Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006359.1 Hibiscus syriacus cultivar Beakdansim tig00015244_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: 39438
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:431 original size:3 final size:3
Alignment explanation
Indices: 423--513 Score: 98
Period size: 3 Copynumber: 30.0 Consensus size: 3
413 GCATGAAATG
*
423 TAA TAA TAA TATT TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
468 TAA TAA -AA GTAAA TAAA TAA TAA TAA TAA TTT TAA T-A TAA TAA TAA
1 TAA TAA TAA -T-AA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
514 CAAATGAATA
Statistics
Matches: 76, Mismatches: 6, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
2 6 0.08
3 61 0.80
4 7 0.09
5 2 0.03
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:468 original size:23 final size:23
Alignment explanation
Indices: 423--513 Score: 102
Period size: 23 Copynumber: 4.1 Consensus size: 23
413 GCATGAAATG
* *
423 TAATAATAATATTTA-ATAATAA
1 TAATAATAATAATAATATAATAA
445 TAATAATAATAATAATATAATAA
1 TAATAATAATAATAATATAATAA
468 TAATAA-AAGT-A-AATA-AATAA
1 TAATAATAA-TAATAATATAATAA
**
488 TAATAATAATTTTAATATAATAA
1 TAATAATAATAATAATATAATAA
511 TAA
1 TAA
514 CAAATGAATA
Statistics
Matches: 60, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
20 12 0.20
21 6 0.10
22 20 0.33
23 22 0.37
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (23 bp):
TAATAATAATAATAATATAATAA
Found at i:524 original size:37 final size:37
Alignment explanation
Indices: 446--524 Score: 99
Period size: 37 Copynumber: 2.1 Consensus size: 37
436 TAATAATAAT
*
446 AATAATAATAATAATATAATAATAATAAAAGTAAATA
1 AATAATAATAATAATATAATAATAATAAAAGCAAATA
* *
483 AATAATAATAATAATTTTAAT-ATAATAATAA-CAAATG
1 AATAATAATAATAA-TATAATAATAATAA-AAGCAAATA
520 AATAA
1 AATAA
525 AAAAATTAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
37 30 0.81
38 7 0.19
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.32
Consensus pattern (37 bp):
AATAATAATAATAATATAATAATAATAAAAGCAAATA
Found at i:535 original size:43 final size:43
Alignment explanation
Indices: 440--535 Score: 120
Period size: 43 Copynumber: 2.2 Consensus size: 43
430 AATATTTAAT
* *
440 AATAATAATAATAATAATAATATAATAATAATAAAAGTAAATA
1 AATAATAATAATAATAATAATATAATAATAACAAAAATAAATA
** *
483 AATAATAATAATAATTTTAATATAATAATAACAAATGAATAAAAA
1 AATAATAATAATAATAATAATATAATAATAACAAA--AATAAATA
528 AATTAATA
1 AA-TAATA
536 TTCAGCTGCC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
43 32 0.71
45 8 0.18
46 5 0.11
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.31
Consensus pattern (43 bp):
AATAATAATAATAATAATAATATAATAATAACAAAAATAAATA
Found at i:808 original size:16 final size:16
Alignment explanation
Indices: 755--811 Score: 69
Period size: 16 Copynumber: 3.4 Consensus size: 16
745 TTGAACAAGC
755 TCTTCTCATTATGAAT
1 TCTTCTCATTATGAAT
* *
771 TGCTTCTCCTTATATGAGT
1 T-CTTCT-CAT-TATGAAT
790 TCTTCTCATTATGAAT
