Multiple sequence alignment - TraesCS4A01G154600

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 TraesCS4A01G154600 chr4A 100.000 2414 0 0 1 2414 310736829 310739242 0 4458
1 TraesCS4A01G154600 chr4A 93.567 2425 122 15 1 2413 309513372 309515774 0 3583
2 TraesCS4A01G154600 chr3D 95.618 2419 76 14 1 2414 589281292 589278899 0 3853
3 TraesCS4A01G154600 chr5D 95.494 2419 82 12 1 2414 6187189 6189585 0 3838
4 TraesCS4A01G154600 chr5D 95.492 2418 83 12 1 2414 503279976 503277581 0 3838
5 TraesCS4A01G154600 chr5D 94.793 2420 95 16 1 2414 432405246 432402852 0 3742
6 TraesCS4A01G154600 chr5D 95.794 2116 63 11 303 2414 503216770 503218863 0 3391
7 TraesCS4A01G154600 chr1A 95.331 2420 77 15 1 2414 554510504 554512893 0 3810
8 TraesCS4A01G154600 chr1D 95.248 2420 87 14 1 2414 254399861 254397464 0 3807
9 TraesCS4A01G154600 chr5A 94.750 2419 101 12 1 2414 607272648 607275045 0 3740
10 TraesCS4A01G154600 chr4B 93.391 2421 117 15 1 2414 308694731 308697115 0 3544
11 TraesCS4A01G154600 chrUn 95.890 2117 59 14 303 2414 93411079 93408986 0 3402
12 TraesCS4A01G154600 chrUn 95.120 1004 31 6 1411 2414 346596834 346595849 0 1567
13 TraesCS4A01G154600 chrUn 94.809 944 31 6 1471 2414 389444756 389445681 0 1456
14 TraesCS4A01G154600 chrUn 96.383 553 18 2 1 552 239346015 239345464 0 909
15 TraesCS4A01G154600 chr6D 95.749 2117 63 13 303 2414 168253477 168255571 0 3386
16 TraesCS4A01G154600 chr6D 95.458 1453 39 12 303 1750 168253213 168251783 0 2292
17 TraesCS4A01G154600 chr3B 95.701 2117 63 14 303 2414 201525576 201527669 0 3380
18 TraesCS4A01G154600 chr3A 95.324 2117 73 12 303 2414 672911457 672909362 0 3338


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 TraesCS4A01G154600 chr4A 310736829 310739242 2413 False 4458 4458 100.000 1 2414 1 chr4A.!!$F2 2413
1 TraesCS4A01G154600 chr4A 309513372 309515774 2402 False 3583 3583 93.567 1 2413 1 chr4A.!!$F1 2412
2 TraesCS4A01G154600 chr3D 589278899 589281292 2393 True 3853 3853 95.618 1 2414 1 chr3D.!!$R1 2413
3 TraesCS4A01G154600 chr5D 6187189 6189585 2396 False 3838 3838 95.494 1 2414 1 chr5D.!!$F1 2413
4 TraesCS4A01G154600 chr5D 503277581 503279976 2395 True 3838 3838 95.492 1 2414 1 chr5D.!!$R2 2413
5 TraesCS4A01G154600 chr5D 432402852 432405246 2394 True 3742 3742 94.793 1 2414 1 chr5D.!!$R1 2413
6 TraesCS4A01G154600 chr5D 503216770 503218863 2093 False 3391 3391 95.794 303 2414 1 chr5D.!!$F2 2111
