Multiple sequence alignment - TraesCS2D01G416800

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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 TraesCS2D01G416800 chr2D 100.000 3161 0 0 1 3161 531234310 531237470 0.000000e+00 5838.0
1 TraesCS2D01G416800 chr2D 78.400 1250 220 31 935 2153 529693926 529695156 0.000000e+00 767.0
2 TraesCS2D01G416800 chr2D 85.144 626 91 2 1594 2217 531316373 531316998 9.560000e-180 640.0
3 TraesCS2D01G416800 chr2D 76.447 1261 234 46 974 2213 459322002 459323220 2.680000e-175 625.0
4 TraesCS2D01G416800 chr2D 81.864 590 83 18 975 1549 531322957 531323537 2.850000e-130 475.0
5 TraesCS2D01G416800 chr2D 82.738 168 25 4 6 172 465570142 465570306 2.540000e-31 147.0
6 TraesCS2D01G416800 chr2D 75.434 346 27 26 537 857 531255812 531256124 7.160000e-22 115.0
7 TraesCS2D01G416800 chr2D 86.567 67 1 1 267 333 531314889 531314947 2.030000e-07 67.6
8 TraesCS2D01G416800 chr2A 96.596 2468 81 2 697 3161 675708124 675710591 0.000000e+00 4089.0
9 TraesCS2D01G416800 chr2A 90.985 721 40 10 1 711 675707046 675707751 0.000000e+00 948.0
10 TraesCS2D01G416800 chr2A 79.320 1030 175 25 975 1975 675839952 675840972 0.000000e+00 688.0
11 TraesCS2D01G416800 chr2A 79.912 906 134 32 935 1810 674545591 674546478 3.460000e-174 621.0
12 TraesCS2D01G416800 chr2A 84.602 591 86 4 1627 2214 675834518 675835106 1.630000e-162 582.0
13 TraesCS2D01G416800 chr2A 79.813 535 95 10 956 1482 602489292 602489821 8.280000e-101 377.0
14 TraesCS2D01G416800 chr2A 80.117 342 36 16 537 857 675818895 675819225 3.170000e-55 226.0
15 TraesCS2D01G416800 chr2B 96.051 1418 55 1 822 2238 630882719 630884136 0.000000e+00 2307.0
16 TraesCS2D01G416800 chr2B 78.335 1237 227 28 975 2179 631140353 631141580 0.000000e+00 761.0
17 TraesCS2D01G416800 chr2B 77.938 1038 189 29 956 1970 540730755 540731775 2.080000e-171 612.0
18 TraesCS2D01G416800 chr2B 88.706 425 31 8 7 415 630881612 630882035 1.310000e-138 503.0
19 TraesCS2D01G416800 chr2B 92.000 150 8 1 640 785 630882568 630882717 1.150000e-49 207.0
20 TraesCS2D01G416800 chr2B 79.402 301 26 15 583 857 631133069 631133359 2.500000e-41 180.0
21 TraesCS2D01G416800 chr2B 88.372 129 12 3 414 540 76099615 76099742 5.460000e-33 152.0
22 TraesCS2D01G416800 chr2B 88.393 112 4 2 267 378 631132894 631132996 3.310000e-25 126.0
23 TraesCS2D01G416800 chr2B 98.387 62 1 0 575 636 630882057 630882118 3.330000e-20 110.0
24 TraesCS2D01G416800 chr2B 100.000 45 0 0 209 253 773875078 773875034 2.020000e-12 84.2
25 TraesCS2D01G416800 chr2B 87.879 66 5 3 210 272 73555127 73555062 1.220000e-09 75.0
26 TraesCS2D01G416800 chr5D 92.122 622 47 2 2539 3160 281684720 281685339 0.000000e+00 876.0
