Multiple sequence alignment - TraesCS3A01G271400

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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 TraesCS3A01G271400 chr3A 100.000 3018 0 0 1 3018 500528298 500525281 0.000000e+00 5574
1 TraesCS3A01G271400 chr3B 94.787 3031 105 20 3 3018 489982317 489979325 0.000000e+00 4673
2 TraesCS3A01G271400 chr3B 79.372 223 41 5 167 385 5747896 5747675 5.210000e-33 152
3 TraesCS3A01G271400 chr3D 93.756 3027 80 31 15 3018 375724260 375721320 0.000000e+00 4442
4 TraesCS3A01G271400 chr1B 87.574 338 42 0 1012 1349 643567684 643567347 2.820000e-105 392
5 TraesCS3A01G271400 chr1B 79.213 178 35 2 205 381 50898127 50898303 4.090000e-24 122
6 TraesCS3A01G271400 chr1D 86.111 360 49 1 990 1349 467002349 467002707 1.310000e-103 387
7 TraesCS3A01G271400 chr1D 79.352 247 42 9 156 397 387470235 387469993 6.690000e-37 165
8 TraesCS3A01G271400 chr1A 86.167 347 48 0 1003 1349 558954615 558954961 2.840000e-100 375
9 TraesCS3A01G271400 chr5A 82.479 234 34 7 156 384 594138031 594138262 6.600000e-47 198
10 TraesCS3A01G271400 chr5A 80.000 170 31 3 202 370 594134811 594134978 4.090000e-24 122
11 TraesCS3A01G271400 chr5B 84.302 172 23 4 167 334 582157827 582157998 6.690000e-37 165
12 TraesCS3A01G271400 chr7D 80.851 188 33 3 204 390 580011302 580011117 8.720000e-31 145
13 TraesCS3A01G271400 chr5D 76.818 220 45 5 167 382 475004972 475005189 5.290000e-23 119


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 TraesCS3A01G271400 chr3A 500525281 500528298 3017 True 5574 5574 100.000 1 3018 1 chr3A.!!$R1 3017
1 TraesCS3A01G271400 chr3B 489979325 489982317 2992 True 4673 4673 94.787 3 3018 1 chr3B.!!$R2 3015
2 TraesCS3A01G271400 chr3D 375721320 375724260 2940 True 4442 4442 93.756 15 3018 1 chr3D.!!$R1 3003

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
144 145 0.027586 GCGTGGACATTAATGGCGTC 59.972 55.0 19.37 11.44 36.40 5.19 F
473 476 0.816825 CCATGCATCCCCGAAGTCTG 60.817 60.0 0.00 0.00 0.00 3.51 F
485 488 1.282930 GAAGTCTGCGAACCCACGTC 61.283 60.0 0.00 0.00 35.59 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1533 1553 0.678684 TGTAGCCATCGTCCGAGTCA 60.679 55.000 0.0 0.0 0.0 3.41 R
1695 1718 0.991920 CTAGCTCCCCAAAACCTCCA 59.008 55.000 0.0 0.0 0.0 3.86 R
2191 2216 2.111384 GTCAGGCCTTGGTCTCTCATA 58.889 52.381 0.0 0.0 0.0 2.15 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
29 30 1.490621 GCAGTTTGTGTGTGCATTCC 58.509 50.000 0.00 0.00 37.16 3.01
40 41 4.740822 GCATTCCGGCTGTGGGGT 62.741 66.667 0.00 0.00 0.00 4.95
45 46 2.002018 TTCCGGCTGTGGGGTTTCTT 62.002 55.000 0.00 0.00 0.00 2.52
59 60 3.364664 GGGTTTCTTCCATCGAACGAAAC 60.365 47.826 14.05 14.05 40.60 2.78
73 74 2.463592 GAAACCGTTCGGTGGGATC 58.536 57.895 17.59 10.02 38.70 3.36
84 85 1.658717 GTGGGATCGATCGCTCGTG 60.659 63.158 33.83 0.00 45.25 4.35
125 126 0.179108 GGGGATCTCCAGAACGAACG 60.179 60.000 6.79 0.00 37.91 3.95
