Multiple sequence alignment - TraesCS2B01G212700

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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 TraesCS2B01G212700 chr2B 100.000 3311 0 0 1 3311 197213413 197210103 0.000000e+00 6115
1 TraesCS2B01G212700 chr2D 95.769 2458 78 9 77 2519 138756873 138754427 0.000000e+00 3940
2 TraesCS2B01G212700 chr2D 93.552 791 33 9 2536 3311 138754441 138753654 0.000000e+00 1162
3 TraesCS2B01G212700 chr2D 90.355 197 17 2 19 215 138756983 138756789 1.180000e-64 257
4 TraesCS2B01G212700 chr2A 94.387 2530 92 24 19 2519 162290457 162292965 0.000000e+00 3840
5 TraesCS2B01G212700 chr2A 95.897 780 30 2 2533 3311 162292948 162293726 0.000000e+00 1262


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 TraesCS2B01G212700 chr2B 197210103 197213413 3310 True 6115.000000 6115 100.000000 1 3311 1 chr2B.!!$R1 3310
1 TraesCS2B01G212700 chr2D 138753654 138756983 3329 True 1786.333333 3940 93.225333 19 3311 3 chr2D.!!$R1 3292
2 TraesCS2B01G212700 chr2A 162290457 162293726 3269 False 2551.000000 3840 95.142000 19 3311 2 chr2A.!!$F1 3292

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
492 554 1.280133 CCTGCTTCAATCCACCTCTCA 59.720 52.381 0.0 0.0 0.0 3.27 F
1260 1335 0.035056 CCAGTTTCCTTGATCCGGCT 60.035 55.000 0.0 0.0 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1595 1670 0.388520 TCGATGTCGTTGCTGGTGAG 60.389 55.0 2.04 0.00 40.80 3.51 R
2689 2780 0.977108 TTACCGGCGGTAACTGGGAT 60.977 55.0 39.49 15.67 42.44 3.85 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
65 66 9.226345 GTCTTTCTTCAACATGTAAAGAACTTG 57.774 33.333 24.94 19.58 38.40 3.16
143 144 7.719633 ACCACTTACAAGTTATTTGATCACTGT 59.280 33.333 0.00 0.00 39.21 3.55
159 216 7.860613 TGATCACTGTTGTTTTGTGTACATAG 58.139 34.615 0.00 0.00 33.82 2.23
301 359 7.765695 AAGAATGAAGGCAGAAATTCTGTTA 57.234 32.000 22.28 2.37 45.94 2.41
472 534 7.530426 AACTAAATTCCCATAATGATCCTGC 57.470 36.000 0.00 0.00 0.00 4.85
480 542 3.483421 CATAATGATCCTGCCTGCTTCA 58.517 45.455 0.00 0.00 0.00 3.02
482 544 2.750141 ATGATCCTGCCTGCTTCAAT 57.250 45.000 0.00 0.00 0.00 2.57
483 545 2.048444 TGATCCTGCCTGCTTCAATC 57.952 50.000 0.00 0.00 0.00 2.67
484 546 1.316651 GATCCTGCCTGCTTCAATCC 58.683 55.000 0.00 0.00 0.00 3.01
492 554 1.280133 CCTGCTTCAATCCACCTCTCA 59.720 52.381 0.00 0.00 0.00 3.27
613 678 6.160459 ACCTCCAACATAAACATATCTTCCCT 59.840 38.462 0.00 0.00 0.00 4.20
616 681 5.536161 CCAACATAAACATATCTTCCCTGGG 59.464 44.000 6.33 6.33 0.00 4.45
