Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003972.1 Hibiscus syriacus cultivar Beakdansim tig00008616_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: 173427
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:861 original size:29 final size:30
Alignment explanation
Indices: 810--867 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
800 ATTTAGAATA
* *
810 AATACTTTGTAATATAATTTAATAAAAAAT
1 AATAATTTGTAATATAATATAATAAAAAAT
*
840 AATAATTTG-AATCTAATATAATAAAAAA
1 AATAATTTGTAATATAATATAATAAAAAA
868 CAAAATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.36
Consensus pattern (30 bp):
AATAATTTGTAATATAATATAATAAAAAAT
Found at i:19497 original size:48 final size:48
Alignment explanation
Indices: 19428--19538 Score: 127
Period size: 48 Copynumber: 2.3 Consensus size: 48
19418 AAATATTTTA
* * *
19428 TCTGATTTCCGACT-TGAATTCTGTTCTGAT-ACATTACCTGAATTTTGT
1 TCTGATTTCTGA-TATGAATTCTGTTCTGATGAC-TGACCTGAATTCTGT
* * *
19476 TCTGATTTCTGATATGGATTCTGTTCTGATGTCTGATCTGAATTCTGT
1 TCTGATTTCTGATATGAATTCTGTTCTGATGACTGACCTGAATTCTGT
*
19524 TTTGATTTCTGATAT
1 TCTGATTTCTGATAT
19539 CTCTGGTTAC
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 1 0.02
48 52 0.96
49 1 0.02
ACGTcount: A:0.19, C:0.15, G:0.17, T:0.49
Consensus pattern (48 bp):
TCTGATTTCTGATATGAATTCTGTTCTGATGACTGACCTGAATTCTGT
Found at i:19500 original size:24 final size:24
Alignment explanation
Indices: 19466--19538 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 24
19456 ATACATTACC
*
19466 TGAATTTTGTTCTGATTTCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
* * *
19490 TGGATTCTGTTCTGATGTCTGATC
1 TGAATTCTGTTCTGATTTCTGATA
*
19514 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
19538 T
1 T
19539 CTCTGGTTAC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.18, C:0.11, G:0.19, T:0.52
Consensus pattern (24 bp):
TGAATTCTGTTCTGATTTCTGATA
Found at i:19533 original size:12 final size:12
Alignment explanation
Indices: 19469--19534 Score: 55
Period size: 12 Copynumber: 5.6 Consensus size: 12
19459 CATTACCTGA
19469 ATTT-TGTTCTG
1 ATTTCTGTTCTG
* *
19480 ATTTCTGATATGG
1 ATTTCTGTTCT-G
19493 A-TTCTGTTCTG
1 ATTTCTGTTCTG
* *
19504 ATGTCTGATCTG
1 ATTTCTGTTCTG
* *
19516 AATTCTGTTTTG
1 ATTTCTGTTCTG
19528 ATTTCTG
1 ATTTCTG
19535 ATATCTCTGG
Statistics
Matches: 41, Mismatches: 11, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
11 6 0.15
12 33 0.80
13 2 0.05
ACGTcount: A:0.15, C:0.12, G:0.20, T:0.53
Consensus pattern (12 bp):
ATTTCTGTTCTG
Found at i:25663 original size:39 final size:39
Alignment explanation
Indices: 25620--25740 Score: 163
Period size: 39 Copynumber: 3.1 Consensus size: 39
25610 TATTGGTCTA
*
25620 AAGACGTCGTACACTCTTGGGGTCTTC-TCAATTTGCCTG
1 AAGACGTCGTGCACTCTTGGGGTCTTCTTC-ATTTGCCTG
* *
25659 AAGACGTCGTGCACTCTTGGGGTCTTCTTCATTTACCCG
1 AAGACGTCGTGCACTCTTGGGGTCTTCTTCATTTGCCTG
* ** *
25698 AAGACGTCATGCAGACGTGGGGTCTTCTTCATTTGCCTG
1 AAGACGTCGTGCACTCTTGGGGTCTTCTTCATTTGCCTG
25737 AAGA
1 AAGA
25741 TGTTATGCAG
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
39 70 0.97
40 2 0.03
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.31
Consensus pattern (39 bp):
AAGACGTCGTGCACTCTTGGGGTCTTCTTCATTTGCCTG
Found at i:30412 original size:19 final size:20
Alignment explanation
Indices: 30388--30435 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 20
30378 TACGATAAGC
30388 TAAATTTAT-TGAAT-TATTT
1 TAAATTTATAT-AATATATTT
*
30407 TAAATTAATATAATATATTT
1 TAAATTTATATAATATATTT
