Multiple sequence alignment - TraesCS3D01G179500

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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 TraesCS3D01G179500 chr3D 100.000 3305 0 0 1 3305 161499700 161496396 0.000000e+00 6104.0
1 TraesCS3D01G179500 chr3D 94.690 1563 73 9 1745 3305 161596221 161594667 0.000000e+00 2418.0
2 TraesCS3D01G179500 chr3D 90.304 1578 107 30 1746 3292 161401331 161399769 0.000000e+00 2025.0
3 TraesCS3D01G179500 chr3D 92.322 1094 58 15 13 1104 161403647 161402578 0.000000e+00 1531.0
4 TraesCS3D01G179500 chr3D 90.341 528 33 7 1170 1682 161401874 161401350 0.000000e+00 676.0
5 TraesCS3D01G179500 chr3D 89.381 452 41 3 1231 1682 161596674 161596230 2.230000e-156 562.0
6 TraesCS3D01G179500 chr3B 93.459 2385 108 25 937 3292 237973779 237971414 0.000000e+00 3496.0
7 TraesCS3D01G179500 chr3B 93.084 1576 84 13 1745 3305 238113156 238111591 0.000000e+00 2283.0
8 TraesCS3D01G179500 chr3B 91.567 1672 106 19 13 1680 237735457 237733817 0.000000e+00 2274.0
9 TraesCS3D01G179500 chr3B 88.980 1579 108 35 1746 3292 237733796 237732252 0.000000e+00 1892.0
10 TraesCS3D01G179500 chr3B 88.285 717 73 7 46 761 237978033 237977327 0.000000e+00 848.0
11 TraesCS3D01G179500 chr3B 85.249 522 45 17 1177 1682 238113670 238113165 2.940000e-140 508.0
12 TraesCS3D01G179500 chr3B 84.112 107 2 3 850 941 237977215 237977109 4.540000e-14 89.8
13 TraesCS3D01G179500 chr3A 93.938 1699 60 19 1 1687 191008779 191007112 0.000000e+00 2527.0
14 TraesCS3D01G179500 chr3A 95.463 1587 60 8 1727 3305 191006623 191005041 0.000000e+00 2521.0
15 TraesCS3D01G179500 chr3A 93.110 1582 78 13 1745 3305 190228524 190226953 0.000000e+00 2289.0
16 TraesCS3D01G179500 chr3A 93.320 1542 80 10 1745 3269 191253506 191251971 0.000000e+00 2255.0
17 TraesCS3D01G179500 chr3A 89.051 1580 123 35 1746 3292 190094122 190092560 0.000000e+00 1914.0
18 TraesCS3D01G179500 chr3A 95.098 816 33 3 1746 2561 188112691 188113499 0.000000e+00 1279.0
19 TraesCS3D01G179500 chr3A 91.410 943 62 6 1 943 190096099 190095176 0.000000e+00 1275.0
20 TraesCS3D01G179500 chr3A 88.355 833 71 14 13 843 188100263 188101071 0.000000e+00 977.0
21 TraesCS3D01G179500 chr3A 90.078 766 48 12 940 1681 190094903 190094142 0.000000e+00 968.0
22 TraesCS3D01G179500 chr3A 91.162 611 35 9 843 1435 188101147 188101756 0.000000e+00 811.0
23 TraesCS3D01G179500 chr3A 88.521 453 42 4 1231 1683 190228974 190228532 1.040000e-149 540.0
24 TraesCS3D01G179500 chr3A 88.521 453 42 4 1231 1683 191253956 191253514 1.040000e-149 540.0
25 TraesCS3D01G179500 chr3A 93.281 253 14 1 1427 1679 188112420 188112669 1.450000e-98 370.0
26 TraesCS3D01G179500 chr3A 98.214 56 1 0 970 1025 190229119 190229064 7.550000e-17 99.0
27 TraesCS3D01G179500 chr3A 100.000 53 0 0 1673 1725 191006650 191006598 7.550000e-17 99.0
28 TraesCS3D01G179500 chr3A 98.214 56 1 0 970 1025 191254101 191254046 7.550000e-17 99.0
29 TraesCS3D01G179500 chr3A 96.364 55 2 0 971 1025 190583047 190582993 1.260000e-14 91.6
30 TraesCS3D01G179500 chr3A 100.000 40 0 0 3266 3305 191251868 191251829 1.270000e-09 75.0
31 TraesCS3D01G179500 chr4D 85.042 361 39 7 484 843 9548103 9548449 1.460000e-93 353.0
32 TraesCS3D01G179500 chr4A 88.688 221 22 3 480 698 555535884 555536103 1.960000e-67 267.0
33 TraesCS3D01G179500 chr6D 89.571 163 16 1 477 639 281926087 281926248 4.320000e-49 206.0
34 TraesCS3D01G179500 chr6D 100.000 35 0 0 809 843 452414538 452414572 7.660000e-07 65.8
35 TraesCS3D01G179500 chr7B 83.036 224 32 6 13 232 640231080 640230859 7.230000e-47 198.0
36 TraesCS3D01G179500 chr1B 83.871 124 19 1 47 169 93952669 93952546 2.080000e-22 117.0
37 TraesCS3D01G179500 chr7A 83.065 124 20 1 47 169 611770147 611770024 9.690000e-21 111.0
38 TraesCS3D01G179500 chr7D 76.042 192 29 12 655 843 579794562 579794385 2.110000e-12 84.2
39 TraesCS3D01G179500 chr2D 81.928 83 12 3 762 843 124318391 124318311 2.130000e-07 67.6


