Multiple sequence alignment - TraesCS3A01G379600

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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 TraesCS3A01G379600 chr3A 100.000 3050 0 0 1 3050 629105153 629108202 0.000000e+00 5633
1 TraesCS3A01G379600 chr2D 97.837 3051 51 6 1 3050 645428152 645431188 0.000000e+00 5254
2 TraesCS3A01G379600 chr2D 94.003 717 40 3 858 1573 586830966 586831680 0.000000e+00 1083
3 TraesCS3A01G379600 chr7B 95.272 3046 138 5 1 3046 575978084 575975045 0.000000e+00 4822
4 TraesCS3A01G379600 chr7B 94.545 2255 99 10 795 3046 515591354 515593587 0.000000e+00 3461
5 TraesCS3A01G379600 chr6B 94.895 2860 132 8 1 2857 671453404 671456252 0.000000e+00 4460
6 TraesCS3A01G379600 chr6B 94.835 1181 40 10 1869 3046 58115535 58116697 0.000000e+00 1823
7 TraesCS3A01G379600 chr1B 95.695 1951 78 5 1099 3045 665424813 665422865 0.000000e+00 3133
8 TraesCS3A01G379600 chr1B 93.138 1778 100 11 1286 3049 232329633 232331402 0.000000e+00 2588
9 TraesCS3A01G379600 chr1B 90.235 553 51 2 71 623 232293645 232294194 0.000000e+00 719
10 TraesCS3A01G379600 chr1B 81.208 596 45 33 126 683 470778525 470779091 4.700000e-113 418
11 TraesCS3A01G379600 chr7D 96.982 1756 51 2 1292 3046 41752458 41750704 0.000000e+00 2948
12 TraesCS3A01G379600 chr7D 95.015 662 30 1 1 662 41764029 41763371 0.000000e+00 1037
13 TraesCS3A01G379600 chr7D 92.211 475 31 2 1478 1952 486202416 486201948 0.000000e+00 667
14 TraesCS3A01G379600 chr7D 93.812 404 23 2 1957 2359 486200977 486200575 9.350000e-170 606
15 TraesCS3A01G379600 chr4D 92.256 1498 72 13 858 2354 437505855 437507309 0.000000e+00 2084
16 TraesCS3A01G379600 chr2B 94.920 1181 41 8 1869 3046 81564407 81565571 0.000000e+00 1831
17 TraesCS3A01G379600 chr3B 94.915 1180 39 10 1869 3045 684608140 684609301 0.000000e+00 1827
18 TraesCS3A01G379600 chr3B 95.298 1106 45 4 868 1973 749193609 749192511 0.000000e+00 1748
19 TraesCS3A01G379600 chr5D 93.733 718 42 3 858 1573 556578709 556577993 0.000000e+00 1074
20 TraesCS3A01G379600 chr3D 93.724 717 43 2 858 1573 10933418 10932703 0.000000e+00 1074
21 TraesCS3A01G379600 chr3D 93.584 717 44 2 858 1573 588696155 588696870 0.000000e+00 1068
22 TraesCS3A01G379600 chr1D 82.787 488 47 18 125 591 349184412 349184883 4.740000e-108 401
23 TraesCS3A01G379600 chr1D 84.559 272 20 8 601 856 349185177 349185442 1.820000e-62 250
24 TraesCS3A01G379600 chr1A 78.853 558 56 31 207 735 449556498 449557022 1.360000e-83 320


