Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005253.1 Hibiscus syriacus cultivar Beakdansim tig00011877_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: 51496
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:2656 original size:18 final size:18
Alignment explanation
Indices: 2632--2712 Score: 110
Period size: 18 Copynumber: 4.6 Consensus size: 18
2622 AAGGGATTAT
*
2632 CAGTGGTCCTTTGGGACA
1 CAGTGGTCCTTCGGGACA
*
2650 TAGTGGTCCTTCGGGACA
1 CAGTGGTCCTTCGGGACA
*
2668 TA-TGGTCCTTCGGGACA
1 CAGTGGTCCTTCGGGACA
*
2685 CGGTGGTCCTTCGGGACA
1 CAGTGGTCCTTCGGGACA
*
2703 CGGTGGTCCT
1 CAGTGGTCCT
2713 ACGAGACAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
17 15 0.26
18 43 0.74
ACGTcount: A:0.14, C:0.25, G:0.35, T:0.27
Consensus pattern (18 bp):
CAGTGGTCCTTCGGGACA
Found at i:2683 original size:35 final size:35
Alignment explanation
Indices: 2635--2702 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
2625 GGATTATCAG
* *
2635 TGGTCCTTTGGGACATAGTGGTCCTTCGGGACATA
1 TGGTCCTTCGGGACACAGTGGTCCTTCGGGACATA
*
2670 TGGTCCTTCGGGACACGGTGGTCCTTCGGGACA
1 TGGTCCTTCGGGACACAGTGGTCCTTCGGGACA
2703 CGGTGGTCCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.15, C:0.24, G:0.34, T:0.28
Consensus pattern (35 bp):
TGGTCCTTCGGGACACAGTGGTCCTTCGGGACATA
Found at i:8127 original size:26 final size:28
Alignment explanation
Indices: 8095--8148 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
8085 GGAATTTCAA
8095 AATAATGGA-T-TTGATATCAGGTATTT
1 AATAATGGATTCTTGATATCAGGTATTT
8121 AATAATGGATTCTTGATATCAGGTATTT
1 AATAATGGATTCTTGATATCAGGTATTT
8149 GAAAATGAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 9 0.35
27 1 0.04
28 16 0.62
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.43
Consensus pattern (28 bp):
AATAATGGATTCTTGATATCAGGTATTT
Found at i:8833 original size:2 final size:2
Alignment explanation
Indices: 8826--8869 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
8816 TTTGTAACAC
8826 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
8868 AT
1 AT
8870 TTTCAAGGCC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12525 original size:11 final size:11
Alignment explanation
Indices: 12509--12543 Score: 52
Period size: 11 Copynumber: 3.0 Consensus size: 11
12499 ATGGGTTCTC
12509 ATTTATTATTA
1 ATTTATTATTA
12520 ATTTATTATTA
1 ATTTATTATTA
12531 ATACTTATTATTA
1 AT--TTATTATTA
12544 TTATATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 13 0.59
13 9 0.41
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (11 bp):
ATTTATTATTA
Found at i:12980 original size:11 final size:11
Alignment explanation
Indices: 12960--12992 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
12950 CCACTATTAT
*
12960 CATCAGAAATC
1 CATCATAAATC
12971 CATCATAAATC
1 CATCATAAATC
12982 CATCATAAATC
1 CATCATAAATC
12993 AACATGCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.45, C:0.27, G:0.03, T:0.24
Consensus pattern (11 bp):
CATCATAAATC
Found at i:19880 original size:66 final size:66
Alignment explanation
Indices: 19766--20162 Score: 647
Period size: 66 Copynumber: 6.0 Consensus size: 66
19756 AAACAAATTG
* *
19766 ATAAACCTTTGAGATTGTTTCTCGTTGAAACAAATTTTGTCTCGCTTGAGATAGTTTCTCTTGAA
