Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000488.1 Hibiscus syriacus cultivar Beakdansim tig00000930_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: 49475
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4757 original size:3 final size:3
Alignment explanation
Indices: 4749--4801 Score: 65
Period size: 3 Copynumber: 18.0 Consensus size: 3
4739 ATTTATTTAT
* *
4749 TTA TTA TTA TTA -TA TAA TAA TTA TTA TTA TTA -TA TATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
4793 TTA TTA TTA
1 TTA TTA TTA
4802 AAATATAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 4 0.09
3 38 0.84
4 3 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:4772 original size:24 final size:22
Alignment explanation
Indices: 4749--4810 Score: 81
Period size: 21 Copynumber: 2.8 Consensus size: 22
4739 ATTTATTTAT
4749 TTATTATTATTATATAATAATTA
1 TTATTATTA-TATATAATAATTA
*
4772 TTATTATTATATAT-ATTATTA
1 TTATTATTATATATAATAATTA
*
4793 TTATTATTAAAATATAAT
1 TTATTATT-ATATATAAT
4811 TACAGGCCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.40
22 10 0.29
23 11 0.31
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTATTATTATATATAATAATTA
Found at i:8109 original size:14 final size:14
Alignment explanation
Indices: 8071--8124 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
8061 ATTTTAAATA
*
8071 ATTTACATTTACAT
1 ATTTACATTTGCAT
*
8085 TTTTACATTTGCAT
1 ATTTACATTTGCAT
8099 ATTTACATTTGGCAT
1 ATTTACATTT-GCAT
* *
8114 CTTTGCATTTG
1 ATTTACATTTG
8125 TATTTTTATG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.52
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:11677 original size:26 final size:27
Alignment explanation
Indices: 11647--11701 Score: 103
Period size: 26 Copynumber: 2.1 Consensus size: 27
11637 TCATATACTC
11647 ATCCAGCAAAGAAAG-AAAAAAGAAAA
1 ATCCAGCAAAGAAAGAAAAAAAGAAAA
11673 ATCCAGCAAAGAAAGAAAAAAAGAAAA
1 ATCCAGCAAAGAAAGAAAAAAAGAAAA
11700 AT
1 AT
11702 AAAAGAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 15 0.54
27 13 0.46
ACGTcount: A:0.69, C:0.11, G:0.15, T:0.05
Consensus pattern (27 bp):
ATCCAGCAAAGAAAGAAAAAAAGAAAA
Found at i:11711 original size:20 final size:19
Alignment explanation
Indices: 11684--11740 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 19
11674 TCCAGCAAAG
11684 AAAG-AAAAAAAGAAAAATA
1 AAAGAAAAAAAAGAAAAA-A
11703 AAAGAAAAAAAAGAAAAAA
1 AAAGAAAAAAAAGAAAAAA
*
11722 AAAGAAGGAAAAAGAAAAA
1 AAAGAA-AAAAAAGAAAAA
11741 GGGAGAAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
19 11 0.31
20 24 0.69
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (19 bp):
AAAGAAAAAAAAGAAAAAA
Found at i:11713 original size:14 final size:13
Alignment explanation
Indices: 11684--11741 Score: 62
Period size: 13 Copynumber: 4.3 Consensus size: 13
11674 TCCAGCAAAG
11684 AAAGAAAAAAAGAA
1 AAAGAAAAAAA-AA
*
11698 AAATAAAAGAAAAA
1 AAAGAAAA-AAAAA
11712 AAAGAAAAAAAAA
1 AAAGAAAAAAAAA
* * *
11725 GAAGGAAAAAGAA
1 AAAGAAAAAAAAA
11738 AAAG
1 AAAG
11742 GGAGAAATTG
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
13 18 0.49
14 16 0.43
15 3 0.08
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.02
Consensus pattern (13 bp):
AAAGAAAAAAAAA
Found at i:11719 original size:27 final size:26
Alignment explanation
Indices: 11658--11721 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 26
11648 TCCAGCAAAG
** * *
11658 AAAGAAAAAAGAAAAATCCAGCAAAG
1 AAAGAAAAAAGAAAAATAAAGAAAAA
11684 AAAGAAAAAAAGAAAAATAAAAGAAAAA
1 AAAG-AAAAAAGAAAAAT-AAAGAAAAA
11712 AAAGAAAAAA
1 AAAGAAAAAA
11722 AAAGAAGGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 4 0.12
27 19 0.59
28 9 0.28
ACGTcount: A:0.80, C:0.05, G:0.12, T:0.03
Consensus pattern (26 bp):
AAAGAAAAAAGAAAAATAAAGAAAAA
Found at i:11720 original size:10 final size:10
Alignment explanation
Indices: 11688--11740 Score: 72
Period size: 10 Copynumber: 5.3 Consensus size: 10
11678 GCAAAGAAAG
11688 AAAAAAAGAA
1 AAAAAAAGAA
11698 AAATAAAAG-A
1 AAA-AAAAGAA
11708 AAAAAAAGAA
1 AAAAAAAGAA
11718 AAAAAAAGAA
1 AAAAAAAGAA
**
11728 GGAAAAAGAA
1 AAAAAAAGAA
