Multiple sequence alignment - TraesCS3B01G468800

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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 TraesCS3B01G468800 chr3B 100.000 2261 0 0 1 2261 713989209 713986949 0.000000e+00 4176.0
1 TraesCS3B01G468800 chr3B 93.480 1595 63 11 1 1558 713969803 713968213 0.000000e+00 2331.0
2 TraesCS3B01G468800 chr3B 79.415 1025 137 40 471 1457 713392472 713391484 0.000000e+00 656.0
3 TraesCS3B01G468800 chr3B 80.567 494 78 10 1554 2039 226784793 226785276 4.590000e-97 364.0
4 TraesCS3B01G468800 chr3D 93.429 1187 42 11 401 1558 538688044 538686865 0.000000e+00 1727.0
5 TraesCS3B01G468800 chr3D 90.095 838 59 14 729 1558 538699820 538698999 0.000000e+00 1066.0
6 TraesCS3B01G468800 chr3D 89.352 648 47 13 1 632 538700551 538699910 0.000000e+00 795.0
7 TraesCS3B01G468800 chr3D 79.843 1017 135 44 471 1457 538516249 538515273 0.000000e+00 678.0
8 TraesCS3B01G468800 chr3D 85.179 614 70 12 871 1471 538574192 538573587 5.340000e-171 610.0
9 TraesCS3B01G468800 chr3D 80.435 184 24 6 1 174 538688522 538688341 1.820000e-26 130.0
10 TraesCS3B01G468800 chr3A 88.853 1247 80 18 358 1558 674026202 674024969 0.000000e+00 1478.0
11 TraesCS3B01G468800 chr3A 90.435 690 49 8 874 1558 674061300 674060623 0.000000e+00 893.0
12 TraesCS3B01G468800 chr3A 79.959 973 122 44 536 1457 673923927 673922977 0.000000e+00 649.0
13 TraesCS3B01G468800 chr3A 86.493 422 30 3 424 819 674061737 674061317 2.670000e-119 438.0
14 TraesCS3B01G468800 chr3A 84.122 296 29 6 38 316 674068342 674068048 1.030000e-68 270.0
15 TraesCS3B01G468800 chr3A 78.008 241 33 12 1 229 674026725 674026493 1.410000e-27 134.0
16 TraesCS3B01G468800 chr4B 89.385 716 64 10 1553 2259 163843264 163842552 0.000000e+00 891.0
17 TraesCS3B01G468800 chr4B 82.087 709 97 15 1553 2254 87610498 87611183 1.510000e-161 579.0
18 TraesCS3B01G468800 chr5B 90.342 673 62 2 1565 2234 470036099 470035427 0.000000e+00 880.0
19 TraesCS3B01G468800 chr5B 88.365 636 69 4 1556 2187 101859717 101860351 0.000000e+00 760.0
20 TraesCS3B01G468800 chr6B 89.296 710 58 6 1553 2261 575333514 575332822 0.000000e+00 874.0
21 TraesCS3B01G468800 chr6B 89.086 678 67 5 1565 2236 646202780 646203456 0.000000e+00 835.0
22 TraesCS3B01G468800 chr6B 84.923 650 82 10 1554 2199 647942172 647942809 0.000000e+00 643.0
23 TraesCS3B01G468800 chrUn 87.948 614 54 13 1553 2155 31794494 31795098 0.000000e+00 706.0
24 TraesCS3B01G468800 chr1B 86.655 562 68 3 1553 2114 474275322 474275876 1.150000e-172 616.0
25 TraesCS3B01G468800 chr2D 98.039 51 1 0 428 478 615472775 615472725 3.090000e-14 89.8
26 TraesCS3B01G468800 chr2A 97.222 36 1 0 443 478 745431456 745431421 6.740000e-06 62.1


