Multiple sequence alignment - TraesCS2D01G297400

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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 TraesCS2D01G297400 chr2D 100.000 4502 0 0 1 4502 380073093 380077594 0.000000e+00 8314
1 TraesCS2D01G297400 chr2B 94.495 4523 200 35 1 4502 451449019 451453513 0.000000e+00 6927
2 TraesCS2D01G297400 chr2B 74.791 837 192 14 2578 3403 8321388 8320560 4.280000e-95 359
3 TraesCS2D01G297400 chr2B 74.405 840 194 15 2578 3405 9145205 9146035 1.550000e-89 340
4 TraesCS2D01G297400 chr2B 71.749 1069 251 35 1154 2183 117994132 117993076 2.080000e-63 254
5 TraesCS2D01G297400 chr2A 93.695 3886 186 28 1 3867 515297496 515301341 0.000000e+00 5764
6 TraesCS2D01G297400 chr2A 95.000 320 13 2 4183 4502 515301343 515301659 2.420000e-137 499
7 TraesCS2D01G297400 chr2A 76.313 857 187 14 2578 3426 514861261 514862109 1.150000e-120 444
8 TraesCS2D01G297400 chr7D 73.463 2359 529 72 1160 3465 543640313 543637999 0.000000e+00 798


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 TraesCS2D01G297400 chr2D 380073093 380077594 4501 False 8314.0 8314 100.0000 1 4502 1 chr2D.!!$F1 4501
1 TraesCS2D01G297400 chr2B 451449019 451453513 4494 False 6927.0 6927 94.4950 1 4502 1 chr2B.!!$F2 4501
2 TraesCS2D01G297400 chr2B 8320560 8321388 828 True 359.0 359 74.7910 2578 3403 1 chr2B.!!$R1 825
3 TraesCS2D01G297400 chr2B 9145205 9146035 830 False 340.0 340 74.4050 2578 3405 1 chr2B.!!$F1 827
4 TraesCS2D01G297400 chr2B 117993076 117994132 1056 True 254.0 254 71.7490 1154 2183 1 chr2B.!!$R2 1029
5 TraesCS2D01G297400 chr2A 515297496 515301659 4163 False 3131.5 5764 94.3475 1 4502 2 chr2A.!!$F2 4501
6 TraesCS2D01G297400 chr2A 514861261 514862109 848 False 444.0 444 76.3130 2578 3426 1 chr2A.!!$F1 848
7 TraesCS2D01G297400 chr7D 543637999 543640313 2314 True 798.0 798 73.4630 1160 3465 1 chr7D.!!$R1 2305

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
443 454 1.071385 AGAGCAGTTGGACACTTGGAG 59.929 52.381 0.00 0.0 30.92 3.86 F
1050 1078 0.861837 CACAACAGTTGCGGTCTCTC 59.138 55.000 13.56 0.0 0.00 3.20 F
3270 3340 0.972883 AGAAGCTTCTCGAAGGCAGT 59.027 50.000 23.49 0.0 38.80 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2288 2346 0.802494 AAGTAATTCGCCGTGCCAAG 59.198 50.000 0.0 0.0 0.0 3.61 R
3274 3344 0.982852 TGATCCACCAAGCTCCCGAT 60.983 55.000 0.0 0.0 0.0 4.18 R
4284 4360 1.200020 CTTTGAGGTTTGACCGATGGC 59.800 52.381 0.0 0.0 44.9 4.40 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
