Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005942.1 Hibiscus syriacus cultivar Beakdansim tig00013956_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: 66075
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:4899 original size:21 final size:21
Alignment explanation
Indices: 4858--4900 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
4848 TTCTGGGTTG
*
4858 TGTGCATCGATGCATATTCAA
1 TGTGCATCGATGCATACTCAA
*
4879 TGTGTATCGATGCACT-CTCAA
1 TGTGCATCGATGCA-TACTCAA
4900 T
1 T
4901 TAAAGGAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.35
Consensus pattern (21 bp):
TGTGCATCGATGCATACTCAA
Found at i:8909 original size:64 final size:64
Alignment explanation
Indices: 8841--9061 Score: 234
Period size: 64 Copynumber: 3.5 Consensus size: 64
8831 TTGAAGGTGT
** * * *
8841 ATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATTCGTG
1 ATCGATGCATAAGTAGTGCATCGATGCATC-CTATTAATAAGAAA-ACATCGAATGCAATTAGTG
8904 C
64 C
*
8905 ATCGATGCATAAGTAGTGCATCGATGCATCCTATTAATAAGGAAACATCGAATGCAATTAGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCTATTAATAAGAAAACATCGAATGCAATTAGTGC
* * * * * * * *
8969 ATCGATGAATAAGGCA-TGCATCGATGCATCCCAGTAATAATAAAACATCAAATACATTTTA-TG
1 ATCGATGCATAA-GTAGTGCATCGATGCATCCTATTAATAAGAAAACATCGAATGCA-ATTAGTG
9032 C
64 C
* *
9033 ACCGATGCATCAGTAGTGCATCGATGCAT
1 ATCGATGCATAAGTAGTGCATCGATGCAT
9062 ACCTTCATTA
Statistics
Matches: 133, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
63 2 0.02
64 121 0.91
65 10 0.08
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCCTATTAATAAGAAAACATCGAATGCAATTAGTGC
Found at i:9861 original size:30 final size:29
Alignment explanation
Indices: 9820--9885 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
9810 GTGGTCCTTA
*
9820 TGGACAGTTACCAAGGATCTTTATGACCTC
1 TGGATAGTTACC-AGGATCTTTATGACCTC
* * *
9850 TGGATAGTTACCGGGGTCTTTGTGACCTC
1 TGGATAGTTACCAGGATCTTTATGACCTC
9879 TGGATAG
1 TGGATAG
9886 GTCCTTCGGG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 21 0.66
30 11 0.34
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (29 bp):
TGGATAGTTACCAGGATCTTTATGACCTC
Found at i:10299 original size:2 final size:2
Alignment explanation
Indices: 10294--10321 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
10284 ATGTATATGT
10294 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
10322 ATGTTATATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14891 original size:29 final size:30
Alignment explanation
Indices: 14818--14897 Score: 126
Period size: 30 Copynumber: 2.7 Consensus size: 30
14808 GCATAAGCCC
*
14818 ATCTTTATGACCTCTGGACAGTTACCGAGG
1 ATCTTTATGACCTCTGGATAGTTACCGAGG
14848 ATCTTTATGACCTCTGGATAGTTACCG-GG
1 ATCTTTATGACCTCTGGATAGTTACCGAGG
* *
14877 GTCTTTGTGACCTCTGGATAG
1 ATCTTTATGACCTCTGGATAG
14898 GTCCTTTGGG
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 21 0.45
30 26 0.55
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.34
Consensus pattern (30 bp):
ATCTTTATGACCTCTGGATAGTTACCGAGG
Found at i:16938 original size:20 final size:20
Alignment explanation
Indices: 16913--16951 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
16903 TCATATGTTA
*
16913 AAGAATGCATCGATGCACTG
1 AAGAATGCACCGATGCACTG
*
16933 AAGAATGCACCTATGCACT
1 AAGAATGCACCGATGCACT
16952 TCAATGGGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.21
Consensus pattern (20 bp):
AAGAATGCACCGATGCACTG
Found at i:24687 original size:2 final size:2
Alignment explanation
Indices: 24675--24705 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
24665 CTTGACATCT
*
24675 TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
24706 TGTTTTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:27306 original size:46 final size:46
Alignment explanation
Indices: 27239--27341 Score: 188
Period size: 46 Copynumber: 2.2 Consensus size: 46
27229 AACAATATTT
27239 AATTAATTTGAATAAAAGAATGTTAAGCTAATCTAATTTTTTATCA
1 AATTAATTTGAATAAAAGAATGTTAAGCTAATCTAATTTTTTATCA
*
27285 AATTAATTTGAATAAAAGAATGTTAAGTTAATCTAATTTTTTATCA
1 AATTAATTTGAATAAAAGAATGTTAAGCTAATCTAATTTTTTATCA
