Multiple sequence alignment - TraesCS2B01G095400

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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 TraesCS2B01G095400 chr2B 100.000 3269 0 0 1 3269 55700255 55696987 0.000000e+00 6037.0
1 TraesCS2B01G095400 chr2B 85.578 1366 123 47 857 2168 55227617 55226272 0.000000e+00 1363.0
2 TraesCS2B01G095400 chr2B 84.644 1348 118 53 888 2168 55855927 55854602 0.000000e+00 1260.0
3 TraesCS2B01G095400 chr2B 86.778 1142 79 37 857 1951 55210378 55209262 0.000000e+00 1206.0
4 TraesCS2B01G095400 chr2B 93.574 747 29 4 1 734 55211200 55210460 0.000000e+00 1096.0
5 TraesCS2B01G095400 chr2B 86.371 653 75 9 2606 3248 55224778 55224130 0.000000e+00 701.0
6 TraesCS2B01G095400 chr2B 86.893 618 71 9 2659 3269 55512938 55512324 0.000000e+00 684.0
7 TraesCS2B01G095400 chr2B 88.624 545 55 6 2727 3269 55208574 55208035 0.000000e+00 656.0
8 TraesCS2B01G095400 chr2B 90.392 510 33 5 1 502 55538113 55537612 0.000000e+00 656.0
9 TraesCS2B01G095400 chr2B 93.171 410 25 2 1177 1583 55203319 55202910 1.680000e-167 599.0
10 TraesCS2B01G095400 chr2B 88.235 493 47 8 2662 3148 55854304 55853817 2.190000e-161 579.0
11 TraesCS2B01G095400 chr2B 87.860 486 48 9 2727 3208 55201903 55201425 7.920000e-156 560.0
12 TraesCS2B01G095400 chr2B 82.332 566 68 24 1605 2145 55202821 55202263 2.300000e-126 462.0
13 TraesCS2B01G095400 chr2B 79.477 726 83 41 857 1522 122992225 122992944 3.850000e-124 455.0
14 TraesCS2B01G095400 chr2B 88.604 351 22 6 2030 2368 55207618 55207274 8.440000e-111 411.0
15 TraesCS2B01G095400 chr2B 84.055 439 28 9 540 945 55537615 55537186 5.120000e-103 385.0
16 TraesCS2B01G095400 chr2B 86.014 286 26 14 891 1172 54888293 54888018 8.870000e-76 294.0
17 TraesCS2B01G095400 chr2B 87.861 173 16 1 242 409 55167043 55166871 7.150000e-47 198.0
18 TraesCS2B01G095400 chr2B 93.684 95 6 0 2454 2548 122994152 122994246 3.400000e-30 143.0
19 TraesCS2B01G095400 chr2B 92.632 95 7 0 2454 2548 122928374 122928468 1.580000e-28 137.0
20 TraesCS2B01G095400 chr2B 100.000 66 0 0 2387 2452 55697828 55697763 4.430000e-24 122.0
21 TraesCS2B01G095400 chr2B 100.000 66 0 0 2428 2493 55697869 55697804 4.430000e-24 122.0
22 TraesCS2B01G095400 chr2B 98.305 59 1 0 2196 2254 55854599 55854541 1.600000e-18 104.0
23 TraesCS2B01G095400 chr2B 97.500 40 1 0 2413 2452 122928374 122928413 5.850000e-08 69.4
24 TraesCS2B01G095400 chr2B 97.500 40 1 0 2413 2452 122994152 122994191 5.850000e-08 69.4
25 TraesCS2B01G095400 chr2D 93.290 1073 50 13 888 1949 33581160 33580099 0.000000e+00 1563.0
26 TraesCS2B01G095400 chr2D 91.209 1001 70 11 1186 2171 33373920 33372923 0.000000e+00 1345.0
27 TraesCS2B01G095400 chr2D 86.364 1122 88 22 888 1951 33242152 33241038 0.000000e+00 1164.0
28 TraesCS2B01G095400 chr2D 95.093 428 20 1 2843 3269 33579247 33578820 0.000000e+00 673.0
