Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000104.1 Hibiscus syriacus cultivar Beakdansim tig00000188_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: 63075
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:2153 original size:14 final size:14
Alignment explanation
Indices: 2134--2160 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2124 ACTTAATATC
2134 ACACAAGAATCATA
1 ACACAAGAATCATA
2148 ACACAAGAATCAT
1 ACACAAGAATCAT
2161 GTTAAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.22, G:0.07, T:0.15
Consensus pattern (14 bp):
ACACAAGAATCATA
Found at i:4301 original size:16 final size:13
Alignment explanation
Indices: 4266--4322 Score: 60
Period size: 13 Copynumber: 4.2 Consensus size: 13
4256 ACTATCTTCT
4266 ATTTAATAACTCA
1 ATTTAATAACTCA
4279 ATTTAATAACTCA
1 ATTTAATAACTCA
4292 ACTGTTTAATAACTCA
1 A---TTTAATAACTCA
***
4308 AGAAAATAACTCA
1 ATTTAATAACTCA
4321 AT
1 AT
4323 CTGGCCCTCG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
13 24 0.65
16 13 0.35
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33
Consensus pattern (13 bp):
ATTTAATAACTCA
Found at i:5361 original size:83 final size:83
Alignment explanation
Indices: 5222--5413 Score: 267
Period size: 83 Copynumber: 2.3 Consensus size: 83
5212 TAAATTAGCG
* * ** * *
5222 GCGTTTATATCACAAACGCTTCAATAGATTATAAATTTTGCGGCGATTTAGCCAAAACGCCGCAA
1 GCGTTTTTACCACAAACGCCACAATAGAGTATAAATTTTGCGGCGATTGAGCCAAAACGCCGCAA
*
5287 TATAGTGGTAAACTGGCA
66 TAGAGTGGTAAACTGGCA
*
5305 GCGTTTTTACCACAAACGCCACAATAGAGTATAAATTTTGCGGCGATTGAGTCAAAACGCCGCAA
1 GCGTTTTTACCACAAACGCCACAATAGAGTATAAATTTTGCGGCGATTGAGCCAAAACGCCGCAA
* *
5370 TAGAGTGGTAAATTGGCT
66 TAGAGTGGTAAACTGGCA
* * *
5388 GCGTTTTGACCAAAAACGCCGCAATA
1 GCGTTTTTACCACAAACGCCACAATA
5414 TATTACACAT
Statistics
Matches: 96, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
83 96 1.00
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (83 bp):
GCGTTTTTACCACAAACGCCACAATAGAGTATAAATTTTGCGGCGATTGAGCCAAAACGCCGCAA
TAGAGTGGTAAACTGGCA
Found at i:5375 original size:41 final size:41
Alignment explanation
Indices: 5243--5375 Score: 135
Period size: 41 Copynumber: 3.2 Consensus size: 41
5233 ACAAACGCTT
*
5243 CAATAGATTATAAATTTTGCGGCGATTTAGCCAAAACGCCG
1 CAATAGAGTATAAATTTTGCGGCGATTTAGCCAAAACGCCG
* * * * * * *
5284 CAATATAGTGGTAAA-CTGGCAGCGTTTTTA-CCACAAACGCCA
1 CAATAGAGT-ATAAATTTTGCGGCG-ATTTAGCCA-AAACGCCG
* *
5326 CAATAGAGTATAAATTTTGCGGCGATTGAGTCAAAACGCCG
1 CAATAGAGTATAAATTTTGCGGCGATTTAGCCAAAACGCCG
5367 CAATAGAGT
1 CAATAGAGT
5376 GGTAAATTGG
Statistics
Matches: 70, Mismatches: 17, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
41 39 0.56
42 31 0.44
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.25
Consensus pattern (41 bp):
CAATAGAGTATAAATTTTGCGGCGATTTAGCCAAAACGCCG
Found at i:5402 original size:41 final size:41
Alignment explanation
Indices: 5273--5413 Score: 142
Period size: 42 Copynumber: 3.4 Consensus size: 41
5263 GGCGATTTAG
* * *
5273 CCAAAACGCCGCAATATAGTGGTAAACTGGCAGCGTTTTTA
1 CCAAAACGCCGCAATAGAGTGGTAAATTGGCAGCGTTTTGA
* * * * *
5314 CCACAAACGCCACAATAGAGT-ATAAATTTTGCGGCG-ATTGA
