Multiple sequence alignment - TraesCS6D01G240600

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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 TraesCS6D01G240600 chr6D 100.000 3245 0 0 1 3245 342474244 342471000 0.000000e+00 5993
1 TraesCS6D01G240600 chr6A 96.309 2980 85 9 1 2959 482621479 482618504 0.000000e+00 4870
2 TraesCS6D01G240600 chr6A 87.245 196 18 6 3050 3245 482618457 482618269 1.960000e-52 217
3 TraesCS6D01G240600 chr6B 91.044 3305 140 44 3 3245 516881483 516878273 0.000000e+00 4320
4 TraesCS6D01G240600 chr2A 80.959 751 112 24 1036 1776 645311189 645311918 1.690000e-157 566
5 TraesCS6D01G240600 chr2D 80.764 759 111 25 1036 1776 500362437 500363178 7.860000e-156 560
6 TraesCS6D01G240600 chr2D 89.565 460 9 12 592 1029 114646639 114647081 6.120000e-152 547
7 TraesCS6D01G240600 chr2B 80.504 754 107 28 1036 1770 588067176 588067908 2.850000e-150 542
8 TraesCS6D01G240600 chrUn 88.604 351 36 3 1261 1609 365429968 365429620 1.080000e-114 424
9 TraesCS6D01G240600 chr4B 88.604 351 36 3 1261 1609 641891314 641890966 1.080000e-114 424
10 TraesCS6D01G240600 chr5A 88.034 351 38 3 1261 1609 679875216 679874868 2.330000e-111 412
11 TraesCS6D01G240600 chr5A 86.431 339 42 3 1258 1594 685432403 685432739 5.110000e-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 TraesCS6D01G240600 chr6D 342471000 342474244 3244 True 5993.0 5993 100.000 1 3245 1 chr6D.!!$R1 3244
1 TraesCS6D01G240600 chr6A 482618269 482621479 3210 True 2543.5 4870 91.777 1 3245 2 chr6A.!!$R1 3244
2 TraesCS6D01G240600 chr6B 516878273 516881483 3210 True 4320.0 4320 91.044 3 3245 1 chr6B.!!$R1 3242
3 TraesCS6D01G240600 chr2A 645311189 645311918 729 False 566.0 566 80.959 1036 1776 1 chr2A.!!$F1 740
4 TraesCS6D01G240600 chr2D 500362437 500363178 741 False 560.0 560 80.764 1036 1776 1 chr2D.!!$F2 740
5 TraesCS6D01G240600 chr2B 588067176 588067908 732 False 542.0 542 80.504 1036 1770 1 chr2B.!!$F1 734

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
402 418 0.809241 GAGGATCGAACTGCAGCAGG 60.809 60.0 26.38 9.03 35.51 4.85 F
1202 1278 0.970937 CCGTCTGGAAGTAGCCCTCA 60.971 60.0 0.00 0.00 37.49 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2134 2225 0.905357 GGGAACTCTAGCAGCCTCAA 59.095 55.0 0.00 0.0 0.00 3.02 R
3142 3272 0.036483 GGGGTTGGCATTTGCGAAAT 60.036 50.0 1.42 0.0 40.32 2.17 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
