Multiple sequence alignment - TraesCS6D01G311500

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 TraesCS6D01G311500 chr6D 100.000 2592 0 0 1 2592 420934724 420937315 0.000000e+00 4787.0
1 TraesCS6D01G311500 chr6D 85.137 1312 135 37 478 1760 420898646 420899926 0.000000e+00 1288.0
2 TraesCS6D01G311500 chr6D 84.481 799 53 26 804 1590 420956415 420957154 0.000000e+00 723.0
3 TraesCS6D01G311500 chr6D 77.561 205 19 14 1644 1842 420957151 420957334 5.900000e-17 99.0
4 TraesCS6D01G311500 chr6B 93.920 2352 97 20 1 2317 634320914 634323254 0.000000e+00 3509.0
5 TraesCS6D01G311500 chr6B 85.768 1321 120 43 473 1760 634315160 634316445 0.000000e+00 1336.0
6 TraesCS6D01G311500 chr6B 89.088 669 40 19 923 1590 634329895 634330531 0.000000e+00 800.0
7 TraesCS6D01G311500 chr6B 86.869 297 21 2 2314 2592 634323378 634323674 1.500000e-82 316.0
8 TraesCS6D01G311500 chr6B 96.825 63 2 0 661 723 634324412 634324474 3.530000e-19 106.0
9 TraesCS6D01G311500 chr6A 92.726 2337 105 27 1 2317 564131452 564133743 0.000000e+00 3314.0
10 TraesCS6D01G311500 chr6A 91.552 1740 78 25 600 2317 564238306 564239998 0.000000e+00 2335.0
11 TraesCS6D01G311500 chr6A 91.412 1735 86 21 600 2317 564190851 564192539 0.000000e+00 2320.0
12 TraesCS6D01G311500 chr6A 85.234 1219 121 39 683 1874 564117558 564118744 0.000000e+00 1199.0
13 TraesCS6D01G311500 chr6A 84.871 542 54 17 804 1340 564259894 564260412 2.960000e-144 521.0
14 TraesCS6D01G311500 chr6A 86.131 274 20 10 2322 2592 564240339 564240597 1.960000e-71 279.0
15 TraesCS6D01G311500 chr6A 80.342 351 48 13 343 690 564115287 564115619 1.990000e-61 246.0
16 TraesCS6D01G311500 chr6A 82.400 125 11 7 1722 1842 564260678 564260795 5.900000e-17 99.0
17 TraesCS6D01G311500 chr6A 93.651 63 4 0 661 723 564134848 564134910 7.640000e-16 95.3
18 TraesCS6D01G311500 chr3A 73.352 364 70 17 1974 2316 36888887 36889244 2.730000e-20 110.0


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 TraesCS6D01G311500 chr6D 420934724 420937315 2591 False 4787.000000 4787 100.0000 1 2592 1 chr6D.!!$F2 2591
1 TraesCS6D01G311500 chr6D 420898646 420899926 1280 False 1288.000000 1288 85.1370 478 1760 1 chr6D.!!$F1 1282
2 TraesCS6D01G311500 chr6D 420956415 420957334 919 False 411.000000 723 81.0210 804 1842 2 chr6D.!!$F3 1038
3 TraesCS6D01G311500 chr6B 634315160 634316445 1285 False 1336.000000 1336 85.7680 473 1760 1 chr6B.!!$F1 1287
4 TraesCS6D01G311500 chr6B 634320914 634324474 3560 False 1310.333333 3509 92.5380 1 2592 3 chr6B.!!$F3 2591
5 TraesCS6D01G311500 chr6B 634329895 634330531 636 False 800.000000 800 89.0880 923 1590 1 chr6B.!!$F2 667
6 TraesCS6D01G311500 chr6A 564190851 564192539 1688 False 2320.000000 2320 91.4120 600 2317 1 chr6A.!!$F1 1717
7 TraesCS6D01G311500 chr6A 564131452 564134910 3458 False 1704.650000 3314 93.1885 1 2317 2 chr6A.!!$F3 2316
8 TraesCS6D01G311500 chr6A 564238306 564240597 2291 False 1307.000000 2335 88.8415 600 2592 2 chr6A.!!$F4 1992
