Multiple sequence alignment - TraesCS4D01G237300

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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 TraesCS4D01G237300 chr4D 100.000 5682 0 0 1 5682 399530191 399535872 0.000000e+00 10493.0
1 TraesCS4D01G237300 chr4B 93.972 4678 157 62 289 4918 493526470 493531070 0.000000e+00 6961.0
2 TraesCS4D01G237300 chr4B 97.625 421 7 1 5203 5620 493533113 493533533 0.000000e+00 719.0
3 TraesCS4D01G237300 chr4B 86.207 348 29 10 2809 3148 184601057 184601393 5.410000e-95 359.0
4 TraesCS4D01G237300 chr4B 86.833 281 32 2 3 283 493526156 493526431 5.530000e-80 309.0
5 TraesCS4D01G237300 chr4B 82.383 193 12 8 4915 5107 493531119 493531289 1.280000e-31 148.0
6 TraesCS4D01G237300 chr4A 92.491 4701 180 66 289 4918 57162509 57167107 0.000000e+00 6565.0
7 TraesCS4D01G237300 chr4A 90.848 743 31 8 4918 5639 57167165 57167891 0.000000e+00 961.0
8 TraesCS4D01G237300 chr2D 86.000 350 27 13 2809 3148 579178697 579179034 7.000000e-94 355.0
9 TraesCS4D01G237300 chr2D 82.671 277 41 6 2 277 442013474 442013744 7.360000e-59 239.0
10 TraesCS4D01G237300 chr1D 86.040 351 26 12 2809 3148 403278483 403278145 7.000000e-94 355.0
11 TraesCS4D01G237300 chr7D 82.971 276 43 3 3 277 230911907 230912179 4.400000e-61 246.0
12 TraesCS4D01G237300 chr7D 80.660 212 24 11 2941 3148 559288469 559288271 1.280000e-31 148.0
13 TraesCS4D01G237300 chr7D 89.157 83 2 2 2809 2884 559288546 559288464 4.690000e-16 97.1
14 TraesCS4D01G237300 chr5B 83.394 277 35 9 2 275 16474552 16474284 4.400000e-61 246.0
15 TraesCS4D01G237300 chr5B 83.032 277 33 11 2 275 16730652 16730387 7.360000e-59 239.0
16 TraesCS4D01G237300 chr5B 82.671 277 37 10 2 275 16813514 16813246 9.520000e-58 235.0
17 TraesCS4D01G237300 chr5B 88.189 127 13 2 4053 4178 585475640 585475765 3.550000e-32 150.0
18 TraesCS4D01G237300 chr3D 83.206 262 34 9 1 260 114339060 114338807 1.230000e-56 231.0
19 TraesCS4D01G237300 chr3D 94.872 39 2 0 5644 5682 491639776 491639738 1.710000e-05 62.1
20 TraesCS4D01G237300 chrUn 81.949 277 39 10 2 275 355474873 355474605 2.060000e-54 224.0
21 TraesCS4D01G237300 chr7B 80.836 287 38 14 1 284 641747904 641748176 5.770000e-50 209.0
22 TraesCS4D01G237300 chr1A 87.013 154 16 3 5011 5162 120379953 120380104 2.720000e-38 171.0
23 TraesCS4D01G237300 chr1A 100.000 29 0 0 5644 5672 22278374 22278346 3.000000e-03 54.7
24 TraesCS4D01G237300 chr2B 90.625 128 10 1 5034 5159 195678206 195678079 9.790000e-38 169.0
25 TraesCS4D01G237300 chr5D 87.402 127 14 2 4053 4178 477986488 477986613 1.650000e-30 145.0
26 TraesCS4D01G237300 chr5D 97.674 43 1 0 5640 5682 217976744 217976702 2.200000e-09 75.0
27 TraesCS4D01G237300 chr5D 97.674 43 1 0 5640 5682 379580422 379580380 2.200000e-09 75.0
28 TraesCS4D01G237300 chr5D 94.286 35 2 0 5633 5667 75726087 75726121 3.000000e-03 54.7
29 TraesCS4D01G237300 chr5A 87.402 127 14 2 4053 4178 597256923 597257048 1.650000e-30 145.0
30 TraesCS4D01G237300 chr5A 88.679 106 6 1 2809 2908 615832880 615832775 2.150000e-24 124.0
31 TraesCS4D01G237300 chr5A 87.736 106 7 1 2809 2908 615773768 615773663 1.000000e-22 119.0
32 TraesCS4D01G237300 chr5A 100.000 31 0 0 5640 5670 291135193 291135223 2.210000e-04 58.4
33 TraesCS4D01G237300 chr2A 90.000 70 5 2 5011 5080 140366702 140366635 7.840000e-14 89.8
34 TraesCS4D01G237300 chr6D 95.349 43 2 0 5640 5682 362985289 362985331 1.020000e-07 69.4
35 TraesCS4D01G237300 chr3A 92.308 39 3 0 5644 5682 673718692 673718654 7.950000e-04 56.5
36 TraesCS4D01G237300 chr3A 94.286 35 2 0 5644 5678 743469937 743469903 3.000000e-03 54.7


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 TraesCS4D01G237300 chr4D 399530191 399535872 5681 False 10493.00 10493 100.00000 1 5682 1 chr4D.!!$F1 5681
1 TraesCS4D01G237300 chr4B 493526156 493533533 7377 False 2034.25 6961 90.20325 3 5620 4 chr4B.!!$F2 5617
2 TraesCS4D01G237300 chr4A 57162509 57167891 5382 False 3763.00 6565 91.66950 289 5639 2 chr4A.!!$F1 5350

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
759 815 0.396060 GCATTAGGGCTCAGGAGAGG 59.604 60.0 0.0 0.0 42.33 3.69 F
1588 1666 0.034059 ACTTCCAGCACTTGACGGAG 59.966 55.0 0.0 0.0 0.00 4.63 F
