Multiple sequence alignment - TraesCS2D01G413000

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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 TraesCS2D01G413000 chr2D 100.000 3634 0 0 1 3634 527641933 527645566 0.000000e+00 6711.0
1 TraesCS2D01G413000 chr2D 79.235 366 69 7 25 387 333505551 333505912 7.790000e-62 248.0
2 TraesCS2D01G413000 chr2A 89.915 2479 168 46 6 2434 672425099 672427545 0.000000e+00 3118.0
3 TraesCS2D01G413000 chr2A 90.290 1205 84 14 2459 3634 672641797 672642997 0.000000e+00 1546.0
4 TraesCS2D01G413000 chr2B 94.354 2037 89 11 555 2575 624994797 624996823 0.000000e+00 3101.0
5 TraesCS2D01G413000 chr2B 91.205 614 49 4 2726 3335 624996815 624997427 0.000000e+00 830.0
6 TraesCS2D01G413000 chr2B 91.318 311 21 3 3329 3634 625006141 625006450 1.560000e-113 420.0
7 TraesCS2D01G413000 chr7B 80.172 464 78 11 3156 3609 159122916 159122457 5.810000e-88 335.0
8 TraesCS2D01G413000 chr7B 80.308 325 57 6 29 350 42572 42892 4.690000e-59 239.0
9 TraesCS2D01G413000 chr1A 83.596 317 47 5 25 339 469307111 469307424 3.550000e-75 292.0
10 TraesCS2D01G413000 chr1A 77.378 473 81 21 4 456 21987892 21987426 1.290000e-64 257.0
11 TraesCS2D01G413000 chr7D 78.829 444 78 12 25 456 234181787 234181348 5.940000e-73 285.0
12 TraesCS2D01G413000 chr5D 79.135 393 75 7 4 393 434036257 434035869 7.740000e-67 265.0
13 TraesCS2D01G413000 chr3D 80.110 362 64 5 1 360 13491002 13491357 2.780000e-66 263.0
14 TraesCS2D01G413000 chr1D 78.701 385 69 7 4 386 414270542 414270169 1.010000e-60 244.0
15 TraesCS2D01G413000 chr6D 77.273 374 74 10 25 393 147644995 147644628 3.680000e-50 209.0
16 TraesCS2D01G413000 chr6D 90.000 60 6 0 1391 1450 318078765 318078824 1.080000e-10 78.7
17 TraesCS2D01G413000 chr3A 81.022 137 15 7 2576 2702 719266973 719267108 8.300000e-17 99.0
18 TraesCS2D01G413000 chr6B 90.000 60 6 0 1391 1450 506383239 506383180 1.080000e-10 78.7
19 TraesCS2D01G413000 chr6A 90.909 55 5 0 1391 1445 455495273 455495327 1.400000e-09 75.0


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 TraesCS2D01G413000 chr2D 527641933 527645566 3633 False 6711.0 6711 100.0000 1 3634 1 chr2D.!!$F2 3633
1 TraesCS2D01G413000 chr2A 672425099 672427545 2446 False 3118.0 3118 89.9150 6 2434 1 chr2A.!!$F1 2428
2 TraesCS2D01G413000 chr2A 672641797 672642997 1200 False 1546.0 1546 90.2900 2459 3634 1 chr2A.!!$F2 1175
3 TraesCS2D01G413000 chr2B 624994797 624997427 2630 False 1965.5 3101 92.7795 555 3335 2 chr2B.!!$F2 2780

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
193 195 0.028505 CATTTGAATGCGGCGAGGAG 59.971 55.0 12.98 0.00 0.00 3.69 F
505 522 0.034477 GTTGGATGGGGTTCCGTGAT 60.034 55.0 0.00 0.00 38.74 3.06 F
567 584 0.038709 CCCTAGCATAGCACGCTCTC 60.039 60.0 0.00 0.00 40.96 3.20 F
2271 2325 0.440371 CCTGCGACGAAGAGCTTTTC 59.560 55.0 3.77 6.92 35.99 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1489 1525 0.034896 TCGGTGACCTTGGAAGAAGC 59.965 55.0 0.00 0.00 0.00 3.86 R
2253 2307 0.092014 CGAAAAGCTCTTCGTCGCAG 59.908 55.0 14.04 0.00 42.53 5.18 R
2485 2540 1.438651 GCGCACACTTATTCCACTGA 58.561 50.0 0.30 0.00 0.00 3.41 R
3232 3314 0.831288 TCTTGGGCCCAACACCAATG 60.831 55.0 34.07 21.27 45.03 2.82 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 21 2.595009 GAAGATGGGGAGCGGTGGAC 62.595 65.000 0.00 0.00 0.00 4.02
27 28 2.741092 GAGCGGTGGACTTGGTGA 59.259 61.111 0.00 0.00 0.00 4.02
28 29 1.296715 GAGCGGTGGACTTGGTGAT 59.703 57.895 0.00 0.00 0.00 3.06
42 43 1.031571 GGTGATGCGATTCTTGCCCA 61.032 55.000 0.00 0.00 0.00 5.36
