Multiple sequence alignment - TraesCS5D01G051900

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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 TraesCS5D01G051900 chr5D 100.000 4127 0 0 1 4127 49761433 49757307 0.000000e+00 7622
1 TraesCS5D01G051900 chr5D 98.109 4072 43 7 1 4043 50037023 50032957 0.000000e+00 7062
2 TraesCS5D01G051900 chr5D 97.840 4074 55 6 1 4043 50198124 50194053 0.000000e+00 7005
3 TraesCS5D01G051900 chr5D 97.647 85 2 0 4043 4127 50190142 50190058 3.320000e-31 147
4 TraesCS5D01G051900 chr5D 96.471 85 3 0 4043 4127 50028694 50028610 1.550000e-29 141
5 TraesCS5D01G051900 chr5D 91.765 85 7 0 4043 4127 171683332 171683416 7.250000e-23 119
6 TraesCS5D01G051900 chr5B 98.462 2211 31 2 1836 4043 52632193 52629983 0.000000e+00 3892
7 TraesCS5D01G051900 chr5B 96.674 902 15 8 579 1471 52646625 52645730 0.000000e+00 1485
8 TraesCS5D01G051900 chr5B 93.676 506 17 1 1 506 52647362 52646872 0.000000e+00 743
9 TraesCS5D01G051900 chr5B 93.291 477 17 1 1 477 52917582 52918043 0.000000e+00 689
10 TraesCS5D01G051900 chr5B 97.354 378 7 2 1463 1840 52642139 52641765 1.250000e-179 640
11 TraesCS5D01G051900 chr5B 91.034 290 26 0 948 1237 676178044 676177755 3.870000e-105 392
12 TraesCS5D01G051900 chr5B 96.471 85 3 0 4043 4127 52619691 52619607 1.550000e-29 141
13 TraesCS5D01G051900 chr5B 100.000 53 0 0 528 580 52646698 52646646 9.440000e-17 99
14 TraesCS5D01G051900 chr4A 91.820 2445 179 13 1586 4026 419960558 419962985 0.000000e+00 3387
15 TraesCS5D01G051900 chr4A 86.652 914 76 18 995 1893 629586414 629587296 0.000000e+00 970
16 TraesCS5D01G051900 chr4A 91.030 301 25 1 1287 1587 419884282 419884580 4.970000e-109 405
17 TraesCS5D01G051900 chr4A 88.839 224 19 4 723 940 261150484 261150707 1.890000e-68 270
18 TraesCS5D01G051900 chr5A 96.396 1554 26 8 1 1526 39242084 39240533 0.000000e+00 2532
19 TraesCS5D01G051900 chr5A 98.466 1434 18 4 1571 3004 39240533 39239104 0.000000e+00 2523
20 TraesCS5D01G051900 chr5A 98.294 1055 17 1 2989 4043 39221959 39220906 0.000000e+00 1847
21 TraesCS5D01G051900 chr5A 86.711 903 71 18 995 1884 551344177 551343311 0.000000e+00 957
22 TraesCS5D01G051900 chr5A 92.857 574 31 7 3474 4043 329383695 329383128 0.000000e+00 824
23 TraesCS5D01G051900 chr5A 88.318 214 15 5 737 940 708833762 708833549 8.860000e-62 248
24 TraesCS5D01G051900 chr5A 98.824 85 1 0 4043 4127 39108726 39108642 7.150000e-33 152
25 TraesCS5D01G051900 chr5A 98.824 85 1 0 4043 4127 39217830 39217746 7.150000e-33 152
26 TraesCS5D01G051900 chr5A 86.364 110 12 2 579 685 490149677 490149786 2.610000e-22 117
27 TraesCS5D01G051900 chr7A 91.874 1243 70 17 2818 4043 599246787 599248015 0.000000e+00 1707
28 TraesCS5D01G051900 chr7A 91.459 1241 81 14 2818 4043 597754254 597753024 0.000000e+00 1681
29 TraesCS5D01G051900 chr7A 90.538 1226 92 14 1477 2689 599245574 599246788 0.000000e+00 1600
30 TraesCS5D01G051900 chr7A 90.049 1216 101 10 1486 2689 597755460 597754253 0.000000e+00 1557
31 TraesCS5D01G051900 chr7A 87.829 912 68 15 995 1893 668651065 668650184 0.000000e+00 1029
32 TraesCS5D01G051900 chr7A 89.199 287 31 0 951 1237 422041561 422041847 3.920000e-95 359
33 TraesCS5D01G051900 chr7A 91.765 85 7 0 4043 4127 454757160 454757244 7.250000e-23 119
34 TraesCS5D01G051900 chr7A 86.364 110 12 2 579 685 454755080 454755189 2.610000e-22 117
35 TraesCS5D01G051900 chr2A 79.610 2256 305 63 1894 4043 273372313 273374519 0.000000e+00 1474
36 TraesCS5D01G051900 chr2A 88.466 919 63 21 988 1893 527320832 527321720 0.000000e+00 1070
37 TraesCS5D01G051900 chr2A 85.567 291 30 2 948 1237 740649763 740649484 1.120000e-75 294
38 TraesCS5D01G051900 chr2A 84.545 110 14 2 579 685 720953656 720953765 5.640000e-19 106
39 TraesCS5D01G051900 chr2B 83.168 1515 180 36 1899 3354 686502477 686500979 0.000000e+00 1315
40 TraesCS5D01G051900 chr6B 93.253 830 42 9 3220 4043 533517662 533518483 0.000000e+00 1210
41 TraesCS5D01G051900 chrUn 100.000 399 0 0 1767 2165 478833283 478833681 0.000000e+00 737
42 TraesCS5D01G051900 chrUn 93.291 477 17 1 1 477 371432021 371431560 0.000000e+00 689
43 TraesCS5D01G051900 chr2D 83.087 745 102 13 2085 2808 543764747 543765488 0.000000e+00 656
44 TraesCS5D01G051900 chr1D 82.440 746 106 14 2085 2808 23168562 23169304 2.710000e-176 628
45 TraesCS5D01G051900 chr1D 82.239 259 23 7 1894 2134 23168315 23168568 7.000000e-48 202
46 TraesCS5D01G051900 chr1D 90.226 133 9 2 1146 1277 149064671 149064800 1.970000e-38 171
47 TraesCS5D01G051900 chr6A 90.233 215 15 2 732 940 15380607 15380821 4.060000e-70 276
48 TraesCS5D01G051900 chr6D 87.946 224 20 5 723 940 14025586 14025808 1.470000e-64 257
49 TraesCS5D01G051900 chr7D 88.060 134 9 3 1146 1277 99878634 99878762 7.150000e-33 152
50 TraesCS5D01G051900 chr3B 90.826 109 7 2 580 685 458277540 458277432 4.300000e-30 143
51 TraesCS5D01G051900 chr3B 94.048 84 5 0 4043 4126 143588108 143588191 1.200000e-25 128
52 TraesCS5D01G051900 chr3B 91.765 85 7 0 4043 4127 458275461 458275377 7.250000e-23 119


