Multiple sequence alignment - TraesCS5D01G204500

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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 TraesCS5D01G204500 chr5D 100.000 3243 0 0 1 3243 309693532 309696774 0.000000e+00 5989.0
1 TraesCS5D01G204500 chr5D 85.938 64 6 3 2443 2504 117066758 117066820 7.510000e-07 65.8
2 TraesCS5D01G204500 chr5B 93.242 3196 134 35 1 3151 355233752 355236910 0.000000e+00 4630.0
3 TraesCS5D01G204500 chr5B 86.842 76 1 3 3166 3241 355237069 355237135 3.470000e-10 76.8
4 TraesCS5D01G204500 chr5A 90.381 2464 109 45 833 3241 403028158 403030548 0.000000e+00 3120.0
5 TraesCS5D01G204500 chr5A 86.282 831 55 25 1 809 403027367 403028160 0.000000e+00 848.0
6 TraesCS5D01G204500 chr5A 86.364 66 8 1 2443 2507 293767749 293767814 1.610000e-08 71.3
7 TraesCS5D01G204500 chr7B 89.394 66 6 1 2443 2507 310256692 310256757 7.460000e-12 82.4
8 TraesCS5D01G204500 chr7B 85.714 70 9 1 1966 2034 28505762 28505693 4.490000e-09 73.1
9 TraesCS5D01G204500 chr7D 87.143 70 8 1 1966 2034 80979335 80979266 9.650000e-11 78.7
10 TraesCS5D01G204500 chr7D 84.848 66 9 1 2443 2507 537122858 537122923 7.510000e-07 65.8
11 TraesCS5D01G204500 chr6B 86.111 72 9 1 2443 2513 449057997 449057926 3.470000e-10 76.8
12 TraesCS5D01G204500 chr6B 86.111 72 9 1 2443 2513 449104143 449104072 3.470000e-10 76.8
13 TraesCS5D01G204500 chr7A 85.714 70 9 1 1966 2034 83635422 83635353 4.490000e-09 73.1
14 TraesCS5D01G204500 chr2A 84.848 66 9 1 2443 2507 149519828 149519763 7.510000e-07 65.8


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 TraesCS5D01G204500 chr5D 309693532 309696774 3242 False 5989.0 5989 100.0000 1 3243 1 chr5D.!!$F2 3242
1 TraesCS5D01G204500 chr5B 355233752 355237135 3383 False 2353.4 4630 90.0420 1 3241 2 chr5B.!!$F1 3240
2 TraesCS5D01G204500 chr5A 403027367 403030548 3181 False 1984.0 3120 88.3315 1 3241 2 chr5A.!!$F2 3240

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
864 906 0.671796 AAGGTTTAGGTTTGGTGCGC 59.328 50.0 0.0 0.0 0.0 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2311 2378 0.391263 ATCCACTTCCGAGGAAACGC 60.391 55.0 6.01 0.0 37.48 4.84 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
60 63 3.083349 TCCATGGCTCCACCTCCG 61.083 66.667 6.96 0.00 40.22 4.63
97 100 1.149148 GCTCGGTTTGAACAGTCTCC 58.851 55.000 0.00 0.00 0.00 3.71
104 107 1.827399 TTGAACAGTCTCCCCGGAGC 61.827 60.000 0.73 1.87 41.71 4.70
121 124 2.429930 CTCCCACGGGACAAGCAA 59.570 61.111 0.00 0.00 39.76 3.91
137 140 1.080025 CAAACGTCCGTCCTCCCTC 60.080 63.158 0.00 0.00 0.00 4.30
160 170 2.835431 TTGGTTGGTTGGCACCCG 60.835 61.111 0.00 0.00 43.49 5.28
502 529 2.435059 GAGCCTCAACCCGACTGC 60.435 66.667 0.00 0.00 0.00 4.40