1 CCA-AAACGCCGCAATAGAGTGGTAAA-TTGGCAGCGTTTTGA
* *
5355 GTCAAAACGCCGCAATAGAGTGGTAAATTGGCTGCGTTTTGA
1 -CCAAAACGCCGCAATAGAGTGGTAAATTGGCAGCGTTTTGA
5397 CCAAAAACGCCGCAATA
1 CC-AAAACGCCGCAATA
5414 TATTACACAT
Statistics
Matches: 79, Mismatches: 15, Indels: 11
0.75 0.14 0.10
Matches are distributed among these distances:
41 34 0.43
42 45 0.57
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (41 bp):
CCAAAACGCCGCAATAGAGTGGTAAATTGGCAGCGTTTTGA
Found at i:6179 original size:23 final size:21
Alignment explanation
Indices: 6132--6171 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
6122 CGAGCAATTA
6132 GTTTTTTACTGAACACGAAAT
1 GTTTTTTACTGAACACGAAAT
6153 GTTTTTTACTGAACACGAA
1 GTTTTTTACTGAACACGAA
6172 TGATGTTTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (21 bp):
GTTTTTTACTGAACACGAAAT
Found at i:7420 original size:12 final size:12
Alignment explanation
Indices: 7403--7428 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
7393 TTTAGTTCAT
7403 CATTTCATCACC
1 CATTTCATCACC
7415 CATTTCATCACC
1 CATTTCATCACC
7427 CA
1 CA
7429 CTAAAACTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.42, G:0.00, T:0.31
Consensus pattern (12 bp):
CATTTCATCACC
Found at i:11082 original size:21 final size:21
Alignment explanation
Indices: 11058--11143 Score: 93
Period size: 21 Copynumber: 4.1 Consensus size: 21
11048 ATGAAGCAAG
*
11058 GGAAACAGAGAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
** *
11079 GGAAGCAGCTAGAGCAACAGC
1 GGAAGCAGAGAGAGCAGCAGC
*
11100 GGAAGCAGAGAGAGAAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
* *
11121 GGCAGCATAGAGAG-AGGCAGC
1 GGAAGCAGAGAGAGCA-GCAGC
11142 GG
1 GG
11144 CAGAACAGAG
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
20 1 0.02
21 53 0.98
ACGTcount: A:0.38, C:0.19, G:0.41, T:0.02
Consensus pattern (21 bp):
GGAAGCAGAGAGAGCAGCAGC
Found at i:11144 original size:21 final size:21
Alignment explanation
Indices: 11066--11158 Score: 82
Period size: 21 Copynumber: 4.4 Consensus size: 21
11056 AGGGAAACAG
* *
11066 AGAGAGCAGCAGCGGAAGCAGC
1 AGAGAGAAGCAGCGGCAGCA-C
* * *
11088 TAGAG-CAA-CAGCGGAAGCAG
1 -AGAGAGAAGCAGCGGCAGCAC
*
11108 AGAGAGAAGCAGCGGCAGCAT
1 AGAGAGAAGCAGCGGCAGCAC
* *
11129 AGAGAGAGGCAGCGGCAGAAC
1 AGAGAGAAGCAGCGGCAGCAC
11150 AGAGAGAAG
1 AGAGAGAAG
11159 TAATATATCA
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
19 4 0.07
20 2 0.03
21 47 0.81
22 1 0.02
23 4 0.07
ACGTcount: A:0.40, C:0.18, G:0.40, T:0.02
Consensus pattern (21 bp):
AGAGAGAAGCAGCGGCAGCAC
Found at i:11629 original size:43 final size:43
Alignment explanation
Indices: 11496--11726 Score: 138
Period size: 43 Copynumber: 5.3 Consensus size: 43
11486 CATACAGTTA
* *
11496 GCGGCGTTTTTGATA-AAAACGCCGCAAAATC-TCAAGATA-TATTCT
1 GCGGCGTTTTTGA-AGAAAACGCCGCTAAA-CATCAACA-ACTA-T-T
* * * * * *
11541 GCGGCGTTTGT-AGGAAAACGCCGGTAAAAAT-AAAAATCTACT
1 GCGGCGTTTTTGAAGAAAACGCCGCTAAACATCAACAA-CTATT
11583 GCGGCGTTTTTGAAGAAAACGCCGCTAAACATCAACAACTATT
1 GCGGCGTTTTTGAAGAAAACGCCGCTAAACATCAACAACTATT
** * * * *
11626 GCGGCGTTTGTCTG--CCAAATGCCGTTAAATATCAACACCTATT
1 GCGGCGTTT-T-TGAAGAAAACGCCGCTAAACATCAACAACTATT
* * * *
