Multiple sequence alignment - TraesCS1A01G274100

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 TraesCS1A01G274100 chr1A 100.000 3785 0 0 1 3785 468412208 468408424 0.000000e+00 6990.0
1 TraesCS1A01G274100 chr1A 98.997 3788 35 1 1 3785 468463382 468459595 0.000000e+00 6782.0
2 TraesCS1A01G274100 chr1A 95.277 741 32 1 1 738 276261850 276261110 0.000000e+00 1171.0
3 TraesCS1A01G274100 chr1A 96.429 644 19 4 3143 3785 23414976 23414336 0.000000e+00 1059.0
4 TraesCS1A01G274100 chr1A 81.596 451 47 21 1096 1516 588664111 588664555 1.300000e-89 340.0
5 TraesCS1A01G274100 chr1A 88.186 237 27 1 1105 1340 587846020 587846256 8.000000e-72 281.0
6 TraesCS1A01G274100 chr1A 88.571 175 17 3 3135 3309 554838758 554838929 3.830000e-50 209.0
7 TraesCS1A01G274100 chr1A 84.270 89 14 0 1827 1915 588664354 588664442 1.870000e-13 87.9
8 TraesCS1A01G274100 chr1A 94.000 50 2 1 858 906 587663666 587663617 1.460000e-09 75.0
9 TraesCS1A01G274100 chr1D 94.836 1433 40 13 753 2155 368676061 368674633 0.000000e+00 2206.0
10 TraesCS1A01G274100 chr1D 97.601 542 10 3 2595 3134 368674293 368673753 0.000000e+00 926.0
11 TraesCS1A01G274100 chr1D 93.802 484 24 2 3308 3785 450583917 450584400 0.000000e+00 723.0
12 TraesCS1A01G274100 chr1D 95.963 322 13 0 2266 2587 368674648 368674327 1.200000e-144 523.0
13 TraesCS1A01G274100 chr1D 81.871 513 50 21 963 1451 489326973 489326480 3.540000e-105 392.0
14 TraesCS1A01G274100 chr1D 81.871 513 50 21 963 1451 489434697 489434204 3.540000e-105 392.0
15 TraesCS1A01G274100 chr1D 82.463 479 48 20 997 1451 489301825 489301359 1.650000e-103 387.0
16 TraesCS1A01G274100 chr1D 81.663 469 52 12 1011 1451 489755856 489756318 3.590000e-95 359.0
17 TraesCS1A01G274100 chr1D 82.785 395 48 14 963 1351 488589351 488589731 6.060000e-88 335.0
18 TraesCS1A01G274100 chr1D 89.130 92 8 2 2095 2185 407673101 407673011 3.090000e-21 113.0
19 TraesCS1A01G274100 chr1D 84.298 121 12 5 2747 2860 488513036 488512916 1.110000e-20 111.0
20 TraesCS1A01G274100 chr1D 96.429 56 2 0 846 901 488544153 488544098 4.030000e-15 93.5
21 TraesCS1A01G274100 chr1D 88.525 61 7 0 840 900 489301990 489301930 1.460000e-09 75.0
22 TraesCS1A01G274100 chrUn 94.197 741 39 2 1 738 385763869 385764608 0.000000e+00 1127.0
23 TraesCS1A01G274100 chrUn 94.062 741 40 2 1 738 385776872 385776133 0.000000e+00 1122.0
24 TraesCS1A01G274100 chrUn 75.000 256 43 14 2607 2844 8748857 8748605 8.650000e-17 99.0
25 TraesCS1A01G274100 chrUn 82.955 88 8 4 1672 1759 111025288 111025368 5.240000e-09 73.1
26 TraesCS1A01G274100 chr3B 94.476 706 31 4 17 718 25915416 25914715 0.000000e+00 1081.0
27 TraesCS1A01G274100 chr3B 94.476 706 31 4 17 718 26051525 26050824 0.000000e+00 1081.0
28 TraesCS1A01G274100 chr3B 94.460 704 31 4 17 716 26393750 26393051 0.000000e+00 1077.0
29 TraesCS1A01G274100 chr3B 93.909 706 35 4 17 718 26240527 26239826 0.000000e+00 1059.0
30 TraesCS1A01G274100 chr6B 91.680 649 47 5 98 739 711318152 711317504 0.000000e+00 893.0
31 TraesCS1A01G274100 chr6B 86.117 461 29 10 3337 3785 715685812 715686249 7.410000e-127 464.0
32 TraesCS1A01G274100 chr5B 93.018 487 25 3 3308 3785 37035276 37034790 0.000000e+00 702.0
33 TraesCS1A01G274100 chr5B 78.261 437 72 15 3337 3759 481200913 481201340 3.750000e-65 259.0
34 TraesCS1A01G274100 chr5A 96.834 379 9 3 3129 3505 540383482 540383859 6.900000e-177 630.0
35 TraesCS1A01G274100 chr5A 90.431 209 4 3 3389 3597 540383845 540384037 1.040000e-65 261.0
36 TraesCS1A01G274100 chr5A 88.660 97 11 0 2096 2192 407937800 407937704 6.640000e-23 119.0
37 TraesCS1A01G274100 chr5A 91.489 47 4 0 3546 3592 89281641 89281687 8.780000e-07 65.8
38 TraesCS1A01G274100 chr7B 87.500 504 37 15 3308 3785 585868245 585867742 3.300000e-155 558.0
39 TraesCS1A01G274100 chr7B 83.299 485 64 8 3308 3776 90516783 90517266 7.510000e-117 431.0
40 TraesCS1A01G274100 chr7B 92.353 170 8 4 3143 3309 585871763 585871596 1.760000e-58 237.0
41 TraesCS1A01G274100 chr7B 90.110 91 7 2 2096 2185 605072494 605072405 2.390000e-22 117.0
42 TraesCS1A01G274100 chr7B 90.000 60 4 2 1702 1760 641326191 641326249 4.050000e-10 76.8
43 TraesCS1A01G274100 chr1B 80.200 500 39 30 950 1401 680744540 680744053 1.700000e-83 320.0
44 TraesCS1A01G274100 chr1B 84.397 141 22 0 2421 2561 681076275 681076135 5.100000e-29 139.0
45 TraesCS1A01G274100 chr1B 88.764 89 10 0 2097 2185 507850378 507850466 4.000000e-20 110.0
46 TraesCS1A01G274100 chr1B 97.826 46 1 0 858 903 681802533 681802578 3.130000e-11 80.5
47 TraesCS1A01G274100 chr1B 89.796 49 3 2 841 887 682003088 682003136 1.140000e-05 62.1
48 TraesCS1A01G274100 chr2A 92.857 168 10 2 3142 3309 724411504 724411339 3.780000e-60 243.0
49 TraesCS1A01G274100 chr3A 89.773 176 15 3 3135 3309 487445504 487445677 4.920000e-54 222.0
50 TraesCS1A01G274100 chr7D 88.398 181 12 5 3135 3309 254897349 254897172 3.830000e-50 209.0
51 TraesCS1A01G274100 chr4D 88.268 179 15 4 3135 3309 240931028 240931204 3.830000e-50 209.0
52 TraesCS1A01G274100 chr4D 83.529 85 7 5 1676 1760 307492699 307492622 5.240000e-09 73.1
53 TraesCS1A01G274100 chr4B 93.333 90 6 0 2096 2185 19086548 19086459 2.370000e-27 134.0
54 TraesCS1A01G274100 chr4B 79.762 84 8 7 1677 1760 639455500 639455574 7.000000e-03 52.8
55 TraesCS1A01G274100 chr3D 88.889 90 10 0 2096 2185 23667592 23667503 1.110000e-20 111.0
56 TraesCS1A01G274100 chr3D 84.146 82 6 5 1677 1758 499945097 499945171 5.240000e-09 73.1
57 TraesCS1A01G274100 chr2D 87.629 97 4 7 2095 2187 192181496 192181588 5.170000e-19 106.0
58 TraesCS1A01G274100 chr2D 82.353 85 8 4 1676 1760 37236629 37236552 2.440000e-07 67.6
59 TraesCS1A01G274100 chr2D 82.353 85 8 5 1676 1760 534121428 534121351 2.440000e-07 67.6
60 TraesCS1A01G274100 chr5D 83.529 85 7 4 1676 1760 41816896 41816819 5.240000e-09 73.1


