Multiple sequence alignment - TraesCS3B01G215900

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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 TraesCS3B01G215900 chr3B 100.000 3599 0 0 1 3599 257040108 257036510 0.000000e+00 6647.0
1 TraesCS3B01G215900 chr3D 95.481 3629 116 24 1 3599 178594269 178590659 0.000000e+00 5749.0
2 TraesCS3B01G215900 chr3A 95.417 3011 117 14 1 3007 220889702 220886709 0.000000e+00 4776.0
3 TraesCS3B01G215900 chr3A 95.537 605 22 4 2997 3599 220886637 220886036 0.000000e+00 963.0
4 TraesCS3B01G215900 chr3A 96.970 33 1 0 3343 3375 220886258 220886226 5.020000e-04 56.5
5 TraesCS3B01G215900 chrUn 86.512 215 22 4 3377 3584 28822558 28822344 2.790000e-56 230.0
6 TraesCS3B01G215900 chr4B 92.208 77 6 0 3377 3453 421725725 421725649 3.800000e-20 110.0
7 TraesCS3B01G215900 chr5B 91.549 71 6 0 3377 3447 461494076 461494146 8.220000e-17 99.0
8 TraesCS3B01G215900 chr4A 77.564 156 31 3 3378 3532 1744666 1744818 1.380000e-14 91.6
9 TraesCS3B01G215900 chr1A 92.683 41 3 0 615 655 459098830 459098790 3.880000e-05 60.2


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 TraesCS3B01G215900 chr3B 257036510 257040108 3598 True 6647.000000 6647 100.000000 1 3599 1 chr3B.!!$R1 3598
1 TraesCS3B01G215900 chr3D 178590659 178594269 3610 True 5749.000000 5749 95.481000 1 3599 1 chr3D.!!$R1 3598
2 TraesCS3B01G215900 chr3A 220886036 220889702 3666 True 1931.833333 4776 95.974667 1 3599 3 chr3A.!!$R1 3598

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
716 738 0.752009 TAGGTAGGCAGAGCTCCACG 60.752 60.0 10.93 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2692 2722 0.625849 GAACACCACCAGGATCCCAT 59.374 55.0 8.55 0.0 38.69 4.0 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 1.153823 GCATTTCTGCTGCTGGCTG 60.154 57.895 6.69 3.71 45.32 4.85
56 57 2.126071 CGTGGTCGTCGCCAATCT 60.126 61.111 9.50 0.00 40.68 2.40
70 71 1.089920 CAATCTTAGCAGCGGCAACT 58.910 50.000 12.44 0.86 44.61 3.16
101 102 1.967762 CGAATTGCATCGCTTGTTGT 58.032 45.000 0.00 0.00 35.85 3.32
123 124 0.860533 CAAAACAACATTGCGGCCAG 59.139 50.000 2.24 0.00 0.00 4.85
169 171 2.190578 GCATAGCCGGTTCCAGCT 59.809 61.111 1.90 4.92 43.20 4.24
191 193 2.280797 GCGTCACTGGTTCCAGCA 60.281 61.111 17.55 3.20 37.57 4.41
192 194 1.891919 GCGTCACTGGTTCCAGCAA 60.892 57.895 17.55 4.47 37.57 3.91
193 195 1.444119 GCGTCACTGGTTCCAGCAAA 61.444 55.000 17.55 2.12 37.57 3.68
296 298 3.372730 GCCATGGCCGCAGAAACA 61.373 61.111 27.24 0.00 34.56 2.83
