Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008928.1 Hibiscus syriacus cultivar Beakdansim tig00112233_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: 39296
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:1793 original size:19 final size:19
Alignment explanation
Indices: 1771--2057 Score: 311
Period size: 19 Copynumber: 16.4 Consensus size: 19
1761 CGGAAAATAC
*
1771 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1790 AATCCCAA--C---ATG-A
1 AATCGCAATGCGAAATGAA
1803 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
1823 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1837 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1856 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1875 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1889 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1908 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
1927 AATCG-AA-CCGACAT---
1 AATCGCAATGCGAAATGAA
*
1941 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
1960 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
1979 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1998 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2017 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
2031 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2050 AATCGCAA
1 AATCGCAA
2058 CGAGATAATC
Statistics
Matches: 228, Mismatches: 13, Indels: 54
0.77 0.04 0.18
Matches are distributed among these distances:
13 8 0.04
14 36 0.16
15 5 0.02
16 15 0.07
17 15 0.07
18 5 0.02
19 135 0.59
20 9 0.04
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1822 original size:33 final size:33
Alignment explanation
Indices: 1771--2001 Score: 132
Period size: 33 Copynumber: 6.7 Consensus size: 33
1761 CGGAAAATAC
*
1771 AATCGCAACGCGAAATGAAAATCCCAAC-ATGA-
1 AATCGCAATGCGAAATGAAAATCCCAACGA-GAG
*
1803 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCCCAACGAGAG
* * *
1837 AATCGCAATGCGAAATGAAAATCGCAATGCGA-
1 AATCGCAATGCGAAATGAAAATCCCAACGAGAG
* * * * *
1869 AAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCG-CAATGCGAAATGA-A-AATCCCAA--CG--A-GAG
* * *
1908 AATCGCAATGCGAAATGAAAAT-CGAACCGACAT
1 AATCGCAATGCGAAATGAAAATCCCAA-CGAGAG
* * *
1941 AATCGCAATGCGAAATTAAAATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAAAATC-CCA-ACG--A-GAG
1979 AATCGCAATGCGAAATGAAAATC
1 AATCGCAATGCGAAATGAAAATC
2002 GCAATGCGAA
Statistics
Matches: 157, Mismatches: 22, Indels: 34
0.74 0.10 0.16
Matches are distributed among these distances:
31 7 0.04
32 17 0.11
33 67 0.43
34 13 0.08
35 5 0.03
36 3 0.02
37 3 0.02
38 28 0.18
39 7 0.04
40 7 0.04
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.15
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCCCAACGAGAG
Found at i:1830 original size:52 final size:52
Alignment explanation
Indices: 1771--1998 Score: 227
Period size: 52 Copynumber: 4.4 Consensus size: 52
1761 CGGAAAATAC
1771 AATCGCAACGCGA-AAT-GAAAATCCCAACATG-AAATCGCAATGCGGAAATGAA
1 AATCGCAACGCGAGAATCG-AAATCCCAA-ATGAAAATCGCAATGC-GAAATGAA
* * * *
1823 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGCGAGAATCGAAATCCCAAATGAAAATCGCAATGCGAAATGAA
* * * *
1875 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGCGAGAATCGAAATCCCAAATGAAAATCGCAATGCGAAATGAA
* * * * * *
1927 AATCG-AAC-CGACATAATCGCAATGCGAAATTAAAATCGCAATACGAAATGAA
1 AATCGCAACGCG--AGAATCGAAATCCCAAATGAAAATCGCAATGCGAAATGAA
*
1979 AATCGCAATGCGA-AAT-GAAA
1 AATCGCAACGCGAGAATCGAAA
1999 ATCGCAATGC
Statistics
Matches: 159, Mismatches: 10, Indels: 16
0.86 0.05 0.09
Matches are distributed among these distances:
50 4 0.03
51 6 0.04
52 123 0.77
53 23 0.14
54 3 0.02
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (52 bp):
AATCGCAACGCGAGAATCGAAATCCCAAATGAAAATCGCAATGCGAAATGAA
Found at i:1989 original size:123 final size:122
Alignment explanation
Indices: 1837--2089 Score: 365
Period size: 123 Copynumber: 2.1 Consensus size: 122
1827 GCAACGAGAG
* *
1837 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CG-A-GAGAATCGCAATG
1 AATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAAATCGCAA--
1899 CGAAATGAAAATCGCAATGCGAAATGAAAATCG-AACCGACATAATCGCAATGCGAAATTA-A
64 CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAA-CGACATAATCGCAATGCGAAATTATA
1960 AATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAA
*
2025 CGAAAGAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATTATA
64 CGAAAGAATCGCAATGCGAAATGAAAATCGCAACGACATAATCGCAATGCGAAATTATA
2084 AA-CGCA
1 AATCGCA
2090 TTGCGATTTT
Statistics
Matches: 120, Mismatches: 3, Indels: 14
0.88 0.02 0.10
Matches are distributed among these distances:
123 96 0.80
124 5 0.04
125 3 0.03
126 5 0.04
127 1 0.01
128 10 0.08
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (122 bp):
AATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAAATCGCAACG
AAAGAATCGCAATGCGAAATGAAAATCGCAACGACATAATCGCAATGCGAAATTATA
Found at i:2035 original size:33 final size:34
Alignment explanation
Indices: 1837--2079 Score: 223
Period size: 33 Copynumber: 6.9 Consensus size: 34
1827 GCAACGAGAG
1837 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA-GCGAAA-G--AATCGCAATGCGAAATGAA
*
1875 AATCGCAA-CGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAAGCGAAAGAATCGCAATGCGAAATGAA
**
1908 AATCGCAATGCGAAATGAA----AAT-CGAACCGACA
1 AATCGCAA-GCGAAA-GAATCGCAATGCGAAATGA-A
* *
1940 TAATCGCAATGCGAAATTAAAATCGCAATACGAAATGAA
1 -AATCGCAA-GCG-AA--AGAATCGCAATGCGAAATGAA
1979 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA-GCGAAA-G--AATCGCAATGCGAAATGAA
2017 AATCGCAA-CGAAAGAATCGCAATGCGAAATGAA
1 AATCGCAAGCGAAAGAATCGCAATGCGAAATGAA
* *
2050 AATCGCAA-CGAGATAATCGCAATGCGAAAT
1 AATCGCAAGCGAAAGAATCGCAATGCGAAAT
2080 TATAAACGCA
Statistics
Matches: 178, Mismatches: 11, Indels: 37
0.79 0.05 0.16
Matches are distributed among these distances:
31 6 0.03
32 4 0.02
33 86 0.48
34 2 0.01
35 9 0.05
36 13 0.07
37 2 0.01
38 46 0.26
39 4 0.02
40 6 0.03
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (34 bp):
AATCGCAAGCGAAAGAATCGCAATGCGAAATGAA
Found at i:2056 original size:52 final size:54
Alignment explanation
Indices: 1802--2057 Score: 254
Period size: 52 Copynumber: 4.8 Consensus size: 54
1792 TCCCAACATG
*
1802 AAATCGCAATGCGGAAATGAAAATCGCAA-CG--A-GAGAATCGCAATGCGAAATGA
1 AAATCGCAA-GC-GAAATG-AAATCGCAATCGAAATGAAAATCGCAATGCGAAATGA
*
1855 AAATCGCAATGCGAAATGAAAATCGCAA-CG--A-GAGAATCGCAATGCGAAATGA
1 AAATCGCAA-GCGAAATG-AAATCGCAATCGAAATGAAAATCGCAATGCGAAATGA
* * *
1907 AAATCGCAATGCGAAATGAAAATCG-AACCGACAT---AATCGCAATGCGAAATTA
1 AAATCGCAA-GCGAAATG-AAATCGCAATCGAAATGAAAATCGCAATGCGAAATGA
*
1959 AAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGA
1 AAATCGCAA-GCGAAATG-AAATCGCAAT-CGAAATGAAAATCGCAATGCGAAATGA
2016 AAATCGCAA-CGAAA-G-AATCGCAATGCGAAATGAAAATCGCAA
1 AAATCGCAAGCGAAATGAAATCGCAAT-CGAAATGAAAATCGCAA
2058 CGAGATAATC
Statistics
Matches: 189, Mismatches: 5, Indels: 19
0.89 0.02 0.09
Matches are distributed among these distances:
51 2 0.01
52 135 0.71
53 14 0.07
54 7 0.04
55 5 0.03
57 26 0.14
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (54 bp):
AAATCGCAAGCGAAATGAAATCGCAATCGAAATGAAAATCGCAATGCGAAATGA
Found at i:2195 original size:19 final size:19
Alignment explanation
Indices: 2086--2187 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
2076 AAATTATAAA
2086 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
2105 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
2125 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
2141 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
2158 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
2177 CGCATTGCGAT
1 CGCATTGCGAT
2188 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:2313 original size:14 final size:14
Alignment explanation
Indices: 2294--2330 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2284 CATCAATTAC
2294 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2308 ACAAATCATCTTTT
1 ACAAATCAACTTTT
2322 ACAAATCAA
1 ACAAATCAA
2331 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:2342 original size:12 final size:12
Alignment explanation
Indices: 2325--2397 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
2315 ATCTTTTACA
2325 AATCAATTAAAC
1 AATCAATTAAAC
*
2337 AATCAA--AAATTG
1 AATCAATTAAA--C
**
2349 AATCAACTTTTAC
1 AATCAA-TTAAAC
2362 AAATCAATTAAAC
1 A-ATCAATTAAAC
*
2375 AATCAA-AAAAC
1 AATCAATTAAAC
2386 AATCAATTAAAC
1 AATCAATTAAAC
2398 TATTGAATCA
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
10 3 0.07
11 10 0.22
12 21 0.46
13 6 0.13
14 5 0.11
15 1 0.02
ACGTcount: A:0.58, C:0.16, G:0.01, T:0.25
Consensus pattern (12 bp):
AATCAATTAAAC
Found at i:2359 original size:38 final size:38
Alignment explanation
Indices: 2311--2383 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
2301 AACTTTTACA
*
2311 AATCATCTTTTACAAATCAATTAAACAATCAAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
2349 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
2384 ACAATCAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.29
Consensus pattern (38 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
Found at i:4260 original size:14 final size:14
Alignment explanation
Indices: 4241--4297 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
4231 GCGAAATGAA
*
4241 AATCGCAACGACAG
1 AATCGCAACGAAAG
4255 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
4272 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
4288 AATCGCAACG
1 AATCGCAACG
4298 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:4268 original size:33 final size:33
