Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000525.1 Hibiscus syriacus cultivar Beakdansim tig00001007_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: 91137
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:3582 original size:15 final size:16
Alignment explanation
Indices: 3558--3598 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
3548 TAACTTGAAG
*
3558 CCTCTATTTTA-TTTT
1 CCTCTCTTTTATTTTT
3573 CCTCTCTTTTATTTTT
1 CCTCTCTTTTATTTTT
3589 CCTCTCTTTT
1 CCTCTCTTTT
3599 CACACCCTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.66
Consensus pattern (16 bp):
CCTCTCTTTTATTTTT
Found at i:12833 original size:31 final size:31
Alignment explanation
Indices: 12798--12858 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
12788 TAGCATAGGA
12798 AGGCATTTGCTCGATAGCTTCAAAAAAGGGC
1 AGGCATTTGCTCGATAGCTTCAAAAAAGGGC
* *
12829 AGGCATTTGCTCGATGGCTTCAAGAAAGGG
1 AGGCATTTGCTCGATAGCTTCAAAAAAGGG
12859 TATATTGATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.30, C:0.18, G:0.30, T:0.23
Consensus pattern (31 bp):
AGGCATTTGCTCGATAGCTTCAAAAAAGGGC
Found at i:13435 original size:21 final size:20
Alignment explanation
Indices: 13402--13440 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
13392 CATCAAGATC
*
13402 TTTGTAGATGCCATGAAATAT
1 TTTGTAGAGGCCAT-AAATAT
*
13423 TTTGTCGAGGCCATAAAT
1 TTTGTAGAGGCCATAAAT
13441 TCCTGCAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.36
Consensus pattern (20 bp):
TTTGTAGAGGCCATAAATAT
Found at i:16878 original size:84 final size:82
Alignment explanation
Indices: 16697--16865 Score: 259
Period size: 84 Copynumber: 2.0 Consensus size: 82
16687 AAACTCATGT
* *
16697 TTTAAGATATTATTTT-AAATATTATATTTTATCTTTGTTTTAGGTATTTAGTTTAAATAATTTT
1 TTTAGGATATTATTTTAAAATATTATATCTTATCTTTGTTTTAGGTATTTAGTTTAAATAATTTT
*
16761 AAGTGTTTTAATTAGGA
66 AAGTATTTTAATTAGGA
* *
16778 TTTAGGATATTATTTTAAATATATTTTATCTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTT
1 TTTAGGATATTATTTTAAA-ATATTATATCTTATCTTTGTTTTAGGTA-TTTAGTTTAAATAATT
*
16843 TTAAGTATTTTAATTAGGT
64 TTAAGTATTTTAATTAGGA
16862 TTTA
1 TTTA
16866 TTTTTTTATT
Statistics
Matches: 79, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
81 15 0.19
82 2 0.03
83 26 0.33
84 36 0.46
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (82 bp):
TTTAGGATATTATTTTAAAATATTATATCTTATCTTTGTTTTAGGTATTTAGTTTAAATAATTTT
AAGTATTTTAATTAGGA
Found at i:20232 original size:18 final size:18
Alignment explanation
Indices: 20209--20263 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 18
20199 TATAATCGAT
20209 TCCTTCTCGTTGAGTGAA
1 TCCTTCTCGTTGAGTGAA
*
20227 TCCTTCTCATTGAGTGAA
1 TCCTTCTCGTTGAGTGAA
* * *
20245 TCATTCTCGCTGCGTGAA
1 TCCTTCTCGTTGAGTGAA
20263 T
1 T
20264 TCTGTCATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.38
Consensus pattern (18 bp):
TCCTTCTCGTTGAGTGAA
Found at i:21825 original size:31 final size:31
Alignment explanation
Indices: 21766--21825 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
21756 TTGATGGATG
* * *
21766 GGGGACTAAAATTGAATGAATCGGTAACGTT
1 GGGGACTAAAATCGAACGAATCGATAACGTT
* *
21797 GGGGACTAAAATCGAACGGATTGATAACG
1 GGGGACTAAAATCGAACGAATCGATAACG