709 774 2.033448 AAGAATCCGGCGGCAACA 59.967 55.556 23.83 3.71 0.00 3.33
793 862 3.897239 TCCAAACAGACAACTTGGTGAT 58.103 40.909 0.00 0.00 40.47 3.06
812 881 6.183360 TGGTGATTGAATGATAAGGTGATTGC 60.183 38.462 0.00 0.00 0.00 3.56
893 968 2.949177 ACAAATACCCTGCACAGACA 57.051 45.000 0.00 0.00 0.00 3.41
939 1014 4.039124 AGGCATTCTCTCTCTAAAGCTAGC 59.961 45.833 6.62 6.62 0.00 3.42
948 1023 4.219115 TCTCTAAAGCTAGCATACTGCCT 58.781 43.478 18.83 0.00 46.52 4.75
1206 1281 1.152589 TCCACAATGCTGGCCACAA 60.153 52.632 0.00 0.00 0.00 3.33
1260 1335 0.035056 CCAGTTTCCTTGATCCGGCT 60.035 55.000 0.00 0.00 0.00 5.52
1287 1362 4.478206 CTATGAGAGCTTTGAGTTCCCA 57.522 45.455 0.00 0.00 0.00 4.37
1303 1378 0.916358 CCCAGTGATGGACCCCTTCT 60.916 60.000 0.00 0.00 0.00 2.85
1344 1419 1.140312 ATTGCACCGACATCCCCTAT 58.860 50.000 0.00 0.00 0.00 2.57
1348 1423 1.704641 CACCGACATCCCCTATCTCA 58.295 55.000 0.00 0.00 0.00 3.27
1357 1432 2.574018 CCCTATCTCATCGGCGGCA 61.574 63.158 10.53 0.00 0.00 5.69
1359 1434 1.662608 CTATCTCATCGGCGGCAGT 59.337 57.895 10.53 0.00 0.00 4.40
1431 1506 2.954318 AGCAGCAAATGATCATACACCC 59.046 45.455 9.04 0.00 0.00 4.61
1595 1670 3.407424 AAAAGGCTGCCAAAAAGGATC 57.593 42.857 22.65 0.00 41.22 3.36
1690 1765 2.090380 AGATGGGGATTTGGATGGCAAT 60.090 45.455 0.00 0.00 0.00 3.56
1777 1852 3.799232 GCCTCTATGCAAGGGTAAGTACG 60.799 52.174 5.09 0.00 34.26 3.67
1795 1870 0.385098 CGCAGCACACAACATCACAG 60.385 55.000 0.00 0.00 0.00 3.66
1808 1883 4.032703 ACATCACAGAGTGCAACAAAAC 57.967 40.909 0.00 0.00 41.43 2.43
1821 1896 6.040842 AGTGCAACAAAACAGATGATAAAGGT 59.959 34.615 0.00 0.00 41.43 3.50
1830 1905 4.400251 ACAGATGATAAAGGTTGCATGGTG 59.600 41.667 0.00 0.00 0.00 4.17
1831 1906 4.641541 CAGATGATAAAGGTTGCATGGTGA 59.358 41.667 0.00 0.00 0.00 4.02
1834 1909 5.327616 TGATAAAGGTTGCATGGTGAATG 57.672 39.130 0.00 0.00 39.49 2.67
1837 1912 3.947910 AAGGTTGCATGGTGAATGAAG 57.052 42.857 0.00 0.00 38.72 3.02
1838 1913 2.173519 AGGTTGCATGGTGAATGAAGG 58.826 47.619 0.00 0.00 38.72 3.46
1839 1914 1.205417 GGTTGCATGGTGAATGAAGGG 59.795 52.381 0.00 0.00 38.72 3.95
1840 1915 0.896923 TTGCATGGTGAATGAAGGGC 59.103 50.000 0.00 0.00 38.72 5.19
1841 1916 0.040058 TGCATGGTGAATGAAGGGCT 59.960 50.000 0.00 0.00 38.72 5.19
2102 2178 5.248477 AGAGGAAGCAGTGGAGTATGTTAAA 59.752 40.000 0.00 0.00 0.00 1.52
2283 2365 3.994392 GGATTAACGTCAGCAGTCTTGAA 59.006 43.478 0.00 0.00 0.00 2.69
2509 2592 8.352137 TGTAAATGATCAAAGGTCACAATGAT 57.648 30.769 0.00 0.00 35.33 2.45
