Multiple sequence alignment - TraesCS6A01G222400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6A01G222400 chr6A 100.000 2216 0 0 1 2216 416253926 416251711 0.000000e+00 4093
1 TraesCS6A01G222400 chr3A 96.145 1816 53 6 408 2215 191842888 191841082 0.000000e+00 2950
2 TraesCS6A01G222400 chr3A 93.333 195 12 1 217 411 94957194 94957001 1.000000e-73 287
3 TraesCS6A01G222400 chr7D 89.646 1188 107 11 576 1751 503287783 503288966 0.000000e+00 1498
4 TraesCS6A01G222400 chr7D 91.095 539 36 12 1685 2216 503288977 503289510 0.000000e+00 719
5 TraesCS6A01G222400 chr7D 92.500 200 12 3 213 411 279727260 279727063 1.300000e-72 283
6 TraesCS6A01G222400 chr7D 93.333 165 10 1 402 566 578518494 578518331 2.200000e-60 243
7 TraesCS6A01G222400 chr7D 90.625 160 15 0 407 566 503287576 503287735 1.720000e-51 213
8 TraesCS6A01G222400 chr4D 81.532 1175 144 31 576 1719 172018896 172017764 0.000000e+00 900
9 TraesCS6A01G222400 chr4D 83.479 914 114 17 854 1751 333258316 333257424 0.000000e+00 817
10 TraesCS6A01G222400 chr4D 86.787 666 77 10 1501 2159 464366882 464367543 0.000000e+00 732
11 TraesCS6A01G222400 chr6D 83.265 980 129 19 786 1751 132003190 132004148 0.000000e+00 869
12 TraesCS6A01G222400 chr6D 85.425 247 29 3 615 854 132002972 132003218 1.310000e-62 250
13 TraesCS6A01G222400 chr5D 90.116 516 43 8 1706 2216 283105948 283106460 0.000000e+00 664
14 TraesCS6A01G222400 chr5D 85.981 535 56 18 1220 1747 283105414 283105936 2.490000e-154 555
15 TraesCS6A01G222400 chr5D 90.127 314 27 4 1439 1750 46648640 46648329 2.650000e-109 405
16 TraesCS6A01G222400 chr5D 93.333 195 12 1 217 411 475494856 475495049 1.000000e-73 287
17 TraesCS6A01G222400 chr2B 84.812 665 85 13 1505 2162 79358095 79358750 0.000000e+00 654
18 TraesCS6A01G222400 chr2B 83.550 693 74 25 1501 2159 34582633 34583319 1.450000e-171 612
19 TraesCS6A01G222400 chr2B 87.170 530 54 12 1688 2213 761289564 761290083 6.820000e-165 590
20 TraesCS6A01G222400 chr2B 85.859 495 58 11 1661 2149 761250162 761250650 1.170000e-142 516
21 TraesCS6A01G222400 chr4B 87.671 511 56 7 1709 2216 109396872 109396366 2.450000e-164 588
22 TraesCS6A01G222400 chr1D 82.857 630 67 22 1501 2121 342450080 342450677 5.420000e-146 527
23 TraesCS6A01G222400 chr1D 89.831 59 4 2 405 462 195189890 195189833 8.490000e-10 75
24 TraesCS6A01G222400 chr3D 93.069 202 13 1 210 411 342505063 342504863 5.980000e-76 294
25 TraesCS6A01G222400 chr3D 93.333 195 12 1 217 411 445127054 445127247 1.000000e-73 287
26 TraesCS6A01G222400 chr2D 94.241 191 11 0 217 407 317754181 317754371 2.150000e-75 292
27 TraesCS6A01G222400 chr2D 93.333 195 12 1 217 411 275869992 275869799 1.000000e-73 287
28 TraesCS6A01G222400 chr7B 93.333 195 12 1 217 411 218956360 218956553 1.000000e-73 287
29 TraesCS6A01G222400 chr2A 92.462 199 13 2 210 407 462493825 462494022 1.300000e-72 283
30 TraesCS6A01G222400 chr6B 90.686 204 15 1 3 206 466186380 466186579 3.630000e-68 268


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G222400 chr6A 416251711 416253926 2215 True 4093.0 4093 100.000000 1 2216 1 chr6A.!!$R1 2215
1 TraesCS6A01G222400 chr3A 191841082 191842888 1806 True 2950.0 2950 96.145000 408 2215 1 chr3A.!!$R2 1807
2 TraesCS6A01G222400 chr7D 503287576 503289510 1934 False 810.0 1498 90.455333 407 2216 3 chr7D.!!$F1 1809
3 TraesCS6A01G222400 chr4D 172017764 172018896 1132 True 900.0 900 81.532000 576 1719 1 chr4D.!!$R1 1143
4 TraesCS6A01G222400 chr4D 333257424 333258316 892 True 817.0 817 83.479000 854 1751 1 chr4D.!!$R2 897
5 TraesCS6A01G222400 chr4D 464366882 464367543 661 False 732.0 732 86.787000 1501 2159 1 chr4D.!!$F1 658
6 TraesCS6A01G222400 chr6D 132002972 132004148 1176 False 559.5 869 84.345000 615 1751 2 chr6D.!!$F1 1136
7 TraesCS6A01G222400 chr5D 283105414 283106460 1046 False 609.5 664 88.048500 1220 2216 2 chr5D.!!$F2 996
8 TraesCS6A01G222400 chr2B 79358095 79358750 655 False 654.0 654 84.812000 1505 2162 1 chr2B.!!$F2 657
9 TraesCS6A01G222400 chr2B 34582633 34583319 686 False 612.0 612 83.550000 1501 2159 1 chr2B.!!$F1 658
10 TraesCS6A01G222400 chr2B 761289564 761290083 519 False 590.0 590 87.170000 1688 2213 1 chr2B.!!$F4 525
11 TraesCS6A01G222400 chr4B 109396366 109396872 506 True 588.0 588 87.671000 1709 2216 1 chr4B.!!$R1 507
12 TraesCS6A01G222400 chr1D 342450080 342450677 597 False 527.0 527 82.857000 1501 2121 1 chr1D.!!$F1 620

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
397 398 0.033228 TGGGCTGAAAATTTGCGGTG 59.967 50.0 6.85 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1227 1329 0.905357 CGACCTCCCCAGATCTTGTT 59.095 55.0 0.0 0.0 0.0 2.83 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 6.219302 GCAAGTCATTGAAGGAAAATGTTG 57.781 37.500 0.00 0.00 38.83 3.33
24 25 5.754890 GCAAGTCATTGAAGGAAAATGTTGT 59.245 36.000 0.00 0.00 38.83 3.32
25 26 6.258507 GCAAGTCATTGAAGGAAAATGTTGTT 59.741 34.615 0.00 0.00 38.83 2.83
26 27 7.623770 CAAGTCATTGAAGGAAAATGTTGTTG 58.376 34.615 0.00 0.00 38.83 3.33
27 28 5.754890 AGTCATTGAAGGAAAATGTTGTTGC 59.245 36.000 0.00 0.00 36.58 4.17
28 29 5.523188 GTCATTGAAGGAAAATGTTGTTGCA 59.477 36.000 0.00 0.00 36.58 4.08
29 30 6.203338 GTCATTGAAGGAAAATGTTGTTGCAT 59.797 34.615 0.00 0.00 36.58 3.96
