Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021822.1 Corchorus olitorius cultivar O-4 contig21855, 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: 5807
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Found at i:3819 original size:30 final size:30
Alignment explanation
Indices: 3783--4157 Score: 386
Period size: 30 Copynumber: 12.2 Consensus size: 30
3773 ACTGATGATA
3783 CAATGATCCTAAACCAGGATTAAAATAAAG
1 CAATGATCCTAAACCAGGATTAAAATAAAG
* * *
3813 CAATGATCCTCAACCAAGATTAAAATGAAG
1 CAATGATCCTAAACCAGGATTAAAATAAAG
*
3843 CAATGATCCTAAACTAGGATTAAAATAAAG
1 CAATGATCCTAAACCAGGATTAAAATAAAG
*
3873 CAAGGATCCTCAAA-CAGGATTAAAATAAAG
1 CAATGATCCT-AAACCAGGATTAAAATAAAG
3903 CAATGATCCTCAAA-CAGGATT-AAATAAAG
1 CAATGATCCT-AAACCAGGATTAAAATAAAG
3932 CAATGATCCTCAAA-CAGGATTAAAATAAAG
1 CAATGATCCT-AAACCAGGATTAAAATAAAG
*
3962 CAAAGATCCTCAAA-CAGGATTAAAATAAAG
1 CAATGATCCT-AAACCAGGATTAAAATAAAG
* *
3992 CAAAGATCCTCAAA-CATGATTAATAATAAAG
1 CAATGATCCT-AAACCAGGATTAA-AATAAAG
* * *
4023 CAATAATCCTCAACCAGGATTAAAACAAAG
1 CAATGATCCTAAACCAGGATTAAAATAAAG
* * *
4053 CAACGATCCT-CACACAGGATTAAAACAAAG
1 CAATGATCCTAAAC-CAGGATTAAAATAAAG
* *
4083 CAATGAAGCAAATATCCTTAACCAGGATTTAAATAAAG
1 CAAT---G-----ATCCTAAACCAGGATTAAAATAAAG
* ** *
4121 TAATGATCCTAAACCAGGATCGAAATGAAG
1 CAATGATCCTAAACCAGGATTAAAATAAAG
4151 CAATGAT
1 CAATGAT
4158 GCAATGATCC
Statistics
Matches: 301, Mismatches: 30, Indels: 28
0.84 0.08 0.08
Matches are distributed among these distances:
29 31 0.10
30 218 0.72
31 26 0.09
33 1 0.00
35 1 0.00
38 22 0.07
39 2 0.01
ACGTcount: A:0.49, C:0.18, G:0.14, T:0.20
Consensus pattern (30 bp):
CAATGATCCTAAACCAGGATTAAAATAAAG
Found at i:3862 original size:60 final size:59
Alignment explanation
Indices: 3783--4088 Score: 434
Period size: 60 Copynumber: 5.1 Consensus size: 59
3773 ACTGATGATA
* * *
3783 CAATGATCCTAAACCAGGATTAAAATAAAGCAATGATCCTCAACCAAGATTAAAATGAAG
1 CAATGATCCTAAA-CAGGATTAAAATAAAGCAATGATCCTCAAACAGGATTAAAATAAAG
*
3843 CAATGATCCTAAACTAGGATTAAAATAAAGCAAGGATCCTCAAACAGGATTAAAATAAAG
1 CAATGATCCTAAAC-AGGATTAAAATAAAGCAATGATCCTCAAACAGGATTAAAATAAAG
3903 CAATGATCCTCAAACAGGATT-AAATAAAGCAATGATCCTCAAACAGGATTAAAATAAAG
1 CAATGATCCT-AAACAGGATTAAAATAAAGCAATGATCCTCAAACAGGATTAAAATAAAG
* * *
3962 CAAAGATCCTCAAACAGGATTAAAATAAAGCAAAGATCCTCAAACATGATTAATAATAAAG
1 CAATGATCCT-AAACAGGATTAAAATAAAGCAATGATCCTCAAACAGGATTAA-AATAAAG
* * * * * *
4023 CAATAATCCTCAACCAGGATTAAAACAAAGCAACGATCCTCACACAGGATTAAAACAAAG
1 CAATGATCCT-AAACAGGATTAAAATAAAGCAATGATCCTCAAACAGGATTAAAATAAAG
4083 CAATGA
1 CAATGA
4089 AGCAAATATC
Statistics
Matches: 225, Mismatches: 17, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
