Multiple sequence alignment - TraesCS2B01G287100

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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 TraesCS2B01G287100 chr2B 100.000 4479 0 0 1 4479 396194216 396189738 0.000000e+00 8272.0
1 TraesCS2B01G287100 chr2A 96.604 3769 98 12 727 4479 390882043 390885797 0.000000e+00 6224.0
2 TraesCS2B01G287100 chr2D 96.210 3773 106 16 727 4479 326459484 326455729 0.000000e+00 6141.0
3 TraesCS2B01G287100 chr2D 100.000 29 0 0 698 726 186809112 186809140 2.000000e-03 54.7
4 TraesCS2B01G287100 chr3D 94.094 745 25 11 1 734 404977950 404977214 0.000000e+00 1114.0
5 TraesCS2B01G287100 chr1D 89.407 708 33 17 33 728 54936495 54937172 0.000000e+00 854.0
6 TraesCS2B01G287100 chr1D 91.481 270 16 3 472 734 10950306 10950037 9.160000e-97 364.0
7 TraesCS2B01G287100 chr1D 88.830 188 12 7 176 360 10950500 10950319 5.830000e-54 222.0
8 TraesCS2B01G287100 chr1D 78.750 320 46 17 1 309 54936501 54936809 1.270000e-45 195.0
9 TraesCS2B01G287100 chr1D 88.189 127 9 5 1 123 10950494 10950370 3.610000e-31 147.0
10 TraesCS2B01G287100 chr7D 79.627 751 86 29 25 726 371785926 371786658 1.130000e-130 477.0
11 TraesCS2B01G287100 chr4A 92.857 168 10 1 467 634 667367715 667367880 4.480000e-60 243.0
12 TraesCS2B01G287100 chrUn 90.698 172 16 0 520 691 329546476 329546305 3.480000e-56 230.0
13 TraesCS2B01G287100 chr1B 84.277 159 22 2 471 629 488480735 488480890 7.760000e-33 152.0
14 TraesCS2B01G287100 chr6B 79.839 124 15 9 5 122 659586790 659586671 1.030000e-11 82.4


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 TraesCS2B01G287100 chr2B 396189738 396194216 4478 True 8272.0 8272 100.0000 1 4479 1 chr2B.!!$R1 4478
1 TraesCS2B01G287100 chr2A 390882043 390885797 3754 False 6224.0 6224 96.6040 727 4479 1 chr2A.!!$F1 3752
2 TraesCS2B01G287100 chr2D 326455729 326459484 3755 True 6141.0 6141 96.2100 727 4479 1 chr2D.!!$R1 3752
3 TraesCS2B01G287100 chr3D 404977214 404977950 736 True 1114.0 1114 94.0940 1 734 1 chr3D.!!$R1 733
4 TraesCS2B01G287100 chr1D 54936495 54937172 677 False 524.5 854 84.0785 1 728 2 chr1D.!!$F1 727
5 TraesCS2B01G287100 chr7D 371785926 371786658 732 False 477.0 477 79.6270 25 726 1 chr7D.!!$F1 701

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
993 1077 0.177373 AGGATTCTTACCGGCCGTTC 59.823 55.0 26.12 1.33 0.00 3.95 F
1474 1570 0.032416 GCCTCCTACAGGTACCTCCA 60.032 60.0 12.84 1.12 45.61 3.86 F
