Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005327.1 Hibiscus syriacus cultivar Beakdansim tig00012064_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: 76676
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3291 original size:21 final size:22
Alignment explanation
Indices: 3262--3303 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
3252 GTTAGTCTCC
3262 TAACTAACTACGCTGAGCTGGA
1 TAACTAACTACGCTGAGCTGGA
**
3284 TAAC-AACTGTGCTGAGCTGG
1 TAACTAACTACGCTGAGCTGG
3304 CATCTTCCAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (22 bp):
TAACTAACTACGCTGAGCTGGA
Found at i:13286 original size:24 final size:23
Alignment explanation
Indices: 13239--13286 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
13229 ATATATAAAC
* *
13239 TTTTTACTTTTTTAAAAAATATA
1 TTTTTAATTTTTTAAAAAAAATA
*
13262 TTTTTAATATTTTTAAAAACAATA
1 TTTTTAAT-TTTTTAAAAAAAATA
13286 T
1 T
13287 GAATTTCATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTTTAATTTTTTAAAAAAAATA
Found at i:13695 original size:60 final size:59
Alignment explanation
Indices: 13619--13735 Score: 137
Period size: 59 Copynumber: 2.0 Consensus size: 59
13609 ATATGTCCCT
* *
13619 AAACTATAGCCCTCATTTCAAATT-GGTCTTTAAAATTTTAAATATTACAATCTCATCCTC
1 AAACTATAACCCTCA-TTCAAATTAGTTC-TTAAAATTTTAAATATTACAATCTCATCCTC
* * * * * *
13679 AAACTATAACTCTCATTCTAATTAGTTCTTAAAATTTTGATTATTTCAATTTCATCC
1 AAACTATAACCCTCATTCAAATTAGTTCTTAAAATTTTAAATATTACAATCTCATCC
13736 CTGAAATATG
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
59 32 0.67
60 16 0.33
ACGTcount: A:0.34, C:0.20, G:0.04, T:0.42
Consensus pattern (59 bp):
AAACTATAACCCTCATTCAAATTAGTTCTTAAAATTTTAAATATTACAATCTCATCCTC
Found at i:16841 original size:22 final size:21
Alignment explanation
Indices: 16805--16868 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
16795 CATATGAGAT
* *
16805 TTGTTCCGAAGGACCTGTGAA
1 TTGTCCCGAAGGACCTATGAA
* *
16826 TATGTCCCGAATGACCTATGAG
1 T-TGTCCCGAAGGACCTATGAA
*
16848 TTGTCTCGAAGGACCTATGAA
1 TTGTCCCGAAGGACCTATGAA
16869 ACCCTCAACT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
21 18 0.51
22 17 0.49
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAA
Found at i:17933 original size:30 final size:30
Alignment explanation
Indices: 17864--17921 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
17854 AATTTAAGGC
17864 AAAATGTTTTTGGACTTGAATTGAATTTGA
1 AAAATGTTTTTGGACTTGAATTGAATTTGA
*
17894 AAAATGTTTTTGGATTTGAATTGAATTT
1 AAAATGTTTTTGGACTTGAATTGAATTT
17922 ATTCAAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.33, C:0.02, G:0.19, T:0.47
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTGA
Found at i:18031 original size:21 final size:21
Alignment explanation
Indices: 18005--18103 Score: 105
Period size: 21 Copynumber: 4.7 Consensus size: 21
17995 GGTGTCAAAG
18005 TGCATCCATGCATCCCTGCAA
1 TGCATCCATGCATCCCTGCAA
*
18026 TGCATCCATGCATCCCTGCAG
1 TGCATCCATGCATCCCTGCAA
*
18047 TGCATCCATGCAT--TTGCACTAA
1 TGCATCCATGCATCCCTG--C-AA
* **
18069 TGCATCGATGCAT-CAGGCAA
1 TGCATCCATGCATCCCTGCAA
18089 TGCATCCATGCATCC
