Multiple sequence alignment - TraesCS3D01G437500

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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 TraesCS3D01G437500 chr3D 100.000 3310 0 0 1 3310 548681247 548684556 0.000000e+00 6113
1 TraesCS3D01G437500 chr3B 93.067 2380 109 29 1 2336 727471667 727474034 0.000000e+00 3430
2 TraesCS3D01G437500 chr3B 87.042 764 43 17 2348 3067 727474070 727474821 0.000000e+00 811
3 TraesCS3D01G437500 chr3B 88.444 675 67 8 1636 2306 732908091 732907424 0.000000e+00 804
4 TraesCS3D01G437500 chr3B 85.217 690 73 21 890 1559 732908938 732908258 0.000000e+00 682
5 TraesCS3D01G437500 chr3B 97.200 250 7 0 3061 3310 727474851 727475100 1.100000e-114 424
6 TraesCS3D01G437500 chr3A 91.819 2188 106 33 361 2523 686169700 686171839 0.000000e+00 2981
7 TraesCS3D01G437500 chr3A 93.333 375 13 6 1 364 686169037 686169410 8.080000e-151 544
8 TraesCS3D01G437500 chr3A 82.993 588 78 11 1759 2343 686174003 686173435 2.280000e-141 512
9 TraesCS3D01G437500 chr6D 74.451 501 85 26 967 1452 287956 288428 3.390000e-40 176


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 TraesCS3D01G437500 chr3D 548681247 548684556 3309 False 6113.0 6113 100.000000 1 3310 1 chr3D.!!$F1 3309
1 TraesCS3D01G437500 chr3B 727471667 727475100 3433 False 1555.0 3430 92.436333 1 3310 3 chr3B.!!$F1 3309
2 TraesCS3D01G437500 chr3B 732907424 732908938 1514 True 743.0 804 86.830500 890 2306 2 chr3B.!!$R1 1416
3 TraesCS3D01G437500 chr3A 686169037 686171839 2802 False 1762.5 2981 92.576000 1 2523 2 chr3A.!!$F1 2522
4 TraesCS3D01G437500 chr3A 686173435 686174003 568 True 512.0 512 82.993000 1759 2343 1 chr3A.!!$R1 584

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
487 798 1.663695 ATTTGTGCCCCGTCGATAAG 58.336 50.000 0.0 0.0 0.0 1.73 F
1983 2471 1.519234 GAGGTCGCATCGCATCACA 60.519 57.895 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2043 2535 0.744874 CCGTCGGTCACCATCTACAT 59.255 55.0 2.08 0.0 0.00 2.29 R
3111 3713 0.168128 GGCCGAAGTGGTCAATTTCG 59.832 55.0 0.00 0.0 44.04 3.46 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
198 209 3.594603 ACGATCTTGACCGAAATGAGT 57.405 42.857 0.00 0.00 0.00 3.41
240 251 6.464222 ACTCTTTCATTTCTTGTCCGTATGA 58.536 36.000 0.00 0.00 0.00 2.15
350 363 4.963276 TTCATGCTACGGAAGGAAAATG 57.037 40.909 0.00 0.00 0.00 2.32
