Multiple sequence alignment - TraesCS5D01G532700

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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 TraesCS5D01G532700 chr5D 100.000 5441 0 0 1 5441 547611710 547606270 0.000000e+00 10048.0
1 TraesCS5D01G532700 chr5D 88.664 247 25 1 371 617 375170681 375170924 1.150000e-76 298.0
2 TraesCS5D01G532700 chr5D 88.618 123 14 0 1005 1127 547615891 547615769 3.400000e-32 150.0
3 TraesCS5D01G532700 chrUn 99.155 2603 20 1 2556 5158 68497064 68494464 0.000000e+00 4684.0
4 TraesCS5D01G532700 chrUn 97.642 1908 30 4 1 1907 68510227 68508334 0.000000e+00 3260.0
5 TraesCS5D01G532700 chrUn 97.975 889 16 1 4553 5441 68494469 68493583 0.000000e+00 1541.0
6 TraesCS5D01G532700 chrUn 97.545 448 7 1 2111 2558 68508317 68507874 0.000000e+00 763.0
7 TraesCS5D01G532700 chrUn 90.090 111 11 0 1017 1127 68522329 68522219 1.580000e-30 145.0
8 TraesCS5D01G532700 chr4A 94.095 2337 78 20 2936 5238 621565519 621563209 0.000000e+00 3496.0
9 TraesCS5D01G532700 chr4A 90.527 1594 56 36 614 2158 621567871 621566324 0.000000e+00 2019.0
10 TraesCS5D01G532700 chr4A 92.267 750 26 7 2216 2933 621566310 621565561 0.000000e+00 1035.0
11 TraesCS5D01G532700 chr4A 88.088 638 63 10 3102 3735 24765543 24764915 0.000000e+00 745.0
12 TraesCS5D01G532700 chr4A 84.803 533 60 15 1050 1572 24768065 24767544 2.910000e-142 516.0
13 TraesCS5D01G532700 chr4A 86.972 284 30 5 331 612 731081923 731081645 4.090000e-81 313.0
14 TraesCS5D01G532700 chr4A 88.211 246 29 0 1639 1884 24767410 24767165 1.480000e-75 294.0
15 TraesCS5D01G532700 chr4A 91.892 185 14 1 5257 5441 621563222 621563039 1.940000e-64 257.0
16 TraesCS5D01G532700 chr4A 86.911 191 25 0 4264 4454 24764450 24764260 1.190000e-51 215.0
17 TraesCS5D01G532700 chr4A 80.220 273 43 10 4727 4997 621542943 621542680 1.550000e-45 195.0
18 TraesCS5D01G532700 chr5B 91.714 1762 91 14 2933 4666 690908014 690909748 0.000000e+00 2394.0
19 TraesCS5D01G532700 chr5B 90.541 888 54 19 1005 1884 690906323 690907188 0.000000e+00 1147.0
20 TraesCS5D01G532700 chr5B 88.991 654 60 6 4785 5438 690909878 690910519 0.000000e+00 798.0
21 TraesCS5D01G532700 chr5B 84.563 732 75 17 2225 2933 690907259 690907975 0.000000e+00 691.0
22 TraesCS5D01G532700 chr5B 86.505 289 22 6 614 886 690905935 690906222 8.860000e-78 302.0
23 TraesCS5D01G532700 chr5B 97.727 44 1 0 889 932 416331611 416331654 5.840000e-10 76.8
