Multiple sequence alignment - TraesCS4A01G345300

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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 TraesCS4A01G345300 chr4A 100.000 4584 0 0 1 4584 624922754 624918171 0.000000e+00 8466.0
1 TraesCS4A01G345300 chr4A 77.730 696 109 25 2219 2896 624875176 624874509 7.190000e-103 385.0
2 TraesCS4A01G345300 chr4A 77.778 675 105 24 2219 2875 624899099 624898452 1.560000e-99 374.0
3 TraesCS4A01G345300 chr4A 90.588 85 8 0 1868 1952 11296174 11296090 3.750000e-21 113.0
4 TraesCS4A01G345300 chr4A 89.412 85 9 0 1868 1952 170810923 170810839 1.740000e-19 108.0
5 TraesCS4A01G345300 chr4A 87.324 71 7 2 3517 3585 741849593 741849663 3.800000e-11 80.5
6 TraesCS4A01G345300 chr1A 97.721 2677 41 6 1 2676 570158278 570160935 0.000000e+00 4588.0
7 TraesCS4A01G345300 chr1A 98.230 1130 5 1 3455 4584 570161504 570162618 0.000000e+00 1962.0
8 TraesCS4A01G345300 chr1A 99.258 539 3 1 2669 3207 570160969 570161506 0.000000e+00 972.0
9 TraesCS4A01G345300 chr1A 77.630 675 106 24 2219 2875 570181666 570182313 7.250000e-98 368.0
10 TraesCS4A01G345300 chr1A 77.481 675 107 24 2219 2875 569192970 569193617 3.370000e-96 363.0
11 TraesCS4A01G345300 chr1A 94.475 181 10 0 673 853 41895322 41895142 3.490000e-71 279.0
12 TraesCS4A01G345300 chr1A 90.769 130 11 1 543 671 303946672 303946801 6.100000e-39 172.0
13 TraesCS4A01G345300 chr1A 100.000 31 0 0 3340 3370 569193797 569193827 1.780000e-04 58.4
14 TraesCS4A01G345300 chr1A 100.000 31 0 0 3340 3370 570182493 570182523 1.780000e-04 58.4
15 TraesCS4A01G345300 chr1A 100.000 29 0 0 3530 3558 6899323 6899295 2.000000e-03 54.7
16 TraesCS4A01G345300 chr5B 91.068 1657 109 17 2669 4299 687738429 687736786 0.000000e+00 2204.0
17 TraesCS4A01G345300 chr5B 93.798 903 39 6 968 1870 687740075 687739190 0.000000e+00 1341.0
18 TraesCS4A01G345300 chr5B 94.490 726 33 2 1950 2669 687739193 687738469 0.000000e+00 1112.0
19 TraesCS4A01G345300 chr5B 80.510 549 78 26 1299 1846 687745641 687746161 1.200000e-105 394.0
20 TraesCS4A01G345300 chr5B 91.667 180 15 0 1987 2166 687746210 687746389 2.740000e-62 250.0
21 TraesCS4A01G345300 chr5B 90.977 133 11 1 543 674 599701585 599701453 1.310000e-40 178.0
22 TraesCS4A01G345300 chr5B 85.047 107 13 3 18 123 687740542 687740438 6.270000e-19 106.0
23 TraesCS4A01G345300 chr5D 85.638 1504 117 40 3126 4584 545121369 545119920 0.000000e+00 1489.0
24 TraesCS4A01G345300 chr5D 94.613 724 30 5 1951 2669 545123985 545123266 0.000000e+00 1112.0
25 TraesCS4A01G345300 chr5D 92.920 452 25 4 2669 3116 545123227 545122779 0.000000e+00 651.0
26 TraesCS4A01G345300 chr5D 87.326 576 42 8 1282 1853 545124539 545123991 8.370000e-177 630.0
27 TraesCS4A01G345300 chr5D 90.741 324 20 4 968 1287 545124891 545124574 1.520000e-114 424.0
28 TraesCS4A01G345300 chr5D 86.466 133 18 0 2669 2801 545119440 545119308 3.700000e-31 147.0
29 TraesCS4A01G345300 chr6A 96.196 184 7 0 673 856 11769718 11769535 7.450000e-78 302.0
30 TraesCS4A01G345300 chr6A 93.370 181 12 0 673 853 61705313 61705493 7.560000e-68 268.0