11669 GCGGCG-TTTT-AATGATAAACGCCGCTAAATATCAATACCTTTT
1 GCGGCGTTTTTGAA-GA-AAACGCCGCTAAACATCAACAACTATT
11712 GCGGCGTTTGTTGAA
1 GCGGCGTTT-TTGAA
11727 CAATCGCCGC
Statistics
Matches: 146, Mismatches: 25, Indels: 29
0.73 0.12 0.14
Matches are distributed among these distances:
40 1 0.01
41 1 0.01
42 14 0.10
43 91 0.62
44 23 0.16
45 14 0.10
46 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (43 bp):
GCGGCGTTTTTGAAGAAAACGCCGCTAAACATCAACAACTATT
Found at i:11735 original size:43 final size:43
Alignment explanation
Indices: 11582--11764 Score: 137
Period size: 43 Copynumber: 4.3 Consensus size: 43
11572 AAAAATCTAC
* * * *
11582 TGCGGCGTTTT-TGAAGAAAACGCCGCTAAACATCAACAACTAT
1 TGCGGCGTTTTATGAA-CAATCGCCGCTAAATATCAACACCTAT
* * *
11625 TGCGGCGTTTGTCTG-CCAAAT-GCCGTTAAATATCAACACCTAT
1 TGCGGCGTTT-TATGAAC-AATCGCCGCTAAATATCAACACCTAT
* *
11668 TGCGGCGTTTTAATGATA-AA-CGCCGCTAAATATCAATACCTTT
1 TGCGGCGTTTT-ATGA-ACAATCGCCGCTAAATATCAACACCTAT
* * **
11711 TGCGGCGTTTGT-TGAACAATCGCCGCTATATGTTGTA-ACCTAT
1 TGCGGCGTTT-TATGAACAATCGCCGCTAAAT-ATCAACACCTAT
11754 TGCGGCGTTTT
1 TGCGGCGTTTT
11765 TTTGTTGAAA
Statistics
Matches: 113, Mismatches: 16, Indels: 23
0.74 0.11 0.15
Matches are distributed among these distances:
41 1 0.01
42 7 0.06
43 97 0.86
44 6 0.05
45 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.31
Consensus pattern (43 bp):
TGCGGCGTTTTATGAACAATCGCCGCTAAATATCAACACCTAT
Found at i:13170 original size:19 final size:19
Alignment explanation
Indices: 13148--13223 Score: 66
Period size: 19 Copynumber: 3.8 Consensus size: 19
13138 CCCTAATCCA
13148 TTAAAAAAACCTAAACAAC
1 TTAAAAAAACCTAAACAAC
13167 TTAAATAAAACCCTAATACAA-
1 TTAAA-AAAA-CCTAA-ACAAC
* *
13188 TTAGAAAATCCTAAATC-AC
1 TTAAAAAAACCTAAA-CAAC
*
13207 ATAAAAAAACTCTAAAC
1 TTAAAAAAAC-CTAAAC
13224 CGCTTTAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
18 2 0.04
19 19 0.41
20 12 0.26
21 9 0.20
22 4 0.09
ACGTcount: A:0.58, C:0.20, G:0.01, T:0.21
Consensus pattern (19 bp):
TTAAAAAAACCTAAACAAC
Found at i:13181 original size:21 final size:20
Alignment explanation
Indices: 13109--13201 Score: 59
Period size: 21 Copynumber: 4.7 Consensus size: 20
13099 CCCTAAACCA
* *
13109 TTAAAATAAACCGAATACAAT
1 TTAAAA-AAACCTAATACAAC
* ** *
13130 TTTAAAAGCCCTAAT-CCA-
1 TTAAAAAAACCTAATACAAC
13148 TTAAAAAAACCTAA-ACAAC
1 TTAAAAAAACCTAATACAAC
13167 TTAAATAAAACCCTAATACAA-
1 TTAAA-AAAA-CCTAATACAAC
* *
13188 TTAGAAAATCCTAA
1 TTAAAAAAACCTAA
13202 ATCACATAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
18 13 0.23
19 12 0.21
20 13 0.23
21 14 0.25
22 4 0.07
ACGTcount: A:0.54, C:0.19, G:0.03, T:0.24
Consensus pattern (20 bp):
TTAAAAAAACCTAATACAAC
Found at i:13181 original size:39 final size:37
Alignment explanation
Indices: 13099--13202 Score: 93
Period size: 39 Copynumber: 2.7 Consensus size: 37
13089 TTTATCTATC
* * *
13099 CCCTAAACCATTAAAATAAACCGAATACAATTTTAAAAG
1 CCCTAATCCATTAAAA-AAACCTAA-ACAATTATAAAAG
13138 CCCTAATCCATTAAAAAAACCTAAACAACTTAAATAAAA-
1 CCCTAATCCATTAAAAAAACCTAAACAA-TT--ATAAAAG
* * *
13177 CCCTAATACAATTAGAAAATCCTAAA
1 CCCTAAT-CCATTAAAAAAACCTAAA
