Multiple sequence alignment - TraesCS6D01G360200

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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 TraesCS6D01G360200 chr6D 100.000 3458 0 0 1 3458 452076277 452079734 0.000000e+00 6386.0
1 TraesCS6D01G360200 chr6D 98.097 1997 28 4 1 1992 462403930 462405921 0.000000e+00 3469.0
2 TraesCS6D01G360200 chr6D 99.242 792 4 1 2250 3039 462405922 462406713 0.000000e+00 1428.0
3 TraesCS6D01G360200 chr6D 97.418 426 7 2 3037 3458 462406786 462407211 0.000000e+00 723.0
4 TraesCS6D01G360200 chr6D 94.118 340 19 1 478 816 245042211 245041872 1.840000e-142 516.0
5 TraesCS6D01G360200 chr6A 92.990 1726 68 26 810 2513 609157298 609158992 0.000000e+00 2468.0
6 TraesCS6D01G360200 chr6A 89.270 233 21 4 56 287 609156720 609156949 4.370000e-74 289.0
7 TraesCS6D01G360200 chr6A 83.983 231 23 10 3039 3266 609160121 609160340 3.500000e-50 209.0
8 TraesCS6D01G360200 chr6A 88.235 51 2 4 2774 2824 595481199 595481245 1.340000e-04 58.4
9 TraesCS6D01G360200 chr6B 93.156 1651 88 16 834 2474 704853152 704851517 0.000000e+00 2399.0
10 TraesCS6D01G360200 chr6B 92.053 151 4 4 3124 3266 704858757 704858907 4.520000e-49 206.0
11 TraesCS6D01G360200 chr6B 84.615 91 8 4 3039 3127 704858592 704858678 6.150000e-13 86.1
12 TraesCS6D01G360200 chr6B 90.196 51 1 1 2774 2824 681924214 681924260 2.880000e-06 63.9
13 TraesCS6D01G360200 chr1D 95.719 327 14 0 478 804 490705950 490706276 8.500000e-146 527.0
14 TraesCS6D01G360200 chr1D 98.182 55 1 0 1 55 176355923 176355869 2.840000e-16 97.1
15 TraesCS6D01G360200 chr1D 98.039 51 1 0 1 51 356876367 356876317 4.750000e-14 89.8
16 TraesCS6D01G360200 chr2B 95.441 329 15 0 476 804 754549792 754550120 3.060000e-145 525.0
17 TraesCS6D01G360200 chr2B 72.354 803 163 43 1535 2317 298515209 298514446 7.570000e-47 198.0
18 TraesCS6D01G360200 chr3D 95.413 327 15 0 478 804 127227917 127228243 3.950000e-144 521.0
19 TraesCS6D01G360200 chr3D 95.122 328 16 0 477 804 586505050 586505377 5.120000e-143 518.0
20 TraesCS6D01G360200 chr3D 94.065 337 19 1 469 805 123864675 123865010 8.560000e-141 510.0
21 TraesCS6D01G360200 chr3D 76.596 705 119 30 1354 2026 593236143 593236833 2.550000e-91 346.0
22 TraesCS6D01G360200 chr4D 94.864 331 17 0 477 807 55583311 55582981 5.120000e-143 518.0
23 TraesCS6D01G360200 chr2D 95.122 328 16 0 477 804 136422672 136422345 5.120000e-143 518.0
24 TraesCS6D01G360200 chr5D 75.025 997 190 41 1352 2317 491527759 491528727 1.160000e-109 407.0
25 TraesCS6D01G360200 chr5D 74.504 1008 189 53 1352 2316 45379067 45378085 3.260000e-100 375.0
26 TraesCS6D01G360200 chr5D 72.189 996 219 49 1355 2321 356090452 356091418 5.730000e-63 252.0
27 TraesCS6D01G360200 chr5D 72.753 712 141 35 1354 2028 1542432 1541737 1.270000e-44 191.0
28 TraesCS6D01G360200 chr5B 74.575 999 191 41 1352 2317 606301630 606302598 2.520000e-101 379.0
29 TraesCS6D01G360200 chr5B 73.909 1008 195 51 1352 2316 45393554 45394536 3.300000e-90 342.0
30 TraesCS6D01G360200 chr5A 74.423 997 196 40 1352 2317 613700670 613701638 1.170000e-99 374.0
