Multiple sequence alignment - TraesCS3D01G186500

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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 TraesCS3D01G186500 chr3D 100.000 3443 0 0 1 3443 172384220 172380778 0.000000e+00 6359.0
1 TraesCS3D01G186500 chr3B 96.749 2738 62 12 710 3443 250819677 250816963 0.000000e+00 4538.0
2 TraesCS3D01G186500 chr3B 87.952 664 60 10 11 673 250820907 250820263 0.000000e+00 765.0
3 TraesCS3D01G186500 chr3B 79.167 240 42 7 243 479 586858444 586858678 3.560000e-35 159.0
4 TraesCS3D01G186500 chr3B 79.091 110 17 5 397 505 139470449 139470553 1.710000e-08 71.3
5 TraesCS3D01G186500 chr3A 95.760 2712 79 17 736 3443 210261293 210258614 0.000000e+00 4338.0
6 TraesCS3D01G186500 chr3A 75.256 489 94 15 31 505 686941489 686941014 1.250000e-49 207.0
7 TraesCS3D01G186500 chr3A 75.964 441 81 19 75 498 592143602 592144034 1.620000e-48 204.0
8 TraesCS3D01G186500 chr3A 90.411 73 5 2 620 690 210261577 210261505 1.020000e-15 95.3
9 TraesCS3D01G186500 chr7B 76.059 472 94 13 30 488 319591273 319591738 9.610000e-56 228.0
10 TraesCS3D01G186500 chr7B 75.647 464 88 17 49 495 50631105 50631560 1.250000e-49 207.0
11 TraesCS3D01G186500 chr1D 73.824 489 105 18 5 487 481468236 481467765 4.570000e-39 172.0
12 TraesCS3D01G186500 chr1B 75.000 364 66 21 131 487 105201755 105201410 9.960000e-31 145.0
13 TraesCS3D01G186500 chr6B 79.082 196 38 3 304 498 663764103 663763910 7.750000e-27 132.0
14 TraesCS3D01G186500 chr2D 80.556 144 25 3 241 383 80326771 80326630 1.310000e-19 108.0
15 TraesCS3D01G186500 chr6D 74.242 264 55 12 240 499 355301334 355301588 7.860000e-17 99.0
16 TraesCS3D01G186500 chr7A 78.750 160 22 11 11 165 733348865 733348713 2.830000e-16 97.1


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 TraesCS3D01G186500 chr3D 172380778 172384220 3442 True 6359.00 6359 100.0000 1 3443 1 chr3D.!!$R1 3442
1 TraesCS3D01G186500 chr3B 250816963 250820907 3944 True 2651.50 4538 92.3505 11 3443 2 chr3B.!!$R1 3432
2 TraesCS3D01G186500 chr3A 210258614 210261577 2963 True 2216.65 4338 93.0855 620 3443 2 chr3A.!!$R2 2823

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
319 320 0.039035 GCATTGGTCCTGTGGGGTTA 59.961 55.0 0.00 0.00 36.25 2.85 F
427 429 0.108396 TGCTTCAGTGCTTGTAGCCA 59.892 50.0 14.35 4.33 46.29 4.75 F