59 58 0.26
60 110 0.49
61 57 0.25
ACGTcount: A:0.50, C:0.18, G:0.13, T:0.19
Consensus pattern (59 bp):
CAATGATCCTAAACAGGATTAAAATAAAGCAATGATCCTCAAACAGGATTAAAATAAAG
Found at i:3972 original size:89 final size:90
Alignment explanation
Indices: 3787--4088 Score: 448
Period size: 89 Copynumber: 3.4 Consensus size: 90
3777 ATGATACAAT
* *
3787 GATCCT-AAACCAGGATTAAAATAAAGCAATGATCCTCAACCAAGATTAAAATGAAGCAATGATC
1 GATCCTCAAA-CAGGATTAAAATAAAGCAATGATCCTCAAACAAGATTAAAATAAAGCAATGATC
*
3851 CT-AAACTAGGATTAAAATAAAGCAAG
65 CTCAAAC-AGGATTAAAATAAAGCAAA
*
3877 GATCCTCAAACAGGATTAAAATAAAGCAATGATCCTCAAACAGGATT-AAATAAAGCAATGATCC
1 GATCCTCAAACAGGATTAAAATAAAGCAATGATCCTCAAACAAGATTAAAATAAAGCAATGATCC
3941 TCAAACAGGATTAAAATAAAGCAAA
66 TCAAACAGGATTAAAATAAAGCAAA
* * *
3966 GATCCTCAAACAGGATTAAAATAAAGCAAAGATCCTCAAACATGATTAATAATAAAGCAATAATC
1 GATCCTCAAACAGGATTAAAATAAAGCAATGATCCTCAAACAAGATTAA-AATAAAGCAATGATC
* * *
4031 CTCAACCAGGATTAAAACAAAGCAAC
65 CTCAAACAGGATTAAAATAAAGCAAA
* *
4057 GATCCTCACACAGGATTAAAACAAAGCAATGA
1 GATCCTCAAACAGGATTAAAATAAAGCAATGA
4089 AGCAAATATC
Statistics
Matches: 195, Mismatches: 13, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
89 80 0.41
90 46 0.24
91 69 0.35
ACGTcount: A:0.50, C:0.18, G:0.13, T:0.19
Consensus pattern (90 bp):
GATCCTCAAACAGGATTAAAATAAAGCAATGATCCTCAAACAAGATTAAAATAAAGCAATGATCC
TCAAACAGGATTAAAATAAAGCAAA
Found at i:4168 original size:68 final size:67
Alignment explanation
Indices: 4020--4168 Score: 156
Period size: 68 Copynumber: 2.2 Consensus size: 67
4010 ATTAATAATA
* *
4020 AAGCAATAATCCTCAACCAGGATTAAAACAAAGCAACGATCCTCACACAGGATTAAAACAAAGCA
1 AAGCAAT-ATCCTCAACCAGGATTAAAACAAAGCAACGATCCTAACACAGGATCAAAACAAAGCA
4085 ATG
65 ATG
* * * * * * **
4088 AAGCAAATATCCTTAACCAGGATTTAAATAAAGTAATGATCCTAA-ACCAGGATCGAAATGAAGC
1 AAGC-AATATCCTCAACCAGGATTAAAACAAAGCAACGATCCTAACA-CAGGATCAAAACAAAGC
4152 AATG
64 AATG
*
4156 ATGCAATGATCCT
1 AAGCAAT-ATCCT
4169 ACCCGGATCG
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
67 4 0.06
68 60 0.90
69 3 0.04
ACGTcount: A:0.46, C:0.20, G:0.15, T:0.19
Consensus pattern (67 bp):
AAGCAATATCCTCAACCAGGATTAAAACAAAGCAACGATCCTAACACAGGATCAAAACAAAGCAA
TG
Found at i:4698 original size:31 final size:32
Alignment explanation
Indices: 4626--4696 Score: 79
Period size: 36 Copynumber: 2.1 Consensus size: 32
4616 TAAACTGAAG
* * *
4626 AAAAGATTGCCCTGGATCCATTGAAATAAATT
1 AAAAGATTGCCCTGAATCAACTGAAATAAATT
4658 AAAGAAAAGATTGCCCTGAATCAACTGAAATAAATT
1 ----AAAAGATTGCCCTGAATCAACTGAAATAAATT
4694 AAA
1 AAA
4697 GAAAGACCGC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
32 3 0.09
36 29 0.91
