Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002991.1 Hibiscus syriacus cultivar Beakdansim tig00006185_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: 152125
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:4808 original size:33 final size:33
Alignment explanation
Indices: 4766--4829 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
4756 TTTATCCACC
4766 ATCTGTGCAAGACAAAGGGAAACAGAGCACACA
1 ATCTGTGCAAGACAAAGGGAAACAGAGCACACA
4799 ATCTGTGCAAGACAAAGGGAAACAGAGCACA
1 ATCTGTGCAAGACAAAGGGAAACAGAGCACA
4830 GCAAACGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.45, C:0.20, G:0.25, T:0.09
Consensus pattern (33 bp):
ATCTGTGCAAGACAAAGGGAAACAGAGCACACA
Found at i:5365 original size:42 final size:42
Alignment explanation
Indices: 5314--5564 Score: 179
Period size: 42 Copynumber: 5.9 Consensus size: 42
5304 TATAAAAGAT
*
5314 GATTGAAAAAATTAAGGGTCTCAATTTTAAAGATAAAAATGA
1 GATTGAAAAAATTAAGGGTCTCAATTATAAAGATAAAAATGA
* * * ** * *
5356 GATTAAAAAAAATT-AGATGCCTTGATTTTAAAGGTAAAAAGTGA
1 GATT-GAAAAAATTAAG-GGTCTCAATTATAAAGATAAAAA-TGA
* * * * * * *
5400 -ATTAAAAAAAATATGGGCCTCAATTGTAAAGGTAAAATGTGA
1 GATTGAAAAAATTAAGGGTCTCAATTATAAAGATAAAA-ATGA
* * *
5442 TATTGAAAAAATTATGAGT-TCAATTATAAAGATAAAAATGA
1 GATTGAAAAAATTAAGGGTCTCAATTATAAAGATAAAAATGA
* * *
5483 GTTTGAAAAAATT-AGGGTCATCAATTATAAATATAAAAAATTA
1 GATTGAAAAAATTAAGGGTC-TCAATTATAAAGAT-AAAAATGA
** * *
5526 GGATTG-AAAAATTAATAGTCCCAATTATCAAGATAAAAA
1 -GATTGAAAAAATTAAGGGTCTCAATTATAAAGATAAAAA
5565 GTGTGACTAC
Statistics
Matches: 166, Mismatches: 32, Indels: 22
0.75 0.15 0.10
Matches are distributed among these distances:
40 3 0.02
41 14 0.08
42 69 0.42
43 69 0.42
44 11 0.07
ACGTcount: A:0.50, C:0.06, G:0.15, T:0.29
Consensus pattern (42 bp):
GATTGAAAAAATTAAGGGTCTCAATTATAAAGATAAAAATGA
Found at i:11147 original size:18 final size:18
Alignment explanation
Indices: 11124--11162 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
11114 TATAAGTATA
* *
11124 ATTTAAGAATATATTACT
1 ATTTAAAAATATATTAAT
11142 ATTTAAAAATATATTAAT
1 ATTTAAAAATATATTAAT
11160 ATT
1 ATT
11163 AATTATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (18 bp):
ATTTAAAAATATATTAAT
Found at i:11715 original size:20 final size:20
Alignment explanation
Indices: 11689--11740 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
11679 ATTCGTGTTG
11689 CATTTCGCGTTG-AGATTTTT
1 CATTTCGCGTTGTA-ATTTTT
*
11709 TATTTCGCGTTGTAATTTTT
1 CATTTCGCGTTGTAATTTTT
*
11729 CATTTCACGTTG
1 CATTTCGCGTTG
11741 CGATAGTTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.15, C:0.15, G:0.17, T:0.52
Consensus pattern (20 bp):
CATTTCGCGTTGTAATTTTT
Found at i:11782 original size:22 final size:22
Alignment explanation
Indices: 11729--11809 Score: 78
Period size: 22 Copynumber: 3.7 Consensus size: 22
11719 TGTAATTTTT
*
11729 CATTTCACGTTGCGATAGT-TGA
1 CATTTCGCGTTGCGATAGTCT-A
**
11751 -AAATCGCGTTGCGATAGTCTA
1 CATTTCGCGTTGCGATAGTCTA
*
11772 CATTTCGCGTTGCGGTAGTCTA
1 CATTTCGCGTTGCGATAGTCTA
*
11794 CAGTT-GTCGTTGCGAT
1 CATTTCG-CGTTGCGAT
11810 TTTTCAAATT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
21 17 0.35
22 31 0.65
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.35
Consensus pattern (22 bp):
CATTTCGCGTTGCGATAGTCTA
Found at i:11824 original size:19 final size:19
Alignment explanation
Indices: 11800--11868 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
11790 TCTACAGTTG
*
11800 TCGTTGCGATTTTTCAAAT
1 TCGTTGCGATTTTACAAAT
* **
11819 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTACAAAT
*
11840 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTACAAAT
11860 TCGTTGCGA
1 TCGTTGCGA
11869 AAATTCGTTG
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 19 0.49
20 5 0.13
21 5 0.13
22 10 0.26
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.41
