Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001704.1 Hibiscus syriacus cultivar Beakdansim tig00003418_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: 79354
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:3883 original size:15 final size:15
Alignment explanation
Indices: 3863--3892 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3853 CAATTTATGC
3863 CTCTAAATTAGAAAA
1 CTCTAAATTAGAAAA
*
3878 CTCTAAGTTAGAAAA
1 CTCTAAATTAGAAAA
3893 GATACTAATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.13, G:0.10, T:0.27
Consensus pattern (15 bp):
CTCTAAATTAGAAAA
Found at i:6192 original size:15 final size:16
Alignment explanation
Indices: 6172--6213 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
6162 ACAAGAAAAC
*
6172 AAAAAAAGTAA-ATGA
1 AAAAAAAGTAAGATAA
*
6187 AAAAAAATTAAGATAA
1 AAAAAAAGTAAGATAA
6203 AAGAAAAAGTA
1 AA-AAAAAGTA
6214 TTTATCTTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 10 0.45
16 5 0.23
17 7 0.32
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.14
Consensus pattern (16 bp):
AAAAAAAGTAAGATAA
Found at i:8502 original size:6 final size:6
Alignment explanation
Indices: 8485--8809 Score: 486
Period size: 6 Copynumber: 56.3 Consensus size: 6
8475 CATTCATAGG
8485 TGTATA TG--TA TGTATA TGTATA --TATA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
8529 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TG--TATA TGTATA
*
8579 TGTATA TGTATA TGTGTA TG--TA TGTATA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
8625 TGTATA TG--TA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
8671 TGTATA TGTATA TG--TA TGTATA TG--TA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
8715 TGTATATA TGTATA TG--TA TGTATA TGTATA --TATA TGTATA TGTATA
1 TG--TATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
8761 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA -GTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
8808 TG
1 TG
8810 CATTAAACCT
Statistics
Matches: 297, Mismatches: 1, Indels: 42
0.87 0.00 0.12
Matches are distributed among these distances:
4 32 0.11
5 5 0.02
6 248 0.84
8 12 0.04
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
TGTATA
Found at i:10534 original size:29 final size:30
Alignment explanation
Indices: 10480--10539 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
10470 CTCCTAAAAA
*
10480 TAAATTTGAAAACTCTTATTTTCTTA-TGT
1 TAAATTTGAAAACTCTTATTTGCTTACTGT
*
10509 TAAATTTGAAAACT-TTCTTCTGCTTACTGT
1 TAAATTTGAAAACTCTTATT-TGCTTACTGT
10539 T
1 T
10540 TAGTGGTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 4 0.15
29 19 0.70
30 4 0.15
ACGTcount: A:0.28, C:0.13, G:0.08, T:0.50
Consensus pattern (30 bp):
TAAATTTGAAAACTCTTATTTGCTTACTGT
Found at i:10683 original size:7 final size:7
Alignment explanation
Indices: 10667--10699 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
10657 TATGGCTTTT
10667 CTTA-TG
1 CTTACTG
10673 CTTACTG
1 CTTACTG
10680 CTTACTG
1 CTTACTG
10687 CTTACTG
1 CTTACTG
10694 CTTACT
1 CTTACT
10700 TATTGCACGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.15
7 22 0.85
ACGTcount: A:0.15, C:0.27, G:0.12, T:0.45
Consensus pattern (7 bp):
CTTACTG
Found at i:10814 original size:17 final size:17
Alignment explanation
Indices: 10793--10847 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
10783 ATATGTTTAT
10793 TGATAGAATATATGTTC
1 TGATAGAATATATGTTC
* * * *
10810 CGATAAAATAT-TTTTT
1 TGATAGAATATATGTTC
*
10826 TTATAGAATATATGTTC
1 TGATAGAATATATGTTC
10843 TGATA
1 TGATA
10848 TGTTTATTTG
Statistics
Matches: 27, Mismatches: 10, Indels: 2
0.69 0.26 0.05
Matches are distributed among these distances:
16 11 0.41
17 16 0.59
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.45
Consensus pattern (17 bp):
TGATAGAATATATGTTC
Found at i:10885 original size:17 final size:17
