Multiple sequence alignment - TraesCS6B01G313800

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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 TraesCS6B01G313800 chr6B 100.000 4166 0 0 1 4166 561691299 561695464 0.000000e+00 7694
1 TraesCS6B01G313800 chr6D 94.369 4191 122 52 1 4157 375014789 375018899 0.000000e+00 6327
2 TraesCS6B01G313800 chr6A 96.225 3682 96 19 1 3670 516407443 516411093 0.000000e+00 5989
3 TraesCS6B01G313800 chr6A 93.952 248 14 1 3911 4157 516411382 516411629 1.410000e-99 374
4 TraesCS6B01G313800 chr6A 95.536 224 8 2 3696 3918 516411088 516411310 1.420000e-94 357


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 TraesCS6B01G313800 chr6B 561691299 561695464 4165 False 7694 7694 100.000000 1 4166 1 chr6B.!!$F1 4165
1 TraesCS6B01G313800 chr6D 375014789 375018899 4110 False 6327 6327 94.369000 1 4157 1 chr6D.!!$F1 4156
2 TraesCS6B01G313800 chr6A 516407443 516411629 4186 False 2240 5989 95.237667 1 4157 3 chr6A.!!$F1 4156

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
405 406 0.246635 CTAGGTGGCACGTGCTTAGT 59.753 55.0 36.84 22.36 41.7 2.24 F
1882 1898 0.462581 GCGTGATCCTGAAGCCATGA 60.463 55.0 0.00 0.00 0.0 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2325 2341 3.390639 ACATGAATCCAAAGGTGGCAAAA 59.609 39.13 0.00 0.0 45.54 2.44 R
3213 3229 0.332632 CCTTCCCAGGCCAGATCAAA 59.667 55.00 5.01 0.0 31.53 2.69 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
19 20 1.065600 TTGGTTCGCTGCTGCAAAC 59.934 52.632 16.29 13.40 39.64 2.93
22 23 1.370900 GTTCGCTGCTGCAAACTGG 60.371 57.895 16.29 0.00 39.64 4.00
23 24 1.823470 TTCGCTGCTGCAAACTGGT 60.823 52.632 16.29 0.00 39.64 4.00
24 25 1.383456 TTCGCTGCTGCAAACTGGTT 61.383 50.000 16.29 0.00 39.64 3.67
95 96 1.370172 GGTTCGGATCGATCGACCG 60.370 63.158 33.82 33.82 46.71 4.79
122 123 1.073284 CCTTTCTCCTCCCCGTTTCAA 59.927 52.381 0.00 0.00 0.00 2.69
276 277 1.803334 CGATTCGGGAGTGGTTTTCA 58.197 50.000 0.00 0.00 0.00 2.69
277 278 1.732259 CGATTCGGGAGTGGTTTTCAG 59.268 52.381 0.00 0.00 0.00 3.02
309 310 0.733909 GCCGAGCAAATGTTTGAGCC 60.734 55.000 9.53 0.00 40.55 4.70
311 312 1.203052 CCGAGCAAATGTTTGAGCCAT 59.797 47.619 9.53 0.00 40.55 4.40
405 406 0.246635 CTAGGTGGCACGTGCTTAGT 59.753 55.000 36.84 22.36 41.70 2.24
452 453 6.251376 CACGTTAGATTTAGCCTTTGCATTTC 59.749 38.462 0.00 0.00 41.13 2.17
547 552 0.901827 TTGTTAGCGAGCATCTGGGA 59.098 50.000 0.00 0.00 0.00 4.37
