Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005959.1 Hibiscus syriacus cultivar Beakdansim tig00014003_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: 62975
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4515 original size:14 final size:15
Alignment explanation
Indices: 4467--4515 Score: 50
Period size: 14 Copynumber: 3.3 Consensus size: 15
4457 TTCTTATTAA
4467 ATATTAAATTATAACT
1 ATATTAAATTATAA-T
4483 A-A-TAAATATATAAT
1 ATATTAAAT-TATAAT
4497 AATATTAAATTA-AAT
1 -ATATTAAATTATAAT
4512 ATAT
1 ATAT
4516 ATACTTATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
14 10 0.34
15 10 0.34
16 4 0.14
17 5 0.17
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (15 bp):
ATATTAAATTATAAT
Found at i:4863 original size:62 final size:60
Alignment explanation
Indices: 4797--5073 Score: 196
Period size: 62 Copynumber: 4.5 Consensus size: 60
4787 CATATTCGCA
*
4797 TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAA-TT-CG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTT--CGTTGCGA--TAGTCCAAGTTCCG
* *
4859 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTTC-AAGTTCGTTGCGATAGTCGAAGTTCACG
1 TTGCGATAGTCCAAGTTCGCGTTGCGA--TA-GTCGAAGTTCGTTGCGATAGTCCAAGTTC-CG
* * * *
4922 TTGCGATTTATTCCAA-TT--CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCG
1 TTGCGA--TAGTCCAAGTTCGCGTTGCGA--TAGTCGAAGTTCGTTGCGATAGTCCAAGTTC-CG
* * * * * *
4984 TTGCAATTTATTCTAAGTT--CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT-T
1 TTGCGA--TAGTCCAAGTTCGCGTTGCGATAGTCGAAGTT--CGTTGCGA--TAGTCCAAGTTCC
5046 G
60 G
5047 TTGCGATAGTCCAA-TTCGCGTTGCGAT
1 TTGCGATAGTCCAAGTTCGCGTTGCGAT
5074 TTATTCCAAG
Statistics
Matches: 181, Mismatches: 18, Indels: 32
0.78 0.08 0.14
Matches are distributed among these distances:
60 8 0.04
61 19 0.10
62 95 0.52
63 32 0.18
64 9 0.05
65 18 0.10
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (60 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGTTGCGATAGTCCAAGTTCCG
Found at i:4917 original size:42 final size:41
Alignment explanation
Indices: 4816--4948 Score: 230
Period size: 41 Copynumber: 3.2 Consensus size: 41
4806 TCCAAGTTCG
4816 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAATT
* *
4857 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTTCAAGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAA-TT
*
4899 CGTTGCGATAGTCGAAGTTCACGTTGCGATTTATTCCAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAATT
4940 CGTTGCGAT
1 CGTTGCGAT
4949 TTATTCCAAA
Statistics
Matches: 86, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
41 48 0.56
42 38 0.44
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.37
Consensus pattern (41 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAATT
Found at i:4961 original size:104 final size:103
Alignment explanation
Indices: 4797--5089 Score: 389
Period size: 104 Copynumber: 2.8 Consensus size: 103
4787 CATATTCGCA
* * *
4797 TTGCGATAGTCCAAGTTCGCGTTGCGA--TAGTCGAAGTTCGCGTTGCGATTTATTCCAATTCGT
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAA-TT--CGTTGCGATTTATTCCAATTCGT
*
4860 TGCGATAGTCCAAGTTCGCGTTGCGATTTATT-TCAAGTTCG
63 TGCGATAGTCCAAGTTCGCGTTGCAATTTATTCT-AAGTTCG
*
4901 TTGCGATAGTCGAAGTTCACGTTGCGATTTATTCCAATTCGTTGCGATTTATTCCAAATTCGTTG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAATTCGTTGCGATTTATTCC-AATTCGTTG
4966 CGATAGTCCAAGTTCGCGTTGCAATTTATTCTAAGTTCG
65 CGATAGTCCAAGTTCGCGTTGCAATTTATTCTAAGTTCG
* *
