Multiple sequence alignment - TraesCS2B01G513300

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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 TraesCS2B01G513300 chr2B 100.000 3716 0 0 1 3716 708383993 708387708 0.000000e+00 6863.0
1 TraesCS2B01G513300 chr2D 95.071 3104 122 15 1 3092 586901950 586905034 0.000000e+00 4855.0
2 TraesCS2B01G513300 chr2D 92.160 625 48 1 3093 3716 586904999 586905623 0.000000e+00 881.0
3 TraesCS2B01G513300 chr2A 95.756 1508 51 6 775 2275 721652701 721654202 0.000000e+00 2418.0
4 TraesCS2B01G513300 chr2A 91.746 1478 101 10 2244 3715 721654262 721655724 0.000000e+00 2034.0
5 TraesCS2B01G513300 chr2A 92.947 794 41 8 1 785 721650845 721651632 0.000000e+00 1142.0
6 TraesCS2B01G513300 chr3B 75.052 485 100 16 3095 3572 758227701 758228171 4.860000e-49 206.0
7 TraesCS2B01G513300 chr3B 89.091 55 5 1 3039 3092 818310318 818310372 2.400000e-07 67.6
8 TraesCS2B01G513300 chr6D 92.500 40 2 1 3054 3092 456665264 456665225 5.180000e-04 56.5


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 TraesCS2B01G513300 chr2B 708383993 708387708 3715 False 6863.000000 6863 100.0000 1 3716 1 chr2B.!!$F1 3715
1 TraesCS2B01G513300 chr2D 586901950 586905623 3673 False 2868.000000 4855 93.6155 1 3716 2 chr2D.!!$F1 3715
2 TraesCS2B01G513300 chr2A 721650845 721655724 4879 False 1864.666667 2418 93.4830 1 3715 3 chr2A.!!$F1 3714