Consensus pattern (19 bp):
TCGTTGCGATTTTACAAAT
Found at i:11832 original size:41 final size:41
Alignment explanation
Indices: 11779--11868 Score: 162
Period size: 41 Copynumber: 2.2 Consensus size: 41
11769 CTACATTTCG
* *
11779 CGTTGCGGTAGTCTACAGTTGTCGTTGCGATTTTTCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
11820 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
11861 CGTTGCGA
1 CGTTGCGA
11869 AAATTCGTTG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.39
Consensus pattern (41 bp):
CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
Found at i:11847 original size:22 final size:22
Alignment explanation
Indices: 11757--11850 Score: 97
Period size: 22 Copynumber: 4.4 Consensus size: 22
11747 TTGAAAATCG
*
11757 CGTTGCGATAGTCTACATTTCG-
1 CGTTGCGATAGTCTACAGTT-GT
*
11779 CGTTGCGGTAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
11801 CGTTGCGAT--TTTTCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
11820 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
11842 CGTTGCGAT
1 CGTTGCGAT
11851 TTTCCAAATT
Statistics
Matches: 57, Mismatches: 11, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
19 10 0.18
20 5 0.09
21 6 0.11
22 36 0.63
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:12621 original size:22 final size:22
Alignment explanation
Indices: 12596--12649 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
12586 AATTTAGAAA
*
12596 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAAATGTAGACT
* *
12618 ATCGCAACAACAAATGTAGTCT
1 ATCGCAACGACAAATGTAGACT
12640 ATCGCAACGA
1 ATCGCAACGA
12650 ATTTGGAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.39, C:0.26, G:0.17, T:0.19
Consensus pattern (22 bp):
ATCGCAACGACAAATGTAGACT
Found at i:12662 original size:19 final size:19
Alignment explanation
Indices: 12640--12687 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
12630 AATGTAGTCT
12640 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
* *
12659 ATCGCCATGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
12678 ATCGCAACGA
1 ATCGCAACGA
12688 CAACAGTAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.21
Consensus pattern (19 bp):
ATCGCAACGAATTTGGAAA
Found at i:16074 original size:27 final size:27
Alignment explanation
Indices: 16032--16099 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
16022 GTGTAGGAAT
16032 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
16057 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
16084 TATAGAGATATGATTT
1 TATAGAGATATGATTT
16100 TGTAAATAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 7 0.17
27 34 0.83
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:17300 original size:31 final size:31
Alignment explanation
Indices: 17262--17384 Score: 212
Period size: 31 Copynumber: 4.0 Consensus size: 31
17252 CCCGAAGGAC
* *
17262 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
17293 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
17324 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
17355 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
17385 CCCTCGACCC
Statistics
Matches: 89, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
31 88 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:21665 original size:31 final size:31
Alignment explanation
Indices: 21627--21718 Score: 150
Period size: 31 Copynumber: 3.0 Consensus size: 31
21617 CCCGAAGGAC
* *
21627 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
21658 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
21689 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
21719 CCCTCGACCC
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
31 57 0.98
32 1 0.02
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:25711 original size:25 final size:25