1 TCTTCTCATTATGAAT
806 TCTTCT
1 TCTTCT
812 GGAAATATTG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
16 13 0.38
17 7 0.21
18 7 0.21
19 7 0.21
ACGTcount: A:0.19, C:0.21, G:0.09, T:0.51
Consensus pattern (16 bp):
TCTTCTCATTATGAAT
Found at i:1099 original size:121 final size:119
Alignment explanation
Indices: 873--1182 Score: 446
Period size: 121 Copynumber: 2.6 Consensus size: 119
863 GAATTAAGGC
*
873 AAGGTTGAA-AATTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTACTCATTATG
1 AAGGTTGAACAATTCTTCT-ATTATGAACTTCTT-TCCTTCTTCAGATGAGTTCTTCTCATTATG
* * *
937 AACATTTCTAGAAATGTTGATGCTGATCTATCTCTTTATGTGATAGAGTCATACAA
64 AACTTTTCTAGAAAAGTTGATGCTGATCTATCTCCTTATGTGATAGAGTCATACAA
* *
993 AAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTTCCTT-TTCAGATAAGTTCTTCTAATTATG
1 AAGGTTGAACAA-TTCTTC-TATTATGAACTTCTTTCCTTCTTCAGATGAGTTCTTCTCATTATG
* *
1057 AACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTATGTGATAGAGTCATGCAA
64 AACTTT-TCTAGAAAAGTTGATGCTGATCTATCTCCTTATGTGATAGAGTCATACAA
*
1114 AAGGTTGAACAAATTCTTC-ATTATTAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAAC-AATTCTTCTATTATGAACTTC-T-TTCCTTCTTCAGATGAGTTCTTCTCATTAT
1178 GAACT
63 GAACT
1183 CTACCTGGCA
Statistics
Matches: 171, Mismatches: 11, Indels: 14
0.87 0.06 0.07
Matches are distributed among these distances:
119 11 0.06
120 36 0.21
121 75 0.44
122 48 0.28
123 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (119 bp):
AAGGTTGAACAATTCTTCTATTATGAACTTCTTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
CTTTTCTAGAAAAGTTGATGCTGATCTATCTCCTTATGTGATAGAGTCATACAA
Found at i:1938 original size:49 final size:52
Alignment explanation
Indices: 1884--1982 Score: 141
Period size: 49 Copynumber: 1.9 Consensus size: 52
1874 TTACTGGTTT
* *
1884 GTAAAACATTTGAC-ATACATTCAT-TTCCTGTGA-TTCTGCATAGATGTCC
1 GTAAAACATTTGACAACACATTCATCTTCCTGTGATTTCTGCACAGATGTCC
*
1933 GTAAAATATTTGACAACACATTCATCCTTCCTGTGATTTCTGCACAGATG
1 GTAAAACATTTGACAACACATTCAT-CTTCCTGTGATTTCTGCACAGATG
1983 CCTCATTAGT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
49 13 0.30
50 9 0.21
52 9 0.21
53 12 0.28
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.35
Consensus pattern (52 bp):
GTAAAACATTTGACAACACATTCATCTTCCTGTGATTTCTGCACAGATGTCC
Found at i:2484 original size:20 final size:19
Alignment explanation
Indices: 2441--2488 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 19
2431 ATGTTTATAT
2441 AAAATAATAAATTGAATTCG
1 AAAA-AATAAATTGAATTCG
*
2461 --AAAATAAATTGAATTTTG
1 AAAAAATAAATTGAA-TTCG
2479 AAAAAATAAA
1 AAAAAATAAA
2489 CTTGTAATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
17 11 0.46
18 5 0.21
20 8 0.33
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.29
Consensus pattern (19 bp):
AAAAAATAAATTGAATTCG
Found at i:2855 original size:10 final size:9
Alignment explanation
Indices: 2829--2886 Score: 73
Period size: 9 Copynumber: 6.3 Consensus size: 9
2819 CTGACCCTCC
