Multiple sequence alignment - TraesCS1B01G222900

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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 TraesCS1B01G222900 chr1B 100.000 3104 0 0 1 3104 400421584 400418481 0.000000e+00 5733
1 TraesCS1B01G222900 chr1B 96.165 3103 115 4 2 3104 98648535 98651633 0.000000e+00 5068
2 TraesCS1B01G222900 chr1B 95.715 3104 132 1 1 3104 91435352 91432250 0.000000e+00 4994
3 TraesCS1B01G222900 chr1B 95.563 293 13 0 2812 3104 647409910 647410202 1.300000e-128 470
4 TraesCS1B01G222900 chr6B 95.935 3100 125 1 5 3104 692888675 692885577 0.000000e+00 5025
5 TraesCS1B01G222900 chr5B 95.662 3089 130 3 18 3104 419027037 419023951 0.000000e+00 4959
6 TraesCS1B01G222900 chr5B 95.451 2814 126 2 1 2814 230942009 230939198 0.000000e+00 4486
7 TraesCS1B01G222900 chr5B 96.246 293 11 0 2812 3104 92758939 92758647 6.020000e-132 481
8 TraesCS1B01G222900 chr2B 95.421 3101 132 5 1 3101 635822598 635825688 0.000000e+00 4931
9 TraesCS1B01G222900 chr4B 95.593 2814 120 3 1 2814 16600517 16597708 0.000000e+00 4506
10 TraesCS1B01G222900 chr4B 94.670 2814 146 3 1 2814 127613236 127610427 0.000000e+00 4362
11 TraesCS1B01G222900 chr7B 94.927 2819 142 1 1 2819 529757476 529760293 0.000000e+00 4412
12 TraesCS1B01G222900 chr4A 96.928 293 9 0 2812 3104 655929773 655929481 2.780000e-135 492
13 TraesCS1B01G222900 chr3B 95.222 293 14 0 2812 3104 746729923 746730215 6.060000e-127 464


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 TraesCS1B01G222900 chr1B 400418481 400421584 3103 True 5733 5733 100.000 1 3104 1 chr1B.!!$R2 3103
1 TraesCS1B01G222900 chr1B 98648535 98651633 3098 False 5068 5068 96.165 2 3104 1 chr1B.!!$F1 3102
2 TraesCS1B01G222900 chr1B 91432250 91435352 3102 True 4994 4994 95.715 1 3104 1 chr1B.!!$R1 3103
3 TraesCS1B01G222900 chr6B 692885577 692888675 3098 True 5025 5025 95.935 5 3104 1 chr6B.!!$R1 3099
4 TraesCS1B01G222900 chr5B 419023951 419027037 3086 True 4959 4959 95.662 18 3104 1 chr5B.!!$R3 3086
5 TraesCS1B01G222900 chr5B 230939198 230942009 2811 True 4486 4486 95.451 1 2814 1 chr5B.!!$R2 2813
6 TraesCS1B01G222900 chr2B 635822598 635825688 3090 False 4931 4931 95.421 1 3101 1 chr2B.!!$F1 3100
7 TraesCS1B01G222900 chr4B 16597708 16600517 2809 True 4506 4506 95.593 1 2814 1 chr4B.!!$R1 2813
8 TraesCS1B01G222900 chr4B 127610427 127613236 2809 True 4362 4362 94.670 1 2814 1 chr4B.!!$R2 2813
9 TraesCS1B01G222900 chr7B 529757476 529760293 2817 False 4412 4412 94.927 1 2819 1 chr7B.!!$F1 2818

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
905 908 0.109551 ACAGTGAGATCGTGCACTCG 60.11 55.0 16.19 2.27 43.06 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2360 2364 0.538287 GGGGCCATGGCTTATGAGTC 60.538 60.0 34.7 16.14 39.21 3.36 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