29 TraesCS2B01G095400 chr2D 85.766 555 69 6 2657 3205 33372559 33372009 2.190000e-161 579.0
30 TraesCS2B01G095400 chr2D 85.949 548 61 13 2727 3269 33313702 33313166 3.660000e-159 571.0
31 TraesCS2B01G095400 chr2D 92.583 391 9 6 2082 2452 33580031 33579641 7.980000e-151 544.0
32 TraesCS2B01G095400 chr2D 90.986 355 24 5 1605 1951 33314636 33314282 3.820000e-129 472.0
33 TraesCS2B01G095400 chr2D 79.230 727 84 40 857 1522 79084913 79085633 8.320000e-121 444.0
34 TraesCS2B01G095400 chr2D 97.881 236 5 0 2552 2787 33579479 33579244 3.040000e-110 409.0
35 TraesCS2B01G095400 chr2D 90.458 262 20 4 2030 2287 33240084 33239824 1.120000e-89 340.0
36 TraesCS2B01G095400 chr2D 83.562 292 28 11 891 1170 33049675 33049392 4.190000e-64 255.0
37 TraesCS2B01G095400 chr2D 98.400 125 2 0 2424 2548 33579710 33579586 1.530000e-53 220.0
38 TraesCS2B01G095400 chr2D 87.302 189 8 4 1973 2145 33371908 33371720 5.530000e-48 202.0
39 TraesCS2B01G095400 chr2D 85.535 159 7 8 2219 2368 33372902 33372751 5.650000e-33 152.0
40 TraesCS2B01G095400 chr2A 88.266 1142 66 19 857 1949 36411890 36410768 0.000000e+00 1304.0
41 TraesCS2B01G095400 chr2A 87.209 1118 83 29 888 1951 36400210 36399099 0.000000e+00 1218.0
42 TraesCS2B01G095400 chr2A 87.664 762 55 16 857 1584 36392769 36392013 0.000000e+00 850.0
43 TraesCS2B01G095400 chr2A 86.252 531 59 9 2657 3180 36410242 36409719 6.120000e-157 564.0
44 TraesCS2B01G095400 chr2A 81.907 713 76 26 857 1522 79342346 79343052 1.330000e-153 553.0
45 TraesCS2B01G095400 chr2A 88.732 355 26 5 1605 1951 36391963 36391615 3.900000e-114 422.0
46 TraesCS2B01G095400 chr2A 89.492 295 18 6 2082 2368 36410700 36410411 8.620000e-96 361.0
47 TraesCS2B01G095400 chr2A 81.865 193 20 12 2074 2261 1212129 1212311 7.310000e-32 148.0
48 TraesCS2B01G095400 chr4A 89.041 219 21 2 1605 1820 723918001 723917783 5.380000e-68 268.0
49 TraesCS2B01G095400 chr7D 82.143 196 20 12 2074 2264 239730614 239730429 1.570000e-33 154.0
50 TraesCS2B01G095400 chr5A 81.122 196 22 12 2074 2264 565537280 565537095 3.400000e-30 143.0
51 TraesCS2B01G095400 chr6A 80.612 196 23 13 2074 2264 108079691 108079506 1.580000e-28 137.0


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 TraesCS2B01G095400 chr2B 55696987 55700255 3268 True 2093.666667 6037 100.000000 1 3269 3 chr2B.!!$R7 3268
1 TraesCS2B01G095400 chr2B 55224130 55227617 3487 True 1032.000000 1363 85.974500 857 3248 2 chr2B.!!$R5 2391
2 TraesCS2B01G095400 chr2B 55201425 55211200 9775 True 712.857143 1206 88.706143 1 3269 7 chr2B.!!$R4 3268
3 TraesCS2B01G095400 chr2B 55512324 55512938 614 True 684.000000 684 86.893000 2659 3269 1 chr2B.!!$R3 610
4 TraesCS2B01G095400 chr2B 55853817 55855927 2110 True 647.666667 1260 90.394667 888 3148 3 chr2B.!!$R8 2260
5 TraesCS2B01G095400 chr2B 55537186 55538113 927 True 520.500000 656 87.223500 1 945 2 chr2B.!!$R6 944
