Multiple sequence alignment - TraesCS7B01G223900

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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 TraesCS7B01G223900 chr7B 100.000 2966 0 0 1 2966 423548407 423551372 0.000000e+00 5478
1 TraesCS7B01G223900 chr7D 94.818 2991 79 23 1 2966 409162020 409164959 0.000000e+00 4595
2 TraesCS7B01G223900 chr7A 95.011 2726 50 23 291 2966 469356415 469359104 0.000000e+00 4202
3 TraesCS7B01G223900 chr7A 89.456 294 28 2 1 294 469353937 469354227 4.670000e-98 368


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 TraesCS7B01G223900 chr7B 423548407 423551372 2965 False 5478 5478 100.0000 1 2966 1 chr7B.!!$F1 2965
1 TraesCS7B01G223900 chr7D 409162020 409164959 2939 False 4595 4595 94.8180 1 2966 1 chr7D.!!$F1 2965
2 TraesCS7B01G223900 chr7A 469353937 469359104 5167 False 2285 4202 92.2335 1 2966 2 chr7A.!!$F1 2965

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
723 2917 0.038251 CGAGCTGCTTACCTCACACA 60.038 55.0 2.53 0.0 0.0 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2085 4303 0.168568 GAAGAAGAAGCAGCAGCAGC 59.831 55.0 3.17 0.46 45.49 5.25 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
61 62 5.177511 CCATGCAGTTAACTCCATGTATACG 59.822 44.000 29.15 15.35 39.82 3.06
63 64 4.403113 TGCAGTTAACTCCATGTATACGGA 59.597 41.667 4.77 0.00 0.00 4.69
138 139 5.245301 GGCGGGCCCTAATTTTAGATTTTAT 59.755 40.000 22.43 0.00 32.47 1.40
242 243 0.604243 TGGTCGACCCAAATGAACGG 60.604 55.000 31.19 0.00 41.50 4.44
268 269 3.383761 GGAAAAGACGGACGTCAGTTTA 58.616 45.455 22.15 0.00 46.76 2.01
274 275 1.334054 CGGACGTCAGTTTAAGGTCG 58.666 55.000 18.91 3.45 33.44 4.79
278 279 0.788391 CGTCAGTTTAAGGTCGTGCC 59.212 55.000 0.00 0.00 37.58 5.01
289 290 1.966451 GTCGTGCCTTGGAGTTGGG 60.966 63.158 0.00 0.00 0.00 4.12
305 2497 0.714180 TGGGCTAACAGAGGTAGGGA 59.286 55.000 0.00 0.00 0.00 4.20
340 2534 4.097418 CAAGAAGGGAAGGTAGAGGAGAA 58.903 47.826 0.00 0.00 0.00 2.87
394 2588 1.926511 GATGTGTGAAAGCCTGCGGG 61.927 60.000 7.41 7.41 0.00 6.13
518 2712 6.270695 TCATCATCATTATTCTAGTGCTCCCA 59.729 38.462 0.00 0.00 0.00 4.37
647 2841 5.135383 CCATCAGCCATAAATTCTTCTCCA 58.865 41.667 0.00 0.00 0.00 3.86
723 2917 0.038251 CGAGCTGCTTACCTCACACA 60.038 55.000 2.53 0.00 0.00 3.72
793 2987 0.684535 GGCTAGCCTTCTCCTCCATC 59.315 60.000 27.17 0.00 0.00 3.51
842 3040 1.331214 CTCATGGGCTCTCTCTCTCC 58.669 60.000 0.00 0.00 0.00 3.71
