Multiple sequence alignment - TraesCS3D01G040500

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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 TraesCS3D01G040500 chr3D 100.000 3699 0 0 1 3699 15369085 15365387 0.000000e+00 6831
1 TraesCS3D01G040500 chr3D 89.516 1755 122 14 1032 2769 15389627 15387918 0.000000e+00 2165
2 TraesCS3D01G040500 chr3D 94.415 931 45 3 2769 3699 15387882 15386959 0.000000e+00 1424
3 TraesCS3D01G040500 chr3D 80.843 830 129 9 1053 1876 15345020 15344215 3.140000e-175 625
4 TraesCS3D01G040500 chr3D 83.735 664 91 12 2771 3430 15342050 15341400 2.440000e-171 612
5 TraesCS3D01G040500 chr3D 88.530 279 29 2 2492 2767 15342371 15342093 5.920000e-88 335
6 TraesCS3D01G040500 chr3D 82.759 290 42 8 46 331 539245283 539244998 6.130000e-63 252
7 TraesCS3D01G040500 chr3D 88.387 155 18 0 1962 2116 15343996 15343842 1.750000e-43 187
8 TraesCS3D01G040500 chr3B 93.878 2695 120 17 1025 3699 22516630 22519299 0.000000e+00 4021
9 TraesCS3D01G040500 chr3B 87.451 1020 77 16 3 1003 22515318 22516305 0.000000e+00 1127
10 TraesCS3D01G040500 chr3B 80.552 1450 210 44 1037 2433 22323141 22321711 0.000000e+00 1050
11 TraesCS3D01G040500 chr3B 83.512 934 123 19 2771 3699 22459170 22458263 0.000000e+00 843
12 TraesCS3D01G040500 chr3B 83.280 933 126 19 2771 3699 22321271 22320365 0.000000e+00 832
13 TraesCS3D01G040500 chr3B 81.272 865 120 14 1053 1899 22461455 22460615 0.000000e+00 662
14 TraesCS3D01G040500 chr3B 88.889 279 28 2 2492 2767 22459491 22459213 1.270000e-89 340
15 TraesCS3D01G040500 chr3B 88.462 156 17 1 1962 2116 22460496 22460341 1.750000e-43 187
16 TraesCS3D01G040500 chr3A 93.269 2704 132 21 1017 3699 20914047 20916721 0.000000e+00 3940
17 TraesCS3D01G040500 chr3A 88.661 1755 141 24 1032 2766 20841791 20843507 0.000000e+00 2085
18 TraesCS3D01G040500 chr3A 91.708 1013 52 9 3 1003 20912813 20913805 0.000000e+00 1376
19 TraesCS3D01G040500 chr3A 93.140 933 55 5 2769 3699 20843546 20844471 0.000000e+00 1360
20 TraesCS3D01G040500 chr3A 83.996 931 124 14 2771 3699 20938666 20939573 0.000000e+00 870
21 TraesCS3D01G040500 chr3A 81.995 872 118 17 1040 1899 20936815 20937659 0.000000e+00 704
22 TraesCS3D01G040500 chr3A 83.519 449 60 11 1962 2400 20937778 20938222 1.240000e-109 407
23 TraesCS3D01G040500 chr3A 91.935 248 20 0 2521 2768 20938377 20938624 7.600000e-92 348
24 TraesCS3D01G040500 chr5D 83.909 1187 158 22 2516 3699 558340694 558339538 0.000000e+00 1103
25 TraesCS3D01G040500 chr5D 80.164 852 122 21 1031 1866 558342300 558341480 8.840000e-166 593
26 TraesCS3D01G040500 chr5D 83.247 388 41 9 10 384 561617487 561617863 5.920000e-88 335
27 TraesCS3D01G040500 chr5D 79.716 493 66 19 1901 2368 558341366 558340883 3.560000e-85 326
28 TraesCS3D01G040500 chr5D 81.159 276 44 6 12 284 418530870 418531140 8.050000e-52 215
