Multiple sequence alignment - TraesCS5B01G248200

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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 TraesCS5B01G248200 chr5B 100.000 3206 0 0 1 3206 430471137 430474342 0.000000e+00 5921.0
1 TraesCS5B01G248200 chr5A 94.188 3252 120 29 1 3206 465546256 465549484 0.000000e+00 4894.0
2 TraesCS5B01G248200 chr5A 95.000 40 2 0 2506 2545 465548832 465548871 2.670000e-06 63.9
3 TraesCS5B01G248200 chr5D 97.457 2477 46 5 1 2472 364399651 364402115 0.000000e+00 4209.0
4 TraesCS5B01G248200 chr5D 90.588 680 44 5 2544 3205 364402155 364402832 0.000000e+00 883.0
5 TraesCS5B01G248200 chr5D 100.000 37 0 0 2506 2542 364402183 364402219 5.740000e-08 69.4
6 TraesCS5B01G248200 chr7D 88.369 834 95 2 1045 1877 318252547 318251715 0.000000e+00 1002.0
7 TraesCS5B01G248200 chr7B 87.049 803 101 3 1076 1877 302512526 302513326 0.000000e+00 904.0
8 TraesCS5B01G248200 chr7B 86.325 819 109 3 1045 1862 302545710 302546526 0.000000e+00 889.0


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 TraesCS5B01G248200 chr5B 430471137 430474342 3205 False 5921.000000 5921 100.000 1 3206 1 chr5B.!!$F1 3205
1 TraesCS5B01G248200 chr5A 465546256 465549484 3228 False 2478.950000 4894 94.594 1 3206 2 chr5A.!!$F1 3205
2 TraesCS5B01G248200 chr5D 364399651 364402832 3181 False 1720.466667 4209 96.015 1 3205 3 chr5D.!!$F1 3204
3 TraesCS5B01G248200 chr7D 318251715 318252547 832 True 1002.000000 1002 88.369 1045 1877 1 chr7D.!!$R1 832
4 TraesCS5B01G248200 chr7B 302512526 302513326 800 False 904.000000 904 87.049 1076 1877 1 chr7B.!!$F1 801
5 TraesCS5B01G248200 chr7B 302545710 302546526 816 False 889.000000 889 86.325 1045 1862 1 chr7B.!!$F2 817

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
198 199 0.036010 CCAGTCCTGCAGTCCGATTT 60.036 55.0 13.81 0.0 0.0 2.17 F
264 265 0.542702 AATCAACAGCCACCCCCTTG 60.543 55.0 0.00 0.0 0.0 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2196 2202 1.001706 CCCATCAGCATTCATTCAGCG 60.002 52.381 0.0 0.0 0.00 5.18 R
2298 2306 2.812011 GACAAGGCGTCCAATTACAACT 59.188 45.455 0.0 0.0 38.85 3.16 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
198 199 0.036010 CCAGTCCTGCAGTCCGATTT 60.036 55.000 13.81 0.00 0.00 2.17
225 226 1.481056 CCTCCCCATACGGATCCACC 61.481 65.000 13.41 0.00 0.00 4.61
240 241 1.734477 CACCAACTCCGCGAGTCTG 60.734 63.158 8.23 10.00 42.59 3.51
