Multiple sequence alignment - TraesCS2B01G281400

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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 TraesCS2B01G281400 chr2B 100.000 4199 0 0 1 4199 388598540 388594342 0 7755
1 TraesCS2B01G281400 chr2D 95.333 4200 132 16 1 4199 320284602 320280466 0 6612
2 TraesCS2B01G281400 chr2A 95.907 3274 102 12 94 3362 410850696 410853942 0 5275
3 TraesCS2B01G281400 chr2A 93.026 846 49 5 3357 4199 410853986 410854824 0 1227


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 TraesCS2B01G281400 chr2B 388594342 388598540 4198 True 7755 7755 100.0000 1 4199 1 chr2B.!!$R1 4198
1 TraesCS2B01G281400 chr2D 320280466 320284602 4136 True 6612 6612 95.3330 1 4199 1 chr2D.!!$R1 4198
2 TraesCS2B01G281400 chr2A 410850696 410854824 4128 False 3251 5275 94.4665 94 4199 2 chr2A.!!$F1 4105

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
416 420 0.388649 CGACGCTACTTCCAGCTGTT 60.389 55.000 13.81 0.00 39.51 3.16 F
418 422 0.679505 ACGCTACTTCCAGCTGTTGA 59.320 50.000 13.81 0.01 39.51 3.18 F
2232 2239 1.003718 GACCCCGAGACAACCAAGG 60.004 63.158 0.00 0.00 0.00 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1909 1916 0.178068 TTCGCAGGGAGCAGATTACC 59.822 55.0 0.0 0.0 46.13 2.85 R
2260 2267 0.463620 CTCTCCCTTCTAGTGCCAGC 59.536 60.0 0.0 0.0 0.00 4.85 R
4092 4150 0.036952 AAGGACGGCATCAGTCACTG 60.037 55.0 0.0 0.0 40.20 3.66 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
27 28 4.331968 TGATTGTCTATTGTTGTGGGGAC 58.668 43.478 0.00 0.00 0.00 4.46
34 35 0.753479 TTGTTGTGGGGACGTGCATT 60.753 50.000 9.96 0.00 0.00 3.56
59 60 1.548719 TCCCATGTTGGAGACAGTACG 59.451 52.381 0.00 0.00 40.96 3.67
74 75 4.193865 ACAGTACGTTAATATGGTTGGCC 58.806 43.478 0.00 0.00 0.00 5.36
80 81 0.466543 TAATATGGTTGGCCGCTCGT 59.533 50.000 0.00 0.00 37.67 4.18
133 134 6.266168 CCACACATTGGCAACTAATTAAGA 57.734 37.500 0.00 0.00 39.07 2.10
326 327 1.203441 AGCCCACATGAGAAGAGCCA 61.203 55.000 0.00 0.00 0.00 4.75
333 337 2.503356 ACATGAGAAGAGCCAAGTAGGG 59.497 50.000 0.00 0.00 38.09 3.53
399 403 3.096852 AGTAGTGAATGTGATGGGTCGA 58.903 45.455 0.00 0.00 0.00 4.20
408 412 0.454600 TGATGGGTCGACGCTACTTC 59.545 55.000 29.62 20.70 0.00 3.01
411 415 1.139095 GGGTCGACGCTACTTCCAG 59.861 63.158 23.96 0.00 0.00 3.86
416 420 0.388649 CGACGCTACTTCCAGCTGTT 60.389 55.000 13.81 0.00 39.51 3.16
417 421 1.071605 GACGCTACTTCCAGCTGTTG 58.928 55.000 13.81 4.66 39.51 3.33
418 422 0.679505 ACGCTACTTCCAGCTGTTGA 59.320 50.000 13.81 0.01 39.51 3.18
