Multiple sequence alignment - TraesCS7B01G189000

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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 TraesCS7B01G189000 chr7B 100.000 3458 0 0 1 3458 322474390 322477847 0.000000e+00 6386.0
1 TraesCS7B01G189000 chr7D 94.165 3445 107 23 1 3423 363038284 363041656 0.000000e+00 5162.0
2 TraesCS7B01G189000 chr7D 97.059 34 1 0 3425 3458 363044149 363044182 1.340000e-04 58.4
3 TraesCS7B01G189000 chr7A 94.743 3215 80 28 266 3458 394837024 394833877 0.000000e+00 4918.0
4 TraesCS7B01G189000 chr7A 90.114 263 21 5 1 258 394856809 394856547 1.540000e-88 337.0


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 TraesCS7B01G189000 chr7B 322474390 322477847 3457 False 6386.0 6386 100.000 1 3458 1 chr7B.!!$F1 3457
1 TraesCS7B01G189000 chr7D 363038284 363044182 5898 False 2610.2 5162 95.612 1 3458 2 chr7D.!!$F1 3457
2 TraesCS7B01G189000 chr7A 394833877 394837024 3147 True 4918.0 4918 94.743 266 3458 1 chr7A.!!$R1 3192

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
842 855 0.453282 CATCGCCGTTGCAGTTCTTG 60.453 55.0 0.0 0.0 37.32 3.02 F
1686 1699 1.630126 AAGCCATCCAGCGGTCTCAT 61.630 55.0 0.0 0.0 38.01 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1746 1759 0.249868 CGTCCTTCTTGACAGCACCA 60.250 55.0 0.0 0.0 34.88 4.17 R
3146 3178 0.387929 CAATGTGCCCCATGAGATGC 59.612 55.0 0.0 0.0 32.82 3.91 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
292 295 1.815132 GAGCGTTTGATTTGCGATCC 58.185 50.000 0.00 0.00 35.38 3.36
309 312 4.921515 GCGATCCGTGCAAGTAATCTAATA 59.078 41.667 0.00 0.00 0.00 0.98
311 314 6.400091 GCGATCCGTGCAAGTAATCTAATAAG 60.400 42.308 0.00 0.00 0.00 1.73
312 315 6.641314 CGATCCGTGCAAGTAATCTAATAAGT 59.359 38.462 0.00 0.00 0.00 2.24
412 415 9.759473 ATAATTCATGGGTATTTATGAAGAGGG 57.241 33.333 0.00 0.00 43.97 4.30
544 555 0.833949 GAAGAAGGGAAGAGGGCGAT 59.166 55.000 0.00 0.00 0.00 4.58
625 637 1.600636 CACTCGAGCAGCCCCAAAA 60.601 57.895 13.61 0.00 0.00 2.44
763 776 1.301401 CGTGGACAAAAGCCCTCGA 60.301 57.895 0.00 0.00 40.61 4.04
785 798 3.067833 CCGACTCTCCCAACTTCTTTTC 58.932 50.000 0.00 0.00 0.00 2.29
805 818 1.078759 CTGTTCGTCCTGACCATCGC 61.079 60.000 0.00 0.00 0.00 4.58
842 855 0.453282 CATCGCCGTTGCAGTTCTTG 60.453 55.000 0.00 0.00 37.32 3.02
904 917 3.611674 CCGCGGCCTTTGGGTTTT 61.612 61.111 14.67 0.00 34.45 2.43
1166 1179 2.420129 CGGTTCCGGAATCTCCAAGAAT 60.420 50.000 24.58 0.00 35.91 2.40
1183 1196 2.158842 AGAATGGATGAGCCTGCAGTAC 60.159 50.000 13.81 4.26 37.63 2.73
