Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003572.1 Hibiscus syriacus cultivar Beakdansim tig00007541_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: 62458
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:1339 original size:23 final size:21
Alignment explanation
Indices: 1278--1351 Score: 87
Period size: 23 Copynumber: 3.5 Consensus size: 21
1268 CGATACCTAG
* *
1278 GTATCGATACCCCTTG-TTAT
1 GTATCGATACACCTTGAATAT
*
1298 GTATCGATACACCTTGAATGT
1 GTATCGATACACCTTGAATAT
*
1319 GTACCGATACATTCCTTGAATAT
1 GTATCGATACA--CCTTGAATAT
1342 GTATCGATAC
1 GTATCGATAC
1352 CCCTCACGGT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
20 15 0.33
21 12 0.27
23 18 0.40
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (21 bp):
GTATCGATACACCTTGAATAT
Found at i:3590 original size:13 final size:13
Alignment explanation
Indices: 3559--3592 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
3549 GGAGTATTTT
*
3559 TTTTCAAAATTGA
1 TTTTCAAAACTGA
3572 -TTTCAAAACTGA
1 TTTTCAAAACTGA
3584 TTTTCAAAA
1 TTTTCAAAA
3593 AGAAAATCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (13 bp):
TTTTCAAAACTGA
Found at i:3732 original size:17 final size:18
Alignment explanation
Indices: 3699--3735 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
3689 TTTAAGATTT
3699 TATATTCGATTCAAAATTA
1 TATATTCGATT-AAAATTA
3718 TATATTCGATT-AAATTA
1 TATATTCGATTAAAATTA
3735 T
1 T
3736 TCGAATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
19 11 0.61
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (18 bp):
TATATTCGATTAAAATTA
Found at i:7586 original size:20 final size:20
Alignment explanation
Indices: 7558--7612 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
7548 CAACTCAAAG
*
7558 TCAATTCGAGTCGAGCTTTT
1 TCAAATCGAGTCGAGCTTTT
*
7578 TCAAATCGAATCGAGCTTTT
1 TCAAATCGAGTCGAGCTTTT
*
7598 TCGAATCGAGTCGAG
1 TCAAATCGAGTCGAG
7613 TCGAAAAGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (20 bp):
TCAAATCGAGTCGAGCTTTT
Found at i:10320 original size:258 final size:258
Alignment explanation
Indices: 9857--10592 Score: 964
Period size: 258 Copynumber: 2.8 Consensus size: 258
9847 CAACACTATT
* * * * ** *
9857 CATAAGACCTACGGGTAGGATG-TTTCACATGATTTTCAAAAGATAAGAAAGTGATTTCTAAAGT
1 CATAAGAACTTCGGGCAGGATGTTTTCACATGATTTTCAAAAGATGAGAAAACGATTTC-CAAGT
* * * ** *
9921 TTCTCATTTAAATCTTGTGTGAAAATTGAAATTTTTGAAAAAAAGAGAAACCAATTTCCAAAGTT
65 TTCTCATTTAAATCTTTTCTGAAAATTGAAATTTTGGAAAGTAAGA-AAA-CGATTTCCAAAGTT
* * * *
9986 TCTTATCTAGTAAACTATTTCCAAAATTGGTAAGTCATTTGAGCCATCAGTAAGTCTTTCGAGCA
128 TATTACCTAGTAAACTATTTCCAAAATTGGTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCA
**
10051 TGAGGATTAAATCATTCGGGTCATCTATAAGCCTTTCGAGCAAGATGATAAGCCCTTAGGGCCAT
193 TGATAATTAAATCATTCGGGTCATCTATAAGCCTTTCGAGCAAGATGATAAGCCCTTAGGGCCAT
10116 C
258 C
* * * *
10117 CATAAGAACTTCGGGCGGGATGTTTTCACATGATTTTCAAATGATGAGAAAACGATTACCAATTT
1 CATAAGAACTTCGGGCAGGATGTTTTCACATGATTTTCAAAAGATGAGAAAACGATTTCCAAGTT
*
10182 TCTCATTTAAATCTTTTTTG-AAATTGAAATATTTGGAAAGTAAGAAAACGATTTCCAAAGTTTA
66 TCTCATTTAAATCTTTTCTGAAAATTGAAAT-TTTGGAAAGTAAGAAAACGATTTCCAAAGTTTA
* *
10246 TTACCTAGTAAACTATTTCTAAAATTGGTAAGTCATTCGGGCCATCAATAAGTCTTTCGAGCATG
130 TTACCTAGTAAACTATTTCCAAAATTGGTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATG
* ** * * * * *