1 TGCATCCATGCATCC
18104 AAACATCGAA
Statistics
Matches: 66, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
19 2 0.03
20 14 0.21
21 36 0.55
22 13 0.20
23 1 0.02
ACGTcount: A:0.24, C:0.33, G:0.17, T:0.25
Consensus pattern (21 bp):
TGCATCCATGCATCCCTGCAA
Found at i:18561 original size:34 final size:33
Alignment explanation
Indices: 18522--18592 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 33
18512 TTTTGTAAAG
* *
18522 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAACCCGTG-AAAAACTA
*
18556 GGGAAAGGTTCTAGTTTAACCCGTGAAAAACTA
1 GGGAAAGGTTCTAGCTTAACCCGTGAAAAACTA
18589 GGGA
1 GGGA
18593 GTTGTAAGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 11 0.32
34 23 0.68
ACGTcount: A:0.32, C:0.15, G:0.30, T:0.23
Consensus pattern (33 bp):
GGGAAAGGTTCTAGCTTAACCCGTGAAAAACTA
Found at i:19398 original size:19 final size:20
Alignment explanation
Indices: 19374--19421 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
19364 AACGATTTTC
*
19374 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
19393 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
19413 TTTTGAAAA
1 TTTTGAAAA
19422 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:20763 original size:30 final size:30
Alignment explanation
Indices: 20694--20751 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
20684 AATTTAAGGC
20694 AAAATGTTTTTGGACTTGAATTGAATTTGA
1 AAAATGTTTTTGGACTTGAATTGAATTTGA
*
20724 AAAATGTTTTTGGATTTGAATTGAATTT
1 AAAATGTTTTTGGACTTGAATTGAATTT
20752 ATTCAAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.33, C:0.02, G:0.19, T:0.47
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTGA
Found at i:20861 original size:21 final size:21
Alignment explanation
Indices: 20835--20933 Score: 114
Period size: 21 Copynumber: 4.7 Consensus size: 21
20825 GGTGTCAAAG
20835 TGCATCCATGCATCCCTGCAA
1 TGCATCCATGCATCCCTGCAA
*
20856 TGCATCCATGCATCCCTGCAG
1 TGCATCCATGCATCCCTGCAA
20877 TGCATCCATGCAT--CTGCACTAA
1 TGCATCCATGCATCCCTG--C-AA
* **
20899 TGCATCGATGCAT-CAGGCAA
1 TGCATCCATGCATCCCTGCAA
20919 TGCATCCATGCATCC
1 TGCATCCATGCATCC
20934 AAACATCGAA
Statistics
Matches: 67, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
19 3 0.04
20 14 0.21
21 36 0.54
22 13 0.19
23 1 0.01
ACGTcount: A:0.24, C:0.34, G:0.17, T:0.24
Consensus pattern (21 bp):
TGCATCCATGCATCCCTGCAA
Found at i:32865 original size:16 final size:16
Alignment explanation
Indices: 32844--32895 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
32834 AGGTTTTTTC
*
32844 TTGTAAGTTTGCAAAT
1 TTGTAATTTTGCAAAT
32860 TTGTAATTTTGCAAAT
1 TTGTAATTTTGCAAAT
32876 TTGTAATTTTGCAAAT
1 TTGTAATTTTGCAAAT
32892 TTGT
1 TTGT
32896 GTAATCTTCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.29, C:0.06, G:0.15, T:0.50
Consensus pattern (16 bp):
TTGTAATTTTGCAAAT
Found at i:45690 original size:3 final size:3
Alignment explanation
Indices: 45658--45717 Score: 65
Period size: 3 Copynumber: 20.7 Consensus size: 3
45648 AACGGGAAAA
*
45658 AAT AA- AAT AA- AAT AAGT GAT AA- AA- AAT AAT AAT AAAT AAT AAT
