Multiple sequence alignment - TraesCS4D01G141400

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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 TraesCS4D01G141400 chr4D 100.000 2375 0 0 1 2375 125803740 125801366 0.000000e+00 4386.0
1 TraesCS4D01G141400 chr4D 98.109 1322 18 2 1 1315 125905298 125903977 0.000000e+00 2296.0
2 TraesCS4D01G141400 chr4D 97.169 989 18 5 1390 2375 125903980 125902999 0.000000e+00 1663.0
3 TraesCS4D01G141400 chr4D 93.846 975 36 4 901 1875 236671757 236670807 0.000000e+00 1447.0
4 TraesCS4D01G141400 chr4D 93.884 883 28 5 1 858 125913355 125912474 0.000000e+00 1308.0
5 TraesCS4D01G141400 chr4D 93.658 883 30 5 1 858 125811645 125810764 0.000000e+00 1297.0
6 TraesCS4D01G141400 chr4D 93.545 883 32 4 1 858 125895994 125896876 0.000000e+00 1291.0
7 TraesCS4D01G141400 chr4D 85.900 539 65 8 10 542 247983435 247983968 4.430000e-157 564.0
8 TraesCS4D01G141400 chr5D 96.663 1019 26 2 858 1875 140952366 140951355 0.000000e+00 1687.0
9 TraesCS4D01G141400 chr5D 95.984 1021 27 6 858 1875 29766787 29765778 0.000000e+00 1646.0
10 TraesCS4D01G141400 chr5D 94.799 1019 31 4 858 1875 384511228 384510231 0.000000e+00 1568.0
11 TraesCS4D01G141400 chr5D 94.216 1020 36 11 858 1875 401783456 401784454 0.000000e+00 1535.0
12 TraesCS4D01G141400 chr5D 94.268 471 20 5 1868 2332 29765753 29765284 0.000000e+00 713.0
13 TraesCS4D01G141400 chr5D 93.139 481 30 3 1856 2333 401784467 401784947 0.000000e+00 702.0
14 TraesCS4D01G141400 chr5D 82.548 785 105 24 1573 2332 161384091 161383314 0.000000e+00 662.0
15 TraesCS4D01G141400 chr5D 95.556 45 2 0 2331 2375 198210991 198211035 3.270000e-09 73.1
16 TraesCS4D01G141400 chr6D 95.191 1019 21 5 858 1875 297170608 297169617 0.000000e+00 1585.0
17 TraesCS4D01G141400 chr6D 84.799 1046 95 38 858 1875 46519801 46518792 0.000000e+00 992.0
18 TraesCS4D01G141400 chr6D 94.255 470 21 6 1868 2332 297169592 297169124 0.000000e+00 713.0
19 TraesCS4D01G141400 chr6D 95.556 45 2 0 2331 2375 106403350 106403394 3.270000e-09 73.1
20 TraesCS4D01G141400 chr1D 94.112 1019 38 7 858 1875 336729334 336728337 0.000000e+00 1530.0
21 TraesCS4D01G141400 chr1D 91.941 881 41 10 4 858 237119120 237118244 0.000000e+00 1206.0
22 TraesCS4D01G141400 chr1D 93.196 485 27 5 1856 2334 463791798 463791314 0.000000e+00 708.0
23 TraesCS4D01G141400 chr1D 93.004 486 29 4 1856 2336 336728324 336727839 0.000000e+00 704.0
24 TraesCS4D01G141400 chr7B 90.359 1058 58 27 859 1875 551235761 551236815 0.000000e+00 1349.0
25 TraesCS4D01G141400 chr7B 90.267 1048 62 23 859 1875 615588675 615587637 0.000000e+00 1334.0
26 TraesCS4D01G141400 chr7B 87.185 874 85 18 4 858 268049733 268048868 0.000000e+00 968.0
