Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007174.1 Hibiscus syriacus cultivar Beakdansim tig00018829_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: 77728
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:5396 original size:2 final size:2
Alignment explanation
Indices: 5389--5416 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5379 AAACTTAATC
5389 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5417 GTGTATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12143 original size:12 final size:12
Alignment explanation
Indices: 12126--12156 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
12116 CTACTTAGAT
12126 GGGATGAGAAAG
1 GGGATGAGAAAG
12138 GGGATGAGAAAG
1 GGGATGAGAAAG
12150 GGGATGA
1 GGGATGA
12157 AAGAGGAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.52, T:0.10
Consensus pattern (12 bp):
GGGATGAGAAAG
Found at i:17624 original size:7 final size:7
Alignment explanation
Indices: 17596--17820 Score: 112
Period size: 7 Copynumber: 31.7 Consensus size: 7
17586 TGTCCGATAG
17596 TATATATT
1 TATATA-T
17604 TATATAT
1 TATATAT
17611 TATTATAT
1 TA-TATAT
*
17619 TATATAG
1 TATATAT
*
17626 TA-GTAT
1 TATATAT
17632 TATATAT
1 TATATAT
17639 TATAT-T
1 TATATAT
*
17645 CCATAT-T
1 -TATATAT
17652 ATATATAT
1 -TATATAT
*
17660 TATAGTAG
1 TATA-TAT
17668 TAT-TAT
1 TATATAT
*
17674 T-TATAC
1 TATATAT
17680 TATATAT
1 TATATAT
*
17687 TATATGT
1 TATATAT
*
17694 TATATAGCA
1 TATATA--T
*
17703 TATACAT
1 TATATAT
* *
17710 TATAAAA
1 TATATAT
17717 TATATAT
1 TATATAT
*
17724 TATA-CT
1 TATATAT
17730 TAT-TA-
1 TATATAT
17735 TATATAT
1 TATATAT
* *
17742 TACATAG
1 TATATAT
*
17749 TACATAT
1 TATATAT
17756 TAAAGTATAT
1 T--A-TATAT
*
17766 TATTATAC
1 TA-TATAT
17774 T-TATAT
1 TATATAT
17780 TATATAT
1 TATATAT
17787 TATAGTA-
1 TATA-TAT
17794 TATTATAT
1 TA-TATAT
17802 TA-ATAT
1 TATATAT
17808 TATAGTAT
1 TATA-TAT
17816 TATAT
1 TATAT
17821 TATATTAGTT
Statistics
Matches: 167, Mismatches: 29, Indels: 43
0.70 0.12 0.18
Matches are distributed among these distances:
5 4 0.02
6 28 0.17
7 86 0.51
8 38 0.23
9 6 0.04
10 5 0.03
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (7 bp):
TATATAT
Found at i:17637 original size:36 final size:36
Alignment explanation
Indices: 17596--17700 Score: 108
Period size: 39 Copynumber: 2.8 Consensus size: 36
17586 TGTCCGATAG
17596 TATATATTTATATATTATTATATTATATAGTAGTAT
1 TATATATTTATATATTATTATATTATATAGTAGTAT
17632 TATATA-TTATAT-TCCATATTATATATATTATAGTAGTAT
1 TATATATTTATATAT---TATTATAT-TA-TATAGTAGTAT
* * *
17671 TATTTATACTATATATTA-TATGTTATATAG
1 TATATAT-TTATATATTATTATATTATATAG
17701 CATATACATT
Statistics
Matches: 58, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
34 1 0.02
35 6 0.10
36 11 0.19
37 10 0.17
38 6 0.10
39 18 0.31
41 5 0.09
42 1 0.02
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (36 bp):
TATATATTTATATATTATTATATTATATAGTAGTAT
Found at i:17788 original size:31 final size:30
Alignment explanation
Indices: 17611--17849 Score: 134
Period size: 31 Copynumber: 7.6 Consensus size: 30
17601 ATTTATATAT
* *
17611 TATTATATTATATAGTAGTATTATA-TATTA
1 TATTATATTATATATTA-TAGTATATTATTA
17641 TATTCCATATTATATATATTATAGTAGTATTATTTA
1 TATT--ATA-T-TATATATTATAGTA-TATTA-TTA
