Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004300.1 Hibiscus syriacus cultivar Beakdansim tig00009432_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: 45905
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:5532 original size:183 final size:182
Alignment explanation
Indices: 5224--5590 Score: 725
Period size: 183 Copynumber: 2.0 Consensus size: 182
5214 GTTTTTGCTG
5224 CTTCATATGTAGACCAGCAGATTGCAGCAGCAGGAGCATGGAAAAGCATTCGGGGAATCCATCCC
1 CTTCATATGTAGACCAGCAGATTGCAGCAGCAGGAGCATGGAAAAGCATTCGGGGAATCCATCCC
5289 CTCATGAGGCCCTTGTAGCCGTCCTTTCGCACAATTGTTTCAACCACATCCCCAATAGAACTACT
66 CTCATGAGGCCCTTGTAGCCGTCCTTTCGCACAATTGTTTCAACCACATCCCCAATAGAACTACT
5354 CTTAAATCTATCACACCCGCATACACCCTGTTATACAATTTTTAATAACAATA
131 CTT-AATCTATCACACCCGCATACACCCTGTTATACAATTTTTAATAACAATA
5407 CTTCATATGTAGACCAGCAGATTGCAGCAGCAGGAGCATGGAAAAGCATTCGGGGAATCCATCCC
1 CTTCATATGTAGACCAGCAGATTGCAGCAGCAGGAGCATGGAAAAGCATTCGGGGAATCCATCCC
5472 CTCATGAGGCCCTTGTAGCCGTCCTTTCGCACAATTGTTTCAACCACATCCCCAATAGAACTACT
66 CTCATGAGGCCCTTGTAGCCGTCCTTTCGCACAATTGTTTCAACCACATCCCCAATAGAACTACT
5537 CTTAATCTATCACACCCGCATACACCCTGTTATACAATTTTTAATAACAATA
131 CTTAATCTATCACACCCGCATACACCCTGTTATACAATTTTTAATAACAATA
5589 CT
1 CT
5591 AAACAGTCAG
Statistics
Matches: 184, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
182 51 0.28
183 133 0.72
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (182 bp):
CTTCATATGTAGACCAGCAGATTGCAGCAGCAGGAGCATGGAAAAGCATTCGGGGAATCCATCCC
CTCATGAGGCCCTTGTAGCCGTCCTTTCGCACAATTGTTTCAACCACATCCCCAATAGAACTACT
CTTAATCTATCACACCCGCATACACCCTGTTATACAATTTTTAATAACAATA
Found at i:16793 original size:21 final size:20
Alignment explanation
Indices: 16707--16864 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
16697 AAATGACCAA
**
16707 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
16726 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
16746 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
16766 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
16787 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
16808 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
16828 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
16849 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
16865 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:16893 original size:20 final size:20
Alignment explanation
Indices: 16831--17023 Score: 219
Period size: 20 Copynumber: 9.7 Consensus size: 20
16821 CGATTTTCCA
* ** *
16831 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
16851 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
16871 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
16891 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
16911 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
* *
16931 AAATCGCAATGCATATCCGT
1 AAATCGCAACGCGTATCCGT
*
16951 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
16971 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* *
16991 AAATCGCAACGAGAATCCGT
1 AAATCGCAACGCGTATCCGT
17011 AAATCGCAACGCG
1 AAATCGCAACGCG
17024 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
19 2 0.01
20 142 0.97
21 2 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:17443 original size:33 final size:33
Alignment explanation
Indices: 17404--17474 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
17394 TTCACTTAGA
*
17404 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* * *
17437 TTTCATTTCGTGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
17470 TTTCA
1 TTTCA
17475 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.21, G:0.18, T:0.49
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:17600 original size:20 final size:20
Alignment explanation
Indices: 17554--17663 Score: 99
Period size: 21 Copynumber: 5.8 Consensus size: 20
17544 TGCAGAAGAG
* *
17554 TCGCAACGAGATAAATTAAAA
1 TCGCAACGAGA-GAATGAAAA
***
17575 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
17595 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
17616 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
17630 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
17649 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
17664 CGCAACGCGA
Statistics
Matches: 72, Mismatches: 9, Indels: 17
0.73 0.09 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.06
17 2 0.03
19 15 0.21
20 19 0.26
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:17616 original size:41 final size:38
Alignment explanation
Indices: 17547--17663 Score: 136
Period size: 41 Copynumber: 3.1 Consensus size: 38
17537 TTCAATTTGC
* * *
17547 AGAAGAGTCGCAACGAGATAAATTAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
17585 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
17626 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
17659 AGAAT
1 AGAAT
17664 CGCAACGCGA
Statistics
Matches: 70, Mismatches: 4, Indels: 13
0.80 0.05 0.15
Matches are distributed among these distances:
33 23 0.33
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 32 0.46
ACGTcount: A:0.46, C:0.17, G:0.25, T:0.12
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:17633 original size:14 final size:14
Alignment explanation
Indices: 17614--17670 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
17604 GAGAAATGAA
17614 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
17628 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
17647 AATCGCAACGAGAG
1 AATCGCAACGAGAG
17661 AATCGCAACG
1 AATCGCAACG