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 TraesCS3D01G179500 chr3D 161496396 161499700 3304 True 6104.000000 6104 100.000000 1 3305 1 chr3D.!!$R1 3304
1 TraesCS3D01G179500 chr3D 161594667 161596674 2007 True 1490.000000 2418 92.035500 1231 3305 2 chr3D.!!$R3 2074
2 TraesCS3D01G179500 chr3D 161399769 161403647 3878 True 1410.666667 2025 90.989000 13 3292 3 chr3D.!!$R2 3279
3 TraesCS3D01G179500 chr3B 237732252 237735457 3205 True 2083.000000 2274 90.273500 13 3292 2 chr3B.!!$R1 3279
4 TraesCS3D01G179500 chr3B 237971414 237978033 6619 True 1477.933333 3496 88.618667 46 3292 3 chr3B.!!$R2 3246
5 TraesCS3D01G179500 chr3B 238111591 238113670 2079 True 1395.500000 2283 89.166500 1177 3305 2 chr3B.!!$R3 2128
6 TraesCS3D01G179500 chr3A 191005041 191008779 3738 True 1715.666667 2527 96.467000 1 3305 3 chr3A.!!$R4 3304
7 TraesCS3D01G179500 chr3A 190092560 190096099 3539 True 1385.666667 1914 90.179667 1 3292 3 chr3A.!!$R2 3291
8 TraesCS3D01G179500 chr3A 190226953 190229119 2166 True 976.000000 2289 93.281667 970 3305 3 chr3A.!!$R3 2335
9 TraesCS3D01G179500 chr3A 188100263 188101756 1493 False 894.000000 977 89.758500 13 1435 2 chr3A.!!$F1 1422
10 TraesCS3D01G179500 chr3A 188112420 188113499 1079 False 824.500000 1279 94.189500 1427 2561 2 chr3A.!!$F2 1134
11 TraesCS3D01G179500 chr3A 191251829 191254101 2272 True 742.250000 2255 95.013750 970 3305 4 chr3A.!!$R5 2335

