Multiple sequence alignment - TraesCS5D01G337700

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 TraesCS5D01G337700 chr5D 100.000 3251 0 0 1 3251 426297508 426294258 0.000000e+00 6004.0
1 TraesCS5D01G337700 chr5D 98.113 53 1 0 2598 2650 426294879 426294827 3.450000e-15 93.5
2 TraesCS5D01G337700 chr5D 98.113 53 1 0 2630 2682 426294911 426294859 3.450000e-15 93.5
3 TraesCS5D01G337700 chr5A 95.481 3275 95 16 1 3251 540395958 540392713 0.000000e+00 5179.0
4 TraesCS5D01G337700 chr5A 98.113 53 1 0 2598 2650 540393350 540393298 3.450000e-15 93.5
5 TraesCS5D01G337700 chr5A 98.113 53 1 0 2630 2682 540393382 540393330 3.450000e-15 93.5
6 TraesCS5D01G337700 chr5B 96.461 2458 65 13 1 2448 516094581 516092136 0.000000e+00 4037.0
7 TraesCS5D01G337700 chr5B 88.043 644 29 16 2630 3251 516091930 516091313 0.000000e+00 719.0
8 TraesCS5D01G337700 chr5B 95.909 220 9 0 2431 2650 516092097 516091878 1.110000e-94 357.0
9 TraesCS5D01G337700 chr4D 91.887 604 25 15 2029 2615 24335268 24334672 0.000000e+00 822.0
10 TraesCS5D01G337700 chr4D 90.717 614 36 8 2657 3251 24334555 24333944 0.000000e+00 798.0
11 TraesCS5D01G337700 chr7D 86.391 338 37 2 311 648 8974728 8975056 8.570000e-96 361.0
12 TraesCS5D01G337700 chr7D 87.446 231 25 2 418 648 615365605 615365831 2.490000e-66 263.0
13 TraesCS5D01G337700 chr7D 91.772 158 12 1 32 189 8974543 8974699 5.460000e-53 219.0
14 TraesCS5D01G337700 chr7D 95.062 81 4 0 32 112 615365422 615365502 9.470000e-26 128.0
15 TraesCS5D01G337700 chr2D 89.529 191 19 1 320 510 30410279 30410090 1.170000e-59 241.0
16 TraesCS5D01G337700 chr3A 91.139 158 14 0 32 189 382372004 382372161 7.060000e-52 215.0
17 TraesCS5D01G337700 chr4B 87.209 86 8 3 3166 3251 111990437 111990519 9.600000e-16 95.3
18 TraesCS5D01G337700 chr3B 87.209 86 8 3 3166 3251 74186247 74186329 9.600000e-16 95.3
19 TraesCS5D01G337700 chr2B 87.209 86 8 3 3166 3251 53573791 53573873 9.600000e-16 95.3
20 TraesCS5D01G337700 chr7B 86.420 81 8 3 3169 3249 707757179 707757102 5.780000e-13 86.1


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 TraesCS5D01G337700 chr5D 426294258 426297508 3250 True 2063.666667 6004 98.742000 1 3251 3 chr5D.!!$R1 3250
1 TraesCS5D01G337700 chr5A 540392713 540395958 3245 True 1788.666667 5179 97.235667 1 3251 3 chr5A.!!$R1 3250
2 TraesCS5D01G337700 chr5B 516091313 516094581 3268 True 1704.333333 4037 93.471000 1 3251 3 chr5B.!!$R1 3250
3 TraesCS5D01G337700 chr4D 24333944 24335268 1324 True 810.000000 822 91.302000 2029 3251 2 chr4D.!!$R1 1222