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 TraesCS3A01G379600 chr3A 629105153 629108202 3049 False 5633.0 5633 100.0000 1 3050 1 chr3A.!!$F1 3049
1 TraesCS3A01G379600 chr2D 645428152 645431188 3036 False 5254.0 5254 97.8370 1 3050 1 chr2D.!!$F2 3049
2 TraesCS3A01G379600 chr2D 586830966 586831680 714 False 1083.0 1083 94.0030 858 1573 1 chr2D.!!$F1 715
3 TraesCS3A01G379600 chr7B 575975045 575978084 3039 True 4822.0 4822 95.2720 1 3046 1 chr7B.!!$R1 3045
4 TraesCS3A01G379600 chr7B 515591354 515593587 2233 False 3461.0 3461 94.5450 795 3046 1 chr7B.!!$F1 2251
5 TraesCS3A01G379600 chr6B 671453404 671456252 2848 False 4460.0 4460 94.8950 1 2857 1 chr6B.!!$F2 2856
6 TraesCS3A01G379600 chr6B 58115535 58116697 1162 False 1823.0 1823 94.8350 1869 3046 1 chr6B.!!$F1 1177
7 TraesCS3A01G379600 chr1B 665422865 665424813 1948 True 3133.0 3133 95.6950 1099 3045 1 chr1B.!!$R1 1946
8 TraesCS3A01G379600 chr1B 232329633 232331402 1769 False 2588.0 2588 93.1380 1286 3049 1 chr1B.!!$F2 1763
9 TraesCS3A01G379600 chr1B 232293645 232294194 549 False 719.0 719 90.2350 71 623 1 chr1B.!!$F1 552
10 TraesCS3A01G379600 chr1B 470778525 470779091 566 False 418.0 418 81.2080 126 683 1 chr1B.!!$F3 557
11 TraesCS3A01G379600 chr7D 41750704 41752458 1754 True 2948.0 2948 96.9820 1292 3046 1 chr7D.!!$R1 1754
12 TraesCS3A01G379600 chr7D 41763371 41764029 658 True 1037.0 1037 95.0150 1 662 1 chr7D.!!$R2 661
13 TraesCS3A01G379600 chr7D 486200575 486202416 1841 True 636.5 667 93.0115 1478 2359 2 chr7D.!!$R3 881
14 TraesCS3A01G379600 chr4D 437505855 437507309 1454 False 2084.0 2084 92.2560 858 2354 1 chr4D.!!$F1 1496
15 TraesCS3A01G379600 chr2B 81564407 81565571 1164 False 1831.0 1831 94.9200 1869 3046 1 chr2B.!!$F1 1177
16 TraesCS3A01G379600 chr3B 684608140 684609301 1161 False 1827.0 1827 94.9150 1869 3045 1 chr3B.!!$F1 1176
17 TraesCS3A01G379600 chr3B 749192511 749193609 1098 True 1748.0 1748 95.2980 868 1973 1 chr3B.!!$R1 1105
18 TraesCS3A01G379600 chr5D 556577993 556578709 716 True 1074.0 1074 93.7330 858 1573 1 chr5D.!!$R1 715
19 TraesCS3A01G379600 chr3D 10932703 10933418 715 True 1074.0 1074 93.7240 858 1573 1 chr3D.!!$R1 715
20 TraesCS3A01G379600 chr3D 588696155 588696870 715 False 1068.0 1068 93.5840 858 1573 1 chr3D.!!$F1 715
21 TraesCS3A01G379600 chr1D 349184412 349185442 1030 False 325.5 401 83.6730 125 856 2 chr1D.!!$F1 731
22 TraesCS3A01G379600 chr1A 449556498 449557022 524 False 320.0 320 78.8530 207 735 1 chr1A.!!$F1 528

