Multiple sequence alignment - TraesCS5A01G140300

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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 TraesCS5A01G140300 chr5A 100.000 2695 0 0 1 2695 312501085 312498391 0 4977
1 TraesCS5A01G140300 chr5A 94.401 2697 149 2 1 2695 264257248 264259944 0 4143
2 TraesCS5A01G140300 chr5A 94.177 2696 156 1 1 2695 407235824 407233129 0 4108
3 TraesCS5A01G140300 chr3A 94.549 2697 143 4 1 2695 113570895 113568201 0 4163
4 TraesCS5A01G140300 chr3A 94.290 2697 152 2 1 2695 157087533 157090229 0 4126
5 TraesCS5A01G140300 chr3A 93.662 2698 168 3 1 2695 612367275 612369972 0 4032
6 TraesCS5A01G140300 chr3A 93.655 2695 165 5 1 2694 422976502 422973813 0 4024
7 TraesCS5A01G140300 chr1A 94.436 2696 149 1 1 2695 111333219 111330524 0 4146
8 TraesCS5A01G140300 chr1A 94.360 2695 146 6 1 2694 512511411 512514100 0 4130
9 TraesCS5A01G140300 chr6A 93.657 2696 169 2 1 2695 269382436 269385130 0 4030


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 TraesCS5A01G140300 chr5A 312498391 312501085 2694 True 4977 4977 100.000 1 2695 1 chr5A.!!$R1 2694
1 TraesCS5A01G140300 chr5A 264257248 264259944 2696 False 4143 4143 94.401 1 2695 1 chr5A.!!$F1 2694
2 TraesCS5A01G140300 chr5A 407233129 407235824 2695 True 4108 4108 94.177 1 2695 1 chr5A.!!$R2 2694
3 TraesCS5A01G140300 chr3A 113568201 113570895 2694 True 4163 4163 94.549 1 2695 1 chr3A.!!$R1 2694
4 TraesCS5A01G140300 chr3A 157087533 157090229 2696 False 4126 4126 94.290 1 2695 1 chr3A.!!$F1 2694
5 TraesCS5A01G140300 chr3A 612367275 612369972 2697 False 4032 4032 93.662 1 2695 1 chr3A.!!$F2 2694
6 TraesCS5A01G140300 chr3A 422973813 422976502 2689 True 4024 4024 93.655 1 2694 1 chr3A.!!$R2 2693
7 TraesCS5A01G140300 chr1A 111330524 111333219 2695 True 4146 4146 94.436 1 2695 1 chr1A.!!$R1 2694
8 TraesCS5A01G140300 chr1A 512511411 512514100 2689 False 4130 4130 94.360 1 2694 1 chr1A.!!$F1 2693
9 TraesCS5A01G140300 chr6A 269382436 269385130 2694 False 4030 4030 93.657 1 2695 1 chr6A.!!$F1 2694

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
942 945 0.032912 TGACCGGTATGGACCTGCTA 60.033 55.0 7.34 0.0 44.46 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2460 2470 0.530744 CACTTAGCGTGCCCTCACTA 59.469 55.0 0.0 0.0 40.99 2.74 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
60 61 1.529152 GGCGTTGGACGGGGATTTTT 61.529 55.000 2.48 0.00 42.82 1.94
204 205 2.048127 GGAGCGTGCGAAGAAGGT 60.048 61.111 0.00 0.00 0.00 3.50
253 254 2.721167 CCAGGGCGGATCTTCGTCA 61.721 63.158 0.00 0.00 36.35 4.35
291 293 0.691078 GGCTGGATCCAGGGTGACTA 60.691 60.000 36.92 3.13 43.77 2.59
338 340 2.166459 GACATCGATGACCTGGTTGAGA 59.834 50.000 31.33 0.00 0.00 3.27