Alignment explanation
Indices: 25683--25736 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
25673 GAAGGACTTG
25683 TGATCAACCAAAAAAAATATGTACT
1 TGATCAACCAAAAAAAATATGTACT
** *
25708 TGATTTACTAAAAAAAATATGTACT
1 TGATCAACCAAAAAAAATATGTACT
25733 TGAT
1 TGAT
25737 TTATTCAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.31
Consensus pattern (25 bp):
TGATCAACCAAAAAAAATATGTACT
Found at i:25737 original size:25 final size:25
Alignment explanation
Indices: 25692--25739 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
25682 GTGATCAACC
25692 AAAAAAAATATGTACTTGATTTACT
1 AAAAAAAATATGTACTTGATTTACT
25717 AAAAAAAATATGTACTTGATTTA
1 AAAAAAAATATGTACTTGATTTA
25740 TTCAAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.35
Consensus pattern (25 bp):
AAAAAAAATATGTACTTGATTTACT
Found at i:26572 original size:27 final size:27
Alignment explanation
Indices: 26530--26624 Score: 167
Period size: 27 Copynumber: 3.6 Consensus size: 27
26520 GTGTAGGAAT
26530 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
26555 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
26582 TATAGAGATATGATTTGTTACAATTCC
1 TATAGAGATATGATTTGTTACCATTCC
26609 TATAGAGATATGATTT
1 TATAGAGATATGATTT
26625 TGTAAATAGA
Statistics
Matches: 67, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
25 7 0.10
27 60 0.90
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.41
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:30361 original size:27 final size:27
Alignment explanation
Indices: 30319--30386 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
30309 GTGTATGAAT
30319 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
30344 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
30371 TATAGAGATATGATTT
1 TATAGAGATATGATTT
30387 TGTAAATAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 7 0.17
27 34 0.83
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:33816 original size:17 final size:17
Alignment explanation
Indices: 33790--33834 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
33780 TAAAATAAAT
33790 ATTTTTT-AAAGAGTAA
1 ATTTTTTAAAAGAGTAA
33806 ATTTGTTTAAAAGAGT--
1 ATTT-TTTAAAAGAGTAA
*
33822 ATTATTTAAAAGA
1 ATTTTTTAAAAGA
33835 ACACAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 9 0.35
16 7 0.27
17 3 0.12
18 7 0.27
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.42
Consensus pattern (17 bp):
ATTTTTTAAAAGAGTAA
Found at i:41991 original size:4 final size:4
Alignment explanation
Indices: 41984--42012 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
41974 CAAAACTAAC
41984 TCTT TCTT TCTT TCTT TCTT TCTT TCTT T
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT T
42013 TCGTCAATGT
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:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TCTT
Found at i:42417 original size:26 final size:26
Alignment explanation
Indices: 42359--42430 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 26
42349 CCTTATACAT
* *
42359 AATATTTA-TATTTAATAACTTATGG
1 AATATTTATTATTTTATAATTTATGG
42384 AATAATTTATTATTTTATAATTTAT-G
1 AAT-ATTTATTATTTTATAATTTATGG
*
42410 ATATATTTTTTATTTT-TAATT
1 A-ATATTTATTATTTTATAATT
42431 ATTCTTAGTA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
25 8 0.20
26 18 0.44
27 15 0.37
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.58
Consensus pattern (26 bp):
AATATTTATTATTTTATAATTTATGG
Found at i:50562 original size:37 final size:37
Alignment explanation
Indices: 50512--50586 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
50502 TCATACTGGC
50512 GCAAGATCAGATAGTTCCAACACCGATCGGAGAGAAG
1 GCAAGATCAGATAGTTCCAACACCGATCGGAGAGAAG
*
50549 GCAAGATCGGATAGTTCCAACACCGATCGGAGAGAAG
1 GCAAGATCAGATAGTTCCAACACCGATCGGAGAGAAG
50586 G
1 G