864 3074 3.133362 CCTCTCTCTCTCGTGTAGGTAGT 59.867 52.174 0.00 0.00 0.00 2.73
865 3075 4.341806 CCTCTCTCTCTCGTGTAGGTAGTA 59.658 50.000 0.00 0.00 0.00 1.82
866 3076 5.508489 CCTCTCTCTCTCGTGTAGGTAGTAG 60.508 52.000 0.00 0.00 0.00 2.57
931 3141 4.146075 GCTCAGCTCAGCTCGGCT 62.146 66.667 0.67 4.31 36.40 5.52
944 3154 2.405143 TCGGCTCATCGTCGATCTT 58.595 52.632 4.34 0.00 46.20 2.40
956 3166 2.538861 CGTCGATCTTCGTCTAGCTACA 59.461 50.000 0.00 0.00 41.35 2.74
1095 3305 2.232298 CTCTGCTCTTCGACCACCCC 62.232 65.000 0.00 0.00 0.00 4.95
1098 3308 2.663196 CTCTTCGACCACCCCACC 59.337 66.667 0.00 0.00 0.00 4.61
1099 3309 2.926242 TCTTCGACCACCCCACCC 60.926 66.667 0.00 0.00 0.00 4.61
1100 3310 4.029809 CTTCGACCACCCCACCCC 62.030 72.222 0.00 0.00 0.00 4.95
1101 3311 4.902258 TTCGACCACCCCACCCCA 62.902 66.667 0.00 0.00 0.00 4.96
1102 3312 4.902258 TCGACCACCCCACCCCAA 62.902 66.667 0.00 0.00 0.00 4.12
1103 3313 4.653888 CGACCACCCCACCCCAAC 62.654 72.222 0.00 0.00 0.00 3.77
1104 3314 3.503839 GACCACCCCACCCCAACA 61.504 66.667 0.00 0.00 0.00 3.33
1105 3315 3.507377 GACCACCCCACCCCAACAG 62.507 68.421 0.00 0.00 0.00 3.16
1106 3316 4.299796 CCACCCCACCCCAACAGG 62.300 72.222 0.00 0.00 0.00 4.00
1173 3383 2.780693 CCTCCTCCTCCTCCACCA 59.219 66.667 0.00 0.00 0.00 4.17
1272 3482 3.966543 CCTCACCACCACCCCCAC 61.967 72.222 0.00 0.00 0.00 4.61
1990 4200 0.179134 TAAAGAAGAGCGAGCGAGCC 60.179 55.000 2.87 0.00 38.01 4.70
2085 4303 6.677781 TGATTTAATTTCCTCCTAACGCTG 57.322 37.500 0.00 0.00 0.00 5.18
2088 4306 2.029838 ATTTCCTCCTAACGCTGCTG 57.970 50.000 0.00 0.00 0.00 4.41
2091 4309 1.812922 CCTCCTAACGCTGCTGCTG 60.813 63.158 14.03 9.56 36.97 4.41
2094 4312 2.747822 CCTAACGCTGCTGCTGCTG 61.748 63.158 25.43 20.66 40.48 4.41
2232 4468 6.338214 TGTGATCTATCTAGCTTCATGGTC 57.662 41.667 0.00 0.00 0.00 4.02
2245 4481 5.047802 AGCTTCATGGTCAATTTTGTACTGG 60.048 40.000 0.00 0.00 0.00 4.00
2350 4586 6.433404 ACTGCTACACATACACAGTACTAGTT 59.567 38.462 0.00 0.00 39.69 2.24
2432 4668 1.200020 GCTTGCATGTTGACCACTACC 59.800 52.381 1.14 0.00 0.00 3.18
2464 4700 2.418471 GGCACTGGTTCATGAGAGAGAG 60.418 54.545 0.00 0.00 0.00 3.20
2465 4701 2.495270 GCACTGGTTCATGAGAGAGAGA 59.505 50.000 0.00 0.00 0.00 3.10
2466 4702 3.429272 GCACTGGTTCATGAGAGAGAGAG 60.429 52.174 0.00 0.00 0.00 3.20
2467 4703 4.015764 CACTGGTTCATGAGAGAGAGAGA 58.984 47.826 0.00 0.00 0.00 3.10
2546 4806 5.816258 AGTTTGTCATGCTGAGATCATAGTG 59.184 40.000 0.00 0.00 0.00 2.74
