Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006764.1 Hibiscus syriacus cultivar Beakdansim tig00017095_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: 58450
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5455 original size:24 final size:24
Alignment explanation
Indices: 5411--5460 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
5401 ATAAAGAACC
*
5411 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
5435 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACATACCATTA
5459 AA
1 AA
5461 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:7074 original size:25 final size:24
Alignment explanation
Indices: 7032--7079 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
7022 TACATTTATA
7032 TGAGACACCAAAGCCATACCTTTTT
1 TGAGACACCAAAGCCATA-CTTTTT
*
7057 TGAGATACCAAA-CTCATACTTTT
1 TGAGACACCAAAGC-CATACTTTT
7080 ACCTTCTCGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.33, C:0.25, G:0.10, T:0.31
Consensus pattern (24 bp):
TGAGACACCAAAGCCATACTTTTT
Found at i:7845 original size:8 final size:7
Alignment explanation
Indices: 7808--7945 Score: 88
Period size: 7 Copynumber: 19.4 Consensus size: 7
7798 ATAAAGTCAT
7808 AGAAAAA
1 AGAAAAA
7815 AG--AAA
1 AGAAAAA
*
7820 AGATAAA
1 AGAAAAA
7827 AG-AAAA
1 AGAAAAA
7833 AGAAAAA
1 AGAAAAA
7840 ATGAAAAA
1 A-GAAAAA
* * *
7848 ATAACAT
1 AGAAAAA
7855 AGAAAAA
1 AGAAAAA
*
7862 GATACAAAA
1 -AGA-AAAA
7871 AGAAAAA
1 AGAAAAA
7878 AGAAAAAA
1 AG-AAAAA
*
7886 AGAAAAC
1 AGAAAAA
*
7893 AGAAAAG
1 AGAAAAA
7900 AGAAAAGA
1 AGAAAA-A
7908 TAG-AAAA
1 -AGAAAAA
*
7915 AGAAGAA
1 AGAAAAA
*
7922 A-AAAAG
1 AGAAAAA
7928 AGAAAAAA
1 AG-AAAAA
*
7936 ATAAAAA
1 AGAAAAA
7943 AGA
1 AGA
7946 GGAAACGAAA
Statistics
Matches: 101, Mismatches: 18, Indels: 24
0.71 0.13 0.17
Matches are distributed among these distances:
5 5 0.05
6 11 0.11
7 53 0.52
8 26 0.26
9 6 0.06
ACGTcount: A:0.78, C:0.02, G:0.15, T:0.05
Consensus pattern (7 bp):
AGAAAAA
Found at i:7897 original size:38 final size:37
Alignment explanation
Indices: 7829--7928 Score: 96
Period size: 38 Copynumber: 2.6 Consensus size: 37
7819 AAGATAAAAG
* * *
7829 AAAAAGAAAAAATG-AAAAAATAACATAGAAAA-AGATA
1 AAAAAGAAAAAA-GAAAAAAAGAAAACAGAAAAGAGA-A
7866 CAAAAAGAAAAAAGAAAAAAAGAAAACAGAAAAGAGAA
1 -AAAAAGAAAAAAGAAAAAAAGAAAACAGAAAAGAGAA
*
7904 AAGATAGAAAAAGAAGAAAAAAAGA
1 AA-AAAG-AAAA-AAGAAAAAAAGA
7929 GAAAAAAATA
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
37 3 0.06
38 31 0.58
39 7 0.13
40 12 0.23
ACGTcount: A:0.77, C:0.03, G:0.15, T:0.05
Consensus pattern (37 bp):
AAAAAGAAAAAAGAAAAAAAGAAAACAGAAAAGAGAA
Found at i:7927 original size:11 final size:10
Alignment explanation
Indices: 7873--7936 Score: 53
Period size: 10 Copynumber: 6.5 Consensus size: 10
7863 ATACAAAAAG
7873 AAAAA-AGAA
1 AAAAAGAGAA
*
7882 AAAAAGAAAA
1 AAAAAGAGAA
7892 CAGAAAAGAG-A
1 -A-AAAAGAGAA
* *
7903 AAAGATAGAA
1 AAAAAGAGAA
*
7913 AAAGA-AGAA
1 AAAAAGAGAA
7922 AAAAAGAGAA
1 AAAAAGAGAA
7932 AAAAA
1 AAAAA
7937 TAAAAAAGAG
