Multiple sequence alignment - TraesCS3B01G027400

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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 TraesCS3B01G027400 chr3B 100.000 3063 0 0 1 3063 11923405 11926467 0.000000e+00 5657.0
1 TraesCS3B01G027400 chr3B 95.798 119 5 0 2368 2486 11959419 11959301 3.120000e-45 193.0
2 TraesCS3B01G027400 chrUn 95.254 2065 58 15 450 2483 36300718 36298663 0.000000e+00 3234.0
3 TraesCS3B01G027400 chrUn 95.085 590 20 4 2482 3063 36298559 36297971 0.000000e+00 920.0
4 TraesCS3B01G027400 chrUn 96.305 433 13 1 1112 1544 476365717 476365288 0.000000e+00 708.0
5 TraesCS3B01G027400 chrUn 88.215 594 38 14 1 591 36303899 36303335 0.000000e+00 680.0
6 TraesCS3B01G027400 chrUn 88.215 594 38 14 1 591 325223519 325222955 0.000000e+00 680.0
7 TraesCS3B01G027400 chrUn 89.427 454 36 7 450 901 36317787 36318230 2.060000e-156 562.0
8 TraesCS3B01G027400 chrUn 90.557 413 35 2 1835 2246 35513625 35514034 7.470000e-151 544.0
9 TraesCS3B01G027400 chrUn 88.262 443 33 13 1 430 35513184 35513620 2.110000e-141 512.0
10 TraesCS3B01G027400 chrUn 87.443 438 39 12 1 430 36301123 36300694 9.870000e-135 490.0
11 TraesCS3B01G027400 chrUn 94.118 119 7 0 2368 2486 36476640 36476758 6.750000e-42 182.0
12 TraesCS3B01G027400 chr3D 93.071 1703 78 18 551 2246 5816106 5814437 0.000000e+00 2455.0
13 TraesCS3B01G027400 chr3D 92.446 556 37 4 2511 3063 609880374 609879821 0.000000e+00 789.0
14 TraesCS3B01G027400 chr3D 92.182 550 43 0 2514 3063 84507376 84506827 0.000000e+00 778.0
15 TraesCS3B01G027400 chr3D 86.386 404 39 9 6 401 5816574 5816179 7.850000e-116 427.0
16 TraesCS3B01G027400 chr3D 84.680 359 34 14 59 402 104021264 104020912 3.780000e-89 339.0
17 TraesCS3B01G027400 chr3D 88.679 53 6 0 1188 1240 29308931 29308879 7.090000e-07 65.8
18 TraesCS3B01G027400 chr3D 100.000 32 0 0 2345 2376 5814658 5814627 3.300000e-05 60.2
19 TraesCS3B01G027400 chr3A 90.132 1814 122 33 701 2486 15429025 15430809 0.000000e+00 2305.0
20 TraesCS3B01G027400 chr3A 92.694 1355 75 14 848 2196 12177445 12176109 0.000000e+00 1932.0
21 TraesCS3B01G027400 chr3A 85.671 656 51 20 1 640 15428404 15429032 0.000000e+00 651.0
22 TraesCS3B01G027400 chr3A 82.326 430 31 20 163 582 12180492 12180098 6.330000e-87 331.0
23 TraesCS3B01G027400 chr3A 92.021 188 9 3 575 756 12179526 12179339 3.030000e-65 259.0
24 TraesCS3B01G027400 chr3A 95.098 102 4 1 753 853 12179034 12178933 3.160000e-35 159.0
25 TraesCS3B01G027400 chr3A 95.238 42 2 0 2445 2486 12175949 12175990 1.970000e-07 67.6
26 TraesCS3B01G027400 chr3A 88.679 53 6 0 1188 1240 38621385 38621437 7.090000e-07 65.8
27 TraesCS3B01G027400 chr7D 91.014 1736 90 20 762 2486 42197400 42195720 0.000000e+00 2281.0
28 TraesCS3B01G027400 chr7D 91.501 553 45 2 2513 3063 565435433 565435985 0.000000e+00 760.0
29 TraesCS3B01G027400 chr7D 82.278 790 121 12 1366 2141 81760047 81760831 0.000000e+00 665.0
30 TraesCS3B01G027400 chr7D 78.779 655 134 5 1421 2071 317625779 317625126 4.690000e-118 435.0
