Multiple sequence alignment - TraesCS2D01G254400

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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 TraesCS2D01G254400 chr2D 100.000 3837 0 0 1 3837 306534039 306530203 0.000000e+00 7086.0
1 TraesCS2D01G254400 chr2D 85.057 174 19 5 811 978 537188020 537188192 1.830000e-38 171.0
2 TraesCS2D01G254400 chr2D 83.799 179 25 2 804 978 110401898 110402076 2.370000e-37 167.0
3 TraesCS2D01G254400 chr2A 95.754 2779 76 15 977 3737 386297224 386294470 0.000000e+00 4440.0
4 TraesCS2D01G254400 chr2A 83.654 624 62 25 1 620 386298459 386297872 5.600000e-153 551.0
5 TraesCS2D01G254400 chr2B 95.488 2017 64 14 977 2985 374803304 374801307 0.000000e+00 3195.0
6 TraesCS2D01G254400 chr2B 96.005 826 21 7 2923 3737 374801226 374800402 0.000000e+00 1332.0
7 TraesCS2D01G254400 chr2B 91.748 206 15 2 1 204 374805011 374804806 6.270000e-73 285.0
8 TraesCS2D01G254400 chr2B 93.651 63 3 1 2923 2985 374801297 374801236 4.080000e-15 93.5
9 TraesCS2D01G254400 chr2B 81.522 92 17 0 211 302 727730717 727730808 4.110000e-10 76.8
10 TraesCS2D01G254400 chr3A 86.705 173 21 2 806 977 47845615 47845786 1.410000e-44 191.0
11 TraesCS2D01G254400 chr3A 86.364 66 7 2 3605 3670 335471216 335471153 1.910000e-08 71.3
12 TraesCS2D01G254400 chr3A 84.722 72 10 1 3619 3690 468533875 468533805 1.910000e-08 71.3
13 TraesCS2D01G254400 chr6B 86.905 168 20 2 813 978 610828023 610827856 1.820000e-43 187.0
14 TraesCS2D01G254400 chrUn 86.207 174 19 5 804 974 97103530 97103701 2.350000e-42 183.0
15 TraesCS2D01G254400 chr5D 85.795 176 22 2 804 977 544719106 544718932 2.350000e-42 183.0
16 TraesCS2D01G254400 chr5D 99.000 100 0 1 3735 3833 443898318 443898219 1.100000e-40 178.0
17 TraesCS2D01G254400 chr5D 96.040 101 4 0 3733 3833 551088630 551088730 8.530000e-37 165.0
18 TraesCS2D01G254400 chr5D 84.146 82 12 1 3605 3686 267617436 267617516 1.140000e-10 78.7
19 TraesCS2D01G254400 chr7A 85.632 174 19 4 804 977 576119950 576120117 1.100000e-40 178.0
20 TraesCS2D01G254400 chr7A 82.222 90 16 0 211 300 458979843 458979932 1.140000e-10 78.7
21 TraesCS2D01G254400 chr6A 97.143 105 3 0 3729 3833 249162344 249162448 1.100000e-40 178.0
22 TraesCS2D01G254400 chr3D 98.990 99 1 0 3735 3833 615080013 615079915 1.100000e-40 178.0
23 TraesCS2D01G254400 chr3D 83.957 187 18 7 804 978 433426756 433426570 6.590000e-38 169.0
24 TraesCS2D01G254400 chr3D 93.269 104 6 1 3730 3833 22917750 22917852 6.640000e-33 152.0
25 TraesCS2D01G254400 chr3D 86.364 66 7 2 3605 3670 254109869 254109932 1.910000e-08 71.3
26 TraesCS2D01G254400 chr7D 98.000 100 1 1 3735 3833 75800853 75800754 5.100000e-39 172.0
27 TraesCS2D01G254400 chr3B 83.978 181 23 3 804 978 638359827 638360007 6.590000e-38 169.0
28 TraesCS2D01G254400 chr6D 95.238 105 5 0 3729 3833 185191910 185192014 2.370000e-37 167.0
29 TraesCS2D01G254400 chr4B 91.071 112 6 4 3724 3833 207094054 207093945 8.590000e-32 148.0
30 TraesCS2D01G254400 chr1D 90.909 110 9 1 3728 3836 314506385 314506276 3.090000e-31 147.0
31 TraesCS2D01G254400 chr1A 74.830 147 34 2 211 355 12258100 12257955 3.200000e-06 63.9
32 TraesCS2D01G254400 chr7B 100.000 33 0 0 2088 2120 714534007 714533975 1.150000e-05 62.1


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 TraesCS2D01G254400 chr2D 306530203 306534039 3836 True 7086.000 7086 100.000 1 3837 1 chr2D.!!$R1 3836
1 TraesCS2D01G254400 chr2A 386294470 386298459 3989 True 2495.500 4440 89.704 1 3737 2 chr2A.!!$R1 3736
2 TraesCS2D01G254400 chr2B 374800402 374805011 4609 True 1226.375 3195 94.223 1 3737 4 chr2B.!!$R1 3736

