Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003766.1 Hibiscus syriacus cultivar Beakdansim tig00008066_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: 68977
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:10313 original size:21 final size:21
Alignment explanation
Indices: 10287--10339 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
10277 GTTTCCAGAT
10287 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACATCGACTA
*
10308 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACATCGACTA
*
10329 TCGCAATGCGA
1 TCGCAACGCGA
10340 TAGTCCAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.32, G:0.21, T:0.17
Consensus pattern (21 bp):
TCGCAACGCGAACATCGACTA
Found at i:10395 original size:42 final size:42
Alignment explanation
Indices: 10343--10529 Score: 252
Period size: 42 Copynumber: 4.5 Consensus size: 42
10333 AATGCGATAG
* *
10343 TCCAAGTTCGTTGTGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTAT
* * *
10385 TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGAGA--TAG
1 TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTAT
* *
10425 TCGAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTAT
* * *
10469 TCTAAATTCGTTGCAATAGTCCAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTAT
10511 TCCAAGTTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
10530 AGAATAAGGG
Statistics
Matches: 124, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
40 8 0.06
42 108 0.87
44 8 0.06
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (42 bp):
TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTAT
Found at i:10417 original size:21 final size:21
Alignment explanation
Indices: 10335--10529 Score: 172
Period size: 21 Copynumber: 9.4 Consensus size: 21
10325 ACTATCGCAA
10335 TGCGATAGTCCAAGTT--CGT
1 TGCGATAGTCCAAGTTCGCGT
* *
10354 TGTGATAGTCGAAGTTCGCGT
1 TGCGATAGTCCAAGTTCGCGT
* *
10375 TGCGATTTATTCCAAATT--CGT
1 TGCGA--TAGTCCAAGTTCGCGT
10396 TGCGATAGTCCAAGTTCGCGT
1 TGCGATAGTCCAAGTTCGCGT
* *
10417 TGAGATAGTCGAAGTTCGCGT
1 TGCGATAGTCCAAGTTCGCGT
*
10438 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCCAAGTTCGCGT
* * *
10459 TGCGATTTATTCTAAATT--CGT
1 TGCGA--TAGTCCAAGTTCGCGT
*
10480 TGCAATAGTCCAAGTTCGCGT
1 TGCGATAGTCCAAGTTCGCGT
*
10501 TGCGATTTATTCCAAGTT--CGT
1 TGCGA--TAGTCCAAGTTCGCGT
10522 TGCGATAG
1 TGCGATAG
10530 AGAATAAGGG
Statistics
Matches: 143, Mismatches: 21, Indels: 24
0.76 0.11 0.13
Matches are distributed among these distances:
19 33 0.23
21 84 0.59
23 26 0.18
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (21 bp):
TGCGATAGTCCAAGTTCGCGT
Found at i:10477 original size:84 final size:82
Alignment explanation
Indices: 10338--10529 Score: 294
Period size: 84 Copynumber: 2.3 Consensus size: 82
10328 ATCGCAATGC
* *
10338 GATAGTCCAAGTTCGTTGTGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATA
1 GATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCAATA
10403 GTCCAAGTTCGCGTTGA
66 GTCCAAGTTCGCGTTGA
* *
10420 GATAGTCGAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCTAAATTCGTTGCAA
1 GATAGTCCAAGTT--CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCAA
*
10485 TAGTCCAAGTTCGCGTTGC
64 TAGTCCAAGTTCGCGTTGA
*
10504 GATTTATTCCAAGTTCGTTGCGATAG
1 GA--TAGTCCAAGTTCGTTGCGATAG
10530 AGAATAAGGG
Statistics
Matches: 99, Mismatches: 7, Indels: 6
0.88 0.06 0.05
Matches are distributed among these distances:
82 12 0.12
84 78 0.79
86 9 0.09
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (82 bp):
GATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCAATA
GTCCAAGTTCGCGTTGA
Found at i:10777 original size:20 final size:20
Alignment explanation
