Multiple sequence alignment - TraesCS6A01G184500

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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 TraesCS6A01G184500 chr6A 100.000 3532 0 0 1 3532 215526836 215530367 0.000000e+00 6523.0
1 TraesCS6A01G184500 chr6B 91.140 3578 199 53 1 3532 280051054 280047549 0.000000e+00 4743.0
2 TraesCS6A01G184500 chr6B 82.222 90 11 5 586 673 657948048 657947962 4.890000e-09 73.1
3 TraesCS6A01G184500 chr6D 94.517 2079 53 19 713 2770 157168505 157166467 0.000000e+00 3151.0
4 TraesCS6A01G184500 chr6D 87.549 506 10 8 3051 3532 157166171 157165695 1.440000e-148 536.0
5 TraesCS6A01G184500 chr6D 93.898 295 3 4 2741 3020 157166465 157166171 7.000000e-117 431.0
6 TraesCS6A01G184500 chr7D 76.224 715 151 16 1349 2054 459873478 459872774 9.320000e-96 361.0
7 TraesCS6A01G184500 chr7B 75.838 716 152 18 1349 2054 482175897 482175193 9.390000e-91 344.0
8 TraesCS6A01G184500 chr7A 75.770 714 154 17 1350 2054 539652067 539652770 3.380000e-90 342.0
9 TraesCS6A01G184500 chrUn 98.077 52 1 0 586 637 300921614 300921665 1.350000e-14 91.6
10 TraesCS6A01G184500 chr2B 98.077 52 1 0 586 637 81550492 81550543 1.350000e-14 91.6
11 TraesCS6A01G184500 chr2B 84.783 92 5 7 590 679 12993636 12993552 2.260000e-12 84.2
12 TraesCS6A01G184500 chr3B 84.524 84 11 2 589 672 428195456 428195375 8.130000e-12 82.4
13 TraesCS6A01G184500 chr3A 82.979 94 9 6 584 675 668876204 668876292 1.050000e-10 78.7
14 TraesCS6A01G184500 chr1B 82.609 92 13 3 584 674 100643236 100643147 1.050000e-10 78.7
15 TraesCS6A01G184500 chr1B 79.798 99 15 5 195 290 28761979 28762075 2.280000e-07 67.6
16 TraesCS6A01G184500 chr3D 82.418 91 12 4 584 672 481916108 481916196 3.780000e-10 76.8


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 TraesCS6A01G184500 chr6A 215526836 215530367 3531 False 6523.000000 6523 100.000 1 3532 1 chr6A.!!$F1 3531
1 TraesCS6A01G184500 chr6B 280047549 280051054 3505 True 4743.000000 4743 91.140 1 3532 1 chr6B.!!$R1 3531
2 TraesCS6A01G184500 chr6D 157165695 157168505 2810 True 1372.666667 3151 91.988 713 3532 3 chr6D.!!$R1 2819
3 TraesCS6A01G184500 chr7D 459872774 459873478 704 True 361.000000 361 76.224 1349 2054 1 chr7D.!!$R1 705
4 TraesCS6A01G184500 chr7B 482175193 482175897 704 True 344.000000 344 75.838 1349 2054 1 chr7B.!!$R1 705
5 TraesCS6A01G184500 chr7A 539652067 539652770 703 False 342.000000 342 75.770 1350 2054 1 chr7A.!!$F1 704

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
634 643 0.246635 GGGTGAGTGTATGCTCGTGT 59.753 55.0 0.00 0.0 38.28 4.49 F
1500 1531 0.100146 GATCTACACCGTGACCGACC 59.900 60.0 5.28 0.0 35.63 4.79 F
2214 2249 0.255318 GGTACGTCCTCTCCTCCTCA 59.745 60.0 0.00 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2339 2381 0.393077 ACACCCAGTTCTTCCACTCG 59.607 55.0 0.00 0.0 0.0 4.18 R
