Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000824.1 Hibiscus syriacus cultivar Beakdansim tig00001592_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: 65895
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1762 original size:17 final size:18
Alignment explanation
Indices: 1727--1762 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1717 GTTAAATTAC
*
1727 ATTAAGTTCATATTTATT
1 ATTAAGTTCATATTAATT
1745 ATTAAGTT-ATATTAATT
1 ATTAAGTTCATATTAATT
1762 A
1 A
1763 GATTAGATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.53
Consensus pattern (18 bp):
ATTAAGTTCATATTAATT
Found at i:2482 original size:28 final size:28
Alignment explanation
Indices: 2450--2505 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
2440 ATTTCTAAGT
2450 ATATTCAATACAA-CTATTCAAATATCAA
1 ATATT-AATACAAGCTATTCAAATATCAA
* * *
2478 ATATTACTCCAAGCTTTTCAAATATCAA
1 ATATTAATACAAGCTATTCAAATATCAA
2506 TTTTAATTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.45, C:0.20, G:0.02, T:0.34
Consensus pattern (28 bp):
ATATTAATACAAGCTATTCAAATATCAA
Found at i:4205 original size:23 final size:21
Alignment explanation
Indices: 4175--4222 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
4165 TTGAAGAAGG
4175 ATTTAAAGCT-TTCAAAAATGAA
1 ATTTAAAG-TATTCAAAAA-GAA
*
4197 ATTTGAAAGTATTGAAAAAGAA
1 ATTT-AAAGTATTCAAAAAGAA
4219 ATTT
1 ATTT
4223 CGATTTGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.50, C:0.04, G:0.12, T:0.33
Consensus pattern (21 bp):
ATTTAAAGTATTCAAAAAGAA
Found at i:8139 original size:23 final size:23
Alignment explanation
Indices: 8104--8156 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
8094 CAGGAGGCAT
8104 CGATA-CCCCTTTGAATGGGTAC
1 CGATACCCCCTTTGAATGGGTAC
8126 CGATACCCCCTTTGAATGGGTAC
1 CGATACCCCCTTTGAATGGGTAC
*
8149 AGATACCC
1 CGATACCC
8157 TCCACGAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 5 0.17
23 24 0.83
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.25
Consensus pattern (23 bp):
CGATACCCCCTTTGAATGGGTAC
Found at i:13591 original size:129 final size:125
Alignment explanation
Indices: 13377--13810 Score: 599
Period size: 118 Copynumber: 3.5 Consensus size: 125
13367 TAGTATAATC
13377 TTAAATTCTTAACTATAAAAATATATATTTTATTATTTTTCTTAATTTATCGAATATATATATTT
1 TTAAATTCTTAACTATAAAAATATATATTTTATTATTTTTCTTAATTTATCGAATATATATATTT
* * *
13442 TGGTTTAAAGTAAGCTAAGTTTATTATTTTAGGTAAGAATATATTCAAAATATTTTAAAATAT
66 TGGTTTAAAGTAGGC-AAGTTTATTATTTAAGTTAAGAATATATT-AAAATA-TTTAAAATAT
13505 TTAAATTCTTAACTATAAAAATATATATTTTATTATTTTTTCTTAATTTATCGAATATATATATT
1 TTAAATTCTTAACTATAAAAATATATATTTTATTA-TTTTTCTTAATTTATCGAATATATATATT
