Multiple sequence alignment - TraesCS4A01G199600

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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 TraesCS4A01G199600 chr4A 100.000 5195 0 0 890 6084 487862038 487867232 0.000000e+00 9594
1 TraesCS4A01G199600 chr4A 100.000 508 0 0 1 508 487861149 487861656 0.000000e+00 939
2 TraesCS4A01G199600 chr4A 81.511 741 118 12 3532 4261 486641621 486642353 5.250000e-165 592
3 TraesCS4A01G199600 chr4A 80.918 697 91 30 910 1596 486639789 486640453 4.210000e-141 512
4 TraesCS4A01G199600 chr4A 76.822 535 83 24 2515 3024 486640461 486640979 4.680000e-66 263
5 TraesCS4A01G199600 chr4A 84.766 256 36 2 3239 3492 486641241 486641495 2.810000e-63 254
6 TraesCS4A01G199600 chr4B 95.994 2696 57 15 890 3565 132338528 132335864 0.000000e+00 4333
7 TraesCS4A01G199600 chr4B 95.779 2085 72 11 3563 5639 132335771 132333695 0.000000e+00 3349
8 TraesCS4A01G199600 chr4B 95.813 406 9 2 104 508 132339043 132338645 0.000000e+00 649
9 TraesCS4A01G199600 chr4B 81.157 743 119 13 3532 4264 132854647 132853916 1.470000e-160 577
10 TraesCS4A01G199600 chr4B 79.953 424 51 17 2621 3024 132855682 132855273 1.290000e-71 281
11 TraesCS4A01G199600 chr4B 81.418 409 14 17 5709 6084 132333695 132333316 1.670000e-70 278
12 TraesCS4A01G199600 chr4B 84.109 258 37 4 3237 3492 132855018 132854763 4.710000e-61 246
13 TraesCS4A01G199600 chr4B 98.095 105 1 1 1 105 132339269 132339166 1.350000e-41 182
14 TraesCS4A01G199600 chr4D 94.741 2434 87 16 2513 4933 93846603 93844198 0.000000e+00 3747
15 TraesCS4A01G199600 chr4D 96.050 1595 47 10 891 2476 93848189 93846602 0.000000e+00 2582
16 TraesCS4A01G199600 chr4D 89.897 1168 58 26 4939 6077 93844093 93842957 0.000000e+00 1448
17 TraesCS4A01G199600 chr4D 81.316 760 121 12 3518 4265 94260321 94259571 1.130000e-166 597
18 TraesCS4A01G199600 chr4D 81.530 693 94 26 910 1596 94262240 94261576 1.930000e-149 540
19 TraesCS4A01G199600 chr4D 95.331 257 8 2 1 257 93848956 93848704 7.340000e-109 405
20 TraesCS4A01G199600 chr4D 90.830 229 7 6 283 508 93848711 93848494 1.660000e-75 294
21 TraesCS4A01G199600 chr4D 82.663 323 32 11 2714 3024 94261240 94260930 1.300000e-66 265
22 TraesCS4A01G199600 chr4D 84.766 256 38 1 3237 3492 94260676 94260422 7.830000e-64 255
23 TraesCS4A01G199600 chr2B 79.790 1049 146 45 3197 4231 511275970 511276966 0.000000e+00 702
24 TraesCS4A01G199600 chr2B 81.781 494 68 16 910 1387 511273381 511273868 1.590000e-105 394
25 TraesCS4A01G199600 chr2A 79.042 1107 160 48 3151 4231 553487490 553486430 0.000000e+00 693
26 TraesCS4A01G199600 chr2A 80.000 660 110 20 909 1558 553489981 553489334 9.230000e-128 468
