Multiple sequence alignment - TraesCS7D01G250000

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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 TraesCS7D01G250000 chr7D 100.000 2252 0 0 1 2252 221992190 221989939 0.000000e+00 4159.0
1 TraesCS7D01G250000 chr4A 93.433 1401 40 7 1 1374 420015979 420017354 0.000000e+00 2030.0
2 TraesCS7D01G250000 chr4A 92.580 283 17 3 1970 2252 494066377 494066099 9.690000e-109 403.0
3 TraesCS7D01G250000 chr4A 93.023 43 2 1 251 293 104128999 104129040 6.720000e-06 62.1
4 TraesCS7D01G250000 chr5B 92.812 1266 52 15 140 1394 166590937 166592174 0.000000e+00 1797.0
5 TraesCS7D01G250000 chr5B 96.865 319 9 1 140 457 166586182 166586500 1.180000e-147 532.0
6 TraesCS7D01G250000 chr5B 96.000 150 6 0 1 150 166585364 166585513 6.210000e-61 244.0
7 TraesCS7D01G250000 chr5B 95.918 147 6 0 1 147 166590131 166590277 2.890000e-59 239.0
8 TraesCS7D01G250000 chr4D 97.659 897 19 2 1357 2252 102381211 102382106 0.000000e+00 1539.0
9 TraesCS7D01G250000 chr5D 95.815 908 25 5 1356 2252 551061484 551060579 0.000000e+00 1454.0
10 TraesCS7D01G250000 chr5D 83.553 1441 140 48 1 1394 196319195 196320585 0.000000e+00 1258.0
11 TraesCS7D01G250000 chr5D 95.922 613 14 2 1401 2013 445192953 445193554 0.000000e+00 983.0
12 TraesCS7D01G250000 chr5D 85.759 632 55 15 640 1248 196319790 196320409 8.770000e-179 636.0
13 TraesCS7D01G250000 chr5D 87.526 473 46 8 1 463 527081292 527080823 3.290000e-148 534.0
14 TraesCS7D01G250000 chr5D 86.588 425 36 9 701 1109 527080594 527080175 1.230000e-122 449.0
15 TraesCS7D01G250000 chr5D 77.824 478 77 14 11 459 548640433 548640910 3.690000e-68 268.0
16 TraesCS7D01G250000 chr1A 92.731 963 39 7 458 1394 490470942 490469985 0.000000e+00 1362.0
17 TraesCS7D01G250000 chr1A 96.129 775 23 5 1 773 558017945 558017176 0.000000e+00 1258.0
18 TraesCS7D01G250000 chr1A 91.783 645 21 5 760 1377 558016883 558016244 0.000000e+00 869.0
19 TraesCS7D01G250000 chr1A 95.047 424 15 4 1580 1999 12038132 12037711 0.000000e+00 662.0
20 TraesCS7D01G250000 chr1A 96.721 305 10 0 132 436 490473022 490472718 2.000000e-140 508.0
21 TraesCS7D01G250000 chr1A 88.085 235 14 7 1356 1579 12038449 12038218 1.330000e-67 267.0
22 TraesCS7D01G250000 chr1A 94.891 137 7 0 1 137 490473278 490473142 4.870000e-52 215.0
23 TraesCS7D01G250000 chr2B 85.401 1096 68 17 350 1394 15466160 15465106 0.000000e+00 1053.0
24 TraesCS7D01G250000 chr3D 92.730 619 17 5 1383 2001 593316669 593317259 0.000000e+00 869.0
25 TraesCS7D01G250000 chr3D 88.273 469 44 5 1 461 593315356 593315821 3.270000e-153 551.0
26 TraesCS7D01G250000 chr3D 83.904 584 40 24 701 1235 593316012 593316590 2.000000e-140 508.0
27 TraesCS7D01G250000 chr5A 95.047 424 15 3 1580 1999 483537867 483537446 0.000000e+00 662.0
28 TraesCS7D01G250000 chr5A 93.805 339 17 4 1630 1967 694508462 694508797 7.180000e-140 507.0