760 1338 0.176680 CCAGGAGACGACAGGGATTG 59.823 60.0 0.00 0.00 0.00 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1476 2057 3.238497 TCCACGGTGGTGTCCCAG 61.238 66.667 25.53 0.0 42.94 4.45 R
2340 2921 0.327924 CAGGCATTCCAGGTACACCA 59.672 55.000 0.38 0.0 38.89 4.17 R
2448 3029 1.265905 GGACACATCGACCAACCAAAC 59.734 52.381 0.00 0.0 0.00 2.93 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
44 45 3.072330 TGCTCATGTTCTTGTTAGGTCCA 59.928 43.478 0.00 0.00 0.00 4.02
54 55 4.039973 TCTTGTTAGGTCCAACGTCTTGAT 59.960 41.667 0.00 0.00 0.00 2.57
69 70 2.040145 TCTTGATTGAGGTCATGTGGCA 59.960 45.455 0.00 0.00 0.00 4.92
89 90 1.937223 AGCGACGATGTCTCTCAGTAG 59.063 52.381 0.00 0.00 0.00 2.57
102 103 7.350382 TGTCTCTCAGTAGGAATAATGTCTCT 58.650 38.462 0.00 0.00 0.00 3.10
107 108 7.782168 TCTCAGTAGGAATAATGTCTCTCATGT 59.218 37.037 0.00 0.00 36.81 3.21
114 115 8.592809 AGGAATAATGTCTCTCATGTCTAATCC 58.407 37.037 0.00 0.00 36.81 3.01
128 129 3.808174 GTCTAATCCCGTTCCAATAGTGC 59.192 47.826 0.00 0.00 0.00 4.40
131 132 0.108520 TCCCGTTCCAATAGTGCGTC 60.109 55.000 0.00 0.00 0.00 5.19
164 165 1.153429 GGCGTGTGGAGGTATGTCC 60.153 63.158 0.00 0.00 37.10 4.02
167 168 1.261938 CGTGTGGAGGTATGTCCCCA 61.262 60.000 0.00 0.00 35.49 4.96
180 181 3.467226 CCCCATCGGGTAGCACGT 61.467 66.667 0.00 0.00 45.50 4.49
194 195 0.796312 GCACGTGATTCAATCGGTGT 59.204 50.000 22.23 3.89 38.10 4.16
206 207 1.259609 ATCGGTGTTGGTCTTCGGTA 58.740 50.000 0.00 0.00 0.00 4.02
228 229 8.979574 CGGTAGATTTGTTTGGATCTAGTATTC 58.020 37.037 0.00 0.00 35.99 1.75
229 230 9.832445 GGTAGATTTGTTTGGATCTAGTATTCA 57.168 33.333 0.00 0.00 35.99 2.57
235 236 6.561614 TGTTTGGATCTAGTATTCAGTCGTC 58.438 40.000 0.00 0.00 0.00 4.20
237 238 7.555195 TGTTTGGATCTAGTATTCAGTCGTCTA 59.445 37.037 0.00 0.00 0.00 2.59
280 281 5.334182 CCGATCTACGATTCTCTTTCATCGA 60.334 44.000 8.46 0.00 44.18 3.59
281 282 6.136743 CGATCTACGATTCTCTTTCATCGAA 58.863 40.000 8.46 0.00 44.18 3.71
302 303 0.179032 ATGGTTATTGATCGGGCGCA 60.179 50.000 10.83 0.00 0.00 6.09
319 320 0.039035 GCATTGGTCCTGTGGGGTTA 59.961 55.000 0.00 0.00 36.25 2.85
326 327 1.212935 GTCCTGTGGGGTTATCAGCAT 59.787 52.381 0.00 0.00 36.25 3.79
347 349 6.696411 GCATGATGCTTCCTAACTATCTACT 58.304 40.000 10.72 0.00 40.96 2.57
363 365 4.425180 TCTACTACAACAAGGTTTGCCA 57.575 40.909 0.00 0.00 37.19 4.92
375 377 1.677217 GGTTTGCCAGGCTCTAGTGAG 60.677 57.143 14.15 0.00 37.79 3.51
