Multiple sequence alignment - TraesCS6A01G126600

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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 TraesCS6A01G126600 chr6A 100.000 2638 0 0 1 2638 99978784 99976147 0.000000e+00 4872.0
1 TraesCS6A01G126600 chr3A 97.445 1996 33 5 646 2638 662139640 662141620 0.000000e+00 3387.0
2 TraesCS6A01G126600 chr3A 96.610 649 21 1 1 649 482050223 482049576 0.000000e+00 1075.0
3 TraesCS6A01G126600 chr3A 96.451 648 21 2 1 648 533918678 533918033 0.000000e+00 1068.0
4 TraesCS6A01G126600 chr1D 96.803 2002 33 8 646 2638 156777378 156779357 0.000000e+00 3314.0
5 TraesCS6A01G126600 chr5A 97.140 1888 35 4 754 2638 299774058 299772187 0.000000e+00 3169.0
6 TraesCS6A01G126600 chr5A 96.759 648 20 1 1 648 493694461 493695107 0.000000e+00 1079.0
7 TraesCS6A01G126600 chr5A 96.462 650 20 3 1 648 543097982 543098630 0.000000e+00 1070.0
8 TraesCS6A01G126600 chr4A 96.891 1351 23 4 646 1993 41895908 41897242 0.000000e+00 2244.0
9 TraesCS6A01G126600 chr4A 91.036 1071 50 14 1571 2638 725869206 725868179 0.000000e+00 1404.0
10 TraesCS6A01G126600 chr4A 96.308 650 23 1 1 650 418685792 418685144 0.000000e+00 1066.0
11 TraesCS6A01G126600 chr4A 93.597 531 34 0 646 1176 725869986 725869456 0.000000e+00 793.0
12 TraesCS6A01G126600 chr4A 94.667 225 11 1 1252 1475 725869454 725869230 5.400000e-92 348.0
13 TraesCS6A01G126600 chr4A 98.000 50 1 0 1474 1523 725869244 725869195 1.300000e-13 87.9
14 TraesCS6A01G126600 chr1A 96.779 1335 25 4 646 1978 452025973 452024655 0.000000e+00 2211.0
15 TraesCS6A01G126600 chr1A 92.760 1395 58 11 1252 2636 548228465 548227104 0.000000e+00 1977.0
16 TraesCS6A01G126600 chr1A 94.915 531 27 0 646 1176 548228997 548228467 0.000000e+00 832.0
17 TraesCS6A01G126600 chr2B 91.379 1392 59 18 1252 2638 493242792 493244127 0.000000e+00 1849.0
18 TraesCS6A01G126600 chr2B 94.539 531 29 0 646 1176 493242260 493242790 0.000000e+00 821.0
19 TraesCS6A01G126600 chr2D 97.527 647 14 2 1 647 628116830 628116186 0.000000e+00 1105.0
20 TraesCS6A01G126600 chr7A 97.063 647 18 1 1 647 488413192 488413837 0.000000e+00 1088.0
21 TraesCS6A01G126600 chr7A 96.754 647 20 1 1 647 680881569 680882214 0.000000e+00 1077.0
22 TraesCS6A01G126600 chr7A 95.764 661 23 5 1 660 650677139 650676483 0.000000e+00 1061.0
23 TraesCS6A01G126600 chr4B 90.369 758 57 6 646 1402 570344511 570345253 0.000000e+00 981.0
24 TraesCS6A01G126600 chr5B 85.932 263 28 7 1474 1734 468630232 468629977 3.350000e-69 272.0
25 TraesCS6A01G126600 chr5D 88.800 125 11 1 646 767 421914678 421914802 1.640000e-32 150.0
26 TraesCS6A01G126600 chr5D 89.362 94 8 2 2545 2637 419805005 419804913 1.660000e-22 117.0
27 TraesCS6A01G126600 chrUn 87.037 108 12 2 2347 2454 31522499 31522394 1.280000e-23 121.0
28 TraesCS6A01G126600 chr7B 87.912 91 10 1 2548 2637 521177405 521177315 3.590000e-19 106.0


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 TraesCS6A01G126600 chr6A 99976147 99978784 2637 True 4872.000 4872 100.0000 1 2638 1 chr6A.!!$R1 2637
1 TraesCS6A01G126600 chr3A 662139640 662141620 1980 False 3387.000 3387 97.4450 646 2638 1 chr3A.!!$F1 1992
2 TraesCS6A01G126600 chr3A 482049576 482050223 647 True 1075.000 1075 96.6100 1 649 1 chr3A.!!$R1 648
