Multiple sequence alignment - TraesCS7A01G283900

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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 TraesCS7A01G283900 chr7A 100.000 3489 0 0 1 3489 317898006 317894518 0.000000e+00 6444.0
1 TraesCS7A01G283900 chr7A 91.988 1036 66 16 844 1873 554473662 554474686 0.000000e+00 1437.0
2 TraesCS7A01G283900 chr7A 85.921 277 16 8 3234 3489 195524173 195523899 1.230000e-69 274.0
3 TraesCS7A01G283900 chr1B 95.987 3514 82 14 1 3489 512629255 512625776 0.000000e+00 5653.0
4 TraesCS7A01G283900 chr4A 95.475 3536 74 13 1 3489 726567218 726563722 0.000000e+00 5565.0
5 TraesCS7A01G283900 chr4A 87.976 1339 85 23 1 1268 24021392 24020059 0.000000e+00 1511.0
6 TraesCS7A01G283900 chr4A 87.685 1348 86 30 1 1274 2907829 2909170 0.000000e+00 1496.0
7 TraesCS7A01G283900 chr4A 81.439 431 49 22 1 420 726661928 726662338 1.210000e-84 324.0
8 TraesCS7A01G283900 chr3B 94.655 3536 94 30 1 3489 781353741 781350254 0.000000e+00 5395.0
9 TraesCS7A01G283900 chr3B 94.572 3537 86 33 1 3489 85345789 85342311 0.000000e+00 5371.0
10 TraesCS7A01G283900 chr6B 97.550 3102 71 4 389 3489 300672072 300675169 0.000000e+00 5302.0
11 TraesCS7A01G283900 chr6B 89.736 2309 113 44 1 2220 720763421 720765694 0.000000e+00 2837.0
12 TraesCS7A01G283900 chr6B 87.681 414 18 2 1 391 300671546 300671949 5.310000e-123 451.0
13 TraesCS7A01G283900 chr6B 79.262 569 82 18 2455 2998 720765832 720766389 7.120000e-97 364.0
14 TraesCS7A01G283900 chr7B 96.737 2544 58 4 970 3489 582698263 582695721 0.000000e+00 4215.0
15 TraesCS7A01G283900 chr7B 94.508 965 18 10 1 941 582699213 582698260 0.000000e+00 1456.0
16 TraesCS7A01G283900 chr2A 92.145 2037 109 24 254 2272 343417779 343419782 0.000000e+00 2828.0
17 TraesCS7A01G283900 chr2A 86.854 677 38 13 2381 3012 343420320 343420990 0.000000e+00 710.0
18 TraesCS7A01G283900 chr2A 93.013 229 14 2 1 228 343417470 343417697 2.010000e-87 333.0
19 TraesCS7A01G283900 chr2A 88.983 118 8 3 2270 2387 343419863 343419975 1.310000e-29 141.0
20 TraesCS7A01G283900 chr3A 91.924 2006 92 28 254 2220 109880503 109882477 0.000000e+00 2743.0
21 TraesCS7A01G283900 chr3A 92.766 235 13 1 1 231 109880200 109880434 1.550000e-88 337.0
22 TraesCS7A01G283900 chr3A 86.643 277 15 6 3234 3489 422616518 422616243 1.580000e-73 287.0
23 TraesCS7A01G283900 chr1A 90.508 2128 111 36 153 2220 22856541 22854445 0.000000e+00 2726.0
24 TraesCS7A01G283900 chr1A 92.672 232 10 2 1 228 22856728 22856500 9.340000e-86 327.0
25 TraesCS7A01G283900 chr1A 91.549 71 6 0 3144 3214 548997528 548997458 7.970000e-17 99.0
26 TraesCS7A01G283900 chr4D 94.482 1468 66 9 614 2073 211757210 211758670 0.000000e+00 2248.0
27 TraesCS7A01G283900 chr4D 93.886 229 12 2 1 228 211756490 211756717 9.270000e-91 344.0
28 TraesCS7A01G283900 chr5D 94.178 292 16 1 2097 2388 553776950 553776660 8.890000e-121 444.0
29 TraesCS7A01G283900 chr1D 86.643 277 15 3 3234 3489 470573177 470572902 1.580000e-73 287.0
30 TraesCS7A01G283900 chr1D 88.261 230 22 4 1 228 79815918 79816144 1.600000e-68 270.0
31 TraesCS7A01G283900 chr1D 92.754 69 4 1 3144 3212 455092592 455092525 7.970000e-17 99.0
32 TraesCS7A01G283900 chr1D 90.141 71 7 0 3144 3214 455092515 455092445 3.710000e-15 93.5
33 TraesCS7A01G283900 chr7D 88.158 228 25 2 1 228 588566438 588566663 1.600000e-68 270.0