10311 ATAATTAAATCTTTCGCTTAATCTATAAGCCTTTCGAGCAAGATGATAAGTCTTTCGGGTCATC
195 ATAATTAAATCATTCGGGTCATCTATAAGCCTTTCGAGCAAGATGATAAGCCCTTAGGGCCATC
* *
10375 CATAAGACCTTCGGGCATGATGTTTTCACATGATTTTCAAAAGATGAGAAAACGATTTCCAAAGT
1 CATAAGAACTTCGGGCAGGATGTTTTCACATGATTTTCAAAAGATGAGAAAACGATTTCC-AAGT
* * *
10440 TTCTCATTTAAATCTTTTCTGAAAATTGAATTTTTTGAAAAAGTAAG-AAACGATTTCCAAAATT
65 TTCTCATTTAAATCTTTTCTGAAAATTGAA-ATTTTG-GAAAGTAAGAAAACGATTTCCAAAGTT
* * *
10504 TATTACCTAGTAAACTATTTCCAAGA-TGATTAAGTCATTCAGGCCAT--GTAAGTCTTTCGAGC
128 TATTACCTAGTAAACTATTTCCAAAATTG-GTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGC
10566 ATGATGAA-TAAATCATTCGGGTCATCT
192 ATGAT-AATTAAATCATTCGGGTCATCT
10593 GGTAGTATCA
Statistics
Matches: 416, Mismatches: 52, Indels: 18
0.86 0.11 0.04
Matches are distributed among these distances:
258 217 0.52
259 40 0.10
260 119 0.29
261 40 0.10
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (258 bp):
CATAAGAACTTCGGGCAGGATGTTTTCACATGATTTTCAAAAGATGAGAAAACGATTTCCAAGTT
TCTCATTTAAATCTTTTCTGAAAATTGAAATTTTGGAAAGTAAGAAAACGATTTCCAAAGTTTAT
TACCTAGTAAACTATTTCCAAAATTGGTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGA
TAATTAAATCATTCGGGTCATCTATAAGCCTTTCGAGCAAGATGATAAGCCCTTAGGGCCATC
Found at i:10759 original size:6 final size:6
Alignment explanation
Indices: 10737--10806 Score: 62
Period size: 5 Copynumber: 12.5 Consensus size: 6
10727 TTAATTTAAC
* *
10737 TATTAT TATTAT TATTAT CATTAAT TATTTT TATT-T TATT-T TATT-T
1 TATTAT TATTAT TATTAT TATT-AT TATTAT TATTAT TATTAT TATTAT
*
10783 TATT-T TATT-T TATT-T TATTTT TAT
1 TATTAT TATTAT TATTAT TATTAT TAT
10807 CTTATTTTGC
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
5 30 0.51
6 24 0.41
7 5 0.08
ACGTcount: A:0.26, C:0.01, G:0.00, T:0.73
Consensus pattern (6 bp):
TATTAT
Found at i:10775 original size:5 final size:5
Alignment explanation
Indices: 10765--10814 Score: 82
Period size: 5 Copynumber: 9.8 Consensus size: 5
10755 CATTAATTAT
*
10765 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTTA TCTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA TTTT
10815 GCAGGTTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
5 37 0.88
6 5 0.12
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:21486 original size:20 final size:22
Alignment explanation
Indices: 21441--21498 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
21431 GCATGGGTAG
21441 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
21465 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
21485 TGTATCGATGCACT
1 TGCATCGATGCACT
21499 TCAAGGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:22505 original size:20 final size:20
Alignment explanation
Indices: 22477--22517 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
22467 TGTATATGTT
* *
22477 ATAAGATATATGATATGAAC
1 ATAAGATATATCATATAAAC
*
22497 ATAATATATATCATATAAAC
1 ATAAGATATATCATATAAAC
22517 A
1 A
22518 AGAGAATAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.07, G:0.07, T:0.32
Consensus pattern (20 bp):
ATAAGATATATCATATAAAC
Found at i:25885 original size:12 final size:12
Alignment explanation
Indices: 25868--25897 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
25858 TTGGTGTATC
25868 GATGCATGGGTA
1 GATGCATGGGTA
25880 GATGCATGGGTA
1 GATGCATGGGTA
25892 G-TGCAT
1 GATGCAT