1 ATAAACCTTTGAGATTGTTTCTC-TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAA
19831 AC
65 AC
*
19833 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGAAAGTTTCTCTTGAAA
1 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
19898 C
66 C
* * *
19899 ATAAACCTTTGAGTTTGTTTCTCTTGAAAGAAA-TTT-TCCCTCTTGAGACAGTTTCTCTTGAAA
1 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
*
19962 T
66 C
19963 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
1 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
20028 C
66 C
*
20029 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAAATTTTGTCTCTCTTGAGACATTTTCTCTTGAA
1 ATAAACCTTTGAGATTGTTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAA
20094 AC
65 AC
* * *
20096 ATAAATCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCT-TGCTTGAGACAATTTCTCTTGAA
1 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCT-CTTGAGACAGTTTCTCTTGAA
20160 AC
65 AC
20162 A
1 A
20163 AATTATCTCT
Statistics
Matches: 311, Mismatches: 15, Indels: 9
0.93 0.04 0.03
Matches are distributed among these distances:
64 56 0.18
65 7 0.02
66 162 0.52
67 86 0.28
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (66 bp):
ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
C
Found at i:19889 original size:36 final size:36
Alignment explanation
Indices: 19774--20166 Score: 232
Period size: 30 Copynumber: 11.8 Consensus size: 36
19764 TGATAAACCT
* *
19774 TTGAGATTGTTTCTCGTTGAAACAAATTTTGTCTCGC
1 TTGAGATAGTTTCTC-TTGAAACAAATTTTGTCTCTC
*
19811 TTGAGATAGTTTCTCTTGAAACATAA-----AC-CT-
1 TTGAGATAGTTTCTCTTGAAACA-AATTTTGTCTCTC
*
19841 TTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTC
1 TTGAGATAGTTTCTCTTGAAACAAATTTTGTCTCTC
* *
19877 TTGAGAAAGTTTCTCTTGAAACATAA-----AC-CT-
1 TTGAGATAGTTTCTCTTGAAACA-AATTTTGTCTCTC
* * * *
19907 TTGAGTTTGTTTCTCTTGAAAGAAA-TTT-TCCCTC
1 TTGAGATAGTTTCTCTTGAAACAAATTTTGTCTCTC
* * *
19941 TTGAGACAGTTTCTCTTGAAATATAA-----AC-CT-
1 TTGAGATAGTTTCTCTTGAAACA-AATTTTGTCTCTC
*
19971 TTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTC
1 TTGAGATAGTTTCTCTTGAAACAAATTTTGTCTCTC
* *
20007 TTGAGACAGTTTCTCTTGAAACATAA-----AC-CT-
1 TTGAGATAGTTTCTCTTGAAACA-AATTTTGTCTCTC
*
20037 TTGAGATTGTTTCTCTTGAAACAAAATTTTGTCTCTC
1 TTGAGATAGTTTCTCTTGAAAC-AAATTTTGTCTCTC
* * *
20074 TTGAGACATTTTCTCTTGAAACATAA------ATCT-
1 TTGAGATAGTTTCTCTTGAAACA-AATTTTGTCTCTC
* *
20104 TTGAGATTGTTTCCCTTGAAACAAATTTTGTCT-TGC
1 TTGAGATAGTTTCTCTTGAAACAAATTTTGTCTCT-C
* *
20140 TTGAGACAATTTCTCTTGAAACAAATT
1 TTGAGATAGTTTCTCTTGAAACAAATT
20167 ATCTCTAAAG
Statistics
Matches: 275, Mismatches: 41, Indels: 81
0.69 0.10 0.20
Matches are distributed among these distances:
29 8 0.03
30 102 0.37
31 11 0.04
32 5 0.02
33 2 0.01
34 22 0.08
35 8 0.03
36 76 0.28
37 41 0.15
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (36 bp):
TTGAGATAGTTTCTCTTGAAACAAATTTTGTCTCTC
Found at i:19967 original size:130 final size:132
Alignment explanation
Indices: 19766--20162 Score: 631
Period size: 130 Copynumber: 3.0 Consensus size: 132
19756 AAACAAATTG
* * *
19766 ATAAACCTTTGAGATTGTTTCTCGTTGAAACAAATTTTGTCTCGCTTGAGATAGTTTCTCTTGAA
1 ATAAACCTTTGAGATTGTTTCTC-TTGAAAAAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAA
19831 ACATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGAAAGTTTCTCTTGA
65 ACATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGAAAGTTTCTCTTGA
19896 AAC
130 AAC
* * *
19899 ATAAACCTTTGAGTTTGTTTCTCTTGAAAGAAA-TTT-TCCCTCTTGAGACAGTTTCTCTTGAAA
1 ATAAACCTTTGAGATTGTTTCTCTTGAAAAAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
* *
19962 TATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAA
66 CATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGAAAGTTTCTCTTGAA
20027 AC
131 AC
*
20029 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAAATTTTGTCTCTCTTGAGACATTTTCTCTTGAA
1 ATAAACCTTTGAGATTGTTTCTCTTGAAA-AAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAA
* *
20094 ACATAAATCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCT-TGCTTGAGACAA-TTTCTCTT
65 ACATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCT-CTTGAGA-AAGTTTCTCTT
20157 GAAAC
128 GAAAC
20162 A
1 A
20163 AATTATCTCT
Statistics
Matches: 244, Mismatches: 15, Indels: 10
0.91 0.06 0.04
Matches are distributed among these distances:
130 117 0.48
131 6 0.02
132 13 0.05
133 107 0.44
134 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (132 bp):
ATAAACCTTTGAGATTGTTTCTCTTGAAAAAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
CATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGAAAGTTTCTCTTGAA
AC
Found at i:25227 original size:14 final size:15
Alignment explanation
Indices: 25197--25226 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
25187 CACATTTATA
25197 TATTTTAAAATTTTT
1 TATTTTAAAATTTTT
25212 TATTTTAAAATTTTT
1 TATTTTAAAATTTTT
25227 AAAATAACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTTTAAAATTTTT
Found at i:26083 original size:23 final size:23
Alignment explanation
Indices: 26052--26096 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
26042 ATTCACTTCC
26052 TAAAAATTTAGTT-TTTTATATTT
1 TAAAAATTT-GTTATTTTATATTT
* *
26075 TAAATATTTTTTATTTTATATT
1 TAAAAATTTGTTATTTTATATT
26097 GATTATATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (23 bp):
TAAAAATTTGTTATTTTATATTT
Found at i:26169 original size:26 final size:25
Alignment explanation
Indices: 26123--26174 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
26113 CTCTAAATTT
*
26123 TTTTATAAGTTTATTGTTATTAAAA
1 TTTTATAAGTTTATTGCTATTAAAA
26148 TTTTATAAGTTTTATCT-CTATTAAAA
1 TTTTATAAG-TTTAT-TGCTATTAAAA
26174 T
1 T
26175 CTTACGCTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 9 0.38
26 14 0.58
27 1 0.04
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.56
Consensus pattern (25 bp):
TTTTATAAGTTTATTGCTATTAAAA
Found at i:27122 original size:130 final size:132
Alignment explanation
Indices: 26958--27212 Score: 435
Period size: 130 Copynumber: 1.9 Consensus size: 132
26948 ATTAGAGATC
26958 TAAATTGATTTAAAAAATTTAAATAACTAAATATAAAAATGTGTAATTTATATA-TTTTCTGTAT
1 TAAATTGATTTAAAAAATTTAAATAACTAAATATAAAAATGTGTAATTTATATATTTTTCTGTAT
*
27022 TAAATTAAAAATATATAAATTTGCTACAAGAAATTCTATTGATAATAGATCGAATATATATATAT
66 TAAATTAAAAATATATAAATTTGCTACAA-AAACTCTATTGATAATAGATCGAATATATATATAT
27087 ATA
130 ATA
*
27090 TAAATTGA-TTAAAAAA-TTAAATAATTAAATATAAAAATGTGTAATTTATATATTTTTCTGTAT
1 TAAATTGATTTAAAAAATTTAAATAACTAAATATAAAAATGTGTAATTTATATATTTTTCTGTAT
* * *