1957 2055 0.890996 CCTCCAACTGCCTTCCACAC 60.891 60.0 0.00 0.00 0.00 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2186 2284 0.538057 CAAAGAACTGGCTGCTGGGA 60.538 55.000 0.00 0.00 0.00 4.37 R
2377 2475 1.089920 CTGCACTTGTACCTGGCATC 58.910 55.000 0.00 0.00 33.50 3.91 R
3630 3728 1.203994 GCACAAGCTTGCCATCAGAAT 59.796 47.619 26.27 0.04 36.42 2.40 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
219 241 6.215495 AGGGAAAAAGTTCGTTGAATTTGA 57.785 33.333 0.00 0.00 34.28 2.69
415 481 6.984740 TTCAATTTGAATTAGTTCGTGCAC 57.015 33.333 6.82 6.82 37.15 4.57
491 559 5.196341 GGAAAAACCGTTCCAGAAAGAAT 57.804 39.130 0.00 0.00 45.57 2.40
533 604 2.038387 ACCGCCTGGCAAACTATAAG 57.962 50.000 20.29 0.00 39.70 1.73
846 924 0.250166 CGTTTCCTTTCCCTCCACGT 60.250 55.000 0.00 0.00 0.00 4.49
913 991 1.033202 ACCAACAAAAACCGCCGAGT 61.033 50.000 0.00 0.00 0.00 4.18
929 1007 2.219325 GAGTCGCACACAGAGGGAGG 62.219 65.000 0.00 0.00 0.00 4.30
950 1030 3.189702 GGGAGAGATAGAAAGACGATCGG 59.810 52.174 20.98 1.23 36.11 4.18
954 1034 6.452494 AGAGATAGAAAGACGATCGGAAAA 57.548 37.500 20.98 0.00 36.11 2.29
955 1035 6.864342 AGAGATAGAAAGACGATCGGAAAAA 58.136 36.000 20.98 0.00 36.11 1.94
993 1077 0.177373 AGGATTCTTACCGGCCGTTC 59.823 55.000 26.12 1.33 0.00 3.95
1281 1377 4.945645 TCCCTCAAGGAGTCACGT 57.054 55.556 0.00 0.00 40.93 4.49
1472 1568 1.108132 CCGCCTCCTACAGGTACCTC 61.108 65.000 12.84 0.00 45.61 3.85
1474 1570 0.032416 GCCTCCTACAGGTACCTCCA 60.032 60.000 12.84 1.12 45.61 3.86
1498 1594 4.974721 CACCCTGTGCACCCCACC 62.975 72.222 15.69 0.00 44.01 4.61
1541 1638 7.494298 TGCTAGTCTATGCGATTGTTATTTTCA 59.506 33.333 0.00 0.00 0.00 2.69
1657 1754 6.844696 AAGTGTGTACTGTCATAAGTTGTG 57.155 37.500 0.00 0.00 37.19 3.33
1695 1792 7.810766 TTTTTGTTTAGTTTCTGAACTGCAG 57.189 32.000 13.48 13.48 45.46 4.41
1740 1837 4.778213 AGCACACCAGTTACATGGATAT 57.222 40.909 0.00 0.00 43.57 1.63
1758 1855 8.582437 CATGGATATTAGATGGCTTGTCAATTT 58.418 33.333 0.00 0.00 0.00 1.82
1924 2022 6.481644 TGTATTTCCATTTGAAAAACTGGCAC 59.518 34.615 0.00 0.00 45.67 5.01
1957 2055 0.890996 CCTCCAACTGCCTTCCACAC 60.891 60.000 0.00 0.00 0.00 3.82
2009 2107 4.621274 GCTTTTGCCATCCATACATTGTGT 60.621 41.667 0.00 0.00 40.15 3.72
2015 2113 6.003326 TGCCATCCATACATTGTGTATTAGG 58.997 40.000 0.00 1.10 40.40 2.69
2023 2121 8.612619 CCATACATTGTGTATTAGGTTTCAGTC 58.387 37.037 0.00 0.00 40.40 3.51
