Multiple sequence alignment - TraesCS5D01G536600

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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 TraesCS5D01G536600 chr5D 100.000 1792 0 0 1 1792 549805411 549807202 0.000000e+00 3310.0
1 TraesCS5D01G536600 chr5D 100.000 606 0 0 2049 2654 549807459 549808064 0.000000e+00 1120.0
2 TraesCS5D01G536600 chr4A 94.813 1793 76 5 1 1792 621428071 621429847 0.000000e+00 2780.0
3 TraesCS5D01G536600 chr4A 93.433 335 17 5 2125 2456 621430243 621430575 2.370000e-135 492.0
4 TraesCS5D01G536600 chr4A 94.558 147 8 0 2508 2654 621430571 621430717 7.390000e-56 228.0
5 TraesCS5D01G536600 chr4A 97.500 80 2 0 2049 2128 621429920 621429999 1.280000e-28 137.0
6 TraesCS5D01G536600 chr5B 93.774 1317 69 9 483 1792 701392477 701393787 0.000000e+00 1965.0
7 TraesCS5D01G536600 chr5B 94.825 599 23 6 2049 2640 701393860 701394457 0.000000e+00 928.0
8 TraesCS5D01G536600 chr5B 86.041 437 54 3 1 435 701392045 701392476 1.860000e-126 462.0
9 TraesCS5D01G536600 chr1D 77.821 257 40 13 744 996 10404461 10404704 2.750000e-30 143.0
10 TraesCS5D01G536600 chr7D 84.397 141 13 4 2519 2653 131113364 131113501 2.140000e-26 130.0
11 TraesCS5D01G536600 chr4D 89.706 68 6 1 474 540 410294541 410294474 4.710000e-13 86.1
12 TraesCS5D01G536600 chr2B 87.879 66 7 1 474 538 779037320 779037385 2.830000e-10 76.8
13 TraesCS5D01G536600 chr1B 100.000 29 0 0 560 588 689386694 689386722 1.000000e-03 54.7


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 TraesCS5D01G536600 chr5D 549805411 549808064 2653 False 2215.000000 3310 100.000000 1 2654 2 chr5D.!!$F1 2653
1 TraesCS5D01G536600 chr4A 621428071 621430717 2646 False 909.250000 2780 95.076000 1 2654 4 chr4A.!!$F1 2653
2 TraesCS5D01G536600 chr5B 701392045 701394457 2412 False 1118.333333 1965 91.546667 1 2640 3 chr5B.!!$F1 2639

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
303 307 0.035725 TTCCCACAGCTGCTCATCTG 60.036 55.0 15.27 2.87 36.45 2.90 F
455 459 0.539051 ACATGCTCCTCCGGAAAGAG 59.461 55.0 21.62 21.62 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1114 1120 1.772836 AAGGCCTTCTTGATGGATGC 58.227 50.000 13.78 0.00 33.76 3.91 R
1723 1733 1.901159 CCTGTTTCCATGCATGGGAAA 59.099 47.619 36.09 30.29 46.64 3.13 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
28 29 3.314913 TCATTTGTGACTGCGTTGTCAAT 59.685 39.130 12.71 3.06 46.77 2.57
29 30 2.753989 TTGTGACTGCGTTGTCAATG 57.246 45.000 12.71 0.00 46.77 2.82
39 40 2.524034 CGTTGTCAATGTGTGTTGCAA 58.476 42.857 0.00 0.00 0.00 4.08
61 63 2.035155 TCGTCGGCTCCCTCTGAA 59.965 61.111 0.00 0.00 0.00 3.02
