Multiple sequence alignment - TraesCS3D01G509400

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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 TraesCS3D01G509400 chr3D 100.000 3500 0 0 1 3500 594955512 594952013 0.000000e+00 6464
1 TraesCS3D01G509400 chr3D 96.687 2596 51 14 924 3500 590153646 590156225 0.000000e+00 4285
2 TraesCS3D01G509400 chr3D 95.541 314 14 0 594 907 590160366 590160053 1.450000e-138 503
3 TraesCS3D01G509400 chr3D 94.888 313 15 1 594 906 594947122 594947433 4.060000e-134 488
4 TraesCS3D01G509400 chr3D 92.698 315 16 3 594 906 590153061 590153370 6.890000e-122 448
5 TraesCS3D01G509400 chr3D 84.598 448 48 8 13 451 594893349 594892914 3.230000e-115 425
6 TraesCS3D01G509400 chr2D 96.648 2924 61 13 594 3500 380678115 380681018 0.000000e+00 4822
7 TraesCS3D01G509400 chr4D 96.310 2927 65 17 593 3500 108842223 108845125 0.000000e+00 4767
8 TraesCS3D01G509400 chr4D 91.903 704 33 11 811 1509 488848780 488849464 0.000000e+00 963
9 TraesCS3D01G509400 chr1D 96.900 2484 50 8 921 3386 7180817 7183291 0.000000e+00 4135
10 TraesCS3D01G509400 chr1D 96.555 2003 51 5 1511 3500 42896308 42894311 0.000000e+00 3301
11 TraesCS3D01G509400 chr1D 96.270 1394 29 7 935 2315 4307997 4306614 0.000000e+00 2265
12 TraesCS3D01G509400 chr1D 92.225 926 47 8 594 1509 42897256 42896346 0.000000e+00 1288
13 TraesCS3D01G509400 chr5D 96.776 2388 58 7 1127 3500 449488326 449490708 0.000000e+00 3965
14 TraesCS3D01G509400 chr5D 97.389 1532 30 7 1971 3500 406909575 406911098 0.000000e+00 2599
15 TraesCS3D01G509400 chr5D 95.211 1399 42 8 593 1980 406899476 406900860 0.000000e+00 2189
16 TraesCS3D01G509400 chr5D 93.930 313 18 1 594 906 406945365 406945054 4.090000e-129 472
17 TraesCS3D01G509400 chr5D 93.375 317 18 2 593 908 449495588 449495274 1.900000e-127 466
18 TraesCS3D01G509400 chr5A 96.685 1991 58 4 1511 3500 573011281 573009298 0.000000e+00 3304
19 TraesCS3D01G509400 chr5A 91.145 926 44 11 593 1509 573012215 573011319 0.000000e+00 1221
20 TraesCS3D01G509400 chr2B 91.808 1123 63 6 2379 3478 80549106 80547990 0.000000e+00 1537
21 TraesCS3D01G509400 chr7A 93.043 1035 38 18 2478 3478 689938334 689939368 0.000000e+00 1482
22 TraesCS3D01G509400 chr3A 96.464 707 22 1 2794 3500 22759190 22758487 0.000000e+00 1164
23 TraesCS3D01G509400 chr3A 89.965 568 27 6 3 562 725904875 725904330 0.000000e+00 706