2039 2137 1.556911 CAGTCTATCACCTGGTGGCTT 59.443 52.381 25.67 13.72 36.63 4.35
2049 2147 2.017049 CCTGGTGGCTTGTGCTATTAC 58.983 52.381 0.00 0.00 39.59 1.89
2059 2157 5.007136 GGCTTGTGCTATTACTCATCTTGAC 59.993 44.000 0.00 0.00 39.59 3.18
2071 2169 8.918202 TTACTCATCTTGACATTAACAAGGTT 57.082 30.769 0.00 0.00 43.11 3.50
2186 2284 3.324268 TCAAATGCCAACAACATGTCCAT 59.676 39.130 0.00 0.00 0.00 3.41
2280 2378 3.370846 CCAAGAGAATATGTGCTGGACCA 60.371 47.826 0.00 0.00 0.00 4.02
2377 2475 5.639506 CACCAGTTATTGACTTACTGTCCTG 59.360 44.000 0.00 0.00 44.75 3.86
2415 2513 1.141657 AGCCTCTCAACTGCAAACTGA 59.858 47.619 0.00 0.00 0.00 3.41
2416 2514 1.534595 GCCTCTCAACTGCAAACTGAG 59.465 52.381 11.39 11.39 38.34 3.35
2565 2663 2.818921 TCCCATGGGAAATGAACTTGG 58.181 47.619 32.09 0.00 42.05 3.61
2755 2853 2.322355 AATCAAGCACCCAGAGATCG 57.678 50.000 0.00 0.00 0.00 3.69
3186 3284 1.527034 TGAAGCCAATGTCAGCAGAC 58.473 50.000 1.64 1.64 45.19 3.51
3303 3401 4.641989 ACAAATCTTCCATGCATACCTGTC 59.358 41.667 0.00 0.00 0.00 3.51
3375 3473 7.516209 AGGATAAAGATTGTTAGCCCTGGTATA 59.484 37.037 0.00 0.00 39.85 1.47
3426 3524 8.402472 TCTCATGTACAACAGGTTTTAAAGTTG 58.598 33.333 13.55 13.55 45.02 3.16
3516 3614 3.189910 TGAACATCACAAAGAGCAGATGC 59.810 43.478 0.00 0.00 41.08 3.91
3518 3616 2.290768 ACATCACAAAGAGCAGATGCCT 60.291 45.455 0.14 0.00 41.08 4.75
3522 3620 2.818432 CACAAAGAGCAGATGCCTTCTT 59.182 45.455 0.14 2.48 43.38 2.52
3630 3728 3.419943 TCTTTCAGCATTACACATGGCA 58.580 40.909 0.00 0.00 0.00 4.92
3820 3918 4.448732 GCTTTTGGTGCTCCTAAAATGTTG 59.551 41.667 13.91 5.17 37.81 3.33
3948 4047 0.035152 TTGTGCTGGCTGGTCCTATG 60.035 55.000 0.00 0.00 35.26 2.23
4088 4196 9.661187 CATCTCTTGCATCATGTAAATTTCTAC 57.339 33.333 0.00 0.00 0.00 2.59
4090 4198 7.549134 TCTCTTGCATCATGTAAATTTCTACGT 59.451 33.333 0.00 0.00 0.00 3.57
4093 4201 8.667987 TTGCATCATGTAAATTTCTACGTTTC 57.332 30.769 0.00 0.00 0.00 2.78
4097 4208 7.731882 TCATGTAAATTTCTACGTTTCCACA 57.268 32.000 0.00 0.00 0.00 4.17
4106 4217 2.240493 ACGTTTCCACACTCTCCTTG 57.760 50.000 0.00 0.00 0.00 3.61
4216 4327 7.004086 AGGGAGATACAGTTCTAAGATGAGAG 58.996 42.308 0.00 0.00 0.00 3.20
4430 4541 3.847602 CTCCGAGCCAGCTCCAGG 61.848 72.222 13.83 10.20 39.77 4.45
4431 4542 4.382541 TCCGAGCCAGCTCCAGGA 62.383 66.667 13.83 12.28 39.77 3.86
4432 4543 4.154347 CCGAGCCAGCTCCAGGAC 62.154 72.222 13.83 0.00 39.77 3.85