382 384 1.458588 GGCTCTAGTGAGGGAGGGG 60.459 68.421 0.00 0.00 40.53 4.79
388 390 0.790993 TAGTGAGGGAGGGGTGAAGT 59.209 55.000 0.00 0.00 0.00 3.01
396 398 1.226746 GAGGGGTGAAGTCAACAACG 58.773 55.000 0.00 0.00 34.61 4.10
398 400 1.278637 GGGTGAAGTCAACAACGCG 59.721 57.895 3.53 3.53 34.61 6.01
408 410 0.575390 CAACAACGCGTCTTCGACTT 59.425 50.000 14.44 0.00 39.71 3.01
427 429 0.108396 TGCTTCAGTGCTTGTAGCCA 59.892 50.000 14.35 4.33 46.29 4.75
443 445 1.090052 GCCATCGCTAAGTGGTCCAC 61.090 60.000 14.68 14.68 37.81 4.02
491 493 9.690913 TTACTTCTAGTGTTCCTTATACTGCTA 57.309 33.333 0.00 0.00 30.13 3.49
518 520 0.754217 TTATGACTCCCTCCGTCCCG 60.754 60.000 0.00 0.00 0.00 5.14
519 521 1.929860 TATGACTCCCTCCGTCCCGT 61.930 60.000 0.00 0.00 0.00 5.28
523 525 0.325016 ACTCCCTCCGTCCCGTATTT 60.325 55.000 0.00 0.00 0.00 1.40
614 616 3.267900 CGAGTAATTCGGTGCGGAT 57.732 52.632 0.00 0.00 45.54 4.18
622 624 0.681887 TTCGGTGCGGATGGAGTAGA 60.682 55.000 0.00 0.00 0.00 2.59
623 625 0.467474 TCGGTGCGGATGGAGTAGAT 60.467 55.000 0.00 0.00 0.00 1.98
624 626 1.202842 TCGGTGCGGATGGAGTAGATA 60.203 52.381 0.00 0.00 0.00 1.98
625 627 1.611977 CGGTGCGGATGGAGTAGATAA 59.388 52.381 0.00 0.00 0.00 1.75
626 628 2.351835 CGGTGCGGATGGAGTAGATAAG 60.352 54.545 0.00 0.00 0.00 1.73
657 659 6.976636 TTTTGCAAAAGAAAAACACCCTAG 57.023 33.333 20.46 0.00 0.00 3.02
759 1337 0.978146 CCCAGGAGACGACAGGGATT 60.978 60.000 0.00 0.00 42.25 3.01
760 1338 0.176680 CCAGGAGACGACAGGGATTG 59.823 60.000 0.00 0.00 0.00 2.67
761 1339 1.186200 CAGGAGACGACAGGGATTGA 58.814 55.000 0.00 0.00 0.00 2.57
762 1340 1.759445 CAGGAGACGACAGGGATTGAT 59.241 52.381 0.00 0.00 0.00 2.57
818 1396 6.800890 AGGAAAGGAAAACACCCATATAAGT 58.199 36.000 0.00 0.00 0.00 2.24
859 1439 3.284617 AGGAAAACACCCATATAACGGC 58.715 45.455 0.00 0.00 0.00 5.68
862 1442 0.179468 AACACCCATATAACGGCGCT 59.821 50.000 6.90 0.00 0.00 5.92
872 1452 0.599558 TAACGGCGCTGTGAACTAGT 59.400 50.000 25.11 7.76 0.00 2.57
921 1501 0.251341 GCCTTGTCACCCAACCATCT 60.251 55.000 0.00 0.00 0.00 2.90
928 1508 3.181466 TGTCACCCAACCATCTCATATCG 60.181 47.826 0.00 0.00 0.00 2.92
1141 1722 0.395448 AGCCGAGTACTACCCCACTC 60.395 60.000 0.00 0.00 38.24 3.51
1338 1919 3.267860 GCTTCGATCCAGGCGCTG 61.268 66.667 7.64 3.34 0.00 5.18
2340 2921 1.770110 TGGAGCTCTTGGTGGTGGT 60.770 57.895 14.64 0.00 0.00 4.16
