Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005228.1 Hibiscus syriacus cultivar Beakdansim tig00011838_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: 52850
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:4542 original size:49 final size:49
Alignment explanation
Indices: 4306--4544 Score: 271
Period size: 49 Copynumber: 4.9 Consensus size: 49
4296 ATACCATGAG
* * * * *
4306 TGGCACCTTTTGTGTCGATAATGCATCGTTATGCATTTAACTGTCATTAA
1 TGGCACCTTTTATGCCGA-AATGCACCGTTATGCATTTAATTTTCATTAA
* * ** *
4356 TGGCACCTTTTACGTCGAAATGCACCGTTATGCATTTAACATTCATTAG
1 TGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAATTTTCATTAA
* * * * *
4405 TTGCACCTTTTATGCCTAAATGCACCGTTGTGCATTTTATTTTCGTTAA
1 TGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAATTTTCATTAA
* * *
4454 TGGCACCTTTTATGCCTAAATTCACCGTTATGCATTTAATTTTCATTAG
1 TGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAATTTTCATTAA
* * * *
4503 TGGTACATTTTATGCCGAAATTCACCGTTATGCCTTTAATTT
1 TGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAATTT
4545 GGCAATCATT
Statistics
Matches: 163, Mismatches: 26, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
49 147 0.90
50 16 0.10
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (49 bp):
TGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAATTTTCATTAA
Found at i:12159 original size:16 final size:17
Alignment explanation
Indices: 12131--12166 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
12121 AAAGCGAAAA
12131 AAATATGAAAAAGAACG
1 AAATATGAAAAAGAACG
*
12148 AAATAT-AAAAAGAATG
1 AAATATGAAAAAGAACG
12164 AAA
1 AAA
12167 AGAAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.69, C:0.03, G:0.14, T:0.14
Consensus pattern (17 bp):
AAATATGAAAAAGAACG
Found at i:13087 original size:18 final size:19
Alignment explanation
Indices: 13064--13106 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
13054 ATAGTTTAAC
*
13064 TATTTTCA-TTAGGATTTA
1 TATTTTCATTTAGGAATTA
*
13082 TATTTTTATTTTAGGAATTA
1 TATTTTCA-TTTAGGAATTA
13102 TATTT
1 TATTT
13107 CCTTATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.33
20 14 0.67
ACGTcount: A:0.28, C:0.02, G:0.09, T:0.60
Consensus pattern (19 bp):
TATTTTCATTTAGGAATTA
Found at i:13856 original size:15 final size:16
Alignment explanation
Indices: 13836--13865 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
13826 ATTTATTTAA
13836 TTATTTT-TTTTTTTC
1 TTATTTTATTTTTTTC
13851 TTATTTTATTTTTTT
1 TTATTTTATTTTTTT
13866 AAAAATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.87
Consensus pattern (16 bp):
TTATTTTATTTTTTTC
Found at i:15725 original size:21 final size:21
Alignment explanation
Indices: 15701--15752 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
15691 CGAACCTCAG
*
15701 TTTCCAAATTCGCATTGCGCT
1 TTTCCAAATTCGCATTGCGAT
*
15722 TTTCCAAATTCGCGTTGCGAT
1 TTTCCAAATTCGCATTGCGAT
15743 TTTCCAAATT
1 TTTCCAAATT
15753 TACAACACTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.21, C:0.25, G:0.13, T:0.40
