Multiple sequence alignment - TraesCS5B01G172700

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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 TraesCS5B01G172700 chr5B 100.000 4538 0 0 1 4538 317268789 317273326 0.000000e+00 8381
1 TraesCS5B01G172700 chr5B 96.324 925 34 0 3614 4538 479453227 479452303 0.000000e+00 1520
2 TraesCS5B01G172700 chr7B 88.566 2475 255 18 1115 3575 645128655 645131115 0.000000e+00 2977
3 TraesCS5B01G172700 chr3B 87.844 2542 271 23 1067 3578 792489817 792487284 0.000000e+00 2948
4 TraesCS5B01G172700 chr3B 96.324 925 34 0 3614 4538 248700241 248699317 0.000000e+00 1520
5 TraesCS5B01G172700 chr3B 96.220 926 33 2 3613 4538 490533581 490534504 0.000000e+00 1515
6 TraesCS5B01G172700 chr3B 96.022 930 36 1 3609 4538 688919215 688918287 0.000000e+00 1511
7 TraesCS5B01G172700 chr3D 88.228 2438 256 22 1128 3540 74632216 74629785 0.000000e+00 2883
8 TraesCS5B01G172700 chr3D 94.851 1573 64 7 1051 2613 268046864 268048429 0.000000e+00 2440
9 TraesCS5B01G172700 chr3D 95.648 1011 41 3 2605 3613 268049602 268050611 0.000000e+00 1620
10 TraesCS5B01G172700 chr3D 92.476 824 60 2 2791 3613 16421624 16420802 0.000000e+00 1177
11 TraesCS5B01G172700 chr3D 88.348 678 60 15 119 787 268046193 268046860 0.000000e+00 797
12 TraesCS5B01G172700 chr3D 83.596 317 32 12 15 314 16421936 16421623 3.460000e-71 279
13 TraesCS5B01G172700 chr3D 85.348 273 31 8 780 1046 377811616 377811347 1.610000e-69 274
14 TraesCS5B01G172700 chr3D 94.355 124 7 0 1 124 267984500 267984623 1.670000e-44 191
15 TraesCS5B01G172700 chr5D 87.047 2540 292 23 1067 3575 24807250 24809783 0.000000e+00 2833
16 TraesCS5B01G172700 chr6D 94.943 1305 53 7 1051 2347 444669720 444668421 0.000000e+00 2032
17 TraesCS5B01G172700 chr6D 95.451 1275 46 6 2347 3613 444668103 444666833 0.000000e+00 2023
18 TraesCS5B01G172700 chr6D 90.387 801 46 10 1 791 444670498 444669719 0.000000e+00 1024
19 TraesCS5B01G172700 chr1B 95.099 1265 59 2 1113 2374 31159818 31158554 0.000000e+00 1989
20 TraesCS5B01G172700 chr1B 92.961 895 57 6 2722 3613 31158524 31157633 0.000000e+00 1299
21 TraesCS5B01G172700 chr1B 83.271 801 87 24 16 788 31160641 31159860 0.000000e+00 693
22 TraesCS5B01G172700 chr1B 82.684 231 38 2 1065 1294 36719358 36719587 2.140000e-48 204
23 TraesCS5B01G172700 chrUn 96.324 925 34 0 3614 4538 219034287 219033363 0.000000e+00 1520
24 TraesCS5B01G172700 chr6B 96.328 926 33 1 3613 4538 647647156 647648080 0.000000e+00 1520
25 TraesCS5B01G172700 chr6B 88.561 271 24 5 779 1046 3408231 3407965 5.660000e-84 322
26 TraesCS5B01G172700 chr2B 96.324 925 34 0 3614 4538 218299290 218300214 0.000000e+00 1520
27 TraesCS5B01G172700 chr2B 81.566 396 51 16 1 380 140501169 140501558 1.590000e-79 307
28 TraesCS5B01G172700 chr2B 93.000 200 14 0 1071 1270 140502085 140502284 4.440000e-75 292
29 TraesCS5B01G172700 chr4B 96.324 925 33 1 3614 4538 144361525 144362448 0.000000e+00 1519
30 TraesCS5B01G172700 chr4B 96.216 925 35 0 3614 4538 126980368 126981292 0.000000e+00 1515
31 TraesCS5B01G172700 chr7D 78.119 2116 401 41 1441 3534 540516397 540518472 0.000000e+00 1286
32 TraesCS5B01G172700 chr7D 85.874 269 32 6 780 1045 568803251 568802986 9.610000e-72 281
33 TraesCS5B01G172700 chr1A 77.909 2114 412 36 1441 3534 16080528 16082606 0.000000e+00 1266
34 TraesCS5B01G172700 chr5A 77.684 2124 407 44 1441 3539 355170164 355168083 0.000000e+00 1234
35 TraesCS5B01G172700 chr3A 90.762 801 67 3 2791 3585 33605956 33605157 0.000000e+00 1062
36 TraesCS5B01G172700 chr3A 90.909 132 11 1 16 147 33607597 33607467 4.670000e-40 176
