Multiple sequence alignment - TraesCS3A01G434300

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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 TraesCS3A01G434300 chr3A 100.000 2735 0 0 1 2735 676109112 676106378 0.000000e+00 5051.0
1 TraesCS3A01G434300 chr3D 92.779 2368 103 35 405 2734 540937554 540935217 0.000000e+00 3363.0
2 TraesCS3A01G434300 chr3D 89.610 308 26 5 2 307 540963462 540963159 1.190000e-103 387.0
3 TraesCS3A01G434300 chr3B 89.623 1590 87 35 356 1896 716340528 716338968 0.000000e+00 1951.0
4 TraesCS3A01G434300 chr3B 95.035 846 35 6 1894 2735 716337579 716336737 0.000000e+00 1323.0
5 TraesCS3A01G434300 chr3B 90.764 314 27 2 2 313 716343942 716343629 4.210000e-113 418.0
6 TraesCS3A01G434300 chr5D 74.257 303 60 11 29 313 446164512 446164210 8.010000e-21 111.0
7 TraesCS3A01G434300 chr4A 79.412 136 28 0 2514 2649 347411306 347411441 2.240000e-16 97.1
8 TraesCS3A01G434300 chr1A 87.500 56 5 2 340 393 588272372 588272317 2.270000e-06 63.9
9 TraesCS3A01G434300 chr1D 92.857 42 3 0 340 381 490053560 490053601 8.180000e-06 62.1


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 TraesCS3A01G434300 chr3A 676106378 676109112 2734 True 5051.000000 5051 100.000000 1 2735 1 chr3A.!!$R1 2734
1 TraesCS3A01G434300 chr3D 540935217 540937554 2337 True 3363.000000 3363 92.779000 405 2734 1 chr3D.!!$R1 2329
2 TraesCS3A01G434300 chr3B 716336737 716343942 7205 True 1230.666667 1951 91.807333 2 2735 3 chr3B.!!$R1 2733

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
47 49 0.622665 CCCTTTCAGTGGATGGCTCT 59.377 55.0 0.0 0.0 0.0 4.09 F
1037 4121 0.415429 TCTCCAGCTCCTCCTTCCTT 59.585 55.0 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1500 4611 0.103937 GGAACAGAGCTCATCGGAGG 59.896 60.0 17.77 0.0 41.67 4.30 R
2295 6812 0.036306 CTTTAGTTGGCCCACTCCGT 59.964 55.0 13.76 0.0 0.00 4.69 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
31 32 3.637273 GCCCGACTGGTTCACCCT 61.637 66.667 0.00 0.00 36.04 4.34
47 49 0.622665 CCCTTTCAGTGGATGGCTCT 59.377 55.000 0.00 0.00 0.00 4.09
54 56 1.558756 CAGTGGATGGCTCTTTCTCCT 59.441 52.381 0.00 0.00 0.00 3.69
95 97 1.868519 GCGGGTATGATCCTTCGTGAC 60.869 57.143 0.00 0.00 0.00 3.67
120 122 4.890581 ACAATGGTGGTGTTACTTTTGCTA 59.109 37.500 0.00 0.00 0.00 3.49