5005 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTTGTTGCGA--TAGTCCAATTCGCGT
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCC-AATTCGTTGCGATTTATTCCAATT--CGT
*
5068 TGCGATTTATTCCAAGTTCGCG
63 TGCGA--TAGTCCAAGTTCGCG
5090 ATAATCCCAA
Statistics
Matches: 171, Mismatches: 9, Indels: 16
0.87 0.05 0.08
Matches are distributed among these distances:
102 4 0.02
103 21 0.12
104 112 0.65
105 14 0.08
106 20 0.12
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (103 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAATTCGTTGCGATTTATTCCAATTCGTTGC
GATAGTCCAAGTTCGCGTTGCAATTTATTCTAAGTTCG
Found at i:4965 original size:83 final size:82
Alignment explanation
Indices: 4816--4969 Score: 247
Period size: 83 Copynumber: 1.9 Consensus size: 82
4806 TCCAAGTTCG
* *
4816 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAATTCGTTGCGATAGTCCAAGTTCGCGT
1 CGTTGCGATAGTCGAAGTTCACGTTGCGATTTATTCCAATTCGTTGCGATAGTCCAAATTC-CGT
4881 TGCGATTTATTTCAAGTT
65 TGCGATTTATTTCAAGTT
*
4899 CGTTGCGATAGTCGAAGTTCACGTTGCGATTTATTCCAATTCGTTGCGATTTATTCCAAATT-CG
1 CGTTGCGATAGTCGAAGTTCACGTTGCGATTTATTCCAATTCGTTGCGA--TAGTCCAAATTCCG
4963 TTGCGAT
64 TTGCGAT
4970 AGTCCAAGTT
Statistics
Matches: 66, Mismatches: 3, Indels: 4
0.90 0.04 0.05
Matches are distributed among these distances:
83 57 0.86
85 9 0.14
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (82 bp):
CGTTGCGATAGTCGAAGTTCACGTTGCGATTTATTCCAATTCGTTGCGATAGTCCAAATTCCGTT
GCGATTTATTTCAAGTT
Found at i:4993 original size:42 final size:42
Alignment explanation
Indices: 4940--5087 Score: 235
Period size: 42 Copynumber: 3.5 Consensus size: 42
4930 TATTCCAATT
4940 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCG
* * * *
4982 CGTTGCAATTTATTCTAAGTTCGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCG
*
5024 CGTTGCGATTTATTCCAAATTTGTTGCGATAGTCCAA-TTCG
1 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCG
*
5065 CGTTGCGATTTATTCCAAGTTCG
1 CGTTGCGATTTATTCCAAATTCG
5088 CGATAATCCC
Statistics
Matches: 95, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
41 25 0.26
42 70 0.74
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.38
Consensus pattern (42 bp):
CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCG
Found at i:5199 original size:6 final size:6
Alignment explanation
Indices: 5183--5217 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
5173 AGACACGATT
5183 ACCAC- ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
5218 GGACGGCGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.34, C:0.51, G:0.14, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:5831 original size:21 final size:21
Alignment explanation
Indices: 5805--5937 Score: 166
Period size: 21 Copynumber: 6.4 Consensus size: 21
5795 ATTTTGGACT
5805 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* *
5826 ATCGCAACGAACTTGGACT--
1 ATCGCAACGAATTTGGAATAA
5845 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * * *
5866 ATCGTAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTGGAATAA
5887 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
5908 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
5929 ATCGCAACG
1 ATCGCAACG
5938 CGAACTTCGA
Statistics
Matches: 94, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
19 26 0.28
21 59 0.63
23 9 0.10
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:5923 original size:63 final size:61
Alignment explanation
Indices: 5826--5977 Score: 232