50587 TTTACTATGG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.36, C:0.21, G:0.29, T:0.13
Consensus pattern (37 bp):
GCAAGATCAGATAGTTCCAACACCGATCGGAGAGAAG
Found at i:51923 original size:37 final size:37
Alignment explanation
Indices: 51846--51926 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 37
51836 ACAAGTTTGG
**
51846 AAAATATTTATAGATTTTCTTTAAAAATTTTAATTCAT
1 AAAAT-TTTATAGATTTTCTTTAAAAATTGAAATTCAT
*
51884 AAAATTTATATA-ATTTTTTTTACAAAATTGAAATT-AT
1 AAAATTT-TATAGATTTTCTTTA-AAAATTGAAATTCAT
51921 AAAATT
1 AAAATT
51927 GTTTAATGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
37 19 0.50
38 19 0.50
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (37 bp):
AAAATTTTATAGATTTTCTTTAAAAATTGAAATTCAT
Found at i:54019 original size:36 final size:36
Alignment explanation
Indices: 53965--54075 Score: 172
Period size: 36 Copynumber: 3.1 Consensus size: 36
53955 CAACTTTAAA
53965 AAAATGG-TTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAATGGTTTTTCAAAGTTTGGTAAATGTTTCTTTG
54000 AAAATGGTTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAATGGTTTTTCAAAGTTTGGTAAATGTTTCTTTG
* * *
54036 AAAAATAGTTTTTCAAAGTTTGGTAGATGTTT-GTTG
1 -AAAATGGTTTTTCAAAGTTTGGTAAATGTTTCTTTG
54072 AAAA
1 AAAA
54076 ATGATAATAG
Statistics
Matches: 71, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
35 11 0.15
36 31 0.44
37 29 0.41
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.44
Consensus pattern (36 bp):
AAAATGGTTTTTCAAAGTTTGGTAAATGTTTCTTTG
Found at i:54343 original size:16 final size:16
Alignment explanation
Indices: 54322--54353 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
54312 ACTATTCACA
*
54322 TGAATAGTGAATTTCG
1 TGAATAGTGAAATTCG
54338 TGAATAGTGAAATTCG
1 TGAATAGTGAAATTCG
54354 GTCGGCGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.34
Consensus pattern (16 bp):
TGAATAGTGAAATTCG
Found at i:58511 original size:37 final size:37
Alignment explanation
Indices: 58419--58538 Score: 174
Period size: 36 Copynumber: 3.3 Consensus size: 37
58409 TGCTAACCAA
*
58419 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATA-GTTTTTCAAAGTTTGGTAAATGTTT
*
58456 CTTTG-AAAATGGTTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAAATGTTT
*
58492 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAAATGTTT
*
58529 -GTTGAAAAAT
1 CTTTGAAAAAT
58539 GATAATGGGA
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
36 42 0.55
37 34 0.45
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (37 bp):
CTTTGAAAAATAGTTTTTCAAAGTTTGGTAAATGTTT
Found at i:59784 original size:24 final size:25
Alignment explanation
Indices: 59739--59785 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
59729 TTTAAGAATT
*
59739 AAAAAAGAGGTTAAATTTATGATTG
1 AAAAAAGAGGTTAAATTCATGATTG
59764 AAAAAAGAGGTTAAA-TCATGAT
1 AAAAAAGAGGTTAAATTCATGAT
59786 AAACTAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.51, C:0.02, G:0.19, T:0.28
Consensus pattern (25 bp):
AAAAAAGAGGTTAAATTCATGATTG
Found at i:77653 original size:22 final size:23
Alignment explanation
Indices: 77622--77677 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
77612 TATATTAAAA
*
77622 TAAAAA-TGTTATAT-TATATTT
1 TAAAAATTGTTATATATATATAT
77643 TAAAAATTGTTA-ATATATATAT
1 TAAAAATTGTTATATATATATAT
*
77665 TAAATATT-TTATA
1 TAAAAATTGTTATA
77678 ATTCAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 11 0.37
22 19 0.63
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (23 bp):
TAAAAATTGTTATATATATATAT
Found at i:77659 original size:20 final size:21
Alignment explanation
Indices: 77622--77665 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
77612 TATATTAAAA
77622 TAAAAATGTTATATTATATTT
1 TAAAAATGTTATATTATATTT
77643 TAAAAATTGTTAATATATATATT
1 TAAAAA-TGTT-ATAT-TATATT
77666 AAATATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 6 0.30
