Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004276.1 Hibiscus syriacus cultivar Beakdansim tig00009373_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 124863
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:1800 original size:185 final size:181
Alignment explanation
Indices: 1572--1948 Score: 677
Period size: 185 Copynumber: 2.1 Consensus size: 181
1562 TAGATTGCTT
1572 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1637 TTTGTCTTT-TTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAA--TGTTCGGTTGCTGCCAATTCTGCTAAACT
1701 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
129 GTGTATTC---AACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
1756 AGTAAATTTGTTCGGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGT
1 AGTAAATTTATTCGG-TTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGT
1821 ATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATGTTCGGTTGCTGCCAATTCTGCTAAACTG
65 ATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATGTTCGGTTGCTGCCAATTCTGCTAAACTG
1886 TGTATTCAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
130 TGTATTCAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1938 AGTAAATTTAT
1 AGTAAATTTAT
1949 CCATTCAAGT
Statistics
Matches: 188, Mismatches: 2, Indels: 8
0.95 0.01 0.04
Matches are distributed among these distances:
181 14 0.07
182 40 0.21
184 51 0.27
185 59 0.31
186 24 0.13
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (181 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATGTTCGGTTGCTGCCAATTCTGCTAAACTGT
GTATTCAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1817 original size:93 final size:93
Alignment explanation
Indices: 1572--1946 Score: 683
Period size: 92 Copynumber: 4.1 Consensus size: 93
1562 TAGATTGCTT
*
1572 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1637 TTTGTCTTT-TTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1664 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1728 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1756 AGTAAATTTGTTCGGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGT
1 AGTAAATTTGTTCGG-TTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGT
1821 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
65 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1850 AGTAAA--TGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTC---AACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1910 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1938 AGTAAATTT
1 AGTAAATTT
1947 ATCCATTCAA
Statistics
Matches: 277, Mismatches: 1, Indels: 12
0.96 0.00 0.04
Matches are distributed among these distances:
88 51 0.18
90 1 0.00
91 41 0.15
92 101 0.36
93 47 0.17
94 36 0.13
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:2030 original size:19 final size:19
Alignment explanation
Indices: 1990--2117 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
1980 TAGTTTACTT
* *
1990 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
2010 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
2029 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
2048 TCGCAA--CG--A-C-AGA
1 TCGCAACGCGAAACCAAAA
2061 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
2080 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
2094 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
2113 TCGCA
1 TCGCA
2118 TTGCGATTTT
Statistics
Matches: 88, Mismatches: 9, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
13 8 0.09
14 10 0.11
15 4 0.05
16 2 0.02
17 5 0.06
18 2 0.02
19 44 0.50
20 13 0.15
ACGTcount: A:0.45, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:2069 original size:32 final size:33
Alignment explanation
Indices: 2028--2117 Score: 155
Period size: 32 Copynumber: 2.8 Consensus size: 33
2018 CGAAACCAAA
**
2028 ATCGCAACGCGAAATGAAAATCGCAACGAC-AG
1 ATCGCAACGCGAAACCAAAATCGCAACGACAAG
2060 ATCGCAACGCGAAACCAAAATCGCAACGACAAG
1 ATCGCAACGCGAAACCAAAATCGCAACGACAAG
2093 ATCGCAACGCGAAACCAAAATCGCA
1 ATCGCAACGCGAAACCAAAATCGCA
2118 TTGCGATTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 28 0.51
33 27 0.49
ACGTcount: A:0.44, C:0.29, G:0.19, T:0.08
Consensus pattern (33 bp):
ATCGCAACGCGAAACCAAAATCGCAACGACAAG
Found at i:2135 original size:19 final size:19
Alignment explanation
Indices: 2113--2246 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
2103 GAAACCAAAA
*
2113 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2132 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
2148 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
2165 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
2181 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
2198 TCGCGTTGCGATTTT-GTT
1 TCGCGTTGCGATTTTCATT
*
2216 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
2236 TCGTGTTGCGA
1 TCGCGTTGCGA
2247 AAGTAAACTA
Statistics
Matches: 97, Mismatches: 6, Indels: 23
0.77 0.05 0.18
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
18 17 0.18
19 30 0.31
20 12 0.12
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2154 original size:14 final size:14
Alignment explanation
Indices: 2135--2191 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2125 TTTCATTTCG
2135 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
2149 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
2166 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
2182 CGTTGCGATT
1 CGTTGCGATT
2192 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.09, C:0.21, G:0.25, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:2160 original size:33 final size:33
Alignment explanation
Indices: 2118--2246 Score: 177
Period size: 33 Copynumber: 3.8 Consensus size: 33
2108 CAAAATCGCA
2118 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
*
2151 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
*
2184 TTGCGATTTTCATTTCGCGTTGCGATTTTGTTTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGA--TTCTTT--CG
* *
2221 TTGCGATTTTAAGTTTCGTGTTGCGA
1 TTGCGATTTTCA-TTTCGCGTTGCGA
2247 AAGTAAACTA
Statistics
Matches: 86, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
33 57 0.66
35 4 0.05
37 13 0.15
38 12 0.14
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
Found at i:4088 original size:38 final size:38
Alignment explanation
Indices: 4046--4118 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
4036 AATTGATTGT
*
4046 TTTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
4084 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
4119 TGTAAAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.53
Consensus pattern (38 bp):
TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
Found at i:4105 original size:19 final size:19
Alignment explanation
Indices: 4041--4105 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
4031 AGTTTAATTG
*
4041 ATTGTTTTTTGATTGTTTA
1 ATTGATTTTTGATTGTTTA
* * ** *
4060 ATTGATTTGTAAAAG-TTG
1 ATTGATTTTTGATTGTTTA
*
4078 ATTCAATTTTTGATTGTTTA
1 ATT-GATTTTTGATTGTTTA
4098 ATTGATTT
1 ATTGATTT
4106 GTAAAAGATG
Statistics
Matches: 31, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
18 5 0.16
19 21 0.68
20 5 0.16
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (19 bp):
ATTGATTTTTGATTGTTTA
Found at i:4119 original size:14 final size:14
Alignment explanation
Indices: 4100--4135 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
4090 ATTGTTTAAT
4100 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
4114 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
4128 TGATTTGT
1 TGATTTGT
4136 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:4254 original size:19 final size:19
Alignment explanation
Indices: 4238--4339 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
4228 AAAAATGACT
4238 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
4257 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
4276 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
4290 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
4309 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
4329 ATCGCAATGCG
1 ATCGCAATGCG
4340 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:4392 original size:19 final size:19
Alignment explanation
Indices: 4368--4693 Score: 396
Period size: 19 Copynumber: 18.4 Consensus size: 19
4358 GATTATCTCG
4368 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4387 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4406 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
4420 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4439 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
4458 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
4477 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
4496 TTGCGCTTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
4515 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
4529 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4548 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
4567 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
4581 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4600 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
4619 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
4633 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
4653 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
4667 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
4686 TTGCGATT
1 TTGCGATT
4694 GTATTTTCCG
Statistics
Matches: 267, Mismatches: 14, Indels: 52
0.80 0.04 0.16
Matches are distributed among these distances:
14 35 0.13
16 31 0.12
17 28 0.10
18 3 0.01
19 158 0.59
20 12 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:4408 original size:52 final size:52
Alignment explanation
Indices: 4346--4665 Score: 541
Period size: 52 Copynumber: 6.0 Consensus size: 52
4336 TGCGTTTATA
*
4346 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
4398 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* * *
4450 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGCTTTTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
4507 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
4559 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
4611 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
4664 AT
1 AT
4666 GTTGGGATTT
Statistics
Matches: 255, Mismatches: 7, Indels: 11
0.93 0.03 0.04
Matches are distributed among these distances:
52 181 0.71
53 17 0.07
54 7 0.03
55 8 0.03
57 42 0.16
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:4443 original size:71 final size:72
Alignment explanation
Indices: 4368--4693 Score: 380
Period size: 71 Copynumber: 4.6 Consensus size: 72
4358 GATTATCTCG
4368 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCG-TTGCGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCA
4432 TTTCGCA
66 TTTCGCA
* * *
4439 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGCTT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TT-CTTTCG-ATTGCGATT
4504 TTCATTTCGCA
62 TTCATTTCGCA
*
4515 TTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG-ATTGCGATT
*
4573 TTC-TCTCG--
62 TTCATTTCGCA
*
4581 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG-TTGCGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCA
4645 TTTCCGCA
66 TTT-CGCA
* *
4653 TTGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
4694 GTATTTTCCG
Statistics
Matches: 225, Mismatches: 13, Indels: 38
0.82 0.05 0.14
Matches are distributed among these distances:
66 12 0.05
67 25 0.11
68 14 0.06
69 13 0.06
70 3 0.01
71 108 0.48
72 12 0.05
73 6 0.03
74 8 0.04
76 24 0.11
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (72 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCA
TTTCGCA
Found at i:4611 original size:161 final size:157
Alignment explanation
Indices: 4346--4665 Score: 543
Period size: 161 Copynumber: 2.0 Consensus size: 157
4336 TGCGTTTATA
4346 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
* *
4411 ATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGT
66 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG-
*
4476 ATTGCGATTTTAATTT-CGCATTGCGCTTTTC
127 -TTGCGATTTTAATTTCCGCATTGCGATTTTC
*
4507 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
4572 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
66 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
*
4637 GATTTTCATTTCCGCATTGCGATTTTC
131 GATTTTAATTTCCGCATTGCGATTTTC
4664 AT
1 AT
4666 GTTGGGATTT
Statistics
Matches: 153, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
156 14 0.09
157 16 0.10
158 4 0.03
159 3 0.02
161 116 0.76
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (157 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
GATTTTAATTTCCGCATTGCGATTTTC
Found at i:4637 original size:33 final size:33
Alignment explanation
Indices: 4387--4693 Score: 271
Period size: 33 Copynumber: 8.8 Consensus size: 33
4377 TCATTTCGCA
*
4387 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
4420 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * *
4456 CATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCG
1 --TTGCGATTTTCATTTCGCATTGCGA--TT-CTCTCG
*
4494 CATTGCGCTTTTCATTTCGCATTGCGATTCTCTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