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.24
Consensus pattern (32 bp):
AAAAGATTGCCCTGAATCAACTGAAATAAATT
Found at i:4709 original size:35 final size:35
Alignment explanation
Indices: 4570--5192 Score: 508
Period size: 35 Copynumber: 18.0 Consensus size: 35
4560 CAATTTGCGG
* * *
4570 TCAACTGAAATAAACTGCAGAAAAGATCACCCTGGA
1 TCAACTGAAATAAACTGAAG-AAAGACCGCCCTGGA
* **
4606 TCAATTGAAATAAACTGAAGAAAAGATTGCCCTGGA
1 TCAACTGAAATAAACTGAAG-AAAGACCGCCCTGGA
* * * * ** *
4642 TCCATTGAAATAAATTAAAGAAAAGATTGCCCTGAA
1 TCAACTGAAATAAACTGAAG-AAAGACCGCCCTGGA
* * *
4678 TCAACTGAAATAAATTAAAGAAAGACCGCCCTGGG
1 TCAACTGAAATAAACTGAAGAAAGACCGCCCTGGA
* * * *
4713 GCAACTAAAATAAACTGAAGAAAGGATCGCCCTGGG
1 TCAACTGAAATAAACTGAAGAAA-GACCGCCCTGGA
* *
4749 TCCACTGAAATAAACTGAAGAAAGAGCGCCCTGGA
1 TCAACTGAAATAAACTGAAGAAAGACCGCCCTGGA
4784 TCAACTG------A-T---GAAAGACCGCCCT-GA
1 TCAACTGAAATAAACTGAAGAAAGACCGCCCTGGA
* * *
4808 GTCAACTGAAATAAACTAAAGAAAGGATCACCCTGGA
1 -TCAACTGAAATAAACTGAAGAAA-GACCGCCCTGGA
* * * *
4845 TCAACT-AGAGTGAATTGAAGAAAGACCGCCCTGGG
1 TCAACTGA-AATAAACTGAAGAAAGACCGCCCTGGA
*
4880 TCAACTGAAATAAACTGAAGAAAGACCGCCCTGGG
1 TCAACTGAAATAAACTGAAGAAAGACCGCCCTGGA
* *
4915 TCAACTGAAATAAACTAAAGAAAGGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAGAAA-GACCGCCCTGGA
* * * * *
4951 TCAACTGGAGTGAATTGAAGAAAGACCGCCCTGGG
1 TCAACTGAAATAAACTGAAGAAAGACCGCCCTGGA
* *
4986 TCAACTAAAATAAACTGAAGAACGACCGCCCTGGA
1 TCAACTGAAATAAACTGAAGAAAGACCGCCCTGGA
* * * *
5021 TTAACTGAAATAAACTGGAGAAAGACAGCCCTGGG
1 TCAACTGAAATAAACTGAAGAAAGACCGCCCTGGA
* *
5056 TCAA--G---TAAGCTGAAGAAAAGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAG-AAAGACCGCCCTGGA
* * * * * * *
5087 TCCATTAAAATGAATTGAAGAAGGACCGCCCTGGG
1 TCAACTGAAATAAACTGAAGAAAGACCGCCCTGGA
* *
5122 TCAACTGAAATAAACTGAAATAAAGATCGCCCTGGA
1 TCAACTGAAATAAACTG-AAGAAAGACCGCCCTGGA
* * * *
5158 TCAACTGAAGTAAA-TGAGGAAAGATCACCCTGGA
1 TCAACTGAAATAAACTGAAGAAAGACCGCCCTGGA
5192 T
1 T
5193 GACTCTCAAA
Statistics
Matches: 475, Mismatches: 88, Indels: 50
0.77 0.14 0.08
Matches are distributed among these distances:
24 2 0.00
25 19 0.04
28 1 0.00
29 1 0.00
30 8 0.02
31 16 0.03
32 1 0.00
33 1 0.00
34 16 0.03
35 208 0.44
36 200 0.42
37 2 0.00
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.17
Consensus pattern (35 bp):
TCAACTGAAATAAACTGAAGAAAGACCGCCCTGGA
Found at i:4745 original size:71 final size:71
Alignment explanation
Indices: 4568--5190 Score: 561
Period size: 71 Copynumber: 9.0 Consensus size: 71
4558 ACCAATTTGC
* * * *
4568 GGTCAACTGAAATAAACTGCAGAAAAGATCACCCTGGATCAATTGAAATAAACTGAAGAAAAGAT
1 GGTCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAG-AAAGAC