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
275 279 1.595382 CCACCGGCCGAGATCATTC 60.595 63.158 30.73 0.0 0.0 2.67 F
1155 4964 0.668535 GCAACCTGGTGACCAACTTC 59.331 55.000 5.53 0.0 30.8 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1837 6802 1.110518 AATCGCGGGTTGTTTGGGTT 61.111 50.000 6.13 0.0 0.0 4.11 R
2671 7647 3.146104 AGTGAACCCAAGGAACAGATG 57.854 47.619 0.00 0.0 0.0 2.90 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
142 145 1.606668 GTTTCAAGGACGTCCATGCAA 59.393 47.619 35.00 26.53 38.89 4.08
175 178 3.742640 GCCCTTGCGTAGATCTTCATTCT 60.743 47.826 0.00 0.00 0.00 2.40
275 279 1.595382 CCACCGGCCGAGATCATTC 60.595 63.158 30.73 0.00 0.00 2.67
303 307 2.100631 GGGATGACGTGGTCAAGCG 61.101 63.158 0.00 0.00 45.96 4.68
368 372 2.281208 CTCGCCCGACCACCAAAA 60.281 61.111 0.00 0.00 0.00 2.44
397 401 2.672996 GCCGTCACCATGCCAAGT 60.673 61.111 0.00 0.00 0.00 3.16
453 457 4.353383 ACCCTACAAACAAAGAGAGGAC 57.647 45.455 0.00 0.00 0.00 3.85
454 458 3.244112 ACCCTACAAACAAAGAGAGGACG 60.244 47.826 0.00 0.00 0.00 4.79
622 628 4.154195 AGCAAAACTACAGAGTATTTGGCG 59.846 41.667 0.00 0.00 35.93 5.69
639 645 2.224185 TGGCGAGCACAGTCTTTCTAAA 60.224 45.455 0.00 0.00 0.00 1.85
737 743 6.310711 CCTCACTTTTGAAGATACTACGGTTC 59.689 42.308 0.00 0.00 0.00 3.62
932 1110 2.818274 CCTGTTTACGGAGCGGCC 60.818 66.667 0.00 0.00 0.00 6.13
1155 4964 0.668535 GCAACCTGGTGACCAACTTC 59.331 55.000 5.53 0.00 30.80 3.01
1716 6666 1.630148 CGGAAGGTGACGAAGATGAC 58.370 55.000 0.00 0.00 0.00 3.06
1717 6667 1.630148 GGAAGGTGACGAAGATGACG 58.370 55.000 0.00 0.00 0.00 4.35
1718 6668 1.201647 GGAAGGTGACGAAGATGACGA 59.798 52.381 0.00 0.00 34.70 4.20
1719 6669 2.352421 GGAAGGTGACGAAGATGACGAA 60.352 50.000 0.00 0.00 34.70 3.85
1720 6670 2.638556 AGGTGACGAAGATGACGAAG 57.361 50.000 0.00 0.00 34.70 3.79
1721 6671 1.202582 AGGTGACGAAGATGACGAAGG 59.797 52.381 0.00 0.00 34.70 3.46
1837 6802 1.282653 TGTGGTTGTCTTGGACCCCA 61.283 55.000 0.00 0.00 34.99 4.96
2498 7473 9.878599 CCTGTATTTTGATCGTTTATGGTAATC 57.121 33.333 0.00 0.00 0.00 1.75
2561 7537 4.640647 GGGTGAATTACTTCATCTGTTCCC 59.359 45.833 6.09 4.13 43.08 3.97
2659 7635 4.690280 CCAAACTTCCCATTTACATTGTGC 59.310 41.667 0.00 0.00 0.00 4.57
2671 7647 7.008266 CCATTTACATTGTGCGTGAATTACTTC 59.992 37.037 0.00 0.00 0.00 3.01
2689 7665 3.138283 ACTTCATCTGTTCCTTGGGTTCA 59.862 43.478 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
142 145 2.912025 CAAGGGCGCCACCAAGTT 60.912 61.111 30.85 8.17 42.05 2.66
175 178 3.441101 ACCATCTAGCACAACTGACCTA 58.559 45.455 0.00 0.00 0.00 3.08
397 401 1.212751 CTCACAGATGGCGTCACGA 59.787 57.895 0.00 1.29 0.00 4.35
589 595 6.463049 ACTCTGTAGTTTTGCTAAAGCAGAGA 60.463 38.462 31.28 19.32 42.37 3.10
622 628 4.319839 GCTGGTTTTAGAAAGACTGTGCTC 60.320 45.833 0.00 0.00 0.00 4.26
639 645 1.293498 CACTCACGCCTAGCTGGTT 59.707 57.895 0.00 0.00 38.35 3.67
932 1110 6.098124 ACTCAGTCTGATCTAGAAGGAAATGG 59.902 42.308 2.22 0.00 37.12 3.16
1713 6663 1.883926 TCATCTTCGTCACCTTCGTCA 59.116 47.619 0.00 0.00 0.00 4.35
1714 6664 2.251893 GTCATCTTCGTCACCTTCGTC 58.748 52.381 0.00 0.00 0.00 4.20
1715 6665 1.401148 CGTCATCTTCGTCACCTTCGT 60.401 52.381 0.00 0.00 0.00 3.85
1716 6666 1.135774 TCGTCATCTTCGTCACCTTCG 60.136 52.381 0.00 0.00 0.00 3.79
1717 6667 2.631418 TCGTCATCTTCGTCACCTTC 57.369 50.000 0.00 0.00 0.00 3.46
1718 6668 2.417379 CCATCGTCATCTTCGTCACCTT 60.417 50.000 0.00 0.00 0.00 3.50
1719 6669 1.135139 CCATCGTCATCTTCGTCACCT 59.865 52.381 0.00 0.00 0.00 4.00
1720 6670 1.135083 ACCATCGTCATCTTCGTCACC 60.135 52.381 0.00 0.00 0.00 4.02
1721 6671 1.920574 CACCATCGTCATCTTCGTCAC 59.079 52.381 0.00 0.00 0.00 3.67
1837 6802 1.110518 AATCGCGGGTTGTTTGGGTT 61.111 50.000 6.13 0.00 0.00 4.11
1884 6849 3.571401 AGCTGTGAAAACCTTCCAGATTG 59.429 43.478 0.00 0.00 34.39 2.67
2498 7473 6.715464 AGTTTGATAACAGAAGACAACAACG 58.285 36.000 0.00 0.00 36.70 4.10
2561 7537 9.029243 GAGTTATCACTGAATACTGAATGTCAG 57.971 37.037 3.71 3.71 41.10 3.51
2607 7583 6.816640 CAGAAGACAACCCAATTACGATAGAA 59.183 38.462 0.00 0.00 41.38 2.10
2609 7585 5.523916 CCAGAAGACAACCCAATTACGATAG 59.476 44.000 0.00 0.00 46.19 2.08
2659 7635 6.402550 CCAAGGAACAGATGAAGTAATTCACG 60.403 42.308 7.92 2.75 33.23 4.35
2671 7647 3.146104 AGTGAACCCAAGGAACAGATG 57.854 47.619 0.00 0.00 0.00 2.90
2689 7665 4.641094 CCAATACCGAGAAGAGACAGTAGT 59.359 45.833 0.00 0.00 0.00 2.73
2749 7731 8.082852 GTCAAGAACACTAATCTTACAGACAGA 58.917 37.037 0.00 0.00 35.43 3.41
3247 8286 5.950544 ATACTACTGTGTATTTGCTGGGA 57.049 39.130 0.00 0.00 29.70 4.37


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

AutoCloner maintained by Alex Coulton.