Multiple sequence alignment - TraesCS4B01G188200

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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 TraesCS4B01G188200 chr4B 100.000 6763 0 0 1 6763 408985351 408978589 0.000000e+00 12490.0
1 TraesCS4B01G188200 chr4B 92.934 1670 97 9 2966 4619 147075653 147073989 0.000000e+00 2410.0
2 TraesCS4B01G188200 chr4B 94.957 1170 42 6 2964 4130 182238966 182237811 0.000000e+00 1818.0
3 TraesCS4B01G188200 chr4B 93.622 1176 68 4 2962 4130 471722459 471721284 0.000000e+00 1749.0
4 TraesCS4B01G188200 chr4D 95.703 2211 49 14 797 2965 329140607 329138401 0.000000e+00 3515.0
5 TraesCS4B01G188200 chr4D 97.372 1408 37 0 4620 6027 329138405 329136998 0.000000e+00 2396.0
6 TraesCS4B01G188200 chr4D 88.778 401 19 13 6277 6659 329136845 329136453 1.030000e-127 468.0
7 TraesCS4B01G188200 chr4D 93.277 119 5 2 6022 6140 329136967 329136852 9.020000e-39 172.0
8 TraesCS4B01G188200 chr6B 98.225 1690 7 6 2953 4621 346318345 346316658 0.000000e+00 2933.0
9 TraesCS4B01G188200 chr6B 93.487 1689 75 9 2966 4620 552131979 552133666 0.000000e+00 2477.0
10 TraesCS4B01G188200 chr6B 96.764 989 18 3 3645 4620 124082530 124083517 0.000000e+00 1637.0
11 TraesCS4B01G188200 chr6B 95.648 988 28 4 3646 4620 113651066 113652051 0.000000e+00 1572.0
12 TraesCS4B01G188200 chr7A 98.140 1667 21 1 2966 4622 692307686 692306020 0.000000e+00 2898.0
13 TraesCS4B01G188200 chr7A 85.008 1294 147 30 4620 5897 661594039 661595301 0.000000e+00 1271.0
14 TraesCS4B01G188200 chr7A 85.314 606 69 12 1140 1735 661589392 661589987 5.800000e-170 608.0
15 TraesCS4B01G188200 chr7A 83.427 356 44 9 2398 2747 661590777 661591123 3.940000e-82 316.0
16 TraesCS4B01G188200 chr7A 85.477 241 27 5 1766 2006 661590247 661590479 1.880000e-60 244.0
17 TraesCS4B01G188200 chr3B 93.954 1687 77 8 2966 4628 276489240 276490925 0.000000e+00 2527.0
18 TraesCS4B01G188200 chr3B 93.493 1168 71 3 2966 4130 104382382 104381217 0.000000e+00 1731.0
19 TraesCS4B01G188200 chr3B 84.091 88 10 2 6188 6274 727790667 727790751 1.560000e-11 82.4
20 TraesCS4B01G188200 chr2B 93.321 1677 94 7 2963 4625 197585326 197586998 0.000000e+00 2460.0
21 TraesCS4B01G188200 chr2B 94.383 997 32 7 3651 4624 463928426 463927431 0.000000e+00 1509.0
22 TraesCS4B01G188200 chr2B 75.500 200 37 9 529 717 781578584 781578386 3.360000e-13 87.9
23 TraesCS4B01G188200 chr7B 92.857 1680 95 10 2963 4625 234647197 234645526 0.000000e+00 2414.0
24 TraesCS4B01G188200 chr7B 94.128 1141 64 1 2993 4130 457412591 457411451 0.000000e+00 1733.0
25 TraesCS4B01G188200 chr7B 87.050 1112 117 18 4671 5767 629580846 629579747 0.000000e+00 1230.0
26 TraesCS4B01G188200 chr7B 83.759 665 79 20 1092 1735 629582717 629582061 2.700000e-168 603.0
27 TraesCS4B01G188200 chr7B 87.409 413 44 5 2548 2956 629581295 629580887 1.030000e-127 468.0
28 TraesCS4B01G188200 chr7B 93.333 120 8 0 1890 2009 629581576 629581457 1.940000e-40 178.0
29 TraesCS4B01G188200 chr4A 93.135 1646 96 6 2987 4619 661533954 661535595 0.000000e+00 2398.0
30 TraesCS4B01G188200 chr4A 96.449 1408 49 1 4620 6027 140978531 140979937 0.000000e+00 2322.0
31 TraesCS4B01G188200 chr4A 95.128 862 33 6 793 1653 140975853 140976706 0.000000e+00 1351.0
32 TraesCS4B01G188200 chr4A 91.371 591 45 5 210 799 140974603 140975188 0.000000e+00 804.0
