Multiple sequence alignment - TraesCS3B01G275000

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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 TraesCS3B01G275000 chr3B 100.000 4972 0 0 644 5615 443803307 443808278 0.000000e+00 9182.0
1 TraesCS3B01G275000 chr3B 100.000 165 0 0 1 165 443802664 443802828 7.070000e-79 305.0
2 TraesCS3B01G275000 chr3B 74.344 686 157 17 3653 4330 82625646 82626320 1.990000e-69 274.0
3 TraesCS3B01G275000 chr3D 96.546 5038 82 29 644 5615 344337883 344342894 0.000000e+00 8255.0
4 TraesCS3B01G275000 chr3D 89.697 165 10 2 1 165 344337563 344337720 2.650000e-48 204.0
5 TraesCS3B01G275000 chr3A 94.149 5059 122 69 644 5615 458683103 458678132 0.000000e+00 7542.0
6 TraesCS3B01G275000 chr3A 74.355 620 149 10 3653 4267 64281568 64282182 7.220000e-64 255.0
7 TraesCS3B01G275000 chr3A 80.488 328 39 13 1386 1713 12525890 12525588 1.570000e-55 228.0
8 TraesCS3B01G275000 chr3A 84.831 178 6 9 2 165 458683425 458683255 5.820000e-35 159.0
9 TraesCS3B01G275000 chr1B 84.217 849 91 25 1217 2050 534298215 534299035 0.000000e+00 785.0
10 TraesCS3B01G275000 chr7A 85.417 528 62 5 1248 1769 33657522 33658040 8.280000e-148 534.0
11 TraesCS3B01G275000 chr7A 91.416 233 19 1 1815 2046 33658041 33658273 9.080000e-83 318.0
12 TraesCS3B01G275000 chr7B 84.888 536 60 12 1241 1769 622301295 622300774 6.450000e-144 521.0
13 TraesCS3B01G275000 chr7B 94.059 202 11 1 1815 2015 622300773 622300572 7.070000e-79 305.0
14 TraesCS3B01G275000 chr5A 78.582 691 139 8 3593 4277 374646543 374645856 1.110000e-121 448.0
15 TraesCS3B01G275000 chr5D 78.520 689 140 8 3593 4277 282152986 282152302 3.990000e-121 446.0
16 TraesCS3B01G275000 chr5B 77.971 690 145 6 3593 4277 320153339 320152652 5.200000e-115 425.0
17 TraesCS3B01G275000 chr4A 81.111 540 62 17 1241 1769 716835122 716834612 4.080000e-106 396.0
18 TraesCS3B01G275000 chr4A 89.431 246 17 3 1815 2051 716834611 716834366 9.140000e-78 302.0
19 TraesCS3B01G275000 chr6B 80.741 540 63 18 1241 1769 244561784 244562293 3.170000e-102 383.0
20 TraesCS3B01G275000 chr6B 92.437 238 17 1 1815 2051 244562294 244562531 6.970000e-89 339.0
21 TraesCS3B01G275000 chr6B 89.623 106 10 1 1815 1919 693888104 693887999 3.530000e-27 134.0
22 TraesCS3B01G275000 chr6B 88.608 79 7 1 1972 2050 693888012 693887936 1.670000e-15 95.3
23 TraesCS3B01G275000 chr4B 92.083 240 17 2 1815 2052 613388609 613388848 2.510000e-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 TraesCS3B01G275000 chr3B 443802664 443808278 5614 False 4743.5 9182 100.0000 1 5615 2 chr3B.!!$F2 5614
1 TraesCS3B01G275000 chr3B 82625646 82626320 674 False 274.0 274 74.3440 3653 4330 1 chr3B.!!$F1 677