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
9 18 0.40
10 19 0.42
11 2 0.04
12 6 0.13
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.02
Consensus pattern (10 bp):
AAAAAGAGAA
Found at i:7945 original size:45 final size:43
Alignment explanation
Indices: 7810--7946 Score: 124
Period size: 44 Copynumber: 3.2 Consensus size: 43
7800 AAAGTCATAG
* *
7810 AAAAA-AGAAAAGATAAAAGAAAAAG-AAAAAATG-AAAAAATA
1 AAAAAGAGAAAAGATAAAA-AAGAAGAAAAAAAAGAAAAAAATA
* * *
7851 ACATAGA-AAAAGATACAAAAAGAA-AAAAGAAAA-AAAGAAAACA
1 AAAAAGAGAAAAGATA-AAAAAGAAGAAAA-AAAAGAAA-AAAATA
*
7894 GAAAAGAGAAAAGATAGAAAAAGAAGAAAAAAAGAGAAAAAAATA
1 AAAAAGAGAAAAGATA-AAAAAGAAGAAAAAAA-AGAAAAAAATA
7939 AAAAAGAG
1 AAAAAGAG
7947 GAAACGAAAA
Statistics
Matches: 75, Mismatches: 11, Indels: 16
0.74 0.11 0.16
Matches are distributed among these distances:
41 18 0.24
42 9 0.12
43 9 0.12
44 19 0.25
45 17 0.23
46 3 0.04
ACGTcount: A:0.77, C:0.02, G:0.15, T:0.05
Consensus pattern (43 bp):
AAAAAGAGAAAAGATAAAAAAGAAGAAAAAAAAGAAAAAAATA
Found at i:9791 original size:22 final size:22
Alignment explanation
Indices: 9763--9807 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
9753 TTTTACATAT
9763 TTCCAGTGAAAGAGAAGATCCA
1 TTCCAGTGAAAGAGAAGATCCA
9785 TTCCAGTGAAAGAGAAGATCCA
1 TTCCAGTGAAAGAGAAGATCCA
9807 T
1 T
9808 GATGTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.18, G:0.22, T:0.20
Consensus pattern (22 bp):
TTCCAGTGAAAGAGAAGATCCA
Found at i:10394 original size:229 final size:233
Alignment explanation
Indices: 9965--10898 Score: 1142
Period size: 228 Copynumber: 4.1 Consensus size: 233
9955 TTTTATAATT
* *
9965 AAAAATGAGAAAGGTTTCTCATTTAAATCTAAAAATTGAATTTTTTGAAAAGTAAGAAAAGTTTC
1 AAAAATGAGAAAAGTTTCTCATTTAAATCTAAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTC
* ** * *
10030 TTACCTAG-AAATTA-TTCTGAAATTGGTAAGTCATTCGGGCCATCA--AAGTCTTTCGAACCAT
66 TTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCG-AGCAT
* * * *
10091 GATGCTTAAATCCTTCGGGTAATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTTGAGCCATC
130 GATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCAAGCAAGATGATAAGTCCTTTGGGCCATC
** *
10156 CAT-AGACCTTCGTACAGGATGTTTTCACATGTTTTCCA
195 CATAAGACCTTCGGGCAAGATGTTTTCACATGTTTTCCA
* * * *
10194 AAAAATGAGAAAGGTTTCTTATTTAAATCTGAAAATTGAAATTTTTGAAAAGT-AGAAAAGTTTA
1 AAAAATGAGAAAAGTTTCTCATTTAAATCTAAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTC
* *
10258 TTACCTAGTAAACT-TTT-CAAAATTAGTAAGTCCTTC-GGCTATCAGTAAGTCTTTCGAGCATG
66 TTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATG
* * *
10320 ATGCTTAAATCCTTCGAGTCATCTATAAGTCTTTCAAGCAAGGTGATAAGTCCTTTGGGCTATCC
131 ATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCAAGCAAGATGATAAGTCCTTTGGGCCATCC
* *
10385 ATAAGACCTTCGGGCATGATATTTTCACATGTTTT-C-
196 ATAAGACCTTCGGGCAAGATGTTTTCACATGTTTTCCA
* * * ** *
10421 AAAAATGAGAAAAGTTTCTCATTTAAGTCT-GAAGTTGAAATTTTCAAAAAGTAAGAAATGTTTC
1 AAAAATGAGAAAAGTTTCTCATTTAAATCTAAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTC
* * * * *
