Multiple sequence alignment - TraesCS6B01G155900

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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 TraesCS6B01G155900 chr6B 100.000 3358 0 0 1 3358 158290106 158286749 0.000000e+00 6202.0
1 TraesCS6B01G155900 chr6B 85.540 2130 249 41 283 2372 159284004 159286114 0.000000e+00 2172.0
2 TraesCS6B01G155900 chr6B 88.155 1545 154 13 753 2274 159371667 159373205 0.000000e+00 1812.0
3 TraesCS6B01G155900 chr6D 94.761 3245 140 9 138 3358 83225811 83222573 0.000000e+00 5024.0
4 TraesCS6B01G155900 chr6D 85.976 2460 246 56 288 2681 83489240 83491666 0.000000e+00 2540.0
5 TraesCS6B01G155900 chr6D 95.960 99 2 1 9 105 83225907 83225809 3.470000e-35 159.0
6 TraesCS6B01G155900 chr6A 91.729 2551 163 13 9 2554 100427351 100424844 0.000000e+00 3498.0
7 TraesCS6B01G155900 chr6A 87.614 1534 136 22 753 2261 100734186 100735690 0.000000e+00 1731.0
8 TraesCS6B01G155900 chr6A 88.845 251 18 3 3012 3261 100424566 100424325 1.960000e-77 300.0
9 TraesCS6B01G155900 chr6A 82.738 336 41 12 593 925 100733353 100733674 1.970000e-72 283.0
10 TraesCS6B01G155900 chr6A 76.712 292 38 20 2429 2696 100735898 100736183 5.840000e-28 135.0
11 TraesCS6B01G155900 chr6A 85.714 119 12 1 2309 2422 100735709 100735827 1.640000e-23 121.0
12 TraesCS6B01G155900 chr7D 91.371 197 17 0 731 927 45072495 45072299 1.540000e-68 270.0
13 TraesCS6B01G155900 chr7B 89.706 68 5 1 44 109 486668898 486668831 5.970000e-13 86.1
14 TraesCS6B01G155900 chr7B 94.231 52 3 0 58 109 486668930 486668879 2.780000e-11 80.5


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 TraesCS6B01G155900 chr6B 158286749 158290106 3357 True 6202.0 6202 100.0000 1 3358 1 chr6B.!!$R1 3357
1 TraesCS6B01G155900 chr6B 159284004 159286114 2110 False 2172.0 2172 85.5400 283 2372 1 chr6B.!!$F1 2089
2 TraesCS6B01G155900 chr6B 159371667 159373205 1538 False 1812.0 1812 88.1550 753 2274 1 chr6B.!!$F2 1521
3 TraesCS6B01G155900 chr6D 83222573 83225907 3334 True 2591.5 5024 95.3605 9 3358 2 chr6D.!!$R1 3349
4 TraesCS6B01G155900 chr6D 83489240 83491666 2426 False 2540.0 2540 85.9760 288 2681 1 chr6D.!!$F1 2393
5 TraesCS6B01G155900 chr6A 100424325 100427351 3026 True 1899.0 3498 90.2870 9 3261 2 chr6A.!!$R1 3252
6 TraesCS6B01G155900 chr6A 100733353 100736183 2830 False 567.5 1731 83.1945 593 2696 4 chr6A.!!$F1 2103

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
453 470 0.247460 TGTCGAGAGATGTTGGCTGG 59.753 55.000 0.0 0.0 45.19 4.85 F
713 770 1.065851 CATGTGCTTGTGCTGTTGTGA 59.934 47.619 0.0 0.0 40.48 3.58 F
1695 2455 1.022735 GAATGGCATGAGGACAGCAG 58.977 55.000 0.0 0.0 38.50 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1577 2337 0.105224 TGATGGTAATACCGCCACCG 59.895 55.0 4.83 0.0 42.58 4.94 R
1919 2680 0.107654 GGTCAGCAAGCCGGATAACT 60.108 55.0 5.05 0.0 0.00 2.24 R
