Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000734.1 Hibiscus syriacus cultivar Beakdansim tig00001424_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: 86144
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:5909 original size:165 final size:166
Alignment explanation
Indices: 5556--6231 Score: 941
Period size: 165 Copynumber: 4.1 Consensus size: 166
5546 CGAACTCGTC
* * * * *
5556 AGGTC-TTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTCGGA
1 AGGTCTTTTGGTTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAA
* * * * * * * * * **
5619 GCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGCAAATAGCCCTTCTTGCCTTGAGTTATGTT
66 GCTGAGTGTAATCGAACTCGAGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATACT
*
5684 GCAAATGATGTACCTTGGAGCTGAGCGTAGTCGAACTCAA
127 GCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAA
* *
5724 AGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAA
1 AGGTCTTTTGGTTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAA
*
5788 GCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATACTGCAA
66 GCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAA
* *
5853 ATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCAA
131 ATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAA
* * * *
5889 AGGTCTTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCGAA
1 AGGTCTTTTGGTTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAA
* *
5953 GCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAA
66 GCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAA
*
6018 ATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGA
131 ATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAA
* * **
6054 AGGTCTTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATGTGCCCTCGAA
1 AGGTCTTTTGGTTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAA
*
6118 GCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATATCCCTTCTCGACTTAAGCTATACTGCAA
66 GCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAA
* * *
6183 ATGATGTGCCTTGGAGTTGAGCATAGTCGAACTCGA
131 ATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAA
6219 AGGTC-TTTGGTTG
1 AGGTCTTTTGGTTG
6232 GCAAATAGTC
Statistics
Matches: 470, Mismatches: 35, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
164 5 0.01
165 377 0.80
166 5 0.01
167 1 0.00
168 54 0.11
169 28 0.06
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.30
Consensus pattern (166 bp):
AGGTCTTTTGGTTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAA
GCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAA
ATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAA
Found at i:6269 original size:84 final size:84
Alignment explanation
Indices: 5545--6246 Score: 766
Period size: 84 Copynumber: 8.5 Consensus size: 84
5535 CTGAATGAAA
* *
5545 TCGAACTCGTCAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATG
1 TCGAACTCG-AAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATG
5610 TGCCTCGGAGCTGAGCGTAG
65 TGCCTCGGAGCTGAGCGTAG
* * * * * *
5630 TCAAACTCGAAGGTCTTTGGTTGGCAAATAGCCCTTCTTGCCTTGAGTTATGTTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
* *
5695 ACCTTGGAGCTGAGCGTAG
66 GCCTCGGAGCTGAGCGTAG
* *
5714 TCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
* * *
5779 GCCCTCGAAGCTGAGTGTAA
66 G-CCTCGGAGCTGAGCGTAG
* * *
5799 TCGAACTCGAGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGTTATACTGCAAATGATAT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
**
5860 GCCTTAGAGCTGAGCGTAG
66 GCCTCGGAGCTGAGCGTAG
* * * * * * * *
5879 TCGAACTCAAAGGTCTTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATG
1 TCGAACTCGAAGGTC-TTTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATG
* * *
5943 TGCCCTCGAAGCTGAGTGTAA
65 TG-CCTCGGAGCTGAGCGTAG
** *
5964 TCGAACTCGGGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
*
6025 GCCTTGGAGCTGAGCGTAG
66 GCCTCGGAGCTGAGCGTAG
* * * * * **
6044 TCGAACTCGAAGGTCTTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATG
1 TCGAACTCGAAGGTC-TTTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATG
* * *
6108 TGCCCTCGAAGCTGAGTGTAA
65 TG-CCTCGGAGCTGAGCGTAG
* * * *
