Multiple sequence alignment - TraesCS5B01G118500

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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 TraesCS5B01G118500 chr5B 100.000 2438 0 0 1 2438 208769155 208766718 0.000000e+00 4503.0
1 TraesCS5B01G118500 chr5B 93.785 1609 75 9 1 1595 512585383 512583786 0.000000e+00 2394.0
2 TraesCS5B01G118500 chr5B 88.482 191 9 5 1621 1811 512583679 512583502 4.080000e-53 219.0
3 TraesCS5B01G118500 chr5B 90.511 137 11 2 511 647 512584758 512584624 1.930000e-41 180.0
4 TraesCS5B01G118500 chr5B 90.511 137 11 2 633 767 512584880 512584744 1.930000e-41 180.0
5 TraesCS5B01G118500 chr5B 89.051 137 13 2 511 647 208768523 208768389 4.170000e-38 169.0
6 TraesCS5B01G118500 chr5B 89.051 137 13 2 633 767 208768645 208768509 4.170000e-38 169.0
7 TraesCS5B01G118500 chr2B 93.654 1828 72 15 1 1811 357880701 357882501 0.000000e+00 2693.0
8 TraesCS5B01G118500 chr2B 91.642 670 19 17 1803 2438 198424541 198425207 0.000000e+00 893.0
9 TraesCS5B01G118500 chr2B 86.583 559 69 3 1150 1704 711218358 711217802 1.600000e-171 612.0
10 TraesCS5B01G118500 chr2B 90.511 137 11 2 511 647 357881314 357881448 1.930000e-41 180.0
11 TraesCS5B01G118500 chr2B 90.071 141 8 6 633 767 357881188 357881328 6.930000e-41 178.0
12 TraesCS5B01G118500 chr2B 91.818 110 7 2 1803 1910 539705391 539705500 4.200000e-33 152.0
13 TraesCS5B01G118500 chr3B 94.970 1312 50 5 515 1811 324238090 324236780 0.000000e+00 2043.0
14 TraesCS5B01G118500 chr3B 89.793 676 62 4 1136 1811 393843024 393843692 0.000000e+00 859.0
15 TraesCS5B01G118500 chr3B 92.949 468 22 3 1 467 324238542 324238085 0.000000e+00 671.0
16 TraesCS5B01G118500 chr3B 85.822 663 56 13 1 647 393754730 393755370 0.000000e+00 669.0
17 TraesCS5B01G118500 chr3B 87.374 396 25 7 630 1014 393755247 393755628 4.820000e-117 431.0
18 TraesCS5B01G118500 chr3B 90.511 137 11 2 511 647 324237968 324237834 1.930000e-41 180.0
19 TraesCS5B01G118500 chr3B 89.051 137 9 3 637 767 324238090 324237954 5.390000e-37 165.0
20 TraesCS5B01G118500 chr6B 91.629 669 21 15 1803 2438 384179338 384180004 0.000000e+00 893.0
21 TraesCS5B01G118500 chr2D 83.836 928 106 17 904 1808 117194281 117193375 0.000000e+00 843.0
22 TraesCS5B01G118500 chr2D 88.511 235 20 7 1803 2030 458734746 458734980 6.640000e-71 278.0
23 TraesCS5B01G118500 chr2D 84.375 288 23 10 633 908 117194665 117194388 1.860000e-66 263.0
24 TraesCS5B01G118500 chr7B 83.752 757 96 12 899 1637 381905571 381906318 0.000000e+00 691.0
25 TraesCS5B01G118500 chr7B 92.544 228 4 2 1835 2062 353971054 353971268 5.060000e-82 315.0
26 TraesCS5B01G118500 chr7B 83.916 286 25 9 635 908 381905195 381905471 1.120000e-63 254.0
27 TraesCS5B01G118500 chr3A 83.665 753 98 11 904 1640 442907134 442906391 0.000000e+00 686.0
28 TraesCS5B01G118500 chr3A 84.528 265 21 8 656 908 442907497 442907241 6.730000e-61 244.0
