Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006669.1 Hibiscus syriacus cultivar Beakdansim tig00016522_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: 62312
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:12015 original size:91 final size:90
Alignment explanation
Indices: 11877--12405 Score: 695
Period size: 91 Copynumber: 5.8 Consensus size: 90
11867 TTATAGCGAG
* *
11877 GAGTTCATAATGAGAAGAACTCATCCAACAAGGGAGAAAAAGTTCATAATGAGAAGAATTTGTTC
1 GAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTTC
* *
11942 AACCTTGGCTCAACATTTCCAGTAGA
66 AACCTTGGCTCAATATTTCCAAT-GA
* * *
11968 GAGTTCATAATGAGAAGAACTCATCCAATGAGAGA-AAATAATTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAA-AAGTTCATAATGAGAAGAACTTGTT
*
12032 CAACCTTGGCTCAATATTTCCATTGGA
65 CAACCTTGGCTCAATATTTCCAAT-GA
* * * *
12059 GAGTTCATAATGAGAAGAACTCATCCGATGAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 GAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTTC
* * * *
12124 AACCTTTGATCAATGTCTCCAATGAA
66 AACCTTGGCTCAATATTTCCAATG-A
* * *
12150 GAGTTCATAATGAGAAGAACTCATCCAACAAGGGAGAAAAAGTTCATAATTAGAAGAGCTTGTTC
1 GAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTTC
** *
12215 AACCTTGATTCAATATTCCCAATAGA
66 AACCTTGGCTCAATATTTCCAAT-GA
* * *
12241 GAGTTCATAATGAGAAGAACTCGTCCTACGAGGGAGAAAAAGTTCATAATAAGAAGAACTTGTTC
1 GAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTTC
* * *
12306 GACCTTGGAC-CAACATTTCCAGTGTA
66 AACCTTGG-CTCAATATTTCCAATG-A
* *
12332 GAGTTCATAATGAGAAGAACTCATCCGACGA-GGAAAAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAA-AAGTTCATAATGAGAAGAACTTGTT
12396 CAACCTTGGC
65 CAACCTTGGC
12406 GATTCCTTCA
Statistics
Matches: 384, Mismatches: 47, Indels: 15
0.86 0.11 0.03
Matches are distributed among these distances:
90 12 0.03
91 369 0.96
92 3 0.01
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (90 bp):
GAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTTC
AACCTTGGCTCAATATTTCCAATGA
Found at i:12123 original size:20 final size:19
Alignment explanation
Indices: 12061--12124 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 19
12051 CCATTGGAGA
12061 GTTCATAATGAGAAGAACT
1 GTTCATAATGAGAAGAACT
* * *
12080 CATCCGATGAAGGAGAAGAA--
1 -GTTC-AT-AATGAGAAGAACT
12100 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAAC-T
12120 GTTCA
1 GTTCA
12125 ACCTTTGATC
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
17 10 0.30
18 2 0.06
19 2 0.06
20 7 0.21
21 2 0.06
22 10 0.30
ACGTcount: A:0.41, C:0.12, G:0.23, T:0.23
Consensus pattern (19 bp):
GTTCATAATGAGAAGAACT
Found at i:12374 original size:273 final size:273
Alignment explanation
Indices: 11877--12402 Score: 824
Period size: 273 Copynumber: 1.9 Consensus size: 273
11867 TTATAGCGAG
*
11877 GAGTTCATAATGAGAAGAACTCATCCAACAAGGGAGAAAAAGTTCATAATGAGAAGAATTTGTTC
1 GAGTTCATAATGAGAAGAACTCATCCAACAAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTTC
* * * *
11942 AACCTTGGCTCAACATTTCCAGTAGAGAGTTCATAATGAGAAGAACTCATCCAATGAGAGAAAAT
66 AACCTTGACTCAACATTCCCAATAGAGAGTTCATAATGAGAAGAACTCATCCAACGAGAGAAAAT
* * * *
12007 AATTTCATAATGAGAAGAACTTGTTCAACCTTGGCTCAATATTTCCATTGGAGAGTTCATAATGA
131 AAGTTCATAATAAGAAGAACTTGTTCAACCTTGGCTCAACATTTCCAGTGGAGAGTTCATAATGA
* *
12072 GAAGAACTCATCCGATGAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTGATCAA
196 GAAGAACTCATCCGACGAAGGAAAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTGATCAA
12137 TGTCTCCAATGAA
261 TGTCTCCAATGAA
* *
12150 GAGTTCATAATGAGAAGAACTCATCCAACAAGGGAGAAAAAGTTCATAATTAGAAGAGCTTGTTC
1 GAGTTCATAATGAGAAGAACTCATCCAACAAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTTC
* * * * *
12215 AACCTTGATTCAATATTCCCAATAGAGAGTTCATAATGAGAAGAACTCGTCCTACGAGGGAGAAA
66 AACCTTGACTCAACATTCCCAATAGAGAGTTCATAATGAGAAGAACTCATCCAACGAGAGA-AAA
* *
12280 -AAGTTCATAATAAGAAGAACTTGTTCGACCTTGGAC-CAACATTTCCAGTGTAGAGTTCATAAT
130 TAAGTTCATAATAAGAAGAACTTGTTCAACCTTGG-CTCAACATTTCCAGTGGAGAGTTCATAAT
12343 GAGAAGAACTCATCCGACG-AGGAAAAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
194 GAGAAGAACTCATCCGACGAAGG-AAAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
12403 GGCGATTCCT
Statistics
Matches: 230, Mismatches: 20, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
272 3 0.01
273 223 0.97
274 4 0.02
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (273 bp):
GAGTTCATAATGAGAAGAACTCATCCAACAAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTTC
AACCTTGACTCAACATTCCCAATAGAGAGTTCATAATGAGAAGAACTCATCCAACGAGAGAAAAT
AAGTTCATAATAAGAAGAACTTGTTCAACCTTGGCTCAACATTTCCAGTGGAGAGTTCATAATGA
GAAGAACTCATCCGACGAAGGAAAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTGATCAA
TGTCTCCAATGAA
Found at i:12441 original size:36 final size:36
Alignment explanation
Indices: 12395--12472 Score: 147
Period size: 36 Copynumber: 2.2 Consensus size: 36
12385 AAGAACTTGT
*
12395 TCAACCTTGGCGATTCCTTCATATACGGAGGTTAGA
1 TCAACATTGGCGATTCCTTCATATACGGAGGTTAGA
12431 TCAACATTGGCGATTCCTTCATATACGGAGGTTAGA
1 TCAACATTGGCGATTCCTTCATATACGGAGGTTAGA
12467 TCAACA
1 TCAACA
12473 CCGACATCTC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (36 bp):
TCAACATTGGCGATTCCTTCATATACGGAGGTTAGA
Found at i:12956 original size:4 final size:4
Alignment explanation
Indices: 12947--12975 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
12937 ATAGCAATAA
12947 TATT TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT T
12976 GTTCAATTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:17226 original size:38 final size:38
Alignment explanation
Indices: 17167--17253 Score: 124
Period size: 38 Copynumber: 2.3 Consensus size: 38
17157 ATTCATATAT
* *
17167 TCGGGTC-GGATTTTTTAAGTGTGATATTCGGGTC-GA
1 TCGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCGGA
*
17203 GTCGGGTTGGGTTTTTTTAAGTGTGATATTCAGGTCGGA
1 -TCGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCGGA
17242 TCGGGTCGGGTT
1 TCGGGTCGGGTT
17254 CGGGTTTATG
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
37 6 0.14
38 36 0.82
39 2 0.05
ACGTcount: A:0.14, C:0.10, G:0.37, T:0.39
Consensus pattern (38 bp):
TCGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCGGA
Found at i:17676 original size:37 final size:38
Alignment explanation
Indices: 17634--17719 Score: 120
Period size: 38 Copynumber: 2.3 Consensus size: 38
17624 TTTATTTTAT
* *
17634 TCGGGTCGG-GTTTTTTAAGTGTGATATTCTGGTCGAG
1 TCGGGTCGGAGTTTTTTAAGTGTGATATTCGGGTCGAA
* *
17671 TCGGGTTGGATTTTTTTAAGTGTGATATTCGGGTCGAA
1 TCGGGTCGGAGTTTTTTAAGTGTGATATTCGGGTCGAA
17709 TCGGGGTCGGA
