAA
1 ACTATCACATGCTGGATCTAAGGGTTGACATGTGTACTTTAGGGAATAGTTTTAAATTTTAAAAA
*
10056 CAAAATTAATTAAAAAAAAGGTAATATGTGTCAACTCCCCAGCCTGCTTGTGGAGTCCAAAATTT
66 CAAAATTAATTAAAAAAAAGGTAATATGTGTCAACTCCCCAGCCCGCTTGTGGAGTCCAAAATTT
10121 AC
131 AC
10123 ACTATCA
1 ACTATCA
10130 GTGTATCAAA
Statistics
Matches: 131, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
131 118 0.90
132 13 0.10
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.31
Consensus pattern (132 bp):
ACTATCACATGCTGGATCTAAGGGTTGACATGTGTACTTTAGGGAATAGTTTTAAATTTTAAAAA
CAAAATTAATTAAAAAAAAGGTAATATGTGTCAACTCCCCAGCCCGCTTGTGGAGTCCAAAATTT
AC
Found at i:10327 original size:75 final size:78
Alignment explanation
Indices: 10200--10365 Score: 259
Period size: 75 Copynumber: 2.2 Consensus size: 78
10190 CCAAAAAAAC
* * *
10200 TTTTA-TAGTTTTACACAACTAAAAACTCTATTTTTATTTAATTAAGTCT-A-ATA-TTATAACT
1 TTTTACTA-TTTTACACAACTAAAAAATCTATTTTTATTTAATTAAATATAATATACTTATAACT
10261 ATTTTATTTTACCA
65 ATTTTATTTTACCA
*
10275 TTTTACTATTTTACTCAACTAAAAAATCTATTTTTATTTAATTAAATATAATATACTTATAACTA
1 TTTTACTATTTTACACAACTAAAAAATCTATTTTTATTTAATTAAATATAATATACTTATAACTA
10340 TTTTATTTTACCA
66 TTTTATTTTACCA
10353 TTTTACTATTTTA
1 TTTTACTATTTTA
10366 ATTAAAAAAC
Statistics
Matches: 83, Mismatches: 4, Indels: 5
0.90 0.04 0.05
Matches are distributed among these distances:
75 42 0.51
76 3 0.04
77 3 0.04
78 35 0.42
ACGTcount: A:0.36, C:0.11, G:0.01, T:0.51
Consensus pattern (78 bp):
TTTTACTATTTTACACAACTAAAAAATCTATTTTTATTTAATTAAATATAATATACTTATAACTA
TTTTATTTTACCA
Found at i:10374 original size:75 final size:74
Alignment explanation
Indices: 10215--10367 Score: 225
Period size: 78 Copynumber: 2.0 Consensus size: 74
10205 TAGTTTTACA
* * *
10215 CAACTAAAAACTCTATTTTTATTTAATTAAGTCTAATATTATAACTATTTTATTTTACCATTTTA
1 CAAC-AAAAAATCTATTTTTATTTAATTAAATATAATATTATAACTATTTTATTTTACCATTTTA
*
10280 CTATTTTACT
65 CTATTTTAAT
10290 CAACTAAAAAATCTATTTTTATTTAATTAAATATAATATACTTATAACTATTTTATTTTACCATT
1 CAAC-AAAAAATCTATTTTTATTTAATTAAATAT-A-ATA-TTATAACTATTTTATTTTACCATT
10355 TTACTATTTTAAT
62 TTACTATTTTAAT
10368 TAAAAAACTT
Statistics
Matches: 71, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
75 31 0.44
76 1 0.01
77 3 0.04
78 36 0.51
ACGTcount: A:0.37, C:0.12, G:0.01, T:0.50
Consensus pattern (74 bp):
CAACAAAAAATCTATTTTTATTTAATTAAATATAATATTATAACTATTTTATTTTACCATTTTAC
TATTTTAAT
Found at i:10515 original size:256 final size:253
Alignment explanation
Indices: 10149--10720 Score: 729
Period size: 256 Copynumber: 2.2 Consensus size: 253
10139 ATAATTATCC
* ** * * * * *
10149 TTTCTTAAATGCAATTGTTTAAACTTTTATAGTTTTTTGT-GCCAAAAAAACTTTTATAGTTTTA
1 TTTCTTAAATGAAATTAATTAAACTTTTACAGTTTTTT-TAG--AGATAAACCTTTACAGTTTTA
** * ** * *
10213 CACAACTAAAAACTCTATTTTTATTTAATTAAGTCTAATATTATAACTATTTTATTTTACCATTT
63 TTCTACTAAAAACTCTATTTTTATTTAATTAAACCTAATATTATAACTACTATATTTTACCATTT
* *
10278 TACTATTTTACTCAACTAAAAAATCTATTTTTATTTAATTAAATATAATATACTTATAACTATTT
128 TACTATTTCACTCAACTAAAAAATCTATGTTTATTTAATTAAATATAATATACTTATAACTATTT
* * *
10343 TATTTTACCATTTTACTATTTTAATTAAAAAACTTGATATATTAGAAATTT-TTTAAATATA
193 TATTTTACCATTTTACTATTTTAATTAAAAAAATTGATATATAAG-AATTTAGTTAAATATA
* * *
10404 TTTCTTAAATGACATCT-TTTAAAACTTTTACAGTTTTTTTAGATATAAACCTTTACAGTTTTAT
1 TTTCTTAAATGAAAT-TAATT-AAACTTTTACAGTTTTTTTAGAGATAAACCTTTACAGTTTTAT
10468 TCTACTAAAAACTCTA-TTTTATTTAATTAAACCTAATATCTTTATAACTACTATATTTTACCAT
64 TCTACTAAAAACTCTATTTTTATTTAATTAAACCTAATA---TTATAACTACTATATTTTACCAT
* * * * * * *
10532 TTTACTATTTCATTCAACTACAAATTCTATGTTTATTTAATTAAGTGTAATATCCTTTTAACTAT
126 TTTACTATTTCACTCAACTAAAAAATCTATGTTTATTTAATTAAATATAATATACTTATAACTAT
* *
10597 TTTATTTTACCATTTTACTATTTTAATTAAAAAAATTTATATATAAGAATTTAGTTAAATTTA
191 TTTATTTTACCATTTTACTATTTTAATTAAAAAAATTGATATATAAGAATTTAGTTAAATATA
* *
10660 TTTCTTAAATGAAATTAATTAAACTTTTACAGTTTTTTTAGAGATAATCTTTTACAGTTTT
1 TTTCTTAAATGAAATTAATTAAACTTTTACAGTTTTTTTAGAGATAAACCTTTACAGTTTT
10721 TATTGCCAAA
Statistics
