Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001923.1 Hibiscus syriacus cultivar Beakdansim tig00003891_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: 58106
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:4336 original size:48 final size:48
Alignment explanation
Indices: 4244--4336 Score: 116
Period size: 49 Copynumber: 1.9 Consensus size: 48
4234 CACACTCCAA
* * * * *
4244 TTTGCCTTTCATCGTGACTAGGAGGGTTGGTTAGAGCCATTTATCGAT
1 TTTGCCTTTCATCGCGACTAGGAGGGTTCGATAGAGACACTTATCGAT
*
4292 TTTGCCTTTTCATTGCGACTAGGAGGGTTCGATAG-GACACTTATC
1 TTTGCC-TTTCATCGCGACTAGGAGGGTTCGATAGAGACACTTATC
4337 CATCTATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
48 14 0.37
49 24 0.63
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (48 bp):
TTTGCCTTTCATCGCGACTAGGAGGGTTCGATAGAGACACTTATCGAT
Found at i:5654 original size:17 final size:17
Alignment explanation
Indices: 5632--5664 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5622 AGTTTTCATT
5632 TTTTATTTTATTTTAAG
1 TTTTATTTTATTTTAAG
*
5649 TTTTATTTTTTTTTAA
1 TTTTATTTTATTTTAA
5665 ATTCTAAGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (17 bp):
TTTTATTTTATTTTAAG
Found at i:5672 original size:24 final size:25
Alignment explanation
Indices: 5621--5673 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
5611 ATCTCTTTTC
* *
5621 AAGTTTTCATTTTTTATTTTATTTT
1 AAGTTTTCATTTTTTATTTAATTCT
5646 AAGTTTT-ATTTTTT-TTTAAATTCT
1 AAGTTTTCATTTTTTATTT-AATTCT
5670 AAGT
1 AAGT
5674 GTCATAACGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 3 0.12
24 15 0.60
25 7 0.28
ACGTcount: A:0.25, C:0.04, G:0.06, T:0.66
Consensus pattern (25 bp):
AAGTTTTCATTTTTTATTTAATTCT
Found at i:6698 original size:29 final size:29
Alignment explanation
Indices: 6617--6781 Score: 134
Period size: 29 Copynumber: 5.9 Consensus size: 29
6607 AAATATGATT
*
6617 AACAAAAATTTAAGAGG-CT-AAATAG--A
1 AACAAAAACTTAA-AGGACTAAAATAGCAA
* *
6643 AA-AAAAACTTAAGGGA--ATAATCAGCAA
1 AACAAAAACTTAAAGGACTAAAAT-AGCAA
* * *
6670 AACAGAAACCTAAATGACTAAAATAGCAAA
1 AACAAAAACTTAAAGGACTAAAATAGC-AA
*
6700 AACAAAAACTTAAAGGACT-AAACAGCAA
1 AACAAAAACTTAAAGGACTAAAATAGCAA
* *
6728 AA-AAAAACTTAAAGGACTAAAATGGCATG
1 AACAAAAACTTAAAGGACTAAAATAGCA-A
*
6757 AA-TAAAACTTAAAGGACTAAAATAG
1 AACAAAAACTTAAAGGACTAAAATAG
6782 AAATTTTAAA
Statistics
Matches: 111, Mismatches: 17, Indels: 19
0.76 0.12 0.13
Matches are distributed among these distances:
24 5 0.05
25 11 0.10
26 2 0.02
27 19 0.17
28 20 0.18
29 32 0.29
30 22 0.20
ACGTcount: A:0.59, C:0.12, G:0.13, T:0.16
Consensus pattern (29 bp):
AACAAAAACTTAAAGGACTAAAATAGCAA
Found at i:6719 original size:30 final size:29
Alignment explanation
Indices: 6642--6781 Score: 135
Period size: 29 Copynumber: 4.9 Consensus size: 29
6632 GGCTAAATAG
* *
6642 AAAAAAAACTTAAGGGA--ATAATCAGCAA
1 AAAAAAAACTTAAAGGACTAAAAT-AGCAA
* * * *
6670 AACAGAAACCTAAATGACTAAAATAGCAA
1 AAAAAAAACTTAAAGGACTAAAATAGCAA
*
6699 AAACAAAAACTTAAAGGACT-AAACAGC-A
1 AAA-AAAAACTTAAAGGACTAAAATAGCAA
* *
6727 AAAAAAAACTTAAAGGACTAAAATGGCAT
1 AAAAAAAACTTAAAGGACTAAAATAGCAA
* *
6756 GAATAAAACTTAAAGGACTAAAATAG
1 AAAAAAAACTTAAAGGACTAAAATAG
6782 AAATTTTAAA
Statistics
Matches: 90, Mismatches: 17, Indels: 9
0.78 0.15 0.08
Matches are distributed among these distances:
27 16 0.18
28 21 0.23
29 36 0.40
30 17 0.19
ACGTcount: A:0.59, C:0.13, G:0.13, T:0.15
Consensus pattern (29 bp):
AAAAAAAACTTAAAGGACTAAAATAGCAA
Found at i:6726 original size:58 final size:56
Alignment explanation
Indices: 6642--6777 Score: 164
Period size: 57 Copynumber: 2.4 Consensus size: 56
6632 GGCTAAATAG
* * * * *
6642 AAAAAAAACTTAAGGGAATAATCAGCAAAACAGAAACCTAAATGACTAAAATAGCAA
1 AAAAAAAACTTAAAGGACTAAACAGCAAAA-AAAAACCTAAAGGACTAAAATAGCAA
* * *
6699 AAACAAAAACTTAAAGGACTAAACAGCAAAAAAAAACTTAAAGGACTAAAATGGCAT
1 AAA-AAAAACTTAAAGGACTAAACAGCAAAAAAAAACCTAAAGGACTAAAATAGCAA
* *
6756 GAATAAAACTTAAAGGACTAAA
1 AAAAAAAACTTAAAGGACTAAA
6778 ATAGAAATTT
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
56 18 0.26
57 26 0.38
58 24 0.35
ACGTcount: A:0.60, C:0.13, G:0.12, T:0.15
Consensus pattern (56 bp):
AAAAAAAACTTAAAGGACTAAACAGCAAAAAAAAACCTAAAGGACTAAAATAGCAA
Found at i:6806 original size:14 final size:14
Alignment explanation
