Multiple sequence alignment - TraesCS5A01G136900

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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 TraesCS5A01G136900 chr5A 100.000 2537 0 0 1 2537 308541498 308538962 0.000000e+00 4686.0
1 TraesCS5A01G136900 chr5D 91.577 1484 73 20 1 1442 243077461 243078934 0.000000e+00 2001.0
2 TraesCS5A01G136900 chr5D 92.473 1116 56 16 1449 2537 243082791 243083905 0.000000e+00 1570.0
3 TraesCS5A01G136900 chr5D 74.559 397 67 21 97 492 557249633 557249270 2.630000e-30 143.0
4 TraesCS5A01G136900 chr5D 72.996 474 78 33 21 480 225585622 225586059 1.230000e-23 121.0
5 TraesCS5A01G136900 chr5B 91.901 1420 83 16 931 2339 255337933 255336535 0.000000e+00 1956.0
6 TraesCS5A01G136900 chr5B 88.344 326 30 5 18 336 255392447 255392123 3.960000e-103 385.0
7 TraesCS5A01G136900 chr5B 88.439 173 20 0 332 504 255378211 255378039 2.560000e-50 209.0
8 TraesCS5A01G136900 chr5B 84.146 82 11 2 21 102 69636977 69637056 7.520000e-11 78.7
9 TraesCS5A01G136900 chr4A 78.356 365 64 9 137 492 616705775 616706133 3.290000e-54 222.0
10 TraesCS5A01G136900 chr1A 75.789 380 59 21 133 484 119705889 119705515 7.260000e-36 161.0
11 TraesCS5A01G136900 chr1D 75.269 372 58 22 143 484 112464509 112464142 2.030000e-31 147.0
12 TraesCS5A01G136900 chr1B 82.456 114 20 0 371 484 317842449 317842562 1.610000e-17 100.0
13 TraesCS5A01G136900 chr3D 78.102 137 30 0 167 303 104208583 104208447 1.250000e-13 87.9
14 TraesCS5A01G136900 chr7B 86.842 76 10 0 387 462 495023694 495023619 4.500000e-13 86.1
15 TraesCS5A01G136900 chr6A 78.505 107 19 4 379 484 18352550 18352447 1.630000e-07 67.6


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 TraesCS5A01G136900 chr5A 308538962 308541498 2536 True 4686.0 4686 100.000 1 2537 1 chr5A.!!$R1 2536
1 TraesCS5A01G136900 chr5D 243077461 243083905 6444 False 1785.5 2001 92.025 1 2537 2 chr5D.!!$F2 2536
2 TraesCS5A01G136900 chr5B 255336535 255337933 1398 True 1956.0 1956 91.901 931 2339 1 chr5B.!!$R1 1408

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
175 176 0.103208 GCAGAGGATGACCACCTACG 59.897 60.0 0.0 0.0 37.93 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1864 5778 0.674534 GAGGCCTGGACCGTATGTAG 59.325 60.0 12.0 0.0 33.69 2.74 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
40 41 3.003763 GAGGGGTCAAGTCCGGCT 61.004 66.667 0.00 0.00 0.00 5.52
