Multiple sequence alignment - TraesCS5D01G246000

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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 TraesCS5D01G246000 chr5D 100.000 2765 0 0 1 2765 354258497 354261261 0.000000e+00 5107.0
1 TraesCS5D01G246000 chr5D 90.608 362 33 1 706 1067 412722495 412722135 1.930000e-131 479.0
2 TraesCS5D01G246000 chr5A 94.238 1857 70 16 37 1868 455088090 455089934 0.000000e+00 2802.0
3 TraesCS5D01G246000 chr5A 96.311 244 9 0 2521 2764 455091310 455091553 4.290000e-108 401.0
4 TraesCS5D01G246000 chr5A 87.607 234 19 4 2113 2343 455090405 455090631 2.110000e-66 263.0
5 TraesCS5D01G246000 chr5A 95.395 152 7 0 1936 2087 455090271 455090422 2.750000e-60 243.0
6 TraesCS5D01G246000 chr5A 100.000 30 0 0 1905 1934 455090221 455090250 3.850000e-04 56.5
7 TraesCS5D01G246000 chr5B 94.758 1774 81 7 103 1868 418470977 418472746 0.000000e+00 2750.0
8 TraesCS5D01G246000 chr5B 95.640 367 15 1 2398 2764 418507519 418507884 3.070000e-164 588.0
9 TraesCS5D01G246000 chr5B 91.033 368 29 3 700 1067 709933557 709933920 6.880000e-136 494.0
10 TraesCS5D01G246000 chr5B 89.130 184 12 5 2163 2343 418506606 418506784 3.580000e-54 222.0
11 TraesCS5D01G246000 chr5B 100.000 46 0 0 1861 1906 418472764 418472809 4.910000e-13 86.1


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 TraesCS5D01G246000 chr5D 354258497 354261261 2764 False 5107.00 5107 100.0000 1 2765 1 chr5D.!!$F1 2764
1 TraesCS5D01G246000 chr5A 455088090 455091553 3463 False 753.10 2802 94.7102 37 2764 5 chr5A.!!$F1 2727
2 TraesCS5D01G246000 chr5B 418470977 418472809 1832 False 1418.05 2750 97.3790 103 1906 2 chr5B.!!$F2 1803
3 TraesCS5D01G246000 chr5B 418506606 418507884 1278 False 405.00 588 92.3850 2163 2764 2 chr5B.!!$F3 601

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
569 583 0.38539 GTTGGTGCTGTCTGTTTGGG 59.615 55.0 0.0 0.0 0.0 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2030 2324 1.140652 TGCCACATTGTCAGTGTCTCA 59.859 47.619 0.0 0.0 35.24 3.27 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
81 82 3.372822 CCCTGAAATGCATCAAATGTTGC 59.627 43.478 0.00 9.05 40.24 4.17
94 95 7.168972 GCATCAAATGTTGCACTTAACTGTAAA 59.831 33.333 10.71 0.00 39.75 2.01
96 97 7.990917 TCAAATGTTGCACTTAACTGTAAAGA 58.009 30.769 0.00 0.00 0.00 2.52
