Multiple sequence alignment - TraesCS1B01G233300

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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 TraesCS1B01G233300 chr1B 100.000 2828 0 0 1 2828 418820208 418823035 0.000000e+00 5223
1 TraesCS1B01G233300 chr1D 94.049 2638 88 34 241 2828 309087072 309089690 0.000000e+00 3938
2 TraesCS1B01G233300 chr1D 94.422 251 13 1 1 250 309086639 309086889 4.420000e-103 385
3 TraesCS1B01G233300 chr1A 92.155 2065 64 33 824 2828 388848966 388850992 0.000000e+00 2826
4 TraesCS1B01G233300 chr1A 92.910 268 9 3 567 831 388847442 388847702 5.720000e-102 381
5 TraesCS1B01G233300 chr2A 86.909 275 31 4 1251 1524 672265685 672265415 1.270000e-78 303
6 TraesCS1B01G233300 chr6A 85.911 291 32 8 1235 1522 465389758 465390042 4.580000e-78 302
7 TraesCS1B01G233300 chr6A 87.352 253 30 2 1261 1512 465316699 465316950 3.560000e-74 289
8 TraesCS1B01G233300 chr6B 85.324 293 34 8 1233 1522 495543804 495543518 7.660000e-76 294
9 TraesCS1B01G233300 chr6D 87.402 254 28 4 1261 1512 326572805 326573056 3.560000e-74 289
10 TraesCS1B01G233300 chr6D 84.880 291 35 8 1235 1522 326760682 326760966 4.610000e-73 285
11 TraesCS1B01G233300 chr2D 85.766 274 36 2 1251 1524 527272567 527272297 1.280000e-73 287


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 TraesCS1B01G233300 chr1B 418820208 418823035 2827 False 5223.0 5223 100.0000 1 2828 1 chr1B.!!$F1 2827
1 TraesCS1B01G233300 chr1D 309086639 309089690 3051 False 2161.5 3938 94.2355 1 2828 2 chr1D.!!$F1 2827
2 TraesCS1B01G233300 chr1A 388847442 388850992 3550 False 1603.5 2826 92.5325 567 2828 2 chr1A.!!$F1 2261

