Multiple sequence alignment - TraesCS5D01G082600

Loading Multiple Alignment...

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 TraesCS5D01G082600 chr5D 100.000 1688 0 0 892 2579 84407544 84409231 0.000000e+00 3118
1 TraesCS5D01G082600 chr5D 95.853 1664 51 8 929 2579 84452268 84453926 0.000000e+00 2675
2 TraesCS5D01G082600 chr5D 100.000 494 0 0 1 494 84406653 84407146 0.000000e+00 913
3 TraesCS5D01G082600 chr5D 94.904 471 24 0 1 471 84451139 84451609 0.000000e+00 737
4 TraesCS5D01G082600 chr5D 93.645 299 19 0 196 494 53755584 53755882 5.060000e-122 448
5 TraesCS5D01G082600 chr5D 92.459 305 22 1 190 494 359546425 359546728 3.940000e-118 435
6 TraesCS5D01G082600 chr5D 92.929 297 20 1 198 494 497306138 497305843 5.100000e-117 431
7 TraesCS5D01G082600 chr3D 94.664 937 38 8 927 1854 486147213 486146280 0.000000e+00 1443
8 TraesCS5D01G082600 chr3D 94.382 890 41 5 949 1832 338869956 338869070 0.000000e+00 1358
9 TraesCS5D01G082600 chr3D 95.336 729 33 1 1852 2579 594702325 594703053 0.000000e+00 1157
10 TraesCS5D01G082600 chr3D 95.199 729 33 2 1852 2579 184296219 184295492 0.000000e+00 1151
11 TraesCS5D01G082600 chr3D 94.000 300 13 2 193 491 486147836 486147541 1.410000e-122 449
12 TraesCS5D01G082600 chr7D 94.046 907 43 7 956 1855 582089019 582089921 0.000000e+00 1365
13 TraesCS5D01G082600 chr7D 95.616 730 30 2 1852 2579 376023875 376023146 0.000000e+00 1170
14 TraesCS5D01G082600 chr7D 95.062 729 34 2 1852 2579 481350384 481349657 0.000000e+00 1146
15 TraesCS5D01G082600 chr7D 92.929 297 20 1 198 494 549747873 549747578 5.100000e-117 431
16 TraesCS5D01G082600 chr7D 97.512 201 5 0 1 201 376024070 376023870 6.830000e-91 344
17 TraesCS5D01G082600 chr3A 94.098 898 46 4 962 1856 418754018 418753125 0.000000e+00 1358
18 TraesCS5D01G082600 chr7A 93.189 925 51 9 951 1868 700256716 700257635 0.000000e+00 1349
19 TraesCS5D01G082600 chr7A 92.612 934 50 13 928 1857 705128373 705127455 0.000000e+00 1325
20 TraesCS5D01G082600 chr6D 93.209 913 52 6 949 1852 424649060 424648149 0.000000e+00 1334
21 TraesCS5D01G082600 chr6D 95.199 729 33 2 1852 2579 181646735 181646008 0.000000e+00 1151
22 TraesCS5D01G082600 chr6D 97.980 198 4 0 1 198 314808494 314808691 6.830000e-91 344
23 TraesCS5D01G082600 chr6D 97.015 201 6 0 1 201 137262871 137262671 3.180000e-89 339
24 TraesCS5D01G082600 chr6D 96.117 206 7 1 1 206 244692563 244692359 4.110000e-88 335
25 TraesCS5D01G082600 chr5B 92.169 945 52 11 928 1854 56361516 56362456 0.000000e+00 1315
26 TraesCS5D01G082600 chr4D 95.205 730 33 2 1852 2579 290903955 290904684 0.000000e+00 1153
27 TraesCS5D01G082600 chr1D 95.212 731 32 2 1852 2579 294767970 294768700 0.000000e+00 1153
28 TraesCS5D01G082600 chr1D 95.199 729 33 2 1852 2579 31639204 31638477 0.000000e+00 1151
29 TraesCS5D01G082600 chr1D 95.062 729 35 1 1852 2579 62492256 62492984 0.000000e+00 1146
30 TraesCS5D01G082600 chr1D 97.980 198 4 0 1 198 342257650 342257847 6.830000e-91 344
31 TraesCS5D01G082600 chr3B 93.878 294 18 0 196 489 207205132 207204839 6.550000e-121 444
32 TraesCS5D01G082600 chr3B 97.980 198 4 0 1 198 100437326 100437523 6.830000e-91 344
33 TraesCS5D01G082600 chr4B 95.636 275 12 0 198 472 577064128 577063854 2.360000e-120 442
34 TraesCS5D01G082600 chrUn 92.929 297 21 0 198 494 105321379 105321083 1.420000e-117 433
35 TraesCS5D01G082600 chrUn 97.475 198 5 0 1 198 98152581 98152778 3.180000e-89 339
36 TraesCS5D01G082600 chr6B 97.980 198 4 0 1 198 149218724 149218921 6.830000e-91 344