Matches: 276, Mismatches: 33, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
253 20 0.07
254 31 0.11
255 61 0.22
256 164 0.59
ACGTcount: A:0.36, C:0.11, G:0.04, T:0.49
Consensus pattern (253 bp):
TTTCTTAAATGAAATTAATTAAACTTTTACAGTTTTTTTAGAGATAAACCTTTACAGTTTTATTC
TACTAAAAACTCTATTTTTATTTAATTAAACCTAATATTATAACTACTATATTTTACCATTTTAC
TATTTCACTCAACTAAAAAATCTATGTTTATTTAATTAAATATAATATACTTATAACTATTTTAT
TTTACCATTTTACTATTTTAATTAAAAAAATTGATATATAAGAATTTAGTTAAATATA
Found at i:10574 original size:78 final size:77
Alignment explanation
Indices: 10466--10619 Score: 211
Period size: 78 Copynumber: 2.0 Consensus size: 77
10456 TTACAGTTTT
*
10466 ATTCTACTAAAAACTCTATTTTATTTAATTAAACCTAATAT-CTTTATAACTACTATATTTTACC
1 ATTCAACTAAAAACTCTATTTTATTTAATTAAACCTAATATCCTTT-TAACTACTATATTTTACC
10530 ATTTTACTATTTC
65 ATTTTACTATTTC
* * *** * *
10543 ATTCAACTACAAATTCTATGTTTATTTAATTAAGTGTAATATCCTTTTAACTATTTTATTTTACC
1 ATTCAACTAAAAACTCTAT-TTTATTTAATTAAACCTAATATCCTTTTAACTACTATATTTTACC
10608 ATTTTACTATTT
65 ATTTTACTATTT
10620 TAATTAAAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
77 16 0.24
78 47 0.70
79 4 0.06
ACGTcount: A:0.33, C:0.15, G:0.02, T:0.50
Consensus pattern (77 bp):
ATTCAACTAAAAACTCTATTTTATTTAATTAAACCTAATATCCTTTTAACTACTATATTTTACCA
TTTTACTATTTC
Found at i:19894 original size:27 final size:28
Alignment explanation
Indices: 19864--19916 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
19854 GCATTAGGGT
*
19864 CATCCA-GGGGCATTTTGGTCATTTTCA
1 CATCCAGGGGGCATTTTAGTCATTTTCA
*
19891 CATCTAGGGGGCATTTTAGTCATTTT
1 CATCCAGGGGGCATTTTAGTCATTTT
19917 TGCATTTAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.40
Consensus pattern (28 bp):
CATCCAGGGGGCATTTTAGTCATTTTCA
Found at i:19902 original size:28 final size:28
Alignment explanation
Indices: 19870--19942 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 28
19860 GGGTCATCCA
19870 GGGGCATTTTGGTCATTTTCACATCTAG
1 GGGGCATTTTGGTCATTTTCACATCTAG
* ** *
19898 GGGGCATTTTAGTCATTTTTGCATTTAG
1 GGGGCATTTTGGTCATTTTCACATCTAG
*
19926 GGGGTATTTTGGTCATT
1 GGGGCATTTTGGTCATT
19943 CTTAATCTAC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.16, C:0.12, G:0.27, T:0.44
Consensus pattern (28 bp):
GGGGCATTTTGGTCATTTTCACATCTAG
Found at i:23285 original size:45 final size:44
Alignment explanation
Indices: 23253--23366 Score: 121
Period size: 45 Copynumber: 2.6 Consensus size: 44
23243 AAAGGTGATT
23253 AGTAAAGAGAAGTAAA-GGTAATCAGTAAAAGAATAAAAGGCAATC
1 AGTAAAGAGAA--AAATGGTAATCAGTAAAAGAATAAAAGGCAATC
* * *
23298 AGTAAAGAGAAAAATGGTAATTAGT-AAAGAAACAAAAAGGTAATC
1 AGTAAAGAGAAAAATGGTAATCAGTAAAAG-AA-TAAAAGGCAATC
*
23343 AGT-AAGCG--AAATGGTAATCAGTAA
1 AGTAAAGAGAAAAATGGTAATCAGTAA
23367 GAGTAAAATA
Statistics
Matches: 60, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
42 13 0.22
43 8 0.13
44 15 0.25
45 24 0.40
ACGTcount: A:0.54, C:0.06, G:0.22, T:0.18
Consensus pattern (44 bp):
AGTAAAGAGAAAAATGGTAATCAGTAAAAGAATAAAAGGCAATC
Found at i:23304 original size:21 final size:22
Alignment explanation
Indices: 23188--23564 Score: 230
Period size: 22 Copynumber: 17.8 Consensus size: 22
23178 TAATCAGTAA
23188 AATCAGT-AAG-AGTAAAAGGT
1 AATCAGTAAAGAAGTAAAAGGT
* * *
23208 CATCAAT-AAG-AGTAAAATAGT
1 AATCAGTAAAGAAGTAAAA-GGT
*
23229 AGTCAGT-AAGAAGT-AAAGGT
1 AATCAGTAAAGAAGTAAAAGGT
* *
23249 GATTAGTAAAGAGAAGT-AAAGGT
1 AATCAGT-AA-AGAAGTAAAAGGT
*
23272 AATCAGTAAAAGAA-TAAAAGGC
1 AATCAGT-AAAGAAGTAAAAGGT
*
23294 AATCAGTAAAG-AGAAAAATGGT
1 AATCAGTAAAGAAGTAAAA-GGT
* **
23316 AATTAGTAAAGAAACAAAAAGGT
1 AATCAGTAAAG-AAGTAAAAGGT
* *
23339 AATCAGT-AAG-CG-AAATGGT
1 AATCAGTAAAGAAGTAAAAGGT
*
23358 AATCAGT-AAG-AGTAAAATAGT
1 AATCAGTAAAGAAGTAAAA-GGT
* * *
23379 AATCGGCAAA-AAGTAAAAAGT
1 AATCAGTAAAGAAGTAAAAGGT
23400 AATCAGT-AAGAAGT-AAAGGT
1 AATCAGTAAAGAAGTAAAAGGT
*
23420 AAACAGT-AAG-AGTATAAAGGT
1 AATCAGTAAAGAAGTA-AAAGGT
* * *
23441 AATCAATGAAG-AGTAAAAAGCT
1 AATCAGTAAAGAAGT-AAAAGGT
*
23463 AATCAAT-AAGAAGTAAAAGGT
1 AATCAGTAAAGAAGTAAAAGGT
*
23484 AATCAGTAAA-AAGCGAAAAGGT
