Multiple sequence alignment - TraesCS5D01G080000

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 TraesCS5D01G080000 chr5D 100.000 2546 0 0 1 2546 80119734 80117189 0 4702
1 TraesCS5D01G080000 chrUn 97.368 1938 45 5 615 2546 246703147 246701210 0 3291
2 TraesCS5D01G080000 chrUn 96.880 609 19 0 5 613 266183737 266184345 0 1020
3 TraesCS5D01G080000 chrUn 96.716 609 20 0 5 613 246703580 246704188 0 1014
4 TraesCS5D01G080000 chr6B 97.216 1940 48 5 613 2546 128896137 128894198 0 3278
5 TraesCS5D01G080000 chr6B 96.880 609 19 0 5 613 128896567 128897175 0 1020
6 TraesCS5D01G080000 chr5B 97.216 1940 48 5 613 2546 695879848 695877909 0 3278
7 TraesCS5D01G080000 chr5B 96.804 1940 56 5 613 2546 713089606 713091545 0 3234
8 TraesCS5D01G080000 chr5B 96.701 1940 58 5 613 2546 127825154 127823215 0 3223
9 TraesCS5D01G080000 chr5B 97.030 606 18 0 8 613 695892682 695892077 0 1020
10 TraesCS5D01G080000 chr5B 96.388 609 22 0 5 613 127825582 127826190 0 1003
11 TraesCS5D01G080000 chr3D 97.165 1940 49 5 613 2546 202630375 202628436 0 3273
12 TraesCS5D01G080000 chr7B 97.062 1940 51 5 613 2546 698132765 698130826 0 3262
13 TraesCS5D01G080000 chr7B 97.062 1940 51 5 613 2546 742931331 742933270 0 3262
14 TraesCS5D01G080000 chr7B 96.959 1940 53 5 613 2546 716801999 716800060 0 3251
15 TraesCS5D01G080000 chr7B 97.030 606 18 0 8 613 742930898 742930293 0 1020
16 TraesCS5D01G080000 chr7A 96.880 609 19 0 5 613 200013558 200014166 0 1020
17 TraesCS5D01G080000 chr6D 96.880 609 19 0 5 613 430474785 430475393 0 1020
18 TraesCS5D01G080000 chr1D 96.535 606 21 0 8 613 141351837 141351232 0 1003


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 TraesCS5D01G080000 chr5D 80117189 80119734 2545 True 4702 4702 100.000 1 2546 1 chr5D.!!$R1 2545
1 TraesCS5D01G080000 chrUn 246701210 246703147 1937 True 3291 3291 97.368 615 2546 1 chrUn.!!$R1 1931
2 TraesCS5D01G080000 chrUn 266183737 266184345 608 False 1020 1020 96.880 5 613 1 chrUn.!!$F2 608
3 TraesCS5D01G080000 chrUn 246703580 246704188 608 False 1014 1014 96.716 5 613 1 chrUn.!!$F1 608
4 TraesCS5D01G080000 chr6B 128894198 128896137 1939 True 3278 3278 97.216 613 2546 1 chr6B.!!$R1 1933
5 TraesCS5D01G080000 chr6B 128896567 128897175 608 False 1020 1020 96.880 5 613 1 chr6B.!!$F1 608
6 TraesCS5D01G080000 chr5B 695877909 695879848 1939 True 3278 3278 97.216 613 2546 1 chr5B.!!$R2 1933