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 TraesCS5D01G082600 chr5D 84406653 84409231 2578 False 2015.5 3118 100.0000 1 2579 2 chr5D.!!$F3 2578
1 TraesCS5D01G082600 chr5D 84451139 84453926 2787 False 1706.0 2675 95.3785 1 2579 2 chr5D.!!$F4 2578
2 TraesCS5D01G082600 chr3D 338869070 338869956 886 True 1358.0 1358 94.3820 949 1832 1 chr3D.!!$R2 883
3 TraesCS5D01G082600 chr3D 594702325 594703053 728 False 1157.0 1157 95.3360 1852 2579 1 chr3D.!!$F1 727
4 TraesCS5D01G082600 chr3D 184295492 184296219 727 True 1151.0 1151 95.1990 1852 2579 1 chr3D.!!$R1 727
5 TraesCS5D01G082600 chr3D 486146280 486147836 1556 True 946.0 1443 94.3320 193 1854 2 chr3D.!!$R3 1661
6 TraesCS5D01G082600 chr7D 582089019 582089921 902 False 1365.0 1365 94.0460 956 1855 1 chr7D.!!$F1 899
7 TraesCS5D01G082600 chr7D 481349657 481350384 727 True 1146.0 1146 95.0620 1852 2579 1 chr7D.!!$R1 727
8 TraesCS5D01G082600 chr7D 376023146 376024070 924 True 757.0 1170 96.5640 1 2579 2 chr7D.!!$R3 2578
9 TraesCS5D01G082600 chr3A 418753125 418754018 893 True 1358.0 1358 94.0980 962 1856 1 chr3A.!!$R1 894
10 TraesCS5D01G082600 chr7A 700256716 700257635 919 False 1349.0 1349 93.1890 951 1868 1 chr7A.!!$F1 917
11 TraesCS5D01G082600 chr7A 705127455 705128373 918 True 1325.0 1325 92.6120 928 1857 1 chr7A.!!$R1 929
12 TraesCS5D01G082600 chr6D 424648149 424649060 911 True 1334.0 1334 93.2090 949 1852 1 chr6D.!!$R4 903
13 TraesCS5D01G082600 chr6D 181646008 181646735 727 True 1151.0 1151 95.1990 1852 2579 1 chr6D.!!$R2 727
14 TraesCS5D01G082600 chr5B 56361516 56362456 940 False 1315.0 1315 92.1690 928 1854 1 chr5B.!!$F1 926
15 TraesCS5D01G082600 chr4D 290903955 290904684 729 False 1153.0 1153 95.2050 1852 2579 1 chr4D.!!$F1 727
16 TraesCS5D01G082600 chr1D 294767970 294768700 730 False 1153.0 1153 95.2120 1852 2579 1 chr1D.!!$F2 727
17 TraesCS5D01G082600 chr1D 31638477 31639204 727 True 1151.0 1151 95.1990 1852 2579 1 chr1D.!!$R1 727
18 TraesCS5D01G082600 chr1D 62492256 62492984 728 False 1146.0 1146 95.0620 1852 2579 1 chr1D.!!$F1 727