30427 TAAAATTTA
1 T-AAATTTA
30436 GAAGTTACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 11 0.46
20 7 0.29
21 6 0.25
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TAAATTTATATAATATATTT
Found at i:31994 original size:6 final size:6
Alignment explanation
Indices: 31985--32022 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
31975 TATATATATA
31985 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TG
32023 CTTGTACTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.16, C:0.00, G:0.34, T:0.50
Consensus pattern (6 bp):
TGTATG
Found at i:39869 original size:33 final size:33
Alignment explanation
Indices: 39830--39900 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 33
39820 GTGATGGTTT
39830 GGGGAGAAGAGCATGGAGATGCAGTAGAAATTG
1 GGGGAGAAGAGCATGGAGATGCAGTAGAAATTG
*
39863 GGGGAGAAGAGCGTGGAGATGCAGTAGAAATTG
1 GGGGAGAAGAGCATGGAGATGCAGTAGAAATTG
39896 GGGGA
1 GGGGA
39901 AATTGAGGTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.34, C:0.06, G:0.46, T:0.14
Consensus pattern (33 bp):
GGGGAGAAGAGCATGGAGATGCAGTAGAAATTG
Found at i:47342 original size:17 final size:17
Alignment explanation
Indices: 47320--47354 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
47310 ATGGATTTTA
47320 TTGTATTGTAATCGTAT
1 TTGTATTGTAATCGTAT
*
47337 TTGTATTGTAATCTTAT
1 TTGTATTGTAATCGTAT
47354 T
1 T
47355 AATGGATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.23, C:0.06, G:0.14, T:0.57
Consensus pattern (17 bp):
TTGTATTGTAATCGTAT
Found at i:50764 original size:44 final size:46
Alignment explanation
Indices: 50693--50795 Score: 147
Period size: 44 Copynumber: 2.2 Consensus size: 46
50683 ATTTATTTTC
*
50693 GTTTTTTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAG
1 GTTTATTTTT-GAATAAATGCATGCGAACTAGATATCATGCGGTTAG
*
50740 GTTTATTTTTGAAT-AA-GCATGCGAATTAGATATCATGCGGTTAG
1 GTTTATTTTTGAATAAATGCATGCGAACTAGATATCATGCGGTTAG
*
50784 GATTTCTTTTTG
1 G-TTTATTTTTG
50796 TGGATAACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
44 28 0.54
45 11 0.21
46 4 0.08
47 9 0.17
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.42
Consensus pattern (46 bp):
GTTTATTTTTGAATAAATGCATGCGAACTAGATATCATGCGGTTAG
Found at i:60472 original size:16 final size:15
Alignment explanation
Indices: 60453--60563 Score: 55
Period size: 16 Copynumber: 6.7 Consensus size: 15
60443 AAGAAGAAAT
60453 AAAAGAGAAAAGAAGA
1 AAAAGAGAAAA-AAGA
60469 AAAA-ATGAGAAAAAGA
1 AAAAGA-GA-AAAAAGA
60485 AAAATGATGGAAAAAACG-
1 AAAA-GA--GAAAAAA-GA
*
60503 AAAAGAAAAAATAAGAGA
1 AAAAG-AGAAA-AA-AGA
*
60521 AAAAGAGAAAAATGGAA
1 AAAAGAGAAAAA-AG-A
**
60538 AAAAGAGAAAAGTGAA
1 AAAAGAGAAAAAAG-A
60554 AAAAGAGAAA
1 AAAAGAGAAA
60564 TAAAAGGAGG
Statistics
Matches: 77, Mismatches: 7, Indels: 22
0.73 0.07 0.21
Matches are distributed among these distances:
15 1 0.01
16 33 0.43
17 23 0.30
18 17 0.22
19 3 0.04
ACGTcount: A:0.72, C:0.01, G:0.22, T:0.05
Consensus pattern (15 bp):
AAAAGAGAAAAAAGA
Found at i:60488 original size:25 final size:25
Alignment explanation
Indices: 60453--60559 Score: 71
Period size: 25 Copynumber: 4.2 Consensus size: 25
60443 AAGAAGAAAT
60453 AAAAGAGAAAAGAAGA-AAAAATGAGA
1 AAAAGA-AAAAGAAGAGAAAAATGA-A
* *
60479 AAAAGAAAAATGATG-GAAAAAACGAA
1 AAAAGAAAAA-GAAGAG-AAAAATGAA
* *
60505 AAGA-AAAAATAAGAGAAAAA-GAGA
1 AAAAGAAAAAGAAGAGAAAAATGA-A
* *
60529 AAAATGGAAAA-AAGAGAAAAGTGAA
1 AAAA-GAAAAAGAAGAGAAAAATGAA
60554 AAAAGA
1 AAAAGA
60560 GAAATAAAAG
Statistics
Matches: 64, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
