Multiple sequence alignment - TraesCS2B01G247300

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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 TraesCS2B01G247300 chr2B 100.000 2585 0 0 1 2585 253716993 253714409 0.000000e+00 4774.0
1 TraesCS2B01G247300 chr2B 98.319 714 11 1 1 713 741577788 741577075 0.000000e+00 1251.0
2 TraesCS2B01G247300 chr2B 94.746 571 22 8 1988 2554 749538431 749538997 0.000000e+00 881.0
3 TraesCS2B01G247300 chr2B 96.449 535 12 7 2023 2554 722829894 722830424 0.000000e+00 876.0
4 TraesCS2B01G247300 chr2B 87.153 576 45 16 149 700 222003916 222004486 6.070000e-176 627.0
5 TraesCS2B01G247300 chr2B 89.691 291 19 3 2274 2554 543503528 543503239 6.800000e-96 361.0
6 TraesCS2B01G247300 chr2B 89.384 292 18 5 2274 2554 544913766 544913477 3.160000e-94 355.0
7 TraesCS2B01G247300 chr2B 90.654 107 10 0 1 107 222003490 222003596 2.680000e-30 143.0
8 TraesCS2B01G247300 chr2B 94.118 85 5 0 134 218 222003862 222003946 2.090000e-26 130.0
9 TraesCS2B01G247300 chr7B 95.494 1043 28 11 1529 2554 143200570 143199530 0.000000e+00 1648.0
10 TraesCS2B01G247300 chr7B 90.558 1112 69 21 1463 2554 661716304 661715209 0.000000e+00 1439.0
11 TraesCS2B01G247300 chr5B 89.947 1134 67 19 1463 2554 620760832 620761960 0.000000e+00 1419.0
12 TraesCS2B01G247300 chr5B 95.514 535 16 6 2023 2554 688549990 688550519 0.000000e+00 848.0
13 TraesCS2B01G247300 chr5B 93.636 110 7 0 1463 1572 89200771 89200662 5.720000e-37 165.0
14 TraesCS2B01G247300 chr5B 88.462 52 4 2 2533 2583 604670237 604670287 7.720000e-06 62.1
15 TraesCS2B01G247300 chr5B 91.304 46 0 4 2539 2583 218039536 218039578 2.780000e-05 60.2
16 TraesCS2B01G247300 chr1B 88.609 1071 73 31 1511 2554 42322733 42321685 0.000000e+00 1256.0
17 TraesCS2B01G247300 chr1B 95.514 535 20 4 2023 2554 298078758 298078225 0.000000e+00 852.0
18 TraesCS2B01G247300 chr7A 97.339 714 18 1 1 713 735862667 735863380 0.000000e+00 1212.0
19 TraesCS2B01G247300 chr7A 82.836 268 35 5 456 714 620853718 620853983 2.000000e-56 230.0
20 TraesCS2B01G247300 chr7A 89.583 48 2 3 2537 2583 556950585 556950630 9.990000e-05 58.4
21 TraesCS2B01G247300 chr2D 95.586 725 25 4 745 1462 196437247 196436523 0.000000e+00 1155.0
22 TraesCS2B01G247300 chr2D 90.036 843 40 12 1463 2273 144465064 144465894 0.000000e+00 1051.0
23 TraesCS2B01G247300 chr2D 88.442 199 22 1 506 703 87591691 87591493 3.320000e-59 239.0
24 TraesCS2B01G247300 chr6B 88.984 935 54 21 1663 2554 647362783 647363711 0.000000e+00 1110.0
25 TraesCS2B01G247300 chr6B 93.182 44 1 2 2540 2583 505256327 505256286 2.150000e-06 63.9
26 TraesCS2B01G247300 chr2A 87.811 804 70 22 1487 2273 10517641 10518433 0.000000e+00 917.0
27 TraesCS2B01G247300 chr2A 87.484 767 40 22 1515 2273 5647714 5648432 0.000000e+00 833.0