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
427 434 0.333312 AGACCACCACCTCTCTCGAT 59.667 55.000 0.0 0.0 0.0 3.59 F
1120 2633 0.034059 CACTCCACACTCCACACCTC 59.966 60.000 0.0 0.0 0.0 3.85 F
1321 2837 1.135141 TGTGCTTGTTGTTCCTTGTGC 60.135 47.619 0.0 0.0 0.0 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2314 3837 0.385390 GAACCCAAGCCAACACTGTG 59.615 55.000 6.19 6.19 0.00 3.66 R
2319 3843 1.144708 TGATCTGAACCCAAGCCAACA 59.855 47.619 0.00 0.00 0.00 3.33 R
3084 4774 1.667724 CTAAGTGCATGCGCTTAAGCT 59.332 47.619 38.76 25.18 44.92 3.74 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
45 46 5.362263 ACAATACGTGAAAGTACACTTGGT 58.638 37.500 0.00 0.00 38.47 3.67
48 49 8.306038 ACAATACGTGAAAGTACACTTGGTATA 58.694 33.333 0.00 0.00 38.47 1.47
185 188 4.141711 CCCTCCATCGAGACAGGAAAAATA 60.142 45.833 7.70 0.00 38.52 1.40
195 198 9.893634 TCGAGACAGGAAAAATATTACCAAATA 57.106 29.630 8.33 0.00 32.20 1.40
225 228 5.978814 AGATGTCCGCCTTATTATGGTATC 58.021 41.667 0.00 0.00 0.00 2.24
228 231 7.565398 AGATGTCCGCCTTATTATGGTATCTAT 59.435 37.037 0.00 0.00 30.51 1.98
259 262 9.927668 ATGTAGAAATGATGTTGTTTTTAAGGG 57.072 29.630 0.00 0.00 0.00 3.95
261 264 6.825610 AGAAATGATGTTGTTTTTAAGGGCA 58.174 32.000 0.00 0.00 0.00 5.36
265 268 6.917217 TGATGTTGTTTTTAAGGGCAAAAG 57.083 33.333 0.00 0.00 0.00 2.27
279 282 5.995446 AGGGCAAAAGTTAATCTCCTCTAG 58.005 41.667 0.00 0.00 0.00 2.43
281 284 6.052360 GGGCAAAAGTTAATCTCCTCTAGAG 58.948 44.000 13.18 13.18 44.75 2.43
321 324 5.874810 ACGTATTGTCTTTGCATGTGTCTAT 59.125 36.000 0.00 0.00 0.00 1.98
364 368 1.515081 CGATGTTTAACACGGGTGGT 58.485 50.000 0.00 0.00 34.19 4.16
378 385 1.836166 GGGTGGTTAGAGAGGTTACCC 59.164 57.143 0.00 0.00 39.45 3.69
386 393 2.915869 AGAGAGGTTACCCAACATGGA 58.084 47.619 0.00 0.00 40.96 3.41
392 399 2.073816 GTTACCCAACATGGACGACAG 58.926 52.381 0.00 0.00 40.96 3.51
399 406 4.750098 CCCAACATGGACGACAGTATAATC 59.250 45.833 0.00 0.00 40.96 1.75
406 413 7.885922 ACATGGACGACAGTATAATCTCTAGAT 59.114 37.037 0.00 0.00 36.07 1.98
413 420 7.604545 CGACAGTATAATCTCTAGATCAGACCA 59.395 40.741 0.00 0.00 32.75 4.02
414 421 8.630054 ACAGTATAATCTCTAGATCAGACCAC 57.370 38.462 0.00 0.00 32.75 4.16
415 422 7.668052 ACAGTATAATCTCTAGATCAGACCACC 59.332 40.741 0.00 0.00 32.75 4.61
416 423 7.667635 CAGTATAATCTCTAGATCAGACCACCA 59.332 40.741 0.00 0.00 32.75 4.17
417 424 6.909550 ATAATCTCTAGATCAGACCACCAC 57.090 41.667 0.00 0.00 32.75 4.16
419 426 2.583101 TCTCTAGATCAGACCACCACCT 59.417 50.000 0.00 0.00 0.00 4.00
420 427 2.955660 CTCTAGATCAGACCACCACCTC 59.044 54.545 0.00 0.00 0.00 3.85
421 428 2.583101 TCTAGATCAGACCACCACCTCT 59.417 50.000 0.00 0.00 0.00 3.69
423 430 1.360852 AGATCAGACCACCACCTCTCT 59.639 52.381 0.00 0.00 0.00 3.10
424 431 1.754226 GATCAGACCACCACCTCTCTC 59.246 57.143 0.00 0.00 0.00 3.20
425 432 0.609406 TCAGACCACCACCTCTCTCG 60.609 60.000 0.00 0.00 0.00 4.04
427 434 0.333312 AGACCACCACCTCTCTCGAT 59.667 55.000 0.00 0.00 0.00 3.59
435 442 5.007034 CACCACCTCTCTCGATATAGACAT 58.993 45.833 0.00 0.00 0.00 3.06
439 446 7.180587 ACCACCTCTCTCGATATAGACATAGTA 59.819 40.741 0.00 0.00 0.00 1.82
442 449 8.983789 ACCTCTCTCGATATAGACATAGTATCA 58.016 37.037 0.00 0.00 0.00 2.15
514 1544 3.438781 TGTCGGATAGTTCATGTTTTGGC 59.561 43.478 0.00 0.00 0.00 4.52
570 1600 2.429250 TGTCCATCGTGATTGTATCCGT 59.571 45.455 0.00 0.00 0.00 4.69
572 1602 3.869246 GTCCATCGTGATTGTATCCGTTT 59.131 43.478 0.00 0.00 0.00 3.60
587 1622 9.944663 TTGTATCCGTTTGATGCTATATTTTTC 57.055 29.630 0.00 0.00 37.04 2.29
651 2143 2.807967 CACATACTGCCATGGAATACCG 59.192 50.000 18.40 1.13 39.42 4.02
