Multiple sequence alignment - TraesCS2D01G327700

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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 TraesCS2D01G327700 chr2D 100.000 3011 0 0 1 3011 420902165 420899155 0.000000e+00 5561.0
1 TraesCS2D01G327700 chr2A 90.339 2391 141 41 170 2527 566860694 566858361 0.000000e+00 3053.0
2 TraesCS2D01G327700 chr2A 88.975 517 27 17 2522 3011 566856791 566856278 1.980000e-171 612.0
3 TraesCS2D01G327700 chr2B 92.299 1714 54 36 716 2374 493567581 493565891 0.000000e+00 2362.0
4 TraesCS2D01G327700 chr2B 92.130 648 36 9 1 641 493568612 493567973 0.000000e+00 900.0
5 TraesCS2D01G327700 chr2B 89.450 673 43 15 2362 3011 493565803 493565136 0.000000e+00 824.0
6 TraesCS2D01G327700 chr3D 90.411 73 7 0 1339 1411 170659625 170659697 2.470000e-16 97.1
7 TraesCS2D01G327700 chr3A 90.411 73 7 0 1339 1411 208222074 208222146 2.470000e-16 97.1
8 TraesCS2D01G327700 chr3A 87.671 73 9 0 1339 1411 208089767 208089695 5.350000e-13 86.1
9 TraesCS2D01G327700 chr6D 93.333 60 4 0 1352 1411 72405979 72406038 4.130000e-14 89.8
10 TraesCS2D01G327700 chr6B 93.333 60 4 0 1352 1411 147056516 147056575 4.130000e-14 89.8
11 TraesCS2D01G327700 chr6B 90.909 44 3 1 1179 1222 89513877 89513919 1.170000e-04 58.4
12 TraesCS2D01G327700 chr3B 87.671 73 9 0 1339 1411 245969780 245969708 5.350000e-13 86.1
13 TraesCS2D01G327700 chr3B 86.301 73 10 0 1339 1411 245964036 245963964 2.490000e-11 80.5
14 TraesCS2D01G327700 chr5B 72.240 317 64 14 187 496 321561410 321561709 3.220000e-10 76.8
15 TraesCS2D01G327700 chrUn 93.182 44 2 1 1179 1222 114968230 114968188 2.510000e-06 63.9
16 TraesCS2D01G327700 chr6A 93.182 44 2 1 1179 1222 50034779 50034821 2.510000e-06 63.9


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 TraesCS2D01G327700 chr2D 420899155 420902165 3010 True 5561.0 5561 100.000 1 3011 1 chr2D.!!$R1 3010
1 TraesCS2D01G327700 chr2A 566856278 566860694 4416 True 1832.5 3053 89.657 170 3011 2 chr2A.!!$R1 2841
2 TraesCS2D01G327700 chr2B 493565136 493568612 3476 True 1362.0 2362 91.293 1 3011 3 chr2B.!!$R1 3010

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
367 375 0.098552 CTTGTTGTGCTTGCGTGACA 59.901 50.0 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2048 2412 0.522076 GGACTAGCGACGGTACAACG 60.522 60.0 1.96 0.0 40.31 4.1 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
41 42 5.848406 AGAGAACCTATTTTATCCGCTCTG 58.152 41.667 0.00 0.00 0.00 3.35
