Multiple sequence alignment - TraesCS4A01G241300

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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 TraesCS4A01G241300 chr4A 100.000 3440 0 0 1 3440 551131424 551134863 0.000000e+00 6353
1 TraesCS4A01G241300 chr4A 85.325 1247 146 22 808 2035 542533688 542532460 0.000000e+00 1254
2 TraesCS4A01G241300 chr4A 87.470 830 80 13 960 1767 542555949 542555122 0.000000e+00 935
3 TraesCS4A01G241300 chr4A 86.862 784 55 17 2119 2884 542532428 542531675 0.000000e+00 833
4 TraesCS4A01G241300 chr4A 82.534 521 54 15 89 604 542534360 542533872 1.140000e-114 424
5 TraesCS4A01G241300 chr4A 80.383 209 17 14 168 368 542556553 542556361 1.660000e-28 137
6 TraesCS4A01G241300 chr4D 84.717 2277 244 57 883 3122 54604229 54606438 0.000000e+00 2182
7 TraesCS4A01G241300 chr4D 90.874 1304 89 18 2108 3397 47334700 47333413 0.000000e+00 1722
8 TraesCS4A01G241300 chr4D 91.988 986 53 14 802 1771 47336955 47335980 0.000000e+00 1360
9 TraesCS4A01G241300 chr4D 85.714 1295 117 22 808 2072 54474744 54476000 0.000000e+00 1304
10 TraesCS4A01G241300 chr4D 86.801 841 77 18 963 1771 54446539 54447377 0.000000e+00 907
11 TraesCS4A01G241300 chr4D 87.436 780 60 18 2119 2884 54476003 54476758 0.000000e+00 863
12 TraesCS4A01G241300 chr4D 86.066 610 31 19 2 604 47337789 47337227 1.060000e-169 606
13 TraesCS4A01G241300 chr4D 94.222 225 13 0 604 828 47337195 47336971 9.140000e-91 344
14 TraesCS4A01G241300 chr4D 83.607 366 45 10 2694 3058 54479578 54479929 2.560000e-86 329
15 TraesCS4A01G241300 chr4D 85.714 294 28 8 314 604 54603698 54603980 7.220000e-77 298
16 TraesCS4A01G241300 chr4D 77.462 528 39 35 89 604 54474092 54474551 3.430000e-60 243
17 TraesCS4A01G241300 chr4D 90.511 137 11 2 604 738 54604011 54604147 2.730000e-41 180
18 TraesCS4A01G241300 chr4B 94.752 1353 52 10 2085 3430 68730217 68728877 0.000000e+00 2087
19 TraesCS4A01G241300 chr4B 89.575 1554 77 27 237 1771 68962463 68960976 0.000000e+00 1893
20 TraesCS4A01G241300 chr4B 84.115 1322 134 42 2119 3415 80594768 80596038 0.000000e+00 1208
21 TraesCS4A01G241300 chr4B 89.224 928 66 15 2477 3397 68959248 68958348 0.000000e+00 1129
22 TraesCS4A01G241300 chr4B 82.542 842 96 22 955 1771 80556952 80557767 0.000000e+00 693
23 TraesCS4A01G241300 chr4B 82.542 842 96 22 955 1771 80585622 80586437 0.000000e+00 693
24 TraesCS4A01G241300 chr4B 88.732 497 50 2 1173 1666 80593783 80594276 1.370000e-168 603
25 TraesCS4A01G241300 chr4B 88.258 511 22 10 2 480 68730883 68730379 8.280000e-161 577
26 TraesCS4A01G241300 chr4B 86.686 353 34 7 805 1149 80593372 80593719 2.510000e-101 379