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
277 289 0.257616 AAGACGAGGAGGAGGAGGAG 59.742 60.0 0.00 0.00 0.00 3.69 F
439 466 0.530870 TTTGTGCATCGGTCGACACA 60.531 50.0 18.91 9.06 41.04 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1231 1590 1.589716 GCTGTTCGCCAAGCCTGAAT 61.590 55.000 0.0 0.0 0.00 2.57 R
2108 3488 3.008049 TGGAAACCTAGAAGAAGGACAGC 59.992 47.826 0.0 0.0 39.15 4.40 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
62 63 4.361971 TCCGTCTCCTCCCGCAGT 62.362 66.667 0.00 0.00 0.00 4.40
276 288 0.705253 AAAGACGAGGAGGAGGAGGA 59.295 55.000 0.00 0.00 0.00 3.71
277 289 0.257616 AAGACGAGGAGGAGGAGGAG 59.742 60.000 0.00 0.00 0.00 3.69
278 290 1.152839 GACGAGGAGGAGGAGGAGG 60.153 68.421 0.00 0.00 0.00 4.30
432 459 3.959535 ATCCAATTTTTGTGCATCGGT 57.040 38.095 0.00 0.00 0.00 4.69
439 466 0.530870 TTTGTGCATCGGTCGACACA 60.531 50.000 18.91 9.06 41.04 3.72
508 538 5.359009 CCTGTTACCATCTGCAATCTTTGAT 59.641 40.000 0.00 0.00 0.00 2.57
818 1166 4.332428 AGTAGTACATTATCGTTGGCCC 57.668 45.455 0.00 0.00 0.00 5.80
819 1167 3.707611 AGTAGTACATTATCGTTGGCCCA 59.292 43.478 0.00 0.00 0.00 5.36
820 1168 2.914059 AGTACATTATCGTTGGCCCAC 58.086 47.619 0.00 0.00 0.00 4.61
959 1314 2.611292 GCTTGTTGCTAGCTGTAGGATG 59.389 50.000 17.23 0.21 38.95 3.51
1136 1494 2.834549 ACCTCTACAATGTCCACTCCTG 59.165 50.000 0.00 0.00 0.00 3.86
1231 1590 0.987613 TGCTATGGGGCTGATGTGGA 60.988 55.000 0.00 0.00 0.00 4.02
1556 1970 1.739466 ACTTGTGGCACTAATGATGCG 59.261 47.619 19.83 0.00 44.37 4.73
2095 3475 6.727231 TGTAAATAGTCCCTTACTCCACTCAA 59.273 38.462 0.00 0.00 39.80 3.02
2518 3917 2.769663 AGTACAACCAGGACAACTGTGA 59.230 45.455 0.00 0.00 46.06 3.58
2559 3958 5.321934 AGGTCCAAGGACGACTATATACT 57.678 43.478 12.77 0.00 45.41 2.12
2865 4264 2.764269 TGGGCTCTAGAAAGGCTATGT 58.236 47.619 5.66 0.00 41.37 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 5.439828 CAAATCGATGACAAAACGACTTGA 58.560 37.500 14.29 0.00 42.79 3.02
276 288 0.032217 CTTCTCCTCCTGCTCCTCCT 60.032 60.000 0.00 0.00 0.00 3.69
277 289 1.685355 GCTTCTCCTCCTGCTCCTCC 61.685 65.000 0.00 0.00 0.00 4.30
278 290 0.975040 TGCTTCTCCTCCTGCTCCTC 60.975 60.000 0.00 0.00 0.00 3.71
432 459 1.346395 AGGGTAGCAAATGTGTGTCGA 59.654 47.619 0.00 0.00 0.00 4.20
439 466 4.382386 AACCAAGTAGGGTAGCAAATGT 57.618 40.909 0.00 0.00 41.32 2.71
508 538 4.400251 GGAATCAAGTTCTTGATGGATGCA 59.600 41.667 23.09 0.00 40.51 3.96
599 663 5.866633 CCATCAACACTTCAGTTCTACTCTC 59.133 44.000 0.00 0.00 0.00 3.20
770 1117 1.732405 CGAGCTCTTACACGTGATGCA 60.732 52.381 25.01 0.83 0.00 3.96
818 1166 6.319658 ACCAGGATCAAAATGTAGCAATAGTG 59.680 38.462 0.00 0.00 0.00 2.74
819 1167 6.319658 CACCAGGATCAAAATGTAGCAATAGT 59.680 38.462 0.00 0.00 0.00 2.12
820 1168 6.543465 TCACCAGGATCAAAATGTAGCAATAG 59.457 38.462 0.00 0.00 0.00 1.73
959 1314 4.752604 ACCAAAACAACAACCAAAAGTCAC 59.247 37.500 0.00 0.00 0.00 3.67
1136 1494 1.897641 CTACGGACTCGAGAACTTGC 58.102 55.000 21.68 0.06 40.11 4.01
1231 1590 1.589716 GCTGTTCGCCAAGCCTGAAT 61.590 55.000 0.00 0.00 0.00 2.57
1627 2041 5.290493 TGCGTCTATCATTTCCTAACCAT 57.710 39.130 0.00 0.00 0.00 3.55
2095 3475 7.837187 AGAAGAAGGACAGCTTATAGAGTTACT 59.163 37.037 0.00 0.00 0.00 2.24
2108 3488 3.008049 TGGAAACCTAGAAGAAGGACAGC 59.992 47.826 0.00 0.00 39.15 4.40
2518 3917 1.004745 CTTGGGAGCTACCACCAACAT 59.995 52.381 20.36 0.00 41.03 2.71
2559 3958 2.481795 GCTTGGCTCTTTGCTGTCAAAA 60.482 45.455 0.00 0.00 41.22 2.44


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

AutoCloner maintained by Alex Coulton.