Multiple sequence alignment - TraesCS3A01G205500

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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 TraesCS3A01G205500 chr3A 100.000 2765 0 0 1 2765 361614373 361611609 0.000000e+00 5107.0
1 TraesCS3A01G205500 chr3D 96.746 1598 35 4 674 2263 277930640 277932228 0.000000e+00 2647.0
2 TraesCS3A01G205500 chr3D 92.843 503 30 5 2264 2765 277932386 277932883 0.000000e+00 725.0
3 TraesCS3A01G205500 chr7B 96.746 676 21 1 1 675 377594886 377594211 0.000000e+00 1125.0
4 TraesCS3A01G205500 chr5B 96.450 676 23 1 1 675 585013268 585012593 0.000000e+00 1114.0
5 TraesCS3A01G205500 chr5B 95.266 676 30 1 1 674 660928735 660928060 0.000000e+00 1070.0
6 TraesCS3A01G205500 chr4B 96.000 675 26 1 1 674 177225693 177225019 0.000000e+00 1096.0
7 TraesCS3A01G205500 chr3B 94.805 693 33 3 1 692 740858800 740859490 0.000000e+00 1077.0
8 TraesCS3A01G205500 chr3B 95.238 42 1 1 637 678 194627323 194627283 6.390000e-07 65.8
9 TraesCS3A01G205500 chrUn 95.538 650 27 2 25 674 12455938 12455291 0.000000e+00 1038.0
10 TraesCS3A01G205500 chr7A 96.055 507 18 1 1 507 40833661 40833157 0.000000e+00 824.0
11 TraesCS3A01G205500 chr7A 93.007 143 10 0 532 674 40832896 40832754 2.790000e-50 209.0
12 TraesCS3A01G205500 chr2D 87.329 513 35 8 32 540 12868856 12868370 6.690000e-156 560.0
13 TraesCS3A01G205500 chr2A 83.236 513 44 16 32 540 14957221 14956747 1.520000e-117 433.0


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 TraesCS3A01G205500 chr3A 361611609 361614373 2764 True 5107.0 5107 100.0000 1 2765 1 chr3A.!!$R1 2764
1 TraesCS3A01G205500 chr3D 277930640 277932883 2243 False 1686.0 2647 94.7945 674 2765 2 chr3D.!!$F1 2091
2 TraesCS3A01G205500 chr7B 377594211 377594886 675 True 1125.0 1125 96.7460 1 675 1 chr7B.!!$R1 674
3 TraesCS3A01G205500 chr5B 585012593 585013268 675 True 1114.0 1114 96.4500 1 675 1 chr5B.!!$R1 674
4 TraesCS3A01G205500 chr5B 660928060 660928735 675 True 1070.0 1070 95.2660 1 674 1 chr5B.!!$R2 673
5 TraesCS3A01G205500 chr4B 177225019 177225693 674 True 1096.0 1096 96.0000 1 674 1 chr4B.!!$R1 673
6 TraesCS3A01G205500 chr3B 740858800 740859490 690 False 1077.0 1077 94.8050 1 692 1 chr3B.!!$F1 691
7 TraesCS3A01G205500 chrUn 12455291 12455938 647 True 1038.0 1038 95.5380 25 674 1 chrUn.!!$R1 649
8 TraesCS3A01G205500 chr7A 40832754 40833661 907 True 516.5 824 94.5310 1 674 2 chr7A.!!$R1 673