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
417 418 0.678950 CCCAACCGCCACTTCATTTT 59.321 50.000 0.0 0.0 0.0 1.82 F
1130 1634 2.203877 ACGTACCCCTCTGCCCAA 60.204 61.111 0.0 0.0 0.0 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1401 1910 0.617935 GCCCCTTCTTCTTCTGCTCT 59.382 55.0 0.0 0.0 0.00 4.09 R
2169 2693 0.933097 CAAAGCATCATCGAGGACCG 59.067 55.0 0.0 0.0 40.25 4.79 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
62 63 6.039717 ACAATGGAATGCACATGTATTAGGTC 59.960 38.462 0.00 0.00 30.53 3.85
70 71 4.279169 GCACATGTATTAGGTCATGCCATT 59.721 41.667 0.00 0.00 43.34 3.16
252 253 8.907222 AAAATAACTAACTTTTGGACCGTCTA 57.093 30.769 0.00 0.00 0.00 2.59
334 335 4.699735 TCCTCGTGATGTAAAATGCAACAT 59.300 37.500 1.37 1.37 39.00 2.71
417 418 0.678950 CCCAACCGCCACTTCATTTT 59.321 50.000 0.00 0.00 0.00 1.82
1130 1634 2.203877 ACGTACCCCTCTGCCCAA 60.204 61.111 0.00 0.00 0.00 4.12
1292 1801 6.410540 AGAAGAAGATAATGAAGAAGCCGTT 58.589 36.000 0.00 0.00 0.00 4.44
1458 1967 2.494918 GGTCCCTCGACGGTGATG 59.505 66.667 0.15 0.00 40.17 3.07
1569 2084 1.516603 GCAGTTCCGTAGCTCCGAC 60.517 63.158 0.00 0.00 0.00 4.79
1596 2111 7.777095 AGGAGTAGTTTATCTAGCAGTTTGAG 58.223 38.462 0.00 0.00 0.00 3.02
1785 2300 2.292292 GAGCTCCAAAACGCACCTTTTA 59.708 45.455 0.87 0.00 0.00 1.52
1787 2302 2.034179 GCTCCAAAACGCACCTTTTAGT 59.966 45.455 0.00 0.00 0.00 2.24
1945 2468 4.817517 TCGGGTAGAAGCTCACTAAAAAG 58.182 43.478 0.00 0.00 0.00 2.27
1989 2513 4.720649 TGACTCTGTTGTCTGCCTATAC 57.279 45.455 0.00 0.00 37.79 1.47
2013 2537 3.130869 ACACTCAAAATGCAACTGCTCAA 59.869 39.130 2.95 0.00 42.66 3.02
2146 2670 3.706373 GGTTCCTCCAGCGAGCCA 61.706 66.667 0.00 0.00 34.49 4.75
2169 2693 2.692368 TCTGGTCCCATCTGGCCC 60.692 66.667 0.00 0.00 31.41 5.80
2186 2710 1.443407 CCGGTCCTCGATGATGCTT 59.557 57.895 0.00 0.00 42.43 3.91
2240 2764 1.094073 CAAATCTCCCTGGCTGCTCG 61.094 60.000 0.00 0.00 0.00 5.03
2415 2940 3.341291 GCCTTGAGGTGCTGTTGAAGC 62.341 57.143 0.00 0.00 43.59 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
263 264 2.031012 CCGTCTGTTGGAGCAGCA 59.969 61.111 0.00 0.00 36.49 4.41
334 335 4.385748 GTGATGTATATTTGCATCGCGAGA 59.614 41.667 16.66 0.00 45.03 4.04
1019 1521 2.748058 GAAGCCCGACTTGCCCTTCA 62.748 60.000 0.00 0.00 39.29 3.02
1292 1801 1.227527 CCAGCACTGACGACAACCA 60.228 57.895 0.00 0.00 0.00 3.67
1401 1910 0.617935 GCCCCTTCTTCTTCTGCTCT 59.382 55.000 0.00 0.00 0.00 4.09
1458 1967 1.443828 GGAAGAGGACTCGATGGGC 59.556 63.158 0.00 0.00 34.09 5.36
1490 1999 1.491332 CCTCCTCCTCCGAGAAGTCTA 59.509 57.143 0.00 0.00 38.52 2.59
1569 2084 6.380095 AACTGCTAGATAAACTACTCCTCG 57.620 41.667 0.00 0.00 0.00 4.63
1785 2300 5.183140 CCGAAGATGTAAAATTTGGACCACT 59.817 40.000 0.00 0.00 30.14 4.00
1787 2302 5.074115 ACCGAAGATGTAAAATTTGGACCA 58.926 37.500 0.00 0.00 32.63 4.02
1945 2468 2.488836 TCACTATTCCCCTTCCCTTCC 58.511 52.381 0.00 0.00 0.00 3.46
1989 2513 4.023792 TGAGCAGTTGCATTTTGAGTGTAG 60.024 41.667 6.90 0.00 45.16 2.74
2013 2537 2.842462 TCAGGTGTGACGTGGGCT 60.842 61.111 0.00 0.00 34.95 5.19
2146 2670 1.074926 AGATGGGACCAGAGGCGAT 60.075 57.895 0.00 0.00 0.00 4.58
2169 2693 0.933097 CAAAGCATCATCGAGGACCG 59.067 55.000 0.00 0.00 40.25 4.79
2186 2710 1.486310 CCATGTAGCCTAGCTGGACAA 59.514 52.381 0.00 0.00 40.10 3.18
2415 2940 2.422479 CACCTTGTTGGATGAGCTCATG 59.578 50.000 33.33 17.94 39.71 3.07


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

AutoCloner maintained by Alex Coulton.