Multiple sequence alignment - TraesCS6A01G319000

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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 TraesCS6A01G319000 chr6A 100.000 3238 0 0 1 3238 554786279 554789516 0.000000e+00 5980
1 TraesCS6A01G319000 chr6A 87.031 2267 165 58 37 2250 554714992 554717182 0.000000e+00 2438
2 TraesCS6A01G319000 chr6B 95.308 2579 85 12 1 2559 614126429 614128991 0.000000e+00 4060
3 TraesCS6A01G319000 chr6B 85.274 1331 111 52 102 1413 613609295 613610559 0.000000e+00 1293
4 TraesCS6A01G319000 chr6B 92.611 785 44 5 1466 2250 613610567 613611337 0.000000e+00 1116
5 TraesCS6A01G319000 chr6B 91.977 698 37 17 2551 3238 614129020 614129708 0.000000e+00 961
6 TraesCS6A01G319000 chr6D 88.279 2167 152 55 102 2250 408944641 408946723 0.000000e+00 2501
7 TraesCS6A01G319000 chr6D 95.694 1138 44 2 1425 2559 409288306 409289441 0.000000e+00 1825
8 TraesCS6A01G319000 chr6D 93.406 1107 48 18 329 1429 409287253 409288340 0.000000e+00 1616
9 TraesCS6A01G319000 chr6D 93.840 698 27 12 2551 3238 409289470 409290161 0.000000e+00 1037
10 TraesCS6A01G319000 chr6D 95.268 317 12 3 16 331 409286815 409287129 1.730000e-137 499
11 TraesCS6A01G319000 chr2D 85.484 124 12 5 1251 1371 627974070 627974190 1.220000e-24 124
12 TraesCS6A01G319000 chr2B 86.275 102 12 2 1251 1351 771043285 771043385 3.420000e-20 110


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 TraesCS6A01G319000 chr6A 554786279 554789516 3237 False 5980.00 5980 100.0000 1 3238 1 chr6A.!!$F2 3237
1 TraesCS6A01G319000 chr6A 554714992 554717182 2190 False 2438.00 2438 87.0310 37 2250 1 chr6A.!!$F1 2213
2 TraesCS6A01G319000 chr6B 614126429 614129708 3279 False 2510.50 4060 93.6425 1 3238 2 chr6B.!!$F2 3237
3 TraesCS6A01G319000 chr6B 613609295 613611337 2042 False 1204.50 1293 88.9425 102 2250 2 chr6B.!!$F1 2148
4 TraesCS6A01G319000 chr6D 408944641 408946723 2082 False 2501.00 2501 88.2790 102 2250 1 chr6D.!!$F1 2148
5 TraesCS6A01G319000 chr6D 409286815 409290161 3346 False 1244.25 1825 94.5520 16 3238 4 chr6D.!!$F2 3222

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
95 96 1.541233 GCCTGTCATCTTATGGTCCCG 60.541 57.143 0.0 0.0 0.0 5.14 F
1165 1396 0.095417 GCATCCGTTTTCTGTCTCGC 59.905 55.000 0.0 0.0 0.0 5.03 F
1845 2087 0.541863 CACCATCCCCACTGACCTAC 59.458 60.000 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1175 1406 0.462759 AAAGCTAGCCACGGCATCTC 60.463 55.000 12.13 0.00 44.88 2.75 R