30 31 5.987777 TTGAAGGAAAATGTTGTTGCATG 57.012 34.783 0.00 0.00 0.00 4.06
31 32 5.021033 TGAAGGAAAATGTTGTTGCATGT 57.979 34.783 0.00 0.00 0.00 3.21
32 33 5.049167 TGAAGGAAAATGTTGTTGCATGTC 58.951 37.500 0.00 0.00 0.00 3.06
33 34 4.942761 AGGAAAATGTTGTTGCATGTCT 57.057 36.364 0.00 0.00 0.00 3.41
34 35 5.280654 AGGAAAATGTTGTTGCATGTCTT 57.719 34.783 0.00 0.00 0.00 3.01
35 36 5.291971 AGGAAAATGTTGTTGCATGTCTTC 58.708 37.500 0.00 0.00 0.00 2.87
36 37 5.049167 GGAAAATGTTGTTGCATGTCTTCA 58.951 37.500 0.00 0.00 0.00 3.02
37 38 5.523188 GGAAAATGTTGTTGCATGTCTTCAA 59.477 36.000 0.00 0.00 0.00 2.69
38 39 6.203338 GGAAAATGTTGTTGCATGTCTTCAAT 59.797 34.615 0.00 0.00 0.00 2.57
39 40 7.384660 GGAAAATGTTGTTGCATGTCTTCAATA 59.615 33.333 0.00 0.00 0.00 1.90
40 41 8.836268 AAAATGTTGTTGCATGTCTTCAATAT 57.164 26.923 0.00 0.00 0.00 1.28
41 42 8.470040 AAATGTTGTTGCATGTCTTCAATATC 57.530 30.769 0.00 0.00 0.00 1.63
42 43 6.822667 TGTTGTTGCATGTCTTCAATATCT 57.177 33.333 0.00 0.00 0.00 1.98
43 44 7.218228 TGTTGTTGCATGTCTTCAATATCTT 57.782 32.000 0.00 0.00 0.00 2.40
44 45 7.307694 TGTTGTTGCATGTCTTCAATATCTTC 58.692 34.615 0.00 0.00 0.00 2.87
45 46 6.441093 TGTTGCATGTCTTCAATATCTTCC 57.559 37.500 0.00 0.00 0.00 3.46
46 47 6.182627 TGTTGCATGTCTTCAATATCTTCCT 58.817 36.000 0.00 0.00 0.00 3.36
47 48 7.337938 TGTTGCATGTCTTCAATATCTTCCTA 58.662 34.615 0.00 0.00 0.00 2.94
48 49 7.496920 TGTTGCATGTCTTCAATATCTTCCTAG 59.503 37.037 0.00 0.00 0.00 3.02
49 50 6.528321 TGCATGTCTTCAATATCTTCCTAGG 58.472 40.000 0.82 0.82 0.00 3.02
50 51 6.100279 TGCATGTCTTCAATATCTTCCTAGGT 59.900 38.462 9.08 0.00 0.00 3.08
51 52 6.648725 GCATGTCTTCAATATCTTCCTAGGTC 59.351 42.308 9.08 0.00 0.00 3.85
52 53 7.687837 GCATGTCTTCAATATCTTCCTAGGTCA 60.688 40.741 9.08 0.00 0.00 4.02
53 54 7.113658 TGTCTTCAATATCTTCCTAGGTCAC 57.886 40.000 9.08 0.00 0.00 3.67
54 55 6.098409 TGTCTTCAATATCTTCCTAGGTCACC 59.902 42.308 9.08 0.00 0.00 4.02
55 56 5.602978 TCTTCAATATCTTCCTAGGTCACCC 59.397 44.000 9.08 0.00 0.00 4.61
56 57 4.890988 TCAATATCTTCCTAGGTCACCCA 58.109 43.478 9.08 0.00 0.00 4.51
57 58 5.476983 TCAATATCTTCCTAGGTCACCCAT 58.523 41.667 9.08 0.00 0.00 4.00
58 59 5.911178 TCAATATCTTCCTAGGTCACCCATT 59.089 40.000 9.08 0.53 0.00 3.16
59 60 6.389869 TCAATATCTTCCTAGGTCACCCATTT 59.610 38.462 9.08 0.00 0.00 2.32
60 61 4.510167 ATCTTCCTAGGTCACCCATTTG 57.490 45.455 9.08 0.00 0.00 2.32
61 62 2.576191 TCTTCCTAGGTCACCCATTTGG 59.424 50.000 9.08 0.00 41.37 3.28
62 63 0.623723 TCCTAGGTCACCCATTTGGC 59.376 55.000 9.08 0.00 37.83 4.52
63 64 0.625849 CCTAGGTCACCCATTTGGCT 59.374 55.000 0.00 0.00 37.83 4.75
64 65 1.683011 CCTAGGTCACCCATTTGGCTG 60.683 57.143 0.00 0.00 37.83 4.85
65 66 0.331278 TAGGTCACCCATTTGGCTGG 59.669 55.000 0.00 0.00 37.83 4.85
66 67 1.076549 GGTCACCCATTTGGCTGGA 59.923 57.895 0.00 0.00 38.69 3.86
67 68 0.541764 GGTCACCCATTTGGCTGGAA 60.542 55.000 0.00 0.00 38.69 3.53
68 69 0.890683 GTCACCCATTTGGCTGGAAG 59.109 55.000 0.00 0.00 38.69 3.46
69 70 0.251742 TCACCCATTTGGCTGGAAGG 60.252 55.000 0.00 0.00 38.69 3.46
79 80 2.612115 CTGGAAGGCCCTCCCAGT 60.612 66.667 18.20 0.00 41.81 4.00
80 81 2.935481 TGGAAGGCCCTCCCAGTG 60.935 66.667 18.20 0.00 34.22 3.66
81 82 4.432741 GGAAGGCCCTCCCAGTGC 62.433 72.222 9.53 0.00 35.39 4.40
82 83 3.650950 GAAGGCCCTCCCAGTGCA 61.651 66.667 0.00 0.00 35.39 4.57
83 84 2.943265 AAGGCCCTCCCAGTGCAT 60.943 61.111 0.00 0.00 35.39 3.96
84 85 3.292481 AAGGCCCTCCCAGTGCATG 62.292 63.158 0.00 0.00 35.39 4.06
85 86 3.731728 GGCCCTCCCAGTGCATGA 61.732 66.667 0.00 0.00 0.00 3.07
86 87 2.124403 GCCCTCCCAGTGCATGAG 60.124 66.667 0.00 0.00 0.00 2.90
87 88 2.124403 CCCTCCCAGTGCATGAGC 60.124 66.667 0.00 0.00 42.57 4.26
100 101 2.416747 GCATGAGCACTTGTGTAGACA 58.583 47.619 0.00 0.00 41.58 3.41
101 102 3.005554 GCATGAGCACTTGTGTAGACAT 58.994 45.455 0.00 1.78 41.58 3.06
102 103 4.183865 GCATGAGCACTTGTGTAGACATA 58.816 43.478 0.00 0.00 41.58 2.29
103 104 4.033358 GCATGAGCACTTGTGTAGACATAC 59.967 45.833 0.00 0.00 41.58 2.39
104 105 4.188247 TGAGCACTTGTGTAGACATACC 57.812 45.455 0.00 0.00 30.13 2.73
105 106 3.576550 TGAGCACTTGTGTAGACATACCA 59.423 43.478 0.00 0.00 30.13 3.25
106 107 3.926616 AGCACTTGTGTAGACATACCAC 58.073 45.455 0.00 0.00 30.13 4.16
107 108 3.578716 AGCACTTGTGTAGACATACCACT 59.421 43.478 0.00 0.00 30.13 4.00
108 109 4.770531 AGCACTTGTGTAGACATACCACTA 59.229 41.667 0.00 0.00 30.13 2.74
109 110 5.422331 AGCACTTGTGTAGACATACCACTAT 59.578 40.000 0.00 0.00 30.13 2.12
110 111 5.749109 GCACTTGTGTAGACATACCACTATC 59.251 44.000 0.00 0.00 30.13 2.08
111 112 6.405953 GCACTTGTGTAGACATACCACTATCT 60.406 42.308 0.00 0.00 30.13 1.98
112 113 7.548097 CACTTGTGTAGACATACCACTATCTT 58.452 38.462 0.00 0.00 30.13 2.40
113 114 7.489435 CACTTGTGTAGACATACCACTATCTTG 59.511 40.741 0.00 0.00 30.13 3.02
114 115 7.396339 ACTTGTGTAGACATACCACTATCTTGA 59.604 37.037 0.00 0.00 30.13 3.02
115 116 7.898014 TGTGTAGACATACCACTATCTTGAT 57.102 36.000 0.00 0.00 0.00 2.57
116 117 7.716612 TGTGTAGACATACCACTATCTTGATG 58.283 38.462 0.00 0.00 0.00 3.07
117 118 7.559897 TGTGTAGACATACCACTATCTTGATGA 59.440 37.037 0.00 0.00 0.00 2.92
118 119 8.414003 GTGTAGACATACCACTATCTTGATGAA 58.586 37.037 0.00 0.00 0.00 2.57
119 120 8.414003 TGTAGACATACCACTATCTTGATGAAC 58.586 37.037 0.00 0.00 0.00 3.18
