Multiple sequence alignment - TraesCS3D01G403500

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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 TraesCS3D01G403500 chr3D 100.000 3474 0 0 1 3474 517487139 517490612 0.000000e+00 6416
1 TraesCS3D01G403500 chr3D 86.364 110 14 1 645 753 46257311 46257202 6.090000e-23 119
2 TraesCS3D01G403500 chr3B 92.048 2427 104 33 379 2750 681209804 681212196 0.000000e+00 3330
3 TraesCS3D01G403500 chr3B 89.959 727 52 12 2753 3474 681493922 681494632 0.000000e+00 918
4 TraesCS3D01G403500 chr3B 88.580 324 24 11 1 315 681209204 681209523 7.040000e-102 381
5 TraesCS3D01G403500 chr3B 88.591 298 26 7 141 431 681209522 681209818 4.260000e-94 355
6 TraesCS3D01G403500 chr3B 87.273 110 13 1 645 753 72457562 72457453 1.310000e-24 124
7 TraesCS3D01G403500 chr3A 92.784 1857 69 26 824 2647 653330721 653332545 0.000000e+00 2627
8 TraesCS3D01G403500 chr3A 88.401 638 24 12 2843 3474 653332814 653333407 0.000000e+00 723
9 TraesCS3D01G403500 chr3A 87.021 339 30 11 3 330 653329775 653330110 1.520000e-98 370
10 TraesCS3D01G403500 chr3A 87.786 262 22 8 180 432 653330113 653330373 7.290000e-77 298
11 TraesCS3D01G403500 chr3A 79.635 329 43 17 2714 3038 72287771 72287463 7.550000e-52 215
12 TraesCS3D01G403500 chr7D 81.271 598 80 19 2714 3304 571875068 571874496 4.090000e-124 455
13 TraesCS3D01G403500 chr7B 82.172 488 69 15 2714 3197 628461783 628461310 1.500000e-108 403
14 TraesCS3D01G403500 chr2A 76.690 562 94 31 1802 2334 580385010 580385563 9.500000e-71 278
15 TraesCS3D01G403500 chr2D 77.200 500 82 28 1802 2276 413353626 413354118 2.660000e-66 263
16 TraesCS3D01G403500 chr2B 75.593 590 105 32 1715 2276 486843653 486844231 4.450000e-64 255


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 TraesCS3D01G403500 chr3D 517487139 517490612 3473 False 6416.000000 6416 100.000000 1 3474 1 chr3D.!!$F1 3473
1 TraesCS3D01G403500 chr3B 681209204 681212196 2992 False 1355.333333 3330 89.739667 1 2750 3 chr3B.!!$F2 2749
2 TraesCS3D01G403500 chr3B 681493922 681494632 710 False 918.000000 918 89.959000 2753 3474 1 chr3B.!!$F1 721
3 TraesCS3D01G403500 chr3A 653329775 653333407 3632 False 1004.500000 2627 88.998000 3 3474 4 chr3A.!!$F1 3471
4 TraesCS3D01G403500 chr7D 571874496 571875068 572 True 455.000000 455 81.271000 2714 3304 1 chr7D.!!$R1 590
5 TraesCS3D01G403500 chr2A 580385010 580385563 553 False 278.000000 278 76.690000 1802 2334 1 chr2A.!!$F1 532
6 TraesCS3D01G403500 chr2B 486843653 486844231 578 False 255.000000 255 75.593000 1715 2276 1 chr2B.!!$F1 561


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
892 1256 0.040058 AACCTGCATGGATCAAGGCA 59.96 50.0 9.46 9.46 39.71 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2486 2934 1.207791 GAGACATGACATGAGGGGGT 58.792 55.0 22.19 0.0 0.0 4.95 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