24 25 7.467557 GAGCATCTCTTTGAGAAGTAATGAG 57.532 40.000 1.20 0.00 42.27 2.90
28 29 8.725148 GCATCTCTTTGAGAAGTAATGAGAAAA 58.275 33.333 1.20 0.00 42.27 2.29
88 89 7.448588 TGAACATTTATTTTCATATGCGTGC 57.551 32.000 0.00 0.00 0.00 5.34
135 137 6.500684 ACACTTCATTTCCACATACATGAC 57.499 37.500 0.00 0.00 0.00 3.06
215 221 7.038729 TCCCTGGATATTGTATTTTTGCAACAA 60.039 33.333 0.00 0.00 37.51 2.83
402 413 1.884067 GGTAAGCTTTGCTCACCAGCT 60.884 52.381 3.20 0.00 45.81 4.24
443 454 1.071385 AGAGCAGTTGGACACTTGGAG 59.929 52.381 0.00 0.00 30.92 3.86
498 509 6.220201 ACAGCCAAAATTGCTTAATTTACGT 58.780 32.000 0.00 0.00 36.81 3.57
500 511 5.867174 AGCCAAAATTGCTTAATTTACGTCC 59.133 36.000 0.00 0.00 34.87 4.79
506 517 7.810766 AATTGCTTAATTTACGTCCATTGTG 57.189 32.000 0.00 0.00 0.00 3.33
659 687 6.464222 TGTTTCAGGTTGGTCAAGAGTATAG 58.536 40.000 0.00 0.00 0.00 1.31
1050 1078 0.861837 CACAACAGTTGCGGTCTCTC 59.138 55.000 13.56 0.00 0.00 3.20
1419 1465 1.344438 CGGTCCAGCAGCTCCATAATA 59.656 52.381 0.00 0.00 0.00 0.98
1439 1485 2.175878 TGGTCTTCTCAAGCAAGAGC 57.824 50.000 6.10 6.10 44.97 4.09
1444 1490 1.805345 CTTCTCAAGCAAGAGCCACAG 59.195 52.381 0.90 0.00 43.56 3.66
1464 1510 1.577328 CCACCGACACCATTGCTGTC 61.577 60.000 2.54 2.54 35.61 3.51
1860 1912 1.164411 TGCATGATGAAACCACGGTC 58.836 50.000 0.00 0.00 0.00 4.79
2008 2060 1.269174 CCACCATTTGCGATGACAACA 59.731 47.619 1.75 0.00 0.00 3.33
2100 2152 1.915141 CCAGTGGGTGCTTGAGAAAT 58.085 50.000 0.00 0.00 0.00 2.17
2242 2300 1.748122 GCACAGATCTGCCTGGGTG 60.748 63.158 22.83 12.91 39.68 4.61
2434 2492 7.611213 AGAGGAAAAACCAATGTTATACTCG 57.389 36.000 0.00 0.00 36.88 4.18
2724 2782 1.012841 GAGAGAAGCAATTCAGGGCG 58.987 55.000 0.00 0.00 34.54 6.13
3270 3340 0.972883 AGAAGCTTCTCGAAGGCAGT 59.027 50.000 23.49 0.00 38.80 4.40
3274 3344 0.319900 GCTTCTCGAAGGCAGTGACA 60.320 55.000 0.00 0.00 38.80 3.58
3548 3618 7.609532 GGAGTATTTCTATTCTGGAATCCATGG 59.390 40.741 4.97 4.97 30.82 3.66
3723 3794 0.107703 TTCCCGTAGCTTGGATGCTG 60.108 55.000 6.27 0.00 43.87 4.41
3773 3844 8.507249 CCATTCTCAAAAGTTAGTGTCTAAAGG 58.493 37.037 0.00 0.00 0.00 3.11
3894 3965 1.090052 GGCGTTTCGGAGGGATGAAG 61.090 60.000 0.00 0.00 0.00 3.02
3899 3970 2.436173 GTTTCGGAGGGATGAAGATCCT 59.564 50.000 0.00 0.00 46.88 3.24
3900 3971 3.612795 TTCGGAGGGATGAAGATCCTA 57.387 47.619 0.00 0.00 46.88 2.94
3904 3975 3.699038 CGGAGGGATGAAGATCCTAGATC 59.301 52.174 0.00 0.00 46.88 2.75
