Multiple sequence alignment - TraesCS2D01G253200

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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 TraesCS2D01G253200 chr2D 100.000 2097 0 0 390 2486 305507021 305504925 0.000000e+00 3873.0
1 TraesCS2D01G253200 chr2D 87.705 244 29 1 1549 1792 305442761 305442519 1.460000e-72 283.0
2 TraesCS2D01G253200 chr2D 100.000 132 0 0 1 132 305507410 305507279 6.870000e-61 244.0
3 TraesCS2D01G253200 chr2D 81.250 192 22 9 2208 2389 95532246 95532433 2.580000e-30 143.0
4 TraesCS2D01G253200 chr2D 80.435 184 24 10 2208 2382 637752639 637752819 2.010000e-26 130.0
5 TraesCS2D01G253200 chr2A 92.593 1809 93 13 670 2459 384331638 384329852 0.000000e+00 2560.0
6 TraesCS2D01G253200 chr2A 90.722 291 17 6 390 671 384332185 384331896 1.800000e-101 379.0
7 TraesCS2D01G253200 chr2A 96.212 132 5 0 1 132 384332403 384332272 1.500000e-52 217.0
8 TraesCS2D01G253200 chr2B 94.597 1203 28 12 707 1875 373747928 373746729 0.000000e+00 1827.0
9 TraesCS2D01G253200 chr2B 92.881 295 19 2 2165 2459 373746390 373746098 6.350000e-116 427.0
10 TraesCS2D01G253200 chr2B 91.176 306 14 7 390 683 373748469 373748165 1.070000e-108 403.0
11 TraesCS2D01G253200 chr2B 88.506 261 23 5 1910 2168 373746726 373746471 2.400000e-80 309.0
12 TraesCS2D01G253200 chr2B 100.000 132 0 0 1 132 373748691 373748560 6.870000e-61 244.0
13 TraesCS2D01G253200 chr4A 83.270 263 22 13 2208 2459 342449476 342449727 3.220000e-54 222.0
14 TraesCS2D01G253200 chr4A 95.122 41 2 0 1749 1789 604032225 604032185 5.740000e-07 65.8
15 TraesCS2D01G253200 chr4B 82.949 217 25 8 2208 2416 50454028 50454240 4.220000e-43 185.0
16 TraesCS2D01G253200 chr4B 95.455 44 2 0 1749 1792 277407906 277407949 1.230000e-08 71.3
17 TraesCS2D01G253200 chr4B 100.000 30 0 0 2457 2486 75177650 75177621 3.450000e-04 56.5
18 TraesCS2D01G253200 chr4B 96.970 33 0 1 2454 2486 94000928 94000959 1.000000e-03 54.7
19 TraesCS2D01G253200 chr7B 83.060 183 16 10 2208 2379 630895032 630894854 4.280000e-33 152.0
20 TraesCS2D01G253200 chr7B 94.444 36 1 1 2451 2486 636140221 636140187 1.000000e-03 54.7
21 TraesCS2D01G253200 chr7B 94.444 36 1 1 2451 2486 636197832 636197798 1.000000e-03 54.7
22 TraesCS2D01G253200 chr3A 80.093 216 28 10 2211 2416 308787851 308787641 1.990000e-31 147.0
23 TraesCS2D01G253200 chr6D 78.879 232 28 18 2201 2418 166168309 166168533 1.200000e-28 137.0
24 TraesCS2D01G253200 chr6D 100.000 30 0 0 2457 2486 469512862 469512891 3.450000e-04 56.5
25 TraesCS2D01G253200 chr5A 77.358 265 39 13 2208 2459 633641469 633641213 1.200000e-28 137.0
26 TraesCS2D01G253200 chr3B 78.733 221 29 14 2209 2418 752701263 752701050 5.580000e-27 132.0
27 TraesCS2D01G253200 chrUn 95.556 45 2 0 1745 1789 73917631 73917587 3.430000e-09 73.1
28 TraesCS2D01G253200 chr3D 95.556 45 2 0 1745 1789 143960763 143960807 3.430000e-09 73.1
