Multiple sequence alignment - TraesCS7B01G141500

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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 TraesCS7B01G141500 chr7B 100.000 3367 0 0 1 3367 179707426 179704060 0.000000e+00 6218
1 TraesCS7B01G141500 chr6B 96.798 3373 95 7 1 3367 158274405 158271040 0.000000e+00 5618
2 TraesCS7B01G141500 chr6B 93.590 78 5 0 3290 3367 666887771 666887694 2.120000e-22 117
3 TraesCS7B01G141500 chr6B 89.873 79 6 2 3290 3367 42919864 42919787 2.140000e-17 100
4 TraesCS7B01G141500 chr6B 90.000 80 4 3 3290 3367 71659498 71659421 2.140000e-17 100
5 TraesCS7B01G141500 chr4A 96.376 2732 87 7 645 3367 672472755 672470027 0.000000e+00 4486
6 TraesCS7B01G141500 chr4A 96.349 2027 67 5 1347 3367 660057154 660059179 0.000000e+00 3326
7 TraesCS7B01G141500 chr3B 96.157 2732 90 10 645 3367 713896361 713893636 0.000000e+00 4449
8 TraesCS7B01G141500 chr3B 96.455 2003 65 4 624 2622 306836432 306834432 0.000000e+00 3301
9 TraesCS7B01G141500 chr3B 95.153 1403 56 1 1 1391 18314317 18315719 0.000000e+00 2204
10 TraesCS7B01G141500 chr3B 95.753 989 42 0 624 1612 731043935 731044923 0.000000e+00 1594
11 TraesCS7B01G141500 chr3B 97.051 712 21 0 38 749 459507352 459506641 0.000000e+00 1199
12 TraesCS7B01G141500 chr3B 98.251 343 6 0 1 343 821806783 821806441 4.810000e-168 601
13 TraesCS7B01G141500 chr3B 96.330 327 8 1 1 323 731043596 731043922 4.940000e-148 534
14 TraesCS7B01G141500 chr3B 97.949 195 4 0 129 323 306836639 306836445 4.160000e-89 339
15 TraesCS7B01G141500 chr3B 96.923 195 6 0 129 323 27361098 27360904 9.010000e-86 327
16 TraesCS7B01G141500 chr3B 96.923 195 6 0 129 323 713896550 713896356 9.010000e-86 327
17 TraesCS7B01G141500 chr3B 97.403 154 4 0 1 154 17005167 17005320 2.580000e-66 263
18 TraesCS7B01G141500 chr3B 93.785 177 7 1 3 179 326636071 326635899 2.580000e-66 263
19 TraesCS7B01G141500 chr3B 96.753 154 5 0 1 154 768521661 768521508 1.200000e-64 257
20 TraesCS7B01G141500 chr3B 80.175 343 51 13 268 603 87728797 87728465 1.210000e-59 241
21 TraesCS7B01G141500 chr5B 96.339 2704 88 9 624 3321 682755397 682758095 0.000000e+00 4434
22 TraesCS7B01G141500 chr5B 94.054 555 16 5 2814 3367 695581864 695581326 0.000000e+00 826
23 TraesCS7B01G141500 chr5B 95.395 456 17 3 2913 3367 36654540 36654992 0.000000e+00 723
24 TraesCS7B01G141500 chr5B 95.395 456 17 3 2913 3367 36688062 36688514 0.000000e+00 723
25 TraesCS7B01G141500 chr5B 96.599 147 5 0 2656 2802 9024588 9024734 9.330000e-61 244
26 TraesCS7B01G141500 chr2B 96.588 2579 81 5 447 3021 636832644 636830069 0.000000e+00 4268
