Multiple sequence alignment - TraesCS3A01G419300

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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 TraesCS3A01G419300 chr3A 100.000 3485 0 0 1 3485 661472693 661476177 0.000000e+00 6436
1 TraesCS3A01G419300 chr3B 94.939 3497 153 14 2 3485 696327537 696331022 0.000000e+00 5456
2 TraesCS3A01G419300 chr3D 93.493 3012 125 22 1 2974 526973931 526976909 0.000000e+00 4410
3 TraesCS3A01G419300 chr3D 95.022 462 15 6 3031 3485 526976906 526977366 0.000000e+00 719
4 TraesCS3A01G419300 chr7D 92.271 1048 80 1 966 2013 496314147 496315193 0.000000e+00 1485
5 TraesCS3A01G419300 chr7B 96.094 128 5 0 472 599 312023750 312023623 3.520000e-50 209
6 TraesCS3A01G419300 chr7B 95.312 128 6 0 472 599 311927075 311926948 1.640000e-48 204
7 TraesCS3A01G419300 chr2D 92.523 107 6 2 3379 3485 317593007 317593111 6.020000e-33 152
8 TraesCS3A01G419300 chr2B 90.654 107 8 2 3379 3485 385199439 385199543 1.300000e-29 141
9 TraesCS3A01G419300 chr2A 90.741 108 7 3 3379 3485 416919561 416919456 1.300000e-29 141


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 TraesCS3A01G419300 chr3A 661472693 661476177 3484 False 6436.0 6436 100.0000 1 3485 1 chr3A.!!$F1 3484
1 TraesCS3A01G419300 chr3B 696327537 696331022 3485 False 5456.0 5456 94.9390 2 3485 1 chr3B.!!$F1 3483
2 TraesCS3A01G419300 chr3D 526973931 526977366 3435 False 2564.5 4410 94.2575 1 3485 2 chr3D.!!$F1 3484
3 TraesCS3A01G419300 chr7D 496314147 496315193 1046 False 1485.0 1485 92.2710 966 2013 1 chr7D.!!$F1 1047

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
144 145 0.603707 TCAAGAAAGCAGGCAGGTCG 60.604 55.0 0.00 0.0 0.0 4.79 F
1797 1842 0.665835 CAGGTAGTAGGCGCTCTCTG 59.334 60.0 7.64 2.5 0.0 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2058 2103 0.178891 TCTTGGCCAACTCCTCCTCT 60.179 55.0 16.05 0.0 0.0 3.69 R
2675 2728 0.390472 GCACTCCTTGAACCTCCTCG 60.390 60.0 0.00 0.0 0.0 4.63 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
64 65 2.653702 GCTCCGCAGTCTCTGTGT 59.346 61.111 9.01 0.00 39.99 3.72
139 140 2.816087 GTTGAGATCAAGAAAGCAGGCA 59.184 45.455 0.00 0.00 36.39 4.75
143 144 1.742268 GATCAAGAAAGCAGGCAGGTC 59.258 52.381 0.00 0.00 0.00 3.85
144 145 0.603707 TCAAGAAAGCAGGCAGGTCG 60.604 55.000 0.00 0.00 0.00 4.79
146 147 3.435186 GAAAGCAGGCAGGTCGGC 61.435 66.667 0.00 0.00 41.61 5.54
189 190 1.871126 CTCCGAGCTGCTCTGTGTCA 61.871 60.000 25.59 4.31 0.00 3.58
343 352 4.488126 TCAGCATTGAAGAAAGTTTCCG 57.512 40.909 12.05 0.00 0.00 4.30
349 358 5.570589 GCATTGAAGAAAGTTTCCGAGAATG 59.429 40.000 12.05 14.53 0.00 2.67
384 404 5.961272 AGGAAACGAACAAAACAAATCACT 58.039 33.333 0.00 0.00 0.00 3.41
385 405 7.090953 AGGAAACGAACAAAACAAATCACTA 57.909 32.000 0.00 0.00 0.00 2.74
