Multiple sequence alignment - TraesCS2D01G007300

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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 TraesCS2D01G007300 chr2D 100.000 6272 0 0 1 6272 4030551 4024280 0.000000e+00 11583.0
1 TraesCS2D01G007300 chr2D 98.566 6277 74 12 1 6272 3972952 3966687 0.000000e+00 11079.0
2 TraesCS2D01G007300 chr2D 92.892 408 21 5 5287 5688 341646960 341646555 2.520000e-163 586.0
3 TraesCS2D01G007300 chr2D 82.353 119 14 6 402 517 60072639 60072525 5.180000e-16 97.1
4 TraesCS2D01G007300 chr2B 95.106 1880 82 9 3420 5294 6957662 6955788 0.000000e+00 2953.0
5 TraesCS2D01G007300 chr2B 94.941 1878 86 8 3420 5293 454693265 454691393 0.000000e+00 2933.0
6 TraesCS2D01G007300 chr2B 94.149 1880 100 9 3420 5294 454719232 454717358 0.000000e+00 2854.0
7 TraesCS2D01G007300 chr2B 94.992 1777 80 8 3420 5191 6871036 6869264 0.000000e+00 2780.0
8 TraesCS2D01G007300 chr2B 89.769 2209 137 26 1 2158 6959827 6957657 0.000000e+00 2745.0
9 TraesCS2D01G007300 chr2B 94.601 1741 86 7 3420 5155 7001540 7003277 0.000000e+00 2687.0
10 TraesCS2D01G007300 chr2B 90.292 1988 118 25 1 1952 6873243 6871295 0.000000e+00 2532.0
11 TraesCS2D01G007300 chr2B 93.441 1357 80 8 3420 4770 7087573 7088926 0.000000e+00 2004.0
12 TraesCS2D01G007300 chr2B 92.552 1356 79 14 3420 4770 7161822 7163160 0.000000e+00 1925.0
13 TraesCS2D01G007300 chr2B 90.380 1237 89 17 947 2158 454694491 454693260 0.000000e+00 1598.0
14 TraesCS2D01G007300 chr2B 89.849 1261 95 16 923 2158 7086326 7087578 0.000000e+00 1589.0
15 TraesCS2D01G007300 chr2B 89.770 1261 96 16 923 2158 7048515 7049767 0.000000e+00 1583.0
16 TraesCS2D01G007300 chr2B 89.374 1261 101 16 923 2158 7160575 7161827 0.000000e+00 1555.0
17 TraesCS2D01G007300 chr2B 89.294 1261 102 16 923 2158 454720479 454719227 0.000000e+00 1550.0
18 TraesCS2D01G007300 chr2B 92.289 830 30 7 96 905 454695306 454694491 0.000000e+00 1147.0
19 TraesCS2D01G007300 chr2B 92.965 597 22 6 5676 6272 454691343 454690767 0.000000e+00 852.0
20 TraesCS2D01G007300 chr2B 92.630 597 27 1 5676 6272 6998041 6997462 0.000000e+00 843.0
21 TraesCS2D01G007300 chr2B 91.803 610 28 8 5664 6272 7003741 7004329 0.000000e+00 830.0
22 TraesCS2D01G007300 chr2B 91.960 597 28 6 5676 6272 454717309 454716733 0.000000e+00 819.0
23 TraesCS2D01G007300 chr2B 91.275 596 32 2 5676 6271 6955707 6955132 0.000000e+00 795.0
24 TraesCS2D01G007300 chr2B 94.758 496 24 1 4799 5294 6998579 6998086 0.000000e+00 771.0