37 TraesCS5B01G172700 chr4A 78.440 1359 269 18 2012 3355 571306367 571305018 0.000000e+00 865
38 TraesCS5B01G172700 chr6A 87.868 272 25 5 779 1046 311138 310871 3.410000e-81 313
39 TraesCS5B01G172700 chr6A 87.361 269 29 5 780 1046 459050315 459050580 2.050000e-78 303
40 TraesCS5B01G172700 chr2D 86.617 269 31 5 780 1045 380558228 380558494 4.440000e-75 292
41 TraesCS5B01G172700 chr1D 86.397 272 27 10 780 1046 298892903 298893169 5.740000e-74 289
42 TraesCS5B01G172700 chr4D 85.926 270 30 8 780 1045 64907525 64907790 9.610000e-72 281
43 TraesCS5B01G172700 chr4D 84.559 272 35 7 779 1046 130066788 130066520 3.480000e-66 263


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 TraesCS5B01G172700 chr5B 317268789 317273326 4537 False 8381.0 8381 100.000000 1 4538 1 chr5B.!!$F1 4537
1 TraesCS5B01G172700 chr5B 479452303 479453227 924 True 1520.0 1520 96.324000 3614 4538 1 chr5B.!!$R1 924
2 TraesCS5B01G172700 chr7B 645128655 645131115 2460 False 2977.0 2977 88.566000 1115 3575 1 chr7B.!!$F1 2460
3 TraesCS5B01G172700 chr3B 792487284 792489817 2533 True 2948.0 2948 87.844000 1067 3578 1 chr3B.!!$R3 2511
4 TraesCS5B01G172700 chr3B 248699317 248700241 924 True 1520.0 1520 96.324000 3614 4538 1 chr3B.!!$R1 924
5 TraesCS5B01G172700 chr3B 490533581 490534504 923 False 1515.0 1515 96.220000 3613 4538 1 chr3B.!!$F1 925
6 TraesCS5B01G172700 chr3B 688918287 688919215 928 True 1511.0 1511 96.022000 3609 4538 1 chr3B.!!$R2 929
7 TraesCS5B01G172700 chr3D 74629785 74632216 2431 True 2883.0 2883 88.228000 1128 3540 1 chr3D.!!$R1 2412
8 TraesCS5B01G172700 chr3D 268046193 268050611 4418 False 1619.0 2440 92.949000 119 3613 3 chr3D.!!$F2 3494
9 TraesCS5B01G172700 chr3D 16420802 16421936 1134 True 728.0 1177 88.036000 15 3613 2 chr3D.!!$R3 3598
10 TraesCS5B01G172700 chr5D 24807250 24809783 2533 False 2833.0 2833 87.047000 1067 3575 1 chr5D.!!$F1 2508
11 TraesCS5B01G172700 chr6D 444666833 444670498 3665 True 1693.0 2032 93.593667 1 3613 3 chr6D.!!$R1 3612
12 TraesCS5B01G172700 chr1B 31157633 31160641 3008 True 1327.0 1989 90.443667 16 3613 3 chr1B.!!$R1 3597
13 TraesCS5B01G172700 chrUn 219033363 219034287 924 True 1520.0 1520 96.324000 3614 4538 1 chrUn.!!$R1 924
14 TraesCS5B01G172700 chr6B 647647156 647648080 924 False 1520.0 1520 96.328000 3613 4538 1 chr6B.!!$F1 925
15 TraesCS5B01G172700 chr2B 218299290 218300214 924 False 1520.0 1520 96.324000 3614 4538 1 chr2B.!!$F1 924
16 TraesCS5B01G172700 chr2B 140501169 140502284 1115 False 299.5 307 87.283000 1 1270 2 chr2B.!!$F2 1269
17 TraesCS5B01G172700 chr4B 144361525 144362448 923 False 1519.0 1519 96.324000 3614 4538 1 chr4B.!!$F2 924
18 TraesCS5B01G172700 chr4B 126980368 126981292 924 False 1515.0 1515 96.216000 3614 4538 1 chr4B.!!$F1 924
19 TraesCS5B01G172700 chr7D 540516397 540518472 2075 False 1286.0 1286 78.119000 1441 3534 1 chr7D.!!$F1 2093
20 TraesCS5B01G172700 chr1A 16080528 16082606 2078 False 1266.0 1266 77.909000 1441 3534 1 chr1A.!!$F1 2093
21 TraesCS5B01G172700 chr5A 355168083 355170164 2081 True 1234.0 1234 77.684000 1441 3539 1 chr5A.!!$R1 2098
22 TraesCS5B01G172700 chr3A 33605157 33607597 2440 True 619.0 1062 90.835500 16 3585 2 chr3A.!!$R1 3569
23 TraesCS5B01G172700 chr4A 571305018 571306367 1349 True 865.0 865 78.440000 2012 3355 1 chr4A.!!$R1 1343

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
870 2371 0.196118 AAGGTTCCCCAAGAGGAGGA 59.804 55.0 0.00 0.0 37.20 3.71 F
1639 3172 0.030638 TTTGCGCAAGAGAAGGTTGC 59.969 50.0 23.68 0.0 45.68 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1754 3287 2.057137 TACTTGCCATCATCTTGCCC 57.943 50.000 0.0 0.0 0.0 5.36 R
