Multiple sequence alignment - TraesCS1D01G206400

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 TraesCS1D01G206400 chr1D 100.000 2468 0 0 1 2468 291840765 291843232 0.000000e+00 4558.0
1 TraesCS1D01G206400 chr1D 99.195 994 8 0 1 994 291800700 291799707 0.000000e+00 1792.0
2 TraesCS1D01G206400 chr1D 88.667 1050 69 28 510 1553 291799707 291798702 0.000000e+00 1234.0
3 TraesCS1D01G206400 chr1D 81.818 121 16 4 1521 1641 291857500 291857614 2.020000e-16 97.1
4 TraesCS1D01G206400 chr1A 90.108 1567 87 24 5 1556 364041130 364039617 0.000000e+00 1973.0
5 TraesCS1D01G206400 chr1A 90.638 235 20 2 999 1232 101335647 101335414 6.630000e-81 311.0
6 TraesCS1D01G206400 chr1A 89.041 146 16 0 162 307 364041056 364040911 5.420000e-42 182.0
7 TraesCS1D01G206400 chr7D 98.237 624 11 0 1845 2468 224462474 224463097 0.000000e+00 1092.0
8 TraesCS1D01G206400 chr7D 92.157 459 36 0 999 1457 91054792 91055250 0.000000e+00 649.0
9 TraesCS1D01G206400 chr7D 83.486 327 49 5 1145 1470 548808640 548808962 1.430000e-77 300.0
10 TraesCS1D01G206400 chr3D 98.086 627 12 0 1842 2468 491627750 491628376 0.000000e+00 1092.0
11 TraesCS1D01G206400 chr3D 97.917 624 13 0 1845 2468 32733485 32734108 0.000000e+00 1081.0
12 TraesCS1D01G206400 chr3D 97.917 624 13 0 1845 2468 46546748 46547371 0.000000e+00 1081.0
13 TraesCS1D01G206400 chr3D 97.468 632 16 0 1837 2468 288041809 288042440 0.000000e+00 1079.0
14 TraesCS1D01G206400 chr3D 97.615 629 14 1 1841 2468 39038528 39037900 0.000000e+00 1077.0
15 TraesCS1D01G206400 chr5D 98.077 624 12 0 1845 2468 43964091 43964714 0.000000e+00 1086.0
16 TraesCS1D01G206400 chr4D 98.077 624 12 0 1845 2468 449193366 449193989 0.000000e+00 1086.0
17 TraesCS1D01G206400 chr4D 98.077 624 12 0 1845 2468 488033678 488033055 0.000000e+00 1086.0
18 TraesCS1D01G206400 chr1B 91.629 657 31 13 1003 1641 392738608 392737958 0.000000e+00 887.0
19 TraesCS1D01G206400 chr1B 87.223 767 60 20 162 913 392747653 392746910 0.000000e+00 839.0
20 TraesCS1D01G206400 chr1B 90.125 638 48 8 766 1400 392837326 392837951 0.000000e+00 815.0
21 TraesCS1D01G206400 chr1B 93.682 459 18 2 245 695 392833955 392834410 0.000000e+00 676.0
22 TraesCS1D01G206400 chr1B 85.684 475 18 7 1391 1846 392838890 392839333 2.890000e-124 455.0
23 TraesCS1D01G206400 chr1B 95.625 160 7 0 1 160 392833879 392834038 8.760000e-65 257.0
24 TraesCS1D01G206400 chr1B 82.869 251 26 3 2 244 392747737 392747496 2.490000e-50 209.0
25 TraesCS1D01G206400 chr1B 94.872 39 0 2 720 758 392834485 392834521 2.650000e-05 60.2
26 TraesCS1D01G206400 chr7A 92.157 459 36 0 999 1457 93064874 93065332 0.000000e+00 649.0
