Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001176.1 Hibiscus syriacus cultivar Beakdansim tig00002342_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: 73013
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:8862 original size:32 final size:32
Alignment explanation
Indices: 8826--8902 Score: 118
Period size: 32 Copynumber: 2.4 Consensus size: 32
8816 GTGACATAGT
**
8826 TGAGGGACTAAAATCGAACGGGAATTAATGGC
1 TGAGGGACTAAAATCGAACGACAATTAATGGC
8858 TGAGGGACTAAAATCGAACGACAATTAATGGC
1 TGAGGGACTAAAATCGAACGACAATTAATGGC
* *
8890 TGAAGGATTAAAA
1 TGAGGGACTAAAA
8903 CCAAATGGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.42, C:0.12, G:0.27, T:0.19
Consensus pattern (32 bp):
TGAGGGACTAAAATCGAACGACAATTAATGGC
Found at i:10674 original size:11 final size:11
Alignment explanation
Indices: 10632--10703 Score: 51
Period size: 11 Copynumber: 6.6 Consensus size: 11
10622 TGATATAAAA
10632 ATAAT-ATTTT
1 ATAATAATTTT
* *
10642 TTAATAAATTT
1 ATAATAATTTT
* *
10653 AAAGATTATTTT
1 ATA-ATAATTTT
*
10665 ATAATAATTTG
1 ATAATAATTTT
10676 AT-A-AATTTT
1 ATAATAATTTT
*
10685 AATAATTATTTT
1 -ATAATAATTTT
10697 ATAATAA
1 ATAATAA
10704 CGTAATAAAA
Statistics
Matches: 45, Mismatches: 12, Indels: 9
0.68 0.18 0.14
Matches are distributed among these distances:
9 5 0.11
10 7 0.16
11 20 0.44
12 13 0.29
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (11 bp):
ATAATAATTTT
Found at i:10695 original size:21 final size:20
Alignment explanation
Indices: 10660--10700 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
10650 TTTAAAGATT
10660 ATTTTATAATAATTTGATAA
1 ATTTTATAATAATTTGATAA
* *
10680 ATTTTAATAATTATTTTATAA
1 ATTTT-ATAATAATTTGATAA
10701 TAACGTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
ATTTTATAATAATTTGATAA
Found at i:10712 original size:32 final size:31
Alignment explanation
Indices: 10643--10712 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 31
10633 TAATATTTTT
**
10643 TAATAAATTTAAAGATTATTTTATAATAATT
1 TAATAAATTTAAAGATTATTTTATAATAACG
*
10674 TGATAAATTTTAATA-ATTATTTTATAATAACG
1 TAATAAA-TTTAA-AGATTATTTTATAATAACG
10706 TAATAAA
1 TAATAAA
10713 ATATAATATC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
31 6 0.18
32 26 0.79
33 1 0.03
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (31 bp):
TAATAAATTTAAAGATTATTTTATAATAACG
Found at i:10720 original size:32 final size:32
Alignment explanation
Indices: 10657--10720 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
10647 AAATTTAAAG
** * * *
10657 ATTATTTTATAATAATTTGATAAATTTTAATA
1 ATTATTTTATAATAACGTAATAAAATATAATA
10689 ATTATTTTATAATAACGTAATAAAATATAATA
1 ATTATTTTATAATAACGTAATAAAATATAATA
10721 TCAATTTCAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (32 bp):
ATTATTTTATAATAACGTAATAAAATATAATA
Found at i:16806 original size:11 final size:11
Alignment explanation
Indices: 16763--16804 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
16753 GCATTGATGC
16763 ACTGCTACAAT
1 ACTGCTACAAT
16774 ACTGCTACAAT
1 ACTGCTACAAT
* * *
16785 ATTGTTACAGT
1 ACTGCTACAAT
16796 ACTGCTACA
1 ACTGCTACA
16805 GTGATTTCGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.31
Consensus pattern (11 bp):
ACTGCTACAAT
Found at i:17357 original size:22 final size:22
Alignment explanation
Indices: 17323--17373 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
17313 CTGAGTGGCA
*
17323 TATGAAGTTTGTCCCGAAGGACC
1 TATGAA-TATGTCCCGAAGGACC
*
17346 TGTGAATATGTCCCGAAGGACC
1 TATGAATATGTCCCGAAGGACC
17368 TATGAA
1 TATGAA
17374 ACCCTCGACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (22 bp):
