Multiple sequence alignment - TraesCS7A01G554900

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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 TraesCS7A01G554900 chr7A 100.000 2357 0 0 1 2357 727004755 727007111 0.000000e+00 4353
1 TraesCS7A01G554900 chr7A 91.753 194 16 0 164 357 727006868 727006675 1.070000e-68 270
2 TraesCS7A01G554900 chrUn 97.007 2372 41 11 1 2357 83676224 83678580 0.000000e+00 3960
3 TraesCS7A01G554900 chrUn 90.418 407 37 2 1701 2106 321125430 321125025 3.450000e-148 534
4 TraesCS7A01G554900 chrUn 90.418 407 37 2 1701 2106 321128748 321128343 3.450000e-148 534
5 TraesCS7A01G554900 chrUn 90.418 407 37 2 1701 2106 336388979 336389384 3.450000e-148 534
6 TraesCS7A01G554900 chrUn 91.457 199 16 1 165 363 89951892 89952089 2.980000e-69 272
7 TraesCS7A01G554900 chr1D 95.701 884 38 0 675 1558 60171768 60170885 0.000000e+00 1423
8 TraesCS7A01G554900 chr1D 95.465 882 40 0 675 1556 205134649 205133768 0.000000e+00 1408
9 TraesCS7A01G554900 chr1D 95.136 884 43 0 675 1558 247505710 247504827 0.000000e+00 1395
10 TraesCS7A01G554900 chr1D 88.272 486 33 6 158 642 342219903 342220365 5.690000e-156 560
11 TraesCS7A01G554900 chr1D 90.315 413 38 2 1701 2113 342220511 342220921 7.410000e-150 540
12 TraesCS7A01G554900 chr3D 95.249 884 42 0 675 1558 613711318 613712201 0.000000e+00 1400
13 TraesCS7A01G554900 chr2D 95.249 884 42 0 675 1558 73126824 73125941 0.000000e+00 1400
14 TraesCS7A01G554900 chr2D 96.341 82 3 0 2 83 508794430 508794349 4.090000e-28 135
15 TraesCS7A01G554900 chr7D 93.972 929 42 7 642 1557 497560908 497561835 0.000000e+00 1393
16 TraesCS7A01G554900 chr7D 90.985 477 35 1 166 642 555077264 555077732 9.190000e-179 636
17 TraesCS7A01G554900 chr7D 90.777 412 37 1 1701 2112 555077878 555078288 1.230000e-152 549
18 TraesCS7A01G554900 chr7D 93.122 189 12 1 165 353 22992536 22992723 2.310000e-70 276
19 TraesCS7A01G554900 chr7D 93.233 133 9 0 1573 1705 83866289 83866421 1.850000e-46 196
20 TraesCS7A01G554900 chr7D 96.386 83 3 0 2 84 474045756 474045838 1.140000e-28 137
21 TraesCS7A01G554900 chr7B 95.136 884 42 1 675 1558 720163341 720162459 0.000000e+00 1393
22 TraesCS7A01G554900 chr6D 93.871 930 44 5 642 1558 57791141 57790212 0.000000e+00 1389
23 TraesCS7A01G554900 chr6D 89.144 479 24 5 164 642 365457338 365457788 2.630000e-159 571
24 TraesCS7A01G554900 chr6D 91.727 411 34 0 1701 2111 365457949 365458359 2.630000e-159 571
25 TraesCS7A01G554900 chr6D 95.082 183 7 2 461 642 59711088 59711269 1.070000e-73 287
26 TraesCS7A01G554900 chr6D 92.537 134 10 0 1572 1705 365457773 365457906 2.390000e-45 193
27 TraesCS7A01G554900 chr6D 96.386 83 3 0 2 84 468661146 468661064 1.140000e-28 137
28 TraesCS7A01G554900 chr4A 95.229 545 25 1 1572 2116 532598415 532597872 0.000000e+00 861
29 TraesCS7A01G554900 chr4A 93.265 490 25 2 153 642 532598881 532598400 0.000000e+00 715
30 TraesCS7A01G554900 chr4A 88.075 478 48 3 166 642 78156824 78157293 2.050000e-155 558
