Multiple sequence alignment - TraesCS2D01G510100

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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 TraesCS2D01G510100 chr2D 100.000 6549 0 0 1 6549 602133734 602140282 0.000000e+00 12094.0
1 TraesCS2D01G510100 chr2D 99.774 3103 7 0 1 3103 602107137 602110239 0.000000e+00 5692.0
2 TraesCS2D01G510100 chr2D 96.439 2668 59 13 468 3103 602080255 602082918 0.000000e+00 4368.0
3 TraesCS2D01G510100 chr2D 96.429 2184 68 4 921 3103 602236281 602238455 0.000000e+00 3592.0
4 TraesCS2D01G510100 chr2D 98.612 1801 22 2 1305 3103 602178822 602180621 0.000000e+00 3184.0
5 TraesCS2D01G510100 chr2D 97.249 1781 31 4 3102 4873 602181019 602182790 0.000000e+00 3001.0
6 TraesCS2D01G510100 chr2D 99.758 1241 3 0 3100 4340 602110635 602111875 0.000000e+00 2276.0
7 TraesCS2D01G510100 chr2D 97.394 1151 24 5 3100 4245 602083314 602084463 0.000000e+00 1954.0
8 TraesCS2D01G510100 chr2D 97.164 1093 30 1 5457 6549 602114722 602115813 0.000000e+00 1845.0
9 TraesCS2D01G510100 chr2D 97.072 1093 31 1 5457 6549 602087265 602088356 0.000000e+00 1840.0
10 TraesCS2D01G510100 chr2D 96.889 1093 31 1 5457 6549 602184827 602185916 0.000000e+00 1827.0
11 TraesCS2D01G510100 chr2D 98.928 933 10 0 1 933 602227539 602228471 0.000000e+00 1668.0
12 TraesCS2D01G510100 chr2D 99.479 768 2 1 4108 4873 602111917 602112684 0.000000e+00 1395.0
13 TraesCS2D01G510100 chr2D 98.951 572 6 0 4871 5442 602086607 602087178 0.000000e+00 1024.0
14 TraesCS2D01G510100 chr2D 98.601 572 8 0 4871 5442 602114064 602114635 0.000000e+00 1013.0
15 TraesCS2D01G510100 chr2D 97.759 580 8 2 4298 4873 602084647 602085225 0.000000e+00 994.0
16 TraesCS2D01G510100 chr2D 97.203 572 16 0 4871 5442 602184169 602184740 0.000000e+00 968.0
17 TraesCS2D01G510100 chr2D 89.500 200 20 1 4396 4595 634588300 634588102 1.090000e-62 252.0
18 TraesCS2D01G510100 chr2D 100.000 53 0 0 1 53 602171225 602171277 1.500000e-16 99.0
19 TraesCS2D01G510100 chr2B 96.300 2189 71 4 613 2800 732341925 732344104 0.000000e+00 3585.0
20 TraesCS2D01G510100 chr2B 94.404 1090 42 11 3319 4393 732347684 732348769 0.000000e+00 1657.0
21 TraesCS2D01G510100 chr2B 92.091 569 43 2 4871 5438 732349990 732350557 0.000000e+00 800.0
22 TraesCS2D01G510100 chr2B 89.754 488 49 1 5462 5948 732350653 732351140 2.010000e-174 623.0
23 TraesCS2D01G510100 chr2B 97.764 313 7 0 2791 3103 732346468 732346780 2.080000e-149 540.0
24 TraesCS2D01G510100 chr2B 95.964 223 8 1 3100 3321 732347176 732347398 1.740000e-95 361.0
25 TraesCS2D01G510100 chr2B 98.701 154 1 1 468 621 732341735 732341887 8.370000e-69 272.0
26 TraesCS2D01G510100 chr2B 98.561 139 2 0 3962 4100 288972059 288971921 5.070000e-61 246.0
27 TraesCS2D01G510100 chr2B 87.931 116 14 0 854 969 732341974 732342089 3.180000e-28 137.0