2773 2889 0.179062 ATCTCTGGCTCGAATGGTGC 60.179 55.0 0.0 0.0 0.00 5.01 F
4060 4200 0.324285 CCACTCAGGAAGAAGCAGCT 59.676 55.0 0.0 0.0 41.22 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2685 2801 0.396811 ACAAGGTGACTGGTGCCTAC 59.603 55.0 0.0 0.0 45.23 3.18 R
3097 3224 1.967319 AGTGTGCAACGAATTCCTGT 58.033 45.0 0.0 0.0 42.39 4.00 R
4616 4759 0.036671 GAATTCGGTCCCCTCAACGT 60.037 55.0 0.0 0.0 0.00 3.99 R
5363 7315 0.387929 AAAGGACGTGAGACAAGCGA 59.612 50.0 0.0 0.0 0.00 4.93 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
18 19 1.912983 CGAGATCATCACGTGCACG 59.087 57.895 35.99 35.99 46.33 5.34
19 20 1.633171 GAGATCATCACGTGCACGC 59.367 57.895 37.35 19.83 44.43 5.34
55 56 3.266510 TCTTGTGGAGCATATGTGGAC 57.733 47.619 4.29 0.00 0.00 4.02
88 89 8.870075 AGAAACCAAAGAGCTAATATTTGAGT 57.130 30.769 12.34 7.57 41.66 3.41
98 99 6.846350 AGCTAATATTTGAGTTGTGCACTTC 58.154 36.000 19.41 13.20 35.01 3.01
109 110 9.809096 TTGAGTTGTGCACTTCAAATAAATTTA 57.191 25.926 19.41 0.00 35.01 1.40
158 159 8.065407 TCAGTAACAACATTTTTGCTACTTACG 58.935 33.333 0.00 0.00 31.25 3.18
161 162 4.973663 ACAACATTTTTGCTACTTACGTGC 59.026 37.500 0.00 0.00 0.00 5.34
171 172 1.057636 ACTTACGTGCGACATTGACG 58.942 50.000 0.00 4.15 39.03 4.35
184 185 4.102649 GACATTGACGTGTATGATCGACA 58.897 43.478 12.12 0.00 31.16 4.35
185 186 4.682787 ACATTGACGTGTATGATCGACAT 58.317 39.130 12.12 0.00 42.39 3.06
186 187 5.827666 ACATTGACGTGTATGATCGACATA 58.172 37.500 12.12 0.00 40.07 2.29
208 209 9.093970 ACATACATGAATTTGCATGAATTTGAG 57.906 29.630 12.68 0.00 46.64 3.02
209 210 9.308318 CATACATGAATTTGCATGAATTTGAGA 57.692 29.630 12.68 0.00 46.64 3.27
210 211 9.878667 ATACATGAATTTGCATGAATTTGAGAA 57.121 25.926 12.68 0.00 46.64 2.87
215 216 5.641783 TTTGCATGAATTTGAGAATCCGA 57.358 34.783 0.00 0.00 0.00 4.55
238 239 7.012704 CCGAATTTAAGATATATGGATGCAGGG 59.987 40.741 0.00 0.00 0.00 4.45
244 245 4.477581 AGATATATGGATGCAGGGCAGAAT 59.522 41.667 0.00 0.00 43.65 2.40
249 250 5.981494 ATGGATGCAGGGCAGAATATATA 57.019 39.130 0.00 0.00 43.65 0.86
250 251 5.981494 TGGATGCAGGGCAGAATATATAT 57.019 39.130 0.00 0.00 43.65 0.86
251 252 7.637548 ATGGATGCAGGGCAGAATATATATA 57.362 36.000 0.00 0.00 43.65 0.86
258 259 3.008049 GGGCAGAATATATATAGGGCCGG 59.992 52.174 18.04 0.00 41.00 6.13
283 284 4.937781 CGTCCGCGGACTTATAGG 57.062 61.111 44.83 29.74 42.54 2.57
285 286 1.229428 CGTCCGCGGACTTATAGGTA 58.771 55.000 44.83 14.19 42.54 3.08
286 287 1.196354 CGTCCGCGGACTTATAGGTAG 59.804 57.143 44.83 27.77 42.54 3.18
287 288 1.538950 GTCCGCGGACTTATAGGTAGG 59.461 57.143 43.32 6.97 41.57 3.18
299 333 3.810721 ATAGGTAGGCGGATACACTCT 57.189 47.619 0.00 0.00 0.00 3.24
303 337 2.308690 GTAGGCGGATACACTCTCCTT 58.691 52.381 0.00 0.00 31.99 3.36
403 441 0.811915 CTACGTCTAGGCAGCAGTGT 59.188 55.000 0.00 0.00 0.00 3.55
515 553 8.902806 TCCACGATTAAATTCTTGCATCTTTAT 58.097 29.630 0.00 0.00 0.00 1.40
519 557 9.831737 CGATTAAATTCTTGCATCTTTATAGGG 57.168 33.333 0.00 0.00 0.00 3.53
521 559 9.660544 ATTAAATTCTTGCATCTTTATAGGGGT 57.339 29.630 0.00 0.00 0.00 4.95
522 560 7.978099 AAATTCTTGCATCTTTATAGGGGTT 57.022 32.000 0.00 0.00 0.00 4.11
524 562 8.697507 AATTCTTGCATCTTTATAGGGGTTAG 57.302 34.615 0.00 0.00 0.00 2.34
728 779 3.279434 CCCTAGATTTTATATGCCCGCC 58.721 50.000 0.00 0.00 0.00 6.13
759 815 0.396060 GCATTAGGGCTCAGGAGAGG 59.604 60.000 0.00 0.00 42.33 3.69
845 905 2.681778 CAGCTCACGGGTCCCTCT 60.682 66.667 6.29 0.00 0.00 3.69
846 906 2.363147 AGCTCACGGGTCCCTCTC 60.363 66.667 6.29 0.00 0.00 3.20
847 907 3.827898 GCTCACGGGTCCCTCTCG 61.828 72.222 6.29 0.00 46.72 4.04
848 908 3.827898 CTCACGGGTCCCTCTCGC 61.828 72.222 6.29 0.00 44.96 5.03
1083 1146 2.063378 GGTGCCCTCCTCCTCTGAG 61.063 68.421 0.00 0.00 38.42 3.35
1158 1227 2.360475 GCCACCTGCAACCTCCTC 60.360 66.667 0.00 0.00 40.77 3.71
1166 1235 1.201429 TGCAACCTCCTCTTCTCCCC 61.201 60.000 0.00 0.00 0.00 4.81
1167 1236 0.912006 GCAACCTCCTCTTCTCCCCT 60.912 60.000 0.00 0.00 0.00 4.79
1171 1240 1.598856 CCTCCTCTTCTCCCCTCCCT 61.599 65.000 0.00 0.00 0.00 4.20
1215 1284 1.937391 CTACTACTACGTCGGCGGG 59.063 63.158 16.39 8.92 43.45 6.13
1312 1381 1.100510 CCTGTGCATCATGGAAGGTG 58.899 55.000 0.00 0.00 0.00 4.00
