Multiple sequence alignment - TraesCS5B01G531500

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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 TraesCS5B01G531500 chr5B 100.000 2537 0 0 1 2537 689486168 689488704 0.000000e+00 4686
1 TraesCS5B01G531500 chr2B 87.318 2200 153 43 1 2108 371166742 371168907 0.000000e+00 2401
2 TraesCS5B01G531500 chr2B 87.719 114 4 6 2302 2413 371169026 371169131 9.530000e-25 124
3 TraesCS5B01G531500 chr2A 87.447 1649 104 36 735 2315 376076746 376075133 0.000000e+00 1803
4 TraesCS5B01G531500 chr2A 87.549 771 66 15 1 750 376077525 376076764 0.000000e+00 865
5 TraesCS5B01G531500 chr5D 92.950 1149 38 9 735 1863 546365626 546366751 0.000000e+00 1633
6 TraesCS5B01G531500 chr5D 91.617 668 33 9 1873 2537 546371656 546372303 0.000000e+00 902
7 TraesCS5B01G531500 chr5D 91.011 445 29 7 202 636 546358592 546359035 7.820000e-165 590
8 TraesCS5B01G531500 chr5D 94.030 67 4 0 634 700 546361501 546361567 4.470000e-18 102
9 TraesCS5B01G531500 chr2D 90.743 713 38 7 820 1510 299887959 299887253 0.000000e+00 926
10 TraesCS5B01G531500 chr2D 86.940 781 56 19 1 750 299888851 299888086 0.000000e+00 835
11 TraesCS5B01G531500 chr2D 87.240 768 52 27 1569 2315 299886927 299886185 0.000000e+00 833
12 TraesCS5B01G531500 chr3A 83.523 528 50 22 820 1325 724300391 724300903 2.300000e-125 459
13 TraesCS5B01G531500 chr3A 82.407 540 55 22 1439 1960 724301038 724301555 3.880000e-118 435
14 TraesCS5B01G531500 chr3A 83.631 336 36 10 1946 2274 724303069 724303392 5.310000e-77 298


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 TraesCS5B01G531500 chr5B 689486168 689488704 2536 False 4686.000000 4686 100.000000 1 2537 1 chr5B.!!$F1 2536
1 TraesCS5B01G531500 chr2B 371166742 371169131 2389 False 1262.500000 2401 87.518500 1 2413 2 chr2B.!!$F1 2412
2 TraesCS5B01G531500 chr2A 376075133 376077525 2392 True 1334.000000 1803 87.498000 1 2315 2 chr2A.!!$R1 2314
3 TraesCS5B01G531500 chr5D 546365626 546366751 1125 False 1633.000000 1633 92.950000 735 1863 1 chr5D.!!$F1 1128
4 TraesCS5B01G531500 chr5D 546371656 546372303 647 False 902.000000 902 91.617000 1873 2537 1 chr5D.!!$F2 664
5 TraesCS5B01G531500 chr5D 546358592 546361567 2975 False 346.000000 590 92.520500 202 700 2 chr5D.!!$F3 498
6 TraesCS5B01G531500 chr2D 299886185 299888851 2666 True 864.666667 926 88.307667 1 2315 3 chr2D.!!$R1 2314
7 TraesCS5B01G531500 chr3A 724300391 724303392 3001 False 397.333333 459 83.187000 820 2274 3 chr3A.!!$F1 1454

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
417 449 0.106819 CTGCCCCCTCTCCATCTTTG 60.107 60.0 0.0 0.0 0.0 2.77 F