Alignment explanation
Indices: 4222--4314 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
4212 GCGAAACCAA
*
4222 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
4255 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
4288 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
4315 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:4279 original size:19 final size:19
Alignment explanation
Indices: 4185--4319 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
4175 TAGTTTACTT
* *
4185 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
4205 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
4224 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
4243 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
4257 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
4276 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
4290 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
4309 TCGCAATGCGA
1 TCGCAACGCGA
4320 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:4337 original size:19 final size:19
Alignment explanation
Indices: 4315--4442 Score: 123
Period size: 19 Copynumber: 7.3 Consensus size: 19
4305 AAAATCGCAA
4315 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
4334 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
4348 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
4367 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
4381 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
4400 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
** *
4419 TGCGATTTAAGTTTCGTGT
1 TGCGATTTTGGTTTCGCGT
4438 TGCGA
1 TGCGA
4443 AAGTAAACTA
Statistics
Matches: 89, Mismatches: 10, Indels: 20
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.25
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 60 0.67
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.45
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:4357 original size:33 final size:33
Alignment explanation
Indices: 4315--4406 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
4305 AAAATCGCAA
4315 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
4348 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
4381 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
4407 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:4648 original size:92 final size:93
Alignment explanation
Indices: 4486--4864 Score: 744
Period size: 92 Copynumber: 4.1 Consensus size: 93
4476 TTGAATGGAT
4486 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
4551 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
4579 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
4643 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
4671 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
4735 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
4763 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
4828 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
4856 AAATTTACT
1 AAATTTACT
4865 AAGCAATCTA
Statistics
Matches: 284, Mismatches: 0, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
92 184 0.65
93 100 0.35
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:4810 original size:185 final size:185
Alignment explanation
Indices: 4486--4864 Score: 742
Period size: 185 Copynumber: 2.0 Consensus size: 185
4476 TTGAATGGAT
4486 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
4551 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAT
4616 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
4671 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
4735 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AA
4800 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
130 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
4856 AAATTTACT
1 AAATTTACT
4865 AAGCAATCTA
Statistics
Matches: 193, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
184 87 0.45
185 106 0.55
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (185 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAT
ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:5445 original size:19 final size:19
Alignment explanation
Indices: 5429--5530 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
5419 CAAAATGACT
5429 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
5448 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
5467 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
5481 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
5500 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
5520 ATCGCAATGCG
1 ATCGCAATGCG
5531 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:5579 original size:33 final size:33
Alignment explanation
Indices: 5537--5864 Score: 210
Period size: 33 Copynumber: 9.5 Consensus size: 33