4529 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
4565 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
4600 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
4633 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
* *
4667 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
4694 GTATTTTCCG
Statistics
Matches: 233, Mismatches: 22, Indels: 38
0.80 0.08 0.13
Matches are distributed among these distances:
31 9 0.04
32 5 0.02
33 86 0.37
34 29 0.12
35 13 0.06
36 11 0.05
37 2 0.01
38 66 0.28
39 3 0.01
40 9 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:7218 original size:24 final size:24
Alignment explanation
Indices: 7184--7230 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
7174 CTGAAACATC
7184 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
7208 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
7231 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:7929 original size:20 final size:20
Alignment explanation
Indices: 7901--8269 Score: 449
Period size: 20 Copynumber: 18.4 Consensus size: 20
7891 AAAATTCAGT
* * * *
7901 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
7921 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
7941 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
7961 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
7981 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
8001 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
8021 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
8041 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
8061 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
8081 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
8101 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
8121 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
8141 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* * **
8161 ATTGTGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
8181 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
8201 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
8221 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
8241 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
8261 GTTGCGATT
1 GTTGCGATT
8270 ATGGAAAATC
Statistics
Matches: 307, Mismatches: 34, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
19 5 0.02
20 297 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:10943 original size:31 final size:32
Alignment explanation
Indices: 10880--10944 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 32
10870 ATTTGGGTTT
**
10880 GGATTTTTTTTAAAAAAAATCGGGATTGAGTC
1 GGATTTTTTTTAAAAAAAATCGGGATCAAGTC
10912 GGATTTTTTTT-AAAAAAATCGAGG-TCAAGTC
1 GGATTTTTTTTAAAAAAAATCG-GGATCAAGTC
10943 GG
1 GG
10945 GTCGGGTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
31 17 0.57
32 13 0.43
ACGTcount: A:0.34, C:0.08, G:0.23, T:0.35
Consensus pattern (32 bp):
GGATTTTTTTTAAAAAAAATCGGGATCAAGTC
Found at i:11564 original size:18 final size:18
Alignment explanation
Indices: 11541--11588 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
11531 AAACAGGTTT
*
11541 CAGATTCTAGTTCCTTCA
1 CAGATTCTAATTCCTTCA
*
11559 CAGATT-TCAATTCTTTCA
1 CAGATTCT-AATTCCTTCA
11577 CAGATTCTAATT
1 CAGATTCTAATT
11589 TCCTCATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 1 0.04
18 24 0.92
19 1 0.04
ACGTcount: A:0.27, C:0.23, G:0.08, T:0.42
Consensus pattern (18 bp):
CAGATTCTAATTCCTTCA
Found at i:28044 original size:33 final size:33
Alignment explanation
Indices: 27979--28044 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
27969 AATTTAAAAG
**
27979 AAAGATTTATAGAAATAAAGTGGGTTTTAAATT
1 AAAGATTTATAGAAATAAAGTGGGTTCAAAATT
*
28012 AAAGATTTATAGTAATAAAGTGGGTTCAAAATT
1 AAAGATTTATAGAAATAAAGTGGGTTCAAAATT
28045 GAGTTGTGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.45, C:0.02, G:0.18, T:0.35
Consensus pattern (33 bp):
AAAGATTTATAGAAATAAAGTGGGTTCAAAATT
Found at i:28955 original size:30 final size:30
Alignment explanation
Indices: 28837--28985 Score: 126
Period size: 31 Copynumber: 4.8 Consensus size: 30
28827 ATTATTTATA
* *
28837 TATCTTAACTTTAAAAATATATTTTGTTTCT
1 TATCTTTACTTTAAAAATATATTTT-ATTCT
*
28868 GT-TTTAATTA-TTTAAAAATATATTTTATTCT
1 -TATCT--TTACTTTAAAAATATATTTTATTCT
28899 TATCTTTAC-TTAAACATATATATTTTATTCT
1 TATCTTTACTTTAAA-A-ATATATTTTATTCT
* *
28930 TAT-TTTACCTTTAAAAATGTTTTTTATTCT
1 TATCTTTA-CTTTAAAAATATATTTTATTCT
* * *
28960 TACCTTAATTTTTAAAAATATATTTT
1 TATCTTTA-CTTTAAAAATATATTTT
28986 TAAAATATAT
Statistics
Matches: 96, Mismatches: 12, Indels: 19
0.76 0.09 0.15
Matches are distributed among these distances:
29 8 0.08
30 20 0.21
31 44 0.46
32 22 0.23
33 2 0.02
ACGTcount: A:0.33, C:0.09, G:0.02, T:0.56
Consensus pattern (30 bp):
TATCTTTACTTTAAAAATATATTTTATTCT
Found at i:28990 original size:13 final size:14
Alignment explanation
Indices: 28967--28996 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
28957 TCTTACCTTA
28967 ATTTTTAAAAATAT
1 ATTTTTAAAAATAT
28981 ATTTTT-AAAATAT
1 ATTTTTAAAAATAT
28994 ATT
1 ATT
28997 AGCTTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTTTTAAAAATAT
Found at i:29061 original size:25 final size:24
Alignment explanation
Indices: 29027--29100 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 24
29017 AAGATATTTT
*
29027 AGAAAAAAATATATTTTTAAAATCA
1 AGAATAAAATATATTTTTAAAAT-A
29052 AGAATAAAATATATTTTTAAGTTGAAATA
1 AGAATAAAATATATTTTT-A----AAATA
29081 AGAATAAAATATATTTTTAA
1 AGAATAAAATATATTTTTAA
29101 GTGAATATAT
Statistics
Matches: 43, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
24 1 0.02
25 17 0.40
26 1 0.02
28 1 0.02
29 19 0.44
30 4 0.09
ACGTcount: A:0.55, C:0.01, G:0.07, T:0.36
Consensus pattern (24 bp):
AGAATAAAATATATTTTTAAAATA
Found at i:29087 original size:29 final size:29
Alignment explanation
Indices: 29043--29343 Score: 157
Period size: 29 Copynumber: 9.8 Consensus size: 29
29033 AAATATATTT
29043 TTAAAATCAAGAATAAAATATATTTTTA-A
1 TTAAAAT-AAGAATAAAATATATTTTTATA
*
29072 GTTGAAATAAGAATAAAATATATTTTTA-A
1 -TTAAAATAAGAATAAAATATATTTTTATA
* * * *
29101 GTGAATATATGAA-AAAAGTATATATATTATA
1 -TTAAAATAAGAATAAAA-TATAT-TTTTATA
* *
29132 TTAAAATAAGAATAATATATATATATATATA
1 TTAAAATAAGAATAA-A-ATATATTTTTATA
* *
29163 TTAAAATAAGAATAAAATAT-TTAAATATATT
1 TTAAAATAAGAATAAAATATATT---TTTATA
*** ** *
29194 TTATGCTAAGACATTTTAAAGCATATATTTTAAAAAA
1 TTAAAATAAGA-A---TAAAATATAT-TTTT---ATA
* *
29231 GTTAAGATAA-AATAAAATATATTTTTCAAA
1 -TTAAAATAAGAATAAAATATATTTTT-ATA
*
29261 TTAAAATAAGAATACAATATA-TTTTA-A
1 TTAAAATAAGAATAAAATATATTTTTATA
* *