97 98 8.629158 TCAAATGTTGCACTTAACTGTAAAGAT 58.371 29.630 0.00 0.00 0.00 2.40
98 99 8.693504 CAAATGTTGCACTTAACTGTAAAGATG 58.306 33.333 0.00 0.00 0.00 2.90
100 101 6.724263 TGTTGCACTTAACTGTAAAGATGTG 58.276 36.000 0.00 0.00 0.00 3.21
101 102 6.540551 TGTTGCACTTAACTGTAAAGATGTGA 59.459 34.615 0.00 0.00 0.00 3.58
124 125 9.525409 GTGATACTAACTAATAACGACCACAAT 57.475 33.333 0.00 0.00 0.00 2.71
168 177 6.415573 ACCTGATACATGGAAGGTTAAACTC 58.584 40.000 0.00 0.00 40.14 3.01
213 227 5.018539 TGGAGGTGTCTTACATTATTCCG 57.981 43.478 0.00 0.00 0.00 4.30
368 382 5.355071 TCTTGACATCTTGTTCATACCATGC 59.645 40.000 0.00 0.00 0.00 4.06
415 429 6.549952 CATTCAGTACATTCCTTCTGAAAGC 58.450 40.000 9.82 0.00 45.58 3.51
424 438 3.632333 TCCTTCTGAAAGCGATCTAGGA 58.368 45.455 0.00 0.00 0.00 2.94
489 503 6.431198 TTTGTAGGCTATGTTCGGAAAATC 57.569 37.500 0.00 0.00 0.00 2.17
498 512 3.666274 TGTTCGGAAAATCACATACCGT 58.334 40.909 0.00 0.00 43.36 4.83
528 542 6.897986 AGCTGAAAATCTGGATGAGTTAGAT 58.102 36.000 0.00 0.00 32.22 1.98
569 583 0.385390 GTTGGTGCTGTCTGTTTGGG 59.615 55.000 0.00 0.00 0.00 4.12
572 586 1.150536 GTGCTGTCTGTTTGGGGGA 59.849 57.895 0.00 0.00 0.00 4.81
577 591 1.149854 GTCTGTTTGGGGGACGGTT 59.850 57.895 0.00 0.00 0.00 4.44
610 624 5.772521 ACTGGTGCTGAATATTTTGTGTTC 58.227 37.500 0.00 0.00 0.00 3.18
617 631 7.860373 GTGCTGAATATTTTGTGTTCACTACAA 59.140 33.333 4.59 0.00 38.80 2.41
618 632 8.409371 TGCTGAATATTTTGTGTTCACTACAAA 58.591 29.630 4.59 0.00 43.88 2.83
632 646 8.134895 TGTTCACTACAAATGATTCTTTTCACC 58.865 33.333 0.00 0.00 32.64 4.02
638 652 6.275335 ACAAATGATTCTTTTCACCACACAG 58.725 36.000 0.00 0.00 0.00 3.66
655 669 4.516698 CACACAGTTTCTATTTCAGGCACT 59.483 41.667 0.00 0.00 43.88 4.40
690 704 6.552350 AGGATGCCATTCTTTAAGCATTGTAT 59.448 34.615 0.00 0.00 45.57 2.29
692 706 8.359642 GGATGCCATTCTTTAAGCATTGTATAA 58.640 33.333 0.00 0.00 45.57 0.98
693 707 9.748708 GATGCCATTCTTTAAGCATTGTATAAA 57.251 29.630 0.00 0.00 45.57 1.40
694 708 8.925161 TGCCATTCTTTAAGCATTGTATAAAC 57.075 30.769 0.00 0.00 0.00 2.01
813 828 2.576615 GCTTTGGACCAGTTCTCAAGT 58.423 47.619 0.00 0.00 0.00 3.16
822 837 5.365619 GACCAGTTCTCAAGTAACCTTTCA 58.634 41.667 0.00 0.00 0.00 2.69
1013 1033 2.009051 TCTGTTCAGCACACAACAGTG 58.991 47.619 10.71 0.00 46.51 3.66
1084 1104 3.699411 ATAGCCTTCTCCATCATCTGC 57.301 47.619 0.00 0.00 0.00 4.26
