Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000301.1 Hibiscus syriacus cultivar Beakdansim tig00000555_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: 102180
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:1928 original size:11 final size:12
Alignment explanation
Indices: 1907--1952 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
1897 TCCGGATAAA
1907 AACCGGTTTTTT
1 AACCGGTTTTTT
1919 AACCGGTTTTTTT
1 AACCGG-TTTTTT
1932 CAAACCGGTTTTTT
1 --AACCGGTTTTTT
*
1946 ATCCGGT
1 AACCGGT
1953 AAAAAACCGG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 12 0.40
13 6 0.20
14 6 0.20
15 6 0.20
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:1937 original size:15 final size:14
Alignment explanation
Indices: 1906--1945 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
1896 TTCCGGATAA
1906 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
1919 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
1932 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
1946 ATCCGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
15 12 0.50
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:3059 original size:22 final size:23
Alignment explanation
Indices: 3028--3076 Score: 91
Period size: 22 Copynumber: 2.2 Consensus size: 23
3018 AACTACCATG
3028 GCACTAAAGGAAAACCAGTAGTA
1 GCACTAAAGGAAAACCAGTAGTA
3051 GCACT-AAGGAAAACCAGTAGTA
1 GCACTAAAGGAAAACCAGTAGTA
3073 GCAC
1 GCAC
3077 GAATTGTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.12
Consensus pattern (23 bp):
GCACTAAAGGAAAACCAGTAGTA
Found at i:4365 original size:21 final size:21
Alignment explanation
Indices: 4332--4371 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
4322 AAAATTAACT
*
4332 CCAAGATCGCTCAGATGGATA
1 CCAAGATCACTCAGATGGATA
* *
4353 CCAAGCTCACTCAGGTGGA
1 CCAAGATCACTCAGATGGA
4372 GTCTAAGGTG
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:0.30, C:0.28, G:0.25, T:0.17
Consensus pattern (21 bp):
CCAAGATCACTCAGATGGATA
Found at i:29234 original size:44 final size:44
Alignment explanation
Indices: 29157--29267 Score: 145
Period size: 44 Copynumber: 2.5 Consensus size: 44
29147 TTTATGCGCA
* * * *
29157 ATGCATCAATAAACTATGACAGTGTACCGATGCATCCCTTGAAT
1 ATGCATCGATACACTATGACAGTGCACCAATGCATCCCTTGAAT
*
29201 ATGCATCGATACACTATGA-AGGTGCACCAATGCATTCCTTGAAT
1 ATGCATCGATACACTATGACA-GTGCACCAATGCATCCCTTGAAT
*
29245 GTGCATCGATACACTATG-CAGTG
1 ATGCATCGATACACTATGACAGTG
29268 TATCGATACA
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
43 4 0.07
44 55 0.93
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.27
Consensus pattern (44 bp):
ATGCATCGATACACTATGACAGTGCACCAATGCATCCCTTGAAT
Found at i:29765 original size:13 final size:13
Alignment explanation
Indices: 29747--29784 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
29737 TCCATATTAA
29747 TTTTCAAACATTG
1 TTTTCAAACATTG
*
29760 TTTTCAAACATAG
1 TTTTCAAACATTG
29773 TTTTCAAA-ATTG
1 TTTTCAAACATTG
29785 CCCATTAGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 3 0.13
13 20 0.87
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (13 bp):
TTTTCAAACATTG
Found at i:31221 original size:18 final size:16
Alignment explanation
Indices: 31200--31244 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 16
31190 GATTGATATA
31200 TTTTGGATGTTTGATTG
1 TTTTGGATGTTTGA-TG
31217 TTTTTGGA--TTT-ATG