2369 2411 0.852777 CGTTTATCATCAGGTCGCCG 59.147 55.0 0.00 0.0 0.0 6.46 R
3494 3618 1.028905 GCCAATTATGCGCAACCCTA 58.971 50.0 17.11 0.0 0.0 3.53 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
46 47 3.704061 AGAAGAGGAAGAAGAAGGATCGG 59.296 47.826 0.00 0.00 0.00 4.18
49 50 0.460311 GGAAGAAGAAGGATCGGCGA 59.540 55.000 13.87 13.87 0.00 5.54
89 90 1.080705 GTGTCGCTTACCTGCTCGT 60.081 57.895 0.00 0.00 0.00 4.18
128 129 1.671901 GACAGAGAGCTCGAAGGGGG 61.672 65.000 8.37 0.00 34.09 5.40
178 179 0.756903 TGGACGAGGGCTAAATAGGC 59.243 55.000 5.49 5.49 47.00 3.93
201 202 1.808411 TCAAATTGGCGAGAGGTGAC 58.192 50.000 0.00 0.00 0.00 3.67
214 215 1.566231 GAGGTGACCCAATTCCTCCAT 59.434 52.381 0.00 0.00 40.14 3.41
215 216 1.566231 AGGTGACCCAATTCCTCCATC 59.434 52.381 0.00 0.00 0.00 3.51
304 305 1.898574 CCCTTGCAAGCCGAACACT 60.899 57.895 21.43 0.00 0.00 3.55
321 322 4.078639 ACACTTGGTTGAGAGGAAAGAG 57.921 45.455 0.00 0.00 0.00 2.85
324 325 3.181450 ACTTGGTTGAGAGGAAAGAGTGG 60.181 47.826 0.00 0.00 0.00 4.00
332 333 2.507471 AGAGGAAAGAGTGGGCCAATAG 59.493 50.000 8.40 0.00 0.00 1.73
354 355 3.274281 TGGATATAGGTCAGGCATCCA 57.726 47.619 0.00 0.00 42.16 3.41
386 387 1.490910 GCCACATTCCTAGGCCTAACT 59.509 52.381 14.85 0.00 42.58 2.24
390 391 2.436173 ACATTCCTAGGCCTAACTGAGC 59.564 50.000 14.85 0.00 0.00 4.26
412 413 3.119673 CCATACGCAAGCAACCAAACATA 60.120 43.478 0.00 0.00 45.62 2.29
577 578 5.981088 TTGCTTGTCATCAATACCACAAT 57.019 34.783 0.00 0.00 32.82 2.71
581 582 2.942376 TGTCATCAATACCACAATCCGC 59.058 45.455 0.00 0.00 0.00 5.54
615 624 1.012671 GCGTGCGTGCGTTTATAGG 60.013 57.895 3.11 0.00 0.00 2.57
617 626 1.758319 CGTGCGTGCGTTTATAGGGG 61.758 60.000 0.00 0.00 0.00 4.79
634 643 0.246635 GGGTGAGTGTATGCTCGTGT 59.753 55.000 0.00 0.00 38.28 4.49
638 647 2.535984 GTGAGTGTATGCTCGTGTATGC 59.464 50.000 0.00 0.00 38.28 3.14
657 666 2.224670 TGCGAGGGACTTTGGTTGTAAT 60.225 45.455 0.00 0.00 41.55 1.89
671 680 9.796120 CTTTGGTTGTAATGTGTTTAGAAGAAA 57.204 29.630 0.00 0.00 0.00 2.52
733 744 1.098050 GGCAGAATTCATGCGTTCCT 58.902 50.000 17.79 0.00 44.80 3.36
865 876 0.529378 AATACCACCTCGACGGTCAC 59.471 55.000 9.10 0.00 44.93 3.67
976 991 2.350772 CGAGCTACCCAAACAAAGCAAG 60.351 50.000 0.00 0.00 37.44 4.01
1000 1015 7.063593 AGCATACCACAAGATAGAGAGTTAGA 58.936 38.462 0.00 0.00 0.00 2.10
1122 1137 1.044790 CGTACAACCCCGACCCCTAT 61.045 60.000 0.00 0.00 0.00 2.57
1128 1143 2.571216 CCCCGACCCCTATAGCGTG 61.571 68.421 0.00 0.00 0.00 5.34
1279 1299 1.066787 TGGCATTGGCATGAACATGTG 60.067 47.619 9.11 7.46 43.71 3.21
1489 1520 2.911484 CCTCAAGGGCAAGATCTACAC 58.089 52.381 0.00 0.00 0.00 2.90
1500 1531 0.100146 GATCTACACCGTGACCGACC 59.900 60.000 5.28 0.00 35.63 4.79
