Multiple sequence alignment - TraesCS7A01G245300

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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 TraesCS7A01G245300 chr7A 100.000 2729 0 0 1 2729 223470966 223473694 0.000000e+00 5040
1 TraesCS7A01G245300 chr7D 90.534 2155 125 45 1 2100 211404939 211407069 0.000000e+00 2776
2 TraesCS7A01G245300 chr7D 88.939 443 47 2 2285 2726 211598133 211598574 1.850000e-151 545
3 TraesCS7A01G245300 chr7B 90.476 1932 94 43 1 1870 190117711 190115808 0.000000e+00 2466
4 TraesCS7A01G245300 chr7B 84.310 580 70 8 1936 2504 190099878 190099309 5.140000e-152 547
5 TraesCS7A01G245300 chr7B 85.897 390 51 3 2342 2728 190099256 190098868 1.960000e-111 412
6 TraesCS7A01G245300 chr7B 93.333 210 14 0 1740 1949 190101306 190101097 7.340000e-81 311
7 TraesCS7A01G245300 chr7B 81.858 226 31 7 1986 2207 717535419 717535200 6.000000e-42 182
8 TraesCS7A01G245300 chr7B 81.308 214 36 3 1986 2197 188001543 188001332 1.300000e-38 171
9 TraesCS7A01G245300 chr7B 81.081 222 35 4 1986 2203 573930545 573930327 1.300000e-38 171
10 TraesCS7A01G245300 chr4A 83.260 227 27 9 1986 2203 514421805 514421581 5.960000e-47 198
11 TraesCS7A01G245300 chr4A 81.448 221 38 2 1986 2203 121480413 121480193 7.770000e-41 178
12 TraesCS7A01G245300 chr5A 82.533 229 34 6 1983 2208 338221686 338221461 2.140000e-46 196
13 TraesCS7A01G245300 chr1B 81.778 225 36 3 1983 2204 667683062 667683284 1.670000e-42 183
14 TraesCS7A01G245300 chr1A 80.531 226 36 7 1986 2204 52234676 52234452 1.680000e-37 167


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 TraesCS7A01G245300 chr7A 223470966 223473694 2728 False 5040.000000 5040 100.000000 1 2729 1 chr7A.!!$F1 2728
1 TraesCS7A01G245300 chr7D 211404939 211407069 2130 False 2776.000000 2776 90.534000 1 2100 1 chr7D.!!$F1 2099
2 TraesCS7A01G245300 chr7B 190115808 190117711 1903 True 2466.000000 2466 90.476000 1 1870 1 chr7B.!!$R2 1869
3 TraesCS7A01G245300 chr7B 190098868 190101306 2438 True 423.333333 547 87.846667 1740 2728 3 chr7B.!!$R5 988

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
787 850 0.17902 TGATAATTGGGCCGGCTCAG 60.179 55.0 31.0 0.0 0.0 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2287 3609 0.035458 ACCTCAAACTGGAAGCTCGG 59.965 55.0 0.0 0.0 37.6 4.63 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
