Multiple sequence alignment - TraesCS7D01G514000

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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 TraesCS7D01G514000 chr7D 100.000 3239 0 0 1 3239 614816016 614819254 0 5982
1 TraesCS7D01G514000 chr7D 94.718 3029 105 16 264 3239 614795704 614798730 0 4656
2 TraesCS7D01G514000 chr7D 87.283 2249 258 16 1 2227 14414307 14412065 0 2543
3 TraesCS7D01G514000 chr7D 95.302 1490 48 7 531 1998 614740509 614741998 0 2344
4 TraesCS7D01G514000 chr7D 93.387 1240 50 7 2032 3239 614741984 614743223 0 1807
5 TraesCS7D01G514000 chrUn 92.489 2250 148 9 1 2229 81311244 81313493 0 3199
6 TraesCS7D01G514000 chrUn 91.945 1018 78 4 2225 3239 81313518 81314534 0 1423
7 TraesCS7D01G514000 chr6D 91.719 2246 163 11 1 2224 380504525 380502281 0 3096
8 TraesCS7D01G514000 chr6D 92.709 1015 70 4 2228 3239 380502248 380501235 0 1461
9 TraesCS7D01G514000 chr2D 90.917 2180 170 16 1 2157 563782954 563780780 0 2904
10 TraesCS7D01G514000 chr2D 91.535 1016 74 5 2228 3239 563764769 563763762 0 1389
11 TraesCS7D01G514000 chr7A 87.455 2240 255 18 13 2229 641424895 641422659 0 2556
12 TraesCS7D01G514000 chr4A 85.377 2120 283 14 133 2228 688501519 688503635 0 2172
13 TraesCS7D01G514000 chr4A 87.387 999 123 3 2236 3231 688503672 688504670 0 1144
14 TraesCS7D01G514000 chr5D 93.164 1302 89 0 928 2229 533247454 533248755 0 1912
15 TraesCS7D01G514000 chr5D 92.338 1018 75 3 2225 3239 533248780 533249797 0 1445
16 TraesCS7D01G514000 chr5D 92.134 1017 76 4 2225 3237 311468907 311469923 0 1432
17 TraesCS7D01G514000 chr5D 90.797 1054 73 8 1 1031 311466336 311467388 0 1387
18 TraesCS7D01G514000 chr5D 93.557 714 44 2 57 768 533246262 533246975 0 1062
19 TraesCS7D01G514000 chr5D 82.338 1189 173 24 1 1159 32755451 32754270 0 998
20 TraesCS7D01G514000 chr4B 87.587 1007 122 3 2236 3239 5581814 5580808 0 1164


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 TraesCS7D01G514000 chr7D 614816016 614819254 3238 False 5982.0 5982 100.000000 1 3239 1 chr7D.!!$F2 3238
1 TraesCS7D01G514000 chr7D 614795704 614798730 3026 False 4656.0 4656 94.718000 264 3239 1 chr7D.!!$F1 2975
2 TraesCS7D01G514000 chr7D 14412065 14414307 2242 True 2543.0 2543 87.283000 1 2227 1 chr7D.!!$R1 2226
3 TraesCS7D01G514000 chr7D 614740509 614743223 2714 False 2075.5 2344 94.344500 531 3239 2 chr7D.!!$F3 2708
4 TraesCS7D01G514000 chrUn 81311244 81314534 3290 False 2311.0 3199 92.217000 1 3239 2 chrUn.!!$F1 3238
5 TraesCS7D01G514000 chr6D 380501235 380504525 3290 True 2278.5 3096 92.214000 1 3239 2 chr6D.!!$R1 3238
6 TraesCS7D01G514000 chr2D 563780780 563782954 2174 True 2904.0 2904 90.917000 1 2157 1 chr2D.!!$R2 2156
7 TraesCS7D01G514000 chr2D 563763762 563764769 1007 True 1389.0 1389 91.535000 2228 3239 1 chr2D.!!$R1 1011
