Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001518.1 Hibiscus syriacus cultivar Beakdansim tig00002966_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: 63081
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:4132 original size:21 final size:22
Alignment explanation
Indices: 4088--4135 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
4078 AATTAATAAG
4088 TTATATTTTATAATTTAAAAATT
1 TTATATTTTATAATTT-AAAATT
*
4111 TTATATTTTGTAATTT-AAATT
1 TTATATTTTATAATTTAAAATT
4132 TTAT
1 TTAT
4136 TTTAGATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 9 0.38
23 15 0.62
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
TTATATTTTATAATTTAAAATT
Found at i:4159 original size:25 final size:26
Alignment explanation
Indices: 4108--4159 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
4098 TAATTTAAAA
* * *
4108 ATTTTATATTTTGTAATTTAAATTTT
1 ATTTTAGATTTTGTAAGTTAAAATTT
4134 ATTTTAGATTTT-TAAGTTAAAATTT
1 ATTTTAGATTTTGTAAGTTAAAATTT
4159 A
1 A
4160 CAAAATTACG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.60
Consensus pattern (26 bp):
ATTTTAGATTTTGTAAGTTAAAATTT
Found at i:4518 original size:19 final size:20
Alignment explanation
Indices: 4494--4535 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
4484 CTACAATTAA
4494 TTATAAAAGTTTAAT-AAAT
1 TTATAAAAGTTTAATAAAAT
* *
4513 TTATAATATTTTAATAAAAT
1 TTATAAAAGTTTAATAAAAT
4533 TTA
1 TTA
4536 ATGTTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
TTATAAAAGTTTAATAAAAT
Found at i:4860 original size:23 final size:22
Alignment explanation
Indices: 4834--4877 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
4824 TTGTAAATTT
4834 ATAATATTT-TAATAAATTTAATG
1 ATAAT-TTTATAAT-AATTTAATG
4857 ATAATTTTATAATAATTTAAT
1 ATAATTTTATAATAATTTAAT
4878 AATTATAACG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
ATAATTTTATAATAATTTAATG
Found at i:4862 original size:11 final size:11
Alignment explanation
Indices: 4829--4880 Score: 56
Period size: 11 Copynumber: 5.0 Consensus size: 11
4819 AATTTTTGTA
4829 AATTT-ATAAT
1 AATTTAATAAT
*
4839 ATTTTAAT-A-
1 AATTTAATAAT
*
4848 AATTTAATGAT
1 AATTTAATAAT
*
4859 AATTTTATAAT
1 AATTTAATAAT
4870 AATTTAATAAT
1 AATTTAATAAT
4881 TATAACGGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
9 7 0.21
10 6 0.18
11 21 0.62
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (11 bp):
AATTTAATAAT
Found at i:7175 original size:21 final size:21
Alignment explanation
Indices: 7151--7197 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
7141 AGTGCCCAAC
*
7151 AATAACAAAATCGGTAGAAAA-
1 AATAACAAAACCGGTA-AAAAT
*
7172 AATATCAAAACCGGTAAAAAT
1 AATAACAAAACCGGTAAAAAT
7193 AATAA
1 AATAA
7198 TATTTCAGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.62, C:0.11, G:0.11, T:0.17
Consensus pattern (21 bp):
AATAACAAAACCGGTAAAAAT
Found at i:7595 original size:32 final size:32
Alignment explanation
Indices: 7559--7624 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
7549 GTCACTCGAC
7559 TATTTATTATGTTTCAAACTCATCATTTTTGG
1 TATTTATTATGTTTCAAACTCATCATTTTTGG
7591 TATTTATTATGTTTCAAACTCATCATTTTTGG
1 TATTTATTATGTTTCAAACTCATCATTTTTGG
7623 TA
1 TA
7625 AAAATTGATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.26, C:0.12, G:0.09, T:0.53
Consensus pattern (32 bp):
TATTTATTATGTTTCAAACTCATCATTTTTGG
Found at i:12886 original size:579 final size:579
Alignment explanation
Indices: 11788--12948 Score: 2214
Period size: 579 Copynumber: 2.0 Consensus size: 579
11778 TTGATGCTGG
*
11788 ATAAATCCAGTAATCTTGTCCATATACAATATCTTATGTTTTTGGTTAACTTTTTTATTACCCGT
1 ATAAATCCAGTAATCTTGTCCATATACAATATCTTATGTTTTTGATTAACTTTTTTATTACCCGT
** * *
11853 CAGTGTAGTTGGGGATCGACAATATTGGTGTTCTTGTATTGCGAGATGTACACTGATTCATTACT
66 CAGTGTAGTTGAAGATCGACAATATTGGCGTTCTTGTATTGCGAGATGTACAATGATTCATTACT
11918 TGTAAATGATGTGTATACGATTGAAATCATTGGATGCACGATATTATTACAATCGTGGGAATGTC