386 406 7.540299 AGGAAACGAACAAAACAAATCACTAA 58.460 30.769 0.00 0.00 0.00 2.24
387 407 8.194769 AGGAAACGAACAAAACAAATCACTAAT 58.805 29.630 0.00 0.00 0.00 1.73
388 408 8.813282 GGAAACGAACAAAACAAATCACTAATT 58.187 29.630 0.00 0.00 0.00 1.40
833 859 1.747745 CCGAATCCAAACCCCCGAC 60.748 63.158 0.00 0.00 0.00 4.79
1383 1428 3.854669 CTCCGCCGCCTCCTTGAT 61.855 66.667 0.00 0.00 0.00 2.57
1386 1431 4.514577 CGCCGCCTCCTTGATCGT 62.515 66.667 0.00 0.00 0.00 3.73
1675 1720 3.249189 GGGGCTGCGATGGGGATA 61.249 66.667 0.00 0.00 0.00 2.59
1773 1818 2.568546 TTATCAGGAAGGGGCTGAGA 57.431 50.000 0.00 0.00 0.00 3.27
1797 1842 0.665835 CAGGTAGTAGGCGCTCTCTG 59.334 60.000 7.64 2.50 0.00 3.35
1827 1872 1.619654 TGCTTGCTGTGCTTACCATT 58.380 45.000 0.00 0.00 0.00 3.16
1938 1983 3.525619 CGAGGGACGGTTGAATGAA 57.474 52.632 0.00 0.00 38.46 2.57
2226 2271 7.925483 CGAAAGGAGACATTCTCTATCTTGATT 59.075 37.037 3.30 0.00 42.95 2.57
2232 2277 8.774546 AGACATTCTCTATCTTGATTAGTGGA 57.225 34.615 0.00 0.00 0.00 4.02
2246 2291 6.768483 TGATTAGTGGATTGTGTTCAGAAGA 58.232 36.000 0.00 0.00 0.00 2.87
2256 2301 7.545615 GGATTGTGTTCAGAAGAAAAGTTTGTT 59.454 33.333 0.00 0.00 35.08 2.83
2313 2358 2.355108 CCACCATCGTCCTGACAGAAAT 60.355 50.000 3.32 0.00 0.00 2.17
2532 2577 1.401761 TGCAGCACACCAAAGACAAT 58.598 45.000 0.00 0.00 0.00 2.71
2586 2631 6.426327 GCTGAAGAGAAAAAGAAAGACAGTC 58.574 40.000 0.00 0.00 0.00 3.51
2627 2672 5.295431 TGAATTCTTGCCAGTTTGTATCG 57.705 39.130 7.05 0.00 0.00 2.92
2636 2681 3.560068 GCCAGTTTGTATCGGTATGAAGG 59.440 47.826 0.00 0.00 0.00 3.46
2639 2684 3.135895 AGTTTGTATCGGTATGAAGGGGG 59.864 47.826 0.00 0.00 0.00 5.40
2668 2721 2.831526 TGAGCTAGCTATGTTGTGTCCA 59.168 45.455 19.38 4.14 0.00 4.02
2670 2723 2.093447 AGCTAGCTATGTTGTGTCCACC 60.093 50.000 17.69 0.00 0.00 4.61
2719 2772 1.301677 GCTTCTGTTTCGGCCTGAGG 61.302 60.000 0.00 0.00 0.00 3.86
2765 2818 3.264104 GCCATCACAATGAAAACCATGG 58.736 45.455 11.19 11.19 35.24 3.66
2830 2883 2.342179 CTGAAGGAAAGAGAAGACCGC 58.658 52.381 0.00 0.00 0.00 5.68
2866 2919 5.073965 ACTTTCTTTATACACCCCCACAAGA 59.926 40.000 0.00 0.00 0.00 3.02
2869 2922 1.587066 TATACACCCCCACAAGACCC 58.413 55.000 0.00 0.00 0.00 4.46
2904 2957 3.483959 GAGCAGCCAAGAAGCTCG 58.516 61.111 0.00 0.00 44.37 5.03
2933 2986 8.078596 GGTATCAATTCTTATTTCTGATGGCAC 58.921 37.037 0.00 0.00 0.00 5.01
2974 3028 3.735237 TCTTGAGAGTGAACACAGACC 57.265 47.619 7.68 0.00 0.00 3.85
3206 3262 1.637338 TGCTGTCATGTGGAGAGACT 58.363 50.000 0.00 0.00 39.20 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 3.253188 CGGCTCTGAAATTGTTTGAGGAA 59.747 43.478 0.00 0.00 0.00 3.36
115 116 4.022503 GCCTGCTTTCTTGATCTCAACTTT 60.023 41.667 0.00 0.00 0.00 2.66
143 144 4.003788 ACAACACCCTCCTCGCCG 62.004 66.667 0.00 0.00 0.00 6.46