487 798 1.663695 ATTTGTGCCCCGTCGATAAG 58.336 50.000 0.00 0.00 0.00 1.73
522 833 8.117370 ACACAATTAAAACAATAACCGCAAAAC 58.883 29.630 0.00 0.00 0.00 2.43
589 900 3.981416 CGTATTCAGATACACATCCACGG 59.019 47.826 0.00 0.00 38.42 4.94
634 949 4.917415 CGGTGGCAATTTCTTTAGAAACAG 59.083 41.667 7.05 4.67 45.55 3.16
653 968 5.138125 ACAGATGCAATTTCCGACAAAAT 57.862 34.783 0.00 0.00 0.00 1.82
748 1072 5.933463 TGAAAATGTTCATTTTGCCATCCTC 59.067 36.000 22.60 10.28 38.88 3.71
884 1214 6.048509 GTGCCTTCTCAATCAAAAAGGAAAA 58.951 36.000 4.23 0.00 40.63 2.29
938 1280 9.794719 ATAAGTGCATGTGATAGAGTAGTAGTA 57.205 33.333 0.00 0.00 0.00 1.82
998 1346 4.023707 CGAAGCCAACAAGAAAAGTGAGAT 60.024 41.667 0.00 0.00 0.00 2.75
1053 1401 1.736645 CCTGCCGGACAAGTACGTG 60.737 63.158 5.05 7.29 34.48 4.49
1152 1500 2.203126 GCTCTTGGAGATGGCCGG 60.203 66.667 0.00 0.00 0.00 6.13
1173 1521 2.890808 GACAGGTCATTGGCGAGATA 57.109 50.000 0.00 0.00 0.00 1.98
1342 1722 2.190578 GTGATCCAGGGCTTCCGG 59.809 66.667 0.00 0.00 35.17 5.14
1983 2471 1.519234 GAGGTCGCATCGCATCACA 60.519 57.895 0.00 0.00 0.00 3.58
1984 2472 1.756375 GAGGTCGCATCGCATCACAC 61.756 60.000 0.00 0.00 0.00 3.82
1987 2475 2.100031 TCGCATCGCATCACACCAC 61.100 57.895 0.00 0.00 0.00 4.16
2011 2499 5.534654 CCTATCCTGTGGAAGAAGAGAGTAG 59.465 48.000 0.00 0.00 34.34 2.57
2012 2500 4.390129 TCCTGTGGAAGAAGAGAGTAGT 57.610 45.455 0.00 0.00 0.00 2.73
2013 2501 5.516059 TCCTGTGGAAGAAGAGAGTAGTA 57.484 43.478 0.00 0.00 0.00 1.82
2016 2504 6.215023 TCCTGTGGAAGAAGAGAGTAGTAGTA 59.785 42.308 0.00 0.00 0.00 1.82
2017 2505 7.057894 CCTGTGGAAGAAGAGAGTAGTAGTAT 58.942 42.308 0.00 0.00 0.00 2.12
2141 2633 2.709475 GCAACGCTTATCAGGCCG 59.291 61.111 0.00 0.00 0.00 6.13
2301 2793 3.940852 TGAAATGTTCAGGATCCATCACG 59.059 43.478 15.82 0.00 34.08 4.35
2315 2807 2.464865 CATCACGCCAAGTAGCTAGAC 58.535 52.381 0.00 0.00 0.00 2.59
2324 2816 0.613853 AGTAGCTAGACCCAACGCCA 60.614 55.000 0.00 0.00 0.00 5.69
2325 2817 0.248289 GTAGCTAGACCCAACGCCAA 59.752 55.000 0.00 0.00 0.00 4.52
2350 2868 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2370 2889 2.416547 CACACATCCTTCGACCATTGTC 59.583 50.000 0.00 0.00 38.18 3.18
2383 2902 5.694910 TCGACCATTGTCTTCTTAAGTTCAC 59.305 40.000 1.63 0.00 39.47 3.18
2393 2916 4.794278 TCTTAAGTTCACAGTGCCGATA 57.206 40.909 1.63 0.00 0.00 2.92