2 TraesCS3B01G275000 chr3D 344337563 344342894 5331 False 4229.5 8255 93.1215 1 5615 2 chr3D.!!$F1 5614
3 TraesCS3B01G275000 chr3A 458678132 458683425 5293 True 3850.5 7542 89.4900 2 5615 2 chr3A.!!$R2 5613
4 TraesCS3B01G275000 chr3A 64281568 64282182 614 False 255.0 255 74.3550 3653 4267 1 chr3A.!!$F1 614
5 TraesCS3B01G275000 chr1B 534298215 534299035 820 False 785.0 785 84.2170 1217 2050 1 chr1B.!!$F1 833
6 TraesCS3B01G275000 chr7A 33657522 33658273 751 False 426.0 534 88.4165 1248 2046 2 chr7A.!!$F1 798
7 TraesCS3B01G275000 chr7B 622300572 622301295 723 True 413.0 521 89.4735 1241 2015 2 chr7B.!!$R1 774
8 TraesCS3B01G275000 chr5A 374645856 374646543 687 True 448.0 448 78.5820 3593 4277 1 chr5A.!!$R1 684
9 TraesCS3B01G275000 chr5D 282152302 282152986 684 True 446.0 446 78.5200 3593 4277 1 chr5D.!!$R1 684
10 TraesCS3B01G275000 chr5B 320152652 320153339 687 True 425.0 425 77.9710 3593 4277 1 chr5B.!!$R1 684
11 TraesCS3B01G275000 chr4A 716834366 716835122 756 True 349.0 396 85.2710 1241 2051 2 chr4A.!!$R1 810
12 TraesCS3B01G275000 chr6B 244561784 244562531 747 False 361.0 383 86.5890 1241 2051 2 chr6B.!!$F1 810

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
86 96 1.009675 CCGAACCGTATCCGTACCG 60.010 63.158 0.0 0.00 0.00 4.02 F
938 1002 1.130561 CCGTGCTTAGCTTTGGTTAGC 59.869 52.381 5.6 1.56 41.53 3.09 F
1701 1817 0.173708 AGACGTTGAATCTCTCCGGC 59.826 55.000 0.0 0.00 0.00 6.13 F
3114 3241 0.824109 TTCTGTCTGGTGCTATCCCG 59.176 55.000 0.0 0.00 0.00 5.14 F
3123 3250 0.249238 GTGCTATCCCGACAGAGCTG 60.249 60.000 0.0 0.00 35.89 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1181 1265 1.477558 GGGAGCAGAGAGAGAGAGAGG 60.478 61.905 0.00 0.0 0.00 3.69 R
2628 2755 0.538057 CCAAGTTGCTGAGCTTCCCA 60.538 55.000 5.83 0.0 0.00 4.37 R
3123 3250 1.583477 GAGCTTCTTTGCACCAGCC 59.417 57.895 0.00 0.0 41.13 4.85 R
4314 4444 0.034186 TGTGCATCTTCACCCATCCC 60.034 55.000 0.00 0.0 36.17 3.85 R
5068 5211 0.369931 TTTCGATCAACTGATGCGCG 59.630 50.000 0.00 0.0 34.37 6.86 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
69 79 1.208358 GAAACTAAACCACGGCGCC 59.792 57.895 19.07 19.07 0.00 6.53
82 92 4.860261 GCGCCGAACCGTATCCGT 62.860 66.667 0.00 0.00 0.00 4.69
83 93 2.715005 CGCCGAACCGTATCCGTA 59.285 61.111 0.00 0.00 0.00 4.02
84 94 1.655350 CGCCGAACCGTATCCGTAC 60.655 63.158 0.00 0.00 0.00 3.67
85 95 1.299392 GCCGAACCGTATCCGTACC 60.299 63.158 0.00 0.00 0.00 3.34
86 96 1.009675 CCGAACCGTATCCGTACCG 60.010 63.158 0.00 0.00 0.00 4.02
743 765 2.776913 CGACCTCGCTCCTCCTTCC 61.777 68.421 0.00 0.00 0.00 3.46
785 817 1.470098 CCAAAGCAGTCATTTCCTCCG 59.530 52.381 0.00 0.00 0.00 4.63
938 1002 1.130561 CCGTGCTTAGCTTTGGTTAGC 59.869 52.381 5.60 1.56 41.53 3.09
