Multiple sequence alignment - TraesCS5D01G073600

Loading Multiple Alignment...

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 TraesCS5D01G073600 chr5D 100.000 3254 0 0 1 3254 72870392 72873645 0 6010
1 TraesCS5D01G073600 chr5A 93.739 2731 99 27 574 3254 67326590 67329298 0 4030
2 TraesCS5D01G073600 chr5A 89.673 581 40 4 1 562 67325866 67326445 0 723
3 TraesCS5D01G073600 chr5B 93.472 2252 77 32 562 2772 79765890 79768112 0 3280
4 TraesCS5D01G073600 chr5B 87.931 580 53 4 1 564 79765217 79765795 0 667


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 TraesCS5D01G073600 chr5D 72870392 72873645 3253 False 6010.0 6010 100.0000 1 3254 1 chr5D.!!$F1 3253
1 TraesCS5D01G073600 chr5A 67325866 67329298 3432 False 2376.5 4030 91.7060 1 3254 2 chr5A.!!$F1 3253
2 TraesCS5D01G073600 chr5B 79765217 79768112 2895 False 1973.5 3280 90.7015 1 2772 2 chr5B.!!$F1 2771

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
737 924 0.030101 TTTCCGCGCCTCAGTTTTTG 59.970 50.000 0.0 0.0 0.0 2.44 F
947 1147 1.075600 CCTCCTCCACCTCCTCCTC 60.076 68.421 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1818 2019 0.179097 GGTTGAGCTGATCGGGACTC 60.179 60.0 3.14 3.05 0.0 3.36 R
2889 3113 0.400213 ATTTGGGGAAGCTCACGACA 59.600 50.0 0.00 0.00 0.0 4.35 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
59 60 1.530013 GGGTCACCCTCGAACGAGAA 61.530 60.000 22.96 5.41 44.53 2.87
62 63 1.443872 CACCCTCGAACGAGAACGG 60.444 63.158 22.96 17.71 44.53 4.44
71 72 2.096417 CGAACGAGAACGGCAAGAAAAT 60.096 45.455 0.00 0.00 44.46 1.82
128 132 7.845037 TGAGATATCTCGAATTGCCTTCATAT 58.155 34.615 24.27 0.00 45.72 1.78
155 159 9.872684 AAAATTCATATATGACCCAGAGATTGT 57.127 29.630 15.10 3.35 36.36 2.71
213 230 2.979678 AGCTCTTAGGTGGAAACAAGGA 59.020 45.455 0.00 0.00 46.06 3.36
220 237 1.273327 GGTGGAAACAAGGAATGCTGG 59.727 52.381 0.00 0.00 46.06 4.85
272 289 2.271800 CACTAAGACATCGAAGGGTGC 58.728 52.381 0.00 0.00 0.00 5.01
277 294 0.955428 GACATCGAAGGGTGCAGCAA 60.955 55.000 19.06 0.00 0.00 3.91
305 325 0.546122 TTTAGGCACGAGCATGGGAT 59.454 50.000 7.26 0.00 44.61 3.85
324 344 4.081476 GGGATTTTATCAAGTGCTTTGGCT 60.081 41.667 2.44 0.00 37.39 4.75
326 346 6.036470 GGATTTTATCAAGTGCTTTGGCTAC 58.964 40.000 2.44 0.00 37.39 3.58