1 AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT -AAT AAT AAT
45701 AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
45718 ATATAAAAAC
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
2 8 0.16
3 37 0.74
4 5 0.10
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:45691 original size:25 final size:24
Alignment explanation
Indices: 45654--45723 Score: 81
Period size: 24 Copynumber: 2.8 Consensus size: 24
45644 CTGAAACGGG
*
45654 AAAAAATAA-AATAAAATAAGTGAT
1 AAAAAATAATAATAAAATAA-TAAT
45678 AAAAAATAATAAT-AAATAATAAT
1 AAAAAATAATAATAAAATAATAAT
45701 AATAATAATAATAATAAATATAA
1 AA-AA-AATAATAATAAA-ATAA
45724 AAACTATATA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
23 5 0.12
24 17 0.43
25 12 0.30
26 2 0.05
27 4 0.10
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (24 bp):
AAAAAATAATAATAAAATAATAAT
Found at i:45837 original size:32 final size:32
Alignment explanation
Indices: 45796--45861 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
45786 TAAAAAAATA
*
45796 TTTTAAAAAACTATATAATTTTCAAAAATGTT
1 TTTTAAAAAACCATATAATTTTCAAAAATGTT
* *
45828 TTTTTAAAAACCATATAATTTTTAAAAATGTT
1 TTTTAAAAAACCATATAATTTTCAAAAATGTT
45860 TT
1 TT
45862 AAAAATTACA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (32 bp):
TTTTAAAAAACCATATAATTTTCAAAAATGTT
Found at i:45892 original size:36 final size:36
Alignment explanation
Indices: 45840--46097 Score: 235
Period size: 34 Copynumber: 7.2 Consensus size: 36
45830 TTTAAAAACC
* *
45840 ATATA-AT-TTTTAAAAATGTTTTAAAAATTACATA
1 ATATATATATTTTCAAAATGTTTTAAAAATTATATA
* **
45874 TTATATATGCTTTCAAAATGTTTTTCAAAAAATTATATA
1 ATATATATATTTTCAAAATG-TTTT--AAAAATTATATA
* * *
45913 TTATATATTAATTTTCAAAACGTTTTAAAAACTATATA
1 ATATATA-T-ATTTTCAAAATGTTTTAAAAATTATATA
*
45951 ATATATATATTTTCAAAAATGTTTTGAAAATTATAT-
1 ATATATATATTTTC-AAAATGTTTTAAAAATTATATA
* * *
45987 ATAT-T-TCTTTTCAAAAACGTTTT-AAAACTATATA
1 ATATATATATTTTC-AAAATGTTTTAAAAATTATATA
* * * *
46021 ATATAAATGTTTTTAAAATGTTTTAAAAACTATAT-
1 ATATATATATTTTCAAAATGTTTTAAAAATTATATA
* *
46056 AT-CATATATTTTCAAAATGTTTTCAAAATTATATA
1 ATATATATATTTTCAAAATGTTTTAAAAATTATATA
46091 ATATATA
1 ATATATA
46098 AATAAAAAAA
Statistics
Matches: 184, Mismatches: 26, Indels: 26
0.78 0.11 0.11
Matches are distributed among these distances:
33 9 0.05
34 50 0.27
35 16 0.09
36 37 0.20
37 23 0.12
38 17 0.09
39 18 0.10
40 5 0.03
41 9 0.05
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (36 bp):
ATATATATATTTTCAAAATGTTTTAAAAATTATATA
Found at i:45998 original size:70 final size:68
Alignment explanation
Indices: 45914--46097 Score: 233
Period size: 70 Copynumber: 2.6 Consensus size: 68
45904 AATTATATAT
* *
45914 TATATATTAATTTTCAAAACGTTTTAAAAACTATATAATATATATATTTTCAAAAATGTTTTGAA
1 TATATATTTATTTTCAAAACGTTTT-AAAACTATATAATATATATATTTT-AAAAATGTTTTAAA
*
45979 AATTA
64 AACTA
* * * *
45984 TATATATTTCTTTTCAAAAACGTTTTAAAACTATATAATATAAATGTTTTTAAAATGTTTTAAAA
1 TATATATTTATTTTC-AAAACGTTTTAAAACTATATAATATATATATTTTAAAAATGTTTTAAAA
46049 ACTA
65 ACTA
* * *
46053 TATATCATATATTTTCAAAATGTTTTCAAAATTATATAATATATA
