Multiple sequence alignment - TraesCS7B01G119100

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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 TraesCS7B01G119100 chr7B 100.000 2354 0 0 1 2354 138609059 138606706 0.000000e+00 4348
1 TraesCS7B01G119100 chr7B 93.592 1342 65 7 499 1821 7206210 7204871 0.000000e+00 1982
2 TraesCS7B01G119100 chr7B 93.297 1104 56 5 738 1824 743287309 743286207 0.000000e+00 1613
3 TraesCS7B01G119100 chr7B 95.431 394 18 0 1 394 7207313 7206920 1.540000e-176 628
4 TraesCS7B01G119100 chrUn 93.134 1835 109 5 1 1819 56310160 56308327 0.000000e+00 2675
5 TraesCS7B01G119100 chr3A 92.716 1826 108 6 1 1817 590360803 590362612 0.000000e+00 2612
6 TraesCS7B01G119100 chr3A 90.991 1332 104 8 499 1818 739083034 739084361 0.000000e+00 1781
7 TraesCS7B01G119100 chr3A 90.816 196 13 1 306 501 268524439 268524629 8.350000e-65 257
8 TraesCS7B01G119100 chr4D 92.817 1601 80 18 245 1817 185820859 185822452 0.000000e+00 2287
9 TraesCS7B01G119100 chr4D 91.562 1268 97 8 499 1759 13600144 13601408 0.000000e+00 1740
10 TraesCS7B01G119100 chr4D 89.822 1346 99 18 499 1834 178224945 178223628 0.000000e+00 1692
11 TraesCS7B01G119100 chr4D 94.041 537 30 2 1819 2354 248851813 248852348 0.000000e+00 813
12 TraesCS7B01G119100 chr4D 95.032 463 23 0 1 463 79148451 79147989 0.000000e+00 728
13 TraesCS7B01G119100 chr4D 95.122 246 8 1 1 246 185820524 185820765 3.670000e-103 385
14 TraesCS7B01G119100 chr7A 91.504 1330 96 10 499 1818 69432364 69433686 0.000000e+00 1814
15 TraesCS7B01G119100 chr3B 91.512 1343 68 14 497 1817 328544445 328543127 0.000000e+00 1807
16 TraesCS7B01G119100 chr3B 94.212 501 27 2 1 501 328545485 328544987 0.000000e+00 763
17 TraesCS7B01G119100 chr3B 93.014 501 35 0 1 501 150098558 150099058 0.000000e+00 732
18 TraesCS7B01G119100 chr3D 90.998 1333 103 9 499 1818 606824964 606826292 0.000000e+00 1781
19 TraesCS7B01G119100 chr3D 93.309 538 34 2 1818 2354 445691556 445691020 0.000000e+00 793
20 TraesCS7B01G119100 chr4B 90.723 1175 96 10 655 1821 592725500 592724331 0.000000e+00 1554
21 TraesCS7B01G119100 chr2A 93.787 676 27 2 7 682 279140707 279140047 0.000000e+00 1002
22 TraesCS7B01G119100 chr7D 94.238 538 30 1 1818 2354 145984986 145984449 0.000000e+00 821
23 TraesCS7B01G119100 chr7D 94.052 538 31 1 1818 2354 420928197 420927660 0.000000e+00 815
24 TraesCS7B01G119100 chr7D 93.494 538 33 2 1818 2354 93058933 93058397 0.000000e+00 798
25 TraesCS7B01G119100 chr7D 93.506 539 32 3 1817 2354 411871825 411871289 0.000000e+00 798
26 TraesCS7B01G119100 chr7D 93.321 539 33 3 1818 2354 406365458 406365995 0.000000e+00 793
27 TraesCS7B01G119100 chr2D 92.973 555 35 4 1803 2354 123791755 123791202 0.000000e+00 806
28 TraesCS7B01G119100 chr1D 93.680 538 33 1 1818 2354 395534239 395533702 0.000000e+00 804
29 TraesCS7B01G119100 chr2B 88.224 501 26 2 1 501 763434567 763435034 3.400000e-158 568
30 TraesCS7B01G119100 chr2B 95.057 263 13 0 239 501 738934697 738934435 4.680000e-112 414
31 TraesCS7B01G119100 chr4A 85.437 515 51 19 1322 1817 256502579 256502070 4.490000e-142 514


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 TraesCS7B01G119100 chr7B 138606706 138609059 2353 True 4348 4348 100.0000 1 2354 1 chr7B.!!$R1 2353