25898 CGATGCACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.28
12 13 0.72
ACGTcount: A:0.23, C:0.10, G:0.40, T:0.27
Consensus pattern (12 bp):
GATGCATGGGTA
Found at i:25938 original size:20 final size:22
Alignment explanation
Indices: 25893--25950 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
25883 GCATGGGTAG
25893 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
25917 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
25937 TGTATCGATGCACT
1 TGCATCGATGCACT
25951 TCAAGGGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:26790 original size:8 final size:8
Alignment explanation
Indices: 26777--26816 Score: 53
Period size: 8 Copynumber: 4.8 Consensus size: 8
26767 TACAAACAAT
26777 TTTAAATA
1 TTTAAATA
26785 TTTAAATA
1 TTTAAATA
26793 TTTTAAATAA
1 -TTTAAAT-A
*
26803 TTAAAATA
1 TTTAAATA
26811 TTTAAA
1 TTTAAA
26817 GGTTAAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 14 0.50
9 13 0.46
10 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
TTTAAATA
Found at i:26797 original size:9 final size:9
Alignment explanation
Indices: 26775--26813 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
26765 TGTACAAACA
26775 ATTTTAAAT
1 ATTTTAAAT
26784 A-TTTAAAT
1 ATTTTAAAT
26792 ATTTTAAAT
1 ATTTTAAAT
* *
26801 AATTAAAAT
1 ATTTTAAAT
26810 ATTT
1 ATTT
26814 AAAGGTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
8 8 0.31
9 18 0.69
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
ATTTTAAAT
Found at i:26797 original size:17 final size:18
Alignment explanation
Indices: 26775--26813 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
26765 TGTACAAACA
*
26775 ATTTTAAAT-ATTTAAAT
1 ATTTTAAATAATTAAAAT
26792 ATTTTAAATAATTAAAAT
1 ATTTTAAATAATTAAAAT
26810 ATTT
1 ATTT
26814 AAAGGTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTTAAATAATTAAAAT
Found at i:36350 original size:18 final size:18
Alignment explanation
Indices: 36329--36375 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
36319 ATATTATATC
36329 TTAACTTAAATTCACATA
1 TTAACTTAAATTCACATA
* *
36347 TTAAGTTAAATTCACATC
1 TTAACTTAAATTCACATA
36365 TTAACATTAAA
1 TTAAC-TTAAA
36376 CAATATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 20 0.80
19 5 0.20
ACGTcount: A:0.45, C:0.15, G:0.02, T:0.38
Consensus pattern (18 bp):
TTAACTTAAATTCACATA
Found at i:36646 original size:56 final size:55
Alignment explanation
Indices: 36581--36690 Score: 132
Period size: 56 Copynumber: 2.0 Consensus size: 55
36571 TTATTAAATA
* * *
36581 TTAATATATATATTATATTCCTACCTTAAATT-ATTAATATTTATTTTTATTTTAAC
1 TTAAAATATATATTATATTCCTACCTTAAATTAAAT-ATATTTA-TTATATTTTAAC
* * * *
36637 TTAAAATATATATTTTATTCTTATCTTAATTTAAATATATTTATTATATTTTAA
1 TTAAAATATATATTATATTCCTACCTTAAATTAAATATATTTATTATATTTTAA
36691 TTTTAATTTA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
55 10 0.22
56 34 0.74
57 2 0.04
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.56
Consensus pattern (55 bp):
TTAAAATATATATTATATTCCTACCTTAAATTAAATATATTTATTATATTTTAAC
Found at i:36650 original size:25 final size:25
Alignment explanation
Indices: 36616--36665 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
36606 TTAAATTATT
*
36616 AATATTTATTTTTATT-TTAACTTAA
1 AATATATA-TTTTATTCTTAACTTAA
*
36641 AATATATATTTTATTCTTATCTTAA
1 AATATATATTTTATTCTTAACTTAA