11738 AAA
1 AAA
11741 GGGAGAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
9 5 0.14
10 27 0.73
11 5 0.14
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:11733 original size:28 final size:29
Alignment explanation
Indices: 11684--11740 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
11674 TCCAGCAAAG
*
11684 AAAGAAAAAAAGAAAAA-TAAAAGAAAAA
1 AAAGAAAAAAAGAAAAAGAAAAAGAAAAA
*
11712 AAAGAAAAAAA-AAGAAGGAAAAAGAAAAA
1 AAAGAAAAAAAGAA-AAAGAAAAAGAAAAA
11741 GGGAGAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 2 0.08
28 13 0.52
29 10 0.40
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (29 bp):
AAAGAAAAAAAGAAAAAGAAAAAGAAAAA
Found at i:15243 original size:76 final size:76
Alignment explanation
Indices: 15117--15308 Score: 332
Period size: 76 Copynumber: 2.5 Consensus size: 76
15107 ACAAGAAGCG
* *
15117 AATGTT-GTGGCATGCTGAAAACCCCTTTCAATTAGAATCATGAATATTAAAGTATTCTGAATAT
1 AATGTTAG-GGCATGCTGAAAACCCCTTTCAATCAGAATCAGGAATATTAAAGTATTCTGAATAT
*
15181 TTATATCAGCAA
65 TTATATCAACAA
15193 AATGTTAGGGCATGCTGAAAACCCCTTTCAATCAGAATCAGGAATATTAAAGTATTCTGAATATT
1 AATGTTAGGGCATGCTGAAAACCCCTTTCAATCAGAATCAGGAATATTAAAGTATTCTGAATATT
15258 TATATCAACAA
66 TATATCAACAA
*
15269 AATGTTAGGGCATGCTGAAAGCCCCTTTCAATCAGAATCA
1 AATGTTAGGGCATGCTGAAAACCCCTTTCAATCAGAATCA
15309 AGACTGTTGA
Statistics
Matches: 111, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
76 110 0.99
77 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.31
Consensus pattern (76 bp):
AATGTTAGGGCATGCTGAAAACCCCTTTCAATCAGAATCAGGAATATTAAAGTATTCTGAATATT
TATATCAACAA
Found at i:16320 original size:54 final size:54
Alignment explanation
Indices: 16235--16392 Score: 182
Period size: 54 Copynumber: 3.0 Consensus size: 54
16225 TAATTGAGAA
* *
16235 ATCTGAGTAGAAGCCAC-AGAAAAGGATGAATGTGTTGTCAAATGCTTTACGAAC
1 ATCTGAGCAGAAGCCACAAG-AAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
* * * *
16289 ATCTGAGCAGAAGCTACAAGAAAGGAAGAATGTGTTTTCAAATGTTTTAC-ATC
1 ATCTGAGCAGAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
* * * *
16342 -TC-GA-CAGAAACCACAGGAAAAGATGAATGTATTGTCAAATGTTTTACGAAC
1 ATCTGAGCAGAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
16393 CAGTGATTAT
Statistics
Matches: 88, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
50 36 0.41
51 4 0.05
52 2 0.02
53 2 0.02
54 42 0.48
55 2 0.02
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.25
Consensus pattern (54 bp):
ATCTGAGCAGAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
Found at i:17552 original size:227 final size:226
Alignment explanation
Indices: 17135--18607 Score: 2351
Period size: 227 Copynumber: 6.5 Consensus size: 226
17125 TTCAAAATAT
17135 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
*
17200 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCAAATCCATCATTTGA
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGA
* * *
17265 TGGATCAACTTTTCCAGAAAAAAGTTCATAATGAGAAGAATTCATCTGAAGAATGAAGAAGAAAT
131 TGGATCAGCTTTTCCAG-AAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAAT
17330 TCATAATGAGAAGAATTTGTTCAACCTTTTGC
195 TCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
17362 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAG-AAAAAGTTCATAATGAGAAGAACTCATCTG
*
17427 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAAACCATCATTTG
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTG
* * *
17492 ATGGATTAGCTTTTCCAGAAAAAGTTCATAATGAGAATAACTCGTCTGAAGAAGGAAGAAGAAAT
130 ATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAAT
17557 TCATAATGAGAAGAATTTGTTCAACCTTTTGC
195 TCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
17589 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAG-AAAAAGTTCATAATGAGAAGAACTCATCTG
*
17654 AAGAAGGAAGAAGAAATTCATAATAAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTG
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTG
17719 ATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAAT
130 ATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAAT
* *
17784 TCATAATGAGAAGAAATTGTTCAACCTTTT-T