49 50 0.179111 CGATTCTTGCCCAGCGTCTA 60.179 55.000 0.00 0.00 0.00 2.59
71 72 3.215151 GCCTCCTTTAAATAGAGGGTGC 58.785 50.000 25.00 13.77 46.14 5.01
74 75 3.869065 TCCTTTAAATAGAGGGTGCACG 58.131 45.455 11.45 0.00 33.73 5.34
76 77 2.702592 TTAAATAGAGGGTGCACGGG 57.297 50.000 11.45 0.00 0.00 5.28
90 91 3.721706 CGGGAGGAGCTTTGCCCT 61.722 66.667 14.44 4.45 38.46 5.19
93 94 2.034687 GAGGAGCTTTGCCCTGCA 59.965 61.111 0.00 0.00 36.47 4.41
111 112 2.258755 GCATTGTGTTTAATGTCGGCC 58.741 47.619 0.00 0.00 39.62 6.13
113 114 1.982660 TTGTGTTTAATGTCGGCCCA 58.017 45.000 0.00 0.00 0.00 5.36
122 124 1.899437 ATGTCGGCCCACTCGTGAAT 61.899 55.000 1.09 0.00 0.00 2.57
127 129 1.003839 GCCCACTCGTGAATGGACA 60.004 57.895 0.00 0.00 38.34 4.02
132 134 2.612721 CCACTCGTGAATGGACATGTGA 60.613 50.000 1.15 0.00 38.34 3.58
142 144 0.460311 GGACATGTGACCGGAGTAGG 59.540 60.000 9.46 0.00 37.30 3.18
146 148 2.289444 ACATGTGACCGGAGTAGGTTTG 60.289 50.000 9.46 0.00 46.09 2.93
154 156 2.593257 CGGAGTAGGTTTGTCGTCTTC 58.407 52.381 0.00 0.00 0.00 2.87
157 159 3.315418 GAGTAGGTTTGTCGTCTTCCAC 58.685 50.000 0.00 0.00 0.00 4.02
158 160 2.696707 AGTAGGTTTGTCGTCTTCCACA 59.303 45.455 0.00 0.00 0.00 4.17
159 161 1.949465 AGGTTTGTCGTCTTCCACAC 58.051 50.000 0.00 0.00 0.00 3.82
160 162 0.942252 GGTTTGTCGTCTTCCACACC 59.058 55.000 0.00 0.00 0.00 4.16
165 167 0.531311 GTCGTCTTCCACACCGGTTT 60.531 55.000 2.97 0.00 35.57 3.27
169 171 2.158841 CGTCTTCCACACCGGTTTAATG 59.841 50.000 2.97 0.43 35.57 1.90
180 182 2.757868 CCGGTTTAATGGAGGCATTTGA 59.242 45.455 0.00 0.00 0.00 2.69
193 195 0.028505 CATTTGAATGCGGCGAGGAG 59.971 55.000 12.98 0.00 0.00 3.69
195 197 4.838152 TGAATGCGGCGAGGAGGC 62.838 66.667 12.98 0.00 42.76 4.70
202 204 2.586792 GGCGAGGAGGCATGTTCT 59.413 61.111 0.00 0.00 45.92 3.01
251 253 1.173444 TGGTGCGCCGTTTTAATGGT 61.173 50.000 12.58 0.00 37.40 3.55
259 261 1.396996 CCGTTTTAATGGTCGAGGCAG 59.603 52.381 0.00 0.00 0.00 4.85
265 267 0.247736 AATGGTCGAGGCAGTGAGAC 59.752 55.000 0.00 0.00 0.00 3.36
267 269 2.627737 GGTCGAGGCAGTGAGACGT 61.628 63.158 0.00 0.00 34.68 4.34
270 272 2.505118 GAGGCAGTGAGACGTCGC 60.505 66.667 12.80 12.80 0.00 5.19
272 274 4.702081 GGCAGTGAGACGTCGCGT 62.702 66.667 14.68 4.60 45.10 6.01
290 292 1.626747 GTCCGTTCTAAGCCGTCTTC 58.373 55.000 0.00 0.00 33.85 2.87
294 296 3.444742 TCCGTTCTAAGCCGTCTTCAATA 59.555 43.478 0.00 0.00 33.85 1.90
300 302 2.918712 AGCCGTCTTCAATATGGAGG 57.081 50.000 0.00 0.00 0.00 4.30
302 304 1.543429 GCCGTCTTCAATATGGAGGGG 60.543 57.143 0.00 0.00 36.07 4.79
304 306 1.140852 CGTCTTCAATATGGAGGGGCA 59.859 52.381 0.00 0.00 0.00 5.36
307 309 0.465460 TTCAATATGGAGGGGCACGC 60.465 55.000 0.00 0.00 43.76 5.34
326 328 3.128465 GCTCTACAGCAACAAGAATGC 57.872 47.619 0.00 0.00 46.06 3.56
381 383 1.553690 ATGGAGGAGTGGTTCGGGTG 61.554 60.000 0.00 0.00 0.00 4.61
411 419 2.260434 CGGGTGTGGGTAGTGTCG 59.740 66.667 0.00 0.00 0.00 4.35
413 421 1.909781 GGGTGTGGGTAGTGTCGGA 60.910 63.158 0.00 0.00 0.00 4.55
415 423 0.611714 GGTGTGGGTAGTGTCGGAAT 59.388 55.000 0.00 0.00 0.00 3.01
429 437 3.381136 GAATGCCCGCAAAGCCCA 61.381 61.111 0.00 0.00 0.00 5.36
430 438 2.684655 AATGCCCGCAAAGCCCAT 60.685 55.556 0.00 0.00 0.00 4.00
431 439 1.381056 AATGCCCGCAAAGCCCATA 60.381 52.632 0.00 0.00 0.00 2.74
439 448 2.166254 CCGCAAAGCCCATATTTGTCTT 59.834 45.455 0.96 0.00 39.36 3.01
441 450 3.438360 GCAAAGCCCATATTTGTCTTCG 58.562 45.455 0.96 0.00 39.36 3.79
447 456 4.638865 AGCCCATATTTGTCTTCGGTTTAC 59.361 41.667 0.00 0.00 0.00 2.01
449 458 4.034742 CCCATATTTGTCTTCGGTTTACGG 59.965 45.833 0.00 0.00 44.45 4.02
