Multiple sequence alignment - TraesCS7B01G188200

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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 TraesCS7B01G188200 chr7B 100.000 2519 0 0 1 2519 318839814 318842332 0.000000e+00 4652
1 TraesCS7B01G188200 chr7A 93.037 2140 98 18 405 2519 414185846 414183733 0.000000e+00 3079
2 TraesCS7B01G188200 chr7D 94.224 1887 58 16 579 2437 371267661 371269524 0.000000e+00 2833
3 TraesCS7B01G188200 chr7D 88.567 586 57 8 1 581 371265084 371265664 0.000000e+00 702
4 TraesCS7B01G188200 chr7D 100.000 85 0 0 2435 2519 371269682 371269766 9.330000e-35 158


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 TraesCS7B01G188200 chr7B 318839814 318842332 2518 False 4652 4652 100.000000 1 2519 1 chr7B.!!$F1 2518
1 TraesCS7B01G188200 chr7A 414183733 414185846 2113 True 3079 3079 93.037000 405 2519 1 chr7A.!!$R1 2114
2 TraesCS7B01G188200 chr7D 371265084 371269766 4682 False 1231 2833 94.263667 1 2519 3 chr7D.!!$F1 2518

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
500 506 0.03467 AAAGGCCCAGCTCAGATGAC 60.035 55.0 0.0 0.0 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2148 4194 0.252197 GTCCATCCACCACCTACACC 59.748 60.0 0.0 0.0 0.0 4.16 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
20 21 0.109504 CCAATTTGTTACGGGTGGCG 60.110 55.000 0.00 0.00 0.00 5.69
24 25 3.534054 TTGTTACGGGTGGCGGGAC 62.534 63.158 0.00 0.00 0.00 4.46
60 61 2.229543 TGTCGCAACCTACTACAACGAT 59.770 45.455 0.00 0.00 0.00 3.73
68 69 1.867233 CTACTACAACGATGGCCATGC 59.133 52.381 26.56 13.83 0.00 4.06
81 82 0.536006 GCCATGCCGGAAGCTAGAAT 60.536 55.000 5.05 0.00 44.23 2.40
83 84 1.143305 CATGCCGGAAGCTAGAATCG 58.857 55.000 5.05 0.00 44.23 3.34
101 104 2.016165 GGCAGCCGTTTTTGCGAAG 61.016 57.895 0.00 0.00 41.17 3.79
113 116 1.171549 TTGCGAAGTGGCTTGCATCA 61.172 50.000 0.00 0.00 37.17 3.07
126 130 1.742880 GCATCAGAGCTGCAACCGA 60.743 57.895 1.02 0.00 39.46 4.69
131 135 0.460811 CAGAGCTGCAACCGATAGCA 60.461 55.000 1.02 0.00 39.84 3.49
148 152 0.246635 GCAGGAGAAGCTACAACCGA 59.753 55.000 0.00 0.00 0.00 4.69
149 153 1.997669 CAGGAGAAGCTACAACCGAC 58.002 55.000 0.00 0.00 0.00 4.79
228 232 2.191786 AAATGCGACATCCCCGGTGA 62.192 55.000 0.00 0.00 0.00 4.02
232 236 1.594833 CGACATCCCCGGTGAAAGA 59.405 57.895 0.00 0.00 0.00 2.52
248 252 0.463116 AAGAAGTTGCAACCGTCGGT 60.463 50.000 25.62 12.23 37.65 4.69