33 TraesCS4B01G188200 chr4A 93.750 496 17 9 2469 2963 140978051 140978533 0.000000e+00 732.0
34 TraesCS4B01G188200 chr4A 94.866 448 22 1 4620 5067 253273794 253274240 0.000000e+00 699.0
35 TraesCS4B01G188200 chr4A 94.231 364 18 2 1655 2016 140976975 140977337 2.760000e-153 553.0
36 TraesCS4B01G188200 chr4A 87.683 479 30 15 2017 2483 140977469 140977930 1.290000e-146 531.0
37 TraesCS4B01G188200 chr4A 84.980 506 36 17 6272 6763 140980148 140980627 1.710000e-130 477.0
38 TraesCS4B01G188200 chr4A 96.491 114 3 1 6027 6140 140980035 140980147 3.220000e-43 187.0
39 TraesCS4B01G188200 chr4A 90.000 70 7 0 1 70 140797734 140797803 2.600000e-14 91.6
40 TraesCS4B01G188200 chr4A 88.000 75 7 2 6202 6274 743374387 743374461 3.360000e-13 87.9
41 TraesCS4B01G188200 chr4A 100.000 28 0 0 6202 6229 70811589 70811562 1.200000e-02 52.8
42 TraesCS4B01G188200 chr1B 96.233 1407 51 2 4620 6025 135816366 135817771 0.000000e+00 2303.0
43 TraesCS4B01G188200 chr1B 93.782 1351 61 6 3295 4622 141118536 141119886 0.000000e+00 2008.0
44 TraesCS4B01G188200 chr1B 93.545 1100 34 9 925 2016 135814266 135815336 0.000000e+00 1604.0
45 TraesCS4B01G188200 chr1B 91.104 978 51 19 2018 2965 135815399 135816370 0.000000e+00 1291.0
46 TraesCS4B01G188200 chr1B 85.057 87 10 3 6188 6273 549520470 549520554 1.210000e-12 86.1
47 TraesCS4B01G188200 chr5B 95.467 1103 35 4 3531 4619 216657113 216658214 0.000000e+00 1746.0
48 TraesCS4B01G188200 chr7D 85.714 1225 140 20 4682 5897 572553697 572554895 0.000000e+00 1260.0
49 TraesCS4B01G188200 chr7D 83.387 939 115 28 1083 2006 572549022 572549934 0.000000e+00 832.0
50 TraesCS4B01G188200 chr7D 95.556 45 2 0 6188 6232 632891066 632891110 9.410000e-09 73.1
51 TraesCS4B01G188200 chr2D 78.283 198 31 6 530 716 553759049 553759245 4.290000e-22 117.0
52 TraesCS4B01G188200 chr2D 79.231 130 26 1 505 633 377120569 377120698 9.340000e-14 89.8
53 TraesCS4B01G188200 chr2D 87.931 58 3 2 6197 6253 348194639 348194693 1.570000e-06 65.8
54 TraesCS4B01G188200 chr6D 81.818 88 11 2 6188 6273 453809351 453809435 1.220000e-07 69.4
55 TraesCS4B01G188200 chr3D 88.525 61 2 3 6202 6261 105124434 105124490 1.220000e-07 69.4


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 TraesCS4B01G188200 chr4B 408978589 408985351 6762 True 12490.000000 12490 100.000000 1 6763 1 chr4B.!!$R3 6762
1 TraesCS4B01G188200 chr4B 147073989 147075653 1664 True 2410.000000 2410 92.934000 2966 4619 1 chr4B.!!$R1 1653
2 TraesCS4B01G188200 chr4B 182237811 182238966 1155 True 1818.000000 1818 94.957000 2964 4130 1 chr4B.!!$R2 1166
3 TraesCS4B01G188200 chr4B 471721284 471722459 1175 True 1749.000000 1749 93.622000 2962 4130 1 chr4B.!!$R4 1168
4 TraesCS4B01G188200 chr4D 329136453 329140607 4154 True 1637.750000 3515 93.782500 797 6659 4 chr4D.!!$R1 5862
5 TraesCS4B01G188200 chr6B 346316658 346318345 1687 True 2933.000000 2933 98.225000 2953 4621 1 chr6B.!!$R1 1668
6 TraesCS4B01G188200 chr6B 552131979 552133666 1687 False 2477.000000 2477 93.487000 2966 4620 1 chr6B.!!$F3 1654
7 TraesCS4B01G188200 chr6B 124082530 124083517 987 False 1637.000000 1637 96.764000 3645 4620 1 chr6B.!!$F2 975
8 TraesCS4B01G188200 chr6B 113651066 113652051 985 False 1572.000000 1572 95.648000 3646 4620 1 chr6B.!!$F1 974
