Multiple sequence alignment - TraesCS3A01G048600

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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 TraesCS3A01G048600 chr3A 100.000 3242 0 0 1 3242 25912590 25909349 0.000000e+00 5987
1 TraesCS3A01G048600 chr3A 88.060 134 14 1 68 201 19063569 19063438 1.200000e-34 158
2 TraesCS3A01G048600 chr3B 95.459 2907 109 8 1 2902 25282675 25279787 0.000000e+00 4615
3 TraesCS3A01G048600 chr3B 96.183 2384 72 7 530 2902 16035411 16037786 0.000000e+00 3880
4 TraesCS3A01G048600 chr3B 83.795 1481 208 16 1001 2454 16049143 16050618 0.000000e+00 1376
5 TraesCS3A01G048600 chr3B 81.781 1471 240 12 1001 2454 16055675 16057134 0.000000e+00 1206
6 TraesCS3A01G048600 chr3B 84.720 661 90 6 1001 1651 25259761 25259102 0.000000e+00 651
7 TraesCS3A01G048600 chr3B 96.721 305 8 2 2940 3242 16037793 16038097 1.040000e-139 507
8 TraesCS3A01G048600 chr3B 96.066 305 10 2 2940 3242 25279780 25279476 2.250000e-136 496
9 TraesCS3A01G048600 chr3B 85.151 431 46 7 551 980 25283711 25283298 2.990000e-115 425
10 TraesCS3A01G048600 chr3D 95.715 2357 92 7 553 2902 11361057 11363411 0.000000e+00 3784
11 TraesCS3A01G048600 chr3D 84.758 1509 196 19 969 2449 11772893 11771391 0.000000e+00 1482
12 TraesCS3A01G048600 chr3D 83.198 1476 214 20 1001 2449 11370269 11371737 0.000000e+00 1321
13 TraesCS3A01G048600 chr3D 96.700 303 7 3 2940 3240 11363418 11363719 4.830000e-138 501


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 TraesCS3A01G048600 chr3A 25909349 25912590 3241 True 5987.000000 5987 100.000000 1 3242 1 chr3A.!!$R2 3241
1 TraesCS3A01G048600 chr3B 16035411 16038097 2686 False 2193.500000 3880 96.452000 530 3242 2 chr3B.!!$F3 2712
2 TraesCS3A01G048600 chr3B 25279476 25283711 4235 True 1845.333333 4615 92.225333 1 3242 3 chr3B.!!$R2 3241
3 TraesCS3A01G048600 chr3B 16049143 16050618 1475 False 1376.000000 1376 83.795000 1001 2454 1 chr3B.!!$F1 1453
4 TraesCS3A01G048600 chr3B 16055675 16057134 1459 False 1206.000000 1206 81.781000 1001 2454 1 chr3B.!!$F2 1453
5 TraesCS3A01G048600 chr3B 25259102 25259761 659 True 651.000000 651 84.720000 1001 1651 1 chr3B.!!$R1 650
6 TraesCS3A01G048600 chr3D 11361057 11363719 2662 False 2142.500000 3784 96.207500 553 3240 2 chr3D.!!$F2 2687
7 TraesCS3A01G048600 chr3D 11771391 11772893 1502 True 1482.000000 1482 84.758000 969 2449 1 chr3D.!!$R1 1480
8 TraesCS3A01G048600 chr3D 11370269 11371737 1468 False 1321.000000 1321 83.198000 1001 2449 1 chr3D.!!$F1 1448