210 213 5.457473 CCCGTCCATTTTATAAATTTGCGAC 59.543 40.000 0.00 8.61 0.00 5.19
211 214 6.262601 CCGTCCATTTTATAAATTTGCGACT 58.737 36.000 0.00 0.00 0.00 4.18
225 228 4.647424 TTGCGACTCAAATTTCAAAGGT 57.353 36.364 0.00 0.00 0.00 3.50
228 231 4.278170 TGCGACTCAAATTTCAAAGGTGAT 59.722 37.500 0.00 0.00 32.48 3.06
325 346 7.213678 TGGGAACATGTTTTGAAATTCCTAAC 58.786 34.615 13.36 0.00 36.62 2.34
350 371 7.934120 ACCATTTTATCAATTCGGGAAAACAAA 59.066 29.630 0.00 0.00 0.00 2.83
361 383 6.777526 TCGGGAAAACAAATAAATGCAAAG 57.222 33.333 0.00 0.00 0.00 2.77
362 384 6.516718 TCGGGAAAACAAATAAATGCAAAGA 58.483 32.000 0.00 0.00 0.00 2.52
702 765 4.540502 AGGCTAGAAGGTTCCTAAAACCAT 59.459 41.667 9.45 0.00 42.69 3.55
732 795 3.367190 GGACTGGAACCTTCTAGAACGTC 60.367 52.174 0.00 4.33 37.94 4.34
733 796 2.228343 ACTGGAACCTTCTAGAACGTCG 59.772 50.000 0.00 0.00 37.94 5.12
734 797 1.068055 TGGAACCTTCTAGAACGTCGC 60.068 52.381 0.00 0.77 0.00 5.19
787 850 0.179020 TGATAATTGGGCCGGCTCAG 60.179 55.000 31.00 0.00 0.00 3.35
800 863 3.877357 CTCAGGTCGCTCGCGCTA 61.877 66.667 5.56 0.00 39.59 4.26
815 878 3.691702 GCTATGCGAATCAACGACG 57.308 52.632 0.00 0.00 35.09 5.12
912 975 1.649390 CCTCGCCGATCTCCTATCCG 61.649 65.000 0.00 0.00 0.00 4.18
916 979 1.244697 GCCGATCTCCTATCCGCTCA 61.245 60.000 0.00 0.00 0.00 4.26
954 1017 1.544777 AAATCGCGCGCAAAAACCAC 61.545 50.000 32.61 0.00 0.00 4.16
1032 1108 0.341609 CTTCCCTCTTCTCCCCCTCT 59.658 60.000 0.00 0.00 0.00 3.69
1167 1243 4.154347 GCCGGTCTCCTCCTGCTG 62.154 72.222 1.90 0.00 35.38 4.41
1314 1390 4.410400 GTGCCCGAGGGGTGGAAG 62.410 72.222 10.61 0.00 46.51 3.46
1320 1396 2.683933 GAGGGGTGGAAGGAGCGA 60.684 66.667 0.00 0.00 0.00 4.93
1470 1546 2.344203 CGACAACCTCGCCCTCTCT 61.344 63.158 0.00 0.00 35.06 3.10
1569 1645 0.035630 ACTACGAGTACGAGGTGGCT 60.036 55.000 0.00 0.00 42.66 4.75
1984 3303 9.707957 TTATCCAATCATGTAAATTTACCCTGT 57.292 29.630 22.47 6.71 32.72 4.00
2002 3321 3.086733 TCACACGTGTGGCATGAAA 57.913 47.368 39.88 21.78 45.65 2.69
2012 3331 0.611618 TGGCATGAAACAATCCGGCT 60.612 50.000 0.00 0.00 0.00 5.52
2013 3332 0.532115 GGCATGAAACAATCCGGCTT 59.468 50.000 0.00 0.00 0.00 4.35
2018 3337 1.269448 TGAAACAATCCGGCTTTGAGC 59.731 47.619 19.86 10.74 41.46 4.26
2033 3352 6.474102 CGGCTTTGAGCTTTTTACAACTAAAA 59.526 34.615 0.00 0.00 41.99 1.52