107 109 6.602009 GGTATAAAACTCAGTTGCCATTACCT 59.398 38.462 0.00 0.00 0.00 3.08
121 123 3.683340 CCATTACCTGCATCTCATCATCG 59.317 47.826 0.00 0.00 0.00 3.84
126 128 2.223994 CCTGCATCTCATCATCGTCAGT 60.224 50.000 0.00 0.00 0.00 3.41
143 145 1.745489 GTGCACCTCGTCCCATTCC 60.745 63.158 5.22 0.00 0.00 3.01
148 150 0.978146 ACCTCGTCCCATTCCCTCTG 60.978 60.000 0.00 0.00 0.00 3.35
213 217 1.926108 TTGGAAATACCGGGGGTTTG 58.074 50.000 6.32 0.00 42.61 2.93
269 273 1.933853 CGCTGCCTACACATAACTTCC 59.066 52.381 0.00 0.00 0.00 3.46
272 276 3.369471 GCTGCCTACACATAACTTCCTCA 60.369 47.826 0.00 0.00 0.00 3.86
274 278 3.580895 TGCCTACACATAACTTCCTCACA 59.419 43.478 0.00 0.00 0.00 3.58
289 293 3.907474 TCCTCACACTCATAAACTTCCCA 59.093 43.478 0.00 0.00 0.00 4.37
293 297 3.189287 CACACTCATAAACTTCCCACAGC 59.811 47.826 0.00 0.00 0.00 4.40
303 307 0.035725 TTCCCACAGCTGCTCATCTG 60.036 55.000 15.27 2.87 36.45 2.90
363 367 4.222114 CCGTTCTTTTGCATCTCAAAGTC 58.778 43.478 8.14 3.69 44.62 3.01
411 415 3.037549 TGAATTGACCCCAAAACAGCTT 58.962 40.909 0.00 0.00 35.67 3.74
445 449 2.764007 TGTCCAGTGACATGCTCCT 58.236 52.632 0.00 0.00 46.40 3.69
448 452 1.153489 CCAGTGACATGCTCCTCCG 60.153 63.158 0.00 0.00 0.00 4.63
455 459 0.539051 ACATGCTCCTCCGGAAAGAG 59.461 55.000 21.62 21.62 0.00 2.85
463 467 2.963782 TCCTCCGGAAAGAGTATAAGCC 59.036 50.000 5.23 0.00 31.53 4.35
472 476 6.405508 CGGAAAGAGTATAAGCCTTGACACTA 60.406 42.308 0.00 0.00 0.00 2.74
493 497 6.873605 CACTAGTGAGACACCATGTTGAAATA 59.126 38.462 18.45 0.00 34.49 1.40
544 548 7.615403 TGAGCCATGCTTATTATACTAGGAAG 58.385 38.462 0.00 0.00 39.88 3.46
680 685 2.093447 ACAGGCTAGTAAGACATGCACC 60.093 50.000 0.00 0.00 30.50 5.01
871 876 2.866085 AAGCTCTCATGGCCTCACGC 62.866 60.000 3.32 0.00 0.00 5.34
1008 1014 3.356290 AGGTCAACTTACAATGGCCATC 58.644 45.455 21.08 1.50 43.88 3.51
1036 1042 3.388345 ACATTGCATGCACATTGTTCA 57.612 38.095 22.58 2.84 31.85 3.18
1325 1331 2.116827 AAACCCGCCGACAAATATGA 57.883 45.000 0.00 0.00 0.00 2.15
1353 1359 1.743252 CAAGACCTTCAGCGAGGCC 60.743 63.158 0.00 0.00 40.65 5.19
1499 1505 4.059459 CGTCGTCGCTGCCAACAC 62.059 66.667 0.00 0.00 0.00 3.32
1534 1540 6.149474 GTCTGCAAAGGACAAGAAGCTATTTA 59.851 38.462 0.00 0.00 34.23 1.40
1667 1677 1.593787 CATGAGTGGCACCTCGTCT 59.406 57.895 15.27 0.00 34.04 4.18
1683 1693 1.375908 TCTGGCCTTCGATGCACAC 60.376 57.895 3.32 0.00 0.00 3.82
1691 1701 3.478394 CGATGCACACGACCACCG 61.478 66.667 9.10 0.00 45.44 4.94
1758 1768 6.279882 TGGAAACAGGCAATAGTTCTTTTTG 58.720 36.000 0.00 0.00 35.01 2.44
2118 2128 6.044046 GCATGTGATTTCTGATGGCATAAAA 58.956 36.000 0.00 2.24 0.00 1.52