Period size: 63 Copynumber: 2.4 Consensus size: 61
5816 TTTGGAATAA
* *
5826 ATCGCAACGAACTTGGACTATCGCAACGAATTTGGAATAAATCGTAACGCGAACTTCGACT
1 ATCGCAACGAACTTGGAATATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
*
5887 ATCGCAACGAATTTGGAATAAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAACTTGGAAT--ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
*
5950 ATCGCAACGCGAACTTGGACTATCGCAA
1 ATCGCAA--CGAACTTGGAATATCGCAA
5978 TGCGAATATG
Statistics
Matches: 82, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
61 17 0.21
63 55 0.67
65 10 0.12
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.22
Consensus pattern (61 bp):
ATCGCAACGAACTTGGAATATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
Found at i:5933 original size:42 final size:40
Alignment explanation
Indices: 5798--5977 Score: 211
Period size: 42 Copynumber: 4.3 Consensus size: 40
5788 CGTTGCGATT
5798 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGAAC
*
5838 TTGGACTATCGCAACGAATTTGGAATAAATCGTAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAA--CGAAC
* *
5880 TTCGACTATCGCAACGAATTTGGAATAAATCGCAACGAAT
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGAAC
* * * *
5920 TTGGAATAAATCGCAACGCGAACTTCGACT--ATCGCAACGCGAAC
1 TTGGACT--ATCGCAA--CGAATTTGGAATAAATCGCAA--CGAAC
5964 TTGGACTATCGCAA
1 TTGGACTATCGCAA
5978 TGCGAATATG
Statistics
Matches: 121, Mismatches: 11, Indels: 14
0.83 0.08 0.10
Matches are distributed among these distances:
40 43 0.36
42 59 0.49
44 19 0.16
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.23
Consensus pattern (40 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGAAC
Found at i:5953 original size:21 final size:21
Alignment explanation
Indices: 5929--5983 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
5919 TTTGGAATAA
5929 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
*
5950 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
*
5971 ATCGCAATGCGAA
1 ATCGCAACGCGAA
5984 TATGTAAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.18
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:7088 original size:24 final size:24
Alignment explanation
Indices: 7025--7088 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 24
7015 TGAATATAAT
* *
7025 AATATTTTATATTAT-AT-TTATA
1 AATATTTTATATTTTAATAATATA
* *
7047 ACTATTTT-TATTTAAATAATATA
1 AATATTTTATATTTTAATAATATA
7070 AATATTTTATATTTTAATA
1 AATATTTTATATTTTAATA
7089 GTGAGATTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
21 4 0.12
22 9 0.27
23 11 0.33
24 9 0.27
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
AATATTTTATATTTTAATAATATA
Found at i:7845 original size:16 final size:17
Alignment explanation
Indices: 7824--7865 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
7814 TGATTATATA
7824 TATATATATAATATT-T
1 TATATATATAATATTAT
* *
7840 TATATATTTTATATTAAT
1 TATATATATAATATT-AT
7858 TATATATA
1 TATATATA
7866 ATACAAACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 13 0.62
18 8 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TATATATATAATATTAT
Found at i:7863 original size:20 final size:20
Alignment explanation
Indices: 7816--7865 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
7806 CTCCGCCTTG
7816 ATTATATATATATATATAAT
1 ATTATATATATATATATAAT
* * *
7836 ATTTTATATAT-TTTATATT
1 ATTATATATATATATATAAT
7855 AATTATATATA
1 -ATTATATATA
7866 ATACAAACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 6 0.24
