Multiple sequence alignment - TraesCS6A01G177900

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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 TraesCS6A01G177900 chr6A 100.000 3536 0 0 1 3536 199457111 199460646 0.000000e+00 6530
1 TraesCS6A01G177900 chr6D 95.207 2775 116 13 2 2768 148081252 148078487 0.000000e+00 4372
2 TraesCS6A01G177900 chr6D 89.047 703 51 9 2841 3534 148077003 148076318 0.000000e+00 848
3 TraesCS6A01G177900 chr6B 93.691 2441 106 23 329 2751 260782702 260780292 0.000000e+00 3611
4 TraesCS6A01G177900 chr6B 84.203 690 76 19 2790 3463 260779884 260779212 1.070000e-179 640
5 TraesCS6A01G177900 chr6B 91.098 337 25 3 2 336 260820775 260820442 5.380000e-123 451
6 TraesCS6A01G177900 chr6B 92.429 317 19 3 22 336 260820290 260819977 6.960000e-122 448


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 TraesCS6A01G177900 chr6A 199457111 199460646 3535 False 6530.0 6530 100.0000 1 3536 1 chr6A.!!$F1 3535
1 TraesCS6A01G177900 chr6D 148076318 148081252 4934 True 2610.0 4372 92.1270 2 3534 2 chr6D.!!$R1 3532
2 TraesCS6A01G177900 chr6B 260779212 260782702 3490 True 2125.5 3611 88.9470 329 3463 2 chr6B.!!$R1 3134
3 TraesCS6A01G177900 chr6B 260819977 260820775 798 True 449.5 451 91.7635 2 336 2 chr6B.!!$R2 334

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
986 1460 0.039527 CACCCGCTTAAACCACTTGC 60.04 55.0 0.0 0.0 0.0 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2950 4984 0.107831 TGTCTTCGAGGGTGTTTGGG 59.892 55.0 0.0 0.0 0.0 4.12 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
98 565 9.890629 TTTGAGTTCATGTATTTGACTAGCTAT 57.109 29.630 0.00 0.00 0.00 2.97
102 570 8.924303 AGTTCATGTATTTGACTAGCTATGGTA 58.076 33.333 0.00 0.00 0.00 3.25
110 578 4.215908 TGACTAGCTATGGTAAGAGGGTG 58.784 47.826 0.00 0.00 0.00 4.61
131 599 3.160269 GCCCTAGGATCCATCAATTTGG 58.840 50.000 15.82 2.16 38.18 3.28
156 624 5.359756 TCCATAATTGAAGATGACTGGTCG 58.640 41.667 0.00 0.00 0.00 4.79
204 672 1.478471 CCACCAAGTGTCCATGTTCCA 60.478 52.381 0.00 0.00 0.00 3.53
265 733 0.392327 GAGACAAGGGCTCCTTCTGC 60.392 60.000 3.71 0.00 42.67 4.26
272 740 1.521616 GGCTCCTTCTGCCTCAGAG 59.478 63.158 0.00 0.00 46.38 3.35
302 770 6.365970 AGGTTCTCAAGTCAATGACTACAT 57.634 37.500 17.04 5.47 42.59 2.29
317 785 4.390603 TGACTACATCATGTTTAACCGTGC 59.609 41.667 0.00 0.00 29.99 5.34
354 822 3.999663 GCAGAAGGCGCATCTATAATCTT 59.000 43.478 10.83 0.00 0.00 2.40
426 894 6.546395 CATGCTCTAAATGACAACACCTAAC 58.454 40.000 0.00 0.00 0.00 2.34
431 899 7.519328 GCTCTAAATGACAACACCTAACGAAAA 60.519 37.037 0.00 0.00 0.00 2.29