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
936 1177 1.254954 GTCCGTGTAGGTCTCTTGGT 58.745 55.0 0.0 0.0 41.99 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2686 3097 0.602562 CCGCAACACAAATGGGATGT 59.397 50.0 0.0 0.0 32.93 3.06 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
204 205 8.907829 ATATTATGGAGATGGTCACTGTAGAT 57.092 34.615 0.00 0.00 0.00 1.98
205 206 9.997172 ATATTATGGAGATGGTCACTGTAGATA 57.003 33.333 0.00 0.00 0.00 1.98
324 329 1.630126 ATGGTTGAGCGAGCCAGGAT 61.630 55.000 0.00 0.00 35.56 3.24
345 350 7.543520 CAGGATTTTCTGGTCTTTTGCTATTTC 59.456 37.037 0.00 0.00 0.00 2.17
415 420 9.807649 CAGCTACATATGTACATATTGCTATGA 57.192 33.333 28.47 8.77 38.49 2.15
607 848 1.708341 AAGGTGCAATGAGGTGCTTT 58.292 45.000 0.00 0.00 45.17 3.51
687 928 8.215050 CCCAACCACTAGTATGGAATTATTGTA 58.785 37.037 18.41 0.00 43.02 2.41
697 938 3.465210 TGGAATTATTGTATGGGGCCAGA 59.535 43.478 4.39 0.00 0.00 3.86
719 960 3.129300 CCAGGGCGCTCGAATCTA 58.871 61.111 7.64 0.00 0.00 1.98
722 963 1.402984 CCAGGGCGCTCGAATCTATAC 60.403 57.143 7.64 0.00 0.00 1.47
847 1088 9.807649 GCAATTATCTTAACAAATCAAGTGGAT 57.192 29.630 0.00 0.00 38.05 3.41
859 1100 3.371034 TCAAGTGGATGAGTAATCGGGA 58.629 45.455 0.00 0.00 35.99 5.14
936 1177 1.254954 GTCCGTGTAGGTCTCTTGGT 58.745 55.000 0.00 0.00 41.99 3.67
1656 1897 1.737838 CCGATGGCTGTACAACACAT 58.262 50.000 0.00 1.59 36.29 3.21
1683 1924 1.264557 AGATTAGAGCCGTCATCGTCG 59.735 52.381 0.00 0.00 35.01 5.12
1939 2188 3.684788 GGCGGCCTTGTGAACTATATATG 59.315 47.826 12.87 0.00 0.00 1.78
1945 2194 6.992715 GGCCTTGTGAACTATATATGTTCTGT 59.007 38.462 19.63 0.00 42.86 3.41
2098 2347 7.171167 CAGGAGAAGTAGATGCATTTACTGATG 59.829 40.741 25.72 16.89 30.85 3.07
2108 2357 5.893687 TGCATTTACTGATGGCTTGTTATG 58.106 37.500 0.00 0.00 0.00 1.90
2109 2358 4.741676 GCATTTACTGATGGCTTGTTATGC 59.258 41.667 0.00 0.00 0.00 3.14
2110 2359 5.679382 GCATTTACTGATGGCTTGTTATGCA 60.679 40.000 0.00 0.00 34.13 3.96
2111 2360 6.509656 CATTTACTGATGGCTTGTTATGCAT 58.490 36.000 3.79 3.79 0.00 3.96
2112 2361 7.650890 CATTTACTGATGGCTTGTTATGCATA 58.349 34.615 1.16 1.16 0.00 3.14
2113 2362 7.822161 TTTACTGATGGCTTGTTATGCATAT 57.178 32.000 7.36 0.00 0.00 1.78
2124 2373 9.143631 GGCTTGTTATGCATATCATATTTTTCC 57.856 33.333 16.28 7.89 37.49 3.13
2146 2395 1.478631 GCCTGCTTATTTTGGCTCCT 58.521 50.000 0.00 0.00 41.92 3.69
2232 2481 5.959618 AACTACAGTATTGTTTTCTGGGC 57.040 39.130 0.00 0.00 38.76 5.36