Indices: 10752--10804 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
10742 GAACTTGGAC
10752 TATCGCAATGCGAATATGTA
1 TATCGCAATGCGAATATGTA
10772 TATCGCAATGCGAATATGTA
1 TATCGCAATGCGAATATGTA
*
10792 AATCGCAATGCGA
1 TATCGCAATGCGA
10805 TAGTCGAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (20 bp):
TATCGCAATGCGAATATGTA
Found at i:12868 original size:16 final size:19
Alignment explanation
Indices: 12847--12891 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 19
12837 AAGAAATTTA
12847 TTTTTATATTAG-TA-T-T
1 TTTTTATATTAGTTATTAT
*
12863 TTTTTA-AATAGTTATTAT
1 TTTTTATATTAGTTATTAT
12881 TTTTTATATTA
1 TTTTTATATTA
12892 ATATATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
15 4 0.17
16 8 0.35
17 1 0.04
18 7 0.30
19 3 0.13
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (19 bp):
TTTTTATATTAGTTATTAT
Found at i:12888 original size:34 final size:34
Alignment explanation
Indices: 12842--12948 Score: 96
Period size: 34 Copynumber: 3.1 Consensus size: 34
12832 GTGGTAAGAA
* *
12842 ATTTATTTTTATATTAGTAT-TTT-TTTAAATAGTT
1 ATTT-TTTTTATATTAATATATTTATGTAAATA-TT
12876 ATTATTTTTTATATTAATATATTTATGTAAATATT
1 ATT-TTTTTTATATTAATATATTTATGTAAATATT
* * *
12911 A-TTTTTTTAT-TAAAATAATATTTATATAATTATT
1 ATTTTTTTTATAT-TAAT-ATATTTATGTAAATATT
12945 ATTT
1 ATTT
12949 ATTTAGAATT
Statistics
Matches: 62, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
32 1 0.02
33 11 0.18
34 34 0.55
35 9 0.15
36 7 0.11
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (34 bp):
ATTTTTTTTATATTAATATATTTATGTAAATATT
Found at i:12930 original size:36 final size:34
Alignment explanation
Indices: 12875--12953 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
12865 TTTAAATAGT
*
12875 TATTATTTTTTATATT--AAT-ATATTTATGTAAA
1 TATTATTTTTT-TATTAAAATAATATTTATATAAA
*
12907 TATTATTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTTATTAAAATAATATTTATATAAA
*
12941 TATTATTTATTTA
1 TATTATTTTTTTA
12954 GAATTATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
31 4 0.10
32 11 0.27
33 3 0.07
34 23 0.56
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (34 bp):
TATTATTTTTTTATTAAAATAATATTTATATAAA
Found at i:14658 original size:21 final size:21
Alignment explanation
Indices: 14628--14675 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
14618 GCAGGGGTAC
* *
14628 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
14649 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
14670 ATGCCA
1 ATGCCA
14676 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:14705 original size:21 final size:21
Alignment explanation
Indices: 14679--14772 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
14669 TATGCCATCT
* *
14679 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
14700 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
14721 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
14742 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
14763 CCGCAGGGTT
1 CCGCAGGGTT
14773 TTATACCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.03
21 65 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.35, G:0.27, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:15344 original size:33 final size:34
Alignment explanation
Indices: 15294--15390 Score: 135
Period size: 33 Copynumber: 2.9 Consensus size: 34
15284 TAAATGTTTT
*
15294 TAAAATACAAATTATATTATTCGAAATTTAAA-A
1 TAAAATAAAAATTATATTATTCGAAATTTAAATA
* *
15327 TAAAATAAAAATAATATTATTC-AAATTTAAATT
1 TAAAATAAAAATTATATTATTCGAAATTTAAATA
* *
15360 TAAAATATAAATTATAGTATTCGAAATTTAA
1 TAAAATAAAAATTATATTATTCGAAATTTAA
15391 CATTAAATTT
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
32 9 0.16
33 39 0.70
34 8 0.14
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.38