475 943 0.314898 GACGTCCTATCGTGTCGTCG 60.315 60.000 3.51 0.00 44.21 5.12
580 1048 4.739716 GTGCGCCCATTCAAATTGTATAAG 59.260 41.667 4.18 0.00 0.00 1.73
603 1071 3.432933 GGCGTGTACCTTTCAATAACGAA 59.567 43.478 0.00 0.00 0.00 3.85
607 1075 5.613142 CGTGTACCTTTCAATAACGAACACC 60.613 44.000 0.00 0.00 0.00 4.16
610 1078 5.432885 ACCTTTCAATAACGAACACCAAG 57.567 39.130 0.00 0.00 0.00 3.61
624 1092 3.088532 ACACCAAGCTCACAAAAGACAA 58.911 40.909 0.00 0.00 0.00 3.18
634 1102 1.597663 ACAAAAGACAACCGCTCTTCG 59.402 47.619 0.00 0.00 38.08 3.79
787 1256 0.988063 AGAAGGTGGAGAAGAAGGCC 59.012 55.000 0.00 0.00 0.00 5.19
851 1324 3.787001 GAGGGTGAGGAAGCGGGG 61.787 72.222 0.00 0.00 0.00 5.73
859 1332 3.081409 GGAAGCGGGGGCAGAGTA 61.081 66.667 0.00 0.00 0.00 2.59
936 1410 5.959618 AGTGCCTTTTACTTGACCATTAC 57.040 39.130 0.00 0.00 0.00 1.89
986 1460 0.039527 CACCCGCTTAAACCACTTGC 60.040 55.000 0.00 0.00 0.00 4.01
990 1464 3.767287 GCTTAAACCACTTGCGACC 57.233 52.632 0.00 0.00 0.00 4.79
1026 1500 2.203408 TCCACAATGGCGCCAACA 60.203 55.556 36.33 11.20 37.47 3.33
1089 1563 2.579738 GTCTTGGTCCCTCTCGCC 59.420 66.667 0.00 0.00 0.00 5.54
1323 1797 3.254654 ATGATCGCCGACAACGCG 61.255 61.111 3.53 3.53 39.12 6.01
1347 1821 1.296715 GCTCCCCTTCTTTCTCGCA 59.703 57.895 0.00 0.00 0.00 5.10
1445 1919 1.174078 TGTAACTCGTGGACAGCCGA 61.174 55.000 0.00 0.00 36.79 5.54
1491 1965 3.170362 CTGTTCTTCCAGGGGCCA 58.830 61.111 4.39 0.00 0.00 5.36
1698 2172 3.192922 GCCATGCGTACGTCCCAC 61.193 66.667 17.90 0.00 0.00 4.61
1731 2205 0.900647 ACACCTTCCTGGACCTCGAG 60.901 60.000 5.13 5.13 39.71 4.04
1823 2297 4.778415 CCGTGACGGCGAGGACAG 62.778 72.222 16.62 0.00 41.17 3.51
1825 2299 3.371063 GTGACGGCGAGGACAGGA 61.371 66.667 16.62 0.00 0.00 3.86
2053 2527 0.315568 GGCTCGTATGTGGCTAGAGG 59.684 60.000 0.00 0.00 0.00 3.69
2054 2528 0.319125 GCTCGTATGTGGCTAGAGGC 60.319 60.000 0.00 0.00 41.50 4.70
2181 2655 1.536943 GGAACTCGGTGCTGGAGTCT 61.537 60.000 5.56 0.00 43.66 3.24
2266 2740 3.680786 CTGTGGACGTGCTCGGGA 61.681 66.667 13.32 0.00 41.85 5.14
2379 2853 1.614525 AGAGCTCATGCAGGGTGGA 60.615 57.895 17.77 0.00 42.74 4.02
2391 2865 3.151022 GGTGGAGAGGAGGCCGAG 61.151 72.222 0.00 0.00 0.00 4.63
2468 2942 0.919300 GGAGGCGATTCGTACGAAAC 59.081 55.000 32.12 27.62 37.69 2.78
2565 3040 7.461107 GTGAATATTGCACAATTGTACGTAGT 58.539 34.615 11.53 2.46 39.40 2.73
2628 3107 4.029529 CGTAATCATGTCGCTCGATGTATG 59.970 45.833 0.00 2.24 0.00 2.39
2702 3193 3.854666 ACACGATGGAGAGATGTTTCAG 58.145 45.455 0.00 0.00 0.00 3.02
2706 3197 5.233902 CACGATGGAGAGATGTTTCAGAATC 59.766 44.000 0.00 0.00 0.00 2.52