6 TraesCS2B01G095400 chr2B 122992225 122994246 2021 False 222.466667 455 90.220333 857 2548 3 chr2B.!!$F2 1691
7 TraesCS2B01G095400 chr2D 33239824 33242152 2328 True 752.000000 1164 88.411000 888 2287 2 chr2D.!!$R2 1399
8 TraesCS2B01G095400 chr2D 33578820 33581160 2340 True 681.800000 1563 95.449400 888 3269 5 chr2D.!!$R5 2381
9 TraesCS2B01G095400 chr2D 33371720 33373920 2200 True 569.500000 1345 87.453000 1186 3205 4 chr2D.!!$R4 2019
10 TraesCS2B01G095400 chr2D 33313166 33314636 1470 True 521.500000 571 88.467500 1605 3269 2 chr2D.!!$R3 1664
11 TraesCS2B01G095400 chr2D 79084913 79085633 720 False 444.000000 444 79.230000 857 1522 1 chr2D.!!$F1 665
12 TraesCS2B01G095400 chr2A 36399099 36400210 1111 True 1218.000000 1218 87.209000 888 1951 1 chr2A.!!$R1 1063
13 TraesCS2B01G095400 chr2A 36409719 36411890 2171 True 743.000000 1304 88.003333 857 3180 3 chr2A.!!$R3 2323
14 TraesCS2B01G095400 chr2A 36391615 36392769 1154 True 636.000000 850 88.198000 857 1951 2 chr2A.!!$R2 1094
15 TraesCS2B01G095400 chr2A 79342346 79343052 706 False 553.000000 553 81.907000 857 1522 1 chr2A.!!$F2 665

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
496 510 0.181114 CCATGGGTCCACGTCATGAT 59.819 55.0 13.96 0.0 40.28 2.45 F
813 839 0.321653 AACACTTCCATGGGACTCGC 60.322 55.0 13.02 0.0 0.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1511 1706 1.003839 GGTCATGGCGAACTCACCA 60.004 57.895 0.0 0.0 41.06 4.17 R
2436 4783 1.274728 GTCTCTCAGCAGGAAAGCAGA 59.725 52.381 0.0 0.0 36.85 4.26 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
325 339 2.842496 TCCATTGAGAAGAGGCAGATGT 59.158 45.455 0.00 0.00 0.00 3.06
467 481 8.540388 TGATATACTCTTATCCTTGCATTACCC 58.460 37.037 0.00 0.00 0.00 3.69
468 482 8.686739 ATATACTCTTATCCTTGCATTACCCT 57.313 34.615 0.00 0.00 0.00 4.34
469 483 9.784376 ATATACTCTTATCCTTGCATTACCCTA 57.216 33.333 0.00 0.00 0.00 3.53
470 484 6.824958 ACTCTTATCCTTGCATTACCCTAA 57.175 37.500 0.00 0.00 0.00 2.69
471 485 6.592870 ACTCTTATCCTTGCATTACCCTAAC 58.407 40.000 0.00 0.00 0.00 2.34
472 486 5.937111 TCTTATCCTTGCATTACCCTAACC 58.063 41.667 0.00 0.00 0.00 2.85
496 510 0.181114 CCATGGGTCCACGTCATGAT 59.819 55.000 13.96 0.00 40.28 2.45
537 551 9.349713 ACCATTCTAGAATAAAAACACACTCAA 57.650 29.630 17.53 0.00 0.00 3.02
551 565 6.048732 ACACACTCAACATGTATATCCACA 57.951 37.500 0.00 0.00 0.00 4.17
552 566 6.653020 ACACACTCAACATGTATATCCACAT 58.347 36.000 0.00 0.00 39.76 3.21
556 570 6.426025 CACTCAACATGTATATCCACATCCTG 59.574 42.308 0.00 0.00 37.02 3.86
571 585 6.267699 TCCACATCCTGTTCGACATATTATCT 59.732 38.462 0.00 0.00 0.00 1.98
572 586 6.931281 CCACATCCTGTTCGACATATTATCTT 59.069 38.462 0.00 0.00 0.00 2.40
591 605 2.263540 GCTAAAGGCGACCACCGA 59.736 61.111 0.00 0.00 41.76 4.69
593 607 0.952010 GCTAAAGGCGACCACCGAAA 60.952 55.000 0.00 0.00 41.76 3.46
709 735 8.954950 AAAGATACATAAATCTGAGACACTGG 57.045 34.615 0.00 0.00 36.34 4.00