1313 1382 0.454600 CTGTGCATCATGGAAGGTGC 59.545 55.000 0.00 0.00 38.05 5.01
1316 1385 2.711311 CATCATGGAAGGTGCGCG 59.289 61.111 0.00 0.00 0.00 6.86
1504 1573 3.738246 CACCAGCAGCAGCAGCAG 61.738 66.667 12.92 3.65 45.49 4.24
1588 1666 0.034059 ACTTCCAGCACTTGACGGAG 59.966 55.000 0.00 0.00 0.00 4.63
1782 1860 2.515523 GCATCAGATGGCTGCGGT 60.516 61.111 12.54 0.00 42.01 5.68
1998 2082 7.920738 ACAGATATTTAGCTTTTCGATTCACC 58.079 34.615 0.00 0.00 0.00 4.02
2026 2128 5.738619 TCTCAACTTGCTCAATAGTACCA 57.261 39.130 0.00 0.00 0.00 3.25
2027 2129 6.299805 TCTCAACTTGCTCAATAGTACCAT 57.700 37.500 0.00 0.00 0.00 3.55
2028 2130 6.711277 TCTCAACTTGCTCAATAGTACCATT 58.289 36.000 0.00 0.00 0.00 3.16
2029 2131 7.168219 TCTCAACTTGCTCAATAGTACCATTT 58.832 34.615 0.00 0.00 0.00 2.32
2030 2132 7.665559 TCTCAACTTGCTCAATAGTACCATTTT 59.334 33.333 0.00 0.00 0.00 1.82
2031 2133 8.177119 TCAACTTGCTCAATAGTACCATTTTT 57.823 30.769 0.00 0.00 0.00 1.94
2070 2172 8.969260 TGATCATTTAGCATTAGTCATCTTGT 57.031 30.769 0.00 0.00 0.00 3.16
2071 2173 8.833493 TGATCATTTAGCATTAGTCATCTTGTG 58.167 33.333 0.00 0.00 0.00 3.33
2072 2174 7.019774 TCATTTAGCATTAGTCATCTTGTGC 57.980 36.000 0.00 0.00 34.97 4.57
2091 2193 5.708948 TGTGCTGCAAATAAACTAATGTCC 58.291 37.500 2.77 0.00 0.00 4.02
2107 2209 4.927267 ATGTCCACTAATTCCTGGTTCA 57.073 40.909 0.00 3.95 0.00 3.18
2108 2210 4.715534 TGTCCACTAATTCCTGGTTCAA 57.284 40.909 0.00 0.00 0.00 2.69
2110 2212 5.640147 TGTCCACTAATTCCTGGTTCAATT 58.360 37.500 0.00 0.00 0.00 2.32
2111 2213 6.785076 TGTCCACTAATTCCTGGTTCAATTA 58.215 36.000 0.00 0.00 0.00 1.40
2151 2253 7.797121 AATAAGTTCCTGGTTCATTTGGAAT 57.203 32.000 0.00 0.00 40.20 3.01
2165 2272 9.826574 GTTCATTTGGAATATGTAGTGGTAGTA 57.173 33.333 0.00 0.00 37.93 1.82
2166 2273 9.826574 TTCATTTGGAATATGTAGTGGTAGTAC 57.173 33.333 0.00 0.00 0.00 2.73
2201 2314 4.646945 TCTGTTTGAATGTTTTGCCCTGTA 59.353 37.500 0.00 0.00 0.00 2.74
2221 2334 6.879458 CCTGTAATTTTGTCCTAGTTAGCAGT 59.121 38.462 0.00 0.00 0.00 4.40
2240 2353 5.466432 CAGTATTGATGTCTGCAGTCTTG 57.534 43.478 14.67 0.00 0.00 3.02
2304 2417 4.014406 AGGACCCATATTTCGTTCCAAAC 58.986 43.478 0.00 0.00 0.00 2.93
2305 2418 3.759618 GGACCCATATTTCGTTCCAAACA 59.240 43.478 0.00 0.00 0.00 2.83
2316 2431 4.551388 TCGTTCCAAACAAAATATGCCAC 58.449 39.130 0.00 0.00 0.00 5.01
2342 2457 6.095021 GGAACAGTTAGATTTATTCACCCACC 59.905 42.308 0.00 0.00 0.00 4.61
2343 2458 6.134535 ACAGTTAGATTTATTCACCCACCA 57.865 37.500 0.00 0.00 0.00 4.17
2344 2459 5.944007 ACAGTTAGATTTATTCACCCACCAC 59.056 40.000 0.00 0.00 0.00 4.16
2371 2486 3.751175 TGCTTAGTTTGTTTCATCCCTCG 59.249 43.478 0.00 0.00 0.00 4.63
2677 2793 9.463443 AACTTCTAGCACAAATTGTATCAAAAC 57.537 29.630 0.00 0.00 0.00 2.43
2683 2799 7.895759 AGCACAAATTGTATCAAAACCATACT 58.104 30.769 0.00 0.00 0.00 2.12
2684 2800 9.019656 AGCACAAATTGTATCAAAACCATACTA 57.980 29.630 0.00 0.00 0.00 1.82
2685 2801 9.289303 GCACAAATTGTATCAAAACCATACTAG 57.711 33.333 0.00 0.00 0.00 2.57
2703 2819 0.687354 AGTAGGCACCAGTCACCTTG 59.313 55.000 0.00 0.00 34.92 3.61
2773 2889 0.179062 ATCTCTGGCTCGAATGGTGC 60.179 55.000 0.00 0.00 0.00 5.01
2798 2914 7.201652 GCCTTCTTGCAGTTTATCTAGGTAAAG 60.202 40.741 8.49 0.00 0.00 1.85
2940 3067 1.411501 GCTCTGAAATATTGGGGGCCA 60.412 52.381 4.39 0.00 0.00 5.36
2975 3102 3.275617 TTTCCCGGTATGGATGACAAG 57.724 47.619 0.00 0.00 42.00 3.16
3000 3127 6.588719 TGGATTGGTTCATGGAAACTAAAG 57.411 37.500 1.13 0.00 34.00 1.85
3022 3149 5.391736 AAGCCGTCGATATCGGTTTCTATAG 60.392 44.000 24.12 0.00 45.64 1.31
3097 3224 4.914983 AGGAGATGAAAAGCATGACAAGA 58.085 39.130 0.00 0.00 37.34 3.02
3130 3257 5.505654 CGTTGCACACTTGAGAAGGTAAAAT 60.506 40.000 0.00 0.00 0.00 1.82
3286 3414 3.585289 TGCCTACACATTTCCCTCAACTA 59.415 43.478 0.00 0.00 0.00 2.24
3287 3415 4.042311 TGCCTACACATTTCCCTCAACTAA 59.958 41.667 0.00 0.00 0.00 2.24
3288 3416 4.636206 GCCTACACATTTCCCTCAACTAAG 59.364 45.833 0.00 0.00 0.00 2.18
3289 3417 5.570844 GCCTACACATTTCCCTCAACTAAGA 60.571 44.000 0.00 0.00 0.00 2.10
3290 3418 6.472887 CCTACACATTTCCCTCAACTAAGAA 58.527 40.000 0.00 0.00 0.00 2.52
3637 3765 4.575236 TGCTAGAGAATGTAGTAGACACCG 59.425 45.833 0.00 0.00 42.17 4.94
3680 3808 1.873591 CCTCTAGTTTTGTGCGTTGCT 59.126 47.619 0.00 0.00 0.00 3.91