9 TraesCS4B01G188200 chr7A 692306020 692307686 1666 True 2898.000000 2898 98.140000 2966 4622 1 chr7A.!!$R1 1656
10 TraesCS4B01G188200 chr7A 661589392 661595301 5909 False 609.750000 1271 84.806500 1140 5897 4 chr7A.!!$F1 4757
11 TraesCS4B01G188200 chr3B 276489240 276490925 1685 False 2527.000000 2527 93.954000 2966 4628 1 chr3B.!!$F1 1662
12 TraesCS4B01G188200 chr3B 104381217 104382382 1165 True 1731.000000 1731 93.493000 2966 4130 1 chr3B.!!$R1 1164
13 TraesCS4B01G188200 chr2B 197585326 197586998 1672 False 2460.000000 2460 93.321000 2963 4625 1 chr2B.!!$F1 1662
14 TraesCS4B01G188200 chr2B 463927431 463928426 995 True 1509.000000 1509 94.383000 3651 4624 1 chr2B.!!$R1 973
15 TraesCS4B01G188200 chr7B 234645526 234647197 1671 True 2414.000000 2414 92.857000 2963 4625 1 chr7B.!!$R1 1662
16 TraesCS4B01G188200 chr7B 457411451 457412591 1140 True 1733.000000 1733 94.128000 2993 4130 1 chr7B.!!$R2 1137
17 TraesCS4B01G188200 chr7B 629579747 629582717 2970 True 619.750000 1230 87.887750 1092 5767 4 chr7B.!!$R3 4675
18 TraesCS4B01G188200 chr4A 661533954 661535595 1641 False 2398.000000 2398 93.135000 2987 4619 1 chr4A.!!$F3 1632
19 TraesCS4B01G188200 chr4A 140974603 140980627 6024 False 869.625000 2322 92.510375 210 6763 8 chr4A.!!$F5 6553
20 TraesCS4B01G188200 chr1B 141118536 141119886 1350 False 2008.000000 2008 93.782000 3295 4622 1 chr1B.!!$F1 1327
21 TraesCS4B01G188200 chr1B 135814266 135817771 3505 False 1732.666667 2303 93.627333 925 6025 3 chr1B.!!$F3 5100
22 TraesCS4B01G188200 chr5B 216657113 216658214 1101 False 1746.000000 1746 95.467000 3531 4619 1 chr5B.!!$F1 1088
23 TraesCS4B01G188200 chr7D 572549022 572554895 5873 False 1046.000000 1260 84.550500 1083 5897 2 chr7D.!!$F2 4814


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
46 47 0.096976 CGCTACAGTGCATTTTCCGG 59.903 55.000 0.00 0.00 0.00 5.14 F
139 140 0.105039 CGTCACATAAGAGCTCCCCC 59.895 60.000 10.93 0.00 0.00 5.40 F
360 361 0.171231 CTCGCGTCTCTCACATGGAA 59.829 55.000 5.77 0.00 0.00 3.53 F
1011 1687 0.179171 CGACGACGATGGCAACTACT 60.179 55.000 0.00 0.00 42.66 2.57 F
1138 1814 1.022451 AGCTCGACGAGTCACTCTCC 61.022 60.000 24.80 6.73 39.84 3.71 F
1586 2274 1.134670 GGTGACACTACTGAGCCCATC 60.135 57.143 5.39 0.00 0.00 3.51 F
2740 4359 3.055240 CAGGTTCAGAATGCCTCTTCTCT 60.055 47.826 0.00 0.00 33.18 3.10 F
4801 11337 4.758773 TGAATACATGAGATGCAGTCCA 57.241 40.909 0.00 0.00 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1345 2032 0.321741 TGGCATTCCGCGAAACCTTA 60.322 50.000 8.23 0.00 43.84 2.69 R
1586 2274 1.676006 GCATTTGTTATGACCTCCGGG 59.324 52.381 0.00 0.00 38.88 5.73 R
1808 2997 2.411547 GCAAAGATGTGTACTGTGTCGC 60.412 50.000 0.00 0.00 0.00 5.19 R
2612 4231 1.247567 TTGCTGCCCTTAGTTTCTGC 58.752 50.000 0.00 0.00 0.00 4.26 R
2740 4359 6.681729 AACATGAACAGTAGACTAAAGGGA 57.318 37.500 0.00 0.00 0.00 4.20 R
3265 6928 3.621805 TGACCGGCAGCGGAAGAA 61.622 61.111 8.49 0.00 0.00 2.52 R
4700 11236 6.015180 ACACTTGAATCAACATATGCCTGTTT 60.015 34.615 1.58 2.34 37.25 2.83 R
6158 12803 0.031449 GGCTCTCTCCAGTGTATCGC 59.969 60.000 0.00 0.00 0.00 4.58 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)



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AutoCloner maintained by Alex Coulton.