29 TraesCS7D01G250000 chr5A 94.275 262 12 2 1991 2252 694513913 694514171 4.510000e-107 398.0
30 TraesCS7D01G250000 chr5A 93.050 259 14 3 1994 2252 490149218 490149472 2.110000e-100 375.0
31 TraesCS7D01G250000 chr5A 92.562 242 14 3 1630 1869 490148903 490149142 5.950000e-91 344.0
32 TraesCS7D01G250000 chr5A 87.611 226 23 4 1357 1579 483538176 483537953 7.980000e-65 257.0
33 TraesCS7D01G250000 chr5A 98.113 53 1 0 1582 1634 694508195 694508247 2.380000e-15 93.5
34 TraesCS7D01G250000 chr7A 87.636 550 45 10 701 1233 123205684 123206227 3.180000e-173 617.0
35 TraesCS7D01G250000 chr7A 91.506 259 17 3 1994 2252 454754623 454754876 3.560000e-93 351.0
36 TraesCS7D01G250000 chr7A 88.298 188 19 3 2016 2201 389348538 389348352 2.910000e-54 222.0
37 TraesCS7D01G250000 chr7A 100.000 33 0 0 1547 1579 454753929 454753961 6.720000e-06 62.1
38 TraesCS7D01G250000 chr1B 87.273 550 47 10 701 1233 62430345 62429802 6.880000e-170 606.0
39 TraesCS7D01G250000 chr1B 87.091 550 48 10 701 1233 229526251 229525708 3.200000e-168 601.0
40 TraesCS7D01G250000 chr1B 89.873 79 6 2 521 598 62430544 62430467 1.420000e-17 100.0
41 TraesCS7D01G250000 chr2D 87.261 471 47 9 1 461 610357247 610357714 1.980000e-145 525.0
42 TraesCS7D01G250000 chr2D 86.505 289 23 8 701 978 610357897 610358180 1.010000e-78 303.0
43 TraesCS7D01G250000 chr2D 94.118 51 2 1 1345 1394 233671136 233671086 2.400000e-10 76.8
44 TraesCS7D01G250000 chr2D 80.672 119 6 6 520 622 610357713 610357830 2.400000e-10 76.8
45 TraesCS7D01G250000 chr3A 92.183 371 22 5 1630 1999 521576424 521576060 3.320000e-143 518.0
46 TraesCS7D01G250000 chr3A 96.296 54 1 1 1581 1634 521576690 521576638 1.110000e-13 87.9
47 TraesCS7D01G250000 chr3A 100.000 32 0 0 1547 1578 521576810 521576779 2.420000e-05 60.2
48 TraesCS7D01G250000 chr7B 95.730 281 10 2 1630 1909 53712546 53712825 3.410000e-123 451.0
49 TraesCS7D01G250000 chr7B 88.679 53 1 2 1582 1634 53712138 53712185 2.420000e-05 60.2
50 TraesCS7D01G250000 chr7B 97.143 35 0 1 254 288 7017032 7016999 8.690000e-05 58.4
51 TraesCS7D01G250000 chrUn 93.559 295 16 3 1630 1923 309170780 309171072 9.550000e-119 436.0
52 TraesCS7D01G250000 chrUn 93.506 154 10 0 1395 1548 309170261 309170414 1.740000e-56 230.0
53 TraesCS7D01G250000 chrUn 92.857 154 11 0 1395 1548 385138071 385138224 8.090000e-55 224.0
54 TraesCS7D01G250000 chr2A 91.892 259 17 3 1994 2252 720953195 720953449 2.130000e-95 359.0
55 TraesCS7D01G250000 chr1D 90.661 257 16 5 2001 2252 126206288 126206035 3.580000e-88 335.0
56 TraesCS7D01G250000 chr4B 93.750 160 9 1 1389 1548 522415997 522416155 2.890000e-59 239.0
57 TraesCS7D01G250000 chr4B 100.000 33 0 0 1547 1579 522416199 522416231 6.720000e-06 62.1
58 TraesCS7D01G250000 chr6A 97.143 35 0 1 254 288 606314161 606314128 8.690000e-05 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 TraesCS7D01G250000 chr7D 221989939 221992190 2251 True 4159.000000 4159 100.000000 1 2252 1 chr7D.!!$R1 2251