1 -TTTTGGATGTTTGATG
31231 TTTTGGATGTTTGA
1 TTTTGGATGTTTGA
31245 ACTTGAATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
13 7 0.29
14 2 0.08
15 4 0.17
16 4 0.17
18 7 0.29
ACGTcount: A:0.13, C:0.00, G:0.27, T:0.60
Consensus pattern (16 bp):
TTTTGGATGTTTGATG
Found at i:31238 original size:31 final size:31
Alignment explanation
Indices: 31177--31244 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
31167 GTTAAAACAT
31177 TTTGATGTTTTTGGATTGATATATTTTGGATG
1 TTTGATGTTTTTGGATT-ATATATTTTGGATG
*
31209 TTTGATTGTTTTTGGATT-TATGTTTTGGATG
1 TTTGA-TGTTTTTGGATTATATATTTTGGATG
31240 TTTGA
1 TTTGA
31245 ACTTGAATGC
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
31 17 0.50
32 5 0.15
33 12 0.35
ACGTcount: A:0.16, C:0.00, G:0.25, T:0.59
Consensus pattern (31 bp):
TTTGATGTTTTTGGATTATATATTTTGGATG
Found at i:31568 original size:13 final size:13
Alignment explanation
Indices: 31538--31570 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
31528 TAATTTTCTA
*
31538 ATTTTCAAAATTG
1 ATTTTCAAAAATG
31551 A-TTTCAAAAATG
1 ATTTTCAAAAATG
31563 ATTTTCAA
1 ATTTTCAA
31571 TGAAAATCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.42
Consensus pattern (13 bp):
ATTTTCAAAAATG
Found at i:31864 original size:64 final size:65
Alignment explanation
Indices: 31785--31930 Score: 181
Period size: 65 Copynumber: 2.3 Consensus size: 65
31775 TTTGAATGTG
* * * *
31785 TTTTGTGTACCGATGCACA-ACCATGCATTGATGCACTCAT-GATTTTATTGAAACATCGAATGC
1 TTTTATGTACCGATGCACAGACCATGCATCGAAGCACTCATGGATCTT-TTGAAACATCGAATGC
31848 A
65 A
* * *
31849 TTTTATGTACCGATGCACAGACCATGCATCGAAGCACTCCTGGCTCTTTTGAAACATCGAATGTA
1 TTTTATGTACCGATGCACAGACCATGCATCGAAGCACTCATGGATCTTTTGAAACATCGAATGCA
*
31914 -ATTAGTGTACCGATGCA
1 TTTTA-TGTACCGATGCA
31931 TACAAAGTGT
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
64 21 0.30
65 46 0.65
66 4 0.06
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (65 bp):
TTTTATGTACCGATGCACAGACCATGCATCGAAGCACTCATGGATCTTTTGAAACATCGAATGCA
Found at i:33095 original size:47 final size:45
Alignment explanation
Indices: 33040--33176 Score: 195
Period size: 45 Copynumber: 3.0 Consensus size: 45
33030 TTCCGATGGA
33040 GTGCTACCTAAAATGTTATTCTTTTCTACCGAAAATATTAATATCG
1 GTGCTACCTAAAATGTTATT-TTTTCTACCGAAAATATTAATATCG
* *
33086 GATGCTACCTAAAATGTTA-TTTTCCTACCAAAAATATTAATATCG
1 G-TGCTACCTAAAATGTTATTTTTTCTACCGAAAATATTAATATCG
* **
33131 GTCGCTATCTAAAATGTTATTTTTTCTATAGAAAATATTAATATCG
1 GT-GCTACCTAAAATGTTATTTTTTCTACCGAAAATATTAATATCG
33177 AAAATATTCA
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
44 1 0.01
45 39 0.48
46 24 0.30
47 17 0.21
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.39
Consensus pattern (45 bp):
GTGCTACCTAAAATGTTATTTTTTCTACCGAAAATATTAATATCG
Found at i:33210 original size:22 final size:22
Alignment explanation
Indices: 33185--33240 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
33175 CGAAAATATT
*
33185 CATTTTAGGTA-AAAACAATTAA
1 CATTTTAGGTAGAAAA-AAATAA
* *
33207 CATTTCATGTAGAAAAAAATAA
1 CATTTTAGGTAGAAAAAAATAA
33229 CATTTTAGGTAG
1 CATTTTAGGTAG
33241 CACCCTACTG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
22 24 0.86
23 4 0.14
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.32
Consensus pattern (22 bp):
CATTTTAGGTAGAAAAAAATAA
Found at i:37001 original size:23 final size:23
Alignment explanation