4 TraesCS5D01G337700 chr7D 8974543 8975056 513 False 290.000000 361 89.081500 32 648 2 chr7D.!!$F1 616

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
796 804 0.098200 GGCGAGGTTTTATTGCGGAC 59.902 55.0 0.00 0.00 0.00 4.79 F
806 814 0.465460 TATTGCGGACTTGATGGGCC 60.465 55.0 0.00 0.00 0.00 5.80 F
945 954 0.689745 AATAGCCCGGCTAGTCCACA 60.690 55.0 23.37 1.57 44.66 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1941 1956 1.028905 TTGGTAGCATAAATGGCCGC 58.971 50.000 0.0 0.0 0.00 6.53 R
2106 2121 2.046285 CACCCCAACAGGAATCGGC 61.046 63.158 0.0 0.0 38.24 5.54 R
2774 2968 2.257207 AGGACTACACTAGCAGGCAAA 58.743 47.619 0.0 0.0 0.00 3.68 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
586 587 4.531351 TGGGACACGATGAGGTCA 57.469 55.556 0.00 0.00 35.74 4.02
796 804 0.098200 GGCGAGGTTTTATTGCGGAC 59.902 55.000 0.00 0.00 0.00 4.79
806 814 0.465460 TATTGCGGACTTGATGGGCC 60.465 55.000 0.00 0.00 0.00 5.80
870 879 6.039616 CCCAGATCTCTCTAAAAGAAAGTCG 58.960 44.000 0.00 0.00 32.23 4.18
912 921 1.692762 GCCCAGGATCCCACTAAGAGA 60.693 57.143 8.55 0.00 0.00 3.10
923 932 3.261897 CCCACTAAGAGAACCTCATGTGT 59.738 47.826 0.00 0.00 32.06 3.72
943 952 1.146359 TCTAATAGCCCGGCTAGTCCA 59.854 52.381 22.25 8.01 44.66 4.02
944 953 1.272769 CTAATAGCCCGGCTAGTCCAC 59.727 57.143 22.25 0.00 44.66 4.02
945 954 0.689745 AATAGCCCGGCTAGTCCACA 60.690 55.000 23.37 1.57 44.66 4.17
946 955 0.689745 ATAGCCCGGCTAGTCCACAA 60.690 55.000 23.37 0.79 44.66 3.33
947 956 1.610554 TAGCCCGGCTAGTCCACAAC 61.611 60.000 15.59 0.00 40.44 3.32
948 957 2.267961 CCCGGCTAGTCCACAACC 59.732 66.667 0.00 0.00 34.01 3.77
1011 1026 3.589881 GCCGCCATGATGCAGTCC 61.590 66.667 0.00 0.00 0.00 3.85
1452 1467 4.742201 GTCGCCGAGCTGCAGGAA 62.742 66.667 17.12 2.74 0.00 3.36
1851 1866 3.896888 AGTTTGCTGATTTGGATGTTGGA 59.103 39.130 0.00 0.00 0.00 3.53
2106 2121 0.179056 AGGAACAACGACCCAGTGTG 60.179 55.000 0.00 0.00 0.00 3.82
2277 2293 7.072177 CTTTTGTAAGCTCGACCATTTCATA 57.928 36.000 0.00 0.00 0.00 2.15
2312 2328 6.994421 TCCATATCCAGTGTAGCTCATTTA 57.006 37.500 0.00 0.00 0.00 1.40
2382 2411 5.009911 ACTGCTGCAACACAAAATCTATTCA 59.990 36.000 3.02 0.00 0.00 2.57
2774 2968 8.730680 GTTCATCATTGTAGGTTTCAGTTGTAT 58.269 33.333 0.00 0.00 0.00 2.29
2908 3109 0.519961 GCCTTCGTTAATGGCGTGTT 59.480 50.000 0.00 0.00 37.11 3.32
2962 3166 7.434927 TGATTCCTCTCTTCATCTCTGATTT 57.565 36.000 0.00 0.00 0.00 2.17
2989 3195 5.991328 AATATAGCGACTTCACATGGTTG 57.009 39.130 0.00 0.00 0.00 3.77
3070 3276 9.691362 GTTCAGCTTATTTGAGATTTGGTTTTA 57.309 29.630 0.00 0.00 0.00 1.52