1278 1291 2.711542 TCGCTGATAGATCCGATGCTA 58.288 47.619 0.00 0.00 0.00 3.49
1377 1390 2.357009 GTCCTCACATGATGCCAATGTC 59.643 50.000 0.00 0.00 0.00 3.06
1416 1429 1.839994 CCATTGTCTCTTCCTGGGCTA 59.160 52.381 0.00 0.00 0.00 3.93
1632 1645 1.647084 GTCAGTGAACCGCAACCAC 59.353 57.895 0.00 0.00 0.00 4.16
1686 1699 1.630126 AAGCCATCCAGCGGTCTCAT 61.630 55.000 0.00 0.00 38.01 2.90
1746 1759 3.698040 GTGATGGCAAGATGACAGGAATT 59.302 43.478 0.00 0.00 39.76 2.17
1752 1765 3.087031 CAAGATGACAGGAATTGGTGCT 58.913 45.455 0.00 0.00 0.00 4.40
1914 1927 1.757306 CCACTCTGAGTGCCCTGTT 59.243 57.895 28.14 0.00 44.63 3.16
1980 1993 1.229529 AGGAGGTGGTGAACGGGAT 60.230 57.895 0.00 0.00 0.00 3.85
1985 1998 2.040544 GTGGTGAACGGGATGCCTG 61.041 63.158 0.28 0.00 35.68 4.85
2010 2023 0.833287 ATGATGTTCCTCCCAGACCG 59.167 55.000 0.00 0.00 0.00 4.79
2283 2296 3.173540 CAATCAGGTCCGATTGCCA 57.826 52.632 17.61 0.00 44.13 4.92
2658 2679 8.537728 AATTTCCCTGATATTGCATCTGTTTA 57.462 30.769 0.00 0.00 0.00 2.01
2703 2724 5.420739 TGTTATCTCTGTACTGTGTATGCCA 59.579 40.000 0.00 0.00 0.00 4.92
2704 2725 6.098266 TGTTATCTCTGTACTGTGTATGCCAT 59.902 38.462 0.00 0.00 0.00 4.40
2705 2726 5.620738 ATCTCTGTACTGTGTATGCCATT 57.379 39.130 0.00 0.00 0.00 3.16
2706 2727 6.731292 ATCTCTGTACTGTGTATGCCATTA 57.269 37.500 0.00 0.00 0.00 1.90
2707 2728 5.902681 TCTCTGTACTGTGTATGCCATTAC 58.097 41.667 0.00 0.00 0.00 1.89
2708 2729 4.678622 TCTGTACTGTGTATGCCATTACG 58.321 43.478 0.00 0.00 0.00 3.18
2709 2730 4.158949 TCTGTACTGTGTATGCCATTACGT 59.841 41.667 0.00 0.00 0.00 3.57
2710 2731 4.823157 TGTACTGTGTATGCCATTACGTT 58.177 39.130 0.00 0.00 0.00 3.99
2711 2732 5.239351 TGTACTGTGTATGCCATTACGTTT 58.761 37.500 0.00 0.00 0.00 3.60
2712 2733 4.939509 ACTGTGTATGCCATTACGTTTC 57.060 40.909 0.00 0.00 0.00 2.78
2713 2734 4.575885 ACTGTGTATGCCATTACGTTTCT 58.424 39.130 0.00 0.00 0.00 2.52
2714 2735 5.001232 ACTGTGTATGCCATTACGTTTCTT 58.999 37.500 0.00 0.00 0.00 2.52
2715 2736 5.106712 ACTGTGTATGCCATTACGTTTCTTG 60.107 40.000 0.00 0.00 0.00 3.02
2716 2737 4.155099 TGTGTATGCCATTACGTTTCTTGG 59.845 41.667 0.00 0.00 0.00 3.61
2717 2738 4.155280 GTGTATGCCATTACGTTTCTTGGT 59.845 41.667 0.00 0.00 0.00 3.67
2718 2739 5.352016 GTGTATGCCATTACGTTTCTTGGTA 59.648 40.000 0.00 0.00 0.00 3.25
2719 2740 4.957759 ATGCCATTACGTTTCTTGGTAC 57.042 40.909 0.00 0.00 0.00 3.34
2720 2741 4.010667 TGCCATTACGTTTCTTGGTACT 57.989 40.909 0.00 0.00 0.00 2.73
2721 2742 5.149973 TGCCATTACGTTTCTTGGTACTA 57.850 39.130 0.00 0.00 0.00 1.82