31 TraesCS3B01G027400 chr7D 92.359 301 20 2 446 743 42197920 42197620 2.820000e-115 425.0
32 TraesCS3B01G027400 chr7D 88.390 267 22 8 174 433 42198153 42197889 2.290000e-81 313.0
33 TraesCS3B01G027400 chr7D 90.604 149 10 2 33 181 42199465 42199321 8.670000e-46 195.0
34 TraesCS3B01G027400 chr7D 80.478 251 37 6 61 303 598525436 598525682 6.750000e-42 182.0
35 TraesCS3B01G027400 chr7D 82.439 205 26 6 64 266 169967545 169967349 1.460000e-38 171.0
36 TraesCS3B01G027400 chr7D 96.970 66 1 1 2181 2246 42195987 42195923 3.230000e-20 110.0
37 TraesCS3B01G027400 chr7D 85.185 81 9 1 67 147 42945265 42945188 2.530000e-11 80.5
38 TraesCS3B01G027400 chr5B 92.532 549 39 2 2517 3063 473887282 473886734 0.000000e+00 785.0
39 TraesCS3B01G027400 chr5B 88.732 71 6 2 91 161 710654559 710654491 5.440000e-13 86.1
40 TraesCS3B01G027400 chr5D 92.196 551 41 2 2515 3063 7054352 7054902 0.000000e+00 778.0
41 TraesCS3B01G027400 chr5D 84.109 258 20 10 165 402 416797886 416798142 2.380000e-56 230.0
42 TraesCS3B01G027400 chr5D 88.679 53 5 1 83 134 114976377 114976429 2.550000e-06 63.9
43 TraesCS3B01G027400 chr7B 92.168 549 39 3 2517 3063 376806745 376806199 0.000000e+00 773.0
44 TraesCS3B01G027400 chr7B 92.015 551 40 3 2514 3063 477607279 477607826 0.000000e+00 771.0
45 TraesCS3B01G027400 chr7B 80.978 757 128 10 1366 2110 28686732 28687484 1.220000e-163 586.0
46 TraesCS3B01G027400 chr5A 91.470 551 37 9 2517 3063 211614961 211614417 0.000000e+00 749.0
47 TraesCS3B01G027400 chr2D 79.586 725 128 8 1357 2071 267847899 267848613 4.560000e-138 501.0
48 TraesCS3B01G027400 chr2D 77.169 219 37 6 1976 2190 158030724 158030933 6.940000e-22 115.0
49 TraesCS3B01G027400 chr4D 80.451 665 117 8 1530 2190 148543629 148542974 2.120000e-136 496.0
50 TraesCS3B01G027400 chr4D 85.772 246 20 9 171 402 64085248 64085492 2.360000e-61 246.0
51 TraesCS3B01G027400 chr6A 84.956 113 12 3 53 164 535538215 535538107 3.230000e-20 110.0
52 TraesCS3B01G027400 chr6A 86.022 93 10 2 60 152 71527491 71527580 2.510000e-16 97.1
53 TraesCS3B01G027400 chr6B 85.000 100 9 3 60 159 127376244 127376337 2.510000e-16 97.1
54 TraesCS3B01G027400 chr1A 92.593 54 4 0 85 138 333886694 333886641 9.110000e-11 78.7
55 TraesCS3B01G027400 chr4B 89.655 58 6 0 99 156 167934224 167934167 1.180000e-09 75.0
56 TraesCS3B01G027400 chr1D 93.878 49 3 0 103 151 412220893 412220845 1.180000e-09 75.0
57 TraesCS3B01G027400 chr6D 87.931 58 6 1 86 142 26367203 26367260 1.970000e-07 67.6


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 TraesCS3B01G027400 chr3B 11923405 11926467 3062 False 5657.000000 5657 100.000000 1 3063 1 chr3B.!!$F1 3062
1 TraesCS3B01G027400 chrUn 36297971 36303899 5928 True 1331.000000 3234 91.499250 1 3063 4 chrUn.!!$R3 3062
2 TraesCS3B01G027400 chrUn 325222955 325223519 564 True 680.000000 680 88.215000 1 591 1 chrUn.!!$R1 590
3 TraesCS3B01G027400 chrUn 35513184 35514034 850 False 528.000000 544 89.409500 1 2246 2 chrUn.!!$F3 2245