1 TATAT-ATTTATTTTCAAAACGTTTT-AAAACTATATAATATATA
46098 AATAAAAAAA
Statistics
Matches: 99, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
69 30 0.30
70 59 0.60
71 10 0.10
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.45
Consensus pattern (68 bp):
TATATATTTATTTTCAAAACGTTTTAAAACTATATAATATATATATTTTAAAAATGTTTTAAAAA
CTA
Found at i:47071 original size:85 final size:85
Alignment explanation
Indices: 46706--47431 Score: 867
Period size: 85 Copynumber: 8.7 Consensus size: 85
46696 AAGTTGAATA
* * * *
46706 TAATCGAACTCGAAGGTC--T--TTAGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGA
1 TAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
* *
46767 TGTGCCGTTG-AGCTGAGCG
66 TGTGCCCTCGAAGCTGAGCG
* * * * * *
46786 TAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGA
1 TAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
* *
46851 TATGCCCT-GGAGCTGAGCG
66 TGTGCCCTCGAAGCTGAGCG
* ** * *
46870 TAGTCGAACTCGGGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGA
1 TAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
* *
46931 TGTGCCGTTG-AGCTGAGCG
66 TGTGCCCTCGAAGCTGAGCG
* * ** * * * *
46950 TAGTCGAACTCAAAGGTCTTTTGG-TCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG
1 TAATCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATG
*
47014 ATGTGCCCTCGAAGCTGAGTG
65 ATGTGCCCTCGAAGCTGAGCG
**
47035 TAATCGAACTCGGGGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
1 TAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
* *
47100 TGTGCCCTCGATGCTGAGTG
66 TGTGCCCTCGAAGCTGAGCG
47120 TAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
1 TAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
*
47185 TGTGCCCTCGAAGCTGAGTG
66 TGTGCCCTCGAAGCTGAGCG
* ** *
47205 TAATCAAACTCGGGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGA
1 TAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
* *
47266 TGTGCCGTTG-AGCTGAGCG
66 TGTGCCCTCGAAGCTGAGCG
* * *
47285 TAGTCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
1 TAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
*
47350 TGTGCCCTCGAAGCTGAGTG
66 TGTGCCCTCGAAGCTGAGCG
* * * * *
47370 TAATCGAACTCGAAGGTCTTTGG-TGACAGATAACCCTTATAGCCTTGAGTTATGCTGCAAAT
1 TAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAAT
47432 AATTTGTTTA
Statistics
Matches: 555, Mismatches: 73, Indels: 32
0.84 0.11 0.05
Matches are distributed among these distances:
80 104 0.19
81 50 0.09
82 3 0.01
83 3 0.01
84 194 0.35
85 201 0.36
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.29
Consensus pattern (85 bp):
TAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
TGTGCCCTCGAAGCTGAGCG
Found at i:47262 original size:335 final size:332
Alignment explanation
Indices: 46706--47431 Score: 1107
Period size: 335 Copynumber: 2.2 Consensus size: 332
46696 AAGTTGAATA
* * * *
46706 TAATCGAACTCGAAGGTC-TT--TAGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGAT
1 TAATCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGAT
* * * *
46768 GTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTT
66 GTGCCCTCGAGCTGAGCGTAATCGAACTCAAAGGTCTTTGGTTGGCAGACAACCCTTCTAGACTT
* * * *
46833 AAGTTGTGCTGCAAATGATATGCCCTGGAGCTGAGCGTAGTCGAACTCGGGGGTCTTTGGCAGAT
131 AAGTTATGCTGCAAATGATATGCCCTGAAGCTGAGCGTAATCAAACTCGGGGGTCTTTGGCAGAT
46898 AGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAA
196 AGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAA
* * *
46963 AGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAG
261 AGGTCTTTTGGTCACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAG
47028 CTGAGTG
326 CTGAGTG
**
47035 TAATCGAACTCGGGGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
1 TAATCGAACTCGAAGGTCTTTGG-TGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
* * * *
47100 TGTGCCCTCGATGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGAC
65 TGTGCCCTCGA-GCTGAGCGTAATCGAACTCAAAGGTCTTTGGTTGGCAGACAACCCTTCTAGAC
* *
47165 TTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCAAACTCGGGGGTCTTTGGCA
129 TTAAGTTATGCTGCAAATGATATGCCCT-GAAGCTGAGCGTAATCAAACTCGGGGGTCTTTGGCA
*
47230 GATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACT
193 GATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACT
* ** *
47295 CAAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCG
258 CAAAGGTCTTTTGGTCACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCG
47360 AAGCTGAGTG
323 AAGCTGAGTG
* * * * *
47370 TAATCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTATAGCCTTGAGTTATGCTGCAAAT
1 TAATCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAAT
47432 AATTTGTTTA
Statistics
Matches: 356, Mismatches: 35, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
329 16 0.04
330 2 0.01
333 46 0.13
334 107 0.30
335 185 0.52
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.29
Consensus pattern (332 bp):
TAATCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGAT
GTGCCCTCGAGCTGAGCGTAATCGAACTCAAAGGTCTTTGGTTGGCAGACAACCCTTCTAGACTT
AAGTTATGCTGCAAATGATATGCCCTGAAGCTGAGCGTAATCAAACTCGGGGGTCTTTGGCAGAT
AGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAA
AGGTCTTTTGGTCACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAG
CTGAGTG
Found at i:50332 original size:17 final size:17
Alignment explanation
Indices: 50299--50332 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
50289 TTAGTGAGAT
*
50299 AATGATGATAATAAAAA
1 AATGATGAAAATAAAAA
50316 AATGATGAAAATGAAAA
1 AATGATGAAAAT-AAAA
50333 GTCTTACCCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.21
Consensus pattern (17 bp):
AATGATGAAAATAAAAA
Found at i:58518 original size:17 final size:17
Alignment explanation
Indices: 58496--58539 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
58486 TTTCAACATT
*
58496 TTTGATATTT-TGGGTTG
1 TTTGAT-TTTGTGGATTG
58513 TTTGATTTTGTGGATTG
1 TTTGATTTTGTGGATTG
*
58530 TTGGATTTTG
1 TTTGATTTTG
58540 GATTTATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.11, C:0.00, G:0.30, T:0.59
Consensus pattern (17 bp):
TTTGATTTTGTGGATTG
Found at i:58816 original size:30 final size:31
Alignment explanation
Indices: 58782--58845 Score: 112
Period size: 30 Copynumber: 2.1 Consensus size: 31