3697 3827 4.094442 CGTTGCTTTTGGGATCTAGTAACC 59.906 45.833 0.00 0.00 32.00 2.85
3822 3960 3.592059 TGTACAAAGCTATCGGTTGACC 58.408 45.455 2.16 0.00 0.00 4.02
3906 4044 6.529125 TCAGATCGGAAATCGTACTTTACAAC 59.471 38.462 0.00 0.00 40.32 3.32
3989 4127 6.750963 GTCTTCTAAAGTAACATACCTCACCG 59.249 42.308 0.00 0.00 0.00 4.94
3992 4130 7.701539 TCTAAAGTAACATACCTCACCGTTA 57.298 36.000 0.00 0.00 0.00 3.18
4023 4163 8.677300 TGTATGAAGATCTTAACAAAATCTGCC 58.323 33.333 8.25 0.00 30.35 4.85
4033 4173 4.853924 ACAAAATCTGCCGAATCTTTGT 57.146 36.364 9.20 9.20 33.39 2.83
4034 4174 5.200368 ACAAAATCTGCCGAATCTTTGTT 57.800 34.783 9.20 0.00 34.27 2.83
4035 4175 4.984161 ACAAAATCTGCCGAATCTTTGTTG 59.016 37.500 9.20 0.00 34.27 3.33
4060 4200 0.324285 CCACTCAGGAAGAAGCAGCT 59.676 55.000 0.00 0.00 41.22 4.24
4078 4218 2.327244 GAGGCCTACGACGTAGCG 59.673 66.667 26.14 20.03 35.06 4.26
4223 4363 2.740055 CAGCCAGCCACGTGTCTC 60.740 66.667 15.65 3.17 0.00 3.36
4414 4557 2.740826 ATTGCCGGGTTCGACGTG 60.741 61.111 2.18 0.00 39.00 4.49
4627 4770 3.948719 GCCCACACGTTGAGGGGA 61.949 66.667 16.20 0.00 46.71 4.81
4646 4789 1.490910 GACCGAATTCCTCCATCCCTT 59.509 52.381 0.00 0.00 0.00 3.95
4648 4791 1.771255 CCGAATTCCTCCATCCCTTCT 59.229 52.381 0.00 0.00 0.00 2.85
4691 4834 2.358125 ACGCATAGCCGTGTTGCA 60.358 55.556 0.00 0.00 40.40 4.08
4726 4869 1.881925 GCTGTCACTGGCCATGTTGTA 60.882 52.381 5.51 0.00 0.00 2.41
4755 4898 1.334243 GAGCTGGATTAGTAGCGTCGT 59.666 52.381 0.00 0.00 44.43 4.34
4757 4900 1.852895 GCTGGATTAGTAGCGTCGTTG 59.147 52.381 0.00 0.00 0.00 4.10
4758 4901 1.852895 CTGGATTAGTAGCGTCGTTGC 59.147 52.381 0.00 0.00 0.00 4.17
4760 4903 2.117910 GGATTAGTAGCGTCGTTGCTC 58.882 52.381 2.48 1.43 45.87 4.26
4761 4904 2.479049 GGATTAGTAGCGTCGTTGCTCA 60.479 50.000 2.48 0.00 45.87 4.26
4762 4905 2.933495 TTAGTAGCGTCGTTGCTCAT 57.067 45.000 2.48 1.61 45.87 2.90
4763 4906 2.188837 TAGTAGCGTCGTTGCTCATG 57.811 50.000 2.48 0.00 45.87 3.07
4766 4909 0.796870 TAGCGTCGTTGCTCATGTCG 60.797 55.000 7.40 0.00 45.87 4.35
4767 4910 2.391821 CGTCGTTGCTCATGTCGC 59.608 61.111 0.00 0.00 0.00 5.19
4768 4911 2.088763 CGTCGTTGCTCATGTCGCT 61.089 57.895 10.24 0.00 0.00 4.93
4770 4913 1.346365 GTCGTTGCTCATGTCGCTTA 58.654 50.000 10.24 0.00 0.00 3.09
4771 4914 1.724623 GTCGTTGCTCATGTCGCTTAA 59.275 47.619 10.24 0.00 0.00 1.85
4772 4915 1.992667 TCGTTGCTCATGTCGCTTAAG 59.007 47.619 0.00 0.00 0.00 1.85
4778 4921 6.314784 GTTGCTCATGTCGCTTAAGTTTAAT 58.685 36.000 4.02 0.00 0.00 1.40
4812 4960 4.396790 TGGTTAATTGGTTATCACGAAGGC 59.603 41.667 0.00 0.00 0.00 4.35
4850 4998 2.736347 AGTGGTACGTAGGAGAAGCAT 58.264 47.619 0.00 0.00 0.00 3.79
4918 5067 9.269453 GTTCTTACTTACTTTCTTTTGAGCCTA 57.731 33.333 0.00 0.00 0.00 3.93
4974 5182 1.144093 TGAAAGGGTTTGTGGGATCGT 59.856 47.619 0.00 0.00 0.00 3.73
5004 5212 2.750712 TGATGTGTCTTCATCCGTACGA 59.249 45.455 18.76 3.10 42.24 3.43
5007 5222 3.507786 TGTGTCTTCATCCGTACGATTG 58.492 45.455 18.76 13.57 0.00 2.67
5009 5224 3.303495 GTGTCTTCATCCGTACGATTGTG 59.697 47.826 18.76 9.57 0.00 3.33
5030 5245 3.949031 TTTTTGCCGACGAAAAGGG 57.051 47.368 0.00 0.00 34.80 3.95
5032 5247 1.457009 TTTTGCCGACGAAAAGGGGG 61.457 55.000 0.00 0.00 0.00 5.40
5109 5324 2.235761 GGGGAGGTTGGGTAAGCCA 61.236 63.158 0.00 0.00 34.90 4.75
5113 7043 0.034089 GAGGTTGGGTAAGCCAGCAT 60.034 55.000 0.00 0.00 34.90 3.79
5162 7094 2.749621 CGCTAAAGAATCTGCAACCCTT 59.250 45.455 0.00 0.00 0.00 3.95
5163 7095 3.181506 CGCTAAAGAATCTGCAACCCTTC 60.182 47.826 0.00 0.00 0.00 3.46
5165 7097 5.186198 GCTAAAGAATCTGCAACCCTTCTA 58.814 41.667 0.00 0.00 0.00 2.10
5166 7098 5.065346 GCTAAAGAATCTGCAACCCTTCTAC 59.935 44.000 0.00 0.00 0.00 2.59
5167 7099 3.252974 AGAATCTGCAACCCTTCTACG 57.747 47.619 0.00 0.00 0.00 3.51
5168 7100 2.832129 AGAATCTGCAACCCTTCTACGA 59.168 45.455 0.00 0.00 0.00 3.43
5169 7101 2.674796 ATCTGCAACCCTTCTACGAC 57.325 50.000 0.00 0.00 0.00 4.34
5170 7102 1.629043 TCTGCAACCCTTCTACGACT 58.371 50.000 0.00 0.00 0.00 4.18
5171 7103 2.799017 TCTGCAACCCTTCTACGACTA 58.201 47.619 0.00 0.00 0.00 2.59
5244 7196 2.376032 GTACGCTCGTTTATCCGTACC 58.624 52.381 10.12 0.00 45.97 3.34