21826 ATAAGGTTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.37, C:0.12, G:0.30, T:0.22
Consensus pattern (31 bp):
GGGGACTAAAATCGAACGAATCGATAACGTT
Found at i:22983 original size:56 final size:55
Alignment explanation
Indices: 22901--23005 Score: 133
Period size: 56 Copynumber: 1.9 Consensus size: 55
22891 TTAATATATG
* * *
22901 GTATTAAATATATGATATTTGATAAATATAACTA-CTAAATTGAATTAAAAAAATAA
1 GTATCAAATATATGAAATTTGATAAATATAAATATC-AAATT-AATTAAAAAAATAA
*
22957 GTATCAAATATAT-AAAGTTTGTTAAATATAAATATCAAATTAATTAAAA
1 GTATCAAATATATGAAA-TTTGATAAATATAAATATCAAATTAATTAAAA
23006 CGATATATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
55 10 0.23
56 32 0.74
57 1 0.02
ACGTcount: A:0.53, C:0.04, G:0.07, T:0.36
Consensus pattern (55 bp):
GTATCAAATATATGAAATTTGATAAATATAAATATCAAATTAATTAAAAAAATAA
Found at i:23401 original size:60 final size:58
Alignment explanation
Indices: 23328--23458 Score: 154
Period size: 59 Copynumber: 2.2 Consensus size: 58
23318 ATAAAAACGT
* * *
23328 AAAGTACACAAATGGTCCCCCGACTATATGATATTGTTTTATTGAGTCCCTTGACTATTA
1 AAAGTACA-AAATGGT-CCCCAACTATAGGATATTGTTTTATTGAGTCCCTCGACTATTA
* * * * *
23388 AAAGTAACAAAATGGTCCTCAACTATAGGGTGTTGTTTTGTTGAGTCTCTCGACTATTA
1 AAAGT-ACAAAATGGTCCCCAACTATAGGATATTGTTTTATTGAGTCCCTCGACTATTA
23447 AAAGTTACAAAA
1 AAAG-TACAAAA
23459 CGTTCACCTG
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
59 45 0.74
60 13 0.21
61 3 0.05
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Consensus pattern (58 bp):
AAAGTACAAAATGGTCCCCAACTATAGGATATTGTTTTATTGAGTCCCTCGACTATTA
Found at i:28791 original size:55 final size:54
Alignment explanation
Indices: 28730--28945 Score: 190
Period size: 55 Copynumber: 3.9 Consensus size: 54
28720 GACTTGAAAC
* * *
28730 ATCTTCAAATGACGAGCCTGCTCCCTATTCCTTCAG-GAAGTATAAGACTCGAGCA
1 ATCTTCAAA-AACGAGCCTGCTCTCTATTCCTTCAGAG-AGTATAAGACTCGAACA
* * * * *
28785 ATCTTCATAAAATGTGTCTGCTCTCTATTCATTCAGAGAGTATAAGACTTGAACA
1 ATCTTCA-AAAACGAGCCTGCTCTCTATTCCTTCAGAGAGTATAAGACTCGAACA
* *
28840 ATCTTCAATAAAACGGGTCC-GCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAAAA
1 ATCTTC-A-AAAACGAG-CCTGCTCTCTATTCCTTCAGAGAGTATAAG-ACTCGAACA
* * *
28896 ATCTTCAATAAAC-AGGTCC-GCTCCCTATTCTTTCAGAGAGTATAGGACTC
1 ATCTTCAA-AAACGA-G-CCTGCTCTCTATTCCTTCAGAGAGTATAAGACTC
28946 AATCTTTAAC
Statistics
Matches: 135, Mismatches: 18, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
54 1 0.01
55 85 0.63
56 48 0.36
57 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (54 bp):
ATCTTCAAAAACGAGCCTGCTCTCTATTCCTTCAGAGAGTATAAGACTCGAACA
Found at i:28876 original size:56 final size:56
Alignment explanation
Indices: 28749--29200 Score: 282
Period size: 51 Copynumber: 8.6 Consensus size: 56
28739 TGACGAGCCT
* * * *
28749 GCTCCCTATTCCTTCAG-GAAGTATAAGACTCGAGCAATCTTC-ATAAAATGTGTCT
1 GCTCCCTATTCCTTCAGAG-AGTATAAGACTCGAACAATCTTCAATAAAACGGGTCC
* * *
28804 GCTCTCTATTCATTCAGAGAGTATAAGACTTGAACAATCTTCAATAAAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAACGGGTCC
* * *
28860 GCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAAAAATCTTCAAT-AAACAGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAATAAAACGGGTCC
* * * * * *
