Multiple sequence alignment - TraesCS2A01G503400

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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 TraesCS2A01G503400 chr2A 100.000 3592 0 0 1 3592 732854578 732850987 0.000000e+00 6634.0
1 TraesCS2A01G503400 chr2A 94.665 1387 55 3 1244 2630 732599375 732600742 0.000000e+00 2134.0
2 TraesCS2A01G503400 chr2A 77.485 1026 181 28 1588 2597 722072238 722071247 1.450000e-158 569.0
3 TraesCS2A01G503400 chr2B 97.218 3163 64 5 1 3155 727207695 727204549 0.000000e+00 5332.0
4 TraesCS2A01G503400 chr2B 97.190 1388 36 3 1244 2630 727084905 727086290 0.000000e+00 2344.0
5 TraesCS2A01G503400 chr2B 78.028 1065 187 25 1547 2597 709784373 709783342 8.470000e-176 627.0
6 TraesCS2A01G503400 chr2B 92.449 437 21 3 3156 3592 727204469 727204045 6.590000e-172 614.0
7 TraesCS2A01G503400 chr2B 86.567 67 9 0 1701 1767 101073273 101073339 1.380000e-09 75.0
8 TraesCS2A01G503400 chr1B 79.598 1392 218 45 1239 2602 656422870 656421517 0.000000e+00 937.0
9 TraesCS2A01G503400 chr2D 80.544 478 74 12 1538 2000 587257903 587257430 2.050000e-92 350.0
10 TraesCS2A01G503400 chr2D 77.456 621 108 15 1987 2602 587242009 587241416 3.430000e-90 342.0
11 TraesCS2A01G503400 chr2D 78.512 121 24 2 1648 1767 64732666 64732785 1.070000e-10 78.7
12 TraesCS2A01G503400 chr4B 85.088 114 17 0 786 899 143894817 143894930 2.270000e-22 117.0


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 TraesCS2A01G503400 chr2A 732850987 732854578 3591 True 6634 6634 100.0000 1 3592 1 chr2A.!!$R2 3591
1 TraesCS2A01G503400 chr2A 732599375 732600742 1367 False 2134 2134 94.6650 1244 2630 1 chr2A.!!$F1 1386
2 TraesCS2A01G503400 chr2A 722071247 722072238 991 True 569 569 77.4850 1588 2597 1 chr2A.!!$R1 1009
3 TraesCS2A01G503400 chr2B 727204045 727207695 3650 True 2973 5332 94.8335 1 3592 2 chr2B.!!$R2 3591
4 TraesCS2A01G503400 chr2B 727084905 727086290 1385 False 2344 2344 97.1900 1244 2630 1 chr2B.!!$F2 1386
5 TraesCS2A01G503400 chr2B 709783342 709784373 1031 True 627 627 78.0280 1547 2597 1 chr2B.!!$R1 1050
6 TraesCS2A01G503400 chr1B 656421517 656422870 1353 True 937 937 79.5980 1239 2602 1 chr1B.!!$R1 1363
7 TraesCS2A01G503400 chr2D 587241416 587242009 593 True 342 342 77.4560 1987 2602 1 chr2D.!!$R1 615

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
472 473 0.320771 CCTCTTGGTGGAACAGGTCG 60.321 60.0 0.00 0.0 41.80 4.79 F
1077 1078 0.477204 CCCATGGCTCTGACATCCAT 59.523 55.0 6.09 0.0 40.98 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2387 2411 0.172803 CTTTCAGGCTGCCTTCATGC 59.827 55.0 20.79 0.0 0.00 4.06 R