27 TraesCS4A01G241300 chr4B 91.414 198 14 3 2 197 68980748 68980552 5.660000e-68 268
28 TraesCS4A01G241300 chr4B 88.136 236 10 6 295 524 80592780 80593003 7.320000e-67 265
29 TraesCS4A01G241300 chr4B 90.756 119 9 1 604 720 80593165 80593283 1.280000e-34 158
30 TraesCS4A01G241300 chr4B 87.970 133 6 1 1626 1748 68730350 68730218 7.690000e-32 148


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 TraesCS4A01G241300 chr4A 551131424 551134863 3439 False 6353.000000 6353 100.000000 1 3440 1 chr4A.!!$F1 3439
1 TraesCS4A01G241300 chr4A 542531675 542534360 2685 True 837.000000 1254 84.907000 89 2884 3 chr4A.!!$R1 2795
2 TraesCS4A01G241300 chr4A 542555122 542556553 1431 True 536.000000 935 83.926500 168 1767 2 chr4A.!!$R2 1599
3 TraesCS4A01G241300 chr4D 47333413 47337789 4376 True 1008.000000 1722 90.787500 2 3397 4 chr4D.!!$R1 3395
4 TraesCS4A01G241300 chr4D 54446539 54447377 838 False 907.000000 907 86.801000 963 1771 1 chr4D.!!$F1 808
5 TraesCS4A01G241300 chr4D 54603698 54606438 2740 False 886.666667 2182 86.980667 314 3122 3 chr4D.!!$F3 2808
6 TraesCS4A01G241300 chr4D 54474092 54479929 5837 False 684.750000 1304 83.554750 89 3058 4 chr4D.!!$F2 2969
7 TraesCS4A01G241300 chr4B 68958348 68962463 4115 True 1511.000000 1893 89.399500 237 3397 2 chr4B.!!$R3 3160
8 TraesCS4A01G241300 chr4B 68728877 68730883 2006 True 937.333333 2087 90.326667 2 3430 3 chr4B.!!$R2 3428
9 TraesCS4A01G241300 chr4B 80556952 80557767 815 False 693.000000 693 82.542000 955 1771 1 chr4B.!!$F1 816
10 TraesCS4A01G241300 chr4B 80585622 80586437 815 False 693.000000 693 82.542000 955 1771 1 chr4B.!!$F2 816
11 TraesCS4A01G241300 chr4B 80592780 80596038 3258 False 522.600000 1208 87.685000 295 3415 5 chr4B.!!$F3 3120

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
610 818 1.070134 GCCCTTTTGTTGGGGAAACTC 59.930 52.381 1.8 0.0 45.18 3.01 F
1644 2067 1.248785 CCTTCGGAGGGTTCGTCAGA 61.249 60.000 0.0 0.0 39.55 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1878 3294 0.250640 GATCGGATGCAATGGCTCCT 60.251 55.0 0.0 0.0 41.91 3.69 R
2891 4625 0.173481 TCTTGCGATCTTCCACTCGG 59.827 55.0 0.0 0.0 35.48 4.63 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
21 22 3.857194 CGAAGTCCTACGTTTTGTTGTG 58.143 45.455 0.00 0.00 0.00 3.33
610 818 1.070134 GCCCTTTTGTTGGGGAAACTC 59.930 52.381 1.80 0.00 45.18 3.01
725 998 5.405269 GGCGTTTGTAATTTTGCTTGATCTT 59.595 36.000 0.00 0.00 0.00 2.40
770 1043 6.024552 TCCCTGTAATTTTGCTTGATGTTC 57.975 37.500 0.00 0.00 0.00 3.18
811 1131 4.444536 ACTTAGGCGTTTGTACAAACTCA 58.555 39.130 35.97 21.47 46.21 3.41
