Multiple sequence alignment - TraesCS4D01G257400

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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 TraesCS4D01G257400 chr4D 100.000 3188 0 0 1 3188 427013531 427016718 0.000000e+00 5888.0
1 TraesCS4D01G257400 chr4D 96.693 1542 36 2 669 2197 427322331 427323870 0.000000e+00 2551.0
2 TraesCS4D01G257400 chr4D 94.102 1543 61 18 700 2231 428558578 428557055 0.000000e+00 2318.0
3 TraesCS4D01G257400 chr4D 87.306 1544 142 18 723 2227 428398146 428396618 0.000000e+00 1716.0
4 TraesCS4D01G257400 chr4D 83.688 1269 134 25 958 2186 427267891 427269126 0.000000e+00 1129.0
5 TraesCS4D01G257400 chr4D 95.303 660 21 6 1 653 427320138 427320794 0.000000e+00 1038.0
6 TraesCS4D01G257400 chr4D 95.614 228 5 1 2455 2682 427020835 427021057 8.410000e-96 361.0
7 TraesCS4D01G257400 chr4D 92.275 233 10 3 2221 2446 428396678 428396447 1.100000e-84 324.0
8 TraesCS4D01G257400 chr4D 97.273 110 3 0 2337 2446 427323907 427324016 1.510000e-43 187.0
9 TraesCS4D01G257400 chr4D 88.732 142 15 1 2305 2446 57841978 57842118 4.230000e-39 172.0
10 TraesCS4D01G257400 chr4D 92.727 110 8 0 2337 2446 428557039 428556930 3.290000e-35 159.0
11 TraesCS4D01G257400 chr4D 85.507 138 12 4 2311 2441 424168263 424168127 1.540000e-28 137.0
12 TraesCS4D01G257400 chr4A 93.914 1758 60 22 700 2446 38663617 38661896 0.000000e+00 2610.0
13 TraesCS4D01G257400 chr4A 91.270 1764 92 36 700 2446 37833404 37835122 0.000000e+00 2348.0
14 TraesCS4D01G257400 chr4A 88.490 1755 155 17 723 2446 37999746 38001484 0.000000e+00 2078.0
15 TraesCS4D01G257400 chr4A 89.510 143 11 4 2305 2446 539140642 539140781 9.090000e-41 178.0
16 TraesCS4D01G257400 chr4A 95.283 106 5 0 2339 2444 38661427 38661322 5.470000e-38 169.0
17 TraesCS4D01G257400 chr4B 94.386 1532 70 7 700 2231 522681944 522683459 0.000000e+00 2338.0
18 TraesCS4D01G257400 chr4B 86.114 1750 156 31 723 2446 524901114 524899426 0.000000e+00 1805.0
19 TraesCS4D01G257400 chr4B 83.914 1206 134 24 901 2074 522677162 522678339 0.000000e+00 1098.0
20 TraesCS4D01G257400 chr4B 93.976 166 2 2 700 859 526960248 526960411 8.830000e-61 244.0
21 TraesCS4D01G257400 chr4B 99.091 110 1 0 2337 2446 522683475 522683584 6.980000e-47 198.0
22 TraesCS4D01G257400 chr4B 85.340 191 25 3 507 695 636988297 636988486 9.020000e-46 195.0
23 TraesCS4D01G257400 chr2B 93.030 703 42 3 2458 3159 768790827 768790131 0.000000e+00 1020.0
24 TraesCS4D01G257400 chr6B 87.465 710 77 6 2454 3159 82634792 82634091 0.000000e+00 808.0
25 TraesCS4D01G257400 chr6B 84.286 70 9 2 626 694 695905405 695905473 2.050000e-07 67.6
26 TraesCS4D01G257400 chr1A 88.604 623 41 10 77 693 405483073 405483671 0.000000e+00 730.0
27 TraesCS4D01G257400 chr1B 84.870 694 85 16 2460 3148 43988449 43989127 0.000000e+00 682.0