1 AATCAGTAAAGAAG-TAAAAGGT
*
23506 AATCAGTAAA-AAGTAAAGGAGT
1 AATCAGTAAAGAAGTAAAAG-GT
*
23528 AATCAGTAAAGAA--AAATGGT
1 AATCAGTAAAGAAGTAAAAGGT
**
23548 AAAGAGTAAAG-AGTAAA
1 AATCAGTAAAGAAGTAAA
23565 GAAAAATGGT
Statistics
Matches: 290, Mismatches: 41, Indels: 51
0.76 0.11 0.13
Matches are distributed among these distances:
19 21 0.07
20 52 0.18
21 80 0.28
22 99 0.34
23 32 0.11
24 6 0.02
ACGTcount: A:0.54, C:0.06, G:0.22, T:0.19
Consensus pattern (22 bp):
AATCAGTAAAGAAGTAAAAGGT
Found at i:23453 original size:84 final size:81
Alignment explanation
Indices: 23333--23492 Score: 196
Period size: 84 Copynumber: 1.9 Consensus size: 81
23323 AAAGAAACAA
* * * * **
23333 AAAGGTAATCAGTAAGCGAAATGGTAATCAGTAAGAGTAAAATAG-TAATCGGCAAAAAGTAAAA
1 AAAGGTAAACAGTAAGAGAAAAGGTAATCAATAAGAGTAAAA-AGCTAATCAACAAAAAGTAAAA
23397 AGTAATCAGTAAGAAGT
65 AGTAATCAGTAAGAAGT
* *
23414 AAAGGTAAACAGTAAGAGTATAAAGGTAATCAATGAAGAGTAAAAAGCTAATCAATAAGAAGTAA
1 AAAGGTAAACAGTAAGAG-A-AAAGGTAATCAAT-AAGAGTAAAAAGCTAATCAACAAAAAGTAA
*
23479 AAGGTAATCAGTAA
63 AAAGTAATCAGTAA
23493 AAAGCGAAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
81 16 0.24
82 1 0.02
83 13 0.20
84 36 0.55
ACGTcount: A:0.53, C:0.07, G:0.21, T:0.19
Consensus pattern (81 bp):
AAAGGTAAACAGTAAGAGAAAAGGTAATCAATAAGAGTAAAAAGCTAATCAACAAAAAGTAAAAA
GTAATCAGTAAGAAGT
Found at i:23503 original size:43 final size:42
Alignment explanation
Indices: 23260--23537 Score: 174
Period size: 43 Copynumber: 6.5 Consensus size: 42
23250 ATTAGTAAAG
** *
23260 AGAAGT-AAAGGTAATCAGTAAAAGAATAAAAGGCAATCAGTA
1 AGAAGTAAAAGGTAATCAGTAAAA-AGGAAAAGGTAATCAGTA
* * **
23302 A-AGAGAAAAATGGTAATTAGTAAAGAAACAAAAAGGTAATCAGTA
1 AGA-AGTAAAA-GGTAATCAGT-AA-AAAGGAAAAGGTAATCAGTA
* * * * * * *
23347 AG-CG-AAATGGTAATCAGT-AAGAGTAAAATAGTAATCGGCA
1 AGAAGTAAAAGGTAATCAGTAAAAAGGAAAA-GGTAATCAGTA
* * * * *
23387 AAAAGTAAAAAGTAATCAGTAAGAA-GTAAAGGTAAACAGTA
1 AGAAGTAAAAGGTAATCAGTAAAAAGGAAAAGGTAATCAGTA
* * * * * *
23428 AG-AGTATAAAGGTAATCAATGAAGAGTAAAAAGCTAATCAATA
1 AGAAGTA-AAAGGTAATCAGTAAAAAG-GAAAAGGTAATCAGTA
23471 AGAAGTAAAAGGTAATCAGTAAAAAGCGAAAAGGTAATCAGTA
1 AGAAGTAAAAGGTAATCAGTAAAAAG-GAAAAGGTAATCAGTA
* *
23514 AAAAGTAAAGGAGTAATCAGTAAA
1 AGAAGTAAAAG-GTAATCAGTAAA
23538 GAAAAATGGT
Statistics
Matches: 175, Mismatches: 46, Indels: 28
0.70 0.18 0.11
Matches are distributed among these distances:
39 6 0.03
40 14 0.08
41 23 0.13
42 27 0.15
43 59 0.34
44 26 0.15
45 18 0.10
46 2 0.01
ACGTcount: A:0.54, C:0.06, G:0.21, T:0.18
Consensus pattern (42 bp):
AGAAGTAAAAGGTAATCAGTAAAAAGGAAAAGGTAATCAGTA
Found at i:23543 original size:27 final size:27
Alignment explanation
Indices: 23518--23592 Score: 123
Period size: 27 Copynumber: 2.7 Consensus size: 27
23508 TCAGTAAAAA
**
23518 GTAAAGGAGTAATCAGTAAAGAAAAATG
1 GTAAA-GAGTAAAGAGTAAAGAAAAATG
23546 GTAAAGAGTAAAGAGTAAAGAAAAATG
1 GTAAAGAGTAAAGAGTAAAGAAAAATG
23573 GTAAAGAGTAAAGAGTAAAG
1 GTAAAGAGTAAAGAGTAAAG
23593 TAGAGAGTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
27 40 0.89
28 5 0.11
ACGTcount: A:0.56, C:0.01, G:0.27, T:0.16
Consensus pattern (27 bp):
GTAAAGAGTAAAGAGTAAAGAAAAATG
Found at i:23556 original size:148 final size:147
Alignment explanation
Indices: 23260--23533 Score: 313
Period size: 148 Copynumber: 1.9 Consensus size: 147
23250 ATTAGTAAAG
* * * * *
23260 AGAAGTAAAGGTAATCAGTAAAAGAATAAAAGGCAATCAGTAAAGAGAAAAATGGTAATTAGTAA
1 AGAAGTAAAGGTAAACAGTAAAAGAATAAAAGGCAATCAATAAAGAGAAAAATGCTAATCAATAA
* * * *
23325 AGAAACAAAAAGGTAATCAGTAAGCGAAATGGTAATCAGTAAGAGTAAAATAGTAATCGGCAAAA
66 AGAAACAAAAAGGTAATCAGTAAGCGAAAAGGTAATCAGTAAAAGTAAAAGAGTAATCAG-AAAA
*
23390 AGTAAAAAGTAATCAGTA
130 AGTAAAAAGTAAACAGTA
* * * *
23408 AGAAGTAAAGGTAAACAGTAAGAGTAT-AAAGGTAATCAATGAAGAGTAAAAA-GCTAATCAAT-
1 AGAAGTAAAGGTAAACAGTAAAAGAATAAAAGGCAATCAATAAAGAG-AAAAATGCTAATCAATA
** *
23470 AAG-AAGTAAAAGGTAATCAGTAAAAAGCGAAAAGGTAATCAGTAAAAAGTAAAGGAGTAATCAG
65 AAGAAACAAAAAGGTAATCAGT---AAGCGAAAAGGTAATCAGT-AAAAGTAAAAGAGTAATCAG