7 TraesCS4A01G154600 chr1A 554510504 554512893 2389 False 3810 3810 95.331 1 2414 1 chr1A.!!$F1 2413
8 TraesCS4A01G154600 chr1D 254397464 254399861 2397 True 3807 3807 95.248 1 2414 1 chr1D.!!$R1 2413
9 TraesCS4A01G154600 chr5A 607272648 607275045 2397 False 3740 3740 94.750 1 2414 1 chr5A.!!$F1 2413
10 TraesCS4A01G154600 chr4B 308694731 308697115 2384 False 3544 3544 93.391 1 2414 1 chr4B.!!$F1 2413
11 TraesCS4A01G154600 chrUn 93408986 93411079 2093 True 3402 3402 95.890 303 2414 1 chrUn.!!$R1 2111
12 TraesCS4A01G154600 chrUn 346595849 346596834 985 True 1567 1567 95.120 1411 2414 1 chrUn.!!$R3 1003
13 TraesCS4A01G154600 chrUn 389444756 389445681 925 False 1456 1456 94.809 1471 2414 1 chrUn.!!$F1 943
14 TraesCS4A01G154600 chrUn 239345464 239346015 551 True 909 909 96.383 1 552 1 chrUn.!!$R2 551
15 TraesCS4A01G154600 chr6D 168253477 168255571 2094 False 3386 3386 95.749 303 2414 1 chr6D.!!$F1 2111
16 TraesCS4A01G154600 chr6D 168251783 168253213 1430 True 2292 2292 95.458 303 1750 1 chr6D.!!$R1 1447
17 TraesCS4A01G154600 chr3B 201525576 201527669 2093 False 3380 3380 95.701 303 2414 1 chr3B.!!$F1 2111
18 TraesCS4A01G154600 chr3A 672909362 672911457 2095 True 3338 3338 95.324 303 2414 1 chr3A.!!$R1 2111

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
828 844 0.676466 ATGCGCGGGTTCAATTCTCA 60.676 50.0 8.83 0.0 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1755 1778 1.673009 CGGAAGCGCCCCTTGTTTA 60.673 57.895 2.29 0.0 32.78 2.01 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
31 32 6.323225 ACTGCTTTCGGTATTAGTACTATGGT 59.677 38.462 2.79 0.00 0.00 3.55
32 33 6.509656 TGCTTTCGGTATTAGTACTATGGTG 58.490 40.000 2.79 0.00 0.00 4.17
85 93 5.008331 TCTGTAGTTGATAGTCAAGGTCGT 58.992 41.667 0.00 0.00 37.00 4.34
117 125 3.202818 ACTTGGGCTGATATCATCAACCA 59.797 43.478 5.72 9.40 45.25 3.67
153 161 2.988493 TGGAAGTAATGCACGAACGTAC 59.012 45.455 0.00 0.00 0.00 3.67
180 188 5.642165 TCACAACTTCCCTCTAGACTTAGT 58.358 41.667 0.00 0.00 0.00 2.24
412 421 2.301870 ACTTGTGAAATGCCGAGTAGGA 59.698 45.455 0.00 0.00 45.00 2.94
434 443 2.943033 ACGAATTCCCCTAATTTGCGAG 59.057 45.455 0.00 0.00 41.13 5.03
643 655 4.776795 TTCGTGTCACAGCTGATTACTA 57.223 40.909 23.35 3.20 0.00 1.82
666 681 9.470399 ACTACTTTTTCCTTTTTAAAGAGTGGA 57.530 29.630 5.15 1.77 38.28 4.02
