Multiple sequence alignment - TraesCS5A01G207300

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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 TraesCS5A01G207300 chr5A 100.000 2819 0 0 1 2819 419206299 419209117 0 5206
1 TraesCS5A01G207300 chr5D 94.912 2850 73 36 1 2816 322576217 322579028 0 4394
2 TraesCS5A01G207300 chr5B 94.372 2221 69 32 614 2816 374190765 374192947 0 3358
3 TraesCS5A01G207300 chr5B 95.731 609 18 3 12 616 374190058 374190662 0 974


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 TraesCS5A01G207300 chr5A 419206299 419209117 2818 False 5206 5206 100.0000 1 2819 1 chr5A.!!$F1 2818
1 TraesCS5A01G207300 chr5D 322576217 322579028 2811 False 4394 4394 94.9120 1 2816 1 chr5D.!!$F1 2815
2 TraesCS5A01G207300 chr5B 374190058 374192947 2889 False 2166 3358 95.0515 12 2816 2 chr5B.!!$F1 2804

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
783 911 0.253044 ATCAGTGGGAATGGACACCG 59.747 55.0 0.0 0.0 38.34 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2245 2382 0.520404 CTGACTGCATGTGCTGAACC 59.48 55.0 17.09 7.49 41.71 3.62 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
111 113 2.592194 CACAATTGTGCAGCTAGCTTG 58.408 47.619 24.69 11.68 45.94 4.01
112 114 2.030540 CACAATTGTGCAGCTAGCTTGT 60.031 45.455 24.69 12.39 45.94 3.16
114 116 3.820467 ACAATTGTGCAGCTAGCTTGTTA 59.180 39.130 16.46 0.00 45.94 2.41
196 207 2.902523 CACACTGCATATGCTGAGACT 58.097 47.619 33.30 14.04 41.71 3.24
342 355 1.995484 CCAACATCAGACAGCTACGTG 59.005 52.381 0.00 0.00 0.00 4.49
358 374 0.464373 CGTGCCTACCTACCTACGGA 60.464 60.000 0.00 0.00 0.00 4.69
518 534 2.362717 CTGCCCTCTGTAACCTAGCTAC 59.637 54.545 0.00 0.00 0.00 3.58
588 604 2.441378 CGTACACATCGCACCCACG 61.441 63.158 0.00 0.00 0.00 4.94
783 911 0.253044 ATCAGTGGGAATGGACACCG 59.747 55.000 0.00 0.00 38.34 4.94
885 1013 2.564947 TGTGAAAGAGGAAGAGGAGAGC 59.435 50.000 0.00 0.00 0.00 4.09
1197 1325 4.783621 GCGGTGCTCATGAGGCCA 62.784 66.667 23.89 11.59 0.00 5.36
1338 1466 4.514577 AGCAAGATCCGGACGGCG 62.515 66.667 6.12 4.80 34.68 6.46
1419 1547 1.905354 GCAGGACCAGCTTGGCTTT 60.905 57.895 0.77 0.00 42.67 3.51
1611 1742 3.335729 TCGGGAAAGGGGGAAGCC 61.336 66.667 0.00 0.00 0.00 4.35
1616 1747 2.043953 AAAGGGGGAAGCCGATGC 60.044 61.111 0.00 0.00 37.95 3.91
1631 1762 1.290203 GATGCGGAGAAAGCGATGAA 58.710 50.000 0.00 0.00 37.44 2.57
1776 1913 2.954020 AATGCGACGACGATGGCGAT 62.954 55.000 12.29 0.00 42.66 4.58
1995 2132 2.071778 TCTTTGCTTTGAGGTGCCTT 57.928 45.000 0.00 0.00 0.00 4.35
