Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005797.1 Hibiscus syriacus cultivar Beakdansim tig00013588_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: 56310
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:4794 original size:9 final size:8
Alignment explanation
Indices: 4769--4793 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
4759 CTCATTCATC
4769 AGAAAAAA
1 AGAAAAAA
4777 AGAAAAAA
1 AGAAAAAA
4785 AGAAAAAA
1 AGAAAAAA
4793 A
1 A
4794 AATATTACAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AGAAAAAA
Found at i:6431 original size:51 final size:52
Alignment explanation
Indices: 6352--6486 Score: 220
Period size: 51 Copynumber: 2.6 Consensus size: 52
6342 ATCTATCTGG
6352 GGCATCTTAAAGGCTCACATCAGCATGAAAAAGACAGAAGTAATCCATGTG-
1 GGCATCTTAAAGGCTCACATCAGCATGAAAAAGACAGAAGTAATCCATGTGA
* *
6403 GGTATCTTAAAGGCTCACATTAGCATGAAAAAGACAGAAGTAATCCATGTGA
1 GGCATCTTAAAGGCTCACATCAGCATGAAAAAGACAGAAGTAATCCATGTGA
* *
6455 GGCATCTTGAAGGCTCACACCAGCAT-AAAAAG
1 GGCATCTTAAAGGCTCACATCAGCATGAAAAAG
6487 GTTGGGATAT
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
51 55 0.71
52 22 0.29
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.20
Consensus pattern (52 bp):
GGCATCTTAAAGGCTCACATCAGCATGAAAAAGACAGAAGTAATCCATGTGA
Found at i:7722 original size:42 final size:42
Alignment explanation
Indices: 7654--7735 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
7644 CACAAATTCG
* * *
7654 TAAATCCTTCGGGTCATCTGTTAGTCTTTCAAGCATGATGCT
1 TAAAACCTTCGGGTCATCTGTCAGTCTTTCAAGCAAGATGCT
*
7696 TAAAACCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATG
1 TAAAACCTTCGGGTCATCTGTCAGTCTTTCAAGCAAGATG
7736 ATAAGTCCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (42 bp):
TAAAACCTTCGGGTCATCTGTCAGTCTTTCAAGCAAGATGCT
Found at i:8028 original size:249 final size:249
Alignment explanation
Indices: 7568--8432 Score: 1487
Period size: 249 Copynumber: 3.5 Consensus size: 249
7558 CCCAACCAAC
* * * * *
7568 AAGTTTCTCATTTAATCTTTTTTAGAAAATGAAATTCTTGAAAAGTAAAAAGTTTCTTACCCAGT
1 AAGTTTCTCATTTAA--TGTTCTAGAAAATCAAATTCTTGAAAAGTAAGAAGTTTCTTACCTAGT
* *
7633 AAAGTATTTCCCACAAATTCGTAAATCCTTCGGGTCATCTGTTAGTCTTTCAAGCATGATGCTTA
64 AAAGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGCTTA
7698 AAACCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCTTAGGGCCATCCGTAAAGC
129 AAACCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCTTAGGGCCATCCGTAAAGC
* *
7763 CTTTGGGTAGGATGTTCACATATGATTTTTGCATGAAAATGAGATAGCAATTTTCA
194 CTTTGGGTAGGATGTTCACATATGATTTTCGCATGAAAATGAGATAGCGATTTTCA
* * *
7819 AAATTTCTCATTTAATGTTCTAGAAAATAAAATTCTTGAAAAGTAAGAAGCTTCTTACCTAGTAA
1 AAGTTTCTCATTTAATGTTCTAGAAAATCAAATTCTTGAAAAGTAAGAAGTTTCTTACCTAGTAA
7884 AGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGCTTAAA
66 AGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGCTTAAA
** * * *
7949 ACCTTCGGGTCATCTACCAGTCTTTCAAGAAAGATGATAAGTCCTTAGGGCCATTCGTAAAGCCT
131 ACCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCTTAGGGCCATCCGTAAAGCCT
*
8014 TTGGGTAGGATGTTCACATATGATTTTCGCATGAAAATGAGATATCGATTTTCA
196 TTGGGTAGGATGTTCACATATGATTTTCGCATGAAAATGAGATAGCGATTTTCA
* * *
8068 AAGTTTCTCATTTAATGTTCTAAAAAAGCAAATTCTTGAAAGGTAAGAAGTTTCTTACCTAGTAA
1 AAGTTTCTCATTTAATGTTCTAGAAAATCAAATTCTTGAAAAGTAAGAAGTTTCTTACCTAGTAA
8133 AGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGCTTAAA
66 AGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGCTTAAA
*
8198 ACCTTCGGGTTATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCTTAGGGCCATCCGTAAAGCCT
