Multiple sequence alignment - TraesCS1B01G005000

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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 TraesCS1B01G005000 chr1B 100.000 2624 0 0 1 2624 3172351 3169728 0.000000e+00 4846
1 TraesCS1B01G005000 chr6A 95.386 2644 78 13 1 2624 27214626 27217245 0.000000e+00 4167
2 TraesCS1B01G005000 chr2B 87.565 1914 155 53 298 2167 733833106 733831232 0.000000e+00 2139
3 TraesCS1B01G005000 chr2B 87.975 1630 144 31 316 1921 637724821 637723220 0.000000e+00 1877
4 TraesCS1B01G005000 chr2B 95.638 298 13 0 1 298 637750694 637750397 1.830000e-131 479
5 TraesCS1B01G005000 chr2B 94.295 298 16 1 1 298 733833452 733833156 3.080000e-124 455
6 TraesCS1B01G005000 chr2B 85.000 440 37 10 2209 2624 733831047 733830613 1.120000e-113 420
7 TraesCS1B01G005000 chr2B 90.945 254 17 6 1916 2167 637714952 637714703 1.160000e-88 337
8 TraesCS1B01G005000 chr5B 76.304 882 158 32 656 1512 170640327 170639472 8.680000e-115 424


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 TraesCS1B01G005000 chr1B 3169728 3172351 2623 True 4846.000000 4846 100.000000 1 2624 1 chr1B.!!$R1 2623
1 TraesCS1B01G005000 chr6A 27214626 27217245 2619 False 4167.000000 4167 95.386000 1 2624 1 chr6A.!!$F1 2623
2 TraesCS1B01G005000 chr2B 637723220 637724821 1601 True 1877.000000 1877 87.975000 316 1921 1 chr2B.!!$R2 1605
3 TraesCS1B01G005000 chr2B 733830613 733833452 2839 True 1004.666667 2139 88.953333 1 2624 3 chr2B.!!$R4 2623
4 TraesCS1B01G005000 chr5B 170639472 170640327 855 True 424.000000 424 76.304000 656 1512 1 chr5B.!!$R1 856

