Multiple sequence alignment - TraesCS1B01G185200

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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 TraesCS1B01G185200 chr1B 100.000 3513 0 0 1 3513 332155547 332152035 0.000000e+00 6488.0
1 TraesCS1B01G185200 chr1B 94.947 950 34 1 831 1780 169942250 169941315 0.000000e+00 1476.0
2 TraesCS1B01G185200 chr1B 95.228 901 20 4 1 878 390430145 390429245 0.000000e+00 1404.0
3 TraesCS1B01G185200 chr1B 94.875 761 33 2 1842 2602 169941319 169940565 0.000000e+00 1184.0
4 TraesCS1B01G185200 chr1B 95.333 300 13 1 2302 2601 390429242 390428944 3.170000e-130 475.0
5 TraesCS1B01G185200 chr1B 88.889 324 32 2 2278 2601 122922064 122921745 2.540000e-106 396.0
6 TraesCS1B01G185200 chr1B 90.476 42 3 1 566 607 536572266 536572306 2.000000e-03 54.7
7 TraesCS1B01G185200 chr5B 95.025 1769 67 4 831 2599 704279303 704277556 0.000000e+00 2760.0
8 TraesCS1B01G185200 chr5B 92.077 1035 74 6 1570 2599 252300984 252299953 0.000000e+00 1450.0
9 TraesCS1B01G185200 chr5B 93.656 930 57 2 645 1573 252302712 252301784 0.000000e+00 1389.0
10 TraesCS1B01G185200 chr5B 93.811 921 40 2 645 1548 127501862 127502782 0.000000e+00 1369.0
11 TraesCS1B01G185200 chr5B 95.147 783 35 3 1570 2349 127503632 127504414 0.000000e+00 1232.0
12 TraesCS1B01G185200 chr5B 94.949 297 13 2 820 1114 678674092 678673796 6.870000e-127 464.0
13 TraesCS1B01G185200 chr4B 94.867 1773 70 4 831 2602 564198861 564197109 0.000000e+00 2750.0
14 TraesCS1B01G185200 chr4B 94.935 1757 69 3 831 2587 175549896 175548160 0.000000e+00 2734.0
15 TraesCS1B01G185200 chr6B 95.764 897 19 4 1 878 631947961 631948857 0.000000e+00 1428.0
16 TraesCS1B01G185200 chr6B 94.966 298 15 0 2302 2599 631948860 631949157 5.310000e-128 468.0
17 TraesCS1B01G185200 chr1A 93.649 929 37 9 2600 3513 306643999 306644920 0.000000e+00 1369.0
18 TraesCS1B01G185200 chr1A 94.349 814 43 2 645 1457 483640986 483641797 0.000000e+00 1245.0
19 TraesCS1B01G185200 chr1A 90.476 42 3 1 566 607 496170451 496170491 2.000000e-03 54.7
20 TraesCS1B01G185200 chr4A 93.672 885 56 0 1717 2601 321129404 321128520 0.000000e+00 1325.0
21 TraesCS1B01G185200 chr4A 95.332 557 26 0 1003 1559 321175767 321175211 0.000000e+00 885.0
22 TraesCS1B01G185200 chr4A 94.823 367 15 4 645 1008 321184442 321184077 1.410000e-158 569.0
23 TraesCS1B01G185200 chr4A 94.667 150 8 0 1570 1719 321174405 321174256 2.110000e-57 233.0
24 TraesCS1B01G185200 chr5D 92.034 954 47 10 645 1569 115947871 115948824 0.000000e+00 1314.0
25 TraesCS1B01G185200 chr5D 93.121 785 44 4 1572 2349 115949629 115950410 0.000000e+00 1142.0
26 TraesCS1B01G185200 chr5A 91.509 954 49 8 645 1569 122953982 122954932 0.000000e+00 1284.0
27 TraesCS1B01G185200 chr5A 93.606 782 44 5 1570 2349 122955741 122956518 0.000000e+00 1162.0
