Multiple sequence alignment - TraesCS3A01G099200

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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 TraesCS3A01G099200 chr3A 100.000 3534 0 0 1 3534 64030824 64027291 0.000000e+00 6527
1 TraesCS3A01G099200 chr3D 93.513 3607 117 44 2 3534 51104306 51100743 0.000000e+00 5256
2 TraesCS3A01G099200 chr3B 96.880 1282 39 1 2253 3534 82053453 82052173 0.000000e+00 2145
3 TraesCS3A01G099200 chr3B 94.432 1365 53 13 862 2207 82054787 82053427 0.000000e+00 2078
4 TraesCS3A01G099200 chr3B 89.335 872 53 18 1 848 82055881 82055026 0.000000e+00 1059
5 TraesCS3A01G099200 chr5B 84.269 1176 128 33 1466 2605 527336695 527335541 0.000000e+00 1094
6 TraesCS3A01G099200 chr5B 81.041 269 20 3 2664 2908 527335515 527335254 6.020000e-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 TraesCS3A01G099200 chr3A 64027291 64030824 3533 True 6527.000000 6527 100.000 1 3534 1 chr3A.!!$R1 3533
1 TraesCS3A01G099200 chr3D 51100743 51104306 3563 True 5256.000000 5256 93.513 2 3534 1 chr3D.!!$R1 3532
2 TraesCS3A01G099200 chr3B 82052173 82055881 3708 True 1760.666667 2145 93.549 1 3534 3 chr3B.!!$R1 3533
3 TraesCS3A01G099200 chr5B 527335254 527336695 1441 True 639.500000 1094 82.655 1466 2908 2 chr5B.!!$R1 1442

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
141 142 0.103937 CCGAGGCTCTTGTCCATCTC 59.896 60.0 13.5 0.0 0.00 2.75 F
231 234 0.464735 CGTCAACCCCACCAAACTCA 60.465 55.0 0.0 0.0 0.00 3.41 F
1635 1948 0.466124 AGGATAGCCCTGCTTCGTTC 59.534 55.0 0.0 0.0 45.61 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1368 1669 0.173481 TGAATCTCGCCGAACTCCAG 59.827 55.000 0.00 0.0 0.00 3.86 R
1774 2093 1.079127 AGCAACCGAATCAGGACCG 60.079 57.895 0.00 0.0 34.73 4.79 R
3466 3839 2.008242 AAAGCACCTTGTATGGCCAA 57.992 45.000 10.96 0.0 0.00 4.52 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
26 27 7.362487 CGAGGCACATACTCTCATGTCTATATT 60.362 40.741 0.00 0.00 37.02 1.28
78 79 0.974010 TCTACCGCGGGGTCTCAAAT 60.974 55.000 31.76 7.29 46.01 2.32
86 87 0.251787 GGGGTCTCAAATGGCAACCT 60.252 55.000 3.96 0.00 0.00 3.50
126 127 2.030562 AAGACAACCGCCACCGAG 59.969 61.111 0.00 0.00 36.29 4.63
139 140 0.460987 CACCGAGGCTCTTGTCCATC 60.461 60.000 13.50 0.00 0.00 3.51
141 142 0.103937 CCGAGGCTCTTGTCCATCTC 59.896 60.000 13.50 0.00 0.00 2.75
150 151 2.567169 TCTTGTCCATCTCCAACGTCAT 59.433 45.455 0.00 0.00 0.00 3.06
231 234 0.464735 CGTCAACCCCACCAAACTCA 60.465 55.000 0.00 0.00 0.00 3.41
266 269 6.451064 AATTTGACGAGGGAATTTACATCC 57.549 37.500 0.00 0.00 36.16 3.51
284 287 2.202905 TCGGTTTCGCCAACACGT 60.203 55.556 0.00 0.00 37.07 4.49
289 292 1.745864 TTTCGCCAACACGTGTGGT 60.746 52.632 24.16 4.10 34.19 4.16
393 397 4.021192 CAGCATTCCAAACAAACCCTACAT 60.021 41.667 0.00 0.00 0.00 2.29
395 399 4.620567 GCATTCCAAACAAACCCTACATCC 60.621 45.833 0.00 0.00 0.00 3.51
