Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007027.1 Hibiscus syriacus cultivar Beakdansim tig00018191_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: 263012
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
File 2 of 2
Found at i:211228 original size:19 final size:19
Alignment explanation
Indices: 211176--211235 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
211166 GCAACGAGAT
211176 CAACGCGAAATGAAAATCG
1 CAACGCGAAATGAAAATCG
*
211195 CAA--CG--A-GAGAATCG
1 CAACGCGAAATGAAAATCG
211209 CAACGCGAAATGAAAATCG
1 CAACGCGAAATGAAAATCG
*
211228 CAATGCGA
1 CAACGCGA
211236 TTTTGGTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.45, C:0.22, G:0.23, T:0.10
Consensus pattern (19 bp):
CAACGCGAAATGAAAATCG
Found at i:211317 original size:33 final size:32
Alignment explanation
Indices: 211242--211321 Score: 99
Period size: 33 Copynumber: 2.4 Consensus size: 32
211232 GCGATTTTGG
**
211242 TTTCGCGTTGCGATTCTCTCGTTGCGATTTCCA
1 TTTCGCGTTGCGA-TCTCTCGTTGCGAAGTCCA
211275 TTTCGCGTTGCGATCTCTCGTTGCGACAGT-CA
1 TTTCGCGTTGCGATCTCTCGTTGCGA-AGTCCA
*
211307 TTCTCTCGTTGCGAT
1 TT-TCGCGTTGCGAT
211322 TTTCATTTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
32 17 0.40
33 25 0.60
ACGTcount: A:0.10, C:0.28, G:0.23, T:0.40
Consensus pattern (32 bp):
TTTCGCGTTGCGATCTCTCGTTGCGAAGTCCA
Found at i:211327 original size:20 final size:21
Alignment explanation
Indices: 211288--211342 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
211278 CGCGTTGCGA
211288 TCTCTCGTTGCGACAGTCA-T
1 TCTCTCGTTGCGACAGTCATT
***
211308 TCTCTCGTTGCGATTTTCATT
1 TCTCTCGTTGCGACAGTCATT
*
211329 TATCTCGTTGCGAC
1 TCTCTCGTTGCGAC
211343 TCTTCTGCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.13, C:0.27, G:0.18, T:0.42
Consensus pattern (21 bp):
TCTCTCGTTGCGACAGTCATT
Found at i:211462 original size:33 final size:33
Alignment explanation
Indices: 211420--211490 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
211410 AATACTAACT
*
211420 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
211453 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
211486 TGAAA
1 TGAAA
211491 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:211720 original size:22 final size:22
Alignment explanation
Indices: 211668--211722 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
211658 TGGTTGTGAG
**
211668 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
211690 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
211712 GGATTTCTTCG
1 GGATTTCTTCG
211723 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:211890 original size:20 final size:20
Alignment explanation
Indices: 211865--212058 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
211855 CTTTAAATAT
211865 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
211885 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
211907 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
211926 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
211946 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
211966 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
211986 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
212006 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
212026 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
212046 CGCGTTGCGATTT
1 CGCGTTGCGATTT
212059 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:212052 original size:60 final size:60
Alignment explanation
Indices: 211865--212058 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
211855 CTTTAAATAT
**
211865 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
211926 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
211986 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
212046 CGCGTTGCGATTT
1 CGCGTTGCGATTT
212059 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:212075 original size:21 final size:20
Alignment explanation
Indices: 212051--212127 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
212041 ATATTCGCGT
212051 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
212072 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
212092 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