131 TGTAAATGATGTGTATACGATTGAAATCATTGGATGCACGATATTATTACAATCGTGGGAATGTC
11983 ACAGAATTCCATGGTTAACACCGATTAGCCGAACTGCAGTTGACTTTCCTCTTACCGGAAGGTAA
196 ACAGAATTCCATGGTTAACACCGATTAGCCGAACTGCAGTTGACTTTCCTCTTACCGGAAGGTAA
12048 TTTTTTATTTAAAATATTTGATCTTAAATTAATTAAAGAATATATTGTAAAGGAAAAATAATTAC
261 TTTTTTATTTAAAATATTTGATCTTAAATTAATTAAAGAATATATTGTAAAGGAAAAATAATTAC
12113 AGAATTTTATTTTGATTCGTATACAGATGGAGGCATAAAATAGAAAGAACGGGGTTGATGCACAA
326 AGAATTTTATTTTGATTCGTATACAGATGGAGGCATAAAATAGAAAGAACGGGGTTGATGCACAA
* *
12178 TAACGTGAAAGAGTTTAGGTTTAAGATTGACATCAAATGCAAAGTTGATGTATATATATAATTAA
391 TAACGTGAAAGAGTTTAGGTTTAAGATTGACATCAAATGCAAAGTTGAGGTATATATAAAATTAA
12243 TTAGCGAATTTATTTTTTATTATGTTTATATTATAATATTGTTGTTTATTTATTTAGTTGAATTT
456 TTAGCGAATTTATTTTTTATTATGTTTATATTATAATATTGTTGTTTATTTATTTAGTTGAATTT
12308 TATAATTATTTAATTAAATAATAACTATATAATTTTGTTTTATAGTTTATTTGGAGGCC
521 TATAATTATTTAATTAAATAATAACTATATAATTTTGTTTTATAGTTTATTTGGAGGCC
12367 ATAAATCCAGTAATCTTGTCCATATACAATATCTTATGTTTTTGATTAACTTTTTTATTACCCGT
1 ATAAATCCAGTAATCTTGTCCATATACAATATCTTATGTTTTTGATTAACTTTTTTATTACCCGT
12432 CAGTGTAGTTGAAGATCGACAATATTGGCGTTCTTGTATTGCGAGATGTACAATGATTCATTACT
66 CAGTGTAGTTGAAGATCGACAATATTGGCGTTCTTGTATTGCGAGATGTACAATGATTCATTACT
*
12497 TGTAAATGATGTGTATACGATTGAAATCGTTGGATGCACGATATTATTACAATCGTGGGAATGTC
131 TGTAAATGATGTGTATACGATTGAAATCATTGGATGCACGATATTATTACAATCGTGGGAATGTC
* *
12562 ACAGAATTCCATGGTTAACACCGATTAGCCGAACTGCAGTTGACTTTTCTCTTACCGGAATGTAA
196 ACAGAATTCCATGGTTAACACCGATTAGCCGAACTGCAGTTGACTTTCCTCTTACCGGAAGGTAA
12627 TTTTTTATTTAAAATATTTGATCTTAAATTAATTAAAGAATATATTGTAAAGGAAAAATAATTAC
261 TTTTTTATTTAAAATATTTGATCTTAAATTAATTAAAGAATATATTGTAAAGGAAAAATAATTAC
*
12692 ATAATTTTATTTTGATTCGTATACAGATGGAGGCATAAAATAGAAAGAACGGGGTTGATGCACAA
326 AGAATTTTATTTTGATTCGTATACAGATGGAGGCATAAAATAGAAAGAACGGGGTTGATGCACAA
12757 TAACGTGAAAGAGTTTAGGTTTAAGATTGACATCAAATGCAAAGTTGAGGTATATATAAAATTAA
391 TAACGTGAAAGAGTTTAGGTTTAAGATTGACATCAAATGCAAAGTTGAGGTATATATAAAATTAA
12822 TTAGCGAATTTATTTTTTATTATGTTTATATTATAATATTGTTGTTTATTTATTTAGTTGAATTT
456 TTAGCGAATTTATTTTTTATTATGTTTATATTATAATATTGTTGTTTATTTATTTAGTTGAATTT
*
12887 TATAATTATTTAATTAAATAATAACTATATAATTTTGTTTTATAGTTTATTTGGAGGTC
521 TATAATTATTTAATTAAATAATAACTATATAATTTTGTTTTATAGTTTATTTGGAGGCC
12946 ATA
1 ATA
12949 CGATGATGGA
Statistics
Matches: 570, Mismatches: 12, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
579 570 1.00
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (579 bp):
ATAAATCCAGTAATCTTGTCCATATACAATATCTTATGTTTTTGATTAACTTTTTTATTACCCGT
CAGTGTAGTTGAAGATCGACAATATTGGCGTTCTTGTATTGCGAGATGTACAATGATTCATTACT
TGTAAATGATGTGTATACGATTGAAATCATTGGATGCACGATATTATTACAATCGTGGGAATGTC
ACAGAATTCCATGGTTAACACCGATTAGCCGAACTGCAGTTGACTTTCCTCTTACCGGAAGGTAA
TTTTTTATTTAAAATATTTGATCTTAAATTAATTAAAGAATATATTGTAAAGGAAAAATAATTAC
AGAATTTTATTTTGATTCGTATACAGATGGAGGCATAAAATAGAAAGAACGGGGTTGATGCACAA
TAACGTGAAAGAGTTTAGGTTTAAGATTGACATCAAATGCAAAGTTGAGGTATATATAAAATTAA
TTAGCGAATTTATTTTTTATTATGTTTATATTATAATATTGTTGTTTATTTATTTAGTTGAATTT
TATAATTATTTAATTAAATAATAACTATATAATTTTGTTTTATAGTTTATTTGGAGGCC
Found at i:13941 original size:27 final size:28
Alignment explanation
Indices: 13895--13952 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 28
13885 AATATTAAAA
*
13895 TAAAAATTAAAGATATAATTTAAATATT
1 TAAAAATTAAAGATAAAATTTAAATATT
*
13923 TAAATATT-AAGATAAAATTTAAATATT
1 TAAAAATTAAAGATAAAATTTAAATATT
13950 TAA
1 TAA
13953 TCATTATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
27 21 0.75
28 7 0.25
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (28 bp):
TAAAAATTAAAGATAAAATTTAAATATT
Found at i:13982 original size:24 final size:24
Alignment explanation
Indices: 13946--14030 Score: 100
Period size: 24 Copynumber: 3.5 Consensus size: 24
13936 AAAATTTAAA
*
13946 TATTTAATCATTATTAGTAATAAT
1 TATTAAATCATTATTAGTAATAAT
