Multiple sequence alignment - TraesCS3A01G303800

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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 TraesCS3A01G303800 chr3A 100.000 5015 0 0 1 5015 538017913 538012899 0.000000e+00 9262
1 TraesCS3A01G303800 chr3D 97.167 4765 98 15 1 4747 412085186 412089931 0.000000e+00 8017
2 TraesCS3A01G303800 chr3D 90.947 243 8 3 4786 5015 412089922 412090163 1.050000e-81 315
3 TraesCS3A01G303800 chr3B 95.553 4497 150 14 2 4477 539061665 539066132 0.000000e+00 7151
4 TraesCS3A01G303800 chr3B 95.541 471 18 2 4465 4935 539066173 539066640 0.000000e+00 750


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 TraesCS3A01G303800 chr3A 538012899 538017913 5014 True 9262.0 9262 100.000 1 5015 1 chr3A.!!$R1 5014
1 TraesCS3A01G303800 chr3D 412085186 412090163 4977 False 4166.0 8017 94.057 1 5015 2 chr3D.!!$F1 5014
2 TraesCS3A01G303800 chr3B 539061665 539066640 4975 False 3950.5 7151 95.547 2 4935 2 chr3B.!!$F1 4933

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
61 64 0.179169 GTCTACTGAACGGAGGCGTC 60.179 60.000 0.00 0.0 0.0 5.19 F
624 649 0.322816 TCGTCCTGGGCGTACTACTT 60.323 55.000 21.33 0.0 0.0 2.24 F
791 816 0.668535 AGCTTGGTTGTTTCTTCGCC 59.331 50.000 0.00 0.0 0.0 5.54 F
1173 1201 1.004277 GTCCAGCACAATAACTCCCCA 59.996 52.381 0.00 0.0 0.0 4.96 F
2637 2668 1.066573 AGTGACCGATGCTTTGAGGAG 60.067 52.381 0.00 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1211 1239 1.067283 CCTGCTGTACCAGAGTGTCAG 60.067 57.143 1.10 0.0 34.77 3.51 R
2103 2134 1.630878 GAGAGCTCCTTTTTCCTCCCA 59.369 52.381 10.93 0.0 0.00 4.37 R
2637 2668 1.101331 CAATGGCTTCCTCTTCCTGC 58.899 55.000 0.00 0.0 0.00 4.85 R
2883 2914 0.392461 GCGGGTATTCCTTGACAGCA 60.392 55.000 0.00 0.0 0.00 4.41 R
4546 4631 0.036732 TGAGTGGACAACAGGATGGC 59.963 55.000 0.00 0.0 43.62 4.40 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
19 22 2.044793 TTCCTTCTGGGTCATGGAGT 57.955 50.000 0.00 0.00 36.25 3.85
20 23 2.044793 TCCTTCTGGGTCATGGAGTT 57.955 50.000 0.00 0.00 36.25 3.01
38 41 2.361737 GTCCCTCTTGCTTGGCCC 60.362 66.667 0.00 0.00 0.00 5.80
61 64 0.179169 GTCTACTGAACGGAGGCGTC 60.179 60.000 0.00 0.00 0.00 5.19
71 74 2.438795 GAGGCGTCCTCTCGAGGT 60.439 66.667 13.56 0.00 46.41 3.85
105 108 2.398252 TCTGCTTTGCCAGATCTGAG 57.602 50.000 24.62 13.95 36.96 3.35
106 109 0.733729 CTGCTTTGCCAGATCTGAGC 59.266 55.000 24.62 22.75 34.77 4.26
147 154 0.787787 CGCGATCTTGTTCGGTTTCA 59.212 50.000 0.00 0.00 39.49 2.69
150 157 2.159827 GCGATCTTGTTCGGTTTCAGTC 60.160 50.000 0.00 0.00 39.49 3.51