22 4 0.20
23 4 0.20
24 6 0.30
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (21 bp):
TAAAAATGTTATATTATATTT
Found at i:81069 original size:15 final size:16
Alignment explanation
Indices: 81051--81103 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 16
81041 ATGATACTTC
81051 TGATGA-ACTTGAAAA
1 TGATGATACTTGAAAA
*
81066 TGATGATACTT----C
1 TGATGATACTTGAAAA
81078 TGATGA-ACTTGAAAA
1 TGATGATACTTGAAAA
81093 TGATGATACTT
1 TGATGATACTT
81104 CTGATGAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 11
0.70 0.05 0.26
Matches are distributed among these distances:
11 4 0.13
12 6 0.20
15 12 0.40
16 8 0.27
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (16 bp):
TGATGATACTTGAAAA
Found at i:81073 original size:27 final size:27
Alignment explanation
Indices: 81038--81126 Score: 153
Period size: 27 Copynumber: 3.3 Consensus size: 27
81028 CCTGCAAAAG
81038 ATGATGATACTTCTGATGAACTTGAAA
1 ATGATGATACTTCTGATGAACTTGAAA
81065 ATGATGATACTTCTGATGAACTTGAAA
1 ATGATGATACTTCTGATGAACTTGAAA
*
81092 ATGATGATACTTCTGATGAA-TTCGAAG
1 ATGATGATACTTCTGATGAACTT-GAAA
81119 ATGATGAT
1 ATGATGAT
81127 GATGAAACCT
Statistics
Matches: 60, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
26 2 0.03
27 58 0.97
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.34
Consensus pattern (27 bp):
ATGATGATACTTCTGATGAACTTGAAA
Found at i:91119 original size:28 final size:28
Alignment explanation
Indices: 91079--91159 Score: 144
Period size: 28 Copynumber: 2.9 Consensus size: 28
91069 GAATGACCAC
91079 TATGTCCCGAAGGACCACATAGAACACA
1 TATGTCCCGAAGGACCACATAGAACACA
*
91107 TATGTCCTGAAGGACCACATAGAACACA
1 TATGTCCCGAAGGACCACATAGAACACA
*
91135 TATGTCCCGAAAGACCACATAGAAC
1 TATGTCCCGAAGGACCACATAGAAC
91160 CCTCGACTCT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 50 1.00
ACGTcount: A:0.40, C:0.27, G:0.17, T:0.16
Consensus pattern (28 bp):
TATGTCCCGAAGGACCACATAGAACACA
Found at i:92505 original size:21 final size:21
Alignment explanation
Indices: 92481--92534 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
92471 TTGATGTTTA
92481 AAGCTTATATAAACTTTCCTT
1 AAGCTTATATAAACTTTCCTT
92502 AAGCTTATATAAACTTTCCTT
1 AAGCTTATATAAACTTTCCTT
92523 AAGCTTATATAA
1 AAGCTTATATAA
92535 CACCCAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.41
Consensus pattern (21 bp):
AAGCTTATATAAACTTTCCTT
Found at i:92674 original size:4 final size:4
Alignment explanation
Indices: 92665--92714 Score: 91
Period size: 4 Copynumber: 12.5 Consensus size: 4
92655 TAGACTTTTC
*
92665 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTCT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
92713 CT
1 CT
92715 CTTAATCCCA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (4 bp):
CTTT
Found at i:93006 original size:22 final size:21
Alignment explanation
Indices: 92976--93016 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
92966 TTTTTGTATT
* *
92976 ATATTATATTTTATATAAATAA
1 ATATCATA-TTTATAAAAATAA
92998 ATATCATATTTATAAAAAT
1 ATATCATATTTATAAAAAT
93017 TATTTAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
ATATCATATTTATAAAAATAA
Found at i:95058 original size:20 final size:20
Alignment explanation
Indices: 95030--95084 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
95020 TATTCGTTCG
*
95030 TTTATGTTTGTTTATATTCA
1 TTTACGTTTGTTTATATTCA
* *
95050 TTTACGTTTGTTTGTATTCG
1 TTTACGTTTGTTTATATTCA
95070 TTTACGTTTGTTTAT
1 TTTACGTTTGTTTAT
95085 TTGTATTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.15, C:0.07, G:0.15, T:0.64
Consensus pattern (20 bp):
TTTACGTTTGTTTATATTCA
Found at i:95061 original size:24 final size:23
Alignment explanation
Indices: 95034--95097 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 23
95024 CGTTCGTTTA
*
95034 TGTTTGTTTATATTCATTTACGTT
1 TGTTTGTTT-TATTCGTTTACGTT
