Multiple sequence alignment - TraesCS5B01G416300

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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 TraesCS5B01G416300 chr5B 100.000 4231 0 0 1 4231 590808808 590804578 0.000000e+00 7814.0
1 TraesCS5B01G416300 chr5B 87.598 1016 82 22 2767 3747 590183537 590182531 0.000000e+00 1138.0
2 TraesCS5B01G416300 chr5B 80.759 764 83 30 811 1556 590184915 590184198 4.810000e-149 538.0
3 TraesCS5B01G416300 chr5B 88.326 454 38 5 2768 3206 590256468 590256015 8.050000e-147 531.0
4 TraesCS5B01G416300 chr5B 82.731 498 53 15 2050 2545 590503167 590502701 3.040000e-111 412.0
5 TraesCS5B01G416300 chr5B 86.943 314 29 6 1073 1380 590530763 590530456 4.050000e-90 342.0
6 TraesCS5B01G416300 chr5B 89.051 274 20 6 2502 2773 590256789 590256524 8.770000e-87 331.0
7 TraesCS5B01G416300 chr5B 79.825 456 65 16 3007 3450 590613630 590613190 1.480000e-79 307.0
8 TraesCS5B01G416300 chr5B 85.294 272 37 3 2436 2706 590184037 590183768 1.160000e-70 278.0
9 TraesCS5B01G416300 chr5B 85.075 201 20 8 1266 1458 590455654 590455456 3.340000e-46 196.0
10 TraesCS5B01G416300 chr5B 87.857 140 17 0 1087 1226 590456604 590456465 9.410000e-37 165.0
11 TraesCS5B01G416300 chr5B 83.766 154 21 2 3748 3898 590606212 590606060 4.410000e-30 143.0
12 TraesCS5B01G416300 chr5A 93.036 1479 70 13 2766 4231 601341918 601340460 0.000000e+00 2130.0
13 TraesCS5B01G416300 chr5A 85.901 2142 137 65 483 2580 601343960 601341940 0.000000e+00 2130.0
14 TraesCS5B01G416300 chr5A 90.636 865 68 7 3370 4229 601255751 601254895 0.000000e+00 1136.0
15 TraesCS5B01G416300 chr5A 87.043 1011 86 18 2766 3744 600503634 600502637 0.000000e+00 1099.0
16 TraesCS5B01G416300 chr5A 85.504 952 84 27 1839 2771 601257297 601256381 0.000000e+00 944.0
17 TraesCS5B01G416300 chr5A 84.032 1002 102 39 2767 3745 601086741 601085775 0.000000e+00 911.0
18 TraesCS5B01G416300 chr5A 93.836 584 35 1 2767 3350 601256321 601255739 0.000000e+00 878.0
19 TraesCS5B01G416300 chr5A 81.620 827 104 24 2909 3713 601483987 601483187 3.570000e-180 641.0
20 TraesCS5B01G416300 chr5A 90.496 484 31 9 917 1389 601258328 601257849 3.590000e-175 625.0
21 TraesCS5B01G416300 chr5A 88.400 500 41 6 2801 3285 601166997 601166500 1.690000e-163 586.0
22 TraesCS5B01G416300 chr5A 81.737 668 69 24 2140 2772 600504337 600503688 3.770000e-140 508.0
23 TraesCS5B01G416300 chr5A 84.766 512 43 16 2050 2550 601087308 601086821 8.230000e-132 481.0
24 TraesCS5B01G416300 chr5A 94.097 288 15 2 45 331 601345640 601345354 1.810000e-118 436.0
25 TraesCS5B01G416300 chr5A 81.703 552 66 18 3677 4226 601254477 601253959 1.090000e-115 427.0
26 TraesCS5B01G416300 chr5A 85.646 418 39 4 905 1311 600504863 600504456 1.820000e-113 420.0
27 TraesCS5B01G416300 chr5A 77.445 634 107 16 2159 2773 601485079 601484463 3.130000e-91 346.0
28 TraesCS5B01G416300 chr5A 81.058 359 57 8 3841 4193 600502493 600502140 4.170000e-70 276.0
29 TraesCS5B01G416300 chr5A 89.706 204 11 4 4035 4230 601245332 601245131 7.020000e-63 252.0
30 TraesCS5B01G416300 chr5A 82.955 264 30 5 1568 1819 601257674 601257414 1.530000e-54 224.0
31 TraesCS5B01G416300 chr5A 77.358 424 46 21 3522 3898 601155977 601155557 5.550000e-49 206.0
32 TraesCS5B01G416300 chr5A 93.162 117 8 0 371 487 601344933 601344817 5.620000e-39 172.0
33 TraesCS5B01G416300 chr5A 76.393 305 50 13 1643 1931 601485000 601484702 1.230000e-30 145.0
34 TraesCS5B01G416300 chr5A 78.166 229 43 7 92 319 601428703 601428481 5.700000e-29 139.0
35 TraesCS5B01G416300 chr5A 97.368 38 1 0 3861 3898 600502535 600502498 9.820000e-07 65.8