56 57 1.654774 GCTATTTAAGCCGGGCAGC 59.345 57.895 23.09 16.13 46.25 5.25
95 96 3.007635 CCGTCCCCATTTCTACACTTTC 58.992 50.000 0.00 0.00 0.00 2.62
126 127 1.754803 ACGTCGCATCCTTCTAATCCA 59.245 47.619 0.00 0.00 0.00 3.41
138 139 3.179443 TCTAATCCAATCACCGTCAGC 57.821 47.619 0.00 0.00 0.00 4.26
165 166 3.804153 ATGGCTCGCGCAGAGGATG 62.804 63.158 23.77 6.62 46.91 3.51
175 176 0.103208 GCAGAGGATGACCACCTACG 59.897 60.000 0.00 0.00 37.93 3.51
178 179 1.305802 AGGATGACCACCTACGCCA 60.306 57.895 0.00 0.00 38.94 5.69
199 200 1.065600 CTCACTCTAGAGCAGCGGC 59.934 63.158 19.97 0.00 41.61 6.53
219 220 0.694771 TGCAACTGCTGGAGGAGATT 59.305 50.000 1.72 0.00 42.66 2.40
267 268 2.124320 GGCCTGCCTGCGGATTTA 60.124 61.111 0.00 0.00 0.00 1.40
292 299 2.015081 CTGGAGGAGGAGGAGGAGT 58.985 63.158 0.00 0.00 0.00 3.85
295 302 0.481128 GGAGGAGGAGGAGGAGTAGG 59.519 65.000 0.00 0.00 0.00 3.18
297 304 1.423921 GAGGAGGAGGAGGAGTAGGAG 59.576 61.905 0.00 0.00 0.00 3.69
308 315 0.452585 GAGTAGGAGCAGGACGTGAC 59.547 60.000 0.00 0.00 0.00 3.67
312 319 1.153549 GGAGCAGGACGTGACCATC 60.154 63.158 0.00 0.00 0.00 3.51
313 320 1.591703 GAGCAGGACGTGACCATCA 59.408 57.895 0.00 0.00 0.00 3.07
351 358 1.377856 GGTGGAAGAGGCAGAAGGC 60.378 63.158 0.00 0.00 43.74 4.35
372 379 2.351276 GCTGATCCGGTTGTGGGT 59.649 61.111 0.00 0.00 0.00 4.51
379 386 2.902846 CGGTTGTGGGTTTCGCCA 60.903 61.111 0.00 0.00 39.65 5.69
417 424 1.377202 GTTCGAGATGGCCCAAGCA 60.377 57.895 0.00 0.00 42.56 3.91
462 469 0.331616 TCCTCGACTCCATCCAGTCA 59.668 55.000 1.78 0.00 42.75 3.41
463 470 1.186200 CCTCGACTCCATCCAGTCAA 58.814 55.000 1.78 0.00 42.75 3.18
468 475 2.029020 CGACTCCATCCAGTCAAAGACA 60.029 50.000 0.00 0.00 42.75 3.41
484 491 1.768684 GACAGAGGTGGAGGCCAACA 61.769 60.000 5.01 0.00 45.07 3.33
485 492 1.352622 ACAGAGGTGGAGGCCAACAA 61.353 55.000 5.01 0.00 45.07 2.83
488 495 0.890996 GAGGTGGAGGCCAACAACTG 60.891 60.000 20.40 0.00 45.07 3.16
489 496 2.564721 GGTGGAGGCCAACAACTGC 61.565 63.158 5.01 0.00 41.64 4.40
490 497 1.529244 GTGGAGGCCAACAACTGCT 60.529 57.895 5.01 0.00 34.18 4.24
491 498 1.109323 GTGGAGGCCAACAACTGCTT 61.109 55.000 5.01 0.00 34.18 3.91
501 524 3.434319 AACTGCTTGCATCCGCGG 61.434 61.111 22.12 22.12 42.97 6.46
502 525 3.899981 AACTGCTTGCATCCGCGGA 62.900 57.895 33.12 33.12 42.97 5.54
517 540 0.527565 GCGGACATTTGGCAACTCAT 59.472 50.000 0.00 0.00 37.61 2.90