7 TraesCS5D01G080000 chr5B 713089606 713091545 1939 False 3234 3234 96.804 613 2546 1 chr5B.!!$F2 1933
8 TraesCS5D01G080000 chr5B 127823215 127825154 1939 True 3223 3223 96.701 613 2546 1 chr5B.!!$R1 1933
9 TraesCS5D01G080000 chr5B 695892077 695892682 605 True 1020 1020 97.030 8 613 1 chr5B.!!$R3 605
10 TraesCS5D01G080000 chr5B 127825582 127826190 608 False 1003 1003 96.388 5 613 1 chr5B.!!$F1 608
11 TraesCS5D01G080000 chr3D 202628436 202630375 1939 True 3273 3273 97.165 613 2546 1 chr3D.!!$R1 1933
12 TraesCS5D01G080000 chr7B 698130826 698132765 1939 True 3262 3262 97.062 613 2546 1 chr7B.!!$R1 1933
13 TraesCS5D01G080000 chr7B 742931331 742933270 1939 False 3262 3262 97.062 613 2546 1 chr7B.!!$F1 1933
14 TraesCS5D01G080000 chr7B 716800060 716801999 1939 True 3251 3251 96.959 613 2546 1 chr7B.!!$R2 1933
15 TraesCS5D01G080000 chr7B 742930293 742930898 605 True 1020 1020 97.030 8 613 1 chr7B.!!$R3 605
16 TraesCS5D01G080000 chr7A 200013558 200014166 608 False 1020 1020 96.880 5 613 1 chr7A.!!$F1 608
17 TraesCS5D01G080000 chr6D 430474785 430475393 608 False 1020 1020 96.880 5 613 1 chr6D.!!$F1 608
18 TraesCS5D01G080000 chr1D 141351232 141351837 605 True 1003 1003 96.535 8 613 1 chr1D.!!$R1 605

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
200 201 0.888285 GCTTGAAGGCACAGCTCACT 60.888 55.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1790 1795 1.136529 CACGACAACATCACGCTTCTG 60.137 52.381 0.0 0.0 0.0 3.02 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
25 26 3.373830 CCAAATAATTCAAGGAGGGGCA 58.626 45.455 0.00 0.00 0.00 5.36
28 29 3.979501 ATAATTCAAGGAGGGGCACAT 57.020 42.857 0.00 0.00 0.00 3.21
66 67 2.996249 TAGTAGATGACTCGTCGGGT 57.004 50.000 0.00 0.00 39.81 5.28
91 92 2.093447 CAGAGCGGGACTTCTTTGGTAT 60.093 50.000 0.00 0.00 0.00 2.73
200 201 0.888285 GCTTGAAGGCACAGCTCACT 60.888 55.000 0.00 0.00 0.00 3.41
349 350 3.330720 CCCCCGGCCTCTCACTTT 61.331 66.667 0.00 0.00 0.00 2.66
354 355 1.318576 CCGGCCTCTCACTTTGTTTT 58.681 50.000 0.00 0.00 0.00 2.43
387 388 3.197766 TGTACCCTCGCTTGAATGAAGAT 59.802 43.478 0.00 0.00 32.82 2.40
443 444 2.304761 CCAGCCCTTTTCCTGTAGTACA 59.695 50.000 2.36 2.36 0.00 2.90
478 479 7.367159 TCTTGTCTTGTTTTCGTTTTAGTCA 57.633 32.000 0.00 0.00 0.00 3.41
496 497 2.675242 ATGGTGATCGCCCGGGAAA 61.675 57.895 29.31 11.99 0.00 3.13
728 729 4.687483 CGGGTACAACTCTTATTTGAACGT 59.313 41.667 0.00 0.00 0.00 3.99
1133 1135 9.512588 CAAAATAAGAAGGGATGTGCTATATCT 57.487 33.333 0.00 0.00 0.00 1.98