Consensus pattern (21 bp):
TTTCCAAATTCGCATTGCGAT
Found at i:15815 original size:20 final size:20
Alignment explanation
Indices: 15792--15867 Score: 127
Period size: 20 Copynumber: 3.9 Consensus size: 20
15782 GATTTCTAAA
*
15792 TTCGCAACGCGAATTTTGTT
1 TTCGCAACTCGAATTTTGTT
15812 TTCGCAACTCGAATTTTGTT
1 TTCGCAACTCGAATTTTGTT
*
15832 TTCTCAACTCGAATTTTGTT
1 TTCGCAACTCGAATTTTGTT
15852 TTCGCAACTCG-ATTTT
1 TTCGCAACTCGAATTTT
15868 CGAATTTGCA
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
19 5 0.09
20 48 0.91
ACGTcount: A:0.20, C:0.21, G:0.14, T:0.45
Consensus pattern (20 bp):
TTCGCAACTCGAATTTTGTT
Found at i:15817 original size:40 final size:39
Alignment explanation
Indices: 15772--15899 Score: 143
Period size: 40 Copynumber: 3.2 Consensus size: 39
15762 GAATTTCAAA
*
15772 TTCGCAACTCGATTTCTAAATTCGCAACGCGAATTTTGTT
1 TTCGCAACTCGATTT-TGAATTCGCAACGCGAATTTTGTT
** * *
15812 TTCGCAACTCGAATTTTGTTTTCTCAACTCGAATTTTGTT
1 TTCGCAACTCG-ATTTTGAATTCGCAACGCGAATTTTGTT
*
15852 TTCGCAACTCGATTTTCGAATTTGCAACAG-GAATTTT-TAT
1 TTCGCAACTCGATTTT-GAATTCGCAAC-GCGAATTTTGT-T
15892 TTCGCAAC
1 TTCGCAAC
15900 AGGTTTTAGT
Statistics
Matches: 74, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
39 6 0.08
40 64 0.86
41 4 0.05
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (39 bp):
TTCGCAACTCGATTTTGAATTCGCAACGCGAATTTTGTT
Found at i:17051 original size:64 final size:64
Alignment explanation
Indices: 16893--17044 Score: 193
Period size: 64 Copynumber: 2.4 Consensus size: 64
16883 AATTTAAAAC
* * *
16893 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAACAATAAGAATTATTTATACATTAATTA
1 AACAAATCAACTTTTACAAATCAATTAAATAAGCAAAAAATAAGAATTATTTATACATCAATTA
* *** *
16957 AACAAATCAACTTTTACAAATTAATTAAATAAGCAAAAAATAATTCTTATTT-TCTCA-CAATTA
1 AACAAATCAACTTTTACAAATCAATTAAATAAGCAAAAAATAAGAATTATTTAT-ACATCAATTA
*
17020 AATAAATCAAC-TTTACAAATCAATT
1 AACAAATCAACTTTTACAAATCAATT
17045 GTAAATACAT
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
62 13 0.17
63 16 0.21
64 48 0.62
ACGTcount: A:0.51, C:0.14, G:0.02, T:0.32
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAATAAGCAAAAAATAAGAATTATTTATACATCAATTA
Found at i:18415 original size:21 final size:21
Alignment explanation
Indices: 18386--18498 Score: 93
Period size: 21 Copynumber: 5.4 Consensus size: 21
18376 GTGAATCGGT
* *
18386 CTCTCGAACGGTGGGAGGGAC
1 CTCTTGAACGGTGGGAGGGGC
* **
18407 CTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
*
18428 CTCTTTAACGGTGGGAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
**
18449 CTCTTGAA-GGATGATAGGGGC
1 CTCTTGAACGG-TGGGAGGGGC
* * * **
18470 CTCTTAAACGATAGGAGATGC
1 CTCTTGAACGGTGGGAGGGGC
18491 CTCTTGAA
1 CTCTTGAA
18499 TGATGACAGG
Statistics
Matches: 70, Mismatches: 20, Indels: 4
0.74 0.21 0.04
Matches are distributed among these distances:
20 2 0.03
21 67 0.96
22 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.35, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGC
Found at i:18452 original size:42 final size:42