9 TraesCS6D01G311500 chr6A 564115287 564118744 3457 False 722.500000 1199 82.7880 343 1874 2 chr6A.!!$F2 1531
10 TraesCS6D01G311500 chr6A 564259894 564260795 901 False 310.000000 521 83.6355 804 1842 2 chr6A.!!$F5 1038

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
880 2868 0.53578 TGCTTGAAGCTGGTGTCAGG 60.536 55.0 18.94 0.0 42.97 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2146 4219 0.616395 TGGCGAGGGTGAAGTGGATA 60.616 55.0 0.0 0.0 0.0 2.59 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
247 248 2.973419 TTAGCGCCTTTGGTTAAACG 57.027 45.000 2.29 0.00 0.00 3.60
250 251 1.655329 CGCCTTTGGTTAAACGCCA 59.345 52.632 0.00 0.00 0.00 5.69
267 268 0.612229 CCAGCCAGTGACTGTCATCT 59.388 55.000 14.37 9.99 33.09 2.90
297 298 2.092211 CACGAAATTACGACACAGCTCC 59.908 50.000 0.00 0.00 37.03 4.70
319 320 8.188139 GCTCCATAGCTCAACTCTAAGATATAC 58.812 40.741 0.00 0.00 45.85 1.47
320 321 9.461312 CTCCATAGCTCAACTCTAAGATATACT 57.539 37.037 0.00 0.00 0.00 2.12
519 537 7.038799 AGGTGAATTAGTTGCCAATGAAAGAAT 60.039 33.333 0.00 0.00 0.00 2.40
815 2799 5.399052 ACCTATACTCCAGGTGCTTACTA 57.601 43.478 0.00 0.00 44.89 1.82
880 2868 0.535780 TGCTTGAAGCTGGTGTCAGG 60.536 55.000 18.94 0.00 42.97 3.86
904 2892 5.499004 TCAGGGTCTATAAATATGGCCAC 57.501 43.478 8.16 0.00 0.00 5.01
983 2992 5.122396 GCACTAATAACTAGTTGCAGCAGTT 59.878 40.000 18.56 17.41 38.92 3.16
984 2993 6.537566 CACTAATAACTAGTTGCAGCAGTTG 58.462 40.000 18.56 11.17 38.92 3.16
1078 3097 1.672356 GCATTGGTCGTGGTCTGCT 60.672 57.895 0.00 0.00 0.00 4.24
1319 3339 4.745125 CCAGGTACGTACTCATATGCTTTG 59.255 45.833 24.07 7.10 0.00 2.77
1400 3424 2.202298 CGCGTTGTTTGATCGGCC 60.202 61.111 0.00 0.00 0.00 6.13
1403 3427 2.874751 GTTGTTTGATCGGCCGGG 59.125 61.111 27.83 0.00 0.00 5.73
1602 3629 0.179127 CAGGACTGATCACGCACGAT 60.179 55.000 0.00 0.00 0.00 3.73
1687 3727 6.103997 TCAGTAGTACCGGCAAGAATAAAAG 58.896 40.000 0.00 0.00 0.00 2.27
1771 3819 7.084486 TCCGATTCTGAATATCTCGTTATGTG 58.916 38.462 2.28 0.00 0.00 3.21
1779 3827 3.694535 ATCTCGTTATGTGACTCGGAC 57.305 47.619 0.00 0.00 0.00 4.79
1780 3828 1.395954 TCTCGTTATGTGACTCGGACG 59.604 52.381 0.00 0.00 0.00 4.79
1781 3829 0.448990 TCGTTATGTGACTCGGACGG 59.551 55.000 0.00 0.00 0.00 4.79
1782 3830 0.448990 CGTTATGTGACTCGGACGGA 59.551 55.000 0.00 0.00 0.00 4.69
2079 4132 5.847111 AGGTAGCACAATTCGATACACTA 57.153 39.130 0.00 0.00 0.00 2.74
2146 4219 0.918983 TCGGCCATGATTTTCTCCCT 59.081 50.000 2.24 0.00 0.00 4.20
2166 4239 1.488705 ATCCACTTCACCCTCGCCAA 61.489 55.000 0.00 0.00 0.00 4.52
2257 4337 0.810823 GACAGCTCAGCCTCATCTGC 60.811 60.000 0.00 0.00 34.19 4.26
2276 4356 2.823747 TGCCTTCTTGTAGAGCTCGTAA 59.176 45.455 8.37 4.22 0.00 3.18
2290 4370 0.901580 TCGTAAACCCGGAGCTCCTT 60.902 55.000 29.73 19.20 0.00 3.36
2351 4798 2.182014 TGTCAATATCTTCGCACGACG 58.818 47.619 0.00 0.00 45.62 5.12
2391 4847 0.318360 CACGTCGTAAGTGTGAGCCA 60.318 55.000 0.00 0.00 43.82 4.75
2415 4871 2.965831 TGCTCCACTGACTAGAACAAGT 59.034 45.455 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 1.874019 CGGCTTCGGTCGTCAGATG 60.874 63.158 0.00 0.00 38.37 2.90