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
156 157 2.307768 GTCATGTACCTCGGAGGATGA 58.692 52.381 30.13 23.24 37.67 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1946 2061 2.316108 ACACTTAAGCAACAAAGGGGG 58.684 47.619 1.29 0.0 30.05 5.4 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
118 119 4.768448 TCATGCACAATCTTCCATTGTTCT 59.232 37.500 0.00 0.00 39.94 3.01
156 157 2.307768 GTCATGTACCTCGGAGGATGA 58.692 52.381 30.13 23.24 37.67 2.92
216 217 5.123979 GCTCAGGGTAATAAGTTTCCTGTTG 59.876 44.000 0.00 0.00 43.83 3.33
300 349 6.147821 GTGCAAGTATGTTCTTTTGCTCTCTA 59.852 38.462 9.14 0.00 44.59 2.43
309 358 9.635520 ATGTTCTTTTGCTCTCTATTTTCATTG 57.364 29.630 0.00 0.00 0.00 2.82
314 363 7.642071 TTTGCTCTCTATTTTCATTGTTTGC 57.358 32.000 0.00 0.00 0.00 3.68
323 372 8.346300 TCTATTTTCATTGTTTGCGTTTGTAGA 58.654 29.630 0.00 0.00 0.00 2.59
482 532 3.059352 AGCTACCGAAATCTTGCAACT 57.941 42.857 0.00 0.00 0.00 3.16
608 658 7.335627 TCTCTTACATTGGGGTAAGTTGTATG 58.664 38.462 11.52 0.00 46.54 2.39
1014 1089 6.092092 TCGTGATGCAATGGTATTCAAAAAG 58.908 36.000 0.00 0.00 0.00 2.27
1017 1092 7.116090 CGTGATGCAATGGTATTCAAAAAGAAA 59.884 33.333 0.00 0.00 40.22 2.52
1020 1103 9.763465 GATGCAATGGTATTCAAAAAGAAATTG 57.237 29.630 0.00 0.00 40.22 2.32
1221 1312 9.634021 AATTGGTACTTCTTCTCTTTTCTCTTT 57.366 29.630 0.00 0.00 0.00 2.52
1229 1320 6.115446 TCTTCTCTTTTCTCTTTTCAGTGCA 58.885 36.000 0.00 0.00 0.00 4.57
1618 1713 6.016610 GCCTATTTTTGTTGTACAGGTCAAGA 60.017 38.462 0.00 0.00 0.00 3.02
1629 1724 7.828508 TGTACAGGTCAAGACTTAGAGTTTA 57.171 36.000 0.00 0.00 0.00 2.01
1641 1736 6.328672 AGACTTAGAGTTTATGGGAGATGCAT 59.671 38.462 0.00 0.00 0.00 3.96
1650 1745 6.452757 TTATGGGAGATGCATTGGAAGATA 57.547 37.500 0.00 0.00 0.00 1.98
1756 1863 3.515502 TGTTGATGGTTTGGTGTTTTCCA 59.484 39.130 0.00 0.00 35.49 3.53
1794 1901 6.267817 CGACAATATAGTAGTCCCGAAACAA 58.732 40.000 0.00 0.00 0.00 2.83
1946 2061 2.861147 AGTCAAGGTTCTTACCCAGC 57.139 50.000 0.00 0.00 46.28 4.85
1962 2077 1.337118 CAGCCCCCTTTGTTGCTTAA 58.663 50.000 0.00 0.00 30.08 1.85
2144 2265 6.677913 ACTCTTCCCATTTATTTTCGTGTTG 58.322 36.000 0.00 0.00 0.00 3.33
2230 2494 5.385198 TGTCTACTTGCCTTTCTGGAATTT 58.615 37.500 0.00 0.00 38.35 1.82
2231 2495 5.241506 TGTCTACTTGCCTTTCTGGAATTTG 59.758 40.000 0.00 0.00 38.35 2.32
2232 2496 5.473504 GTCTACTTGCCTTTCTGGAATTTGA 59.526 40.000 0.00 0.00 38.35 2.69
2291 2555 4.080863 AGGCTGTCTGAAATTAGGTACCAG 60.081 45.833 15.94 0.20 0.00 4.00
2328 2610 8.446394 TGCTAATACATTAGTAGTACTCCCTCT 58.554 37.037 5.96 0.00 41.34 3.69
2329 2611 8.949177 GCTAATACATTAGTAGTACTCCCTCTC 58.051 40.741 5.96 0.00 41.34 3.20
2331 2613 8.694581 AATACATTAGTAGTACTCCCTCTCAC 57.305 38.462 5.96 0.00 32.86 3.51
2332 2614 6.330178 ACATTAGTAGTACTCCCTCTCACT 57.670 41.667 5.96 0.00 0.00 3.41
2333 2615 7.448915 ACATTAGTAGTACTCCCTCTCACTA 57.551 40.000 5.96 0.00 0.00 2.74
2334 2616 7.281841 ACATTAGTAGTACTCCCTCTCACTAC 58.718 42.308 5.96 3.17 42.30 2.73
2339 2621 5.114764 AGTACTCCCTCTCACTACTAACC 57.885 47.826 0.00 0.00 0.00 2.85
2340 2622 4.789702 AGTACTCCCTCTCACTACTAACCT 59.210 45.833 0.00 0.00 0.00 3.50
2341 2623 4.678538 ACTCCCTCTCACTACTAACCTT 57.321 45.455 0.00 0.00 0.00 3.50
2342 2624 5.013258 ACTCCCTCTCACTACTAACCTTT 57.987 43.478 0.00 0.00 0.00 3.11
2343 2625 5.018149 ACTCCCTCTCACTACTAACCTTTC 58.982 45.833 0.00 0.00 0.00 2.62
2344 2626 5.222379 ACTCCCTCTCACTACTAACCTTTCT 60.222 44.000 0.00 0.00 0.00 2.52
2345 2627 5.262804 TCCCTCTCACTACTAACCTTTCTC 58.737 45.833 0.00 0.00 0.00 2.87
