Multiple sequence alignment - TraesCS7B01G186000

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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 TraesCS7B01G186000 chr7B 100.000 2549 0 0 1 2549 304994146 304991598 0.000000e+00 4708.0
1 TraesCS7B01G186000 chr5A 93.580 1729 100 9 1 1724 671915645 671913923 0.000000e+00 2567.0
2 TraesCS7B01G186000 chr5A 95.558 833 32 4 1720 2549 671892831 671892001 0.000000e+00 1328.0
3 TraesCS7B01G186000 chr4A 92.121 1726 131 4 1 1724 28974510 28972788 0.000000e+00 2429.0
4 TraesCS7B01G186000 chr4A 92.784 1649 107 6 1 1645 374434029 374435669 0.000000e+00 2375.0
5 TraesCS7B01G186000 chr4A 95.084 834 38 3 1717 2549 374436405 374437236 0.000000e+00 1310.0
6 TraesCS7B01G186000 chr4A 94.826 831 40 3 1720 2549 28886971 28886143 0.000000e+00 1293.0
7 TraesCS7B01G186000 chr1A 89.625 1735 155 16 7 1724 13270012 13268286 0.000000e+00 2183.0
8 TraesCS7B01G186000 chr1A 80.916 262 48 2 1004 1264 250648792 250648532 3.320000e-49 206.0
9 TraesCS7B01G186000 chr3B 87.356 1740 177 25 1 1724 648187226 648185514 0.000000e+00 1954.0
10 TraesCS7B01G186000 chr3B 92.467 823 55 5 1727 2549 648181096 648180281 0.000000e+00 1170.0
11 TraesCS7B01G186000 chr1D 90.385 1404 119 9 334 1724 20334354 20332954 0.000000e+00 1831.0
12 TraesCS7B01G186000 chr6B 95.293 956 44 1 742 1697 706187961 706187007 0.000000e+00 1515.0
13 TraesCS7B01G186000 chr6B 96.029 831 30 3 1720 2549 706162143 706161315 0.000000e+00 1349.0
14 TraesCS7B01G186000 chr6B 88.750 160 17 1 856 1014 706188115 706187956 7.200000e-46 195.0
15 TraesCS7B01G186000 chr6B 79.412 136 28 0 2285 2420 658559605 658559470 2.090000e-16 97.1
16 TraesCS7B01G186000 chr1B 96.064 559 19 3 1 557 566990944 566991501 0.000000e+00 907.0
17 TraesCS7B01G186000 chr1B 92.009 463 35 2 553 1014 566993531 566993992 0.000000e+00 649.0
18 TraesCS7B01G186000 chr2A 82.320 543 77 10 505 1045 767551357 767551882 1.080000e-123 453.0
19 TraesCS7B01G186000 chr2A 82.396 409 61 10 1 404 767528165 767528567 1.880000e-91 346.0
20 TraesCS7B01G186000 chr7A 76.093 732 167 7 996 1723 675494267 675494994 2.390000e-100 375.0
21 TraesCS7B01G186000 chr2D 76.039 722 165 8 1007 1724 431392367 431391650 4.010000e-98 368.0
22 TraesCS7B01G186000 chr6A 78.857 175 37 0 2243 2417 615376622 615376796 4.450000e-23 119.0
23 TraesCS7B01G186000 chr4B 80.488 123 24 0 2267 2389 63806066 63806188 7.510000e-16 95.3
24 TraesCS7B01G186000 chr2B 77.953 127 25 3 2292 2417 314764330 314764454 2.720000e-10 76.8