6129 TCGAACTCGAGGGTC--T--TTGGCAGATATCCCTTCTCGACTTAAGCTATACTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
* * *
6190 GCCTTGGAGTTGAGCATAG
66 GCCTCGGAGCTGAGCGTAG
* *
6209 TCGAACTCGAAGGTCTTTGGTTGGCAAATAGTCCTTCT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCT
6247 TGTCTTGAGC
Statistics
Matches: 500, Mismatches: 98, Indels: 39
0.78 0.15 0.06
Matches are distributed among these distances:
80 79 0.16
81 116 0.23
82 3 0.01
83 3 0.01
84 211 0.42
85 88 0.18
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (84 bp):
TCGAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
GCCTCGGAGCTGAGCGTAG
Found at i:10063 original size:6 final size:6
Alignment explanation
Indices: 10047--10081 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
10037 TTAATTGCGA
* *
10047 AAATTT GAATTT AAATTT AAATTT AAACTT AAATT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATT
10082 ATTCGATCTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (6 bp):
AAATTT
Found at i:10162 original size:20 final size:21
Alignment explanation
Indices: 10121--10162 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
10111 AAATTACCCC
*
10121 TAAAAAGATAAAAATATTATA
1 TAAAAAGATAAAAATATAATA
10142 TAAAAA-ATAAGAAATA-AATA
1 TAAAAAGATAA-AAATATAATA
10162 T
1 T
10163 TAAATAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (21 bp):
TAAAAAGATAAAAATATAATA
Found at i:11656 original size:84 final size:84
Alignment explanation
Indices: 11522--12246 Score: 715
Period size: 84 Copynumber: 8.7 Consensus size: 84
11512 CTGAATGAAA
*
11522 TCGAACTCGTCAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATG
1 TCGAACTCG-AAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATG
11587 TGCCTCGGAGCTGAGCGTAG
65 TGCCTCGGAGCTGAGCGTAG
* * *** * *
11607 TCAAACTCGAAGGTCTTTGGTTGGCAAATAGCCCTTCTTTCCTTGAGCTATGTTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
* * *
11672 ACCTTGGAGCTGAGAGTAG
66 GCCTCGGAGCTGAGCGTAG
* * *
11691 TCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
* * *
11756 GCCCTCGAAGCTGAGTGTAA
66 G-CCTCGGAGCTGAGCGTAG
* * *
11776 TCGAACTCGAGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATAT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
**
11837 GCCTTAGAGCTGAGCGTAG
66 GCCTCGGAGCTGAGCGTAG
* * * * * * * * * *
11856 TCGAACTCAAAGGTCTTTTGG-TGACATATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATG
1 TCGAACTCGAAGGTC-TTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATG
** * *
11920 TGCCCTCAAAGCTGAGTGTAA
65 TG-CCTCGGAGCTGAGCGTAG
**
11941 TCGAACTCGGGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
* *
12002 GCCTTGGAGCTGAGCGCAG
66 GCCTCGGAGCTGAGCGTAG
* * * * * * **
12021 TCGAACTCGAAGGTCTTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATG
1 TCGAACTCGAAGGTC-TTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATG
* * *
12085 TGCCCTCGAAGCTGAGTGTAA
65 TG-CCTCGGAGCTGAGCGTAG
* *
12106 TCGAACTCG-AGTGTC--T--TTGGCAGATATCCCTTCTCGACTTAAGCTATACTGCAAATGATG
1 TCGAACTCGAAG-GTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATG
* * *
12166 TGCCTTGGAGTTGAGCATAG
65 TGCCTCGGAGCTGAGCGTAG
* * * * * **
12186 TCGAACTCGAAGGTCTTTGGTTGGCAAATAGTCCTTCTTGTCTTGAGCTATATTGCAAATG
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATG
12247 TTGCCTAAAA
Statistics
Matches: 510, Mismatches: 109, Indels: 43
0.77 0.16 0.06
Matches are distributed among these distances:
80 75 0.15
81 116 0.23
82 3 0.01
83 3 0.01
84 227 0.45
85 86 0.17
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (84 bp):
TCGAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
GCCTCGGAGCTGAGCGTAG
Found at i:11889 original size:165 final size:165
Alignment explanation
Indices: 11533--12203 Score: 898
Period size: 165 Copynumber: 4.0 Consensus size: 165
11523 CGAACTCGTC
* * * * *
11533 AGGTC-TTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTCGGA
1 AGGTCTTTTGG-TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAA
* * * * * *** * **
11596 GCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGCAAATAGCCCTTCTTTCCTTGAGCTATGTT
65 GCTGAGTGTAATCGAACTCGAGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATACT
* *
11661 GCAAATGATGTACCTTGGAGCTGAGAGTAGTCGAACTCAA