10485 TTTCCTAGTAAACTATTTCCAAAATTGATATGCCCTTCGGGCCATCAGTATGTCTTTCGAGCATG
66 TTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATG
* * ** * **
10550 CTGGTT-AATCCTTC-GGTCATCTATAAGTCTTTTGAGCGAGATGATAAGTCCTTCAGGCCATCC
131 ATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCAAGCAAGATGATAAGTCCTTTGGGCCATCC
* * * * **
10613 ACAAGATCTTTGGGCAAGATGTTTTCACGTGTTTTTTA
196 ATAAGACCTTCGGGCAAGATGTTTTCACATGTTTTCCA
* ** * *
10651 AAAAAGGAGAAAAAATTATCATTTAAATCTAAAAAATTGAAGTTTTTGAAAAGTAA-AGAAAGTT
1 AAAAATGAGAAAAGTTTCTCATTTAAATCT-AAAAATTGAAATTTTTGAAAAGTAAGA-AAAGTT
** **
10715 TCTTACCTAGTAAACTATTTCCAAAGCTGGTAAGTCCTTCGGGTAATCAGTAAGTCTTTCGAGCA
64 TCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCA
* * *
10780 TGATGCTTAAGTCCTTCAGGGTCATCTATAAGCCTTTCAAGCAAGATGATAAGTCTTTTGGGCCA
129 TGATGCTTAAATCCTTC-GGGTCATCTATAAGTCTTTCAAGCAAGATGATAAGTCCTTTGGGCCA
* *
10845 TCCATAATACCTTCGGGCAAAATGTTTTCACATGGTTTTCCA
193 TCCATAAGACCTTCGGGCAAGATGTTTTCACAT-GTTTTCCA
*
10887 AAATATGAGAAA
1 AAAAATGAGAAA
10899 CAATTTCCAA
Statistics
Matches: 592, Mismatches: 95, Indels: 29
0.83 0.13 0.04
Matches are distributed among these distances:
226 18 0.03
227 56 0.09
228 172 0.29
229 117 0.20
230 53 0.09
231 1 0.00
232 86 0.15
233 7 0.01
235 66 0.11
236 16 0.03
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (233 bp):
AAAAATGAGAAAAGTTTCTCATTTAAATCTAAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTC
TTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATG
ATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCAAGCAAGATGATAAGTCCTTTGGGCCATCC
ATAAGACCTTCGGGCAAGATGTTTTCACATGTTTTCCA
Found at i:10792 original size:42 final size:43
Alignment explanation
Indices: 10745--10827 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 43
10735 CCAAAGCTGG
* * *
10745 TAAGTCCTTC-GGGTAATC-AGTAAGTCTTTCGAGCATGATGCT
1 TAAGTCCTTCAGGGTAATCTA-TAAGCCTTTCAAGCAAGATGCT
*
10787 TAAGTCCTTCAGGGTCATCTATAAGCCTTTCAAGCAAGATG
1 TAAGTCCTTCAGGGTAATCTATAAGCCTTTCAAGCAAGATG
10828 ATAAGTCTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
42 10 0.29
43 24 0.69
44 1 0.03
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (43 bp):
TAAGTCCTTCAGGGTAATCTATAAGCCTTTCAAGCAAGATGCT
Found at i:10927 original size:463 final size:453
Alignment explanation
Indices: 10012--10905 Score: 1121
Period size: 457 Copynumber: 1.9 Consensus size: 453
10002 GAATTTTTTG
* ** * *
10012 AAAAGTAAGAAAAGTTTCTTACCTAGAAATTATTCTGAAATTGGTAAGTCATTCGGGCCATCAAA
1 AAAAGTAAGAAAAGTTTCTTACCTAGAAACTATTCCAAAATTGATAAGCCATTCGGGCCATCAAA
*
10077 GTCTTTCGAACCATGATGCTTAAATCCTTCGGGTAATCTGTAAGTCTTTCGAGCAAGATGATAAG
66 GTCTTTCGAACCATGATGCTTAAATCCTTCGGGTAATCTATAAGTCTTTCGAGCAAGATGATAAG
* * * * * *
10142 TCCTTTGAGCCATCCATAGACCTTCGTACAGGATGTTTTCACATGTTTTCCAAAAAATGAGAAAG
131 TCCTTAGAGCCATCCAAAGACCTTCGGACAAGATGTTTTCACATGTTTTCCAAAAAAGGAGAAAA
** * * * *
10207 GTTTCTTATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAGAAAAGTTTATTACCTAGTAAACT
196 AATTATCATTTAAATCTAAAAATTGAAATTTTTGAAAAGTAAAAAAGTTTATTACCTAGTAAACT