42 43 4.381411 AGAACCTATTTTATCCGCTCTGC 58.619 43.478 0.00 0.00 0.00 4.26
58 59 3.378427 GCTCTGCCCCTAAAATTGTGTAG 59.622 47.826 0.00 0.00 0.00 2.74
76 77 5.892119 TGTGTAGTCTACTATTCCCCTCAAG 59.108 44.000 11.28 0.00 0.00 3.02
84 85 3.782523 ACTATTCCCCTCAAGCTTCATCA 59.217 43.478 0.00 0.00 0.00 3.07
85 86 2.795231 TTCCCCTCAAGCTTCATCAG 57.205 50.000 0.00 0.00 0.00 2.90
96 97 0.803768 CTTCATCAGTGAGGCCGTCG 60.804 60.000 0.00 0.00 35.39 5.12
101 102 2.915659 AGTGAGGCCGTCGGTTCA 60.916 61.111 13.94 14.09 0.00 3.18
108 109 1.595929 GCCGTCGGTTCACTTTCCA 60.596 57.895 13.94 0.00 0.00 3.53
112 113 1.076332 GTCGGTTCACTTTCCATCCG 58.924 55.000 0.00 0.00 39.40 4.18
116 117 2.094390 CGGTTCACTTTCCATCCGTCTA 60.094 50.000 0.00 0.00 34.38 2.59
181 182 6.479884 TCTTCTCCGACTAGTAGTTTAGGTT 58.520 40.000 3.85 0.00 0.00 3.50
363 371 1.469079 GGTTTCTTGTTGTGCTTGCGT 60.469 47.619 0.00 0.00 0.00 5.24
367 375 0.098552 CTTGTTGTGCTTGCGTGACA 59.901 50.000 0.00 0.00 0.00 3.58
369 377 1.024046 TGTTGTGCTTGCGTGACAGT 61.024 50.000 0.00 0.00 0.00 3.55
396 407 3.558931 TGGTGCCAGATGTTTATCGAT 57.441 42.857 2.16 2.16 38.38 3.59
400 411 3.802139 GTGCCAGATGTTTATCGATCGAA 59.198 43.478 23.50 5.25 38.38 3.71
408 419 6.816640 AGATGTTTATCGATCGAAAGGTTCAA 59.183 34.615 23.50 0.00 38.38 2.69
413 424 1.153353 GATCGAAAGGTTCAACGGCA 58.847 50.000 0.00 0.00 0.00 5.69
418 429 2.095263 CGAAAGGTTCAACGGCAATGAT 60.095 45.455 0.00 0.00 0.00 2.45
470 481 2.167487 ACATGCACAAAAACTTTCCGGT 59.833 40.909 0.00 0.00 0.00 5.28
606 619 5.154932 CGTTTGGTGTGTTTTGTACTTTGA 58.845 37.500 0.00 0.00 0.00 2.69
778 1122 3.827898 CTCGAGCTCCACCCCGTC 61.828 72.222 8.47 0.00 0.00 4.79
781 1125 2.943978 CGAGCTCCACCCCGTCTTT 61.944 63.158 8.47 0.00 0.00 2.52
782 1126 1.601419 CGAGCTCCACCCCGTCTTTA 61.601 60.000 8.47 0.00 0.00 1.85
876 1231 1.490910 CCCACTAATCCTCCCACTTCC 59.509 57.143 0.00 0.00 0.00 3.46
877 1232 2.196595 CCACTAATCCTCCCACTTCCA 58.803 52.381 0.00 0.00 0.00 3.53
880 1235 2.196595 CTAATCCTCCCACTTCCACCA 58.803 52.381 0.00 0.00 0.00 4.17
1812 2176 4.333690 ACGAGCTCTACTTCAAGAACCTA 58.666 43.478 12.85 0.00 0.00 3.08
1928 2292 0.321671 TTCTTCCAGGACTTCGCCAG 59.678 55.000 0.00 0.00 0.00 4.85
1944 2308 2.124819 AGGGCGATGCAGAAGCTG 60.125 61.111 10.04 0.00 42.74 4.24
2045 2409 0.663269 GCGTTGCTACAACTTTGCCC 60.663 55.000 8.66 0.00 0.00 5.36
2048 2412 0.948678 TTGCTACAACTTTGCCCGAC 59.051 50.000 0.00 0.00 0.00 4.79