833 1153 6.223852 TCACTGTACTCTGTTTCTTGATTCC 58.776 40.000 0.00 0.00 0.00 3.01
852 1179 9.573166 TTGATTCCATCTTAATATACCACAAGG 57.427 33.333 0.00 0.00 42.21 3.61
853 1180 7.665559 TGATTCCATCTTAATATACCACAAGGC 59.334 37.037 0.00 0.00 39.06 4.35
854 1181 6.508030 TCCATCTTAATATACCACAAGGCA 57.492 37.500 0.00 0.00 39.06 4.75
855 1182 6.296026 TCCATCTTAATATACCACAAGGCAC 58.704 40.000 0.00 0.00 39.06 5.01
856 1183 6.061441 CCATCTTAATATACCACAAGGCACA 58.939 40.000 0.00 0.00 39.06 4.57
857 1184 6.545666 CCATCTTAATATACCACAAGGCACAA 59.454 38.462 0.00 0.00 39.06 3.33
858 1185 7.255242 CCATCTTAATATACCACAAGGCACAAG 60.255 40.741 0.00 0.00 39.06 3.16
946 1276 6.601217 GCAGAGGATACCAAGATTTTCTTTCT 59.399 38.462 0.00 0.00 33.78 2.52
1264 1664 2.579410 TTGAACTAGAAGCCCCCAAC 57.421 50.000 0.00 0.00 0.00 3.77
1348 1762 4.130857 GCGTTTGTCGATGCCAAC 57.869 55.556 0.00 0.00 42.86 3.77
1644 2067 1.248785 CCTTCGGAGGGTTCGTCAGA 61.249 60.000 0.00 0.00 39.55 3.27
1666 2089 8.826710 TCAGATTAACTTTACAACTGACTTGTG 58.173 33.333 0.00 0.00 43.38 3.33
1750 2269 1.637338 AGACAGTCCAGATGAGCACA 58.363 50.000 0.00 0.00 0.00 4.57
1774 2963 7.440556 ACAAGTCATCTGAATCCGAAGATATTG 59.559 37.037 0.00 6.40 31.87 1.90
1778 2967 7.439356 GTCATCTGAATCCGAAGATATTGAACA 59.561 37.037 0.00 0.00 31.87 3.18
1869 3285 5.300752 CAAGTGCAGGAGAAGAAAGTTCTA 58.699 41.667 0.00 0.00 36.28 2.10
1878 3294 9.765795 CAGGAGAAGAAAGTTCTAAAGAAAGTA 57.234 33.333 0.00 0.00 36.28 2.24
1893 3309 2.355010 AAGTAGGAGCCATTGCATCC 57.645 50.000 0.00 0.00 41.13 3.51
1927 3343 2.103042 GTCGCAGTCATGACCAGGC 61.103 63.158 22.21 20.53 0.00 4.85
1931 3347 1.450848 CAGTCATGACCAGGCGCAT 60.451 57.895 22.21 0.00 0.00 4.73
1991 3407 4.829064 TTCTTCTGATTTTGGGTTGACG 57.171 40.909 0.00 0.00 0.00 4.35
1996 3412 4.658063 TCTGATTTTGGGTTGACGGTTAT 58.342 39.130 0.00 0.00 0.00 1.89
2021 3438 6.377327 TTGTTTTGAGAGAAATCAGTCCAC 57.623 37.500 0.00 0.00 0.00 4.02
2030 3447 6.240894 AGAGAAATCAGTCCACATAAGCAAA 58.759 36.000 0.00 0.00 0.00 3.68
2295 3786 1.298041 GTTGCACGACACCAAACGG 60.298 57.895 0.00 0.00 0.00 4.44
2311 3802 1.705873 ACGGACCCTGAGGATATGTC 58.294 55.000 0.00 0.00 36.73 3.06
2376 3867 1.678627 GACATCTGCCTCTTCGAGCTA 59.321 52.381 0.00 0.00 0.00 3.32
2600 4323 5.307976 ACCTATATCTGCATGGCAAACTAGA 59.692 40.000 0.00 0.00 38.41 2.43
2689 4423 7.561021 TGAATTTAAACTAGTTGTGCTGACA 57.439 32.000 9.34 2.60 0.00 3.58
2738 4472 7.823745 ATTGTTTGTATCCTCTGAAGTTTGT 57.176 32.000 0.00 0.00 0.00 2.83
2891 4625 4.322567 AGACAGCATTCAAGAAGAAGGAC 58.677 43.478 0.00 0.00 40.35 3.85