31 TraesCS6D01G360200 chr5A 74.356 1010 184 55 1352 2316 36330859 36331838 9.120000e-96 361.0
32 TraesCS6D01G360200 chr5A 72.060 995 222 45 1355 2321 457790979 457791945 2.670000e-61 246.0
33 TraesCS6D01G360200 chr3B 77.019 718 115 38 1354 2037 795839886 795840587 1.960000e-97 366.0
34 TraesCS6D01G360200 chr3B 74.568 405 82 16 1919 2317 130115289 130115678 1.280000e-34 158.0
35 TraesCS6D01G360200 chr3A 76.503 715 124 32 1354 2037 724515610 724516311 1.970000e-92 350.0
36 TraesCS6D01G360200 chrUn 72.113 710 149 31 1354 2028 146272474 146271779 5.940000e-38 169.0
37 TraesCS6D01G360200 chr7A 98.182 55 1 0 1 55 439781317 439781263 2.840000e-16 97.1
38 TraesCS6D01G360200 chr2A 96.364 55 2 0 1 55 77797599 77797545 1.320000e-14 91.6
39 TraesCS6D01G360200 chr4A 94.872 39 2 0 2544 2582 708602998 708603036 1.040000e-05 62.1


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 TraesCS6D01G360200 chr6D 452076277 452079734 3457 False 6386.000000 6386 100.000000 1 3458 1 chr6D.!!$F1 3457
1 TraesCS6D01G360200 chr6D 462403930 462407211 3281 False 1873.333333 3469 98.252333 1 3458 3 chr6D.!!$F2 3457
2 TraesCS6D01G360200 chr6A 609156720 609160340 3620 False 988.666667 2468 88.747667 56 3266 3 chr6A.!!$F2 3210
3 TraesCS6D01G360200 chr6B 704851517 704853152 1635 True 2399.000000 2399 93.156000 834 2474 1 chr6B.!!$R1 1640
4 TraesCS6D01G360200 chr3D 593236143 593236833 690 False 346.000000 346 76.596000 1354 2026 1 chr3D.!!$F4 672
5 TraesCS6D01G360200 chr5D 491527759 491528727 968 False 407.000000 407 75.025000 1352 2317 1 chr5D.!!$F2 965
6 TraesCS6D01G360200 chr5D 45378085 45379067 982 True 375.000000 375 74.504000 1352 2316 1 chr5D.!!$R2 964
7 TraesCS6D01G360200 chr5D 356090452 356091418 966 False 252.000000 252 72.189000 1355 2321 1 chr5D.!!$F1 966
8 TraesCS6D01G360200 chr5B 606301630 606302598 968 False 379.000000 379 74.575000 1352 2317 1 chr5B.!!$F2 965
9 TraesCS6D01G360200 chr5B 45393554 45394536 982 False 342.000000 342 73.909000 1352 2316 1 chr5B.!!$F1 964
10 TraesCS6D01G360200 chr5A 613700670 613701638 968 False 374.000000 374 74.423000 1352 2317 1 chr5A.!!$F3 965
11 TraesCS6D01G360200 chr5A 36330859 36331838 979 False 361.000000 361 74.356000 1352 2316 1 chr5A.!!$F1 964
12 TraesCS6D01G360200 chr5A 457790979 457791945 966 False 246.000000 246 72.060000 1355 2321 1 chr5A.!!$F2 966
13 TraesCS6D01G360200 chr3B 795839886 795840587 701 False 366.000000 366 77.019000 1354 2037 1 chr3B.!!$F2 683
14 TraesCS6D01G360200 chr3A 724515610 724516311 701 False 350.000000 350 76.503000 1354 2037 1 chr3A.!!$F1 683

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
927 1108 1.004918 GAGGGACACCAACCACGAG 60.005 63.158 0.0 0.00 40.13 4.18 F
2067 2288 1.202568 CAACGACAAGCAGCTCACG 59.797 57.895 0.0 4.82 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2152 2382 1.143183 CGTACTGGATGTTCCCCGG 59.857 63.158 0.0 0.0 35.03 5.73 R
3063 3927 1.726248 GTTTTTGCATGATTGTCCGCC 59.274 47.619 0.0 0.0 0.00 6.13 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
