Multiple sequence alignment - TraesCS4A01G316100

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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 TraesCS4A01G316100 chr4A 100.000 2880 0 0 1 2880 606338516 606341395 0.000000e+00 5319.0
1 TraesCS4A01G316100 chr4A 76.000 550 70 31 1244 1735 605750936 605750391 8.030000e-56 228.0
2 TraesCS4A01G316100 chr4A 86.408 206 15 4 979 1184 605765450 605765258 2.250000e-51 213.0
3 TraesCS4A01G316100 chr4A 92.969 128 8 1 2748 2875 89954254 89954380 4.900000e-43 185.0
4 TraesCS4A01G316100 chr4A 87.302 63 5 2 378 438 641983627 641983566 5.150000e-08 69.4
5 TraesCS4A01G316100 chr4A 95.238 42 1 1 394 435 405552412 405552452 6.660000e-07 65.8
6 TraesCS4A01G316100 chr3A 97.608 1672 18 13 1210 2880 744098214 744096564 0.000000e+00 2846.0
7 TraesCS4A01G316100 chr3A 90.909 132 5 2 62 186 671091475 671091344 1.370000e-38 171.0
8 TraesCS4A01G316100 chr5D 92.655 708 32 8 501 1197 564787954 564788652 0.000000e+00 1002.0
9 TraesCS4A01G316100 chr5D 91.877 714 39 11 1319 2018 564789293 564790001 0.000000e+00 979.0
10 TraesCS4A01G316100 chr5D 93.598 453 20 4 63 506 564777931 564778383 0.000000e+00 667.0
11 TraesCS4A01G316100 chr5D 81.349 697 85 23 1343 2014 564750898 564750222 2.540000e-145 525.0
12 TraesCS4A01G316100 chr5D 80.505 554 85 19 1395 1934 564748123 564747579 1.240000e-108 403.0
13 TraesCS4A01G316100 chr5D 78.211 615 106 21 1237 1832 483810778 483811383 4.530000e-98 368.0
14 TraesCS4A01G316100 chr5D 89.493 276 20 7 2075 2347 564789992 564790261 9.880000e-90 340.0
15 TraesCS4A01G316100 chr5D 78.284 571 85 19 1395 1934 557283556 557282994 5.950000e-87 331.0
16 TraesCS4A01G316100 chr5D 87.372 293 28 6 911 1197 564749144 564748855 7.690000e-86 327.0
17 TraesCS4A01G316100 chr5D 83.333 318 26 10 894 1197 564752258 564751954 4.730000e-68 268.0
18 TraesCS4A01G316100 chr5D 80.741 270 23 13 931 1197 528280011 528279768 1.760000e-42 183.0
19 TraesCS4A01G316100 chr5D 92.188 128 3 2 63 183 503278045 503278172 1.060000e-39 174.0
20 TraesCS4A01G316100 chr5D 88.679 106 11 1 1212 1317 564751480 564751376 8.380000e-26 128.0
21 TraesCS4A01G316100 chr5D 79.275 193 30 7 2193 2376 557323794 557323603 3.010000e-25 126.0
22 TraesCS4A01G316100 chr5D 79.275 193 30 7 2193 2376 557354644 557354453 3.010000e-25 126.0
23 TraesCS4A01G316100 chr5D 79.275 193 30 7 2193 2376 557375082 557374891 3.010000e-25 126.0
24 TraesCS4A01G316100 chr5D 79.275 193 30 7 2193 2376 564726991 564726800 3.010000e-25 126.0
25 TraesCS4A01G316100 chr5D 92.308 65 4 1 1 64 564777845 564777909 1.100000e-14 91.6