1728 1752 1.959899 GCTCGTCTCCATTGCGTGTG 61.960 60.000 0.00 0.00 0.00 3.82
1795 1820 3.577805 AAACGCCCCTATGCTTCTAAT 57.422 42.857 0.00 0.00 0.00 1.73
1934 2209 3.761897 TGGATAGGACACAAACCTTTGG 58.238 45.455 2.94 0.00 42.34 3.28
1990 2284 6.821665 ACTATAAGCAAACTAATTTCGCAGGA 59.178 34.615 0.00 0.00 0.00 3.86
2004 2298 2.880268 TCGCAGGATATTGATGCTTTGG 59.120 45.455 6.29 0.00 37.81 3.28
2030 2324 8.268605 GGATTTACTAGAAGATTCCCAAGACTT 58.731 37.037 0.00 0.00 0.00 3.01
2040 2334 2.677914 TCCCAAGACTTGAGACACTGA 58.322 47.619 16.99 0.00 0.00 3.41
2073 2367 1.067213 GCCTGCAGGAGCTAGCTATAC 60.067 57.143 37.21 11.28 42.74 1.47
2087 2381 5.921408 GCTAGCTATACTCGCAAGTATGTTT 59.079 40.000 7.70 0.00 46.07 2.83
2088 2382 6.421202 GCTAGCTATACTCGCAAGTATGTTTT 59.579 38.462 7.70 0.00 46.07 2.43
2089 2383 7.042658 GCTAGCTATACTCGCAAGTATGTTTTT 60.043 37.037 7.70 0.00 46.07 1.94
2141 2435 4.211389 GCAAGTATGTTGACACGTGAAAG 58.789 43.478 25.01 0.00 0.00 2.62
2177 2471 1.753903 TTCAAGGAGGATGAACCCCA 58.246 50.000 0.00 0.00 40.05 4.96
2250 2547 7.739825 TCCATATAGGAAAATCCTCTCAACAG 58.260 38.462 1.36 0.00 45.66 3.16
2265 2562 8.424918 TCCTCTCAACAGTATCATAAAATCCTC 58.575 37.037 0.00 0.00 0.00 3.71
2266 2563 8.428063 CCTCTCAACAGTATCATAAAATCCTCT 58.572 37.037 0.00 0.00 0.00 3.69
2296 2593 2.823747 TGACCGGCGATATAGCAATAGT 59.176 45.455 9.30 1.11 39.27 2.12
2328 2625 1.692519 ACACTCCTAGACAACGCCTTT 59.307 47.619 0.00 0.00 0.00 3.11
2329 2626 2.069273 CACTCCTAGACAACGCCTTTG 58.931 52.381 0.00 0.00 41.49 2.77
2378 2717 1.474143 GCTATCACCCCTGAAGCAGAC 60.474 57.143 0.00 0.00 33.86 3.51
2443 3420 2.836262 ACTCTGCATGATCAAGCTAGC 58.164 47.619 22.26 6.62 0.00 3.42
2495 3973 6.867662 TTTGGATTTTCTCACTTGAGTCTC 57.132 37.500 6.15 0.00 42.60 3.36
2498 3976 5.070981 TGGATTTTCTCACTTGAGTCTCTGT 59.929 40.000 6.15 0.00 42.60 3.41
2723 4201 5.048846 TCTTGTCCCTTGGCTAAATATCC 57.951 43.478 0.00 0.00 0.00 2.59
2764 4242 9.057089 GTGTAGCTTTAGGTATCAATGCTAAAT 57.943 33.333 0.00 0.00 39.15 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.009681 ACATTTTGGTTCAGACCCCC 57.990 50.000 0.00 0.00 45.92 5.40
20 21 4.415881 AAAACATTTTGGTTCAGACCCC 57.584 40.909 0.00 0.00 45.92 4.95
21 22 5.670485 AGAAAAACATTTTGGTTCAGACCC 58.330 37.500 0.00 0.00 45.92 4.46