23 2 0.03
24 12 0.19
25 24 0.38
26 19 0.30
27 7 0.11
ACGTcount: A:0.72, C:0.01, G:0.21, T:0.06
Consensus pattern (25 bp):
AAAAGAAAAAGAAGAGAAAAATGAA
Found at i:60523 original size:10 final size:9
Alignment explanation
Indices: 60503--60563 Score: 58
Period size: 9 Copynumber: 7.1 Consensus size: 9
60493 GGAAAAAACG
*
60503 AAAAGAAAA
1 AAAAGAGAA
60512 AATAAGAG-A
1 AA-AAGAGAA
60521 AAAAGAGAA
1 AAAAGAGAA
*
60530 AAATG-GAA
1 AAAAGAGAA
60538 AAAAGAG--
1 AAAAGAGAA
*
60545 AAAAGTGAA
1 AAAAGAGAA
60554 AAAAGAGAA
1 AAAAGAGAA
60563 A
1 A
60564 TAAAAGGAGG
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
7 6 0.14
8 12 0.29
9 20 0.48
10 4 0.10
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (9 bp):
AAAAGAGAA
Found at i:60540 original size:17 final size:16
Alignment explanation
Indices: 60453--60563 Score: 77
Period size: 17 Copynumber: 6.6 Consensus size: 16
60443 AAGAAGAAAT
*
60453 AAAAGAGAAAAGAAGAA
1 AAAAGAGAAAA-ATGAA
60470 AAAATGAGAAAAA-GAA
1 AAAA-GAGAAAAATGAA
* *
60486 AAATGATGGAAAAA--ACG
1 AAAAGA--GAAAAATGA-A
60503 AAAAGA-AAAAATAAGAGA
1 AAAAGAGAAAAAT--GA-A
60521 AAAAGAGAAAAATGGAA
1 AAAAGAGAAAAAT-GAA
*
60538 AAAAGAGAAAAGTGAA
1 AAAAGAGAAAAATGAA
60554 AAAAGAGAAA
1 AAAAGAGAAA
60564 TAAAAGGAGG
Statistics
Matches: 78, Mismatches: 7, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
14 5 0.06
15 2 0.03
16 20 0.26
17 29 0.37
18 16 0.21
19 6 0.08
ACGTcount: A:0.72, C:0.01, G:0.22, T:0.05
Consensus pattern (16 bp):
AAAAGAGAAAAATGAA
Found at i:60548 original size:50 final size:49
Alignment explanation
Indices: 60453--60548 Score: 115
Period size: 50 Copynumber: 1.9 Consensus size: 49
60443 AAGAAGAAAT
* *
60453 AAAAGAGAAAAGAAGAAAAAATGAGAAAAAGAAAAATGATGGAAAAAACG
1 AAAAGAAAAAAGAAGAAAAAATGAGAAAAAGAAAAAAGA-GGAAAAAACG
*
60503 AAAAGAAAAAATAAGAGAAAAA-GAGAAAAATGGAAAAAAGA-GAAAA
1 AAAAGAAAAAAGAAGA-AAAAATGAGAAAAA--GAAAAAAGAGGAAAA
60549 GTGAAAAAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
50 27 0.68
51 5 0.12
52 8 0.20
ACGTcount: A:0.73, C:0.01, G:0.21, T:0.05
Consensus pattern (49 bp):
AAAAGAAAAAAGAAGAAAAAATGAGAAAAAGAAAAAAGAGGAAAAAACG
Found at i:61761 original size:51 final size:51
Alignment explanation
Indices: 61700--62269 Score: 753
Period size: 51 Copynumber: 10.9 Consensus size: 51
61690 AAATTTGTTT
*
61700 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGAGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
61751 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
*
61802 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
*
61853 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGAGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
*
61904 GTTGAGGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
61955 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
* *
62006 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
* * ** *
62057 GTTAAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACCTGTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
* * * * ** *
62108 ATTGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACTCGTTTT
1 GTTGAAGA---TT-GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTC
* * * * ** *
62164 ATTGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACTCGTTTT
1 GTTGAAGA---TT-GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTC
* * * *
62220 ATTGAAGATTGTTCAAGTCTTATACTCTCTGAATGAATAGAGAGCAGACA
1 GTTGAAGATTG----AGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
