Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003195.1 Hibiscus syriacus cultivar Beakdansim tig00006724_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: 79225
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.32
Found at i:4167 original size:56 final size:56
Alignment explanation
Indices: 4095--4201 Score: 144
Period size: 56 Copynumber: 1.9 Consensus size: 56
4085 TGAAAAAGAG
* * * *
4095 ACCATAATCACGATAAATGA-AAAACAACTGAAAAAGCGACTGCAACCGCAACCGCA
1 ACCATAATCACAATAAA-CACAAAACAACTGAAAAAACGACGGCAACCGCAACCGCA
* *
4151 ACCATAATCACAATAAACACAAAGCAACTGAAAAAACGACGGCATCCGCAA
1 ACCATAATCACAATAAACACAAAACAACTGAAAAAACGACGGCAACCGCAA
4202 TTTAAATCTC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
55 1 0.02
56 43 0.98
ACGTcount: A:0.50, C:0.27, G:0.13, T:0.10
Consensus pattern (56 bp):
ACCATAATCACAATAAACACAAAACAACTGAAAAAACGACGGCAACCGCAACCGCA
Found at i:4541 original size:21 final size:21
Alignment explanation
Indices: 4504--4543 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4494 TTGGATGAAA
*
4504 AATTAGGGATTGAGGGTCAAG
1 AATTAGGAATTGAGGGTCAAG
4525 AATTAGGAATT-ACGGGTCA
1 AATTAGGAATTGA-GGGTCA
4544 GAAAATTGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.07, G:0.33, T:0.25
Consensus pattern (21 bp):
AATTAGGAATTGAGGGTCAAG
Found at i:10298 original size:16 final size:17
Alignment explanation
Indices: 10277--10312 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
10267 TATGCAGATA
10277 TTAAAA-AAATATTATT
1 TTAAAATAAATATTATT
10293 TTAAAATAAATATTATT
1 TTAAAATAAATATTATT
10310 TTA
1 TTA
10313 TATATTTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAAAATAAATATTATT
Found at i:11892 original size:14 final size:14
Alignment explanation
Indices: 11873--11926 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 14
11863 CAGTTATTAT
11873 GTTCGTTTATATTC
1 GTTCGTTTATATTC
*
11887 GTTCGTTTGTATTC
1 GTTCGTTTATATTC
*
11901 GTTTACGTTCATATAT-
1 G-TT-CGTTTATAT-TC
11917 GTTCGTTTAT
1 GTTCGTTTAT
11927 CATTTAAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
14 20 0.61
15 4 0.12
16 8 0.24
17 1 0.03
ACGTcount: A:0.15, C:0.13, G:0.17, T:0.56
Consensus pattern (14 bp):
GTTCGTTTATATTC
Found at i:11982 original size:16 final size:16
Alignment explanation
Indices: 11961--11993 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
11951 AAAAAAATTT
11961 TGTTCGCTTATGTTCG
1 TGTTCGCTTATGTTCG
*
11977 TGTTCGTTTATGTTCG
1 TGTTCGCTTATGTTCG
11993 T
1 T
11994 TTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.15, G:0.24, T:0.55
Consensus pattern (16 bp):
TGTTCGCTTATGTTCG
Found at i:12482 original size:15 final size:16
Alignment explanation
Indices: 12455--12486 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
12445 TATAAAAATC
12455 AAATAACTATTTTATA
1 AAATAACTATTTTATA
12471 AAATAA-TATTTTATA
1 AAATAACTATTTTATA
12486 A
1 A
12487 TCAAAACACC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
AAATAACTATTTTATA
Found at i:26247 original size:24 final size:24
Alignment explanation
Indices: 26184--26247 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
26174 CGTTAAAATG
**
26184 ATAAACAAACACAAATGAACGAAC
1 ATAAACAAACACAAACAAACGAAC
* ** *