969 1033 1.763634 GCACCGCGGATTACTACTAC 58.236 55.000 35.90 0.00 0.00 2.73
970 1034 1.601412 GCACCGCGGATTACTACTACC 60.601 57.143 35.90 0.00 0.00 3.18
971 1035 1.677576 CACCGCGGATTACTACTACCA 59.322 52.381 35.90 0.00 0.00 3.25
977 1041 4.614946 GCGGATTACTACTACCACGATTT 58.385 43.478 0.00 0.00 0.00 2.17
1085 1149 2.036475 CCTCTCTCCTCTCTCTCTCTCG 59.964 59.091 0.00 0.00 0.00 4.04
1088 1152 1.837439 TCTCCTCTCTCTCTCTCGCTT 59.163 52.381 0.00 0.00 0.00 4.68
1089 1153 2.158957 TCTCCTCTCTCTCTCTCGCTTC 60.159 54.545 0.00 0.00 0.00 3.86
1090 1154 1.837439 TCCTCTCTCTCTCTCGCTTCT 59.163 52.381 0.00 0.00 0.00 2.85
1092 1156 2.614057 CCTCTCTCTCTCTCGCTTCTTC 59.386 54.545 0.00 0.00 0.00 2.87
1093 1157 3.535561 CTCTCTCTCTCTCGCTTCTTCT 58.464 50.000 0.00 0.00 0.00 2.85
1133 1217 2.941025 CCCCCACCACCACCATCT 60.941 66.667 0.00 0.00 0.00 2.90
1134 1218 2.677228 CCCCACCACCACCATCTC 59.323 66.667 0.00 0.00 0.00 2.75
1178 1262 1.133792 CCACTCTCTCCCTCCTCTCTC 60.134 61.905 0.00 0.00 0.00 3.20
1179 1263 1.133792 CACTCTCTCCCTCCTCTCTCC 60.134 61.905 0.00 0.00 0.00 3.71
1180 1264 1.275002 ACTCTCTCCCTCCTCTCTCCT 60.275 57.143 0.00 0.00 0.00 3.69
1181 1265 1.421646 CTCTCTCCCTCCTCTCTCCTC 59.578 61.905 0.00 0.00 0.00 3.71
1243 1327 0.461961 ATGGTCTCAAGGTAGAGCGC 59.538 55.000 0.00 0.00 45.03 5.92
1701 1817 0.173708 AGACGTTGAATCTCTCCGGC 59.826 55.000 0.00 0.00 0.00 6.13
2179 2306 2.759783 CACTTCAGTGGCTCCATCG 58.240 57.895 0.00 0.00 42.10 3.84
2592 2719 2.421952 GCTCAACTGGATATCCTTGGCA 60.422 50.000 22.35 0.84 36.82 4.92
2772 2899 1.401905 GGATCAATTCCACCGCAACTC 59.598 52.381 0.00 0.00 44.74 3.01
3114 3241 0.824109 TTCTGTCTGGTGCTATCCCG 59.176 55.000 0.00 0.00 0.00 5.14
3123 3250 0.249238 GTGCTATCCCGACAGAGCTG 60.249 60.000 0.00 0.00 35.89 4.24
4038 4168 3.575256 ACAACTGCATTCCACACATCATT 59.425 39.130 0.00 0.00 0.00 2.57
4098 4228 1.943730 ATCTGGAGGCGAGGGTCTCT 61.944 60.000 0.00 0.00 44.49 3.10
4314 4444 2.213499 GGCGAGGACCATAATCTTGTG 58.787 52.381 0.00 0.00 0.00 3.33
4350 4480 3.242706 TGCACACAAAGTTGAAGATCACG 60.243 43.478 0.00 0.00 0.00 4.35
4760 4899 4.927782 TCCCACGCAACGCAAGCT 62.928 61.111 0.00 0.00 45.62 3.74
4978 5121 1.541588 GTGGATTCTCTTGGGTGCAAC 59.458 52.381 0.00 0.00 0.00 4.17
5068 5211 2.412770 GCTGGCATTTTGTACAATGTGC 59.587 45.455 25.72 25.72 36.63 4.57
5102 5246 1.735018 TCGAAACATGGTACCATTGCG 59.265 47.619 25.25 21.61 33.90 4.85
5119 5263 1.995991 CGGATGCACGGTAGAAACG 59.004 57.895 0.00 0.00 37.36 3.60
5120 5264 0.457166 CGGATGCACGGTAGAAACGA 60.457 55.000 0.00 0.00 34.93 3.85
5121 5265 1.717194 GGATGCACGGTAGAAACGAA 58.283 50.000 0.00 0.00 34.93 3.85
5127 5271 2.610232 GCACGGTAGAAACGAAACCCTA 60.610 50.000 0.00 0.00 34.93 3.53
