Multiple sequence alignment - TraesCS2D01G310700

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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 TraesCS2D01G310700 chr2D 100.000 3386 0 0 1 3386 398784612 398781227 0.000000e+00 6253.0
1 TraesCS2D01G310700 chr2D 95.455 264 12 0 1179 1442 642836772 642837035 4.040000e-114 422.0
2 TraesCS2D01G310700 chr2D 95.076 264 13 0 1179 1442 585381610 585381873 1.880000e-112 416.0
3 TraesCS2D01G310700 chr2D 96.154 156 5 1 937 1092 585381458 585381612 1.560000e-63 254.0
4 TraesCS2D01G310700 chr2D 94.375 160 7 1 935 1092 642836615 642836774 9.390000e-61 244.0
5 TraesCS2D01G310700 chr2B 96.689 2779 56 16 615 3386 472902435 472899686 0.000000e+00 4590.0
6 TraesCS2D01G310700 chr2B 88.494 478 40 10 1 470 472904074 472903604 6.340000e-157 564.0
7 TraesCS2D01G310700 chr2B 88.372 86 5 1 477 562 760299973 760299893 7.730000e-17 99.0
8 TraesCS2D01G310700 chr2B 84.314 102 9 4 490 584 609150427 609150528 3.600000e-15 93.5
9 TraesCS2D01G310700 chr2A 93.592 1982 89 20 482 2431 536627797 536625822 0.000000e+00 2922.0
10 TraesCS2D01G310700 chr2A 84.060 941 92 39 2466 3386 536625744 536624842 0.000000e+00 854.0
11 TraesCS2D01G310700 chr2A 90.294 340 25 4 1 339 536642004 536641672 4.010000e-119 438.0
12 TraesCS2D01G310700 chr1B 93.182 264 18 0 1179 1442 642618914 642618651 4.100000e-104 388.0
13 TraesCS2D01G310700 chr4A 91.875 160 11 1 935 1092 347399515 347399674 4.400000e-54 222.0
14 TraesCS2D01G310700 chr4A 92.982 114 7 1 1335 1447 347399738 347399851 7.520000e-37 165.0
15 TraesCS2D01G310700 chr4A 96.000 75 3 0 1179 1253 347399672 347399746 4.590000e-24 122.0
16 TraesCS2D01G310700 chr4A 94.737 38 1 1 1 38 356725659 356725623 1.310000e-04 58.4
17 TraesCS2D01G310700 chr5D 85.841 113 9 5 473 584 519340255 519340361 2.760000e-21 113.0
18 TraesCS2D01G310700 chr5D 83.193 119 9 6 477 584 64718951 64718833 7.730000e-17 99.0
19 TraesCS2D01G310700 chr3B 85.124 121 7 5 475 584 752304795 752304675 2.760000e-21 113.0
20 TraesCS2D01G310700 chr3B 95.000 40 1 1 1 39 229002793 229002832 1.010000e-05 62.1
21 TraesCS2D01G310700 chr3A 87.778 90 9 1 473 560 661928917 661929006 1.660000e-18 104.0
22 TraesCS2D01G310700 chr5B 88.636 88 5 5 478 560 581220975 581220888 5.980000e-18 102.0
23 TraesCS2D01G310700 chr3D 86.022 93 8 4 475 562 140625358 140625266 1.000000e-15 95.3