663 2155 2.288579 TGGAATACCGCGCGAGATAATT 60.289 45.455 34.63 21.03 39.42 1.40
688 2180 1.223417 CGTTTTCGCCGGTGGTTACT 61.223 55.000 16.49 0.00 36.22 2.24
802 2314 2.434185 TGCCGCGGATTCACAGTC 60.434 61.111 33.48 8.18 0.00 3.51
803 2315 3.554692 GCCGCGGATTCACAGTCG 61.555 66.667 33.48 0.00 0.00 4.18
804 2316 2.885644 CCGCGGATTCACAGTCGG 60.886 66.667 24.07 0.00 0.00 4.79
805 2317 2.885644 CGCGGATTCACAGTCGGG 60.886 66.667 0.00 0.00 0.00 5.14
806 2318 2.264794 GCGGATTCACAGTCGGGT 59.735 61.111 0.00 0.00 0.00 5.28
807 2319 1.810030 GCGGATTCACAGTCGGGTC 60.810 63.158 0.00 0.00 0.00 4.46
808 2320 1.890894 CGGATTCACAGTCGGGTCT 59.109 57.895 0.00 0.00 0.00 3.85
809 2321 1.100510 CGGATTCACAGTCGGGTCTA 58.899 55.000 0.00 0.00 0.00 2.59
810 2322 1.681793 CGGATTCACAGTCGGGTCTAT 59.318 52.381 0.00 0.00 0.00 1.98
811 2323 2.100916 CGGATTCACAGTCGGGTCTATT 59.899 50.000 0.00 0.00 0.00 1.73
812 2324 3.430374 CGGATTCACAGTCGGGTCTATTT 60.430 47.826 0.00 0.00 0.00 1.40
813 2325 4.202080 CGGATTCACAGTCGGGTCTATTTA 60.202 45.833 0.00 0.00 0.00 1.40
814 2326 5.290386 GGATTCACAGTCGGGTCTATTTAG 58.710 45.833 0.00 0.00 0.00 1.85
815 2327 4.730949 TTCACAGTCGGGTCTATTTAGG 57.269 45.455 0.00 0.00 0.00 2.69
816 2328 3.972133 TCACAGTCGGGTCTATTTAGGA 58.028 45.455 0.00 0.00 0.00 2.94
817 2329 3.698040 TCACAGTCGGGTCTATTTAGGAC 59.302 47.826 0.00 0.00 0.00 3.85
818 2330 3.446161 CACAGTCGGGTCTATTTAGGACA 59.554 47.826 0.00 0.00 35.61 4.02
819 2331 3.446516 ACAGTCGGGTCTATTTAGGACAC 59.553 47.826 0.00 0.00 35.61 3.67
820 2332 3.446161 CAGTCGGGTCTATTTAGGACACA 59.554 47.826 0.00 0.00 36.98 3.72
821 2333 4.099573 CAGTCGGGTCTATTTAGGACACAT 59.900 45.833 0.00 0.00 36.98 3.21
822 2334 4.341520 AGTCGGGTCTATTTAGGACACATC 59.658 45.833 0.00 0.00 36.98 3.06
823 2335 4.341520 GTCGGGTCTATTTAGGACACATCT 59.658 45.833 0.00 0.00 36.98 2.90
824 2336 5.533903 GTCGGGTCTATTTAGGACACATCTA 59.466 44.000 0.00 0.00 36.98 1.98
825 2337 5.768662 TCGGGTCTATTTAGGACACATCTAG 59.231 44.000 0.00 0.00 36.98 2.43
826 2338 5.768662 CGGGTCTATTTAGGACACATCTAGA 59.231 44.000 0.00 0.00 36.98 2.43
827 2339 6.434652 CGGGTCTATTTAGGACACATCTAGAT 59.565 42.308 0.00 0.00 36.98 1.98
828 2340 7.575909 CGGGTCTATTTAGGACACATCTAGATG 60.576 44.444 27.63 27.63 44.15 2.90
867 2379 5.350504 CATCTAAACTGATGTCCACTCCT 57.649 43.478 0.00 0.00 39.05 3.69
868 2380 5.738909 CATCTAAACTGATGTCCACTCCTT 58.261 41.667 0.00 0.00 39.05 3.36
869 2381 5.407407 TCTAAACTGATGTCCACTCCTTC 57.593 43.478 0.00 0.00 0.00 3.46
870 2382 5.087323 TCTAAACTGATGTCCACTCCTTCT 58.913 41.667 0.00 0.00 0.00 2.85
871 2383 3.692257 AACTGATGTCCACTCCTTCTG 57.308 47.619 0.00 0.00 0.00 3.02
872 2384 2.614259 ACTGATGTCCACTCCTTCTGT 58.386 47.619 0.00 0.00 0.00 3.41
873 2385 2.301296 ACTGATGTCCACTCCTTCTGTG 59.699 50.000 0.00 0.00 35.39 3.66
884 2396 5.799213 CACTCCTTCTGTGGTCTATTTTCT 58.201 41.667 0.00 0.00 0.00 2.52
885 2397 6.234177 CACTCCTTCTGTGGTCTATTTTCTT 58.766 40.000 0.00 0.00 0.00 2.52
886 2398 7.386851 CACTCCTTCTGTGGTCTATTTTCTTA 58.613 38.462 0.00 0.00 0.00 2.10
887 2399 8.043710 CACTCCTTCTGTGGTCTATTTTCTTAT 58.956 37.037 0.00 0.00 0.00 1.73
888 2400 8.606830 ACTCCTTCTGTGGTCTATTTTCTTATT 58.393 33.333 0.00 0.00 0.00 1.40
889 2401 9.103861 CTCCTTCTGTGGTCTATTTTCTTATTC 57.896 37.037 0.00 0.00 0.00 1.75
890 2402 8.826765 TCCTTCTGTGGTCTATTTTCTTATTCT 58.173 33.333 0.00 0.00 0.00 2.40
938 2450 6.854496 ATTTGTAAAAGCTTAGACGTGACA 57.146 33.333 0.00 0.00 0.00 3.58
939 2451 6.854496 TTTGTAAAAGCTTAGACGTGACAT 57.146 33.333 0.00 0.00 0.00 3.06
940 2452 6.854496 TTGTAAAAGCTTAGACGTGACATT 57.146 33.333 0.00 0.00 0.00 2.71
941 2453 6.854496 TGTAAAAGCTTAGACGTGACATTT 57.146 33.333 0.00 0.00 0.00 2.32