13203 TCACATAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
37 4 0.07
38 9 0.16
39 22 0.40
40 20 0.36
ACGTcount: A:0.53, C:0.22, G:0.03, T:0.22
Consensus pattern (37 bp):
CCCTAATCCATTAAAAAAACCTAAACAATTATAAAAG
Found at i:13216 original size:39 final size:38
Alignment explanation
Indices: 13133--13221 Score: 90
Period size: 40 Copynumber: 2.3 Consensus size: 38
13123 ATACAATTTT
* * *
13133 AAAAGCCCTAATCCATTAAAAAAACCTAAACAACTTAA
1 AAAAACCCTAATCAATTAAAAAAACCTAAACAACATAA
* *
13171 ATAAAACCCTAATACAATTAGAAAATCCTAAATC-ACATAA
1 A-AAAACCCTAAT-CAATTAAAAAAACCTAAA-CAACATAA
*
13211 AAAAACTCTAA
1 AAAAACCCTAA
13222 ACCGCTTTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
38 1 0.02
39 19 0.45
40 21 0.50
41 1 0.02
ACGTcount: A:0.56, C:0.21, G:0.02, T:0.20
Consensus pattern (38 bp):
AAAAACCCTAATCAATTAAAAAAACCTAAACAACATAA
Found at i:13388 original size:20 final size:20
Alignment explanation
Indices: 13363--13423 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 20
13353 CTAAATCACA
13363 TAAAAAACTCTAAACCACTT
1 TAAAAAACTCTAAACCACTT
13383 TAAAAAAAAC-CTAAACCACTT
1 T--AAAAAACTCTAAACCACTT
*
13404 T-AAAAACTCCTAAACTACTT
1 TAAAAAACT-CTAAACCACTT
13424 CAACATTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
18 6 0.17
20 11 0.31
21 12 0.33
22 7 0.19
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.25
Consensus pattern (20 bp):
TAAAAAACTCTAAACCACTT
Found at i:13392 original size:22 final size:21
Alignment explanation
Indices: 13364--13409 Score: 83
Period size: 21 Copynumber: 2.1 Consensus size: 21
13354 TAAATCACAT
13364 AAAAAACTCTAAACCACTTTAA
1 AAAAAAC-CTAAACCACTTTAA
13386 AAAAAACCTAAACCACTTTAA
1 AAAAAACCTAAACCACTTTAA
13407 AAA
1 AAA
13410 CTCCTAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.59, C:0.22, G:0.00, T:0.20
Consensus pattern (21 bp):
AAAAAACCTAAACCACTTTAA
Found at i:13397 original size:40 final size:41
Alignment explanation
Indices: 13347--13423 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 41
13337 ATACAATTAG
* *
13347 AAAATCCTAAATCACATAAAAAACT-CTAAACCACTTTAAA
1 AAAAACCTAAACCACATAAAAAACTCCTAAACCACTTTAAA
* * *
13387 AAAAACCTAAACCACTTTAAAAACTCCTAAACTACTT
1 AAAAACCTAAACCACATAAAAAACTCCTAAACCACTT
13424 CAACATTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
40 21 0.68
41 10 0.32
ACGTcount: A:0.52, C:0.25, G:0.00, T:0.23
Consensus pattern (41 bp):
AAAAACCTAAACCACATAAAAAACTCCTAAACCACTTTAAA
Found at i:13520 original size:179 final size:175
Alignment explanation
Indices: 13208--13661 Score: 787
Period size: 179 Copynumber: 2.6 Consensus size: 175
13198 CTAAATCACA
*
13208 TAAAAAAACTCTAAACCGCTTTAAAAACTCCTAAACTACTTCAACATTAAAAAAACCCTAACCCT
1 TAAAAAAAC-CTAAACCACTTTAAAAACTCCTAAACTACTTCAACATTAAAAAAACCCTAACCCT
*
13273 AAACCACTTTAA-CCCCAAAAAAACCTAAACCAAAAACTTTATAAACAACTTAAATAAAACCCTA
65 AAACCACTTTAACCCCCAAAAAAACCTAAACCAGAAACTTTATAAACAACTTAAATAAAACCCTA
13337 ATACAATTAGAAAATCCTAAATCACATAAAAAACTCTAAACCACTT
130 ATACAATTAGAAAATCCTAAATCACATAAAAAACTCTAAACCACTT
13383 TAAAAAAAACCTAAACCACTTTAAAAACTCCTAAACTACTTCAACATTAAAAAAATACCCTAACC
1 T-AAAAAAACCTAAACCACTTTAAAAACTCCTAAACTACTTCAACATT-AAAAAA-ACCCTAACC