450 459 4.034742 CCATATTTGTCTTCGGTTTACGGG 59.965 45.833 0.00 0.00 44.45 5.28
452 461 2.443887 TTGTCTTCGGTTTACGGGAG 57.556 50.000 0.00 0.00 44.45 4.30
456 465 2.733552 GTCTTCGGTTTACGGGAGAAAC 59.266 50.000 0.52 0.00 44.45 2.78
457 466 2.364970 TCTTCGGTTTACGGGAGAAACA 59.635 45.455 0.00 0.00 44.45 2.83
459 468 2.482864 TCGGTTTACGGGAGAAACAAC 58.517 47.619 0.00 0.00 44.45 3.32
467 476 1.877443 CGGGAGAAACAACGTCCAAAT 59.123 47.619 0.00 0.00 31.31 2.32
469 478 2.882137 GGGAGAAACAACGTCCAAATCA 59.118 45.455 0.00 0.00 31.31 2.57
471 480 4.202070 GGGAGAAACAACGTCCAAATCAAA 60.202 41.667 0.00 0.00 31.31 2.69
473 482 5.317733 AGAAACAACGTCCAAATCAAACA 57.682 34.783 0.00 0.00 0.00 2.83
477 486 1.588674 ACGTCCAAATCAAACAGCGA 58.411 45.000 0.00 0.00 0.00 4.93
481 498 2.293399 GTCCAAATCAAACAGCGAAGGT 59.707 45.455 0.00 0.00 41.48 3.50
498 515 3.642503 TCCGCGTTGGATGGGGTT 61.643 61.111 4.92 0.00 43.74 4.11
500 517 3.131478 CGCGTTGGATGGGGTTCC 61.131 66.667 0.00 0.00 36.24 3.62
501 518 3.131478 GCGTTGGATGGGGTTCCG 61.131 66.667 0.00 0.00 38.74 4.30
502 519 2.349755 CGTTGGATGGGGTTCCGT 59.650 61.111 0.00 0.00 38.74 4.69
504 521 1.377229 GTTGGATGGGGTTCCGTGA 59.623 57.895 0.00 0.00 38.74 4.35
505 522 0.034477 GTTGGATGGGGTTCCGTGAT 60.034 55.000 0.00 0.00 38.74 3.06
506 523 0.254747 TTGGATGGGGTTCCGTGATC 59.745 55.000 0.00 0.00 38.74 2.92
507 524 1.148498 GGATGGGGTTCCGTGATCC 59.852 63.158 0.00 0.00 35.24 3.36
510 527 1.268992 ATGGGGTTCCGTGATCCGAA 61.269 55.000 5.32 0.00 39.56 4.30
511 528 1.449070 GGGGTTCCGTGATCCGAAC 60.449 63.158 5.32 6.94 39.56 3.95
512 529 1.808390 GGGTTCCGTGATCCGAACG 60.808 63.158 5.32 1.51 39.56 3.95
513 530 1.080298 GGTTCCGTGATCCGAACGT 60.080 57.895 5.32 0.00 39.38 3.99
514 531 0.171007 GGTTCCGTGATCCGAACGTA 59.829 55.000 5.32 0.00 39.38 3.57
515 532 1.202336 GGTTCCGTGATCCGAACGTAT 60.202 52.381 5.32 0.00 39.38 3.06
517 534 0.248743 TCCGTGATCCGAACGTATGC 60.249 55.000 5.32 0.00 39.38 3.14
518 535 1.537289 CCGTGATCCGAACGTATGCG 61.537 60.000 0.19 0.19 39.38 4.73
531 548 5.418310 AACGTATGCGGATGATTTAAAGG 57.582 39.130 8.39 0.00 43.45 3.11
532 549 4.448210 ACGTATGCGGATGATTTAAAGGT 58.552 39.130 8.39 0.00 43.45 3.50
533 550 5.603596 ACGTATGCGGATGATTTAAAGGTA 58.396 37.500 8.39 0.00 43.45 3.08
534 551 6.050432 ACGTATGCGGATGATTTAAAGGTAA 58.950 36.000 8.39 0.00 43.45 2.85
537 554 4.850680 TGCGGATGATTTAAAGGTAAGGT 58.149 39.130 0.00 0.00 0.00 3.50
538 555 4.638421 TGCGGATGATTTAAAGGTAAGGTG 59.362 41.667 0.00 0.00 0.00 4.00
539 556 4.638865 GCGGATGATTTAAAGGTAAGGTGT 59.361 41.667 0.00 0.00 0.00 4.16
540 557 5.220796 GCGGATGATTTAAAGGTAAGGTGTC 60.221 44.000 0.00 0.00 0.00 3.67
541 558 5.006358 CGGATGATTTAAAGGTAAGGTGTCG 59.994 44.000 0.00 0.00 0.00 4.35
542 559 6.110707 GGATGATTTAAAGGTAAGGTGTCGA 58.889 40.000 0.00 0.00 0.00 4.20
553 570 1.115467 AGGTGTCGAAGATGCCCTAG 58.885 55.000 0.00 0.00 40.67 3.02
567 584 0.038709 CCCTAGCATAGCACGCTCTC 60.039 60.000 0.00 0.00 40.96 3.20
581 598 1.074752 GCTCTCTTTTCTGGAGCGTG 58.925 55.000 0.00 0.00 42.03 5.34
588 605 0.603707 TTTCTGGAGCGTGCCTGAAG 60.604 55.000 14.17 0.00 43.69 3.02
634 651 2.608268 GACTTCTACGTCCTTTCAGCC 58.392 52.381 0.00 0.00 0.00 4.85
637 654 0.543410 TCTACGTCCTTTCAGCCCCA 60.543 55.000 0.00 0.00 0.00 4.96
666 683 3.370104 TCCAAAGTCCAAGCTTCCAAAA 58.630 40.909 0.00 0.00 0.00 2.44
680 697 3.063510 TCCAAAACAGAGGAGCTCATG 57.936 47.619 17.19 13.18 32.06 3.07
762 779 2.264455 AGGAGAGCCATGGACCATATC 58.736 52.381 18.40 6.06 36.29 1.63
1022 1052 2.773993 TAAATTCTTTCCGTCCGCCT 57.226 45.000 0.00 0.00 0.00 5.52
1088 1124 1.523711 GAGCGCGGATTCCATTCCA 60.524 57.895 8.83 0.00 35.34 3.53