131 ACCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCTTAGGGCCATCCGTAAAGCCT
8263 TTGGGTAGGATGTTCACATATGATTTTCGCATGAAAATGAGATAGCGATTTTCA
196 TTGGGTAGGATGTTCACATATGATTTTCGCATGAAAATGAGATAGCGATTTTCA
*
8317 AAGTTTCTCATTTAATGTTCTAGAAAATCAAATTATTGAAAAGTAAGAAGTTTCTTACCTAGTAA
1 AAGTTTCTCATTTAATGTTCTAGAAAATCAAATTCTTGAAAAGTAAGAAGTTTCTTACCTAGTAA
* *
8382 AGTATTTCCCACAAATTTGTATATCCTTCGGGTCATCTGTCAGTCTTTCGA
66 AGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTGTTAGTCTTTCGA
8433 ACAAGATGAT
Statistics
Matches: 578, Mismatches: 36, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
249 564 0.98
251 14 0.02
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (249 bp):
AAGTTTCTCATTTAATGTTCTAGAAAATCAAATTCTTGAAAAGTAAGAAGTTTCTTACCTAGTAA
AGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGCTTAAA
ACCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCTTAGGGCCATCCGTAAAGCCT
TTGGGTAGGATGTTCACATATGATTTTCGCATGAAAATGAGATAGCGATTTTCA
Found at i:8220 original size:42 final size:42
Alignment explanation
Indices: 8152--8233 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
8142 CACAAATTTG
* * *
8152 TAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGCT
1 TAAAACCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGCT
*
8194 TAAAACCTTCGGGTTATCTGTCAGTCTTTCGAGCAAGATG
1 TAAAACCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATG
8234 ATAAGTCCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (42 bp):
TAAAACCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGCT
Found at i:8652 original size:48 final size:46
Alignment explanation
Indices: 8572--8667 Score: 147
Period size: 48 Copynumber: 2.0 Consensus size: 46
8562 GGTAATTTGT
*
8572 AAAACCTTCGGGTCATCCATAAGACCTTCAGTGCAGGAAGTTTTTCA
1 AAAACCTTCGGGTCATCCATAAGACCTTCAGTGCAAGAAG-TTTTCA
* *
8619 AAAAGCCTTTGGGTCATCCATAAGACCTTCAGTGCAAGATGTTTTCA
1 AAAA-CCTTCGGGTCATCCATAAGACCTTCAGTGCAAGAAGTTTTCA
8666 AA
1 AA
8668 TGAGATTTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
47 12 0.27
48 33 0.73
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (46 bp):
AAAACCTTCGGGTCATCCATAAGACCTTCAGTGCAAGAAGTTTTCA
Found at i:9008 original size:20 final size:20
Alignment explanation
Indices: 8983--9028 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
8973 ATCTGAAGAG
8983 GAAGAAGAAATTCATAATCT
1 GAAGAAGAAATTCATAATCT
9003 GAAGAAGAAATTCATAATCT
1 GAAGAAGAAATTCATAATCT
9023 GAAGAA
1 GAAGAA
9029 CTTATTCAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.52, C:0.09, G:0.17, T:0.22
Consensus pattern (20 bp):
GAAGAAGAAATTCATAATCT
Found at i:9935 original size:20 final size:21
Alignment explanation
Indices: 9891--9935 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 21
9881 CTATATTTTT
*
9891 ATTTTCCTTTATTTTGATCTC
1 ATTTTCCTTTATTTTGATATC
9912 -TTTT-CTTTATTTT-ATTATC
1 ATTTTCCTTTATTTTGA-TATC
9931 ATTTT
1 ATTTT
9936 AGTCATTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
18 1 0.05
19 12 0.57
20 8 0.38
ACGTcount: A:0.16, C:0.13, G:0.02, T:0.69
Consensus pattern (21 bp):
ATTTTCCTTTATTTTGATATC
Found at i:10119 original size:24 final size:24
Alignment explanation
Indices: 10086--10144 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 24
10076 TTTGTGCCCC
*
10086 TTTTTGTTTTATTT-ATATTTAAGT-
1 TTTTTATTTTATTTAATA-TTAA-TA
10110 TTTTTATTTT-TTTAATATTAATA
1 TTTTTATTTTATTTAATATTAATA
*
10133 CTTTTATTTTAT
1 TTTTTATTTTAT
10145 GCAATTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
22 1 0.03
23 16 0.53
24 13 0.43
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.71
