Multiple sequence alignment - TraesCS7B01G418500

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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 TraesCS7B01G418500 chr7B 100.000 3454 0 0 1 3454 686889545 686886092 0.000000e+00 6379.0
1 TraesCS7B01G418500 chr7B 83.209 1739 156 64 532 2199 686849485 686851158 0.000000e+00 1469.0
2 TraesCS7B01G418500 chr7B 85.500 1131 121 22 1088 2199 688163057 688164163 0.000000e+00 1140.0
3 TraesCS7B01G418500 chr7B 85.062 1138 120 22 1088 2199 686966476 686965363 0.000000e+00 1114.0
4 TraesCS7B01G418500 chr7B 84.350 377 35 9 530 895 686966933 686966570 7.090000e-92 348.0
5 TraesCS7B01G418500 chr7B 91.176 136 11 1 535 670 688162672 688162806 2.120000e-42 183.0
6 TraesCS7B01G418500 chr7D 88.869 2273 182 36 235 2486 603981712 603983934 0.000000e+00 2730.0
7 TraesCS7B01G418500 chr7D 88.466 1604 118 33 614 2199 604530609 604532163 0.000000e+00 1875.0
8 TraesCS7B01G418500 chr7D 84.013 1520 151 47 715 2199 603847518 603848980 0.000000e+00 1376.0
9 TraesCS7B01G418500 chr7D 84.725 1329 136 40 923 2199 604475133 604476446 0.000000e+00 1267.0
10 TraesCS7B01G418500 chr7D 86.740 181 7 4 3288 3454 603984703 603984880 5.890000e-43 185.0
11 TraesCS7B01G418500 chr7D 89.147 129 11 3 535 663 604472276 604472401 1.280000e-34 158.0
12 TraesCS7B01G418500 chr7D 85.965 57 5 2 527 580 604530559 604530615 1.340000e-04 58.4
13 TraesCS7B01G418500 chr7A 89.740 2115 150 35 392 2484 696624168 696622099 0.000000e+00 2641.0
14 TraesCS7B01G418500 chr7A 84.711 1282 135 34 953 2199 696552496 696553751 0.000000e+00 1225.0
15 TraesCS7B01G418500 chr7A 86.567 1139 110 21 1086 2199 696723497 696722377 0.000000e+00 1216.0
16 TraesCS7B01G418500 chr7A 85.185 378 26 12 535 897 696723995 696723633 9.110000e-96 361.0
17 TraesCS7B01G418500 chr7A 83.768 345 23 11 535 857 696552150 696552483 2.610000e-76 296.0
18 TraesCS7B01G418500 chr7A 83.025 324 47 8 209 527 433744575 433744895 1.570000e-73 287.0
19 TraesCS7B01G418500 chr7A 89.247 186 13 5 3271 3454 696621242 696621062 3.470000e-55 226.0
20 TraesCS7B01G418500 chr7A 92.593 81 6 0 3033 3113 696621847 696621767 2.180000e-22 117.0
21 TraesCS7B01G418500 chr2D 83.133 332 50 5 209 538 357443068 357443395 7.250000e-77 298.0
22 TraesCS7B01G418500 chr2D 82.609 322 53 3 209 527 618691287 618691608 7.300000e-72 281.0
23 TraesCS7B01G418500 chr6D 83.386 319 50 3 211 527 460272519 460272202 3.370000e-75 292.0
24 TraesCS7B01G418500 chr6D 93.939 99 6 0 2115 2213 104454152 104454054 2.150000e-32 150.0
25 TraesCS7B01G418500 chr3B 83.333 324 45 8 209 527 71346822 71347141 1.210000e-74 291.0
26 TraesCS7B01G418500 chr1B 83.282 323 47 7 209 527 57805344 57805025 1.210000e-74 291.0
27 TraesCS7B01G418500 chr1B 82.972 323 48 7 209 527 30713618 30713299 5.640000e-73 285.0
28 TraesCS7B01G418500 chr4A 82.866 321 52 3 209 527 94978615 94978296 5.640000e-73 285.0
29 TraesCS7B01G418500 chr6A 93.939 99 6 0 2115 2213 126345536 126345438 2.150000e-32 150.0


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 TraesCS7B01G418500 chr7B 686886092 686889545 3453 True 6379.000000 6379 100.000000 1 3454 1 chr7B.!!$R1 3453
1 TraesCS7B01G418500 chr7B 686849485 686851158 1673 False 1469.000000 1469 83.209000 532 2199 1 chr7B.!!$F1 1667
2 TraesCS7B01G418500 chr7B 686965363 686966933 1570 True 731.000000 1114 84.706000 530 2199 2 chr7B.!!$R2 1669
3 TraesCS7B01G418500 chr7B 688162672 688164163 1491 False 661.500000 1140 88.338000 535 2199 2 chr7B.!!$F2 1664
4 TraesCS7B01G418500 chr7D 603981712 603984880 3168 False 1457.500000 2730 87.804500 235 3454 2 chr7D.!!$F2 3219
5 TraesCS7B01G418500 chr7D 603847518 603848980 1462 False 1376.000000 1376 84.013000 715 2199 1 chr7D.!!$F1 1484
6 TraesCS7B01G418500 chr7D 604530559 604532163 1604 False 966.700000 1875 87.215500 527 2199 2 chr7D.!!$F4 1672
7 TraesCS7B01G418500 chr7D 604472276 604476446 4170 False 712.500000 1267 86.936000 535 2199 2 chr7D.!!$F3 1664
8 TraesCS7B01G418500 chr7A 696621062 696624168 3106 True 994.666667 2641 90.526667 392 3454 3 chr7A.!!$R1 3062
9 TraesCS7B01G418500 chr7A 696722377 696723995 1618 True 788.500000 1216 85.876000 535 2199 2 chr7A.!!$R2 1664
10 TraesCS7B01G418500 chr7A 696552150 696553751 1601 False 760.500000 1225 84.239500 535 2199 2 chr7A.!!$F2 1664


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
192 193 0.107945 GTCTGGCATCACTGGAGGAC 60.108 60.0 0.00 0.0 32.07 3.85 F
1732 4389 0.040067 CCTCGTGATCATCGATCGCA 60.040 55.0 11.09 0.0 46.25 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1784 4456 0.036010 CCATCCTTCACGACCTGCTT 60.036 55.0 0.0 0.0 0.0 3.91 R
2782 5486 0.034477 TCCGATTCTTTTGCCCCTCC 60.034 55.0 0.0 0.0 0.0 4.30 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)



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AutoCloner maintained by Alex Coulton.