Multiple sequence alignment - TraesCS2D01G523500

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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 TraesCS2D01G523500 chr2D 100.000 3377 0 0 1 3377 612346123 612342747 0.000000e+00 6237.0
1 TraesCS2D01G523500 chr2A 95.044 3087 124 15 300 3377 744450768 744447702 0.000000e+00 4826.0
2 TraesCS2D01G523500 chr2A 83.415 205 23 4 5 209 744451330 744451137 2.680000e-41 180.0
3 TraesCS2D01G523500 chr2B 94.839 3081 126 20 301 3377 747182575 747179524 0.000000e+00 4778.0
4 TraesCS2D01G523500 chr2B 89.855 207 21 0 1 207 747183150 747182944 2.000000e-67 267.0
5 TraesCS2D01G523500 chr5B 87.935 489 58 1 1638 2125 382333099 382332611 2.920000e-160 575.0
6 TraesCS2D01G523500 chr7D 83.202 381 34 15 2250 2628 618084818 618084466 4.200000e-84 322.0
7 TraesCS2D01G523500 chr7B 80.741 405 34 23 2238 2635 712467983 712467616 3.320000e-70 276.0
8 TraesCS2D01G523500 chr7A 79.874 318 26 21 2320 2635 711814462 711814181 7.390000e-47 198.0
9 TraesCS2D01G523500 chr3A 74.395 496 79 31 1906 2371 587878227 587878704 5.800000e-38 169.0
10 TraesCS2D01G523500 chr3D 85.906 149 16 4 1902 2046 446064953 446065100 1.620000e-33 154.0
11 TraesCS2D01G523500 chr5A 77.863 131 23 5 416 544 609293522 609293648 3.610000e-10 76.8
12 TraesCS2D01G523500 chr6B 90.385 52 5 0 470 521 646278300 646278351 6.050000e-08 69.4


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 TraesCS2D01G523500 chr2D 612342747 612346123 3376 True 6237.0 6237 100.0000 1 3377 1 chr2D.!!$R1 3376
1 TraesCS2D01G523500 chr2A 744447702 744451330 3628 True 2503.0 4826 89.2295 5 3377 2 chr2A.!!$R1 3372
2 TraesCS2D01G523500 chr2B 747179524 747183150 3626 True 2522.5 4778 92.3470 1 3377 2 chr2B.!!$R1 3376

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
897 1198 1.103398 CGTTCCCTCCATGCCATTCC 61.103 60.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2673 2982 0.107214 TTGAGGCCGACATTCCATCC 60.107 55.0 0.0 0.0 0.0 3.51 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
179 180 5.478407 TGTCGTATTCACAGACATGTCAAT 58.522 37.500 27.02 18.76 39.63 2.57
186 187 6.407475 TTCACAGACATGTCAATATGTTCG 57.593 37.500 27.02 11.59 41.15 3.95
266 269 7.834068 ACTAATGTATGATTATAGGCGCTTG 57.166 36.000 7.64 0.00 0.00 4.01
267 270 7.386851 ACTAATGTATGATTATAGGCGCTTGT 58.613 34.615 7.64 0.00 0.00 3.16
268 271 6.486253 AATGTATGATTATAGGCGCTTGTG 57.514 37.500 7.64 0.00 0.00 3.33
269 272 4.956085 TGTATGATTATAGGCGCTTGTGT 58.044 39.130 7.64 0.00 0.00 3.72
270 273 6.091718 TGTATGATTATAGGCGCTTGTGTA 57.908 37.500 7.64 0.00 0.00 2.90
271 274 6.697395 TGTATGATTATAGGCGCTTGTGTAT 58.303 36.000 7.64 0.00 0.00 2.29
272 275 7.832769 TGTATGATTATAGGCGCTTGTGTATA 58.167 34.615 7.64 0.00 0.00 1.47
273 276 8.308207 TGTATGATTATAGGCGCTTGTGTATAA 58.692 33.333 7.64 0.67 0.00 0.98
274 277 9.314321 GTATGATTATAGGCGCTTGTGTATAAT 57.686 33.333 7.64 6.15 32.96 1.28