31 TraesCS4A01G345300 chr6A 78.970 233 38 10 754 978 48638764 48638993 1.030000e-31 148.0
32 TraesCS4A01G345300 chr6A 91.011 89 8 0 1865 1953 445839011 445839099 2.240000e-23 121.0
33 TraesCS4A01G345300 chr7A 94.624 186 10 0 673 858 79811562 79811377 5.800000e-74 289.0
34 TraesCS4A01G345300 chr7A 92.437 119 8 1 854 971 383096112 383095994 7.890000e-38 169.0
35 TraesCS4A01G345300 chr7A 91.954 87 7 0 1868 1954 636701742 636701656 6.230000e-24 122.0
36 TraesCS4A01G345300 chr7A 90.110 91 8 1 1863 1952 1900094 1900184 2.900000e-22 117.0
37 TraesCS4A01G345300 chr7A 89.552 67 7 0 3509 3575 603560155 603560221 8.170000e-13 86.1
38 TraesCS4A01G345300 chr7A 91.228 57 5 0 1325 1381 692762431 692762487 1.370000e-10 78.7
39 TraesCS4A01G345300 chr2A 93.889 180 11 0 673 852 65086476 65086655 5.840000e-69 272.0
40 TraesCS4A01G345300 chr2A 86.631 187 25 0 1309 1495 107316622 107316808 1.670000e-49 207.0
41 TraesCS4A01G345300 chr2A 90.769 130 11 1 543 671 634878775 634878646 6.100000e-39 172.0
42 TraesCS4A01G345300 chr3B 92.818 181 13 0 673 853 827034062 827034242 3.520000e-66 263.0
43 TraesCS4A01G345300 chr3B 92.818 181 13 0 673 853 827580114 827580294 3.520000e-66 263.0
44 TraesCS4A01G345300 chr3B 90.769 130 11 1 543 671 254760819 254760690 6.100000e-39 172.0
45 TraesCS4A01G345300 chr3B 90.076 131 11 2 854 982 188638590 188638460 7.890000e-38 169.0
46 TraesCS4A01G345300 chr3B 92.437 119 8 1 854 971 377803487 377803369 7.890000e-38 169.0
47 TraesCS4A01G345300 chr3B 83.607 122 15 5 745 863 764529020 764528901 4.850000e-20 110.0
48 TraesCS4A01G345300 chr3B 81.944 72 13 0 3500 3571 279661155 279661084 1.380000e-05 62.1
49 TraesCS4A01G345300 chrUn 92.350 183 14 0 673 855 52887722 52887540 1.260000e-65 261.0
50 TraesCS4A01G345300 chrUn 90.476 126 11 1 543 667 17254995 17255120 1.020000e-36 165.0
51 TraesCS4A01G345300 chr2B 84.925 199 16 6 664 861 215794474 215794289 6.050000e-44 189.0
52 TraesCS4A01G345300 chr2D 91.538 130 10 1 543 671 385285516 385285387 1.310000e-40 178.0
53 TraesCS4A01G345300 chr2D 92.437 119 8 1 743 861 387733848 387733731 7.890000e-38 169.0
54 TraesCS4A01G345300 chr2D 89.412 85 9 0 1868 1952 57162645 57162729 1.740000e-19 108.0
55 TraesCS4A01G345300 chr3D 93.162 117 7 1 854 969 209677610 209677726 2.190000e-38 171.0
56 TraesCS4A01G345300 chr3D 90.000 130 12 1 543 671 79250504 79250375 2.840000e-37 167.0
57 TraesCS4A01G345300 chr3D 83.969 131 10 9 733 857 574280299 574280424 1.040000e-21 115.0
58 TraesCS4A01G345300 chr3D 82.895 76 11 2 3500 3574 196933151 196933077 2.960000e-07 67.6
59 TraesCS4A01G345300 chr1B 92.437 119 8 1 854 971 271369423 271369305 7.890000e-38 169.0
60 TraesCS4A01G345300 chr1B 80.508 118 13 9 743 855 470430248 470430360 1.060000e-11 82.4
61 TraesCS4A01G345300 chr7B 88.406 138 13 3 538 672 715795625 715795488 3.670000e-36 163.0
62 TraesCS4A01G345300 chr7B 79.259 135 28 0 1310 1444 679930676 679930542 1.360000e-15 95.3
63 TraesCS4A01G345300 chr4B 91.597 119 9 1 854 971 445751737 445751855 3.670000e-36 163.0