1213 3816 0.108138 GTTCATGTCGTGGGAGGAGG 60.108 60.0 0.0 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1436 4042 1.127567 AGCCTGCTCAACCACTACCA 61.128 55.000 0.0 0.0 0.00 3.25 R
2503 7066 1.950909 TCGGTGTTTTGTGAATCCCAC 59.049 47.619 0.0 0.0 45.88 4.61 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
24 32 4.281688 ACTTTTGTGTGGAATGGAGAATGG 59.718 41.667 0.00 0.00 0.00 3.16
45 53 3.270877 GTCCAACTATTGCGGAACTCAT 58.729 45.455 0.00 0.00 0.00 2.90
46 54 3.063997 GTCCAACTATTGCGGAACTCATG 59.936 47.826 0.00 0.00 0.00 3.07
61 69 2.236146 ACTCATGGCTCCGTTGAACATA 59.764 45.455 0.00 0.00 0.00 2.29
161 169 0.319383 AGATTATCTGCAGGAGCGCG 60.319 55.000 15.13 0.00 46.23 6.86
173 181 1.643832 GAGCGCGATCATCAAACCC 59.356 57.895 21.13 0.00 0.00 4.11
175 183 1.091771 AGCGCGATCATCAAACCCTG 61.092 55.000 12.10 0.00 0.00 4.45
179 187 2.083774 GCGATCATCAAACCCTGACAA 58.916 47.619 0.00 0.00 36.69 3.18
198 206 3.716872 ACAAGAATATGTCCCCGGAAGAT 59.283 43.478 0.73 0.00 0.00 2.40
200 208 2.907042 AGAATATGTCCCCGGAAGATCC 59.093 50.000 0.73 0.00 0.00 3.36
245 262 1.900585 GCATTTCGCGTGAGAGCACA 61.901 55.000 5.77 0.00 45.41 4.57
289 315 4.383861 TGCAGTGAGCTCAGCGGG 62.384 66.667 18.89 8.05 45.94 6.13
352 378 2.281761 CTTGTCCAAGTGCCGGCT 60.282 61.111 29.70 4.80 33.87 5.52
354 380 3.113514 TTGTCCAAGTGCCGGCTGA 62.114 57.895 29.70 13.17 0.00 4.26
411 437 2.610859 GGTTCTGCCCCCTCTCCA 60.611 66.667 0.00 0.00 0.00 3.86
416 448 0.253347 TCTGCCCCCTCTCCATCTTT 60.253 55.000 0.00 0.00 0.00 2.52
417 449 0.106819 CTGCCCCCTCTCCATCTTTG 60.107 60.000 0.00 0.00 0.00 2.77
433 465 5.105877 CCATCTTTGTTCACGTACTCCTCTA 60.106 44.000 0.00 0.00 0.00 2.43
520 552 2.616458 GGCAGGAGAATGGGGTGGT 61.616 63.158 0.00 0.00 0.00 4.16
587 622 3.945285 TGGAAGTTGTTGAGGTTGAAGTC 59.055 43.478 0.00 0.00 0.00 3.01
646 3150 1.002087 GGTGAAGGAAAGAGCGGAAGA 59.998 52.381 0.00 0.00 0.00 2.87
702 3206 4.473643 GCTTGGTGCTGTGGTGTA 57.526 55.556 0.00 0.00 38.95 2.90
754 3293 5.405063 TCCTTATTGCCTACTCCTAGTCT 57.595 43.478 0.00 0.00 0.00 3.24
814 3353 0.804989 CGGGGCTCTGTTGCTAAAAG 59.195 55.000 0.00 0.00 0.00 2.27
830 3394 7.648039 TGCTAAAAGAAAAACTAAAGACCCA 57.352 32.000 0.00 0.00 0.00 4.51
833 3397 7.648112 GCTAAAAGAAAAACTAAAGACCCACTG 59.352 37.037 0.00 0.00 0.00 3.66
964 3545 2.351706 AACGCTTCTTTTACCCACCA 57.648 45.000 0.00 0.00 0.00 4.17
965 3546 2.351706 ACGCTTCTTTTACCCACCAA 57.648 45.000 0.00 0.00 0.00 3.67
966 3547 2.657143 ACGCTTCTTTTACCCACCAAA 58.343 42.857 0.00 0.00 0.00 3.28
1198 3801 1.896660 GGTTGCAAGGAGGCGTTCA 60.897 57.895 0.00 0.00 36.28 3.18
1213 3816 0.108138 GTTCATGTCGTGGGAGGAGG 60.108 60.000 0.00 0.00 0.00 4.30
1214 3817 0.252057 TTCATGTCGTGGGAGGAGGA 60.252 55.000 0.00 0.00 0.00 3.71