23534 TAAAGAAAAA
Statistics
Matches: 105, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
145 16 0.15
146 3 0.03
147 23 0.22
148 47 0.45
149 16 0.15
ACGTcount: A:0.54, C:0.07, G:0.22, T:0.18
Consensus pattern (147 bp):
AGAAGTAAAGGTAAACAGTAAAAGAATAAAAGGCAATCAATAAAGAGAAAAATGCTAATCAATAA
AGAAACAAAAAGGTAATCAGTAAGCGAAAAGGTAATCAGTAAAAGTAAAAGAGTAATCAGAAAAA
GTAAAAAGTAAACAGTA
Found at i:23558 original size:7 final size:7
Alignment explanation
Indices: 23510--23592 Score: 66
Period size: 7 Copynumber: 12.0 Consensus size: 7
23500 AAAGGTAATC
*
23510 AGTAAAA
1 AGTAAAG
23517 AGTAAAGG
1 AGTAAA-G
**
23525 AGTAATC
1 AGTAAAG
23532 AGTAAAG
1 AGTAAAG
*
23539 A-AAAATG
1 AGTAAA-G
23546 -GTAAAG
1 AGTAAAG
23552 AGTAAAG
1 AGTAAAG
23559 AGTAAAG
1 AGTAAAG
*
23566 A-AAAATG
1 AGTAAA-G
23573 -GTAAAG
1 AGTAAAG
23579 AGTAAAG
1 AGTAAAG
23586 AGTAAAG
1 AGTAAAG
23593 TAGAGAGTAA
Statistics
Matches: 60, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
6 8 0.13
7 47 0.78
8 5 0.08
ACGTcount: A:0.58, C:0.01, G:0.25, T:0.16
Consensus pattern (7 bp):
AGTAAAG
Found at i:33693 original size:92 final size:92
Alignment explanation
Indices: 33517--33695 Score: 254
Period size: 92 Copynumber: 1.9 Consensus size: 92
33507 TTAGGATTTA
* **
33517 ACCTATTCTTTTGCAGATTTCTCGAAAAATAAAAGACTTTTATTTGCATAAAATAAATGACTCCT
1 ACCTATTCTTTTGCAGATTTCTCG-AAAAGAAAAGACACTTATTTGCATAAAATAAATGACTCCT
33582 CTTTTAAATCGTCTTAGACTTTAGTATTG
65 C-TTTAAATCGTCTTAGACTTTAGTATTG
* * *
33611 ACCTTTTCTTTTGCAGATTTTTCG-AAAGAAAAGACACTTATTTGCATGAAATAAATGACTCCTC
1 ACCTATTCTTTTGCAGATTTCTCGAAAAGAAAAGACACTTATTTGCATAAAATAAATGACTCCTC
33675 -TTAAATCGTCTTTAAGACTTT
66 TTTAAATCGTC-TT-AGACTTT
33696 TAATAGTATA
Statistics
Matches: 77, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
90 10 0.13
91 2 0.03
92 43 0.56
94 22 0.29
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40
Consensus pattern (92 bp):
ACCTATTCTTTTGCAGATTTCTCGAAAAGAAAAGACACTTATTTGCATAAAATAAATGACTCCTC
TTTAAATCGTCTTAGACTTTAGTATTG
Found at i:34592 original size:6 final size:6
Alignment explanation
Indices: 34581--34610 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
34571 ATTCTGCTTC
*
34581 AGATTT AGATTT ACATTT AGATTT AGATTT
1 AGATTT AGATTT AGATTT AGATTT AGATTT
34611 CCTTTGCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.50
Consensus pattern (6 bp):
AGATTT
Found at i:35345 original size:182 final size:182
Alignment explanation
Indices: 34730--35565 Score: 1172
Period size: 182 Copynumber: 4.6 Consensus size: 182
34720 AAATAACAAT
* *
34730 AGATAAAAGATATCTTACCTTAACTTAAAGTGTGTCGAGATATGGAATAGATTCGAAAAATAGCT
1 AGATAAAAGATATCTTACCTTAACTTAAAGTGTGTTGAAATATGGAATAGATTCGAAAAATAGCT
* * *
34795 CTATAGACTTGAGAAGCCCTTAAGTGTCTTGGGATAGATTTCCTGCATATACAAAAGAAAAAAAA
66 CTCTAGACTTGAGAAGCCCTTAAGTGTATTGGAATAGATTTCCTGCATATACAAAAGAAAAAAAA
* * *
34860 AAAGAGTTAGTATGAAATAAGTATTCAGATAAAGAAAAATAAAACA-ACAAC
131 AAAGAGTTAGTATGAAATAAGTATTCAGATAAAGAAAAAAAAAACAGATAAA
* *
34911 AGATAAAAGATATCTTACCTTAACTTAAAGTGTGTTGAAATATGGAAAAGATTCGAAAAATAGTT
1 AGATAAAAGATATCTTACCTTAACTTAAAGTGTGTTGAAATATGGAATAGATTCGAAAAATAGCT
* *
34976 GTCTAGAGTTGAGAAGCCCTTAAGTGTATTGGAATAGATTTCCTGCATATACAAAAG--AAAAAA
66 CTCTAGACTTGAGAAGCCCTTAAGTGTATTGGAATAGATTTCCTGCATATACAAAAGAAAAAAAA
*
35039 AAAGAGTTAGTATGAAATAAGTATTCGGATAAAGAAAAAAAAAACAACAATAGATAAA
131 AAAGAGTTAGTATGAAATAAGTATTCAGATAAAG--AAAAAAAA-AAC---AGATAAA
*
35097 AGATAAAAGATATATTACCTTAACTTAAAGTGTGTTGAAATATGGAATAGATTCGAAAAATAGCT
1 AGATAAAAGATATCTTACCTTAACTTAAAGTGTGTTGAAATATGGAATAGATTCGAAAAATAGCT
** **
35162 CTCTAGACTTGAGAAGCAATTAAGTGTATTGGGGTAGATTTCCTGCATATACAAAAGAAAAAAAA
66 CTCTAGACTTGAGAAGCCCTTAAGTGTATTGGAATAGATTTCCTGCATATACAAAAGAAAAAAAA
35227 AAAGAGTTAGTACT-AAATAAGTATTCAGATAAAGAAAAAAAAAACAGATAAA
131 AAAGAGTTAGTA-TGAAATAAGTATTCAGATAAAGAAAAAAAAAACAGATAAA
35279 AGATAAAAGATATCTTACCTTAACTTAAAGTGTGTTGAAATATGGAATAGATTCGAAAAATAGCT
1 AGATAAAAGATATCTTACCTTAACTTAAAGTGTGTTGAAATATGGAATAGATTCGAAAAATAGCT
*