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
634 833 0.032017 TCTCCCTTGTCCTAGCTCCC 60.032 60.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2551 4089 0.10104 TTTTGTCTGCACTGCACTGC 59.899 50.0 10.99 10.99 37.7 4.4 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
37 38 9.640963 ACTTGTACTGTTGAATATCTAGTGTTC 57.359 33.333 0.00 0.00 0.00 3.18
40 41 8.033038 TGTACTGTTGAATATCTAGTGTTCACC 58.967 37.037 0.00 2.54 37.62 4.02
45 46 7.658167 TGTTGAATATCTAGTGTTCACCGAAAA 59.342 33.333 0.00 0.00 37.62 2.29
169 171 5.063017 TCGGATCTAGACCTGGTCTTATT 57.937 43.478 32.49 17.75 40.28 1.40
178 180 4.341520 AGACCTGGTCTTATTCCATACGTC 59.658 45.833 23.49 0.00 40.28 4.34
190 192 9.104965 CTTATTCCATACGTCTCCACAAATAAA 57.895 33.333 0.00 0.00 0.00 1.40
227 229 4.326278 CATATAAGCACCGCTTGTATACCG 59.674 45.833 14.94 0.00 46.05 4.02
292 486 7.816995 GCTCCCAATTTCATAAACACACATTTA 59.183 33.333 0.00 0.00 0.00 1.40
396 591 9.843334 ACAAAAGAAACAAAAACGTGAATAGTA 57.157 25.926 0.00 0.00 0.00 1.82
468 663 6.625532 ATTTGCATCTGGAAATTTTAGGGT 57.374 33.333 4.09 0.00 42.20 4.34
477 672 4.706476 TGGAAATTTTAGGGTCTGCAGATG 59.294 41.667 21.47 0.00 0.00 2.90
634 833 0.032017 TCTCCCTTGTCCTAGCTCCC 60.032 60.000 0.00 0.00 0.00 4.30
731 930 2.615493 GCATGTAGTACCACAAGGCACT 60.615 50.000 13.71 0.00 43.97 4.40
737 936 3.626930 AGTACCACAAGGCACTGAAAAA 58.373 40.909 0.00 0.00 40.12 1.94
865 2335 3.746492 CAGTAAACTTTTCTCCCACCTCG 59.254 47.826 0.00 0.00 0.00 4.63
914 2387 0.461163 CGAACAGACACACACCACCA 60.461 55.000 0.00 0.00 0.00 4.17
919 2392 0.107214 AGACACACACCACCACAAGG 60.107 55.000 0.00 0.00 42.21 3.61
951 2424 3.552839 CGAGAGCTCGCTTGCAGC 61.553 66.667 15.76 8.30 46.50 5.25
952 2425 2.433838 GAGAGCTCGCTTGCAGCA 60.434 61.111 10.55 0.00 42.58 4.41
953 2426 2.031516 GAGAGCTCGCTTGCAGCAA 61.032 57.895 10.55 7.81 42.58 3.91
1038 2511 1.269998 CTCCAAGAAACCTCGTCGTCT 59.730 52.381 0.00 0.00 0.00 4.18
1226 2699 1.681327 CGGAGGAGGGGAAGACGAA 60.681 63.158 0.00 0.00 0.00 3.85
1536 3021 3.033764 GCCGCGTTCACGTCTTCA 61.034 61.111 4.92 0.00 42.22 3.02
1791 3285 1.874019 CGTCGAGGAGGTCAATGCG 60.874 63.158 0.00 0.00 0.00 4.73
2259 3782 4.561105 CAAGAAGCTCGAAGTTAAGAGGT 58.439 43.478 6.69 6.69 45.77 3.85
2264 3787 4.333690 AGCTCGAAGTTAAGAGGTCACTA 58.666 43.478 6.69 0.00 40.72 2.74
2398 3928 4.122776 GCATCAGATCCTGTCGTAAACAT 58.877 43.478 0.00 0.00 37.23 2.71
2421 3951 9.410556 ACATCATGTTGAACTTTATTAGTTTGC 57.589 29.630 10.74 0.00 47.00 3.68
2548 4086 1.676529 CCTCCATGATCAAGCAAGCAG 59.323 52.381 0.00 0.00 0.00 4.24
2549 4087 2.640184 CTCCATGATCAAGCAAGCAGA 58.360 47.619 0.00 0.00 0.00 4.26
2550 4088 2.614520 CTCCATGATCAAGCAAGCAGAG 59.385 50.000 0.00 0.00 0.00 3.35
2551 4089 1.676529 CCATGATCAAGCAAGCAGAGG 59.323 52.381 0.00 0.00 0.00 3.69
2552 4090 1.065701 CATGATCAAGCAAGCAGAGGC 59.934 52.381 0.00 0.00 41.61 4.70
2555 4093 0.037877 ATCAAGCAAGCAGAGGCAGT 59.962 50.000 0.00 0.00 44.61 4.40
2573 4111 0.595825 GTGCAGTGCAGACAAAAGGC 60.596 55.000 20.42 0.00 40.08 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.196193 TCAACAGTACAAGTTCAAGTGGG 58.804 43.478 0.00 0.00 0.00 4.61
8 9 9.639601 CACTAGATATTCAACAGTACAAGTTCA 57.360 33.333 0.00 0.00 0.00 3.18
37 38 6.735130 AGTTAGATTTCCAAACTTTTCGGTG 58.265 36.000 0.00 0.00 29.25 4.94
40 41 8.770828 TGTCTAGTTAGATTTCCAAACTTTTCG 58.229 33.333 0.00 0.00 35.23 3.46
123 124 7.041303 CGAGTCATCTTAAGTAGGTGCACTATA 60.041 40.741 17.98 7.51 34.80 1.31
129 130 3.380637 TCCGAGTCATCTTAAGTAGGTGC 59.619 47.826 1.63 0.00 34.80 5.01
169 171 6.231951 TGTTTTATTTGTGGAGACGTATGGA 58.768 36.000 0.00 0.00 0.00 3.41
178 180 9.507280 GTATGATGTCATGTTTTATTTGTGGAG 57.493 33.333 5.78 0.00 37.15 3.86
190 192 7.118245 CGGTGCTTATATGTATGATGTCATGTT 59.882 37.037 5.78 0.00 37.15 2.71
246 248 3.548745 CATGAGAGCATGTGAAGGGTA 57.451 47.619 0.00 0.00 45.41 3.69