2510 2593 9.460019 TGTAAATGATCAAAGGTCACAATGATA 57.540 29.630 0.00 0.00 32.90 2.15
2513 2596 8.756486 AATGATCAAAGGTCACAATGATATGA 57.244 30.769 0.00 0.00 32.90 2.15
2514 2597 8.935614 ATGATCAAAGGTCACAATGATATGAT 57.064 30.769 0.00 0.00 32.90 2.45
2515 2598 8.756486 TGATCAAAGGTCACAATGATATGATT 57.244 30.769 0.00 0.00 32.90 2.57
2516 2599 8.626526 TGATCAAAGGTCACAATGATATGATTG 58.373 33.333 12.69 12.69 38.97 2.67
2517 2600 7.337480 TCAAAGGTCACAATGATATGATTGG 57.663 36.000 17.61 8.05 37.60 3.16
2518 2601 5.779529 AAGGTCACAATGATATGATTGGC 57.220 39.130 17.61 8.32 37.60 4.52
2519 2602 4.147321 AGGTCACAATGATATGATTGGCC 58.853 43.478 17.61 15.22 37.60 5.36
2520 2603 4.141088 AGGTCACAATGATATGATTGGCCT 60.141 41.667 17.61 16.80 37.60 5.19
2521 2604 4.586001 GGTCACAATGATATGATTGGCCTT 59.414 41.667 17.61 0.00 37.60 4.35
2522 2605 5.069516 GGTCACAATGATATGATTGGCCTTT 59.930 40.000 17.61 0.00 37.60 3.11
2523 2606 6.407299 GGTCACAATGATATGATTGGCCTTTT 60.407 38.462 17.61 0.00 37.60 2.27
2524 2607 7.043565 GTCACAATGATATGATTGGCCTTTTT 58.956 34.615 17.61 0.00 37.60 1.94
2589 2672 6.385649 TTCTTTTTCATGTCACAGGGTTAC 57.614 37.500 0.00 0.00 0.00 2.50
2591 2674 2.465860 TTCATGTCACAGGGTTACGG 57.534 50.000 0.00 0.00 0.00 4.02
2594 2677 2.898612 TCATGTCACAGGGTTACGGTTA 59.101 45.455 0.00 0.00 0.00 2.85
2657 2740 5.062528 TGCATGACTTCATAACAACACTGA 58.937 37.500 0.00 0.00 34.26 3.41
2689 2780 4.141251 GGAAGGGCAGAAAATATACCAGGA 60.141 45.833 0.00 0.00 0.00 3.86
2745 2838 8.527810 AGTATTCAAACAAAACTTGGAAGTCAA 58.472 29.630 0.00 0.00 38.57 3.18
2853 2947 1.595311 ACACCTCCTTGATGCCCATA 58.405 50.000 0.00 0.00 0.00 2.74
2900 2997 6.424812 TCAGTCACAGACACTTATTCATGTTG 59.575 38.462 0.00 0.00 34.60 3.33
2992 3089 4.803098 ACCTAGTTACTGCCACTAACAG 57.197 45.455 0.00 0.00 41.08 3.16
3122 3219 1.769026 CATCGTTCTCCTCCTCCTCA 58.231 55.000 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 90 2.948979 TCTTGCACCAGGTACAAAACTG 59.051 45.455 6.70 0.00 34.54 3.16
90 91 3.290948 TCTTGCACCAGGTACAAAACT 57.709 42.857 6.70 0.00 0.00 2.66
143 144 6.685527 TCTTGCACTATGTACACAAAACAA 57.314 33.333 0.00 0.00 0.00 2.83
159 216 1.181098 AGTGGTGGCCAATCTTGCAC 61.181 55.000 7.24 0.00 34.18 4.57
224 282 3.538392 GCGATGTCGTTTTAAGATTGTGC 59.462 43.478 4.20 0.00 42.22 4.57
301 359 1.779092 CAGATCCTCAACATGGGGGAT 59.221 52.381 3.20 3.20 38.96 3.85
472 534 1.280133 TGAGAGGTGGATTGAAGCAGG 59.720 52.381 0.00 0.00 0.00 4.85
480 542 1.630878 GGTTGAGGTGAGAGGTGGATT 59.369 52.381 0.00 0.00 0.00 3.01