746 772 1.638529 TTTTTGCATGGGATTCGGGT 58.361 45.000 0.00 0.00 0.00 5.28
747 773 1.638529 TTTTGCATGGGATTCGGGTT 58.361 45.000 0.00 0.00 0.00 4.11
748 774 1.638529 TTTGCATGGGATTCGGGTTT 58.361 45.000 0.00 0.00 0.00 3.27
749 775 1.638529 TTGCATGGGATTCGGGTTTT 58.361 45.000 0.00 0.00 0.00 2.43
750 776 1.638529 TGCATGGGATTCGGGTTTTT 58.361 45.000 0.00 0.00 0.00 1.94
779 805 7.408132 TTTTTGAGAACTTACATGAGACTCG 57.592 36.000 0.00 0.00 31.70 4.18
780 806 5.707242 TTGAGAACTTACATGAGACTCGT 57.293 39.130 0.00 0.00 31.70 4.18
813 839 0.321653 AACACTTCCATGGGACTCGC 60.322 55.000 13.02 0.00 0.00 5.03
829 855 1.676529 CTCGCGGGAACAGAGAGATAA 59.323 52.381 0.00 0.00 37.03 1.75
832 858 2.799917 CGCGGGAACAGAGAGATAAAGG 60.800 54.545 0.00 0.00 0.00 3.11
906 961 1.379527 GCACCTTGAAATACCTCCGG 58.620 55.000 0.00 0.00 0.00 5.14
1140 1246 3.204827 GCGCACGCCTCCATGAAT 61.205 61.111 0.30 0.00 34.56 2.57
1201 1367 1.229177 TACCTGCTCCTCCACAGCA 60.229 57.895 0.00 0.00 44.80 4.41
1294 1460 3.807538 GCGACTACGACCAGCCGA 61.808 66.667 0.00 0.00 42.66 5.54
1341 1507 4.208686 GAGTCGGGCTTCGCGGAT 62.209 66.667 6.13 0.00 40.17 4.18
1490 1685 2.729479 CCGCCAGAGAGGACATGCT 61.729 63.158 0.00 0.00 41.22 3.79
1542 1752 0.174845 CATGACCGACCGGCTTCTTA 59.825 55.000 8.55 0.00 39.32 2.10
1878 2499 4.086178 CGCTCGTCGTCGACCTGT 62.086 66.667 19.29 0.00 41.35 4.00
2003 2689 8.137437 TGGTCTTTGATTGAATTTTCTTCAGAC 58.863 33.333 0.00 0.00 0.00 3.51
2021 2710 2.234661 AGACTTTGGTGCAGATCGATGA 59.765 45.455 0.54 0.00 0.00 2.92
2027 2716 3.346315 TGGTGCAGATCGATGATGTTTT 58.654 40.909 0.54 0.00 0.00 2.43
2028 2717 3.758023 TGGTGCAGATCGATGATGTTTTT 59.242 39.130 0.54 0.00 0.00 1.94
2034 4290 4.156556 CAGATCGATGATGTTTTTGGGTGT 59.843 41.667 0.54 0.00 0.00 4.16
2037 4293 5.621197 TCGATGATGTTTTTGGGTGTTAG 57.379 39.130 0.00 0.00 0.00 2.34
2065 4349 6.346096 ACTTGTCTTACTGAAGCTGTTACAA 58.654 36.000 0.00 0.00 32.21 2.41
2066 4350 6.258068 ACTTGTCTTACTGAAGCTGTTACAAC 59.742 38.462 0.00 0.00 32.21 3.32
2070 4354 2.851195 ACTGAAGCTGTTACAACCTGG 58.149 47.619 0.00 0.00 0.00 4.45
2145 4429 4.127171 TGAAGTCTGAAACTGTTAGGTGC 58.873 43.478 0.00 0.00 38.58 5.01
2287 4622 4.917415 CACGAAATTCAGGTTCCAACAATC 59.083 41.667 0.00 0.00 0.00 2.67
2408 4755 2.574006 TGTTCATCTGCTTTCCTGCT 57.426 45.000 0.00 0.00 0.00 4.24
2409 4756 2.156917 TGTTCATCTGCTTTCCTGCTG 58.843 47.619 0.00 0.00 0.00 4.41
2410 4757 2.224597 TGTTCATCTGCTTTCCTGCTGA 60.225 45.455 0.00 0.00 43.15 4.26
2411 4758 2.398252 TCATCTGCTTTCCTGCTGAG 57.602 50.000 0.00 0.00 42.48 3.35
2412 4759 1.904537 TCATCTGCTTTCCTGCTGAGA 59.095 47.619 0.00 0.00 42.48 3.27
2413 4760 2.093606 TCATCTGCTTTCCTGCTGAGAG 60.094 50.000 0.00 0.00 42.48 3.20
2414 4761 1.637338 TCTGCTTTCCTGCTGAGAGA 58.363 50.000 0.00 0.00 36.30 3.10
2415 4762 1.274728 TCTGCTTTCCTGCTGAGAGAC 59.725 52.381 0.00 0.00 36.30 3.36
2416 4763 1.275856 CTGCTTTCCTGCTGAGAGACT 59.724 52.381 0.00 0.00 34.47 3.24