327 347 6.350110 GGATTTTATCAAGTGCTTTGGCTACA 60.350 38.462 2.44 0.00 37.39 2.74
351 371 5.366768 AGTCTATGAGGGAATTTTCGATCCA 59.633 40.000 5.21 0.00 37.46 3.41
356 376 5.076873 TGAGGGAATTTTCGATCCAGTTTT 58.923 37.500 5.21 0.00 37.46 2.43
424 447 4.082274 TGTTCACTTGAATTATGCGCAG 57.918 40.909 18.32 1.10 36.33 5.18
441 464 1.678101 GCAGGTGGCTATGGATTGTTC 59.322 52.381 0.00 0.00 40.25 3.18
444 467 1.940613 GGTGGCTATGGATTGTTCGAC 59.059 52.381 0.00 0.00 0.00 4.20
537 560 2.353803 CCACTAGGCAAGCGTAGAGTTT 60.354 50.000 23.72 3.42 37.70 2.66
557 580 4.868172 TTGGACATGGAGGATGAGAAAT 57.132 40.909 0.00 0.00 35.80 2.17
665 823 7.266922 TCAGGTTAAACAAATTGGAGTACAC 57.733 36.000 0.00 0.00 0.00 2.90
678 865 4.862371 TGGAGTACACAAGAAAACCCTTT 58.138 39.130 0.00 0.00 0.00 3.11
685 872 7.783119 AGTACACAAGAAAACCCTTTATTTCCT 59.217 33.333 0.00 0.00 36.44 3.36
696 883 4.436332 CCTTTATTTCCTTGCCTCAATGC 58.564 43.478 0.00 0.00 0.00 3.56
731 918 2.464459 GGTGATTTCCGCGCCTCAG 61.464 63.158 0.00 0.00 33.20 3.35
737 924 0.030101 TTTCCGCGCCTCAGTTTTTG 59.970 50.000 0.00 0.00 0.00 2.44
761 949 5.733620 TTTGAAGGACGGACATTAGTACT 57.266 39.130 0.00 0.00 31.81 2.73
947 1147 1.075600 CCTCCTCCACCTCCTCCTC 60.076 68.421 0.00 0.00 0.00 3.71
1070 1271 2.832201 CTCTCCGTCCCCGTACCC 60.832 72.222 0.00 0.00 0.00 3.69
1821 2022 3.148279 GAGATCACCCCGGCGAGT 61.148 66.667 9.30 1.73 0.00 4.18
1884 2085 4.796231 TCCTTCGGCTTCGAGCGC 62.796 66.667 0.00 0.00 43.62 5.92
2325 2530 1.227556 GGTGTCGTGCACTGTCCTT 60.228 57.895 16.19 0.00 46.86 3.36
2487 2695 4.036352 CGTTCGAAATTTTCAACCCGAAA 58.964 39.130 0.00 0.00 41.95 3.46
2583 2793 2.224205 GAAAACGAACGGCTCTCGGC 62.224 60.000 9.44 0.00 44.45 5.54
2653 2875 2.856000 AGGGCAGCAGTGGAACCT 60.856 61.111 0.00 0.00 37.80 3.50
2675 2897 3.334583 TGCCATGTGTTCTTCTCTACC 57.665 47.619 0.00 0.00 0.00 3.18
2724 2948 5.965918 GCAGTGTGTTTGAGTTTAAGAAGTC 59.034 40.000 0.00 0.00 36.05 3.01
2726 2950 5.293569 AGTGTGTTTGAGTTTAAGAAGTCGG 59.706 40.000 0.00 0.00 37.92 4.79
2739 2963 1.659098 GAAGTCGGCGTCCTATTTGTG 59.341 52.381 6.85 0.00 0.00 3.33
2743 2967 1.758280 TCGGCGTCCTATTTGTGGTAT 59.242 47.619 6.85 0.00 0.00 2.73
2813 3037 4.665833 ATATTCATCTTCGTTGACCGGA 57.334 40.909 9.46 0.00 37.11 5.14
2931 3155 1.976045 CGTGTATTGCGGCTTTTTCAC 59.024 47.619 0.00 4.01 0.00 3.18