26 TraesCS4A01G316100 chr5B 80.537 447 77 7 1389 1832 595019210 595019649 4.600000e-88 335.0
27 TraesCS4A01G316100 chr5B 81.984 383 56 9 1645 2014 708657461 708657079 2.150000e-81 313.0
28 TraesCS4A01G316100 chr5B 84.229 279 24 8 926 1197 708657809 708657544 1.320000e-63 254.0
29 TraesCS4A01G316100 chr5B 87.895 190 21 2 510 698 270633570 270633758 3.740000e-54 222.0
30 TraesCS4A01G316100 chr5B 81.675 191 24 7 1008 1197 683655323 683655503 6.430000e-32 148.0
31 TraesCS4A01G316100 chr5B 96.000 50 2 0 1267 1316 708611036 708610987 6.610000e-12 82.4
32 TraesCS4A01G316100 chr5B 94.000 50 3 0 1267 1316 708453526 708453477 3.080000e-10 76.8
33 TraesCS4A01G316100 chr5B 94.000 50 3 0 1267 1316 708532949 708532900 3.080000e-10 76.8
34 TraesCS4A01G316100 chr5B 94.000 50 3 0 1267 1316 708570544 708570495 3.080000e-10 76.8
35 TraesCS4A01G316100 chr5B 100.000 32 0 0 306 337 34245266 34245235 3.100000e-05 60.2
36 TraesCS4A01G316100 chr5A 76.708 644 118 23 1210 1832 605249725 605250357 2.140000e-86 329.0
37 TraesCS4A01G316100 chr5A 84.667 300 34 5 901 1197 656216714 656216424 3.630000e-74 289.0
38 TraesCS4A01G316100 chr5A 96.053 152 6 0 186 337 16595222 16595373 6.160000e-62 248.0
39 TraesCS4A01G316100 chr5A 94.872 39 2 0 2496 2534 445200108 445200070 8.620000e-06 62.1
40 TraesCS4A01G316100 chr7A 77.027 592 119 12 1256 1838 91497366 91497949 9.950000e-85 324.0
41 TraesCS4A01G316100 chr7A 87.958 191 21 2 508 697 30660910 30660721 1.040000e-54 224.0
42 TraesCS4A01G316100 chr1D 91.053 190 16 1 508 696 457175411 457175600 3.680000e-64 255.0
43 TraesCS4A01G316100 chr1D 90.476 189 14 3 513 700 28560008 28560193 2.220000e-61 246.0
44 TraesCS4A01G316100 chr1D 86.154 130 14 2 2752 2878 481407315 481407187 1.390000e-28 137.0
45 TraesCS4A01G316100 chr6B 96.644 149 5 0 189 337 394516587 394516439 6.160000e-62 248.0
46 TraesCS4A01G316100 chr6B 87.786 131 15 1 2748 2878 528290249 528290378 4.970000e-33 152.0
47 TraesCS4A01G316100 chr6B 81.818 66 12 0 2497 2562 469832167 469832102 4.010000e-04 56.5
48 TraesCS4A01G316100 chr2D 94.079 152 9 0 186 337 391003874 391004025 6.210000e-57 231.0
49 TraesCS4A01G316100 chr2D 90.341 176 15 2 530 704 647674776 647674602 2.230000e-56 230.0
50 TraesCS4A01G316100 chr2D 78.818 203 30 4 509 698 536924678 536924476 1.080000e-24 124.0
51 TraesCS4A01G316100 chr1B 92.857 154 11 0 184 337 583604398 583604551 1.040000e-54 224.0
52 TraesCS4A01G316100 chr1B 90.909 44 4 0 2493 2536 152317639 152317682 3.100000e-05 60.2
53 TraesCS4A01G316100 chr1B 90.909 44 4 0 2493 2536 170294825 170294868 3.100000e-05 60.2