95058 TGTTTG---TATTCGTTTACGTT
1 TGTTTGTTTTATTCGTTTACGTT
*
95078 TGTTTATTTGTATTCGTTTA
1 TGTTTGTTT-TATTCGTTTA
95098 TTATTTAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
20 18 0.53
24 16 0.47
ACGTcount: A:0.14, C:0.08, G:0.16, T:0.62
Consensus pattern (23 bp):
TGTTTGTTTTATTCGTTTACGTT
Found at i:97453 original size:17 final size:17
Alignment explanation
Indices: 97431--97463 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
97421 ACAACATGCA
97431 TCAAGGAGGTCATTGTG
1 TCAAGGAGGTCATTGTG
97448 TCAAGGAGGTCATTGT
1 TCAAGGAGGTCATTGT
97464 ACATGCGTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.12, G:0.33, T:0.30
Consensus pattern (17 bp):
TCAAGGAGGTCATTGTG
Found at i:98638 original size:25 final size:25
Alignment explanation
Indices: 98609--98687 Score: 122
Period size: 25 Copynumber: 3.2 Consensus size: 25
98599 AAGAGTTTAA
*
98609 AGATGAAAGGAATGTGTTGTGTAAG
1 AGATGAAAGGAGTGTGTTGTGTAAG
*
98634 AGATGAAAGGAGTGTGCTGTGTAAG
1 AGATGAAAGGAGTGTGTTGTGTAAG
* *
98659 AGATGAAAAGAGTGTGTTATGTAAG
1 AGATGAAAGGAGTGTGTTGTGTAAG
98684 AGAT
1 AGAT
98688 TGAATATAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 49 1.00
ACGTcount: A:0.37, C:0.01, G:0.35, T:0.27
Consensus pattern (25 bp):
AGATGAAAGGAGTGTGTTGTGTAAG
Found at i:99273 original size:17 final size:17
Alignment explanation
Indices: 99251--99306 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
99241 ACTATTATTT
99251 TAATTTTAAAAATAAAA
1 TAATTTTAAAAATAAAA
***
99268 TAA-TTTATTCATAATAA
1 TAATTTTAAAAATAA-AA
99285 T-ATTTTAAAAATAAAA
1 TAATTTTAAAAATAAAA
99301 TAATTT
1 TAATTT
99307 ATTTATAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
16 12 0.40
17 18 0.60
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
TAATTTTAAAAATAAAA
Found at i:99281 original size:16 final size:16
Alignment explanation
Indices: 99261--99314 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
99251 TAATTTTAAA
99261 AATAAAATAATTTATT
1 AATAAAATAATTTATT
* * **
99277 CATAATAATATTTTAAA
1 AATAA-AATAATTTATT
99294 AATAAAATAATTTATT
1 AATAAAATAATTTATT
*
99310 TATAA
1 AATAA
99315 TAAGTTATTC
Statistics
Matches: 28, Mismatches: 9, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
16 16 0.57
17 12 0.43
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
AATAAAATAATTTATT
Found at i:99295 original size:33 final size:33
Alignment explanation
Indices: 99253--99317 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
99243 TATTATTTTA
99253 ATTTTAAAAATAAAATAATTTATTCATAATAAT
1 ATTTTAAAAATAAAATAATTTATTCATAATAAT
*
99286 ATTTTAAAAATAAAATAATTTATTTATAATAA
1 ATTTTAAAAATAAAATAATTTATTCATAATAA
99318 GTTATTCAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (33 bp):
ATTTTAAAAATAAAATAATTTATTCATAATAAT
Found at i:99316 original size:19 final size:19
Alignment explanation
Indices: 99256--99317 Score: 53
Period size: 19 Copynumber: 3.5 Consensus size: 19
99246 TATTTTAATT
*
99256 TTAAAAATAAAATAATTTA
1 TTAATAATAAAATAATTTA
*
99275 TTCATAAT--AAT-A-TT-
1 TTAATAATAAAATAATTTA
*
99289 TTAAAAATAAAATAATTTA
1 TTAATAATAAAATAATTTA
*
99308 TTTATAATAA
1 TTAATAATAA
99318 GTTATTCAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
14 6 0.19
15 2 0.06
16 4 0.12
17 4 0.12
18 2 0.06
19 14 0.44
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
TTAATAATAAAATAATTTA
Found at i:107877 original size:32 final size:33
Alignment explanation
Indices: 107813--107877 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
107803 GCAGACTATG
*
107813 CTGCTTGAATCCGAGTCACCATTGGAGAATAAA
1 CTGCTTGAATCCGAGTCACCATGGGAGAATAAA
*
107846 CTGCTTGAATCCGGGAT-ACCA-GGGAGAATAAA
1 CTGCTTGAATCCGAG-TCACCATGGGAGAATAAA
107878 ATTTGCTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 10 0.34
33 18 0.62
34 1 0.03
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.22