2448 3029 7.998964 AGAAATTACATGGGTCATTAGGTAAGG 59.001 37.037 0.00 0.00 0.00 2.69
2712 3295 6.734104 AAGTTCTCTAATGTGCATTCTGAC 57.266 37.500 0.18 0.00 32.50 3.51
2750 3333 6.369615 GTGCCTGAATGCATTTGTCTAATTTT 59.630 34.615 14.33 0.00 44.30 1.82
2763 3346 5.312895 TGTCTAATTTTCTGCCTTACTGCA 58.687 37.500 0.00 0.00 39.37 4.41
2844 3427 8.547967 TGAAATTGTAGGTCATCTGTTAAGTC 57.452 34.615 0.00 0.00 0.00 3.01
2878 3461 6.959639 ACTTCCTGACAAATTGCTTCTTAA 57.040 33.333 0.00 0.00 0.00 1.85
2948 3531 3.813443 AGCCAAGCTAACATTGATCGAT 58.187 40.909 0.00 0.00 36.99 3.59
2957 3540 5.277058 GCTAACATTGATCGATGTTGAGGTC 60.277 44.000 36.25 22.05 46.60 3.85
3016 3599 0.808060 GAGGCTAGAAGCGAAGGTGC 60.808 60.000 0.00 0.00 43.62 5.01
3181 3766 2.809696 CAAAGAATTTTTGGCAGGCCTG 59.190 45.455 29.34 29.34 35.03 4.85
3204 3789 7.541091 CCTGATCATTTTTGTCATCTCACAAAG 59.459 37.037 0.00 0.00 44.92 2.77
3217 3802 7.536622 GTCATCTCACAAAGATTGTTTCACATC 59.463 37.037 0.00 0.00 42.30 3.06
3266 3851 4.393834 TGCAGGTTTCAGTGCTTACATAA 58.606 39.130 0.00 0.00 40.54 1.90
3324 3909 6.668645 ACCCCAAACTATGAGTTATGCATTA 58.331 36.000 3.54 0.00 37.47 1.90
3426 4012 7.227314 TGCTATTTGACAGGATGCTTATAACTG 59.773 37.037 0.00 0.00 42.53 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.273324 GGGATCCCTCCTATCGGTGAT 60.273 57.143 24.69 0.00 41.74 3.06
1 2 0.114560 GGGATCCCTCCTATCGGTGA 59.885 60.000 24.69 0.00 41.74 4.02
2 3 0.905337 GGGGATCCCTCCTATCGGTG 60.905 65.000 30.08 0.00 41.34 4.94
4 5 4.463043 GGGGATCCCTCCTATCGG 57.537 66.667 30.08 0.00 41.34 4.18
22 23 3.072330 TGGACCTAACAAGAACATGAGCA 59.928 43.478 0.00 0.00 0.00 4.26
23 24 3.674997 TGGACCTAACAAGAACATGAGC 58.325 45.455 0.00 0.00 0.00 4.26
24 25 4.152402 CGTTGGACCTAACAAGAACATGAG 59.848 45.833 0.00 0.00 0.00 2.90
25 26 4.062293 CGTTGGACCTAACAAGAACATGA 58.938 43.478 0.00 0.00 0.00 3.07
26 27 3.813166 ACGTTGGACCTAACAAGAACATG 59.187 43.478 0.00 0.00 0.00 3.21
27 28 4.062991 GACGTTGGACCTAACAAGAACAT 58.937 43.478 0.00 0.00 0.00 2.71
44 45 3.748048 CACATGACCTCAATCAAGACGTT 59.252 43.478 0.00 0.00 30.82 3.99
54 55 1.672030 CGCTGCCACATGACCTCAA 60.672 57.895 0.00 0.00 0.00 3.02
69 70 1.937223 CTACTGAGAGACATCGTCGCT 59.063 52.381 0.00 0.00 44.70 4.93
89 90 7.821846 GGGATTAGACATGAGAGACATTATTCC 59.178 40.741 0.00 0.00 37.07 3.01
102 103 4.771114 ATTGGAACGGGATTAGACATGA 57.229 40.909 0.00 0.00 0.00 3.07