5527 TGCGTTTATA
5537 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
*
5570 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
*
5606 -TTTCG--TTGCGATTTTCATTTCGCATTGCGA-TTTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
* *
5640 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTA
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
*
5678 ATTTCGCATTGCGATTATGTCGGTT-CGATTTTC
1 ATTTCGCATTGCGATTATCTC-GTTGCGATTTTC
*
5711 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATT-T-TC
* * * * *
5751 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTATCTCGTTGCGATTTTC
*
5782 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
* *
5815 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTATC-TCGTTGCGATTTTC
*
5849 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
5865 GTATTTTCCG
Statistics
Matches: 250, Mismatches: 20, Indels: 50
0.78 0.06 0.16
Matches are distributed among these distances:
31 9 0.04
32 5 0.02
33 97 0.39
34 34 0.14
35 22 0.09
36 15 0.06
37 28 0.11
38 28 0.11
39 3 0.01
40 9 0.04
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (33 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
Found at i:5583 original size:19 final size:19
Alignment explanation
Indices: 5559--5864 Score: 349
Period size: 19 Copynumber: 17.4 Consensus size: 19
5549 GATTATCTCG
5559 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5578 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5597 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
5611 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5630 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
5648 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
5667 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
5686 TTGCGA--TT-ATGTCG-G
1 TTGCGATTTTCATTTCGCA
5701 TT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5719 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
5738 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
5752 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5771 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
5790 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
5804 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
5824 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
5838 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
5857 TTGCGATT
1 TTGCGATT
5865 GTATTTTCCG
Statistics
Matches: 247, Mismatches: 13, Indels: 54
0.79 0.04 0.17
Matches are distributed among these distances:
14 32 0.13
15 2 0.01
16 31 0.13
17 28 0.11
18 23 0.09
19 119 0.48
20 12 0.05
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:5803 original size:52 final size:52
Alignment explanation
Indices: 5559--5836 Score: 361
Period size: 52 Copynumber: 5.2 Consensus size: 52
5549 GATTATCTCG
*
5559 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* *
5611 TTGCGATTTTCATTTCGCATTGCGATTTCATTTCGCATTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCATTGCGA-TTC-TCTCG--TTGCGATTTTCATTTCGCA
* * *
5667 TTGCGATTTTAATTTCGCATTGCGATTATGTCGGTT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTC-GTTGCGATTTTCATTTCGCA
5719 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
5771 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCA
5824 TTGCGATTTTCAT
1 TTGCGATTTTCAT
5837 GTTGGGATTT
Statistics
Matches: 211, Mismatches: 7, Indels: 15
0.91 0.03 0.06
Matches are distributed among these distances:
51 21 0.10
52 133 0.63
53 22 0.10
54 8 0.04
55 3 0.01
56 24 0.11
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:8396 original size:24 final size:24
Alignment explanation
Indices: 8362--8408 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
8352 CTGAAACATC
8362 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
8386 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
8409 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:9109 original size:20 final size:20
Alignment explanation
Indices: 9081--9449 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
9071 AAATTTCAGT
* * * *
9081 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
9101 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
9121 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
9141 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
9161 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
9181 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
9201 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
9221 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
9241 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
9261 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
9281 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
9301 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
