Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008413.1 Hibiscus syriacus cultivar Beakdansim tig00111191_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: 2772818
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 10
Found at i:2762955 original size:153 final size:153
Alignment explanation
Indices: 2762714--2762997 Score: 459
Period size: 153 Copynumber: 1.8 Consensus size: 153
2762704 CCCAACATGA
*
2762714 AATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGGAAATGAAAATCGCAACGAAAGAATCGCAA-GCGAAATG-AAATCGCAATGCG
*
2762779 AAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCA
64 AAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCA
2762844 ATGCGAAATGAAATCGCAACGACAG
129 ATGCGAAATGAAATCGCAACGACAG
*
2762869 AATCGCAATGC-GAAATTAAAATCGCAATGCGAAATGAAATCGCAA-CGAAA-G-AATCGCAATG
1 AATCGCAATGCGGAAATGAAAATCGCAA--CGAAA-G-AATCGCAAGCGAAATGAAATCGCAATG
2762930 CGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCG
62 CGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCG
2762995 CAA
127 CAA
2762998 CGAGATAATC
Statistics
Matches: 122, Mismatches: 3, Indels: 10
0.90 0.02 0.07
Matches are distributed among these distances:
153 77 0.63
154 15 0.12
155 12 0.10
156 9 0.07
157 1 0.01
158 8 0.07
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (153 bp):
AATCGCAATGCGGAAATGAAAATCGCAACGAAAGAATCGCAAGCGAAATGAAATCGCAATGCGAA
ATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAAT
GCGAAATGAAATCGCAACGACAG
Found at i:2762976 original size:33 final size:35
Alignment explanation
Indices: 2762683--2762997 Score: 287
Period size: 33 Copynumber: 9.2 Consensus size: 35
2762673 CGGAAAATAC
* * *
2762683 AATCGCAACGCG-AATGAAAATCCCAA-C--ATGA
1 AATCGCAATGCGAAATGAAAATCGCAAGCGAAAGA
*
2762714 AATCGCAATGCGGAAATGAAAATCGCAA-CGAGAG-
1 AATCGCAATGC-GAAATGAAAATCGCAAGCGAAAGA
2762748 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA-GCGAAA-G-A
*
2762786 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA-GCGAAA-G-A
2762819 AATCGCAATGCGAAATG-AAATCGCAATGCGAAATGA
1 AATCGCAATGCGAAATGAAAATCGCAA-GCGAAA-GA
* *
2762855 AATCGCAA--CGACA-G--AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAA-GCGAAA--GA
2762888 AATCGCAATGCGAAATG-AAATCGCAA-CGAAAG-
1 AATCGCAATGCGAAATGAAAATCGCAAGCGAAAGA
2762920 AATCGCAATGCGAAATGAAAATCGCAA-CGAAAG-
1 AATCGCAATGCGAAATGAAAATCGCAAGCGAAAGA
2762953 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGA
1 AATCGCAATGCGAAATGAAAATCGCAA-GCGAAA-GA
2762990 AATCGCAA
1 AATCGCAA
2762998 CGAGATAATC
Statistics
Matches: 249, Mismatches: 11, Indels: 42
0.82 0.04 0.14
Matches are distributed among these distances:
31 10 0.04
32 33 0.13
33 112 0.45
34 16 0.06
35 21 0.08
36 14 0.06
37 34 0.14
38 9 0.04
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.14
Consensus pattern (35 bp):
AATCGCAATGCGAAATGAAAATCGCAAGCGAAAGA
Found at i:2763035 original size:51 final size:52
Alignment explanation
Indices: 2762713--2763019 Score: 400
Period size: 51 Copynumber: 6.0 Consensus size: 52
2762703 TCCCAACATG
2762713 AAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
1 AAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
2762766 AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
* * * * *
2762818 AAATCGCAATGCGAAATG-AAATCGCAATGCGA-AAT-GAAAT-CGCAACGA
1 AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
* *
2762866 CAGAATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAAATCGCAA--CGAAA-G-
1 -A-AATCGCAATGCGAAATGAAAATCGCAA--CGAGA-G-AATCGCAATGCGAAATGA
*
2762920 -AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
*
2762971 AAATCGCAATGCGAAATG-AAATCGCAACGAGATAATCGCAATGCGAAAT
1 AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAT
2763020 TATAAACGCA
Statistics
Matches: 226, Mismatches: 14, Indels: 30
0.84 0.05 0.11
Matches are distributed among these distances:
47 8 0.04
48 7 0.03
49 15 0.07
50 20 0.09
51 76 0.34
52 75 0.33
53 14 0.06
55 1 0.00
56 7 0.03
57 3 0.01
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (52 bp):
AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
Found at i:2763135 original size:19 final size:19
Alignment explanation
Indices: 2763026--2763127 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
2763016 AAATTATAAA
2763026 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
2763045 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
2763065 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
2763081 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
2763098 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
2763117 CGCATTGCGAT
1 CGCATTGCGAT
2763128 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:2763252 original size:14 final size:14
Alignment explanation
Indices: 2763233--2763269 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2763223 CATCAATTAC
2763233 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2763247 ACAAATCATCTTTT
1 ACAAATCAACTTTT
2763261 ACAAATCAA
1 ACAAATCAA
2763270 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2765234 original size:14 final size:14
Alignment explanation
Indices: 2765215--2765271 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2765205 GCGAAATGAA
*
2765215 AATCGCAACGACAG
1 AATCGCAACGAAAG
2765229 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
2765246 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
2765262 AATCGCAACG
1 AATCGCAACG
2765272 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:2765242 original size:33 final size:33