22 23 7.609760 AAAGAAAAACATTTTGGTTCAGACC 57.390 32.000 0.00 0.00 46.71 3.85
49 50 1.547675 GCATTTCAGGGTTCCACTGGA 60.548 52.381 0.00 0.00 36.62 3.86
50 51 0.890683 GCATTTCAGGGTTCCACTGG 59.109 55.000 0.00 0.00 36.62 4.00
51 52 1.619654 TGCATTTCAGGGTTCCACTG 58.380 50.000 0.00 0.00 37.30 3.66
52 53 2.225091 TGATGCATTTCAGGGTTCCACT 60.225 45.455 0.00 0.00 0.00 4.00
53 54 2.170166 TGATGCATTTCAGGGTTCCAC 58.830 47.619 0.00 0.00 0.00 4.02
54 55 2.601240 TGATGCATTTCAGGGTTCCA 57.399 45.000 0.00 0.00 0.00 3.53
94 95 9.128404 TGGTCGTTATTAGTTAGTATCACATCT 57.872 33.333 0.00 0.00 0.00 2.90
96 97 8.689061 TGTGGTCGTTATTAGTTAGTATCACAT 58.311 33.333 0.00 0.00 0.00 3.21
97 98 8.054152 TGTGGTCGTTATTAGTTAGTATCACA 57.946 34.615 0.00 0.00 0.00 3.58
98 99 8.915871 TTGTGGTCGTTATTAGTTAGTATCAC 57.084 34.615 0.00 0.00 0.00 3.06
124 125 6.436218 TCAGGTCAGAATAGTTGCAGTACTAA 59.564 38.462 2.47 0.00 34.50 2.24
168 177 3.132160 GTCATGTGCAGATCTCATCAGG 58.868 50.000 0.00 0.00 0.00 3.86
213 227 1.047801 ACCCATCCACTGGCAAAAAC 58.952 50.000 0.00 0.00 44.46 2.43
312 326 2.564947 ACAAGCTCTACTGGAAGGTCTG 59.435 50.000 0.00 0.00 39.30 3.51
383 397 5.473931 AGGAATGTACTGAATGCTATAGCG 58.526 41.667 19.55 7.56 45.83 4.26
389 403 5.426689 TCAGAAGGAATGTACTGAATGCT 57.573 39.130 0.00 0.00 36.63 3.79
415 429 4.647424 AAAGAAGTCAGCTCCTAGATCG 57.353 45.455 0.00 0.00 0.00 3.69
424 438 2.659428 AGGCACAAAAAGAAGTCAGCT 58.341 42.857 0.00 0.00 0.00 4.24
498 512 2.269023 TCCAGATTTTCAGCTCCCTCA 58.731 47.619 0.00 0.00 0.00 3.86
528 542 6.086011 ACAAATTATGGTGGTCTCCCATTA 57.914 37.500 0.00 0.00 44.35 1.90
569 583 6.678655 GCACCAGTTAATAAAATAACCGTCCC 60.679 42.308 0.00 0.00 36.62 4.46
572 586 6.655848 TCAGCACCAGTTAATAAAATAACCGT 59.344 34.615 0.00 0.00 36.62 4.83
601 615 9.868277 AAAGAATCATTTGTAGTGAACACAAAA 57.132 25.926 7.68 5.58 45.95 2.44
602 616 9.868277 AAAAGAATCATTTGTAGTGAACACAAA 57.132 25.926 7.68 3.39 46.64 2.83
610 624 7.379529 GTGTGGTGAAAAGAATCATTTGTAGTG 59.620 37.037 0.00 0.00 0.00 2.74
617 631 6.469782 AACTGTGTGGTGAAAAGAATCATT 57.530 33.333 0.00 0.00 0.00 2.57
618 632 6.322201 AGAAACTGTGTGGTGAAAAGAATCAT 59.678 34.615 0.00 0.00 0.00 2.45
632 646 4.516698 AGTGCCTGAAATAGAAACTGTGTG 59.483 41.667 0.00 0.00 0.00 3.82
638 652 5.122396 CCTGTACAGTGCCTGAAATAGAAAC 59.878 44.000 21.18 0.00 35.18 2.78