27 TraesCS4A01G199600 chr2D 82.186 668 100 15 3576 4231 433506432 433507092 1.920000e-154 556
28 TraesCS4A01G199600 chr2D 79.909 662 108 22 909 1558 433503414 433504062 4.300000e-126 462
29 TraesCS4A01G199600 chr2D 82.609 299 45 5 3151 3445 433505893 433506188 2.180000e-64 257
30 TraesCS4A01G199600 chrUn 84.184 392 53 8 996 1383 477061841 477062227 7.450000e-99 372


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 TraesCS4A01G199600 chr4A 487861149 487867232 6083 False 5266.50 9594 100.000000 1 6084 2 chr4A.!!$F2 6083
1 TraesCS4A01G199600 chr4A 486639789 486642353 2564 False 405.25 592 81.004250 910 4261 4 chr4A.!!$F1 3351
2 TraesCS4A01G199600 chr4B 132333316 132339269 5953 True 1758.20 4333 93.419800 1 6084 5 chr4B.!!$R1 6083
3 TraesCS4A01G199600 chr4B 132853916 132855682 1766 True 368.00 577 81.739667 2621 4264 3 chr4B.!!$R2 1643
4 TraesCS4A01G199600 chr4D 93842957 93848956 5999 True 1695.20 3747 93.369800 1 6077 5 chr4D.!!$R1 6076
5 TraesCS4A01G199600 chr4D 94259571 94262240 2669 True 414.25 597 82.568750 910 4265 4 chr4D.!!$R2 3355
6 TraesCS4A01G199600 chr2B 511273381 511276966 3585 False 548.00 702 80.785500 910 4231 2 chr2B.!!$F1 3321
7 TraesCS4A01G199600 chr2A 553486430 553489981 3551 True 580.50 693 79.521000 909 4231 2 chr2A.!!$R1 3322
8 TraesCS4A01G199600 chr2D 433503414 433507092 3678 False 425.00 556 81.568000 909 4231 3 chr2D.!!$F1 3322


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
78 79 0.321564 CCTTGAACGCCATGGACTCA 60.322 55.000 18.40 11.31 41.31 3.41 F
462 594 0.542333 GTACCTTCCTCCTGCCTTCC 59.458 60.000 0.00 0.00 0.00 3.46 F
1818 1978 3.365969 GGTTCCATTTTTCTGTACCAGCG 60.366 47.826 0.00 0.00 0.00 5.18 F
2530 2906 1.765074 GCCCTTGACCCCAGTGTTA 59.235 57.895 0.00 0.00 0.00 2.41 F
3847 5300 2.103537 TTACTACGCCTTGAAAGGGC 57.896 50.000 11.03 0.00 46.56 5.19 F
4801 6277 2.036098 TTGCCAGACTGCCATGGG 59.964 61.111 15.13 0.00 37.05 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1696 1855 0.528017 TGTTTGGCGTGCAGAAAACA 59.472 45.000 12.66 12.66 39.51 2.83 R
2063 2233 1.153524 ACATGACCAGCCCAAGCAA 59.846 52.632 0.00 0.00 43.56 3.91 R
3281 4386 1.338973 AGAACATGCAAACTGTGGCTG 59.661 47.619 0.00 5.05 0.00 4.85 R
4081 5537 3.365472 TCTGCTGCTACTTGTGAGGATA 58.635 45.455 0.00 0.00 0.00 2.59 R
4814 6290 0.540597 GAGCCTTGCCTTTCAGGGTT 60.541 55.000 0.00 0.00 43.37 4.11 R
5621 7213 0.662374 ATAGATAAACGACGGCCGCG 60.662 55.000 30.82 30.82 43.32 6.46 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
78 79 0.321564 CCTTGAACGCCATGGACTCA 60.322 55.000 18.40 11.31 41.31 3.41
236 361 7.605691 TCTTTTGTTTGTTGTTTTGTCATCCAT 59.394 29.630 0.00 0.00 0.00 3.41