17671 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:17646 original size:33 final size:33
Alignment explanation
Indices: 17606--17686 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
17596 CGCAACGAGA
17606 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
17639 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
17672 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
17687 TTGCGATTTC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:17741 original size:19 final size:18
Alignment explanation
Indices: 17682--17753 Score: 80
Period size: 19 Copynumber: 4.1 Consensus size: 18
17672 GAAACCAAAA
*
17682 TCGCATTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
17700 TCGCGTTGCGA-TT-A--
1 TCGCGTTGCGATTTCATT
*
17714 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATT-TCATT
17733 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATT
17752 TC
1 TC
17754 AACCAAAAGA
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
14 10 0.22
15 1 0.02
16 2 0.04
17 3 0.07
18 10 0.22
19 17 0.38
20 2 0.04
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.44
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATT
Found at i:19680 original size:185 final size:186
Alignment explanation
Indices: 19449--19793 Score: 665
Period size: 185 Copynumber: 1.9 Consensus size: 186
19439 TAGATTGCTT
19449 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
19514 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGCTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
19579 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
19635 AGTAAA-TTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
19699 TTTGTCTTTGCTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGCTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
19764 GTGTATTCTTTAACACTGTGAAATAGTATT
131 GTGTATTCTTTAACACTGTGAAATAGTATT
19794 GCGATTTTCA
Statistics
Matches: 157, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
185 151 0.96
186 6 0.04
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.45
Consensus pattern (186 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGCTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:19706 original size:92 final size:93
Alignment explanation
Indices: 19449--19793 Score: 665
Period size: 93 Copynumber: 3.7 Consensus size: 93
19439 TAGATTGCTT
*
19449 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
19514 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
19542 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
19607 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
19635 AGTAAA-TTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
19699 TTTGTCTTTGCTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
19727 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
19792 TT
66 TT
19794 GCGATTTTCA
Statistics
Matches: 249, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
92 91 0.37
93 158 0.63
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:19816 original size:19 final size:19
Alignment explanation
Indices: 19792--19921 Score: 127
Period size: 19 Copynumber: 7.3 Consensus size: 19
19782 TGAAATAGTA
19792 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
19811 TTGCGA--TTC-TTT--CG
1 TTGCGATTTTCATTTCGCG
*
19825 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCG
*
19844 TTGCGA--TTC-TGT--CG
1 TTGCGATTTTCATTTCGCG
19858 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
**
19877 TTGCGATTTTGGTTTCGCG
1 TTGCGATTTTCATTTCGCG
* *
19896 TTGCGATTTTAAGTTTCGTG
1 TTGCGATTTTCA-TTTCGCG
19916 TTGCGA
1 TTGCGA
19922 AGTAACTATT
Statistics
Matches: 91, Mismatches: 9, Indels: 21
0.75 0.07 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 42 0.46
20 12 0.13
ACGTcount: A:0.11, C:0.18, G:0.24, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:19828 original size:14 final size:14
Alignment explanation
Indices: 19809--19865 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
19799 TTTCATTTCG
19809 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
19823 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
19840 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
19856 CGTTGCGATT
1 CGTTGCGATT
19866 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:19834 original size:33 final size:33
Alignment explanation
Indices: 19792--19884 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
19782 TGAAATAGTA
*
19792 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
19825 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
19858 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
19885 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:21862 original size:14 final size:14
Alignment explanation
Indices: 21843--21878 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
21833 ATTGTTTAAT
21843 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
21857 TGATTTGTATAAGT
1 TGATTTGTAAAAGA
21871 TGATTTGT
1 TGATTTGT
21879 GTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:22081 original size:19 final size:19
Alignment explanation
Indices: 22057--22221 Score: 189
Period size: 19 Copynumber: 9.4 Consensus size: 19
22047 GATTCTCTCG
22057 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
22076 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
22095 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
22109 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
22128 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
22147 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
