Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003874.1 Hibiscus syriacus cultivar Beakdansim tig00008348_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: 42751
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:2011 original size:19 final size:19
Alignment explanation
Indices: 1958--2212 Score: 247
Period size: 19 Copynumber: 14.7 Consensus size: 19
1948 GCAACGAGAG
1958 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
*
1976 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1990 AATCGCAATGCGGAAATG-A
1 AATCGCAATGC-GAAATGAA
2009 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2028 AATCG-AA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
2041 AATCGCAATGCGGAAATG-A
1 AATCGCAATGC-GAAATGAA
2060 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
*
2078 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
2092 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2111 AATCGCAATGCG-AATGAA
1 AATCGCAATGCGAAATGAA
2129 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2148 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
2167 AATCGC-A-CCG--A-GAG
1 AATCGCAATGCGAAATGAA
*
2181 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
2200 AATCGCATTGCGA
1 AATCGCAATGCGA
2213 TTCTCTCGTT
Statistics
Matches: 198, Mismatches: 12, Indels: 53
0.75 0.05 0.20
Matches are distributed among these distances:
13 11 0.06
14 28 0.14
15 2 0.01
16 11 0.06
17 3 0.02
18 51 0.26
19 88 0.44
20 4 0.02
ACGTcount: A:0.44, C:0.18, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:2016 original size:51 final size:52
Alignment explanation
Indices: 1958--2173 Score: 266
Period size: 51 Copynumber: 4.1 Consensus size: 52
1948 GCAACGAGAG
1958 AATCGCAATGCGAAATG-AAATCCCAAC-ATGAAAATCGCAATGCGGAAATG-A
1 AATCGCAATGCGAAATGAAAATCCCAACGA-GAAAATCGCAATGC-GAAATGAA
* *
2009 AATCGCAATGCGAAATGAAAAT-CGAACGAGAGAATCGCAATGCGGAAATG-A
1 AATCGCAATGCGAAATGAAAATCCCAACGAGAAAATCGCAATGC-GAAATGAA
* *
2060 AATCGCAATGCGAAATG-AAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAACGAGAAAATCGCAATGCGAAATGAA
*
2111 AATCGCAATGCG-AATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAA--CG--A-GAAAATCGCAATGCGAAATGAA
2167 AATCGCA
1 AATCGCA
2174 CCGAGAGAAT
Statistics
Matches: 150, Mismatches: 5, Indels: 15
0.88 0.03 0.09
Matches are distributed among these distances:
50 14 0.09
51 100 0.67
52 5 0.03
53 2 0.01
55 1 0.01
56 28 0.19
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCCCAACGAGAAAATCGCAATGCGAAATGAA
Found at i:2064 original size:70 final size:68
Alignment explanation
Indices: 1989--2212 Score: 267
Period size: 70 Copynumber: 3.2 Consensus size: 68
1979 CCCAACATGA
1989 AAATCGCAATGCGGAAATGAAATCGCAATGCGAAATGAAAATCGAACGAGAGAATCGCAATGCGG
1 AAATCGCAATGC-GAAATGAAATCGCAATGCGAAATGAAAATCGAACGAGAGAATCGCAATGC-G
2054 AAATG
64 AAATG
* * * *
2059 AAATCGCAATGCGAAATGAAATCGCAACGAGAGAATCG-CAATGCGAA--ATGAAAATCGCAATG
1 AAATCGCAATGCGAAATGAAATCGCAATGCGA-AAT-GAAAAT-CGAACGA-GAGAATCGCAATG
2121 CG-AATG
62 CGAAATG
*
2127 AAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCACCGAGAGAATCGCAATGC
1 -AAATCGCAATGCGAAATG-AAATCGCAATGCGAAATGAAAATCG-AACGAGAGAATCGCAATGC
*
2192 GAAATTA
63 GAAA-TG
*
2199 AAATCGCATTGCGA
1 AAATCGCAATGCGA
2213 TTCTCTCGTT
Statistics
Matches: 131, Mismatches: 11, Indels: 23
0.79 0.07 0.14
Matches are distributed among these distances:
68 7 0.05
69 45 0.34
70 57 0.44
71 21 0.16
72 1 0.01
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.15
Consensus pattern (68 bp):
AAATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGAACGAGAGAATCGCAATGCGAA
ATG
Found at i:2202 original size:89 final size:88
Alignment explanation
Indices: 2041--2212 Score: 292
Period size: 89 Copynumber: 1.9 Consensus size: 88
2031 CGAACGAGAG
2041 AATCGCAATGCGGAAATGAAATCGCAATGCGAAATGAAATCGCAACGAGAGAATCGCAATGCGAA
1 AATCGCAATGCGGAAATGAAATCGCAATGCGAAATGAAATCGCAACGAGAGAATCGCAATGCGAA
2106 ATGAAAATCGCAATGCGAATGAA
66 ATGAAAATCGCAATGCGAATGAA
*
2129 AATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAAAATCGCACCGAGAGAATCGCAATGCG