27 TraesCS4D01G141400 chr7D 92.332 952 36 11 925 1875 103542349 103543264 0.000000e+00 1319.0
28 TraesCS4D01G141400 chr7D 93.333 45 3 0 2331 2375 507057026 507056982 1.520000e-07 67.6
29 TraesCS4D01G141400 chr5A 90.098 1020 50 13 858 1875 178859781 178858811 0.000000e+00 1277.0
30 TraesCS4D01G141400 chr5A 91.086 976 37 13 901 1875 235675994 235676920 0.000000e+00 1275.0
31 TraesCS4D01G141400 chr3D 92.672 887 37 6 1 860 215676660 215677545 0.000000e+00 1253.0
32 TraesCS4D01G141400 chr3D 97.778 45 1 0 2331 2375 50173656 50173612 7.040000e-11 78.7
33 TraesCS4D01G141400 chr3D 95.556 45 2 0 2331 2375 460887662 460887618 3.270000e-09 73.1
34 TraesCS4D01G141400 chr2D 94.864 701 28 2 858 1557 239257741 239258434 0.000000e+00 1088.0
35 TraesCS4D01G141400 chr2D 93.429 487 26 5 1856 2336 645234811 645234325 0.000000e+00 717.0
36 TraesCS4D01G141400 chr4A 89.583 864 74 12 4 856 235344830 235343972 0.000000e+00 1083.0
37 TraesCS4D01G141400 chr4A 89.298 869 78 11 1 858 235352154 235351290 0.000000e+00 1075.0
38 TraesCS4D01G141400 chr1A 88.417 872 86 12 1 863 485653316 485654181 0.000000e+00 1037.0
39 TraesCS4D01G141400 chrUn 92.789 527 25 4 859 1384 38473555 38474069 0.000000e+00 750.0
40 TraesCS4D01G141400 chrUn 95.319 235 10 1 859 1092 312612934 312612700 2.880000e-99 372.0
41 TraesCS4D01G141400 chrUn 89.963 269 20 4 957 1222 281295904 281295640 8.130000e-90 340.0
42 TraesCS4D01G141400 chrUn 89.963 269 20 4 957 1222 281302824 281302560 8.130000e-90 340.0
43 TraesCS4D01G141400 chrUn 89.963 269 20 4 957 1222 291784071 291784335 8.130000e-90 340.0
44 TraesCS4D01G141400 chrUn 89.963 269 20 4 957 1222 291787076 291786812 8.130000e-90 340.0
45 TraesCS4D01G141400 chrUn 89.963 269 20 4 957 1222 389950698 389950434 8.130000e-90 340.0
46 TraesCS4D01G141400 chrUn 96.970 66 1 1 859 923 34512012 34512077 2.500000e-20 110.0
47 TraesCS4D01G141400 chrUn 96.970 66 1 1 859 923 281295966 281295901 2.500000e-20 110.0
48 TraesCS4D01G141400 chrUn 96.970 66 1 1 859 923 281302886 281302821 2.500000e-20 110.0
49 TraesCS4D01G141400 chrUn 96.970 66 1 1 859 923 291784009 291784074 2.500000e-20 110.0
50 TraesCS4D01G141400 chrUn 96.970 66 1 1 859 923 291787138 291787073 2.500000e-20 110.0
51 TraesCS4D01G141400 chrUn 96.970 66 1 1 859 923 301821960 301821895 2.500000e-20 110.0
52 TraesCS4D01G141400 chr6B 85.795 704 75 17 13 703 67065182 67064491 0.000000e+00 723.0
53 TraesCS4D01G141400 chr3A 93.139 481 29 4 1856 2332 702242556 702243036 0.000000e+00 702.0
54 TraesCS4D01G141400 chr3A 93.842 341 12 6 1538 1875 702242209 702242543 2.720000e-139 505.0