29288 ATAAAGATAAGAATAAGATATATGTTTTTATA
1 TTAAA-ATAAGAATAA-A-ATATATTTTTATA
*
29320 TTAAAATAAGAATAAATTATATTT
1 TTAAAATAAGAATAAAATATATTT
29344 AATAAGGTAA
Statistics
Matches: 211, Mismatches: 35, Indels: 51
0.71 0.12 0.17
Matches are distributed among these distances:
27 5 0.02
28 15 0.07
29 58 0.27
30 38 0.18
31 50 0.24
32 16 0.08
33 9 0.04
34 2 0.01
35 6 0.03
36 2 0.01
37 3 0.01
38 7 0.03
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (29 bp):
TTAAAATAAGAATAAAATATATTTTTATA
Found at i:29166 original size:31 final size:31
Alignment explanation
Indices: 29035--29371 Score: 127
Period size: 31 Copynumber: 11.0 Consensus size: 31
29025 TTAGAAAAAA
*
29035 ATATAT-TTTTAAAATCAAGAATAAAATATAT
1 ATATATATATTAAAAT-AAGAATAAAATATAT
* *
29066 -T-TTTA-AGTTGAAATAAGAATAAAATATAT
1 ATATATATA-TTAAAATAAGAATAAAATATAT
* * * *
29095 -T-TTTA-AGTGAATATATGAA-AAAAGTATAT
1 ATATATATA-TTAAAATAAGAATAAAA-TATAT
*
29124 ATAT-TATATTAAAATAAGAATAATATATAT
1 ATATATATATTAAAATAAGAATAAAATATAT
*
29154 ATATATATATTAAAATAAGAATAAAATATTT
1 ATATATATATTAAAATAAGAATAAAATATAT
* * ***
29185 AAATATATTTTATGCTAAGACATTTTAAAGCATATAT
1 ATATATATATTAAAATAAGA-A---TAAA--ATATAT
* * * *
29222 -TTTAAAAAAGTTAAGATAA-AATAAAATATAT
1 ATAT-ATATA-TTAAAATAAGAATAAAATATAT
* * *
29253 -T-TTTCAAATTAAAATAAGAATACAATATAT
1 ATATAT-ATATTAAAATAAGAATAAAATATAT
* *
29283 -T-T-TA-AATAAAGATAAGAATAAGATATAT
1 ATATATATATTAAA-ATAAGAATAAAATATAT
* * * *
29311 GTTTTTATATTAAAATAAGAATAAATTATAT
1 ATATATATATTAAAATAAGAATAAAATATAT
* * * *
29342 TTA-ATA-AGGTAAGATAAAAATAAAATATAT
1 ATATATATA-TTAAAATAAGAATAAAATATAT
29372 TTGAAAAAAT
Statistics
Matches: 239, Mismatches: 43, Indels: 49
0.72 0.13 0.15
Matches are distributed among these distances:
27 5 0.02
28 20 0.08
29 48 0.20
30 66 0.28
31 69 0.29
32 6 0.03
33 4 0.02
35 4 0.02
36 2 0.01
37 8 0.03
38 7 0.03
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (31 bp):
ATATATATATTAAAATAAGAATAAAATATAT
Found at i:29288 original size:61 final size:59
Alignment explanation
Indices: 29216--29373 Score: 180
Period size: 61 Copynumber: 2.6 Consensus size: 59
29206 ATTTTAAAGC
29216 ATATATTTTAAAAAAGTTAAGATAAAATAAAATATATTTTTCAAATTAAAATAAGAATACA
1 ATATATTTT-AAAAAGTTAAGATAAAATAAAATATATTTTTCAAATTAAAATAAGAATA-A
* * * *
29277 ATATATTTT--AAA-TAAAGATAAGAATAAGATATATGTTTTTATATTAAAATAAGAATAA
1 ATATATTTTAAAAAGTTAAGATAA-AATAAAATATAT-TTTTCAAATTAAAATAAGAATAA
* *
29335 AT-TATATTTAATAAGGTAAGATAAAAATAAAATATATTT
1 ATATAT-TTTAAAAAGTTAAGAT-AAAATAAAATATATTT
29374 GAAAAAATTA
Statistics
Matches: 82, Mismatches: 8, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
57 11 0.13
58 20 0.24
59 20 0.24
60 4 0.05
61 25 0.30
62 2 0.02
ACGTcount: A:0.55, C:0.01, G:0.07, T:0.37
Consensus pattern (59 bp):
ATATATTTTAAAAAGTTAAGATAAAATAAAATATATTTTTCAAATTAAAATAAGAATAA
Found at i:29297 original size:28 final size:29
Alignment explanation
Indices: 29234--29343 Score: 104
Period size: 28 Copynumber: 3.7 Consensus size: 29
29224 TAAAAAAGTT
29234 AAGATAA-AATAAAATATATTTTTCAAATTA
1 AAGATAAGAAT-AAATATA-TTTTCAAATTA
29264 AA-ATAAGAATACAATATATTTT-AAA-TA
1 AAGATAAGAATA-AATATATTTTCAAATTA
* *
29291 AAGATAAGAATAAGATATATGTTTTTATATTA
1 AAGATAAGAATAA-ATATA--TTTTCAAATTA
29323 AA-ATAAGAATAAATTATATTT
1 AAGATAAGAATAAA-TATATTT
29344 AATAAGGTAA
Statistics
Matches: 70, Mismatches: 1, Indels: 19
0.78 0.01 0.21
Matches are distributed among these distances:
27 5 0.07
28 17 0.24
29 12 0.17
30 16 0.23
31 16 0.23
32 4 0.06
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (29 bp):
AAGATAAGAATAAATATATTTTCAAATTA
Found at i:29330 original size:59 final size:57
Alignment explanation
Indices: 29234--29373 Score: 167
Period size: 59 Copynumber: 2.4 Consensus size: 57
29224 TAAAAAAGTT
29234 AAGATAAAATAAAATATATTTTTCAAATTAAAATAAGAATACAA-TATATTTTAAATA
1 AAGATAAAATAAAATATATTTTTCAAATTAAAATAAGAATA-AATTATATTTTAAATA
* * * *
29291 AAGATAAGAATAAGATATATGTTTTTATATTAAAATAAGAATAAATTATATTTAATAAGGT-
1 AAGATAA-AATAAAATATAT-TTTTCAAATTAAAATAAGAATAAATTATATTT--TAA-ATA
29352 AAGATAAAAATAAAATATATTT
1 AAGAT-AAAATAAAATATATTT
29374 GAAAAAATTA
Statistics
Matches: 71, Mismatches: 5, Indels: 11
0.82 0.06 0.13
Matches are distributed among these distances:
57 7 0.10
58 13 0.18
59 27 0.38
60 2 0.03
61 19 0.27
62 3 0.04
ACGTcount: A:0.56, C:0.01, G:0.07, T:0.36
Consensus pattern (57 bp):
AAGATAAAATAAAATATATTTTTCAAATTAAAATAAGAATAAATTATATTTTAAATA
Found at i:32264 original size:27 final size:26
Alignment explanation
Indices: 32226--32281 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
32216 AATAAAAAAA
* * *
32226 TAAAAAATTAATTTCATGATTATAAT
1 TAAAAAATTAATATAAGGATTATAAT
*
32252 TAAAAATTATAATATAAGGATTATAAT
1 TAAAAAAT-TAATATAAGGATTATAAT
32279 TAA
1 TAA
32282 GATAATTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (26 bp):
TAAAAAATTAATATAAGGATTATAAT
Found at i:32282 original size:13 final size:13
Alignment explanation
Indices: 32243--32282 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
32233 TTAATTTCAT
*
32243 GATTATAATTAAA
1 GATTATAATTAAG
*
32256 AATTATAATATAAG
1 GATTATAAT-TAAG
32270 GATTATAATTAAG
1 GATTATAATTAAG
32283 ATAATTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.38
Consensus pattern (13 bp):
GATTATAATTAAG
Found at i:40714 original size:26 final size:28
Alignment explanation
Indices: 40684--40745 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 28
40674 AAAAATTTTA
40684 AGCTC-GC-GAGTTTTCGAGTCGAGTCG
1 AGCTCTGCAGAGTTTTCGAGTCGAGTCG
*
40710 AGCTCCATTTCAGAGTTTTCGAGTCGAGTCG
1 AGCT-C--TGCAGAGTTTTCGAGTCGAGTCG
40741 AGCTC
1 AGCTC
40746 AACAATACTC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
26 4 0.13
27 1 0.03
30 2 0.07
31 23 0.77
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (28 bp):
AGCTCTGCAGAGTTTTCGAGTCGAGTCG
Found at i:42914 original size:30 final size:30
Alignment explanation
Indices: 42875--42931 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
42865 CTATCTTGTG
* *
42875 TTTTCTTGCATTTTAGTCAATATAATTAGA
1 TTTTATTGCATTTTAGTCAACATAATTAGA
42905 TTTTATTGCATTTTAGTCAACATAATT
1 TTTTATTGCATTTTAGTCAACATAATT
42932 TTATGTTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.51
Consensus pattern (30 bp):
TTTTATTGCATTTTAGTCAACATAATTAGA
Found at i:43148 original size:30 final size:29
Alignment explanation
Indices: 43114--43209 Score: 88
Period size: 28 Copynumber: 3.3 Consensus size: 29
43104 TTATTATTTG
*
43114 GTCCTTTAACTCTCTATTTTTTCTATTTTA
1 GTCCTTTAACT-TCTATTTTTACTATTTTA
* *
43144 GTCCTTTAAGTTTTATTTTTACTA-TTTA
1 GTCCTTTAACTTCTATTTTTACTATTTTA
* * *
43172 ATCCCTTAAGTT-TATGTTTTACTATTTTA
1 GTCCTTTAACTTCTAT-TTTTACTATTTTA
* *
43201 CTCTTTTAA
