Multiple sequence alignment - TraesCS7D01G435000

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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 TraesCS7D01G435000 chr7D 100.000 2669 0 0 1 2669 554531666 554528998 0.000000e+00 4929.0
1 TraesCS7D01G435000 chr7D 90.826 981 53 18 950 1915 554474716 554473758 0.000000e+00 1279.0
2 TraesCS7D01G435000 chr7D 86.425 1105 94 26 761 1827 554421532 554420446 0.000000e+00 1158.0
3 TraesCS7D01G435000 chr7D 86.373 932 83 18 761 1661 554500782 554499864 0.000000e+00 977.0
4 TraesCS7D01G435000 chr7D 93.461 627 34 2 1334 1954 554486278 554485653 0.000000e+00 924.0
5 TraesCS7D01G435000 chr7D 98.824 425 4 1 542 966 554475533 554475110 0.000000e+00 756.0
6 TraesCS7D01G435000 chr7D 96.499 457 14 2 1 457 554476002 554475548 0.000000e+00 754.0
7 TraesCS7D01G435000 chr7D 91.068 459 38 3 1 457 554468677 554468220 3.770000e-173 617.0
8 TraesCS7D01G435000 chr7D 90.625 384 30 6 1 381 554519839 554519459 3.070000e-139 505.0
9 TraesCS7D01G435000 chr7D 90.104 384 32 6 1 381 554513567 554513187 6.640000e-136 494.0
10 TraesCS7D01G435000 chr7D 94.203 69 2 2 535 601 554519405 554519337 1.310000e-18 104.0
11 TraesCS7D01G435000 chr7D 94.118 68 3 1 535 601 554468213 554468146 4.700000e-18 102.0
12 TraesCS7D01G435000 chr7B 90.652 1380 87 17 588 1954 600350756 600352106 0.000000e+00 1796.0
13 TraesCS7D01G435000 chr7B 90.611 1374 89 16 588 1954 600389086 600390426 0.000000e+00 1786.0
14 TraesCS7D01G435000 chr7B 88.957 1313 91 26 588 1893 600363740 600365005 0.000000e+00 1572.0
15 TraesCS7D01G435000 chr7B 88.652 1313 95 21 588 1893 600311113 600312378 0.000000e+00 1550.0
16 TraesCS7D01G435000 chr7B 92.566 834 43 9 910 1728 600093538 600094367 0.000000e+00 1179.0
17 TraesCS7D01G435000 chr7B 92.045 616 23 6 3 601 600028381 600028987 0.000000e+00 843.0
18 TraesCS7D01G435000 chr7B 89.737 380 36 3 223 601 600310140 600310517 1.440000e-132 483.0
19 TraesCS7D01G435000 chr7B 88.201 339 30 6 635 968 600093206 600093539 1.930000e-106 396.0
20 TraesCS7D01G435000 chr7B 91.878 197 16 0 1758 1954 600094365 600094561 2.620000e-70 276.0
21 TraesCS7D01G435000 chr7B 85.593 118 10 2 588 699 600388246 600388362 1.680000e-22 117.0
22 TraesCS7D01G435000 chr7A 87.085 1115 80 32 761 1826 639740847 639741946 0.000000e+00 1203.0
23 TraesCS7D01G435000 chr7A 88.797 964 101 7 1707 2667 639580214 639581173 0.000000e+00 1175.0
24 TraesCS7D01G435000 chr7A 90.723 830 37 11 635 1432 639654380 639655201 0.000000e+00 1070.0
25 TraesCS7D01G435000 chr7A 90.413 751 39 17 771 1521 639579098 639579815 0.000000e+00 957.0