212114 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
212128 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:212138 original size:20 final size:20
Alignment explanation
Indices: 212113--212164 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
212103 AAGAATCGCG
*
212113 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
212133 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
212153 TTGCGATTCTGG
1 TTGCGATTCTGG
212165 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:212747 original size:22 final size:23
Alignment explanation
Indices: 212722--212776 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
212712 TGATGGCATT
212722 AATTAATATGAATATACTTTT-A
1 AATTAATATGAATATACTTTTAA
* * *
212744 AATTAGTATTAATATATTTTTAA
1 AATTAATATGAATATACTTTTAA
212767 AATTATATAT
1 AATTA-ATAT
212777 TTCATATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 18 0.67
23 6 0.22
24 3 0.11
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (23 bp):
AATTAATATGAATATACTTTTAA
Found at i:212799 original size:22 final size:22
Alignment explanation
Indices: 212774--212815 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
212764 TAAAATTATA
212774 TATTTCATATTTTACTTAAACG
1 TATTTCATATTTTACTTAAACG
* *
212796 TATTTGATATTTTATTTAAA
1 TATTTCATATTTTACTTAAA
212816 AATATATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (22 bp):
TATTTCATATTTTACTTAAACG
Found at i:216663 original size:3 final size:3
Alignment explanation
Indices: 216655--216695 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
216645 ATGAACGCAA
*
216655 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAA AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
216696 AAGGATCCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:218362 original size:106 final size:106
Alignment explanation
Indices: 218177--219466 Score: 2222
Period size: 106 Copynumber: 12.3 Consensus size: 106
218167 GTATTGTTCC
* *** * * *
218177 GAGTCCAATATCCTCCACCGTGAAGTTGAAATTGGCTCTGGAACTG-GAAAATTGTTTATTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AAGTTGTTTATTGACA
* *
218241 ACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG-CATG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
218283 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
218348 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
218389 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG-TATTGAAATTGAGAAGTTGTTTATTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT-CTGAAATTGAGAAGTTGTTTATTGACA
218453 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
218495 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTT-TTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
218559 CCAGCGGTCCCTTCGTCGTGAAG-TGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
218599 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
218664 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
218705 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG-TCTTGAAATTGAGAAGTTGTTTATTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC-TGAAATTGAGAAGTTGTTTATTGACA
218769 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
218811 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
218876 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
218917 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
218982 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
219023 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATT-G----G-----GA-AA-TTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
219076 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
219117 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
219182 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
219223 GAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
219288 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
219329 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
* * *
219394 CCAGTGGTCCCTTTGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
219435 GAGT-CAAGATCCTTCGTTGAGAAGTTGAAATT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
219467 TACTCTCGAG
Statistics
Matches: 1137, Mismatches: 27, Indels: 41
0.94 0.02 0.03
Matches are distributed among these distances:
94 88 0.08
95 3 0.00
96 2 0.00
99 1 0.00
101 1 0.00
104 75 0.07
105 92 0.08
106 870 0.77
107 5 0.00
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:219052 original size:43 final size:43
Alignment explanation
Indices: 218991--219146 Score: 141
Period size: 43 Copynumber: 3.4 Consensus size: 43
218981 ACCAGCGGTC
218991 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * * * ** ***
219034 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGT
1 CCTTCGTCGTGAAGTTGAACTTGCG---TTG--TCTGGA-GTCCA-ATAT
219084 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 -CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
219128 CCTTCGTTGTGAAGTTGAA
1 CCTTCGTCGTGAAGTTGAA
219147 ATTGGCTCTG
Statistics
Matches: 84, Mismatches: 21, Indels: 16
0.69 0.17 0.13
Matches are distributed among these distances:
43 40 0.48
44 1 0.01
45 3 0.04
46 7 0.08
48 7 0.08
49 3 0.04
50 1 0.01
51 22 0.26
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.35
Consensus pattern (43 bp):
CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
Found at i:219244 original size:412 final size:414
Alignment explanation
Indices: 218225--219466 Score: 2185
Period size: 412 Copynumber: 3.0 Consensus size: 414
218215 TGGAACTGGA
* *
218225 AAATTGTTTATTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG-CATGGAGTCC
1 AAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TGGAGTCC
218289 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCG
65 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCG
*
218354 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAA
130 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCATTCGTTGTGAAGTTGAA
*
218419 ATTGG-TATTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
195 ATTGGCT-CTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
218483 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTT
259 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTT
*
218548 GGTTTTGACAACCAGCGGTCCCTTCGTCGTGAAG-TGAACTTGCGTTGTCTGGAGTCCAATATCC
324 GTTTTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
218612 TTCGTTGTGAAGTTGAAATTGGCTCTGAAATTG
389 TTCGTTGTGAAGTTGAAATTGG--C-G--A--G
218645 AGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTC
1 A-AA-TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTC
218710 CAATATCCTTCGTTGTGAAGTTGAAATTGG-TCTTGAAATTGAGAAGTTGTTTATTGACAACCAG
64 CAATATCCTTCGTTGTGAAGTTGAAATTGGCTC-TGAAATTGAGAAGTTGTTTATTGACAACCAG
218774 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCATTCGTTGTGAAGTTG
128 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCATTCGTTGTGAAGTTG
*
218839 AAATTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
193 AAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
218904 CTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGT
258 CTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGT
218969 TGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
323 TGTTT-TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
219034 CCTTCGTTGTGAAGTTGAAATT-G-G-G
387 CCTTCGTTGTGAAGTTGAAATTGGCGAG
219059 AAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 AAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
*
219124 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
66 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGG
*
219189 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCTTTCGTTGTGAAGTTGAAA
131 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCATTCGTTGTGAAGTTGAAA
219254 TTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
196 TTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
219319 GCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGT
261 GCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGT
* * * *
219384 TTGTTGACAACCAGTGGTCCCTTTGTCGTGAAGTTGAACTTGCGTTGTCTAGAGT-CAAGATCCT
326 TT-TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCT
*
219448 TCGTTGAGAAGTTGAAATT
390 TCGTTGTGAAGTTGAAATT
219467 TACTCTCGAG
Statistics
Matches: 799, Mismatches: 15, Indels: 25
0.95 0.02 0.03
Matches are distributed among these distances:
411 26 0.03
412 367 0.46
413 4 0.01
414 2 0.00
419 1 0.00
420 1 0.00
421 4 0.01
422 311 0.39
423 33 0.04
424 50 0.06