29 TraesCS3D01G040500 chr4A 83.501 1194 152 28 2516 3699 611265364 611264206 0.000000e+00 1072
30 TraesCS3D01G040500 chr4A 80.816 490 63 17 1901 2368 611266036 611265556 4.540000e-94 355
31 TraesCS3D01G040500 chr4A 77.533 454 74 21 8 441 24979660 24979215 7.930000e-62 248
32 TraesCS3D01G040500 chr4A 79.167 312 49 13 7 317 140751904 140751608 6.260000e-48 202
33 TraesCS3D01G040500 chr5B 83.221 1192 162 25 2513 3699 704311695 704312853 0.000000e+00 1059
34 TraesCS3D01G040500 chr5B 79.454 842 124 25 1036 1860 704310154 704310963 5.400000e-153 551
35 TraesCS3D01G040500 chr5B 85.644 404 41 12 2 391 287475921 287476321 3.440000e-110 409
36 TraesCS3D01G040500 chr5B 81.647 425 52 13 1962 2368 704311092 704311508 2.750000e-86 329
37 TraesCS3D01G040500 chr7D 85.610 549 69 8 463 1003 617516706 617516160 5.360000e-158 568
38 TraesCS3D01G040500 chr7D 78.692 535 72 21 473 1003 116468665 116469161 5.960000e-83 318
39 TraesCS3D01G040500 chr7B 84.981 526 70 7 474 994 711738501 711737980 3.270000e-145 525
40 TraesCS3D01G040500 chr2D 83.765 425 52 8 7 418 643953224 643952804 1.610000e-103 387
41 TraesCS3D01G040500 chr2D 85.802 162 19 3 2196 2355 2450240 2450081 6.350000e-38 169
42 TraesCS3D01G040500 chr2A 79.287 449 77 8 493 940 597865116 597864683 2.160000e-77 300
43 TraesCS3D01G040500 chr2B 85.441 261 33 5 61 317 195622379 195622638 2.190000e-67 267
44 TraesCS3D01G040500 chr1B 78.507 442 63 18 10 435 616600502 616600927 1.020000e-65 261
45 TraesCS3D01G040500 chr1B 84.834 211 27 5 7 215 308636499 308636292 1.350000e-49 207
46 TraesCS3D01G040500 chr1A 85.586 222 28 3 10 227 12120252 12120473 2.870000e-56 230
47 TraesCS3D01G040500 chr1A 83.333 228 33 5 2 227 372032034 372032258 4.840000e-49 206


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 TraesCS3D01G040500 chr3D 15365387 15369085 3698 True 6831.000000 6831 100.000000 1 3699 1 chr3D.!!$R1 3698
1 TraesCS3D01G040500 chr3D 15386959 15389627 2668 True 1794.500000 2165 91.965500 1032 3699 2 chr3D.!!$R4 2667
2 TraesCS3D01G040500 chr3D 15341400 15345020 3620 True 439.750000 625 85.373750 1053 3430 4 chr3D.!!$R3 2377
3 TraesCS3D01G040500 chr3B 22515318 22519299 3981 False 2574.000000 4021 90.664500 3 3699 2 chr3B.!!$F1 3696
4 TraesCS3D01G040500 chr3B 22320365 22323141 2776 True 941.000000 1050 81.916000 1037 3699 2 chr3B.!!$R1 2662
5 TraesCS3D01G040500 chr3B 22458263 22461455 3192 True 508.000000 843 85.533750 1053 3699 4 chr3B.!!$R2 2646
6 TraesCS3D01G040500 chr3A 20912813 20916721 3908 False 2658.000000 3940 92.488500 3 3699 2 chr3A.!!$F2 3696
7 TraesCS3D01G040500 chr3A 20841791 20844471 2680 False 1722.500000 2085 90.900500 1032 3699 2 chr3A.!!$F1 2667
8 TraesCS3D01G040500 chr3A 20936815 20939573 2758 False 582.250000 870 85.361250 1040 3699 4 chr3A.!!$F3 2659
9 TraesCS3D01G040500 chr5D 558339538 558342300 2762 True 674.000000 1103 81.263000 1031 3699 3 chr5D.!!$R1 2668