13448 CTAAACCACTTTAACCCCCAAAAAAAACCTAAACCAGAAACTTTATAAACAACTTAAATAAAACC
63 CTAAACCACTTTAACCCCC-AAAAAAACCTAAACCAGAAACTTTATAAACAACTTAAATAAAACC
13513 CTAATACAATTAGAAAATCCTAAATCACATAAAAAACTCTAAACCACTT
127 CTAATACAATTAGAAAATCCTAAATCACATAAAAAACTCTAAACCACTT
*
13562 T-AAAAAGCCTAAACCACTTT-AAAACTCCTAAACTACTTCAACATTAAAAAAA---T-ACCCTA
1 TAAAAAAACCTAAACCACTTTAAAAACTCCTAAACTACTTCAACATTAAAAAAACCCTAACCCTA
13621 AACCACTTTAACCCCCAAAAAAACCTAAACCAGAAACTTTA
66 AACCACTTTAACCCCCAAAAAAACCTAAACCAGAAACTTTA
13662 AACCGTAAAT
Statistics
Matches: 271, Mismatches: 3, Indels: 16
0.93 0.01 0.06
Matches are distributed among these distances:
169 25 0.09
170 22 0.08
171 1 0.00
174 1 0.00
175 44 0.16
176 39 0.14
177 41 0.15
178 4 0.01
179 94 0.35
ACGTcount: A:0.51, C:0.26, G:0.01, T:0.21
Consensus pattern (175 bp):
TAAAAAAACCTAAACCACTTTAAAAACTCCTAAACTACTTCAACATTAAAAAAACCCTAACCCTA
AACCACTTTAACCCCCAAAAAAACCTAAACCAGAAACTTTATAAACAACTTAAATAAAACCCTAA
TACAATTAGAAAATCCTAAATCACATAAAAAACTCTAAACCACTT
Found at i:13548 original size:19 final size:19
Alignment explanation
Indices: 13526--13599 Score: 78
Period size: 19 Copynumber: 3.9 Consensus size: 19
13516 ATACAATTAG
* *
13526 AAAATCCTAAATCAC-ATA
1 AAAATCCTAAACCACTTTA
*
13544 AAAAACTCTAAACCACTTTA
1 AAAATC-CTAAACCACTTTA
*
13564 AAAAGCCTAAACCACTTTA
1 AAAATCCTAAACCACTTTA
* *
13583 AAACTCCTAAACTACTT
1 AAAATCCTAAACCACTT
13600 CAACATTAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
18 5 0.11
19 35 0.74
20 7 0.15
ACGTcount: A:0.49, C:0.26, G:0.01, T:0.24
Consensus pattern (19 bp):
AAAATCCTAAACCACTTTA
Found at i:22649 original size:2 final size:2
Alignment explanation
Indices: 22644--22706 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
22634 TTTTTTTAAA
22644 AT AT AT AT AT AT 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 AT AT AT AT AT AT
22686 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
22707 ATTTTTAATT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:22855 original size:20 final size:20
Alignment explanation
Indices: 22830--22901 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
22820 GACCAACAAA
22830 TTCGCAACGCGAATTCCAAT
1 TTCGCAACGCGAATTCCAAT
* *
22850 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGA-ATTCCAAT
* * *
22870 TTCGAAACGCGAAAGT-CAAA
1 TTCGCAACGCG-AATTCCAAT
22890 TTCGCAACGCGA
1 TTCGCAACGCGA
22902 TAGTCAAATT
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
19 3 0.07
20 35 0.85
21 2 0.05
22 1 0.02
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (20 bp):
TTCGCAACGCGAATTCCAAT
Found at i:22906 original size:20 final size:20
Alignment explanation
Indices: 22870--22915 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
22860 AGTTTCCAAT
*
22870 TTCGAAACGCGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
*
22890 TTCGCAACGCGATAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
22910 TTCGCA
1 TTCGCA
22916 GCTCGAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
TTCGCAACGCGAAAGTCAAA
Found at i:23214 original size:20 final size:20
Alignment explanation
Indices: 23191--23228 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