*
27331 AATGAATTTGA
1 AATTAATTTGA
27342 GTGAAATAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 55 1.00
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.42
Consensus pattern (46 bp):
AATTAATTTGAATAAAAGAATGTTAAGCTAATCTAATTTTTTATCA
Found at i:27754 original size:26 final size:25
Alignment explanation
Indices: 27708--27764 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
27698 TATAATTTAT
**
27708 TTAAAAAAATCTAAATGTAAAAGTA
1 TTAAAAAAATCTAAATGTAAAAAAA
*
27733 TTAAAAAAAT-TAAATTATTAAAAAAA
1 TTAAAAAAATCTAAA-T-GTAAAAAAA
27759 TTAAAA
1 TTAAAA
27765 TATAAATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 4 0.15
25 11 0.41
26 12 0.44
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (25 bp):
TTAAAAAAATCTAAATGTAAAAAAA
Found at i:27765 original size:18 final size:18
Alignment explanation
Indices: 27720--27765 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
27710 AAAAAAATCT
*
27720 AAATGTAAAAGTATTAAAA
1 AAAT-TAAAATTATTAAAA
27739 AAATT-AAATTATTAAAA
1 AAATTAAAATTATTAAAA
27756 AAATTAAAAT
1 AAATTAAAAT
27766 ATAAATTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 16 0.64
18 5 0.20
19 4 0.16
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.30
Consensus pattern (18 bp):
AAATTAAAATTATTAAAA
Found at i:38976 original size:31 final size:29
Alignment explanation
Indices: 38938--39028 Score: 80
Period size: 31 Copynumber: 3.1 Consensus size: 29
38928 TCAACAAAAG
38938 GGAATACCTTAGGGCCTTAGAGCCTACCCAA
1 GGAATACCTT-GGGCC-TAGAGCCTACCCAA
* * *
38969 GGAATACCTTGGG---AGAACTTACACAA
1 GGAATACCTTGGGCCTAGAGCCTACCCAA
*
38995 GGGAGTACCTTGGGGCCTAAGAGCCTACCCAA
1 -GGAATACCTT-GGGCCT-AGAGCCTACCCAA
39027 GG
1 GG
39029 GAGCATCTCG
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
26 10 0.21
27 9 0.19
28 3 0.06
30 3 0.06
31 12 0.26
32 10 0.21
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (29 bp):
GGAATACCTTGGGCCTAGAGCCTACCCAA
Found at i:48604 original size:41 final size:40
Alignment explanation
Indices: 48545--48638 Score: 143
Period size: 40 Copynumber: 2.3 Consensus size: 40
48535 TTAAATCAAT
* * *
48545 TAAGGATCTAATTGAGAAAATCTTATTTTTATTTGATAAAA
1 TAAGGATATAATTAAG-AAATCTTACTTTTATTTGATAAAA
*
48586 TAAGGATATTATTAAGAAATCTTACTTTTATTTGATAAAA
1 TAAGGATATAATTAAGAAATCTTACTTTTATTTGATAAAA
48626 TAAGGATATAATT
1 TAAGGATATAATT
48639 GTCTAATTGC
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 35 0.73
41 13 0.27
ACGTcount: A:0.43, C:0.04, G:0.12, T:0.41
Consensus pattern (40 bp):
TAAGGATATAATTAAGAAATCTTACTTTTATTTGATAAAA
Found at i:49940 original size:19 final size:19
Alignment explanation
Indices: 49916--49968 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
49906 AGGGAAACAA
*
49916 AAAGAAGAAATTCAAAATT
1 AAAGAATAAATTCAAAATT
49935 AAAGAATAAATTCAAAATT
1 AAAGAATAAATTCAAAATT
49954 AAAGAATAAATTCAA
1 AAAGAATAAATTCAA
49969 TAACCATGGC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.64, C:0.06, G:0.08, T:0.23
Consensus pattern (19 bp):
AAAGAATAAATTCAAAATT
Found at i:51815 original size:40 final size:40
Alignment explanation
Indices: 51769--51849 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
51759 TTTTAACATT
51769 TATTTTTTTA-TTTTTTAAAATTAAATTAAATTACATAAA
1 TATTTTTTTATTTTTTTAAAATTAAATTAAATTACATAAA
*
51808 TATTTTTTTATTTTTTTAAAATTACATTAAATTACATAAA
1 TATTTTTTTATTTTTTTAAAATTAAATTAAATTACATAAA
51848 TA
1 TA
51850 ATAAACTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
39 10 0.25
40 30 0.75
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (40 bp):
TATTTTTTTATTTTTTTAAAATTAAATTAAATTACATAAA
Found at i:55816 original size:127 final size:127
Alignment explanation
Indices: 55590--56243 Score: 1166
Period size: 127 Copynumber: 5.2 Consensus size: 127
55580 TTCATATGAC
* * *
55590 GGCGCATTCCCGGGGGCGCGTCTTCCATTATTTTATCAGAGAATATGTTATCATTACCCTATTAT
1 GGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTAT
*
55655 GTCACTTATGTCCCCCAGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGTGAA
66 GTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGTGAA
55717 GGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTAT
1 GGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTAT
55782 GTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGTGAA
66 GTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGTGAA
* * *
55844 GGCACGTTCCCGGGGGCGTGCCTTCCATTATTTTGTCAGAGAA-ATATTATCATTACCCTATTAT
1 GGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTAT
55908 GTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGTGAA
66 GTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGTGAA
* *
55970 CGCGCGTTCCCGGGGGCACGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTAT
1 GGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTAT
*
56035 GTCACTTATGTCCCCCGAGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGTGAA
66 GTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGTGAA
* *
56097 GGCGCGTTTCCGGGGGCACGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTAT
1 GGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTAT
***
56162 GTCACTTATGTCCCCTAAGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGTGAA
66 GTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGTGAA
56224 GGCGCGTTCCCGGGGGCGCG
1 GGCGCGTTCCCGGGGGCGCG
56244 TTCCTGGGGA
Statistics
Matches: 507, Mismatches: 19, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
126 121 0.24
127 386 0.76
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (127 bp):
GGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTAT
GTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGTGAA
Found at i:56045 original size:253 final size:254
Alignment explanation
Indices: 55596--56240 Score: 1166
Period size: 253 Copynumber: 2.5 Consensus size: 254
55586 TGACGGCGCA
* *
55596 TTCCCGGGGGCGCGTCTTCCATTATTTTATCAGAGAATATGTTATCATTACCCTATTATGTCACT
1 TTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGTCACT
55661 TATGTCCCCCAGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGTGAAGGCGCGTTC
66 TATGTCCCCCAGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGTGAAGGCGCGTTC
*
55726 CCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGTCACTTAT
131 CCGGGGGCACGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGTCACTTAT
*
55791 GTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGTGAAGGCACG
196 GTCCCCCGAGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGTGAAGGCACG
* *
55850 TTCCCGGGGGCGTGCCTTCCATTATTTTGTCAGAGAA-ATATTATCATTACCCTATTATGTCACT
1 TTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGTCACT
* *
55914 TATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGTGAACGCGCGTTC
66 TATGTCCCCCAGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGTGAAGGCGCGTTC
55979 CCGGGGGCACGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGTCACTTAT
131 CCGGGGGCACGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGTCACTTAT
*
56044 GTCCCCCGAGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGTGAAGGCGCG
196 GTCCCCCGAGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGTGAAGGCACG
* *
56103 TTTCCGGGGGCACGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGTCACT
1 TTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGTCACT
* *
56168 TATGTCCCCTAAGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGTGAAGGCGCGTTC
66 TATGTCCCCCAGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGTGAAGGCGCGTTC
56233 CCGGGGGC
131 CCGGGGGC
56241 GCGTTCCTGG
Statistics
Matches: 373, Mismatches: 17, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
253 244 0.65
254 129 0.35
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (254 bp):
TTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGTCACT
TATGTCCCCCAGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGTGAAGGCGCGTTC
CCGGGGGCACGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGTCACTTAT
GTCCCCCGAGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGTGAAGGCACG
Found at i:56342 original size:2 final size:2
Alignment explanation
Indices: 56335--56384 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
56325 AGGATAAAAT