120 121 7.423844 AGACATACCACTATCTTGATGAACA 57.576 36.000 0.00 0.00 0.00 3.18
121 122 7.851228 AGACATACCACTATCTTGATGAACAA 58.149 34.615 0.00 0.00 36.97 2.83
122 123 7.766278 AGACATACCACTATCTTGATGAACAAC 59.234 37.037 0.00 0.00 34.56 3.32
123 124 6.535150 ACATACCACTATCTTGATGAACAACG 59.465 38.462 0.00 0.00 34.56 4.10
124 125 3.684788 ACCACTATCTTGATGAACAACGC 59.315 43.478 0.00 0.00 34.56 4.84
125 126 3.242091 CCACTATCTTGATGAACAACGCG 60.242 47.826 3.53 3.53 34.56 6.01
126 127 2.348666 ACTATCTTGATGAACAACGCGC 59.651 45.455 5.73 0.00 34.56 6.86
127 128 0.447801 ATCTTGATGAACAACGCGCC 59.552 50.000 5.73 0.00 34.56 6.53
128 129 0.882484 TCTTGATGAACAACGCGCCA 60.882 50.000 5.73 0.00 34.56 5.69
129 130 0.040514 CTTGATGAACAACGCGCCAA 60.041 50.000 5.73 0.00 34.56 4.52
130 131 0.040514 TTGATGAACAACGCGCCAAG 60.041 50.000 5.73 0.00 33.18 3.61
131 132 1.797537 GATGAACAACGCGCCAAGC 60.798 57.895 5.73 0.00 43.95 4.01
143 144 1.153958 GCCAAGCGAGAATGGTTGC 60.154 57.895 0.44 0.00 43.99 4.17
144 145 1.508088 CCAAGCGAGAATGGTTGCC 59.492 57.895 0.44 0.00 43.99 4.52
145 146 1.135315 CAAGCGAGAATGGTTGCCG 59.865 57.895 0.00 0.00 40.06 5.69
146 147 2.040544 AAGCGAGAATGGTTGCCGG 61.041 57.895 0.00 0.00 0.00 6.13
147 148 4.179579 GCGAGAATGGTTGCCGGC 62.180 66.667 22.73 22.73 0.00 6.13
148 149 2.436646 CGAGAATGGTTGCCGGCT 60.437 61.111 29.70 5.42 0.00 5.52
149 150 2.753966 CGAGAATGGTTGCCGGCTG 61.754 63.158 29.70 0.34 0.00 4.85
150 151 1.377202 GAGAATGGTTGCCGGCTGA 60.377 57.895 29.70 13.94 0.00 4.26
151 152 1.372087 GAGAATGGTTGCCGGCTGAG 61.372 60.000 29.70 0.00 0.00 3.35
152 153 3.056313 GAATGGTTGCCGGCTGAGC 62.056 63.158 29.70 24.39 0.00 4.26
166 167 2.144952 TGAGCCATGTGGTCAGTGT 58.855 52.632 10.74 0.00 46.14 3.55
167 168 0.035317 TGAGCCATGTGGTCAGTGTC 59.965 55.000 10.74 0.00 46.14 3.67
168 169 0.035317 GAGCCATGTGGTCAGTGTCA 59.965 55.000 0.35 0.00 41.24 3.58
169 170 0.473755 AGCCATGTGGTCAGTGTCAA 59.526 50.000 0.35 0.00 37.57 3.18
170 171 1.074405 AGCCATGTGGTCAGTGTCAAT 59.926 47.619 0.35 0.00 37.57 2.57
171 172 2.305635 AGCCATGTGGTCAGTGTCAATA 59.694 45.455 0.35 0.00 37.57 1.90
172 173 2.420022 GCCATGTGGTCAGTGTCAATAC 59.580 50.000 0.35 0.00 37.57 1.89
173 174 3.673902 CCATGTGGTCAGTGTCAATACA 58.326 45.455 0.00 0.00 0.00 2.29
174 175 4.264253 CCATGTGGTCAGTGTCAATACAT 58.736 43.478 0.00 0.00 38.08 2.29
175 176 5.427378 CCATGTGGTCAGTGTCAATACATA 58.573 41.667 0.00 0.00 38.08 2.29
176 177 6.057533 CCATGTGGTCAGTGTCAATACATAT 58.942 40.000 0.00 0.00 38.08 1.78
177 178 6.017687 CCATGTGGTCAGTGTCAATACATATG 60.018 42.308 0.00 0.00 38.08 1.78
178 179 5.427378 TGTGGTCAGTGTCAATACATATGG 58.573 41.667 7.80 0.00 38.08 2.74
179 180 5.045942 TGTGGTCAGTGTCAATACATATGGT 60.046 40.000 7.80 0.00 38.08 3.55
180 181 6.155393 TGTGGTCAGTGTCAATACATATGGTA 59.845 38.462 7.80 0.00 38.08 3.25
181 182 6.701841 GTGGTCAGTGTCAATACATATGGTAG 59.298 42.308 7.80 0.00 38.08 3.18
182 183 6.183360 TGGTCAGTGTCAATACATATGGTAGG 60.183 42.308 7.80 0.00 38.08 3.18
183 184 6.223852 GTCAGTGTCAATACATATGGTAGGG 58.776 44.000 7.80 0.00 38.08 3.53
184 185 6.041637 GTCAGTGTCAATACATATGGTAGGGA 59.958 42.308 7.80 0.00 38.08 4.20
185 186 6.267699 TCAGTGTCAATACATATGGTAGGGAG 59.732 42.308 7.80 0.00 38.08 4.30
186 187 6.267699 CAGTGTCAATACATATGGTAGGGAGA 59.732 42.308 7.80 0.00 38.08 3.71
187 188 7.019388 AGTGTCAATACATATGGTAGGGAGAT 58.981 38.462 7.80 0.00 38.08 2.75
188 189 7.179338 AGTGTCAATACATATGGTAGGGAGATC 59.821 40.741 7.80 0.00 38.08 2.75
189 190 6.440647 TGTCAATACATATGGTAGGGAGATCC 59.559 42.308 7.80 0.00 34.92 3.36
190 191 5.656859 TCAATACATATGGTAGGGAGATCCG 59.343 44.000 7.80 0.00 41.52 4.18
191 192 3.827817 ACATATGGTAGGGAGATCCGA 57.172 47.619 7.80 0.00 41.52 4.55
192 193 3.432378 ACATATGGTAGGGAGATCCGAC 58.568 50.000 7.80 0.00 41.52 4.79
197 198 0.318762 GTAGGGAGATCCGACCATGC 59.681 60.000 0.00 0.00 41.52 4.06
198 199 0.832135 TAGGGAGATCCGACCATGCC 60.832 60.000 0.00 0.00 41.52 4.40
199 200 2.143419 GGGAGATCCGACCATGCCT 61.143 63.158 0.00 0.00 36.71 4.75
200 201 1.369321 GGAGATCCGACCATGCCTC 59.631 63.158 0.00 0.00 0.00 4.70
201 202 1.006805 GAGATCCGACCATGCCTCG 60.007 63.158 4.46 4.46 0.00 4.63
206 207 3.486263 CGACCATGCCTCGGAAAC 58.514 61.111 3.67 0.00 0.00 2.78
207 208 1.375396 CGACCATGCCTCGGAAACA 60.375 57.895 3.67 0.00 0.00 2.83
208 209 0.953471 CGACCATGCCTCGGAAACAA 60.953 55.000 3.67 0.00 0.00 2.83
209 210 1.243902 GACCATGCCTCGGAAACAAA 58.756 50.000 0.00 0.00 0.00 2.83
210 211 1.818674 GACCATGCCTCGGAAACAAAT 59.181 47.619 0.00 0.00 0.00 2.32
211 212 1.545582 ACCATGCCTCGGAAACAAATG 59.454 47.619 0.00 0.00 0.00 2.32
212 213 1.135024 CCATGCCTCGGAAACAAATGG 60.135 52.381 0.00 0.00 0.00 3.16
213 214 1.545582 CATGCCTCGGAAACAAATGGT 59.454 47.619 0.00 0.00 0.00 3.55
214 215 1.698506 TGCCTCGGAAACAAATGGTT 58.301 45.000 0.00 0.00 42.98 3.67
225 226 4.345271 AACAAATGGTTTATACGTCGCC 57.655 40.909 0.00 0.00 35.82 5.54
226 227 3.336468 ACAAATGGTTTATACGTCGCCA 58.664 40.909 0.00 0.00 0.00 5.69
227 228 3.752222 ACAAATGGTTTATACGTCGCCAA 59.248 39.130 0.00 0.00 32.54 4.52
228 229 4.092816 CAAATGGTTTATACGTCGCCAAC 58.907 43.478 0.00 0.00 32.54 3.77
241 242 5.817616 CGTCGCCAACGTATCTATAATTT 57.182 39.130 0.00 0.00 46.42 1.82
242 243 6.916401 CGTCGCCAACGTATCTATAATTTA 57.084 37.500 0.00 0.00 46.42 1.40