655 669 3.266772 AGAATGGCATCCTTTCCTGTACA 59.733 43.478 0.00 0.00 38.10 2.90
664 678 5.188359 ACAATGCTTAAAGAATGGCATCCTT 59.812 36.000 0.00 0.00 43.39 3.36
697 711 9.355215 CGTGTACAATAACTAGACAGAAAAGAT 57.645 33.333 0.00 0.00 0.00 2.40
699 713 7.328737 AGCGTGTACAATAACTAGACAGAAAAG 59.671 37.037 0.00 0.00 0.00 2.27
784 798 2.005451 CTGGTCCAAAGCGATCTCTTG 58.995 52.381 0.00 0.00 0.00 3.02
1013 1033 3.570125 GCCCTTGATGAAGGTTTATAGGC 59.430 47.826 10.28 0.47 46.84 3.93
1201 1221 4.021925 GACTGCTGCCGGTCCCTT 62.022 66.667 1.90 0.00 40.73 3.95
1223 1243 3.056179 TCGTCAGGCTTGTACATCATCAA 60.056 43.478 0.00 0.00 0.00 2.57
1318 1338 0.251386 TCTCGAACCTCTGCAGGAGT 60.251 55.000 15.13 8.86 43.65 3.85
1510 1530 1.433879 GACGTCCATCACCTCCTCG 59.566 63.158 3.51 0.00 0.00 4.63
1728 1752 7.708998 TGGGTTTACAAGTTTCAGTTTATGTC 58.291 34.615 0.00 0.00 0.00 3.06
1795 1820 5.187772 AGTCTGTCATATGTGCTGGTTAAGA 59.812 40.000 1.90 0.00 0.00 2.10
1934 2209 6.282199 TGGTTCAGAGGAAGACTGTATAAC 57.718 41.667 0.00 0.00 36.81 1.89
1968 2262 6.699575 ATCCTGCGAAATTAGTTTGCTTAT 57.300 33.333 6.20 0.00 45.70 1.73
1973 2267 7.113965 GCATCAATATCCTGCGAAATTAGTTTG 59.886 37.037 0.00 0.00 0.00 2.93
1990 2284 9.866655 TTCTAGTAAATCCCAAAGCATCAATAT 57.133 29.630 0.00 0.00 0.00 1.28
2004 2298 7.797062 AGTCTTGGGAATCTTCTAGTAAATCC 58.203 38.462 0.00 0.00 0.00 3.01
2030 2324 1.140652 TGCCACATTGTCAGTGTCTCA 59.859 47.619 0.00 0.00 35.24 3.27
2109 2403 8.696175 CGTGTCAACATACTTGCGAATATATTA 58.304 33.333 0.00 0.00 0.00 0.98
2110 2404 7.223971 ACGTGTCAACATACTTGCGAATATATT 59.776 33.333 0.00 0.00 0.00 1.28
2111 2405 6.700081 ACGTGTCAACATACTTGCGAATATAT 59.300 34.615 0.00 0.00 0.00 0.86
2112 2406 6.020201 CACGTGTCAACATACTTGCGAATATA 60.020 38.462 7.58 0.00 0.00 0.86
2113 2407 4.868171 ACGTGTCAACATACTTGCGAATAT 59.132 37.500 0.00 0.00 0.00 1.28
2114 2408 4.090786 CACGTGTCAACATACTTGCGAATA 59.909 41.667 7.58 0.00 0.00 1.75
2115 2409 3.064207 ACGTGTCAACATACTTGCGAAT 58.936 40.909 0.00 0.00 0.00 3.34
2116 2410 2.219903 CACGTGTCAACATACTTGCGAA 59.780 45.455 7.58 0.00 0.00 4.70
2117 2411 1.790043 CACGTGTCAACATACTTGCGA 59.210 47.619 7.58 0.00 0.00 5.10
2118 2412 1.790043 TCACGTGTCAACATACTTGCG 59.210 47.619 16.51 0.00 0.00 4.85
2119 2413 3.870723 TTCACGTGTCAACATACTTGC 57.129 42.857 16.51 0.00 0.00 4.01