157 164 1.048601 TTCGGTTTCAGTCCAGAGCT 58.951 50.000 0.00 0.00 0.00 4.09
192 199 4.419921 ATTCGTTGGGACCCGGCC 62.420 66.667 5.91 0.00 0.00 6.13
230 237 2.420890 CAGATCTGGAGCCTCGGC 59.579 66.667 15.38 0.00 42.33 5.54
331 341 4.335400 TGGAAAGAGTTGCCATTTTTCC 57.665 40.909 7.22 7.22 44.38 3.13
332 342 3.966665 TGGAAAGAGTTGCCATTTTTCCT 59.033 39.130 13.53 0.00 44.41 3.36
336 346 2.158325 AGAGTTGCCATTTTTCCTCCCA 60.158 45.455 0.00 0.00 0.00 4.37
416 426 1.134431 TGGTACGCTGTGCATCATCAT 60.134 47.619 0.00 0.00 0.00 2.45
418 428 1.262417 GTACGCTGTGCATCATCATGG 59.738 52.381 0.00 0.00 0.00 3.66
419 429 1.099295 ACGCTGTGCATCATCATGGG 61.099 55.000 0.00 0.00 0.00 4.00
420 430 1.362717 GCTGTGCATCATCATGGGC 59.637 57.895 0.00 0.00 0.00 5.36
421 431 1.388837 GCTGTGCATCATCATGGGCA 61.389 55.000 1.27 1.27 0.00 5.36
517 538 4.121691 GCGCACAGCTCATCTCAT 57.878 55.556 0.30 0.00 44.04 2.90
519 540 0.530211 GCGCACAGCTCATCTCATCT 60.530 55.000 0.30 0.00 44.04 2.90
520 541 1.489574 CGCACAGCTCATCTCATCTC 58.510 55.000 0.00 0.00 0.00 2.75
521 542 1.202382 CGCACAGCTCATCTCATCTCA 60.202 52.381 0.00 0.00 0.00 3.27
522 543 2.737679 CGCACAGCTCATCTCATCTCAA 60.738 50.000 0.00 0.00 0.00 3.02
523 544 2.608546 GCACAGCTCATCTCATCTCAAC 59.391 50.000 0.00 0.00 0.00 3.18
524 545 3.196463 CACAGCTCATCTCATCTCAACC 58.804 50.000 0.00 0.00 0.00 3.77
525 546 3.106054 ACAGCTCATCTCATCTCAACCT 58.894 45.455 0.00 0.00 0.00 3.50
526 547 3.518705 ACAGCTCATCTCATCTCAACCTT 59.481 43.478 0.00 0.00 0.00 3.50
527 548 3.872182 CAGCTCATCTCATCTCAACCTTG 59.128 47.826 0.00 0.00 0.00 3.61
528 549 3.118334 AGCTCATCTCATCTCAACCTTGG 60.118 47.826 0.00 0.00 0.00 3.61
587 612 9.020813 CAAAATCAGAGTATCATCAAGCAATTG 57.979 33.333 0.00 0.00 37.82 2.32
614 639 2.300437 AGTTTTTCTCTCTCGTCCTGGG 59.700 50.000 0.00 0.00 0.00 4.45
619 644 1.716826 CTCTCTCGTCCTGGGCGTAC 61.717 65.000 21.33 0.00 0.00 3.67
624 649 0.322816 TCGTCCTGGGCGTACTACTT 60.323 55.000 21.33 0.00 0.00 2.24
674 699 3.995199 TGCTCTATCCGAATGACCAATC 58.005 45.455 0.00 0.00 0.00 2.67
791 816 0.668535 AGCTTGGTTGTTTCTTCGCC 59.331 50.000 0.00 0.00 0.00 5.54
888 916 1.560923 CCGGCTACGAACTGATTGAG 58.439 55.000 0.00 0.00 44.60 3.02
935 963 5.359860 TGTTTCTATCTTCTGCAGATACCGA 59.640 40.000 19.04 12.07 40.85 4.69
936 964 6.040955 TGTTTCTATCTTCTGCAGATACCGAT 59.959 38.462 19.04 17.72 40.85 4.18
937 965 6.656632 TTCTATCTTCTGCAGATACCGATT 57.343 37.500 19.04 1.43 40.85 3.34
938 966 6.656632 TCTATCTTCTGCAGATACCGATTT 57.343 37.500 19.04 1.41 40.85 2.17
939 967 6.450545 TCTATCTTCTGCAGATACCGATTTG 58.549 40.000 19.04 12.43 40.85 2.32