*
10272 TTTCAAAATTAGTAAGTCCTTCGGCTATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGA
261 TTTCAAAACTAGTAAGTCCTTCGGCTATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGA
* * * *
10337 GTCATCTATAAGTCTTTCAAGCAAGGTGATAAGTCCTTTGGGCTATCCATAAGACCTTCGGGCAT
326 GTCATCTATAAGCCTTTCAAGCAAGATGATAAGTCCTTTGGGCCATCCATAAGACCTTCGGGCAA
* * *
10402 GATATTTTCACATGTTTTCAAAAATGAGAAAAGTTTCTCATTTAAGTCTGAAGTTGAAATTTTCA
391 AATATTTTCACATGTTTTCAAAAATGAGAAAAATTTCTCA--TAAGTCTGAAGTTAAAATTTTCA
* * * *
10467 AAAAGTAAGAAATGTTTCTTTCCTAGTAAACTATTTCCAAAATTGATATGCCCTTCGGGCCATCA
1 AAAAGTAAGAAAAGTTTCTTACCTAG-AAACTA-TTCCAAAATTGATAAGCCATTCGGGCCATCA
* * * * * * *
10532 GTATGTCTTTCG-AGCATGCTGGTT-AATCCTTC-GGTCATCTATAAGTCTTTTGAGCGAGATGA
64 --AAGTCTTTCGAACCATGATGCTTAAATCCTTCGGGTAATCTATAAGTCTTTCGAGCAAGATGA
* * * * **
10594 TAAGTCCTTCAG-GCCATCCACAAGATCTTTGGGCAAGATGTTTTCACGTGTTTTTTAAAAAAGG
127 TAAGTCCTT-AGAGCCATCCA-AAGACCTTCGGACAAGATGTTTTCACATGTTTTCCAAAAAAGG
* *
10658 AGAAAAAATTATCATTTAAATCTAAAAAATTGAAGTTTTTGAAAAGTAAAGAAAGTTTCTTACCT
190 AGAAAAAATTATCATTTAAATCT-AAAAATTGAAATTTTTGAAAAGTAAA-AAAGTTTATTACCT
* * *
10723 AGTAAACTATTTCCAAAGCTGGTAAGTCCTTCGGGTAATCAGTAAGTCTTTCGAGCATGATGCTT
253 AGTAAACT-TTT-CAAAACTAGTAAGTCCTTCGGCT-ATCAGTAAGTCTTTCGAGCATGATGCTT
* * * *
10788 AAGTCCTTCAGGGTCATCTATAAGCCTTTCAAGCAAGATGATAAGTCTTTTGGGCCATCCATAAT
315 AAATCCTTC-GAGTCATCTATAAGCCTTTCAAGCAAGATGATAAGTCCTTTGGGCCATCCATAAG
*
10853 ACCTTCGGGCAAAATGTTTTCACATGGTTTTCCAAAATATGAGAAACAATTTC
379 ACCTTCGGGCAAAATATTTTCACAT-GTTTT-CAAAA-ATGAGAAA-AATTTC
10906 CAAAGTTTCT
Statistics
Matches: 371, Mismatches: 52, Indels: 20
0.84 0.12 0.05
Matches are distributed among these distances:
455 24 0.06
456 48 0.13
457 85 0.23
458 32 0.09
459 30 0.08
460 3 0.01
461 19 0.05
462 36 0.10
463 71 0.19
464 5 0.01
465 5 0.01
466 8 0.02
467 5 0.01
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (453 bp):
AAAAGTAAGAAAAGTTTCTTACCTAGAAACTATTCCAAAATTGATAAGCCATTCGGGCCATCAAA
GTCTTTCGAACCATGATGCTTAAATCCTTCGGGTAATCTATAAGTCTTTCGAGCAAGATGATAAG
TCCTTAGAGCCATCCAAAGACCTTCGGACAAGATGTTTTCACATGTTTTCCAAAAAAGGAGAAAA
AATTATCATTTAAATCTAAAAATTGAAATTTTTGAAAAGTAAAAAAGTTTATTACCTAGTAAACT
TTTCAAAACTAGTAAGTCCTTCGGCTATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGA
GTCATCTATAAGCCTTTCAAGCAAGATGATAAGTCCTTTGGGCCATCCATAAGACCTTCGGGCAA
AATATTTTCACATGTTTTCAAAAATGAGAAAAATTTCTCATAAGTCTGAAGTTAAAATTTTCA
Found at i:11467 original size:135 final size:134
Alignment explanation
Indices: 11178--11619 Score: 507
Period size: 134 Copynumber: 3.3 Consensus size: 134
11168 GCAAATTGAA
* * * * *
11178 CTCGATTCAATCTTCCCTAAGGAACAGTGGAATGAAACAACATTT-CCAGATCTGATTTTTCCTC
1 CTCGATTCAATCTTCCCTGAGTAACAGTGGAATGAATC-ACCTTTCCCAGATCTGATTTTCCCTC
* * ** *
11242 AAGAAGAAGTGGAACATATCCCA-CTCTTTTTAGATTTGATATT-CCTAGAGTAACAGCGGAACA
65 AAGAAGAAGCGGAACAGAT-CCATCTCTTTCAAGATTTGATATTCCCT-GAGTAACAGTGGAACA
11305 AGTCTGC
128 AGTCTGC
* *
11312 CTCGATTCAATCTTCCCTGAGTAACAGTGGAATGAATCACCTTTCCCAGGTCTGATTTTCCCTCT