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 TraesCS5D01G051900 chr5D 49757307 49761433 4126 True 7622.00 7622 100.0000 1 4127 1 chr5D.!!$R1 4126
1 TraesCS5D01G051900 chr5D 50032957 50037023 4066 True 7062.00 7062 98.1090 1 4043 1 chr5D.!!$R3 4042
2 TraesCS5D01G051900 chr5D 50190058 50198124 8066 True 3576.00 7005 97.7435 1 4127 2 chr5D.!!$R4 4126
3 TraesCS5D01G051900 chr5B 52629983 52632193 2210 True 3892.00 3892 98.4620 1836 4043 1 chr5B.!!$R2 2207
4 TraesCS5D01G051900 chr5B 52641765 52647362 5597 True 741.75 1485 96.9260 1 1840 4 chr5B.!!$R4 1839
5 TraesCS5D01G051900 chr4A 419960558 419962985 2427 False 3387.00 3387 91.8200 1586 4026 1 chr4A.!!$F3 2440
6 TraesCS5D01G051900 chr4A 629586414 629587296 882 False 970.00 970 86.6520 995 1893 1 chr4A.!!$F4 898
7 TraesCS5D01G051900 chr5A 39239104 39242084 2980 True 2527.50 2532 97.4310 1 3004 2 chr5A.!!$R6 3003
8 TraesCS5D01G051900 chr5A 39217746 39221959 4213 True 999.50 1847 98.5590 2989 4127 2 chr5A.!!$R5 1138
9 TraesCS5D01G051900 chr5A 551343311 551344177 866 True 957.00 957 86.7110 995 1884 1 chr5A.!!$R3 889
10 TraesCS5D01G051900 chr5A 329383128 329383695 567 True 824.00 824 92.8570 3474 4043 1 chr5A.!!$R2 569
11 TraesCS5D01G051900 chr7A 599245574 599248015 2441 False 1653.50 1707 91.2060 1477 4043 2 chr7A.!!$F3 2566
12 TraesCS5D01G051900 chr7A 597753024 597755460 2436 True 1619.00 1681 90.7540 1486 4043 2 chr7A.!!$R2 2557
13 TraesCS5D01G051900 chr7A 668650184 668651065 881 True 1029.00 1029 87.8290 995 1893 1 chr7A.!!$R1 898
14 TraesCS5D01G051900 chr2A 273372313 273374519 2206 False 1474.00 1474 79.6100 1894 4043 1 chr2A.!!$F1 2149
15 TraesCS5D01G051900 chr2A 527320832 527321720 888 False 1070.00 1070 88.4660 988 1893 1 chr2A.!!$F2 905
16 TraesCS5D01G051900 chr2B 686500979 686502477 1498 True 1315.00 1315 83.1680 1899 3354 1 chr2B.!!$R1 1455
17 TraesCS5D01G051900 chr6B 533517662 533518483 821 False 1210.00 1210 93.2530 3220 4043 1 chr6B.!!$F1 823
18 TraesCS5D01G051900 chr2D 543764747 543765488 741 False 656.00 656 83.0870 2085 2808 1 chr2D.!!$F1 723
19 TraesCS5D01G051900 chr1D 23168315 23169304 989 False 415.00 628 82.3395 1894 2808 2 chr1D.!!$F2 914