25 TraesCS7B01G186000 chr2B 79.439 107 18 3 2045 2149 358776567 358776671 3.520000e-09 73.1


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 TraesCS7B01G186000 chr7B 304991598 304994146 2548 True 4708.0 4708 100.0000 1 2549 1 chr7B.!!$R1 2548
1 TraesCS7B01G186000 chr5A 671913923 671915645 1722 True 2567.0 2567 93.5800 1 1724 1 chr5A.!!$R2 1723
2 TraesCS7B01G186000 chr5A 671892001 671892831 830 True 1328.0 1328 95.5580 1720 2549 1 chr5A.!!$R1 829
3 TraesCS7B01G186000 chr4A 28972788 28974510 1722 True 2429.0 2429 92.1210 1 1724 1 chr4A.!!$R2 1723
4 TraesCS7B01G186000 chr4A 374434029 374437236 3207 False 1842.5 2375 93.9340 1 2549 2 chr4A.!!$F1 2548
5 TraesCS7B01G186000 chr4A 28886143 28886971 828 True 1293.0 1293 94.8260 1720 2549 1 chr4A.!!$R1 829
6 TraesCS7B01G186000 chr1A 13268286 13270012 1726 True 2183.0 2183 89.6250 7 1724 1 chr1A.!!$R1 1717
7 TraesCS7B01G186000 chr3B 648185514 648187226 1712 True 1954.0 1954 87.3560 1 1724 1 chr3B.!!$R2 1723
8 TraesCS7B01G186000 chr3B 648180281 648181096 815 True 1170.0 1170 92.4670 1727 2549 1 chr3B.!!$R1 822
9 TraesCS7B01G186000 chr1D 20332954 20334354 1400 True 1831.0 1831 90.3850 334 1724 1 chr1D.!!$R1 1390
10 TraesCS7B01G186000 chr6B 706161315 706162143 828 True 1349.0 1349 96.0290 1720 2549 1 chr6B.!!$R2 829
11 TraesCS7B01G186000 chr6B 706187007 706188115 1108 True 855.0 1515 92.0215 742 1697 2 chr6B.!!$R3 955
12 TraesCS7B01G186000 chr1B 566990944 566993992 3048 False 778.0 907 94.0365 1 1014 2 chr1B.!!$F1 1013
13 TraesCS7B01G186000 chr2A 767551357 767551882 525 False 453.0 453 82.3200 505 1045 1 chr2A.!!$F2 540
14 TraesCS7B01G186000 chr7A 675494267 675494994 727 False 375.0 375 76.0930 996 1723 1 chr7A.!!$F1 727
15 TraesCS7B01G186000 chr2D 431391650 431392367 717 True 368.0 368 76.0390 1007 1724 1 chr2D.!!$R1 717

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
887 2937 0.179018 CCTCGCCCCCTCCTATTTTG 60.179 60.0 0.0 0.0 0.0 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1864 4582 1.160137 GTGAGAGCGCAAATCACCTT 58.84 50.0 21.93 0.0 37.88 3.5 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
34 35 0.970427 AAACGCCATGTGGATTCCCC 60.970 55.000 2.55 0.00 37.39 4.81
119 122 4.637534 CACACATGCAAAAGTCTATAGGCT 59.362 41.667 0.00 0.00 0.00 4.58
145 148 0.456142 TCGCAGCTGACATGTACGAC 60.456 55.000 20.43 0.00 0.00 4.34
153 156 3.502920 CTGACATGTACGACCAGAACTC 58.497 50.000 0.00 0.00 0.00 3.01
167 170 0.610687 GAACTCTGGGCAGCTGTACT 59.389 55.000 16.64 0.00 0.00 2.73