1 AATCGCAATGCGGAAATG-AAATCGCAATGCGAAATG-AAATCGCAACGAGAGAATCGCAATGCG
* *
2193 AAATTAAAATCGCATTGCGA
64 AAATGAAAATCGCAATGCGA
2213 TTCTCTCGTT
Statistics
Matches: 79, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
87 6 0.08
88 29 0.37
89 44 0.56
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.16
Consensus pattern (88 bp):
AATCGCAATGCGGAAATGAAATCGCAATGCGAAATGAAATCGCAACGAGAGAATCGCAATGCGAA
ATGAAAATCGCAATGCGAATGAA
Found at i:2259 original size:52 final size:52
Alignment explanation
Indices: 2202--2317 Score: 216
Period size: 52 Copynumber: 2.2 Consensus size: 52
2192 GAAATTAAAA
2202 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCA-T
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
2254 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
2306 TCGCATTGCGAT
1 TCGCATTGCGAT
2318 AGTCATTTTT
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
51 16 0.25
52 47 0.75
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
Found at i:2325 original size:19 final size:19
Alignment explanation
Indices: 2221--2317 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
2211 GATTCTCTCG
2221 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
2241 TTGCGATTTTCA-TTCGCA
1 TTGCGATTTTCATTTCGCA
*
2259 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2273 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2292 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2311 TTGCGAT
1 TTGCGAT
2318 AGTCATTTTT
Statistics
Matches: 69, Mismatches: 2, Indels: 13
0.82 0.02 0.15
Matches are distributed among these distances:
14 6 0.09
16 9 0.13
17 4 0.06
18 10 0.14
19 28 0.41
20 12 0.17
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:4387 original size:18 final size:18
Alignment explanation
Indices: 4362--4514 Score: 133
Period size: 18 Copynumber: 8.8 Consensus size: 18
4352 ACGAAACTTA
4362 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
* * **
4380 AGATCGCAACGAGAAACCA
1 AAATCGCAACGCGAAA-TG
**
4399 AAATCGCAACGCGAAACC
1 AAATCGCAACGCGAAATG
4417 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
*
4435 AAATCGCAA--CGACAT-
1 AAATCGCAACGCGAAATG
*
4450 -AATCGCAATGCGAAATG
1 AAATCGCAACGCGAAATG
*
4467 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAAATG
4483 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
*
4500 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
4515 TTTTGGTTTC
Statistics
Matches: 110, Mismatches: 14, Indels: 21
0.76 0.10 0.14
Matches are distributed among these distances:
14 16 0.15
16 15 0.14
17 5 0.05
18 40 0.36
19 34 0.31
ACGTcount: A:0.45, C:0.24, G:0.21, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAAATG
Found at i:4409 original size:37 final size:36
Alignment explanation
Indices: 4361--4445 Score: 107
Period size: 37 Copynumber: 2.3 Consensus size: 36
4351 CACGAAACTT
** *
4361 AAAATCGCAACGCGAAATGAGATCGCAACGAGAAACC
1 AAAATCGCAACGCGAAACCAAATCGCAACGAGAAA-C
* *
4398 AAAATCGCAACGCGAAACCAAATCGCAACGCGAAAT
1 AAAATCGCAACGCGAAACCAAATCGCAACGAGAAAC
*
4434 GAAATCGCAACG
1 AAAATCGCAACG
4446 ACATAATCGC
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 11 0.26
37 31 0.74
ACGTcount: A:0.46, C:0.26, G:0.20, T:0.08
Consensus pattern (36 bp):
AAAATCGCAACGCGAAACCAAATCGCAACGAGAAAC
Found at i:4477 original size:33 final size:33
Alignment explanation
Indices: 4418--4509 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
4408 CGCGAAACCA
*
4418 AATCGCAACGCGAAATG-AAATCGCAACGACAT
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* *
4450 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
4483 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
4510 TGCGATTTTG
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
32 16 0.29
33 39 0.71
ACGTcount: A:0.46, C:0.22, G:0.21, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:4563 original size:19 final size:18
Alignment explanation
Indices: 4510--4600 Score: 74
Period size: 19 Copynumber: 5.4 Consensus size: 18
4500 AAAATCGCAA