453 648 4.335416 TCTGCAGACCCTAAAATTTCCAG 58.665 43.478 13.74 0.00 0.00 3.86
456 651 4.676546 GCATCTGCAGACCCTAAAATTTC 58.323 43.478 20.97 0.00 41.59 2.17
505 700 8.805175 ACATTCAAATGGTTCACAAATATCTGA 58.195 29.630 7.58 0.00 40.70 3.27
506 701 8.865978 CACATTCAAATGGTTCACAAATATCTG 58.134 33.333 7.58 0.00 40.70 2.90
507 702 8.036575 CCACATTCAAATGGTTCACAAATATCT 58.963 33.333 7.58 0.00 40.70 1.98
508 703 7.278424 CCCACATTCAAATGGTTCACAAATATC 59.722 37.037 7.58 0.00 40.70 1.63
509 704 7.104939 CCCACATTCAAATGGTTCACAAATAT 58.895 34.615 7.58 0.00 40.70 1.28
510 705 6.042552 ACCCACATTCAAATGGTTCACAAATA 59.957 34.615 7.58 0.00 40.70 1.40
511 706 5.163216 ACCCACATTCAAATGGTTCACAAAT 60.163 36.000 7.58 0.00 40.70 2.32
550 746 7.228507 GCTCCTAATTTTGAAAACCCACATTTT 59.771 33.333 0.00 0.00 34.46 1.82
554 750 4.651503 TGCTCCTAATTTTGAAAACCCACA 59.348 37.500 0.00 0.00 0.00 4.17
645 844 1.069049 ACAAATTTGAGTGGCTGTGGC 59.931 47.619 24.64 0.00 37.82 5.01
646 845 3.305335 GGTACAAATTTGAGTGGCTGTGG 60.305 47.826 24.64 0.00 0.00 4.17
647 846 3.609175 CGGTACAAATTTGAGTGGCTGTG 60.609 47.826 24.64 0.00 0.00 3.66
648 847 2.552315 CGGTACAAATTTGAGTGGCTGT 59.448 45.455 24.64 2.76 0.00 4.40
649 848 2.552315 ACGGTACAAATTTGAGTGGCTG 59.448 45.455 24.64 14.61 0.00 4.85
650 849 2.858745 ACGGTACAAATTTGAGTGGCT 58.141 42.857 24.64 3.62 0.00 4.75
651 850 3.003897 TCAACGGTACAAATTTGAGTGGC 59.996 43.478 24.64 8.90 0.00 5.01
710 909 1.737793 GTGCCTTGTGGTACTACATGC 59.262 52.381 20.49 20.49 44.16 4.06
737 936 3.167485 AGGGCACATGTTCATCATTGTT 58.833 40.909 0.00 0.00 34.09 2.83
738 937 2.811410 AGGGCACATGTTCATCATTGT 58.189 42.857 0.00 0.00 34.09 2.71
865 2335 3.648545 AGTGGGGGTTTATATGAGAGAGC 59.351 47.826 0.00 0.00 0.00 4.09
947 2420 0.529378 AGTATGGCTTTGCTTGCTGC 59.471 50.000 0.00 0.00 43.25 5.25
948 2421 1.133790 GGAGTATGGCTTTGCTTGCTG 59.866 52.381 0.00 0.00 0.00 4.41
949 2422 1.005215 AGGAGTATGGCTTTGCTTGCT 59.995 47.619 0.00 0.00 0.00 3.91
950 2423 1.467920 AGGAGTATGGCTTTGCTTGC 58.532 50.000 0.00 0.00 0.00 4.01
951 2424 2.424956 GGAAGGAGTATGGCTTTGCTTG 59.575 50.000 0.00 0.00 0.00 4.01
952 2425 2.621668 GGGAAGGAGTATGGCTTTGCTT 60.622 50.000 0.00 0.00 0.00 3.91
953 2426 1.064389 GGGAAGGAGTATGGCTTTGCT 60.064 52.381 0.00 0.00 0.00 3.91
955 2428 2.743183 CGAGGGAAGGAGTATGGCTTTG 60.743 54.545 0.00 0.00 0.00 2.77
958 2431 0.032017 ACGAGGGAAGGAGTATGGCT 60.032 55.000 0.00 0.00 0.00 4.75
959 2432 0.389757 GACGAGGGAAGGAGTATGGC 59.610 60.000 0.00 0.00 0.00 4.40
960 2433 0.669077 CGACGAGGGAAGGAGTATGG 59.331 60.000 0.00 0.00 0.00 2.74
961 2434 1.065701 CACGACGAGGGAAGGAGTATG 59.934 57.143 0.00 0.00 0.00 2.39
1187 2660 4.806339 CCTCCCGCCCTCCCTCTT 62.806 72.222 0.00 0.00 0.00 2.85
1226 2699 1.667467 GCTTGCTCTTCTTCGTCGTCT 60.667 52.381 0.00 0.00 0.00 4.18
1968 3466 7.720957 TCACTACGTACTCCCTTATGCTTATTA 59.279 37.037 0.00 0.00 0.00 0.98
1969 3467 6.548622 TCACTACGTACTCCCTTATGCTTATT 59.451 38.462 0.00 0.00 0.00 1.40
2183 3706 4.675510 CATGGCATGGAACTCAAATGTAC 58.324 43.478 19.80 0.00 0.00 2.90
2259 3782 7.391148 AAGTTTTCAAAGTCAGCTTTAGTGA 57.609 32.000 0.00 0.00 42.54 3.41
2421 3951 4.314121 CTTCTTCTCCCAACTTCACTGAG 58.686 47.826 0.00 0.00 0.00 3.35
2548 4086 2.031616 TCTGCACTGCACTGCCTC 59.968 61.111 14.65 0.00 36.21 4.70
2549 4087 2.281345 GTCTGCACTGCACTGCCT 60.281 61.111 14.65 0.00 36.21 4.75
2550 4088 1.727511 TTTGTCTGCACTGCACTGCC 61.728 55.000 14.65 1.80 36.21 4.85
2551 4089 0.101040 TTTTGTCTGCACTGCACTGC 59.899 50.000 10.99 10.99 37.70 4.40
2552 4090 1.268896 CCTTTTGTCTGCACTGCACTG 60.269 52.381 0.00 0.00 33.79 3.66
2555 4093 1.735360 GCCTTTTGTCTGCACTGCA 59.265 52.632 3.11 3.11 36.92 4.41
2573 4111 2.821366 GCCACATGAGGAGTGCCG 60.821 66.667 13.99 0.00 39.96 5.69


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

AutoCloner maintained by Alex Coulton.