238 363 5.114780 TGTTTGTTGTTTTGTCATCCATGG 58.885 37.500 4.97 4.97 0.00 3.66
452 584 3.182152 ACATGCCTAGTTGTACCTTCCT 58.818 45.455 0.00 0.00 0.00 3.36
453 585 3.197983 ACATGCCTAGTTGTACCTTCCTC 59.802 47.826 0.00 0.00 0.00 3.71
454 586 2.185387 TGCCTAGTTGTACCTTCCTCC 58.815 52.381 0.00 0.00 0.00 4.30
455 587 2.225547 TGCCTAGTTGTACCTTCCTCCT 60.226 50.000 0.00 0.00 0.00 3.69
456 588 2.168728 GCCTAGTTGTACCTTCCTCCTG 59.831 54.545 0.00 0.00 0.00 3.86
457 589 2.168728 CCTAGTTGTACCTTCCTCCTGC 59.831 54.545 0.00 0.00 0.00 4.85
458 590 0.984995 AGTTGTACCTTCCTCCTGCC 59.015 55.000 0.00 0.00 0.00 4.85
459 591 0.984995 GTTGTACCTTCCTCCTGCCT 59.015 55.000 0.00 0.00 0.00 4.75
460 592 1.351350 GTTGTACCTTCCTCCTGCCTT 59.649 52.381 0.00 0.00 0.00 4.35
461 593 1.276622 TGTACCTTCCTCCTGCCTTC 58.723 55.000 0.00 0.00 0.00 3.46
462 594 0.542333 GTACCTTCCTCCTGCCTTCC 59.458 60.000 0.00 0.00 0.00 3.46
1029 1172 4.005650 TCATGCAGACAAGTGATTCTTCC 58.994 43.478 0.00 0.00 33.63 3.46
1696 1855 3.795877 CAAGTGTTTGGTTCAAAGCCAT 58.204 40.909 0.00 0.00 33.82 4.40
1818 1978 3.365969 GGTTCCATTTTTCTGTACCAGCG 60.366 47.826 0.00 0.00 0.00 5.18
2063 2233 2.806434 TGTGATAGGTTGCCAAGCATT 58.194 42.857 9.58 0.00 38.76 3.56
2492 2820 3.123620 CAAGCGGCTCTGTCAGGC 61.124 66.667 1.45 2.47 44.60 4.85
2526 2902 2.169810 ATTGGCCCTTGACCCCAGT 61.170 57.895 0.00 0.00 0.00 4.00
2527 2903 2.445492 ATTGGCCCTTGACCCCAGTG 62.445 60.000 0.00 0.00 0.00 3.66
2528 2904 3.580319 GGCCCTTGACCCCAGTGT 61.580 66.667 0.00 0.00 0.00 3.55
2530 2906 1.765074 GCCCTTGACCCCAGTGTTA 59.235 57.895 0.00 0.00 0.00 2.41
2611 2992 6.183360 GGTGATCACATGACATCCTTGTTTAG 60.183 42.308 26.47 0.00 35.79 1.85
2612 2993 5.355071 TGATCACATGACATCCTTGTTTAGC 59.645 40.000 0.00 0.00 35.79 3.09
2645 3026 8.562892 CAACAGAAGAGATCAAACACTGTTTAT 58.437 33.333 16.52 2.44 42.47 1.40
3143 3816 4.769688 TCTTGTTCAGTTCTGCAGAAGAA 58.230 39.130 29.13 24.47 42.83 2.52
3281 4386 2.426522 TCATTACAACCTGCAGACAGC 58.573 47.619 17.39 0.00 43.02 4.40
3583 5033 7.672983 ATGGTAGTTGAGACTATTTGTGTTG 57.327 36.000 0.00 0.00 40.33 3.33
3847 5300 2.103537 TTACTACGCCTTGAAAGGGC 57.896 50.000 11.03 0.00 46.56 5.19
4309 5783 5.664457 TGCACAGGAGTACTCTAATGAATG 58.336 41.667 21.88 13.51 0.00 2.67
4499 5974 5.490139 CTGGTAAGCAGTATTGTCCATTG 57.510 43.478 0.00 0.00 0.00 2.82
4558 6034 3.606777 CACATTTGATGCTCTTTCTTGCG 59.393 43.478 0.00 0.00 0.00 4.85
4801 6277 2.036098 TTGCCAGACTGCCATGGG 59.964 61.111 15.13 0.00 37.05 4.00
4860 6336 2.832129 AGAGGATAGCACAAACCGAAGA 59.168 45.455 0.00 0.00 0.00 2.87
5041 6616 1.376553 GAAGGAGCACAGGAGCCAC 60.377 63.158 0.00 0.00 34.23 5.01
5051 6626 2.887568 GGAGCCACGATCACAGCG 60.888 66.667 0.00 0.00 0.00 5.18