280 283 3.871594 AGGCGCTTGTGTATAATTGTCTC 59.128 43.478 7.64 0.00 0.00 3.36
287 290 7.254117 CGCTTGTGTATAATTGTCTCCTTGTAG 60.254 40.741 0.00 0.00 0.00 2.74
292 295 9.601217 GTGTATAATTGTCTCCTTGTAGTCATT 57.399 33.333 0.00 0.00 0.00 2.57
503 802 5.830991 TCACTTGCCTAAAATTAACACCACT 59.169 36.000 0.00 0.00 0.00 4.00
604 903 9.157104 GTTTTAAAATTCAAAAGGACCAAGACA 57.843 29.630 3.52 0.00 0.00 3.41
610 909 6.597832 TTCAAAAGGACCAAGACAGAAAAA 57.402 33.333 0.00 0.00 0.00 1.94
624 923 8.766151 CAAGACAGAAAAAGTACTTCTAGAACC 58.234 37.037 8.95 0.00 31.84 3.62
625 924 7.443477 AGACAGAAAAAGTACTTCTAGAACCC 58.557 38.462 8.95 0.00 31.84 4.11
645 944 9.981460 AGAACCCTTCTCATAAATTAAAGTGAT 57.019 29.630 0.00 0.00 34.07 3.06
666 965 7.172532 AGTGATGTTAATTAAACGAACAGCAGA 59.827 33.333 14.82 0.00 46.59 4.26
677 976 5.847670 ACGAACAGCAGACTCTTAAATTC 57.152 39.130 0.00 0.00 0.00 2.17
897 1198 1.103398 CGTTCCCTCCATGCCATTCC 61.103 60.000 0.00 0.00 0.00 3.01
901 1202 2.203394 CTCCATGCCATTCCCCCG 60.203 66.667 0.00 0.00 0.00 5.73
903 1204 2.203394 CCATGCCATTCCCCCGAG 60.203 66.667 0.00 0.00 0.00 4.63
1964 2265 3.414700 GTTCGTGGACGGCTGCAG 61.415 66.667 10.11 10.11 40.29 4.41
2046 2347 2.097038 CGCCTTCAAGTCCGAGCTG 61.097 63.158 0.00 0.00 0.00 4.24
2049 2350 1.743252 CTTCAAGTCCGAGCTGGCC 60.743 63.158 0.00 0.00 37.80 5.36
2430 2739 2.744741 GGCTAAAGTTCTCCTGCTGTTC 59.255 50.000 0.00 0.00 0.00 3.18
2580 2889 7.214467 TCTATGAGGTCAAATTTTGTTGGTC 57.786 36.000 8.89 3.65 0.00 4.02
2623 2932 6.374613 GCCATATAAATTTAGTACCCAGCCTC 59.625 42.308 3.94 0.00 0.00 4.70
2673 2982 8.147642 AGAATTTTATCTGAATCTGCGTTAGG 57.852 34.615 0.00 0.00 0.00 2.69
2674 2983 6.867662 ATTTTATCTGAATCTGCGTTAGGG 57.132 37.500 0.00 0.00 0.00 3.53
2675 2984 5.607939 TTTATCTGAATCTGCGTTAGGGA 57.392 39.130 0.00 0.00 0.00 4.20
2676 2985 5.808366 TTATCTGAATCTGCGTTAGGGAT 57.192 39.130 0.00 0.00 0.00 3.85
2677 2986 3.459232 TCTGAATCTGCGTTAGGGATG 57.541 47.619 0.00 0.00 0.00 3.51
2782 3103 7.760340 ACTCGAATAAACCAGAGTATCAGAAAC 59.240 37.037 0.00 0.00 41.57 2.78
2796 3117 4.790765 TCAGAAACGTCAGAGACATGAT 57.209 40.909 0.00 0.00 32.09 2.45
2804 3125 2.346847 GTCAGAGACATGATTGCACGAC 59.653 50.000 0.00 0.00 32.09 4.34
3017 3339 0.865769 CTGTTCGAACGGGGAGTTTG 59.134 55.000 26.35 4.03 44.35 2.93
3106 3428 1.043816 CGGACACCATCATAGCTCCT 58.956 55.000 0.00 0.00 0.00 3.69
3193 3515 4.169271 ACGGTCTTGGTCGTCTCA 57.831 55.556 0.00 0.00 34.20 3.27
3253 3575 2.125753 CCAGCGCTGACTCTGTCC 60.126 66.667 38.06 0.00 0.00 4.02
3262 3584 2.203640 ACTCTGTCCGTCAGGCCA 60.204 61.111 5.01 0.00 43.76 5.36
3367 3689 2.194271 GCGTCCTTGCTCAGTATGTAC 58.806 52.381 0.00 0.00 37.40 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 5.416013 TGTTGTTGTAGTGTTTGATGGTTGA 59.584 36.000 0.00 0.00 0.00 3.18
102 103 8.674607 GTTATACCCCACAACTCTAAGATTTTG 58.325 37.037 0.00 0.00 0.00 2.44