177 180 1.060713 CAGCTGTACTTGTTCGACCG 58.939 55.000 5.25 0.00 0.00 4.79
316 319 5.068067 GCAAGTTGGTTTCCTTTAGGTACAA 59.932 40.000 4.75 0.00 36.34 2.41
367 371 9.575783 TGTTTTGTTTCACTAATTTTCAGGTAC 57.424 29.630 0.00 0.00 0.00 3.34
390 394 3.695556 TGCCCATGATATTGACAAGTGTG 59.304 43.478 0.00 0.00 0.00 3.82
454 458 5.772521 CATGATGCATGTCATGTGATGATT 58.227 37.500 18.29 0.00 46.56 2.57
492 504 6.337356 AGTTAAACACTTGGTTGGAACATTG 58.663 36.000 0.00 0.00 40.35 2.82
579 2625 4.273480 GCCAGTTCAGTTATTATGCGTGAT 59.727 41.667 0.00 0.00 0.00 3.06
643 2689 7.496263 GGTTCTCTTTTTAGGGTCATGTATCTC 59.504 40.741 0.00 0.00 0.00 2.75
675 2721 4.308458 CGCCGTCACCTCACCCAA 62.308 66.667 0.00 0.00 0.00 4.12
780 2826 4.500116 GAGCACCGACTCCCTCGC 62.500 72.222 0.00 0.00 41.46 5.03
821 2868 0.400213 ACGAGGTTGATTCTTGGCCA 59.600 50.000 0.00 0.00 0.00 5.36
884 2934 2.122369 CCCTCGCCCCCTCCTATT 60.122 66.667 0.00 0.00 0.00 1.73
887 2937 0.179018 CCTCGCCCCCTCCTATTTTG 60.179 60.000 0.00 0.00 0.00 2.44
927 2977 1.340248 TCCTTCTCTGTTCGTGGTGTC 59.660 52.381 0.00 0.00 0.00 3.67
1349 3400 1.152963 AGGGCGTGCTTGAACTGTT 60.153 52.632 0.00 0.00 0.00 3.16
1434 3485 1.523258 CGAGCCATCAGAAGCCTGG 60.523 63.158 0.00 0.00 40.76 4.45
1457 3508 0.249398 GAGTACACCCGAATGGCAGT 59.751 55.000 0.00 0.00 37.83 4.40
1546 3597 0.542232 AGCGTCCTCCCAAGTACAGT 60.542 55.000 0.00 0.00 0.00 3.55
1602 3653 2.352422 GGTCATGTGCTGGCTCCA 59.648 61.111 0.00 0.00 0.00 3.86
1647 3698 3.285484 CATAGATTTCTGGGCTGCACTT 58.715 45.455 2.50 0.00 0.00 3.16
1724 4439 3.799366 TGTTTCAAGCCGTCAGAAAGTA 58.201 40.909 0.00 0.00 32.48 2.24
1725 4440 3.558418 TGTTTCAAGCCGTCAGAAAGTAC 59.442 43.478 0.00 0.00 32.48 2.73
1813 4529 5.464168 CGGTCAAATTGAAGCTTCTCAAAT 58.536 37.500 26.09 15.08 38.75 2.32
1840 4558 2.421424 GAGGAACAGATGCATTGGACAC 59.579 50.000 0.00 0.00 0.00 3.67
1864 4582 1.229082 AGGCACGTACCCCTTCAGA 60.229 57.895 0.00 0.00 0.00 3.27
1891 4609 0.603707 TTGCGCTCTCACTCCTTTGG 60.604 55.000 9.73 0.00 0.00 3.28
1897 4615 0.397941 TCTCACTCCTTTGGGTGCTG 59.602 55.000 0.00 0.00 33.91 4.41
1924 4642 4.901197 TTTAGCACAGAAGACACCCATA 57.099 40.909 0.00 0.00 0.00 2.74
1966 4684 2.304092 TGCCGGACTTCGTATATCTGT 58.696 47.619 5.05 0.00 37.11 3.41
2201 4919 1.748950 TGCAATTTCCATAGAGCGCA 58.251 45.000 11.47 0.00 0.00 6.09
2257 4975 4.382685 CCACCAACCATACGTATGAACTCT 60.383 45.833 32.19 11.96 35.75 3.24
2360 5078 2.285083 CACCAACGAAGAGACCAAACA 58.715 47.619 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 4.344474 GAGGGATACGCGGCGAGG 62.344 72.222 30.94 3.44 37.60 4.63