1215 3818 0.684479 TCATGTCGTGGGAGGAGGAG 60.684 60.000 0.00 0.00 0.00 3.69
1303 3906 0.957395 CAAGAAGTGCATGGACGCCT 60.957 55.000 12.02 9.91 0.00 5.52
1344 3947 2.716017 GCTACAGGCTGAGCGGACT 61.716 63.158 23.66 0.00 38.06 3.85
1366 3969 4.394712 CCGACCAAGCCGAAGCCT 62.395 66.667 0.00 0.00 41.25 4.58
1436 4042 1.562672 CCCTCCCCGGACACTGATTT 61.563 60.000 0.73 0.00 33.16 2.17
1657 4592 6.220930 GGGAAATAAAGGTTGTTCTTCCAAC 58.779 40.000 0.00 0.00 43.15 3.77
1742 4684 3.928727 ACTCATCATGTTTGTGCTTGG 57.071 42.857 0.00 0.00 0.00 3.61
1863 4822 2.431782 ACCAAGTTTGTTGCTTGATGCT 59.568 40.909 6.62 0.00 44.29 3.79
1907 4869 0.251354 CCTGGTGACTGGGATGTCTG 59.749 60.000 0.00 0.00 45.15 3.51
1978 6468 3.915437 ATTGGTTTCAGCTTGTTACCG 57.085 42.857 0.00 0.00 0.00 4.02
1979 6469 2.623878 TGGTTTCAGCTTGTTACCGA 57.376 45.000 0.00 0.00 0.00 4.69
1980 6470 2.215196 TGGTTTCAGCTTGTTACCGAC 58.785 47.619 0.00 0.00 0.00 4.79
1981 6471 2.158871 TGGTTTCAGCTTGTTACCGACT 60.159 45.455 0.00 0.00 0.00 4.18
1982 6472 2.876550 GGTTTCAGCTTGTTACCGACTT 59.123 45.455 0.00 0.00 0.00 3.01
1983 6473 4.060205 GGTTTCAGCTTGTTACCGACTTA 58.940 43.478 0.00 0.00 0.00 2.24
1984 6474 4.084171 GGTTTCAGCTTGTTACCGACTTAC 60.084 45.833 0.00 0.00 0.00 2.34
1985 6475 3.308438 TCAGCTTGTTACCGACTTACC 57.692 47.619 0.00 0.00 0.00 2.85
1996 6486 1.990563 CCGACTTACCGTCATTGACAC 59.009 52.381 16.61 0.00 42.98 3.67
2024 6514 5.622346 TGGTTTGCCTTCATTTACCTTTT 57.378 34.783 0.00 0.00 35.27 2.27
2104 6594 5.529800 TCTTTTAACTAGTCACTTGGCCAAC 59.470 40.000 16.05 5.46 0.00 3.77
2175 6665 8.761575 ATAATCAGTTGCATAAACAAAACAGG 57.238 30.769 0.00 0.00 41.61 4.00
2180 6670 4.935352 TGCATAAACAAAACAGGAGCTT 57.065 36.364 0.00 0.00 0.00 3.74
2187 6677 9.061610 CATAAACAAAACAGGAGCTTATTTACG 57.938 33.333 0.00 0.00 0.00 3.18
2202 6696 8.900781 AGCTTATTTACGTAGTCTTATGTGAGA 58.099 33.333 0.00 0.00 43.93 3.27
2262 6757 8.125978 AGTTTCCTGAATTTTTATCTGATGCA 57.874 30.769 0.00 0.00 0.00 3.96
2354 6915 3.503363 TCCAGTTGATTGCTGTCATTGAC 59.497 43.478 9.93 9.93 32.41 3.18
2355 6916 3.253921 CCAGTTGATTGCTGTCATTGACA 59.746 43.478 18.08 18.08 40.50 3.58
2356 6917 4.082408 CCAGTTGATTGCTGTCATTGACAT 60.082 41.667 19.29 5.17 41.94 3.06
2357 6918 4.857037 CAGTTGATTGCTGTCATTGACATG 59.143 41.667 19.29 14.00 41.94 3.21
2358 6919 4.763279 AGTTGATTGCTGTCATTGACATGA 59.237 37.500 19.29 9.17 41.94 3.07
2359 6920 5.417894 AGTTGATTGCTGTCATTGACATGAT 59.582 36.000 19.29 13.06 41.94 2.45
2360 6921 5.243426 TGATTGCTGTCATTGACATGATG 57.757 39.130 19.29 9.32 41.94 3.07
2361 6922 4.944930 TGATTGCTGTCATTGACATGATGA 59.055 37.500 19.29 6.19 41.94 2.92
2418 6980 1.196808 ACAAAACAGCGATTAGTGCCG 59.803 47.619 0.00 0.00 0.00 5.69