67 69 2.159114 GCACCCGGATAAACAAATGCAT 60.159 45.455 0.73 0.00 0.00 3.96
73 75 6.603997 ACCCGGATAAACAAATGCATAAGTAA 59.396 34.615 0.73 0.00 0.00 2.24
110 112 4.881273 ACATGTTCACTTGTTCTAGTTGCA 59.119 37.500 0.00 0.00 31.23 4.08
167 352 8.336080 GTTGCTCCATAAAAACTATAGTGCTAC 58.664 37.037 6.06 5.65 0.00 3.58
168 353 6.700081 TGCTCCATAAAAACTATAGTGCTACG 59.300 38.462 6.06 0.00 0.00 3.51
228 415 3.213506 TCTCAGACCACCACAAATGTTG 58.786 45.455 0.00 0.00 0.00 3.33
280 467 7.435068 AACAAGCATACAAGTTAGTTACCAG 57.565 36.000 0.00 0.00 0.00 4.00
286 473 9.953565 AGCATACAAGTTAGTTACCAGAAAATA 57.046 29.630 0.00 0.00 0.00 1.40
340 534 2.746277 GTCCATCCGGGTGCACAC 60.746 66.667 20.43 15.50 38.11 3.82
415 647 6.183361 ACACTAAGAGGATGGTTTGTAAGGTT 60.183 38.462 0.00 0.00 0.00 3.50
419 651 5.701224 AGAGGATGGTTTGTAAGGTTGAAA 58.299 37.500 0.00 0.00 0.00 2.69
446 678 5.384063 TTGCACAAACCGATATTGTCAAT 57.616 34.783 3.06 3.06 38.90 2.57
557 789 8.937207 ACTCCCTCTGTAACTTAATATACGAT 57.063 34.615 0.00 0.00 0.00 3.73
561 793 7.749570 CCCTCTGTAACTTAATATACGATGTCG 59.250 40.741 0.11 0.11 46.33 4.35
674 908 4.065088 TGTCAGAGCAATTAGTCGCTTTT 58.935 39.130 0.00 0.00 38.99 2.27
686 920 1.662446 CGCTTTTGGCAGTGGCTTG 60.662 57.895 18.53 6.37 41.91 4.01
697 937 0.392998 AGTGGCTTGCATTCCCTACG 60.393 55.000 0.00 0.00 0.00 3.51
698 938 1.748879 TGGCTTGCATTCCCTACGC 60.749 57.895 0.00 0.00 0.00 4.42
699 939 1.748879 GGCTTGCATTCCCTACGCA 60.749 57.895 0.00 0.00 0.00 5.24
744 1092 4.632153 AGCAGTGATTTTCAAGTAGTCGT 58.368 39.130 0.00 0.00 0.00 4.34
793 1141 1.755179 CAGCAAAATGATCCGAGGGT 58.245 50.000 0.00 0.00 0.00 4.34
858 1222 6.401477 CGTTTTTCACGTAACAGTCAAATC 57.599 37.500 0.00 0.00 44.49 2.17
859 1223 6.189567 CGTTTTTCACGTAACAGTCAAATCT 58.810 36.000 0.00 0.00 44.49 2.40
881 1245 1.812571 GTGGTTCGATTCAACCTGCAT 59.187 47.619 14.81 0.00 45.54 3.96
892 1256 0.040058 AACCTGCATGGATCAAGGCA 59.960 50.000 9.46 9.46 39.71 4.75
916 1281 3.005897 CGTCTGTTATCCGATCCATCCTT 59.994 47.826 0.00 0.00 0.00 3.36
962 1327 2.165437 CTCTCTCTGGAGTGCTAACCAC 59.835 54.545 0.00 0.00 45.01 4.16
974 1339 4.140663 AGTGCTAACCACCCTCCTCTATAT 60.141 45.833 0.00 0.00 45.83 0.86
1217 1607 3.095347 GCCACCATCCTCTCCGTCC 62.095 68.421 0.00 0.00 0.00 4.79
1219 1609 1.753078 CACCATCCTCTCCGTCCGA 60.753 63.158 0.00 0.00 0.00 4.55
1253 1643 0.103208 CGGTACTGGCTGCTCTTAGG 59.897 60.000 0.00 0.00 0.00 2.69
1300 1699 3.058450 GTTGAGATGGAGATGCTGATCG 58.942 50.000 0.00 0.00 33.34 3.69
1370 1769 4.667519 GTACAAGACCATCGGAGGTTAT 57.332 45.455 1.25 0.00 43.38 1.89
1399 1798 3.304257 CGCTGCTTGATCTTGAACTGTTT 60.304 43.478 0.00 0.00 0.00 2.83