243 244 7.502177 CGTCGCCAACGTATCTATAATTTAT 57.498 36.000 0.00 0.00 46.42 1.40
244 245 7.381079 CGTCGCCAACGTATCTATAATTTATG 58.619 38.462 0.00 0.00 46.42 1.90
245 246 7.271868 CGTCGCCAACGTATCTATAATTTATGA 59.728 37.037 0.00 0.00 46.42 2.15
246 247 8.918658 GTCGCCAACGTATCTATAATTTATGAA 58.081 33.333 0.00 0.00 41.18 2.57
247 248 9.135843 TCGCCAACGTATCTATAATTTATGAAG 57.864 33.333 0.00 0.00 41.18 3.02
248 249 8.922676 CGCCAACGTATCTATAATTTATGAAGT 58.077 33.333 0.00 0.00 33.53 3.01
267 268 8.938801 ATGAAGTATCCATGCCATATTTACAA 57.061 30.769 0.00 0.00 0.00 2.41
268 269 8.165239 TGAAGTATCCATGCCATATTTACAAC 57.835 34.615 0.00 0.00 0.00 3.32
269 270 7.777440 TGAAGTATCCATGCCATATTTACAACA 59.223 33.333 0.00 0.00 0.00 3.33
270 271 8.532186 AAGTATCCATGCCATATTTACAACAA 57.468 30.769 0.00 0.00 0.00 2.83
271 272 8.710749 AGTATCCATGCCATATTTACAACAAT 57.289 30.769 0.00 0.00 0.00 2.71
272 273 9.146586 AGTATCCATGCCATATTTACAACAATT 57.853 29.630 0.00 0.00 0.00 2.32
273 274 9.762933 GTATCCATGCCATATTTACAACAATTT 57.237 29.630 0.00 0.00 0.00 1.82
304 305 9.308000 TGGTTTTGGTATCATTTGATTAGAACT 57.692 29.630 0.00 0.00 36.05 3.01
309 310 8.974060 TGGTATCATTTGATTAGAACTAACCC 57.026 34.615 0.00 0.00 36.05 4.11
310 311 7.713507 TGGTATCATTTGATTAGAACTAACCCG 59.286 37.037 0.00 0.00 36.05 5.28
311 312 7.172703 GGTATCATTTGATTAGAACTAACCCGG 59.827 40.741 0.00 0.00 36.05 5.73
312 313 6.302535 TCATTTGATTAGAACTAACCCGGA 57.697 37.500 0.73 0.00 0.00 5.14
313 314 6.110707 TCATTTGATTAGAACTAACCCGGAC 58.889 40.000 0.73 0.00 0.00 4.79
314 315 5.750352 TTTGATTAGAACTAACCCGGACT 57.250 39.130 0.73 0.00 0.00 3.85
315 316 4.730949 TGATTAGAACTAACCCGGACTG 57.269 45.455 0.73 0.00 0.00 3.51
316 317 4.346730 TGATTAGAACTAACCCGGACTGA 58.653 43.478 0.73 0.00 0.00 3.41
317 318 4.159135 TGATTAGAACTAACCCGGACTGAC 59.841 45.833 0.73 0.00 0.00 3.51
318 319 0.886563 AGAACTAACCCGGACTGACG 59.113 55.000 0.73 0.00 0.00 4.35
319 320 0.735287 GAACTAACCCGGACTGACGC 60.735 60.000 0.73 0.00 0.00 5.19
320 321 1.183676 AACTAACCCGGACTGACGCT 61.184 55.000 0.73 0.00 0.00 5.07
321 322 0.322816 ACTAACCCGGACTGACGCTA 60.323 55.000 0.73 0.00 0.00 4.26
322 323 1.030457 CTAACCCGGACTGACGCTAT 58.970 55.000 0.73 0.00 0.00 2.97
323 324 1.407979 CTAACCCGGACTGACGCTATT 59.592 52.381 0.73 0.00 0.00 1.73
324 325 0.611714 AACCCGGACTGACGCTATTT 59.388 50.000 0.73 0.00 0.00 1.40
325 326 0.611714 ACCCGGACTGACGCTATTTT 59.388 50.000 0.73 0.00 0.00 1.82
326 327 1.287425 CCCGGACTGACGCTATTTTC 58.713 55.000 0.73 0.00 0.00 2.29
327 328 1.404986 CCCGGACTGACGCTATTTTCA 60.405 52.381 0.73 0.00 0.00 2.69
328 329 1.927174 CCGGACTGACGCTATTTTCAG 59.073 52.381 0.00 0.00 44.19 3.02
329 330 1.324736 CGGACTGACGCTATTTTCAGC 59.675 52.381 0.00 0.00 42.67 4.26
330 331 2.346803 GGACTGACGCTATTTTCAGCA 58.653 47.619 0.00 0.00 42.67 4.41
331 332 2.349886 GGACTGACGCTATTTTCAGCAG 59.650 50.000 0.00 0.00 42.67 4.24
332 333 3.254060 GACTGACGCTATTTTCAGCAGA 58.746 45.455 0.00 0.00 42.67 4.26
333 334 3.664107 ACTGACGCTATTTTCAGCAGAA 58.336 40.909 0.00 0.00 42.67 3.02
334 335 3.433615 ACTGACGCTATTTTCAGCAGAAC 59.566 43.478 0.00 0.00 42.67 3.01
335 336 3.664107 TGACGCTATTTTCAGCAGAACT 58.336 40.909 0.00 0.00 41.88 3.01
336 337 4.816392 TGACGCTATTTTCAGCAGAACTA 58.184 39.130 0.00 0.00 41.88 2.24
337 338 4.625742 TGACGCTATTTTCAGCAGAACTAC 59.374 41.667 0.00 0.00 41.88 2.73
338 339 3.933332 ACGCTATTTTCAGCAGAACTACC 59.067 43.478 0.00 0.00 41.88 3.18
339 340 3.000322 CGCTATTTTCAGCAGAACTACCG 60.000 47.826 0.00 0.00 41.88 4.02
340 341 3.933332 GCTATTTTCAGCAGAACTACCGT 59.067 43.478 0.00 0.00 41.40 4.83
341 342 4.033014 GCTATTTTCAGCAGAACTACCGTC 59.967 45.833 0.00 0.00 41.40 4.79
342 343 2.060326 TTTCAGCAGAACTACCGTCG 57.940 50.000 0.00 0.00 32.39 5.12
343 344 0.956633 TTCAGCAGAACTACCGTCGT 59.043 50.000 0.00 0.00 0.00 4.34
344 345 0.240145 TCAGCAGAACTACCGTCGTG 59.760 55.000 0.00 0.00 0.00 4.35
345 346 0.039437 CAGCAGAACTACCGTCGTGT 60.039 55.000 0.00 0.00 0.00 4.49
346 347 0.240411 AGCAGAACTACCGTCGTGTC 59.760 55.000 0.00 0.00 0.00 3.67
347 348 0.039798 GCAGAACTACCGTCGTGTCA 60.040 55.000 0.00 0.00 0.00 3.58
348 349 1.402456 GCAGAACTACCGTCGTGTCAT 60.402 52.381 0.00 0.00 0.00 3.06
349 350 2.925306 GCAGAACTACCGTCGTGTCATT 60.925 50.000 0.00 0.00 0.00 2.57
350 351 3.314553 CAGAACTACCGTCGTGTCATTT 58.685 45.455 0.00 0.00 0.00 2.32
351 352 3.739300 CAGAACTACCGTCGTGTCATTTT 59.261 43.478 0.00 0.00 0.00 1.82
352 353 4.210537 CAGAACTACCGTCGTGTCATTTTT 59.789 41.667 0.00 0.00 0.00 1.94
379 380 9.672086 TGTGTAGAAATAAAAGTTTTCGGAATG 57.328 29.630 3.60 0.00 37.98 2.67
380 381 9.124807 GTGTAGAAATAAAAGTTTTCGGAATGG 57.875 33.333 3.60 0.00 37.98 3.16
381 382 8.301002 TGTAGAAATAAAAGTTTTCGGAATGGG 58.699 33.333 3.60 0.00 37.98 4.00
382 383 6.163476 AGAAATAAAAGTTTTCGGAATGGGC 58.837 36.000 3.60 0.00 37.98 5.36
383 384 5.738619 AATAAAAGTTTTCGGAATGGGCT 57.261 34.783 3.60 0.00 0.00 5.19
384 385 3.385193 AAAAGTTTTCGGAATGGGCTG 57.615 42.857 0.00 0.00 0.00 4.85
385 386 2.286365 AAGTTTTCGGAATGGGCTGA 57.714 45.000 0.00 0.00 0.00 4.26
386 387 2.286365 AGTTTTCGGAATGGGCTGAA 57.714 45.000 0.00 0.00 0.00 3.02
387 388 2.593026 AGTTTTCGGAATGGGCTGAAA 58.407 42.857 0.00 0.00 40.39 2.69
388 389 2.962421 AGTTTTCGGAATGGGCTGAAAA 59.038 40.909 0.00 0.00 45.75 2.29
