Multiple sequence alignment - TraesCS1B01G398300

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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 TraesCS1B01G398300 chr1B 100.000 2483 0 0 1 2483 629473262 629470780 0.000000e+00 4586.0
1 TraesCS1B01G398300 chr1B 91.509 212 15 2 1 210 656522447 656522237 3.120000e-74 289.0
2 TraesCS1B01G398300 chr1B 80.822 292 39 7 1386 1675 33004096 33003820 1.930000e-51 213.0
3 TraesCS1B01G398300 chr5D 95.854 1978 44 10 1 1944 462801633 462803606 0.000000e+00 3164.0
4 TraesCS1B01G398300 chr5D 95.969 1439 29 5 533 1944 388395300 388393864 0.000000e+00 2309.0
5 TraesCS1B01G398300 chr5D 88.723 470 39 6 887 1342 546919534 546920003 1.670000e-156 562.0
6 TraesCS1B01G398300 chr5D 90.683 161 15 0 1739 1899 9084843 9084683 5.380000e-52 215.0
7 TraesCS1B01G398300 chr3D 95.248 1978 45 9 1 1944 22230197 22232159 0.000000e+00 3086.0
8 TraesCS1B01G398300 chr4B 94.541 916 24 8 1054 1944 626627893 626626979 0.000000e+00 1391.0
9 TraesCS1B01G398300 chr4B 96.552 87 3 0 905 991 626627976 626627890 7.160000e-31 145.0
10 TraesCS1B01G398300 chr2B 95.125 841 29 3 1 830 485758477 485759316 0.000000e+00 1315.0
11 TraesCS1B01G398300 chr2B 94.418 842 30 5 1 830 632383121 632382285 0.000000e+00 1279.0
12 TraesCS1B01G398300 chr2B 90.361 166 15 1 1735 1899 237983331 237983496 1.500000e-52 217.0
13 TraesCS1B01G398300 chr2B 87.261 157 20 0 1743 1899 87531396 87531552 1.960000e-41 180.0
14 TraesCS1B01G398300 chr2D 94.781 843 30 4 1 830 617125075 617124234 0.000000e+00 1301.0
15 TraesCS1B01G398300 chr6B 94.636 839 35 5 1 830 681261872 681261035 0.000000e+00 1291.0
16 TraesCS1B01G398300 chr6D 94.222 623 25 3 218 830 423499016 423498395 0.000000e+00 941.0
17 TraesCS1B01G398300 chr6D 93.504 508 30 1 1977 2481 28289782 28289275 0.000000e+00 752.0
18 TraesCS1B01G398300 chr1A 92.435 542 38 1 1945 2483 24860432 24859891 0.000000e+00 771.0
19 TraesCS1B01G398300 chr1A 97.872 47 1 0 1898 1944 581505094 581505140 5.690000e-12 82.4
20 TraesCS1B01G398300 chr6A 91.713 543 36 3 1944 2483 41342691 41343227 0.000000e+00 745.0
21 TraesCS1B01G398300 chr6A 91.864 295 15 3 2192 2483 41403725 41404013 1.070000e-108 403.0
22 TraesCS1B01G398300 chr5B 91.650 503 32 7 218 716 415046900 415047396 0.000000e+00 688.0
23 TraesCS1B01G398300 chr5B 88.387 465 40 9 892 1342 690091585 690092049 4.670000e-152 547.0
24 TraesCS1B01G398300 chr4D 86.379 580 60 6 218 788 48415815 48416384 1.260000e-172 616.0
25 TraesCS1B01G398300 chr4D 90.566 212 17 2 1 210 49769692 49769902 6.760000e-71 278.0
26 TraesCS1B01G398300 chr1D 93.932 412 15 1 218 619 495445890 495445479 4.540000e-172 614.0
27 TraesCS1B01G398300 chr4A 88.486 469 41 5 887 1342 621818351 621817883 2.790000e-154 555.0
28 TraesCS1B01G398300 chr4A 92.073 164 11 1 1734 1897 739280650 739280489 1.920000e-56 230.0
29 TraesCS1B01G398300 chr3B 90.566 212 17 2 1 210 174459541 174459331 6.760000e-71 278.0
30 TraesCS1B01G398300 chr7D 99.083 109 1 0 2375 2483 55262125 55262233 1.950000e-46 196.0
31 TraesCS1B01G398300 chr7D 87.349 166 18 3 1734 1899 415220925 415220763 1.170000e-43 187.0
32 TraesCS1B01G398300 chr7D 95.745 47 2 0 1898 1944 415220307 415220353 2.650000e-10 76.8
33 TraesCS1B01G398300 chr7D 91.837 49 2 2 1898 1944 415038270 415038318 1.590000e-07 67.6
34 TraesCS1B01G398300 chr5A 95.833 48 2 0 1897 1944 168276209 168276256 7.360000e-11 78.7
35 TraesCS1B01G398300 chr5A 95.745 47 1 1 1898 1944 671540819 671540774 9.520000e-10 75.0