55 TraesCS4D01G141400 chr3B 85.481 489 33 16 1411 1875 318305174 318305648 2.140000e-130 475.0
56 TraesCS4D01G141400 chr3B 93.333 45 3 0 2331 2375 440688905 440688949 1.520000e-07 67.6
57 TraesCS4D01G141400 chr2B 95.556 45 2 0 2331 2375 144204193 144204149 3.270000e-09 73.1
58 TraesCS4D01G141400 chr4B 97.297 37 1 0 2331 2367 576381223 576381187 1.970000e-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 TraesCS4D01G141400 chr4D 125801366 125803740 2374 True 4386.0 4386 100.0000 1 2375 1 chr4D.!!$R1 2374
1 TraesCS4D01G141400 chr4D 125902999 125905298 2299 True 1979.5 2296 97.6390 1 2375 2 chr4D.!!$R5 2374
2 TraesCS4D01G141400 chr4D 236670807 236671757 950 True 1447.0 1447 93.8460 901 1875 1 chr4D.!!$R4 974
3 TraesCS4D01G141400 chr4D 125912474 125913355 881 True 1308.0 1308 93.8840 1 858 1 chr4D.!!$R3 857
4 TraesCS4D01G141400 chr4D 125810764 125811645 881 True 1297.0 1297 93.6580 1 858 1 chr4D.!!$R2 857
5 TraesCS4D01G141400 chr4D 125895994 125896876 882 False 1291.0 1291 93.5450 1 858 1 chr4D.!!$F1 857
6 TraesCS4D01G141400 chr4D 247983435 247983968 533 False 564.0 564 85.9000 10 542 1 chr4D.!!$F2 532
7 TraesCS4D01G141400 chr5D 140951355 140952366 1011 True 1687.0 1687 96.6630 858 1875 1 chr5D.!!$R1 1017
8 TraesCS4D01G141400 chr5D 384510231 384511228 997 True 1568.0 1568 94.7990 858 1875 1 chr5D.!!$R3 1017
9 TraesCS4D01G141400 chr5D 29765284 29766787 1503 True 1179.5 1646 95.1260 858 2332 2 chr5D.!!$R4 1474
10 TraesCS4D01G141400 chr5D 401783456 401784947 1491 False 1118.5 1535 93.6775 858 2333 2 chr5D.!!$F2 1475
11 TraesCS4D01G141400 chr5D 161383314 161384091 777 True 662.0 662 82.5480 1573 2332 1 chr5D.!!$R2 759
12 TraesCS4D01G141400 chr6D 297169124 297170608 1484 True 1149.0 1585 94.7230 858 2332 2 chr6D.!!$R2 1474
13 TraesCS4D01G141400 chr6D 46518792 46519801 1009 True 992.0 992 84.7990 858 1875 1 chr6D.!!$R1 1017
14 TraesCS4D01G141400 chr1D 237118244 237119120 876 True 1206.0 1206 91.9410 4 858 1 chr1D.!!$R1 854
15 TraesCS4D01G141400 chr1D 336727839 336729334 1495 True 1117.0 1530 93.5580 858 2336 2 chr1D.!!$R3 1478
16 TraesCS4D01G141400 chr7B 551235761 551236815 1054 False 1349.0 1349 90.3590 859 1875 1 chr7B.!!$F1 1016
17 TraesCS4D01G141400 chr7B 615587637 615588675 1038 True 1334.0 1334 90.2670 859 1875 1 chr7B.!!$R2 1016
18 TraesCS4D01G141400 chr7B 268048868 268049733 865 True 968.0 968 87.1850 4 858 1 chr7B.!!$R1 854
19 TraesCS4D01G141400 chr7D 103542349 103543264 915 False 1319.0 1319 92.3320 925 1875 1 chr7D.!!$F1 950
20 TraesCS4D01G141400 chr5A 178858811 178859781 970 True 1277.0 1277 90.0980 858 1875 1 chr5A.!!$R1 1017