940 968 3.198068 TCTTCTGCAGATACCGATTTGC 58.802 45.455 19.04 0.00 42.25 3.68
942 970 2.279741 TCTGCAGATACCGATTTGCAC 58.720 47.619 13.74 0.00 45.52 4.57
943 971 2.009051 CTGCAGATACCGATTTGCACA 58.991 47.619 8.42 0.00 45.52 4.57
1077 1105 1.479709 ACCTGTCATCCTCTTCCTCG 58.520 55.000 0.00 0.00 0.00 4.63
1173 1201 1.004277 GTCCAGCACAATAACTCCCCA 59.996 52.381 0.00 0.00 0.00 4.96
1211 1239 7.083875 TGAAAATCGGTGATATTCTTTCCAC 57.916 36.000 0.00 0.00 0.00 4.02
1939 1970 2.223852 GCTCTTTCTCGGGTGGTAGATC 60.224 54.545 0.00 0.00 0.00 2.75
2103 2134 1.468520 CCTCGCAATGGTGATTTCGTT 59.531 47.619 0.00 0.00 31.16 3.85
2637 2668 1.066573 AGTGACCGATGCTTTGAGGAG 60.067 52.381 0.00 0.00 0.00 3.69
2730 2761 6.380414 TGATAATCTGGAGAGTGAGAAGGAT 58.620 40.000 0.00 0.00 0.00 3.24
2883 2914 2.827921 GGCAATGACTTTGATGAAGGGT 59.172 45.455 5.31 0.00 39.79 4.34
3141 3172 4.387256 GTCTGCCTATCGATATTTGAGCAC 59.613 45.833 5.40 0.00 0.00 4.40
3363 3394 1.471287 GCAGCTGCAATGTTGATGAGA 59.529 47.619 33.36 0.00 41.59 3.27
3849 3880 2.241160 TCTGTACTAGAAACACGGGCA 58.759 47.619 0.00 0.00 30.84 5.36
3915 3946 5.241403 TGATACGGAAGGCCATATTCATT 57.759 39.130 5.01 0.00 0.00 2.57
3999 4030 7.942894 AGTAAACTAACAAGGCTCCTTACAAAT 59.057 33.333 0.11 0.00 34.50 2.32
4303 4335 4.036734 TGCACAGAAGACTTTGAATTGGTC 59.963 41.667 0.00 0.00 0.00 4.02
4332 4364 6.805016 AAGTTCTGTCCTGTCTGATGATAT 57.195 37.500 0.00 0.00 0.00 1.63
4392 4424 1.117749 TCGGCTCTGATGGGAGATGG 61.118 60.000 0.00 0.00 35.52 3.51
4397 4429 2.550423 GCTCTGATGGGAGATGGATGTG 60.550 54.545 0.00 0.00 35.52 3.21
4415 4447 2.226200 TGTGGAATTGACGCATGAACTG 59.774 45.455 0.00 0.00 0.00 3.16
4513 4598 1.064505 CGTATGCTGCCACTGGAATTG 59.935 52.381 0.00 0.00 0.00 2.32
4542 4627 1.586154 GAACATGTGGCCCCTGAACG 61.586 60.000 0.00 0.00 0.00 3.95
4543 4628 2.034066 CATGTGGCCCCTGAACGT 59.966 61.111 0.00 0.00 0.00 3.99
4661 4746 7.118535 TCACTTTTAGCATTGTATAGTTCGCAA 59.881 33.333 0.00 0.00 0.00 4.85
4675 4760 3.560068 AGTTCGCAAAACTTAGTGACTGG 59.440 43.478 0.00 0.00 0.00 4.00
4721 4806 5.537300 TTATCTGAATGCTAGAGTGACCC 57.463 43.478 0.00 0.00 0.00 4.46
4796 4881 1.308783 GCTACCTGTTGCTGAAGGGC 61.309 60.000 4.51 0.00 37.94 5.19
4815 4900 2.159379 GGCGGCTGGAGAAACATAAAAG 60.159 50.000 0.00 0.00 0.00 2.27
4816 4901 2.747446 GCGGCTGGAGAAACATAAAAGA 59.253 45.455 0.00 0.00 0.00 2.52
4818 4903 4.731773 GCGGCTGGAGAAACATAAAAGATG 60.732 45.833 0.00 0.00 0.00 2.90
4916 5001 6.365970 TTCATAATTCTCCTCTAGATGGCC 57.634 41.667 0.00 0.00 33.05 5.36
4976 5073 6.698380 TCCAGAAGACAAGAATTAGTACCAC 58.302 40.000 0.00 0.00 0.00 4.16