56 57 7.449086 TGGAAAACATTCCGGAAAATAGTAACT 59.551 33.333 23.08 0.00 44.02 2.24
116 117 6.128661 CGACGTTCATTCCTTTGTCATAGAAA 60.129 38.462 0.00 0.00 0.00 2.52
304 305 0.460311 GCCTCACGTAGCACCATAGT 59.540 55.000 0.00 0.00 0.00 2.12
320 321 5.815222 CACCATAGTAACGAATTGACATCCA 59.185 40.000 0.00 0.00 0.00 3.41
345 346 2.273370 TCACGTAACTTCATCTCCGC 57.727 50.000 0.00 0.00 0.00 5.54
586 589 2.166459 TGAAAACAATTGCCACGACCAA 59.834 40.909 5.05 0.00 0.00 3.67
621 624 3.724374 CCCGTGTGTCTGAGAGTTAAAA 58.276 45.455 0.00 0.00 0.00 1.52
813 816 5.592104 AGAAAAACCACGATCAAAAACCT 57.408 34.783 0.00 0.00 0.00 3.50
905 908 0.109551 ACAGTGAGATCGTGCACTCG 60.110 55.000 16.19 2.27 43.06 4.18
939 943 4.524053 CCCGCCCTTAAATTTAGACTTCT 58.476 43.478 0.00 0.00 0.00 2.85
1008 1012 2.099098 CACTCACTGTTCCCCACAAAAC 59.901 50.000 0.00 0.00 33.87 2.43
1036 1040 2.271940 CAGGAGGACGAACTGCTCT 58.728 57.895 2.63 0.00 37.01 4.09
1252 1256 1.241990 CCTCGTCCAACTCTCCGTCA 61.242 60.000 0.00 0.00 0.00 4.35
1254 1258 1.213013 CGTCCAACTCTCCGTCAGG 59.787 63.158 0.00 0.00 39.46 3.86
1273 1277 2.575279 AGGAAAGATCATCTGGTGCTGT 59.425 45.455 0.00 0.00 0.00 4.40
1344 1348 3.315949 GCCGACCCCAGGTACACA 61.316 66.667 0.00 0.00 35.25 3.72
1404 1408 1.381928 GCCACGTCGGACTGGAGATA 61.382 60.000 22.58 0.00 36.56 1.98
1412 1416 1.044611 GGACTGGAGATAGCCCACTC 58.955 60.000 0.00 0.00 0.00 3.51
1446 1450 0.044855 AGGAATGGAGGGTGCCTACT 59.955 55.000 0.00 0.00 34.99 2.57
1585 1589 1.153289 ACCATGAGGCACATCGAGC 60.153 57.895 0.00 0.00 37.07 5.03
1601 1605 2.560861 GCACGCGGCAAAAGATGA 59.439 55.556 12.47 0.00 43.97 2.92
1603 1607 0.863119 GCACGCGGCAAAAGATGATC 60.863 55.000 12.47 0.00 43.97 2.92
1734 1738 1.896465 GACTACTGAAGCAGGTGGTCT 59.104 52.381 0.00 0.00 35.51 3.85
1823 1827 3.311322 TCAAGACTACCGTTTGCTTGTTG 59.689 43.478 0.00 0.00 37.71 3.33
1917 1921 5.850557 TTATTTCCGATGCAATGTTGGAT 57.149 34.783 0.00 0.00 42.18 3.41
2196 2200 5.761234 TCCTTGCAAAACATTACTTACGTCT 59.239 36.000 0.00 0.00 0.00 4.18
2278 2282 0.188342 AACACCCATGGAGGCACTTT 59.812 50.000 15.22 0.00 41.55 2.66
2360 2364 2.347697 TGACTTCGAAGACACATCGG 57.652 50.000 31.08 2.81 40.59 4.18
2488 2492 0.108520 TTAGAATCACGTCCGTGCCC 60.109 55.000 14.64 6.43 45.04 5.36
3047 3051 2.092592 TCTGTCCATCTGGTAGCGTCTA 60.093 50.000 0.00 0.00 36.34 2.59
3051 3055 3.068307 GTCCATCTGGTAGCGTCTATTGT 59.932 47.826 0.00 0.00 36.34 2.71
3075 3079 1.095228 CGGACACACAACAGTGCCTT 61.095 55.000 0.00 0.00 43.23 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 2.499693 TGAGGATTGACAATAGGCGTCA 59.500 45.455 0.00 3.96 41.53 4.35