1 GTCCTTTAA
43210 GCTTATAAAC
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
27 3 0.05
28 22 0.39
29 21 0.38
30 10 0.18
ACGTcount: A:0.21, C:0.16, G:0.05, T:0.58
Consensus pattern (29 bp):
GTCCTTTAACTTCTATTTTTACTATTTTA
Found at i:43171 original size:28 final size:28
Alignment explanation
Indices: 43108--43198 Score: 94
Period size: 28 Copynumber: 3.2 Consensus size: 28
43098 CTTTAATTAT
* * * *
43108 TATTTGGTCCTTTAACTCTCTATTTTTTC
1 TATTTAGTCCTTTAAGT-TTTATTTTTAC
43137 TATTTTAGTCCTTTAAGTTTTATTTTTAC
1 TA-TTTAGTCCTTTAAGTTTTATTTTTAC
* *
43166 TATTTAATCCCTTAAG-TTTATGTTTTAC
1 TATTTAGTCCTTTAAGTTTTAT-TTTTAC
43194 TATTT
1 TATTT
43199 TACTCTTTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
27 5 0.09
28 23 0.43
29 13 0.24
30 13 0.24
ACGTcount: A:0.20, C:0.14, G:0.07, T:0.59
Consensus pattern (28 bp):
TATTTAGTCCTTTAAGTTTTATTTTTAC
Found at i:43200 original size:29 final size:29
Alignment explanation
Indices: 43128--43200 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 29
43118 TTTAACTCTC
* * *
43128 TATTTTTTCTATTTTAGTCCTTTAAGTTT
1 TATTTTTACTATTTTAATCCCTTAAGTTT
43157 TATTTTTACTA-TTTAATCCCTTAAG-TT
1 TATTTTTACTATTTTAATCCCTTAAGTTT
43184 TATGTTTTACTATTTTA
1 TAT-TTTTACTATTTTA
43201 CTCTTTTAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
27 5 0.13
28 20 0.51
29 14 0.36
ACGTcount: A:0.22, C:0.11, G:0.05, T:0.62
Consensus pattern (29 bp):
TATTTTTACTATTTTAATCCCTTAAGTTT
Found at i:43209 original size:29 final size:28
Alignment explanation
Indices: 43128--43215 Score: 97
Period size: 29 Copynumber: 3.1 Consensus size: 28
43118 TTTAACTCTC
* *
43128 TATTTTTTCTATTTTAGTCCTTTAAGTTT
1 TATTTTTACTATTTTAATCCTTTAAG-TT
*
43157 TATTTTTACTA-TTTAATCCCTTAAGTT
1 TATTTTTACTATTTTAATCCTTTAAGTT
* * *
43184 TATGTTTTACTATTTTACTCTTTTAAGCT
1 TAT-TTTTACTATTTTAATCCTTTAAGTT
43213 TAT
1 TAT
43216 AAACGTCAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
27 5 0.10
28 20 0.40
29 25 0.50
ACGTcount: A:0.22, C:0.12, G:0.06, T:0.60
Consensus pattern (28 bp):
TATTTTTACTATTTTAATCCTTTAAGTT
Found at i:45392 original size:16 final size:17
Alignment explanation
Indices: 45356--45393 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
45346 GGATAAAAAA
*
45356 TAAATAAATTATTTGTT
1 TAAATAAATTATTTATT
45373 TAAATAAATTA-TTATT
1 TAAATAAATTATTTATT
45389 TAAAT
1 TAAAT
45394 TGTAAAATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TAAATAAATTATTTATT
Found at i:45612 original size:29 final size:29
Alignment explanation
Indices: 45558--45628 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
45548 AAAAAAATCG
* * * *
45558 ATTAATTTGGTTTGGTTAATACTTTTCAA
1 ATTAATTTTGTTTGGTTAAAAATTTTAAA
45587 ATTAATTTTGTTTGGTTAAAAATTTTAAA
1 ATTAATTTTGTTTGGTTAAAAATTTTAAA
*
45616 ATAAAATTTTGTT
1 AT-TAATTTTGTT
45629 CGATTAACCG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 27 0.75
30 9 0.25
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.52
Consensus pattern (29 bp):
ATTAATTTTGTTTGGTTAAAAATTTTAAA
Found at i:45742 original size:29 final size:29
Alignment explanation
Indices: 45698--45767 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
45688 GAAAAATCGG
*
45698 TTAATTCGGTTCGGTTAATAATTTTTAAA
1 TTAATTTGGTTCGGTTAATAATTTTTAAA
*
45727 TTAATTTGGTTTGGTTAATAATTTTTAAA
1 TTAATTTGGTTCGGTTAATAATTTTTAAA
*
45756 TAAATTTTGGTT
1 TTAA-TTTGGTT
45768 ATATTAACCG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
29 30 0.81
30 7 0.19
ACGTcount: A:0.30, C:0.03, G:0.14, T:0.53
Consensus pattern (29 bp):
TTAATTTGGTTCGGTTAATAATTTTTAAA
Found at i:45775 original size:125 final size:126
Alignment explanation
Indices: 45645--45911 Score: 358
Period size: 127 Copynumber: 2.1 Consensus size: 126
45635 ACCGAACCGA
* *
45645 ATTAACCGAATTTTTGTTTCGATTAATTCAATTAATAATTTT-AGAAAAA-TCGGTTAATTCGGT
1 ATTAACCGAATTTTTGTTTCGATTAATTCAATTAATAATTTTCA-AAAAAGTAGGTTAATTCGGG
* * * * * * *
45708 TCGGTTAATAATTTTTAAATTAATTTGGTTTGGTTAATAATTTTTAAATAAATTTTGGTTAT
65 TCGGTTAATAATTTTCAAAATAATTCGGTTCGGTTAATAATTTTCAAATAAATTTTGGGTAG
*** * *
45770 ATTAACCGAATTTTTGTTTCGATTAATTTGGTTAATAATTTTCAAAAAAGTTATGTTAATTTGGG
1 ATTAACCGAATTTTTGTTTCGATTAATTCAATTAATAATTTTCAAAAAAG-TAGGTTAATTCGGG
*
45835 TCGGTTAATAATTTTCAAAATAATTCGGTTCGGTTAATAATTTTCAAATAAATTTTGGGTCG
65 TCGGTTAATAATTTTCAAAATAATTCGGTTCGGTTAATAATTTTCAAATAAATTTTGGGTAG
*
45897 ATTGACCGAATTTTT
1 ATTAACCGAATTTTT
45912 TTCTTTAATC
Statistics
Matches: 123, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
125 44 0.36
126 1 0.01
127 78 0.63
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.46
Consensus pattern (126 bp):
ATTAACCGAATTTTTGTTTCGATTAATTCAATTAATAATTTTCAAAAAAGTAGGTTAATTCGGGT
CGGTTAATAATTTTCAAAATAATTCGGTTCGGTTAATAATTTTCAAATAAATTTTGGGTAG
Found at i:45868 original size:29 final size:29
Alignment explanation
Indices: 45826--45882 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
45816 AAAGTTATGT
*
45826 TAATTTGGGTCGGTTAATAATTTTCAAAA
1 TAATTCGGGTCGGTTAATAATTTTCAAAA
*
45855 TAATTCGGTTCGGTTAATAATTTTCAAA
1 TAATTCGGGTCGGTTAATAATTTTCAAA
45883 TAAATTTTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (29 bp):
TAATTCGGGTCGGTTAATAATTTTCAAAA
Found at i:46603 original size:29 final size:29
Alignment explanation
Indices: 46545--46612 Score: 66
Period size: 29 Copynumber: 2.3 Consensus size: 29
46535 ACGGGTGGTT
*
46545 TGATTGAATTAATTAAATAGTTAGGTGGTC
1 TGATTG-ATTAATTAAATAGTTAGGCGGTC
* *
46575 TGATTGATTCAATTGAA-AGTTCGGCGGTC
1 TGATTGATT-AATTAAATAGTTAGGCGGTC
**
46604 ACATTGATT
1 TGATTGATT
46613 TTTTACCATA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
29 20 0.62
30 12 0.38
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (29 bp):
TGATTGATTAATTAAATAGTTAGGCGGTC
Found at i:46913 original size:18 final size:18
Alignment explanation
Indices: 46890--46931 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
46880 GTGTAATGTG
46890 ATCGTTTTAAGTGCTTAA
1 ATCGTTTTAAGTGCTTAA
46908 ATCGTTTTAAGTGCTTAA
1 ATCGTTTTAAGTGCTTAA
46926 ATCGTT
1 ATCGTT
46932 AACTGTGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.45
Consensus pattern (18 bp):
ATCGTTTTAAGTGCTTAA
Found at i:58624 original size:64 final size:63
Alignment explanation
Indices: 58556--58735 Score: 204
Period size: 65 Copynumber: 2.8 Consensus size: 63
58546 TTGGACCCTT
*
58556 AGTGCATCGGTGCACTAAG-AGTGCATCGATGCATAAAATGCATTCGATGTTTCA-AAATAGC-C
1 AGTGCATCGATGCA-T-AGTAGTGCATCGATGCATAAAATGCATTCGATGTTTCATAAA-A-CTC
58618 AG
62 AG
* * *
58620 AGTGCATCGATGCATAGCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACTCTG
1 AGTGCATCGATGCATAG-TAGTGCATCGATGCATAAAATGCATTCGATG-TTTCATAAAACTCAG
* * * *