2294 2700 4.148871 CGTAATATGCATCTTCTGACACCG 59.851 45.833 0.19 0.00 0.00 4.94
2314 2721 8.161699 ACACCGTTGTAGTTTAATTTCTTCAT 57.838 30.769 0.00 0.00 32.60 2.57
2346 2753 7.230849 AGATTTACTCAATTTGTTGATGGCA 57.769 32.000 0.00 0.00 0.00 4.92
2375 2782 4.396166 CACCCATCCACTTGATTACTGTTC 59.604 45.833 0.00 0.00 0.00 3.18
2549 2956 6.122277 ACCACACCACTCTAATCCAATAATG 58.878 40.000 0.00 0.00 0.00 1.90
2562 2969 7.951347 AATCCAATAATGAAGCTGAAGACTT 57.049 32.000 0.00 0.00 0.00 3.01
2596 3003 5.571357 CACGTCCTTTATTTTAACATGGCAC 59.429 40.000 0.00 0.00 0.00 5.01
2598 3005 6.655848 ACGTCCTTTATTTTAACATGGCACTA 59.344 34.615 0.00 0.00 0.00 2.74
2599 3006 7.148306 ACGTCCTTTATTTTAACATGGCACTAG 60.148 37.037 0.00 0.00 0.00 2.57
2615 3022 3.847467 GCACTAGCAAATGAAGCTATGCG 60.847 47.826 0.00 0.00 43.08 4.73
2627 3034 4.096231 TGAAGCTATGCGTTGCAACATTAT 59.904 37.500 28.01 19.48 43.62 1.28
2665 3076 5.943416 CACACCCCTAAATAACAATGACTCA 59.057 40.000 0.00 0.00 0.00 3.41
2666 3077 6.432783 CACACCCCTAAATAACAATGACTCAA 59.567 38.462 0.00 0.00 0.00 3.02
2667 3078 6.659242 ACACCCCTAAATAACAATGACTCAAG 59.341 38.462 0.00 0.00 0.00 3.02
2668 3079 6.884295 CACCCCTAAATAACAATGACTCAAGA 59.116 38.462 0.00 0.00 0.00 3.02
2669 3080 6.884836 ACCCCTAAATAACAATGACTCAAGAC 59.115 38.462 0.00 0.00 0.00 3.01
2670 3081 6.318900 CCCCTAAATAACAATGACTCAAGACC 59.681 42.308 0.00 0.00 0.00 3.85
2671 3082 7.112779 CCCTAAATAACAATGACTCAAGACCT 58.887 38.462 0.00 0.00 0.00 3.85
2686 3097 4.707934 TCAAGACCTCAATATGTCCACGTA 59.292 41.667 0.00 0.00 31.76 3.57
2711 3122 2.529151 CCATTTGTGTTGCGGCTTATC 58.471 47.619 0.00 0.00 0.00 1.75
2727 3138 4.567747 GGCTTATCTTCCTTCCAACCTTCA 60.568 45.833 0.00 0.00 0.00 3.02
2735 3146 0.834612 TTCCAACCTTCACTGACGGT 59.165 50.000 1.26 1.26 35.67 4.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
249 252 9.317936 CATACAACACTATGATACTGACATTGT 57.682 33.333 0.00 0.00 35.07 2.71
407 412 8.969260 ATTGACAATATGAAGTCTCATAGCAA 57.031 30.769 0.00 0.00 45.56 3.91
719 960 2.100631 GGACGTTGCTGCTGCGTAT 61.101 57.895 18.28 0.00 43.34 3.06
847 1088 1.514087 GCACGGTCCCGATTACTCA 59.486 57.895 13.54 0.00 42.83 3.41
859 1100 2.660552 CCGACAAGAACGCACGGT 60.661 61.111 0.00 0.00 38.97 4.83
916 1157 0.170561 CCAAGAGACCTACACGGACG 59.829 60.000 0.00 0.00 36.31 4.79
917 1158 1.254954 ACCAAGAGACCTACACGGAC 58.745 55.000 0.00 0.00 36.31 4.79