Indices: 6774--6811 Score: 69
Period size: 13 Copynumber: 2.8 Consensus size: 14
6764 CTTAAAGGAC
6774 TAAAATAGAAATTT
1 TAAAATAGAAATTT
6788 T-AAATAGAAATTT
1 TAAAATAGAAATTT
6801 TAAAATAGAAA
1 TAAAATAGAAA
6812 AAATAGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 13 0.57
14 10 0.43
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.32
Consensus pattern (14 bp):
TAAAATAGAAATTT
Found at i:7340 original size:14 final size:14
Alignment explanation
Indices: 7321--7349 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
7311 AATCAGAAAG
7321 AGAGAGAGAGAGAA
1 AGAGAGAGAGAGAA
7335 AGAGAGAGAGAGAA
1 AGAGAGAGAGAGAA
7349 A
1 A
7350 AACCTCTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (14 bp):
AGAGAGAGAGAGAA
Found at i:8182 original size:3 final size:3
Alignment explanation
Indices: 8169--8205 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
8159 AATAAATGTA
8169 AAT AAT AAAT AAT AAT AA- AAT AAT AAT AAT AAT AAT A
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
8206 TATTATTAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:8187 original size:17 final size:16
Alignment explanation
Indices: 8169--8205 Score: 60
Period size: 14 Copynumber: 2.4 Consensus size: 16
8159 AATAAATGTA
8169 AATAATAAATAATAAT
1 AATAATAAATAATAAT
8185 AA-AAT-AATAATAAT
1 AATAATAAATAATAAT
8199 AATAATA
1 AATAATA
8206 TATTATTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 11 0.58
15 6 0.32
16 2 0.11
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AATAATAAATAATAAT
Found at i:9390 original size:22 final size:21
Alignment explanation
Indices: 9329--9393 Score: 58
Period size: 26 Copynumber: 2.9 Consensus size: 21
9319 TGTTTTATTT
9329 TCAAAAGTTTGAAAATATCAA
1 TCAAAAGTTTGAAAATATCAA
* * *
9350 TTAAAAGGATGTTGAAAAATGTTTAA
1 TCAAAA-G-T-TTG-AAAAT-ATCAA
9376 TCAAAAGTTTGAAAATAT
1 TCAAAAGTTTGAAAATAT
9394 TACTCCTTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
21 6 0.18
22 6 0.18
23 4 0.12
24 4 0.12
25 6 0.18
26 8 0.24
ACGTcount: A:0.49, C:0.05, G:0.14, T:0.32
Consensus pattern (21 bp):
TCAAAAGTTTGAAAATATCAA
Found at i:9721 original size:79 final size:79
Alignment explanation
Indices: 9631--9788 Score: 298
Period size: 79 Copynumber: 2.0 Consensus size: 79
9621 ATGAAGTGGC
*
9631 TTCTGTACTCATTTATTGGAAGTGTTCTCCGACTCCCAGCTCTCATGTTCTCATTCAAGTTTTTC
1 TTCTGTACTCATTTATTGGAAGTGTTCTCCGACTCCCAGCTCTCATGTTCTCATTCAAGTTGTTC
9696 GATGCCTTATCAAG
66 GATGCCTTATCAAG
9710 TTCTGTACTCATTTATTGGAAGTGTTCTCCGACTCCCAGCTCTCATGTTCTCATTCAAGTTGTTC
1 TTCTGTACTCATTTATTGGAAGTGTTCTCCGACTCCCAGCTCTCATGTTCTCATTCAAGTTGTTC
*
9775 GATGCTTTATCAAG
66 GATGCCTTATCAAG
9789 GGATTTGTGT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
79 77 1.00
ACGTcount: A:0.19, C:0.25, G:0.16, T:0.41
Consensus pattern (79 bp):
TTCTGTACTCATTTATTGGAAGTGTTCTCCGACTCCCAGCTCTCATGTTCTCATTCAAGTTGTTC
GATGCCTTATCAAG
Found at i:9764 original size:42 final size:42
Alignment explanation
Indices: 9638--9764 Score: 96
Period size: 42 Copynumber: 3.1 Consensus size: 42
9628 GGCTTCTGTA
9638 CTCATTTATTGGAAGTGTTCTCCGACTCCCAGCTCTCATGTT
1 CTCATTTATTGGAAGTGTTCTCCGACTCCCAGCTCTCATGTT
* * *
9680 CTC----ATT-CAAGT-TT-TTCGA-TGCCTTATCAAG-T-TC-TGTA
1 CTCATTTATTGGAAGTGTTCTCCGACT-CC----C-AGCTCTCATGTT
9717 CTCATTTATTGGAAGTGTTCTCCGACTCCCAGCTCTCATGTT
1 CTCATTTATTGGAAGTGTTCTCCGACTCCCAGCTCTCATGTT
9759 CTCATT
1 CTCATT
9765 CAAGTTGTTC
Statistics
Matches: 62, Mismatches: 6, Indels: 34
0.61 0.06 0.33
Matches are distributed among these distances:
34 1 0.02
35 6 0.10
36 2 0.03
37 10 0.16
38 5 0.08
39 4 0.06
40 4 0.06
41 5 0.08
42 16 0.26
43 2 0.03
44 6 0.10
45 1 0.02
ACGTcount: A:0.18, C:0.27, G:0.15, T:0.40
Consensus pattern (42 bp):
CTCATTTATTGGAAGTGTTCTCCGACTCCCAGCTCTCATGTT
Found at i:10503 original size:2 final size:2
Alignment explanation
Indices: 10496--10521 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10486 GCTTTATTGC
10496 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
10522 TAATTGCCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11717 original size:20 final size:20
Alignment explanation
Indices: 11692--11732 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
11682 TGATAAATGC
11692 AATGTTTCAAGGTCTCAAAG
1 AATGTTTCAAGGTCTCAAAG