Consensus pattern (34 bp):
TAAAATAAAAATTATATTATTCGAAATTTAAATA
Found at i:16576 original size:126 final size:128
Alignment explanation
Indices: 15782--16787 Score: 1877
Period size: 128 Copynumber: 7.9 Consensus size: 128
15772 AGTTATTCAA
15782 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
15847 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
15910 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
15975 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
*
16038 ACTGATATATCTAGTGTCCCCGAGGGACAT--GTGACATAATAGGGCAATGATAACATATTCTTT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
16101 GACGAAATAATGGAAGGCGCG-CCCC-GGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
*
16162 ACTGATATATCTAGTGTCCCC-AGGGACATGAGTGACATAATAGGGTAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
*
16226 GACGAAATAATGGAAGGCGCACCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
16289 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
* *
16354 GACGAAATAATGGAAGGCGCGCCCCCGGGAATGCGACTTCATGTGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
*
16417 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGACAATGATAACATA-T-TCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
16480 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
16543 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
*
16608 GACGAAATAATGGAA-G-GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGAT
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
*
16669 ACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
16734 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
16788 CCGATTATAG
Statistics
Matches: 855, Mismatches: 14, Indels: 18
0.96 0.02 0.02
Matches are distributed among these distances:
123 8 0.01
124 57 0.07
125 55 0.06
126 302 0.35
127 61 0.07
128 372 0.44
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (128 bp):
ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
Found at i:28260 original size:19 final size:19
Alignment explanation
Indices: 28236--28290 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 19
28226 AATGACCAAC
*
28236 TAAATCGTAATGCGATCGA
1 TAAATCGAAATGCGATCGA
*
28255 TAAATCAAAATGCGATCGA
1 TAAATCGAAATGCGATCGA
* * *
28274 TAATTCGCAACGCGATC
1 TAAATCGAAATGCGATC
28291 TCCGGTATCG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (19 bp):
TAAATCGAAATGCGATCGA
Found at i:28416 original size:20 final size:20
Alignment explanation
Indices: 28391--28537 Score: 190
Period size: 20 Copynumber: 7.3 Consensus size: 20
28381 TTTTCCTAAT
28391 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
28411 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
28432 TCAG-AATGCGATTACGTAAA
1 TC-GCAATGCGAATACGTAAA
28452 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
28472 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
28492 TCGTAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
28512 TCGCAATGCGAAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
28532 TCGCAA
1 TCGCAA
28538 CGAGATTCTG
Statistics
Matches: 109, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.02
20 93 0.85
21 13 0.12
22 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:28522 original size:60 final size:61
Alignment explanation
Indices: 28391--28539 Score: 223
Period size: 60 Copynumber: 2.5 Consensus size: 61
28381 TTTTCCTAAT
**
28391 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTGGAAAATCAGAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATTACGAAAATCAGAATGCGATTACGTAAA
* *
28452 TCGCAATGCGAATACGTAAATCGCAATGCGAA-TACGTAAATC-GTAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATTACGAAAATCAG-AATGCGATTACGTAAA