3617 6685 1.001633 AGATACGCCGGTTTTGACACT 59.998 47.619 1.9 0.0 0.0 3.55 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
20 22 1.420430 AGGAGAAACGTGGACAGGAA 58.580 50.000 0.00 0.00 0.00 3.36
39 42 5.047164 CAGGAAAATCCATTGAACATCACCA 60.047 40.000 0.00 0.00 39.61 4.17
69 72 6.183360 GCCATTTGGTAAGCTACATGTTACAT 60.183 38.462 2.30 0.00 37.57 2.29
134 137 4.235939 TGTTGGTTTTGGATGATGAACG 57.764 40.909 0.00 0.00 0.00 3.95
279 1631 2.567985 ACCCAAACAACAGAACCTACG 58.432 47.619 0.00 0.00 0.00 3.51
282 1634 3.379057 CCCAAACAACAGAACCTACGTTT 59.621 43.478 0.00 0.00 30.30 3.60
285 1637 5.524646 CCAAACAACAGAACCTACGTTTCTA 59.475 40.000 0.00 0.00 30.30 2.10
328 1697 8.657074 AAAATAACTAGTTGAAAAACTTGGGC 57.343 30.769 18.56 0.00 34.37 5.36
329 1698 6.969993 ATAACTAGTTGAAAAACTTGGGCA 57.030 33.333 18.56 0.00 34.37 5.36
330 1699 4.649088 ACTAGTTGAAAAACTTGGGCAC 57.351 40.909 0.00 0.00 34.37 5.01
331 1700 4.020543 ACTAGTTGAAAAACTTGGGCACA 58.979 39.130 0.00 0.00 34.37 4.57
332 1701 3.971245 AGTTGAAAAACTTGGGCACAA 57.029 38.095 0.00 0.00 34.87 3.33
333 1702 4.278975 AGTTGAAAAACTTGGGCACAAA 57.721 36.364 1.48 0.00 35.89 2.83
334 1703 4.646572 AGTTGAAAAACTTGGGCACAAAA 58.353 34.783 1.48 0.00 35.89 2.44
335 1704 5.066593 AGTTGAAAAACTTGGGCACAAAAA 58.933 33.333 1.48 0.00 35.89 1.94
392 1874 7.645402 TCAAGATATGAATGCTAACATTGCTG 58.355 34.615 0.00 0.00 46.59 4.41
425 1907 3.508012 ACAGGTAGCCGCTTCTATATGAG 59.492 47.826 0.00 0.00 0.00 2.90
434 1916 5.237344 GCCGCTTCTATATGAGTTTCATGTT 59.763 40.000 1.94 0.00 37.70 2.71
590 2072 5.817816 CCTATTCAAGTACCTGGATGTGAAC 59.182 44.000 0.00 0.00 0.00 3.18
592 2074 6.620877 ATTCAAGTACCTGGATGTGAACTA 57.379 37.500 0.00 0.00 0.00 2.24
619 2102 1.475213 GGGACAAGACCGGATTCATCC 60.475 57.143 9.46 9.45 43.65 3.51
696 2180 7.026631 TGTTAGAACCATTTTCAGAACACTG 57.973 36.000 0.00 0.00 0.00 3.66
717 2218 8.426489 ACACTGTTGACTATTTTCCTTAGTACA 58.574 33.333 0.00 0.00 30.15 2.90
718 2219 9.436957 CACTGTTGACTATTTTCCTTAGTACAT 57.563 33.333 0.00 0.00 30.15 2.29
719 2220 9.654663 ACTGTTGACTATTTTCCTTAGTACATC 57.345 33.333 0.00 0.00 30.15 3.06
720 2221 9.877178 CTGTTGACTATTTTCCTTAGTACATCT 57.123 33.333 0.00 0.00 30.15 2.90
746 2247 2.725811 TGCTGGTGCATTCGGAAAA 58.274 47.368 0.00 0.00 45.31 2.29
803 2304 2.859165 TTACCTGGAAGACTGCAAGG 57.141 50.000 1.65 1.65 39.30 3.61
823 2324 3.333029 GCTTATGCCCCACAACATTTT 57.667 42.857 0.00 0.00 0.00 1.82
824 2325 4.464069 GCTTATGCCCCACAACATTTTA 57.536 40.909 0.00 0.00 0.00 1.52
825 2326 5.022282 GCTTATGCCCCACAACATTTTAT 57.978 39.130 0.00 0.00 0.00 1.40
826 2327 5.427378 GCTTATGCCCCACAACATTTTATT 58.573 37.500 0.00 0.00 0.00 1.40
827 2328 6.578023 GCTTATGCCCCACAACATTTTATTA 58.422 36.000 0.00 0.00 0.00 0.98
828 2329 7.044798 GCTTATGCCCCACAACATTTTATTAA 58.955 34.615 0.00 0.00 0.00 1.40
829 2330 7.550906 GCTTATGCCCCACAACATTTTATTAAA 59.449 33.333 0.00 0.00 0.00 1.52
830 2331 9.442047 CTTATGCCCCACAACATTTTATTAAAA 57.558 29.630 4.16 4.16 34.41 1.52
831 2332 9.793259 TTATGCCCCACAACATTTTATTAAAAA 57.207 25.926 5.73 0.00 38.87 1.94
857 2358 9.758651 AAATAACAAGGTACAAATGAAAGGTTC 57.241 29.630 0.00 0.00 0.00 3.62
858 2359 5.784578 ACAAGGTACAAATGAAAGGTTCC 57.215 39.130 0.00 0.00 0.00 3.62
859 2360 4.587262 ACAAGGTACAAATGAAAGGTTCCC 59.413 41.667 0.00 0.00 0.00 3.97
860 2361 3.774734 AGGTACAAATGAAAGGTTCCCC 58.225 45.455 0.00 0.00 0.00 4.81
861 2362 3.141272 AGGTACAAATGAAAGGTTCCCCA 59.859 43.478 0.00 0.00 0.00 4.96
862 2363 3.898741 GGTACAAATGAAAGGTTCCCCAA 59.101 43.478 0.00 0.00 0.00 4.12
863 2364 4.021456 GGTACAAATGAAAGGTTCCCCAAG 60.021 45.833 0.00 0.00 0.00 3.61
