Multiple sequence alignment - TraesCS2A01G029200

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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 TraesCS2A01G029200 chr2A 100.000 2541 0 0 1 2541 13069952 13067412 0.000000e+00 4693.0
1 TraesCS2A01G029200 chr2A 95.260 865 11 8 79 931 13652851 13653697 0.000000e+00 1343.0
2 TraesCS2A01G029200 chr2A 94.302 860 22 7 79 927 19259413 19260256 0.000000e+00 1291.0
3 TraesCS2A01G029200 chr2A 93.750 864 14 8 79 931 18277516 18278350 0.000000e+00 1260.0
4 TraesCS2A01G029200 chr2A 93.837 860 14 6 79 927 16895432 16896263 0.000000e+00 1258.0
5 TraesCS2A01G029200 chr2A 93.837 860 13 11 79 927 19838350 19839180 0.000000e+00 1258.0
6 TraesCS2A01G029200 chr2A 93.080 867 30 10 79 933 19370706 19369858 0.000000e+00 1242.0
7 TraesCS2A01G029200 chr2A 80.221 1537 269 22 953 2473 13013266 13014783 0.000000e+00 1122.0
8 TraesCS2A01G029200 chr2A 82.328 945 167 0 1527 2471 13004110 13003166 0.000000e+00 821.0
9 TraesCS2A01G029200 chr2A 95.167 269 10 2 662 930 17636185 17635920 3.020000e-114 422.0
10 TraesCS2A01G029200 chr2B 91.001 1589 140 2 956 2541 19102532 19100944 0.000000e+00 2139.0
11 TraesCS2A01G029200 chr2B 93.883 1128 67 1 961 2088 18913718 18914843 0.000000e+00 1700.0
12 TraesCS2A01G029200 chr2B 86.285 1327 156 17 1239 2541 19084579 19083255 0.000000e+00 1419.0
13 TraesCS2A01G029200 chr2B 88.589 999 105 3 1543 2541 19077488 19076499 0.000000e+00 1205.0
14 TraesCS2A01G029200 chr2B 79.551 1560 296 18 968 2509 19075067 19073513 0.000000e+00 1092.0
15 TraesCS2A01G029200 chr2B 80.026 1522 263 28 968 2473 18950267 18948771 0.000000e+00 1088.0
16 TraesCS2A01G029200 chr2B 79.040 1541 288 20 956 2472 18955473 18953944 0.000000e+00 1024.0
17 TraesCS2A01G029200 chr2B 81.485 983 182 0 1524 2506 18922761 18923743 0.000000e+00 808.0
18 TraesCS2A01G029200 chr2B 73.634 421 94 12 981 1391 405262379 405262792 2.040000e-31 147.0
19 TraesCS2A01G029200 chr2D 89.827 983 85 2 1193 2174 12584193 12583225 0.000000e+00 1247.0
20 TraesCS2A01G029200 chr2D 80.365 1533 263 26 956 2473 12556630 12558139 0.000000e+00 1129.0
21 TraesCS2A01G029200 chr2D 79.737 1594 287 18 956 2531 12581474 12579899 0.000000e+00 1122.0
22 TraesCS2A01G029200 chr2D 79.571 1537 276 24 956 2465 12550685 12552210 0.000000e+00 1064.0
23 TraesCS2A01G029200 chr2D 91.862 639 21 6 79 717 72957176 72957783 0.000000e+00 863.0
24 TraesCS2A01G029200 chr2D 90.751 346 32 0 2196 2541 12583236 12582891 1.780000e-126 462.0
25 TraesCS2A01G029200 chr2D 76.471 442 102 2 1905 2345 406261787 406262227 3.270000e-59 239.0