* *
13970 TATTAAATAATTATTAGTAATTAT
1 TATTAAATCATTATTAGTAATAAT
* * *
13994 TA-TAATTTCATTATTAATAATCAT
1 TATTAA-ATCATTATTAGTAATAAT
14018 TATTAAATCATTA
1 TATTAAATCATTA
14031 AATATCAAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
23 3 0.06
24 45 0.88
25 3 0.06
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (24 bp):
TATTAAATCATTATTAGTAATAAT
Found at i:14019 original size:13 final size:13
Alignment explanation
Indices: 13950--14158 Score: 85
Period size: 13 Copynumber: 17.0 Consensus size: 13
13940 TTTAAATATT
*
13950 TAATCATTATTAG
1 TAATCATTATTAA
*
13963 TAATAATTATT-A
1 TAATCATTATTAA
* *
13975 -AATAATTATTAG
1 TAATCATTATTAA
*
13987 TAATTATTA-TAA
1 TAATCATTATTAA
*
13999 T-TTCATTATTAA
1 TAATCATTATTAA
14011 TAATCATTATT-A
1 TAATCATTATTAA
*
14023 -AATCATTA-AATA
1 TAATCATTATTA-A
14035 TCAAATCATTAAATTAA
1 T--AATCATT--ATTAA
* *
14052 TAATAATTAGT-A
1 TAATCATTATTAA
*
14064 -AAT-ATTATTAT
1 TAATCATTATTAA
*
14075 TAATCATTATTAG
1 TAATCATTATTAA
14088 TAATCA-TATTACA
1 TAATCATTATTA-A
* *
14101 T--T-AGTA-TCA
1 TAATCATTATTAA
** *
14110 -AATCAAAATTGA
1 TAATCATTATTAA
14122 TAATCATTATT-A
1 TAATCATTATTAA
*
14134 -AATCATTATTAG
1 TAATCATTATTAA
14146 TAATCATTATTAA
1 TAATCATTATTAA
14159 ATTATTAGTA
Statistics
Matches: 148, Mismatches: 24, Indels: 48
0.67 0.11 0.22
Matches are distributed among these distances:
9 1 0.01
10 8 0.05
11 41 0.28
12 21 0.14
13 60 0.41
15 13 0.09
17 3 0.02
18 1 0.01
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (13 bp):
TAATCATTATTAA
Found at i:14137 original size:24 final size:24
Alignment explanation
Indices: 14109--14160 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
14099 CATTAGTATC
14109 AAATCAAAATT-GATAATCATTATT
1 AAATCAAAATTAG-TAATCATTATT
**
14133 AAATCATTATTAGTAATCATTATT
1 AAATCAAAATTAGTAATCATTATT
14157 AAAT
1 AAAT
14161 TATTAGTATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (24 bp):
AAATCAAAATTAGTAATCATTATT
Found at i:14182 original size:22 final size:21
Alignment explanation
Indices: 14138--14187 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
14128 TTATTAAATC
*
14138 ATTATTAGTAATCATTATTAA
1 ATTATTAGTAATCATCATTAA
14159 ATTATTAGT-ATCAAATCATTAA
1 ATTATTAGTAATC--ATCATTAA
14181 ATTATTA
1 ATTATTA
14188 TTATTTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 3 0.12
21 9 0.35
22 14 0.54
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (21 bp):
ATTATTAGTAATCATCATTAA
Found at i:14558 original size:13 final size:13
Alignment explanation
Indices: 14505--14563 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
14495 ATGTTATCAA
*
14505 ATTAATAGTAATC
1 ATTATTAGTAATC
14518 ATTATTA--AATC
1 ATTATTAGTAATC
** *
14529 ATTAAAATTCAAATC
1 ATTATTAGT--AATC
14544 ATTATTAGTAATC
1 ATTATTAGTAATC
14557 ATTATTA
1 ATTATTA
14564 TCAAATCATT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
11 9 0.25
13 17 0.47
15 10 0.28
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.42
Consensus pattern (13 bp):
ATTATTAGTAATC
Found at i:14578 original size:22 final size:22
Alignment explanation
Indices: 14553--14596 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
14543 CATTATTAGT
*
14553 AATCATTATTATCAAATCATTA
1 AATCACTATTATCAAATCATTA
* *
14575 AATCGCTATTATTAAATCATTA
1 AATCACTATTATCAAATCATTA
14597 GTAGTAAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.14, G:0.02, T:0.41
Consensus pattern (22 bp):
AATCACTATTATCAAATCATTA
Found at i:14610 original size:22 final size:22
Alignment explanation
Indices: 14585--14630 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
14575 AATCGCTATT
*
14585 ATTAAATCATTAGTAGTAAATC
1 ATTAAATCATTAGTAATAAATC
*
14607 ATTAAATCATTATTAATAAATC
1 ATTAAATCATTAGTAATAAATC
14629 AT
1 AT
14631 ATCATTACTA
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:0.48, C:0.09, G:0.04, T:0.39
Consensus pattern (22 bp):