TATGAATATGTCCCGAAGGACC
Found at i:20636 original size:106 final size:107
Alignment explanation
Indices: 20491--20689 Score: 269
Period size: 106 Copynumber: 1.9 Consensus size: 107
20481 AAAAACCCTG
* * * *
20491 ATACTATAAGATCAATCTGGTCGAAATCTGTAGAGTCTAGGTCACATGATCAT-CTTTAG-TAGG
1 ATACTACAAGATCAATCTGGTCGAAATCTGTAGAGTCTAGGTCACATCACCATAC-CTAGTTAGG
*
20554 GTGATGTGTCATGAGACTATTATTTTAGATAAGACGTTACCTA
65 GTGATGTGTCATGAGACAATTATTTTAGATAAGACGTTACCTA
* ** *
20597 ATACTACAGGATCAATCTGGTCGAAATCTG-AGGAGTCTAGGTTGCATCCCCATACCTAGTTAGG
1 ATACTACAAGATCAATCTGGTCGAAATCTGTA-GAGTCTAGGTCACATCACCATACCTAGTTAGG
*
20661 GTGATTTGTCATGAGACAATTATTTTAGA
65 GTGATGTGTCATGAGACAATTATTTTAGA
20690 CAGGGCGCTA
Statistics
Matches: 80, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
105 1 0.01
106 47 0.59
107 32 0.40
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.33
Consensus pattern (107 bp):
ATACTACAAGATCAATCTGGTCGAAATCTGTAGAGTCTAGGTCACATCACCATACCTAGTTAGGG
TGATGTGTCATGAGACAATTATTTTAGATAAGACGTTACCTA
Found at i:21083 original size:35 final size:35
Alignment explanation
Indices: 21042--21110 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
21032 AAAAACTTGT
*
21042 TGCTCGTTGCTCGCCTCTTTGCTCGTTAAGCTCAA
1 TGCTCGTTGCTCGCCTCGTTGCTCGTTAAGCTCAA
* * *
21077 TGCTCGTTGCTTGCCTCGTTGCTTGTTAATCTCA
1 TGCTCGTTGCTCGCCTCGTTGCTCGTTAAGCTCA
21111 CTAAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.10, C:0.29, G:0.20, T:0.41
Consensus pattern (35 bp):
TGCTCGTTGCTCGCCTCGTTGCTCGTTAAGCTCAA
Found at i:31525 original size:23 final size:23
Alignment explanation
Indices: 31491--31574 Score: 123
Period size: 23 Copynumber: 3.7 Consensus size: 23
31481 CTCATATAAA
* *
31491 TGCACCGAAGTGCCATGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
* *
31514 TGCACTGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
*
31537 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
31560 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
31575 TATAATAATG
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.24, C:0.25, G:0.29, T:0.23
Consensus pattern (23 bp):
TGCACCGTAGTGCCACGTAGAAT
Found at i:37322 original size:38 final size:36
Alignment explanation
Indices: 37229--37336 Score: 171
Period size: 36 Copynumber: 2.9 Consensus size: 36
37219 TTTCAATTTG
*
37229 CATAGTTTTATTATTACGTCATTTATAAATACTTTC
1 CATATTTTTATTATTACGTCATTTATAAATACTTTC
* *
37265 CATATTTTTATTATAACGTCATTTATAAATACTTTG
1 CATATTTTTATTATTACGTCATTTATAAATACTTTC
37301 CATATTTTTTTATTATTACGTCATTTATAAATACTT
1 CATA--TTTTTATTATTACGTCATTTATAAATACTT
37337 AACGTATTAT
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
36 37 0.56
38 29 0.44
ACGTcount: A:0.31, C:0.12, G:0.05, T:0.52
Consensus pattern (36 bp):
CATATTTTTATTATTACGTCATTTATAAATACTTTC
Found at i:37600 original size:10 final size:10
Alignment explanation
Indices: 37587--37621 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
37577 CTTTCGGTAA
37587 TATGTTCGTT
1 TATGTTCGTT
*
37597 TATGTTCATT
1 TATGTTCGTT
37607 TATGTTCGTT
1 TATGTTCGTT
37617 TATGT
1 TATGT
37622 GTGTTAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.14, C:0.09, G:0.17, T:0.60
Consensus pattern (10 bp):
TATGTTCGTT
Found at i:37818 original size:10 final size:10
Alignment explanation
Indices: 37805--37933 Score: 51
Period size: 10 Copynumber: 11.5 Consensus size: 10
37795 ATTATTTTCA
37805 TTTATGTTCG
1 TTTATGTTCG
** *
37815 TTTACATTCA
1 TTTATGTTCG
*
37825 TTTATGTTCA
1 TTTATGTTCG
37835 TTTATTGTGTTCG
1 TTTA---TGTTCG
37848 TTTATGTTCGTTCG
1 TTTA---T-GTTCG
* *
37862 TTTGTGTTTG