36666 TTTAAATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (25 bp):
AATATATATTTTATTCTTAACTTAA
Found at i:36690 original size:25 final size:26
Alignment explanation
Indices: 36617--36693 Score: 75
Period size: 30 Copynumber: 2.8 Consensus size: 26
36607 TAAATTATTA
*
36617 ATATTTATTTTTATTTTAACTTAAAATAT
1 ATATTTA-TTTTATTTTAA-TT-TAATAT
*
36646 ATATTTTATTCTTATCTTAATTTAA-AT
1 ATA-TTTATT-TTATTTTAATTTAATAT
*
36673 ATATTTATTATATTTTAATTT
1 ATATTTATTTTATTTTAATTT
36694 TAATTTAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
25 10 0.24
26 6 0.14
27 5 0.12
28 2 0.05
29 7 0.17
30 12 0.29
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (26 bp):
ATATTTATTTTATTTTAATTTAATAT
Found at i:36700 original size:31 final size:30
Alignment explanation
Indices: 36620--36799 Score: 168
Period size: 31 Copynumber: 5.9 Consensus size: 30
36610 ATTATTAATA
* *
36620 TTTATTTTTATTTTAACTTAAAATATATAT
1 TTTATTCTTATTTTAATTTAAAATATATAT
* *
36650 TTTATTCTTATCTTAATTTAAATATATTTAT
1 TTTATTCTTATTTTAATTTAAA-ATATATAT
* *
36681 TATATT-TTAATTTTAATTTAAAAATGTATAT
1 TTTATTCTT-ATTTTAATTT-AAAATATATAT
*
36712 TTTATTCTTATTTTAATTTAAGAA-ATAAAT
1 TTTATTCTTATTTTAATTTAA-AATATATAT
* * * *
36742 TTTATTTTTATCTTAACTATAAAAAATATAT
1 TTTATTCTTATTTTAA-TTTAAAATATATAT
*
36773 TTTATT-TTCATCTTAATTTTAAAATAT
1 TTTATTCTT-ATTTTAA-TTTAAAATAT
36800 TATAAGAATA
Statistics
Matches: 124, Mismatches: 18, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
30 45 0.36
31 74 0.60
32 5 0.04
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (30 bp):
TTTATTCTTATTTTAATTTAAAATATATAT
Found at i:36728 original size:62 final size:60
Alignment explanation
Indices: 36618--36800 Score: 201
Period size: 61 Copynumber: 3.0 Consensus size: 60
36608 AAATTATTAA
*
36618 TATTTATTTTTATTTTAACTTAAAATATATATTTTATTCTTATCTTAATTTAAATATATT
1 TATTTATTTTAATTTTAACTTAAAATATATATTTTATTCTTATCTTAATTTAAATATATT
* * * * **
36678 TATTATATTTTAATTTTAATTTAAAAATGTATATTTTATTCTTATTTTAATTTAAGAAATAAA
1 TATT-TATTTTAATTTTAACTT-AAAATATATATTTTATTCTTATCTTAATTTAA-ATATATT
* * *
36741 T-TTTATTTTTATCTTAACTATAAAAAATATATTTTATT-TTCATCTTAATTTTAAA-ATATT
1 TATTTATTTTAATTTTAACT-TAAAATATATATTTTATTCTT-ATCTTAA-TTTAAATATATT
36801 ATAAGAATAA
Statistics
Matches: 102, Mismatches: 15, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
60 9 0.09
61 50 0.49
62 38 0.37
63 5 0.05
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (60 bp):
TATTTATTTTAATTTTAACTTAAAATATATATTTTATTCTTATCTTAATTTAAATATATT
Found at i:36744 original size:92 final size:92
Alignment explanation
Indices: 36620--36797 Score: 225
Period size: 92 Copynumber: 1.9 Consensus size: 92
36610 ATTATTAATA
* * * * *
36620 TTTATTTTTATTTTAACTTAAAATATATATTTTATTCTTATCTTAA-TTTAAATATATTTATTAT
1 TTTATTCTTATTTTAACTTAAAATATAAATTTTATTCTTATCTTAACTATAAA-AAATATATTAT
*
36684 ATTTTAATTTTAATTTAAAAATGTATAT
65 ATTTTAATCTTAATTTAAAAATGTATAT
* * *
36712 TTTATTCTTATTTTAATTTAAGAA-ATAAATTTTATTTTTATCTTAACTATAAAAAATATATTTT
1 TTTATTCTTATTTTAACTTAA-AATATAAATTTTATTCTTATCTTAACTATAAAAAATATATTAT
* *
36776 ATTTTCATCTTAATTTTAAAAT
65 ATTTTAATCTTAATTTAAAAAT
36798 ATTATAAGAA
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
92 66 0.90
93 7 0.10
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (92 bp):
TTTATTCTTATTTTAACTTAAAATATAAATTTTATTCTTATCTTAACTATAAAAAATATATTATA
