Multiple sequence alignment - TraesCS4A01G222700

Loading Multiple Alignment...

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 TraesCS4A01G222700 chr4A 100.000 3158 0 0 1 3158 530120870 530124027 0.000000e+00 5832.0
1 TraesCS4A01G222700 chr4D 94.619 3178 118 28 1 3158 65579124 65575980 0.000000e+00 4872.0
2 TraesCS4A01G222700 chr4D 85.849 106 14 1 2678 2783 65100685 65100789 9.260000e-21 111.0
3 TraesCS4A01G222700 chr4B 93.639 2531 99 22 272 2793 96273102 96270625 0.000000e+00 3725.0
4 TraesCS4A01G222700 chr4B 77.990 209 33 9 2655 2851 671694966 671695173 5.530000e-23 119.0
5 TraesCS4A01G222700 chr5D 91.981 212 17 0 1266 1477 205995758 205995969 6.620000e-77 298.0
6 TraesCS4A01G222700 chr5D 83.957 187 26 4 1285 1469 539014529 539014713 3.240000e-40 176.0
7 TraesCS4A01G222700 chr5D 100.000 28 0 0 1808 1835 205996261 205996288 6.000000e-03 52.8
8 TraesCS4A01G222700 chr5A 91.509 212 18 0 1266 1477 264421478 264421689 3.080000e-75 292.0
9 TraesCS4A01G222700 chr5A 100.000 28 0 0 1808 1835 264421981 264422008 6.000000e-03 52.8
10 TraesCS4A01G222700 chr5B 90.367 218 21 0 1266 1483 206102422 206102205 1.430000e-73 287.0
11 TraesCS4A01G222700 chr6D 84.519 239 32 4 1264 1498 393936217 393935980 6.810000e-57 231.0
12 TraesCS4A01G222700 chr6A 84.519 239 32 4 1264 1498 540145669 540145432 6.810000e-57 231.0
13 TraesCS4A01G222700 chr2D 82.979 188 27 5 1285 1469 520537008 520536823 7.010000e-37 165.0
14 TraesCS4A01G222700 chr2D 77.844 167 35 2 2687 2852 76651164 76650999 5.570000e-18 102.0
15 TraesCS4A01G222700 chr1B 81.188 202 31 4 2658 2852 495146792 495146993 4.220000e-34 156.0
16 TraesCS4A01G222700 chr3D 86.364 110 11 4 2686 2793 432507737 432507630 1.990000e-22 117.0
17 TraesCS4A01G222700 chr3A 83.761 117 17 2 2685 2800 569953813 569953698 3.330000e-20 110.0
18 TraesCS4A01G222700 chr2B 75.449 167 35 4 2687 2852 117930662 117930501 3.380000e-10 76.8
19 TraesCS4A01G222700 chr6B 100.000 32 0 0 1617 1648 12118379 12118348 3.400000e-05 60.2


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 TraesCS4A01G222700 chr4A 530120870 530124027 3157 False 5832 5832 100.000 1 3158 1 chr4A.!!$F1 3157
1 TraesCS4A01G222700 chr4D 65575980 65579124 3144 True 4872 4872 94.619 1 3158 1 chr4D.!!$R1 3157
2 TraesCS4A01G222700 chr4B 96270625 96273102 2477 True 3725 3725 93.639 272 2793 1 chr4B.!!$R1 2521

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
428 442 0.683973 GATGGTGATCCGATGGCTCT 59.316 55.000 0.0 0.0 36.3 4.09 F
990 1009 1.067846 TGTAACTGTGCCTAGCTGTCG 60.068 52.381 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1254 1273 1.355066 GCTTCGCCACCTTCTTCTCG 61.355 60.0 0.0 0.0 0.00 4.04 R