Alignment explanation
Indices: 18392--18508 Score: 153
Period size: 42 Copynumber: 2.8 Consensus size: 42
18382 CGGTCTCTCG
* *
18392 AACGGTGGGAGGGACCTCTTGAACGATGACAGGGGCCTCTTT
1 AACGGTGGGAGGGGCCTCTTGAACGATGACAGGGGCCTCTTA
* *
18434 AACGGTGGGAGGGGCCTCTTGAAGGATGATAGGGGCCTCTTA
1 AACGGTGGGAGGGGCCTCTTGAACGATGACAGGGGCCTCTTA
* * ** *
18476 AACGATAGGAGATGCCTCTTGAATGATGACAGG
1 AACGGTGGGAGGGGCCTCTTGAACGATGACAGG
18509 TGAATCGGGC
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.25, C:0.18, G:0.36, T:0.21
Consensus pattern (42 bp):
AACGGTGGGAGGGGCCTCTTGAACGATGACAGGGGCCTCTTA
Found at i:18903 original size:21 final size:21
Alignment explanation
Indices: 18879--18928 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
18869 ACTATTGTCT
* *
18879 TCACGTAAAGTATTGACCTCC
1 TCACGTAAAGCATTGACCTCA
18900 TCACGTAAAGCATTGACCTCA
1 TCACGTAAAGCATTGACCTCA
18921 TCACGTAA
1 TCACGTAA
18929 CTCCCCTAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (21 bp):
TCACGTAAAGCATTGACCTCA
Found at i:21008 original size:20 final size:21
Alignment explanation
Indices: 20983--21022 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
20973 TCTGAGAGAT
20983 GGAGAT-AGACGGATTTCGGC
1 GGAGATGAGACGGATTTCGGC
21003 GGAGATGGAGACGGATTTCG
1 GGAGAT-GAGACGGATTTCG
21023 TCATAGATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
22 12 0.67
ACGTcount: A:0.25, C:0.12, G:0.42, T:0.20
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGGC
Found at i:21016 original size:22 final size:22
Alignment explanation
Indices: 20989--21040 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
20979 AGATGGAGAT
*
20989 AGACGGATTTCGGCGGAGATGG
1 AGACGGATTTCGGCAGAGATGG
* *
21011 AGACGGATTTCGTCATAGATGG
1 AGACGGATTTCGGCAGAGATGG
*
21033 GGACGGAT
1 AGACGGAT
21041 GTCACCGTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.25, C:0.13, G:0.40, T:0.21
Consensus pattern (22 bp):
AGACGGATTTCGGCAGAGATGG
Found at i:22992 original size:19 final size:20
Alignment explanation
Indices: 22951--23025 Score: 68
Period size: 19 Copynumber: 3.9 Consensus size: 20
22941 ATGACCAACA
*
22951 AATTT-GCAACGCG-ATCTCA
1 AATTTCGCAACGCGAAT-TCC
22970 AATTT-GCAACGCGAATTCC
1 AATTTCGCAACGCGAATTCC
* * *
22989 AATTTCGTAAC-CCAGTTTCC
1 AATTTCGCAACGCGA-ATTCC
23009 AATTTCGCAACGCGAAT
1 AATTTCGCAACGCGAAT
23026 ATGTAAATCG
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
19 22 0.49
20 21 0.47
21 2 0.04
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.28
Consensus pattern (20 bp):
AATTTCGCAACGCGAATTCC
Found at i:23072 original size:20 final size:20
Alignment explanation
Indices: 23049--23113 Score: 96
Period size: 20 Copynumber: 3.2 Consensus size: 20
23039 TGCGATTTTC
23049 CAAATTCGCAACGCGGAAGT
1 CAAATTCGCAACGCGGAAGT
*
23069 CAAATTCGCAACGC-GATAAT
1 CAAATTCGCAACGCGGA-AGT
*
23089 CAAATTCGTAACGCGGAAGT
1 CAAATTCGCAACGCGGAAGT
23109 CAAAT
1 CAAAT
23114 ATAAATGCAT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
19 2 0.05
20 36 0.90
21 2 0.05