2174 2435 2.066262 ACTACGTTTCGCCTCACAATG 58.934 47.619 0.00 0.00 0.00 2.82
2185 2446 2.826428 CCTCACAATGTAGCGTGCTAT 58.174 47.619 4.68 0.00 33.03 2.97
2195 2456 0.741326 AGCGTGCTATGATGTCGTCT 59.259 50.000 0.00 0.00 0.00 4.18
2196 2457 1.135139 AGCGTGCTATGATGTCGTCTT 59.865 47.619 0.00 0.00 0.00 3.01
2235 2496 7.172190 ACATTGACAGTTTGACACTATCTTCTG 59.828 37.037 0.00 0.00 29.26 3.02
2262 2524 2.806945 TCCCTATGTTTTGCCTCTGG 57.193 50.000 0.00 0.00 0.00 3.86
2434 2698 5.799435 CGCACTATGAGCATATCTACTTCTG 59.201 44.000 0.00 0.00 0.00 3.02
2547 2811 3.556633 CCACAGTGTGAGAAATCTCTGCT 60.557 47.826 24.99 4.58 43.25 4.24
2557 2821 5.769662 TGAGAAATCTCTGCTTTTAAAGCCA 59.230 36.000 24.45 11.80 45.76 4.75
2596 2860 2.290847 CCTCTCAGGGCAGTTGCTA 58.709 57.895 3.88 0.00 41.70 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 1.024046 ACGAGCTGTTGCAACACACA 61.024 50.000 27.96 8.56 42.74 3.72
29 30 0.316196 GACGAGCTGTTGCAACACAC 60.316 55.000 27.96 21.51 42.74 3.82
61 63 0.693049 AGCTTTTCATGTCGGAGGGT 59.307 50.000 0.00 0.00 0.00 4.34
107 109 2.817901 CACTGACGATGATGAGATGCA 58.182 47.619 0.00 0.00 0.00 3.96
121 123 2.048127 GGGACGAGGTGCACTGAC 60.048 66.667 17.98 7.42 0.00 3.51
126 128 2.668632 GGAATGGGACGAGGTGCA 59.331 61.111 0.00 0.00 0.00 4.57
143 145 4.003648 ACCGTTTGAGCTTTAATCAGAGG 58.996 43.478 0.00 0.00 0.00 3.69
148 150 5.358298 AGAACACCGTTTGAGCTTTAATC 57.642 39.130 0.00 0.00 0.00 1.75
176 179 1.470098 CAAAACCGAGCTTCTCATGGG 59.530 52.381 0.00 0.00 0.00 4.00
177 180 1.470098 CCAAAACCGAGCTTCTCATGG 59.530 52.381 0.00 0.00 0.00 3.66
179 182 2.859165 TCCAAAACCGAGCTTCTCAT 57.141 45.000 0.00 0.00 0.00 2.90
208 212 0.804989 CAAGGCAGACGATCCAAACC 59.195 55.000 0.00 0.00 0.00 3.27
213 217 1.522580 GGCTCAAGGCAGACGATCC 60.523 63.158 0.00 0.00 44.01 3.36
269 273 4.641396 TGTGGGAAGTTTATGAGTGTGAG 58.359 43.478 0.00 0.00 0.00 3.51
272 276 3.073062 AGCTGTGGGAAGTTTATGAGTGT 59.927 43.478 0.00 0.00 0.00 3.55
274 278 3.679389 CAGCTGTGGGAAGTTTATGAGT 58.321 45.455 5.25 0.00 0.00 3.41
293 297 5.021033 AGATAAAGGACACAGATGAGCAG 57.979 43.478 0.00 0.00 0.00 4.24
303 307 6.651225 GGGTATCAAGCATAGATAAAGGACAC 59.349 42.308 0.00 0.00 30.37 3.67
363 367 4.585364 CAGATAGCAAAACTGCGAGAATG 58.415 43.478 0.00 0.00 40.27 2.67
411 415 0.250234 GACATGCAGTAGTGGAGCCA 59.750 55.000 0.00 0.00 0.00 4.75
444 448 4.099573 TCAAGGCTTATACTCTTTCCGGAG 59.900 45.833 3.34 0.00 39.09 4.63
445 449 4.028131 TCAAGGCTTATACTCTTTCCGGA 58.972 43.478 0.00 0.00 0.00 5.14
448 452 5.735766 AGTGTCAAGGCTTATACTCTTTCC 58.264 41.667 0.00 0.00 0.00 3.13
455 459 6.127703 TGTCTCACTAGTGTCAAGGCTTATAC 60.128 42.308 21.99 1.94 0.00 1.47