22161 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
22181 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
*
22195 TTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
22214 TTGCGATT
1 TTGCGATT
22222 CTCTCGTTGC
Statistics
Matches: 124, Mismatches: 6, Indels: 32
0.77 0.04 0.20
Matches are distributed among these distances:
14 23 0.19
16 16 0.13
17 13 0.10
18 3 0.02
19 57 0.46
20 12 0.10
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:22091 original size:52 final size:52
Alignment explanation
Indices: 22035--22193 Score: 309
Period size: 52 Copynumber: 3.0 Consensus size: 52
22025 TGCGTTTATA
22035 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
22087 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
22139 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
22192 AT
1 AT
22194 GTTGGGATTT
Statistics
Matches: 106, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
52 89 0.84
53 17 0.16
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:22243 original size:33 final size:33
Alignment explanation
Indices: 22035--22235 Score: 212
Period size: 33 Copynumber: 5.9 Consensus size: 33
22025 TGCGTTTATA
22035 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
22068 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TC
* * * * *
22108 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
22139 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
* *
22172 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTC
22206 ATTTCGCATTGCGATTCTCTCGTTGCGATT
1 ATTTCGCATTGCGATTCTCTCGTTGCGATT
22236 GTAATTTCCG
Statistics
Matches: 138, Mismatches: 16, Indels: 28
0.76 0.09 0.15
Matches are distributed among these distances:
31 9 0.07
32 6 0.04
33 62 0.45
34 29 0.21
35 6 0.04
36 4 0.03
37 2 0.01
38 8 0.06
39 3 0.02
40 9 0.07
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:24535 original size:12 final size:12
Alignment explanation
Indices: 24518--24542 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24508 TTCTTCGGGA
24518 CTTTTTCTTCTT
1 CTTTTTCTTCTT
24530 CTTTTTCTTCTT
1 CTTTTTCTTCTT
24542 C
1 C
24543 AGGATATATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:24750 original size:24 final size:24
Alignment explanation
Indices: 24716--24762 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
24706 CTGAAACATC
24716 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
24740 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
24763 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:25472 original size:20 final size:20
Alignment explanation
Indices: 25444--25673 Score: 228
Period size: 20 Copynumber: 11.5 Consensus size: 20
25434 AAATTTCAGT
* * *
25444 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
25464 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* **
25484 GTTGCGATTTACAGATTCTT
1 GTTGCGATTTACGGATTCGC
**
25504 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
25524 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
25544 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
25564 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
25584 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
25604 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
25624 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
25644 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
25664 GTTGCGATTT
1 GTTGCGATTT
25674 TGGAAAATCG
Statistics
Matches: 180, Mismatches: 28, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
20 179 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:25690 original size:21 final size:21
Alignment explanation
Indices: 25660--25742 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
25650 ATTTTCATAT
*
25660 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
25681 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
25702 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
25723 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
25743 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:25733 original size:42 final size:43
Alignment explanation
Indices: 25640--25738 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
25630 ATTTATGTGT
* *
25640 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
25681 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
25723 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
25739 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:39586 original size:17 final size:17
Alignment explanation
Indices: 39564--39602 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
39554 ACAAGAATCT
*
39564 TCTTCCGCCTTACTGCC
1 TCTTCCGCCTAACTGCC
39581 TCTTCCGCCTAACTGCC
1 TCTTCCGCCTAACTGCC
39598 TCTTC
1 TCTTC
39603 TCGCTCGACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.08, C:0.46, G:0.10, T:0.36
Consensus pattern (17 bp):
TCTTCCGCCTAACTGCC
Found at i:42156 original size:36 final size:38
Alignment explanation
Indices: 42101--42191 Score: 105
Period size: 40 Copynumber: 2.4 Consensus size: 38
42091 GAAAAATTAT
*
42101 TAACTTTATTTACACCTGTGTGAG-A-CTTTTTTCCCTC
1 TAAC-TTATTTACACCTGTGTGAGAAGCCTTTTTCCCTC
* * *
42138 TAACTTATTTATAGCTGTGTGAGATAGTCCTTTTTCCCTT
1 TAACTTATTTACACCTGTGTGAGA-AG-CCTTTTTCCCTC
42178 TAACTTATTTACAC
1 TAACTTATTTACAC
42192 TGGTGTAAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
36 17 0.39
37 4 0.09
38 1 0.02
40 22 0.50
ACGTcount: A:0.22, C:0.21, G:0.11, T:0.46
Consensus pattern (38 bp):
TAACTTATTTACACCTGTGTGAGAAGCCTTTTTCCCTC
Done.