2088 3410 3.656559 CTGAAAGTTGCCATCCAAAAGG 58.343 45.455 0.00 0.00 34.68 3.11
2102 3424 3.960102 TCCAAAAGGAAAGTTGTCATGCT 59.040 39.130 0.00 0.00 0.00 3.79
2138 3460 3.568007 TGCAATCCTTGTGTCACTAAACC 59.432 43.478 4.27 0.00 0.00 3.27
2140 3462 5.001232 GCAATCCTTGTGTCACTAAACCTA 58.999 41.667 4.27 0.00 0.00 3.08
2141 3463 5.648092 GCAATCCTTGTGTCACTAAACCTAT 59.352 40.000 4.27 0.00 0.00 2.57
2170 3492 1.368850 GTTCGAAGTTGCCACGTGC 60.369 57.895 10.91 6.53 41.77 5.34
2190 3512 0.684535 TCGTGTCCCATGTGTGACAT 59.315 50.000 11.60 0.00 42.90 3.06
2195 3517 4.201812 CGTGTCCCATGTGTGACATTTATC 60.202 45.833 11.60 1.11 42.90 1.75
2213 3535 9.990868 ACATTTATCAGGGTCCTTAATTTAACT 57.009 29.630 0.00 0.00 0.00 2.24
2245 3567 8.659925 ATTTTGCATGAATTTCACTTAACACA 57.340 26.923 0.15 0.00 0.00 3.72
2250 3572 6.086765 GCATGAATTTCACTTAACACAGTTCG 59.913 38.462 0.15 0.00 0.00 3.95
2258 3580 3.744426 ACTTAACACAGTTCGATTTCCGG 59.256 43.478 0.00 0.00 39.14 5.14
2259 3581 0.872388 AACACAGTTCGATTTCCGGC 59.128 50.000 0.00 0.00 39.14 6.13
2268 3590 0.316196 CGATTTCCGGCGATTTGCTC 60.316 55.000 9.30 0.00 45.43 4.26
2287 3609 3.628017 CTCGACATTTTTGGTGTTCCAC 58.372 45.455 0.00 0.00 44.22 4.02
2336 3658 1.688311 CCATCTCCTTGGTCCGAGGTA 60.688 57.143 22.84 13.77 36.45 3.08
2337 3659 2.108168 CATCTCCTTGGTCCGAGGTAA 58.892 52.381 22.84 13.45 36.45 2.85
2338 3660 2.314071 TCTCCTTGGTCCGAGGTAAA 57.686 50.000 22.84 8.56 36.45 2.01
2340 3662 0.611714 TCCTTGGTCCGAGGTAAAGC 59.388 55.000 22.84 0.00 36.45 3.51
2345 3667 0.745468 GGTCCGAGGTAAAGCGAGAT 59.255 55.000 0.00 0.00 0.00 2.75
2416 3954 3.240134 ATGCAACACCTCGCGTCCT 62.240 57.895 5.77 0.00 0.00 3.85
2514 4053 3.695022 ATCCCGCGTCTTCCGAACG 62.695 63.158 4.92 0.00 42.87 3.95
2529 4068 0.248289 GAACGAATCGGAGGTTCCCA 59.752 55.000 7.80 0.00 35.24 4.37
2536 4075 2.652095 CGGAGGTTCCCAACGGCTA 61.652 63.158 0.00 0.00 31.13 3.93
2545 4084 0.537371 CCCAACGGCTAATCCATCCC 60.537 60.000 0.00 0.00 34.01 3.85
2548 4087 4.675404 CGGCTAATCCATCCCGTC 57.325 61.111 0.00 0.00 36.18 4.79
2549 4088 1.745890 CGGCTAATCCATCCCGTCA 59.254 57.895 0.00 0.00 36.18 4.35
2575 4114 1.811645 GAGGCGTCTAGGAGGGATGC 61.812 65.000 0.00 0.00 42.86 3.91
2577 4116 1.365633 GCGTCTAGGAGGGATGCTG 59.634 63.158 0.00 0.00 41.08 4.41