2933 3157 1.068885 TGTATTGCGGCTTTTTCACGG 60.069 47.619 0.00 0.00 0.00 4.94
2978 3206 0.239879 TTCGCTTCGAATGGTTTGGC 59.760 50.000 0.00 0.00 41.05 4.52
3038 3266 4.333649 CACCGTGATTTCAGCATGTAGAAT 59.666 41.667 0.00 0.00 37.40 2.40
3044 3272 7.533426 GTGATTTCAGCATGTAGAATTGTTCT 58.467 34.615 0.00 0.00 38.27 3.01
3076 3304 3.609853 TGCATCGGAAGCAGAATTAAGT 58.390 40.909 3.44 0.00 37.02 2.24
3082 3310 2.742053 GGAAGCAGAATTAAGTGCGTGA 59.258 45.455 1.04 0.00 44.78 4.35
3083 3311 3.375299 GGAAGCAGAATTAAGTGCGTGAT 59.625 43.478 1.04 0.00 44.78 3.06
3084 3312 4.337763 GAAGCAGAATTAAGTGCGTGATG 58.662 43.478 1.04 0.00 44.78 3.07
3086 3314 2.677836 GCAGAATTAAGTGCGTGATGGA 59.322 45.455 0.00 0.00 0.00 3.41
3088 3316 4.201950 GCAGAATTAAGTGCGTGATGGAAT 60.202 41.667 0.00 0.00 0.00 3.01
3089 3317 5.677091 GCAGAATTAAGTGCGTGATGGAATT 60.677 40.000 0.00 0.00 0.00 2.17
3090 3318 6.324819 CAGAATTAAGTGCGTGATGGAATTT 58.675 36.000 0.00 0.00 0.00 1.82
3091 3319 6.808212 CAGAATTAAGTGCGTGATGGAATTTT 59.192 34.615 0.00 0.00 0.00 1.82
3092 3320 7.008628 CAGAATTAAGTGCGTGATGGAATTTTC 59.991 37.037 0.00 0.00 0.00 2.29
3093 3321 5.697473 TTAAGTGCGTGATGGAATTTTCA 57.303 34.783 0.00 0.00 0.00 2.69
3095 3323 4.582701 AGTGCGTGATGGAATTTTCAAA 57.417 36.364 0.00 0.00 0.00 2.69
3096 3324 4.942852 AGTGCGTGATGGAATTTTCAAAA 58.057 34.783 0.00 0.00 0.00 2.44
3098 3326 5.234116 AGTGCGTGATGGAATTTTCAAAAAC 59.766 36.000 0.00 0.00 0.00 2.43
3099 3327 5.006165 GTGCGTGATGGAATTTTCAAAAACA 59.994 36.000 0.00 0.00 0.00 2.83
3100 3328 5.582269 TGCGTGATGGAATTTTCAAAAACAA 59.418 32.000 0.00 0.00 0.00 2.83
3101 3329 6.092670 TGCGTGATGGAATTTTCAAAAACAAA 59.907 30.769 0.00 0.00 0.00 2.83
3102 3330 6.963805 GCGTGATGGAATTTTCAAAAACAAAA 59.036 30.769 0.00 0.00 0.00 2.44
3104 3332 8.997960 CGTGATGGAATTTTCAAAAACAAAAAG 58.002 29.630 0.00 0.00 0.00 2.27
3107 3335 8.686397 ATGGAATTTTCAAAAACAAAAAGTGC 57.314 26.923 0.00 0.00 33.34 4.40
3108 3336 6.798959 TGGAATTTTCAAAAACAAAAAGTGCG 59.201 30.769 0.00 0.00 34.77 5.34
3109 3337 6.799441 GGAATTTTCAAAAACAAAAAGTGCGT 59.201 30.769 0.00 0.00 0.00 5.24
3110 3338 7.201224 GGAATTTTCAAAAACAAAAAGTGCGTG 60.201 33.333 0.00 0.00 0.00 5.34
3111 3339 5.907197 TTTCAAAAACAAAAAGTGCGTGA 57.093 30.435 0.00 0.00 0.00 4.35