4 TraesCS3B01G027400 chr3D 5814437 5816574 2137 True 980.733333 2455 93.152333 6 2376 3 chr3D.!!$R5 2370
5 TraesCS3B01G027400 chr3D 609879821 609880374 553 True 789.000000 789 92.446000 2511 3063 1 chr3D.!!$R4 552
6 TraesCS3B01G027400 chr3D 84506827 84507376 549 True 778.000000 778 92.182000 2514 3063 1 chr3D.!!$R2 549
7 TraesCS3B01G027400 chr3A 15428404 15430809 2405 False 1478.000000 2305 87.901500 1 2486 2 chr3A.!!$F3 2485
8 TraesCS3B01G027400 chr3A 12176109 12180492 4383 True 670.250000 1932 90.534750 163 2196 4 chr3A.!!$R1 2033
9 TraesCS3B01G027400 chr7D 565435433 565435985 552 False 760.000000 760 91.501000 2513 3063 1 chr7D.!!$F2 550
10 TraesCS3B01G027400 chr7D 81760047 81760831 784 False 665.000000 665 82.278000 1366 2141 1 chr7D.!!$F1 775
11 TraesCS3B01G027400 chr7D 42195720 42199465 3745 True 664.800000 2281 91.867400 33 2486 5 chr7D.!!$R4 2453
12 TraesCS3B01G027400 chr7D 317625126 317625779 653 True 435.000000 435 78.779000 1421 2071 1 chr7D.!!$R3 650
13 TraesCS3B01G027400 chr5B 473886734 473887282 548 True 785.000000 785 92.532000 2517 3063 1 chr5B.!!$R1 546
14 TraesCS3B01G027400 chr5D 7054352 7054902 550 False 778.000000 778 92.196000 2515 3063 1 chr5D.!!$F1 548
15 TraesCS3B01G027400 chr7B 376806199 376806745 546 True 773.000000 773 92.168000 2517 3063 1 chr7B.!!$R1 546
16 TraesCS3B01G027400 chr7B 477607279 477607826 547 False 771.000000 771 92.015000 2514 3063 1 chr7B.!!$F2 549
17 TraesCS3B01G027400 chr7B 28686732 28687484 752 False 586.000000 586 80.978000 1366 2110 1 chr7B.!!$F1 744
18 TraesCS3B01G027400 chr5A 211614417 211614961 544 True 749.000000 749 91.470000 2517 3063 1 chr5A.!!$R1 546
19 TraesCS3B01G027400 chr2D 267847899 267848613 714 False 501.000000 501 79.586000 1357 2071 1 chr2D.!!$F2 714
20 TraesCS3B01G027400 chr4D 148542974 148543629 655 True 496.000000 496 80.451000 1530 2190 1 chr4D.!!$R1 660

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
934 7325 1.006639 AGTCTCACCCTTCCTCCTCTC 59.993 57.143 0.0 0.0 0.0 3.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2508 9181 1.145803 GTGAGTTGGCCTAACGTGTC 58.854 55.0 3.32 2.03 44.15 3.67 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
259 1444 7.868906 CAAATATGCATGGGAATTTCCTTTT 57.131 32.000 14.95 0.00 36.57 2.27
261 1446 7.868906 AATATGCATGGGAATTTCCTTTTTG 57.131 32.000 14.95 8.67 36.57 2.44
413 4382 9.090692 GTTGCAAACTACTCCTAATTAATACGA 57.909 33.333 0.00 0.00 45.32 3.43
414 4383 8.638685 TGCAAACTACTCCTAATTAATACGAC 57.361 34.615 0.00 0.00 0.00 4.34
415 4384 8.252417 TGCAAACTACTCCTAATTAATACGACA 58.748 33.333 0.00 0.00 0.00 4.35
420 4389 9.798994 ACTACTCCTAATTAATACGACAAACAG 57.201 33.333 0.00 0.00 0.00 3.16
422 4391 8.928270 ACTCCTAATTAATACGACAAACAGAG 57.072 34.615 0.00 0.00 0.00 3.35
423 4392 8.746530 ACTCCTAATTAATACGACAAACAGAGA 58.253 33.333 0.00 0.00 0.00 3.10
424 4393 9.582431 CTCCTAATTAATACGACAAACAGAGAA 57.418 33.333 0.00 0.00 0.00 2.87
425 4394 9.932207 TCCTAATTAATACGACAAACAGAGAAA 57.068 29.630 0.00 0.00 0.00 2.52