Alignment explanation
Indices: 2765196--2765288 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
2765186 GCGAAACCAA
*
2765196 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
2765229 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
2765262 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
2765289 TGCGATTTTG
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:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:2765253 original size:19 final size:19
Alignment explanation
Indices: 2765159--2765293 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
2765149 TAGTTTACTT
* *
2765159 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
2765179 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
2765198 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2765217 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
2765231 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
2765250 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
2765264 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2765283 TCGCAATGCGA
1 TCGCAACGCGA
2765294 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:2765311 original size:19 final size:19
Alignment explanation
Indices: 2765289--2765400 Score: 102
Period size: 19 Copynumber: 6.5 Consensus size: 19
2765279 AAAATCGCAA
2765289 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2765308 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
2765322 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2765341 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
2765355 TGCGA-TTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2765373 TGTGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
2765392 TGCGATTTT
1 TGCGATTTT
2765401 TTTAAGTTTC
Statistics
Matches: 73, Mismatches: 9, Indels: 22
0.70 0.09 0.21
Matches are distributed among these distances:
13 2 0.03
14 19 0.26
15 1 0.01
16 3 0.04
17 1 0.01
18 9 0.12
19 38 0.52
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:2765331 original size:33 final size:33
Alignment explanation
Indices: 2765289--2765379 Score: 132
Period size: 33 Copynumber: 2.8 Consensus size: 33
2765279 AAAATCGCAA
2765289 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
2765322 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
2765355 TGCGA-TTTCATTTCGCGTTGTGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
2765380 TTGGTTTCGC
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
32 17 0.31
33 35 0.65
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.29, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:2765897 original size:92 final size:92
Alignment explanation
Indices: 2765450--2765910 Score: 867
Period size: 91 Copynumber: 5.0 Consensus size: 92
2765440 GCAAATTGAA
2765450 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACC-AAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
2765515 GCAGAATTGGCAGCAACCGAACAAATTT
65 GCAGAATTGGCAGCAACCGAACAAATTT
2765543 ACTTTCAACC-AAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAG
1 ACTTTCAACCAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAG
2765607 CAGAATTGGCAGCAACCGAACAAATTT
66 CAGAATTGGCAGCAACCGAACAAATTT
2765634 ACTTTCAACCAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAG
1 ACTTTCAACCAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAG
2765699 CAG-ATTGGCAGCAACCGAACAAATTT
66 CAGAATTGGCAGCAACCGAACAAATTT
2765725 ACTTTCAACCAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACACAGTTTAG
1 ACTTTCAACCAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAG
2765789 CAGAATTGGCAGCAACCGAAC-AATTT
66 CAGAATTGGCAGCAACCGAACAAATTT
2765815 ACTTTCAACCAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAGACAAAACAAAGACAAATACTATTTCACAGTG-TTAAAGAATACACAGTTTA
*
2765880 GCAGAATTGGCAGCAACCGAATAAATTT
65 GCAGAATTGGCAGCAACCGAACAAATTT
2765908 ACT
1 ACT
2765911 AAGCAATCTA
Statistics
Matches: 362, Mismatches: 1, Indels: 10
0.97 0.00 0.03
Matches are distributed among these distances:
90 72 0.20
91 175 0.48
92 97 0.27
93 18 0.05
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.22
Consensus pattern (92 bp):
ACTTTCAACCAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAG
CAGAATTGGCAGCAACCGAACAAATTT
Found at i:2767597 original size:14 final size:14
Alignment explanation
Indices: 2767578--2767669 Score: 58
Period size: 14 Copynumber: 5.7 Consensus size: 14
2767568 GTTGAAATGA
2767578 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2767592 AATCGCAACGCGCGAGATG
1 AATCGCAA----CGAGA-G
2767611 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
2767627 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
2767646 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2767660 AATCACAACG
1 AATCGCAACG
2767670 CGAAATGAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 24
0.70 0.03 0.27
Matches are distributed among these distances:
14 27 0.43
15 1 0.02
16 3 0.05
17 7 0.11
18 6 0.10
19 11 0.17
21 8 0.13
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2767650 original size:33 final size:33
Alignment explanation
Indices: 2767571--2767686 Score: 180
Period size: 33 Copynumber: 3.5 Consensus size: 33
2767561 TCTTTTGGTT
2767571 GAAATG-AAATCGCAACGAGAGAATCGCAACGCGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAA--CGC
* *
2767605 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