* *
17677 TACTATATATTATATGTTATA-TAGCA-TA-TA
1 TA-T-TATATTATATATTATAGTA-TATTATTA
* * *
17707 CATTATAAAATATATATTATACT-TATTATATA
1 TATTAT--ATTATATATTATAGTATATTAT-TA
* * *
17739 TATTACATAGTACATATTAAAGTATATTATTA
1 TATT--ATATTATATATTATAGTATATTATTA
17771 TACTTATATTATATATTATAGTATATTA-TA
1 TA-TTATATTATATATTATAGTATATTATTA
* *
17801 T-TAATATTATAGTATTATATTATATTAGTTA
1 TATTATATTATA-TATTATAGTATATTA-TTA
*
17832 TAGTTATATTCTAT-TTAT
1 TA-TTATATTATATATTAT
17850 TATTATACTA
Statistics
Matches: 165, Mismatches: 20, Indels: 47
0.71 0.09 0.20
Matches are distributed among these distances:
28 12 0.07
29 16 0.10
30 23 0.14
31 28 0.17
32 26 0.16
33 25 0.15
34 22 0.13
35 3 0.02
36 8 0.05
37 1 0.01
38 1 0.01
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.51
Consensus pattern (30 bp):
TATTATATTATATATTATAGTATATTATTA
Found at i:17825 original size:39 final size:37
Alignment explanation
Indices: 17592--17866 Score: 120
Period size: 36 Copynumber: 7.9 Consensus size: 37
17582 TTTTTGTCCG
17592 ATAGTATA-TAT-TTATA-TAT-TATTATATTATA-T
1 ATAGTATATTATATTATATTATATATTATATTATATT
**
17624 AGTAGTAT-TATATATTATATTCCATATTATA-TATATT
1 A-TAGTATAT-TATATTATATTATATATTATATTATATT
*
17661 ATAGTAGTATTAT-TTATACTATATATTATATGT-TA-T
1 ATAGTA-TATTATATTATATTATATATTATAT-TATATT
* * *
17697 ATAGCATA-TACATTATA--AAATA-TATATTATACTT
1 ATAGTATATTATATTATATTATATATTATATTATA-TT
* * * * *
17731 AT--TATA-TATATTACA-TA-GTA-CATATTAAAGT
1 ATAGTATATTATATTATATTATATATTATATTATATT
*
17762 ATA-T-TATTATACTTATATTATATATTATAGTATATT
1 ATAGTATATTATA-TTATATTATATATTATATTATATT
* *
17798 ATA-T-TA--ATATTATAGTATTATATTATATTA-GTT
1 ATAGTATATTATATTATATTA-TATATTATATTATATT
* *
17831 ATAGTTATATTCTATT-TATTATTATACTAATATTAT
1 ATAG-TATATTATATTATATTA-TATA-TTATATTAT
17867 TTTTTCAATT
Statistics
Matches: 186, Mismatches: 27, Indels: 53
0.70 0.10 0.20
Matches are distributed among these distances:
31 6 0.03
32 32 0.17
33 27 0.15
34 24 0.13
35 15 0.08
36 45 0.24
37 24 0.13
38 13 0.07
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.51
Consensus pattern (37 bp):
ATAGTATATTATATTATATTATATATTATATTATATT
Found at i:18344 original size:33 final size:32
Alignment explanation
Indices: 18287--18368 Score: 85
Period size: 33 Copynumber: 2.5 Consensus size: 32
18277 CAACCAAGCA
*
18287 AACAAAGCAAAAACAAGCAATCGAAACAACAAG
1 AACAAAGCAAAAA-AAACAATCGAAACAACAAG
* * *
18320 AACAAAGCAGAAAAAAACATTCGAAATAGCAAG
1 AACAAAGCA-AAAAAAACAATCGAAACAACAAG
*
18353 AA-AAATCACAAAAAAA
1 AACAAAGCA-AAAAAAA
18369 ATCAAGGATT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
32 12 0.29
33 26 0.62
34 4 0.10
ACGTcount: A:0.66, C:0.17, G:0.11, T:0.06
Consensus pattern (32 bp):
AACAAAGCAAAAAAAACAATCGAAACAACAAG
Found at i:19681 original size:21 final size:23
Alignment explanation
Indices: 19637--19683 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
19627 TGTATAATTA
*
19637 TAAATTAGTTAAAAATTTAAAGG
1 TAAATTAGTTAAAAATTAAAAGG
*
19660 TAAATTA-TTTAAAA-TAAAAGG
1 TAAATTAGTTAAAAATTAAAAGG
19681 TAA
1 TAA
19684 CTATATCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 6 0.27
23 7 0.32
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (23 bp):
TAAATTAGTTAAAAATTAAAAGG