26 TraesCS7D01G435000 chr7A 88.690 725 79 3 1942 2664 639600428 639601151 0.000000e+00 881.0
27 TraesCS7D01G435000 chr7A 93.934 577 29 4 945 1521 639598929 639599499 0.000000e+00 867.0
28 TraesCS7D01G435000 chr7A 91.068 459 34 5 1 457 639595726 639596179 4.880000e-172 614.0
29 TraesCS7D01G435000 chr7A 89.070 430 28 10 1439 1854 639599486 639599910 1.420000e-142 516.0
30 TraesCS7D01G435000 chr7A 79.156 782 130 29 1899 2665 16638412 16639175 6.590000e-141 510.0
31 TraesCS7D01G435000 chr7A 92.945 326 15 3 588 913 639598614 639598931 4.020000e-128 468.0
32 TraesCS7D01G435000 chr7A 92.994 314 19 3 143 455 639695769 639696080 3.130000e-124 455.0
33 TraesCS7D01G435000 chr7A 86.247 429 38 10 1446 1866 639659228 639659643 1.890000e-121 446.0
34 TraesCS7D01G435000 chr7A 92.787 305 21 1 299 602 639578027 639578331 8.770000e-120 440.0
35 TraesCS7D01G435000 chr7A 91.481 270 14 7 189 457 639645282 639645543 1.950000e-96 363.0
36 TraesCS7D01G435000 chr7A 91.353 266 16 3 3 266 639577772 639578032 9.090000e-95 357.0
37 TraesCS7D01G435000 chr7A 92.135 89 6 1 1 88 639691551 639691639 1.000000e-24 124.0
38 TraesCS7D01G435000 chr7A 86.792 106 10 2 596 699 639578990 639579093 6.040000e-22 115.0
39 TraesCS7D01G435000 chr7A 92.647 68 3 2 535 601 639645550 639645616 2.190000e-16 97.1
40 TraesCS7D01G435000 chr7A 89.706 68 6 1 535 601 639696090 639696157 4.730000e-13 86.1
41 TraesCS7D01G435000 chr6B 79.507 771 126 23 1909 2665 132935688 132936440 1.100000e-143 520.0
42 TraesCS7D01G435000 chr4A 79.064 769 136 18 1909 2665 555797972 555797217 3.070000e-139 505.0
43 TraesCS7D01G435000 chr2B 79.319 764 116 35 1909 2650 741143623 741144366 5.130000e-137 497.0
44 TraesCS7D01G435000 chr3D 79.265 762 115 33 1909 2648 573450875 573450135 2.390000e-135 492.0
45 TraesCS7D01G435000 chr2D 79.058 764 120 32 1908 2650 566283367 566284111 3.090000e-134 488.0
46 TraesCS7D01G435000 chr4B 78.682 774 129 25 1909 2665 546723582 546724336 1.440000e-132 483.0
47 TraesCS7D01G435000 chr6D 88.235 85 10 0 457 541 20756840 20756756 4.700000e-18 102.0


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 TraesCS7D01G435000 chr7D 554528998 554531666 2668 True 4929.000000 4929 100.000000 1 2669 1 chr7D.!!$R5 2668
1 TraesCS7D01G435000 chr7D 554420446 554421532 1086 True 1158.000000 1158 86.425000 761 1827 1 chr7D.!!$R1 1066
2 TraesCS7D01G435000 chr7D 554499864 554500782 918 True 977.000000 977 86.373000 761 1661 1 chr7D.!!$R3 900
3 TraesCS7D01G435000 chr7D 554473758 554476002 2244 True 929.666667 1279 95.383000 1 1915 3 chr7D.!!$R7 1914