390 391 4.615588 TTTTCGGAATGGGCTGAAAATT 57.384 36.364 0.00 0.00 44.11 1.82
391 392 4.615588 TTTCGGAATGGGCTGAAAATTT 57.384 36.364 0.00 0.00 39.49 1.82
392 393 3.591196 TCGGAATGGGCTGAAAATTTG 57.409 42.857 0.00 0.00 0.00 2.32
393 394 2.001872 CGGAATGGGCTGAAAATTTGC 58.998 47.619 0.00 0.00 0.00 3.68
394 395 2.001872 GGAATGGGCTGAAAATTTGCG 58.998 47.619 0.00 0.00 0.00 4.85
395 396 2.001872 GAATGGGCTGAAAATTTGCGG 58.998 47.619 0.00 0.00 0.00 5.69
396 397 0.975887 ATGGGCTGAAAATTTGCGGT 59.024 45.000 6.85 0.00 0.00 5.68
397 398 0.033228 TGGGCTGAAAATTTGCGGTG 59.967 50.000 6.85 0.00 0.00 4.94
398 399 0.316841 GGGCTGAAAATTTGCGGTGA 59.683 50.000 6.85 0.00 0.00 4.02
399 400 1.066929 GGGCTGAAAATTTGCGGTGAT 60.067 47.619 6.85 0.00 0.00 3.06
400 401 2.612721 GGGCTGAAAATTTGCGGTGATT 60.613 45.455 6.85 0.00 0.00 2.57
401 402 3.066380 GGCTGAAAATTTGCGGTGATTT 58.934 40.909 6.85 0.00 0.00 2.17
402 403 3.498018 GGCTGAAAATTTGCGGTGATTTT 59.502 39.130 6.85 0.00 37.96 1.82
403 404 4.024133 GGCTGAAAATTTGCGGTGATTTTT 60.024 37.500 6.85 0.00 36.04 1.94
452 453 3.000078 CCGGTATTTTCACATCTCGTTCG 60.000 47.826 0.00 0.00 0.00 3.95
566 593 2.580601 CGAACGAACCCCACTCCCT 61.581 63.158 0.00 0.00 0.00 4.20
778 824 0.465278 GAGCAGCCTTCATCTTCCCC 60.465 60.000 0.00 0.00 0.00 4.81
784 830 0.983378 CCTTCATCTTCCCCTCCCGT 60.983 60.000 0.00 0.00 0.00 5.28
788 834 1.305887 ATCTTCCCCTCCCGTCGTT 60.306 57.895 0.00 0.00 0.00 3.85
922 1023 1.450491 GCGAGAAGAGCCCCTTTCC 60.450 63.158 0.00 0.00 34.68 3.13
1051 1152 3.307108 TGACGGCCGGTGACATCA 61.307 61.111 31.76 19.91 0.00 3.07
1073 1174 2.026522 CTTCCGTCCTAGAGCTCCG 58.973 63.158 10.93 6.20 0.00 4.63
1227 1329 2.184322 GGATGAGTTGCGGCTCGA 59.816 61.111 0.00 0.00 38.28 4.04
1255 1357 4.222847 GGGAGGTCGGCGGCTTAG 62.223 72.222 12.73 0.00 0.00 2.18
1268 1371 2.289565 CGGCTTAGTCTTCCATTTCCC 58.710 52.381 0.00 0.00 0.00 3.97
1306 1422 1.694150 AGGAACTGCTACTGTTGCTCA 59.306 47.619 14.81 0.00 38.96 4.26
1388 1510 4.215399 GCAGTGTTTTTGCTATGGTGACTA 59.785 41.667 0.00 0.00 38.51 2.59
2161 2480 6.549952 TGTTCAAAAACATGGAACATTTTGC 58.450 32.000 9.55 3.58 44.14 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 6.258507 GCAACAACATTTTCCTTCAATGACTT 59.741 34.615 0.00 0.00 35.51 3.01
3 4 5.754890 GCAACAACATTTTCCTTCAATGACT 59.245 36.000 0.00 0.00 35.51 3.41
4 5 5.523188 TGCAACAACATTTTCCTTCAATGAC 59.477 36.000 0.00 0.00 35.51 3.06
5 6 5.668471 TGCAACAACATTTTCCTTCAATGA 58.332 33.333 0.00 0.00 35.51 2.57
6 7 5.987777 TGCAACAACATTTTCCTTCAATG 57.012 34.783 0.00 0.00 37.60 2.82
7 8 6.056884 ACATGCAACAACATTTTCCTTCAAT 58.943 32.000 0.00 0.00 0.00 2.57
8 9 5.426504 ACATGCAACAACATTTTCCTTCAA 58.573 33.333 0.00 0.00 0.00 2.69
9 10 5.021033 ACATGCAACAACATTTTCCTTCA 57.979 34.783 0.00 0.00 0.00 3.02
10 11 5.291971 AGACATGCAACAACATTTTCCTTC 58.708 37.500 0.00 0.00 0.00 3.46
11 12 5.280654 AGACATGCAACAACATTTTCCTT 57.719 34.783 0.00 0.00 0.00 3.36
12 13 4.942761 AGACATGCAACAACATTTTCCT 57.057 36.364 0.00 0.00 0.00 3.36
13 14 5.049167 TGAAGACATGCAACAACATTTTCC 58.951 37.500 0.00 0.00 0.00 3.13
14 15 6.586868 TTGAAGACATGCAACAACATTTTC 57.413 33.333 0.00 0.00 0.00 2.29
15 16 8.836268 ATATTGAAGACATGCAACAACATTTT 57.164 26.923 0.00 0.00 0.00 1.82
16 17 8.308931 AGATATTGAAGACATGCAACAACATTT 58.691 29.630 0.00 0.00 0.00 2.32
17 18 7.833786 AGATATTGAAGACATGCAACAACATT 58.166 30.769 0.00 0.00 0.00 2.71
18 19 7.400599 AGATATTGAAGACATGCAACAACAT 57.599 32.000 0.00 0.00 0.00 2.71
19 20 6.822667 AGATATTGAAGACATGCAACAACA 57.177 33.333 0.00 0.00 0.00 3.33
20 21 6.749118 GGAAGATATTGAAGACATGCAACAAC 59.251 38.462 0.00 0.00 0.00 3.32
21 22 6.660521 AGGAAGATATTGAAGACATGCAACAA 59.339 34.615 0.00 0.00 0.00 2.83
22 23 6.182627 AGGAAGATATTGAAGACATGCAACA 58.817 36.000 0.00 0.00 0.00 3.33
23 24 6.690194 AGGAAGATATTGAAGACATGCAAC 57.310 37.500 0.00 0.00 0.00 4.17
24 25 6.994496 CCTAGGAAGATATTGAAGACATGCAA 59.006 38.462 1.05 0.00 0.00 4.08
25 26 6.100279 ACCTAGGAAGATATTGAAGACATGCA 59.900 38.462 17.98 0.00 0.00 3.96
26 27 6.529220 ACCTAGGAAGATATTGAAGACATGC 58.471 40.000 17.98 0.00 0.00 4.06
27 28 7.655328 GTGACCTAGGAAGATATTGAAGACATG 59.345 40.741 17.98 0.00 0.00 3.21
28 29 7.202047 GGTGACCTAGGAAGATATTGAAGACAT 60.202 40.741 17.98 0.00 0.00 3.06
29 30 6.098409 GGTGACCTAGGAAGATATTGAAGACA 59.902 42.308 17.98 0.00 0.00 3.41
30 31 6.517605 GGTGACCTAGGAAGATATTGAAGAC 58.482 44.000 17.98 0.00 0.00 3.01
31 32 6.732896 GGTGACCTAGGAAGATATTGAAGA 57.267 41.667 17.98 0.00 0.00 2.87
53 54 3.302129 GCCTTCCAGCCAAATGGG 58.698 61.111 0.90 0.00 41.01 4.00
63 64 2.935481 CACTGGGAGGGCCTTCCA 60.935 66.667 31.91 31.91 36.67 3.53
64 65 4.432741 GCACTGGGAGGGCCTTCC 62.433 72.222 25.31 25.31 39.15 3.46
65 66 2.988839 ATGCACTGGGAGGGCCTTC 61.989 63.158 7.89 4.90 46.16 3.46
66 67 2.943265 ATGCACTGGGAGGGCCTT 60.943 61.111 7.89 0.00 46.16 4.35
67 68 3.736224 CATGCACTGGGAGGGCCT 61.736 66.667 5.25 5.25 46.16 5.19
68 69 3.711059 CTCATGCACTGGGAGGGCC 62.711 68.421 0.00 0.00 46.16 5.80
70 71 2.124403 GCTCATGCACTGGGAGGG 60.124 66.667 0.00 0.00 39.41 4.30
71 72 2.672908 TGCTCATGCACTGGGAGG 59.327 61.111 0.00 0.00 45.31 4.30
79 80 3.557686 ATGTCTACACAAGTGCTCATGCA 60.558 43.478 0.00 0.00 40.84 3.96
80 81 2.416747 TGTCTACACAAGTGCTCATGC 58.583 47.619 0.00 0.00 40.20 4.06
