Multiple sequence alignment - TraesCS3B01G594600

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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 TraesCS3B01G594600 chr3B 100.000 4278 0 0 1 4278 817853968 817849691 0.000000e+00 7901
1 TraesCS3B01G594600 chr3B 93.624 643 36 3 3641 4278 373864207 373863565 0.000000e+00 955
2 TraesCS3B01G594600 chr6A 97.310 1933 51 1 1713 3644 58834562 58832630 0.000000e+00 3280
3 TraesCS3B01G594600 chr6A 97.156 1934 53 2 1713 3644 73467774 73465841 0.000000e+00 3265
4 TraesCS3B01G594600 chr6A 97.050 1932 57 0 1713 3644 530170019 530168088 0.000000e+00 3253
5 TraesCS3B01G594600 chr6A 96.219 1534 55 3 181 1713 464136759 464135228 0.000000e+00 2508
6 TraesCS3B01G594600 chr6A 97.812 640 12 2 3641 4278 73465692 73465053 0.000000e+00 1103
7 TraesCS3B01G594600 chr6A 95.938 640 23 3 3641 4278 58832482 58831844 0.000000e+00 1035
8 TraesCS3B01G594600 chr6A 95.781 640 25 2 3641 4278 530167939 530167300 0.000000e+00 1031
9 TraesCS3B01G594600 chr7A 97.205 1932 53 1 1713 3644 157162525 157164455 0.000000e+00 3267
10 TraesCS3B01G594600 chr7A 96.948 1933 57 2 1713 3644 50325575 50327506 0.000000e+00 3241
11 TraesCS3B01G594600 chr7A 95.625 640 26 2 3641 4278 157164604 157165243 0.000000e+00 1026
12 TraesCS3B01G594600 chr1A 96.999 1933 57 1 1713 3644 380303294 380305226 0.000000e+00 3247
13 TraesCS3B01G594600 chr1A 96.250 640 22 2 3641 4278 380305374 380306013 0.000000e+00 1048
14 TraesCS3B01G594600 chr1A 96.094 640 23 2 3641 4278 3565837 3566476 0.000000e+00 1042
15 TraesCS3B01G594600 chr1A 89.680 562 36 5 320 878 488634663 488635205 0.000000e+00 697
16 TraesCS3B01G594600 chr1A 92.810 306 21 1 873 1177 488647365 488647670 3.930000e-120 442
17 TraesCS3B01G594600 chr1A 94.009 217 11 1 18 232 488634446 488634662 1.150000e-85 327
18 TraesCS3B01G594600 chr1A 79.134 254 27 8 20 261 358352911 358352672 7.410000e-33 152
19 TraesCS3B01G594600 chrUn 96.793 1933 60 2 1713 3644 82369597 82371528 0.000000e+00 3225
20 TraesCS3B01G594600 chr2A 96.793 1933 60 2 1713 3644 721512004 721510073 0.000000e+00 3225
21 TraesCS3B01G594600 chr2A 96.719 640 19 2 3641 4278 721509925 721509286 0.000000e+00 1064
22 TraesCS3B01G594600 chr3A 96.532 1932 67 0 1713 3644 80119907 80121838 0.000000e+00 3197
23 TraesCS3B01G594600 chr3A 96.714 639 20 1 3641 4278 80121987 80122625 0.000000e+00 1062
24 TraesCS3B01G594600 chr3A 85.824 910 102 11 823 1714 198163722 198164622 0.000000e+00 941
25 TraesCS3B01G594600 chr3A 88.496 113 12 1 714 825 390143678 390143790 7.460000e-28 135
26 TraesCS3B01G594600 chr5D 96.214 1717 59 4 3 1714 106891820 106890105 0.000000e+00 2806
27 TraesCS3B01G594600 chr5D 84.556 913 112 11 822 1714 47734252 47735155 0.000000e+00 878
28 TraesCS3B01G594600 chr7B 96.098 1717 55 5 3 1714 703151908 703150199 0.000000e+00 2789
29 TraesCS3B01G594600 chr7B 79.412 238 23 7 36 261 670704324 670704547 1.240000e-30 145