918 1159 1.891150 GAACCAAGAGACCTACACGGA 59.109 52.381 0.00 0.00 36.31 4.69
919 1160 1.893801 AGAACCAAGAGACCTACACGG 59.106 52.381 0.00 0.00 39.35 4.94
951 1192 0.538287 GGAATAGCCAGGGTGGATGC 60.538 60.000 0.00 0.00 40.96 3.91
958 1199 2.102578 CAGTTTTGGGAATAGCCAGGG 58.897 52.381 0.00 0.00 38.95 4.45
1324 1565 1.805254 TCTGTAAGAGGCCGTACGC 59.195 57.895 10.49 5.40 38.67 4.42
1564 1805 1.989966 ATTGTCGCGTCCTCGTCGAT 61.990 55.000 5.77 0.00 42.95 3.59
1641 1882 2.224329 ACCGTAATGTGTTGTACAGCCA 60.224 45.455 7.29 5.42 43.80 4.75
1683 1924 1.062206 CGAAGACCGGTAGCTCGAC 59.938 63.158 21.70 3.06 33.91 4.20
1786 2027 3.762288 ACACGATTACTAACTCTCAGCCA 59.238 43.478 0.00 0.00 0.00 4.75
1870 2119 9.583765 CAATGACAAATTTGGGAAATTTTGTTT 57.416 25.926 21.74 0.00 46.01 2.83
1939 2188 5.752098 GCATTTTGTAGATGCAACAGAAC 57.248 39.130 0.00 0.00 46.96 3.01
2044 2293 4.142924 CCGACGTGAATGAATCAACATCAA 60.143 41.667 0.00 0.00 40.50 2.57
2098 2347 9.143631 GGAAAAATATGATATGCATAACAAGCC 57.856 33.333 19.09 9.82 42.45 4.35
2108 2357 5.717119 CAGGCCAGGAAAAATATGATATGC 58.283 41.667 5.01 0.00 0.00 3.14
2109 2358 5.479375 AGCAGGCCAGGAAAAATATGATATG 59.521 40.000 5.01 0.00 0.00 1.78
2110 2359 5.648247 AGCAGGCCAGGAAAAATATGATAT 58.352 37.500 5.01 0.00 0.00 1.63
2111 2360 5.065613 AGCAGGCCAGGAAAAATATGATA 57.934 39.130 5.01 0.00 0.00 2.15
2112 2361 3.919834 AGCAGGCCAGGAAAAATATGAT 58.080 40.909 5.01 0.00 0.00 2.45
2113 2362 3.386932 AGCAGGCCAGGAAAAATATGA 57.613 42.857 5.01 0.00 0.00 2.15
2124 2373 3.746900 GCCAAAATAAGCAGGCCAG 57.253 52.632 5.01 0.00 41.25 4.85
2146 2395 4.706842 AAGCTACCAGAGTCCAGAAAAA 57.293 40.909 0.00 0.00 0.00 1.94
2212 2461 3.374058 CCGCCCAGAAAACAATACTGTAG 59.626 47.826 0.00 0.00 33.45 2.74
2232 2481 4.925576 CCGCTACCGCTACTGCCG 62.926 72.222 0.00 0.00 35.36 5.69
2245 2494 3.097614 ACTTGAGTAGTTCCATACCGCT 58.902 45.455 0.00 0.00 31.29 5.52
2248 2497 4.870991 GCTCAACTTGAGTAGTTCCATACC 59.129 45.833 18.16 0.00 45.29 2.73
2252 2501 2.364324 ACGCTCAACTTGAGTAGTTCCA 59.636 45.455 18.16 0.00 45.29 3.53
2294 2700 9.530129 CGAGTGATGAAGAAATTAAACTACAAC 57.470 33.333 0.00 0.00 0.00 3.32
2314 2721 8.708742 CAACAAATTGAGTAAATCTACGAGTGA 58.291 33.333 0.00 0.00 38.15 3.41
2346 2753 5.589367 AATCAAGTGGATGGGTGCTATAT 57.411 39.130 0.00 0.00 36.02 0.86
2375 2782 7.687005 TTTTGGTTGAATTAAACAACGCTAG 57.313 32.000 7.99 0.00 45.24 3.42
2403 2810 4.623647 GCCCCATTGAAATGCAACAGTTAT 60.624 41.667 0.00 0.00 39.78 1.89