24 TraesCS2D01G310700 chr7D 97.368 38 0 1 1 38 523738884 523738920 2.820000e-06 63.9
25 TraesCS2D01G310700 chr1D 94.737 38 1 1 1 38 358251633 358251597 1.310000e-04 58.4
26 TraesCS2D01G310700 chr6B 96.970 33 0 1 1 33 662818239 662818208 2.000000e-03 54.7
27 TraesCS2D01G310700 chr5A 83.929 56 9 0 1 56 344550218 344550273 2.000000e-03 54.7


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 TraesCS2D01G310700 chr2D 398781227 398784612 3385 True 6253 6253 100.0000 1 3386 1 chr2D.!!$R1 3385
1 TraesCS2D01G310700 chr2B 472899686 472904074 4388 True 2577 4590 92.5915 1 3386 2 chr2B.!!$R2 3385
2 TraesCS2D01G310700 chr2A 536624842 536627797 2955 True 1888 2922 88.8260 482 3386 2 chr2A.!!$R2 2904

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
385 394 0.107214 TTTCCATCCTGCCGGTCATC 60.107 55.000 1.9 0.0 0.0 2.92 F
470 479 0.591170 AAAACGATTGTGGCTGGACG 59.409 50.000 0.0 0.0 0.0 4.79 F
708 1750 0.853530 AGTTGCCACCCTTTTCTCCT 59.146 50.000 0.0 0.0 0.0 3.69 F
876 1919 1.078426 CTGGGTAGCAGTTTCCGGG 60.078 63.158 0.0 0.0 0.0 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1800 2858 0.956633 AGTCCTTGCAGTCGTACGAA 59.043 50.000 21.39 0.45 0.00 3.85 R
2061 3119 2.104859 CACGAGGCTGATGTGCAGG 61.105 63.158 0.00 0.00 45.03 4.85 R
2208 3266 4.191243 TGGTCGAGCCAGAAGACA 57.809 55.556 12.85 0.00 43.61 3.41 R
2820 3928 2.456594 TTCGTCAGCCATGCGTTTGC 62.457 55.000 0.00 0.00 43.20 3.68 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
63 64 0.467844 ATGCACTTTCACAGGCACCA 60.468 50.000 0.00 0.00 39.34 4.17
75 76 4.148825 GCACCACGAGAGGGCGAT 62.149 66.667 0.00 0.00 34.83 4.58
114 115 4.091509 CGACCACAACCTTCTTCTTATTCG 59.908 45.833 0.00 0.00 0.00 3.34
132 134 2.657296 CACCGACGTCGTGCTGTT 60.657 61.111 33.49 9.98 37.74 3.16
152 161 3.794270 CCGCATTGGTCGACGATT 58.206 55.556 9.92 0.00 0.00 3.34
153 162 1.348250 CCGCATTGGTCGACGATTG 59.652 57.895 15.48 15.48 0.00 2.67
169 178 4.883083 ACGATTGACTCTCAAGTTTGCTA 58.117 39.130 0.00 0.00 40.05 3.49
175 184 1.996191 CTCTCAAGTTTGCTAGTCGGC 59.004 52.381 0.00 0.00 0.00 5.54
180 189 1.192146 AGTTTGCTAGTCGGCTGGGA 61.192 55.000 0.00 0.00 0.00 4.37
216 225 1.969064 TTGTGGCGGCGCAATAGTT 60.969 52.632 34.36 0.00 0.00 2.24
217 226 2.100216 GTGGCGGCGCAATAGTTG 59.900 61.111 34.36 0.00 0.00 3.16
263 272 2.226200 TGTCGATGATGTTGTTGCCTTG 59.774 45.455 0.00 0.00 0.00 3.61
