Multiple sequence alignment - TraesCS2D01G448200

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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 TraesCS2D01G448200 chr2D 100.000 4186 0 0 1 4186 557959243 557955058 0.000000e+00 7731.0
1 TraesCS2D01G448200 chr2D 100.000 3055 0 0 4651 7705 557954593 557951539 0.000000e+00 5642.0
2 TraesCS2D01G448200 chr2D 79.153 307 26 17 3209 3498 557953338 557953053 2.210000e-40 178.0
3 TraesCS2D01G448200 chr2D 79.153 307 26 17 5906 6191 557956035 557955746 2.210000e-40 178.0
4 TraesCS2D01G448200 chr2D 87.591 137 14 2 7565 7700 420742003 420741869 1.040000e-33 156.0
5 TraesCS2D01G448200 chr2A 96.372 1075 36 3 5670 6742 698183583 698182510 0.000000e+00 1766.0
6 TraesCS2D01G448200 chr2A 96.569 816 26 2 1781 2595 698190973 698190159 0.000000e+00 1351.0
7 TraesCS2D01G448200 chr2A 93.843 877 41 6 5685 6553 698184453 698183582 0.000000e+00 1308.0
8 TraesCS2D01G448200 chr2A 95.630 778 24 2 959 1726 698192018 698191241 0.000000e+00 1240.0
9 TraesCS2D01G448200 chr2A 94.399 607 25 4 2616 3214 698189794 698189189 0.000000e+00 924.0
10 TraesCS2D01G448200 chr2A 91.050 581 40 3 7127 7703 698179847 698179275 0.000000e+00 774.0
11 TraesCS2D01G448200 chr2A 91.762 522 35 6 3209 3724 698189131 698188612 0.000000e+00 719.0
12 TraesCS2D01G448200 chr2A 79.236 785 115 29 1818 2571 698315398 698314631 3.210000e-138 503.0
13 TraesCS2D01G448200 chr2A 75.500 1049 144 56 5596 6580 698313068 698312069 7.200000e-110 409.0
14 TraesCS2D01G448200 chr2A 75.149 837 105 44 5799 6573 698302636 698301841 1.630000e-76 298.0
15 TraesCS2D01G448200 chr2A 92.537 201 15 0 6742 6942 698180119 698179919 9.780000e-74 289.0
16 TraesCS2D01G448200 chr2A 90.625 192 18 0 3023 3214 698314134 698313943 9.920000e-64 255.0
17 TraesCS2D01G448200 chr2A 73.574 526 81 37 3209 3724 698302529 698302052 1.730000e-31 148.0
18 TraesCS2D01G448200 chr2A 77.273 308 31 18 3209 3498 698183347 698183061 2.240000e-30 145.0
19 TraesCS2D01G448200 chr2A 77.163 289 39 15 3209 3495 698312763 698312500 8.060000e-30 143.0
20 TraesCS2D01G448200 chr2A 76.603 312 26 23 3209 3498 698184232 698183946 2.260000e-25 128.0
21 TraesCS2D01G448200 chr2A 80.921 152 18 6 6950 7090 572050944 572051095 8.170000e-20 110.0
22 TraesCS2D01G448200 chr2A 100.000 30 0 0 72 101 767805206 767805177 1.000000e-03 56.5
23 TraesCS2D01G448200 chr2B 94.583 1126 48 7 5983 7102 666403167 666402049 0.000000e+00 1729.0
24 TraesCS2D01G448200 chr2B 94.583 1126 48 7 5983 7102 666428387 666427269 0.000000e+00 1729.0
25 TraesCS2D01G448200 chr2B 94.853 816 39 3 1781 2595 666430834 666430021 0.000000e+00 1271.0
26 TraesCS2D01G448200 chr2B 91.749 909 34 12 840 1726 666431996 666431107 0.000000e+00 1225.0
27 TraesCS2D01G448200 chr2B 89.685 921 60 10 4702 5588 796324123 796323204 0.000000e+00 1142.0
28 TraesCS2D01G448200 chr2B 88.382 964 71 17 4651 5576 636178637 636177677 0.000000e+00 1122.0
29 TraesCS2D01G448200 chr2B 94.737 627 24 4 2596 3214 666404717 666404092 0.000000e+00 966.0
30 TraesCS2D01G448200 chr2B 94.737 627 24 4 2596 3214 666429937 666429312 0.000000e+00 966.0
31 TraesCS2D01G448200 chr2B 91.806 598 40 6 3209 3799 666404034 666403439 0.000000e+00 824.0
32 TraesCS2D01G448200 chr2B 91.806 598 40 6 3209 3799 666429254 666428659 0.000000e+00 824.0