28512 TCGCAATGCGAAT-CTGTAAATCGCAACG
1 TCGCAATGCGAATAC-GTAAATCGCAACG
28540 AGATTCTGAC
Statistics
Matches: 81, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
59 2 0.02
60 48 0.59
61 31 0.38
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (61 bp):
TCGCAATGCGAATACGTAAATCGCAACGCGAATTACGAAAATCAGAATGCGATTACGTAAA
Found at i:28547 original size:20 final size:20
Alignment explanation
Indices: 28507--28547 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
28497 ATGCGATTAC
* *
28507 GTAAATCGCAATGCGAATCT
1 GTAAATCGCAACGAGAATCT
*
28527 GTAAATCGCAACGAGATTCT
1 GTAAATCGCAACGAGAATCT
28547 G
1 G
28548 ACTATCGCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (20 bp):
GTAAATCGCAACGAGAATCT
Found at i:29425 original size:24 final size:24
Alignment explanation
Indices: 29398--29451 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
29388 GTATTCAAAA
29398 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
29422 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
29446 TTTGAT
1 TTTGAT
29452 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:32737 original size:42 final size:42
Alignment explanation
Indices: 32672--32783 Score: 122
Period size: 42 Copynumber: 2.7 Consensus size: 42
32662 TCTAGAATGT
*
32672 TGGGAGGGACCTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGGGACCTCTTCAACGATGACAGGGGCCTCTTGAACGG
** * *
32714 TGGGAGGGGA-CTCTTCAGGGATGATAGGGGCCTCTTGAACGA
1 TGGGA-GGGACCTCTTCAACGATGACAGGGGCCTCTTGAACGG
*
32756 TAGGG-GAGG-CCTCTTGAACGATGACAGG
1 T-GGGAG-GGACCTCTTCAACGATGACAGG
32784 TGAGTCGGGC
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
41 1 0.02
42 49 0.86
43 7 0.12
ACGTcount: A:0.22, C:0.20, G:0.38, T:0.21
Consensus pattern (42 bp):
TGGGAGGGACCTCTTCAACGATGACAGGGGCCTCTTGAACGG
Found at i:33320 original size:33 final size:33
Alignment explanation
Indices: 33260--33343 Score: 114
Period size: 33 Copynumber: 2.5 Consensus size: 33
33250 TCTGAAACTT
** * *
33260 AAAATCGCAACGCGAAAATGACTATCGCAACGAG
1 AAAATCGCAACGCG-AAATGAAAATCGCAACAAC
*
33294 AGAATCGCAACGCGAAATGAAAATCGCAACAAC
1 AAAATCGCAACGCGAAATGAAAATCGCAACAAC
33327 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
33344 ATGACTATCG
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 31 0.70
34 13 0.30
ACGTcount: A:0.48, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
AAAATCGCAACGCGAAATGAAAATCGCAACAAC
Found at i:33355 original size:20 final size:20
Alignment explanation
Indices: 33330--33378 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
33320 CAACAACAAA
33330 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
33350 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
33370 ATCGCAACG
1 ATCGCAACG
33379 AGAGAATCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:33441 original size:34 final size:34
Alignment explanation
Indices: 33402--33515 Score: 120
Period size: 34 Copynumber: 3.2 Consensus size: 34
33392 GCTATTTTCA
** *
33402 TTTCGCATTACGATTCTTTCATTGCAATAGTCAT
1 TTTCGCATTGTGATTCTTTCATTGCGATAGTCAT
*
33436 TTTCGCATTGTGATAGTCATTTTCGCATTGCGATAATCAT
1 TTTCGCATTGTGAT--TC--TTT--CATTGCGATAGTCAT
* *
33476 TTTCGCATTGTGATTCTCTCGTTGCGATAGTCAT
1 TTTCGCATTGTGATTCTTTCATTGCGATAGTCAT
33510 TTTCGC
1 TTTCGC
33516 GTTGAGATAG
Statistics
Matches: 67, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
34 31 0.46
36 4 0.06
38 5 0.07
40 27 0.40
ACGTcount: A:0.19, C:0.20, G:0.17, T:0.44
Consensus pattern (34 bp):
TTTCGCATTGTGATTCTTTCATTGCGATAGTCAT
Found at i:33451 original size:20 final size:20
Alignment explanation
Indices: 33421--33546 Score: 147
Period size: 20 Copynumber: 6.6 Consensus size: 20
33411 ACGATTCTTT
*