942 2454 7.254227 TGTAAAAGCTTAGACGTGACATTTT 57.746 32.000 0.00 0.00 0.00 1.82
943 2455 7.699566 TGTAAAAGCTTAGACGTGACATTTTT 58.300 30.769 0.00 0.00 0.00 1.94
944 2456 8.828644 TGTAAAAGCTTAGACGTGACATTTTTA 58.171 29.630 0.00 0.00 0.00 1.52
945 2457 9.654417 GTAAAAGCTTAGACGTGACATTTTTAA 57.346 29.630 0.00 0.00 0.00 1.52
947 2459 9.575783 AAAAGCTTAGACGTGACATTTTTAAAA 57.424 25.926 0.00 0.00 0.00 1.52
948 2460 9.575783 AAAGCTTAGACGTGACATTTTTAAAAA 57.424 25.926 15.38 15.38 0.00 1.94
981 2493 9.394767 AGATATGCATTATACAAACTGTTCACA 57.605 29.630 3.54 0.00 0.00 3.58
991 2503 2.203139 TGTTCACAGCCACACGGG 60.203 61.111 0.00 0.00 40.85 5.28
1110 2623 0.037232 GACTAGCCCACACTCCACAC 60.037 60.000 0.00 0.00 0.00 3.82
1111 2624 0.471971 ACTAGCCCACACTCCACACT 60.472 55.000 0.00 0.00 0.00 3.55
1112 2625 0.247736 CTAGCCCACACTCCACACTC 59.752 60.000 0.00 0.00 0.00 3.51
1113 2626 1.192146 TAGCCCACACTCCACACTCC 61.192 60.000 0.00 0.00 0.00 3.85
1114 2627 2.818169 GCCCACACTCCACACTCCA 61.818 63.158 0.00 0.00 0.00 3.86
1115 2628 1.071471 CCCACACTCCACACTCCAC 59.929 63.158 0.00 0.00 0.00 4.02
1116 2629 1.695114 CCCACACTCCACACTCCACA 61.695 60.000 0.00 0.00 0.00 4.17
1117 2630 0.532862 CCACACTCCACACTCCACAC 60.533 60.000 0.00 0.00 0.00 3.82
1118 2631 0.532862 CACACTCCACACTCCACACC 60.533 60.000 0.00 0.00 0.00 4.16
1119 2632 0.691078 ACACTCCACACTCCACACCT 60.691 55.000 0.00 0.00 0.00 4.00
1120 2633 0.034059 CACTCCACACTCCACACCTC 59.966 60.000 0.00 0.00 0.00 3.85
1130 2643 1.552792 CTCCACACCTCCTTCTCCTTC 59.447 57.143 0.00 0.00 0.00 3.46
1142 2655 3.195396 CCTTCTCCTTCTCTCCAGAACAG 59.805 52.174 0.00 0.00 34.71 3.16
1321 2837 1.135141 TGTGCTTGTTGTTCCTTGTGC 60.135 47.619 0.00 0.00 0.00 4.57
1718 3237 2.288025 GGGACGAACTGGGTAGCCA 61.288 63.158 14.12 14.12 0.00 4.75
1751 3270 3.847184 CTCTTCCTTTTCCCCTCTACCTT 59.153 47.826 0.00 0.00 0.00 3.50
1759 3278 2.202756 CCTCTACCTTGTCGGCGC 60.203 66.667 0.00 0.00 35.61 6.53
1785 3304 2.614057 GGCGACATTGCTAAGCACTTAT 59.386 45.455 0.00 0.00 38.71 1.73
1881 3404 3.195698 GCCGTCAATGAGACCCGC 61.196 66.667 0.00 0.00 44.66 6.13
2012 3535 5.407407 ACCAGTCTCGTGATATTTCTGTT 57.593 39.130 0.00 0.00 0.00 3.16
2125 3648 6.954944 TGCATTAGTACTTGTGTTCTTGAAC 58.045 36.000 0.00 6.56 0.00 3.18
2139 3662 6.195798 GTGTTCTTGAACCATTGTTACGTTTC 59.804 38.462 10.51 0.00 33.97 2.78
2260 3783 5.646467 CTGCAAGTTCAGGTTCAAAATTG 57.354 39.130 0.00 0.00 34.52 2.32
2285 3808 8.522830 TGAAAATCACACCCTGAATTTCTAATC 58.477 33.333 10.63 0.00 44.40 1.75
2307 3830 2.766263 TCTCCTCAATCAAGCACGGTAT 59.234 45.455 0.00 0.00 0.00 2.73
2314 3837 2.273370 TCAAGCACGGTATTCGACTC 57.727 50.000 0.00 0.00 42.43 3.36
2319 3843 1.402456 GCACGGTATTCGACTCACAGT 60.402 52.381 0.00 0.00 42.43 3.55
2544 4068 1.972872 ATCGATTCCCTCAATGTGGC 58.027 50.000 0.00 0.00 0.00 5.01
2545 4069 0.617935 TCGATTCCCTCAATGTGGCA 59.382 50.000 0.00 0.00 0.00 4.92
2546 4070 1.004161 TCGATTCCCTCAATGTGGCAA 59.996 47.619 0.00 0.00 0.00 4.52
2547 4071 1.818060 CGATTCCCTCAATGTGGCAAA 59.182 47.619 0.00 0.00 0.00 3.68
2548 4072 2.415893 CGATTCCCTCAATGTGGCAAAC 60.416 50.000 0.00 0.00 0.00 2.93
2549 4073 1.337118 TTCCCTCAATGTGGCAAACC 58.663 50.000 0.00 0.00 0.00 3.27
2550 4074 0.187117 TCCCTCAATGTGGCAAACCA 59.813 50.000 0.00 0.00 46.51 3.67
2644 4180 4.389077 GCATCTCAGGTTAGTACAACACAC 59.611 45.833 0.00 0.00 0.00 3.82
3777 5468 7.069852 CATCTAGATGTGCCATAAGTATTGC 57.930 40.000 22.42 0.00 34.23 3.56
3778 5469 6.173427 TCTAGATGTGCCATAAGTATTGCA 57.827 37.500 0.00 0.00 32.69 4.08
3786 5477 6.866010 TGCCATAAGTATTGCACATCTAAG 57.134 37.500 0.00 0.00 30.49 2.18