2829 TTTTATTTT
1 TTTTATTTT
*
2838 CCTTT-TTTT
1 -TTTTATTTT
*
2847 TTTAATTTT
1 TTTTATTTT
2856 TTTTATTTT
1 TTTTATTTT
2865 TTTTATTTT
1 TTTTATTTT
2874 TTTTCATTTT
1 TTTT-ATTTT
2884 TTT
1 TTT
2887 CTTCTTCAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
8 2 0.05
9 29 0.69
10 11 0.26
ACGTcount: A:0.10, C:0.05, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTATTTT
Found at i:2864 original size:19 final size:19
Alignment explanation
Indices: 2842--2886 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
2832 TATTTTCCTT
2842 TTTTTTTTAATTTTTTTT-A
1 TTTTTTTT-ATTTTTTTTCA
2861 TTTTTTTTATTTTTTTTCA
1 TTTTTTTTATTTTTTTTCA
2880 TTTTTTT
1 TTTTTTT
2887 CTTCTTCAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.11, C:0.02, G:0.00, T:0.87
Consensus pattern (19 bp):
TTTTTTTTATTTTTTTTCA
Found at i:13066 original size:46 final size:46
Alignment explanation
Indices: 13008--13228 Score: 354
Period size: 46 Copynumber: 4.8 Consensus size: 46
12998 AATAAATGCT
13008 TGCGAACTAGATATCATGCGGTTAGGTTTATTTTTTCGAACAAGCA
1 TGCGAACTAGATATCATGCGGTTAGGTTTATTTTTTCGAACAAGCA
* *
13054 TGCAAACTAGATATCATACGGTTAGGTTTATTTTTTCGAACAAGCA
1 TGCGAACTAGATATCATGCGGTTAGGTTTATTTTTTCGAACAAGCA
13100 TGCGAACTAGATATCATGCGGTTAGGTTTATTTTTTCGAACAAGCA
1 TGCGAACTAGATATCATGCGGTTAGGTTTATTTTTTCGAACAAGCA
* * *
13146 TGCGAACTAGATATCATGCGGTTAGGTTTA-TTTTTAGAATAAATGCT
1 TGCGAACTAGATATCATGCGGTTAGGTTTATTTTTTCGAA-CAA-GCA
*
13193 TGCGAACTAGATATCATGCGGTTAGGATTTCTTTTT
1 TGCGAACTAGATATCATGCGGTTAGG-TTTATTTTT
13229 GTGAATAACA
Statistics
Matches: 163, Mismatches: 8, Indels: 5
0.93 0.05 0.03
Matches are distributed among these distances:
45 8 0.05
46 120 0.74
47 28 0.17
48 3 0.02
49 4 0.02
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.37
Consensus pattern (46 bp):
TGCGAACTAGATATCATGCGGTTAGGTTTATTTTTTCGAACAAGCA
Found at i:14902 original size:25 final size:23
Alignment explanation
Indices: 14871--14916 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
14861 AAGGGATTGG
14871 AGATTGAAATTCAAAAGAGTAGACC
1 AGATTG-AATTCAAAA-AGTAGACC
*
14896 AGATTGAATTGAAAAAGTAGA
1 AGATTGAATTCAAAAAGTAGA
14917 GAAGCAACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 8 0.40
25 6 0.30
ACGTcount: A:0.50, C:0.07, G:0.22, T:0.22
Consensus pattern (23 bp):
AGATTGAATTCAAAAAGTAGACC
Found at i:22982 original size:17 final size:17
Alignment explanation
Indices: 22906--22983 Score: 50
Period size: 17 Copynumber: 4.2 Consensus size: 17
22896 AAAAAATAAT
*
22906 AAAAATGAGAAGAAGAA
1 AAAAATGAAAAGAAGAA
*
22923 AAAGAA-GAAAAGAAAATTGAG
1 AAA-AATGAAAAG--AA--GAA
* *
22944 AAAAATGAAAAATGATGGA
1 AAAAATG-AAAA-GAAGAA
22963 AAAAATGAAAAGAAGAA
1 AAAAATGAAAAGAAGAA
22980 AAAA
1 AAAA
22984 TAATAATAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 16
0.67 0.10 0.23
Matches are distributed among these distances:
17 16 0.35
18 6 0.13
19 10 0.22
20 2 0.04
21 7 0.15
22 4 0.09
23 1 0.02