1241 1243 3.569194 TGGCACCAAAAGTTGTAGAGA 57.431 42.857 0.00 0.00 0.00 3.10
1323 1325 1.665679 CGTGCTATGAGCGGACAATTT 59.334 47.619 0.00 0.00 46.26 1.82
1326 1328 1.261619 GCTATGAGCGGACAATTTCGG 59.738 52.381 0.00 0.00 0.00 4.30
1432 1437 1.674322 CCGACGGGTTGGATTGCTT 60.674 57.895 5.81 0.00 36.15 3.91
1486 1491 4.648762 TGGATGGTGTGAGTTTGTCAAATT 59.351 37.500 0.40 0.00 36.74 1.82
1543 1548 4.506886 TGTTCGTCAACCAAGTTTGTTT 57.493 36.364 0.00 0.00 0.00 2.83
1586 1591 4.664479 GGGGAAAAACCGGGCCGA 62.664 66.667 30.79 0.00 40.11 5.54
1599 1604 1.876416 CGGGCCGAGACTCAAAAGAAA 60.876 52.381 24.41 0.00 0.00 2.52
1610 1615 5.763204 AGACTCAAAAGAAATTGGCGAAGTA 59.237 36.000 0.00 0.00 0.00 2.24
1657 1662 3.053359 AGACAAAGAGGGATAGGGAGG 57.947 52.381 0.00 0.00 0.00 4.30
1694 1699 5.866335 TTTGTAATCGCCGAAATTGTACT 57.134 34.783 0.00 0.00 0.00 2.73
1870 1875 7.119553 ACTGTTGCATTGTTTCAATTTCTGTTT 59.880 29.630 0.00 0.00 0.00 2.83
1883 1888 8.450578 TCAATTTCTGTTTGTACTCTGATTGT 57.549 30.769 0.00 0.00 0.00 2.71
2054 2059 0.325671 TGGGAAAAAGGCAACCACCA 60.326 50.000 0.00 0.00 37.17 4.17
2122 2127 3.701664 TCTCTTCTAGTGAGCATGACCA 58.298 45.455 0.00 0.00 0.00 4.02
2148 2153 5.641209 GCACTTTTCACTCATACATCTGACT 59.359 40.000 0.00 0.00 0.00 3.41
2166 2171 1.626654 CTGCGGTCGTACCTTGCTTG 61.627 60.000 3.15 0.00 35.66 4.01
2178 2183 5.408604 CGTACCTTGCTTGTTCTCTATGTTT 59.591 40.000 0.00 0.00 0.00 2.83
2373 2378 3.345508 TCTCACGCTCAGGTCTTACTA 57.654 47.619 0.00 0.00 0.00 1.82
2375 2380 4.077108 TCTCACGCTCAGGTCTTACTAAA 58.923 43.478 0.00 0.00 0.00 1.85
2502 2509 2.725127 TACCTCACTGTGACCCGGCT 62.725 60.000 6.36 1.56 0.00 5.52
2532 2539 2.815503 CTCATGCAGTCCACATTGTCAA 59.184 45.455 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.540715 CCCTCCTTGAATTATTTGGCTCT 58.459 43.478 0.00 0.00 0.00 4.09
1 2 3.638627 CCCCTCCTTGAATTATTTGGCTC 59.361 47.826 0.00 0.00 0.00 4.70
2 3 3.646534 CCCCTCCTTGAATTATTTGGCT 58.353 45.455 0.00 0.00 0.00 4.75
3 4 2.103094 GCCCCTCCTTGAATTATTTGGC 59.897 50.000 0.00 0.00 0.00 4.52
6 7 4.059773 TGTGCCCCTCCTTGAATTATTT 57.940 40.909 0.00 0.00 0.00 1.40
25 26 0.044855 AAGGACCCTCCCTGCTATGT 59.955 55.000 0.00 0.00 37.19 2.29
28 29 1.755200 AAAAAGGACCCTCCCTGCTA 58.245 50.000 0.00 0.00 37.19 3.49
32 33 4.431158 TCTACTAAAAAGGACCCTCCCT 57.569 45.455 0.00 0.00 37.19 4.20
66 67 0.894184 AAGAAGTCCCGCTCTGACGA 60.894 55.000 0.00 0.00 37.80 4.20