419 423 1.070134 ACGCTACTTCCAGCTGTTGAA 59.930 47.619 13.81 9.02 39.51 2.69
420 424 2.143122 CGCTACTTCCAGCTGTTGAAA 58.857 47.619 13.81 0.61 39.51 2.69
463 467 4.277174 CCAACAATATAGGCGCCAAATACA 59.723 41.667 31.54 7.98 0.00 2.29
494 498 6.293790 CCGTTAGGAGTATGTGTCGATATCAA 60.294 42.308 3.12 0.00 41.02 2.57
498 502 5.594725 AGGAGTATGTGTCGATATCAACACT 59.405 40.000 23.72 13.75 44.78 3.55
605 609 1.468054 CCACCGCTAAGAAAATGCAGC 60.468 52.381 0.00 0.00 0.00 5.25
667 671 6.563422 CATGGTGAATGTGGTTAGGTATTTG 58.437 40.000 0.00 0.00 0.00 2.32
712 716 4.885325 AGTCACAAAACTAACAACCGGATT 59.115 37.500 9.46 1.42 0.00 3.01
716 720 1.541379 AACTAACAACCGGATTGGCC 58.459 50.000 9.46 0.00 43.20 5.36
794 798 1.560146 AGCCAAGAAAGGTACTAGGCC 59.440 52.381 0.00 0.00 38.49 5.19
903 907 4.662394 CGTCGTCGCTTCGTCTTTTTAATT 60.662 41.667 0.00 0.00 0.00 1.40
1043 1050 2.620115 CACTCTGCTTCACAACCATTGT 59.380 45.455 0.00 0.00 46.75 2.71
1236 1243 4.404098 GACATGCGGTCCCGGGTT 62.404 66.667 22.86 0.00 40.83 4.11
1267 1274 2.451493 TCCCTTCCCAACCCAGCA 60.451 61.111 0.00 0.00 0.00 4.41
1314 1321 4.101448 GTGGCAGGCCTCACCGAT 62.101 66.667 12.58 0.00 46.52 4.18
1335 1342 6.095720 CCGATCTCAAAGTACTTTCTCTACCT 59.904 42.308 18.00 0.12 0.00 3.08
1367 1374 1.068250 GCGGAGAGATACCTGGTGC 59.932 63.158 10.23 1.18 0.00 5.01
1554 1561 2.205074 CTCCGGATGTCTTCCAATTCG 58.795 52.381 3.57 0.00 45.78 3.34
1815 1822 1.189752 GTCTGGGTCAGCTGAGATCA 58.810 55.000 18.89 14.26 0.00 2.92
1909 1916 1.268899 ACACCGTTCTACTCCTTGACG 59.731 52.381 0.00 0.00 0.00 4.35
1912 1919 2.086869 CCGTTCTACTCCTTGACGGTA 58.913 52.381 5.16 0.00 34.93 4.02
2036 2043 6.090088 CACTCTGCTGAAGTATTTACAGTCAC 59.910 42.308 0.00 0.00 34.60 3.67
2169 2176 2.095919 GGTGTTAGTCGTCATTGTTGCC 60.096 50.000 0.00 0.00 0.00 4.52
2232 2239 1.003718 GACCCCGAGACAACCAAGG 60.004 63.158 0.00 0.00 0.00 3.61
2236 2243 2.664851 CGAGACAACCAAGGCGCA 60.665 61.111 10.83 0.00 0.00 6.09
3038 3045 4.034163 GCTAATCCAAAGCGGTAGAGTTTC 59.966 45.833 0.00 0.00 35.57 2.78
3153 3160 6.074648 TCTTTCTTCTAGGCCCAAAATGAAA 58.925 36.000 0.00 3.26 0.00 2.69
3215 3222 6.500751 TCTTACTAGGGAAGAACAAGAATGGT 59.499 38.462 6.84 0.00 29.97 3.55
3269 3276 3.819564 TCCACTTCTTATCCATGGACG 57.180 47.619 18.99 8.92 34.50 4.79
3270 3277 3.371034 TCCACTTCTTATCCATGGACGA 58.629 45.455 18.99 11.32 34.50 4.20
3271 3278 3.132289 TCCACTTCTTATCCATGGACGAC 59.868 47.826 18.99 0.00 34.50 4.34
3429 3486 6.148150 CCTATGGTTAGTGCGTCAGTTTTAAA 59.852 38.462 0.00 0.00 0.00 1.52
3612 3669 2.710096 TTAGGCTGCCCTATGTGTTC 57.290 50.000 16.57 0.00 43.15 3.18