3787 5478 6.356556 TGCCATAAGTATTGCACATCTAAGT 58.643 36.000 0.00 0.00 30.49 2.24
3788 5479 6.483307 TGCCATAAGTATTGCACATCTAAGTC 59.517 38.462 0.00 0.00 30.49 3.01
3789 5480 6.073003 GCCATAAGTATTGCACATCTAAGTCC 60.073 42.308 0.00 0.00 0.00 3.85
3790 5481 7.220030 CCATAAGTATTGCACATCTAAGTCCT 58.780 38.462 0.00 0.00 0.00 3.85
3791 5482 7.172190 CCATAAGTATTGCACATCTAAGTCCTG 59.828 40.741 0.00 0.00 0.00 3.86
3792 5483 5.683876 AGTATTGCACATCTAAGTCCTGT 57.316 39.130 0.00 0.00 0.00 4.00
3793 5484 6.791867 AGTATTGCACATCTAAGTCCTGTA 57.208 37.500 0.00 0.00 0.00 2.74
3794 5485 7.366847 AGTATTGCACATCTAAGTCCTGTAT 57.633 36.000 0.00 0.00 0.00 2.29
3795 5486 7.437748 AGTATTGCACATCTAAGTCCTGTATC 58.562 38.462 0.00 0.00 0.00 2.24
3796 5487 5.675684 TTGCACATCTAAGTCCTGTATCA 57.324 39.130 0.00 0.00 0.00 2.15
3797 5488 5.876651 TGCACATCTAAGTCCTGTATCAT 57.123 39.130 0.00 0.00 0.00 2.45
3798 5489 6.239217 TGCACATCTAAGTCCTGTATCATT 57.761 37.500 0.00 0.00 0.00 2.57
3799 5490 6.051074 TGCACATCTAAGTCCTGTATCATTG 58.949 40.000 0.00 0.00 0.00 2.82
3800 5491 6.127083 TGCACATCTAAGTCCTGTATCATTGA 60.127 38.462 0.00 0.00 0.00 2.57
3801 5492 6.933521 GCACATCTAAGTCCTGTATCATTGAT 59.066 38.462 4.28 4.28 0.00 2.57
3802 5493 7.117523 GCACATCTAAGTCCTGTATCATTGATC 59.882 40.741 1.55 0.00 0.00 2.92
3803 5494 8.366401 CACATCTAAGTCCTGTATCATTGATCT 58.634 37.037 1.55 0.00 0.00 2.75
3804 5495 8.932610 ACATCTAAGTCCTGTATCATTGATCTT 58.067 33.333 1.55 2.28 0.00 2.40
3807 5498 9.421399 TCTAAGTCCTGTATCATTGATCTTACA 57.579 33.333 1.55 1.71 0.00 2.41
3808 5499 9.469807 CTAAGTCCTGTATCATTGATCTTACAC 57.530 37.037 1.55 0.00 0.00 2.90
3809 5500 6.507900 AGTCCTGTATCATTGATCTTACACG 58.492 40.000 1.55 0.00 0.00 4.49
3810 5501 6.321435 AGTCCTGTATCATTGATCTTACACGA 59.679 38.462 1.55 0.00 0.00 4.35
3811 5502 6.978659 GTCCTGTATCATTGATCTTACACGAA 59.021 38.462 1.55 0.00 0.00 3.85
3812 5503 7.168302 GTCCTGTATCATTGATCTTACACGAAG 59.832 40.741 1.55 0.00 36.38 3.79
3829 5520 4.939509 CGAAGATTCGTGTGGGTATTTT 57.060 40.909 6.81 0.00 45.09 1.82
3830 5521 4.893795 CGAAGATTCGTGTGGGTATTTTC 58.106 43.478 6.81 0.00 45.09 2.29
3831 5522 4.630069 CGAAGATTCGTGTGGGTATTTTCT 59.370 41.667 6.81 0.00 45.09 2.52
3832 5523 5.121768 CGAAGATTCGTGTGGGTATTTTCTT 59.878 40.000 6.81 0.00 45.09 2.52
3833 5524 6.311935 CGAAGATTCGTGTGGGTATTTTCTTA 59.688 38.462 6.81 0.00 45.09 2.10
3834 5525 6.980051 AGATTCGTGTGGGTATTTTCTTAC 57.020 37.500 0.00 0.00 0.00 2.34
3835 5526 6.708285 AGATTCGTGTGGGTATTTTCTTACT 58.292 36.000 0.00 0.00 0.00 2.24
3836 5527 7.844009 AGATTCGTGTGGGTATTTTCTTACTA 58.156 34.615 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 8.133024 TCCATTGTTGATAGCCTTTAACAAAT 57.867 30.769 9.60 0.00 43.59 2.32
185 188 7.387948 GCGGACATCTTACATCTATTTGGTAAT 59.612 37.037 0.00 0.00 0.00 1.89
195 198 5.552870 AATAAGGCGGACATCTTACATCT 57.447 39.130 0.00 0.00 0.00 2.90
204 207 7.344612 TCATAGATACCATAATAAGGCGGACAT 59.655 37.037 0.00 0.00 0.00 3.06
205 208 6.666113 TCATAGATACCATAATAAGGCGGACA 59.334 38.462 0.00 0.00 0.00 4.02
209 212 9.684448 CATAGTCATAGATACCATAATAAGGCG 57.316 37.037 0.00 0.00 0.00 5.52
246 249 9.104965 AGATTAACTTTTGCCCTTAAAAACAAC 57.895 29.630 0.00 0.00 0.00 3.32
288 291 4.266502 GCAAAGACAATACGTGCAACAAAA 59.733 37.500 0.00 0.00 35.74 2.44
296 299 4.083855 AGACACATGCAAAGACAATACGTG 60.084 41.667 0.00 0.00 0.00 4.49
321 324 4.350368 TGATACTCAGTTTGGTGAAGCA 57.650 40.909 0.00 0.00 0.00 3.91
325 328 3.322541 TCGGTTGATACTCAGTTTGGTGA 59.677 43.478 0.00 0.00 0.00 4.02
352 355 2.173519 CCTCTCTAACCACCCGTGTTA 58.826 52.381 0.00 0.00 0.00 2.41