25 TraesCS2D01G007300 chr2B 86.977 622 51 14 1555 2158 7000936 7001545 0.000000e+00 673.0
26 TraesCS2D01G007300 chr2B 95.854 410 16 1 40 449 454788487 454788079 0.000000e+00 662.0
27 TraesCS2D01G007300 chr2B 95.400 413 18 1 34 446 7044487 7044898 0.000000e+00 656.0
28 TraesCS2D01G007300 chr2B 95.400 413 18 1 34 446 7157544 7157955 0.000000e+00 656.0
29 TraesCS2D01G007300 chr2B 90.617 373 15 2 5900 6272 6867183 6866831 1.580000e-130 477.0
30 TraesCS2D01G007300 chr2B 79.805 614 120 4 4638 5249 7579152 7579763 1.600000e-120 444.0
31 TraesCS2D01G007300 chr2B 93.258 178 12 0 5676 5853 6867353 6867176 4.820000e-66 263.0
32 TraesCS2D01G007300 chr2B 90.256 195 18 1 1964 2158 6871224 6871031 2.900000e-63 254.0
33 TraesCS2D01G007300 chr2B 94.355 124 5 2 5171 5294 7003583 7003704 8.300000e-44 189.0
34 TraesCS2D01G007300 chr2B 97.849 93 0 2 5202 5294 6867544 6867454 6.510000e-35 159.0
35 TraesCS2D01G007300 chr2B 100.000 44 0 0 785 828 7048409 7048452 1.450000e-11 82.4
36 TraesCS2D01G007300 chr2B 100.000 44 0 0 785 828 7086220 7086263 1.450000e-11 82.4
37 TraesCS2D01G007300 chrUn 94.474 1140 57 6 4143 5279 11589951 11588815 0.000000e+00 1751.0
38 TraesCS2D01G007300 chrUn 83.603 866 80 34 1 828 11580973 11581814 0.000000e+00 756.0
39 TraesCS2D01G007300 chrUn 83.603 866 80 34 1 828 440301383 440300542 0.000000e+00 756.0
40 TraesCS2D01G007300 chrUn 95.854 410 16 1 40 449 360049887 360049479 0.000000e+00 662.0
41 TraesCS2D01G007300 chrUn 95.610 410 17 1 40 449 268875214 268874806 0.000000e+00 656.0
42 TraesCS2D01G007300 chrUn 93.333 210 14 0 5813 6022 398109863 398110072 1.700000e-80 311.0
43 TraesCS2D01G007300 chrUn 93.333 210 14 0 5813 6022 468075067 468075276 1.700000e-80 311.0
44 TraesCS2D01G007300 chrUn 92.754 138 9 1 5676 5812 11588753 11588616 1.380000e-46 198.0
45 TraesCS2D01G007300 chrUn 100.000 44 0 0 785 828 385833006 385833049 1.450000e-11 82.4
46 TraesCS2D01G007300 chrUn 97.619 42 1 0 40 81 424078558 424078517 8.720000e-09 73.1
47 TraesCS2D01G007300 chr5B 95.052 384 17 2 5300 5681 101020313 101020696 2.500000e-168 603.0
48 TraesCS2D01G007300 chr1D 94.041 386 19 2 5300 5681 174199601 174199216 3.260000e-162 582.0
49 TraesCS2D01G007300 chr4D 94.026 385 19 3 5300 5681 441294481 441294098 1.170000e-161 580.0
50 TraesCS2D01G007300 chr4A 94.241 382 19 2 5300 5678 311248599 311248980 1.170000e-161 580.0
51 TraesCS2D01G007300 chr4A 93.947 380 20 2 5302 5678 510712328 510712707 7.050000e-159 571.0
