Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003537.1 Hibiscus syriacus cultivar Beakdansim tig00007463_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: 60516
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5774 original size:11 final size:11
Alignment explanation
Indices: 5758--5784 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
5748 GGTGTTTTAT
5758 AAAAAAATTAA
1 AAAAAAATTAA
5769 AAAAAAATTAA
1 AAAAAAATTAA
5780 AAAAA
1 AAAAA
5785 TAAAATGACG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAAAATTAA
Found at i:8743 original size:15 final size:15
Alignment explanation
Indices: 8725--8759 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
8715 TAAAATTGTA
8725 AAATTTAAATTACAG
1 AAATTTAAATTACAG
* *
8740 AAATTTAGATTACTG
1 AAATTTAAATTACAG
8755 AAATT
1 AAATT
8760 AAGACTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.37
Consensus pattern (15 bp):
AAATTTAAATTACAG
Found at i:9566 original size:2 final size:2
Alignment explanation
Indices: 9559--9607 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
9549 TATACAAATA
*
9559 AT AT AT AT AT AC 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
9601 AT AT AT A
1 AT AT AT A
9608 CGATAATTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12539 original size:14 final size:15
Alignment explanation
Indices: 12520--12551 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
12510 ATTGCGGATG
12520 CGGTTGCGG-TGTTA
1 CGGTTGCGGATGTTA
12534 CGGTTGCGGATGTTA
1 CGGTTGCGGATGTTA
12549 CGG
1 CGG
12552 ACGTTACGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.09, C:0.16, G:0.44, T:0.31
Consensus pattern (15 bp):
CGGTTGCGGATGTTA
Found at i:12826 original size:22 final size:22
Alignment explanation
Indices: 12796--12837 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
12786 GAGCTCGTTC
12796 GTTCATTTACGTTCGGTAATAT
1 GTTCATTTACGTTCGGTAATAT
* * *
12818 GTTCGTTTATGTTCGTTAAT
1 GTTCATTTACGTTCGGTAAT
12838 TTATGTTTAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.50
Consensus pattern (22 bp):
GTTCATTTACGTTCGGTAATAT
Found at i:13080 original size:57 final size:58
Alignment explanation
Indices: 13011--13119 Score: 150
Period size: 57 Copynumber: 1.9 Consensus size: 58
13001 AAAATCTATT
*
13011 TTCATTTATGTTCGCTTACGA-TCATTTATGTTAGTTTA-TTGTGTTTGTTTACGTTCG
1 TTCATTTATGTTCGCTTAC-ATTCATTTATGTTAGTTCATTTGTGTTTGTTTACGTTCG
* * * *
13068 TTCATTTGTGTTCGTTTACATTCGTTTATGTTCGTTCATTTGTGTTTGTTTA
1 TTCATTTATGTTCGCTTACATTCATTTATGTTAGTTCATTTGTGTTTGTTTA
13120 TCATTTAAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
56 1 0.02
57 31 0.69
58 13 0.29
ACGTcount: A:0.14, C:0.12, G:0.17, T:0.57
Consensus pattern (58 bp):
TTCATTTATGTTCGCTTACATTCATTTATGTTAGTTCATTTGTGTTTGTTTACGTTCG
Found at i:13101 original size:34 final size:35
Alignment explanation
Indices: 13057--13124 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 35
13047 TATTGTGTTT
13057 GTTTACGTTCGTTCATTTGTGTTCGTTTA-CATTC
1 GTTTACGTTCGTTCATTTGTGTTCGTTTATCATTC
* *
13091 GTTTATGTTCGTTCATTTGTGTTTGTTTATCATT
1 GTTTACGTTCGTTCATTTGTGTTCGTTTATCATT
13125 TAAATGAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 27 0.87
35 4 0.13
ACGTcount: A:0.12, C:0.13, G:0.18, T:0.57
Consensus pattern (35 bp):
GTTTACGTTCGTTCATTTGTGTTCGTTTATCATTC
Found at i:15247 original size:34 final size:34
Alignment explanation
Indices: 15209--15288 Score: 160
Period size: 34 Copynumber: 2.4 Consensus size: 34
15199 ATTGTGCACC
15209 GATGCATCGATGATAAATACCAGAAATTGTTTAA
1 GATGCATCGATGATAAATACCAGAAATTGTTTAA