686 701 8.267620 AGTGGAATTCTATGTCCAATATCTCA 57.732 34.615 5.23 0.00 45.42 3.27
765 781 3.145559 TCCTTTAGCTGGATAAGGGGT 57.854 47.619 14.75 0.00 39.12 4.95
826 842 1.656818 CCATGCGCGGGTTCAATTCT 61.657 55.000 8.83 0.00 0.00 2.40
828 844 0.676466 ATGCGCGGGTTCAATTCTCA 60.676 50.000 8.83 0.00 0.00 3.27
851 867 1.601903 GTTCGCCCATCGCATTATTGA 59.398 47.619 0.00 0.00 37.30 2.57
861 877 6.201425 CCCATCGCATTATTGAAAATTCCAAG 59.799 38.462 0.00 0.00 0.00 3.61
923 939 5.961395 GGCGACGAAGAATAAAACTATCA 57.039 39.130 0.00 0.00 0.00 2.15
1062 1084 4.470304 ACAAGGTTCATAACTACCCCTCTC 59.530 45.833 0.00 0.00 34.90 3.20
1073 1095 2.363795 CCCTCTCACTACGGGGCA 60.364 66.667 0.00 0.00 34.22 5.36
1080 1102 1.208535 CTCACTACGGGGCATTTACCA 59.791 52.381 0.00 0.00 0.00 3.25
1102 1124 1.656652 CCAACACTTAGATCCGGCTG 58.343 55.000 0.00 0.00 0.00 4.85
1232 1254 5.163519 CCGATTTACCCTCTTTTGCAATGAT 60.164 40.000 0.00 0.00 0.00 2.45
1513 1536 3.079960 TCTACCGAATCGCTCATGTTC 57.920 47.619 0.00 0.00 0.00 3.18
1516 1539 0.806102 CCGAATCGCTCATGTTCCGT 60.806 55.000 0.00 0.00 0.00 4.69
1517 1540 0.572590 CGAATCGCTCATGTTCCGTC 59.427 55.000 0.00 0.00 0.00 4.79
1518 1541 1.640428 GAATCGCTCATGTTCCGTCA 58.360 50.000 0.00 0.00 0.00 4.35
1519 1542 2.205074 GAATCGCTCATGTTCCGTCAT 58.795 47.619 0.00 0.00 0.00 3.06
1520 1543 2.315925 ATCGCTCATGTTCCGTCATT 57.684 45.000 0.00 0.00 0.00 2.57
1521 1544 2.093306 TCGCTCATGTTCCGTCATTT 57.907 45.000 0.00 0.00 0.00 2.32
1522 1545 1.731709 TCGCTCATGTTCCGTCATTTG 59.268 47.619 0.00 0.00 0.00 2.32
1523 1546 1.202065 CGCTCATGTTCCGTCATTTGG 60.202 52.381 0.00 0.00 0.00 3.28
1524 1547 1.468054 GCTCATGTTCCGTCATTTGGC 60.468 52.381 0.00 0.00 0.00 4.52
1525 1548 2.086869 CTCATGTTCCGTCATTTGGCT 58.913 47.619 0.00 0.00 0.00 4.75
1526 1549 2.489329 CTCATGTTCCGTCATTTGGCTT 59.511 45.455 0.00 0.00 0.00 4.35
1527 1550 3.680490 TCATGTTCCGTCATTTGGCTTA 58.320 40.909 0.00 0.00 0.00 3.09
1528 1551 4.269183 TCATGTTCCGTCATTTGGCTTAT 58.731 39.130 0.00 0.00 0.00 1.73
1529 1552 4.096231 TCATGTTCCGTCATTTGGCTTATG 59.904 41.667 0.00 0.00 0.00 1.90
1530 1553 2.752354 TGTTCCGTCATTTGGCTTATGG 59.248 45.455 0.00 0.00 0.00 2.74
1531 1554 1.388547 TCCGTCATTTGGCTTATGGC 58.611 50.000 0.00 0.00 40.90 4.40
1532 1555 1.064758 TCCGTCATTTGGCTTATGGCT 60.065 47.619 3.78 0.00 41.46 4.75
1533 1556 1.750778 CCGTCATTTGGCTTATGGCTT 59.249 47.619 3.78 0.00 41.46 4.35