3112 3340 6.473397 TTTCAAAAACAAAAAGTGCGTGAT 57.527 29.167 0.00 0.00 0.00 3.06
3113 3341 5.447478 TCAAAAACAAAAAGTGCGTGATG 57.553 34.783 0.00 0.00 0.00 3.07
3127 3355 1.086634 GTGATGGAGAACCGAGCTGC 61.087 60.000 0.00 0.00 39.42 5.25
3135 3363 3.288308 AACCGAGCTGCCTGTCGAG 62.288 63.158 10.81 4.58 38.50 4.04
3145 3373 2.575993 CTGTCGAGCTGGAGGTGG 59.424 66.667 0.00 0.00 0.00 4.61
3194 3422 2.560981 TGTCCAGCGACAGTGAAAGATA 59.439 45.455 0.00 0.00 44.20 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 3.770040 CCCCAGCCGACGACATCA 61.770 66.667 0.00 0.00 0.00 3.07
59 60 3.982576 ACTTTTCGATTTTCTTGCCGT 57.017 38.095 0.00 0.00 0.00 5.68
62 63 9.180678 TGAATAAGAACTTTTCGATTTTCTTGC 57.819 29.630 15.77 9.21 38.47 4.01
71 72 8.361139 AGAGTCTCTTGAATAAGAACTTTTCGA 58.639 33.333 0.00 0.00 42.11 3.71
147 151 1.135546 CACTCTCGCGTGACAATCTCT 60.136 52.381 5.77 0.00 37.06 3.10
155 159 4.103103 CGCCTCACTCTCGCGTGA 62.103 66.667 10.80 10.80 41.33 4.35
256 273 0.674895 GCTGCACCCTTCGATGTCTT 60.675 55.000 0.00 0.00 0.00 3.01
272 289 5.030295 CGTGCCTAAAAATAGTCATTGCTG 58.970 41.667 0.00 0.00 0.00 4.41
277 294 4.513442 TGCTCGTGCCTAAAAATAGTCAT 58.487 39.130 7.05 0.00 38.71 3.06
305 325 5.534654 ACTGTAGCCAAAGCACTTGATAAAA 59.465 36.000 0.38 0.00 43.56 1.52
324 344 6.785337 TCGAAAATTCCCTCATAGACTGTA 57.215 37.500 0.00 0.00 0.00 2.74
326 346 5.698545 GGATCGAAAATTCCCTCATAGACTG 59.301 44.000 0.00 0.00 0.00 3.51
327 347 5.366768 TGGATCGAAAATTCCCTCATAGACT 59.633 40.000 0.41 0.00 0.00 3.24
351 371 4.838423 AGGCCATAGCTTTTTACCAAAACT 59.162 37.500 5.01 0.00 39.73 2.66
356 376 2.099405 GCAGGCCATAGCTTTTTACCA 58.901 47.619 5.01 0.00 39.73 3.25
396 416 6.237019 CGCATAATTCAAGTGAACAACATTCG 60.237 38.462 0.00 0.00 36.80 3.34
424 447 1.940613 GTCGAACAATCCATAGCCACC 59.059 52.381 0.00 0.00 0.00 4.61
537 560 5.974156 TTATTTCTCATCCTCCATGTCCA 57.026 39.130 0.00 0.00 33.66 4.02
655 813 4.513406 AGGGTTTTCTTGTGTACTCCAA 57.487 40.909 0.00 0.00 0.00 3.53
678 865 2.722094 ACGCATTGAGGCAAGGAAATA 58.278 42.857 0.00 0.00 0.00 1.40
685 872 4.202060 TGTTAGAAAAACGCATTGAGGCAA 60.202 37.500 0.00 0.00 0.00 4.52
696 883 7.043656 GGAAATCACCTTTGTGTTAGAAAAACG 60.044 37.037 0.00 0.00 43.26 3.60
731 918 4.487019 TGTCCGTCCTTCAAAACAAAAAC 58.513 39.130 0.00 0.00 0.00 2.43