2578 4117 1.365633 CGTCTAGGAGGGATGCTGC 59.634 63.158 0.00 0.00 0.00 5.25
2586 4125 1.383664 AGGGATGCTGCTGCTCCTA 60.384 57.895 23.23 5.23 40.48 2.94
2591 4130 0.822532 ATGCTGCTGCTCCTATTGGC 60.823 55.000 17.00 0.00 40.48 4.52
2592 4131 2.192187 GCTGCTGCTCCTATTGGCC 61.192 63.158 8.53 0.00 36.03 5.36
2602 4141 0.546598 CCTATTGGCCGGTTTCTCCT 59.453 55.000 1.90 0.00 0.00 3.69
2603 4142 1.064685 CCTATTGGCCGGTTTCTCCTT 60.065 52.381 1.90 0.00 0.00 3.36
2625 4164 1.301716 GTCACCTTTGGCTCGCTCA 60.302 57.895 0.00 0.00 0.00 4.26
2629 4168 0.326264 ACCTTTGGCTCGCTCAGATT 59.674 50.000 0.00 0.00 0.00 2.40
2630 4169 1.012841 CCTTTGGCTCGCTCAGATTC 58.987 55.000 0.00 0.00 0.00 2.52
2649 4188 1.586154 CGTCCATGGAGGGTTGCAAC 61.586 60.000 24.05 21.59 38.24 4.17
2651 4190 2.568090 CATGGAGGGTTGCAACGC 59.432 61.111 32.68 32.68 41.65 4.84
2670 4209 2.031857 CGCTATCTCTAAGGTGGTCGTC 60.032 54.545 0.00 0.00 0.00 4.20
2687 4228 1.867233 CGTCCACTTGTTCTGTCTTGG 59.133 52.381 0.00 0.00 0.00 3.61
2690 4231 3.312697 GTCCACTTGTTCTGTCTTGGAAC 59.687 47.826 0.00 0.00 42.17 3.62
2710 4251 0.034380 ACTAGCAGCGAGTGACCCTA 60.034 55.000 7.46 0.00 0.00 3.53
2711 4252 1.323412 CTAGCAGCGAGTGACCCTAT 58.677 55.000 0.00 0.00 0.00 2.57
2713 4254 1.884926 GCAGCGAGTGACCCTATGC 60.885 63.158 0.00 0.00 0.00 3.14
2716 4257 2.782222 GCGAGTGACCCTATGCCGA 61.782 63.158 0.00 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
169 172 2.657184 CGGGAATTTCACGTTCCAAAC 58.343 47.619 12.86 0.00 45.56 2.93
296 299 8.435982 AGGAATTTCAAAACATGTTCCCAAATA 58.564 29.630 12.39 0.00 34.00 1.40
297 300 7.289310 AGGAATTTCAAAACATGTTCCCAAAT 58.711 30.769 12.39 12.45 34.00 2.32
325 346 7.897575 TTGTTTTCCCGAATTGATAAAATGG 57.102 32.000 0.00 0.00 0.00 3.16
339 360 6.777526 TCTTTGCATTTATTTGTTTTCCCG 57.222 33.333 0.00 0.00 0.00 5.14
393 415 8.637986 ACTACTTTGCAAAATGTTCCAAGATTA 58.362 29.630 13.84 0.00 0.00 1.75
397 419 6.272318 TCACTACTTTGCAAAATGTTCCAAG 58.728 36.000 13.84 5.60 0.00 3.61
556 590 9.625747 TTCCCTTTGCTTTCTTCATTTTATTTT 57.374 25.926 0.00 0.00 0.00 1.82
557 591 9.625747 TTTCCCTTTGCTTTCTTCATTTTATTT 57.374 25.926 0.00 0.00 0.00 1.40
558 592 9.625747 TTTTCCCTTTGCTTTCTTCATTTTATT 57.374 25.926 0.00 0.00 0.00 1.40
559 593 9.625747 TTTTTCCCTTTGCTTTCTTCATTTTAT 57.374 25.926 0.00 0.00 0.00 1.40