2907 4641 1.511305 GACCGAGTGGAAGATCGCA 59.489 57.895 0.00 0.00 39.21 5.10
2931 4665 1.605710 CAATTCGTCTGGATGGATGGC 59.394 52.381 0.00 0.00 0.00 4.40
2948 4682 3.490439 TGGCTCTTGTCTTCAATGTCA 57.510 42.857 0.00 0.00 32.82 3.58
3279 5027 6.707161 CCATTGAGTGGTTTGAACATTTTCAT 59.293 34.615 0.00 0.00 41.13 2.57
3406 5156 6.748132 TCTTGTTCAGAAAATTTCATGGTCC 58.252 36.000 8.55 0.00 0.00 4.46
3431 5181 7.824289 CCTCACTTCTAATTGACTGGTTTGATA 59.176 37.037 0.00 0.00 0.00 2.15
3432 5182 9.388506 CTCACTTCTAATTGACTGGTTTGATAT 57.611 33.333 0.00 0.00 0.00 1.63
3438 5188 9.699410 TCTAATTGACTGGTTTGATATTTCCAT 57.301 29.630 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.552699 TCACAACAAAACGTAGGACTTCG 59.447 43.478 0.00 0.00 0.00 3.79
30 31 7.993821 TTGAATGAAAACAAATCACGCTTTA 57.006 28.000 0.00 0.00 0.00 1.85
43 45 6.616774 TTGGAGCCAAATTTGAATGAAAAC 57.383 33.333 19.86 2.47 32.44 2.43
45 47 7.820578 ATTTTGGAGCCAAATTTGAATGAAA 57.179 28.000 19.86 11.78 44.14 2.69
79 84 6.957631 TCAGATTTAAGAGCAAGGGTGATTA 58.042 36.000 0.00 0.00 0.00 1.75
87 92 7.869800 AGTCTTGTTTCAGATTTAAGAGCAAG 58.130 34.615 0.00 0.00 33.69 4.01
153 160 2.049888 ACGAGGTACTAGTAGGGTGC 57.950 55.000 1.87 0.00 43.92 5.01
511 619 2.031120 CAACCAAAAGCCAAGGACTCA 58.969 47.619 0.00 0.00 0.00 3.41
512 620 1.269778 GCAACCAAAAGCCAAGGACTC 60.270 52.381 0.00 0.00 0.00 3.36
513 621 0.752658 GCAACCAAAAGCCAAGGACT 59.247 50.000 0.00 0.00 0.00 3.85
514 622 0.752658 AGCAACCAAAAGCCAAGGAC 59.247 50.000 0.00 0.00 0.00 3.85
610 818 4.826274 TCTCCCTGTGGTAAATTCTGAG 57.174 45.455 0.00 0.00 0.00 3.35
656 866 5.688807 CACCCATCAAATTACCTGATCTCT 58.311 41.667 0.00 0.00 30.99 3.10
725 998 2.039818 TTGTACAAACGACCAGCCAA 57.960 45.000 5.64 0.00 0.00 4.52
770 1043 4.553330 AGTACTGGGAGTTTGTACCATG 57.447 45.455 0.00 0.00 37.76 3.66
786 1059 5.912360 GTTTGTACAAACGCCTAAGTACT 57.088 39.130 29.96 0.00 40.85 2.73
811 1131 6.174720 TGGAATCAAGAAACAGAGTACAGT 57.825 37.500 0.00 0.00 0.00 3.55
833 1153 7.566760 TTGTGCCTTGTGGTATATTAAGATG 57.433 36.000 0.00 0.00 35.27 2.90
946 1276 8.049117 AGAAAAACATAGATTATGACTGGCAGA 58.951 33.333 23.66 0.00 39.45 4.26
1264 1664 1.202020 CCAACATCGTACACATTGCCG 60.202 52.381 0.00 0.00 0.00 5.69
1348 1762 8.100508 TCAATGAGTCGTTCTCTACTATATGG 57.899 38.462 0.00 0.00 43.13 2.74
1666 2089 6.860023 GCAGCAAAATGGTATGATCAATAGTC 59.140 38.462 0.00 0.00 0.00 2.59
1750 2269 7.730084 TCAATATCTTCGGATTCAGATGACTT 58.270 34.615 4.88 1.07 36.01 3.01
1774 2963 5.333111 GCTCGGGTGTTAATCGAATATGTTC 60.333 44.000 0.00 0.00 32.35 3.18
1778 2967 4.330944 TGCTCGGGTGTTAATCGAATAT 57.669 40.909 0.00 0.00 32.35 1.28