864 2365 3.922375 ACAAATGAAAGGTTCCCCAAGA 58.078 40.909 0.00 0.00 0.00 3.02
865 2366 3.897505 ACAAATGAAAGGTTCCCCAAGAG 59.102 43.478 0.00 0.00 0.00 2.85
866 2367 2.907458 ATGAAAGGTTCCCCAAGAGG 57.093 50.000 0.00 0.00 0.00 3.69
867 2368 1.827792 TGAAAGGTTCCCCAAGAGGA 58.172 50.000 0.00 0.00 38.24 3.71
868 2369 1.705186 TGAAAGGTTCCCCAAGAGGAG 59.295 52.381 0.00 0.00 37.20 3.69
869 2370 1.004862 GAAAGGTTCCCCAAGAGGAGG 59.995 57.143 0.00 0.00 37.20 4.30
870 2371 0.196118 AAGGTTCCCCAAGAGGAGGA 59.804 55.000 0.00 0.00 37.20 3.71
871 2372 0.196118 AGGTTCCCCAAGAGGAGGAA 59.804 55.000 0.00 0.00 40.06 3.36
873 2374 3.589232 TTCCCCAAGAGGAGGAACA 57.411 52.632 0.00 0.00 38.52 3.18
874 2375 1.827792 TTCCCCAAGAGGAGGAACAA 58.172 50.000 0.00 0.00 38.52 2.83
875 2376 1.827792 TCCCCAAGAGGAGGAACAAA 58.172 50.000 0.00 0.00 38.24 2.83
876 2377 1.705186 TCCCCAAGAGGAGGAACAAAG 59.295 52.381 0.00 0.00 38.24 2.77
877 2378 1.705186 CCCCAAGAGGAGGAACAAAGA 59.295 52.381 0.00 0.00 38.24 2.52
878 2379 2.108250 CCCCAAGAGGAGGAACAAAGAA 59.892 50.000 0.00 0.00 38.24 2.52
879 2380 3.436470 CCCCAAGAGGAGGAACAAAGAAA 60.436 47.826 0.00 0.00 38.24 2.52
880 2381 3.570125 CCCAAGAGGAGGAACAAAGAAAC 59.430 47.826 0.00 0.00 38.24 2.78
881 2382 4.207165 CCAAGAGGAGGAACAAAGAAACA 58.793 43.478 0.00 0.00 36.89 2.83
882 2383 4.276926 CCAAGAGGAGGAACAAAGAAACAG 59.723 45.833 0.00 0.00 36.89 3.16
883 2384 4.092116 AGAGGAGGAACAAAGAAACAGG 57.908 45.455 0.00 0.00 0.00 4.00
884 2385 3.716872 AGAGGAGGAACAAAGAAACAGGA 59.283 43.478 0.00 0.00 0.00 3.86
885 2386 4.166144 AGAGGAGGAACAAAGAAACAGGAA 59.834 41.667 0.00 0.00 0.00 3.36
886 2387 4.867086 AGGAGGAACAAAGAAACAGGAAA 58.133 39.130 0.00 0.00 0.00 3.13
887 2388 5.269189 AGGAGGAACAAAGAAACAGGAAAA 58.731 37.500 0.00 0.00 0.00 2.29
888 2389 5.719563 AGGAGGAACAAAGAAACAGGAAAAA 59.280 36.000 0.00 0.00 0.00 1.94
979 2480 9.732130 AAAGAAAGAGGATACATATAAGATGGC 57.268 33.333 0.00 0.00 41.41 4.40
980 2481 7.856415 AGAAAGAGGATACATATAAGATGGCC 58.144 38.462 0.00 0.00 41.41 5.36
981 2482 6.567602 AAGAGGATACATATAAGATGGCCC 57.432 41.667 0.00 0.00 41.41 5.80
982 2483 5.859429 AGAGGATACATATAAGATGGCCCT 58.141 41.667 0.00 0.00 41.41 5.19
983 2484 5.902431 AGAGGATACATATAAGATGGCCCTC 59.098 44.000 0.00 0.00 41.41 4.30
984 2485 5.603750 AGGATACATATAAGATGGCCCTCA 58.396 41.667 10.92 0.00 41.41 3.86
985 2486 6.032039 AGGATACATATAAGATGGCCCTCAA 58.968 40.000 10.92 0.00 41.41 3.02
986 2487 6.157645 AGGATACATATAAGATGGCCCTCAAG 59.842 42.308 10.92 0.00 41.41 3.02
987 2488 4.647564 ACATATAAGATGGCCCTCAAGG 57.352 45.455 10.92 0.00 39.47 3.61
997 2498 3.180282 CCTCAAGGGGGCAGGAAA 58.820 61.111 0.00 0.00 0.00 3.13
998 2499 1.699752 CCTCAAGGGGGCAGGAAAT 59.300 57.895 0.00 0.00 0.00 2.17
999 2500 0.396278 CCTCAAGGGGGCAGGAAATC 60.396 60.000 0.00 0.00 0.00 2.17
1000 2501 0.332632 CTCAAGGGGGCAGGAAATCA 59.667 55.000 0.00 0.00 0.00 2.57
1001 2502 0.783206 TCAAGGGGGCAGGAAATCAA 59.217 50.000 0.00 0.00 0.00 2.57
1002 2503 1.362237 TCAAGGGGGCAGGAAATCAAT 59.638 47.619 0.00 0.00 0.00 2.57
1003 2504 1.758862 CAAGGGGGCAGGAAATCAATC 59.241 52.381 0.00 0.00 0.00 2.67
1004 2505 0.262876 AGGGGGCAGGAAATCAATCC 59.737 55.000 0.00 0.00 39.96 3.01
1005 2506 0.032217 GGGGGCAGGAAATCAATCCA 60.032 55.000 0.00 0.00 42.27 3.41
1006 2507 1.413517 GGGGGCAGGAAATCAATCCAT 60.414 52.381 0.00 0.00 42.27 3.41
1007 2508 2.401568 GGGGCAGGAAATCAATCCATT 58.598 47.619 0.00 0.00 42.27 3.16
1008 2509 2.773661 GGGGCAGGAAATCAATCCATTT 59.226 45.455 0.00 0.00 42.27 2.32
1009 2510 3.432608 GGGGCAGGAAATCAATCCATTTG 60.433 47.826 0.00 0.00 42.27 2.32
1020 2521 5.028549 TCAATCCATTTGAGTAGAGCCTC 57.971 43.478 0.00 0.00 39.44 4.70