3911 3982 7.516906 AGGGATGAAGATCCTAGATCAGATTTT 59.483 37.037 7.30 0.00 46.88 1.82
3912 3983 7.607223 GGGATGAAGATCCTAGATCAGATTTTG 59.393 40.741 7.30 0.00 46.88 2.44
3917 3988 9.691362 GAAGATCCTAGATCAGATTTTGAGTAC 57.309 37.037 7.30 0.00 39.68 2.73
3924 3995 9.311916 CTAGATCAGATTTTGAGTACAAAGGAG 57.688 37.037 0.00 0.00 44.97 3.69
3933 4004 8.608844 TTTTGAGTACAAAGGAGATTCTCTTC 57.391 34.615 13.22 0.00 44.97 2.87
3945 4016 6.654161 AGGAGATTCTCTTCAACACATCTTTG 59.346 38.462 13.22 0.00 0.00 2.77
3982 4053 6.688813 GCTCTAACAAACAAACAGAGACAAAG 59.311 38.462 1.23 0.00 35.77 2.77
4016 4088 4.553330 ACTTGTCACCCTGTACATAAGG 57.447 45.455 0.00 0.17 34.31 2.69
4021 4093 0.828677 ACCCTGTACATAAGGCGTCC 59.171 55.000 0.00 0.00 33.07 4.79
4026 4098 3.945285 CCTGTACATAAGGCGTCCATTTT 59.055 43.478 0.00 0.00 0.00 1.82
4027 4099 4.201910 CCTGTACATAAGGCGTCCATTTTG 60.202 45.833 0.00 0.00 0.00 2.44
4040 4113 6.089417 GGCGTCCATTTTGTTTTTCTTCTATG 59.911 38.462 0.00 0.00 0.00 2.23
4072 4145 2.815647 GCTCCTGCCGGTTTCTCG 60.816 66.667 1.90 0.00 0.00 4.04
4076 4149 1.153745 CCTGCCGGTTTCTCGAGAG 60.154 63.158 15.94 4.69 0.00 3.20
4100 4173 7.050377 AGAAAAACACAGAGACAAGATCTTCA 58.950 34.615 4.57 0.00 38.00 3.02
4101 4174 6.857777 AAAACACAGAGACAAGATCTTCAG 57.142 37.500 4.57 0.00 38.00 3.02
4102 4175 4.533919 ACACAGAGACAAGATCTTCAGG 57.466 45.455 4.57 0.00 38.00 3.86
4103 4176 3.900601 ACACAGAGACAAGATCTTCAGGT 59.099 43.478 4.57 0.20 38.00 4.00
4105 4178 4.928615 CACAGAGACAAGATCTTCAGGTTC 59.071 45.833 4.57 0.00 38.00 3.62
4152 4227 2.125512 GATGGTCTTCGCCACGCT 60.126 61.111 0.00 0.00 41.94 5.07
4155 4230 0.530650 ATGGTCTTCGCCACGCTATG 60.531 55.000 0.00 0.00 41.94 2.23
4284 4360 4.981806 TCAAGGCCTTAATCCAAAATCG 57.018 40.909 20.00 0.67 0.00 3.34
4431 4513 4.074970 CCTTAATTTCACTGCAGTGGACT 58.925 43.478 39.04 26.90 45.65 3.85
4488 4570 3.753797 GACCCAGGCTTTAGTTTCAAGAG 59.246 47.826 0.00 0.00 0.00 2.85
4490 4572 4.043435 ACCCAGGCTTTAGTTTCAAGAGAT 59.957 41.667 0.00 0.00 0.00 2.75
4491 4573 5.250774 ACCCAGGCTTTAGTTTCAAGAGATA 59.749 40.000 0.00 0.00 0.00 1.98
4493 4575 6.410540 CCAGGCTTTAGTTTCAAGAGATAGT 58.589 40.000 0.00 0.00 0.00 2.12
4495 4577 6.314896 CAGGCTTTAGTTTCAAGAGATAGTGG 59.685 42.308 0.00 0.00 0.00 4.00
4496 4578 6.213600 AGGCTTTAGTTTCAAGAGATAGTGGA 59.786 38.462 0.00 0.00 0.00 4.02
4499 4581 7.387948 GCTTTAGTTTCAAGAGATAGTGGAACA 59.612 37.037 0.00 0.00 41.43 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
