Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000925.1 Hibiscus syriacus cultivar Beakdansim tig00001847_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: 60235
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:16935 original size:45 final size:45
Alignment explanation
Indices: 16886--17000 Score: 176
Period size: 45 Copynumber: 2.5 Consensus size: 45
16876 TGACATCCAA
16886 TCATACCAATTATGCATTGTTATACATTATATATATGGCATCCTT
1 TCATACCAATTATGCATTGTTATACATTATATATATGGCATCCTT
* * *
16931 TCATACCACTTATGCATTGTTGTACATTATATATATGTCATCCTT
1 TCATACCAATTATGCATTGTTATACATTATATATATGGCATCCTT
* *
16976 TTATACCAACTATGCATTGTGTATA
1 TCATACCAATTATGCATTGT-TATA
17001 TAAAAATGCA
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
45 59 0.95
46 3 0.05
ACGTcount: A:0.30, C:0.18, G:0.10, T:0.43
Consensus pattern (45 bp):
TCATACCAATTATGCATTGTTATACATTATATATATGGCATCCTT
Found at i:17139 original size:81 final size:81
Alignment explanation
Indices: 17026--17638 Score: 874
Period size: 81 Copynumber: 7.6 Consensus size: 81
17016 TTTCCTTTAG
* * *
17026 TCTTTTACTCAACGGAATTTAACCGTTCATCTAAATGGCATAATTGACACCTTTCTTCCAAATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
*
17091 ATAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * * * * * *
17107 TATTTTACTCAACGGTATTTAATCGTTAATCTAACTAGTATAATTGACACCTTTTTTCCAAATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
* *
17172 ATAGCTAGACCATTAA
66 ACAGCTAGGCCATTAA
* *
17188 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTTGCATAATTGACACCTTTCTGCCAAATGT
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
*
17253 ACAGCTATGCCATTAA
66 ACAGCTAGGCCATTAA
* * * **
17269 TATTTTACTCAATGGTATTTAATCGTTCATCTAACTATCATAATTGACACCTTTCTGCCAAATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
17334 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
** *
17350 TCTTTTACTCAACGGTATTTAACTATTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
* *
17415 ACAGTTAAGCCATTAA
66 ACAGCTAGGCCATTAA
* *
17431 TCTTTTACTCAATGATATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
* *
17496 ATAGCTAGGTCATTAA
66 ACAGCTAGGCCATTAA
* * *
17512 TCTTTTACTCAACGGTATTTAACCATTCATCTAACTGG----ATTGACACCTCTCTTCCAAATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
17573 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * *
17589 TCTTTTACTCAATGATATTTAATCGTTCATCTAACTGGCATAATTGACAC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACAC
17639 ATGCCAAATG
Statistics
Matches: 471, Mismatches: 57, Indels: 8
0.88 0.11 0.01
Matches are distributed among these distances:
77 69 0.15
81 402 0.85
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.36
Consensus pattern (81 bp):
TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
ACAGCTAGGCCATTAA
Found at i:24346 original size:39 final size:39
Alignment explanation
Indices: 24288--24441 Score: 164
Period size: 39 Copynumber: 3.9 Consensus size: 39
24278 CTGTACACCA
* * * *
24288 AGTAAGGGCTTATCCTGTGCACAAAGCAAAGAAGCCTGC