1021 2522 4.133078 CAATCCATTTGAGTAGAGCCTCC 58.867 47.826 0.00 0.00 37.53 4.30
1022 2523 3.121929 TCCATTTGAGTAGAGCCTCCT 57.878 47.619 0.00 0.00 0.00 3.69
1023 2524 3.454858 TCCATTTGAGTAGAGCCTCCTT 58.545 45.455 0.00 0.00 0.00 3.36
1024 2525 3.198635 TCCATTTGAGTAGAGCCTCCTTG 59.801 47.826 0.00 0.00 0.00 3.61
1025 2526 3.054802 CCATTTGAGTAGAGCCTCCTTGT 60.055 47.826 0.00 0.00 0.00 3.16
1026 2527 4.162320 CCATTTGAGTAGAGCCTCCTTGTA 59.838 45.833 0.00 0.00 0.00 2.41
1027 2528 5.163258 CCATTTGAGTAGAGCCTCCTTGTAT 60.163 44.000 0.00 0.00 0.00 2.29
1028 2529 5.599999 TTTGAGTAGAGCCTCCTTGTATC 57.400 43.478 0.00 0.00 0.00 2.24
1029 2530 4.528076 TGAGTAGAGCCTCCTTGTATCT 57.472 45.455 0.00 0.00 0.00 1.98
1030 2531 4.211125 TGAGTAGAGCCTCCTTGTATCTG 58.789 47.826 0.00 0.00 0.00 2.90
1031 2532 3.571590 AGTAGAGCCTCCTTGTATCTGG 58.428 50.000 0.00 0.00 0.00 3.86
1032 2533 2.559381 AGAGCCTCCTTGTATCTGGT 57.441 50.000 0.00 0.00 0.00 4.00
1033 2534 2.393646 AGAGCCTCCTTGTATCTGGTC 58.606 52.381 0.00 0.00 0.00 4.02
1034 2535 2.023501 AGAGCCTCCTTGTATCTGGTCT 60.024 50.000 0.00 0.00 0.00 3.85
1035 2536 2.769095 GAGCCTCCTTGTATCTGGTCTT 59.231 50.000 0.00 0.00 0.00 3.01
1036 2537 2.503356 AGCCTCCTTGTATCTGGTCTTG 59.497 50.000 0.00 0.00 0.00 3.02
1037 2538 2.501723 GCCTCCTTGTATCTGGTCTTGA 59.498 50.000 0.00 0.00 0.00 3.02
1038 2539 3.135530 GCCTCCTTGTATCTGGTCTTGAT 59.864 47.826 0.00 0.00 0.00 2.57
1039 2540 4.742138 GCCTCCTTGTATCTGGTCTTGATC 60.742 50.000 0.00 0.00 0.00 2.92
1040 2541 4.202305 CCTCCTTGTATCTGGTCTTGATCC 60.202 50.000 0.00 0.00 0.00 3.36
1041 2542 4.361783 TCCTTGTATCTGGTCTTGATCCA 58.638 43.478 0.00 0.00 0.00 3.41
1069 2581 5.581126 TTTTGATTGTGTTGTTGCTCTCT 57.419 34.783 0.00 0.00 0.00 3.10
1091 2603 7.657761 TCTCTTGAAAAGCTAACTCTTAGTTGG 59.342 37.037 2.59 0.91 45.70 3.77
1104 2616 2.122783 TAGTTGGCCCTGCATGTAAC 57.877 50.000 0.00 0.00 0.00 2.50
1106 2618 0.243636 GTTGGCCCTGCATGTAACAC 59.756 55.000 0.00 0.00 0.00 3.32
1110 2622 1.133792 GGCCCTGCATGTAACACCTAT 60.134 52.381 0.00 0.00 0.00 2.57
1262 2776 4.563337 ACTCATGTTCATATGTGCATGC 57.437 40.909 24.14 11.82 38.72 4.06
1480 3013 5.623368 GCCTGAGTATGATGATAGCCTACAC 60.623 48.000 0.00 0.00 0.00 2.90
1483 3016 4.752063 AGTATGATGATAGCCTACACCCA 58.248 43.478 0.00 0.00 0.00 4.51
1639 3172 0.030638 TTTGCGCAAGAGAAGGTTGC 59.969 50.000 23.68 0.00 45.68 4.17
1685 3218 5.178096 TGGCCAAGATACTCAAGAAATGA 57.822 39.130 0.61 0.00 36.38 2.57
1754 3287 3.007290 TGAGGCTATGATCGGATTGAAGG 59.993 47.826 0.00 0.00 0.00 3.46
1781 3314 3.713248 AGATGATGGCAAGTATGAGGTCA 59.287 43.478 0.00 0.00 0.00 4.02
1836 3370 7.397476 ACTTATCTCACCAAGTAAGAGACATCA 59.603 37.037 0.00 0.00 40.83 3.07
1926 3460 4.332268 GCTTGGCACATCAAAAACTTTTCA 59.668 37.500 0.00 0.00 39.30 2.69
1947 3481 8.902540 TTTCACTTGCTTAGTATTGAGAAAGA 57.097 30.769 4.91 0.00 34.56 2.52
1991 3525 3.118542 ACGAAACGTGACTTACAGAACC 58.881 45.455 0.00 0.00 39.18 3.62
2310 3849 6.913132 GTCAAATGAGAAGATTGCATCATCAG 59.087 38.462 1.40 0.00 31.31 2.90
2532 4393 2.300956 TTTATGGCATGTGTGTGGGT 57.699 45.000 10.98 0.00 0.00 4.51
2580 4444 6.780457 ATCAAGGTGGTCAATAATTTCTGG 57.220 37.500 0.00 0.00 0.00 3.86
2614 5659 8.827832 TTGAGGATAATGAATGGTTGAAAGAT 57.172 30.769 0.00 0.00 0.00 2.40
2731 5779 2.286713 TGCATTTTTCCGACACTTCACG 60.287 45.455 0.00 0.00 0.00 4.35
2953 6002 3.143728 AGGGACCGTTGTCATGTAAAAC 58.856 45.455 0.00 0.00 43.65 2.43
2991 6040 0.460284 ATGTCCGAACCACGAGCATC 60.460 55.000 0.00 0.00 45.77 3.91
3038 6087 5.747951 GTAGTCCGCTACAACACTAGTAT 57.252 43.478 0.00 0.00 45.18 2.12
3633 6701 1.153329 TCAGTGTCAAAACCGGCGT 60.153 52.632 6.01 0.00 0.00 5.68