129 131 5.505159 GGTGTTACTTTTGCTACTTGTCACC 60.505 44.000 0.00 0.00 34.73 4.02
150 153 2.802816 CTGCTCTTCGTTTGCAACTAGT 59.197 45.455 0.00 0.00 36.22 2.57
186 189 8.267183 GGGAATGACCTTAATTGGAAATTCAAT 58.733 33.333 0.00 0.00 37.60 2.57
193 196 9.034800 ACCTTAATTGGAAATTCAATGCTCTAA 57.965 29.630 0.00 0.00 37.42 2.10
208 211 8.055181 TCAATGCTCTAATCTCCTTATTTTGGT 58.945 33.333 0.00 0.00 0.00 3.67
239 242 2.202676 GTGGGCGCTCTCTCTTCG 60.203 66.667 9.62 0.00 0.00 3.79
244 247 2.179517 CGCTCTCTCTTCGCCGTT 59.820 61.111 0.00 0.00 0.00 4.44
259 262 2.414138 CGCCGTTAAATTCTTTCCTCGT 59.586 45.455 0.00 0.00 0.00 4.18
264 267 6.608610 CCGTTAAATTCTTTCCTCGTCAAAT 58.391 36.000 0.00 0.00 0.00 2.32
268 271 5.532025 AATTCTTTCCTCGTCAAATCGTC 57.468 39.130 0.00 0.00 0.00 4.20
274 277 4.041740 TCCTCGTCAAATCGTCTTATGG 57.958 45.455 0.00 0.00 0.00 2.74
282 285 5.869888 GTCAAATCGTCTTATGGTCTCTTGT 59.130 40.000 0.00 0.00 0.00 3.16
285 288 7.759886 TCAAATCGTCTTATGGTCTCTTGTTAG 59.240 37.037 0.00 0.00 0.00 2.34
295 298 6.777213 TGGTCTCTTGTTAGAGGAGATTAC 57.223 41.667 0.00 0.00 46.57 1.89
302 305 5.401531 TGTTAGAGGAGATTACGTTGCTT 57.598 39.130 0.00 0.00 0.00 3.91
339 446 7.484744 AGGGCCACCAGTTATTCTATACTATA 58.515 38.462 6.18 0.00 40.13 1.31
340 447 8.129656 AGGGCCACCAGTTATTCTATACTATAT 58.870 37.037 6.18 0.00 40.13 0.86
341 448 8.422566 GGGCCACCAGTTATTCTATACTATATC 58.577 40.741 4.39 0.00 36.50 1.63
342 449 9.203163 GGCCACCAGTTATTCTATACTATATCT 57.797 37.037 0.00 0.00 0.00 1.98
358 3421 7.831691 ACTATATCTTGTATCAGCAGACTGT 57.168 36.000 3.99 0.00 44.77 3.55
369 3432 9.314133 TGTATCAGCAGACTGTAATCCTATTAT 57.686 33.333 3.99 0.00 44.77 1.28
394 3457 8.970859 TTTTGGAATAAATCTCTTTTGCCAAA 57.029 26.923 0.00 0.00 39.65 3.28
395 3458 9.571816 TTTTGGAATAAATCTCTTTTGCCAAAT 57.428 25.926 0.00 0.00 40.26 2.32
398 3461 9.874205 TGGAATAAATCTCTTTTGCCAAATAAG 57.126 29.630 0.00 0.00 0.00 1.73
616 3694 2.639286 CAGCCACACAGAAACGCC 59.361 61.111 0.00 0.00 0.00 5.68
620 3699 1.071471 CCACACAGAAACGCCTCCT 59.929 57.895 0.00 0.00 0.00 3.69
741 3820 4.471548 TCTCTTCTTTACCCTATCCGGAG 58.528 47.826 11.34 0.00 33.16 4.63
929 4011 2.192175 CGGGCCCCAACTGGATAC 59.808 66.667 18.66 0.00 37.39 2.24
1009 4091 0.751643 CCGGCGATTCCCATTCCTTT 60.752 55.000 9.30 0.00 0.00 3.11