482 544 0.191064 AGGTTGAGGTGAGAGGTGGA 59.809 55.000 0.00 0.00 0.00 4.02
483 545 0.610687 GAGGTTGAGGTGAGAGGTGG 59.389 60.000 0.00 0.00 0.00 4.61
484 546 1.342074 TGAGGTTGAGGTGAGAGGTG 58.658 55.000 0.00 0.00 0.00 4.00
492 554 0.401395 TGAGGGGTTGAGGTTGAGGT 60.401 55.000 0.00 0.00 0.00 3.85
632 697 1.165907 ATTATGCCGCGATGGTGTGG 61.166 55.000 8.23 0.00 42.55 4.17
664 729 4.878439 TGATATCGACGGGATAAACAAGG 58.122 43.478 0.00 0.00 40.87 3.61
793 862 6.883756 TGTACAGCAATCACCTTATCATTCAA 59.116 34.615 0.00 0.00 0.00 2.69
812 881 3.994392 ACAAAGTACGGAAGCATGTACAG 59.006 43.478 0.33 0.00 42.62 2.74
893 968 0.882042 CTTGAGTGCTTCTGCCGTGT 60.882 55.000 0.00 0.00 38.71 4.49
939 1014 0.179034 GGCAAGGGAGAGGCAGTATG 60.179 60.000 0.00 0.00 40.87 2.39
948 1023 2.665000 CGCTCAAGGCAAGGGAGA 59.335 61.111 0.00 0.00 41.91 3.71
970 1045 2.291865 GGAGAATTGGAAGGGAAGGCTT 60.292 50.000 0.00 0.00 0.00 4.35
1269 1344 2.050144 ACTGGGAACTCAAAGCTCTCA 58.950 47.619 0.00 0.00 0.00 3.27
1287 1362 1.617947 GCGAGAAGGGGTCCATCACT 61.618 60.000 0.00 0.00 0.00 3.41
1303 1378 1.078497 ACTGGAATTCGGCATGCGA 60.078 52.632 12.44 9.85 0.00 5.10
1344 1419 3.068064 TCACTGCCGCCGATGAGA 61.068 61.111 0.00 0.00 0.00 3.27
1348 1423 3.157217 GATCCTCACTGCCGCCGAT 62.157 63.158 0.00 0.00 0.00 4.18
1431 1506 3.005472 TGGACTTCCTCTTGTTAGTCACG 59.995 47.826 0.00 0.00 38.96 4.35
1584 1659 2.517959 TGCTGGTGAGATCCTTTTTGG 58.482 47.619 0.00 0.00 37.10 3.28
1595 1670 0.388520 TCGATGTCGTTGCTGGTGAG 60.389 55.000 2.04 0.00 40.80 3.51
1700 1775 1.016653 GTGCCTGTCTTCTTCGAGCC 61.017 60.000 0.00 0.00 0.00 4.70
1777 1852 0.946528 TCTGTGATGTTGTGTGCTGC 59.053 50.000 0.00 0.00 0.00 5.25
1795 1870 6.583806 CCTTTATCATCTGTTTTGTTGCACTC 59.416 38.462 0.00 0.00 0.00 3.51
1808 1883 4.641541 TCACCATGCAACCTTTATCATCTG 59.358 41.667 0.00 0.00 0.00 2.90
1821 1896 0.896923 GCCCTTCATTCACCATGCAA 59.103 50.000 0.00 0.00 32.13 4.08
1830 1905 4.853924 TTCAGAAACAAGCCCTTCATTC 57.146 40.909 0.00 0.00 0.00 2.67
1831 1906 5.541484 AGAATTCAGAAACAAGCCCTTCATT 59.459 36.000 8.44 0.00 0.00 2.57
1834 1909 6.575162 TTAGAATTCAGAAACAAGCCCTTC 57.425 37.500 8.44 0.00 0.00 3.46
1837 1912 5.394553 CCCATTAGAATTCAGAAACAAGCCC 60.395 44.000 8.44 0.00 0.00 5.19
1838 1913 5.185828 ACCCATTAGAATTCAGAAACAAGCC 59.814 40.000 8.44 0.00 0.00 4.35
1839 1914 6.095377 CACCCATTAGAATTCAGAAACAAGC 58.905 40.000 8.44 0.00 0.00 4.01
1840 1915 7.219484 ACACCCATTAGAATTCAGAAACAAG 57.781 36.000 8.44 0.00 0.00 3.16
1841 1916 8.698973 TTACACCCATTAGAATTCAGAAACAA 57.301 30.769 8.44 0.00 0.00 2.83