264 265 0.542702 AATCAACAGCCACCCCCTTG 60.543 55.000 0.00 0.00 0.00 3.61
477 478 0.753867 GGTTCTCGGAATCCTCCTCC 59.246 60.000 0.00 0.00 39.93 4.30
957 958 5.620654 CGCTCCACTGATCAAATTGAAACAT 60.621 40.000 0.00 0.00 0.00 2.71
973 974 1.142688 ACATTGAGCCCCCAACTCCT 61.143 55.000 0.00 0.00 32.98 3.69
1458 1463 3.561213 CCGCTCATGTGCTCGCTG 61.561 66.667 16.99 1.89 0.00 5.18
2196 2202 1.527844 GGATCCCAGGCACAGCATC 60.528 63.158 0.00 0.00 0.00 3.91
2298 2306 6.015350 GGCTCAGCTAGTCCATACTTGTATTA 60.015 42.308 0.00 0.00 37.15 0.98
2395 2406 8.227791 TGAAAATACGCTCATGTTAGAAACTTC 58.772 33.333 0.00 0.00 0.00 3.01
2488 2516 4.473520 CGGCGGGAGATGGCAACT 62.474 66.667 0.00 0.00 37.61 3.16
2489 2517 2.514824 GGCGGGAGATGGCAACTC 60.515 66.667 15.71 15.71 37.61 3.01
2495 2523 0.460987 GGAGATGGCAACTCCGACTG 60.461 60.000 25.45 0.00 43.25 3.51
2498 2526 1.137872 AGATGGCAACTCCGACTGATC 59.862 52.381 0.00 0.00 37.80 2.92
2509 2537 1.070821 CGACTGATCGCAGCAGAAAA 58.929 50.000 8.13 0.00 46.26 2.29
2510 2538 1.201855 CGACTGATCGCAGCAGAAAAC 60.202 52.381 8.13 0.00 46.26 2.43
2512 2540 2.481952 GACTGATCGCAGCAGAAAACTT 59.518 45.455 8.13 0.00 46.26 2.66
2513 2541 2.225019 ACTGATCGCAGCAGAAAACTTG 59.775 45.455 8.13 0.00 46.26 3.16
2515 2543 3.076621 TGATCGCAGCAGAAAACTTGAT 58.923 40.909 0.00 0.00 0.00 2.57
2516 2544 4.252878 TGATCGCAGCAGAAAACTTGATA 58.747 39.130 0.00 0.00 0.00 2.15
2517 2545 4.877823 TGATCGCAGCAGAAAACTTGATAT 59.122 37.500 0.00 0.00 0.00 1.63
2519 2547 4.252878 TCGCAGCAGAAAACTTGATATCA 58.747 39.130 0.00 0.00 0.00 2.15
2520 2548 4.093408 TCGCAGCAGAAAACTTGATATCAC 59.907 41.667 4.48 0.00 0.00 3.06
2521 2549 4.337763 GCAGCAGAAAACTTGATATCACG 58.662 43.478 4.48 6.26 0.00 4.35
2523 2551 4.631377 CAGCAGAAAACTTGATATCACGGA 59.369 41.667 13.25 0.00 0.00 4.69
2525 2553 4.034510 GCAGAAAACTTGATATCACGGAGG 59.965 45.833 13.25 1.80 0.00 4.30
2527 2555 5.874810 CAGAAAACTTGATATCACGGAGGAA 59.125 40.000 13.25 0.00 0.00 3.36
2528 2556 6.036517 CAGAAAACTTGATATCACGGAGGAAG 59.963 42.308 13.25 5.61 0.00 3.46
2529 2557 5.677319 AAACTTGATATCACGGAGGAAGA 57.323 39.130 13.25 0.00 0.00 2.87
2530 2558 5.677319 AACTTGATATCACGGAGGAAGAA 57.323 39.130 13.25 0.00 0.00 2.52
2531 2559 5.269505 ACTTGATATCACGGAGGAAGAAG 57.730 43.478 13.25 3.63 0.00 2.85
2532 2560 3.735237 TGATATCACGGAGGAAGAAGC 57.265 47.619 0.00 0.00 0.00 3.86
