Multiple sequence alignment - TraesCS2D01G288400

Loading Multiple Alignment...

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 TraesCS2D01G288400 chr2D 100.000 4552 0 0 1 4552 369484496 369479945 0.000000e+00 8407
1 TraesCS2D01G288400 chr2A 95.566 3924 112 21 1 3899 500534922 500531036 0.000000e+00 6226
2 TraesCS2D01G288400 chr2A 93.819 631 34 3 3925 4552 500531043 500530415 0.000000e+00 944
3 TraesCS2D01G288400 chr2B 95.695 2741 80 11 1 2732 439228364 439225653 0.000000e+00 4373
4 TraesCS2D01G288400 chr2B 88.883 1826 109 29 2766 4552 439225656 439223886 0.000000e+00 2161
5 TraesCS2D01G288400 chr4A 93.921 658 35 4 1335 1988 564748298 564747642 0.000000e+00 989
6 TraesCS2D01G288400 chr7B 92.537 670 46 2 1319 1988 443642860 443643525 0.000000e+00 957
7 TraesCS2D01G288400 chr6A 93.301 627 40 1 1335 1961 449825189 449824565 0.000000e+00 924
8 TraesCS2D01G288400 chr6A 90.855 667 44 8 1335 1988 22029326 22029988 0.000000e+00 878
9 TraesCS2D01G288400 chr4B 91.053 380 27 3 1319 1691 605164390 605164011 1.460000e-139 507
10 TraesCS2D01G288400 chr4B 92.647 136 9 1 1853 1988 605164008 605163874 1.290000e-45 195


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 TraesCS2D01G288400 chr2D 369479945 369484496 4551 True 8407 8407 100.0000 1 4552 1 chr2D.!!$R1 4551
1 TraesCS2D01G288400 chr2A 500530415 500534922 4507 True 3585 6226 94.6925 1 4552 2 chr2A.!!$R1 4551
2 TraesCS2D01G288400 chr2B 439223886 439228364 4478 True 3267 4373 92.2890 1 4552 2 chr2B.!!$R1 4551
3 TraesCS2D01G288400 chr4A 564747642 564748298 656 True 989 989 93.9210 1335 1988 1 chr4A.!!$R1 653
4 TraesCS2D01G288400 chr7B 443642860 443643525 665 False 957 957 92.5370 1319 1988 1 chr7B.!!$F1 669
5 TraesCS2D01G288400 chr6A 449824565 449825189 624 True 924 924 93.3010 1335 1961 1 chr6A.!!$R1 626
6 TraesCS2D01G288400 chr6A 22029326 22029988 662 False 878 878 90.8550 1335 1988 1 chr6A.!!$F1 653
7 TraesCS2D01G288400 chr4B 605163874 605164390 516 True 351 507 91.8500 1319 1988 2 chr4B.!!$R1 669

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
419 423 1.063806 GCACAGCTCGTACAACTCAG 58.936 55.000 0.00 0.00 0.00 3.35 F
1692 1721 1.396653 AGCAACAAGATGGCCTATGC 58.603 50.000 3.32 4.12 32.51 3.14 F
2638 2678 4.251543 CAACCCAATTGTAGAAACACCC 57.748 45.455 4.43 0.00 34.61 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1792 1825 0.111061 AGGCAATTCAGCACACCAGA 59.889 50.0 0.0 0.0 35.83 3.86 R
3148 3190 0.391661 GCCTCTTCTTGTGATCGGCA 60.392 55.0 0.0 0.0 36.16 5.69 R
4435 4510 0.030908 CCTCCGACGAGCCTGATAAC 59.969 60.0 0.0 0.0 34.49 1.89 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