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
613 1650 0.038166 AAGTCATGCAACCCCGATGT 59.962 50.000 0.00 0.00 0.0 3.06 F
1337 2392 1.743252 CCACTCCCTTGAAGCGCTC 60.743 63.158 12.06 4.99 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2013 3071 0.606401 CTGCCACAAATGACCCGTCT 60.606 55.0 0.00 0.0 0.00 4.18 R
2920 4004 0.180171 GGCTTGTTTTGGCCTTTGGT 59.820 50.0 3.32 0.0 44.48 3.67 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
23 1060 2.911509 TGTTGCTTGCGCCACCAT 60.912 55.556 4.18 0.00 31.18 3.55
109 1146 1.476085 CAACAAGGACCTGCAAACACA 59.524 47.619 0.00 0.00 0.00 3.72
123 1160 6.797995 CCTGCAAACACAAATATTTTTCATGC 59.202 34.615 0.00 6.83 0.00 4.06
149 1186 0.780637 TTGGATAACAACCAGGGGCA 59.219 50.000 0.00 0.00 38.70 5.36
158 1195 1.357272 AACCAGGGGCACAGGTACAA 61.357 55.000 3.48 0.00 34.63 2.41
215 1252 2.689646 GACCACCTGAAGAGCTACAAC 58.310 52.381 0.00 0.00 0.00 3.32
454 1491 0.603975 AACCGCAAGAGAACAGGCTC 60.604 55.000 0.00 0.00 43.02 4.70
455 1492 2.097038 CCGCAAGAGAACAGGCTCG 61.097 63.158 0.00 0.00 39.87 5.03
466 1503 3.080121 AGGCTCGGGCTCTCCAAG 61.080 66.667 7.48 0.00 38.73 3.61
494 1531 0.714180 TAGGCTCCAGGGTAGGTGAA 59.286 55.000 0.00 0.00 0.00 3.18
593 1630 3.817647 AGTTAGAGCACTTCTGCAAAAGG 59.182 43.478 4.51 0.00 46.97 3.11
609 1646 0.609131 AAGGAAGTCATGCAACCCCG 60.609 55.000 0.00 0.00 0.00 5.73
613 1650 0.038166 AAGTCATGCAACCCCGATGT 59.962 50.000 0.00 0.00 0.00 3.06
800 1845 4.504864 CCTTATGCTAACCATTGATCCCGA 60.505 45.833 0.00 0.00 35.34 5.14
819 1864 3.242739 CCGAGTCAAATTTAGATTGGCCG 60.243 47.826 0.00 0.00 32.88 6.13
828 1873 2.921853 TAGATTGGCCGGCGGAGAGA 62.922 60.000 33.44 12.37 0.00 3.10
901 1947 8.792830 TCTCAACCACACCTTATATATACCTT 57.207 34.615 0.00 0.00 0.00 3.50
902 1948 9.886337 TCTCAACCACACCTTATATATACCTTA 57.114 33.333 0.00 0.00 0.00 2.69
928 1974 5.799213 ACCTGATCTCTACAAGGTGAAAAG 58.201 41.667 0.00 0.00 0.00 2.27
976 2022 3.010420 GCATTCCCCTTCAGTTCAGTAC 58.990 50.000 0.00 0.00 0.00 2.73
995 2041 5.007724 CAGTACTCACTCAACCAAAAGTTCC 59.992 44.000 0.00 0.00 31.39 3.62
998 2044 3.020984 TCACTCAACCAAAAGTTCCCAC 58.979 45.455 0.00 0.00 36.18 4.61
1337 2392 1.743252 CCACTCCCTTGAAGCGCTC 60.743 63.158 12.06 4.99 0.00 5.03
1761 2819 4.767928 AGGGCATTGGTCGTTGTTAAATTA 59.232 37.500 0.00 0.00 0.00 1.40
1801 2859 7.405292 TGATGAGGACTGGAAATCATTTTACT 58.595 34.615 0.00 0.00 32.68 2.24
2013 3071 6.240894 AGCAGGAGAGTTCATCAAATTGTTA 58.759 36.000 0.00 0.00 0.00 2.41
2201 3259 4.079730 AGACTTCACCAACTTTCTTCCCTT 60.080 41.667 0.00 0.00 0.00 3.95