2120 2414 4.272504 ACCTTTCACGTGTCAACATACTTG 59.727 41.667 16.51 0.00 0.00 3.16
2121 2415 4.272504 CACCTTTCACGTGTCAACATACTT 59.727 41.667 16.51 0.00 0.00 2.24
2122 2416 3.807622 CACCTTTCACGTGTCAACATACT 59.192 43.478 16.51 0.00 0.00 2.12
2123 2417 3.805422 TCACCTTTCACGTGTCAACATAC 59.195 43.478 16.51 0.00 32.86 2.39
2124 2418 4.061357 TCACCTTTCACGTGTCAACATA 57.939 40.909 16.51 0.00 32.86 2.29
2125 2419 2.912771 TCACCTTTCACGTGTCAACAT 58.087 42.857 16.51 0.00 32.86 2.71
2126 2420 2.388310 TCACCTTTCACGTGTCAACA 57.612 45.000 16.51 0.00 32.86 3.33
2127 2421 3.750639 TTTCACCTTTCACGTGTCAAC 57.249 42.857 16.51 0.00 32.86 3.18
2128 2422 3.942115 TGATTTCACCTTTCACGTGTCAA 59.058 39.130 16.51 8.96 32.86 3.18
2129 2423 3.536570 TGATTTCACCTTTCACGTGTCA 58.463 40.909 16.51 4.74 32.86 3.58
2130 2424 4.749245 ATGATTTCACCTTTCACGTGTC 57.251 40.909 16.51 1.88 32.86 3.67
2131 2425 5.514274 AAATGATTTCACCTTTCACGTGT 57.486 34.783 16.51 0.00 32.86 4.49
2132 2426 6.208644 AGAAAATGATTTCACCTTTCACGTG 58.791 36.000 9.94 9.94 46.03 4.49
2133 2427 6.391227 AGAAAATGATTTCACCTTTCACGT 57.609 33.333 14.57 0.00 46.03 4.49
2134 2428 7.698836 AAAGAAAATGATTTCACCTTTCACG 57.301 32.000 14.57 0.00 46.03 4.35
2155 2449 3.092301 GGGGTTCATCCTCCTTGAAAAG 58.908 50.000 0.00 0.00 39.03 2.27
2177 2471 2.434884 CGGCCTGTTCGATGCACT 60.435 61.111 0.00 0.00 0.00 4.40
2265 2562 5.862924 ATATCGCCGGTCAATTTGATAAG 57.137 39.130 1.90 0.00 0.00 1.73
2266 2563 5.350365 GCTATATCGCCGGTCAATTTGATAA 59.650 40.000 1.90 0.00 0.00 1.75
2274 2571 2.831685 ATTGCTATATCGCCGGTCAA 57.168 45.000 1.90 0.00 0.00 3.18
2296 2593 2.343758 GAGTGTTGCGCCCTCTGA 59.656 61.111 4.18 0.00 0.00 3.27
2328 2625 4.835056 TCTGACTCAAGTGATTCCTTCTCA 59.165 41.667 0.00 0.00 0.00 3.27
2329 2626 5.398603 TCTGACTCAAGTGATTCCTTCTC 57.601 43.478 0.00 0.00 0.00 2.87
2378 2717 1.961793 TGAAGGTGTTGGTTCGAAGG 58.038 50.000 0.00 0.00 0.00 3.46
2464 3942 6.773976 AGTGAGAAAATCCAAAACTTGTCA 57.226 33.333 0.00 0.00 0.00 3.58
2466 3944 7.093771 ACTCAAGTGAGAAAATCCAAAACTTGT 60.094 33.333 15.15 0.00 44.74 3.16
2517 3995 1.893801 TGAAAGGGAAGTCGACTCTCC 59.106 52.381 26.00 26.00 0.00 3.71
2680 4158 5.776744 AGAAAAGAACAAATGCTCCATCAC 58.223 37.500 0.00 0.00 0.00 3.06
2681 4159 6.183360 ACAAGAAAAGAACAAATGCTCCATCA 60.183 34.615 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.