28 TraesCS2B01G247300 chr2A 93.566 373 18 3 1095 1462 212630532 212630161 3.760000e-153 551.0
29 TraesCS2B01G247300 chr2A 90.606 330 27 4 717 1046 212633035 212632710 3.950000e-118 435.0
30 TraesCS2B01G247300 chr2A 76.139 746 118 38 1559 2273 17917152 17916436 1.150000e-88 337.0
31 TraesCS2B01G247300 chr2A 91.379 58 5 0 1469 1526 125629553 125629610 2.130000e-11 80.5
32 TraesCS2B01G247300 chr2A 84.746 59 6 3 2527 2583 112548476 112548533 3.590000e-04 56.5
33 TraesCS2B01G247300 chr4A 95.888 535 16 6 2023 2554 731504157 731503626 0.000000e+00 861.0
34 TraesCS2B01G247300 chr4A 91.071 112 5 3 1515 1621 522061015 522061126 2.070000e-31 147.0
35 TraesCS2B01G247300 chr4A 89.583 48 5 0 2536 2583 660406116 660406069 7.720000e-06 62.1
36 TraesCS2B01G247300 chr1D 90.432 533 42 7 188 714 30291343 30290814 0.000000e+00 693.0
37 TraesCS2B01G247300 chr1D 90.654 107 10 0 1 107 30291981 30291875 2.680000e-30 143.0
38 TraesCS2B01G247300 chr1D 92.941 85 6 0 134 218 30291599 30291515 9.710000e-25 124.0
39 TraesCS2B01G247300 chr6D 87.188 601 43 17 1641 2231 7328930 7329506 0.000000e+00 652.0
40 TraesCS2B01G247300 chr6D 92.174 115 6 2 1487 1598 7328816 7328930 2.660000e-35 159.0
41 TraesCS2B01G247300 chr5D 92.287 376 25 3 340 714 294158455 294158083 4.900000e-147 531.0
42 TraesCS2B01G247300 chr5D 79.953 429 62 15 310 715 379220858 379220431 7.000000e-76 294.0
43 TraesCS2B01G247300 chr5D 90.654 107 10 0 1 107 294159878 294159772 2.680000e-30 143.0
44 TraesCS2B01G247300 chr5D 92.941 85 6 0 134 218 294159496 294159412 9.710000e-25 124.0
45 TraesCS2B01G247300 chr3B 89.384 292 19 4 2274 2554 667720796 667720506 8.800000e-95 357.0
46 TraesCS2B01G247300 chr3B 89.003 291 21 3 2274 2554 434312107 434311818 1.470000e-92 350.0
47 TraesCS2B01G247300 chr4D 91.133 203 17 1 506 707 103490270 103490472 9.110000e-70 274.0
48 TraesCS2B01G247300 chr4D 85.366 123 16 1 67 187 103489853 103489975 2.700000e-25 126.0
49 TraesCS2B01G247300 chrUn 90.654 107 10 0 1 107 480179689 480179583 2.680000e-30 143.0
50 TraesCS2B01G247300 chr1A 97.333 75 2 0 1117 1191 19088569 19088643 7.510000e-26 128.0
51 TraesCS2B01G247300 chr1A 95.122 41 1 1 2544 2583 161731345 161731385 2.150000e-06 63.9
52 TraesCS2B01G247300 chr5A 82.927 123 16 3 67 187 619949368 619949487 3.520000e-19 106.0
53 TraesCS2B01G247300 chr3A 87.037 54 3 3 2530 2583 113241004 113241053 9.990000e-05 58.4
54 TraesCS2B01G247300 chr6A 85.714 56 3 5 2530 2583 258955963 258955911 1.000000e-03 54.7


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 TraesCS2B01G247300 chr2B 253714409 253716993 2584 True 4774.0 4774 100.000000 1 2585 1 chr2B.!!$R1 2584