2175 2417 0.753111 CAAATAGGGAGCTGGGTGCC 60.753 60.000 0.00 2.12 44.23 5.01 R
2947 3253 2.433970 CCCTCTTTTGACAGGGCAAAAA 59.566 45.455 13.54 5.18 44.40 1.94 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
95 96 1.541233 GCCTGTCATCTTATGGTCCCG 60.541 57.143 0.00 0.00 0.00 5.14
148 150 7.256655 CCAACATGTACTATGATATCCCAGGAA 60.257 40.741 0.00 0.00 0.00 3.36
298 330 5.222079 TGCTACAACTACATTCCAAGACA 57.778 39.130 0.00 0.00 0.00 3.41
312 344 4.447290 TCCAAGACACGAATTGAAGTTGA 58.553 39.130 0.00 0.00 0.00 3.18
350 508 7.912250 CAGTTATGTCTTTGGAATTGATACAGC 59.088 37.037 0.00 0.00 0.00 4.40
352 510 8.408601 GTTATGTCTTTGGAATTGATACAGCAT 58.591 33.333 0.00 0.00 0.00 3.79
426 620 2.738743 CCCCCAGCAAGTAATCACAAT 58.261 47.619 0.00 0.00 0.00 2.71
431 625 6.151648 CCCCCAGCAAGTAATCACAATATATG 59.848 42.308 0.00 0.00 0.00 1.78
432 626 6.151648 CCCCAGCAAGTAATCACAATATATGG 59.848 42.308 0.00 0.00 0.00 2.74
460 654 3.806521 GGACATGTCACATGATGAGCTAC 59.193 47.826 24.98 0.00 38.28 3.58
829 1048 8.024285 CACTCGAATAATCTAATCCTGACCTAC 58.976 40.741 0.00 0.00 0.00 3.18
1071 1296 0.685097 CACCCGAAGAGGACCAGAAA 59.315 55.000 0.00 0.00 45.00 2.52
1148 1374 4.953868 AGGTACGCAACGCACGCA 62.954 61.111 0.00 0.00 0.00 5.24
1165 1396 0.095417 GCATCCGTTTTCTGTCTCGC 59.905 55.000 0.00 0.00 0.00 5.03
1168 1399 3.448686 CATCCGTTTTCTGTCTCGCTAT 58.551 45.455 0.00 0.00 0.00 2.97
1169 1400 3.146618 TCCGTTTTCTGTCTCGCTATC 57.853 47.619 0.00 0.00 0.00 2.08
1170 1401 1.846782 CCGTTTTCTGTCTCGCTATCG 59.153 52.381 0.00 0.00 0.00 2.92
1175 1406 1.007964 CTGTCTCGCTATCGGGCAG 60.008 63.158 0.00 0.00 35.80 4.85
1571 1813 5.070981 TGAGATCAAGAACTTCTGGAACACT 59.929 40.000 0.00 1.38 28.71 3.55
1724 1966 3.294493 GACCAAAGCGCCAGCCAA 61.294 61.111 2.29 0.00 46.67 4.52
1778 2020 2.611518 GAGTACTTACAGTGCCTGCTG 58.388 52.381 0.00 0.95 41.92 4.41
1845 2087 0.541863 CACCATCCCCACTGACCTAC 59.458 60.000 0.00 0.00 0.00 3.18
2060 2302 3.003763 AGCGGTGAGGGGGAGAAC 61.004 66.667 0.00 0.00 0.00 3.01
2111 2353 3.249189 TCCCTTCCGCCACTTGCT 61.249 61.111 0.00 0.00 38.05 3.91
2175 2417 3.414700 GTGACGCTGAGGGCAACG 61.415 66.667 0.00 0.00 41.91 4.10
2342 2584 5.997746 TGATTTCCATTATAGTGCTGTAGCC 59.002 40.000 0.80 0.00 41.18 3.93
2441 2683 7.372451 TGCCAAAACACTTGTACATATAGAC 57.628 36.000 0.00 0.00 0.00 2.59