11712 AATGTTTCAAGGTCTCAAAG
1 AATGTTTCAAGGTCTCAAAG
11732 A
1 A
11733 GAGGGAATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.29
Consensus pattern (20 bp):
AATGTTTCAAGGTCTCAAAG
Found at i:12966 original size:210 final size:212
Alignment explanation
Indices: 12582--12972 Score: 524
Period size: 210 Copynumber: 1.8 Consensus size: 212
12572 TCCTCAAAAA
* * *
12582 TGATGCCCCTCAAGCGATCTGTAACCTAACTCCATTAATGCCTCGATGGTACTGAAGTCAGTGTG
1 TGATGCCCCTCAAGC-ATCTGTAAACTAACTCCATTAATGCCTCGACGGTACTGAAGCCAGTGT-
** * *
12647 CCACTCACTCCTTGATGGTTAGTGATGGAATGATCGTAGATAAGACTCTACTACTGGATTACTCC
64 -CACTCACTCCTTGATGACTAGTGATGGAATGATCGTAGATAAGACTCCACTACTAGATTACTCC
* * * *
12712 TCGGATTAGTGGATCTTCATTTCAGTCTCGAATGTTGCACGATCTTCGAGCTCACTGTTTTGTCT
128 TCGAATCAATGGATCATCATTTCAGTCTCGAATGTTGCACGATCTTCGAGCTCACTGTTTTGTCT
12777 CAGATCTTTGTATTTGGAAC
193 CAGATCTTTGTATTTGGAAC
*
12797 TGATGCCCCTCAATGC-TCTGTAAACTAACTCCATTAATGCCTC-AGCGGTGCTGAAGCCA-T-T
1 TGATGCCCCTCAA-GCATCTGTAAACTAACTCCATTAATGCCTCGA-CGGTACTGAAGCCAGTGT
* * *
12858 -ACGTCACTCCTTGATGACTAGTGAT-GACATGATTGTAGATAAGATTCCACTGCTAGATTACTC
64 CAC-TCACTCCTTGATGACTAGTGATGGA-ATGATCGTAGATAAGACTCCACTACTAGATTACTC
* *
12921 CTCGAATCAATGGATCATCATTTCAGTCTTGAATGTTGTACGATCTTCGAGC
127 CTCGAATCAATGGATCATCATTTCAGTCTCGAATGTTGCACGATCTTCGAGC
12973 AAGTTTTATT
Statistics
Matches: 155, Mismatches: 17, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
209 4 0.03
210 96 0.62
212 1 0.01
213 2 0.01
214 37 0.24
215 13 0.08
216 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.32
Consensus pattern (212 bp):
TGATGCCCCTCAAGCATCTGTAAACTAACTCCATTAATGCCTCGACGGTACTGAAGCCAGTGTCA
CTCACTCCTTGATGACTAGTGATGGAATGATCGTAGATAAGACTCCACTACTAGATTACTCCTCG
AATCAATGGATCATCATTTCAGTCTCGAATGTTGCACGATCTTCGAGCTCACTGTTTTGTCTCAG
ATCTTTGTATTTGGAAC
Found at i:15154 original size:30 final size:30
Alignment explanation
Indices: 15058--15236 Score: 175
Period size: 30 Copynumber: 6.0 Consensus size: 30
15048 AAATATGATT
*
15058 AATAGAAATTTAAGAGG-CTAAAATAGCAAAA
1 AATAGAAACTTAA-AGGACTAAAATAG-AAAA
* * * * *
15089 AATAGATACTTAAGGGACTAATA-AGCAAT
1 AATAGAAACTTAAAGGACTAAAATAGAAAA
* *
15118 AATAGAAACATAAAGGACTAAAATATAAAA
1 AATAGAAACTTAAAGGACTAAAATAGAAAA
* * *
15148 AATAGAACCTTAAAGGA-TTAAATAGCAAA
1 AATAGAAACTTAAAGGACTAAAATAGAAAA
* * *
15177 AATAGAAACTTAAAGGACTAAAATGGTACA
1 AATAGAAACTTAAAGGACTAAAATAGAAAA
* *
15207 AACAAAAACTTAAAGGACTAAAATAGAAAA
1 AATAGAAACTTAAAGGACTAAAATAGAAAA
15237 TAAAAAATTA
Statistics
Matches: 117, Mismatches: 28, Indels: 7
0.77 0.18 0.05
Matches are distributed among these distances:
29 46 0.39
30 55 0.47
31 16 0.14
ACGTcount: A:0.58, C:0.09, G:0.14, T:0.19
Consensus pattern (30 bp):
AATAGAAACTTAAAGGACTAAAATAGAAAA
Found at i:15181 original size:59 final size:60
Alignment explanation
Indices: 15058--15200 Score: 177
Period size: 59 Copynumber: 2.4 Consensus size: 60
15048 AAATATGATT
* * *
15058 AATAGAAATTTAAGAGG-CTAAAATAGCAAAAAATAGATACTTAAGGGACTAATAAGCAAT
1 AATAGAAACTTAA-AGGACTAAAATAGCAAAAAATAGATACTTAAAGGACTAATAAGCAAA
* * *
15118 AATAGAAACATAAAGGACTAAAATA-TAAAAAATAGA-ACCTTAAAGGATTAA-ATAGCAAA
1 AATAGAAACTTAAAGGACTAAAATAGCAAAAAATAGATA-CTTAAAGGACTAATA-AGCAAA
15177 AATAGAAACTTAAAGGACTAAAAT
1 AATAGAAACTTAAAGGACTAAAAT
15201 GGTACAAACA
Statistics
Matches: 73, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
58 2 0.03
59 52 0.71
60 19 0.26
ACGTcount: A:0.57, C:0.08, G:0.14, T:0.20
Consensus pattern (60 bp):
AATAGAAACTTAAAGGACTAAAATAGCAAAAAATAGATACTTAAAGGACTAATAAGCAAA
Found at i:15219 original size:59 final size:59
Alignment explanation
Indices: 15096--15286 Score: 171
Period size: 59 Copynumber: 3.3 Consensus size: 59
15086 AAAAATAGAT
* * * * *
15096 ACTTAAGGGACTAATA-AGCAATAATAGAAACATAAAGGACTAAAAT-ATAAAA-AATAGA
1 ACTTAAAGGACTAAAATAGCAAAAATAGAAACTTAAAGGACTAAAATGGTAAAACAA-A-A
*
15154 ACCTTAAAGGA-TTAAATAGCAAAAATAGAAACTTAAAGGACTAAAATGGTACAAACAAAA
1 A-CTTAAAGGACTAAAATAGCAAAAATAGAAACTTAAAGGACTAAAATGGTA-AAACAAAA
* * * * *
15214 ACTTAAAGGACTAAAATAG--AAAATAAAAAATT-AAGGACAAAAATGGTATTAACATAA
1 ACTTAAAGGACTAAAATAGCAAAAATAGAAACTTAAAGGACTAAAATGGTA-AAACAAAA
* *
15271 ACTAAAAGGGCTAAAA
1 ACTTAAAGGACTAAAA
15287 GTAATTACAA
Statistics
Matches: 112, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