62270 CATTTTATGA
Statistics
Matches: 487, Mismatches: 23, Indels: 13
0.93 0.04 0.02
Matches are distributed among these distances:
51 351 0.72
52 1 0.00
53 2 0.00
54 2 0.00
55 34 0.07
56 97 0.20
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.29
Consensus pattern (51 bp):
GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
Found at i:62349 original size:55 final size:54
Alignment explanation
Indices: 61710--62349 Score: 445
Period size: 51 Copynumber: 12.1 Consensus size: 54
61700 GTTGAAGATT
* * ** **
61710 GAGTCCTATACTCTCTGAATGAATAGAGAGCGGACAAGTTCGTTGAAGA--TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACTCGTTTATTGAAGATTTTC
* * * ** **
61761 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA--TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACTCGTTTATTGAAGATTTTC
* * ** **
61812 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGA--TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACTCGTTTATTGAAGATTTTC
* * ** ** *
61863 GAGTCCTATACTCTCTGAATGAATAGAGAGCGGACAAGTTCGTTGAGGA--TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACTCGTTTATTGAAGATTTTC
* * * ** **
61914 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA--TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACTCGTTTATTGAAGATTTTC
* * * ** **
61965 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA--TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACTCGTTTATTGAAGATTTTC
* * ** * *
62016 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTTGTTAAAGA--TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACTCGTTTATTGAAGATTTTC
* *
62067 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC-CTGTTTATTGAAGATTTTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACTC-GTTTATTGAAGA-TTTTC
62122 GAGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACTCGTTTTATTGAAGATTTTTC
1 GAGTCT-TATACTCTCTGAAGGAATAGAGAGCGGACTCG-TTTATTGAAGA-TTTTC
62178 GAGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACTCGTTTTATTGAAGATTGTTC
1 GAGTCT-TATACTCTCTGAAGGAATAGAGAGCGGACTCG-TTTATTGAAGATT-TTC
* * * * * *
62234 AAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACATTT-TATGAAGATTGCTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACTCGTTTAT-TGAAGATT-TTC
* *
62289 GAGTCTTATACT-TCCTGAAGGAATAGGGAGCAGG-CTCG-TCATTTGAAGATGTTTC
1 GAGTCTTATACTCT-CTGAAGGAATAGAGAGC-GGACTCGTTTA-TTGAAGAT-TTTC
*
62344 AAGTCT
1 GAGTCT
62350 CATTTATCCT
Statistics
Matches: 543, Mismatches: 30, Indels: 28
0.90 0.05 0.05
Matches are distributed among these distances:
51 341 0.63
54 5 0.01
55 91 0.17
56 105 0.19
57 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (54 bp):
GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACTCGTTTATTGAAGATTTTC
Found at i:66493 original size:17 final size:17
Alignment explanation
Indices: 66471--66505 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
66461 GTGTATTGGG
66471 TTGTATTGTAATCGTAT
1 TTGTATTGTAATCGTAT
*
66488 TTGTATTGTAATCTTAT
1 TTGTATTGTAATCGTAT
66505 T
1 T
66506 GGTGTGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.23, C:0.06, G:0.14, T:0.57
Consensus pattern (17 bp):
TTGTATTGTAATCGTAT
Found at i:68024 original size:30 final size:31
Alignment explanation
Indices: 67984--68043 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
67974 AAAAGGGACC
*
67984 ATTTTATAATATTTTGAT-AAATTTAATAAT
1 ATTTTATAATAATTTGATCAAATTTAATAAT
* *
68014 ATTTTTTAATAATTTGATCAATTTTAATAA
1 ATTTTATAATAATTTGATCAAATTTAATAA