426 4395 9.968743 CCTAATTAATACGACAAACAGAGAAAC 57.031 33.333 0.00 0.00 0.00 2.78
435 4404 4.377021 ACAAACAGAGAAACTATCGTGCA 58.623 39.130 0.00 0.00 0.00 4.57
439 4408 1.134670 AGAGAAACTATCGTGCAGGGC 60.135 52.381 6.56 0.00 0.00 5.19
456 4428 4.154195 GCAGGGCATCACCTAATTAATACG 59.846 45.833 0.00 0.00 39.34 3.06
503 4477 9.010029 ACCCTCTATTACTTAATGTTGTGTTTG 57.990 33.333 0.00 0.00 0.00 2.93
554 4536 7.102847 ACTTTGTCCAAATTTACGGAGAAAA 57.897 32.000 16.09 10.75 42.16 2.29
871 7247 2.084546 GGGTGTCACATTAACTCAGCC 58.915 52.381 5.12 0.00 38.99 4.85
934 7325 1.006639 AGTCTCACCCTTCCTCCTCTC 59.993 57.143 0.00 0.00 0.00 3.20
1001 7419 4.424842 AGAGAGAGAGAGGTTTGTTCCAT 58.575 43.478 0.00 0.00 0.00 3.41
1085 7509 4.083581 AGCAAGAAATCGTTGTGCATAC 57.916 40.909 0.00 0.00 0.00 2.39
1302 7740 5.195940 ACATCCCATGAACTGAATCGAATT 58.804 37.500 0.00 0.00 0.00 2.17
1516 7964 3.509137 GAAGTGCGACCACCACGGA 62.509 63.158 0.00 0.00 43.09 4.69
2508 9181 4.756642 TGACTAAGAATGCAGTTTGTCAGG 59.243 41.667 14.90 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 0.178995 TTGATGAGCAGTGTTGGGCA 60.179 50.000 0.00 0.00 0.00 5.36
214 1398 2.887152 GCATGTGGAGGTGAGTCTTTTT 59.113 45.455 0.00 0.00 0.00 1.94
358 4327 5.902681 TCGATGAGATTCCTTGTACGAAAT 58.097 37.500 0.00 0.00 0.00 2.17
363 4332 6.313905 ACACATTTCGATGAGATTCCTTGTAC 59.686 38.462 0.00 0.00 0.00 2.90
398 4367 9.582431 TTCTCTGTTTGTCGTATTAATTAGGAG 57.418 33.333 0.00 0.00 0.00 3.69
399 4368 9.932207 TTTCTCTGTTTGTCGTATTAATTAGGA 57.068 29.630 0.00 0.00 0.00 2.94
405 4374 9.069078 CGATAGTTTCTCTGTTTGTCGTATTAA 57.931 33.333 0.00 0.00 0.00 1.40
406 4375 8.610855 CGATAGTTTCTCTGTTTGTCGTATTA 57.389 34.615 0.00 0.00 0.00 0.98
407 4376 7.507672 CGATAGTTTCTCTGTTTGTCGTATT 57.492 36.000 0.00 0.00 0.00 1.89
426 4395 0.882042 GGTGATGCCCTGCACGATAG 60.882 60.000 0.00 0.00 43.04 2.08
427 4396 1.146041 GGTGATGCCCTGCACGATA 59.854 57.895 0.00 0.00 43.04 2.92
429 4398 1.549243 TTAGGTGATGCCCTGCACGA 61.549 55.000 0.00 0.00 43.04 4.35
435 4404 5.071250 TGTCGTATTAATTAGGTGATGCCCT 59.929 40.000 0.00 0.00 38.26 5.19
439 4408 7.438160 TCTGCTTGTCGTATTAATTAGGTGATG 59.562 37.037 0.00 0.00 0.00 3.07
456 4428 7.501844 AGGGTATTATAGTTTCTCTGCTTGTC 58.498 38.462 0.00 0.00 0.00 3.18
554 4536 7.112122 TCTTGGCATTGTAGATGTAGATGTTT 58.888 34.615 0.00 0.00 0.00 2.83
556 4538 6.239217 TCTTGGCATTGTAGATGTAGATGT 57.761 37.500 0.00 0.00 0.00 3.06
821 5704 3.951979 ACAGTCAAAGAGCAAAACGAG 57.048 42.857 0.00 0.00 0.00 4.18
871 7247 0.166814 GCACAGTAAAGGAGCAAGCG 59.833 55.000 0.00 0.00 0.00 4.68
934 7325 0.179150 CGGCTGGAGAAGAGAAGACG 60.179 60.000 0.00 0.00 34.38 4.18
1085 7509 1.378250 CTTCCTTGGGCTCCTGCAG 60.378 63.158 6.78 6.78 41.91 4.41
2253 8819 5.351465 CAGCCACAAGATACTAACGTCAAAT 59.649 40.000 0.00 0.00 0.00 2.32
2508 9181 1.145803 GTGAGTTGGCCTAACGTGTC 58.854 55.000 3.32 2.03 44.15 3.67


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

AutoCloner maintained by Alex Coulton.