2202 3260 4.207955 ACTTCACCAACTTTCTTCCCTTC 58.792 43.478 0.00 0.00 0.00 3.46
2203 3261 3.223674 TCACCAACTTTCTTCCCTTCC 57.776 47.619 0.00 0.00 0.00 3.46
2298 3368 3.463825 TCATTGAGAATCCCTCCCTTCA 58.536 45.455 0.00 0.00 41.25 3.02
2339 3409 5.698741 ATTAGTGACATGGGAATCACAGA 57.301 39.130 14.50 5.01 46.34 3.41
2340 3410 5.698741 TTAGTGACATGGGAATCACAGAT 57.301 39.130 14.50 0.07 46.34 2.90
2341 3411 6.806668 TTAGTGACATGGGAATCACAGATA 57.193 37.500 14.50 0.00 46.34 1.98
2342 3412 5.028549 AGTGACATGGGAATCACAGATAC 57.971 43.478 14.50 0.00 46.34 2.24
2343 3413 4.130118 GTGACATGGGAATCACAGATACC 58.870 47.826 8.81 0.00 43.89 2.73
2344 3414 4.040047 TGACATGGGAATCACAGATACCT 58.960 43.478 0.00 0.00 0.00 3.08
2345 3415 4.101585 TGACATGGGAATCACAGATACCTC 59.898 45.833 0.00 0.00 0.00 3.85
2346 3416 3.392616 ACATGGGAATCACAGATACCTCC 59.607 47.826 0.00 0.00 0.00 4.30
2347 3417 3.421394 TGGGAATCACAGATACCTCCT 57.579 47.619 0.00 0.00 0.00 3.69
2348 3418 3.736094 TGGGAATCACAGATACCTCCTT 58.264 45.455 0.00 0.00 0.00 3.36
2603 3687 8.359642 ACATGTTTGCAATTCTTTAAGAAGCTA 58.640 29.630 13.07 6.32 37.69 3.32
2647 3731 7.201992 GGATATATGCAGGGGAAACAATTTGAA 60.202 37.037 2.79 0.00 0.00 2.69
2693 3777 3.327757 AGTTAAGTCATTGCCAGTGGAGA 59.672 43.478 15.20 0.00 0.00 3.71
2694 3778 2.191128 AAGTCATTGCCAGTGGAGAC 57.809 50.000 15.20 14.06 0.00 3.36
2785 3869 4.741676 CCACTTGTTTCAGTTGAGAATTGC 59.258 41.667 0.00 0.00 0.00 3.56
2797 3881 4.263018 TGAGAATTGCGATAGATCCTGG 57.737 45.455 0.00 0.00 39.76 4.45
2816 3900 1.527034 GAGAATCAGTGGTGCAGCAA 58.473 50.000 22.04 5.57 33.17 3.91
2902 3986 2.628696 CCTTGTTCAGCATGGCGCA 61.629 57.895 10.83 0.00 46.13 6.09
2904 3988 0.318869 CTTGTTCAGCATGGCGCAAA 60.319 50.000 10.83 0.00 46.13 3.68
2905 3989 0.597118 TTGTTCAGCATGGCGCAAAC 60.597 50.000 10.83 0.00 46.13 2.93
2908 3992 0.804364 TTCAGCATGGCGCAAACTAG 59.196 50.000 10.83 0.00 46.13 2.57
2909 3993 0.321564 TCAGCATGGCGCAAACTAGT 60.322 50.000 10.83 0.00 46.13 2.57
2910 3994 0.523072 CAGCATGGCGCAAACTAGTT 59.477 50.000 10.83 1.12 46.13 2.24
2911 3995 1.068333 CAGCATGGCGCAAACTAGTTT 60.068 47.619 15.22 15.22 46.13 2.66
2912 3996 5.449486 TCAGCATGGCGCAAACTAGTTTG 62.449 47.826 34.22 34.22 46.13 2.93
2934 4018 3.313012 GGTATGACCAAAGGCCAAAAC 57.687 47.619 5.01 0.00 38.42 2.43
2935 4019 2.630580 GGTATGACCAAAGGCCAAAACA 59.369 45.455 5.01 0.00 38.42 2.83
2936 4020 3.070302 GGTATGACCAAAGGCCAAAACAA 59.930 43.478 5.01 0.00 38.42 2.83
2937 4021 2.977772 TGACCAAAGGCCAAAACAAG 57.022 45.000 5.01 0.00 0.00 3.16