54 TraesCS4A01G316100 chr4D 89.143 175 17 2 530 703 258893484 258893657 1.740000e-52 217.0
55 TraesCS4A01G316100 chr4D 90.179 112 4 2 82 186 19928737 19928626 3.870000e-29 139.0
56 TraesCS4A01G316100 chr3D 86.911 191 23 2 510 698 43776890 43776700 2.250000e-51 213.0
57 TraesCS4A01G316100 chr3D 88.571 175 18 2 530 702 317203565 317203391 8.080000e-51 211.0
58 TraesCS4A01G316100 chr3D 83.916 143 21 2 1056 1197 609232339 609232480 5.010000e-28 135.0
59 TraesCS4A01G316100 chr3D 97.222 36 0 1 504 538 317203604 317203569 3.100000e-05 60.2
60 TraesCS4A01G316100 chr1A 90.789 152 14 0 186 337 115873604 115873755 1.350000e-48 204.0
61 TraesCS4A01G316100 chr1A 95.238 42 2 0 394 435 104385886 104385845 1.850000e-07 67.6
62 TraesCS4A01G316100 chrUn 92.188 128 3 2 63 183 346596313 346596440 1.060000e-39 174.0
63 TraesCS4A01G316100 chrUn 91.406 128 4 2 63 183 93409450 93409577 4.940000e-38 169.0
64 TraesCS4A01G316100 chrUn 91.406 128 4 2 63 183 216518421 216518548 4.940000e-38 169.0
65 TraesCS4A01G316100 chrUn 91.406 128 4 2 63 183 216521809 216521936 4.940000e-38 169.0
66 TraesCS4A01G316100 chrUn 90.840 131 5 2 63 186 422745236 422745106 4.940000e-38 169.0
67 TraesCS4A01G316100 chrUn 79.275 193 30 7 2193 2376 376645900 376645709 3.010000e-25 126.0
68 TraesCS4A01G316100 chrUn 79.275 193 30 7 2193 2376 404505858 404505667 3.010000e-25 126.0
69 TraesCS4A01G316100 chrUn 94.545 55 3 0 189 243 417578679 417578625 5.110000e-13 86.1
70 TraesCS4A01G316100 chr6D 90.840 131 5 2 63 186 168251719 168251589 4.940000e-38 169.0
71 TraesCS4A01G316100 chr6D 95.960 99 4 0 62 160 263916310 263916212 8.260000e-36 161.0
72 TraesCS4A01G316100 chr2A 81.951 205 25 3 506 698 749834235 749834439 2.300000e-36 163.0
73 TraesCS4A01G316100 chr2A 88.281 128 14 1 2751 2878 605336137 605336011 4.970000e-33 152.0
74 TraesCS4A01G316100 chr2A 97.059 34 1 0 2491 2524 778141018 778141051 1.110000e-04 58.4
75 TraesCS4A01G316100 chr4B 88.722 133 13 2 2746 2877 632331106 632331237 8.260000e-36 161.0
76 TraesCS4A01G316100 chr4B 86.466 133 17 1 2746 2877 632393713 632393845 8.320000e-31 145.0
77 TraesCS4A01G316100 chr4B 83.969 131 20 1 2748 2878 43183205 43183334 1.080000e-24 124.0
78 TraesCS4A01G316100 chr4B 93.878 49 2 1 398 446 611405370 611405417 3.980000e-09 73.1
79 TraesCS4A01G316100 chr3B 82.051 195 27 6 1009 1196 819948241 819948434 2.970000e-35 159.0
80 TraesCS4A01G316100 chr3B 85.827 127 17 1 2752 2878 573644005 573644130 1.800000e-27 134.0
81 TraesCS4A01G316100 chr3B 90.909 44 4 0 2493 2536 171510073 171510116 3.100000e-05 60.2