81 82 4.568359 GGTATGTCTACACAAGTGCTCATG 59.432 45.833 0.00 0.00 35.64 3.07
82 83 4.222810 TGGTATGTCTACACAAGTGCTCAT 59.777 41.667 0.00 3.39 35.64 2.90
83 84 3.576550 TGGTATGTCTACACAAGTGCTCA 59.423 43.478 0.00 0.00 35.64 4.26
84 85 3.927142 GTGGTATGTCTACACAAGTGCTC 59.073 47.826 0.00 0.00 35.64 4.26
85 86 3.578716 AGTGGTATGTCTACACAAGTGCT 59.421 43.478 0.00 0.00 35.64 4.40
86 87 3.926616 AGTGGTATGTCTACACAAGTGC 58.073 45.455 0.00 0.00 35.64 4.40
87 88 7.101652 AGATAGTGGTATGTCTACACAAGTG 57.898 40.000 0.00 0.00 35.64 3.16
88 89 7.396339 TCAAGATAGTGGTATGTCTACACAAGT 59.604 37.037 0.00 0.00 35.64 3.16
89 90 7.772166 TCAAGATAGTGGTATGTCTACACAAG 58.228 38.462 0.00 0.00 35.64 3.16
90 91 7.712204 TCAAGATAGTGGTATGTCTACACAA 57.288 36.000 0.00 0.00 35.64 3.33
91 92 7.559897 TCATCAAGATAGTGGTATGTCTACACA 59.440 37.037 0.00 0.00 36.78 3.72
92 93 7.941919 TCATCAAGATAGTGGTATGTCTACAC 58.058 38.462 0.00 0.00 0.00 2.90
93 94 8.414003 GTTCATCAAGATAGTGGTATGTCTACA 58.586 37.037 0.00 0.00 0.00 2.74
94 95 8.414003 TGTTCATCAAGATAGTGGTATGTCTAC 58.586 37.037 0.00 0.00 0.00 2.59
95 96 8.533569 TGTTCATCAAGATAGTGGTATGTCTA 57.466 34.615 0.00 0.00 0.00 2.59
96 97 7.423844 TGTTCATCAAGATAGTGGTATGTCT 57.576 36.000 0.00 0.00 0.00 3.41
97 98 7.254117 CGTTGTTCATCAAGATAGTGGTATGTC 60.254 40.741 0.00 0.00 36.66 3.06
98 99 6.535150 CGTTGTTCATCAAGATAGTGGTATGT 59.465 38.462 0.00 0.00 36.66 2.29
99 100 6.510157 GCGTTGTTCATCAAGATAGTGGTATG 60.510 42.308 0.00 0.00 36.66 2.39
100 101 5.523916 GCGTTGTTCATCAAGATAGTGGTAT 59.476 40.000 0.00 0.00 36.66 2.73
101 102 4.868171 GCGTTGTTCATCAAGATAGTGGTA 59.132 41.667 0.00 0.00 36.66 3.25
102 103 3.684788 GCGTTGTTCATCAAGATAGTGGT 59.315 43.478 0.00 0.00 36.66 4.16
103 104 3.242091 CGCGTTGTTCATCAAGATAGTGG 60.242 47.826 0.00 0.00 36.66 4.00
104 105 3.782250 GCGCGTTGTTCATCAAGATAGTG 60.782 47.826 8.43 0.00 36.66 2.74
105 106 2.348666 GCGCGTTGTTCATCAAGATAGT 59.651 45.455 8.43 0.00 36.66 2.12
106 107 2.285834 GGCGCGTTGTTCATCAAGATAG 60.286 50.000 8.43 0.00 36.66 2.08
107 108 1.663643 GGCGCGTTGTTCATCAAGATA 59.336 47.619 8.43 0.00 36.66 1.98
108 109 0.447801 GGCGCGTTGTTCATCAAGAT 59.552 50.000 8.43 0.00 36.66 2.40
109 110 0.882484 TGGCGCGTTGTTCATCAAGA 60.882 50.000 8.43 0.00 36.66 3.02
110 111 0.040514 TTGGCGCGTTGTTCATCAAG 60.041 50.000 8.43 0.00 36.66 3.02
111 112 0.040514 CTTGGCGCGTTGTTCATCAA 60.041 50.000 8.43 0.00 0.00 2.57
112 113 1.573932 CTTGGCGCGTTGTTCATCA 59.426 52.632 8.43 0.00 0.00 3.07
113 114 1.797537 GCTTGGCGCGTTGTTCATC 60.798 57.895 8.43 0.00 0.00 2.92
114 115 2.255252 GCTTGGCGCGTTGTTCAT 59.745 55.556 8.43 0.00 0.00 2.57
125 126 1.153958 GCAACCATTCTCGCTTGGC 60.154 57.895 0.00 0.00 36.41 4.52
126 127 1.508088 GGCAACCATTCTCGCTTGG 59.492 57.895 0.00 0.00 39.02 3.61
127 128 1.135315 CGGCAACCATTCTCGCTTG 59.865 57.895 0.00 0.00 0.00 4.01
128 129 2.040544 CCGGCAACCATTCTCGCTT 61.041 57.895 0.00 0.00 0.00 4.68
129 130 2.436646 CCGGCAACCATTCTCGCT 60.437 61.111 0.00 0.00 0.00 4.93
130 131 4.179579 GCCGGCAACCATTCTCGC 62.180 66.667 24.80 0.00 0.00 5.03
131 132 2.436646 AGCCGGCAACCATTCTCG 60.437 61.111 31.54 0.00 0.00 4.04
132 133 1.372087 CTCAGCCGGCAACCATTCTC 61.372 60.000 31.54 0.00 0.00 2.87
133 134 1.377725 CTCAGCCGGCAACCATTCT 60.378 57.895 31.54 0.76 0.00 2.40
134 135 3.056313 GCTCAGCCGGCAACCATTC 62.056 63.158 31.54 6.74 0.00 2.67
135 136 3.064324 GCTCAGCCGGCAACCATT 61.064 61.111 31.54 2.66 0.00 3.16
146 147 1.002868 ACTGACCACATGGCTCAGC 60.003 57.895 20.96 0.00 42.15 4.26
147 148 0.035881 ACACTGACCACATGGCTCAG 59.964 55.000 20.08 20.08 43.08 3.35
148 149 0.035317 GACACTGACCACATGGCTCA 59.965 55.000 0.00 0.88 39.32 4.26
149 150 0.035317 TGACACTGACCACATGGCTC 59.965 55.000 0.00 0.00 39.32 4.70
150 151 0.473755 TTGACACTGACCACATGGCT 59.526 50.000 0.00 0.00 39.32 4.75
151 152 1.538047 ATTGACACTGACCACATGGC 58.462 50.000 0.00 0.00 39.32 4.40
152 153 3.673902 TGTATTGACACTGACCACATGG 58.326 45.455 0.00 0.00 42.17 3.66
153 154 6.017687 CCATATGTATTGACACTGACCACATG 60.018 42.308 1.24 0.00 38.76 3.21
154 155 6.057533 CCATATGTATTGACACTGACCACAT 58.942 40.000 1.24 0.00 38.76 3.21
155 156 5.045942 ACCATATGTATTGACACTGACCACA 60.046 40.000 1.24 0.00 38.76 4.17
156 157 5.428253 ACCATATGTATTGACACTGACCAC 58.572 41.667 1.24 0.00 38.76 4.16
157 158 5.692115 ACCATATGTATTGACACTGACCA 57.308 39.130 1.24 0.00 38.76 4.02
158 159 6.223852 CCTACCATATGTATTGACACTGACC 58.776 44.000 1.24 0.00 38.76 4.02
159 160 6.041637 TCCCTACCATATGTATTGACACTGAC 59.958 42.308 1.24 0.00 38.76 3.51
160 161 6.140377 TCCCTACCATATGTATTGACACTGA 58.860 40.000 1.24 0.00 38.76 3.41
161 162 6.267699 TCTCCCTACCATATGTATTGACACTG 59.732 42.308 1.24 0.00 38.76 3.66
162 163 6.382087 TCTCCCTACCATATGTATTGACACT 58.618 40.000 1.24 0.00 38.76 3.55
163 164 6.665992 TCTCCCTACCATATGTATTGACAC 57.334 41.667 1.24 0.00 38.76 3.67
164 165 6.440647 GGATCTCCCTACCATATGTATTGACA 59.559 42.308 1.24 0.00 40.72 3.58
165 166 6.405953 CGGATCTCCCTACCATATGTATTGAC 60.406 46.154 1.24 0.00 0.00 3.18
166 167 5.656859 CGGATCTCCCTACCATATGTATTGA 59.343 44.000 1.24 0.00 0.00 2.57
167 168 5.656859 TCGGATCTCCCTACCATATGTATTG 59.343 44.000 1.24 0.00 0.00 1.90
168 169 5.657302 GTCGGATCTCCCTACCATATGTATT 59.343 44.000 1.24 0.00 0.00 1.89