4510 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
4529 TGCGA-TTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
4542 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
4561 TGCGATTCT-TTT---GT
1 TGCGATTTTGTTTCGCGT
*
4575 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
4594 TGCGATT
1 TGCGATT
4601 CTCTCGTTGC
Statistics
Matches: 59, Mismatches: 2, Indels: 22
0.71 0.02 0.27
Matches are distributed among these distances:
13 8 0.14
14 13 0.22
15 2 0.03
16 3 0.05
17 5 0.08
18 3 0.05
19 25 0.42
ACGTcount: A:0.08, C:0.16, G:0.27, T:0.48
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:4582 original size:33 final size:33
Alignment explanation
Indices: 4510--4632 Score: 167
Period size: 33 Copynumber: 3.7 Consensus size: 33
4500 AAAATCGCAA
*
4510 TGCGATTTTGGTTTCGCGTTGCGATT-TGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
* *
4542 TGCGATTTTGGTTTCGCGTTGCGATTCTTTTGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
**
4575 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
* *
4608 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
4633 AAGTAAACTA
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
32 26 0.32
33 42 0.52
34 12 0.15
ACGTcount: A:0.09, C:0.17, G:0.27, T:0.47
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
Found at i:4815 original size:93 final size:93
Alignment explanation
Indices: 4679--4868 Score: 364
Period size: 93 Copynumber: 2.1 Consensus size: 93
4669 ATGGATTGCA
4679 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
4743 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
4771 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
4836 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
4864 TTACT
1 TTACT
4869 AAGCAATCTA
Statistics
Matches: 96, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
92 4 0.04
93 92 0.96
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.23
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:6573 original size:20 final size:20
Alignment explanation
Indices: 6542--6638 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
6532 TTTTGGTTGA
6542 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
6562 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
6582 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
6601 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
6616 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
6636 AAT
1 AAT
6639 CGCAACGCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.06
17 2 0.03
19 15 0.24
20 20 0.32
21 12 0.19
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:6594 original size:21 final size:21
Alignment explanation
Indices: 6540--6604 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
6530 TCTTTTGGTT
6540 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
6561 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
6581 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
6602 GAA
1 GAA
6605 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:6608 original size:14 final size:14
Alignment explanation
Indices: 6589--6645 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
6579 GAGAAATGAA
6589 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
6603 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
6622 AATCGCAACGAGAG
1 AATCGCAACGAGAG
6636 AATCGCAACG
1 AATCGCAACG
6646 CGAAATGAAA
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:6621 original size:33 final size:33
Alignment explanation
Indices: 6540--6662 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
6530 TCTTTTGGTT
*
6540 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GC
6581 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
6614 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
6647 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
6663 TGCGATTTTG
Statistics
Matches: 81, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
33 50 0.62
35 7 0.09
38 1 0.01
40 1 0.01
41 22 0.27