23181 AATTCGCAAC
23191 GCGAATTTGACTTTCGCGTT
1 GCGAATTTGACTTTCGCGTT
23211 GCGAATTTGACTTTCGCG
1 GCGAATTTGACTTTCGCG
23229 ACGCTAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.16, C:0.21, G:0.26, T:0.37
Consensus pattern (20 bp):
GCGAATTTGACTTTCGCGTT
Found at i:23237 original size:20 final size:20
Alignment explanation
Indices: 23183--23237 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
23173 ATTTTGACAA
*
23183 TTCGCAACGCGAATTTGACT
1 TTCGCGACGCGAATTTGACT
**
23203 TTCGCGTTGCGAATTTGACT
1 TTCGCGACGCGAATTTGACT
*
23223 TTCGCGACGCTAATT
1 TTCGCGACGCGAATT
23238 ACCTATATAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.35
Consensus pattern (20 bp):
TTCGCGACGCGAATTTGACT
Found at i:29693 original size:26 final size:26
Alignment explanation
Indices: 29662--29731 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
29652 AACAATTAAA
*
29662 TTTTAAAATGTACTTTTCTACAGTAC
1 TTTTAAAATGTACTTTTCTACAGCAC
* * *
29688 TTTTAAAAAGCT-TTTTTTTACAGCAC
1 TTTTAAAATG-TACTTTTCTACAGCAC
29714 TTTTAAAAAT-TACTTTTC
1 TTTT-AAAATGTACTTTTC
29732 AAAAGTTGGT
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
25 1 0.03
26 28 0.82
27 5 0.15
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.49
Consensus pattern (26 bp):
TTTTAAAATGTACTTTTCTACAGCAC
Found at i:30643 original size:2 final size:2
Alignment explanation
Indices: 30633--30685 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
30623 TTAAAAAAAT
*
30633 TA TA AA TA TA TA TA TA TA TA TA TA 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 TA TA TA
30675 TA TA TA TA TA T
1 TA TA TA TA TA T
30686 TAAAAAGAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:41991 original size:38 final size:38
Alignment explanation
Indices: 41940--42015 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
41930 GTAGTATTTG
41940 TGTACTCACAAAGCGGGTAATGTTACGTGTAATTACAT
1 TGTACTCACAAAGCGGGTAATGTTACGTGTAATTACAT
41978 TGTACTCACAAAGCGGGTAATGTTACGTGTAATTACAT
1 TGTACTCACAAAGCGGGTAATGTTACGTGTAATTACAT
42016 AGATCGGTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Consensus pattern (38 bp):
TGTACTCACAAAGCGGGTAATGTTACGTGTAATTACAT
Found at i:42095 original size:17 final size:17
Alignment explanation
Indices: 42070--42108 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
42060 ACCCTTAAAA
42070 ATTTAAAATTATCATAT
1 ATTTAAAATTATCATAT
* * *
42087 ATTTTAAATTTTTATAT
1 ATTTAAAATTATCATAT
42104 ATTTA
1 ATTTA
42109 TTAAAATAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTAAAATTATCATAT
Found at i:42247 original size:37 final size:37
Alignment explanation
Indices: 42185--42288 Score: 127
Period size: 37 Copynumber: 2.8 Consensus size: 37
42175 CATTTTCGTC
* *
42185 CTACTAGGATTCAAACTCCTAAAAATATGACAGAATT
1 CTACTATGATTTAAACTCCTAAAAATATGACAGAATT
* * * * *
42222 TTGCTATGATTTAAACTCCTAAAAATAGGATAGAGTT
1 CTACTATGATTTAAACTCCTAAAAATATGACAGAATT
* *
42259 CTACTATTATTTAAACTCCTAAAGATATGA
1 CTACTATGATTTAAACTCCTAAAAATATGA
42289 TCCACAAGCA
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (37 bp):
CTACTATGATTTAAACTCCTAAAAATATGACAGAATT
Found at i:42726 original size:15 final size:15
Alignment explanation