126 GCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAA
* *
11701 AGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAA
1 AGGTCTTTTGG-TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAA
11765 GCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAA
65 GCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAA
* *
11830 ATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCAA
130 ATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAA
* * * * * *
11866 AGGTCTTTTGGTGACATATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCAAAG
1 AGGTCTTTTGGTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAG
* *
11931 CTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAA
66 CTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAA
* *
11996 TGATGTGCCTTGGAGCTGAGCGCAGTCGAACTCGA
131 TGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAA
* * **
12031 AGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATGTGCCCTCGAAG
1 AGGTCTTTTGGTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAG
* *
12096 CTGAGTGTAATCGAACTCGAGTGTCTTTGGCAGATATCCCTTCTCGACTTAAGCTATACTGCAAA
66 CTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAA
* * *
12161 TGATGTGCCTTGGAGTTGAGCATAGTCGAACTCGA
131 TGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAA
12196 AGGTCTTT
1 AGGTCTTT
12204 GGTTGGCAAA
Statistics
Matches: 458, Mismatches: 43, Indels: 7
0.90 0.08 0.01
Matches are distributed among these distances:
165 370 0.81
166 5 0.01
167 1 0.00
168 54 0.12
169 28 0.06
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (165 bp):
AGGTCTTTTGGTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAG
CTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAA
TGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAA
Found at i:12083 original size:249 final size:249
Alignment explanation
Indices: 11520--12113 Score: 678
Period size: 249 Copynumber: 2.4 Consensus size: 249
11510 AGCTGAATGA
*
11520 AATCGAACTCGTCAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGA
1 AATCGAACTCG-AAGGTCTTTGG-T-GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGA
** * * * * **
11585 TGTGCCTCGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGCAAATAGCCCTTCTTTCCT
63 TGTGCCTTAGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGACAAATAACCCTTCTAGCCT
*** *
11650 TGAGCTATGTTGCAAATGATGTACCTTGGAGCTGAGAGTAGTCGAACTCAAAGGTCTTTGGTTGG
128 TGAGCTATGTTGCAAATGATGTACCTCAAAGCTGAGAGTAATCGAACTCAAAGGTC-TT-GTTGG
* * *
11715 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGT
191 CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGC
* * *
11774 AATCGAACTCGAGGGTCTTT-G-GCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATAT
1 AATCGAACTCGAAGGTCTTTGGTGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
*
11837 GCCTTAGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGG-TGACATATAACCCTTCTAGCCTTG
66 GCCTTAGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGGTTGACAAATAACCCTTCTAGCCTTG
* * * * ***
11901 AGTTATGTTGTAAATGATGTGCCCTCAAAGCTGAGTGTAATCGAACTCGGGGGTC-T-TTGGCAG
130 AGCTATGTTGCAAATGATGT-ACCTCAAAGCTGAGAGTAATCGAACTCAAAGGTCTTGTTGGCAG
* * *
11964 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGC
194 ATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGC
* * * * * * **
12019 AGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGAT
1 AATCGAACTCGAAGGTC-TTTGGTG-CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGAT
* * * *
12084 GTGCCCTCGAAGCTGAGTGTAATCGAACTC
64 GTGCCTTAG-AGCTGAGCGTAGTCGAACTC
12114 GAGTGTCTTT
Statistics
Matches: 288, Mismatches: 45, Indels: 18
0.82 0.13 0.05
Matches are distributed among these distances:
245 27 0.09
246 47 0.16
247 1 0.00
248 2 0.01
249 144 0.50
250 48 0.17
252 1 0.00
253 7 0.02
254 11 0.04
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.29
Consensus pattern (249 bp):
AATCGAACTCGAAGGTCTTTGGTGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
GCCTTAGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGACAAATAACCCTTCTAGCCTTGA
GCTATGTTGCAAATGATGTACCTCAAAGCTGAGAGTAATCGAACTCAAAGGTCTTGTTGGCAGAT
AACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGC
Found at i:15986 original size:6 final size:6