58772 AGAATAGGTG
58782 AATGTTTTACATAATAAATTGAAG-GTGTTA
1 AATGTTTTACATAATAAATTGAAGAGTGTTA
58812 AATGTTTTACATAATAAATTGAAGAAGTGTTA
1 AATGTTTTACATAATAAATTGAAG-AGTGTTA
58844 AA
1 AA
58846 GTAAGGGGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 24 0.75
32 8 0.25
ACGTcount: A:0.44, C:0.03, G:0.16, T:0.38
Consensus pattern (31 bp):
AATGTTTTACATAATAAATTGAAGAGTGTTA
Found at i:59320 original size:75 final size:76
Alignment explanation
Indices: 59152--59357 Score: 290
Period size: 76 Copynumber: 2.7 Consensus size: 76
59142 CAAAGCCAAA
* * * * **
59152 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATCCCCCCTAAATGGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
59217 TTGGCCCCGAG
66 TTGGCCCCGAG
*
59228 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
*
59293 TT-GCTCCGAG
66 TTGGCCCCGAG
* * * *
59303 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCC
59358 CTTGTACAAC
Statistics
Matches: 117, Mismatches: 13, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
74 17 0.15
75 40 0.34
76 60 0.51
ACGTcount: A:0.25, C:0.32, G:0.24, T:0.19
Consensus pattern (76 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
TTGGCCCCGAG
Found at i:61328 original size:25 final size:25
Alignment explanation
Indices: 61251--61317 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 25
61241 AACGGGAAAA
*
61251 AATAA-AATAAA-ATAAGTGATAA-AA
1 AATAATAATAAATATAA-T-ATAATAT
61275 AATAATAATAAATATAATATAATAT
1 AATAATAATAAATATAATATAATAT
61300 AATAATATATAAATATAA
1 AATAATA-ATAAATATAA
61318 ACTATATAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
24 9 0.24
25 15 0.39
26 14 0.37
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (25 bp):
AATAATAATAAATATAATATAATAT
Found at i:61416 original size:32 final size:33
Alignment explanation
Indices: 61380--61447 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 33
61370 TATAAACATA
*
61380 AAAAAAAC-ATTTTAAAAAACTATATAATTTTC
1 AAAAAAACTATTTTAAAAAACCATATAATTTTC
* * * *
61412 -AAAAATCTTTTTTTAAAAACCATATAATTTTT
1 AAAAAAACTATTTTAAAAAACCATATAATTTTC
61444 AAAA
1 AAAA
61448 TGTTTTAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
31 6 0.21
32 20 0.69
33 3 0.10
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (33 bp):
AAAAAAACTATTTTAAAAAACCATATAATTTTC
Found at i:61571 original size:37 final size:36
Alignment explanation
Indices: 61433--61687 Score: 231
Period size: 37 Copynumber: 7.1 Consensus size: 36
61423 TTTAAAAACC
* *
61433 ATATA-ATTTTTAAAATGTTTTAAAAATTACAT-AT
1 ATATATATTTTCAAAATGTTTTAAAAATTATATAAT
**
61467 -TATATGCTTTC-AAATGTTTTTCAAAAATTATAT-AT
1 ATATATATTTTCAAAATG-TTTT-AAAAATTATATAAT
* *
61502 ATAT-TAATTTTCAAAACGTTTTAAAAACTATATAAT
1 ATATAT-ATTTTCAAAATGTTTTAAAAATTATATAAT
* *
61538 ATATATATTTTCAAAAATGTTTTGAAAATTATATATT
1 ATATATATTTTC-AAAATGTTTTAAAAATTATATAAT
* * * *
61575 ATATTTCTTTTCAAAAACGTTTT-AAAACTATATAAT
1 ATATATATTTTC-AAAATGTTTTAAAAATTATATAAT
* * *
61611 ATATAAATGTTTTTAAAATGTTTTAAAAACTATAT-AT
1 ATAT--ATATTTTCAAAATGTTTTAAAAATTATATAAT
* *
61648 -CATATATTTTCAAAATGTTTTCAAAATTATATAAT