57 35 0.31
58 15 0.13
59 45 0.40
60 11 0.10
61 4 0.04
62 2 0.02
ACGTcount: A:0.58, C:0.09, G:0.14, T:0.19
Consensus pattern (59 bp):
ACTTAAAGGACTAAAATAGCAAAAATAGAAACTTAAAGGACTAAAATGGTAAAACAAAA
Found at i:15259 original size:57 final size:59
Alignment explanation
Indices: 15156--15286 Score: 151
Period size: 57 Copynumber: 2.3 Consensus size: 59
15146 AAAATAGAAC
* * * *
15156 CTTAAAGGA-TTAAATAGCAAAAATAGAAACTTAAAGGACTAAAATGGTACAAACAAAAA
1 CTTAAAGGACTAAAATAG-AAAAATAAAAAATTAAAGGACAAAAATGGTACAAACAAAAA
** *
15215 CTTAAAGGACTAAAATAG-AAAATAAAAAATT-AAGGACAAAAATGGTATTAACATAAA
1 CTTAAAGGACTAAAATAGAAAAATAAAAAATTAAAGGACAAAAATGGTACAAACAAAAA
* *
15272 CTAAAAGGGCTAAAA
1 CTTAAAGGACTAAAA
15287 GTAATTACAA
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
57 35 0.56
58 11 0.18
59 9 0.15
60 7 0.11
ACGTcount: A:0.58, C:0.09, G:0.14, T:0.19
Consensus pattern (59 bp):
CTTAAAGGACTAAAATAGAAAAATAAAAAATTAAAGGACAAAAATGGTACAAACAAAAA
Found at i:16610 original size:3 final size:3
Alignment explanation
Indices: 16591--16636 Score: 58
Period size: 3 Copynumber: 15.3 Consensus size: 3
16581 GTAAAATGTA
* *
16591 AAT AAT AAAT AAA AAT AAT AAT AAT AAT AAT AAT -AT AAT ATT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16636 A
1 A
16637 GTTTTGTAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:23033 original size:15 final size:15
Alignment explanation
Indices: 23013--23042 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
23003 AACTTTAAGC
23013 ATTGTATAACTTATA
1 ATTGTATAACTTATA
*
23028 ATTGTATAATTTATA
1 ATTGTATAACTTATA
23043 TCATTGAACT
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:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (15 bp):
ATTGTATAACTTATA
Found at i:23070 original size:29 final size:29
Alignment explanation
Indices: 23038--23117 Score: 81
Period size: 31 Copynumber: 2.7 Consensus size: 29
23028 ATTGTATAAT
23038 TTATATCATTGAACTTTTAATTT-TGTCAA
1 TTATA-CATTGAACTTTTAATTTCTGTCAA
* * *
23067 TTATAGATTTGAACTTTGATTTTCGTGTCAA
1 TTATACA-TTGAACTTTTAATTTC-TGTCAA
*
23098 TTATACTATTGAACTGTTAA
1 TTATAC-ATTGAACTTTTAA
23118 ATCGTTAACG
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
28 1 0.03
29 18 0.45
31 20 0.50
32 1 0.03
ACGTcount: A:0.30, C:0.10, G:0.11, T:0.49
Consensus pattern (29 bp):
TTATACATTGAACTTTTAATTTCTGTCAA
Found at i:23627 original size:105 final size:101
Alignment explanation
Indices: 23440--23640 Score: 267
Period size: 105 Copynumber: 2.0 Consensus size: 101
23430 ATGGGTTCTC
* * * *
23440 ATGTTATTAATTTAAACCAACTAGTAGTATTATAAAAGTATAACTAATTTATACCAAACTAAAAT
1 ATGTTATCAACTTAAACCAACTAATAGCATTATAAAAGTATAACTAATTTATACCAAACTAAAAT
* *
23505 AGATGGGTTAACTCCTAAGTTTCAACATAATTAATG
66 AGATGGGTTAACGCCTAAATTTCAACATAATTAATG
* ** *
23541 ATGTTATCAACTTAAACCAACTAATGGCATTATAAAAAGTAGTAGGACTAATTTATGTCAAATTA
1 ATGTTATCAACTTAAACCAACTAATAGCATTAT-AAAAGTA-TA--ACTAATTTATACCAAACTA
*
23606 AAATAGATGGTTTAACGCCTAAATTTCAACATAAT
62 AAATAGATGGGTTAACGCCTAAATTTCAACATAAT
23641 AAAGGGCCTA
Statistics
Matches: 85, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
101 28 0.33
102 7 0.08
103 2 0.02
105 48 0.56
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.33
Consensus pattern (101 bp):
ATGTTATCAACTTAAACCAACTAATAGCATTATAAAAGTATAACTAATTTATACCAAACTAAAAT
AGATGGGTTAACGCCTAAATTTCAACATAATTAATG
Found at i:26872 original size:3 final size:3
Alignment explanation
Indices: 26864--26893 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
26854 AATAAATGTA
*
26864 AAT AAT AAT AAT AAT AAT AAT AAT CAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
26894 GGAGGACCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:28393 original size:14 final size:15
Alignment explanation
Indices: 28370--28423 Score: 60
Period size: 14 Copynumber: 3.8 Consensus size: 15
28360 TGCCATTGCA
28370 ATAAACCCTAAACT-
1 ATAAACCCTAAACTC
*
28384 ATAAATCCTAAA-TC
1 ATAAACCCTAAACTC
28398 ATAAACCCTAAAC-C
1 ATAAACCCTAAACTC
* *
28412 CTAAACACTAAA
1 ATAAACCCTAAA
28424 TTGTACTTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
13 1 0.03
14 33 0.97
ACGTcount: A:0.52, C:0.28, G:0.00, T:0.20
Consensus pattern (15 bp):
ATAAACCCTAAACTC
Found at i:28395 original size:7 final size:7