68044 CTAATTTGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (31 bp):
ATTTTATAATAATTTGATCAAATTTAATAAT
Found at i:73087 original size:17 final size:16
Alignment explanation
Indices: 73060--73094 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
73050 TTCAATCATA
73060 ATCAATGATATCCTTC
1 ATCAATGATATCCTTC
*
73076 ATCAAGTGATATTCTTC
1 ATCAA-TGATATCCTTC
73093 AT
1 AT
73095 ATCAAAGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (16 bp):
ATCAATGATATCCTTC
Found at i:79835 original size:23 final size:22
Alignment explanation
Indices: 79808--79851 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
79798 ACATTTGATT
79808 AAAAACCCATACTCCTTGACATG
1 AAAAACCCATA-TCCTTGACATG
**
79831 AAAAATTCATATCCTTGACAT
1 AAAAACCCATATCCTTGACAT
79852 AAATTTTACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.41, C:0.25, G:0.07, T:0.27
Consensus pattern (22 bp):
AAAAACCCATATCCTTGACATG
Found at i:80433 original size:60 final size:59
Alignment explanation
Indices: 80291--80454 Score: 150
Period size: 60 Copynumber: 2.7 Consensus size: 59
80281 TCAATGAGCC
* * ** * **
80291 TCATTTTAAATTAATCCCTAAACTTTTAAACAATTCAATTCCATCCTTAAACTAAGACTA
1 TCATTCTAAATTAATCCC-AAACTTTTAAACATTTCAATTTTACCCCCAAACTAAGACTA
* * * * *
80351 TAATTCTAAATTAGTCTTCAAACTTTTAAACATTTCATTTTTACCCCCAAACTATGATCT-
1 TCATTCTAAATTAATC-CCAAACTTTTAAACATTTCAATTTTACCCCCAAACTAAGA-CTA
* *
80411 TCATTCTAAATTAATCCACAAACATTTTGAATATTTCAATTTTA
1 TCATTCTAAATTAATCC-CAAAC-TTTTAAACATTTCAATTTTA
80455 TCCTAAATTA
Statistics
Matches: 82, Mismatches: 18, Indels: 7
0.77 0.17 0.07
Matches are distributed among these distances:
60 62 0.76
61 20 0.24
ACGTcount: A:0.37, C:0.20, G:0.02, T:0.40
Consensus pattern (59 bp):
TCATTCTAAATTAATCCCAAACTTTTAAACATTTCAATTTTACCCCCAAACTAAGACTA
Found at i:86704 original size:44 final size:44
Alignment explanation
Indices: 86654--86744 Score: 182
Period size: 44 Copynumber: 2.1 Consensus size: 44
86644 GTTGGAGAAA
86654 TCGCGTGATTTCAAGTTGGCGTTAGTAAGAAGCGGACTCTTCAC
1 TCGCGTGATTTCAAGTTGGCGTTAGTAAGAAGCGGACTCTTCAC
86698 TCGCGTGATTTCAAGTTGGCGTTAGTAAGAAGCGGACTCTTCAC
1 TCGCGTGATTTCAAGTTGGCGTTAGTAAGAAGCGGACTCTTCAC
86742 TCG
1 TCG
86745 ATGGCGCCAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (44 bp):
TCGCGTGATTTCAAGTTGGCGTTAGTAAGAAGCGGACTCTTCAC
Found at i:96869 original size:21 final size:21
Alignment explanation
Indices: 96827--96869 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
96817 TTTCTGGGCT
* *
96827 AGGGGAATTGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
96848 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
96869 A
1 A
96870 ACAAATATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:96922 original size:20 final size:20
Alignment explanation
Indices: 96897--96934 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
96887 TAACGCTAGA
*
96897 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
96917 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
96935 TAAAAAAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:97741 original size:103 final size:103
Alignment explanation
Indices: 97413--97733 Score: 588
Period size: 103 Copynumber: 3.1 Consensus size: 103
97403 GTAGAGGGTC
*
97413 TATGTGGTCCTTCGGAACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
97478 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
97516 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
97581 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* * *