526 529 3.221771 CCACTTTCTCCAAACACCATCA 58.778 45.455 0.00 0.00 0.00 3.07
778 781 1.625818 CCTGGTTCTACTGCAAGGACT 59.374 52.381 0.00 0.00 39.30 3.85
860 863 2.465813 CTCCACCTTGAGAGTGATCCT 58.534 52.381 0.00 0.00 37.42 3.24
876 879 2.856760 TCCTAGAGGAGAAGGTGCAT 57.143 50.000 0.00 0.00 39.78 3.96
892 895 1.133823 TGCATGTGAAGGTGTTGGTCT 60.134 47.619 0.00 0.00 0.00 3.85
899 902 2.436115 GGTGTTGGTCTAGCGGGC 60.436 66.667 0.00 0.00 0.00 6.13
917 920 4.351938 TGTCCAACTCGTCCGCGG 62.352 66.667 22.12 22.12 38.89 6.46
942 945 0.032912 TGACCGGTATGGACCTGCTA 60.033 55.000 7.34 0.00 44.46 3.49
1027 1030 2.241430 TCAGGACTCGAGGATTCCACTA 59.759 50.000 18.41 1.86 34.40 2.74
1169 1177 2.000447 GGAACAGGTACGATTCTGCAC 59.000 52.381 0.00 0.00 34.57 4.57
1189 1198 3.917380 CACTGTCGAGTGTCTTCTTGATC 59.083 47.826 0.00 0.00 44.15 2.92
1204 1213 7.748683 GTCTTCTTGATCTACTATGTAGCATCG 59.251 40.741 0.00 0.00 0.00 3.84
1273 1282 6.653020 TCTTGTTGATATGTACTCAATGCCT 58.347 36.000 0.00 0.00 35.26 4.75
1353 1363 1.760086 ACTCGGATGCAGAGGAGGG 60.760 63.158 13.27 0.00 39.90 4.30
1366 1376 2.909965 GAGGGCGAGGAGAGCGAT 60.910 66.667 0.00 0.00 35.00 4.58
1404 1414 1.228894 AGGTTGACTCGCCTCCTCA 60.229 57.895 0.00 0.00 0.00 3.86
1495 1505 1.374252 GTCTTCAAAGCGCCCTCGA 60.374 57.895 2.29 0.00 38.10 4.04
1512 1522 0.039074 CGAACGTCTTCTCCAGTGCT 60.039 55.000 0.00 0.00 0.00 4.40
1690 1700 1.686052 TGGGTAACAGAACGTAACCGT 59.314 47.619 0.00 0.00 45.89 4.83
1714 1724 3.181484 TGAATGCTGATATTTGCAGTGCC 60.181 43.478 13.72 0.00 42.74 5.01
1842 1852 6.316140 TGGTCGATTAAATTCTGGTGATTCAG 59.684 38.462 0.00 0.00 36.17 3.02
1853 1863 1.271163 GGTGATTCAGTTGGGGTCGAA 60.271 52.381 0.00 0.00 0.00 3.71
1988 1998 1.021202 CTGGCGACAAAACCAACAGA 58.979 50.000 0.00 0.00 42.06 3.41
1993 2003 2.014128 CGACAAAACCAACAGACCAGT 58.986 47.619 0.00 0.00 0.00 4.00
2047 2057 0.828022 TGTTGTCCCAGTGTCGAGTT 59.172 50.000 0.00 0.00 0.00 3.01
2050 2060 3.070446 TGTTGTCCCAGTGTCGAGTTAAT 59.930 43.478 0.00 0.00 0.00 1.40
2090 2100 4.873827 TGTACCAGTGTTTTCTTCAGTCAC 59.126 41.667 0.00 0.00 0.00 3.67
2179 2189 1.885560 TGTTCCGAAAAGCCAATCGA 58.114 45.000 4.41 0.00 41.43 3.59
2189 2199 3.118454 CCAATCGAACGCCGCTGT 61.118 61.111 0.00 0.00 38.37 4.40
2202 2212 1.081108 CGCTGTAGAGGCTATCCGC 60.081 63.158 0.00 0.00 37.47 5.54
2250 2260 0.324943 AGGCGGTGCAAGACAATAGT 59.675 50.000 0.00 0.00 0.00 2.12
2384 2394 8.097038 ACAATCTCTTGTTGTCTGCTTCTAATA 58.903 33.333 0.00 0.00 43.05 0.98
2460 2470 4.952335 GTCTGGTTGAATGGGATCTGAATT 59.048 41.667 0.00 0.00 0.00 2.17
2465 2475 6.122277 GGTTGAATGGGATCTGAATTAGTGA 58.878 40.000 0.00 0.00 0.00 3.41
2504 2514 2.038329 TGGGTGTAGTCCCCGAGG 59.962 66.667 0.00 0.00 45.86 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.922369 AGTGGCTGACTCATGGGCT 60.922 57.895 0.00 0.00 0.00 5.19