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 TraesCS1A01G274100 chr1A 468408424 468412208 3784 True 6990.000000 6990 100.000000 1 3785 1 chr1A.!!$R3 3784
1 TraesCS1A01G274100 chr1A 468459595 468463382 3787 True 6782.000000 6782 98.997000 1 3785 1 chr1A.!!$R4 3784
2 TraesCS1A01G274100 chr1A 276261110 276261850 740 True 1171.000000 1171 95.277000 1 738 1 chr1A.!!$R2 737
3 TraesCS1A01G274100 chr1A 23414336 23414976 640 True 1059.000000 1059 96.429000 3143 3785 1 chr1A.!!$R1 642
4 TraesCS1A01G274100 chr1D 368673753 368676061 2308 True 1218.333333 2206 96.133333 753 3134 3 chr1D.!!$R6 2381
5 TraesCS1A01G274100 chr1D 489301359 489301990 631 True 231.000000 387 85.494000 840 1451 2 chr1D.!!$R7 611
6 TraesCS1A01G274100 chrUn 385763869 385764608 739 False 1127.000000 1127 94.197000 1 738 1 chrUn.!!$F2 737
7 TraesCS1A01G274100 chrUn 385776133 385776872 739 True 1122.000000 1122 94.062000 1 738 1 chrUn.!!$R2 737
8 TraesCS1A01G274100 chr3B 25914715 25915416 701 True 1081.000000 1081 94.476000 17 718 1 chr3B.!!$R1 701
9 TraesCS1A01G274100 chr3B 26050824 26051525 701 True 1081.000000 1081 94.476000 17 718 1 chr3B.!!$R2 701
10 TraesCS1A01G274100 chr3B 26393051 26393750 699 True 1077.000000 1077 94.460000 17 716 1 chr3B.!!$R4 699
11 TraesCS1A01G274100 chr3B 26239826 26240527 701 True 1059.000000 1059 93.909000 17 718 1 chr3B.!!$R3 701
12 TraesCS1A01G274100 chr6B 711317504 711318152 648 True 893.000000 893 91.680000 98 739 1 chr6B.!!$R1 641
13 TraesCS1A01G274100 chr5A 540383482 540384037 555 False 445.500000 630 93.632500 3129 3597 2 chr5A.!!$F2 468
14 TraesCS1A01G274100 chr7B 585867742 585871763 4021 True 397.500000 558 89.926500 3143 3785 2 chr7B.!!$R2 642