8 TraesCS7D01G514000 chr7A 641422659 641424895 2236 True 2556.0 2556 87.455000 13 2229 1 chr7A.!!$R1 2216
9 TraesCS7D01G514000 chr4A 688501519 688504670 3151 False 1658.0 2172 86.382000 133 3231 2 chr4A.!!$F1 3098
10 TraesCS7D01G514000 chr5D 533246262 533249797 3535 False 1473.0 1912 93.019667 57 3239 3 chr5D.!!$F2 3182
11 TraesCS7D01G514000 chr5D 311466336 311469923 3587 False 1409.5 1432 91.465500 1 3237 2 chr5D.!!$F1 3236
12 TraesCS7D01G514000 chr5D 32754270 32755451 1181 True 998.0 998 82.338000 1 1159 1 chr5D.!!$R1 1158
13 TraesCS7D01G514000 chr4B 5580808 5581814 1006 True 1164.0 1164 87.587000 2236 3239 1 chr4B.!!$R1 1003

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
649 655 0.107752 CAAAATGCCGGAATTGGGGG 60.108 55.0 8.93 0.00 0.00 5.40 F
650 656 0.252467 AAAATGCCGGAATTGGGGGA 60.252 50.0 8.93 0.00 0.00 4.81 F
1259 1891 1.133809 TGCTTTACCTGTGGAGGCCT 61.134 55.0 3.86 3.86 44.33 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1682 2314 1.057471 TGGGTCAATTGTACCGGTCA 58.943 50.000 12.4 6.49 37.93 4.02 R
2058 2693 1.202746 GGTTCCTCTCCATCATCCAGC 60.203 57.143 0.0 0.00 0.00 4.85 R
2364 3038 1.254284 CGTCCTCCAGCTCTTCCTGT 61.254 60.000 0.0 0.00 0.00 4.00 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
22 23 3.315949 GGTCCCACAGGCGGTGTA 61.316 66.667 16.41 1.66 46.44 2.90
34 35 1.374885 CGGTGTACATGGCGTCCAA 60.375 57.895 0.00 0.00 36.95 3.53
99 100 2.225791 CTTCGAGTGGATCCGGTGCA 62.226 60.000 7.39 0.00 0.00 4.57
112 113 1.748122 GGTGCATGCAGGAGTGGAG 60.748 63.158 23.41 0.00 0.00 3.86
242 243 1.135083 GCACGGAGAATCTTCGAGGAA 60.135 52.381 18.94 0.00 35.79 3.36
541 545 4.262894 CCAAAGGGACAAGTTAGTCAGCTA 60.263 45.833 0.00 0.00 40.29 3.32
637 641 2.125952 GCGGTGAGGCCAAAATGC 60.126 61.111 5.01 0.00 36.97 3.56
649 655 0.107752 CAAAATGCCGGAATTGGGGG 60.108 55.000 8.93 0.00 0.00 5.40
650 656 0.252467 AAAATGCCGGAATTGGGGGA 60.252 50.000 8.93 0.00 0.00 4.81
915 1220 6.757010 GCTCAGGAAAGATATAGTTCGTTTGA 59.243 38.462 0.00 0.00 0.00 2.69
916 1221 7.439655 GCTCAGGAAAGATATAGTTCGTTTGAT 59.560 37.037 0.00 0.00 0.00 2.57
917 1222 8.873215 TCAGGAAAGATATAGTTCGTTTGATC 57.127 34.615 0.00 0.00 0.00 2.92
918 1223 7.926555 TCAGGAAAGATATAGTTCGTTTGATCC 59.073 37.037 0.00 0.00 0.00 3.36
919 1224 7.928706 CAGGAAAGATATAGTTCGTTTGATCCT 59.071 37.037 0.00 0.00 0.00 3.24
920 1225 8.145122 AGGAAAGATATAGTTCGTTTGATCCTC 58.855 37.037 0.00 0.00 0.00 3.71
921 1226 7.385478 GGAAAGATATAGTTCGTTTGATCCTCC 59.615 40.741 0.00 0.00 0.00 4.30
924 1229 4.674281 ATAGTTCGTTTGATCCTCCTCC 57.326 45.455 0.00 0.00 0.00 4.30
925 1230 1.204941 AGTTCGTTTGATCCTCCTCCG 59.795 52.381 0.00 0.00 0.00 4.63
1001 1326 2.845345 GGATTGGGGCGGGATCCAT 61.845 63.158 15.23 0.00 39.30 3.41
1008 1333 1.227973 GGCGGGATCCATGTCCTTC 60.228 63.158 15.23 0.00 38.38 3.46
1089 1718 1.961180 CTCTGCCGAAGAATCCGGGT 61.961 60.000 0.00 0.00 46.55 5.28