26208 GTAAATGAATACAAACAAACGAAC
1 ATAAACAAACACAAACAAACGAAC
*
26232 ATAAACAAACATAAAC
1 ATAAACAAACACAAAC
26248 GAGCGAATAT
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.62, C:0.19, G:0.08, T:0.11
Consensus pattern (24 bp):
ATAAACAAACACAAACAAACGAAC
Found at i:29406 original size:45 final size:48
Alignment explanation
Indices: 29339--29444 Score: 164
Period size: 45 Copynumber: 2.2 Consensus size: 48
29329 TATTTTCGTT
29339 TTTTTTGAATAAATGCATGCGAACTAGATATCATGCGGTTAGG-TTTA
1 TTTTTTGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
* *
29386 TTTTTTGAA-CAA-GCATGCGAATTAGATATCATGCGGTTAGGATTTA
1 TTTTTTGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
29432 TTTTTGTGAATAA
1 TTTTT-TGAATAA
29445 CAAAGCATGG
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
45 28 0.53
46 11 0.21
47 13 0.25
48 1 0.02
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (48 bp):
TTTTTTGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
Found at i:31883 original size:16 final size:18
Alignment explanation
Indices: 31862--31894 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
31852 TTGCATATGC
31862 ATTTTTA-AT-GCATTTA
1 ATTTTTACATCGCATTTA
31878 ATTTTTACATCGCATTT
1 ATTTTTACATCGCATTT
31895 TATTCATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.27, C:0.12, G:0.06, T:0.55
Consensus pattern (18 bp):
ATTTTTACATCGCATTTA
Found at i:39101 original size:9 final size:9
Alignment explanation
Indices: 39089--39165 Score: 50
Period size: 9 Copynumber: 8.3 Consensus size: 9
39079 AAGAAGAAAT
39089 AAAAGAGAAA
1 AAAAGAG-AA
39099 AAAATGAGAA
1 AAAA-GAGAA
*
39109 AAATGATGGAA
1 AAAAGA--GAA
* *
39120 AAACGAAAA
1 AAAAGAGAA
*
39129 AAAAAAGAA
1 AAAAGAGAA
*
39138 AAAA-TGAA
1 AAAAGAGAA
*
39146 AAATGA-AA
1 AAAAGAGAA
39154 AAAAGAGAA
1 AAAAGAGAA
39163 AAA
1 AAA
39166 TAAAAAGAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 11
0.71 0.14 0.15
Matches are distributed among these distances:
8 13 0.25
9 19 0.37
10 9 0.17
11 11 0.21
ACGTcount: A:0.75, C:0.01, G:0.17, T:0.06
Consensus pattern (9 bp):
AAAAGAGAA
Found at i:39129 original size:7 final size:6
Alignment explanation
Indices: 39117--39201 Score: 52
Period size: 7 Copynumber: 13.8 Consensus size: 6
39107 AAAAATGATG
*
39117 GAAAAA CGAAAAA -AAAAA GAAAAAA TGAAAAA TG-AAAA -AAAGA GAAAAA
1 GAAAAA -GAAAAA GAAAAA G-AAAAA -GAAAAA -GAAAAA GAAAAA GAAAAA
* * *
39166 TAAAAA GAAAAAA TGAAAAA -ATAAA GAAAAA TAAAA
1 GAAAAA G-AAAAA -GAAAAA GAAAAA GAAAAA GAAAA
39202 GGGGGGTTCA
Statistics
Matches: 63, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
5 12 0.19
6 21 0.33
7 28 0.44
8 2 0.03
ACGTcount: A:0.80, C:0.01, G:0.12, T:0.07
Consensus pattern (6 bp):
GAAAAA
Found at i:39129 original size:8 final size:8
Alignment explanation
Indices: 39128--39187 Score: 65
Period size: 8 Copynumber: 7.9 Consensus size: 8
39118 AAAAACGAAA
*
39128 AAAAAAAG
1 AAAAAATG
39136 AAAAAATG
1 AAAAAATG
39144 -AAAAATG
1 AAAAAATG
*
39151 AAAAAAAG
1 AAAAAATG
39159 AGAAAAAT-
1 A-AAAAATG
39167 -AAAAA-G
1 AAAAAATG
39173 AAAAAATG
1 AAAAAATG
39181 AAAAAAT
1 AAAAAAT
39188 AAAGAAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
6 5 0.11
7 12 0.27
