Multiple sequence alignment - TraesCS2B01G092200

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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 TraesCS2B01G092200 chr2B 100.000 3580 0 0 1 3580 53083465 53087044 0.000000e+00 6612.0
1 TraesCS2B01G092200 chr2B 96.335 1610 37 6 10 1598 53197873 53199481 0.000000e+00 2627.0
2 TraesCS2B01G092200 chr2B 96.335 1610 37 6 10 1598 53219850 53221458 0.000000e+00 2627.0
3 TraesCS2B01G092200 chr2B 88.613 1572 137 21 869 2438 53045911 53047442 0.000000e+00 1873.0
4 TraesCS2B01G092200 chr2B 97.774 1078 24 0 613 1690 53308106 53309183 0.000000e+00 1858.0
5 TraesCS2B01G092200 chr2B 85.999 1407 159 20 1038 2437 53055591 53056966 0.000000e+00 1472.0
6 TraesCS2B01G092200 chr2B 91.455 983 49 8 1594 2574 53199901 53200850 0.000000e+00 1317.0
7 TraesCS2B01G092200 chr2B 91.141 982 54 8 1594 2574 53221878 53222827 0.000000e+00 1301.0
8 TraesCS2B01G092200 chr2B 92.951 837 49 3 1740 2574 53309181 53310009 0.000000e+00 1210.0
9 TraesCS2B01G092200 chr2B 95.326 599 23 5 12 607 53307220 53307816 0.000000e+00 946.0
10 TraesCS2B01G092200 chr2B 81.055 512 76 13 10 505 53313786 53314292 4.330000e-104 388.0
11 TraesCS2B01G092200 chr2B 81.511 503 63 18 10 502 53050018 53050500 1.560000e-103 387.0
12 TraesCS2B01G092200 chr2B 80.385 520 81 13 15 518 53105558 53106072 3.370000e-100 375.0
13 TraesCS2B01G092200 chr2D 94.018 1237 67 5 997 2227 32427365 32428600 0.000000e+00 1868.0
14 TraesCS2B01G092200 chr2D 88.303 1556 137 19 885 2438 32400642 32402154 0.000000e+00 1823.0
15 TraesCS2B01G092200 chr2D 86.022 930 104 15 938 1865 32409092 32409997 0.000000e+00 974.0
16 TraesCS2B01G092200 chr2D 90.141 710 40 9 90 789 32426413 32427102 0.000000e+00 896.0
17 TraesCS2B01G092200 chr2D 88.583 254 21 1 2222 2475 32429096 32429341 5.810000e-78 302.0
18 TraesCS2B01G092200 chr2D 79.310 116 13 7 800 911 32427252 32427360 1.780000e-08 71.3
19 TraesCS2B01G092200 chr2A 88.546 1554 136 18 880 2431 35384144 35385657 0.000000e+00 1845.0
20 TraesCS2B01G092200 chr2A 86.182 1498 165 22 945 2437 35474244 35475704 0.000000e+00 1581.0
21 TraesCS2B01G092200 chr2A 94.106 492 23 5 10 499 35487706 35488193 0.000000e+00 743.0
22 TraesCS2B01G092200 chr2A 86.292 445 57 4 1795 2236 35476092 35476535 6.950000e-132 481.0
23 TraesCS2B01G092200 chr2A 83.936 498 56 13 9 501 35393716 35394194 4.210000e-124 455.0
24 TraesCS2B01G092200 chr5D 94.542 971 46 5 2611 3580 381694843 381693879 0.000000e+00 1493.0
25 TraesCS2B01G092200 chr1B 89.715 982 82 12 2612 3580 323618158 323619133 0.000000e+00 1236.0
26 TraesCS2B01G092200 chr6D 94.992 659 29 4 2607 3264 464650286 464649631 0.000000e+00 1031.0
27 TraesCS2B01G092200 chr6D 85.635 362 26 4 3244 3580 464649616 464649256 1.220000e-94 357.0
28 TraesCS2B01G092200 chr6D 73.832 214 42 13 3320 3525 464649626 464649419 4.960000e-09 73.1