195 TCATAATGAGAAGAATTTGTTCAACCTTTTGC
** *
17815 TTGAATTCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
*
17880 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATTCATCATTTGA
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGA
* * * *
17945 TGGATCAACTTTTCTAGAAAAAGTTCATAATGAGAAGAACTCATTTGAAGAAGGAAGAAAAAATT
131 TGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATT
18010 CATAATGAGAAGAATTTGTTCAACCTTTTGC
196 CATAATGAGAAGAATTTGTTCAACCTTTTGC
* * *
18041 TCAAATCCATCA-TCTGATGAATCAGCTTTTCCAGAAAAAAGTTTATAATGAGAAGAACTCATTT
1 TCAAATCCATCACT-TGATGGATCAGCTTTTCCAG-AAAAAGTTCATAATGAGAAGAACTCATCT
*
18105 GAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAATCTTTTGCTCAAATCCATCATTT
64 GAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTT
18170 GATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAA
129 GATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAA
* * *
18235 TTCATAATGAGAATAAATTGTTCAACCTTTTGT
194 TTCATAATGAGAAGAATTTGTTCAACCTTTTGC
** * *
18268 TTGAATTCATCACTTGATAGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* * ** *
18333 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGA
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGA
* * * *
18398 TGGATCAGC-ATCCCAGTGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
131 TGGATCAGCTTTTCCA--GAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAA
*
18462 TTCATAATGAGAAGAACTTGTTCAA-CTTTTCGC
194 TTCATAATGAGAAGAATTTGTTCAACCTTTT-GC
* * * * * * *
18495 TCGAATTCATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATTTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* * ** * *
18560 AGAAAGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACGTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
18608 ATGACTCTAT
Statistics
Matches: 1162, Mismatches: 76, Indels: 16
0.93 0.06 0.01
Matches are distributed among these distances:
225 188 0.16
226 160 0.14
227 704 0.61
228 110 0.09
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (226 bp):
TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGA
TGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATT
CATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:18620 original size:113 final size:113
Alignment explanation
Indices: 17135--18607 Score: 2340
Period size: 113 Copynumber: 13.0 Consensus size: 113
17125 TTCAAAATAT
*
17135 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
*
17200 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
17248 TCAAATCCATCATTTGATGGATCAACTTTTCCAGAAAAAAGTTCATAATGAGAAGAATTCATCTG
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAG-AAAAAGTTCATAATGAGAAGAACTCATCTG
*
17313 AAGAATGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
17362 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAG-AAAAAGTTCATAATGAGAAGAACTCATCTG
17427 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * *
17476 TCAAAACCATCATTTGATGGATTAGCTTTTCCAGAAAAAGTTCATAATGAGAATAACTCGTCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
17541 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
17589 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAG-AAAAAGTTCATAATGAGAAGAACTCATCTG
*
17654 AAGAAGGAAGAAGAAATTCATAATAAGAAGAATTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
17703 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* *
17768 AGAAGGAAGAAGAAATTCATAATGAGAAGAAATTGTTCAACCTTTT-T
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
** * *
17815 TTGAATTCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
17880 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * *
17928 TCAAATTCATCATTTGATGGATCAACTTTTCTAGAAAAAGTTCATAATGAGAAGAACTCATTTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
*
17993 AGAAGGAAGAAAAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * *
18041 TCAAATCCATCATCTGATGAATCAGCTTTTCCAGAAAAAAGTTTATAATGAGAAGAACTCATTTG
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAG-AAAAAGTTCATAATGAGAAGAACTCATCTG
*
18106 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAATCTTTTGC
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