2533 2561 2.034685 TGATATCACGGAGGAAGAAGCG 59.965 50.000 0.00 0.00 0.00 4.68
2535 2563 0.173708 ATCACGGAGGAAGAAGCGAC 59.826 55.000 0.00 0.00 0.00 5.19
2536 2564 0.894184 TCACGGAGGAAGAAGCGACT 60.894 55.000 0.00 0.00 0.00 4.18
2537 2565 0.456995 CACGGAGGAAGAAGCGACTC 60.457 60.000 0.00 0.00 0.00 3.36
2539 2567 1.316706 CGGAGGAAGAAGCGACTCCT 61.317 60.000 7.83 0.02 45.71 3.69
2540 2568 0.458260 GGAGGAAGAAGCGACTCCTC 59.542 60.000 15.04 15.04 44.74 3.71
2541 2569 1.470051 GAGGAAGAAGCGACTCCTCT 58.530 55.000 15.73 2.81 42.58 3.69
2542 2570 2.645802 GAGGAAGAAGCGACTCCTCTA 58.354 52.381 15.73 0.00 42.58 2.43
2576 2604 1.340017 TGGAGGAAGCCATCGGAAAAG 60.340 52.381 0.00 0.00 31.66 2.27
2586 2614 5.380043 AGCCATCGGAAAAGTTGATATCAT 58.620 37.500 6.17 0.00 0.00 2.45
2641 2669 5.448496 CGATTCTGTTGAGTGTTCAAAACCA 60.448 40.000 0.00 0.00 44.49 3.67
2642 2670 4.963276 TCTGTTGAGTGTTCAAAACCAG 57.037 40.909 0.00 0.00 44.49 4.00
2643 2671 3.694072 TCTGTTGAGTGTTCAAAACCAGG 59.306 43.478 6.56 0.00 44.49 4.45
2644 2672 3.691575 TGTTGAGTGTTCAAAACCAGGA 58.308 40.909 0.00 0.00 44.49 3.86
2645 2673 4.082845 TGTTGAGTGTTCAAAACCAGGAA 58.917 39.130 0.00 0.00 44.49 3.36
2646 2674 4.709397 TGTTGAGTGTTCAAAACCAGGAAT 59.291 37.500 0.00 0.00 44.49 3.01
2670 2715 8.761575 ATGTCTTTATCGCAATTTGTTTCATT 57.238 26.923 0.00 0.00 0.00 2.57
2674 2721 8.423973 TCTTTATCGCAATTTGTTTCATTTTCG 58.576 29.630 0.00 0.00 0.00 3.46
2690 2737 3.579147 TTTCGGACAATATTTAGCGCG 57.421 42.857 0.00 0.00 0.00 6.86
2774 2821 8.049117 TGTTATAGGCTGAATTTGAATCTCAGT 58.951 33.333 0.00 0.00 39.05 3.41
2775 2822 8.897752 GTTATAGGCTGAATTTGAATCTCAGTT 58.102 33.333 0.00 0.04 39.05 3.16
2781 2828 6.127814 GCTGAATTTGAATCTCAGTTGGATCA 60.128 38.462 0.00 0.00 39.05 2.92
2805 2852 1.374758 CGTGTCTGGGAAGGCTCAC 60.375 63.158 0.00 0.00 0.00 3.51
2990 3037 0.316841 TCCTTTGCAAATTGACCCGC 59.683 50.000 13.23 0.00 0.00 6.13
3022 3069 4.422057 TCTAAGGGTTCATGTCACCACTA 58.578 43.478 15.86 7.59 35.80 2.74
3078 3125 0.727398 GATTCGGCAAGAAGGAACCG 59.273 55.000 0.00 0.00 46.97 4.44
3137 3185 6.016777 ACCTCACTTTTGCTTTTCATCTAGTG 60.017 38.462 0.00 0.00 33.09 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.819208 CTGGATCAATTGCCGCCGA 60.819 57.895 0.00 0.00 0.00 5.54
198 199 1.271762 CCGTATGGGGAGGAGATACGA 60.272 57.143 11.32 0.00 44.94 3.43