398 402 4.340617 TCCAAACAAACCCTACATCCATC 58.659 43.478 0.00 0.00 0.00 3.51
400 404 4.399303 CCAAACAAACCCTACATCCATCTC 59.601 45.833 0.00 0.00 0.00 2.75
401 405 5.256474 CAAACAAACCCTACATCCATCTCT 58.744 41.667 0.00 0.00 0.00 3.10
402 406 5.520748 AACAAACCCTACATCCATCTCTT 57.479 39.130 0.00 0.00 0.00 2.85
435 460 6.738114 ACATCACACGAAAAATGTTGAGATT 58.262 32.000 0.00 0.00 0.00 2.40
458 483 1.681486 CCTCTCCCGCTCCCTCTTTC 61.681 65.000 0.00 0.00 0.00 2.62
517 547 1.844771 CGCCCGACGGTGATACGATA 61.845 60.000 13.94 0.00 42.83 2.92
718 782 1.597027 CACTCGTGTTGACCCACCC 60.597 63.158 0.00 0.00 31.47 4.61
1029 1329 2.124695 GGTAGCAAGCGGGAAGGG 60.125 66.667 0.00 0.00 0.00 3.95
1077 1377 2.603652 GGAACCACTCCCTCCACCC 61.604 68.421 0.00 0.00 38.44 4.61
1100 1401 1.520787 CTCTATCCCGCCGCGTTTT 60.521 57.895 12.58 0.00 0.00 2.43
1212 1513 3.440173 CGTGAAACATGCCCATCTAAAGT 59.560 43.478 0.00 0.00 35.74 2.66
1368 1669 2.046217 GCCTTCTCGGTTGGGGAC 60.046 66.667 0.00 0.00 34.25 4.46
1394 1695 2.964389 GGCGAGATTCAGAGCGGC 60.964 66.667 0.00 0.00 41.85 6.53
1635 1948 0.466124 AGGATAGCCCTGCTTCGTTC 59.534 55.000 0.00 0.00 45.61 3.95
2148 2467 1.303561 TGGCACCTCCATTGCTGAC 60.304 57.895 0.00 0.00 40.72 3.51
2229 2548 6.326064 TCTCCTCCTTCTCTTATCTCAAATGG 59.674 42.308 0.00 0.00 0.00 3.16
2455 2796 7.621428 AGTTCTTGACATGATAATTGTGGAG 57.379 36.000 0.00 0.00 0.00 3.86
2630 2979 2.024176 TTATCTGCAACCCGAAGCTC 57.976 50.000 0.00 0.00 0.00 4.09
2795 3168 9.305925 GATATCTTTTCTTATTTGTTTGGCTGG 57.694 33.333 0.00 0.00 0.00 4.85
3044 3417 1.503542 CACACTCCATTCAAGCCGC 59.496 57.895 0.00 0.00 0.00 6.53
3081 3454 3.136626 AGAGGTCCTTTGTGTGTTAAGCT 59.863 43.478 0.00 0.00 0.00 3.74
3155 3528 0.868406 CTTCACGGCAGACCTTTCAC 59.132 55.000 0.00 0.00 0.00 3.18
3229 3602 3.078097 TGAATGGACGGTACACATTTGG 58.922 45.455 0.00 0.00 35.17 3.28
3466 3839 3.922171 GGAAGACAGAGGTCAATCCAT 57.078 47.619 12.15 0.00 46.80 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 4.019950 TGGCTCTTGTTTGAGATCTCATGA 60.020 41.667 25.64 14.72 39.64 3.07
38 39 1.014352 GTCACACGTGGCTCTTGTTT 58.986 50.000 21.57 0.00 31.34 2.83
66 67 1.595093 GGTTGCCATTTGAGACCCCG 61.595 60.000 0.00 0.00 0.00 5.73
78 79 1.884075 ATAGACACGCGAGGTTGCCA 61.884 55.000 15.93 0.00 0.00 4.92
86 87 1.538075 TGTCAACAGATAGACACGCGA 59.462 47.619 15.93 0.00 39.65 5.87
126 127 1.743996 GTTGGAGATGGACAAGAGCC 58.256 55.000 0.00 0.00 0.00 4.70
139 140 1.732259 CGGGAAAAGATGACGTTGGAG 59.268 52.381 0.00 0.00 0.00 3.86
141 142 0.168128 GCGGGAAAAGATGACGTTGG 59.832 55.000 0.00 0.00 0.00 3.77
150 151 4.404098 GAGGCGGGCGGGAAAAGA 62.404 66.667 0.00 0.00 0.00 2.52
174 175 0.529378 GACACGTATGACCTTCCCGT 59.471 55.000 0.00 0.00 0.00 5.28
214 216 0.184933 CCTGAGTTTGGTGGGGTTGA 59.815 55.000 0.00 0.00 0.00 3.18
224 227 0.679640 TATTGGCGCCCCTGAGTTTG 60.680 55.000 26.77 0.00 0.00 2.93
231 234 1.111277 GTCAAATTATTGGCGCCCCT 58.889 50.000 26.77 13.97 37.15 4.79