2967 2991 0.116342 GGGTTTTTCCTCCCCCACAT 59.884 55.0 0.0 0.0 37.89 3.21 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
22 23 3.997021 ACAACTTCTCCGAATGTCATGTC 59.003 43.478 0.00 0.00 0.00 3.06
23 24 4.248859 CAACTTCTCCGAATGTCATGTCT 58.751 43.478 0.00 0.00 0.00 3.41
24 25 3.854666 ACTTCTCCGAATGTCATGTCTG 58.145 45.455 0.00 0.00 0.00 3.51
123 124 9.665264 AAACATTTGACGTTCTCTAAGAAATTC 57.335 29.630 0.00 0.00 35.75 2.17
136 137 8.322091 TCTCTAAGAAATTCAGAAAAGGGGTAG 58.678 37.037 0.00 0.00 0.00 3.18
287 292 2.419673 CGAATGTCTAAGTTGCCATGCA 59.580 45.455 0.00 0.00 36.47 3.96
377 385 1.001487 TGTGCAAAGAAATGGCAGACG 60.001 47.619 0.00 0.00 38.38 4.18
392 400 2.006888 CAGACGAATTACCACGCCATT 58.993 47.619 0.00 0.00 0.00 3.16
394 402 1.735571 GACGAATTACCACGCCATTGT 59.264 47.619 0.00 0.00 0.00 2.71
405 413 1.612950 ACGCCATTGTGAGAAATTGCA 59.387 42.857 0.00 0.00 29.75 4.08
412 425 5.231357 CCATTGTGAGAAATTGCATTCGATG 59.769 40.000 0.00 0.00 34.46 3.84
428 442 0.683973 GATGGTGATCCGATGGCTCT 59.316 55.000 0.00 0.00 36.30 4.09
440 454 2.739932 CGATGGCTCTGAGGAAATTCGT 60.740 50.000 6.83 0.00 0.00 3.85
535 550 9.211485 CAGCTGTATTTCCATTTCAAAATCTTT 57.789 29.630 5.25 0.00 0.00 2.52
561 576 1.909700 TTCACAAATCCCAGCCTCAC 58.090 50.000 0.00 0.00 0.00 3.51
739 756 2.364002 GAGAGGAAAGCTAGGTAGGCTG 59.636 54.545 0.00 0.00 40.19 4.85
990 1009 1.067846 TGTAACTGTGCCTAGCTGTCG 60.068 52.381 0.00 0.00 0.00 4.35
1182 1201 2.202878 GGCTCGCTTGCGATGGTA 60.203 61.111 18.05 0.00 0.00 3.25
1479 1498 2.742372 CCCGCCAACTTCTCCACG 60.742 66.667 0.00 0.00 0.00 4.94
1668 1687 4.838152 GCGCCGCAAGATCCTGGA 62.838 66.667 3.15 0.00 43.02 3.86
2094 2113 3.445518 GATGGATCAGCACCGCCGA 62.446 63.158 0.00 0.00 0.00 5.54
2247 2266 2.003301 GTGTGGAGCACTTTAGCTAGC 58.997 52.381 6.62 6.62 46.75 3.42
2378 2397 1.490490 TGATGATTAGCAGTGGGTCCC 59.510 52.381 0.00 0.00 0.00 4.46
2449 2468 9.638300 GCACATTTTATCGTATCAGTTTTCTAG 57.362 33.333 0.00 0.00 0.00 2.43
2457 2476 7.987268 TCGTATCAGTTTTCTAGTATTGCTG 57.013 36.000 0.00 0.00 0.00 4.41
2487 2506 3.882888 TGGGGAATCTATTTGTTCGATGC 59.117 43.478 0.00 0.00 0.00 3.91
2591 2610 4.848357 ACAGAACTAGCTAATTGCCATGT 58.152 39.130 0.00 0.00 44.23 3.21
2603 2622 0.754587 TGCCATGTGTTGCAACAGGA 60.755 50.000 31.81 21.31 40.05 3.86
2623 2646 7.743749 ACAGGAGCATATTCTAGTGATTCAAT 58.256 34.615 0.00 0.00 0.00 2.57
2639 2662 9.246670 AGTGATTCAATATCAATTTTGTCCTCA 57.753 29.630 0.00 0.00 0.00 3.86
2640 2663 9.512435 GTGATTCAATATCAATTTTGTCCTCAG 57.488 33.333 0.00 0.00 0.00 3.35
2641 2664 9.246670 TGATTCAATATCAATTTTGTCCTCAGT 57.753 29.630 0.00 0.00 0.00 3.41