1152 1188 1.241315 CGATCAAACAAACCCGGCCT 61.241 55.000 0.00 0.00 0.00 5.19
1276 1312 1.278985 ACGATGTCATTTCTGCCAGGA 59.721 47.619 0.00 0.00 0.00 3.86
1311 1347 2.168728 GGAGCTCTTGTTCCCGTCTAAT 59.831 50.000 14.64 0.00 37.58 1.73
1504 1540 1.302511 GCCGCTTCTTCCAAGGTCA 60.303 57.895 0.00 0.00 0.00 4.02
1505 1541 1.578206 GCCGCTTCTTCCAAGGTCAC 61.578 60.000 0.00 0.00 0.00 3.67
1816 1861 4.444306 CCAAGGAAGAAATAGGATACGGCA 60.444 45.833 0.00 0.00 46.39 5.69
1860 1905 2.749044 CCGTCCTCCGTCCTCGAA 60.749 66.667 0.00 0.00 39.71 3.71
2069 2114 0.832135 AGGAGGAGCACTTTCACCGA 60.832 55.000 0.00 0.00 0.00 4.69
2082 2127 1.092348 TCACCGACTACGATCCTGTG 58.908 55.000 0.00 0.00 42.66 3.66
2253 2307 2.617274 GCGGCAAGGTGACAACTCC 61.617 63.158 0.00 0.00 0.00 3.85
2271 2325 0.440371 CCTGCGACGAAGAGCTTTTC 59.560 55.000 3.77 6.92 35.99 2.29
2373 2427 1.699054 TTAGGATGCAGCGGGCTCAT 61.699 55.000 0.00 0.00 45.15 2.90
2485 2540 4.405358 ACAACCTGAACAAATGGTGTCAAT 59.595 37.500 0.00 0.00 40.60 2.57
2498 2553 5.241403 TGGTGTCAATCAGTGGAATAAGT 57.759 39.130 0.00 0.00 0.00 2.24
2502 2557 4.455533 TGTCAATCAGTGGAATAAGTGTGC 59.544 41.667 0.00 0.00 0.00 4.57
2536 2591 2.421424 GCGCATCCTCTTTTTCTCACAT 59.579 45.455 0.30 0.00 0.00 3.21
2602 2657 8.993121 AGTAATGCTGCACATACATAGATTTAC 58.007 33.333 22.03 14.55 38.34 2.01
2603 2658 6.808008 ATGCTGCACATACATAGATTTACC 57.192 37.500 3.57 0.00 37.17 2.85
2606 2661 5.538118 CTGCACATACATAGATTTACCGGA 58.462 41.667 9.46 0.00 0.00 5.14
2607 2662 5.294356 TGCACATACATAGATTTACCGGAC 58.706 41.667 9.46 0.00 0.00 4.79
2610 2665 7.149973 GCACATACATAGATTTACCGGACTTA 58.850 38.462 9.46 0.00 0.00 2.24
2611 2666 7.328737 GCACATACATAGATTTACCGGACTTAG 59.671 40.741 9.46 0.00 0.00 2.18
2628 2687 3.826729 ACTTAGGCAGTTGGGTTTTGATC 59.173 43.478 0.00 0.00 27.32 2.92
2635 2694 3.758554 CAGTTGGGTTTTGATCGGAGATT 59.241 43.478 0.00 0.00 45.12 2.40
2639 2698 6.151144 AGTTGGGTTTTGATCGGAGATTAAAG 59.849 38.462 1.39 0.00 45.12 1.85
2643 2702 3.857157 TTGATCGGAGATTAAAGGGGG 57.143 47.619 0.00 0.00 45.12 5.40
2755 2837 6.015519 ACAACATAGCAAAAGCATAACCAGAA 60.016 34.615 0.00 0.00 0.00 3.02
2762 2844 2.270434 AGCATAACCAGAAGAGGGGA 57.730 50.000 0.00 0.00 0.00 4.81
2763 2845 2.122768 AGCATAACCAGAAGAGGGGAG 58.877 52.381 0.00 0.00 0.00 4.30
2829 2911 6.183360 GCAGTTTTTGTCACTCAACTTCAAAG 60.183 38.462 0.00 0.00 35.61 2.77
2872 2954 3.304458 GCTAAACTACACAACTTGCACCC 60.304 47.826 0.00 0.00 0.00 4.61
2938 3020 6.403866 TGAATGCTAACTCATTGTGGTTTT 57.596 33.333 0.00 0.00 36.85 2.43
2946 3028 6.723298 AACTCATTGTGGTTTTGACCAATA 57.277 33.333 0.00 0.00 42.10 1.90
2948 3030 5.132897 TCATTGTGGTTTTGACCAATAGC 57.867 39.130 0.00 0.00 42.10 2.97
2957 3039 1.898574 GACCAATAGCCGCCCATGG 60.899 63.158 4.14 4.14 37.19 3.66
3023 3105 6.264067 CCACACTTTCTTCTCTCTCCATTTTT 59.736 38.462 0.00 0.00 0.00 1.94
3024 3106 7.137426 CACACTTTCTTCTCTCTCCATTTTTG 58.863 38.462 0.00 0.00 0.00 2.44
3025 3107 6.148264 CACTTTCTTCTCTCTCCATTTTTGC 58.852 40.000 0.00 0.00 0.00 3.68
3026 3108 5.829924 ACTTTCTTCTCTCTCCATTTTTGCA 59.170 36.000 0.00 0.00 0.00 4.08
3027 3109 6.322201 ACTTTCTTCTCTCTCCATTTTTGCAA 59.678 34.615 0.00 0.00 0.00 4.08
3067 3149 1.487976 GGACTGATGAGATGGAGGCAA 59.512 52.381 0.00 0.00 0.00 4.52
3069 3151 1.911357 ACTGATGAGATGGAGGCAACA 59.089 47.619 0.00 0.00 41.41 3.33
3094 3176 2.349580 CGTTGTGACATCGATGATTGCT 59.650 45.455 31.33 8.90 0.00 3.91
3110 3192 2.820059 TGCTTAGGATACATCGCCTG 57.180 50.000 0.00 0.00 41.41 4.85
3116 3198 0.956633 GGATACATCGCCTGGTACGA 59.043 55.000 0.00 0.00 44.75 3.43