28 TraesCS4D01G257400 chr1B 84.648 697 89 13 2460 3152 44004600 44005282 0.000000e+00 678.0
29 TraesCS4D01G257400 chr1B 82.476 719 100 20 2446 3154 392152743 392153445 9.780000e-170 606.0
30 TraesCS4D01G257400 chr5D 83.618 702 92 18 2460 3154 48055129 48055814 3.470000e-179 638.0
31 TraesCS4D01G257400 chr3A 84.488 606 80 9 2578 3181 373339402 373339995 1.270000e-163 586.0
32 TraesCS4D01G257400 chr6A 84.463 605 80 9 2579 3181 67638552 67637960 4.580000e-163 584.0
33 TraesCS4D01G257400 chr6A 82.953 569 60 24 135 682 51721250 51721802 2.220000e-131 479.0
34 TraesCS4D01G257400 chr6A 82.074 569 65 24 135 682 40649231 40648679 4.850000e-123 451.0
35 TraesCS4D01G257400 chr5B 83.677 631 92 9 2532 3157 547067863 547068487 4.580000e-163 584.0
36 TraesCS4D01G257400 chr7A 81.338 568 62 22 137 693 728455458 728455992 3.800000e-114 422.0
37 TraesCS4D01G257400 chr7A 80.844 569 65 22 137 693 728240483 728239947 1.060000e-109 407.0
38 TraesCS4D01G257400 chr7A 86.387 191 20 5 507 693 669330033 669329845 1.500000e-48 204.0
39 TraesCS4D01G257400 chr7D 94.737 228 7 2 2455 2682 555547888 555547666 1.820000e-92 350.0
40 TraesCS4D01G257400 chr2A 77.500 480 66 22 171 641 726215959 726216405 1.900000e-62 250.0
41 TraesCS4D01G257400 chr3B 72.446 323 62 15 40 357 744321866 744321566 9.480000e-11 78.7
42 TraesCS4D01G257400 chr5A 93.023 43 3 0 652 694 565725224 565725182 2.650000e-06 63.9


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 TraesCS4D01G257400 chr4D 427013531 427016718 3187 False 5888.000000 5888 100.000000 1 3188 1 chr4D.!!$F2 3187
1 TraesCS4D01G257400 chr4D 427320138 427324016 3878 False 1258.666667 2551 96.423000 1 2446 3 chr4D.!!$F5 2445
2 TraesCS4D01G257400 chr4D 428556930 428558578 1648 True 1238.500000 2318 93.414500 700 2446 2 chr4D.!!$R3 1746
3 TraesCS4D01G257400 chr4D 427267891 427269126 1235 False 1129.000000 1129 83.688000 958 2186 1 chr4D.!!$F4 1228
4 TraesCS4D01G257400 chr4D 428396447 428398146 1699 True 1020.000000 1716 89.790500 723 2446 2 chr4D.!!$R2 1723
5 TraesCS4D01G257400 chr4A 37833404 37835122 1718 False 2348.000000 2348 91.270000 700 2446 1 chr4A.!!$F1 1746
6 TraesCS4D01G257400 chr4A 37999746 38001484 1738 False 2078.000000 2078 88.490000 723 2446 1 chr4A.!!$F2 1723
7 TraesCS4D01G257400 chr4A 38661322 38663617 2295 True 1389.500000 2610 94.598500 700 2446 2 chr4A.!!$R1 1746
8 TraesCS4D01G257400 chr4B 524899426 524901114 1688 True 1805.000000 1805 86.114000 723 2446 1 chr4B.!!$R1 1723
9 TraesCS4D01G257400 chr4B 522677162 522683584 6422 False 1211.333333 2338 92.463667 700 2446 3 chr4B.!!$F3 1746
10 TraesCS4D01G257400 chr2B 768790131 768790827 696 True 1020.000000 1020 93.030000 2458 3159 1 chr2B.!!$R1 701