8 22 0.50
9 5 0.11
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (8 bp):
AAAAAATG
Found at i:39151 original size:37 final size:37
Alignment explanation
Indices: 39080--39185 Score: 117
Period size: 37 Copynumber: 2.7 Consensus size: 37
39070 TTTTGCTTGA
*
39080 AGAAGAAATAAAAGAGAAAAAAATGAGAAAAATGATGGAAAAA-
1 AGAA-AAATAAAA-AG-AAAAAAT--GAAAAATGA--AAAAAAG
*
39123 CGAAAAA-AAAAAGAAAAAATGAAAAATGAAAAAAAG
1 AGAAAAATAAAAAGAAAAAATGAAAAATGAAAAAAAG
39159 AGAAAAATAAAAAGAAAAAATGAAAAA
1 AGAAAAATAAAAAGAAAAAATGAAAAA
39186 ATAAAGAAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
35 5 0.09
36 6 0.10
37 28 0.48
39 7 0.12
40 2 0.03
41 4 0.07
42 3 0.05
43 3 0.05
ACGTcount: A:0.75, C:0.01, G:0.16, T:0.08
Consensus pattern (37 bp):
AGAAAAATAAAAAGAAAAAATGAAAAATGAAAAAAAG
Found at i:39171 original size:30 final size:31
Alignment explanation
Indices: 39144--39201 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 31
39134 AGAAAAAATG
*
39144 AAAAATGAAAAAA-AGAGAAAAATAAAAAGA
1 AAAAATGAAAAAATAAAGAAAAATAAAAAGA
39174 AAAAATGAAAAAATAAAGAAAAATAAAA
1 AAAAATGAAAAAATAAAGAAAAATAAAA
39202 GGGGGGTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 13 0.50
31 13 0.50
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.09
Consensus pattern (31 bp):
AAAAATGAAAAAATAAAGAAAAATAAAAAGA
Found at i:39171 original size:31 final size:32
Alignment explanation
Indices: 39130--39201 Score: 96
Period size: 30 Copynumber: 2.3 Consensus size: 32
39120 AAACGAAAAA
* *
39130 AAAAAGAAAAAATG-AAAAATGAAAAAA-AGAG
1 AAAAATAAAAAA-GAAAAAATGAAAAAATAAAG
39161 AAAAAT-AAAAAGAAAAAATGAAAAAATAAAG
1 AAAAATAAAAAAGAAAAAATGAAAAAATAAAG
39192 AAAAATAAAA
1 AAAAATAAAA
39202 GGGGGGTTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
29 1 0.03
30 18 0.50
31 14 0.39
32 3 0.08
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.08
Consensus pattern (32 bp):
AAAAATAAAAAAGAAAAAATGAAAAAATAAAG
Found at i:40523 original size:37 final size:37
Alignment explanation
Indices: 40473--40545 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
40463 TCGAAACAAG
40473 TCAATCTTAAGCCTTCACGAAAGAGTAGTGAAGCAAT
1 TCAATCTTAAGCCTTCACGAAAGAGTAGTGAAGCAAT
*
40510 TCAATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAA
1 TCAATCTTAAGCCTTCACGAAAGAGTAGTGAAGCAA
40546 ACTAATTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (37 bp):
TCAATCTTAAGCCTTCACGAAAGAGTAGTGAAGCAAT
Found at i:40636 original size:55 final size:55
Alignment explanation
Indices: 40562--41042 Score: 684
Period size: 55 Copynumber: 8.7 Consensus size: 55
40552 TTTATGAAGA
* * * *
40562 TCGAGTTCTATACTCTCTGATAAAATAGAGAGAGGACCCATTTGTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGATAGAATAGGGAGCGGACCCGTTTGTTGAAGATTGT
*
40617 TCGAGTTCTATACTCTCTGATAGAATAGGGAGCAGACCCGTTTGTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGATAGAATAGGGAGCGGACCCGTTTGTTGAAGATTGT
*
40672 TCGAGTTCTATACTCTCTGATAGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGATAGAATAGGGAGCGGACCCGTTTGTTGAAGATTGT
*
40727 TCGAGTTCTATACTCTCTGATAGAATAGGGAGCGAACCCGTTTGTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGATAGAATAGGGAGCGGACCCGTTTGTTGAAGATTGT
*