3761 6829 7.010339 ACCCTACTCCTGCTTGATTAATATC 57.990 40.000 0.00 0.00 0.00 1.63
3856 6924 5.640357 GGTATGATTGTTGTTCGTCCTACAA 59.360 40.000 6.57 6.57 35.25 2.41
3872 6940 1.612676 ACAAACTAAAACCCTCCGGC 58.387 50.000 0.00 0.00 0.00 6.13
3917 6985 6.070938 GGTTAGGGTTACACAGAGTCAGTTAT 60.071 42.308 0.00 0.00 0.00 1.89
3965 7033 2.629656 CCAAGCTTGCCTTCCACGG 61.630 63.158 21.43 0.00 0.00 4.94
3976 7044 1.318576 CTTCCACGGCAAGGAAAGTT 58.681 50.000 8.72 0.00 44.07 2.66
4030 7098 6.897966 TCTTGTATCTTCATAGTCCAGGAGTT 59.102 38.462 0.79 0.00 0.00 3.01
4115 7183 2.290260 TGAACCAGGCTTCAATGACGAT 60.290 45.455 0.00 0.00 0.00 3.73
4183 7251 6.072175 CCTCCTCCGAATACTTCATAGAAGAG 60.072 46.154 13.23 0.00 0.00 2.85
4212 7280 3.055530 CACAAGGATAGTGTCTGGCTCTT 60.056 47.826 0.00 0.00 32.44 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 22 5.066893 CGAGATGGTGATGTTCAATGGATTT 59.933 40.000 0.00 0.00 0.00 2.17
39 42 2.717639 AGCTTACCAAATGGCGAGAT 57.282 45.000 0.00 0.00 39.32 2.75
69 72 9.877178 TCTTGCTTACAACAATAAAAAGGAAAA 57.123 25.926 0.00 0.00 29.01 2.29
84 87 5.125417 GCCATACAAAGGATCTTGCTTACAA 59.875 40.000 0.00 0.00 0.00 2.41
87 90 4.207165 GGCCATACAAAGGATCTTGCTTA 58.793 43.478 0.00 0.00 0.00 3.09
220 1570 2.110011 ACTAAGTTGTTCCAGGGGCAAT 59.890 45.455 0.90 0.00 0.00 3.56
221 1571 1.497286 ACTAAGTTGTTCCAGGGGCAA 59.503 47.619 0.00 0.00 0.00 4.52
333 1702 2.114616 TGGATGCCACACAACCTTTTT 58.885 42.857 0.00 0.00 41.72 1.94
334 1703 1.786937 TGGATGCCACACAACCTTTT 58.213 45.000 0.00 0.00 41.72 2.27
335 1704 1.786937 TTGGATGCCACACAACCTTT 58.213 45.000 0.00 0.00 41.72 3.11
404 1886 3.508012 ACTCATATAGAAGCGGCTACCTG 59.492 47.826 1.35 0.00 0.00 4.00
425 1907 3.632145 AGACCAGACAACCAACATGAAAC 59.368 43.478 0.00 0.00 0.00 2.78
434 1916 3.714798 AGTTTCCTTAGACCAGACAACCA 59.285 43.478 0.00 0.00 0.00 3.67
590 2072 2.346803 CGGTCTTGTCCCAACATGTAG 58.653 52.381 0.00 0.00 34.73 2.74
592 2074 0.250727 CCGGTCTTGTCCCAACATGT 60.251 55.000 0.00 0.00 34.73 3.21
619 2102 5.484173 AGTCACACACAATTGTACAGTTG 57.516 39.130 24.70 24.70 33.30 3.16
731 2232 4.280677 AGAGAAAATTTTCCGAATGCACCA 59.719 37.500 24.01 0.00 37.92 4.17
785 2286 0.324943 GCCTTGCAGTCTTCCAGGTA 59.675 55.000 0.57 0.00 0.00 3.08
790 2291 1.403323 GCATAAGCCTTGCAGTCTTCC 59.597 52.381 1.28 0.00 39.90 3.46
803 2304 3.333029 AAAATGTTGTGGGGCATAAGC 57.667 42.857 0.00 0.00 41.10 3.09
804 2305 9.442047 TTTTAATAAAATGTTGTGGGGCATAAG 57.558 29.630 0.00 0.00 0.00 1.73
805 2306 9.793259 TTTTTAATAAAATGTTGTGGGGCATAA 57.207 25.926 0.00 0.00 0.00 1.90
831 2332 9.758651 GAACCTTTCATTTGTACCTTGTTATTT 57.241 29.630 0.00 0.00 0.00 1.40
832 2333 8.364894 GGAACCTTTCATTTGTACCTTGTTATT 58.635 33.333 0.00 0.00 0.00 1.40
833 2334 7.892609 GGAACCTTTCATTTGTACCTTGTTAT 58.107 34.615 0.00 0.00 0.00 1.89
834 2335 7.279750 GGAACCTTTCATTTGTACCTTGTTA 57.720 36.000 0.00 0.00 0.00 2.41
835 2336 6.156748 GGAACCTTTCATTTGTACCTTGTT 57.843 37.500 0.00 0.00 0.00 2.83
836 2337 5.784578 GGAACCTTTCATTTGTACCTTGT 57.215 39.130 0.00 0.00 0.00 3.16
854 2355 3.959433 GTTCCTCCTCTTGGGGAAC 57.041 57.895 8.13 8.13 46.34 3.62
855 2356 1.827792 TTGTTCCTCCTCTTGGGGAA 58.172 50.000 0.00 0.00 39.06 3.97
856 2357 1.705186 CTTTGTTCCTCCTCTTGGGGA 59.295 52.381 0.00 0.00 35.23 4.81
857 2358 1.705186 TCTTTGTTCCTCCTCTTGGGG 59.295 52.381 0.00 0.00 35.33 4.96
858 2359 3.508845 TTCTTTGTTCCTCCTCTTGGG 57.491 47.619 0.00 0.00 0.00 4.12
859 2360 4.207165 TGTTTCTTTGTTCCTCCTCTTGG 58.793 43.478 0.00 0.00 0.00 3.61
860 2361 4.276926 CCTGTTTCTTTGTTCCTCCTCTTG 59.723 45.833 0.00 0.00 0.00 3.02
861 2362 4.166144 TCCTGTTTCTTTGTTCCTCCTCTT 59.834 41.667 0.00 0.00 0.00 2.85