33 TraesCS2D01G448200 chr2B 93.860 456 26 2 2141 2595 666405255 666404801 0.000000e+00 686.0
34 TraesCS2D01G448200 chr2B 80.556 648 81 22 5575 6194 666404370 666403740 2.530000e-124 457.0
35 TraesCS2D01G448200 chr2B 80.556 648 81 22 5575 6194 666429590 666428960 2.530000e-124 457.0
36 TraesCS2D01G448200 chr2B 93.208 265 17 1 5686 5949 666403430 666403166 9.380000e-104 388.0
37 TraesCS2D01G448200 chr2B 92.830 265 18 1 5686 5949 666428650 666428386 4.360000e-102 383.0
38 TraesCS2D01G448200 chr2B 91.011 178 14 2 7528 7703 666401982 666401805 9.990000e-59 239.0
39 TraesCS2D01G448200 chr2B 91.011 178 14 2 7528 7703 666427202 666427025 9.990000e-59 239.0
40 TraesCS2D01G448200 chr2B 75.926 486 61 31 3051 3498 666428650 666428183 1.700000e-46 198.0
41 TraesCS2D01G448200 chr2B 95.283 106 4 1 563 667 17113321 17113216 4.780000e-37 167.0
42 TraesCS2D01G448200 chr2B 87.050 139 15 2 7565 7703 493331300 493331165 3.720000e-33 154.0
43 TraesCS2D01G448200 chr2B 81.053 190 14 10 3325 3498 666403146 666402963 1.740000e-26 132.0
44 TraesCS2D01G448200 chr2B 78.846 156 33 0 3656 3811 666639955 666639800 1.060000e-18 106.0
45 TraesCS2D01G448200 chr5B 94.503 946 32 7 4653 5580 457985607 457984664 0.000000e+00 1441.0
46 TraesCS2D01G448200 chr5B 94.055 942 36 3 4651 5574 531949724 531950663 0.000000e+00 1411.0
47 TraesCS2D01G448200 chr5B 89.278 886 60 9 4727 5578 469811367 469810483 0.000000e+00 1077.0
48 TraesCS2D01G448200 chr5B 87.097 124 15 1 6917 7040 530948026 530948148 1.040000e-28 139.0
49 TraesCS2D01G448200 chr7A 94.725 910 29 6 4685 5576 676968120 676969028 0.000000e+00 1397.0
50 TraesCS2D01G448200 chr7A 88.791 910 66 12 4698 5573 427515837 427516744 0.000000e+00 1083.0
51 TraesCS2D01G448200 chr7A 89.262 149 15 1 7130 7277 609265476 609265624 1.320000e-42 185.0
52 TraesCS2D01G448200 chrUn 93.100 942 46 6 4652 5575 284643456 284644396 0.000000e+00 1362.0
53 TraesCS2D01G448200 chrUn 92.997 871 42 6 4723 5575 300772552 300773421 0.000000e+00 1253.0
54 TraesCS2D01G448200 chrUn 79.888 179 18 2 582 742 94210070 94210248 1.760000e-21 115.0
55 TraesCS2D01G448200 chr1D 92.479 944 49 10 4651 5576 470824342 470825281 0.000000e+00 1330.0
56 TraesCS2D01G448200 chr1D 89.604 808 44 9 4807 5580 155854411 155855212 0.000000e+00 990.0
57 TraesCS2D01G448200 chr7D 91.121 946 60 13 4651 5577 102729526 102728586 0.000000e+00 1260.0
58 TraesCS2D01G448200 chr7D 80.000 185 18 7 575 741 90306473 90306656 1.360000e-22 119.0
59 TraesCS2D01G448200 chr7D 78.977 176 20 2 582 740 47395725 47395900 3.800000e-18 104.0
60 TraesCS2D01G448200 chr5A 91.937 893 52 13 4699 5574 639095369 639094480 0.000000e+00 1232.0
61 TraesCS2D01G448200 chr5A 92.683 123 8 1 6921 7043 545602824 545602945 7.950000e-40 176.0
62 TraesCS2D01G448200 chr5A 87.200 125 15 1 6916 7040 370194805 370194928 2.900000e-29 141.0
63 TraesCS2D01G448200 chr5A 88.034 117 14 0 7125 7241 545603174 545603290 1.040000e-28 139.0
64 TraesCS2D01G448200 chr5A 85.484 124 18 0 3598 3721 54759090 54759213 6.270000e-26 130.0
65 TraesCS2D01G448200 chr5A 85.484 124 18 0 3598 3721 456982352 456982475 6.270000e-26 130.0
66 TraesCS2D01G448200 chr7B 89.396 943 76 12 4651 5574 10953180 10952243 0.000000e+00 1166.0