378 385 6.507900 AGAGATTATACTGTCGTCCATGTTG 58.492 40.000 0.00 0.00 0.00 3.33
386 393 7.604927 GGTCTGATCTAGAGATTATACTGTCGT 59.395 40.741 0.00 0.00 35.70 4.34
392 399 7.094118 GGTGGTGGTCTGATCTAGAGATTATAC 60.094 44.444 0.00 0.00 35.70 1.47
399 406 2.955660 GAGGTGGTGGTCTGATCTAGAG 59.044 54.545 0.00 0.00 35.70 2.43
406 413 0.609406 CGAGAGAGGTGGTGGTCTGA 60.609 60.000 0.00 0.00 0.00 3.27
420 427 9.810545 TGAGTGATACTATGTCTATATCGAGAG 57.189 37.037 0.00 0.00 0.00 3.20
421 428 9.589111 GTGAGTGATACTATGTCTATATCGAGA 57.411 37.037 0.00 0.00 0.00 4.04
488 495 6.582295 CCAAAACATGAACTATCCGACAAAAG 59.418 38.462 0.00 0.00 0.00 2.27
505 1535 1.687660 TCATGCACACAGCCAAAACAT 59.312 42.857 0.00 0.00 44.83 2.71
606 1641 8.730680 GTGGAACAACACATACTCTGATAAAAT 58.269 33.333 0.00 0.00 44.16 1.82
633 2125 1.608025 CGCGGTATTCCATGGCAGTAT 60.608 52.381 6.96 0.33 0.00 2.12
636 2128 2.896801 GCGCGGTATTCCATGGCAG 61.897 63.158 8.83 0.00 0.00 4.85
637 2129 2.899838 GCGCGGTATTCCATGGCA 60.900 61.111 8.83 0.00 0.00 4.92
651 2143 0.782384 CGTACCCAATTATCTCGCGC 59.218 55.000 0.00 0.00 0.00 6.86
663 2155 2.357275 CCGGCGAAAACGTACCCA 60.357 61.111 9.30 0.00 0.00 4.51
757 2253 7.818930 CCACCAAGAAAAATACAGTATTTGCAT 59.181 33.333 17.62 8.62 38.32 3.96
767 2276 2.298729 GGCAGCCACCAAGAAAAATACA 59.701 45.455 6.55 0.00 0.00 2.29
791 2303 3.821421 AATAGACCCGACTGTGAATCC 57.179 47.619 0.00 0.00 0.00 3.01
802 2314 4.939052 AGATGTGTCCTAAATAGACCCG 57.061 45.455 0.00 0.00 33.09 5.28
803 2315 7.607250 CATCTAGATGTGTCCTAAATAGACCC 58.393 42.308 22.42 0.00 34.23 4.46
846 2358 5.723887 AGAAGGAGTGGACATCAGTTTAGAT 59.276 40.000 0.00 0.00 0.00 1.98
847 2359 5.047021 CAGAAGGAGTGGACATCAGTTTAGA 60.047 44.000 0.00 0.00 0.00 2.10
848 2360 5.174395 CAGAAGGAGTGGACATCAGTTTAG 58.826 45.833 0.00 0.00 0.00 1.85
849 2361 4.593206 ACAGAAGGAGTGGACATCAGTTTA 59.407 41.667 0.00 0.00 0.00 2.01
850 2362 3.392616 ACAGAAGGAGTGGACATCAGTTT 59.607 43.478 0.00 0.00 0.00 2.66
851 2363 2.975489 ACAGAAGGAGTGGACATCAGTT 59.025 45.455 0.00 0.00 0.00 3.16
852 2364 2.301296 CACAGAAGGAGTGGACATCAGT 59.699 50.000 0.00 0.00 33.43 3.41
853 2365 2.969990 CACAGAAGGAGTGGACATCAG 58.030 52.381 0.00 0.00 33.43 2.90
861 2373 5.799213 AGAAAATAGACCACAGAAGGAGTG 58.201 41.667 0.00 0.00 36.76 3.51
862 2374 6.441088 AAGAAAATAGACCACAGAAGGAGT 57.559 37.500 0.00 0.00 0.00 3.85
863 2375 9.103861 GAATAAGAAAATAGACCACAGAAGGAG 57.896 37.037 0.00 0.00 0.00 3.69
864 2376 8.826765 AGAATAAGAAAATAGACCACAGAAGGA 58.173 33.333 0.00 0.00 0.00 3.36
912 2424 9.642327 TGTCACGTCTAAGCTTTTACAAATATA 57.358 29.630 3.20 0.00 0.00 0.86
913 2425 8.542497 TGTCACGTCTAAGCTTTTACAAATAT 57.458 30.769 3.20 0.00 0.00 1.28
914 2426 7.949903 TGTCACGTCTAAGCTTTTACAAATA 57.050 32.000 3.20 0.00 0.00 1.40
915 2427 6.854496 TGTCACGTCTAAGCTTTTACAAAT 57.146 33.333 3.20 0.00 0.00 2.32
916 2428 6.854496 ATGTCACGTCTAAGCTTTTACAAA 57.146 33.333 3.20 0.00 0.00 2.83
917 2429 6.854496 AATGTCACGTCTAAGCTTTTACAA 57.146 33.333 3.20 0.00 0.00 2.41
918 2430 6.854496 AAATGTCACGTCTAAGCTTTTACA 57.146 33.333 3.20 0.00 0.00 2.41
919 2431 9.654417 TTAAAAATGTCACGTCTAAGCTTTTAC 57.346 29.630 3.20 2.26 0.00 2.01
921 2433 9.575783 TTTTAAAAATGTCACGTCTAAGCTTTT 57.424 25.926 3.20 0.00 0.00 2.27
922 2434 9.575783 TTTTTAAAAATGTCACGTCTAAGCTTT 57.424 25.926 3.20 0.00 0.00 3.51
955 2467 9.394767 TGTGAACAGTTTGTATAATGCATATCT 57.605 29.630 0.00 0.00 0.00 1.98
956 2468 9.655769 CTGTGAACAGTTTGTATAATGCATATC 57.344 33.333 0.00 0.00 39.09 1.63
957 2469 8.131100 GCTGTGAACAGTTTGTATAATGCATAT 58.869 33.333 11.87 0.00 45.45 1.78
958 2470 7.415095 GGCTGTGAACAGTTTGTATAATGCATA 60.415 37.037 11.87 0.00 45.45 3.14