2626 4886 7.309499 GGAGTGAATAAAAGAGAGAGACAGACA 60.309 40.741 0.00 0.00 0.00 3.41
2627 4887 7.601856 AGTGAATAAAAGAGAGAGACAGACAG 58.398 38.462 0.00 0.00 0.00 3.51
2809 5071 2.376855 AGTAAAGAAAGGAGGCTGGCTT 59.623 45.455 4.82 0.00 0.00 4.35
2810 5072 2.388526 AAAGAAAGGAGGCTGGCTTT 57.611 45.000 4.82 0.00 0.00 3.51
2811 5073 1.916506 AAGAAAGGAGGCTGGCTTTC 58.083 50.000 4.82 5.61 36.42 2.62
2812 5074 0.322008 AGAAAGGAGGCTGGCTTTCG 60.322 55.000 4.82 0.00 39.82 3.46
2813 5075 0.606673 GAAAGGAGGCTGGCTTTCGT 60.607 55.000 4.82 0.00 0.00 3.85
2814 5076 0.178990 AAAGGAGGCTGGCTTTCGTT 60.179 50.000 4.82 3.29 0.00 3.85
2815 5077 0.890996 AAGGAGGCTGGCTTTCGTTG 60.891 55.000 4.82 0.00 0.00 4.10
2816 5078 2.335712 GGAGGCTGGCTTTCGTTGG 61.336 63.158 4.82 0.00 0.00 3.77
2817 5079 1.302511 GAGGCTGGCTTTCGTTGGA 60.303 57.895 4.82 0.00 0.00 3.53
2818 5080 1.301677 GAGGCTGGCTTTCGTTGGAG 61.302 60.000 4.82 0.00 0.00 3.86
2819 5081 1.302511 GGCTGGCTTTCGTTGGAGA 60.303 57.895 0.00 0.00 0.00 3.71
2820 5082 1.301677 GGCTGGCTTTCGTTGGAGAG 61.302 60.000 0.00 0.00 0.00 3.20
2821 5083 0.603975 GCTGGCTTTCGTTGGAGAGT 60.604 55.000 0.00 0.00 0.00 3.24
2822 5084 1.884235 CTGGCTTTCGTTGGAGAGTT 58.116 50.000 0.00 0.00 0.00 3.01
2823 5085 1.801178 CTGGCTTTCGTTGGAGAGTTC 59.199 52.381 0.00 0.00 0.00 3.01
2824 5086 1.157585 GGCTTTCGTTGGAGAGTTCC 58.842 55.000 0.00 0.00 44.31 3.62
2825 5087 1.157585 GCTTTCGTTGGAGAGTTCCC 58.842 55.000 0.00 0.00 43.33 3.97
2826 5088 1.542547 GCTTTCGTTGGAGAGTTCCCA 60.543 52.381 0.00 0.00 43.33 4.37
2827 5089 2.417719 CTTTCGTTGGAGAGTTCCCAG 58.582 52.381 0.00 0.00 43.33 4.45
2828 5090 1.712056 TTCGTTGGAGAGTTCCCAGA 58.288 50.000 0.00 0.00 43.33 3.86
2829 5091 1.257743 TCGTTGGAGAGTTCCCAGAG 58.742 55.000 0.00 0.00 43.33 3.35
2830 5092 1.203013 TCGTTGGAGAGTTCCCAGAGA 60.203 52.381 0.00 0.00 43.33 3.10
2962 5249 2.836262 ACGTCCTCTCCAGTATACTCG 58.164 52.381 1.26 3.68 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 0.250338 GGGGAAGAACGTGCAGACTT 60.250 55.000 0.00 0.00 0.00 3.01
44 45 4.293415 CGGTCCGTATACATGGAGTTAAC 58.707 47.826 2.08 0.00 40.67 2.01
61 62 4.767255 CCAGAGTGCCAGCGGTCC 62.767 72.222 0.00 0.00 0.00 4.46
171 172 4.715523 GGCTAGTGCGCCCAACCA 62.716 66.667 4.18 0.00 44.41 3.67
238 239 1.141455 TCCGTCTTTTCCCTTTCCGTT 59.859 47.619 0.00 0.00 0.00 4.44
242 243 1.797046 GACGTCCGTCTTTTCCCTTTC 59.203 52.381 12.31 0.00 41.57 2.62
278 279 2.616510 CCTCTGTTAGCCCAACTCCAAG 60.617 54.545 1.01 0.00 38.05 3.61