Alignment explanation
Indices: 28371--28423 Score: 52
Period size: 7 Copynumber: 7.6 Consensus size: 7
28361 GCCATTGCAA
28371 TAAACCC
1 TAAACCC
**
28378 TAAACTA
1 TAAACCC
*
28385 TAAATCC
1 TAAACCC
* *
28392 TAAATCA
1 TAAACCC
28399 TAAACCC
1 TAAACCC
28406 TAAACCC
1 TAAACCC
*
28413 TAAACAC
1 TAAACCC
28420 TAAA
1 TAAA
28424 TTGTACTTAC
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.21
Consensus pattern (7 bp):
TAAACCC
Found at i:28416 original size:28 final size:28
Alignment explanation
Indices: 28370--28424 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
28360 TGCCATTGCA
*
28370 ATAAACCCTAAACTATAAATC-CTAAATC
1 ATAAACCCTAAACCATAAA-CACTAAATC
*
28398 ATAAACCCTAAACCCTAAACACTAAAT
1 ATAAACCCTAAACCATAAACACTAAAT
28425 TGTACTTACC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 1 0.04
28 23 0.96
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (28 bp):
ATAAACCCTAAACCATAAACACTAAATC
Found at i:28488 original size:7 final size:7
Alignment explanation
Indices: 28476--28542 Score: 98
Period size: 7 Copynumber: 9.6 Consensus size: 7
28466 GTCTTTGCAA
28476 TAAACCC
1 TAAACCC
28483 TAAACCC
1 TAAACCC
28490 TAAACCC
1 TAAACCC
* *
28497 TAAATCT
1 TAAACCC
*
28504 TAAACTC
1 TAAACCC
28511 TAAACCC
1 TAAACCC
*
28518 TAATCCC
1 TAAACCC
28525 TAAACCC
1 TAAACCC
28532 TAAACCC
1 TAAACCC
28539 TAAA
1 TAAA
28543 ATCTAAATCC
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 52 1.00
ACGTcount: A:0.43, C:0.36, G:0.00, T:0.21
Consensus pattern (7 bp):
TAAACCC
Found at i:28548 original size:21 final size:21
Alignment explanation
Indices: 28482--28549 Score: 84
Period size: 21 Copynumber: 3.2 Consensus size: 21
28472 GCAATAAACC
28482 CTAAACCCTAAACCCT-AAAT
1 CTAAACCCTAAACCCTAAAAT
* ***
28502 CTTAAACTCTAAACCCTAATCC
1 C-TAAACCCTAAACCCTAAAAT
28524 CTAAACCCTAAACCCTAAAAT
1 CTAAACCCTAAACCCTAAAAT
28545 CTAAA
1 CTAAA
28550 TCCAATTATG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
20 1 0.03
21 35 0.92
22 2 0.05
ACGTcount: A:0.44, C:0.34, G:0.00, T:0.22
Consensus pattern (21 bp):
CTAAACCCTAAACCCTAAAAT
Found at i:30069 original size:23 final size:21
Alignment explanation
Indices: 30026--30078 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 21
30016 TAACCCGTCT
30026 TCGAGCTTCAAACGAGATTGAA
1 TCGAGC-TCAAACGAGATTGAA
*
30048 TCGAGCTCAAAGTCGAGCTTGAA
1 TCGAGCTCAAA--CGAGATTGAA
*
30071 TCTAGCTC
1 TCGAGCTC
30079 GAGTCTCGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 5 0.19
22 6 0.22
23 16 0.59
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (21 bp):
TCGAGCTCAAACGAGATTGAA
Found at i:31412 original size:15 final size:15
Alignment explanation
Indices: 31394--31423 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31384 TTCTTTTTAT
31394 TCTTTTTTTATCTTA
1 TCTTTTTTTATCTTA
*
31409 TCTTTTTTTCTCTTA
1 TCTTTTTTTATCTTA
31424 CCTCTCTAAC
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:0.10, C:0.17, G:0.00, T:0.73
Consensus pattern (15 bp):
TCTTTTTTTATCTTA
Found at i:33193 original size:28 final size:29
Alignment explanation
Indices: 33148--33204 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
33138 TAATACTATT
*
33148 AATATGTATATATTAAAAACTATATAATA
1 AATATGTATATATTAAAAACAATATAATA
33177 AATAT-TATAT-TTCAAAAACAATATAATA
1 AATATGTATATATT-AAAAACAATATAATA
33205 TGTTTTCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 2 0.08
28 19 0.73
29 5 0.19
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (29 bp):
AATATGTATATATTAAAAACAATATAATA
Found at i:33324 original size:2 final size:2
Alignment explanation
Indices: 33319--33358 Score: 55
Period size: 2 Copynumber: 19.5 Consensus size: 2
33309 TATATATTGA
33319 AT AT AT AT AT AT AT AT AT AT AT -T AT CAT AT AT ACT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT A-T AT AT A
33359 ATGTAATAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 1 0.03
2 30 0.86
3 4 0.11
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:33802 original size:79 final size:80
Alignment explanation
Indices: 33656--33808 Score: 191
Period size: 80 Copynumber: 1.9 Consensus size: 80
33646 GAGTTACGGA
* * * * * * * *
33656 TGACTCCTTTGTCATGAAGTCGAGTCGATATTGGATGACTTTGAGCCCGACATCCTTCGTCTTGA
1 TGACCCCTTCGTCATGAAGTCGAGTCAATATTGAATGACTTTGAGCACAACATCCTTCGCCGTGA