40782 TCCAGTTCTATACTCTCTGATAGAATAGGGAGCGGACCCGTTTGTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGATAGAATAGGGAGCGGACCCGTTTGTTGAAGATTGT
* * *
40837 TCGAGTTCTATACTCCCTGA-ACGAATAGGGAGCGGACCCATTTATTGAAGATTGT
1 TCGAGTTCTATACTCTCTGATA-GAATAGGGAGCGGACCCGTTTGTTGAAGATTGT
* * *
40892 TCGAGTTCTATACTCTCTGATAGAATAGAGAGCGGACTCGTTTGCTGAAGATTGT
1 TCGAGTTCTATACTCTCTGATAGAATAGGGAGCGGACCCGTTTGTTGAAGATTGT
* * * * * *
40947 TCGAG-TCTTATACTCCCT-AAACGAATAGGGAGCAGACACATTTGCTGAAGATTGT
1 TCGAGTTC-TATACTCTCTGATA-GAATAGGGAGCGGACCCGTTTGTTGAAGATTGT
* *
41002 TCGAG-TCTTATACTCCCTGA-AGGAATATGGAGCGGACCCGT
1 TCGAGTTC-TATACTCTCTGATA-GAATAGGGAGCGGACCCGT
41043 CATCCGAAGC
Statistics
Matches: 389, Mismatches: 32, Indels: 10
0.90 0.07 0.02
Matches are distributed among these distances:
54 5 0.01
55 382 0.98
56 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.31
Consensus pattern (55 bp):
TCGAGTTCTATACTCTCTGATAGAATAGGGAGCGGACCCGTTTGTTGAAGATTGT
Found at i:44249 original size:67 final size:67
Alignment explanation
Indices: 44137--44682 Score: 788
Period size: 67 Copynumber: 8.1 Consensus size: 67
44127 TAAAACCTGA
* **
44137 AGCTGAATTAACTCATGTCACATTGAGCAAGGCCTTTATACGATAGAAAGCAACAACGAAAGGCT
1 AGCTGAATTAGCTCATGTCACACCGAGCAAGGCCTTTATACGATAGAAAGCAACAACGAAAGGCT
*
44202 GG
66 GC
* * * * * *
44204 AGCTGAATTAGCTCATGTTACACCGAGGAAGGCCTTCATAAGATAGAAAACAACAATGAAAGGCT
1 AGCTGAATTAGCTCATGTCACACCGAGCAAGGCCTTTATACGATAGAAAGCAACAACGAAAGGCT
*
44269 GA
66 GC
* * *
44271 AGTTGAATTAGCTCATGTCACACCAAGCAAGGCCTTTATATGATAGAAAGCAACAAC-ATAAGGC
1 AGCTGAATTAGCTCATGTCACACCGAGCAAGGCCTTTATACGATAGAAAGCAACAACGA-AAGGC
44335 TGC
65 TGC
* * *
44338 AGCTGAATTAGCTCATGCCACACTGAGCAAGGCCTTTATACGATAGAAAGCAACAACGAATGGCT
1 AGCTGAATTAGCTCATGTCACACCGAGCAAGGCCTTTATACGATAGAAAGCAACAACGAAAGGCT
*
44403 GG
66 GC
* * * * *
44405 AGTTGAATTAGCTCATGTCACACTGAGCAAGGCCTTTATACAATAGAGAGCAACAACGAGAGGCT
1 AGCTGAATTAGCTCATGTCACACCGAGCAAGGCCTTTATACGATAGAAAGCAACAACGAAAGGCT
44470 GC
66 GC
* *
44472 AGTTGAATTAGCTCATGTCACACCTAGCAAGGCCTTTATACGATAGAAAGCAACAACGAAAGGCT
1 AGCTGAATTAGCTCATGTCACACCGAGCAAGGCCTTTATACGATAGAAAGCAACAACGAAAGGCT
44537 GC
66 GC
*
44539 AGCTGAATTAGCTCATGTCACACCGAACAAGGCCTTTATACGATAGAAAGCAACAACGAAAGGCT
1 AGCTGAATTAGCTCATGTCACACCGAGCAAGGCCTTTATACGATAGAAAGCAACAACGAAAGGCT
44604 GC
66 GC
* * * *
44606 ATCTGAATTAGCTCATGTCACACCGAACAAGGCCTTTATACAATAGAAAGCAACAACTAAAGGCT
1 AGCTGAATTAGCTCATGTCACACCGAGCAAGGCCTTTATACGATAGAAAGCAACAACGAAAGGCT
*
44671 GA
66 GC
*
44673 AGTTGAATTA
1 AGCTGAATTA
44683 ATTTAGGTCA
Statistics
Matches: 430, Mismatches: 47, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
66 1 0.00
67 428 1.00
68 1 0.00
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (67 bp):
AGCTGAATTAGCTCATGTCACACCGAGCAAGGCCTTTATACGATAGAAAGCAACAACGAAAGGCT
GC
Found at i:54927 original size:2 final size:2
Alignment explanation
Indices: 54920--54949 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
54910 CTGAATCTTT
54920 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
54950 AAGAAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:59013 original size:23 final size:23
Alignment explanation
Indices: 58950--59013 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