ATTAAATCATTAGTAATAAATC
Found at i:16771 original size:60 final size:60
Alignment explanation
Indices: 16703--16819 Score: 173
Period size: 60 Copynumber: 1.9 Consensus size: 60
16693 TCGTTCTCGC
* * *
16703 CCCCACCTATTCACGCATGCAGAGATTCTC-GACCCCCCAACATGCAGCAGGGATCACATT
1 CCCCACCTATTCACACATGCAGAGATTCTCGGA-CCCCAAACATACAGCAGGGATCACATT
* *
16763 CCCCACCTATTCATACATGCAGTGATTCTCGGACCCCAAACATACAGCAGGGATCAC
1 CCCCACCTATTCACACATGCAGAGATTCTCGGACCCCAAACATACAGCAGGGATCAC
16820 GTTCTCGGCC
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
60 49 0.96
61 2 0.04
ACGTcount: A:0.28, C:0.37, G:0.16, T:0.19
Consensus pattern (60 bp):
CCCCACCTATTCACACATGCAGAGATTCTCGGACCCCAAACATACAGCAGGGATCACATT
Found at i:18967 original size:26 final size:26
Alignment explanation
Indices: 18908--18967 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
18898 CTTAACGAGT
18908 ACTGCTGAGCACCATTAACGATGAGC
1 ACTGCTGAGCACCATTAACGATGAGC
* *
18934 ACTACTGAGCACTATTAACGATGAGC
1 ACTGCTGAGCACCATTAACGATGAGC
*
18960 ATTGCTGA
1 ACTGCTGA
18968 ACAAAAAACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (26 bp):
ACTGCTGAGCACCATTAACGATGAGC
Found at i:21008 original size:11 final size:11
Alignment explanation
Indices: 20992--21016 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20982 AATTCTACGT
20992 GTAAATAAAGA
1 GTAAATAAAGA
21003 GTAAATAAAGA
1 GTAAATAAAGA
21014 GTA
1 GTA
21017 GACGGCTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (11 bp):
GTAAATAAAGA
Found at i:22863 original size:21 final size:21
Alignment explanation
Indices: 22838--22880 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
22828 AAGCAAGGAG
22838 TGTTAAATATTTGAACATCCC
1 TGTTAAATATTTGAACATCCC
22859 TGTTAAATATTTGAACATCCC
1 TGTTAAATATTTGAACATCCC
22880 T
1 T
22881 ATCATTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.40
Consensus pattern (21 bp):
TGTTAAATATTTGAACATCCC
Found at i:26840 original size:23 final size:23
Alignment explanation
Indices: 26814--26882 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
26804 CACCACAGCT
*
26814 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
26837 CGTAGAATTGCACC-AGAGTGCCG
1 CGTAGAATTGCACCGA-AGTGCCA
* *
26860 CGTAGAATTGCACTGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
26883 TATAATAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
22 1 0.03
23 38 0.97
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:27077 original size:103 final size:103
Alignment explanation
Indices: 26898--27110 Score: 390
Period size: 103 Copynumber: 2.1 Consensus size: 103
26888 TAATTTCCAT
* *
26898 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
26963 GACTTCACACATGTTCCAAAGAATACATATATGTCCTG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
27001 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
27066 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
27104 AAGGACC
1 AAGGACC
27111 GCGTAGACCC
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 106 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:32082 original size:23 final size:23
Alignment explanation
Indices: 32056--32124 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
32046 CACCACAGCT
*
32056 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
32079 CGTAGAATTGCACCGGAGTGTCG
1 CGTAGAATTGCACCGAAGTGCCA
* *
32102 CGTAGAATTGCACTGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
32125 TATAATAATG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:32270 original size:103 final size:103
Alignment explanation
Indices: 32144--32344 Score: 348
Period size: 103 Copynumber: 2.0 Consensus size: 103
32134 GTCCATAAGG
*
32144 ACCACATATCATTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTCAACAGACT
1 ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCAACAGACT
*
32209 TCACACATGTTCCAAATAATACATATATGTCCCAAAGA