21 TraesCS4D01G141400 chr5A 235675994 235676920 926 False 1275.0 1275 91.0860 901 1875 1 chr5A.!!$F1 974
22 TraesCS4D01G141400 chr3D 215676660 215677545 885 False 1253.0 1253 92.6720 1 860 1 chr3D.!!$F1 859
23 TraesCS4D01G141400 chr2D 239257741 239258434 693 False 1088.0 1088 94.8640 858 1557 1 chr2D.!!$F1 699
24 TraesCS4D01G141400 chr4A 235343972 235344830 858 True 1083.0 1083 89.5830 4 856 1 chr4A.!!$R1 852
25 TraesCS4D01G141400 chr4A 235351290 235352154 864 True 1075.0 1075 89.2980 1 858 1 chr4A.!!$R2 857
26 TraesCS4D01G141400 chr1A 485653316 485654181 865 False 1037.0 1037 88.4170 1 863 1 chr1A.!!$F1 862
27 TraesCS4D01G141400 chrUn 38473555 38474069 514 False 750.0 750 92.7890 859 1384 1 chrUn.!!$F2 525
28 TraesCS4D01G141400 chr6B 67064491 67065182 691 True 723.0 723 85.7950 13 703 1 chr6B.!!$R1 690
29 TraesCS4D01G141400 chr3A 702242209 702243036 827 False 603.5 702 93.4905 1538 2332 2 chr3A.!!$F1 794

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
192 193 2.16301 CCATGACATGAGACTTGGCAAC 59.837 50.0 17.24 0.0 35.3 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2068 2387 1.920574 CTGACGTGGCAGAATTACGAG 59.079 52.381 0.0 0.0 40.01 4.18 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
192 193 2.163010 CCATGACATGAGACTTGGCAAC 59.837 50.000 17.24 0.00 35.30 4.17
669 720 7.105588 GTCCTATACACATGGCATGATCATTA 58.894 38.462 32.74 15.38 0.00 1.90
1259 1316 1.098050 GCGGCAATCAAGATGAAGGT 58.902 50.000 0.00 0.00 0.00 3.50
1270 1327 3.625649 AGATGAAGGTGGAAGAAGCTC 57.374 47.619 0.00 0.00 0.00 4.09
2021 2340 4.567318 GGCTTGCCCCATGTAGAG 57.433 61.111 0.00 0.00 0.00 2.43
2277 2600 5.861222 AAAAGGTCACAAAAGCAAAACTG 57.139 34.783 0.00 0.00 0.00 3.16
2347 2670 0.178068 AGTGTATGCCCGAATCGCTT 59.822 50.000 0.00 0.00 0.00 4.68
2368 2691 2.606519 TAGCGACTGGGGGCTGTT 60.607 61.111 0.00 0.00 40.32 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 121 7.441017 CCTCAAAACCATTTCTGTCCATTTTA 58.559 34.615 0.00 0.0 0.00 1.52
192 193 7.427214 TGCCACATATGACATGTTTGATAATG 58.573 34.615 10.38 1.8 0.00 1.90
195 196 6.515365 GCATGCCACATATGACATGTTTGATA 60.515 38.462 24.93 0.0 41.51 2.15
669 720 6.077322 TCTCATTGATCCAAAAACCTTTCCT 58.923 36.000 0.00 0.0 0.00 3.36
1270 1327 2.127496 CTTGTCGCGTGCAGCTTG 60.127 61.111 5.77 0.0 45.59 4.01
2021 2340 2.513897 CCCGGTCCATTTCGGCTC 60.514 66.667 0.00 0.0 44.45 4.70
2068 2387 1.920574 CTGACGTGGCAGAATTACGAG 59.079 52.381 0.00 0.0 40.01 4.18
2277 2600 4.393062 CACTATTGGTCACTGAATGGTCAC 59.607 45.833 0.00 0.0 0.00 3.67
2347 2670 1.075525 AGCCCCCAGTCGCTACATA 60.076 57.895 0.00 0.0 32.26 2.29


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

AutoCloner maintained by Alex Coulton.