579 612 4.564110 GGTGCCCGCCCAGGTATC 62.564 72.222 0.00 0.00 38.74 2.24
580 613 4.564110 GTGCCCGCCCAGGTATCC 62.564 72.222 0.00 0.00 38.74 2.59
685 722 3.913799 CCCCTCCATAACCATACCATACA 59.086 47.826 0.00 0.00 0.00 2.29
686 723 4.263331 CCCCTCCATAACCATACCATACAC 60.263 50.000 0.00 0.00 0.00 2.90
687 724 4.263331 CCCTCCATAACCATACCATACACC 60.263 50.000 0.00 0.00 0.00 4.16
864 906 0.671796 AAGGTTTAGGTTTGGTGCGC 59.328 50.000 0.00 0.00 0.00 6.09
910 956 4.519350 AGGGATCTTTTGTTTCTTTCCGTC 59.481 41.667 0.00 0.00 0.00 4.79
977 1024 1.885887 CTAGCGAGCCAGAGAGCTATT 59.114 52.381 0.00 0.00 45.15 1.73
1009 1056 2.034305 CGGCGGTAGTGGATATATAGCC 59.966 54.545 10.23 10.23 38.73 3.93
1101 1148 4.106925 GAGGAGGGTGGCAGGCTG 62.107 72.222 10.94 10.94 0.00 4.85
1141 1188 2.203070 AAGACCGGCGATGATGGC 60.203 61.111 9.30 0.00 0.00 4.40
1285 1335 2.580815 CTGCTCCACATCCTGCGA 59.419 61.111 0.00 0.00 0.00 5.10
1288 1338 2.887568 CTCCACATCCTGCGACGC 60.888 66.667 14.19 14.19 0.00 5.19
1686 1736 4.933064 GCCGGACATCGAGGAGCG 62.933 72.222 5.05 0.00 42.43 5.03
1791 1847 0.820871 GTCCAGGGCAACAACAACAA 59.179 50.000 0.00 0.00 39.74 2.83
1876 1938 2.577112 CAGTACGTGCTCGCCGAG 60.577 66.667 10.36 10.36 41.18 4.63
2033 2095 4.827087 AGATCTGGCAGTGGCGCG 62.827 66.667 15.27 0.00 42.47 6.86
2298 2365 6.616774 TTTTGATGAATCTTTTTGGGCAAC 57.383 33.333 0.00 0.00 0.00 4.17
2311 2378 0.872388 GGGCAACGTTGAGTAGTTGG 59.128 55.000 31.62 2.06 45.52 3.77
2354 2422 0.730265 AACGAACGCACTTTGCTGAA 59.270 45.000 0.00 0.00 42.25 3.02
2356 2424 1.333619 ACGAACGCACTTTGCTGAAAT 59.666 42.857 0.00 0.00 42.25 2.17
2380 2452 1.509162 GTTGCGACGATCAAACGGC 60.509 57.895 0.00 0.00 38.00 5.68
2390 2462 1.798813 GATCAAACGGCGACAGTTTCT 59.201 47.619 16.62 0.62 39.50 2.52
2405 2477 2.758423 AGTTTCTGTCCGTTTTTGCCTT 59.242 40.909 0.00 0.00 0.00 4.35
2413 2485 6.477360 TCTGTCCGTTTTTGCCTTAAATTTTC 59.523 34.615 0.00 0.00 0.00 2.29
2417 2489 6.824196 TCCGTTTTTGCCTTAAATTTTCCTTT 59.176 30.769 0.00 0.00 0.00 3.11
2440 2512 4.142609 TCTCAGAAGTTACCATGCATCC 57.857 45.455 0.00 0.00 0.00 3.51
2496 2577 0.107410 ACCCTTGCAGTGAACGTTCA 60.107 50.000 26.53 26.53 34.20 3.18
2558 2639 6.091577 CGAAGCCATGTATACAAGTACAACAA 59.908 38.462 10.14 0.00 38.03 2.83
2596 2697 9.929180 TCAAAACTCATATGGCTACTCATATAC 57.071 33.333 2.13 0.00 38.02 1.47
2597 2698 9.935241 CAAAACTCATATGGCTACTCATATACT 57.065 33.333 2.13 0.00 38.02 2.12
2661 2762 2.632377 CGGTGTTTATCATCTGCCTGT 58.368 47.619 0.00 0.00 0.00 4.00
2802 2915 0.680280 GGCGTCTCCTCACTCACCTA 60.680 60.000 0.00 0.00 0.00 3.08
2844 2957 3.117738 CCATTAAACTCAGGATCTGGGCT 60.118 47.826 0.00 0.00 34.91 5.19
2998 3111 3.426568 GCCAGCAACCGCAGACTC 61.427 66.667 0.00 0.00 42.27 3.36