58940 CATTATTATA
58950 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* * *
58973 CGGCACTCCGATGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
58996 TGGCACTTCGGTGTAATT
1 TGGCACTACGGTGCAATT
59014 ATATGAGCTA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:62082 original size:18 final size:18
Alignment explanation
Indices: 62059--62147 Score: 124
Period size: 18 Copynumber: 4.9 Consensus size: 18
62049 AGGGATTATC
* *
62059 AGTGGTCTTTCGGGATAT
1 AGTGGTCATTCGGGACAT
62077 AGTGGTCATTCGGGACAT
1 AGTGGTCATTCGGGACAT
*
62095 AGTGGTCATTCGGGATAT
1 AGTGGTCATTCGGGACAT
* *
62113 AGTGGTCCTTCAGGACAT
1 AGTGGTCATTCGGGACAT
*
62131 AGTGGTCATACGGGACA
1 AGTGGTCATTCGGGACA
62148 AATTCTATGC
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 62 1.00
ACGTcount: A:0.22, C:0.16, G:0.33, T:0.29
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:62107 original size:36 final size:36
Alignment explanation
Indices: 62059--62145 Score: 138
Period size: 36 Copynumber: 2.4 Consensus size: 36
62049 AGGGATTATC
* *
62059 AGTGGTCTTTCGGGATATAGTGGTCATTCGGGACAT
1 AGTGGTCATTCGGGATATAGTGGTCATTCAGGACAT
*
62095 AGTGGTCATTCGGGATATAGTGGTCCTTCAGGACAT
1 AGTGGTCATTCGGGATATAGTGGTCATTCAGGACAT
*
62131 AGTGGTCATACGGGA
1 AGTGGTCATTCGGGA
62146 CAAATTCTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.22, C:0.15, G:0.33, T:0.30
Consensus pattern (36 bp):
AGTGGTCATTCGGGATATAGTGGTCATTCAGGACAT
Found at i:65278 original size:18 final size:17
Alignment explanation
Indices: 65239--65281 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
65229 AAATGGTAAC
*
65239 AAAATAAATAACATAAG
1 AAAATAAATAAAATAAG
* *
65256 GAAATCAAATAAAATAAT
1 AAAAT-AAATAAAATAAG
65274 AAAATAAA
1 AAAATAAA
65282 CAAACATGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.72, C:0.05, G:0.05, T:0.19
Consensus pattern (17 bp):
AAAATAAATAAAATAAG
Found at i:68287 original size:18 final size:18
Alignment explanation
Indices: 68264--68316 Score: 97
Period size: 18 Copynumber: 2.9 Consensus size: 18
68254 AGGGATTATC
68264 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
68282 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
68300 AGTGGTCCTACGGGACA
1 AGTGGTCCTTCGGGACA
68317 AATTCTACGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.19, C:0.23, G:0.34, T:0.25
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:70301 original size:23 final size:23
Alignment explanation
Indices: 70266--70338 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
70256 ATACTTTACA
*
70266 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
70289 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
70312 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
70335 ATAT
1 ATAT
70339 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:71863 original size:30 final size:31
Alignment explanation
Indices: 71797--71863 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
71787 ACAATGATAG
* * **
71797 AGTGACCATTTTTTTACAAATCGATAACGTT
1 AGTGACCATTTTATTACAAACCGATAAAATT
71828 AGTGACCA-TTTATTACAAACCGATAAAATT
1 AGTGACCATTTTATTACAAACCGATAAAATT
*
71858 GGTGAC
1 AGTGAC
