Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004252.1 Hibiscus syriacus cultivar Beakdansim tig00009323_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: 65802
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:4189 original size:21 final size:21
Alignment explanation
Indices: 4165--4204 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
4155 TTTATTTTAT
4165 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
4186 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
4205 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:4253 original size:33 final size:32
Alignment explanation
Indices: 4199--4297 Score: 153
Period size: 33 Copynumber: 3.0 Consensus size: 32
4189 TTTGTTTCAA
4199 TTATCGAACTTGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGAAGTTTTTAAGTATTTGAAT
4231 TTATCGAACTTGAAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTG-AAGTTTTTAAGTATTTGAAT
* * *
4264 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
4297 T
1 T
4298 ATGTTGAGTT
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
32 12 0.19
33 49 0.79
34 1 0.02
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.45
Consensus pattern (32 bp):
TTATCGAACTTGAAGTTTTTAAGTATTTGAAT
Found at i:4326 original size:13 final size:13
Alignment explanation
Indices: 4283--4337 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
4273 TTGGAAGTAT
4283 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
4296 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
4310 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
4323 TTAAGTATTTGAA
1 TTAAGTATTTCAA
4336 TT
1 TT
4338 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:4554 original size:21 final size:21
Alignment explanation
Indices: 4528--4567 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4518 TGGAGCATGG
4528 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTACCCTCTCATA
**
4549 GGGAATCGGTTTCCTCTCA
1 GGGAATCGGTACCCTCTCA
4568 AATACTTGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.28, G:0.25, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTACCCTCTCATA
Found at i:4733 original size:17 final size:17
Alignment explanation
Indices: 4707--4755 Score: 80
Period size: 17 Copynumber: 2.9 Consensus size: 17
4697 CCGGTTTCGG
*
4707 TTTTTAAAAAAACCGGC
1 TTTTTTAAAAAACCGGC
*
4724 TTTTTTAAAAAACCGGT
1 TTTTTTAAAAAACCGGC
4741 TTTTTTAAAAAACCG
1 TTTTTTAAAAAACCG
4756 TTATAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (17 bp):
TTTTTTAAAAAACCGGC
Found at i:4988 original size:21 final size:21
Alignment explanation
Indices: 4934--4990 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
4924 TTTTACACTT
*
4934 AGGGAACCGATTACCTATGAG
1 AGGGAACCGATTCCCTATGAG
*
4955 AGGAAACCGATTCCCTATGAG
1 AGGGAACCGATTCCCTATGAG
*
4976 AGGGTACCGATTCCC
1 AGGGAACCGATTCCC
4991 CATGCTCCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGAACCGATTCCCTATGAG
Found at i:5317 original size:32 final size:33
Alignment explanation
Indices: 5221--5319 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
5211 AACTCAACAT
* * *
5221 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
5254 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
5287 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
5319 A
1 A
5320 TTGAACAAAG
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:7632 original size:11 final size:12
Alignment explanation
Indices: 7611--7656 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
7601 TCCGGATAAA
7611 AACCGGTTTTTT
1 AACCGGTTTTTT
7623 AACCGGTTTTTTT
1 AACCGG-TTTTTT
7636 CAAACCGGTTTTTT
1 --AACCGGTTTTTT
*
7650 ATCCGGT
1 AACCGGT
7657 AAAAAAACCG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 12 0.40
13 6 0.20
14 6 0.20