2707 3198 5.105187 ACGATGGAGAGATGTTTCAGAATCA 60.105 40.000 0.00 0.00 0.00 2.57
2708 3199 5.990386 CGATGGAGAGATGTTTCAGAATCAT 59.010 40.000 6.44 6.44 0.00 2.45
2709 3200 6.145858 CGATGGAGAGATGTTTCAGAATCATC 59.854 42.308 20.27 20.27 38.43 2.92
2738 3229 4.537135 AAAGAGTCAAGACGGCTGATAA 57.463 40.909 0.00 0.00 36.20 1.75
2743 3236 2.093783 GTCAAGACGGCTGATAAAACGG 59.906 50.000 0.00 0.00 0.00 4.44
2797 4831 0.530650 AGACTGCAACGTCACCACTG 60.531 55.000 8.62 0.00 36.38 3.66
2798 4832 2.105960 GACTGCAACGTCACCACTGC 62.106 60.000 0.71 0.71 34.11 4.40
2801 4835 2.186826 GCAACGTCACCACTGCCTT 61.187 57.895 0.00 0.00 0.00 4.35
2806 4840 3.497115 TCACCACTGCCTTGCCCA 61.497 61.111 0.00 0.00 0.00 5.36
2807 4841 2.521465 CACCACTGCCTTGCCCAA 60.521 61.111 0.00 0.00 0.00 4.12
2823 4857 1.280998 CCCAATGAACCGAACCTAGGT 59.719 52.381 9.21 9.21 45.29 3.08
2831 4865 1.356527 CCGAACCTAGGTTTTCGCCG 61.357 60.000 27.72 23.46 42.62 6.46
2832 4866 1.792301 GAACCTAGGTTTTCGCCGC 59.208 57.895 27.72 9.88 38.60 6.53
2865 4899 3.385111 GGAAATGGACTAGACCGAGACAT 59.615 47.826 6.76 0.00 0.00 3.06
2866 4900 4.141914 GGAAATGGACTAGACCGAGACATT 60.142 45.833 6.76 0.00 32.75 2.71
2941 4975 1.734465 CGCGAGGCAGAAATTTCTTCT 59.266 47.619 18.16 17.14 34.74 2.85
2950 4984 3.992427 CAGAAATTTCTTCTTGGCCAAGC 59.008 43.478 36.24 20.56 35.41 4.01
2963 4997 2.268076 CCAAGCCCAAACACCCTCG 61.268 63.158 0.00 0.00 0.00 4.63
2994 5028 2.364324 AGAGCGACACAAAACTGGAGTA 59.636 45.455 0.00 0.00 0.00 2.59
2996 5030 2.364324 AGCGACACAAAACTGGAGTAGA 59.636 45.455 0.00 0.00 0.00 2.59
3016 5050 2.057922 AGGAGGAAAAGTGCCTTCTCA 58.942 47.619 0.00 0.00 36.63 3.27
3031 5065 4.141620 GCCTTCTCAGACCATTGATTAGGA 60.142 45.833 0.00 0.00 33.03 2.94
3042 5076 5.614402 ACCATTGATTAGGAAGGAGATCCAT 59.386 40.000 0.92 0.00 42.27 3.41
3081 5115 2.032681 GGAGCACCGACAAGGCTT 59.967 61.111 0.00 0.00 46.52 4.35
3084 5118 1.362406 GAGCACCGACAAGGCTTAGC 61.362 60.000 0.00 0.00 46.52 3.09
3197 5239 1.374190 GAGATCCAGGCGCCATCAT 59.626 57.895 31.54 16.72 0.00 2.45
3214 5256 6.903479 CGCCATCATGATTGACGAATATATTG 59.097 38.462 10.85 0.00 33.85 1.90
3224 5266 9.616634 GATTGACGAATATATTGATGCATTTGT 57.383 29.630 0.00 0.00 0.00 2.83
3275 5318 4.445448 CCATGGGTTTGAAAAATGTTCCCA 60.445 41.667 2.85 4.47 45.73 4.37
3286 5329 8.436046 TGAAAAATGTTCCCAGATTTTGAAAG 57.564 30.769 0.00 0.00 36.31 2.62
3304 5347 7.789202 TTGAAAGAAATGGGTCATGGATTTA 57.211 32.000 0.00 0.00 0.00 1.40
3368 5414 8.672214 AAAAAGTTCACACATTTGAAAAATGC 57.328 26.923 11.62 0.00 37.24 3.56