52 TraesCS2D01G007300 chr3D 93.750 384 21 2 5301 5681 545201577 545201960 1.960000e-159 573.0
53 TraesCS2D01G007300 chr7D 93.734 383 21 3 5301 5681 391324565 391324184 7.050000e-159 571.0
54 TraesCS2D01G007300 chr2A 78.098 936 165 28 1006 1924 551721513 551722425 1.980000e-154 556.0
55 TraesCS2D01G007300 chr5D 73.476 328 57 25 264 571 288573677 288573994 5.180000e-16 97.1
56 TraesCS2D01G007300 chr7B 81.301 123 16 7 416 534 707593226 707593345 6.690000e-15 93.5


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 TraesCS2D01G007300 chr2D 4024280 4030551 6271 True 11583.000000 11583 100.000000 1 6272 1 chr2D.!!$R2 6271
1 TraesCS2D01G007300 chr2D 3966687 3972952 6265 True 11079.000000 11079 98.566000 1 6272 1 chr2D.!!$R1 6271
2 TraesCS2D01G007300 chr2B 6955132 6959827 4695 True 2164.333333 2953 92.050000 1 6271 3 chr2B.!!$R3 6270
3 TraesCS2D01G007300 chr2B 454716733 454720479 3746 True 1741.000000 2854 91.801000 923 6272 3 chr2B.!!$R6 5349
4 TraesCS2D01G007300 chr2B 454690767 454695306 4539 True 1632.500000 2933 92.643750 96 6272 4 chr2B.!!$R5 6176
5 TraesCS2D01G007300 chr2B 7157544 7163160 5616 False 1378.666667 1925 92.442000 34 4770 3 chr2B.!!$F5 4736
6 TraesCS2D01G007300 chr2B 7086220 7088926 2706 False 1225.133333 2004 94.430000 785 4770 3 chr2B.!!$F4 3985
7 TraesCS2D01G007300 chr2B 7000936 7004329 3393 False 1094.750000 2687 91.934000 1555 6272 4 chr2B.!!$F2 4717
8 TraesCS2D01G007300 chr2B 6866831 6873243 6412 True 1077.500000 2780 92.877333 1 6272 6 chr2B.!!$R2 6271
9 TraesCS2D01G007300 chr2B 6997462 6998579 1117 True 807.000000 843 93.694000 4799 6272 2 chr2B.!!$R4 1473
10 TraesCS2D01G007300 chr2B 7044487 7049767 5280 False 773.800000 1583 95.056667 34 2158 3 chr2B.!!$F3 2124
11 TraesCS2D01G007300 chr2B 7579152 7579763 611 False 444.000000 444 79.805000 4638 5249 1 chr2B.!!$F1 611
12 TraesCS2D01G007300 chrUn 11588616 11589951 1335 True 974.500000 1751 93.614000 4143 5812 2 chrUn.!!$R5 1669
13 TraesCS2D01G007300 chrUn 11580973 11581814 841 False 756.000000 756 83.603000 1 828 1 chrUn.!!$F1 827
14 TraesCS2D01G007300 chrUn 440300542 440301383 841 True 756.000000 756 83.603000 1 828 1 chrUn.!!$R4 827
15 TraesCS2D01G007300 chr2A 551721513 551722425 912 False 556.000000 556 78.098000 1006 1924 1 chr2A.!!$F1 918

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
151 157 5.701290 AGTATTAAAAGATACATCAGGCGGC 59.299 40.0 0.0 0.0 35.43 6.53 F
446 479 7.936496 AAATGTCCAAACTTCACCAAATTTT 57.064 28.0 0.0 0.0 0.00 1.82 F