36 TraesCS5B01G416300 chr5D 91.107 1473 109 13 2771 4227 481761179 481759713 0.000000e+00 1975.0
37 TraesCS5B01G416300 chr5D 84.720 1250 110 45 2766 3948 481564295 481563060 0.000000e+00 1175.0
38 TraesCS5B01G416300 chr5D 86.615 777 73 18 2767 3533 481643421 481642666 0.000000e+00 830.0
39 TraesCS5B01G416300 chr5D 89.568 671 34 15 897 1556 481762901 481762256 0.000000e+00 819.0
40 TraesCS5B01G416300 chr5D 85.062 723 42 21 1565 2231 481762196 481761484 0.000000e+00 676.0
41 TraesCS5B01G416300 chr5D 79.161 739 77 24 828 1555 481565730 481565058 1.400000e-119 440.0
42 TraesCS5B01G416300 chr5D 84.889 450 39 21 2341 2773 481564785 481564348 1.090000e-115 427.0
43 TraesCS5B01G416300 chr5D 78.963 694 85 26 3254 3898 481738197 481737516 2.350000e-112 416.0
44 TraesCS5B01G416300 chr5D 87.429 350 30 6 2410 2747 481643840 481643493 1.430000e-104 390.0
45 TraesCS5B01G416300 chr5D 94.650 243 12 1 2338 2580 481761480 481761239 3.990000e-100 375.0
46 TraesCS5B01G416300 chr5D 88.327 257 20 5 4 250 481763630 481763374 2.470000e-77 300.0
47 TraesCS5B01G416300 chr5D 80.968 310 51 5 3841 4145 481738829 481738523 5.470000e-59 239.0
48 TraesCS5B01G416300 chr5D 80.829 193 33 3 126 318 481808441 481808253 9.480000e-32 148.0
49 TraesCS5B01G416300 chr5D 78.355 231 24 13 3522 3729 481749490 481749263 4.440000e-25 126.0


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 TraesCS5B01G416300 chr5B 590804578 590808808 4230 True 7814.000000 7814 100.000000 1 4231 1 chr5B.!!$R5 4230
1 TraesCS5B01G416300 chr5B 590182531 590184915 2384 True 651.333333 1138 84.550333 811 3747 3 chr5B.!!$R6 2936
2 TraesCS5B01G416300 chr5B 590256015 590256789 774 True 431.000000 531 88.688500 2502 3206 2 chr5B.!!$R7 704
3 TraesCS5B01G416300 chr5A 601340460 601345640 5180 True 1217.000000 2130 91.549000 45 4231 4 chr5A.!!$R8 4186
4 TraesCS5B01G416300 chr5A 601253959 601258328 4369 True 705.666667 1136 87.521667 917 4229 6 chr5A.!!$R7 3312
5 TraesCS5B01G416300 chr5A 601085775 601087308 1533 True 696.000000 911 84.399000 2050 3745 2 chr5A.!!$R6 1695
6 TraesCS5B01G416300 chr5A 600502140 600504863 2723 True 473.760000 1099 86.570400 905 4193 5 chr5A.!!$R5 3288
7 TraesCS5B01G416300 chr5A 601483187 601485079 1892 True 377.333333 641 78.486000 1643 3713 3 chr5A.!!$R9 2070
8 TraesCS5B01G416300 chr5D 481759713 481763630 3917 True 829.000000 1975 89.742800 4 4227 5 chr5D.!!$R6 4223
9 TraesCS5B01G416300 chr5D 481563060 481565730 2670 True 680.666667 1175 82.923333 828 3948 3 chr5D.!!$R3 3120
10 TraesCS5B01G416300 chr5D 481642666 481643840 1174 True 610.000000 830 87.022000 2410 3533 2 chr5D.!!$R4 1123
11 TraesCS5B01G416300 chr5D 481737516 481738829 1313 True 327.500000 416 79.965500 3254 4145 2 chr5D.!!$R5 891

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
887 2271 0.039978 CACTCACTCGCTCGTTCACT 60.040 55.0 0.0 0.0 0.0 3.41 F
893 2277 0.108615 CTCGCTCGTTCACTCCCATT 60.109 55.0 0.0 0.0 0.0 3.16 F
1316 2723 0.179089 CCAGATCTCCTTGCTCCACG 60.179 60.0 0.0 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2375 4038 1.826385 AAGGACAAAGGAAGGCATCG 58.174 50.000 0.0 0.0 0.00 3.84 R
2672 5068 3.894759 ACGTAGAGCTTATGGAGTGGTA 58.105 45.455 0.0 0.0 0.00 3.25 R
3298 6191 1.282930 GACAAGGGAACTCGTCGTGC 61.283 60.000 0.0 0.0 42.68 5.34 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
42 43 1.455849 CTGAGCTTGGGACCAACCA 59.544 57.895 0.00 0.00 41.20 3.67
124 131 4.097589 CCATCTTTTCTCAAGGATTCTGGC 59.902 45.833 0.00 0.00 0.00 4.85
162 172 6.013379 TCCTCTTCTTCACATGTTCCAATACT 60.013 38.462 0.00 0.00 0.00 2.12