15 6 0.20
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:7641 original size:15 final size:14
Alignment explanation
Indices: 7610--7649 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
7600 TTCCGGATAA
7610 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
7623 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
7636 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
7650 ATCCGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
15 12 0.50
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:7770 original size:27 final size:28
Alignment explanation
Indices: 7739--7796 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
7729 AAAAAACCTG
*
7739 TTTTTC-CCAAATCCGAT-TTCGAATATT
1 TTTTTCGCAAAATCCGATATTCGAAT-TT
*
7766 TTTTTCGCAAAATCGGATATTCGAATTT
1 TTTTTCGCAAAATCCGATATTCGAATTT
7794 TTT
1 TTT
7797 GTGCACCCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 6 0.22
28 14 0.52
29 7 0.26
ACGTcount: A:0.26, C:0.17, G:0.10, T:0.47
Consensus pattern (28 bp):
TTTTTCGCAAAATCCGATATTCGAATTT
Found at i:8660 original size:13 final size:13
Alignment explanation
Indices: 8614--8660 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
8604 ATTCAAATTT
8614 AAAATTTAAACT-
1 AAAATTTAAACTC
*
8626 AATTATTTAAACTTC
1 AA-AATTTAAAC-TC
8641 TAAAATTTAAACTC
1 -AAAATTTAAACTC
8655 AAAATT
1 AAAATT
8661 CAAATTGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
12 2 0.07
13 14 0.48
14 3 0.10
15 8 0.28
16 2 0.07
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (13 bp):
AAAATTTAAACTC
Found at i:20854 original size:35 final size:35
Alignment explanation
Indices: 20808--20879 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
20798 TGGCAGTGCA
20808 CATGTCATAATCATGCAACATTGGTGAGCTAGGGC
1 CATGTCATAATCATGCAACATTGGTGAGCTAGGGC
20843 CATGTCATAATCATGCAACATTGGTGAGCTAGGGC
1 CATGTCATAATCATGCAACATTGGTGAGCTAGGGC
20878 CA
1 CA
20880 ACTGCATATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (35 bp):
CATGTCATAATCATGCAACATTGGTGAGCTAGGGC
Found at i:21568 original size:6 final size:6
Alignment explanation
Indices: 21557--21590 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
21547 GGGGCCTACA
*
21557 AAAAAT AAAAAT AAAAAT AATAAT AATAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AA-AAAT AAA
21591 TAAATAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (6 bp):
AAAAAT
Found at i:21584 original size:15 final size:14
Alignment explanation
Indices: 21556--21599 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
21546 TGGGGCCTAC
*
21556 AAAAAATAAAAATA
1 AAAAAATAATAATA
21570 AAAATAATAATAATA
1 AAAA-AATAATAATA
*
21585 AATAAATAAATAATA
1 AAAAAAT-AATAATA
21600 TAATATAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 7 0.27
15 19 0.73
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAAAATAATAATA
Found at i:21607 original size:18 final size:18
Alignment explanation
Indices: 21560--21607 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
21550 GCCTACAAAA
* *
21560 AATAAAAATAAAAATAAT
1 AATAATAATATAAATAAT
21578 AATAATAA-ATAAATAAAT
1 AATAATAATATAAAT-AAT
21596 AAT-ATAATATAA
1 AATAATAATATAA
21608 TGTTTTTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 9 0.35
18 17 0.65
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (18 bp):
AATAATAATATAAATAAT
Found at i:22011 original size:84 final size:84
Alignment explanation
Indices: 21864--22236 Score: 379
Period size: 84 Copynumber: 4.4 Consensus size: 84
21854 TTGTTGACAT
* * * * * **
21864 ATAACCCTTCTCA-CCTTGAGCTATGATGTAAATTTGATTTGCCTTTGAGTTGAATGTAATCGAA
1 ATAACCCTTCT-AGCCTTGAGTTATGCTGCAAA--TGATGTGCCTTTGAGCTGAGCGTAATCGAA
* * * *
21928 GTCAAAGGTCTTTGGTTGCCAG
63 CTCGAAGGTCTTTGGTTGGCAA
* * * * ** * *