1033 4117 0.682855 CTCGTCTCCAGCTCCTCCTT 60.683 60.000 0.00 0.00 0.00 3.36
1035 4119 1.671901 CGTCTCCAGCTCCTCCTTCC 61.672 65.000 0.00 0.00 0.00 3.46
1037 4121 0.415429 TCTCCAGCTCCTCCTTCCTT 59.585 55.000 0.00 0.00 0.00 3.36
1048 4138 4.803426 CTTCCTTCCTCGCGCGCT 62.803 66.667 30.48 0.00 0.00 5.92
1388 4490 4.778415 GTCGCGCTGCTCTTCGGA 62.778 66.667 5.56 0.00 0.00 4.55
1461 4572 1.841556 TCCTCCAAGGAGCAACGGT 60.842 57.895 10.68 0.00 40.06 4.83
1499 4610 4.406173 CGTGTCCGCGTCTCTGCT 62.406 66.667 4.92 0.00 0.00 4.24
1500 4611 2.505118 GTGTCCGCGTCTCTGCTC 60.505 66.667 4.92 0.00 0.00 4.26
1501 4612 3.749064 TGTCCGCGTCTCTGCTCC 61.749 66.667 4.92 0.00 0.00 4.70
1502 4613 3.444805 GTCCGCGTCTCTGCTCCT 61.445 66.667 4.92 0.00 0.00 3.69
1517 4628 1.110442 CTCCTCCGATGAGCTCTGTT 58.890 55.000 16.19 0.00 37.29 3.16
1535 4646 1.609635 TTCCGGATAAGCTCGTGGCA 61.610 55.000 4.15 0.00 44.79 4.92
1564 4675 7.572759 CGTTGAGCTGTTCTTGAAATTTAGTA 58.427 34.615 0.00 0.00 0.00 1.82
1565 4676 7.742089 CGTTGAGCTGTTCTTGAAATTTAGTAG 59.258 37.037 0.00 0.00 0.00 2.57
1566 4677 8.560374 GTTGAGCTGTTCTTGAAATTTAGTAGT 58.440 33.333 0.00 0.00 0.00 2.73
1568 4679 9.772973 TGAGCTGTTCTTGAAATTTAGTAGTTA 57.227 29.630 0.00 0.00 0.00 2.24
1588 4699 7.770366 AGTTAATTAATTAATTAGGGCGGGG 57.230 36.000 23.20 0.00 38.80 5.73
1756 4870 2.568935 GATGGCAACGTGCTTCGCTC 62.569 60.000 9.31 0.00 44.28 5.03
1932 6445 1.035932 AGCATGGCTTGAGATGCACC 61.036 55.000 9.10 0.00 46.21 5.01
2213 6728 4.357947 GCACGCCTGACTCACGGA 62.358 66.667 0.00 0.00 0.00 4.69
2214 6729 2.430921 CACGCCTGACTCACGGAC 60.431 66.667 0.00 0.00 0.00 4.79
2217 6732 4.436998 GCCTGACTCACGGACCCG 62.437 72.222 6.94 6.94 46.03 5.28
2218 6733 4.436998 CCTGACTCACGGACCCGC 62.437 72.222 8.55 0.00 44.19 6.13
2219 6734 3.680786 CTGACTCACGGACCCGCA 61.681 66.667 8.55 0.00 44.19 5.69
2285 6802 2.903350 AAACGACCCAACCCACGC 60.903 61.111 0.00 0.00 0.00 5.34
2342 6865 0.522180 CGACACTACTTCAGGCGACT 59.478 55.000 0.00 0.00 46.44 4.18
2405 6928 0.764752 GCATCAGCTACCCCTACCCT 60.765 60.000 0.00 0.00 37.91 4.34
2472 6995 5.849510 TCTCTTGTACTCGAATCAAACCAA 58.150 37.500 0.00 0.00 0.00 3.67
2483 7006 7.824289 ACTCGAATCAAACCAAAGATTGAGATA 59.176 33.333 15.06 0.00 38.80 1.98
2509 7032 8.095169 AGTTGTTGTAATAGAGATTCTCGGTTT 58.905 33.333 8.01 6.14 35.36 3.27