3370 5416 6.592798 AGTTCACACATTTGAAAAATGCTG 57.407 33.333 11.62 11.14 37.24 4.41
3383 5429 9.903682 TTTGAAAAATGCTGTCAATTTGAAAAA 57.096 22.222 0.00 0.00 31.66 1.94
3452 5498 7.948137 TGAAAAACACGAATTTGAGAAAAGTG 58.052 30.769 0.00 0.00 33.56 3.16
3456 5502 6.189677 ACACGAATTTGAGAAAAGTGTTCA 57.810 33.333 0.00 0.00 35.55 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.470709 CACCACAAGATCAACACTCAGT 58.529 45.455 0.00 0.00 0.00 3.41
110 578 3.160269 CCAAATTGATGGATCCTAGGGC 58.840 50.000 14.23 1.10 43.54 5.19
131 599 6.146837 CGACCAGTCATCTTCAATTATGGATC 59.853 42.308 0.00 0.00 0.00 3.36
141 609 0.532573 GGAGCGACCAGTCATCTTCA 59.467 55.000 0.00 0.00 38.79 3.02
156 624 0.390472 CTTGAGTTGGTCCGAGGAGC 60.390 60.000 13.90 13.90 42.37 4.70
204 672 1.351350 GACAAGGTTAGTTGCTCCCCT 59.649 52.381 0.00 0.00 0.00 4.79
265 733 4.082845 TGAGAACCTACAAGTCTCTGAGG 58.917 47.826 4.59 0.00 0.00 3.86
296 764 4.320023 TGCACGGTTAAACATGATGTAGT 58.680 39.130 0.00 0.00 0.00 2.73
302 770 2.811431 CTCCTTGCACGGTTAAACATGA 59.189 45.455 9.36 0.00 0.00 3.07
317 785 3.806521 CCTTCTGCATATTCGACTCCTTG 59.193 47.826 0.00 0.00 0.00 3.61
372 840 7.452880 TGTGCTTCAGCTACAAGAAATTAAT 57.547 32.000 8.48 0.00 42.66 1.40
426 894 4.260656 GTGCATCTAATTGAGCGTTTTTCG 59.739 41.667 0.00 0.00 43.12 3.46
431 899 3.338249 ACTGTGCATCTAATTGAGCGTT 58.662 40.909 0.00 0.00 0.00 4.84
475 943 7.208225 AGATTAGACTTCAAGCCAAGAAAAC 57.792 36.000 0.00 0.00 0.00 2.43
580 1048 2.094734 CGTTATTGAAAGGTACACGCCC 59.905 50.000 0.00 0.00 0.00 6.13
603 1071 2.722094 TGTCTTTTGTGAGCTTGGTGT 58.278 42.857 0.00 0.00 0.00 4.16
607 1075 2.719798 CGGTTGTCTTTTGTGAGCTTG 58.280 47.619 0.00 0.00 0.00 4.01
610 1078 0.663153 AGCGGTTGTCTTTTGTGAGC 59.337 50.000 0.00 0.00 0.00 4.26
624 1092 4.579340 TCAGAATTCTATACGAAGAGCGGT 59.421 41.667 7.86 0.00 46.49 5.68
851 1324 1.204146 TCCCACATTCCTACTCTGCC 58.796 55.000 0.00 0.00 0.00 4.85
859 1332 0.394352 GCAACGGATCCCACATTCCT 60.394 55.000 6.06 0.00 0.00 3.36
936 1410 6.342111 GTCTGAAGGAAGAGTTGGGTATTAG 58.658 44.000 0.00 0.00 0.00 1.73
986 1460 0.243907 ACTCATCAACGTCCTGGTCG 59.756 55.000 11.71 11.71 0.00 4.79
990 1464 0.667487 ACGCACTCATCAACGTCCTG 60.667 55.000 0.00 0.00 32.37 3.86
1092 1566 2.111878 GGGATGAGATGGCCGTGG 59.888 66.667 0.00 0.00 0.00 4.94
1281 1755 2.847234 TTCTGGCAGTCCGGTGGT 60.847 61.111 15.27 0.00 39.81 4.16
1323 1797 1.064832 AGAAAGAAGGGGAGCATCTGC 60.065 52.381 0.00 0.00 42.49 4.26
1491 1965 0.814457 AGAGCGAGAAGAAGCACGAT 59.186 50.000 0.00 0.00 35.48 3.73
1731 2205 2.109126 GCATGCCACGGACTTCTCC 61.109 63.158 6.36 0.00 0.00 3.71