144 145 2.185310 ATCACAACACCCTCCTCGCC 62.185 60.000 0.00 0.00 0.00 5.54
146 147 0.321671 ACATCACAACACCCTCCTCG 59.678 55.000 0.00 0.00 0.00 4.63
148 149 3.497942 GGTTAACATCACAACACCCTCCT 60.498 47.826 8.10 0.00 0.00 3.69
149 150 2.817844 GGTTAACATCACAACACCCTCC 59.182 50.000 8.10 0.00 0.00 4.30
150 151 3.751518 AGGTTAACATCACAACACCCTC 58.248 45.455 8.10 0.00 0.00 4.30
151 152 3.497942 GGAGGTTAACATCACAACACCCT 60.498 47.826 20.75 0.00 0.00 4.34
152 153 2.817844 GGAGGTTAACATCACAACACCC 59.182 50.000 20.75 0.00 0.00 4.61
157 158 2.301870 AGCTCGGAGGTTAACATCACAA 59.698 45.455 20.75 5.62 0.00 3.33
254 255 3.430895 TGCGATCCTCGTTTGTTTCTAAC 59.569 43.478 0.00 0.00 42.81 2.34
256 257 3.306917 TGCGATCCTCGTTTGTTTCTA 57.693 42.857 0.00 0.00 42.81 2.10
274 276 4.621068 TGAATTGATTCGTTCCTCATGC 57.379 40.909 0.00 0.00 39.62 4.06
275 277 6.025896 CAGTTGAATTGATTCGTTCCTCATG 58.974 40.000 0.00 0.00 39.62 3.07
279 281 3.191371 GGCAGTTGAATTGATTCGTTCCT 59.809 43.478 0.00 0.00 39.62 3.36
280 282 3.057596 TGGCAGTTGAATTGATTCGTTCC 60.058 43.478 0.00 0.00 39.62 3.62
281 283 4.083324 TCTGGCAGTTGAATTGATTCGTTC 60.083 41.667 15.27 0.00 39.62 3.95
282 284 3.820467 TCTGGCAGTTGAATTGATTCGTT 59.180 39.130 15.27 0.00 39.62 3.85
343 352 3.559069 TCCTTCCATGCCATTCATTCTC 58.441 45.455 0.00 0.00 31.79 2.87
349 358 2.091541 TCGTTTCCTTCCATGCCATTC 58.908 47.619 0.00 0.00 0.00 2.67
387 407 8.725405 TTAACTGCCGATTAATCAGTGATTAA 57.275 30.769 30.83 30.83 44.88 1.40
388 408 8.902540 ATTAACTGCCGATTAATCAGTGATTA 57.097 30.769 19.51 19.51 40.54 1.75
389 409 7.807977 ATTAACTGCCGATTAATCAGTGATT 57.192 32.000 21.57 21.57 40.54 2.57
390 410 7.807977 AATTAACTGCCGATTAATCAGTGAT 57.192 32.000 15.57 0.00 40.54 3.06
391 411 7.225931 GGTAATTAACTGCCGATTAATCAGTGA 59.774 37.037 15.57 0.00 40.54 3.41
392 412 7.226720 AGGTAATTAACTGCCGATTAATCAGTG 59.773 37.037 15.57 4.54 40.54 3.66
393 413 7.280356 AGGTAATTAACTGCCGATTAATCAGT 58.720 34.615 15.57 9.04 42.28 3.41
394 414 7.730364 AGGTAATTAACTGCCGATTAATCAG 57.270 36.000 15.57 8.43 32.31 2.90
400 420 4.331717 CGACAAGGTAATTAACTGCCGATT 59.668 41.667 3.17 0.00 0.00 3.34
403 423 3.255725 TCGACAAGGTAATTAACTGCCG 58.744 45.455 3.17 8.24 0.00 5.69
671 696 2.040359 CCCTCCCTCCTTCCCTCC 60.040 72.222 0.00 0.00 0.00 4.30
672 697 0.692756 CTTCCCTCCCTCCTTCCCTC 60.693 65.000 0.00 0.00 0.00 4.30
673 698 1.398234 CTTCCCTCCCTCCTTCCCT 59.602 63.158 0.00 0.00 0.00 4.20
674 699 1.694525 CCTTCCCTCCCTCCTTCCC 60.695 68.421 0.00 0.00 0.00 3.97
675 700 1.694525 CCCTTCCCTCCCTCCTTCC 60.695 68.421 0.00 0.00 0.00 3.46
676 701 1.694525 CCCCTTCCCTCCCTCCTTC 60.695 68.421 0.00 0.00 0.00 3.46
677 702 2.461637 CCCCTTCCCTCCCTCCTT 59.538 66.667 0.00 0.00 0.00 3.36
678 703 3.711782 CCCCCTTCCCTCCCTCCT 61.712 72.222 0.00 0.00 0.00 3.69