2510 7033 9.362539 GTTGTTGTAATAGAGATTCTCGGTTTA 57.637 33.333 8.01 5.29 35.36 2.01
2562 7085 2.203280 CCCTTCCACCGCAACACA 60.203 61.111 0.00 0.00 0.00 3.72
2635 7158 1.451504 GCCATGGACCCATCGATCA 59.548 57.895 18.40 0.00 33.90 2.92
2728 7251 1.710013 GACCAAAATCGACGAGCTCA 58.290 50.000 15.40 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 3.560025 GGAGAAAGAGCCATCCACTGAAA 60.560 47.826 0.00 0.00 0.00 2.69
47 49 1.681327 CCCGTCCTCCGAGGAGAAA 60.681 63.158 18.00 5.51 46.90 2.52
70 72 1.068741 GAAGGATCATACCCGCTTCGT 59.931 52.381 0.00 0.00 0.00 3.85
72 74 1.068741 ACGAAGGATCATACCCGCTTC 59.931 52.381 0.00 0.00 0.00 3.86
76 78 1.407618 TGTCACGAAGGATCATACCCG 59.592 52.381 0.00 0.00 0.00 5.28
83 85 3.074412 ACCATTGTTGTCACGAAGGATC 58.926 45.455 0.00 0.00 30.54 3.36
95 97 4.269844 GCAAAAGTAACACCACCATTGTTG 59.730 41.667 0.00 0.00 37.73 3.33
120 122 0.753262 ACGAAGAGCAGGTGACAAGT 59.247 50.000 0.00 0.00 0.00 3.16
150 153 2.398588 AGGTCATTCCCTCTCGCATTA 58.601 47.619 0.00 0.00 36.75 1.90
186 189 7.857456 TGTACCAAAATAAGGAGATTAGAGCA 58.143 34.615 0.00 0.00 0.00 4.26
193 196 6.884836 GTCAGGTTGTACCAAAATAAGGAGAT 59.115 38.462 0.00 0.00 41.95 2.75
208 211 0.685097 GCCCACTGAGTCAGGTTGTA 59.315 55.000 23.79 0.00 35.51 2.41
212 215 4.008933 GCGCCCACTGAGTCAGGT 62.009 66.667 23.79 7.20 35.51 4.00
213 216 3.655810 GAGCGCCCACTGAGTCAGG 62.656 68.421 23.79 12.48 35.51 3.86
239 242 3.434299 TGACGAGGAAAGAATTTAACGGC 59.566 43.478 0.00 0.00 39.27 5.68
244 247 6.872020 AGACGATTTGACGAGGAAAGAATTTA 59.128 34.615 0.00 0.00 36.22 1.40
259 262 6.037786 ACAAGAGACCATAAGACGATTTGA 57.962 37.500 0.00 0.00 0.00 2.69
264 267 5.357314 CCTCTAACAAGAGACCATAAGACGA 59.643 44.000 3.98 0.00 38.13 4.20
268 271 7.595819 ATCTCCTCTAACAAGAGACCATAAG 57.404 40.000 3.98 0.00 39.36 1.73
274 277 6.439675 ACGTAATCTCCTCTAACAAGAGAC 57.560 41.667 3.98 0.00 39.36 3.36
282 285 7.108841 ACATAAGCAACGTAATCTCCTCTAA 57.891 36.000 0.00 0.00 0.00 2.10
285 288 5.502544 GCAACATAAGCAACGTAATCTCCTC 60.503 44.000 0.00 0.00 0.00 3.71
295 298 2.628972 CGCTGCAACATAAGCAACG 58.371 52.632 0.00 0.00 43.68 4.10
302 305 2.124736 GGCCCTCGCTGCAACATA 60.125 61.111 0.00 0.00 34.44 2.29
314 421 4.567857 AGTATAGAATAACTGGTGGCCCT 58.432 43.478 0.00 0.00 0.00 5.19