29 TraesCS5B01G118500 chr3A 82.011 189 24 6 272 455 292181049 292180866 4.200000e-33 152.0
30 TraesCS5B01G118500 chrUn 86.047 559 67 5 1150 1704 94937093 94937644 7.510000e-165 590.0
31 TraesCS5B01G118500 chr2A 81.113 683 71 29 1803 2438 602124288 602124959 6.060000e-136 494.0
32 TraesCS5B01G118500 chr2A 81.152 191 26 8 1803 1991 277137306 277137124 7.030000e-31 145.0
33 TraesCS5B01G118500 chr1B 95.614 228 6 1 1835 2062 359604236 359604459 1.780000e-96 363.0
34 TraesCS5B01G118500 chr5A 83.217 286 26 10 635 908 691995954 691995679 2.420000e-60 243.0
35 TraesCS5B01G118500 chr4A 88.652 141 16 0 1581 1721 738580811 738580671 3.220000e-39 172.0
36 TraesCS5B01G118500 chr6D 81.818 99 12 3 328 420 28036347 28036249 7.230000e-11 78.7
37 TraesCS5B01G118500 chr1A 79.412 102 15 4 325 420 8167074 8167175 1.560000e-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 TraesCS5B01G118500 chr5B 208766718 208769155 2437 True 1613.666667 4503 92.700667 1 2438 3 chr5B.!!$R1 2437
1 TraesCS5B01G118500 chr5B 512583502 512585383 1881 True 743.250000 2394 90.822250 1 1811 4 chr5B.!!$R2 1810
2 TraesCS5B01G118500 chr2B 357880701 357882501 1800 False 1017.000000 2693 91.412000 1 1811 3 chr2B.!!$F3 1810
3 TraesCS5B01G118500 chr2B 198424541 198425207 666 False 893.000000 893 91.642000 1803 2438 1 chr2B.!!$F1 635
4 TraesCS5B01G118500 chr2B 711217802 711218358 556 True 612.000000 612 86.583000 1150 1704 1 chr2B.!!$R1 554
5 TraesCS5B01G118500 chr3B 393843024 393843692 668 False 859.000000 859 89.793000 1136 1811 1 chr3B.!!$F1 675
6 TraesCS5B01G118500 chr3B 324236780 324238542 1762 True 764.750000 2043 91.870250 1 1811 4 chr3B.!!$R1 1810
7 TraesCS5B01G118500 chr3B 393754730 393755628 898 False 550.000000 669 86.598000 1 1014 2 chr3B.!!$F2 1013
8 TraesCS5B01G118500 chr6B 384179338 384180004 666 False 893.000000 893 91.629000 1803 2438 1 chr6B.!!$F1 635
9 TraesCS5B01G118500 chr2D 117193375 117194665 1290 True 553.000000 843 84.105500 633 1808 2 chr2D.!!$R1 1175
10 TraesCS5B01G118500 chr7B 381905195 381906318 1123 False 472.500000 691 83.834000 635 1637 2 chr7B.!!$F2 1002
11 TraesCS5B01G118500 chr3A 442906391 442907497 1106 True 465.000000 686 84.096500 656 1640 2 chr3A.!!$R2 984
12 TraesCS5B01G118500 chrUn 94937093 94937644 551 False 590.000000 590 86.047000 1150 1704 1 chrUn.!!$F1 554
13 TraesCS5B01G118500 chr2A 602124288 602124959 671 False 494.000000 494 81.113000 1803 2438 1 chr2A.!!$F1 635

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
978 1126 0.326264 ATGGAGCTTTTCGAGGCAGT 59.674 50.0 9.16 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2321 2628 2.437085 ACCCCTATAGCAGCCAAAAC 57.563 50.0 0.0 0.0 0.0 2.43 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
34 35 2.131067 GCTTCCCTCCTCCCTCTCG 61.131 68.421 0.00 0.00 0.00 4.04
35 36 1.308326 CTTCCCTCCTCCCTCTCGT 59.692 63.158 0.00 0.00 0.00 4.18