1 AGTAAGGACTTACCCTGAGCACAAAGCAAAGGAGCCTGC
* * * * * * *
24327 AGTAAGGTCTTATCATGTGCACAAAGTAGAGGAGCCTAC
1 AGTAAGGACTTACCCTGAGCACAAAGCAAAGGAGCCTGC
* * *
24366 AGTAAGGACTTACCTTGAGCACAAAGCCACGGAGCCTGC
1 AGTAAGGACTTACCCTGAGCACAAAGCAAAGGAGCCTGC
* *
24405 GGTAAGGACTTACCCTGAGCACAAAGCAGAGGAGCCT
1 AGTAAGGACTTACCCTGAGCACAAAGCAAAGGAGCCT
24442 ACGGAAAGCG
Statistics
Matches: 95, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 95 1.00
ACGTcount: A:0.32, C:0.23, G:0.27, T:0.18
Consensus pattern (39 bp):
AGTAAGGACTTACCCTGAGCACAAAGCAAAGGAGCCTGC
Found at i:24402 original size:78 final size:78
Alignment explanation
Indices: 24288--24443 Score: 197
Period size: 78 Copynumber: 2.0 Consensus size: 78
24278 CTGTACACCA
* * * * *
24288 AGTAAGGGCTTATCCTGTGCACAAAGCAAAGAAGCCTGCAGTAAGGTCTTATCATGTGCACAAAG
1 AGTAAGGACTTATCCTGAGCACAAAGCAAAGAAGCCTGCAGTAAGGACTTACCATGAGCACAAAG
*
24353 TAGAGGAGCCTAC
66 CAGAGGAGCCTAC
* * * * *
24366 AGTAAGGACTTA-CCTTGAGCACAAAGCCACGGAGCCTGCGGTAAGGACTTACCCTGAGCACAAA
1 AGTAAGGACTTATCC-TGAGCACAAAGCAAAGAAGCCTGCAGTAAGGACTTACCATGAGCACAAA
24430 GCAGAGGAGCCTAC
65 GCAGAGGAGCCTAC
24444 GGAAAGCGAT
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
77 2 0.03
78 64 0.97
ACGTcount: A:0.33, C:0.24, G:0.26, T:0.17
Consensus pattern (78 bp):
AGTAAGGACTTATCCTGAGCACAAAGCAAAGAAGCCTGCAGTAAGGACTTACCATGAGCACAAAG
CAGAGGAGCCTAC
Found at i:30045 original size:39 final size:38
Alignment explanation
Indices: 30001--30156 Score: 136
Period size: 39 Copynumber: 4.1 Consensus size: 38
29991 CCCGTACACC
* * * *
30001 CAGTAAGGGCTTACCCTATGCACAAAGTAAAGGAGATTA
1 CAGTAAGGACTTACCCTAAGCACAAAG-AAAGGAGCTTG
* * * ** * *
30040 TAGTAAGGTCTTATCCTGTGCAAAAAGAAGAGGAGCCTG
1 CAGTAAGGACTTACCCTAAGCACAAAGAA-AGGAGCTTG
*
30079 CAGTAAGGACTTACCCTAAGAACAAAG-AA-GAGCTTG
1 CAGTAAGGACTTACCCTAAGCACAAAGAAAGGAGCTTG
* * *
30115 CAGTAAGGACTTTCCCTAAGCACAAAGTATAGGAGCCTG
1 CAGTAAGGACTTACCCTAAGCACAAAG-AAAGGAGCTTG
30154 CAG
1 CAG
30157 AAAGCGGTAA
Statistics
Matches: 93, Mismatches: 20, Indels: 8
0.77 0.17 0.07
Matches are distributed among these distances:
36 31 0.33
37 1 0.01
38 4 0.04
39 57 0.61
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.20
Consensus pattern (38 bp):
CAGTAAGGACTTACCCTAAGCACAAAGAAAGGAGCTTG
Found at i:30124 original size:36 final size:36
Alignment explanation
Indices: 30067--30156 Score: 117
Period size: 36 Copynumber: 2.4 Consensus size: 36
30057 GTGCAAAAAG
*
30067 AAGAGGAGCCTGCAGTAAGGACTTACCCTAAGAACA
1 AAGAAGAGCCTGCAGTAAGGACTTACCCTAAGAACA
* * *
30103 AAGAAGAGCTTGCAGTAAGGACTTTCCCTAAGCACA
1 AAGAAGAGCCTGCAGTAAGGACTTACCCTAAGAACA
30139 AAGTATAGGAGCCTGCAG
1 AAG-A-A-GAGCCTGCAG
30157 AAAGCGGTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
36 35 0.76
37 1 0.02
38 1 0.02
39 9 0.20
ACGTcount: A:0.37, C:0.21, G:0.26, T:0.17
Consensus pattern (36 bp):
AAGAAGAGCCTGCAGTAAGGACTTACCCTAAGAACA
Found at i:32054 original size:82 final size:82
Alignment explanation