239 240 0.887387 TCACTGGCTGGCGTTTAACC 60.887 55.000 0.00 0.00 0.00 2.85
247 248 1.002868 ATGACAGTCACTGGCTGGC 60.003 57.895 13.20 12.63 40.76 4.85
250 251 2.369860 TGAAAGATGACAGTCACTGGCT 59.630 45.455 13.20 0.00 40.76 4.75
267 268 5.396947 GTGTCGTAATTTCGTGCAAATGAAA 59.603 36.000 11.12 11.12 38.35 2.69
319 320 7.384932 TCATGGCGTTGTTATTCTACATCATAG 59.615 37.037 0.00 0.00 0.00 2.23
320 321 7.213678 TCATGGCGTTGTTATTCTACATCATA 58.786 34.615 0.00 0.00 0.00 2.15
321 322 6.054941 TCATGGCGTTGTTATTCTACATCAT 58.945 36.000 0.00 0.00 0.00 2.45
519 537 2.609747 AGTTGACAGTGGCCTCTCTTA 58.390 47.619 3.81 0.00 0.00 2.10
880 2868 6.069963 AGTGGCCATATTTATAGACCCTGATC 60.070 42.308 9.72 0.00 0.00 2.92
952 2961 9.542462 CTGCAACTAGTTATTAGTGCCTAATTA 57.458 33.333 8.04 2.44 41.80 1.40
983 2992 1.690893 CCATGCCTCTTCTAGCTAGCA 59.309 52.381 18.83 10.59 34.28 3.49
984 2993 1.607767 GCCATGCCTCTTCTAGCTAGC 60.608 57.143 16.35 6.62 0.00 3.42
1044 3063 3.414700 GCCACGAGAACCAGCACG 61.415 66.667 0.00 0.00 0.00 5.34
1218 3238 4.514577 CCGTACCTCTGCCGCCAG 62.515 72.222 0.00 0.00 40.54 4.85
1319 3339 2.072298 GATGCATTGACGGAGATAGGC 58.928 52.381 0.00 0.00 0.00 3.93
1400 3424 2.034879 GGTGACATGACAGTGCCCG 61.035 63.158 0.00 0.00 0.00 6.13
1403 3427 0.250467 ACCTGGTGACATGACAGTGC 60.250 55.000 0.00 0.00 41.51 4.40
1779 3827 4.368315 TGTCATTTCGACTATGGATTCCG 58.632 43.478 6.82 0.00 45.60 4.30
1780 3828 5.601662 TCTGTCATTTCGACTATGGATTCC 58.398 41.667 0.00 0.00 45.60 3.01
1781 3829 7.721286 AATCTGTCATTTCGACTATGGATTC 57.279 36.000 6.82 0.00 45.60 2.52
1782 3830 8.511604 AAAATCTGTCATTTCGACTATGGATT 57.488 30.769 6.82 5.75 45.60 3.01
1897 3945 3.116746 AGGGCCTAAATTTAAGGGATGGG 60.117 47.826 2.82 1.34 34.46 4.00
1898 3946 4.152647 GAGGGCCTAAATTTAAGGGATGG 58.847 47.826 5.73 1.97 34.46 3.51
2017 4070 9.917129 TGTTTGAATCGAGTAGTTCTATGTTTA 57.083 29.630 0.00 0.00 0.00 2.01
2033 4086 8.107564 CCTTTGTTTAACTTTGTGTTTGAATCG 58.892 33.333 0.00 0.00 39.89 3.34
2079 4132 9.817809 ATCGAGTAGTTTATGTTCATGTTATGT 57.182 29.630 0.00 0.00 0.00 2.29
2127 4200 0.918983 AGGGAGAAAATCATGGCCGA 59.081 50.000 0.00 0.00 0.00 5.54
2146 4219 0.616395 TGGCGAGGGTGAAGTGGATA 60.616 55.000 0.00 0.00 0.00 2.59
2257 4337 4.174762 GGTTTACGAGCTCTACAAGAAGG 58.825 47.826 12.85 0.00 0.00 3.46
2276 4356 4.035102 GCCAAGGAGCTCCGGGTT 62.035 66.667 33.50 20.33 42.08 4.11
2290 4370 2.755876 ATCCAGAGCTCGTCGCCA 60.756 61.111 8.37 0.00 40.39 5.69
2351 4798 3.311110 TGGTCTGCCTCCACGACC 61.311 66.667 0.00 0.00 45.76 4.79
2391 4847 2.965831 TGTTCTAGTCAGTGGAGCAAGT 59.034 45.455 0.00 0.00 0.00 3.16
2400 4856 5.305644 ACTGGATCAACTTGTTCTAGTCAGT 59.694 40.000 11.27 7.78 34.25 3.41
2402 4858 5.808366 ACTGGATCAACTTGTTCTAGTCA 57.192 39.130 11.27 0.00 34.25 3.41
2415 4871 1.559682 GGGGAAGCTGTACTGGATCAA 59.440 52.381 1.65 0.00 0.00 2.57
2542 5008 3.252284 CCACCCTGAGCACCCACT 61.252 66.667 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.