3300 3382 1.692519 ACTCTAACAAGGTGGCTTCGT 59.307 47.619 0.00 0.00 0.00 3.85
3350 3432 4.630894 TTGGATCGCATTGGTGTTATTC 57.369 40.909 0.00 0.00 0.00 1.75
3408 3490 6.957631 TGATCATACCACTCATAGTTTGGTT 58.042 36.000 0.00 0.00 40.98 3.67
3466 3548 5.458779 CGATCTCTATACGACAATGTTTGCA 59.541 40.000 0.00 0.00 0.00 4.08
3467 3549 6.560433 CGATCTCTATACGACAATGTTTGCAC 60.560 42.308 0.00 0.00 0.00 4.57
3469 3551 5.805486 TCTCTATACGACAATGTTTGCACTC 59.195 40.000 0.00 0.00 0.00 3.51
3473 3555 6.985188 ATACGACAATGTTTGCACTCTATT 57.015 33.333 0.00 0.00 0.00 1.73
3489 3571 6.017523 GCACTCTATTCCAAGCCTTCTTATTC 60.018 42.308 0.00 0.00 0.00 1.75
3497 3579 6.068010 TCCAAGCCTTCTTATTCAAAGACAA 58.932 36.000 0.00 0.00 0.00 3.18
3519 3601 3.080319 GCTTTCATCCTTGCAAGAGTCT 58.920 45.455 28.05 6.14 28.72 3.24
3556 3640 6.204852 TCATATAGCTGATTTCATTGGGGT 57.795 37.500 0.00 0.00 0.00 4.95
3595 3679 3.181491 TGGAGCCTTTTGAACAGTTTTCG 60.181 43.478 0.00 0.00 0.00 3.46
3596 3680 3.066203 GGAGCCTTTTGAACAGTTTTCGA 59.934 43.478 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.190578 CCACCGCTCCCCATCTTC 59.809 66.667 0.00 0.00 0.00 2.87
2 3 2.285368 TCCACCGCTCCCCATCTT 60.285 61.111 0.00 0.00 0.00 2.40
4 5 2.670148 AAGTCCACCGCTCCCCATC 61.670 63.158 0.00 0.00 0.00 3.51
8 9 3.637273 ACCAAGTCCACCGCTCCC 61.637 66.667 0.00 0.00 0.00 4.30
15 16 1.398390 GAATCGCATCACCAAGTCCAC 59.602 52.381 0.00 0.00 0.00 4.02
16 17 1.278985 AGAATCGCATCACCAAGTCCA 59.721 47.619 0.00 0.00 0.00 4.02
20 21 1.202222 GGCAAGAATCGCATCACCAAG 60.202 52.381 0.00 0.00 0.00 3.61
27 28 2.475466 CGCTGGGCAAGAATCGCAT 61.475 57.895 0.00 0.00 0.00 4.73
28 29 3.126879 CGCTGGGCAAGAATCGCA 61.127 61.111 0.00 0.00 0.00 5.10
42 43 4.894114 TCTATTTAAAGGAGGCTAGACGCT 59.106 41.667 0.00 0.00 39.13 5.07
49 50 3.117851 GCACCCTCTATTTAAAGGAGGCT 60.118 47.826 23.75 14.23 43.66 4.58
69 70 2.032528 CAAAGCTCCTCCCGTGCA 59.967 61.111 0.00 0.00 33.25 4.57
71 72 2.747855 GGCAAAGCTCCTCCCGTG 60.748 66.667 0.00 0.00 0.00 4.94
74 75 2.044551 CAGGGCAAAGCTCCTCCC 60.045 66.667 8.62 8.62 39.05 4.30
76 77 0.969409 AATGCAGGGCAAAGCTCCTC 60.969 55.000 0.00 0.00 43.62 3.71
90 91 2.352225 GGCCGACATTAAACACAATGCA 60.352 45.455 0.00 0.00 39.13 3.96
93 94 2.230266 GTGGGCCGACATTAAACACAAT 59.770 45.455 13.75 0.00 0.00 2.71
111 112 1.733912 CACATGTCCATTCACGAGTGG 59.266 52.381 0.00 2.27 39.31 4.00
113 114 2.612972 GGTCACATGTCCATTCACGAGT 60.613 50.000 0.00 0.00 0.00 4.18
122 124 1.182667 CTACTCCGGTCACATGTCCA 58.817 55.000 0.00 0.00 0.00 4.02
127 129 1.975680 ACAAACCTACTCCGGTCACAT 59.024 47.619 0.00 0.00 35.89 3.21
132 134 0.600057 GACGACAAACCTACTCCGGT 59.400 55.000 0.00 0.00 39.48 5.28
142 144 0.580104 CGGTGTGGAAGACGACAAAC 59.420 55.000 0.00 0.00 36.59 2.93
146 148 0.531311 AAACCGGTGTGGAAGACGAC 60.531 55.000 8.52 0.00 42.00 4.34
154 156 1.459450 CCTCCATTAAACCGGTGTGG 58.541 55.000 8.52 14.83 46.41 4.17
157 159 1.762708 ATGCCTCCATTAAACCGGTG 58.237 50.000 8.52 0.00 0.00 4.94
158 160 2.495669 CAAATGCCTCCATTAAACCGGT 59.504 45.455 0.00 0.00 40.69 5.28
159 161 2.757868 TCAAATGCCTCCATTAAACCGG 59.242 45.455 0.00 0.00 40.69 5.28
160 162 4.448537 TTCAAATGCCTCCATTAAACCG 57.551 40.909 0.00 0.00 40.69 4.44
180 182 4.181010 ATGCCTCCTCGCCGCATT 62.181 61.111 0.00 0.00 40.23 3.56
185 187 1.817099 CAGAACATGCCTCCTCGCC 60.817 63.158 0.00 0.00 0.00 5.54
195 197 4.465512 GCACGCCGGCAGAACATG 62.466 66.667 28.98 14.64 0.00 3.21
230 232 0.239879 CATTAAAACGGCGCACCAGT 59.760 50.000 10.83 0.00 34.57 4.00
232 234 1.173444 ACCATTAAAACGGCGCACCA 61.173 50.000 10.83 0.00 34.57 4.17