29 TraesCS2B01G092200 chr7D 97.368 38 0 1 468 505 27554151 27554115 2.980000e-06 63.9
30 TraesCS2B01G092200 chr3D 97.368 38 0 1 468 505 589873527 589873491 2.980000e-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 TraesCS2B01G092200 chr2B 53083465 53087044 3579 False 6612.000000 6612 100.000000 1 3580 1 chr2B.!!$F2 3579
1 TraesCS2B01G092200 chr2B 53197873 53200850 2977 False 1972.000000 2627 93.895000 10 2574 2 chr2B.!!$F5 2564
2 TraesCS2B01G092200 chr2B 53219850 53222827 2977 False 1964.000000 2627 93.738000 10 2574 2 chr2B.!!$F6 2564
3 TraesCS2B01G092200 chr2B 53055591 53056966 1375 False 1472.000000 1472 85.999000 1038 2437 1 chr2B.!!$F1 1399
4 TraesCS2B01G092200 chr2B 53045911 53050500 4589 False 1130.000000 1873 85.062000 10 2438 2 chr2B.!!$F4 2428
5 TraesCS2B01G092200 chr2B 53307220 53314292 7072 False 1100.500000 1858 91.776500 10 2574 4 chr2B.!!$F7 2564
6 TraesCS2B01G092200 chr2B 53105558 53106072 514 False 375.000000 375 80.385000 15 518 1 chr2B.!!$F3 503
7 TraesCS2B01G092200 chr2D 32400642 32402154 1512 False 1823.000000 1823 88.303000 885 2438 1 chr2D.!!$F1 1553
8 TraesCS2B01G092200 chr2D 32409092 32409997 905 False 974.000000 974 86.022000 938 1865 1 chr2D.!!$F2 927
9 TraesCS2B01G092200 chr2D 32426413 32429341 2928 False 784.325000 1868 88.013000 90 2475 4 chr2D.!!$F3 2385
10 TraesCS2B01G092200 chr2A 35384144 35385657 1513 False 1845.000000 1845 88.546000 880 2431 1 chr2A.!!$F1 1551
11 TraesCS2B01G092200 chr2A 35474244 35476535 2291 False 1031.000000 1581 86.237000 945 2437 2 chr2A.!!$F4 1492
12 TraesCS2B01G092200 chr5D 381693879 381694843 964 True 1493.000000 1493 94.542000 2611 3580 1 chr5D.!!$R1 969
13 TraesCS2B01G092200 chr1B 323618158 323619133 975 False 1236.000000 1236 89.715000 2612 3580 1 chr1B.!!$F1 968
14 TraesCS2B01G092200 chr6D 464649256 464650286 1030 True 487.033333 1031 84.819667 2607 3580 3 chr6D.!!$R1 973

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
195 200 0.250684 TGGACTGCGGAAATTCAGCA 60.251 50.0 18.78 18.78 44.85 4.41 F
1519 2065 0.039437 ACGACGATGACGACTGCTTT 60.039 50.0 0.00 0.00 42.66 3.51 F
1921 3969 0.455295 CTCGAGAAGAGCGGACACAC 60.455 60.0 6.58 0.00 40.54 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1990 4042 0.107654 CATTCTCTCCACGAACCCCC 60.108 60.000 0.00 0.00 0.0 5.40 R
2332 4884 1.144057 CTACATCTCCGCGGCCTTT 59.856 57.895 23.51 5.76 0.0 3.11 R
3378 7754 1.770294 TTCAAAAAGCTGGAACCGGT 58.230 45.000 0.00 0.00 0.0 5.28 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
83 84 5.934625 AGTTGTTCATGTCCATCTCTACAAC 59.065 40.000 0.00 0.00 42.51 3.32
105 108 1.273886 GGACACTTGGTGAGACTCCTC 59.726 57.143 4.62 0.00 36.96 3.71
181 185 0.793617 TCTTCCCCTTCCTCTGGACT 59.206 55.000 0.00 0.00 0.00 3.85
195 200 0.250684 TGGACTGCGGAAATTCAGCA 60.251 50.000 18.78 18.78 44.85 4.41