126 127 0.806492 GGGATCTCCAGAACGAACGC 60.806 60.000 0.00 0.00 37.91 4.84
139 140 2.071604 CGAACGCGTGGACATTAATG 57.928 50.000 14.98 14.01 0.00 1.90
144 145 0.027586 GCGTGGACATTAATGGCGTC 59.972 55.000 19.37 11.44 36.40 5.19
160 161 3.886505 TGGCGTCCAAACATTTTTACTCT 59.113 39.130 0.00 0.00 0.00 3.24
188 189 5.559417 CGTTTTGTTTAGTCCGCACATTACT 60.559 40.000 0.00 0.00 0.00 2.24
196 197 4.890088 AGTCCGCACATTACTTTTGACTA 58.110 39.130 0.00 0.00 30.56 2.59
198 199 5.938125 AGTCCGCACATTACTTTTGACTAAT 59.062 36.000 0.00 0.00 30.56 1.73
201 202 8.231837 GTCCGCACATTACTTTTGACTAATTTA 58.768 33.333 0.00 0.00 0.00 1.40
409 412 1.349973 GCTGAAGAGCCGAAATCGC 59.650 57.895 0.00 0.00 39.57 4.58
458 461 1.449726 CGCACCCATCCATGACCATG 61.450 60.000 0.00 3.11 38.51 3.66
473 476 0.816825 CCATGCATCCCCGAAGTCTG 60.817 60.000 0.00 0.00 0.00 3.51
484 487 1.300697 GAAGTCTGCGAACCCACGT 60.301 57.895 0.00 0.00 35.59 4.49
485 488 1.282930 GAAGTCTGCGAACCCACGTC 61.283 60.000 0.00 0.00 35.59 4.34
486 489 3.103911 GTCTGCGAACCCACGTCG 61.104 66.667 0.00 0.00 35.59 5.12
551 554 1.727335 GTTTCTCTCTCCTTTTCGGCG 59.273 52.381 0.00 0.00 0.00 6.46
553 556 1.811679 CTCTCTCCTTTTCGGCGCC 60.812 63.158 19.07 19.07 0.00 6.53
709 718 2.943033 CCGATTTTAATTCGGCTCCACT 59.057 45.455 14.02 0.00 40.25 4.00
733 742 2.671963 GGCCGGTCAGTCAAACCC 60.672 66.667 0.00 0.00 32.89 4.11
734 743 3.047877 GCCGGTCAGTCAAACCCG 61.048 66.667 1.90 0.00 40.12 5.28
927 937 2.355126 CCGACTCGCATCCATCCG 60.355 66.667 0.00 0.00 0.00 4.18
1648 1671 1.761174 GGTCCTCCTGTTCTTGGCA 59.239 57.895 0.00 0.00 0.00 4.92
2105 2130 2.198827 TGCTTAGGTGTTCACCCATG 57.801 50.000 17.06 8.31 0.00 3.66
2112 2137 2.028130 GGTGTTCACCCATGTTGAACA 58.972 47.619 25.39 25.39 46.30 3.18
2138 2163 3.983533 AACCAGAGATCTAGGCTACCT 57.016 47.619 12.46 0.00 37.71 3.08
2139 2164 3.983533 ACCAGAGATCTAGGCTACCTT 57.016 47.619 12.46 0.00 34.61 3.50
2178 2203 7.543172 AGCAATGCTCAAGTAATTGTATGTTTG 59.457 33.333 0.00 4.05 30.62 2.93
2191 2216 4.564041 TGTATGTTTGGCGATTTTGCATT 58.436 34.783 0.00 0.00 36.28 3.56
2207 2232 2.225467 GCATTATGAGAGACCAAGGCC 58.775 52.381 0.00 0.00 0.00 5.19
2380 2405 1.068588 TGCTCTGCGTATAGGCGAATT 59.931 47.619 12.43 0.00 35.06 2.17
2571 2603 4.318332 TCTGTTGTGAGTAGGAAATGCTG 58.682 43.478 0.00 0.00 0.00 4.41
2916 2952 1.978454 TGTGGTGCACATGTTGATCA 58.022 45.000 20.43 1.18 39.62 2.92
2995 3031 8.650714 GTTTATTAACTGTTACAGTCCGTTAGG 58.349 37.037 18.89 0.00 44.62 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.094597 CACACAAACTGCCCCATACATG 60.095 50.000 0.00 0.00 0.00 3.21
1 2 2.170166 CACACAAACTGCCCCATACAT 58.830 47.619 0.00 0.00 0.00 2.29
11 12 1.600164 CCGGAATGCACACACAAACTG 60.600 52.381 0.00 0.00 0.00 3.16
12 13 0.667993 CCGGAATGCACACACAAACT 59.332 50.000 0.00 0.00 0.00 2.66
13 14 0.939106 GCCGGAATGCACACACAAAC 60.939 55.000 5.05 0.00 0.00 2.93
29 30 1.971695 GGAAGAAACCCCACAGCCG 60.972 63.158 0.00 0.00 0.00 5.52