60 61 0.587768 CAATGAGAACGCACTGTGCA 59.412 50.000 29.86 11.81 45.36 4.57
204 205 2.736995 CTTTCGCCTTCGCCGTCA 60.737 61.111 0.00 0.00 35.26 4.35
286 288 1.746470 TTGTCGAGCGGATCTAGTCA 58.254 50.000 0.00 0.00 0.00 3.41
291 293 0.249238 GCTGATTGTCGAGCGGATCT 60.249 55.000 0.00 0.00 0.00 2.75
374 376 1.260538 TGCGGCTCAGTCTCATTCCT 61.261 55.000 0.00 0.00 0.00 3.36
379 381 4.074526 GGCTGCGGCTCAGTCTCA 62.075 66.667 18.85 0.00 43.90 3.27
526 529 2.066262 CACGAAAGCGACAAGGTACAT 58.934 47.619 0.00 0.00 41.64 2.29
860 863 2.820178 TCACATGCACCTTCTCCTCTA 58.180 47.619 0.00 0.00 0.00 2.43
876 879 1.270094 CGCTAGACCAACACCTTCACA 60.270 52.381 0.00 0.00 0.00 3.58
892 895 2.978824 GAGTTGGACAGCCCGCTA 59.021 61.111 0.00 0.00 37.93 4.26
899 902 2.805353 CGCGGACGAGTTGGACAG 60.805 66.667 0.00 0.00 43.93 3.51
1027 1030 1.460305 CATCCTCCGGGTGGATCCT 60.460 63.158 24.24 5.85 45.33 3.24
1169 1177 4.433186 AGATCAAGAAGACACTCGACAG 57.567 45.455 0.00 0.00 0.00 3.51
1204 1213 0.030369 AGACAGTCGACCGTCAACAC 59.970 55.000 28.59 7.02 34.48 3.32
1353 1363 2.026879 GGTCATCGCTCTCCTCGC 59.973 66.667 0.00 0.00 0.00 5.03
1366 1376 2.493675 CTCTTCTTCATCACTCGGGTCA 59.506 50.000 0.00 0.00 0.00 4.02
1404 1414 1.349357 GCTTGGACCTCCTTTCTCTGT 59.651 52.381 0.00 0.00 36.82 3.41
1440 1450 2.352805 CCAGGTCAGGGGTGCTTC 59.647 66.667 0.00 0.00 0.00 3.86
1472 1482 2.260869 GGCGCTTTGAAGACTGCCA 61.261 57.895 7.64 0.00 42.03 4.92
1495 1505 1.040646 TCAGCACTGGAGAAGACGTT 58.959 50.000 0.00 0.00 0.00 3.99
1512 1522 2.821378 TGTTTCGATACCTTCTCGGTCA 59.179 45.455 3.47 0.00 44.93 4.02
1690 1700 4.201980 GCACTGCAAATATCAGCATTCAGA 60.202 41.667 0.00 0.00 40.42 3.27
1714 1724 0.250295 TGGAAGTTCCAGAAGTGGCG 60.250 55.000 21.05 0.00 42.67 5.69
1842 1852 4.485163 CAAAGAAATCATTCGACCCCAAC 58.515 43.478 0.00 0.00 40.63 3.77
1853 1863 1.551883 GTGGGGCTGCAAAGAAATCAT 59.448 47.619 0.50 0.00 0.00 2.45
1963 1973 1.281656 GTTTTGTCGCCAGTTCCGG 59.718 57.895 0.00 0.00 0.00 5.14
1978 1988 1.774856 AGGCTACTGGTCTGTTGGTTT 59.225 47.619 0.00 0.00 0.00 3.27
1988 1998 1.209019 CTGCATCTTCAGGCTACTGGT 59.791 52.381 0.00 0.00 44.99 4.00
2047 2057 2.203139 CGATGGTGCGGGGCATTA 60.203 61.111 0.00 0.00 41.91 1.90
2090 2100 2.124570 CCGAGGCATGAGGTTGGG 60.125 66.667 0.00 0.00 0.00 4.12
2202 2212 1.168407 CCATCATTACGCCAGCCTGG 61.168 60.000 6.32 6.32 41.55 4.45
2250 2260 3.409201 GGCATCATAAGCAGCCTGA 57.591 52.632 0.00 0.00 43.70 3.86
2282 2292 3.157087 CAACTTACCTGGACATTGGCTT 58.843 45.455 0.00 0.00 0.00 4.35
2460 2470 0.530744 CACTTAGCGTGCCCTCACTA 59.469 55.000 0.00 0.00 40.99 2.74
2588 2598 3.099905 CCACTAGTTCAGATCCCACTCA 58.900 50.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.