463 467 4.240888 CATGGTGTCTCACTAGTGTCAAG 58.759 47.826 21.99 12.63 34.40 3.02
472 476 5.934625 GTCTATTTCAACATGGTGTCTCACT 59.065 40.000 11.27 0.00 34.40 3.41
493 497 2.293122 GCTCTGCTGATCTACATCGTCT 59.707 50.000 0.00 0.00 0.00 4.18
544 548 1.199097 CCGTGCAAAACCTACCATGTC 59.801 52.381 0.00 0.00 0.00 3.06
590 595 3.844640 TCCATTGATCGATCCTGGAGTA 58.155 45.455 29.30 16.34 34.58 2.59
680 685 4.305769 TCTGGTTTTGCGATTGATTTTGG 58.694 39.130 0.00 0.00 0.00 3.28
723 728 4.698583 ATCATTCTTTCAAGAGCACAGC 57.301 40.909 0.00 0.00 36.22 4.40
851 856 0.392193 CGTGAGGCCATGAGAGCTTT 60.392 55.000 5.01 0.00 0.00 3.51
871 876 3.379452 AGGAGATGGTGTCTAAAGAGGG 58.621 50.000 0.00 0.00 37.29 4.30
1036 1042 1.976898 CCACCACAATGGCAGCAAT 59.023 52.632 0.00 0.00 42.67 3.56
1114 1120 1.772836 AAGGCCTTCTTGATGGATGC 58.227 50.000 13.78 0.00 33.76 3.91
1325 1331 3.746492 GCTGAAGGTCTTGTCAAATACGT 59.254 43.478 0.00 0.00 0.00 3.57
1338 1344 4.821589 CCGGCCTCGCTGAAGGTC 62.822 72.222 0.00 0.00 38.79 3.85
1499 1505 2.979676 TTGCAGACTGGGCAAGCG 60.980 61.111 4.26 0.00 45.57 4.68
1667 1677 2.741985 CGTGTGCATCGAAGGCCA 60.742 61.111 5.01 5.12 0.00 5.36
1683 1693 3.733344 ATCAATCCGCCGGTGGTCG 62.733 63.158 32.48 21.26 38.88 4.79
1691 1701 2.292267 ACATCAAGTGATCAATCCGCC 58.708 47.619 0.00 0.00 31.21 6.13
1723 1733 1.901159 CCTGTTTCCATGCATGGGAAA 59.099 47.619 36.09 30.29 46.64 3.13
1742 1752 8.648557 AGAAAACTTCAAAAAGAACTATTGCC 57.351 30.769 0.00 0.00 36.30 4.52
1758 1768 5.607119 TCGCCAATACAAGAGAAAACTTC 57.393 39.130 0.00 0.00 0.00 3.01
2155 2416 2.066262 ACATTGTGAGGCGAAACGTAG 58.934 47.619 0.00 0.00 0.00 3.51
2174 2435 2.044860 GACGACATCATAGCACGCTAC 58.955 52.381 0.00 0.00 0.00 3.58
2185 2446 3.511699 CGGAAGATCAAAGACGACATCA 58.488 45.455 0.00 0.00 0.00 3.07
2195 2456 2.487762 GTCAATGTGCCGGAAGATCAAA 59.512 45.455 5.05 0.00 0.00 2.69
2196 2457 2.083774 GTCAATGTGCCGGAAGATCAA 58.916 47.619 5.05 0.00 0.00 2.57
2235 2496 3.119495 GGCAAAACATAGGGATCACACAC 60.119 47.826 0.00 0.00 0.00 3.82
2418 2682 8.385898 ACTACAGTACAGAAGTAGATATGCTC 57.614 38.462 16.55 0.00 38.79 4.26
2434 2698 7.807687 TCTGCGAGAATTTAAACTACAGTAC 57.192 36.000 0.00 0.00 0.00 2.73
2547 2811 3.304829 AGCTTTGGAGGTGGCTTTAAAA 58.695 40.909 0.00 0.00 31.08 1.52
2557 2821 0.960861 GGCGCTAAAGCTTTGGAGGT 60.961 55.000 25.01 0.00 39.32 3.85
2591 2855 0.480690 TTTGGGCTTGGAGGTAGCAA 59.519 50.000 0.00 0.00 40.42 3.91
2596 2860 0.178924 AGCATTTTGGGCTTGGAGGT 60.179 50.000 0.00 0.00 38.81 3.85


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

AutoCloner maintained by Alex Coulton.