800 863 1.854743 CAGATCGTCGTTGATTCGCAT 59.145 47.619 0.00 0.00 0.00 4.73
828 891 1.271054 GGACAATCCTATCTGCCGCAT 60.271 52.381 0.00 0.00 32.53 4.73
912 975 0.235926 GTGGTTTTGTCTCGCTGAGC 59.764 55.000 0.00 0.00 0.00 4.26
916 979 1.745232 TTGTGTGGTTTTGTCTCGCT 58.255 45.000 0.00 0.00 0.00 4.93
985 1061 1.303806 TCATGGTGGACCTCGACGA 60.304 57.895 0.00 0.00 36.82 4.20
1032 1108 2.680352 GCGGTGGTGAGGAGAGGA 60.680 66.667 0.00 0.00 0.00 3.71
1155 1231 2.039624 GGGGTCAGCAGGAGGAGA 59.960 66.667 0.00 0.00 0.00 3.71
1320 1396 1.507140 TCTCCACCTTTGACACCAGT 58.493 50.000 0.00 0.00 0.00 4.00
1998 3317 1.269448 GCTCAAAGCCGGATTGTTTCA 59.731 47.619 5.31 0.00 34.48 2.69
2002 3321 1.620822 AAAGCTCAAAGCCGGATTGT 58.379 45.000 5.31 0.00 43.77 2.71
2013 3332 9.862371 TGACAATTTTAGTTGTAAAAAGCTCAA 57.138 25.926 0.00 0.00 42.08 3.02
2018 3337 9.672086 TCGGATGACAATTTTAGTTGTAAAAAG 57.328 29.630 0.00 0.00 42.08 2.27
2082 3404 5.350633 TCAAGCATGACAACTTTCCTTTTG 58.649 37.500 0.00 0.00 0.00 2.44
2083 3405 5.596836 TCAAGCATGACAACTTTCCTTTT 57.403 34.783 0.00 0.00 0.00 2.27
2151 3473 2.010670 CACGTGGCAACTTCGAACA 58.989 52.632 7.95 0.00 38.01 3.18
2176 3498 4.525996 CCTGATAAATGTCACACATGGGA 58.474 43.478 0.00 0.00 37.97 4.37
2178 3500 4.272489 ACCCTGATAAATGTCACACATGG 58.728 43.478 0.00 0.00 37.97 3.66
2181 3503 3.587061 AGGACCCTGATAAATGTCACACA 59.413 43.478 0.00 0.00 0.00 3.72
2226 3548 7.351981 TCGAACTGTGTTAAGTGAAATTCATG 58.648 34.615 0.00 0.00 0.00 3.07
2245 3567 1.396996 CAAATCGCCGGAAATCGAACT 59.603 47.619 5.05 0.00 42.43 3.01
2250 3572 0.316196 CGAGCAAATCGCCGGAAATC 60.316 55.000 5.05 0.00 45.98 2.17
2287 3609 0.035458 ACCTCAAACTGGAAGCTCGG 59.965 55.000 0.00 0.00 37.60 4.63
2336 3658 4.155826 CGATCCTAGATCTCATCTCGCTTT 59.844 45.833 0.00 0.00 40.76 3.51
2337 3659 3.689161 CGATCCTAGATCTCATCTCGCTT 59.311 47.826 0.00 0.00 40.76 4.68
2338 3660 3.270027 CGATCCTAGATCTCATCTCGCT 58.730 50.000 0.00 0.00 40.76 4.93
2340 3662 3.006247 TGCGATCCTAGATCTCATCTCG 58.994 50.000 0.00 5.93 40.76 4.04
2345 3667 2.242926 CCCTTGCGATCCTAGATCTCA 58.757 52.381 0.00 0.00 0.00 3.27
2481 4020 0.250081 GGGATGAGCGGGAAGATGAC 60.250 60.000 0.00 0.00 0.00 3.06
2482 4021 1.748329 CGGGATGAGCGGGAAGATGA 61.748 60.000 0.00 0.00 0.00 2.92
2492 4031 2.586357 GGAAGACGCGGGATGAGC 60.586 66.667 12.47 0.00 0.00 4.26