2396 2919 2.656560 AGTTCACAGTGCCGATAGTC 57.343 50.000 0.00 0.00 0.00 2.59
2397 2920 1.204941 AGTTCACAGTGCCGATAGTCC 59.795 52.381 0.00 0.00 0.00 3.85
2398 2921 0.172578 TTCACAGTGCCGATAGTCCG 59.827 55.000 0.00 0.00 0.00 4.79
2400 2923 0.736636 CACAGTGCCGATAGTCCGTA 59.263 55.000 0.00 0.00 0.00 4.02
2401 2924 1.022735 ACAGTGCCGATAGTCCGTAG 58.977 55.000 0.00 0.00 0.00 3.51
2404 2927 2.097825 AGTGCCGATAGTCCGTAGTTT 58.902 47.619 0.00 0.00 0.00 2.66
2405 2928 3.065786 CAGTGCCGATAGTCCGTAGTTTA 59.934 47.826 0.00 0.00 0.00 2.01
2406 2929 3.887716 AGTGCCGATAGTCCGTAGTTTAT 59.112 43.478 0.00 0.00 0.00 1.40
2407 2930 4.340381 AGTGCCGATAGTCCGTAGTTTATT 59.660 41.667 0.00 0.00 0.00 1.40
2408 2931 5.532406 AGTGCCGATAGTCCGTAGTTTATTA 59.468 40.000 0.00 0.00 0.00 0.98
2446 2969 6.771076 TGATTGTTAAATCGTGTATGCTGAC 58.229 36.000 0.00 0.00 44.47 3.51
2477 3000 3.296628 CAGTCGGTGGTTTTGATTTTCG 58.703 45.455 0.00 0.00 0.00 3.46
2480 3003 4.998672 AGTCGGTGGTTTTGATTTTCGATA 59.001 37.500 0.00 0.00 0.00 2.92
2481 3004 5.646360 AGTCGGTGGTTTTGATTTTCGATAT 59.354 36.000 0.00 0.00 0.00 1.63
2529 3054 4.100373 AGGAACAGAGTAATTGGAGCTCT 58.900 43.478 14.64 0.00 39.89 4.09
2611 3161 6.769512 ACAAACTTCAGTGGTACATGATAGT 58.230 36.000 0.00 0.83 44.52 2.12
2635 3185 9.793259 AGTTTCTCTTATGTGAAATAAACCTCA 57.207 29.630 8.53 0.00 37.78 3.86
2672 3222 2.777536 ACTGGATCCTTCAGTGGCA 58.222 52.632 14.23 0.00 43.07 4.92
2676 3226 1.034292 GGATCCTTCAGTGGCAAGGC 61.034 60.000 3.84 0.00 40.43 4.35
2677 3227 0.034670 GATCCTTCAGTGGCAAGGCT 60.035 55.000 5.85 0.00 40.43 4.58
2692 3259 1.130054 AGGCTGCACTGGAGGAGAAA 61.130 55.000 0.50 0.00 0.00 2.52
2696 3263 1.301293 GCACTGGAGGAGAAAGGGG 59.699 63.158 0.00 0.00 0.00 4.79
2741 3308 3.740832 TGTTTGATTAGAGTCACTGCGTG 59.259 43.478 0.00 2.79 34.45 5.34
2743 3310 3.217599 TGATTAGAGTCACTGCGTGTC 57.782 47.619 8.22 3.86 34.79 3.67
2744 3311 2.820197 TGATTAGAGTCACTGCGTGTCT 59.180 45.455 7.79 7.79 34.96 3.41
2745 3312 2.706555 TTAGAGTCACTGCGTGTCTG 57.293 50.000 11.51 0.00 32.72 3.51
2746 3313 0.241213 TAGAGTCACTGCGTGTCTGC 59.759 55.000 11.51 5.71 32.72 4.26
2747 3314 2.355126 AGTCACTGCGTGTCTGCG 60.355 61.111 8.22 0.00 37.81 5.18
2748 3315 2.658593 GTCACTGCGTGTCTGCGT 60.659 61.111 8.22 0.00 37.81 5.24
2749 3316 2.354656 TCACTGCGTGTCTGCGTC 60.355 61.111 8.22 0.00 37.81 5.19
2750 3317 2.355126 CACTGCGTGTCTGCGTCT 60.355 61.111 1.24 0.00 37.81 4.18