2446 2688 5.277857 ACACTTGTACATATAGACCTGCC 57.722 43.478 0.00 0.00 0.00 4.85
2540 2795 0.908198 AGACTGGGATCTTGCTCACC 59.092 55.000 0.00 0.00 0.00 4.02
2645 2942 6.983890 CAGTTATGCACCCTAAGTTTGTTTTT 59.016 34.615 0.00 0.00 0.00 1.94
2757 3061 5.460091 CGGAGCATATATGTATTGATCCACG 59.540 44.000 14.14 1.38 0.00 4.94
2769 3073 8.873186 TGTATTGATCCACGGTATATAGAGAA 57.127 34.615 0.00 0.00 0.00 2.87
2770 3074 8.957466 TGTATTGATCCACGGTATATAGAGAAG 58.043 37.037 0.00 0.00 0.00 2.85
2774 3079 7.883217 TGATCCACGGTATATAGAGAAGAAAC 58.117 38.462 0.00 0.00 0.00 2.78
2789 3094 7.036220 AGAGAAGAAACAGATAACGTATGTGG 58.964 38.462 0.00 0.00 34.06 4.17
2796 3101 6.963049 ACAGATAACGTATGTGGTCTTTTC 57.037 37.500 0.00 0.00 34.06 2.29
2845 3151 7.966204 GCTGCAAATGCTTTATTGAAAAATGAT 59.034 29.630 6.97 0.00 42.66 2.45
2943 3249 4.363999 CGAGGCAGTTATAGGAAGTTGAG 58.636 47.826 0.00 0.00 0.00 3.02
2947 3253 7.439108 AGGCAGTTATAGGAAGTTGAGTAAT 57.561 36.000 0.00 0.00 0.00 1.89
3034 3340 3.126831 GACATATGCTGCTGTCACTACC 58.873 50.000 13.63 0.00 41.13 3.18
3066 3372 2.351706 TGCTAATCATGCATGAGCCA 57.648 45.000 31.36 21.59 40.64 4.75
3160 3466 4.572985 TCTCACAGCTTCAAACCATTTG 57.427 40.909 0.00 0.00 41.96 2.32
3173 3479 9.437045 CTTCAAACCATTTGCATTTTAGTTTTC 57.563 29.630 0.00 0.00 40.43 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 96 9.828852 CGTATATCCTCTTCTCAAGTATGTAAC 57.171 37.037 0.00 0.00 0.00 2.50
199 227 8.133627 CACCCATCTTATGCATTTCTTTTAGAG 58.866 37.037 3.54 0.00 0.00 2.43
213 241 2.620115 GGCACATGACACCCATCTTATG 59.380 50.000 0.00 0.00 31.94 1.90
221 249 1.165270 GTACTTGGCACATGACACCC 58.835 55.000 0.00 0.00 39.30 4.61
298 330 6.215121 TGCAATTTCATCAACTTCAATTCGT 58.785 32.000 0.00 0.00 0.00 3.85
312 344 7.762615 CCAAAGACATAACTGATGCAATTTCAT 59.237 33.333 0.00 0.00 39.39 2.57
350 508 0.038744 AGTGGGTTCCTGGAAGCATG 59.961 55.000 32.48 0.00 41.18 4.06
352 510 0.110486 GAAGTGGGTTCCTGGAAGCA 59.890 55.000 32.48 19.49 41.18 3.91
426 620 7.947890 TCATGTGACATGTCCTACTACCATATA 59.052 37.037 23.39 0.00 0.00 0.86
431 625 5.069119 TCATCATGTGACATGTCCTACTACC 59.931 44.000 23.39 0.00 0.00 3.18
432 626 6.149129 TCATCATGTGACATGTCCTACTAC 57.851 41.667 23.39 13.98 0.00 2.73
460 654 7.761409 TGTTGATTTTTAAGTAGCATAGCCAG 58.239 34.615 0.00 0.00 0.00 4.85
476 670 7.383687 AGCACAATCAGATCATTGTTGATTTT 58.616 30.769 8.33 0.00 43.17 1.82