2494 4033 2.344981 TTCGGAAGACGCGGGATGA 61.345 57.895 12.47 0.00 43.86 2.92
2523 4062 1.947456 GATGGATTAGCCGTTGGGAAC 59.053 52.381 0.00 0.00 40.66 3.62
2529 4068 0.106149 GACGGGATGGATTAGCCGTT 59.894 55.000 0.00 0.00 40.66 4.44
2536 4075 0.179009 CAGCCATGACGGGATGGATT 60.179 55.000 16.87 3.62 45.24 3.01
2545 4084 4.457496 ACGCCTCCAGCCATGACG 62.457 66.667 0.00 0.00 38.78 4.35
2548 4087 1.068753 CTAGACGCCTCCAGCCATG 59.931 63.158 0.00 0.00 38.78 3.66
2549 4088 2.136878 CCTAGACGCCTCCAGCCAT 61.137 63.158 0.00 0.00 38.78 4.40
2561 4100 0.392336 CAGCAGCATCCCTCCTAGAC 59.608 60.000 0.00 0.00 0.00 2.59
2575 4114 1.890979 CGGCCAATAGGAGCAGCAG 60.891 63.158 2.24 0.00 36.89 4.24
2577 4116 2.592861 CCGGCCAATAGGAGCAGC 60.593 66.667 2.24 0.00 36.89 5.25
2578 4117 0.394352 AAACCGGCCAATAGGAGCAG 60.394 55.000 0.00 0.00 36.89 4.24
2586 4125 1.064685 CCTAAGGAGAAACCGGCCAAT 60.065 52.381 0.00 0.00 44.74 3.16
2591 4130 1.066358 GTGACCCTAAGGAGAAACCGG 60.066 57.143 0.00 0.00 44.74 5.28
2592 4131 1.066358 GGTGACCCTAAGGAGAAACCG 60.066 57.143 0.00 0.00 44.74 4.44
2602 4141 0.323629 CGAGCCAAAGGTGACCCTAA 59.676 55.000 0.00 0.00 41.56 2.69
2603 4142 1.980052 CGAGCCAAAGGTGACCCTA 59.020 57.895 0.00 0.00 41.56 3.53
2615 4154 1.139734 GACGAATCTGAGCGAGCCA 59.860 57.895 9.27 0.00 0.00 4.75
2625 4164 1.210478 CAACCCTCCATGGACGAATCT 59.790 52.381 11.44 0.00 38.35 2.40
2629 4168 1.773856 TTGCAACCCTCCATGGACGA 61.774 55.000 11.44 0.00 38.35 4.20
2630 4169 1.303236 TTGCAACCCTCCATGGACG 60.303 57.895 11.44 7.10 38.35 4.79
2649 4188 1.948145 ACGACCACCTTAGAGATAGCG 59.052 52.381 0.00 0.00 0.00 4.26
2651 4190 3.552875 TGGACGACCACCTTAGAGATAG 58.447 50.000 1.37 0.00 41.77 2.08
2652 4191 3.657398 TGGACGACCACCTTAGAGATA 57.343 47.619 1.37 0.00 41.77 1.98
2670 4209 3.971032 GTTCCAAGACAGAACAAGTGG 57.029 47.619 0.00 0.00 42.58 4.00
2687 4228 1.341606 GTCACTCGCTGCTAGTGTTC 58.658 55.000 26.93 19.22 43.88 3.18
2690 4231 1.153745 GGGTCACTCGCTGCTAGTG 60.154 63.158 23.74 23.74 44.66 2.74
2692 4233 1.000827 CATAGGGTCACTCGCTGCTAG 60.001 57.143 0.00 0.00 39.66 3.42
2693 4234 1.032794 CATAGGGTCACTCGCTGCTA 58.967 55.000 0.00 0.00 39.66 3.49
2694 4235 1.819229 CATAGGGTCACTCGCTGCT 59.181 57.895 0.00 0.00 39.66 4.24


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

AutoCloner maintained by Alex Coulton.