Alignment explanation
Indices: 10865--10909 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
10855 TTGGATAATT
10865 TATATTTTTTGATAGAA
1 TATATTTTTTGATAGAA
* *
10882 TATATGTTGTGATAGAA
1 TATATTTTTTGATAGAA
10899 T-TATTTGTTTG
1 TATATTT-TTTG
10910 CATGAATAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (17 bp):
TATATTTTTTGATAGAA
Found at i:10979 original size:17 final size:17
Alignment explanation
Indices: 10939--10982 Score: 56
Period size: 15 Copynumber: 2.7 Consensus size: 17
10929 CATGAAATCA
10939 ATGAATATATGTACTGC
1 ATGAATATATGTACTGC
*
10956 ATG--TATATGTTCTGC
1 ATGAATATATGTACTGC
*
10971 GTGAATATATGT
1 ATGAATATATGT
10983 GTTTAGTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 13 0.57
17 10 0.43
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (17 bp):
ATGAATATATGTACTGC
Found at i:11640 original size:15 final size:15
Alignment explanation
Indices: 11622--11763 Score: 83
Period size: 15 Copynumber: 9.5 Consensus size: 15
11612 CAAAACCAGT
*
11622 TGAACCAGAAATTAG
1 TGAACCAGAAATTAA
*
11637 TGAACCCGAAATTAA
1 TGAACCAGAAATTAA
* *
11652 TGAACCAG-AACTAGT
1 TGAACCAGAAATTA-A
* *
11667 TGAGCCTGAAATTAA
1 TGAACCAGAAATTAA
** *
11682 TGAACCA-AAACCAGC
1 TGAACCAGAAATTA-A
*
11697 TGAGCCAGAAATTAA
1 TGAACCAGAAATTAA
** *
11712 TGAACCAG-AACCAGC
1 TGAACCAGAAATTA-A
* *
11727 CGAGCCAGAAATTAA
1 TGAACCAGAAATTAA
* *
11742 TGAACCTGAAATTGA
1 TGAACCAGAAATTAA
11757 TGAACCA
1 TGAACCA
11764 TAACCTGTTG
Statistics
Matches: 89, Mismatches: 32, Indels: 12
0.67 0.24 0.09
Matches are distributed among these distances:
14 11 0.12
15 67 0.75
16 11 0.12
ACGTcount: A:0.44, C:0.20, G:0.18, T:0.18
Consensus pattern (15 bp):
TGAACCAGAAATTAA
Found at i:11656 original size:30 final size:31
Alignment explanation
Indices: 11622--11752 Score: 153
Period size: 30 Copynumber: 4.4 Consensus size: 31
11612 CAAAACCAGT
* * *
11622 TGAACCAGAAATTAG-TGAACCCGAAATTAA
1 TGAACCAGAAACTAGCTGAGCCAGAAATTAA
* *
11652 TGAACCAG-AACTAGTTGAGCCTGAAATTAA
1 TGAACCAGAAACTAGCTGAGCCAGAAATTAA
*
11682 TGAACCA-AAACCAGCTGAGCCAGAAATTAA
1 TGAACCAGAAACTAGCTGAGCCAGAAATTAA
* *
11712 TGAACCAG-AACCAGCCGAGCCAGAAATTAA
1 TGAACCAGAAACTAGCTGAGCCAGAAATTAA
*
11742 TGAACCTGAAA
1 TGAACCAGAAA
11753 TTGATGAACC
Statistics
Matches: 89, Mismatches: 8, Indels: 7
0.86 0.08 0.07
Matches are distributed among these distances:
29 5 0.06
30 82 0.92
31 2 0.02
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.17
Consensus pattern (31 bp):
TGAACCAGAAACTAGCTGAGCCAGAAATTAA
Found at i:11687 original size:45 final size:45
Alignment explanation
Indices: 11589--11687 Score: 117
Period size: 45 Copynumber: 2.2 Consensus size: 45
11579 GGTCTGAACA
** * *
11589 TAATGAACATGAAATTGATGAAGCAAAACCAGTTGAACCAGAAAT
1 TAATGAACCCGAAATTAATGAACCAAAACCAGTTGAACCAGAAAT
* * * * *
11634 TAGTGAACCCGAAATTAATGAACCAGAACTAGTTGAGCCTGAAAT
1 TAATGAACCCGAAATTAATGAACCAAAACCAGTTGAACCAGAAAT
11679 TAATGAACC
1 TAATGAACC
11688 AAAACCAGCT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.44, C:0.16, G:0.18, T:0.21
Consensus pattern (45 bp):
TAATGAACCCGAAATTAATGAACCAAAACCAGTTGAACCAGAAAT
Found at i:11735 original size:75 final size:75
Alignment explanation
Indices: 11589--11768 Score: 184
Period size: 75 Copynumber: 2.4 Consensus size: 75
11579 GGTCTGAACA
* * * * * ** *
11589 TAATGAACATGAAATTGATGAAGCAAAACCAGTTGAACCAGAAATTAGTGAACCCGAAATTAATG
1 TAATGAACCTGAAATTGATGAACCAAAACCAGCTGAACCAGAAATTAATGAACCAGAAACCAACG
11654 AACCAG-AAC
66 AACCAGAAAC
* * * * *
11663 TAGTTGAGCCTGAAATTAATGAACCAAAACCAGCTGAGCCAGAAATTAATGAACCAG-AACCAGC
1 TA-ATGAACCTGAAATTGATGAACCAAAACCAGCTGAACCAGAAATTAATGAACCAGAAACCA-A
* *
11727 CGAGCCAGAAAT
64 CGAACCAGAAAC
*
11739 TAATGAACCTGAAATTGATGAACCATAACC
1 TAATGAACCTGAAATTGATGAACCAAAACC
11769 TGTTGAGGTG
Statistics
Matches: 84, Mismatches: 19, Indels: 5
0.78 0.18 0.05