1 TraesCS2B01G247300 chr2B 741577075 741577788 713 True 1251.0 1251 98.319000 1 713 1 chr2B.!!$R4 712
2 TraesCS2B01G247300 chr2B 749538431 749538997 566 False 881.0 881 94.746000 1988 2554 1 chr2B.!!$F2 566
3 TraesCS2B01G247300 chr2B 722829894 722830424 530 False 876.0 876 96.449000 2023 2554 1 chr2B.!!$F1 531
4 TraesCS2B01G247300 chr2B 222003490 222004486 996 False 300.0 627 90.641667 1 700 3 chr2B.!!$F3 699
5 TraesCS2B01G247300 chr7B 143199530 143200570 1040 True 1648.0 1648 95.494000 1529 2554 1 chr7B.!!$R1 1025
6 TraesCS2B01G247300 chr7B 661715209 661716304 1095 True 1439.0 1439 90.558000 1463 2554 1 chr7B.!!$R2 1091
7 TraesCS2B01G247300 chr5B 620760832 620761960 1128 False 1419.0 1419 89.947000 1463 2554 1 chr5B.!!$F3 1091
8 TraesCS2B01G247300 chr5B 688549990 688550519 529 False 848.0 848 95.514000 2023 2554 1 chr5B.!!$F4 531
9 TraesCS2B01G247300 chr1B 42321685 42322733 1048 True 1256.0 1256 88.609000 1511 2554 1 chr1B.!!$R1 1043
10 TraesCS2B01G247300 chr1B 298078225 298078758 533 True 852.0 852 95.514000 2023 2554 1 chr1B.!!$R2 531
11 TraesCS2B01G247300 chr7A 735862667 735863380 713 False 1212.0 1212 97.339000 1 713 1 chr7A.!!$F3 712
12 TraesCS2B01G247300 chr2D 196436523 196437247 724 True 1155.0 1155 95.586000 745 1462 1 chr2D.!!$R2 717
13 TraesCS2B01G247300 chr2D 144465064 144465894 830 False 1051.0 1051 90.036000 1463 2273 1 chr2D.!!$F1 810
14 TraesCS2B01G247300 chr6B 647362783 647363711 928 False 1110.0 1110 88.984000 1663 2554 1 chr6B.!!$F1 891
15 TraesCS2B01G247300 chr2A 10517641 10518433 792 False 917.0 917 87.811000 1487 2273 1 chr2A.!!$F2 786
16 TraesCS2B01G247300 chr2A 5647714 5648432 718 False 833.0 833 87.484000 1515 2273 1 chr2A.!!$F1 758
17 TraesCS2B01G247300 chr2A 212630161 212633035 2874 True 493.0 551 92.086000 717 1462 2 chr2A.!!$R2 745
18 TraesCS2B01G247300 chr2A 17916436 17917152 716 True 337.0 337 76.139000 1559 2273 1 chr2A.!!$R1 714
19 TraesCS2B01G247300 chr4A 731503626 731504157 531 True 861.0 861 95.888000 2023 2554 1 chr4A.!!$R2 531
20 TraesCS2B01G247300 chr1D 30290814 30291981 1167 True 320.0 693 91.342333 1 714 3 chr1D.!!$R1 713
21 TraesCS2B01G247300 chr6D 7328816 7329506 690 False 405.5 652 89.681000 1487 2231 2 chr6D.!!$F1 744
22 TraesCS2B01G247300 chr5D 294158083 294159878 1795 True 266.0 531 91.960667 1 714 3 chr5D.!!$R2 713

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
780 1897 1.529152 TACGCCATGTCCACGAGTGT 61.529 55.0 2.36 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1635 4901 0.037232 GGTTAGTGCCTTCGCTGACT 60.037 55.0 1.84 0.0 38.77 3.41 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
193 443 7.566760 TTGACATGTACTCAACAATTGTTCT 57.433 32.000 20.85 9.03 42.70 3.01
411 1527 8.461222 TCAAGTTTCTGGCATAATTAGTTGATG 58.539 33.333 4.40 0.00 0.00 3.07