1 CTCGATTCAATCTTCCCTGAGTAACAGTGGAATGAATCACCTTTCCCAGATCTGATTTTCCCTCA
* * * *
11377 ACAAGAAGCGTAACAGATCCATTTCTTTCAAAGATTTGATATTCCCTGAGTAACAGTGGAACAAA
66 AGAAGAAGCGGAACAGATCCATCTCTTTC-AAGATTTGATATTCCCTGAGTAACAGTGGAACAAG
11442 TCTGC
130 TCTGC
* * * * ** *
11447 CTTGATTTAATCTTCTCTGAGTGACAGCAGAATGAATCA-CGTTCCCAGATCTGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAGTAACAGTGGAATGAATCACCTTTCCCAGATCTGATTTTCCCTCA
* ** * *
11511 AGAATAAGCGGAGTAGATCCCTCTCTTTTCAAGATTTGATATTCCCTGAGCAACAGTGGAACAAG
66 AGAAGAAGCGGAACAGATCCATCTC-TTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAG
* *
11576 TATAC
130 TCTGC
* *
11581 CTCGATTCAATCTTCCTTGAAG-AACAATGGAATGAATCA
1 CTCGATTCAATCTTCCCTG-AGTAACAGTGGAATGAATCA
11620 ACGTTTCTCG
Statistics
Matches: 258, Mismatches: 44, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
133 8 0.03
134 175 0.68
135 72 0.28
136 3 0.01
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.30
Consensus pattern (134 bp):
CTCGATTCAATCTTCCCTGAGTAACAGTGGAATGAATCACCTTTCCCAGATCTGATTTTCCCTCA
AGAAGAAGCGGAACAGATCCATCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
CTGC
Found at i:14366 original size:31 final size:31
Alignment explanation
Indices: 14323--14386 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
14313 AAAGCTAACA
*
14323 GATGAATGATTGATT-TCAAGTATGCGTGATT
1 GATGAATGATTGATTCT-AAGTATGCATGATT
* *
14354 GATGCATGATTGATTCTAAGTATGTATGATT
1 GATGAATGATTGATTCTAAGTATGCATGATT
14385 GA
1 GA
14387 ACGCAAGTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 28 0.97
32 1 0.03
ACGTcount: A:0.30, C:0.06, G:0.25, T:0.39
Consensus pattern (31 bp):
GATGAATGATTGATTCTAAGTATGCATGATT
Found at i:21044 original size:27 final size:28
Alignment explanation
Indices: 20990--21044 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
20980 GTCATATTTC
20990 ATATAGTATATAATAACTGCATGAGATAGT
1 ATATAGTATATAAT-A-TGCATGAGATAGT
*
21020 ATATAGTATATAAT-TGCATGTGATA
1 ATATAGTATATAATATGCATGAGATA
21045 TTACATCTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 10 0.42
30 14 0.58
ACGTcount: A:0.42, C:0.05, G:0.16, T:0.36
Consensus pattern (28 bp):
ATATAGTATATAATATGCATGAGATAGT
Found at i:29960 original size:21 final size:20
Alignment explanation
Indices: 29924--29965 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
29914 CAGACTAGTT
* *
29924 TTATTATATTATGATATTAA
1 TTATTATATGATGATACTAA
29944 TTATTATTATGATGATACTAA
1 TTATTA-TATGATGATACTAA
29965 T
1 T
29966 CGATATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.52
Consensus pattern (20 bp):
TTATTATATGATGATACTAA
Found at i:30440 original size:94 final size:94
Alignment explanation
Indices: 30279--30463 Score: 352
Period size: 94 Copynumber: 2.0 Consensus size: 94
30269 GAGATGAAAC
* *
30279 AGAAATTTCAATAGTGTTTCGGTGATATCGCTTACCTCCTGGTTGTCGATATAGAGGATGATTTA
1 AGAAATTTCAACAGTGTTTCAGTGATATCGCTTACCTCCTGGTTGTCGATATAGAGGATGATTTA
30344 TTGAGGGCACTGATTCAGTTTTGTAAAAT
66 TTGAGGGCACTGATTCAGTTTTGTAAAAT
30373 AGAAATTTCAACAGTGTTTCAGTGATATCGCTTACCTCCTGGTTGTCGATATAGAGGATGATTTA