11 TraesCS4D01G257400 chr6B 82634091 82634792 701 True 808.000000 808 87.465000 2454 3159 1 chr6B.!!$R1 705
12 TraesCS4D01G257400 chr1A 405483073 405483671 598 False 730.000000 730 88.604000 77 693 1 chr1A.!!$F1 616
13 TraesCS4D01G257400 chr1B 43988449 43989127 678 False 682.000000 682 84.870000 2460 3148 1 chr1B.!!$F1 688
14 TraesCS4D01G257400 chr1B 44004600 44005282 682 False 678.000000 678 84.648000 2460 3152 1 chr1B.!!$F2 692
15 TraesCS4D01G257400 chr1B 392152743 392153445 702 False 606.000000 606 82.476000 2446 3154 1 chr1B.!!$F3 708
16 TraesCS4D01G257400 chr5D 48055129 48055814 685 False 638.000000 638 83.618000 2460 3154 1 chr5D.!!$F1 694
17 TraesCS4D01G257400 chr3A 373339402 373339995 593 False 586.000000 586 84.488000 2578 3181 1 chr3A.!!$F1 603
18 TraesCS4D01G257400 chr6A 67637960 67638552 592 True 584.000000 584 84.463000 2579 3181 1 chr6A.!!$R2 602
19 TraesCS4D01G257400 chr6A 51721250 51721802 552 False 479.000000 479 82.953000 135 682 1 chr6A.!!$F1 547
20 TraesCS4D01G257400 chr6A 40648679 40649231 552 True 451.000000 451 82.074000 135 682 1 chr6A.!!$R1 547
21 TraesCS4D01G257400 chr5B 547067863 547068487 624 False 584.000000 584 83.677000 2532 3157 1 chr5B.!!$F1 625
22 TraesCS4D01G257400 chr7A 728455458 728455992 534 False 422.000000 422 81.338000 137 693 1 chr7A.!!$F1 556
23 TraesCS4D01G257400 chr7A 728239947 728240483 536 True 407.000000 407 80.844000 137 693 1 chr7A.!!$R2 556

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
651 686 2.479656 CCAACAAAATCAATGGCCAACG 59.52 45.455 10.96 3.4 0.0 4.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2487 6785 0.036164 TCTAACCATGCCGCACAAGT 59.964 50.0 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
62 63 5.619220 GAGAGAGGATTTTCTACCATGCAT 58.381 41.667 0.00 0.00 0.00 3.96
122 124 4.079500 TGTTTTGTGGGCCCATAGATATCA 60.080 41.667 31.45 17.00 0.00 2.15
160 162 8.300286 TGTCTCTAGTCACTAAGTTTCATTCAG 58.700 37.037 0.00 0.00 0.00 3.02
263 268 6.145048 GCAAGATCTTCAAAACAAGACCAATG 59.855 38.462 4.57 0.00 35.18 2.82
643 678 8.369424 TGAATGTGAATCTCCAACAAAATCAAT 58.631 29.630 0.00 0.00 0.00 2.57
651 686 2.479656 CCAACAAAATCAATGGCCAACG 59.520 45.455 10.96 3.40 0.00 4.10
748 4845 2.924290 CGAAGAACCTGAATTCGAGTCC 59.076 50.000 0.04 0.00 46.57 3.85
767 4864 2.864946 TCCGAAATGAACGAAACGTGAA 59.135 40.909 0.00 0.00 39.99 3.18
768 4865 3.495377 TCCGAAATGAACGAAACGTGAAT 59.505 39.130 0.00 0.00 39.99 2.57
2039 6208 1.179152 TGGTTCGATGCTCCTCGTTA 58.821 50.000 0.00 0.00 39.62 3.18
2074 6249 2.182030 CGAAGGTCGACCCTCTGC 59.818 66.667 30.82 10.71 45.47 4.26
2196 6432 6.506464 CAAAAAGTGCAATGAAACTCTCTG 57.494 37.500 0.00 0.00 0.00 3.35
2215 6469 2.671888 CTGCTAGATGTGACTGTGCTTG 59.328 50.000 0.00 0.00 0.00 4.01