4977 5074 6.269077 TCCAGAAGACAAGAATTAGTACCACA 59.731 38.462 0.00 0.00 0.00 4.17
5007 5104 8.508800 TTTTGCATTAAAAGGTGTTATACACG 57.491 30.769 4.08 0.00 40.25 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 15 1.004044 AGCAAGAGGGACAACTCCATG 59.996 52.381 0.00 0.00 38.52 3.66
13 16 1.366319 AGCAAGAGGGACAACTCCAT 58.634 50.000 0.00 0.00 38.52 3.41
19 22 1.228552 GGCCAAGCAAGAGGGACAA 60.229 57.895 0.00 0.00 0.00 3.18
20 23 2.436109 GGCCAAGCAAGAGGGACA 59.564 61.111 0.00 0.00 0.00 4.02
38 41 0.170561 CCTCCGTTCAGTAGACCACG 59.829 60.000 0.00 0.00 0.00 4.94
71 74 1.242076 GCAGAAAGCCAGCAGAGAAA 58.758 50.000 0.00 0.00 37.23 2.52
130 137 2.412089 GGACTGAAACCGAACAAGATCG 59.588 50.000 0.00 0.00 42.37 3.69
147 154 2.158549 AGAAAAAGGCAAGCTCTGGACT 60.159 45.455 0.00 0.00 0.00 3.85
150 157 1.543358 GGAGAAAAAGGCAAGCTCTGG 59.457 52.381 0.00 0.00 0.00 3.86
157 164 1.909700 ATCAGCGGAGAAAAAGGCAA 58.090 45.000 0.00 0.00 0.00 4.52
234 241 3.414700 GATCTAATGGCGCCCGCG 61.415 66.667 26.77 9.99 43.06 6.46
278 285 5.048507 GTCGCAACCTTTAATAGTAGGAGG 58.951 45.833 0.00 1.50 35.45 4.30
331 341 3.449227 TACGGCTCAGCGTGGGAG 61.449 66.667 4.64 0.00 35.47 4.30
332 342 3.755628 GTACGGCTCAGCGTGGGA 61.756 66.667 4.64 0.00 0.00 4.37
418 428 1.322538 ATGGCGAGAATTGGGTTGCC 61.323 55.000 4.06 4.06 42.76 4.52
419 429 0.179129 CATGGCGAGAATTGGGTTGC 60.179 55.000 0.00 0.00 0.00 4.17
420 430 1.176527 ACATGGCGAGAATTGGGTTG 58.823 50.000 0.00 0.00 0.00 3.77
421 431 1.923356 AACATGGCGAGAATTGGGTT 58.077 45.000 0.00 0.00 0.00 4.11
528 549 1.964448 CCGGCAGGAAAAGGGAAAC 59.036 57.895 0.00 0.00 41.02 2.78
614 639 0.108804 TGGCTCAGCAAGTAGTACGC 60.109 55.000 0.00 0.00 0.00 4.42
619 644 4.024218 GCTCAATAATGGCTCAGCAAGTAG 60.024 45.833 0.00 0.00 0.00 2.57
624 649 1.064537 TGGCTCAATAATGGCTCAGCA 60.065 47.619 0.00 0.00 0.00 4.41
654 679 2.989840 CGATTGGTCATTCGGATAGAGC 59.010 50.000 7.20 3.37 32.47 4.09
742 767 5.987953 ACAGCAGTATAGCATACACATTCTG 59.012 40.000 8.40 0.00 36.85 3.02
791 816 4.561213 TGACGTATGAGTAATTCAACAGCG 59.439 41.667 0.00 0.00 39.77 5.18
840 868 7.421530 ACATATACATTGGAAATACACGCTC 57.578 36.000 0.00 0.00 0.00 5.03
888 916 6.592607 ACAAGTCCATCATGATTTGAAATTGC 59.407 34.615 19.80 4.05 38.03 3.56
935 963 5.571784 ATTCAACTGATCGATGTGCAAAT 57.428 34.783 0.54 0.00 0.00 2.32
936 964 5.375417 AATTCAACTGATCGATGTGCAAA 57.625 34.783 0.54 0.00 0.00 3.68
937 965 5.411053 TGTAATTCAACTGATCGATGTGCAA 59.589 36.000 0.54 0.00 0.00 4.08
938 966 4.934602 TGTAATTCAACTGATCGATGTGCA 59.065 37.500 0.54 0.00 0.00 4.57
