Multiple sequence alignment - TraesCS7D01G405100

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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 TraesCS7D01G405100 chr7D 100.000 2978 0 0 1 2978 522512591 522515568 0 5500
1 TraesCS7D01G405100 chr7A 93.992 2996 133 15 1 2978 602808733 602811699 0 4492
2 TraesCS7D01G405100 chr7B 93.961 2484 118 19 511 2978 556461609 556464076 0 3727
3 TraesCS7D01G405100 chr7B 94.055 471 15 3 13 471 556460917 556461386 0 702


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 TraesCS7D01G405100 chr7D 522512591 522515568 2977 False 5500.0 5500 100.000 1 2978 1 chr7D.!!$F1 2977
1 TraesCS7D01G405100 chr7A 602808733 602811699 2966 False 4492.0 4492 93.992 1 2978 1 chr7A.!!$F1 2977
2 TraesCS7D01G405100 chr7B 556460917 556464076 3159 False 2214.5 3727 94.008 13 2978 2 chr7B.!!$F1 2965

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
729 938 0.233074 CAGGCGCGTGCTTGTATATG 59.767 55.0 23.37 6.74 42.78 1.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2476 2706 0.107752 CTGAGGAAGCCTGAAGCCTC 60.108 60.0 0.0 0.0 45.47 4.7 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
54 55 2.081462 GCAAAGTGCCAACCGTACTAT 58.919 47.619 0.00 0.00 36.24 2.12
58 59 2.037144 AGTGCCAACCGTACTATAGGG 58.963 52.381 4.43 0.00 35.38 3.53
87 88 7.872113 ATTGAAAATACAGAGATTGTCCTCC 57.128 36.000 0.00 0.00 41.29 4.30
110 111 5.983118 CCCATTTTTGTTAAGTCACTGTTCC 59.017 40.000 0.00 0.00 0.00 3.62
152 153 4.157289 AGCAAGCTGTTACCAATTGATCTG 59.843 41.667 7.12 0.00 0.00 2.90
153 154 4.082571 GCAAGCTGTTACCAATTGATCTGT 60.083 41.667 7.12 0.00 0.00 3.41
154 155 5.565439 GCAAGCTGTTACCAATTGATCTGTT 60.565 40.000 7.12 0.00 0.00 3.16
155 156 6.449698 CAAGCTGTTACCAATTGATCTGTTT 58.550 36.000 7.12 0.82 0.00 2.83
156 157 7.592938 CAAGCTGTTACCAATTGATCTGTTTA 58.407 34.615 7.12 0.00 0.00 2.01
157 158 7.759489 AGCTGTTACCAATTGATCTGTTTAA 57.241 32.000 7.12 0.00 0.00 1.52
158 159 8.177119 AGCTGTTACCAATTGATCTGTTTAAA 57.823 30.769 7.12 0.00 0.00 1.52
159 160 8.806146 AGCTGTTACCAATTGATCTGTTTAAAT 58.194 29.630 7.12 0.00 0.00 1.40
160 161 9.423061 GCTGTTACCAATTGATCTGTTTAAATT 57.577 29.630 7.12 0.00 0.00 1.82
257 272 6.142798 CACAAGTGCATGTTCTAAAATGTGAC 59.857 38.462 12.23 0.00 37.27 3.67
