Multiple sequence alignment - TraesCS2D01G061800

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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 TraesCS2D01G061800 chr2D 100.000 3639 0 0 1 3639 25620995 25624633 0.000000e+00 6721.0
1 TraesCS2D01G061800 chr2D 100.000 637 0 0 3943 4579 25624937 25625573 0.000000e+00 1177.0
2 TraesCS2D01G061800 chr2D 85.426 892 96 18 632 1507 30258022 30257149 0.000000e+00 896.0
3 TraesCS2D01G061800 chr2D 86.052 803 75 21 2600 3368 549931671 549930872 0.000000e+00 828.0
4 TraesCS2D01G061800 chr2D 85.679 803 78 22 2600 3368 550660884 550661683 0.000000e+00 811.0
5 TraesCS2D01G061800 chr2D 85.448 804 79 21 2600 3368 549741125 549740325 0.000000e+00 802.0
6 TraesCS2D01G061800 chr2D 85.536 802 77 22 2603 3368 551152063 551151265 0.000000e+00 802.0
7 TraesCS2D01G061800 chr2D 84.837 798 78 20 2600 3362 550253876 550253087 0.000000e+00 763.0
8 TraesCS2D01G061800 chr2D 83.607 671 70 17 3943 4577 550662546 550663212 1.100000e-165 593.0
9 TraesCS2D01G061800 chr2D 83.631 672 67 16 3943 4577 549930008 549929343 3.950000e-165 592.0
10 TraesCS2D01G061800 chr2D 83.206 655 71 8 3943 4560 551150401 551149749 8.600000e-157 564.0
11 TraesCS2D01G061800 chr2D 83.243 555 63 19 1 539 30258569 30258029 2.480000e-132 483.0
12 TraesCS2D01G061800 chr2D 87.037 162 18 2 1589 1747 30257150 30256989 3.640000e-41 180.0
13 TraesCS2D01G061800 chr2D 86.806 144 11 3 3482 3618 551872992 551872850 2.210000e-33 154.0
14 TraesCS2D01G061800 chr2D 85.417 144 13 3 3482 3618 551429694 551429836 4.780000e-30 143.0
15 TraesCS2D01G061800 chr2D 86.364 132 11 2 3482 3606 549739735 549739604 2.220000e-28 137.0
16 TraesCS2D01G061800 chr2D 86.364 132 11 2 3482 3606 550252492 550252361 2.220000e-28 137.0
17 TraesCS2D01G061800 chr2D 92.727 55 4 0 3389 3443 549740326 549740272 3.800000e-11 80.5
18 TraesCS2D01G061800 chr2D 94.444 36 2 0 2566 2601 25623594 25623629 6.400000e-04 56.5
19 TraesCS2D01G061800 chr2B 98.314 3617 55 6 1 3615 41199763 41196151 0.000000e+00 6336.0
20 TraesCS2D01G061800 chr2B 97.671 644 7 5 3943 4579 41195732 41195090 0.000000e+00 1099.0
21 TraesCS2D01G061800 chr2B 85.314 892 97 22 632 1507 49087806 49088679 0.000000e+00 891.0
22 TraesCS2D01G061800 chr2B 85.821 804 76 21 2600 3368 656000007 655999207 0.000000e+00 819.0
23 TraesCS2D01G061800 chr2B 83.614 653 70 7 3943 4560 656360378 656359728 3.070000e-161 579.0
24 TraesCS2D01G061800 chr2B 86.252 531 58 6 4059 4577 656239078 656238551 3.090000e-156 562.0
25 TraesCS2D01G061800 chr2B 85.380 513 55 13 35 539 49087299 49087799 8.780000e-142 514.0
26 TraesCS2D01G061800 chr2B 87.273 165 18 2 1586 1747 49088675 49088839 7.820000e-43 185.0