2499 2906 1.914634 TTTTCATTGCAACGCACGTT 58.085 40.000 0.00 1.93 38.71 3.99
2500 2907 1.914634 TTTTTCATTGCAACGCACGT 58.085 40.000 0.00 0.00 38.71 4.49
2523 2930 5.975988 ATTGGATTAGAGTGGTGTGGTAT 57.024 39.130 0.00 0.00 0.00 2.73
2524 2931 6.877668 TTATTGGATTAGAGTGGTGTGGTA 57.122 37.500 0.00 0.00 0.00 3.25
2525 2932 5.772393 TTATTGGATTAGAGTGGTGTGGT 57.228 39.130 0.00 0.00 0.00 4.16
2527 2934 7.467811 GCTTCATTATTGGATTAGAGTGGTGTG 60.468 40.741 0.00 0.00 0.00 3.82
2528 2935 6.543831 GCTTCATTATTGGATTAGAGTGGTGT 59.456 38.462 0.00 0.00 0.00 4.16
2529 2936 6.769822 AGCTTCATTATTGGATTAGAGTGGTG 59.230 38.462 0.00 0.00 0.00 4.17
2530 2937 6.769822 CAGCTTCATTATTGGATTAGAGTGGT 59.230 38.462 0.00 0.00 0.00 4.16
2531 2938 6.994496 TCAGCTTCATTATTGGATTAGAGTGG 59.006 38.462 0.00 0.00 0.00 4.00
2533 2940 8.489489 TCTTCAGCTTCATTATTGGATTAGAGT 58.511 33.333 0.00 0.00 0.00 3.24
2537 2944 9.113838 GAAGTCTTCAGCTTCATTATTGGATTA 57.886 33.333 7.76 0.00 41.29 1.75
2549 2956 4.873259 GGGTCTATTGAAGTCTTCAGCTTC 59.127 45.833 14.75 6.79 41.38 3.86
2562 2969 5.687166 AATAAAGGACGTGGGTCTATTGA 57.313 39.130 0.00 0.00 42.97 2.57
2569 2976 5.184287 CCATGTTAAAATAAAGGACGTGGGT 59.816 40.000 0.00 0.00 41.49 4.51
2570 2977 5.646606 CCATGTTAAAATAAAGGACGTGGG 58.353 41.667 0.00 0.00 41.49 4.61
2596 3003 4.277258 CAACGCATAGCTTCATTTGCTAG 58.723 43.478 0.00 0.00 44.77 3.42
2598 3005 2.733227 GCAACGCATAGCTTCATTTGCT 60.733 45.455 0.00 0.00 43.79 3.91
2599 3006 1.585214 GCAACGCATAGCTTCATTTGC 59.415 47.619 0.00 0.00 0.00 3.68
2665 3076 4.464951 TGTACGTGGACATATTGAGGTCTT 59.535 41.667 0.00 0.00 36.60 3.01
2666 3077 4.021229 TGTACGTGGACATATTGAGGTCT 58.979 43.478 0.00 0.00 36.60 3.85
2667 3078 4.380841 TGTACGTGGACATATTGAGGTC 57.619 45.455 0.00 0.00 35.59 3.85
2668 3079 4.202223 GGATGTACGTGGACATATTGAGGT 60.202 45.833 3.97 0.00 40.18 3.85
2669 3080 4.307432 GGATGTACGTGGACATATTGAGG 58.693 47.826 3.97 0.00 40.18 3.86
2670 3081 4.202212 TGGGATGTACGTGGACATATTGAG 60.202 45.833 3.97 0.00 40.18 3.02
2671 3082 3.707102 TGGGATGTACGTGGACATATTGA 59.293 43.478 3.97 0.00 40.18 2.57
2686 3097 0.602562 CCGCAACACAAATGGGATGT 59.397 50.000 0.00 0.00 32.93 3.06
2711 3122 3.142174 GTCAGTGAAGGTTGGAAGGAAG 58.858 50.000 0.00 0.00 0.00 3.46
2727 3138 2.041976 CACAGAGGTCACCGTCAGT 58.958 57.895 0.00 0.00 0.00 3.41



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

AutoCloner maintained by Alex Coulton.