700 1817 4.253685 GCACCACAAGCTGTTCTTCTATA 58.746 43.478 0.00 0.00 31.27 1.31
714 1831 6.602406 TGTTCTTCTATAGTAGTCACTCCCAC 59.398 42.308 6.31 0.00 36.14 4.61
715 1832 6.323210 TCTTCTATAGTAGTCACTCCCACA 57.677 41.667 6.31 0.00 36.14 4.17
723 1840 5.445964 AGTAGTCACTCCCACAAAAACAAT 58.554 37.500 0.00 0.00 0.00 2.71
730 1847 4.202070 ACTCCCACAAAAACAATACCAACG 60.202 41.667 0.00 0.00 0.00 4.10
780 1897 1.529152 TACGCCATGTCCACGAGTGT 61.529 55.000 2.36 0.00 0.00 3.55
974 2095 4.276926 AGCAAAGCTAACAGAACAAGAAGG 59.723 41.667 0.00 0.00 36.99 3.46
991 2112 4.714632 AGAAGGCAGCACTAGTTTACAAA 58.285 39.130 0.00 0.00 0.00 2.83
1016 2137 0.955428 CCCATGGATTACCCGATGCG 60.955 60.000 15.22 0.00 37.93 4.73
1263 4517 1.153647 GGCCGTGACATCGACATGA 60.154 57.895 0.00 0.00 33.72 3.07
1289 4546 2.107178 GTACGTTCGATTAGGCGTGAG 58.893 52.381 0.00 0.00 38.10 3.51
1488 4745 1.596752 CTATATGGCGCCCGTTGCA 60.597 57.895 26.77 3.54 41.33 4.08
1628 4894 4.196193 ACAAGATTCGAACACAAGACCAA 58.804 39.130 0.00 0.00 0.00 3.67
1635 4901 2.608546 CGAACACAAGACCAACCGTTTA 59.391 45.455 0.00 0.00 0.00 2.01
1793 5069 2.294233 TCTGGACAGCTTTTTGTGATGC 59.706 45.455 0.00 0.00 0.00 3.91
2410 5891 5.398122 ACGATGAACAATTTTTAACTGCACG 59.602 36.000 0.00 0.00 0.00 5.34
2554 6047 7.984391 TGAACAATTTTGTGATATACGCTGAT 58.016 30.769 0.00 0.00 41.31 2.90
2555 6048 7.909641 TGAACAATTTTGTGATATACGCTGATG 59.090 33.333 0.00 0.00 41.31 3.07
2556 6049 7.320443 ACAATTTTGTGATATACGCTGATGT 57.680 32.000 0.00 0.00 40.49 3.06
2557 6050 7.409697 ACAATTTTGTGATATACGCTGATGTC 58.590 34.615 0.00 0.00 40.49 3.06
2558 6051 5.635549 TTTTGTGATATACGCTGATGTCG 57.364 39.130 0.00 0.00 0.00 4.35
2559 6052 3.282831 TGTGATATACGCTGATGTCGG 57.717 47.619 0.00 0.00 0.00 4.79
2560 6053 2.621526 TGTGATATACGCTGATGTCGGT 59.378 45.455 0.00 0.00 0.00 4.69
2561 6054 2.980476 GTGATATACGCTGATGTCGGTG 59.020 50.000 1.01 1.01 38.63 4.94
2562 6055 2.621526 TGATATACGCTGATGTCGGTGT 59.378 45.455 12.21 12.21 46.56 4.16
2564 6057 2.486951 ATACGCTGATGTCGGTGTAC 57.513 50.000 15.31 0.00 46.94 2.90
2565 6058 1.456296 TACGCTGATGTCGGTGTACT 58.544 50.000 10.37 0.00 43.49 2.73
2566 6059 1.456296 ACGCTGATGTCGGTGTACTA 58.544 50.000 6.26 0.00 43.49 1.82
2567 6060 1.400846 ACGCTGATGTCGGTGTACTAG 59.599 52.381 6.26 0.00 43.49 2.57
2568 6061 1.669265 CGCTGATGTCGGTGTACTAGA 59.331 52.381 0.00 0.00 0.00 2.43
2569 6062 2.286477 CGCTGATGTCGGTGTACTAGAG 60.286 54.545 0.00 0.00 0.00 2.43
2570 6063 2.683867 GCTGATGTCGGTGTACTAGAGT 59.316 50.000 0.00 0.00 0.00 3.24
2571 6064 3.875727 GCTGATGTCGGTGTACTAGAGTA 59.124 47.826 0.00 0.00 0.00 2.59
2572 6065 4.024725 GCTGATGTCGGTGTACTAGAGTAG 60.025 50.000 0.00 0.00 0.00 2.57
2573 6066 4.449131 TGATGTCGGTGTACTAGAGTAGG 58.551 47.826 0.00 0.00 0.00 3.18