Indices: 31917--32078 Score: 245
Period size: 82 Copynumber: 2.0 Consensus size: 82
31907 TCCTCACACA
* * * *
31917 CTGGCGATAAAGGATATAAGAATGACACTGGTGGACTCGGGACGATGCAAGGAACACAATGGTGT
1 CTGGCGATAAAGGAGAAAAGAAGGACACTGGTGGACTCGAGACGATGCAAGGAACACAATGGTGT
* *
31982 GGGTGGTGTCGAAAACG
66 GGGAGGTGTCAAAAACG
*
31999 CTGGCGATAAAGGAGAAAAGAAGGACACTGGTGGACTCGAGA-TACTGCAAGGAACACAATGGTG
1 CTGGCGATAAAGGAGAAAAGAAGGACACTGGTGGACTCGAGACGA-TGCAAGGAACACAATGGTG
32063 TGGGAGGTGTCAAAAA
65 TGGGAGGTGTCAAAAA
32079 TAGAGCAACG
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
81 1 0.01
82 71 0.99
ACGTcount: A:0.35, C:0.14, G:0.35, T:0.17
Consensus pattern (82 bp):
CTGGCGATAAAGGAGAAAAGAAGGACACTGGTGGACTCGAGACGATGCAAGGAACACAATGGTGT
GGGAGGTGTCAAAAACG
Found at i:46644 original size:44 final size:45
Alignment explanation
Indices: 46546--46688 Score: 209
Period size: 45 Copynumber: 3.2 Consensus size: 45
46536 TTTAATTTAC
* * * *
46546 TAAATGAAATACATAATGATGCATTATCGTCATGAAAGGACGCCA
1 TAAATGAAATGCATAATGGTGCATTATCGACATGAAAGGATGCCA
46591 TAAATGAAATGCATAATGGTGCATTATC-AGCATG-AAGGATGCCA
1 TAAATGAAATGCATAATGGTGCATTATCGA-CATGAAAGGATGCCA
*
46635 TAAATGAAATGCATAACGGTGCATTATCGACATGAAAGGATGCCA
1 TAAATGAAATGCATAATGGTGCATTATCGACATGAAAGGATGCCA
*
46680 TAGATGAAA
1 TAAATGAAA
46689 ATAAAGTATA
Statistics
Matches: 89, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
44 40 0.45
45 49 0.55
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (45 bp):
TAAATGAAATGCATAATGGTGCATTATCGACATGAAAGGATGCCA
Found at i:52048 original size:45 final size:44
Alignment explanation
Indices: 51938--52264 Score: 411
Period size: 45 Copynumber: 7.2 Consensus size: 44
51928 ATTTAATTTA
* *
51938 ATAAATGAAATGTATAACGGTGCATTATCGACATGAAAGGATATGTC
1 ATAAATGAAATGCATAACGGTGCATTATCG-CATGAAAGG--ATGCC
* ** *
51985 ATAAATAAAATATATAACGATGCATTATCAGCATGAAAGGATGCC
1 ATAAATGAAATGCATAACGGTGCATTATC-GCATGAAAGGATGCC
* *
52030 ATAAATGAAATGCATAACGGTGCATTATCGACATGAAAAGATGTC
1 ATAAATGAAATGCATAACGGTGCATTATCG-CATGAAAGGATGCC
* *
52075 ATAAATAAAATGCATAACGGTGCATTATCGGCATGAAAGGATACC
1 ATAAATGAAATGCATAACGGTGCATTATC-GCATGAAAGGATGCC
*
52120 ATAAATGAAATGCATAACGGTGCATTATCGGTATGAAAGGATGCC
1 ATAAATGAAATGCATAACGGTGCATTATC-GCATGAAAGGATGCC
* * *
52165 ATAAATGAAATACATAACGGTGCATTATCGACATGAAAGGATTCA
1 ATAAATGAAATGCATAACGGTGCATTATCG-CATGAAAGGATGCC
* * *
52210 ATAAATGAAATCCATAATGATGCATTATCGGCATGAAAGGATGCC
1 ATAAATGAAATGCATAACGGTGCATTATC-GCATGAAAGGATGCC
*
52255 ATACATGAAA
1 ATAAATGAAA
52265 AAGTATAATT
Statistics
Matches: 248, Mismatches: 27, Indels: 12
0.86 0.09 0.04
Matches are distributed among these distances:
44 2 0.01
45 208 0.84
46 2 0.01
47 35 0.14
48 1 0.00
ACGTcount: A:0.43, C:0.13, G:0.20, T:0.24
Consensus pattern (44 bp):
ATAAATGAAATGCATAACGGTGCATTATCGCATGAAAGGATGCC
Found at i:52182 original size:135 final size:135
Alignment explanation
Indices: 51937--52264 Score: 469
Period size: 135 Copynumber: 2.4 Consensus size: 135
51927 GATTTAATTT
* * * * *