249 260 4.468510 TGATCAAATACTCGGTACCCAAGT 59.531 41.667 16.52 16.52 0.00 3.16
250 261 4.196626 TCAAATACTCGGTACCCAAGTG 57.803 45.455 19.98 7.56 0.00 3.16
252 263 3.604875 AATACTCGGTACCCAAGTGTG 57.395 47.619 19.98 4.94 0.00 3.82
253 264 1.999648 TACTCGGTACCCAAGTGTGT 58.000 50.000 19.98 9.79 0.00 3.72
254 265 1.999648 ACTCGGTACCCAAGTGTGTA 58.000 50.000 12.63 0.00 0.00 2.90
255 266 2.532843 ACTCGGTACCCAAGTGTGTAT 58.467 47.619 12.63 0.00 0.00 2.29
256 267 2.494870 ACTCGGTACCCAAGTGTGTATC 59.505 50.000 12.63 0.00 0.00 2.24
258 269 2.494471 TCGGTACCCAAGTGTGTATCTG 59.506 50.000 6.25 0.00 0.00 2.90
259 270 2.232941 CGGTACCCAAGTGTGTATCTGT 59.767 50.000 6.25 0.00 0.00 3.41
261 272 4.098960 CGGTACCCAAGTGTGTATCTGTAT 59.901 45.833 6.25 0.00 0.00 2.29
262 273 5.300034 CGGTACCCAAGTGTGTATCTGTATA 59.700 44.000 6.25 0.00 0.00 1.47
263 274 6.015688 CGGTACCCAAGTGTGTATCTGTATAT 60.016 42.308 6.25 0.00 0.00 0.86
266 277 6.817184 ACCCAAGTGTGTATCTGTATATGAC 58.183 40.000 0.00 0.00 0.00 3.06
268 279 7.093068 ACCCAAGTGTGTATCTGTATATGACAA 60.093 37.037 0.00 0.00 37.70 3.18
269 280 7.439356 CCCAAGTGTGTATCTGTATATGACAAG 59.561 40.741 0.00 0.00 37.70 3.16
270 281 8.197439 CCAAGTGTGTATCTGTATATGACAAGA 58.803 37.037 0.00 0.00 37.70 3.02
271 282 9.242477 CAAGTGTGTATCTGTATATGACAAGAG 57.758 37.037 0.00 0.00 37.70 2.85
272 283 8.753497 AGTGTGTATCTGTATATGACAAGAGA 57.247 34.615 0.00 0.00 37.70 3.10
273 284 9.190317 AGTGTGTATCTGTATATGACAAGAGAA 57.810 33.333 0.00 0.00 37.70 2.87
274 285 9.457110 GTGTGTATCTGTATATGACAAGAGAAG 57.543 37.037 0.00 0.00 37.70 2.85
275 286 9.408648 TGTGTATCTGTATATGACAAGAGAAGA 57.591 33.333 0.00 0.00 37.70 2.87
276 287 9.672086 GTGTATCTGTATATGACAAGAGAAGAC 57.328 37.037 0.00 0.00 37.70 3.01
280 291 9.761504 ATCTGTATATGACAAGAGAAGACAATG 57.238 33.333 0.00 0.00 37.70 2.82
282 293 9.591792 CTGTATATGACAAGAGAAGACAATGAA 57.408 33.333 0.00 0.00 37.70 2.57
283 294 9.591792 TGTATATGACAAGAGAAGACAATGAAG 57.408 33.333 0.00 0.00 34.15 3.02
284 295 9.809096 GTATATGACAAGAGAAGACAATGAAGA 57.191 33.333 0.00 0.00 0.00 2.87
285 296 8.945481 ATATGACAAGAGAAGACAATGAAGAG 57.055 34.615 0.00 0.00 0.00 2.85
286 297 6.166984 TGACAAGAGAAGACAATGAAGAGT 57.833 37.500 0.00 0.00 0.00 3.24
287 298 6.586344 TGACAAGAGAAGACAATGAAGAGTT 58.414 36.000 0.00 0.00 0.00 3.01
288 299 6.703607 TGACAAGAGAAGACAATGAAGAGTTC 59.296 38.462 0.00 0.00 0.00 3.01
290 301 5.815233 AGAGAAGACAATGAAGAGTTCCA 57.185 39.130 0.00 0.00 0.00 3.53
291 302 6.179906 AGAGAAGACAATGAAGAGTTCCAA 57.820 37.500 0.00 0.00 0.00 3.53
292 303 5.994668 AGAGAAGACAATGAAGAGTTCCAAC 59.005 40.000 0.00 0.00 0.00 3.77
323 378 3.003378 GGAACAATGCTTACGAATAGGCC 59.997 47.826 0.00 0.00 32.46 5.19
324 379 3.275617 ACAATGCTTACGAATAGGCCA 57.724 42.857 5.01 0.00 32.46 5.36
325 380 3.820557 ACAATGCTTACGAATAGGCCAT 58.179 40.909 5.01 0.00 32.46 4.40
326 381 4.207165 ACAATGCTTACGAATAGGCCATT 58.793 39.130 5.01 2.34 32.46 3.16
327 382 4.644685 ACAATGCTTACGAATAGGCCATTT 59.355 37.500 5.01 0.00 32.46 2.32
328 383 5.127031 ACAATGCTTACGAATAGGCCATTTT 59.873 36.000 5.01 0.00 32.46 1.82
329 384 5.852282 ATGCTTACGAATAGGCCATTTTT 57.148 34.783 5.01 0.00 32.46 1.94
380 850 4.062293 CTGGTTACATTCACAGGTTTCGA 58.938 43.478 0.00 0.00 0.00 3.71
397 867 4.880886 TTCGACACAATAAGATGCATGG 57.119 40.909 2.46 0.00 0.00 3.66
406 887 1.098050 AAGATGCATGGGAAAGACGC 58.902 50.000 2.46 0.00 0.00 5.19
426 907 7.086376 AGACGCGTAGTTTCAACTTAGAATTA 58.914 34.615 13.97 0.00 40.37 1.40
449 930 3.837146 AGAGGCATCGGAATGACATATCT 59.163 43.478 0.00 0.00 44.06 1.98
509 1851 3.751175 CAGCATAGTTCAACGGGAGAAAA 59.249 43.478 0.00 0.00 0.00 2.29