225 226 2.811317 GCCAGACTCGCGGAGTTG 60.811 66.667 6.13 9.37 43.53 3.16
240 241 1.293179 GGTGGCTGTTGATTTGGCC 59.707 57.895 0.00 0.00 44.31 5.36
264 265 1.747745 CCGGGATTTGACGAACCCC 60.748 63.158 0.00 0.00 39.20 4.95
329 330 3.776781 CCACGATACCGGTGCCCA 61.777 66.667 19.93 0.00 40.78 5.36
957 958 2.231380 GGAGGAGTTGGGGGCTCAA 61.231 63.158 0.00 0.00 34.83 3.02
2196 2202 1.001706 CCCATCAGCATTCATTCAGCG 60.002 52.381 0.00 0.00 0.00 5.18
2298 2306 2.812011 GACAAGGCGTCCAATTACAACT 59.188 45.455 0.00 0.00 38.85 3.16
2395 2406 2.846827 AGAGGGTATTGGTTTCAGGGAG 59.153 50.000 0.00 0.00 0.00 4.30
2437 2465 1.745115 CGCCCTGCCGAAGATCAAA 60.745 57.895 0.00 0.00 0.00 2.69
2495 2523 3.754188 ATCAAGTTTTCTGCTGCGATC 57.246 42.857 0.00 0.00 0.00 3.69
2498 2526 4.337763 GTGATATCAAGTTTTCTGCTGCG 58.662 43.478 7.07 0.00 0.00 5.18
2509 2537 4.442192 GCTTCTTCCTCCGTGATATCAAGT 60.442 45.833 16.05 0.00 0.00 3.16
2510 2538 4.054671 GCTTCTTCCTCCGTGATATCAAG 58.945 47.826 7.07 9.46 0.00 3.02
2512 2540 2.034685 CGCTTCTTCCTCCGTGATATCA 59.965 50.000 0.00 0.00 0.00 2.15
2513 2541 2.293677 TCGCTTCTTCCTCCGTGATATC 59.706 50.000 0.00 0.00 0.00 1.63
2515 2543 1.404391 GTCGCTTCTTCCTCCGTGATA 59.596 52.381 0.00 0.00 0.00 2.15
2516 2544 0.173708 GTCGCTTCTTCCTCCGTGAT 59.826 55.000 0.00 0.00 0.00 3.06
2517 2545 0.894184 AGTCGCTTCTTCCTCCGTGA 60.894 55.000 0.00 0.00 0.00 4.35
2519 2547 1.596895 GGAGTCGCTTCTTCCTCCGT 61.597 60.000 0.00 0.00 34.62 4.69
2520 2548 1.139947 GGAGTCGCTTCTTCCTCCG 59.860 63.158 0.00 0.00 34.62 4.63
2521 2549 0.458260 GAGGAGTCGCTTCTTCCTCC 59.542 60.000 8.27 0.00 43.14 4.30
2523 2551 2.025699 ACTAGAGGAGTCGCTTCTTCCT 60.026 50.000 0.00 0.00 34.41 3.36
2525 2553 3.486209 CGAACTAGAGGAGTCGCTTCTTC 60.486 52.174 0.00 0.00 37.44 2.87
2527 2555 2.011222 CGAACTAGAGGAGTCGCTTCT 58.989 52.381 0.00 0.00 37.44 2.85
2528 2556 1.064357 CCGAACTAGAGGAGTCGCTTC 59.936 57.143 0.00 0.00 37.44 3.86
2529 2557 1.096416 CCGAACTAGAGGAGTCGCTT 58.904 55.000 0.00 0.00 37.44 4.68
2530 2558 1.378124 GCCGAACTAGAGGAGTCGCT 61.378 60.000 0.00 0.00 37.44 4.93
2531 2559 1.064458 GCCGAACTAGAGGAGTCGC 59.936 63.158 0.00 0.00 37.44 5.19
2532 2560 1.352404 CGCCGAACTAGAGGAGTCG 59.648 63.158 0.00 0.00 37.44 4.18
2533 2561 0.377905 GACGCCGAACTAGAGGAGTC 59.622 60.000 18.07 18.07 46.68 3.36
2535 2563 0.378962 CTGACGCCGAACTAGAGGAG 59.621 60.000 0.00 1.23 0.00 3.69