27 TraesCS1D01G206400 chr7A 93.333 45 3 0 1648 1692 452295494 452295538 1.580000e-07 67.6
28 TraesCS1D01G206400 chr7A 94.737 38 2 0 1642 1679 678929830 678929867 2.650000e-05 60.2
29 TraesCS1D01G206400 chr7B 91.295 471 41 0 999 1469 43949108 43948638 0.000000e+00 643.0
30 TraesCS1D01G206400 chr7B 90.433 439 41 1 1031 1469 43896940 43896503 5.920000e-161 577.0
31 TraesCS1D01G206400 chrUn 90.638 235 20 2 999 1232 478858121 478857888 6.630000e-81 311.0
32 TraesCS1D01G206400 chrUn 92.982 57 4 0 937 993 183180786 183180842 1.570000e-12 84.2
33 TraesCS1D01G206400 chrUn 92.982 57 4 0 937 993 254878547 254878603 1.570000e-12 84.2
34 TraesCS1D01G206400 chrUn 94.444 54 3 0 940 993 339676665 339676612 1.570000e-12 84.2
35 TraesCS1D01G206400 chrUn 94.444 54 3 0 940 993 391943831 391943778 1.570000e-12 84.2
36 TraesCS1D01G206400 chrUn 92.982 57 4 0 937 993 391959373 391959429 1.570000e-12 84.2
37 TraesCS1D01G206400 chr2B 83.396 265 42 2 998 1261 613037668 613037405 6.820000e-61 244.0
38 TraesCS1D01G206400 chr5A 89.730 185 18 1 1659 1843 322859911 322860094 4.100000e-58 235.0
39 TraesCS1D01G206400 chr6D 93.103 145 9 1 1699 1843 38460752 38460609 6.910000e-51 211.0
40 TraesCS1D01G206400 chr2D 88.276 145 17 0 1659 1803 315481505 315481361 9.070000e-40 174.0
41 TraesCS1D01G206400 chr5B 83.908 87 14 0 1370 1456 397834730 397834644 1.570000e-12 84.2


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 TraesCS1D01G206400 chr1D 291840765 291843232 2467 False 4558.00 4558 100.0000 1 2468 1 chr1D.!!$F1 2467
1 TraesCS1D01G206400 chr1D 291798702 291800700 1998 True 1513.00 1792 93.9310 1 1553 2 chr1D.!!$R1 1552
2 TraesCS1D01G206400 chr1A 364039617 364041130 1513 True 1077.50 1973 89.5745 5 1556 2 chr1A.!!$R2 1551
3 TraesCS1D01G206400 chr7D 224462474 224463097 623 False 1092.00 1092 98.2370 1845 2468 1 chr7D.!!$F2 623
4 TraesCS1D01G206400 chr3D 491627750 491628376 626 False 1092.00 1092 98.0860 1842 2468 1 chr3D.!!$F4 626
5 TraesCS1D01G206400 chr3D 32733485 32734108 623 False 1081.00 1081 97.9170 1845 2468 1 chr3D.!!$F1 623
6 TraesCS1D01G206400 chr3D 46546748 46547371 623 False 1081.00 1081 97.9170 1845 2468 1 chr3D.!!$F2 623
7 TraesCS1D01G206400 chr3D 288041809 288042440 631 False 1079.00 1079 97.4680 1837 2468 1 chr3D.!!$F3 631
8 TraesCS1D01G206400 chr3D 39037900 39038528 628 True 1077.00 1077 97.6150 1841 2468 1 chr3D.!!$R1 627
9 TraesCS1D01G206400 chr5D 43964091 43964714 623 False 1086.00 1086 98.0770 1845 2468 1 chr5D.!!$F1 623
10 TraesCS1D01G206400 chr4D 449193366 449193989 623 False 1086.00 1086 98.0770 1845 2468 1 chr4D.!!$F1 623