Consensus pattern (33 bp):
CTGCTTGAATCCGAGTCACCATGGGAGAATAAA
Found at i:108163 original size:32 final size:33
Alignment explanation
Indices: 108099--108163 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
108089 GCAGACTATG
*
108099 CTGCTTGAATCCGAGTCACCATTGGAGAATAAA
1 CTGCTTGAATCCGAGTCACCATGGGAGAATAAA
*
108132 CTGCTTGAATCCGGGAT-ACCA-GGGAGAATAAA
1 CTGCTTGAATCCGAG-TCACCATGGGAGAATAAA
108164 ATTTGCTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 10 0.34
33 18 0.62
34 1 0.03
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.22
Consensus pattern (33 bp):
CTGCTTGAATCCGAGTCACCATGGGAGAATAAA
Found at i:108305 original size:286 final size:286
Alignment explanation
Indices: 107793--108367 Score: 1132
Period size: 286 Copynumber: 2.0 Consensus size: 286
107783 ATCTAAACTC
107793 ACACACACGTGCAGACTATGCTGCTTGAATCCGAGTCACCATTGGAGAATAAACTGCTTGAATCC
1 ACACACACGTGCAGACTATGCTGCTTGAATCCGAGTCACCATTGGAGAATAAACTGCTTGAATCC
107858 GGGATACCAGGGAGAATAAAATTTGCTTTTACAACTTAGACCACTTAAAAGGTTCTAATTTCAGA
66 GGGATACCAGGGAGAATAAAATTTGCTTTTACAACTTAGACCACTTAAAAGGTTCTAATTTCAGA
107923 TTCTTGAATGAGAGATACAAGGTGATTTTTTCCTCTTCAAAATAAGCCATAGTTTGGGATCTGAA
131 TTCTTGAATGAGAGATACAAGGTGATTTTTTCCTCTTCAAAATAAGCCATAGTTTGGGATCTGAA
107988 TCGCATGGGTCACTCTTACTTCAATAAGCTCTATGGAATCATGCATGACGAAGAGTCAAACCTGG
196 TCGCATGGGTCACTCTTACTTCAATAAGCTCTATGGAATCATGCATGACGAAGAGTCAAACCTGG
108053 AATTATATCTAAAAAATAGAATTACA
261 AATTATATCTAAAAAATAGAATTACA
108079 ACACACACGTGCAGACTATGCTGCTTGAATCCGAGTCACCATTGGAGAATAAACTGCTTGAATCC
1 ACACACACGTGCAGACTATGCTGCTTGAATCCGAGTCACCATTGGAGAATAAACTGCTTGAATCC
108144 GGGATACCAGGGAGAATAAAATTTGCTTTTACAACTTAGACCACTTAAAAGGTTCTAATTTCAGA
66 GGGATACCAGGGAGAATAAAATTTGCTTTTACAACTTAGACCACTTAAAAGGTTCTAATTTCAGA
* *
108209 TTCTTGAATGAGAGATACACGGTGATTTTTTCCTCTTCAAAATGAGCCATAGTTTGGGATCTGAA
131 TTCTTGAATGAGAGATACAAGGTGATTTTTTCCTCTTCAAAATAAGCCATAGTTTGGGATCTGAA
108274 TCGCATGGGTCACTCTTACTTCAATAAGCTCTATGGAATCATGCATGACGAAGAGTCAAACCTGG
196 TCGCATGGGTCACTCTTACTTCAATAAGCTCTATGGAATCATGCATGACGAAGAGTCAAACCTGG
108339 AATTATATCTAAAAAATAGAATTACA
261 AATTATATCTAAAAAATAGAATTACA
108365 ACA
1 ACA
108368 GCTATACTTA
Statistics
Matches: 287, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
286 287 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (286 bp):
ACACACACGTGCAGACTATGCTGCTTGAATCCGAGTCACCATTGGAGAATAAACTGCTTGAATCC
GGGATACCAGGGAGAATAAAATTTGCTTTTACAACTTAGACCACTTAAAAGGTTCTAATTTCAGA
TTCTTGAATGAGAGATACAAGGTGATTTTTTCCTCTTCAAAATAAGCCATAGTTTGGGATCTGAA
TCGCATGGGTCACTCTTACTTCAATAAGCTCTATGGAATCATGCATGACGAAGAGTCAAACCTGG
AATTATATCTAAAAAATAGAATTACA
Found at i:118053 original size:15 final size:15
Alignment explanation
Indices: 118035--118064 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
118025 CCACGGTGCT
118035 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
118050 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
118065 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:125471 original size:60 final size:60
Alignment explanation
Indices: 125405--125518 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
125395 AATTGTCCCT
** * *
125405 TGACTATAGGGTATTGCTTTATTTAGTCTATTGACTATTAAAAGTTACAAAATGATCTTA
1 TGACTATAGAATATTGCTCTATTGAGTCTATTGACTATTAAAAGTTACAAAATGATCTTA
* * *
125465 TGACTATAGAATGTTGCTCTGTTGAGTCTCTTGACTATTAAAAGTTACAAAATG
1 TGACTATAGAATATTGCTCTATTGAGTCTATTGACTATTAAAAGTTACAAAATG
125519 GTCACCCAAC
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 47 1.00
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.39
Consensus pattern (60 bp):
TGACTATAGAATATTGCTCTATTGAGTCTATTGACTATTAAAAGTTACAAAATGATCTTA
Found at i:126364 original size:20 final size:20
Alignment explanation
Indices: 126336--126380 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
126326 GATCAATATT