2054 2418 0.938713 CAACTTTGCCCGACGTTGTA 59.061 50.000 1.30 0.00 33.82 2.41
2107 2476 5.975693 TTAGGATTGGATTTTGGTGTGTC 57.024 39.130 0.00 0.00 0.00 3.67
2109 2478 3.828451 AGGATTGGATTTTGGTGTGTCTG 59.172 43.478 0.00 0.00 0.00 3.51
2111 2480 2.363306 TGGATTTTGGTGTGTCTGCT 57.637 45.000 0.00 0.00 0.00 4.24
2116 2485 2.245159 TTTGGTGTGTCTGCTCTCTG 57.755 50.000 0.00 0.00 0.00 3.35
2117 2486 1.413118 TTGGTGTGTCTGCTCTCTGA 58.587 50.000 0.00 0.00 0.00 3.27
2280 2679 1.164662 GGCTCATCTCGTGCATGCAT 61.165 55.000 25.64 3.87 35.77 3.96
2301 2711 7.359595 TGCATTTGTTACTTTCAGTCATACAC 58.640 34.615 0.00 0.00 0.00 2.90
2442 2957 1.375908 TGACACGAGCAGATTGCCC 60.376 57.895 0.00 0.00 46.52 5.36
2550 4640 1.808411 TCATGTCGGGTGAAGCTTTC 58.192 50.000 0.00 0.00 0.00 2.62
2611 4702 2.822399 GGTACGGGGAGGCATCTG 59.178 66.667 0.00 0.00 0.00 2.90
2673 4764 5.476599 CCTTCCATTGTGACAGTTTGGATAA 59.523 40.000 12.67 1.89 36.42 1.75
2720 4821 3.106827 CCATTTCCAGGGCCAATAGTTT 58.893 45.455 6.18 0.00 0.00 2.66
2721 4822 3.132824 CCATTTCCAGGGCCAATAGTTTC 59.867 47.826 6.18 0.00 0.00 2.78
2737 4838 1.720852 GTTTCCGTCATTGCACAATGC 59.279 47.619 16.74 11.51 45.77 3.56
2763 4864 1.507141 AAGAAAGAACTGGCGCACGG 61.507 55.000 10.83 6.44 0.00 4.94
2780 4881 4.043200 GCAGCTTGCACGGGTTCC 62.043 66.667 0.00 0.00 44.26 3.62
2813 4914 2.200067 CTACTCAGCTGCAGTGCATAC 58.800 52.381 20.10 14.10 38.13 2.39
2814 4915 0.322648 ACTCAGCTGCAGTGCATACA 59.677 50.000 20.10 2.11 38.13 2.29
2815 4916 1.065636 ACTCAGCTGCAGTGCATACAT 60.066 47.619 20.10 1.78 38.13 2.29
2823 4924 3.009026 TGCAGTGCATACATAACCAGTG 58.991 45.455 15.37 0.00 31.71 3.66
2869 4970 5.793030 AACGCTGCTCTATCCTAGTAATT 57.207 39.130 0.00 0.00 0.00 1.40
2872 4973 5.478679 ACGCTGCTCTATCCTAGTAATTCAT 59.521 40.000 0.00 0.00 0.00 2.57
2874 4975 6.349694 CGCTGCTCTATCCTAGTAATTCATGA 60.350 42.308 0.00 0.00 0.00 3.07
2875 4976 7.035004 GCTGCTCTATCCTAGTAATTCATGAG 58.965 42.308 0.00 0.00 0.00 2.90
2877 4978 6.033341 GCTCTATCCTAGTAATTCATGAGCG 58.967 44.000 0.00 0.00 34.83 5.03
2878 4979 6.349777 GCTCTATCCTAGTAATTCATGAGCGT 60.350 42.308 0.00 0.00 34.83 5.07
2879 4980 7.526142 TCTATCCTAGTAATTCATGAGCGTT 57.474 36.000 0.00 0.00 0.00 4.84
2880 4981 7.594714 TCTATCCTAGTAATTCATGAGCGTTC 58.405 38.462 0.00 0.00 0.00 3.95
2881 4982 5.854010 TCCTAGTAATTCATGAGCGTTCT 57.146 39.130 0.00 0.00 0.00 3.01
2894 5012 3.427528 TGAGCGTTCTAACATCGTTCAAC 59.572 43.478 0.00 0.00 40.47 3.18