1744 1775 3.353029 CCACGTGCACGGCATCAA 61.353 61.111 39.21 0.00 41.91 2.57
1745 1776 2.174107 CACGTGCACGGCATCAAG 59.826 61.111 39.21 17.62 41.91 3.02
1887 1918 0.813610 TAATTGCGAGGACGGCATGG 60.814 55.000 0.00 0.00 40.15 3.66
1889 1920 2.819984 ATTGCGAGGACGGCATGGTT 62.820 55.000 0.00 0.00 40.15 3.67
2212 2247 2.712640 AGGTACGTCCTCTCCTCCT 58.287 57.895 0.00 0.00 44.42 3.69
2213 2248 0.547553 AGGTACGTCCTCTCCTCCTC 59.452 60.000 0.00 0.00 44.42 3.71
2214 2249 0.255318 GGTACGTCCTCTCCTCCTCA 59.745 60.000 0.00 0.00 0.00 3.86
2283 2325 0.707822 ATTCAAATTCAAACGCGCGC 59.292 45.000 32.58 23.91 0.00 6.86
2311 2353 0.333993 ATTGAATGGCTGGAGCAGGT 59.666 50.000 0.20 0.00 44.36 4.00
2324 2366 3.414700 CAGGTGACCAAGCGCGAC 61.415 66.667 12.10 0.04 0.00 5.19
2339 2381 4.549516 GACTACGCGCCCGAGTCC 62.550 72.222 5.73 3.40 36.51 3.85
2369 2411 1.120530 ACTGGGTGTGGATATCGGAC 58.879 55.000 0.00 0.00 0.00 4.79
2568 2615 2.735772 ATACCTGCCAGGCGGAGTG 61.736 63.158 23.25 7.69 39.63 3.51
2716 2764 1.306654 AATGTAGGAGGGTGGCCGA 60.307 57.895 0.00 0.00 0.00 5.54
2739 2816 1.750206 TCATCAGTCTGCTGCTCTCTC 59.250 52.381 0.00 0.00 42.29 3.20
2790 2880 7.275920 TCACTACTTGCTTTTCTTCTTCTTCT 58.724 34.615 0.00 0.00 0.00 2.85
2878 2970 5.865552 TGTACTGTAACCGCTCTTGTTTATC 59.134 40.000 0.00 0.00 0.00 1.75
2880 2972 5.488341 ACTGTAACCGCTCTTGTTTATCAT 58.512 37.500 0.00 0.00 0.00 2.45
2881 2973 5.938125 ACTGTAACCGCTCTTGTTTATCATT 59.062 36.000 0.00 0.00 0.00 2.57
2925 3019 4.424061 TCCATGTTCAGAAAGAAATGCG 57.576 40.909 0.00 0.00 38.13 4.73
3033 3127 7.186804 AGACAAAATGAACACTCAACTAAACG 58.813 34.615 0.00 0.00 34.49 3.60
3039 3133 4.802039 TGAACACTCAACTAAACGAGTCAC 59.198 41.667 0.00 0.00 40.50 3.67
3163 3281 6.423905 CGGAAGACAAGAAAAGTTGATCACTA 59.576 38.462 0.00 0.00 32.94 2.74
3259 3377 4.021192 TCCCTGCATCAATTTCCTGAAAAC 60.021 41.667 0.00 0.00 33.56 2.43
3353 3476 5.370584 TGATGATGGGGTCAAGAGATACAAT 59.629 40.000 0.00 0.00 40.97 2.71
3382 3505 8.534333 TTTACTTACAAAGCATGTAGAGTCAG 57.466 34.615 14.54 7.96 43.63 3.51
3442 3566 9.717942 AGTAAGGTAATTGATATCTCTGCATTC 57.282 33.333 3.98 0.00 0.00 2.67
3494 3618 7.482169 TGTCACAAGGAGTTCAGACTATAAT 57.518 36.000 0.00 0.00 35.88 1.28
3507 3631 5.479027 TCAGACTATAATAGGGTTGCGCATA 59.521 40.000 12.75 0.00 0.00 3.14
3513 3637 1.028905 TAGGGTTGCGCATAATTGGC 58.971 50.000 12.75 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 5.026790 CCTTCTTCTTCCTCTTCTTCCCTA 58.973 45.833 0.00 0.00 0.00 3.53
79 80 0.607217 TCTTCACCGACGAGCAGGTA 60.607 55.000 0.00 0.00 39.00 3.08
89 90 1.140161 CGGGCGTATTCTTCACCGA 59.860 57.895 0.00 0.00 43.69 4.69
128 129 2.440247 CCCCGCCACCATTTCCTC 60.440 66.667 0.00 0.00 0.00 3.71
178 179 0.940126 CCTCTCGCCAATTTGATCGG 59.060 55.000 0.00 0.00 0.00 4.18