2423 2706 7.353414 TCACTCCTAATCCTACTCATCTTTG 57.647 40.000 0.00 0.00 0.00 2.77
2479 2785 9.071276 TCTGCTATCTTGTTTTCTTCATTCTTT 57.929 29.630 0.00 0.00 0.00 2.52
2490 2796 5.995565 TCTTCATTCTTTCGGAGGTTCTA 57.004 39.130 0.00 0.00 0.00 2.10
2532 2838 3.682718 CGTCATATTGCCCTTCCTCTTGT 60.683 47.826 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
118 119 2.894765 TGACCGTGAGATGAACCACTAA 59.105 45.455 0.00 0.0 0.00 2.24
156 157 4.660303 TGAGGTATATCTGCCAGGAACAAT 59.340 41.667 0.00 0.0 0.00 2.71
216 217 2.096013 GGTGACGCCTTTCTTGATTAGC 59.904 50.000 0.00 0.0 0.00 3.09
300 349 7.945033 ATCTACAAACGCAAACAATGAAAAT 57.055 28.000 0.00 0.0 0.00 1.82
309 358 9.601971 TTACATAGAAAATCTACAAACGCAAAC 57.398 29.630 0.00 0.0 30.79 2.93
482 532 5.445069 TCCACATCTTCTTTGGACTTCAAA 58.555 37.500 0.00 0.0 42.50 2.69
695 763 8.229253 TGAAATGCATTAGCTACAATCTCAAT 57.771 30.769 13.39 0.0 42.74 2.57
847 920 7.280652 AGCTGCAAAAACAACACAAGAATAATT 59.719 29.630 1.02 0.0 0.00 1.40
1014 1089 7.019774 TCCATCGAATGAATCACTCAATTTC 57.980 36.000 0.00 0.0 37.67 2.17
1017 1092 6.293698 TGATCCATCGAATGAATCACTCAAT 58.706 36.000 0.00 0.0 37.67 2.57
1020 1103 6.609237 TTTGATCCATCGAATGAATCACTC 57.391 37.500 0.00 0.0 0.00 3.51
1170 1258 3.461378 TGCTGAGGTACACTAGGGTAA 57.539 47.619 6.38 0.0 0.00 2.85
1221 1312 8.635765 AGAAAATTAATAGAAGGTGCACTGAA 57.364 30.769 17.98 0.0 0.00 3.02
1542 1637 8.470040 TTGTTTCCATCTGTATTACGTTCTAC 57.530 34.615 0.00 0.0 0.00 2.59
1554 1649 5.754890 GCTGAAAAACATTGTTTCCATCTGT 59.245 36.000 14.80 0.0 34.67 3.41
1593 1688 5.699097 TGACCTGTACAACAAAAATAGGC 57.301 39.130 0.00 0.0 0.00 3.93
1618 1713 5.957771 TGCATCTCCCATAAACTCTAAGT 57.042 39.130 0.00 0.0 0.00 2.24
1629 1724 3.897657 ATCTTCCAATGCATCTCCCAT 57.102 42.857 0.00 0.0 0.00 4.00
1641 1736 3.110705 AGCAGAGCCTTCTATCTTCCAA 58.889 45.455 0.00 0.0 30.73 3.53
1650 1745 4.322567 CTCAAAACTAAGCAGAGCCTTCT 58.677 43.478 0.00 0.0 0.00 2.85
1756 1863 6.826741 ACTATATTGTCGGCTTACAAACCAAT 59.173 34.615 8.18 0.0 42.33 3.16
1946 2061 2.316108 ACACTTAAGCAACAAAGGGGG 58.684 47.619 1.29 0.0 30.05 5.40
2328 2610 8.488308 AAAACTAGGAGAAAGGTTAGTAGTGA 57.512 34.615 0.00 0.0 0.00 3.41
2329 2611 7.818446 GGAAAACTAGGAGAAAGGTTAGTAGTG 59.182 40.741 0.00 0.0 0.00 2.74
2330 2612 7.733955 AGGAAAACTAGGAGAAAGGTTAGTAGT 59.266 37.037 0.00 0.0 0.00 2.73
2331 2613 8.136563 AGGAAAACTAGGAGAAAGGTTAGTAG 57.863 38.462 0.00 0.0 0.00 2.57
2332 2614 8.502047 AAGGAAAACTAGGAGAAAGGTTAGTA 57.498 34.615 0.00 0.0 0.00 1.82
2333 2615 7.292827 AGAAGGAAAACTAGGAGAAAGGTTAGT 59.707 37.037 0.00 0.0 0.00 2.24
2334 2616 7.681679 AGAAGGAAAACTAGGAGAAAGGTTAG 58.318 38.462 0.00 0.0 0.00 2.34
2335 2617 7.628501 AGAAGGAAAACTAGGAGAAAGGTTA 57.371 36.000 0.00 0.0 0.00 2.85
2336 2618 6.517013 AGAAGGAAAACTAGGAGAAAGGTT 57.483 37.500 0.00 0.0 0.00 3.50
2337 2619 7.628501 TTAGAAGGAAAACTAGGAGAAAGGT 57.371 36.000 0.00 0.0 0.00 3.50
2338 2620 8.322091 TGATTAGAAGGAAAACTAGGAGAAAGG 58.678 37.037 0.00 0.0 0.00 3.11
2339 2621 9.898152 ATGATTAGAAGGAAAACTAGGAGAAAG 57.102 33.333 0.00 0.0 0.00 2.62
2423 2706 7.708752 TGAGAGAAGAAGAAAAGAAGACAGAAC 59.291 37.037 0.00 0.0 0.00 3.01
2479 2785 5.768662 CACAATCCTATAGTAGAACCTCCGA 59.231 44.000 0.00 0.0 0.00 4.55
2490 2796 2.561569 GGCGCAACACAATCCTATAGT 58.438 47.619 10.83 0.0 0.00 2.12
2532 2838 0.823356 GGCAACCAGAGGAGCAACAA 60.823 55.000 7.33 0.0 0.00 2.83


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

AutoCloner maintained by Alex Coulton.