153 156 1.160137 GAACAAGTACAGCTGCCCAG 58.840 55.000 15.27 2.77 0.00 4.45
167 170 3.993584 CGTCCCCCGGTCGAACAA 61.994 66.667 0.00 0.00 36.43 2.83
316 319 1.802365 GTTTGGTTCAGTACGGCGAAT 59.198 47.619 16.62 0.00 0.00 3.34
366 370 3.949754 CACTTGTCAATATCATGGGCAGT 59.050 43.478 0.00 0.00 0.00 4.40
367 371 3.949754 ACACTTGTCAATATCATGGGCAG 59.050 43.478 0.00 0.00 0.00 4.85
390 394 2.640184 GGGCACATCTTACTAACCCAC 58.360 52.381 0.00 0.00 35.84 4.61
492 504 1.000233 TGAACGCGTCGTCTACTTGC 61.000 55.000 14.44 0.00 39.99 4.01
643 2689 3.619483 TGACGGCGTAGTAAATTCCAATG 59.381 43.478 14.74 0.00 0.00 2.82
802 2848 0.400213 TGGCCAAGAATCAACCTCGT 59.600 50.000 0.61 0.00 0.00 4.18
884 2934 0.171455 GACACCACAACGCCAACAAA 59.829 50.000 0.00 0.00 0.00 2.83
887 2937 1.152989 TACGACACCACAACGCCAAC 61.153 55.000 0.00 0.00 0.00 3.77
927 2977 0.599728 GCGAGCTAGGGATGAGCAAG 60.600 60.000 0.00 0.00 42.69 4.01
977 3028 4.161189 TCCTCACTTCTCTAATTGCCTCAG 59.839 45.833 0.00 0.00 0.00 3.35
1231 3282 2.615912 GCCATGCCTTCACATCTAGAAC 59.384 50.000 0.00 0.00 0.00 3.01
1239 3290 0.401356 TCTTCTGCCATGCCTTCACA 59.599 50.000 0.00 0.00 0.00 3.58
1326 3377 1.153066 TTCAAGCACGCCCTGTTCA 60.153 52.632 0.00 0.00 0.00 3.18
1349 3400 9.393249 CAAAAACATAATTAAGCTTCTGTTCGA 57.607 29.630 0.00 0.00 28.67 3.71
1434 3485 1.868519 GCCATTCGGGTGTACTCGATC 60.869 57.143 7.92 0.00 39.65 3.69
1457 3508 2.225491 GTGCCTTTGTCGCTGAATGTTA 59.775 45.455 0.00 0.00 0.00 2.41
1546 3597 6.265196 ACAAATGCAATCTTGAAACAGTCCTA 59.735 34.615 12.07 0.00 0.00 2.94
1647 3698 8.886719 CAACTCTTGATCTTGCTAATGTCATTA 58.113 33.333 5.19 5.19 0.00 1.90
1725 4440 1.161843 AAAACTCCATACGTTGCCCG 58.838 50.000 0.00 0.00 44.03 6.13
1813 4529 2.275134 TGCATCTGTTCCTCAAGCAA 57.725 45.000 0.00 0.00 0.00 3.91
1840 4558 3.782443 GGGTACGTGCCTCCAGGG 61.782 72.222 22.50 0.00 35.18 4.45
1864 4582 1.160137 GTGAGAGCGCAAATCACCTT 58.840 50.000 21.93 0.00 37.88 3.50
1897 4615 4.083271 GGTGTCTTCTGTGCTAAAATGACC 60.083 45.833 0.00 0.00 0.00 4.02
2201 4919 8.812972 TCCACAAACTATACTTACAGATCAAGT 58.187 33.333 0.00 0.00 39.50 3.16
2257 4975 1.487142 TCTTTCAAGTGGGTGTTCCGA 59.513 47.619 0.00 0.00 38.76 4.55
2350 5068 5.468072 CCTATATGACATGCTGTTTGGTCTC 59.532 44.000 0.00 0.00 0.00 3.36
2360 5078 4.357918 GGACCAACCTATATGACATGCT 57.642 45.455 0.00 0.00 35.41 3.79
2431 5149 1.519246 GGTTACGAGTAGGGGGTGC 59.481 63.158 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.