959 2471 6.324819 GCTGTGAACAGTTTGTATAATGCAT 58.675 36.000 11.87 0.00 45.45 3.96
960 2472 5.335583 GGCTGTGAACAGTTTGTATAATGCA 60.336 40.000 11.87 0.00 45.45 3.96
961 2473 5.095490 GGCTGTGAACAGTTTGTATAATGC 58.905 41.667 11.87 0.00 45.45 3.56
962 2474 6.086222 GTGGCTGTGAACAGTTTGTATAATG 58.914 40.000 11.87 0.00 45.45 1.90
963 2475 5.767665 TGTGGCTGTGAACAGTTTGTATAAT 59.232 36.000 11.87 0.00 45.45 1.28
964 2476 5.008217 GTGTGGCTGTGAACAGTTTGTATAA 59.992 40.000 11.87 0.00 45.45 0.98
965 2477 4.513692 GTGTGGCTGTGAACAGTTTGTATA 59.486 41.667 11.87 0.00 45.45 1.47
966 2478 3.315191 GTGTGGCTGTGAACAGTTTGTAT 59.685 43.478 11.87 0.00 45.45 2.29
967 2479 2.680841 GTGTGGCTGTGAACAGTTTGTA 59.319 45.455 11.87 0.00 45.45 2.41
968 2480 1.472480 GTGTGGCTGTGAACAGTTTGT 59.528 47.619 11.87 0.00 45.45 2.83
969 2481 1.531677 CGTGTGGCTGTGAACAGTTTG 60.532 52.381 11.87 0.00 45.45 2.93
970 2482 0.732571 CGTGTGGCTGTGAACAGTTT 59.267 50.000 11.87 0.00 45.45 2.66
971 2483 1.095228 CCGTGTGGCTGTGAACAGTT 61.095 55.000 11.87 0.00 45.45 3.16
972 2484 1.523711 CCGTGTGGCTGTGAACAGT 60.524 57.895 11.87 0.00 45.45 3.55
973 2485 2.253758 CCCGTGTGGCTGTGAACAG 61.254 63.158 6.08 6.08 46.40 3.16
974 2486 2.203139 CCCGTGTGGCTGTGAACA 60.203 61.111 0.00 0.00 0.00 3.18
983 2495 4.953868 TCGTTGTCGCCCGTGTGG 62.954 66.667 0.00 0.00 36.96 4.17
1110 2623 1.552792 GAAGGAGAAGGAGGTGTGGAG 59.447 57.143 0.00 0.00 0.00 3.86
1111 2624 1.150135 AGAAGGAGAAGGAGGTGTGGA 59.850 52.381 0.00 0.00 0.00 4.02
1112 2625 1.552792 GAGAAGGAGAAGGAGGTGTGG 59.447 57.143 0.00 0.00 0.00 4.17
1113 2626 2.495669 GAGAGAAGGAGAAGGAGGTGTG 59.504 54.545 0.00 0.00 0.00 3.82
1114 2627 2.558800 GGAGAGAAGGAGAAGGAGGTGT 60.559 54.545 0.00 0.00 0.00 4.16
1115 2628 2.107366 GGAGAGAAGGAGAAGGAGGTG 58.893 57.143 0.00 0.00 0.00 4.00
1116 2629 1.719378 TGGAGAGAAGGAGAAGGAGGT 59.281 52.381 0.00 0.00 0.00 3.85
1117 2630 2.024464 TCTGGAGAGAAGGAGAAGGAGG 60.024 54.545 0.00 0.00 0.00 4.30
1118 2631 3.380471 TCTGGAGAGAAGGAGAAGGAG 57.620 52.381 0.00 0.00 0.00 3.69
1119 2632 3.181417 TGTTCTGGAGAGAAGGAGAAGGA 60.181 47.826 0.00 0.00 38.95 3.36
1120 2633 3.169099 TGTTCTGGAGAGAAGGAGAAGG 58.831 50.000 0.00 0.00 38.95 3.46
1130 2643 1.675415 GCCAAGCTCTGTTCTGGAGAG 60.675 57.143 3.98 0.00 40.10 3.20
1271 2787 5.143376 AGAAACAAATCAATTGGGCAGAG 57.857 39.130 5.42 0.00 43.66 3.35
1272 2788 5.549742 AAGAAACAAATCAATTGGGCAGA 57.450 34.783 5.42 0.00 43.66 4.26
1759 3278 0.647410 CTTAGCAATGTCGCCGTCTG 59.353 55.000 0.00 0.00 0.00 3.51
1785 3304 7.441760 TCAGCCGAAACTATACACAAACTTAAA 59.558 33.333 0.00 0.00 0.00 1.52
2012 3535 2.819608 CCGATCCCTTCTTTTCTGCAAA 59.180 45.455 0.00 0.00 0.00 3.68
2125 3648 6.140110 CACCAAACTAGAAACGTAACAATGG 58.860 40.000 0.00 0.00 0.00 3.16
2139 3662 3.750371 TCAACCATCCACACCAAACTAG 58.250 45.455 0.00 0.00 0.00 2.57
2260 3783 8.743714 AGATTAGAAATTCAGGGTGTGATTTTC 58.256 33.333 11.68 11.68 46.64 2.29
2285 3808 1.066573 ACCGTGCTTGATTGAGGAGAG 60.067 52.381 0.00 0.00 0.00 3.20
2307 3830 0.464036 AGCCAACACTGTGAGTCGAA 59.536 50.000 15.86 0.00 0.00 3.71
2314 3837 0.385390 GAACCCAAGCCAACACTGTG 59.615 55.000 6.19 6.19 0.00 3.66
2319 3843 1.144708 TGATCTGAACCCAAGCCAACA 59.855 47.619 0.00 0.00 0.00 3.33
2544 4068 4.024725 CACCATTGTTTTGCATCTGGTTTG 60.025 41.667 0.00 0.00 39.81 2.93
2545 4069 4.128643 CACCATTGTTTTGCATCTGGTTT 58.871 39.130 0.00 0.00 39.81 3.27
2546 4070 3.134442 ACACCATTGTTTTGCATCTGGTT 59.866 39.130 0.00 0.00 39.81 3.67
2547 4071 2.699846 ACACCATTGTTTTGCATCTGGT 59.300 40.909 0.00 0.00 41.40 4.00
2548 4072 3.006110 AGACACCATTGTTTTGCATCTGG 59.994 43.478 0.00 0.00 35.47 3.86