Matches are distributed among these distances:
74 5 0.06
75 75 0.89
76 4 0.05
ACGTcount: A:0.44, C:0.19, G:0.18, T:0.18
Consensus pattern (75 bp):
TAATGAACCTGAAATTGATGAACCAAAACCAGCTGAACCAGAAATTAATGAACCAGAAACCAACG
AACCAGAAAC
Found at i:13692 original size:26 final size:25
Alignment explanation
Indices: 13663--13745 Score: 87
Period size: 26 Copynumber: 3.2 Consensus size: 25
13653 ATGCTTAGTA
13663 TTATTACATATTGTTACTAT-ATAATG
1 TTATTACATATTGTT-C-ATCATAATG
* *
13689 TTATTGCATATTGTTCATGCATACTG
1 TTATTACATATTGTTCAT-CATAATG
* *
13715 TTATTACATGTTGTTCATGCATACTG
1 TTATTACATATTGTTCAT-CATAATG
13741 TTATT
1 TTATT
13746 GTATATTAGA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
24 2 0.04
25 1 0.02
26 48 0.94
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.49
Consensus pattern (25 bp):
TTATTACATATTGTTCATCATAATG
Found at i:13703 original size:13 final size:13
Alignment explanation
Indices: 13663--13752 Score: 58
Period size: 13 Copynumber: 6.9 Consensus size: 13
13653 ATGCTTAGTA
*
13663 TTATTACATATTG
1 TTATTGCATATTG
* ** *
13676 TTACTATATAATG
1 TTATTGCATATTG
13689 TTATTGCATATTG
1 TTATTGCATATTG
*
13702 TTCA-TGCATACTG
1 TT-ATTGCATATTG
* *
13715 TTATTACATGTTG
1 TTATTGCATATTG
*
13728 TTCA-TGCATACTG
1 TT-ATTGCATATTG
*
13741 TTATTGTATATT
1 TTATTGCATATT
13753 AGAATAATTG
Statistics
Matches: 57, Mismatches: 16, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
12 2 0.04
13 53 0.93
14 2 0.04
ACGTcount: A:0.27, C:0.11, G:0.12, T:0.50
Consensus pattern (13 bp):
TTATTGCATATTG
Found at i:14516 original size:14 final size:15
Alignment explanation
Indices: 14483--14565 Score: 51
Period size: 16 Copynumber: 5.3 Consensus size: 15
14473 TGTATTTGTT
*
14483 TTTTTATTGAGTTTG
1 TTTTTATTGAATTTG
*
14498 TTTTTCTTGAATTTG
1 TTTTTATTGAATTTG
* * *
14513 TTTTAGACTGACTTTG
1 TTTT-TATTGAATTTG
* *
14529 -TTTTAGCTTGTATTTA
1 TTTTTA--TTGAATTTG
*
14545 TTTTAGATTGAATTTG
1 TTTT-TATTGAATTTG
14561 TTTTT
1 TTTTT
14566 TATTATAGTT
Statistics
Matches: 48, Mismatches: 15, Indels: 10
0.66 0.21 0.14
Matches are distributed among these distances:
14 1 0.02
15 20 0.42
16 23 0.48
17 3 0.06
18 1 0.02
ACGTcount: A:0.17, C:0.05, G:0.16, T:0.63
Consensus pattern (15 bp):
TTTTTATTGAATTTG
Found at i:14530 original size:16 final size:15
Alignment explanation
Indices: 14508--14564 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 15
14498 TTTTTCTTGA
14508 ATTTGTTTTAGACTG
1 ATTTGTTTTAGACTG
14523 ACTTTGTTTTAG-CTTG
1 A-TTTGTTTTAGAC-TG
* *
14539 TATTTATTTTAGATTG
1 -ATTTGTTTTAGACTG
14555 AATTTGTTTT
1 -ATTTGTTTT
14565 TTATTATAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
15 2 0.06
16 31 0.91
17 1 0.03
ACGTcount: A:0.19, C:0.05, G:0.16, T:0.60
Consensus pattern (15 bp):
ATTTGTTTTAGACTG
Found at i:14561 original size:32 final size:31
Alignment explanation
Indices: 14488--14564 Score: 91
Period size: 32 Copynumber: 2.5 Consensus size: 31
14478 TTGTTTTTTT
* * *
14488 ATTGAGTTTGTTTTTCTTGAATTTGTTTTAG
1 ATTGAATTTGTTTTGCTTGAATTTATTTTAG
* * *
14519 ACTGACTTTGTTTTAGCTTGTATTTATTTTAG
1 ATTGAATTTGTTTT-GCTTGAATTTATTTTAG
14551 ATTGAATTTGTTTT
1 ATTGAATTTGTTTT
14565 TTATTATAGT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 12 0.32
32 26 0.68
ACGTcount: A:0.18, C:0.05, G:0.17, T:0.60
Consensus pattern (31 bp):
ATTGAATTTGTTTTGCTTGAATTTATTTTAG
Found at i:16085 original size:18 final size:18
Alignment explanation
Indices: 16059--16133 Score: 96
Period size: 18 Copynumber: 3.9 Consensus size: 18
16049 AGGGTTATAC
16059 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
16077 AGTGATCCTTCGGGACATAT
1 AGTGGTCCTTCGGGAC--AT
*
16097 ACAGTGGTCCTTCGGGATAT
1 --AGTGGTCCTTCGGGACAT
16117 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
16134 AATATTCAGT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
18 31 0.63
20 4 0.08
22 14 0.29