Alignment explanation
Indices: 15970--16010 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
15960 TTAATTGCGA
* *
15970 AAATTT GAATTT AAATTT AAATTT AAATTT AAACTT AAATT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATT
16011 ATTCGATCTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (6 bp):
AAATTT
Found at i:16091 original size:20 final size:21
Alignment explanation
Indices: 16050--16091 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
16040 AAATTACCCC
*
16050 TAAAAAGATAAAAATATTATA
1 TAAAAAGATAAAAATATAATA
16071 TAAAAA-ATAAGAAATA-AATA
1 TAAAAAGATAA-AAATATAATA
16091 T
1 T
16092 TAAATAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (21 bp):
TAAAAAGATAAAAATATAATA
Found at i:17226 original size:23 final size:22
Alignment explanation
Indices: 17186--17240 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
17176 TGGACCTGCA
17186 AAAATAAAAAATATTAATAAT-
1 AAAATAAAAAATATTAATAATG
17207 AATAATAAATAAAT-TATAATAATG
1 AA-AATAAA-AAATAT-TAATAATG
17231 AAAATAAAAA
1 AAAATAAAAA
17241 TATAAAACCC
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
21 2 0.07
22 9 0.30
23 17 0.57
24 2 0.07
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (22 bp):
AAAATAAAAAATATTAATAATG
Found at i:17994 original size:39 final size:39
Alignment explanation
Indices: 17942--18124 Score: 285
Period size: 39 Copynumber: 4.7 Consensus size: 39
17932 ATTTTGAAAG
* *
17942 GGGTACTAAAATGAAACAAAAGCTAAAGTTTTTAACGGT
1 GGGTACTAAAATGAAACAAAAACTAAAATTTTTAACGGT
* * *
17981 GGGCACTAAAATGAAACAAAAACTAAAATTTTTAACTGC
1 GGGTACTAAAATGAAACAAAAACTAAAATTTTTAACGGT
* *
18020 GGGTACTAAAATGAAACAAAAACTAAAGTTTTTAACGAT
1 GGGTACTAAAATGAAACAAAAACTAAAATTTTTAACGGT
**
18059 GGGTACTAAAATGAAACAAAAACTAAAATTTTTAACATT
1 GGGTACTAAAATGAAACAAAAACTAAAATTTTTAACGGT
18098 GGGTACTAAAATGAAACAAAAACTAAA
1 GGGTACTAAAATGAAACAAAAACTAAA
18125 TTGTAGGTAT
Statistics
Matches: 131, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 131 1.00
ACGTcount: A:0.50, C:0.11, G:0.15, T:0.24
Consensus pattern (39 bp):
GGGTACTAAAATGAAACAAAAACTAAAATTTTTAACGGT
Found at i:18071 original size:78 final size:78
Alignment explanation
Indices: 17942--18124 Score: 314
Period size: 78 Copynumber: 2.3 Consensus size: 78
17932 ATTTTGAAAG
* *
17942 GGGTACTAAAATGAAACAAAAGCTAAAGTTTTTAACGGTGGGCACTAAAATGAAACAAAAACTAA
1 GGGTACTAAAATGAAACAAAAACTAAAGTTTTTAACGATGGGCACTAAAATGAAACAAAAACTAA
18007 AATTTTTAAC-TGC
66 AATTTTTAACAT-C
*
18020 GGGTACTAAAATGAAACAAAAACTAAAGTTTTTAACGATGGGTACTAAAATGAAACAAAAACTAA
1 GGGTACTAAAATGAAACAAAAACTAAAGTTTTTAACGATGGGCACTAAAATGAAACAAAAACTAA
*
18085 AATTTTTAACATT
66 AATTTTTAACATC
18098 GGGTACTAAAATGAAACAAAAACTAAA
1 GGGTACTAAAATGAAACAAAAACTAAA
18125 TTGTAGGTAT
Statistics
Matches: 100, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
78 99 0.99
79 1 0.01
ACGTcount: A:0.50, C:0.11, G:0.15, T:0.24
Consensus pattern (78 bp):
GGGTACTAAAATGAAACAAAAACTAAAGTTTTTAACGATGGGCACTAAAATGAAACAAAAACTAA
AATTTTTAACATC
Found at i:19366 original size:58 final size:58
Alignment explanation
Indices: 19244--19366 Score: 144
Period size: 58 Copynumber: 2.1 Consensus size: 58
19234 ACCATTTTGG
* * * *
19244 AACTTTTAATAGTCGATGGACTTAATAAAGTAACATTCTATAGTTGAAGGATCATTTGT
1 AACTTTTAATAGTCGATGGACTTAATAAAGTAACA-TCTATAATCGAAGGACCATTTAT
*
19303 AACTTTTAATAGTCGATGG-CTTAATAAAGTAGTACA-CTATAATCG-GGGACCATTTAT
1 AACTTTTAATAGTCGATGGACTTAATAAAGTA--ACATCTATAATCGAAGGACCATTTAT
19360 ATACTTT
1 A-ACTTT
19367 ACGTAGAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
57 10 0.18
58 24 0.43
59 19 0.34
60 3 0.05
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (58 bp):
AACTTTTAATAGTCGATGGACTTAATAAAGTAACATCTATAATCGAAGGACCATTTAT
Found at i:19620 original size:19 final size:19
Alignment explanation
Indices: 19596--19636 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
19586 TTGAACATTA
19596 TATAA-TTTTATCCTTAAAT
1 TATAATTTTTATCC-TAAAT
*
19615 TATAATTTTTATTCTAAAT
1 TATAATTTTTATCCTAAAT
19634 TAT
1 TAT
19637 TTCTCAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (19 bp):
TATAATTTTTATCCTAAAT
Found at i:19663 original size:122 final size:120
Alignment explanation
Indices: 19476--19714 Score: 252