1536 1559 4.539870 CGTCATTTGGCTTATGGCTTATG 58.460 43.478 3.78 7.10 41.46 1.90
1647 1670 9.042450 TCGATACTTCCACATATTATGGGTAAT 57.958 33.333 8.48 0.00 37.85 1.89
1671 1694 2.707554 GGAGACATCCCTATTTCCCCT 58.292 52.381 0.00 0.00 40.03 4.79
1674 1697 2.090719 AGACATCCCTATTTCCCCTCGA 60.091 50.000 0.00 0.00 0.00 4.04
1750 1773 1.138464 GTGAATAACCCGTCCTCCTCC 59.862 57.143 0.00 0.00 0.00 4.30
1751 1774 1.273381 TGAATAACCCGTCCTCCTCCA 60.273 52.381 0.00 0.00 0.00 3.86
1755 1778 1.073098 AACCCGTCCTCCTCCATTTT 58.927 50.000 0.00 0.00 0.00 1.82
1891 1914 4.824537 TGCTGCCATTACTCAACAGTTTTA 59.175 37.500 0.00 0.00 33.62 1.52
1920 1943 4.040706 AGGTCTATCCTGTAGAGGTAGTCG 59.959 50.000 5.71 0.00 46.19 4.18
2016 2039 2.103432 TCAAACCGCACTCAAAGGTAGA 59.897 45.455 0.00 0.00 37.26 2.59
2046 2069 8.893563 TTCCCATTGATATAGGAACTTTTGTT 57.106 30.769 0.00 0.00 46.75 2.83
2152 2175 5.376854 AATGTATGCATTTCGATTAGGGC 57.623 39.130 3.54 0.00 42.19 5.19
2395 2418 5.921408 GGTGTTTTGTATAAATGTTTCGCCA 59.079 36.000 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 6.698766 GGTTGAACACCATAGTACTAATACCG 59.301 42.308 6.70 0.00 46.42 4.02
43 45 6.484364 ACAGATTGGTTGAAATTGAAACCT 57.516 33.333 18.51 4.70 45.12 3.50
117 125 4.862641 ACTTCCATACCAAGGTTAGCAT 57.137 40.909 0.00 0.00 0.00 3.79
153 161 2.828520 TCTAGAGGGAAGTTGTGAGCAG 59.171 50.000 0.00 0.00 0.00 4.24
180 188 7.994425 TTAATAGATGGAACTTCAACAGCAA 57.006 32.000 0.00 0.00 0.00 3.91
257 265 9.474313 TTGCTAGAACAAGATATTGGGTATTTT 57.526 29.630 4.88 0.00 0.00 1.82
386 395 4.323417 ACTCGGCATTTCACAAGTTATGA 58.677 39.130 0.00 0.00 0.00 2.15
394 403 2.695359 GTTCCTACTCGGCATTTCACA 58.305 47.619 0.00 0.00 0.00 3.58
412 421 3.349022 TCGCAAATTAGGGGAATTCGTT 58.651 40.909 0.00 0.00 36.71 3.85
424 433 4.948341 TCCTATGGTAGCTCGCAAATTA 57.052 40.909 0.00 0.00 0.00 1.40
765 781 2.195727 TGATCCACTTGGCTACATCCA 58.804 47.619 0.00 0.00 34.44 3.41
826 842 2.584970 GCGATGGGCGAACGATGA 60.585 61.111 2.92 0.00 44.57 2.92
1062 1084 2.014128 CTTGGTAAATGCCCCGTAGTG 58.986 52.381 0.00 0.00 0.00 2.74
1073 1095 5.652452 GGATCTAAGTGTTGGCTTGGTAAAT 59.348 40.000 0.00 0.00 0.00 1.40
1080 1102 1.679032 GCCGGATCTAAGTGTTGGCTT 60.679 52.381 5.05 0.00 38.00 4.35
1513 1536 1.392589 AGCCATAAGCCAAATGACGG 58.607 50.000 0.00 0.00 45.47 4.79
1516 1539 5.893255 AGAACATAAGCCATAAGCCAAATGA 59.107 36.000 0.00 0.00 45.47 2.57