Indices: 42706--42738 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
42696 TATATATATA
42706 ATTAT-ATTTTTTATT
1 ATTATAATTTTTT-TT
42721 ATTATAATTTTTTTT
1 ATTATAATTTTTTTT
42736 ATT
1 ATT
42739 TTTCTTTGCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
ATTATAATTTTTTTT
Found at i:42801 original size:8 final size:9
Alignment explanation
Indices: 42771--42803 Score: 50
Period size: 10 Copynumber: 3.7 Consensus size: 9
42761 AATTTTCTAT
42771 TATTATATA
1 TATTATATA
42780 TATATATATA
1 TAT-TATATA
42790 TATTATAT-
1 TATTATATA
42798 TATTAT
1 TATTAT
42804 TTTTTATCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 6 0.26
9 8 0.35
10 9 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
TATTATATA
Found at i:43012 original size:26 final size:30
Alignment explanation
Indices: 42981--43042 Score: 85
Period size: 27 Copynumber: 2.2 Consensus size: 30
42971 TTATACATAC
42981 ATTTTTATATTTT-TATATA-TATTT-TTT
1 ATTTTTATATTTTATATATACTATTTATTT
* *
43008 ATTTTTTTATTTTATTTATACTATTTATTT
1 ATTTTTATATTTTATATATACTATTTATTT
43038 ATTTT
1 ATTTT
43043 CATTATGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 12 0.40
28 5 0.17
29 5 0.17
30 8 0.27
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (30 bp):
ATTTTTATATTTTATATATACTATTTATTT
Found at i:43014 original size:20 final size:21
Alignment explanation
Indices: 42961--43014 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
42951 CTATTTAGTA
42961 TTTTATTTTATTATACATACAT
1 TTTTATTTT-TTATACATACAT
* *
42983 TTTTATATTTTTATATATA-TT
1 TTTTAT-TTTTTATACATACAT
43004 TTTTATTTTTT
1 TTTTATTTTTT
43015 TATTTTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 5 0.17
21 7 0.24
22 14 0.48
23 3 0.10
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTATTTTTTATACATACAT
Found at i:43147 original size:18 final size:19
Alignment explanation
Indices: 43124--43169 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
43114 TTTTTTTATA
*
43124 TATTTTTTTTTCTTC-ATT
1 TATTTTTTTTTATTCAATT
*
43142 TATTTTATTTTATTCAATT
1 TATTTTTTTTTATTCAATT
43161 TCATTTTTT
1 T-ATTTTTT
43170 AAAATATTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 13 0.57
19 4 0.17
20 6 0.26
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (19 bp):
TATTTTTTTTTATTCAATT
Found at i:44375 original size:19 final size:20
Alignment explanation
Indices: 44339--44376 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
44329 ACCTTACTAA
*
44339 CTCTTTTCATTTTTTTTCCT
1 CTCTTTTCATTTTATTTCCT
44359 CTCTTTT-ATTTTATTTCC
1 CTCTTTTCATTTTATTTCC
44377 ATCATCTGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (20 bp):
CTCTTTTCATTTTATTTCCT
Found at i:48655 original size:22 final size:22
Alignment explanation
Indices: 48630--48677 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
48620 TATCAAACTG
*
48630 TTGAGCATCAAGTGCCAAACCT
1 TTGAGCATCAAATGCCAAACCT
48652 TTGAGCATCAAATGCCAAACCT
1 TTGAGCATCAAATGCCAAACCT
48674 TTGA
1 TTGA
48678 CCAAACATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (22 bp):
TTGAGCATCAAATGCCAAACCT
Found at i:49638 original size:106 final size:106
Alignment explanation
Indices: 49481--50755 Score: 1994