24 TraesCS5D01G532700 chr4D 89.343 685 56 8 3055 3737 442897547 442898216 0.000000e+00 845.0
25 TraesCS5D01G532700 chr4D 85.605 521 59 11 1050 1565 442895147 442895656 2.890000e-147 532.0
26 TraesCS5D01G532700 chr4D 89.837 246 25 0 1639 1884 442895792 442896037 3.160000e-82 316.0
27 TraesCS5D01G532700 chr4D 86.926 283 31 5 331 612 418391518 418391795 4.090000e-81 313.0
28 TraesCS5D01G532700 chr4D 90.000 160 16 0 4283 4442 442898703 442898862 1.990000e-49 207.0
29 TraesCS5D01G532700 chr4D 97.727 44 1 0 889 932 167119141 167119184 5.840000e-10 76.8
30 TraesCS5D01G532700 chr4D 95.455 44 2 0 889 932 229525558 229525601 2.720000e-08 71.3
31 TraesCS5D01G532700 chr4B 88.743 684 57 10 3055 3735 552016607 552017273 0.000000e+00 819.0
32 TraesCS5D01G532700 chr4B 86.762 491 51 9 1078 1564 552014241 552014721 8.020000e-148 534.0
33 TraesCS5D01G532700 chr4B 88.211 246 29 0 1639 1884 552014861 552015106 1.480000e-75 294.0
34 TraesCS5D01G532700 chr4B 86.592 179 24 0 4264 4442 552017694 552017872 1.200000e-46 198.0
35 TraesCS5D01G532700 chr7D 95.668 277 7 1 1353 1624 180440130 180440406 1.800000e-119 440.0
36 TraesCS5D01G532700 chr3A 93.863 277 12 1 1353 1624 703853064 703852788 3.920000e-111 412.0
37 TraesCS5D01G532700 chr3A 85.567 291 32 7 331 619 8568250 8568532 4.120000e-76 296.0
38 TraesCS5D01G532700 chr3D 93.502 277 12 2 1353 1624 86080900 86080625 1.820000e-109 407.0
39 TraesCS5D01G532700 chr2B 87.234 282 31 3 331 612 754885727 754886003 3.160000e-82 316.0
40 TraesCS5D01G532700 chr7B 89.712 243 21 2 372 613 626587170 626586931 1.900000e-79 307.0
41 TraesCS5D01G532700 chr2D 85.461 282 37 3 331 612 569089138 569088861 1.920000e-74 291.0
42 TraesCS5D01G532700 chr3B 85.252 278 36 4 331 606 576048158 576048432 1.150000e-71 281.0
43 TraesCS5D01G532700 chr2A 83.444 302 30 12 331 612 543620764 543621065 4.180000e-66 263.0
44 TraesCS5D01G532700 chr2A 82.065 184 17 8 330 497 649006555 649006738 5.680000e-30 143.0
45 TraesCS5D01G532700 chr1A 97.727 44 1 0 889 932 94626274 94626317 5.840000e-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 TraesCS5D01G532700 chr5D 547606270 547611710 5440 True 10048.00 10048 100.00000 1 5441 1 chr5D.!!$R1 5440
1 TraesCS5D01G532700 chrUn 68493583 68497064 3481 True 3112.50 4684 98.56500 2556 5441 2 chrUn.!!$R2 2885
2 TraesCS5D01G532700 chrUn 68507874 68510227 2353 True 2011.50 3260 97.59350 1 2558 2 chrUn.!!$R3 2557