4 TraesCS7D01G435000 chr7D 554485653 554486278 625 True 924.000000 924 93.461000 1334 1954 1 chr7D.!!$R2 620
5 TraesCS7D01G435000 chr7D 554468146 554468677 531 True 359.500000 617 92.593000 1 601 2 chr7D.!!$R6 600
6 TraesCS7D01G435000 chr7D 554519337 554519839 502 True 304.500000 505 92.414000 1 601 2 chr7D.!!$R8 600
7 TraesCS7D01G435000 chr7B 600350756 600352106 1350 False 1796.000000 1796 90.652000 588 1954 1 chr7B.!!$F2 1366
8 TraesCS7D01G435000 chr7B 600363740 600365005 1265 False 1572.000000 1572 88.957000 588 1893 1 chr7B.!!$F3 1305
9 TraesCS7D01G435000 chr7B 600310140 600312378 2238 False 1016.500000 1550 89.194500 223 1893 2 chr7B.!!$F5 1670
10 TraesCS7D01G435000 chr7B 600388246 600390426 2180 False 951.500000 1786 88.102000 588 1954 2 chr7B.!!$F6 1366
11 TraesCS7D01G435000 chr7B 600028381 600028987 606 False 843.000000 843 92.045000 3 601 1 chr7B.!!$F1 598
12 TraesCS7D01G435000 chr7B 600093206 600094561 1355 False 617.000000 1179 90.881667 635 1954 3 chr7B.!!$F4 1319
13 TraesCS7D01G435000 chr7A 639740847 639741946 1099 False 1203.000000 1203 87.085000 761 1826 1 chr7A.!!$F5 1065
14 TraesCS7D01G435000 chr7A 639654380 639655201 821 False 1070.000000 1070 90.723000 635 1432 1 chr7A.!!$F2 797
15 TraesCS7D01G435000 chr7A 639595726 639601151 5425 False 669.200000 881 91.141400 1 2664 5 chr7A.!!$F7 2663
16 TraesCS7D01G435000 chr7A 639577772 639581173 3401 False 608.800000 1175 90.028400 3 2667 5 chr7A.!!$F6 2664
17 TraesCS7D01G435000 chr7A 16638412 16639175 763 False 510.000000 510 79.156000 1899 2665 1 chr7A.!!$F1 766
18 TraesCS7D01G435000 chr6B 132935688 132936440 752 False 520.000000 520 79.507000 1909 2665 1 chr6B.!!$F1 756
19 TraesCS7D01G435000 chr4A 555797217 555797972 755 True 505.000000 505 79.064000 1909 2665 1 chr4A.!!$R1 756
20 TraesCS7D01G435000 chr2B 741143623 741144366 743 False 497.000000 497 79.319000 1909 2650 1 chr2B.!!$F1 741
21 TraesCS7D01G435000 chr3D 573450135 573450875 740 True 492.000000 492 79.265000 1909 2648 1 chr3D.!!$R1 739
22 TraesCS7D01G435000 chr2D 566283367 566284111 744 False 488.000000 488 79.058000 1908 2650 1 chr2D.!!$F1 742
23 TraesCS7D01G435000 chr4B 546723582 546724336 754 False 483.000000 483 78.682000 1909 2665 1 chr4B.!!$F1 756

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
344 368 1.067846 TGACAGTGTGCTACGATGACC 60.068 52.381 0.0 0.0 0.0 4.02 F
1263 4728 1.377202 GCGGCTGGAGATGGACAAA 60.377 57.895 0.0 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1471 5002 0.411452 TCTCTGCCAGTCTCCTCCTT 59.589 55.0 0.0 0.0 0.0 3.36 R