21950 ATAGCCCTTCTCGACTTAAACTATGCTGCAAATGATGTGGCTTTGAGCTGAGTGTAATCGAACTC
1 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAATCGAACTC
* * *
22015 GAAGGTATTTTGTTGGCAG
66 GAAGGTCTTTGGTTGGCAA
* * * *
22034 ATAAACCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCATAGTCGAACTC
1 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAATCGAACTC
22099 GAAGGTCTTTGGTTGGCAA
66 GAAGGTCTTTGGTTGGCAA
* * *
22118 ATAACGCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTTGAGCTGAGCGTAGTCGAACTC
1 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAATCGAACTC
* *
22183 GAAGGTCTTTTGTTGACAA
66 GAAGGTCTTTGGTTGGCAA
* ** * * *
22202 ATAGCCCTTCTTTCCTTGAGCTATGTTACAAATGA
1 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGA
22237 ACACGATATC
Statistics
Matches: 241, Mismatches: 45, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
84 217 0.90
86 24 0.10
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (84 bp):
ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAATCGAACTC
GAAGGTCTTTGGTTGGCAA
Found at i:22436 original size:124 final size:123
Alignment explanation
Indices: 22287--22885 Score: 521
Period size: 124 Copynumber: 4.8 Consensus size: 123
22277 ATTGCTACTT
* * * * * * * **
22287 GTGGGCATGATATCCTTCGTTGTGAAGTTGAAATCGTGGAGGGCCCTTTCGTTGTGAAAATGAGC
1 GTGGGCACGAT-TCCTTCGTCGTGAAGTTGAAACCGTGGATGACCCATTCATTGTGAAGTTGAGC
* * * * *
22352 CTTGAATTGGATATCCTTCATCATGAAGTTGAAATCCAATATGAAGATGAATGTTGCTG
65 CTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTA
* *
22411 GTGGGCACGATTCCTTTCGTCGTGAAGTTGAAACCATGGATGACCCCTTCATTGTGAAGTTGAGC
1 GTGGGCACGATTCC-TTCGTCGTGAAGTTGAAACCGTGGATGACCCATTCATTGTGAAGTTGAGC
* * *
22476 CTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATTCGATCTAAAGATGAATGTTACTA
65 CTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTA
* * *
22535 GTGAGCACGATTTCCTTCGTCGTGAAGTTGAAACCGTGGATGACCCAATCTTTGTGAAGTTGAGC
1 GTGGGCACGA-TTCCTTCGTCGTGAAGTTGAAACCGTGGATGACCCATTCATTGTGAAGTTGAGC
22600 CTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTTCAA
65 CTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGC-T--A
* * * * * *
22662 GT--CCA-AAATCCTTCGCCGTGAAGTTGAAATTGGCTCTGAATGAAACTGGGAAGCCCATTCAC
1 GTGGGCACGATTCCTTCGTCGTGAAGTTGAAA----C-C-G--TG-GA-T--G-A-CCCATTCAT
* *
22724 CGTGAAGTTGAGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCT----A-G-A-
52 TGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAAT
22782 ---G-T-
117 GTTGCTA
* * * * * *
22784 -T-GGCACGATATCCTTCGTCGTGAAGTTGAAATCGTAGACGACCCCTTCGTTGTGAAGCTGAGC
1 GTGGGCACGAT-TCCTTCGTCGTGAAGTTGAAACCGTGGATGACCCATTCATTGTGAAGTTGAGC
* * * * *
22847 CTTGACTTGAATATCTTTCGTCGTAAAGTTGATATCCAA
65 CTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAA
22886 GCTTGTATTG
Statistics
Matches: 398, Mismatches: 55, Indels: 58
0.78 0.11 0.11
Matches are distributed among these distances:
110 50 0.13
111 1 0.00
112 1 0.00
115 1 0.00
116 1 0.00
118 1 0.00
119 1 0.00
121 1 0.00
122 2 0.01
123 24 0.06
124 232 0.58
125 8 0.02
127 5 0.01
128 1 0.00
129 1 0.00
131 3 0.01
132 2 0.01
133 2 0.01
135 1 0.00
136 1 0.00
137 59 0.15
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.31
Consensus pattern (123 bp):
GTGGGCACGATTCCTTCGTCGTGAAGTTGAAACCGTGGATGACCCATTCATTGTGAAGTTGAGCC
TTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTA
Found at i:22969 original size:240 final size:242
Alignment explanation
Indices: 22539--23126 Score: 838
Period size: 240 Copynumber: 2.4 Consensus size: 242
22529 TTACTAGTGA
* * * *
22539 GCACGATTTCCTTCGTCGTGAAGTTGAAACCGTGGATGACCCAATCTTTGTGAAGTTGAGCCTTG
1 GCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTG
* * * *
22604 AATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTTCAAGTCCAAA
66 ACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCT----ATG-ATATTGCTTCAAGTCCAAA
* *
22669 ATCCTTCGCCGTGAAGTTGAAATTGGCTCTGAATGAAACTGGGAAGCCCATTCACCGTGAAGTTG
126 ATCCTTCGCAGTGAAGTTAAAATTGGCTCTGAATGAAACTGGGAAGCCCATTCACCGTGAAGTTG
* *
22734 AGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGTTG
191 AGCTTTGAATTGGATATCCTTCATCATGAAGTTGAAATCCAATCTAGAGTTG
* * * *
22786 GCACGATATCCTTCGTCGTGAAGTTGAAATCGTAGACGACCCCTTCGTTGTGAAGCTGAGCCTTG
1 GCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTG
* * * * * *
22851 ACTTGAATATCTTTCGTCGTAAAGTTGATATCCAAGCT-TG-TATTGTTTCGAGTCCAATATCCT
66 ACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCTATGATATTGCTTCAAGTCCAAAATCCT
*
22914 TCGCAGTGAAGTTAAAATTGGCTCTGAATGAAACTGGGAAGCCCCTTCACCGTGAAGTTGAGCTT
131 TCGCAGTGAAGTTAAAATTGGCTCTGAATGAAACTGGGAAGCCCATTCACCGTGAAGTTGAGCTT
* *
22979 TGAATTGGATATCCTTCATCATGAATTTGAAATCCAATCTAGAGTTT
196 TGAATTGGATATCCTTCATCATGAAGTTGAAATCCAATCTAGAGTTG
* * * * *
23026 ACATGATATCCTTTGTCGTGAAGTTGAAATCGTGGATGGCCCATTCGTTGTGAAGTTGAGCATTG
1 GCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTG
*
23091 ACTTGAATATCCTTCGTCGTGAAGTTGAAATTCAAG
66 ACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAG
23127 TATTGTATGT
Statistics
Matches: 303, Mismatches: 38, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
240 212 0.70
242 2 0.01
247 89 0.29
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.32
Consensus pattern (242 bp):
GCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTG
ACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCTATGATATTGCTTCAAGTCCAAAATCCT
TCGCAGTGAAGTTAAAATTGGCTCTGAATGAAACTGGGAAGCCCATTCACCGTGAAGTTGAGCTT
TGAATTGGATATCCTTCATCATGAAGTTGAAATCCAATCTAGAGTTG
Found at i:24391 original size:95 final size:95
Alignment explanation
Indices: 24266--24465 Score: 319
Period size: 95 Copynumber: 2.1 Consensus size: 95
24256 ATTGTATAGG
*
24266 TATTATAATCACCTTTATCATGCTAACTGAATATTATCTATAAAGTAGAGGCGTTTAACCAATTG
1 TATTATAATCACCTTTATCATGCTAACTGAATATTATCTATAAAGCAGAGGCGTTTAACCAATTG
24331 CTCTAGAGGAACAACTCAAGCTTTATTGTA
66 CTCTAGAGGAACAACTCAAGCTTTATTGTA
* * * * * *
24361 TATTATAATCACCTTTATCATGCTAGCTGAATCTTATTTATAAAGCCGGGGCGTTTAACCAATTT
1 TATTATAATCACCTTTATCATGCTAACTGAATATTATCTATAAAGCAGAGGCGTTTAACCAATTG
*
24426 CTCTAGAGGGACAACTCAAGCTTTATTGTA
66 CTCTAGAGGAACAACTCAAGCTTTATTGTA
24456 TATATATAAT
1 TAT-TATAAT
24466 ATTATAATCT
Statistics
Matches: 96, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
95 90 0.94
96 6 0.06
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (95 bp):
TATTATAATCACCTTTATCATGCTAACTGAATATTATCTATAAAGCAGAGGCGTTTAACCAATTG
CTCTAGAGGAACAACTCAAGCTTTATTGTA
Found at i:28174 original size:3 final size:3
Alignment explanation
Indices: 28166--28203 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
28156 GCCTACAAAA
28166 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
28204 TTTTTTACAG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.12
3 29 0.88
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:29328 original size:27 final size:26
Alignment explanation
Indices: 29273--29332 Score: 93
Period size: 27 Copynumber: 2.3 Consensus size: 26
29263 ATATTAAATA
*
29273 AATTAAAATTATATAAAAAGCTCTCC
1 AATTATAATTATATAAAAAGCTCTCC
*
29299 AATTATAATTATATAAAAAAGCTCTTC
1 AATTATAATTATAT-AAAAAGCTCTCC
29326 AATTATA
1 AATTATA
29333 TGATGACACG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 13 0.42
27 18 0.58
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.35
Consensus pattern (26 bp):
AATTATAATTATATAAAAAGCTCTCC
Found at i:38946 original size:18 final size:18
Alignment explanation
Indices: 38923--38978 Score: 103
Period size: 18 Copynumber: 3.1 Consensus size: 18
38913 ATGATAATGT
*
38923 CCTAATTCTACAACCATG