27 TraesCS7B01G141500 chr2B 96.003 2452 82 5 624 3060 371495428 371492978 0.000000e+00 3971
28 TraesCS7B01G141500 chr2B 97.101 1966 49 6 1407 3367 731752848 731750886 0.000000e+00 3308
29 TraesCS7B01G141500 chr1B 96.515 746 22 1 1 746 526003651 526004392 0.000000e+00 1230


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 TraesCS7B01G141500 chr7B 179704060 179707426 3366 True 6218 6218 100.0000 1 3367 1 chr7B.!!$R1 3366
1 TraesCS7B01G141500 chr6B 158271040 158274405 3365 True 5618 5618 96.7980 1 3367 1 chr6B.!!$R3 3366
2 TraesCS7B01G141500 chr4A 672470027 672472755 2728 True 4486 4486 96.3760 645 3367 1 chr4A.!!$R1 2722
3 TraesCS7B01G141500 chr4A 660057154 660059179 2025 False 3326 3326 96.3490 1347 3367 1 chr4A.!!$F1 2020
4 TraesCS7B01G141500 chr3B 713893636 713896550 2914 True 2388 4449 96.5400 129 3367 2 chr3B.!!$R8 3238
5 TraesCS7B01G141500 chr3B 18314317 18315719 1402 False 2204 2204 95.1530 1 1391 1 chr3B.!!$F2 1390
6 TraesCS7B01G141500 chr3B 306834432 306836639 2207 True 1820 3301 97.2020 129 2622 2 chr3B.!!$R7 2493
7 TraesCS7B01G141500 chr3B 459506641 459507352 711 True 1199 1199 97.0510 38 749 1 chr3B.!!$R4 711
8 TraesCS7B01G141500 chr3B 731043596 731044923 1327 False 1064 1594 96.0415 1 1612 2 chr3B.!!$F3 1611
9 TraesCS7B01G141500 chr5B 682755397 682758095 2698 False 4434 4434 96.3390 624 3321 1 chr5B.!!$F4 2697
10 TraesCS7B01G141500 chr5B 695581326 695581864 538 True 826 826 94.0540 2814 3367 1 chr5B.!!$R1 553
11 TraesCS7B01G141500 chr2B 636830069 636832644 2575 True 4268 4268 96.5880 447 3021 1 chr2B.!!$R2 2574
12 TraesCS7B01G141500 chr2B 371492978 371495428 2450 True 3971 3971 96.0030 624 3060 1 chr2B.!!$R1 2436
13 TraesCS7B01G141500 chr2B 731750886 731752848 1962 True 3308 3308 97.1010 1407 3367 1 chr2B.!!$R3 1960
14 TraesCS7B01G141500 chr1B 526003651 526004392 741 False 1230 1230 96.5150 1 746 1 chr1B.!!$F1 745

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
730 743 1.407618 GGGCAGGACGTTTGAGTTTTT 59.592 47.619 5.32 0.0 0.00 1.94 F
2247 2280 0.179137 CAAGCTCATCGAGTACGCCA 60.179 55.000 0.00 0.0 39.58 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2252 2285 0.097499 CGTAGGTGTCGTACGCATCA 59.903 55.0 19.94 12.57 40.31 3.07 R
3267 3309 0.787084 CTCCCCCTAGCTATCCTCCA 59.213 60.0 0.00 0.00 0.00 3.86 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 3.420893 CCAGTCAGGCAGGAAATAAACA 58.579 45.455 0.00 0.00 0.00 2.83
169 182 8.430801 AATGCATGCAAGTTTAAAGTAAAACA 57.569 26.923 26.68 0.00 40.97 2.83