1 TC-GGGTCGGA
17720 TTCGGGTTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
37 8 0.19
38 27 0.64
39 7 0.17
ACGTcount: A:0.15, C:0.10, G:0.36, T:0.38
Consensus pattern (38 bp):
TCGGGTCGGAGTTTTTTAAGTGTGATATTCGGGTCGAA
Found at i:17904 original size:5 final size:5
Alignment explanation
Indices: 17894--17925 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
17884 TTTATTTTGT
17894 TCGGG TCGGG TCGGG TCGGG TCGGG TTCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG -TCGGG T
17926 TTAGGGTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.00, C:0.19, G:0.56, T:0.25
Consensus pattern (5 bp):
TCGGG
Found at i:17929 original size:199 final size:199
Alignment explanation
Indices: 17712--18103 Score: 631
Period size: 199 Copynumber: 2.0 Consensus size: 199
17702 GGTCGAATCG
*
17712 GGGTCGGATTCGGGTTTAGGGTAAAAAAAACCGGACCGACCTGAAAATATATATAATGCGGGTCG
1 GGGTCGGATTCGGGTTTAGGGTAAAAAAAACCGGACCGACCCGAAAATATATATAATGCGGGTCG
* * *
17777 GGTCAGATTAAGTCACTGTTTTTATTAAATAAGAATAATTCTTTATTATTTTGGGTCGGGTCGGG
66 GGTCAGATTAAGTCACTATTTTTATTAAATAAAAATAATTCTTTATTATTTCGGGTCGGGTCGGG
*
17842 TAGGATTTCTAATTCATATATTCAGATCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTCG
131 TAGGATTTCTAATTCATATATTCAGATCGGGTCAGATGAAACTTTATTTTGTTCGGGTCGGGTCG
17907 GGTC
196 GGTC
* * * * *
17911 GGGTCGGGTTCGGGTTTAGGGTGAAAAAAACTGGACCGACCCGAAAATATATATAATTCGGGTCT
1 GGGTCGGATTCGGGTTTAGGGTAAAAAAAACCGGACCGACCCGAAAATATATATAATGCGGGTCG
* *
17976 GGTCGGATTAAGTCACTATTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGG
66 GGTCAGATTAAGTCACTATTTTTATTAAATAAAAATAATTCTTTATTATTTCGGGTCGGGTCGGG
** * * *
18041 TCTGATTTCTAATTCATATATTCGGGTCGGGTTAGATGAAACTTTATTTTGTTCGGGTCGGGT
131 TAGGATTTCTAATTCATATATTCAGATCGGGTCAGATGAAACTTTATTTTGTTCGGGTCGGGT
18104 TTTTTAAGTG
Statistics
Matches: 176, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
199 176 1.00
ACGTcount: A:0.26, C:0.13, G:0.27, T:0.35
Consensus pattern (199 bp):
GGGTCGGATTCGGGTTTAGGGTAAAAAAAACCGGACCGACCCGAAAATATATATAATGCGGGTCG
GGTCAGATTAAGTCACTATTTTTATTAAATAAAAATAATTCTTTATTATTTCGGGTCGGGTCGGG
TAGGATTTCTAATTCATATATTCAGATCGGGTCAGATGAAACTTTATTTTGTTCGGGTCGGGTCG
GGTC
Found at i:18135 original size:37 final size:38
Alignment explanation
Indices: 18093--18165 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
18083 TTTATTTTGT
18093 TCGGGTC-GGGTTTTTTAAGTGTGATATTCGGGTCGAG
1 TCGGGTCAGGGTTTTTTAAGTGTGATATTCGGGTCGAG
*
18130 TCGGGTCAGGTTTTTTTAAGTGTGATATTCGGGTCG
1 TCGGGTCAGGGTTTTTTAAGTGTGATATTCGGGTCG
18166 GGTTCAGGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
37 7 0.21
38 27 0.79
ACGTcount: A:0.14, C:0.11, G:0.36, T:0.40
Consensus pattern (38 bp):
TCGGGTCAGGGTTTTTTAAGTGTGATATTCGGGTCGAG
Found at i:18777 original size:18 final size:16
Alignment explanation
Indices: 18741--18785 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 16
18731 TATGAAATTG
18741 GATTCCAATTCTTACA
1 GATTCCAATTCTTACA
*
18757 GATTTCAATTCTTTCACA
1 GATTCCAATTC-TT-ACA
*
18775 GATTCTAATTC
1 GATTCCAATTC
18786 CCTCGTAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 10 0.42
17 2 0.08
18 12 0.50
ACGTcount: A:0.29, C:0.22, G:0.07, T:0.42
Consensus pattern (16 bp):
GATTCCAATTCTTACA
Found at i:20721 original size:3 final size:3
Alignment explanation