289 298 2.616842 CGGCTTTTTAGTGGTTGTGACT 59.383 45.455 0.00 0.00 0.00 3.41
290 299 3.066203 CGGCTTTTTAGTGGTTGTGACTT 59.934 43.478 0.00 0.00 0.00 3.01
291 300 4.359706 GGCTTTTTAGTGGTTGTGACTTG 58.640 43.478 0.00 0.00 0.00 3.16
292 301 4.142249 GGCTTTTTAGTGGTTGTGACTTGT 60.142 41.667 0.00 0.00 0.00 3.16
293 302 4.798387 GCTTTTTAGTGGTTGTGACTTGTG 59.202 41.667 0.00 0.00 0.00 3.33
294 303 5.392595 GCTTTTTAGTGGTTGTGACTTGTGA 60.393 40.000 0.00 0.00 0.00 3.58
295 304 5.554822 TTTTAGTGGTTGTGACTTGTGAC 57.445 39.130 0.00 0.00 0.00 3.67
296 305 2.779755 AGTGGTTGTGACTTGTGACA 57.220 45.000 0.00 0.00 0.00 3.58
297 306 2.356135 AGTGGTTGTGACTTGTGACAC 58.644 47.619 0.00 0.00 38.85 3.67
298 307 1.400494 GTGGTTGTGACTTGTGACACC 59.600 52.381 2.45 0.00 37.90 4.16
299 308 1.280710 TGGTTGTGACTTGTGACACCT 59.719 47.619 2.45 0.00 37.90 4.00
331 340 1.746615 CGGTGGGTCTCCAATGCTG 60.747 63.158 0.00 0.00 46.04 4.41
356 365 4.340246 TGGCCAGAGGTGCAGCAG 62.340 66.667 19.63 7.34 0.00 4.24
377 386 2.054453 GTGGGGCTTTCCATCCTGC 61.054 63.158 0.00 0.00 39.26 4.85
378 387 2.442830 GGGGCTTTCCATCCTGCC 60.443 66.667 0.00 0.00 44.22 4.85
380 389 2.830370 GGCTTTCCATCCTGCCGG 60.830 66.667 0.00 0.00 35.79 6.13
385 394 0.107214 TTTCCATCCTGCCGGTCATC 60.107 55.000 1.90 0.00 0.00 2.92
386 395 2.280389 CCATCCTGCCGGTCATCG 60.280 66.667 1.90 0.00 38.88 3.84
421 430 4.733542 AACATCGGGGTTGGGCGG 62.734 66.667 0.00 0.00 0.00 6.13
431 440 1.901464 GTTGGGCGGAAAAGCTCCA 60.901 57.895 0.00 0.00 45.74 3.86
433 442 2.282180 GGGCGGAAAAGCTCCACA 60.282 61.111 0.00 0.00 45.74 4.17
434 443 1.901464 GGGCGGAAAAGCTCCACAA 60.901 57.895 0.00 0.00 45.74 3.33
470 479 0.591170 AAAACGATTGTGGCTGGACG 59.409 50.000 0.00 0.00 0.00 4.79
472 481 0.949105 AACGATTGTGGCTGGACGAC 60.949 55.000 0.00 0.00 0.00 4.34
473 482 2.444624 CGATTGTGGCTGGACGACG 61.445 63.158 0.00 0.00 0.00 5.12
477 593 2.149803 TTGTGGCTGGACGACGTAGG 62.150 60.000 0.00 0.00 0.00 3.18
504 621 6.821160 TCTTATGTTGAGATCCGTGCAAAATA 59.179 34.615 0.00 0.00 0.00 1.40
513 630 7.754924 TGAGATCCGTGCAAAATATTCTTTTTC 59.245 33.333 0.00 0.00 0.00 2.29
514 631 7.830739 AGATCCGTGCAAAATATTCTTTTTCT 58.169 30.769 0.00 0.00 0.00 2.52
562 686 6.984474 TCACTTGACTTAGACTTGGTTAAGTG 59.016 38.462 23.49 23.49 46.79 3.16
564 688 6.761714 ACTTGACTTAGACTTGGTTAAGTGTG 59.238 38.462 13.06 0.21 46.79 3.82
566 690 6.278363 TGACTTAGACTTGGTTAAGTGTGAC 58.722 40.000 1.97 0.00 46.79 3.67