66 TCACACATGTTCCAAAGAATACATATATGTCCCAAAGA
* * *
32247 ACCACATATCATTCCTTAAGAATCATCTACATATGCCAAGGATCAAGTATGTGTCTCACCAGACT
1 ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCAACAGACT
*
32312 TCATACATGTTCCAAAGAATACATATATGTCCC
66 TCACACATGTTCCAAAGAATACATATATGTCCC
32345 GAAGGACCGC
Statistics
Matches: 92, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 92 1.00
ACGTcount: A:0.37, C:0.24, G:0.10, T:0.28
Consensus pattern (103 bp):
ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCAACAGACT
TCACACATGTTCCAAAGAATACATATATGTCCCAAAGA
Found at i:35771 original size:12 final size:12
Alignment explanation
Indices: 35751--35785 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
35741 CATTGATGCA
35751 CTACAGTAATTG
1 CTACAGTAATTG
* *
35763 CTACCGTAACTG
1 CTACAGTAATTG
35775 CTACAGTAATT
1 CTACAGTAATT
35786 TCAGCATTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.31
Consensus pattern (12 bp):
CTACAGTAATTG
Found at i:36306 original size:22 final size:21
Alignment explanation
Indices: 36281--36332 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 21
36271 GGTATACGAG
36281 TAAAATACCTGCACCGTAGTGC
1 TAAAA-ACCTGCACCGTAGTGC
*
36303 T--AAACCTGCACCGTAGTGG
1 TAAAAACCTGCACCGTAGTGC
36322 T--AAACCTGCAC
1 TAAAAACCTGCAC
36333 TAAGCTTACG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 26 0.90
20 2 0.07
22 1 0.03
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (21 bp):
TAAAAACCTGCACCGTAGTGC
Found at i:36311 original size:19 final size:19
Alignment explanation
Indices: 36287--36332 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
36277 CGAGTAAAAT
36287 ACCTGCACCGTAGTGCTAA
1 ACCTGCACCGTAGTGCTAA
*
36306 ACCTGCACCGTAGTGGTAA
1 ACCTGCACCGTAGTGCTAA
36325 ACCTGCAC
1 ACCTGCAC
36333 TAAGCTTACG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.26, C:0.33, G:0.22, T:0.20
Consensus pattern (19 bp):
ACCTGCACCGTAGTGCTAA
Found at i:39236 original size:29 final size:30
Alignment explanation
Indices: 39165--39224 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
39155 CAATTTAAGG
*
39165 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACGTGAATTGAATTTA
39196 CAAAATGTTTTTGGACGT-AATTGAATTTA
1 CAAAATGTTTTTGGACGTGAATTGAATTTA
39225 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.42
Consensus pattern (30 bp):
CAAAATGTTTTTGGACGTGAATTGAATTTA
Found at i:39340 original size:22 final size:22
Alignment explanation
Indices: 39314--39394 Score: 88
Period size: 22 Copynumber: 4.0 Consensus size: 22
39304 TTCAAGATTG
* *
39314 CCCAGGGGGTATAGATTCCCCC
1 CCCAGGGGGTACAGATACCCCC
39336 CCCAGGGGGTACAGATA----C
1 CCCAGGGGGTACAGATACCCCC
39354 CCC---GGGTACAGATACC-CC
1 CCCAGGGGGTACAGATACCCCC
39372 CCCAGGGGGTACAGATACCCCC
1 CCCAGGGGGTACAGATACCCCC
39394 C
1 C
39395 TGCAGGTTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
15 11 0.22
18 8 0.16
21 13 0.26
22 18 0.36
ACGTcount: A:0.22, C:0.38, G:0.27, T:0.12
Consensus pattern (22 bp):
CCCAGGGGGTACAGATACCCCC
Found at i:39356 original size:21 final size:21
Alignment explanation
Indices: 39314--39394 Score: 93
Period size: 21 Copynumber: 4.1 Consensus size: 21
39304 TTCAAGATTG
* *
39314 CCCAGGGGGTATAGATTCCCCC
1 CCCAGGGGGTACAGA-TACCCC
39336 CCCAGGGGGTACAGATA---C
1 CCCAGGGGGTACAGATACCCC
39354 CCC---GGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
39372 CCCAGGGGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
39393 CC
1 CC
39395 TGCAGGTTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
15 11 0.22
18 8 0.16
21 18 0.35
22 14 0.27
ACGTcount: A:0.22, C:0.38, G:0.27, T:0.12
Consensus pattern (21 bp):
CCCAGGGGGTACAGATACCCC
Found at i:39362 original size:15 final size:15
Alignment explanation
Indices: 39342--39371 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
39332 CCCCCCCAGG
39342 GGGTACAGATACCCC
1 GGGTACAGATACCCC