27153 TAAATTAAAATTATATAAATTTGCTCCAAAAACTCTATTGATAGTAGATCGAATATATAT
66 TAAATTAAAAATATATAAATTTGCTACAAAAACTCTATTGATAATAGATCGAATATATAT
27213 GTCCATATTT
Statistics
Matches: 117, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
130 64 0.55
131 45 0.38
132 8 0.07
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.40
Consensus pattern (132 bp):
TAAATTGATTTAAAAAATTTAAATAACTAAATATAAAAATGTGTAATTTATATATTTTTCTGTAT
TAAATTAAAAATATATAAATTTGCTACAAAAACTCTATTGATAATAGATCGAATATATATATATA
TA
Found at i:28828 original size:36 final size:36
Alignment explanation
Indices: 28778--28864 Score: 165
Period size: 36 Copynumber: 2.4 Consensus size: 36
28768 TCAAATCGTC
28778 TTGGGGACTCTATTAGCACGATTGTAATCAGCACAG
1 TTGGGGACTCTATTAGCACGATTGTAATCAGCACAG
*
28814 TTGGGGACTTTATTAGCACGATTGTAATCAGCACAG
1 TTGGGGACTCTATTAGCACGATTGTAATCAGCACAG
28850 TTGGGGACTCTATTA
1 TTGGGGACTCTATTA
28865 ACATGATGGT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.31
Consensus pattern (36 bp):
TTGGGGACTCTATTAGCACGATTGTAATCAGCACAG
Found at i:30067 original size:14 final size:14
Alignment explanation
Indices: 30034--30072 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
30024 AAACAAATAA
*
30034 GAATAAAAGAACAT
1 GAATAAATGAACAT
30048 GAATAAATGAACAT
1 GAATAAATGAACAT
30062 -ATATAAATGAA
1 GA-ATAAATGAA
30073 TTATTGAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 1 0.04
14 22 0.96
ACGTcount: A:0.62, C:0.05, G:0.13, T:0.21
Consensus pattern (14 bp):
GAATAAATGAACAT
Found at i:35631 original size:21 final size:21
Alignment explanation
Indices: 35607--35648 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
35597 CAGGTTTCTT
**
35607 GGCATTTGTTCGGTCTTTGAA
1 GGCATTTGTTCAATCTTTGAA
35628 GGCATTTGTTCAATCTTTGAA
1 GGCATTTGTTCAATCTTTGAA
35649 AGTGAACTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.14, G:0.24, T:0.43
Consensus pattern (21 bp):
GGCATTTGTTCAATCTTTGAA
Found at i:36250 original size:2 final size:2
Alignment explanation
Indices: 36243--36294 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
36233 CCTCCAATTG
36243 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
36285 TA TA TA TA TA
1 TA TA TA TA TA
36295 GATACACACA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:37248 original size:20 final size:20
Alignment explanation
Indices: 37207--37248 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
37197 AGATAAAAAA
*
37207 AAACAACAACAAAAAACTGT
1 AAACAACAACAAAAAACCGT
* *
37227 AAACAACGACAAAAACCCGT
1 AAACAACAACAAAAAACCGT
37247 AA
1 AA
37249 GCTACCAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.62, C:0.24, G:0.07, T:0.07
Consensus pattern (20 bp):
AAACAACAACAAAAAACCGT
Found at i:39552 original size:32 final size:32
Alignment explanation
Indices: 39441--39582 Score: 98
Period size: 32 Copynumber: 4.4 Consensus size: 32
39431 GTGATTATAG
*
39441 GATCAGTT-ATTTTTTCAGTTCGGATCAATATCA
1 GATCAGTTGA-TTTTTGA-TTCGGATCAATATCA
* ** *
39474 TA-C-GATTGATTTTTGGGTCGGATTAATATCA
1 GATCAG-TTGATTTTTGATTCGGATCAATATCA
* *
39505 GATCAGTT-ACATTTTGATTCGGGTCAATATCA
1 GATCAGTTGA-TTTTTGATTCGGATCAATATCA
* *
39537 GATCAGTTGATTTTTGGA-TC-AAGTCAATACCA
1 GATCAGTTGATTTTT-GATTCGGA-TCAATATCA
*
39569 GATTAGTTGATTTT
1 GATCAGTTGATTTT
39583 CAGTTTGTGT
Statistics