28 TraesCS2D01G510100 chr2B 97.674 43 1 0 331 373 732341689 732341731 2.530000e-09 75.0
29 TraesCS2D01G510100 chr2B 93.750 48 2 1 3254 3300 16027866 16027913 3.280000e-08 71.3
30 TraesCS2D01G510100 chr6D 91.939 521 39 2 6028 6548 289511266 289510749 0.000000e+00 726.0
31 TraesCS2D01G510100 chr6D 84.472 322 23 11 4391 4700 450570313 450570619 6.420000e-75 292.0
32 TraesCS2D01G510100 chr6D 94.737 38 0 2 3261 3296 413768723 413768760 2.550000e-04 58.4
33 TraesCS2D01G510100 chr3D 90.758 541 47 3 6008 6548 598603826 598603289 0.000000e+00 719.0
34 TraesCS2D01G510100 chr5B 90.538 539 48 2 6010 6548 712875070 712875605 0.000000e+00 710.0
35 TraesCS2D01G510100 chr5B 90.388 541 48 3 6008 6548 693954321 693953785 0.000000e+00 708.0
36 TraesCS2D01G510100 chr5B 96.377 138 5 0 3963 4100 472662987 472663124 1.840000e-55 228.0
37 TraesCS2D01G510100 chr7D 90.353 539 48 3 6010 6548 72464383 72463849 0.000000e+00 704.0
38 TraesCS2D01G510100 chr1A 89.945 547 48 7 6002 6548 589613371 589613910 0.000000e+00 699.0
39 TraesCS2D01G510100 chr3A 85.580 319 39 3 3538 3853 10665678 10665364 1.760000e-85 327.0
40 TraesCS2D01G510100 chr3A 87.342 237 28 2 3264 3498 10665919 10665683 3.010000e-68 270.0
41 TraesCS2D01G510100 chr5D 75.789 570 95 24 3258 3802 488886121 488886672 1.410000e-61 248.0
42 TraesCS2D01G510100 chr7B 97.857 140 3 0 3961 4100 445291239 445291378 6.560000e-60 243.0
43 TraesCS2D01G510100 chr7B 95.683 139 6 0 3962 4100 508191349 508191487 2.380000e-54 224.0
44 TraesCS2D01G510100 chr7B 77.528 267 57 3 1156 1420 750148664 750148929 2.440000e-34 158.0
45 TraesCS2D01G510100 chr4D 94.444 144 8 0 3961 4104 469431040 469430897 8.550000e-54 222.0
46 TraesCS2D01G510100 chr6B 74.854 171 31 10 4394 4562 646751647 646751487 4.240000e-07 67.6
47 TraesCS2D01G510100 chr6A 87.719 57 5 2 3246 3300 559742774 559742830 1.520000e-06 65.8
48 TraesCS2D01G510100 chr7A 94.444 36 1 1 3261 3295 51087956 51087921 3.000000e-03 54.7


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 TraesCS2D01G510100 chr2D 602133734 602140282 6548 False 12094.00 12094 100.00000 1 6549 1 chr2D.!!$F1 6548
1 TraesCS2D01G510100 chr2D 602236281 602238455 2174 False 3592.00 3592 96.42900 921 3103 1 chr2D.!!$F4 2182
2 TraesCS2D01G510100 chr2D 602107137 602115813 8676 False 2444.20 5692 98.95520 1 6549 5 chr2D.!!$F6 6548
3 TraesCS2D01G510100 chr2D 602178822 602185916 7094 False 2245.00 3184 97.48825 1305 6549 4 chr2D.!!$F7 5244
4 TraesCS2D01G510100 chr2D 602080255 602088356 8101 False 2036.00 4368 97.52300 468 6549 5 chr2D.!!$F5 6081
5 TraesCS2D01G510100 chr2D 602227539 602228471 932 False 1668.00 1668 98.92800 1 933 1 chr2D.!!$F3 932
6 TraesCS2D01G510100 chr2B 732341689 732344104 2415 False 1017.25 3585 95.15150 331 2800 4 chr2B.!!$F2 2469