39357 GGGTACAGATACCCC
1 GGGTACAGATACCCC
39372 CCCAGGGGGT
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:0.27, C:0.33, G:0.27, T:0.13
Consensus pattern (15 bp):
GGGTACAGATACCCC
Found at i:39512 original size:21 final size:21
Alignment explanation
Indices: 39486--39549 Score: 119
Period size: 21 Copynumber: 3.0 Consensus size: 21
39476 ATTTGAATAT
39486 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTATCGATTCCC
39507 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTATCGATTCCC
*
39528 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTATCGATTCCC
39549 T
1 T
39550 CTATTCTGGA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTATCGATTCCC
Found at i:39606 original size:21 final size:21
Alignment explanation
Indices: 39577--39616 Score: 64
Period size: 20 Copynumber: 1.9 Consensus size: 21
39567 TTTGAGTATA
39577 AAAATCATCCCCAAACGGCTCC
1 AAAATCAT-CCCAAACGGCTCC
39599 AAAA-CATCCCAAACGGCT
1 AAAATCATCCCAAACGGCT
39617 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.61
21 3 0.17
22 4 0.22
ACGTcount: A:0.40, C:0.38, G:0.10, T:0.12
Consensus pattern (21 bp):
AAAATCATCCCAAACGGCTCC
Found at i:39870 original size:34 final size:32
Alignment explanation
Indices: 39831--39900 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
39821 TTTTGTAAAG
*
39831 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
39865 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
39897 GGGA
1 GGGA
39901 GTTGTAAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:40784 original size:19 final size:20
Alignment explanation
Indices: 40760--40807 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
40750 AACAATTTTC
*
40760 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
40779 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
40799 TTTTGAAAA
1 TTTTGAAAA
40808 AGGATTTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:42142 original size:29 final size:30
Alignment explanation
Indices: 42071--42130 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
42061 CAATTTAAGG
*
42071 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACGTGAATTGAATTTA
42102 CAAAATGTTTTTGGACGT-AATTGAATTTA
1 CAAAATGTTTTTGGACGTGAATTGAATTTA
42131 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.42
Consensus pattern (30 bp):
CAAAATGTTTTTGGACGTGAATTGAATTTA
Found at i:42245 original size:21 final size:21
Alignment explanation
Indices: 42220--42299 Score: 100
Period size: 21 Copynumber: 4.1 Consensus size: 21
42210 TTCAAGATTG
* *
42220 CCCAGGGGGTATAGATTCCCC
1 CCCAGGGGGTACAGATACCCC
42241 CCCAGGGGGTACAGATA---C
1 CCCAGGGGGTACAGATACCCC
42259 CCC---GGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
42277 CCCAGGGGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
42298 CC
1 CC
42300 TGCAGGTTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
15 11 0.22
18 8 0.16
21 32 0.63
ACGTcount: A:0.23, C:0.38, G:0.28, T:0.12
Consensus pattern (21 bp):
CCCAGGGGGTACAGATACCCC
Found at i:42266 original size:36 final size:36
Alignment explanation
Indices: 42226--42297 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
42216 ATTGCCCAGG
* *
42226 GGGTATAGATTCCCCCCCAGGGGGTACAGATACCCC
1 GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
42262 GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
1 GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
42298 CCTGCAGGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.24, C:0.35, G:0.28, T:0.14
Consensus pattern (36 bp):
GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
Found at i:42267 original size:15 final size:15
Alignment explanation
Indices: 42247--42276 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
42237 CCCCCCCAGG
42247 GGGTACAGATACCCC
1 GGGTACAGATACCCC
42262 GGGTACAGATACCCC
1 GGGTACAGATACCCC
42277 CCCAGGGGGT