ACGTcount: A:0.20, C:0.21, G:0.31, T:0.28
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:16098 original size:40 final size:40
Alignment explanation
Indices: 16054--16133 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
16044 AGTCGAGGGT
16054 TATACAGTGGTCCTTCGGGACATAGTGATCCTTCGGGACA
1 TATACAGTGGTCCTTCGGGACATAGTGATCCTTCGGGACA
* *
16094 TATACAGTGGTCCTTCGGGATATAGTGGTCCTTCGGGACA
1 TATACAGTGGTCCTTCGGGACATAGTGATCCTTCGGGACA
16134 AATATTCAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (40 bp):
TATACAGTGGTCCTTCGGGACATAGTGATCCTTCGGGACA
Found at i:16736 original size:22 final size:22
Alignment explanation
Indices: 16711--16756 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
16701 TGTAGCAGTA
*
16711 CTGTAGTAGGGGAATCGGCTCC
1 CTGTAGCAGGGGAATCGGCTCC
*
16733 CTGTAGCAGGGGAATCGGTTCC
1 CTGTAGCAGGGGAATCGGCTCC
16755 CT
1 CT
16757 ATTTGCAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.17, C:0.24, G:0.35, T:0.24
Consensus pattern (22 bp):
CTGTAGCAGGGGAATCGGCTCC
Found at i:16825 original size:22 final size:22
Alignment explanation
Indices: 16800--16843 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
16790 TGTAGCAGGG
*
16800 TATTGTTCACGGTACTGTTCAT
1 TATTGTTCACGATACTGTTCAT
*
16822 TATTGTTCACGATATTGTTCAT
1 TATTGTTCACGATACTGTTCAT
16844 ACCGTATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.48
Consensus pattern (22 bp):
TATTGTTCACGATACTGTTCAT
Found at i:20219 original size:50 final size:50
Alignment explanation
Indices: 20160--20258 Score: 180
Period size: 50 Copynumber: 2.0 Consensus size: 50
20150 GACGTAAGTT
*
20160 AATTCATATTAGGAGCAAGAATGATTTCTATAAAGAATAAAGTGATGTGC
1 AATTCATATTAGGAGCAAGAATGATTTCTATAAAGAAAAAAGTGATGTGC
*
20210 AATTCATATTAGGAGCAAGAATGATTTCTATAAAGAAAAAAGTGTTGTG
1 AATTCATATTAGGAGCAAGAATGATTTCTATAAAGAAAAAAGTGATGTG
20259 ATAATTAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.42, C:0.07, G:0.20, T:0.30
Consensus pattern (50 bp):
AATTCATATTAGGAGCAAGAATGATTTCTATAAAGAAAAAAGTGATGTGC
Found at i:21179 original size:20 final size:20
Alignment explanation
Indices: 21151--21196 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
21141 AAATGGATTT
* *
21151 ATTTAGTGACCAAATTATAA
1 ATTTGGTGACCAAAGTATAA
21171 ATTTGGTGACCAAAGTATAA
1 ATTTGGTGACCAAAGTATAA
21191 ACTTTG
1 A-TTTG
21197 AAAAGTTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (20 bp):
ATTTGGTGACCAAAGTATAA
Found at i:22447 original size:24 final size:24
Alignment explanation
Indices: 22420--22465 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
22410 GCATGACATG
22420 GTACATAAATGTGTTATACATCGT
1 GTACATAAATGTGTTATACATCGT
* *
22444 GTACATAGATGTTTTATACATC
1 GTACATAAATGTGTTATACATC
22466 ATCTGGAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (24 bp):
GTACATAAATGTGTTATACATCGT
Found at i:23260 original size:22 final size:22
Alignment explanation
Indices: 23235--23279 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
23225 GCATTGGTAT
*
23235 ATTGTTCACGGTAATGTTCATC
1 ATTGTTCACGGTAATGTGCATC
*
23257 ATTGTTCACGGTACTGTGCATC
1 ATTGTTCACGGTAATGTGCATC
23279 A
1 A
23280 CTATTCATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (22 bp):
ATTGTTCACGGTAATGTGCATC
Found at i:23286 original size:22 final size:22
Alignment explanation
Indices: 23239--23286 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
23229 TGGTATATTG
* * *
23239 TTCACGGTAATGTTCATCATTG
1 TTCACGGTAATGTGCATCACTA
*
23261 TTCACGGTACTGTGCATCACTA
1 TTCACGGTAATGTGCATCACTA
23283 TTCA
1 TTCA
23287 TAAAATAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.38
Consensus pattern (22 bp):
TTCACGGTAATGTGCATCACTA
Found at i:23967 original size:18 final size:17
Alignment explanation
Indices: 23939--23972 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
23929 ATAACGAGAA
*
23939 TTAAGTTTTCTTTAAGT
1 TTAAGTTTTCTCTAAGT