18155 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* * *
18220 AGAAGGAAGAAGAAATTCATAATGAGAATAAATTGTTCAACCTTTTGT
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
** * * *
18268 TTGAATTCATCACTTGATAGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* *
18333 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
** * * * *
18381 TTGAATTCATCATTTGATGGATCAGC-ATCCCAGTGAAAGAGTTCATAATGAGAAGAACTCATCT
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCA--GAAAAAGTTCATAATGAGAAGAACTCATCT
* *
18445 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGC
64 GAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTT-GC
* * * * * * * *
18495 TCGAATTCATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATTTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* * ** * *
18560 AGAAAGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACGTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
18608 ATGACTCTAT
Statistics
Matches: 1275, Mismatches: 76, Indels: 18
0.93 0.06 0.01
Matches are distributed among these distances:
112 110 0.09
113 627 0.49
114 534 0.42
115 4 0.00
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (113 bp):
TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:18671 original size:124 final size:119
Alignment explanation
Indices: 18522--18750 Score: 311
Period size: 120 Copynumber: 1.9 Consensus size: 119
18512 TGGATCAACT
* * *
18522 TTTCCAGAGAGAGTTCATAATGAGAAGAACTCATTTGAAGAAAGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAGAGTTCACAATGAGAAGAACTCATCT---G-AAGAAGAAGAAGTTCACAATGAGA
* *
18587 AGAGCTTGTTCGACGTTTTGC-ATGACT-CTATCACAGAAGGAGATATATCATCATCAGCA
62 AGAGCTTGTTCAAC-CTTTGCTA-GACTAC-ATCACAGAAGGAGATATATCATCATCAGCA
18646 TTTCCAGA-AGAAGTTCACAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCACAATGAGAAGA
1 TTTCCAGAGAG-AGTTCACAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCACAATGAGAAGA
*
18710 GCTTGTTCAACCTTTGCTAGATTACATCACAGAAGGAGATA
65 GCTTGTTCAACCTTTGCTAGACTACATCACAGAAGGAGATA
18751 AATTGTCATC
Statistics
Matches: 96, Mismatches: 6, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
119 24 0.25
120 38 0.40
121 1 0.01
123 2 0.02
124 31 0.32
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.24
Consensus pattern (119 bp):
TTTCCAGAGAGAGTTCACAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCACAATGAGAAGAG
CTTGTTCAACCTTTGCTAGACTACATCACAGAAGGAGATATATCATCATCAGCA
Found at i:18673 original size:17 final size:17
Alignment explanation
Indices: 18651--18709 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
18641 CAGCATTTCC
18651 AGAAGAAGTTCACAATG
1 AGAAGAAGTTCACAATG
*
18668 AGAAGAA-CTCATCTGAA-G
1 AGAAGAAGTTCA-C--AATG
18686 AAGAAGAAGTTCACAATG
1 -AGAAGAAGTTCACAATG
18704 AGAAGA
1 AGAAGA
18710 GCTTGTTCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
16 3 0.09
17 16 0.47
18 2 0.06
19 10 0.29
20 3 0.09
ACGTcount: A:0.49, C:0.12, G:0.24, T:0.15
Consensus pattern (17 bp):
AGAAGAAGTTCACAATG
Found at i:18959 original size:3 final size:3
Alignment explanation
Indices: 18951--19011 Score: 97
Period size: 3 Copynumber: 20.0 Consensus size: 3
18941 CCCATTTTAT
18951 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
18996 TATA TTA TTA TTA TTA
1 T-TA TTA TTA TTA TTA
19012 AAAAATAATT
Statistics
Matches: 56, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.04
3 47 0.84
4 7 0.12
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:23514 original size:2 final size:2
Alignment explanation
Indices: 23507--23536 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
23497 AATTTTTAAA
23507 AT 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 AT
23537 TGTCATAACG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25492 original size:21 final size:19
Alignment explanation
Indices: 25450--25504 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 19
25440 AAAGAAATAA
**
25450 ATTTCTAATTAAATTTTTT
1 ATTTCTAATTAAATTTAAT
25469 ATTTCTAATTATAAATTTAAT
1 ATTTCTAA-T-TAAATTTAAT
*
25490 ATTT-TTATTAAATTT
1 ATTTCTAATTAAATTT