5276 7228 3.139077 GGTCAAGTAGTGGACAGGTTTG 58.861 50.000 7.40 0.00 35.74 2.93
5363 7315 2.771943 TCTTTTGACCAGTGTCTCAGGT 59.228 45.455 0.00 0.00 42.28 4.00
5420 7372 2.416747 GCGGCACTTGCTCATATGATA 58.583 47.619 5.72 0.00 41.70 2.15
5421 7373 2.807967 GCGGCACTTGCTCATATGATAA 59.192 45.455 5.72 4.31 41.70 1.75
5509 7461 1.545582 CGGTGCCAATCATTCCAAAGT 59.454 47.619 0.00 0.00 0.00 2.66
5621 7584 1.839994 CCAAAGTGGAGGAGGATGCTA 59.160 52.381 0.00 0.00 40.96 3.49
5626 7589 1.137872 GTGGAGGAGGATGCTAGTGTG 59.862 57.143 0.00 0.00 36.27 3.82
5648 7611 2.961768 CGGCTGCCGGACAAATTT 59.038 55.556 32.37 0.00 44.15 1.82
5649 7612 1.154035 CGGCTGCCGGACAAATTTC 60.154 57.895 32.37 0.00 44.15 2.17
5650 7613 1.154035 GGCTGCCGGACAAATTTCG 60.154 57.895 5.05 0.00 0.00 3.46
5651 7614 1.579429 GCTGCCGGACAAATTTCGT 59.421 52.632 5.05 0.00 0.00 3.85
5652 7615 0.729140 GCTGCCGGACAAATTTCGTG 60.729 55.000 5.05 0.00 0.00 4.35
5653 7616 0.591170 CTGCCGGACAAATTTCGTGT 59.409 50.000 5.05 0.00 0.00 4.49
5654 7617 1.001815 CTGCCGGACAAATTTCGTGTT 60.002 47.619 5.05 0.00 0.00 3.32
5655 7618 1.405821 TGCCGGACAAATTTCGTGTTT 59.594 42.857 5.05 0.00 0.00 2.83
5656 7619 2.159226 TGCCGGACAAATTTCGTGTTTT 60.159 40.909 5.05 0.00 0.00 2.43
5657 7620 2.217620 GCCGGACAAATTTCGTGTTTTG 59.782 45.455 5.05 0.00 38.49 2.44
5658 7621 3.696898 CCGGACAAATTTCGTGTTTTGA 58.303 40.909 0.00 0.00 36.54 2.69
5659 7622 3.484285 CCGGACAAATTTCGTGTTTTGAC 59.516 43.478 0.00 6.99 36.54 3.18
5660 7623 3.484285 CGGACAAATTTCGTGTTTTGACC 59.516 43.478 11.62 12.61 41.29 4.02
5661 7624 3.799963 GGACAAATTTCGTGTTTTGACCC 59.200 43.478 11.62 8.97 39.88 4.46
5662 7625 4.440940 GGACAAATTTCGTGTTTTGACCCT 60.441 41.667 11.62 0.00 39.88 4.34
5663 7626 5.079689 ACAAATTTCGTGTTTTGACCCTT 57.920 34.783 11.62 0.00 36.54 3.95
5664 7627 5.483811 ACAAATTTCGTGTTTTGACCCTTT 58.516 33.333 11.62 0.00 36.54 3.11
5665 7628 5.935206 ACAAATTTCGTGTTTTGACCCTTTT 59.065 32.000 11.62 0.00 36.54 2.27
5666 7629 6.091577 ACAAATTTCGTGTTTTGACCCTTTTC 59.908 34.615 11.62 0.00 36.54 2.29
5667 7630 5.592104 ATTTCGTGTTTTGACCCTTTTCT 57.408 34.783 0.00 0.00 0.00 2.52
5668 7631 4.625972 TTCGTGTTTTGACCCTTTTCTC 57.374 40.909 0.00 0.00 0.00 2.87
5669 7632 3.611970 TCGTGTTTTGACCCTTTTCTCA 58.388 40.909 0.00 0.00 0.00 3.27
5670 7633 4.011023 TCGTGTTTTGACCCTTTTCTCAA 58.989 39.130 0.00 0.00 0.00 3.02
5671 7634 4.459685 TCGTGTTTTGACCCTTTTCTCAAA 59.540 37.500 0.00 0.00 35.14 2.69
5672 7635 5.126384 TCGTGTTTTGACCCTTTTCTCAAAT 59.874 36.000 0.00 0.00 36.51 2.32
5673 7636 5.458779 CGTGTTTTGACCCTTTTCTCAAATC 59.541 40.000 0.00 0.00 36.51 2.17
5674 7637 6.573434 GTGTTTTGACCCTTTTCTCAAATCT 58.427 36.000 0.00 0.00 36.51 2.40
5675 7638 7.468084 CGTGTTTTGACCCTTTTCTCAAATCTA 60.468 37.037 0.00 0.00 36.51 1.98
5676 7639 8.360390 GTGTTTTGACCCTTTTCTCAAATCTAT 58.640 33.333 0.00 0.00 36.51 1.98
5677 7640 8.923270 TGTTTTGACCCTTTTCTCAAATCTATT 58.077 29.630 0.00 0.00 36.51 1.73
5678 7641 9.411801 GTTTTGACCCTTTTCTCAAATCTATTC 57.588 33.333 0.00 0.00 36.51 1.75
5679 7642 6.985188 TGACCCTTTTCTCAAATCTATTCG 57.015 37.500 0.00 0.00 0.00 3.34
5680 7643 6.707290 TGACCCTTTTCTCAAATCTATTCGA 58.293 36.000 0.00 0.00 0.00 3.71
5681 7644 6.818644 TGACCCTTTTCTCAAATCTATTCGAG 59.181 38.462 0.00 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.912983 CGTGCACGTGATGATCTCG 59.087 57.895 30.50 14.46 39.05 4.04
1 2 1.633171 GCGTGCACGTGATGATCTC 59.367 57.895 36.80 15.74 42.22 2.75
26 27 0.723981 GCTCCACAAGATCGTTGAGC 59.276 55.000 9.87 9.87 44.41 4.26
55 56 4.082125 AGCTCTTTGGTTTCTATTGTGGG 58.918 43.478 0.00 0.00 0.00 4.61
64 65 9.346725 CAACTCAAATATTAGCTCTTTGGTTTC 57.653 33.333 0.00 0.00 32.15 2.78
158 159 1.989864 TCATACACGTCAATGTCGCAC 59.010 47.619 0.00 0.00 33.85 5.34
161 162 3.177838 GTCGATCATACACGTCAATGTCG 59.822 47.826 16.64 16.64 33.85 4.35
184 185 9.878667 TTCTCAAATTCATGCAAATTCATGTAT 57.121 25.926 6.93 1.57 43.18 2.29
185 186 9.878667 ATTCTCAAATTCATGCAAATTCATGTA 57.121 25.926 6.93 0.00 43.18 2.29
186 187 8.786826 ATTCTCAAATTCATGCAAATTCATGT 57.213 26.923 6.93 0.00 43.18 3.21
209 210 9.685276 TGCATCCATATATCTTAAATTCGGATT 57.315 29.630 0.00 0.00 0.00 3.01
210 211 9.334947 CTGCATCCATATATCTTAAATTCGGAT 57.665 33.333 0.00 0.00 0.00 4.18