3 TraesCS6A01G126600 chr3A 533918033 533918678 645 True 1068.000 1068 96.4510 1 648 1 chr3A.!!$R2 647
4 TraesCS6A01G126600 chr1D 156777378 156779357 1979 False 3314.000 3314 96.8030 646 2638 1 chr1D.!!$F1 1992
5 TraesCS6A01G126600 chr5A 299772187 299774058 1871 True 3169.000 3169 97.1400 754 2638 1 chr5A.!!$R1 1884
6 TraesCS6A01G126600 chr5A 493694461 493695107 646 False 1079.000 1079 96.7590 1 648 1 chr5A.!!$F1 647
7 TraesCS6A01G126600 chr5A 543097982 543098630 648 False 1070.000 1070 96.4620 1 648 1 chr5A.!!$F2 647
8 TraesCS6A01G126600 chr4A 41895908 41897242 1334 False 2244.000 2244 96.8910 646 1993 1 chr4A.!!$F1 1347
9 TraesCS6A01G126600 chr4A 418685144 418685792 648 True 1066.000 1066 96.3080 1 650 1 chr4A.!!$R1 649
10 TraesCS6A01G126600 chr4A 725868179 725869986 1807 True 658.225 1404 94.3250 646 2638 4 chr4A.!!$R2 1992
11 TraesCS6A01G126600 chr1A 452024655 452025973 1318 True 2211.000 2211 96.7790 646 1978 1 chr1A.!!$R1 1332
12 TraesCS6A01G126600 chr1A 548227104 548228997 1893 True 1404.500 1977 93.8375 646 2636 2 chr1A.!!$R2 1990
13 TraesCS6A01G126600 chr2B 493242260 493244127 1867 False 1335.000 1849 92.9590 646 2638 2 chr2B.!!$F1 1992
14 TraesCS6A01G126600 chr2D 628116186 628116830 644 True 1105.000 1105 97.5270 1 647 1 chr2D.!!$R1 646
15 TraesCS6A01G126600 chr7A 488413192 488413837 645 False 1088.000 1088 97.0630 1 647 1 chr7A.!!$F1 646
16 TraesCS6A01G126600 chr7A 680881569 680882214 645 False 1077.000 1077 96.7540 1 647 1 chr7A.!!$F2 646
17 TraesCS6A01G126600 chr7A 650676483 650677139 656 True 1061.000 1061 95.7640 1 660 1 chr7A.!!$R1 659
18 TraesCS6A01G126600 chr4B 570344511 570345253 742 False 981.000 981 90.3690 646 1402 1 chr4B.!!$F1 756

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
471 476 0.593618 CAGGAGAAGCGCGCTATAGA 59.406 55.0 36.73 0.0 0.0 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2159 2230 0.475906 GGCATAGGGATCAGGCAAGT 59.524 55.0 0.0 0.0 0.0 3.16 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
105 106 1.550524 TGCATAGTTCCGCTCTCACTT 59.449 47.619 0.00 0.00 0.00 3.16
110 111 3.719173 AGTTCCGCTCTCACTTATAGC 57.281 47.619 0.00 0.00 0.00 2.97
186 187 6.398234 AGTATTCGAGACTTGCATGTATCT 57.602 37.500 20.83 9.18 0.00 1.98
317 318 7.641760 TGTATGTGTATCATGATGACATTTGC 58.358 34.615 27.21 20.58 37.91 3.68
347 348 8.267894 TGCTAAAGATTCTTCTATAAAGCCTGT 58.732 33.333 0.00 0.00 0.00 4.00
471 476 0.593618 CAGGAGAAGCGCGCTATAGA 59.406 55.000 36.73 0.00 0.00 1.98
583 588 5.251601 GCTATAGCGCCTTATTAGTAGCT 57.748 43.478 9.40 0.00 36.57 3.32
677 682 2.557056 CCACTACTCAACTTCAGGTCGA 59.443 50.000 0.00 0.00 0.00 4.20
938 943 3.404224 TGCATGTTGTTTGGATTGCAT 57.596 38.095 0.00 0.00 35.36 3.96
1135 1140 4.225942 ACATGATCTAGAAGCCCTCAAACA 59.774 41.667 0.00 0.00 0.00 2.83
1466 1472 5.904984 AGTGGTTAAGTATGGGATATGCA 57.095 39.130 0.00 0.00 0.00 3.96
1467 1473 5.621193 AGTGGTTAAGTATGGGATATGCAC 58.379 41.667 0.00 0.00 0.00 4.57
1468 1474 4.760204 GTGGTTAAGTATGGGATATGCACC 59.240 45.833 0.00 0.00 0.00 5.01
1469 1475 4.663120 TGGTTAAGTATGGGATATGCACCT 59.337 41.667 0.00 0.00 0.00 4.00
1470 1476 5.003804 GGTTAAGTATGGGATATGCACCTG 58.996 45.833 0.00 0.00 0.00 4.00
1471 1477 2.867109 AGTATGGGATATGCACCTGC 57.133 50.000 0.00 0.00 42.50 4.85