15243 GATGCATCGATGATAAATACCAGAAATTGTTTAA
1 GATGCATCGATGATAAATACCAGAAATTGTTTAA
15277 GATGCATCGATG
1 GATGCATCGATG
15289 CATGAATTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (34 bp):
GATGCATCGATGATAAATACCAGAAATTGTTTAA
Found at i:15354 original size:64 final size:63
Alignment explanation
Indices: 15279--15419 Score: 169
Period size: 64 Copynumber: 2.2 Consensus size: 63
15269 TTGTTTAAGA
* * ** *
15279 TGCATCGATGCAT-GAATTTAAATAGAAAACATCGAATAGGA-TTTATGCATTGATGCATAAGGA
1 TGCATCGATGCATCCAA-TTAAATA-AAAACATCGAAT-GCATTTTATGCACCGATGCACAAGGA
15342 G
63 G
* *
15343 TGCATCGATGCATCCCCATTAAATAAAAACATCGAATGCATTTTATGCACCGATGCACAAGTAG
1 TGCATCGATGCAT-CCAATTAAATAAAAACATCGAATGCATTTTATGCACCGATGCACAAGGAG
15407 TGCATCGATGCAT
1 TGCATCGATGCAT
15420 ACATTCATTG
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
63 2 0.03
64 57 0.85
65 7 0.10
66 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCATCCAATTAAATAAAAACATCGAATGCATTTTATGCACCGATGCACAAGGAG
Found at i:16139 original size:30 final size:30
Alignment explanation
Indices: 16103--16166 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
16093 AAGGAACATA
* *
16103 TGGATAGTTGCCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
* * *
16133 TGGATAGTTACCGGGGTTCTTTGTAACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
16163 TGGA
1 TGGA
16167 CAGGTCCTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATAACCTC
Found at i:17657 original size:15 final size:15
Alignment explanation
Indices: 17634--17663 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17624 GATATGAAAA
17634 AAATCAATTTAATTT
1 AAATCAATTTAATTT
*
17649 AAATTAATTTAATTT
1 AAATCAATTTAATTT
17664 TAAAATAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
AAATCAATTTAATTT
Found at i:21103 original size:24 final size:25
Alignment explanation
Indices: 21051--21101 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 25
21041 AAAGTTCTTC
21051 TTTT-CTTTATTTTCAAGTTTTCGT
1 TTTTACTTTATTTTCAAGTTTTCGT
21075 TTTTACTTTATTTT-AAGTTTT-GT
1 TTTTACTTTATTTTCAAGTTTTCGT
21098 TTTT
1 TTTT
21102 TAACATGCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 6 0.23
24 11 0.42
25 9 0.35
ACGTcount: A:0.14, C:0.08, G:0.08, T:0.71
Consensus pattern (25 bp):
TTTTACTTTATTTTCAAGTTTTCGT
Found at i:33315 original size:4 final size:4
Alignment explanation
Indices: 33306--33360 Score: 96
Period size: 4 Copynumber: 14.2 Consensus size: 4
33296 TTTCTTGTTT
33306 TTCC TTCC TTCC TTCC TTCC TTCC TTCC TTCC TTCC TTCC TTCC -T-C
1 TTCC TTCC TTCC TTCC TTCC TTCC TTCC TTCC TTCC TTCC TTCC TTCC
33352 TTCC TTCC T
1 TTCC TTCC T
33361 CTTCGCTTCG
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 1 0.02
3 2 0.04
4 46 0.94
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (4 bp):
TTCC
Found at i:37329 original size:19 final size:19
Alignment explanation
Indices: 37314--37349 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
37304 TTTAATATAT
*
37314 TTAATTTATTAAAATAAAG
1 TTAATATATTAAAATAAAG
37333 TTAATATATT-AAATAAA
1 TTAATATATTAAAATAAA
37350 AATATTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
TTAATATATTAAAATAAAG
Found at i:42201 original size:47 final size:47
Alignment explanation
Indices: 42127--42222 Score: 138
Period size: 47 Copynumber: 2.0 Consensus size: 47
42117 TAAAATAAAA
* * * *
42127 TAAATATTAATAAAAATAAGGTGTTCACTATGTTACTATGATAAATT
1 TAAATATTAATAAAAATAAGATATTCACTATGCTACGATGATAAATT
* *
42174 TAAATATTAATAAAAGTAAGATATTCACTATGCTGCGATGATAAATT
1 TAAATATTAATAAAAATAAGATATTCACTATGCTACGATGATAAATT
42221 TA
1 TA