2258 6542 9.618890 AAATGCTAGCATAAACTCTCTTGATAA 57.381 29.630 29.77 0.00 35.31 1.75
2296 6587 1.335810 CCATCAACAATCATGAGCCCG 59.664 52.381 0.09 0.00 0.00 6.13
2454 6752 5.497474 AGGTTGTGTTCAGAGTGTTAAACT 58.503 37.500 0.00 0.00 43.85 2.66
2624 6932 1.148498 GGTGTGCCCCTGCCTATAC 59.852 63.158 0.00 0.00 36.33 1.47
2625 6933 1.345715 GGTGTGCCCCTGCCTATACT 61.346 60.000 0.00 0.00 36.33 2.12
2626 6934 1.420430 GTGTGCCCCTGCCTATACTA 58.580 55.000 0.00 0.00 36.33 1.82
2627 6935 1.978580 GTGTGCCCCTGCCTATACTAT 59.021 52.381 0.00 0.00 36.33 2.12
2628 6936 3.170717 GTGTGCCCCTGCCTATACTATA 58.829 50.000 0.00 0.00 36.33 1.31
3037 7638 3.110705 AGAGGTGCTGATAATGGTGACT 58.889 45.455 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 2.861462 AGAAAATCCTCTCTCGCTCG 57.139 50.000 0.00 0.0 0.00 5.03
38 39 4.054671 GCATGGTAGAAAATCCTCTCTCG 58.945 47.826 0.00 0.0 0.00 4.04
62 63 0.613572 TACATGCACGAGAGGTCCCA 60.614 55.000 0.00 0.0 0.00 4.37
748 4845 5.671140 GGATATTCACGTTTCGTTCATTTCG 59.329 40.000 0.00 0.0 38.32 3.46
1797 5963 2.124570 GGCATCCCGAGCACACAT 60.125 61.111 0.00 0.0 0.00 3.21
1910 6079 3.481453 AGCTTGTCTTCAGGGAAAGAAC 58.519 45.455 0.00 0.0 37.04 3.01
2083 6258 2.026262 TGATCCTTGGTGCCCTCTTTAC 60.026 50.000 0.00 0.0 0.00 2.01
2084 6259 2.274542 TGATCCTTGGTGCCCTCTTTA 58.725 47.619 0.00 0.0 0.00 1.85
2090 6265 1.177401 GAACTTGATCCTTGGTGCCC 58.823 55.000 0.00 0.0 0.00 5.36
2182 6357 6.035866 GTCACATCTAGCAGAGAGTTTCATTG 59.964 42.308 0.00 0.0 37.70 2.82
2196 6432 2.005451 CCAAGCACAGTCACATCTAGC 58.995 52.381 0.00 0.0 0.00 3.42
2215 6469 7.011857 GCTAGCATTTACATAGATGGCTTATCC 59.988 40.741 10.63 0.0 36.40 2.59
2257 6541 2.633967 TGGCTCATCCAAGCACAATTTT 59.366 40.909 0.00 0.0 43.21 1.82
2258 6542 2.250031 TGGCTCATCCAAGCACAATTT 58.750 42.857 0.00 0.0 43.21 1.82
2296 6587 7.819900 ACTTCTACTTGATGGATCAACACTAAC 59.180 37.037 0.00 0.0 41.51 2.34
2454 6752 0.963225 TAGGCTGTCACGCTACACAA 59.037 50.000 0.00 0.0 0.00 3.33
2481 6779 3.287222 ACCATGCCGCACAAGTTTATAT 58.713 40.909 0.00 0.0 0.00 0.86
2487 6785 0.036164 TCTAACCATGCCGCACAAGT 59.964 50.000 0.00 0.0 0.00 3.16
2545 6845 6.323996 TGAGGGCGAAGAAAGATAGAGATAAA 59.676 38.462 0.00 0.0 0.00 1.40
2564 6864 3.350219 TGGAGATTACAACTTGAGGGC 57.650 47.619 0.00 0.0 0.00 5.19
2624 6932 1.070577 GGACGCGCTGCATGTTTATAG 60.071 52.381 5.73 0.0 0.00 1.31
2625 6933 0.934496 GGACGCGCTGCATGTTTATA 59.066 50.000 5.73 0.0 0.00 0.98
2626 6934 1.714899 GGGACGCGCTGCATGTTTAT 61.715 55.000 5.73 0.0 0.00 1.40
2627 6935 2.395360 GGGACGCGCTGCATGTTTA 61.395 57.895 5.73 0.0 0.00 2.01
2628 6936 3.737172 GGGACGCGCTGCATGTTT 61.737 61.111 5.73 0.0 0.00 2.83
2970 7571 3.325753 GCACCTGCTGGTCCTCCT 61.326 66.667 13.09 0.0 46.60 3.69


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

AutoCloner maintained by Alex Coulton.