2815 3701 0.394899 CTGCCCCTCCTTCATCCAAC 60.395 60.0 0.00 0.0 0.00 3.77 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
85 88 4.165950 TGCCATGGTTGTATAGGACTCATT 59.834 41.667 14.67 0.00 0.00 2.57
111 114 4.019792 ACTGCCATGAGTGTATGAACAA 57.980 40.909 0.00 0.00 37.36 2.83
118 121 6.968904 GCCATGAGTGTATGAACAAATTACAG 59.031 38.462 0.00 0.00 37.36 2.74
121 124 5.943416 TGAGTGTATGAACAAATTACAGGGG 59.057 40.000 0.00 0.00 37.36 4.79
174 177 0.474660 AAGCTGGAGGGACAGGAACT 60.475 55.000 0.00 0.00 38.90 3.01
221 224 2.239907 AGGGACTTATTTCCACAGGAGC 59.760 50.000 0.00 0.00 37.40 4.70
229 232 3.634397 TTTCCACAGGAGCTTATCTGG 57.366 47.619 14.33 6.42 35.47 3.86
240 243 4.895889 GGAGCTTATCTGGGGCTTATTTTT 59.104 41.667 0.00 0.00 36.37 1.94
394 405 0.435008 GCGTTCTGCTTGTAGTCGTG 59.565 55.000 0.00 0.00 41.73 4.35
422 436 9.173939 GGAGCGAAAACAGATTGATTATTTATG 57.826 33.333 0.00 0.00 0.00 1.90
453 470 0.247460 TGTCGAGAGATGTTGGCTGG 59.753 55.000 0.00 0.00 45.19 4.85
458 475 2.613977 CGAGAGATGTTGGCTGGTTCTT 60.614 50.000 0.00 0.00 0.00 2.52
510 533 1.827789 GGCTCACAACCTGCAACCA 60.828 57.895 0.00 0.00 0.00 3.67
544 567 2.408704 GCTATAGTGCCGCATAAACTCG 59.591 50.000 0.00 0.00 0.00 4.18
556 580 4.284485 GCATAAACTCGAACAACCGTTTT 58.716 39.130 3.90 0.00 34.75 2.43
617 666 6.379133 TGTTCTTCTTATAGTCGTATGTGGGT 59.621 38.462 0.00 0.00 0.00 4.51
713 770 1.065851 CATGTGCTTGTGCTGTTGTGA 59.934 47.619 0.00 0.00 40.48 3.58
729 1442 4.202040 TGTTGTGATTCTTTTGGCTCACAG 60.202 41.667 4.63 0.00 46.07 3.66
744 1457 2.023673 TCACAGCCTTCAACAGTTTGG 58.976 47.619 0.00 0.00 33.06 3.28
758 1492 5.304686 ACAGTTTGGAGTCCTAAACATCA 57.695 39.130 25.76 0.00 38.82 3.07
781 1515 4.517832 ACAAAGGGTATGACGAACTTTTCC 59.482 41.667 0.00 0.00 29.64 3.13
834 1569 2.758009 GTTGACTTAACGGTAGTGCCA 58.242 47.619 0.00 0.00 36.97 4.92
859 1595 8.586273 CATACATGGCAAAAATAGAAGAAAACG 58.414 33.333 0.00 0.00 0.00 3.60
971 1709 5.070770 ACTTATCAGAACTCAGCTGACAG 57.929 43.478 13.74 6.89 44.39 3.51
1094 1853 1.305297 TGTCCTGGGAGTCGCTGAT 60.305 57.895 14.56 0.00 0.00 2.90
1109 1868 1.203994 GCTGATTGCTGATTTGCTGGT 59.796 47.619 0.00 0.00 38.95 4.00
1161 1920 2.430465 CTGCTGCACTATGTCTGGTTT 58.570 47.619 0.00 0.00 0.00 3.27
1329 2088 3.834813 TCTGCTTCCTCAACATCTACACT 59.165 43.478 0.00 0.00 0.00 3.55
1553 2313 3.021695 TGATCTTCGACTACGGATGGTT 58.978 45.455 0.00 0.00 40.21 3.67
1577 2337 1.153549 GGCTGTCTCCGTCCATGTC 60.154 63.158 0.00 0.00 0.00 3.06
1678 2438 3.244665 ACTCACACAAGCTGGATGATGAA 60.245 43.478 0.00 0.00 0.00 2.57
1695 2455 1.022735 GAATGGCATGAGGACAGCAG 58.977 55.000 0.00 0.00 38.50 4.24
1919 2680 2.483876 GACAGACACTTGCAGCTTGTA 58.516 47.619 0.00 0.00 0.00 2.41
1991 2752 3.319198 ATCGGTGACCACGCCCTT 61.319 61.111 1.11 0.00 43.10 3.95
2039 2800 0.987294 ACTGCAGCAACCTACCATCT 59.013 50.000 15.27 0.00 0.00 2.90
