Multiple sequence alignment - TraesCS2D01G331900

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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 TraesCS2D01G331900 chr2D 100.000 3595 0 0 1 3595 424636142 424639736 0.000000e+00 6639.0
1 TraesCS2D01G331900 chr2A 92.310 3524 129 61 1 3426 563949912 563946433 0.000000e+00 4876.0
2 TraesCS2D01G331900 chr2A 95.858 169 7 0 3420 3588 563946380 563946212 1.270000e-69 274.0
3 TraesCS2D01G331900 chr2B 91.737 3183 129 63 69 3207 499538784 499541876 0.000000e+00 4298.0
4 TraesCS2D01G331900 chr2B 94.083 169 10 0 3420 3588 499542383 499542551 1.280000e-64 257.0
5 TraesCS2D01G331900 chr2B 98.611 72 0 1 1 72 499538690 499538760 3.770000e-25 126.0
6 TraesCS2D01G331900 chr6B 84.891 503 26 26 384 860 362490935 362491413 2.530000e-126 462.0
7 TraesCS2D01G331900 chr6B 87.814 279 13 7 69 346 362490672 362490930 1.250000e-79 307.0
8 TraesCS2D01G331900 chr6B 97.297 37 1 0 36 72 362490613 362490649 3.000000e-06 63.9


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 TraesCS2D01G331900 chr2D 424636142 424639736 3594 False 6639.000000 6639 100.000000 1 3595 1 chr2D.!!$F1 3594
1 TraesCS2D01G331900 chr2A 563946212 563949912 3700 True 2575.000000 4876 94.084000 1 3588 2 chr2A.!!$R1 3587
2 TraesCS2D01G331900 chr2B 499538690 499542551 3861 False 1560.333333 4298 94.810333 1 3588 3 chr2B.!!$F1 3587
3 TraesCS2D01G331900 chr6B 362490613 362491413 800 False 277.633333 462 90.000667 36 860 3 chr6B.!!$F1 824

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
752 827 0.172352 GTGAGCTCTCTCTTGGTCCG 59.828 60.0 16.19 0.00 40.03 4.79 F
1489 1586 0.109226 GTGCTCGAGTCCACCTACAC 60.109 60.0 15.13 7.03 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2184 2290 0.251564 ATCTGGAGATCCTCGCCGAT 60.252 55.000 0.00 0.00 39.36 4.18 R
3246 3387 1.207593 CGTCTGCGCAGGGAAAAAG 59.792 57.895 35.36 15.46 0.00 2.27 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
479 518 3.698029 TTTGACAGAGAAAAGCTGCAC 57.302 42.857 1.02 0.00 36.86 4.57
481 520 1.202521 TGACAGAGAAAAGCTGCACGA 60.203 47.619 1.02 0.00 36.86 4.35
590 633 1.770294 AGCTAGCTAGGTGGAGTGTC 58.230 55.000 24.15 3.01 31.96 3.67
608 660 4.578516 AGTGTCACTAGTATCAGCTAGCTG 59.421 45.833 34.48 34.48 41.49 4.24
622 674 8.868522 ATCAGCTAGCTGGAGATCTATATATC 57.131 38.462 37.60 0.00 43.75 1.63