305 307 1.998257 CGCAGAAACACAACACGCG 60.998 57.895 3.53 3.53 34.89 6.01
352 355 1.139734 CTAGTCGCAGCATCCGTGT 59.860 57.895 0.00 0.00 0.00 4.49
453 456 3.498777 GTGGAAAGAAGAAAAGACGAGGG 59.501 47.826 0.00 0.00 0.00 4.30
486 489 6.149616 AGAAGATAGTGATTGAGGGGAAGAT 58.850 40.000 0.00 0.00 0.00 2.40
495 498 0.767375 GAGGGGAAGATGGCTATGCA 59.233 55.000 0.00 0.00 0.00 3.96
500 503 1.202976 GGAAGATGGCTATGCATGGGT 60.203 52.381 10.16 0.00 0.00 4.51
503 506 2.624495 AGATGGCTATGCATGGGTCTA 58.376 47.619 10.16 0.00 0.00 2.59
518 522 2.134346 GGTCTACAAAAACGCGTGGTA 58.866 47.619 14.98 12.47 0.00 3.25
582 586 2.898840 CCGATGCAATGCTCGGCT 60.899 61.111 24.64 0.04 46.87 5.52
583 587 2.326897 CGATGCAATGCTCGGCTG 59.673 61.111 15.64 0.00 0.00 4.85
590 594 1.066605 GCAATGCTCGGCTGATTGATT 59.933 47.619 10.84 0.74 30.03 2.57
628 650 2.348218 CGACTACAGTGTCAAAAACGCC 60.348 50.000 0.00 0.00 39.30 5.68
640 662 6.416750 GTGTCAAAAACGCCCTTATATTATGC 59.583 38.462 0.00 0.00 31.92 3.14
666 688 2.355244 GAGTAGATCCTGCGCGCC 60.355 66.667 30.77 12.97 0.00 6.53
716 738 0.752009 TAGGTAGGCAGAGCTCCACG 60.752 60.000 10.93 0.00 0.00 4.94
788 818 2.097791 AGTGATCGCTTACGGAACTCTC 59.902 50.000 2.02 0.00 40.63 3.20
948 978 2.847234 TCCTGACGCCACCACCTT 60.847 61.111 0.00 0.00 0.00 3.50
1078 1108 4.150454 AGGGCGAGGAGGAGGAGG 62.150 72.222 0.00 0.00 0.00 4.30
1079 1109 4.144727 GGGCGAGGAGGAGGAGGA 62.145 72.222 0.00 0.00 0.00 3.71
1080 1110 2.520741 GGCGAGGAGGAGGAGGAG 60.521 72.222 0.00 0.00 0.00 3.69
1361 1391 1.077357 AGGATGAGGACGACGAGCT 60.077 57.895 0.00 0.00 0.00 4.09
1640 1670 1.591703 GACAGGCTGTCGATGACCA 59.408 57.895 29.91 0.00 37.67 4.02
1716 1746 4.137879 GCTGATGGCGAAGATGCT 57.862 55.556 0.00 0.00 34.52 3.79
1782 1812 4.367023 TGGCGTTCGTCCCTTCCG 62.367 66.667 0.00 0.00 0.00 4.30
1917 1947 4.051922 TCAGCGTTGAAGAGAGAAAAGAC 58.948 43.478 0.00 0.00 0.00 3.01
2084 2114 0.392998 CTCGTAAGCAGGGCCATGTT 60.393 55.000 20.22 10.77 37.18 2.71
2130 2160 0.962489 GGGAGGTCGATGATGACGAT 59.038 55.000 0.00 0.00 41.62 3.73
2138 2168 5.183904 AGGTCGATGATGACGATGATGATAA 59.816 40.000 0.00 0.00 41.62 1.75
2246 2276 5.132144 AGGTTGAGGGAAAACAAGAAGTAGA 59.868 40.000 0.00 0.00 0.00 2.59
2249 2279 5.063880 TGAGGGAAAACAAGAAGTAGAAGC 58.936 41.667 0.00 0.00 0.00 3.86
2295 2325 7.141758 AGATAAGGAGATGATTTTGGTAGCA 57.858 36.000 0.00 0.00 0.00 3.49
2427 2457 1.092348 TATCACTGGTGTCTCGACCG 58.908 55.000 0.53 0.00 39.07 4.79