253 257 1.885388 TTGCAACCGTCGGTGACAG 60.885 57.895 19.67 9.71 35.34 3.51
256 260 1.372997 CAACCGTCGGTGACAGAGG 60.373 63.158 19.67 0.00 35.34 3.69
266 270 1.208052 GGTGACAGAGGCTGCTATCAA 59.792 52.381 0.00 0.00 34.37 2.57
287 291 0.897621 GGATGACAAAAAGGGGGCAG 59.102 55.000 0.00 0.00 0.00 4.85
289 293 1.273327 GATGACAAAAAGGGGGCAGTG 59.727 52.381 0.00 0.00 0.00 3.66
300 304 4.008933 GGCAGTGACGGGTGCTCT 62.009 66.667 0.00 0.00 39.76 4.09
301 305 2.740055 GCAGTGACGGGTGCTCTG 60.740 66.667 0.00 0.00 36.71 3.35
302 306 2.740055 CAGTGACGGGTGCTCTGC 60.740 66.667 0.00 0.00 0.00 4.26
366 370 1.830368 CGTTGAGCGCATGTGTGTGA 61.830 55.000 11.47 0.00 38.10 3.58
386 391 2.734079 GAGGAGAGAGTTGACTTTTGCG 59.266 50.000 0.00 0.00 0.00 4.85
388 393 1.801178 GAGAGAGTTGACTTTTGCGGG 59.199 52.381 0.00 0.00 0.00 6.13
394 399 1.710996 TTGACTTTTGCGGGGGAGGA 61.711 55.000 0.00 0.00 0.00 3.71
395 400 1.377333 GACTTTTGCGGGGGAGGAG 60.377 63.158 0.00 0.00 0.00 3.69
396 401 2.044946 CTTTTGCGGGGGAGGAGG 60.045 66.667 0.00 0.00 0.00 4.30
397 402 2.530661 TTTTGCGGGGGAGGAGGA 60.531 61.111 0.00 0.00 0.00 3.71
500 506 0.034670 AAAGGCCCAGCTCAGATGAC 60.035 55.000 0.00 0.00 0.00 3.06
508 514 2.357075 CAGCTCAGATGACTTGTGCAT 58.643 47.619 0.00 0.00 0.00 3.96
516 522 4.692155 CAGATGACTTGTGCATGTTACTCA 59.308 41.667 0.00 0.00 0.00 3.41
589 2608 4.772100 GGCCCATATATGTAACAAAGCCAT 59.228 41.667 11.73 0.00 36.67 4.40
633 2652 0.320946 TAACTACGGGTTGCACTGCC 60.321 55.000 0.00 0.00 38.75 4.85
701 2720 2.280524 TGATATTTCCGGCGGCGG 60.281 61.111 41.57 41.57 0.00 6.13
809 2833 3.896648 TTCTCGCTTGACATGTTTTCC 57.103 42.857 0.00 0.00 0.00 3.13
925 2949 1.316266 CCACCTCTCCTCCCCTCAT 59.684 63.158 0.00 0.00 0.00 2.90
1056 3080 2.270205 CAGCCGCTCATCCTGGTT 59.730 61.111 0.00 0.00 0.00 3.67
1219 3243 1.120530 GTCCTCTTTATCCCTGGCGA 58.879 55.000 0.00 0.00 0.00 5.54
1615 3639 0.761802 CTAGGCCCTTCTCCATCCAC 59.238 60.000 0.00 0.00 0.00 4.02
1655 3679 2.964740 TCCATGCTTTCACGAGAGAAG 58.035 47.619 0.00 0.00 0.00 2.85
1676 3700 4.171234 AGTCAAAAGGGGATGAGAGAGAA 58.829 43.478 0.00 0.00 0.00 2.87
1684 3728 3.966665 GGGGATGAGAGAGAAAGAGACAT 59.033 47.826 0.00 0.00 0.00 3.06
1921 3967 5.860648 TTGTAATTTCCTTCCCCTTCTCT 57.139 39.130 0.00 0.00 0.00 3.10
1964 4010 8.736244 TCTATTAACTTATTTTGTGAGGGCAAC 58.264 33.333 0.00 0.00 0.00 4.17