42223 GTTTTAGTCG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.36
Consensus pattern (47 bp):
TAAATATTAATAAAAATAAGATATTCACTATGCTACGATGATAAATT
Found at i:45929 original size:24 final size:24
Alignment explanation
Indices: 45859--45911 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
45849 TTATTTTCTT
*
45859 AGTTTGAGAGTTTCAAAGTTTGAA
1 AGTTTGAAAGTTTCAAAGTTTGAA
45883 AGTTTGAAAGTTTCAAAGTTTGAA
1 AGTTTGAAAGTTTCAAAGTTTGAA
45907 AGTTT
1 AGTTT
45912 ACACGTTTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.34, C:0.04, G:0.23, T:0.40
Consensus pattern (24 bp):
AGTTTGAAAGTTTCAAAGTTTGAA
Found at i:45931 original size:8 final size:8
Alignment explanation
Indices: 45859--45929 Score: 81
Period size: 8 Copynumber: 8.9 Consensus size: 8
45849 TTATTTTCTT
*
45859 AGTTTGAG
1 AGTTTGAA
*
45867 AGTTTCAA
1 AGTTTGAA
45875 AGTTTGAA
1 AGTTTGAA
45883 AGTTTGAA
1 AGTTTGAA
*
45891 AGTTTCAA
1 AGTTTGAA
45899 AGTTTGAA
1 AGTTTGAA
45907 AGTTT-ACA
1 AGTTTGA-A
* *
45915 CGTTTGAG
1 AGTTTGAA
45923 AGTTTGA
1 AGTTTGA
45930 GATTTCAAAG
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
7 1 0.02
8 51 0.96
9 1 0.02
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.38
Consensus pattern (8 bp):
AGTTTGAA
Found at i:46219 original size:83 final size:83
Alignment explanation
Indices: 46052--46492 Score: 503
Period size: 83 Copynumber: 5.4 Consensus size: 83
46042 TGCACATTTT
* * * *
46052 ATTTCGGATGGGATGGAACACTATGACATGACAAAGA-T-TCTGAATAATAATGGAAAACGCTTT
1 ATTTCGGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAATGGAAAATGCTTC
*
46115 CCCTGAAACGCGCCTTTC
66 CCCTGGAACGCGCCTTTC
* *
46133 ATTTTGGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAATGGAAAATGTTTC
1 ATTTCGGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAATGGAAAATGCTTC
* *
46198 CCTTGGAATGCGCCTTTC
66 CCCTGGAACGCGCCTTTC
* * **
46216 ATTTCGGATGGGATGGAACATTATGACATGGCAGAGATTCTCCGAATAATAATGGAAAATAATTC
1 ATTTCGGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAATGGAAAATGCTTC
* *
46281 CTCTAGAACGCGCCTTTC
66 CCCTGGAACGCGCCTTTC
* * ** * *
46299 ATTTCGGATGGGATAGAACACTATAACATTACAGAGATTCTCTAAATAATAA--AAAAATGCTTC
1 ATTTCGGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAATGGAAAATGCTTC
* ** *
46362 CCCTAGAACATGCCTCTC
66 CCCTGGAACGCGCCTTTC
** * * * * *
46380 ATTTAAGATGGGATGGAACACTATGACATGGTAGATATTCTCTCATTAATAATGGAAAACGCTTC
1 ATTTCGGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAATGGAAAATGCTTC
* ** *
46445 CCCTGAAACATGTCTTTC
66 CCCTGGAACGCGCCTTTC
** *
46463 ATTTAAGATGGGATAGAACACTATGACATG
1 ATTTCGGATGGGATGGAACACTATGACATG
46493 ACAAATATTT
Statistics
Matches: 307, Mismatches: 49, Indels: 6
0.85 0.14 0.02
Matches are distributed among these distances:
81 98 0.32
82 1 0.00
83 208 0.68
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.29
Consensus pattern (83 bp):
ATTTCGGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAATGGAAAATGCTTC
CCCTGGAACGCGCCTTTC
Found at i:46393 original size:164 final size:164
Alignment explanation
Indices: 46058--46495 Score: 499
Period size: 164 Copynumber: 2.7 Consensus size: 164
46048 TTTTATTTCG
* * **
46058 GATGGGATGGAACACTATGACATGACAAAGATTCT--GAATAATAATGGAAAACGCTTTCCCTGA
1 GATGGGATGGAACACTATGACATGGCAGAGATTCTCCGAATAATAATGGAAAAC-AATTCCCTGA
* * * *
46121 AACGCGCCTTTCATTTTGGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAAT
65 AACGCGCCTTTCATTTAGGATGGGATAGAACACTATGACATGACAGAGATTCTCTAAATAATAA-
* * * * ** * **
46186 GGAAAATGTTTCCCTTGGAATGCGCCTTTCATTTCG
129 GAAAAATGCTTCCCCTAGAACACGCCTCTCATTTAA
* *