289 290 3.367321 ACTCTTCCCTACCTCTGTTAGC 58.633 50.000 0.00 0.00 0.00 3.09
305 2497 3.652869 TCCCTTCTTGGTCATCAACTCTT 59.347 43.478 0.00 0.00 0.00 2.85
340 2534 5.101529 TCCTTCTCTTTCCCTTGTATCCTT 58.898 41.667 0.00 0.00 0.00 3.36
451 2645 4.093011 CAGGAGGAAGAAGAAAGAGGAGA 58.907 47.826 0.00 0.00 0.00 3.71
518 2712 2.945080 ATCTGGCAATGGTGATCGAT 57.055 45.000 0.00 0.00 0.00 3.59
723 2917 4.384647 GGCTGGTAGAAGAAGATGATGGTT 60.385 45.833 0.00 0.00 0.00 3.67
793 2987 5.251700 ACATAAGGGATGGCTTTATAGGAGG 59.748 44.000 0.00 0.00 40.18 4.30
842 3040 2.702592 ACCTACACGAGAGAGAGAGG 57.297 55.000 0.00 0.00 35.64 3.69
864 3074 3.197766 CCAAAGTGTGTCCCTATGAGCTA 59.802 47.826 0.00 0.00 0.00 3.32
865 3075 2.026822 CCAAAGTGTGTCCCTATGAGCT 60.027 50.000 0.00 0.00 0.00 4.09
866 3076 2.027192 TCCAAAGTGTGTCCCTATGAGC 60.027 50.000 0.00 0.00 0.00 4.26
929 3139 1.003331 AGACGAAGATCGACGATGAGC 60.003 52.381 16.49 0.52 43.74 4.26
931 3141 2.221286 GCTAGACGAAGATCGACGATGA 59.779 50.000 16.49 0.00 43.74 2.92
944 3154 6.183360 TGGAGTAAGTAGATGTAGCTAGACGA 60.183 42.308 0.00 0.00 0.00 4.20
956 3166 4.698304 GCGAGCTAGATGGAGTAAGTAGAT 59.302 45.833 0.00 0.00 0.00 1.98
1095 3305 2.917227 GTTGGGCCTGTTGGGGTG 60.917 66.667 4.53 0.00 35.12 4.61
1098 3308 2.283173 GGAGTTGGGCCTGTTGGG 60.283 66.667 4.53 0.00 38.36 4.12
1099 3309 2.672996 CGGAGTTGGGCCTGTTGG 60.673 66.667 4.53 0.00 0.00 3.77
1100 3310 3.365265 GCGGAGTTGGGCCTGTTG 61.365 66.667 4.53 0.00 0.00 3.33
1101 3311 4.660938 GGCGGAGTTGGGCCTGTT 62.661 66.667 4.53 0.00 45.93 3.16
1173 3383 1.352017 TGCTGATGGTGTTGATGAGGT 59.648 47.619 0.00 0.00 0.00 3.85
1272 3482 0.972983 AGTCGAGGTGGTGGAGATGG 60.973 60.000 0.00 0.00 0.00 3.51
1371 3581 2.841988 GAGCCCTCCTCCATCGCT 60.842 66.667 0.00 0.00 34.35 4.93
1449 3659 1.542030 GCGATCCGGTACATCATCTCT 59.458 52.381 0.00 0.00 0.00 3.10
1473 3683 1.146041 GATGTCCACCGGCTGCATA 59.854 57.895 0.00 0.00 0.00 3.14
1990 4200 1.275666 TCCATGGCCTATATGGGACG 58.724 55.000 18.12 0.00 44.18 4.79
2004 4222 5.251468 TCCATCCCTAGTTAATCCATCCATG 59.749 44.000 0.00 0.00 0.00 3.66
2085 4303 0.168568 GAAGAAGAAGCAGCAGCAGC 59.831 55.000 3.17 0.46 45.49 5.25
2088 4306 2.425539 AGAAGAAGAAGAAGCAGCAGC 58.574 47.619 0.00 0.00 42.56 5.25
2091 4309 3.684305 GGAGAAGAAGAAGAAGAAGCAGC 59.316 47.826 0.00 0.00 0.00 5.25
2094 4312 4.154015 GCAAGGAGAAGAAGAAGAAGAAGC 59.846 45.833 0.00 0.00 0.00 3.86