1 AGAAATTTCAACAGTGTTTCAGTGATATCGCTTACCTCCTGGTTGTCGATATAGAGGATGATTTA
30438 TTGAGGGCACTGATTCAGTTTTGTAA
66 TTGAGGGCACTGATTCAGTTTTGTAA
30464 TCCAAGCTAA
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 89 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (94 bp):
AGAAATTTCAACAGTGTTTCAGTGATATCGCTTACCTCCTGGTTGTCGATATAGAGGATGATTTA
TTGAGGGCACTGATTCAGTTTTGTAAAAT
Found at i:33791 original size:22 final size:23
Alignment explanation
Indices: 33755--33799 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
33745 TTTTTTTTCA
*
33755 TTTGTTTTATTTATTATTATTAT
1 TTTGTTTTATATATTATTATTAT
33778 TTTGTTTTA-ATATTATTATTAT
1 TTTGTTTTATATATTATTATTAT
33800 ATTATTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (23 bp):
TTTGTTTTATATATTATTATTAT
Found at i:33835 original size:3 final size:3
Alignment explanation
Indices: 33765--33815 Score: 63
Period size: 3 Copynumber: 18.0 Consensus size: 3
33755 TTTGTTTTAT
* *
33765 TTA TTA TTA TTA TT- TTG TT- TTA ATA TTA TTA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
33810 TTA TTA
1 TTA TTA
33816 AATAAATAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 6 0.14
3 37 0.86
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:35229 original size:3 final size:3
Alignment explanation
Indices: 35221--35250 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
35211 TTTACTTTTA
*
35221 ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
35251 TAGCTATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:39374 original size:15 final size:15
Alignment explanation
Indices: 39354--39385 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
39344 ATCAATACCT
39354 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
39369 TTTTGCATACATTCA
1 TTTTGCATACATGCA
39384 TT
1 TT
39386 ATTCATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:46269 original size:20 final size:18
Alignment explanation
Indices: 46246--46312 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 18
46236 ATTATGCTTG
46246 AAGAAAAAATGAAATGAAAA
1 AAGAAAAAA-GAAA-GAAAA
* *
46266 AAGAAAAAAAAAAAGAAGAG
1 AAG-AAAAAAGAAAGAA-AA
46286 AAGAAAAAAAGAAA-AAAA
1 AAG-AAAAAAGAAAGAAAA
46304 AGAGAAAAA
1 A-AGAAAAA
46313 GGAGGGTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
18 7 0.17
19 7 0.17
20 20 0.50
21 6 0.15
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (18 bp):
AAGAAAAAAGAAAGAAAA
Found at i:46300 original size:24 final size:24
Alignment explanation
Indices: 46246--46303 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
46236 ATTATGCTTG
*
46246 AAGAAAAAATGAAATGAAAAAAGA
1 AAGAAAAAAAGAAATGAAAAAAGA
*
46270 AAAAAAAAAAGAAGA-GAAGAAAA-A
1 AAGAAAAAAAGAA-ATGAA-AAAAGA
46294 AAGAAAAAAA
1 AAGAAAAAAA
46304 AGAGAAAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 24 0.83
25 5 0.17
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (24 bp):
AAGAAAAAAAGAAATGAAAAAAGA
Found at i:48028 original size:113 final size:113
Alignment explanation
Indices: 47819--48236 Score: 534