2042 2179 6.363088 TCGCTCTTTTTAATTTCATGCAACAG 59.637 34.615 0.00 0.00 0.00 3.16
2091 2228 8.785329 TTGGGGATTATTTTGTAAGATTTTGC 57.215 30.769 0.00 0.00 0.00 3.68
2098 2235 8.532977 TTATTTTGTAAGATTTTGCTGAAGCC 57.467 30.769 0.00 0.00 41.18 4.35
2118 2255 4.217550 AGCCGATCATCTTAAGCTAGAGAC 59.782 45.833 0.00 0.00 0.00 3.36
2126 2263 4.846040 TCTTAAGCTAGAGACGGAGAAGT 58.154 43.478 0.00 0.00 0.00 3.01
2130 2267 5.979288 AAGCTAGAGACGGAGAAGTTAAA 57.021 39.130 0.00 0.00 0.00 1.52
2131 2268 6.532988 AAGCTAGAGACGGAGAAGTTAAAT 57.467 37.500 0.00 0.00 0.00 1.40
2132 2269 5.897050 AGCTAGAGACGGAGAAGTTAAATG 58.103 41.667 0.00 0.00 0.00 2.32
2133 2270 4.504826 GCTAGAGACGGAGAAGTTAAATGC 59.495 45.833 0.00 0.00 0.00 3.56
2140 2277 5.250200 ACGGAGAAGTTAAATGCATGGTTA 58.750 37.500 0.00 0.00 0.00 2.85
2143 2280 6.555315 GGAGAAGTTAAATGCATGGTTAGTG 58.445 40.000 0.00 0.00 0.00 2.74
2166 2303 3.865164 TGTTCACTGCGCTTATACTCATG 59.135 43.478 9.73 0.00 0.00 3.07
2167 2304 4.112634 GTTCACTGCGCTTATACTCATGA 58.887 43.478 9.73 0.00 0.00 3.07
2168 2305 3.969899 TCACTGCGCTTATACTCATGAG 58.030 45.455 21.37 21.37 0.00 2.90
2169 2306 3.632145 TCACTGCGCTTATACTCATGAGA 59.368 43.478 29.27 12.98 0.00 3.27
2170 2307 4.279420 TCACTGCGCTTATACTCATGAGAT 59.721 41.667 29.27 18.59 0.00 2.75
2171 2308 5.473504 TCACTGCGCTTATACTCATGAGATA 59.526 40.000 29.27 17.65 0.00 1.98
2172 2309 5.570973 CACTGCGCTTATACTCATGAGATAC 59.429 44.000 29.27 10.55 0.00 2.24
2173 2310 5.475220 ACTGCGCTTATACTCATGAGATACT 59.525 40.000 29.27 9.25 0.00 2.12
2174 2311 5.944013 TGCGCTTATACTCATGAGATACTC 58.056 41.667 29.27 11.60 0.00 2.59
2175 2312 5.473504 TGCGCTTATACTCATGAGATACTCA 59.526 40.000 29.27 12.27 44.99 3.41
2188 2325 6.388435 TGAGATACTCATGAGATGACAGTG 57.612 41.667 29.27 0.11 35.39 3.66
2197 2334 7.340487 ACTCATGAGATGACAGTGTATGTAGAA 59.660 37.037 29.27 0.00 44.17 2.10
2228 2365 5.605488 AGGTACTTCAGGTAAAGGAAAGTGA 59.395 40.000 0.00 0.00 27.25 3.41
2229 2366 6.100714 AGGTACTTCAGGTAAAGGAAAGTGAA 59.899 38.462 0.00 0.00 27.25 3.18
2230 2367 6.940867 GGTACTTCAGGTAAAGGAAAGTGAAT 59.059 38.462 0.00 0.00 31.56 2.57
2241 2378 5.599999 AGGAAAGTGAATACAGAGCGTAT 57.400 39.130 0.00 0.00 42.91 3.06
2245 2382 7.707035 AGGAAAGTGAATACAGAGCGTATAAAG 59.293 37.037 0.00 0.00 40.04 1.85
2301 2438 5.568620 AACACAAGAGTATCAGGAAACCT 57.431 39.130 0.00 0.00 37.82 3.50
2376 2517 6.484977 CCTTCTTGACCTAGAATAAAGATGGC 59.515 42.308 10.60 0.00 36.19 4.40
2382 2523 4.978388 ACCTAGAATAAAGATGGCCTTCCT 59.022 41.667 14.77 6.55 33.02 3.36
2383 2524 5.072464 ACCTAGAATAAAGATGGCCTTCCTC 59.928 44.000 14.77 4.95 33.02 3.71