Period size: 122 Copynumber: 2.0 Consensus size: 120
19466 TTAAATATTT
* * * * * **
19476 TAATTTTATCTTTAAATTATGACTTTTTTTTAAAGTTACTTCTTAAATTATTGAACGTTTTAATT
1 TAATTTTATCCTTAAATTATGAATTTTTTTTAAAGTTACTTCTCAAATTACTGAACATTCCAATT
* * *
19541 TCATCTTCAAACTAGGACGATCATTTTAAATT-AGTCTTTAAATGTTTGAACATTATA
66 TCATCCTAAAACTA-GA-AATCATTTTAAATTGA-TCTTTAAATGTTTGAACATTATA
*
19598 TAATTTTATCCTTAAATTAT-AATTTTTATTCTAAA-TTATTTCTCAAACTT-CTGAACATTCCA
1 TAATTTTATCCTTAAATTATGAATTTTT-TT-TAAAGTTACTTCTCAAA-TTACTGAACATTCCA
* * * * *
19660 ATTTTATCCTAAAACTATAAATTATTTTATATTGATCTTTAAATTTTTGAACATT
63 ATTTCATCCTAAAACTAGAAATCATTTTAAATTGATCTTTAAATGTTTGAACATT
19715 CTAATTCCAT
Statistics
Matches: 97, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
120 30 0.31
121 8 0.08
122 53 0.55
123 6 0.06
ACGTcount: A:0.34, C:0.12, G:0.05, T:0.49
Consensus pattern (120 bp):
TAATTTTATCCTTAAATTATGAATTTTTTTTAAAGTTACTTCTCAAATTACTGAACATTCCAATT
TCATCCTAAAACTAGAAATCATTTTAAATTGATCTTTAAATGTTTGAACATTATA
Found at i:27207 original size:68 final size:69
Alignment explanation
Indices: 27097--27232 Score: 215
Period size: 68 Copynumber: 2.0 Consensus size: 69
27087 GGTTGGGTCG
*
27097 GGTTCGGATTTTCTATCAAAAAATTGGAACGAATTCAGATCGGTAGAGAATATATATTTTTCAGA
1 GGTTCAGATTTTCTATCAAAAAATTGGAACGAATTCAGATCGGTAGAGAATATATATTTTTCAGA
27162 TCAA
66 TCAA
*
27166 GGTTCAGATTTTCTAT-AAAAAATTAGG-ACGAATTC-GAATCGGTGGAGAATATATATTTTTCA
1 GGTTCAGATTTTCTATCAAAAAATT-GGAACGAATTCAG-ATCGGTAGAGAATATATATTTTTCA
27228 GATCA
64 GATCA
27233 TGTTAAGTTG
Statistics
Matches: 63, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
67 1 0.02
68 45 0.71
69 17 0.27
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (69 bp):
GGTTCAGATTTTCTATCAAAAAATTGGAACGAATTCAGATCGGTAGAGAATATATATTTTTCAGA
TCAA
Found at i:30309 original size:17 final size:17
Alignment explanation
Indices: 30287--30325 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
30277 TGAATCAAAT
30287 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
30304 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
30321 -AATTA
1 TAATTA
30326 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:35153 original size:3 final size:3
Alignment explanation
Indices: 35145--35195 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
35135 TAGAATTCAA
35145 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
35192 AAT A
1 AAT A
35196 TAAAAAATAG
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:43929 original size:14 final size:15
Alignment explanation
Indices: 43905--43933 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
43895 AAAGTAAGAA
43905 TGGGCAGAGGGAGAG
1 TGGGCAGAGGGAGAG
43920 TGGG-AGAGGGAGAG
1 TGGGCAGAGGGAGAG
43934 AGAGAGAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.03, G:0.62, T:0.07
Consensus pattern (15 bp):
TGGGCAGAGGGAGAG
Found at i:48731 original size:60 final size:60
Alignment explanation
Indices: 48667--48813 Score: 179
Period size: 60 Copynumber: 2.4 Consensus size: 60
48657 TGGTTTTTAC
* * *
48667 ACTTTTTAATATTTCAATTCCATCCCTAAACTATGACTCTCATTCTAAATTAGTC-CTTAA
1 ACTTTTTAACATTTCAATTCCATCCCTAAACTATGACCCTCATTCTAAATTAGTCTC-CAA
* * * * *
48727 ACTTTTAAACATTTCAATTTCATTCCTAAACTATGACCCTCTTTCTAAATTGGTCTCCAA
1 ACTTTTTAACATTTCAATTCCATCCCTAAACTATGACCCTCATTCTAAATTAGTCTCCAA
* *
48787 ACTTTTTAAACATTCCCATTCCATCCC
1 ACTTTTT-AACATTTCAATTCCATCCC
48814 AAATTCATCC
Statistics
Matches: 72, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
60 56 0.78
61 16 0.22
ACGTcount: A:0.30, C:0.27, G:0.03, T:0.40
Consensus pattern (60 bp):
ACTTTTTAACATTTCAATTCCATCCCTAAACTATGACCCTCATTCTAAATTAGTCTCCAA
Found at i:49029 original size:60 final size:60
Alignment explanation
Indices: 48965--49112 Score: 142
Period size: 60 Copynumber: 2.5 Consensus size: 60
48955 GTTCAACAAA
* * * **
48965 TTTGAAGACCAATTTAAAATGACGGTCATAGTTTGGGGATGAA-ATTAAAATTTTTAAAAG
1 TTTGAAGACCAATTTAAAATGAAGGTCATAGTTTAGAGAT-AAGATTAAAACATTTAAAAG
* ** * *
49025 TTTGAGGATTAATTTAGAATGATA-GTCATAGTTTAGATATAAGATTAAAACATTTAAAAG
1 TTTGAAGACCAATTTAAAATGA-AGGTCATAGTTTAGAGATAAGATTAAAACATTTAAAAG
49085 TTT-AGAGACCGAA-TTAAAATGAAGGTCA
1 TTTGA-AGACC-AATTTAAAATGAAGGTCA
49113 AATTTTTTAA