23956 TTAAGTTTTTCTCTAAG
1 TTAAG-TTTTCTCTAAG
23973 ATTATTTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.24, C:0.09, G:0.12, T:0.56
Consensus pattern (17 bp):
TTAAGTTTTCTCTAAGT
Found at i:27673 original size:11 final size:11
Alignment explanation
Indices: 27659--27684 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
27649 TTTTCGTTCT
27659 TTTTATTTTTA
1 TTTTATTTTTA
27670 TTTTATTTTTA
1 TTTTATTTTTA
27681 TTTT
1 TTTT
27685 TTCCTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:27685 original size:18 final size:17
Alignment explanation
Indices: 27658--27697 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
27648 ATTTTCGTTC
*
27658 TTTTTATTTTTATTTTA
1 TTTTTATTTTTACTTTA
*
27675 TTTTTATTTTTTCCTTTA
1 TTTTTA-TTTTTACTTTA
27693 TTTTT
1 TTTTT
27698 TGGAGTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.12, C:0.05, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTATTTTTACTTTA
Found at i:38053 original size:2 final size:2
Alignment explanation
Indices: 38046--38102 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
38036 GTGTATCTTT
38046 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38088 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
38103 GAAGGAATTC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:38820 original size:42 final size:42
Alignment explanation
Indices: 38773--38955 Score: 192
Period size: 42 Copynumber: 4.4 Consensus size: 42
38763 TACTTTATTA
38773 GCGTTTTTGTAATAAACACCGCAATAGTCATACACCTTAGTG
1 GCGTTTTTGTAATAAACACCGCAATAGTCATACACCTTAGTG
* **
38815 GCGTTTTT-TAATAAACACCGCAATAGTGATGTACCTTAGTG
1 GCGTTTTTGTAATAAACACCGCAATAGTCATACACCTTAGTG
* * ** * *
38856 GCGTCTTTGTGATAAATGCCACAATAGTCATGA-ATCTTAGTG
1 GCGTTTTTGTAATAAACACCGCAATAGTCAT-ACACCTTAGTG
* ** * * *
38898 GTGTTTTTGTAATGGACGCCGCAACAGTCATACACTTTAGTG
1 GCGTTTTTGTAATAAACACCGCAATAGTCATACACCTTAGTG
*
38940 ACG-TTTTGTAATAAAC
1 GCGTTTTTGTAATAAAC
38956 GTCGCACCAG
Statistics
Matches: 113, Mismatches: 25, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
41 49 0.43
42 64 0.57
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (42 bp):
GCGTTTTTGTAATAAACACCGCAATAGTCATACACCTTAGTG
Found at i:38979 original size:41 final size:42
Alignment explanation
Indices: 38774--38979 Score: 161
Period size: 41 Copynumber: 5.0 Consensus size: 42
38764 ACTTTATTAG
* * * *
38774 CGTTTTTGTAATAAACACCGCAATAGTCAT-ACACCTTAGTGG
1 CGTTTTTGTAATAAACGCCGCAACAGTCATGA-ATCTTAGTGA
* * * * * *
38816 CGTTTTT-TAATAAACACCGCAATAGTGATGTACCTTAGTGG
1 CGTTTTTGTAATAAACGCCGCAACAGTCATGAATCTTAGTGA
* * * * * *
38857 CGTCTTTGTGATAAATGCCACAATAGTCATGAATCTTAGTGG
1 CGTTTTTGTAATAAACGCCGCAACAGTCATGAATCTTAGTGA
* **
38899 TGTTTTTGTAATGGACGCCGCAACAGTCAT-ACA-CTTTAGTGA
1 CGTTTTTGTAATAAACGCCGCAACAGTCATGA-ATC-TTAGTGA
* *
38941 CG-TTTTGTAATAAACGTCGCACCAGTCATGAATCTTAGT
1 CGTTTTTGTAATAAACGCCGCAACAGTCATGAATCTTAGT
38980 TTTGTACAAT
Statistics
Matches: 134, Mismatches: 24, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
41 68 0.51
42 66 0.49
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (42 bp):
CGTTTTTGTAATAAACGCCGCAACAGTCATGAATCTTAGTGA
Found at i:47138 original size:54 final size:54
Alignment explanation
Indices: 47054--47186 Score: 212
Period size: 54 Copynumber: 2.4 Consensus size: 54
47044 AGTGTACCGA
*
47054 TACACATGAGATGTACTGATACACTAGGTCAACTAACGGTCAAAATATTTGAATTT
1 TACAC-TGAG-TGTACCGATACACTAGGTCAACTAACGGTCAAAATATTTGAATTT
* *
47110 TACACTGAGTGTACCGATACATTAGGTCAACTAACGGTCGAAATATTTGAATTT
1 TACACTGAGTGTACCGATACACTAGGTCAACTAACGGTCAAAATATTTGAATTT
*
47164 TATACTGAGTGTACCGATACACT
1 TACACTGAGTGTACCGATACACT
47187 TGATAATGTA
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
54 63 0.88
55 4 0.06
56 5 0.07
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (54 bp):
TACACTGAGTGTACCGATACACTAGGTCAACTAACGGTCAAAATATTTGAATTT