2107 6305 1.029681 ACAGCACAGACACGTAGACA 58.970 50.0 0.0 0.0 0.0 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
27 28 7.696872 CGATCTTGTTATCGTATTCGGATACAT 59.303 37.037 14.22 8.82 42.93 2.29
344 368 1.067846 TGACAGTGTGCTACGATGACC 60.068 52.381 0.00 0.00 0.00 4.02
528 552 3.740832 GCCATTTTAACCACAGCAAACTC 59.259 43.478 0.00 0.00 0.00 3.01
655 3624 9.774742 GATGGATATATTTGCTATTTTCCGTTC 57.225 33.333 0.00 0.00 0.00 3.95
1116 4578 2.494918 GTCTATGTCACCGGCGCT 59.505 61.111 7.64 0.00 0.00 5.92
1201 4666 2.890961 GGAACCTCCTTAGCGCGC 60.891 66.667 26.66 26.66 32.53 6.86
1263 4728 1.377202 GCGGCTGGAGATGGACAAA 60.377 57.895 0.00 0.00 0.00 2.83
1471 5002 0.525882 TGACGACGACAACGCAGAAA 60.526 50.000 0.00 0.00 43.96 2.52
1769 5518 3.485381 GGTTTAATCGAAGAGGAAAGCGC 60.485 47.826 0.00 0.00 43.63 5.92
1830 5579 1.143889 TGGTTGGTGAATGTGGCTGTA 59.856 47.619 0.00 0.00 0.00 2.74
1954 6144 8.144478 GCACAGTTGATCTATTATAGACCAAGA 58.856 37.037 9.16 0.00 38.94 3.02
2107 6305 2.594592 GCACACGCCACCTCCTTT 60.595 61.111 0.00 0.00 0.00 3.11
2108 6306 2.908073 GCACACGCCACCTCCTTTG 61.908 63.158 0.00 0.00 0.00 2.77
2112 6310 0.320374 CACGCCACCTCCTTTGTCTA 59.680 55.000 0.00 0.00 0.00 2.59
2125 6323 2.134201 TTGTCTACGTGTCTGTGCTG 57.866 50.000 0.00 0.00 0.00 4.41
2236 6440 6.944234 ATCTACACATCATACGACTCAGAA 57.056 37.500 0.00 0.00 0.00 3.02
2242 6446 5.987953 CACATCATACGACTCAGAATCCAAT 59.012 40.000 0.00 0.00 0.00 3.16
2249 6453 9.476202 CATACGACTCAGAATCCAATTATAACA 57.524 33.333 0.00 0.00 0.00 2.41
2296 6502 6.725834 ACAATCCTAACAAATTCCACCTTGAT 59.274 34.615 0.00 0.00 0.00 2.57
2312 6518 5.301045 CACCTTGATGAATATTCTGCACCAT 59.699 40.000 16.24 1.16 0.00 3.55
2315 6521 6.072618 CCTTGATGAATATTCTGCACCATCTC 60.073 42.308 16.24 1.44 33.55 2.75
2321 6527 2.787473 TTCTGCACCATCTCGGATTT 57.213 45.000 0.00 0.00 38.63 2.17
2333 6539 6.267699 ACCATCTCGGATTTATCTATGTGTCA 59.732 38.462 0.00 0.00 38.63 3.58
2390 6598 1.825474 GAGCACTGCTACTACTCCCAA 59.175 52.381 2.71 0.00 39.88 4.12
2430 6643 4.187694 CTGCAACTGTAGATCCTTCCTTC 58.812 47.826 0.00 0.00 0.00 3.46
2453 6666 1.002792 GTCTTTTCCGCAGTCAACACC 60.003 52.381 0.00 0.00 0.00 4.16
2492 6706 6.842437 TTCTCATTACTCTAGTTGTGCTCT 57.158 37.500 0.00 0.00 0.00 4.09
2541 6756 2.510613 TCACACACCGATCACTGTCTA 58.489 47.619 0.00 0.00 0.00 2.59
2545 6760 2.417586 CACACCGATCACTGTCTACGTA 59.582 50.000 0.00 0.00 0.00 3.57
2557 6773 8.343974 TCACTGTCTACGTAAAAGTAAACAAG 57.656 34.615 0.00 0.00 28.51 3.16
2667 6886 0.320374 GTCATCCTGTGTCACCCGAA 59.680 55.000 0.00 0.00 0.00 4.30