112 113 6.980416 AGATAGAGTTATACCCCACAACTC 57.020 41.667 5.73 5.73 45.49 3.01
148 149 6.340522 TGTCTGTGAATACGACAATCATGAT 58.659 36.000 1.18 1.18 37.38 2.45
156 157 4.513198 TGACATGTCTGTGAATACGACA 57.487 40.909 25.55 0.00 41.18 4.35
157 158 7.222805 ACATATTGACATGTCTGTGAATACGAC 59.777 37.037 25.55 0.00 41.96 4.34
162 163 6.818142 TCGAACATATTGACATGTCTGTGAAT 59.182 34.615 25.55 18.17 41.32 2.57
165 166 6.594284 ATCGAACATATTGACATGTCTGTG 57.406 37.500 25.55 16.76 38.19 3.66
213 214 7.209471 TGTGCCAAAATAGACTACGATTTTT 57.791 32.000 0.00 0.00 38.54 1.94
214 215 6.811253 TGTGCCAAAATAGACTACGATTTT 57.189 33.333 0.00 0.00 40.19 1.82
215 216 6.597672 TGATGTGCCAAAATAGACTACGATTT 59.402 34.615 0.00 0.00 33.94 2.17
216 217 6.112734 TGATGTGCCAAAATAGACTACGATT 58.887 36.000 0.00 0.00 0.00 3.34
217 218 5.670485 TGATGTGCCAAAATAGACTACGAT 58.330 37.500 0.00 0.00 0.00 3.73
223 226 8.840321 ACATTAGTATGATGTGCCAAAATAGAC 58.160 33.333 0.00 0.00 36.43 2.59
252 255 8.029642 ACAATTATACACAAGCGCCTATAATC 57.970 34.615 2.29 0.00 0.00 1.75
256 259 5.611374 AGACAATTATACACAAGCGCCTAT 58.389 37.500 2.29 0.00 0.00 2.57
257 260 5.018539 AGACAATTATACACAAGCGCCTA 57.981 39.130 2.29 0.00 0.00 3.93
258 261 3.871594 GAGACAATTATACACAAGCGCCT 59.128 43.478 2.29 0.00 0.00 5.52
259 262 3.002348 GGAGACAATTATACACAAGCGCC 59.998 47.826 2.29 0.00 0.00 6.53
260 263 3.871594 AGGAGACAATTATACACAAGCGC 59.128 43.478 0.00 0.00 0.00 5.92
261 264 5.351465 ACAAGGAGACAATTATACACAAGCG 59.649 40.000 0.00 0.00 0.00 4.68
262 265 6.743575 ACAAGGAGACAATTATACACAAGC 57.256 37.500 0.00 0.00 0.00 4.01
263 266 9.088512 GACTACAAGGAGACAATTATACACAAG 57.911 37.037 0.00 0.00 0.00 3.16
264 267 8.590204 TGACTACAAGGAGACAATTATACACAA 58.410 33.333 0.00 0.00 0.00 3.33
265 268 8.129496 TGACTACAAGGAGACAATTATACACA 57.871 34.615 0.00 0.00 0.00 3.72
266 269 9.601217 AATGACTACAAGGAGACAATTATACAC 57.399 33.333 0.00 0.00 0.00 2.90
400 699 7.624549 TGCATCCCTATGAGTTATATTCCTTC 58.375 38.462 0.00 0.00 34.84 3.46
407 706 4.322725 CCGCTTGCATCCCTATGAGTTATA 60.323 45.833 0.00 0.00 34.84 0.98
411 710 0.107456 CCGCTTGCATCCCTATGAGT 59.893 55.000 0.00 0.00 34.84 3.41
412 711 1.233285 GCCGCTTGCATCCCTATGAG 61.233 60.000 0.00 0.00 40.77 2.90
414 713 3.348236 GCCGCTTGCATCCCTATG 58.652 61.111 0.00 0.00 40.77 2.23
503 802 3.674682 GCGGGCAATAACATAGCACAAAA 60.675 43.478 0.00 0.00 0.00 2.44
579 878 9.377312 CTGTCTTGGTCCTTTTGAATTTTAAAA 57.623 29.630 2.51 2.51 0.00 1.52
590 889 6.890268 AGTACTTTTTCTGTCTTGGTCCTTTT 59.110 34.615 0.00 0.00 0.00 2.27
604 903 8.265108 AGAAGGGTTCTAGAAGTACTTTTTCT 57.735 34.615 10.02 5.17 38.49 2.52
610 909 8.896722 TTTATGAGAAGGGTTCTAGAAGTACT 57.103 34.615 5.12 1.56 40.87 2.73
645 944 6.704493 AGAGTCTGCTGTTCGTTTAATTAACA 59.296 34.615 0.00 0.00 36.50 2.41
666 965 8.446273 CAGATGTTGATTGACGAATTTAAGAGT 58.554 33.333 0.00 0.00 0.00 3.24