3700 3757 2.022195 TGACATAGTACCCTGTCGCTC 58.978 52.381 16.37 0.13 43.74 5.03
3778 3835 6.202954 AGTGCGTAATTTAGTATGCAGGAATC 59.797 38.462 4.51 0.00 44.56 2.52
3893 3950 7.359181 GGTTGTATTTTTGAAGCTGCACATAAC 60.359 37.037 0.00 0.00 0.00 1.89
3899 3956 1.394917 GAAGCTGCACATAACTGGTCG 59.605 52.381 1.02 0.00 0.00 4.79
3913 3970 3.220110 ACTGGTCGTCGATGTGGTATAT 58.780 45.455 4.21 0.00 0.00 0.86
3936 3993 7.972832 ATATATTTTCCGCGTTATTCAAGGA 57.027 32.000 4.92 0.00 0.00 3.36
3944 4001 4.332819 CCGCGTTATTCAAGGAAAATCTCT 59.667 41.667 4.92 0.00 0.00 3.10
4070 4128 7.994911 AGTTTCATAATGTTGCATCCAGATAGA 59.005 33.333 0.00 0.00 0.00 1.98
4095 4153 8.554490 AGATAGTCATGGTTACCTTTATCAGT 57.446 34.615 2.07 0.00 0.00 3.41
4179 4237 0.822532 AGTGGTCGGTCGTCTGTTCT 60.823 55.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.073816 CACGTCCCCACAACAATAGAC 58.926 52.381 0.00 0.00 0.00 2.59
12 13 0.802494 GCACGTCCCCACAACAATAG 59.198 55.000 0.00 0.00 0.00 1.73
27 28 0.677731 ACATGGGAGGACAATGCACG 60.678 55.000 0.00 0.00 0.00 5.34
59 60 1.263217 CGAGCGGCCAACCATATTAAC 59.737 52.381 2.24 0.00 34.57 2.01
74 75 0.729116 ATGCCAGATTTTGACGAGCG 59.271 50.000 0.00 0.00 0.00 5.03
133 134 6.545666 TGTGTTCACCAGAAAGAATGTGTATT 59.454 34.615 0.37 0.00 35.08 1.89
191 192 6.961554 CCTTCAACGCTAGATTATGTTTTGTC 59.038 38.462 0.00 0.00 0.00 3.18
341 345 1.478510 TCTCCGCAACCTCATTCTCTC 59.521 52.381 0.00 0.00 0.00 3.20
342 346 1.205893 GTCTCCGCAACCTCATTCTCT 59.794 52.381 0.00 0.00 0.00 3.10
343 347 1.646189 GTCTCCGCAACCTCATTCTC 58.354 55.000 0.00 0.00 0.00 2.87
369 373 2.159627 CACATTCACTACTTTCGTGGCC 59.840 50.000 0.00 0.00 33.31 5.36
371 375 4.093408 CCATCACATTCACTACTTTCGTGG 59.907 45.833 0.00 0.00 33.31 4.94
408 412 3.731652 TGGTTTCATTTCAACAGCTGG 57.268 42.857 19.93 0.36 0.00 4.85
411 415 7.164008 CGAAAATTTTGGTTTCATTTCAACAGC 59.836 33.333 8.47 0.00 35.17 4.40
416 420 5.008118 GGCCGAAAATTTTGGTTTCATTTCA 59.992 36.000 8.47 0.00 35.17 2.69
417 421 5.448438 GGCCGAAAATTTTGGTTTCATTTC 58.552 37.500 8.47 0.00 35.17 2.17
418 422 4.277174 GGGCCGAAAATTTTGGTTTCATTT 59.723 37.500 8.47 0.00 35.17 2.32
419 423 3.818210 GGGCCGAAAATTTTGGTTTCATT 59.182 39.130 8.47 0.00 35.17 2.57
420 424 3.181450 TGGGCCGAAAATTTTGGTTTCAT 60.181 39.130 8.47 0.00 35.17 2.57
463 467 2.124411 ACATACTCCTAACGGCCCATT 58.876 47.619 0.00 0.00 0.00 3.16
605 609 3.705043 ATACCGTGCTAGGTTTCTACG 57.295 47.619 8.87 0.00 43.00 3.51
667 671 9.474920 TGACTGTTTGTTCCATATTTGATTTTC 57.525 29.630 0.00 0.00 0.00 2.29