11 TraesCS1D01G206400 chr4D 488033055 488033678 623 True 1086.00 1086 98.0770 1845 2468 1 chr4D.!!$R1 623
12 TraesCS1D01G206400 chr1B 392737958 392738608 650 True 887.00 887 91.6290 1003 1641 1 chr1B.!!$R1 638
13 TraesCS1D01G206400 chr1B 392746910 392747737 827 True 524.00 839 85.0460 2 913 2 chr1B.!!$R2 911
14 TraesCS1D01G206400 chr1B 392833879 392839333 5454 False 452.64 815 91.9976 1 1846 5 chr1B.!!$F1 1845

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
970 4335 0.320374 TCGTGAGGACTCGCCAAAAT 59.68 50.0 7.25 0.0 40.02 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2100 6454 1.06643 GTCAGGTTCGGGTGCTTCATA 60.066 52.381 0.0 0.0 0.0 2.15 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
536 1039 3.760035 GGCAGACGGAGCGGAAGA 61.760 66.667 0.00 0.00 0.00 2.87
593 1096 0.914417 GATGGGTTCCAGGAGGTCCA 60.914 60.000 9.20 9.20 36.75 4.02
636 1139 3.687102 TTCGGCCATCGTCGTGGT 61.687 61.111 2.24 0.00 41.47 4.16
637 1140 3.925362 TTCGGCCATCGTCGTGGTG 62.925 63.158 2.24 8.09 41.47 4.17
668 1174 3.984200 GACGTACGGCAGGAGCACC 62.984 68.421 18.23 0.00 44.61 5.01
696 1246 4.069304 GGCAAAGGTATATATGCACGGAA 58.931 43.478 8.02 0.00 40.51 4.30
697 1247 4.154195 GGCAAAGGTATATATGCACGGAAG 59.846 45.833 8.02 0.00 40.51 3.46
713 1267 5.656213 ACGGAAGTAGTATGTTTGTAGCT 57.344 39.130 0.00 0.00 46.88 3.32
717 1271 6.043411 GGAAGTAGTATGTTTGTAGCTCCAG 58.957 44.000 0.00 0.00 0.00 3.86
722 1276 6.354794 AGTATGTTTGTAGCTCCAGTACAA 57.645 37.500 0.00 0.00 38.36 2.41
723 1277 6.164176 AGTATGTTTGTAGCTCCAGTACAAC 58.836 40.000 0.00 0.00 39.53 3.32
725 1279 5.031066 TGTTTGTAGCTCCAGTACAACTT 57.969 39.130 0.00 0.00 39.53 2.66
726 1280 6.164417 TGTTTGTAGCTCCAGTACAACTTA 57.836 37.500 0.00 0.00 39.53 2.24
970 4335 0.320374 TCGTGAGGACTCGCCAAAAT 59.680 50.000 7.25 0.00 40.02 1.82
1006 4371 1.354337 CGACGACAACCAGATGCAGG 61.354 60.000 0.00 0.00 0.00 4.85
1053 4418 1.296392 CATCACGCTGGAGGTGGAA 59.704 57.895 0.00 0.00 36.09 3.53
1155 4520 2.790791 CGGGAAGCAGCTCGAGGAT 61.791 63.158 15.58 0.00 0.00 3.24
1196 4570 1.531149 CAACGTGCAAAAGGAGTCGAT 59.469 47.619 0.00 0.00 0.00 3.59
1726 6080 2.688507 AGACGTTCATCGACTTGCAAT 58.311 42.857 0.00 0.00 41.07 3.56
1738 6092 1.002746 TTGCAATAGCGACTGGGCA 60.003 52.632 0.00 0.00 46.23 5.36
1838 6192 1.549203 TACGGTTTCCTTCGCTAGGT 58.451 50.000 3.73 0.00 45.03 3.08
1887 6241 5.826601 TGCTTATTGATAATTTGGTGCGA 57.173 34.783 0.00 0.00 0.00 5.10
2020 6374 3.173240 GCAGGCTCGACGACGTTC 61.173 66.667 0.13 0.40 40.69 3.95
2100 6454 1.867363 AACTGAGCCGTAGAGGGAAT 58.133 50.000 0.00 0.00 41.48 3.01
2331 6685 0.246635 ACAACGCGATACTCAGCCTT 59.753 50.000 15.93 0.00 0.00 4.35