2417 4764 1.274728 TGCTTTCCTGCTGAGAGACTC 59.725 52.381 0.00 0.00 0.00 3.36
2418 4765 1.550072 GCTTTCCTGCTGAGAGACTCT 59.450 52.381 4.14 4.14 0.00 3.24
2419 4766 2.674747 GCTTTCCTGCTGAGAGACTCTG 60.675 54.545 10.44 0.00 33.52 3.35
2420 4767 2.593925 TTCCTGCTGAGAGACTCTGA 57.406 50.000 10.44 0.00 32.36 3.27
2421 4768 2.127271 TCCTGCTGAGAGACTCTGAG 57.873 55.000 14.05 14.05 32.36 3.35
2422 4769 1.632920 TCCTGCTGAGAGACTCTGAGA 59.367 52.381 21.57 6.95 28.58 3.27
2423 4770 2.241941 TCCTGCTGAGAGACTCTGAGAT 59.758 50.000 21.57 0.00 28.58 2.75
2424 4771 3.025978 CCTGCTGAGAGACTCTGAGATT 58.974 50.000 21.57 0.00 28.58 2.40
2425 4772 3.448301 CCTGCTGAGAGACTCTGAGATTT 59.552 47.826 21.57 0.00 28.58 2.17
2426 4773 4.644234 CCTGCTGAGAGACTCTGAGATTTA 59.356 45.833 21.57 4.70 28.58 1.40
2427 4774 5.126869 CCTGCTGAGAGACTCTGAGATTTAA 59.873 44.000 21.57 1.82 28.58 1.52
2428 4775 6.350864 CCTGCTGAGAGACTCTGAGATTTAAA 60.351 42.308 21.57 0.00 28.58 1.52
2429 4776 7.180322 TGCTGAGAGACTCTGAGATTTAAAT 57.820 36.000 21.57 0.00 28.58 1.40
2430 4777 7.619050 TGCTGAGAGACTCTGAGATTTAAATT 58.381 34.615 21.57 0.00 28.58 1.82
2431 4778 7.548427 TGCTGAGAGACTCTGAGATTTAAATTG 59.452 37.037 21.57 0.00 28.58 2.32
2432 4779 7.548780 GCTGAGAGACTCTGAGATTTAAATTGT 59.451 37.037 21.57 0.00 28.58 2.71
2433 4780 9.434420 CTGAGAGACTCTGAGATTTAAATTGTT 57.566 33.333 13.20 0.00 28.58 2.83
2434 4781 9.429359 TGAGAGACTCTGAGATTTAAATTGTTC 57.571 33.333 10.44 2.35 0.00 3.18
2435 4782 9.429359 GAGAGACTCTGAGATTTAAATTGTTCA 57.571 33.333 10.44 6.50 0.00 3.18
2436 4783 9.956640 AGAGACTCTGAGATTTAAATTGTTCAT 57.043 29.630 12.44 0.00 0.00 2.57
2438 4785 9.956640 AGACTCTGAGATTTAAATTGTTCATCT 57.043 29.630 12.44 5.11 0.00 2.90
2439 4786 9.985318 GACTCTGAGATTTAAATTGTTCATCTG 57.015 33.333 12.44 4.03 0.00 2.90
2440 4787 8.457261 ACTCTGAGATTTAAATTGTTCATCTGC 58.543 33.333 12.44 0.00 0.00 4.26
2441 4788 8.571461 TCTGAGATTTAAATTGTTCATCTGCT 57.429 30.769 1.43 0.00 0.00 4.24
2442 4789 9.017509 TCTGAGATTTAAATTGTTCATCTGCTT 57.982 29.630 1.43 0.00 0.00 3.91
2443 4790 9.635520 CTGAGATTTAAATTGTTCATCTGCTTT 57.364 29.630 1.43 0.00 0.00 3.51
2444 4791 9.630098 TGAGATTTAAATTGTTCATCTGCTTTC 57.370 29.630 1.43 0.00 0.00 2.62
2445 4792 8.992835 AGATTTAAATTGTTCATCTGCTTTCC 57.007 30.769 1.43 0.00 0.00 3.13
2446 4793 8.810041 AGATTTAAATTGTTCATCTGCTTTCCT 58.190 29.630 1.43 0.00 0.00 3.36
2447 4794 8.767478 ATTTAAATTGTTCATCTGCTTTCCTG 57.233 30.769 0.00 0.00 0.00 3.86
2448 4795 3.863142 ATTGTTCATCTGCTTTCCTGC 57.137 42.857 0.00 0.00 0.00 4.85
2449 4796 2.574006 TGTTCATCTGCTTTCCTGCT 57.426 45.000 0.00 0.00 0.00 4.24
2548 4895 6.689554 TGAATGTGTTATGAACAATGCACAT 58.310 32.000 0.00 0.00 44.16 3.21
2549 4896 7.153315 TGAATGTGTTATGAACAATGCACATT 58.847 30.769 21.26 21.26 46.74 2.71
2582 5051 5.353394 ACTGTTGTTGTCCTGTAGAAAGA 57.647 39.130 0.00 0.00 0.00 2.52