2899 5017 4.896238 CGTTCTAACATCGTTCAACAACAC 59.104 41.667 0.00 0.00 32.14 3.32
2924 5047 0.111639 TGAAAACCTGGGGTACTGGC 59.888 55.000 0.00 0.00 41.59 4.85
2977 5100 2.634453 TGGCAGAGAATGACAGTTGAGA 59.366 45.455 0.00 0.00 44.15 3.27
2978 5101 3.071457 TGGCAGAGAATGACAGTTGAGAA 59.929 43.478 0.00 0.00 44.15 2.87
2989 5112 6.618287 TGACAGTTGAGAAAAATGTAGGTG 57.382 37.500 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 1.502690 TTTAGGGGCAGAGCGGATAA 58.497 50.000 0.00 0.00 0.00 1.75
41 42 5.742063 AGTAGACTACACAATTTTAGGGGC 58.258 41.667 14.95 0.00 0.00 5.80
42 43 9.543783 GAATAGTAGACTACACAATTTTAGGGG 57.456 37.037 14.95 0.00 0.00 4.79
58 59 4.406003 TGAAGCTTGAGGGGAATAGTAGAC 59.594 45.833 2.10 0.00 0.00 2.59
76 77 1.078848 ACGGCCTCACTGATGAAGC 60.079 57.895 0.00 0.00 40.97 3.86
84 85 2.915659 TGAACCGACGGCCTCACT 60.916 61.111 15.39 0.00 0.00 3.41
85 86 2.710724 AAGTGAACCGACGGCCTCAC 62.711 60.000 29.32 29.32 38.41 3.51
92 93 1.076332 GGATGGAAAGTGAACCGACG 58.924 55.000 0.00 0.00 0.00 5.12
96 97 2.474410 AGACGGATGGAAAGTGAACC 57.526 50.000 0.00 0.00 0.00 3.62
101 102 2.496470 GAGTGGTAGACGGATGGAAAGT 59.504 50.000 0.00 0.00 0.00 2.66
152 153 1.823797 ACTAGTCGGAGAAGAAGCGT 58.176 50.000 0.00 0.00 39.69 5.07
353 361 1.153469 TCACTGTCACGCAAGCACA 60.153 52.632 0.00 0.00 45.62 4.57
363 371 1.142667 TGGCACCAAATCTCACTGTCA 59.857 47.619 0.00 0.00 0.00 3.58
367 375 2.040813 ACATCTGGCACCAAATCTCACT 59.959 45.455 0.00 0.00 0.00 3.41
369 377 2.885135 ACATCTGGCACCAAATCTCA 57.115 45.000 0.00 0.00 0.00 3.27
396 407 1.265635 CATTGCCGTTGAACCTTTCGA 59.734 47.619 0.00 0.00 0.00 3.71
400 411 3.302365 CAATCATTGCCGTTGAACCTT 57.698 42.857 0.00 0.00 0.00 3.50
413 424 1.454479 CCCTGGAGCCGCAATCATT 60.454 57.895 0.00 0.00 0.00 2.57
470 481 2.013563 GCCTGATCTTGCCGATGACAA 61.014 52.381 0.00 0.00 30.84 3.18
492 503 4.246458 GTTGTTGCTCCTCTATCGAAGTT 58.754 43.478 0.00 0.00 0.00 2.66
512 523 1.022451 ACCGTTGACACGCTGTTGTT 61.022 50.000 0.00 0.00 45.72 2.83
777 1121 2.349755 GCGGTGGCCTGGTAAAGA 59.650 61.111 3.32 0.00 0.00 2.52
778 1122 2.033448 TGCGGTGGCCTGGTAAAG 59.967 61.111 3.32 0.00 38.85 1.85
876 1231 0.329261 TGGGCTGGAGAAGAATGGTG 59.671 55.000 0.00 0.00 0.00 4.17
877 1232 0.329596 GTGGGCTGGAGAAGAATGGT 59.670 55.000 0.00 0.00 0.00 3.55
880 1235 1.604378 CGGTGGGCTGGAGAAGAAT 59.396 57.895 0.00 0.00 0.00 2.40
1281 1645 4.162690 AGGTTGATCTCCGCGGCC 62.163 66.667 23.51 14.45 0.00 6.13