97619 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAATATGTGTGAAGTTTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
97684 TTGATCCTTGGCATATGCATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
97722 TATGTGGTCCTT
1 TATGTGGTCCTT
97734 ATGGACATTA
Statistics
Matches: 211, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 211 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:97788 original size:23 final size:23
Alignment explanation
Indices: 97762--97812 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
97752 CACTACGGTA
97762 CAATTCTACGCGGCACTCT-GGTG
1 CAATTCTACGCGGCACT-TAGGTG
*
97785 CAATTCTACGTGGCACTTAGGTG
1 CAATTCTACGCGGCACTTAGGTG
97808 CAATT
1 CAATT
97813 ATATGAGCTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 1 0.04
23 25 0.96
ACGTcount: A:0.22, C:0.25, G:0.24, T:0.29
Consensus pattern (23 bp):
CAATTCTACGCGGCACTTAGGTG
Found at i:103889 original size:21 final size:21
Alignment explanation
Indices: 103847--103889 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
103837 TTTCTGGGCT
*
103847 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
103868 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
103889 A
1 A
103890 ACGAATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:103942 original size:20 final size:20
Alignment explanation
Indices: 103917--103954 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
103907 GAATGCTAGA
*
103917 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
103937 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
103955 TAAAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:104738 original size:103 final size:103
Alignment explanation
Indices: 104429--104730 Score: 577
Period size: 103 Copynumber: 2.9 Consensus size: 103
104419 AGGGTAGATG
*
104429 TATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCTTGGTATATGTA
1 TATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCTTGGCATATGTA
104494 TATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACA
66 TATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACA
104532 TATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCTTGGCATATGTA
1 TATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCTTGGCATATGTA
*
104597 TATGATTCTTAAGGAATGATATGTGGTCATTCGGGACA
66 TATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACA
*
104635 TATATGTATTCTTTGGAATATGTGTGAAGTCTGGTGAGACACATACTTGATCCTTGGCATATGTA
1 TATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCTTGGCATATGTA
104700 TATGATTCTTAAGGAATGATATGTGGTCCTT
66 TATGATTCTTAAGGAATGATATGTGGTCCTT
104731 ATGGACATTA
Statistics
Matches: 195, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 195 1.00
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.37
Consensus pattern (103 bp):
TATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCTTGGCATATGTA
TATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACA
Found at i:104780 original size:23 final size:23
Alignment explanation
Indices: 104747--104809 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
104737 ATTATTATAT
*
104747 GGCACTACGGTGTAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
104770 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
104793 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
104810 ATATGAGATG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 34 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.25, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:129014 original size:10 final size:10