46222 GATGGGATGGAACATTATGACATGGCAGAGATTCTCCGAATAATAATGGAAAATAATTCCTCT-A
1 GATGGGATGGAACACTATGACATGGCAGAGATTCTCCGAATAATAATGGAAAACAATTCC-CTGA
* * *
46286 GAACGCGCCTTTCATTTCGGATGGGATAGAACACTATAACATTACAGAGATTCTCTAAATAATAA
65 -AACGCGCCTTTCATTTAGGATGGGATAGAACACTATGACATGACAGAGATTCTCTAAATAATAA
*
46351 -AAAAATGCTTCCCCTAGAACATGCCTCTCATTTAA
129 GAAAAATGCTTCCCCTAGAACACGCCTCTCATTTAA
* * * **
46386 GATGGGATGGAACACTATGACATGGTAGATATTCTCTC-ATTAATAATGGAAAACGCTTCCCCTG
1 GATGGGATGGAACACTATGACATGGCAGAGATTCTC-CGAATAATAATGGAAAACAATT-CCCTG
** * *
46450 AAACATGTCTTTCATTTAAGATGGGATAGAACACTATGACATGACA
64 AAACGCGCCTTTCATTTAGGATGGGATAGAACACTATGACATGACA
46496 AATATTTTCT
Statistics
Matches: 231, Mismatches: 36, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
164 146 0.63
165 9 0.04
166 76 0.33
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (164 bp):
GATGGGATGGAACACTATGACATGGCAGAGATTCTCCGAATAATAATGGAAAACAATTCCCTGAA
ACGCGCCTTTCATTTAGGATGGGATAGAACACTATGACATGACAGAGATTCTCTAAATAATAAGA
AAAATGCTTCCCCTAGAACACGCCTCTCATTTAA
Found at i:47430 original size:26 final size:27
Alignment explanation
Indices: 47395--47446 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
47385 TGAACTATAA
*
47395 AAACAACAAACCA-TAAACATTACATT
1 AAACAACAAACCATTAAACATGACATT
*
47421 AAACAACAAACTATTAAACATGACAT
1 AAACAACAAACCATTAAACATGACAT
47447 GAAGCATACC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.58, C:0.21, G:0.02, T:0.19
Consensus pattern (27 bp):
AAACAACAAACCATTAAACATGACATT
Found at i:47549 original size:31 final size:32
Alignment explanation
Indices: 47494--47567 Score: 123
Period size: 31 Copynumber: 2.3 Consensus size: 32
47484 TCTTTCACAG
* *
47494 ACCTTAAACAGTAAATAAAAGCATACACATAC
1 ACCTAAAATAGTAAATAAAAGCATACACATAC
47526 ACCTAAAATAGTAAAT-AAAGCATACACATAC
1 ACCTAAAATAGTAAATAAAAGCATACACATAC
47557 ACCTAAAATAG
1 ACCTAAAATAG
47568 ACTTTTCTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 26 0.65
32 14 0.35
ACGTcount: A:0.54, C:0.20, G:0.07, T:0.19
Consensus pattern (32 bp):
ACCTAAAATAGTAAATAAAAGCATACACATAC
Found at i:48379 original size:24 final size:24
Alignment explanation
Indices: 48352--48401 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
48342 TATAAACAGT
* *
48352 TCCTCTTCATCCCCATTATCGTCA
1 TCCTCATCATCCCCATCATCGTCA
* *
48376 TCCTCATCCTCCTCATCATCGTCA
1 TCCTCATCATCCCCATCATCGTCA
48400 TC
1 TC
48402 ATTATCTTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.16, C:0.44, G:0.04, T:0.36
Consensus pattern (24 bp):
TCCTCATCATCCCCATCATCGTCA
Found at i:48390 original size:9 final size:9
Alignment explanation
Indices: 48373--48444 Score: 51
Period size: 9 Copynumber: 8.3 Consensus size: 9
48363 CCCATTATCG
48373 TCATCCTCA
1 TCATCCTCA
*
48382 TCCTCCTCA
1 TCATCCTCA
*
48391 TCATCGTCA
1 TCATCCTCA
** *
48400 TCATTATCT
1 TCATCCTCA
48409 TCATCCTCA
1 TCATCCTCA
*
48418 TCCTCCT--
1 TCATCCTCA
48425 TC-TCCTCA
1 TCATCCTCA
* *
48433 TCGTCATCA
1 TCATCCTCA
48442 TCA
1 TCA
48445 CTTTCAACAA
Statistics
Matches: 48, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
6 4 0.08
7 2 0.04
8 2 0.04
9 40 0.83
ACGTcount: A:0.18, C:0.42, G:0.03, T:0.38
Consensus pattern (9 bp):
TCATCCTCA
Found at i:48413 original size:36 final size:38
Alignment explanation
Indices: 48365--48442 Score: 115
Period size: 36 Copynumber: 2.1 Consensus size: 38
48355 TCTTCATCCC
48365 CATTATCGTCATCCTCATCCT-C-CTCATCATCGTCAT
1 CATTATCGTCATCCTCATCCTCCTCTCATCATCGTCAT
* *
48401 CATTATCTTCATCCTCATCCTCCTTCTCCTCATCGTCAT
1 CATTATCGTCATCCTCATCCTCC-TCTCATCATCGTCAT
48440 CAT
1 CAT