33721 AGTTGAAATCGTGGC
66 AGTTGAAATCGTGGC
* * * *
33736 TGACCCCTTCGTCGTGAAGTCGAGTCAATCTTGAATGAC-TTGAGCATAATATCCTTCGCCGTGA
1 TGACCCCTTCGTCATGAAGTCGAGTCAATATTGAATGACTTTGAGCACAACATCCTTCGCCGTGA
33800 AGTTGAAAT
66 AGTTGAAAT
33809 TGAGCTCGAA
Statistics
Matches: 61, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
79 28 0.46
80 33 0.54
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.31
Consensus pattern (80 bp):
TGACCCCTTCGTCATGAAGTCGAGTCAATATTGAATGACTTTGAGCACAACATCCTTCGCCGTGA
AGTTGAAATCGTGGC
Found at i:38007 original size:28 final size:29
Alignment explanation
Indices: 37965--38027 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 29
37955 AATACTAATG
*
37965 ATAATA-ATATGTATATAT-TAAAAACTAT
1 ATAATATATATGTATAT-TGTAAAAACAAT
*
37993 ATAATATATAT-TATATTGTGAAAACAAT
1 ATAATATATATGTATATTGTAAAAACAAT
38021 ATAATAT
1 ATAATAT
38028 GTTTTCAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 1 0.03
28 26 0.84
29 4 0.13
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.40
Consensus pattern (29 bp):
ATAATATATATGTATATTGTAAAAACAAT
Found at i:38186 original size:21 final size:21
Alignment explanation
Indices: 38162--38201 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
38152 GTTTAAAAAC
*
38162 TATATATTATGTTTTCAAATT
1 TATATAATATGTTTTCAAATT
38183 TATATAATATGTTTTCAAA
1 TATATAATATGTTTTCAAA
38202 AACTATATTG
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:0.38, C:0.05, G:0.05, T:0.53
Consensus pattern (21 bp):
TATATAATATGTTTTCAAATT
Found at i:38823 original size:10 final size:10
Alignment explanation
Indices: 38808--38837 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
38798 TTATTACCCC
38808 AATTGAAATG
1 AATTGAAATG
38818 AATTGAAATG
1 AATTGAAATG
38828 AATTGAAATG
1 AATTGAAATG
38838 TAGAGATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.20, T:0.30
Consensus pattern (10 bp):
AATTGAAATG
Found at i:41165 original size:3 final size:3
Alignment explanation
Indices: 41157--41220 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
41147 AAACAAAAAT
41157 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
41205 ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA A
41221 AGGCGGGACA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:41505 original size:140 final size:140
Alignment explanation
Indices: 41249--41518 Score: 364
Period size: 140 Copynumber: 1.9 Consensus size: 140
41239 TGTCGACAGG
* * *
41249 TGCCCCTCTTTGCCCAGTATTGTGTCAACAAGAATAGGGCAAAGATGAAGAGACAATGAGTTTTC
1 TGCCCCTCTTTGCCCAGTATTGTGTCAACAAGAATAAGGCAAAGACGAAGAGACAATGAGATTTC
* * *
41314 ATCCGGTCAACTCCATGTTTTGAAATCTGATAAGGGAGATGCTCTACTGTTTCTTGAGGGTAGAT
66 ATCCGGTCAACTCCATGCTTTGAAATCTAATAAGGGACATGCTCTACTGTTTCTTGAGGGTAGAT
41379 CAGATCGAGC
131 CAGATCGAGC
* * * * *
41389 TGCCCCTCTTTTCCCATTCTTGTGTTAACAAGGATAAGGCAAAGACGAAGAGACAATGAGATTTC
1 TGCCCCTCTTTGCCCAGTATTGTGTCAACAAGAATAAGGCAAAGACGAAGAGACAATGAGATTTC
* * * * *
41454 ATCTGGCTGAA-TCTATGCTTTGAAATCTAATAAGGGACATGCT-TCATTGTTTCTTTAGGGTAG
66 ATCCGG-TCAACTCCATGCTTTGAAATCTAATAAGGGACATGCTCT-ACTGTTTCTTGAGGGTAG
41517 AT
129 AT
41519 TGAATCAAGG
Statistics
Matches: 112, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
139 1 0.01
140 108 0.96
141 3 0.03
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.31
Consensus pattern (140 bp):
TGCCCCTCTTTGCCCAGTATTGTGTCAACAAGAATAAGGCAAAGACGAAGAGACAATGAGATTTC
ATCCGGTCAACTCCATGCTTTGAAATCTAATAAGGGACATGCTCTACTGTTTCTTGAGGGTAGAT
CAGATCGAGC
Found at i:41776 original size:136 final size:134
Alignment explanation
Indices: 41504--41930 Score: 468
Period size: 136 Copynumber: 3.2 Consensus size: 134
41494 GCTTCATTGT
* * * * * *
41504 TTCTTTAGGGTAGATTGAATCAAGGTAGACTTGTTCCACTATTCCTCAGGGAAGATCAAATCTGG
1 TTCTTCAGGGAAGATTGAATCGA-GAAGACTTGTTCCACTATTCCTCAAGGAATATCAAATCTGG
* * * * * *
41569 A-AAAAGAGGGATCTATTCCACTGCTTCTTGAGGGAAAATTAGATCTGGAAATGTTGATTCATTC
65 AGAAAAGAGGGATATGTTCCTCTTCTTATTGAGGGAAAATCAGATCTGGAAATGTTGATTCATTC
41633 CACTG
130 CACTG
* *
41638 TTCTTCAGGGAAGATTGAATCGAGACAGACTTGTTCCACTGTTCCTCAAAGAATATCAAATCTGG
1 TTCTTCAGGGAAGATTGAATCGAGA-AGACTTGTTCCACTATTCCTCAAGGAATATCAAATCTGG
* * *
41703 AGAAAATGAGGGATTTGTTCCTCTTCTTATTGAGGGAAAATCAAATCTGGAAATTTTGATTCATT