Statistics
Matches: 69, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
59 4 0.06
60 63 0.91
61 2 0.03
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (60 bp):
TTTGAAGACCAATTTAAAATGAAGGTCATAGTTTAGAGATAAGATTAAAACATTTAAAAG
Found at i:53300 original size:21 final size:22
Alignment explanation
Indices: 53271--53317 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
53261 ATTCATTGTA
* * *
53271 TTGATGTGGCGGTCTACTGT-G
1 TTGACGTGGCAGTCCACTGTGG
53292 TTGACGTGGCAGTCCACTGTGG
1 TTGACGTGGCAGTCCACTGTGG
53314 TTGA
1 TTGA
53318 TAATGTGGCG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.13, C:0.17, G:0.36, T:0.34
Consensus pattern (22 bp):
TTGACGTGGCAGTCCACTGTGG
Found at i:56464 original size:32 final size:31
Alignment explanation
Indices: 56428--56504 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
56418 CGGGGCCGTG
*
56428 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
56460 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
56491 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
56505 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:56487 original size:63 final size:63
Alignment explanation
Indices: 56381--56504 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
56371 CCCTAAGGGA
* * ** *
56381 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
56444 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
56505 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.26, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:57386 original size:7 final size:7
Alignment explanation
Indices: 57374--57404 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
57364 GTCAAAGAAA
57374 GTCAACG
1 GTCAACG
57381 GTCAACG
1 GTCAACG
*
57388 GTCAACA
1 GTCAACG
57395 GTCAACG
1 GTCAACG
57402 GTC
1 GTC
57405 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:57423 original size:22 final size:22
Alignment explanation
Indices: 57395--57436 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
57385 ACGGTCAACA
57395 GTCAACGGTCGGGTCGGGTCGG
1 GTCAACGGTCGGGTCGGGTCGG
57417 GTCAACGGTCGGGTCGGGTC
1 GTCAACGGTCGGGTCGGGTC
57437 AGACCGGTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.10, C:0.24, G:0.48, T:0.19
Consensus pattern (22 bp):
GTCAACGGTCGGGTCGGGTCGG
Found at i:57451 original size:9 final size:9
Alignment explanation
Indices: 57433--57531 Score: 90
Period size: 9 Copynumber: 10.3 Consensus size: 9
57423 GGTCGGGTCG
*
57433 GGTCAGACC
1 GGTCAAACC
57442 GGTCAAACC
1 GGTCAAACC
* *
57451 GATTCAGACC
1 G-GTCAAACC
57461 GGTCAAACC
1 GGTCAAACC
*
57470 GGTTCGAACC
1 GG-TCAAACC
*
57480 GGTTGAAACC
1 GG-TCAAACC
57490 GGTCAAACC
1 GGTCAAACC
57499 GGTCAGAACC
1 GGTCA-AACC
*
57509 GGTTGAAAACC
1 GG-T-CAAACC
57520 GGTCAAACC
1 GGTCAAACC
57529 GGT
1 GGT
57532 TTCCAGCAGC
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
9 36 0.49
10 30 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:57457 original size:19 final size:19
Alignment explanation
Indices: 57435--57532 Score: 101
Period size: 19 Copynumber: 5.1 Consensus size: 19
57425 TCGGGTCGGG
*
57435 TCAGACCGGTCAAACCGAT
1 TCAGACCGGTCAAACCGGT
57454 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
57473 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
57492 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
* *
57512 TGAAAACCGGTCAAACCGGT
1 T-CAGACCGGTCAAACCGGT
57532 T
1 T
57533 TCCAGCAGCC
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
18 3 0.04
19 38 0.56
20 17 0.25
21 10 0.15
ACGTcount: A:0.30, C:0.29, G:0.26, T:0.16
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:57490 original size:29 final size:31
Alignment explanation
Indices: 57458--57532 Score: 129
Period size: 29 Copynumber: 2.5 Consensus size: 31
57448 ACCGATTCAG
57458 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
57487 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
57517 ACCGGTCAAACCGGTT
1 ACCGGTCAAACCGGTT
57533 TCCAGCAGCC
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.56
30 16 0.37
31 1 0.02
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.16
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:63279 original size:32 final size:31