339 446 6.326064 AGGATTACAGTCTGCTGATACAAGAT 59.674 38.462 0.00 0.00 45.28 2.40
340 447 5.658634 AGGATTACAGTCTGCTGATACAAGA 59.341 40.000 0.00 0.00 45.28 3.02
341 448 5.911752 AGGATTACAGTCTGCTGATACAAG 58.088 41.667 0.00 0.00 45.28 3.16
342 449 5.939764 AGGATTACAGTCTGCTGATACAA 57.060 39.130 0.00 0.00 45.28 2.41
369 3432 8.970859 TTTGGCAAAAGAGATTTATTCCAAAA 57.029 26.923 10.83 0.00 39.02 2.44
381 3444 5.065988 GCGGTATCTTATTTGGCAAAAGAGA 59.934 40.000 22.56 22.56 33.05 3.10
393 3456 9.337396 TGAGAAATGTTAATGCGGTATCTTATT 57.663 29.630 0.00 0.00 0.00 1.40
394 3457 8.902540 TGAGAAATGTTAATGCGGTATCTTAT 57.097 30.769 0.00 0.00 0.00 1.73
395 3458 8.725405 TTGAGAAATGTTAATGCGGTATCTTA 57.275 30.769 0.00 0.00 0.00 2.10
398 3461 8.682128 TTTTTGAGAAATGTTAATGCGGTATC 57.318 30.769 0.00 0.00 0.00 2.24
400 3463 7.877003 TCTTTTTGAGAAATGTTAATGCGGTA 58.123 30.769 0.00 0.00 0.00 4.02
402 3465 7.669098 CATCTTTTTGAGAAATGTTAATGCGG 58.331 34.615 0.00 0.00 38.06 5.69
403 3466 7.148771 TGCATCTTTTTGAGAAATGTTAATGCG 60.149 33.333 0.00 0.00 38.06 4.73
638 3717 1.946984 TATCCGTTCCCTGACAGGTT 58.053 50.000 20.24 0.00 31.93 3.50
756 3836 3.810896 GGCATTCCGTTGGGTCGC 61.811 66.667 0.00 0.00 33.83 5.19
788 3868 2.041115 TCAGCGAGTGGGACGAGAG 61.041 63.158 0.00 0.00 0.00 3.20
821 3901 4.082523 CATGCGGGACCAGGACGT 62.083 66.667 0.00 0.00 0.00 4.34
954 4036 1.696097 ATATGCCCCACGTCCCAGTC 61.696 60.000 0.00 0.00 0.00 3.51
961 4043 3.826637 GCGTATATATGCCCCACGT 57.173 52.632 14.96 0.00 35.17 4.49
997 4079 2.642807 ACGAGAGGAAAAGGAATGGGAA 59.357 45.455 0.00 0.00 0.00 3.97
1009 4091 0.681564 GGAGCTGGAGACGAGAGGAA 60.682 60.000 0.00 0.00 0.00 3.36
1048 4138 1.077357 GCACGAGGAGAGGAGGAGA 60.077 63.158 0.00 0.00 0.00 3.71
1490 4601 1.098129 TCATCGGAGGAGCAGAGACG 61.098 60.000 0.00 0.00 0.00 4.18
1492 4603 3.108292 CTCATCGGAGGAGCAGAGA 57.892 57.895 6.75 0.00 37.51 3.10
1499 4610 1.107114 GAACAGAGCTCATCGGAGGA 58.893 55.000 17.77 0.00 41.67 3.71
1500 4611 0.103937 GGAACAGAGCTCATCGGAGG 59.896 60.000 17.77 0.00 41.67 4.30
1501 4612 0.248825 CGGAACAGAGCTCATCGGAG 60.249 60.000 17.77 0.00 44.33 4.63
1502 4613 1.667154 CCGGAACAGAGCTCATCGGA 61.667 60.000 17.77 0.00 38.42 4.55
1517 4628 1.399744 ATGCCACGAGCTTATCCGGA 61.400 55.000 6.61 6.61 44.23 5.14