Consensus pattern (24 bp):
TTTTTATTTTATTTAATATTAATA
Found at i:12860 original size:66 final size:67
Alignment explanation
Indices: 12779--12917 Score: 199
Period size: 66 Copynumber: 2.1 Consensus size: 67
12769 GTCATTGCTA
* * * *
12779 GTTAAGCTCGTTAAAATGTTGCTCGACTCGTTCTCATTAAGAAG-TTTGTTGCTTGACTCGTTGA
1 GTTAAGCTCGTTAAAATGTTGCTCGACTCGTACTCATTAAGAAGTTTTGTTGCTCGACTCCTCGA
12843 TC
66 TC
* * * *
12845 GTTAAGCTTGTTAAAATTTTTCTCGACTTGTACTCATTAAGAAGTTTTGTTGCTCGACTCCTCGA
1 GTTAAGCTCGTTAAAATGTTGCTCGACTCGTACTCATTAAGAAGTTTTGTTGCTCGACTCCTCGA
12910 TC
66 TC
12912 GTTAAG
1 GTTAAG
12918 TTCATTATTC
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
66 39 0.61
67 25 0.39
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.40
Consensus pattern (67 bp):
GTTAAGCTCGTTAAAATGTTGCTCGACTCGTACTCATTAAGAAGTTTTGTTGCTCGACTCCTCGA
TC
Found at i:13559 original size:20 final size:19
Alignment explanation
Indices: 13536--13589 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 19
13526 GTTGCGATTT
13536 AGAAAATCGCAACGTAAAAA
1 AGAAAATCGCAACGT-AAAA
*
13556 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAAC-GTAAAA
13576 AGAAAATCGCAACG
1 AGAAAATCGCAACG
13590 CGAGCTTCCA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 1 0.03
20 29 0.91
21 2 0.06
ACGTcount: A:0.54, C:0.19, G:0.19, T:0.09
Consensus pattern (19 bp):
AGAAAATCGCAACGTAAAA
Found at i:13649 original size:20 final size:20
Alignment explanation
Indices: 13624--13857 Score: 261
Period size: 20 Copynumber: 11.4 Consensus size: 20
13614 TTTAGAAGAA
*
13624 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGAGAG
*
13644 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGAGAG
*
13664 ATTCGCAATGCGATTGAGAAGAG
1 AATCGCAATGCGATT--G-AGAG
*
13687 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGAGAG
*
13707 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGAGAG
* *
13727 AATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGAGAG
* *
13747 AATCGCAACGCGATTAAGAG
1 AATCGCAATGCGATTGAGAG
* * *
13767 ATTCGCAACGCGATTAAGAG
1 AATCGCAATGCGATTGAGAG
* *
13787 ATTCGCAACGCGATTGAGAG
1 AATCGCAATGCGATTGAGAG
* *
13807 ATTCGCAACGCGATTTAGAAGAG
1 AATCGCAATGCGA-TT-G-AGAG
*
13830 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAG
13850 AATCGCAA
1 AATCGCAA
13858 CGTTGAAAAT
Statistics
Matches: 195, Mismatches: 13, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
20 156 0.80
21 4 0.02
22 3 0.02
23 32 0.16
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (20 bp):
AATCGCAATGCGATTGAGAG
Found at i:13691 original size:63 final size:61
Alignment explanation
Indices: 13602--13859 Score: 268
Period size: 63 Copynumber: 4.1 Consensus size: 61
13592 AGCTTCCAAG
* * * *
13602 TTCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAGA
1 TTCGCAACGCGA-TT-GAAGAGAATCGCAACGCGATTGAGAGAATCGCAATGCGATTGAGAGA
* * * *
13665 TTCGCAATGCGATTGAGAAGAGAATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAGA
1 TTCGCAACGCGATT--GAAGAGAATCGCAACGCGATTGAGAGAATCGCAATGCGATTGAGAGA
* * * * * * * *
13728 ATCGCAATGCGATT-TATAGAATCGCAACGCGATTAAGAGATTCGCAACGCGATTAAGAGA
1 TTCGCAACGCGATTGAAGAGAATCGCAACGCGATTGAGAGAATCGCAATGCGATTGAGAGA
* *
13788 TTCGCAACGCGATTG-AGAGATTCGCAACGCGATTTAGAAGAGAATCGCAATGCGACTGAGAGA
1 TTCGCAACGCGATTGAAGAGAATCGCAACGCGA-TT-G-AGAGAATCGCAATGCGATTGAGAGA
*
13851 ATCGCAACG
1 TTCGCAACG
13860 TTGAAAATAA
Statistics
Matches: 168, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
60 64 0.38
61 2 0.01
62 2 0.01
63 100 0.60
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (61 bp):