169 170 5.202004 GTCGGATCTCCCTACCATATGTAT 58.798 45.833 1.24 0.00 0.00 2.29
170 171 4.569228 GGTCGGATCTCCCTACCATATGTA 60.569 50.000 1.24 0.00 46.99 2.29
171 172 3.432378 GTCGGATCTCCCTACCATATGT 58.568 50.000 1.24 0.00 0.00 2.29
172 173 2.761208 GGTCGGATCTCCCTACCATATG 59.239 54.545 9.50 0.00 46.99 1.78
173 174 3.103080 GGTCGGATCTCCCTACCATAT 57.897 52.381 9.50 0.00 46.99 1.78
174 175 2.599408 GGTCGGATCTCCCTACCATA 57.401 55.000 9.50 0.00 46.99 2.74
175 176 3.459386 GGTCGGATCTCCCTACCAT 57.541 57.895 9.50 0.00 46.99 3.55
178 179 0.318762 GCATGGTCGGATCTCCCTAC 59.681 60.000 0.00 0.00 0.00 3.18
179 180 0.832135 GGCATGGTCGGATCTCCCTA 60.832 60.000 0.00 0.00 0.00 3.53
180 181 2.143419 GGCATGGTCGGATCTCCCT 61.143 63.158 0.00 0.00 0.00 4.20
181 182 2.105806 GAGGCATGGTCGGATCTCCC 62.106 65.000 0.00 0.00 0.00 4.30
182 183 1.369321 GAGGCATGGTCGGATCTCC 59.631 63.158 0.00 0.00 0.00 3.71
183 184 1.006805 CGAGGCATGGTCGGATCTC 60.007 63.158 0.00 0.00 33.66 2.75
184 185 3.133014 CGAGGCATGGTCGGATCT 58.867 61.111 0.00 0.00 33.66 2.75
189 190 0.953471 TTGTTTCCGAGGCATGGTCG 60.953 55.000 0.00 0.00 37.17 4.79
190 191 1.243902 TTTGTTTCCGAGGCATGGTC 58.756 50.000 0.00 0.00 0.00 4.02
191 192 1.545582 CATTTGTTTCCGAGGCATGGT 59.454 47.619 0.00 0.00 0.00 3.55
192 193 1.135024 CCATTTGTTTCCGAGGCATGG 60.135 52.381 0.00 0.00 0.00 3.66
193 194 1.545582 ACCATTTGTTTCCGAGGCATG 59.454 47.619 0.00 0.00 0.00 4.06
194 195 1.923356 ACCATTTGTTTCCGAGGCAT 58.077 45.000 0.00 0.00 0.00 4.40
195 196 1.698506 AACCATTTGTTTCCGAGGCA 58.301 45.000 0.00 0.00 31.47 4.75
196 197 2.812358 AAACCATTTGTTTCCGAGGC 57.188 45.000 0.00 0.00 43.74 4.70
197 198 5.122711 ACGTATAAACCATTTGTTTCCGAGG 59.877 40.000 0.00 0.00 43.74 4.63
198 199 6.173191 ACGTATAAACCATTTGTTTCCGAG 57.827 37.500 0.00 0.00 43.74 4.63
199 200 5.163972 CGACGTATAAACCATTTGTTTCCGA 60.164 40.000 0.00 0.00 43.74 4.55
200 201 5.016985 CGACGTATAAACCATTTGTTTCCG 58.983 41.667 0.00 0.00 43.74 4.30
201 202 4.789629 GCGACGTATAAACCATTTGTTTCC 59.210 41.667 0.00 0.00 43.74 3.13
202 203 4.789629 GGCGACGTATAAACCATTTGTTTC 59.210 41.667 0.00 0.00 43.74 2.78
204 205 3.752222 TGGCGACGTATAAACCATTTGTT 59.248 39.130 0.00 0.00 39.43 2.83
205 206 3.336468 TGGCGACGTATAAACCATTTGT 58.664 40.909 0.00 0.00 0.00 2.83
206 207 4.092816 GTTGGCGACGTATAAACCATTTG 58.907 43.478 0.00 0.00 0.00 2.32
207 208 3.181518 CGTTGGCGACGTATAAACCATTT 60.182 43.478 19.03 0.00 46.49 2.32
208 209 2.349275 CGTTGGCGACGTATAAACCATT 59.651 45.455 19.03 0.00 46.49 3.16
209 210 1.928503 CGTTGGCGACGTATAAACCAT 59.071 47.619 19.03 0.00 46.49 3.55
210 211 1.348276 CGTTGGCGACGTATAAACCA 58.652 50.000 19.03 0.00 46.49 3.67
220 221 8.456904 TCATAAATTATAGATACGTTGGCGAC 57.543 34.615 0.00 0.00 42.00 5.19
221 222 9.135843 CTTCATAAATTATAGATACGTTGGCGA 57.864 33.333 0.00 0.00 42.00 5.54
222 223 8.922676 ACTTCATAAATTATAGATACGTTGGCG 58.077 33.333 0.00 0.00 44.93 5.69
242 243 8.796475 GTTGTAAATATGGCATGGATACTTCAT 58.204 33.333 10.98 0.00 37.61 2.57
243 244 7.777440 TGTTGTAAATATGGCATGGATACTTCA 59.223 33.333 10.98 9.88 37.61 3.02
244 245 8.165239 TGTTGTAAATATGGCATGGATACTTC 57.835 34.615 10.98 7.88 37.61 3.01
245 246 8.532186 TTGTTGTAAATATGGCATGGATACTT 57.468 30.769 10.98 0.00 37.61 2.24
246 247 8.710749 ATTGTTGTAAATATGGCATGGATACT 57.289 30.769 10.98 0.00 37.61 2.12
247 248 9.762933 AAATTGTTGTAAATATGGCATGGATAC 57.237 29.630 10.98 10.28 0.00 2.24
278 279 9.308000 AGTTCTAATCAAATGATACCAAAACCA 57.692 29.630 0.00 0.00 33.73 3.67
283 284 9.403583 GGGTTAGTTCTAATCAAATGATACCAA 57.596 33.333 8.96 0.00 33.73 3.67
284 285 7.713507 CGGGTTAGTTCTAATCAAATGATACCA 59.286 37.037 8.96 0.00 33.73 3.25
285 286 7.172703 CCGGGTTAGTTCTAATCAAATGATACC 59.827 40.741 0.00 0.00 33.73 2.73
286 287 7.929785 TCCGGGTTAGTTCTAATCAAATGATAC 59.070 37.037 0.00 0.00 33.73 2.24
287 288 7.929785 GTCCGGGTTAGTTCTAATCAAATGATA 59.070 37.037 0.00 0.00 33.73 2.15
288 289 6.766467 GTCCGGGTTAGTTCTAATCAAATGAT 59.234 38.462 0.00 0.00 36.07 2.45
289 290 6.070424 AGTCCGGGTTAGTTCTAATCAAATGA 60.070 38.462 0.00 0.00 0.00 2.57
290 291 6.037172 CAGTCCGGGTTAGTTCTAATCAAATG 59.963 42.308 0.00 0.00 0.00 2.32
291 292 6.070424 TCAGTCCGGGTTAGTTCTAATCAAAT 60.070 38.462 0.00 0.00 0.00 2.32
292 293 5.246656 TCAGTCCGGGTTAGTTCTAATCAAA 59.753 40.000 0.00 0.00 0.00 2.69
293 294 4.773674 TCAGTCCGGGTTAGTTCTAATCAA 59.226 41.667 0.00 0.00 0.00 2.57
294 295 4.159135 GTCAGTCCGGGTTAGTTCTAATCA 59.841 45.833 0.00 0.00 0.00 2.57
295 296 4.680702 GTCAGTCCGGGTTAGTTCTAATC 58.319 47.826 0.00 0.00 0.00 1.75
296 297 3.129988 CGTCAGTCCGGGTTAGTTCTAAT 59.870 47.826 0.00 0.00 0.00 1.73
297 298 2.489329 CGTCAGTCCGGGTTAGTTCTAA 59.511 50.000 0.00 0.00 0.00 2.10
298 299 2.086869 CGTCAGTCCGGGTTAGTTCTA 58.913 52.381 0.00 0.00 0.00 2.10
299 300 0.886563 CGTCAGTCCGGGTTAGTTCT 59.113 55.000 0.00 0.00 0.00 3.01
300 301 0.735287 GCGTCAGTCCGGGTTAGTTC 60.735 60.000 0.00 0.00 0.00 3.01
301 302 1.183676 AGCGTCAGTCCGGGTTAGTT 61.184 55.000 0.00 0.00 0.00 2.24
302 303 0.322816 TAGCGTCAGTCCGGGTTAGT 60.323 55.000 0.00 0.00 0.00 2.24
303 304 1.030457 ATAGCGTCAGTCCGGGTTAG 58.970 55.000 0.00 0.00 0.00 2.34
304 305 1.477553 AATAGCGTCAGTCCGGGTTA 58.522 50.000 0.00 0.00 0.00 2.85
305 306 0.611714 AAATAGCGTCAGTCCGGGTT 59.388 50.000 0.00 0.00 0.00 4.11