623 675 7.810260 TCAGCTAGCTGGAGATCTATATATCA 58.190 38.462 37.60 14.94 43.75 2.15
627 679 7.814107 GCTAGCTGGAGATCTATATATCATTGC 59.186 40.741 7.70 0.93 0.00 3.56
724 785 9.905713 AAATTGAGCATCTACCTTATTTAGACA 57.094 29.630 0.00 0.00 34.92 3.41
744 815 5.183713 AGACATGCTATATGTGAGCTCTCTC 59.816 44.000 16.19 6.25 40.76 3.20
750 825 4.935352 ATATGTGAGCTCTCTCTTGGTC 57.065 45.455 16.19 0.00 40.03 4.02
752 827 0.172352 GTGAGCTCTCTCTTGGTCCG 59.828 60.000 16.19 0.00 40.03 4.79
799 874 8.626526 TGGAAACTCACTTTTGGTATTCTTTAC 58.373 33.333 0.00 0.00 0.00 2.01
906 983 1.144057 CTGCGGCGTAAAGGAGGAT 59.856 57.895 9.37 0.00 0.00 3.24
972 1052 4.028131 AGAAACGGATACAGTACCCATCA 58.972 43.478 0.00 0.00 0.00 3.07
993 1073 3.256960 TGAGAAGCCCACACCCCC 61.257 66.667 0.00 0.00 0.00 5.40
994 1074 3.256960 GAGAAGCCCACACCCCCA 61.257 66.667 0.00 0.00 0.00 4.96
995 1075 3.569200 GAGAAGCCCACACCCCCAC 62.569 68.421 0.00 0.00 0.00 4.61
996 1076 3.580319 GAAGCCCACACCCCCACT 61.580 66.667 0.00 0.00 0.00 4.00
1186 1283 2.438434 GGTGGGGATGAACAGCGG 60.438 66.667 0.00 0.00 0.00 5.52
1378 1475 1.294659 GCGAGGAAACTGCTGTGGAG 61.295 60.000 0.00 0.00 44.43 3.86
1489 1586 0.109226 GTGCTCGAGTCCACCTACAC 60.109 60.000 15.13 7.03 0.00 2.90
1521 1618 2.331132 GCTGCCAACACTCTCCTGC 61.331 63.158 0.00 0.00 0.00 4.85
1527 1624 1.475751 CCAACACTCTCCTGCACTTGT 60.476 52.381 0.00 0.00 0.00 3.16
1533 1630 1.673665 CTCCTGCACTTGTCCCAGC 60.674 63.158 0.00 0.00 0.00 4.85
1535 1632 3.664495 CTGCACTTGTCCCAGCAG 58.336 61.111 0.00 0.00 46.98 4.24
1750 1856 2.842256 GCATCATCTTGCAGCCCCG 61.842 63.158 0.00 0.00 42.31 5.73
1806 1912 1.079503 GTCGGAGCCTGTGAACAATC 58.920 55.000 0.00 0.00 0.00 2.67
1921 2027 2.443016 AGATTCCTCTCGGCCGCT 60.443 61.111 23.51 5.96 0.00 5.52
2069 2175 1.379916 CCACAACAGGGCCATCAGA 59.620 57.895 6.18 0.00 0.00 3.27
2480 2592 1.139498 TGCCTTGGGAGTGATTGGGA 61.139 55.000 0.00 0.00 0.00 4.37
2481 2593 0.394899 GCCTTGGGAGTGATTGGGAG 60.395 60.000 0.00 0.00 0.00 4.30
2482 2594 0.995024 CCTTGGGAGTGATTGGGAGT 59.005 55.000 0.00 0.00 0.00 3.85
2530 2642 1.273327 GGGACATTTGTCTGCTTTGGG 59.727 52.381 10.32 0.00 44.20 4.12
2578 2700 3.118775 GCATGTGGTAGTGGTGTATCAGA 60.119 47.826 0.00 0.00 0.00 3.27
2579 2701 4.686972 CATGTGGTAGTGGTGTATCAGAG 58.313 47.826 0.00 0.00 0.00 3.35