546 1888 1.680651 CCTAATGCGGTTGGCCCAA 60.681 57.895 0.00 0.00 42.61 4.12
596 1947 4.655963 TCCTCTTTAAGCAGAAGCACAAT 58.344 39.130 0.00 0.00 45.49 2.71
607 1958 4.482386 CAGAAGCACAATCACAATTCTGG 58.518 43.478 5.11 0.00 39.80 3.86
609 1960 4.828939 AGAAGCACAATCACAATTCTGGAA 59.171 37.500 0.00 0.00 0.00 3.53
610 1961 4.510038 AGCACAATCACAATTCTGGAAC 57.490 40.909 0.00 0.00 0.00 3.62
611 1962 4.147321 AGCACAATCACAATTCTGGAACT 58.853 39.130 0.00 0.00 0.00 3.01
612 1963 4.022589 AGCACAATCACAATTCTGGAACTG 60.023 41.667 0.00 0.00 0.00 3.16
613 1964 4.801891 CACAATCACAATTCTGGAACTGG 58.198 43.478 0.00 0.00 0.00 4.00
614 1965 4.279169 CACAATCACAATTCTGGAACTGGT 59.721 41.667 0.00 0.00 0.00 4.00
617 1968 4.974645 TCACAATTCTGGAACTGGTAGT 57.025 40.909 0.00 0.00 0.00 2.73
619 1970 3.189287 CACAATTCTGGAACTGGTAGTGC 59.811 47.826 0.00 0.00 0.00 4.40
620 1971 3.073062 ACAATTCTGGAACTGGTAGTGCT 59.927 43.478 0.00 0.00 0.00 4.40
652 2010 0.940126 CTGTGTGCGTGCTTCTTTCT 59.060 50.000 0.00 0.00 0.00 2.52
653 2011 1.331756 CTGTGTGCGTGCTTCTTTCTT 59.668 47.619 0.00 0.00 0.00 2.52
705 2063 7.872483 AGTCAAAAGAAAAGAAAAAGTGCTGAA 59.128 29.630 0.00 0.00 0.00 3.02
706 2064 8.164790 GTCAAAAGAAAAGAAAAAGTGCTGAAG 58.835 33.333 0.00 0.00 0.00 3.02
723 2107 2.194271 GAAGCTGACACATACGTAGGC 58.806 52.381 7.23 0.00 0.00 3.93
730 2114 1.202268 ACACATACGTAGGCGCTTCTC 60.202 52.381 7.64 0.00 42.83 2.87
750 2134 2.027625 GCCGTGGGACGAACTGAAG 61.028 63.158 0.00 0.00 46.05 3.02
798 2182 0.613260 TCTCCAGATTTGGTCACCCG 59.387 55.000 1.59 0.00 45.26 5.28
799 2183 0.324943 CTCCAGATTTGGTCACCCGT 59.675 55.000 1.59 0.00 45.26 5.28
800 2184 0.323629 TCCAGATTTGGTCACCCGTC 59.676 55.000 1.59 0.00 45.26 4.79
834 2218 4.796495 ATCTGGGTTTCGGGCCGC 62.796 66.667 23.83 7.37 0.00 6.53
881 2265 3.062466 TCCCCACTCACTCGCTCG 61.062 66.667 0.00 0.00 0.00 5.03
882 2266 3.374402 CCCCACTCACTCGCTCGT 61.374 66.667 0.00 0.00 0.00 4.18
883 2267 2.651361 CCCACTCACTCGCTCGTT 59.349 61.111 0.00 0.00 0.00 3.85
884 2268 1.444553 CCCACTCACTCGCTCGTTC 60.445 63.158 0.00 0.00 0.00 3.95
885 2269 1.285950 CCACTCACTCGCTCGTTCA 59.714 57.895 0.00 0.00 0.00 3.18
886 2270 1.004277 CCACTCACTCGCTCGTTCAC 61.004 60.000 0.00 0.00 0.00 3.18
887 2271 0.039978 CACTCACTCGCTCGTTCACT 60.040 55.000 0.00 0.00 0.00 3.41
888 2272 0.238817 ACTCACTCGCTCGTTCACTC 59.761 55.000 0.00 0.00 0.00 3.51
889 2273 0.455295 CTCACTCGCTCGTTCACTCC 60.455 60.000 0.00 0.00 0.00 3.85
890 2274 1.444553 CACTCGCTCGTTCACTCCC 60.445 63.158 0.00 0.00 0.00 4.30
891 2275 1.901948 ACTCGCTCGTTCACTCCCA 60.902 57.895 0.00 0.00 0.00 4.37
892 2276 1.251527 ACTCGCTCGTTCACTCCCAT 61.252 55.000 0.00 0.00 0.00 4.00
893 2277 0.108615 CTCGCTCGTTCACTCCCATT 60.109 55.000 0.00 0.00 0.00 3.16
901 2285 0.613260 TTCACTCCCATTCCCACTCG 59.387 55.000 0.00 0.00 0.00 4.18
925 2309 1.279749 CCCCCTCTTTACTCCCCACC 61.280 65.000 0.00 0.00 0.00 4.61
1016 2411 2.177580 CGCGGCCGTACCATCAATT 61.178 57.895 28.70 0.00 39.03 2.32
1022 2417 1.400494 GCCGTACCATCAATTCACCAC 59.600 52.381 0.00 0.00 0.00 4.16
1316 2723 0.179089 CCAGATCTCCTTGCTCCACG 60.179 60.000 0.00 0.00 0.00 4.94
1339 2758 3.431725 GCCCTTCTTTCCGTGCCG 61.432 66.667 0.00 0.00 0.00 5.69
1392 2813 1.132640 GCGTTTGTAGCCGCTCAAG 59.867 57.895 0.00 0.00 46.08 3.02
1398 2819 0.744414 TGTAGCCGCTCAAGATTGCC 60.744 55.000 0.00 0.00 0.00 4.52
1452 2878 3.370527 GGATAGGCTAAGAACTTGGCACA 60.371 47.826 20.62 10.42 46.97 4.57
1511 2941 1.939980 AGGGACTCTAACCTGTGACC 58.060 55.000 0.00 0.00 35.30 4.02
1534 2964 5.277490 CCTGAATGTCCTACAATAATGCACG 60.277 44.000 0.00 0.00 0.00 5.34