518 541 1.067635 GCGGACATTTGGCAACTCATT 60.068 47.619 0.00 0.00 37.61 2.57
519 542 2.163412 GCGGACATTTGGCAACTCATTA 59.837 45.455 0.00 0.00 37.61 1.90
520 543 3.731867 GCGGACATTTGGCAACTCATTAG 60.732 47.826 0.00 0.00 37.61 1.73
528 554 9.845740 ACATTTGGCAACTCATTAGTATATGTA 57.154 29.630 0.00 0.00 33.75 2.29
564 590 2.005971 AGTCGCTTTCATACCGAACC 57.994 50.000 0.00 0.00 31.73 3.62
611 637 2.939103 GTGGCTAAATTGAGCGTCAGAT 59.061 45.455 8.77 0.00 43.83 2.90
661 687 0.821711 TTCAACCCAAGCCTGGAACG 60.822 55.000 1.80 0.00 46.92 3.95
669 695 4.704833 GCCTGGAACGGAGCAGCA 62.705 66.667 0.00 0.00 36.31 4.41
704 730 2.896854 CACCGGCCCATCGTCATG 60.897 66.667 0.00 0.00 0.00 3.07
750 779 1.404315 GGGAGTTCGATCGAGCAAGTT 60.404 52.381 29.72 12.37 0.00 2.66
766 795 1.133869 GTTGGCAATGGCGACGTAC 59.866 57.895 11.51 0.00 42.47 3.67
817 853 2.346803 GTGGCGCTCAAATCAAGTCTA 58.653 47.619 7.64 0.00 0.00 2.59
955 998 3.900601 CCATTCTCTGCTATACCCACTCT 59.099 47.826 0.00 0.00 0.00 3.24
1390 1433 4.435436 AGTTCGATGGCGCTGCGA 62.435 61.111 28.07 11.57 37.46 5.10
1686 5597 2.305009 GAAGCAGATGATTTCCCCTGG 58.695 52.381 0.00 0.00 0.00 4.45
1846 5758 5.695851 AAAAATGCTTCAGTACAGTCCTG 57.304 39.130 0.00 0.00 0.00 3.86
1847 5759 3.340814 AATGCTTCAGTACAGTCCTGG 57.659 47.619 0.00 0.00 34.19 4.45
1859 5773 3.878778 ACAGTCCTGGAATACAGCAATC 58.121 45.455 0.00 0.00 46.14 2.67
1864 5778 3.131396 CCTGGAATACAGCAATCCGTAC 58.869 50.000 0.00 0.00 46.14 3.67
1885 5804 0.617820 ACATACGGTCCAGGCCTCTT 60.618 55.000 0.00 0.00 0.00 2.85
1889 5808 2.747855 GGTCCAGGCCTCTTTGCG 60.748 66.667 0.00 0.00 0.00 4.85
1956 5878 4.823419 TAATCCCGCCGTGTGCCG 62.823 66.667 0.00 0.00 36.24 5.69
2025 5947 2.103373 CCCATTGTCTTCCTCTCGAGA 58.897 52.381 15.70 15.70 0.00 4.04
2063 5987 1.067060 CCTAGCGACGATGGATCACAA 59.933 52.381 0.00 0.00 0.00 3.33
2105 6029 1.063027 CGCAAGTGGTAGACGACGATA 59.937 52.381 0.00 0.00 0.00 2.92
2148 6072 3.681897 CGTGAGATCTGTAGCTGCTTTTT 59.318 43.478 7.79 0.00 0.00 1.94
2167 6091 6.560253 TTTTTGAACTTGGAGATGCTCTAC 57.440 37.500 0.00 0.00 0.00 2.59
2168 6092 4.890158 TTGAACTTGGAGATGCTCTACA 57.110 40.909 0.00 0.00 35.03 2.74
2198 6122 2.113986 GGATTGCTATGGCGGCCT 59.886 61.111 21.46 8.36 42.25 5.19
2203 6127 2.203015 GCTATGGCGGCCTCGAAA 60.203 61.111 21.46 0.00 39.00 3.46
2236 6160 1.139455 TGAATGATCGGAGATGCAGCA 59.861 47.619 4.07 0.00 45.12 4.41