9321 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
9341 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
9361 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
9381 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
9401 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
9421 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
9441 GTTGCGATT
1 GTTGCGATT
9450 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:15195 original size:14 final size:14
Alignment explanation
Indices: 15147--15197 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
15137 TAAATTATCT
*
15147 ATATAGTAATTTAA
1 ATATAATAATTTAA
*
15161 GTAT-ATAATTT-A
1 ATATAATAATTTAA
*
15173 ATCTAAATAATTTAA
1 ATAT-AATAATTTAA
15188 ATATAATAAT
1 ATATAATAAT
15198 AGAAATATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
12 3 0.10
13 6 0.21
14 16 0.55
15 4 0.14
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (14 bp):
ATATAATAATTTAA
Found at i:28980 original size:16 final size:18
Alignment explanation
Indices: 28959--28993 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
28949 AAAAAAAATA
28959 TAATTTT-AAT-TTTTTT
1 TAATTTTAAATATTTTTT
28975 TAATTTTAAATATTTTTT
1 TAATTTTAAATATTTTTT
28993 T
1 T
28994 TAAAAATTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 3 0.18
18 7 0.41
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TAATTTTAAATATTTTTT
Found at i:29161 original size:29 final size:29
Alignment explanation
Indices: 29106--29162 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
29096 TCATTCAAAA
* *
29106 AATAGTTTAAACATCTATTCTTAAAAAGT
1 AATAATTTAAACATCTATTCGTAAAAAGT
29135 AATAATTTAAACA-CTTATTCGTGAAAAA
1 AATAATTTAAACATC-TATTCGT-AAAAA
29163 ACGTTAATAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 1 0.04
29 18 0.75
30 5 0.21
ACGTcount: A:0.47, C:0.11, G:0.07, T:0.35
Consensus pattern (29 bp):
AATAATTTAAACATCTATTCGTAAAAAGT
Found at i:32077 original size:20 final size:20
Alignment explanation
Indices: 32054--32092 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
32044 TTAAATTATG
*
32054 AAATTATTGATATAATAGTT
1 AAATAATTGATATAATAGTT
*
32074 AAATAATTTATATAATAGT
1 AAATAATTGATATAATAGT
32093 AATTTGGATA
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:0.49, C:0.00, G:0.08, T:0.44
Consensus pattern (20 bp):
AAATAATTGATATAATAGTT
Found at i:35303 original size:20 final size:21
Alignment explanation
Indices: 35278--35327 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
35268 ACTAAGGTAG
*
35278 GGTTTAGGGTTAAAGA-TTAT
1 GGTTTAGGGTCAAAGAGTTAT
*
35298 GGTTTAGAGGTCATAGAGTTAT
1 GGTTTAG-GGTCAAAGAGTTAT
*
35320 GATTTAGG
1 GGTTTAGG
35328 ATTTAGGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 7 0.28
21 8 0.32
22 10 0.40
ACGTcount: A:0.28, C:0.02, G:0.32, T:0.38
Consensus pattern (21 bp):
GGTTTAGGGTCAAAGAGTTAT
Found at i:37720 original size:53 final size:52
Alignment explanation
Indices: 37603--37710 Score: 173
Period size: 53 Copynumber: 2.1 Consensus size: 52
37593 AAATTTAAGC
*
37603 TCGAGACATTACTT-AAGTGATATCAATCATTTATCACTTGAATCAACCCATA
1 TCGAGACATT-GTTCAAGTGATATCAATCATTTATCACTTGAATCAACCCATA
*
37655 TCGAGATATTGTTCAAGTGATATCAATCTATTTATCACTTGAATCAACCCATA
1 TCGAGACATTGTTCAAGTGATATCAATC-ATTTATCACTTGAATCAACCCATA
37708 TCG
1 TCG
37711 TAACGTTGTT
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
51 2 0.04
52 23 0.44
53 27 0.52
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.34
Consensus pattern (52 bp):
TCGAGACATTGTTCAAGTGATATCAATCATTTATCACTTGAATCAACCCATA
Found at i:37926 original size:2 final size:2
Alignment explanation
Indices: 37916--38018 Score: 197
Period size: 2 Copynumber: 51.5 Consensus size: 2
37906 AAAGGTAAAA
*
37916 AG AG CG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
37958 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
38000 AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG A
38019 ACAGATTCGA
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 99 1.00
ACGTcount: A:0.50, C:0.01, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:38609 original size:30 final size:31
Alignment explanation
Indices: 38573--38675 Score: 117
Period size: 29 Copynumber: 3.5 Consensus size: 31
38563 CGTGACAGAT
*
38573 AACATGACAGATGAGTT-AATTAGTAACTCA
1 AACATGACAGATGAGTTAAATTGGTAACTCA
* *
38603 AACATGACAG-TGAATTAAATTGGCAACTCA
1 AACATGACAGATGAGTTAAATTGGTAACTCA
* *
38633 AATA-G-CAGATGAGTTAAATTGGTACCTCA
1 AACATGACAGATGAGTTAAATTGGTAACTCA
38662 AACAT-AGCAGATGA
1 AACATGA-CAGATGA
38676 AGCCACCTAT
Statistics
Matches: 60, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
28 3 0.05
29 26 0.43
30 24 0.40
31 7 0.12
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.24
Consensus pattern (31 bp):
AACATGACAGATGAGTTAAATTGGTAACTCA
Done.