4433 4544 4.154347 CGAGCCAGCTCCAGGACC 62.154 72.222 13.83 0.00 39.77 4.46
4434 4545 3.005539 GAGCCAGCTCCAGGACCA 61.006 66.667 8.51 0.00 37.11 4.02
4435 4546 3.007920 AGCCAGCTCCAGGACCAG 61.008 66.667 0.00 0.00 0.00 4.00
4453 4564 4.660168 ACCAGAATGTCTTGAGAGCAAAT 58.340 39.130 0.00 0.00 32.73 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
225 247 6.381801 GTGAACTGTTTCAAATCCGATGAAT 58.618 36.000 0.00 0.00 43.52 2.57
242 283 4.734917 TGTTTTACAAAACCGGTGAACTG 58.265 39.130 8.52 5.85 45.82 3.16
479 547 3.318839 CCTGTTGTGCATTCTTTCTGGAA 59.681 43.478 0.00 0.00 0.00 3.53
517 588 3.251972 GCATCTCTTATAGTTTGCCAGGC 59.748 47.826 3.66 3.66 32.64 4.85
533 604 4.440663 GGCAATTACCTTCCTTTGCATCTC 60.441 45.833 8.53 0.00 44.77 2.75
604 676 1.339929 GATTTGAACCCGCAACCTGTT 59.660 47.619 0.00 0.00 0.00 3.16
691 763 3.053291 CTAACGGGCGCCTTTGCA 61.053 61.111 28.56 7.26 37.32 4.08
846 924 4.286297 ACGAATGGAATTGGAGTGAGAA 57.714 40.909 0.00 0.00 36.07 2.87
913 991 2.997315 CCCTCCCTCTGTGTGCGA 60.997 66.667 0.00 0.00 0.00 5.10
929 1007 4.066490 TCCGATCGTCTTTCTATCTCTCC 58.934 47.826 15.09 0.00 0.00 3.71
954 1034 5.947663 TCCTAGATCTCGATCTCTCCTTTT 58.052 41.667 12.39 0.00 44.37 2.27
955 1035 5.576563 TCCTAGATCTCGATCTCTCCTTT 57.423 43.478 12.39 0.00 44.37 3.11
1472 1568 0.179020 TGCACAGGGTGAAAGAGTGG 60.179 55.000 0.00 0.00 35.23 4.00
1474 1570 0.179018 GGTGCACAGGGTGAAAGAGT 60.179 55.000 20.43 0.00 35.23 3.24
1541 1638 4.741928 AACAAGGGGTTGGAATCTAGTT 57.258 40.909 0.00 0.00 38.60 2.24
1695 1792 6.952773 TGTGGCCCAAAATATATCTAACAC 57.047 37.500 0.00 0.00 0.00 3.32
1740 1837 7.230510 ACTGTAACAAATTGACAAGCCATCTAA 59.769 33.333 0.00 0.00 0.00 2.10
1758 1855 8.402472 CACAGTCCAATTCTAAAAACTGTAACA 58.598 33.333 5.72 0.00 43.91 2.41
1924 2022 4.334759 CAGTTGGAGGAGAAATACTGCATG 59.665 45.833 0.00 0.00 39.46 4.06
1957 2055 1.032794 TAGGACATGACTAGGCTGCG 58.967 55.000 0.00 0.00 0.00 5.18
2009 2107 6.901300 ACCAGGTGATAGACTGAAACCTAATA 59.099 38.462 0.00 0.00 39.24 0.98
2015 2113 3.600388 CCACCAGGTGATAGACTGAAAC 58.400 50.000 22.37 0.00 36.86 2.78
2023 2121 1.742761 CACAAGCCACCAGGTGATAG 58.257 55.000 22.37 10.10 35.23 2.08
2039 2137 9.098355 GTTAATGTCAAGATGAGTAATAGCACA 57.902 33.333 0.00 0.00 0.00 4.57
2049 2147 6.656693 AGGAACCTTGTTAATGTCAAGATGAG 59.343 38.462 6.00 0.00 43.17 2.90
2059 2157 9.981114 AATAACAGAAAAGGAACCTTGTTAATG 57.019 29.630 15.26 9.79 36.26 1.90