1 TraesCS7B01G119100 chr7B 743286207 743287309 1102 True 1613 1613 93.2970 738 1824 1 chr7B.!!$R2 1086
2 TraesCS7B01G119100 chr7B 7204871 7207313 2442 True 1305 1982 94.5115 1 1821 2 chr7B.!!$R3 1820
3 TraesCS7B01G119100 chrUn 56308327 56310160 1833 True 2675 2675 93.1340 1 1819 1 chrUn.!!$R1 1818
4 TraesCS7B01G119100 chr3A 590360803 590362612 1809 False 2612 2612 92.7160 1 1817 1 chr3A.!!$F2 1816
5 TraesCS7B01G119100 chr3A 739083034 739084361 1327 False 1781 1781 90.9910 499 1818 1 chr3A.!!$F3 1319
6 TraesCS7B01G119100 chr4D 13600144 13601408 1264 False 1740 1740 91.5620 499 1759 1 chr4D.!!$F1 1260
7 TraesCS7B01G119100 chr4D 178223628 178224945 1317 True 1692 1692 89.8220 499 1834 1 chr4D.!!$R2 1335
8 TraesCS7B01G119100 chr4D 185820524 185822452 1928 False 1336 2287 93.9695 1 1817 2 chr4D.!!$F3 1816
9 TraesCS7B01G119100 chr4D 248851813 248852348 535 False 813 813 94.0410 1819 2354 1 chr4D.!!$F2 535
10 TraesCS7B01G119100 chr7A 69432364 69433686 1322 False 1814 1814 91.5040 499 1818 1 chr7A.!!$F1 1319
11 TraesCS7B01G119100 chr3B 328543127 328545485 2358 True 1285 1807 92.8620 1 1817 2 chr3B.!!$R1 1816
12 TraesCS7B01G119100 chr3B 150098558 150099058 500 False 732 732 93.0140 1 501 1 chr3B.!!$F1 500
13 TraesCS7B01G119100 chr3D 606824964 606826292 1328 False 1781 1781 90.9980 499 1818 1 chr3D.!!$F1 1319
14 TraesCS7B01G119100 chr3D 445691020 445691556 536 True 793 793 93.3090 1818 2354 1 chr3D.!!$R1 536
15 TraesCS7B01G119100 chr4B 592724331 592725500 1169 True 1554 1554 90.7230 655 1821 1 chr4B.!!$R1 1166
16 TraesCS7B01G119100 chr2A 279140047 279140707 660 True 1002 1002 93.7870 7 682 1 chr2A.!!$R1 675
17 TraesCS7B01G119100 chr7D 145984449 145984986 537 True 821 821 94.2380 1818 2354 1 chr7D.!!$R2 536
18 TraesCS7B01G119100 chr7D 420927660 420928197 537 True 815 815 94.0520 1818 2354 1 chr7D.!!$R4 536
19 TraesCS7B01G119100 chr7D 93058397 93058933 536 True 798 798 93.4940 1818 2354 1 chr7D.!!$R1 536
20 TraesCS7B01G119100 chr7D 411871289 411871825 536 True 798 798 93.5060 1817 2354 1 chr7D.!!$R3 537
21 TraesCS7B01G119100 chr7D 406365458 406365995 537 False 793 793 93.3210 1818 2354 1 chr7D.!!$F1 536
22 TraesCS7B01G119100 chr2D 123791202 123791755 553 True 806 806 92.9730 1803 2354 1 chr2D.!!$R1 551
23 TraesCS7B01G119100 chr1D 395533702 395534239 537 True 804 804 93.6800 1818 2354 1 chr1D.!!$R1 536
24 TraesCS7B01G119100 chr4A 256502070 256502579 509 True 514 514 85.4370 1322 1817 1 chr4A.!!$R1 495

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
196 197 0.602905 CGGTCTTGCCTTTTCGGAGT 60.603 55.0 0.00 0.0 34.25 3.85 F
1151 2121 0.806868 GTGATCGACGTGGACTACCA 59.193 55.0 1.11 0.0 44.76 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1227 2197 1.600957 GCAATGACCTGGACGATCATG 59.399 52.381 0.00 0.00 33.37 3.07 R
2254 3303 1.117142 ATGCTGCAGCCTGGTTGTTT 61.117 50.000 34.64 6.34 41.18 2.83 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
30 31 6.786122 AGGTCTCTAGAAGAAAGTAGTCTGT 58.214 40.000 0.00 0.00 35.21 3.41
196 197 0.602905 CGGTCTTGCCTTTTCGGAGT 60.603 55.000 0.00 0.00 34.25 3.85
272 368 8.896320 TTGTTTGTAGAAAAGTATAGCTGACA 57.104 30.769 0.00 0.00 0.00 3.58
432 764 4.402056 TCCCGATGTCCTGATAAGTTTC 57.598 45.455 0.00 0.00 0.00 2.78
528 1490 9.922305 CTTAGTGTAGCATTGTAGCTTTATTTC 57.078 33.333 0.00 0.00 43.70 2.17