Alignment explanation
Indices: 63243--63319 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
63233 CGGGGCCGTG
*
63243 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
63275 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
63306 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
63320 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:63302 original size:63 final size:63
Alignment explanation
Indices: 63196--63319 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
63186 CCCTAAGGGA
* * ** *
63196 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
63259 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
63320 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.26, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:64202 original size:7 final size:7
Alignment explanation
Indices: 64190--64227 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
64180 GTCAAAGAAA
64190 GTCAACG
1 GTCAACG
64197 GTCAACG
1 GTCAACG
64204 GTCAACG
1 GTCAACG
64211 GTCAACG
1 GTCAACG
64218 GTCAACG
1 GTCAACG
64225 GTC
1 GTC
64228 GGGTCGGGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:64252 original size:22 final size:22
Alignment explanation
Indices: 64224--64276 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
64214 AACGGTCAAC
*
64224 GGTCGGGTCGGGTTAACGGTCG
1 GGTCGGGTCGGGTCAACGGTCG
64246 GGTCGGGTCGGGTCAACGGTCG
1 GGTCGGGTCGGGTCAACGGTCG
64268 GGTCGGGTC
1 GGTCGGGTC
64277 AGACCGGTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.08, C:0.21, G:0.51, T:0.21
Consensus pattern (22 bp):
GGTCGGGTCGGGTCAACGGTCG
Found at i:64266 original size:17 final size:17
Alignment explanation
Indices: 64217--64277 Score: 68
Period size: 17 Copynumber: 3.3 Consensus size: 17
64207 AACGGTCAAC
64217 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
64234 GGTTAACGGTCGGGTCGGGTCG
1 GGTCAA----C-GGTCGGGTCG
64256 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
64273 GGTCA
1 GGTCA
64278 GACCGGTTCG
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
17 20 0.54
18 1 0.03
21 1 0.03
22 15 0.41
ACGTcount: A:0.11, C:0.21, G:0.48, T:0.20
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:64306 original size:29 final size:31
Alignment explanation
Indices: 64273--64344 Score: 114
Period size: 29 Copynumber: 2.4 Consensus size: 31
64263 GGTCGGGTCG
*
64273 GGTCAGACCGGTTC-GAACCGGTTG-AAACC
1 GGTCAAACCGGTTCAGAACCGGTTGAAAACC
64302 GGTCAAACCGG-TCAGAACCGGTTGAAAACC
1 GGTCAAACCGGTTCAGAACCGGTTGAAAACC
64332 GGTCAAACCGGTT
1 GGTCAAACCGGTT
64345 TCCAGCAGCC
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 20 0.51
30 16 0.41
31 1 0.03
ACGTcount: A:0.28, C:0.26, G:0.29, T:0.17
Consensus pattern (31 bp):
GGTCAAACCGGTTCAGAACCGGTTGAAAACC
Found at i:64311 original size:9 final size:9
Alignment explanation
Indices: 64273--64343 Score: 61
Period size: 10 Copynumber: 7.3 Consensus size: 9
64263 GGTCGGGTCG
*
64273 GGTCAGACC
1 GGTCAAACC
*
64282 GGTTCGAACC
1 GG-TCAAACC
*
64292 GGTTGAAACC
1 GG-TCAAACC
64302 GGTCAAACC
1 GGTCAAACC
64311 GGTCAGAACC
1 GGTCA-AACC
*
64321 GGTTGAAAACC
1 GG-T-CAAACC
64332 GGTCAAACC
1 GGTCAAACC
64341 GGT
1 GGT
64344 TTCCAGCAGC
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
9 21 0.41
10 22 0.43
11 7 0.14
12 1 0.02
ACGTcount: A:0.28, C:0.27, G:0.30, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:64342 original size:20 final size:21
Alignment explanation
Indices: 64306--64344 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
64296 GAAACCGGTC
64306 AAACCGGTCAGAACCGGTTGA
1 AAACCGGTCAGAACCGGTTGA
64327 AAACCGGTCA-AACCGGTT
1 AAACCGGTCAGAACCGGTT
64345 TCCAGCAGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.33, C:0.26, G:0.26, T:0.15
Consensus pattern (21 bp):
AAACCGGTCAGAACCGGTTGA
Found at i:65688 original size:2 final size:2
Alignment explanation
Indices: 65681--65717 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
65671 TTATAATTTT
65681 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
65718 GATAAATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:65968 original size:52 final size:51
Alignment explanation
Indices: 65862--66052 Score: 197