Period size: 113 Copynumber: 3.8 Consensus size: 113
47809 ATCCATCACA
47819 ATGGATCAGCTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
1 ATGGATCAGC-TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
* * *
47884 TTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAA-TCTATCACTTG
65 TTCATAATGAGAAGAACTTGTTCAACATTTTGCTTAAATTC-ATCACTTG
*
47933 ATGGATCAGCTTTTCCAGAGAAACTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
1 ATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
* **
47998 TCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCAC-CC
66 TCATAATGAGAAGAACTTGTTCAACATTTTGCTTAAATTCATCACTTG
* ** * ** * * *
48045 AGTGGATTAGCAGTGCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAA
1 A-TGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
* *
48110 TTCATAATGAGAAGAATTTGTTCAACATTTTGTTTAAATTCATCACTTG
65 TTCATAATGAGAAGAACTTGTTCAACATTTTGCTTAAATTCATCACTTG
* * *
48159 ATGGATTAACTTTTCCAGAGAAAGTTCATAAT---------TCATCTGAAGAAAGAAGAAGAAGT
1 ATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
*
48215 TCATAATGAGAAGAGCTTGTTC
66 TCATAATGAGAAGAACTTGTTC
48237 GACCTTTGCA
Statistics
Matches: 268, Mismatches: 33, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
104 41 0.15
112 1 0.00
113 213 0.79
114 13 0.05
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (113 bp):
ATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
TCATAATGAGAAGAACTTGTTCAACATTTTGCTTAAATTCATCACTTG
Found at i:48636 original size:17 final size:17
Alignment explanation
Indices: 48587--48642 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
48577 TTCATTTGTT
*
48587 TTATT-TATTATTGTTA
1 TTATTATATTATTATTA
* * *
48603 TT-TTGTTTTAATATTA
1 TTATTATATTATTATTA
48619 TTATTATATTATTATTA
1 TTATTATATTATTATTA
48636 TTATTAT
1 TTATTAT
48643 TAAATAAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
15 2 0.06
16 12 0.38
17 18 0.56
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.68
Consensus pattern (17 bp):
TTATTATATTATTATTA
Found at i:48664 original size:3 final size:3
Alignment explanation
Indices: 48591--48644 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
48581 TTTGTTTTAT
* * *
48591 TTA TTA TTG TTA TT- TTG TT- TTA ATA TTA TTA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
48636 TTA TTA TTA
1 TTA TTA TTA
48645 AATAAATAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
2 6 0.14
3 38 0.86
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:50126 original size:20 final size:20
Alignment explanation
Indices: 50101--50149 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
50091 TAAATAATAT
50101 TTATTTTATTTA-TTTAAATC
1 TTATTTTATTTACTTTAAA-C
* *
50121 TTA-TTTAATTACTTTTAAC
1 TTATTTTATTTACTTTAAAC
50140 TTATTTTATT
1 TTATTTTATT
50150 CATGTTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTTATTTACTTTAAAC
Found at i:50278 original size:19 final size:19
Alignment explanation
Indices: 50256--50292 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
50246 TATTTTATAA