235 237 0.949588 TCGACCATTAAAACGGCGCA 60.950 50.000 10.83 0.00 0.00 6.09
241 243 3.071479 TCACTGCCTCGACCATTAAAAC 58.929 45.455 0.00 0.00 0.00 2.43
242 244 3.007506 TCTCACTGCCTCGACCATTAAAA 59.992 43.478 0.00 0.00 0.00 1.52
251 253 2.677979 CGACGTCTCACTGCCTCGA 61.678 63.158 14.70 0.00 0.00 4.04
265 267 2.494591 GCTTAGAACGGACGCGACG 61.495 63.158 15.93 19.85 37.36 5.12
267 269 2.180017 GGCTTAGAACGGACGCGA 59.820 61.111 15.93 0.00 0.00 5.87
270 272 0.109412 AAGACGGCTTAGAACGGACG 60.109 55.000 0.00 0.00 40.16 4.79
272 274 1.250328 TGAAGACGGCTTAGAACGGA 58.750 50.000 1.76 0.00 33.61 4.69
274 276 4.209288 CCATATTGAAGACGGCTTAGAACG 59.791 45.833 1.76 0.00 33.61 3.95
276 278 5.453339 CCTCCATATTGAAGACGGCTTAGAA 60.453 44.000 1.76 0.00 33.61 2.10
277 279 4.039245 CCTCCATATTGAAGACGGCTTAGA 59.961 45.833 1.76 0.00 33.61 2.10
280 282 2.158755 CCCTCCATATTGAAGACGGCTT 60.159 50.000 1.10 1.10 36.96 4.35
290 292 0.886490 GAGCGTGCCCCTCCATATTG 60.886 60.000 0.00 0.00 0.00 1.90
294 296 2.041922 TAGAGCGTGCCCCTCCAT 60.042 61.111 0.00 0.00 0.00 3.41
307 309 2.094894 CCGCATTCTTGTTGCTGTAGAG 59.905 50.000 0.00 0.00 37.96 2.43
312 314 1.444895 GCCCGCATTCTTGTTGCTG 60.445 57.895 0.00 0.00 37.96 4.41
313 315 1.870055 CTGCCCGCATTCTTGTTGCT 61.870 55.000 0.00 0.00 37.96 3.91
314 316 1.444895 CTGCCCGCATTCTTGTTGC 60.445 57.895 0.00 0.00 36.74 4.17
315 317 1.444895 GCTGCCCGCATTCTTGTTG 60.445 57.895 0.00 0.00 38.92 3.33
316 318 1.604593 AGCTGCCCGCATTCTTGTT 60.605 52.632 0.00 0.00 42.61 2.83
363 365 2.203182 ACCCGAACCACTCCTCCA 59.797 61.111 0.00 0.00 0.00 3.86
365 367 2.663196 CCACCCGAACCACTCCTC 59.337 66.667 0.00 0.00 0.00 3.71
390 392 2.993264 ACTACCCACACCCGTCCG 60.993 66.667 0.00 0.00 0.00 4.79
391 393 2.163601 GACACTACCCACACCCGTCC 62.164 65.000 0.00 0.00 0.00 4.79
393 395 2.567497 CGACACTACCCACACCCGT 61.567 63.158 0.00 0.00 0.00 5.28
395 397 1.474332 TTCCGACACTACCCACACCC 61.474 60.000 0.00 0.00 0.00 4.61
397 399 1.722011 CATTCCGACACTACCCACAC 58.278 55.000 0.00 0.00 0.00 3.82
398 400 0.036765 GCATTCCGACACTACCCACA 60.037 55.000 0.00 0.00 0.00 4.17
411 419 4.147449 GGGCTTTGCGGGCATTCC 62.147 66.667 0.00 0.00 0.00 3.01
413 421 0.760189 ATATGGGCTTTGCGGGCATT 60.760 50.000 0.00 0.00 0.00 3.56
415 423 0.975040 AAATATGGGCTTTGCGGGCA 60.975 50.000 0.00 0.00 0.00 5.36
420 428 3.438360 CGAAGACAAATATGGGCTTTGC 58.562 45.455 0.00 0.00 37.15 3.68
429 437 5.088680 TCCCGTAAACCGAAGACAAATAT 57.911 39.130 0.00 0.00 39.56 1.28
430 438 4.220382 TCTCCCGTAAACCGAAGACAAATA 59.780 41.667 0.00 0.00 39.56 1.40
431 439 3.007182 TCTCCCGTAAACCGAAGACAAAT 59.993 43.478 0.00 0.00 39.56 2.32
439 448 2.482864 GTTGTTTCTCCCGTAAACCGA 58.517 47.619 0.00 0.00 39.56 4.69
441 450 2.212652 ACGTTGTTTCTCCCGTAAACC 58.787 47.619 0.00 0.00 36.26 3.27
447 456 1.301423 TTTGGACGTTGTTTCTCCCG 58.699 50.000 0.00 0.00 0.00 5.14
449 458 4.561735 TTGATTTGGACGTTGTTTCTCC 57.438 40.909 0.00 0.00 0.00 3.71
450 459 5.336744 TGTTTGATTTGGACGTTGTTTCTC 58.663 37.500 0.00 0.00 0.00 2.87
452 461 4.026886 GCTGTTTGATTTGGACGTTGTTTC 60.027 41.667 0.00 0.00 0.00 2.78
456 465 2.043411 CGCTGTTTGATTTGGACGTTG 58.957 47.619 0.00 0.00 0.00 4.10
457 466 1.944024 TCGCTGTTTGATTTGGACGTT 59.056 42.857 0.00 0.00 0.00 3.99
459 468 2.574322 CTTCGCTGTTTGATTTGGACG 58.426 47.619 0.00 0.00 0.00 4.79
467 476 4.354155 CGGACCTTCGCTGTTTGA 57.646 55.556 0.00 0.00 0.00 2.69
485 502 2.038269 CACGGAACCCCATCCAACG 61.038 63.158 0.00 0.00 39.61 4.10
494 511 1.808390 CGTTCGGATCACGGAACCC 60.808 63.158 14.23 0.00 46.41 4.11
496 513 1.850441 CATACGTTCGGATCACGGAAC 59.150 52.381 8.68 10.19 45.99 3.62