27 TraesCS2D01G416800 chr5D 91.586 618 52 0 2544 3161 277668306 277667689 0.000000e+00 854.0
28 TraesCS2D01G416800 chr5D 82.353 102 17 1 2405 2506 497178036 497177936 1.560000e-13 87.9
29 TraesCS2D01G416800 chr5D 97.872 47 1 0 212 258 439643669 439643623 7.270000e-12 82.4
30 TraesCS2D01G416800 chr3D 92.233 618 48 0 2544 3161 416180772 416180155 0.000000e+00 876.0
31 TraesCS2D01G416800 chr4D 91.922 619 50 0 2542 3160 403304465 403305083 0.000000e+00 867.0
32 TraesCS2D01G416800 chr7D 91.761 619 50 1 2544 3161 422614821 422614203 0.000000e+00 859.0
33 TraesCS2D01G416800 chr7D 91.200 625 53 2 2539 3161 385572586 385573210 0.000000e+00 848.0
34 TraesCS2D01G416800 chr7D 91.304 621 52 2 2541 3161 266911972 266912590 0.000000e+00 846.0
35 TraesCS2D01G416800 chr7D 91.228 114 9 1 429 541 251036035 251035922 1.520000e-33 154.0
36 TraesCS2D01G416800 chr1D 91.748 618 51 0 2544 3161 479379760 479379143 0.000000e+00 859.0
37 TraesCS2D01G416800 chr1D 83.158 95 11 4 78 172 322476746 322476657 7.270000e-12 82.4
38 TraesCS2D01G416800 chrUn 79.061 1256 207 37 941 2162 357782192 357780959 0.000000e+00 811.0
39 TraesCS2D01G416800 chrUn 86.667 135 17 1 406 539 33215653 33215519 7.060000e-32 148.0
40 TraesCS2D01G416800 chrUn 97.059 34 1 0 139 172 433066317 433066350 1.220000e-04 58.4
41 TraesCS2D01G416800 chr3A 86.957 138 17 1 406 542 580812819 580812682 1.520000e-33 154.0
42 TraesCS2D01G416800 chr3A 84.906 106 10 4 72 172 76319585 76319689 5.580000e-18 102.0
43 TraesCS2D01G416800 chr3A 90.000 60 3 3 201 259 354424210 354424267 1.220000e-09 75.0
44 TraesCS2D01G416800 chr6B 89.344 122 12 1 414 534 632245463 632245584 5.460000e-33 152.0
45 TraesCS2D01G416800 chr6B 76.786 168 36 3 6 172 132739945 132740110 1.210000e-14 91.6
46 TraesCS2D01G416800 chr3B 86.861 137 17 1 407 542 153542316 153542452 5.460000e-33 152.0
47 TraesCS2D01G416800 chr4B 89.076 119 12 1 424 541 661262952 661262834 2.540000e-31 147.0
48 TraesCS2D01G416800 chr4A 86.131 137 17 2 406 541 66317649 66317784 2.540000e-31 147.0
49 TraesCS2D01G416800 chr4A 88.172 93 11 0 5 97 47129981 47129889 9.270000e-21 111.0
50 TraesCS2D01G416800 chr4A 100.000 29 0 0 144 172 688325731 688325759 2.000000e-03 54.7
51 TraesCS2D01G416800 chr6A 89.189 74 7 1 99 172 11114413 11114485 1.210000e-14 91.6
52 TraesCS2D01G416800 chr1A 86.420 81 10 1 93 172 585251176 585251256 1.560000e-13 87.9
53 TraesCS2D01G416800 chr6D 95.833 48 2 0 209 256 310400745 310400792 9.400000e-11 78.7
54 TraesCS2D01G416800 chr5A 94.000 50 3 0 200 249 195632093 195632142 3.380000e-10 76.8