129 130 4.826274 TCCCTTCTCACTTCAGGTTATG 57.174 45.455 0.00 0.00 0.00 1.90
130 131 3.519510 TCCCTTCTCACTTCAGGTTATGG 59.480 47.826 0.00 0.00 0.00 2.74
152 153 2.711542 TCTCTTCCCATTCGCCTTTTC 58.288 47.619 0.00 0.00 0.00 2.29
191 192 1.204467 GTTCCTCTGCAGAGTCCTGAG 59.796 57.143 35.47 22.17 43.02 3.35
193 194 1.516892 CTCTGCAGAGTCCTGAGGC 59.483 63.158 31.71 0.00 43.02 4.70
419 423 1.063806 GCACAGCTCGTACAACTCAG 58.936 55.000 0.00 0.00 0.00 3.35
499 508 6.169094 AGTAGGTAATACATGATGCAGATGC 58.831 40.000 0.00 0.00 36.79 3.91
774 788 9.777843 GTATTGCTGAAACTTTTAATTTCGTTG 57.222 29.630 0.00 0.00 38.64 4.10
815 829 7.645340 GGCTGTTTATCATGTTTATGCTAACTG 59.355 37.037 0.00 0.00 34.21 3.16
819 833 9.869844 GTTTATCATGTTTATGCTAACTGCTAG 57.130 33.333 0.00 0.00 43.37 3.42
856 870 6.693315 TGTATTTAGCTAATGGTTTGGCTC 57.307 37.500 7.08 0.00 45.51 4.70
1042 1056 1.499056 GGCAACACTGATCACAGCG 59.501 57.895 0.00 0.00 46.95 5.18
1221 1235 3.853671 CACGAAATGGCTCATTTACTTGC 59.146 43.478 11.58 1.62 43.05 4.01
1353 1367 5.293079 CAGAAAAATCGTCTCTTCTCCATCC 59.707 44.000 0.00 0.00 0.00 3.51
1692 1721 1.396653 AGCAACAAGATGGCCTATGC 58.603 50.000 3.32 4.12 32.51 3.14
1734 1767 7.013846 TCCCTTAATGGTGTTAAAAGTGAGTTG 59.986 37.037 0.00 0.00 0.00 3.16
2214 2251 5.930405 TGTGATGAAAACTCATGACATTCG 58.070 37.500 3.68 0.00 38.83 3.34
2277 2314 5.107607 GCAGAAAAAGTTCAATGATGCACTG 60.108 40.000 0.00 0.00 33.14 3.66
2638 2678 4.251543 CAACCCAATTGTAGAAACACCC 57.748 45.455 4.43 0.00 34.61 4.61
2986 3028 6.260271 AGCAAGTAAAACTAACACCAACTCTC 59.740 38.462 0.00 0.00 0.00 3.20
3148 3190 5.005779 GCATCAACTTCGATATGAAAGACGT 59.994 40.000 0.00 0.00 35.79 4.34
3156 3198 2.951457 TATGAAAGACGTGCCGATCA 57.049 45.000 0.00 0.00 0.00 2.92
3171 3213 2.266554 CGATCACAAGAAGAGGCTGTC 58.733 52.381 0.00 0.00 0.00 3.51
3201 3243 7.102993 GCATAAAATTTTGTGGGTGTTAGGAT 58.897 34.615 23.79 0.06 31.00 3.24
3338 3385 2.042686 TGCTCCGCTTAATTCTGCAT 57.957 45.000 0.00 0.00 0.00 3.96
3341 3388 1.672363 CTCCGCTTAATTCTGCATGCA 59.328 47.619 21.29 21.29 0.00 3.96
3423 3470 2.574006 TGTGATGCCTTTCAGCTCTT 57.426 45.000 0.00 0.00 31.07 2.85
3431 3478 2.941720 GCCTTTCAGCTCTTATGACCTG 59.058 50.000 0.00 0.00 0.00 4.00
3439 3486 3.713764 AGCTCTTATGACCTGGCACTATT 59.286 43.478 0.00 0.00 0.00 1.73
3456 3503 5.278266 GCACTATTTGTGGTGAAGCTTTACA 60.278 40.000 21.43 11.96 46.27 2.41
3458 3505 4.853924 ATTTGTGGTGAAGCTTTACAGG 57.146 40.909 21.43 0.00 0.00 4.00
3554 3608 0.740737 GGGATGCATTTGCTTAGCGT 59.259 50.000 0.00 0.00 42.66 5.07