*
4633 TGCCCTG
65 CGCCCTG
* * * * * * * * *
4640 GATCCATTGAAATAAATTAAAGAAAAGATTGCCCTGAATCAACTGAAATAAATTAAAGAAAGACC
1 GGTCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGACC
4705 GCCCTG
66 GCCCTG
* * * * * *
4711 GGGCAACTAAAATAAACTGAAGAAAGGATCGCCCTGGGTCCACTGAAATAAACTGAAGAAAGAGC
1 GGTCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGACC
4776 GCCCTG
66 GCCCTG
* * *
4782 GATCAACTG------A-T---G-AAAGACCGCCCT-GAGTCAACTGAAATAAACTAAAGAAAGGA
1 GGTCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA-TCAACTGAAATAAACTGAAGAAA-GA
* *
4835 TCACCCTG
64 CCGCCCTG
* * * * * *
4843 GATCAACT-AGAGTGAATTGAAG-AAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAAGAC
1 GGTCAACTGA-AATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGAC
4906 CGCCCTG
65 CGCCCTG
* * * * * *
4913 GGTCAACTGAAATAAACTAAAGAAAGGATCGCCCTGGATCAACTGGAGTGAATTGAAGAAAGACC
1 GGTCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGACC
4978 GCCCTG
66 GCCCTG
* * * * * *
4984 GGTCAACTAAAATAAACTGAAG-AACGACCGCCCTGGATTAACTGAAATAAACTGGAGAAAGACA
1 GGTCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGACC
5048 GCCCTG
66 GCCCTG
* * * * * * *
5054 GGTCAA--G---TAAGCTGAAGAAAAGATCGCCCTGGATCCATTAAAATGAATTGAAGAAGGACC
1 GGTCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGACC
5114 GCCCTG
66 GCCCTG
* * *
5120 GGTCAACTGAAATAAACTGAA-ATAAAGATCGCCCTGGATCAACTGAAGTAAA-TGAGGAAAGAT
1 GGTCAACTGAAATAAACTGAAGA-AAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGAC
*
5183 CACCCTG
65 CGCCCTG
5190 G
1 G
5191 ATGACTCTCA
Statistics
Matches: 439, Mismatches: 89, Indels: 48
0.76 0.15 0.08
Matches are distributed among these distances:
59 1 0.00
60 31 0.07
61 17 0.04
64 1 0.00
65 10 0.02
66 43 0.10
67 1 0.00
68 2 0.00
70 84 0.19
71 202 0.46
72 47 0.11
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.17
Consensus pattern (71 bp):
GGTCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGACC
GCCCTG
Found at i:4796 original size:25 final size:25
Alignment explanation
Indices: 4761--4817 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
4751 CACTGAAATA
*
4761 AACTGAAGAAAGAGCGCCCTG-GATC
1 AACTGAAGAAAGACCGCCCTGAG-TC
*
4786 AACTGATGAAAGACCGCCCTGAGTC
1 AACTGAAGAAAGACCGCCCTGAGTC
4811 AACTGAA
1 AACTGAA
4818 ATAAACTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 27 0.96
26 1 0.04
ACGTcount: A:0.37, C:0.25, G:0.25, T:0.14
Consensus pattern (25 bp):
AACTGAAGAAAGACCGCCCTGAGTC
Found at i:4897 original size:131 final size:131
Alignment explanation
Indices: 4670--5192 Score: 392
Period size: 131 Copynumber: 3.9 Consensus size: 131
4660 AGAAAAGATT
* * *