10 TraesCS3D01G040500 chr4A 611264206 611266036 1830 True 713.500000 1072 82.158500 1901 3699 2 chr4A.!!$R3 1798
11 TraesCS3D01G040500 chr5B 704310154 704312853 2699 False 646.333333 1059 81.440667 1036 3699 3 chr5B.!!$F2 2663
12 TraesCS3D01G040500 chr7D 617516160 617516706 546 True 568.000000 568 85.610000 463 1003 1 chr7D.!!$R1 540
13 TraesCS3D01G040500 chr7B 711737980 711738501 521 True 525.000000 525 84.981000 474 994 1 chr7B.!!$R1 520

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
219 224 0.906066 GAGGGAGAAGAGGGGACAAC 59.094 60.0 0.00 0.0 0.00 3.32 F
438 455 1.058428 TCCCCCATGGAGATGCTCTG 61.058 60.0 15.22 0.0 38.61 3.35 F
1518 1933 0.249699 TCAACACGGTGAACATCGCT 60.250 50.0 16.29 0.0 38.78 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1228 1622 0.590481 GTCCCGTTTGTGTTTGCGTC 60.590 55.000 0.0 0.0 0.00 5.19 R
1770 2194 0.896940 AGGCCTCGAACCTGACGTTA 60.897 55.000 0.0 0.0 35.72 3.18 R
3177 5476 1.002257 CAGGTGCCATGTAGCCACA 60.002 57.895 0.0 0.0 39.52 4.17 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
59 60 5.272283 TCCTCTGGTATATGTCCGTTTTC 57.728 43.478 0.00 0.00 0.00 2.29
70 71 2.242047 TCCGTTTTCATGTTCGGACA 57.758 45.000 0.00 0.00 45.49 4.02
194 196 4.620589 TTATGGTTTAGTGTCCGGTTGA 57.379 40.909 0.00 0.00 0.00 3.18
219 224 0.906066 GAGGGAGAAGAGGGGACAAC 59.094 60.000 0.00 0.00 0.00 3.32
358 375 4.345854 ACTTCGAGGACTGATAAAGGTCT 58.654 43.478 0.00 0.00 33.46 3.85
385 402 8.557864 CCATTGAATTGCAAAAGTGAACAAATA 58.442 29.630 1.71 0.00 40.48 1.40
392 409 6.215121 TGCAAAAGTGAACAAATATGTCCAG 58.785 36.000 0.00 0.00 39.40 3.86
421 438 6.639563 ACAAATACCAATATTTTGCAGGTCC 58.360 36.000 0.00 0.00 38.67 4.46
425 442 2.465813 CAATATTTTGCAGGTCCCCCA 58.534 47.619 0.00 0.00 0.00 4.96
435 452 2.081161 GGTCCCCCATGGAGATGCT 61.081 63.158 15.22 0.00 46.38 3.79
438 455 1.058428 TCCCCCATGGAGATGCTCTG 61.058 60.000 15.22 0.00 38.61 3.35
460 477 8.239681 TCTGAAATATCTGAAACACAAGTACG 57.760 34.615 0.00 0.00 31.42 3.67
600 620 1.974236 CCCTTCTACATGGGGAGCTAG 59.026 57.143 0.00 0.00 42.58 3.42
632 654 3.863086 ACAATATTCCTCTCCCTCGGAT 58.137 45.455 0.00 0.00 0.00 4.18
634 656 3.551635 ATATTCCTCTCCCTCGGATGT 57.448 47.619 0.00 0.00 0.00 3.06
678 702 6.769512 AGAAATTCCTAGCTAAGAACACACA 58.230 36.000 6.94 0.00 0.00 3.72
681 705 4.785511 TCCTAGCTAAGAACACACACTC 57.214 45.455 0.00 0.00 0.00 3.51
682 706 4.408276 TCCTAGCTAAGAACACACACTCT 58.592 43.478 0.00 0.00 0.00 3.24
683 707 4.833380 TCCTAGCTAAGAACACACACTCTT 59.167 41.667 0.00 0.00 35.99 2.85
684 708 5.304614 TCCTAGCTAAGAACACACACTCTTT 59.695 40.000 0.00 0.00 33.89 2.52
869 898 6.016527 ACATGTTCAGTTCTACTGTTACTCGA 60.017 38.462 6.71 0.00 46.03 4.04
944 973 2.038295 CCTCCTGAAGACAGAAAGCAGT 59.962 50.000 0.00 0.00 46.03 4.40
947 976 4.825422 TCCTGAAGACAGAAAGCAGTATG 58.175 43.478 0.00 0.00 46.03 2.39