153 154 0.392729 TACGCCGGGGTTGTAAATGG 60.393 55.000 30.49 0.00 0.00 3.16
272 273 0.322997 ACGAAATCCGGATTTGGCCA 60.323 50.000 39.98 0.00 40.77 5.36
349 350 4.165372 AGGGTACAGAGGAAGAACAAAACA 59.835 41.667 0.00 0.00 0.00 2.83
354 355 2.168496 CGAGGGTACAGAGGAAGAACA 58.832 52.381 0.00 0.00 0.00 3.18
387 388 4.511246 AGTCGGGCCGATCGGGTA 62.511 66.667 33.54 4.08 38.42 3.69
443 444 7.275560 CGAAAACAAGACAAGAAATCAAAACCT 59.724 33.333 0.00 0.00 0.00 3.50
447 448 8.527567 AAACGAAAACAAGACAAGAAATCAAA 57.472 26.923 0.00 0.00 0.00 2.69
478 479 2.204865 TTTTCCCGGGCGATCACCAT 62.205 55.000 18.49 0.00 0.00 3.55
496 497 9.059260 CCAAAAGGACATTCATTCATTTCTTTT 57.941 29.630 0.00 0.00 33.81 2.27
1122 1124 5.488645 TCGTACGTTTCAGATATAGCACA 57.511 39.130 16.05 0.00 0.00 4.57
1241 1243 3.553096 GGCTCGATATGAAAGACGACCAT 60.553 47.826 0.00 0.00 0.00 3.55
1323 1325 7.289317 ACTCTTACCCATATCTTACAATTCCGA 59.711 37.037 0.00 0.00 0.00 4.55
1384 1389 5.693769 TTTCCTCTTCCCATTCGAACTAT 57.306 39.130 0.00 0.00 0.00 2.12
1385 1390 5.488341 CTTTTCCTCTTCCCATTCGAACTA 58.512 41.667 0.00 0.00 0.00 2.24
1486 1491 4.560136 CTAATCTAGCAGCTTGTCGAGA 57.440 45.455 0.00 0.00 0.00 4.04
1543 1548 4.782019 ACCAATTACGTTACGACCACTA 57.218 40.909 13.03 0.00 0.00 2.74
1586 1591 4.580580 ACTTCGCCAATTTCTTTTGAGTCT 59.419 37.500 0.00 0.00 0.00 3.24
1599 1604 4.331968 TCAGGAACAAATACTTCGCCAAT 58.668 39.130 0.00 0.00 0.00 3.16
1694 1699 2.026262 GCCTGGAACAAGAAGGGTCATA 60.026 50.000 0.00 0.00 38.70 2.15
1790 1795 1.136529 CACGACAACATCACGCTTCTG 60.137 52.381 0.00 0.00 0.00 3.02
1846 1851 6.981762 AACAGAAATTGAAACAATGCAACA 57.018 29.167 0.00 0.00 0.00 3.33
1852 1857 9.520204 CAGAGTACAAACAGAAATTGAAACAAT 57.480 29.630 0.00 0.00 0.00 2.71
1870 1875 3.402110 CAGCCACAACAATCAGAGTACA 58.598 45.455 0.00 0.00 0.00 2.90
1883 1888 1.742880 GATCGAGCTGCAGCCACAA 60.743 57.895 34.39 18.19 43.38 3.33
2054 2059 2.542907 CCGCTCAAACCAAGCACGT 61.543 57.895 0.00 0.00 39.81 4.49
2122 2127 6.093219 GTCAGATGTATGAGTGAAAAGTGCAT 59.907 38.462 0.00 0.00 0.00 3.96
2148 2153 1.666553 CAAGCAAGGTACGACCGCA 60.667 57.895 0.00 0.00 44.90 5.69
2196 2201 6.231258 AGCAATGTACTTCTGATCATCTCA 57.769 37.500 0.00 0.00 0.00 3.27
2373 2378 1.676006 GGTGTAGCAGCAGTGTGTTTT 59.324 47.619 0.00 0.00 0.00 2.43
2375 2380 0.535102 GGGTGTAGCAGCAGTGTGTT 60.535 55.000 0.00 0.00 33.07 3.32


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

AutoCloner maintained by Alex Coulton.