2655 2682 0.179032 ACAAGCCGAATGGACACACA 60.179 50.0 0.00 0.0 37.49 3.72 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
34 35 3.118112 TCATTTCAGGAAGCAGGAGGATC 60.118 47.826 0.00 0.00 0.00 3.36
64 65 4.349342 CCCCTCCTAAGCATCTCTTACAAT 59.651 45.833 0.00 0.00 36.25 2.71
145 146 4.966787 TGGCGACAACCTTGGGGC 62.967 66.667 0.00 0.00 37.44 5.80
148 149 3.966543 CGACAACCTTGGGGCCCT 61.967 66.667 25.93 0.00 35.63 5.19
149 150 2.283173 GACAACCTTGGGGCCCTG 60.283 66.667 25.93 15.90 35.63 4.45
263 264 1.073474 AGCTGCCCAGGGATATGGA 60.073 57.895 10.89 0.00 43.57 3.41
377 378 4.479993 GACCCAGCAGCAGCCGAT 62.480 66.667 0.00 0.00 43.56 4.18
441 442 1.767681 GAGCCAGAGGTTGAGATGGAT 59.232 52.381 0.00 0.00 34.60 3.41
442 443 1.489649 AGCCAGAGGTTGAGATGGATG 59.510 52.381 0.00 0.00 34.60 3.51
461 462 0.322546 GGACGCAAATCCCTCTTGGT 60.323 55.000 0.00 0.00 34.77 3.67
472 473 0.320771 CCTCTTGGTGGAACAGGTCG 60.321 60.000 0.00 0.00 41.80 4.79
596 597 2.220313 GCTCAAAGAGATGATGGAGGC 58.780 52.381 0.00 0.00 0.00 4.70
870 871 2.549778 GCAGCAGTCTCAACTTCTTCCT 60.550 50.000 0.00 0.00 31.71 3.36
975 976 3.797269 AGGGGCATAAGAAGGGGAAATAA 59.203 43.478 0.00 0.00 0.00 1.40
1030 1031 1.062121 AGATGGAAGAGGAATCCGGGA 60.062 52.381 0.00 0.00 39.98 5.14
1077 1078 0.477204 CCCATGGCTCTGACATCCAT 59.523 55.000 6.09 0.00 40.98 3.41
1089 1090 6.239148 GCTCTGACATCCATAGTAGTGATCAA 60.239 42.308 0.00 0.00 0.00 2.57
1125 1126 1.602311 AGGTTGACAAGCAGAAGCAG 58.398 50.000 18.93 0.00 45.49 4.24
1217 1218 3.198068 CCAAGGTTGAGATGGACATACG 58.802 50.000 0.00 0.00 36.27 3.06
1221 1222 3.133003 AGGTTGAGATGGACATACGGAAG 59.867 47.826 0.00 0.00 0.00 3.46
1272 1273 3.209410 GGACATAGGCAAATCAGTCCAG 58.791 50.000 0.00 0.00 43.74 3.86
1321 1322 5.461935 AGCCGCTGAGGAAGAGGATTTTT 62.462 47.826 0.09 0.00 42.45 1.94
1471 1480 5.566469 TCCTTTTACCTTTGGTTGATCGAT 58.434 37.500 0.00 0.00 37.09 3.59
1558 1567 6.500684 TTGATTTCTAACACATGCTTCTCC 57.499 37.500 0.00 0.00 0.00 3.71
2065 2087 0.989890 GCAACTCGCGATTTCTACGT 59.010 50.000 10.36 0.00 0.00 3.57
2303 2327 0.706433 ATGCCCCATCTGGTGAAGTT 59.294 50.000 0.00 0.00 0.00 2.66
2387 2411 0.171455 GGCGTGTGGTCTCTGTAGAG 59.829 60.000 2.45 2.45 43.36 2.43
2472 2499 0.107508 ACATGTCTCCTTGGCATCCG 60.108 55.000 0.00 0.00 39.27 4.18
2635 2662 4.153117 GCGGAGGCAATGTATTTATCTGAG 59.847 45.833 0.00 0.00 39.62 3.35
2776 2805 2.806244 ACTTATGTTGTGCGAGTTGACC 59.194 45.455 0.00 0.00 0.00 4.02