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:6698 original size:14 final size:14
Alignment explanation
Indices: 6679--6735 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
6669 TTTGGTTTCG
6679 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
6693 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
6712 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
6726 CGTTGCGATT
1 CGTTGCGATT
6736 TTCATTTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:6711 original size:33 final size:33
Alignment explanation
Indices: 6663--6742 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
6653 AAAATCGCAA
**
6663 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
6696 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
6729 TGCGATTTTCATTT
1 TGCGATTTTCATTT
6743 TTCTCGTTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.21, G:0.23, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:6748 original size:21 final size:21
Alignment explanation
Indices: 6723--6796 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
6713 GTTGCGATTC
6723 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
6744 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
6765 TCACGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTT
6786 TCTCGTTGCGA
1 TCTCGTTGCGA
6797 CTCTTCTGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.14
21 32 0.73
22 6 0.14
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:6918 original size:33 final size:33
Alignment explanation
Indices: 6876--6946 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
6866 AATACTAACT
6876 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
6909 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
6942 TGAAA
1 TGAAA
6947 TCTAAGTGAA
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:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:7351 original size:20 final size:20
Alignment explanation
Indices: 7326--7499 Score: 224
Period size: 20 Copynumber: 8.6 Consensus size: 20
7316 CTTTAAAAAT
7326 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
7346 CGCGTTGCGATTTTTACGGATA
1 CGCGTTGCGA--TTTACGGATA
* *
7368 CGCGTTGCGATATACGGACA
1 CGCGTTGCGATTTACGGATA
*
7388 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
7408 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
7428 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
7448 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
7468 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
7488 CGCGTTGCGATT
1 CGCGTTGCGATT
7500 CTGGAAAATC
Statistics
Matches: 136, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
20 115 0.85
21 1 0.01
22 20 0.15
ACGTcount: A:0.19, C:0.20, G:0.28, T:0.33
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:8107 original size:21 final size:21
Alignment explanation
Indices: 8078--8117 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
8068 TTTTTATTAT
* *
8078 TTTATTAAAAGAATTGGTATG
1 TTTAGTAAAACAATTGGTATG
*
8099 TTTAGTAAAACATTTGGTA
1 TTTAGTAAAACAATTGGTA
8118 CATTTAGACA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.17, T:0.42
Consensus pattern (21 bp):
TTTAGTAAAACAATTGGTATG
Found at i:15066 original size:16 final size:16
Alignment explanation
Indices: 15047--15081 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
15037 GACTGTAATG
15047 AACAAAAATTGTTCAT
1 AACAAAAATTGTTCAT
*
15063 AACAAAAATTGTTTAT
1 AACAAAAATTGTTCAT
15079 AAC
1 AAC
15082 TGTTATTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.51, C:0.11, G:0.06, T:0.31
Consensus pattern (16 bp):
AACAAAAATTGTTCAT
Found at i:15769 original size:5 final size:5
Alignment explanation
Indices: 15761--15786 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
15751 AATGTATTGT
15761 ATAAC ATAAC ATAAC ATAAC ATAAC A
1 ATAAC ATAAC ATAAC ATAAC ATAAC A
15787 CAATTTTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.19, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAC
Found at i:23611 original size:105 final size:101
Alignment explanation