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
781 969 2.629137 TGTTGAGCATGCAGGTTTTGAT 59.371 40.909 21.98 0.0 0.00 2.57 F
2215 6130 5.163561 GCTAGCAAGTAGTCTCATCTCTTGT 60.164 44.000 10.63 0.0 38.09 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2539 6492 1.939934 TGACAACAGCTTCAAACTCCG 59.060 47.619 0.00 0.00 0.00 4.63 R
4050 12080 2.231964 CACCCTTGACAATGACATTGGG 59.768 50.000 27.46 21.36 44.42 4.12 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
701 888 4.664150 TTTTCTGAATTCAACCGGCTTT 57.336 36.364 9.88 0.00 0.00 3.51
781 969 2.629137 TGTTGAGCATGCAGGTTTTGAT 59.371 40.909 21.98 0.00 0.00 2.57
1313 1522 8.143835 AGTTCATGAACAAATAAAACTGGAAGG 58.856 33.333 33.92 0.00 43.47 3.46
1344 1553 7.490000 CGATAGGTTTTATCCTGTACTGAACT 58.510 38.462 0.60 0.00 38.41 3.01
2215 6130 5.163561 GCTAGCAAGTAGTCTCATCTCTTGT 60.164 44.000 10.63 0.00 38.09 3.16
2428 6381 5.530543 TGACAACAGCACTGAAACATCAATA 59.469 36.000 4.31 0.00 0.00 1.90
2511 6464 7.624077 AGTTCTATTATCAGACCAGGGTAAGTT 59.376 37.037 0.00 0.00 0.00 2.66
2932 6916 1.555075 TCGAGTGGGAAGCTGCTATTT 59.445 47.619 0.90 0.00 0.00 1.40
3701 7756 7.273320 TCTATGAGTACTGTTAGGTATGTGC 57.727 40.000 0.00 0.00 0.00 4.57
3908 7968 8.492415 TTTAGGCAGGTCTATCTTACATATGT 57.508 34.615 13.93 13.93 0.00 2.29
4050 12080 3.686726 AGTTTCTTCCGATCTTGATGCAC 59.313 43.478 0.00 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
701 888 2.151202 GGTGCAAGTCGATTTGGAAGA 58.849 47.619 20.52 0.00 29.97 2.87
781 969 5.071788 GGGGATGGTGATAGTGATTAGACAA 59.928 44.000 0.00 0.00 0.00 3.18
1139 1334 5.275067 ACAAAATTTCTTGCTGGTGCTTA 57.725 34.783 0.00 0.00 40.48 3.09
1313 1522 5.057149 ACAGGATAAAACCTATCGCATGAC 58.943 41.667 0.00 0.00 38.32 3.06
2215 6130 4.837860 AGGATTCCTGTGGCAAACAAATAA 59.162 37.500 3.86 0.00 38.67 1.40
2258 6175 9.469097 AATAACTACCTACCATACAATTTGCAA 57.531 29.630 0.00 0.00 0.00 4.08
2511 6464 2.371510 TGGCATCCATCATATCAACGGA 59.628 45.455 0.00 0.00 0.00 4.69
2539 6492 1.939934 TGACAACAGCTTCAAACTCCG 59.060 47.619 0.00 0.00 0.00 4.63
2932 6916 5.834169 CAGTATTTGCATGCATCCATTGTA 58.166 37.500 23.37 0.00 0.00 2.41
3701 7756 7.426929 ACTTCTAAGCATAACTTGTTGACAG 57.573 36.000 0.00 0.00 39.58 3.51
3908 7968 4.012374 GGAAAATGCCTGAGATGAGTTCA 58.988 43.478 0.00 0.00 0.00 3.18
4050 12080 2.231964 CACCCTTGACAATGACATTGGG 59.768 50.000 27.46 21.36 44.42 4.12


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

AutoCloner maintained by Alex Coulton.