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.09
Consensus pattern (17 bp):
AAAAATGAAAAGAAGAA
Found at i:23027 original size:29 final size:29
Alignment explanation
Indices: 22970--23028 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 29
22960 GGAAAAAATG
*
22970 AAAAGAAGAAAAAATAATAATAAATAAAA
1 AAAAGAAGAAAAAATAATAATAAAGAAAA
*
22999 AAAAGAAAGAGAAAAATGA-AA-AAAGAAAA
1 AAAAG-AAGA-AAAAATAATAATAAAGAAAA
23028 A
1 A
23029 GAAAATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
29 13 0.50
30 6 0.23
31 7 0.27
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (29 bp):
AAAAGAAGAAAAAATAATAATAAAGAAAA
Found at i:23042 original size:20 final size:20
Alignment explanation
Indices: 22991--23043 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
22981 AAATAATAAT
*
22991 AAATAAAAAAAAGAAAGAGAA
1 AAAT-AAAAAAAGAAAAAGAA
*
23012 AAATGAAAAAAGAAAAAG-A
1 AAATAAAAAAAGAAAAAGAA
23031 AAATAAATAAAAG
1 AAATAAA-AAAAG
23044 GGGGTTCAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 7 0.25
20 17 0.61
21 4 0.14
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (20 bp):
AAATAAAAAAAGAAAAAGAA
Found at i:24428 original size:55 final size:56
Alignment explanation
Indices: 24361--24726 Score: 317
Period size: 55 Copynumber: 6.7 Consensus size: 56
24351 TGTATGAAGA
* * * *
24361 TCGAGTCTTATACTCTCTTGTA-GAATAGGGAGCATACTCGTTTGGTGAAGATTGT
1 TCGAGTCTTATACTCTCTTGAATGAATAGGGAGCAGACACGTTTGTTGAAGATTGT
* * * * *
24416 TCGAGT-TCTATACTCTCTGGTA-GAATAGGGAGCGGACTCGTTTGTTGAAGACTGT
1 TCGAGTCT-TATACTCTCTTGAATGAATAGGGAGCAGACACGTTTGTTGAAGATTGT
* * * * * *
24471 TCGAGT-TCTATACTCTCTGGTA-GAATAGAGAGCGGAC-CCTTT-TATGAAGATTAT
1 TCGAGTCT-TATACTCTCTTGAATGAATAGGGAGCAGACACGTTTGT-TGAAGATTGT
* * * * *
24525 TCGAGT-TCTATACTC-CCTGAACGAATAGGGAGCAGACCCGTTTATTGACGATTGAT
1 TCGAGTCT-TATACTCTCTTGAATGAATAGGGAGCAGACACGTTTGTTGAAGATTG-T
* * * * *
24581 T-GAGTCTTATACTC-CCTAAATGAATAGGGAGTAGACACGCTTGTTGAAGATTGA
1 TCGAGTCTTATACTCTCTTGAATGAATAGGGAGCAGACACGTTTGTTGAAGATTGT
* *
24635 TCGAGTCTTATACTCTC-TGAATGAATAGGGAGCAGACACGTTTGCTGAAGATTGG
1 TCGAGTCTTATACTCTCTTGAATGAATAGGGAGCAGACACGTTTGTTGAAGATTGT
* * * *
24690 TCGAGTCTTATACTC-CCTAAAGGGATAGGGAGCAGAC
1 TCGAGTCTTATACTCTCTTGAATGAATAGGGAGCAGAC
24727 CCGTCATTCG
Statistics
Matches: 268, Mismatches: 33, Indels: 20
0.83 0.10 0.06
Matches are distributed among these distances:
53 4 0.01
54 43 0.16
55 216 0.81
56 5 0.02
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (56 bp):
TCGAGTCTTATACTCTCTTGAATGAATAGGGAGCAGACACGTTTGTTGAAGATTGT
Found at i:24708 original size:110 final size:109
Alignment explanation
Indices: 24359--24727 Score: 356
Period size: 110 Copynumber: 3.4 Consensus size: 109
24349 ATTGTATGAA
* ** * * * *
24359 GATCGAGTCTTATACTCTCTTGTAGAATAGGGAGCATACTCGTTTGGTGAAGATTGTTCGAGTTC
1 GATCGAGTCTTATACTCCCTAATAGAATAGGGAGCAGAC-CGCTTGTTGAAGATTGATCGAGTTC
* * * *
24424 TATACTCTCTG-GTAGAATAGGGAGCGGACTCGTTTGTTGAAGACT