3 TraesCS5D01G532700 chr4A 621563039 621567871 4832 True 1701.75 3496 92.19525 614 5441 4 chr4A.!!$R4 4827
4 TraesCS5D01G532700 chr4A 24764260 24768065 3805 True 442.50 745 87.00325 1050 4454 4 chr4A.!!$R3 3404
5 TraesCS5D01G532700 chr5B 690905935 690910519 4584 False 1066.40 2394 88.46280 614 5438 5 chr5B.!!$F2 4824
6 TraesCS5D01G532700 chr4D 442895147 442898862 3715 False 475.00 845 88.69625 1050 4442 4 chr4D.!!$F4 3392
7 TraesCS5D01G532700 chr4B 552014241 552017872 3631 False 461.25 819 87.57700 1078 4442 4 chr4B.!!$F1 3364

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
317 319 0.598158 TGTCGGCGTGTTGGAGTTAC 60.598 55.000 6.85 0.0 0.0 2.50 F
580 582 0.828677 GGGCTGGGTATACGACTGTT 59.171 55.000 0.00 0.0 0.0 3.16 F
581 583 1.208776 GGGCTGGGTATACGACTGTTT 59.791 52.381 0.00 0.0 0.0 2.83 F
2007 2670 3.449737 TCCTAGTTCATTAAGGGGTGTCG 59.550 47.826 0.00 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2145 2832 0.465705 TGCGGCAAATTTTGGTTCCA 59.534 45.000 10.96 0.00 0.00 3.53 R
2399 3097 2.293122 TCCAATGTGCAAGCTGTTGTAC 59.707 45.455 0.13 0.13 46.37 2.90 R
2529 3248 2.689471 AGTTCAACAAGCAGCACATGAA 59.311 40.909 0.00 0.00 0.00 2.57 R
4805 5838 7.500892 ACAGTCAAATACACACTGGTTTATTGA 59.499 33.333 3.52 0.00 41.66 2.57 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
23 24 2.311463 CCCGTATGTCTCCATGACTCT 58.689 52.381 0.00 0.00 45.54 3.24
47 48 1.860484 GCTTCCACTCACTGCCAAGC 61.860 60.000 0.00 0.00 30.90 4.01
98 99 1.414919 TGACTGTAGTGGTGGTTGGAC 59.585 52.381 0.00 0.00 0.00 4.02
103 104 4.572571 GTGGTGGTTGGACGGCCA 62.573 66.667 5.41 5.41 44.17 5.36
159 161 2.504244 GCGTCCGTCTTCTGTCCG 60.504 66.667 0.00 0.00 0.00 4.79
274 276 2.567564 TTTTCGTCCGCTCCGATCCC 62.568 60.000 0.00 0.00 33.81 3.85
317 319 0.598158 TGTCGGCGTGTTGGAGTTAC 60.598 55.000 6.85 0.00 0.00 2.50
332 334 4.164604 TGGAGTTACCCTAACACAGTGTTT 59.835 41.667 23.88 8.80 41.07 2.83
512 514 2.744202 AGAAAGCGCATCGTCAGAAATT 59.256 40.909 11.47 0.00 0.00 1.82
537 539 9.806203 TTCTGAAATAAATCCAGCAATAATGTG 57.194 29.630 0.00 0.00 0.00 3.21
538 540 9.187996 TCTGAAATAAATCCAGCAATAATGTGA 57.812 29.630 0.00 0.00 0.00 3.58
539 541 9.459640 CTGAAATAAATCCAGCAATAATGTGAG 57.540 33.333 0.00 0.00 0.00 3.51
545 547 2.098607 CCAGCAATAATGTGAGCACCAG 59.901 50.000 0.00 0.00 0.00 4.00
554 556 1.230324 GTGAGCACCAGGACTTGAAC 58.770 55.000 0.00 0.00 0.00 3.18
580 582 0.828677 GGGCTGGGTATACGACTGTT 59.171 55.000 0.00 0.00 0.00 3.16