315 328 7.024340 TCAGTTTCGTCAGATATAGGTGTAC 57.976 40.000 0.00 0.00 0.00 2.90
357 370 6.889301 TTCATCAGAGAAGTTTGCTTTCAT 57.111 33.333 0.00 0.00 34.61 2.57
579 592 7.906327 AGAAGAGAAATAGAGAGCAGAAAAGT 58.094 34.615 0.00 0.00 0.00 2.66
583 596 4.935885 AATAGAGAGCAGAAAAGTTGCG 57.064 40.909 0.00 0.00 45.98 4.85
592 605 4.044426 GCAGAAAAGTTGCGAAGTTGAAT 58.956 39.130 0.00 0.00 0.00 2.57
688 701 1.834263 CTCCCCTCCAGAGTTTTCGAT 59.166 52.381 0.00 0.00 0.00 3.59
730 743 1.407618 GGGCAGGACGTTTGAGTTTTT 59.592 47.619 5.32 0.00 0.00 1.94
777 790 2.351276 GGCAACTCCCCATGACGT 59.649 61.111 0.00 0.00 0.00 4.34
828 841 2.061061 CTCCCCTCCTATTCCATTGCT 58.939 52.381 0.00 0.00 0.00 3.91
848 871 1.575788 TGCTCCATCTTCCTCCCTCTA 59.424 52.381 0.00 0.00 0.00 2.43
882 905 1.645455 CATTGCCGCTCCATCTTCG 59.355 57.895 0.00 0.00 0.00 3.79
1104 1127 3.368571 GACGACGTTCCGGTCCCT 61.369 66.667 0.13 0.00 33.30 4.20
1114 1137 3.322466 CGGTCCCTGGGCAGAAGT 61.322 66.667 8.22 0.00 0.00 3.01
1246 1269 2.359850 TCGGCGGCATGCTTTCTT 60.360 55.556 18.92 0.00 45.43 2.52
1311 1334 1.199789 CCGCAAATTGCTGCAGTTCTA 59.800 47.619 16.64 0.00 42.25 2.10
1325 1348 2.930040 CAGTTCTACAGTTATGCGTGGG 59.070 50.000 0.00 0.00 0.00 4.61
1336 1359 3.148279 GCGTGGGGGATCTCGTCT 61.148 66.667 0.00 0.00 0.00 4.18
1541 1565 8.977505 TGAAGTTTTTGAAGTTTCTGAAGTTTG 58.022 29.630 0.00 0.00 0.00 2.93
1810 1842 9.378551 TCATTTAGTAGTTGTTGTGATCATACC 57.621 33.333 0.00 0.00 0.00 2.73
1813 1845 5.408356 AGTAGTTGTTGTGATCATACCGTC 58.592 41.667 0.00 0.00 0.00 4.79
1929 1962 5.357878 TGAAGTAGATGAATTTGATGCACCC 59.642 40.000 0.00 0.00 0.00 4.61
1945 1978 3.384146 TGCACCCGATTAATTTGATGCAT 59.616 39.130 0.00 0.00 36.94 3.96
2125 2158 2.736670 AAGAAGTGGCAGTCTTTGGT 57.263 45.000 7.40 0.00 29.67 3.67
2198 2231 1.191535 TCGACAGGAATTCGGACCAT 58.808 50.000 0.00 0.00 37.09 3.55
2247 2280 0.179137 CAAGCTCATCGAGTACGCCA 60.179 55.000 0.00 0.00 39.58 5.69
2252 2285 0.736636 TCATCGAGTACGCCACGAAT 59.263 50.000 10.24 0.62 39.38 3.34
2263 2296 1.143373 GCCACGAATGATGCGTACGA 61.143 55.000 21.65 4.52 40.44 3.43
2498 2532 7.224362 TGAACAAGTTTGCTTTTGTAATGATGG 59.776 33.333 0.00 0.00 36.56 3.51
2737 2771 7.455058 TGTAGTTACACATTCCAACCAATACT 58.545 34.615 0.00 0.00 0.00 2.12
2743 2777 3.056607 ACATTCCAACCAATACTTGCAGC 60.057 43.478 0.00 0.00 0.00 5.25
2792 2826 9.499585 CATCAATGACTAAGTGAAGCAAATAAG 57.500 33.333 0.00 0.00 0.00 1.73
3267 3309 1.535202 GGGATCTGGCGAGAGGGAT 60.535 63.158 4.31 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 7.093945 GGAAAGTAATGTTTATTTCCTGCCTGA 60.094 37.037 8.03 0.00 44.72 3.86