1626 3110 9.554395 TTTCACTTATTCAGAAGTCATAACACA 57.446 29.630 0.00 0.00 37.57 3.72
1711 3245 6.093219 ACATGACATGCTACTGAAATCTTGTC 59.907 38.462 15.49 0.00 35.49 3.18
1714 3248 5.181748 ACATGCTACTGAAATCTTGTCTCC 58.818 41.667 0.00 0.00 0.00 3.71
1770 3310 3.795688 TTGATTCTCAAGCTCCACCTT 57.204 42.857 0.00 0.00 31.83 3.50
1777 3317 0.693049 CAAGCTCCACCTTGGGTAGT 59.307 55.000 0.00 0.00 38.78 2.73
1798 3338 7.014134 GGTAGTATCCTTTGTCCTTAGTCTACC 59.986 44.444 0.00 0.00 36.81 3.18
1876 3521 9.683069 CTTATGTTTATTGTTCTCTTTGCACTT 57.317 29.630 0.00 0.00 0.00 3.16
1932 3577 9.246670 TGCCTTGTCAGTAGTTTAACTAGTATA 57.753 33.333 11.60 1.98 32.84 1.47
1981 3626 6.494146 GGTAGTACTGTGGATAGGCTAAGAAT 59.506 42.308 5.39 0.00 0.00 2.40
1998 3643 8.025445 GGCTAAGAATTTGGCATGATATGTAAG 58.975 37.037 0.00 0.00 45.01 2.34
2056 3701 7.337942 GGGATTCTAACTTGTGATCTGAATGTT 59.662 37.037 0.00 0.00 0.00 2.71
2084 3729 2.874701 AGCATGCATAGCTTAACTTCCG 59.125 45.455 21.98 0.00 39.87 4.30
2132 3777 2.883386 CAGATTTTCTATGCCTGGCCTC 59.117 50.000 17.53 0.41 0.00 4.70
2133 3778 2.511218 AGATTTTCTATGCCTGGCCTCA 59.489 45.455 17.53 0.00 0.00 3.86
2136 3781 0.621571 TTCTATGCCTGGCCTCACCT 60.622 55.000 17.53 0.00 40.22 4.00
2173 3833 1.276138 GCTTGAAATTTGGGGGTGAGG 59.724 52.381 0.00 0.00 0.00 3.86
2196 3856 6.071728 AGGCCAAGATGTTTTCAGTTATTCAG 60.072 38.462 5.01 0.00 0.00 3.02
2198 3858 7.363268 GGCCAAGATGTTTTCAGTTATTCAGAT 60.363 37.037 0.00 0.00 0.00 2.90
2234 3894 4.402056 TCAGGTTGTAGCCTTATACTGC 57.598 45.455 0.00 0.00 36.58 4.40
2243 3904 6.213677 TGTAGCCTTATACTGCGAGTAATTG 58.786 40.000 0.00 0.00 33.89 2.32
2253 3915 6.795098 ACTGCGAGTAATTGTGTATTTCAA 57.205 33.333 0.00 0.00 0.00 2.69
2321 3984 1.808945 GATGCCTGTCTTGTCTTGGTG 59.191 52.381 0.00 0.00 0.00 4.17
2322 3985 0.819259 TGCCTGTCTTGTCTTGGTGC 60.819 55.000 0.00 0.00 0.00 5.01
2375 4038 6.906659 TCTTTGATTCTCAAGTTCAATCTGC 58.093 36.000 0.00 0.00 37.70 4.26
2424 4781 6.597832 AAAGATGTCTACTGCTCTAGTTGT 57.402 37.500 0.00 0.00 40.89 3.32
2509 4878 6.136155 TCCATGATATACTCTGTCCTGTCAA 58.864 40.000 0.00 0.00 0.00 3.18
2515 4884 8.851145 TGATATACTCTGTCCTGTCAATAGTTC 58.149 37.037 0.00 0.00 0.00 3.01
2540 4916 9.772973 TCAACTAAGTAGCTCAGTTATTTTTCA 57.227 29.630 0.00 0.00 31.46 2.69
2694 5090 3.894759 ACCACTCCATAAGCTCTACGTA 58.105 45.455 0.00 0.00 0.00 3.57
2780 5381 7.339466 CCTGTAAACATAGGCACTTATTTTCCT 59.661 37.037 0.00 0.00 41.75 3.36
2799 5400 5.266733 TCCTGAGCCATATTTTGCAATTC 57.733 39.130 0.00 0.00 0.00 2.17
2806 5407 5.188359 AGCCATATTTTGCAATTCTCTGGTT 59.812 36.000 0.00 0.00 0.00 3.67
3298 6191 1.856265 GACCTTGCCTCACTTTGCGG 61.856 60.000 0.00 0.00 0.00 5.69
3323 6217 2.758979 GACGAGTTCCCTTGTCCATAGA 59.241 50.000 0.00 0.00 43.65 1.98
3354 6249 5.587388 ATTGGGTTTGTCAGCATTATCAG 57.413 39.130 0.00 0.00 0.00 2.90
3417 6326 5.678583 CCATAGAATGACACTCATCACCTT 58.321 41.667 0.00 0.00 35.76 3.50
3546 6465 5.155509 TGAGTTGTGACATTCTGTTTTCG 57.844 39.130 0.00 0.00 0.00 3.46
3587 6525 9.911788 ATTTTGAGATGAAGATGGTGTAGTATT 57.088 29.630 0.00 0.00 0.00 1.89
3651 6595 3.060602 GACTGTCAAAGAAAGGGAGACG 58.939 50.000 2.24 0.00 32.08 4.18
3670 6619 0.332972 GCCCCCAGACTTCTCCAAAT 59.667 55.000 0.00 0.00 0.00 2.32
3703 6653 4.933505 TTTCCATTTGAACTGTGCATGA 57.066 36.364 0.00 0.00 31.05 3.07
3829 6810 1.341209 CCAACTCTTGAAACCTTGGCC 59.659 52.381 0.00 0.00 0.00 5.36
3839 6820 1.990160 AACCTTGGCCGAGTTCACCA 61.990 55.000 19.14 0.00 0.00 4.17
3987 7048 7.169591 TCGGGAAAATGGTAAAGATTGTTAGA 58.830 34.615 0.00 0.00 0.00 2.10
4036 7097 3.960571 CAGAAGGTGGAATGGATTCTGT 58.039 45.455 5.33 0.00 41.12 3.41