433 459 2.805194 ACCTAGTGTCTCTACGGCTTT 58.195 47.619 0.00 0.00 0.00 3.51
456 482 0.610232 GAGCAGCAACCACCAGGAAT 60.610 55.000 0.00 0.00 38.69 3.01
489 515 1.488812 TCTAAACGCCCCAGCATGTAT 59.511 47.619 0.00 0.00 39.83 2.29
534 743 4.578871 TGATGAAGATGTACACTGTTGGG 58.421 43.478 0.00 0.00 0.00 4.12
535 744 3.417069 TGAAGATGTACACTGTTGGGG 57.583 47.619 0.00 0.00 0.00 4.96
536 745 2.039746 TGAAGATGTACACTGTTGGGGG 59.960 50.000 0.00 0.00 0.00 5.40
568 777 2.280797 TGGAGTGCACGAGTTGGC 60.281 61.111 12.01 0.00 0.00 4.52
630 839 1.076350 AGGAGATATCCAGGAGGGTCG 59.924 57.143 9.50 0.00 38.11 4.79
688 897 0.676466 TGGGGCGCAATACAAGACAG 60.676 55.000 10.83 0.00 0.00 3.51
699 908 2.645730 ACAAGACAGAGCACGAGATC 57.354 50.000 0.00 0.00 0.00 2.75
707 916 2.723658 CAGAGCACGAGATCTTTATCGC 59.276 50.000 0.00 0.00 38.74 4.58
713 922 2.294791 ACGAGATCTTTATCGCCTCAGG 59.705 50.000 0.00 0.00 42.61 3.86
714 923 2.682836 GAGATCTTTATCGCCTCAGGC 58.317 52.381 5.22 5.22 46.75 4.85
729 938 0.233074 CAGGCGCGTGCTTGTATATG 59.767 55.000 23.37 6.74 42.78 1.78
744 953 4.155709 TGTATATGAAGCCTGAGGAGAGG 58.844 47.826 0.65 0.00 36.03 3.69
745 954 3.627041 ATATGAAGCCTGAGGAGAGGA 57.373 47.619 0.65 0.00 34.69 3.71
762 971 3.511540 AGAGGAACATTTAAAGCCAAGGC 59.488 43.478 2.02 2.02 42.33 4.35
791 1000 2.023223 GCAGTTGCCAATTGGTGCG 61.023 57.895 25.19 10.98 37.57 5.34
794 1003 2.916703 TTGCCAATTGGTGCGCCT 60.917 55.556 25.19 0.00 37.57 5.52
805 1014 1.686325 GGTGCGCCTGGATAAGAGGA 61.686 60.000 9.68 0.00 31.48 3.71
813 1022 3.942115 GCCTGGATAAGAGGAAAACAGTC 59.058 47.826 0.00 0.00 31.48 3.51
814 1023 4.323868 GCCTGGATAAGAGGAAAACAGTCT 60.324 45.833 0.00 0.00 31.48 3.24
992 1205 2.150390 TGCAAGCTGAAATTCTGCGTA 58.850 42.857 17.01 3.46 44.61 4.42
1056 1275 7.559486 TGAACATAGAGCAAGAGTATGTCAAT 58.441 34.615 0.00 0.00 36.57 2.57
1198 1417 2.159476 GCTGAAATTGAGCTCGCAATGA 60.159 45.455 9.64 0.00 38.42 2.57
1200 1419 3.076621 TGAAATTGAGCTCGCAATGACT 58.923 40.909 9.64 0.00 38.42 3.41
1221 1440 1.202348 GGTTACTTTGATGCCAGTGCC 59.798 52.381 0.00 0.00 36.33 5.01
1269 1488 4.696479 ACTGAGGAACATCAAGAACACT 57.304 40.909 0.00 0.00 0.00 3.55
1621 1840 3.282920 GGCTCTGCCCTATTGCGC 61.283 66.667 0.00 0.00 44.06 6.09
1629 1848 0.179073 GCCCTATTGCGCTCAAGAGA 60.179 55.000 12.47 0.00 42.50 3.10