2536 2564 0.035725 TCTGACGCCGAACTAGAGGA 60.036 55.000 0.00 0.00 0.00 3.71
2537 2565 1.025812 ATCTGACGCCGAACTAGAGG 58.974 55.000 0.00 0.00 0.00 3.69
2539 2567 0.738975 CCATCTGACGCCGAACTAGA 59.261 55.000 0.00 0.00 0.00 2.43
2540 2568 0.738975 TCCATCTGACGCCGAACTAG 59.261 55.000 0.00 0.00 0.00 2.57
2541 2569 0.738975 CTCCATCTGACGCCGAACTA 59.261 55.000 0.00 0.00 0.00 2.24
2542 2570 1.513158 CTCCATCTGACGCCGAACT 59.487 57.895 0.00 0.00 0.00 3.01
2569 2597 5.368145 TCCTCCATGATATCAACTTTTCCG 58.632 41.667 9.99 0.00 0.00 4.30
2576 2604 4.450419 CGCTTCTTCCTCCATGATATCAAC 59.550 45.833 9.99 0.00 0.00 3.18
2586 2614 0.251832 AGGAGTCGCTTCTTCCTCCA 60.252 55.000 7.25 0.00 44.85 3.86
2641 2669 6.515272 ACAAATTGCGATAAAGACATTCCT 57.485 33.333 0.00 0.00 0.00 3.36
2642 2670 7.328249 TGAAACAAATTGCGATAAAGACATTCC 59.672 33.333 0.00 0.00 0.00 3.01
2643 2671 8.226543 TGAAACAAATTGCGATAAAGACATTC 57.773 30.769 0.00 0.00 0.00 2.67
2644 2672 8.761575 ATGAAACAAATTGCGATAAAGACATT 57.238 26.923 0.00 0.00 0.00 2.71
2645 2673 8.761575 AATGAAACAAATTGCGATAAAGACAT 57.238 26.923 0.00 0.00 0.00 3.06
2646 2674 8.586570 AAATGAAACAAATTGCGATAAAGACA 57.413 26.923 0.00 0.00 0.00 3.41
2670 2715 2.285950 GCGCGCTAAATATTGTCCGAAA 60.286 45.455 26.67 0.00 0.00 3.46
2674 2721 2.659291 CGAAGCGCGCTAAATATTGTCC 60.659 50.000 36.73 11.67 0.00 4.02
2683 2730 3.380671 GCTAACGAAGCGCGCTAA 58.619 55.556 36.73 16.25 46.04 3.09
2774 2821 3.599343 CCAGACACGATCTTTGATCCAA 58.401 45.455 0.00 0.00 34.41 3.53
2775 2822 2.093500 CCCAGACACGATCTTTGATCCA 60.093 50.000 0.00 0.00 34.41 3.41
2781 2828 1.339151 GCCTTCCCAGACACGATCTTT 60.339 52.381 0.00 0.00 34.41 2.52
2830 2877 5.689383 TTCCTCAAACTCCTTCAAAATCG 57.311 39.130 0.00 0.00 0.00 3.34
2935 2982 4.051922 CGATCTACTTCAAGCCCATGTAC 58.948 47.826 0.00 0.00 0.00 2.90
2948 2995 3.251479 TGCATGCTTGTCGATCTACTT 57.749 42.857 20.33 0.00 0.00 2.24
2949 2996 2.932614 GTTGCATGCTTGTCGATCTACT 59.067 45.455 20.33 0.00 0.00 2.57
2990 3037 2.039348 TGAACCCTTAGAAAACCTCCCG 59.961 50.000 0.00 0.00 0.00 5.14
3022 3069 4.820173 CCTTCTCAAGGGTTTCTTTACGTT 59.180 41.667 0.00 0.00 45.27 3.99
3049 3096 5.389859 TTCTTGCCGAATCAATCACAAAT 57.610 34.783 0.00 0.00 0.00 2.32
3177 3225 2.556114 CCAGTTGCCTTCCTCATCCTTT 60.556 50.000 0.00 0.00 0.00 3.11


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

AutoCloner maintained by Alex Coulton.