2274 6198 0.916086 TATTGGGCGATGTTGGAGGT 59.084 50.000 0.00 0.00 0.00 3.85
2290 6215 1.896465 GAGGTATGGAGAGGGGATTCG 59.104 57.143 0.00 0.00 0.00 3.34
2325 6250 2.260434 GCCCGCGTACAAGTCTCA 59.740 61.111 4.92 0.00 0.00 3.27
2341 6266 4.680237 CACGCTCTGAACCCGCCA 62.680 66.667 0.00 0.00 0.00 5.69
2342 6267 3.706373 ACGCTCTGAACCCGCCAT 61.706 61.111 0.00 0.00 0.00 4.40
2346 6271 1.450312 CTCTGAACCCGCCATGTCC 60.450 63.158 0.00 0.00 0.00 4.02
2429 6355 1.600013 TGTGTTGGATGAAACGAACCG 59.400 47.619 0.00 0.00 32.47 4.44
2431 6357 1.232119 GTTGGATGAAACGAACCGGT 58.768 50.000 0.00 0.00 0.00 5.28
2435 6361 0.165944 GATGAAACGAACCGGTGCTG 59.834 55.000 8.52 5.20 0.00 4.41
2437 6363 3.249973 GAAACGAACCGGTGCTGCC 62.250 63.158 8.52 0.00 0.00 4.85
2455 6384 0.617413 CCAAGGAGGAGAGTGCATGT 59.383 55.000 0.00 0.00 41.22 3.21
2462 6391 0.835941 GGAGAGTGCATGTGAGGGAT 59.164 55.000 0.00 0.00 0.00 3.85
2530 6459 2.104530 GTAGCCCTCGGTCGCTTC 59.895 66.667 0.00 0.00 36.53 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.308458 CCCTCGGGTTGTGTGCGA 62.308 66.667 0.00 0.00 0.00 5.10
28 29 3.946308 GCTTAAATAGCCGGACTTGAC 57.054 47.619 5.05 0.00 44.48 3.18
40 41 4.134623 CGCTGCCCGGCTTAAATA 57.865 55.556 11.61 0.00 0.00 1.40
56 57 2.125106 GCTAGGGTTGGACTGCCG 60.125 66.667 0.00 0.00 36.79 5.69
62 63 2.686106 GGACGGGCTAGGGTTGGA 60.686 66.667 0.00 0.00 0.00 3.53
156 157 0.103208 CGTAGGTGGTCATCCTCTGC 59.897 60.000 0.00 0.00 36.60 4.26
165 166 1.521681 GAGCATGGCGTAGGTGGTC 60.522 63.158 0.00 0.00 33.88 4.02
193 194 4.400109 CAGCAGTTGCAGCCGCTG 62.400 66.667 21.96 21.96 45.17 5.18
199 200 0.252479 ATCTCCTCCAGCAGTTGCAG 59.748 55.000 6.90 0.00 45.16 4.41
205 206 1.445095 CCCGAATCTCCTCCAGCAG 59.555 63.158 0.00 0.00 0.00 4.24
266 267 0.395862 CTCCTCCTCCAGCTTCGGTA 60.396 60.000 0.00 0.00 0.00 4.02
267 268 1.684049 CTCCTCCTCCAGCTTCGGT 60.684 63.158 0.00 0.00 0.00 4.69
274 275 1.144913 CTACTCCTCCTCCTCCTCCAG 59.855 61.905 0.00 0.00 0.00 3.86
275 276 1.227249 CTACTCCTCCTCCTCCTCCA 58.773 60.000 0.00 0.00 0.00 3.86
276 277 0.481128 CCTACTCCTCCTCCTCCTCC 59.519 65.000 0.00 0.00 0.00 4.30
292 299 0.324368 ATGGTCACGTCCTGCTCCTA 60.324 55.000 0.00 0.00 0.00 2.94
295 302 0.037326 TTGATGGTCACGTCCTGCTC 60.037 55.000 0.00 0.00 0.00 4.26
297 304 1.021390 CCTTGATGGTCACGTCCTGC 61.021 60.000 0.00 0.00 0.00 4.85