2767638 GAAATGAAAATCGCAACGAGAGAATCACAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2767671 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
2767687 TGCGATTTTG
Statistics
Matches: 76, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
33 49 0.64
34 5 0.07
35 22 0.29
ACGTcount: A:0.45, C:0.22, G:0.24, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:2767651 original size:19 final size:19
Alignment explanation
Indices: 2767627--2767691 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
2767617 GCAACGAGAG
2767627 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
2767646 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
*
2767660 AATCACAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
2767679 AATCGCAATGCGA
1 AATCGCAACGCGA
2767692 TTTTGGTTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
14 9 0.25
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 21 0.58
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:2767722 original size:14 final size:14
Alignment explanation
Indices: 2767703--2767757 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
2767693 TTTGGTTTCG
2767703 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2767717 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2767736 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2767750 CGTTGCGA
1 CGTTGCGA
2767758 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2767735 original size:33 final size:33
Alignment explanation
Indices: 2767687--2767757 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
2767677 AAAATCGCAA
**
2767687 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
2767720 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
2767753 TGCGA
1 TGCGA
2767758 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:2767765 original size:33 final size:33
Alignment explanation
Indices: 2767698--2767779 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
2767688 GCGATTTTGG
***
2767698 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
2767731 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
2767764 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
2767780 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:2767784 original size:20 final size:20
Alignment explanation
Indices: 2767710--2767798 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
2767700 TCGCGTTGCG
2767710 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
2767730 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
2767743 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
2767763 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
2767783 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
2767799 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:2767918 original size:32 final size:31
Alignment explanation
Indices: 2767877--2767946 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 31
2767867 AATACTAACT
*
2767877 TGAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAATCGCAACGACAGAATAGCAACGC-AAA
* *
2767909 TGAAATCGCAACGACAGAATCGTAACGCAAA
1 TGAAATCGCAACGACAGAATAGCAACGCAAA
2767940 TGAAATC
1 TGAAATC
2767947 TAAGTGAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
31 10 0.29
32 25 0.71
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.13
Consensus pattern (31 bp):
TGAAATCGCAACGACAGAATAGCAACGCAAA
Found at i:2768171 original size:22 final size:22
Alignment explanation
Indices: 2768119--2768173 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
2768109 TGGTTGTGAG
**
2768119 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
2768141 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
2768163 GGATTTCTTCG
1 GGATTTCTTCG
2768174 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:2768343 original size:20 final size:20
Alignment explanation
Indices: 2768318--2768510 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
2768308 CTTTAAATAT
2768318 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2768338 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
2768360 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2768379 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
2768399 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
2768419 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2768439 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2768459 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
2768479 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
2768499 CGCGTTGCGATT
1 CGCGTTGCGATT
2768511 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:2768505 original size:60 final size:60
Alignment explanation
Indices: 2768318--2768510 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
2768308 CTTTAAATAT
**
2768318 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
2768379 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
2768439 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
2768499 CGCGTTGCGATT
1 CGCGTTGCGATT
2768511 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:2768591 original size:20 final size:20
Alignment explanation
Indices: 2768566--2768617 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
2768556 AAGAATCGCG
*
2768566 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
2768586 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
2768606 TTGCGATTCTGG
1 TTGCGATTCTGG
2768618 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Done.