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 TraesCS1B01G398300 chr1B 629470780 629473262 2482 True 4586 4586 100.0000 1 2483 1 chr1B.!!$R2 2482
1 TraesCS1B01G398300 chr5D 462801633 462803606 1973 False 3164 3164 95.8540 1 1944 1 chr5D.!!$F1 1943
2 TraesCS1B01G398300 chr5D 388393864 388395300 1436 True 2309 2309 95.9690 533 1944 1 chr5D.!!$R2 1411
3 TraesCS1B01G398300 chr3D 22230197 22232159 1962 False 3086 3086 95.2480 1 1944 1 chr3D.!!$F1 1943
4 TraesCS1B01G398300 chr4B 626626979 626627976 997 True 768 1391 95.5465 905 1944 2 chr4B.!!$R1 1039
5 TraesCS1B01G398300 chr2B 485758477 485759316 839 False 1315 1315 95.1250 1 830 1 chr2B.!!$F3 829
6 TraesCS1B01G398300 chr2B 632382285 632383121 836 True 1279 1279 94.4180 1 830 1 chr2B.!!$R1 829
7 TraesCS1B01G398300 chr2D 617124234 617125075 841 True 1301 1301 94.7810 1 830 1 chr2D.!!$R1 829
8 TraesCS1B01G398300 chr6B 681261035 681261872 837 True 1291 1291 94.6360 1 830 1 chr6B.!!$R1 829
9 TraesCS1B01G398300 chr6D 423498395 423499016 621 True 941 941 94.2220 218 830 1 chr6D.!!$R2 612
10 TraesCS1B01G398300 chr6D 28289275 28289782 507 True 752 752 93.5040 1977 2481 1 chr6D.!!$R1 504
11 TraesCS1B01G398300 chr1A 24859891 24860432 541 True 771 771 92.4350 1945 2483 1 chr1A.!!$R1 538
12 TraesCS1B01G398300 chr6A 41342691 41343227 536 False 745 745 91.7130 1944 2483 1 chr6A.!!$F1 539
13 TraesCS1B01G398300 chr4D 48415815 48416384 569 False 616 616 86.3790 218 788 1 chr4D.!!$F1 570