343 501 8.123639 TCATATATGAAGAGTGGCCTAACTAC 57.876 38.462 13.12 0.00 33.08 2.73
344 502 7.950684 TCATATATGAAGAGTGGCCTAACTACT 59.049 37.037 13.12 0.00 36.98 2.57
400 558 5.250774 ACAATGTGTAGGTGGTAAAGGAGAT 59.749 40.000 0.00 0.00 0.00 2.75
530 692 6.729690 ATTCAAAAATCTCACCAACCAAGA 57.270 33.333 0.00 0.00 0.00 3.02
546 708 4.494091 CCAAGATAGATGGTGAGTGGTT 57.506 45.455 0.00 0.00 33.08 3.67
669 831 9.723601 ATAAAGTACATGCATTGGTCAATTTTT 57.276 25.926 0.00 0.00 0.00 1.94
726 888 3.960571 AGAATCTGAACTTGTGATGGGG 58.039 45.455 0.00 0.00 0.00 4.96
753 915 8.776376 ACAACCAAATTGAGCCTTATAAAATG 57.224 30.769 0.00 0.00 41.23 2.32
754 916 7.823799 ACAACCAAATTGAGCCTTATAAAATGG 59.176 33.333 0.00 0.00 41.23 3.16
926 1107 2.513259 GGAGGGACACCAACCACGA 61.513 63.158 0.00 0.00 39.49 4.35
927 1108 1.004918 GAGGGACACCAACCACGAG 60.005 63.158 0.00 0.00 40.13 4.18
928 1109 2.668550 GGGACACCAACCACGAGC 60.669 66.667 0.00 0.00 36.50 5.03
929 1110 2.426023 GGACACCAACCACGAGCT 59.574 61.111 0.00 0.00 0.00 4.09
2060 2281 1.452145 GGAAAGGGCAACGACAAGCA 61.452 55.000 0.00 0.00 37.60 3.91
2065 2286 2.253758 GGCAACGACAAGCAGCTCA 61.254 57.895 0.00 0.00 0.00 4.26
2067 2288 1.202568 CAACGACAAGCAGCTCACG 59.797 57.895 0.00 4.82 0.00 4.35
2133 2354 4.821589 GACGAGGCCGCCAAGGAG 62.822 72.222 13.15 0.13 45.00 3.69
2152 2382 2.282745 AGGGCAAGGACAAGCTGC 60.283 61.111 0.00 0.00 35.28 5.25
2721 3037 1.325476 GCCCCAAAGAAGATGGCCAG 61.325 60.000 13.05 0.00 36.58 4.85
3063 3927 4.074970 ACAGGTGCTGGAATCACTAAAAG 58.925 43.478 0.00 0.00 35.51 2.27
3274 4140 6.070824 ACAGTCCATGTATTCAGTGTGATACA 60.071 38.462 17.93 17.93 41.60 2.29
3412 4280 3.246226 CCAGTGGATCGAATTTCGTGATC 59.754 47.826 17.61 13.62 41.35 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
400 558 7.078249 ACTGGTGCAGGTATATTGATCAATA 57.922 36.000 26.24 26.24 35.47 1.90
530 692 9.975218 AAAAGTATTTAACCACTCACCATCTAT 57.025 29.630 0.00 0.00 37.28 1.98
705 867 3.588842 TCCCCATCACAAGTTCAGATTCT 59.411 43.478 0.00 0.00 0.00 2.40
726 888 8.825667 TTTTATAAGGCTCAATTTGGTTGTTC 57.174 30.769 0.00 0.00 38.95 3.18
764 926 7.230712 CCGGTTTATAGGGCTTATCTCAAAATT 59.769 37.037 0.00 0.00 0.00 1.82
796 958 2.897350 GCATGCGCAGTACTCCCC 60.897 66.667 18.32 0.00 38.36 4.81
829 991 2.084546 GGAGTTTCACCCATTTCTCCG 58.915 52.381 0.00 0.00 33.44 4.63
926 1107 1.341156 GGGATCTGGTGGTGCTAGCT 61.341 60.000 17.23 0.00 0.00 3.32
927 1108 1.147153 GGGATCTGGTGGTGCTAGC 59.853 63.158 8.10 8.10 0.00 3.42
928 1109 0.911769 TTGGGATCTGGTGGTGCTAG 59.088 55.000 0.00 0.00 0.00 3.42
929 1110 0.618458 GTTGGGATCTGGTGGTGCTA 59.382 55.000 0.00 0.00 0.00 3.49
2133 2354 1.676967 CAGCTTGTCCTTGCCCTCC 60.677 63.158 0.00 0.00 0.00 4.30
2152 2382 1.143183 CGTACTGGATGTTCCCCGG 59.857 63.158 0.00 0.00 35.03 5.73
2153 2383 1.520787 GCGTACTGGATGTTCCCCG 60.521 63.158 0.00 0.00 35.03 5.73
2721 3037 1.795286 CTTCGTTCACTGTCTTCAGGC 59.205 52.381 0.47 0.00 45.14 4.85
3063 3927 1.726248 GTTTTTGCATGATTGTCCGCC 59.274 47.619 0.00 0.00 0.00 6.13
3298 4166 6.067217 AGCAGTTCATTAGTCCAAGGTATT 57.933 37.500 0.00 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.