2642 2665 9.727627 GATTCAATATCAATTTTGTCCTCAGTC 57.272 33.333 0.00 0.00 0.00 3.51
2643 2666 7.307493 TCAATATCAATTTTGTCCTCAGTCG 57.693 36.000 0.00 0.00 0.00 4.18
2644 2667 5.741388 ATATCAATTTTGTCCTCAGTCGC 57.259 39.130 0.00 0.00 0.00 5.19
2645 2668 2.844946 TCAATTTTGTCCTCAGTCGCA 58.155 42.857 0.00 0.00 0.00 5.10
2646 2669 3.210227 TCAATTTTGTCCTCAGTCGCAA 58.790 40.909 0.00 0.00 0.00 4.85
2647 2670 3.629855 TCAATTTTGTCCTCAGTCGCAAA 59.370 39.130 0.00 0.00 0.00 3.68
2648 2671 4.097135 TCAATTTTGTCCTCAGTCGCAAAA 59.903 37.500 0.00 0.00 42.48 2.44
2649 2672 4.647424 ATTTTGTCCTCAGTCGCAAAAA 57.353 36.364 0.00 0.00 41.89 1.94
2681 2704 9.898152 TCAATTTTGTCTGACATATATACACCA 57.102 29.630 11.86 0.00 0.00 4.17
2742 2765 8.792830 TTAAGTATAGATAGGGAAAGGCAAGA 57.207 34.615 0.00 0.00 0.00 3.02
2746 2769 8.557450 AGTATAGATAGGGAAAGGCAAGAAAAA 58.443 33.333 0.00 0.00 0.00 1.94
2747 2770 5.984695 AGATAGGGAAAGGCAAGAAAAAC 57.015 39.130 0.00 0.00 0.00 2.43
2748 2771 5.393866 AGATAGGGAAAGGCAAGAAAAACA 58.606 37.500 0.00 0.00 0.00 2.83
2800 2823 3.857157 TTGATTGAGGTATGGGTAGGC 57.143 47.619 0.00 0.00 0.00 3.93
2815 2838 4.067192 GGGTAGGCGAAGTCAAGTAAAAA 58.933 43.478 0.00 0.00 0.00 1.94
2826 2849 8.798153 CGAAGTCAAGTAAAAATTTGATATGGC 58.202 33.333 0.00 0.00 35.91 4.40
2863 2887 6.894339 AGATTTGATTTGGAAAAGTACCGT 57.106 33.333 0.00 0.00 0.00 4.83
2867 2891 7.758613 TTTGATTTGGAAAAGTACCGTTTTC 57.241 32.000 10.41 10.41 43.08 2.29
2885 2909 8.398665 ACCGTTTTCATTTAGATTATCTCAAGC 58.601 33.333 0.00 0.00 0.00 4.01
2900 2924 9.680315 ATTATCTCAAGCTACTGTATTTACGTC 57.320 33.333 0.00 0.00 0.00 4.34
2909 2933 7.008992 AGCTACTGTATTTACGTCGCTTTTTAG 59.991 37.037 0.00 0.00 32.54 1.85
2930 2954 2.064434 TTGTGTGCCAATGGTTGAGA 57.936 45.000 0.00 0.00 0.00 3.27
2984 3013 1.077169 AGGATGTGGGGGAGGAAAAAC 59.923 52.381 0.00 0.00 0.00 2.43
2994 3023 1.357761 GGAGGAAAAACCCCATGGAGA 59.642 52.381 15.22 0.00 40.05 3.71
3022 3051 5.422145 GCGAACCTACTAACCATCCTTTAA 58.578 41.667 0.00 0.00 0.00 1.52
3038 3067 7.398024 CATCCTTTAATAGTAGAGATTGGGGG 58.602 42.308 0.00 0.00 0.00 5.40
3049 3078 3.986134 AGAGATTGGGGGAGCAAGATATT 59.014 43.478 0.00 0.00 0.00 1.28
3052 3081 1.507140 TGGGGGAGCAAGATATTCGT 58.493 50.000 0.00 0.00 0.00 3.85
3075 3104 6.421202 CGTTCTAGCATTCCAAATAGACCTAC 59.579 42.308 0.00 0.00 0.00 3.18
3077 3106 7.432148 TCTAGCATTCCAAATAGACCTACAA 57.568 36.000 0.00 0.00 0.00 2.41
3079 3108 6.067217 AGCATTCCAAATAGACCTACAACT 57.933 37.500 0.00 0.00 0.00 3.16
3080 3109 6.116126 AGCATTCCAAATAGACCTACAACTC 58.884 40.000 0.00 0.00 0.00 3.01
3082 3111 6.653989 CATTCCAAATAGACCTACAACTCCT 58.346 40.000 0.00 0.00 0.00 3.69