4037 7098 3.944015 CAGAAGGTGGAATGGATTCTGTC 59.056 47.826 5.33 0.00 41.12 3.51
4058 7119 4.062293 TCTGTGCACAAAGTGGTGTATAC 58.938 43.478 21.98 0.00 40.89 1.47
4138 7200 6.040247 CAGGGTCAACAAAGAAGGTAAAAAC 58.960 40.000 0.00 0.00 0.00 2.43
4148 7210 6.803154 AAGAAGGTAAAAACGATGAGAAGG 57.197 37.500 0.00 0.00 0.00 3.46
4196 8199 1.608025 CCTCTAAACCTTGAGCACGCA 60.608 52.381 0.00 0.00 0.00 5.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.350057 TTTTGTGGGTCGGATTGTGA 57.650 45.000 0.00 0.00 0.00 3.58
2 3 2.352617 CCATTTTGTGGGTCGGATTGTG 60.353 50.000 0.00 0.00 44.79 3.33
18 19 0.613012 GGTCCCAAGCTCAGCCATTT 60.613 55.000 0.00 0.00 0.00 2.32
42 43 5.012664 TGTCTAACATGATGGGTACAAGTGT 59.987 40.000 0.00 0.00 0.00 3.55
124 131 7.726291 TGTGAAGAAGAGGAGGTAATATAGGAG 59.274 40.741 0.00 0.00 0.00 3.69
162 172 4.222145 GGGAATATGTATAGAGGCGGTTGA 59.778 45.833 0.00 0.00 0.00 3.18
188 199 8.833231 AATCATATAGAATCACGGTAGGTTTG 57.167 34.615 0.00 0.00 0.00 2.93
189 200 9.490379 GAAATCATATAGAATCACGGTAGGTTT 57.510 33.333 0.00 0.00 0.00 3.27
249 260 9.408648 TCTTCTCTTGTCATATACAGATACACA 57.591 33.333 0.00 0.00 39.87 3.72
250 261 9.672086 GTCTTCTCTTGTCATATACAGATACAC 57.328 37.037 0.00 0.00 39.87 2.90
254 265 9.761504 CATTGTCTTCTCTTGTCATATACAGAT 57.238 33.333 0.00 0.00 39.87 2.90
255 266 8.971073 TCATTGTCTTCTCTTGTCATATACAGA 58.029 33.333 0.00 0.00 39.87 3.41
256 267 9.591792 TTCATTGTCTTCTCTTGTCATATACAG 57.408 33.333 0.00 0.00 39.87 2.74
258 269 9.809096 TCTTCATTGTCTTCTCTTGTCATATAC 57.191 33.333 0.00 0.00 0.00 1.47
261 272 7.901029 ACTCTTCATTGTCTTCTCTTGTCATA 58.099 34.615 0.00 0.00 0.00 2.15
262 273 6.767456 ACTCTTCATTGTCTTCTCTTGTCAT 58.233 36.000 0.00 0.00 0.00 3.06
263 274 6.166984 ACTCTTCATTGTCTTCTCTTGTCA 57.833 37.500 0.00 0.00 0.00 3.58
266 277 5.994054 TGGAACTCTTCATTGTCTTCTCTTG 59.006 40.000 0.00 0.00 0.00 3.02
268 279 5.815233 TGGAACTCTTCATTGTCTTCTCT 57.185 39.130 0.00 0.00 0.00 3.10
269 280 5.994668 AGTTGGAACTCTTCATTGTCTTCTC 59.005 40.000 0.00 0.00 32.86 2.87
270 281 5.934781 AGTTGGAACTCTTCATTGTCTTCT 58.065 37.500 0.00 0.00 32.86 2.85
271 282 6.706270 TGTAGTTGGAACTCTTCATTGTCTTC 59.294 38.462 0.00 0.00 40.37 2.87
272 283 6.591935 TGTAGTTGGAACTCTTCATTGTCTT 58.408 36.000 0.00 0.00 40.37 3.01
273 284 6.174720 TGTAGTTGGAACTCTTCATTGTCT 57.825 37.500 0.00 0.00 40.37 3.41
274 285 6.650807 TCATGTAGTTGGAACTCTTCATTGTC 59.349 38.462 0.00 0.00 40.37 3.18
275 286 6.533730 TCATGTAGTTGGAACTCTTCATTGT 58.466 36.000 0.00 0.00 40.37 2.71
276 287 7.414873 CCATCATGTAGTTGGAACTCTTCATTG 60.415 40.741 0.00 0.00 39.08 2.82
278 289 6.070021 TCCATCATGTAGTTGGAACTCTTCAT 60.070 38.462 0.00 0.00 41.91 2.57
279 290 5.248248 TCCATCATGTAGTTGGAACTCTTCA 59.752 40.000 0.00 0.00 41.91 3.02
280 291 5.734720 TCCATCATGTAGTTGGAACTCTTC 58.265 41.667 0.00 0.00 41.91 2.87
282 293 5.762179 TTCCATCATGTAGTTGGAACTCT 57.238 39.130 14.06 0.00 46.29 3.24
287 298 4.398988 GCATTGTTCCATCATGTAGTTGGA 59.601 41.667 0.00 0.00 42.89 3.53
288 299 4.400251 AGCATTGTTCCATCATGTAGTTGG 59.600 41.667 0.00 0.00 38.26 3.77
290 301 6.183360 CGTAAGCATTGTTCCATCATGTAGTT 60.183 38.462 0.00 0.00 0.00 2.24
291 302 5.294306 CGTAAGCATTGTTCCATCATGTAGT 59.706 40.000 0.00 0.00 0.00 2.73
292 303 5.523552 TCGTAAGCATTGTTCCATCATGTAG 59.476 40.000 0.00 0.00 37.18 2.74
349 404 0.679960 AATGTAACCAGGCCTTCCGC 60.680 55.000 0.00 0.00 37.47 5.54
350 405 1.339631 TGAATGTAACCAGGCCTTCCG 60.340 52.381 0.00 0.00 37.47 4.30
351 406 2.092323 GTGAATGTAACCAGGCCTTCC 58.908 52.381 0.00 0.00 0.00 3.46
352 407 2.749621 CTGTGAATGTAACCAGGCCTTC 59.250 50.000 0.00 0.00 0.00 3.46