2784 2813 0.033504 TGCGAGTTGACCCTGACTTC 59.966 55.000 0.00 0.00 0.00 3.01
2815 2844 4.240888 TGTTTTGTTGTGTGATTGGTGTG 58.759 39.130 0.00 0.00 0.00 3.82
2916 2950 5.906113 TGTCTGGTTTTTGTGTATGTGTT 57.094 34.783 0.00 0.00 0.00 3.32
2926 2960 8.491950 GTTTTTGTGTATGTGTTTTGTTGTCTT 58.508 29.630 0.00 0.00 0.00 3.01
2927 2961 9.692749 TTTTTGTGTATGTGTTTTGTTGTCTTA 57.307 25.926 0.00 0.00 0.00 2.10
2928 2962 8.903570 TTTGTGTATGTGTTTTGTTGTCTTAG 57.096 30.769 0.00 0.00 0.00 2.18
2929 2963 6.491394 TGTGTATGTGTTTTGTTGTCTTAGC 58.509 36.000 0.00 0.00 0.00 3.09
2930 2964 6.094186 TGTGTATGTGTTTTGTTGTCTTAGCA 59.906 34.615 0.00 0.00 0.00 3.49
2931 2965 6.413818 GTGTATGTGTTTTGTTGTCTTAGCAC 59.586 38.462 0.00 0.00 0.00 4.40
2932 2966 5.574891 ATGTGTTTTGTTGTCTTAGCACA 57.425 34.783 0.00 0.00 39.44 4.57
2933 2967 5.574891 TGTGTTTTGTTGTCTTAGCACAT 57.425 34.783 0.00 0.00 31.76 3.21
2934 2968 5.960113 TGTGTTTTGTTGTCTTAGCACATT 58.040 33.333 0.00 0.00 31.76 2.71
2935 2969 6.393990 TGTGTTTTGTTGTCTTAGCACATTT 58.606 32.000 0.00 0.00 31.76 2.32
2936 2970 6.309980 TGTGTTTTGTTGTCTTAGCACATTTG 59.690 34.615 0.00 0.00 31.76 2.32
2937 2971 6.310224 GTGTTTTGTTGTCTTAGCACATTTGT 59.690 34.615 0.00 0.00 0.00 2.83
2938 2972 6.870965 TGTTTTGTTGTCTTAGCACATTTGTT 59.129 30.769 0.00 0.00 0.00 2.83
2939 2973 7.062839 TGTTTTGTTGTCTTAGCACATTTGTTC 59.937 33.333 0.00 0.00 0.00 3.18
2940 2974 6.449635 TTGTTGTCTTAGCACATTTGTTCT 57.550 33.333 0.00 0.00 0.00 3.01
3018 3052 2.018542 TTTGGCGGTTTAGAGATCGG 57.981 50.000 0.00 0.00 0.00 4.18
3139 3173 1.195448 TCGTTCGGTAGTGAACTCGTC 59.805 52.381 5.25 0.00 44.76 4.20
3180 3293 4.054780 TGCCCAACGTAGACATATTCTC 57.945 45.455 0.00 0.00 35.55 2.87
3247 3360 9.769093 CTTAAATTTGTGTTAGATTTAGGTCGG 57.231 33.333 0.00 0.00 29.82 4.79
3296 3409 4.764823 TCTGTCCATTCGCATAACCTTTTT 59.235 37.500 0.00 0.00 0.00 1.94
3392 3505 2.107141 GCCTACGCGCTTCTCCAT 59.893 61.111 5.73 0.00 0.00 3.41
3404 3517 1.203441 TTCTCCATGCTCACCCTGCT 61.203 55.000 0.00 0.00 0.00 4.24
3432 3545 4.144727 TCTCTCTCCCCCTCGCCC 62.145 72.222 0.00 0.00 0.00 6.13
3504 3617 1.845809 CTGGTGTGCGGTTTGAGCTC 61.846 60.000 6.82 6.82 35.28 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.644299 TGCTTCCTGAAATGAGGAGGAA 59.356 45.455 2.27 0.00 43.26 3.36
17 18 0.043183 TGGATCCTCCTGCTTCCTGA 59.957 55.000 14.23 0.00 37.46 3.86
34 35 0.914417 TGCTTAGGAGGGGGAACTGG 60.914 60.000 0.00 0.00 0.00 4.00
41 42 3.309296 TGTAAGAGATGCTTAGGAGGGG 58.691 50.000 0.00 0.00 39.66 4.79
64 65 2.703416 CACAGATGGTTGCTTCTGCTA 58.297 47.619 0.00 0.00 42.51 3.49