27 TraesCS2D01G061800 chr2B 87.121 132 10 2 3482 3606 655998617 655998486 4.780000e-30 143.0
28 TraesCS2D01G061800 chr2B 84.507 142 14 3 3484 3618 657078881 657078741 2.870000e-27 134.0
29 TraesCS2D01G061800 chr2B 92.727 55 4 0 3389 3443 655999208 655999154 3.800000e-11 80.5
30 TraesCS2D01G061800 chr2B 96.970 33 1 0 2569 2601 41197160 41197128 6.400000e-04 56.5
31 TraesCS2D01G061800 chr2A 97.756 3521 62 11 1 3519 28021034 28017529 0.000000e+00 6048.0
32 TraesCS2D01G061800 chr2A 97.645 637 14 1 3943 4579 28017071 28016436 0.000000e+00 1092.0
33 TraesCS2D01G061800 chr2A 84.624 891 104 21 632 1507 32150693 32149821 0.000000e+00 856.0
34 TraesCS2D01G061800 chr2A 85.979 485 49 12 63 539 32151173 32150700 6.840000e-138 501.0
35 TraesCS2D01G061800 chr2A 96.575 146 0 1 3483 3623 28017529 28017384 2.130000e-58 237.0
36 TraesCS2D01G061800 chr2A 88.889 162 15 2 1589 1747 32149822 32149661 3.610000e-46 196.0
37 TraesCS2D01G061800 chr2A 93.333 105 5 2 3482 3585 692643284 692643181 2.210000e-33 154.0
38 TraesCS2D01G061800 chr2A 87.059 85 10 1 1506 1590 744446983 744447066 1.360000e-15 95.3
39 TraesCS2D01G061800 chr2A 96.970 33 1 0 2569 2601 28018441 28018409 6.400000e-04 56.5
40 TraesCS2D01G061800 chr5D 85.947 797 81 15 2600 3368 395722909 395723702 0.000000e+00 822.0
41 TraesCS2D01G061800 chr5D 85.445 797 85 15 2600 3368 395921148 395921941 0.000000e+00 800.0
42 TraesCS2D01G061800 chr5D 94.545 55 3 0 3389 3443 395723701 395723755 8.160000e-13 86.1
43 TraesCS2D01G061800 chr5D 94.545 55 3 0 3389 3443 395921940 395921994 8.160000e-13 86.1
44 TraesCS2D01G061800 chr5B 85.571 797 82 17 2600 3368 475987558 475988349 0.000000e+00 804.0
45 TraesCS2D01G061800 chr5B 84.720 661 70 11 3943 4577 475989213 475989868 2.320000e-177 632.0
46 TraesCS2D01G061800 chr5A 84.289 802 88 20 2601 3368 501824461 501825258 0.000000e+00 749.0
47 TraesCS2D01G061800 chr5A 85.354 635 61 15 3943 4551 501817765 501818393 3.010000e-176 628.0
48 TraesCS2D01G061800 chr5A 85.354 635 61 15 3943 4551 501826121 501826749 3.010000e-176 628.0
49 TraesCS2D01G061800 chrUn 100.000 396 0 0 1662 2057 479220824 479220429 0.000000e+00 732.0
50 TraesCS2D01G061800 chr6A 100.000 31 0 0 1501 1531 581806258 581806288 1.780000e-04 58.4
51 TraesCS2D01G061800 chr6A 100.000 29 0 0 1503 1531 499207211 499207183 2.000000e-03 54.7
52 TraesCS2D01G061800 chr1A 90.698 43 3 1 1551 1593 10211060 10211101 6.400000e-04 56.5
53 TraesCS2D01G061800 chr7B 100.000 28 0 0 1507 1534 701170285 701170258 8.000000e-03 52.8


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 TraesCS2D01G061800 chr2D 25620995 25625573 4578 False 2651.500000 6721 98.148000 1 4579 3 chr2D.!!$F2 4578
1 TraesCS2D01G061800 chr2D 549929343 549931671 2328 True 710.000000 828 84.841500 2600 4577 2 chr2D.!!$R4 1977