*
126336 GATACTGAT-TGAAGAGTATC
1 GATATTGATGTGAAG-GTATC
*
126356 GATATTGATGTGGAGGTATC
1 GATATTGATGTGAAGGTATC
126376 GATAT
1 GATAT
126381 CAAGAGGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.31, C:0.07, G:0.29, T:0.33
Consensus pattern (20 bp):
GATATTGATGTGAAGGTATC
Found at i:129220 original size:44 final size:43
Alignment explanation
Indices: 129171--129268 Score: 126
Period size: 43 Copynumber: 2.3 Consensus size: 43
129161 TGGTATATGG
* *
129171 TTATGGAATAATGACAAGTGTATTGGTAAAATAAGCTTACGAGC
1 TTATGGAATAATGACAAGTATATCGGT-AAATAAGCTTACGAGC
**
129215 TTATGGACA-AATGGTAAGTATATCGGTAAATAAGCTTACGAGC
1 TTATGGA-ATAATGACAAGTATATCGGTAAATAAGCTTACGAGC
*
129258 TTATGGGATAA
1 TTATGGAATAA
129269 ATGGTAAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
42 1 0.02
43 24 0.51
44 21 0.45
45 1 0.02
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.30
Consensus pattern (43 bp):
TTATGGAATAATGACAAGTATATCGGTAAATAAGCTTACGAGC
Found at i:129887 original size:19 final size:19
Alignment explanation
Indices: 129859--129901 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
129849 TTAAGAAAAT
*
129859 AAATTTTAAATCACTTTT-G
1 AAATTGTAAAT-ACTTTTAG
*
129878 AAATTGTAAATAGTTTTAG
1 AAATTGTAAATACTTTTAG
129897 AAATT
1 AAATT
129902 CGGGTGACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (19 bp):
AAATTGTAAATACTTTTAG
Found at i:130096 original size:23 final size:23
Alignment explanation
Indices: 129984--130082 Score: 171
Period size: 23 Copynumber: 4.3 Consensus size: 23
129974 TCAAGGGTTT
* * *
129984 TATGTGGTCCTTTGAGACAAATC
1 TATGTGGTCCTTCGGGACAAACC
130007 TATGTGGTCCTTCGGGACAAACC
1 TATGTGGTCCTTCGGGACAAACC
130030 TATGTGGTCCTTCGGGACAAACC
1 TATGTGGTCCTTCGGGACAAACC
130053 TATGTGGTCCTTCGGGACAAACC
1 TATGTGGTCCTTCGGGACAAACC
130076 TATGTGG
1 TATGTGG
130083 CACTTTGGTG
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 73 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.29
Consensus pattern (23 bp):
TATGTGGTCCTTCGGGACAAACC
Found at i:131331 original size:59 final size:60
Alignment explanation
Indices: 131255--131368 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
131245 CCCAGGTGAC
*
131255 CATTTTGTAACTGTTAATAGTCG-GGGACTTAACAAAACAACATTC-TATAGTCGAAGAAT
1 CATTTTATAACTGTTAATAGTCGAGGGACTTAACAAAACAACA-TCATATAGTCGAAGAAT
* * * *
131314 CATTTTATAACTTTTAATAGTCGAGGGTCTTAATAAAACAATATCATATAGTCGA
1 CATTTTATAACTGTTAATAGTCGAGGGACTTAACAAAACAACATCATATAGTCGA
131369 GGGACCATTC
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 23 0.48
60 25 0.52
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (60 bp):
CATTTTATAACTGTTAATAGTCGAGGGACTTAACAAAACAACATCATATAGTCGAAGAAT
Found at i:131387 original size:60 final size:59
Alignment explanation
Indices: 131253--131387 Score: 139
Period size: 60 Copynumber: 2.3 Consensus size: 59
131243 AACCCAGGTG
** *
131253 ACCATTTTGTAACTGTTAATAGTCGGGGACTTAACAAAACAACATTCTATAGTCGAAGA
1 ACCATTTCATAACTTTTAATAGTCGGGGACTTAACAAAACAACATTCTATAGTCGAAGA
* * * * * * *
131312 ATCATTTTATAACTTTTAATAGTCGAGGGTCTTAATAAAACAATA-TCATATAGTCGAGGG
1 ACCATTTCATAACTTTTAATAGTCG-GGGACTTAACAAAACAACATTC-TATAGTCGAAGA
131372 ACCA-TTCATACACTTT
1 ACCATTTCATA-ACTTT
131388 ACCCTAAATA
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
59 29 0.46
60 34 0.54
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (59 bp):
ACCATTTCATAACTTTTAATAGTCGGGGACTTAACAAAACAACATTCTATAGTCGAAGA
Found at i:132852 original size:17 final size:18
Alignment explanation
Indices: 132832--132865 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
132822 ACATTTATCG
*
132832 TTTTAGTTGTTT-TAATA
1 TTTTAATTGTTTGTAATA
132849 TTTTAATTGTTTGTAAT
1 TTTTAATTGTTTGTAAT
132866 GCGAATGGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.65
Consensus pattern (18 bp):
TTTTAATTGTTTGTAATA
Done.