263 264 8.522830 CACCATCCAATATGTCTAACTTGTTTT 58.477 33.333 0.00 0.00 0.00 2.43
377 378 3.568007 GTCTAACTTGTTTGCCACATCCA 59.432 43.478 0.00 0.00 34.43 3.41
441 442 0.322456 CCAAGAGGGATTTGCGTCCA 60.322 55.000 5.16 0.00 40.17 4.02
442 443 0.322546 ACCAAGAGGGATTTGCGTCC 60.323 55.000 0.00 0.00 41.15 4.79
461 462 2.039418 CCATATCCTCGACCTGTTCCA 58.961 52.381 0.00 0.00 0.00 3.53
472 473 2.032178 GCGACTTGTTTGCCATATCCTC 59.968 50.000 0.00 0.00 0.00 3.71
870 871 2.373169 ACTCTGAATCTGAAGGCCACAA 59.627 45.455 5.01 0.00 0.00 3.33
975 976 1.456331 AGCAGCAGCACAAACCCTT 60.456 52.632 3.17 0.00 45.49 3.95
1008 1009 2.042464 CCGGATTCCTCTTCCATCTCA 58.958 52.381 0.00 0.00 32.45 3.27
1046 1047 2.692041 GAGCCATGGGGAAGAAATCTTG 59.308 50.000 15.13 0.00 36.11 3.02
1089 1090 2.680312 CCTTCAGGTCGATCATGTGT 57.320 50.000 0.00 0.00 0.00 3.72
1125 1126 3.129462 TGTCGATCTCAACCTCAGTCATC 59.871 47.826 0.00 0.00 0.00 2.92
1217 1218 2.203126 CCTCGGCCATCTGCTTCC 60.203 66.667 2.24 0.00 40.92 3.46
1221 1222 3.781770 CTCGACCTCGGCCATCTGC 62.782 68.421 2.24 0.00 40.29 4.26
1272 1273 4.166144 TCCTCCTTCTCCATGGTTAATTCC 59.834 45.833 12.58 0.00 0.00 3.01
1321 1322 0.615331 CAGGCCCTTCTGTAGCAAGA 59.385 55.000 0.00 0.00 0.00 3.02
1369 1373 4.755411 TCACTTGTGTCTTCGAAGAAACT 58.245 39.130 36.31 21.58 45.90 2.66
1471 1480 0.394938 TGCCGCTTGTACAAGGAAGA 59.605 50.000 31.42 10.23 38.80 2.87
1558 1567 1.736645 GCTGCATGCAAGCACCAAG 60.737 57.895 26.77 14.00 40.11 3.61
1577 1586 2.211250 AGTGCATGGAGCTCAATTGT 57.789 45.000 17.19 0.00 45.94 2.71
2065 2087 0.324614 ATGCACACCAGGATGACGAA 59.675 50.000 0.00 0.00 39.69 3.85
2303 2327 4.560136 TTTTAAACGATCAAGCAGCACA 57.440 36.364 0.00 0.00 0.00 4.57
2328 2352 0.251297 TCTGAACCACTGGGCATTGG 60.251 55.000 0.00 0.00 37.90 3.16
2387 2411 0.172803 CTTTCAGGCTGCCTTCATGC 59.827 55.000 20.79 0.00 0.00 4.06
2497 2524 4.966366 GCTCAGCATCATCAACGTTAAATC 59.034 41.667 0.00 0.00 0.00 2.17
2653 2680 1.237285 AAGCCGAATGGACACACAGC 61.237 55.000 0.00 0.00 37.49 4.40
2654 2681 0.518636 CAAGCCGAATGGACACACAG 59.481 55.000 0.00 0.00 37.49 3.66
2655 2682 0.179032 ACAAGCCGAATGGACACACA 60.179 50.000 0.00 0.00 37.49 3.72
2776 2805 8.594687 CAACAAAACATTAACTTTGAAGTCAGG 58.405 33.333 11.49 0.00 38.57 3.86
2784 2813 9.475505 CAATCACACAACAAAACATTAACTTTG 57.524 29.630 5.42 5.42 38.29 2.77
2877 2911 6.119536 ACCAGACAAGACAAAATACAGTTGA 58.880 36.000 0.00 0.00 0.00 3.18
2916 2950 6.751425 CAGAACAAATGTGCTAAGACAACAAA 59.249 34.615 0.00 0.00 30.45 2.83
2926 2960 3.751175 GTGCTACCAGAACAAATGTGCTA 59.249 43.478 0.00 0.00 30.45 3.49