306 307 0.611714 AAAATAGCGTCAGTCCGGGT 59.388 50.000 0.00 0.00 0.00 5.28
307 308 1.287425 GAAAATAGCGTCAGTCCGGG 58.713 55.000 0.00 0.00 0.00 5.73
308 309 1.927174 CTGAAAATAGCGTCAGTCCGG 59.073 52.381 0.00 0.00 37.16 5.14
309 310 1.324736 GCTGAAAATAGCGTCAGTCCG 59.675 52.381 2.90 0.00 42.72 4.79
310 311 2.346803 TGCTGAAAATAGCGTCAGTCC 58.653 47.619 2.90 0.00 46.61 3.85
311 312 3.254060 TCTGCTGAAAATAGCGTCAGTC 58.746 45.455 2.90 0.00 46.61 3.51
312 313 3.319137 TCTGCTGAAAATAGCGTCAGT 57.681 42.857 2.90 0.00 46.61 3.41
313 314 3.681897 AGTTCTGCTGAAAATAGCGTCAG 59.318 43.478 7.68 0.00 46.61 3.51
314 315 3.664107 AGTTCTGCTGAAAATAGCGTCA 58.336 40.909 7.68 0.00 46.61 4.35
315 316 4.033014 GGTAGTTCTGCTGAAAATAGCGTC 59.967 45.833 7.68 0.00 46.61 5.19
316 317 3.933332 GGTAGTTCTGCTGAAAATAGCGT 59.067 43.478 7.68 0.00 46.61 5.07
317 318 3.000322 CGGTAGTTCTGCTGAAAATAGCG 60.000 47.826 23.75 23.75 46.61 4.26
318 319 3.933332 ACGGTAGTTCTGCTGAAAATAGC 59.067 43.478 7.68 11.81 43.95 2.97
319 320 4.265556 CGACGGTAGTTCTGCTGAAAATAG 59.734 45.833 7.68 2.28 33.52 1.73
320 321 4.171005 CGACGGTAGTTCTGCTGAAAATA 58.829 43.478 7.68 1.94 33.52 1.40
321 322 2.993899 CGACGGTAGTTCTGCTGAAAAT 59.006 45.455 7.68 2.88 33.52 1.82
322 323 2.223876 ACGACGGTAGTTCTGCTGAAAA 60.224 45.455 7.68 0.00 33.52 2.29
323 324 1.338973 ACGACGGTAGTTCTGCTGAAA 59.661 47.619 7.68 0.00 33.52 2.69
324 325 0.956633 ACGACGGTAGTTCTGCTGAA 59.043 50.000 1.33 1.33 0.00 3.02
325 326 0.240145 CACGACGGTAGTTCTGCTGA 59.760 55.000 0.00 0.00 0.00 4.26
326 327 0.039437 ACACGACGGTAGTTCTGCTG 60.039 55.000 0.00 0.00 0.00 4.41
327 328 0.240411 GACACGACGGTAGTTCTGCT 59.760 55.000 0.00 0.00 0.00 4.24
328 329 0.039798 TGACACGACGGTAGTTCTGC 60.040 55.000 0.00 0.00 0.00 4.26
329 330 2.631418 ATGACACGACGGTAGTTCTG 57.369 50.000 0.00 0.00 0.00 3.02
330 331 3.655276 AAATGACACGACGGTAGTTCT 57.345 42.857 0.00 0.00 0.00 3.01
331 332 4.720530 AAAAATGACACGACGGTAGTTC 57.279 40.909 0.00 0.00 0.00 3.01
353 354 9.672086 CATTCCGAAAACTTTTATTTCTACACA 57.328 29.630 0.00 0.00 35.19 3.72
354 355 9.124807 CCATTCCGAAAACTTTTATTTCTACAC 57.875 33.333 0.00 0.00 35.19 2.90
355 356 8.301002 CCCATTCCGAAAACTTTTATTTCTACA 58.699 33.333 0.00 0.00 35.19 2.74
356 357 7.274904 GCCCATTCCGAAAACTTTTATTTCTAC 59.725 37.037 0.00 0.00 35.19 2.59
357 358 7.177744 AGCCCATTCCGAAAACTTTTATTTCTA 59.822 33.333 0.00 0.00 35.19 2.10
358 359 6.014584 AGCCCATTCCGAAAACTTTTATTTCT 60.015 34.615 0.00 0.00 35.19 2.52
359 360 6.090763 CAGCCCATTCCGAAAACTTTTATTTC 59.909 38.462 0.00 0.00 34.25 2.17
360 361 5.931724 CAGCCCATTCCGAAAACTTTTATTT 59.068 36.000 0.00 0.00 0.00 1.40
361 362 5.245075 TCAGCCCATTCCGAAAACTTTTATT 59.755 36.000 0.00 0.00 0.00 1.40
362 363 4.770010 TCAGCCCATTCCGAAAACTTTTAT 59.230 37.500 0.00 0.00 0.00 1.40
363 364 4.145807 TCAGCCCATTCCGAAAACTTTTA 58.854 39.130 0.00 0.00 0.00 1.52
364 365 2.962421 TCAGCCCATTCCGAAAACTTTT 59.038 40.909 0.00 0.00 0.00 2.27
365 366 2.593026 TCAGCCCATTCCGAAAACTTT 58.407 42.857 0.00 0.00 0.00 2.66
366 367 2.286365 TCAGCCCATTCCGAAAACTT 57.714 45.000 0.00 0.00 0.00 2.66
367 368 2.286365 TTCAGCCCATTCCGAAAACT 57.714 45.000 0.00 0.00 0.00 2.66
368 369 3.378911 TTTTCAGCCCATTCCGAAAAC 57.621 42.857 0.00 0.00 33.61 2.43
369 370 4.615588 AATTTTCAGCCCATTCCGAAAA 57.384 36.364 0.00 0.00 40.50 2.29
370 371 4.314121 CAAATTTTCAGCCCATTCCGAAA 58.686 39.130 0.00 0.00 0.00 3.46
371 372 3.864160 GCAAATTTTCAGCCCATTCCGAA 60.864 43.478 0.00 0.00 0.00 4.30
372 373 2.353605 GCAAATTTTCAGCCCATTCCGA 60.354 45.455 0.00 0.00 0.00 4.55
373 374 2.001872 GCAAATTTTCAGCCCATTCCG 58.998 47.619 0.00 0.00 0.00 4.30
374 375 2.001872 CGCAAATTTTCAGCCCATTCC 58.998 47.619 0.00 0.00 0.00 3.01
375 376 2.001872 CCGCAAATTTTCAGCCCATTC 58.998 47.619 0.00 0.00 0.00 2.67
376 377 1.347378 ACCGCAAATTTTCAGCCCATT 59.653 42.857 0.00 0.00 0.00 3.16
377 378 0.975887 ACCGCAAATTTTCAGCCCAT 59.024 45.000 0.00 0.00 0.00 4.00
378 379 0.033228 CACCGCAAATTTTCAGCCCA 59.967 50.000 0.00 0.00 0.00 5.36
379 380 0.316841 TCACCGCAAATTTTCAGCCC 59.683 50.000 0.00 0.00 0.00 5.19
380 381 2.368655 ATCACCGCAAATTTTCAGCC 57.631 45.000 0.00 0.00 0.00 4.85
381 382 4.730600 AAAATCACCGCAAATTTTCAGC 57.269 36.364 0.00 0.00 31.17 4.26
452 453 1.733399 GTGGCTCTCGACACGTTCC 60.733 63.158 0.00 0.00 39.83 3.62
566 593 3.144068 TGGAGTGGGGAGAATGGATAA 57.856 47.619 0.00 0.00 0.00 1.75
622 661 2.752238 CGCCTCACTCGGGTCTCT 60.752 66.667 0.00 0.00 0.00 3.10
979 1080 1.302112 TTGCCGCTTGTTGGATCGA 60.302 52.632 0.00 0.00 0.00 3.59
1034 1135 3.307108 TGATGTCACCGGCCGTCA 61.307 61.111 26.12 17.19 0.00 4.35
1167 1268 3.691342 CAACAGCTCCCCCGACGA 61.691 66.667 0.00 0.00 0.00 4.20
1201 1303 1.134995 CGCAACTCATCCTCTAGCACA 60.135 52.381 0.00 0.00 0.00 4.57
1227 1329 0.905357 CGACCTCCCCAGATCTTGTT 59.095 55.000 0.00 0.00 0.00 2.83
1268 1371 4.899239 GCTGGCTCGATCGTGGGG 62.899 72.222 15.94 5.50 0.00 4.96
1300 1416 1.097232 GCAGCATACCACATGAGCAA 58.903 50.000 0.00 0.00 0.00 3.91
1306 1422 1.352352 GGGGATAGCAGCATACCACAT 59.648 52.381 8.01 0.00 29.30 3.21
1388 1510 3.675228 CGGTACTCGTGGCAACTTAATCT 60.675 47.826 0.00 0.00 37.61 2.40
2063 2380 3.679502 GCCATGGCAACTTTACATGTTTC 59.320 43.478 32.08 0.00 40.16 2.78


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.