24 TraesCS3D01G509400 chr3A 86.283 452 45 12 13 451 725842715 725842268 3.160000e-130 475
25 TraesCS3D01G509400 chr3A 87.302 126 16 0 3 128 725911531 725911406 1.010000e-30 145
26 TraesCS3D01G509400 chr3B 94.464 560 31 0 3 562 798404055 798403496 0.000000e+00 863


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 TraesCS3D01G509400 chr3D 594952013 594955512 3499 True 6464.0 6464 100.0000 1 3500 1 chr3D.!!$R3 3499
1 TraesCS3D01G509400 chr3D 590153061 590156225 3164 False 2366.5 4285 94.6925 594 3500 2 chr3D.!!$F2 2906
2 TraesCS3D01G509400 chr2D 380678115 380681018 2903 False 4822.0 4822 96.6480 594 3500 1 chr2D.!!$F1 2906
3 TraesCS3D01G509400 chr4D 108842223 108845125 2902 False 4767.0 4767 96.3100 593 3500 1 chr4D.!!$F1 2907
4 TraesCS3D01G509400 chr4D 488848780 488849464 684 False 963.0 963 91.9030 811 1509 1 chr4D.!!$F2 698
5 TraesCS3D01G509400 chr1D 7180817 7183291 2474 False 4135.0 4135 96.9000 921 3386 1 chr1D.!!$F1 2465
6 TraesCS3D01G509400 chr1D 42894311 42897256 2945 True 2294.5 3301 94.3900 594 3500 2 chr1D.!!$R2 2906
7 TraesCS3D01G509400 chr1D 4306614 4307997 1383 True 2265.0 2265 96.2700 935 2315 1 chr1D.!!$R1 1380
8 TraesCS3D01G509400 chr5D 449488326 449490708 2382 False 3965.0 3965 96.7760 1127 3500 1 chr5D.!!$F3 2373
9 TraesCS3D01G509400 chr5D 406909575 406911098 1523 False 2599.0 2599 97.3890 1971 3500 1 chr5D.!!$F2 1529
10 TraesCS3D01G509400 chr5D 406899476 406900860 1384 False 2189.0 2189 95.2110 593 1980 1 chr5D.!!$F1 1387
11 TraesCS3D01G509400 chr5A 573009298 573012215 2917 True 2262.5 3304 93.9150 593 3500 2 chr5A.!!$R1 2907
12 TraesCS3D01G509400 chr2B 80547990 80549106 1116 True 1537.0 1537 91.8080 2379 3478 1 chr2B.!!$R1 1099
13 TraesCS3D01G509400 chr7A 689938334 689939368 1034 False 1482.0 1482 93.0430 2478 3478 1 chr7A.!!$F1 1000
14 TraesCS3D01G509400 chr3A 22758487 22759190 703 True 1164.0 1164 96.4640 2794 3500 1 chr3A.!!$R1 706
15 TraesCS3D01G509400 chr3A 725904330 725904875 545 True 706.0 706 89.9650 3 562 1 chr3A.!!$R3 559
16 TraesCS3D01G509400 chr3B 798403496 798404055 559 True 863.0 863 94.4640 3 562 1 chr3B.!!$R1 559

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
233 234 0.038251 TCTCTACCTGCGTGCTGTTG 60.038 55.0 0.0 0.0 0.0 3.33 F
236 237 0.319900 CTACCTGCGTGCTGTTGTCT 60.320 55.0 0.0 0.0 0.0 3.41 F