28915 GCTCCCTATTCTTTCAGAGAGTATAGGACT----CAATCTTTAA-CAAACGTGTTC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAACGGGTCC
* ** **
28966 GCTCCCTA-TCCGTTCAGGGAGTAT-AGAACTCG----ATCTTCAA-CGAACTTGTCC
1 GCTCCCTATTCC-TTCAGAGAGTATAAG-ACTCGAACAATCTTCAATAAAACGGGTCC
* * ** **
29017 GCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCAA-CGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAACGGGTCC
* * ** **
29068 GCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCAA-CGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAACGGGTCC
* * ** **
29119 GCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCAA-CGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAACGGGTCC
* *
29170 GCTCCCTATTCATTCAGAGAGTATAGGACTC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTC
29201 AATCTTCAAC
Statistics
Matches: 354, Mismatches: 29, Indels: 31
0.86 0.07 0.07
Matches are distributed among these distances:
50 3 0.01
51 225 0.64
52 3 0.01
55 72 0.20
56 51 0.14
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (56 bp):
GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAACGGGTCC
Found at i:28973 original size:51 final size:51
Alignment explanation
Indices: 28799--29215 Score: 537
Period size: 51 Copynumber: 8.0 Consensus size: 51
28789 TCATAAAATG
* * * ** *
28799 TGTCTGCTCTCTATTCATTCAGAGAGTATAAGACTTGAACAATCTTCAATAAAACG
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGAC-T---CAATCTTCAA-CGAACT
* * * * ** *
28855 GGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAATAAACA
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTC----AATCTTCAACGAACT
* * * * *
28910 GGTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTTAACAAACG
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
* * * * * *
28961 TGTTCGCTCCCTATCCGTTCAGGGAGTATAGAACTCGATCTTCAACGAACT
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
29012 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
29063 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
29114 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
29165 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
29216 AATTTGCTTC
Statistics
Matches: 328, Mismatches: 29, Indels: 13
0.89 0.08 0.04
Matches are distributed among these distances:
51 251 0.77
52 1 0.00
55 38 0.12
56 38 0.12
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (51 bp):
TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
Found at i:30621 original size:18 final size:16
Alignment explanation
Indices: 30536--30634 Score: 73
Period size: 14 Copynumber: 6.1 Consensus size: 16
30526 TTTATTTCTT
30536 TTTTTTCTC-TTTTT-
1 TTTTTTCTCATTTTTC
*
30550 GTTTTT-TCATTTTTC
1 TTTTTTCTCATTTTTC
*
30565 ATTTTTTTCTTCCATTTTCC
1 --TTTTTTC-T-CATTTTTC
*
30585 ATTTTTTC-C-TTTTTG
1 -TTTTTTCTCATTTTTC
30600 TTTTTTCCATCATTTTTC
1 TTTTTT-C-TCATTTTTC
30618 TTTTTTCTCATTTTTC
1 TTTTTTCTCATTTTTC
30634 T
1 T
30635 CATTTTTTTC
Statistics
Matches: 67, Mismatches: 7, Indels: 20
0.71 0.07 0.21
Matches are distributed among these distances:
13 2 0.03
14 16 0.24
15 5 0.07
16 11 0.16
17 7 0.10
18 11 0.16
19 8 0.12
20 7 0.10
ACGTcount: A:0.07, C:0.18, G:0.02, T:0.73
Consensus pattern (16 bp):
TTTTTTCTCATTTTTC
Found at i:30632 original size:34 final size:37