13570 TTGGTTTAAAGTAGGTCAAGTTTATTATTTAAGTTAAG-A-ATA-T---ATATTTAAAATAT
65 TTGGTTTAAAGTAGG-CAAGTTTATTATTTAAGTTAAGAATATATTAAAATATTTAAAATAT
* *
13626 TTAAATTATTAACTATAAAAATATATA--TTATTATTTTTCTTAATTTATCGAATATATATTTTT
1 TTAAATTCTTAACTATAAAAATATATATTTTATTATTTTTCTTAATTTATCGAATATATATATTT
*
13689 TGGTTTAAAGTAGGCCAAGTTTATTATTTAAGTTAAGTATATATATTTAAAATA-TT----TGT
66 TGGTTTAAAGTAGG-CAAGTTTATTATTTAAGTTAAG-A-ATATA-TTAAAATATTTAAAATAT
*
13748 TTAAATTCTTAAC-AGTAAAAATATATATTTTATTATTTTTTTCTTAATTTATTGAATATATAT
1 TTAAATTCTTAACTA-TAAAAATATATATTTTATTA--TTTTTCTTAATTTATCGAATATATAT
13811 TTTAAAGTAG
Statistics
Matches: 281, Mismatches: 9, Indels: 34
0.87 0.03 0.10
Matches are distributed among these distances:
118 65 0.23
119 6 0.02
121 38 0.14
122 32 0.11
124 7 0.02
126 28 0.10
127 6 0.02
128 36 0.13
129 62 0.22
130 1 0.00
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (125 bp):
TTAAATTCTTAACTATAAAAATATATATTTTATTATTTTTCTTAATTTATCGAATATATATATTT
TGGTTTAAAGTAGGCAAGTTTATTATTTAAGTTAAGAATATATTAAAATATTTAAAATAT
Found at i:23032 original size:15 final size:15
Alignment explanation
Indices: 23012--23041 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
23002 TATCCTAATA
*
23012 CTTATCTACGCCATC
1 CTTATCTACACCATC
23027 CTTATCTACACCATC
1 CTTATCTACACCATC
23042 TTTTTTTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.40, G:0.03, T:0.33
Consensus pattern (15 bp):
CTTATCTACACCATC
Found at i:29567 original size:656 final size:656
Alignment explanation
Indices: 28314--29616 Score: 2489
Period size: 656 Copynumber: 2.0 Consensus size: 656
28304 CTACATATAT
28314 ATACATACAAGTTAAAAAGTAAAGATCTGGTTGACTCAATTTTTTCATCTTGAATTCGAATATGA
1 ATACATACAAGTTAAAAAGTAAAGATCTGGTTGACTCAATTTTTTCATCTTGAATTCGAATATGA
*
28379 TTTAAAGTTAACTCAATTTAATCTAAACATAAATTTTAAAAATAAAAAATTGATTTAATTGAATT
66 TTTAAAGTTAACTCAATTTAATCTAAACATAAATTTTAAAAATAAAAAATTGATTTAATTGAATC
28444 GAGTCAGAATAAAACTCGTCAAGTCGGGTGAAATATTCCTCCCTTGGTGGATCATGCCAACAATA
131 GAGTCAGAATAAAACTCGTCAAGTCGGGTGAAATATTCCTCCCTTGGTGGATCATGCCAACAATA
28509 GAAGGTTTTGCTCTGACTAAACTGGATCGACCTGGGTTGCACACCTGATTTTGGTGGGTGAGTCT
196 GAAGGTTTTGCTCTGACTAAACTGGATCGACCTGGGTTGCACACCTGATTTTGGTGGGTGAGTCT
*
28574 CCCAGTGGGATTTTTTGCATACACAAGGACTCGAACCTAAGATCTTACTTAAGCAATATCAAGTT
261 CCCAGTGGGATTTTCTGCATACACAAGGACTCGAACCTAAGATCTTACTTAAGCAATATCAAGTT
28639 GCTTACTATTTGAACCAATCCTCATTTGTCACTTTTGTTTGATGTTAGTTTTCAAACATGTGACT
326 GCTTACTATTTGAACCAATCCTCATTTGTCACTTTTGTTTGATGTTAGTTTTCAAACATGTGACT
*
28704 TTAATAAGGTAGGAATAGGAAATTCTTATATGTTTTTAGGGAATTAAAAATGTAATATAAGAAAA
391 TTAATAAGGTAGGAATAGGAAATTCTTATATATTTTTAGGGAATTAAAAATGTAATATAAGAAAA