2 TraesCS2D01G061800 chr2D 550660884 550663212 2328 False 702.000000 811 84.643000 2600 4577 2 chr2D.!!$F3 1977
3 TraesCS2D01G061800 chr2D 551149749 551152063 2314 True 683.000000 802 84.371000 2603 4560 2 chr2D.!!$R6 1957
4 TraesCS2D01G061800 chr2D 30256989 30258569 1580 True 519.666667 896 85.235333 1 1747 3 chr2D.!!$R2 1746
5 TraesCS2D01G061800 chr2D 550252361 550253876 1515 True 450.000000 763 85.600500 2600 3606 2 chr2D.!!$R5 1006
6 TraesCS2D01G061800 chr2D 549739604 549741125 1521 True 339.833333 802 88.179667 2600 3606 3 chr2D.!!$R3 1006
7 TraesCS2D01G061800 chr2B 41195090 41199763 4673 True 2497.166667 6336 97.651667 1 4579 3 chr2B.!!$R4 4578
8 TraesCS2D01G061800 chr2B 656359728 656360378 650 True 579.000000 579 83.614000 3943 4560 1 chr2B.!!$R2 617
9 TraesCS2D01G061800 chr2B 656238551 656239078 527 True 562.000000 562 86.252000 4059 4577 1 chr2B.!!$R1 518
10 TraesCS2D01G061800 chr2B 49087299 49088839 1540 False 530.000000 891 85.989000 35 1747 3 chr2B.!!$F1 1712
11 TraesCS2D01G061800 chr2B 655998486 656000007 1521 True 347.500000 819 88.556333 2600 3606 3 chr2B.!!$R5 1006
12 TraesCS2D01G061800 chr2A 28016436 28021034 4598 True 1858.375000 6048 97.236500 1 4579 4 chr2A.!!$R2 4578
13 TraesCS2D01G061800 chr2A 32149661 32151173 1512 True 517.666667 856 86.497333 63 1747 3 chr2A.!!$R3 1684
14 TraesCS2D01G061800 chr5D 395722909 395723755 846 False 454.050000 822 90.246000 2600 3443 2 chr5D.!!$F1 843
15 TraesCS2D01G061800 chr5D 395921148 395921994 846 False 443.050000 800 89.995000 2600 3443 2 chr5D.!!$F2 843
16 TraesCS2D01G061800 chr5B 475987558 475989868 2310 False 718.000000 804 85.145500 2600 4577 2 chr5B.!!$F1 1977
17 TraesCS2D01G061800 chr5A 501824461 501826749 2288 False 688.500000 749 84.821500 2601 4551 2 chr5A.!!$F2 1950
18 TraesCS2D01G061800 chr5A 501817765 501818393 628 False 628.000000 628 85.354000 3943 4551 1 chr5A.!!$F1 608

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
25 26 2.361104 TGCGGCTGGGTTTCCATC 60.361 61.111 0.0 0.0 43.11 3.51 F
1273 1316 0.035152 TCATGGTGATGCTGTGGTCC 60.035 55.000 0.0 0.0 0.00 4.46 F
1459 1502 1.404181 GCTGATAGGTGTTCGTGCTGA 60.404 52.381 0.0 0.0 0.00 4.26 F
2340 2470 2.101209 GACGTGGGTTGCTGTTGACG 62.101 60.000 0.0 0.0 0.00 4.35 F
3250 3418 2.543777 TTATTGGGCGAGGATGCTAC 57.456 50.000 0.0 0.0 34.52 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1525 1568 1.141053 GGAACCAGCGGGACATCTTAT 59.859 52.381 10.86 0.0 38.05 1.73 R
2571 2701 2.084610 TCACTGATGAGTTCAAGGCG 57.915 50.000 0.00 0.0 32.78 5.52 R
2867 2999 2.923121 TGCAACTTTGACTCTGAAGCT 58.077 42.857 0.00 0.0 0.00 3.74 R
3329 3506 3.677424 GCCAAAACCAACAGTAAAGTGCA 60.677 43.478 0.00 0.0 0.00 4.57 R