737 924 5.930569 AGTACTAATGTCCGTCCTTCAAAAC 59.069 40.000 0.00 0.00 0.00 2.43
761 949 2.632602 ATTTCGCCACCACCACCACA 62.633 55.000 0.00 0.00 0.00 4.17
947 1147 1.154016 CACCGTCTCAGTGCGTAGG 60.154 63.158 0.00 0.00 0.00 3.18
1818 2019 0.179097 GGTTGAGCTGATCGGGACTC 60.179 60.000 3.14 3.05 0.00 3.36
1821 2022 2.721167 CGGGTTGAGCTGATCGGGA 61.721 63.158 3.14 0.00 0.00 5.14
1971 2172 2.985456 CTCCAGAAGCTTCGGCCT 59.015 61.111 23.98 6.33 43.01 5.19
2130 2331 0.613260 CGGAGGACAGGGACATGAAA 59.387 55.000 0.00 0.00 0.00 2.69
2311 2516 2.661537 CGCAAGGACAGTGCACGA 60.662 61.111 12.01 0.00 42.33 4.35
2543 2753 3.157217 ATCGGACGGCTCAGATGGC 62.157 63.158 0.00 0.00 30.87 4.40
2583 2793 2.582498 GGTCCATCGCCTTCGTCG 60.582 66.667 0.00 0.00 36.96 5.12
2584 2794 2.582498 CGGTCCATCGCCTTCGTC 60.582 66.667 0.00 0.00 36.96 4.20
2585 2795 4.143333 CCGGTCCATCGCCTTCGT 62.143 66.667 0.00 0.00 36.96 3.85
2586 2796 3.774959 CTCCGGTCCATCGCCTTCG 62.775 68.421 0.00 0.00 0.00 3.79
2587 2797 2.107141 CTCCGGTCCATCGCCTTC 59.893 66.667 0.00 0.00 0.00 3.46
2588 2798 4.162690 GCTCCGGTCCATCGCCTT 62.163 66.667 0.00 0.00 0.00 4.35
2591 2801 4.814294 AACGCTCCGGTCCATCGC 62.814 66.667 0.00 0.00 0.00 4.58
2592 2802 2.582498 GAACGCTCCGGTCCATCG 60.582 66.667 0.00 1.62 37.65 3.84
2593 2803 2.582498 CGAACGCTCCGGTCCATC 60.582 66.667 0.00 0.00 40.86 3.51
2594 2804 2.444700 AAACGAACGCTCCGGTCCAT 62.445 55.000 0.00 0.00 40.86 3.41
2597 2807 0.942884 AGAAAACGAACGCTCCGGTC 60.943 55.000 0.00 0.00 40.50 4.79
2653 2875 4.072131 GGTAGAGAAGAACACATGGCAAA 58.928 43.478 0.00 0.00 0.00 3.68
2675 2897 9.182933 GCTTCTATATAACTGAGTTTTCTACCG 57.817 37.037 1.97 0.00 0.00 4.02
2724 2948 2.234300 ATACCACAAATAGGACGCCG 57.766 50.000 0.00 0.00 0.00 6.46
2779 3003 8.514594 ACGAAGATGAATATTCTTTTTCTTGCA 58.485 29.630 21.93 0.00 33.65 4.08
2889 3113 0.400213 ATTTGGGGAAGCTCACGACA 59.600 50.000 0.00 0.00 0.00 4.35
2931 3155 1.301716 CGGCAATAGGATGGACCCG 60.302 63.158 0.00 0.00 40.05 5.28
2933 3157 0.693049 ATCCGGCAATAGGATGGACC 59.307 55.000 0.00 0.00 46.01 4.46
2988 3216 1.061411 CGCATCTCGCAACACCATG 59.939 57.895 0.00 0.00 42.60 3.66
3044 3272 1.675552 TCCGATGCATCTCTACACGA 58.324 50.000 23.73 5.55 0.00 4.35
3076 3304 5.111989 TGTTTTTGAAAATTCCATCACGCA 58.888 33.333 0.00 0.00 0.00 5.24
