Multiple sequence alignment - TraesCS7A01G436100

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 TraesCS7A01G436100 chr7A 100.000 2157 0 0 390 2546 630389598 630391754 0.000000e+00 3984.0
1 TraesCS7A01G436100 chr7A 94.930 1637 63 14 919 2544 631961088 631959461 0.000000e+00 2545.0
2 TraesCS7A01G436100 chr7A 87.576 990 108 7 725 1712 632908816 632907840 0.000000e+00 1133.0
3 TraesCS7A01G436100 chr7A 87.475 990 109 7 725 1712 633037810 633036834 0.000000e+00 1127.0
4 TraesCS7A01G436100 chr7A 87.625 800 96 2 913 1712 632588107 632587311 0.000000e+00 926.0
5 TraesCS7A01G436100 chr7A 86.230 748 99 2 931 1678 630035649 630036392 0.000000e+00 808.0
6 TraesCS7A01G436100 chr7A 92.713 494 17 1 428 921 631961645 631961171 0.000000e+00 695.0
7 TraesCS7A01G436100 chr7A 92.625 339 22 2 397 732 632971744 632971406 3.810000e-133 484.0
8 TraesCS7A01G436100 chr7A 92.625 339 22 2 397 732 633038185 633037847 3.810000e-133 484.0
9 TraesCS7A01G436100 chr7A 92.330 339 23 2 397 732 632588769 632588431 1.770000e-131 479.0
10 TraesCS7A01G436100 chr7A 91.509 318 24 2 418 732 632909170 632908853 3.890000e-118 435.0
11 TraesCS7A01G436100 chr7A 100.000 86 0 0 1 86 630389209 630389294 2.620000e-35 159.0
12 TraesCS7A01G436100 chr7A 88.722 133 12 1 725 857 632588397 632588268 2.620000e-35 159.0
13 TraesCS7A01G436100 chr7A 97.619 84 2 0 3 86 631963145 631963062 7.340000e-31 145.0
14 TraesCS7A01G436100 chr7B 87.247 988 117 4 725 1712 592362020 592361042 0.000000e+00 1118.0
15 TraesCS7A01G436100 chr7B 91.343 335 26 2 397 728 592362392 592362058 2.990000e-124 455.0
16 TraesCS7A01G436100 chr7D 87.045 988 113 8 725 1712 548805334 548804362 0.000000e+00 1101.0
17 TraesCS7A01G436100 chr7D 85.027 748 107 3 931 1678 546754399 546755141 0.000000e+00 756.0
18 TraesCS7A01G436100 chr7D 94.387 481 16 4 397 868 548132004 548131526 0.000000e+00 728.0
19 TraesCS7A01G436100 chr7D 81.328 723 131 4 911 1631 548138165 548138885 3.650000e-163 584.0
20 TraesCS7A01G436100 chr7D 86.804 485 37 16 1449 1909 548129991 548129510 1.350000e-142 516.0
21 TraesCS7A01G436100 chr7D 91.329 346 20 7 397 732 548805713 548805368 4.960000e-127 464.0
22 TraesCS7A01G436100 chr7D 86.154 260 32 2 455 714 546753961 546754216 6.940000e-71 278.0
23 TraesCS7A01G436100 chr7D 95.349 86 4 0 1 86 548132192 548132107 1.230000e-28 137.0
24 TraesCS7A01G436100 chr4D 86.207 87 10 1 838 924 432765544 432765460 2.700000e-15 93.5
25 TraesCS7A01G436100 chr6B 84.884 86 11 1 838 923 59825853 59825770 4.510000e-13 86.1
26 TraesCS7A01G436100 chr1D 83.908 87 12 2 836 922 69266554 69266638 5.840000e-12 82.4


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 TraesCS7A01G436100 chr7A 630389209 630391754 2545 False 2071.500000 3984 100.000000 1 2546 2 chr7A.!!$F2 2545
1 TraesCS7A01G436100 chr7A 631959461 631963145 3684 True 1128.333333 2545 95.087333 3 2544 3 chr7A.!!$R2 2541
2 TraesCS7A01G436100 chr7A 630035649 630036392 743 False 808.000000 808 86.230000 931 1678 1 chr7A.!!$F1 747