1783 2972 1.934589 TCATGCTCGGGTGTTAATCG 58.065 50.000 0.00 0.00 0.00 3.34
1855 3271 9.984190 TCCTACTTTCTTTAGAACTTTCTTCTC 57.016 33.333 0.00 0.00 38.70 2.87
1869 3285 3.766545 TGCAATGGCTCCTACTTTCTTT 58.233 40.909 0.00 0.00 41.91 2.52
1878 3294 0.250640 GATCGGATGCAATGGCTCCT 60.251 55.000 0.00 0.00 41.91 3.69
1893 3309 1.389853 CGACGTAGATGTGCAGATCG 58.610 55.000 17.31 9.71 0.00 3.69
1927 3343 1.519455 GGGAGACGAGGACAATGCG 60.519 63.158 0.00 0.00 0.00 4.73
1931 3347 3.009916 ACTTACTAGGGAGACGAGGACAA 59.990 47.826 0.00 0.00 0.00 3.18
1984 3400 6.267070 TCTCAAAACAAAATAACCGTCAACC 58.733 36.000 0.00 0.00 0.00 3.77
1991 3407 9.750125 ACTGATTTCTCTCAAAACAAAATAACC 57.250 29.630 0.00 0.00 0.00 2.85
1996 3412 7.093988 TGTGGACTGATTTCTCTCAAAACAAAA 60.094 33.333 0.00 0.00 0.00 2.44
2295 3786 1.889829 CCTCGACATATCCTCAGGGTC 59.110 57.143 0.00 0.00 0.00 4.46
2311 3802 0.519077 GCAAAAGAAGTCCAGCCTCG 59.481 55.000 0.00 0.00 0.00 4.63
2376 3867 1.203001 TGCTCCCCCTCGTTTTTCATT 60.203 47.619 0.00 0.00 0.00 2.57
2617 4346 8.287439 TGAAGAAAGAAATCACAACCTGTTTA 57.713 30.769 0.00 0.00 0.00 2.01
2619 4348 6.378280 ACTGAAGAAAGAAATCACAACCTGTT 59.622 34.615 0.00 0.00 0.00 3.16
2620 4349 5.888161 ACTGAAGAAAGAAATCACAACCTGT 59.112 36.000 0.00 0.00 0.00 4.00
2621 4350 6.204359 CACTGAAGAAAGAAATCACAACCTG 58.796 40.000 0.00 0.00 0.00 4.00
2622 4351 5.300286 CCACTGAAGAAAGAAATCACAACCT 59.700 40.000 0.00 0.00 0.00 3.50
2623 4352 5.523369 CCACTGAAGAAAGAAATCACAACC 58.477 41.667 0.00 0.00 0.00 3.77
2624 4353 4.978580 GCCACTGAAGAAAGAAATCACAAC 59.021 41.667 0.00 0.00 0.00 3.32
2689 4423 2.812011 GTGGCTTCCTCATACAAACGTT 59.188 45.455 0.00 0.00 0.00 3.99
2691 4425 2.699954 AGTGGCTTCCTCATACAAACG 58.300 47.619 0.00 0.00 0.00 3.60
2737 4471 5.645497 AGAAACTAGGCATCATGAGTTCAAC 59.355 40.000 0.09 0.00 30.98 3.18
2738 4472 5.809001 AGAAACTAGGCATCATGAGTTCAA 58.191 37.500 0.09 0.00 30.98 2.69
2891 4625 0.173481 TCTTGCGATCTTCCACTCGG 59.827 55.000 0.00 0.00 35.48 4.63
2931 4665 8.545229 AATAGAAGTGACATTGAAGACAAGAG 57.455 34.615 0.00 0.00 39.46 2.85
2959 4694 8.201242 TGTCTAGGCCAAAAAGGAAATAAAAT 57.799 30.769 5.01 0.00 41.22 1.82
2964 4699 5.086621 ACATGTCTAGGCCAAAAAGGAAAT 58.913 37.500 5.01 0.00 41.22 2.17
3142 4880 9.834628 CTAATTGTTTTTGCCTCGTTAAGATTA 57.165 29.630 0.00 0.00 0.00 1.75
3379 5129 9.912634 GACCATGAAATTTTCTGAACAAGAATA 57.087 29.630 10.33 0.00 44.46 1.75
3406 5156 7.678947 ATCAAACCAGTCAATTAGAAGTGAG 57.321 36.000 0.00 0.00 33.24 3.51


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

AutoCloner maintained by Alex Coulton.