720 729 7.710907 TCATTCTGAAGTAGGTGTATGTTATGC 59.289 37.037 0.00 0.00 0.00 3.14
721 730 6.791867 TCTGAAGTAGGTGTATGTTATGCT 57.208 37.500 0.00 0.00 0.00 3.79
722 731 7.182817 TCTGAAGTAGGTGTATGTTATGCTT 57.817 36.000 0.00 0.00 0.00 3.91
723 732 8.301252 TCTGAAGTAGGTGTATGTTATGCTTA 57.699 34.615 0.00 0.00 0.00 3.09
724 733 8.924303 TCTGAAGTAGGTGTATGTTATGCTTAT 58.076 33.333 0.00 0.00 0.00 1.73
725 734 8.887036 TGAAGTAGGTGTATGTTATGCTTATG 57.113 34.615 0.00 0.00 0.00 1.90
772 781 9.148879 AGTTATCAACTAGCCATATTGTAGTCT 57.851 33.333 0.00 0.00 40.69 3.24
773 782 9.765795 GTTATCAACTAGCCATATTGTAGTCTT 57.234 33.333 0.00 0.00 0.00 3.01
776 785 9.935241 ATCAACTAGCCATATTGTAGTCTTATG 57.065 33.333 0.00 0.00 0.00 1.90
777 786 9.143155 TCAACTAGCCATATTGTAGTCTTATGA 57.857 33.333 0.00 0.00 0.00 2.15
778 787 9.764363 CAACTAGCCATATTGTAGTCTTATGAA 57.236 33.333 0.00 0.00 0.00 2.57
809 818 3.130160 GAAGCCCCTCAGCAAGCG 61.130 66.667 0.00 0.00 34.23 4.68
810 819 3.909086 GAAGCCCCTCAGCAAGCGT 62.909 63.158 0.00 0.00 34.23 5.07
870 879 1.376553 GGACCTTGCTGCCAGTCTC 60.377 63.158 11.80 1.83 0.00 3.36
1038 1047 6.017026 TGTGTGGTCGTTTGCTTTATTTATCA 60.017 34.615 0.00 0.00 0.00 2.15
1472 1482 5.676811 ACCAGATTGATAATTCCCCTTACCT 59.323 40.000 0.00 0.00 0.00 3.08
1802 1812 2.560105 TGATCTCAGACACTGACACTGG 59.440 50.000 0.00 0.00 35.39 4.00
1882 1898 0.462581 GCGTGATCCTGAAGCCATGA 60.463 55.000 0.00 0.00 0.00 3.07
2325 2341 3.959535 ATGGCGATTGTCACCATTTTT 57.040 38.095 0.00 0.00 35.93 1.94
2446 2462 2.950874 GCTGTTAGGCTCTGGAGGACTA 60.951 54.545 0.00 0.00 0.00 2.59
2736 2752 5.163581 CCCTTCAAAGAATTACTCATGGCTG 60.164 44.000 0.00 0.00 0.00 4.85
3129 3145 4.637977 GGGTTCCTGACATCATTCTCTTTC 59.362 45.833 0.00 0.00 0.00 2.62
3147 3163 5.909477 TCTTTCGTTCACTACCTTTTCTCA 58.091 37.500 0.00 0.00 0.00 3.27
3168 3184 6.705825 TCTCAAACGTCAAGATTGATTGAAGA 59.294 34.615 8.92 7.74 40.19 2.87
3170 3186 5.613358 AACGTCAAGATTGATTGAAGACC 57.387 39.130 8.92 0.00 40.72 3.85
3171 3187 4.899502 ACGTCAAGATTGATTGAAGACCT 58.100 39.130 8.92 0.00 40.72 3.85
3172 3188 5.308825 ACGTCAAGATTGATTGAAGACCTT 58.691 37.500 8.92 0.00 40.72 3.50
3173 3189 6.464222 ACGTCAAGATTGATTGAAGACCTTA 58.536 36.000 8.92 0.00 40.72 2.69
3174 3190 7.106239 ACGTCAAGATTGATTGAAGACCTTAT 58.894 34.615 8.92 0.00 40.72 1.73
3175 3191 7.278868 ACGTCAAGATTGATTGAAGACCTTATC 59.721 37.037 8.92 0.00 40.72 1.75
3176 3192 7.493971 CGTCAAGATTGATTGAAGACCTTATCT 59.506 37.037 0.00 0.00 40.72 1.98