Alignment explanation
Indices: 30551--30642 Score: 88
Period size: 35 Copynumber: 2.6 Consensus size: 37
30541 TCTCTTTTTG
* *
30551 TTTTT-TCATTTTTCATTTTTTTCTTCCATTTTCCAT
1 TTTTTCTCATTTTTCATTTTTTCCATCCATTTTCCAT
* *
30587 TTTTTC-C-TTTTT-GTTTTTTCCAT-CATTTTTC-T
1 TTTTTCTCATTTTTCATTTTTTCCATCCATTTTCCAT
30619 TTTTTCTCATTTTTCTCATTTTTT
1 TTTTTCTCA-TTTT-TCATTTTTT
30643 TCTCTTTTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
32 7 0.16
33 8 0.18
34 8 0.18
35 9 0.20
36 7 0.16
37 6 0.13
ACGTcount: A:0.09, C:0.18, G:0.01, T:0.72
Consensus pattern (37 bp):
TTTTTCTCATTTTTCATTTTTTCCATCCATTTTCCAT
Found at i:46648 original size:44 final size:43
Alignment explanation
Indices: 46553--46693 Score: 207
Period size: 44 Copynumber: 3.3 Consensus size: 43
46543 ATAGGTCAAG
** *
46553 ATCTATAGCGGCGTTTTTAAAACTAACGC-CACAAAAGGTTGAT
1 ATCTATAGCGGCGTTTTTGGAACAAACGCGCA-AAAAGGTTGAT
46596 ATCTATAGCGGCGTTTTTGGAACAAACGTCGCAAAAAGGTTGAT
1 ATCTATAGCGGCGTTTTTGGAACAAACG-CGCAAAAAGGTTGAT
46640 ATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAA-GTT-AT
1 ATCTATAGCGGCGTTTTTGGAACAAACG-CGCAAAAAGGTTGAT
46682 ATCTATAGCGGC
1 ATCTATAGCGGC
46694 CGCGAACGGT
Statistics
Matches: 92, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
42 14 0.15
43 28 0.30
44 48 0.52
45 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (43 bp):
ATCTATAGCGGCGTTTTTGGAACAAACGCGCAAAAAGGTTGAT
Found at i:46779 original size:43 final size:43
Alignment explanation
Indices: 46708--46996 Score: 413
Period size: 43 Copynumber: 6.8 Consensus size: 43
46698 AACGGTCGAG
* * * *
46708 ATCTATAACGGCATTTTTGGA-ATAAACGCCGCAAAAGTTCAT
1 ATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAT
* *
46750 ATCTATAGCAGCGTTTTTGGATACAAACGCCGCAAAAGGTCGAG
1 ATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTC-AT
* *
46794 ATCTATAGCGGCGTTTTTGGA-ACAAACGTCGCAAAAGGACAT
1 ATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAT
**
46836 ATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAATTCAT
1 ATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAT
*
46879 ATCTATAGCGGCGTTTTTGGATACAAATGCCGCAAAAGGTCAT
1 ATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAT
* * *
46922 ATCTATAGCTGCGTTTTTGGA-ACAAACGTCGGAAAAGGTCAT
1 ATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAT
*
46964 ATCTATAGCGGCGTTTTTGGATACAAATGCCGC
1 ATCTATAGCGGCGTTTTTGGATACAAACGCCGC
46997 TAATTACCTT
Statistics
Matches: 218, Mismatches: 25, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
42 78 0.36
43 119 0.55
44 21 0.10
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.27
Consensus pattern (43 bp):
ATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAT
Found at i:46798 original size:112 final size:112
Alignment explanation
Indices: 46596--46805 Score: 307
Period size: 112 Copynumber: 1.9 Consensus size: 112
46586 AAAGGTTGAT
* * * * *
46596 ATCTATAGCGGCGTTTTTGGAACAAACGTCGCAAAAAGGTTGATATCTATAGCGGCGTTTTTGGA
1 ATCTATAACGGCATTTTTGGAACAAACGCCGCAAAAAGGTTCATATCTATAGCAGCGTTTTTGGA
* *
46661 ACAAACGCCGCAAAAAGTTATATCTATAGCGGCCGCGAACGGTCGAG
66 ACAAACGCCGCAAAAAGTGAGATCTATAGCGGCCGCGAACGGTCGAG
*
46708 ATCTATAACGGCATTTTTGGAATAAACGCCGC-AAAA-GTTCATATCTATAGCAGCGTTTTTGGA