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:0.27, C:0.33, G:0.27, T:0.13
Consensus pattern (15 bp):
GGGTACAGATACCCC
Found at i:42420 original size:21 final size:21
Alignment explanation
Indices: 42394--42433 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
42384 TGAATATTAT
*
42394 GAAGGGGTATCGATTCCCTAA
1 GAAGGGGTACCGATTCCCTAA
42415 GAAGGGGTACCGATTCCCT
1 GAAGGGGTACCGATTCCCT
42434 CTATTCTGGG
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:0.25, C:0.23, G:0.30, T:0.23
Consensus pattern (21 bp):
GAAGGGGTACCGATTCCCTAA
Found at i:42499 original size:20 final size:22
Alignment explanation
Indices: 42461--42500 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
42451 TTTGAGTATA
42461 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
42483 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
42501 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:42754 original size:34 final size:32
Alignment explanation
Indices: 42715--42784 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
42705 TTTTGTAAAG
*
42715 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
42749 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
42781 GGGA
1 GGGA
42785 GTTGTAAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:43103 original size:20 final size:20
Alignment explanation
Indices: 43078--43116 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
43068 TTTGCCCCAA
43078 TTCATCTAGTATCGATATTG
1 TTCATCTAGTATCGATATTG
43098 TTCATCTAGTATCGATATT
1 TTCATCTAGTATCGATATT
43117 CGAACCCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (20 bp):
TTCATCTAGTATCGATATTG
Found at i:45517 original size:18 final size:20
Alignment explanation
Indices: 45496--45542 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
45486 ACCTGACCCG
45496 AAATAATATATTTATT-AA-
1 AAATAATATATTTATTCAAT
* *
45514 AAATATTATTTTTATTCAAT
1 AAATAATATATTTATTCAAT
45534 AAA-AATATA
1 AAATAATATA
45543 GATTTAATTG
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 14 0.61
19 6 0.26
20 3 0.13
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
AAATAATATATTTATTCAAT
Found at i:47566 original size:16 final size:17
Alignment explanation
Indices: 47540--47583 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
47530 ATAGTAGTAA
47540 AATATTA-TTTTA-AAT
1 AATATTATTTTTACAAT
47555 AAT-TATATTTTTACAAT
1 AATAT-TATTTTTACAAT
47572 AATATTATTTTT
1 AATATTATTTTT
47584 TTCATCACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 1 0.04
15 5 0.20
16 5 0.20
17 13 0.52
18 1 0.04
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
AATATTATTTTTACAAT
Found at i:47597 original size:23 final size:23
Alignment explanation
Indices: 47567--47612 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
47557 TTATATTTTT
*
47567 ACAATAATATTATTTTTTTCATC
1 ACAATAATACTATTTTTTTCATC
47590 ACAATAATACTATTTTTTTCATC
1 ACAATAATACTATTTTTTTCATC
47613 CAAAAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (23 bp):
ACAATAATACTATTTTTTTCATC
Found at i:48801 original size:56 final size:56
Alignment explanation
Indices: 48719--48890 Score: 247
Period size: 56 Copynumber: 3.1 Consensus size: 56
48709 CTATTTTTTA
* * * *
48719 ATATATTCAATTTTGGG-CTCCTATTTTTATGCTTCTTAATGGCAACAATTGATAG
1 ATATATTCGATTTCGGGACCCCTATTTTTATGCTTCTTAATGGCAACAACTGATAG
*
48774 ATATATTCGATTTCGGGACCCCTATTTTTATGTTTCTTAATGGCAACAACTGATAG
1 ATATATTCGATTTCGGGACCCCTATTTTTATGCTTCTTAATGGCAACAACTGATAG
* * ** *
48830 ATATACTCGATTTCGGGACCCCTATTTTTATGCTTATTAATGATAACAACTAATAG
1 ATATATTCGATTTCGGGACCCCTATTTTTATGCTTCTTAATGGCAACAACTGATAG
48886 ATATA
1 ATATA
48891 CTCAATTCCG
Statistics
Matches: 105, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
55 15 0.14
56 90 0.86
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (56 bp):
ATATATTCGATTTCGGGACCCCTATTTTTATGCTTCTTAATGGCAACAACTGATAG