Indices: 23323--23629 Score: 416
Period size: 102 Copynumber: 3.0 Consensus size: 101
23313 AAGTTGTGCA
* * * * * *
23323 TTCTTAAAATTGTAAACTGTATAAGTTACATTATGTCAACCTTTTTAATTTTACAATTATAAGAT
1 TTCTTGAAATGGTAAAC-GTATAAATTACATTATGTAAACCTTTTTTATTTTAAAATTATAAGAT
* *
23388 AAATCAAGTTTACATTTATAATAATATAGATATCGCC
65 AAATCAAGTTTACATTTATAATAATATAGGTAGCGCC
** * * * *
23425 TTCTTGGTATGGAAAACCATATAAATTACATTGTGTAAACCTTTTTTATTTTAAAATTATAACAT
1 TTCTTGAAATGGTAAA-CGTATAAATTACATTATGTAAACCTTTTTTATTTTAAAATTATAAGAT
* *
23490 AATTCAAGTTTACATTTATAATAATATAGGTAGCTCC
65 AAATCAAGTTTACATTTATAATAATATAGGTAGCGCC
23527 TTCTTGAAATGGTAAATCGTATAAATTACATTATGTAAACCTTTTTTTTTATTTTAAAATTATAA
1 TTCTTGAAATGGTAAA-CGTATAAATTACATTATGTAAACC---TTTTTTATTTTAAAATTATAA
23592 GATAAATCAAGTTTACATTTATAATAATATAGGTAGCG
62 GATAAATCAAGTTTACATTTATAATAATATAGGTAGCG
23630 ACACTACCGT
Statistics
Matches: 176, Mismatches: 25, Indels: 5
0.85 0.12 0.02
Matches are distributed among these distances:
102 119 0.68
103 1 0.01
105 56 0.32
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.42
Consensus pattern (101 bp):
TTCTTGAAATGGTAAACGTATAAATTACATTATGTAAACCTTTTTTATTTTAAAATTATAAGATA
AATCAAGTTTACATTTATAATAATATAGGTAGCGCC
Found at i:24608 original size:37 final size:36
Alignment explanation
Indices: 24550--24631 Score: 105
Period size: 37 Copynumber: 2.3 Consensus size: 36
24540 TGGCAACCAA
24550 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATATTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATATTT
* * *
24585 CTTTGAAAAATGATTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATG-GTTTTCAAAGTTTGGTAAATATTT
*
24622 -GTTGAAAAAT
1 CTTTGAAAAAT
24632 TGTAATGGGG
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
35 5 0.12
36 15 0.37
37 21 0.51
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATATTT
Found at i:24627 original size:36 final size:37
Alignment explanation
Indices: 24562--24631 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
24552 TTGAAAATGG
*
24562 TTTTCAAAGTTTGGTAAATATTTCTTTGAAAAATGAT
1 TTTTCAAAGTTTGGTAAATATTTCGTTGAAAAATGAT
* *
24599 TTTTCAAAGTTTGGTAGATGTTT-GTTGAAAAAT
1 TTTTCAAAGTTTGGTAAATATTTCGTTGAAAAAT
24632 TGTAATGGGG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
36 9 0.30
37 21 0.70
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (37 bp):
TTTTCAAAGTTTGGTAAATATTTCGTTGAAAAATGAT
Found at i:29164 original size:36 final size:36
Alignment explanation
Indices: 29115--29186 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 36
29105 TGGCAACCAA
29115 CTTTGAAAATGG-TTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTTCAAAGTTTGGTAAATGTTT
*
29150 CTTTGAAAAATGGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTG-AAAATGGTTTTTCAAAGTTTGGTAAATGTTT
29187 GTTGACAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
35 5 0.15
36 7 0.21
37 22 0.65
ACGTcount: A:0.28, C:0.06, G:0.21, T:0.46
Consensus pattern (36 bp):
CTTTGAAAATGGTTTTTCAAAGTTTGGTAAATGTTT
Found at i:29568 original size:20 final size:20
Alignment explanation
Indices: 29540--29578 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
29530 CATTAGGTAA
*
29540 TTGAGGTGATAATTTAGCAG
1 TTGAGGTGATAATATAGCAG
*
29560 TTGATGTGATAATATAGCA
1 TTGAGGTGATAATATAGCA
29579 AGTGAAGAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.36
Consensus pattern (20 bp):
TTGAGGTGATAATATAGCAG
Found at i:31997 original size:14 final size:14
Alignment explanation
Indices: 31965--32005 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
31955 GGTGTTTCAT
31965 TTCTT-ATATCTTC
1 TTCTTCATATCTTC
*
31978 -TCTTCATTTCTTC
1 TTCTTCATATCTTC
31991 TTCTTCATATCTTC
1 TTCTTCATATCTTC
32005 T
1 T
32006 ACCTTCGTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 4 0.17
13 7 0.29
14 13 0.54
ACGTcount: A:0.12, C:0.27, G:0.00, T:0.61
Consensus pattern (14 bp):
TTCTTCATATCTTC
Found at i:32756 original size:20 final size:19
Alignment explanation
Indices: 32727--32780 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
32717 TCGACTAAGG
* *
32727 CTGATCTCCATACCGTAGGA