Indices: 20709--20753 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
20699 AAGATAATTG
20709 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
20754 GTTTAGGAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:23764 original size:12 final size:12
Alignment explanation
Indices: 23747--23772 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
23737 ATTACCCGGT
23747 TACCCGGCCCGA
1 TACCCGGCCCGA
23759 TACCCGGCCCGA
1 TACCCGGCCCGA
23771 TA
1 TA
23773 AATATTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.46, G:0.23, T:0.12
Consensus pattern (12 bp):
TACCCGGCCCGA
Found at i:23800 original size:4 final size:4
Alignment explanation
Indices: 23791--23889 Score: 68
Period size: 4 Copynumber: 26.5 Consensus size: 4
23781 AAATAATTAT
* * *
23791 TATA TATA TATA TATA TATA TA-A TAT- TA-A TAAA TTTA -ATT TA-A
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * * *
23834 TTTA AATA TATA TATA TATA TATA TA-A TATT TATA TATT TA-A TTTA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
*
23880 AATA TATA TA
1 TATA TATA TA
23890 CCTGACCCGA
Statistics
Matches: 71, Mismatches: 17, Indels: 14
0.70 0.17 0.14
Matches are distributed among these distances:
3 13 0.18
4 58 0.82
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (4 bp):
TATA
Found at i:23802 original size:6 final size:6
Alignment explanation
Indices: 23791--23889 Score: 68
Period size: 6 Copynumber: 17.7 Consensus size: 6
23781 AAATAATTAT
* * *
23791 TATATA TATATA TATATA TATA-A TAT-TA -ATAAA TTTA-A TTTA-A
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * *
23834 TTTAAA TATATA TATATA TATATA TA-ATA TTTATA TATTTA -ATTTA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
*
23880 AATATA TATA
1 TATATA TATA
23890 CCTGACCCGA
Statistics
Matches: 78, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
4 2 0.03
5 25 0.32
6 51 0.65
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
TATATA
Found at i:26872 original size:18 final size:17
Alignment explanation
Indices: 26830--26872 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
26820 TGAATGTGCA
26830 TGATATG-TATTATATG
1 TGATATGATATTATATG
*
26846 TGATGTGATATGTATATG
1 TGATATGATAT-TATATG
*
26864 TTATATGAT
1 TGATATGAT
26873 GATGATCTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 6 0.27
17 3 0.14
18 13 0.59
ACGTcount: A:0.30, C:0.00, G:0.21, T:0.49
Consensus pattern (17 bp):
TGATATGATATTATATG
Found at i:37334 original size:127 final size:127
Alignment explanation
Indices: 37108--37615 Score: 890
Period size: 127 Copynumber: 4.0 Consensus size: 127
37098 GTACTATTCA
* * *
37108 CGTGAAGGCGCGTTCCCGGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATTATTGCCC
1 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
*
37173 TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAT
66 TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
* * *
37235 CGTGAAGGCGCGTTCTCGGGGGTGCGCCTTCTATTATTTTGTCAGAGAATATGTTATCATTACCC
1 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
* *
37300 TATTATATCACTTATGTCACCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
66 TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
* *
37362 CGTGAAGGTGCATTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