1 TraesCS7D01G250000 chr4A 420015979 420017354 1375 False 2030.000000 2030 93.433000 1 1374 1 chr4A.!!$F2 1373
2 TraesCS7D01G250000 chr5B 166585364 166592174 6810 False 703.000000 1797 95.398750 1 1394 4 chr5B.!!$F1 1393
3 TraesCS7D01G250000 chr4D 102381211 102382106 895 False 1539.000000 1539 97.659000 1357 2252 1 chr4D.!!$F1 895
4 TraesCS7D01G250000 chr5D 551060579 551061484 905 True 1454.000000 1454 95.815000 1356 2252 1 chr5D.!!$R1 896
5 TraesCS7D01G250000 chr5D 445192953 445193554 601 False 983.000000 983 95.922000 1401 2013 1 chr5D.!!$F1 612
6 TraesCS7D01G250000 chr5D 196319195 196320585 1390 False 947.000000 1258 84.656000 1 1394 2 chr5D.!!$F3 1393
7 TraesCS7D01G250000 chr5D 527080175 527081292 1117 True 491.500000 534 87.057000 1 1109 2 chr5D.!!$R2 1108
8 TraesCS7D01G250000 chr1A 558016244 558017945 1701 True 1063.500000 1258 93.956000 1 1377 2 chr1A.!!$R3 1376
9 TraesCS7D01G250000 chr1A 490469985 490473278 3293 True 695.000000 1362 94.781000 1 1394 3 chr1A.!!$R2 1393
10 TraesCS7D01G250000 chr1A 12037711 12038449 738 True 464.500000 662 91.566000 1356 1999 2 chr1A.!!$R1 643
11 TraesCS7D01G250000 chr2B 15465106 15466160 1054 True 1053.000000 1053 85.401000 350 1394 1 chr2B.!!$R1 1044
12 TraesCS7D01G250000 chr3D 593315356 593317259 1903 False 642.666667 869 88.302333 1 2001 3 chr3D.!!$F1 2000
13 TraesCS7D01G250000 chr5A 483537446 483538176 730 True 459.500000 662 91.329000 1357 1999 2 chr5A.!!$R1 642
14 TraesCS7D01G250000 chr5A 490148903 490149472 569 False 359.500000 375 92.806000 1630 2252 2 chr5A.!!$F2 622
15 TraesCS7D01G250000 chr5A 694508195 694508797 602 False 300.250000 507 95.959000 1582 1967 2 chr5A.!!$F3 385
16 TraesCS7D01G250000 chr7A 123205684 123206227 543 False 617.000000 617 87.636000 701 1233 1 chr7A.!!$F1 532
17 TraesCS7D01G250000 chr7A 454753929 454754876 947 False 206.550000 351 95.753000 1547 2252 2 chr7A.!!$F2 705
18 TraesCS7D01G250000 chr1B 229525708 229526251 543 True 601.000000 601 87.091000 701 1233 1 chr1B.!!$R1 532
19 TraesCS7D01G250000 chr1B 62429802 62430544 742 True 353.000000 606 88.573000 521 1233 2 chr1B.!!$R2 712
20 TraesCS7D01G250000 chr2D 610357247 610358180 933 False 301.600000 525 84.812667 1 978 3 chr2D.!!$F1 977
21 TraesCS7D01G250000 chr3A 521576060 521576810 750 True 222.033333 518 96.159667 1547 1999 3 chr3A.!!$R1 452
22 TraesCS7D01G250000 chr7B 53712138 53712825 687 False 255.600000 451 92.204500 1582 1909 2 chr7B.!!$F1 327
23 TraesCS7D01G250000 chrUn 309170261 309171072 811 False 333.000000 436 93.532500 1395 1923 2 chrUn.!!$F2 528

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
621 6685 1.416401 TCGCATGATTTCTACCCTCCC 59.584 52.381 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2049 9186 3.748048 CACCGATCAATTGCTAGGTATGG 59.252 47.826 12.87 0.0 0.0 2.74 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