20 19 0.76
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTATATATATATATATAAT
Found at i:11893 original size:64 final size:64
Alignment explanation
Indices: 11787--11920 Score: 214
Period size: 64 Copynumber: 2.1 Consensus size: 64
11777 ATATTCAGGT
* * *
11787 GGCAAAATCCAAATCGGTAGAAAAGGGTTATGGACCAAATTGAATGAAAGGGCTTAATTAAGGA
1 GGCAAAATCCAAATCGGTAAAAAAGAGTTATGGACCAAATTGAATGAAAGGGATTAATTAAGGA
* * *
11851 GGCAGAATCCAAATTGGTAAAAAAGAGTTATGGACCAAATTGAATGAAAGGGATTAATTCAGGA
1 GGCAAAATCCAAATCGGTAAAAAAGAGTTATGGACCAAATTGAATGAAAGGGATTAATTAAGGA
11915 GGCAAA
1 GGCAAA
11921 TAAGGTTTAT
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.43, C:0.10, G:0.26, T:0.20
Consensus pattern (64 bp):
GGCAAAATCCAAATCGGTAAAAAAGAGTTATGGACCAAATTGAATGAAAGGGATTAATTAAGGA
Found at i:12753 original size:4 final size:4
Alignment explanation
Indices: 12734--12779 Score: 67
Period size: 4 Copynumber: 11.8 Consensus size: 4
12724 TTGTTTGTTC
* *
12734 ATTT ATTC ATTC ATTT ATTT A-TT ATTT ATTT ATTT ATTT ATTT ATT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATT
12780 ACTGTAGTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 3 0.08
4 36 0.92
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (4 bp):
ATTT
Found at i:12768 original size:19 final size:19
Alignment explanation
Indices: 12736--12775 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
12726 GTTTGTTCAT
12736 TTATTCATTCATTTATTTA
1 TTATTCATTCATTTATTTA
* *
12755 TTATTTATTTATTTATTTA
1 TTATTCATTCATTTATTTA
12774 TT
1 TT
12776 TATTACTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (19 bp):
TTATTCATTCATTTATTTA
Found at i:12772 original size:23 final size:23
Alignment explanation
Indices: 12734--12780 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
12724 TTGTTTGTTC
12734 ATTTATTCATTCATTTATTTATT
1 ATTTATTCATTCATTTATTTATT
* *
12757 ATTTATTTATTTATTTATTTATT
1 ATTTATTCATTCATTTATTTATT
12780 A
1 A
12781 CTGTAGTGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (23 bp):
ATTTATTCATTCATTTATTTATT
Found at i:20965 original size:21 final size:22
Alignment explanation
Indices: 20927--20981 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
20917 TCCTGTAAGG
*
20927 AAAGGGATCAAT-TCTTTTGCT
1 AAAGGGATCGATCTCTTTTGCT
* *
20948 CAAGGGATCGATCT-TTTTGGT
1 AAAGGGATCGATCTCTTTTGCT
20969 AAAGGGATCGATC
1 AAAGGGATCGATC
20982 CCAAACTCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (22 bp):
AAAGGGATCGATCTCTTTTGCT
Found at i:21045 original size:21 final size:21
Alignment explanation
Indices: 21002--21078 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
20992 TGGAATCCAA
* * *
21002 GGGATCAATCCTTT-TTAAAG
1 GGGATCTATCCTTTGGTCAAG
21022 GGGATCTATCCTTTGGTCAAG
1 GGGATCTATCCTTTGGTCAAG
*
21043 GGGATCTATCCTTTGGTCAAA
1 GGGATCTATCCTTTGGTCAAG
*
21064 GGGATCGATCCTTTG
1 GGGATCTATCCTTTG
21079 AGCTAAAAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 13 0.25
21 38 0.75
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (21 bp):
GGGATCTATCCTTTGGTCAAG
Found at i:21553 original size:25 final size:25
Alignment explanation
Indices: 21525--21592 Score: 64
Period size: 25 Copynumber: 2.6 Consensus size: 25
21515 ATCGATAAGC
*
21525 ATATTAAAGTGTCAAAAGCATAAAT
1 ATATTAAAGTATCAAAAGCATAAAT
* * * *
21550 ATATCAAAATATCAAATGCATATAT
1 ATATTAAAGTATCAAAAGCATAAAT
21575 ATAAGTTAAAGTACTCAA
1 AT-A-TTAAAGTA-TCAA
21593 CAAGATACTC
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