2435 5829 0.263765 AGGTATTCTAGCCCGTCCCA 59.736 55.0 0.0 0.0 0.00 4.37 F
2436 5830 1.125633 GGTATTCTAGCCCGTCCCAA 58.874 55.0 0.0 0.0 0.00 4.12 F
3977 7376 2.458592 GTGACATCACATAAAGGCGC 57.541 50.0 0.0 0.0 45.75 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1209 4541 0.963962 GGTGCATCATTGGCCCATAG 59.036 55.000 0.0 0.0 0.00 2.23 R
1515 4847 2.282391 TTGATGCTGTTGCGGGCT 60.282 55.556 0.0 0.0 43.34 5.19 R
4019 7418 1.281899 GGCGAGACTTATGACACTGC 58.718 55.000 0.0 0.0 0.00 4.40 R
4149 7548 1.334419 CGCATGATTTCCTCGATTGCC 60.334 52.381 0.0 0.0 0.00 4.52 R
5828 11255 0.179124 GAGTGAGGCAGTGATCGACC 60.179 60.000 0.0 0.0 0.00 4.79 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
151 157 5.701290 AGTATTAAAAGATACATCAGGCGGC 59.299 40.000 0.00 0.00 35.43 6.53
446 479 7.936496 AAATGTCCAAACTTCACCAAATTTT 57.064 28.000 0.00 0.00 0.00 1.82
2435 5829 0.263765 AGGTATTCTAGCCCGTCCCA 59.736 55.000 0.00 0.00 0.00 4.37
2436 5830 1.125633 GGTATTCTAGCCCGTCCCAA 58.874 55.000 0.00 0.00 0.00 4.12
2715 6109 7.361457 TCCTATGTTACTATTCCTGGTCTTG 57.639 40.000 0.00 0.00 0.00 3.02
2972 6366 4.499865 GCTAAGCATCACGATACTTCCAGA 60.500 45.833 0.00 0.00 0.00 3.86
2985 6379 6.456988 CGATACTTCCAGACCATTTGCTAAAC 60.457 42.308 0.00 0.00 0.00 2.01
2986 6380 4.469657 ACTTCCAGACCATTTGCTAAACA 58.530 39.130 0.00 0.00 0.00 2.83
3143 6538 8.757877 AGTGGGCTATTTGAAGCAAATTTAATA 58.242 29.630 10.26 0.00 40.60 0.98
3225 6620 8.274322 AGGAGATCATATCACAAATTGTAACCA 58.726 33.333 0.00 0.00 0.00 3.67
3795 7194 3.571401 CCATGGCATTGACCTTAATCCTC 59.429 47.826 0.00 0.00 0.00 3.71
3977 7376 2.458592 GTGACATCACATAAAGGCGC 57.541 50.000 0.00 0.00 45.75 6.53
4094 7493 3.640967 GCAACCCATGAATAATAAGCCCA 59.359 43.478 0.00 0.00 0.00 5.36
4287 7687 8.808529 CGACTATAAAGTGGTGATGTTTTCTAG 58.191 37.037 0.00 0.00 35.56 2.43
4542 7945 7.429636 TCCTTTAGTTCACTTCAAAATACCG 57.570 36.000 0.00 0.00 0.00 4.02
4562 7967 6.949578 ACCGCATACAATTTTTCAAATGAG 57.050 33.333 0.00 0.00 0.00 2.90
4984 8389 3.975312 TCCAAAGTACTGGAAACACCCTA 59.025 43.478 0.00 0.00 42.69 3.53
5347 10751 4.652421 GGTAGTTACCCCACATGTCTCATA 59.348 45.833 0.00 0.00 40.53 2.15
6098 11525 6.817765 TCTTTGATGGAAGTTGTACATTCC 57.182 37.500 17.81 17.81 44.42 3.01
6165 11592 3.882888 TGCTCAAATGGTCGGATTATTCC 59.117 43.478 0.00 0.00 38.81 3.01
6178 11622 4.566987 GGATTATTCCGGTATCAGTGGTC 58.433 47.826 0.00 0.00 30.72 4.02
6179 11623 4.283722 GGATTATTCCGGTATCAGTGGTCT 59.716 45.833 0.00 0.00 30.72 3.85
6180 11624 5.221661 GGATTATTCCGGTATCAGTGGTCTT 60.222 44.000 0.00 0.00 30.72 3.01