1240 1634 3.943034 CCGCCGACGCAAACACAA 61.943 61.111 0.00 0.00 38.22 3.33
1241 1635 2.023461 CGCCGACGCAAACACAAA 59.977 55.556 0.00 0.00 34.03 2.83
1243 1637 2.283058 GCCGACGCAAACACAAACG 61.283 57.895 0.00 0.00 34.03 3.60
1244 1638 1.652930 CCGACGCAAACACAAACGG 60.653 57.895 0.00 0.00 0.00 4.44
1246 1640 1.722677 GACGCAAACACAAACGGGA 59.277 52.632 0.00 0.00 0.00 5.14
1247 1641 0.590481 GACGCAAACACAAACGGGAC 60.590 55.000 0.00 0.00 0.00 4.46
1248 1642 1.298788 CGCAAACACAAACGGGACC 60.299 57.895 0.00 0.00 0.00 4.46
1249 1643 1.298788 GCAAACACAAACGGGACCG 60.299 57.895 9.56 9.56 46.03 4.79
1518 1933 0.249699 TCAACACGGTGAACATCGCT 60.250 50.000 16.29 0.00 38.78 4.93
1653 2077 2.955881 AACACTCTACGCCCTGGCC 61.956 63.158 1.86 0.00 37.98 5.36
1770 2194 3.077556 ATCTTCCGGCTCCGCTGT 61.078 61.111 0.00 0.00 38.24 4.40
2222 3405 5.047021 TCACGAGTTTCAAGAAGGAGATGAT 60.047 40.000 0.00 0.00 0.00 2.45
2273 3456 5.383130 GCCGAGTTTTCAGTATTTGACTTC 58.617 41.667 0.00 0.00 35.64 3.01
2392 3743 6.981708 ACGTTACGTAATAATCCTCGTTTTG 58.018 36.000 9.22 0.00 38.73 2.44
2415 3766 2.615447 AGGCAAGATAACATGCATCACG 59.385 45.455 0.00 0.00 41.66 4.35
2433 3785 7.970614 TGCATCACGATTATCATCAGAGTATAC 59.029 37.037 0.00 0.00 0.00 1.47
2698 4952 6.133356 AGGAGAGGAGAAAATACTGGTCTAG 58.867 44.000 0.00 0.00 0.00 2.43
2808 5106 8.548721 TCTCGTCTTTTGATTGTTTCTTTAGAC 58.451 33.333 0.00 0.00 0.00 2.59
2809 5107 8.203937 TCGTCTTTTGATTGTTTCTTTAGACA 57.796 30.769 0.00 0.00 31.56 3.41
2858 5157 8.824159 TTAACTTATGAGCAGATGAAGATAGC 57.176 34.615 0.00 0.00 0.00 2.97
3002 5301 6.037610 ACATTCTCTTGGATAGCGAAATGAAC 59.962 38.462 0.00 0.00 31.77 3.18
3210 5509 0.839946 ACCTGAGTATGCATCCCACC 59.160 55.000 0.19 0.00 0.00 4.61
3211 5510 0.839277 CCTGAGTATGCATCCCACCA 59.161 55.000 0.19 0.00 0.00 4.17
3463 5769 1.739466 GGAGCGAACTCATTGATGCAA 59.261 47.619 0.00 0.00 45.42 4.08
3555 5861 2.183478 ATGCAGTTGATCGACCAACA 57.817 45.000 24.32 4.53 46.48 3.33
3562 5868 4.024133 CAGTTGATCGACCAACAATGTTGA 60.024 41.667 24.32 7.65 46.48 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 71 1.068588 CGTATCATGTCCACGGACCAT 59.931 52.381 13.60 5.84 43.97 3.55
78 79 0.263468 TCCCTCCCGTATCATGTCCA 59.737 55.000 0.00 0.00 0.00 4.02
109 110 7.094762 CCTCTCAGCCGAATACTTTTTAACTTT 60.095 37.037 0.00 0.00 0.00 2.66
111 112 5.875359 CCTCTCAGCCGAATACTTTTTAACT 59.125 40.000 0.00 0.00 0.00 2.24
116 117 3.769844 TCTCCTCTCAGCCGAATACTTTT 59.230 43.478 0.00 0.00 0.00 2.27
120 121 3.802948 TTTCTCCTCTCAGCCGAATAC 57.197 47.619 0.00 0.00 0.00 1.89
162 164 6.059484 ACACTAAACCATAAATATCCCACCG 58.941 40.000 0.00 0.00 0.00 4.94
194 196 0.933700 CCCTCTTCTCCCTCTCCTCT 59.066 60.000 0.00 0.00 0.00 3.69
336 343 4.345854 AGACCTTTATCAGTCCTCGAAGT 58.654 43.478 0.00 0.00 33.29 3.01
358 375 5.668471 TGTTCACTTTTGCAATTCAATGGA 58.332 33.333 0.00 0.00 34.12 3.41