1 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
*
37427 TATTATGTCACTTATGTCCCCCGGGAACTATTCATGCCAATACCTATTATTCCTTAGGGGAC
66 TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
* *
37489 CGTGAAAGCGCGTTCCTGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
1 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
37554 TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
66 TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
37616 TTTAAAGCGC
Statistics
Matches: 360, Mismatches: 21, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
127 360 1.00
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (127 bp):
CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
Found at i:38121 original size:34 final size:34
Alignment explanation
Indices: 38044--38149 Score: 160
Period size: 34 Copynumber: 3.1 Consensus size: 34
38034 TTAACTTGAA
* *
38044 TTTAATGTTAAATTTCGAAT-ATATAATTTATAT
1 TTTAATTTTAAATTTCGAATAATATAATTTGTAT
* *
38077 TTTAAATTTAAATTTCGAATAATATTATTTGTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTGTAT
*
38111 TTTAATTTTAAATTTCGAATACTATAATTTGTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTGTAT
38145 TTTAA
1 TTTAA
38150 AAACATTTAA
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 18 0.28
34 47 0.72
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.53
Consensus pattern (34 bp):
TTTAATTTTAAATTTCGAATAATATAATTTGTAT
Found at i:38750 original size:42 final size:42
Alignment explanation
Indices: 38684--38764 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
38674 GGCATGTAAC
* * *
38684 CTGGTGGGCTAGGAATGTAACCCTGCGGAGATGACATATGAA
1 CTGGTGGGCTAGGAATATAACCCTGAGGAAATGACATATGAA
* * * *
38726 CTGGTGGGCTTGGCATATACCCCTGAGGAAATGGCATAT
1 CTGGTGGGCTAGGAATATAACCCTGAGGAAATGACATAT
38765 ATCCCTGAGG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.23
Consensus pattern (42 bp):
CTGGTGGGCTAGGAATATAACCCTGAGGAAATGACATATGAA
Found at i:38760 original size:21 final size:21
Alignment explanation
Indices: 38736--38775 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
38726 CTGGTGGGCT
38736 TGGCATATACCCCTGAGGAAA
1 TGGCATATACCCCTGAGGAAA
*
38757 TGGCATATATCCCTGAGGA
1 TGGCATATACCCCTGAGGA
38776 GATAACATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.23, G:0.25, T:0.23
Consensus pattern (21 bp):
TGGCATATACCCCTGAGGAAA
Found at i:38784 original size:21 final size:21
Alignment explanation
Indices: 38739--38785 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
38729 GTGGGCTTGG
**
38739 CATATACCCCTGAGGAAATGG
1 CATATACCCCTGAGGAAATAA
* *
38760 CATATATCCCTGAGGAGATAA
1 CATATACCCCTGAGGAAATAA
38781 CATAT
1 CATAT
38786 GAAGTGGAGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.23
Consensus pattern (21 bp):
CATATACCCCTGAGGAAATAA
Found at i:40419 original size:17 final size:17
Alignment explanation
Indices: 40371--40419 Score: 57
Period size: 15 Copynumber: 3.0 Consensus size: 17
40361 AAATTTAAAG
*
40371 AAATAATAATTATATAA
1 AAATAATATTTATATAA
* *
40388 ATATTAT-TTTA-ATAA
1 AAATAATATTTATATAA
40403 AAATAATATTTATATAA
1 AAATAATATTTATATAA
40420 TTATATTAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
15 9 0.36
16 7 0.28
17 9 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATAATATTTATATAA
Found at i:40422 original size:29 final size:33
Alignment explanation
Indices: 40371--40441 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 33
40361 AAATTTAAAG
*
40371 AAATAATAATTATATAAATATTATTTTAATA-A
1 AAATAATAATTATATAAATATTATATTAATATA
*
40403 AAATAAT-ATT-TATATA-ATTATATTAATATA
1 AAATAATAATTATATAAATATTATATTAATATA
40433 AAAT-ATAAT
1 AAATAATAAT
40442 AACTATTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 13 0.37
30 12 0.34
31 3 0.09
32 7 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (33 bp):
AAATAATAATTATATAAATATTATATTAATATA
Found at i:40441 original size:32 final size:32
Alignment explanation
Indices: 40371--40452 Score: 87
Period size: 32 Copynumber: 2.6 Consensus size: 32
40361 AAATTTAAAG
*
40371 AAATAATAATTATATAAATATTATTTTAATAA
1 AAATAATAATTATATAAATATTATTATAATAA
* *
40403 AAATAATATTTATATAATTA-TATTA-ATATAA
1 AAATAATAATTATATAAATATTATTATA-ATAA
* *
40434 AATATAATAACTATTTAAA
1 AA-ATAATAATTATATAAA
40453 AAAAATAACT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
30 1 0.02
31 10 0.24
32 30 0.73
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (32 bp):
AAATAATAATTATATAAATATTATTATAATAA
Found at i:45331 original size:31 final size:31
Alignment explanation
Indices: 45296--45358 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
45286 CAGTTACGTC
45296 GGGGACCATATTGCAAACAGACTAAATGTTG
1 GGGGACCATATTGCAAACAGACTAAATGTTG
*
45327 GGGGATCATATTGCAAACAGACTAAATGTTG
1 GGGGACCATATTGCAAACAGACTAAATGTTG
45358 G
1 G
45359 AGAACTGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.14, G:0.27, T:0.24
Consensus pattern (31 bp):
GGGGACCATATTGCAAACAGACTAAATGTTG
Found at i:47390 original size:31 final size:31
Alignment explanation
Indices: 47341--47467 Score: 177
Period size: 31 Copynumber: 4.2 Consensus size: 31
47331 TGCAATACAA
*
47341 TCCCCAAACA-TTAGTCCGTTTGCAATATGG
1 TCCCCCAACATTTAGTCCGTTTGCAATATGG
* *
47371 TCCCCCAACATTTAATCCGTTTGCAATATAG
1 TCCCCCAACATTTAGTCCGTTTGCAATATGG
* * *
47402 TCTCTCAACATTTAGTCTGTTTGCAATAT-G
1 TCCCCCAACATTTAGTCCGTTTGCAATATGG
*
47432 ACCCCCAACATTTAGTCCGTTTGCAATATGG
1 TCCCCCAACATTTAGTCCGTTTGCAATATGG
47463 TCCCC
1 TCCCC
47468 GACGTAACTA
Statistics
Matches: 83, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
30 35 0.42
31 48 0.58
ACGTcount: A:0.25, C:0.28, G:0.13, T:0.33
Consensus pattern (31 bp):
TCCCCCAACATTTAGTCCGTTTGCAATATGG
Found at i:48423 original size:15 final size:15
Alignment explanation
Indices: 48400--48433 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
48390 ATATTTAGCT
* *
48400 GGGCGGGCGGATGTG
1 GGGCAGGCGGATGCG
48415 GGGCAGGCGGATGCG
1 GGGCAGGCGGATGCG
48430 GGGC
1 GGGC
48434 GGGTAATGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.18, G:0.65, T:0.09
Consensus pattern (15 bp):
GGGCAGGCGGATGCG
Found at i:61814 original size:30 final size:30
Alignment explanation
Indices: 61778--61838 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
61768 ACACACCAGT
61778 CCCCAGTTGAGAGGATTTGGAGGTATCAGA
1 CCCCAGTTGAGAGGATTTGGAGGTATCAGA
61808 CCCCAGTTGAGAGGATTTGGAGGTATCAGA
1 CCCCAGTTGAGAGGATTTGGAGGTATCAGA
61838 C
1 C
61839 TAAAAACTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.18, G:0.33, T:0.23
Consensus pattern (30 bp):
CCCCAGTTGAGAGGATTTGGAGGTATCAGA
Done.