58685 AATGCATCAATGCATAGTATGTGCATCGGTGCATGAAATGCATTCGATGTT
1 AGTGCATCGATGCATAGTA-GTGCATCGATGCATAAAATGCATTCGATGTT
58736 CAATTTATTC
Statistics
Matches: 101, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
62 2 0.02
63 1 0.01
64 45 0.45
65 50 0.50
66 3 0.03
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (63 bp):
AGTGCATCGATGCATAGTAGTGCATCGATGCATAAAATGCATTCGATGTTTCATAAAACTCAG
Found at i:58779 original size:65 final size:64
Alignment explanation
Indices: 58576--58777 Score: 191
Period size: 65 Copynumber: 3.1 Consensus size: 64
58566 TGCACTAAGA
* * *
58576 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCCA-GAGTGCATCGATGCATAGCTG
1 GTGCATCGATGCATAAAATGCATTCGATGTTTC-AATTAACCATGAGTGCATCGATGCATAGTTG
* * * *
58640 GTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAACTC-TGAATGCATCAATGCATAGT
1 GTGCATCGATGCATAAAATGCATTCGATG-TTTCAAT-TAAC-CATGAGTGCATCGATGCATAGT
58703 AT-
63 -TG
* * * *
58705 GTGCATCGGTGCATGAAATGCATTCGATG-TTCAATTTATTCCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAA-TTA-ACCATGAGTGCATCGATGCATAG-T
58768 TG
63 TG
58770 GTGCATCG
1 GTGCATCG
58778 GTACATCACT
Statistics
Matches: 113, Mismatches: 14, Indels: 21
0.76 0.09 0.14
Matches are distributed among these distances:
63 4 0.04
64 47 0.42
65 61 0.54
66 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCAATTAACCATGAGTGCATCGATGCATAGTTG
Found at i:62093 original size:19 final size:19
Alignment explanation
Indices: 62069--62120 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
62059 AATAGCCAGA
62069 GTGCATCGATGCATAGCTG
1 GTGCATCGATGCATAGCTG
**
62088 GTGCATCGATGTGTAGCTG
1 GTGCATCGATGCATAGCTG
62107 GTGCATCGATGCAT
1 GTGCATCGATGCAT
62121 GAAATGCATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.33, T:0.29
Consensus pattern (19 bp):
GTGCATCGATGCATAGCTG
Found at i:64879 original size:21 final size:22
Alignment explanation
Indices: 64817--64898 Score: 69
Period size: 23 Copynumber: 3.6 Consensus size: 22
64807 GCATGGCCTT
64817 GTGCATCGATGCACATTCAAGGC
1 GTGCATCGATGCACATTC-AGGC
* * * *
64840 GTGCATTGGTGCACCTTCATG-
1 GTGCATCGATGCACATTCAGGC
*
64861 GTGTATCGATGCACATTCAAAGG-
1 GTGCATCGATGCACATTC--AGGC
64884 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
64899 TGTTAAGTAT
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
21 14 0.30
22 2 0.04
23 18 0.39
24 12 0.26
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAGGC
Found at i:69085 original size:10 final size:11
Alignment explanation
Indices: 69054--69099 Score: 53
Period size: 10 Copynumber: 4.5 Consensus size: 11
69044 TATTGGTCAA
69054 ATAAT-TAAAT
1 ATAATATAAAT
*
69064 ATAAAATAAAT
1 ATAATATAAAT
69075 ATAATAT-AAT
1 ATAATATAAAT
*
69085 ATAATA-AAAA
1 ATAATATAAAT
69095 ATAAT
1 ATAAT
69100 TTTGTCTTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
10 20 0.65
11 11 0.35
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:72155 original size:11 final size:11
Alignment explanation
Indices: 72139--72163 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
72129 TATATTTGAT
72139 ATTAATTATTA
1 ATTAATTATTA
72150 ATTAATTATTA
1 ATTAATTATTA
72161 ATT
1 ATT
72164 TATGCATCCA
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:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATTAATTATTA
Found at i:72645 original size:61 final size:61
Alignment explanation
Indices: 72575--72697 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
72565 TATCTTTTAT
72575 TATTTTATTTGTTTAAAGAGAATAAATAAGCATTTTAATTTTGTGGACTTAAATAAAACCC
1 TATTTTATTTGTTTAAAGAGAATAAATAAGCATTTTAATTTTGTGGACTTAAATAAAACCC
72636 TATTTTATTTGTTTAAAGAGAATAAATAAGCATTTTAATTTTGTGGACTTAAATAAAACCC
1 TATTTTATTTGTTTAAAGAGAATAAATAAGCATTTTAATTTTGTGGACTTAAATAAAACCC
72697 T
1 T
72698 TTTAAATTAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.41
Consensus pattern (61 bp):
TATTTTATTTGTTTAAAGAGAATAAATAAGCATTTTAATTTTGTGGACTTAAATAAAACCC
Found at i:72671 original size:30 final size:30
Alignment explanation
Indices: 72576--72672 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
72566 ATCTTTTATT
72576 ATTTTATTTGTTTAAAGAGAATAAATAAGC
1 ATTTTATTTGTTTAAAGAGAATAAATAAGC
** *** **
72606 ATTTTAATTTTGTGGACTTA-AATAAA-ACCC
1 ATTTT-A-TTTGTTTAAAGAGAATAAATAAGC
72636 TATTTTATTTGTTTAAAGAGAATAAATAAGC
1 -ATTTTATTTGTTTAAAGAGAATAAATAAGC
72667 ATTTTA
1 ATTTTA
72673 ATTTTGTGGA
Statistics
Matches: 48, Mismatches: 14, Indels: 10
0.67 0.19 0.14
Matches are distributed among these distances:
29 7 0.15
30 20 0.42
31 14 0.29
32 7 0.15
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.42
Consensus pattern (30 bp):
ATTTTATTTGTTTAAAGAGAATAAATAAGC
Found at i:76993 original size:2 final size:2
Alignment explanation
Indices: 76986--77072 Score: 174
Period size: 2 Copynumber: 43.5 Consensus size: 2
76976 TTGACCAGAA
76986 AT AT AT AT AT AT 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 AT AT AT AT AT AT
77028 AT AT AT AT AT AT 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 AT AT AT AT AT AT
77070 AT A
1 AT A
77073 AAGAAATGTT
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 85 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:78861 original size:15 final size:16
Alignment explanation
Indices: 78829--78871 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
78819 ATTTATGAAT
*
78829 ACAAAAAAAAATATAA
1 ACAAATAAAAATATAA
*
78845 ACAAATAAAATTA-AA
1 ACAAATAAAAATATAA
78860 AC-AATAAAAATA
1 ACAAATAAAAATA
78872 ACACTAAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 9 0.38
15 4 0.17
16 11 0.46
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.16
Consensus pattern (16 bp):
ACAAATAAAAATATAA
Found at i:78870 original size:20 final size:20
Alignment explanation
Indices: 78847--78885 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
78837 AAATATAAAC
*
78847 AAATAAAATTAAAACAATAA
1 AAATAAAACTAAAACAATAA
*
78867 AAATAACACTAAAACAATA
1 AAATAAAACTAAAACAATA
78886 TATTTTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.72, C:0.10, G:0.00, T:0.18
Consensus pattern (20 bp):
AAATAAAACTAAAACAATAA
Found at i:79769 original size:20 final size:20
Alignment explanation
Indices: 79744--79782 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
79734 TCTCTGTTGT
79744 TTTTTTTTTCTGTCTCTCTC
1 TTTTTTTTTCTGTCTCTCTC
79764 TTTTTTTTTCTGTCTCTCT
1 TTTTTTTTTCTGTCTCTCT
79783 GTCCCGTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.00, C:0.23, G:0.05, T:0.72
Consensus pattern (20 bp):
TTTTTTTTTCTGTCTCTCTC
Found at i:80266 original size:3 final size:3
Alignment explanation
Indices: 80258--80350 Score: 150
Period size: 3 Copynumber: 30.7 Consensus size: 3
80248 AATATATATT
* *