1928 2292 3.207669 CCAGCTTCTGCATCGCCC 61.208 66.667 0.00 0.00 42.74 6.13
2023 2387 0.996727 CAAAGTTGTAGCAACGCGCC 60.997 55.000 5.73 0.00 44.04 6.53
2037 2401 0.881600 GGTACAACGTCGGGCAAAGT 60.882 55.000 0.00 0.00 0.00 2.66
2048 2412 0.522076 GGACTAGCGACGGTACAACG 60.522 60.000 1.96 0.00 40.31 4.10
2107 2476 5.875910 AGTTCATTCAGAAATCAGAGAGCAG 59.124 40.000 0.00 0.00 38.13 4.24
2116 2485 7.269937 CACAATTCACGAGTTCATTCAGAAATC 59.730 37.037 0.00 0.00 45.35 2.17
2117 2486 7.041167 TCACAATTCACGAGTTCATTCAGAAAT 60.041 33.333 0.00 0.00 38.13 2.17
2263 2662 2.096980 ACAAATGCATGCACGAGATGAG 59.903 45.455 25.37 9.58 0.00 2.90
2301 2711 1.588404 GTGATGACTACGCGGAATGTG 59.412 52.381 12.47 0.00 0.00 3.21
2354 2764 0.668096 CCGTTAGCTGCGTAACCACA 60.668 55.000 0.00 0.00 30.30 4.17
2419 2934 1.462283 CAATCTGCTCGTGTCACCTTG 59.538 52.381 0.00 0.00 0.00 3.61
2453 2968 2.672996 CCAACGCCCAAGTCCCAG 60.673 66.667 0.00 0.00 0.00 4.45
2550 4640 2.977169 CACCATTAAAACGCAACCGAAG 59.023 45.455 0.00 0.00 38.29 3.79
2673 4764 5.622007 CGTGAATGTTTGGCCTAATCATTGT 60.622 40.000 22.15 8.45 38.29 2.71
2737 4838 3.120511 GCGCCAGTTCTTTCTTCTGTTAG 60.121 47.826 0.00 0.00 0.00 2.34
2763 4864 4.043200 GGAACCCGTGCAAGCTGC 62.043 66.667 0.00 0.00 45.29 5.25
2823 4924 7.496529 TTAACATCATGAATTACTAGCAGGC 57.503 36.000 0.00 0.00 0.00 4.85
2869 4970 3.503827 ACGATGTTAGAACGCTCATGA 57.496 42.857 0.00 0.00 0.00 3.07
2872 4973 3.291809 TGAACGATGTTAGAACGCTCA 57.708 42.857 0.00 0.00 31.50 4.26
2874 4975 3.386486 TGTTGAACGATGTTAGAACGCT 58.614 40.909 0.00 0.00 0.00 5.07
2875 4976 3.781341 TGTTGAACGATGTTAGAACGC 57.219 42.857 0.00 0.00 0.00 4.84
2877 4978 5.007332 AGGTGTTGTTGAACGATGTTAGAAC 59.993 40.000 0.00 0.00 34.49 3.01
2878 4979 5.120399 AGGTGTTGTTGAACGATGTTAGAA 58.880 37.500 0.00 0.00 34.49 2.10
2879 4980 4.699637 AGGTGTTGTTGAACGATGTTAGA 58.300 39.130 0.00 0.00 34.49 2.10
2880 4981 6.533819 TTAGGTGTTGTTGAACGATGTTAG 57.466 37.500 0.00 0.00 34.49 2.34
2881 4982 7.226918 TCAATTAGGTGTTGTTGAACGATGTTA 59.773 33.333 0.00 0.00 34.49 2.41
2894 5012 4.262420 CCCCAGGTTTTCAATTAGGTGTTG 60.262 45.833 0.00 0.00 0.00 3.33
2899 5017 4.705023 CAGTACCCCAGGTTTTCAATTAGG 59.295 45.833 0.00 0.00 37.09 2.69
2924 5047 4.094887 GTCCATAGTTGTGTTGCCTGTATG 59.905 45.833 0.00 0.00 0.00 2.39
2977 5100 3.181434 TGACTGCTCCCACCTACATTTTT 60.181 43.478 0.00 0.00 0.00 1.94
2978 5101 2.375174 TGACTGCTCCCACCTACATTTT 59.625 45.455 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.