Alignment explanation
Indices: 128999--129025 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
128989 GAGAAAGACT
128999 GCCTGTGGAA
1 GCCTGTGGAA
129009 GCCTGTGGAA
1 GCCTGTGGAA
129019 GCCTGTG
1 GCCTGTG
129026 AAGTATCGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.15, C:0.22, G:0.41, T:0.22
Consensus pattern (10 bp):
GCCTGTGGAA
Found at i:129689 original size:17 final size:17
Alignment explanation
Indices: 129667--129700 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
129657 TTTTTCGGAT
*
129667 AAAAAATCAGTTTTTTA
1 AAAAAACCAGTTTTTTA
*
129684 AAAAAACCGGTTTTTTA
1 AAAAAACCAGTTTTTTA
129701 TCCGGTTTCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (17 bp):
AAAAAACCAGTTTTTTA
Found at i:129742 original size:24 final size:25
Alignment explanation
Indices: 129681--129745 Score: 87
Period size: 27 Copynumber: 2.6 Consensus size: 25
129671 AATCAGTTTT
*
129681 TTAAAAAAACCGGTTTTTTATCCGG
1 TTAAAAAAACCGGTTTTTAATCCGG
*
129706 TTTCAAAAAAACCGGTTTTTAATCTGG
1 -TT-AAAAAAACCGGTTTTTAATCCGG
129733 -TAAAAAAACCGGT
1 TTAAAAAAACCGGT
129746 CGTTCAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
24 12 0.33
25 1 0.03
26 2 0.06
27 21 0.58
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (25 bp):
TTAAAAAAACCGGTTTTTAATCCGG
Found at i:135744 original size:3 final size:3
Alignment explanation
Indices: 135738--135775 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
135728 GATTTTTTTC
135738 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
135776 TATTATTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:136843 original size:5 final size:5
Alignment explanation
Indices: 136833--136858 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
136823 CAATTTTAAA
136833 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
136859 ATTTATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:139834 original size:21 final size:22
Alignment explanation
Indices: 139810--139854 Score: 56
Period size: 25 Copynumber: 2.0 Consensus size: 22
139800 ATAATGATAA
139810 AAAC-ATCAATTAATATATCCT
1 AAACAATCAATTAATATATCCT
139831 AAACTTAAATCAATTAATATATCC
1 AAAC---AATCAATTAATATATCC
139855 ATAACTGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 4 0.20
25 16 0.80
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (22 bp):
AAACAATCAATTAATATATCCT
Found at i:146507 original size:61 final size:60
Alignment explanation
Indices: 146403--146559 Score: 235
Period size: 61 Copynumber: 2.6 Consensus size: 60
146393 GTGAGTGACC
*
146403 ATTTTATAATTTTTAATAGTCGAATGACTCAACAAATCAACACTCTATAGCCGAAGGACT
1 ATTTTATAATTTTTAATAGTCGAAGGACTCAACAAATCAACACTCTATAGCCGAAGGACT
* * * *
146463 ATTTTGTAACTTTTTAATAGTCGAAGGACTCCACAAAGT-AACACTCTATAGTCGAATGACT
1 ATTTTATAA-TTTTTAATAGTCGAAGGACTCAACAAA-TCAACACTCTATAGCCGAAGGACT
*
146524 ATTTTATAATTTTTAATAGTCGATGGACTCAACAAA
1 ATTTTATAATTTTTAATAGTCGAAGGACTCAACAAA
146560 ATAGTAACCT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
60 33 0.38
61 53 0.61
62 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.34
Consensus pattern (60 bp):
ATTTTATAATTTTTAATAGTCGAAGGACTCAACAAATCAACACTCTATAGCCGAAGGACT
Found at i:146572 original size:60 final size:60
Alignment explanation
Indices: 146403--146586 Score: 225
Period size: 61 Copynumber: 3.1 Consensus size: 60
146393 GTGAGTGACC
*
146403 ATTTTATAATTTTTAATAGTCGAAT-GACTCAAC-AAATCAACACTCTATAGCCGAAGGACT
1 ATTTTATAATTTTTAATAGTCG-ATGGACTCAACAAAAT-AACACTCTATAGTCGAAGGACT
* * * * *