1638 1857 0.318441 CGCTCAAGAGAAGGGTCACA 59.682 55.000 0.32 0.00 0.00 3.58
1653 1872 1.002792 GTCACAAGGCTGAAACGTTCC 60.003 52.381 0.00 0.00 0.00 3.62
1660 1879 1.673920 GGCTGAAACGTTCCAAGACAA 59.326 47.619 0.00 0.00 0.00 3.18
1675 1894 2.648059 AGACAAAGTCTTTGCAGCAGT 58.352 42.857 22.58 4.59 40.28 4.40
1734 1953 0.984230 TTCTTGGCAGGGACTTCGAT 59.016 50.000 0.00 0.00 34.60 3.59
1846 2065 2.124983 CGGTGCAGGAGATGGTGG 60.125 66.667 0.00 0.00 0.00 4.61
1942 2161 5.713792 TGCTACAATCCATAGAGCTAGAC 57.286 43.478 0.00 0.00 34.19 2.59
2030 2252 9.871238 GACATTATGTTTAGGAGTACTTCAGAA 57.129 33.333 3.42 0.00 0.00 3.02
2057 2280 7.863666 TGTTTATACTTTTTGTTAGACCGTGG 58.136 34.615 0.00 0.00 0.00 4.94
2227 2451 6.267471 AGGGAAATTGATGCTTTCTTGTACAA 59.733 34.615 8.28 8.28 33.93 2.41
2346 2575 9.195411 ACAGTTGTTAGCAATTTATGTTCAATG 57.805 29.630 0.00 0.00 36.92 2.82
2353 2582 9.624697 TTAGCAATTTATGTTCAATGTCTGTTC 57.375 29.630 0.00 0.00 0.00 3.18
2370 2599 8.620116 TGTCTGTTCATGATTGAAGTTCAATA 57.380 30.769 27.01 16.94 46.20 1.90
2428 2657 6.593382 GGCAAACCAAACAGCATTAATATTGA 59.407 34.615 0.00 0.00 35.26 2.57
2455 2685 6.888632 AGAAAATGGTCAAGAGACTATGCAAT 59.111 34.615 0.00 0.00 44.12 3.56
2460 2690 7.071069 TGGTCAAGAGACTATGCAATATGAT 57.929 36.000 0.00 0.00 44.36 2.45
2481 2711 7.701539 TGATATTTTGTTTACACATGAGGCT 57.298 32.000 0.00 0.00 31.06 4.58
2482 2712 8.121305 TGATATTTTGTTTACACATGAGGCTT 57.879 30.769 0.00 0.00 31.06 4.35
2483 2713 8.243426 TGATATTTTGTTTACACATGAGGCTTC 58.757 33.333 0.00 0.00 31.06 3.86
2498 2728 1.447945 GCTTCAGGCTTCCTCAGAAC 58.552 55.000 0.00 0.00 38.06 3.01
2507 2737 2.480802 GCTTCCTCAGAACGGAGAAAAC 59.519 50.000 3.75 0.00 37.05 2.43
2509 2739 3.386768 TCCTCAGAACGGAGAAAACTG 57.613 47.619 3.75 0.00 37.05 3.16
2517 2747 5.049405 CAGAACGGAGAAAACTGCTGTATTT 60.049 40.000 0.00 0.57 0.00 1.40
2760 2990 1.821753 AGAACTGATAGACGTGCTGCT 59.178 47.619 0.00 0.00 0.00 4.24
2814 3044 7.541162 ACACTCTAATACTGCGTACAAACATA 58.459 34.615 0.00 0.00 0.00 2.29
2844 3074 9.398170 CATGAATTCAAACTGGTTAAGTACAAG 57.602 33.333 13.09 0.00 38.56 3.16
2905 3135 5.835280 AGTGGAATTCTGAATTTGTGTTCCT 59.165 36.000 16.14 4.48 35.75 3.36
2931 3161 1.026182 TTATTGCACTGCTGAGGCCG 61.026 55.000 0.00 0.00 37.74 6.13