Matches: 85, Mismatches: 16, Indels: 17
0.72 0.14 0.14
Matches are distributed among these distances:
31 16 0.19
32 63 0.74
33 6 0.07
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (32 bp):
GATCAGTTGATTTTTGATTCGGATCAATATCA
Found at i:40800 original size:20 final size:21
Alignment explanation
Indices: 40758--40800 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
40748 CAAAATATCA
*
40758 TTCATGTTAAACATCGTATATG
1 TTCATGATAAACATCG-ATATG
40780 TTCATGATAAACATC-ATATG
1 TTCATGATAAACATCGATATG
40800 T
1 T
40801 AACGAAGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
22 14 0.70
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.40
Consensus pattern (21 bp):
TTCATGATAAACATCGATATG
Found at i:42263 original size:23 final size:23
Alignment explanation
Indices: 42233--42284 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
42223 TTATGATTAT
42233 ATTCAAGCATGAAATCAACATCG
1 ATTCAAGCATGAAATCAACATCG
* *
42256 ATTCAAGCATGAAATCAGCATCT
1 ATTCAAGCATGAAATCAACATCG
42279 ATTCAA
1 ATTCAA
42285 CCTTATACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.25
Consensus pattern (23 bp):
ATTCAAGCATGAAATCAACATCG
Found at i:46166 original size:23 final size:23
Alignment explanation
Indices: 46140--46208 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
46130 CACCACAGCT
*
46140 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
46163 CGTAGAATTGCACC-AGAGTGCCG
1 CGTAGAATTGCACCGA-AGTGCCA
*
46186 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
46209 TATAATAATG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
22 1 0.03
23 39 0.98
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:46392 original size:100 final size:102
Alignment explanation
Indices: 46224--46434 Score: 372
Period size: 100 Copynumber: 2.1 Consensus size: 102
46214 TAATGTCCAT
* *
46224 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAA-CATATACATATACCAAGGATCAAGTATGTGTCTCACCA
46289 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
65 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
46327 AAGGACCACATATCATTCCTTAAG-A-ATATACATATGCCAAGGATCAAGTATGTGTCTCACCAG
1 AAGGACCACATATCATTCCTTAAGAACATATACATATACCAAGGATCAAGTATGTGTCTCACCAG
46390 ACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 ACTTCACACATGTTCCAAAGAATACATATATGTCCCG
46427 AAGGACCA
1 AAGGACCA
46435 TATAGACCCT
Statistics
Matches: 105, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
100 80 0.76
102 1 0.01
103 24 0.23
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (102 bp):
AAGGACCACATATCATTCCTTAAGAACATATACATATACCAAGGATCAAGTATGTGTCTCACCAG
ACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:51328 original size:22 final size:23
Alignment explanation
Indices: 51264--51331 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
51254 CACCACAGCT
*
51264 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
51287 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
* *
51310 CGTAGAA-TGTACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
51332 TAATAATGTC
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
22 12 0.31
23 27 0.69
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.21
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Done.