51937 AATAAATGAAATGTATAACGGTGCATTATCGACATGAAAGGATATGTCATAAATAAAATATATAA
1 AATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATA--CCATAAATGAAATACATAA
*
52002 CGATGCATTATCAGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCATTATCGACATGAA
64 CGATGCATTATCAGCATGAAAGGATGCCATAAATGAAATACATAACGGTGCATTATCGACATGAA
52067 AAGATGTC
129 AAGAT-TC
* *
52075 -ATAAATAAAATGCATAACGGTGCATTATCGGCATGAAAGGATACCATAAATGAAATGCATAACG
1 AATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATACCATAAATGAAATACATAACG
* * * *
52139 GTGCATTATCGGTATGAAAGGATGCCATAAATGAAATACATAACGGTGCATTATCGACATGAAAG
66 ATGCATTATCAGCATGAAAGGATGCCATAAATGAAATACATAACGGTGCATTATCGACATGAAAA
52204 GATTC
131 GATTC
* * * * *
52209 AATAAATGAAATCCATAATGATGCATTATCGGCATGAAAGGATGCCATACATGAAA
1 AATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATACCATAAATGAAA
52265 AAGTATAATT
Statistics
Matches: 171, Mismatches: 18, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
134 2 0.01
135 129 0.75
137 40 0.23
ACGTcount: A:0.43, C:0.13, G:0.20, T:0.24
Consensus pattern (135 bp):
AATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATACCATAAATGAAATACATAACG
ATGCATTATCAGCATGAAAGGATGCCATAAATGAAATACATAACGGTGCATTATCGACATGAAAA
GATTC
Found at i:54028 original size:66 final size:65
Alignment explanation
Indices: 53958--54148 Score: 195
Period size: 66 Copynumber: 2.9 Consensus size: 65
53948 TAAATGAAAT
* * * * * *
53958 GCATGAAAGGATGCATTAA-GGAATGAAAGGAAGCCATATATGAAATGCATGAAAGGATGCGTTA
1 GCATGAAAGGATGCATAAATGAAATGAAAGAAAG-CATACAT-AAAGGCATGAAAGGATGCATTA
54022 AG
64 AG
* * * * *
54024 GCATGAAAGGATGTCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCATTAA
1 GCATGAAAGGATG-CATAAATGAAATGAAAGAAAGCATACATAAAGGCATGAAAGGATGCATTAA
54089 G
65 G
* * * * *
54090 GCATGAAAGGATGCCATAAATGAAATGCATGAAAGAATGCATTAAGGCATGAAAGGATG
1 GCATGAAAGGATG-CATAAATGAAATGAAAGAAAGCATACATAAAGGCATGAAAGGATG
54149 TCATAAATGA
Statistics
Matches: 110, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
66 91 0.83
67 9 0.08
68 10 0.09
ACGTcount: A:0.43, C:0.09, G:0.28, T:0.20
Consensus pattern (65 bp):
GCATGAAAGGATGCATAAATGAAATGAAAGAAAGCATACATAAAGGCATGAAAGGATGCATTAAG
Found at i:54077 original size:112 final size:112
Alignment explanation
Indices: 53958--54267 Score: 465
Period size: 112 Copynumber: 2.8 Consensus size: 112
53948 TAAATGAAAT
* * *
53958 GCATGAAAGGATGCATTAAGGAATGAAAGGAAGCCATATATGAAATGCATGAAAGGATGCGTTAA
1 GCATGAAAGGATGCATTAAGGAATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAA
*
54023 GGCATGAAAGGATGTCATAAATGAAATGCATGAAAGGATGCATTAAG
66 GGCATGAAAGGATGTCATAAATGAAATGCATGAAAGGATACATTAAG
* *
54070 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATGAAATGCATGAAAGAATGCATTAA
1 GCATGAAAGGATGCATTAAGGAATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAA
54135 GGCATGAAAGGATGTCATAAATGAAATGCATGAAAGGATACATTAAG
66 GGCATGAAAGGATGTCATAAATGAAATGCATGAAAGGATACATTAAG
*
54182 GCATGAAAGGATGCCA-T-A--AATGAATGCG-TG--A-AAATGAAATGCATGAAAGGATGCATT