2973 3203 5.235850 TCCACATTGTGTTTAGGCTAGAA 57.764 39.130 15.34 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 88 6.805713 AGGAACAGTGACTTAACAAAAATGG 58.194 36.000 0.00 0.00 0.00 3.16
110 111 6.417930 GCTTGCTTAAACTACTGGACAAAAAG 59.582 38.462 0.00 0.00 0.00 2.27
152 153 4.627035 GCAAGCCACCAGATCAATTTAAAC 59.373 41.667 0.00 0.00 0.00 2.01
153 154 4.282957 TGCAAGCCACCAGATCAATTTAAA 59.717 37.500 0.00 0.00 0.00 1.52
154 155 3.831333 TGCAAGCCACCAGATCAATTTAA 59.169 39.130 0.00 0.00 0.00 1.52
155 156 3.429492 TGCAAGCCACCAGATCAATTTA 58.571 40.909 0.00 0.00 0.00 1.40
156 157 2.250031 TGCAAGCCACCAGATCAATTT 58.750 42.857 0.00 0.00 0.00 1.82
157 158 1.927487 TGCAAGCCACCAGATCAATT 58.073 45.000 0.00 0.00 0.00 2.32
158 159 2.029623 GATGCAAGCCACCAGATCAAT 58.970 47.619 0.00 0.00 0.00 2.57
159 160 1.466856 GATGCAAGCCACCAGATCAA 58.533 50.000 0.00 0.00 0.00 2.57
160 161 0.394762 GGATGCAAGCCACCAGATCA 60.395 55.000 4.23 0.00 46.15 2.92
161 162 2.412605 GGATGCAAGCCACCAGATC 58.587 57.895 4.23 0.00 46.15 2.75
162 163 4.672251 GGATGCAAGCCACCAGAT 57.328 55.556 4.23 0.00 46.15 2.90
257 272 3.761140 TGCATTGTGGGCATGCCG 61.761 61.111 29.90 16.17 40.34 5.69
433 459 1.545428 CCTGGTGGTTGCTGCTCTAAA 60.545 52.381 0.00 0.00 0.00 1.85
456 482 3.304391 GGCGTTTAGATTGTGTGCAAGAA 60.304 43.478 0.00 0.00 38.10 2.52
489 515 2.349755 GTCCTTTACCAGCCGCCA 59.650 61.111 0.00 0.00 0.00 5.69
534 743 0.745845 CCACATCACTGTAGCAGCCC 60.746 60.000 0.00 0.00 34.37 5.19
535 744 0.250234 TCCACATCACTGTAGCAGCC 59.750 55.000 0.00 0.00 34.37 4.85
536 745 1.066573 ACTCCACATCACTGTAGCAGC 60.067 52.381 0.00 0.00 34.37 5.25
568 777 3.670625 TCCACGGTGTATTCTTTTCTGG 58.329 45.455 7.45 0.00 0.00 3.86
630 839 0.888619 GCTTAAGTTTGGCACTCCCC 59.111 55.000 4.02 0.00 32.94 4.81
688 897 2.055100 GGCGATAAAGATCTCGTGCTC 58.945 52.381 0.00 0.00 37.23 4.26
707 916 3.808148 TATACAAGCACGCGCCTGAGG 62.808 57.143 5.73 0.00 39.83 3.86
713 922 1.657538 GCTTCATATACAAGCACGCGC 60.658 52.381 5.73 0.00 44.87 6.86
714 923 1.070577 GGCTTCATATACAAGCACGCG 60.071 52.381 16.46 3.53 46.94 6.01
715 924 2.032549 CAGGCTTCATATACAAGCACGC 60.033 50.000 16.46 3.82 46.94 5.34
716 925 3.457234 TCAGGCTTCATATACAAGCACG 58.543 45.455 16.46 9.05 46.94 5.34
729 938 1.270907 TGTTCCTCTCCTCAGGCTTC 58.729 55.000 0.00 0.00 32.91 3.86
744 953 3.588955 CCTGCCTTGGCTTTAAATGTTC 58.411 45.455 13.18 0.00 0.00 3.18