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
793 804 1.32868 CGTGCAGAGATGGATTTTCGG 59.671 52.381 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3687 7281 6.202226 GCTGAAGTATCCCGATTTTTGATTC 58.798 40.0 0.0 0.0 0.0 2.52 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
311 312 2.852075 TTGAACCCGGCCTCCTGT 60.852 61.111 0.00 0.0 0.00 4.00
793 804 1.328680 CGTGCAGAGATGGATTTTCGG 59.671 52.381 0.00 0.0 0.00 4.30
1229 1316 4.749310 CTCCAGCGAACGCAGGCT 62.749 66.667 22.13 0.0 45.75 4.58
1387 1483 6.477688 CAGCCATAATCGAATTCTTTGCAATT 59.522 34.615 0.00 0.0 0.00 2.32
1527 1625 1.271054 CCTGACCTAGTGCTGCTTGTT 60.271 52.381 0.00 0.0 0.00 2.83
3204 3330 7.120579 ACGGCAATTTCTAGAAACATCAATACA 59.879 33.333 19.94 0.0 32.51 2.29
3715 7309 2.732412 ATCGGGATACTTCAGCGATG 57.268 50.000 0.00 0.0 0.00 3.84
3719 7313 1.606737 GGGATACTTCAGCGATGCCTC 60.607 57.143 0.00 0.0 0.00 4.70
3766 7360 2.579873 AGTATCGGCCACGTACAGTAT 58.420 47.619 2.24 0.0 41.85 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
311 312 1.352017 AGATCGGCATGGGATATTGCA 59.648 47.619 0.00 0.00 40.66 4.08
1387 1483 1.283487 CACGCATGCTGCTGTTTCA 59.717 52.632 17.13 0.00 42.25 2.69
1527 1625 2.141312 TGCAGTACCTCCTGTTGCA 58.859 52.632 0.02 0.02 41.97 4.08
3687 7281 6.202226 GCTGAAGTATCCCGATTTTTGATTC 58.798 40.000 0.00 0.00 0.00 2.52
3719 7313 1.983972 GCCTGATACGGCTTCGATAG 58.016 55.000 0.00 0.00 46.63 2.08


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

AutoCloner maintained by Alex Coulton.