TTCGCAACGCGATTGAAGAGAATCGCAACGCGATTGAGAGAATCGCAATGCGATTGAGAGA
Found at i:13978 original size:6 final size:6
Alignment explanation
Indices: 13967--14079 Score: 198
Period size: 6 Copynumber: 19.5 Consensus size: 6
13957 GACACGTATT
13967 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
14015 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
14062 ACC-CG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACC
14080 CGAGACGAGA
Statistics
Matches: 107, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 20 0.19
6 87 0.81
ACGTcount: A:0.31, C:0.52, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:14787 original size:6 final size:6
Alignment explanation
Indices: 14776--14856 Score: 144
Period size: 6 Copynumber: 13.5 Consensus size: 6
14766 TCTCGTCTCG
14776 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
**
14824 GGTCGT GGTCGT GGTCGT GGTAAT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
14857 AATACGTGTC
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 71 1.00
ACGTcount: A:0.02, C:0.15, G:0.49, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:14967 original size:20 final size:20
Alignment explanation
Indices: 14944--15241 Score: 175
Period size: 20 Copynumber: 14.6 Consensus size: 20
14934 TTCTTTTTAA
14944 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
14964 CGTTGCGATTCTCTCAATCA
1 CGTTGCGATTTTCTAAATCG
* * *
14984 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
15004 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
15024 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
* * *
15047 CGTTGCGAATCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
15067 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
15087 CATTGCGATTCTATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
15107 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
15130 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
*** **
15151 CGTTGCGATTTTCTTTTTAA
1 CGTTGCGATTTTCTAAATCG
*** **
15171 CGTTGCGATTTTCTTTTTAA
1 CGTTGCGATTTTCTAAATCG
15191 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
15211 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
15230 CGTTGCGATTTT
1 CGTTGCGATTTT
15242 ATTGGTTATT
Statistics
Matches: 224, Mismatches: 47, Indels: 15
0.78 0.16 0.05
Matches are distributed among these distances:
19 17 0.08
20 161 0.72
21 14 0.06
22 4 0.02
23 28 0.12
ACGTcount: A:0.20, C:0.22, G:0.18, T:0.40
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:14990 original size:40 final size:40
Alignment explanation
Indices: 14946--15137 Score: 240
Period size: 40 Copynumber: 4.7 Consensus size: 40
14936 CTTTTTAACG
*
14946 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCACA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
* * * *
14986 TTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
*
15026 TTGCGATTTTCTTCTAAATCGCGTTGCGAATCTCTCAATCGCA
1 TTGCGA--TT-TTCTAAATCGCGTTGCGATTCTCTCAATCGCA
* * * *
15069 TTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
15109 TTGCGATTTTCTTCTAAATCGCGTTGCGA
1 TTGCGA--TT-TTCTAAATCGCGTTGCGA
15138 ACTTGGAAGC
Statistics
Matches: 128, Mismatches: 18, Indels: 9
0.83 0.12 0.06
Matches are distributed among these distances:
40 74 0.58
41 2 0.02
42 4 0.03
43 48 0.38
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (40 bp):
TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
Found at i:15054 original size:83 final size:83
Alignment explanation
Indices: 14954--15138 Score: 334
Period size: 83 Copynumber: 2.2 Consensus size: 83