5167 6745 4.552674 ACAACCAGGGTGAAAACCTATTT 58.447 39.130 13.01 0.00 36.32 1.40
5211 6789 1.115467 CTATCTCGGTCCTTGCTGGT 58.885 55.000 0.00 0.00 37.07 4.00
5254 6832 5.050490 CGTGATTCGAGAATATGGTTTCCT 58.950 41.667 0.00 0.00 42.86 3.36
5334 6918 2.096565 CGTGATGCGAGAATTATGCAGG 60.097 50.000 0.00 0.00 42.65 4.85
5505 7089 1.282248 TGCTGCGAACTCGTAACTGC 61.282 55.000 0.51 1.37 42.22 4.40
5508 7092 0.238025 TGCGAACTCGTAACTGCGTA 59.762 50.000 0.51 0.00 42.22 4.42
5510 7094 2.095692 TGCGAACTCGTAACTGCGTATA 59.904 45.455 0.51 0.00 42.22 1.47
5594 7186 0.179062 AGCTGGCGGATCATCAAGAC 60.179 55.000 0.00 0.00 0.00 3.01
5621 7213 2.105960 GAACGTGCACTGCTGTCCAC 62.106 60.000 16.19 7.68 0.00 4.02
5649 7242 6.746364 GGCCGTCGTTTATCTATAATAGACAG 59.254 42.308 13.58 7.38 37.69 3.51
5680 7273 1.305930 ACGAGAAGCAATTTCCCGCC 61.306 55.000 0.00 0.00 40.27 6.13
5835 7428 0.745468 AAGGAGGAAGGCGACGTATC 59.255 55.000 0.00 0.00 0.00 2.24
5887 7480 3.282885 CCTAATCCTGCACCTCCTTTTC 58.717 50.000 0.00 0.00 0.00 2.29
6080 7706 9.903682 AACTGCTAATAATGCATTAACATGATC 57.096 29.630 22.37 9.13 39.86 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
236 361 6.983307 CAGTAATTGAACAAATTTGTGACCCA 59.017 34.615 23.93 15.79 41.31 4.51
238 363 6.423604 CCCAGTAATTGAACAAATTTGTGACC 59.576 38.462 23.93 15.87 41.31 4.02
452 584 2.038863 TAAACAGGAGGAAGGCAGGA 57.961 50.000 0.00 0.00 0.00 3.86
453 585 2.648059 CATAAACAGGAGGAAGGCAGG 58.352 52.381 0.00 0.00 0.00 4.85
454 586 2.019984 GCATAAACAGGAGGAAGGCAG 58.980 52.381 0.00 0.00 0.00 4.85
455 587 1.354031 TGCATAAACAGGAGGAAGGCA 59.646 47.619 0.00 0.00 0.00 4.75
456 588 2.019984 CTGCATAAACAGGAGGAAGGC 58.980 52.381 0.00 0.00 33.85 4.35
894 1026 1.390123 CATAAACACAGTGACGGAGCG 59.610 52.381 7.81 0.00 0.00 5.03
1029 1172 6.404734 GGCTGTTTTCTACAACTCCATATTGG 60.405 42.308 0.00 0.00 35.97 3.16
1396 1550 6.437928 TGACGATGAAACAAGAAAGAAATGG 58.562 36.000 0.00 0.00 0.00 3.16
1397 1551 7.431960 TGTTGACGATGAAACAAGAAAGAAATG 59.568 33.333 0.00 0.00 33.50 2.32
1696 1855 0.528017 TGTTTGGCGTGCAGAAAACA 59.472 45.000 12.66 12.66 39.51 2.83
1721 1881 1.674322 GCGCTTGGAACCCAGCTAA 60.674 57.895 13.57 0.00 33.81 3.09
1838 1998 5.482908 CAGCCTAAGACTGTGTAAGATGTT 58.517 41.667 0.00 0.00 0.00 2.71
1847 2007 1.929836 GATTCGCAGCCTAAGACTGTG 59.070 52.381 0.00 0.00 45.03 3.66
2063 2233 1.153524 ACATGACCAGCCCAAGCAA 59.846 52.632 0.00 0.00 43.56 3.91
2477 2805 1.617018 TTATGCCTGACAGAGCCGCT 61.617 55.000 3.32 0.00 0.00 5.52
2478 2806 1.153369 TTATGCCTGACAGAGCCGC 60.153 57.895 3.32 0.00 0.00 6.53
2484 2812 4.331168 GTGCTAAGAAGTTATGCCTGACAG 59.669 45.833 0.00 0.00 0.00 3.51