2580 2702 3.774734 TGTGGTAGTGGTGTATCAGAGT 58.225 45.455 0.00 0.00 0.00 3.24
2729 2851 1.405821 GTTCGATCGATCTGGACTGGT 59.594 52.381 20.18 0.00 0.00 4.00
2740 2862 7.578203 TCGATCTGGACTGGTGATATAGATAT 58.422 38.462 0.00 0.00 0.00 1.63
2741 2863 8.714906 TCGATCTGGACTGGTGATATAGATATA 58.285 37.037 0.00 0.00 0.00 0.86
2742 2864 9.513906 CGATCTGGACTGGTGATATAGATATAT 57.486 37.037 0.00 0.00 0.00 0.86
2814 2940 2.482721 CTGTAATGTCCGGCTTCGTTTT 59.517 45.455 0.00 0.00 0.00 2.43
2815 2941 3.661944 TGTAATGTCCGGCTTCGTTTTA 58.338 40.909 0.00 0.00 0.00 1.52
2887 3015 9.155975 GTGTGTAGTTAAATGATTGTCAGATCT 57.844 33.333 0.00 0.00 0.00 2.75
3009 3139 7.049799 AGAGTAATCAAGCTGACTTCCTATC 57.950 40.000 0.00 0.00 32.29 2.08
3010 3140 6.609212 AGAGTAATCAAGCTGACTTCCTATCA 59.391 38.462 0.00 0.00 32.29 2.15
3011 3141 6.578023 AGTAATCAAGCTGACTTCCTATCAC 58.422 40.000 0.00 0.00 32.29 3.06
3012 3142 5.690464 AATCAAGCTGACTTCCTATCACT 57.310 39.130 0.00 0.00 32.29 3.41
3013 3143 6.798427 AATCAAGCTGACTTCCTATCACTA 57.202 37.500 0.00 0.00 32.29 2.74
3014 3144 5.584253 TCAAGCTGACTTCCTATCACTAC 57.416 43.478 0.00 0.00 32.29 2.73
3051 3189 2.017138 TGCCGCGACATGATTTTCTA 57.983 45.000 8.23 0.00 0.00 2.10
3120 3258 3.498397 CACTCATGTTCCAAGTACCACAC 59.502 47.826 0.00 0.00 0.00 3.82
3125 3263 5.596361 TCATGTTCCAAGTACCACACAATTT 59.404 36.000 0.00 0.00 0.00 1.82
3204 3345 2.558313 GCACCTGCTGCTCGAAAC 59.442 61.111 0.00 0.00 43.33 2.78
3205 3346 2.253758 GCACCTGCTGCTCGAAACA 61.254 57.895 0.00 0.00 43.33 2.83
3208 3349 0.035317 ACCTGCTGCTCGAAACATGA 59.965 50.000 0.00 0.00 0.00 3.07
3209 3350 0.725686 CCTGCTGCTCGAAACATGAG 59.274 55.000 0.00 0.00 36.53 2.90
3210 3351 1.436600 CTGCTGCTCGAAACATGAGT 58.563 50.000 0.00 0.00 35.85 3.41
3212 3353 0.445436 GCTGCTCGAAACATGAGTGG 59.555 55.000 0.00 0.00 35.85 4.00
3213 3354 1.941209 GCTGCTCGAAACATGAGTGGA 60.941 52.381 0.00 0.00 35.85 4.02
3215 3356 2.807967 CTGCTCGAAACATGAGTGGAAA 59.192 45.455 0.00 0.00 35.85 3.13
3216 3357 3.210227 TGCTCGAAACATGAGTGGAAAA 58.790 40.909 0.00 0.00 35.85 2.29
3218 3359 4.083324 TGCTCGAAACATGAGTGGAAAATC 60.083 41.667 0.00 0.00 35.85 2.17
3219 3360 4.672801 GCTCGAAACATGAGTGGAAAATCC 60.673 45.833 0.00 0.00 35.85 3.01
3220 3361 4.393834 TCGAAACATGAGTGGAAAATCCA 58.606 39.130 0.00 0.00 45.98 3.41