2529 2672 3.498841 GCTAGTGTCCCTATGAGCCTAGA 60.499 52.174 0.00 0.00 30.91 2.43
2539 2682 9.594936 GTCCCTATGAGCCTAGATAACATATAT 57.405 37.037 0.00 0.00 0.00 0.86
2572 2719 9.489084 TGGTGTATATGCATGAGTTATTAGTTC 57.511 33.333 10.16 0.00 0.00 3.01
2595 2742 6.694447 TCCAGTCTACAAAGTACATGGTTAC 58.306 40.000 0.00 0.00 0.00 2.50
2626 2773 6.600882 ATCTTTCCAGAAGCAATCATTTGT 57.399 33.333 0.00 0.00 31.85 2.83
2669 2816 6.614694 TGGTTAGCTGGAGTTATACAAGAA 57.385 37.500 0.00 0.00 0.00 2.52
2679 2826 6.422701 TGGAGTTATACAAGAACACGACAAAG 59.577 38.462 0.00 0.00 0.00 2.77
2682 2829 2.702592 ACAAGAACACGACAAAGGGA 57.297 45.000 0.00 0.00 0.00 4.20
2683 2830 3.208747 ACAAGAACACGACAAAGGGAT 57.791 42.857 0.00 0.00 0.00 3.85
2686 2835 5.127491 ACAAGAACACGACAAAGGGATAAA 58.873 37.500 0.00 0.00 0.00 1.40
2739 2888 4.134563 TGAAAGAAGTTGGAAGTACAGGC 58.865 43.478 0.00 0.00 0.00 4.85
2804 2953 5.643379 TGATTTAGCCTCATTTGTCAACC 57.357 39.130 0.00 0.00 0.00 3.77
2805 2954 5.324409 TGATTTAGCCTCATTTGTCAACCT 58.676 37.500 0.00 0.00 0.00 3.50
2806 2955 5.774690 TGATTTAGCCTCATTTGTCAACCTT 59.225 36.000 0.00 0.00 0.00 3.50
2808 2957 6.817765 TTTAGCCTCATTTGTCAACCTTAG 57.182 37.500 0.00 0.00 0.00 2.18
2809 2958 4.640771 AGCCTCATTTGTCAACCTTAGA 57.359 40.909 0.00 0.00 0.00 2.10
2810 2959 4.985538 AGCCTCATTTGTCAACCTTAGAA 58.014 39.130 0.00 0.00 0.00 2.10
2811 2960 5.385198 AGCCTCATTTGTCAACCTTAGAAA 58.615 37.500 0.00 0.00 0.00 2.52
2812 2961 5.241728 AGCCTCATTTGTCAACCTTAGAAAC 59.758 40.000 0.00 0.00 0.00 2.78
2813 2962 5.241728 GCCTCATTTGTCAACCTTAGAAACT 59.758 40.000 0.00 0.00 0.00 2.66
2814 2963 6.239036 GCCTCATTTGTCAACCTTAGAAACTT 60.239 38.462 0.00 0.00 0.00 2.66
2815 2964 7.040686 GCCTCATTTGTCAACCTTAGAAACTTA 60.041 37.037 0.00 0.00 0.00 2.24
2816 2965 8.846211 CCTCATTTGTCAACCTTAGAAACTTAA 58.154 33.333 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
190 201 8.966868 TGTGACATGTAAATCTATGTAGTCTCA 58.033 33.333 0.00 0.00 37.63 3.27
518 534 0.109643 TTTTGCTGCGTGCTATGCTG 60.110 50.000 0.00 0.00 43.37 4.41
588 604 1.633774 TAGTGGAGCTAGCATAGGGC 58.366 55.000 18.83 1.77 39.70 5.19
629 750 2.755952 TGGGAGTGATGAGCTAGCTA 57.244 50.000 19.38 6.79 0.00 3.32
630 751 2.100128 ATGGGAGTGATGAGCTAGCT 57.900 50.000 19.45 19.45 0.00 3.32
631 752 3.768757 AGATATGGGAGTGATGAGCTAGC 59.231 47.826 6.62 6.62 0.00 3.42
632 753 5.999205 AAGATATGGGAGTGATGAGCTAG 57.001 43.478 0.00 0.00 0.00 3.42
640 768 4.141620 GGAAGCTGAAAGATATGGGAGTGA 60.142 45.833 0.00 0.00 34.07 3.41
783 911 3.987547 TGATATAAGCTCAGCTCAGCAC 58.012 45.455 13.67 0.00 42.40 4.40