581 583 1.208776 GGGCTGGGTATACGACTGTTT 59.791 52.381 0.00 0.00 0.00 2.83
592 594 7.263496 GGTATACGACTGTTTCTCTAACCATT 58.737 38.462 0.00 0.00 35.81 3.16
635 637 4.181578 CCCTAACACAGTGTTAATCCTCG 58.818 47.826 23.46 12.63 41.70 4.63
1897 2052 4.784710 GCTGAGGTACGTATACAGTTCGAC 60.785 50.000 19.62 0.00 32.40 4.20
1900 2055 4.002982 AGGTACGTATACAGTTCGACACA 58.997 43.478 0.00 0.00 32.40 3.72
1903 2058 5.801947 GGTACGTATACAGTTCGACACATTT 59.198 40.000 0.00 0.00 32.40 2.32
1904 2059 6.966632 GGTACGTATACAGTTCGACACATTTA 59.033 38.462 0.00 0.00 32.40 1.40
1905 2060 7.645340 GGTACGTATACAGTTCGACACATTTAT 59.355 37.037 0.00 0.00 32.40 1.40
1987 2641 9.266127 CAGTGAACCTGTGAAGTTTGTACTTCC 62.266 44.444 13.69 7.31 44.17 3.46
2007 2670 3.449737 TCCTAGTTCATTAAGGGGTGTCG 59.550 47.826 0.00 0.00 0.00 4.35
2106 2792 5.049398 GTTTTCCAACGGCATACATTACA 57.951 39.130 0.00 0.00 0.00 2.41
2116 2802 6.403878 ACGGCATACATTACAGTAGAGTTTT 58.596 36.000 0.00 0.00 0.00 2.43
2306 3001 7.223777 GCAGGAGAACTTTATGAGTGATTCTAC 59.776 40.741 0.00 0.00 39.00 2.59
2399 3097 6.525121 TTTTGACTTTGACAGTAGATCACG 57.475 37.500 0.00 0.00 35.01 4.35
2437 3136 6.968904 CACATTGGAATAGTTCAAAATCGAGG 59.031 38.462 0.00 0.00 0.00 4.63
4137 5115 6.756074 TGATTTTCTTGGATTGTTCACACAAC 59.244 34.615 0.00 0.00 45.88 3.32
4805 5838 2.544267 CACTTTCCGAGCTTTTCTTCGT 59.456 45.455 0.00 0.00 0.00 3.85
4816 5849 6.002062 AGCTTTTCTTCGTCAATAAACCAG 57.998 37.500 0.00 0.00 0.00 4.00
5238 6903 4.394610 ACCACAACCAAATTTTGAGTTTGC 59.605 37.500 10.72 0.00 35.71 3.68
5239 6904 4.394300 CCACAACCAAATTTTGAGTTTGCA 59.606 37.500 10.72 0.00 35.71 4.08
5240 6905 5.106396 CCACAACCAAATTTTGAGTTTGCAA 60.106 36.000 10.72 0.00 35.71 4.08
5241 6906 6.022821 CACAACCAAATTTTGAGTTTGCAAG 58.977 36.000 10.72 4.29 35.71 4.01
5242 6907 5.704978 ACAACCAAATTTTGAGTTTGCAAGT 59.295 32.000 10.72 4.78 35.71 3.16
5243 6908 5.799681 ACCAAATTTTGAGTTTGCAAGTG 57.200 34.783 10.72 0.00 35.71 3.16
5244 6909 5.244755 ACCAAATTTTGAGTTTGCAAGTGT 58.755 33.333 10.72 0.00 35.71 3.55
5245 6910 5.351189 ACCAAATTTTGAGTTTGCAAGTGTC 59.649 36.000 10.72 0.00 35.71 3.67
5246 6911 5.350914 CCAAATTTTGAGTTTGCAAGTGTCA 59.649 36.000 10.72 1.18 35.71 3.58
5247 6912 6.037391 CCAAATTTTGAGTTTGCAAGTGTCAT 59.963 34.615 10.72 0.00 35.71 3.06
5248 6913 6.833342 AATTTTGAGTTTGCAAGTGTCATC 57.167 33.333 0.00 0.00 0.00 2.92
5249 6914 4.979943 TTTGAGTTTGCAAGTGTCATCA 57.020 36.364 0.00 0.00 0.00 3.07