833 859 2.897350 GGATCCTGGAAAGGCGCG 60.897 66.667 3.84 0.00 0.00 6.86
914 942 4.828925 GGCTCGGTCCAGCTCAGC 62.829 72.222 11.55 0.00 39.58 4.26
915 943 4.504916 CGGCTCGGTCCAGCTCAG 62.505 72.222 11.55 3.02 39.58 3.35
938 966 0.251653 TCACTTCCGGCTCCAGTAGT 60.252 55.000 0.00 0.00 0.00 2.73
1380 1425 2.764128 GGGAGGAGGCCACGATCA 60.764 66.667 5.01 0.00 0.00 2.92
1668 1713 1.065053 CGGAACACCACAATATCCCCA 60.065 52.381 0.00 0.00 0.00 4.96
1675 1720 2.671619 CGCCCGGAACACCACAAT 60.672 61.111 0.73 0.00 0.00 2.71
1827 1872 3.797353 GCTTCCCGGGCATCCTCA 61.797 66.667 18.49 0.00 0.00 3.86
1875 1920 1.227556 AAAGCTCGCAACAGTCCGT 60.228 52.632 0.00 0.00 0.00 4.69
1938 1983 3.953612 TGTCCTGAAACAAATTGTCTGCT 59.046 39.130 0.00 0.00 0.00 4.24
2058 2103 0.178891 TCTTGGCCAACTCCTCCTCT 60.179 55.000 16.05 0.00 0.00 3.69
2226 2271 7.054124 ACTTTTCTTCTGAACACAATCCACTA 58.946 34.615 0.00 0.00 31.02 2.74
2232 2277 8.087750 TCAACAAACTTTTCTTCTGAACACAAT 58.912 29.630 0.00 0.00 31.02 2.71
2246 2291 0.820871 TGCCGCCTCAACAAACTTTT 59.179 45.000 0.00 0.00 0.00 2.27
2256 2301 1.077787 CATAACCCTTGCCGCCTCA 60.078 57.895 0.00 0.00 0.00 3.86
2313 2358 5.240623 ACCTTCAATAACGTTGCTGAATTCA 59.759 36.000 20.50 8.12 0.00 2.57
2586 2631 5.344743 TTCAGGTTAATCTCTACAGGCAG 57.655 43.478 0.00 0.00 0.00 4.85
2639 2684 2.373502 ACATAGCTAGCTCAATTCCCCC 59.626 50.000 23.26 0.00 0.00 5.40
2668 2721 0.834612 TTGAACCTCCTCGTGTTGGT 59.165 50.000 0.00 0.00 0.00 3.67
2670 2723 1.070134 TCCTTGAACCTCCTCGTGTTG 59.930 52.381 0.00 0.00 0.00 3.33
2675 2728 0.390472 GCACTCCTTGAACCTCCTCG 60.390 60.000 0.00 0.00 0.00 4.63
2719 2772 2.557924 TCCACCTGTTCATCAAACATGC 59.442 45.455 0.00 0.00 46.53 4.06
2741 2794 2.288948 TGGTTTTCATTGTGATGGCAGC 60.289 45.455 0.00 0.00 33.93 5.25
2765 2818 1.817941 ACCACGTCCACAACAGCAC 60.818 57.895 0.00 0.00 0.00 4.40
2830 2883 3.778954 AAAGAAAGTCACCTCTCCTGG 57.221 47.619 0.00 0.00 0.00 4.45
2866 2919 1.762957 CTCCACGAATCCATACTGGGT 59.237 52.381 0.00 0.00 38.32 4.51
2869 2922 2.546795 GCTCCTCCACGAATCCATACTG 60.547 54.545 0.00 0.00 0.00 2.74
2879 2932 2.922503 TTGGCTGCTCCTCCACGA 60.923 61.111 0.00 0.00 35.26 4.35
2882 2935 1.681666 CTTCTTGGCTGCTCCTCCA 59.318 57.895 0.00 0.00 35.26 3.86
2884 2937 0.744057 GAGCTTCTTGGCTGCTCCTC 60.744 60.000 0.00 0.00 45.12 3.71
2904 2957 8.295288 CCATCAGAAATAAGAATTGATACCTGC 58.705 37.037 0.00 0.00 0.00 4.85
2970 3024 1.005215 CCCTGATCAAAAGCTGGGTCT 59.995 52.381 7.20 0.00 43.19 3.85
2974 3028 0.529378 GCACCCTGATCAAAAGCTGG 59.471 55.000 0.00 0.00 0.00 4.85
3206 3262 6.783708 ACACAAAACAAAGTCTGGGATTTA 57.216 33.333 0.00 0.00 0.00 1.40
3369 3429 5.007332 ACGAACAACAGGACATTGTTAGTTC 59.993 40.000 9.60 15.82 46.86 3.01
3380 3440 1.533129 GCAAACCACGAACAACAGGAC 60.533 52.381 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.