885 1013 0.809385 TTCTACTCCTTGGTCGAGCG 59.191 55.000 10.46 0.00 0.00 5.03
942 1070 9.250624 CACTTGAGTACTTTATATGTTCCTAGC 57.749 37.037 0.00 0.00 0.00 3.42
943 1071 9.250624 GCACTTGAGTACTTTATATGTTCCTAG 57.749 37.037 0.00 0.00 0.00 3.02
944 1072 8.755028 TGCACTTGAGTACTTTATATGTTCCTA 58.245 33.333 0.00 0.00 0.00 2.94
945 1073 7.620880 TGCACTTGAGTACTTTATATGTTCCT 58.379 34.615 0.00 0.00 0.00 3.36
1155 1283 0.039437 GCGTCTCGGAGTTGAACTGA 60.039 55.000 0.90 0.00 0.00 3.41
1236 1364 2.677979 GCCGGTTCTTGCCTCGTTC 61.678 63.158 1.90 0.00 0.00 3.95
1290 1418 1.078848 CCTGAACGGCCTCTTCCTG 60.079 63.158 0.00 0.00 0.00 3.86
1413 1541 2.202395 GCTGGCCTTGTCAAAGCCA 61.202 57.895 23.48 23.48 37.30 4.75
1419 1547 1.597854 CGTCTTGCTGGCCTTGTCA 60.598 57.895 3.32 0.00 0.00 3.58
1611 1742 0.871592 TCATCGCTTTCTCCGCATCG 60.872 55.000 0.00 0.00 0.00 3.84
1616 1747 1.756375 CGCCTTCATCGCTTTCTCCG 61.756 60.000 0.00 0.00 0.00 4.63
1631 1762 4.974438 TTCCACCACCCCTCGCCT 62.974 66.667 0.00 0.00 0.00 5.52
1776 1913 2.995466 AATCACCGTCTTCGTCGTAA 57.005 45.000 0.00 0.00 35.01 3.18
1995 2132 7.174946 AGCGATGGACTTCAAGAAAATCTTAAA 59.825 33.333 0.00 0.00 33.78 1.52
2042 2179 3.930634 AAGACATGAAAGAAAGCCAGC 57.069 42.857 0.00 0.00 0.00 4.85
2091 2228 3.726607 AGCTTAAGATGATCGGCTTCAG 58.273 45.455 6.67 4.27 0.00 3.02
2098 2235 4.452795 TCCGTCTCTAGCTTAAGATGATCG 59.547 45.833 6.67 8.25 31.44 3.69
2118 2255 4.701956 AACCATGCATTTAACTTCTCCG 57.298 40.909 0.00 0.00 0.00 4.63
2126 2263 6.264292 AGTGAACACACTAACCATGCATTTAA 59.736 34.615 0.00 0.00 42.17 1.52
2130 2267 3.503363 CAGTGAACACACTAACCATGCAT 59.497 43.478 7.68 0.00 42.09 3.96
2131 2268 2.877786 CAGTGAACACACTAACCATGCA 59.122 45.455 7.68 0.00 42.09 3.96
2132 2269 2.350772 GCAGTGAACACACTAACCATGC 60.351 50.000 7.68 2.41 42.09 4.06
2133 2270 2.096268 CGCAGTGAACACACTAACCATG 60.096 50.000 7.68 0.00 42.09 3.66
2140 2277 2.169832 ATAAGCGCAGTGAACACACT 57.830 45.000 11.47 0.00 44.39 3.55
2143 2280 3.250744 TGAGTATAAGCGCAGTGAACAC 58.749 45.455 11.47 0.19 0.00 3.32
2166 2303 6.389830 ACACTGTCATCTCATGAGTATCTC 57.610 41.667 21.92 10.64 40.53 2.75
2167 2304 7.505248 ACATACACTGTCATCTCATGAGTATCT 59.495 37.037 21.92 3.62 40.53 1.98
2168 2305 7.656412 ACATACACTGTCATCTCATGAGTATC 58.344 38.462 21.92 11.56 40.53 2.24
2169 2306 7.594351 ACATACACTGTCATCTCATGAGTAT 57.406 36.000 21.92 11.47 40.53 2.12
2170 2307 7.993183 TCTACATACACTGTCATCTCATGAGTA 59.007 37.037 21.92 9.67 40.53 2.59
2171 2308 5.929058 ACATACACTGTCATCTCATGAGT 57.071 39.130 21.92 7.26 40.53 3.41