292 309 5.313520 TGCAATACTTGTGTGAATCCATG 57.686 39.130 0.00 0.00 0.00 3.66
302 319 9.295825 ACTTGTGTGAATCCATGTTATAAAAGA 57.704 29.630 0.00 0.00 0.00 2.52
373 390 5.757320 CGCTTATGAGTTCCATCTGAAGATT 59.243 40.000 0.00 0.00 36.71 2.40
414 431 5.869753 AACTCTTCACAAAATGATCCTCG 57.130 39.130 0.00 0.00 37.11 4.63
559 595 2.427232 GGGAAAAACTGCCCGTAAAC 57.573 50.000 0.00 0.00 34.00 2.01
603 639 6.128363 GGAATCGATTTTACGGGATGGTAATC 60.128 42.308 12.81 0.00 32.79 1.75
660 980 8.776119 AGACTAGCTTGGCCATATATAATTCAT 58.224 33.333 6.09 0.00 0.00 2.57
1362 1902 2.430075 CGATGTGCACGTCGTGGA 60.430 61.111 40.13 21.30 46.84 4.02
1513 2059 1.393597 CCAACGACGACGATGACGAC 61.394 60.000 17.82 0.00 43.20 4.34
1519 2065 0.039437 ACGACGATGACGACTGCTTT 60.039 50.000 0.00 0.00 42.66 3.51
1670 2640 4.228567 TGCTCGTCAACACCGCCA 62.229 61.111 0.00 0.00 0.00 5.69
1739 2761 1.288127 GTCCCGATATTCCCGGTCG 59.712 63.158 0.00 1.94 45.14 4.79
1849 3895 1.284715 CTCGGTGCTGTACGTGTCA 59.715 57.895 0.00 0.00 0.00 3.58
1921 3969 0.455295 CTCGAGAAGAGCGGACACAC 60.455 60.000 6.58 0.00 40.54 3.82
2310 4862 3.800863 GCTCGGCGAGACGTCTGA 61.801 66.667 38.56 12.97 34.94 3.27
2332 4884 4.735132 CGGGCCGCAAAGAGACGA 62.735 66.667 15.42 0.00 0.00 4.20
2348 4900 2.125106 GAAAGGCCGCGGAGATGT 60.125 61.111 33.48 8.45 0.00 3.06
2519 5097 1.338337 ACGGATTCGATAGTGCTCCTG 59.662 52.381 0.00 0.00 40.11 3.86
2615 5256 4.735338 GCGACATATTGCTTAAGAAAAGGC 59.265 41.667 6.67 0.00 31.75 4.35
2616 5257 5.449177 GCGACATATTGCTTAAGAAAAGGCT 60.449 40.000 6.67 0.00 31.75 4.58
2712 6818 0.745486 TACACAGCGCCGCTCTACTA 60.745 55.000 9.54 0.00 36.40 1.82
2747 6861 5.042979 TCTCCTCTCCTTATCCTTTCCTTCT 60.043 44.000 0.00 0.00 0.00 2.85
2813 6931 1.639298 GCTCCAAGCTACTGCGTTGG 61.639 60.000 10.67 10.67 45.42 3.77
2839 6957 2.260524 AAGGCCTCCTCCTCTCCCT 61.261 63.158 5.23 0.00 34.82 4.20
2847 6965 0.471022 CCTCCTCTCCCTTAGCTCCC 60.471 65.000 0.00 0.00 0.00 4.30
2979 7098 4.347453 CTGCCGCTGGTTGTTGCC 62.347 66.667 0.00 0.00 0.00 4.52
3013 7132 2.196925 CGCGGTAGGAGCAGGAGAT 61.197 63.158 0.00 0.00 34.19 2.75
3199 7537 2.607635 TGCATCCTTCTAAATCGCGTTC 59.392 45.455 5.77 0.00 0.00 3.95
3293 7669 3.502211 CCGGTTGTAGCTTTTTGATCAGT 59.498 43.478 0.00 0.00 0.00 3.41
3378 7754 6.094742 TCAGCCGATTGCAACTTTTATAATCA 59.905 34.615 0.00 0.00 44.83 2.57
3425 7823 5.175859 CGGTTCCAGCTTCTGATTAGTTTA 58.824 41.667 0.00 0.00 32.44 2.01
3461 7862 1.392510 CGCCGGTAGTAGCTTTTTGAC 59.607 52.381 1.90 0.00 0.00 3.18
3463 7864 3.072211 GCCGGTAGTAGCTTTTTGACTT 58.928 45.455 1.90 0.00 0.00 3.01
3513 7915 2.098870 GCATCGTTTTAAATCGCCGAC 58.901 47.619 12.72 0.00 0.00 4.79
3549 7956 1.862827 ACTCACCGTTTTGTAACTCGC 59.137 47.619 0.00 0.00 31.89 5.03
3570 7977 1.579429 GCCACCGGTTTTGCTACAG 59.421 57.895 2.97 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.636206 CCCAAAACAAGTATGAGAGGCTAC 59.364 45.833 0.00 0.00 0.00 3.58