6181 11625 6.014840 GGATTATTCCGGTATCAGTGGTCTTA 60.015 42.308 0.00 0.00 30.72 2.10
6182 11626 6.795144 TTATTCCGGTATCAGTGGTCTTAA 57.205 37.500 0.00 0.00 0.00 1.85
6183 11627 5.888982 ATTCCGGTATCAGTGGTCTTAAT 57.111 39.130 0.00 0.00 0.00 1.40
6184 11628 6.989155 ATTCCGGTATCAGTGGTCTTAATA 57.011 37.500 0.00 0.00 0.00 0.98
6185 11629 6.989155 TTCCGGTATCAGTGGTCTTAATAT 57.011 37.500 0.00 0.00 0.00 1.28
6186 11630 6.989155 TCCGGTATCAGTGGTCTTAATATT 57.011 37.500 0.00 0.00 0.00 1.28
6187 11631 6.755206 TCCGGTATCAGTGGTCTTAATATTG 58.245 40.000 0.00 0.00 0.00 1.90
6188 11632 5.408604 CCGGTATCAGTGGTCTTAATATTGC 59.591 44.000 0.00 0.00 0.00 3.56
6189 11633 5.989168 CGGTATCAGTGGTCTTAATATTGCA 59.011 40.000 0.00 0.00 0.00 4.08
6190 11634 6.481976 CGGTATCAGTGGTCTTAATATTGCAA 59.518 38.462 0.00 0.00 0.00 4.08
6191 11635 7.173218 CGGTATCAGTGGTCTTAATATTGCAAT 59.827 37.037 17.56 17.56 0.00 3.56
6192 11636 8.292448 GGTATCAGTGGTCTTAATATTGCAATG 58.708 37.037 22.27 4.76 0.00 2.82
6193 11637 6.698008 TCAGTGGTCTTAATATTGCAATGG 57.302 37.500 22.27 6.96 0.00 3.16
6194 11638 6.186957 TCAGTGGTCTTAATATTGCAATGGT 58.813 36.000 22.27 11.58 0.00 3.55
6202 11646 6.324512 TCTTAATATTGCAATGGTGGCTTGAT 59.675 34.615 22.27 0.87 0.00 2.57
6236 11680 5.360714 GGATTTGCTTCCTTCCACATCATTA 59.639 40.000 0.00 0.00 32.68 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
145 151 0.534873 ACAAGTTGTTTTTGCCGCCT 59.465 45.000 1.64 0.00 0.00 5.52
151 157 9.264782 CTTCAAAAAGCATACAAGTTGTTTTTG 57.735 29.630 24.21 24.21 42.31 2.44
446 479 2.432456 GTGCGAGATGTCCGTGCA 60.432 61.111 0.00 0.00 0.00 4.57
1209 4541 0.963962 GGTGCATCATTGGCCCATAG 59.036 55.000 0.00 0.00 0.00 2.23
1515 4847 2.282391 TTGATGCTGTTGCGGGCT 60.282 55.556 0.00 0.00 43.34 5.19
1874 5206 3.942115 GCTCTTTGTGGTTAGAGGGAATC 59.058 47.826 0.00 0.00 38.63 2.52
2715 6109 8.784043 ACAAAATAGGTACAAATGAACTCTGAC 58.216 33.333 0.00 0.00 0.00 3.51
3143 6538 2.949177 TGCAAAGTGTGGGACTATGT 57.051 45.000 0.00 0.00 33.09 2.29
3342 6737 3.000222 CGGCAGAGCAAAAACTCAAAAAC 60.000 43.478 0.00 0.00 39.26 2.43
3404 6799 6.385176 TGAGGTCATTTCTGAGATATCCAAGT 59.615 38.462 0.00 0.00 30.18 3.16
3795 7194 8.600449 TGTTGGTTGCAATATTAAAAGAAAGG 57.400 30.769 0.59 0.00 0.00 3.11
3977 7376 5.636121 CACAACCAATGTTCATGGAATCTTG 59.364 40.000 0.00 0.00 41.46 3.02
4019 7418 1.281899 GGCGAGACTTATGACACTGC 58.718 55.000 0.00 0.00 0.00 4.40
4094 7493 8.537728 TTTCATGCTAGGAAAATATTGTGGAT 57.462 30.769 0.00 0.00 31.72 3.41