1145 1777 2.811799 GCCCGGCAAAAGTGTTGT 59.188 55.556 3.91 0.00 0.00 3.32
1259 1891 1.133809 TGCTTTACCTGTGGAGGCCT 61.134 55.000 3.86 3.86 44.33 5.19
1343 1975 4.155644 TCACAATGTCAATAATTGCGCAGA 59.844 37.500 11.31 0.00 38.36 4.26
1348 1980 2.420022 GTCAATAATTGCGCAGACTGGT 59.580 45.455 11.31 0.00 0.00 4.00
1384 2016 1.981256 TGCCACTTTCTTTGGGAGTC 58.019 50.000 0.00 0.00 34.35 3.36
1543 2175 7.121168 TCTCTGGTATATTCTGCAAAAACAAGG 59.879 37.037 0.00 0.00 0.00 3.61
1670 2302 2.964740 CATCGATGGAGTGTCTGTGTT 58.035 47.619 17.96 0.00 0.00 3.32
1682 2314 4.522789 AGTGTCTGTGTTTGTGGAAAAGTT 59.477 37.500 0.00 0.00 0.00 2.66
2019 2651 6.330004 ACTGACATAGCTGTAGATGATGAG 57.670 41.667 0.00 0.00 35.14 2.90
2058 2693 5.835819 TGAGGAGGAACTAGATAAGGACATG 59.164 44.000 0.00 0.00 41.55 3.21
2194 2829 1.022735 GTTGGAGGCATGCATCTCTG 58.977 55.000 29.25 0.00 0.00 3.35
2195 2830 0.622136 TTGGAGGCATGCATCTCTGT 59.378 50.000 29.25 0.22 0.00 3.41
2214 2849 7.896811 TCTCTGTTGTGAGAGCTAATAAGAAA 58.103 34.615 0.00 0.00 39.59 2.52
2337 3002 3.535561 CTGCTATTACTTCCCCAGTGTG 58.464 50.000 0.00 0.00 35.97 3.82
2364 3038 6.542370 GCTCAAAAATATACTGTTCTGGCCTA 59.458 38.462 3.32 0.00 0.00 3.93
2366 3040 7.398829 TCAAAAATATACTGTTCTGGCCTACA 58.601 34.615 3.32 4.98 0.00 2.74
2398 3072 3.568853 GGAGGACGCTGCTTCTAATACTA 59.431 47.826 6.09 0.00 0.00 1.82
2408 3082 9.197694 CGCTGCTTCTAATACTAATAGTGAAAT 57.802 33.333 2.68 0.00 0.00 2.17
2525 3199 1.153756 CCAAGAACAAGTGGGGCCT 59.846 57.895 0.84 0.00 0.00 5.19
2871 3549 2.234908 ACTCCAAAGAGAGACATTCCCG 59.765 50.000 0.00 0.00 43.39 5.14
2893 3571 2.118076 CAACACACCAGGGGGCAT 59.882 61.111 0.00 0.00 37.90 4.40
2983 3661 7.587037 TCAAAATCCCATGATTGGTATCTTC 57.413 36.000 0.00 0.00 40.34 2.87
3042 3721 5.163343 ACAGTGCCTGTCTGACTTAGTTAAA 60.163 40.000 9.51 0.00 41.21 1.52
3093 3772 9.853177 TTTCAAGAAATTAAGAGAGAGACCTTT 57.147 29.630 0.00 0.00 0.00 3.11
3155 3834 7.966812 ACTTATGAATGACATATGCTACCTGA 58.033 34.615 1.58 0.00 40.56 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 4.312052 GGCTTTGGACGCCATGTA 57.688 55.556 0.00 0.00 46.77 2.29
99 100 1.992519 GCCATCCTCCACTCCTGCAT 61.993 60.000 0.00 0.00 0.00 3.96
242 243 3.073735 CTCTCCTCCAGCGTGGCT 61.074 66.667 0.00 0.00 40.77 4.75
392 393 0.179119 CCACCCGTAACGATCCTCAC 60.179 60.000 0.00 0.00 0.00 3.51
454 458 4.077184 TCGCCGCGGTCTCCAAAT 62.077 61.111 28.70 0.00 0.00 2.32
488 492 5.677319 ATCCCTTTGTTAGATCTCGAACA 57.323 39.130 0.00 2.23 39.18 3.18
529 533 7.097192 TCGATTGTGAAAATAGCTGACTAACT 58.903 34.615 0.00 0.00 30.45 2.24
629 633 0.107752 CCCCAATTCCGGCATTTTGG 60.108 55.000 14.13 14.13 38.66 3.28
631 635 0.252467 TCCCCCAATTCCGGCATTTT 60.252 50.000 0.00 0.00 0.00 1.82
636 640 0.464036 GAAAATCCCCCAATTCCGGC 59.536 55.000 0.00 0.00 0.00 6.13
637 641 1.119684 GGAAAATCCCCCAATTCCGG 58.880 55.000 0.00 0.00 32.72 5.14