308 315 1.277273 TCAGCTCTGTGTCCTTGATGG 59.723 52.381 0.00 0.00 37.10 3.51
312 319 1.345741 TCCTTCAGCTCTGTGTCCTTG 59.654 52.381 0.00 0.00 0.00 3.61
313 320 1.622811 CTCCTTCAGCTCTGTGTCCTT 59.377 52.381 0.00 0.00 0.00 3.36
322 329 1.206849 CTCTTCCACCTCCTTCAGCTC 59.793 57.143 0.00 0.00 0.00 4.09
351 358 0.179073 CCACAACCGGATCAGCCTAG 60.179 60.000 9.46 0.00 0.00 3.02
385 392 3.482783 GAACTCTGCCAGCGCGTC 61.483 66.667 8.43 0.00 38.08 5.19
417 424 1.178534 GCTGCTCTATCGCCTCCTCT 61.179 60.000 0.00 0.00 0.00 3.69
426 433 0.321475 GGATGGCCTGCTGCTCTATC 60.321 60.000 3.32 3.43 40.92 2.08
462 469 0.768221 TGGCCTCCACCTCTGTCTTT 60.768 55.000 3.32 0.00 0.00 2.52
463 470 0.768221 TTGGCCTCCACCTCTGTCTT 60.768 55.000 3.32 0.00 30.78 3.01
468 475 1.062488 AGTTGTTGGCCTCCACCTCT 61.062 55.000 3.32 0.00 30.78 3.69
484 491 3.434319 CCGCGGATGCAAGCAGTT 61.434 61.111 24.07 0.00 42.97 3.16
485 492 4.393155 TCCGCGGATGCAAGCAGT 62.393 61.111 27.28 0.00 42.97 4.40
488 495 2.270297 AAATGTCCGCGGATGCAAGC 62.270 55.000 33.58 17.93 42.97 4.01
489 496 0.523968 CAAATGTCCGCGGATGCAAG 60.524 55.000 33.58 17.71 42.97 4.01
490 497 1.505807 CAAATGTCCGCGGATGCAA 59.494 52.632 33.58 17.79 42.97 4.08
491 498 2.405805 CCAAATGTCCGCGGATGCA 61.406 57.895 33.58 25.76 42.97 3.96
501 524 8.840321 ACATATACTAATGAGTTGCCAAATGTC 58.160 33.333 0.00 0.00 37.10 3.06
502 525 8.752005 ACATATACTAATGAGTTGCCAAATGT 57.248 30.769 0.00 0.00 37.10 2.71
528 554 5.238583 AGCGACTTTAGAGCATTTACAACT 58.761 37.500 0.00 0.00 0.00 3.16
611 637 1.039068 TCGGGAAGGTTGAACGTACA 58.961 50.000 0.00 0.00 0.00 2.90
644 670 2.268076 CCGTTCCAGGCTTGGGTTG 61.268 63.158 15.86 4.66 45.10 3.77
704 730 1.787847 CCGAATCACACACGAAGCC 59.212 57.895 0.00 0.00 0.00 4.35
705 731 1.132640 GCCGAATCACACACGAAGC 59.867 57.895 0.00 0.00 0.00 3.86
707 733 0.865111 CTTGCCGAATCACACACGAA 59.135 50.000 0.00 0.00 0.00 3.85
708 734 0.948623 CCTTGCCGAATCACACACGA 60.949 55.000 0.00 0.00 0.00 4.35
710 736 1.875963 CCCTTGCCGAATCACACAC 59.124 57.895 0.00 0.00 0.00 3.82
750 779 1.739929 CAGTACGTCGCCATTGCCA 60.740 57.895 0.00 0.00 0.00 4.92
766 795 5.713822 GTTTTAGAACCCTATGCGTACAG 57.286 43.478 0.00 0.00 0.00 2.74
817 853 2.382746 CGCTGTGTACACGCATGCT 61.383 57.895 28.95 0.00 35.63 3.79
850 893 1.679305 GAGAGGAGGAGACACGGCA 60.679 63.158 0.00 0.00 0.00 5.69