2492 2820 4.202050 GGGCCAATGTGCTAAGAAGTTATG 60.202 45.833 4.39 0.00 0.00 1.90
2611 2992 2.638556 TCTCTTCTGTTGTCGCTAGC 57.361 50.000 4.06 4.06 0.00 3.42
2612 2993 4.362932 TGATCTCTTCTGTTGTCGCTAG 57.637 45.455 0.00 0.00 0.00 3.42
2645 3026 9.699703 GACACATAAAGGCCTAAACAAAAATAA 57.300 29.630 5.16 0.00 0.00 1.40
3032 3587 2.816087 CTGCCTACAAGTGACAGCAAAT 59.184 45.455 0.00 0.00 0.00 2.32
3185 4150 5.290643 CCCAAATAACAAATTGTATGCCACG 59.709 40.000 0.00 0.00 0.00 4.94
3281 4386 1.338973 AGAACATGCAAACTGTGGCTG 59.661 47.619 0.00 5.05 0.00 4.85
3583 5033 4.072131 TCATAGACTTCCTGCACAAAACC 58.928 43.478 0.00 0.00 0.00 3.27
4062 5518 9.584008 TGAGGATAAGAAATACTATCCTTACGT 57.416 33.333 11.06 0.00 46.25 3.57
4081 5537 3.365472 TCTGCTGCTACTTGTGAGGATA 58.635 45.455 0.00 0.00 0.00 2.59
4499 5974 3.452474 AGAGCATCAGTTCTTGATACGC 58.548 45.455 0.00 0.00 44.76 4.42
4558 6034 7.548427 GGGTCCTTAGTGTGTCTTTTATACTTC 59.452 40.741 0.00 0.00 0.00 3.01
4801 6277 1.202806 TCAGGGTTATGCTGGCTATGC 60.203 52.381 0.00 0.00 0.00 3.14
4806 6282 1.106285 CCTTTCAGGGTTATGCTGGC 58.894 55.000 0.00 0.00 0.00 4.85
4814 6290 0.540597 GAGCCTTGCCTTTCAGGGTT 60.541 55.000 0.00 0.00 43.37 4.11
5041 6616 2.653448 CTCTCGCCGCTGTGATCG 60.653 66.667 0.00 0.00 0.00 3.69
5051 6626 0.747852 CTCTTAAGGTCCCTCTCGCC 59.252 60.000 1.85 0.00 0.00 5.54
5078 6653 9.403583 GGTGGTTATGAATACTTCCTTTTATGA 57.596 33.333 0.00 0.00 0.00 2.15
5211 6789 2.500229 GGTTCAAAACTCCCGACATGA 58.500 47.619 0.00 0.00 0.00 3.07
5334 6918 5.874810 TGTGTATGACTAATGTTTCTCAGGC 59.125 40.000 0.00 0.00 0.00 4.85
5505 7089 2.677199 ACTGATGGCAGCGATTATACG 58.323 47.619 0.00 0.00 46.26 3.06
5508 7092 2.874701 GACAACTGATGGCAGCGATTAT 59.125 45.455 0.00 0.00 46.26 1.28
5510 7094 1.089920 GACAACTGATGGCAGCGATT 58.910 50.000 0.00 0.00 46.26 3.34
5519 7103 3.489813 TCGTCACCGACAACTGATG 57.510 52.632 0.00 0.00 38.40 3.07
5594 7186 1.069765 AGTGCACGTTCTCCTGTGG 59.930 57.895 12.01 0.00 36.61 4.17
5621 7213 0.662374 ATAGATAAACGACGGCCGCG 60.662 55.000 30.82 30.82 43.32 6.46
5649 7242 4.012319 TGCTTCTCGTTACGTATCTGTC 57.988 45.455 4.24 0.00 0.00 3.51
5656 7249 2.740447 GGGAAATTGCTTCTCGTTACGT 59.260 45.455 4.24 0.00 34.17 3.57
5692 7285 7.007905 CGAGAATGAAAAAGTTTGTTGACGAAA 59.992 33.333 0.00 0.00 0.00 3.46
5887 7480 4.326766 CGGTGGCGTTGCTTGTGG 62.327 66.667 0.00 0.00 0.00 4.17
5992 7618 7.010738 GCGTAATGCATTTCCAAACTAGTACTA 59.989 37.037 18.75 1.89 45.45 1.82
5993 7619 6.183360 GCGTAATGCATTTCCAAACTAGTACT 60.183 38.462 18.75 0.00 45.45 2.73
5994 7620 5.963586 GCGTAATGCATTTCCAAACTAGTAC 59.036 40.000 18.75 3.92 45.45 2.73



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

AutoCloner maintained by Alex Coulton.