3259 3400 0.951558 TGACTTCTTTTTCCCTGCGC 59.048 50.000 0.00 0.00 0.00 6.09
3316 3688 4.096311 CAGGTAGCACGTACGCATATATC 58.904 47.826 16.72 3.94 31.59 1.63
3588 4038 1.135139 TCTCGCTTGAGCACCTCATAC 59.865 52.381 3.65 0.00 40.39 2.39
3589 4039 0.179137 TCGCTTGAGCACCTCATACG 60.179 55.000 3.65 9.68 40.39 3.06
3590 4040 0.179137 CGCTTGAGCACCTCATACGA 60.179 55.000 3.65 0.00 40.39 3.43
3591 4041 1.565305 GCTTGAGCACCTCATACGAG 58.435 55.000 0.00 0.00 40.39 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
331 361 9.387257 GGGAGAGGATTAATTAAAGTTAACGAA 57.613 33.333 1.21 0.00 0.00 3.85
332 362 7.707893 CGGGAGAGGATTAATTAAAGTTAACGA 59.292 37.037 1.21 0.00 0.00 3.85
479 518 0.108138 GTGACAGGGGGTGATCTTCG 60.108 60.000 0.00 0.00 0.00 3.79
481 520 0.178861 AGGTGACAGGGGGTGATCTT 60.179 55.000 0.00 0.00 0.00 2.40
590 633 4.393834 TCTCCAGCTAGCTGATACTAGTG 58.606 47.826 40.03 23.74 46.30 2.74
608 660 7.868922 CAGCTGAGCAATGATATATAGATCTCC 59.131 40.741 8.42 0.00 0.00 3.71
646 698 6.099125 TGAGCTAGCTTTGGGTGTATATAACA 59.901 38.462 20.42 3.00 35.06 2.41
647 699 6.522054 TGAGCTAGCTTTGGGTGTATATAAC 58.478 40.000 20.42 0.07 0.00 1.89
648 700 6.740944 TGAGCTAGCTTTGGGTGTATATAA 57.259 37.500 20.42 0.00 0.00 0.98
649 701 6.496911 TCATGAGCTAGCTTTGGGTGTATATA 59.503 38.462 20.42 0.00 0.00 0.86
650 702 5.307976 TCATGAGCTAGCTTTGGGTGTATAT 59.692 40.000 20.42 0.00 0.00 0.86
651 703 4.653801 TCATGAGCTAGCTTTGGGTGTATA 59.346 41.667 20.42 0.00 0.00 1.47
652 704 3.455910 TCATGAGCTAGCTTTGGGTGTAT 59.544 43.478 20.42 1.34 0.00 2.29
653 705 2.837591 TCATGAGCTAGCTTTGGGTGTA 59.162 45.455 20.42 1.16 0.00 2.90
654 706 1.630369 TCATGAGCTAGCTTTGGGTGT 59.370 47.619 20.42 0.00 0.00 4.16
655 707 2.408271 TCATGAGCTAGCTTTGGGTG 57.592 50.000 20.42 12.99 0.00 4.61
656 708 3.659183 AATCATGAGCTAGCTTTGGGT 57.341 42.857 20.42 4.49 0.00 4.51
657 709 4.996788 AAAATCATGAGCTAGCTTTGGG 57.003 40.909 20.42 9.33 0.00 4.12
658 710 5.919141 GCATAAAATCATGAGCTAGCTTTGG 59.081 40.000 20.42 11.17 0.00 3.28
659 711 6.736123 AGCATAAAATCATGAGCTAGCTTTG 58.264 36.000 20.42 18.92 0.00 2.77
660 712 6.956202 AGCATAAAATCATGAGCTAGCTTT 57.044 33.333 20.42 9.72 0.00 3.51
661 713 6.956202 AAGCATAAAATCATGAGCTAGCTT 57.044 33.333 20.42 13.65 34.16 3.74
662 714 6.956202 AAAGCATAAAATCATGAGCTAGCT 57.044 33.333 19.45 19.45 0.00 3.32