48 49 1.791103 CTCTCGTCGGCCTCATCTCC 61.791 65.000 0.00 0.00 0.00 3.71
142 143 1.361993 GCGTCATCTCGAGAGGCAT 59.638 57.895 21.83 0.77 44.01 4.40
202 219 0.898320 CCTCCTCATCAGTCCAACGT 59.102 55.000 0.00 0.00 0.00 3.99
240 257 1.003580 GCCTCCTCTTTGGTGTCATCA 59.996 52.381 0.00 0.00 37.07 3.07
277 297 5.623956 TTTTTCTTCTAGGCCGATGGATA 57.376 39.130 0.00 0.00 0.00 2.59
487 508 2.489722 GCCCAACCTCTGTTCTTTGATC 59.510 50.000 0.00 0.00 30.42 2.92
604 629 9.787435 TTTTATTGGCAGTAAGAAGTTAAGAGA 57.213 29.630 2.62 0.00 0.00 3.10
618 643 4.218635 AGTTAAGAGATCAAGCGTGAGACA 59.781 41.667 8.63 0.00 37.14 3.41
622 647 3.194329 AGAGATCAAGCGTGAGACATCAA 59.806 43.478 8.63 0.00 37.14 2.57
691 716 1.211567 ACGGTGGGATGGGGATTCAA 61.212 55.000 0.00 0.00 0.00 2.69
728 753 3.844211 TGGCAGTATGAGGTTAAGAGGTT 59.156 43.478 0.00 0.00 39.69 3.50
820 846 7.935405 ACTGGTTTAAAGGGAATCCATACTTA 58.065 34.615 0.09 0.00 34.83 2.24
944 1092 3.784178 TCACTGAGGTGGAAATCTCTCT 58.216 45.455 0.00 0.00 43.17 3.10
978 1126 0.326264 ATGGAGCTTTTCGAGGCAGT 59.674 50.000 9.16 0.00 0.00 4.40
979 1127 0.603707 TGGAGCTTTTCGAGGCAGTG 60.604 55.000 9.16 0.00 0.00 3.66
1028 1176 2.114625 CATGCCCATCCCGATGCT 59.885 61.111 0.00 0.00 37.49 3.79
1065 1213 1.815421 GAGCATCACCGCCGACAAT 60.815 57.895 0.00 0.00 33.17 2.71
1153 1313 0.106015 AAGCAAGAAGGCCAAGGTGT 60.106 50.000 5.01 0.00 0.00 4.16
1185 1345 0.753479 ACAACGGCATGGTCACCAAA 60.753 50.000 0.00 0.00 36.95 3.28
1282 1442 5.107913 CCGTCAATTGTTTAATGTTGCACTG 60.108 40.000 5.13 0.00 0.00 3.66
1325 1485 0.957395 CAGTTTGGCCTGTCGAGCAT 60.957 55.000 3.32 0.00 0.00 3.79
1466 1634 3.205338 AGTTTCCTGCAACATTTTTGGC 58.795 40.909 0.00 0.00 0.00 4.52
1956 2216 7.014808 GGTTATCAGTCTAGGAGCTTTATCTGT 59.985 40.741 0.00 0.00 0.00 3.41
2002 2262 9.806203 TGCCATGTAAATATTCAAATTCAGAAG 57.194 29.630 0.00 0.00 0.00 2.85
2068 2347 6.934048 AAGCTAGAGATAAGTTTTCCATGC 57.066 37.500 0.00 0.00 0.00 4.06
2069 2348 5.994250 AGCTAGAGATAAGTTTTCCATGCA 58.006 37.500 0.00 0.00 0.00 3.96
2071 2350 6.485984 AGCTAGAGATAAGTTTTCCATGCATG 59.514 38.462 20.19 20.19 0.00 4.06
2074 2353 9.330063 CTAGAGATAAGTTTTCCATGCATGTAA 57.670 33.333 24.58 13.43 0.00 2.41
2075 2354 8.579850 AGAGATAAGTTTTCCATGCATGTAAA 57.420 30.769 24.58 18.74 0.00 2.01
2076 2355 9.193806 AGAGATAAGTTTTCCATGCATGTAAAT 57.806 29.630 24.58 12.20 0.00 1.40
2127 2431 1.429930 TTCCCAGTGGACTGTTGCTA 58.570 50.000 11.95 0.00 41.57 3.49
2202 2509 4.514401 CAATCCTTAGCGGTAGGAAACTT 58.486 43.478 14.09 4.97 44.59 2.66
2240 2547 1.334599 CCCGTTCCATTTTGTGACACG 60.335 52.381 0.22 0.00 34.63 4.49
2321 2628 0.949105 GTAGGGTTGTGTGCTGGACG 60.949 60.000 0.00 0.00 0.00 4.79
2333 2640 1.234615 GCTGGACGTTTTGGCTGCTA 61.235 55.000 0.00 0.00 0.00 3.49
2423 2730 7.391620 TGTCTTGATTATCGTAGAAAGGGTTT 58.608 34.615 0.00 0.00 43.58 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 1.758514 TGGAGGAGATGAGGCCGAC 60.759 63.158 0.00 0.00 0.00 4.79