35344 CTCTAGACTTGAGAAGCCCTTGAGTGTATTGGAATAGATTTCCTGCATATACAAAAGAAAAAAAA
66 CTCTAGACTTGAGAAGCCCTTAAGTGTATTGGAATAGATTTCCTGCATATACAAAAGAAAAAAAA
* * * * * * * *
35409 GAA-A-TAAATATTCAGATAAAG-A--AAAATAAA-ACAACAACAGATAAA-AAATAAA
131 AAAGAGTTAGTA-TGAAAT-AAGTATTCAGATAAAGA-AA-AA-A-A-AAACAGATAAA
* ** *
35461 AGATAAAAGATATCTTACCTTAAGTTAAAGTGTGTTTTAATATTGAATAGATTCGAAAAATAGCT
1 AGATAAAAGATATCTTACCTTAACTTAAAGTGTGTTGAAATATGGAATAGATTCGAAAAATAGCT
* *
35526 GTTTAGACTTGAGAAGCCCTTAAGTGTATTGGAATAGATT
66 CTCTAGACTTGAGAAGCCCTTAAGTGTATTGGAATAGATT
35566 CGAAAAAAAC
Statistics
Matches: 594, Mismatches: 44, Indels: 33
0.89 0.07 0.05
Matches are distributed among these distances:
178 1 0.00
179 47 0.08
180 7 0.01
181 126 0.21
182 244 0.41
183 3 0.01
185 4 0.01
186 124 0.21
188 37 0.06
189 1 0.00
ACGTcount: A:0.47, C:0.10, G:0.17, T:0.27
Consensus pattern (182 bp):
AGATAAAAGATATCTTACCTTAACTTAAAGTGTGTTGAAATATGGAATAGATTCGAAAAATAGCT
CTCTAGACTTGAGAAGCCCTTAAGTGTATTGGAATAGATTTCCTGCATATACAAAAGAAAAAAAA
AAAGAGTTAGTATGAAATAAGTATTCAGATAAAGAAAAAAAAAACAGATAAA
Found at i:35407 original size:367 final size:362
Alignment explanation
Indices: 34730--35565 Score: 1272
Period size: 367 Copynumber: 2.3 Consensus size: 362
34720 AAATAACAAT
* *
34730 AGATAAAAGATATCTTACCTTAACTTAAAGTGTGTCGAGATATGGAATAGATTCGAAAAATAGCT
1 AGATAAAAGATATCTTACCTTAACTTAAAGTGTGTTGAAATATGGAATAGATTCGAAAAATAGCT
*
34795 CTATAGACTTGAGAAGCCCTTAAGTGTCTTGGGATAGATTTCCTGCATATACAAAAGAAAAAAAA
66 CTATAGACTTGAGAAGCCCTTAAGTGTATTGGGATAGATTTCCTGCATATACAAAAGAAAAAAAA
* *
34860 AAAGAGTTAGTATGAAATAAGTATTCAGATAAAGAAAAATAAAACAACAACAGATAAAAGATATC
131 AAAGAGTTAGTATGAAATAAGTATTCAGATAAAGAAAAAAAAAACAACAAAAGATAAAAGATATC
* * *
34925 TTACCTTAACTTAAAGTGTGTTGAAATATGGAAAAGATTCGAAAAATAGTTGTCTAGAGTTGAGA
196 TTACCTTAACTTAAAGTGTGTTGAAATATGGAAAAGATTCGAAAAATAGCTCTCTAGACTTGAGA
34990 AGCCCTTAAGTGTATTGGAATAGATTTCCTGCATATACAAAAGAAAAAAAAAGAGTTAGTATGAA
261 AGCCCTTAAGTGTATTGGAATAGATTTCCTGCATATACAAAAGAAAAAAAAAGA---A--AT---
* *
35055 ATAAGTATTCGGATAAAG-AAAA-AAAA-AACAACA-AT-AGATAAA
318 A-AA-TATTCAGATAAAGAAAAATAAAACAACAACAGATAAAATAAA
*
35097 AGATAAAAGATATATTACCTTAACTTAAAGTGTGTTGAAATATGGAATAGATTCGAAAAATAGCT
1 AGATAAAAGATATCTTACCTTAACTTAAAGTGTGTTGAAATATGGAATAGATTCGAAAAATAGCT
* ** *
35162 CTCTAGACTTGAGAAGCAATTAAGTGTATTGGGGTAGATTTCCTGCATATACAAAAGAAAAAAAA
66 CTATAGACTTGAGAAGCCCTTAAGTGTATTGGGATAGATTTCCTGCATATACAAAAGAAAAAAAA
*
35227 AAAGAGTTAGTACT-AAATAAGTATTCAGATAAAGAAAAAAAAAACAGATAAAAGATAAAAGATA
131 AAAGAGTTAGTA-TGAAATAAGTATTCAGATAAAGAAAAAAAAAACA-ACAAAAGATAAAAGATA
*
35291 TCTTACCTTAACTTAAAGTGTGTTGAAATATGGAATAGATTCGAAAAATAGCTCTCTAGACTTGA
194 TCTTACCTTAACTTAAAGTGTGTTGAAATATGGAAAAGATTCGAAAAATAGCTCTCTAGACTTGA
*
35356 GAAGCCCTTGAGTGTATTGGAATAGATTTCCTGCATATACAAAAG-AAAAAAAAGAAATAAATAT
259 GAAGCCCTTAAGTGTATTGGAATAGATTTCCTGCATATACAAAAGAAAAAAAAAGAAATAAATAT
35420 TCAGATAAAGAAAAATAAAACAACAACAGATAAAAAATAAA
324 TCAGATAAAGAAAAATAAAACAACAACAGAT--AAAATAAA
* ** *
35461 AGATAAAAGATATCTTACCTTAAGTTAAAGTGTGTTTTAATATTGAATAGATTCGAAAAATAGCT
1 AGATAAAAGATATCTTACCTTAACTTAAAGTGTGTTGAAATATGGAATAGATTCGAAAAATAGCT
* * *
35526 GTTTAGACTTGAGAAGCCCTTAAGTGTATTGGAATAGATT
66 CTATAGACTTGAGAAGCCCTTAAGTGTATTGGGATAGATT
35566 CGAAAAAAAC
Statistics
Matches: 431, Mismatches: 29, Indels: 21
0.90 0.06 0.04
Matches are distributed among these distances:
357 12 0.03
358 6 0.01
359 5 0.01
360 7 0.02
361 2 0.00
362 2 0.00
364 101 0.23
367 175 0.41
368 121 0.28
ACGTcount: A:0.47, C:0.10, G:0.17, T:0.27
Consensus pattern (362 bp):
AGATAAAAGATATCTTACCTTAACTTAAAGTGTGTTGAAATATGGAATAGATTCGAAAAATAGCT
CTATAGACTTGAGAAGCCCTTAAGTGTATTGGGATAGATTTCCTGCATATACAAAAGAAAAAAAA
AAAGAGTTAGTATGAAATAAGTATTCAGATAAAGAAAAAAAAAACAACAAAAGATAAAAGATATC
TTACCTTAACTTAAAGTGTGTTGAAATATGGAAAAGATTCGAAAAATAGCTCTCTAGACTTGAGA
AGCCCTTAAGTGTATTGGAATAGATTTCCTGCATATACAAAAGAAAAAAAAAGAAATAAATATTC
AGATAAAGAAAAATAAAACAACAACAGATAAAATAAA
Found at i:41740 original size:53 final size:55
Alignment explanation