30 TraesCS3B01G594600 chr3D 96.631 1603 49 3 116 1714 5451629 5450028 0.000000e+00 2656
31 TraesCS3B01G594600 chr3D 96.458 960 33 1 755 1714 226702136 226701178 0.000000e+00 1583
32 TraesCS3B01G594600 chr3D 96.197 710 26 1 3 711 226703030 226702321 0.000000e+00 1160
33 TraesCS3B01G594600 chr3D 94.958 119 5 1 3 120 5460386 5460268 7.310000e-43 185
34 TraesCS3B01G594600 chr5A 92.824 1073 66 5 3 1073 399311579 399310516 0.000000e+00 1544
35 TraesCS3B01G594600 chr5A 91.977 511 34 3 1204 1714 399308730 399308227 0.000000e+00 710
36 TraesCS3B01G594600 chr5B 85.149 909 103 12 822 1707 669600017 669599118 0.000000e+00 902
37 TraesCS3B01G594600 chr4D 87.075 441 35 10 294 716 350249006 350248570 2.990000e-131 479
38 TraesCS3B01G594600 chr4D 87.059 255 22 2 822 1066 95515363 95515110 1.170000e-70 278
39 TraesCS3B01G594600 chr4D 92.920 113 7 1 714 825 350248540 350248428 3.420000e-36 163
40 TraesCS3B01G594600 chr4A 85.714 469 49 9 262 716 114742526 114742990 2.990000e-131 479


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 TraesCS3B01G594600 chr3B 817849691 817853968 4277 True 7901.0 7901 100.0000 1 4278 1 chr3B.!!$R2 4277
1 TraesCS3B01G594600 chr3B 373863565 373864207 642 True 955.0 955 93.6240 3641 4278 1 chr3B.!!$R1 637
2 TraesCS3B01G594600 chr6A 464135228 464136759 1531 True 2508.0 2508 96.2190 181 1713 1 chr6A.!!$R1 1532
3 TraesCS3B01G594600 chr6A 73465053 73467774 2721 True 2184.0 3265 97.4840 1713 4278 2 chr6A.!!$R3 2565
4 TraesCS3B01G594600 chr6A 58831844 58834562 2718 True 2157.5 3280 96.6240 1713 4278 2 chr6A.!!$R2 2565
5 TraesCS3B01G594600 chr6A 530167300 530170019 2719 True 2142.0 3253 96.4155 1713 4278 2 chr6A.!!$R4 2565
6 TraesCS3B01G594600 chr7A 50325575 50327506 1931 False 3241.0 3241 96.9480 1713 3644 1 chr7A.!!$F1 1931
7 TraesCS3B01G594600 chr7A 157162525 157165243 2718 False 2146.5 3267 96.4150 1713 4278 2 chr7A.!!$F2 2565
8 TraesCS3B01G594600 chr1A 380303294 380306013 2719 False 2147.5 3247 96.6245 1713 4278 2 chr1A.!!$F3 2565
9 TraesCS3B01G594600 chr1A 3565837 3566476 639 False 1042.0 1042 96.0940 3641 4278 1 chr1A.!!$F1 637
10 TraesCS3B01G594600 chr1A 488634446 488635205 759 False 512.0 697 91.8445 18 878 2 chr1A.!!$F4 860
11 TraesCS3B01G594600 chrUn 82369597 82371528 1931 False 3225.0 3225 96.7930 1713 3644 1 chrUn.!!$F1 1931
12 TraesCS3B01G594600 chr2A 721509286 721512004 2718 True 2144.5 3225 96.7560 1713 4278 2 chr2A.!!$R1 2565
13 TraesCS3B01G594600 chr3A 80119907 80122625 2718 False 2129.5 3197 96.6230 1713 4278 2 chr3A.!!$F3 2565
14 TraesCS3B01G594600 chr3A 198163722 198164622 900 False 941.0 941 85.8240 823 1714 1 chr3A.!!$F1 891
15 TraesCS3B01G594600 chr5D 106890105 106891820 1715 True 2806.0 2806 96.2140 3 1714 1 chr5D.!!$R1 1711
16 TraesCS3B01G594600 chr5D 47734252 47735155 903 False 878.0 878 84.5560 822 1714 1 chr5D.!!$F1 892