56335 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
56377 TA TA TA TA
1 TA TA TA TA
56385 AATTTAAGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:56736 original size:34 final size:34
Alignment explanation
Indices: 56698--56798 Score: 166
Period size: 34 Copynumber: 3.0 Consensus size: 34
56688 GAATTTAATG
*
56698 TTAAATTTTGAATACTATAATTTATATTTTAAAT
1 TTAAATTTTGAATACTATAATTTGTATTTTAAAT
* * *
56732 TTAAATTTTGAATAATATTATTTGTATTTTAATT
1 TTAAATTTTGAATACTATAATTTGTATTTTAAAT
56766 TTAAATTTTGAATACTATAATTTGTATTTTAAA
1 TTAAATTTTGAATACTATAATTTGTATTTTAAA
56799 AAGATTTATT
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 60 1.00
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (34 bp):
TTAAATTTTGAATACTATAATTTGTATTTTAAAT
Found at i:57344 original size:21 final size:21
Alignment explanation
Indices: 57318--57367 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
57308 TATGGTATAA
*
57318 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
57339 AACCCTGCGGGCTAGGAATGT
1 AACCCTGCGGGCTAGGAATGT
57360 AACCCTGC
1 AACCCTGC
57368 AGAGATGACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.22, C:0.30, G:0.30, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:59228 original size:29 final size:31
Alignment explanation
Indices: 59173--59248 Score: 86
Period size: 29 Copynumber: 2.5 Consensus size: 31
59163 TTAATAAATT
*
59173 TAAATAATAATAATTATATAAATATTATTTTAA
1 TAAA-AATAAT-ATTATATAAATATTATATTAA
*
59206 TAAAAATAATATT-TATATA-ATTATATTAA
1 TAAAAATAATATTATATAAATATTATATTAA
59235 TATAAAAT-ATATTA
1 TA-AAAATAATATTA
59249 ACTATTTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
29 16 0.41
30 10 0.26
31 3 0.08
32 6 0.15
33 4 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (31 bp):
TAAAAATAATATTATATAAATATTATATTAA
Found at i:59247 original size:15 final size:15
Alignment explanation
Indices: 59152--59249 Score: 61
Period size: 15 Copynumber: 6.8 Consensus size: 15
59142 ATTAGCACAA
59152 AAAATA-ATTAAT-T
1 AAAATATATTAATAT
59165 AATAA-AT-TTAA-AT
1 AA-AATATATTAATAT
59178 AATAATA-ATT-ATAT
1 AA-AATATATTAATAT
*
59192 AAATATTATTTTAATA-
1 AAA-A-TATATTAATAT
*
59208 AAAATAATATTTATAT
1 AAAAT-ATATTAATAT
*
59224 -AATTATATTAATAT
1 AAAATATATTAATAT
59238 AAAATATATTAA
1 AAAATATATTAA
59250 CTATTTAAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 24
0.69 0.06 0.25
Matches are distributed among these distances:
13 15 0.23
14 20 0.30
15 23 0.35
16 5 0.08
17 3 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AAAATATATTAATAT
Found at i:59596 original size:61 final size:59
Alignment explanation
Indices: 59452--59596 Score: 177
Period size: 59 Copynumber: 2.4 Consensus size: 59
59442 CTAATGAAAG
*
59452 GCGCATCCCCGGGGATGCGCCTTTCACACGTGGCAACTGAATCAACAAATAAAGGTAAA
1 GCGCATCCCCGGGGATGCGCCTTTCACACGTGGCAACTCAATCAACAAATAAAGGTAAA
* * ** *
59511 GCGCGTCCCCGGGGATGCGCCTTTCACACGTGGCATC-CAACTCAGTGTAAA-ACCAGGTAAA
1 GCGCATCCCCGGGGATGCGCCTTTCACACGTGGCAACTCAA-TCA--ACAAATA-AAGGTAAA
*
59572 GCGCATCCCCGGGGATGCGTCTTTC
1 GCGCATCCCCGGGGATGCGCCTTTC
59597 GCCACCTCAA
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
58 2 0.03
59 38 0.51
60 1 0.01
61 33 0.45
ACGTcount: A:0.25, C:0.30, G:0.26, T:0.19
Consensus pattern (59 bp):
GCGCATCCCCGGGGATGCGCCTTTCACACGTGGCAACTCAATCAACAAATAAAGGTAAA
Found at i:61681 original size:2 final size:2
Alignment explanation
Indices: 61674--61705 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
61664 AGGTATAGTA
61674 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
61706 TAAAAAAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:64533 original size:27 final size:28
Alignment explanation
Indices: 64489--64541 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
64479 ACATGTATTA
* *
64489 ACTAACTTTTTTTCTTTTGTTTGTGTAC
1 ACTAACTTTGTTTCTTTTGATTGTGTAC
64517 ACTAAC-TTGTTTCTTTTGATTGTGT
1 ACTAACTTTGTTTCTTTTGATTGTGT
64542 CATTTTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 17 0.74
28 6 0.26
ACGTcount: A:0.15, C:0.13, G:0.13, T:0.58
Consensus pattern (28 bp):
ACTAACTTTGTTTCTTTTGATTGTGTAC
Done.