862 2363 3.716872 TCCTGTTTCTTTGTTCCTCCTCT 59.283 43.478 0.00 0.00 0.00 3.69
863 2364 4.086706 TCCTGTTTCTTTGTTCCTCCTC 57.913 45.455 0.00 0.00 0.00 3.71
864 2365 4.519906 TTCCTGTTTCTTTGTTCCTCCT 57.480 40.909 0.00 0.00 0.00 3.69
865 2366 5.592104 TTTTCCTGTTTCTTTGTTCCTCC 57.408 39.130 0.00 0.00 0.00 4.30
953 2454 9.732130 GCCATCTTATATGTATCCTCTTTCTTT 57.268 33.333 0.00 0.00 0.00 2.52
954 2455 8.325046 GGCCATCTTATATGTATCCTCTTTCTT 58.675 37.037 0.00 0.00 0.00 2.52
955 2456 7.092668 GGGCCATCTTATATGTATCCTCTTTCT 60.093 40.741 4.39 0.00 0.00 2.52
956 2457 7.051000 GGGCCATCTTATATGTATCCTCTTTC 58.949 42.308 4.39 0.00 0.00 2.62
957 2458 6.737608 AGGGCCATCTTATATGTATCCTCTTT 59.262 38.462 6.18 0.00 0.00 2.52
958 2459 6.275461 AGGGCCATCTTATATGTATCCTCTT 58.725 40.000 6.18 0.00 0.00 2.85
959 2460 5.859429 AGGGCCATCTTATATGTATCCTCT 58.141 41.667 6.18 0.00 0.00 3.69
960 2461 5.663106 TGAGGGCCATCTTATATGTATCCTC 59.337 44.000 19.75 3.31 37.97 3.71
961 2462 5.603750 TGAGGGCCATCTTATATGTATCCT 58.396 41.667 19.75 0.00 0.00 3.24
962 2463 5.957771 TGAGGGCCATCTTATATGTATCC 57.042 43.478 19.75 0.00 0.00 2.59
963 2464 6.352516 CCTTGAGGGCCATCTTATATGTATC 58.647 44.000 19.75 0.00 0.00 2.24
964 2465 6.319048 CCTTGAGGGCCATCTTATATGTAT 57.681 41.667 19.75 0.00 0.00 2.29
965 2466 5.762179 CCTTGAGGGCCATCTTATATGTA 57.238 43.478 19.75 0.00 0.00 2.29
966 2467 4.647564 CCTTGAGGGCCATCTTATATGT 57.352 45.455 19.75 0.00 0.00 2.29
980 2481 0.396278 GATTTCCTGCCCCCTTGAGG 60.396 60.000 0.00 0.00 0.00 3.86
981 2482 0.332632 TGATTTCCTGCCCCCTTGAG 59.667 55.000 0.00 0.00 0.00 3.02
982 2483 0.783206 TTGATTTCCTGCCCCCTTGA 59.217 50.000 0.00 0.00 0.00 3.02
983 2484 1.758862 GATTGATTTCCTGCCCCCTTG 59.241 52.381 0.00 0.00 0.00 3.61
984 2485 1.343377 GGATTGATTTCCTGCCCCCTT 60.343 52.381 0.00 0.00 32.68 3.95
985 2486 0.262876 GGATTGATTTCCTGCCCCCT 59.737 55.000 0.00 0.00 32.68 4.79
986 2487 0.032217 TGGATTGATTTCCTGCCCCC 60.032 55.000 0.00 0.00 36.68 5.40
987 2488 2.092598 ATGGATTGATTTCCTGCCCC 57.907 50.000 0.00 0.00 36.68 5.80
988 2489 3.451902 TCAAATGGATTGATTTCCTGCCC 59.548 43.478 0.00 0.00 43.08 5.36
989 2490 4.161001 ACTCAAATGGATTGATTTCCTGCC 59.839 41.667 0.00 0.00 46.62 4.85
990 2491 5.334724 ACTCAAATGGATTGATTTCCTGC 57.665 39.130 0.00 0.00 46.62 4.85
991 2492 7.468357 GCTCTACTCAAATGGATTGATTTCCTG 60.468 40.741 0.00 0.00 46.62 3.86
992 2493 6.545298 GCTCTACTCAAATGGATTGATTTCCT 59.455 38.462 0.00 0.00 46.62 3.36
993 2494 6.238869 GGCTCTACTCAAATGGATTGATTTCC 60.239 42.308 0.00 0.00 46.62 3.13
994 2495 6.545298 AGGCTCTACTCAAATGGATTGATTTC 59.455 38.462 0.00 0.00 46.62 2.17
995 2496 6.430007 AGGCTCTACTCAAATGGATTGATTT 58.570 36.000 0.00 0.00 46.62 2.17
996 2497 6.011122 AGGCTCTACTCAAATGGATTGATT 57.989 37.500 0.00 0.00 46.62 2.57
997 2498 5.455899 GGAGGCTCTACTCAAATGGATTGAT 60.456 44.000 15.23 0.00 46.62 2.57
998 2499 4.141620 GGAGGCTCTACTCAAATGGATTGA 60.142 45.833 15.23 0.00 45.71 2.57
999 2500 4.133078 GGAGGCTCTACTCAAATGGATTG 58.867 47.826 15.23 0.00 39.27 2.67
1000 2501 4.043596 AGGAGGCTCTACTCAAATGGATT 58.956 43.478 15.23 0.00 39.27 3.01
1001 2502 3.663198 AGGAGGCTCTACTCAAATGGAT 58.337 45.455 15.23 0.00 39.27 3.41
1002 2503 3.121929 AGGAGGCTCTACTCAAATGGA 57.878 47.619 15.23 0.00 39.27 3.41
1003 2504 3.054802 ACAAGGAGGCTCTACTCAAATGG 60.055 47.826 15.23 0.00 39.27 3.16
1004 2505 4.213564 ACAAGGAGGCTCTACTCAAATG 57.786 45.455 15.23 1.99 39.27 2.32
1005 2506 5.902431 AGATACAAGGAGGCTCTACTCAAAT 59.098 40.000 15.23 0.11 39.27 2.32
1006 2507 5.127845 CAGATACAAGGAGGCTCTACTCAAA 59.872 44.000 15.23 0.00 39.27 2.69
1007 2508 4.646945 CAGATACAAGGAGGCTCTACTCAA 59.353 45.833 15.23 0.00 39.27 3.02