1 CTGATATCCATACCG-AAGA
32747 CTGATATCCATACCGAAGA
1 CTGATATCCATACCGAAGA
*
32766 TTGAGTATCCATACC
1 CTGA-TATCCATACC
32781 AAAGGCTCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 6 0.20
20 24 0.80
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (19 bp):
CTGATATCCATACCGAAGA
Found at i:33864 original size:32 final size:32
Alignment explanation
Indices: 33819--33908 Score: 108
Period size: 32 Copynumber: 2.8 Consensus size: 32
33809 TAGATACTAG
*
33819 TCAGGTTTGCATTCAGATAATGCACAATATGT
1 TCAGGTTTGCATTCAGACAATGCACAATATGT
* * * * *
33851 TCAGGTCTACATTCAGACAATGTATAGTATGT
1 TCAGGTTTGCATTCAGACAATGCACAATATGT
* *
33883 TTAGGTTTGCATTAAGACAATGCACA
1 TCAGGTTTGCATTCAGACAATGCACA
33909 TGAATGTCAG
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (32 bp):
TCAGGTTTGCATTCAGACAATGCACAATATGT
Found at i:38159 original size:20 final size:20
Alignment explanation
Indices: 38136--38180 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
38126 TAATATCAAT
38136 ATCGGATGCTCAGTATCGAG
1 ATCGGATGCTCAGTATCGAG
* ** *
38156 ATCGTATGCTTGGTCTCGAG
1 ATCGGATGCTCAGTATCGAG
38176 ATCGG
1 ATCGG
38181 CTGGTCTCCA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (20 bp):
ATCGGATGCTCAGTATCGAG
Found at i:38209 original size:20 final size:19
Alignment explanation
Indices: 38184--38254 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 19
38174 AGATCGGCTG
*
38184 GTCTCCATACTGTAGGACTA
1 GTCTCCATAC-GAAGGACTA
*
38204 GTCTCCATAACGAAGAACTA
1 GTCTCCAT-ACGAAGGACTA
38224 GTCTCCA-AGCCGAAGGACTA
1 GTCTCCATA--CGAAGGACTA
*
38244 GTATCCATACG
1 GTCTCCATACG
38255 GAAGATTGAG
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
18 1 0.02
19 2 0.05
20 37 0.86
21 3 0.07
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.23
Consensus pattern (19 bp):
GTCTCCATACGAAGGACTA
Found at i:38258 original size:20 final size:19
Alignment explanation
Indices: 38187--38273 Score: 61
Period size: 20 Copynumber: 4.4 Consensus size: 19
38177 TCGGCTGGTC
* *
38187 TCCATACTGTAGGACTAGTC
1 TCCATAC-GAAGGACTAGTA
* *
38207 TCCATAACGAAGAACTAGTC
1 TCCAT-ACGAAGGACTAGTA
38227 TCCA-AGCCGAAGGACTAGTA
1 TCCATA--CGAAGGACTAGTA
*
38247 TCCATACGGAA-GATTGAGTA
1 TCCATAC-GAAGGACT-AGTA
38267 TCCATAC
1 TCCATAC
38274 CAAATGCTCG
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
18 1 0.02
19 4 0.07
20 48 0.86
21 3 0.05
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (19 bp):
TCCATACGAAGGACTAGTA
Found at i:42488 original size:214 final size:215
Alignment explanation
Indices: 42092--42525 Score: 852
Period size: 214 Copynumber: 2.0 Consensus size: 215
42082 ATCATCTGCT
42092 TCTCCCAATGGTAATCTTTTCTCCGATTCTTCTTCTGTTTCTTTTGTTTACTTTGGATAAATTTT
1 TCTCCCAATGGTAATCTTTTCTCCGATTCTTCTTCTGTTTCTTTTGTTTACTTTGGATAAATTTT
42157 TTTTCTAAGATTTGTTTAATTTGGGATTTTTTTTCAGATGAGAATGATAGACCCAATCTGCAAAG
66 TTTTCTAAGATTTGTTTAATTTGGGATTTTTTTTCAGATGAGAATGATAGACCCAATCTGCAAAG
42222 GGATTTGAATTTGCAGAAACCGATGAAACAAAATGTGAAGACTTTCAGTTTTCCAAGAAAGAAAG
131 GGATTTGAATTTGCAGAAACCGATGAAACAAAATGTGAAGACTTTCAGTTTTCCAAGAAAGAAAG
*
42287 TCTTGGGTGAAAGAAATGAA
196 TCTTAGGTGAAAGAAATGAA
42307 TCTCCCAATGGTAATCTTTTCTCCGATTCTTCTTCTGTTTCTTTTGTTTACTTTGGATAAATTTT
1 TCTCCCAATGGTAATCTTTTCTCCGATTCTTCTTCTGTTTCTTTTGTTTACTTTGGATAAATTTT
42372 TTTTCTAAGATTTGTTTAATTTGGGA-TTTTTTTCAGATGAGAATGATAGACCCAATCTGCAAAG
66 TTTTCTAAGATTTGTTTAATTTGGGATTTTTTTTCAGATGAGAATGATAGACCCAATCTGCAAAG
42436 GGATTTGAATTTGCAGAAACCGATGAAACAAAATGTGAAGACTTTCAGTTTTCCAAGAAAGAAAG
131 GGATTTGAATTTGCAGAAACCGATGAAACAAAATGTGAAGACTTTCAGTTTTCCAAGAAAGAAAG
42501 TCTTAGGTGAAAGAAATGAA
196 TCTTAGGTGAAAGAAATGAA
42521 TCTCC
1 TCTCC
42526 AGGATCAAAT
Statistics
Matches: 218, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
214 127 0.58
215 91 0.42
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (215 bp):
TCTCCCAATGGTAATCTTTTCTCCGATTCTTCTTCTGTTTCTTTTGTTTACTTTGGATAAATTTT
TTTTCTAAGATTTGTTTAATTTGGGATTTTTTTTCAGATGAGAATGATAGACCCAATCTGCAAAG
GGATTTGAATTTGCAGAAACCGATGAAACAAAATGTGAAGACTTTCAGTTTTCCAAGAAAGAAAG
TCTTAGGTGAAAGAAATGAA
Done.