2722 2743 4.931002 TGCCATTACGTTTCTTGGTACTAC 59.069 41.667 0.00 0.00 0.00 2.73
2723 2744 5.173664 GCCATTACGTTTCTTGGTACTACT 58.826 41.667 0.00 0.00 0.00 2.57
2724 2745 5.640783 GCCATTACGTTTCTTGGTACTACTT 59.359 40.000 0.00 0.00 0.00 2.24
2725 2746 6.813152 GCCATTACGTTTCTTGGTACTACTTA 59.187 38.462 0.00 0.00 0.00 2.24
2726 2747 7.009907 GCCATTACGTTTCTTGGTACTACTTAG 59.990 40.741 0.00 0.00 0.00 2.18
2727 2748 8.031277 CCATTACGTTTCTTGGTACTACTTAGT 58.969 37.037 0.00 0.00 40.24 2.24
2728 2749 9.415544 CATTACGTTTCTTGGTACTACTTAGTT 57.584 33.333 0.00 0.00 37.73 2.24
2729 2750 9.987272 ATTACGTTTCTTGGTACTACTTAGTTT 57.013 29.630 0.00 0.00 37.73 2.66
2762 2783 9.601217 TTGAAGATAGTTAATTTCCTCAGCTAC 57.399 33.333 0.00 0.00 0.00 3.58
2765 2787 7.213678 AGATAGTTAATTTCCTCAGCTACAGC 58.786 38.462 0.00 0.00 42.49 4.40
2862 2884 7.489757 GTCTTAATGACTTGATCTAGTGTCCAC 59.510 40.741 14.73 0.64 42.21 4.02
2922 2944 7.324935 TGTTTTTCCCATGATCTGAAATGATG 58.675 34.615 0.00 0.00 0.00 3.07
2951 2981 7.915397 CCAATGTAATTTGCAGTATAAGTCACC 59.085 37.037 0.00 0.00 31.22 4.02
2992 3022 5.806654 ATTTTTCCTTTAAGCTCCTGCAA 57.193 34.783 0.00 0.00 42.74 4.08
3001 3031 5.528043 TTAAGCTCCTGCAAAACATGAAA 57.472 34.783 0.00 0.00 42.74 2.69
3089 3119 4.654091 AGGTTGTCAATGTTTGGAACAG 57.346 40.909 0.00 0.00 45.95 3.16
3146 3178 2.989840 CAGCTGTCCAGTTTTAGTCGAG 59.010 50.000 5.25 0.00 0.00 4.04
3160 3192 2.065789 TCGAGCATCTCATGGGGCA 61.066 57.895 0.00 0.00 0.00 5.36
3161 3193 1.890979 CGAGCATCTCATGGGGCAC 60.891 63.158 0.00 0.00 0.00 5.01
3229 3263 2.422276 AAGAACCAGCATCGTTTTGC 57.578 45.000 0.00 0.53 43.09 3.68
3237 3271 1.490621 GCATCGTTTTGCTGCAAACT 58.509 45.000 25.99 9.59 39.51 2.66
3238 3272 1.190763 GCATCGTTTTGCTGCAAACTG 59.809 47.619 25.99 20.20 39.51 3.16
3239 3273 2.730069 CATCGTTTTGCTGCAAACTGA 58.270 42.857 25.99 24.10 32.79 3.41
3350 3386 9.168451 CACTAGAGTATATCACAGATATTCCGT 57.832 37.037 0.00 0.00 0.00 4.69
3423 5949 2.031944 GGGTCAGCGTCAAAAAGAGTTC 60.032 50.000 0.00 0.00 0.00 3.01
3426 5952 4.451096 GGTCAGCGTCAAAAAGAGTTCATA 59.549 41.667 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
263 265 2.642154 TCAAACGCTCCACCCTTTAA 57.358 45.000 0.00 0.00 0.00 1.52
264 266 2.871096 ATCAAACGCTCCACCCTTTA 57.129 45.000 0.00 0.00 0.00 1.85
269 272 0.729140 CGCAAATCAAACGCTCCACC 60.729 55.000 0.00 0.00 0.00 4.61
279 282 0.877743 TTGCACGGATCGCAAATCAA 59.122 45.000 4.28 0.00 45.91 2.57
292 295 6.533723 TGTGGACTTATTAGATTACTTGCACG 59.466 38.462 0.00 0.00 0.00 5.34
309 312 4.707030 TCGTCGTTATATGTGTGGACTT 57.293 40.909 0.00 0.00 0.00 3.01