Found at i:56073 original size:20 final size:21
Alignment explanation
Indices: 56038--56088 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
56028 ATTTTTCAAA
* *
56038 TTTTTAATTTCGAAATA-TTT
1 TTTTTAATTTCAAAATAGTTG
*
56058 TTTTTAATTTTAAAATAGTTG
1 TTTTTAATTTCAAAATAGTTG
*
56079 TTTTTGATTT
1 TTTTTAATTT
56089 AATTATGTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.27, C:0.02, G:0.08, T:0.63
Consensus pattern (21 bp):
TTTTTAATTTCAAAATAGTTG
Found at i:58264 original size:229 final size:228
Alignment explanation
Indices: 57859--58292 Score: 778
Period size: 229 Copynumber: 1.9 Consensus size: 228
57849 AGAATAAAGT
* *
57859 AAGGAGGAGATTGTTGAAAATATTTTGATGTTTCGATATAACAAATAAAGTCCTATTAATTTTAA
1 AAGGAGGAGATTGTTAAAAACATTTTGATGTTTCGATATAACAAATAAAGTCCTATTAATTTTAA
*
57924 GATTTTATATTTGATTTTGAAATTAATATTCGAGTAAATTATTCGAATATAAAAAATAATACTCC
66 GATTTTATATTCGATTTTGAAATTAATATTCGAGTAAATTATTCGAATATAAAAAATAATACTCC
*
57989 AAGTTTTCAAATGCCAATTTTAATCCTTACTTAAGTGTAAAATTGTGTTTTAGTCTTAAAATATT
131 AAGTTTTCAAATGCAAATTTTAATCCTTACTTAAGTGTAAAATTGTGTTTTAGTCTTAAAATATT
*
58054 TTTGAAACAACTTAAATGTTTTGTTATATCAAA
196 TTCGAAACAACTTAAATGTTTTGTTATATCAAA
*
58087 AAGGGGGAGATTGTTAAAAACATTTTGATGTTTCGATATAACAAATAAAGTCCTATTGAATTTTA
1 AAGGAGGAGATTGTTAAAAACATTTTGATGTTTCGATATAACAAATAAAGTCCTATT-AATTTTA
* * *
58152 AGATTTTATATTCGATTTTGAAATTAATATTCGAGTAAATTTTTCGAATATCAAAAATATTACTC
65 AGATTTTATATTCGATTTTGAAATTAATATTCGAGTAAATTATTCGAATATAAAAAATAATACTC
58217 CAAGTTTTCAAATGCAAATTTTAATCCTTACTTAAGTGTAAAATTGTGTTTTAGTCTTAAAATAT
130 CAAGTTTTCAAATGCAAATTTTAATCCTTACTTAAGTGTAAAATTGTGTTTTAGTCTTAAAATAT
58282 TTTCGAAACAA
195 TTTCGAAACAA
58293 TTTTGATAAA
Statistics
Matches: 196, Mismatches: 9, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
228 54 0.28
229 142 0.72
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (228 bp):
AAGGAGGAGATTGTTAAAAACATTTTGATGTTTCGATATAACAAATAAAGTCCTATTAATTTTAA
GATTTTATATTCGATTTTGAAATTAATATTCGAGTAAATTATTCGAATATAAAAAATAATACTCC
AAGTTTTCAAATGCAAATTTTAATCCTTACTTAAGTGTAAAATTGTGTTTTAGTCTTAAAATATT
TTCGAAACAACTTAAATGTTTTGTTATATCAAA
Found at i:63579 original size:3 final size:3
Alignment explanation
Indices: 63567--63624 Score: 100
Period size: 3 Copynumber: 19.7 Consensus size: 3
63557 TTTACAAAAC
*
63567 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
63614 TAT TAT TAT TA
1 TAT TAT TAT TA
63625 CCATATCTAA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 50 0.96
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:65164 original size:30 final size:30
Alignment explanation
Indices: 65123--65312 Score: 126
Period size: 30 Copynumber: 6.5 Consensus size: 30
65113 TGAGTTTCTA
* *
65123 TTTTTGTTATTTTAATCCTTTAAATGTTTG
1 TTTTTGCTATTTTAGTCCTTTAAATGTTTG
* * *
65153 TATTTGCTA-TTTAGTCCCTT-AA-GCTCTG
1 TTTTTGCTATTTTAGTCCTTTAAATG-TTTG
* * * *
65181 TTTTTGCTGTTTTAGCCCTCTAAAT-TTCTA
1 TTTTTGCTATTTTAGTCCTTTAAATGTT-TG
* *
65211 TTTTTACTATTTTAGTCTTTTAAAAT-TTTG
1 TTTTTGCTATTTTAGTCCTTT-AAATGTTTG
* * * * * *
65241 TTTTTACTGTTTTAGCCCTTTAAGTTTTTA
1 TTTTTGCTATTTTAGTCCTTTAAATGTTTG
*
65271 TTTTT-CTATTTTAATCCTTTAAAT-TTATG
1 TTTTTGCTATTTTAGTCCTTTAAATGTT-TG
65300 TTTTT-CTATTTTA
1 TTTTTGCTATTTTA
65313 ACCCTTAAAG
Statistics
Matches: 124, Mismatches: 28, Indels: 17
0.73 0.17 0.10
Matches are distributed among these distances:
27 1 0.01
28 14 0.11
29 50 0.40
30 53 0.43
31 6 0.05
ACGTcount: A:0.19, C:0.13, G:0.08, T:0.59
Consensus pattern (30 bp):
TTTTTGCTATTTTAGTCCTTTAAATGTTTG
Found at i:65268 original size:29 final size:29
Alignment explanation
Indices: 65130--65326 Score: 125
Period size: 29 Copynumber: 6.8 Consensus size: 29
65120 CTATTTTTGT
** * *
65130 TATTTTAATCCTTTAAATGTTTGTATTTGC
1 TATTTTAGCCCTTTAAAT-TTTGTTTTTAC
** * *
65160 TA-TTTAGTCCC-TTAAGCTCTGTTTTTGC
1 TATTTTAG-CCCTTTAAATTTTGTTTTTAC
* * *
65188 TGTTTTAGCCCTCTAAATTTCTATTTTTAC