2751 3318 2.355126 ACTGCGTGTCTGCGTCTG 60.355 61.111 0.00 0.00 37.81 3.51
2752 3319 2.050077 CTGCGTGTCTGCGTCTGA 60.050 61.111 0.00 0.00 37.81 3.27
2753 3320 1.445066 CTGCGTGTCTGCGTCTGAT 60.445 57.895 0.00 0.00 37.81 2.90
2763 3330 2.237143 TCTGCGTCTGATTTTGAGGGAT 59.763 45.455 0.00 0.00 0.00 3.85
2787 3354 0.676466 TATCCCAACTTGCGCCACTG 60.676 55.000 4.18 0.00 0.00 3.66
2793 3360 2.743928 CTTGCGCCACTGTCCTCC 60.744 66.667 4.18 0.00 0.00 4.30
2816 3383 1.534235 AGCCTTCCACGTCTGGTCT 60.534 57.895 0.00 0.00 38.90 3.85
2817 3384 1.374758 GCCTTCCACGTCTGGTCTG 60.375 63.158 0.00 0.00 38.90 3.51
2922 3489 0.040058 TTGGCATGGGAGATTGTGCT 59.960 50.000 0.00 0.00 37.70 4.40
2928 3495 0.325933 TGGGAGATTGTGCTGAGGTG 59.674 55.000 0.00 0.00 0.00 4.00
2955 3522 1.537202 CTGCCTGTACTTGCCAGAAAC 59.463 52.381 0.00 0.00 31.38 2.78
2961 3528 2.942376 TGTACTTGCCAGAAACTGTGTG 59.058 45.455 0.00 0.00 0.00 3.82
2967 3534 1.534595 GCCAGAAACTGTGTGCACAAG 60.535 52.381 23.59 21.60 41.33 3.16
2968 3535 1.066002 CCAGAAACTGTGTGCACAAGG 59.934 52.381 23.59 18.87 41.33 3.61
3014 3581 5.224888 TCTCGTAAACACGTTTAAGCAGAT 58.775 37.500 9.78 0.00 36.86 2.90
3070 3672 1.616725 GGGTCACATGGATCTTGCCAA 60.617 52.381 0.00 0.00 42.16 4.52
3095 3697 9.745018 AACAAAAAGGAGATCAAAGATCAGATA 57.255 29.630 9.43 0.00 0.00 1.98
3108 3710 4.529897 AGATCAGATAAGCATTTGCCACA 58.470 39.130 0.00 0.00 43.38 4.17
3111 3713 3.691118 TCAGATAAGCATTTGCCACAGAC 59.309 43.478 0.00 0.00 43.38 3.51
3184 3786 6.317391 CAGTCAAGTTTTGAAGAAACTCCTCT 59.683 38.462 4.80 2.14 42.15 3.69
3286 3888 2.197875 ACCGCCGCTCCCTAGTAT 59.802 61.111 0.00 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
198 209 4.720046 AGAGTAATGGTGCTCTAGATCGA 58.280 43.478 0.00 0.00 44.18 3.59
240 251 3.282745 CTGCGTCACGTGGCTACCT 62.283 63.158 19.37 0.00 0.00 3.08
397 705 0.759436 TTGGATCGGAGGGAGTAGCC 60.759 60.000 0.00 0.00 0.00 3.93
589 900 5.293569 CCGTCCCATATTGTGAAAGAGTAAC 59.706 44.000 0.00 0.00 0.00 2.50
634 949 6.811170 TCCTTAATTTTGTCGGAAATTGCATC 59.189 34.615 12.29 0.00 39.05 3.91
653 968 6.183360 TGGCAATTTTTACAGCAAGTCCTTAA 60.183 34.615 0.00 0.00 0.00 1.85
748 1072 5.972107 ATTCAATGAAAGTTCACTGGGAG 57.028 39.130 0.00 0.00 40.49 4.30
810 1134 3.122297 GCATCTCTTCTTCGACATGGAG 58.878 50.000 0.00 0.00 0.00 3.86