**
28769 AAAAGAAATATCGATGATGATTATAAACATCAAGGTTAGTTGCCTATTGATCAAAAATGAAGAAA
456 AAAAGAAATATCGATGATGATTATAAACATCAAGGCCAGTTGCCTATTGATCAAAAATGAAGAAA
28834 AGTTTAATGTTTCAGAGAGAAAAAGTTAAACTAAACATTTAATATCCTCCAAACAGAGGTAGTAA
521 AGTTTAATGTTTCAGAGAGAAAAAGTTAAACTAAACATTTAATATCCTCCAAACAGAGGTAGTAA
* *
28899 TAGGAAATTGTTATATAGCACGTAAAATTAATATCAACAAGTTCTGGAGTGGTATAGGAAGTTCT
586 TAGGAAATTGTTATATAGCACGTAAAATTAACATCAACAAGTTATGGAGTGGTATAGGAAGTTCT
28964 ACATAC
651 ACATAC
28970 ATACATACAAGTTAAAAAGTAAAGATCTGGTTGACTCAATTTTTTCATCTTGAATTCGAATATGA
1 ATACATACAAGTTAAAAAGTAAAGATCTGGTTGACTCAATTTTTTCATCTTGAATTCGAATATGA
29035 TTTAAAGTTAACTCAATTTAATCTAAACATAAATTTTAAAAATAAAAAATTGATTTAATTGAATC
66 TTTAAAGTTAACTCAATTTAATCTAAACATAAATTTTAAAAATAAAAAATTGATTTAATTGAATC
*
29100 GAGTCAGAATAAAACTCGTCAAGTCGGGTGAAATATTTCTCCCTTGGTGGATCATGCCAACAATA
131 GAGTCAGAATAAAACTCGTCAAGTCGGGTGAAATATTCCTCCCTTGGTGGATCATGCCAACAATA
29165 GAAGGTTTTGCTCTGACTAAACTGGATCGACCTGGGTTGCACACCTGATTTTGGTGGGTGAGTCT
196 GAAGGTTTTGCTCTGACTAAACTGGATCGACCTGGGTTGCACACCTGATTTTGGTGGGTGAGTCT
*
29230 CCCAGTGGGATTTTCTGCATACACAAGGACTCGAACCTAAGATCTTACTTAAGCAATATCGAGTT
261 CCCAGTGGGATTTTCTGCATACACAAGGACTCGAACCTAAGATCTTACTTAAGCAATATCAAGTT
*
29295 GCTTTCTATTTGAACCAATCCTCATTTGTCACTTTTGTTTGATGTTAGTTTTCAAACATGTGACT
326 GCTTACTATTTGAACCAATCCTCATTTGTCACTTTTGTTTGATGTTAGTTTTCAAACATGTGACT
29360 TTAATAAGGTAGGAATAGGAAATTCTTATATATTTTTAGGGAATTAAAAATGTAATATAAGAAAA
391 TTAATAAGGTAGGAATAGGAAATTCTTATATATTTTTAGGGAATTAAAAATGTAATATAAGAAAA
* *
29425 ATAAGAAATATCGATGATGATTATAAACATCAAGGCCAGTTTCCTATTGATCAAAAATGAAGAAA
456 AAAAGAAATATCGATGATGATTATAAACATCAAGGCCAGTTGCCTATTGATCAAAAATGAAGAAA
*
29490 AGTTTAATGTTTCAGAGAGAAAAAGTTAAACTAAACCTTTAATATCCTCCAAACAGAGGTAGTAA
521 AGTTTAATGTTTCAGAGAGAAAAAGTTAAACTAAACATTTAATATCCTCCAAACAGAGGTAGTAA
29555 TAGGAAATTGTTATATAGCACGTAAAATTAACATCAACAAGTTATGGAGTGGTATAGGAAGT
586 TAGGAAATTGTTATATAGCACGTAAAATTAACATCAACAAGTTATGGAGTGGTATAGGAAGT
29617 GCTGTTAGAA
Statistics
Matches: 634, Mismatches: 13, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
656 634 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.32
Consensus pattern (656 bp):
ATACATACAAGTTAAAAAGTAAAGATCTGGTTGACTCAATTTTTTCATCTTGAATTCGAATATGA
TTTAAAGTTAACTCAATTTAATCTAAACATAAATTTTAAAAATAAAAAATTGATTTAATTGAATC
GAGTCAGAATAAAACTCGTCAAGTCGGGTGAAATATTCCTCCCTTGGTGGATCATGCCAACAATA
GAAGGTTTTGCTCTGACTAAACTGGATCGACCTGGGTTGCACACCTGATTTTGGTGGGTGAGTCT
CCCAGTGGGATTTTCTGCATACACAAGGACTCGAACCTAAGATCTTACTTAAGCAATATCAAGTT
GCTTACTATTTGAACCAATCCTCATTTGTCACTTTTGTTTGATGTTAGTTTTCAAACATGTGACT
TTAATAAGGTAGGAATAGGAAATTCTTATATATTTTTAGGGAATTAAAAATGTAATATAAGAAAA