1 TATTTTAGCCCTTTAAATTT-TGTTTTTAC
* *
65218 TATTTTAGTCTTTTAAAATTTTGTTTTTAC
1 TATTTTAGCCCTTT-AAATTTTGTTTTTAC
* * *
65248 TGTTTTAGCCCTTTAAGTTTT-TATTTTTC
1 TATTTTAGCCCTTTAAATTTTGT-TTTTAC
**
65277 TATTTTAATCCTTTAAATTTATGTTTTT-C
1 TATTTTAGCCCTTTAAATTT-TGTTTTTAC
* *
65306 TATTTTAACCC-TTAAAGTTTG
1 TATTTTAGCCCTTTAAATTTTG
65327 GTTAAATATC
Statistics
Matches: 130, Mismatches: 29, Indels: 19
0.73 0.16 0.11
Matches are distributed among these distances:
27 2 0.02
28 21 0.16
29 55 0.42
30 45 0.35
31 7 0.05
ACGTcount: A:0.21, C:0.14, G:0.09, T:0.57
Consensus pattern (29 bp):
TATTTTAGCCCTTTAAATTTTGTTTTTAC
Found at i:66339 original size:22 final size:20
Alignment explanation
Indices: 66301--66344 Score: 70
Period size: 22 Copynumber: 2.1 Consensus size: 20
66291 TAAACCGCTC
66301 AAATTTCAACAGATGAGGAG
1 AAATTTCAACAGATGAGGAG
66321 AAATTTCCAACAAGATGAGGAG
1 AAATTT-CAAC-AGATGAGGAG
66343 AA
1 AA
66345 CCACAAGTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 6 0.27
21 4 0.18
22 12 0.55
ACGTcount: A:0.48, C:0.11, G:0.23, T:0.18
Consensus pattern (20 bp):
AAATTTCAACAGATGAGGAG
Found at i:67508 original size:69 final size:68
Alignment explanation
Indices: 67423--67569 Score: 267
Period size: 69 Copynumber: 2.1 Consensus size: 68
67413 TACTCTAATC
67423 AAAATAAAGAAATATTAAAATTCAATTACAAAGTTCATTAATGTTAAATTCAAATACATAAATAA
1 AAAATAAA-AAATATTAAAATTCAATTACAAAGTTCATTAATGTTAAATTCAAATACATAAATAA
67488 CAAT
65 CAAT
*
67492 AAAATAAAAATATATTAAAATTCAATTACAAAGTTCATTAATTTTAAATTCAAATACATAAATAA
1 AAAATAAAAA-ATATTAAAATTCAATTACAAAGTTCATTAATGTTAAATTCAAATACATAAATAA
67557 CAAT
65 CAAT
67561 AAAATAAAA
1 AAAATAAAA
67570 CAAAGTAAAT
Statistics
Matches: 76, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
68 2 0.03
69 74 0.97
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.31
Consensus pattern (68 bp):
AAAATAAAAAATATTAAAATTCAATTACAAAGTTCATTAATGTTAAATTCAAATACATAAATAAC
AAT
Found at i:68339 original size:21 final size:21
Alignment explanation
Indices: 68313--68386 Score: 58
Period size: 21 Copynumber: 3.4 Consensus size: 21
68303 ATAAAACCAA
68313 GGGTATCGGTACCTCTCAAGG
1 GGGTATCGGTACCTCTCAAGG
* * * * **
68334 GGGTATCGATACTTATATGTAAAT
1 GGGTATCGGTAC--CTCT-CAAGG
*
68358 AGGTATCGGTACCTCTCAAGG
1 GGGTATCGGTACCTCTCAAGG
68379 GGGTATCG
1 GGGTATCG
68387 ATACTTATAT
Statistics
Matches: 36, Mismatches: 14, Indels: 6
0.64 0.25 0.11
Matches are distributed among these distances:
21 20 0.56
22 2 0.06
23 2 0.06
24 12 0.33
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (21 bp):
GGGTATCGGTACCTCTCAAGG
Found at i:68363 original size:45 final size:45
Alignment explanation
Indices: 68314--68410 Score: 194
Period size: 45 Copynumber: 2.2 Consensus size: 45
68304 TAAAACCAAG
68314 GGTATCGGTACCTCTCAAGGGGGTATCGATACTTATATGTAAATA
1 GGTATCGGTACCTCTCAAGGGGGTATCGATACTTATATGTAAATA
68359 GGTATCGGTACCTCTCAAGGGGGTATCGATACTTATATGTAAATA
1 GGTATCGGTACCTCTCAAGGGGGTATCGATACTTATATGTAAATA
68404 GGTATCG
1 GGTATCG
68411 ATACATATCA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (45 bp):
GGTATCGGTACCTCTCAAGGGGGTATCGATACTTATATGTAAATA
Found at i:68412 original size:24 final size:24
Alignment explanation
Indices: 68335--68414 Score: 76
Period size: 24 Copynumber: 3.5 Consensus size: 24
68325 CTCTCAAGGG
68335 GGTATCGATACTTATATGTAAATA
1 GGTATCGATACTTATATGTAAATA
* * * * ***
68359 GGTATCGGTAC--CTCT-CAAGGG
1 GGTATCGATACTTATATGTAAATA
68380 GGTATCGATACTTATATGTAAATA
1 GGTATCGATACTTATATGTAAATA
68404 GGTATCGATAC
1 GGTATCGATAC
68415 ATATCATGGT
Statistics
Matches: 39, Mismatches: 14, Indels: 6
0.66 0.24 0.10
Matches are distributed among these distances:
21 12 0.31
22 2 0.05
23 2 0.05
24 23 0.59
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.33
Consensus pattern (24 bp):
GGTATCGATACTTATATGTAAATA
Found at i:68503 original size:21 final size:21