649 655 2.162408 CCTCGCAACTCAAGGGAAAATC 59.838 50.000 0.00 0.00 0.00 2.17
650 656 2.162681 CCTCGCAACTCAAGGGAAAAT 58.837 47.619 0.00 0.00 0.00 1.82
761 767 1.020333 CGTCGTCTCGAGGAGGAAGT 61.020 60.000 13.56 0.00 43.12 3.01
915 1220 0.755686 GATGCTTGTCGGAGGAGGAT 59.244 55.000 0.00 0.00 0.00 3.24
916 1221 0.324738 AGATGCTTGTCGGAGGAGGA 60.325 55.000 0.00 0.00 0.00 3.71
917 1222 0.103937 GAGATGCTTGTCGGAGGAGG 59.896 60.000 0.00 0.00 0.00 4.30
918 1223 0.103937 GGAGATGCTTGTCGGAGGAG 59.896 60.000 0.00 0.00 0.00 3.69
919 1224 1.667154 CGGAGATGCTTGTCGGAGGA 61.667 60.000 0.00 0.00 0.00 3.71
920 1225 1.227089 CGGAGATGCTTGTCGGAGG 60.227 63.158 0.00 0.00 0.00 4.30
921 1226 1.880340 GCGGAGATGCTTGTCGGAG 60.880 63.158 8.20 0.00 0.00 4.63
924 1229 2.892425 GGGCGGAGATGCTTGTCG 60.892 66.667 0.00 0.00 34.52 4.35
925 1230 2.892425 CGGGCGGAGATGCTTGTC 60.892 66.667 0.00 0.00 34.52 3.18
1024 1350 3.864686 CGGCGCATTCTTGTCCGG 61.865 66.667 10.83 0.00 37.42 5.14
1138 1770 1.344953 TGTGCAGGAGGGACAACACT 61.345 55.000 0.00 0.00 45.55 3.55
1145 1777 1.150536 GTGGTTTGTGCAGGAGGGA 59.849 57.895 0.00 0.00 0.00 4.20
1259 1891 1.417145 AGTTACCAACGTAGTGGCCAA 59.583 47.619 7.24 0.00 45.00 4.52
1348 1980 2.637382 TGGCAACTAGATGAGGTTGTGA 59.363 45.455 3.85 0.00 43.07 3.58
1397 2029 2.420129 GCGTCAATGTGATAGAACCCCT 60.420 50.000 0.00 0.00 0.00 4.79
1543 2175 1.134699 TCTGATCTGCCACGTCCATTC 60.135 52.381 0.00 0.00 0.00 2.67
1670 2302 2.131776 ACCGGTCAACTTTTCCACAA 57.868 45.000 0.00 0.00 0.00 3.33
1682 2314 1.057471 TGGGTCAATTGTACCGGTCA 58.943 50.000 12.40 6.49 37.93 4.02
2019 2651 5.745227 TCCTCCTCATCAATTACCTTGTTC 58.255 41.667 0.00 0.00 36.20 3.18
2058 2693 1.202746 GGTTCCTCTCCATCATCCAGC 60.203 57.143 0.00 0.00 0.00 4.85
2194 2829 8.311650 TCAGTTTTCTTATTAGCTCTCACAAC 57.688 34.615 0.00 0.00 0.00 3.32
2195 2830 8.902540 TTCAGTTTTCTTATTAGCTCTCACAA 57.097 30.769 0.00 0.00 0.00 3.33
2337 3002 6.030228 GCCAGAACAGTATATTTTTGAGCAC 58.970 40.000 0.00 0.00 0.00 4.40
2364 3038 1.254284 CGTCCTCCAGCTCTTCCTGT 61.254 60.000 0.00 0.00 0.00 4.00
2366 3040 2.355193 GCGTCCTCCAGCTCTTCCT 61.355 63.158 0.00 0.00 0.00 3.36
2398 3072 8.579850 TCATCTGGTTTAGCAATTTCACTATT 57.420 30.769 0.00 0.00 0.00 1.73
2408 3082 4.706476 CCATTTCCTCATCTGGTTTAGCAA 59.294 41.667 0.00 0.00 0.00 3.91
2413 3087 4.082125 GTGTCCATTTCCTCATCTGGTTT 58.918 43.478 0.00 0.00 0.00 3.27
2871 3549 1.528309 CCCCTGGTGTGTTGGTGTC 60.528 63.158 0.00 0.00 0.00 3.67
2893 3571 2.113774 CACCCTCAGCACCAGCAA 59.886 61.111 0.00 0.00 45.49 3.91
2983 3661 3.138283 TGGCCCAAACCTCTATATTCCAG 59.862 47.826 0.00 0.00 0.00 3.86
3093 3772 3.560025 GGGCATTGAGGAAAGAGTCAGAA 60.560 47.826 0.00 0.00 0.00 3.02
3130 3809 7.966812 TCAGGTAGCATATGTCATTCATAAGT 58.033 34.615 4.29 0.00 41.57 2.24
3155 3834 1.997874 CCCCCAGCAGAGCCTACTT 60.998 63.158 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.