1400 1799 4.083855 CGCTGCTTGATCTTGAACTGTTTA 60.084 41.667 0.00 0.00 0.00 2.01
1446 1849 1.062525 GTGCCGCCGACATTGATTC 59.937 57.895 0.00 0.00 0.00 2.52
1467 1870 7.647715 TGATTCGTTTGTTTGATCCTTTCTTTC 59.352 33.333 0.00 0.00 0.00 2.62
1470 1873 7.543756 TCGTTTGTTTGATCCTTTCTTTCTTT 58.456 30.769 0.00 0.00 0.00 2.52
2369 2808 3.682792 GGATCCGATCCGATCCGT 58.317 61.111 22.21 0.00 46.73 4.69
2486 2934 3.751246 CGTTACGGCCGGTGAGGA 61.751 66.667 31.76 5.12 45.00 3.71
2507 2955 1.140452 CCCCCTCATGTCATGTCTCAG 59.860 57.143 12.54 2.83 0.00 3.35
2514 2962 1.247567 TGTCATGTCTCAGTCGCTCA 58.752 50.000 0.00 0.00 0.00 4.26
2589 3037 1.740025 GCTTGGTGTCTAGGATTGTGC 59.260 52.381 0.00 0.00 0.00 4.57
2638 3086 6.838090 TGGGCATCCATATTTTAGAATTCACA 59.162 34.615 8.44 0.00 38.32 3.58
2641 3089 8.579006 GGCATCCATATTTTAGAATTCACATCA 58.421 33.333 8.44 0.00 0.00 3.07
2660 3108 6.048509 ACATCAATTGTGTCTCGCATATACA 58.951 36.000 5.13 0.00 37.11 2.29
2664 3112 6.202762 TCAATTGTGTCTCGCATATACATTCC 59.797 38.462 5.13 0.00 0.00 3.01
2669 3117 3.086282 TCTCGCATATACATTCCGCCTA 58.914 45.455 0.00 0.00 0.00 3.93
2670 3118 3.119602 TCTCGCATATACATTCCGCCTAC 60.120 47.826 0.00 0.00 0.00 3.18
2676 3124 6.210078 GCATATACATTCCGCCTACTATCTC 58.790 44.000 0.00 0.00 0.00 2.75
2677 3125 6.039941 GCATATACATTCCGCCTACTATCTCT 59.960 42.308 0.00 0.00 0.00 3.10
2678 3126 5.906113 ATACATTCCGCCTACTATCTCTG 57.094 43.478 0.00 0.00 0.00 3.35
2680 3128 3.823873 ACATTCCGCCTACTATCTCTGAG 59.176 47.826 0.00 0.00 0.00 3.35
2681 3129 3.859061 TTCCGCCTACTATCTCTGAGA 57.141 47.619 10.23 10.23 0.00 3.27
2710 3259 6.056236 GTCTCCCCAATCTAATCTTACCAAC 58.944 44.000 0.00 0.00 0.00 3.77
2730 3281 2.198304 CTCCCTTACACTGCCACCCC 62.198 65.000 0.00 0.00 0.00 4.95
2750 3301 3.987220 CCCCACACTTTGAATTTAAAGCG 59.013 43.478 19.50 14.07 40.48 4.68
2758 3309 9.632807 ACACTTTGAATTTAAAGCGCATAATTA 57.367 25.926 19.50 0.06 40.48 1.40
2946 3500 3.760684 GAGCTCACAAAATGGACCTGAAT 59.239 43.478 9.40 0.00 0.00 2.57
3039 3599 4.335594 AGCAAATCGGTAGTTAAATGCTCC 59.664 41.667 0.00 0.00 38.42 4.70
3129 3693 5.122239 CCTTTGCATAGAACATTCGTCTTCA 59.878 40.000 5.65 0.00 0.00 3.02
3160 3724 0.751277 TGGGTCAATATGGCTTGGCG 60.751 55.000 0.00 0.00 31.42 5.69
3249 3813 6.849305 GCCGAATATTTTATTTCCGTGTACTG 59.151 38.462 0.00 0.00 0.00 2.74
3306 3872 9.405587 GATGTCGGACAATAAAATTGAAAAAGA 57.594 29.630 15.72 0.00 0.00 2.52
3361 3928 2.952310 GTTTTGTGCCAGAAGAAGACCT 59.048 45.455 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 0.467290 AGGAGCCAAAACTTCGCCAA 60.467 50.000 0.00 0.00 0.00 4.52
73 75 9.912634 CAAGTGAACATGTTTATTGTTAATCCT 57.087 29.630 13.36 0.00 37.43 3.24
97 99 6.760298 TGAAAATTTGCATGCAACTAGAACAA 59.240 30.769 31.99 15.70 35.46 2.83
110 112 7.218614 TGTCATTTCTCCTTGAAAATTTGCAT 58.781 30.769 0.00 0.00 46.32 3.96