Found at i:34849 original size:23 final size:25
Alignment explanation
Indices: 34809--34854 Score: 78
Period size: 23 Copynumber: 1.9 Consensus size: 25
34799 TGTGACATGA
34809 TTTTTCTCTACTCTTGTAGCACGCG
1 TTTTTCTCTACTCTTGTAGCACGCG
34834 TTTTTCT-T-CTCTTGTAGCACG
1 TTTTTCTCTACTCTTGTAGCACG
34855 ATCCTCATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 13 0.62
24 1 0.05
25 7 0.33
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (25 bp):
TTTTTCTCTACTCTTGTAGCACGCG
Found at i:37373 original size:29 final size:29
Alignment explanation
Indices: 37338--37419 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
37328 AAACTAAATT
*
37338 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
37367 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
37396 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
37420 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:42135 original size:29 final size:29
Alignment explanation
Indices: 42100--42181 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
42090 AAACTAAATT
*
42100 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
42129 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
42158 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
42182 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:50208 original size:27 final size:26
Alignment explanation
Indices: 50178--50229 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
50168 ATAACAAATA
50178 TTAAAT-ATATTTAAACTTAATATTTTT
1 TTAAATGA-ATTTAAACTTAA-ATTTTT
*
50205 TTAATTGAATTTAAACTTAAATTTT
1 TTAAATGAATTTAAACTTAAATTTT
50230 CGTATAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 5 0.22
27 17 0.74
28 1 0.04
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (26 bp):
TTAAATGAATTTAAACTTAAATTTTT
Found at i:55521 original size:24 final size:20
Alignment explanation
Indices: 55494--55551 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
55484 GCATGGGTAG
55494 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG---AAGAA
* *
55518 TGCATTGATGCACTGCAGAA
1 TGCATCGATGCACTGAAGAA
55538 TGCATCGATGCACT
1 TGCATCGATGCACT
55552 TCAAAGGGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 17 0.55
23 2 0.06
24 12 0.39
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (20 bp):
TGCATCGATGCACTGAAGAA
Found at i:55539 original size:20 final size:20
Alignment explanation
Indices: 55514--55551 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
55504 CACATGTTAA
*
55514 AGAATGCATTGATGCACTGC
1 AGAATGCATCGATGCACTGC
55534 AGAATGCATCGATGCACT
1 AGAATGCATCGATGCACT
55552 TCAAAGGGAA
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:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGC
Found at i:59881 original size:63 final size:63
Alignment explanation
Indices: 59808--59929 Score: 226
Period size: 63 Copynumber: 1.9 Consensus size: 63
59798 CTTCATCCAT
* *
59808 TACCGATACTTCAAGAATAAAACAGTGATATTTGGTAAAGGGGTATTGATACTGGTTGAGAAG
1 TACCGATACTTCAAGAACAAAACAATGATATTTGGTAAAGGGGTATTGATACTGGTTGAGAAG
59871 TACCGATACTTCAAGAACAAAACAATGATATTTGGTAAAGGGGTATTGATACTGGTTGA
1 TACCGATACTTCAAGAACAAAACAATGATATTTGGTAAAGGGGTATTGATACTGGTTGA
59930 ACAATATTGA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.29