311 314 4.856664 AGATCGTCGTTATATGTGTGGAC 58.143 43.478 0.00 0.00 0.00 4.02
312 315 6.622833 TTAGATCGTCGTTATATGTGTGGA 57.377 37.500 0.00 0.00 0.00 4.02
324 327 5.121768 CCCTCAAAACATTTTAGATCGTCGT 59.878 40.000 0.00 0.00 0.00 4.34
499 503 2.952310 GCTGTCTTCCCTCAACAAACTT 59.048 45.455 0.00 0.00 0.00 2.66
544 555 6.717997 AGGAGAGGTTTTATTTTCGGCTTTTA 59.282 34.615 0.00 0.00 0.00 1.52
612 624 3.373565 CCGGTTTTGGGGCTGCTC 61.374 66.667 0.00 0.00 0.00 4.26
763 776 1.718280 AAGAAGTTGGGAGAGTCGGT 58.282 50.000 0.00 0.00 0.00 4.69
785 798 0.458543 CGATGGTCAGGACGAACAGG 60.459 60.000 0.00 0.00 46.98 4.00
842 855 0.248296 GATGTCCAGACGAGACGAGC 60.248 60.000 0.00 0.00 37.04 5.03
891 904 2.003937 TACCTCAAAACCCAAAGGCC 57.996 50.000 0.00 0.00 36.11 5.19
1104 1117 0.250295 GCGGGCAATCCATAGCTACA 60.250 55.000 0.00 0.00 34.36 2.74
1166 1179 1.757118 GTAGTACTGCAGGCTCATCCA 59.243 52.381 19.93 0.00 37.29 3.41
1183 1196 0.757188 ATCTCCTCTGGTGCCGGTAG 60.757 60.000 1.90 0.00 0.00 3.18
1357 1370 2.240414 AGACATTGGCATCATGTGAGGA 59.760 45.455 9.43 0.00 0.00 3.71
1416 1429 0.698818 ATTCAAGGCGAACCCCTTCT 59.301 50.000 0.00 0.00 43.23 2.85
1611 1624 2.112297 TTGCGGTTCACTGACCCC 59.888 61.111 0.00 0.00 36.28 4.95
1686 1699 3.257873 GCCTTGATGCATCTAGAGAGCTA 59.742 47.826 31.52 6.60 32.51 3.32
1746 1759 0.249868 CGTCCTTCTTGACAGCACCA 60.250 55.000 0.00 0.00 34.88 4.17
1752 1765 1.070134 CAGTTCCCGTCCTTCTTGACA 59.930 52.381 0.00 0.00 34.88 3.58
1914 1927 1.376466 GAGCACCTCTCCCTTGCAA 59.624 57.895 0.00 0.00 38.81 4.08
1968 1981 2.350895 CAGGCATCCCGTTCACCA 59.649 61.111 0.00 0.00 35.76 4.17
1985 1998 0.743097 GGGAGGAACATCATTGCTGC 59.257 55.000 0.00 0.00 0.00 5.25
2010 2023 3.300667 CTCACTCCTGTTTGCGCGC 62.301 63.158 27.26 27.26 0.00 6.86
2283 2296 5.822519 TGCAGCATTAACGGAATTAGAAGAT 59.177 36.000 0.00 0.00 0.00 2.40
2560 2581 6.304356 TGAGCAAAGCAATAGCATATACAC 57.696 37.500 0.00 0.00 45.49 2.90
2703 2724 9.987272 AAACTAAGTAGTACCAAGAAACGTAAT 57.013 29.630 6.52 0.00 34.99 1.89
2706 2727 8.850156 TCTAAACTAAGTAGTACCAAGAAACGT 58.150 33.333 6.52 0.00 34.99 3.99
2707 2728 9.683069 TTCTAAACTAAGTAGTACCAAGAAACG 57.317 33.333 6.52 0.00 34.99 3.60
2762 2783 4.811024 TCAGTCTTGACAGTACAAAAGCTG 59.189 41.667 3.49 5.60 38.58 4.24
2765 2787 7.482654 TTCATCAGTCTTGACAGTACAAAAG 57.517 36.000 3.49 0.00 35.83 2.27
2774 2796 5.151297 TGCTACATTCATCAGTCTTGACA 57.849 39.130 3.49 0.00 35.83 3.58
2862 2884 4.933330 CAAGATCTGGATGCCAATCTTTG 58.067 43.478 15.11 10.41 38.26 2.77