663 715 7.042925 CCAAAAAGCATAAAATCATGAGCTAGC 60.043 37.037 6.62 6.62 0.00 3.42
664 716 7.977853 ACCAAAAAGCATAAAATCATGAGCTAG 59.022 33.333 0.09 0.00 0.00 3.42
665 717 7.839907 ACCAAAAAGCATAAAATCATGAGCTA 58.160 30.769 0.09 0.00 0.00 3.32
666 718 6.704310 ACCAAAAAGCATAAAATCATGAGCT 58.296 32.000 0.09 0.00 0.00 4.09
720 781 5.078949 AGAGAGCTCACATATAGCATGTCT 58.921 41.667 17.77 1.82 42.62 3.41
722 783 5.078949 AGAGAGAGCTCACATATAGCATGT 58.921 41.667 17.77 0.00 43.81 3.21
723 784 5.648178 AGAGAGAGCTCACATATAGCATG 57.352 43.478 17.77 0.00 43.81 4.06
724 785 5.047164 CCAAGAGAGAGCTCACATATAGCAT 60.047 44.000 17.77 0.00 43.81 3.79
744 815 1.138036 CATGCATGCACGGACCAAG 59.862 57.895 25.37 1.78 0.00 3.61
750 825 1.099295 ATCTGGACATGCATGCACGG 61.099 55.000 25.37 22.14 0.00 4.94
752 827 4.295870 CAAATATCTGGACATGCATGCAC 58.704 43.478 25.37 18.96 0.00 4.57
799 874 0.322456 TCGGAAAGTGGCCAATCAGG 60.322 55.000 7.24 2.83 41.84 3.86
906 983 7.492994 GGCAAGCGAATTAATTAAAACCCAATA 59.507 33.333 1.21 0.00 0.00 1.90
972 1052 1.073897 GGTGTGGGCTTCTCAGCTT 59.926 57.895 0.00 0.00 46.44 3.74
993 1073 1.436195 CGGTTGTGGTGTGGTGAGTG 61.436 60.000 0.00 0.00 0.00 3.51
994 1074 1.153249 CGGTTGTGGTGTGGTGAGT 60.153 57.895 0.00 0.00 0.00 3.41
995 1075 1.891919 CCGGTTGTGGTGTGGTGAG 60.892 63.158 0.00 0.00 0.00 3.51
996 1076 2.190843 CCGGTTGTGGTGTGGTGA 59.809 61.111 0.00 0.00 0.00 4.02
1289 1386 2.513897 CGGATCGCCCCCTTGTTC 60.514 66.667 0.00 0.00 0.00 3.18
1368 1465 0.979709 TCATCCTCCCTCCACAGCAG 60.980 60.000 0.00 0.00 0.00 4.24
1521 1618 2.674380 GGCCTGCTGGGACAAGTG 60.674 66.667 12.06 0.00 44.40 3.16
1601 1698 2.106938 TCGGCGACATGATCAGCC 59.893 61.111 4.99 12.56 41.09 4.85
1921 2027 3.147595 CGTCCTCGGGATCTGGCA 61.148 66.667 0.00 0.00 32.73 4.92
2184 2290 0.251564 ATCTGGAGATCCTCGCCGAT 60.252 55.000 0.00 0.00 39.36 4.18
2306 2415 4.025858 GCCTGCAGCCTGTCCTCA 62.026 66.667 8.66 0.00 34.35 3.86
2429 2538 2.925162 GATCAAAGTCCCGGGGAGCG 62.925 65.000 23.50 6.05 29.39 5.03
2480 2592 3.133183 GCTAGGGTTTTGCTAGCTCTACT 59.867 47.826 17.23 9.04 41.82 2.57
2481 2593 3.459145 GCTAGGGTTTTGCTAGCTCTAC 58.541 50.000 17.23 10.32 41.82 2.59
2482 2594 2.434702 GGCTAGGGTTTTGCTAGCTCTA 59.565 50.000 17.23 7.17 43.81 2.43
2578 2700 2.099921 GACACTGACAGACACTGACACT 59.900 50.000 10.08 0.00 33.33 3.55