215 216 7.184161 TGCCCTGCATCCATATATCTTAAATT 58.816 34.615 0.00 0.00 31.71 1.82
227 228 4.875578 ATATATTCTGCCCTGCATCCAT 57.124 40.909 0.00 0.00 38.13 3.41
232 233 4.103153 GCCCTATATATATTCTGCCCTGCA 59.897 45.833 0.00 0.00 36.92 4.41
238 239 4.503296 CCACCGGCCCTATATATATTCTGC 60.503 50.000 0.00 1.59 0.00 4.26
244 245 2.658285 CGTCCACCGGCCCTATATATA 58.342 52.381 0.00 0.00 0.00 0.86
267 268 1.538950 CCTACCTATAAGTCCGCGGAC 59.461 57.143 43.92 43.92 44.86 4.79
271 272 0.243095 CCGCCTACCTATAAGTCCGC 59.757 60.000 0.00 0.00 0.00 5.54
277 278 5.251764 GAGAGTGTATCCGCCTACCTATAA 58.748 45.833 0.00 0.00 0.00 0.98
283 284 1.984066 AGGAGAGTGTATCCGCCTAC 58.016 55.000 0.00 0.00 42.02 3.18
285 286 1.063567 AGAAGGAGAGTGTATCCGCCT 60.064 52.381 0.00 0.00 42.02 5.52
286 287 1.338655 GAGAAGGAGAGTGTATCCGCC 59.661 57.143 0.00 0.00 42.02 6.13
287 288 2.292292 GAGAGAAGGAGAGTGTATCCGC 59.708 54.545 0.00 0.00 42.02 5.54
299 333 2.093181 CGTGAGAGGAGAGAGAGAAGGA 60.093 54.545 0.00 0.00 0.00 3.36
303 337 3.516300 AGTTACGTGAGAGGAGAGAGAGA 59.484 47.826 0.00 0.00 0.00 3.10
403 441 4.882842 TCAACCTGTCATGCACTAGTAA 57.117 40.909 0.00 0.00 0.00 2.24
515 553 3.013188 ACATACCCACAGACTAACCCCTA 59.987 47.826 0.00 0.00 0.00 3.53
516 554 2.225805 ACATACCCACAGACTAACCCCT 60.226 50.000 0.00 0.00 0.00 4.79
517 555 2.093128 CACATACCCACAGACTAACCCC 60.093 54.545 0.00 0.00 0.00 4.95
518 556 2.679930 GCACATACCCACAGACTAACCC 60.680 54.545 0.00 0.00 0.00 4.11
519 557 2.629051 GCACATACCCACAGACTAACC 58.371 52.381 0.00 0.00 0.00 2.85
520 558 2.629051 GGCACATACCCACAGACTAAC 58.371 52.381 0.00 0.00 0.00 2.34
521 559 1.206132 CGGCACATACCCACAGACTAA 59.794 52.381 0.00 0.00 0.00 2.24
522 560 0.821517 CGGCACATACCCACAGACTA 59.178 55.000 0.00 0.00 0.00 2.59
523 561 1.596934 CGGCACATACCCACAGACT 59.403 57.895 0.00 0.00 0.00 3.24
524 562 2.106683 GCGGCACATACCCACAGAC 61.107 63.158 0.00 0.00 0.00 3.51
845 905 2.046023 TACGAGGAAGACGGGCGA 60.046 61.111 0.00 0.00 34.93 5.54
846 906 1.930908 AACTACGAGGAAGACGGGCG 61.931 60.000 0.00 0.00 34.93 6.13
847 907 0.179142 GAACTACGAGGAAGACGGGC 60.179 60.000 0.00 0.00 34.93 6.13
848 908 1.135460 GTGAACTACGAGGAAGACGGG 60.135 57.143 0.00 0.00 34.93 5.28
1143 1212 0.689623 AGAAGAGGAGGTTGCAGGTG 59.310 55.000 0.00 0.00 0.00 4.00
1158 1227 1.553690 TTTGCGAGGGAGGGGAGAAG 61.554 60.000 0.00 0.00 0.00 2.85
1166 1235 3.204827 CGGCCATTTGCGAGGGAG 61.205 66.667 2.24 0.00 42.61 4.30
1171 1240 4.713735 TGGAGCGGCCATTTGCGA 62.714 61.111 2.24 0.00 43.33 5.10
1248 1317 0.615544 CGGGGTGGTGGGAGTAGTAA 60.616 60.000 0.00 0.00 0.00 2.24
1502 1571 1.127567 TCCTGGTCCTGTTGGTCCTG 61.128 60.000 0.00 0.00 41.29 3.86
1503 1572 0.838122 CTCCTGGTCCTGTTGGTCCT 60.838 60.000 0.00 0.00 41.29 3.85
1504 1573 1.679898 CTCCTGGTCCTGTTGGTCC 59.320 63.158 0.00 0.00 41.13 4.46
1524 1593 2.837591 TGGTGCTGGTAGATTCTGCTTA 59.162 45.455 1.69 0.00 0.00 3.09
1809 1887 2.858476 TGCCTCCCTGGGAAGCAA 60.858 61.111 31.78 17.78 44.91 3.91
1990 2074 5.050499 GCAAGTTGAGATCATAGGTGAATCG 60.050 44.000 7.16 0.00 38.01 3.34
1998 2082 9.190858 GTACTATTGAGCAAGTTGAGATCATAG 57.809 37.037 7.16 11.73 0.00 2.23
2054 2156 2.681848 GCAGCACAAGATGACTAATGCT 59.318 45.455 0.00 0.00 43.54 3.79
2055 2157 2.421073 TGCAGCACAAGATGACTAATGC 59.579 45.455 0.00 0.00 37.37 3.56
2060 2162 5.242393 AGTTTATTTGCAGCACAAGATGACT 59.758 36.000 0.00 0.00 40.06 3.41
2061 2163 5.464168 AGTTTATTTGCAGCACAAGATGAC 58.536 37.500 0.00 0.00 40.06 3.06
2063 2165 7.543172 ACATTAGTTTATTTGCAGCACAAGATG 59.457 33.333 0.00 0.00 40.06 2.90
2070 2172 5.476599 AGTGGACATTAGTTTATTTGCAGCA 59.523 36.000 0.00 0.00 0.00 4.41
2071 2173 5.954335 AGTGGACATTAGTTTATTTGCAGC 58.046 37.500 0.00 0.00 0.00 5.25
2132 2234 6.530019 ACATATTCCAAATGAACCAGGAAC 57.470 37.500 0.00 0.00 42.42 3.62
2165 2272 8.179509 ACATTCAAACAGACTAGTACTAGTGT 57.820 34.615 34.67 28.98 45.63 3.55
2166 2273 9.477484 AAACATTCAAACAGACTAGTACTAGTG 57.523 33.333 34.67 24.39 45.63 2.74
2201 2314 9.686683 ATCAATACTGCTAACTAGGACAAAATT 57.313 29.630 0.00 0.00 0.00 1.82
2284 2397 5.379732 TTGTTTGGAACGAAATATGGGTC 57.620 39.130 0.00 0.00 0.00 4.46
2292 2405 5.463724 GTGGCATATTTTGTTTGGAACGAAA 59.536 36.000 8.26 8.26 45.91 3.46