TTTTAATCTTAATTTAAAAATGTATAT
Found at i:42790 original size:60 final size:60
Alignment explanation
Indices: 42689--42869 Score: 274
Period size: 60 Copynumber: 3.0 Consensus size: 60
42679 TTATCTAAAT
*
42689 ACTATGAATCTCATTCTAAATTGGTCCTTCAACTTTTGAACATTCCAATTTCATCCCCAA
1 ACTATGACTCTCATTCTAAATTGGTCCTTCAACTTTTGAACATTCCAATTTCATCCCCAA
* *
42749 ACTGTGACTCTCATTTTAAATTGGTCCTTCAACTTTTGAACATTCCAATTTCATCCCCAA
1 ACTATGACTCTCATTCTAAATTGGTCCTTCAACTTTTGAACATTCCAATTTCATCCCCAA
* * * **
42809 ACTATGACTCTCATTCTAAATTTGTCC-CCAAACTTTTTATTATTCCAATTTCATCCCCAA
1 ACTATGACTCTCATTCTAAATTGGTCCTTC-AACTTTTGAACATTCCAATTTCATCCCCAA
42869 A
1 A
42870 TTCATCCAAA
Statistics
Matches: 110, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
59 1 0.01
60 109 0.99
ACGTcount: A:0.29, C:0.27, G:0.06, T:0.38
Consensus pattern (60 bp):
ACTATGACTCTCATTCTAAATTGGTCCTTCAACTTTTGAACATTCCAATTTCATCCCCAA
Found at i:42824 original size:31 final size:30
Alignment explanation
Indices: 42789--42869 Score: 78
Period size: 31 Copynumber: 2.7 Consensus size: 30
42779 AACTTTTGAA
42789 CATTCCAATTTCATCCCCAAAC-TATGACTCT
1 CATTCCAATTTCATCCCCAAACTTATGA-T-T
* * * *
42820 CATTCTAAATTT-GTCCCCAAACTTTTTATT
1 CATTC-CAATTTCATCCCCAAACTTATGATT
42850 -ATTCCAATTTCATCCCCAAA
1 CATTCCAATTTCATCCCCAAA
42870 TTCATCCAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
28 5 0.12
29 12 0.29
30 1 0.02
31 15 0.37
32 8 0.20
ACGTcount: A:0.30, C:0.31, G:0.02, T:0.37
Consensus pattern (30 bp):
CATTCCAATTTCATCCCCAAACTTATGATT
Found at i:52479 original size:21 final size:20
Alignment explanation
Indices: 52408--52481 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 20
52398 TAACGCGAAC
* *
52408 TCCAATTTCGCAACACAGTT
1 TCCAAATTCGCAACACATTT
*
52428 TCCAAATTCGCAACTCAATTT
1 TCCAAATTCGCAACAC-ATTT
* *
52449 CTGC-AA-TCGCAACGCGATTT
1 -TCCAAATTCGCAACAC-ATTT
52469 TCCAAATTCGCAA
1 TCCAAATTCGCAA
52482 TATAGAATTC
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
19 2 0.05
20 28 0.65
21 11 0.26
22 2 0.05
ACGTcount: A:0.31, C:0.30, G:0.11, T:0.28
Consensus pattern (20 bp):
TCCAAATTCGCAACACATTT
Found at i:52516 original size:20 final size:20
Alignment explanation
Indices: 52426--52532 Score: 65
Period size: 20 Copynumber: 5.2 Consensus size: 20
52416 CGCAACACAG
* *
52426 TTTCCAAATTCGCAACTCAA
1 TTTCTAAATTCGCAACTCGA
* *
52446 TTTCTGCAA-TCGCAACGCGA
1 TTTCT-AAATTCGCAACTCGA
* * *
52466 TTTTCCAAATTCGCAATATAGA
1 -TTTCTAAATTCGCAA-CTCGA
*
52488 ATTC-AAATTCGCAACTCGA
1 TTTCTAAATTCGCAACTCGA
* * *
52507 TTTCTGAATTCTCAACGCGAA
1 TTTCTAAATTCGCAACTCG-A
52528 TTTCT
1 TTTCT
52533 TTTCGCAACA
Statistics
Matches: 65, Mismatches: 16, Indels: 11
0.71 0.17 0.12
Matches are distributed among these distances:
19 6 0.09
20 36 0.55
21 21 0.32
22 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (20 bp):
TTTCTAAATTCGCAACTCGA
Found at i:52599 original size:20 final size:20
Alignment explanation
Indices: 52576--52641 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 20
52566 TTTTCTAAAC
*
52576 CGCAACACGAATTTTGTTTT
1 CGCAACACGAATTTTGATTT
* * *
52596 CGCAACTCG-ATTTCGAATT
1 CGCAACACGAATTTTGATTT
* *
52615 CGCAACACAAATTTTAATTT
1 CGCAACACGAATTTTGATTT
52635 CGCAACA
1 CGCAACA
52642 GCTTTTATTT
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
19 14 0.39