498 515 0.248743 GCATACGTTCGGATCACGGA 60.249 55.000 8.68 0.44 44.45 4.69
500 517 1.837450 CGCATACGTTCGGATCACG 59.163 57.895 0.00 2.79 43.52 4.35
506 523 1.497991 AATCATCCGCATACGTTCGG 58.502 50.000 14.77 14.77 46.52 4.30
507 524 4.702247 TTAAATCATCCGCATACGTTCG 57.298 40.909 0.00 0.00 37.70 3.95
510 527 4.448210 ACCTTTAAATCATCCGCATACGT 58.552 39.130 0.00 0.00 37.70 3.57
511 528 6.347402 CCTTACCTTTAAATCATCCGCATACG 60.347 42.308 0.00 0.00 39.67 3.06
512 529 6.485648 ACCTTACCTTTAAATCATCCGCATAC 59.514 38.462 0.00 0.00 0.00 2.39
513 530 6.485313 CACCTTACCTTTAAATCATCCGCATA 59.515 38.462 0.00 0.00 0.00 3.14
514 531 5.299279 CACCTTACCTTTAAATCATCCGCAT 59.701 40.000 0.00 0.00 0.00 4.73
515 532 4.638421 CACCTTACCTTTAAATCATCCGCA 59.362 41.667 0.00 0.00 0.00 5.69
517 534 5.006358 CGACACCTTACCTTTAAATCATCCG 59.994 44.000 0.00 0.00 0.00 4.18
518 535 6.110707 TCGACACCTTACCTTTAAATCATCC 58.889 40.000 0.00 0.00 0.00 3.51
520 537 7.391620 TCTTCGACACCTTACCTTTAAATCAT 58.608 34.615 0.00 0.00 0.00 2.45
521 538 6.761312 TCTTCGACACCTTACCTTTAAATCA 58.239 36.000 0.00 0.00 0.00 2.57
522 539 7.676572 GCATCTTCGACACCTTACCTTTAAATC 60.677 40.741 0.00 0.00 0.00 2.17
523 540 6.093633 GCATCTTCGACACCTTACCTTTAAAT 59.906 38.462 0.00 0.00 0.00 1.40
524 541 5.410439 GCATCTTCGACACCTTACCTTTAAA 59.590 40.000 0.00 0.00 0.00 1.52
527 544 3.335579 GCATCTTCGACACCTTACCTTT 58.664 45.455 0.00 0.00 0.00 3.11
531 548 1.207329 AGGGCATCTTCGACACCTTAC 59.793 52.381 0.00 0.00 0.00 2.34
532 549 1.568504 AGGGCATCTTCGACACCTTA 58.431 50.000 0.00 0.00 0.00 2.69
533 550 1.482593 CTAGGGCATCTTCGACACCTT 59.517 52.381 0.00 0.00 0.00 3.50
534 551 1.115467 CTAGGGCATCTTCGACACCT 58.885 55.000 0.00 0.00 0.00 4.00
537 554 2.590704 TGCTAGGGCATCTTCGACA 58.409 52.632 0.00 0.00 44.28 4.35
553 570 2.030213 CAGAAAAGAGAGCGTGCTATGC 59.970 50.000 0.00 0.00 0.00 3.14
567 584 0.603707 TCAGGCACGCTCCAGAAAAG 60.604 55.000 0.00 0.00 0.00 2.27
581 598 0.108615 TTCAGTCGCTAGCTTCAGGC 60.109 55.000 13.93 0.00 42.19 4.85
588 605 0.320421 TGGGTTGTTCAGTCGCTAGC 60.320 55.000 4.06 4.06 0.00 3.42
634 651 2.437359 CTTTGGAGCCGAGCTGGG 60.437 66.667 10.99 10.99 39.88 4.45
637 654 1.768684 TTGGACTTTGGAGCCGAGCT 61.769 55.000 0.00 0.00 43.88 4.09
861 890 1.213094 CGAAAAGGACTCGTGTGCGT 61.213 55.000 3.43 0.00 39.62 5.24
1022 1052 2.029964 GGTCGGGAAGCAACACGA 59.970 61.111 3.52 3.52 43.49 4.35
1088 1124 2.029828 CGATCGAGAAGGAAATCCGGAT 60.030 50.000 12.38 12.38 42.08 4.18
1162 1198 4.452733 GACTTGGGGTCTCGGGCG 62.453 72.222 0.00 0.00 41.46 6.13
1276 1312 4.172512 CTCCAGAGCCCGCTGCAT 62.173 66.667 0.00 0.00 44.83 3.96
1489 1525 0.034896 TCGGTGACCTTGGAAGAAGC 59.965 55.000 0.00 0.00 0.00 3.86
1504 1540 3.418068 GGACTCGTCGTCGTCGGT 61.418 66.667 11.74 8.53 43.79 4.69
1505 1541 4.495939 CGGACTCGTCGTCGTCGG 62.496 72.222 11.74 5.61 43.79 4.79
1860 1905 3.394836 GAGAGGGTCAAGCCGGCT 61.395 66.667 27.08 27.08 38.44 5.52
2069 2114 1.384989 CGGAGCCACAGGATCGTAGT 61.385 60.000 0.00 0.00 39.27 2.73
2082 2127 2.938539 CTTGATCGTCGGACGGAGCC 62.939 65.000 28.07 15.53 42.81 4.70
2239 2293 0.249868 TCGCAGGAGTTGTCACCTTG 60.250 55.000 0.00 0.00 32.49 3.61
2253 2307 0.092014 CGAAAAGCTCTTCGTCGCAG 59.908 55.000 14.04 0.00 42.53 5.18
2293 2347 3.141488 CACCTCGTCCTCCTCCGG 61.141 72.222 0.00 0.00 0.00 5.14
2485 2540 1.438651 GCGCACACTTATTCCACTGA 58.561 50.000 0.30 0.00 0.00 3.41
2498 2553 2.468670 GCACAATATCCCGCGCACA 61.469 57.895 8.75 0.00 0.00 4.57
2536 2591 9.907576 CAATAAAACGTGCTTTATCAAACAAAA 57.092 25.926 5.86 0.00 31.66 2.44