28 TraesCS1B01G185200 chr5A 94.080 473 25 3 645 1114 504720314 504719842 0.000000e+00 715.0
29 TraesCS1B01G185200 chr3B 97.302 630 8 2 1 624 250145518 250144892 0.000000e+00 1061.0
30 TraesCS1B01G185200 chr1D 98.440 577 6 1 2937 3513 245982729 245983302 0.000000e+00 1013.0
31 TraesCS1B01G185200 chr1D 95.335 343 15 1 2600 2941 245982273 245982615 8.580000e-151 544.0
32 TraesCS1B01G185200 chr1D 90.476 42 3 1 566 607 399810473 399810513 2.000000e-03 54.7
33 TraesCS1B01G185200 chr3D 93.185 631 35 3 1 624 171151960 171151331 0.000000e+00 920.0
34 TraesCS1B01G185200 chr3A 91.601 631 45 3 1 624 208736578 208735949 0.000000e+00 865.0
35 TraesCS1B01G185200 chr2A 92.000 300 19 3 820 1114 97847976 97847677 1.950000e-112 416.0


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 TraesCS1B01G185200 chr1B 332152035 332155547 3512 True 6488.0 6488 100.0000 1 3513 1 chr1B.!!$R2 3512
1 TraesCS1B01G185200 chr1B 169940565 169942250 1685 True 1330.0 1476 94.9110 831 2602 2 chr1B.!!$R3 1771
2 TraesCS1B01G185200 chr1B 390428944 390430145 1201 True 939.5 1404 95.2805 1 2601 2 chr1B.!!$R4 2600
3 TraesCS1B01G185200 chr5B 704277556 704279303 1747 True 2760.0 2760 95.0250 831 2599 1 chr5B.!!$R2 1768
4 TraesCS1B01G185200 chr5B 252299953 252302712 2759 True 1419.5 1450 92.8665 645 2599 2 chr5B.!!$R3 1954
5 TraesCS1B01G185200 chr5B 127501862 127504414 2552 False 1300.5 1369 94.4790 645 2349 2 chr5B.!!$F1 1704
6 TraesCS1B01G185200 chr4B 564197109 564198861 1752 True 2750.0 2750 94.8670 831 2602 1 chr4B.!!$R2 1771
7 TraesCS1B01G185200 chr4B 175548160 175549896 1736 True 2734.0 2734 94.9350 831 2587 1 chr4B.!!$R1 1756
8 TraesCS1B01G185200 chr6B 631947961 631949157 1196 False 948.0 1428 95.3650 1 2599 2 chr6B.!!$F1 2598
9 TraesCS1B01G185200 chr1A 306643999 306644920 921 False 1369.0 1369 93.6490 2600 3513 1 chr1A.!!$F1 913
10 TraesCS1B01G185200 chr1A 483640986 483641797 811 False 1245.0 1245 94.3490 645 1457 1 chr1A.!!$F2 812
11 TraesCS1B01G185200 chr4A 321128520 321129404 884 True 1325.0 1325 93.6720 1717 2601 1 chr4A.!!$R1 884
12 TraesCS1B01G185200 chr4A 321174256 321175767 1511 True 559.0 885 94.9995 1003 1719 2 chr4A.!!$R3 716
13 TraesCS1B01G185200 chr5D 115947871 115950410 2539 False 1228.0 1314 92.5775 645 2349 2 chr5D.!!$F1 1704
14 TraesCS1B01G185200 chr5A 122953982 122956518 2536 False 1223.0 1284 92.5575 645 2349 2 chr5A.!!$F1 1704
15 TraesCS1B01G185200 chr3B 250144892 250145518 626 True 1061.0 1061 97.3020 1 624 1 chr3B.!!$R1 623
16 TraesCS1B01G185200 chr1D 245982273 245983302 1029 False 778.5 1013 96.8875 2600 3513 2 chr1D.!!$F2 913
17 TraesCS1B01G185200 chr3D 171151331 171151960 629 True 920.0 920 93.1850 1 624 1 chr3D.!!$R1 623