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 TraesCS7A01G283900 chr7A 317894518 317898006 3488 True 6444.0 6444 100.00000 1 3489 1 chr7A.!!$R2 3488
1 TraesCS7A01G283900 chr7A 554473662 554474686 1024 False 1437.0 1437 91.98800 844 1873 1 chr7A.!!$F1 1029
2 TraesCS7A01G283900 chr1B 512625776 512629255 3479 True 5653.0 5653 95.98700 1 3489 1 chr1B.!!$R1 3488
3 TraesCS7A01G283900 chr4A 726563722 726567218 3496 True 5565.0 5565 95.47500 1 3489 1 chr4A.!!$R2 3488
4 TraesCS7A01G283900 chr4A 24020059 24021392 1333 True 1511.0 1511 87.97600 1 1268 1 chr4A.!!$R1 1267
5 TraesCS7A01G283900 chr4A 2907829 2909170 1341 False 1496.0 1496 87.68500 1 1274 1 chr4A.!!$F1 1273
6 TraesCS7A01G283900 chr3B 781350254 781353741 3487 True 5395.0 5395 94.65500 1 3489 1 chr3B.!!$R2 3488
7 TraesCS7A01G283900 chr3B 85342311 85345789 3478 True 5371.0 5371 94.57200 1 3489 1 chr3B.!!$R1 3488
8 TraesCS7A01G283900 chr6B 300671546 300675169 3623 False 2876.5 5302 92.61550 1 3489 2 chr6B.!!$F1 3488
9 TraesCS7A01G283900 chr6B 720763421 720766389 2968 False 1600.5 2837 84.49900 1 2998 2 chr6B.!!$F2 2997
10 TraesCS7A01G283900 chr7B 582695721 582699213 3492 True 2835.5 4215 95.62250 1 3489 2 chr7B.!!$R1 3488
11 TraesCS7A01G283900 chr2A 343417470 343420990 3520 False 1003.0 2828 90.24875 1 3012 4 chr2A.!!$F1 3011
12 TraesCS7A01G283900 chr3A 109880200 109882477 2277 False 1540.0 2743 92.34500 1 2220 2 chr3A.!!$F1 2219
13 TraesCS7A01G283900 chr1A 22854445 22856728 2283 True 1526.5 2726 91.59000 1 2220 2 chr1A.!!$R2 2219
14 TraesCS7A01G283900 chr4D 211756490 211758670 2180 False 1296.0 2248 94.18400 1 2073 2 chr4D.!!$F1 2072