3177 3193 9.171877 GTCAAGATTGATTGAAGACCTTATCTT 57.828 33.333 0.00 0.00 44.08 2.40
3178 3194 9.170734 TCAAGATTGATTGAAGACCTTATCTTG 57.829 33.333 16.76 16.76 44.35 3.02
3193 3209 5.832060 CCTTATCTTGCAAATCTCCAAGGAT 59.168 40.000 0.00 0.00 39.07 3.24
3212 3228 4.456911 AGGATTGTACACAGTGCTTTGATG 59.543 41.667 0.00 0.00 30.63 3.07
3213 3229 4.216257 GGATTGTACACAGTGCTTTGATGT 59.784 41.667 0.00 0.00 0.00 3.06
3214 3230 5.278463 GGATTGTACACAGTGCTTTGATGTT 60.278 40.000 0.00 0.00 0.00 2.71
3215 3231 5.574891 TTGTACACAGTGCTTTGATGTTT 57.425 34.783 0.00 0.00 0.00 2.83
3216 3232 4.919206 TGTACACAGTGCTTTGATGTTTG 58.081 39.130 0.00 0.00 0.00 2.93
3217 3233 4.637977 TGTACACAGTGCTTTGATGTTTGA 59.362 37.500 0.00 0.00 0.00 2.69
3218 3234 4.924305 ACACAGTGCTTTGATGTTTGAT 57.076 36.364 0.00 0.00 0.00 2.57
3224 3240 2.231964 TGCTTTGATGTTTGATCTGGCC 59.768 45.455 0.00 0.00 0.00 5.36
3226 3242 3.675228 GCTTTGATGTTTGATCTGGCCTG 60.675 47.826 3.32 2.92 0.00 4.85
3387 3405 3.247442 ACATTCGTTGATGCAAATGCTG 58.753 40.909 6.97 0.00 42.66 4.41
3394 3413 4.556135 CGTTGATGCAAATGCTGTCTTAAG 59.444 41.667 6.97 0.00 42.66 1.85
3398 3417 4.604843 TGCAAATGCTGTCTTAAGATCG 57.395 40.909 8.75 4.15 42.66 3.69
3445 3465 2.030363 TGTGCGATTGTTGGTTCCATTC 60.030 45.455 0.00 0.00 0.00 2.67
3460 3480 5.047731 GGTTCCATTCTTCTCTTTTCCAAGG 60.048 44.000 0.00 0.00 0.00 3.61
3472 3492 5.701224 TCTTTTCCAAGGTAGGTTTGTCAT 58.299 37.500 0.00 0.00 0.00 3.06
3559 3580 2.860136 GTTTGTGCTTTTCTGACTTGCC 59.140 45.455 0.00 0.00 0.00 4.52
3741 3762 0.398318 AGGTTTGCTCCTCTGTCCAC 59.602 55.000 0.00 0.00 31.32 4.02
3778 3799 8.292448 TGAGTTAAAGTTGATTCTGAAATCTGC 58.708 33.333 0.00 0.00 41.63 4.26
3846 3869 4.084066 GCATATCGCACCATAATTTCGACA 60.084 41.667 0.00 0.00 41.79 4.35
3986 4109 7.365741 CAGATATTGCCTAGTTATTTGCTTGG 58.634 38.462 0.00 0.00 33.14 3.61
3998 4121 7.739825 AGTTATTTGCTTGGATCTAGAGCATA 58.260 34.615 10.68 12.35 44.95 3.14
4005 4128 5.279406 GCTTGGATCTAGAGCATATCAGTGT 60.279 44.000 10.68 0.00 36.45 3.55
4128 4255 5.587289 TGCCTTACAAAAAGAACATGTGAC 58.413 37.500 0.00 0.00 0.00 3.67
4132 4259 4.695217 ACAAAAAGAACATGTGACGTGT 57.305 36.364 4.28 4.28 0.00 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 105 2.642807 AGATTGAAACGGGGAGGAGAAA 59.357 45.455 0.00 0.00 0.00 2.52
145 146 2.737830 GCCGCCCCAGATCTAGAC 59.262 66.667 0.00 0.00 0.00 2.59
146 147 2.524394 GGCCGCCCCAGATCTAGA 60.524 66.667 0.00 0.00 0.00 2.43
276 277 0.748729 CTCGGCTCGACCCTAGAACT 60.749 60.000 0.00 0.00 33.26 3.01