3555 3609 1.268743 GGGATGCATTTGCTTAGCGTC 60.269 52.381 0.00 0.00 42.14 5.19
3556 3610 1.672881 GGATGCATTTGCTTAGCGTCT 59.327 47.619 0.00 0.00 42.41 4.18
3557 3611 2.098117 GGATGCATTTGCTTAGCGTCTT 59.902 45.455 0.00 0.00 42.41 3.01
3558 3612 3.312421 GGATGCATTTGCTTAGCGTCTTA 59.688 43.478 0.00 0.00 42.41 2.10
3559 3613 4.521943 GATGCATTTGCTTAGCGTCTTAG 58.478 43.478 0.00 0.00 40.28 2.18
3560 3614 2.095853 TGCATTTGCTTAGCGTCTTAGC 59.904 45.455 0.00 9.81 42.66 3.09
3561 3615 2.847254 GCATTTGCTTAGCGTCTTAGCG 60.847 50.000 0.00 0.00 38.73 4.26
3594 3648 1.833055 ATGTGGTAGGGGAGGGGTGA 61.833 60.000 0.00 0.00 0.00 4.02
3624 3682 2.549992 GGTCACATCACACAAGCTACCA 60.550 50.000 0.00 0.00 0.00 3.25
3750 3813 2.414559 CCAATGCACACCACGAATTCTC 60.415 50.000 3.52 0.00 0.00 2.87
3817 3887 3.655615 ATTCTGACGAGTCTCCTACCT 57.344 47.619 4.78 0.00 0.00 3.08
3847 3917 6.013379 ACAAGAAGAGACAAGAATGGGTATCA 60.013 38.462 0.00 0.00 0.00 2.15
3915 3985 0.744771 GCTTTCCCCGTAAGCAGAGG 60.745 60.000 0.00 0.00 45.64 3.69
3933 4003 3.092403 CTGCGCGCTTATTGCTCA 58.908 55.556 33.29 7.29 40.11 4.26
3955 4025 3.514309 ACCCAGCTTCGAAGTGTAGTTAT 59.486 43.478 25.24 2.72 0.00 1.89
3959 4029 6.331061 CCAGCTTCGAAGTGTAGTTATTAGT 58.669 40.000 25.24 0.00 0.00 2.24
3962 4032 5.805994 GCTTCGAAGTGTAGTTATTAGTGCT 59.194 40.000 25.24 0.00 0.00 4.40
4051 4123 3.976902 GACCAATGGCAGCTTGCGC 62.977 63.158 0.00 0.00 46.21 6.09
4125 4200 4.675565 CAGACCAGTCGTAGTATAATTGCG 59.324 45.833 0.00 0.00 34.09 4.85
4183 4258 2.369394 CCATGTTAGGACTTTGGAGGC 58.631 52.381 0.00 0.00 33.95 4.70
4197 4272 0.033011 GGAGGCAGGAGTAGTCCAGA 60.033 60.000 19.00 0.00 46.80 3.86
4216 4291 4.937620 CCAGAATCGGAGAGAGATAGAGAG 59.062 50.000 0.00 0.00 43.63 3.20
4222 4297 2.224426 GGAGAGAGATAGAGAGGCGTCA 60.224 54.545 9.41 0.00 0.00 4.35
4287 4362 0.398381 GTGAGGAGGGAGCAGAGGAT 60.398 60.000 0.00 0.00 0.00 3.24
4293 4368 2.328319 GAGGGAGCAGAGGATGAAGAT 58.672 52.381 0.00 0.00 0.00 2.40
4298 4373 2.102757 GAGCAGAGGATGAAGATGCAGA 59.897 50.000 0.00 0.00 39.34 4.26
4422 4497 1.141881 GCATCTCACCGTCGTCCAT 59.858 57.895 0.00 0.00 0.00 3.41
4424 4499 0.455815 CATCTCACCGTCGTCCATCA 59.544 55.000 0.00 0.00 0.00 3.07
4427 4502 0.455815 CTCACCGTCGTCCATCATCA 59.544 55.000 0.00 0.00 0.00 3.07
4435 4510 0.031314 CGTCCATCATCAGGTCTCCG 59.969 60.000 0.00 0.00 0.00 4.63
4436 4511 1.115467 GTCCATCATCAGGTCTCCGT 58.885 55.000 0.00 0.00 0.00 4.69
4437 4512 1.482593 GTCCATCATCAGGTCTCCGTT 59.517 52.381 0.00 0.00 0.00 4.44
4455 4530 0.106868 TTATCAGGCTCGTCGGAGGA 60.107 55.000 0.00 0.00 40.80 3.71
4497 4575 1.150567 CGCCTCTTCGATTGCCTGAG 61.151 60.000 0.00 0.00 0.00 3.35