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.18
Consensus pattern (20 bp):
CAAATTCGCAACGCGGAAGT
Found at i:23078 original size:41 final size:41
Alignment explanation
Indices: 22949--23113 Score: 119
Period size: 40 Copynumber: 4.1 Consensus size: 41
22939 AAATGACCAA
* * * *
22949 CAAATTTGCAACGCGA-TCT-CAAATTTGCAACGC-GAATT
1 CAAATTCGCAACGCGATTTTCCAAATTCGCAACGCGGAAGT
* * * * * *
22987 CCAATTTCGTAAC-CCAGTTTCCAATTTCGCAACGCGAATATGT
1 -CAAATTCGCAACGCGATTTTCCAAATTCGCAACGCGGA-A-GT
**
23030 -AAA-TCGCATTGCGATTTTCCAAATTCGCAACGCGGAAGT
1 CAAATTCGCAACGCGATTTTCCAAATTCGCAACGCGGAAGT
** *
23069 CAAATTCGCAACGCGATAAT-CAAATTCGTAACGCGGAAGT
1 CAAATTCGCAACGCGATTTTCCAAATTCGCAACGCGGAAGT
23109 CAAAT
1 CAAAT
23114 ATAAATGCAT
Statistics
Matches: 96, Mismatches: 22, Indels: 15
0.72 0.17 0.11
Matches are distributed among these distances:
38 2 0.02
39 13 0.14
40 44 0.46
41 35 0.36
42 1 0.01
43 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.25
Consensus pattern (41 bp):
CAAATTCGCAACGCGATTTTCCAAATTCGCAACGCGGAAGT
Found at i:23806 original size:40 final size:39
Alignment explanation
Indices: 23747--23845 Score: 128
Period size: 40 Copynumber: 2.5 Consensus size: 39
23737 AAGAGAGAGC
23747 ATTTC-ATTTGTGTTGCGAAAGTGAAATTCGCAACGCGA
1 ATTTCAATTTGTGTTGCGAAAGTGAAATTCGCAACGCGA
* * *
23785 ATTTCAATTGTGTGTTGCGAAATTGAAATTTGCAATGCGA
1 ATTTCAATT-TGTGTTGCGAAAGTGAAATTCGCAACGCGA
* *
23825 ATTTTAATTATATGTTGCGAA
1 ATTTCAATT-TGTGTTGCGAA
23846 TTTTATGTTG
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
38 5 0.09
39 3 0.06
40 45 0.85
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.37
Consensus pattern (39 bp):
ATTTCAATTTGTGTTGCGAAAGTGAAATTCGCAACGCGA
Found at i:25139 original size:20 final size:21
Alignment explanation
Indices: 25123--25338 Score: 250
Period size: 20 Copynumber: 10.7 Consensus size: 21
25113 TACACAAATT
*
25123 CGCGTTGCG-ATTTACAAATC
1 CGCGTTGCGAATTTACAGATC
25143 CGCGTTGCGAATTT-CAGATC
1 CGCGTTGCGAATTTACAGATC
* **
25163 TGCGTTGCGAAAAT-CAGATC
1 CGCGTTGCGAATTTACAGATC
25183 CGCGTTGCGAATTT-CAGATC
1 CGCGTTGCGAATTTACAGATC
* *
25203 TGCGTTGCGAATTT-CAGATT
1 CGCGTTGCGAATTTACAGATC
**
25223 CGCGTTGCGAAAAT-CAGATC
1 CGCGTTGCGAATTTACAGATC
25243 CGCGTTGCGAATTT-CAGATC
1 CGCGTTGCGAATTTACAGATC
*
25263 CGCGTTGCGAATTT-CATATC
1 CGCGTTGCGAATTTACAGATC
* *
25283 CGCGTTGCGTATTTACATATC
1 CGCGTTGCGAATTTACAGATC
* *
25304 CGCGTTGCGAATTTACATATT
1 CGCGTTGCGAATTTACAGATC
*
25325 CGCGTTGCAAATTT
1 CGCGTTGCGAATTT
25339 GGAAAATCGC
Statistics
Matches: 174, Mismatches: 20, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
20 132 0.76
21 42 0.24
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.32
Consensus pattern (21 bp):
CGCGTTGCGAATTTACAGATC
Found at i:25192 original size:60 final size:60
Alignment explanation
Indices: 25123--25338 Score: 283
Period size: 60 Copynumber: 3.6 Consensus size: 60
25113 TACACAAATT
*
25123 CGCGTTGCG-ATTTACAAATCCGCGTTGCGAATTTCAGATCTGCGTTGCGAAAATCAGATC