1008 2509 4.211125 CAGATACAAGGAGGCTCTACTCA 58.789 47.826 15.23 0.00 39.27 3.41
1009 2510 3.572255 CCAGATACAAGGAGGCTCTACTC 59.428 52.174 15.23 0.00 36.76 2.59
1010 2511 3.052490 ACCAGATACAAGGAGGCTCTACT 60.052 47.826 15.23 0.38 0.00 2.57
1011 2512 3.301274 ACCAGATACAAGGAGGCTCTAC 58.699 50.000 15.23 0.00 0.00 2.59
1012 2513 3.205507 AGACCAGATACAAGGAGGCTCTA 59.794 47.826 15.23 0.00 0.00 2.43
1013 2514 2.023501 AGACCAGATACAAGGAGGCTCT 60.024 50.000 15.23 0.00 0.00 4.09
1014 2515 2.393646 AGACCAGATACAAGGAGGCTC 58.606 52.381 5.78 5.78 0.00 4.70
1015 2516 2.503356 CAAGACCAGATACAAGGAGGCT 59.497 50.000 0.00 0.00 0.00 4.58
1016 2517 2.501723 TCAAGACCAGATACAAGGAGGC 59.498 50.000 0.00 0.00 0.00 4.70
1017 2518 4.202305 GGATCAAGACCAGATACAAGGAGG 60.202 50.000 0.00 0.00 0.00 4.30
1018 2519 4.406972 TGGATCAAGACCAGATACAAGGAG 59.593 45.833 0.00 0.00 33.51 3.69
1019 2520 4.361783 TGGATCAAGACCAGATACAAGGA 58.638 43.478 0.00 0.00 33.51 3.36
1020 2521 4.760530 TGGATCAAGACCAGATACAAGG 57.239 45.455 0.00 0.00 33.51 3.61
1062 2574 5.220710 AGAGTTAGCTTTTCAAGAGAGCA 57.779 39.130 0.00 0.00 38.85 4.26
1069 2581 5.240844 GGCCAACTAAGAGTTAGCTTTTCAA 59.759 40.000 0.00 0.00 41.50 2.69
1091 2603 2.222027 GATAGGTGTTACATGCAGGGC 58.778 52.381 2.31 0.00 0.00 5.19
1104 2616 7.281774 ACTCTGTGCAGATAAAAATGATAGGTG 59.718 37.037 2.06 0.00 36.76 4.00
1106 2618 7.798596 ACTCTGTGCAGATAAAAATGATAGG 57.201 36.000 2.06 0.00 36.76 2.57
1110 2622 7.840931 TCTCTACTCTGTGCAGATAAAAATGA 58.159 34.615 2.06 0.00 36.76 2.57
1262 2776 6.710744 AGGTTGTTAGAACTTTAGTGACATGG 59.289 38.462 0.00 0.00 0.00 3.66
1483 3016 3.804786 TCAAATCGCATGCCAATTGAT 57.195 38.095 11.20 5.55 0.00 2.57
1639 3172 4.144297 TGTCCACTGATTTTTCCTTCCTG 58.856 43.478 0.00 0.00 0.00 3.86
1754 3287 2.057137 TACTTGCCATCATCTTGCCC 57.943 50.000 0.00 0.00 0.00 5.36
1781 3314 4.644234 TGTGTGTGATTGAACAAACTGGAT 59.356 37.500 0.00 0.00 38.81 3.41
1836 3370 3.375699 ACCTCTCTATTTGACCGGATGT 58.624 45.455 9.46 0.00 0.00 3.06
1926 3460 6.825721 CCCATCTTTCTCAATACTAAGCAAGT 59.174 38.462 0.00 0.00 42.62 3.16
1947 3481 3.099141 CAACCTATGTTTCCTTGCCCAT 58.901 45.455 0.00 0.00 30.42 4.00
1991 3525 3.731867 GCTGCCTTAAAATCACGGTCATG 60.732 47.826 0.00 0.00 0.00 3.07
2310 3849 8.239998 CTTTCAAGAAAGTCTGGAATAACCATC 58.760 37.037 13.12 0.00 43.58 3.51
2580 4444 3.541632 TCATTATCCTCAAGGCCGAAAC 58.458 45.455 0.00 0.00 34.44 2.78
2614 5659 8.002984 TCCATGATTGTCGTAAGTCATACTTA 57.997 34.615 0.00 0.00 39.51 2.24
2953 6002 2.787473 TCACCAACCTGCTCAATAGG 57.213 50.000 0.00 0.00 41.22 2.57
2991 6040 2.509336 CTGCCGCTAAGGTCACCG 60.509 66.667 0.00 0.00 43.70 4.94
3038 6087 2.553602 CAAGTACATTGTGCAGCCTTCA 59.446 45.455 7.64 0.00 33.95 3.02
3598 6666 4.649674 ACACTGACACTCTACAAAGAAGGA 59.350 41.667 0.00 0.00 0.00 3.36
3617 6685 1.001633 AGATACGCCGGTTTTGACACT 59.998 47.619 1.90 0.00 0.00 3.55
3633 6701 1.733387 GGGACCCCCTACCCGAGATA 61.733 65.000 0.00 0.00 41.34 1.98
3761 6829 6.576662 ACTCTTGTACTACCCATATCATCG 57.423 41.667 0.00 0.00 0.00 3.84
3872 6940 3.833070 ACCCTCTTCGGTGCCTATATAAG 59.167 47.826 0.00 0.00 33.77 1.73
3917 6985 7.640313 ACGGATATGTAGATCTCCTACCATTA 58.360 38.462 0.00 0.00 45.60 1.90
3976 7044 2.431454 CGTCCCATGTCCGGATGGA 61.431 63.158 23.27 16.32 45.24 3.41
4030 7098 1.404986 CGAACTATCACCTTTGGCCGA 60.405 52.381 0.00 0.00 0.00 5.54
4115 7183 3.439513 AATATGCGCGCCGGACTCA 62.440 57.895 30.77 8.32 0.00 3.41
4212 7280 5.413213 CGGTGGTATGTGGAACTTATTTTGA 59.587 40.000 0.00 0.00 38.04 2.69


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

AutoCloner maintained by Alex Coulton.