Indices: 36959--37003 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
36949 CAAAGTGACA
36959 CGTAGAACTGCACCGGAGTGCCG
1 CGTAGAACTGCACCGGAGTGCCG
* * *
36982 CGTAGAATTGCATCGTAGTGCC
1 CGTAGAACTGCACCGGAGTGCC
37004 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.27, G:0.31, T:0.20
Consensus pattern (23 bp):
CGTAGAACTGCACCGGAGTGCCG
Found at i:42464 original size:23 final size:23
Alignment explanation
Indices: 42438--42506 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
42428 CACCACAGCT
* *
42438 CGTATAATTACACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
42461 CGTAGAATTGCATC-AGAGTGCCG
1 CGTAGAATTGCACCGA-AGTGCCA
*
42484 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
42507 TATAATAATG
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
22 1 0.03
23 36 0.97
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:46424 original size:47 final size:47
Alignment explanation
Indices: 46329--46435 Score: 115
Period size: 47 Copynumber: 2.3 Consensus size: 47
46319 TTGAATGACC
* ** * *
46329 TCTGAAAAGTTGTAGAAGATGATAATACGTCACTATTTCACCCGTTT
1 TCTGAAAAGTTGCAGAAGATGATAATACACCACTATTTCACACATTT
* * * *
46376 TCTGAAAAGTTGCAGAATATGATAATGCACCACTTTTTCACATATTT
1 TCTGAAAAGTTGCAGAAGATGATAATACACCACTATTTCACACATTT
*
46423 TCTAAAAAAGTTG
1 TCT-GAAAAGTTG
46436 TTTAAATTAT
Statistics
Matches: 49, Mismatches: 10, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
47 41 0.84
48 8 0.16
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Consensus pattern (47 bp):
TCTGAAAAGTTGCAGAAGATGATAATACACCACTATTTCACACATTT
Found at i:46481 original size:130 final size:129
Alignment explanation
Indices: 46249--46484 Score: 321
Period size: 130 Copynumber: 1.8 Consensus size: 129
46239 GATACATCAT
* * *
46249 TGAAAAGTTGCGAAAGATGATAATGCACCACTATTTCACCCGTTGTCTGAAAAGTTATTTAAATG
1 TGAAAAGTTGCGAAAGATGATAATGCACCACTATTTCACACATTGTCTAAAAAGTTATTTAAATG
** * *
46314 ATGCATTGAATGACCTCTGAAAAGTTGTAGAAGATGATAATACGTCACTATTTCACCCGTTTTC
66 ATGCATTGAATGACCTCTGAAAAGTTACAAAAAATGATAATACGTCACTATTTCACCCGTTTTC
* * * * *
46378 TGAAAAGTTGC-AGAATATGATAATGCACCACTTTTTCACATATTTTCTAAAAAAGTTGTTTAAA
1 TGAAAAGTTGCGA-AAGATGATAATGCACCACTATTTCACACATTGTCT-AAAAAGTTATTTAAA
* *
46442 TTATGCATTGAATGACCTTTGAAAAGTTACAAAAAATGATAAT
64 TGATGCATTGAATGACCTCTGAAAAGTTACAAAAAATGATAAT
46485 GCACCACCAT
Statistics
Matches: 91, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
128 1 0.01
129 40 0.44
130 50 0.55
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (129 bp):
TGAAAAGTTGCGAAAGATGATAATGCACCACTATTTCACACATTGTCTAAAAAGTTATTTAAATG
ATGCATTGAATGACCTCTGAAAAGTTACAAAAAATGATAATACGTCACTATTTCACCCGTTTTC
Found at i:53538 original size:30 final size:28
Alignment explanation
Indices: 53462--53546 Score: 98
Period size: 31 Copynumber: 2.9 Consensus size: 28
53452 TAAAGCTTAA
53462 TTTTTTATCTTAAATAAAAATAATAAAT
1 TTTTTTATCTTAAATAAAAATAATAAAT
* * * * *
53490 TTTTTTATCTCATGATAAATACTATTTAATT
1 TTTTTTATCTTA-AATAAA-AATA-ATAAAT
53521 TTTTTTATCTTAAATAAAAATAATAA
1 TTTTTTATCTTAAATAAAAATAATAA
53547 TAAAGGAGTG
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
28 14 0.31
29 8 0.18
30 8 0.18
31 15 0.33
ACGTcount: A:0.44, C:0.06, G:0.01, T:0.49
Consensus pattern (28 bp):
TTTTTTATCTTAAATAAAAATAATAAAT
Found at i:53845 original size:2 final size:2
Alignment explanation
Indices: 53838--53915 Score: 147