3091 3120 9.725206 AATAGACCTACAACTCCTTTCCTAATA 57.275 33.333 0.00 0.00 0.00 0.98
3135 3164 1.321474 AGTCGTGGTAGTTTCCGTCA 58.679 50.000 0.00 0.00 0.00 4.35
3149 3178 9.595357 GTAGTTTCCGTCAAATTTTAGAAGAAG 57.405 33.333 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 1.402968 CCTTCATGGATCAAACGCCAG 59.597 52.381 0.00 0.00 37.64 4.85
23 24 1.462616 CCTTCATGGATCAAACGCCA 58.537 50.000 0.00 0.00 38.35 5.69
24 25 0.740737 CCCTTCATGGATCAAACGCC 59.259 55.000 0.00 0.00 38.35 5.68
123 124 2.094675 CCATGTGCTACCCCTTTTCTG 58.905 52.381 0.00 0.00 0.00 3.02
136 137 7.969536 ATAATCTACTTGTATCACCATGTGC 57.030 36.000 0.00 0.00 32.98 4.57
186 187 9.337396 GACACCATGTTGTTCATCCTATTATTA 57.663 33.333 0.00 0.00 34.09 0.98
225 230 3.775316 AGACGTAGACCATCAATTTCCCT 59.225 43.478 0.00 0.00 0.00 4.20
365 372 3.485216 CGTGGTAATTCGTCTGCCATTTC 60.485 47.826 0.00 0.00 0.00 2.17
377 385 3.006940 TCTCACAATGGCGTGGTAATTC 58.993 45.455 0.00 0.00 37.50 2.17
392 400 3.758023 ACCATCGAATGCAATTTCTCACA 59.242 39.130 0.00 0.00 36.07 3.58
394 402 4.009002 TCACCATCGAATGCAATTTCTCA 58.991 39.130 0.00 0.00 36.07 3.27
405 413 1.609061 GCCATCGGATCACCATCGAAT 60.609 52.381 0.00 0.00 36.49 3.34
412 425 0.033228 CTCAGAGCCATCGGATCACC 59.967 60.000 0.54 0.00 41.08 4.02
428 442 2.510613 GGTTCCCAACGAATTTCCTCA 58.489 47.619 0.00 0.00 31.67 3.86
458 472 3.791993 TTAATAACGTGTGAACGCCAC 57.208 42.857 0.00 1.98 45.88 5.01
486 500 8.961092 GCTGTTTGTTAGCATGTATATTCATTG 58.039 33.333 0.00 0.00 40.81 2.82
490 504 7.697691 ACAGCTGTTTGTTAGCATGTATATTC 58.302 34.615 15.25 0.00 43.53 1.75
555 570 2.354821 GGATTTGTGGTAATCGTGAGGC 59.645 50.000 0.00 0.00 35.76 4.70
739 756 2.656069 TTGGGACCTACTGCTCCGC 61.656 63.158 0.00 0.00 0.00 5.54
871 888 4.035102 GAGGTGTGGGGCTGGGAC 62.035 72.222 0.00 0.00 0.00 4.46
990 1009 1.552337 TGCTGGTCCATGAGAAGAGAC 59.448 52.381 0.00 0.00 0.00 3.36
1026 1045 2.596631 CTGGTGCTGGTGCTGCTT 60.597 61.111 0.00 0.00 40.48 3.91
1254 1273 1.355066 GCTTCGCCACCTTCTTCTCG 61.355 60.000 0.00 0.00 0.00 4.04
1668 1687 2.370445 CCTCATGAACTCCCCGGCT 61.370 63.158 0.00 0.00 0.00 5.52
2316 2335 3.876914 TGGATTAATGAACGGCAAGCTAG 59.123 43.478 0.00 0.00 0.00 3.42
2320 2339 3.381272 ACCATGGATTAATGAACGGCAAG 59.619 43.478 21.47 0.00 0.00 4.01
2378 2397 9.398170 CTTAAACAAATAGTGTCTGGTTCAATG 57.602 33.333 0.00 0.00 40.60 2.82
2389 2408 6.512297 CCTTGTTGCCTTAAACAAATAGTGT 58.488 36.000 4.28 0.00 46.43 3.55
2449 2468 7.341805 AGATTCCCCATGATATACAGCAATAC 58.658 38.462 0.00 0.00 0.00 1.89
2457 2476 8.883731 CGAACAAATAGATTCCCCATGATATAC 58.116 37.037 0.00 0.00 0.00 1.47