201 202 2.664402 AATCGGATGGAGGAATTGGG 57.336 50.000 0.00 0.00 0.00 4.12
214 215 1.803334 CGTGTCCCTGAAAAATCGGA 58.197 50.000 0.00 0.00 0.00 4.55
215 216 0.168128 GCGTGTCCCTGAAAAATCGG 59.832 55.000 0.00 0.00 0.00 4.18
251 252 1.276820 CGAGCTCATGCGAGATGCTC 61.277 60.000 15.40 14.11 46.63 4.26
253 254 2.308769 CCGAGCTCATGCGAGATGC 61.309 63.158 15.40 0.00 42.34 3.91
288 289 0.318107 CCAAGTGTTCGGCTTGCAAG 60.318 55.000 22.44 22.44 41.27 4.01
304 305 2.106511 CCCACTCTTTCCTCTCAACCAA 59.893 50.000 0.00 0.00 0.00 3.67
332 333 3.327757 TGGATGCCTGACCTATATCCAAC 59.672 47.826 0.00 0.00 43.02 3.77
383 384 0.321564 TGCTTGCGTATGGCTCAGTT 60.322 50.000 1.51 0.00 44.05 3.16
386 387 1.305219 GGTTGCTTGCGTATGGCTCA 61.305 55.000 1.51 0.00 44.05 4.26
390 391 1.000827 TGTTTGGTTGCTTGCGTATGG 60.001 47.619 0.00 0.00 0.00 2.74
396 397 1.618343 AGGGTATGTTTGGTTGCTTGC 59.382 47.619 0.00 0.00 0.00 4.01
412 413 7.235804 TGCTTTTTGTAACCTTATCTTAGGGT 58.764 34.615 0.00 0.00 40.24 4.34
498 499 8.245195 ACTAAGTTTTATTCCCAAGAGCAAAA 57.755 30.769 0.00 0.00 0.00 2.44
577 578 0.325860 ACACCCTACCCTATTGCGGA 60.326 55.000 0.00 0.00 0.00 5.54
581 582 0.539986 ACGCACACCCTACCCTATTG 59.460 55.000 0.00 0.00 0.00 1.90
615 624 0.246635 ACACGAGCATACACTCACCC 59.753 55.000 0.00 0.00 36.42 4.61
617 626 2.535984 GCATACACGAGCATACACTCAC 59.464 50.000 0.00 0.00 36.42 3.51
634 643 1.349688 ACAACCAAAGTCCCTCGCATA 59.650 47.619 0.00 0.00 0.00 3.14
638 647 3.188460 CACATTACAACCAAAGTCCCTCG 59.812 47.826 0.00 0.00 0.00 4.63
687 698 3.784338 ACGTTCGTTAGGTTGACTCAAA 58.216 40.909 0.00 0.00 0.00 2.69
695 706 2.224784 GCCAATGAACGTTCGTTAGGTT 59.775 45.455 29.88 10.24 37.54 3.50
699 710 2.756829 TCTGCCAATGAACGTTCGTTA 58.243 42.857 29.88 17.06 34.81 3.18
733 744 1.625818 GGAGAGGAGAGCCAAGACAAA 59.374 52.381 0.00 0.00 36.29 2.83
865 876 3.666345 AGGCCTATATACGTAGGAGGG 57.334 52.381 1.29 11.00 43.27 4.30
955 970 1.234821 TGCTTTGTTTGGGTAGCTCG 58.765 50.000 0.00 0.00 34.77 5.03
976 991 7.278461 TCTAACTCTCTATCTTGTGGTATGC 57.722 40.000 0.00 0.00 0.00 3.14
1000 1015 0.765903 AGGCTCCGATCCATGGACAT 60.766 55.000 18.99 0.80 0.00 3.06
1082 1097 3.484547 GGTTGGCGCTCGTTACGG 61.485 66.667 7.64 0.00 0.00 4.02
1083 1098 3.484547 GGGTTGGCGCTCGTTACG 61.485 66.667 7.64 0.00 0.00 3.18
1085 1100 4.745751 CCGGGTTGGCGCTCGTTA 62.746 66.667 7.64 0.00 0.00 3.18
1189 1207 7.454380 ACTCTACTCCGTATATACTGTACTCCT 59.546 40.741 11.05 0.00 0.00 3.69
1190 1208 7.610865 ACTCTACTCCGTATATACTGTACTCC 58.389 42.308 11.05 0.00 0.00 3.85
1191 1209 9.787532 CTACTCTACTCCGTATATACTGTACTC 57.212 40.741 11.05 0.00 0.00 2.59
1192 1210 9.308000 ACTACTCTACTCCGTATATACTGTACT 57.692 37.037 11.05 0.00 0.00 2.73
1193 1211 9.921637 AACTACTCTACTCCGTATATACTGTAC 57.078 37.037 11.05 0.00 0.00 2.90