1 ATATATATTTTCAAAATGTTTTAAAAATTATATAAT
61683 ATATA
1 ATATA
61688 AATAAAAAAA
Statistics
Matches: 180, Mismatches: 27, Indels: 26
0.77 0.12 0.11
Matches are distributed among these distances:
33 9 0.05
34 32 0.18
35 25 0.14
36 43 0.24
37 56 0.31
38 15 0.08
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (36 bp):
ATATATATTTTCAAAATGTTTTAAAAATTATATAAT
Found at i:61679 original size:72 final size:74
Alignment explanation
Indices: 61478--61690 Score: 265
Period size: 74 Copynumber: 2.9 Consensus size: 74
61468 ATATGCTTTC
61478 AAATGTTTTTCAAAAATTATATAT-ATATTAATTTTCAAAACGTTTTAAAAACTATATAATATAT
1 AAATG-TTTT-AAAAATTATATATCATATTAATTTTCAAAACGTTTTAAAAACTATATAATATAT
* **
61542 ATAT-TTTCAA
64 AAATGTTTTTA
* * **
61552 AAATGTTTTGAAAATTATATATTATATTTCTTTTCAAAAACGTTTT-AAAACTATATAATATATA
1 AAATGTTTTAAAAATTATATATCATATTAATTTTC-AAAACGTTTTAAAAACTATATAATATATA
61616 AATGTTTTTA
65 AATGTTTTTA
* * * *
61626 AAATGTTTTAAAAACTATATATCATA-T-ATTTTCAAAATGTTTTCAAAATTATATAATATATAA
1 AAATGTTTTAAAAATTATATATCATATTAATTTTCAAAACGTTTTAAAAACTATATAATATATAA
61689 AT
66 AT
61691 AAAAAAATAT
Statistics
Matches: 123, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
71 9 0.07
72 37 0.30
73 35 0.28
74 42 0.34
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (74 bp):
AAATGTTTTAAAAATTATATATCATATTAATTTTCAAAACGTTTTAAAAACTATATAATATATAA
ATGTTTTTA
Found at i:61752 original size:6 final size:7
Alignment explanation
Indices: 61736--61763 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
61726 CAACGATCAC
61736 AAAAAGA
1 AAAAAGA
61743 AAAAAGA
1 AAAAAGA
61750 AAAAAGA
1 AAAAAGA
61757 AAAAAGA
1 AAAAAGA
61764 GTAGATGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:62989 original size:39 final size:39
Alignment explanation
Indices: 62942--63090 Score: 190
Period size: 39 Copynumber: 3.7 Consensus size: 39
62932 TATCGAACCA
* **
62942 AAGACTCCAAGCTTACATGGCGTCTTCAGGCCAACCAGG
1 AAGACTCCAAGCTTACATGGCGTCTTCAGGCAAAATAGG
* ** *
62981 AATACTCCAAGAGTGCATGGCGTCTTCAGGCAAAATAGG
1 AAGACTCCAAGCTTACATGGCGTCTTCAGGCAAAATAGG
*
63020 AAGACTCCAACAAGCTTACCTGGCGTCTTCAGGCAAAATAGG
1 AAGACT-C--CAAGCTTACATGGCGTCTTCAGGCAAAATAGG
*
63062 AAGACTCCAAGCTTACCTGGCGTCTTCAG
1 AAGACTCCAAGCTTACATGGCGTCTTCAG
63091 TCTAGGGTGA
Statistics
Matches: 95, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
39 59 0.62
40 1 0.01
41 1 0.01
42 34 0.36
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.20
Consensus pattern (39 bp):
AAGACTCCAAGCTTACATGGCGTCTTCAGGCAAAATAGG
Found at i:63768 original size:21 final size:22
Alignment explanation
Indices: 63739--63797 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 22
63729 TTGTAGTAGA
*
63739 AATGTAAAAAAATA-TAATTAT
1 AATGAAAAAAAATATTAATTAT
*
63760 AATGAAAAAAATAATATTTATTAT
1 AATG-AAAAAA-AATATTAATTAT
*
63784 AATGAAGAAAAATA
1 AATGAAAAAAAATA
63798 ATGGCACAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
21 4 0.12
22 9 0.28
23 9 0.28
24 10 0.31
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.31
Consensus pattern (22 bp):
AATGAAAAAAAATATTAATTAT
Done.