2196 2957 5.487433 CATACAGTCTTGTCCACCACATTA 58.513 41.667 0.00 0.00 38.76 1.90
2274 3035 1.197721 GTTCTGAACATCGTTGGCAGG 59.802 52.381 15.34 0.00 33.03 4.85
2276 3037 1.303236 TGAACATCGTTGGCAGGGG 60.303 57.895 0.00 0.00 0.00 4.79
2299 3060 2.359214 TCGCTGCAGTACATAGAAGAGG 59.641 50.000 16.64 0.00 0.00 3.69
2300 3061 2.478831 GCTGCAGTACATAGAAGAGGC 58.521 52.381 16.64 0.00 0.00 4.70
2408 3175 5.983118 CAGCTTCATGTGGTACGAACATATA 59.017 40.000 11.28 2.76 36.10 0.86
2409 3176 6.478673 CAGCTTCATGTGGTACGAACATATAA 59.521 38.462 11.28 8.75 36.10 0.98
2436 3273 6.731467 ACAGATGGTTTAGGATGTATTTGGT 58.269 36.000 0.00 0.00 0.00 3.67
2480 3326 8.827677 ACTGTGTCTACTTTTGTTAAGACATTC 58.172 33.333 7.23 0.00 44.75 2.67
2509 3355 5.986004 AACTCGGATGAATTCGGAAATAC 57.014 39.130 0.04 0.00 33.74 1.89
2667 3553 0.451383 TGCATATTTGTCACGCCAGC 59.549 50.000 0.00 0.00 0.00 4.85
2737 3623 0.951040 GCTCCGGTCCAACTTGACTG 60.951 60.000 0.00 0.00 40.61 3.51
2862 3748 2.638480 AGGCACTGTAGCAGAAACAA 57.362 45.000 2.91 0.00 37.18 2.83
3293 4199 0.041312 CGGAAGCGAACACAGGTTTG 60.041 55.000 0.00 0.00 40.72 2.93
3299 4205 2.290641 AGCGAACACAGGTTTGAATCAC 59.709 45.455 0.00 0.00 40.28 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.014326 TCAGACCCACACTCATATATCTGTAAC 59.986 40.741 0.00 0.00 35.07 2.50
1 2 7.014326 GTCAGACCCACACTCATATATCTGTAA 59.986 40.741 0.00 0.00 35.07 2.41
2 3 6.490381 GTCAGACCCACACTCATATATCTGTA 59.510 42.308 0.00 0.00 35.07 2.74
3 4 5.303078 GTCAGACCCACACTCATATATCTGT 59.697 44.000 0.00 0.00 35.07 3.41
4 5 5.279206 GGTCAGACCCACACTCATATATCTG 60.279 48.000 8.65 0.00 34.87 2.90
5 6 4.835615 GGTCAGACCCACACTCATATATCT 59.164 45.833 8.65 0.00 30.04 1.98
6 7 4.588951 TGGTCAGACCCACACTCATATATC 59.411 45.833 17.59 0.00 37.50 1.63
7 8 4.556697 TGGTCAGACCCACACTCATATAT 58.443 43.478 17.59 0.00 37.50 0.86
85 88 6.127196 TGTTCATACACTCATGGCAGTACATA 60.127 38.462 0.00 0.00 0.00 2.29
111 114 4.862641 AGTCTGTAATGCCCCTGTAATT 57.137 40.909 0.00 0.00 0.00 1.40
118 121 4.580580 CCTATGAAAAGTCTGTAATGCCCC 59.419 45.833 0.00 0.00 0.00 5.80
121 124 9.726438 ATATACCCTATGAAAAGTCTGTAATGC 57.274 33.333 0.00 0.00 0.00 3.56
174 177 0.108585 AAGCCAGCGAGTTCTTTCCA 59.891 50.000 0.00 0.00 0.00 3.53
221 224 8.463930 TCATGTAAAAATAAGCCCCAGATAAG 57.536 34.615 0.00 0.00 0.00 1.73
229 232 6.642540 GCATAAGCTCATGTAAAAATAAGCCC 59.357 38.462 0.00 0.00 37.91 5.19
266 269 5.370679 GCAATAAGGGCCAATTCATTTGAT 58.629 37.500 6.18 0.00 37.53 2.57
272 275 1.846007 ACGCAATAAGGGCCAATTCA 58.154 45.000 6.18 0.00 0.00 2.57
394 405 4.425577 AATCAATCTGTTTTCGCTCCAC 57.574 40.909 0.00 0.00 0.00 4.02
422 436 3.921677 TCTCTCGACAACATAAACACCC 58.078 45.455 0.00 0.00 0.00 4.61
430 444 2.027745 AGCCAACATCTCTCGACAACAT 60.028 45.455 0.00 0.00 0.00 2.71