20 22 0.61
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (20 bp):
CGCAACACGAATTTTGATTT
Found at i:52608 original size:40 final size:39
Alignment explanation
Indices: 52536--52641 Score: 104
Period size: 39 Copynumber: 2.7 Consensus size: 39
52526 AATTTCTTTT
* ** *
52536 CGCAACACAAGTTTCCTTTTCGCAACAAGATTTTCTAAAC
1 CGCAACACAAATTTTATTTTCGCAACAAGA-TTTCGAAAC
* * ** **
52576 CGCAACACGAATTTTGTTTTCGCAACTCGATTTCGAATT
1 CGCAACACAAATTTTATTTTCGCAACAAGATTTCGAAAC
*
52615 CGCAACACAAATTTTAATTTCGCAACA
1 CGCAACACAAATTTTATTTTCGCAACA
52642 GCTTTTATTT
Statistics
Matches: 53, Mismatches: 13, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
39 29 0.55
40 24 0.45
ACGTcount: A:0.32, C:0.25, G:0.11, T:0.31
Consensus pattern (39 bp):
CGCAACACAAATTTTATTTTCGCAACAAGATTTCGAAAC
Found at i:56995 original size:22 final size:21
Alignment explanation
Indices: 56948--56995 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
56938 ACAGAATGTC
* *
56948 AAGGGGGAACTGATACCCCCA
1 AAGGAGGAACCGATACCCCCA
* *
56969 CAGGAGGAACCGATTCCCCCTA
1 AAGGAGGAACCGATACCCCC-A
56991 AAGGA
1 AAGGA
56996 AATTGTGAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.33, C:0.29, G:0.27, T:0.10
Consensus pattern (21 bp):
AAGGAGGAACCGATACCCCCA
Found at i:58812 original size:102 final size:103
Alignment explanation
Indices: 58571--58881 Score: 533
Period size: 102 Copynumber: 3.1 Consensus size: 103
58561 GGGTCTACGC
58571 GGTCCTTCGGGACATATATGTATTCTTTGG-A-ATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
58634 CCTTGGCATA--TATATGATTCTTAAGGAATGATATGT
66 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
*
58670 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTTTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
*
58735 CCTTGGCATATGTATATGATTCTTAAAGAATGATAT-T
66 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
58772 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* * *
58837 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
66 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
*
58875 AGTCCTT
1 GGTCCTT
58882 ATGGACTTAT
Statistics
Matches: 199, Mismatches: 8, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
99 30 0.15
100 1 0.01
101 41 0.21
102 97 0.49
103 30 0.15
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.37
Consensus pattern (103 bp):
GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
Found at i:58930 original size:23 final size:23
Alignment explanation
Indices: 58897--58948 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
58887 CTTATTATAT
58897 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
58920 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
58943 GGCACT
1 GGCACT
58949 TCAGTACAAT
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:0.19, C:0.31, G:0.27, T:0.23
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:58958 original size:23 final size:23
Alignment explanation
Indices: 58909--58964 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
58899 CACTACGGTG
* *
58909 CAATTCTACGCGGCACTCCGGTG
1 CAATTCTACGCGGCACTCCAGTA
* *
58932 CAATTCTACGTGGCACTTCAGTA
1 CAATTCTACGCGGCACTCCAGTA
*
58955 CAATTATACG
1 CAATTCTACG
58965 AGTTGTGGTG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.27
Consensus pattern (23 bp):
CAATTCTACGCGGCACTCCAGTA
Done.