25 22 0.67
26 1 0.03
27 6 0.18
28 4 0.12
ACGTcount: A:0.51, C:0.10, G:0.09, T:0.29
Consensus pattern (25 bp):
ATATTAAAGTATCAAAAGCATAAAT
Found at i:23037 original size:23 final size:21
Alignment explanation
Indices: 23011--23054 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
23001 CCAAAAATAA
23011 CATTTAACGCACAAGGGATCGAT
1 CATTTAACG-A-AAGGGATCGAT
* *
23034 CATTTGATGAAAGGGATCGAT
1 CATTTAACGAAAGGGATCGAT
23055 TTTTTTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 11 0.58
22 1 0.05
23 7 0.37
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (21 bp):
CATTTAACGAAAGGGATCGAT
Found at i:23264 original size:21 final size:21
Alignment explanation
Indices: 23237--23297 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
23227 CGATATTTTT
23237 TAAGGGGATCGATCCTTTGG-
1 TAAGGGGATCGATCCTTTGGC
* * *
23257 TCAAGGGGGTCGAACCTTTTGC
1 T-AAGGGGATCGATCCTTTGGC
* *
23279 TAAGGGGATTGATCTTTTG
1 TAAGGGGATCGATCCTTTG
23298 AGCAAAAAAT
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.20, C:0.15, G:0.33, T:0.33
Consensus pattern (21 bp):
TAAGGGGATCGATCCTTTGGC
Found at i:27189 original size:33 final size:33
Alignment explanation
Indices: 27147--27250 Score: 174
Period size: 33 Copynumber: 3.2 Consensus size: 33
27137 TTCGTTTCAA
27147 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
*
27180 TTATCGAACTTGTAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* *
27213 TTATCGAACTTGGAAGTATTTAAGTATTTCAA-
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
27245 TTATCG
1 TTATCG
27251 TAAACTTTGT
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 6 0.09
33 61 0.91
ACGTcount: A:0.31, C:0.08, G:0.16, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:28309 original size:16 final size:16
Alignment explanation
Indices: 28288--28341 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
28278 TACTTATTTT
28288 ATAATAAAATATATTA
1 ATAATAAAATATATTA
*
28304 ATAATAACATATATT-
1 ATAATAAAATATATTA
*
28319 ATAA-AATAATATAATA
1 ATAATAA-AATATATTA
28335 AT-ATAAA
1 ATAATAAA
28342 TTATTTGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
14 2 0.06
15 12 0.38
16 18 0.56
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAATAAAATATATTA
Found at i:28346 original size:28 final size:27
Alignment explanation
Indices: 28286--28346 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
28276 CTTACTTATT
* *
28286 TTATAATAAAATATATTAATAATAACA
1 TTATTATAAAATATATTAATAATAAAA
28313 TATATTATAAAATA-ATATAATAATATAAA
1 T-TATTATAAAATATAT-TAATAATA-AAA
28342 TTATT
1 TTATT
28347 TGAAATGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
27 3 0.10
28 23 0.79
29 3 0.10
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (27 bp):
TTATTATAAAATATATTAATAATAAAA
Found at i:28585 original size:16 final size:16
Alignment explanation
Indices: 28566--28600 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
28556 ACCCAAATCA
28566 AAAGCAACCCGAACCG
1 AAAGCAACCCGAACCG
* *
28582 AAAGCAATCCGAACTG
1 AAAGCAACCCGAACCG
28598 AAA
1 AAA
28601 TTAACCATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.49, C:0.29, G:0.17, T:0.06
Consensus pattern (16 bp):
AAAGCAACCCGAACCG
Found at i:29418 original size:32 final size:31
Alignment explanation
Indices: 29340--29418 Score: 79
Period size: 32 Copynumber: 2.5 Consensus size: 31
29330 ACCTAAATCG
* * *
29340 AAAATCAATCGATCTGATATTGACCCAACCA
1 AAAATCAATCGATCCGATATTAAACCAACCA
* *
29371 TAAATCTAA-CAGATCCGATATTAAATCAATCCA