25505 TAAAAAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 7 0.23
19 9 0.29
20 3 0.10
21 12 0.39
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTTCTAATTAAATTTAAT
Found at i:25881 original size:16 final size:16
Alignment explanation
Indices: 25860--25899 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
25850 TTCGAGTTTC
*
25860 TTTCGGTTTGGGTTAA
1 TTTCGGTTTAGGTTAA
*
25876 TTTCGGTTTAGTTTAA
1 TTTCGGTTTAGGTTAA
*
25892 TTTTGGTT
1 TTTCGGTT
25900 CTGATTGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.12, C:0.05, G:0.25, T:0.57
Consensus pattern (16 bp):
TTTCGGTTTAGGTTAA
Found at i:39084 original size:16 final size:16
Alignment explanation
Indices: 39055--39111 Score: 57
Period size: 15 Copynumber: 3.6 Consensus size: 16
39045 TAATATTTTT
*
39055 TAAAATTTAATTACT-
1 TAAATTTTAATTACTC
39070 TAAATTTTAAATTACTCC
1 TAAATTTT-AATTACT-C
*
39088 T-AA-TTTAATCACTC
1 TAAATTTTAATTACTC
39102 TAAATTTTAA
1 TAAATTTTAA
39112 ATTTAAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
14 2 0.06
15 15 0.43
16 15 0.43
17 2 0.06
18 1 0.03
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (16 bp):
TAAATTTTAATTACTC
Found at i:44586 original size:17 final size:17
Alignment explanation
Indices: 44542--44586 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
44532 TATTAAAGAC
44542 GAATTTTTGAATTTTAA
1 GAATTTTTGAATTTTAA
**
44559 GAATTGATGAATTTATAA
1 GAATTTTTGAATTT-TAA
44577 -AATTTTTGAA
1 GAATTTTTGAA
44587 ATAATTTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 20 0.87
18 3 0.13
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (17 bp):
GAATTTTTGAATTTTAA
Found at i:44956 original size:36 final size:36
Alignment explanation
Indices: 44916--44998 Score: 123
Period size: 36 Copynumber: 2.3 Consensus size: 36
44906 ATTGGGCCGG
44916 TATATATATATTTAAATTAAATATATAAATATTATA
1 TATATATATATTTAAATTAAATATATAAATATTATA
* * *
44952 TATATAT-TAATTTAAATTAAATTTTTTAATATTATA
1 TATATATAT-ATTTAAATTAAATATATAAATATTATA
44988 TATATATATAT
1 TATATATATAT
44999 AATAATAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
35 1 0.02
36 40 0.95
37 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (36 bp):
TATATATATATTTAAATTAAATATATAAATATTATA
Found at i:45014 original size:36 final size:36
Alignment explanation
Indices: 44943--45025 Score: 100
Period size: 36 Copynumber: 2.3 Consensus size: 36
44933 TAAATATATA
* *
44943 AATATTATATATATATTAATTTAAATTAAATTTTTT
1 AATATTATATATATATTAATATAAAATAAATTTTTT
*
44979 AATATTATATATATA-T-ATATAATAATAATTATTTTT
1 AATATTATATATATATTAATATAA-AATAAAT-TTTTT
45015 AATATT-TATAT
1 AATATTATATAT
45026 GGCCGGATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
34 5 0.12
35 11 0.26
36 26 0.62
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (36 bp):
AATATTATATATATATTAATATAAAATAAATTTTTT
Found at i:45104 original size:30 final size:30
Alignment explanation
Indices: 45064--45137 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
45054 GATTACCAAA
*
45064 CCCGTCCCCGTTTAGCATAAACGGTTTT-T
1 CCCGTCCCCGTTTAGCATAAACGATTTTCT
*
45093 CTCGATCCCCGTTTAGCATAAACGATTTTCT
1 CCCG-TCCCCGTTTAGCATAAACGATTTTCT
45124 CCCGTCCCCGTTTA
1 CCCGTCCCCGTTTA
45138 ATTCGATTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
29 3 0.08
30 33 0.82
31 4 0.10
ACGTcount: A:0.18, C:0.34, G:0.15, T:0.34
Consensus pattern (30 bp):
CCCGTCCCCGTTTAGCATAAACGATTTTCT
Found at i:46006 original size:21 final size:20
Alignment explanation
Indices: 45976--46014 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
45966 TTTAACGTTG
45976 TTAGTCCTAAACTATCAATT
1 TTAGTCCTAAACTATCAATT
*
45996 TTAGTACCTAAACTTTCAA
1 TTAGT-CCTAAACTATCAA
46015 AAAAAAAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.36, C:0.21, G:0.05, T:0.38
Consensus pattern (20 bp):
TTAGTCCTAAACTATCAATT
Found at i:48384 original size:2 final size:2
Alignment explanation
Indices: 48377--48406 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
48367 TGAAAATGAC
48377 AT 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 AT
48407 TTATCTAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.