82 TraesCS4A01G316100 chr7D 94.828 58 3 0 186 243 626728076 626728133 1.100000e-14 91.6
83 TraesCS4A01G316100 chr7D 94.545 55 3 0 189 243 382069763 382069709 5.110000e-13 86.1
84 TraesCS4A01G316100 chr7D 92.683 41 3 0 2497 2537 203884881 203884921 3.100000e-05 60.2
85 TraesCS4A01G316100 chr6A 84.932 73 10 1 2491 2562 6024638 6024710 3.980000e-09 73.1
86 TraesCS4A01G316100 chr6A 100.000 32 0 0 306 337 289136212 289136181 3.100000e-05 60.2
87 TraesCS4A01G316100 chr6A 100.000 32 0 0 306 337 608866863 608866832 3.100000e-05 60.2


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 TraesCS4A01G316100 chr4A 606338516 606341395 2879 False 5319.000000 5319 100.000000 1 2880 1 chr4A.!!$F3 2879
1 TraesCS4A01G316100 chr4A 605750391 605750936 545 True 228.000000 228 76.000000 1244 1735 1 chr4A.!!$R1 491
2 TraesCS4A01G316100 chr3A 744096564 744098214 1650 True 2846.000000 2846 97.608000 1210 2880 1 chr3A.!!$R2 1670
3 TraesCS4A01G316100 chr5D 564787954 564790261 2307 False 773.666667 1002 91.341667 501 2347 3 chr5D.!!$F4 1846
4 TraesCS4A01G316100 chr5D 564777845 564778383 538 False 379.300000 667 92.953000 1 506 2 chr5D.!!$F3 505
5 TraesCS4A01G316100 chr5D 483810778 483811383 605 False 368.000000 368 78.211000 1237 1832 1 chr5D.!!$F1 595
6 TraesCS4A01G316100 chr5D 557282994 557283556 562 True 331.000000 331 78.284000 1395 1934 1 chr5D.!!$R2 539
7 TraesCS4A01G316100 chr5D 564747579 564752258 4679 True 330.200000 525 84.247600 894 2014 5 chr5D.!!$R7 1120
8 TraesCS4A01G316100 chr5B 708657079 708657809 730 True 283.500000 313 83.106500 926 2014 2 chr5B.!!$R6 1088
9 TraesCS4A01G316100 chr5A 605249725 605250357 632 False 329.000000 329 76.708000 1210 1832 1 chr5A.!!$F2 622
10 TraesCS4A01G316100 chr7A 91497366 91497949 583 False 324.000000 324 77.027000 1256 1838 1 chr7A.!!$F1 582


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
224 256 0.818296 GTCGGTCTACTCATGCCTGT 59.182 55.0 0.0 0.0 0.00 4.00 F
1487 2556 0.538584 AGATGAGTGCCGAATCAGCA 59.461 50.0 0.0 0.0 34.32 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1856 2985 1.593196 TGAGTTCGGCCACTCTTTTG 58.407 50.000 20.58 0.0 43.32 2.44 R
2468 4258 1.819288 CACCTTCGAGAGACTTAGCCA 59.181 52.381 0.00 0.0 41.84 4.75 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
28 29 4.126520 TGAAGGAAATGCCCTACCTTTT 57.873 40.909 0.00 0.00 41.90 2.27
29 30 5.263872 TGAAGGAAATGCCCTACCTTTTA 57.736 39.130 0.00 0.00 41.90 1.52
33 34 3.130516 GGAAATGCCCTACCTTTTAGTGC 59.869 47.826 0.00 0.00 0.00 4.40