26 TraesCS2A01G029200 chr5D 91.415 827 43 11 79 889 553354035 553353221 0.000000e+00 1109.0
27 TraesCS2A01G029200 chr5D 96.160 651 12 3 79 716 448608808 448609458 0.000000e+00 1051.0
28 TraesCS2A01G029200 chr5D 72.879 837 177 33 1588 2399 416258495 416257684 2.530000e-60 243.0
29 TraesCS2A01G029200 chrUn 96.319 652 11 3 79 717 132299174 132299825 0.000000e+00 1059.0
30 TraesCS2A01G029200 chrUn 94.090 643 32 6 3 644 26263936 26264573 0.000000e+00 972.0
31 TraesCS2A01G029200 chrUn 94.099 644 31 5 79 717 179792442 179791801 0.000000e+00 972.0
32 TraesCS2A01G029200 chr6D 93.769 658 37 4 3 657 473021220 473021876 0.000000e+00 985.0
33 TraesCS2A01G029200 chr6D 74.428 481 118 5 1893 2372 446103726 446104202 4.290000e-48 202.0
34 TraesCS2A01G029200 chr6D 75.899 278 61 6 956 1230 446102889 446103163 1.230000e-28 137.0
35 TraesCS2A01G029200 chr7D 93.663 647 28 6 79 717 598206060 598205419 0.000000e+00 955.0
36 TraesCS2A01G029200 chr7D 72.980 396 90 14 1920 2305 26559072 26558684 3.430000e-24 122.0
37 TraesCS2A01G029200 chr4D 91.862 639 18 8 79 716 466325000 466325605 0.000000e+00 861.0
38 TraesCS2A01G029200 chr4D 94.815 135 6 1 1 135 241460595 241460462 2.560000e-50 209.0
39 TraesCS2A01G029200 chr4D 100.000 31 0 0 2163 2193 5661341 5661311 9.820000e-05 58.4
40 TraesCS2A01G029200 chr6A 93.190 279 15 3 662 940 32042638 32042912 8.460000e-110 407.0
41 TraesCS2A01G029200 chr6A 94.030 134 8 0 2 135 92160555 92160688 1.190000e-48 204.0
42 TraesCS2A01G029200 chr5B 73.430 892 185 34 1534 2399 503116027 503115162 1.150000e-73 287.0
43 TraesCS2A01G029200 chr3B 96.296 135 4 1 1 135 558065256 558065389 1.180000e-53 220.0
44 TraesCS2A01G029200 chr4A 94.815 135 7 0 1 135 536535527 536535393 7.120000e-51 211.0
45 TraesCS2A01G029200 chr4A 72.281 469 108 19 1920 2377 710676295 710675838 2.650000e-25 126.0
46 TraesCS2A01G029200 chr6B 94.815 135 5 1 1 135 108266995 108267127 2.560000e-50 209.0
47 TraesCS2A01G029200 chr4B 93.382 136 8 1 1 135 598078643 598078508 1.540000e-47 200.0
48 TraesCS2A01G029200 chr4B 100.000 31 0 0 2163 2193 9946507 9946477 9.820000e-05 58.4


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 TraesCS2A01G029200 chr2A 13067412 13069952 2540 True 4693.000000 4693 100.000000 1 2541 1 chr2A.!!$R2 2540
1 TraesCS2A01G029200 chr2A 13652851 13653697 846 False 1343.000000 1343 95.260000 79 931 1 chr2A.!!$F2 852
2 TraesCS2A01G029200 chr2A 19259413 19260256 843 False 1291.000000 1291 94.302000 79 927 1 chr2A.!!$F5 848
3 TraesCS2A01G029200 chr2A 18277516 18278350 834 False 1260.000000 1260 93.750000 79 931 1 chr2A.!!$F4 852