Indices: 41635--41744 Score: 152
Period size: 53 Copynumber: 2.0 Consensus size: 55
41625 ATTGGGGTAG
* *
41635 ATTTCCTGCATATACAAAAGAAAAAAAAAGTGTTAGTATGAAATAAACATTCGGAT
1 ATTTCCTACATATAC-AAAGAAAAAAAAAGAGTTAGTATGAAATAAACATTCGGAT
* * *
41691 ATTTCCTACATATAC-AA-AAAAAAAACGAGTTAGTATGAATTAAATATTCGGAT
1 ATTTCCTACATATACAAAGAAAAAAAAAGAGTTAGTATGAAATAAACATTCGGAT
41744 A
1 A
41745 AAGAAAAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
53 33 0.67
54 2 0.04
56 14 0.29
ACGTcount: A:0.48, C:0.11, G:0.13, T:0.28
Consensus pattern (55 bp):
ATTTCCTACATATACAAAGAAAAAAAAAGAGTTAGTATGAAATAAACATTCGGAT
Found at i:41940 original size:7 final size:7
Alignment explanation
Indices: 41928--41956 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
41918 AAACAACAAC
41928 AAAAGAT
1 AAAAGAT
41935 AAAAGAT
1 AAAAGAT
41942 AAAAGAT
1 AAAAGAT
41949 AAAAGAT
1 AAAAGAT
41956 A
1 A
41957 TCTTACCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (7 bp):
AAAAGAT
Found at i:42174 original size:185 final size:189
Alignment explanation
Indices: 41783--42230 Score: 690
Period size: 185 Copynumber: 2.4 Consensus size: 189
41773 ATAACTTTAT
* * *
41783 TGTGTTGAAATATGGAATAGATTGGAAAATTAGTTGTCTAGACTTAAGAAGCCCTTAAGTGTATT
1 TGTGTTGAAATATGGAATAGATTCGAAAAATAGTTGTCTAGACTTGAGAAGCCCTTAAGTGTATT
*
41848 GGAATATATTTCCCGCATATACAAAAGAAAAAAAAGTTAGTATGAAATAAATATTCGGATAAAGA
66 GGAATAAATTTCCCGCATATACAAAAG-AAAAAAAG-TAG-ATGAAATAAATATTCGGATAAAGA
*
41913 AAAAAAAACAACAACAAAAGATAAAAGATAAAAGATAAAAGATATCTTACCTTAACTTAAAG
128 AAAAAAAACAACAACAAAAGATAAAAAATAAAAGATAAAAGATATCTTACCTTAACTTAAAG
* * * *
41975 TGTGCTGAAATATGGAATAGA-TCGAAAAATAGCTCTCTAGACTTGAGAAGCCCTTGAGTGTATT
1 TGTGTTGAAATATGGAATAGATTCGAAAAATAGTTGTCTAGACTTGAGAAGCCCTTAAGTGTATT
* *
42039 GGAATAAATTTCCTGCATATACAAAAG-AAAAAAG-A-A-GAAATAAATATTCGGATAAATAAAA
66 GGAATAAATTTCCCGCATATACAAAAGAAAAAAAGTAGATGAAATAAATATTCGGATAAAGAAAA
* *
42100 ATAAAACTACAACAACAGATAAAAAATAAAAGATAAAAGATATCTTACCTTAACTTAAAG
131 A-AAAACAACAACAAAAGATAAAAAATAAAAGATAAAAGATATCTTACCTTAACTTAAAG
* *
42160 TGTGTTGTAATATGGAATAGATTCGAAAAATAGTTGTTTAGACTTGAGAAGCCCTTAAGTGTATT
1 TGTGTTGAAATATGGAATAGATTCGAAAAATAGTTGTCTAGACTTGAGAAGCCCTTAAGTGTATT
42225 GGAATA
66 GGAATA
42231 GATTCGAAAA
Statistics
Matches: 235, Mismatches: 19, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
184 25 0.11
185 75 0.32
186 45 0.19
187 1 0.00
189 7 0.03
191 62 0.26
192 20 0.09
ACGTcount: A:0.47, C:0.10, G:0.17, T:0.27
Consensus pattern (189 bp):
TGTGTTGAAATATGGAATAGATTCGAAAAATAGTTGTCTAGACTTGAGAAGCCCTTAAGTGTATT
GGAATAAATTTCCCGCATATACAAAAGAAAAAAAGTAGATGAAATAAATATTCGGATAAAGAAAA
AAAAACAACAACAAAAGATAAAAAATAAAAGATAAAAGATATCTTACCTTAACTTAAAG
Found at i:43967 original size:155 final size:156
Alignment explanation
Indices: 43684--43992 Score: 394
Period size: 155 Copynumber: 2.0 Consensus size: 156
43674 TACCAGTAGG
* * * *
43684 CTTAGATTATCATCTTAAGACTATGGTAAAAATTTCAAGTAAAACCGAGCCCCCCTTGATGGTGA
1 CTTAGATTATCATCATAAGACTATGGAAAAAATTTCAAGTAAAACCGAGACCCCCTTCATGGTGA
* * * *
43749 ACTAGGTTTCTCTCCCTAAATTGTCCTTAAATGAAAAACTAGCATAAATTTTTCATTCTAAGTCT
66 ACTAGGTTTCTCACCCAAAACTGTCCTTAAATGAAAAACTAGCATAAATTTTTCATTCTAAGTCC
*
43814 GTTTCAGATGAAACTTGGCCAAGAGA
131 GTTTCAGATGAAACTTAGCCAAGAGA
* *
43840 CTTAGATTATC-TCCATAA-ACTTATGGAAAAAATTTTAAGTAAAACCGA-ACTCCCTATCATGG
1 CTTAGATTATCAT-CATAAGAC-TATGGAAAAAATTTCAAGTAAAACCGAGACCCCCT-TCATGG
* * * *
43902 TGAAGT-GGTTTCTCACCCAAAACTGTCCTTAATTGAAAAACTTGCATAAGTTTTTCA-TCTTAA
63 TGAACTAGGTTTCTCACCCAAAACTGTCCTTAAATGAAAAACTAGCATAAATTTTTCATTC-TAA
* *
43965 GTCCGTTTGAGATGAAATTTAGCCAAGA
127 GTCCGTTTCAGATGAAACTTAGCCAAGA
43993 TAGTCTACAT
Statistics
Matches: 132, Mismatches: 17, Indels: 9
0.84 0.11 0.06
Matches are distributed among these distances:
154 2 0.02
155 80 0.61
156 50 0.38
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (156 bp):
CTTAGATTATCATCATAAGACTATGGAAAAAATTTCAAGTAAAACCGAGACCCCCTTCATGGTGA
ACTAGGTTTCTCACCCAAAACTGTCCTTAAATGAAAAACTAGCATAAATTTTTCATTCTAAGTCC