29 TraesCS2D01G253200 chr1B 93.750 48 3 0 1745 1792 510225609 510225562 3.430000e-09 73.1
30 TraesCS2D01G253200 chr1B 97.297 37 0 1 2450 2486 616884576 616884611 7.420000e-06 62.1
31 TraesCS2D01G253200 chr1B 92.105 38 1 2 2451 2486 527396360 527396397 4.000000e-03 52.8
32 TraesCS2D01G253200 chr7A 95.349 43 2 0 1747 1789 670237244 670237286 4.440000e-08 69.4
33 TraesCS2D01G253200 chr6B 94.737 38 0 2 2451 2486 671031318 671031281 9.600000e-05 58.4
34 TraesCS2D01G253200 chr1A 100.000 30 0 0 2457 2486 521143375 521143404 3.450000e-04 56.5


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 TraesCS2D01G253200 chr2D 305504925 305507410 2485 True 2058.5 3873 100.000000 1 2486 2 chr2D.!!$R2 2485
1 TraesCS2D01G253200 chr2A 384329852 384332403 2551 True 1052.0 2560 93.175667 1 2459 3 chr2A.!!$R1 2458
2 TraesCS2D01G253200 chr2B 373746098 373748691 2593 True 642.0 1827 93.432000 1 2459 5 chr2B.!!$R1 2458

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
982 1344 0.961857 AGCAATCGCAGCATCCACAA 60.962 50.0 0.0 0.0 42.27 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1951 2350 0.891373 CTCCTCAAAGTCAGCCGAGA 59.109 55.0 0.0 0.0 0.0 4.04 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
458 460 2.327002 AATACAGCTTGCGCATGCCG 62.327 55.000 35.95 30.49 41.78 5.69
481 483 6.091305 CCGTGCTGTTATAATATCAGGTCATG 59.909 42.308 4.33 0.00 0.00 3.07
504 507 7.690952 TGTTGTTGATGATCAATCATTCTCA 57.309 32.000 11.46 0.00 46.84 3.27
519 522 6.856135 TCATTCTCATTATCACAGTGATGC 57.144 37.500 24.15 0.00 37.70 3.91
526 529 2.343484 ATCACAGTGATGCCAGGATG 57.657 50.000 15.67 0.00 35.43 3.51
540 543 2.923121 CAGGATGGGTATTCAGTGTGG 58.077 52.381 0.00 0.00 0.00 4.17
541 544 2.505407 CAGGATGGGTATTCAGTGTGGA 59.495 50.000 0.00 0.00 0.00 4.02
576 587 5.298989 TGGTGTATGTGACCTTACAACTT 57.701 39.130 10.76 0.00 38.85 2.66
619 632 2.808523 TTCATTGGCAAATTCGTGCA 57.191 40.000 3.01 0.00 46.81 4.57
637 650 1.268352 GCATGCCACGTAAAACCAAGA 59.732 47.619 6.36 0.00 0.00 3.02
942 1304 5.181245 CGCTCCACAAGATTTAAGAAAGGAA 59.819 40.000 0.00 0.00 0.00 3.36
982 1344 0.961857 AGCAATCGCAGCATCCACAA 60.962 50.000 0.00 0.00 42.27 3.33
988 1350 1.081906 GCAGCATCCACAACACACG 60.082 57.895 0.00 0.00 0.00 4.49
1027 1389 2.685017 AGCTCTCCGCCATGACCA 60.685 61.111 0.00 0.00 40.39 4.02
1096 1458 4.680237 CCACGCTGCCGTCCTTGA 62.680 66.667 0.00 0.00 46.39 3.02
1097 1459 3.114616 CACGCTGCCGTCCTTGAG 61.115 66.667 0.00 0.00 46.39 3.02
1467 1834 1.180456 TCAAGAACACCGGCGTCCTA 61.180 55.000 6.01 0.00 0.00 2.94
1521 1888 1.756538 TCGATAGCTGTTCTGCATCCA 59.243 47.619 0.00 0.00 34.99 3.41
1610 1981 6.798482 ACAATGTATGTGTATGCATCTTTGG 58.202 36.000 0.19 0.00 41.93 3.28
1757 2128 8.105197 TCCAAAAACTAAATTAGTACTCCCTCC 58.895 37.037 6.04 0.00 38.26 4.30
