Multiple sequence alignment - TraesCS6B01G334600

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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 TraesCS6B01G334600 chr6B 100.000 2415 0 0 1 2415 587797865 587800279 0.000000e+00 4460
1 TraesCS6B01G334600 chr6D 95.182 1785 48 14 1 1767 393298428 393300192 0.000000e+00 2785
2 TraesCS6B01G334600 chr6D 96.256 454 13 2 1963 2415 393300493 393300943 0.000000e+00 741
3 TraesCS6B01G334600 chr6D 99.512 205 1 0 1758 1962 393300254 393300458 8.150000e-100 374
4 TraesCS6B01G334600 chr6A 92.769 1784 70 21 1 1748 539864670 539866430 0.000000e+00 2525
5 TraesCS6B01G334600 chr6A 92.910 677 16 14 1758 2406 539866728 539867400 0.000000e+00 955
6 TraesCS6B01G334600 chr7D 87.898 157 19 0 1254 1410 139829120 139829276 4.100000e-43 185
7 TraesCS6B01G334600 chr7B 87.898 157 19 0 1254 1410 104757901 104758057 4.100000e-43 185


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 TraesCS6B01G334600 chr6B 587797865 587800279 2414 False 4460 4460 100.000000 1 2415 1 chr6B.!!$F1 2414
1 TraesCS6B01G334600 chr6D 393298428 393300943 2515 False 1300 2785 96.983333 1 2415 3 chr6D.!!$F1 2414
2 TraesCS6B01G334600 chr6A 539864670 539867400 2730 False 1740 2525 92.839500 1 2406 2 chr6A.!!$F1 2405