535 1497 7.420800 AGCATTGTAGCTTTATTTCTACATGC 58.579 34.615 18.14 18.14 43.70 4.06
744 1708 9.554395 TTATTATTCAATGTACATCGATGGTGT 57.446 29.630 28.09 12.65 0.00 4.16
1151 2121 0.806868 GTGATCGACGTGGACTACCA 59.193 55.000 1.11 0.00 44.76 3.25
1272 2242 4.131088 GAGGTCGCCGAGGTGGAC 62.131 72.222 2.57 5.09 42.00 4.02
1318 2288 1.267574 GGGACTGCTCAGATCCACCA 61.268 60.000 15.34 0.00 33.30 4.17
1390 2382 7.436118 AGTTGTTTGCATCTGATGTTAAATGT 58.564 30.769 18.19 5.35 0.00 2.71
1481 2491 6.966021 TCTGTGAACTTAGTTTATTTGCACC 58.034 36.000 0.00 0.00 0.00 5.01
1609 2653 3.368248 AGTAGCGTAGGTGTAAATGGGA 58.632 45.455 0.00 0.00 40.22 4.37
1643 2687 9.303116 AGTAGTTAGATAGTAGTAGCGTAGGTA 57.697 37.037 0.00 0.00 40.68 3.08
1680 2726 0.893447 GGGTCACCGTGCTACTACTT 59.107 55.000 0.00 0.00 0.00 2.24
1866 2914 2.529632 TGCTTGCTAGAGAGAAGGTGA 58.470 47.619 0.00 0.00 0.00 4.02
2055 3103 2.097110 ACGCCCTCATGATTACCCTA 57.903 50.000 0.00 0.00 0.00 3.53
2107 3155 2.697751 TGGAACACCACCATTTTCTTGG 59.302 45.455 0.00 0.00 42.82 3.61
2146 3194 6.543735 ACATTCCTATTCCTTATAACCTGGC 58.456 40.000 0.00 0.00 0.00 4.85
2157 3205 6.895204 TCCTTATAACCTGGCTTTTAGCATTT 59.105 34.615 0.00 0.00 44.75 2.32
2202 3251 2.818432 CTGCTCCTGCTTTGTTTGATCT 59.182 45.455 0.00 0.00 40.48 2.75
2273 3322 1.117142 AAACAACCAGGCTGCAGCAT 61.117 50.000 37.63 30.86 44.36 3.79
2310 3359 2.111878 GGATGAGTGGATGCCCGG 59.888 66.667 0.00 0.00 34.29 5.73
2317 3366 2.609299 TGGATGCCCGGTCCTCAA 60.609 61.111 10.68 0.00 36.68 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 4.639731 ACACTAGTACTAGAGGTCCCCTA 58.360 47.826 31.93 0.00 36.97 3.53
148 149 6.538021 ACATGAAAACTAGCAGAAGCAGATAG 59.462 38.462 0.00 0.00 45.49 2.08
224 225 8.758829 ACAAATAGATGGACAGTCAACTATACA 58.241 33.333 2.17 0.00 33.50 2.29
370 466 8.570488 CAATAAATGAACAAGCAGCCTATATGA 58.430 33.333 0.00 0.00 0.00 2.15
414 746 5.043903 ACATCGAAACTTATCAGGACATCG 58.956 41.667 0.00 0.00 0.00 3.84
432 764 6.162079 AGAAGCATGTATCCATCTAACATCG 58.838 40.000 0.00 0.00 31.60 3.84
528 1490 5.482908 ACAGAAGGTAGTTTGAGCATGTAG 58.517 41.667 0.00 0.00 0.00 2.74
744 1708 1.416030 TGACTAGCACAAGTCCAGCAA 59.584 47.619 10.31 0.00 44.40 3.91
1227 2197 1.600957 GCAATGACCTGGACGATCATG 59.399 52.381 0.00 0.00 33.37 3.07
1309 2279 3.139077 GAGTTGAAACGTTGGTGGATCT 58.861 45.455 0.00 0.00 0.00 2.75
1390 2382 6.272822 TCTCAACTCGAGATCTCAAAATCA 57.727 37.500 21.68 1.33 46.18 2.57
1481 2491 1.790755 TGGAAATCAAGACACGTCCG 58.209 50.000 0.00 0.00 0.00 4.79
1643 2687 2.972713 ACCCACGCTATCACTATTCCAT 59.027 45.455 0.00 0.00 0.00 3.41
1882 2930 3.243501 ACGACGTAAAACAGCAAGGTCTA 60.244 43.478 0.00 0.00 0.00 2.59
2055 3103 4.099113 GCGGTCTAGGTAAACCTTAGTCAT 59.901 45.833 7.04 0.00 46.09 3.06
2103 3151 2.496070 TGTCAGGGTAATCTCGTCCAAG 59.504 50.000 0.00 0.00 0.00 3.61
2107 3155 3.385111 AGGAATGTCAGGGTAATCTCGTC 59.615 47.826 0.00 0.00 0.00 4.20
2157 3205 7.387673 CAGGCAATGGAATAATATCACGAGTTA 59.612 37.037 0.00 0.00 0.00 2.24
2254 3303 1.117142 ATGCTGCAGCCTGGTTGTTT 61.117 50.000 34.64 6.34 41.18 2.83
2273 3322 1.537397 ACTGCTGAGGCTCCTCCAA 60.537 57.895 12.86 0.00 42.09 3.53
2310 3359 5.011840 GGATAGTAGTTGGGGTATTGAGGAC 59.988 48.000 0.00 0.00 0.00 3.85
2317 3366 3.116317 AGCCTGGATAGTAGTTGGGGTAT 60.116 47.826 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.