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 TraesCS3B01G468800 chr3B 713986949 713989209 2260 True 4176.0 4176 100.0000 1 2261 1 chr3B.!!$R3 2260
1 TraesCS3B01G468800 chr3B 713968213 713969803 1590 True 2331.0 2331 93.4800 1 1558 1 chr3B.!!$R2 1557
2 TraesCS3B01G468800 chr3B 713391484 713392472 988 True 656.0 656 79.4150 471 1457 1 chr3B.!!$R1 986
3 TraesCS3B01G468800 chr3D 538698999 538700551 1552 True 930.5 1066 89.7235 1 1558 2 chr3D.!!$R4 1557
4 TraesCS3B01G468800 chr3D 538686865 538688522 1657 True 928.5 1727 86.9320 1 1558 2 chr3D.!!$R3 1557
5 TraesCS3B01G468800 chr3D 538515273 538516249 976 True 678.0 678 79.8430 471 1457 1 chr3D.!!$R1 986
6 TraesCS3B01G468800 chr3D 538573587 538574192 605 True 610.0 610 85.1790 871 1471 1 chr3D.!!$R2 600
7 TraesCS3B01G468800 chr3A 674024969 674026725 1756 True 806.0 1478 83.4305 1 1558 2 chr3A.!!$R3 1557
8 TraesCS3B01G468800 chr3A 674060623 674061737 1114 True 665.5 893 88.4640 424 1558 2 chr3A.!!$R4 1134
9 TraesCS3B01G468800 chr3A 673922977 673923927 950 True 649.0 649 79.9590 536 1457 1 chr3A.!!$R1 921
10 TraesCS3B01G468800 chr4B 163842552 163843264 712 True 891.0 891 89.3850 1553 2259 1 chr4B.!!$R1 706
11 TraesCS3B01G468800 chr4B 87610498 87611183 685 False 579.0 579 82.0870 1553 2254 1 chr4B.!!$F1 701
12 TraesCS3B01G468800 chr5B 470035427 470036099 672 True 880.0 880 90.3420 1565 2234 1 chr5B.!!$R1 669
13 TraesCS3B01G468800 chr5B 101859717 101860351 634 False 760.0 760 88.3650 1556 2187 1 chr5B.!!$F1 631
14 TraesCS3B01G468800 chr6B 575332822 575333514 692 True 874.0 874 89.2960 1553 2261 1 chr6B.!!$R1 708
15 TraesCS3B01G468800 chr6B 646202780 646203456 676 False 835.0 835 89.0860 1565 2236 1 chr6B.!!$F1 671
16 TraesCS3B01G468800 chr6B 647942172 647942809 637 False 643.0 643 84.9230 1554 2199 1 chr6B.!!$F2 645
17 TraesCS3B01G468800 chrUn 31794494 31795098 604 False 706.0 706 87.9480 1553 2155 1 chrUn.!!$F1 602
18 TraesCS3B01G468800 chr1B 474275322 474275876 554 False 616.0 616 86.6550 1553 2114 1 chr1B.!!$F1 561