1517 1540 6.152932 AGAACATAAGCCATAAGCCAAATG 57.847 37.500 0.00 0.00 45.47 2.32
1518 1541 6.833416 TGTAGAACATAAGCCATAAGCCAAAT 59.167 34.615 0.00 0.00 45.47 2.32
1519 1542 6.184068 TGTAGAACATAAGCCATAAGCCAAA 58.816 36.000 0.00 0.00 45.47 3.28
1520 1543 5.750524 TGTAGAACATAAGCCATAAGCCAA 58.249 37.500 0.00 0.00 45.47 4.52
1521 1544 5.366482 TGTAGAACATAAGCCATAAGCCA 57.634 39.130 0.00 0.00 45.47 4.75
1522 1545 5.412904 GGATGTAGAACATAAGCCATAAGCC 59.587 44.000 0.00 0.00 40.03 4.35
1523 1546 6.234177 AGGATGTAGAACATAAGCCATAAGC 58.766 40.000 0.00 0.00 39.27 3.09
1524 1547 8.037758 CCTAGGATGTAGAACATAAGCCATAAG 58.962 40.741 1.05 0.00 39.27 1.73
1525 1548 7.512746 ACCTAGGATGTAGAACATAAGCCATAA 59.487 37.037 17.98 0.00 39.27 1.90
1526 1549 7.016914 ACCTAGGATGTAGAACATAAGCCATA 58.983 38.462 17.98 0.00 39.27 2.74
1527 1550 5.846714 ACCTAGGATGTAGAACATAAGCCAT 59.153 40.000 17.98 0.00 39.27 4.40
1528 1551 5.216622 ACCTAGGATGTAGAACATAAGCCA 58.783 41.667 17.98 0.00 39.27 4.75
1529 1552 5.540719 AGACCTAGGATGTAGAACATAAGCC 59.459 44.000 17.98 0.00 39.27 4.35
1530 1553 6.492087 AGAGACCTAGGATGTAGAACATAAGC 59.508 42.308 17.98 0.00 39.27 3.09
1531 1554 7.504238 ACAGAGACCTAGGATGTAGAACATAAG 59.496 40.741 17.98 0.00 39.27 1.73
1532 1555 7.285629 CACAGAGACCTAGGATGTAGAACATAA 59.714 40.741 17.98 0.00 39.27 1.90
1533 1556 6.773200 CACAGAGACCTAGGATGTAGAACATA 59.227 42.308 17.98 0.00 39.27 2.29
1536 1559 4.951094 ACACAGAGACCTAGGATGTAGAAC 59.049 45.833 17.98 0.00 0.00 3.01
1647 1670 4.232091 GGGAAATAGGGATGTCTCCTACA 58.768 47.826 0.00 0.00 43.86 2.74
1689 1712 5.184671 AGAGGCAAATTGAAAGCTAAGAAGG 59.815 40.000 0.00 0.00 0.00 3.46
1692 1715 5.182001 GTCAGAGGCAAATTGAAAGCTAAGA 59.818 40.000 0.00 0.00 0.00 2.10
1750 1773 2.741759 AGCGCCCCTTGTTTAAAATG 57.258 45.000 2.29 0.00 0.00 2.32
1751 1774 2.028476 GGAAGCGCCCCTTGTTTAAAAT 60.028 45.455 2.29 0.00 32.78 1.82
1755 1778 1.673009 CGGAAGCGCCCCTTGTTTA 60.673 57.895 2.29 0.00 32.78 2.01
1920 1943 6.857777 AGAAATCGATCACTGATCCAATTC 57.142 37.500 12.58 9.23 35.83 2.17
1978 2001 6.898189 GCGGTTTGAACTATTGATTTACGTAG 59.102 38.462 0.00 0.00 0.00 3.51
2152 2175 8.528643 TGGTAGAATCGTAACCATAGAATATGG 58.471 37.037 13.15 13.15 44.54 2.74
2215 2238 2.561419 GAGGTCATAAGCGCCTATACCA 59.439 50.000 18.62 0.00 31.89 3.25


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

AutoCloner maintained by Alex Coulton.