2591 2610 3.689347 AGAATATGCTCCTGTTGCAACA 58.311 40.909 29.36 29.36 44.01 3.33
2623 2646 4.574892 TGCGACTGAGGACAAAATTGATA 58.425 39.130 0.00 0.00 0.00 2.15
2655 2678 9.898152 TGGTGTATATATGTCAGACAAAATTGA 57.102 29.630 7.50 0.00 0.00 2.57
2658 2681 9.120538 GGTTGGTGTATATATGTCAGACAAAAT 57.879 33.333 7.50 7.13 0.00 1.82
2659 2682 8.103935 TGGTTGGTGTATATATGTCAGACAAAA 58.896 33.333 7.50 0.00 0.00 2.44
2660 2683 7.625469 TGGTTGGTGTATATATGTCAGACAAA 58.375 34.615 7.50 0.00 0.00 2.83
2661 2684 7.189079 TGGTTGGTGTATATATGTCAGACAA 57.811 36.000 7.50 0.00 0.00 3.18
2662 2685 6.800072 TGGTTGGTGTATATATGTCAGACA 57.200 37.500 5.50 5.50 0.00 3.41
2663 2686 9.944376 AATATGGTTGGTGTATATATGTCAGAC 57.056 33.333 0.00 0.00 0.00 3.51
2786 2809 1.340568 GACTTCGCCTACCCATACCTC 59.659 57.143 0.00 0.00 0.00 3.85
2797 2820 6.385649 TCAAATTTTTACTTGACTTCGCCT 57.614 33.333 0.00 0.00 0.00 5.52
2800 2823 8.798153 GCCATATCAAATTTTTACTTGACTTCG 58.202 33.333 0.00 0.00 34.52 3.79
2881 2905 4.103357 AGCGACGTAAATACAGTAGCTTG 58.897 43.478 13.05 0.00 37.89 4.01
2883 2907 4.367386 AAGCGACGTAAATACAGTAGCT 57.633 40.909 13.05 13.05 40.28 3.32
2885 2909 8.166367 ACTAAAAAGCGACGTAAATACAGTAG 57.834 34.615 0.00 0.00 0.00 2.57
2900 2924 2.803451 TGGCACACAAACTAAAAAGCG 58.197 42.857 0.00 0.00 0.00 4.68
2909 2933 2.100584 TCTCAACCATTGGCACACAAAC 59.899 45.455 1.54 0.00 43.46 2.93
2959 2983 4.448340 TCCCCCACATCCTCCCCC 62.448 72.222 0.00 0.00 0.00 5.40
2964 2988 1.077169 GTTTTTCCTCCCCCACATCCT 59.923 52.381 0.00 0.00 0.00 3.24
2966 2990 1.557099 GGTTTTTCCTCCCCCACATC 58.443 55.000 0.00 0.00 0.00 3.06
2967 2991 0.116342 GGGTTTTTCCTCCCCCACAT 59.884 55.000 0.00 0.00 37.89 3.21
2968 2992 1.544703 GGGTTTTTCCTCCCCCACA 59.455 57.895 0.00 0.00 37.89 4.17
2988 3017 1.689273 GTAGGTTCGCCTCATCTCCAT 59.311 52.381 0.00 0.00 46.86 3.41
2989 3018 1.112113 GTAGGTTCGCCTCATCTCCA 58.888 55.000 0.00 0.00 46.86 3.86
2994 3023 2.463752 TGGTTAGTAGGTTCGCCTCAT 58.536 47.619 0.00 0.00 46.86 2.90
3014 3043 7.321530 TCCCCCAATCTCTACTATTAAAGGAT 58.678 38.462 0.00 0.00 0.00 3.24
3022 3051 3.637821 TGCTCCCCCAATCTCTACTAT 57.362 47.619 0.00 0.00 0.00 2.12
3038 3067 6.128688 GGAATGCTAGAACGAATATCTTGCTC 60.129 42.308 10.37 2.50 43.22 4.26
3049 3078 5.128827 AGGTCTATTTGGAATGCTAGAACGA 59.871 40.000 0.00 0.00 33.97 3.85
3052 3081 7.432148 TGTAGGTCTATTTGGAATGCTAGAA 57.568 36.000 0.00 0.00 0.00 2.10
3075 3104 9.516546 AACCTAAAAGTATTAGGAAAGGAGTTG 57.483 33.333 18.53 0.00 43.24 3.16
3098 3127 6.859508 CCACGACTTTAAGACCAATTAAAACC 59.140 38.462 0.00 0.00 34.97 3.27


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

AutoCloner maintained by Alex Coulton.