Period size: 51 Copynumber: 3.7 Consensus size: 51
65852 GTACATACTT
* * * * * * *
65862 ACACCGATATAAGTAGGTGTTAAGTGTTACA-CTTTTTATTTTATTCACTT
1 ACACCGGTGTAAGTATGTGTTAAGTGCTATATTTTTTTATTTTATTCACTC
* *
65912 ACACCGGTGTAAGTATGTATTAAATGCTATATTTTTTTTATTTTATTCACTC
1 ACACCGGTGTAAGTATGTGTTAAGTGCTATA-TTTTTTTATTTTATTCACTC
* * *
65964 ACACCGGTGTAAGTATGTGTTAAGTGCT-TCACTTATTTATTTTATTCAGTC
1 ACACCGGTGTAAGTATGTGTTAAGTGCTAT-ATTTTTTTATTTTATTCACTC
* ** * *
66015 ACATCATTGTAAGTATGTGTTAAGTGTTATAATTTTTT
1 ACACCGGTGTAAGTATGTGTTAAGTGCTATATTTTTTT
66053 GTAATATGAA
Statistics
Matches: 117, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
50 24 0.21
51 48 0.41
52 45 0.38
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.46
Consensus pattern (51 bp):
ACACCGGTGTAAGTATGTGTTAAGTGCTATATTTTTTTATTTTATTCACTC
Found at i:66017 original size:51 final size:50
Alignment explanation
Indices: 65862--66040 Score: 200
Period size: 52 Copynumber: 3.5 Consensus size: 50
65852 GTACATACTT
* * * *
65862 ACACCGATATAAGTAGGTGTTAAGTG-TTACACTTTTTATTTTATTCACTT
1 ACACCGGTGTAAGTATGTGTTAAGTGCTT-CACTTTTTATTTTATTCACTC
* * *
65912 ACACCGGTGTAAGTATGTATTAAATGCTAT-ATTTTTTTTATTTTATTCACTC
1 ACACCGGTGTAAGTATGTGTTAAGTGCT-TCA--CTTTTTATTTTATTCACTC
*
65964 ACACCGGTGTAAGTATGTGTTAAGTGCTTCACTTATTTATTTTATTCAGTC
1 ACACCGGTGTAAGTATGTGTTAAGTGCTTCACTT-TTTATTTTATTCACTC
* **
66015 ACATCATTGTAAGTATGTGTTAAGTG
1 ACACCGGTGTAAGTATGTGTTAAGTG
66041 TTATAATTTT
Statistics
Matches: 109, Mismatches: 14, Indels: 11
0.81 0.10 0.08
Matches are distributed among these distances:
50 24 0.22
51 40 0.37
52 45 0.41
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.44
Consensus pattern (50 bp):
ACACCGGTGTAAGTATGTGTTAAGTGCTTCACTTTTTATTTTATTCACTC
Found at i:74174 original size:14 final size:14
Alignment explanation
Indices: 74137--74166 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
74127 ATTCATTGAT
*
74137 AATAGCTAAATTTA
1 AATAGCAAAATTTA
74151 AATAGCAAAATTTA
1 AATAGCAAAATTTA
74165 AA
1 AA
74167 AGGGAAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.30
Consensus pattern (14 bp):
AATAGCAAAATTTA
Found at i:76237 original size:31 final size:31
Alignment explanation
Indices: 76199--76269 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
76189 TTAATGGTTG
76199 AGTACTAAAATGAAATAAAATTGATAGTTTA
1 AGTACTAAAATGAAATAAAATTGATAGTTTA
* *
76230 AGTACTAAAATGTATTAAAATTGATAGTTTA
1 AGTACTAAAATGAAATAAAATTGATAGTTTA
*
76261 AGTATTAAA
1 AGTACTAAA
76270 TGCATAGTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.49, C:0.03, G:0.13, T:0.35
Consensus pattern (31 bp):
AGTACTAAAATGAAATAAAATTGATAGTTTA
Found at i:78143 original size:29 final size:29
Alignment explanation
Indices: 78111--78203 Score: 71
Period size: 29 Copynumber: 3.1 Consensus size: 29
78101 TTTTAGATTG
78111 ATCCTTAAACTTTTAAATATTTTAATTTC
1 ATCCTTAAACTTTTAAATATTTTAATTTC
* * * * **
78140 ATCCCTAAACTATGATTATCATTTTAAACT-
1 ATCCTTAAACTTTTA-AAT-ATTTTAATTTC
* * *
78170 AGTCCTCAAACTTTTGAATATTTCAATTTC
1 A-TCCTTAAACTTTTAAATATTTTAATTTC
78200 ATCC
1 ATCC
78204 CCGAATATTG
Statistics
Matches: 45, Mismatches: 15, Indels: 8
0.66 0.22 0.12
Matches are distributed among these distances:
29 22 0.49
30 6 0.13
31 17 0.38
ACGTcount: A:0.33, C:0.19, G:0.03, T:0.44
Consensus pattern (29 bp):
ATCCTTAAACTTTTAAATATTTTAATTTC
Found at i:78222 original size:60 final size:60
Alignment explanation
Indices: 78111--78271 Score: 175
Period size: 60 Copynumber: 2.7 Consensus size: 60
78101 TTTTAGATTG
* * * * *
78111 ATCCTTAAACTTTTAAATATTTTAATTTCATCCCTAAACTATGATTATCATTTTAAACTA
1 ATCCTCAAACTTTTGAATATTTCAATTTCATCCCCAAACTATGATTATCATTCTAAACTA
* * *
78171 GTCCTCAAACTTTTGAATATTTCAATTTCATCCCCGAA-TATTGATCT-TCATTCTAAATTA
1 ATCCTCAAACTTTTGAATATTTCAATTTCATCCCCAAACTA-TGAT-TATCATTCTAAACTA
* * *
78231 ATCCCCAAAGCTTTTGAACATTCCAATTTCAT-CCCAAACTA
1 ATCCTCAAA-CTTTTGAATATTTCAATTTCATCCCCAAACTA
78272 AATGTATATT
Statistics
Matches: 84, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
59 2 0.02
60 59 0.70
61 23 0.27
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.40
Consensus pattern (60 bp):
ATCCTCAAACTTTTGAATATTTCAATTTCATCCCCAAACTATGATTATCATTCTAAACTA
Done.