3082 3310 7.484324 CGCACTTTTTGTTTTTGAAAATTCCAT 59.516 29.630 0.00 0.00 0.00 3.41
3083 3311 6.798959 CGCACTTTTTGTTTTTGAAAATTCCA 59.201 30.769 0.00 0.00 0.00 3.53
3084 3312 6.799441 ACGCACTTTTTGTTTTTGAAAATTCC 59.201 30.769 0.00 0.00 0.00 3.01
3086 3314 7.355778 TCACGCACTTTTTGTTTTTGAAAATT 58.644 26.923 0.00 0.00 0.00 1.82
3088 3316 6.287107 TCACGCACTTTTTGTTTTTGAAAA 57.713 29.167 0.00 0.00 0.00 2.29
3089 3317 5.907197 TCACGCACTTTTTGTTTTTGAAA 57.093 30.435 0.00 0.00 0.00 2.69
3090 3318 5.163913 CCATCACGCACTTTTTGTTTTTGAA 60.164 36.000 0.00 0.00 0.00 2.69
3091 3319 4.328440 CCATCACGCACTTTTTGTTTTTGA 59.672 37.500 0.00 0.00 0.00 2.69
3092 3320 4.328440 TCCATCACGCACTTTTTGTTTTTG 59.672 37.500 0.00 0.00 0.00 2.44
3093 3321 4.499183 TCCATCACGCACTTTTTGTTTTT 58.501 34.783 0.00 0.00 0.00 1.94
3095 3323 3.380004 TCTCCATCACGCACTTTTTGTTT 59.620 39.130 0.00 0.00 0.00 2.83
3096 3324 2.948979 TCTCCATCACGCACTTTTTGTT 59.051 40.909 0.00 0.00 0.00 2.83
3098 3326 3.300009 GTTCTCCATCACGCACTTTTTG 58.700 45.455 0.00 0.00 0.00 2.44
3099 3327 2.293399 GGTTCTCCATCACGCACTTTTT 59.707 45.455 0.00 0.00 0.00 1.94
3100 3328 1.880027 GGTTCTCCATCACGCACTTTT 59.120 47.619 0.00 0.00 0.00 2.27
3101 3329 1.523758 GGTTCTCCATCACGCACTTT 58.476 50.000 0.00 0.00 0.00 2.66
3102 3330 0.670546 CGGTTCTCCATCACGCACTT 60.671 55.000 0.00 0.00 0.00 3.16
3104 3332 1.078759 CTCGGTTCTCCATCACGCAC 61.079 60.000 0.00 0.00 0.00 5.34
3107 3335 0.803768 CAGCTCGGTTCTCCATCACG 60.804 60.000 0.00 0.00 0.00 4.35
3108 3336 1.086634 GCAGCTCGGTTCTCCATCAC 61.087 60.000 0.00 0.00 0.00 3.06
3109 3337 1.219124 GCAGCTCGGTTCTCCATCA 59.781 57.895 0.00 0.00 0.00 3.07
3110 3338 1.522580 GGCAGCTCGGTTCTCCATC 60.523 63.158 0.00 0.00 0.00 3.51
3111 3339 1.992277 AGGCAGCTCGGTTCTCCAT 60.992 57.895 0.00 0.00 0.00 3.41
3112 3340 2.604686 AGGCAGCTCGGTTCTCCA 60.605 61.111 0.00 0.00 0.00 3.86
3113 3341 2.125350 CAGGCAGCTCGGTTCTCC 60.125 66.667 0.00 0.00 0.00 3.71
3127 3355 2.575993 CACCTCCAGCTCGACAGG 59.424 66.667 0.00 0.00 0.00 4.00
3135 3363 0.394899 CAAGGGAATCCACCTCCAGC 60.395 60.000 0.09 0.00 37.35 4.85
3136 3364 1.211457 CTCAAGGGAATCCACCTCCAG 59.789 57.143 0.09 0.00 37.35 3.86


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

AutoCloner maintained by Alex Coulton.