567 691 5.608449 ACTTAGACTTGGTTAAGTGTGACC 58.392 41.667 0.00 0.00 46.79 4.02
568 692 5.365895 ACTTAGACTTGGTTAAGTGTGACCT 59.634 40.000 0.00 0.00 46.79 3.85
582 711 3.418995 TGTGACCTAGACCTAGACACAC 58.581 50.000 20.91 17.75 40.87 3.82
584 713 2.015587 GACCTAGACCTAGACACACCG 58.984 57.143 5.67 0.00 35.21 4.94
585 714 1.632409 ACCTAGACCTAGACACACCGA 59.368 52.381 5.67 0.00 35.21 4.69
587 716 3.457380 ACCTAGACCTAGACACACCGATA 59.543 47.826 5.67 0.00 35.21 2.92
588 717 4.104420 ACCTAGACCTAGACACACCGATAT 59.896 45.833 5.67 0.00 35.21 1.63
590 743 3.223435 AGACCTAGACACACCGATATGG 58.777 50.000 0.00 0.00 46.41 2.74
593 746 8.484453 CTAGACCTAGACACACCGATATGGTAG 61.484 48.148 0.00 0.00 41.66 3.18
605 758 6.540438 CCGATATGGTAGATAGGGCTTAAA 57.460 41.667 0.00 0.00 0.00 1.52
690 1732 1.068055 AGCATGCCTTTCGAAGCAAAG 60.068 47.619 15.66 11.85 43.36 2.77
708 1750 0.853530 AGTTGCCACCCTTTTCTCCT 59.146 50.000 0.00 0.00 0.00 3.69
749 1792 5.885912 ACACATCCAAAGTCAAAAGTAGTGT 59.114 36.000 0.00 0.00 0.00 3.55
775 1818 6.074142 GCCTCAAAGCTTCACTTGTAATTTTG 60.074 38.462 0.00 0.00 39.09 2.44
876 1919 1.078426 CTGGGTAGCAGTTTCCGGG 60.078 63.158 0.00 0.00 0.00 5.73
974 2023 2.839486 AGTTGTTGCCGATCTTCAGA 57.161 45.000 0.00 0.00 0.00 3.27
1009 2058 2.031919 GTGTGGTCATGCACGGGA 59.968 61.111 0.00 0.00 0.00 5.14
1746 2804 2.446994 ACCGTGAACTGGTCCCCA 60.447 61.111 0.00 0.00 33.35 4.96
2229 3287 1.048601 TCTTCTGGCTCGACCACTTT 58.951 50.000 3.02 0.00 46.36 2.66
2644 3751 6.319405 AGCACATGTGAATGCATTCTTGTATA 59.681 34.615 33.23 16.39 44.59 1.47
2694 3801 7.907389 AGTCTCACCAAATCAGTATAGAACAA 58.093 34.615 0.00 0.00 0.00 2.83
2695 3802 8.543774 AGTCTCACCAAATCAGTATAGAACAAT 58.456 33.333 0.00 0.00 0.00 2.71
2820 3928 4.809958 ACTTCGATCAGAAATCTGCATCAG 59.190 41.667 5.53 6.95 43.46 2.90
2954 4098 4.911390 AGACAGTAACTGAAAGGGAATGG 58.089 43.478 0.00 0.00 39.30 3.16
3140 4284 6.540189 TCCACCACATAAAAACAACAAATTGG 59.460 34.615 0.00 0.00 40.42 3.16
3153 4297 5.128499 ACAACAAATTGGTCCAGTTCATGAA 59.872 36.000 3.38 3.38 40.42 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 1.379977 TTCCTCATCGCCCTCTCGT 60.380 57.895 0.00 0.00 0.00 4.18
75 76 4.116328 CGCCTCGACGCTTCCTCA 62.116 66.667 4.89 0.00 0.00 3.86
88 89 0.250338 GAAGAAGGTTGTGGTCGCCT 60.250 55.000 0.00 0.00 0.00 5.52
149 158 5.061560 CGACTAGCAAACTTGAGAGTCAATC 59.938 44.000 17.38 0.00 39.46 2.67