64 TraesCS4A01G345300 chr4B 90.984 122 10 1 854 974 451195747 451195626 3.670000e-36 163.0
65 TraesCS4A01G345300 chr6B 90.678 118 9 2 743 860 644660833 644660718 6.140000e-34 156.0
66 TraesCS4A01G345300 chr5A 81.218 197 16 6 669 865 681236818 681236643 6.180000e-29 139.0
67 TraesCS4A01G345300 chr5A 89.412 85 9 0 1868 1952 477542454 477542370 1.740000e-19 108.0
68 TraesCS4A01G345300 chr6D 92.941 85 6 0 1868 1952 413065931 413065847 1.730000e-24 124.0
69 TraesCS4A01G345300 chr3A 83.562 73 10 2 3500 3571 251328895 251328824 2.960000e-07 67.6


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 TraesCS4A01G345300 chr4A 624918171 624922754 4583 True 8466.000000 8466 100.000000 1 4584 1 chr4A.!!$R5 4583
1 TraesCS4A01G345300 chr4A 624874509 624875176 667 True 385.000000 385 77.730000 2219 2896 1 chr4A.!!$R3 677
2 TraesCS4A01G345300 chr4A 624898452 624899099 647 True 374.000000 374 77.778000 2219 2875 1 chr4A.!!$R4 656
3 TraesCS4A01G345300 chr1A 570158278 570162618 4340 False 2507.333333 4588 98.403000 1 4584 3 chr1A.!!$F3 4583
4 TraesCS4A01G345300 chr1A 570181666 570182523 857 False 213.200000 368 88.815000 2219 3370 2 chr1A.!!$F4 1151
5 TraesCS4A01G345300 chr1A 569192970 569193827 857 False 210.700000 363 88.740500 2219 3370 2 chr1A.!!$F2 1151
6 TraesCS4A01G345300 chr5B 687736786 687740542 3756 True 1190.750000 2204 91.100750 18 4299 4 chr5B.!!$R2 4281
7 TraesCS4A01G345300 chr5B 687745641 687746389 748 False 322.000000 394 86.088500 1299 2166 2 chr5B.!!$F1 867
8 TraesCS4A01G345300 chr5D 545119308 545124891 5583 True 742.166667 1489 89.617333 968 4584 6 chr5D.!!$R1 3616

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
720 740 1.154357 GCGGCGACCCTTAAAAACG 60.154 57.895 12.98 0.0 0.0 3.60 F
1818 1883 1.834263 ACCATCTTCTCCAGCTACCAC 59.166 52.381 0.00 0.0 0.0 4.16 F
2200 2285 0.031043 CGGTACACACAACTCGGTCA 59.969 55.000 0.00 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1820 1885 1.811558 GCGTGCATCACATGGATACCT 60.812 52.381 0.00 0.0 35.67 3.08 R
2624 2714 2.028876 CATCAATTGATGCAGAGGCCA 58.971 47.619 30.11 0.0 44.44 5.36 R
3809 5380 3.238788 TCGGATTAGGATAGCAGGTGA 57.761 47.619 0.00 0.0 0.00 4.02 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
54 56 3.128589 GCGCCCATGTTTCTCAAAAGATA 59.871 43.478 0.00 0.00 28.03 1.98
384 402 7.922382 ACATTAAAAAGGATTGGAGAGAGAGA 58.078 34.615 0.00 0.00 0.00 3.10
385 403 8.046107 ACATTAAAAAGGATTGGAGAGAGAGAG 58.954 37.037 0.00 0.00 0.00 3.20
501 520 5.940192 TTGACGTCTGACTTTGCAATTAT 57.060 34.783 17.92 0.00 0.00 1.28
552 571 5.927115 CGTTTCTTGCTTCTTACTACCTCTT 59.073 40.000 0.00 0.00 0.00 2.85
568 587 6.940867 ACTACCTCTTTTCTGGTTTATTGGTC 59.059 38.462 0.00 0.00 37.74 4.02
569 588 5.953571 ACCTCTTTTCTGGTTTATTGGTCT 58.046 37.500 0.00 0.00 31.62 3.85
571 590 7.523415 ACCTCTTTTCTGGTTTATTGGTCTTA 58.477 34.615 0.00 0.00 31.62 2.10
572 591 8.170730 ACCTCTTTTCTGGTTTATTGGTCTTAT 58.829 33.333 0.00 0.00 31.62 1.73
720 740 1.154357 GCGGCGACCCTTAAAAACG 60.154 57.895 12.98 0.00 0.00 3.60
898 918 6.825284 TTGTTGACATGCACTAACATTTTG 57.175 33.333 0.00 0.00 33.56 2.44