40 41 2.477375 CGGTTTCGTTCGATGGAAGAAA 59.523 45.455 9.39 9.39 32.22 2.52
59 60 1.299926 GATCGATCCCACCGAACGG 60.300 63.158 14.76 11.83 39.62 4.44
103 104 0.252513 TCGTTCTGGAGATCCCCCAA 60.253 55.000 6.00 0.00 32.53 4.12
125 126 0.027586 GACGCCATTAATGTCCACGC 59.972 55.000 14.25 8.80 0.00 5.34
131 132 4.799564 AATGTTTGGACGCCATTAATGT 57.200 36.364 14.25 0.00 31.53 2.71
132 133 6.479095 AAAAATGTTTGGACGCCATTAATG 57.521 33.333 8.58 8.58 31.53 1.90
137 138 4.522789 AGAGTAAAAATGTTTGGACGCCAT 59.477 37.500 0.00 0.00 31.53 4.40
138 139 3.886505 AGAGTAAAAATGTTTGGACGCCA 59.113 39.130 0.00 0.00 0.00 5.69
139 140 4.215613 AGAGAGTAAAAATGTTTGGACGCC 59.784 41.667 0.00 0.00 0.00 5.68
144 145 8.531530 CAAAACGAAGAGAGTAAAAATGTTTGG 58.468 33.333 0.00 0.00 0.00 3.28
146 147 9.634163 AACAAAACGAAGAGAGTAAAAATGTTT 57.366 25.926 0.00 0.00 0.00 2.83
160 161 3.001533 GTGCGGACTAAACAAAACGAAGA 59.998 43.478 0.00 0.00 0.00 2.87
372 375 5.109903 TCAGCTTCCTCGTATTAGCTTTTC 58.890 41.667 0.00 0.00 41.76 2.29
458 461 2.852495 TTCGCAGACTTCGGGGATGC 62.852 60.000 0.00 0.00 34.32 3.91
551 554 0.237498 CGTCTCTTTGGTTTTCGGGC 59.763 55.000 0.00 0.00 0.00 6.13
553 556 0.941542 TGCGTCTCTTTGGTTTTCGG 59.058 50.000 0.00 0.00 0.00 4.30
927 937 2.716017 CCTCTCGGTGGCTGGAGAC 61.716 68.421 0.00 0.00 35.55 3.36
1101 1118 1.138047 CGCGGTTGAGGTCGATGTAC 61.138 60.000 0.00 0.00 0.00 2.90
1524 1544 1.511305 GTCCGAGTCAGAATCCGCA 59.489 57.895 0.00 0.00 0.00 5.69
1533 1553 0.678684 TGTAGCCATCGTCCGAGTCA 60.679 55.000 0.00 0.00 0.00 3.41
1695 1718 0.991920 CTAGCTCCCCAAAACCTCCA 59.008 55.000 0.00 0.00 0.00 3.86
2105 2130 9.469807 CTAGATCTCTGGTTACATATGTTCAAC 57.530 37.037 14.77 12.82 0.00 3.18
2112 2137 6.893005 GGTAGCCTAGATCTCTGGTTACATAT 59.107 42.308 27.03 8.62 38.66 1.78
2113 2138 6.045695 AGGTAGCCTAGATCTCTGGTTACATA 59.954 42.308 27.03 10.24 38.66 2.29
2138 2163 5.526479 TGAGCATTGCTTTGCACAAATAAAA 59.474 32.000 13.35 0.00 45.23 1.52
2139 2164 5.055144 TGAGCATTGCTTTGCACAAATAAA 58.945 33.333 13.35 0.00 45.23 1.40
2178 2203 4.531332 GTCTCTCATAATGCAAAATCGCC 58.469 43.478 0.00 0.00 0.00 5.54
2191 2216 2.111384 GTCAGGCCTTGGTCTCTCATA 58.889 52.381 0.00 0.00 0.00 2.15
2207 2232 4.152580 TCGCTAGTCGCTATCATAAGTCAG 59.847 45.833 2.24 0.00 38.27 3.51
2380 2405 8.305317 TGAGATGCATCATCAACAAATTAAACA 58.695 29.630 27.81 1.47 42.72 2.83
2529 2554 8.352201 CAACAGAAAACTATGAATCAGAAACCA 58.648 33.333 0.00 0.00 0.00 3.67
2544 2569 6.238759 GCATTTCCTACTCACAACAGAAAACT 60.239 38.462 0.00 0.00 0.00 2.66
2571 2603 9.766277 CAGCATAACACTAGAGAAAAGATTTTC 57.234 33.333 9.53 9.53 45.22 2.29
2910 2946 7.658982 GCCAGTATCACAAGAATAGATGATCAA 59.341 37.037 0.00 0.00 33.84 2.57
2915 2951 5.862845 AGGCCAGTATCACAAGAATAGATG 58.137 41.667 5.01 0.00 0.00 2.90
2916 2952 6.506538 AAGGCCAGTATCACAAGAATAGAT 57.493 37.500 5.01 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.