2431 2461 1.081376 CTGGTGTCTCGACCGTCAC 60.081 63.158 0.00 0.00 39.07 3.67
2682 2712 9.758651 GATGTTTCCATAGTTTTAACCTGTTTT 57.241 29.630 0.00 0.00 0.00 2.43
2741 2771 5.470047 TTCTCTTGGAGTTCTGTCTTACC 57.530 43.478 0.00 0.00 0.00 2.85
2781 2811 5.163513 GGTACACTGGCAATTCAAATTCAG 58.836 41.667 0.00 3.78 0.00 3.02
2782 2812 4.942761 ACACTGGCAATTCAAATTCAGT 57.057 36.364 4.74 4.74 35.24 3.41
3015 3128 9.428097 TGCTATATATTCATCTGTTGCTTACTG 57.572 33.333 0.00 0.00 0.00 2.74
3188 3301 7.274447 TCTTCAATTTGTCTTTGGAATTGCTT 58.726 30.769 0.00 0.00 39.44 3.91
3279 3393 2.223340 GCAATATTGGTTCGCTGTGAGG 60.223 50.000 17.02 0.00 0.00 3.86
3288 3402 0.671472 TCGCTGTGAGGTTGCATCTG 60.671 55.000 0.00 0.00 0.00 2.90
3314 3430 1.673920 TCAGTTTGCGGTCACCTTTTC 59.326 47.619 0.00 0.00 0.00 2.29
3370 3486 2.769617 CAACGTCGCTAGCAACCG 59.230 61.111 16.45 15.02 0.00 4.44
3551 3667 3.077359 AGTGTGCAAAGCATAGACTTCC 58.923 45.455 0.00 0.00 41.91 3.46
3574 3690 2.791158 GCTTCACGGAACAACACACTTG 60.791 50.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 0.737715 GACGGTGACAGAGGTGATGC 60.738 60.000 0.00 0.00 0.00 3.91
83 84 2.848302 GCTACAACAAGCGATGCAATTC 59.152 45.455 0.00 0.00 31.76 2.17
101 102 1.604185 GGCCGCAATGTTGTTTTGCTA 60.604 47.619 6.80 0.00 45.67 3.49
123 124 1.000736 GAACACGAAGTCGACGGTCC 61.001 60.000 10.46 0.00 41.61 4.46
169 171 0.687920 TGGAACCAGTGACGCCAATA 59.312 50.000 0.00 0.00 0.00 1.90
305 307 1.883084 CGCTAGGAACCGCATGTCC 60.883 63.158 0.00 0.00 0.00 4.02
352 355 2.187493 CGCAGAGCTCTAGGCCGTA 61.187 63.158 17.75 0.00 43.05 4.02
453 456 5.812642 TCAATCACTATCTTCTTCCTTTCGC 59.187 40.000 0.00 0.00 0.00 4.70
486 489 1.506025 TGTAGACCCATGCATAGCCA 58.494 50.000 0.00 0.00 0.00 4.75
495 498 1.533731 CACGCGTTTTTGTAGACCCAT 59.466 47.619 10.22 0.00 0.00 4.00
500 503 2.134346 GGTACCACGCGTTTTTGTAGA 58.866 47.619 10.22 0.00 0.00 2.59
503 506 1.064357 CAAGGTACCACGCGTTTTTGT 59.936 47.619 10.22 7.40 0.00 2.83
518 522 3.490348 CAGAACCCATCAACTTCAAGGT 58.510 45.455 0.00 0.00 0.00 3.50
569 573 0.677414 TCAATCAGCCGAGCATTGCA 60.677 50.000 11.91 0.00 0.00 4.08
582 586 9.949174 CGGTAAATGATTCAATACAATCAATCA 57.051 29.630 12.37 0.00 44.18 2.57
590 594 8.255206 ACTGTAGTCGGTAAATGATTCAATACA 58.745 33.333 12.37 0.00 0.00 2.29
628 650 5.006153 TCCATCCGTCGCATAATATAAGG 57.994 43.478 0.00 0.00 0.00 2.69
666 688 0.109723 TCCACGGAAGTTTGGGAAGG 59.890 55.000 0.00 0.00 46.40 3.46
716 738 0.470341 GATTAGGGCCAGGTGGACTC 59.530 60.000 6.18 0.00 44.77 3.36