188 193 7.038729 TGTTGCAAAAATACAATATCCAGGGAA 60.039 33.333 0.00 0.00 0.00 3.97
192 197 8.649841 CACTTGTTGCAAAAATACAATATCCAG 58.350 33.333 1.65 0.00 31.96 3.86
201 206 9.553418 AAAAATGTTCACTTGTTGCAAAAATAC 57.447 25.926 1.65 0.53 0.00 1.89
269 279 9.823647 CACATCTCTAAGGACAGTTTTATATGT 57.176 33.333 0.00 0.00 0.00 2.29
270 280 9.265901 CCACATCTCTAAGGACAGTTTTATATG 57.734 37.037 0.00 0.00 0.00 1.78
271 281 9.213777 TCCACATCTCTAAGGACAGTTTTATAT 57.786 33.333 0.00 0.00 0.00 0.86
272 282 8.603898 TCCACATCTCTAAGGACAGTTTTATA 57.396 34.615 0.00 0.00 0.00 0.98
273 283 7.496346 TCCACATCTCTAAGGACAGTTTTAT 57.504 36.000 0.00 0.00 0.00 1.40
274 284 6.928348 TCCACATCTCTAAGGACAGTTTTA 57.072 37.500 0.00 0.00 0.00 1.52
275 285 5.825593 TCCACATCTCTAAGGACAGTTTT 57.174 39.130 0.00 0.00 0.00 2.43
402 413 1.345089 TGCGTTAGGTTTGACTGGCTA 59.655 47.619 0.00 0.00 0.00 3.93
443 454 3.751621 GTGCAGATACATTTGTCAGCAC 58.248 45.455 9.67 9.67 43.27 4.40
498 509 1.179152 CTGCTGATTGCCACAATGGA 58.821 50.000 0.00 0.00 40.96 3.41
500 511 0.459585 GCCTGCTGATTGCCACAATG 60.460 55.000 0.00 0.00 42.00 2.82
659 687 1.302511 AACGATGTGGTCTGGGTGC 60.303 57.895 0.00 0.00 0.00 5.01
1013 1041 0.616679 TGTAGTAGGGTGGGTGCTCC 60.617 60.000 0.00 0.00 0.00 4.70
1050 1078 0.678048 GAGGGGTAGCTTGCAGTTGG 60.678 60.000 0.00 0.00 0.00 3.77
1419 1465 2.617532 GGCTCTTGCTTGAGAAGACCAT 60.618 50.000 10.03 0.00 39.59 3.55
1439 1485 3.551496 ATGGTGTCGGTGGCTGTGG 62.551 63.158 0.00 0.00 0.00 4.17
1444 1490 2.672996 AGCAATGGTGTCGGTGGC 60.673 61.111 0.00 0.00 0.00 5.01
1464 1510 1.912043 AGATTCCCAGTGTTCAGGAGG 59.088 52.381 0.00 0.00 0.00 4.30
2008 2060 1.270839 ACAGTTACAAGATGGCAGCGT 60.271 47.619 0.00 0.00 0.00 5.07
2065 2117 7.509546 CACCCACTGGTTAGATCATATAGTTT 58.490 38.462 0.00 0.00 44.75 2.66
2071 2123 3.384168 AGCACCCACTGGTTAGATCATA 58.616 45.455 0.00 0.00 44.75 2.15
2078 2130 1.429930 TCTCAAGCACCCACTGGTTA 58.570 50.000 0.00 0.00 44.75 2.85
2100 2152 3.260632 TGTTGCTGCAGTCTAATGGAGTA 59.739 43.478 16.64 0.00 40.47 2.59
2242 2300 3.070018 AGTATGCAGTGCAAGAACAGTC 58.930 45.455 23.90 6.51 43.62 3.51
2288 2346 0.802494 AAGTAATTCGCCGTGCCAAG 59.198 50.000 0.00 0.00 0.00 3.61
3270 3340 1.296392 CACCAAGCTCCCGATGTCA 59.704 57.895 0.00 0.00 0.00 3.58
3274 3344 0.982852 TGATCCACCAAGCTCCCGAT 60.983 55.000 0.00 0.00 0.00 4.18
3447 3517 2.286872 CTCATAGCTTGAAGCACCCTG 58.713 52.381 20.45 10.42 45.56 4.45