7 TraesCS2D01G510100 chr2B 732346468 732351140 4672 False 796.20 1657 93.99540 2791 5948 5 chr2B.!!$F3 3157
8 TraesCS2D01G510100 chr6D 289510749 289511266 517 True 726.00 726 91.93900 6028 6548 1 chr6D.!!$R1 520
9 TraesCS2D01G510100 chr3D 598603289 598603826 537 True 719.00 719 90.75800 6008 6548 1 chr3D.!!$R1 540
10 TraesCS2D01G510100 chr5B 712875070 712875605 535 False 710.00 710 90.53800 6010 6548 1 chr5B.!!$F2 538
11 TraesCS2D01G510100 chr5B 693953785 693954321 536 True 708.00 708 90.38800 6008 6548 1 chr5B.!!$R1 540
12 TraesCS2D01G510100 chr7D 72463849 72464383 534 True 704.00 704 90.35300 6010 6548 1 chr7D.!!$R1 538
13 TraesCS2D01G510100 chr1A 589613371 589613910 539 False 699.00 699 89.94500 6002 6548 1 chr1A.!!$F1 546
14 TraesCS2D01G510100 chr3A 10665364 10665919 555 True 298.50 327 86.46100 3264 3853 2 chr3A.!!$R1 589
15 TraesCS2D01G510100 chr5D 488886121 488886672 551 False 248.00 248 75.78900 3258 3802 1 chr5D.!!$F1 544

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
432 433 4.515191 TCCTACTGTCAAACATGCTTCAAC 59.485 41.667 0.00 0.0 0.00 3.18 F
2063 2112 7.492524 TGCCAACTTATGTTTGTGATGTAAAA 58.507 30.769 0.00 0.0 33.52 1.52 F
2455 2506 6.349115 GCTGAATGCTTCATTCCACATATAGG 60.349 42.308 14.68 0.0 46.65 2.57 F
3058 3109 6.372937 CCTTCTTCTATTGGACAACTCCTTTC 59.627 42.308 0.00 0.0 37.48 2.62 F
4921 7738 3.628008 TCTTCAGAGCATCATGCCAAAT 58.372 40.909 5.84 0.0 46.52 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2063 2112 6.120905 CCAAGATTTCTCTTCATCCATGAGT 58.879 40.000 0.00 0.0 39.78 3.41 R
3058 3109 3.937706 CCTCAGATCTACAGTTTGCAAGG 59.062 47.826 0.00 0.0 0.00 3.61 R
4372 5550 2.505405 CTCGACCGATTCATCTCCCTA 58.495 52.381 0.00 0.0 0.00 3.53 R
5258 8075 0.618458 AGTCGAAGGCCCTTGCAATA 59.382 50.000 0.00 0.0 40.13 1.90 R
6330 9220 0.316841 GCTCTGAGGATGGACCGATC 59.683 60.000 6.83 0.0 44.74 3.69 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
432 433 4.515191 TCCTACTGTCAAACATGCTTCAAC 59.485 41.667 0.00 0.00 0.00 3.18
2063 2112 7.492524 TGCCAACTTATGTTTGTGATGTAAAA 58.507 30.769 0.00 0.00 33.52 1.52
2455 2506 6.349115 GCTGAATGCTTCATTCCACATATAGG 60.349 42.308 14.68 0.00 46.65 2.57
2835 2886 9.503427 CCTATCGTTCTTGTTTTCATAATTTCC 57.497 33.333 0.00 0.00 0.00 3.13
3058 3109 6.372937 CCTTCTTCTATTGGACAACTCCTTTC 59.627 42.308 0.00 0.00 37.48 2.62
4372 5550 6.876789 GGAATCGGTGGAAATTTTATTGGTTT 59.123 34.615 0.00 0.00 0.00 3.27
4921 7738 3.628008 TCTTCAGAGCATCATGCCAAAT 58.372 40.909 5.84 0.00 46.52 2.32
5258 8075 3.003689 CGACACTTTTGCTGAAACTGGAT 59.996 43.478 0.00 0.00 0.00 3.41
5391 8208 1.150827 CTCTTCGTGCATGCTCAACA 58.849 50.000 20.33 0.00 0.00 3.33
5394 8211 1.532437 CTTCGTGCATGCTCAACAGAA 59.468 47.619 20.33 12.45 0.00 3.02
5418 8235 2.093075 CCAGGACAGTGCATCTCTCATT 60.093 50.000 0.00 0.00 0.00 2.57