80258 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
80306 TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA TA
1 TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
80351 TGGATAAAAA
Statistics
Matches: 83, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
3 81 0.98
4 2 0.02
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:80883 original size:113 final size:113
Alignment explanation
Indices: 80665--81112 Score: 629
Period size: 113 Copynumber: 3.9 Consensus size: 113
80655 ATAGAATTAT
* * * *
80665 GCAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGACGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTT
* * *
80730 CTCATTATGAAC--TCTACATGGCAATGTTGATCCATCAAATGATGAATTCAA
63 CTCATTATGAACTTTCT-C-TGGAAAAGATGATCCATCAAATGATGAATTCAA
80781 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
80846 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAG
66 ATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAA
*
80894 GTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
80959 ATTATGAACTTTCTCTGGCAAAA-ATAATCCATCAAGTGATGAATTC-A
66 ATTATGAACTTTCTCTGG-AAAAGATGATCCATCAAATGATGAATTCAA
*
81006 GACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCCTTCAGATGATGAGTTCT
1 G-CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC--A-GATGAGTTCT
*
81071 T-TCATTATGAACCTTCTCTGGAAAAGAT-ATCCATCAAATGAT
62 TCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGAT
81113 AGATTTGAAT
Statistics
Matches: 305, Mismatches: 19, Indels: 18
0.89 0.06 0.05
Matches are distributed among these distances:
112 1 0.00
113 196 0.64
114 22 0.07
115 25 0.08
116 61 0.20
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.37
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAA
Found at i:81594 original size:22 final size:22
Alignment explanation
Indices: 81515--81591 Score: 100
Period size: 22 Copynumber: 3.5 Consensus size: 22
81505 GATAAAGCTT
*
81515 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* * *
81537 TCATTTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* *
81559 TCATTTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
81581 TCATCTTTGAA
1 TCATCTTTGAA
81592 GAGTGTAGAT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:82025 original size:50 final size:54
Alignment explanation
Indices: 81963--82105 Score: 188
Period size: 50 Copynumber: 2.7 Consensus size: 54
81953 CACTGGTTCA
*
81963 TAAAACATTTGACAATACATTCATCTTTTCCTGTGGTTTCTG-TC-GA-G-ATG
1 TAAAACATTTGACAACACATTCATCTTTTCCTGTGGTTTCTGCTCAGATGTATG
* * *
82013 TAAAACACTTGACAACACATTCATCCTTTT-CTGTGGCTTCTGCTCAGATGTTTG
1 TAAAACATTTGACAACACATTCAT-CTTTTCCTGTGGTTTCTGCTCAGATGTATG
* *
82067 TAAAACATTTGACAACACATTCATCCTTTCTTGTGGTTT
1 TAAAACATTTGACAACACATTCATCTTTTCCTGTGGTTT
82106 TTGCCAAGAT
Statistics
Matches: 79, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
50 33 0.42
51 7 0.09
52 2 0.03
53 5 0.06
54 32 0.41
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (54 bp):
TAAAACATTTGACAACACATTCATCTTTTCCTGTGGTTTCTGCTCAGATGTATG
Found at i:84528 original size:115 final size:113
Alignment explanation
Indices: 84214--84543 Score: 525
Period size: 114 Copynumber: 2.9 Consensus size: 113
84204 GATCATGCAG
* * * *
84214 TTCATCTTTCAATTCCAATGATCGGTTCTGGGGTTCCTACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTAAAATCCAATGAT-GGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* * *
84279 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAT
65 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
* * * *
84328 TTCATCTTTTAAATCTAATGATTGATTTTGGGGTTCATACCAAACTAGATCAGATAACTCAAAGA
1 TTCATCTTTAAAATCCAATGA-TGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
84393 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
65 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
84442 TTCATCTTTAAAATCCAATGATGGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTAAAATCCAATGAT-GG-TTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
84507 AACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTC
64 AACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTC
84544 AGTTAATGAT
Statistics
Matches: 199, Mismatches: 14, Indels: 5
0.91 0.06 0.02
Matches are distributed among these distances:
113 1 0.01
114 122 0.61
115 76 0.38
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.33
Consensus pattern (113 bp):
TTCATCTTTAAAATCCAATGATGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAA
CACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
Found at i:90040 original size:14 final size:14
Alignment explanation
Indices: 90006--90059 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
89996 TTGTGCAATA
* *
90006 CAAATGCAAAGATG
1 CAAATGTAAATATG
90020 CCAAATGTAAATATG
1 -CAAATGTAAATATG
*
90035 CAAATGTAAAAATG
1 CAAATGTAAATATG
*
90049 TAAATGTAAAT
1 CAAATGTAAAT
90060 TATTTAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:91677 original size:28 final size:29
Alignment explanation
Indices: 91646--91718 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 29
91636 AAAATGAAAC
*
91646 ATATAAATATTATGAAAA-TAATAAGTAA
1 ATATAAATATTATGAAAAGAAATAAGTAA
* * *
91674 ATATAAAAATTTTGAAAAGAAATAATTAA
1 ATATAAATATTATGAAAAGAAATAAGTAA
*
91703 AAATTAAATA-TATGAA
1 ATA-TAAATATTATGAA
91719 CTTTTAATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
28 16 0.44
29 15 0.42
30 5 0.14
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.32
Consensus pattern (29 bp):
ATATAAATATTATGAAAAGAAATAAGTAA
Found at i:92427 original size:20 final size:20
Alignment explanation
Indices: 92404--92442 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
92394 AAAAATAAAC
*
92404 AAATAAAATTAAAACAATAA
1 AAATAAAACTAAAACAATAA
*
92424 AAATAACACTAAAACAATA
1 AAATAAAACTAAAACAATA
92443 TATTTTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.72, C:0.10, G:0.00, T:0.18
Consensus pattern (20 bp):
AAATAAAACTAAAACAATAA
Found at i:93341 original size:20 final size:20
Alignment explanation
Indices: 93316--93354 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
93306 TCTCTGTTGT
93316 TTTTTTTTTCTGTCTCTCTC
1 TTTTTTTTTCTGTCTCTCTC
93336 TTTTTTTTTCTGTCTCTCT
1 TTTTTTTTTCTGTCTCTCT
93355 GTCCCGTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.00, C:0.23, G:0.05, T:0.72
Consensus pattern (20 bp):
TTTTTTTTTCTGTCTCTCTC
Found at i:93835 original size:3 final size:3
Alignment explanation
Indices: 93827--93917 Score: 157
Period size: 3 Copynumber: 30.7 Consensus size: 3
93817 AATATATATT
* *
93827 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAG TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