2765 10360 5.985530 AGCTAAAAAGCCAAATCAAGTTCAC 59.014 36.000 0.00 0.00 34.90 3.18
2803 10405 7.413644 GCCTTTGCAGAGAAGATACTAATTTC 58.586 38.462 5.68 0.00 37.47 2.17
2865 11779 8.409358 AGTGCATAAAATCTTTAGTTCCTTGT 57.591 30.769 0.00 0.00 0.00 3.16
2897 11814 6.436843 TTGTCTCAGGTTTTGTTCTTCTTC 57.563 37.500 0.00 0.00 0.00 2.87
2924 11841 8.852135 ACCTTGTTATTAATTTTTCGTCTTCCA 58.148 29.630 0.00 0.00 0.00 3.53
2984 11901 2.047274 CTGCGACACCCGGATGTT 60.047 61.111 0.91 0.00 38.13 2.71
3090 12009 7.402862 ACTGGACACTTACTTTTGCCTATATT 58.597 34.615 0.00 0.00 0.00 1.28
3184 12112 0.250209 CTGCTGAGAGTGTTGTGCCT 60.250 55.000 0.00 0.00 0.00 4.75
3187 12115 2.158827 TGCTGAGAGTGTTGTGCCTAAA 60.159 45.455 0.00 0.00 0.00 1.85
3210 12138 4.039124 AGGCTGAACAATTTTGTAGGTTGG 59.961 41.667 0.00 0.00 41.31 3.77
3218 12146 1.028905 TTTGTAGGTTGGTGCAGTGC 58.971 50.000 8.58 8.58 0.00 4.40
3259 12187 9.920133 TCATATCTGAGATGTTATTTCTAGTGC 57.080 33.333 11.63 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 58 2.165998 AGGCCTTTTAGCAAAGCTCTG 58.834 47.619 0.00 0.00 40.44 3.35
325 339 3.003897 GCTGTTGTTTCGGTGGTTTATCA 59.996 43.478 0.00 0.00 0.00 2.15
418 432 8.109705 TCATCATTTATGTTTGTGTGCTAGTT 57.890 30.769 0.00 0.00 36.89 2.24
446 460 7.202066 GGTTAGGGTAATGCAAGGATAAGAGTA 60.202 40.741 0.00 0.00 0.00 2.59
467 481 1.146263 GACCCATGGAGGCGGTTAG 59.854 63.158 15.22 0.00 35.39 2.34
468 482 2.372074 GGACCCATGGAGGCGGTTA 61.372 63.158 15.22 0.00 35.39 2.85
469 483 3.728373 GGACCCATGGAGGCGGTT 61.728 66.667 15.22 0.00 35.39 4.44
471 485 4.489771 GTGGACCCATGGAGGCGG 62.490 72.222 15.22 0.00 35.39 6.13
472 486 4.838152 CGTGGACCCATGGAGGCG 62.838 72.222 15.22 6.54 35.39 5.52
551 565 8.128322 AGCTAAGATAATATGTCGAACAGGAT 57.872 34.615 0.00 0.00 0.00 3.24
552 566 7.526142 AGCTAAGATAATATGTCGAACAGGA 57.474 36.000 0.00 0.00 0.00 3.86
556 570 8.648968 GCCTTTAGCTAAGATAATATGTCGAAC 58.351 37.037 6.24 0.00 38.99 3.95
571 585 0.108520 CGGTGGTCGCCTTTAGCTAA 60.109 55.000 0.86 0.86 40.39 3.09
572 586 0.966875 TCGGTGGTCGCCTTTAGCTA 60.967 55.000 0.00 0.00 40.39 3.32
591 605 2.254546 TGATTGCTCGGTGTCACTTT 57.745 45.000 2.35 0.00 0.00 2.66
593 607 2.479566 ATTGATTGCTCGGTGTCACT 57.520 45.000 2.35 0.00 0.00 3.41
694 720 3.172339 AGAGAGCCAGTGTCTCAGATTT 58.828 45.455 3.68 0.00 42.63 2.17
709 735 1.112950 AAAGTAGCGGGGTAGAGAGC 58.887 55.000 0.00 0.00 0.00 4.09
813 839 2.799917 CGCCTTTATCTCTCTGTTCCCG 60.800 54.545 0.00 0.00 0.00 5.14
829 855 0.905357 ACACTATTGAGCTCCGCCTT 59.095 50.000 12.15 0.00 0.00 4.35
832 858 0.811616 CCCACACTATTGAGCTCCGC 60.812 60.000 12.15 0.00 0.00 5.54
1294 1460 1.620589 ACATGATGGCCTCCACCCT 60.621 57.895 3.32 0.00 35.80 4.34
1341 1507 3.733960 CGGAGCAGGACGACGTCA 61.734 66.667 27.77 0.00 33.68 4.35
1441 1616 1.480954 GACGACCCAGTACATCATGGT 59.519 52.381 0.00 0.00 34.58 3.55
1511 1706 1.003839 GGTCATGGCGAACTCACCA 60.004 57.895 0.00 0.00 41.06 4.17