1 CGCGTTGCGAATTT-CAGATCCGCGTTGCGAATTTCAGATCTGCGTTGCGAAAATCAGATC
*
25183 CGCGTTGCGAATTTCAGATCTGCGTTGCGAATTTCAGAT-TCGCGTTGCGAAAATCAGATC
1 CGCGTTGCGAATTTCAGATCCGCGTTGCGAATTTCAGATCT-GCGTTGCGAAAATCAGATC
* * * ** *
25243 CGCGTTGCGAATTTCAGATCCGCGTTGCGAATTTCATATCCGCGTTGCGTATTTACATATC
1 CGCGTTGCGAATTTCAGATCCGCGTTGCGAATTTCAGATCTGCGTTGCGAAAAT-CAGATC
* * *
25304 CGCGTTGCGAATTTACATATTCGCGTTGCAAATTT
1 CGCGTTGCGAATTT-CAGATCCGCGTTGCGAATTT
25339 GGAAAATCGC
Statistics
Matches: 139, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
59 1 0.01
60 98 0.71
61 23 0.17
62 17 0.12
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.32
Consensus pattern (60 bp):
CGCGTTGCGAATTTCAGATCCGCGTTGCGAATTTCAGATCTGCGTTGCGAAAATCAGATC
Found at i:25348 original size:21 final size:21
Alignment explanation
Indices: 25324--25364 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
25314 ATTTACATAT
*
25324 TCGCGTTGCAAATTTGGAAAA
1 TCGCATTGCAAATTTGGAAAA
**
25345 TCGCATTGTGAATTTGGAAA
1 TCGCATTGCAAATTTGGAAA
25365 CTGTATTGCG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (21 bp):
TCGCATTGCAAATTTGGAAAA
Found at i:26406 original size:254 final size:257
Alignment explanation
Indices: 25928--26434 Score: 808
Period size: 254 Copynumber: 2.0 Consensus size: 257
25918 GGTCGCTCGG
*
25928 TTTTTTTAAGTGTGATATTCGGTTCGAGTCGAGTTCGGGTTTAGGCTGAAAAATACCCAACCCGA
1 TTTTTTTAAGTGTGATATTCGGGTCGAGTCGAGTTCGGGTTTAGGCTGAAAAATACCCAACCCGA
* * *
25993 AAATATATATAATTTTACCTTATATATTTAGAAATAATTACAATAATAACCCTCTATATAATTTT
66 AAAAATATATAATTTTACCTTATATACTTAGAAATAATTACAATAATAACCCTCTATATAATATT
* * *
26058 TTTCAATTAAGCTACTGTTTTTATTGAATAAAAATAATTTTTTTATTATTTCGGGTCAGGTCGAA
131 TTCCAATTAAGCTACTATTTTTATTGAATAAAAATAATTTTTTTATTATTTCCGGTCAGGTCGAA
* *
26123 TTTCTAATTCATATATTCGGGTTGGGTCGGGTGAAACTTTATTTTGGTCAGGTCGGGTCAGT
196 TTTCTAATTCATATATTCAGGTCGGGTCGGGTGAAACTTTATTTTGGTCAGGTCGGGTCAGT
* * * *
26185 TTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAATACCCGACCC-A
1 TTTTTTTAAGTGTGATATTCGGGTCGAGTCGAGTTCGGGTTTAGGCTGAAAAATACCCAACCCGA
*
26249 AAAAATATATAATTTTACCTTATATACTTAGGAATAATTACAATAAT-ACCC-CTATATATATAT
66 AAAAATATATAATTTTACCTTATATACTTAGAAATAATTACAATAATAACCCTCTATATA-ATAT
*
26312 TTTCCAATTAAG-TCACTATTTTTATTGAATAAAAAT-ATTTTTTTATTATTTCCGGTCGGGTCG
130 TTTCCAATTAAGCT-ACTATTTTTATTGAATAAAAATAATTTTTTTATTATTTCCGGTCAGGTCG
* *
26375 AGTTTCTAATTCATATATTCAGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGT
194 AATTTCTAATTCATATATTCAGGTCGGGTCGGGTGAAACTTTATTTTGGTCAGGTCGGGT
26435 GAACCCAAAA
Statistics
Matches: 231, Mismatches: 17, Indels: 7
0.91 0.07 0.03
Matches are distributed among these distances:
254 89 0.39
255 39 0.17
256 45 0.19
257 58 0.25
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (257 bp):
TTTTTTTAAGTGTGATATTCGGGTCGAGTCGAGTTCGGGTTTAGGCTGAAAAATACCCAACCCGA
AAAAATATATAATTTTACCTTATATACTTAGAAATAATTACAATAATAACCCTCTATATAATATT
TTCCAATTAAGCTACTATTTTTATTGAATAAAAATAATTTTTTTATTATTTCCGGTCAGGTCGAA
TTTCTAATTCATATATTCAGGTCGGGTCGGGTGAAACTTTATTTTGGTCAGGTCGGGTCAGT