14944 CGTTGCGATT
* *
14954 TTCTAAATCGCGTTGCGATTCTCTCAATCACATTGCGATTCTATAAATCGCATTGCGATTCTCTC
1 TTCTAAATCGCGTTGCGAATCTCTCAATCACATTGCGATTCTATAAATCGCATTGCGATTCTATC
*
15019 AGTCGCATTGCGATTTTC
66 AATCGCATTGCGATTTTC
*
15037 TTCTAAATCGCGTTGCGAATCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATC
1 TTCTAAATCGCGTTGCGAATCTCTCAATCACATTGCGATTCTATAAATCGCATTGCGATTCTATC
15102 AATCGCATTGCGATTTTC
66 AATCGCATTGCGATTTTC
15120 TTCTAAATCGCGTTGCGAA
1 TTCTAAATCGCGTTGCGAA
15139 CTTGGAAGCT
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 98 1.00
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.36
Consensus pattern (83 bp):
TTCTAAATCGCGTTGCGAATCTCTCAATCACATTGCGATTCTATAAATCGCATTGCGATTCTATC
AATCGCATTGCGATTTTC
Found at i:19051 original size:17 final size:17
Alignment explanation
Indices: 19029--19062 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
19019 ATATATTTTA
19029 TTAATT-TAATTTTAATT
1 TTAATTATAA-TTTAATT
19046 TTAATTATAATTTAATT
1 TTAATTATAATTTAATT
19063 AAATAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTAATTATAATTTAATT
Found at i:19063 original size:11 final size:11
Alignment explanation
Indices: 19030--19063 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
19020 TATATTTTAT
*
19030 TAATTTAATTT
1 TAATTTAATTA
19041 TAATTTTAATTA
1 TAA-TTTAATTA
19053 TAATTTAATTA
1 TAATTTAATTA
19064 AATAAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TAATTTAATTA
Found at i:19473 original size:21 final size:23
Alignment explanation
Indices: 19432--19473 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
19422 AATCACTCAA
*
19432 TAAATATAATATTTATTTATAAT
1 TAAATATAATATTTATATATAAT
19455 TAAATAT-AT-TTTATATATA
1 TAAATATAATATTTATATATA
19474 TTATAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 2 0.11
23 7 0.39
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TAAATATAATATTTATATATAAT
Found at i:19527 original size:37 final size:36
Alignment explanation
Indices: 19471--19542 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 36
19461 TATTTTATAT
* * *
19471 ATATTATAAAATAGTAAAAATTTAATAATAAATAATA
1 ATATTATAAAACAGTAAAAA-GTAAAAATAAATAATA
19508 ATATTATAAAACA-TCAAAAAGTAAAAATAAATAAT
1 ATATTATAAAACAGT-AAAAAGTAAAAATAAATAAT
19543 TTCTTTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 14 0.45
37 17 0.55
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (36 bp):
ATATTATAAAACAGTAAAAAGTAAAAATAAATAATA
Found at i:19680 original size:6 final size:6
Alignment explanation
Indices: 19669--19696 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
19659 AAATCTTAAA
19669 TTTATT TTTATT TTTATT TTTATT TTTA
1 TTTATT TTTATT TTTATT TTTATT TTTA
19697 CATTAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTATT
Found at i:19705 original size:18 final size:18
Alignment explanation
Indices: 19669--19711 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
19659 AAATCTTAAA
** *
19669 TTTATTTTTATTTTTATT
1 TTTATTTTTACATTAATT
19687 TTTATTTTTACATTAATT
1 TTTATTTTTACATTAATT
*
19705 TTAATTT
1 TTTATTT
19712 AATATATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATTTTTACATTAATT
Found at i:28133 original size:191 final size:188
Alignment explanation
Indices: 27789--28180 Score: 565
Period size: 191 Copynumber: 2.1 Consensus size: 188
27779 TTTAATTTAA
* * **
27789 AATATTCAAAAGATAAAACTCATTTTATCATTCAAACTTAAATTATATTTTTTAATTTGAAATAT
1 AATAGTCAAAAGGTAAAACTCATTTTATCATTCAAACTTAAAAAATATTTTTTAATTTGAAATAT
* * *
27854 ACAAAAGTATATAATTATCTTTAATATTCAAAGTTAAAAAGATAACAAATACATTTTTAAGTTGA