AAAAGAAATATCGATGATGATTATAAACATCAAGGCCAGTTGCCTATTGATCAAAAATGAAGAAA
AGTTTAATGTTTCAGAGAGAAAAAGTTAAACTAAACATTTAATATCCTCCAAACAGAGGTAGTAA
TAGGAAATTGTTATATAGCACGTAAAATTAACATCAACAAGTTATGGAGTGGTATAGGAAGTTCT
ACATAC
Found at i:34648 original size:2 final size:2
Alignment explanation
Indices: 34643--34680 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
34633 ACACACACAC
34643 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
34681 TAAATTATAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38836 original size:11 final size:10
Alignment explanation
Indices: 38822--38951 Score: 50
Period size: 11 Copynumber: 12.2 Consensus size: 10
38812 ATAATAATAA
38822 ATAAATACTAT
1 ATAAATA-TAT
*
38833 ATAAATGCTAT
1 ATAAAT-ATAT
38844 AATAAATATAT
1 -ATAAATATAT
*
38855 AT-AATATAA
1 ATAAATATAT
38864 ATATAATATAT
1 ATA-AATATAT
**
38875 ACTATGTACTAT
1 A-TAAATA-TAT
*
38887 ATAACGTA-AT
1 ATAA-ATATAT
*
38897 AAAAATACTAT
1 ATAAATA-TAT
38908 ATAATATATAT
1 ATAA-ATATAT
* *
38919 ACTATATAAAAT
1 A-TAAAT-ATAT
* *
38931 CTAAATA-CT
1 ATAAATATAT
38940 ATAAATATAT
1 ATAAATATAT
38950 AT
1 AT
38952 TATATAATAT
Statistics
Matches: 89, Mismatches: 17, Indels: 27
0.67 0.13 0.20
Matches are distributed among these distances:
9 17 0.19
10 11 0.12
11 38 0.43
12 23 0.26
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (10 bp):
ATAAATATAT
Found at i:38850 original size:12 final size:12
Alignment explanation
Indices: 38809--38879 Score: 53
Period size: 11 Copynumber: 6.2 Consensus size: 12
38799 CCTACAAATA
*
38809 ATAAT-AATAAT
1 ATAATAAATACT
38820 A-AATAAATACT
1 ATAATAAATACT
*
38831 AT-ATAAATGCT
1 ATAATAAATACT
38842 ATAATAAATA-T
1 ATAATAAATACT
*
38853 AT-ATAATATAAAT
1 ATAATAA-AT-ACT
*
38866 ATAATATATACT
1 ATAATAAATACT
38878 AT
1 AT
38880 GTACTATATA
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
10 7 0.15
11 22 0.46
12 11 0.23
13 5 0.10
14 3 0.06
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (12 bp):
ATAATAAATACT
Found at i:38938 original size:18 final size:16
Alignment explanation
Indices: 38845--38963 Score: 70
Period size: 18 Copynumber: 7.2 Consensus size: 16
38835 AAATGCTATA
38845 ATAAATA-TATATAAT
1 ATAAATACTATATAAT
38860 ATAAATA-TA-ATATAT
1 ATAAATACTATATA-AT
**
38875 ACTATGTACTATATAACGT
1 A-TAAATACTATATAA--T
38894 AATAAAAATACTATATAAT
1 -AT--AAATACTATATAAT
*
38913 ATATATACTATATAAAAT
1 ATAAATACTATAT--AAT
*
38931 CTAAATACTATA-AAT
1 ATAAATACTATATAAT
*
38946 AT--ATATTATATAAT
1 ATAAATACTATATAAT
38960 ATAA
1 ATAA
38964 CACCATATGC
Statistics
Matches: 81, Mismatches: 9, Indels: 27
0.69 0.08 0.23
