Multiple sequence alignment - TraesCS1B01G373500

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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 TraesCS1B01G373500 chr1B 100.000 3835 0 0 1 3835 604141346 604137512 0.000000e+00 7083
1 TraesCS1B01G373500 chr2B 97.139 3845 96 8 1 3835 671388261 671384421 0.000000e+00 6479
2 TraesCS1B01G373500 chr2B 96.132 3852 128 13 1 3835 23103130 23099283 0.000000e+00 6268
3 TraesCS1B01G373500 chr2B 95.874 3854 132 12 1 3835 679051510 679047665 0.000000e+00 6211
4 TraesCS1B01G373500 chr2B 94.865 3856 159 28 1 3835 740768268 740764431 0.000000e+00 5987
5 TraesCS1B01G373500 chr5B 95.719 3854 137 16 1 3835 711431098 711434942 0.000000e+00 6178
6 TraesCS1B01G373500 chrUn 94.611 3860 171 24 1 3835 294583826 294579979 0.000000e+00 5941
7 TraesCS1B01G373500 chrUn 94.561 3861 172 24 1 3835 294578563 294574715 0.000000e+00 5932
8 TraesCS1B01G373500 chr3B 94.374 3857 178 25 1 3835 710814787 710810948 0.000000e+00 5884
9 TraesCS1B01G373500 chr3B 94.273 3859 174 31 1 3835 587986073 587982238 0.000000e+00 5858
10 TraesCS1B01G373500 chr3A 92.857 280 20 0 3556 3835 164752423 164752144 1.280000e-109 407


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 TraesCS1B01G373500 chr1B 604137512 604141346 3834 True 7083.0 7083 100.000 1 3835 1 chr1B.!!$R1 3834
1 TraesCS1B01G373500 chr2B 671384421 671388261 3840 True 6479.0 6479 97.139 1 3835 1 chr2B.!!$R2 3834
2 TraesCS1B01G373500 chr2B 23099283 23103130 3847 True 6268.0 6268 96.132 1 3835 1 chr2B.!!$R1 3834
3 TraesCS1B01G373500 chr2B 679047665 679051510 3845 True 6211.0 6211 95.874 1 3835 1 chr2B.!!$R3 3834
4 TraesCS1B01G373500 chr2B 740764431 740768268 3837 True 5987.0 5987 94.865 1 3835 1 chr2B.!!$R4 3834
5 TraesCS1B01G373500 chr5B 711431098 711434942 3844 False 6178.0 6178 95.719 1 3835 1 chr5B.!!$F1 3834
6 TraesCS1B01G373500 chrUn 294574715 294583826 9111 True 5936.5 5941 94.586 1 3835 2 chrUn.!!$R1 3834
7 TraesCS1B01G373500 chr3B 710810948 710814787 3839 True 5884.0 5884 94.374 1 3835 1 chr3B.!!$R2 3834
8 TraesCS1B01G373500 chr3B 587982238 587986073 3835 True 5858.0 5858 94.273 1 3835 1 chr3B.!!$R1 3834