35 36 1.758514 GTGGAGGAGATGAGGCCGA 60.759 63.158 0.00 0.00 0.00 5.54
48 49 2.294078 GGAGGTGGTGGAGGTGGAG 61.294 68.421 0.00 0.00 0.00 3.86
142 143 1.302431 CGTCATGGAAGGTGTGGCA 60.302 57.895 0.00 0.00 0.00 4.92
202 219 0.681733 GCGGATCTGCCAATCCTCTA 59.318 55.000 16.13 0.00 42.68 2.43
277 297 0.684805 CACTCCTCTTCGCCTACCCT 60.685 60.000 0.00 0.00 0.00 4.34
448 469 2.610479 GGGCTAAAAGGCAAGAAAGTGC 60.610 50.000 2.75 0.00 43.44 4.40
487 508 6.824553 TCTTTATCCTCTGAATCATGGACAG 58.175 40.000 7.17 0.73 0.00 3.51
604 629 4.005650 ACATTTGATGTCTCACGCTTGAT 58.994 39.130 0.00 0.00 39.92 2.57
618 643 8.655935 AACTAAAATCTCCCTTGACATTTGAT 57.344 30.769 0.00 0.00 0.00 2.57
714 739 1.968493 ACGCTCAACCTCTTAACCTCA 59.032 47.619 0.00 0.00 0.00 3.86
779 804 3.426615 ACCAGTAGTCTCTCTTCACAGG 58.573 50.000 0.00 0.00 0.00 4.00
820 846 6.706295 TGTTGAATTGGAAGAAACCTTGTTT 58.294 32.000 0.00 0.00 0.00 2.83
978 1126 2.438254 GTGCGGCATCATGTCCCA 60.438 61.111 5.72 0.00 0.00 4.37
979 1127 3.576356 CGTGCGGCATCATGTCCC 61.576 66.667 5.72 0.00 0.00 4.46
1153 1313 1.720805 CCGTTGTCACCATCGATGAA 58.279 50.000 26.86 9.61 36.17 2.57
1185 1345 6.117975 ACTTGGGATTTGATTTTGCTGAAT 57.882 33.333 0.00 0.00 0.00 2.57
1282 1442 3.359695 TTGGGCCAAGGTGTTAGTATC 57.640 47.619 16.66 0.00 0.00 2.24
1466 1634 4.813161 AGATATGTGGAAGCAAGATGAACG 59.187 41.667 0.00 0.00 0.00 3.95
1573 1741 2.445525 AGTTACCTTGTCCATGTTGGGT 59.554 45.455 0.00 0.00 38.32 4.51
1693 1949 1.424493 GCAGGCATGTAGTCGTCAGC 61.424 60.000 0.00 0.00 0.00 4.26
1956 2216 6.705302 TGGCAATGCATGGAAAATTAAACTA 58.295 32.000 4.87 0.00 0.00 2.24
2006 2274 6.756542 GCATAGTTGTTTCTTTGTGACCTTTT 59.243 34.615 0.00 0.00 0.00 2.27
2014 2282 3.630312 ACCGTGCATAGTTGTTTCTTTGT 59.370 39.130 0.00 0.00 0.00 2.83
2062 2341 7.758980 GTGTGTTGAAATATTTACATGCATGGA 59.241 33.333 29.41 20.48 0.00 3.41
2063 2342 7.544915 TGTGTGTTGAAATATTTACATGCATGG 59.455 33.333 29.41 12.50 0.00 3.66
2064 2343 8.463456 TGTGTGTTGAAATATTTACATGCATG 57.537 30.769 25.09 25.09 0.00 4.06
2066 2345 8.140628 AGTTGTGTGTTGAAATATTTACATGCA 58.859 29.630 0.00 0.00 0.00 3.96
2071 2350 9.030301 AGCAAAGTTGTGTGTTGAAATATTTAC 57.970 29.630 0.00 0.00 0.00 2.01
2074 2353 6.018832 GCAGCAAAGTTGTGTGTTGAAATATT 60.019 34.615 0.00 0.00 0.00 1.28
2075 2354 5.463061 GCAGCAAAGTTGTGTGTTGAAATAT 59.537 36.000 0.00 0.00 0.00 1.28
2076 2355 4.803088 GCAGCAAAGTTGTGTGTTGAAATA 59.197 37.500 0.00 0.00 0.00 1.40
2077 2356 3.618150 GCAGCAAAGTTGTGTGTTGAAAT 59.382 39.130 0.00 0.00 0.00 2.17
2127 2431 6.406624 CGTAGACAATAGGGTGGTTCACTAAT 60.407 42.308 0.00 0.00 35.50 1.73
2321 2628 2.437085 ACCCCTATAGCAGCCAAAAC 57.563 50.000 0.00 0.00 0.00 2.43
2333 2640 2.633481 GGCGAGACTGAATAACCCCTAT 59.367 50.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.