146463 ATTTTGTAACTTTTTAATAGTCGAAGGACTCCACAAAGTAACACTCTATAGTCGAATGACT
1 ATTTTATAA-TTTTTAATAGTCGATGGACTCAACAAAATAACACTCTATAGTCGAAGGACT
*
146524 ATTTTATAATTTTTAATAGTCGATGGACTCAACAAAATAGTA-AC-CTATAATCG-AGGACT
1 ATTTTATAATTTTTAATAGTCGATGGACTCAACAAAATA--ACACTCTATAGTCGAAGGACT
146583 ATTT
1 ATTT
146587 GCGTTCTTTA
Statistics
Matches: 107, Mismatches: 12, Indels: 11
0.82 0.09 0.08
Matches are distributed among these distances:
59 9 0.08
60 44 0.41
61 50 0.47
62 4 0.04
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (60 bp):
ATTTTATAATTTTTAATAGTCGATGGACTCAACAAAATAACACTCTATAGTCGAAGGACT
Found at i:149156 original size:30 final size:31
Alignment explanation
Indices: 149097--149172 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
149087 CAACATCAGA
* *
149097 TACCAATCTAAGAATTTTTTTAAAGTTTAA-G
1 TACCAATTTGAGAATTTTTTT-AAGTTTAAGG
*
149128 TACTAATTTGAGAATTTGTTTT-AGTTTAAGG
1 TACCAATTTGAGAATTT-TTTTAAGTTTAAGG
149159 TACCAATTTGAGAA
1 TACCAATTTGAGAA
149173 AAAGAATAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 7 0.18
31 28 0.72
32 4 0.10
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (31 bp):
TACCAATTTGAGAATTTTTTTAAGTTTAAGG
Found at i:154056 original size:11 final size:11
Alignment explanation
Indices: 154019--154073 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
154009 TTTATTAAAC
*
154019 TATTATAAAAT
1 TATTATCAAAT
* *
154030 TATCATTAAAT
1 TATTATCAAAT
154041 T-TTATCAAAT
1 TATTATCAAAT
*
154051 TATTAT-AAAA
1 TATTATCAAAT
154061 TATTTATCAAAT
1 TA-TTATCAAAT
154073 T
1 T
154074 TAATGAATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
10 13 0.37
11 18 0.51
12 4 0.11
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (11 bp):
TATTATCAAAT
Found at i:154073 original size:32 final size:31
Alignment explanation
Indices: 153996--154074 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 31
153986 TAAAAATCGT
*
153996 AAATTTTATTAAA-TTTATTAAACTATTATA
1 AAATTTTATTAAATTTTATCAAACTATTATA
* *
154026 AAATTATCATTAAATTTTATCAAATTATTATA
1 AAATT-TTATTAAATTTTATCAAACTATTATA
*
154058 AAATATTTATCAAATTT
1 AAAT-TTTATTAAATTT
154075 AATGAATTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 5 0.12
31 7 0.17
32 28 0.68
33 1 0.02
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (31 bp):
AAATTTTATTAAATTTTATCAAACTATTATA
Found at i:160851 original size:14 final size:14
Alignment explanation
Indices: 160832--160869 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
160822 AATCATCCGT
*
160832 TAAATATTTTTTTA
1 TAAATATTTTTATA
160846 TAAATATTTTTATA
1 TAAATATTTTTATA
160860 TCAAA-ATTTT
1 T-AAATATTTT
160870 CTGTTCACTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 19 0.86
15 3 0.14
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (14 bp):
TAAATATTTTTATA
Found at i:169426 original size:2 final size:2
Alignment explanation
Indices: 169415--169463 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
169405 TCGAAGTTAG
169415 TA TA -A 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
169456 TA TA TA TA
1 TA TA TA TA
169464 ATAACAGCAT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:172009 original size:18 final size:18
Alignment explanation
Indices: 171986--172023 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
171976 AATTTAATCA
171986 CATAATCAAAGTCA-TAAT
1 CATAATCAAA-TCATTAAT
172004 CATAATCAAATCATTAAT
1 CATAATCAAATCATTAAT
172022 CA
1 CA
172024 ACCTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (18 bp):
CATAATCAAATCATTAAT
Done.