Consensus pattern (63 bp):
TACCGATACTTCAAGAACAAAACAATGATATTTGGTAAAGGGGTATTGATACTGGTTGAGAAG
Found at i:60037 original size:35 final size:35
Alignment explanation
Indices: 59998--60076 Score: 158
Period size: 35 Copynumber: 2.3 Consensus size: 35
59988 GGAAGGTATA
59998 ATCGATACCAAGAGTACCGATATCATAAGGTCAGT
1 ATCGATACCAAGAGTACCGATATCATAAGGTCAGT
60033 ATCGATACCAAGAGTACCGATATCATAAGGTCAGT
1 ATCGATACCAAGAGTACCGATATCATAAGGTCAGT
60068 ATCGATACC
1 ATCGATACC
60077 CATTTTTGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.23
Consensus pattern (35 bp):
ATCGATACCAAGAGTACCGATATCATAAGGTCAGT
Found at i:60038 original size:20 final size:20
Alignment explanation
Indices: 60010--60074 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
60000 CGATACCAAG
60010 AGTACCGATATCATAAGGTC
1 AGTACCGATATCATAAGGTC
* *
60030 AGTATCGATA-C-CAA-G--
1 AGTACCGATATCATAAGGTC
60045 AGTACCGATATCATAAGGTC
1 AGTACCGATATCATAAGGTC
*
60065 AGTATCGATA
1 AGTACCGATA
60075 CCCATTTTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
15 9 0.26
16 1 0.03
17 3 0.09
18 3 0.09
19 1 0.03
20 18 0.51
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (20 bp):
AGTACCGATATCATAAGGTC
Found at i:60976 original size:31 final size:31
Alignment explanation
Indices: 60935--61028 Score: 143
Period size: 31 Copynumber: 3.0 Consensus size: 31
60925 AAGAGTCGAG
* *
60935 GGTTACCTATGTCCTTCGAGACATATGGATA
1 GGTTACCTATGTTCTTCGGGACATATGGATA
* * *
60966 GGTTATCTATGTTCTTCGGGACATATAGACA
1 GGTTACCTATGTTCTTCGGGACATATGGATA
60997 GGTTACCTATGTTCTTCGGGACATATGGATA
1 GGTTACCTATGTTCTTCGGGACATATGGATA
61028 G
1 G
61029 TGGTCATTCG
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (31 bp):
GGTTACCTATGTTCTTCGGGACATATGGATA
Found at i:66945 original size:20 final size:19
Alignment explanation
Indices: 66922--66976 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
66912 AAGCTGTTCG
66922 AAAAAGAAAAAAAAGAGAAA
1 AAAAAGAAAAAAAAGA-AAA
* **
66942 AAAAAGACATGAAAGAAAA
1 AAAAAGAAAAAAAAGAAAA
66961 AAAATAGAAAACAAAA
1 AAAA-AGAAAA-AAAA
66977 CAATAAAGTG
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 7 0.26
20 17 0.63
21 3 0.11
ACGTcount: A:0.80, C:0.04, G:0.13, T:0.04
Consensus pattern (19 bp):
AAAAAGAAAAAAAAGAAAA
Found at i:68546 original size:2 final size:2
Alignment explanation
Indices: 68539--68577 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
68529 TCCTAAAACC
* *
68539 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
68578 TCGAGGAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:72782 original size:25 final size:25
Alignment explanation
Indices: 72659--72776 Score: 204
Period size: 25 Copynumber: 4.8 Consensus size: 25
72649 AGTTAGGGGA
72659 TTAGGG-TTGAAACCCTAAATTGTT
1 TTAGGGTTTGAAACCCTAAATTGTT
72683 TTAGGGTTTGAAACCCTAAATTGTT
1 TTAGGGTTTGAAACCCTAAATTGTT
72708 TTAGGGTTTGAAACCCTAAATTGTT
1 TTAGGGTTTGAAACCCTAAATTGTT
*
72733 TTAGGGTTTGAAACCCT-AATCTGAT
1 TTAGGGTTTGAAACCCTAAAT-TGTT
72758 TTAGGGTTTGAAACCCTAA
1 TTAGGGTTTGAAACCCTAA
72777 TCTGATGGGT
Statistics
Matches: 90, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
24 9 0.10
25 80 0.89
26 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAAATTGTT
Found at i:72861 original size:3 final size:3