353 408 2.555227 CCTGTGAATGTAACCAGGCCTT 60.555 50.000 0.00 0.00 38.19 4.35
380 850 5.126061 GTCTTTCCCATGCATCTTATTGTGT 59.874 40.000 0.00 0.00 0.00 3.72
397 867 2.798847 AGTTGAAACTACGCGTCTTTCC 59.201 45.455 26.95 18.00 37.52 3.13
406 887 8.381387 GCCTCTTAATTCTAAGTTGAAACTACG 58.619 37.037 0.00 0.00 38.57 3.51
426 907 4.285517 AGATATGTCATTCCGATGCCTCTT 59.714 41.667 0.00 0.00 33.14 2.85
449 930 2.557056 CCTGAAAGACGGACACTCACTA 59.443 50.000 0.00 0.00 34.07 2.74
491 1833 3.332034 CGGTTTTCTCCCGTTGAACTAT 58.668 45.455 0.00 0.00 40.59 2.12
509 1851 2.140717 GGAGTTTGTCGAATTCACGGT 58.859 47.619 6.22 0.00 0.00 4.83
546 1888 5.922053 AGGCTTTTGCTTCTTTTTCAGAAT 58.078 33.333 0.00 0.00 46.54 2.40
596 1947 4.641396 CACTACCAGTTCCAGAATTGTGA 58.359 43.478 3.74 0.00 0.00 3.58
607 1958 2.338500 GTACAGCAGCACTACCAGTTC 58.662 52.381 0.00 0.00 0.00 3.01
609 1960 0.243907 CGTACAGCAGCACTACCAGT 59.756 55.000 0.00 0.00 0.00 4.00
610 1961 0.243907 ACGTACAGCAGCACTACCAG 59.756 55.000 0.00 0.00 0.00 4.00
611 1962 0.038618 CACGTACAGCAGCACTACCA 60.039 55.000 0.00 0.00 0.00 3.25
612 1963 0.038526 ACACGTACAGCAGCACTACC 60.039 55.000 0.00 0.00 0.00 3.18
613 1964 1.060713 CACACGTACAGCAGCACTAC 58.939 55.000 0.00 0.00 0.00 2.73
614 1965 0.666274 GCACACGTACAGCAGCACTA 60.666 55.000 0.00 0.00 0.00 2.74
617 1968 1.955663 CAGCACACGTACAGCAGCA 60.956 57.895 8.46 0.00 0.00 4.41
619 1970 0.875908 ACACAGCACACGTACAGCAG 60.876 55.000 8.46 3.46 0.00 4.24
620 1971 1.142965 ACACAGCACACGTACAGCA 59.857 52.632 8.46 0.00 0.00 4.41
687 2045 5.230936 GTCAGCTTCAGCACTTTTTCTTTTC 59.769 40.000 0.75 0.00 45.16 2.29
692 2050 3.181497 TGTGTCAGCTTCAGCACTTTTTC 60.181 43.478 0.75 0.00 45.16 2.29
693 2051 2.754552 TGTGTCAGCTTCAGCACTTTTT 59.245 40.909 0.75 0.00 45.16 1.94
694 2052 2.368439 TGTGTCAGCTTCAGCACTTTT 58.632 42.857 0.75 0.00 45.16 2.27
695 2053 2.042686 TGTGTCAGCTTCAGCACTTT 57.957 45.000 0.75 0.00 45.16 2.66
696 2054 2.267174 ATGTGTCAGCTTCAGCACTT 57.733 45.000 0.75 0.84 45.16 3.16
697 2055 2.693069 GTATGTGTCAGCTTCAGCACT 58.307 47.619 0.75 0.00 45.16 4.40
698 2056 1.391485 CGTATGTGTCAGCTTCAGCAC 59.609 52.381 0.75 0.00 45.16 4.40
699 2057 1.000843 ACGTATGTGTCAGCTTCAGCA 59.999 47.619 0.75 0.00 45.16 4.41
705 2063 0.100682 CGCCTACGTATGTGTCAGCT 59.899 55.000 0.00 0.00 33.53 4.24
706 2064 1.480219 GCGCCTACGTATGTGTCAGC 61.480 60.000 12.11 1.57 42.83 4.26
812 2196 0.181350 GCCCGAAACCCAGATGAGAT 59.819 55.000 0.00 0.00 0.00 2.75
834 2218 2.811317 GCGCAAGTGGAGACGGAG 60.811 66.667 0.30 0.00 41.68 4.63
860 2244 3.760035 CGAGTGAGTGGGGACGGG 61.760 72.222 0.00 0.00 0.00 5.28
881 2265 1.676014 CGAGTGGGAATGGGAGTGAAC 60.676 57.143 0.00 0.00 0.00 3.18
882 2266 0.613260 CGAGTGGGAATGGGAGTGAA 59.387 55.000 0.00 0.00 0.00 3.18
883 2267 1.899437 GCGAGTGGGAATGGGAGTGA 61.899 60.000 0.00 0.00 0.00 3.41
884 2268 1.450312 GCGAGTGGGAATGGGAGTG 60.450 63.158 0.00 0.00 0.00 3.51
885 2269 1.918293 TGCGAGTGGGAATGGGAGT 60.918 57.895 0.00 0.00 0.00 3.85
886 2270 1.450312 GTGCGAGTGGGAATGGGAG 60.450 63.158 0.00 0.00 0.00 4.30
887 2271 1.899437 GAGTGCGAGTGGGAATGGGA 61.899 60.000 0.00 0.00 0.00 4.37
888 2272 1.450312 GAGTGCGAGTGGGAATGGG 60.450 63.158 0.00 0.00 0.00 4.00
889 2273 1.450312 GGAGTGCGAGTGGGAATGG 60.450 63.158 0.00 0.00 0.00 3.16
890 2274 1.450312 GGGAGTGCGAGTGGGAATG 60.450 63.158 0.00 0.00 0.00 2.67
891 2275 2.670148 GGGGAGTGCGAGTGGGAAT 61.670 63.158 0.00 0.00 0.00 3.01
892 2276 3.319198 GGGGAGTGCGAGTGGGAA 61.319 66.667 0.00 0.00 0.00 3.97
901 2285 0.542333 GGAGTAAAGAGGGGGAGTGC 59.458 60.000 0.00 0.00 0.00 4.40
997 2387 4.823419 TTGATGGTACGGCCGCGG 62.823 66.667 28.58 24.05 41.21 6.46