1 ATCTATAACGGCATTTTTGGAACAAACGCCGCAAAAAGGTTCATATCTATAGCAGCGTTTTTGGA
*
46771 TACAAACGCCGCAAAAGGTCGAGATCTATAGCGGC
66 -ACAAACGCCGCAAAAAGT-GAGATCTATAGCGGC
46806 GTTTTTGGAA
Statistics
Matches: 87, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
110 25 0.29
111 21 0.24
112 41 0.47
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (112 bp):
ATCTATAACGGCATTTTTGGAACAAACGCCGCAAAAAGGTTCATATCTATAGCAGCGTTTTTGGA
ACAAACGCCGCAAAAAGTGAGATCTATAGCGGCCGCGAACGGTCGAG
Found at i:46838 original size:154 final size:155
Alignment explanation
Indices: 46546--46847 Score: 430
Period size: 154 Copynumber: 2.0 Consensus size: 155
46536 CGCTGCCATA
* * * *
46546 GGTCAAGATCTATAGCGGCGTTTTTAAAACTAACGCCACAAAAGGTTGATATCTATAGCGGCGTT
1 GGTCAAGATCTATAACGGCATTTTTAAAACTAACGCCACAAAAGGTTCATATCTATAGCAGCGTT
* * *
46611 TTTGGAACAAACGTCGCAAAAAGGTTGATATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAA
66 TTTGGAACAAACGCCGCAAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAA
**
46676 AGTTATATCTATAGCGGCCGCGAAC
131 AGACATATCTATAGCGGCCGCGAAC
* ** *
46701 GGTCGAGATCTATAACGGCATTTTTGGAA-TAAACGCCGCAAAA-GTTCATATCTATAGCAGCGT
1 GGTCAAGATCTATAACGGCATTTTTAAAACT-AACGCCACAAAAGGTTCATATCTATAGCAGCGT
*
46764 TTTTGGATACAAACGCCGC-AAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGTCGCAA
65 TTTTGGA-ACAAACGCCGCAAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAA
*
46828 AAGGACATATCTATAGCGGC
129 AAAGACATATCTATAGCGGC
46848 GTTTTTGGAT
Statistics
Matches: 130, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
154 85 0.65
155 45 0.35
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.25
Consensus pattern (155 bp):
GGTCAAGATCTATAACGGCATTTTTAAAACTAACGCCACAAAAGGTTCATATCTATAGCAGCGTT
TTTGGAACAAACGCCGCAAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAA
AGACATATCTATAGCGGCCGCGAAC
Found at i:46965 original size:128 final size:129
Alignment explanation
Indices: 46708--46996 Score: 465
Period size: 128 Copynumber: 2.3 Consensus size: 129
46698 AACGGTCGAG
* * * *
46708 ATCTATAACGGCATTTTTGGA-ATAAACGCCGCAAAAGTTCATATCTATAGCAGCGTTTTTGGAT
1 ATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAATTCATATCTATAGCAGCGTTTTTGGAT
46772 ACAAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGTCGCAAAAGGACAT
66 ACAAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGTCGCAAAAGGACAT
*
46836 ATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAATTCATATCTATAGCGGCGTTTTTGGAT
1 ATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAATTCATATCTATAGCAGCGTTTTTGGAT
* * * * *
46901 ACAAATGCCGCAAAAGGTC-ATATCTATAGCTGCGTTTTTGGAACAAACGTCGGAAAAGGTCAT
66 ACAAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGTCGCAAAAGGACAT
*
46964 ATCTATAGCGGCGTTTTTGGATACAAATGCCGC
1 ATCTATAGCGGCGTTTTTGGATACAAACGCCGC
46997 TAATTACCTT
Statistics
Matches: 149, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
128 91 0.61
129 58 0.39
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.27
Consensus pattern (129 bp):
ATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAATTCATATCTATAGCAGCGTTTTTGGAT
ACAAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGTCGCAAAAGGACAT
Found at i:50557 original size:8 final size:8
Alignment explanation