33421 CATTGCAATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
*
33441 CATTGTGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
*
33461 CATTGCGATAATCATTTTCG
1 CATTGCGATAGTCATTTTCG
* *
33481 CATTGTGAT--TC--TCTCG
1 CATTGCGATAGTCATTTTCG
33497 --TTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
* *
33515 CGTTGAGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
33535 CATTGCGATAGT
1 CATTGCGATAGT
33547 AAACTATTCT
Statistics
Matches: 89, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
14 6 0.07
16 6 0.07
18 6 0.07
20 71 0.80
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41
Consensus pattern (20 bp):
CATTGCGATAGTCATTTTCG
Found at i:33466 original size:40 final size:40
Alignment explanation
Indices: 33421--33546 Score: 165
Period size: 40 Copynumber: 3.3 Consensus size: 40
33411 ACGATTCTTT
*
33421 CATTGCAATAGTCATTTTCGCATTGTGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCGCATTGTGATAGTCATTTTCG
* *
33461 CATTGCGATAATCATTTTCGCATTGTGAT--TC--TCTCG
1 CATTGCGATAGTCATTTTCGCATTGTGATAGTCATTTTCG
* *
33497 --TTGCGATAGTCATTTTCGCGTTGAGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCGCATTGTGATAGTCATTTTCG
33535 CATTGCGATAGT
1 CATTGCGATAGT
33547 AAACTATTCT
Statistics
Matches: 73, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
34 24 0.33
36 6 0.08
38 6 0.08
40 37 0.51
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41
Consensus pattern (40 bp):
CATTGCGATAGTCATTTTCGCATTGTGATAGTCATTTTCG
Found at i:33491 original size:74 final size:74
Alignment explanation
Indices: 33402--33544 Score: 223
Period size: 74 Copynumber: 1.9 Consensus size: 74
33392 GCTATTTTCA
* *
33402 TTTCGCATTACGATTCTTTCATTGCAATAGTCATTTTCGCATTGTGATAGTCATTTTCGCATTGC
1 TTTCGCATTACGATTCTCTCATTGCAATAGTCATTTTCGCATTGAGATAGTCATTTTCGCATTGC
33467 GATAATCAT
66 GATAATCAT
** * * *
33476 TTTCGCATTGTGATTCTCTCGTTGCGATAGTCATTTTCGCGTTGAGATAGTCATTTTCGCATTGC
1 TTTCGCATTACGATTCTCTCATTGCAATAGTCATTTTCGCATTGAGATAGTCATTTTCGCATTGC
33541 GATA
66 GATA
33545 GTAAACTATT
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
74 62 1.00
ACGTcount: A:0.20, C:0.19, G:0.18, T:0.43
Consensus pattern (74 bp):
TTTCGCATTACGATTCTCTCATTGCAATAGTCATTTTCGCATTGAGATAGTCATTTTCGCATTGC
GATAATCAT
Found at i:36003 original size:20 final size:20
Alignment explanation
Indices: 35954--35991 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
35944 CTGAAACTTT
*
35954 AAATCGCAACATGAAAATAA
1 AAATCGCAACACGAAAATAA
35974 AAATCGCAACACGAAAAT
1 AAATCGCAACACGAAAAT
35992 GACTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.58, C:0.18, G:0.11, T:0.13
Consensus pattern (20 bp):
AAATCGCAACACGAAAATAA
Found at i:36074 original size:20 final size:20
Alignment explanation
Indices: 36049--36095 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
36039 GATTCTCTCG
36049 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
36069 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
36089 TTGCGAT
1 TTGCGAT
36096 TCACTCGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:36710 original size:20 final size:20
Alignment explanation
Indices: 36665--36754 Score: 83
Period size: 20 Copynumber: 4.5 Consensus size: 20
36655 GCGCTATGTA
* *
36665 AATCGCATTGCGATAGT-CAT
1 AATCGCATTGCGAT-TTACGT
*
36685 ATTCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACGT
* **
36705 AATCGCATTGCGATTTTCCA
1 AATCGCATTGCGATTTACGT
*
36725 AATTCGCGTTGCGATTTACGT
1 AA-TCGCATTGCGATTTACGT
*
36746 ATTCGCATT
1 AATCGCATT
36755 ACGAATTAGG
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
19 1 0.02
20 39 0.71
21 15 0.27
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (20 bp):
AATCGCATTGCGATTTACGT
Found at i:36740 original size:41 final size:40