2549 4073 3.985279 CAGACACCATTGTTTTGCATCTG 59.015 43.478 0.00 0.00 35.47 2.90
2550 4074 3.638160 ACAGACACCATTGTTTTGCATCT 59.362 39.130 0.00 0.00 35.47 2.90
2551 4075 3.737266 CACAGACACCATTGTTTTGCATC 59.263 43.478 0.00 0.00 35.47 3.91
2552 4076 3.493002 CCACAGACACCATTGTTTTGCAT 60.493 43.478 0.00 0.00 35.47 3.96
2553 4077 2.159128 CCACAGACACCATTGTTTTGCA 60.159 45.455 0.00 0.00 35.47 4.08
2554 4078 2.159114 ACCACAGACACCATTGTTTTGC 60.159 45.455 0.00 0.00 35.47 3.68
2555 4079 3.130164 TCACCACAGACACCATTGTTTTG 59.870 43.478 0.00 0.00 35.47 2.44
2556 4080 3.360867 TCACCACAGACACCATTGTTTT 58.639 40.909 0.00 0.00 35.47 2.43
2918 4457 8.052748 ACATGCCTATTGGAGTTTCAGTTAATA 58.947 33.333 0.00 0.00 34.57 0.98
2980 4661 4.518970 TGCCTATTGGAGTTTCAGTCAAAC 59.481 41.667 0.00 0.00 44.38 2.93
2983 4664 4.263462 ACATGCCTATTGGAGTTTCAGTCA 60.263 41.667 0.00 0.00 34.57 3.41
2984 4665 4.265073 ACATGCCTATTGGAGTTTCAGTC 58.735 43.478 0.00 0.00 34.57 3.51
3064 4754 5.448654 AGCTTGGGAAATAATGTCAGCATA 58.551 37.500 0.00 0.00 34.39 3.14
3071 4761 4.440112 GCGCTTAAGCTTGGGAAATAATGT 60.440 41.667 24.33 0.00 39.32 2.71
3084 4774 1.667724 CTAAGTGCATGCGCTTAAGCT 59.332 47.619 38.76 25.18 44.92 3.74
3281 4971 5.617528 TGTTTGTGAACTAGTGGGACTTA 57.382 39.130 0.00 0.00 36.70 2.24
3763 5454 6.356556 ACTTAGATGTGCAATACTTATGGCA 58.643 36.000 0.00 0.00 40.19 4.92
3764 5455 6.073003 GGACTTAGATGTGCAATACTTATGGC 60.073 42.308 0.00 0.00 33.16 4.40
3765 5456 7.172190 CAGGACTTAGATGTGCAATACTTATGG 59.828 40.741 0.00 0.00 0.00 2.74
3766 5457 7.712639 ACAGGACTTAGATGTGCAATACTTATG 59.287 37.037 0.00 0.00 0.00 1.90
3767 5458 7.796054 ACAGGACTTAGATGTGCAATACTTAT 58.204 34.615 0.00 0.00 0.00 1.73
3768 5459 7.182817 ACAGGACTTAGATGTGCAATACTTA 57.817 36.000 0.00 0.00 0.00 2.24
3769 5460 6.054860 ACAGGACTTAGATGTGCAATACTT 57.945 37.500 0.00 0.00 0.00 2.24
3770 5461 5.683876 ACAGGACTTAGATGTGCAATACT 57.316 39.130 0.00 0.00 0.00 2.12
3771 5462 7.210174 TGATACAGGACTTAGATGTGCAATAC 58.790 38.462 0.00 0.00 0.00 1.89
3772 5463 7.360113 TGATACAGGACTTAGATGTGCAATA 57.640 36.000 0.00 0.00 0.00 1.90
3773 5464 6.239217 TGATACAGGACTTAGATGTGCAAT 57.761 37.500 0.00 0.00 0.00 3.56
3774 5465 5.675684 TGATACAGGACTTAGATGTGCAA 57.324 39.130 0.00 0.00 0.00 4.08
3775 5466 5.876651 ATGATACAGGACTTAGATGTGCA 57.123 39.130 0.00 0.00 0.00 4.57
3776 5467 6.283694 TCAATGATACAGGACTTAGATGTGC 58.716 40.000 0.00 0.00 0.00 4.57
3777 5468 8.366401 AGATCAATGATACAGGACTTAGATGTG 58.634 37.037 0.00 0.00 0.00 3.21
3778 5469 8.489676 AGATCAATGATACAGGACTTAGATGT 57.510 34.615 0.00 0.00 0.00 3.06
3781 5472 9.421399 TGTAAGATCAATGATACAGGACTTAGA 57.579 33.333 0.00 0.00 0.00 2.10
3782 5473 9.469807 GTGTAAGATCAATGATACAGGACTTAG 57.530 37.037 0.00 0.00 0.00 2.18
3783 5474 8.135529 CGTGTAAGATCAATGATACAGGACTTA 58.864 37.037 10.21 4.33 36.67 2.24
3784 5475 6.980978 CGTGTAAGATCAATGATACAGGACTT 59.019 38.462 10.21 5.12 36.67 3.01
3785 5476 6.321435 TCGTGTAAGATCAATGATACAGGACT 59.679 38.462 13.02 0.00 37.89 3.85
3786 5477 6.504398 TCGTGTAAGATCAATGATACAGGAC 58.496 40.000 13.02 2.58 37.89 3.85
3787 5478 6.709018 TCGTGTAAGATCAATGATACAGGA 57.291 37.500 13.02 13.02 39.46 3.86
3788 5479 7.203218 TCTTCGTGTAAGATCAATGATACAGG 58.797 38.462 9.71 9.71 39.36 4.00
3809 5500 6.496338 AAGAAAATACCCACACGAATCTTC 57.504 37.500 0.00 0.00 0.00 2.87
3810 5501 7.166167 AGTAAGAAAATACCCACACGAATCTT 58.834 34.615 0.00 0.00 0.00 2.40
3811 5502 6.708285 AGTAAGAAAATACCCACACGAATCT 58.292 36.000 0.00 0.00 0.00 2.40
3812 5503 6.980051 AGTAAGAAAATACCCACACGAATC 57.020 37.500 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.