3 TraesCS7A01G436100 chr7A 633036834 633038185 1351 True 805.500000 1127 90.050000 397 1712 2 chr7A.!!$R5 1315
4 TraesCS7A01G436100 chr7A 632907840 632909170 1330 True 784.000000 1133 89.542500 418 1712 2 chr7A.!!$R4 1294
5 TraesCS7A01G436100 chr7A 632587311 632588769 1458 True 521.333333 926 89.559000 397 1712 3 chr7A.!!$R3 1315
6 TraesCS7A01G436100 chr7B 592361042 592362392 1350 True 786.500000 1118 89.295000 397 1712 2 chr7B.!!$R1 1315
7 TraesCS7A01G436100 chr7D 548804362 548805713 1351 True 782.500000 1101 89.187000 397 1712 2 chr7D.!!$R2 1315
8 TraesCS7A01G436100 chr7D 548138165 548138885 720 False 584.000000 584 81.328000 911 1631 1 chr7D.!!$F1 720
9 TraesCS7A01G436100 chr7D 546753961 546755141 1180 False 517.000000 756 85.590500 455 1678 2 chr7D.!!$F2 1223
10 TraesCS7A01G436100 chr7D 548129510 548132192 2682 True 460.333333 728 92.180000 1 1909 3 chr7D.!!$R1 1908

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
750 1889 4.48193 TGTTGTGCAGTATGTAAGCAAC 57.518 40.909 4.59 4.59 40.35 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1591 4236 0.323725 GCTCTTGGCCCATTCCTCAA 60.324 55.0 0.0 0.0 34.27 3.02 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
61 62 5.757988 TCCATATGGTTTAAAGTACCCACC 58.242 41.667 21.28 0.00 34.66 4.61
535 1618 6.352516 TGCACCAAGTTTTTATTGTGGAAAT 58.647 32.000 0.00 0.00 33.39 2.17
669 1753 7.244192 CAGCATGAATCATTGCATCACTATAG 58.756 38.462 15.95 0.00 39.69 1.31
728 1815 9.801873 CTTATGTAAAAATTGGGATTCGAACAT 57.198 29.630 0.00 0.00 31.32 2.71
750 1889 4.481930 TGTTGTGCAGTATGTAAGCAAC 57.518 40.909 4.59 4.59 40.35 4.17
795 1934 6.067263 TGTTGGTCAGCAATTGTAAACTAC 57.933 37.500 7.40 3.87 0.00 2.73
872 3412 6.061022 TCCTAAATGTAAGATGTGCCTTGA 57.939 37.500 0.00 0.00 0.00 3.02
1168 3812 2.284952 TGTGCACTCAAATATCGCATCG 59.715 45.455 19.41 0.00 34.66 3.84
1280 3924 2.294233 GCAGTTTTGATCTGTGCTTCCA 59.706 45.455 0.00 0.00 35.60 3.53
1460 4104 1.271840 TACTCCTTCAAGGCGGGCAT 61.272 55.000 0.00 0.00 34.61 4.40
1574 4219 1.807139 TGCAGCGCTTGAATGAAGTA 58.193 45.000 7.50 0.00 33.73 2.24
1591 4236 6.671614 TGAAGTATGTCGAAAAGTTGTGTT 57.328 33.333 0.00 0.00 0.00 3.32
1670 4315 7.228706 ACTGTTGAACTGTTTAGGGTATCTTTG 59.771 37.037 1.78 0.00 0.00 2.77
1678 4323 7.015195 ACTGTTTAGGGTATCTTTGCATGTTTT 59.985 33.333 0.00 0.00 0.00 2.43
1756 4438 3.788227 AATGTGCTTGGTGAACTAGGA 57.212 42.857 0.00 0.00 0.00 2.94
1803 4485 5.332106 TCCAGCTCTAATCCTAGTCTGAT 57.668 43.478 0.00 0.00 33.03 2.90
1806 4488 5.538053 CCAGCTCTAATCCTAGTCTGATTCA 59.462 44.000 0.00 0.00 34.43 2.57
1978 4665 8.015087 TCTTTTAGACACAATGCTTACATTTCG 58.985 33.333 0.00 0.00 44.21 3.46
2015 4702 5.123936 AGGTTTACTGTGGACACTTCTTTC 58.876 41.667 3.91 0.00 0.00 2.62
2016 4703 4.275196 GGTTTACTGTGGACACTTCTTTCC 59.725 45.833 3.91 0.00 0.00 3.13
2030 4717 5.472137 CACTTCTTTCCGGAGTCCAAAAATA 59.528 40.000 10.49 0.00 0.00 1.40
2057 4746 8.696410 TCAAATTTAAAGTGTTTGTGGAGTTC 57.304 30.769 10.86 0.00 35.09 3.01
2118 4807 5.316167 CCTGACTTATGCTATGGCCATTTA 58.684 41.667 26.37 11.17 37.74 1.40