4149 7548 1.334419 CGCATGATTTCCTCGATTGCC 60.334 52.381 0.00 0.00 0.00 4.52
4287 7687 9.912634 TTTGATCAGGATGTTTGTTTATTCTTC 57.087 29.630 0.00 0.00 37.40 2.87
4958 8363 3.435671 GTGTTTCCAGTACTTTGGATCCG 59.564 47.826 7.39 0.00 46.22 4.18
4984 8389 1.966354 CCTCTCTGGCAAAAAGGCTTT 59.034 47.619 6.68 6.68 44.55 3.51
5157 8562 3.612247 CTCTGGACTTGCCCCACCG 62.612 68.421 0.00 0.00 34.97 4.94
5294 10698 1.698874 AGGATGGATTTTCCCCAGGT 58.301 50.000 0.00 0.00 37.08 4.00
5296 10700 2.513738 TGGTAGGATGGATTTTCCCCAG 59.486 50.000 0.00 0.00 37.08 4.45
5580 11005 4.916870 TCAAATCGGAGAGTATGTACGTG 58.083 43.478 0.00 0.00 43.63 4.49
5581 11006 5.769484 ATCAAATCGGAGAGTATGTACGT 57.231 39.130 0.00 0.00 43.63 3.57
5828 11255 0.179124 GAGTGAGGCAGTGATCGACC 60.179 60.000 0.00 0.00 0.00 4.79
6098 11525 6.072728 TGTTGACAATTGTTTAGGAGATTCCG 60.073 38.462 13.36 0.00 42.75 4.30
6165 11592 5.989168 TGCAATATTAAGACCACTGATACCG 59.011 40.000 0.00 0.00 0.00 4.02
6178 11622 5.904941 TCAAGCCACCATTGCAATATTAAG 58.095 37.500 12.53 0.00 0.00 1.85
6179 11623 5.929058 TCAAGCCACCATTGCAATATTAA 57.071 34.783 12.53 0.00 0.00 1.40
6180 11624 5.597594 TGATCAAGCCACCATTGCAATATTA 59.402 36.000 12.53 0.00 0.00 0.98
6181 11625 4.406326 TGATCAAGCCACCATTGCAATATT 59.594 37.500 12.53 0.00 0.00 1.28
6182 11626 3.962063 TGATCAAGCCACCATTGCAATAT 59.038 39.130 12.53 0.00 0.00 1.28
6183 11627 3.363627 TGATCAAGCCACCATTGCAATA 58.636 40.909 12.53 0.00 0.00 1.90
6184 11628 2.181125 TGATCAAGCCACCATTGCAAT 58.819 42.857 5.99 5.99 0.00 3.56
6185 11629 1.630223 TGATCAAGCCACCATTGCAA 58.370 45.000 0.00 0.00 0.00 4.08
6186 11630 1.752498 GATGATCAAGCCACCATTGCA 59.248 47.619 0.00 0.00 0.00 4.08
6187 11631 1.268896 CGATGATCAAGCCACCATTGC 60.269 52.381 0.00 0.00 0.00 3.56
6188 11632 2.289820 CTCGATGATCAAGCCACCATTG 59.710 50.000 0.00 0.00 0.00 2.82
6189 11633 2.171237 TCTCGATGATCAAGCCACCATT 59.829 45.455 0.00 0.00 0.00 3.16
6190 11634 1.764723 TCTCGATGATCAAGCCACCAT 59.235 47.619 0.00 0.00 0.00 3.55
6191 11635 1.194218 TCTCGATGATCAAGCCACCA 58.806 50.000 0.00 0.00 0.00 4.17
6192 11636 2.141517 CATCTCGATGATCAAGCCACC 58.858 52.381 0.00 0.00 41.20 4.61
6193 11637 2.141517 CCATCTCGATGATCAAGCCAC 58.858 52.381 0.00 0.00 41.20 5.01
6194 11638 2.041701 TCCATCTCGATGATCAAGCCA 58.958 47.619 0.00 0.00 41.20 4.75
6202 11646 3.135348 AGGAAGCAAATCCATCTCGATGA 59.865 43.478 8.42 0.00 42.27 2.92
6236 11680 4.373156 AGTTGTTCTTGCCAATACTCCT 57.627 40.909 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.