Period size: 106 Copynumber: 12.0 Consensus size: 106
49471 ATATCGTGTC
* * * * *
49481 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACCACTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
49546 AATTTCAGAGCCAATTTCAACTTAACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
49587 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGATCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
49652 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
49693 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACGACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
49758 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
49799 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGATCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
49864 AATTTTAGAGCCAATTTCAACTTCACAGCGTAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
49905 ACTCAAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
49970 AATTCCAGATCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
50011 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
50076 AATTTCATAGCCAATTTCAACTTCACAACGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
50117 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAA-TAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
**
50181 AATTTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
50222 ACTCAAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
50287 AATTTCAGAGCCAATTTCAACTTCATATCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
50328 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAAGGACCGCTGGTTGTCAACAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
50393 AATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
50434 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
50499 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
50540 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTTTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
50605 AATTTCAGAGCCAATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * * *
50646 ACTCGAAACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * * *
50711 GATTCCAGAGACAATTTCAACTTCACGACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
50752 ACTC
1 ACTC
50756 GGAACAATGC
Statistics
Matches: 1073, Mismatches: 95, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
105 95 0.09
106 978 0.91
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:52321 original size:26 final size:24
Alignment explanation
Indices: 52247--52336 Score: 67
Period size: 24 Copynumber: 3.7 Consensus size: 24
52237 TTATTATTGT
* *
52247 TACTATTTAGTATTTTATTTTATTA
1 TACTATTTATTTTTTTATTTTA-TA
** *
52272 TAC-ATACA-TTTTATATTTTATA
1 TACTATTTATTTTTTTATTTTATA
* *
52294 TATTTTTTATTTTTTTATTTTATTTA
1 TACTATTTATTTTTTTATTTTA--TA
52320 TACTATTTATTTATTTT
1 TACTATTTATTT-TTTT
52337 CATTATGTTT
Statistics
Matches: 49, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
22 4 0.08
23 12 0.24
24 14 0.29
25 3 0.06
26 12 0.24
27 4 0.08
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.68
Consensus pattern (24 bp):
TACTATTTATTTTTTTATTTTATA
Done.