1 CCTAATTCTACAGCCATG
38941 CCTAATTCTACAGCCATG
1 CCTAATTCTACAGCCATG
38959 CCTAATTCTACAGCCATG
1 CCTAATTCTACAGCCATG
38977 CC
1 CC
38979 GGTGAACAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.29, C:0.36, G:0.09, T:0.27
Consensus pattern (18 bp):
CCTAATTCTACAGCCATG
Found at i:41638 original size:284 final size:284
Alignment explanation
Indices: 41121--41680 Score: 1093
Period size: 284 Copynumber: 2.0 Consensus size: 284
41111 ATAAAATATA
41121 CTTACAGAACTATATAACTTGCTTTTATAGAACTATCCTTGTAAATCAGAGCTCAGCAGGCAATC
1 CTTACAGAACTATATAACTTGCTTTTATAGAACTATCCTTGTAAATCAGAGCTCAGCAGGCAATC
41186 TCGCCATATTACTCGCCATCATCTTTCTAAACAAATAAAGGGATAAACGAAACAGTTCTTTGGCC
66 TCGCCATATTACTCGCCATCATCTTTCTAAACAAATAAAGGGATAAACGAAACAGTTCTTTGGCC
41251 TGGAATTTTCCAATTCAATTAAAATGTCAAATAAGTCTAGAAATACTCGGTTATTTGTTGAGGAT
131 TGGAATTTTCCAATTCAATTAAAATGTCAAATAAGTCTAGAAATACTCGGTTATTTGTTGAGGAT
41316 TTAGGGTTTAAAATGTTAAATTTTTATATAAAACTATAAAACATGTGAAGTCATCAAAGTGAGGA
196 TTAGGGTTTAAAATGTTAAATTTTTATATAAAACTATAAAACATGTGAAGTCATCAAAGTGAGGA
41381 TCTAAAGGAAAATTCAGAGCTATC
261 TCTAAAGGAAAATTCAGAGCTATC
*
41405 CTTATAGAACTATATAACTTGCTTTTATAGAACTATCCTTGTAAATCAGAGCTCAGCAGGCAATC
1 CTTACAGAACTATATAACTTGCTTTTATAGAACTATCCTTGTAAATCAGAGCTCAGCAGGCAATC
41470 TCGCCATATTACTCGCCATCATCTTTCTAAACAAATAAAGGGATAAACGAAACAGTTCTTTGGCC
66 TCGCCATATTACTCGCCATCATCTTTCTAAACAAATAAAGGGATAAACGAAACAGTTCTTTGGCC
*
41535 TGGAATTTTCTAATTCAATTAAAATGTCAAATAAGTCTAGAAATACTCGGTTATTTGTTGAGGAT
131 TGGAATTTTCCAATTCAATTAAAATGTCAAATAAGTCTAGAAATACTCGGTTATTTGTTGAGGAT
*
41600 TTAGGGTTTAAAATGTTAAATTTTTATATAATACTATAAAACATGTGAAGTCATCAAAGTGAGGA
196 TTAGGGTTTAAAATGTTAAATTTTTATATAAAACTATAAAACATGTGAAGTCATCAAAGTGAGGA
41665 TCTAAAGGAAAATTCA
261 TCTAAAGGAAAATTCA
41681 ACACTTCAAA
Statistics
Matches: 273, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
284 273 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (284 bp):
CTTACAGAACTATATAACTTGCTTTTATAGAACTATCCTTGTAAATCAGAGCTCAGCAGGCAATC
TCGCCATATTACTCGCCATCATCTTTCTAAACAAATAAAGGGATAAACGAAACAGTTCTTTGGCC
TGGAATTTTCCAATTCAATTAAAATGTCAAATAAGTCTAGAAATACTCGGTTATTTGTTGAGGAT
TTAGGGTTTAAAATGTTAAATTTTTATATAAAACTATAAAACATGTGAAGTCATCAAAGTGAGGA
TCTAAAGGAAAATTCAGAGCTATC
Found at i:45100 original size:20 final size:19
Alignment explanation
Indices: 45067--45105 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
45057 TCAATATTTA
*
45067 TTTATTTTATTAAATTAAT
1 TTTAATTTATTAAATTAAT
45086 TTTAATTTATATAAATTAAT
1 TTTAATTTAT-TAAATTAAT
45106 AATTGGGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTAATTTATTAAATTAAT
Found at i:47719 original size:15 final size:15
Alignment explanation
Indices: 47699--47728 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
47689 TAATAAGGTT
47699 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
47714 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
47729 TGGATTGATT
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:47756 original size:36 final size:33
Alignment explanation
Indices: 47699--47938 Score: 117
Period size: 32 Copynumber: 7.5 Consensus size: 33
47689 TAATAAGGTT
47699 ATTTATTTTAAAATAATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATAATTTA--TT--AATATGGATTG
*
47736 ATTTATTTT-AAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAAATAATTTATTAATATGGATTG
*
47768 ATTTATTTT----T-A---A--AATATAGATTG
1 ATTTATTTTAAAATAATTTATTAATATGGATTG
* * *
47791 ATTTATTTT-AAATCATTTATTAGTATGAATTG
1 ATTTATTTTAAAATAATTTATTAATATGGATTG
47823 ATTTATTTTAAAATATGGATTGATTTATTTTAAATATGGATTG
1 ATTTATTTT-AAA-AT--A---ATTTA--TT-AATATGGATTG
* *
47866 ATTTA--TT---AT--TGTAGTT-GTATGGATTG
1 ATTTATTTTAAAATAATTTA-TTAATATGGATTG
* *
47892 ATTTATTTT-AAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAAATAATTTATTAATATGGATTG
47924 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
47939 TGGATTGATT
Statistics
Matches: 161, Mismatches: 14, Indels: 60
0.69 0.06 0.26
Matches are distributed among these distances:
23 18 0.11
25 1 0.01
26 15 0.09
27 1 0.01
28 5 0.03
29 4 0.02
30 3 0.02
31 2 0.01
32 57 0.35
33 5 0.03
34 4 0.02
35 2 0.01
36 12 0.07
37 9 0.06
40 5 0.03
41 2 0.01
42 2 0.01
43 14 0.09
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (33 bp):
ATTTATTTTAAAATAATTTATTAATATGGATTG
Found at i:47768 original size:32 final size:31
Alignment explanation
Indices: 47676--47834 Score: 126
Period size: 32 Copynumber: 5.3 Consensus size: 31
47666 TATTAAAATA
*
47676 ATTTTAAATAATTTA--ATAAGG-TT-ATTT
1 ATTTTAAATAATTTATTATATGGATTGATTT
47703 ATTTTAAAATAATTTATTTTAAAATATGGATTGATTT
1 ATTTT-AAATAATTTA--TT---ATATGGATTGATTT
47740 ATTTTAAATAATTTATTAGTATGGATTGATTT
1 ATTTTAAATAATTTATTA-TATGGATTGATTT
*
47772 ATTTT---TAA---A--ATATAGATTGATTT
1 ATTTTAAATAATTTATTATATGGATTGATTT
* *
47795 ATTTTAAATCATTTATTAGTATGAATTGATTT
1 ATTTTAAATAATTTATTA-TATGGATTGATTT
47827 ATTTTAAA
1 ATTTTAAA
47835 ATATGGATTG
Statistics
Matches: 107, Mismatches: 5, Indels: 35
0.73 0.03 0.24
Matches are distributed among these distances:
23 17 0.16
24 1 0.01
26 3 0.03
27 5 0.05
28 10 0.09
29 4 0.04
31 2 0.02
32 37 0.35
34 2 0.02
35 5 0.05
36 12 0.11
37 9 0.08
ACGTcount: A:0.38, C:0.01, G:0.09, T:0.52
Consensus pattern (31 bp):
ATTTTAAATAATTTATTATATGGATTGATTT
Found at i:47802 original size:22 final size:22
Alignment explanation
Indices: 47763--47872 Score: 71
Period size: 21 Copynumber: 4.5 Consensus size: 22
47753 TATTAGTATG
47763 GATTGATTTATTTTTAAAATATA
1 GATTGATTTA-TTTTAAAATATA
47786 GATTGATTTATTTTAAATCATTTATTA
1 GATTGATTTATTTTAAA--A--TA-TA
* *
47813 G-TATGAATTGATTTATTTTAAAATATG
1 GAT-TG-ATTTA-TT---TTAAAATATA
*
47840 GATTGATTTATTTT-AAATATG
1 GATTGATTTATTTTAAAATATA
47861 GATTGATTTATT
1 GATTGATTTATT
47873 ATTGTAGTTG
Statistics
Matches: 72, Mismatches: 3, Indels: 26
0.71 0.03 0.26
Matches are distributed among these distances:
21 19 0.26
22 9 0.12
23 10 0.14
24 1 0.01
25 2 0.03
26 7 0.10
27 9 0.12
28 7 0.10
29 2 0.03
30 1 0.01
32 5 0.07
ACGTcount: A:0.35, C:0.01, G:0.12, T:0.53
Consensus pattern (22 bp):
GATTGATTTATTTTAAAATATA
Found at i:47856 original size:54 final size:54
Alignment explanation
Indices: 47714--48006 Score: 413
Period size: 54 Copynumber: 5.5 Consensus size: 54
47704 TTTTAAAATA
*
47714 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTG
* *
47768 ATTTATTTTTAAAATATAGATTGATTTATTTTAAATCATTTATTAGTATGAATTG
1 ATTTA-TTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTG
**
47823 ATTTATTTTAAAATATGGATTGATTTATTTTAAAT-ATGGATT-G-AT---TT-
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTG
* ***
47870 A-TTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTA-AAATATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTG
*
47924 ATTTATTTTAAAATATGGATTGATTTATTTTAGATAATTTATTAGTATGAATTG
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTG
*
47978 ATTTATTTTAAAATATAGATTGATTTATT
1 ATTTATTTTAAAATATGGATTGATTTATT
48007 ATTGTAGTTG
Statistics
Matches: 211, Mismatches: 18, Indels: 20
0.85 0.07 0.08
Matches are distributed among these distances:
46 7 0.03
47 23 0.11
48 7 0.03
49 1 0.00
50 2 0.01
51 2 0.01
52 1 0.00
53 7 0.03
54 103 0.49
55 58 0.27
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTG
Found at i:47928 original size:32 final size:32
Alignment explanation
Indices: 47892--47989 Score: 117
Period size: 32 Copynumber: 3.4 Consensus size: 32
47882 GTATGGATTG
47892 ATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTG
47924 ATTTATTTT-AA-AA--TA-T-G---G-ATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTG
*
47946 ATTTATTTTAGATAATTTATTAGTATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTG
47978 ATTTATTTTAAA
1 ATTTATTTTAAA
47990 ATATAGATTG
Statistics
Matches: 54, Mismatches: 2, Indels: 20
0.71 0.03 0.26
Matches are distributed among these distances:
22 13 0.24
23 2 0.04
24 2 0.04
26 3 0.06
27 2 0.04
28 3 0.06
30 2 0.04
31 3 0.06
32 24 0.44
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATGAATTG
Found at i:47929 original size:18 final size:18
Alignment explanation
Indices: 47906--47984 Score: 58
Period size: 22 Copynumber: 4.4 Consensus size: 18
47896 ATTTTAAATA
47906 ATTTATTAGTATGAATTG
1 ATTTATTAGTATGAATTG
* *
47924 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AGTATGAATTG
* *
47946 ATTTATT-TTA-G-A-TA
1 ATTTATTAGTATGAATTG
47960 ATTTATTAGTATGAATTG
1 ATTTATTAGTATGAATTG
47978 ATTTATT
1 ATTTATT
47985 TTAAAATATA
Statistics
Matches: 47, Mismatches: 6, Indels: 16
0.68 0.09 0.23
Matches are distributed among these distances:
14 8 0.17
15 3 0.06
16 2 0.04
17 3 0.06
18 13 0.28
20 4 0.09
22 14 0.30
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (18 bp):
ATTTATTAGTATGAATTG
Found at i:47999 original size:155 final size:156
Alignment explanation
Indices: 47727--48006 Score: 508
Period size: 155 Copynumber: 1.8 Consensus size: 156
47717 TATTTTAAAA
*
47727 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTTAAAATATAGATTGA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTTAAAATATAGATTGA
* *
47792 TTTATTTTAAATCATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAA
66 TTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTGATTTATTTTAAA
47857 TATGGATTGATTTATTATTGTAGTTG
131 TATGGATTGATTTATTATTGTAGTTG
*
47883 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTA-TTTTAAAATATGGATTGA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTTAAAATATAGATTGA
*
47947 TTTATTTTAGATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTGATTTATT
66 TTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTGATTTATT
48007 ATTGTAGTTG
Statistics
Matches: 119, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
155 74 0.62
156 45 0.38
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (156 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTTAAAATATAGATTGA
TTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTGATTTATTTTAAA
TATGGATTGATTTATTATTGTAGTTG
Found at i:48021 original size:80 final size:80
Alignment explanation
Indices: 47937--48086 Score: 282
Period size: 80 Copynumber: 1.9 Consensus size: 80
47927 TATTTTAAAA
*
47937 TATGGATTGATTTATTTTAGATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTGAT
48002 TTATTATTGTAGTTG
66 TTATTATTGTAGTTG
*
48017 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTGAT
48082 TTATT
66 TTATT
48087 TTAAATAATT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 68 1.00
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (80 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTGAT
TTATTATTGTAGTTG
Found at i:48026 original size:134 final size:134
Alignment explanation
Indices: 47836--48106 Score: 481
Period size: 134 Copynumber: 2.0 Consensus size: 134
47826 TATTTTAAAA
* *
47836 TATGGATTGATTTATTTTAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTT
1 TATGAATTGATTTATTTTAAATATAGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTT
* *
47901 AAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAGATAATTTAT
66 AAATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTGATTTATTTTAAATAATTTAT
47966 TA-G
131 TATG
47969 TATGAATTGATTTATTTTAAAATATAGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTT
1 TATGAATTGATTTATTTT-AAATATAGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTT
*