55 TraesCS2D01G416800 chr7B 91.071 56 4 1 209 264 145374835 145374781 1.220000e-09 75.0


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 TraesCS2D01G416800 chr2D 531234310 531237470 3160 False 5838.00 5838 100.0000 1 3161 1 chr2D.!!$F4 3160
1 TraesCS2D01G416800 chr2D 529693926 529695156 1230 False 767.00 767 78.4000 935 2153 1 chr2D.!!$F3 1218
2 TraesCS2D01G416800 chr2D 459322002 459323220 1218 False 625.00 625 76.4470 974 2213 1 chr2D.!!$F1 1239
3 TraesCS2D01G416800 chr2D 531322957 531323537 580 False 475.00 475 81.8640 975 1549 1 chr2D.!!$F6 574
4 TraesCS2D01G416800 chr2D 531314889 531316998 2109 False 353.80 640 85.8555 267 2217 2 chr2D.!!$F7 1950
5 TraesCS2D01G416800 chr2A 675707046 675710591 3545 False 2518.50 4089 93.7905 1 3161 2 chr2A.!!$F6 3160
6 TraesCS2D01G416800 chr2A 675839952 675840972 1020 False 688.00 688 79.3200 975 1975 1 chr2A.!!$F5 1000
7 TraesCS2D01G416800 chr2A 674545591 674546478 887 False 621.00 621 79.9120 935 1810 1 chr2A.!!$F2 875
8 TraesCS2D01G416800 chr2A 675834518 675835106 588 False 582.00 582 84.6020 1627 2214 1 chr2A.!!$F4 587
9 TraesCS2D01G416800 chr2A 602489292 602489821 529 False 377.00 377 79.8130 956 1482 1 chr2A.!!$F1 526
10 TraesCS2D01G416800 chr2B 630881612 630884136 2524 False 781.75 2307 93.7860 7 2238 4 chr2B.!!$F4 2231
11 TraesCS2D01G416800 chr2B 631140353 631141580 1227 False 761.00 761 78.3350 975 2179 1 chr2B.!!$F3 1204
12 TraesCS2D01G416800 chr2B 540730755 540731775 1020 False 612.00 612 77.9380 956 1970 1 chr2B.!!$F2 1014
13 TraesCS2D01G416800 chr5D 281684720 281685339 619 False 876.00 876 92.1220 2539 3160 1 chr5D.!!$F1 621
14 TraesCS2D01G416800 chr5D 277667689 277668306 617 True 854.00 854 91.5860 2544 3161 1 chr5D.!!$R1 617
15 TraesCS2D01G416800 chr3D 416180155 416180772 617 True 876.00 876 92.2330 2544 3161 1 chr3D.!!$R1 617
16 TraesCS2D01G416800 chr4D 403304465 403305083 618 False 867.00 867 91.9220 2542 3160 1 chr4D.!!$F1 618
17 TraesCS2D01G416800 chr7D 422614203 422614821 618 True 859.00 859 91.7610 2544 3161 1 chr7D.!!$R2 617
18 TraesCS2D01G416800 chr7D 385572586 385573210 624 False 848.00 848 91.2000 2539 3161 1 chr7D.!!$F2 622
19 TraesCS2D01G416800 chr7D 266911972 266912590 618 False 846.00 846 91.3040 2541 3161 1 chr7D.!!$F1 620
20 TraesCS2D01G416800 chr1D 479379143 479379760 617 True 859.00 859 91.7480 2544 3161 1 chr1D.!!$R2 617
21 TraesCS2D01G416800 chrUn 357780959 357782192 1233 True 811.00 811 79.0610 941 2162 1 chrUn.!!$R2 1221

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