745 954 3.683365 CCTGCCTTGGCTTTAAATGTT 57.317 42.857 13.18 0.00 0.00 2.71
762 971 3.031964 GCAACTGCACTAGCGCCTG 62.032 63.158 2.29 0.00 46.23 4.85
791 1000 3.942115 GACTGTTTTCCTCTTATCCAGGC 59.058 47.826 0.00 0.00 0.00 4.85
794 1003 5.544176 AGACAGACTGTTTTCCTCTTATCCA 59.456 40.000 10.01 0.00 0.00 3.41
805 1014 5.070981 TGATCCTTCTGAGACAGACTGTTTT 59.929 40.000 10.01 1.19 40.46 2.43
813 1022 5.404466 AGTTCTTGATCCTTCTGAGACAG 57.596 43.478 0.00 0.00 0.00 3.51
814 1023 5.305386 TCAAGTTCTTGATCCTTCTGAGACA 59.695 40.000 10.67 0.00 0.00 3.41
992 1205 2.224719 GCCAGCATCTCCATACCTGAAT 60.225 50.000 0.00 0.00 0.00 2.57
1186 1405 1.661112 GTAACCAGTCATTGCGAGCTC 59.339 52.381 2.73 2.73 0.00 4.09
1200 1419 1.885887 GCACTGGCATCAAAGTAACCA 59.114 47.619 0.00 0.00 40.72 3.67
1221 1440 1.363443 GCAGATCTCTGAGGCCTCG 59.637 63.158 27.43 21.01 46.59 4.63
1230 1449 2.109774 AGTAGCTGCTTGCAGATCTCT 58.890 47.619 24.67 16.79 45.94 3.10
1269 1488 5.048083 GTCCATTGATTGGTAGTTGCTTTCA 60.048 40.000 0.00 0.00 46.52 2.69
1621 1840 2.873649 GCCTTGTGACCCTTCTCTTGAG 60.874 54.545 0.00 0.00 0.00 3.02
1629 1848 1.692411 GTTTCAGCCTTGTGACCCTT 58.308 50.000 0.00 0.00 0.00 3.95
1638 1857 1.947456 GTCTTGGAACGTTTCAGCCTT 59.053 47.619 9.67 0.00 0.00 4.35
1689 1908 3.409856 CCCTTTGCGGCAGTATCG 58.590 61.111 1.67 0.00 0.00 2.92
1734 1953 1.302192 GGCAAGTTGGCTCACCGTA 60.302 57.895 21.39 0.00 40.14 4.02
1846 2065 0.248843 CAACTCCTCCTCAGCTCCAC 59.751 60.000 0.00 0.00 0.00 4.02
2030 2252 9.887406 CACGGTCTAACAAAAAGTATAAACATT 57.113 29.630 0.00 0.00 0.00 2.71
2040 2262 2.812011 CCCTCCACGGTCTAACAAAAAG 59.188 50.000 0.00 0.00 0.00 2.27
2057 2280 5.643379 TGTATTGAAGTGCAAATTCCCTC 57.357 39.130 9.72 1.17 40.84 4.30
2147 2370 4.092091 GCTCAAACTCTCACAAATAGTCCG 59.908 45.833 0.00 0.00 0.00 4.79
2148 2371 4.997395 TGCTCAAACTCTCACAAATAGTCC 59.003 41.667 0.00 0.00 0.00 3.85
2150 2373 6.942532 TTTGCTCAAACTCTCACAAATAGT 57.057 33.333 0.00 0.00 0.00 2.12
2151 2374 7.614674 GTTTTGCTCAAACTCTCACAAATAG 57.385 36.000 5.19 0.00 41.58 1.73
2288 2512 8.970859 ACAGAATATTTGAGGATAGGTTGAAG 57.029 34.615 0.00 0.00 0.00 3.02
2323 2552 9.410556 AGACATTGAACATAAATTGCTAACAAC 57.589 29.630 0.00 0.00 38.99 3.32
2346 2575 9.499585 CATATTGAACTTCAATCATGAACAGAC 57.500 33.333 18.39 0.00 43.03 3.51