1542 1752 8.281212 ACGAAAGCAATTCAAGAATAGGTATT 57.719 30.769 0.00 0.00 37.96 1.89
1686 2307 2.202401 GTAGTGCCCGTCGTCGAC 60.202 66.667 15.51 15.51 39.71 4.20
1973 2655 7.452880 AGAAAATTCAATCAAAGACCATCGA 57.547 32.000 0.00 0.00 0.00 3.59
2003 2689 2.941064 ACATCATCGATCTGCACCAAAG 59.059 45.455 0.00 0.00 0.00 2.77
2021 2710 6.831868 ACAAGTAGACTAACACCCAAAAACAT 59.168 34.615 0.00 0.00 0.00 2.71
2027 2716 5.881923 AAGACAAGTAGACTAACACCCAA 57.118 39.130 0.00 0.00 0.00 4.12
2028 2717 6.015688 CAGTAAGACAAGTAGACTAACACCCA 60.016 42.308 0.00 0.00 0.00 4.51
2034 4290 7.230913 ACAGCTTCAGTAAGACAAGTAGACTAA 59.769 37.037 0.00 0.00 34.37 2.24
2037 4293 5.774630 ACAGCTTCAGTAAGACAAGTAGAC 58.225 41.667 0.00 0.00 34.37 2.59
2065 4349 3.788227 TCAGTAATCTGTTTGCCAGGT 57.212 42.857 0.00 0.00 41.83 4.00
2066 4350 5.649782 ATTTCAGTAATCTGTTTGCCAGG 57.350 39.130 0.00 0.00 41.83 4.45
2070 4354 9.334693 CTAGAACAATTTCAGTAATCTGTTTGC 57.665 33.333 0.00 0.00 41.91 3.68
2178 4493 9.094578 TGAATCAACTAATTTGGGGTTTCAATA 57.905 29.630 0.00 0.00 35.69 1.90
2287 4622 2.360165 AGCTCAGGTGCAGAAACAAAAG 59.640 45.455 0.00 0.00 34.99 2.27
2382 4729 5.862323 CAGGAAAGCAGATGAACAATTCAAG 59.138 40.000 0.00 0.00 43.95 3.02
2408 4755 9.429359 GAACAATTTAAATCTCAGAGTCTCTCA 57.571 33.333 0.00 0.00 32.06 3.27
2409 4756 9.429359 TGAACAATTTAAATCTCAGAGTCTCTC 57.571 33.333 0.00 0.00 0.00 3.20
2410 4757 9.956640 ATGAACAATTTAAATCTCAGAGTCTCT 57.043 29.630 0.10 0.00 0.00 3.10
2412 4759 9.956640 AGATGAACAATTTAAATCTCAGAGTCT 57.043 29.630 0.10 3.35 0.00 3.24
2413 4760 9.985318 CAGATGAACAATTTAAATCTCAGAGTC 57.015 33.333 0.10 1.40 0.00 3.36
2414 4761 8.457261 GCAGATGAACAATTTAAATCTCAGAGT 58.543 33.333 0.10 0.00 0.00 3.24
2415 4762 8.675504 AGCAGATGAACAATTTAAATCTCAGAG 58.324 33.333 0.10 0.00 0.00 3.35
2416 4763 8.571461 AGCAGATGAACAATTTAAATCTCAGA 57.429 30.769 0.10 0.00 0.00 3.27
2417 4764 9.635520 AAAGCAGATGAACAATTTAAATCTCAG 57.364 29.630 0.10 0.00 0.00 3.35
2418 4765 9.630098 GAAAGCAGATGAACAATTTAAATCTCA 57.370 29.630 0.10 5.73 0.00 3.27
2419 4766 9.080915 GGAAAGCAGATGAACAATTTAAATCTC 57.919 33.333 0.10 0.19 0.00 2.75
2420 4767 8.810041 AGGAAAGCAGATGAACAATTTAAATCT 58.190 29.630 0.10 0.00 0.00 2.40
2421 4768 8.866956 CAGGAAAGCAGATGAACAATTTAAATC 58.133 33.333 0.10 0.00 0.00 2.17
2422 4769 7.332678 GCAGGAAAGCAGATGAACAATTTAAAT 59.667 33.333 0.00 0.00 0.00 1.40
2423 4770 6.646240 GCAGGAAAGCAGATGAACAATTTAAA 59.354 34.615 0.00 0.00 0.00 1.52
2424 4771 6.015180 AGCAGGAAAGCAGATGAACAATTTAA 60.015 34.615 0.00 0.00 36.85 1.52
2425 4772 5.477984 AGCAGGAAAGCAGATGAACAATTTA 59.522 36.000 0.00 0.00 36.85 1.40
2426 4773 4.282703 AGCAGGAAAGCAGATGAACAATTT 59.717 37.500 0.00 0.00 36.85 1.82
2427 4774 3.830755 AGCAGGAAAGCAGATGAACAATT 59.169 39.130 0.00 0.00 36.85 2.32
2428 4775 3.192844 CAGCAGGAAAGCAGATGAACAAT 59.807 43.478 0.00 0.00 36.85 2.71