150 159 4.926238 CGACTAGCAAACTTGAGAGTCAAT 59.074 41.667 17.38 0.00 39.46 2.57
152 161 3.305403 CCGACTAGCAAACTTGAGAGTCA 60.305 47.826 17.38 0.00 39.46 3.41
153 162 3.246619 CCGACTAGCAAACTTGAGAGTC 58.753 50.000 11.39 11.39 37.73 3.36
169 178 2.757077 CCCTTTTCCCAGCCGACT 59.243 61.111 0.00 0.00 0.00 4.18
175 184 2.746277 CGACCGCCCTTTTCCCAG 60.746 66.667 0.00 0.00 0.00 4.45
180 189 4.029809 CCTCCCGACCGCCCTTTT 62.030 66.667 0.00 0.00 0.00 2.27
239 248 1.787989 GCAACAACATCATCGACAGCG 60.788 52.381 0.00 0.00 39.35 5.18
241 250 2.079158 AGGCAACAACATCATCGACAG 58.921 47.619 0.00 0.00 41.41 3.51
272 281 5.473846 TGTCACAAGTCACAACCACTAAAAA 59.526 36.000 0.00 0.00 0.00 1.94
289 298 2.625790 GGCCACAAATTAGGTGTCACAA 59.374 45.455 5.12 0.00 34.46 3.33
290 299 2.235016 GGCCACAAATTAGGTGTCACA 58.765 47.619 5.12 0.00 34.46 3.58
291 300 1.199097 CGGCCACAAATTAGGTGTCAC 59.801 52.381 2.24 0.00 34.46 3.67
292 301 1.072489 TCGGCCACAAATTAGGTGTCA 59.928 47.619 2.24 0.00 34.46 3.58
293 302 1.467342 GTCGGCCACAAATTAGGTGTC 59.533 52.381 2.24 0.00 34.46 3.67
294 303 1.530323 GTCGGCCACAAATTAGGTGT 58.470 50.000 2.24 0.00 34.46 4.16
295 304 0.446222 CGTCGGCCACAAATTAGGTG 59.554 55.000 2.24 3.75 36.03 4.00
296 305 0.675522 CCGTCGGCCACAAATTAGGT 60.676 55.000 2.24 0.00 0.00 3.08
297 306 0.675522 ACCGTCGGCCACAAATTAGG 60.676 55.000 12.28 0.00 0.00 2.69
298 307 0.446222 CACCGTCGGCCACAAATTAG 59.554 55.000 12.28 0.00 0.00 1.73
299 308 0.956410 CCACCGTCGGCCACAAATTA 60.956 55.000 12.28 0.00 0.00 1.40
352 361 3.984732 GAAAGCCCCACCCCTGCT 61.985 66.667 0.00 0.00 36.79 4.24
356 365 2.042944 GATGGAAAGCCCCACCCC 60.043 66.667 0.00 0.00 39.34 4.95
380 389 4.530857 CGTCCTGGCCCCGATGAC 62.531 72.222 0.00 0.00 0.00 3.06
392 401 4.778143 GATGTTGCGGGCCGTCCT 62.778 66.667 28.82 11.22 0.00 3.85
407 416 3.212796 TTTTCCGCCCAACCCCGAT 62.213 57.895 0.00 0.00 0.00 4.18
431 440 1.898574 CGCTGCCTCCCACTTTTGT 60.899 57.895 0.00 0.00 0.00 2.83
433 442 2.985847 GCGCTGCCTCCCACTTTT 60.986 61.111 0.00 0.00 0.00 2.27
434 443 3.790416 TTGCGCTGCCTCCCACTTT 62.790 57.895 9.73 0.00 0.00 2.66
443 452 1.371635 ACAATCGTTTTGCGCTGCC 60.372 52.632 9.73 0.00 41.07 4.85
457 466 0.108804 CTACGTCGTCCAGCCACAAT 60.109 55.000 0.00 0.00 0.00 2.71
461 470 1.379443 ATCCTACGTCGTCCAGCCA 60.379 57.895 0.00 0.00 0.00 4.75
477 593 4.371786 TGCACGGATCTCAACATAAGATC 58.628 43.478 4.85 4.85 45.54 2.75