259 262 2.442236 ATAGTACGGACGAGGGGAAA 57.558 50.000 0.00 0.00 0.00 3.13
264 267 2.609921 GGACGAGGGGAAAGGGGT 60.610 66.667 0.00 0.00 0.00 4.95
296 299 3.321497 GAAAACACAGCGAGATGACTCT 58.679 45.455 0.00 0.00 40.65 3.24
297 300 3.393089 AAACACAGCGAGATGACTCTT 57.607 42.857 0.00 0.00 40.65 2.85
298 301 2.360553 ACACAGCGAGATGACTCTTG 57.639 50.000 0.00 0.00 40.65 3.02
300 303 1.991264 CACAGCGAGATGACTCTTGTG 59.009 52.381 0.00 0.00 43.05 3.33
302 305 2.094803 ACAGCGAGATGACTCTTGTGAG 60.095 50.000 0.00 0.00 45.43 3.51
402 418 0.809241 GAGGATCGAACTGCAGCAGG 60.809 60.000 26.38 9.03 35.51 4.85
534 550 1.540166 CATCCCTGCCACATCCCAT 59.460 57.895 0.00 0.00 0.00 4.00
649 665 2.509336 AACGCGGCTCAAGATCGG 60.509 61.111 12.47 0.00 0.00 4.18
667 683 9.982651 CAAGATCGGTATAGAATTTCTTAGGAA 57.017 33.333 3.86 0.00 0.00 3.36
945 973 3.434596 GGTCTTCCTCCTCTCCTCTAGTC 60.435 56.522 0.00 0.00 0.00 2.59
972 1000 1.961277 GGGATGCCGCAGTAATCCG 60.961 63.158 0.00 0.00 40.75 4.18
986 1014 3.387050 AGTAATCCGCGGGAAGAAGTATT 59.613 43.478 27.83 16.91 34.34 1.89
991 1019 6.195141 ATCCGCGGGAAGAAGTATTCAAGT 62.195 45.833 27.83 0.00 39.97 3.16
1107 1150 2.745884 CCTTTCATGACGGCCGCA 60.746 61.111 28.58 24.37 0.00 5.69
1202 1278 0.970937 CCGTCTGGAAGTAGCCCTCA 60.971 60.000 0.00 0.00 37.49 3.86
1209 1285 1.275573 GGAAGTAGCCCTCACTTTCGT 59.724 52.381 0.00 0.00 36.38 3.85
1212 1288 1.275573 AGTAGCCCTCACTTTCGTTCC 59.724 52.381 0.00 0.00 0.00 3.62
2134 2225 2.995547 GGCCAAGGGACCATACGT 59.004 61.111 0.00 0.00 0.00 3.57
2274 2365 5.180304 AGGAAAGTTCTGCGATTCTTTCTTC 59.820 40.000 20.65 13.31 42.73 2.87
2319 2410 3.372514 TCTTCTCGTCATCTCACTTCTCG 59.627 47.826 0.00 0.00 0.00 4.04
2465 2556 8.037166 AGATTAATGTTTTTCTCCCAAATCAGC 58.963 33.333 0.00 0.00 0.00 4.26
2720 2822 8.374728 CACATTCATGATACAAAACCAAAATCG 58.625 33.333 0.00 0.00 0.00 3.34
2867 2996 9.286170 GAAATAAAAAGAAACTGAGGGAGTACT 57.714 33.333 0.00 0.00 33.09 2.73
2901 3030 2.492881 TGAATCCATCAAAATGCGTGCT 59.507 40.909 0.00 0.00 34.30 4.40
2903 3032 0.109179 TCCATCAAAATGCGTGCTGC 60.109 50.000 0.00 0.00 46.70 5.25
2959 3088 3.628008 TCTAACTGGCGACCATTCTCTA 58.372 45.455 0.00 0.00 30.82 2.43
2960 3089 2.969628 AACTGGCGACCATTCTCTAG 57.030 50.000 0.00 0.00 30.82 2.43
2961 3090 1.115467 ACTGGCGACCATTCTCTAGG 58.885 55.000 0.00 0.00 30.82 3.02
2962 3091 1.342076 ACTGGCGACCATTCTCTAGGA 60.342 52.381 0.00 0.00 30.82 2.94