4670 GCCCTGAATCAACTGAAATAAATTAAAGAAAGACCGCCCTGGGGCAACTAAAATAAACTGAAGAA
1 GCCCTGAATCAACTGAAATAAACTAAAGAAAGACCACCCTGGAGCAACTAAAATAAACTGAAGAA
* * *
4735 AGGATCGCCCTGGGTCCACTGAAATAAACTGAAGAAAGAGCGCCCTGGATCAACTGATGAAAGAC
66 AGGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGATCAACTGATGAAAGAC
4800 C
131 C
* * * * * * *
4801 GCCCTGAGTCAACTGAAATAAACTAAAGAAAGGATCACCCTGGATCAACTAGAGTGAATTGAAGA
1 GCCCTGAATCAACTGAAATAAACTAAAGAAA-GACCACCCTGGAGCAACTAAAATAAACTGAAGA
*
4866 AA-GACCGCCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAAC
65 AAGGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGATCAACTG------A-
*
4930 TAAAGAAAGGATC
123 T---GAAA-GACC
* * * * * * *
4943 GCCCTGGATCAACTGGAGTGAATTGAAGAAAGACCGCCCTGG-GTCAACTAAAATAAACTGAAG-
1 GCCCTGAATCAACTGAAATAAACTAAAGAAAGACCACCCTGGAG-CAACTAAAATAAACTGAAGA
* * * * * * *
5006 AACGACCGCCCTGGATTAACTGAAATAAACTGGAGAAAGACAGCCCTGGGTCAAGTAAGCTGAAG
65 AAGGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGATC----AA-CTGATG
*
5071 AAAAGATC
125 -AAAGACC
* * * * * * * * * *
5079 GCCCTGGATCCATTAAAATGAATTGAAGAAGGACCGCCCTGG-GTCAACTGAAATAAACTGAA-A
1 GCCCTGAATCAACTGAAATAAACTAAAGAAAGACCACCCTGGAG-CAACTAAAATAAACTGAAGA
* * * * * * *
5142 TAAAGATCGCCCTGGATCAACTGAAGTAAA-TGAGGAAAGATCACCCTGGAT
65 -AAGGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGAT
5193 GACTCTCAAA
Statistics
Matches: 319, Mismatches: 51, Indels: 39
0.78 0.12 0.10
Matches are distributed among these distances:
131 79 0.25
132 27 0.08
136 75 0.24
137 29 0.09
138 1 0.00
140 3 0.01
141 73 0.23
142 27 0.08
145 2 0.01
146 3 0.01
ACGTcount: A:0.40, C:0.21, G:0.23, T:0.17
Consensus pattern (131 bp):
GCCCTGAATCAACTGAAATAAACTAAAGAAAGACCACCCTGGAGCAACTAAAATAAACTGAAGAA
AGGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGATCAACTGATGAAAGAC
C
Found at i:4923 original size:106 final size:105
Alignment explanation
Indices: 4786--5163 Score: 480
Period size: 106 Copynumber: 3.6 Consensus size: 105
4776 GCCCTGGATC
* *
4786 AACTGATGAAAGACCGCCCTGAGTCAACTGAAATAAACTAAAGAAAGGATCACCCTGGATCAACT
1 AACTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTAAAGAAA-GATCACCCTGGATCAACT
*
4851 AGAGTGAATTGAAGAAAGACCGCCCTGGGTCAACTGAAATA
65 AGAGTGAATTGAAGAAAGACCGCCCTGGGTCAACTAAAATA
*
4892 AACTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTAAAGAAAGGATCGCCCTGGATCAACT
1 AACTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTAAAGAAA-GATCACCCTGGATCAACT
*
4957 GGAGTGAATTGAAGAAAGACCGCCCTGGGTCAACTAAAATA
65 AGAGTGAATTGAAGAAAGACCGCCCTGGGTCAACTAAAATA
* * * ** * *
4998 AACTGAAGAACGACCGCCCTGGATTAACTGAAATAAACTGGAGAAAGA-CAGCCCTGGGTCAAGT
1 AACTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTAAAGAAAGATCA-CCCTGGATCAACT