562 686 2.754002 GGTGTGTCTAGGTCTAGGTCAC 59.246 54.545 17.84 17.84 38.06 3.67
564 688 2.015587 CGGTGTGTCTAGGTCTAGGTC 58.984 57.143 5.31 1.18 34.06 3.85
566 690 2.414994 TCGGTGTGTCTAGGTCTAGG 57.585 55.000 5.31 0.00 34.06 3.02
567 691 4.456222 CCATATCGGTGTGTCTAGGTCTAG 59.544 50.000 0.00 0.00 34.56 2.43
568 692 4.395625 CCATATCGGTGTGTCTAGGTCTA 58.604 47.826 0.00 0.00 0.00 2.59
582 711 6.338937 GTTTAAGCCCTATCTACCATATCGG 58.661 44.000 0.00 0.00 42.50 4.18
584 713 6.651086 GGGTTTAAGCCCTATCTACCATATC 58.349 44.000 19.59 0.00 45.22 1.63
585 714 6.638021 GGGTTTAAGCCCTATCTACCATAT 57.362 41.667 19.59 0.00 45.22 1.78
587 716 4.995624 GGGTTTAAGCCCTATCTACCAT 57.004 45.455 19.59 0.00 45.22 3.55
690 1732 1.248486 GAGGAGAAAAGGGTGGCAAC 58.752 55.000 0.00 0.00 0.00 4.17
694 1736 0.777446 TTGGGAGGAGAAAAGGGTGG 59.223 55.000 0.00 0.00 0.00 4.61
708 1750 0.257328 TGTGACTGGTTGCTTTGGGA 59.743 50.000 0.00 0.00 0.00 4.37
749 1792 2.057137 ACAAGTGAAGCTTTGAGGCA 57.943 45.000 0.00 0.00 34.69 4.75
775 1818 5.677852 GCTGACAATTTAATCCGGGGTTTAC 60.678 44.000 0.00 0.00 0.00 2.01
876 1919 1.856014 GCTGTTTCCGCATTATCGCAC 60.856 52.381 0.00 0.00 0.00 5.34
1009 2058 0.889186 GTGGTGATCCGGTGCTTTGT 60.889 55.000 0.00 0.00 36.30 2.83
1426 2484 2.496341 CATCTTGAGCTCGCCCGA 59.504 61.111 9.64 2.94 0.00 5.14
1746 2804 3.006537 AGGTGTAGTTCTTGCACGTGTAT 59.993 43.478 18.38 0.00 42.63 2.29
1800 2858 0.956633 AGTCCTTGCAGTCGTACGAA 59.043 50.000 21.39 0.45 0.00 3.85
2061 3119 2.104859 CACGAGGCTGATGTGCAGG 61.105 63.158 0.00 0.00 45.03 4.85
2208 3266 4.191243 TGGTCGAGCCAGAAGACA 57.809 55.556 12.85 0.00 43.61 3.41
2440 3498 7.050377 TCTCTTCTCAATTATAAGCACCCAAG 58.950 38.462 0.00 0.00 0.00 3.61
2481 3582 6.817765 TGTCTCAGGAACCATGTAAAATTC 57.182 37.500 0.00 0.00 0.00 2.17
2667 3774 9.031537 TGTTCTATACTGATTTGGTGAGACTTA 57.968 33.333 0.00 0.00 0.00 2.24
2820 3928 2.456594 TTCGTCAGCCATGCGTTTGC 62.457 55.000 0.00 0.00 43.20 3.68
2872 3980 5.416947 GTTCTGGGTCGTATGTTCTATTGT 58.583 41.667 0.00 0.00 0.00 2.71
2954 4098 6.024049 GTCAGAGTTGTTAATGCTGTTATGC 58.976 40.000 0.00 0.00 0.00 3.14
3140 4284 4.326826 TCCATCTTGTTCATGAACTGGAC 58.673 43.478 29.62 13.50 37.16 4.02
3153 4297 8.827832 TTGGATCATAGAAAAATCCATCTTGT 57.172 30.769 4.28 0.00 46.23 3.16


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

AutoCloner maintained by Alex Coulton.