4398 5255 1.712977 CTGCTTCATGCGCCCTCTTC 61.713 60.000 4.18 0.0 46.63 2.87 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
25 26 2.361104 TGCGGCTGGGTTTCCATC 60.361 61.111 0.00 0.00 43.11 3.51
590 609 6.252599 TGGTCTTATGTTATGAAGCCTCAT 57.747 37.500 2.80 2.80 44.71 2.90
941 977 8.970859 AATCTTAATGTACATCTCCTTTCCTG 57.029 34.615 9.23 0.00 0.00 3.86
942 978 7.496346 TCTTAATGTACATCTCCTTTCCTGT 57.504 36.000 9.23 0.00 0.00 4.00
943 979 8.603898 TCTTAATGTACATCTCCTTTCCTGTA 57.396 34.615 9.23 0.00 0.00 2.74
944 980 9.042450 TCTTAATGTACATCTCCTTTCCTGTAA 57.958 33.333 9.23 0.00 0.00 2.41
945 981 9.667107 CTTAATGTACATCTCCTTTCCTGTAAA 57.333 33.333 9.23 0.00 0.00 2.01
948 984 8.738645 ATGTACATCTCCTTTCCTGTAAATTC 57.261 34.615 1.41 0.00 0.00 2.17
1152 1189 7.624344 GCAGTACTACTAAGCTTCCATTGTTTG 60.624 40.741 0.00 0.00 0.00 2.93
1273 1316 0.035152 TCATGGTGATGCTGTGGTCC 60.035 55.000 0.00 0.00 0.00 4.46
1459 1502 1.404181 GCTGATAGGTGTTCGTGCTGA 60.404 52.381 0.00 0.00 0.00 4.26
1484 1527 4.664688 ACATCCCAAGTTGAGGATTCTT 57.335 40.909 18.14 7.61 41.05 2.52
1509 1552 7.445121 TGAGTTCCTGATCATCCATAATACAC 58.555 38.462 0.00 0.00 0.00 2.90
1555 1598 2.358898 CCCGCTGGTTCCATTTAATCTG 59.641 50.000 0.00 0.00 0.00 2.90
2057 2186 5.057149 GCAATATTACCCAGACAGTAGTGG 58.943 45.833 1.92 0.00 0.00 4.00
2246 2375 6.411376 TCTTATTTTGTAGCTGAATCCCGAA 58.589 36.000 0.00 0.00 0.00 4.30
2340 2470 2.101209 GACGTGGGTTGCTGTTGACG 62.101 60.000 0.00 0.00 0.00 4.35
2571 2701 4.343526 AGACATGGTCAGATCTATGGTCAC 59.656 45.833 7.86 0.00 34.60 3.67
2637 2767 3.072330 TCATCAGTGAAGCACCCTTGTTA 59.928 43.478 0.00 0.00 34.49 2.41
2867 2999 7.194112 TCTATGGTTGATGAATACCAGAACA 57.806 36.000 0.00 0.00 46.82 3.18
3250 3418 2.543777 TTATTGGGCGAGGATGCTAC 57.456 50.000 0.00 0.00 34.52 3.58
3260 3428 3.379240 CGAGGATGCTACTGAATCTGTG 58.621 50.000 2.93 0.00 0.00 3.66
3601 4325 6.311445 AGAGCATACGTAATTCAACAGTTCTG 59.689 38.462 0.00 0.00 0.00 3.02
3632 4402 6.485830 TCTACCTCTTATTGTTGATGAGGG 57.514 41.667 11.35 0.00 46.12 4.30
3638 4408 2.134789 ATTGTTGATGAGGGTGCTCC 57.865 50.000 0.00 0.00 0.00 4.70
4263 5106 6.715280 ACAGTATCACATGAATCCTTCTGTT 58.285 36.000 0.00 0.00 0.00 3.16
4347 5197 5.294306 AGTTGTGATAAGGATTACACATGCG 59.706 40.000 0.00 0.00 39.99 4.73
4398 5255 3.057245 TGTCACTGATGGAAGAGAAGACG 60.057 47.826 0.00 0.00 0.00 4.18
4407 5264 0.528470 AAGAGAAGACGAAGAGGGCG 59.472 55.000 0.00 0.00 0.00 6.13
4515 5374 9.381033 GAACTCTATCCTTCCTTTAACCTTAAC 57.619 37.037 0.00 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 7.719778 TGCTAGCTCTATAACATTCAATGTG 57.280 36.000 17.23 0.00 44.07 3.21
551 570 8.436778 ACATAAGACCATTATTACATGCTACCA 58.563 33.333 0.00 0.00 0.00 3.25