66 ACAAAAGCATATAATTATCTTTAATATTCAAAATTAAAAAGATAACAAATACATTTTTAAATTGA
*
27919 CATATTCAAAGAGTAATTATCCTACTAATATTCAAATTAAATAATAT-ATTGAATTTGC
131 CATATTAAAAGAGTAATTATCCTACTAATATTCAAATTAAA-AATATCATTGAATTTGC
*
27977 AATAGTCAAAAGGT-AAACTCCTTTTA-CTATTCAAACTTAAACAAATATTATTTTAATTTGAAA
1 AATAGTCAAAAGGTAAAACTCATTTTATC-ATTCAAACTTAAA-AAATATT-TTTTAATTTGAAA
* *
28040 TATACAAAAGCATATAATTATATTTTAATATTCAAAATTAAAAAAGATAACAAATACCTTTTTAA
63 TATACAAAAGCATATAATTAT-CTTTAATATTCAAAATT-AAAAAGATAACAAATACATTTTTAA
* * * * *
28105 ATTGACTTATTAAAAGAGTAATTATCCTACTAATATTCAAATTAAAATTATCTTTTAATTTGT
126 ATTGACATATTAAAAGAGTAATTATCCTACTAATATTCAAATTAAAAATATCATTGAATTTGC
28168 AATAGTCAAAAGG
1 AATAGTCAAAAGG
28181 ACTATGAATT
Statistics
Matches: 182, Mismatches: 16, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
186 1 0.01
187 24 0.13
188 17 0.09
189 33 0.18
190 19 0.10
191 88 0.48
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (188 bp):
AATAGTCAAAAGGTAAAACTCATTTTATCATTCAAACTTAAAAAATATTTTTTAATTTGAAATAT
ACAAAAGCATATAATTATCTTTAATATTCAAAATTAAAAAGATAACAAATACATTTTTAAATTGA
CATATTAAAAGAGTAATTATCCTACTAATATTCAAATTAAAAATATCATTGAATTTGC
Found at i:33380 original size:2 final size:2
Alignment explanation
Indices: 33373--33409 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
33363 TAAAATAGGG
33373 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
33410 CACATGATGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:36462 original size:23 final size:21
Alignment explanation
Indices: 36410--36471 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
36400 TTTTGGTGCA
*
36410 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
36430 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
36451 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
36472 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:36479 original size:21 final size:21
Alignment explanation
Indices: 36453--36492 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
36443 CCCCCTTTGA
*
36453 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
36474 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
36493 TGGGTTCTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:40226 original size:21 final size:22
Alignment explanation
Indices: 40191--40237 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
40181 AATAAAATGT
40191 TTAACGAAAAAGATACCAATTG
1 TTAACGAAAAAGATACCAATTG
* *
40213 TTAAC-AAAATGATATCAATTG
1 TTAACGAAAAAGATACCAATTG
40234 TTAA
1 TTAA
40238 AAAGATATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.30
Consensus pattern (22 bp):
TTAACGAAAAAGATACCAATTG
Found at i:40244 original size:18 final size:19
Alignment explanation
Indices: 40197--40250 Score: 74
Period size: 21 Copynumber: 2.8 Consensus size: 19
40187 ATGTTTAACG
*
40197 AAAAAGATACCAATTGTTA
1 AAAAAGATATCAATTGTTA
40216 ACAAAATGATATCAATTGTT-
1 A-AAAA-GATATCAATTGTTA
40236 AAAAAGATATCAATT
1 AAAAAGATATCAATT
40251 TTTACCAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
18 10 0.31
19 5 0.16
20 5 0.16
21 12 0.38
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.30
Consensus pattern (19 bp):
AAAAAGATATCAATTGTTA
Found at i:43205 original size:20 final size:20
Alignment explanation
Indices: 43180--43217 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
43170 CGTTGCAGCT
*
43180 AGGGTGAATTGATGCACTGC
1 AGGGTGAATCGATGCACTGC
*
43200 AGGGTGCATCGATGCACT
1 AGGGTGAATCGATGCACT
43218 AATTGCATTC
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:0.18, G:0.34, T:0.24
Consensus pattern (20 bp):
AGGGTGAATCGATGCACTGC