2579 2701 2.159240 TGACACTGACAGACACTGACAC 60.159 50.000 10.08 0.00 33.33 3.67
2580 2702 2.099405 TGACACTGACAGACACTGACA 58.901 47.619 10.08 0.69 35.27 3.58
2742 2864 9.062524 TGTTTAGAAGAATTTTACTTGCAGCTA 57.937 29.630 0.00 0.00 0.00 3.32
2743 2865 7.940850 TGTTTAGAAGAATTTTACTTGCAGCT 58.059 30.769 0.00 0.00 0.00 4.24
2764 2886 6.150976 TGCTGCTTATAGCTTGTACATTGTTT 59.849 34.615 0.00 0.00 42.97 2.83
2803 2925 8.883789 TCAATTAAAAGTATAAAACGAAGCCG 57.116 30.769 0.00 0.00 42.50 5.52
2839 2965 3.451902 CACCAACATTAAGGGGATGCATT 59.548 43.478 0.00 0.00 0.00 3.56
2842 2968 2.166254 CACACCAACATTAAGGGGATGC 59.834 50.000 0.00 0.00 31.04 3.91
2887 3015 9.477484 GAACTCTGACTGAAAGAACTACATTTA 57.523 33.333 0.00 0.00 37.43 1.40
2969 3099 7.492524 TGATTACTCTAGTGAACCTGCATTAG 58.507 38.462 0.00 0.00 31.55 1.73
3009 3139 7.698130 GGCAATCATGTTTTTAGCTTAGTAGTG 59.302 37.037 0.00 0.00 0.00 2.74
3010 3140 7.414098 CGGCAATCATGTTTTTAGCTTAGTAGT 60.414 37.037 0.00 0.00 0.00 2.73
3011 3141 6.907212 CGGCAATCATGTTTTTAGCTTAGTAG 59.093 38.462 0.00 0.00 0.00 2.57
3012 3142 6.676943 GCGGCAATCATGTTTTTAGCTTAGTA 60.677 38.462 0.00 0.00 0.00 1.82
3013 3143 5.640732 CGGCAATCATGTTTTTAGCTTAGT 58.359 37.500 0.00 0.00 0.00 2.24
3014 3144 4.500477 GCGGCAATCATGTTTTTAGCTTAG 59.500 41.667 0.00 0.00 0.00 2.18
3090 3228 6.420913 ACTTGGAACATGAGTGTAAGTAGT 57.579 37.500 0.00 0.00 39.30 2.73
3097 3235 3.135712 TGTGGTACTTGGAACATGAGTGT 59.864 43.478 0.00 0.00 39.30 3.55
3163 3302 8.179148 GCTATATATGTAGCACTGCAACTAAG 57.821 38.462 22.47 0.00 45.03 2.18
3198 3339 4.393834 TGGATTTTCCACTCATGTTTCGA 58.606 39.130 0.00 0.00 42.67 3.71
3199 3340 4.764679 TGGATTTTCCACTCATGTTTCG 57.235 40.909 0.00 0.00 42.67 3.46
3210 3351 6.445451 TTTTTCATGGGATTGGATTTTCCA 57.555 33.333 0.00 0.00 46.61 3.53
3246 3387 1.207593 CGTCTGCGCAGGGAAAAAG 59.792 57.895 35.36 15.46 0.00 2.27
3251 3392 2.089887 TAACAACGTCTGCGCAGGGA 62.090 55.000 35.36 16.69 42.83 4.20
3259 3400 3.365220 GTGAAGCTAGCTAACAACGTCTG 59.635 47.826 19.70 0.00 0.00 3.51
3316 3688 2.487762 ACCAACAAGCATACACGATTGG 59.512 45.455 0.00 0.00 40.76 3.16
3489 3939 9.190858 GGCTTTTTGAAAATGACTTTTTGTTTT 57.809 25.926 7.62 0.00 37.65 2.43
3502 3952 5.008911 GGCATTTCAGTGGCTTTTTGAAAAT 59.991 36.000 3.38 0.00 42.20 1.82


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

AutoCloner maintained by Alex Coulton.