48034 TAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGATTTATTTTAAATAATTTA
65 TAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTGATTTATTTTAAATAATTTA
48099 TTATG
130 TTATG
48104 TAT
1 TAT
48107 TGTAAAACTA
Statistics
Matches: 131, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
133 17 0.13
134 110 0.84
135 4 0.03
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.53
Consensus pattern (134 bp):
TATGAATTGATTTATTTTAAATATAGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTT
AAATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTGATTTATTTTAAATAATTTAT
TATG
Found at i:48867 original size:31 final size:31
Alignment explanation
Indices: 48822--48903 Score: 112
Period size: 30 Copynumber: 2.6 Consensus size: 31
48812 AGTATGCCCC
48822 TAATAACAAATATTGAAAAAAATTGGACCCT
1 TAATAACAAATATTGAAAAAAATTGGACCCT
* * * *
48853 TGATAATAAATATTG-AAAAAATTGGGCCTT
1 TAATAACAAATATTGAAAAAAATTGGACCCT
48883 TAATAACAAATATTAGAAAAA
1 TAATAACAAATATT-GAAAAA
48904 GCAAAAAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
30 25 0.58
31 14 0.33
32 4 0.09
ACGTcount: A:0.52, C:0.09, G:0.11, T:0.28
Consensus pattern (31 bp):
TAATAACAAATATTGAAAAAAATTGGACCCT
Found at i:57481 original size:20 final size:20
Alignment explanation
Indices: 57458--57503 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
57448 CAGTATTGAA
57458 ACTCCTA-TTAAAGTATCGAT
1 ACTCCTACTT-AAGTATCGAT
57478 ACT-CTACCTTAAGTATCGAT
1 ACTCCTA-CTTAAGTATCGAT
57498 ACTCCT
1 ACTCCT
57504 TTGAGTACCG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
19 3 0.13
20 16 0.70
21 4 0.17
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.35
Consensus pattern (20 bp):
ACTCCTACTTAAGTATCGAT
Found at i:58683 original size:18 final size:17
Alignment explanation
Indices: 58629--58677 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
58619 TTGGACCCTT
* *
58629 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
58647 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
58665 AGTGCATTCGATG
1 AGTGCA-TCGATG
58678 TTTCAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:58718 original size:47 final size:48
Alignment explanation
Indices: 58646--58736 Score: 132
Period size: 47 Copynumber: 1.9 Consensus size: 48
58636 CGGTGCACTA
*
58646 AGAGTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAAAATAGCC
1 AGAGTGCATCAATGCATCAAGTGCATTCGATGTTTTCAAAAAATAGCC
* *
58693 AGAGTGCATCAATGCATGGAA-TGCATTCGATGTTTTCATAAAAT
1 AGAGTGCATCAATGCAT-CAAGTGCATTCGATGTTTTCAAAAAAT
58737 CCTCAGTGCA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
47 27 0.69
48 12 0.31
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (48 bp):
AGAGTGCATCAATGCATCAAGTGCATTCGATGTTTTCAAAAAATAGCC
Found at i:58756 original size:46 final size:47
Alignment explanation
Indices: 58648--58771 Score: 130
Period size: 47 Copynumber: 2.7 Consensus size: 47
58638 GTGCACTAAG
* *
58648 AGTGCATCGATGCAT-CAAGTGCATTCGATGTTTCAAAAAATAGCCAG
1 AGTGCATCGATGCATGGAAGTGCATTCGATGTTTCAAAAAATA-CCAC
* * *
58695 AGTGCATCAATGCATGGAA-TGCATTCGATGTTTTCATAAAAT-CCTC
1 AGTGCATCGATGCATGGAAGTGCATTCGATG-TTTCAAAAAATACCAC
* *
58741 AGTGCATCGGTGCATGGTATGTGCA-TCGATG
1 AGTGCATCGATGCATGG-AAGTGCATTCGATG
58772 CATGAAATGC
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
46 17 0.26
47 32 0.49
48 16 0.25
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (47 bp):
AGTGCATCGATGCATGGAAGTGCATTCGATGTTTCAAAAAATACCAC
Found at i:59888 original size:3 final size:3
Alignment explanation
Indices: 59880--59908 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
59870 GTCGGAGCCA
59880 GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
59909 ACACGAGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (3 bp):
GAG
Done.