4 TraesCS2A01G029200 chr2A 16895432 16896263 831 False 1258.000000 1258 93.837000 79 927 1 chr2A.!!$F3 848
5 TraesCS2A01G029200 chr2A 19838350 19839180 830 False 1258.000000 1258 93.837000 79 927 1 chr2A.!!$F6 848
6 TraesCS2A01G029200 chr2A 19369858 19370706 848 True 1242.000000 1242 93.080000 79 933 1 chr2A.!!$R4 854
7 TraesCS2A01G029200 chr2A 13013266 13014783 1517 False 1122.000000 1122 80.221000 953 2473 1 chr2A.!!$F1 1520
8 TraesCS2A01G029200 chr2A 13003166 13004110 944 True 821.000000 821 82.328000 1527 2471 1 chr2A.!!$R1 944
9 TraesCS2A01G029200 chr2B 19100944 19102532 1588 True 2139.000000 2139 91.001000 956 2541 1 chr2B.!!$R2 1585
10 TraesCS2A01G029200 chr2B 18913718 18914843 1125 False 1700.000000 1700 93.883000 961 2088 1 chr2B.!!$F1 1127
11 TraesCS2A01G029200 chr2B 19083255 19084579 1324 True 1419.000000 1419 86.285000 1239 2541 1 chr2B.!!$R1 1302
12 TraesCS2A01G029200 chr2B 19073513 19077488 3975 True 1148.500000 1205 84.070000 968 2541 2 chr2B.!!$R4 1573
13 TraesCS2A01G029200 chr2B 18948771 18955473 6702 True 1056.000000 1088 79.533000 956 2473 2 chr2B.!!$R3 1517
14 TraesCS2A01G029200 chr2B 18922761 18923743 982 False 808.000000 808 81.485000 1524 2506 1 chr2B.!!$F2 982
15 TraesCS2A01G029200 chr2D 12556630 12558139 1509 False 1129.000000 1129 80.365000 956 2473 1 chr2D.!!$F2 1517
16 TraesCS2A01G029200 chr2D 12550685 12552210 1525 False 1064.000000 1064 79.571000 956 2465 1 chr2D.!!$F1 1509
17 TraesCS2A01G029200 chr2D 12579899 12584193 4294 True 943.666667 1247 86.771667 956 2541 3 chr2D.!!$R1 1585
18 TraesCS2A01G029200 chr2D 72957176 72957783 607 False 863.000000 863 91.862000 79 717 1 chr2D.!!$F3 638
19 TraesCS2A01G029200 chr5D 553353221 553354035 814 True 1109.000000 1109 91.415000 79 889 1 chr5D.!!$R2 810
20 TraesCS2A01G029200 chr5D 448608808 448609458 650 False 1051.000000 1051 96.160000 79 716 1 chr5D.!!$F1 637
21 TraesCS2A01G029200 chr5D 416257684 416258495 811 True 243.000000 243 72.879000 1588 2399 1 chr5D.!!$R1 811
22 TraesCS2A01G029200 chrUn 132299174 132299825 651 False 1059.000000 1059 96.319000 79 717 1 chrUn.!!$F2 638
23 TraesCS2A01G029200 chrUn 26263936 26264573 637 False 972.000000 972 94.090000 3 644 1 chrUn.!!$F1 641
24 TraesCS2A01G029200 chrUn 179791801 179792442 641 True 972.000000 972 94.099000 79 717 1 chrUn.!!$R1 638
25 TraesCS2A01G029200 chr6D 473021220 473021876 656 False 985.000000 985 93.769000 3 657 1 chr6D.!!$F1 654
26 TraesCS2A01G029200 chr7D 598205419 598206060 641 True 955.000000 955 93.663000 79 717 1 chr7D.!!$R2 638