Period size: 2 Copynumber: 39.0 Consensus size: 2
53828 ACCCATACCC
*
53838 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53880 AT AT AT 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 AT AT AT
53916 GAAAAGAAAG
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:56314 original size:19 final size:19
Alignment explanation
Indices: 56279--56316 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
56269 TAAAACTATT
*
56279 TTTTATTATATTATATTTA
1 TTTTATTATATGATATTTA
56298 TTTTA-TATATGATTATTTA
1 TTTTATTATATGA-TATTTA
56317 AATAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (19 bp):
TTTTATTATATGATATTTA
Found at i:56738 original size:20 final size:20
Alignment explanation
Indices: 56713--56755 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
56703 TATAAGAGCC
*
56713 CATTTAGGATCATATAGATG
1 CATTTAGGAGCATATAGATG
*
56733 CATTTAGGAGCATATAGTTG
1 CATTTAGGAGCATATAGATG
56753 CAT
1 CAT
56756 GTGGTGGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGAGCATATAGATG
Found at i:65356 original size:15 final size:15
Alignment explanation
Indices: 65336--65370 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
65326 CTTGAGGGAT
65336 CAACTAGGATCATCC
1 CAACTAGGATCATCC
65351 CAACTAGGATCATCC
1 CAACTAGGATCATCC
65366 CAACT
1 CAACT
65371 TGGACTCCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.34, C:0.34, G:0.11, T:0.20
Consensus pattern (15 bp):
CAACTAGGATCATCC
Found at i:77928 original size:4 final size:4
Alignment explanation
Indices: 77919--77946 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
77909 TAATGTTGAT
77919 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
77947 AGCATGAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:79266 original size:18 final size:20
Alignment explanation
Indices: 79235--79272 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
79225 TGACATTAAT
79235 TTTTTTATATATAAAAAATA
1 TTTTTTATATATAAAAAATA
79255 TTTTTT-TA-ATAAAAAATA
1 TTTTTTATATATAAAAAATA
79273 CATAGATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.56
19 2 0.11
20 6 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTTTTATATATAAAAAATA
Found at i:80587 original size:19 final size:19
Alignment explanation
Indices: 80560--80619 Score: 102
Period size: 19 Copynumber: 3.2 Consensus size: 19
80550 CCAATTTTGG
*
80560 ATACCGTATATTACTGTTC
1 ATACAGTATATTACTGTTC
80579 ATACAGTATATTACTGTTC
1 ATACAGTATATTACTGTTC
*
80598 ATACAATATATTACTGTTC
1 ATACAGTATATTACTGTTC
80617 ATA
1 ATA
80620 AAAAATGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (19 bp):
ATACAGTATATTACTGTTC
Found at i:87592 original size:21 final size:21
Alignment explanation
Indices: 87562--87601 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
87552 GAAGTTACTG
* * *
87562 TAGCAGTGCATCGGTACACTA
1 TAGCAATGCACCGATACACTA
87583 TAGCAATGCACCGATACAC
1 TAGCAATGCACCGATACAC
87602 AATTTATATT
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:0.33, C:0.28, G:0.20, T:0.20
Consensus pattern (21 bp):
TAGCAATGCACCGATACACTA
Found at i:87649 original size:21 final size:21
Alignment explanation
Indices: 87623--87663 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
87613 GATGTTTTTA
87623 TGCATCGGTACACTATAGCAG
1 TGCATCGGTACACTATAGCAG
*
87644 TGCATCGGTACACTGTAGCA
1 TGCATCGGTACACTATAGCA
87664 CTATTCATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (21 bp):