1 TTTATGTTCG
*
37872 TTTACGTTCG
1 TTTATGTTCG
37882 TTTATTGTGTTCG
1 TTTA---TGTTCG
*
37895 TTTATGTTTG
1 TTTATGTTCG
*
37905 TTTACATCTATTCG
1 TTT--A--TGTTCG
37919 TTTATGTTCG
1 TTTATGTTCG
37929 TTTAT
1 TTTAT
37934 CATTTAAATG
Statistics
Matches: 90, Mismatches: 18, Indels: 22
0.69 0.14 0.17
Matches are distributed among these distances:
10 52 0.58
11 1 0.01
12 2 0.02
13 20 0.22
14 15 0.17
ACGTcount: A:0.12, C:0.11, G:0.17, T:0.60
Consensus pattern (10 bp):
TTTATGTTCG
Found at i:37826 original size:20 final size:20
Alignment explanation
Indices: 37801--37838 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
37791 AAAAATTATT
*
37801 TTCATTTATGTTCGTTTACA
1 TTCATTTATGTTCATTTACA
37821 TTCATTTATGTTCATTTA
1 TTCATTTATGTTCATTTA
37839 TTGTGTTCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.13, G:0.08, T:0.58
Consensus pattern (20 bp):
TTCATTTATGTTCATTTACA
Found at i:37874 original size:24 final size:23
Alignment explanation
Indices: 37825--37933 Score: 121
Period size: 24 Copynumber: 4.7 Consensus size: 23
37815 TTTACATTCA
*
37825 TTTATGTTCATTTATTGTGTTCG
1 TTTATGTTCGTTTATTGTGTTCG
*
37848 TTTATGTTCGTTCGT-TTGTGTTTG
1 TTTATGTTCGTT--TATTGTGTTCG
*
37872 TTTACGTTCGTTTATTGTGTTCG
1 TTTATGTTCGTTTATTGTGTTCG
* * * *
37895 TTTATGTTTGTTTACATCTATTCG
1 TTTATGTTCGTTTA-TTGTGTTCG
37919 TTTATGTTCGTTTAT
1 TTTATGTTCGTTTAT
37934 CATTTAAATG
Statistics
Matches: 71, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
22 1 0.01
23 31 0.44
24 38 0.54
25 1 0.01
ACGTcount: A:0.11, C:0.10, G:0.18, T:0.61
Consensus pattern (23 bp):
TTTATGTTCGTTTATTGTGTTCG
Found at i:37903 original size:33 final size:34
Alignment explanation
Indices: 37843--37909 Score: 102
Period size: 33 Copynumber: 2.0 Consensus size: 34
37833 CATTTATTGT
*
37843 GTTCGTTTATGTTCGTTCGTTTGTGTTTGTTTAC
1 GTTCGTTTATGTTCGTTCGTTTATGTTTGTTTAC
37877 GTTCGTTTAT-TGT-GTTCGTTTATGTTTGTTTAC
1 GTTCGTTTATGT-TCGTTCGTTTATGTTTGTTTAC
37910 ATCTATTCGT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
33 20 0.65
34 11 0.35
ACGTcount: A:0.07, C:0.10, G:0.22, T:0.60
Consensus pattern (34 bp):
GTTCGTTTATGTTCGTTCGTTTATGTTTGTTTAC
Found at i:37922 original size:47 final size:47
Alignment explanation
Indices: 37820--37933 Score: 129
Period size: 47 Copynumber: 2.4 Consensus size: 47
37810 GTTCGTTTAC
* * *** *
37820 ATTCATTTATGTTCATTTATTGTGTTCGTTTATGTTCGTTCGTTTGT
1 ATTCGTTTATGTTCGTTTATTGTGTTCGTTTATGTTCGTTCACATCT
* * * * *
37867 GTTTGTTTACGTTCGTTTATTGTGTTCGTTTATGTTTGTTTACATCT
1 ATTCGTTTATGTTCGTTTATTGTGTTCGTTTATGTTCGTTCACATCT
37914 ATTCGTTTATGTTCGTTTAT
1 ATTCGTTTATGTTCGTTTAT
37934 CATTTAAATG
Statistics
Matches: 53, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
47 53 1.00
ACGTcount: A:0.12, C:0.11, G:0.18, T:0.60
Consensus pattern (47 bp):
ATTCGTTTATGTTCGTTTATTGTGTTCGTTTATGTTCGTTCACATCT
Found at i:52828 original size:95 final size:97
Alignment explanation
Indices: 52695--53065 Score: 284
Period size: 109 Copynumber: 3.6 Consensus size: 97
52685 CTGGAACTGG
*
52695 GAAATTGTTGTTGACAACCAACCGTCCCTTCGTTGTGAAGTTGAAC-TG-GTTGTCTCGAGTCCA
1 GAAATTGTTGTTGACAACCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCA
* * *
52758 ATATCCTTCGTTGTG-AGTTGAGATTGGCTCC
66 ATATCCTCCGCTGTGAAGTTGAAATTGGCTCC
** * * * *
52789 GAAATTGTTTGTTGACAGTCAGCCG-CCCTTTCGTTGTGAAGTTGAGCTTGTGCTGTCTTGGGTC
1 GAAATTG-TTGTTGACAACCAACCGTCCC-TTCGTTGTGAAGTTGAACTTGTGCTGTCTCGAGTC
*
52853 CAATATCCTCCGCTGTGAAGTTGAAATTGGTCCTGAAGCTGG
64 CAATATCCTCCGCTGTGAAGTTGAAATTGG--CT----C--C
* * * *
52895 GAAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGGGTAGC
1 GAAATTGTTGTTGACAACCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTCGAGT--C
* * ** **
52960 ACGATATCCTCCG-TCGTGGAGTTGAAATCAGCTTTGAAATTG
64 -CAATATCCTCCGCT-GTGAAGTTG-AA--A---TTG-GCTCC
* * *
53002 GAAAGTTGTTCGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGT
1 GAAA-TTGTT-GTTGACAACCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTCGAGT
53066 GGCACGATAT
Statistics
Matches: 229, Mismatches: 21, Indels: 39
0.79 0.07 0.13
Matches are distributed among these distances:
94 10 0.04
95 31 0.14
96 2 0.01
97 25 0.11
98 11 0.05
100 2 0.01
104 1 0.00
105 47 0.21
106 10 0.04
107 7 0.03
108 24 0.10
109 54 0.24
111 1 0.00
113 1 0.00
114 3 0.01
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (97 bp):
GAAATTGTTGTTGACAACCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCA
ATATCCTCCGCTGTGAAGTTGAAATTGGCTCC
Found at i:52903 original size:200 final size:198
Alignment explanation
Indices: 52593--52951 Score: 571
Period size: 200 Copynumber: 1.8 Consensus size: 198
52583 CTGGAACCGG
52593 GAAATTGTTTATTGACAGTCAGCCGCCCCTTCGCTGCGAAGTTGAGCTTGCTGTCTTGGGTCCAA
1 GAAATTGTTTATTGACAGTCAGCCGCCCCTTCGCTGCGAAGTTGAGCTTGCTGTCTTGGGTCCAA
*
52658 TCCTTCGCTATGAAGTTGAAACTGGCCCTGGAACTGGGAAATTGTTGTTGACAACCAACCGTCCC
66 TCCTCCGCTATGAAGTTGAAACTGGCCCTGGAACTGGGAAATTGTTGTTGACAACCAACCGTCCC
52723 TTCGTTGTGAAGTTGAAC-TG-GTTGTCTCGAGTCCAATATCCTTCGTTGTGAGTTGAGATTGGC
131 TTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAGTTGAGATTGGC
52786 TCC
196 TCC
* * * *
52789 GAAATTGTTTGTTGACAGTCAGCCGCCCTTTCGTTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCC
1 GAAATTGTTTATTGACAGTCAGCCGCCCCTTCGCTGCGAAGTTGAGC-T-TGCTGTCTTGGGTCC
* * * *
52854 AATATCCTCCGCTGTGAAGTTGAAATTGGTCCT-GAAGCTGGGAAATTGTTGTTGACAACCAGCC
64 -A-ATCCTCCGCTATGAAGTTGAAACTGGCCCTGGAA-CTGGGAAATTGTTGTTGACAACCAACC
52918 GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
126 GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
52952 TGGGTAGCAC
Statistics
Matches: 147, Mismatches: 9, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
196 43 0.29
197 1 0.01
198 15 0.10
199 4 0.03
200 75 0.51
201 2 0.01
202 7 0.05
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.33
Consensus pattern (198 bp):
GAAATTGTTTATTGACAGTCAGCCGCCCCTTCGCTGCGAAGTTGAGCTTGCTGTCTTGGGTCCAA
TCCTCCGCTATGAAGTTGAAACTGGCCCTGGAACTGGGAAATTGTTGTTGACAACCAACCGTCCC
TTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAGTTGAGATTGGC
TCC
Found at i:53043 original size:109 final size:108
Alignment explanation
Indices: 52789--53097 Score: 389
Period size: 109 Copynumber: 2.9 Consensus size: 108
52779 GATTGGCTCC
** * *
52789 GAAATTGTTTGTTGACAGTCAGCCG-CCCTTTCGTTGTGAAGTTGAGCTTGTGCTGTCTTGGGT-
1 GAAATTG-TTGTTGACAACCAGCCGTCCC-TTCGTTGTGAAGTTGAACTTGTGTTGTCTTGGGTG
* * * * *
52852 C-CAATATCCTCCG-CTGTGAAGTTGAAAT-TGGTCCTGAAGCTGG
64 CACGATATCCTCCGTC-GTGGAGTTGAAATCAGCTCCTGAAGATGG
52895 GAAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGGGTAGC
1 GAAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGGGT-GC
* *
52960 ACGATATCCTCCGTCGTGGAGTTGAAATCAGCT-TTGAA-ATTG
65 ACGATATCCTCCGTCGTGGAGTTGAAATCAGCTCCTGAAGATGG
*
53002 GAAAGTTGTTCGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTG
1 GAAA-TTGTT-GTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGGGT-
*
53067 GCACGATATCCTCCATCGTGGAGTTGAAATC
63 GCACGATATCCTCCGTCGTGGAGTTGAAATC
53098 GTGGATGTTT
Statistics
Matches: 181, Mismatches: 14, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
105 47 0.26
106 10 0.06
107 7 0.04
108 32 0.18
109 85 0.47