1063 2461 4.029186 CCCCACGACGACGACGAA 62.029 66.667 25.15 0.00 42.66 3.85
1316 2723 2.363018 GGAAAGAAGGGCCAGGGC 60.363 66.667 6.18 3.77 41.06 5.19
1339 2758 3.223157 CACAGAAAAATTGTACGGCGAC 58.777 45.455 16.62 8.31 0.00 5.19
1347 2766 2.098934 TCGCACAGCACAGAAAAATTGT 59.901 40.909 0.00 0.00 0.00 2.71
1398 2819 1.374758 GTCCCGTCCACAGCAGAAG 60.375 63.158 0.00 0.00 0.00 2.85
1427 2853 3.458189 CCAAGTTCTTAGCCTATCCACG 58.542 50.000 0.00 0.00 0.00 4.94
1455 2881 7.294720 TCCACAGATCCCCTAATTTACATACAT 59.705 37.037 0.00 0.00 0.00 2.29
1488 2918 2.378886 TCACAGGTTAGAGTCCCTCAGA 59.621 50.000 0.00 0.00 32.06 3.27
1489 2919 2.494073 GTCACAGGTTAGAGTCCCTCAG 59.506 54.545 0.00 0.00 32.06 3.35
1511 2941 5.277490 CCGTGCATTATTGTAGGACATTCAG 60.277 44.000 0.00 0.00 0.00 3.02
1534 2964 3.990318 ACAAACTGAGCAAGCTAAACC 57.010 42.857 0.00 0.00 0.00 3.27
1626 3110 4.910458 ATTACTGCTACAACCTGAACCT 57.090 40.909 0.00 0.00 0.00 3.50
1777 3317 5.845734 TGGGTAGACTAAGGACAAAGGATA 58.154 41.667 0.00 0.00 0.00 2.59
1798 3338 1.901591 AGAGCACCACACATCTTTGG 58.098 50.000 0.00 0.00 39.00 3.28
1981 3626 7.293828 TCCCATAACTTACATATCATGCCAAA 58.706 34.615 0.00 0.00 0.00 3.28
1998 3643 7.396540 AGTGAAAATCAACAGATCCCATAAC 57.603 36.000 0.00 0.00 0.00 1.89
2084 3729 6.310956 TGCATAATAAGCATTGAACAAACTGC 59.689 34.615 5.36 5.36 37.02 4.40
2132 3777 7.280876 TCAAGCATAGCTAAAGTTATCAAGGTG 59.719 37.037 0.00 0.00 38.25 4.00
2133 3778 7.338710 TCAAGCATAGCTAAAGTTATCAAGGT 58.661 34.615 0.00 0.00 38.25 3.50
2173 3833 6.913170 TCTGAATAACTGAAAACATCTTGGC 58.087 36.000 0.00 0.00 0.00 4.52
2321 3984 5.366829 TTGCAATGCTCATATGTGATAGC 57.633 39.130 6.82 7.94 32.98 2.97
2375 4038 1.826385 AAGGACAAAGGAAGGCATCG 58.174 50.000 0.00 0.00 0.00 3.84
2515 4884 9.813080 GTGAAAAATAACTGAGCTACTTAGTTG 57.187 33.333 13.27 0.00 39.89 3.16
2561 4937 5.536538 CAGAGGTAGCATAGTATCCAAGTCA 59.463 44.000 0.00 0.00 0.00 3.41
2672 5068 3.894759 ACGTAGAGCTTATGGAGTGGTA 58.105 45.455 0.00 0.00 0.00 3.25
2677 5073 7.872881 TGACTTTATACGTAGAGCTTATGGAG 58.127 38.462 0.08 0.00 0.00 3.86
2780 5381 5.163488 CCAGAGAATTGCAAAATATGGCTCA 60.163 40.000 1.71 0.00 0.00 4.26
2799 5400 4.879598 ACGAGTTAAACCAGTAACCAGAG 58.120 43.478 0.00 0.00 35.01 3.35
2806 5407 9.439500 AAGCAATAATAACGAGTTAAACCAGTA 57.561 29.630 0.00 0.00 0.00 2.74
3298 6191 1.282930 GACAAGGGAACTCGTCGTGC 61.283 60.000 0.00 0.00 42.68 5.34
3354 6249 1.535462 ACAAACAGCTATGGACGTTGC 59.465 47.619 0.00 0.00 0.00 4.17
3379 6274 7.275560 GTCATTCTATGGCCATTTTAACACAAC 59.724 37.037 26.37 8.12 0.00 3.32
3417 6326 6.256643 ACTGGTCACCCTTTAAAGACTTAA 57.743 37.500 16.98 0.00 0.00 1.85
3651 6595 0.332972 ATTTGGAGAAGTCTGGGGGC 59.667 55.000 0.00 0.00 0.00 5.80
3670 6619 7.012327 CAGTTCAAATGGAAAAGTACTGACAGA 59.988 37.037 10.08 0.00 37.23 3.41
3780 6761 9.492730 AAGGAAGATATTTCATTTATTGTGGGT 57.507 29.630 0.00 0.00 0.00 4.51
3802 6783 2.693074 GGTTTCAAGAGTTGGCAAAGGA 59.307 45.455 0.00 0.00 0.00 3.36
3829 6810 7.036220 AGAGTTTATGTAAGATGGTGAACTCG 58.964 38.462 0.00 0.00 43.79 4.18
3987 7048 3.284617 GTGGTCCCGTTGCCTATAATTT 58.715 45.455 0.00 0.00 0.00 1.82
3991 7052 2.214235 GGTGGTCCCGTTGCCTATA 58.786 57.895 0.00 0.00 0.00 1.31
4036 7097 2.700722 TACACCACTTTGTGCACAGA 57.299 45.000 20.59 15.19 39.93 3.41
4037 7098 3.120683 CGTATACACCACTTTGTGCACAG 60.121 47.826 20.59 12.15 39.93 3.66
4138 7200 2.169352 AGGTTCCACATCCTTCTCATCG 59.831 50.000 0.00 0.00 0.00 3.84
4148 7210 2.076863 CGTTCCTTGAGGTTCCACATC 58.923 52.381 0.00 0.00 36.34 3.06


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

AutoCloner maintained by Alex Coulton.