228 415 5.351189 ACTGTGCAAAAATTGGTGAAGAAAC 59.649 36.000 0.00 0.00 0.00 2.78
340 534 8.799695 AGAAATTCAATTCTAAGCCTGAGCTCG 61.800 40.741 9.64 3.88 40.79 5.03
352 546 9.393249 CGTGCTTTTAACAGAAATTCAATTCTA 57.607 29.630 0.00 0.00 37.56 2.10
375 569 6.199154 CCTCTTAGTGTGCAATATAGTTCGTG 59.801 42.308 0.00 0.00 0.00 4.35
376 570 6.096423 TCCTCTTAGTGTGCAATATAGTTCGT 59.904 38.462 0.00 0.00 0.00 3.85
415 647 9.676195 CAATATCGGTTTGTGCAATATATTTCA 57.324 29.630 0.00 0.00 0.00 2.69
419 651 8.389779 TGACAATATCGGTTTGTGCAATATAT 57.610 30.769 0.00 0.00 37.43 0.86
494 726 4.941263 TGCGATTGTATTTTTAGCAGGAGT 59.059 37.500 0.00 0.00 0.00 3.85
631 864 9.533253 CTGACAATCATGTATGTATCTGTAACA 57.467 33.333 6.20 0.00 40.74 2.41
634 867 8.084684 GCTCTGACAATCATGTATGTATCTGTA 58.915 37.037 6.20 0.00 40.74 2.74
642 875 8.151141 ACTAATTGCTCTGACAATCATGTATG 57.849 34.615 0.00 0.00 40.74 2.39
644 877 6.476706 CGACTAATTGCTCTGACAATCATGTA 59.523 38.462 0.00 0.00 40.74 2.29
645 878 5.292834 CGACTAATTGCTCTGACAATCATGT 59.707 40.000 0.00 0.00 44.25 3.21
646 879 5.735324 CGACTAATTGCTCTGACAATCATG 58.265 41.667 6.12 0.00 39.32 3.07
653 887 4.398247 CAAAAGCGACTAATTGCTCTGAC 58.602 43.478 0.00 0.00 45.59 3.51
674 908 2.277591 GGAATGCAAGCCACTGCCA 61.278 57.895 0.00 0.00 41.90 4.92
686 920 1.090052 GGTCACTGCGTAGGGAATGC 61.090 60.000 7.16 0.00 38.28 3.56
699 939 3.558931 TTGTTCACATCACAGGTCACT 57.441 42.857 0.00 0.00 0.00 3.41
714 954 7.294676 ACTTGAAAATCACTGCTTTTTGTTC 57.705 32.000 0.00 0.00 0.00 3.18
811 1159 4.524714 GCAACTATCAGGCTCTACTCCATA 59.475 45.833 0.00 0.00 0.00 2.74
858 1222 1.806542 CAGGTTGAATCGAACCACCAG 59.193 52.381 14.99 6.62 46.94 4.00
859 1223 1.890876 CAGGTTGAATCGAACCACCA 58.109 50.000 14.99 0.00 46.94 4.17
881 1245 1.078918 CAGACGCTGCCTTGATCCA 60.079 57.895 0.00 0.00 0.00 3.41
892 1256 1.399714 TGGATCGGATAACAGACGCT 58.600 50.000 0.00 0.00 0.00 5.07
974 1339 6.205464 CGTATACTCTTGTTTCCTCCGGTATA 59.795 42.308 0.00 0.00 0.00 1.47
984 1349 4.174009 TCAGCTGCGTATACTCTTGTTTC 58.826 43.478 9.47 0.00 0.00 2.78
1015 1380 3.881688 CCGCCATGATTCTCTCTCAAAAT 59.118 43.478 0.00 0.00 0.00 1.82
1019 1409 0.105593 GCCGCCATGATTCTCTCTCA 59.894 55.000 0.00 0.00 0.00 3.27
1217 1607 1.443872 CGTTCTTGTCGGGGAGTCG 60.444 63.158 0.00 0.00 0.00 4.18
1219 1609 3.057337 CCGTTCTTGTCGGGGAGT 58.943 61.111 0.00 0.00 43.68 3.85
1253 1643 7.787725 AGAAACATAATCAAGGGAATACGTC 57.212 36.000 0.00 0.00 0.00 4.34
1270 1660 5.125097 GCATCTCCATCTCAACAAGAAACAT 59.875 40.000 0.00 0.00 37.61 2.71
1300 1699 3.069872 TGCCAATTAACCATGGATGCATC 59.930 43.478 21.47 18.81 39.12 3.91
1370 1769 2.281692 ATCAAGCAGCGCACCACA 60.282 55.556 11.47 0.00 0.00 4.17
1415 1814 3.884774 GGCACCACCAGTCCACCA 61.885 66.667 0.00 0.00 38.86 4.17