18 TraesCS1B01G185200 chr3A 208735949 208736578 629 True 865.0 865 91.6010 1 624 1 chr3A.!!$R1 623

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
951 975 2.351276 GGCACCATCTTCACCGGT 59.649 61.111 0.00 0.00 0.00 5.28 F
1307 1347 0.469331 CCATCAAGATGCCCATGCCT 60.469 55.000 4.53 0.00 37.49 4.75 F
1593 3277 0.689080 ATGGATGTCTGACGGCTCCT 60.689 55.000 18.63 7.32 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2234 3928 0.253044 GGCTGAACCCATACAGAGCA 59.747 55.000 0.0 0.0 36.38 4.26 R
2285 3979 1.632409 AGCTTGATCTTCTTCCTGCCA 59.368 47.619 0.0 0.0 0.00 4.92 R
2638 4340 1.682323 GCTACTACTACTCTGGTGCCC 59.318 57.143 0.0 0.0 0.00 5.36 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
951 975 2.351276 GGCACCATCTTCACCGGT 59.649 61.111 0.00 0.00 0.00 5.28
1029 1053 2.185867 GCCGCCTCCGTCAACATA 59.814 61.111 0.00 0.00 0.00 2.29
1042 1066 3.873361 CGTCAACATATCCTGCAAGATGT 59.127 43.478 8.12 0.29 34.07 3.06
1307 1347 0.469331 CCATCAAGATGCCCATGCCT 60.469 55.000 4.53 0.00 37.49 4.75
1479 1531 3.305177 GAGCCGCCCAACTTCGGTA 62.305 63.158 2.58 0.00 46.79 4.02
1593 3277 0.689080 ATGGATGTCTGACGGCTCCT 60.689 55.000 18.63 7.32 0.00 3.69
1600 3284 1.379977 CTGACGGCTCCTAGTGGGA 60.380 63.158 0.00 0.00 42.77 4.37
1610 3294 1.541310 CCTAGTGGGACGGCACTTGA 61.541 60.000 0.00 0.00 37.23 3.02
1875 3569 4.760047 GCGTGGACATCCGGCTGT 62.760 66.667 11.47 11.47 39.43 4.40
1934 3628 1.157870 ACGACCACAACAAGAAGGCG 61.158 55.000 0.00 0.00 0.00 5.52
1938 3632 2.192861 CACAACAAGAAGGCGGGCA 61.193 57.895 3.78 0.00 0.00 5.36
1960 3654 2.125512 GAACGCGCTGGTCAGGAT 60.126 61.111 5.73 0.00 0.00 3.24
2091 3785 1.138883 GACCGCATCTGCTACGTGA 59.861 57.895 0.00 0.00 39.32 4.35
2109 3803 4.699522 AGTTCCCGCAGCGGTTCC 62.700 66.667 31.68 18.06 46.80 3.62
2234 3928 1.889105 CTGCATATTCCGCCGCACT 60.889 57.895 0.00 0.00 0.00 4.40
2285 3979 4.586235 AAGCACCACGGCTGGCTT 62.586 61.111 0.00 0.00 45.07 4.35
2379 4077 3.562141 GGCGTTTTTGCAAAAATAACCCT 59.438 39.130 33.23 0.00 39.75 4.34
2435 4137 1.296715 CGGTCAAAGCCTAGCTGGT 59.703 57.895 0.00 0.00 39.62 4.00
2564 4266 2.708861 AGTGGTACCAAAGTGTCATCCA 59.291 45.455 18.31 0.00 0.00 3.41
2620 4322 4.643784 TCTTCGGAGTAATGTACTTCCTCC 59.356 45.833 13.43 13.43 39.59 4.30
2624 4326 3.952967 GGAGTAATGTACTTCCTCCGTCT 59.047 47.826 10.04 0.00 39.59 4.18
2638 4340 6.896021 TCCTCCGTCTGGAATTACTTATAG 57.104 41.667 0.00 0.00 45.87 1.31
2639 4341 5.773680 TCCTCCGTCTGGAATTACTTATAGG 59.226 44.000 0.00 0.00 45.87 2.57
2664 4366 3.622630 CCAGAGTAGTAGTAGCTGTGGT 58.377 50.000 0.00 0.00 38.43 4.16
2813 4516 2.347697 TTGTGTTGATCTCGTCGGAG 57.652 50.000 0.00 0.00 41.89 4.63
2815 4518 0.171455 GTGTTGATCTCGTCGGAGCT 59.829 55.000 0.00 0.00 40.26 4.09
2820 4523 3.627732 TGATCTCGTCGGAGCTAAATC 57.372 47.619 0.00 0.00 40.26 2.17