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (108 bp):
GAAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGGGTGCA
CGATATCCTCCGTCGTGGAGTTGAAATCAGCTCCTGAAGATGG
Found at i:62460 original size:22 final size:23
Alignment explanation
Indices: 62417--62460 Score: 56
Period size: 22 Copynumber: 1.9 Consensus size: 23
62407 ACTCATCAGG
62417 GTGGTTCTTCATTAATTGCCTTAT
1 GTGGTTC-TCATTAATTGCCTTAT
62441 GTGGTTC-CATTCAATT-CCTT
1 GTGGTTCTCATT-AATTGCCTT
62461 CCCCACTACC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 8 0.42
23 4 0.21
24 7 0.37
ACGTcount: A:0.16, C:0.20, G:0.16, T:0.48
Consensus pattern (23 bp):
GTGGTTCTCATTAATTGCCTTAT
Found at i:63080 original size:4 final size:4
Alignment explanation
Indices: 63066--63095 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
63056 AAAATGTTAG
63066 TAAA GTAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA -TAAA TAAA TAAA TAAA TAAA TAAA T
63096 GACGAAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:66905 original size:11 final size:11
Alignment explanation
Indices: 66891--66927 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
66881 TGCAATCTTC
66891 GTTTGAAGTTT
1 GTTTGAAGTTT
*
66902 GTTTGAAGTTC
1 GTTTGAAGTTT
66913 GTTTGAAGTTT
1 GTTTGAAGTTT
66924 GTTT
1 GTTT
66928 TGATTATTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.16, C:0.03, G:0.27, T:0.54
Consensus pattern (11 bp):
GTTTGAAGTTT
Found at i:70098 original size:4 final size:4
Alignment explanation
Indices: 70089--73013 Score: 5434
Period size: 4 Copynumber: 741.2 Consensus size: 4
70079 CTACCATCCC
70089 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
70137 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
70185 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
70233 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
70281 TACA TAC- -ACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
70327 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
70375 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
70423 TACA TACA TACA TACA TACA TACA T-CA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
70470 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
70518 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
70566 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
70614 TACA TACA TACA TACA TACA TACA TACA TACA TACA TAC- TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
70661 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
70709 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
70757 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
70805 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
70853 TAC- TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
70900 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACC TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
70948 TACA TACA TACA TACA TACA TACA TACA TACA TAC- -ACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
70994 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
71042 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA T-CA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
71089 TACA TACA TACA T-CA TACA TAC- -ACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
71134 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACC
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
71182 TAC- TACA TACA TACA TACA TACA TACA TACA TACA TACA TAC- -ACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
71227 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