17 TraesCS3B01G594600 chr7B 703150199 703151908 1709 True 2789.0 2789 96.0980 3 1714 1 chr7B.!!$R1 1711
18 TraesCS3B01G594600 chr3D 5450028 5451629 1601 True 2656.0 2656 96.6310 116 1714 1 chr3D.!!$R1 1598
19 TraesCS3B01G594600 chr3D 226701178 226703030 1852 True 1371.5 1583 96.3275 3 1714 2 chr3D.!!$R3 1711
20 TraesCS3B01G594600 chr5A 399308227 399311579 3352 True 1127.0 1544 92.4005 3 1714 2 chr5A.!!$R1 1711
21 TraesCS3B01G594600 chr5B 669599118 669600017 899 True 902.0 902 85.1490 822 1707 1 chr5B.!!$R1 885
22 TraesCS3B01G594600 chr4D 350248428 350249006 578 True 321.0 479 89.9975 294 825 2 chr4D.!!$R2 531

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
269 277 0.320683 CTGACCATGTTCTCACCGCA 60.321 55.0 0.00 0.0 0.00 5.69 F
881 1053 2.023015 AGGTACTCCTGGACCATGATCA 60.023 50.0 0.00 0.0 43.33 2.92 F
1954 3844 2.248280 TGCGAAAGAAAGTGGCACTA 57.752 45.0 22.37 0.0 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1954 3844 2.290896 TGCGTTTCCCATCATTCTCCTT 60.291 45.455 0.00 0.0 0.00 3.36 R
2657 4548 4.331968 AGTCAAGTTCTTGGACACACAAA 58.668 39.130 11.82 0.0 34.04 2.83 R
3419 5312 1.060122 CGACGACGGCACCTTTATTTC 59.940 52.381 0.00 0.0 35.72 2.17 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
57 59 6.241207 GCAGTTGCACTTAGATTTCAGTTA 57.759 37.500 0.00 0.00 41.59 2.24
212 217 3.896648 ACAGTTTTGACTATTGCCGTG 57.103 42.857 0.00 0.00 0.00 4.94
269 277 0.320683 CTGACCATGTTCTCACCGCA 60.321 55.000 0.00 0.00 0.00 5.69
736 841 5.178996 GTCTTTGATCAATCTCCATGGATCG 59.821 44.000 16.63 4.55 39.14 3.69
853 1025 4.502016 ACATCTGACACTGCTTGTAGATG 58.498 43.478 20.85 20.85 43.39 2.90
881 1053 2.023015 AGGTACTCCTGGACCATGATCA 60.023 50.000 0.00 0.00 43.33 2.92
933 1108 6.611613 AAATGTGACTCCTCTGATAACTGA 57.388 37.500 0.00 0.00 0.00 3.41
1002 1177 7.646922 GCAAGATTCTGGATTGCTTAAACTATG 59.353 37.037 2.07 0.00 44.57 2.23
1354 3231 9.931698 TCTTAATTCTACAGACCCTACTTATGA 57.068 33.333 0.00 0.00 0.00 2.15
1689 3579 4.610945 CAATGGATATTTCCTTTGGCGAC 58.389 43.478 17.77 0.00 46.23 5.19
1796 3686 5.363580 CCCCCAAGAATATAAATGCAGTGTT 59.636 40.000 0.00 0.00 0.00 3.32
1954 3844 2.248280 TGCGAAAGAAAGTGGCACTA 57.752 45.000 22.37 0.00 0.00 2.74
2343 4233 5.299279 GGTTGCATGGTGCTGTAAGTATTAT 59.701 40.000 3.41 0.00 45.31 1.28
2345 4235 7.307989 GGTTGCATGGTGCTGTAAGTATTATAG 60.308 40.741 3.41 0.00 45.31 1.31
2722 4613 7.181569 ACTTTCCTTTTCATGTGGAAGAAAA 57.818 32.000 0.00 0.00 40.43 2.29
2723 4614 7.619965 ACTTTCCTTTTCATGTGGAAGAAAAA 58.380 30.769 0.00 1.10 41.55 1.94
2736 4627 6.549364 TGTGGAAGAAAAACACTGGATAACAT 59.451 34.615 0.00 0.00 36.16 2.71
2865 4756 9.982651 TTTACATGTAACAAGATAGATAGGAGC 57.017 33.333 17.85 0.00 0.00 4.70
2957 4848 3.400255 GAGGTGAACTCCCTTGTACAAC 58.600 50.000 3.59 0.00 40.49 3.32
3069 4960 6.102897 AGTACTTCTCTTACACAGCAATGT 57.897 37.500 0.00 0.00 36.56 2.71
3076 4967 4.960938 TCTTACACAGCAATGTCTGACTT 58.039 39.130 9.51 0.00 37.51 3.01