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (414 bp):
AAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGG
TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCATTCGTTGTGAAGTTGAAA
TTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
GCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGT
TTTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTT
CGTTGTGAAGTTGAAATTGGCGAG
Found at i:224074 original size:3 final size:3
Alignment explanation
Indices: 224066--224103 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
224056 ATGAACGCAA
224066 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
224104 AAAAAATAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:224978 original size:2 final size:2
Alignment explanation
Indices: 224966--225000 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
224956 TTTTAAAAAC
*
224966 TA TA T- TA TA TA TA TA GA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
225001 AAATAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:227171 original size:29 final size:29
Alignment explanation
Indices: 227129--227194 Score: 132
Period size: 29 Copynumber: 2.3 Consensus size: 29
227119 TCAGGCGTTG
227129 CCCTCTGCGTTTTGACACTGTTACCGAGT
1 CCCTCTGCGTTTTGACACTGTTACCGAGT
227158 CCCTCTGCGTTTTGACACTGTTACCGAGT
1 CCCTCTGCGTTTTGACACTGTTACCGAGT
227187 CCCTCTGC
1 CCCTCTGC
227195 AAGTTCAACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.12, C:0.35, G:0.20, T:0.33
Consensus pattern (29 bp):
CCCTCTGCGTTTTGACACTGTTACCGAGT
Found at i:228845 original size:245 final size:247
Alignment explanation
Indices: 228403--229119 Score: 919
Period size: 245 Copynumber: 2.9 Consensus size: 247
228393 TATTCTGTAC
* * * * * **
228403 TGAGTTCACAAGCCTTCTCTTCAAGCAATGCTTCATAGACAGCAGATATCTGTAGCTCACCAATT
1 TGAGCTCACAATCCTTCTCTTCAAGCAATGCTTCATGGA-AGCAGAAATTTGTAGCTCACCAAAC
* * * *
228468 AATGCAGTAGCCCGAGTCTCCCAAACTTCAACCTCATTTCTTCCCTTTTGTAGTTCAA-CATGCA
65 AATGCAGTAGCCTGAGTCTCCCAAAGTTCAACCTCATTTCTTTCCTTTTGTAGTTCAACCCT-CA
* * * * * ** *
228532 AACTCTCCTCCCTAAGTTTCCGTTCTTGAAGTTCCTC-CAGCAATTTCGATAACTCCCCCACAAG
129 AACTCTTCTCCCTATGTTTCCATTCTTCAAGTTCCTCGC-TCAATTTCGATAACTCAGCCTCAAG
* *
228596 TTTCTGGTTAGTCTGACGAATGCTTTCAATCTCCTTATTTTTAAG-A-T-CACAT
193 TTTCTGGTTAGCCTGACGAATGCTTTCAATCTCCTTATTTTGAAGAATTCCACAT
*
228648 TGAGCTCACAATCCTTCTCTTCAAGCAATGCTTCATGGAGAGCAGAAATTTGTAGCTCACTAAAC
1 TGAGCTCACAATCCTTCTCTTCAAGCAATGCTTCATGGA-AGCAGAAATTTGTAGCTCACCAAAC
228713 AATGCAGTAGCCTGAGTCTCCCAAAGTTCAACCTCATTTCTTTCCTTTTGTAGTTCAACCCTCAA
65 AATGCAGTAGCCTGAGTCTCCCAAAGTTCAACCTCATTTCTTTCCTTTTGTAGTTCAACCCTCAA
* * *
228778 ACTCTTCACCCTATGTTTCCATTCTTCAAGTTCCTCGCTCAAATTCGATAATTCAGCCTCAAGTT
130 ACTCTTCTCCCTATGTTTCCATTCTTCAAGTTCCTCGCTCAATTTCGATAACTCAGCCTCAAGTT
228843 TCTGGTTAGCCTGACGAATGCTTTCAATCTCCTTATTTTGAAGATCAAATTCCACAT
195 TCTGGTTAGCCTGACGAATGCTTTCAATCTCCTTATTTTGAAG----AATTCCACAT
* * * * * *
228900 CGAGCTCATAAGT-TTTCTCTCCTAGCAATGCTTCACGGAATGCAGAAATTTGTAGCTCACCAAA
1 TGAGCTCACAA-TCCTTCTCTTCAAGCAATGCTTCATGGAA-GCAGAAATTTGTAGCTCACCAAA
* * * *
228964 CAGTGCAGTAGCCTGAGTCTCCCAAAGTTCAACCTCATTTCTTTCCTTTTGTAGTTCCACACTCG
64 CAATGCAGTAGCCTGAGTCTCCCAAAGTTCAACCTCATTTCTTTCCTTTTGTAGTTCAACCCTCA
* * *
229029 AACTCTTCTCCCTATGTTTCCTTTCTTCAAGTTCCTCG-TGCAATTTTGATAACTCGGCCTCATA
129 AACTCTTCTCCCTATGTTTCCATTCTTCAAGTTCCTCGCT-CAATTTCGATAACTCAGCCTCA-A
*
229093 -TTTCTGATTAGCCTGACGAATGCTTTC
192 GTTTCTGGTTAGCCTGACGAATGCTTTC
229120 TTTTTTTGAT
Statistics
Matches: 415, Mismatches: 44, Indels: 19
0.87 0.09 0.04
Matches are distributed among these distances:
245 207 0.50
246 3 0.01
250 1 0.00
251 3 0.01
252 199 0.48
253 2 0.00
ACGTcount: A:0.25, C:0.28, G:0.14, T:0.34
Consensus pattern (247 bp):
TGAGCTCACAATCCTTCTCTTCAAGCAATGCTTCATGGAAGCAGAAATTTGTAGCTCACCAAACA
ATGCAGTAGCCTGAGTCTCCCAAAGTTCAACCTCATTTCTTTCCTTTTGTAGTTCAACCCTCAAA
CTCTTCTCCCTATGTTTCCATTCTTCAAGTTCCTCGCTCAATTTCGATAACTCAGCCTCAAGTTT
CTGGTTAGCCTGACGAATGCTTTCAATCTCCTTATTTTGAAGAATTCCACAT
Found at i:241634 original size:2 final size:2
Alignment explanation
Indices: 241627--241662 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
241617 TCTCCTTCTT
*
241627 TC TC TC TC TC TC TC TC TC TC TC CC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