277 278 1.728672 CTCGGCTCGACCCTAGAAC 59.271 63.158 0.00 0.00 33.26 3.01
332 333 4.627058 TCAGCGACAAATCTTGAACAGTA 58.373 39.130 0.00 0.00 0.00 2.74
405 406 2.799562 CGCGAGTTAGAAGCATGGATGA 60.800 50.000 0.00 0.00 0.00 2.92
547 552 8.773033 AGAGAATAGAAATAAAATGCCCATGT 57.227 30.769 0.00 0.00 0.00 3.21
720 729 7.596621 TCGATATTTCTCTGTAAGCAGCATAAG 59.403 37.037 0.00 0.00 42.29 1.73
721 730 7.433680 TCGATATTTCTCTGTAAGCAGCATAA 58.566 34.615 0.00 0.00 42.29 1.90
722 731 6.981722 TCGATATTTCTCTGTAAGCAGCATA 58.018 36.000 0.00 0.00 42.29 3.14
723 732 5.847304 TCGATATTTCTCTGTAAGCAGCAT 58.153 37.500 0.00 0.00 42.29 3.79
724 733 5.163509 ACTCGATATTTCTCTGTAAGCAGCA 60.164 40.000 0.00 0.00 42.29 4.41
725 734 5.285651 ACTCGATATTTCTCTGTAAGCAGC 58.714 41.667 0.00 0.00 42.29 5.25
745 754 9.413048 GACTACAATATGGCTAGTTGATAACTC 57.587 37.037 5.22 0.00 41.77 3.01
772 781 6.101332 GCTTCCATTGCTCACAAATTCATAA 58.899 36.000 0.00 0.00 39.77 1.90
773 782 5.394443 GGCTTCCATTGCTCACAAATTCATA 60.394 40.000 0.00 0.00 39.77 2.15
774 783 4.501071 GCTTCCATTGCTCACAAATTCAT 58.499 39.130 0.00 0.00 39.77 2.57
775 784 3.306225 GGCTTCCATTGCTCACAAATTCA 60.306 43.478 0.00 0.00 39.77 2.57
776 785 3.256558 GGCTTCCATTGCTCACAAATTC 58.743 45.455 0.00 0.00 39.77 2.17
777 786 2.027837 GGGCTTCCATTGCTCACAAATT 60.028 45.455 0.00 0.00 39.77 1.82
778 787 1.551883 GGGCTTCCATTGCTCACAAAT 59.448 47.619 0.00 0.00 39.77 2.32
779 788 0.968405 GGGCTTCCATTGCTCACAAA 59.032 50.000 0.00 0.00 39.77 2.83
786 795 2.421399 GCTGAGGGGCTTCCATTGC 61.421 63.158 0.00 0.00 38.24 3.56
809 818 2.359850 TGGCAGGCCAATCACGAC 60.360 61.111 11.25 0.00 44.12 4.34
870 879 7.928307 TCAAGGAGGATCAAAGAGTAAAATG 57.072 36.000 0.00 0.00 36.25 2.32
902 911 2.294791 CACAAAACACGCCCAGGATAAA 59.705 45.455 0.00 0.00 0.00 1.40
1472 1482 6.807720 CGATTCATTGACATTGACATGGAAAA 59.192 34.615 0.00 0.00 34.27 2.29
1882 1898 5.291128 CCTTTTCATACATCGTAAGCTTCGT 59.709 40.000 0.00 0.00 37.18 3.85
2325 2341 3.390639 ACATGAATCCAAAGGTGGCAAAA 59.609 39.130 0.00 0.00 45.54 2.44
2446 2462 5.492524 TCCATCCCTCAGAAGTTCCTTTTAT 59.507 40.000 0.00 0.00 0.00 1.40
2736 2752 3.019564 AGTTCCAGCACCAAATATGAGC 58.980 45.455 0.00 0.00 0.00 4.26
3129 3145 4.269363 ACGTTTGAGAAAAGGTAGTGAACG 59.731 41.667 0.00 0.00 41.91 3.95
3147 3163 5.765182 AGGTCTTCAATCAATCTTGACGTTT 59.235 36.000 0.00 0.00 40.49 3.60
3176 3192 5.048083 GTGTACAATCCTTGGAGATTTGCAA 60.048 40.000 0.00 0.00 34.19 4.08