Alignment explanation
Indices: 68477--68554 Score: 88
Period size: 21 Copynumber: 3.6 Consensus size: 21
68467 CAACACGAGG
68477 GGTATCGGTACCTTTGAGCTA
1 GGTATCGGTACCTTTGAGCTA
*
68498 GGTATCGGTACCACTATATAGAG--G
1 GGTATCGGTA-C-CT-T-T-GAGCTA
68522 GGTATCGGTACCTTTGAGCTA
1 GGTATCGGTACCTTTGAGCTA
68543 GGTATCGGTACC
1 GGTATCGGTACC
68555 ACTATATAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
19 3 0.06
20 1 0.02
21 23 0.48
22 3 0.06
23 3 0.06
24 11 0.23
25 1 0.02
26 3 0.06
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.29
Consensus pattern (21 bp):
GGTATCGGTACCTTTGAGCTA
Found at i:68530 original size:24 final size:24
Alignment explanation
Indices: 68498--68577 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 24
68488 CTTTGAGCTA
68498 GGTATCGGTACCACTATATAGAGG
1 GGTATCGGTACCACTATATAGAGG
*
68522 GGTATCGGTA-C-CT-T-T-GAGCTA
1 GGTATCGGTACCACTATATAGAG--G
*
68543 GGTATCGGTACCACTATATAAAGG
1 GGTATCGGTACCACTATATAGAGG
*
68567 GGTATTGGTAC
1 GGTATCGGTAC
68578 ATCCCTATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
19 3 0.07
20 1 0.02
21 11 0.24
22 3 0.07
23 3 0.07
24 21 0.47
25 1 0.02
26 2 0.04
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (24 bp):
GGTATCGGTACCACTATATAGAGG
Found at i:68537 original size:45 final size:45
Alignment explanation
Indices: 68473--68577 Score: 192
Period size: 45 Copynumber: 2.3 Consensus size: 45
68463 AAATCAACAC
68473 GAGGGGTATCGGTACCTTTGAGCTAGGTATCGGTACCACTATATA
1 GAGGGGTATCGGTACCTTTGAGCTAGGTATCGGTACCACTATATA
68518 GAGGGGTATCGGTACCTTTGAGCTAGGTATCGGTACCACTATATA
1 GAGGGGTATCGGTACCTTTGAGCTAGGTATCGGTACCACTATATA
* *
68563 AAGGGGTATTGGTAC
1 GAGGGGTATCGGTAC
68578 ATCCCTATTT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 58 1.00
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.29
Consensus pattern (45 bp):
GAGGGGTATCGGTACCTTTGAGCTAGGTATCGGTACCACTATATA
Found at i:68765 original size:13 final size:13
Alignment explanation
Indices: 68749--68775 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
68739 AATCGAATAA
68749 AATCTTAAAATTC
1 AATCTTAAAATTC
68762 AATCTTAAAATTC
1 AATCTTAAAATTC
68775 A
1 A
68776 TTAAAACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (13 bp):
AATCTTAAAATTC
Found at i:71743 original size:20 final size:21
Alignment explanation
Indices: 71717--71776 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
71707 TTGGAGTGTG
71717 GGGGGTATCGGTACCATCTG-A
1 GGGGGTATCGGTACCAT-TGCA
* *
71738 -GGGGTATAGATACCATTGCA
1 GGGGGTATCGGTACCATTGCA
71758 TGGGGGTATCGGTACCATT
1 -GGGGGTATCGGTACCATT
71777 CGAGCATTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
19 2 0.06
20 15 0.47
22 15 0.47
ACGTcount: A:0.22, C:0.17, G:0.35, T:0.27
Consensus pattern (21 bp):
GGGGGTATCGGTACCATTGCA
Found at i:74477 original size:20 final size:22
Alignment explanation
Indices: 74449--74507 Score: 77
Period size: 20 Copynumber: 2.7 Consensus size: 22
74439 CAGACCCCGT
74449 GGAGGGTATCGGTACCA-TCAA
1 GGAGGGTATCGGTACCATTCAA
74470 GG-GGGTATCGGTACCCATTCAA
1 GGAGGGTATCGGTA-CCATTCAA
* *
74492 GGATGGTATCGATACC
1 GGAGGGTATCGGTACC
74508 TATTATAGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
20 11 0.33
21 5 0.15
22 8 0.24
23 9 0.27
ACGTcount: A:0.25, C:0.20, G:0.32, T:0.22
Consensus pattern (22 bp):
GGAGGGTATCGGTACCATTCAA
Found at i:74546 original size:23 final size:21
Alignment explanation
Indices: 74499--74549 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
74489 CAAGGATGGT
* *
74499 ATCGATACCTATTATAGGGGT
1 ATCGATACCTATTAAAGGGGC
*
74520 ATCGATGCCTATTCAAAGGGGGC
1 ATCGATACCTATT-AAA-GGGGC
74543 ATCGATA
1 ATCGATA
74550 ACAGTCTTAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 12 0.50
22 2 0.08
23 10 0.42
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.27
Consensus pattern (21 bp):
ATCGATACCTATTAAAGGGGC
Done.