811 1135 2.497273 TGCATCTCTTCTTCGACATGGA 59.503 45.455 0.00 0.00 0.00 3.41
812 1136 2.864946 CTGCATCTCTTCTTCGACATGG 59.135 50.000 0.00 0.00 0.00 3.66
895 1237 6.070767 TGCACTTATACTAGTTTGAGAAGGCT 60.071 38.462 11.25 0.00 0.00 4.58
965 1313 3.026630 TGTTGGCTTCGACTTCTGTAG 57.973 47.619 0.00 0.00 0.00 2.74
998 1346 3.808466 AGTCGCAGATGAGCTTCATTA 57.192 42.857 0.00 0.00 37.20 1.90
1053 1401 4.084888 CGTTTCTCCGGCGGCAAC 62.085 66.667 23.83 21.07 0.00 4.17
1152 1500 2.434185 TCGCCAATGACCTGTCGC 60.434 61.111 0.00 0.00 0.00 5.19
1173 1521 3.338250 TCCTTGCCGGCCTCCATT 61.338 61.111 26.77 0.00 0.00 3.16
1250 1630 3.251484 AGAACTGGTCAGGATTCAGGAA 58.749 45.455 0.00 0.00 33.19 3.36
1608 2090 2.224257 GGTTGCAACCCATGAACAATGT 60.224 45.455 34.36 0.00 43.43 2.71
1833 2319 1.065928 CGTGAGGATGTAGCGGTCC 59.934 63.158 0.00 0.00 34.64 4.46
1987 2475 4.285863 ACTCTCTTCTTCCACAGGATAGG 58.714 47.826 0.00 0.00 0.00 2.57
2043 2535 0.744874 CCGTCGGTCACCATCTACAT 59.255 55.000 2.08 0.00 0.00 2.29
2141 2633 2.108952 ACCAATCCTGGAGCCCATATTC 59.891 50.000 1.52 0.00 46.92 1.75
2301 2793 1.739371 CGTTGGGTCTAGCTACTTGGC 60.739 57.143 0.00 0.00 0.00 4.52
2315 2807 1.226831 GTGTGTGTTTGGCGTTGGG 60.227 57.895 0.00 0.00 0.00 4.12
2324 2816 1.950216 TGTGTGTGTGTGTGTGTGTTT 59.050 42.857 0.00 0.00 0.00 2.83
2325 2817 1.265635 GTGTGTGTGTGTGTGTGTGTT 59.734 47.619 0.00 0.00 0.00 3.32
2350 2868 2.699954 GACAATGGTCGAAGGATGTGT 58.300 47.619 0.00 0.00 33.68 3.72
2370 2889 3.390135 TCGGCACTGTGAACTTAAGAAG 58.610 45.455 12.86 1.43 0.00 2.85
2383 2902 1.022735 ACTACGGACTATCGGCACTG 58.977 55.000 0.00 0.00 0.00 3.66
2393 2916 4.531732 TGTTGGGGTAATAAACTACGGACT 59.468 41.667 0.00 0.00 0.00 3.85
2396 2919 7.862512 TTATTGTTGGGGTAATAAACTACGG 57.137 36.000 0.00 0.00 0.00 4.02
2397 2920 9.724839 CATTTATTGTTGGGGTAATAAACTACG 57.275 33.333 0.00 0.00 39.89 3.51
2443 2966 4.673403 GACTGCACATGTCGGTCA 57.327 55.556 22.09 8.59 39.13 4.02
2477 3000 9.299963 TGCAGTGCAAAATATAACAACAATATC 57.700 29.630 17.26 0.00 34.76 1.63
2480 3003 7.959689 TTGCAGTGCAAAATATAACAACAAT 57.040 28.000 27.79 0.00 45.96 2.71
2529 3054 3.259876 ACAAAGCTACATGTCGGTCCTTA 59.740 43.478 0.00 0.00 0.00 2.69
2573 3098 9.988350 CACTGAAGTTTGTACCATATATTTCAC 57.012 33.333 0.00 0.00 0.00 3.18
2577 3102 9.609346 GTACCACTGAAGTTTGTACCATATATT 57.391 33.333 8.08 0.00 32.11 1.28