829 1048 3.063452 CCATGAAATCCGGTGTCTAAACG 59.937 47.826 0.00 0.00 0.00 3.60
1020 1245 1.266178 TCTTGAGGCCATTCTCGTCA 58.734 50.000 5.01 0.00 36.61 4.35
1071 1296 2.398252 TCTCGATGTAGTCCGTGAGT 57.602 50.000 0.00 0.00 0.00 3.41
1148 1374 3.707793 GATAGCGAGACAGAAAACGGAT 58.292 45.455 0.00 0.00 0.00 4.18
1175 1406 0.462759 AAAGCTAGCCACGGCATCTC 60.463 55.000 12.13 0.00 44.88 2.75
1216 1447 3.071457 TGAGATGCACAGAAGAACCAGAA 59.929 43.478 0.00 0.00 0.00 3.02
1845 2087 1.078214 TCAGGAGGCCGATTTGCTG 60.078 57.895 5.02 5.02 34.49 4.41
2111 2353 3.055385 CGAGGTTGGAAATAGGGAAGTCA 60.055 47.826 0.00 0.00 0.00 3.41
2175 2417 0.753111 CAAATAGGGAGCTGGGTGCC 60.753 60.000 0.00 2.12 44.23 5.01
2329 2571 1.210478 CAACTGGGGCTACAGCACTAT 59.790 52.381 3.04 0.00 45.56 2.12
2417 2659 6.373216 GGTCTATATGTACAAGTGTTTTGGCA 59.627 38.462 0.00 0.00 0.00 4.92
2439 2681 6.311735 TGGAAAATTTATATAGGGGCAGGTC 58.688 40.000 0.00 0.00 0.00 3.85
2441 2683 5.185828 GCTGGAAAATTTATATAGGGGCAGG 59.814 44.000 0.00 0.00 0.00 4.85
2699 3003 7.332182 GCAACTCTGTTTTACTGCTAGTAGATT 59.668 37.037 15.37 0.00 31.47 2.40
2702 3006 5.926542 TGCAACTCTGTTTTACTGCTAGTAG 59.073 40.000 6.26 6.26 31.47 2.57
2711 3015 4.282873 GCTGTTCTGCAACTCTGTTTTAC 58.717 43.478 0.00 0.00 33.17 2.01
2750 3054 7.883217 TGTTTCTTCTCTATATACCGTGGATC 58.117 38.462 0.00 0.00 0.00 3.36
2751 3055 7.724506 TCTGTTTCTTCTCTATATACCGTGGAT 59.275 37.037 0.00 0.00 0.00 3.41
2752 3056 7.058525 TCTGTTTCTTCTCTATATACCGTGGA 58.941 38.462 0.00 0.00 0.00 4.02
2769 3073 6.282199 AGACCACATACGTTATCTGTTTCT 57.718 37.500 0.00 0.00 0.00 2.52
2770 3074 6.963049 AAGACCACATACGTTATCTGTTTC 57.037 37.500 0.00 0.00 0.00 2.78
2774 3079 6.961359 TGAAAAGACCACATACGTTATCTG 57.039 37.500 0.00 0.00 0.00 2.90
2796 3101 3.772932 TGCAACACAAGCTTTTCTCTTG 58.227 40.909 0.00 1.63 44.71 3.02
2849 3155 4.083057 GAAGGTTCCTTCTTTGAGCATCAC 60.083 45.833 20.45 0.00 41.21 3.06
2853 3159 2.863809 GGAAGGTTCCTTCTTTGAGCA 58.136 47.619 24.77 0.00 44.11 4.26
2943 3249 5.696270 CCTCTTTTGACAGGGCAAAAATTAC 59.304 40.000 13.54 0.00 44.40 1.89
2947 3253 2.433970 CCCTCTTTTGACAGGGCAAAAA 59.566 45.455 13.54 5.18 44.40 1.94
3066 3372 2.751806 GCAGTGCTTAGGAAAAGCTGAT 59.248 45.455 8.18 0.00 43.38 2.90
3173 3479 9.630098 TCAGAAGAAAGCATAGCATTTTAAAAG 57.370 29.630 6.79 0.60 0.00 2.27
3196 3502 2.611473 CCAGTACCTGCTCACAAGTCAG 60.611 54.545 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.