1446 1849 7.755582 AAAGAAAGAAAGGATCAAACAAACG 57.244 32.000 0.00 0.00 0.00 3.60
1470 1873 3.558006 TCATTCTGCGTCGTCAAGAAAAA 59.442 39.130 9.97 1.83 0.00 1.94
1473 1876 2.058798 GTCATTCTGCGTCGTCAAGAA 58.941 47.619 8.81 8.81 0.00 2.52
1474 1877 1.000717 TGTCATTCTGCGTCGTCAAGA 60.001 47.619 0.00 0.00 0.00 3.02
1475 1878 1.125021 GTGTCATTCTGCGTCGTCAAG 59.875 52.381 0.00 0.00 0.00 3.02
1477 1880 0.666274 GGTGTCATTCTGCGTCGTCA 60.666 55.000 0.00 0.00 0.00 4.35
1479 1882 0.944311 GTGGTGTCATTCTGCGTCGT 60.944 55.000 0.00 0.00 0.00 4.34
1480 1883 1.626654 GGTGGTGTCATTCTGCGTCG 61.627 60.000 0.00 0.00 0.00 5.12
1481 1884 0.320771 AGGTGGTGTCATTCTGCGTC 60.321 55.000 0.00 0.00 0.00 5.19
1482 1885 0.973632 TAGGTGGTGTCATTCTGCGT 59.026 50.000 0.00 0.00 0.00 5.24
2353 2788 1.507174 GGACGGATCGGATCGGATC 59.493 63.158 26.93 26.93 41.67 3.36
2354 2789 2.333417 CGGACGGATCGGATCGGAT 61.333 63.158 26.28 15.03 34.17 4.18
2355 2790 2.976350 CGGACGGATCGGATCGGA 60.976 66.667 26.28 5.34 34.17 4.55
2369 2808 1.265635 CATCGAAAACTTGTTGCCGGA 59.734 47.619 5.05 0.00 0.00 5.14
2486 2934 1.207791 GAGACATGACATGAGGGGGT 58.792 55.000 22.19 0.00 0.00 4.95
2507 2955 2.105128 CACGGGAGGATGAGCGAC 59.895 66.667 0.00 0.00 0.00 5.19
2589 3037 3.817647 CTGAGGTTCTGAACAAAAGAGGG 59.182 47.826 21.01 0.82 0.00 4.30
2638 3086 7.095060 GGAATGTATATGCGAGACACAATTGAT 60.095 37.037 13.59 0.00 30.44 2.57
2641 3089 5.177511 CGGAATGTATATGCGAGACACAATT 59.822 40.000 0.00 0.00 30.44 2.32
2660 3108 4.076394 GTCTCAGAGATAGTAGGCGGAAT 58.924 47.826 2.64 0.00 0.00 3.01
2664 3112 3.071479 GGAGTCTCAGAGATAGTAGGCG 58.929 54.545 2.64 0.00 0.00 5.52
2710 3259 1.299976 GGTGGCAGTGTAAGGGAGG 59.700 63.158 0.00 0.00 0.00 4.30
2730 3281 4.047822 TGCGCTTTAAATTCAAAGTGTGG 58.952 39.130 14.60 0.00 44.29 4.17
2878 3432 7.446106 TTTCTAGACCAATATTAGCTTCCCA 57.554 36.000 0.00 0.00 0.00 4.37
2879 3433 8.747538 TTTTTCTAGACCAATATTAGCTTCCC 57.252 34.615 0.00 0.00 0.00 3.97
2880 3434 9.397280 ACTTTTTCTAGACCAATATTAGCTTCC 57.603 33.333 0.00 0.00 0.00 3.46
3013 3573 7.255139 GGAGCATTTAACTACCGATTTGCTTAT 60.255 37.037 0.00 0.00 39.15 1.73
3039 3599 2.968675 ACTCGGGAAAGTTGGTTATCG 58.031 47.619 0.00 0.00 0.00 2.92
3080 3641 7.758076 GGCTATTGTTTTAAGGATGGTGTAAAC 59.242 37.037 0.00 0.00 0.00 2.01
3101 3665 5.126067 ACGAATGTTCTATGCAAAGGCTAT 58.874 37.500 0.00 0.00 41.91 2.97
3147 3711 0.684153 AAGTGCCGCCAAGCCATATT 60.684 50.000 0.00 0.00 0.00 1.28
3249 3813 8.181904 TCCTTCCTCCAATAATATGAAAATGC 57.818 34.615 0.00 0.00 0.00 3.56
3306 3872 8.504005 CCTATTGTCGTTTTATTGTTTCTCAGT 58.496 33.333 0.00 0.00 0.00 3.41
3392 3959 3.766691 GGTCGCTTAGGCCGTCCA 61.767 66.667 0.00 0.00 33.32 4.02



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

AutoCloner maintained by Alex Coulton.