2927 2961 2.554032 GTGCTACCAGAACAAATGTGCT 59.446 45.455 0.00 0.00 33.09 4.40
2928 2962 2.554032 AGTGCTACCAGAACAAATGTGC 59.446 45.455 0.00 0.00 0.00 4.57
2929 2963 4.836125 AAGTGCTACCAGAACAAATGTG 57.164 40.909 0.00 0.00 0.00 3.21
2930 2964 4.887071 TCAAAGTGCTACCAGAACAAATGT 59.113 37.500 0.00 0.00 0.00 2.71
2931 2965 5.437289 TCAAAGTGCTACCAGAACAAATG 57.563 39.130 0.00 0.00 0.00 2.32
2932 2966 5.505654 CGTTCAAAGTGCTACCAGAACAAAT 60.506 40.000 0.00 0.00 36.16 2.32
2933 2967 4.201871 CGTTCAAAGTGCTACCAGAACAAA 60.202 41.667 0.00 0.00 36.16 2.83
2934 2968 3.311322 CGTTCAAAGTGCTACCAGAACAA 59.689 43.478 0.00 0.00 36.16 2.83
2935 2969 2.869801 CGTTCAAAGTGCTACCAGAACA 59.130 45.455 0.00 0.00 36.16 3.18
2936 2970 2.223377 CCGTTCAAAGTGCTACCAGAAC 59.777 50.000 0.00 0.00 33.82 3.01
2937 2971 2.158871 ACCGTTCAAAGTGCTACCAGAA 60.159 45.455 0.00 0.00 0.00 3.02
2938 2972 1.414919 ACCGTTCAAAGTGCTACCAGA 59.585 47.619 0.00 0.00 0.00 3.86
2939 2973 1.878953 ACCGTTCAAAGTGCTACCAG 58.121 50.000 0.00 0.00 0.00 4.00
2940 2974 2.215196 GAACCGTTCAAAGTGCTACCA 58.785 47.619 6.38 0.00 0.00 3.25
2984 3018 4.889409 ACCGCCAAAAATCTGATGTCATAT 59.111 37.500 0.00 0.00 0.00 1.78
2985 3019 4.269183 ACCGCCAAAAATCTGATGTCATA 58.731 39.130 0.00 0.00 0.00 2.15
2986 3020 3.091545 ACCGCCAAAAATCTGATGTCAT 58.908 40.909 0.00 0.00 0.00 3.06
2987 3021 2.513753 ACCGCCAAAAATCTGATGTCA 58.486 42.857 0.00 0.00 0.00 3.58
2988 3022 3.575965 AACCGCCAAAAATCTGATGTC 57.424 42.857 0.00 0.00 0.00 3.06
2996 3030 3.377172 CCGATCTCTAAACCGCCAAAAAT 59.623 43.478 0.00 0.00 0.00 1.82
3108 3142 4.625742 CACTACCGAACGACTGAAAATCAT 59.374 41.667 0.00 0.00 0.00 2.45
3139 3173 3.241900 GCAATATCGCGCTGAGACATATG 60.242 47.826 5.56 0.00 0.00 1.78
3199 3312 2.752903 ACATAAATGGGTCCGAGCAAAC 59.247 45.455 0.00 0.00 0.00 2.93
3245 3358 1.227823 TGGTTTGTGTCCAGCTCCG 60.228 57.895 0.00 0.00 0.00 4.63
3268 3381 5.070446 AGGTTATGCGAATGGACAGAGAATA 59.930 40.000 0.00 0.00 0.00 1.75
3269 3382 4.130118 GGTTATGCGAATGGACAGAGAAT 58.870 43.478 0.00 0.00 0.00 2.40
3296 3409 5.587844 GCATGGCAGATAGAAAAGAGAGAAA 59.412 40.000 0.00 0.00 0.00 2.52
3297 3410 5.104610 AGCATGGCAGATAGAAAAGAGAGAA 60.105 40.000 0.00 0.00 0.00 2.87
3417 3530 2.299727 CTTAGGGCGAGGGGGAGAGA 62.300 65.000 0.00 0.00 0.00 3.10
3440 3553 3.945434 GACATGGCATGGCGAGCG 61.945 66.667 29.49 4.81 33.60 5.03
3463 3576 4.678269 ACGAGGCACGACACGACG 62.678 66.667 12.15 0.00 45.77 5.12


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

AutoCloner maintained by Alex Coulton.