507 6468 4.202284 GCCAATTAAGACCTACGACCCATA 60.202 45.833 0.00 0.00 0.00 2.74
620 6684 2.365617 TCTCGCATGATTTCTACCCTCC 59.634 50.000 0.00 0.00 0.00 4.30
621 6685 1.416401 TCGCATGATTTCTACCCTCCC 59.584 52.381 0.00 0.00 0.00 4.30
624 6688 3.685550 CGCATGATTTCTACCCTCCCTTT 60.686 47.826 0.00 0.00 0.00 3.11
625 6689 4.281657 GCATGATTTCTACCCTCCCTTTT 58.718 43.478 0.00 0.00 0.00 2.27
626 6690 4.711846 GCATGATTTCTACCCTCCCTTTTT 59.288 41.667 0.00 0.00 0.00 1.94
1159 7606 2.655073 ATGGTCCATGGCGTCGACA 61.655 57.895 17.16 1.64 0.00 4.35
1333 7813 7.040340 TGCGGGTTGATTAAATAAAAAGTCAGA 60.040 33.333 0.00 0.00 0.00 3.27
1404 7894 7.227910 CCCGGCTTTATTATTACTAGCAAAAGA 59.772 37.037 0.00 0.00 33.60 2.52
1441 7931 6.620678 CAACGGGAGAAAATAAATCACATGT 58.379 36.000 0.00 0.00 0.00 3.21
1463 7953 7.247456 TGTCCATATGTTGTAGGTCAAGTTA 57.753 36.000 1.24 0.00 36.66 2.24
1480 7970 4.810191 AGTTAAAACAAAAGGTGCCACA 57.190 36.364 0.00 0.00 0.00 4.17
1488 7978 3.706086 ACAAAAGGTGCCACAAGAAAGAT 59.294 39.130 0.00 0.00 0.00 2.40
1653 8646 2.224137 TGGCTGCTTCCATATTCTCTCG 60.224 50.000 0.00 0.00 0.00 4.04
1751 8745 8.535592 CAGACAACTTGAGAACGTATATGAATC 58.464 37.037 0.00 0.00 0.00 2.52
2049 9186 0.966179 CCTAATTAAATGGGCCGGCC 59.034 55.000 38.57 38.57 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
269 1083 0.427685 AAGGGAAGGAGGAGGGGATT 59.572 55.000 0.00 0.00 0.00 3.01
355 1177 4.703897 ACAATCGAAGTTTCAGTCCTCAA 58.296 39.130 0.00 0.00 0.00 3.02
624 6688 9.260002 GGTAGAAATCATTTTGCTCAAAGAAAA 57.740 29.630 0.00 0.00 0.00 2.29
625 6689 7.872483 GGGTAGAAATCATTTTGCTCAAAGAAA 59.128 33.333 0.00 0.00 0.00 2.52
626 6690 7.233348 AGGGTAGAAATCATTTTGCTCAAAGAA 59.767 33.333 0.00 0.00 0.00 2.52
627 6691 6.721208 AGGGTAGAAATCATTTTGCTCAAAGA 59.279 34.615 0.00 0.00 0.00 2.52
628 6692 6.928520 AGGGTAGAAATCATTTTGCTCAAAG 58.071 36.000 0.00 0.00 0.00 2.77
828 7237 1.001503 CTGCTCCTCTCCTCCTGGT 59.998 63.158 0.00 0.00 34.23 4.00
1159 7606 3.692406 GGCGAGGAGTTCACCGGT 61.692 66.667 0.00 0.00 34.73 5.28
1180 7627 0.378962 GGAGACATGGAGAGTCGTCG 59.621 60.000 0.00 0.00 40.84 5.12
1333 7813 0.322648 GGCATTTTTGCAAGAGGCCT 59.677 50.000 24.52 3.86 43.89 5.19
1374 7855 5.334646 GCTAGTAATAATAAAGCCGGGTTGC 60.335 44.000 21.54 10.34 0.00 4.17
1441 7931 9.005777 GTTTTAACTTGACCTACAACATATGGA 57.994 33.333 7.80 0.00 34.56 3.41
1463 7953 3.971245 TCTTGTGGCACCTTTTGTTTT 57.029 38.095 16.26 0.00 0.00 2.43
1653 8646 8.936864 AGATTAGCATAATATAAACGTTGCCTC 58.063 33.333 0.00 0.00 0.00 4.70
1751 8745 5.737290 CGCCAATTTAAACTAATTCTCACCG 59.263 40.000 0.00 0.00 0.00 4.94
2049 9186 3.748048 CACCGATCAATTGCTAGGTATGG 59.252 47.826 12.87 0.00 0.00 2.74
2159 9297 7.201848 CCGAGGTGGTACTAATATTACAGTTCA 60.202 40.741 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.