677 976 1.399440 CTGGCCAGATGTTGATTGACG 59.601 52.381 29.88 0.00 0.00 4.35
901 1202 4.467084 TCACGGCGGGAATGGCTC 62.467 66.667 10.60 0.00 0.00 4.70
1482 1783 1.301401 CGGGTCAAACTCGAAGGCA 60.301 57.895 0.00 0.00 46.98 4.75
1709 2010 1.623359 CTTCTTCTCCTTCTGCGACG 58.377 55.000 0.00 0.00 0.00 5.12
1722 2023 4.430765 TCGGCGCCGTCCTTCTTC 62.431 66.667 44.16 5.75 40.74 2.87
1870 2171 4.596585 CGGCCCCAACACCTTGGT 62.597 66.667 0.00 0.00 45.22 3.67
2390 2698 2.632377 CCTACGGTAGACTGTAACGGA 58.368 52.381 16.59 0.00 37.27 4.69
2430 2739 6.924060 ACACTGTACAAAGTAGAAGCAACTAG 59.076 38.462 0.00 0.00 0.00 2.57
2509 2818 8.151596 GGAGGGAGAAAATTATTACTGTAGGAG 58.848 40.741 0.00 0.00 0.00 3.69
2545 2854 6.471233 TTGACCTCATAGATCTACAACAGG 57.529 41.667 4.10 10.03 0.00 4.00
2580 2889 9.710900 TTATATGGCTGTATGTATTCACTCTTG 57.289 33.333 0.00 0.00 0.00 3.02
2616 2925 1.277273 TCACAGATCAACAGAGGCTGG 59.723 52.381 0.00 0.00 35.51 4.85
2623 2932 8.722480 TGAACCTAAATATCACAGATCAACAG 57.278 34.615 0.00 0.00 0.00 3.16
2657 2966 2.103094 CCATCCCTAACGCAGATTCAGA 59.897 50.000 0.00 0.00 0.00 3.27
2663 2972 1.837439 ACATTCCATCCCTAACGCAGA 59.163 47.619 0.00 0.00 0.00 4.26
2666 2975 1.217882 CGACATTCCATCCCTAACGC 58.782 55.000 0.00 0.00 0.00 4.84
2667 2976 1.865865 CCGACATTCCATCCCTAACG 58.134 55.000 0.00 0.00 0.00 3.18
2668 2977 1.594331 GCCGACATTCCATCCCTAAC 58.406 55.000 0.00 0.00 0.00 2.34
2669 2978 0.472471 GGCCGACATTCCATCCCTAA 59.528 55.000 0.00 0.00 0.00 2.69
2670 2979 0.399949 AGGCCGACATTCCATCCCTA 60.400 55.000 0.00 0.00 0.00 3.53
2671 2980 1.694169 AGGCCGACATTCCATCCCT 60.694 57.895 0.00 0.00 0.00 4.20
2672 2981 1.227973 GAGGCCGACATTCCATCCC 60.228 63.158 0.00 0.00 0.00 3.85
2673 2982 0.107214 TTGAGGCCGACATTCCATCC 60.107 55.000 0.00 0.00 0.00 3.51
2674 2983 1.017387 GTTGAGGCCGACATTCCATC 58.983 55.000 0.00 0.00 0.00 3.51
2675 2984 0.327924 TGTTGAGGCCGACATTCCAT 59.672 50.000 0.00 0.00 31.92 3.41
2676 2985 0.327924 ATGTTGAGGCCGACATTCCA 59.672 50.000 14.28 8.86 43.17 3.53
2677 2986 3.175133 ATGTTGAGGCCGACATTCC 57.825 52.632 14.28 4.52 43.17 3.01
2768 3089 5.106515 TGTCTCTGACGTTTCTGATACTCTG 60.107 44.000 0.00 0.00 34.95 3.35
2782 3103 1.322637 CGTGCAATCATGTCTCTGACG 59.677 52.381 0.00 0.00 34.95 4.35
2796 3117 0.813610 CAGTCAAGGTGGTCGTGCAA 60.814 55.000 0.00 0.00 0.00 4.08
2804 3125 2.227388 GTGCAGAATTCAGTCAAGGTGG 59.773 50.000 8.44 0.00 0.00 4.61
3012 3334 5.598417 AGGCAGAATTAAGTGGAAACAAACT 59.402 36.000 0.00 0.00 46.06 2.66
3017 3339 3.367395 GGCAGGCAGAATTAAGTGGAAAC 60.367 47.826 0.00 0.00 0.00 2.78
3085 3407 1.620819 GGAGCTATGATGGTGTCCGAT 59.379 52.381 0.00 0.00 0.00 4.18
3106 3428 1.216444 CAGCAGCTACTTCTCCGCA 59.784 57.895 0.00 0.00 0.00 5.69
3193 3515 4.021229 TGGACGAGACATACCATGTTACT 58.979 43.478 0.00 0.00 45.03 2.24


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

AutoCloner maintained by Alex Coulton.