31 TraesCS7A01G554900 chr4A 96.429 84 3 0 2 85 358069085 358069168 3.160000e-29 139
32 TraesCS7A01G554900 chr4B 90.024 411 41 0 1701 2111 34539007 34539417 1.240000e-147 532
33 TraesCS7A01G554900 chr4B 91.593 226 14 2 422 642 34538634 34538859 8.180000e-80 307
34 TraesCS7A01G554900 chr3B 84.979 486 42 14 156 611 53221931 53221447 4.590000e-127 464
35 TraesCS7A01G554900 chr3B 93.893 131 8 0 1572 1702 727467924 727467794 5.140000e-47 198
36 TraesCS7A01G554900 chr1A 94.656 131 7 0 1572 1702 578773785 578773915 1.100000e-48 204
37 TraesCS7A01G554900 chr1B 93.846 130 8 0 1573 1702 6308731 6308860 1.850000e-46 196
38 TraesCS7A01G554900 chr4D 92.537 134 10 0 1572 1705 504010503 504010370 2.390000e-45 193
39 TraesCS7A01G554900 chr4D 96.386 83 3 0 2 84 6031253 6031335 1.140000e-28 137
40 TraesCS7A01G554900 chr2B 93.130 131 8 1 1572 1702 773468859 773468988 8.600000e-45 191
41 TraesCS7A01G554900 chr2B 92.473 93 5 1 2 94 566496531 566496621 5.290000e-27 132
42 TraesCS7A01G554900 chr3A 95.402 87 4 0 2 88 303696084 303695998 3.160000e-29 139
43 TraesCS7A01G554900 chr2A 96.386 83 3 0 2 84 585886118 585886036 1.140000e-28 137


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 TraesCS7A01G554900 chr7A 727004755 727007111 2356 False 4353.0 4353 100.0000 1 2357 1 chr7A.!!$F1 2356
1 TraesCS7A01G554900 chrUn 83676224 83678580 2356 False 3960.0 3960 97.0070 1 2357 1 chrUn.!!$F1 2356
2 TraesCS7A01G554900 chrUn 321125025 321128748 3723 True 534.0 534 90.4180 1701 2106 2 chrUn.!!$R1 405
3 TraesCS7A01G554900 chr1D 60170885 60171768 883 True 1423.0 1423 95.7010 675 1558 1 chr1D.!!$R1 883
4 TraesCS7A01G554900 chr1D 205133768 205134649 881 True 1408.0 1408 95.4650 675 1556 1 chr1D.!!$R2 881
5 TraesCS7A01G554900 chr1D 247504827 247505710 883 True 1395.0 1395 95.1360 675 1558 1 chr1D.!!$R3 883
6 TraesCS7A01G554900 chr1D 342219903 342220921 1018 False 550.0 560 89.2935 158 2113 2 chr1D.!!$F1 1955
7 TraesCS7A01G554900 chr3D 613711318 613712201 883 False 1400.0 1400 95.2490 675 1558 1 chr3D.!!$F1 883
8 TraesCS7A01G554900 chr2D 73125941 73126824 883 True 1400.0 1400 95.2490 675 1558 1 chr2D.!!$R1 883
9 TraesCS7A01G554900 chr7D 497560908 497561835 927 False 1393.0 1393 93.9720 642 1557 1 chr7D.!!$F4 915
10 TraesCS7A01G554900 chr7D 555077264 555078288 1024 False 592.5 636 90.8810 166 2112 2 chr7D.!!$F5 1946
11 TraesCS7A01G554900 chr7B 720162459 720163341 882 True 1393.0 1393 95.1360 675 1558 1 chr7B.!!$R1 883
12 TraesCS7A01G554900 chr6D 57790212 57791141 929 True 1389.0 1389 93.8710 642 1558 1 chr6D.!!$R1 916
13 TraesCS7A01G554900 chr6D 365457338 365458359 1021 False 445.0 571 91.1360 164 2111 3 chr6D.!!$F2 1947
14 TraesCS7A01G554900 chr4A 532597872 532598881 1009 True 788.0 861 94.2470 153 2116 2 chr4A.!!$R1 1963
15 TraesCS7A01G554900 chr4B 34538634 34539417 783 False 419.5 532 90.8085 422 2111 2 chr4B.!!$F1 1689

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