2232 4468 7.257722 AGACAAGTTGAACCAGTACAAAATTG 58.742 34.615 10.54 0.00 34.31 2.32
2245 4481 4.305989 TGGCAAATGAGACAAGTTGAAC 57.694 40.909 10.54 3.37 0.00 3.18
2464 4700 4.968259 TGTAGTAGCATCTCTCTCCTCTC 58.032 47.826 0.00 0.00 0.00 3.20
2465 4701 5.104109 AGTTGTAGTAGCATCTCTCTCCTCT 60.104 44.000 0.00 0.00 0.00 3.69
2466 4702 5.130350 AGTTGTAGTAGCATCTCTCTCCTC 58.870 45.833 0.00 0.00 0.00 3.71
2467 4703 5.124036 AGTTGTAGTAGCATCTCTCTCCT 57.876 43.478 0.00 0.00 0.00 3.69
2546 4806 3.175929 GTGTGTGTGTTTGTTAACTGGC 58.824 45.455 7.22 0.00 35.24 4.85
2626 4886 7.423844 AAGGACAAACCAAAATTTTCTCTCT 57.576 32.000 0.00 0.00 42.04 3.10
2627 4887 8.492673 AAAAGGACAAACCAAAATTTTCTCTC 57.507 30.769 0.00 0.00 42.04 3.20
2809 5071 1.618837 CTCTGGGAACTCTCCAACGAA 59.381 52.381 0.00 0.00 44.51 3.85
2810 5072 1.203013 TCTCTGGGAACTCTCCAACGA 60.203 52.381 0.00 0.00 44.51 3.85
2811 5073 1.257743 TCTCTGGGAACTCTCCAACG 58.742 55.000 0.00 0.00 44.51 4.10
2812 5074 2.679349 GCATCTCTGGGAACTCTCCAAC 60.679 54.545 0.00 0.00 44.51 3.77
2813 5075 1.556911 GCATCTCTGGGAACTCTCCAA 59.443 52.381 0.00 0.00 44.51 3.53
2814 5076 1.198713 GCATCTCTGGGAACTCTCCA 58.801 55.000 0.00 0.00 44.51 3.86
2815 5077 1.198713 TGCATCTCTGGGAACTCTCC 58.801 55.000 0.00 0.00 41.59 3.71
2816 5078 3.006247 GTTTGCATCTCTGGGAACTCTC 58.994 50.000 0.00 0.00 0.00 3.20
2817 5079 2.290577 GGTTTGCATCTCTGGGAACTCT 60.291 50.000 0.00 0.00 0.00 3.24
2818 5080 2.087646 GGTTTGCATCTCTGGGAACTC 58.912 52.381 0.00 0.00 0.00 3.01
2819 5081 1.425066 TGGTTTGCATCTCTGGGAACT 59.575 47.619 0.00 0.00 0.00 3.01
2820 5082 1.909700 TGGTTTGCATCTCTGGGAAC 58.090 50.000 0.00 0.00 0.00 3.62
2821 5083 2.238521 GTTGGTTTGCATCTCTGGGAA 58.761 47.619 0.00 0.00 0.00 3.97
2822 5084 1.144708 TGTTGGTTTGCATCTCTGGGA 59.855 47.619 0.00 0.00 0.00 4.37
2823 5085 1.619654 TGTTGGTTTGCATCTCTGGG 58.380 50.000 0.00 0.00 0.00 4.45
2824 5086 2.288395 GGTTGTTGGTTTGCATCTCTGG 60.288 50.000 0.00 0.00 0.00 3.86
2825 5087 2.361757 TGGTTGTTGGTTTGCATCTCTG 59.638 45.455 0.00 0.00 0.00 3.35
2826 5088 2.665165 TGGTTGTTGGTTTGCATCTCT 58.335 42.857 0.00 0.00 0.00 3.10
2827 5089 3.665745 ATGGTTGTTGGTTTGCATCTC 57.334 42.857 0.00 0.00 0.00 2.75
2828 5090 3.387374 TCAATGGTTGTTGGTTTGCATCT 59.613 39.130 0.00 0.00 0.00 2.90
2829 5091 3.726607 TCAATGGTTGTTGGTTTGCATC 58.273 40.909 0.00 0.00 0.00 3.91
2830 5092 3.834489 TCAATGGTTGTTGGTTTGCAT 57.166 38.095 0.00 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.