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
774 787 0.239347 CTCTTCGCCCAAGCAACAAG 59.761 55.0 0.0 0.0 39.83 3.16 F
2124 2148 0.908198 GTCCCTCAATGGCTCTGACT 59.092 55.0 0.0 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2157 2181 1.136305 CCGATGTGTACGTTCTGGGAT 59.864 52.381 0.00 0.0 0.00 3.85 R
3711 9020 2.576615 GCGGGAATCTTCCTTGCTTAT 58.423 47.619 15.08 0.0 46.72 1.73 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
582 594 4.315803 GGACATATCAAAGTCCCGTATGG 58.684 47.826 0.00 0.00 46.79 2.74
654 666 0.802494 GAATCCATGCCGAACACGTT 59.198 50.000 0.00 0.00 0.00 3.99
774 787 0.239347 CTCTTCGCCCAAGCAACAAG 59.761 55.000 0.00 0.00 39.83 3.16
914 929 3.342719 TGATTTCTCATGCGGCAACTTA 58.657 40.909 6.82 0.00 0.00 2.24
1037 1053 3.392882 CAAGATGTTCCAAAAGGGTTGC 58.607 45.455 0.00 0.00 38.11 4.17
1092 1109 7.595130 AGTTCTTTTCTGTGAACACTGTTTTTC 59.405 33.333 6.51 0.00 43.38 2.29
1095 1112 8.087750 TCTTTTCTGTGAACACTGTTTTTCAAT 58.912 29.630 6.51 0.00 33.58 2.57
1144 1161 6.938596 CCTGATCATAACAAGATGGCAATCTA 59.061 38.462 3.37 0.00 42.60 1.98
1209 1226 8.301720 CAACTAGCATAATGACAATATGGCAAT 58.698 33.333 11.58 0.00 39.86 3.56
1298 1315 5.604565 CAACTGCTATCACACTATGATGGA 58.395 41.667 4.62 0.00 46.63 3.41
1341 1358 9.423061 TGGAAACTTTTTCTTTTCTTCTCTTTG 57.577 29.630 0.00 0.00 33.10 2.77
1470 1489 1.135660 AGCTCATGTACGTCGACTGTG 60.136 52.381 14.70 6.71 0.00 3.66
1584 1603 2.110835 TGCTTGCCGCAGACAAGA 59.889 55.556 12.99 0.00 45.99 3.02
1641 1660 2.093394 TCTGGTTTCTTTGTCCACACGA 60.093 45.455 0.00 0.00 0.00 4.35
1711 1730 8.378565 CAGATGACTACCTTTATTATCCATGGT 58.621 37.037 12.58 1.59 0.00 3.55
1846 1870 4.564406 GGCCAAGCATGCTATAGACTACAT 60.564 45.833 23.00 0.00 0.00 2.29
1914 1938 4.020617 CTCCGTCTTGCCCTGCCA 62.021 66.667 0.00 0.00 0.00 4.92
2033 2057 4.803908 GCACAGGCTAGGGCACCC 62.804 72.222 0.00 0.00 44.58 4.61
2113 2137 2.926242 GGGGTGGACGTCCCTCAA 60.926 66.667 31.19 10.44 44.07 3.02
2124 2148 0.908198 GTCCCTCAATGGCTCTGACT 59.092 55.000 0.00 0.00 0.00 3.41
2157 2181 2.742053 GCGAGGCAGTTCACTTCATTTA 59.258 45.455 0.00 0.00 0.00 1.40
2665 2699 1.226802 CTCATACGTGCAGCGAGCT 60.227 57.895 14.18 0.00 45.94 4.09
2745 2779 2.050442 GGTTGAACAAAGGCGCCG 60.050 61.111 23.20 9.91 0.00 6.46
2746 2780 2.729491 GTTGAACAAAGGCGCCGC 60.729 61.111 23.20 0.00 0.00 6.53
2903 2938 9.535270 GACATAGCGCTATATTTTCTTGATTTC 57.465 33.333 28.57 4.33 0.00 2.17
3019 3056 4.844349 AGTGTATGGCAACTCCTATTGT 57.156 40.909 0.00 0.00 35.26 2.71
3207 8508 4.202441 ACTGCTGCTAGATTTTGTATGGG 58.798 43.478 0.00 0.00 0.00 4.00