2172 2309 7.269477 TCTACATACACTGTCATCTCATGAG 57.731 40.000 17.07 17.07 40.53 2.90
2173 2310 7.122650 TGTTCTACATACACTGTCATCTCATGA 59.877 37.037 0.00 0.00 39.39 3.07
2174 2311 7.260603 TGTTCTACATACACTGTCATCTCATG 58.739 38.462 0.00 0.00 39.39 3.07
2175 2312 7.410120 TGTTCTACATACACTGTCATCTCAT 57.590 36.000 0.00 0.00 39.39 2.90
2176 2313 6.625960 GCTGTTCTACATACACTGTCATCTCA 60.626 42.308 0.00 0.00 39.39 3.27
2177 2314 5.746245 GCTGTTCTACATACACTGTCATCTC 59.254 44.000 0.00 0.00 39.39 2.75
2188 2325 5.246145 AGTACCTTCGCTGTTCTACATAC 57.754 43.478 0.00 0.00 0.00 2.39
2197 2334 1.339097 ACCTGAAGTACCTTCGCTGT 58.661 50.000 0.00 0.00 42.78 4.40
2219 2356 3.963428 ACGCTCTGTATTCACTTTCCT 57.037 42.857 0.00 0.00 0.00 3.36
2221 2358 7.491696 ACCTTTATACGCTCTGTATTCACTTTC 59.508 37.037 0.00 0.00 41.01 2.62
2222 2359 7.328737 ACCTTTATACGCTCTGTATTCACTTT 58.671 34.615 0.00 0.00 41.01 2.66
2223 2360 6.875076 ACCTTTATACGCTCTGTATTCACTT 58.125 36.000 0.00 0.00 41.01 3.16
2225 2362 6.755141 TGAACCTTTATACGCTCTGTATTCAC 59.245 38.462 0.00 0.00 41.01 3.18
2226 2363 6.869695 TGAACCTTTATACGCTCTGTATTCA 58.130 36.000 0.00 0.00 41.01 2.57
2228 2365 5.753921 GCTGAACCTTTATACGCTCTGTATT 59.246 40.000 0.00 0.00 41.01 1.89
2229 2366 5.163447 TGCTGAACCTTTATACGCTCTGTAT 60.163 40.000 0.00 0.00 45.68 2.29
2230 2367 4.158949 TGCTGAACCTTTATACGCTCTGTA 59.841 41.667 0.00 0.00 37.49 2.74
2241 2378 2.813754 GACTGCATGTGCTGAACCTTTA 59.186 45.455 17.09 0.00 41.71 1.85
2245 2382 0.520404 CTGACTGCATGTGCTGAACC 59.480 55.000 17.09 7.49 41.71 3.62
2404 2545 9.110502 GTACAACTTAGCAAAAATAGGCTATCT 57.889 33.333 7.63 2.81 41.81 1.98
2408 2549 7.761038 AAGTACAACTTAGCAAAAATAGGCT 57.239 32.000 0.00 0.00 43.94 4.58
2539 2682 7.019656 ACTCATGCATATACACCATCCAATA 57.980 36.000 0.00 0.00 0.00 1.90
2540 2683 5.884322 ACTCATGCATATACACCATCCAAT 58.116 37.500 0.00 0.00 0.00 3.16
2557 2704 9.653287 TTTGTAGACTGGAACTAATAACTCATG 57.347 33.333 0.00 0.00 0.00 3.07
2558 2705 9.877178 CTTTGTAGACTGGAACTAATAACTCAT 57.123 33.333 0.00 0.00 0.00 2.90
2559 2706 8.867097 ACTTTGTAGACTGGAACTAATAACTCA 58.133 33.333 0.00 0.00 0.00 3.41
2572 2719 5.873164 GGTAACCATGTACTTTGTAGACTGG 59.127 44.000 0.00 0.00 0.00 4.00
2626 2773 7.589958 AACCATCCAAAACAATGTGTACTTA 57.410 32.000 0.00 0.00 0.00 2.24
2669 2816 5.556915 TCTGATTTTATCCCTTTGTCGTGT 58.443 37.500 0.00 0.00 0.00 4.49
2708 2857 7.116736 ACTTCCAACTTCTTTCAGTCCTAAAA 58.883 34.615 0.00 0.00 0.00 1.52
2722 2871 5.306394 ACTAAAGCCTGTACTTCCAACTTC 58.694 41.667 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.