169 182 7.398024 AGAGGAGTACTTGCATTAACTGAAAT 58.602 34.615 0.00 0.00 0.00 2.17
315 328 6.481313 TGATGAAACTGACAGAGACTGAAAAG 59.519 38.462 10.08 3.04 35.18 2.27
357 370 4.014847 CGCAGCTCGGATTATTTGAAAA 57.985 40.909 0.00 0.00 33.78 2.29
432 445 1.201647 CCATGACCGTCTAGTTCGTGT 59.798 52.381 0.00 6.62 0.00 4.49
579 592 0.886938 TCCCGCATTCAACTTCGCAA 60.887 50.000 0.00 0.00 0.00 4.85
583 596 2.034053 TGTTTGTCCCGCATTCAACTTC 59.966 45.455 0.00 0.00 0.00 3.01
592 605 4.155099 CAGTTATAATGTGTTTGTCCCGCA 59.845 41.667 0.00 0.00 0.00 5.69
777 790 1.990327 GTGGGAAGAAAACCCCCTCTA 59.010 52.381 0.00 0.00 46.21 2.43
828 841 0.341258 AGAGGGAGGAAGATGGAGCA 59.659 55.000 0.00 0.00 0.00 4.26
848 871 1.849039 CAATGGAATGAGGAGGGAGGT 59.151 52.381 0.00 0.00 0.00 3.85
882 905 0.757561 GCAGAGGGAGGTAGAGGGAC 60.758 65.000 0.00 0.00 0.00 4.46
947 970 1.852157 TTCCTTCGCCATTGCCCTCT 61.852 55.000 0.00 0.00 0.00 3.69
971 994 2.203788 ACGGAGGGGAGTTGCTCA 60.204 61.111 0.00 0.00 31.08 4.26
1032 1055 1.399714 CATGGTGATGCTTGGCAGAT 58.600 50.000 0.00 0.00 43.65 2.90
1104 1127 0.472925 TGTAGTCCCACTTCTGCCCA 60.473 55.000 0.00 0.00 0.00 5.36
1246 1269 2.479837 GACATCAACGCCGATATTCCA 58.520 47.619 0.00 0.00 0.00 3.53
1311 1334 0.180406 GATCCCCCACGCATAACTGT 59.820 55.000 0.00 0.00 0.00 3.55
1325 1348 3.228453 TGGTATACCAAGACGAGATCCC 58.772 50.000 22.59 0.00 44.35 3.85
1541 1565 7.547370 ACTTCAGAACTATTGCATCTACTTCAC 59.453 37.037 0.00 0.00 0.00 3.18
1810 1842 6.539649 TCTGACCAAAATTCAGTTAAGACG 57.460 37.500 0.00 0.00 41.22 4.18
1813 1845 7.930217 TCAGTTCTGACCAAAATTCAGTTAAG 58.070 34.615 0.00 0.00 41.22 1.85
1929 1962 3.979948 TGGGCATGCATCAAATTAATCG 58.020 40.909 21.36 0.00 0.00 3.34
1945 1978 4.344865 GGCGGAGTTCCTTGGGCA 62.345 66.667 0.00 0.00 0.00 5.36
2099 2132 4.640771 AGACTGCCACTTCTTTCCATTA 57.359 40.909 0.00 0.00 0.00 1.90
2125 2158 1.152694 AGGCTGGCTGCAAACTCAA 60.153 52.632 18.32 0.00 45.15 3.02
2247 2280 1.265568 GTGTCGTACGCATCATTCGT 58.734 50.000 11.24 0.00 43.20 3.85
2252 2285 0.097499 CGTAGGTGTCGTACGCATCA 59.903 55.000 19.94 12.57 40.31 3.07
2263 2296 0.537188 CTTCCATGCCTCGTAGGTGT 59.463 55.000 3.38 0.00 37.80 4.16
2410 2443 7.043656 GCAAACTTTTCAACCACATAACTACAC 60.044 37.037 0.00 0.00 0.00 2.90
2498 2532 3.843999 TGACAACCAAAGCAAACTTGTC 58.156 40.909 0.00 0.00 40.67 3.18
2737 2771 6.816134 TCAGTATGAAATTACAAGCTGCAA 57.184 33.333 1.02 0.00 45.97 4.08
2792 2826 2.533266 GTGCCAAGAAATGCATAGCAC 58.467 47.619 0.00 9.13 43.04 4.40
3267 3309 0.787084 CTCCCCCTAGCTATCCTCCA 59.213 60.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.