959 1230 0.332972 TCCTCTGCTCTCCACTGCTA 59.667 55.0 0.0 0.0 0.0 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1290 1573 0.624500 ATTTGCCAGCCCTCTCCCTA 60.625 55.000 0.0 0.0 0.00 3.53 R
1696 2023 8.497745 ACCAAGGTTCTCTTCATGATACATATT 58.502 33.333 0.0 0.0 32.41 1.28 R
2731 3081 1.000396 GCTGCCAAATCCTCCCACT 60.000 57.895 0.0 0.0 0.00 4.00 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
98 99 1.448013 CCTCGCCTTCGTTCCTTCC 60.448 63.158 0.00 0.00 36.96 3.46
193 194 1.271434 GGAGTTTGGTTGTCTCCCCTC 60.271 57.143 0.00 0.00 41.09 4.30
218 219 3.596046 TCTCCTCCTTCTCCTTCTTCTCT 59.404 47.826 0.00 0.00 0.00 3.10
223 224 4.605183 TCCTTCTCCTTCTTCTCTACCTG 58.395 47.826 0.00 0.00 0.00 4.00
233 234 0.038251 TCTCTACCTGCGTGCTGTTG 60.038 55.000 0.00 0.00 0.00 3.33
236 237 0.319900 CTACCTGCGTGCTGTTGTCT 60.320 55.000 0.00 0.00 0.00 3.41
305 306 1.764723 TGCATGATGTCCTCGGAGATT 59.235 47.619 6.58 0.00 33.89 2.40
415 417 2.358898 TCGATCGCAGATGAGTTGATGA 59.641 45.455 11.09 0.00 45.12 2.92
432 434 3.580319 AGGCTTTGGGCTTCGGGT 61.580 61.111 0.00 0.00 46.62 5.28
562 571 3.927163 AATTCCGCGGCGTCTCGTT 62.927 57.895 23.51 3.96 0.00 3.85
563 572 2.546645 AATTCCGCGGCGTCTCGTTA 62.547 55.000 23.51 0.00 0.00 3.18
564 573 3.951655 TTCCGCGGCGTCTCGTTAC 62.952 63.158 23.51 0.00 0.00 2.50
565 574 4.471726 CCGCGGCGTCTCGTTACT 62.472 66.667 22.00 0.00 0.00 2.24
566 575 2.943034 CGCGGCGTCTCGTTACTC 60.943 66.667 15.36 0.00 0.00 2.59
567 576 2.484203 GCGGCGTCTCGTTACTCT 59.516 61.111 9.37 0.00 0.00 3.24
568 577 1.583194 GCGGCGTCTCGTTACTCTC 60.583 63.158 9.37 0.00 0.00 3.20
569 578 1.296722 CGGCGTCTCGTTACTCTCG 60.297 63.158 0.00 0.00 0.00 4.04
570 579 1.792941 GGCGTCTCGTTACTCTCGT 59.207 57.895 0.00 0.00 0.00 4.18
571 580 1.002366 GGCGTCTCGTTACTCTCGTA 58.998 55.000 0.00 0.00 0.00 3.43
572 581 1.005137 GGCGTCTCGTTACTCTCGTAG 60.005 57.143 0.00 0.00 0.00 3.51
573 582 1.923204 GCGTCTCGTTACTCTCGTAGA 59.077 52.381 0.00 0.00 0.00 2.59
574 583 2.284969 GCGTCTCGTTACTCTCGTAGAC 60.285 54.545 0.00 0.00 34.99 2.59
575 584 2.281234 CGTCTCGTTACTCTCGTAGACC 59.719 54.545 0.00 0.00 34.93 3.85
576 585 2.281234 GTCTCGTTACTCTCGTAGACCG 59.719 54.545 0.00 0.00 33.73 4.79
577 586 2.094494 TCTCGTTACTCTCGTAGACCGT 60.094 50.000 0.00 0.00 37.94 4.83
578 587 2.263077 TCGTTACTCTCGTAGACCGTC 58.737 52.381 0.00 0.00 37.94 4.79
579 588 2.094494 TCGTTACTCTCGTAGACCGTCT 60.094 50.000 6.25 6.25 37.94 4.18