1781 2152 9.459640 TCCGTGAAGAAATATAAGATCGTTTAG 57.540 33.333 0.00 0.00 0.00 1.85
1848 2247 8.085909 AGTAACAATAAAAGCGCAAAATAACCT 58.914 29.630 11.47 0.00 0.00 3.50
1873 2272 2.477176 CCTCCTCTCACGGCTCGAG 61.477 68.421 8.45 8.45 0.00 4.04
1906 2305 3.412408 GCCTCCTCTTCCACCCCC 61.412 72.222 0.00 0.00 0.00 5.40
1951 2350 0.670546 CAGAGGTGTTGCCGACGAAT 60.671 55.000 0.00 0.00 43.70 3.34
2056 2456 2.388232 CCGGCGTTAGAGTTGTGCC 61.388 63.158 6.01 0.00 42.29 5.01
2064 2464 4.505191 GCGTTAGAGTTGTGCCGAATATTA 59.495 41.667 0.00 0.00 0.00 0.98
2070 2470 5.690409 AGAGTTGTGCCGAATATTATGTACG 59.310 40.000 0.00 0.00 0.00 3.67
2077 2477 5.474532 TGCCGAATATTATGTACGAGGTAGT 59.525 40.000 0.00 0.00 0.00 2.73
2094 2494 8.046107 ACGAGGTAGTTTATAGTTAGACTCTGT 58.954 37.037 0.00 0.00 0.00 3.41
2122 2522 8.628348 CGTACATCGTGTAGACAGGGTATGTC 62.628 50.000 10.95 0.00 45.27 3.06
2129 2529 1.295423 ACAGGGTATGTCGTGGTGC 59.705 57.895 0.00 0.00 37.75 5.01
2189 2673 6.889722 AGTAACAACCTATGCCAACATAACAT 59.110 34.615 0.00 0.00 38.29 2.71
2277 2761 1.257743 GCTCAGGGATGTAGCCGATA 58.742 55.000 0.00 0.00 0.00 2.92
2304 2788 4.336713 GGTGAACCTCATTAGCAAATCTCC 59.663 45.833 0.00 0.00 0.00 3.71
2323 2807 1.372997 GTGTCGTGCCTCGTGTGAT 60.373 57.895 0.00 0.00 40.80 3.06
2333 2817 2.484264 GCCTCGTGTGATTTGCTTAGTT 59.516 45.455 0.00 0.00 0.00 2.24
2392 2876 2.816087 TCATGAGCAAGTTTCAAGGAGC 59.184 45.455 0.00 0.00 0.00 4.70
2402 2886 5.916661 AGTTTCAAGGAGCTCGTAGATTA 57.083 39.130 9.76 0.00 33.89 1.75
2439 2923 2.490115 GGTGCCAATTTCGTATGGTTCA 59.510 45.455 0.00 0.00 39.00 3.18
2459 2943 2.038295 CACTTGGAAGCAGGAGAGAAGT 59.962 50.000 0.00 0.00 0.00 3.01
2460 2944 2.038295 ACTTGGAAGCAGGAGAGAAGTG 59.962 50.000 0.00 0.00 0.00 3.16
2461 2945 2.015456 TGGAAGCAGGAGAGAAGTGA 57.985 50.000 0.00 0.00 0.00 3.41
2462 2946 1.898472 TGGAAGCAGGAGAGAAGTGAG 59.102 52.381 0.00 0.00 0.00 3.51
2463 2947 1.206849 GGAAGCAGGAGAGAAGTGAGG 59.793 57.143 0.00 0.00 0.00 3.86
2464 2948 1.206849 GAAGCAGGAGAGAAGTGAGGG 59.793 57.143 0.00 0.00 0.00 4.30
2465 2949 0.411452 AGCAGGAGAGAAGTGAGGGA 59.589 55.000 0.00 0.00 0.00 4.20
2466 2950 1.203237 AGCAGGAGAGAAGTGAGGGAA 60.203 52.381 0.00 0.00 0.00 3.97
2467 2951 1.625818 GCAGGAGAGAAGTGAGGGAAA 59.374 52.381 0.00 0.00 0.00 3.13
2468 2952 2.238395 GCAGGAGAGAAGTGAGGGAAAT 59.762 50.000 0.00 0.00 0.00 2.17
2469 2953 3.452627 GCAGGAGAGAAGTGAGGGAAATA 59.547 47.826 0.00 0.00 0.00 1.40
2470 2954 4.102367 GCAGGAGAGAAGTGAGGGAAATAT 59.898 45.833 0.00 0.00 0.00 1.28
2471 2955 5.609423 CAGGAGAGAAGTGAGGGAAATATG 58.391 45.833 0.00 0.00 0.00 1.78
2472 2956 4.102367 AGGAGAGAAGTGAGGGAAATATGC 59.898 45.833 0.00 0.00 0.00 3.14
2473 2957 4.384940 GAGAGAAGTGAGGGAAATATGCC 58.615 47.826 0.00 0.00 37.30 4.40
2474 2958 3.137360 AGAGAAGTGAGGGAAATATGCCC 59.863 47.826 5.89 5.89 46.40 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