5250 6915 5.518848 TTTGAGTTTGCAAGTGTCATCAT 57.481 34.783 0.00 0.00 0.00 2.45
5251 6916 4.492791 TGAGTTTGCAAGTGTCATCATG 57.507 40.909 0.00 0.00 0.00 3.07
5252 6917 4.136051 TGAGTTTGCAAGTGTCATCATGA 58.864 39.130 0.00 0.00 0.00 3.07
5253 6918 4.579753 TGAGTTTGCAAGTGTCATCATGAA 59.420 37.500 0.00 0.00 0.00 2.57
5254 6919 5.067544 TGAGTTTGCAAGTGTCATCATGAAA 59.932 36.000 0.00 0.00 0.00 2.69
5255 6920 6.092955 AGTTTGCAAGTGTCATCATGAAAT 57.907 33.333 0.00 0.00 0.00 2.17
5256 6921 7.040548 TGAGTTTGCAAGTGTCATCATGAAATA 60.041 33.333 0.00 0.00 0.00 1.40
5257 6922 7.660112 AGTTTGCAAGTGTCATCATGAAATAA 58.340 30.769 0.00 0.00 0.00 1.40
5258 6923 8.143193 AGTTTGCAAGTGTCATCATGAAATAAA 58.857 29.630 0.00 0.00 0.00 1.40
5259 6924 8.763356 GTTTGCAAGTGTCATCATGAAATAAAA 58.237 29.630 0.00 0.00 0.00 1.52
5260 6925 9.491675 TTTGCAAGTGTCATCATGAAATAAAAT 57.508 25.926 0.00 0.00 0.00 1.82
5261 6926 9.491675 TTGCAAGTGTCATCATGAAATAAAATT 57.508 25.926 0.00 0.00 0.00 1.82
5262 6927 9.491675 TGCAAGTGTCATCATGAAATAAAATTT 57.508 25.926 0.00 0.00 0.00 1.82
5263 6928 9.749490 GCAAGTGTCATCATGAAATAAAATTTG 57.251 29.630 0.00 0.15 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 0.243907 GCAGTGAGTGGAAGCGTCTA 59.756 55.000 0.00 0.00 0.00 2.59
47 48 2.530701 CTACCTACCATAGAGGGCCTG 58.469 57.143 12.95 0.00 43.89 4.85
159 161 2.553602 TGTGTCTGATTTGCATCCACAC 59.446 45.455 10.58 10.58 40.04 3.82
167 169 4.627035 GGCCTAAATTTGTGTCTGATTTGC 59.373 41.667 0.00 0.00 0.00 3.68
274 276 3.613702 GTCCGCGCGTATCCGTTG 61.614 66.667 29.95 10.76 36.15 4.10
332 334 6.205784 GCTTGCATCTGTACTGTGTTAAAAA 58.794 36.000 0.00 0.00 0.00 1.94
512 514 9.187996 TCACATTATTGCTGGATTTATTTCAGA 57.812 29.630 0.00 0.00 0.00 3.27
528 530 3.614092 AGTCCTGGTGCTCACATTATTG 58.386 45.455 2.21 0.00 0.00 1.90
529 531 4.012374 CAAGTCCTGGTGCTCACATTATT 58.988 43.478 2.21 0.00 0.00 1.40
530 532 3.264193 TCAAGTCCTGGTGCTCACATTAT 59.736 43.478 2.21 0.00 0.00 1.28
531 533 2.637382 TCAAGTCCTGGTGCTCACATTA 59.363 45.455 2.21 0.00 0.00 1.90
532 534 1.421268 TCAAGTCCTGGTGCTCACATT 59.579 47.619 2.21 0.00 0.00 2.71
533 535 1.059098 TCAAGTCCTGGTGCTCACAT 58.941 50.000 2.21 0.00 0.00 3.21
534 536 0.836606 TTCAAGTCCTGGTGCTCACA 59.163 50.000 2.21 0.00 0.00 3.58
535 537 1.230324 GTTCAAGTCCTGGTGCTCAC 58.770 55.000 0.00 0.00 0.00 3.51
536 538 0.108585 GGTTCAAGTCCTGGTGCTCA 59.891 55.000 0.00 0.00 0.00 4.26
537 539 0.606673 GGGTTCAAGTCCTGGTGCTC 60.607 60.000 0.00 0.00 0.00 4.26