1 AAAATC-AATC-GATCCGATATTAAACCAA-CCA
29404 AAAATCAATCGATCC
1 AAAATCAATCGATCC
29419 AGTATTGACC
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
31 6 0.16
32 23 0.61
33 9 0.24
ACGTcount: A:0.44, C:0.24, G:0.08, T:0.24
Consensus pattern (31 bp):
AAAATCAATCGATCCGATATTAAACCAACCA
Found at i:29469 original size:32 final size:32
Alignment explanation
Indices: 29433--29497 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 32
29423 TTGACCCGAC
*
29433 CTGATATTGATCTG-ATCCAAAAATTAATCGAT
1 CTGATATTGATCCGAATCCAAAAA-TAATCGAT
*
29465 CTGATATTGATCCGAATCGAAAAATAATCGAT
1 CTGATATTGATCCGAATCCAAAAATAATCGAT
29497 C
1 C
29498 CAATAATCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 22 0.73
33 8 0.27
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (32 bp):
CTGATATTGATCCGAATCCAAAAATAATCGAT
Found at i:30550 original size:29 final size:29
Alignment explanation
Indices: 30473--30551 Score: 113
Period size: 29 Copynumber: 2.7 Consensus size: 29
30463 AACCCAACCA
* * *
30473 TAGGTCGCCATGCACTCCCAGCGACCTCC
1 TAGGTCGCCATGCACGCCCGGCGACATCC
**
30502 TAGGTCGCCATGCACGCCCGGCGACATGG
1 TAGGTCGCCATGCACGCCCGGCGACATCC
30531 TAGGTCGCCATGCACGCCCGG
1 TAGGTCGCCATGCACGCCCGG
30552 ACTCCCCAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.16, C:0.39, G:0.29, T:0.15
Consensus pattern (29 bp):
TAGGTCGCCATGCACGCCCGGCGACATCC
Found at i:30722 original size:46 final size:46
Alignment explanation
Indices: 30655--30746 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
30645 GCATGAACCG
30655 ATCCTTGGTCGCTCCGAGTGCCCCATGCATGAACCGATCCTTGGTC
1 ATCCTTGGTCGCTCCGAGTGCCCCATGCATGAACCGATCCTTGGTC
*
30701 ATCCTTGGTCGC-CTCGAGTGCCCCATGCATGAACTGATCCTTGGTC
1 ATCCTTGGTCGCTC-CGAGTGCCCCATGCATGAACCGATCCTTGGTC
30747 GCCCCGAGTG
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
45 1 0.02
46 43 0.98
ACGTcount: A:0.15, C:0.34, G:0.24, T:0.27
Consensus pattern (46 bp):
ATCCTTGGTCGCTCCGAGTGCCCCATGCATGAACCGATCCTTGGTC
Found at i:30825 original size:29 final size:29
Alignment explanation
Indices: 30792--30858 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
30782 CATGCATGAA
30792 TCCTTGGTCGCCCCGAGTGCATGGCGACC
1 TCCTTGGTCGCCCCGAGTGCATGGCGACC
**** *
30821 TCCTTGGTCGTTGGGCGTGCATGGCGACC
1 TCCTTGGTCGCCCCGAGTGCATGGCGACC
*
30850 TCTTTGGTC
1 TCCTTGGTC
30859 ACTGTACAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.07, C:0.31, G:0.33, T:0.28
Consensus pattern (29 bp):
TCCTTGGTCGCCCCGAGTGCATGGCGACC
Found at i:33634 original size:16 final size:17
Alignment explanation
Indices: 33610--33642 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
33600 TAAAGTTTCC
*
33610 CTTCTGTTTTT-TTATT
1 CTTCAGTTTTTCTTATT
33626 CTTCAGTTTTTCTTATT
1 CTTCAGTTTTTCTTATT
33643 TGATATCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.09, C:0.15, G:0.06, T:0.70
Consensus pattern (17 bp):
CTTCAGTTTTTCTTATT
Found at i:40548 original size:2 final size:2
Alignment explanation
Indices: 40541--40586 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
40531 ATGGTAAGTT
40541 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40583 TA TA
1 TA TA
40587 GTTCAGTGGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:44510 original size:13 final size:13
Alignment explanation
Indices: 44494--44518 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44484 ATTATTTTTT
44494 TATATTATTTAAA
1 TATATTATTTAAA
44507 TATATTATTTAA
1 TATATTATTTAA