3136 3355 8.064222 CGAAATACTAGGTGCAATCAAATGTAG 58.936 37.037 0.00 0.00 0.00 2.74
3181 3400 3.621682 AAATTGGGGTGGTGGTAAAGA 57.378 42.857 0.00 0.00 0.00 2.52
3208 3427 6.038382 TGCCTTCTGTTATAAACGTCAAACAA 59.962 34.615 0.00 0.00 31.90 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.602605 CCGTTTCCTGTTCCCCACC 60.603 63.158 0.00 0.00 0.00 4.61
15 16 2.114411 GCCGTTTCCTGTTCCCCA 59.886 61.111 0.00 0.00 0.00 4.96
576 577 1.335415 CGGTGCTCTATGACCTCATCG 60.335 57.143 0.00 0.00 37.76 3.84
579 580 1.676678 GCCGGTGCTCTATGACCTCA 61.677 60.000 1.90 0.00 33.53 3.86
586 587 4.143333 AACGCGCCGGTGCTCTAT 62.143 61.111 35.04 16.69 34.43 1.98
651 652 0.911525 CTCCTCCTTCCAGGCCTTCA 60.912 60.000 0.00 0.00 34.61 3.02
654 655 2.690510 GCTCCTCCTTCCAGGCCT 60.691 66.667 0.00 0.00 34.61 5.19
733 740 0.657840 CGATCATTTTGGCGGGAGAC 59.342 55.000 0.00 0.00 39.51 3.36
796 804 4.023137 CCCAACAGGCCCATCAAG 57.977 61.111 0.00 0.00 0.00 3.02
825 833 4.823989 GGGCTTGATGACTTGCATATAGTT 59.176 41.667 0.00 0.00 37.34 2.24
870 879 0.663153 GGCGTGAATATGGGCTTGAC 59.337 55.000 0.00 0.00 0.00 3.18
912 921 3.181465 CGGGCTATTAGACACATGAGGTT 60.181 47.826 0.00 0.00 0.00 3.50
923 932 1.146359 TGGACTAGCCGGGCTATTAGA 59.854 52.381 27.90 8.77 40.54 2.10
943 952 2.031163 GCAGAGGCTCGTGGTTGT 59.969 61.111 9.22 0.00 36.96 3.32
992 1007 4.783621 ACTGCATCATGGCGGCGT 62.784 61.111 9.37 0.00 44.09 5.68
999 1014 0.384309 GCATGTGGGACTGCATCATG 59.616 55.000 0.00 0.00 38.28 3.07
1452 1467 2.203788 TCCTGCAGGTCGAGGGTT 60.204 61.111 31.58 0.00 36.34 4.11
1851 1866 1.153756 CAGGGGTTTCTTGGGCACT 59.846 57.895 0.00 0.00 0.00 4.40
1941 1956 1.028905 TTGGTAGCATAAATGGCCGC 58.971 50.000 0.00 0.00 0.00 6.53
1949 1964 3.278574 GGCACTGTGATTGGTAGCATAA 58.721 45.455 12.86 0.00 0.00 1.90
2106 2121 2.046285 CACCCCAACAGGAATCGGC 61.046 63.158 0.00 0.00 38.24 5.54
2774 2968 2.257207 AGGACTACACTAGCAGGCAAA 58.743 47.619 0.00 0.00 0.00 3.68
2837 3035 5.965033 AGGCAGGAAGATTTGAGAAGATA 57.035 39.130 0.00 0.00 0.00 1.98
2906 3107 8.664079 AGGATGATATTAGGCATATGGGATAAC 58.336 37.037 4.56 0.00 0.00 1.89
2908 3109 8.819122 AAGGATGATATTAGGCATATGGGATA 57.181 34.615 4.56 0.00 0.00 2.59
2962 3166 6.040504 ACCATGTGAAGTCGCTATATTACAGA 59.959 38.462 0.00 0.00 0.00 3.41
2989 3195 1.733526 GGGGCACAACGGCATAATC 59.266 57.895 0.00 0.00 43.60 1.75
3070 3276 6.836527 CCTTCTATCTCAGTCCCCGATTATAT 59.163 42.308 0.00 0.00 0.00 0.86
3136 3355 1.137404 CAGTGGCGCTTTACATGGC 59.863 57.895 7.64 0.00 0.00 4.40
3181 3400 6.811253 TTGACGTTTATAACAGAAGGCAAT 57.189 33.333 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.