50256 ATTATATATTAATTTTTTT
1 ATTATATATTAATTTTTTT
* *
50275 ATTATTTATTTATTTTTT
1 ATTATATATTAATTTTTT
50293 AATATCGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (19 bp):
ATTATATATTAATTTTTTT
Found at i:50288 original size:118 final size:117
Alignment explanation
Indices: 50154--50386 Score: 281
Period size: 118 Copynumber: 2.0 Consensus size: 117
50144 TTTATTCATG
* * * * *
50154 TTTAATATTTATTTATTTTTCAATAT-TAAG-AAAGGGCGGTCTTAAAATAACTAGATGTCCAAT
1 TTTAATATTTATTTATTTTTCAATATCGAAGAAAAGAGCGGTCTCAAAACAACTAGAAGTCC-AT
* *
50217 TTCTGATATTTTTAAATAAATAAATATTCTATTTTATAAATTATATATTAATTTT
65 TTCTGATATTTCTAAATAAATAAATATTCTA-TTTATAAA-TATATATAAATTTT
* * * ** * *
50272 TTTATTATTTATTTATTTTTTAATATCGAAGAAAAGAGCTGTCTCAAGGCACCTAGAAGTCCTTT
1 TTTAATATTTATTTATTTTTCAATATCGAAGAAAAGAGCGGTCTCAAAACAACTAGAAGTCCATT
* *
50337 TCTGATATTTCTAAATAAATAACTATTTTATTTATAAATATATATAAATT
66 TCTGATATTTCTAAATAAATAAATATTCTATTTATAAATATATATAAATT
50387 AATATATATT
Statistics
Matches: 97, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
117 11 0.11
118 32 0.33
119 32 0.33
120 22 0.23
ACGTcount: A:0.37, C:0.09, G:0.08, T:0.46
Consensus pattern (117 bp):
TTTAATATTTATTTATTTTTCAATATCGAAGAAAAGAGCGGTCTCAAAACAACTAGAAGTCCATT
TCTGATATTTCTAAATAAATAAATATTCTATTTATAAATATATATAAATTTT
Found at i:54645 original size:54 final size:53
Alignment explanation
Indices: 54587--54771 Score: 210
Period size: 54 Copynumber: 3.4 Consensus size: 53
54577 AATCTACCAC
* * * *
54587 CTCATTATGAATTACGTGGGATGAACACCTAGTGCCAATACGAAAATTCATAAA
1 CTCATTATGAATTTCTTAGGTTGAA-ACCTAGTGCCAATACGAAAATTCATAAA
* * *
54641 CTCATTATGAATTTCTTAAGTTGCAAACAC-AATGCTAATACGAAAATTCATAAA
1 CTCATTATGAATTTCTTAGGTTG-AAAC-CTAGTGCCAATACGAAAATTCATAAA
* * * *
54695 CTTATTATGAATTTCTTAGGTTGCATACATAGTGCCAATACAAAAATTCATAAA
1 CTCATTATGAATTTCTTAGGTTG-AAACCTAGTGCCAATACGAAAATTCATAAA
* *
54749 CTTATTATGAATTTATTAGGTTG
1 CTCATTATGAATTTCTTAGGTTG
54772 CACACATATT
Statistics
Matches: 113, Mismatches: 15, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
54 110 0.97
55 3 0.03
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (53 bp):
CTCATTATGAATTTCTTAGGTTGAAACCTAGTGCCAATACGAAAATTCATAAA
Found at i:54772 original size:54 final size:54
Alignment explanation
Indices: 54616--54779 Score: 247
Period size: 54 Copynumber: 3.0 Consensus size: 54
54606 GATGAACACC
* *
54616 TAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCAAACA
1 TAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGGTTGCAAACA
* * * *
54670 CAATGCTAATACGAAAATTCATAAACTTATTATGAATTTCTTAGGTTGCATACA
1 TAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGGTTGCAAACA
* * *
54724 TAGTGCCAATACAAAAATTCATAAACTTATTATGAATTTATTAGGTTGCACACA
1 TAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGGTTGCAAACA
54778 TA
1 TA
54780 TTGGCCATTG
Statistics
Matches: 98, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 98 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (54 bp):
TAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGGTTGCAAACA
Done.