2304 2417 3.848272 ACTGTTCCGTGGCATATTTTG 57.152 42.857 0.00 0.00 0.00 2.44
2305 2418 5.250200 TCTAACTGTTCCGTGGCATATTTT 58.750 37.500 0.00 0.00 0.00 1.82
2316 2431 5.878116 TGGGTGAATAAATCTAACTGTTCCG 59.122 40.000 0.00 0.00 0.00 4.30
2342 2457 6.144402 GGATGAAACAAACTAAGCATGTTGTG 59.856 38.462 0.00 0.00 37.36 3.33
2343 2458 6.215845 GGATGAAACAAACTAAGCATGTTGT 58.784 36.000 0.00 0.00 37.36 3.32
2344 2459 5.634859 GGGATGAAACAAACTAAGCATGTTG 59.365 40.000 0.00 0.00 37.36 3.33
2371 2486 4.784710 GCATTGCGCTCAGTCTTTAATCTC 60.785 45.833 9.73 0.00 37.77 2.75
2513 2629 2.426738 CACACACAAACCTTGGTCATGT 59.573 45.455 5.66 5.66 34.12 3.21
2683 2799 1.899814 CAAGGTGACTGGTGCCTACTA 59.100 52.381 0.00 0.00 42.68 1.82
2684 2800 0.687354 CAAGGTGACTGGTGCCTACT 59.313 55.000 0.00 0.00 42.68 2.57
2685 2801 0.396811 ACAAGGTGACTGGTGCCTAC 59.603 55.000 0.00 0.00 45.23 3.18
2687 2803 3.660724 ACAAGGTGACTGGTGCCT 58.339 55.556 0.00 0.00 45.23 4.75
2703 2819 3.657634 TCAGAATGTCAGCTGAAGTCAC 58.342 45.455 20.19 6.78 38.14 3.67
2773 2889 7.824779 ACTTTACCTAGATAAACTGCAAGAAGG 59.175 37.037 0.00 0.00 37.43 3.46
2798 2914 4.470462 CTGCAGCAAAGTATGAAGTCAAC 58.530 43.478 0.00 0.00 0.00 3.18
2940 3067 2.081462 GGGAAATTGGTGTTCGTCGAT 58.919 47.619 0.00 0.00 0.00 3.59
2975 3102 6.773976 TTAGTTTCCATGAACCAATCCATC 57.226 37.500 0.00 0.00 0.00 3.51
3022 3149 4.882671 AACTCAACACATCAGTTCACAC 57.117 40.909 0.00 0.00 0.00 3.82
3097 3224 1.967319 AGTGTGCAACGAATTCCTGT 58.033 45.000 0.00 0.00 42.39 4.00
3488 3616 9.719355 AACTTTGTGAAAATTCTTTTGGTTAGT 57.281 25.926 0.00 0.00 31.94 2.24
3637 3765 7.704271 AGGTTTAACAGTAAAAGCTTCTGTTC 58.296 34.615 26.42 16.57 45.36 3.18
3680 3808 7.392393 GCTAAAGTTGGTTACTAGATCCCAAAA 59.608 37.037 11.47 1.59 38.61 2.44
3697 3827 3.909430 TGTACTCCACGAGCTAAAGTTG 58.091 45.455 0.00 0.00 32.04 3.16
3733 3871 4.043059 AGAATGATCAGGGAAGGATGATGG 59.957 45.833 0.09 0.00 36.30 3.51
3734 3872 5.244189 AGAATGATCAGGGAAGGATGATG 57.756 43.478 0.09 0.00 36.30 3.07
3735 3873 5.926580 AAGAATGATCAGGGAAGGATGAT 57.073 39.130 0.09 0.00 38.84 2.45
3736 3874 5.443283 CAAAGAATGATCAGGGAAGGATGA 58.557 41.667 0.09 0.00 0.00 2.92
3822 3960 1.557832 TCCAAGGGGGTATTCAAGACG 59.442 52.381 0.00 0.00 38.11 4.18
3906 4044 4.576330 AGGAAACCAAGGTAGATTCCTG 57.424 45.455 18.42 0.00 46.10 3.86
4021 4161 2.414161 GGCTGTACAACAAAGATTCGGC 60.414 50.000 0.00 0.00 0.00 5.54
4023 4163 3.498397 AGTGGCTGTACAACAAAGATTCG 59.502 43.478 0.00 0.00 0.00 3.34
4033 4173 2.325484 TCTTCCTGAGTGGCTGTACAA 58.675 47.619 0.00 0.00 35.26 2.41
4034 4174 2.009681 TCTTCCTGAGTGGCTGTACA 57.990 50.000 0.00 0.00 35.26 2.90
4035 4175 2.933056 GCTTCTTCCTGAGTGGCTGTAC 60.933 54.545 0.00 0.00 35.26 2.90
4060 4200 2.466982 CGCTACGTCGTAGGCCTCA 61.467 63.158 28.67 0.00 36.71 3.86
4078 4218 2.750888 GCCACGGAACTTGATCGCC 61.751 63.158 0.00 0.00 0.00 5.54
4212 4352 3.127533 GCATGGGAGACACGTGGC 61.128 66.667 21.57 18.79 0.00 5.01
4220 4360 2.359850 GCCGTTGTGCATGGGAGA 60.360 61.111 0.00 0.00 31.00 3.71
4414 4557 4.819761 TCATGCGCCGCAGACTCC 62.820 66.667 19.64 0.00 43.65 3.85
4616 4759 0.036671 GAATTCGGTCCCCTCAACGT 60.037 55.000 0.00 0.00 0.00 3.99
4627 4770 1.490910 GAAGGGATGGAGGAATTCGGT 59.509 52.381 0.00 0.00 0.00 4.69
4646 4789 1.167851 GCAGCAAACACAGGCATAGA 58.832 50.000 0.00 0.00 0.00 1.98
4648 4791 0.251297 AGGCAGCAAACACAGGCATA 60.251 50.000 0.00 0.00 0.00 3.14
4685 4828 1.612676 AGATTTGAGCAGCTGCAACA 58.387 45.000 38.24 31.70 45.16 3.33
4687 4830 1.336517 GCAAGATTTGAGCAGCTGCAA 60.337 47.619 38.24 25.00 45.16 4.08
4691 4834 1.811359 GACAGCAAGATTTGAGCAGCT 59.189 47.619 0.00 0.00 0.00 4.24
4726 4869 5.163395 GCTACTAATCCAGCTCCAGTTTACT 60.163 44.000 0.00 0.00 34.86 2.24
4755 4898 5.933187 TTAAACTTAAGCGACATGAGCAA 57.067 34.783 17.25 5.87 37.01 3.91
4757 4900 6.188175 CAGATTAAACTTAAGCGACATGAGC 58.812 40.000 0.00 4.59 34.45 4.26
4758 4901 6.238211 CCCAGATTAAACTTAAGCGACATGAG 60.238 42.308 0.00 0.00 34.45 2.90
4759 4902 5.584649 CCCAGATTAAACTTAAGCGACATGA 59.415 40.000 0.00 0.00 34.45 3.07
4760 4903 5.584649 TCCCAGATTAAACTTAAGCGACATG 59.415 40.000 1.29 0.00 34.45 3.21
4761 4904 5.741011 TCCCAGATTAAACTTAAGCGACAT 58.259 37.500 1.29 0.00 34.45 3.06