5128 5272 2.989166 CACGGTAGAAACGAAACCCTAC 59.011 50.000 0.00 0.00 34.93 3.18
5129 5273 2.029020 ACGGTAGAAACGAAACCCTACC 60.029 50.000 0.00 0.00 44.64 3.18
5131 5275 2.568956 GGTAGAAACGAAACCCTACCCT 59.431 50.000 0.00 0.00 43.17 4.34
5132 5276 2.853235 AGAAACGAAACCCTACCCTG 57.147 50.000 0.00 0.00 0.00 4.45
5133 5277 2.332117 AGAAACGAAACCCTACCCTGA 58.668 47.619 0.00 0.00 0.00 3.86
5134 5278 2.302157 AGAAACGAAACCCTACCCTGAG 59.698 50.000 0.00 0.00 0.00 3.35
5135 5279 0.323957 AACGAAACCCTACCCTGAGC 59.676 55.000 0.00 0.00 0.00 4.26
5136 5280 0.544595 ACGAAACCCTACCCTGAGCT 60.545 55.000 0.00 0.00 0.00 4.09
5137 5281 1.272872 ACGAAACCCTACCCTGAGCTA 60.273 52.381 0.00 0.00 0.00 3.32
5138 5282 1.409427 CGAAACCCTACCCTGAGCTAG 59.591 57.143 0.00 0.00 0.00 3.42
5319 5471 2.766925 ATGGCCTGTGTGTGGGTGT 61.767 57.895 3.32 0.00 0.00 4.16
5546 5715 2.607187 CTCGCCTTATTATACTGCCCG 58.393 52.381 0.00 0.00 0.00 6.13
5579 5754 1.250328 CATGGTGCTGTGTCCAATGT 58.750 50.000 0.00 0.00 37.27 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 45 1.732809 GTTTCTTCCAGCCTTCGCTAC 59.267 52.381 0.00 0.00 46.25 3.58
51 61 1.208358 GGCGCCGTGGTTTAGTTTC 59.792 57.895 12.58 0.00 0.00 2.78
80 90 6.910878 GAGATTTGCTTTTCTCTCCGGTACG 61.911 48.000 0.00 0.00 42.70 3.67
82 92 4.504858 GAGATTTGCTTTTCTCTCCGGTA 58.495 43.478 0.00 0.00 36.32 4.02
83 93 3.339141 GAGATTTGCTTTTCTCTCCGGT 58.661 45.455 0.00 0.00 36.32 5.28
84 94 2.680339 GGAGATTTGCTTTTCTCTCCGG 59.320 50.000 0.00 0.00 43.10 5.14
86 96 2.680339 CCGGAGATTTGCTTTTCTCTCC 59.320 50.000 0.00 7.27 46.81 3.71
87 97 2.096657 GCCGGAGATTTGCTTTTCTCTC 59.903 50.000 5.05 0.00 38.71 3.20
88 98 2.087646 GCCGGAGATTTGCTTTTCTCT 58.912 47.619 5.05 0.00 38.71 3.10
89 99 1.133216 GGCCGGAGATTTGCTTTTCTC 59.867 52.381 5.05 2.84 38.10 2.87
90 100 1.177401 GGCCGGAGATTTGCTTTTCT 58.823 50.000 5.05 0.00 0.00 2.52
91 101 0.887933 TGGCCGGAGATTTGCTTTTC 59.112 50.000 5.05 0.00 0.00 2.29
92 102 0.890683 CTGGCCGGAGATTTGCTTTT 59.109 50.000 5.28 0.00 0.00 2.27
735 757 0.107456 CATCATCGTGGGGAAGGAGG 59.893 60.000 0.00 0.00 0.00 4.30
736 758 1.123077 TCATCATCGTGGGGAAGGAG 58.877 55.000 0.00 0.00 0.00 3.69
737 759 1.417517 CATCATCATCGTGGGGAAGGA 59.582 52.381 0.00 0.00 0.00 3.36
739 761 2.916702 TCATCATCATCGTGGGGAAG 57.083 50.000 0.00 0.00 0.00 3.46
740 762 2.705127 TCATCATCATCATCGTGGGGAA 59.295 45.455 0.00 0.00 0.00 3.97
741 763 2.301009 CTCATCATCATCATCGTGGGGA 59.699 50.000 0.00 0.00 0.00 4.81
743 765 3.324117 GTCTCATCATCATCATCGTGGG 58.676 50.000 0.00 0.00 0.00 4.61
977 1041 4.973055 CCCGTCCGCCAACGAACA 62.973 66.667 7.07 0.00 45.37 3.18
1085 1149 3.712016 AAGAAAGAGGGGAGAAGAAGC 57.288 47.619 0.00 0.00 0.00 3.86