Indices: 50544--50571 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
50534 AAGTCAGTAG
50544 AATCCCAA
1 AATCCCAA
50552 AATCCCAA
1 AATCCCAA
50560 AATCCCAA
1 AATCCCAA
50568 AATC
1 AATC
50572 TCGTACACGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.36, G:0.00, T:0.14
Consensus pattern (8 bp):
AATCCCAA
Found at i:51371 original size:82 final size:83
Alignment explanation
Indices: 51178--51374 Score: 245
Period size: 82 Copynumber: 2.4 Consensus size: 83
51168 TATAGCGGAT
* * * *
51178 GTTTTTATAAAAATGCCGCTAAAGTACTAAT-TTATTGTGGCGTTCGTCGAAAAAACGCCACTAT
1 GTTTATATAAAAATGCCGCTAAAGTACTACTCTTATTGTGGCATTCGTCGAAAAAACGCCACTAC
51242 AGATGGACCTATTGCGGC
66 AGATGGACCTATTGCGGC
* * * * * * * *
51260 GTTTGTATGAAAACGACACTAAAGTACTACTCTT-TTGTGGCATTCTTTGAAAAAACGCCATTAC
1 GTTTATATAAAAATGCCGCTAAAGTACTACTCTTATTGTGGCATTCGTCGAAAAAACGCCACTAC
* * *
51324 ATATGTACCTATTGCTGC
66 AGATGGACCTATTGCGGC
51342 GTTTATATAAAAATGCCGCTAAAGTACTACTCT
1 GTTTATATAAAAATGCCGCTAAAGTACTACTCT
51375 ATTACGGCGT
Statistics
Matches: 95, Mismatches: 19, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
82 93 0.98
83 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Consensus pattern (83 bp):
GTTTATATAAAAATGCCGCTAAAGTACTACTCTTATTGTGGCATTCGTCGAAAAAACGCCACTAC
AGATGGACCTATTGCGGC
Found at i:51398 original size:82 final size:82
Alignment explanation
Indices: 51178--51400 Score: 241
Period size: 82 Copynumber: 2.7 Consensus size: 82
51168 TATAGCGGAT
* * * * * *
51178 GTTTTTATAAAAATGCCGCTAAAGTACTAATTTATTGTGGCGTTCGTCGAAAAAACGCCACTATA
1 GTTTATATAAAAATGCCGCTAAAGTACTACTCTATTGTGGCGTTTGTTGAAAAAACGCCACTACA
51243 GATGGACCTATTGCGGC
66 GATGGACCTATTGCGGC
* * * * * * * *
51260 GTTTGTATGAAAACGACACTAAAGTACTACTCTTTTGTGGCATTCT-TTGAAAAAACGCCATTAC
1 GTTTATATAAAAATGCCGCTAAAGTACTACTCTATTGTGGCGTT-TGTTGAAAAAACGCCACTAC
* * *
51324 ATATGTACCTATTGCTGC
65 AGATGGACCTATTGCGGC
** * *
51342 GTTTATATAAAAATGCCGCTAAAGTACTACTCTATTACGGCGTTTGTTTAAGAAACGCC
1 GTTTATATAAAAATGCCGCTAAAGTACTACTCTATTGTGGCGTTTGTTGAAAAAACGCC
51401 GCTATATATT
Statistics
Matches: 112, Mismatches: 27, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
81 1 0.01
82 111 0.99
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (82 bp):
GTTTATATAAAAATGCCGCTAAAGTACTACTCTATTGTGGCGTTTGTTGAAAAAACGCCACTACA
GATGGACCTATTGCGGC
Found at i:64721 original size:18 final size:18
Alignment explanation
Indices: 64698--64740 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
64688 TTGAAGGTAG
* *
64698 CAACAAGGTTTGCTAGCT
1 CAACAAGGTGTGCAAGCT
64716 CAACAAGGTGTGCAAGCT
1 CAACAAGGTGTGCAAGCT
64734 CAACAAG
1 CAACAAG
64741 TCTCTATACG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.19
Consensus pattern (18 bp):
CAACAAGGTGTGCAAGCT
Found at i:71883 original size:19 final size:20
Alignment explanation
Indices: 71851--71888 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
71841 ACTACTATAT
71851 TACTTGCATCGA-TTGTGTA
1 TACTTGCATCGATTTGTGTA
71870 TACTTGCA-CAGATTTGTGT
1 TACTTGCATC-GATTTGTGT
71889 GCCACAACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 1 0.06
19 10 0.59
20 6 0.35
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.42
Consensus pattern (20 bp):
TACTTGCATCGATTTGTGTA
Done.