2602 2657 1.078426 CCCAACTGCCTAAGTCCGG 60.078 63.158 0.00 0.00 38.56 5.14
2603 2658 0.036306 AACCCAACTGCCTAAGTCCG 59.964 55.000 0.00 0.00 38.56 4.79
2606 2661 3.306472 TCAAAACCCAACTGCCTAAGT 57.694 42.857 0.00 0.00 42.60 2.24
2607 2662 3.119849 CGATCAAAACCCAACTGCCTAAG 60.120 47.826 0.00 0.00 0.00 2.18
2610 2665 1.247567 CGATCAAAACCCAACTGCCT 58.752 50.000 0.00 0.00 0.00 4.75
2611 2666 0.243636 CCGATCAAAACCCAACTGCC 59.756 55.000 0.00 0.00 0.00 4.85
2647 2706 1.304134 GATTTTCACGGGGTGCCCT 60.304 57.895 7.26 0.00 42.67 5.19
2657 2716 5.167303 ACTAACCTCTCCCTGATTTTCAC 57.833 43.478 0.00 0.00 0.00 3.18
2755 2837 2.418669 TGAACCTTTTCACTCCCCTCT 58.581 47.619 0.00 0.00 36.79 3.69
2781 2863 4.024809 CACAAGTCGCTATATCGAGAGACA 60.025 45.833 10.74 0.00 45.58 3.41
2789 2871 5.470845 AAAACTGCACAAGTCGCTATATC 57.529 39.130 0.00 0.00 38.56 1.63
2872 2954 3.064271 TCTTGTCCGGTTTGAAAAGTTCG 59.936 43.478 0.00 0.00 32.41 3.95
2912 2994 6.594788 ACCACAATGAGTTAGCATTCAAAT 57.405 33.333 0.00 0.00 36.39 2.32
2938 3020 1.152984 CATGGGCGGCTATTGGTCA 60.153 57.895 9.56 0.00 0.00 4.02
2957 3039 3.648545 AGTAGGGAAGAGATACATTGCCC 59.351 47.826 0.00 0.00 37.61 5.36
3023 3105 2.156917 CTCATTCAGTTCCAGCTTGCA 58.843 47.619 0.00 0.00 0.00 4.08
3024 3106 1.471684 CCTCATTCAGTTCCAGCTTGC 59.528 52.381 0.00 0.00 0.00 4.01
3025 3107 1.471684 GCCTCATTCAGTTCCAGCTTG 59.528 52.381 0.00 0.00 0.00 4.01
3026 3108 1.615384 GGCCTCATTCAGTTCCAGCTT 60.615 52.381 0.00 0.00 0.00 3.74
3027 3109 0.034670 GGCCTCATTCAGTTCCAGCT 60.035 55.000 0.00 0.00 0.00 4.24
3069 3151 1.000394 TCATCGATGTCACAACGGTGT 60.000 47.619 24.09 0.00 45.45 4.16
3094 3176 2.555325 CGTACCAGGCGATGTATCCTAA 59.445 50.000 0.00 0.00 0.00 2.69
3110 3192 5.312120 ACATATCGAATCTCCATCGTACC 57.688 43.478 0.00 0.00 40.99 3.34
3116 3198 6.267699 TCCTACACAACATATCGAATCTCCAT 59.732 38.462 0.00 0.00 0.00 3.41
3222 3304 3.763360 CCCAACACCAATGCTCATCTTTA 59.237 43.478 0.00 0.00 0.00 1.85
3232 3314 0.831288 TCTTGGGCCCAACACCAATG 60.831 55.000 34.07 21.27 45.03 2.82
3315 3397 5.601662 TGCGATCCAATACTTCTCTTAAGG 58.398 41.667 1.85 0.00 0.00 2.69
3368 3450 9.822185 TGGTATGATCATACAGCATATAATGAC 57.178 33.333 35.28 19.63 44.09 3.06
3381 3463 8.150945 ACCAAACTATGAGTGGTATGATCATAC 58.849 37.037 30.03 30.03 43.90 2.39
3382 3464 8.262601 ACCAAACTATGAGTGGTATGATCATA 57.737 34.615 11.49 11.49 43.90 2.15
3384 3466 6.560003 ACCAAACTATGAGTGGTATGATCA 57.440 37.500 0.00 0.00 43.90 2.92
3385 3467 7.865706 AAACCAAACTATGAGTGGTATGATC 57.134 36.000 0.00 0.00 44.99 2.92
3387 3469 6.657541 GGAAAACCAAACTATGAGTGGTATGA 59.342 38.462 0.00 0.00 44.99 2.15
3424 3506 8.183104 AGAGATCGAATACACTCATATTTGGA 57.817 34.615 0.00 0.00 32.59 3.53
3442 3524 5.458779 TGCAAACATTGTCGTATAGAGATCG 59.541 40.000 0.00 0.00 0.00 3.69
3453 3535 4.154015 TGGAATAGAGTGCAAACATTGTCG 59.846 41.667 0.00 0.00 0.00 4.35
3466 3548 7.200434 TGAATAAGAAGGCTTGGAATAGAGT 57.800 36.000 3.46 0.00 35.56 3.24
3467 3549 8.511604 TTTGAATAAGAAGGCTTGGAATAGAG 57.488 34.615 3.46 0.00 35.56 2.43
3469 3551 8.401709 GTCTTTGAATAAGAAGGCTTGGAATAG 58.598 37.037 3.46 0.00 35.56 1.73
3473 3555 5.630121 TGTCTTTGAATAAGAAGGCTTGGA 58.370 37.500 3.46 0.00 35.56 3.53
3489 3571 3.985925 GCAAGGATGAAAGCTTGTCTTTG 59.014 43.478 18.89 18.89 44.58 2.77
3497 3579 3.080319 GACTCTTGCAAGGATGAAAGCT 58.920 45.455 25.73 6.10 41.39 3.74
3595 3679 2.317530 AGCGAATTGTAGGCTTCCTC 57.682 50.000 0.00 0.00 34.61 3.71
3596 3680 2.481449 CGTAGCGAATTGTAGGCTTCCT 60.481 50.000 0.00 0.00 38.19 3.36


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

AutoCloner maintained by Alex Coulton.