2297 4986 9.764363 AGAATCACGAAATCTTTACAGCATATA 57.236 29.630 0.00 0.00 0.00 0.86
2544 5233 4.760047 GCCGGTGGACACGATGCT 62.760 66.667 1.90 0.00 0.00 3.79
2545 5234 2.815211 CCGGTGGACACGATGCTG 60.815 66.667 0.00 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 1.139058 CCTAATGTGAGAACTCCCCCG 59.861 57.143 0.00 0.00 0.00 5.73
390 391 6.165577 GGCCTTACAATGTGAAATGTGAAAT 58.834 36.000 0.00 0.00 0.00 2.17
392 393 4.586421 TGGCCTTACAATGTGAAATGTGAA 59.414 37.500 3.32 0.00 0.00 3.18
394 395 4.517952 TGGCCTTACAATGTGAAATGTG 57.482 40.909 3.32 0.00 0.00 3.21
395 396 5.296748 GTTTGGCCTTACAATGTGAAATGT 58.703 37.500 3.32 0.00 0.00 2.71
426 1017 1.755959 AGTGCTTGTTGTTCCATGCAA 59.244 42.857 0.00 0.00 44.11 4.08
495 1573 1.949525 GTGCAATGGTGGCCTATACAG 59.050 52.381 3.32 0.00 0.00 2.74
669 1753 8.877808 AAATGAGAAGAGAAAACAAAATGACC 57.122 30.769 0.00 0.00 0.00 4.02
728 1815 4.261405 GGTTGCTTACATACTGCACAACAA 60.261 41.667 11.58 0.00 38.08 2.83
750 1889 5.105635 ACATCTTTGCCACATATCAAACTGG 60.106 40.000 0.00 0.00 0.00 4.00
872 3412 7.698130 GCGTCTTAGCAATTCAAATTGAACTAT 59.302 33.333 17.44 0.00 46.72 2.12
1168 3812 2.548178 CTGTGCCACAGTCACCATC 58.452 57.895 16.78 0.00 41.19 3.51
1280 3924 5.875910 TCGTCATAACCACCGATAAAACAAT 59.124 36.000 0.00 0.00 0.00 2.71
1387 4031 3.609409 GCAACCTCGAACTTCAAATCCAC 60.609 47.826 0.00 0.00 0.00 4.02
1439 4083 1.900545 GCCCGCCTTGAAGGAGTAGT 61.901 60.000 16.93 0.00 37.67 2.73
1442 4086 2.606587 ATGCCCGCCTTGAAGGAGT 61.607 57.895 16.93 0.00 37.67 3.85
1460 4104 0.829990 TCGAGTATCAAGCCCATGCA 59.170 50.000 0.00 0.00 35.53 3.96
1574 4219 4.638421 TCCTCAAACACAACTTTTCGACAT 59.362 37.500 0.00 0.00 0.00 3.06
1591 4236 0.323725 GCTCTTGGCCCATTCCTCAA 60.324 55.000 0.00 0.00 34.27 3.02
1709 4354 8.752187 TGCCAAGCAAGAAGATATAAAGATTTT 58.248 29.630 0.00 0.00 34.76 1.82
1712 4357 7.886629 TTGCCAAGCAAGAAGATATAAAGAT 57.113 32.000 0.00 0.00 43.99 2.40
1739 4421 2.841442 AGTCCTAGTTCACCAAGCAC 57.159 50.000 0.00 0.00 0.00 4.40
1803 4485 5.421056 ACGTCCAACTAGAGTGGATTATGAA 59.579 40.000 18.71 0.00 33.91 2.57
1806 4488 6.039493 CAGTACGTCCAACTAGAGTGGATTAT 59.961 42.308 18.71 11.84 33.91 1.28
1918 4603 7.961326 AATGTAATCACTAAGCTTTCCCAAT 57.039 32.000 3.20 0.00 0.00 3.16
2001 4688 1.070289 ACTCCGGAAAGAAGTGTCCAC 59.930 52.381 5.23 0.00 33.10 4.02
2003 4690 1.337917 GGACTCCGGAAAGAAGTGTCC 60.338 57.143 17.92 17.92 36.23 4.02
2015 4702 9.646427 TTAAATTTGATTATTTTTGGACTCCGG 57.354 29.630 0.00 0.00 0.00 5.14
2030 4717 9.665719 AACTCCACAAACACTTTAAATTTGATT 57.334 25.926 16.04 4.02 36.91 2.57
2042 4731 1.202651 CCCTCGAACTCCACAAACACT 60.203 52.381 0.00 0.00 0.00 3.55
2048 4737 3.319198 GCCCCCTCGAACTCCACA 61.319 66.667 0.00 0.00 0.00 4.17
2074 4763 1.269936 GGTGGACCGAAAGAGAACGAA 60.270 52.381 0.00 0.00 0.00 3.85
2474 5163 4.724074 AACCCGTTAGATACAATCACGA 57.276 40.909 0.00 0.00 32.41 4.35
2477 5166 6.325545 AGGACATAACCCGTTAGATACAATCA 59.674 38.462 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.