538 540 1.062488 AGGGTTCAAGTCCTGGTGCT 61.062 55.000 0.00 0.00 31.11 4.40
539 541 0.890996 CAGGGTTCAAGTCCTGGTGC 60.891 60.000 0.00 0.00 44.99 5.01
580 582 4.104102 ACCTGTGGTTGAATGGTTAGAGAA 59.896 41.667 0.00 0.00 27.29 2.87
581 583 3.650942 ACCTGTGGTTGAATGGTTAGAGA 59.349 43.478 0.00 0.00 27.29 3.10
635 637 1.060937 GTCATGCATGCGAACGTCC 59.939 57.895 22.25 0.00 0.00 4.79
684 686 0.392729 AGGTGCTAGCGAGTACGAGT 60.393 55.000 10.77 0.00 39.07 4.18
693 695 2.202623 GTCGTGGAGGTGCTAGCG 60.203 66.667 10.77 0.00 0.00 4.26
1378 1457 1.519455 CGTGACGGCCTGGATCTTC 60.519 63.158 0.00 0.00 0.00 2.87
1987 2641 4.430908 GACGACACCCCTTAATGAACTAG 58.569 47.826 0.00 0.00 0.00 2.57
1988 2642 3.119388 CGACGACACCCCTTAATGAACTA 60.119 47.826 0.00 0.00 0.00 2.24
1990 2644 1.997606 CGACGACACCCCTTAATGAAC 59.002 52.381 0.00 0.00 0.00 3.18
2007 2670 0.595567 TAACACGACTGCACCACGAC 60.596 55.000 8.94 0.00 0.00 4.34
2142 2829 1.069978 CGGCAAATTTTGGTTCCACCT 59.930 47.619 10.96 0.00 39.58 4.00
2143 2830 1.507562 CGGCAAATTTTGGTTCCACC 58.492 50.000 10.96 1.92 39.22 4.61
2144 2831 0.865111 GCGGCAAATTTTGGTTCCAC 59.135 50.000 10.96 0.00 0.00 4.02
2145 2832 0.465705 TGCGGCAAATTTTGGTTCCA 59.534 45.000 10.96 0.00 0.00 3.53
2306 3001 6.629963 GCTCTGTATATCCCTCATGATCCTTG 60.630 46.154 0.00 0.00 0.00 3.61
2399 3097 2.293122 TCCAATGTGCAAGCTGTTGTAC 59.707 45.455 0.13 0.13 46.37 2.90
2437 3136 4.158394 ACATGATTGCCATAACAAGTGTCC 59.842 41.667 0.00 0.00 33.31 4.02
2529 3248 2.689471 AGTTCAACAAGCAGCACATGAA 59.311 40.909 0.00 0.00 0.00 2.57
4805 5838 7.500892 ACAGTCAAATACACACTGGTTTATTGA 59.499 33.333 3.52 0.00 41.66 2.57
4816 5849 5.756347 TCACTACCAACAGTCAAATACACAC 59.244 40.000 0.00 0.00 0.00 3.82
4904 6535 9.116067 TCTCAAAATACCGAAAGAAGAAAAGAA 57.884 29.630 0.00 0.00 0.00 2.52
4905 6536 8.557029 GTCTCAAAATACCGAAAGAAGAAAAGA 58.443 33.333 0.00 0.00 0.00 2.52
4906 6537 8.560374 AGTCTCAAAATACCGAAAGAAGAAAAG 58.440 33.333 0.00 0.00 0.00 2.27
5257 6922 9.743057 TGAACATTTACGATCAAACTCAAATTT 57.257 25.926 0.00 0.00 0.00 1.82
5258 6923 9.912634 ATGAACATTTACGATCAAACTCAAATT 57.087 25.926 0.00 0.00 0.00 1.82
5261 6926 9.986833 CATATGAACATTTACGATCAAACTCAA 57.013 29.630 0.00 0.00 0.00 3.02
5262 6927 9.161629 ACATATGAACATTTACGATCAAACTCA 57.838 29.630 10.38 0.00 0.00 3.41
5263 6928 9.988350 AACATATGAACATTTACGATCAAACTC 57.012 29.630 10.38 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.