Found at i:26797 original size:18 final size:18
Alignment explanation
Indices: 26752--26798 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
26742 TATGGAATTG
*
26752 GATTCCAATT-CTTGACA
1 GATTCCAATTCCTTCACA
*
26769 GATTTCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
*
26787 TATTCCAATTCC
1 GATTCCAATTCC
26799 CTCAGAAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.28, C:0.28, G:0.06, T:0.38
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:32794 original size:3 final size:3
Alignment explanation
Indices: 32779--32857 Score: 95
Period size: 3 Copynumber: 26.0 Consensus size: 3
32769 CCATTTTGAT
* * * *
32779 TTA TTA CTA TTA TTA TTA TAA TAA TTAA TTA TTA TTA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA
* *
32825 TTA TAA ATA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
32858 AAAATAATTA
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
3 62 0.95
4 3 0.05
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:36612 original size:14 final size:14
Alignment explanation
Indices: 36593--36635 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
36583 TTTTAAATAA
36593 TTTACATTTACATT
1 TTTACATTTACATT
* *
36607 TTTACATTCACATA
1 TTTACATTTACATT
*
36621 TTTACATTTGCATT
1 TTTACATTTACATT
36635 T
1 T
36636 GGCATTTGCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.28, C:0.16, G:0.02, T:0.53
Consensus pattern (14 bp):
TTTACATTTACATT
Found at i:44852 original size:22 final size:22
Alignment explanation
Indices: 44822--44897 Score: 100
Period size: 22 Copynumber: 3.5 Consensus size: 22
44812 ACATCTACAT
*
44822 TCTTCAAAGATGATAGATTCTC
1 TCTTTAAAGATGATAGATTCTC
*
44844 TCTTTAAAGATGATAGATTCCC
1 TCTTTAAAGATGATAGATTCTC
* *
44866 TTTTTAAAGATGACAGATTCTC
1 TCTTTAAAGATGATAGATTCTC
44888 T-TTTCAAAGA
1 TCTTT-AAAGA
44898 AAGCTTTATC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 3 0.06
22 45 0.94
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (22 bp):
TCTTTAAAGATGATAGATTCTC
Found at i:45572 original size:113 final size:113
Alignment explanation
Indices: 45333--46404 Score: 1698
Period size: 113 Copynumber: 9.5 Consensus size: 113
45323 TACCAGTTCG
* * *
45333 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAATTCATAAT--GAAGAATTTGTCC
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
* * * * ****
45396 AACCTTTTG-TTCAAATCTATCACTTGATGGATTATCTTTTCCAGTTCG
66 AACCTTTTGCCT-GAATCTATCACTTGATGGATTAGCTTTGCCAGAGAA
* * * *
45444 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTCC
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
* * **
45509 AACCTTTTG-TTCAAATCTAAT-ACCAGATGGATTAGCTTTGCCAGAGAA
66 AACCTTTTGCCT-GAATCT-ATCACTTGATGGATTAGCTTTGCCAGAGAA
45557 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
45622 AACCTTTTGCCTGAATCTATCACTTGATGGATTAGCTTTGCCAGAGAA
66 AACCTTTTGCCTGAATCTATCACTTGATGGATTAGCTTTGCCAGAGAA
45670 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
45735 AACCTTTTGCCTGAATCTATCACTTGATGGATTAGCTTTGCCAGAGAA