53 54 7.209471 AGTGCGGTTTGAACTATTGATTTAA 57.791 32.000 0.00 0.00 33.30 1.52
126 151 4.322801 CGGGATAGACCTCAACAGAAAACT 60.323 45.833 0.00 0.00 38.98 2.66
141 166 5.359576 ACAGAAAACTGTTGAGTAATGGCAA 59.640 36.000 0.00 0.00 33.11 4.52
160 185 4.285292 GCAACAAGTGATTGAGTTCAGTG 58.715 43.478 0.00 0.00 29.75 3.66
182 214 9.770097 CAGTGATAGAAAATTATTGGCTCTAGA 57.230 33.333 0.00 0.00 0.00 2.43
184 216 9.547753 GTGATAGAAAATTATTGGCTCTAGACA 57.452 33.333 0.00 0.00 0.00 3.41
213 245 1.674441 CCGTTGCTATCAGTCGGTCTA 59.326 52.381 0.00 0.00 37.04 2.59
217 249 3.277142 TGCTATCAGTCGGTCTACTCA 57.723 47.619 0.00 0.00 0.00 3.41
224 256 0.818296 GTCGGTCTACTCATGCCTGT 59.182 55.000 0.00 0.00 0.00 4.00
238 270 3.492102 TGCCTGTTGCTTACTTTCTCT 57.508 42.857 0.00 0.00 42.00 3.10
528 562 5.110814 TGTATTAGGCCTTGTACAATGCT 57.889 39.130 27.69 18.67 33.37 3.79
538 572 4.941263 CCTTGTACAATGCTAGGTGCTTAA 59.059 41.667 9.13 0.00 43.37 1.85
579 613 4.901868 TCTAAAGCACCGGTGTCTATTTT 58.098 39.130 33.92 24.90 0.00 1.82
585 619 5.365619 AGCACCGGTGTCTATTTTTATAGG 58.634 41.667 33.92 4.71 0.00 2.57
592 626 6.856938 CGGTGTCTATTTTTATAGGAGAGACG 59.143 42.308 0.00 0.00 35.65 4.18
613 647 2.213499 CCTAATTAAGCGTCTGCCCTG 58.787 52.381 0.00 0.00 44.31 4.45
616 650 3.560636 AATTAAGCGTCTGCCCTGTAT 57.439 42.857 0.00 0.00 44.31 2.29
628 662 3.472652 TGCCCTGTATAAATAAGCACCG 58.527 45.455 0.00 0.00 0.00 4.94
629 663 3.134985 TGCCCTGTATAAATAAGCACCGA 59.865 43.478 0.00 0.00 0.00 4.69
677 712 1.746991 GGCACCTCTGCTAAGCACC 60.747 63.158 0.00 0.00 43.66 5.01
705 740 7.500892 TGCATTGTACAAGACCTTAAGAAGAAA 59.499 33.333 14.65 0.00 0.00 2.52
735 771 9.662545 CAAAAGAAAAGAAGAGATGAGAGAAAC 57.337 33.333 0.00 0.00 0.00 2.78
779 815 9.010029 ACGAAATAGAGAAAAAGGAAAGCATAA 57.990 29.630 0.00 0.00 0.00 1.90
903 940 3.230134 CTCTCTCTGAATCCCGAATCCT 58.770 50.000 0.00 0.00 0.00 3.24
1206 1260 3.718097 CGCGCCGTTAAGCACCAA 61.718 61.111 0.00 0.00 0.00 3.67
1207 1261 2.874751 GCGCCGTTAAGCACCAAT 59.125 55.556 0.00 0.00 0.00 3.16
1208 1262 1.211709 GCGCCGTTAAGCACCAATT 59.788 52.632 0.00 0.00 0.00 2.32
1487 2556 0.538584 AGATGAGTGCCGAATCAGCA 59.461 50.000 0.00 0.00 34.32 4.41
2424 4214 1.060937 GCCGATGATGTGCGTTCAC 59.939 57.895 0.00 0.00 43.40 3.18
2468 4258 4.286549 TCCCCAATTTCAAAATGATGTGCT 59.713 37.500 0.00 0.00 0.00 4.40
2877 5726 1.359848 CTGGTTGTAGCATGTCGTCC 58.640 55.000 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 6.811253 AAATCAATAGTTCAAACCGCACTA 57.189 33.333 0.00 0.00 0.00 2.74
29 30 5.705609 AAATCAATAGTTCAAACCGCACT 57.294 34.783 0.00 0.00 0.00 4.40