580 589 2.281234 CGTTACTCTCGTAGACCGTCTC 59.719 54.545 3.74 0.00 37.94 3.36
581 590 3.520569 GTTACTCTCGTAGACCGTCTCT 58.479 50.000 3.74 0.00 37.94 3.10
582 591 2.012937 ACTCTCGTAGACCGTCTCTG 57.987 55.000 3.74 0.00 37.94 3.35
583 592 1.275856 ACTCTCGTAGACCGTCTCTGT 59.724 52.381 3.74 0.00 37.94 3.41
584 593 1.928503 CTCTCGTAGACCGTCTCTGTC 59.071 57.143 3.74 0.00 37.94 3.51
585 594 1.549620 TCTCGTAGACCGTCTCTGTCT 59.450 52.381 3.74 0.00 44.85 3.41
586 595 1.928503 CTCGTAGACCGTCTCTGTCTC 59.071 57.143 3.74 0.00 41.97 3.36
587 596 1.549620 TCGTAGACCGTCTCTGTCTCT 59.450 52.381 3.74 0.00 41.97 3.10
588 597 1.661617 CGTAGACCGTCTCTGTCTCTG 59.338 57.143 3.74 0.00 41.97 3.35
589 598 2.674462 CGTAGACCGTCTCTGTCTCTGA 60.674 54.545 3.74 0.00 41.97 3.27
590 599 2.799126 AGACCGTCTCTGTCTCTGAT 57.201 50.000 0.00 0.00 38.71 2.90
591 600 3.080300 AGACCGTCTCTGTCTCTGATT 57.920 47.619 0.00 0.00 38.71 2.57
674 685 8.904099 TTTTAAAAACTGACCAAAAACTCCAA 57.096 26.923 0.00 0.00 0.00 3.53
736 748 2.032377 TGATGACCGTTTCAAGCGTTTC 60.032 45.455 0.00 0.00 37.92 2.78
890 904 4.778415 CGCTCGTCGTCCCACCAG 62.778 72.222 0.00 0.00 0.00 4.00
902 922 2.608988 CACCAGCTCACTCCCCCT 60.609 66.667 0.00 0.00 0.00 4.79
907 927 4.423209 GCTCACTCCCCCTCCCCT 62.423 72.222 0.00 0.00 0.00 4.79
908 928 2.041405 CTCACTCCCCCTCCCCTC 60.041 72.222 0.00 0.00 0.00 4.30
909 929 3.695825 TCACTCCCCCTCCCCTCC 61.696 72.222 0.00 0.00 0.00 4.30
910 930 4.825679 CACTCCCCCTCCCCTCCC 62.826 77.778 0.00 0.00 0.00 4.30
956 1227 1.256361 TGCTCCTCTGCTCTCCACTG 61.256 60.000 0.00 0.00 0.00 3.66
957 1228 1.516892 CTCCTCTGCTCTCCACTGC 59.483 63.158 0.00 0.00 0.00 4.40
958 1229 0.971959 CTCCTCTGCTCTCCACTGCT 60.972 60.000 0.00 0.00 0.00 4.24
959 1230 0.332972 TCCTCTGCTCTCCACTGCTA 59.667 55.000 0.00 0.00 0.00 3.49
1117 1394 1.128200 TCTCTCCTCTCCTCTCCTCG 58.872 60.000 0.00 0.00 0.00 4.63
1136 1413 1.412074 CGGCTAGGGTTAGGGTTAGGA 60.412 57.143 0.00 0.00 0.00 2.94
1255 1538 4.228210 TGATAGATCCAAGCTTTTCTGGGT 59.772 41.667 0.00 0.00 37.18 4.51
1273 1556 3.136443 TGGGTTTGTGACTGAATCTGACT 59.864 43.478 0.00 0.00 0.00 3.41
1802 2129 4.943705 GGATTCTCTTGGCAATCAGTACAA 59.056 41.667 0.00 0.00 31.58 2.41
1948 2275 6.627243 CAGGCAAAGATTGAGATTCAAATGA 58.373 36.000 0.00 0.00 40.12 2.57
2202 2530 4.385310 GGTTGGTAAGTGAATATGAGGCCT 60.385 45.833 3.86 3.86 0.00 5.19