67 TraesCS2D01G448200 chr3D 93.082 636 26 4 4959 5576 104294973 104294338 0.000000e+00 915.0
68 TraesCS2D01G448200 chr3D 83.871 124 15 2 6918 7036 606601098 606600975 6.320000e-21 113.0
69 TraesCS2D01G448200 chr3D 95.082 61 3 0 680 740 45552313 45552253 6.360000e-16 97.1
70 TraesCS2D01G448200 chr3D 93.846 65 3 1 680 744 474591271 474591208 6.360000e-16 97.1
71 TraesCS2D01G448200 chr3D 89.394 66 7 0 676 741 561906797 561906862 4.950000e-12 84.2
72 TraesCS2D01G448200 chr3D 100.000 30 0 0 72 101 511407103 511407074 1.000000e-03 56.5
73 TraesCS2D01G448200 chr3A 89.698 728 21 10 69 742 533589314 533588587 0.000000e+00 880.0
74 TraesCS2D01G448200 chr3A 97.183 71 2 0 8 78 533589423 533589353 3.780000e-23 121.0
75 TraesCS2D01G448200 chr6A 89.947 567 29 8 134 674 69029352 69028788 0.000000e+00 706.0
76 TraesCS2D01G448200 chr6A 97.183 71 2 0 8 78 69055662 69055592 3.780000e-23 121.0
77 TraesCS2D01G448200 chr1A 91.029 379 16 9 5216 5576 49302447 49302069 5.370000e-136 496.0
78 TraesCS2D01G448200 chr4A 94.007 267 6 2 69 326 728958015 728957750 5.600000e-106 396.0
79 TraesCS2D01G448200 chr4A 88.500 200 12 1 486 674 728957664 728957465 1.670000e-56 231.0
80 TraesCS2D01G448200 chr4A 98.529 68 1 0 11 78 728958121 728958054 3.780000e-23 121.0
81 TraesCS2D01G448200 chr4A 93.443 61 4 0 367 427 728957753 728957693 2.960000e-14 91.6
82 TraesCS2D01G448200 chr6B 87.402 127 15 1 6914 7040 619037461 619037336 2.240000e-30 145.0
83 TraesCS2D01G448200 chr5D 79.592 196 21 5 557 734 64274095 64274289 1.050000e-23 122.0
84 TraesCS2D01G448200 chr5D 77.723 202 26 7 557 740 68210576 68210376 1.060000e-18 106.0
85 TraesCS2D01G448200 chr5D 78.857 175 20 1 582 739 447941583 447941409 1.370000e-17 102.0
86 TraesCS2D01G448200 chr5D 79.503 161 16 1 595 738 21248403 21248243 1.770000e-16 99.0
87 TraesCS2D01G448200 chr4B 97.143 35 1 0 3124 3158 632122487 632122453 8.350000e-05 60.2
88 TraesCS2D01G448200 chr4B 97.059 34 1 0 3124 3157 631896250 631896217 3.000000e-04 58.4


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 TraesCS2D01G448200 chr2D 557951539 557959243 7704 True 3432.250000 7731 89.576500 1 7705 4 chr2D.!!$R2 7704
1 TraesCS2D01G448200 chr2A 698188612 698192018 3406 True 1058.500000 1351 94.590000 959 3724 4 chr2A.!!$R3 2765
2 TraesCS2D01G448200 chr2A 698179275 698184453 5178 True 735.000000 1766 87.946333 3209 7703 6 chr2A.!!$R2 4494
3 TraesCS2D01G448200 chr2A 698312069 698315398 3329 True 327.500000 503 80.631000 1818 6580 4 chr2A.!!$R5 4762
4 TraesCS2D01G448200 chr2A 698301841 698302636 795 True 223.000000 298 74.361500 3209 6573 2 chr2A.!!$R4 3364
5 TraesCS2D01G448200 chr2B 796323204 796324123 919 True 1142.000000 1142 89.685000 4702 5588 1 chr2B.!!$R5 886
6 TraesCS2D01G448200 chr2B 636177677 636178637 960 True 1122.000000 1122 88.382000 4651 5576 1 chr2B.!!$R3 925
7 TraesCS2D01G448200 chr2B 666427025 666431996 4971 True 810.222222 1729 89.783444 840 7703 9 chr2B.!!$R7 6863
8 TraesCS2D01G448200 chr2B 666401805 666405255 3450 True 677.625000 1729 90.101750 2141 7703 8 chr2B.!!$R6 5562
9 TraesCS2D01G448200 chr5B 457984664 457985607 943 True 1441.000000 1441 94.503000 4653 5580 1 chr5B.!!$R1 927
10 TraesCS2D01G448200 chr5B 531949724 531950663 939 False 1411.000000 1411 94.055000 4651 5574 1 chr5B.!!$F2 923