788 818 2.977914 CCTTACATCAGTGAGGGTGTG 58.022 52.381 9.95 0.00 45.29 3.82
948 978 0.257328 ATCTGGACTCTCGAGGCTGA 59.743 55.000 13.56 3.53 36.46 4.26
1078 1108 3.708220 CTTGCTCGACCTCCCGCTC 62.708 68.421 0.00 0.00 0.00 5.03
1079 1109 3.764466 CTTGCTCGACCTCCCGCT 61.764 66.667 0.00 0.00 0.00 5.52
1088 1118 3.348055 CTCTCCGCTGCTTGCTCGA 62.348 63.158 0.00 0.00 40.11 4.04
1782 1812 2.538512 AACGGGTGTACTTCTTGGAC 57.461 50.000 0.00 0.00 0.00 4.02
1902 1932 6.332735 TCAATCTCGTCTTTTCTCTCTTCA 57.667 37.500 0.00 0.00 0.00 3.02
1917 1947 0.737367 TGAGCACGCCTTCAATCTCG 60.737 55.000 0.00 0.00 0.00 4.04
2084 2114 3.231818 AGTTCTTCCTCGTCTTCCTTCA 58.768 45.455 0.00 0.00 0.00 3.02
2130 2160 9.460019 TGTTTGTAATCACCTTGATTATCATCA 57.540 29.630 10.92 3.36 47.00 3.07
2138 2168 4.832266 TGCCTTGTTTGTAATCACCTTGAT 59.168 37.500 0.00 0.00 39.09 2.57
2149 2179 2.992593 TGTGACAGTGCCTTGTTTGTA 58.007 42.857 0.00 0.00 0.00 2.41
2260 2290 2.435805 TCTCCTTATCTTCCGCTGCATT 59.564 45.455 0.00 0.00 0.00 3.56
2262 2292 1.485124 TCTCCTTATCTTCCGCTGCA 58.515 50.000 0.00 0.00 0.00 4.41
2295 2325 5.422012 GGATTCACCATTATTGTCCTTTGGT 59.578 40.000 0.00 0.00 41.27 3.67
2427 2457 1.830477 AGATCTTCCTCCTGCAGTGAC 59.170 52.381 13.81 0.00 0.00 3.67
2431 2461 2.699846 AGCTAAGATCTTCCTCCTGCAG 59.300 50.000 12.24 6.78 0.00 4.41
2682 2712 4.527816 CACCAGGATCCCATTTTTGAGAAA 59.472 41.667 8.55 0.00 0.00 2.52
2691 2721 1.005924 GAACACCACCAGGATCCCATT 59.994 52.381 8.55 0.00 38.69 3.16
2692 2722 0.625849 GAACACCACCAGGATCCCAT 59.374 55.000 8.55 0.00 38.69 4.00
2741 2771 7.412063 CAGTGTACCATCACAATATTCACATG 58.588 38.462 0.00 0.00 40.37 3.21
2781 2811 3.383505 GGGTAATCAAAATACAGCCCCAC 59.616 47.826 0.00 0.00 0.00 4.61
2782 2812 3.637769 GGGTAATCAAAATACAGCCCCA 58.362 45.455 0.00 0.00 0.00 4.96
2858 2888 2.561478 AGTGGACACTAACCGCAAAT 57.439 45.000 2.58 0.00 40.43 2.32
2952 2982 1.529226 CATGCTTGGTAAACCGGTCA 58.471 50.000 8.04 0.00 39.43 4.02
3015 3128 4.202326 TGAACTCCAGTCAAGTTACCTTCC 60.202 45.833 0.00 0.00 37.10 3.46
3279 3393 5.164158 CGCAAACTGAAAATACAGATGCAAC 60.164 40.000 20.49 0.00 44.94 4.17
3288 3402 3.252458 AGGTGACCGCAAACTGAAAATAC 59.748 43.478 0.00 0.00 0.00 1.89
3370 3486 2.602217 CGTTGCTGCACCAGTTTAGTTC 60.602 50.000 0.00 0.00 33.43 3.01
3551 3667 1.013596 TGTGTTGTTCCGTGAAGCTG 58.986 50.000 0.00 0.00 0.00 4.24
3574 3690 4.595986 TCTTATTTTGTGTAAGGGGAGCC 58.404 43.478 0.00 0.00 31.59 4.70


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

AutoCloner maintained by Alex Coulton.