Multiple sequence alignment - TraesCS7A01G142600

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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 TraesCS7A01G142600 chr7A 100.000 3104 0 0 1 3104 94185694 94188797 0.000000e+00 5733.0
1 TraesCS7A01G142600 chr7A 98.100 3106 55 4 1 3104 94216903 94220006 0.000000e+00 5406.0
2 TraesCS7A01G142600 chr7A 82.601 2368 326 35 332 2655 93898042 93900367 0.000000e+00 2012.0
3 TraesCS7A01G142600 chr7A 82.495 2365 323 37 332 2655 94130890 94133204 0.000000e+00 1989.0
4 TraesCS7A01G142600 chr7A 78.103 1265 243 17 856 2104 63759120 63757874 0.000000e+00 771.0
5 TraesCS7A01G142600 chr7B 92.607 2543 166 9 249 2770 42140039 42137498 0.000000e+00 3635.0
6 TraesCS7A01G142600 chr7B 82.892 2268 318 37 332 2558 42178284 42176046 0.000000e+00 1975.0
7 TraesCS7A01G142600 chr7B 92.962 341 22 2 2765 3104 42128457 42128118 2.150000e-136 496.0
8 TraesCS7A01G142600 chr7D 82.579 2365 318 38 332 2656 91990773 91993083 0.000000e+00 1999.0
9 TraesCS7A01G142600 chr7D 77.172 1266 253 20 856 2104 59162521 59161275 0.000000e+00 704.0
10 TraesCS7A01G142600 chr7D 73.085 457 100 16 332 772 59163084 59162635 1.160000e-29 141.0
11 TraesCS7A01G142600 chr4A 77.215 1264 249 21 859 2104 677113687 677112445 0.000000e+00 702.0
12 TraesCS7A01G142600 chr5D 90.938 320 24 3 1 316 288540386 288540068 2.860000e-115 425.0
13 TraesCS7A01G142600 chr5D 88.955 335 29 7 1 328 426148030 426147697 1.040000e-109 407.0
14 TraesCS7A01G142600 chr4B 89.552 335 28 5 1 329 353942151 353942484 4.790000e-113 418.0
15 TraesCS7A01G142600 chr5A 89.521 334 28 5 1 329 501422784 501422453 1.720000e-112 416.0
16 TraesCS7A01G142600 chr5A 89.222 334 30 4 1 329 315317210 315316878 2.230000e-111 412.0
17 TraesCS7A01G142600 chr5A 88.822 331 31 3 4 329 382052232 382051903 4.820000e-108 401.0
18 TraesCS7A01G142600 chr2A 88.372 344 32 6 1 338 212602875 212603216 1.040000e-109 407.0
19 TraesCS7A01G142600 chr1B 88.922 334 31 4 1 329 367445177 367444845 1.040000e-109 407.0
20 TraesCS7A01G142600 chr2B 92.308 52 3 1 844 894 749424194 749424143 4.290000e-09 73.1


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 TraesCS7A01G142600 chr7A 94185694 94188797 3103 False 5733.0 5733 100.0000 1 3104 1 chr7A.!!$F3 3103
1 TraesCS7A01G142600 chr7A 94216903 94220006 3103 False 5406.0 5406 98.1000 1 3104 1 chr7A.!!$F4 3103
2 TraesCS7A01G142600 chr7A 93898042 93900367 2325 False 2012.0 2012 82.6010 332 2655 1 chr7A.!!$F1 2323
3 TraesCS7A01G142600 chr7A 94130890 94133204 2314 False 1989.0 1989 82.4950 332 2655 1 chr7A.!!$F2 2323
4 TraesCS7A01G142600 chr7A 63757874 63759120 1246 True 771.0 771 78.1030 856 2104 1 chr7A.!!$R1 1248
5 TraesCS7A01G142600 chr7B 42137498 42140039 2541 True 3635.0 3635 92.6070 249 2770 1 chr7B.!!$R2 2521
6 TraesCS7A01G142600 chr7B 42176046 42178284 2238 True 1975.0 1975 82.8920 332 2558 1 chr7B.!!$R3 2226
7 TraesCS7A01G142600 chr7D 91990773 91993083 2310 False 1999.0 1999 82.5790 332 2656 1 chr7D.!!$F1 2324
8 TraesCS7A01G142600 chr7D 59161275 59163084 1809 True 422.5 704 75.1285 332 2104 2 chr7D.!!$R1 1772
9 TraesCS7A01G142600 chr4A 677112445 677113687 1242 True 702.0 702 77.2150 859 2104 1 chr4A.!!$R1 1245