2574 6067 3.272574 TGTCGGTGTACTAGAGTAGGG 57.727 52.381 0.00 0.00 0.00 3.53
2575 6068 2.092753 TGTCGGTGTACTAGAGTAGGGG 60.093 54.545 0.00 0.00 0.00 4.79
2576 6069 2.092699 GTCGGTGTACTAGAGTAGGGGT 60.093 54.545 0.00 0.00 0.00 4.95
2577 6070 3.134804 GTCGGTGTACTAGAGTAGGGGTA 59.865 52.174 0.00 0.00 0.00 3.69
2578 6071 3.134804 TCGGTGTACTAGAGTAGGGGTAC 59.865 52.174 0.00 0.00 36.19 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
193 443 8.453681 TCTACATATCAAACTGGACTATCCCTA 58.546 37.037 0.00 0.00 35.03 3.53
411 1527 2.579410 ACAATACTGGGTTCCACCAC 57.421 50.000 0.00 0.00 41.02 4.16
700 1817 4.497291 TGTTTTTGTGGGAGTGACTACT 57.503 40.909 0.00 0.00 40.66 2.57
714 1831 4.206200 GCTGTGTCGTTGGTATTGTTTTTG 59.794 41.667 0.00 0.00 0.00 2.44
715 1832 4.356289 GCTGTGTCGTTGGTATTGTTTTT 58.644 39.130 0.00 0.00 0.00 1.94
723 1840 0.034337 GAAGGGCTGTGTCGTTGGTA 59.966 55.000 0.00 0.00 0.00 3.25
730 1847 0.889306 ACGACTAGAAGGGCTGTGTC 59.111 55.000 0.00 0.00 0.00 3.67
780 1897 1.381872 GTAGCTGGGAGGGCTCTGA 60.382 63.158 0.00 0.00 40.74 3.27
832 1951 2.875080 AAGCAAAGCGTACGTCAATC 57.125 45.000 17.90 4.13 0.00 2.67
929 2050 3.751479 TGCCGCATCTGTATAGTTCAT 57.249 42.857 0.00 0.00 0.00 2.57
974 2095 6.086871 GGAATCTTTTGTAAACTAGTGCTGC 58.913 40.000 0.00 0.00 0.00 5.25
991 2112 3.053077 TCGGGTAATCCATGGGAATCTT 58.947 45.455 13.02 1.10 34.34 2.40
1026 2148 2.409870 CCGGAATCCTTGGTGCTGC 61.410 63.158 0.00 0.00 0.00 5.25
1034 2156 1.921869 ATGAACCGCCCGGAATCCTT 61.922 55.000 14.44 0.00 38.96 3.36
1263 4517 2.416431 GCCTAATCGAACGTACACCACT 60.416 50.000 0.00 0.00 0.00 4.00
1289 4546 1.127343 CACCCTGATCTCCTCCTTCC 58.873 60.000 0.00 0.00 0.00 3.46
1488 4745 4.060038 CCGACGCCTGTAACGGGT 62.060 66.667 0.00 0.00 41.41 5.28
1628 4894 0.669625 GCCTTCGCTGACTAAACGGT 60.670 55.000 0.00 0.00 0.00 4.83
1635 4901 0.037232 GGTTAGTGCCTTCGCTGACT 60.037 55.000 1.84 0.00 38.77 3.41
2113 5483 8.857694 AAGTAGGAAAAGGTTCATCGATTTTA 57.142 30.769 0.00 0.00 35.25 1.52
2249 5730 6.735678 AAAAAGTTCACCAACCATGAAAAC 57.264 33.333 0.00 0.00 37.80 2.43
2345 5826 9.502145 GTTCATTGTATATTTGAAAATCGCTCA 57.498 29.630 0.00 0.00 31.66 4.26
2410 5891 4.364860 ACTAAACCACAAAAATGTTCGCC 58.635 39.130 0.00 0.00 0.00 5.54
2554 6047 2.092753 CCCCTACTCTAGTACACCGACA 60.093 54.545 0.00 0.00 0.00 4.35
2555 6048 2.092699 ACCCCTACTCTAGTACACCGAC 60.093 54.545 0.00 0.00 0.00 4.79
2556 6049 2.200081 ACCCCTACTCTAGTACACCGA 58.800 52.381 0.00 0.00 0.00 4.69
2557 6050 2.725221 ACCCCTACTCTAGTACACCG 57.275 55.000 0.00 0.00 0.00 4.94
2558 6051 3.826524 GGTACCCCTACTCTAGTACACC 58.173 54.545 0.00 0.00 37.42 4.16


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

AutoCloner maintained by Alex Coulton.