2427 6989 2.408704 GCGATTAGTGCCGCTACATAAG 59.591 50.000 0.00 0.00 46.96 1.73
2495 7058 7.563724 AGTACTAGTTTGTCCTGGGATTTAA 57.436 36.000 0.00 0.00 0.00 1.52
2503 7066 4.960938 TGTCCTGGGATTTAATGATCTCG 58.039 43.478 0.00 0.00 28.66 4.04
2520 7083 2.875933 TCTCGTGGGATTCACAAAACAC 59.124 45.455 0.00 0.00 46.36 3.32
2521 7084 1.950909 TCGTGGGATTCACAAAACACC 59.049 47.619 0.00 0.00 46.36 4.16
2531 7094 2.550606 TCACAAAACACCGATTAGTGCC 59.449 45.455 0.00 0.00 41.67 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 32 2.695359 TGAGTTCCGCAATAGTTGGAC 58.305 47.619 0.00 0.00 0.00 4.02
33 41 1.377202 GGAGCCATGAGTTCCGCAA 60.377 57.895 0.00 0.00 35.98 4.85
45 53 1.557371 TCCATATGTTCAACGGAGCCA 59.443 47.619 1.24 0.00 0.00 4.75
46 54 1.940613 GTCCATATGTTCAACGGAGCC 59.059 52.381 1.24 0.00 0.00 4.70
125 133 6.986817 AGATAATCTATGACAAAACCACCGAG 59.013 38.462 0.00 0.00 0.00 4.63
132 140 7.519649 GCTCCTGCAGATAATCTATGACAAAAC 60.520 40.741 17.39 0.00 39.41 2.43
161 169 7.284034 ACATATTCTTGTCAGGGTTTGATGATC 59.716 37.037 0.00 0.00 38.29 2.92
173 181 2.434336 TCCGGGGACATATTCTTGTCAG 59.566 50.000 0.00 0.00 46.32 3.51
175 183 3.134081 TCTTCCGGGGACATATTCTTGTC 59.866 47.826 0.00 0.00 44.27 3.18
179 187 2.907042 GGATCTTCCGGGGACATATTCT 59.093 50.000 0.00 0.00 0.00 2.40
198 206 5.977635 TCTTCAATTTCTGCTTATCTCGGA 58.022 37.500 0.00 0.00 0.00 4.55
200 208 9.808808 CAATATCTTCAATTTCTGCTTATCTCG 57.191 33.333 0.00 0.00 0.00 4.04
207 215 7.434307 CGAAATGCAATATCTTCAATTTCTGCT 59.566 33.333 0.00 0.00 0.00 4.24
245 262 1.725557 CCGAGGTCGACGATGTCCAT 61.726 60.000 9.92 0.00 43.02 3.41
289 315 2.167900 ACCTACCTTACACCTTCATCGC 59.832 50.000 0.00 0.00 0.00 4.58
292 318 3.308188 GGCAACCTACCTTACACCTTCAT 60.308 47.826 0.00 0.00 0.00 2.57
352 378 5.681437 GCAGTTACTATCCACCGAGAAATCA 60.681 44.000 0.00 0.00 0.00 2.57
354 380 4.694339 GCAGTTACTATCCACCGAGAAAT 58.306 43.478 0.00 0.00 0.00 2.17
403 429 2.289694 ACGTGAACAAAGATGGAGAGGG 60.290 50.000 0.00 0.00 0.00 4.30
411 437 5.944599 TCTAGAGGAGTACGTGAACAAAGAT 59.055 40.000 0.00 0.00 0.00 2.40
416 448 4.080469 AGGATCTAGAGGAGTACGTGAACA 60.080 45.833 0.00 0.00 0.00 3.18
417 449 4.453751 AGGATCTAGAGGAGTACGTGAAC 58.546 47.826 0.00 0.00 0.00 3.18
433 465 7.182060 GGAGAATATTACTCTGAGGAGGATCT 58.818 42.308 9.85 5.40 43.46 2.75
500 532 2.204291 ACCCCATTCTCCTGCCCA 60.204 61.111 0.00 0.00 0.00 5.36
520 552 2.037367 CTCCTCCTCCCACCGTCA 59.963 66.667 0.00 0.00 0.00 4.35
550 585 1.174078 TTCCAGTGGCACTACGTCGA 61.174 55.000 21.59 8.02 0.00 4.20
556 591 2.171659 TCAACAACTTCCAGTGGCACTA 59.828 45.455 21.59 2.23 0.00 2.74
563 598 3.644966 TCAACCTCAACAACTTCCAGT 57.355 42.857 0.00 0.00 0.00 4.00