65 AGAAAA-GAGGGATATGTTCCTCTTCTTATTGAGGGAAAATCAGATCTGGAAATGTTGATTCATT
*
41768 CCAATG
129 CCACTG
* * * * * * * *
41774 TTCTTCAGAGAAGATTGAATTGAGGAAAACTTGTTTCATTATTCCT-TAGGGATGATCGAATCT-
1 TTCTTCAGGGAAGATTGAATCGA-GAAGACTTGTTCCACTATTCCTCAAGGAAT-ATCAAATCTG
* * * * *
41837 -AGAAAAAAGAGATATGTT-CTGCTTCTTATTAAGGGAAAATCAGATCCGAAAATGTTGATTCAT
64 GAGAAAAGAGGGATATGTTCCT-CTTCTTATTGAGGGAAAATCAGATCTGGAAATGTTGATTCAT
41900 TCCACTG
128 TCCACTG
* *
41907 TTCTTTAGGGAATATTGAATCGAG
1 TTCTTCAGGGAAGATTGAATCGAG
41931 CTCGATTCGC
Statistics
Matches: 247, Mismatches: 40, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
132 3 0.01
133 72 0.29
134 62 0.25
135 8 0.03
136 100 0.40
137 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.33
Consensus pattern (134 bp):
TTCTTCAGGGAAGATTGAATCGAGAAGACTTGTTCCACTATTCCTCAAGGAATATCAAATCTGGA
GAAAAGAGGGATATGTTCCTCTTCTTATTGAGGGAAAATCAGATCTGGAAATGTTGATTCATTCC
ACTG
Found at i:43677 original size:15 final size:16
Alignment explanation
Indices: 43651--43680 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
43641 AACAGTGAAC
43651 AAAACAATACTTAATG
1 AAAACAATACTTAATG
43667 AAAAC-ATACTTAAT
1 AAAACAATACTTAAT
43681 AATTCATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.57, C:0.13, G:0.03, T:0.27
Consensus pattern (16 bp):
AAAACAATACTTAATG
Found at i:47989 original size:15 final size:16
Alignment explanation
Indices: 47965--47997 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
47955 CGAATAAATC
47965 TATAAAAATAAA-AAA
1 TATAAAAATAAAGAAA
*
47980 TATAACAATAAAGAAA
1 TATAAAAATAAAGAAA
47996 TA
1 TA
47998 AGATAATGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.21
Consensus pattern (16 bp):
TATAAAAATAAAGAAA
Found at i:56072 original size:20 final size:19
Alignment explanation
Indices: 56049--56116 Score: 61
Period size: 18 Copynumber: 3.5 Consensus size: 19
56039 AAGTGGGGAT
56049 AGAAGAAAAAAAGAGAATCA
1 AGAAGAAAAAAAGAGAAT-A
* *
56069 AGAAAAGAAAAAAGATAA-A
1 AGAAGA-AAAAAAGAGAATA
56088 A-AAGAAAGAAAAGAGAA-A
1 AGAAGAAA-AAAAGAGAATA
56106 AGATAGAAAAA
1 AGA-AGAAAAA
56117 TAAAAGGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
17 2 0.05
18 13 0.32
19 5 0.12
20 10 0.25
21 10 0.25
ACGTcount: A:0.75, C:0.01, G:0.19, T:0.04
Consensus pattern (19 bp):
AGAAGAAAAAAAGAGAATA
Found at i:56081 original size:7 final size:7
Alignment explanation
Indices: 56071--56193 Score: 56
Period size: 7 Copynumber: 17.1 Consensus size: 7
56061 GAGAATCAAG
56071 AAAAGAA
1 AAAAGAA
*
56078 AAAAGAT
1 AAAAGAA
56085 AAAA-AA
1 AAAAGAA
*
56091 GAAAGAA
1 AAAAGAA
*
56098 AAGAGAA
1 AAAAGAA
56105 AAGATAG-A
1 AA-A-AGAA
*
56113 AAAA-TA
1 AAAAGAA
*
56119 AAAGGAA
1 AAAAGAA
*
56126 AAATATAGA
1 AAA-AGA-A
56135 AAAAGAA
1 AAAAGAA
**
56142 AAGTGAA
1 AAAAGAA
56149 AAGATAGAAA
1 AA-A-AG-AA
56159 AAAAGAA
1 AAAAGAA
56166 AAAAG-A
1 AAAAGAA
*
56172 AAAAGAG
1 AAAAGAA
**
56179 AGGAGAA
1 AAAAGAA
56186 AAAAGAA
1 AAAAGAA
56193 A
1 A
56194 GAAAAATGAG
Statistics
Matches: 84, Mismatches: 21, Indels: 22
0.66 0.17 0.17
Matches are distributed among these distances:
6 15 0.18
7 49 0.58
8 8 0.10
9 8 0.10
10 4 0.05
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.06
Consensus pattern (7 bp):
AAAAGAA
Found at i:56088 original size:9 final size:8
Alignment explanation
Indices: 56071--56198 Score: 50
Period size: 9 Copynumber: 15.5 Consensus size: 8
56061 GAGAATCAAG
56071 AAAAG-AA
1 AAAAGAAA
56078 AAAAGATAA
1 AAAAGA-AA
56087 AAAAGAAA
1 AAAAGAAA
*
56095 GAAAAG-AG
1 -AAAAGAAA
*
56103 AAAAGATAG
1 AAAAGA-AA
*
56112 AAAA-ATA
1 AAAAGAAA
*
56119 AAAGGAAA
1 AAAAGAAA
* * *
56127 AATATAGA
1 AAAAGAAA
56135 AAAAG-AA
1 AAAAGAAA
**
56142 AAGTGAAA
1 AAAAGAAA
*
56150 AGATAGAAA
1 A-AAAGAAA
56159 AAAAG-AA
1 AAAAGAAA
56166 AAAAGAAA
1 AAAAGAAA
56174 AAGAGAGGAGAA
1 AA-A-A-GA-AA
56186 AAAAGAAA
1 AAAAGAAA
56194 GAAAA
1 -AAAA
56199 ATGAGAAAAA
Statistics
Matches: 90, Mismatches: 17, Indels: 26
0.68 0.13 0.20
Matches are distributed among these distances:
7 24 0.27
8 25 0.28
9 32 0.36
10 2 0.02
11 3 0.03
12 4 0.04
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.05
Consensus pattern (8 bp):
AAAAGAAA
Found at i:56090 original size:16 final size:15
Alignment explanation
Indices: 56071--56175 Score: 63
Period size: 16 Copynumber: 6.7 Consensus size: 15