65 TATACTCTCTGAAT-GAATAGGGAGCAGACACGTTTGTTGAAGATT
* * ** * * *
24469 GTTCGAGT-TCTATACTCTCTGGTAGAATAGAGAGCGGACC-CTTTTATGAAGATT-ATTCGAGT
1 GATCGAGTCT-TATACTCCCTAATAGAATAGGGAGCAGACCGCTTGT-TGAAGATTGA-TCGAGT
* * * * *
24531 TCTATACTCCCTGAACGAATAGGGAGCAGACCCGTTTATTGACGATT
63 TCTATACTCTCTGAATGAATAGGGAGCAGACACGTTTGTTGAAGATT
* *
24578 GATTGAGTCTTATACTCCCTAA-ATGAATAGGGAGTAGACACGCTTGTTGAAGATTGATCGAG-T
1 GATCGAGTCTTATACTCCCTAATA-GAATAGGGAGCAGAC-CGCTTGTTGAAGATTGATCGAGTT
*
24641 CTTATACTCTCTGAATGAATAGGGAGCAGACACGTTTGCTGAAGATT
64 C-TATACTCTCTGAATGAATAGGGAGCAGACACGTTTGTTGAAGATT
* *
24688 GGTCGAGTCTTATACTCCCTAA-AGGGATAGGGAGCAGACC
1 GATCGAGTCTTATACTCCCTAATA-GAATAGGGAGCAGACC
24728 CGTCATTCGA
Statistics
Matches: 212, Mismatches: 37, Indels: 21
0.79 0.14 0.08
Matches are distributed among these distances:
108 3 0.01
109 84 0.40
110 120 0.57
111 5 0.02
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (109 bp):
GATCGAGTCTTATACTCCCTAATAGAATAGGGAGCAGACCGCTTGTTGAAGATTGATCGAGTTCT
ATACTCTCTGAATGAATAGGGAGCAGACACGTTTGTTGAAGATT
Found at i:24752 original size:55 final size:55
Alignment explanation
Indices: 24516--24753 Score: 211
Period size: 55 Copynumber: 4.3 Consensus size: 55
24506 ACCCTTTTAT
* * * *
24516 GAAGATTATTCGAGT-TCTATACTCCCTGAACGAATAGGGAGCAGACCCGTTTATT-
1 GAAGATTATTCGAGTCT-TATACTCCCTAAATGAATAGGGAGCAGACACG-TCATTC
* * * *
24571 GACGATTGATT-GAGTCTTATACTCCCTAAATGAATAGGGAGTAGACACG-CTTGTT
1 GAAGATT-ATTCGAGTCTTATACTCCCTAAATGAATAGGGAGCAGACACGTCAT-TC
* *
24626 GAAGATTGA-TCGAGTCTTATACTCTCTGAATGAATAGGGAGCAGACACGT--TTGC
1 GAAGATT-ATTCGAGTCTTATACTCCCTAAATGAATAGGGAGCAGACACGTCATT-C
** * * *
24680 TGAAGATTGGTCGAGTCTTATACTCCCTAAAGGGATAGGGAGCAGACCCGTCATTC
1 -GAAGATTATTCGAGTCTTATACTCCCTAAATGAATAGGGAGCAGACACGTCATTC
* *
24736 GAAGATTTTTCAAGTCTT
1 GAAGATTATTCGAGTCTT
24754 GCTTATCCTG
Statistics
Matches: 151, Mismatches: 21, Indels: 22
0.78 0.11 0.11
Matches are distributed among these distances:
53 2 0.01
54 3 0.02
55 139 0.92
56 5 0.03
57 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (55 bp):
GAAGATTATTCGAGTCTTATACTCCCTAAATGAATAGGGAGCAGACACGTCATTC
Found at i:24752 original size:110 final size:110
Alignment explanation
Indices: 24516--24753 Score: 284
Period size: 110 Copynumber: 2.2 Consensus size: 110
24506 ACCCTTTTAT
* * *
24516 GAAGATTATTCGAGT-TCTATACTCCCTGAACGAATAGGGAGCAGACCCGTTTATTGACGATTGA
1 GAAGATTATTCGAGTCT-TATACTCCCTGAACGAATAGGGAGCAGACACGTTTACTGAAGATTGA
* * * * *
24580 TTGAGTCTTATACTCCCTAAATGAATAGGGAGTAGACACGCTTGTT
65 TCGAGTCTTATACTCCCTAAAGGAATAGGGAGCAGACACGCATGTC
* * * *
24626 GAAGATTGA-TCGAGTCTTATACTCTCTGAATGAATAGGGAGCAGACACGTTTGCTGAAGATTGG
1 GAAGATT-ATTCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTACTGAAGATTGA
* *
24690 TCGAGTCTTATACTCCCTAAAGGGATAGGGAGCAGACCCGTCAT-TC
65 TCGAGTCTTATACTCCCTAAAGGAATAGGGAGCAGACACG-CATGTC
* *
24736 GAAGATTTTTCAAGTCTT
1 GAAGATTATTCGAGTCTT
24754 GCTTATCCTG
Statistics