790 817 0.918983 CTCCTACCCCCTTGATGCAA 59.081 55.0 0.0 0.0 0.0 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2267 3888 0.537188 GAGGAACCATCGCTGAAGGA 59.463 55.0 6.79 0.0 0.0 3.36 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
64 65 5.629079 AGATTAGTTGTGGCAAAGTTAGC 57.371 39.130 0.00 0.00 0.00 3.09
76 77 3.989817 GCAAAGTTAGCCATGAACCAAAG 59.010 43.478 0.00 0.00 0.00 2.77
85 86 2.091665 CCATGAACCAAAGAGGCCCTAT 60.092 50.000 0.00 0.00 43.14 2.57
266 267 4.835678 GGTCCCTCAACTATTTAAACCGA 58.164 43.478 0.00 0.00 0.00 4.69
394 395 4.988540 TGTGACAGTAAATGTGCAGTCTAC 59.011 41.667 0.00 0.00 44.17 2.59
408 409 6.934083 TGTGCAGTCTACTTCATCATTTACAA 59.066 34.615 0.00 0.00 0.00 2.41
692 719 4.323417 CCTCTGCATACGGCCATTTTATA 58.677 43.478 2.24 0.00 43.89 0.98
790 817 0.918983 CTCCTACCCCCTTGATGCAA 59.081 55.000 0.00 0.00 0.00 4.08
939 966 4.697756 CGCCGCCTTCTTCCACCA 62.698 66.667 0.00 0.00 0.00 4.17
1197 1224 1.003118 CAACATCTCTCCCCCGAACAA 59.997 52.381 0.00 0.00 0.00 2.83
1341 1368 3.717294 TTCGCCTCCAGGAAGGGC 61.717 66.667 9.38 9.38 42.18 5.19
1488 1515 1.302907 AGATGAAAGAGCCATGGGGT 58.697 50.000 15.13 0.00 36.17 4.95
1546 1573 1.022735 TAGATCTCCAGACGCCGAAC 58.977 55.000 0.00 0.00 0.00 3.95
1873 3494 0.390492 CATGCGACTGGGATGCTCTA 59.610 55.000 0.00 0.00 37.67 2.43
2113 3734 9.557061 GAGGACGAAAAATATACTTATCCCTTT 57.443 33.333 0.00 0.00 0.00 3.11
2129 3750 9.341899 CTTATCCCTTTTTGAAATACTTGTTCG 57.658 33.333 0.00 0.00 0.00 3.95
2258 3879 2.266055 CTCCTGGGTCGGCACTTC 59.734 66.667 0.00 0.00 0.00 3.01
2267 3888 0.318762 GTCGGCACTTCTTGGTCTCT 59.681 55.000 0.00 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 0.040204 AGGGCCTCTTTGGTTCATGG 59.960 55.000 0.00 0.00 38.35 3.66
76 77 4.976540 ATTACCACACTAATAGGGCCTC 57.023 45.455 10.74 0.00 0.00 4.70
85 86 8.029782 ACATTATGGCTCTATTACCACACTAA 57.970 34.615 0.00 0.00 39.19 2.24
266 267 2.606272 GTCGCGAGGGACGAAAAATATT 59.394 45.455 10.24 0.00 45.77 1.28
394 395 8.839947 TGTCGCATTTATTGTAAATGATGAAG 57.160 30.769 20.68 9.56 39.36 3.02
408 409 6.563422 ACTGCACATTTATTGTCGCATTTAT 58.437 32.000 0.00 0.00 39.73 1.40
672 685 6.892658 ATTTATAAAATGGCCGTATGCAGA 57.107 33.333 0.00 0.00 43.89 4.26
673 686 9.638239 AATAATTTATAAAATGGCCGTATGCAG 57.362 29.630 0.00 0.00 43.89 4.41
790 817 1.024579 GTTCGGACATTCGGCACCAT 61.025 55.000 0.00 0.00 0.00 3.55
939 966 4.343526 CAGTACCTGCTCTGTAGATGGATT 59.656 45.833 0.00 0.00 0.00 3.01
1197 1224 2.058675 CCGTCTTGGGAGGAACTGT 58.941 57.895 0.00 0.00 41.55 3.55
1323 1350 2.269241 CCCTTCCTGGAGGCGAAC 59.731 66.667 0.00 0.00 38.35 3.95
1488 1515 2.580322 TCCTCCATTATGCTGGGTTGAA 59.420 45.455 2.87 0.00 36.89 2.69
2113 3734 9.574458 TGAAAAATGTCGAACAAGTATTTCAAA 57.426 25.926 0.00 0.00 32.13 2.69
2258 3879 0.891373 TCGCTGAAGGAGAGACCAAG 59.109 55.000 0.00 0.00 42.04 3.61
2267 3888 0.537188 GAGGAACCATCGCTGAAGGA 59.463 55.000 6.79 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.