Alignment explanation
Indices: 72853--72899 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
72843 TATGTAAAAT
72853 TAA TAA TAA TAA TTAA TAA T-A TAA -AA TAA -AA TAA -AA -AA TAA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
72894 TAA TAA
1 TAA TAA
72900 AAAATATAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
2 10 0.26
3 26 0.67
4 3 0.08
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:72884 original size:32 final size:32
Alignment explanation
Indices: 72847--72910 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
72837 ATGTAATATG
* * * *
72847 TAAAATTAATAATAATAATTAATAATATAAAA
1 TAAAATAAAAAATAATAATAAAAAATATAAAA
72879 TAAAATAAAAAATAATAATAAAAAATATAAAA
1 TAAAATAAAAAATAATAATAAAAAATATAAAA
72911 GACCCGGACA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (32 bp):
TAAAATAAAAAATAATAATAAAAAATATAAAA
Found at i:72900 original size:13 final size:13
Alignment explanation
Indices: 72848--72905 Score: 73
Period size: 13 Copynumber: 4.5 Consensus size: 13
72838 TGTAATATGT
*
72848 AAAATTAATAATA
1 AAAAATAATAATA
* *
72861 ATAATTAATAATA
1 AAAAATAATAATA
*
72874 TAAAATAA-AATA
1 AAAAATAATAATA
72886 AAAAATAATAATA
1 AAAAATAATAATA
72899 AAAAATA
1 AAAAATA
72906 TAAAAGACCC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
12 11 0.28
13 28 0.72
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAAATAATAATA
Found at i:72908 original size:12 final size:12
Alignment explanation
Indices: 72868--72908 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
72858 ATAATAATTA
*
72868 ATAATATAAAAT
1 ATAATAAAAAAT
*
72880 AAAATAAAAAAT
1 ATAATAAAAAAT
72892 AATAATAAAAAAT
1 -ATAATAAAAAAT
72905 ATAA
1 ATAA
72909 AAGACCCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 14 0.56
13 11 0.44
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
ATAATAAAAAAT
Found at i:72908 original size:22 final size:22
Alignment explanation
Indices: 72867--72910 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
72857 AATAATAATT
72867 AATAATATAAAATAAAATAAAA
1 AATAATATAAAATAAAATAAAA
*
72889 AATAATAATAAAA-AATATAAAA
1 AATAAT-ATAAAATAAAATAAAA
72911 GACCCGGACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (22 bp):
AATAATATAAAATAAAATAAAA
Found at i:74375 original size:12 final size:11
Alignment explanation
Indices: 74357--74434 Score: 52
Period size: 11 Copynumber: 7.1 Consensus size: 11
74347 CCTTTATTTA
74357 TTTTCTTTTTT
1 TTTTCTTTTTT
74368 TCTTTCTTTTTT
1 T-TTTCTTTTTT
* ** *
74380 TTTTCATCATA
1 TTTTCTTTTTT
*
74391 TTTTC-ATTTT
1 TTTTCTTTTTT
*
74401 TTTCCTCTTTTT
1 TTTTCT-TTTTT
**
74413 TCCTCTTTTTT
1 TTTTCTTTTTT
74424 TTTT-TTTTTT
1 TTTTCTTTTTT
74434 T
1 T
74435 AAGTGTAATA
Statistics
Matches: 49, Mismatches: 15, Indels: 7
0.69 0.21 0.10
Matches are distributed among these distances:
10 12 0.24
11 19 0.39
12 18 0.37
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:74413 original size:10 final size:10
Alignment explanation
Indices: 74398--74423 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
74388 ATATTTTCAT
74398 TTTTTTCCTC
1 TTTTTTCCTC
74408 TTTTTTCCTC
1 TTTTTTCCTC
74418 TTTTTT
1 TTTTTT
74424 TTTTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTTTCCTC
Done.