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
786 811 2.014128 CCAACACGTCCATGGGAATAC 58.986 52.381 13.02 0.99 31.38 1.89 F
1516 1593 1.537202 GACACAAAGCCATGACTGGTC 59.463 52.381 0.00 0.00 45.10 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1756 1836 2.042686 TCATGTGCCTGATTAGGTGC 57.957 50.0 5.29 0.0 46.41 5.01 R
2693 2792 2.128771 TCAATTACAAGAGGCAGGGC 57.871 50.0 0.00 0.0 0.00 5.19 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
75 76 7.731688 CACCTAGACCCCCTTTAATAGTACATA 59.268 40.741 0.00 0.00 0.00 2.29
786 811 2.014128 CCAACACGTCCATGGGAATAC 58.986 52.381 13.02 0.99 31.38 1.89
1056 1133 3.202097 TGACAAAGAGCGTGATTTCACA 58.798 40.909 11.02 0.00 46.75 3.58
1097 1174 5.390613 CGGTTTGTTTAAGAGTATTGCTGG 58.609 41.667 0.00 0.00 0.00 4.85
1453 1530 7.989741 ACAATCTATCCAATGAAATCTCTCGTT 59.010 33.333 0.00 0.00 0.00 3.85
1516 1593 1.537202 GACACAAAGCCATGACTGGTC 59.463 52.381 0.00 0.00 45.10 4.02
1756 1836 1.743252 GCTTCCCAGCAAGAGACCG 60.743 63.158 0.00 0.00 46.49 4.79
2693 2792 8.657074 TGGTAAATCAAGTTCGTAATAGATGG 57.343 34.615 0.00 0.00 0.00 3.51
2717 2816 5.221126 GCCCTGCCTCTTGTAATTGAAATAG 60.221 44.000 0.00 0.00 0.00 1.73
2933 3032 5.498159 CATACGGACACATCGGTTAATTTG 58.502 41.667 0.00 0.00 39.06 2.32
2973 3072 5.833667 TCTATACAGGAACACCCTACATCTG 59.166 44.000 0.00 0.00 45.60 2.90
2975 3074 2.834549 ACAGGAACACCCTACATCTGAG 59.165 50.000 0.00 0.00 45.60 3.35
3058 3158 4.650972 TTAGGTAAACTGAAGCCATGGT 57.349 40.909 14.67 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
133 134 8.396390 CCTATGAAGAAATTGATGTGAAGACTG 58.604 37.037 0.00 0.0 0.00 3.51
196 197 0.481128 AGACGACCCCCAAAAATGGT 59.519 50.000 0.00 0.0 34.33 3.55
205 206 1.078426 CACATGGAAGACGACCCCC 60.078 63.158 0.00 0.0 0.00 5.40
277 278 9.178758 GTATTGAAGACAAATAGGTTGAGGAAT 57.821 33.333 0.00 0.0 39.87 3.01
1056 1133 2.740714 GCCGCGTCGCTTGAAGAAT 61.741 57.895 16.36 0.0 0.00 2.40
1097 1174 0.965439 ACCAGTGACAGCAGAGAGAC 59.035 55.000 0.00 0.0 0.00 3.36
1453 1530 3.682436 CGATGTCCAATGTCCTCATGGAA 60.682 47.826 0.00 0.0 45.18 3.53
1516 1593 4.768659 TGTTTTGTTTTATGCTTGCACG 57.231 36.364 0.00 0.0 0.00 5.34
1756 1836 2.042686 TCATGTGCCTGATTAGGTGC 57.957 50.000 5.29 0.0 46.41 5.01
2559 2658 5.253330 AGCGGAAATTTGGACTATCTTTCA 58.747 37.500 0.00 0.0 0.00 2.69
2621 2720 5.624900 CGAGTTGTTATTGTTGTTGATGGTG 59.375 40.000 0.00 0.0 0.00 4.17
2693 2792 2.128771 TCAATTACAAGAGGCAGGGC 57.871 50.000 0.00 0.0 0.00 5.19
2717 2816 3.056107 TGGCCACACACATACTCTAGTTC 60.056 47.826 0.00 0.0 0.00 3.01
2911 3010 4.034742 GCAAATTAACCGATGTGTCCGTAT 59.965 41.667 0.00 0.0 0.00 3.06
3058 3158 5.204292 TGGCATGCATTTTATAACTACCCA 58.796 37.500 21.36 0.0 0.00 4.51
3072 3172 3.404224 TGATTTGTGTTTGGCATGCAT 57.596 38.095 21.36 0.0 0.00 3.96


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

AutoCloner maintained by Alex Coulton.