Matches are distributed among these distances:
13 7 0.09
14 8 0.10
15 16 0.20
16 14 0.17
17 3 0.04
18 18 0.22
19 3 0.04
20 1 0.01
21 11 0.14
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.38
Consensus pattern (16 bp):
ATAAATACTATATAAT
Found at i:43042 original size:169 final size:168
Alignment explanation
Indices: 42724--43051 Score: 615
Period size: 169 Copynumber: 1.9 Consensus size: 168
42714 AATAAATGAG
42724 AAAAATAATAATCTATAAATCATAAAGAATAAAAATATGTGCTATATCATGTATCTTAATACTTA
1 AAAAATAATAATCTATAAATCATAAAGAATAAAAATATGTGCTATATCATGTATCTTAATACTTA
42789 ATTTATGTCAATGTATGAAGTATCTATCTCTATAAAACTCATCTCTATAACATAAACACCAAATG
66 ATTTATGTCAATGTATGAAGTATCTATCTCTATAAAACTCATCTCTATAACATAAACACCAAATG
42854 TTGCAAAAGCTATAAAAGGATTACATCTCGAAATAAGC
131 TTGCAAAAGCTATAAAAGGATTACATCTCGAAATAAGC
42892 AAAAATAATAATCTATAAATCATAAAG-A-AAAAATATGTGCTATATCATGTATCTTAATACTTA
1 AAAAATAATAATCTATAAATCATAAAGAATAAAAATATGTGCTATATCATGTATCTTAATACTTA
42955 ATTTATGTCAATGTATGAAGTATCTAATATCTCTATAAAACTCATCTCTATAACATAAACACCAA
66 ATTTATGTCAATGTATGAAGTATC---TATCTCTATAAAACTCATCTCTATAACATAAACACCAA
43020 ATGTTGCAAAAGCTATAAAAGGATTACATCTC
128 ATGTTGCAAAAGCTATAAAAGGATTACATCTC
43052 TCTAAAATAA
Statistics
Matches: 157, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
166 59 0.38
167 1 0.01
168 27 0.17
169 70 0.45
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (168 bp):
AAAAATAATAATCTATAAATCATAAAGAATAAAAATATGTGCTATATCATGTATCTTAATACTTA
ATTTATGTCAATGTATGAAGTATCTATCTCTATAAAACTCATCTCTATAACATAAACACCAAATG
TTGCAAAAGCTATAAAAGGATTACATCTCGAAATAAGC
Found at i:45729 original size:14 final size:15
Alignment explanation
Indices: 45710--45739 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
45700 TTATTCAGAT
45710 TTAAAAAA-ATTAAA
1 TTAAAAAATATTAAA
45724 TTAAAAAATATTAAA
1 TTAAAAAATATTAAA
45739 T
1 T
45740 GCTTAAATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TTAAAAAATATTAAA
Found at i:46432 original size:24 final size:24
Alignment explanation
Indices: 46400--46448 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
46390 ACGGAAGTTA
* *
46400 CTCTCAACCTGGCGTTGGGGGCTG
1 CTCTCAACCTGGCATTAGGGGCTG
46424 CTCTCAACCTGGCATTAGGGGCTG
1 CTCTCAACCTGGCATTAGGGGCTG
46448 C
1 C
46449 CTACTACCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.31, G:0.33, T:0.24
Consensus pattern (24 bp):
CTCTCAACCTGGCATTAGGGGCTG
Found at i:47402 original size:14 final size:14
Alignment explanation
Indices: 47383--47411 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
47373 TCTATGTGGA
47383 GAGTGTACAATTAC
1 GAGTGTACAATTAC
47397 GAGTGTACAATTAC
1 GAGTGTACAATTAC
47411 G
1 G