1459 1522 4.335416 CCAAGGATCTGGCAAAGTTCTAA 58.665 43.478 0.00 0.00 0.00 2.10
1818 1883 1.834263 ACCATCTTCTCCAGCTACCAC 59.166 52.381 0.00 0.00 0.00 4.16
1819 1884 1.139853 CCATCTTCTCCAGCTACCACC 59.860 57.143 0.00 0.00 0.00 4.61
1820 1885 1.833630 CATCTTCTCCAGCTACCACCA 59.166 52.381 0.00 0.00 0.00 4.17
1877 1950 3.570550 GTGCTACCTATGTACTCCCTCTG 59.429 52.174 0.00 0.00 0.00 3.35
2048 2127 0.904649 TCCTGTCAGACATCGCCATT 59.095 50.000 2.97 0.00 0.00 3.16
2182 2261 5.166398 CCCTGTAACTACTTAAGTTCACCG 58.834 45.833 14.49 3.76 45.64 4.94
2200 2285 0.031043 CGGTACACACAACTCGGTCA 59.969 55.000 0.00 0.00 0.00 4.02
2259 2348 2.386249 GCTACTGTAGACACTATGCGC 58.614 52.381 18.64 0.00 0.00 6.09
2260 2349 2.640831 CTACTGTAGACACTATGCGCG 58.359 52.381 9.22 0.00 0.00 6.86
2426 2515 1.274703 GGACTGGATCCTCAAGGGCA 61.275 60.000 14.23 0.00 45.22 5.36
2624 2714 7.104290 GTGGTAATTTAAAGAGAGTACTGCCT 58.896 38.462 0.00 0.00 0.00 4.75
3199 4762 6.255887 CCAAATTCTCCGTGACTTACTGATAC 59.744 42.308 0.00 0.00 0.00 2.24
3287 4851 6.605594 AGCATTATATTTTGAAACGGAGGGAA 59.394 34.615 0.00 0.00 0.00 3.97
3297 4861 1.998222 ACGGAGGGAAGGAGTATAGC 58.002 55.000 0.00 0.00 0.00 2.97
3332 4896 7.557719 AGGAAGAATTAAGGTGTTGATATGTGG 59.442 37.037 0.00 0.00 0.00 4.17
3514 5078 6.839124 ATGTTTCATTGCCTTAGATCAACA 57.161 33.333 0.00 0.00 0.00 3.33
3809 5380 1.004044 ACTTGCATGCAGAGCTAAGGT 59.996 47.619 21.50 0.23 0.00 3.50
4123 5705 3.093717 ACTCTATATGGTTTGCGTCGG 57.906 47.619 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
384 402 4.706476 CACAAAGTCAGATCCTCTCTCTCT 59.294 45.833 0.00 0.00 29.16 3.10
385 403 4.704540 TCACAAAGTCAGATCCTCTCTCTC 59.295 45.833 0.00 0.00 29.16 3.20
571 590 8.538701 TGGTCAAAATTTGGCACAGATTATAAT 58.461 29.630 12.62 0.00 42.53 1.28
572 591 7.901029 TGGTCAAAATTTGGCACAGATTATAA 58.099 30.769 12.62 0.00 42.53 0.98
675 695 8.417273 AAATACCATAGCCCGCTATTTAAAAT 57.583 30.769 6.48 0.00 37.16 1.82
916 936 9.941664 CCTCTATGTAATCTGTGCTAAATTTTG 57.058 33.333 0.00 0.00 0.00 2.44
1818 1883 2.224606 GTGCATCACATGGATACCTGG 58.775 52.381 0.00 0.00 36.39 4.45
1819 1884 1.869132 CGTGCATCACATGGATACCTG 59.131 52.381 0.00 0.00 38.31 4.00
1820 1885 1.811558 GCGTGCATCACATGGATACCT 60.812 52.381 0.00 0.00 35.67 3.08
1877 1950 9.069078 GCCAAAAACGTTTTTATATTCTAGGAC 57.931 33.333 32.12 19.43 38.23 3.85
1923 1996 8.283699 TCCCTTGGTCCTAAAATATAAAAACG 57.716 34.615 0.00 0.00 0.00 3.60
2182 2261 2.029290 AGATGACCGAGTTGTGTGTACC 60.029 50.000 0.00 0.00 0.00 3.34
2200 2285 2.233566 TCAGTTGGGCCTGCCAGAT 61.234 57.895 10.86 0.00 37.98 2.90
2624 2714 2.028876 CATCAATTGATGCAGAGGCCA 58.971 47.619 30.11 0.00 44.44 5.36
3224 4787 8.706322 AAGTTAACCTTTCTATGTTTGACCAT 57.294 30.769 0.88 0.00 0.00 3.55
3260 4824 7.444183 TCCCTCCGTTTCAAAATATAATGCTAG 59.556 37.037 0.00 0.00 0.00 3.42
3263 4827 6.385649 TCCCTCCGTTTCAAAATATAATGC 57.614 37.500 0.00 0.00 0.00 3.56
3514 5078 7.860918 GATGCACACATCCATCTATATTGAT 57.139 36.000 0.00 0.00 45.94 2.57
3809 5380 3.238788 TCGGATTAGGATAGCAGGTGA 57.761 47.619 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.