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
734 981 0.108585 TTTGCACTGGACTCTCCCAC 59.891 55.0 0.0 0.0 35.03 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2210 2547 0.039617 CGGCAAGTTCGGCAAATTGA 60.04 50.0 11.9 0.0 39.48 2.57 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
73 75 6.070656 TCATCTTCACATGGAAAAAGGTTCT 58.929 36.000 0.00 0.00 34.44 3.01
102 104 2.038269 CCCAGCAATTACCGCACGT 61.038 57.895 0.00 0.00 0.00 4.49
504 715 3.580895 GGATAGAGAGGAATCAGGAACCC 59.419 52.174 0.00 0.00 0.00 4.11
727 974 1.227102 TGCCACTTTGCACTGGACT 59.773 52.632 8.20 0.00 36.04 3.85
734 981 0.108585 TTTGCACTGGACTCTCCCAC 59.891 55.000 0.00 0.00 35.03 4.61
769 1016 1.121407 TGTCAGTGACACCTCCCAGG 61.121 60.000 22.06 0.00 37.67 4.45
806 1054 2.210524 AAGTTTCGTCGATGCACGCG 62.211 55.000 3.53 3.53 39.74 6.01
947 1222 1.349259 GCATCGCAAAGCAAAGGCAG 61.349 55.000 0.00 0.00 44.61 4.85
1155 1445 0.108615 CTTCTTCCATCGACGCCACT 60.109 55.000 0.00 0.00 0.00 4.00
1203 1493 4.131088 GTCGACGAGAGGGCCACC 62.131 72.222 6.18 0.00 0.00 4.61
1347 1648 1.770658 TCTTCTGGGTAGCCATGGATG 59.229 52.381 18.40 11.31 0.00 3.51
1395 1705 6.635030 ACACCATGTACTTTTCCTTCTTTC 57.365 37.500 0.00 0.00 0.00 2.62
1457 1770 7.018952 AGTGGGAAGAATGGGATGATAACATAT 59.981 37.037 0.00 0.00 36.82 1.78
1467 1780 8.005831 TGGGATGATAACATATTCCCCATTTA 57.994 34.615 7.48 0.00 39.97 1.40
1562 1880 1.592223 CCGACAGTTCACTCCTCCC 59.408 63.158 0.00 0.00 0.00 4.30
1563 1881 1.592223 CGACAGTTCACTCCTCCCC 59.408 63.158 0.00 0.00 0.00 4.81
1680 2000 1.575244 CGGCATCGTCATCAATGAGT 58.425 50.000 0.00 0.00 37.51 3.41
1725 2045 1.518572 CCTCCGCGCTACGTCAAAT 60.519 57.895 5.56 0.00 41.42 2.32
1910 2230 2.317609 GCAGTTCGAAGCTCGGCAA 61.318 57.895 0.00 0.00 40.88 4.52
1938 2258 2.043852 ACGAGGGAGGCGTCATCT 60.044 61.111 8.91 5.04 37.42 2.90
1951 2271 2.631418 GTCATCTTCCTCGACGACAA 57.369 50.000 0.00 0.00 0.00 3.18
2035 2364 4.003788 CGGCCACGTCAAGGAGGT 62.004 66.667 2.24 0.00 34.81 3.85
2048 2377 2.182030 GAGGTGAAGGCCGACGAG 59.818 66.667 0.00 0.00 0.00 4.18
2087 2416 2.094659 CGACATCGGCAACTTCGCT 61.095 57.895 0.00 0.00 35.37 4.93
2129 2461 2.147958 CCTTAAGTTGTAGTTGCGGCA 58.852 47.619 0.00 0.00 0.00 5.69
2181 2518 5.940192 GAACATGTCGAATATATGCCCAA 57.060 39.130 0.00 0.00 30.12 4.12
2199 2536 3.594134 CCAATTTGCCGAATTTTAGCCA 58.406 40.909 0.00 0.00 35.79 4.75
2210 2547 7.389053 TGCCGAATTTTAGCCAAATAATTTGTT 59.611 29.630 0.00 0.00 38.98 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
504 715 2.989840 GCTCCGAATGTTATCCTCATCG 59.010 50.000 0.00 0.00 0.00 3.84
734 981 1.338105 TGACAAGAGATTCCCGTGCTG 60.338 52.381 0.00 0.00 0.00 4.41
769 1016 0.321298 TTAGCTCCGGCAAAGTGGAC 60.321 55.000 0.00 0.00 41.70 4.02
806 1054 5.779529 AGATGCCAATGGATAATGAACAC 57.220 39.130 2.05 0.00 0.00 3.32
947 1222 1.332904 GCTACGCACTTGTGTTGTGTC 60.333 52.381 0.00 0.00 39.74 3.67
1203 1493 1.138047 GGACGGACAGTATGAACGCG 61.138 60.000 3.53 3.53 40.97 6.01
1347 1648 6.789262 ACCACTTAGACACGTGTATGTATAC 58.211 40.000 25.24 9.54 31.24 1.47
1395 1705 7.793927 ACTGAAGTTACAAAAGGAGAGAAAG 57.206 36.000 0.00 0.00 0.00 2.62
1508 1826 1.944024 CGGCACACAAACTCCACTTAA 59.056 47.619 0.00 0.00 0.00 1.85
1509 1827 1.134340 ACGGCACACAAACTCCACTTA 60.134 47.619 0.00 0.00 0.00 2.24
1510 1828 0.393808 ACGGCACACAAACTCCACTT 60.394 50.000 0.00 0.00 0.00 3.16
1511 1829 0.393808 AACGGCACACAAACTCCACT 60.394 50.000 0.00 0.00 0.00 4.00
1562 1880 1.926426 AATGGGAAGAAGAGCGGGGG 61.926 60.000 0.00 0.00 0.00 5.40
1563 1881 0.464554 GAATGGGAAGAAGAGCGGGG 60.465 60.000 0.00 0.00 0.00 5.73
1725 2045 3.068881 CCCCGGCTCTGTCTTCAA 58.931 61.111 0.00 0.00 0.00 2.69
1938 2258 4.929198 GTCGTTGTCGTCGAGGAA 57.071 55.556 9.78 0.00 37.99 3.36
2035 2364 3.744719 CGTCCTCGTCGGCCTTCA 61.745 66.667 0.00 0.00 0.00 3.02
2048 2377 4.570663 CCATCCTCGCCGTCGTCC 62.571 72.222 0.00 0.00 36.96 4.79
2199 2536 8.376889 AGTTCGGCAAATTGAACAAATTATTT 57.623 26.923 0.00 0.00 45.34 1.40
2210 2547 0.039617 CGGCAAGTTCGGCAAATTGA 60.040 50.000 11.90 0.00 39.48 2.57


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

AutoCloner maintained by Alex Coulton.