3037 3156 1.067364 TGCTGAATTGGTTGCACAGTG 59.933 47.619 0.00 0.00 0.00 3.66
3091 3210 4.344865 ATGGACCACGGCGGCTTT 62.345 61.111 13.24 0.00 39.03 3.51
3105 3224 0.960364 GGCTTTGGATGGAGCGTTGA 60.960 55.000 0.00 0.00 39.78 3.18
3108 3227 2.358957 CTTTGGATGGAGCGTTGATGA 58.641 47.619 0.00 0.00 0.00 2.92
3109 3228 2.715749 TTGGATGGAGCGTTGATGAT 57.284 45.000 0.00 0.00 0.00 2.45
3111 3230 1.143305 GGATGGAGCGTTGATGATCG 58.857 55.000 0.00 0.00 0.00 3.69
3112 3231 1.143305 GATGGAGCGTTGATGATCGG 58.857 55.000 0.00 0.00 0.00 4.18
3113 3232 0.465705 ATGGAGCGTTGATGATCGGT 59.534 50.000 0.00 0.00 40.38 4.69
3164 3437 3.905784 GCTGCTAGCAGACAACATTTTT 58.094 40.909 41.87 0.00 46.30 1.94
3193 3466 8.830915 TTCCTTTATTATTGTTGGCCTTGATA 57.169 30.769 3.32 0.00 0.00 2.15
3205 3478 2.332063 CCTTGATAGGCACGGTGATT 57.668 50.000 13.29 1.02 33.99 2.57
3206 3479 2.213499 CCTTGATAGGCACGGTGATTC 58.787 52.381 13.29 3.00 33.99 2.52
3241 3514 4.887748 TGATTCCTCTTCACTGTCAGTTC 58.112 43.478 1.67 0.00 0.00 3.01
3242 3515 4.590647 TGATTCCTCTTCACTGTCAGTTCT 59.409 41.667 1.67 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 107 1.228124 TTTGCTTGTCCCGTGGGAG 60.228 57.895 8.18 0.00 46.16 4.30
121 124 3.060615 CGAGGGAGGACGGACGTT 61.061 66.667 0.00 0.00 0.00 3.99
137 140 2.727544 CCAACCAACCAACTGCCG 59.272 61.111 0.00 0.00 0.00 5.69
160 170 2.484264 AGTGTTTTCTGCAGGATTACGC 59.516 45.455 15.13 12.92 0.00 4.42
184 194 1.609635 ATACATGGACGTGGACCGCA 61.610 55.000 5.75 0.00 41.42 5.69
577 610 1.535202 GCGGGAGGAGAGGATGGAT 60.535 63.158 0.00 0.00 0.00 3.41
578 611 2.123251 GCGGGAGGAGAGGATGGA 60.123 66.667 0.00 0.00 0.00 3.41
579 612 3.237741 GGCGGGAGGAGAGGATGG 61.238 72.222 0.00 0.00 0.00 3.51
580 613 2.066393 TTGGCGGGAGGAGAGGATG 61.066 63.158 0.00 0.00 0.00 3.51
648 685 4.452733 GGGTCGCCGTGCTAGCTT 62.453 66.667 17.23 0.00 0.00 3.74
666 703 5.163248 TGTGGTGTATGGTATGGTTATGGAG 60.163 44.000 0.00 0.00 0.00 3.86
726 763 4.308526 TGTTGGGCTGTGTATTATTGGA 57.691 40.909 0.00 0.00 0.00 3.53
825 866 0.040514 TTTCCGCGATGCAACAACAG 60.041 50.000 8.23 0.00 0.00 3.16
826 867 0.382158 TTTTCCGCGATGCAACAACA 59.618 45.000 8.23 0.00 0.00 3.33
827 868 1.451651 CTTTTTCCGCGATGCAACAAC 59.548 47.619 8.23 0.00 0.00 3.32
828 869 1.601663 CCTTTTTCCGCGATGCAACAA 60.602 47.619 8.23 0.00 0.00 2.83
864 906 1.376037 GAGGTCAACCGGGAAGCTG 60.376 63.158 6.32 0.00 42.08 4.24
966 1012 2.036992 AGCGATCCCAAATAGCTCTCTG 59.963 50.000 0.00 0.00 31.94 3.35
1009 1056 1.788067 AACCCGAAAAGAAACGCCCG 61.788 55.000 0.00 0.00 0.00 6.13
1216 1266 2.476051 GTGATGAACAGCACCGCG 59.524 61.111 11.41 0.00 41.49 6.46
1219 1269 1.626654 CGACCGTGATGAACAGCACC 61.627 60.000 15.72 3.44 44.19 5.01