2203 2531 5.163237 GGTTGGTAAGTGAATATGAGGCCTA 60.163 44.000 4.42 0.00 0.00 3.93
2204 2532 6.465894 GGTTGGTAAGTGAATATGAGGCCTAT 60.466 42.308 4.42 2.27 0.00 2.57
2205 2533 7.256547 GGTTGGTAAGTGAATATGAGGCCTATA 60.257 40.741 4.42 4.75 0.00 1.31
2347 2683 2.809665 GCCCCTGATCTGTAATGCTCTG 60.810 54.545 0.00 0.00 0.00 3.35
2435 2771 2.472695 TGTTGCTGCTAGGTAGTTGG 57.527 50.000 0.00 0.00 0.00 3.77
2452 2788 7.616935 AGGTAGTTGGTGCTAATACTTACACTA 59.383 37.037 0.00 0.00 33.53 2.74
2476 2818 9.436957 CTAGAATCTAGTAACACCAAACAACAT 57.563 33.333 9.07 0.00 0.00 2.71
2485 2834 4.502962 ACACCAAACAACATTGAAACTGG 58.497 39.130 0.00 2.34 31.84 4.00
2497 2846 8.828644 CAACATTGAAACTGGAAATGAAAATGA 58.171 29.630 1.89 0.00 35.67 2.57
2498 2847 8.961294 ACATTGAAACTGGAAATGAAAATGAA 57.039 26.923 1.89 0.00 35.67 2.57
2499 2848 9.393512 ACATTGAAACTGGAAATGAAAATGAAA 57.606 25.926 1.89 0.00 35.67 2.69
2721 3071 0.463295 CCTGAGCGTCGTACCTCCTA 60.463 60.000 0.00 0.00 0.00 2.94
2731 3081 3.755378 GTCGTACCTCCTACTTCACTTCA 59.245 47.826 0.00 0.00 0.00 3.02
3163 3549 1.692148 CGCGCGCTGAACCATAAAGA 61.692 55.000 30.48 0.00 0.00 2.52
3316 3726 6.150307 TGTGAGTAGAGTAGCTGAAGAAAGAG 59.850 42.308 0.00 0.00 0.00 2.85
3317 3727 5.650266 TGAGTAGAGTAGCTGAAGAAAGAGG 59.350 44.000 0.00 0.00 0.00 3.69
3318 3728 4.953579 AGTAGAGTAGCTGAAGAAAGAGGG 59.046 45.833 0.00 0.00 0.00 4.30
3319 3729 3.103742 AGAGTAGCTGAAGAAAGAGGGG 58.896 50.000 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 4.479993 CTCAAGGGCCAGCCTCCG 62.480 72.222 6.18 0.00 36.10 4.63
76 77 3.872027 GAACGAAGGCGAGGTTCC 58.128 61.111 0.00 0.00 41.64 3.62
98 99 4.541648 ATCTCCGTCCCCCTCCCG 62.542 72.222 0.00 0.00 0.00 5.14
182 183 1.682684 GGAGAGCGAGGGGAGACAA 60.683 63.158 0.00 0.00 0.00 3.18
193 194 0.744281 GAAGGAGAAGGAGGAGAGCG 59.256 60.000 0.00 0.00 0.00 5.03
218 219 0.105964 AAGACAACAGCACGCAGGTA 59.894 50.000 0.00 0.00 0.00 3.08
223 224 0.654472 CGTGAAAGACAACAGCACGC 60.654 55.000 0.00 0.00 44.35 5.34
415 417 2.656698 AAACCCGAAGCCCAAAGCCT 62.657 55.000 0.00 0.00 45.47 4.58
511 518 3.549423 CGGACATAGTCGAAGCGGAATAA 60.549 47.826 0.00 0.00 32.65 1.40
562 571 7.390413 GAGACAGAGACGGTCTACGAGAGTA 62.390 52.000 11.27 0.00 45.21 2.59
563 572 6.693626 GAGACAGAGACGGTCTACGAGAGT 62.694 54.167 11.27 3.76 45.21 3.24
564 573 4.281013 GAGACAGAGACGGTCTACGAGAG 61.281 56.522 11.27 0.60 45.21 3.20