2963 3092 1.339610 CTGGCGACCATTCTCTAGGAG 59.660 57.143 0.00 0.00 30.82 3.69
2964 3093 1.063942 TGGCGACCATTCTCTAGGAGA 60.064 52.381 0.00 0.00 36.86 3.71
2965 3094 1.611491 GGCGACCATTCTCTAGGAGAG 59.389 57.143 0.00 0.00 43.64 3.20
2966 3095 1.000717 GCGACCATTCTCTAGGAGAGC 60.001 57.143 0.00 0.00 42.04 4.09
2967 3096 2.302260 CGACCATTCTCTAGGAGAGCA 58.698 52.381 0.00 0.00 42.04 4.26
2968 3097 2.890311 CGACCATTCTCTAGGAGAGCAT 59.110 50.000 0.00 0.00 42.04 3.79
2969 3098 3.320541 CGACCATTCTCTAGGAGAGCATT 59.679 47.826 0.00 0.00 42.04 3.56
2970 3099 4.558496 CGACCATTCTCTAGGAGAGCATTC 60.558 50.000 0.00 0.00 42.04 2.67
2971 3100 4.293494 ACCATTCTCTAGGAGAGCATTCA 58.707 43.478 0.00 0.00 42.04 2.57
2975 3104 4.844998 TCTCTAGGAGAGCATTCATTCG 57.155 45.455 0.00 0.00 42.04 3.34
2979 3108 2.544685 AGGAGAGCATTCATTCGAACG 58.455 47.619 0.00 0.00 32.81 3.95
3012 3141 7.691213 TGACAATTTTAGTTGTATCAGGGGTA 58.309 34.615 0.00 0.00 42.08 3.69
3013 3142 7.608761 TGACAATTTTAGTTGTATCAGGGGTAC 59.391 37.037 0.00 0.00 42.08 3.34
3015 3144 7.257272 ACAATTTTAGTTGTATCAGGGGTACCT 60.257 37.037 12.72 0.00 44.34 3.08
3046 3175 6.871844 TCAAAACAACATGACATTTTCTGGA 58.128 32.000 0.00 0.00 0.00 3.86
3048 3177 7.821359 TCAAAACAACATGACATTTTCTGGAAA 59.179 29.630 0.00 0.00 0.00 3.13
3064 3193 3.565307 TGGAAAGATGGCAGTTTTGAGT 58.435 40.909 4.02 0.00 0.00 3.41
3072 3201 6.240894 AGATGGCAGTTTTGAGTCTTCATTA 58.759 36.000 0.00 0.00 32.27 1.90
3116 3245 2.368875 TCTGAAGAAACTGTCACCCCTC 59.631 50.000 0.00 0.00 0.00 4.30
3119 3248 0.680061 AGAAACTGTCACCCCTCGAC 59.320 55.000 0.00 0.00 0.00 4.20
3142 3272 7.164230 ACCAACTAAAACTGTGATCAAAACA 57.836 32.000 0.00 0.00 0.00 2.83
3168 3298 1.739608 AAATGCCAACCCCTCCCAGT 61.740 55.000 0.00 0.00 0.00 4.00
3169 3299 0.849094 AATGCCAACCCCTCCCAGTA 60.849 55.000 0.00 0.00 0.00 2.74
3189 3319 1.183549 AACGGTCGCCAGATAAGAGT 58.816 50.000 0.00 0.00 0.00 3.24
3206 3337 5.695424 AAGAGTGTCCTAGTAATTTCCCC 57.305 43.478 0.00 0.00 0.00 4.81
3208 3339 4.717280 AGAGTGTCCTAGTAATTTCCCCTG 59.283 45.833 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 57 6.479331 GTGTAGTAGCTTTATAAAGGGCAGAC 59.521 42.308 23.37 13.87 36.53 3.51
275 278 3.321497 AGAGTCATCTCGCTGTGTTTTC 58.679 45.455 0.00 0.00 44.65 2.29
296 299 3.644966 AGTGGAAGTGGAAACTCACAA 57.355 42.857 0.00 0.00 39.93 3.33
297 300 3.494398 GCTAGTGGAAGTGGAAACTCACA 60.494 47.826 0.00 0.00 39.93 3.58
298 301 3.067833 GCTAGTGGAAGTGGAAACTCAC 58.932 50.000 0.00 0.00 37.89 3.51