Found at i:43262 original size:20 final size:20
Alignment explanation
Indices: 43237--43326 Score: 73
Period size: 20 Copynumber: 4.8 Consensus size: 20
43227 CGGTGTTTGA
43237 GTGCATGGATGCACTGCAGG
1 GTGCATGGATGCACTGCAGG
*
43257 GTGCATCGATGCA---CA--
1 GTGCATGGATGCACTGCAGG
* * **
43272 ATGCATGGATACACTGCAAA
1 GTGCATGGATGCACTGCAGG
*
43292 GTGCATGGATGCACTACAGG
1 GTGCATGGATGCACTGCAGG
* *
43312 GTGTATGGATACACT
1 GTGCATGGATGCACT
43327 TTGACACCCT
Statistics
Matches: 54, Mismatches: 11, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
15 10 0.19
17 2 0.04
18 2 0.04
20 40 0.74
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (20 bp):
GTGCATGGATGCACTGCAGG
Found at i:43280 original size:35 final size:35
Alignment explanation
Indices: 43238--43305 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
43228 GGTGTTTGAG
* **
43238 TGCATGGATGCACTGCAGGGTGCATCGATGCACAA
1 TGCATGGATACACTGCAAAGTGCATCGATGCACAA
*
43273 TGCATGGATACACTGCAAAGTGCATGGATGCAC
1 TGCATGGATACACTGCAAAGTGCATCGATGCAC
43306 TACAGGGTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.28, C:0.22, G:0.29, T:0.21
Consensus pattern (35 bp):
TGCATGGATACACTGCAAAGTGCATCGATGCACAA
Found at i:45209 original size:88 final size:88
Alignment explanation
Indices: 45110--45290 Score: 265
Period size: 88 Copynumber: 2.1 Consensus size: 88
45100 AAAAATATAT
* * *
45110 AATTATTTTTTAATATT-AAAAGTTAAAAAGGCAAAAAATACCTTTTTAAGTTGACATATTCAAA
1 AATTATATTTTAATATTCAAAA-TTAAAAAGACAAAAAATACCTTTTTAAGTTGACATATTAAAA
*
45174 GAGTAATTATCCTATTAATATTCA
65 GAGTAATTATCCTACTAATATTCA
* * * *
45198 AATTATATTTTAATATTCAAAATTAAAAAGATAACAAATACCTTTTTAATTTGACTTATTAAAAG
1 AATTATATTTTAATATTCAAAATTAAAAAGACAAAAAATACCTTTTTAAGTTGACATATTAAAAG
*
45263 AGTAATTATCCTACTAATATTTA
66 AGTAATTATCCTACTAATATTCA
45286 AATTA
1 AATTA
45291 AAAATTATAT
Statistics
Matches: 83, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
88 79 0.95
89 4 0.05
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.40
Consensus pattern (88 bp):
AATTATATTTTAATATTCAAAATTAAAAAGACAAAAAATACCTTTTTAAGTTGACATATTAAAAG
AGTAATTATCCTACTAATATTCA
Found at i:45750 original size:27 final size:26
Alignment explanation
Indices: 45699--45759 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
45689 CGTTTGGTTA
*
45699 TAGAAAATATTTTCTGTTTTTATTTC
1 TAGAAAATATTTTCTGTTTTAATTTC
*
45725 TAGAAAATAGTTTTCAT-TTTTAATTTT
1 TAGAAAATA-TTTTC-TGTTTTAATTTC
*
45752 TTGAAAAT
1 TAGAAAAT
45760 TAGAAAACAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 9 0.30
27 20 0.67
28 1 0.03
ACGTcount: A:0.33, C:0.05, G:0.08, T:0.54
Consensus pattern (26 bp):
TAGAAAATATTTTCTGTTTTAATTTC
Found at i:47341 original size:14 final size:14
Alignment explanation
Indices: 47318--47361 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
47308 TACATTTATG
*
47318 GAAAACATTTTCCA
1 GAAAATATTTTCCA
*
47332 GAAAATATTTTTCAA
1 GAAAATA-TTTTCCA
*
47347 AAAAATATTTTCCA
1 GAAAATATTTTCCA
47361 G
1 G
47362 TATTTGGATG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.34
Consensus pattern (14 bp):
GAAAATATTTTCCA
Found at i:48816 original size:19 final size:21
Alignment explanation
Indices: 48792--48840 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
48782 CCCATTAATA
48792 TTCTAAGT-AA-ATAGTATAT
1 TTCTAAGTAAATATAGTATAT
48811 TTCTAAGTAAATATAGTATAT
1 TTCTAAGTAAATATAGTATAT
48832 TTCATAAGT
1 TTC-TAAGT
48841 TTGGTTTGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.30
20 2 0.07
21 12 0.44
22 5 0.19
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (21 bp):
TTCTAAGTAAATATAGTATAT
Done.