1 GCATGAAAGGATG-CATTAAGGAATGAAAG-GATGCCATAAATGAAATGCATGAAAGGATGCATT
* *
54239 AAGGCATGAAAGGATGCCATAAATAAAAT
64 AAGGCATGAAAGGATGTCATAAATGAAAT
54268 TAAAGAATAA
Statistics
Matches: 185, Mismatches: 11, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
106 52 0.28
107 1 0.01
109 8 0.04
110 1 0.01
111 1 0.01
112 120 0.65
113 2 0.01
ACGTcount: A:0.44, C:0.10, G:0.26, T:0.20
Consensus pattern (112 bp):
GCATGAAAGGATGCATTAAGGAATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAA
GGCATGAAAGGATGTCATAAATGAAATGCATGAAAGGATACATTAAG
Found at i:54082 original size:46 final size:46
Alignment explanation
Indices: 53903--54082 Score: 281
Period size: 46 Copynumber: 3.9 Consensus size: 46
53893 AAATGAATCC
* *
53903 AAATGAAATGCATGAAAAGATGCATTAAGGCATGCAAGGAT-TCCAT
1 AAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGT-CAT
* * *
53949 AAATGAAATGCATGAAAGGATGCATTAAGGAATGAAAGGAAGCCAT
1 AAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGTCAT
* *
53995 ATATGAAATGCATGAAAGGATGCGTTAAGGCATGAAAGGATGTCAT
1 AAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGTCAT
54041 AAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
1 AAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
54083 CATTAAGGCA
Statistics
Matches: 121, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
46 121 1.00
ACGTcount: A:0.44, C:0.09, G:0.26, T:0.21
Consensus pattern (46 bp):
AAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGTCAT
Found at i:54120 original size:46 final size:46
Alignment explanation
Indices: 54070--54214 Score: 247
Period size: 46 Copynumber: 3.2 Consensus size: 46
54060 ATGCATTAAG
54070 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATGAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATGAAAT
* *
54116 GCATGAAAGAATGCATTAAGGCATGAAAGGATGTCATAAATGAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATGAAAT
*
54162 GCATGAAAGGATACATTAAGGCATGAAAGGATGCCATAAATG-AAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATGAAAT
*
54207 GCGTGAAA
1 GCATGAAA
54215 ATGAAATGCA
Statistics
Matches: 93, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
45 10 0.11
46 83 0.89
ACGTcount: A:0.44, C:0.10, G:0.26, T:0.20
Consensus pattern (46 bp):
GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATGAAAT
Found at i:54120 original size:92 final size:90
Alignment explanation
Indices: 53932--54255 Score: 274
Period size: 92 Copynumber: 3.7 Consensus size: 90
53922 ATGCATTAAG
* * * *
53932 GCATGCAAGGATTCCATAAATGAAATGCATGAAAGGATGCATTAAGGAATGAAAGGAAGCCATAT
1 GCATGAAAGGA-TGCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG-C--AT
* * *
53997 ATGAAATGCATGAAAGGATG-CGT---T-AAG
62 -T--AAGGCATGAAAGGATGCCATAAATGAAT
54024 GCATGAAAGGATGTCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCATTAA
1 GCATGAAAGGATG-CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCATTAA
54089 GGCATGAAAGGATGCCATAAATGAAAT
65 GGCATGAAAGGATGCCATAAATG-AAT
* * * *