2353 2582 7.658261 AGCCATCATATTGAACTTCAATCATG 58.342 34.615 18.39 17.80 43.03 3.07
2370 2599 6.041637 TGTTACCTTCGAATAGTAGCCATCAT 59.958 38.462 15.16 0.00 0.00 2.45
2428 2657 5.645497 GCATAGTCTCTTGACCATTTTCTGT 59.355 40.000 0.00 0.00 43.91 3.41
2455 2685 9.407380 AGCCTCATGTGTAAACAAAATATCATA 57.593 29.630 0.00 0.00 0.00 2.15
2460 2690 7.309133 CCTGAAGCCTCATGTGTAAACAAAATA 60.309 37.037 0.00 0.00 0.00 1.40
2464 2694 3.820467 CCTGAAGCCTCATGTGTAAACAA 59.180 43.478 0.00 0.00 0.00 2.83
2476 2706 0.107752 CTGAGGAAGCCTGAAGCCTC 60.108 60.000 0.00 0.00 45.47 4.70
2477 2707 0.546267 TCTGAGGAAGCCTGAAGCCT 60.546 55.000 0.00 0.00 45.47 4.58
2478 2708 0.326264 TTCTGAGGAAGCCTGAAGCC 59.674 55.000 0.00 0.00 45.47 4.35
2479 2709 1.447945 GTTCTGAGGAAGCCTGAAGC 58.552 55.000 0.00 0.00 44.25 3.86
2480 2710 1.674221 CCGTTCTGAGGAAGCCTGAAG 60.674 57.143 0.00 0.00 31.76 3.02
2481 2711 0.321671 CCGTTCTGAGGAAGCCTGAA 59.678 55.000 0.00 0.00 31.76 3.02
2482 2712 0.541998 TCCGTTCTGAGGAAGCCTGA 60.542 55.000 0.00 0.00 34.33 3.86
2483 2713 0.108424 CTCCGTTCTGAGGAAGCCTG 60.108 60.000 0.00 0.00 37.32 4.85
2498 2728 6.147164 TGTCTAAAATACAGCAGTTTTCTCCG 59.853 38.462 0.00 0.00 0.00 4.63
2555 2785 5.357742 ACAATGCACACTATCAGGTATGA 57.642 39.130 0.00 0.00 40.50 2.15
2716 2946 2.627515 TCAGGAATCATGTGCCTAGC 57.372 50.000 0.00 0.00 0.00 3.42
2727 2957 8.973378 CGTCTATCAGTTCTTATTTCAGGAATC 58.027 37.037 0.00 0.00 0.00 2.52
2858 3088 8.405531 CACTCTGTTCCTTTCATTTTGTAAGAA 58.594 33.333 0.00 0.00 27.74 2.52
2862 3092 6.361433 TCCACTCTGTTCCTTTCATTTTGTA 58.639 36.000 0.00 0.00 0.00 2.41
2864 3094 5.772825 TCCACTCTGTTCCTTTCATTTTG 57.227 39.130 0.00 0.00 0.00 2.44
2879 3109 6.015940 GGAACACAAATTCAGAATTCCACTCT 60.016 38.462 8.90 0.00 35.30 3.24
2894 3124 5.183904 GCAATAAGGTCAGAGGAACACAAAT 59.816 40.000 0.00 0.00 31.21 2.32
2895 3125 4.518970 GCAATAAGGTCAGAGGAACACAAA 59.481 41.667 0.00 0.00 31.21 2.83
2901 3131 3.869912 GCAGTGCAATAAGGTCAGAGGAA 60.870 47.826 11.09 0.00 0.00 3.36
2905 3135 2.302733 TCAGCAGTGCAATAAGGTCAGA 59.697 45.455 19.20 0.00 0.00 3.27
2931 3161 6.127479 TGTGGATGGTTTATACAATTCCAAGC 60.127 38.462 0.00 0.00 33.00 4.01


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

AutoCloner maintained by Alex Coulton.