2869 4572 2.155279 GTCCAGCTTCTTTTCCACTCC 58.845 52.381 0.00 0.00 0.00 3.85
2902 4605 0.661020 GTGTTCACAACCCTTCACGG 59.339 55.000 0.00 0.00 0.00 4.94
3285 5107 4.445052 CGAATGAACTCAAAGCAATGCAAA 59.555 37.500 8.35 0.00 0.00 3.68
3323 5145 4.877282 AGAGAGGAAACAAAAGAGACTCG 58.123 43.478 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
669 692 2.284699 ACCCCCTCCTCAAGACCG 60.285 66.667 0.00 0.00 0.00 4.79
674 697 4.733725 CCCGGACCCCCTCCTCAA 62.734 72.222 0.73 0.00 36.80 3.02
807 831 1.372499 GTAGTGCACGAACTCGGCA 60.372 57.895 12.01 10.05 44.95 5.69
1235 1275 0.920763 TCATGGGCATCTGGTCCCTT 60.921 55.000 0.00 0.00 42.20 3.95
1307 1347 3.055719 GGCTTGCCGTTGCTGCTA 61.056 61.111 0.00 0.00 37.64 3.49
1395 1447 2.430244 GCCGTGCTCGTTCTCGAA 60.430 61.111 7.47 0.00 45.61 3.71
1396 1448 4.753877 CGCCGTGCTCGTTCTCGA 62.754 66.667 7.47 0.00 44.12 4.04
1593 3277 0.830444 AGTCAAGTGCCGTCCCACTA 60.830 55.000 1.74 0.00 44.86 2.74
1745 3436 8.442632 TCATCAATCATTTGGAGAAGATACAC 57.557 34.615 0.00 0.00 33.44 2.90
1840 3534 2.178273 CCGTCGTGTCGATCAGCA 59.822 61.111 0.00 0.00 38.42 4.41
1875 3569 2.052891 CGAAACGTACACCAACATCGA 58.947 47.619 0.00 0.00 0.00 3.59
1911 3605 2.224209 CCTTCTTGTTGTGGTCGTACCT 60.224 50.000 5.77 0.00 39.58 3.08
1960 3654 1.026182 GTTCGGCATGATGGCACTCA 61.026 55.000 19.29 0.00 43.94 3.41
1974 3668 2.112815 GGATGAAAGGCCCGTTCGG 61.113 63.158 0.00 4.08 0.00 4.30
1985 3679 2.553028 GCAGTCCAGGTTGAGGATGAAA 60.553 50.000 0.00 0.00 37.52 2.69
2079 3773 1.135083 CGGGAACTTCACGTAGCAGAT 60.135 52.381 5.20 0.00 38.72 2.90
2222 3916 4.087892 AGAGCAGTGCGGCGGAAT 62.088 61.111 9.78 0.47 39.27 3.01
2234 3928 0.253044 GGCTGAACCCATACAGAGCA 59.747 55.000 0.00 0.00 36.38 4.26
2285 3979 1.632409 AGCTTGATCTTCTTCCTGCCA 59.368 47.619 0.00 0.00 0.00 4.92
2379 4077 4.180377 AGGGTGAATACTACTCGATCCA 57.820 45.455 0.00 0.00 0.00 3.41
2620 4322 4.989168 GTGCCCTATAAGTAATTCCAGACG 59.011 45.833 0.00 0.00 0.00 4.18
2624 4326 4.972568 TCTGGTGCCCTATAAGTAATTCCA 59.027 41.667 0.00 0.00 0.00 3.53
2638 4340 1.682323 GCTACTACTACTCTGGTGCCC 59.318 57.143 0.00 0.00 0.00 5.36
2639 4341 2.359531 CAGCTACTACTACTCTGGTGCC 59.640 54.545 0.00 0.00 0.00 5.01
2650 4352 3.181454 ACTTTGCAACCACAGCTACTACT 60.181 43.478 0.00 0.00 0.00 2.57
2813 4516 3.243002 GCTGAATGGTGAGCAGATTTAGC 60.243 47.826 0.00 0.21 33.30 3.09
2815 4518 4.226427 AGCTGAATGGTGAGCAGATTTA 57.774 40.909 0.00 0.00 37.70 1.40
2820 4523 2.012673 GGTTAGCTGAATGGTGAGCAG 58.987 52.381 0.00 0.00 37.70 4.24
2902 4605 2.022129 CACCGAACTCACGAGGTGC 61.022 63.158 0.29 0.00 46.06 5.01
3285 5107 6.627087 TCCTCTCTTACATTTGAGGTCATT 57.373 37.500 7.61 0.00 44.57 2.57
3323 5145 5.163550 GGTTAACCCCATTATCTTTGAGTGC 60.164 44.000 14.16 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.