27 TraesCS2A01G029200 chr4D 466325000 466325605 605 False 861.000000 861 91.862000 79 716 1 chr4D.!!$F1 637
28 TraesCS2A01G029200 chr5B 503115162 503116027 865 True 287.000000 287 73.430000 1534 2399 1 chr5B.!!$R1 865

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
942 1011 1.008652 CCAATGGTGTGTGTGTGCG 60.009 57.895 0.0 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2126 11846 0.39113 GCCTCGTGATGTAGCACCAA 60.391 55.0 0.0 0.0 35.37 3.67 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
35 36 5.937975 AATGGCCATAACTTTTGCATACT 57.062 34.783 21.15 0.00 0.00 2.12
468 492 1.683790 CCGGAAGTTAAGCGTGCTCG 61.684 60.000 0.00 3.31 40.37 5.03
938 1007 4.909696 TTTTCTACCAATGGTGTGTGTG 57.090 40.909 16.41 0.00 36.19 3.82
941 1010 1.266718 CTACCAATGGTGTGTGTGTGC 59.733 52.381 16.41 0.00 36.19 4.57
942 1011 1.008652 CCAATGGTGTGTGTGTGCG 60.009 57.895 0.00 0.00 0.00 5.34
944 1013 3.179869 AATGGTGTGTGTGTGCGCG 62.180 57.895 0.00 0.00 0.00 6.86
978 2433 1.530419 GGTGTGTGTGCCATTCCCA 60.530 57.895 0.00 0.00 0.00 4.37
1401 2892 0.759959 TGGGCTACCACAACTTTCGA 59.240 50.000 0.00 0.00 43.37 3.71
1525 3085 7.760131 ATTGCATGTGTAATATTCAGTTTGC 57.240 32.000 0.00 0.00 0.00 3.68
1538 3099 3.664107 TCAGTTTGCGCAGATAAAGAGT 58.336 40.909 11.31 0.00 0.00 3.24
1761 8511 1.077858 TGGATGCTATGTGCGCCAA 60.078 52.632 4.18 0.00 46.63 4.52
2092 11812 1.381327 CCTAGAGGCGACCAAGGGA 60.381 63.158 0.00 0.00 0.00 4.20
2126 11846 2.031163 GCTGGTGCGAACAGGAGT 59.969 61.111 0.00 0.00 36.48 3.85
2127 11847 1.598130 GCTGGTGCGAACAGGAGTT 60.598 57.895 0.00 0.00 41.64 3.01
2153 11873 0.902984 ACATCACGAGGCAGTGGGTA 60.903 55.000 12.09 0.00 42.10 3.69
2260 11980 0.839946 AGCAGACCAATTCCCGCTAT 59.160 50.000 0.00 0.00 32.83 2.97
2278 11998 4.722700 GCGTGCATGGAGTGGGGT 62.723 66.667 8.27 0.00 0.00 4.95
2349 12072 2.588620 GATACGAGAGGTGATGGGAGT 58.411 52.381 0.00 0.00 0.00 3.85
2350 12073 3.498121 GGATACGAGAGGTGATGGGAGTA 60.498 52.174 0.00 0.00 0.00 2.59
2358 12084 1.044611 GTGATGGGAGTAGGAGAGGC 58.955 60.000 0.00 0.00 0.00 4.70
2395 12121 2.526873 AAGGCGGTGGAGTGGAGT 60.527 61.111 0.00 0.00 0.00 3.85
2484 12210 2.365617 AGGATGTACTATTGAGTGCGGG 59.634 50.000 0.00 0.00 40.92 6.13
2493 12219 2.851263 TTGAGTGCGGGTAAGAATGT 57.149 45.000 0.00 0.00 0.00 2.71
2497 12223 0.170339 GTGCGGGTAAGAATGTTGGC 59.830 55.000 0.00 0.00 0.00 4.52
2534 12268 1.667724 GCAGATCCAACCGACAGAATG 59.332 52.381 0.00 0.00 46.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.791801 AAAGTTATGGCCATTTTTACAAATTCT 57.208 25.926 26.37 1.57 29.41 2.40