2429 4776 2.555325 CAGCAGGAAAGCAGATGAACAA 59.445 45.455 0.00 0.00 36.85 2.83
2430 4777 2.156917 CAGCAGGAAAGCAGATGAACA 58.843 47.619 0.00 0.00 36.85 3.18
2431 4778 2.419324 CTCAGCAGGAAAGCAGATGAAC 59.581 50.000 0.00 0.00 36.85 3.18
2432 4779 2.303890 TCTCAGCAGGAAAGCAGATGAA 59.696 45.455 0.00 0.00 36.85 2.57
2433 4780 1.904537 TCTCAGCAGGAAAGCAGATGA 59.095 47.619 0.00 0.00 36.85 2.92
2434 4781 2.093606 TCTCTCAGCAGGAAAGCAGATG 60.094 50.000 0.00 0.00 36.85 2.90
2435 4782 2.093553 GTCTCTCAGCAGGAAAGCAGAT 60.094 50.000 0.00 0.00 36.85 2.90
2436 4783 1.274728 GTCTCTCAGCAGGAAAGCAGA 59.725 52.381 0.00 0.00 36.85 4.26
2437 4784 1.275856 AGTCTCTCAGCAGGAAAGCAG 59.724 52.381 0.00 0.00 36.85 4.24
2438 4785 1.274728 GAGTCTCTCAGCAGGAAAGCA 59.725 52.381 0.00 0.00 36.85 3.91
2439 4786 1.550072 AGAGTCTCTCAGCAGGAAAGC 59.450 52.381 0.00 0.00 32.06 3.51
2440 4787 2.824936 TCAGAGTCTCTCAGCAGGAAAG 59.175 50.000 0.00 0.00 32.06 2.62
2441 4788 2.824936 CTCAGAGTCTCTCAGCAGGAAA 59.175 50.000 0.00 0.00 32.06 3.13
2442 4789 2.040947 TCTCAGAGTCTCTCAGCAGGAA 59.959 50.000 0.00 0.00 32.06 3.36
2443 4790 1.632920 TCTCAGAGTCTCTCAGCAGGA 59.367 52.381 0.00 0.00 32.06 3.86
2444 4791 2.127271 TCTCAGAGTCTCTCAGCAGG 57.873 55.000 0.00 0.00 32.06 4.85
2445 4792 4.724074 AAATCTCAGAGTCTCTCAGCAG 57.276 45.455 0.00 0.00 32.06 4.24
2446 4793 6.596309 TTTAAATCTCAGAGTCTCTCAGCA 57.404 37.500 0.00 0.00 32.06 4.41
2447 4794 7.548780 ACAATTTAAATCTCAGAGTCTCTCAGC 59.451 37.037 0.00 0.00 32.06 4.26
2448 4795 9.434420 AACAATTTAAATCTCAGAGTCTCTCAG 57.566 33.333 0.00 0.00 32.06 3.35
2449 4796 9.429359 GAACAATTTAAATCTCAGAGTCTCTCA 57.571 33.333 0.00 0.00 32.06 3.27
2548 4895 3.754323 ACAACAACAGTTTCGGACAGAAA 59.246 39.130 0.00 0.00 45.76 2.52
2549 4896 3.340034 ACAACAACAGTTTCGGACAGAA 58.660 40.909 0.00 0.00 37.01 3.02
2582 5051 9.449719 CTACCAGTTTCATCCAACTACTTTTAT 57.550 33.333 0.00 0.00 35.10 1.40
2765 10360 2.421073 TGCAAAGGCGAAATGAGATGAG 59.579 45.455 0.00 0.00 45.35 2.90
2878 11792 4.884164 AGGTGAAGAAGAACAAAACCTGAG 59.116 41.667 0.00 0.00 35.28 3.35
2897 11814 9.124807 GGAAGACGAAAAATTAATAACAAGGTG 57.875 33.333 0.00 0.00 0.00 4.00
2916 11833 2.280628 GAGCCAATTAGGTGGAAGACG 58.719 52.381 0.00 0.00 41.65 4.18
2924 11841 6.131961 AGCAGAAATTATGAGCCAATTAGGT 58.868 36.000 0.00 0.00 40.61 3.08
2984 11901 1.817357 TCTTTCTCTACTCCGCGTCA 58.183 50.000 4.92 0.00 0.00 4.35
3024 11943 2.800544 CGAAACTTGTGGACAGGTGTAG 59.199 50.000 0.00 0.00 36.26 2.74
3184 12112 6.969993 ACCTACAAAATTGTTCAGCCTTTA 57.030 33.333 3.85 0.00 42.35 1.85
3187 12115 4.039124 CCAACCTACAAAATTGTTCAGCCT 59.961 41.667 3.85 0.00 42.35 4.58
3210 12138 1.370900 CAAAAGAGCGGCACTGCAC 60.371 57.895 1.45 0.00 37.31 4.57
3218 12146 5.525012 TCAGATATGAATGTCAAAAGAGCGG 59.475 40.000 0.00 0.00 0.00 5.52


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

AutoCloner maintained by Alex Coulton.