3208 8509 4.202441 CTGCTGCTAGATTTTGTATGGGT 58.798 43.478 0.00 0.00 0.00 4.51
3230 8531 5.163447 GGTACTGCTAACTATGACACATGGA 60.163 44.000 0.00 0.00 0.00 3.41
3755 9064 1.344438 TCTGACACTGATTCCAAGCGT 59.656 47.619 0.00 0.00 0.00 5.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
580 592 3.244215 GCTCGATCTCATTATTGACCCCA 60.244 47.826 0.00 0.00 0.00 4.96
582 594 3.995199 TGCTCGATCTCATTATTGACCC 58.005 45.455 0.00 0.00 0.00 4.46
823 837 3.031013 TGACATCGGAGCCAGAAGATTA 58.969 45.455 0.00 0.00 0.00 1.75
886 900 3.429272 GCCGCATGAGAAATCAAATGGAA 60.429 43.478 0.00 0.00 0.00 3.53
914 929 3.432046 CCACACAAAAGTTCAGGGCAAAT 60.432 43.478 0.00 0.00 0.00 2.32
1092 1109 7.089538 TGCCATGTATGAACAAAAGTGTATTG 58.910 34.615 0.00 0.00 39.58 1.90
1095 1112 6.442952 GTTGCCATGTATGAACAAAAGTGTA 58.557 36.000 0.00 0.00 39.58 2.90
1144 1161 5.716228 TGGAAGTTGCCATCTTGTTATGATT 59.284 36.000 0.00 0.00 31.66 2.57
1188 1205 5.929992 GCAATTGCCATATTGTCATTATGCT 59.070 36.000 20.06 0.00 37.72 3.79
1298 1315 5.186409 AGTTTCCATCTGCATGTGCTAATTT 59.814 36.000 6.55 0.00 42.66 1.82
1340 1357 6.374894 TGATAATCAAGTTGATGTGCATGACA 59.625 34.615 18.94 8.35 37.15 3.58
1341 1358 6.788243 TGATAATCAAGTTGATGTGCATGAC 58.212 36.000 18.94 6.22 37.15 3.06
1470 1489 0.320374 TCCACGGTGGACAGATCAAC 59.680 55.000 25.53 0.00 42.67 3.18
1584 1603 5.755409 TTTCCATATGTGGTGTCAGTAGT 57.245 39.130 8.51 0.00 46.16 2.73
1685 1704 8.378565 ACCATGGATAATAAAGGTAGTCATCTG 58.621 37.037 21.47 0.00 0.00 2.90
2033 2057 3.062763 CTGCCCTATTAGATGCTCAACG 58.937 50.000 0.00 0.00 0.00 4.10
2113 2137 2.182791 CGTCGCAGTCAGAGCCAT 59.817 61.111 0.00 0.00 0.00 4.40
2157 2181 1.136305 CCGATGTGTACGTTCTGGGAT 59.864 52.381 0.00 0.00 0.00 3.85
2418 2445 1.551883 CCCCCTCTTTGATGGCAAAAG 59.448 52.381 5.49 5.49 42.96 2.27
2665 2699 3.051210 CTCGTCCACCAGCTGTCA 58.949 61.111 13.81 0.00 0.00 3.58
2745 2779 2.283101 TGTCACCAGCAATGGGGC 60.283 61.111 0.00 0.00 30.89 5.80
2746 2780 1.978617 GGTGTCACCAGCAATGGGG 60.979 63.158 17.59 0.00 38.42 4.96
2903 2938 3.194116 ACAAGCTAAACAGATGCATTGGG 59.806 43.478 0.00 0.00 0.00 4.12
2994 3031 7.346471 ACAATAGGAGTTGCCATACACTTAAT 58.654 34.615 0.00 0.00 40.02 1.40
3207 8508 5.902681 TCCATGTGTCATAGTTAGCAGTAC 58.097 41.667 0.00 0.00 0.00 2.73
3208 8509 6.538945 TTCCATGTGTCATAGTTAGCAGTA 57.461 37.500 0.00 0.00 0.00 2.74
3711 9020 2.576615 GCGGGAATCTTCCTTGCTTAT 58.423 47.619 15.08 0.00 46.72 1.73
3755 9064 4.947147 GGAGGGCCAACACGCACA 62.947 66.667 6.18 0.00 33.27 4.57


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

AutoCloner maintained by Alex Coulton.