1976 4022 3.704061 GTGAGGGCAACTAAGAGAGAGAT 59.296 47.826 0.00 0.00 0.00 2.75
2081 4127 9.890629 ACTTATCTTATTCTTTGATGTGTGCTA 57.109 29.630 0.00 0.00 0.00 3.49
2361 4410 0.645355 CACTAGTAATGGTGCACGCG 59.355 55.000 11.45 3.53 0.00 6.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.893808 GACATAGTGCCCCGCATGG 60.894 63.158 0.00 0.00 41.91 3.66
27 28 4.830765 GCGACATAGTGCCCCGCA 62.831 66.667 0.00 0.00 44.55 5.69
34 35 4.365899 TGTAGTAGGTTGCGACATAGTG 57.634 45.455 14.97 0.00 29.32 2.74
68 69 0.598680 CTGCCGATTCTAGCTTCCGG 60.599 60.000 0.00 0.00 42.74 5.14
83 84 2.016165 CTTCGCAAAAACGGCTGCC 61.016 57.895 9.11 9.11 35.01 4.85
90 91 0.576798 GCAAGCCACTTCGCAAAAAC 59.423 50.000 0.00 0.00 0.00 2.43
101 104 1.801332 CAGCTCTGATGCAAGCCAC 59.199 57.895 4.49 0.00 39.39 5.01
113 116 1.900351 TGCTATCGGTTGCAGCTCT 59.100 52.632 0.00 0.00 36.26 4.09
123 126 1.957177 TGTAGCTTCTCCTGCTATCGG 59.043 52.381 0.00 0.00 43.66 4.18
126 130 2.101582 CGGTTGTAGCTTCTCCTGCTAT 59.898 50.000 0.00 0.00 43.66 2.97
131 135 0.526662 CGTCGGTTGTAGCTTCTCCT 59.473 55.000 0.00 0.00 0.00 3.69
164 168 0.957395 ACAGGTTTGCAGAGCCATCG 60.957 55.000 2.36 0.00 0.00 3.84
166 170 2.814805 ATACAGGTTTGCAGAGCCAT 57.185 45.000 2.36 0.00 0.00 4.40
167 171 2.584835 AATACAGGTTTGCAGAGCCA 57.415 45.000 2.36 0.00 0.00 4.75
228 232 0.661020 CCGACGGTTGCAACTTCTTT 59.339 50.000 27.64 8.82 0.00 2.52
232 236 1.153329 TCACCGACGGTTGCAACTT 60.153 52.632 27.64 15.86 31.02 2.66
248 252 1.134995 CGTTGATAGCAGCCTCTGTCA 60.135 52.381 0.00 0.00 33.33 3.58
253 257 1.069204 TCATCCGTTGATAGCAGCCTC 59.931 52.381 0.00 0.00 0.00 4.70
256 260 1.939974 TGTCATCCGTTGATAGCAGC 58.060 50.000 0.00 0.00 36.54 5.25
266 270 0.898326 GCCCCCTTTTTGTCATCCGT 60.898 55.000 0.00 0.00 0.00 4.69
336 340 2.432456 CTCAACGCTAGCCGCACA 60.432 61.111 9.66 0.00 41.76 4.57
348 352 0.110509 CTCACACACATGCGCTCAAC 60.111 55.000 9.73 0.00 0.00 3.18
357 361 3.006323 GTCAACTCTCTCCTCACACACAT 59.994 47.826 0.00 0.00 0.00 3.21
362 366 4.697514 CAAAAGTCAACTCTCTCCTCACA 58.302 43.478 0.00 0.00 0.00 3.58
366 370 2.548920 CCGCAAAAGTCAACTCTCTCCT 60.549 50.000 0.00 0.00 0.00 3.69
386 391 2.515853 AGATTTGAATTCCTCCTCCCCC 59.484 50.000 2.27 0.00 0.00 5.40
388 393 4.510167 TCAGATTTGAATTCCTCCTCCC 57.490 45.455 2.27 0.00 0.00 4.30
394 399 5.337009 GCACAACCATCAGATTTGAATTCCT 60.337 40.000 2.27 0.00 36.78 3.36