955 998 1.800586 GCGTGACAAGATTTGAGCTGA 59.199 47.619 0.00 0.00 0.00 4.26
1686 5597 5.408604 TCTTCCAACGAAGCAGAGTAAATTC 59.591 40.000 0.00 0.00 44.50 2.17
1771 5683 7.803189 CGCTGATGTACCAATATGAAATTTACC 59.197 37.037 0.00 0.00 0.00 2.85
1846 5758 4.940463 TGTAGTACGGATTGCTGTATTCC 58.060 43.478 0.00 0.00 38.11 3.01
1847 5759 7.564044 GTATGTAGTACGGATTGCTGTATTC 57.436 40.000 0.00 0.00 38.11 1.75
1864 5778 0.674534 GAGGCCTGGACCGTATGTAG 59.325 60.000 12.00 0.00 33.69 2.74
1889 5808 4.626081 ACTGGACACGTGGCAGCC 62.626 66.667 25.47 16.79 0.00 4.85
1956 5878 1.327690 TGGCCATACAGACGAGGACC 61.328 60.000 0.00 0.00 0.00 4.46
2025 5947 3.915346 AGGGTTAGGGGTTTGTTCAAT 57.085 42.857 0.00 0.00 0.00 2.57
2063 5987 2.126071 CATCTCCGCCGACGTTGT 60.126 61.111 1.30 0.00 37.70 3.32
2089 6013 3.118847 TCTCTGTATCGTCGTCTACCACT 60.119 47.826 0.00 0.00 0.00 4.00
2105 6029 3.382111 CCTGGTCGGCTTCTCTGT 58.618 61.111 0.00 0.00 0.00 3.41
2167 6091 1.753073 GCAATCCCCACTGATTCCTTG 59.247 52.381 0.00 0.00 32.71 3.61
2168 6092 1.642762 AGCAATCCCCACTGATTCCTT 59.357 47.619 0.00 0.00 32.71 3.36
2198 6122 2.987232 TCAGATCGTCTCCTCTTTCGA 58.013 47.619 0.00 0.00 36.77 3.71
2236 6160 0.544697 AGATAAACCCGACCGGCAAT 59.455 50.000 0.00 0.00 33.26 3.56
2274 6198 2.326428 GAACCGAATCCCCTCTCCATA 58.674 52.381 0.00 0.00 0.00 2.74
2290 6215 2.383527 CCAACGCGCTCTCTGAACC 61.384 63.158 5.73 0.00 0.00 3.62
2319 6244 1.867919 CGGGTTCAGAGCGTGAGACT 61.868 60.000 0.00 0.00 36.21 3.24
2325 6250 3.706373 ATGGCGGGTTCAGAGCGT 61.706 61.111 0.00 0.00 0.00 5.07
2346 6271 3.796443 TCGTCGCGTCCTCCTTCG 61.796 66.667 5.77 0.10 0.00 3.79
2360 6285 2.016393 ATCGCCATGACCATCGTCGT 62.016 55.000 0.00 0.00 42.37 4.34
2421 6347 4.555709 TGGCAGCACCGGTTCGTT 62.556 61.111 2.97 0.00 43.94 3.85
2429 6355 2.045536 CTCCTCCTTGGCAGCACC 60.046 66.667 0.00 0.00 39.84 5.01
2431 6357 1.537397 ACTCTCCTCCTTGGCAGCA 60.537 57.895 0.00 0.00 35.26 4.41
2435 6361 0.747283 CATGCACTCTCCTCCTTGGC 60.747 60.000 0.00 0.00 35.26 4.52
2437 6363 1.277273 TCACATGCACTCTCCTCCTTG 59.723 52.381 0.00 0.00 0.00 3.61
2455 6384 2.045634 GCAGCTGCACATCCCTCA 60.046 61.111 33.36 0.00 41.59 3.86
2462 6391 2.188829 GTGACAAGGCAGCTGCACA 61.189 57.895 37.63 24.40 44.36 4.57
2506 6435 0.831307 GACCGAGGGCTACAATCCTT 59.169 55.000 0.00 0.00 32.74 3.36


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

AutoCloner maintained by Alex Coulton.