1472 1478 1.352352 AGTATGGGATATGCACCTGCC 59.648 52.381 0.00 0.00 41.18 4.85
1473 1479 1.073763 GTATGGGATATGCACCTGCCA 59.926 52.381 12.16 12.16 41.18 4.92
1474 1480 0.781920 ATGGGATATGCACCTGCCAT 59.218 50.000 15.21 15.21 38.60 4.40
1475 1481 1.443852 TGGGATATGCACCTGCCATA 58.556 50.000 6.50 0.00 41.18 2.74
1476 1482 1.994794 TGGGATATGCACCTGCCATAT 59.005 47.619 6.50 0.00 41.18 1.78
1477 1483 2.291089 TGGGATATGCACCTGCCATATG 60.291 50.000 6.50 0.00 41.18 1.78
1478 1484 1.747355 GGATATGCACCTGCCATATGC 59.253 52.381 0.00 0.00 41.18 3.14
1596 1654 5.806502 TGTGAAGTTGCTTTGTTTGATTCAG 59.193 36.000 0.00 0.00 0.00 3.02
2159 2230 8.539770 CAGAAAAGCAATCTGTAGAACTTCTA 57.460 34.615 5.52 0.00 39.54 2.10
2221 2298 5.104527 CCATCTAGGTTAACTGTTGGGATGA 60.105 44.000 5.42 0.00 32.47 2.92
2429 2506 5.510520 CCAGCTACATCTCCCTTAGAATCAC 60.511 48.000 0.00 0.00 37.89 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 111 2.884663 ATACGCGAGAAGAGCTATCG 57.115 50.000 15.93 5.92 39.40 2.92
186 187 9.684448 GTATCTTGTCATCATCTCGAAAATAGA 57.316 33.333 0.00 0.00 0.00 1.98
317 318 9.875675 GCTTTATAGAAGAATCTTTAGCACATG 57.124 33.333 0.00 0.00 37.10 3.21
347 348 8.818141 TCGGCATATTTGTTTTGTATTTGAAA 57.182 26.923 0.00 0.00 0.00 2.69
449 454 1.949847 ATAGCGCGCTTCTCCTGTGT 61.950 55.000 41.04 13.70 0.00 3.72
471 476 3.574396 TGGAAGCTCGCTACTGCTAATAT 59.426 43.478 0.00 0.00 38.75 1.28
595 600 4.142093 GCGGGTTTTAGGTGTATCAGTAGA 60.142 45.833 0.00 0.00 0.00 2.59
677 682 5.476254 GGAGGTATACTCTACCGCAAAGTAT 59.524 44.000 2.25 0.00 45.83 2.12
917 922 3.404224 TGCAATCCAAACAACATGCAT 57.596 38.095 0.00 0.00 38.73 3.96
938 943 3.073798 TGCACTTAAGTTCCCTTCCATCA 59.926 43.478 5.07 0.00 31.89 3.07
1103 1108 7.836183 AGGGCTTCTAGATCATGTTTACAAATT 59.164 33.333 0.00 0.00 0.00 1.82
1108 1113 5.918608 TGAGGGCTTCTAGATCATGTTTAC 58.081 41.667 0.00 0.00 0.00 2.01
1135 1140 3.197766 TCCAATGTACCGAGCTTGATCTT 59.802 43.478 1.22 0.00 0.00 2.40
1470 1476 0.754472 AAATGGCAGGTGCATATGGC 59.246 50.000 17.44 17.44 44.36 4.40
1471 1477 3.133362 AGAAAAATGGCAGGTGCATATGG 59.867 43.478 4.56 0.00 44.36 2.74
1472 1478 4.395959 AGAAAAATGGCAGGTGCATATG 57.604 40.909 4.01 0.00 44.36 1.78
1473 1479 5.510179 GCATAGAAAAATGGCAGGTGCATAT 60.510 40.000 4.01 0.00 44.36 1.78
1474 1480 4.202141 GCATAGAAAAATGGCAGGTGCATA 60.202 41.667 4.01 0.00 44.36 3.14
1475 1481 3.431207 GCATAGAAAAATGGCAGGTGCAT 60.431 43.478 4.01 0.00 44.36 3.96
1476 1482 2.094078 GCATAGAAAAATGGCAGGTGCA 60.094 45.455 4.01 0.00 44.36 4.57
1477 1483 2.094078 TGCATAGAAAAATGGCAGGTGC 60.094 45.455 0.00 0.00 41.14 5.01
1478 1484 3.872511 TGCATAGAAAAATGGCAGGTG 57.127 42.857 0.00 0.00 0.00 4.00
1559 1617 4.261741 GCAACTTCACATGAGTCACCAATT 60.262 41.667 0.00 0.00 0.00 2.32
1596 1654 0.958382 TGCCACGGTCTAATTGCACC 60.958 55.000 0.00 0.00 0.00 5.01
1819 1880 9.236006 GCCAACTGATACCTCAAATATGATATT 57.764 33.333 0.00 0.00 34.37 1.28
2159 2230 0.475906 GGCATAGGGATCAGGCAAGT 59.524 55.000 0.00 0.00 0.00 3.16
2160 2231 0.769873 AGGCATAGGGATCAGGCAAG 59.230 55.000 0.00 0.00 0.00 4.01
2241 2318 5.598416 ACATTGATAAGATCGACCAGACA 57.402 39.130 0.00 0.00 0.00 3.41
2332 2409 9.817809 GAAATCAGTAGAACAATGTCCATACTA 57.182 33.333 5.26 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.