395 400 4.866486 GCACAACCATCAGATTTGAATTCC 59.134 41.667 2.27 0.00 36.78 3.01
396 401 5.717119 AGCACAACCATCAGATTTGAATTC 58.283 37.500 0.00 0.00 36.78 2.17
397 402 5.733620 AGCACAACCATCAGATTTGAATT 57.266 34.783 2.36 0.00 36.78 2.17
488 494 1.804601 TGCACAAGTCATCTGAGCTG 58.195 50.000 0.00 0.00 0.00 4.24
549 569 1.523154 GCCGATGACACCTGCCAAAA 61.523 55.000 0.00 0.00 0.00 2.44
589 2608 1.007038 GAAGACGTGCGTGTGGGTA 60.007 57.895 0.67 0.00 0.00 3.69
809 2833 2.448219 GAGGCTACGCGTACTACAAAG 58.552 52.381 16.41 6.73 0.00 2.77
839 2863 1.160870 TTTGGAGGAGAGGGCCAGA 59.839 57.895 6.18 0.00 32.47 3.86
840 2864 1.301293 GTTTGGAGGAGAGGGCCAG 59.699 63.158 6.18 0.00 32.47 4.85
841 2865 0.846427 ATGTTTGGAGGAGAGGGCCA 60.846 55.000 6.18 0.00 0.00 5.36
842 2866 1.141858 CTATGTTTGGAGGAGAGGGCC 59.858 57.143 0.00 0.00 0.00 5.80
843 2867 1.475930 GCTATGTTTGGAGGAGAGGGC 60.476 57.143 0.00 0.00 0.00 5.19
844 2868 1.141858 GGCTATGTTTGGAGGAGAGGG 59.858 57.143 0.00 0.00 0.00 4.30
849 2873 0.255890 GGCAGGCTATGTTTGGAGGA 59.744 55.000 0.00 0.00 0.00 3.71
1056 3080 1.080230 GAAGTCGAGCAGCTGCAGA 60.080 57.895 38.24 31.65 45.16 4.26
1504 3528 3.467803 CGTGAGGTCAGAAGGAAAAAGT 58.532 45.455 0.00 0.00 0.00 2.66
1556 3580 1.899054 CCTATCTCTGGCGGCGAGA 60.899 63.158 26.31 26.31 41.36 4.04
1615 3639 4.227134 CGTGGAGAGATGGGCGGG 62.227 72.222 0.00 0.00 0.00 6.13
1655 3679 4.559862 TTCTCTCTCATCCCCTTTTGAC 57.440 45.455 0.00 0.00 0.00 3.18
1676 3700 4.338118 CCTCTTCTTCTCGCTATGTCTCTT 59.662 45.833 0.00 0.00 0.00 2.85
1684 3728 1.202582 GCACACCTCTTCTTCTCGCTA 59.797 52.381 0.00 0.00 0.00 4.26
1897 3943 6.249192 AGAGAAGGGGAAGGAAATTACAAAG 58.751 40.000 0.00 0.00 0.00 2.77
1976 4022 9.647918 ACCTATGTACATCTCTCTTTCTTGATA 57.352 33.333 12.68 0.00 0.00 2.15
2001 4047 2.609459 CGATATTGTCAAGTGGAGGCAC 59.391 50.000 0.00 0.00 0.00 5.01
2137 4183 3.585289 ACCACCTACACCACATACAATCA 59.415 43.478 0.00 0.00 0.00 2.57
2148 4194 0.252197 GTCCATCCACCACCTACACC 59.748 60.000 0.00 0.00 0.00 4.16
2247 4293 4.039603 AGCAATGCTTATCCTAATCCCC 57.960 45.455 0.00 0.00 33.89 4.81
2278 4324 7.013274 AGTGGCGATTAATTAAGCATTGTACAT 59.987 33.333 13.48 0.00 0.00 2.29
2281 4327 6.724263 CAGTGGCGATTAATTAAGCATTGTA 58.276 36.000 13.48 0.00 0.00 2.41
2285 4331 4.228912 GCAGTGGCGATTAATTAAGCAT 57.771 40.909 13.48 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.