2102 2178 6.604795 ACACCTTAATCTGAAGCTGCATAAAT 59.395 34.615 0.00 0.00 0.00 1.40
2187 2269 5.608449 TGCACATGAATGGTTGATGAAAAA 58.392 33.333 0.00 0.00 0.00 1.94
2198 2280 3.571571 CTCAACAACTGCACATGAATGG 58.428 45.455 0.00 0.00 0.00 3.16
2203 2285 1.068748 GGAGCTCAACAACTGCACATG 60.069 52.381 17.19 0.00 0.00 3.21
2295 2377 6.660949 AGAGTGGTATTTATTTTTGCAGAGCT 59.339 34.615 0.00 0.00 0.00 4.09
2422 2505 8.001881 TGCCAAGAAAAGTATGAAGTAAAACA 57.998 30.769 0.00 0.00 0.00 2.83
2423 2506 9.476202 AATGCCAAGAAAAGTATGAAGTAAAAC 57.524 29.630 0.00 0.00 0.00 2.43
2427 2510 7.669722 AGGAAATGCCAAGAAAAGTATGAAGTA 59.330 33.333 0.00 0.00 40.02 2.24
2524 2607 8.102047 AGCCAATCATATGATTTTGGTCAAAAA 58.898 29.630 27.39 0.96 42.41 1.94
2525 2608 7.622713 AGCCAATCATATGATTTTGGTCAAAA 58.377 30.769 27.39 10.72 42.41 2.44
2526 2609 7.185318 AGCCAATCATATGATTTTGGTCAAA 57.815 32.000 27.39 0.00 42.41 2.69
2527 2610 6.795144 AGCCAATCATATGATTTTGGTCAA 57.205 33.333 27.39 0.00 42.41 3.18
2528 2611 6.380560 TGAAGCCAATCATATGATTTTGGTCA 59.619 34.615 27.39 22.79 42.41 4.02
2529 2612 6.698766 GTGAAGCCAATCATATGATTTTGGTC 59.301 38.462 27.39 21.23 42.41 4.02
2530 2613 6.154877 TGTGAAGCCAATCATATGATTTTGGT 59.845 34.615 27.39 22.55 42.41 3.67
2531 2614 6.575267 TGTGAAGCCAATCATATGATTTTGG 58.425 36.000 25.16 24.94 42.41 3.28
2532 2615 8.657074 AATGTGAAGCCAATCATATGATTTTG 57.343 30.769 25.16 19.82 42.41 2.44
2533 2616 9.321562 GAAATGTGAAGCCAATCATATGATTTT 57.678 29.630 25.16 18.03 42.41 1.82
2534 2617 8.479689 TGAAATGTGAAGCCAATCATATGATTT 58.520 29.630 25.16 13.13 42.41 2.17
2535 2618 8.014070 TGAAATGTGAAGCCAATCATATGATT 57.986 30.769 22.65 22.65 44.93 2.57
2536 2619 7.504574 TCTGAAATGTGAAGCCAATCATATGAT 59.495 33.333 12.62 12.62 32.33 2.45
2537 2620 6.829811 TCTGAAATGTGAAGCCAATCATATGA 59.170 34.615 8.10 8.10 32.33 2.15
2538 2621 7.034685 TCTGAAATGTGAAGCCAATCATATG 57.965 36.000 0.00 0.00 32.33 1.78
2539 2622 7.504574 TGATCTGAAATGTGAAGCCAATCATAT 59.495 33.333 0.00 0.00 33.20 1.78
2689 2780 0.977108 TTACCGGCGGTAACTGGGAT 60.977 55.000 39.49 15.67 42.44 3.85
2822 2915 2.258109 AGGAGGTGTTCTGGAGGTTAC 58.742 52.381 0.00 0.00 0.00 2.50
2853 2947 1.205893 GGAGATCGAGCCACAGAAAGT 59.794 52.381 0.00 0.00 0.00 2.66
2900 2997 2.286294 GGATCATCGTCACACATCAAGC 59.714 50.000 0.00 0.00 0.00 4.01
2992 3089 7.703197 GTGTAGTAACTGAAGAGGAGAATTAGC 59.297 40.741 0.00 0.00 0.00 3.09


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

AutoCloner maintained by Alex Coulton.