61 62 9.627123 TGGATCAATAATCGATTTCTAGGTTTT 57.373 29.630 17.19 0.00 34.99 2.43
74 99 8.383318 AGGTAGTCAAATTGGATCAATAATCG 57.617 34.615 0.00 0.00 32.43 3.34
78 103 8.141909 CGTAGAGGTAGTCAAATTGGATCAATA 58.858 37.037 0.00 0.00 32.43 1.90
80 105 6.338146 CGTAGAGGTAGTCAAATTGGATCAA 58.662 40.000 0.00 0.00 0.00 2.57
136 161 3.286353 TGAACTCAATCACTTGTTGCCA 58.714 40.909 0.00 0.00 33.87 4.92
141 166 6.997655 TCTATCACTGAACTCAATCACTTGT 58.002 36.000 0.00 0.00 33.87 3.16
217 249 7.397287 CGATAGAGAAAGTAAGCAACAGGCAT 61.397 42.308 0.00 0.00 42.82 4.40
254 286 7.449086 TCCTTACGGATGTTAGGTTTTTGAATT 59.551 33.333 0.98 0.00 43.76 2.17
293 325 1.546476 AGAGTAAGGCAACGAGTGAGG 59.454 52.381 0.00 0.00 46.39 3.86
345 377 9.326413 ACAGAAAGAATAGAAAAGAAAACGAGA 57.674 29.630 0.00 0.00 0.00 4.04
354 386 8.862550 AGCAAACAACAGAAAGAATAGAAAAG 57.137 30.769 0.00 0.00 0.00 2.27
368 400 2.287915 AGTACAAGCGAGCAAACAACAG 59.712 45.455 0.00 0.00 0.00 3.16
377 409 1.630244 CCACAGCAGTACAAGCGAGC 61.630 60.000 0.00 0.00 37.01 5.03
476 509 7.230108 CCAATGTATTCAAAGATGATGGCTAGT 59.770 37.037 0.00 0.00 34.96 2.57
548 582 2.745281 CCGGTGCTTTAGAAAAATCCGA 59.255 45.455 0.00 0.00 36.37 4.55
579 613 6.349115 CGCTTAATTAGGCGTCTCTCCTATAA 60.349 42.308 28.00 0.00 45.15 0.98
592 626 0.945099 GGGCAGACGCTTAATTAGGC 59.055 55.000 9.43 9.43 38.60 3.93
643 678 5.884792 AGAGGTGCCTGAAGAAATAAATCAG 59.115 40.000 0.00 0.00 0.00 2.90
663 698 0.321919 TGCAAGGTGCTTAGCAGAGG 60.322 55.000 7.34 0.00 45.31 3.69
677 712 6.801539 TCTTAAGGTCTTGTACAATGCAAG 57.198 37.500 9.13 7.31 43.26 4.01
837 873 1.304962 AACGGGCCCTTTCCATTCC 60.305 57.895 22.43 0.00 0.00 3.01
857 894 9.965902 AGCCTTAATGGGATTTATGTATAGAAG 57.034 33.333 0.00 0.00 36.00 2.85
879 916 0.260230 TCGGGATTCAGAGAGAGCCT 59.740 55.000 0.00 0.00 0.00 4.58
903 940 4.141551 CCATGACTGAGAAAGATGGGATCA 60.142 45.833 0.00 0.00 30.04 2.92
1197 1251 5.007626 GCGTAGATGAATCAATTGGTGCTTA 59.992 40.000 5.42 0.00 0.00 3.09
1198 1252 4.201950 GCGTAGATGAATCAATTGGTGCTT 60.202 41.667 5.42 0.00 0.00 3.91
1199 1253 3.313526 GCGTAGATGAATCAATTGGTGCT 59.686 43.478 5.42 0.00 0.00 4.40
1337 2362 7.503566 TGAATGCCTCCAGATAAATTAAGAAGG 59.496 37.037 0.00 0.00 0.00 3.46
1856 2985 1.593196 TGAGTTCGGCCACTCTTTTG 58.407 50.000 20.58 0.00 43.32 2.44
2424 4214 5.348997 GGGAAGTCATCACGTCTCTTTTTAG 59.651 44.000 0.00 0.00 29.32 1.85
2468 4258 1.819288 CACCTTCGAGAGACTTAGCCA 59.181 52.381 0.00 0.00 41.84 4.75
2739 5185 9.783081 AATTGATTTTTAGCAGTCCAAAAGATT 57.217 25.926 0.00 0.00 0.00 2.40



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

AutoCloner maintained by Alex Coulton.