48443 CACTTTCAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
36 20 0.54
37 1 0.03
39 16 0.43
ACGTcount: A:0.18, C:0.40, G:0.04, T:0.38
Consensus pattern (38 bp):
CATTATCGTCATCCTCATCCTCCTCTCATCATCGTCAT
Found at i:49581 original size:2 final size:2
Alignment explanation
Indices: 49574--49630 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
49564 ACCACCTATT
49574 TA TA TA 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
49616 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
49631 TAATAATCAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:50450 original size:14 final size:14
Alignment explanation
Indices: 50431--50468 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
50421 TCAAATTATT
50431 TAAATAAATTCAAA
1 TAAATAAATTCAAA
*
50445 TAAATAAATTCTAA
1 TAAATAAATTCAAA
50459 TAAATTAAAT
1 TAAA-TAAAT
50469 AATATATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (14 bp):
TAAATAAATTCAAA
Found at i:50847 original size:21 final size:21
Alignment explanation
Indices: 50821--50862 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
50811 GTTAGGGAAA
50821 TAGGT-GAGAGAATTTGACGGG
1 TAGGTGGA-AGAATTTGACGGG
*
50842 TAGGTGGAAGAATTTGGCGGG
1 TAGGTGGAAGAATTTGACGGG
50863 GAATCGGGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.26, C:0.05, G:0.45, T:0.24
Consensus pattern (21 bp):
TAGGTGGAAGAATTTGACGGG
Found at i:55237 original size:21 final size:21
Alignment explanation
Indices: 55208--55254 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
55198 ATTCTGACTA
55208 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
55229 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
55250 TCGCA
1 TCGCA
55255 ACGCGATTAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:55275 original size:20 final size:20
Alignment explanation
Indices: 55250--55343 Score: 107
Period size: 20 Copynumber: 4.7 Consensus size: 20
55240 TTTTCCTAAT
*
55250 TCGCAACGCGATTACGTAAA
1 TCGCAATGCGATTACGTAAA
* *
55270 TCGCAATGTGAATACGTAAA
1 TCGCAATGCGATTACGTAAA
* * *
55290 TCGCAATGTGAATTAGGAAAA
1 TCGCAATGCG-ATTACGTAAA
*
55311 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGATTACGTAAA
*
55331 TCACAATGCGATT
1 TCGCAATGCGATT
55344 TACATAGCGC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 45 0.74
21 16 0.26
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGATTACGTAAA
Found at i:55972 original size:21 final size:21
Alignment explanation
Indices: 55898--55976 Score: 76
Period size: 20 Copynumber: 3.9 Consensus size: 21
55888 TTCTAAACTT
55898 AAAATCGCAAC-ATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
55918 AAAATCGCAAC-ACGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
** *
55938 ACTATCGCAGCGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
*
55959 AAAATCACAACGAGAGAA
1 AAAATCGCAACGAGAGAA
55977 TCACAACGCG
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
20 29 0.59
21 20 0.41
ACGTcount: A:0.52, C:0.18, G:0.19, T:0.11
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:56002 original size:19 final size:19
Alignment explanation
Indices: 55975--56019 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
55965 ACAACGAGAG
* **
55975 AATCACAACGCGAAATTAA
1 AATCGCAACGCGAAACCAA
55994 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
56013 AATCGCA
1 AATCGCA
56020 TTGAGATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.49, C:0.27, G:0.13, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:56085 original size:20 final size:20
Alignment explanation
Indices: 56029--56072 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