1195 1213 9.921637 GTAACTACTCTACTCCGTATATACTGT 57.078 37.037 11.05 9.11 0.00 3.55
1222 1240 3.124128 CACTCACTCGCTACAACGTACTA 59.876 47.826 0.00 0.00 0.00 1.82
1223 1241 2.095869 CACTCACTCGCTACAACGTACT 60.096 50.000 0.00 0.00 0.00 2.73
1224 1242 2.240040 CACTCACTCGCTACAACGTAC 58.760 52.381 0.00 0.00 0.00 3.67
1279 1299 4.357947 TCGACCTGCACGCTCACC 62.358 66.667 0.00 0.00 0.00 4.02
1325 1353 3.807622 TGTACTTTGCCTTCTTCGACTTG 59.192 43.478 0.00 0.00 0.00 3.16
1500 1531 1.068474 GTGAAGTCATCGTCGTTGGG 58.932 55.000 3.59 0.00 0.00 4.12
1887 1918 1.852067 GACATGGCCACCACGTCAAC 61.852 60.000 8.16 0.00 44.82 3.18
1889 1920 2.031919 GACATGGCCACCACGTCA 59.968 61.111 8.16 0.00 44.82 4.35
1971 2002 1.446272 CCTCCGGCTTCTTGTCGTC 60.446 63.158 0.00 0.00 43.10 4.20
1972 2003 1.906824 TCCTCCGGCTTCTTGTCGT 60.907 57.895 0.00 0.00 43.10 4.34
2211 2246 4.852134 CATAGATGGAGTGAGGAGTGAG 57.148 50.000 0.00 0.00 0.00 3.51
2239 2274 2.560542 TGATTTGATTTGAACCGGTGGG 59.439 45.455 8.52 0.00 40.11 4.61
2242 2277 5.720371 TTGATGATTTGATTTGAACCGGT 57.280 34.783 0.00 0.00 0.00 5.28
2243 2278 6.812656 TGAATTGATGATTTGATTTGAACCGG 59.187 34.615 0.00 0.00 0.00 5.28
2283 2325 3.012888 CCATTCAATTCGCGCGCG 61.013 61.111 44.84 44.84 41.35 6.86
2311 2353 2.126618 CGTAGTCGCGCTTGGTCA 60.127 61.111 5.56 0.00 0.00 4.02
2331 2373 1.248785 TTCTTCCACTCGGACTCGGG 61.249 60.000 0.00 0.00 42.67 5.14
2339 2381 0.393077 ACACCCAGTTCTTCCACTCG 59.607 55.000 0.00 0.00 0.00 4.18
2369 2411 0.852777 CGTTTATCATCAGGTCGCCG 59.147 55.000 0.00 0.00 0.00 6.46
2415 2457 2.680577 GTTGAGCTTCTGGCCAATTTG 58.319 47.619 7.01 0.00 43.05 2.32
2420 2462 1.476845 TACCGTTGAGCTTCTGGCCA 61.477 55.000 4.71 4.71 43.05 5.36
2568 2615 1.291877 GACGACATGCATATCCGGCC 61.292 60.000 15.65 0.00 0.00 6.13
2607 2654 5.065474 TGGAACGTTAACTCTTGTTTCCTTG 59.935 40.000 0.00 0.00 37.59 3.61
2716 2764 3.198200 AGAGAGCAGCAGACTGATGAATT 59.802 43.478 24.39 8.56 44.20 2.17
2739 2816 4.790140 GGTACGTACATTGACTACACGAAG 59.210 45.833 26.02 0.00 36.51 3.79
2790 2880 5.174037 ACACAATTCCTATTTCCTCGGAA 57.826 39.130 0.00 0.00 40.75 4.30
2925 3019 7.125536 AGAAGTAATACGTACAAAACAAGCC 57.874 36.000 0.00 0.00 34.88 4.35
3033 3127 4.761739 TGGAATTCTGTGAAATGGTGACTC 59.238 41.667 5.23 0.00 0.00 3.36
3039 3133 6.519679 TTCATCTGGAATTCTGTGAAATGG 57.480 37.500 5.23 0.00 0.00 3.16
3163 3281 5.103771 AGGGCATCTGAAATTAGGTTGAGAT 60.104 40.000 0.00 0.00 0.00 2.75
3259 3377 8.200792 ACAGATTCCTAATACTAGAGTTGCTTG 58.799 37.037 0.00 0.00 0.00 4.01
3382 3505 5.869579 TGCTCTGTGAAAATCCCCTATATC 58.130 41.667 0.00 0.00 0.00 1.63
3442 3566 5.735892 CACAACATGTCGATGATGCTAAAAG 59.264 40.000 0.00 0.00 36.14 2.27
3494 3618 1.028905 GCCAATTATGCGCAACCCTA 58.971 50.000 17.11 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.