1734 2208 1.421410 CGTAGCATGCCACGGACTTC 61.421 60.000 27.68 0.00 34.57 3.01
1746 2220 1.739049 GAGAGCAGCCTCGTAGCAT 59.261 57.895 2.48 0.00 43.05 3.79
1929 2403 3.551496 CTTGGGGAGCTTCCGTGCA 62.551 63.158 4.51 0.00 37.43 4.57
2379 2853 2.600731 CTCTCCTCGGCCTCCTCT 59.399 66.667 0.00 0.00 0.00 3.69
2391 2865 1.764454 GGCCTTCCTCCTCCTCTCC 60.764 68.421 0.00 0.00 0.00 3.71
2494 2968 3.726517 CTTTGCCTCCACGTGCCG 61.727 66.667 10.91 2.42 0.00 5.69
2628 3107 2.713976 CGCTTCATTCACACGAACAAAC 59.286 45.455 0.00 0.00 32.81 2.93
2702 3193 9.388506 TCTTGACTCTTTTTCTATGGATGATTC 57.611 33.333 0.00 0.00 0.00 2.52
2706 3197 6.036517 CCGTCTTGACTCTTTTTCTATGGATG 59.963 42.308 0.00 0.00 0.00 3.51
2707 3198 6.109359 CCGTCTTGACTCTTTTTCTATGGAT 58.891 40.000 0.00 0.00 0.00 3.41
2708 3199 5.479306 CCGTCTTGACTCTTTTTCTATGGA 58.521 41.667 0.00 0.00 0.00 3.41
2709 3200 4.093556 GCCGTCTTGACTCTTTTTCTATGG 59.906 45.833 0.00 0.00 0.00 2.74
2738 3229 2.980568 TCTATCCATCGTTTGCCGTTT 58.019 42.857 0.00 0.00 37.94 3.60
2743 3236 2.030457 CGTGGTTCTATCCATCGTTTGC 59.970 50.000 0.00 0.00 39.81 3.68
2797 4831 1.531739 TTCGGTTCATTGGGCAAGGC 61.532 55.000 0.00 0.00 0.00 4.35
2798 4832 0.243636 GTTCGGTTCATTGGGCAAGG 59.756 55.000 0.00 0.00 0.00 3.61
2801 4835 0.693622 TAGGTTCGGTTCATTGGGCA 59.306 50.000 0.00 0.00 0.00 5.36
2806 4840 3.749609 CGAAAACCTAGGTTCGGTTCATT 59.250 43.478 27.24 15.62 43.66 2.57
2807 4841 3.332034 CGAAAACCTAGGTTCGGTTCAT 58.668 45.455 27.24 7.29 43.66 2.57
2823 4857 0.108089 TACCTATGCAGCGGCGAAAA 60.108 50.000 12.98 0.00 45.35 2.29
2827 4861 2.356313 CCTACCTATGCAGCGGCG 60.356 66.667 0.51 0.51 45.35 6.46
2828 4862 0.179056 TTTCCTACCTATGCAGCGGC 60.179 55.000 0.31 0.31 41.68 6.53
2831 4865 3.142174 GTCCATTTCCTACCTATGCAGC 58.858 50.000 0.00 0.00 0.00 5.25
2832 4866 4.696479 AGTCCATTTCCTACCTATGCAG 57.304 45.455 0.00 0.00 0.00 4.41
2950 4984 0.107831 TGTCTTCGAGGGTGTTTGGG 59.892 55.000 0.00 0.00 0.00 4.12
2963 4997 0.787183 GTGTCGCTCTTGCTGTCTTC 59.213 55.000 0.00 0.00 36.97 2.87
3016 5050 5.309282 GGATCTCCTTCCTAATCAATGGTCT 59.691 44.000 0.00 0.00 32.68 3.85
3042 5076 2.131709 CCTTGTCGGCGGGGAGATA 61.132 63.158 7.21 0.00 0.00 1.98
3081 5115 2.679996 TGGTGCTGCTCCTCGCTA 60.680 61.111 20.19 0.00 40.11 4.26
3084 5118 2.183811 CTCTGGTGCTGCTCCTCG 59.816 66.667 20.19 11.97 0.00 4.63
3128 5170 0.185175 TGAGTATAGGGAGCTGGCGA 59.815 55.000 0.00 0.00 0.00 5.54
3197 5239 9.615295 CAAATGCATCAATATATTCGTCAATCA 57.385 29.630 0.00 0.00 0.00 2.57
3275 5318 6.497954 TCCATGACCCATTTCTTTCAAAATCT 59.502 34.615 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.