2938 4022 1.134551 TGACCAAAGGCCAAAACAAGC 60.135 47.619 5.01 0.00 0.00 4.01
2974 4058 3.755378 AGCAAGCCACATAGAGAGTTTTG 59.245 43.478 0.00 0.00 0.00 2.44
3084 4170 0.906756 TCCAGTCTCAGGGAAGCCTG 60.907 60.000 0.00 0.00 39.01 4.85
3233 4319 5.152623 TGTCAGTCTTAGCAATTACAGCT 57.847 39.130 0.00 0.00 45.77 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 1060 5.354234 GTCGGCAAAGAAATCTTAATCAGGA 59.646 40.000 0.00 0.00 34.61 3.86
109 1146 7.850193 TCCAAAGCTAGGCATGAAAAATATTT 58.150 30.769 0.00 0.00 0.00 1.40
123 1160 3.947834 CCTGGTTGTTATCCAAAGCTAGG 59.052 47.826 0.00 0.00 34.07 3.02
186 1223 2.818432 TCTTCAGGTGGTCGTAAGTCTC 59.182 50.000 0.00 0.00 39.48 3.36
215 1252 1.272769 GGTGCCCCTCTAGTATAAGCG 59.727 57.143 0.00 0.00 0.00 4.68
404 1441 4.305989 TGAAAGAATGTTCTGGTTGCAC 57.694 40.909 0.00 0.00 37.65 4.57
466 1503 0.466124 CCTGGAGCCTACCTAACTGC 59.534 60.000 0.00 0.00 0.00 4.40
467 1504 1.123928 CCCTGGAGCCTACCTAACTG 58.876 60.000 0.00 0.00 0.00 3.16
472 1509 1.229626 ACCTACCCTGGAGCCTACCT 61.230 60.000 0.00 0.00 0.00 3.08
494 1531 2.865119 TGATCATGTGAACCTGTGCT 57.135 45.000 0.00 0.00 0.00 4.40
593 1630 0.734889 CATCGGGGTTGCATGACTTC 59.265 55.000 0.00 0.00 0.00 3.01
800 1845 2.427095 GCCGGCCAATCTAAATTTGACT 59.573 45.455 18.11 0.00 0.00 3.41
819 1864 3.386237 AGCTGGTGTCTCTCCGCC 61.386 66.667 0.00 0.00 35.49 6.13
901 1947 6.928348 TCACCTTGTAGAGATCAGGTTTTA 57.072 37.500 0.00 0.00 0.00 1.52
902 1948 5.825593 TCACCTTGTAGAGATCAGGTTTT 57.174 39.130 0.00 0.00 0.00 2.43
928 1974 8.816144 TGATGTTGAACTAGAAAATTGTTTTGC 58.184 29.630 0.00 0.00 31.94 3.68
976 2022 3.066760 GTGGGAACTTTTGGTTGAGTGAG 59.933 47.826 0.00 0.00 38.41 3.51
995 2041 3.885297 AGACAGAACAACTTCCATTGTGG 59.115 43.478 0.00 0.00 42.01 4.17
998 2044 3.607775 CGCAGACAGAACAACTTCCATTG 60.608 47.826 0.00 0.00 35.59 2.82
1337 2392 1.240641 TACACCAGCATTTGCACGGG 61.241 55.000 13.54 10.04 45.16 5.28
1707 2762 5.880332 GCACCTTTCTGTTTCTACCATATGA 59.120 40.000 3.65 0.00 0.00 2.15
1761 2819 4.533707 TCCTCATCATTGACCTCTGAAACT 59.466 41.667 0.00 0.00 0.00 2.66
1801 2859 1.408683 GCTTATGGATGTCACTGCCCA 60.409 52.381 0.00 0.00 0.00 5.36
2013 3071 0.606401 CTGCCACAAATGACCCGTCT 60.606 55.000 0.00 0.00 0.00 4.18
2201 3259 4.392166 TAGTGGAGCAGCGGGGGA 62.392 66.667 0.00 0.00 0.00 4.81
2202 3260 4.162690 GTAGTGGAGCAGCGGGGG 62.163 72.222 0.00 0.00 0.00 5.40
2203 3261 3.390521 TGTAGTGGAGCAGCGGGG 61.391 66.667 0.00 0.00 0.00 5.73
2298 3368 7.402071 TCACTAATACAAAGTCACCCTTAGGAT 59.598 37.037 0.00 0.00 36.73 3.24