7 8 4.288626 ACCCAAAACAAGTATGAGAGGCTA 59.711 41.667 0.00 0.00 0.00 3.93
8 9 3.074538 ACCCAAAACAAGTATGAGAGGCT 59.925 43.478 0.00 0.00 0.00 4.58
83 84 0.038159 GAGTCTCACCAAGTGTCCGG 60.038 60.000 0.00 0.00 34.79 5.14
105 108 2.048503 GAGTCCACGGTTGGTCGG 60.049 66.667 0.00 0.00 44.35 4.79
181 185 0.237235 GTCGTTGCTGAATTTCCGCA 59.763 50.000 10.94 10.94 0.00 5.69
195 200 3.007940 TCCATCCTTCATCACAAGTCGTT 59.992 43.478 0.00 0.00 0.00 3.85
373 390 5.419155 AGAGTTACATCCTTTGTCGATGAGA 59.581 40.000 4.88 0.00 39.64 3.27
510 528 7.719633 GCAGAAAGGATACCATAGGATGTTTTA 59.280 37.037 0.00 0.00 37.17 1.52
559 595 1.400494 CCCGGTTCGCCTTAAATGAAG 59.600 52.381 0.00 0.00 34.30 3.02
660 980 1.266718 GCATCTTGCCTTTCACGTGAA 59.733 47.619 26.53 26.53 37.42 3.18
830 1309 0.319383 CTCTCTCGGAATGGGATGCG 60.319 60.000 0.00 0.00 35.27 4.73
1513 2059 0.755686 AGCTCGGGAGGATAAAGCAG 59.244 55.000 0.00 0.00 35.42 4.24
1519 2065 1.530891 CGGGAAGCTCGGGAGGATA 60.531 63.158 0.00 0.00 0.00 2.59
1670 2640 0.251519 CCCTTTGGCTCCAGCTTCTT 60.252 55.000 0.00 0.00 41.70 2.52
1849 3895 1.153901 CGTGTACAGCGACCCGAAT 60.154 57.895 10.97 0.00 0.00 3.34
1921 3969 3.061848 GGGCCACCCACACGAATG 61.062 66.667 4.39 0.00 44.65 2.67
1990 4042 0.107654 CATTCTCTCCACGAACCCCC 60.108 60.000 0.00 0.00 0.00 5.40
2247 4799 2.273179 CCACCTCGTCCCTCGTCAA 61.273 63.158 0.00 0.00 40.80 3.18
2276 4828 3.775654 CACCCTCTCCACCGCCTC 61.776 72.222 0.00 0.00 0.00 4.70
2279 4831 4.459089 GAGCACCCTCTCCACCGC 62.459 72.222 0.00 0.00 35.16 5.68
2325 4877 4.436998 CCGCGGCCTTTCGTCTCT 62.437 66.667 14.67 0.00 0.00 3.10
2332 4884 1.144057 CTACATCTCCGCGGCCTTT 59.856 57.895 23.51 5.76 0.00 3.11
2348 4900 2.184830 CGGCGTCGATCACCTCCTA 61.185 63.158 1.44 0.00 39.00 2.94
2416 4968 2.173758 TACGTGCCATCGCCTCCAAA 62.174 55.000 0.00 0.00 0.00 3.28
2519 5097 9.651913 TTTTGAAAATATGGAAATAGAAGTGGC 57.348 29.630 0.00 0.00 0.00 5.01
2574 5152 2.232941 TCGCTATTAACATCCGATCCCC 59.767 50.000 0.00 0.00 0.00 4.81
2615 5256 1.988834 GCGCCGTCCCCAAACATTAG 61.989 60.000 0.00 0.00 0.00 1.73
2616 5257 2.041686 GCGCCGTCCCCAAACATTA 61.042 57.895 0.00 0.00 0.00 1.90
2712 6818 9.100197 GGATAAGGAGAGGAGAGATATTTTCTT 57.900 37.037 0.00 0.00 33.74 2.52
2747 6861 2.053747 AGTGGTGGGGGAGAAATACA 57.946 50.000 0.00 0.00 0.00 2.29
2813 6931 3.978571 GAGGAGGCCTTGGCGGAAC 62.979 68.421 6.77 0.00 31.76 3.62
2847 6965 3.123620 GAAGCAGGTCAGCAGCGG 61.124 66.667 0.00 0.00 36.85 5.52
3293 7669 4.843728 AGGATCCAAAAAGCTACAATCGA 58.156 39.130 15.82 0.00 0.00 3.59
3378 7754 1.770294 TTCAAAAAGCTGGAACCGGT 58.230 45.000 0.00 0.00 0.00 5.28
3425 7823 3.130340 ACCGGCGATAGAAAAATGCAAAT 59.870 39.130 9.30 0.00 39.76 2.32
3437 7837 3.366440 AAAAGCTACTACCGGCGATAG 57.634 47.619 9.30 7.92 0.00 2.08


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

AutoCloner maintained by Alex Coulton.