453 470 7.642669 TCACAATCAGATTCTGACAAAAGAAC 58.357 34.615 18.35 0.00 43.63 3.01
458 475 6.384224 GCAATCACAATCAGATTCTGACAAA 58.616 36.000 18.35 3.93 43.63 2.83
510 533 4.503991 GGCACTATAGCTAGGACTGCAAAT 60.504 45.833 14.13 0.00 30.11 2.32
589 613 7.644551 CCACATACGACTATAAGAAGAACAGAC 59.355 40.741 0.00 0.00 0.00 3.51
591 615 6.918569 CCCACATACGACTATAAGAAGAACAG 59.081 42.308 0.00 0.00 0.00 3.16
729 1442 1.609072 GGACTCCAAACTGTTGAAGGC 59.391 52.381 0.00 0.00 36.83 4.35
744 1457 4.652822 ACCCTTTGTGATGTTTAGGACTC 58.347 43.478 0.00 0.00 0.00 3.36
758 1492 4.517832 GGAAAAGTTCGTCATACCCTTTGT 59.482 41.667 0.00 0.00 0.00 2.83
781 1515 5.583854 ACAGACTTCGGATGATCTGAAAATG 59.416 40.000 16.71 16.03 40.86 2.32
834 1569 8.519526 TCGTTTTCTTCTATTTTTGCCATGTAT 58.480 29.630 0.00 0.00 0.00 2.29
859 1595 3.781079 TGAAAATGCCATCCGTCATTC 57.219 42.857 0.00 0.00 32.27 2.67
868 1604 9.754382 CTTTAGTGCTATTTATGAAAATGCCAT 57.246 29.630 0.00 0.00 36.02 4.40
971 1709 1.003696 CCCCTGAGAAGGAACAAGACC 59.996 57.143 0.00 0.00 0.00 3.85
1065 1824 1.443407 CCAGGACAGGACATAGGCG 59.557 63.158 0.00 0.00 0.00 5.52
1094 1853 0.315886 CAGCACCAGCAAATCAGCAA 59.684 50.000 0.00 0.00 45.49 3.91
1306 2065 3.929610 GTGTAGATGTTGAGGAAGCAGAC 59.070 47.826 0.00 0.00 0.00 3.51
1329 2088 1.815003 CACGCGGATGAAGATGCCA 60.815 57.895 12.47 0.00 0.00 4.92
1577 2337 0.105224 TGATGGTAATACCGCCACCG 59.895 55.000 4.83 0.00 42.58 4.94
1678 2438 0.393944 CACTGCTGTCCTCATGCCAT 60.394 55.000 0.00 0.00 0.00 4.40
1730 2490 3.119779 TGTGTGAGGGTTTGTTTTTCGAC 60.120 43.478 0.00 0.00 0.00 4.20
1919 2680 0.107654 GGTCAGCAAGCCGGATAACT 60.108 55.000 5.05 0.00 0.00 2.24
1991 2752 1.702182 TGCTCCAAGTGCCAATGAAA 58.298 45.000 0.00 0.00 0.00 2.69
2274 3035 0.249489 CTATGTACTGCAGCGACCCC 60.249 60.000 15.27 0.00 0.00 4.95
2276 3037 2.099263 TCTTCTATGTACTGCAGCGACC 59.901 50.000 15.27 0.00 0.00 4.79
2408 3175 4.553330 ACATCCTAAACCATCTGTCGTT 57.447 40.909 0.00 0.00 0.00 3.85
2409 3176 5.871396 ATACATCCTAAACCATCTGTCGT 57.129 39.130 0.00 0.00 0.00 4.34
2436 3273 2.942376 CAGTGTAGAGGCAAACACACAA 59.058 45.455 16.06 0.00 46.71 3.33
2509 3355 1.392589 ATGATAAAGGCAACCCAGCG 58.607 50.000 0.00 0.00 34.64 5.18
2667 3553 4.342378 TCCTAGGTATGCAGTTTAGAGCAG 59.658 45.833 9.08 0.00 44.94 4.24
2759 3645 8.514330 TCTACTCTTGCTCCAAAAGTTAAAAA 57.486 30.769 0.00 0.00 0.00 1.94
2815 3701 0.394899 CTGCCCCTCCTTCATCCAAC 60.395 60.000 0.00 0.00 0.00 3.77
2862 3748 5.009310 TGTTCGTCTACACTGTCAACTACAT 59.991 40.000 0.00 0.00 37.50 2.29
2938 3824 2.808543 GTTGAACATGAAACTCGGCTCT 59.191 45.455 0.00 0.00 0.00 4.09
3293 4199 4.993584 TCAAGCAGAAGACAAGAGTGATTC 59.006 41.667 0.00 0.00 0.00 2.52
3299 4205 5.642491 TGAATCATCAAGCAGAAGACAAGAG 59.358 40.000 0.00 0.00 30.99 2.85


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

AutoCloner maintained by Alex Coulton.