392 409 6.326375 TGCAAAATATTGGTATTTGTCCGAC 58.674 36.000 0.00 0.00 39.75 4.79
435 452 7.870954 ACGTACTTGTGTTTCAGATATTTCAGA 59.129 33.333 0.00 0.00 0.00 3.27
438 455 6.736853 GCACGTACTTGTGTTTCAGATATTTC 59.263 38.462 0.93 0.00 41.94 2.17
480 498 5.007234 CGAAAATTAATAGTCGCCATGGTGA 59.993 40.000 24.20 24.20 0.00 4.02
600 620 6.072783 GGAGAGGAATATTGTAGCTCATTTGC 60.073 42.308 0.00 0.00 0.00 3.68
632 654 9.942850 TTTCTCTCATGTAATCATAGAACAACA 57.057 29.630 0.00 0.00 32.47 3.33
678 702 6.879458 AGAAGTTTCGGCAATATACAAAGAGT 59.121 34.615 0.00 0.00 0.00 3.24
681 705 6.842163 ACAGAAGTTTCGGCAATATACAAAG 58.158 36.000 0.00 0.00 0.00 2.77
682 706 6.401688 CGACAGAAGTTTCGGCAATATACAAA 60.402 38.462 0.00 0.00 0.00 2.83
683 707 5.062934 CGACAGAAGTTTCGGCAATATACAA 59.937 40.000 0.00 0.00 0.00 2.41
684 708 4.565166 CGACAGAAGTTTCGGCAATATACA 59.435 41.667 0.00 0.00 0.00 2.29
947 976 8.635765 TGAGGGCTATGTTAAAATGAATATCC 57.364 34.615 0.00 0.00 0.00 2.59
1010 1330 3.367932 CGTATGTGCTTGTCCTAACTGTG 59.632 47.826 0.00 0.00 0.00 3.66
1011 1331 3.585862 CGTATGTGCTTGTCCTAACTGT 58.414 45.455 0.00 0.00 0.00 3.55
1014 1336 2.928116 GACCGTATGTGCTTGTCCTAAC 59.072 50.000 0.00 0.00 0.00 2.34
1228 1622 0.590481 GTCCCGTTTGTGTTTGCGTC 60.590 55.000 0.00 0.00 0.00 5.19
1229 1623 1.430228 GTCCCGTTTGTGTTTGCGT 59.570 52.632 0.00 0.00 0.00 5.24
1233 1627 2.483197 GGCGGTCCCGTTTGTGTTT 61.483 57.895 7.66 0.00 42.09 2.83
1234 1628 2.903350 GGCGGTCCCGTTTGTGTT 60.903 61.111 7.66 0.00 42.09 3.32
1770 2194 0.896940 AGGCCTCGAACCTGACGTTA 60.897 55.000 0.00 0.00 35.72 3.18
1877 2327 6.715280 AGGATTGTTCATCACATACTCTTGT 58.285 36.000 0.00 0.00 34.43 3.16
2222 3405 4.959210 TCTGTTTCCATTTCCCAAACTTGA 59.041 37.500 0.00 0.00 32.28 3.02
2273 3456 6.018589 TCTGTCGCCTCTAATATCTGATTG 57.981 41.667 0.00 0.00 0.00 2.67
2392 3743 4.319046 CGTGATGCATGTTATCTTGCCTAC 60.319 45.833 2.46 5.22 41.89 3.18
2433 3785 7.775093 TCTTATCCACTGTTCCAAATTCCTATG 59.225 37.037 0.00 0.00 0.00 2.23
2698 4952 6.372981 CAAGCTTTTGTTTGGCAAATATTCC 58.627 36.000 16.74 3.21 45.38 3.01
2808 5106 5.185454 TGTTGGTATAGCAGAGGACAAATG 58.815 41.667 4.57 0.00 0.00 2.32
2809 5107 5.435686 TGTTGGTATAGCAGAGGACAAAT 57.564 39.130 4.57 0.00 0.00 2.32
2843 5142 4.128643 GAGCTTTGCTATCTTCATCTGCT 58.871 43.478 0.00 0.00 39.88 4.24
2858 5157 3.274288 GTCCCAGTCCAATAGAGCTTTG 58.726 50.000 0.00 0.00 0.00 2.77
3002 5301 9.334693 GCTAATCCAAAATCTGATATTTTAGCG 57.665 33.333 0.00 0.00 30.85 4.26
3038 5337 5.673337 TTGTGTCAGTGTTATTTGAGCTC 57.327 39.130 6.82 6.82 0.00 4.09
3177 5476 1.002257 CAGGTGCCATGTAGCCACA 60.002 57.895 0.00 0.00 39.52 4.17
3210 5509 7.923888 ACATCCGATTTGATAGAGAAAATGTG 58.076 34.615 0.00 0.00 0.00 3.21
3211 5510 9.784531 ATACATCCGATTTGATAGAGAAAATGT 57.215 29.630 0.00 0.00 0.00 2.71
3555 5861 8.774890 TTAGCATTGCAATTACATTCAACATT 57.225 26.923 9.83 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.