66 AACCTTTTGCCTGAATCTATCACTTGATGGATTAGCTTTGCCAGAGAA
45783 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAG-AATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
45847 AACCTTTTGCCTGAATCTATCACTTGATGGATTAGCTTTGCCAGAGAA
66 AACCTTTTGCCTGAATCTATCACTTGATGGATTAGCTTTGCCAGAGAA
* *
45895 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
* * * *
45960 AACCTTTTACCTGAAT-TCATCAATTGATGGATCAGCCTTT-CCAGAAAA
66 AACCTTTTGCCTGAATCT-ATCACTTGATGGATTAG-CTTTGCCAGAGAA
46008 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
46073 AACCTTTTGCCTGAATCTATCACTTGATGGATTAGCTTTGCCAGAGAA
66 AACCTTTTGCCTGAATCTATCACTTGATGGATTAGCTTTGCCAGAGAA
46121 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
46186 AACCTTTTGCCTGAATCTATCACTTGATGGATTAGCTTTGCCAGAGAA
66 AACCTTTTGCCTGAATCTATCACTTGATGGATTAGCTTTGCCAGAGAA
* *
46234 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
* * * *
46299 AACCTTTTACCTGAAT-TCATCAATTGATGGATCAGCCTTT-CCAGAAAA
66 AACCTTTTGCCTGAATCT-ATCACTTGATGGATTAG-CTTTGCCAGAGAA
* *
46347 AGTTCATAATGAA-AAGAACTCATCTGAAGAAGGAAGAAGAAGTACATAATGAGAAGAA
1 AGTTCATAAT-AAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAA
46405 CTCATCAAGA
Statistics
Matches: 909, Mismatches: 39, Indels: 24
0.94 0.04 0.02
Matches are distributed among these distances:
111 47 0.05
112 119 0.13
113 730 0.80
114 13 0.01
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (113 bp):
AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
AACCTTTTGCCTGAATCTATCACTTGATGGATTAGCTTTGCCAGAGAA
Found at i:45836 original size:23 final size:23
Alignment explanation
Indices: 45793--45837 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
45783 AGTTCATAAT
*
45793 AAGAAGAACTCATCTGAAGAAGG
1 AAGAAGAACTCATATGAAGAAGG
*
45816 AAGAAGAATTCATAATG-AGAAG
1 AAGAAGAACTCAT-ATGAAGAAG
45838 AATTTGTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.51, C:0.09, G:0.24, T:0.16
Consensus pattern (23 bp):
AAGAAGAACTCATATGAAGAAGG
Found at i:46225 original size:451 final size:448
Alignment explanation
Indices: 45333--46404 Score: 1760
Period size: 451 Copynumber: 2.4 Consensus size: 448
45323 TACCAGTTCG
* *
45333 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAATTCATAAT--GAAGAATTTGTCC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG-AAGAATTCATAATGAGAAGAATTTGTTC
* * * ****
45396 AACCTTTTG-TTCAAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAG
65 AACCTTTTGCCT-GAATCTATCACTTGATGGATTAGC-TTTCCAGAAAAAGTTCATAATGAGAAG
* **
45460 AACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTCCAACCTTTTGTTCAAAT
128 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTCCAACCTTTTCCTCAAAT
* *
45525 CTAATACCAGATGGATTAGCTTTGCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGG
193 CTAAT--CAGATGGATCAGCTTTGCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGG
45590 AAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTGAATCTATCACTTGATGGATT
256 AAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTGAATCTATCACTTGATGGATT
45655 AGCTTTGCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAAT
321 AGCTTTGCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAAT
45720 GAGAAGAATTTGTTCAACCTTTTGCCTGAATCTATCACTTGATGGATTAGCTTTGCCAGAGAA
386 GAGAAGAATTTGTTCAACCTTTTGCCTGAATCTATCACTTGATGGATTAGCTTTGCCAGAGAA
*
45783 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAATTCATAATGAGAAGAATTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAATTCATAATGAGAAGAATTTGTTCA
*
45848 ACCTTTTGCCTGAATCTATCACTTGATGGATTAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAA
66 ACCTTTTGCCTGAATCTATCACTTGATGGATTAGCTTT-CCAGAAAAAGTTCATAATGAGAAGAA
* * *
45913 CTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
130 CTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTCCAACCTTTT-CCTCAAATC
*
45978 ATCAAT-TGATGGATCAGCCTTT-CCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGG
194 -T-AATCAGATGGATCAG-CTTTGCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGG
46041 AAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTGAATCTATCACTTGATGGATT
256 AAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTGAATCTATCACTTGATGGATT
46106 AGCTTTGCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAAT
321 AGCTTTGCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAAT
46171 GAGAAGAATTTGTTCAACCTTTTGCCTGAATCTATCACTTGATGGATTAGCTTTGCCAGAGAA
386 GAGAAGAATTTGTTCAACCTTTTGCCTGAATCTATCACTTGATGGATTAGCTTTGCCAGAGAA
46234 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA-TTCATAATGAGAAGAATTTGTTC
* * * *
46299 AACCTTTTACCTGAAT-TCATCAATTGATGGATCAGCCTTTCCAGAAAAAGTTCATAATGAAAAG
65 AACCTTTTGCCTGAATCT-ATCACTTGATGGATTAG-CTTTCCAGAAAAAGTTCATAATGAGAAG
*
46363 AACTCATCTGAAGAAGGAAGAAGAAGTACATAATGAGAAGAA
128 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
46405 CTCATCAAGA
Statistics
Matches: 585, Mismatches: 26, Indels: 20
0.93 0.04 0.03
Matches are distributed among these distances:
449 12 0.02
450 38 0.06
451 401 0.69
452 126 0.22
453 5 0.01
454 3 0.01
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (448 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAATTCATAATGAGAAGAATTTGTTCA
ACCTTTTGCCTGAATCTATCACTTGATGGATTAGCTTTCCAGAAAAAGTTCATAATGAGAAGAAC
TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTCCAACCTTTTCCTCAAATCTA
ATCAGATGGATCAGCTTTGCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAA
GAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTGAATCTATCACTTGATGGATTAGCTT
TGCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAA
GAATTTGTTCAACCTTTTGCCTGAATCTATCACTTGATGGATTAGCTTTGCCAGAGAA
Found at i:46681 original size:3 final size:3
Alignment explanation
Indices: 46666--46755 Score: 135
Period size: 3 Copynumber: 30.0 Consensus size: 3
46656 CCATTTTGAT
* * * *
46666 TTA TTA CTA TTA TTA TTA TAA TTA TTA TTA TTA TTA TAA TTA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
46714 ATA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
46756 AAAAATTACA
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Done.