Found at i:48891 original size:56 final size:56
Alignment explanation
Indices: 48738--48951 Score: 222
Period size: 56 Copynumber: 3.9 Consensus size: 56
48728 ATTTTGGGCT
* * * * *
48738 CCTATTTTTATGCTTCTTAATGGCAACAATTGATAGATATATTCGATTTCGGGACC
1 CCTATTTTTATGCTTATTAATGACAACAACTAATAGATATACTCGATTTCGGGACC
* * * *
48794 CCTATTTTTATGTTTCTTAATGGCAACAACTGATAGATATACTCGATTTCGGGACC
1 CCTATTTTTATGCTTATTAATGACAACAACTAATAGATATACTCGATTTCGGGACC
* * * *
48850 CCTATTTTTATGCTTATTAATGATAACAACTAATAGATATACTC-AATTC-CGATGC
1 CCTATTTTTATGCTTATTAATGACAACAACTAATAGATATACTCGATTTCGGGA-CC
** * *
48905 TTTATTTTTATGCTTATTTAAT---AATAACTAATAAATATACTCGATTT
1 CCTATTTTTATGCTTA-TTAATGACAACAACTAATAGATATACTCGATTT
48952 TGAAGTACCT
Statistics
Matches: 139, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
53 18 0.13
54 5 0.04
55 19 0.14
56 97 0.70
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (56 bp):
CCTATTTTTATGCTTATTAATGACAACAACTAATAGATATACTCGATTTCGGGACC
Found at i:51492 original size:20 final size:19
Alignment explanation
Indices: 51451--51498 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
51441 AATAAATCAA
* *
51451 AAATAATAATTTAACTACT
1 AAATAATAATTTAACCAAT
*
51470 AAATAGATAATTTATCCAAT
1 AAATA-ATAATTTAACCAAT
51490 AAATTAATA
1 AAA-TAATA
51499 TTTTTTTGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 5 0.21
20 17 0.71
21 2 0.08
ACGTcount: A:0.54, C:0.08, G:0.02, T:0.35
Consensus pattern (19 bp):
AAATAATAATTTAACCAAT
Found at i:58922 original size:14 final size:15
Alignment explanation
Indices: 58902--58943 Score: 77
Period size: 14 Copynumber: 2.9 Consensus size: 15
58892 AGCATTATAT
58902 GTTATGTGATATGAA
1 GTTATGTGATATGAA
58917 -TTATGTGATATGAA
1 GTTATGTGATATGAA
58931 GTTATGTGATATG
1 GTTATGTGATATG
58944 TGTTATAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.31, C:0.00, G:0.26, T:0.43
Consensus pattern (15 bp):
GTTATGTGATATGAA
Found at i:58948 original size:14 final size:14
Alignment explanation
Indices: 58902--58949 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
58892 AGCATTATAT
58902 GTTATGTGATATGA
1 GTTATGTGATATGA
*
58916 ATTATGTGATATGAA
1 GTTATGTGATATG-A
*
58931 GTTATGTGATATGT
1 GTTATGTGATATGA
58945 GTTAT
1 GTTAT
58950 AAGACAATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
14 17 0.57
15 13 0.43
ACGTcount: A:0.29, C:0.00, G:0.25, T:0.46
Consensus pattern (14 bp):
GTTATGTGATATGA
Found at i:59175 original size:21 final size:21
Alignment explanation
Indices: 59149--59191 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
59139 TCGAGGGTTC
*
59149 TATGTGGTCCTTTGGGACAAA
1 TATGTGGTCCTTCGGGACAAA
59170 TATGTGGTCCTTCGGGACAAA
1 TATGTGGTCCTTCGGGACAAA
59191 T
1 T
59192 CCTATGTGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (21 bp):
TATGTGGTCCTTCGGGACAAA
Found at i:61764 original size:59 final size:60
Alignment explanation
Indices: 61615--61747 Score: 220
Period size: 60 Copynumber: 2.3 Consensus size: 60
61605 AGAGATTTTT
* *
61615 TTTGACAAAAAAATAATTGAAGTACTTAAAGTGATTACATATAATAGTTTAAGTAACTAG
1 TTTGACCAAAAAATAATTGAAGTACTTAAAGTAATTACATATAATAGTTTAAGTAACTAG
61675 TTTGACCAAAAAATAATTGAAGTACTTAAAGTAATTACATATAATAG-TTAAGTAA-TAG
1 TTTGACCAAAAAATAATTGAAGTACTTAAAGTAATTACATATAATAGTTTAAGTAACTAG
61733 -TTGACC-AAAAATAAT
1 TTTGACCAAAAAATAAT
61748 AATTTAGTTA
Statistics
Matches: 71, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
56 9 0.13
57 6 0.08
58 3 0.04
59 8 0.11
60 45 0.63
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (60 bp):
TTTGACCAAAAAATAATTGAAGTACTTAAAGTAATTACATATAATAGTTTAAGTAACTAG
Found at i:62142 original size:2 final size:2
Alignment explanation
Indices: 62135--62165 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
62125 TCGATTCAGT
62135 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
62166 TATTTTAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.