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
132 144 4.434593 CGTTTAGTGCGTATGTGGTTTACC 60.435 45.833 0.00 0.00 0.00 2.85 F
338 417 5.584649 TGCACTGTATTTGCTAGTGGAATAC 59.415 40.000 13.49 13.49 39.34 1.89 F
2083 2476 1.285667 TCAATGTGACCAGCATCCCAT 59.714 47.619 0.00 0.00 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1062 1357 4.231426 ACAAAAGGATCCCCATCTGAATCT 59.769 41.667 8.55 0.0 33.88 2.40 R
2161 2554 3.541632 GACACAAGAAAGTGGACAAGGA 58.458 45.455 0.00 0.0 43.72 3.36 R
3239 4203 6.992063 AATGAGTAACACAATCAGGCTAAG 57.008 37.500 0.00 0.0 0.00 2.18 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
65 77 6.695713 CAGTCAATTCGAACGGATGTATTCTA 59.304 38.462 0.00 0.00 0.00 2.10
118 130 4.491676 TCTTCACTGGTATCGTTTAGTGC 58.508 43.478 0.00 0.00 40.15 4.40
132 144 4.434593 CGTTTAGTGCGTATGTGGTTTACC 60.435 45.833 0.00 0.00 0.00 2.85
248 304 8.822805 TCATTGTAACTTTCTAGTGGATAGGTT 58.177 33.333 0.00 0.00 34.01 3.50
338 417 5.584649 TGCACTGTATTTGCTAGTGGAATAC 59.415 40.000 13.49 13.49 39.34 1.89
1062 1357 4.734402 GCTGCTTGTGTTGAAGATTGTGAA 60.734 41.667 0.00 0.00 0.00 3.18
1100 1395 4.657969 TCCTTTTGTCCCCAATGATTTTGT 59.342 37.500 0.00 0.00 0.00 2.83
1140 1502 7.356089 TCAAGCTTCGGAGGTTATATTTCTA 57.644 36.000 8.06 0.00 41.44 2.10
1141 1503 7.788026 TCAAGCTTCGGAGGTTATATTTCTAA 58.212 34.615 8.06 0.00 41.44 2.10
1142 1504 8.429641 TCAAGCTTCGGAGGTTATATTTCTAAT 58.570 33.333 8.06 0.00 41.44 1.73
1143 1505 9.057089 CAAGCTTCGGAGGTTATATTTCTAATT 57.943 33.333 8.06 0.00 41.44 1.40
1144 1506 9.628500 AAGCTTCGGAGGTTATATTTCTAATTT 57.372 29.630 6.31 0.00 41.55 1.82
1145 1507 9.057089 AGCTTCGGAGGTTATATTTCTAATTTG 57.943 33.333 0.00 0.00 0.00 2.32
1146 1508 9.052759 GCTTCGGAGGTTATATTTCTAATTTGA 57.947 33.333 0.00 0.00 0.00 2.69
1239 1601 4.973168 TCTGTTAACTGCAGGAAAGTCAT 58.027 39.130 19.93 0.00 34.89 3.06
1348 1710 7.706607 ACCAGTTTCTTCTGTTAATGCTTTTTC 59.293 33.333 0.00 0.00 34.02 2.29
1369 1732 8.617761 TTTTCGTACCAGTTTCATTTTTGTAC 57.382 30.769 0.00 0.00 0.00 2.90
1438 1802 5.528043 TTTGGCAGAAAGTGAATTGCTTA 57.472 34.783 0.00 0.00 36.79 3.09
1439 1803 5.528043 TTGGCAGAAAGTGAATTGCTTAA 57.472 34.783 0.00 0.00 36.79 1.85
1761 2143 5.189180 GTCTTCTGATTTTCCTGTAGCCAT 58.811 41.667 0.00 0.00 0.00 4.40
1942 2332 5.417754 TGATCTTGCTTCAGAGATTCAGT 57.582 39.130 0.00 0.00 32.96 3.41
2083 2476 1.285667 TCAATGTGACCAGCATCCCAT 59.714 47.619 0.00 0.00 0.00 4.00
2161 2554 8.308931 ACATTTTCATCTGCTTCATGTGTATTT 58.691 29.630 0.00 0.00 0.00 1.40
2220 2613 5.982391 TCTCCTAGTCCCAAATATCTCCAT 58.018 41.667 0.00 0.00 0.00 3.41
2230 2623 9.525826 GTCCCAAATATCTCCATATTTTCAGAT 57.474 33.333 0.00 0.00 40.81 2.90
2502 3377 9.715121 TTTTACAGTGTAATTCTAGGTCGATTT 57.285 29.630 16.26 0.00 0.00 2.17
2576 3451 9.241317 ACACTATAATTGTAGGTCGATTTTACG 57.759 33.333 13.13 0.00 32.85 3.18
2768 3667 3.670625 TCCTACCGGATTTTCAGTGTTG 58.329 45.455 9.46 0.00 33.30 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 77 0.187606 GGGATTAAAGGCCCGGGAAT 59.812 55.000 29.31 15.21 34.00 3.01
118 130 5.295045 GGAATTACAGGGTAAACCACATACG 59.705 44.000 0.81 0.00 43.89 3.06
338 417 7.229306 ACACTGCAATTAGGACATATACATTGG 59.771 37.037 0.00 0.00 0.00 3.16
533 739 7.809546 TCAATTACACTGTAAATCCACAACA 57.190 32.000 5.73 0.00 0.00 3.33
1062 1357 4.231426 ACAAAAGGATCCCCATCTGAATCT 59.769 41.667 8.55 0.00 33.88 2.40
1239 1601 6.768641 TTCTCCAAATCAGGATCATCCATA 57.231 37.500 6.42 0.00 39.61 2.74
1348 1710 6.062434 TGGTACAAAAATGAAACTGGTACG 57.938 37.500 0.00 0.00 31.92 3.67
1369 1732 9.075519 CATTAACTACAAACATGCATTAACTGG 57.924 33.333 0.00 0.00 0.00 4.00
1419 1783 5.107875 CGTTTTAAGCAATTCACTTTCTGCC 60.108 40.000 0.00 0.00 35.33 4.85
1438 1802 5.242838 TCCAGCATTTGTAATCTTCCGTTTT 59.757 36.000 0.00 0.00 0.00 2.43
1439 1803 4.764823 TCCAGCATTTGTAATCTTCCGTTT 59.235 37.500 0.00 0.00 0.00 3.60
1942 2332 9.462606 GGGAATCAGAATAAACTTCTTCCTAAA 57.537 33.333 0.00 0.00 32.75 1.85
2083 2476 7.439381 AGTGTATTGTAGAAGAAAGAAACCGA 58.561 34.615 0.00 0.00 0.00 4.69
2161 2554 3.541632 GACACAAGAAAGTGGACAAGGA 58.458 45.455 0.00 0.00 43.72 3.36
2880 3843 7.306515 CCACACACAATTAAAAAGGAAATGACG 60.307 37.037 0.00 0.00 0.00 4.35
3071 4034 7.051623 AGACAAAGTACAAACCATGTTACAGA 58.948 34.615 0.00 0.00 43.63 3.41
3239 4203 6.992063 AATGAGTAACACAATCAGGCTAAG 57.008 37.500 0.00 0.00 0.00 2.18


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

AutoCloner maintained by Alex Coulton.