241663 GGAGCTGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:245454 original size:22 final size:22
Alignment explanation
Indices: 245412--245454 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
245402 AAATTTCAAT
*
245412 AAATAATATTATTAAATATTTA
1 AAATAATATTAATAAATATTTA
*
245434 AAAT-ATATTAATCAATCATTT
1 AAATAATATTAATAAAT-ATTT
245455 TTAGAGTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (22 bp):
AAATAATATTAATAAATATTTA
Found at i:245531 original size:36 final size:37
Alignment explanation
Indices: 245485--245567 Score: 98
Period size: 37 Copynumber: 2.3 Consensus size: 37
245475 TTAGTATTAT
* *
245485 AATTTTTAATATTA-CAATAATATTCTTATTTTAATA
1 AATTATTAATATAATCAATAATATTCTTATTTTAATA
** *
245521 AATTATTAATATAATTTATAATATTTTTATTTTAATA
1 AATTATTAATATAATCAATAATATTCTTATTTTAATA
*
245558 AAATA-TAATA
1 AATTATTAATA
245568 ATCTTAATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
36 17 0.43
37 23 0.57
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (37 bp):
AATTATTAATATAATCAATAATATTCTTATTTTAATA
Found at i:245555 original size:26 final size:26
Alignment explanation
Indices: 245526--245593 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 26
245516 TAATAAATTA
**
245526 TTAATATAATTTATAATATTTTTATT
1 TTAATATAATTTATAATATTAATATT
* * *
245552 TTAATAAAATATAATAATCTTAATATT
1 TTAATATAAT-TTATAATATTAATATT
*
245579 TT-ATATAAATTATAA
1 TTAATATAATTTATAA
245594 AAATGATATT
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
25 5 0.15
26 14 0.42
27 14 0.42
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (26 bp):
TTAATATAATTTATAATATTAATATT
Found at i:252568 original size:26 final size:26
Alignment explanation
Indices: 252533--252584 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
252523 TTATTGTTAG
*
252533 AAAAAAATAATT-GTGATAGCCTTTC
1 AAAAAAATAATTAATGATAGCCTTTC
*
252558 AAAAAGAATAATTAATGATAGTCTTTC
1 AAAAA-AATAATTAATGATAGCCTTTC
252585 TAAATGTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 5 0.22
26 7 0.30
27 11 0.48
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.33
Consensus pattern (26 bp):
AAAAAAATAATTAATGATAGCCTTTC
Found at i:259351 original size:21 final size:21
Alignment explanation
Indices: 259312--259351 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
259302 AAAATAATTA
* *
259312 AATTTATTTATTTTAAAATCT
1 AATTTAATTATTCTAAAATCT
*
259333 AATTTAATTATTCTGAAAT
1 AATTTAATTATTCTAAAAT
259352 TTATTATACT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.53
Consensus pattern (21 bp):
AATTTAATTATTCTAAAATCT
Found at i:259887 original size:61 final size:60
Alignment explanation
Indices: 259810--259950 Score: 212
Period size: 61 Copynumber: 2.3 Consensus size: 60
259800 CCACAATTCG
*
259810 TGCGTATGTGTTTGTTCTTGTTTCTTTTTTTTTC-TTTTCTAAGTATACAGTTATTCGTAAT
1 TGCGTATGTGTCTGTTCTTGTTTCTTTTTTTTTCATTTTCTAAGTATACAGTTATTCGT--T
* * * *
259871 TTCGTATGTGTCTGTTCTTGTTTTTTTTTTTTTCATTTTTTAAGTATGCAGTTATTCGTT
1 TGCGTATGTGTCTGTTCTTGTTTCTTTTTTTTTCATTTTCTAAGTATACAGTTATTCGTT
259931 TGCGTATGTGTCTGTTCTTG
1 TGCGTATGTGTCTGTTCTTG
259951 ATAATCACAG
Statistics
Matches: 73, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
60 20 0.27
61 31 0.42
62 22 0.30
ACGTcount: A:0.12, C:0.11, G:0.17, T:0.60
Consensus pattern (60 bp):
TGCGTATGTGTCTGTTCTTGTTTCTTTTTTTTTCATTTTCTAAGTATACAGTTATTCGTT
Found at i:261715 original size:10 final size:10
Alignment explanation
Indices: 261696--261729 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
261686 ATAAAGCATT
*
261696 TCTCTGTCTC
1 TCTCTATCTC
261706 TCTCTATCTC
1 TCTCTATCTC
261716 TCTCTATCTC
1 TCTCTATCTC
261726 TCTC
1 TCTC
261730 ATTAGCCGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.06, C:0.41, G:0.03, T:0.50
Consensus pattern (10 bp):
TCTCTATCTC
Found at i:262790 original size:10 final size:10
Alignment explanation
Indices: 262777--262812 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
262767 TGGTTCTCTC
*
262777 CTTTTCTTTT
1 CTTTTATTTT
262787 CTTTTATTTT
1 CTTTTATTTT
262797 CTTTTATTTT
1 CTTTTATTTT
262807 -TTTTAT
1 CTTTTAT
262813 GGTTGAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 6 0.24
10 19 0.76
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.81
Consensus pattern (10 bp):
CTTTTATTTT
Done.