* * * * *
5062 A-AGCTGAA--G-A-AAAGATCGCCCTGGATCCATTAAAATG
65 AGAG-TGAATTGAAGAAAGACCGCCCTGGGTCAACTAAAATA
* * * *
5099 AATTGAAGAAGGACCGCCCTGGGTCAACTGAAATAAACTGAAATAAAGATCGCCCTGGATCAACT
1 AACTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACT-AAAGAAAGATCACCCTGGATCAACT
5164 GAAGTAAATG
Statistics
Matches: 239, Mismatches: 29, Indels: 12
0.85 0.10 0.04
Matches are distributed among these distances:
101 57 0.24
102 18 0.08
103 2 0.01
104 3 0.01
105 17 0.07
106 142 0.59
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.17
Consensus pattern (105 bp):
AACTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTAAAGAAAGATCACCCTGGATCAACTA
GAGTGAATTGAAGAAAGACCGCCCTGGGTCAACTAAAATA
Found at i:5250 original size:31 final size:30
Alignment explanation
Indices: 5197--5312 Score: 153
Period size: 30 Copynumber: 3.8 Consensus size: 30
5187 CTGGATGACT
*
5197 CTCAAACAGGATTAAAATAAAGCAAAGATC
1 CTCAAACAGGATTAAAACAAAGCAAAGATC
* *
5227 CTCAAACATGATTAATAATAAAGCAATA-ATC
1 CTCAAACAGGATTAA-AACAAAGCAA-AGATC
* *
5258 CTCAACCAGGATTAAAACAAAGCAACGATC
1 CTCAAACAGGATTAAAACAAAGCAAAGATC
*
5288 CTCACACAGGATTAAAACAAAGCAA
1 CTCAAACAGGATTAAAACAAAGCAA
5313 TGAAGCAAAT
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
30 49 0.64
31 26 0.34
32 1 0.01
ACGTcount: A:0.51, C:0.21, G:0.11, T:0.17
Consensus pattern (30 bp):
CTCAAACAGGATTAAAACAAAGCAAAGATC
Found at i:5301 original size:61 final size:60
Alignment explanation
Indices: 5197--5313 Score: 171
Period size: 61 Copynumber: 1.9 Consensus size: 60
5187 CTGGATGACT
* * *
5197 CTCAAACAGGATTAAAATAAAGCAAAGATCCTCAAACATGATTAATAATAAAGCAATAATC
1 CTCAAACAGGATTAAAACAAAGCAAAGATCCTCAAACAGGATTAA-AACAAAGCAATAATC
* * *
5258 CTCAACCAGGATTAAAACAAAGCAACGATCCTCACACAGGATTAAAACAAAGCAAT
1 CTCAAACAGGATTAAAACAAAGCAAAGATCCTCAAACAGGATTAAAACAAAGCAAT
5314 GAAGCAAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
60 10 0.20
61 40 0.80
ACGTcount: A:0.50, C:0.21, G:0.11, T:0.18
Consensus pattern (60 bp):
CTCAAACAGGATTAAAACAAAGCAAAGATCCTCAAACAGGATTAAAACAAAGCAATAATC
Found at i:5383 original size:30 final size:30
Alignment explanation
Indices: 5311--5384 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
5301 AAAACAAAGC
* **
5311 AATGAAGCAAAT-ATCCTTAACCAGGATTTA
1 AATGAAG-AAATGATCCTAAACCAGGATCGA
* *
5341 AATAAAGTAATGATCCTAAACCAGGATCGA
1 AATGAAGAAATGATCCTAAACCAGGATCGA
5371 AATGAAGAAATGAT
1 AATGAAGAAATGAT
5385 GCAATGATCC
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 3 0.08
30 33 0.92
ACGTcount: A:0.47, C:0.14, G:0.16, T:0.23
Consensus pattern (30 bp):
AATGAAGAAATGATCCTAAACCAGGATCGA
Done.