813 1696 1.351017 CCCTGGTTTGCCTTCTCTGTA 59.649 52.381 0.0 0.0 35.27 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2445 3747 2.199652 CCGTGGGGTTGCACATGTT 61.2 57.895 0.0 0.0 0.0 2.71 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
47 48 4.320456 CTGAGCCACACTGCGGGT 62.320 66.667 0.00 0.00 36.82 5.28
117 122 7.396418 ACGGATAAAAATTTAGTACCACCTCA 58.604 34.615 0.00 0.00 0.00 3.86
187 204 7.655490 AGAAACGCACGTAGGTAGATATAAAT 58.345 34.615 0.00 0.00 0.00 1.40
416 433 7.604549 TGACAGACGGAAACTTATTATGTACA 58.395 34.615 0.00 0.00 0.00 2.90
636 672 3.607209 CCGAAGCTGAGTCGTAAAAGTAC 59.393 47.826 5.63 0.00 36.77 2.73
637 673 4.474113 CGAAGCTGAGTCGTAAAAGTACT 58.526 43.478 0.00 0.00 33.80 2.73
813 1696 1.351017 CCCTGGTTTGCCTTCTCTGTA 59.649 52.381 0.00 0.00 35.27 2.74
923 2149 5.539582 TCGCTACAAATATCACCAACAAC 57.460 39.130 0.00 0.00 0.00 3.32
949 2175 4.167268 GTTCGATTCTCGTTTCTAGTGCT 58.833 43.478 0.00 0.00 41.35 4.40
1198 2426 2.429236 CGCTTCTGCTCGTGTCGT 60.429 61.111 0.00 0.00 36.97 4.34
1257 2497 4.003788 CCCGACGACAGCTGGGTT 62.004 66.667 19.93 0.01 36.86 4.11
1611 2860 6.582636 CAAAGGTGAGCTATATGGTCTTGTA 58.417 40.000 0.00 0.00 43.13 2.41
1761 3055 2.472909 GCTACACGGCAAGCCATCC 61.473 63.158 12.19 0.00 35.37 3.51
1947 3244 2.124570 ACGGCAGATGGGCATCAC 60.125 61.111 0.00 0.00 43.60 3.06
2239 3541 3.334691 ACCCTCGTAATTCATGTGTGTG 58.665 45.455 0.00 0.00 0.00 3.82
2320 3622 2.874457 GCCATCCAGTACGTTTCCAAGT 60.874 50.000 0.00 0.00 0.00 3.16
2333 3635 4.155826 CGTTTCCAAGTTTGATGCTATGGA 59.844 41.667 0.00 0.00 35.27 3.41
2395 3697 2.874701 GTCCATTCTGACGCATATGCTT 59.125 45.455 24.56 16.48 39.32 3.91
2403 3705 1.658596 GACGCATATGCTTTGTGTCGA 59.341 47.619 24.56 0.00 42.63 4.20
2430 3732 3.600388 GATGAAGACGAATGAACCACCT 58.400 45.455 0.00 0.00 0.00 4.00
2439 3741 3.411446 GAATGAACCACCTGTGTCATCA 58.589 45.455 4.47 2.81 30.45 3.07
2445 3747 1.441738 CACCTGTGTCATCAATCGCA 58.558 50.000 0.00 0.00 0.00 5.10
2508 3812 5.918011 GTGAATTCTGATAGTAAGAGAGGCG 59.082 44.000 7.05 0.00 0.00 5.52
2556 3860 2.450243 GGGGTGAGGGAGTCCTGA 59.550 66.667 9.58 0.00 45.05 3.86
2851 4155 6.829298 TCTCGAGGTAGATCAACTCTTGTAAT 59.171 38.462 13.56 0.00 35.28 1.89
2853 4157 6.829298 TCGAGGTAGATCAACTCTTGTAATCT 59.171 38.462 0.00 0.00 35.28 2.40
2898 4202 5.552870 AGCAGGAAGTATGGTATTACCTG 57.447 43.478 13.90 0.00 43.98 4.00
2911 4215 4.202472 GGTATTACCTGCATTAAGAGGGCT 60.202 45.833 5.56 0.00 34.73 5.19
2971 4277 1.805945 CGACCCTAAGACGCACAGC 60.806 63.158 0.00 0.00 0.00 4.40
3040 4346 5.227569 TGCTTTCATTGAGAGTTCCACTA 57.772 39.130 6.13 0.00 0.00 2.74
3104 4410 0.743345 AATACCGCCGCAAAGGAGAC 60.743 55.000 0.00 0.00 43.02 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 5.264395 AGCCAACCTAGTTATTTTCATGCT 58.736 37.500 0.00 0.00 0.00 3.79