4762 4905 5.155278 TCCCAGATTAAACTTAAGCGACA 57.845 39.130 1.29 0.00 34.45 4.35
4763 4906 5.064834 CCTTCCCAGATTAAACTTAAGCGAC 59.935 44.000 1.29 0.00 34.45 5.19
4766 4909 4.950475 AGCCTTCCCAGATTAAACTTAAGC 59.050 41.667 1.29 0.00 0.00 3.09
4767 4910 5.358160 CCAGCCTTCCCAGATTAAACTTAAG 59.642 44.000 0.00 0.00 0.00 1.85
4768 4911 5.222254 ACCAGCCTTCCCAGATTAAACTTAA 60.222 40.000 0.00 0.00 0.00 1.85
4770 4913 3.076032 ACCAGCCTTCCCAGATTAAACTT 59.924 43.478 0.00 0.00 0.00 2.66
4771 4914 2.649816 ACCAGCCTTCCCAGATTAAACT 59.350 45.455 0.00 0.00 0.00 2.66
4772 4915 3.087370 ACCAGCCTTCCCAGATTAAAC 57.913 47.619 0.00 0.00 0.00 2.01
4778 4921 2.291540 CCAATTAACCAGCCTTCCCAGA 60.292 50.000 0.00 0.00 0.00 3.86
4812 4960 2.163010 CACTACCACTACCACTACACCG 59.837 54.545 0.00 0.00 0.00 4.94
4850 4998 2.359214 CGGTGAGCTAGAGACTAATGCA 59.641 50.000 0.00 0.00 0.00 3.96
4918 5067 2.961062 GCCTCCTTCCATGCATTGTTAT 59.039 45.455 0.00 0.00 0.00 1.89
4974 5182 2.629617 TGAAGACACATCAGCTCAGTCA 59.370 45.455 0.00 0.00 0.00 3.41
5030 5245 5.701224 TGTGAATCTGGAATAAATACCCCC 58.299 41.667 0.00 0.00 0.00 5.40
5032 5247 6.601332 TCCTGTGAATCTGGAATAAATACCC 58.399 40.000 0.00 0.00 40.40 3.69
5080 5295 1.632965 AACCTCCCCCTTGTATCGCC 61.633 60.000 0.00 0.00 0.00 5.54
5085 5300 0.497301 TACCCAACCTCCCCCTTGTA 59.503 55.000 0.00 0.00 0.00 2.41
5113 7043 2.856628 CGTAGCGGGGATAGCTGCA 61.857 63.158 1.02 0.00 45.52 4.41
5162 7094 8.971321 GTAAAAATGTTGTGAACTAGTCGTAGA 58.029 33.333 0.00 0.00 0.00 2.59
5163 7095 8.757789 TGTAAAAATGTTGTGAACTAGTCGTAG 58.242 33.333 0.00 0.00 0.00 3.51
5165 7097 7.254658 CCTGTAAAAATGTTGTGAACTAGTCGT 60.255 37.037 0.00 0.00 0.00 4.34
5166 7098 7.042321 TCCTGTAAAAATGTTGTGAACTAGTCG 60.042 37.037 0.00 0.00 0.00 4.18
5167 7099 8.149973 TCCTGTAAAAATGTTGTGAACTAGTC 57.850 34.615 0.00 0.00 0.00 2.59
5168 7100 7.773690 ACTCCTGTAAAAATGTTGTGAACTAGT 59.226 33.333 0.00 0.00 0.00 2.57
5169 7101 8.070171 CACTCCTGTAAAAATGTTGTGAACTAG 58.930 37.037 0.00 0.00 0.00 2.57
5170 7102 7.012894 CCACTCCTGTAAAAATGTTGTGAACTA 59.987 37.037 0.00 0.00 0.00 2.24
5171 7103 6.183360 CCACTCCTGTAAAAATGTTGTGAACT 60.183 38.462 0.00 0.00 0.00 3.01
5244 7196 3.997021 CACTACTTGACCTGCTAACAAGG 59.003 47.826 0.00 2.74 43.28 3.61
5276 7228 6.645415 CGACCCCACTGATTATTAGATTACAC 59.355 42.308 0.00 0.00 0.00 2.90
5363 7315 0.387929 AAAGGACGTGAGACAAGCGA 59.612 50.000 0.00 0.00 0.00 4.93
5420 7372 6.710744 GGGGAATGTTTATGATACTCATCGTT 59.289 38.462 0.00 0.00 38.26 3.85
5421 7373 6.043243 AGGGGAATGTTTATGATACTCATCGT 59.957 38.462 0.00 0.00 38.26 3.73
5639 7602 3.799963 GGGTCAAAACACGAAATTTGTCC 59.200 43.478 0.00 14.17 41.19 4.02
5640 7603 4.678622 AGGGTCAAAACACGAAATTTGTC 58.321 39.130 0.00 0.00 37.68 3.18
5641 7604 4.729227 AGGGTCAAAACACGAAATTTGT 57.271 36.364 0.00 0.00 37.68 2.83
5642 7605 6.312672 AGAAAAGGGTCAAAACACGAAATTTG 59.687 34.615 0.00 0.00 37.77 2.32
5643 7606 6.403049 AGAAAAGGGTCAAAACACGAAATTT 58.597 32.000 0.00 0.00 32.44 1.82
5644 7607 5.972935 AGAAAAGGGTCAAAACACGAAATT 58.027 33.333 0.00 0.00 32.44 1.82
5645 7608 5.126384 TGAGAAAAGGGTCAAAACACGAAAT 59.874 36.000 0.00 0.00 32.44 2.17
5646 7609 4.459685 TGAGAAAAGGGTCAAAACACGAAA 59.540 37.500 0.00 0.00 32.44 3.46
5647 7610 4.011023 TGAGAAAAGGGTCAAAACACGAA 58.989 39.130 0.00 0.00 32.44 3.85
5648 7611 3.611970 TGAGAAAAGGGTCAAAACACGA 58.388 40.909 0.00 0.00 32.44 4.35
5649 7612 4.364415 TTGAGAAAAGGGTCAAAACACG 57.636 40.909 0.00 0.00 32.44 4.49
5650 7613 6.573434 AGATTTGAGAAAAGGGTCAAAACAC 58.427 36.000 1.92 0.00 43.88 3.32
5651 7614 6.790232 AGATTTGAGAAAAGGGTCAAAACA 57.210 33.333 1.92 0.00 43.88 2.83
5652 7615 9.411801 GAATAGATTTGAGAAAAGGGTCAAAAC 57.588 33.333 1.92 0.18 43.88 2.43
5653 7616 8.296713 CGAATAGATTTGAGAAAAGGGTCAAAA 58.703 33.333 1.92 0.00 43.88 2.44
5654 7617 7.663905 TCGAATAGATTTGAGAAAAGGGTCAAA 59.336 33.333 0.34 0.34 44.57 2.69
5655 7618 7.165485 TCGAATAGATTTGAGAAAAGGGTCAA 58.835 34.615 0.00 0.00 0.00 3.18
5656 7619 6.707290 TCGAATAGATTTGAGAAAAGGGTCA 58.293 36.000 0.00 0.00 0.00 4.02
5657 7620 7.240414 CTCGAATAGATTTGAGAAAAGGGTC 57.760 40.000 12.48 0.00 46.59 4.46


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

AutoCloner maintained by Alex Coulton.