2354 6708 1.129998 CCGACGAACGTGAGACTGTAT 59.870 52.381 4.19 0.00 40.78 2.29
2409 6763 8.664211 TTGTTACCAAGAAAAACACAAAAACT 57.336 26.923 0.00 0.00 33.10 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
536 1039 2.501128 CGTCATGGGAGTCGCCAT 59.499 61.111 4.54 6.06 38.95 4.40
593 1096 2.348998 CTGGCTGAAGCTCCCGTT 59.651 61.111 1.74 0.00 41.70 4.44
636 1139 0.256752 TACGTCCCCTACTAGCAGCA 59.743 55.000 0.00 0.00 0.00 4.41
637 1140 0.667453 GTACGTCCCCTACTAGCAGC 59.333 60.000 0.00 0.00 0.00 5.25
638 1141 0.942962 CGTACGTCCCCTACTAGCAG 59.057 60.000 7.22 0.00 0.00 4.24
668 1174 2.736144 TATATACCTTTGCCTCCGCG 57.264 50.000 0.00 0.00 38.08 6.46
696 1246 6.662234 TGTACTGGAGCTACAAACATACTACT 59.338 38.462 9.26 0.00 0.00 2.57
697 1247 6.860080 TGTACTGGAGCTACAAACATACTAC 58.140 40.000 9.26 0.00 0.00 2.73
699 1249 5.995565 TGTACTGGAGCTACAAACATACT 57.004 39.130 9.26 0.00 0.00 2.12
700 1250 6.164176 AGTTGTACTGGAGCTACAAACATAC 58.836 40.000 13.19 13.13 36.18 2.39
717 1271 8.562052 CGGGTTCCCATAAATAATAAGTTGTAC 58.438 37.037 8.70 0.00 0.00 2.90
722 1276 6.877322 CGATCGGGTTCCCATAAATAATAAGT 59.123 38.462 7.38 0.00 0.00 2.24
723 1277 6.315393 CCGATCGGGTTCCCATAAATAATAAG 59.685 42.308 26.95 0.00 0.00 1.73
725 1279 5.484644 TCCGATCGGGTTCCCATAAATAATA 59.515 40.000 32.79 5.19 37.00 0.98
726 1280 4.287585 TCCGATCGGGTTCCCATAAATAAT 59.712 41.667 32.79 0.00 37.00 1.28
763 4117 2.287103 TCGTGGTCATCTCGTATTCTCG 59.713 50.000 0.00 0.00 0.00 4.04
970 4335 4.157120 GGCGGCCGCTCTTTCCTA 62.157 66.667 45.23 0.00 41.60 2.94
997 4362 1.998315 CTTCACGAAGACCTGCATCTG 59.002 52.381 0.20 0.00 40.79 2.90
1024 4389 2.264480 CGTGATGGTCTTGCCCGA 59.736 61.111 0.00 0.00 36.04 5.14
1222 4596 2.672651 CTTGATGGTGGTGCCGCA 60.673 61.111 4.06 0.00 41.21 5.69
1314 4688 1.682684 GCCCTCCTTCTCCTCGACA 60.683 63.158 0.00 0.00 0.00 4.35
1383 4757 1.131638 AGTCCTTGGCAGTCTTGTCA 58.868 50.000 0.00 0.00 37.08 3.58
1703 6057 3.644823 TGCAAGTCGATGAACGTCTTTA 58.355 40.909 0.00 0.00 44.72 1.85
1707 6061 3.542291 GCTATTGCAAGTCGATGAACGTC 60.542 47.826 4.94 0.00 40.05 4.34
1838 6192 7.039784 ACAGTTTTATTTAGCTTTCAGCCATCA 60.040 33.333 0.00 0.00 43.77 3.07
2020 6374 7.412346 CCGTTTCAAGATATCTGTTTCAGTCTG 60.412 40.741 5.86 0.00 32.61 3.51
2100 6454 1.066430 GTCAGGTTCGGGTGCTTCATA 60.066 52.381 0.00 0.00 0.00 2.15
2300 6654 3.353029 CGTTGTGGCACATGGCGA 61.353 61.111 22.73 2.44 44.52 5.54
2303 6657 1.365368 TATCGCGTTGTGGCACATGG 61.365 55.000 22.73 16.77 44.52 3.66
2331 6685 3.289062 TCTCACGTTCGTCGGCCA 61.289 61.111 2.24 0.00 44.69 5.36


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

AutoCloner maintained by Alex Coulton.