1535 4646 0.877071 CAAGAACAGCTCAACGCCAT 59.123 50.000 0.00 0.00 40.39 4.40
1564 4675 7.299896 ACCCCGCCCTAATTAATTAATTAACT 58.700 34.615 24.08 13.69 37.60 2.24
1565 4676 7.528996 ACCCCGCCCTAATTAATTAATTAAC 57.471 36.000 24.08 17.36 37.60 2.01
1566 4677 9.299465 CTAACCCCGCCCTAATTAATTAATTAA 57.701 33.333 24.08 20.11 37.60 1.40
1568 4679 6.722590 CCTAACCCCGCCCTAATTAATTAATT 59.277 38.462 23.28 23.28 39.14 1.40
1570 4681 5.372066 TCCTAACCCCGCCCTAATTAATTAA 59.628 40.000 9.15 0.00 0.00 1.40
1575 4686 2.493099 TCCTAACCCCGCCCTAATTA 57.507 50.000 0.00 0.00 0.00 1.40
1588 4699 8.570068 TTTTACACAGGAATTACCATCCTAAC 57.430 34.615 0.00 0.00 45.59 2.34
1671 4784 0.794473 GTTGCTTGTGCCGGTAGTAC 59.206 55.000 1.90 0.00 38.71 2.73
1672 4785 0.393448 TGTTGCTTGTGCCGGTAGTA 59.607 50.000 1.90 0.00 38.71 1.82
1673 4786 0.250727 ATGTTGCTTGTGCCGGTAGT 60.251 50.000 1.90 0.00 38.71 2.73
1718 4831 1.204704 TCCGTGCACAGAATTCTCGAT 59.795 47.619 18.64 0.00 0.00 3.59
1756 4870 0.108898 CTGGTCTGACGAAGCAGAGG 60.109 60.000 1.07 0.30 44.92 3.69
1867 4989 2.354510 CTCACCACGACAAAACACACAT 59.645 45.455 0.00 0.00 0.00 3.21
1869 4991 2.004017 TCTCACCACGACAAAACACAC 58.996 47.619 0.00 0.00 0.00 3.82
1932 6445 3.446570 AGTTAGCCCCGACGACCG 61.447 66.667 0.00 0.00 38.18 4.79
1963 6476 1.666599 CGCACACCCAACATTCACATG 60.667 52.381 0.00 0.00 36.34 3.21
2218 6733 3.947132 CTGTGGGAGTCGCTGCCTG 62.947 68.421 15.91 5.54 42.66 4.85
2219 6734 3.699894 CTGTGGGAGTCGCTGCCT 61.700 66.667 15.91 0.00 42.66 4.75
2295 6812 0.036306 CTTTAGTTGGCCCACTCCGT 59.964 55.000 13.76 0.00 0.00 4.69
2311 6828 2.372040 TAGTGTCGTGGCGTGGCTTT 62.372 55.000 0.00 0.00 0.00 3.51
2342 6865 1.487976 GATGCTCCTCCTTCCATGTGA 59.512 52.381 0.00 0.00 0.00 3.58
2391 6914 2.758986 CGGAATTAGGGTAGGGGTAGCT 60.759 54.545 0.00 0.00 0.00 3.32
2483 7006 7.171630 ACCGAGAATCTCTATTACAACAACT 57.828 36.000 8.77 0.00 0.00 3.16
2509 7032 4.552674 TCTGATACCTGGTGTTAGGCATA 58.447 43.478 10.23 0.00 41.75 3.14
2510 7033 3.384168 TCTGATACCTGGTGTTAGGCAT 58.616 45.455 10.23 0.00 41.75 4.40
2562 7085 0.911769 TCTCGATGATTTGGGCCAGT 59.088 50.000 6.23 0.00 0.00 4.00
2635 7158 2.035442 GGCGCTCGAAGAAGGCTTT 61.035 57.895 7.64 0.00 36.98 3.51


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

AutoCloner maintained by Alex Coulton.