3451 3521 0.654683 CCGCTCATAGCTTGAAGCAC 59.345 55.000 20.45 0.50 45.56 4.40
3616 3687 4.957296 ACTCACACAAACGGTCTATCTTT 58.043 39.130 0.00 0.00 0.00 2.52
3618 3689 4.765856 ACTACTCACACAAACGGTCTATCT 59.234 41.667 0.00 0.00 0.00 1.98
3723 3794 1.809684 AAGTTTCCCTAAGCTCGTGC 58.190 50.000 0.07 0.07 40.05 5.34
3773 3844 5.009610 TGGAACTTAAGTTTTGGAGATGTGC 59.990 40.000 21.40 4.75 38.56 4.57
3894 3965 9.823647 TTTGTACTCAAAATCTGATCTAGGATC 57.176 33.333 0.00 1.04 40.08 3.36
3899 3970 9.035890 TCTCCTTTGTACTCAAAATCTGATCTA 57.964 33.333 0.00 0.00 42.02 1.98
3900 3971 7.911651 TCTCCTTTGTACTCAAAATCTGATCT 58.088 34.615 0.00 0.00 42.02 2.75
3904 3975 8.558973 AGAATCTCCTTTGTACTCAAAATCTG 57.441 34.615 0.00 0.00 42.02 2.90
3945 4016 6.494842 TGTTTGTTAGAGCACTTTCATCAAC 58.505 36.000 0.00 0.00 0.00 3.18
3956 4027 5.182487 TGTCTCTGTTTGTTTGTTAGAGCA 58.818 37.500 0.00 0.00 35.89 4.26
3982 4053 3.255888 GGTGACAAGTTTTTGGAGGGATC 59.744 47.826 0.00 0.00 38.66 3.36
4016 4088 6.640907 ACATAGAAGAAAAACAAAATGGACGC 59.359 34.615 0.00 0.00 0.00 5.19
4026 4098 8.855110 TGCCTTTTCATACATAGAAGAAAAACA 58.145 29.630 0.00 0.00 38.88 2.83
4027 4099 9.691362 TTGCCTTTTCATACATAGAAGAAAAAC 57.309 29.630 0.00 0.00 38.88 2.43
4040 4113 3.736126 GCAGGAGCATTGCCTTTTCATAC 60.736 47.826 4.70 0.00 41.58 2.39
4072 4145 6.928492 AGATCTTGTCTCTGTGTTTTTCTCTC 59.072 38.462 0.00 0.00 28.45 3.20
4076 4149 7.251704 TGAAGATCTTGTCTCTGTGTTTTTC 57.748 36.000 14.00 0.00 35.67 2.29
4101 4174 2.814913 AAATCACCTCGCCCCGAACC 62.815 60.000 0.00 0.00 34.74 3.62
4102 4175 1.376812 AAATCACCTCGCCCCGAAC 60.377 57.895 0.00 0.00 34.74 3.95
4103 4176 1.376683 CAAATCACCTCGCCCCGAA 60.377 57.895 0.00 0.00 34.74 4.30
4105 4178 3.508840 GCAAATCACCTCGCCCCG 61.509 66.667 0.00 0.00 0.00 5.73
4152 4227 1.227102 GGTGGCTGGGTGCATCATA 59.773 57.895 0.00 0.00 45.15 2.15
4155 4230 3.667217 ATGGGTGGCTGGGTGCATC 62.667 63.158 0.00 0.00 45.15 3.91
4178 4253 6.192044 GTGGGAAAAATATACTCAAGGGGAA 58.808 40.000 0.00 0.00 0.00 3.97
4180 4255 5.515106 TGTGGGAAAAATATACTCAAGGGG 58.485 41.667 0.00 0.00 0.00 4.79
4232 4308 5.175090 AGATTTATCTTAGGCGCAAAAGC 57.825 39.130 10.83 0.55 31.97 3.51
4284 4360 1.200020 CTTTGAGGTTTGACCGATGGC 59.800 52.381 0.00 0.00 44.90 4.40
4431 4513 5.009610 GTCAAACAATTCTTGCCTAGGTGAA 59.990 40.000 11.31 12.70 0.00 3.18
4461 4543 3.434940 AACTAAAGCCTGGGTCGATTT 57.565 42.857 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.