107 108 3.491964 CGCACTATTGGAACGGGATTAGA 60.492 47.826 0.00 0.00 0.00 2.10
114 115 2.460918 CTAGACGCACTATTGGAACGG 58.539 52.381 0.00 0.00 0.00 4.44
128 129 0.249073 CCTTCCGGTGATGCTAGACG 60.249 60.000 0.00 0.00 0.00 4.18
131 132 1.592669 CGCCTTCCGGTGATGCTAG 60.593 63.158 0.00 0.00 43.70 3.42
139 140 4.003788 CTCCACACGCCTTCCGGT 62.004 66.667 0.00 0.00 42.52 5.28
143 144 0.249398 ACATACCTCCACACGCCTTC 59.751 55.000 0.00 0.00 0.00 3.46
167 168 0.821517 TGAATCACGTGCTACCCGAT 59.178 50.000 11.67 0.00 0.00 4.18
172 173 2.029244 CACCGATTGAATCACGTGCTAC 59.971 50.000 11.67 4.75 0.00 3.58
179 180 3.074412 AGACCAACACCGATTGAATCAC 58.926 45.455 5.95 0.00 0.00 3.06
180 181 3.417069 AGACCAACACCGATTGAATCA 57.583 42.857 5.95 0.00 0.00 2.57
194 195 4.517453 CCAAACAAATCTACCGAAGACCAA 59.483 41.667 0.00 0.00 36.93 3.67
206 207 9.606631 GACTGAATACTAGATCCAAACAAATCT 57.393 33.333 0.00 0.00 36.28 2.40
228 229 6.308282 GGATCAAACTTGTAACTAGACGACTG 59.692 42.308 0.00 0.00 0.00 3.51
229 230 6.208994 AGGATCAAACTTGTAACTAGACGACT 59.791 38.462 0.00 0.00 0.00 4.18
231 232 6.585695 AGGATCAAACTTGTAACTAGACGA 57.414 37.500 0.00 0.00 0.00 4.20
235 236 6.395629 TCGGAAGGATCAAACTTGTAACTAG 58.604 40.000 0.00 0.00 0.00 2.57
237 238 5.223449 TCGGAAGGATCAAACTTGTAACT 57.777 39.130 0.00 0.00 0.00 2.24
280 281 2.494059 CGCCCGATCAATAACCATCTT 58.506 47.619 0.00 0.00 0.00 2.40
281 282 1.878102 GCGCCCGATCAATAACCATCT 60.878 52.381 0.00 0.00 0.00 2.90
302 303 2.242196 CTGATAACCCCACAGGACCAAT 59.758 50.000 0.00 0.00 39.89 3.16
326 327 8.630917 GTTGTAGTAGATAGTTAGGAAGCATCA 58.369 37.037 0.00 0.00 0.00 3.07
336 337 7.820872 GGCAAACCTTGTTGTAGTAGATAGTTA 59.179 37.037 0.00 0.00 0.00 2.24
337 338 6.653740 GGCAAACCTTGTTGTAGTAGATAGTT 59.346 38.462 0.00 0.00 0.00 2.24
347 349 1.036707 GCCTGGCAAACCTTGTTGTA 58.963 50.000 15.17 0.00 36.63 2.41
363 365 1.623625 CCCTCCCTCACTAGAGCCT 59.376 63.158 0.00 0.00 40.68 4.58
375 377 0.476771 TTGTTGACTTCACCCCTCCC 59.523 55.000 0.00 0.00 0.00 4.30
382 384 0.928229 AGACGCGTTGTTGACTTCAC 59.072 50.000 15.53 0.00 0.00 3.18
388 390 4.713980 TCGAAGACGCGTTGTTGA 57.286 50.000 15.53 11.16 39.58 3.18
408 410 0.108396 TGGCTACAAGCACTGAAGCA 59.892 50.000 0.78 0.00 44.75 3.91
427 429 0.968901 TCCGTGGACCACTTAGCGAT 60.969 55.000 22.14 0.00 31.34 4.58
434 436 1.342672 AACCAAGTCCGTGGACCACT 61.343 55.000 22.14 0.24 45.59 4.00