71275 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
71323 TACA TACA TACA TACA TACA TACA TACA TACA T--A TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
71369 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
71417 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
71465 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
71513 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
71561 TACA TACA TACA TACA TACA TACA TACA TACA TACA GACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
71609 TACA TACA TACA TAC- -ACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
71655 TACA TACA TACC TACA TACA TACA TACA TACA TACA T--A TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
71701 TACA TACA TACA TACA TACA TACA TACA TAC- TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
71748 TACA TACA TAC- TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
71795 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
71843 TACA TACA TACA TACA TACA TACA TACA TAC- TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
71890 TACA TACA TACA TACA TACA TACA TACA TAC- TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
71937 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
71985 TACA TACA TACA TACA TACAA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TAC-A TACA TACA TACA TACA TACA TACA TACA
*
72034 -ACA TACA TACA TACA TACA TACA TACA TACA TAC- -ACA GACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
72079 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
72127 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACC
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
72175 TACA TACA TACA TACA TAC- -ACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
72221 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
72269 TAC- TACA TACA TACAA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TAC-A TACA TACA TACA TACA TACA TACA TACA TACA
72317 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
72365 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
72413 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
72461 TACA TACA TACA TACA TACA TACA TACA TAC- TACA TACA TACA TAC-
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
72507 TACA TACA TACA TAC- -ACA TACCA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TA-CA TACA TACA TACA TACA TACA TACA
72554 TACA TAC- TACA TACA TACA TACA TACA TACA TACA TACA TACA TACAA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TAC-A
*
72602 TACA TACA TACA TACA TAC- -ACA TACC TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
72648 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
72696 TACA TACA TAC- -ACA TACA TACA TACA TACA TACA TACA TAC- TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
72741 TACA TACA TACA TACA TACA TACA TACA T-CA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
72788 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
72836 TACA TACA TACA TACA TACA TACA TAC- TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
72883 TACA TACA TACA TACA TACA TACA TACA TACA TACA TAC- -ACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
72929 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
72977 TACA TACA TACA TACC TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA T
Statistics
Matches: 2859, Mismatches: 14, Indels: 96
0.96 0.00 0.03
Matches are distributed among these distances:
2 26 0.01
3 54 0.02
4 2763 0.97
5 16 0.01
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.25
Consensus pattern (4 bp):
TACA
Done.