3157 5049 6.073003 GGAACGGAGATGAATGGATATTTGAC 60.073 42.308 0.00 0.00 0.00 3.18
3175 5067 4.008074 TGACTTTGATCAACCTGAGGTC 57.992 45.455 3.76 3.67 33.12 3.85
3304 5197 1.743394 GATGGGTTTTTGGCTACGAGG 59.257 52.381 0.00 0.00 0.00 4.63
3305 5198 0.250989 TGGGTTTTTGGCTACGAGGG 60.251 55.000 0.00 0.00 0.00 4.30
3520 5413 0.179012 ATGTGATGATGATGCCGCCA 60.179 50.000 0.00 0.00 0.00 5.69
3837 6035 1.998530 CCCAGTATGACAGGCCCAA 59.001 57.895 0.00 0.00 39.69 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.056821 CAGAGCCCGAATTCGATGGTATA 60.057 47.826 28.76 0.00 43.02 1.47
57 59 5.068723 TCGAGCTTTAGGATTCGAATACCTT 59.931 40.000 24.63 10.02 38.92 3.50
269 277 0.249489 GAGTGAGGTCTGCACGTTGT 60.249 55.000 0.00 0.00 41.04 3.32
420 438 1.048601 TGAACCCTTTCTCAGCGACT 58.951 50.000 0.00 0.00 32.36 4.18
540 558 0.322975 GTCAGTGCTCACCTCCATGT 59.677 55.000 0.00 0.00 0.00 3.21
543 561 0.836606 TTTGTCAGTGCTCACCTCCA 59.163 50.000 0.00 0.00 0.00 3.86
736 841 9.787532 TTCAGCACTGCAAAACTAATATAATTC 57.212 29.630 3.30 0.00 0.00 2.17
853 1025 2.289506 GGTCCAGGAGTACCTTCACAAC 60.290 54.545 0.00 0.00 45.36 3.32
881 1053 3.244875 GCCAAACATTTTCCCAAGGGATT 60.245 43.478 9.01 0.00 44.74 3.01
933 1108 1.056700 ATGGTGGCCTCTAATCGCCT 61.057 55.000 3.32 0.00 45.90 5.52
1002 1177 2.570442 TGTTGTTCCGTTTGCCTTTC 57.430 45.000 0.00 0.00 0.00 2.62
1143 3011 6.620678 AGTGTGCATACAAATCCAATGTAAC 58.379 36.000 16.44 0.00 38.82 2.50
1354 3231 3.117888 AGAAGTGGAGGAACACACAATGT 60.118 43.478 0.00 0.00 46.42 2.71
1796 3686 2.671370 ATCGGCGCTAGACCCGTCTA 62.671 60.000 17.52 4.57 44.63 2.59
1954 3844 2.290896 TGCGTTTCCCATCATTCTCCTT 60.291 45.455 0.00 0.00 0.00 3.36
2080 3970 7.547227 AGTAAATAAATTGTGCATGGAAGGAC 58.453 34.615 0.00 0.00 0.00 3.85
2657 4548 4.331968 AGTCAAGTTCTTGGACACACAAA 58.668 39.130 11.82 0.00 34.04 2.83
2722 4613 5.711506 TGCATGAGAAATGTTATCCAGTGTT 59.288 36.000 0.00 0.00 0.00 3.32
2723 4614 5.124457 GTGCATGAGAAATGTTATCCAGTGT 59.876 40.000 0.00 0.00 0.00 3.55
3157 5049 4.380233 GCATTGACCTCAGGTTGATCAAAG 60.380 45.833 10.35 3.73 35.25 2.77
3167 5059 2.089980 CCTTGAAGCATTGACCTCAGG 58.910 52.381 0.00 0.00 0.00 3.86
3175 5067 1.508088 GCGTCCCCTTGAAGCATTG 59.492 57.895 0.00 0.00 46.29 2.82
3304 5197 7.702348 AGTTGCGATAATAAGAAAAAGAATGCC 59.298 33.333 0.00 0.00 0.00 4.40
3305 5198 8.620533 AGTTGCGATAATAAGAAAAAGAATGC 57.379 30.769 0.00 0.00 0.00 3.56
3347 5240 3.252215 TCAAAATTGTTCCTAGTGCCGTG 59.748 43.478 0.00 0.00 0.00 4.94
3397 5290 2.517650 TGCGGACGTGCATAATCATA 57.482 45.000 8.11 0.00 40.62 2.15
3419 5312 1.060122 CGACGACGGCACCTTTATTTC 59.940 52.381 0.00 0.00 35.72 2.17
3520 5413 1.479709 AACTCTACGAGCCAGCAGAT 58.520 50.000 0.00 0.00 32.04 2.90
4121 6322 0.457337 AACATAGCCGACCGTCGTTC 60.457 55.000 19.13 10.62 38.40 3.95


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

AutoCloner maintained by Alex Coulton.