458 460 7.969536 ACATGACCTGATATTATAACAGCAC 57.030 36.000 0.00 2.05 0.00 4.40
462 464 9.898152 TCAACAACATGACCTGATATTATAACA 57.102 29.630 0.00 0.00 0.00 2.41
504 507 4.395625 CATCCTGGCATCACTGTGATAAT 58.604 43.478 21.88 0.00 34.28 1.28
519 522 2.421952 CCACACTGAATACCCATCCTGG 60.422 54.545 0.00 0.00 37.25 4.45
526 529 4.099113 GGTAGTACTCCACACTGAATACCC 59.901 50.000 0.00 0.00 0.00 3.69
576 587 6.839124 AATAAAGTGTGATGCATCTTCCAA 57.161 33.333 26.32 3.81 0.00 3.53
619 632 4.864704 AAATCTTGGTTTTACGTGGCAT 57.135 36.364 0.00 0.00 0.00 4.40
804 1166 1.406887 GCCTGCCAGTTCGGATAAGAA 60.407 52.381 0.00 0.00 36.56 2.52
942 1304 0.250467 AGGTGCAATGCTCAACGAGT 60.250 50.000 6.82 0.00 31.39 4.18
982 1344 2.742372 GGCTGCGGATTCGTGTGT 60.742 61.111 0.00 0.00 38.89 3.72
1095 1457 1.687996 CCCTGAGACCTCTTCCTCCTC 60.688 61.905 0.00 0.00 0.00 3.71
1096 1458 0.338120 CCCTGAGACCTCTTCCTCCT 59.662 60.000 0.00 0.00 0.00 3.69
1097 1459 1.334384 GCCCTGAGACCTCTTCCTCC 61.334 65.000 0.00 0.00 0.00 4.30
1467 1834 2.625790 GTTCTAGCCGATGATCTGGTCT 59.374 50.000 0.00 0.20 0.00 3.85
1521 1888 3.424639 TACATGGAGCGCGCGATGT 62.425 57.895 35.03 35.03 33.64 3.06
1690 2061 0.716108 GCACAAGACGATCTTCACCG 59.284 55.000 1.65 0.00 33.78 4.94
1848 2247 3.749064 GTGAGAGGAGGCGACGCA 61.749 66.667 23.09 0.00 0.00 5.24
1873 2272 3.119096 GCGTCGCTGGTTTCTCCC 61.119 66.667 10.68 0.00 34.77 4.30
1951 2350 0.891373 CTCCTCAAAGTCAGCCGAGA 59.109 55.000 0.00 0.00 0.00 4.04
1960 2359 2.234143 GCCAAAGAAGCTCCTCAAAGT 58.766 47.619 0.00 0.00 0.00 2.66
2037 2437 1.666872 GCACAACTCTAACGCCGGT 60.667 57.895 1.90 0.00 0.00 5.28
2039 2439 3.165498 GGCACAACTCTAACGCCG 58.835 61.111 0.00 0.00 32.14 6.46
2064 2464 9.844257 AGTCTAACTATAAACTACCTCGTACAT 57.156 33.333 0.00 0.00 0.00 2.29
2070 2470 9.176460 ACACAGAGTCTAACTATAAACTACCTC 57.824 37.037 0.00 0.00 0.00 3.85
2077 2477 8.552083 TGTACGACACAGAGTCTAACTATAAA 57.448 34.615 0.00 0.00 45.32 1.40
2094 2494 2.417586 CCTGTCTACACGATGTACGACA 59.582 50.000 17.82 17.82 45.77 4.35
2129 2529 5.327737 AGGATACAAGAGTCCTACTAGGG 57.672 47.826 2.04 0.00 42.93 3.53
2189 2673 1.897423 CTCCCCTGCGTGTATGTCA 59.103 57.895 0.00 0.00 0.00 3.58
2277 2761 3.627395 TGCTAATGAGGTTCACCGAAT 57.373 42.857 0.00 0.00 42.08 3.34
2291 2775 2.930040 CACGACACGGAGATTTGCTAAT 59.070 45.455 0.00 0.00 0.00 1.73
2304 2788 3.394874 CACACGAGGCACGACACG 61.395 66.667 12.15 0.00 45.77 4.49
2323 2807 4.570772 GCGATCCACTGATAACTAAGCAAA 59.429 41.667 0.00 0.00 0.00 3.68
2333 2817 4.422073 AATTTGAGGCGATCCACTGATA 57.578 40.909 0.00 0.00 33.74 2.15
2392 2876 8.673711 CCTTCCTCTAGATCAATAATCTACGAG 58.326 40.741 0.00 10.96 43.17 4.18
2402 2886 2.708325 GGCACCCTTCCTCTAGATCAAT 59.292 50.000 0.00 0.00 0.00 2.57
2439 2923 2.038295 CACTTCTCTCCTGCTTCCAAGT 59.962 50.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.