2905 2927 4.466827 TGGACCATCATTTCAGATCATGG 58.533 43.478 4.80 4.80 40.05 3.66
2922 2944 7.996385 ACTTATACTGCAAATTACATTGGACC 58.004 34.615 0.00 0.00 0.00 4.46
2992 3022 7.225341 GCAAATCCAGAAGAACTTTTCATGTTT 59.775 33.333 0.00 0.00 0.00 2.83
3146 3178 0.387929 CAATGTGCCCCATGAGATGC 59.612 55.000 0.00 0.00 32.82 3.91
3219 3253 2.730069 TCAGTTTGCAGCAAAACGATG 58.270 42.857 22.26 17.00 43.39 3.84
3220 3254 3.435105 TTCAGTTTGCAGCAAAACGAT 57.565 38.095 22.26 6.26 43.39 3.73
3221 3255 2.929531 TTCAGTTTGCAGCAAAACGA 57.070 40.000 22.26 17.46 43.39 3.85
3222 3256 3.178267 TCTTTCAGTTTGCAGCAAAACG 58.822 40.909 22.26 15.51 43.39 3.60
3223 3257 4.805192 TCATCTTTCAGTTTGCAGCAAAAC 59.195 37.500 22.26 15.49 39.80 2.43
3224 3258 4.805192 GTCATCTTTCAGTTTGCAGCAAAA 59.195 37.500 22.26 4.30 35.03 2.44
3225 3259 4.362279 GTCATCTTTCAGTTTGCAGCAAA 58.638 39.130 16.93 16.93 0.00 3.68
3226 3260 3.243501 GGTCATCTTTCAGTTTGCAGCAA 60.244 43.478 2.83 2.83 0.00 3.91
3227 3261 2.294233 GGTCATCTTTCAGTTTGCAGCA 59.706 45.455 0.00 0.00 0.00 4.41
3228 3262 2.294233 TGGTCATCTTTCAGTTTGCAGC 59.706 45.455 0.00 0.00 0.00 5.25
3229 3263 4.572985 TTGGTCATCTTTCAGTTTGCAG 57.427 40.909 0.00 0.00 0.00 4.41
3230 3264 4.998671 TTTGGTCATCTTTCAGTTTGCA 57.001 36.364 0.00 0.00 0.00 4.08
3231 3265 6.258507 ACAAATTTGGTCATCTTTCAGTTTGC 59.741 34.615 21.74 0.00 0.00 3.68
3232 3266 7.775397 ACAAATTTGGTCATCTTTCAGTTTG 57.225 32.000 21.74 0.00 0.00 2.93
3233 3267 8.667463 CAAACAAATTTGGTCATCTTTCAGTTT 58.333 29.630 21.74 6.04 41.39 2.66
3234 3268 8.040132 TCAAACAAATTTGGTCATCTTTCAGTT 58.960 29.630 21.74 0.06 44.61 3.16
3235 3269 7.555087 TCAAACAAATTTGGTCATCTTTCAGT 58.445 30.769 21.74 0.00 44.61 3.41
3236 3270 8.330302 GTTCAAACAAATTTGGTCATCTTTCAG 58.670 33.333 21.74 2.84 44.61 3.02
3237 3271 7.821359 TGTTCAAACAAATTTGGTCATCTTTCA 59.179 29.630 21.74 7.09 44.61 2.69
3238 3272 8.195617 TGTTCAAACAAATTTGGTCATCTTTC 57.804 30.769 21.74 4.84 44.61 2.62
3239 3273 8.040132 TCTGTTCAAACAAATTTGGTCATCTTT 58.960 29.630 21.74 9.32 44.61 2.52
3347 3383 1.475280 TGATACTTTCGGACCTCACGG 59.525 52.381 0.00 0.00 0.00 4.94
3350 3386 2.531771 TGGTGATACTTTCGGACCTCA 58.468 47.619 0.00 0.00 0.00 3.86
3358 3394 4.702131 AGAACTGCCAATGGTGATACTTTC 59.298 41.667 0.00 0.00 0.00 2.62
3423 5949 6.404074 GGTTTGAGAAGCTGGTGAATTCTATG 60.404 42.308 7.05 0.00 33.53 2.23
3426 5952 3.823304 GGTTTGAGAAGCTGGTGAATTCT 59.177 43.478 7.05 0.00 36.02 2.40


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

AutoCloner maintained by Alex Coulton.