1357 1407 3.680786 CCGTCCTCGTGCAGGTGA 61.681 66.667 9.88 3.97 43.95 4.02
1666 1716 2.044352 TCCTCGATGTCCGGCTCA 60.044 61.111 0.00 0.00 39.14 4.26
1686 1736 1.992277 TCCTCCTGCTCCTGCTTCC 60.992 63.158 0.00 0.00 40.48 3.46
2298 2365 1.193874 GGAAACGCCAACTACTCAACG 59.806 52.381 0.00 0.00 36.34 4.10
2311 2378 0.391263 ATCCACTTCCGAGGAAACGC 60.391 55.000 6.01 0.00 37.48 4.84
2354 2422 5.338559 CGTTTGATCGTCGCAACTAAAAATT 59.661 36.000 0.00 0.00 0.00 1.82
2356 2424 4.205334 CGTTTGATCGTCGCAACTAAAAA 58.795 39.130 0.00 0.00 0.00 1.94
2390 2462 5.524281 GGAAAATTTAAGGCAAAAACGGACA 59.476 36.000 0.00 0.00 0.00 4.02
2394 2466 8.903570 AAAAAGGAAAATTTAAGGCAAAAACG 57.096 26.923 0.00 0.00 0.00 3.60
2413 2485 5.241506 TGCATGGTAACTTCTGAGAAAAAGG 59.758 40.000 0.00 0.00 37.61 3.11
2417 2489 4.943705 GGATGCATGGTAACTTCTGAGAAA 59.056 41.667 2.46 0.00 37.61 2.52
2440 2512 5.445845 GTTTTTGCTGGCATTTTCTTCATG 58.554 37.500 0.00 0.00 0.00 3.07
2496 2577 2.711174 AGATGGACCCCAATAGCTGAT 58.289 47.619 0.00 0.00 36.95 2.90
2558 2639 8.793592 CCATATGAGTTTTGATGATGATGATGT 58.206 33.333 3.65 0.00 0.00 3.06
2661 2762 2.975536 GCCCCTGCTGTACGTGTA 59.024 61.111 0.00 0.00 33.53 2.90
2844 2957 1.901159 CCCAAATCTGCCCATCAAACA 59.099 47.619 0.00 0.00 0.00 2.83
2979 3092 3.426568 GTCTGCGGTTGCTGGCTC 61.427 66.667 0.00 0.00 41.00 4.70
3037 3156 2.414293 CGACCACTGCAGACTGTACTAC 60.414 54.545 23.35 1.60 0.00 2.73
3091 3210 1.538849 CGATCATCAACGCTCCATCCA 60.539 52.381 0.00 0.00 0.00 3.41
3105 3224 4.020218 CCACTTGGATACCATACCGATCAT 60.020 45.833 0.00 0.00 37.39 2.45
3108 3227 2.637872 CCCACTTGGATACCATACCGAT 59.362 50.000 0.00 0.00 37.39 4.18
3109 3228 2.043992 CCCACTTGGATACCATACCGA 58.956 52.381 0.00 0.00 37.39 4.69
3111 3230 1.423921 CCCCCACTTGGATACCATACC 59.576 57.143 0.00 0.00 37.39 2.73
3112 3231 1.202891 GCCCCCACTTGGATACCATAC 60.203 57.143 0.00 0.00 37.39 2.39
3113 3232 1.145571 GCCCCCACTTGGATACCATA 58.854 55.000 0.00 0.00 37.39 2.74
3138 3267 2.434884 GTCTGCTAGCAGCCGCAA 60.435 61.111 35.21 18.31 41.51 4.85
3164 3437 8.527810 CAAGGCCAACAATAATAAAGGAAGTAA 58.472 33.333 5.01 0.00 0.00 2.24
3193 3466 1.556911 AGAATCAGAATCACCGTGCCT 59.443 47.619 0.00 0.00 0.00 4.75
3201 3474 7.803131 AGGAATCAGAATCAGAATCAGAATCA 58.197 34.615 0.00 0.00 0.00 2.57
3202 3475 8.152246 AGAGGAATCAGAATCAGAATCAGAATC 58.848 37.037 0.00 0.00 0.00 2.52
3203 3476 8.036585 AGAGGAATCAGAATCAGAATCAGAAT 57.963 34.615 0.00 0.00 0.00 2.40
3204 3477 7.434927 AGAGGAATCAGAATCAGAATCAGAA 57.565 36.000 0.00 0.00 0.00 3.02
3205 3478 7.125356 TGAAGAGGAATCAGAATCAGAATCAGA 59.875 37.037 0.00 0.00 0.00 3.27
3206 3479 7.225145 GTGAAGAGGAATCAGAATCAGAATCAG 59.775 40.741 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.