56019 ATTGAGATTT
56029 TCATTT-CGCGTTGCGATAG
1 TCATTTCCGCGTTGCGATAG
56048 TCATTTCCGCGTTGCGATAG
1 TCATTTCCGCGTTGCGATAG
56068 TCATT
1 TCATT
56073 CTCTCGTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.39
Consensus pattern (20 bp):
TCATTTCCGCGTTGCGATAG
Found at i:59318 original size:13 final size:14
Alignment explanation
Indices: 59287--59319 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
59277 GAATGTTTAA
59287 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
*
59301 ATGATTTGT-AAAG
1 TTGATTTGTAAAAG
59314 TTGATT
1 TTGATT
59320 GTTTAATTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.45
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:59443 original size:19 final size:17
Alignment explanation
Indices: 59427--59477 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 17
59417 AAAAATGACT
59427 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
59446 ATCGCAA--CGAGA-GA
1 ATCGCAATGCGAAATGA
59460 ATCGCAATGCGAAATGA
1 ATCGCAATGCGAAATGA
59477 A
1 A
59478 AATCGCAACG
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 8 0.30
16 5 0.19
17 7 0.26
19 7 0.26
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.14
Consensus pattern (17 bp):
ATCGCAATGCGAAATGA
Found at i:59469 original size:33 final size:33
Alignment explanation
Indices: 59427--59506 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
59417 AAAAATGACT
* *
59427 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
59460 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
59493 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
59507 CTAAATTCGC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:59483 original size:19 final size:19
Alignment explanation
Indices: 59427--59485 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
59417 AAAAATGACT
59427 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
59446 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
59460 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
59479 ATCGCAA
1 ATCGCAA
59486 CGACAAAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 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:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:59603 original size:32 final size:33
Alignment explanation
Indices: 59516--59606 Score: 143
Period size: 33 Copynumber: 2.8 Consensus size: 33
59506 ACTAAATTCG
*
59516 CGTTGC-A-TTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
59547 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
59580 CGTTGCGATTTTCA-TTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
59607 AGTCTTCCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
31 6 0.11
32 14 0.25
33 36 0.64
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:59605 original size:18 final size:18
Alignment explanation
Indices: 59549--59643 Score: 83
Period size: 18 Copynumber: 5.4 Consensus size: 18
59539 GATTCCCTCG
59549 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCA-TTCGCA
*
59568 TTGCGATTCTC--TCG--
1 TTGCGATTTTCATTCGCA
59582 TTGCGATTTTCATTCGCA
1 TTGCGATTTTCATTCGCA
**
59600 TTGCGATAGTC-TTCCGCA
1 TTGCGATTTTCATT-CGCA
* * *
59618 TTGCGATATTAATTCGCG
1 TTGCGATTTTCATTCGCA
59636 TTGCGATT
1 TTGCGATT
59644 GTTGCGATTT
Statistics
Matches: 62, Mismatches: 8, Indels: 13
0.75 0.10 0.16
Matches are distributed among these distances:
14 10 0.16
16 6 0.10
17 2 0.03
18 32 0.52
19 12 0.19
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.42
Consensus pattern (18 bp):
TTGCGATTTTCATTCGCA
Done.