552 571 8.848474 ACATAAGACCATTATTACATGCTACC 57.152 34.615 0.00 0.00 0.00 3.18
590 609 5.227569 TGGTTGAAGCTTCTCTGTAATCA 57.772 39.130 26.09 15.31 0.00 2.57
940 976 4.635765 GCAGCAGATGTACCTGAATTTACA 59.364 41.667 3.57 0.00 36.29 2.41
941 977 4.635765 TGCAGCAGATGTACCTGAATTTAC 59.364 41.667 3.57 0.00 36.29 2.01
942 978 4.842574 TGCAGCAGATGTACCTGAATTTA 58.157 39.130 3.57 0.00 36.29 1.40
943 979 3.689347 TGCAGCAGATGTACCTGAATTT 58.311 40.909 3.57 0.00 36.29 1.82
944 980 3.354948 TGCAGCAGATGTACCTGAATT 57.645 42.857 3.57 0.00 36.29 2.17
945 981 3.276857 CTTGCAGCAGATGTACCTGAAT 58.723 45.455 0.00 0.00 36.29 2.57
946 982 2.703416 CTTGCAGCAGATGTACCTGAA 58.297 47.619 0.00 0.00 36.29 3.02
947 983 1.676916 GCTTGCAGCAGATGTACCTGA 60.677 52.381 0.00 0.00 41.89 3.86
948 984 0.731417 GCTTGCAGCAGATGTACCTG 59.269 55.000 0.00 0.00 41.89 4.00
1152 1189 5.415701 TGGACATATCAGTTGCTTTTCCTTC 59.584 40.000 0.00 0.00 0.00 3.46
1273 1316 6.662414 TGAAATACTGGATTTGCTAGAACG 57.338 37.500 1.80 0.00 37.90 3.95
1459 1502 5.669447 AGAATCCTCAACTTGGGATGTAGAT 59.331 40.000 10.76 0.00 41.00 1.98
1484 1527 7.445121 GTGTATTATGGATGATCAGGAACTCA 58.555 38.462 0.09 0.00 34.60 3.41
1509 1552 9.495572 GGACATCTTATATTTAGAAACAGAGGG 57.504 37.037 0.00 0.00 0.00 4.30
1525 1568 1.141053 GGAACCAGCGGGACATCTTAT 59.859 52.381 10.86 0.00 38.05 1.73
1555 1598 6.903479 CGTTCCTAAATATAAGGCGTTTTGAC 59.097 38.462 0.00 0.00 33.84 3.18
2057 2186 7.121168 TCAAGTTCTTTGATTGATGGTGGATAC 59.879 37.037 0.00 0.00 40.82 2.24
2340 2470 6.015940 ACAATCACTTGGAATTCTTCAGGAAC 60.016 38.462 5.23 0.00 35.27 3.62
2501 2631 4.478206 ACCTCATAGATGTTCCACTGTG 57.522 45.455 0.00 0.00 0.00 3.66
2571 2701 2.084610 TCACTGATGAGTTCAAGGCG 57.915 50.000 0.00 0.00 32.78 5.52
2637 2767 7.178451 CCTGTTACCTCCATGGAAAGTATTTTT 59.822 37.037 17.00 0.00 39.27 1.94
2867 2999 2.923121 TGCAACTTTGACTCTGAAGCT 58.077 42.857 0.00 0.00 0.00 3.74
3250 3418 4.126208 ACAGCTGAGATCACAGATTCAG 57.874 45.455 23.35 12.72 39.94 3.02
3260 3428 3.726607 CCCACATCTTACAGCTGAGATC 58.273 50.000 23.35 0.00 30.43 2.75
3329 3506 3.677424 GCCAAAACCAACAGTAAAGTGCA 60.677 43.478 0.00 0.00 0.00 4.57
3378 3560 6.147821 GCACAAGTAAGAGTTCAGCTTATTCA 59.852 38.462 0.00 0.00 31.22 2.57
3601 4325 7.773149 TCAACAATAAGAGGTAGAGCTAGAAC 58.227 38.462 0.00 0.00 0.00 3.01
4263 5106 7.124573 TCTCATAGCACTTGGAAATAAGCTA 57.875 36.000 0.00 0.00 35.09 3.32
4347 5197 1.798813 CGTGTAGCTGACAAAAGGGAC 59.201 52.381 0.00 0.00 40.66 4.46
4398 5255 1.712977 CTGCTTCATGCGCCCTCTTC 61.713 60.000 4.18 0.00 46.63 2.87
4407 5264 2.736721 TGTTTCTACGACTGCTTCATGC 59.263 45.455 0.00 0.00 43.25 4.06


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

AutoCloner maintained by Alex Coulton.