5443 8260 2.107141 GAGACAGGGCGATTCCGG 59.893 66.667 0.00 0.00 36.06 5.14
5444 8261 3.447025 GAGACAGGGCGATTCCGGG 62.447 68.421 0.00 0.00 36.06 5.73
5447 8264 3.781307 CAGGGCGATTCCGGGTCA 61.781 66.667 0.00 0.00 36.06 4.02
5452 8269 2.582498 CGATTCCGGGTCACGCTC 60.582 66.667 0.00 0.00 42.52 5.03
5453 8270 2.893398 GATTCCGGGTCACGCTCT 59.107 61.111 0.00 0.00 42.52 4.09
5454 8271 1.721664 CGATTCCGGGTCACGCTCTA 61.722 60.000 0.00 0.00 42.52 2.43
5455 8272 0.248949 GATTCCGGGTCACGCTCTAC 60.249 60.000 0.00 0.00 42.52 2.59
5554 8444 5.130477 AGAAATAGACCCGCAGAAATCCTTA 59.870 40.000 0.00 0.00 0.00 2.69
5590 8480 0.749454 GCGAGGGCATTGATCTTGGT 60.749 55.000 0.00 0.00 39.62 3.67
5631 8521 3.504520 GGCGGAAATCTAGTTTTGTTCCA 59.495 43.478 3.50 0.00 38.10 3.53
5783 8673 0.735978 TCTGGTACGTTGCATGCTCG 60.736 55.000 25.30 25.30 0.00 5.03
5787 8677 3.925362 TACGTTGCATGCTCGCCGT 62.925 57.895 26.27 23.73 34.77 5.68
6036 8926 2.206223 GGAAAAGGAGGATGTACCCCT 58.794 52.381 3.80 3.80 39.75 4.79
6330 9220 2.100631 GCCGTCACCACCATCTTCG 61.101 63.158 0.00 0.00 0.00 3.79
6501 9391 2.753043 ACCCACCGTCGACGCTAT 60.753 61.111 31.73 16.46 38.18 2.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
432 433 7.894376 TCTGGTATAAAACTAGTGGAAAACG 57.106 36.000 0.00 0.00 37.89 3.60
2063 2112 6.120905 CCAAGATTTCTCTTCATCCATGAGT 58.879 40.000 0.00 0.00 39.78 3.41
2455 2506 5.594926 CCATTTCTTCCATTGTATGCCTTC 58.405 41.667 0.00 0.00 0.00 3.46
3058 3109 3.937706 CCTCAGATCTACAGTTTGCAAGG 59.062 47.826 0.00 0.00 0.00 3.61
4372 5550 2.505405 CTCGACCGATTCATCTCCCTA 58.495 52.381 0.00 0.00 0.00 3.53
5258 8075 0.618458 AGTCGAAGGCCCTTGCAATA 59.382 50.000 0.00 0.00 40.13 1.90
5391 8208 0.773644 ATGCACTGTCCTGGGTTTCT 59.226 50.000 0.00 0.00 0.00 2.52
5394 8211 0.326264 GAGATGCACTGTCCTGGGTT 59.674 55.000 0.00 0.00 0.00 4.11
5452 8269 2.103143 CAGCTCCTGTCGGCGTAG 59.897 66.667 6.85 6.87 0.00 3.51
5453 8270 4.129737 GCAGCTCCTGTCGGCGTA 62.130 66.667 6.85 0.00 33.43 4.42
5554 8444 0.880278 CGCAGCGTATGGCCACTATT 60.880 55.000 8.16 0.00 45.17 1.73
5590 8480 0.299300 CGAAGTTTTGCACGACACGA 59.701 50.000 0.00 0.00 0.00 4.35
5631 8521 4.202792 TGGGCAGCCCTAAGTATCTAGTAT 60.203 45.833 31.51 0.00 45.70 2.12
5654 8544 4.222336 AGCCTAACTCTAGTGATGCAGAT 58.778 43.478 0.00 0.00 0.00 2.90
5902 8792 1.213537 CCGCCAATTGACCTTGCAG 59.786 57.895 7.12 0.00 0.00 4.41
6036 8926 2.993008 GTCCAGATGCAGAGGCCA 59.007 61.111 5.01 0.00 40.13 5.36
6330 9220 0.316841 GCTCTGAGGATGGACCGATC 59.683 60.000 6.83 0.00 44.74 3.69
6401 9291 3.056328 GGAAGTTGCCTGGCGTCC 61.056 66.667 14.98 13.67 0.00 4.79
6410 9300 2.436824 GCGGGAGGAGGAAGTTGC 60.437 66.667 0.00 0.00 0.00 4.17
6501 9391 2.983030 GCGGTGTGGCATCAACCA 60.983 61.111 14.75 0.00 37.38 3.67


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

AutoCloner maintained by Alex Coulton.