2339 3409 5.703310 ACTGAACTCGGTATAAGGAGGTAT 58.297 41.667 6.33 0.00 34.58 2.73
2340 3410 5.121380 ACTGAACTCGGTATAAGGAGGTA 57.879 43.478 6.33 0.00 34.58 3.08
2341 3411 3.978610 ACTGAACTCGGTATAAGGAGGT 58.021 45.455 6.33 0.00 34.58 3.85
2342 3412 5.221204 GGTAACTGAACTCGGTATAAGGAGG 60.221 48.000 6.33 0.00 34.49 4.30
2343 3413 5.359009 TGGTAACTGAACTCGGTATAAGGAG 59.641 44.000 0.00 0.88 34.49 3.69
2344 3414 5.263599 TGGTAACTGAACTCGGTATAAGGA 58.736 41.667 0.00 0.00 34.49 3.36
2345 3415 5.587388 TGGTAACTGAACTCGGTATAAGG 57.413 43.478 0.00 0.00 34.49 2.69
2346 3416 6.570692 ACATGGTAACTGAACTCGGTATAAG 58.429 40.000 0.00 0.00 34.49 1.73
2347 3417 6.406177 GGACATGGTAACTGAACTCGGTATAA 60.406 42.308 0.00 0.00 34.49 0.98
2348 3418 5.068198 GGACATGGTAACTGAACTCGGTATA 59.932 44.000 0.00 0.00 34.49 1.47
2416 3496 8.682710 CACTAGAGAGAAATAGTAGCTTCACTT 58.317 37.037 0.00 0.00 31.10 3.16
2417 3497 7.832187 ACACTAGAGAGAAATAGTAGCTTCACT 59.168 37.037 0.00 0.00 31.10 3.41
2518 3601 9.498176 TCAGTACTTGTAGCGATATACATAGAA 57.502 33.333 0.00 0.00 35.65 2.10
2535 3619 7.582435 ACTTGACAATCGTAATCAGTACTTG 57.418 36.000 0.00 0.00 0.00 3.16
2564 3648 3.801050 GCAAACATGTATGCAACACACAA 59.199 39.130 0.00 0.00 42.09 3.33
2607 3691 6.600388 TGCATATATCCAAAGAACTAGGCAA 58.400 36.000 0.00 0.00 31.16 4.52
2674 3758 2.906389 AGTCTCCACTGGCAATGACTTA 59.094 45.455 0.00 0.00 31.71 2.24
2684 3768 7.745620 ATTTAGTGTTTTTAGTCTCCACTGG 57.254 36.000 0.00 0.00 37.02 4.00
2785 3869 4.082300 CCACTGATTCTCCAGGATCTATCG 60.082 50.000 0.00 0.00 38.44 2.92
2797 3881 1.527034 TTGCTGCACCACTGATTCTC 58.473 50.000 0.00 0.00 0.00 2.87
2914 3998 2.630580 TGTTTTGGCCTTTGGTCATACC 59.369 45.455 3.32 0.00 37.08 2.73
2915 3999 4.306600 CTTGTTTTGGCCTTTGGTCATAC 58.693 43.478 3.32 0.00 37.08 2.39
2916 4000 3.244044 GCTTGTTTTGGCCTTTGGTCATA 60.244 43.478 3.32 0.00 37.08 2.15
2917 4001 2.485302 GCTTGTTTTGGCCTTTGGTCAT 60.485 45.455 3.32 0.00 37.08 3.06
2918 4002 1.134551 GCTTGTTTTGGCCTTTGGTCA 60.135 47.619 3.32 0.00 34.47 4.02
2919 4003 1.581934 GCTTGTTTTGGCCTTTGGTC 58.418 50.000 3.32 0.00 0.00 4.02
2920 4004 0.180171 GGCTTGTTTTGGCCTTTGGT 59.820 50.000 3.32 0.00 44.48 3.67
2921 4005 3.005205 GGCTTGTTTTGGCCTTTGG 57.995 52.632 3.32 0.00 44.48 3.28
2974 4058 8.358148 AGATCATGGAATTATCATTTTCAGTGC 58.642 33.333 0.00 0.00 29.34 4.40
3084 4170 3.385755 AGGCCCAACTAATGATGATTTGC 59.614 43.478 0.00 0.00 0.00 3.68


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

AutoCloner maintained by Alex Coulton.