47412 CTGGATGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (14 bp):
GAGTGTACAATTAC
Found at i:48782 original size:21 final size:21
Alignment explanation
Indices: 48758--48827 Score: 54
Period size: 21 Copynumber: 3.3 Consensus size: 21
48748 CCGCAAGGAT
48758 ATATGCCCATCCCACCAGTTC
1 ATATGCCCATCCCACCAGTTC
* * ** *
48779 ATATG-TCATCTCTGCAGGGGT-
1 ATATGCCCATCCCACCA--GTTC
*
48800 ATATGCCCAGCCCACCAGTTC
1 ATATGCCCATCCCACCAGTTC
48821 ATATGCC
1 ATATGCC
48828 ATCTCAAAAG
Statistics
Matches: 34, Mismatches: 11, Indels: 8
0.64 0.21 0.15
Matches are distributed among these distances:
20 9 0.26
21 17 0.50
22 8 0.24
ACGTcount: A:0.23, C:0.34, G:0.17, T:0.26
Consensus pattern (21 bp):
ATATGCCCATCCCACCAGTTC
Found at i:48789 original size:42 final size:42
Alignment explanation
Indices: 48718--48832 Score: 167
Period size: 42 Copynumber: 2.7 Consensus size: 42
48708 ACAGGGGTAC
* *
48718 ATGCCCAGCCCACCATTTCAGATGCCATCTCCGCAAGGATAT
1 ATGCCCAGCCCACCAGTTCATATGCCATCTCCGCAAGGATAT
* * * * *
48760 ATGCCCATCCCACCAGTTCATATGTCATCTCTGCAGGGGTAT
1 ATGCCCAGCCCACCAGTTCATATGCCATCTCCGCAAGGATAT
48802 ATGCCCAGCCCACCAGTTCATATGCCATCTC
1 ATGCCCAGCCCACCAGTTCATATGCCATCTC
48833 AAAAGGGTTA
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.23, C:0.36, G:0.17, T:0.24
Consensus pattern (42 bp):
ATGCCCAGCCCACCAGTTCATATGCCATCTCCGCAAGGATAT
Found at i:48854 original size:42 final size:42
Alignment explanation
Indices: 48710--48856 Score: 143
Period size: 42 Copynumber: 3.5 Consensus size: 42
48700 ATGACGCCAC
* * **
48710 AGGGGTACATGCCCAGCCCACCATTTCAGATGCCATCTCCGCA
1 AGGGGTACATGCCCAGCCCACCAGTTCATATGCCATCT-CAAA
* * * * ***
48753 A-GGATATATGCCCATCCCACCAGTTCATATGTCATCTCTGC
1 AGGGGTACATGCCCAGCCCACCAGTTCATATGCCATCTCAAA
*
48794 AGGGGTATATGCCCAGCCCACCAGTTCATATGCCATCTCAAA
1 AGGGGTACATGCCCAGCCCACCAGTTCATATGCCATCTCAAA
* * *
48836 AGGGTTACATTCCTAGCCCAC
1 AGGGGTACATGCCCAGCCCAC
48857 AAGGGTACAT
Statistics
Matches: 84, Mismatches: 19, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
41 2 0.02
42 81 0.96
43 1 0.01
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.23
Consensus pattern (42 bp):
AGGGGTACATGCCCAGCCCACCAGTTCATATGCCATCTCAAA
Found at i:48871 original size:21 final size:22
Alignment explanation
Indices: 48835--48881 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
48825 GCCATCTCAA
*
48835 AAGGGTTACATTCCTAGCCCAC
1 AAGGGTTACATACCTAGCCCAC
*
48857 AAGGG-TACATACCTAGCCCGC
1 AAGGGTTACATACCTAGCCCAC
48878 AAGG
1 AAGG
48882 TTTTATGACA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.30, C:0.30, G:0.23, T:0.17
Consensus pattern (22 bp):
AAGGGTTACATACCTAGCCCAC
Done.