47 48 2.418197 GCTAGAGTTTCGTACATGGCCA 60.418 50.000 8.56 8.56 0.00 5.36
160 165 1.470098 TCTACCTACGTGCGTTTCTCC 59.530 52.381 1.66 0.00 0.00 3.71
509 526 7.626390 TCCTCGTCCCAAAATTCTTATCTTAA 58.374 34.615 0.00 0.00 0.00 1.85
512 529 5.693769 TCCTCGTCCCAAAATTCTTATCT 57.306 39.130 0.00 0.00 0.00 1.98
513 530 5.880887 ACTTCCTCGTCCCAAAATTCTTATC 59.119 40.000 0.00 0.00 0.00 1.75
525 542 3.064931 CAAACAAGTACTTCCTCGTCCC 58.935 50.000 4.77 0.00 0.00 4.46
529 546 3.741344 CACTCCAAACAAGTACTTCCTCG 59.259 47.826 4.77 0.00 0.00 4.63
636 672 1.153549 GAGCTTCAGGGTGCGGTAG 60.154 63.158 0.00 0.00 0.00 3.18
637 673 1.609501 AGAGCTTCAGGGTGCGGTA 60.610 57.895 0.00 0.00 0.00 4.02
773 1651 1.001633 GGAGGAAGCAGGTTACACGAA 59.998 52.381 0.00 0.00 0.00 3.85
813 1696 6.054860 AGTAGAGTCCAAACACTTGCATAT 57.945 37.500 0.00 0.00 0.00 1.78
874 2100 2.161012 TCGATGTGTTACACCGAGTCTC 59.839 50.000 13.29 0.00 32.73 3.36
949 2175 2.258013 GCGGTGGCAAGCACAAGTA 61.258 57.895 10.78 0.00 39.62 2.24
1257 2497 2.202946 TTGTCTGGAACGCGCACA 60.203 55.556 5.73 1.13 0.00 4.57
1550 2799 3.453424 ACAATGAACTTTTCGCCCAAAC 58.547 40.909 0.00 0.00 0.00 2.93
1761 3055 2.291465 CCACCAACGATCTATTGCCATG 59.709 50.000 0.00 0.00 0.00 3.66
1947 3244 4.256920 AGACATGATTTCTCTCCAAACCG 58.743 43.478 0.00 0.00 0.00 4.44
2239 3541 3.000727 CCTTTTCGTACACCATCCTCAC 58.999 50.000 0.00 0.00 0.00 3.51
2320 3622 9.407380 ACTTATACACAAATCCATAGCATCAAA 57.593 29.630 0.00 0.00 0.00 2.69
2359 3661 6.385176 TCAGAATGGACAGAGGTATTTCAGAT 59.615 38.462 0.00 0.00 36.16 2.90
2361 3663 5.814705 GTCAGAATGGACAGAGGTATTTCAG 59.185 44.000 0.00 0.00 37.73 3.02
2403 3705 4.389077 GGTTCATTCGTCTTCATCGACTTT 59.611 41.667 0.00 0.00 37.05 2.66
2430 3732 2.813172 ACATGTTGCGATTGATGACACA 59.187 40.909 0.00 0.00 0.00 3.72
2445 3747 2.199652 CCGTGGGGTTGCACATGTT 61.200 57.895 0.00 0.00 0.00 2.71
2469 3771 6.204688 TCAGAATTCACACCACAATAGTTGAC 59.795 38.462 8.44 0.00 0.00 3.18
2508 3812 3.118112 TGAATCATCAGGCCTCTTTCCTC 60.118 47.826 0.00 0.00 0.00 3.71
2716 4020 3.573695 GGGCTAGGGTTATACAGAGTCA 58.426 50.000 0.00 0.00 0.00 3.41
2775 4079 6.599445 AGCCTATATGATTATGATTGCCTCC 58.401 40.000 0.00 0.00 0.00 4.30
2853 4157 9.617523 TGCTTGATTGATTTTGATGAGTATAGA 57.382 29.630 0.00 0.00 0.00 1.98
2898 4202 1.134371 AGGTTCGAGCCCTCTTAATGC 60.134 52.381 15.45 0.00 0.00 3.56
2911 4215 1.619827 ACGATGTTTACCCAGGTTCGA 59.380 47.619 13.28 0.00 30.75 3.71
3040 4346 2.813908 GCCTTTCGACGACGGCAT 60.814 61.111 24.76 0.00 42.06 4.40
3104 4410 0.817654 GATTTGGCCGGGGAGAAAAG 59.182 55.000 2.18 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.