300 303 3.686916 AGCTAGTGGAAGTGGAAACTC 57.313 47.619 0.00 0.00 0.00 3.01
302 305 4.538746 ACTAGCTAGTGGAAGTGGAAAC 57.461 45.455 25.52 0.00 34.72 2.78
637 653 6.459923 AGAAATTCTATACCGATCTTGAGCC 58.540 40.000 0.00 0.00 0.00 4.70
667 683 4.624336 TGCGTGTATGTGTTGTTTTTCT 57.376 36.364 0.00 0.00 0.00 2.52
668 684 5.910166 TGTATGCGTGTATGTGTTGTTTTTC 59.090 36.000 0.00 0.00 0.00 2.29
972 1000 6.200475 GTGTATACTTGAATACTTCTTCCCGC 59.800 42.308 4.17 0.00 34.13 6.13
986 1014 7.817478 CAGTAAACTCCATGTGTGTATACTTGA 59.183 37.037 4.17 0.00 0.00 3.02
991 1019 5.105675 TCGCAGTAAACTCCATGTGTGTATA 60.106 40.000 0.00 0.00 0.00 1.47
997 1025 2.412870 TGTCGCAGTAAACTCCATGTG 58.587 47.619 0.00 0.00 0.00 3.21
1848 1939 4.008933 ACGAGGAGTGGTGCTGGC 62.009 66.667 0.00 0.00 0.00 4.85
2064 2155 1.605710 GCACTGCCATAATTGCTCGAT 59.394 47.619 0.00 0.00 32.00 3.59
2134 2225 0.905357 GGGAACTCTAGCAGCCTCAA 59.095 55.000 0.00 0.00 0.00 3.02
2178 2269 1.012124 CGACGACGATGGAGACGAG 60.012 63.158 0.00 0.00 42.66 4.18
2187 2278 1.293963 TGGAAGACGACGACGACGAT 61.294 55.000 25.15 10.95 42.66 3.73
2274 2365 5.897377 ACCGAAAATCAAATGGTAGAAGG 57.103 39.130 0.00 0.00 0.00 3.46
2319 2410 9.559958 CATCAAAAGGTTATAACTGAATCACAC 57.440 33.333 15.05 0.00 0.00 3.82
2388 2479 8.383318 TCTCAAACCAACACAAAAATTTCAAA 57.617 26.923 0.00 0.00 0.00 2.69
2432 2523 7.453126 TGGGAGAAAAACATTAATCTGCCTAAA 59.547 33.333 12.39 0.00 46.87 1.85
2465 2556 2.680312 ATGGTGGACAAGAGATGACG 57.320 50.000 0.00 0.00 0.00 4.35
2694 2796 8.374728 CGATTTTGGTTTTGTATCATGAATGTG 58.625 33.333 0.00 0.00 0.00 3.21
2840 2969 9.063615 GTACTCCCTCAGTTTCTTTTTATTTCA 57.936 33.333 0.00 0.00 36.43 2.69
2867 2996 7.582667 TTGATGGATTCAACTCGTATCTCTA 57.417 36.000 0.00 0.00 39.44 2.43
2897 3026 2.813901 TGCTGGTTTTGGCAGCAC 59.186 55.556 0.00 0.00 45.62 4.40
2899 3028 0.039165 GTAGTGCTGGTTTTGGCAGC 60.039 55.000 0.00 0.00 39.22 5.25
2901 3030 1.028905 GTGTAGTGCTGGTTTTGGCA 58.971 50.000 0.00 0.00 36.01 4.92
2903 3032 5.446143 TTAATGTGTAGTGCTGGTTTTGG 57.554 39.130 0.00 0.00 0.00 3.28
2938 3067 2.457598 AGAGAATGGTCGCCAGTTAGA 58.542 47.619 4.90 0.00 36.75 2.10
2959 3088 2.093973 ACGTTCGAATGAATGCTCTCCT 60.094 45.455 23.76 0.00 43.56 3.69
2960 3089 2.271800 ACGTTCGAATGAATGCTCTCC 58.728 47.619 23.76 0.00 43.56 3.71
2961 3090 3.999229 AACGTTCGAATGAATGCTCTC 57.001 42.857 23.76 0.00 43.56 3.20