4543 4625 9.537848 GTTATGTGTGAGGTTAAAGAATAAACG 57.462 33.333 0.00 0.00 0.00 3.60
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
129 130 0.253327 AGGCGAATGGGAAGAGAACC 59.747 55.000 0.00 0.00 0.00 3.62
130 131 2.115343 AAGGCGAATGGGAAGAGAAC 57.885 50.000 0.00 0.00 0.00 3.01
228 229 6.097156 CAAGACATGCCGTTACGTTATTTA 57.903 37.500 3.52 0.00 0.00 1.40
316 320 6.592607 CCTTTTTAAGCTACCACAGACGATAA 59.407 38.462 0.00 0.00 0.00 1.75
419 423 4.755123 ACTACAAACAACCACTATGTGAGC 59.245 41.667 0.00 0.00 35.23 4.26
472 481 8.526978 CATCTGCATCATGTATTACCTACTAGT 58.473 37.037 0.00 0.00 0.00 2.57
499 508 1.308998 ACGAGAAAGCACCAGTTTGG 58.691 50.000 0.00 0.00 45.02 3.28
815 829 7.796958 AAATACAACGCAAAAGAATTCTAGC 57.203 32.000 8.75 12.20 0.00 3.42
819 833 7.796958 AGCTAAATACAACGCAAAAGAATTC 57.203 32.000 0.00 0.00 0.00 2.17
856 870 3.056678 TGCAAACCAGACCTGCAATATTG 60.057 43.478 11.27 11.27 42.84 1.90
910 924 1.477700 TGCTTACTCAAATGCCATGCC 59.522 47.619 0.00 0.00 0.00 4.40
1042 1056 1.135517 GTCTTCGTCCTCAGAGCTGAC 60.136 57.143 0.00 0.00 35.46 3.51
1131 1145 5.356190 GTCATGCTCATCATTTTCAAGAGGA 59.644 40.000 0.00 0.00 31.79 3.71
1221 1235 3.002656 CACTAATTGCGGCACCAGATAAG 59.997 47.826 0.05 0.00 0.00 1.73
1248 1262 4.789012 ATTTGTATTGGCCAGTGTGAAG 57.211 40.909 11.69 0.00 0.00 3.02
1353 1367 2.233271 AGCAAGTCCAACCTTGACATG 58.767 47.619 5.17 0.00 43.65 3.21
1692 1721 0.752054 GGGAGTCCTCTGATGAGCTG 59.248 60.000 9.58 0.00 38.93 4.24
1734 1767 4.098349 TCTGCAATTTCCATGGCTAATGTC 59.902 41.667 6.96 5.74 34.11 3.06
1792 1825 0.111061 AGGCAATTCAGCACACCAGA 59.889 50.000 0.00 0.00 35.83 3.86
2065 2102 7.510685 AGAGTCATTAGGATGGTCAGCTAATAA 59.489 37.037 0.00 0.00 33.93 1.40
2186 2223 5.093457 GTCATGAGTTTTCATCACATGCTG 58.907 41.667 0.00 0.00 42.12 4.41
2202 2239 7.993821 AGTTAAGTCATACGAATGTCATGAG 57.006 36.000 0.00 0.00 34.50 2.90
2214 2251 5.765182 AGCATGGGCATTAGTTAAGTCATAC 59.235 40.000 0.00 0.00 44.61 2.39
2277 2314 2.159085 ACGAACTCGGAGAATTCCCATC 60.159 50.000 12.86 0.00 44.95 3.51
2638 2678 8.908786 TTGCCTTCCTATTATAACATGAGAAG 57.091 34.615 0.00 0.00 0.00 2.85
2986 3028 5.221126 GCAAGGCATAGGAAGAAATTAGTGG 60.221 44.000 0.00 0.00 0.00 4.00
3148 3190 0.391661 GCCTCTTCTTGTGATCGGCA 60.392 55.000 0.00 0.00 36.16 5.69
3156 3198 3.621953 GCTGACAGCCTCTTCTTGT 57.378 52.632 17.01 0.00 34.48 3.16
3171 3213 2.672381 CCCACAAAATTTTATGCGGCTG 59.328 45.455 3.58 0.00 0.00 4.85
3201 3243 6.434028 CACCAGAACCCTGAAAAAGATTCATA 59.566 38.462 0.00 0.00 43.02 2.15
3252 3297 5.538433 CACCCAAAATTTCCGGGATATACAT 59.462 40.000 25.32 5.17 43.21 2.29