GTTTCAGATGAAACTTAGCCAAGAGA
Found at i:51994 original size:155 final size:156
Alignment explanation
Indices: 51711--52019 Score: 414
Period size: 155 Copynumber: 2.0 Consensus size: 156
51701 GACCAGTAGG
* * *
51711 CTTAGATTATCATCCTAAGACTATGGTAAAAATTTCAAGTAAAACCGAGCCCCCATTGATGGTGA
1 CTTAGATTATCATCCTAAGACTATGGAAAAAATTTCAAGTAAAACCGAACCCCCATTCATGGTGA
* * * * *
51776 ACTAGGTTTCTCTCCCTAAATTATCCTTAAATGAAAAACTAGCATAAGTTTTTTATTCTAAGTCT
66 ACTAGGTTTCTCACCCCAAACTATCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCC
51841 GTTTGAGATGAAACTTT-GCCAAGAGA
131 GTTTGAGATGAAA-TTTAGCCAAGAGA
* *
51867 CTTAGATTATC-TCCATAA-ACTTATGGAAAAAATTTTAAGTAAAACCGAACTCCC-TATCATGG
1 CTTAGATTATCATCC-TAAGAC-TATGGAAAAAATTTCAAGTAAAACCGAACCCCCAT-TCATGG
* * *
51929 TGAAGT-GGTTTCTCACCCCAAACTATCCTTAACTGAAAAACTTGCATAAGTTTTTCA-TCTTAA
63 TGAACTAGGTTTCTCACCCCAAACTATCCTTAAATGAAAAACTAGCATAAGTTTTTCATTC-TAA
51992 GTCCGTTTGAGATGAAATTTAGCCAAGA
127 GTCCGTTTGAGATGAAATTTAGCCAAGA
52020 TAGTCCACAT
Statistics
Matches: 135, Mismatches: 13, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
154 5 0.04
155 77 0.57
156 53 0.39
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (156 bp):
CTTAGATTATCATCCTAAGACTATGGAAAAAATTTCAAGTAAAACCGAACCCCCATTCATGGTGA
ACTAGGTTTCTCACCCCAAACTATCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCC
GTTTGAGATGAAATTTAGCCAAGAGA
Found at i:55387 original size:17 final size:17
Alignment explanation
Indices: 55340--55392 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
55330 AGAATACAAT
55340 ATAACCT-TCATAAATTA
1 ATAACCTCTC-TAAATTA
**
55357 AT-A-CTCGATAAATTA
1 ATAACCTCTCTAAATTA
55372 ATAACCTCTCTAAATTA
1 ATAACCTCTCTAAATTA
55389 ATAA
1 ATAA
55393 TTTTTTATAG
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
15 11 0.38
16 2 0.07
17 16 0.55
ACGTcount: A:0.47, C:0.17, G:0.02, T:0.34
Consensus pattern (17 bp):
ATAACCTCTCTAAATTA
Found at i:55447 original size:76 final size:76
Alignment explanation
Indices: 55349--55497 Score: 244
Period size: 76 Copynumber: 2.0 Consensus size: 76
55339 TATAACCTTC
* * *
55349 ATAAATTAATACTCGATAAATTAATAACCTCTCTAAATTAATAATTTTTTATAGTCCCAACATTA
1 ATAAATTAACACTAGATAAATTAATAACCTCTCTAAATTAATAATTTTTCATAGTCCCAACATTA
55414 TTAATTTCCAT
66 TTAATTTCCAT
* * *
55425 ATAAATTAGCACTAGATAAATTAATAACCTCTCTAATTTAATAATTTTTCATGGTCCCAACATTA
1 ATAAATTAACACTAGATAAATTAATAACCTCTCTAAATTAATAATTTTTCATAGTCCCAACATTA
55490 TTAATTTC
66 TTAATTTC
55498 TAGAGGTTTT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
76 67 1.00
ACGTcount: A:0.40, C:0.16, G:0.04, T:0.40
Consensus pattern (76 bp):
ATAAATTAACACTAGATAAATTAATAACCTCTCTAAATTAATAATTTTTCATAGTCCCAACATTA
TTAATTTCCAT
Found at i:58495 original size:166 final size:167
Alignment explanation
Indices: 58185--58506 Score: 452
Period size: 166 Copynumber: 1.9 Consensus size: 167
58175 TTGTCAATTG
* * *
58185 AGAAATGACCAATAAGTTTAGTTATTTAATCCCCTCAAGAATAAAAAATTAGGACATTTAAGTAA
1 AGAAATGACCAAAAAGATTAGTTATTTAATCCCCTCAAGAATAAAAAATTAGAACATTTAAGTAA
* * * * ** * *
58250 TCTGCCAAGTAGGTAAAGACGAAAAAATGTTAGTTCTCTAGCTCATCATCAATCCTTGAAGGGGA
66 TCTGCCAAGTAGGAAAAGACGAAAAAATATAAGTTCTCTAACTCAAAAGCAAGCCTTGAAGGGGA
*
58315 TCATTTATTAATTCCACTACTCTATTCAAATCCATTT
131 TCATTTAGTAATTCCACTACTCTATTCAAATCCATTT
* *
58352 AGAAATGACCAAAAAGATTA-TTATTTAATCCCCTCAAGAATCAAAAGTTAGAACATTTAAGTAA
1 AGAAATGACCAAAAAGATTAGTTATTTAATCCCCTCAAGAATAAAAAATTAGAACATTTAAGTAA
* *
58416 TCTGCCAAGTAGGAAAAGATGAAAAAA-ATAAGTTCTCTAACTCCAAAAGCAAGCCTTGTTA-GG
66 TCTGCCAAGTAGGAAAAGACGAAAAAATATAAGTTCTCTAACT-CAAAAGCAAGCCTTG-AAGGG
*
58479 GATCTTTTAGTAATTCCACTACTCTATT
129 GATCATTTAGTAATTCCACTACTCTATT
58507 AAAGTTTAGG
Statistics
Matches: 136, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
165 12 0.09
166 105 0.77
167 19 0.14
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.30
Consensus pattern (167 bp):
AGAAATGACCAAAAAGATTAGTTATTTAATCCCCTCAAGAATAAAAAATTAGAACATTTAAGTAA
TCTGCCAAGTAGGAAAAGACGAAAAAATATAAGTTCTCTAACTCAAAAGCAAGCCTTGAAGGGGA