71864 TAATTTGCTA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 23 0.74
31 8 0.26
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (31 bp):
AGTGACCATTTTATTACAAACCGATAAAATT
Found at i:72662 original size:7 final size:7
Alignment explanation
Indices: 72650--72694 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
72640 CGATTAATAA
72650 ATCAACT
1 ATCAACT
72657 ATCAACTT
1 ATCAAC-T
72665 AT-AA--
1 ATCAACT
72669 ATCAACT
1 ATCAACT
72676 ATCAACT
1 ATCAACT
72683 ATCAACTT
1 ATCAAC-T
72691 ATCA
1 ATCA
72695 TATTTCGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
4 2 0.06
5 2 0.06
7 21 0.64
8 8 0.24
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.31
Consensus pattern (7 bp):
ATCAACT
Found at i:72670 original size:19 final size:19
Alignment explanation
Indices: 72646--72682 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
72636 TAATCGATTA
72646 ATAAATCAACTATCAACTT
1 ATAAATCAACTATCAACTT
72665 ATAAATCAACTATCAACT
1 ATAAATCAACTATCAACT
72683 ATCAACTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (19 bp):
ATAAATCAACTATCAACTT
Found at i:73140 original size:21 final size:21
Alignment explanation
Indices: 73114--73160 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
73104 TGGACTAATG
* * *
73114 TTTTTTTAAATGAAATTCATA
1 TTTTTTAAAAAGAAATTCAAA
*
73135 TTTTTTAAAAAGAAGTTCAAA
1 TTTTTTAAAAAGAAATTCAAA
73156 TTTTT
1 TTTTT
73161 ACTATTTTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.51
Consensus pattern (21 bp):
TTTTTTAAAAAGAAATTCAAA
Found at i:78057 original size:2 final size:2
Alignment explanation
Indices: 78050--78099 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
78040 CATACCAACC
78050 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
78092 AT AT AT AT
1 AT AT AT AT
78100 GAGAAAATAA
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):
AT
Found at i:78183 original size:43 final size:43
Alignment explanation
Indices: 78136--78221 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
78126 TGCCTTATAA
*
78136 TATACTATTTTAATCAACTTGTTAAAATGACCAACAAAATCGC
1 TATACGATTTTAATCAACTTGTTAAAATGACCAACAAAATCGC
78179 TATACGATTTTAATCAACTTGTTAAAATGACCAACAAAATCGC
1 TATACGATTTTAATCAACTTGTTAAAATGACCAACAAAATCGC
78222 AACGCGACCT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (43 bp):
TATACGATTTTAATCAACTTGTTAAAATGACCAACAAAATCGC
Found at i:78656 original size:19 final size:19
Alignment explanation
Indices: 78632--78668 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
78622 TTATTTTGGA
78632 TTTTTCACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
78651 TTTTTCACTATCGCAACA
1 TTTTTCACTATCGCAACA
78669 ACACGTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.30, G:0.05, T:0.38
Consensus pattern (19 bp):
TTTTTCACTATCGCAACAC
Found at i:78715 original size:18 final size:19
Alignment explanation
Indices: 78682--78718 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
78672 CGTTTTTTCA
*
78682 AACTCTCGCAAACACATTT
1 AACTATCGCAAACACATTT
78701 AACTATCGC-AACACATTT
1 AACTATCGCAAACACATTT
78719 TTCAAAATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.38, C:0.30, G:0.05, T:0.27
Consensus pattern (19 bp):
AACTATCGCAAACACATTT
Done.