2071 2169 5.951747 AGCCTGCAATAATAACAGAAAAGGA 59.048 36.000 0.00 0.00 33.10 3.36
2186 2284 0.538057 CAAAGAACTGGCTGCTGGGA 60.538 55.000 0.00 0.00 0.00 4.37
2280 2378 2.380064 TTGGGTTCAAGCTTGTGGAT 57.620 45.000 25.19 0.00 0.00 3.41
2334 2432 3.273434 GTGATGCTGCAGGAAATGACTA 58.727 45.455 13.45 0.00 0.00 2.59
2377 2475 1.089920 CTGCACTTGTACCTGGCATC 58.910 55.000 0.00 0.00 33.50 3.91
2539 2637 3.795688 TCATTTCCCATGGGATAGCTC 57.204 47.619 34.21 0.00 44.74 4.09
2565 2663 3.068024 TGGCCTTTGTGATTGACAAGAAC 59.932 43.478 3.32 0.00 45.43 3.01
2755 2853 5.049828 CCTTTCACATGTTCCCTTTTTGAC 58.950 41.667 0.00 0.00 0.00 3.18
2997 3095 5.701290 ACAGTAGCATACCTTTGAACTTCAC 59.299 40.000 0.00 0.00 44.47 3.18
3186 3284 3.441572 GTGAATTGATGTCTTCAGTGGGG 59.558 47.826 0.00 0.00 35.27 4.96
3236 3334 5.321959 TGAACAAAATCAAGACAGTGCAA 57.678 34.783 0.00 0.00 0.00 4.08
3303 3401 1.206610 ACAGATGTAGCTCCTGCACAG 59.793 52.381 0.00 0.00 42.74 3.66
3375 3473 6.806217 AGCATGATAGGTAGAGGTTATAGGT 58.194 40.000 0.00 0.00 0.00 3.08
3426 3524 9.869844 CAAACAAATACAGCTAGCATATTAGAC 57.130 33.333 18.83 0.00 0.00 2.59
3516 3614 6.878317 TCAGTTAGTGGTCATATCAAGAAGG 58.122 40.000 0.00 0.00 0.00 3.46
3518 3616 7.718334 TCTCAGTTAGTGGTCATATCAAGAA 57.282 36.000 0.00 0.00 0.00 2.52
3522 3620 7.727634 AGATCATCTCAGTTAGTGGTCATATCA 59.272 37.037 0.00 0.00 0.00 2.15
3630 3728 1.203994 GCACAAGCTTGCCATCAGAAT 59.796 47.619 26.27 0.04 36.42 2.40
3820 3918 5.362556 TGCTCTAATTCACTCAAGCAAAC 57.637 39.130 0.00 0.00 36.86 2.93
4088 4196 1.867233 CACAAGGAGAGTGTGGAAACG 59.133 52.381 0.00 0.00 42.20 3.60
4097 4208 1.734655 ACCATCCACACAAGGAGAGT 58.265 50.000 0.00 0.00 41.90 3.24
4390 4501 2.814919 TGGTACCACTGGTATTTTTGCG 59.185 45.455 11.60 0.00 40.54 4.85
4430 4541 3.325293 TGCTCTCAAGACATTCTGGTC 57.675 47.619 0.00 0.00 38.08 4.02
4431 4542 3.777106 TTGCTCTCAAGACATTCTGGT 57.223 42.857 0.00 0.00 0.00 4.00
4432 4543 4.142447 CCATTTGCTCTCAAGACATTCTGG 60.142 45.833 0.00 0.00 33.12 3.86
4433 4544 4.674623 GCCATTTGCTCTCAAGACATTCTG 60.675 45.833 0.00 0.00 36.87 3.02
4434 4545 3.442977 GCCATTTGCTCTCAAGACATTCT 59.557 43.478 0.00 0.00 36.87 2.40
4435 4546 3.192001 TGCCATTTGCTCTCAAGACATTC 59.808 43.478 0.00 0.00 42.00 2.67
4453 4564 7.541162 CATTTTCTCAAAGACATATTCTGCCA 58.459 34.615 0.00 0.00 33.46 4.92


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

AutoCloner maintained by Alex Coulton.