266 269 2.241880 ACGTGTTGGCGAAACCGAG 61.242 57.895 14.21 3.71 43.94 4.63
284 287 3.374678 GTCGGTTCTGTTTTTACACCACA 59.625 43.478 0.00 0.00 0.00 4.17
311 315 1.072505 TGGACCTCCGCCAACTTTC 59.927 57.895 0.00 0.00 39.43 2.62
334 338 1.616620 CAATTTTCGGCATCGGTGTG 58.383 50.000 0.00 0.00 36.95 3.82
335 339 0.525761 CCAATTTTCGGCATCGGTGT 59.474 50.000 0.00 0.00 36.95 4.16
393 397 4.019411 TGATGTTGCCACTAAAGAGATGGA 60.019 41.667 0.00 0.00 35.33 3.41
395 399 4.696877 TGTGATGTTGCCACTAAAGAGATG 59.303 41.667 0.00 0.00 35.66 2.90
398 402 3.120546 CGTGTGATGTTGCCACTAAAGAG 60.121 47.826 0.00 0.00 35.66 2.85
400 404 2.805671 TCGTGTGATGTTGCCACTAAAG 59.194 45.455 0.00 0.00 35.66 1.85
401 405 2.839975 TCGTGTGATGTTGCCACTAAA 58.160 42.857 0.00 0.00 35.66 1.85
402 406 2.535012 TCGTGTGATGTTGCCACTAA 57.465 45.000 0.00 0.00 35.66 2.24
458 483 1.890174 GCCGTTCCCCTTTTGATGG 59.110 57.895 0.00 0.00 0.00 3.51
517 547 1.500474 TTCCCTCTGGATTCGCTGAT 58.500 50.000 0.00 0.00 41.40 2.90
543 573 1.600636 CAGGCAGCCTTCCAAACGA 60.601 57.895 12.86 0.00 0.00 3.85
677 741 4.803426 GCCGTCACCCGCTCTCTG 62.803 72.222 0.00 0.00 34.38 3.35
1077 1377 3.616721 CGGCGGGATAGAGGTGGG 61.617 72.222 0.00 0.00 0.00 4.61
1100 1401 1.452953 ATGCCCGTAGATTCGAGCGA 61.453 55.000 0.00 0.00 37.37 4.93
1182 1483 0.719465 GCATGTTTCACGGTACCGAG 59.281 55.000 39.52 31.52 42.83 4.63
1190 1491 3.440173 ACTTTAGATGGGCATGTTTCACG 59.560 43.478 0.00 0.00 0.00 4.35
1225 1526 0.945265 CCGCGGTAACAGGAAACGAA 60.945 55.000 19.50 0.00 36.21 3.85
1295 1596 2.380410 CGAACCGAACTGAAGGGCG 61.380 63.158 0.00 0.00 0.00 6.13
1332 1633 2.618709 GGCGGAGGAAACCATAATTCTG 59.381 50.000 0.00 0.00 0.00 3.02
1368 1669 0.173481 TGAATCTCGCCGAACTCCAG 59.827 55.000 0.00 0.00 0.00 3.86
1663 1976 7.664731 CCAGCCAGTCATATAAATCTTTCTCAT 59.335 37.037 0.00 0.00 0.00 2.90
1708 2026 7.596494 CAATCCATATCACAAGTGAAAACACT 58.404 34.615 7.02 0.00 43.58 3.55
1774 2093 1.079127 AGCAACCGAATCAGGACCG 60.079 57.895 0.00 0.00 34.73 4.79
2148 2467 2.469516 GCGGTTGCCCCATTAGACG 61.470 63.158 0.00 0.00 33.98 4.18
2247 2566 2.362397 TCATCCTTAGCATCAGACCGAC 59.638 50.000 0.00 0.00 0.00 4.79
2305 2635 6.906659 TCTCAAATCATTGCTCACTTCTTTC 58.093 36.000 0.00 0.00 36.45 2.62
2455 2796 6.012658 TCCATTTTTACATCAGCACTCAAC 57.987 37.500 0.00 0.00 0.00 3.18
2630 2979 8.553459 AAGATGAAAACCATAAGTGACTACAG 57.447 34.615 0.00 0.00 35.17 2.74
2795 3168 3.314541 TTTCAAGGGCTAACTCGAGTC 57.685 47.619 20.33 6.35 0.00 3.36
3044 3417 3.119566 GGACCTCTTACAGTAAGACACGG 60.120 52.174 17.71 18.50 39.73 4.94
3081 3454 9.144298 CCCAGTCTAGATTTGATTAACCTACTA 57.856 37.037 0.00 0.00 0.00 1.82
3155 3528 2.880268 TGTGCACAGAGACAATTTCTGG 59.120 45.455 17.42 1.76 44.96 3.86
3229 3602 2.092968 TGCAGATTCCATGACAGGTACC 60.093 50.000 2.73 2.73 0.00 3.34
3466 3839 2.008242 AAAGCACCTTGTATGGCCAA 57.992 45.000 10.96 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.