Matches: 108, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
110 104 0.96
111 4 0.04
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (110 bp):
GAAGATTATTCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTACTGAAGATTGAT
CGAGTCTTATACTCCCTAAAGGAATAGGGAGCAGACACGCATGTC
Found at i:31205 original size:8 final size:8
Alignment explanation
Indices: 31192--31219 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
31182 CTATTATTGG
31192 AAATTTAA
1 AAATTTAA
31200 AAATTTAA
1 AAATTTAA
31208 AAATTTAA
1 AAATTTAA
31216 AAAT
1 AAAT
31220 ATATTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
AAATTTAA
Found at i:33404 original size:3 final size:3
Alignment explanation
Indices: 33398--33474 Score: 88
Period size: 3 Copynumber: 26.0 Consensus size: 3
33388 TTTTTATTAT
*
33398 TAA TAA TAA TAA -ATA TAA TAA TAA TAA AAA T-A TAAA TAA T-A TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
**
33442 TAA TAA TAA TTT TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
33475 CAAATGGATA
Statistics
Matches: 63, Mismatches: 6, Indels: 10
0.80 0.08 0.13
Matches are distributed among these distances:
2 5 0.08
3 55 0.87
4 3 0.05
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:39363 original size:88 final size:87
Alignment explanation
Indices: 39259--39438 Score: 281
Period size: 88 Copynumber: 2.1 Consensus size: 87
39249 TAAAAATTCC
* * *
39259 TTACCAATATATTTACCATTTATTCCATAAGCTCGTAAGTTTATTTTA-CAATATACTTACCATT
1 TTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATT
*
39323 ATTCCATAAGCTCGTAAGCCTATT
66 ATCCCATAAG--CGTAAGCCTATT
39347 TTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATT
1 TTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATT
**
39412 ATCCCATAAGCGTAAGGTTATT
66 ATCCCATAAGCGTAAGCCTATT
39434 TTACC
1 TTACC
Statistics
Matches: 85, Mismatches: 6, Indels: 3
0.90 0.06 0.03
Matches are distributed among these distances:
87 15 0.18
88 45 0.53
89 25 0.29
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (87 bp):
TTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATT
ATCCCATAAGCGTAAGCCTATT
Found at i:39386 original size:45 final size:44
Alignment explanation
Indices: 39259--39438 Score: 267
Period size: 45 Copynumber: 4.1 Consensus size: 44
39249 TAAAAATTCC
* * *
39259 TTACCAATATATTTACCATTTATTCCATAAGCTCGTAAGTTTATT
1 TTACCAATATACTTACCA-TTATCCCATAAGCTCGTAAGCTTATT
* *
39304 TTA-CAATATACTTACCATTATTCCATAAGCTCGTAAGCCTATT
1 TTACCAATATACTTACCATTATCCCATAAGCTCGTAAGCTTATT
39347 TTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCA-TTATCCCATAAGCTCGTAAGCTTATT
*
39392 TTACCAATATACTTACCATTATCCCATAAG--CGTAAGGTTATT
1 TTACCAATATACTTACCATTATCCCATAAGCTCGTAAGCTTATT
39434 TTACC
1 TTACC
Statistics
Matches: 127, Mismatches: 6, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
42 16 0.13
43 27 0.21
44 39 0.31
45 45 0.35
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (44 bp):
TTACCAATATACTTACCATTATCCCATAAGCTCGTAAGCTTATT
Done.