681 685 7.148869 GGTTGTTAGTTTTGTGACTGTTTGTTC 60.149 37.037 0.00 0.00 0.00 3.18
716 720 0.822944 TGGTGGTGACAGTGGCAATG 60.823 55.000 14.15 14.15 44.46 2.82
903 907 4.799586 GCCGAATAGTGAAGGCTTAGCATA 60.800 45.833 6.53 0.00 45.67 3.14
1043 1050 2.225779 TGGTGGAGGAGGAATAAGGTGA 60.226 50.000 0.00 0.00 0.00 4.02
1302 1309 0.539051 CTTTGAGATCGGTGAGGCCT 59.461 55.000 3.86 3.86 34.25 5.19
1314 1321 6.210984 GGGAAGGTAGAGAAAGTACTTTGAGA 59.789 42.308 25.17 5.29 32.11 3.27
1367 1374 2.106074 TTCTGCAGCCGCCATAACG 61.106 57.895 9.47 0.00 37.32 3.18
1815 1822 3.074538 AGGACAAATTTAGCACCCTGAGT 59.925 43.478 0.00 0.00 0.00 3.41
1909 1916 0.178068 TTCGCAGGGAGCAGATTACC 59.822 55.000 0.00 0.00 46.13 2.85
1912 1919 1.222936 CCTTCGCAGGGAGCAGATT 59.777 57.895 0.00 0.00 46.13 2.40
2169 2176 1.698506 TGGTGGCCACAACTAAAAGG 58.301 50.000 35.78 0.00 34.61 3.11
2223 2230 2.906897 CCAGTGCGCCTTGGTTGT 60.907 61.111 16.72 0.00 0.00 3.32
2260 2267 0.463620 CTCTCCCTTCTAGTGCCAGC 59.536 60.000 0.00 0.00 0.00 4.85
3153 3160 2.066262 CTTAGACGGCGAACAACATGT 58.934 47.619 16.62 0.00 0.00 3.21
3215 3222 6.821665 GTCCATGTAATAAGTGCTTCTTACCA 59.178 38.462 13.80 6.41 40.80 3.25
3429 3486 7.912719 ACTTAGAAGGAAAGATGCTCTACTTT 58.087 34.615 0.00 0.00 38.74 2.66
3473 3530 5.334724 ACCTGTACGGGTGATTTTACTAG 57.665 43.478 25.96 0.00 38.30 2.57
3572 3629 9.034544 GCCTAAATTTTATTTGCAGAATTCGAT 57.965 29.630 0.00 0.00 0.00 3.59
3612 3669 4.498682 CCAAACTTGCTTCTTTCTCCAGTG 60.499 45.833 0.00 0.00 0.00 3.66
3700 3757 2.693591 TCTCTCTACCGCATTACCAAGG 59.306 50.000 0.00 0.00 0.00 3.61
3778 3835 8.550376 CCACTGACACTTTATTTTGGAAAAATG 58.450 33.333 7.96 0.00 0.00 2.32
3893 3950 3.917329 ATATACCACATCGACGACCAG 57.083 47.619 0.00 0.00 0.00 4.00
3899 3956 7.305820 CGCGGAAAATATATATACCACATCGAC 60.306 40.741 0.00 0.00 0.00 4.20
3913 3970 7.789273 TTCCTTGAATAACGCGGAAAATATA 57.211 32.000 12.47 0.00 31.29 0.86
3936 3993 7.362747 GCATGTTCAGGATCAAAGAGAGATTTT 60.363 37.037 0.00 0.00 0.00 1.82
3944 4001 3.349927 CAGGCATGTTCAGGATCAAAGA 58.650 45.455 0.00 0.00 0.00 2.52
3989 4046 4.790765 ATAGAGCGCACATCTTATGCTA 57.209 40.909 11.47 0.00 41.10 3.49
4070 4128 8.424918 CACTGATAAAGGTAACCATGACTATCT 58.575 37.037 0.00 0.00 37.17 1.98
4092 4150 0.036952 AAGGACGGCATCAGTCACTG 60.037 55.000 0.00 0.00 40.20 3.66
4095 4153 1.204704 CAGTAAGGACGGCATCAGTCA 59.795 52.381 0.00 0.00 40.20 3.41
4179 4237 2.048316 TCGAATCGCTGCTGTGCA 60.048 55.556 0.00 0.00 36.92 4.57


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

AutoCloner maintained by Alex Coulton.