TCATTTAGTAATTCCACTACTCTATTCAAATCCATTT
Found at i:58850 original size:2 final size:2
Alignment explanation
Indices: 58843--58868 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
58833 TAATATGTAG
58843 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
58869 CTAGACACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:63292 original size:36 final size:36
Alignment explanation
Indices: 63245--63316 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
63235 TCGCAGATAG
63245 ATCTTTGGCTAGAAATGTTCTGGCATGTTTCCTTCC
1 ATCTTTGGCTAGAAATGTTCTGGCATGTTTCCTTCC
63281 ATCTTTGGCTAGAAATGTTCTGGCATGTTTCCTTCC
1 ATCTTTGGCTAGAAATGTTCTGGCATGTTTCCTTCC
63317 CCCTCTCCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (36 bp):
ATCTTTGGCTAGAAATGTTCTGGCATGTTTCCTTCC
Found at i:64350 original size:19 final size:19
Alignment explanation
Indices: 64326--64362 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
64316 GGTTCTTTTG
64326 ATTCTTGCTGAAGTTATTT
1 ATTCTTGCTGAAGTTATTT
* *
64345 ATTCTTTCTGGAGTTATT
1 ATTCTTGCTGAAGTTATT
64363 CTTGCAACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.19, C:0.11, G:0.16, T:0.54
Consensus pattern (19 bp):
ATTCTTGCTGAAGTTATTT
Found at i:66109 original size:70 final size:70
Alignment explanation
Indices: 66027--66259 Score: 306
Period size: 70 Copynumber: 3.2 Consensus size: 70
66017 TTGTTTAGGT
* *
66027 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAATT
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAATT
66091 ATTTTA
65 ATTTTA
66097 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAGCTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATAT-CTT-TA--TA
*
66162 TTATATTTTACCA
62 AT-TATTTT---A
* * *
66175 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAATTA
*
66240 TTATA
66 TTTTA
*
66245 TTTTACAATTTTACT
1 TTTTACTATTTTACT
66260 ATTTTAGTTA
Statistics
Matches: 145, Mismatches: 9, Indels: 18
0.84 0.05 0.10
Matches are distributed among these distances:
70 64 0.44
71 5 0.03
72 2 0.01
73 5 0.03
74 5 0.03
75 6 0.04
76 2 0.01
77 2 0.01
78 54 0.37
ACGTcount: A:0.37, C:0.13, G:0.01, T:0.49
Consensus pattern (70 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAATTA
TTTTA
Found at i:66109 original size:78 final size:77
Alignment explanation
Indices: 66027--66265 Score: 350
Period size: 78 Copynumber: 3.2 Consensus size: 77
66017 TTGTTTAGGT
* *
66027 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATAT-CTT-T-A-T
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACT
*
66087 AAT-TATTTT--A
65 ATTATATTTTACA
*
66097 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAGCTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
66162 TTATATTTTACCA
66 TTATATTTTA-CA
*
66175 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
66240 TTATATTTTACAA
66 TTATATTTTAC-A
66253 TTTTACTATTTTA
1 TTTTACTATTTTA
66266 GTTAAAAAAA
Statistics
Matches: 153, Mismatches: 6, Indels: 12
0.89 0.04 0.07
Matches are distributed among these distances:
70 49 0.32
71 5 0.03
72 1 0.01
74 3 0.02
75 6 0.04
77 1 0.01
78 88 0.58
ACGTcount: A:0.37, C:0.13, G:0.01, T:0.50
Consensus pattern (77 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
TTATATTTTACA
Found at i:72431 original size:1 final size:1
Alignment explanation
Indices: 72425--72449 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
72415 TTTTGTTTAG
72425 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
72450 GGCACAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:74724 original size:15 final size:15
Alignment explanation
Indices: 74703--74744 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
74693 CATCAAAGTT
74703 TCTTTTTCTTTTTAAC
1 TCTTTTTCTTTTT-AC
* *
74719 -CTTTTTATTTTTCC
1 TCTTTTTCTTTTTAC
74733 TCTTTTTCTTTT
1 TCTTTTTCTTTT
74745 CCATTTTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 1 0.05
15 21 0.95
ACGTcount: A:0.07, C:0.19, G:0.00, T:0.74
Consensus pattern (15 bp):
TCTTTTTCTTTTTAC
Done.