3262 3307 1.269309 TGTTCGCACCCAAAATTTCCG 60.269 47.619 0.00 0.00 0.00 4.30
3439 3486 3.118038 AGACCTGTAAAGCTTCACCACAA 60.118 43.478 0.00 0.00 0.00 3.33
3456 3503 5.648092 CGGTTTCCATTTTATCTTCAGACCT 59.352 40.000 0.00 0.00 0.00 3.85
3458 3505 5.163652 CCCGGTTTCCATTTTATCTTCAGAC 60.164 44.000 0.00 0.00 0.00 3.51
3554 3608 1.045407 ACACCTTGTGGTCGCTAAGA 58.955 50.000 0.00 0.00 46.60 2.10
3555 3609 1.878953 AACACCTTGTGGTCGCTAAG 58.121 50.000 0.00 0.00 46.60 2.18
3556 3610 3.244284 ACATAACACCTTGTGGTCGCTAA 60.244 43.478 0.00 0.00 46.60 3.09
3557 3611 2.300723 ACATAACACCTTGTGGTCGCTA 59.699 45.455 0.00 0.00 46.60 4.26
3558 3612 1.071699 ACATAACACCTTGTGGTCGCT 59.928 47.619 0.00 0.00 46.60 4.93
3559 3613 1.196808 CACATAACACCTTGTGGTCGC 59.803 52.381 0.00 0.00 46.60 5.19
3594 3648 3.009363 TGTGTGATGTGACCAGGATTCAT 59.991 43.478 0.00 0.00 0.00 2.57
3624 3682 8.655935 AAAAATACTGGAGATGTGGAAAGATT 57.344 30.769 0.00 0.00 0.00 2.40
3658 3717 1.079503 GCGACAGGGAAGTTGATCAC 58.920 55.000 0.00 0.00 0.00 3.06
3696 3759 0.106149 ACAACGGTGTCTTCCAGGTC 59.894 55.000 0.00 0.00 29.49 3.85
3817 3887 6.039717 CCCATTCTTGTCTCTTCTTGTGAAAA 59.960 38.462 0.00 0.00 0.00 2.29
3847 3917 6.025749 TCTTTCACTCTCGTGTATTGTGAT 57.974 37.500 0.00 0.00 41.89 3.06
3874 3944 4.442472 GCAATAATCATGCAGGGCTTTTCT 60.442 41.667 0.00 0.00 43.29 2.52
3875 3945 3.805971 GCAATAATCATGCAGGGCTTTTC 59.194 43.478 0.00 0.00 43.29 2.29
3876 3946 3.453353 AGCAATAATCATGCAGGGCTTTT 59.547 39.130 0.00 0.00 46.22 2.27
3933 4003 1.339097 ACTACACTTCGAAGCTGGGT 58.661 50.000 24.86 18.56 0.00 4.51
4102 4174 4.675565 CGCAATTATACTACGACTGGTCTG 59.324 45.833 0.00 0.00 0.00 3.51
4125 4200 1.600916 ACAAACGCAGAGGAAGGGC 60.601 57.895 0.00 0.00 0.00 5.19
4183 4258 2.621055 CTCCGATTCTGGACTACTCCTG 59.379 54.545 0.00 0.00 37.48 3.86
4197 4272 3.686016 GCCTCTCTATCTCTCTCCGATT 58.314 50.000 0.00 0.00 0.00 3.34
4406 4481 1.338337 GATGATGGACGACGGTGAGAT 59.662 52.381 0.00 0.00 0.00 2.75
4414 4489 1.067821 GGAGACCTGATGATGGACGAC 59.932 57.143 0.00 0.00 0.00 4.34
4422 4497 2.959030 CCTGATAACGGAGACCTGATGA 59.041 50.000 0.00 0.00 0.00 2.92
4424 4499 1.689273 GCCTGATAACGGAGACCTGAT 59.311 52.381 0.00 0.00 0.00 2.90
4427 4502 1.404843 GAGCCTGATAACGGAGACCT 58.595 55.000 0.00 0.00 0.00 3.85
4435 4510 0.030908 CCTCCGACGAGCCTGATAAC 59.969 60.000 0.00 0.00 34.49 1.89
4436 4511 0.106868 TCCTCCGACGAGCCTGATAA 60.107 55.000 0.00 0.00 34.49 1.75
4437 4512 0.106868 TTCCTCCGACGAGCCTGATA 60.107 55.000 0.00 0.00 34.49 2.15


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

AutoCloner maintained by Alex Coulton.