587 622 1.765314 CCATCCCACTCCCTACTTCTG 59.235 57.143 0.00 0.00 0.00 3.02
702 3206 0.603569 AAGAGCGACCGAACACTGAT 59.396 50.000 0.00 0.00 0.00 2.90
754 3293 1.283381 AAGCCCGGCCCAATAGGTAA 61.283 55.000 5.55 0.00 38.26 2.85
814 3353 4.024302 CGGACAGTGGGTCTTTAGTTTTTC 60.024 45.833 0.00 0.00 46.16 2.29
830 3394 2.114625 TCCTCGGACACGGACAGT 59.885 61.111 0.00 0.00 41.39 3.55
889 3469 3.090037 TGGAGGAAGAAGTAGAGTTCGG 58.910 50.000 0.00 0.00 0.00 4.30
965 3546 4.764823 TCGCACTAGATTTGGTGGATTTTT 59.235 37.500 0.00 0.00 36.40 1.94
966 3547 4.331968 TCGCACTAGATTTGGTGGATTTT 58.668 39.130 0.00 0.00 36.40 1.82
982 3563 2.163010 CCATTGCAGAATTTCTCGCACT 59.837 45.455 17.44 12.36 32.93 4.40
1045 3626 2.126580 CGACTCCCCAACGACGAC 60.127 66.667 0.00 0.00 0.00 4.34
1109 3705 4.180946 CCGGCTCTGTCTCGACCG 62.181 72.222 1.67 1.67 43.44 4.79
1198 3801 0.972983 CACTCCTCCTCCCACGACAT 60.973 60.000 0.00 0.00 0.00 3.06
1303 3906 3.409856 GGCGTAGTAGTCGGCGTA 58.590 61.111 6.85 0.00 43.07 4.42
1366 3969 4.783621 GGTGGCAGCAGCGATGGA 62.784 66.667 12.58 0.00 43.41 3.41
1436 4042 1.127567 AGCCTGCTCAACCACTACCA 61.128 55.000 0.00 0.00 0.00 3.25
1657 4592 3.550950 TGCGTACATGTCCAACAATTG 57.449 42.857 0.00 3.24 0.00 2.32
1757 4702 5.068067 GGTCACCAGGAGTAATTCTAGAGAC 59.932 48.000 0.00 0.00 0.00 3.36
1863 4822 5.241949 ACTTGACCAACGTTATAATGCCAAA 59.758 36.000 0.00 0.00 0.00 3.28
1877 4836 1.594331 GTCACCAGGACTTGACCAAC 58.406 55.000 0.00 0.00 43.46 3.77
1907 4869 4.454728 TGCAATCAAAGGCCACTTTATC 57.545 40.909 5.01 0.00 44.84 1.75
1978 6468 4.000988 ATTGGTGTCAATGACGGTAAGTC 58.999 43.478 9.00 0.00 41.62 3.01
1979 6469 3.478857 TTGGTGTCAATGACGGTAAGT 57.521 42.857 9.00 0.00 34.95 2.24
1980 6470 5.007626 CCATATTGGTGTCAATGACGGTAAG 59.992 44.000 9.00 0.00 42.93 2.34
1981 6471 4.878971 CCATATTGGTGTCAATGACGGTAA 59.121 41.667 9.00 3.95 42.93 2.85
1982 6472 4.447290 CCATATTGGTGTCAATGACGGTA 58.553 43.478 9.00 0.00 42.93 4.02
1983 6473 3.278574 CCATATTGGTGTCAATGACGGT 58.721 45.455 9.00 0.00 42.93 4.83
1984 6474 3.969117 CCATATTGGTGTCAATGACGG 57.031 47.619 9.00 0.00 42.93 4.79
1996 6486 6.048509 GGTAAATGAAGGCAAACCATATTGG 58.951 40.000 0.00 0.00 45.02 3.16
2104 6594 5.682862 GCATTCCATGTTTCTTACTATTGCG 59.317 40.000 0.00 0.00 0.00 4.85
2175 6665 9.171701 CTCACATAAGACTACGTAAATAAGCTC 57.828 37.037 0.00 0.00 0.00 4.09
2262 6757 4.817987 GCGACACGCGTATCATATAAAT 57.182 40.909 18.78 0.00 44.55 1.40
2482 7045 4.752101 CACGAGATCATTAAATCCCAGGAC 59.248 45.833 0.00 0.00 0.00 3.85
2503 7066 1.950909 TCGGTGTTTTGTGAATCCCAC 59.049 47.619 0.00 0.00 45.88 4.61


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

AutoCloner maintained by Alex Coulton.