565 574 2.417107 GAGACAGAGACGGTCTACGAGA 60.417 54.545 11.27 0.00 45.21 4.04
566 575 1.928503 GAGACAGAGACGGTCTACGAG 59.071 57.143 11.27 4.06 45.21 4.18
567 576 1.549620 AGAGACAGAGACGGTCTACGA 59.450 52.381 11.27 0.00 45.21 3.43
568 577 1.661617 CAGAGACAGAGACGGTCTACG 59.338 57.143 11.27 7.64 45.21 3.51
569 578 2.975266 TCAGAGACAGAGACGGTCTAC 58.025 52.381 11.27 5.16 45.21 2.59
570 579 3.916359 ATCAGAGACAGAGACGGTCTA 57.084 47.619 11.27 0.00 45.21 2.59
572 581 4.193090 TCTAATCAGAGACAGAGACGGTC 58.807 47.826 0.00 0.00 35.50 4.79
573 582 4.223556 TCTAATCAGAGACAGAGACGGT 57.776 45.455 0.00 0.00 0.00 4.83
674 685 3.000041 TGTCACGAAATCAGCGCTAAAT 59.000 40.909 10.99 3.69 0.00 1.40
890 904 4.423209 AGGGGAGGGGGAGTGAGC 62.423 72.222 0.00 0.00 0.00 4.26
956 1227 3.243068 CGAGAAGAAGAAGAGGAGCTAGC 60.243 52.174 6.62 6.62 0.00 3.42
957 1228 3.243068 GCGAGAAGAAGAAGAGGAGCTAG 60.243 52.174 0.00 0.00 0.00 3.42
958 1229 2.685897 GCGAGAAGAAGAAGAGGAGCTA 59.314 50.000 0.00 0.00 0.00 3.32
959 1230 1.476488 GCGAGAAGAAGAAGAGGAGCT 59.524 52.381 0.00 0.00 0.00 4.09
1015 1289 1.540267 GTCAGAGGTCTCGTTGCTGTA 59.460 52.381 0.00 0.00 34.09 2.74
1117 1394 2.484189 TCCTAACCCTAACCCTAGCC 57.516 55.000 0.00 0.00 0.00 3.93
1136 1413 7.091811 TGGAGAAATCCCTATCCTTCTTCAAAT 60.092 37.037 0.00 0.00 31.81 2.32
1255 1538 5.070446 ACCTACAGTCAGATTCAGTCACAAA 59.930 40.000 0.00 0.00 0.00 2.83
1290 1573 0.624500 ATTTGCCAGCCCTCTCCCTA 60.625 55.000 0.00 0.00 0.00 3.53
1696 2023 8.497745 ACCAAGGTTCTCTTCATGATACATATT 58.502 33.333 0.00 0.00 32.41 1.28
2274 2610 5.428253 TGATCTGAAACCATAGGCAGTTAC 58.572 41.667 0.00 0.00 0.00 2.50
2347 2683 6.603599 GGGGGCATTACAAATAGGATTATCTC 59.396 42.308 0.00 0.00 0.00 2.75
2452 2788 8.567948 CAATGTTGTTTGGTGTTACTAGATTCT 58.432 33.333 0.00 0.00 0.00 2.40
2498 2847 9.255029 ACCTCCTATGTAATGCAAGTTTTAATT 57.745 29.630 0.00 0.00 0.00 1.40
2499 2848 8.823220 ACCTCCTATGTAATGCAAGTTTTAAT 57.177 30.769 0.00 0.00 0.00 1.40
2500 2849 9.391006 CTACCTCCTATGTAATGCAAGTTTTAA 57.609 33.333 0.00 0.00 0.00 1.52
2501 2850 7.497909 GCTACCTCCTATGTAATGCAAGTTTTA 59.502 37.037 0.00 0.00 0.00 1.52
2502 2851 6.318900 GCTACCTCCTATGTAATGCAAGTTTT 59.681 38.462 0.00 0.00 0.00 2.43
2731 3081 1.000396 GCTGCCAAATCCTCCCACT 60.000 57.895 0.00 0.00 0.00 4.00
3168 3554 0.190815 AACTGGCAAGGGATGGGTTT 59.809 50.000 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.