Alignment explanation
Indices: 36665--36754 Score: 126
Period size: 41 Copynumber: 2.2 Consensus size: 40
36655 GCGCTATGTA
*
36665 AATCGCATTGCGATAGTCATATTCGCATTGCGATTTACGT
1 AATCGCATTGCGATAGTCAAATTCGCATTGCGATTTACGT
** *
36705 AATCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACGT
1 AATCGCATTGCGATAGT-CAAATTCGCATTGCGATTTACGT
*
36746 ATTCGCATT
1 AATCGCATT
36755 ACGAATTAGG
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 15 0.34
41 29 0.66
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (40 bp):
AATCGCATTGCGATAGTCAAATTCGCATTGCGATTTACGT
Found at i:36780 original size:21 final size:21
Alignment explanation
Indices: 36756--36795 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
36746 ATTCGCATTA
36756 CGAATTAGGAAAATCGCAACG
1 CGAATTAGGAAAATCGCAACG
* *
36777 CGAATTTGGGAAATCGCAA
1 CGAATTAGGAAAATCGCAA
36796 TACGATAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.17
Consensus pattern (21 bp):
CGAATTAGGAAAATCGCAACG
Found at i:38733 original size:2 final size:2
Alignment explanation
Indices: 38726--38755 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
38716 TAGGAAATTC
38726 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
38756 GTTTAAGAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44155 original size:36 final size:36
Alignment explanation
Indices: 44108--44178 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
44098 AGATTACCAC
* * *
44108 GTCAGAAACGTGAACTGTCACATCAGCACTGTAACA
1 GTCAGAAACGTGAAATGCCACATCAGCACTATAACA
44144 GTCAGAAACGTGAAATGCCACATCAGCACTATAAC
1 GTCAGAAACGTGAAATGCCACATCAGCACTATAAC
44179 TCTTTTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (36 bp):
GTCAGAAACGTGAAATGCCACATCAGCACTATAACA
Found at i:45566 original size:29 final size:29
Alignment explanation
Indices: 45530--45641 Score: 188
Period size: 29 Copynumber: 3.8 Consensus size: 29
45520 CAAACTAAAT
*
45530 TGATGTCATTACTTACATCATTTAATTAA
1 TGATGTCATTGCTTACATCATTTAATTAA
*
45559 AGATGTCATTGCTTACATCATTTAATTAA
1 TGATGTCATTGCTTACATCATTTAATTAA
45588 TGATGTCATTGCTTACATCATTTAATTAA
1 TGATGTCATTGCTTACATCATTTAATTAA
*
45617 TGATGTCATTGCTTTCATCAATTTA
1 TGATGTCATTGCTTACATC-ATTTA
45642 GTTAGGTGAG
Statistics
Matches: 78, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
29 73 0.94
30 5 0.06
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (29 bp):
TGATGTCATTGCTTACATCATTTAATTAA
Found at i:50363 original size:29 final size:29
Alignment explanation
Indices: 50327--50438 Score: 188
Period size: 29 Copynumber: 3.8 Consensus size: 29
50317 CAAACTAAAT
*
50327 TGATGTCATTACTTACATCATTTAATTAA
1 TGATGTCATTGCTTACATCATTTAATTAA
*
50356 AGATGTCATTGCTTACATCATTTAATTAA
1 TGATGTCATTGCTTACATCATTTAATTAA
50385 TGATGTCATTGCTTACATCATTTAATTAA
1 TGATGTCATTGCTTACATCATTTAATTAA
*
50414 TGATGTCATTGCTTTCATCAATTTA
1 TGATGTCATTGCTTACATC-ATTTA
50439 GTTAGGTGAG
Statistics
Matches: 78, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
29 73 0.94
30 5 0.06
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (29 bp):
TGATGTCATTGCTTACATCATTTAATTAA
Found at i:53648 original size:35 final size:35
Alignment explanation
Indices: 53602--53677 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
53592 AAAACAGTCC
* *
53602 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
53637 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
53672 TCAATT
1 TCAATT
53678 AAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:54220 original size:130 final size:128
Alignment explanation
Indices: 54074--54319 Score: 411
Period size: 130 Copynumber: 1.9 Consensus size: 128
54064 TATTTATATA
* **
54074 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
*
54139 TTAGCACATGATCATAACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATAACA--TGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
54204 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * *
54269 TTAACACATGATCATGATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATAACATGTCATTGGTGACACATGTCACCACCTAATTA
54320 GAAGAAAATT
Statistics
Matches: 109, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
128 31 0.28
130 78 0.72
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (128 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATAACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:54640 original size:240 final size:238
Alignment explanation
Indices: 54219--54697 Score: 940
Period size: 240 Copynumber: 2.0 Consensus size: 238
54209 TTTGGTCCTA
54219 AATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCAT
1 AATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCAT
54284 GATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTACAAAGAAGTAAAA
66 GATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTACAAAGAAGTAAAA
54349 TTTGGGTCTTGGGCAAACTCAAACCTGAGTCACGCAAATGAAAGATACAGGGTGGTGCCACTAAG
131 TTTGGGTCTTGGGCAAACTCAAACCTGAGTCACGCAAATGAAAGATACAGGGTGGTGCCACTAAG
54414 CTAACACCATCGTTTGTGTTAAGAGATATACAATAATACATAT
196 CTAACACCATCGTTTGTGTTAAGAGATATACAATAATACATAT
54457 AATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCAT
1 AATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCAT
54522 GATATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTACAAAGAAGTAA
66 G--ATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTACAAAGAAGTAA
54587 AATTTGGGTCTTGGGCAAACTCAAACCTGAGTCACGCAAATGAAAGATACAGGGTGGTGCCACTA
129 AATTTGGGTCTTGGGCAAACTCAAACCTGAGTCACGCAAATGAAAGATACAGGGTGGTGCCACTA
54652 AGCTAACACCATCGTTTGTGTTAAGAGATATACAATAATACATAT
194 AGCTAACACCATCGTTTGTGTTAAGAGATATACAATAATACATAT
54697 A
1 A
54698 CTAATAGTAT
Statistics
Matches: 239, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
238 66 0.28
240 173 0.72
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (238 bp):
AATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCAT
GATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTACAAAGAAGTAAAA
TTTGGGTCTTGGGCAAACTCAAACCTGAGTCACGCAAATGAAAGATACAGGGTGGTGCCACTAAG
CTAACACCATCGTTTGTGTTAAGAGATATACAATAATACATAT
Found at i:54918 original size:28 final size:27
Alignment explanation
Indices: 54887--54949 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
54877 AGTTGATATA
*
54887 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
54915 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
54943 ATATTTT
1 ATATTTT
54950 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:55050 original size:16 final size:18
Alignment explanation
Indices: 55029--55062 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
55019 ATTTCTTATT
55029 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
55045 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
55063 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:59447 original size:2 final size:2
Alignment explanation
Indices: 59442--59491 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
59432 GTGTGTGTGT
* *
59442 GA GA GA GA GA GA GG GA GA GG GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
59484 GA GA GA GA
1 GA GA GA GA
59492 ACTTTAATGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (2 bp):
GA
Found at i:60876 original size:2 final size:2
Alignment explanation
Indices: 60871--60895 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
60861 CGGAGAGGGG
60871 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
60896 GGCAGCAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Done.