939 967 5.469373 TGTAATTCAACTGATCGATGTGC 57.531 39.130 0.54 0.00 0.00 4.57
940 968 5.503031 GCCTGTAATTCAACTGATCGATGTG 60.503 44.000 0.54 0.00 0.00 3.21
941 969 4.572389 GCCTGTAATTCAACTGATCGATGT 59.428 41.667 0.54 0.00 0.00 3.06
942 970 4.024556 GGCCTGTAATTCAACTGATCGATG 60.025 45.833 0.54 0.00 0.00 3.84
943 971 4.130118 GGCCTGTAATTCAACTGATCGAT 58.870 43.478 0.00 0.00 0.00 3.59
1077 1105 3.181476 ACTGGTTGGCAGAAACAAATGTC 60.181 43.478 0.00 0.00 0.00 3.06
1173 1201 1.803334 TTTTCAGCGCGATACCAGTT 58.197 45.000 12.10 0.00 0.00 3.16
1211 1239 1.067283 CCTGCTGTACCAGAGTGTCAG 60.067 57.143 1.10 0.00 34.77 3.51
1939 1970 4.210120 GGTATCATTCGCTTCTAACTGCAG 59.790 45.833 13.48 13.48 0.00 4.41
2103 2134 1.630878 GAGAGCTCCTTTTTCCTCCCA 59.369 52.381 10.93 0.00 0.00 4.37
2637 2668 1.101331 CAATGGCTTCCTCTTCCTGC 58.899 55.000 0.00 0.00 0.00 4.85
2730 2761 6.183361 CCATTATGACTCTCTTATCCCACCAA 60.183 42.308 0.00 0.00 0.00 3.67
2883 2914 0.392461 GCGGGTATTCCTTGACAGCA 60.392 55.000 0.00 0.00 0.00 4.41
3141 3172 4.559063 CTCCTGGGGCCATCTGCG 62.559 72.222 4.39 0.00 42.61 5.18
3876 3907 3.550431 AGGTCATCCCCGATGCCG 61.550 66.667 0.00 0.00 39.63 5.69
3945 3976 4.477975 CGAGCCGAGACCGTGTCC 62.478 72.222 1.06 0.00 32.18 4.02
3999 4030 7.071196 AGCTATATGAATCAACTAAGGTGGACA 59.929 37.037 0.00 0.00 0.00 4.02
4240 4272 9.688592 ACTAGTACAATCTAGTAACAACAACAC 57.311 33.333 0.00 0.00 45.71 3.32
4303 4335 4.039245 TCAGACAGGACAGAACTTACAAGG 59.961 45.833 0.00 0.00 0.00 3.61
4332 4364 4.780275 TTCGAACAAAATCATGGCATCA 57.220 36.364 0.00 0.00 0.00 3.07
4392 4424 3.127548 AGTTCATGCGTCAATTCCACATC 59.872 43.478 0.00 0.00 0.00 3.06
4397 4429 3.559238 AACAGTTCATGCGTCAATTCC 57.441 42.857 0.00 0.00 0.00 3.01
4415 4447 0.296349 GACACGGCAAAAACGCAAAC 59.704 50.000 0.00 0.00 34.00 2.93
4513 4598 1.826385 CCACATGTTCTCCTCAACCC 58.174 55.000 0.00 0.00 0.00 4.11
4542 4627 2.690778 GGACAACAGGATGGCGCAC 61.691 63.158 10.83 0.00 43.62 5.34
4543 4628 2.359850 GGACAACAGGATGGCGCA 60.360 61.111 10.83 0.00 43.62 6.09
4546 4631 0.036732 TGAGTGGACAACAGGATGGC 59.963 55.000 0.00 0.00 43.62 4.40
4652 4737 4.748102 CCAGTCACTAAGTTTTGCGAACTA 59.252 41.667 5.81 0.00 0.00 2.24
4653 4738 3.560068 CCAGTCACTAAGTTTTGCGAACT 59.440 43.478 0.00 0.00 0.00 3.01
4721 4806 2.246719 GCTAGGGCTCCATGTTAGTG 57.753 55.000 0.00 0.00 35.22 2.74
4796 4881 4.396166 ACATCTTTTATGTTTCTCCAGCCG 59.604 41.667 0.00 0.00 0.00 5.52
4897 4982 4.163427 CCTGGCCATCTAGAGGAGAATTA 58.837 47.826 5.51 0.00 37.85 1.40
4916 5001 1.573108 TAGGAACAAGAGAGGGCCTG 58.427 55.000 12.95 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.