93875 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
93918 TGGATAAAAA
Statistics
Matches: 83, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
2 2 0.02
3 81 0.98
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:94239 original size:2 final size:2
Alignment explanation
Indices: 94232--94294 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
94222 AGTGACTTTC
94232 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
94274 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
94295 CAAGTCATTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:97221 original size:20 final size:19
Alignment explanation
Indices: 97192--97240 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
97182 GCAATTTTCT
* *
97192 AAATTCGCAACGCGATAGTC
1 AAATTCGCAACAC-AAAGTC
*
97212 AAATTTGCAACACAAAGTC
1 AAATTCGCAACACAAAGTC
97231 AAATTCGCAA
1 AAATTCGCAA
97241 ATTCGCAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.43, C:0.22, G:0.14, T:0.20
Consensus pattern (19 bp):
AAATTCGCAACACAAAGTC
Found at i:97259 original size:55 final size:56
Alignment explanation
Indices: 97192--97296 Score: 135
Period size: 55 Copynumber: 1.9 Consensus size: 56
97182 GCAATTTTCT
* *
97192 AAATTCGCAACGCG-A-TAGTCAAATTTGCAACACA-AAGTCAAATTCGCAAATTCGC
1 AAATTCACAACGCGAATTAGT-AAA-TCGCAACACAGAAGTCAAATTCGCAAATTCGC
* *
97247 AAATTCACAACGCGAATTTGTAAATCGTAACACAGAAGTCAAATTCGCAA
1 AAATTCACAACGCGAATTAGTAAATCGCAACACAGAAGTCAAATTCGCAA
97297 CGCGAAAGTC
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
55 21 0.49
56 19 0.44
57 3 0.07
ACGTcount: A:0.42, C:0.22, G:0.14, T:0.22
Consensus pattern (56 bp):
AAATTCACAACGCGAATTAGTAAATCGCAACACAGAAGTCAAATTCGCAAATTCGC
Found at i:99565 original size:21 final size:21
Alignment explanation
Indices: 99541--99586 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
99531 AGTTAGGGGA
* *
99541 TTTACGTGATGAGGTCGGTGC
1 TTTACGTCATGAGGTCGGTAC
99562 TTTACGTCATGAGGTCGGTAC
1 TTTACGTCATGAGGTCGGTAC
99583 TTTA
1 TTTA
99587 TGTAAAGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.17, C:0.15, G:0.30, T:0.37
Consensus pattern (21 bp):
TTTACGTCATGAGGTCGGTAC
Found at i:100025 original size:21 final size:21
Alignment explanation
Indices: 99994--100092 Score: 103
Period size: 21 Copynumber: 4.7 Consensus size: 21
99984 GATGCATCTA
* *
99994 TCATCATTCAAGAGGCGCCTC
1 TCATCGTTCAAGAGGCCCCTC
100015 -CTATCGTTCAAGAGGCCCCTC
1 TC-ATCGTTCAAGAGGCCCCTC
* *
100036 TCATC-ATCGAAGAAGCCCCTC
1 TCATCGTTC-AAGAGGCCCCTC
* * *
100057 CCACCGTTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGGCCCCTC
100078 TCATCGTTCAAGAGG
1 TCATCGTTCAAGAGG
100093 TCCCGCCCGC
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
20 3 0.05
21 57 0.90
22 3 0.05
ACGTcount: A:0.23, C:0.35, G:0.20, T:0.21
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:100041 original size:42 final size:42
Alignment explanation
Indices: 99994--100112 Score: 141
Period size: 42 Copynumber: 2.8 Consensus size: 42
99984 GATGCATCTA
* * *
99994 TCATCATTCAAGAGGCGCCTCCTATCGTTCAAGAGGCCCCTC
1 TCATCATTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTC
* *
100036 TCATCA-TCGAAGAAGCCCCTCCCACCGTTCAAGAGGCCCCTG
1 TCATCATTC-AAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTC
* * * *
100078 TCATCGTTCAAGAGGTCCCGCCCGCCGTTCAAGAG
1 TCATCATTCAAGAGGCCCCTCCCACCGTTCAAGAG
100113 ACCGATTCAC
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
41 2 0.03
42 61 0.94
43 2 0.03
ACGTcount: A:0.22, C:0.37, G:0.21, T:0.20
Consensus pattern (42 bp):
TCATCATTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTC
Found at i:101492 original size:61 final size:62
Alignment explanation
Indices: 101392--101531 Score: 196
Period size: 66 Copynumber: 2.2 Consensus size: 62
101382 TTTTACATTG
*
101392 AAAGTTGATTTGTTTAATTGATGATGAAATAAGATTTA-TTTT-TTGATTAATTGATTTGTA
1 AAAGTTGATTTGTTTAATTGATGATGAAATAAGAATTATTTTTCTTGATTAATTGATTTGTA
*
101452 AAAGTTGATTTGTTTAATTTGATG-TGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTG
1 AAAGTTGATTTGTTTAA-TTGATGATG-AAATAAGAATTA--TTTTT-CTTGATTAATTGATTTG
101516 TA
61 TA
101518 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
101532 GTTTCTAAAA
Statistics
Matches: 71, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
60 19 0.27
61 17 0.24
64 4 0.06
66 31 0.44
ACGTcount: A:0.31, C:0.01, G:0.17, T:0.51
Consensus pattern (62 bp):
AAAGTTGATTTGTTTAATTGATGATGAAATAAGAATTATTTTTCTTGATTAATTGATTTGTA
Found at i:101615 original size:20 final size:20
Alignment explanation
Indices: 101590--101679 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
101580 GTTGAAGGTA
101590 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
*
101610 CAAATTTGCAACGCGAAA-T
1 CAAATTCGCAACGCGAAAGT
*** *
101629 --AA---GCGTTGCGATAGT
1 CAAATTCGCAACGCGAAAGT
*
101644 CAAATTCGCAACACGAAAGT
1 CAAATTCGCAACGCGAAAGT
*
101664 CAAATTCGTAACGCGA
1 CAAATTCGCAACGCGA
101680 TTTTTGGTTT
Statistics
Matches: 52, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
14 7 0.13
15 1 0.02
17 4 0.08
19 1 0.02
20 39 0.75
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:102301 original size:18 final size:18
Alignment explanation
Indices: 102278--102316 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
102268 CAAAATTTAT
102278 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
102296 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
102314 ATT
1 ATT
102317 CCAATTACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.36
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:105467 original size:24 final size:24
Alignment explanation
Indices: 105433--105486 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
105423 CCATCACATC
105433 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
105457 ATCAAAGTCCGGGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
105481 ATCAAA
1 ATCAAA
105487 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:106421 original size:2 final size:2
Alignment explanation
Indices: 106414--106441 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
106404 TTATTTTCTC
106414 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
106442 GAAAGTGTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:119736 original size:19 final size:19
Alignment explanation
Indices: 119712--119757 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
119702 AATACGTTTT
119712 TATGAACAGTAAAATACGG
1 TATGAACAGTAAAATACGG
119731 TATGAACAGTAAAATACGG
1 TATGAACAGTAAAATACGG
119750 TATGAACA
1 TATGAACA
119758 ATACTATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.48, C:0.11, G:0.20, T:0.22
Consensus pattern (19 bp):
TATGAACAGTAAAATACGG
Done.