2668 6887 0.608130 TCATCCTGTGTCACCCGAAG 59.392 55.000 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 104 7.765819 CCGAGGTATCATTCAATATATCAGCAA 59.234 37.037 0.00 0.00 0.00 3.91
263 277 5.181748 GCACTATGAGTTCATGTTTCTCCT 58.818 41.667 4.90 0.00 37.15 3.69
344 368 3.570559 ACACCGTGTTGTTTGAAACTTG 58.429 40.909 9.69 0.00 0.00 3.16
528 552 8.946085 TCATATTCTGTTTTACACTTGGCTTAG 58.054 33.333 0.00 0.00 0.00 2.18
655 3624 6.945938 TTATATTTGTTGGAACATACCGGG 57.054 37.500 6.32 0.00 39.30 5.73
699 3670 7.406031 TGGAGATTCGTACTTTAGATTCTGT 57.594 36.000 0.00 0.00 30.22 3.41
904 3880 0.321671 TGTGCTCCTAGTGGCTGAAC 59.678 55.000 5.90 0.00 0.00 3.18
1116 4578 1.738350 CTCTTCGAGTCGAGCAGGTAA 59.262 52.381 15.88 0.00 37.14 2.85
1201 4666 2.811317 GTTCTCCGCCGACAGCAG 60.811 66.667 0.00 0.00 44.04 4.24
1263 4728 0.532862 CCACGTGGAAGCAACACTCT 60.533 55.000 31.31 0.00 36.71 3.24
1471 5002 0.411452 TCTCTGCCAGTCTCCTCCTT 59.589 55.000 0.00 0.00 0.00 3.36
1769 5518 7.475015 CAGGAATTACACAATACCAGAACATG 58.525 38.462 0.00 0.00 0.00 3.21
1830 5579 8.416329 GGTGAAAATGAGCATATATGAAACCTT 58.584 33.333 17.10 2.04 0.00 3.50
1866 6036 3.578282 TCGCATCAGAGATGCCCTTATAA 59.422 43.478 22.11 1.69 41.71 0.98
1903 6073 6.590292 CGCCTCGGATTAATTCTAACATATGT 59.410 38.462 1.41 1.41 0.00 2.29
2027 6224 1.300233 GGAGGAGCGCCGTAATCAG 60.300 63.158 2.29 0.00 39.96 2.90
2103 6301 1.792949 GCACAGACACGTAGACAAAGG 59.207 52.381 0.00 0.00 0.00 3.11
2107 6305 1.029681 ACAGCACAGACACGTAGACA 58.970 50.000 0.00 0.00 0.00 3.41
2108 6306 2.135664 AACAGCACAGACACGTAGAC 57.864 50.000 0.00 0.00 0.00 2.59
2112 6310 2.526304 ACATAACAGCACAGACACGT 57.474 45.000 0.00 0.00 0.00 4.49
2205 6409 7.715686 AGTCGTATGATGTGTAGATAGAAGACA 59.284 37.037 0.00 0.00 0.00 3.41
2285 6491 5.357878 GTGCAGAATATTCATCAAGGTGGAA 59.642 40.000 17.56 0.00 0.00 3.53
2296 6502 3.387699 TCCGAGATGGTGCAGAATATTCA 59.612 43.478 17.56 0.00 39.52 2.57
2312 6518 8.879759 GTTTTTGACACATAGATAAATCCGAGA 58.120 33.333 0.00 0.00 0.00 4.04
2315 6521 8.122952 GGAGTTTTTGACACATAGATAAATCCG 58.877 37.037 0.00 0.00 0.00 4.18
2321 6527 9.378551 GTACATGGAGTTTTTGACACATAGATA 57.621 33.333 0.00 0.00 30.21 1.98
2390 6598 3.181445 TGCAGGTGGAGTCATGTTTAGTT 60.181 43.478 0.00 0.00 0.00 2.24
2430 6643 2.354510 TGTTGACTGCGGAAAAGACAAG 59.645 45.455 0.00 0.00 31.61 3.16
2453 6666 8.237267 AGTAATGAGAAACTTAATTTTGCTCGG 58.763 33.333 0.00 0.00 0.00 4.63
2492 6706 6.510478 CGTTGAACGGATACTTTGAAAGTTGA 60.510 38.462 16.49 0.00 39.29 3.18
2567 6783 5.279506 CGGCTAACTCCTATATGTGGTGATT 60.280 44.000 5.90 1.53 0.00 2.57


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

AutoCloner maintained by Alex Coulton.