10 11 7.167535 AGTATGCAAAAGTTATGGCCATTTTT 58.832 30.769 26.37 20.84 0.00 1.94
18 19 6.537301 TCCGAGTTAGTATGCAAAAGTTATGG 59.463 38.462 0.00 0.00 0.00 2.74
838 907 2.157073 GGTCGCGACTAAAGACCGC 61.157 63.158 35.50 14.31 43.96 5.68
839 908 4.068302 GGTCGCGACTAAAGACCG 57.932 61.111 35.50 0.00 43.96 4.79
841 910 4.171754 ACTAAATGGTCGCGACTAAAGAC 58.828 43.478 35.50 19.90 0.00 3.01
927 996 3.648982 CGCGCACACACACACCAT 61.649 61.111 8.75 0.00 0.00 3.55
967 1036 2.568090 CTGCGTTGGGAATGGCAC 59.432 61.111 0.00 0.00 0.00 5.01
968 1037 2.676121 CCTGCGTTGGGAATGGCA 60.676 61.111 0.00 0.00 0.00 4.92
978 2433 2.672996 GTGATGTGCCCCTGCGTT 60.673 61.111 0.00 0.00 41.78 4.84
1004 2459 2.747855 GGACCTTGGCCAGCTTCG 60.748 66.667 5.11 0.00 0.00 3.79
1525 3085 3.064958 TCGTCACCTACTCTTTATCTGCG 59.935 47.826 0.00 0.00 0.00 5.18
1538 3099 4.456911 GTCCATATATCCGTTCGTCACCTA 59.543 45.833 0.00 0.00 0.00 3.08
1590 3159 2.747460 GGAGGCGCATGTGCTTGA 60.747 61.111 28.86 0.00 39.32 3.02
1700 8450 6.711194 TCGTCAAAGGTGTTAACAATAATGGA 59.289 34.615 10.51 1.69 0.00 3.41
1761 8511 2.772515 GTGTAGATTGGTAGGGGAAGCT 59.227 50.000 0.00 0.00 0.00 3.74
1874 11578 2.026822 ACTCAAGGCATGACCGATCTTT 60.027 45.455 0.00 0.00 46.52 2.52
1999 11703 0.613260 ACAGGAAGTCATAGCCGCAA 59.387 50.000 0.00 0.00 0.00 4.85
2053 11772 2.917227 TCAGGAGGCAGCACGACA 60.917 61.111 0.00 0.00 0.00 4.35
2126 11846 0.391130 GCCTCGTGATGTAGCACCAA 60.391 55.000 0.00 0.00 35.37 3.67
2127 11847 1.218047 GCCTCGTGATGTAGCACCA 59.782 57.895 0.00 0.00 35.37 4.17
2153 11873 4.695560 GCAGTGCGTAAGGAAGGT 57.304 55.556 0.00 0.00 41.83 3.50
2260 11980 4.720902 CCCCACTCCATGCACGCA 62.721 66.667 0.00 0.00 0.00 5.24
2278 11998 1.002624 GCCGACTTCCATCCCAACA 60.003 57.895 0.00 0.00 0.00 3.33
2305 12025 2.592574 TCGACCACCTCACGACGT 60.593 61.111 0.00 0.00 0.00 4.34
2308 12028 1.674651 CTCCTCGACCACCTCACGA 60.675 63.158 0.00 0.00 34.90 4.35
2311 12031 1.000771 CCTCTCCTCGACCACCTCA 60.001 63.158 0.00 0.00 0.00 3.86
2349 12072 1.625879 TCCCTCCCTGCCTCTCCTA 60.626 63.158 0.00 0.00 0.00 2.94
2350 12073 2.955246 TCCCTCCCTGCCTCTCCT 60.955 66.667 0.00 0.00 0.00 3.69
2358 12084 2.506061 CGCCTCATCTCCCTCCCTG 61.506 68.421 0.00 0.00 0.00 4.45
2395 12121 2.506217 GCACGAACGGCGATCTCA 60.506 61.111 16.62 0.00 44.57 3.27
2484 12210 7.849804 TCTCAATTCTAGCCAACATTCTTAC 57.150 36.000 0.00 0.00 0.00 2.34
2493 12219 3.317149 GCATGCATCTCAATTCTAGCCAA 59.683 43.478 14.21 0.00 0.00 4.52
2497 12223 5.122554 GGATCTGCATGCATCTCAATTCTAG 59.877 44.000 22.97 4.74 0.00 2.43


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

AutoCloner maintained by Alex Coulton.