TGCATCGGTACACTATAGCAG
Found at i:89879 original size:24 final size:24
Alignment explanation
Indices: 89848--89896 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
89838 AATAAACCGT
89848 ACAAATTCATAAAATAAAATAAAA
1 ACAAATTCATAAAATAAAATAAAA
89872 ACAAATTCATAAAATAAAATAAAA
1 ACAAATTCATAAAATAAAATAAAA
89896 A
1 A
89897 ACTATCTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.71, C:0.08, G:0.00, T:0.20
Consensus pattern (24 bp):
ACAAATTCATAAAATAAAATAAAA
Found at i:93828 original size:17 final size:17
Alignment explanation
Indices: 93801--93843 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
93791 CTTCATTCAA
*
93801 TAAAGCTAGTTTAATAAT
1 TAAA-CTAGTTCAATAAT
*
93819 TAAACTAGTTCATTAAT
1 TAAACTAGTTCAATAAT
*
93836 CAAACTAG
1 TAAACTAG
93844 CTCCTTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (17 bp):
TAAACTAGTTCAATAAT
Found at i:95448 original size:22 final size:22
Alignment explanation
Indices: 95423--95475 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
95413 CTCGAGAATT
95423 GTTTAAGTCAATAAAATGAGAG
1 GTTTAAGTCAATAAAATGAGAG
*
95445 GTTTAAGCCAATAAAATGAGAG
1 GTTTAAGTCAATAAAATGAGAG
95467 GTTTAAGTC
1 GTTTAAGTC
95476 TCGATTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.28
Consensus pattern (22 bp):
GTTTAAGTCAATAAAATGAGAG
Found at i:95711 original size:21 final size:21
Alignment explanation
Indices: 95685--95729 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
95675 AAATTAGTGC
*
95685 TTGAATTTTATTTGGGTCAAT
1 TTGAATTTTACTTGGGTCAAT
95706 TTGAATTTTACTTGGGTCAAT
1 TTGAATTTTACTTGGGTCAAT
95727 TTG
1 TTG
95730 GACTAAAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.22, C:0.07, G:0.20, T:0.51
Consensus pattern (21 bp):
TTGAATTTTACTTGGGTCAAT
Found at i:96195 original size:119 final size:116
Alignment explanation
Indices: 95965--96197 Score: 367
Period size: 119 Copynumber: 2.0 Consensus size: 116
95955 CTCAGGAGCA
*
95965 GGCGGTATTTTAGAGGCGAAACTGCTGAGTGGGCCTTGGTTTCCGGCGCACTTGGGTATTTGTAC
1 GGCGGTATTTTAGAGGCGAAACTGCTGAGTGGGCCTTGGTTTCCGACGCACTTGGGTATTTGTAC
* *
96030 AAATGTAGCTGCTGAGCTTCATGCAATTAAAATCAGAGTGATAATTGCATG
66 AAATGTAGCTGCCGAGCTTCATGCAATTAAAATCAGAGTGACAATTGCATG
*
96081 GGCGGTATTTTGAGAGGCGAAACTGCTGAGTGGGTCTTGGGTTTCACGACGCACTTGGGTATTTG
1 GGCGGTATTTT-AGAGGCGAAACTGCTGAGTGGGCCTT-GGTTTC-CGACGCACTTGGGTATTTG
* * * *
96146 TATAAATGTAGCTGCCGAGCTTCATGCAATTAAAGTCGGATTGACAATTGCA
63 TACAAATGTAGCTGCCGAGCTTCATGCAATTAAAATCAGAGTGACAATTGCA
96198 GGGGATCATG
Statistics
Matches: 106, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
116 11 0.10
117 25 0.24
118 6 0.06
119 64 0.60
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (116 bp):
GGCGGTATTTTAGAGGCGAAACTGCTGAGTGGGCCTTGGTTTCCGACGCACTTGGGTATTTGTAC
AAATGTAGCTGCCGAGCTTCATGCAATTAAAATCAGAGTGACAATTGCATG
Found at i:100558 original size:35 final size:36
Alignment explanation
Indices: 100493--100566 Score: 107
Period size: 35 Copynumber: 2.1 Consensus size: 36
100483 TTAAACTTTT
*
100493 TTATATTTTAAATTTTGTAAAAAAATTATATAAATA
1 TTATAATTTAAATTTTGTAAAAAAATTATATAAATA
*
100529 TTATAATTT-AATTTTTTAAAGAAAA-TATATAAATA
1 TTATAATTTAAATTTTGTAAA-AAAATTATATAAATA
100564 TTA
1 TTA
100567 CGATTTGTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
35 23 0.66
36 12 0.34
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (36 bp):
TTATAATTTAAATTTTGTAAAAAAATTATATAAATA
Done.