3177 3193 4.458989 GTGTACAATCCTTGGAGATTTGCA 59.541 41.667 0.00 0.00 34.19 4.08
3178 3194 4.458989 TGTGTACAATCCTTGGAGATTTGC 59.541 41.667 0.00 0.00 34.19 3.68
3179 3195 5.707298 ACTGTGTACAATCCTTGGAGATTTG 59.293 40.000 0.00 0.00 34.19 2.32
3180 3196 5.707298 CACTGTGTACAATCCTTGGAGATTT 59.293 40.000 0.00 0.00 34.19 2.17
3181 3197 5.248640 CACTGTGTACAATCCTTGGAGATT 58.751 41.667 0.00 0.00 36.92 2.40
3183 3199 3.557054 GCACTGTGTACAATCCTTGGAGA 60.557 47.826 9.86 0.00 34.12 3.71
3184 3200 2.744202 GCACTGTGTACAATCCTTGGAG 59.256 50.000 9.86 0.00 34.12 3.86
3185 3201 2.371841 AGCACTGTGTACAATCCTTGGA 59.628 45.455 9.86 0.00 34.12 3.53
3186 3202 2.783135 AGCACTGTGTACAATCCTTGG 58.217 47.619 9.86 0.00 34.12 3.61
3193 3209 5.124617 TCAAACATCAAAGCACTGTGTACAA 59.875 36.000 9.86 0.00 0.00 2.41
3212 3228 1.467920 CTTCCCAGGCCAGATCAAAC 58.532 55.000 5.01 0.00 0.00 2.93
3213 3229 0.332632 CCTTCCCAGGCCAGATCAAA 59.667 55.000 5.01 0.00 31.53 2.69
3214 3230 2.001803 CCTTCCCAGGCCAGATCAA 58.998 57.895 5.01 0.00 31.53 2.57
3215 3231 3.745546 CCTTCCCAGGCCAGATCA 58.254 61.111 5.01 0.00 31.53 2.92
3226 3242 1.146263 CCGTGTAGATGGCCTTCCC 59.854 63.158 14.77 6.95 0.00 3.97
3387 3405 5.795441 GTGGCAAAATTCACGATCTTAAGAC 59.205 40.000 7.48 1.32 0.00 3.01
3398 3417 2.393764 CAAGGACGTGGCAAAATTCAC 58.606 47.619 0.00 0.00 0.00 3.18
3429 3448 6.581171 AAGAGAAGAATGGAACCAACAATC 57.419 37.500 0.00 0.00 0.00 2.67
3445 3465 5.828328 ACAAACCTACCTTGGAAAAGAGAAG 59.172 40.000 0.00 0.00 0.00 2.85
3460 3480 7.881775 AATAAATCTCCCATGACAAACCTAC 57.118 36.000 0.00 0.00 0.00 3.18
3472 3492 9.288576 CACTGCATAGATAAAATAAATCTCCCA 57.711 33.333 0.00 0.00 35.36 4.37
3559 3580 6.543465 TGACATACAGAATCTTGGGCAAATAG 59.457 38.462 0.00 0.00 0.00 1.73
3778 3799 7.678947 ACTTCAGAATAATGGAACTGTCTTG 57.321 36.000 0.00 0.00 0.00 3.02
3846 3869 1.279271 GGGCGATATGGGCATAGAACT 59.721 52.381 13.23 0.00 0.00 3.01
3880 3903 3.947196 ACATTATGCATCAGCGAAAAGGA 59.053 39.130 0.19 0.00 46.23 3.36
3998 4121 6.476378 AGTAGCCAACAAAGATTACACTGAT 58.524 36.000 0.00 0.00 0.00 2.90
4043 4166 5.106436 GCACAAATGGTTTACTAGTACCACC 60.106 44.000 17.88 18.10 46.50 4.61
4046 4173 6.812879 AAGCACAAATGGTTTACTAGTACC 57.187 37.500 0.91 4.90 44.10 3.34
4047 4174 7.148356 GGGTAAGCACAAATGGTTTACTAGTAC 60.148 40.741 0.91 0.00 44.10 2.73
4048 4175 6.880529 GGGTAAGCACAAATGGTTTACTAGTA 59.119 38.462 0.00 0.00 44.10 1.82


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

AutoCloner maintained by Alex Coulton.