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
38 39 0.036448 AGAGAGTTGCTGTGCTGCAT 59.964 50.0 5.27 0.0 42.96 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1577 1617 0.179936 CTAGGCAGAAAGGGAGCAGG 59.82 60.0 0.0 0.0 0.0 4.85 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
38 39 0.036448 AGAGAGTTGCTGTGCTGCAT 59.964 50.000 5.27 0.00 42.96 3.96
116 124 0.539518 GAAGGGTGGAGAGAAGAGGC 59.460 60.000 0.00 0.00 0.00 4.70
144 152 4.919774 TCCATGTCCCTGTTTAGCTTTA 57.080 40.909 0.00 0.00 0.00 1.85
145 153 4.585879 TCCATGTCCCTGTTTAGCTTTAC 58.414 43.478 0.00 0.00 0.00 2.01
146 154 4.042311 TCCATGTCCCTGTTTAGCTTTACA 59.958 41.667 0.00 0.00 0.00 2.41
147 155 4.156008 CCATGTCCCTGTTTAGCTTTACAC 59.844 45.833 0.00 0.00 0.00 2.90
149 157 4.980573 TGTCCCTGTTTAGCTTTACACAT 58.019 39.130 0.00 0.00 0.00 3.21
151 159 5.935789 TGTCCCTGTTTAGCTTTACACATAC 59.064 40.000 0.00 0.00 0.00 2.39
199 207 8.066595 CGAAAAGCTTATTACTCCATGATCAAG 58.933 37.037 0.00 0.00 0.00 3.02
250 258 1.402968 GCAATGCCGATGATTGACAGT 59.597 47.619 0.00 0.00 33.36 3.55
254 262 1.552792 TGCCGATGATTGACAGTGGTA 59.447 47.619 0.00 0.00 0.00 3.25
334 354 2.391389 GCCGAGGGACTTTCGCTTG 61.391 63.158 1.34 1.34 41.55 4.01
336 356 1.292223 CGAGGGACTTTCGCTTGGA 59.708 57.895 0.49 0.00 41.55 3.53
363 383 4.578516 ACATCAAATCACAACCTCAAACGA 59.421 37.500 0.00 0.00 0.00 3.85
369 389 4.349663 TCACAACCTCAAACGAAACAAG 57.650 40.909 0.00 0.00 0.00 3.16
374 394 5.105917 ACAACCTCAAACGAAACAAGTGATT 60.106 36.000 0.00 0.00 0.00 2.57
380 400 6.616947 TCAAACGAAACAAGTGATTTTGTCT 58.383 32.000 0.00 0.00 40.24 3.41
459 479 1.888512 GGGTTCTTTCCCGGTAAAACC 59.111 52.381 0.00 2.47 37.93 3.27
566 586 2.438434 CCCCACAAGCCGATGACC 60.438 66.667 0.00 0.00 0.00 4.02
688 709 5.227908 GCTAGTGCTATAATTACTTGCCGA 58.772 41.667 0.00 0.00 37.26 5.54
736 757 0.393944 GTTCCCCAATCCGTTCTCCC 60.394 60.000 0.00 0.00 0.00 4.30
900 921 0.249114 TTTGAGCGTACACACTGCGA 60.249 50.000 0.00 0.00 32.03 5.10
1134 1164 2.791655 ACTTGCTTAAGCTTACCACCC 58.208 47.619 26.90 0.00 42.66 4.61
1135 1165 2.107552 ACTTGCTTAAGCTTACCACCCA 59.892 45.455 26.90 1.54 42.66 4.51
1140 1170 3.305131 GCTTAAGCTTACCACCCAAACAC 60.305 47.826 20.38 0.00 38.21 3.32
1141 1171 1.314730 AAGCTTACCACCCAAACACG 58.685 50.000 0.00 0.00 0.00 4.49
1424 1458 0.382758 CCGCTCGTGATCGTACTACG 60.383 60.000 1.93 1.93 44.19 3.51
1831 2159 3.632604 TGGATCGAGTTGTGTCCTCTATC 59.367 47.826 2.40 0.00 32.95 2.08
2112 2485 8.542132 GGTTAAAAACACGATGATTACGCTATA 58.458 33.333 0.00 0.00 0.00 1.31
2278 2653 0.606604 GTGCAAACCCGGTCTCTCTA 59.393 55.000 0.00 0.00 0.00 2.43
2290 2665 3.357203 GGTCTCTCTATGTGTGTCTCCA 58.643 50.000 0.00 0.00 0.00 3.86
2394 2769 1.289109 GCTTCGCGTCAACTGCCTTA 61.289 55.000 5.77 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
116 124 0.761187 ACAGGGACATGGATCGATGG 59.239 55.000 20.19 6.10 0.00 3.51
144 152 1.225855 CACGCACCTTGTGTATGTGT 58.774 50.000 0.00 0.00 39.36 3.72
151 159 1.670811 AGAAAGAACACGCACCTTGTG 59.329 47.619 0.00 0.00 42.99 3.33
199 207 4.324936 GTCGAGTAGTGCAAATTGAGAGTC 59.675 45.833 0.00 0.00 0.00 3.36
250 258 3.764972 TGTACCACGAACTGATCATACCA 59.235 43.478 0.00 0.00 0.00 3.25
254 262 5.348986 GTGTATGTACCACGAACTGATCAT 58.651 41.667 0.00 0.00 0.00 2.45
281 301 2.095059 TCCGAGCCTTGTTAAGACGTAC 60.095 50.000 0.00 0.00 0.00 3.67
282 302 2.161855 TCCGAGCCTTGTTAAGACGTA 58.838 47.619 0.00 0.00 0.00 3.57
283 303 0.963962 TCCGAGCCTTGTTAAGACGT 59.036 50.000 0.00 0.00 0.00 4.34
284 304 1.630148 CTCCGAGCCTTGTTAAGACG 58.370 55.000 0.00 0.00 0.00 4.18
285 305 1.360820 GCTCCGAGCCTTGTTAAGAC 58.639 55.000 9.42 0.00 34.48 3.01
286 306 3.834732 GCTCCGAGCCTTGTTAAGA 57.165 52.632 9.42 0.00 34.48 2.10
334 354 7.156876 TGAGGTTGTGATTTGATGTTATTCC 57.843 36.000 0.00 0.00 0.00 3.01
336 356 7.594758 CGTTTGAGGTTGTGATTTGATGTTATT 59.405 33.333 0.00 0.00 0.00 1.40
363 383 8.143835 CCAGGAAATAGACAAAATCACTTGTTT 58.856 33.333 0.00 0.00 39.63 2.83
369 389 5.411669 ACGTCCAGGAAATAGACAAAATCAC 59.588 40.000 0.00 0.00 0.00 3.06
374 394 3.500680 GCAACGTCCAGGAAATAGACAAA 59.499 43.478 0.00 0.00 0.00 2.83
380 400 1.626321 TCCAGCAACGTCCAGGAAATA 59.374 47.619 0.00 0.00 0.00 1.40
459 479 1.597854 TGCCTTGCAGGACTGTTCG 60.598 57.895 0.00 0.00 37.67 3.95
494 514 3.653836 ACTTAAATGACCACCCACCACTA 59.346 43.478 0.00 0.00 0.00 2.74
555 575 4.096003 CCCCACGGTCATCGGCTT 62.096 66.667 0.00 0.00 44.45 4.35
578 598 2.041922 ACTGATGAGCCGGGCCTA 60.042 61.111 17.02 5.19 0.00 3.93
584 604 2.389059 CGTCTAATCACTGATGAGCCG 58.611 52.381 0.00 0.00 38.57 5.52
638 659 3.320673 CGGAGAGCAAAAGTAGGAACT 57.679 47.619 0.00 0.00 46.37 3.01
688 709 0.318784 GCGCGGAGATAATTCGACCT 60.319 55.000 8.83 0.00 0.00 3.85
736 757 2.973406 GGAGAGGGTGTCTTTATAGGGG 59.027 54.545 0.00 0.00 34.71 4.79
1134 1164 1.725625 GCGTGTGCATCCGTGTTTG 60.726 57.895 9.31 0.00 42.15 2.93
1135 1165 2.637025 GCGTGTGCATCCGTGTTT 59.363 55.556 9.31 0.00 42.15 2.83
1276 1310 1.739562 GCTGCACGTCTCCTTCAGG 60.740 63.158 0.00 0.00 0.00 3.86
1479 1513 2.490148 CGGAGAGACCCATAGCGCA 61.490 63.158 11.47 0.00 34.64 6.09
1484 1518 1.457643 CTGGCCGGAGAGACCCATA 60.458 63.158 5.28 0.00 34.64 2.74
1577 1617 0.179936 CTAGGCAGAAAGGGAGCAGG 59.820 60.000 0.00 0.00 0.00 4.85
1831 2159 1.855213 TAGTGGTCGGTCGGTTGTCG 61.855 60.000 0.00 0.00 40.90 4.35
2112 2485 9.610705 CTGGATCTATATGCAAGCATAAATAGT 57.389 33.333 17.63 4.85 41.53 2.12
2121 2496 4.013267 ACCACTGGATCTATATGCAAGC 57.987 45.455 0.71 0.00 32.50 4.01
2248 2623 2.034558 CGGGTTTGCACTCTTTTCACAT 59.965 45.455 0.00 0.00 0.00 3.21
2394 2769 1.550072 AGCATTAACAGCCGGCAAAAT 59.450 42.857 31.54 18.37 0.00 1.82


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

AutoCloner maintained by Alex Coulton.