2632 3182 5.928839 AGTGTAGCATACTGAACTTGTTGAG 59.071 40.000 0.00 0.00 43.54 3.02
2635 3185 4.997395 CCAGTGTAGCATACTGAACTTGTT 59.003 41.667 14.27 0.00 46.52 2.83
2672 3222 1.130054 TTCTCCTCCAGTGCAGCCTT 61.130 55.000 0.00 0.00 0.00 4.35
2676 3226 0.035630 CCCTTTCTCCTCCAGTGCAG 60.036 60.000 0.00 0.00 0.00 4.41
2677 3227 1.492133 CCCCTTTCTCCTCCAGTGCA 61.492 60.000 0.00 0.00 0.00 4.57
2681 3248 1.301293 GCACCCCTTTCTCCTCCAG 59.699 63.158 0.00 0.00 0.00 3.86
2692 3259 2.255406 TGCAAAAATGTATGCACCCCT 58.745 42.857 0.00 0.00 46.87 4.79
2741 3308 1.734465 CCCTCAAAATCAGACGCAGAC 59.266 52.381 0.00 0.00 0.00 3.51
2743 3310 2.099141 TCCCTCAAAATCAGACGCAG 57.901 50.000 0.00 0.00 0.00 5.18
2744 3311 2.787473 ATCCCTCAAAATCAGACGCA 57.213 45.000 0.00 0.00 0.00 5.24
2745 3312 3.430218 CGATATCCCTCAAAATCAGACGC 59.570 47.826 0.00 0.00 0.00 5.19
2746 3313 4.621991 ACGATATCCCTCAAAATCAGACG 58.378 43.478 0.00 0.00 0.00 4.18
2747 3314 6.814146 GGATACGATATCCCTCAAAATCAGAC 59.186 42.308 11.03 0.00 32.09 3.51
2748 3315 6.936279 GGATACGATATCCCTCAAAATCAGA 58.064 40.000 11.03 0.00 32.09 3.27
2763 3330 1.539496 GGCGCAAGTTGGGATACGATA 60.539 52.381 22.92 0.00 41.68 2.92
2787 3354 1.079057 GGAAGGCTGAACGGAGGAC 60.079 63.158 0.00 0.00 0.00 3.85
2793 3360 1.006102 AGACGTGGAAGGCTGAACG 60.006 57.895 13.34 13.34 41.64 3.95
2854 3421 4.867599 GGTCGGGTCGATGCCGTC 62.868 72.222 0.00 0.00 38.42 4.79
2891 3458 1.448540 ATGCCAAACTCCTCTCGCG 60.449 57.895 0.00 0.00 0.00 5.87
2939 3506 3.002656 CACACAGTTTCTGGCAAGTACAG 59.997 47.826 0.00 0.00 35.51 2.74
2955 3522 0.669619 TGCATTCCTTGTGCACACAG 59.330 50.000 21.56 18.73 46.76 3.66
2961 3528 3.077359 ACTCTTACTGCATTCCTTGTGC 58.923 45.455 0.00 0.00 42.81 4.57
2967 3534 3.624861 CCATGTGACTCTTACTGCATTCC 59.375 47.826 0.00 0.00 0.00 3.01
2968 3535 4.507710 TCCATGTGACTCTTACTGCATTC 58.492 43.478 0.00 0.00 0.00 2.67
3014 3581 7.814587 GCACTACTCTGCATATGTTATATGTCA 59.185 37.037 4.29 7.70 37.11 3.58
3070 3672 9.745018 TTATCTGATCTTTGATCTCCTTTTTGT 57.255 29.630 8.71 0.00 0.00 2.83
3095 3697 1.317613 TTCGTCTGTGGCAAATGCTT 58.682 45.000 5.25 0.00 41.70 3.91
3108 3710 2.413837 CCGAAGTGGTCAATTTCGTCT 58.586 47.619 4.39 0.00 41.39 4.18
3111 3713 0.168128 GGCCGAAGTGGTCAATTTCG 59.832 55.000 0.00 0.00 44.04 3.46


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

AutoCloner maintained by Alex Coulton.