1088 1152 5.608860 AGAAAGAAAGAAAGAGGGGAGAAGA 59.391 40.000 0.00 0.00 0.00 2.87
1089 1153 5.875224 AGAAAGAAAGAAAGAGGGGAGAAG 58.125 41.667 0.00 0.00 0.00 2.85
1090 1154 5.608860 AGAGAAAGAAAGAAAGAGGGGAGAA 59.391 40.000 0.00 0.00 0.00 2.87
1092 1156 5.487433 GAGAGAAAGAAAGAAAGAGGGGAG 58.513 45.833 0.00 0.00 0.00 4.30
1093 1157 4.287326 GGAGAGAAAGAAAGAAAGAGGGGA 59.713 45.833 0.00 0.00 0.00 4.81
1133 1217 2.284405 GGGGGAGGTCCAACTCGA 60.284 66.667 0.00 0.00 38.39 4.04
1134 1218 2.284699 AGGGGGAGGTCCAACTCG 60.285 66.667 0.00 0.00 38.39 4.18
1178 1262 1.492176 AGCAGAGAGAGAGAGAGGAGG 59.508 57.143 0.00 0.00 0.00 4.30
1179 1263 2.486191 GGAGCAGAGAGAGAGAGAGGAG 60.486 59.091 0.00 0.00 0.00 3.69
1180 1264 1.490490 GGAGCAGAGAGAGAGAGAGGA 59.510 57.143 0.00 0.00 0.00 3.71
1181 1265 1.477558 GGGAGCAGAGAGAGAGAGAGG 60.478 61.905 0.00 0.00 0.00 3.69
2179 2306 3.918220 CGCAGCGACGGAATCAGC 61.918 66.667 9.98 0.00 0.00 4.26
2628 2755 0.538057 CCAAGTTGCTGAGCTTCCCA 60.538 55.000 5.83 0.00 0.00 4.37
2772 2899 3.997064 CTTCCCCGACTGCTCTGCG 62.997 68.421 0.00 0.00 0.00 5.18
3114 3241 2.745492 GCACCAGCCAGCTCTGTC 60.745 66.667 2.09 0.00 32.32 3.51
3123 3250 1.583477 GAGCTTCTTTGCACCAGCC 59.417 57.895 0.00 0.00 41.13 4.85
4038 4168 1.468914 CTCGACTTCATGTCTCGGTGA 59.531 52.381 8.76 0.00 43.25 4.02
4098 4228 1.819208 CCTCGCCATGCCGAAATCA 60.819 57.895 0.00 0.00 36.72 2.57
4314 4444 0.034186 TGTGCATCTTCACCCATCCC 60.034 55.000 0.00 0.00 36.17 3.85
4350 4480 1.305930 GCTCCGGGTCAAACACATCC 61.306 60.000 0.00 0.00 0.00 3.51
4760 4899 8.717821 CGTGTACCATCAGAAGAAAATTCTAAA 58.282 33.333 0.00 0.00 36.28 1.85
4970 5113 1.603739 GTGGAGGGAAGTTGCACCC 60.604 63.158 1.76 1.76 45.88 4.61
4978 5121 1.298014 GCAGTGGAGTGGAGGGAAG 59.702 63.158 0.00 0.00 0.00 3.46
5057 5200 1.294659 TGATGCGCGCACATTGTACA 61.295 50.000 39.05 22.45 0.00 2.90
5068 5211 0.369931 TTTCGATCAACTGATGCGCG 59.630 50.000 0.00 0.00 34.37 6.86
5102 5246 1.717194 TTCGTTTCTACCGTGCATCC 58.283 50.000 0.00 0.00 0.00 3.51
5119 5263 2.468915 ACTAGCTCAGGGTAGGGTTTC 58.531 52.381 0.00 0.00 44.93 2.78
5120 5264 2.644060 ACTAGCTCAGGGTAGGGTTT 57.356 50.000 0.00 0.00 44.93 3.27
5121 5265 3.206866 TCATACTAGCTCAGGGTAGGGTT 59.793 47.826 0.00 0.00 44.93 4.11
5127 5271 5.132043 ACTACTTCATACTAGCTCAGGGT 57.868 43.478 0.00 0.00 0.00 4.34
5128 5272 6.300703 ACTACTACTTCATACTAGCTCAGGG 58.699 44.000 0.00 0.00 0.00 4.45
5129 5273 8.905660 TTACTACTACTTCATACTAGCTCAGG 57.094 38.462 0.00 0.00 0.00 3.86
5579 5754 5.493809 ACGATTAGTTTAGCAAGGCCTAAA 58.506 37.500 5.16 0.00 35.53 1.85


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

AutoCloner maintained by Alex Coulton.