56061 GAGAATCAAG
56071 AAAAGAAAAAAGATAA
1 AAAAGAAAAAA-ATAA
* *
56087 AAAAGAAAGAAAAGAG
1 AAAAGAAA-AAAATAA
56103 AAAAGATAGAAAAAT-A
1 AAAAGA-A-AAAAATAA
* *
56119 AAAGGAAAAATATAGA
1 AAAAGAAAAAAATA-A
*
56135 AAAAG--AAAAGTGAA
1 AAAAGAAAAAAAT-AA
*
56149 AAGATAGAAAAAAAGAA
1 AA-A-AGAAAAAAATAA
56166 AAAAGAAAAA
1 AAAAGAAAAA
56176 GAGAGGAGAA
Statistics
Matches: 68, Mismatches: 11, Indels: 21
0.68 0.11 0.21
Matches are distributed among these distances:
14 12 0.18
15 10 0.15
16 29 0.43
17 12 0.18
18 5 0.07
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (15 bp):
AAAAGAAAAAAATAA
Found at i:56096 original size:25 final size:26
Alignment explanation
Indices: 56068--56116 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
56058 AAAGAGAATC
56068 AAGAAAAGAAAAAAGATA-AAAAAGA
1 AAGAAAAGAAAAAAGATAGAAAAAGA
*
56093 AAGAAAAGAGAAAAGATAGAAAAA
1 AAGAAAAGAAAAAAGATAGAAAAA
56117 TAAAAGGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (26 bp):
AAGAAAAGAAAAAAGATAGAAAAAGA
Found at i:56128 original size:22 final size:22
Alignment explanation
Indices: 56071--56162 Score: 87
Period size: 22 Copynumber: 4.0 Consensus size: 22
56061 GAGAATCAAG
* *
56071 AAAAGAAAAAAGATAAAAAAGAA
1 AAAAGGAAAAAGATAGAAAA-AA
* *
56094 AGAAAAGAGAAAAGATAGAAAAAT
1 A-AAAGGA-AAAAGATAGAAAAAA
* *
56118 AAAAGGAAAAATATAGAAAAAG
1 AAAAGGAAAAAGATAGAAAAAA
56140 AAAAGTG-AAAAGATAGAAAAAA
1 AAAAG-GAAAAAGATAGAAAAAA
56162 A
1 A
56163 GAAAAAAGAA
Statistics
Matches: 57, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
22 32 0.56
23 7 0.12
24 6 0.11
25 12 0.21
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (22 bp):
AAAAGGAAAAAGATAGAAAAAA
Found at i:56186 original size:44 final size:43
Alignment explanation
Indices: 56071--56193 Score: 124
Period size: 44 Copynumber: 2.8 Consensus size: 43
56061 GAGAATCAAG
*
56071 AAAAGAAAAAAGATAAAAAAGAAAGAAAAGAGAAAAGATAGAAA
1 AAAAGAAAAAAGA-AAAAGAGAAAGAAAAGAGAAAAGATAGAAA
* * * *
56115 AATAA-AAGGAAAA-ATATAGAAAAAGAAAAGTGAAAAGATAGAAA
1 AA-AAGAA--AAAAGAAAAAGAGAAAGAAAAGAGAAAAGATAGAAA
* *
56159 AAAAGAAAAAAGAAAAAGAGAGGAGAAAAAAGAAA
1 AAAAGAAAAAAGAAAAAGAGA-AAGAAAAGAGAAA
56194 GAAAAATGAG
Statistics
Matches: 62, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
42 4 0.06
43 8 0.13
44 43 0.69
45 3 0.05
46 4 0.06
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.06
Consensus pattern (43 bp):
AAAAGAAAAAAGAAAAAGAGAAAGAAAAGAGAAAAGATAGAAA
Found at i:56204 original size:20 final size:19
Alignment explanation
Indices: 56056--56209 Score: 91
Period size: 20 Copynumber: 7.7 Consensus size: 19
56046 GATAGAAGAA
**
56056 AAAAAGAGAATCAAGAAAAG
1 AAAAAGAGAAAAAAG-AAAG
*
56076 AAAAAAGATAAAAAAGAAAG
1 -AAAAAGAGAAAAAAGAAAG
56096 -AAAAGAGAAAAGATAGAAA-
1 AAAAAGAGAAAA-A-AGAAAG
* * *
56115 AATAAA-AGGAAAAATATAG
1 AA-AAAGAGAAAAAAGAAAG
* *
56134 AAAAAGAAAAGTGAAAAGATAG
1 AAAAAGAGAA---AAAAGAAAG
*
56156 AAAAAAAGAAAAAAGAAA-
1 AAAAAGAGAAAAAAGAAAG
*
56174 AAGAGAGGAGAAAAAAGAAAG
1 AA-A-AAGAGAAAAAAGAAAG
56195 AAAAATGAGAAAAAA
1 AAAAA-GAGAAAAAA
56210 AATCAAATAT
Statistics
Matches: 104, Mismatches: 16, Indels: 27
0.71 0.11 0.18
Matches are distributed among these distances:
18 18 0.17
19 15 0.14
20 38 0.37
21 17 0.16
22 16 0.15
ACGTcount: A:0.74, C:0.01, G:0.19, T:0.06
Consensus pattern (19 bp):
AAAAAGAGAAAAAAGAAAG
Found at i:56205 original size:13 final size:12
Alignment explanation
Indices: 56068--56211 Score: 54
Period size: 12 Copynumber: 12.2 Consensus size: 12
56058 AAAGAGAATC
56068 AAGA-AAAGAAAA
1 AAGAGAAAG-AAA
* *
56080 AAGATAAAAAAGA
1 AAGAGAAAGAA-A
*
56093 AAGA-AAAGAGA
1 AAGAGAAAGAAA
*
56104 AA-AGATAGAAA
1 AAGAGAAAGAAA
* *
56115 AATA-AAAGGAA
1 AAGAGAAAGAAA
* *
56126 AA-ATATAGAAA
1 AAGAGAAAGAAA
*
56137 AAGA-AAAGTGAA
1 AAGAGAAAG-AAA
*
56149 AAGATAGAA-AAA
1 AAGAGA-AAGAAA
*
56161 AAGAAAAAAGAAA
1 AAG-AGAAAGAAA
*
56174 AAGAGAGGAGAAA
1 AAGAGA-AAGAAA
56187 AA-AGAAAGAAA
1 AAGAGAAAGAAA
56198 AATGAGAAA-AAA
1 AA-GAGAAAGAAA
56210 AA
1 AA
56212 TCAAATATTT
Statistics
Matches: 102, Mismatches: 16, Indels: 28
0.70 0.11 0.19
Matches are distributed among these distances:
10 2 0.02
11 34 0.33
12 35 0.34
13 29 0.28
14 2 0.02
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (12 bp):
AAGAGAAAGAAA
Done.