54116 GCATGAAAGAATGCAT---T--AAGGCATGAAAGGATGTCATAAATGAAATGCATGAAAGGATAC
1 GCATGAAAGGATGCATAAATGAAATGCATGAAAGGATG-CAT---T--AAGGCATGAAAGGATGC
54176 ATTAAGGCATGAAAGGATGCCATAAATGAAT
60 ATTAAGGCATGAAAGGATGCCATAAATGAAT
54207 GC-------G-TG-A-AAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
1 GCATGAAAGGATGCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
54256 CATAAATAAA
Statistics
Matches: 199, Mismatches: 15, Indels: 48
0.76 0.06 0.18
Matches are distributed among these distances:
80 15 0.08
82 2 0.01
83 2 0.01
84 1 0.01
85 3 0.02
86 45 0.23
87 5 0.03
88 2 0.01
89 2 0.01
90 2 0.01
91 10 0.05
92 110 0.55
ACGTcount: A:0.43, C:0.10, G:0.26, T:0.20
Consensus pattern (90 bp):
GCATGAAAGGATGCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCATTAAG
GCATGAAAGGATGCCATAAATGAAT
Found at i:54488 original size:55 final size:56
Alignment explanation
Indices: 54408--54558 Score: 184
Period size: 54 Copynumber: 2.8 Consensus size: 56
54398 AGAATTTGTT
*
54408 CAAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGGGCACTTTGTGTG
1 CAAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGGGCACTATGTGTG
* * * **
54464 CAAAAACTAAG-AATTCTTAATAAGTTTATGAAATTCCT-T-TGTGTGCTATGTGTG
1 CAAAAACTAAGAAATTCATAATAAGTTTATG-AATTTCTGTATGGGCACTATGTGTG
** *
54518 -GGAAACTAAGAAATTCATATTAAGTTTATGAATTTCTGTAT
1 CAAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTAT
54559 TGGTAGTGGG
Statistics
Matches: 80, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
53 14 0.17
54 29 0.36
55 20 0.25
56 17 0.21
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.38
Consensus pattern (56 bp):
CAAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGGGCACTATGTGTG
Found at i:54929 original size:81 final size:81
Alignment explanation
Indices: 54725--54929 Score: 277
Period size: 81 Copynumber: 2.5 Consensus size: 81
54715 ATGGCTTAGT
*
54725 TGTGTATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAA
1 TGTGTATTTGGCAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAA
54790 AGACTAAAAGCCTAAC
66 AGACTAAAAGCCTAAC
* ** * *
54806 TATGCCTTTGGCAGAAAGGTGTCAATCATGCCAGTTAAATGAAAGGTTAAATACCTTTGGGTAAA
1 TGTGTATTTGGCAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAA
* *
54871 AGACTAAATGTCTAA-
66 AGACTAAAAGCCTAAC
* * * * *
54886 TGGTGTATTTGGCAGAAAGATGCCAATAATGCAAGTTGGATGAA
1 T-GTGTATTTGGCAGAAAGGTGTCAATCATGCCAGTTAGATGAA
54930 GGACAAATTG
Statistics
Matches: 106, Mismatches: 17, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
80 1 0.01
81 105 0.99
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.28
Consensus pattern (81 bp):
TGTGTATTTGGCAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAA
AGACTAAAAGCCTAAC
Found at i:56863 original size:3 final size:3
Alignment explanation
Indices: 56855--56889 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
56845 TATGTCTGAC
56855 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
56890 TTCCTTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Done.