11 TraesCS2D01G448200 chr5B 469810483 469811367 884 True 1077.000000 1077 89.278000 4727 5578 1 chr5B.!!$R2 851
12 TraesCS2D01G448200 chr7A 676968120 676969028 908 False 1397.000000 1397 94.725000 4685 5576 1 chr7A.!!$F3 891
13 TraesCS2D01G448200 chr7A 427515837 427516744 907 False 1083.000000 1083 88.791000 4698 5573 1 chr7A.!!$F1 875
14 TraesCS2D01G448200 chrUn 284643456 284644396 940 False 1362.000000 1362 93.100000 4652 5575 1 chrUn.!!$F2 923
15 TraesCS2D01G448200 chrUn 300772552 300773421 869 False 1253.000000 1253 92.997000 4723 5575 1 chrUn.!!$F3 852
16 TraesCS2D01G448200 chr1D 470824342 470825281 939 False 1330.000000 1330 92.479000 4651 5576 1 chr1D.!!$F2 925
17 TraesCS2D01G448200 chr1D 155854411 155855212 801 False 990.000000 990 89.604000 4807 5580 1 chr1D.!!$F1 773
18 TraesCS2D01G448200 chr7D 102728586 102729526 940 True 1260.000000 1260 91.121000 4651 5577 1 chr7D.!!$R1 926
19 TraesCS2D01G448200 chr5A 639094480 639095369 889 True 1232.000000 1232 91.937000 4699 5574 1 chr5A.!!$R1 875
20 TraesCS2D01G448200 chr7B 10952243 10953180 937 True 1166.000000 1166 89.396000 4651 5574 1 chr7B.!!$R1 923
21 TraesCS2D01G448200 chr3D 104294338 104294973 635 True 915.000000 915 93.082000 4959 5576 1 chr3D.!!$R2 617
22 TraesCS2D01G448200 chr3A 533588587 533589423 836 True 500.500000 880 93.440500 8 742 2 chr3A.!!$R1 734
23 TraesCS2D01G448200 chr6A 69028788 69029352 564 True 706.000000 706 89.947000 134 674 1 chr6A.!!$R1 540
24 TraesCS2D01G448200 chr4A 728957465 728958121 656 True 209.900000 396 93.619750 11 674 4 chr4A.!!$R1 663

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
817 964 0.109723 AAACCAGGAAAGTGCGGCTA 59.890 50.0 0.00 0.00 0.00 3.93 F
818 965 0.321653 AACCAGGAAAGTGCGGCTAG 60.322 55.0 0.00 0.00 0.00 3.42 F
2187 2594 0.179001 CTGAGGGACAAAACCGGGTT 60.179 55.0 6.59 6.59 0.00 4.11 F
3878 4890 0.035056 ATGCCTGGTTACCTGCTGTC 60.035 55.0 15.19 1.26 0.00 3.51 F
4048 5060 0.034380 GGGCTAGAAACACCTTCCCC 60.034 60.0 0.00 0.00 34.21 4.81 F
4060 5072 0.107654 CCTTCCCCTGATCAACGGAC 60.108 60.0 9.46 0.00 0.00 4.79 F
4064 5076 0.178068 CCCCTGATCAACGGACGATT 59.822 55.0 9.61 0.00 0.00 3.34 F
4083 5095 0.683504 TAGTTCTCTGGACCCGCTCC 60.684 60.0 0.00 0.00 39.97 4.70 F
6403 7525 0.609131 AGTGGGTTGCCTGTACATGC 60.609 55.0 15.39 15.39 0.00 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2044 2451 0.401738 CTGGGGTTGAAGAAGGCAGA 59.598 55.000 0.00 0.0 0.00 4.26 R
2418 2839 1.334869 GAAAGCTGGTCACAACTGTGG 59.665 52.381 9.87 0.0 45.65 4.17 R
4029 5041 0.034380 GGGGAAGGTGTTTCTAGCCC 60.034 60.000 0.00 0.0 36.03 5.19 R
5700 6766 0.835941 ATGGTCTGTGAGGATGGAGC 59.164 55.000 0.00 0.0 0.00 4.70 R
5921 6987 6.199908 CGAATGCAGGTGTTCAACAAATTTAA 59.800 34.615 0.00 0.0 0.00 1.52 R
6084 7159 4.263639 TGGCAGATATGATCCAAGGGATTC 60.264 45.833 0.00 0.0 43.27 2.52 R
6403 7525 6.034683 CGAAGACCTAGAACCGTAAAAATGAG 59.965 42.308 0.00 0.0 0.00 2.90 R
6418 7540 3.695060 TGGAGTTCTTAGCGAAGACCTAG 59.305 47.826 8.95 0.0 41.52 3.02 R
7237 10754 1.073923 TCTCTCCCAAAAGAACCCAGC 59.926 52.381 0.00 0.0 0.00 4.85 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)


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

AutoCloner maintained by Alex Coulton.