44519 TTATTAAAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TATATTATTTAAA
Found at i:44521 original size:21 final size:21
Alignment explanation
Indices: 44492--44639 Score: 63
Period size: 21 Copynumber: 7.0 Consensus size: 21
44482 TTATTATTTT
44492 TTTATATTATTTAAATATATTA
1 TTTA-ATTATTTAAATATATTA
* * *
44514 TTTAATTATTAAAACATATAA
1 TTTAATTATTTAAATATATTA
*** *
44535 CAAAAATATTTTAAATTATATTA
1 TTTAATTA-TTTAAA-TATATTA
** * *
44558 TTTTAACAATTCAAAATATAATA
1 -TTTAATTATT-TAAATATATTA
*
44581 ATTAATTA--TAAATATATTA
1 TTTAATTATTTAAATATATTA
* *
44600 TTATAA-TATATATATATATATA
1 TT-TAATTATTTAAATATAT-TA
*
44622 TTTAAATA-TT-AATATATT
1 TTTAATTATTTAAATATATT
44640 CGGATTGAGT
Statistics
Matches: 91, Mismatches: 26, Indels: 21
0.66 0.19 0.15
Matches are distributed among these distances:
19 13 0.14
20 9 0.10
21 30 0.33
22 20 0.22
23 13 0.14
24 6 0.07
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (21 bp):
TTTAATTATTTAAATATATTA
Found at i:58523 original size:16 final size:15
Alignment explanation
Indices: 58502--58532 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
58492 CTAATCTTTA
58502 TTATTATTATTATTTT
1 TTATTATT-TTATTTT
58518 TTATTATTTTATTTT
1 TTATTATTTTATTTT
58533 GCATGTGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTATTATTTTATTTT
Found at i:60078 original size:20 final size:21
Alignment explanation
Indices: 60053--60105 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
60043 GACCAACAAA
60053 TTCGCAACGCGAACTT-CAAT
1 TTCGCAACGCGAACTTCCAAT
* **
60073 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGAACTTCCAAT
60093 TTCGCAACGCGAA
1 TTCGCAACGCGAA
60106 TATGTAAATC
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 4 0.15
20 20 0.77
21 2 0.08
ACGTcount: A:0.28, C:0.32, G:0.15, T:0.25
Consensus pattern (21 bp):
TTCGCAACGCGAACTTCCAAT
Found at i:60163 original size:20 final size:20
Alignment explanation
Indices: 60137--60181 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
60127 TTCCAATTTA
60137 ACAACGCGAATCTGTAAATC
1 ACAACGCGAATCTGTAAATC
* *
60157 GCAACGCGAATTTGTAAATC
1 ACAACGCGAATCTGTAAATC
60177 ACAAC
1 ACAAC
60182 ACAAAAGTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (20 bp):
ACAACGCGAATCTGTAAATC
Found at i:60770 original size:20 final size:20
Alignment explanation
Indices: 60706--60782 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 20
60696 GCGATTTTAG
* *
60706 TTTCGCGTTTCTATTTTCAT
1 TTTCGCGTTGCAATTTTCAT
* * **
60726 TTTCACATTGTGATTTTCAT
1 TTTCGCGTTGCAATTTTCAT
60746 TTTCGCGTTGCAATTTTCAT
1 TTTCGCGTTGCAATTTTCAT
*
60766 TTTCGTGTTGCGAATTT
1 TTTCGCGTTGC-AATTT
60783 AAGTTTCAGA
Statistics
Matches: 46, Mismatches: 10, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
20 41 0.89
21 5 0.11
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (20 bp):
TTTCGCGTTGCAATTTTCAT
Found at i:62852 original size:38 final size:42
Alignment explanation
Indices: 62793--62870 Score: 94
Period size: 38 Copynumber: 2.0 Consensus size: 42
62783 CGAACACCTA
* *
62793 TCATCATTCAAGAGGCGCCT-CC-TCG-TC-AGAGGCCCCTC
1 TCATCATTCAAGAAGCCCCTCCCATCGTTCAAGAGGCCCCTC
62831 TCATCA-TCGAAGAAGCCCCTCCCATCGTTCAAGAGGCCCC
1 TCATCATTC-AAGAAGCCCCTCCCATCGTTCAAGAGGCCCC
62871 CGTCATTGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
37 2 0.06
38 15 0.45
39 2 0.06
40 3 0.09
41 2 0.06
42 9 0.27
ACGTcount: A:0.22, C:0.40, G:0.19, T:0.19
Consensus pattern (42 bp):
TCATCATTCAAGAAGCCCCTCCCATCGTTCAAGAGGCCCCTC
Done.