2962 3091 4.749245 AAAACGTTCGAATGAATGCTCT 57.251 36.364 23.76 0.00 43.56 4.09
2963 3092 4.320953 GGAAAAACGTTCGAATGAATGCTC 59.679 41.667 23.76 12.03 43.56 4.26
2964 3093 4.023193 AGGAAAAACGTTCGAATGAATGCT 60.023 37.500 23.76 12.87 43.56 3.79
2965 3094 4.088496 CAGGAAAAACGTTCGAATGAATGC 59.912 41.667 23.76 11.04 43.56 3.56
2966 3095 5.339611 GTCAGGAAAAACGTTCGAATGAATG 59.660 40.000 23.76 10.45 44.95 2.67
2967 3096 5.008217 TGTCAGGAAAAACGTTCGAATGAAT 59.992 36.000 23.76 9.24 36.29 2.57
2968 3097 4.333095 TGTCAGGAAAAACGTTCGAATGAA 59.667 37.500 23.76 0.00 0.00 2.57
2969 3098 3.872182 TGTCAGGAAAAACGTTCGAATGA 59.128 39.130 23.76 6.30 0.00 2.57
2970 3099 4.203950 TGTCAGGAAAAACGTTCGAATG 57.796 40.909 15.80 15.80 0.00 2.67
2971 3100 4.886247 TTGTCAGGAAAAACGTTCGAAT 57.114 36.364 0.00 0.00 0.00 3.34
2975 3104 7.980742 ACTAAAATTGTCAGGAAAAACGTTC 57.019 32.000 0.00 0.00 0.00 3.95
3012 3141 8.006298 TGTCATGTTGTTTTGAAGAAATAGGT 57.994 30.769 0.00 0.00 0.00 3.08
3013 3142 9.480053 AATGTCATGTTGTTTTGAAGAAATAGG 57.520 29.630 0.00 0.00 0.00 2.57
3020 3149 7.492020 TCCAGAAAATGTCATGTTGTTTTGAAG 59.508 33.333 0.00 1.70 0.00 3.02
3025 3154 7.555087 TCTTTCCAGAAAATGTCATGTTGTTT 58.445 30.769 0.00 0.00 0.00 2.83
3032 3161 4.773674 TGCCATCTTTCCAGAAAATGTCAT 59.226 37.500 11.12 0.00 30.76 3.06
3042 3171 3.571401 ACTCAAAACTGCCATCTTTCCAG 59.429 43.478 0.00 0.00 0.00 3.86
3046 3175 4.889409 TGAAGACTCAAAACTGCCATCTTT 59.111 37.500 0.00 0.00 0.00 2.52
3048 3177 4.090761 TGAAGACTCAAAACTGCCATCT 57.909 40.909 0.00 0.00 0.00 2.90
3086 3215 6.706270 GTGACAGTTTCTTCAGAATAACCTGA 59.294 38.462 11.40 0.00 41.06 3.86
3093 3222 3.395941 AGGGGTGACAGTTTCTTCAGAAT 59.604 43.478 0.00 0.00 33.54 2.40
3116 3245 5.666969 TTGATCACAGTTTTAGTTGGTCG 57.333 39.130 0.00 0.00 0.00 4.79
3119 3248 8.647143 AATGTTTTGATCACAGTTTTAGTTGG 57.353 30.769 0.00 0.00 0.00 3.77
3142 3272 0.036483 GGGGTTGGCATTTGCGAAAT 60.036 50.000 1.42 0.00 40.32 2.17
3146 3276 2.573340 GAGGGGTTGGCATTTGCG 59.427 61.111 0.00 0.00 43.26 4.85
3168 3298 2.756760 ACTCTTATCTGGCGACCGTTTA 59.243 45.455 0.00 0.00 0.00 2.01
3169 3299 1.549170 ACTCTTATCTGGCGACCGTTT 59.451 47.619 0.00 0.00 0.00 3.60
3189 3319 4.431378 TGACAGGGGAAATTACTAGGACA 58.569 43.478 0.00 0.00 0.00 4.02
3206 3337 6.591448 TCAGTTCACAAGTAATAGCATGACAG 59.409 38.462 0.00 0.00 0.00 3.51
3208 3339 6.968131 TCAGTTCACAAGTAATAGCATGAC 57.032 37.500 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.