435 437 1.147600 AACCAAGTCCGTGGACCAC 59.852 57.895 15.13 15.13 45.59 4.16
472 474 7.014326 CCAGTCATAGCAGTATAAGGAACACTA 59.986 40.741 0.00 0.00 0.00 2.74
483 485 6.015010 GGAGTCATAACCAGTCATAGCAGTAT 60.015 42.308 0.00 0.00 0.00 2.12
491 493 3.041946 GGAGGGAGTCATAACCAGTCAT 58.958 50.000 0.00 0.00 0.00 3.06
571 573 9.680946 CGTCGCATAAATAGATAGAAATGAATG 57.319 33.333 0.00 0.00 0.00 2.67
574 576 8.297426 ACTCGTCGCATAAATAGATAGAAATGA 58.703 33.333 0.00 0.00 0.00 2.57
582 584 6.527023 CCGAATTACTCGTCGCATAAATAGAT 59.473 38.462 0.00 0.00 46.65 1.98
588 590 3.110358 CACCGAATTACTCGTCGCATAA 58.890 45.455 0.00 0.00 46.65 1.90
606 608 2.891580 TCTTATCTACTCCATCCGCACC 59.108 50.000 0.00 0.00 0.00 5.01
614 616 7.936847 TGCAAAAGAAACTTCTTATCTACTCCA 59.063 33.333 5.16 0.00 46.22 3.86
695 734 2.677848 GGCAAGGACCCTCCCTTC 59.322 66.667 0.00 0.00 44.30 3.46
759 1337 0.546122 ACGGATGGGCTAAGCAATCA 59.454 50.000 0.00 0.00 0.00 2.57
760 1338 1.230324 GACGGATGGGCTAAGCAATC 58.770 55.000 0.00 0.00 0.00 2.67
761 1339 0.532862 CGACGGATGGGCTAAGCAAT 60.533 55.000 0.00 0.00 0.00 3.56
762 1340 1.153449 CGACGGATGGGCTAAGCAA 60.153 57.895 0.00 0.00 0.00 3.91
830 1408 8.459635 GTTATATGGGTGTTTTCCTTCTTCTTC 58.540 37.037 0.00 0.00 0.00 2.87
833 1411 6.183360 CCGTTATATGGGTGTTTTCCTTCTTC 60.183 42.308 0.00 0.00 0.00 2.87
836 1414 4.201980 GCCGTTATATGGGTGTTTTCCTTC 60.202 45.833 0.00 0.00 0.00 3.46
1323 1904 3.774528 AGCAGCGCCTGGATCGAA 61.775 61.111 2.29 0.00 31.21 3.71
1476 2057 3.238497 TCCACGGTGGTGTCCCAG 61.238 66.667 25.53 0.00 42.94 4.45
2340 2921 0.327924 CAGGCATTCCAGGTACACCA 59.672 55.000 0.38 0.00 38.89 4.17
2448 3029 1.265905 GGACACATCGACCAACCAAAC 59.734 52.381 0.00 0.00 0.00 2.93
2712 3295 2.234143 TCAGGCACATCCTAGATCTCG 58.766 52.381 0.00 0.00 45.52 4.04
2763 3346 5.505181 AGTTCAGGTTGTCATATTGGACT 57.495 39.130 0.00 0.00 38.61 3.85
2948 3531 9.793259 ATTAGTTTTATTTCTCAGACCTCAACA 57.207 29.630 0.00 0.00 0.00 3.33
2996 3579 0.532573 CACCTTCGCTTCTAGCCTCA 59.467 55.000 0.00 0.00 38.18 3.86
3016 3599 8.682936 AACTAAAACAGAGCCCATATATTCAG 57.317 34.615 0.00 0.00 0.00 3.02
3181 3766 9.635520 AATCTTTGTGAGATGACAAAAATGATC 57.364 29.630 0.00 0.00 44.41 2.92
3217 3802 8.272545 ACAAGCTATGTATAATGTGCATATGG 57.727 34.615 4.56 0.00 41.63 2.74


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

AutoCloner maintained by Alex Coulton.