143 144 4.157105 GCATTCCGGGTTTTACAAGTGTAT 59.843 41.667 0.00 0.00 0.00 2.29
304 305 7.254286 CGTGATTACATGGATGTCAATTCGTTA 60.254 37.037 0.00 0.00 41.97 3.18
320 321 5.977725 CGGAGATGAAGTTACGTGATTACAT 59.022 40.000 0.00 0.00 0.00 2.29
345 346 4.415332 ACGGTGCTACGTGAGGCG 62.415 66.667 0.00 0.00 46.64 5.52
498 501 6.310467 TCTCGTTGTATAAGTGATGTGCTTTC 59.690 38.462 0.00 0.00 0.00 2.62
586 589 0.742990 CACGGGCGTGGTACATTCAT 60.743 55.000 0.00 0.00 44.52 2.57
621 624 0.538977 AGCATGCTTGAAGTGGCTGT 60.539 50.000 16.30 0.00 0.00 4.40
703 706 2.621338 GGAGATGATCGTTGTCTTGCA 58.379 47.619 0.00 0.00 0.00 4.08
786 789 9.465985 GGTTTTTGATCGTGGTTTTTCTTTATA 57.534 29.630 0.00 0.00 0.00 0.98
813 816 1.373059 TGCGGTTGTGCACATCCTA 59.627 52.632 33.43 23.54 40.62 2.94
833 836 1.001974 CGTGGTTTCATCTCCCTGACA 59.998 52.381 0.00 0.00 0.00 3.58
939 943 2.698274 TGTGGAAGACAAGTCTACAGCA 59.302 45.455 2.72 5.09 39.39 4.41
1008 1012 0.742281 CGTCCTCCTGCAACCTGATG 60.742 60.000 0.00 0.00 0.00 3.07
1036 1040 1.215173 CTTGGTGAATCCCATGGCCTA 59.785 52.381 6.09 0.00 33.60 3.93
1062 1066 4.051167 CCATGGGCCTGCACCTCA 62.051 66.667 2.85 0.00 0.00 3.86
1087 1091 2.557924 TGGTGTGGATCACTTGCAAATC 59.442 45.455 0.00 0.36 45.50 2.17
1168 1172 1.215382 CTCCGACGATCTTGTGGCA 59.785 57.895 0.00 0.00 0.00 4.92
1252 1256 2.575279 ACAGCACCAGATGATCTTTCCT 59.425 45.455 0.00 0.00 34.60 3.36
1254 1258 4.260170 AGAACAGCACCAGATGATCTTTC 58.740 43.478 0.00 0.00 39.83 2.62
1273 1277 1.841663 GCGGCGCTCAGTTGAAAGAA 61.842 55.000 26.86 0.00 0.00 2.52
1412 1416 0.530744 TTCCTTCTGGATGTCGACGG 59.469 55.000 11.62 3.22 42.81 4.79
1585 1589 0.447406 TGATCATCTTTTGCCGCGTG 59.553 50.000 4.92 0.00 0.00 5.34
1601 1605 3.304726 CCATATCTCGTACGCAGTGTGAT 60.305 47.826 11.24 9.13 45.73 3.06
1603 1607 2.032924 TCCATATCTCGTACGCAGTGTG 59.967 50.000 11.24 1.11 45.73 3.82
1734 1738 4.811969 TGTAGATACTTTTCTTGGCCGA 57.188 40.909 0.00 0.00 0.00 5.54
1962 1966 7.371159 GCTAATCATGTAGCATCTGTACTGTA 58.629 38.462 9.79 0.00 44.94 2.74
1988 1992 8.522830 ACAAAGTTATTAGTGCATGTGCTTTAT 58.477 29.630 6.55 0.00 42.66 1.40
1992 1996 5.335897 CCACAAAGTTATTAGTGCATGTGCT 60.336 40.000 6.55 0.00 42.66 4.40
2005 2009 2.420022 GACGCTGCATCCACAAAGTTAT 59.580 45.455 0.00 0.00 0.00 1.89
2196 2200 3.199946 AGTGTTCTTCTTTGAGGGTCACA 59.800 43.478 0.00 0.00 0.00 3.58
2278 2282 0.911769 CCATAGGAGTGGAGGCACAA 59.088 55.000 0.00 0.00 42.02 3.33
2360 2364 0.538287 GGGGCCATGGCTTATGAGTC 60.538 60.000 34.70 16.14 39.21 3.36
3047 3051 3.271729 TGTTGTGTGTCCGTGTTACAAT 58.728 40.909 0.00 0.00 34.27 2.71
3051 3055 2.272678 CACTGTTGTGTGTCCGTGTTA 58.727 47.619 0.00 0.00 39.24 2.41
3075 3079 3.128589 GGAGCAGTGTTGTGTTTCTTCAA 59.871 43.478 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.