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
972 997 0.696501 TTCCTTACCTGGGCCTTGAC 59.303 55.0 4.53 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1901 1953 0.253044 TTAGCAGAGCGGAAAGGCAT 59.747 50.0 0.0 0.0 34.64 4.4 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
295 297 6.409524 TGATTGGTTTCTCTTTCTGCATTT 57.590 33.333 0.00 0.00 0.00 2.32
374 376 3.181434 TGGGTTGTCAGATGCTTTACCTT 60.181 43.478 0.00 0.00 0.00 3.50
475 487 2.709213 TGATGTTGCATCGACCAATGA 58.291 42.857 3.95 0.00 0.00 2.57
512 524 5.294734 AGAACTAAAAGTTGGTTACCCGA 57.705 39.130 0.00 0.00 38.80 5.14
544 566 6.016555 ACCTTATAAAAAGGCAAGATGTGGT 58.983 36.000 3.69 0.00 41.10 4.16
701 724 6.042781 GGGGATATATCAAGGTAGTGTGTTGA 59.957 42.308 14.60 0.00 34.79 3.18
885 910 2.009774 CCGTCCAAGCATTGTCCTTAG 58.990 52.381 0.00 0.00 46.99 2.18
972 997 0.696501 TTCCTTACCTGGGCCTTGAC 59.303 55.000 4.53 0.00 0.00 3.18
1060 1085 4.043750 TGTCGAAAAAGATTGCAAGCTTG 58.956 39.130 28.99 22.44 34.43 4.01
1202 1227 0.472471 TGCACGGTTCCTCTTTTCCT 59.528 50.000 0.00 0.00 0.00 3.36
1539 1564 1.005037 CACTGCACTTCCACGCCTA 60.005 57.895 0.00 0.00 0.00 3.93
1758 1808 7.455641 TTTATTTTCGATAAACTGGCAGGAA 57.544 32.000 20.34 8.43 0.00 3.36
1876 1928 1.591594 CGGCATGCGGATTACTCGT 60.592 57.895 19.74 0.00 0.00 4.18
1901 1953 4.356405 TGAGAAAGCAACTGGATCTTGA 57.644 40.909 0.00 0.00 0.00 3.02
1962 2014 2.496470 CCCGAGCTCTTTTACTGTACCT 59.504 50.000 12.85 0.00 0.00 3.08
1968 2020 5.850614 AGCTCTTTTACTGTACCTCGAAAA 58.149 37.500 0.00 0.00 0.00 2.29
1999 2051 2.364324 CCGTCCATTTCTTCCGATCCTA 59.636 50.000 0.00 0.00 0.00 2.94
2060 2112 3.609853 AGTGCTGACTTGAAAACACTCA 58.390 40.909 0.00 0.00 33.25 3.41
2092 2144 4.585581 TCACTTAAGGGGCAAAAAGGTAAC 59.414 41.667 4.54 0.00 0.00 2.50
2097 2149 1.616865 GGGGCAAAAAGGTAACCTCAC 59.383 52.381 0.00 0.00 30.89 3.51
2242 2294 4.488911 AGATCGGGGCTGAGGGCT 62.489 66.667 0.00 0.00 41.46 5.19
2376 2431 1.133761 AGCTAGCCTCTCGGTATGTCA 60.134 52.381 12.13 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
295 297 6.009589 TGCCAAATGAGACCATAGAAAAAGA 58.990 36.000 0.00 0.00 31.59 2.52
374 376 1.493446 AGGAATCTCATCATGCTGCCA 59.507 47.619 0.00 0.00 0.00 4.92
512 524 6.909550 TGCCTTTTTATAAGGTGTGTTGAT 57.090 33.333 3.57 0.00 39.60 2.57
544 566 9.823647 GAATGAACCAAATTCTACTCTAGATGA 57.176 33.333 0.00 0.00 38.25 2.92
885 910 2.298729 CTCCCTAAGATCTGCAGTAGCC 59.701 54.545 14.67 1.59 41.13 3.93
972 997 1.605710 CACTTGGCTTGTGAAGTGGAG 59.394 52.381 6.73 0.00 43.55 3.86
1060 1085 2.618709 GGCCCTTGATAACTGTGTATGC 59.381 50.000 0.00 0.00 0.00 3.14
1202 1227 1.699083 TCAGACAACCTGCAATCTGGA 59.301 47.619 10.11 0.00 42.62 3.86
1289 1314 5.565439 CGGAAGAAATGGAAAGTGAAGCAAT 60.565 40.000 0.00 0.00 0.00 3.56
1758 1808 2.037251 TCTTCTACTTGAAAGGCAGCGT 59.963 45.455 0.00 0.00 33.79 5.07
1876 1928 4.914983 AGATCCAGTTGCTTTCTCATTCA 58.085 39.130 0.00 0.00 0.00 2.57
1901 1953 0.253044 TTAGCAGAGCGGAAAGGCAT 59.747 50.000 0.00 0.00 34.64 4.40
1962 2014 9.199982 GAAATGGACGGACTATATTATTTTCGA 57.800 33.333 0.00 0.00 0.00 3.71
1968 2020 7.177921 TCGGAAGAAATGGACGGACTATATTAT 59.822 37.037 0.00 0.00 37.03 1.28
1999 2051 4.469227 GGAGTACCAGATCATATGAGCCAT 59.531 45.833 17.12 5.97 35.97 4.40
2042 2094 3.873952 ACTCTGAGTGTTTTCAAGTCAGC 59.126 43.478 10.00 0.00 40.30 4.26
2050 2102 5.602628 AGTGAAGGTACTCTGAGTGTTTTC 58.397 41.667 20.19 17.84 38.49 2.29
2125 2177 5.476945 AGGTCGGTCAAAATTATTTCAGCTT 59.523 36.000 0.00 0.00 0.00 3.74
2126 2178 5.010282 AGGTCGGTCAAAATTATTTCAGCT 58.990 37.500 0.00 0.00 0.00 4.24
2212 2264 2.203070 GATCTGTTCGGCCGCCAT 60.203 61.111 23.51 7.07 0.00 4.40
2376 2431 6.306987 AGGACACAGAATGACAAATTACCTT 58.693 36.000 0.00 0.00 39.69 3.50


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

AutoCloner maintained by Alex Coulton.