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
340 349 1.484444 GGGTGTGAGAGGCCTCTGTT 61.484 60.000 39.86 17.28 40.61 3.16 F
406 415 3.001939 GCACACGTAAGCAAAACTACTGT 59.998 43.478 6.53 0.00 45.62 3.55 F
1753 2848 0.307453 TTGTGCTGCTTGCTTGTACG 59.693 50.000 0.00 0.00 43.37 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1343 2433 2.988010 TCACCTGTCAGCCATATCAC 57.012 50.000 0.0 0.0 0.0 3.06 R
2191 3292 3.678289 TGCTTCTTCTGCTGCTTGAATA 58.322 40.909 0.0 0.0 0.0 1.75 R
3551 4750 0.036732 ACGCATGAGGATGGTTGTGT 59.963 50.000 0.0 0.0 0.0 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
39 40 7.058023 ACCGCCATGTAGATGTAATAGTTAA 57.942 36.000 0.00 0.00 0.00 2.01
136 139 9.807921 AGGAAAGTTTGTCCTATCTCAAAATAA 57.192 29.630 0.00 0.00 43.99 1.40
207 211 7.729116 TCCCTATTTTAGATACTTAACACGGG 58.271 38.462 0.00 0.00 0.00 5.28
224 228 1.583054 GGGCTTTACGGCTACATGAG 58.417 55.000 0.00 0.00 38.46 2.90
316 325 7.432350 AAACAAACAAAGTTGCAATCAAAGA 57.568 28.000 0.59 0.00 33.37 2.52
326 335 5.481473 AGTTGCAATCAAAGATAATGGGTGT 59.519 36.000 0.59 0.00 33.37 4.16
327 336 5.327616 TGCAATCAAAGATAATGGGTGTG 57.672 39.130 0.00 0.00 0.00 3.82
340 349 1.484444 GGGTGTGAGAGGCCTCTGTT 61.484 60.000 39.86 17.28 40.61 3.16
406 415 3.001939 GCACACGTAAGCAAAACTACTGT 59.998 43.478 6.53 0.00 45.62 3.55
427 436 4.515567 TGTTGATACATGGCAAACAACGTA 59.484 37.500 0.00 3.38 39.89 3.57
561 570 3.492102 TGGAAGTTAAGCTGAAGTGCT 57.508 42.857 0.00 0.00 46.40 4.40
573 582 4.514441 AGCTGAAGTGCTGATAATACATGC 59.486 41.667 0.00 0.00 42.33 4.06
773 783 7.759489 ACTTTCATAATCTACCAAACTGCAA 57.241 32.000 0.00 0.00 0.00 4.08
854 1944 9.703892 AATATCTACTATTCACAGTCATGCTTC 57.296 33.333 0.00 0.00 0.00 3.86
954 2044 8.711170 TGGTTATATTCTTAGTGGTTTCCTAGG 58.289 37.037 0.82 0.82 0.00 3.02
959 2049 6.803366 TTCTTAGTGGTTTCCTAGGTATCC 57.197 41.667 9.08 8.60 0.00 2.59
963 2053 3.197116 AGTGGTTTCCTAGGTATCCAACG 59.803 47.826 17.25 0.00 0.00 4.10
1008 2098 8.052141 TCATAACCACACATTCTAATGGAATCA 58.948 33.333 7.56 0.00 42.20 2.57
1343 2433 6.402550 GCCGACAATGCAATTCACTATATAGG 60.403 42.308 14.25 3.67 31.22 2.57
1499 2594 9.733556 TGTACATGTGAACTTTAAGATGGTTAT 57.266 29.630 9.11 0.00 0.00 1.89
1676 2771 7.274250 GGATAACATAAAGCTTCAAGCAACAAG 59.726 37.037 13.10 0.75 45.56 3.16
1753 2848 0.307453 TTGTGCTGCTTGCTTGTACG 59.693 50.000 0.00 0.00 43.37 3.67
1802 2897 8.121086 GGCTCGAACTATAAAAGGTATGAAAAC 58.879 37.037 0.00 0.00 0.00 2.43
2191 3292 4.160252 ACACTTGGAATGTCAAACAAAGCT 59.840 37.500 0.00 0.00 0.00 3.74
2348 3541 5.391950 CGAAGGGTGTCAATTGTGGAATTAG 60.392 44.000 5.13 0.00 30.20 1.73
2513 3708 8.545472 TGACAAGGTTGCTATTAAAGGTAGTAT 58.455 33.333 0.00 0.00 0.00 2.12
2677 3873 3.402110 TGTAATTATGCTCCATGGCTCG 58.598 45.455 6.96 0.00 0.00 5.03
2740 3936 8.668510 AGTATAGAATCCAACATGATGTCAAC 57.331 34.615 0.00 0.00 0.00 3.18
2815 4013 7.962964 ACTGGTTGGTTCATCAATATATACG 57.037 36.000 0.00 0.00 0.00 3.06
2870 4068 8.212317 ACCCATTTTATTTAATGCAGCAATTC 57.788 30.769 0.00 0.00 34.81 2.17
2947 4145 8.688151 GTCTCACCACTAAAGAGTAGACATATT 58.312 37.037 0.00 0.00 37.45 1.28
2997 4195 0.036671 CACACTCAGCCTCTGCATGA 60.037 55.000 0.00 0.00 41.13 3.07
3023 4221 0.244994 TGCACACAACCAACACCAAC 59.755 50.000 0.00 0.00 0.00 3.77
3024 4222 0.244994 GCACACAACCAACACCAACA 59.755 50.000 0.00 0.00 0.00 3.33
3025 4223 1.989430 CACACAACCAACACCAACAC 58.011 50.000 0.00 0.00 0.00 3.32
3026 4224 1.270826 CACACAACCAACACCAACACA 59.729 47.619 0.00 0.00 0.00 3.72
3027 4225 1.271102 ACACAACCAACACCAACACAC 59.729 47.619 0.00 0.00 0.00 3.82
3028 4226 1.270826 CACAACCAACACCAACACACA 59.729 47.619 0.00 0.00 0.00 3.72
3029 4227 1.271102 ACAACCAACACCAACACACAC 59.729 47.619 0.00 0.00 0.00 3.82
3030 4228 1.270826 CAACCAACACCAACACACACA 59.729 47.619 0.00 0.00 0.00 3.72
3031 4229 0.885196 ACCAACACCAACACACACAC 59.115 50.000 0.00 0.00 0.00 3.82
3032 4230 0.884514 CCAACACCAACACACACACA 59.115 50.000 0.00 0.00 0.00 3.72
3033 4231 1.402194 CCAACACCAACACACACACAC 60.402 52.381 0.00 0.00 0.00 3.82
3034 4232 1.268079 CAACACCAACACACACACACA 59.732 47.619 0.00 0.00 0.00 3.72
3035 4233 0.878416 ACACCAACACACACACACAC 59.122 50.000 0.00 0.00 0.00 3.82
3076 4274 4.094887 CGCCAACAACTAGCAAAGTCATAT 59.905 41.667 0.00 0.00 37.50 1.78
3081 4279 8.391106 CCAACAACTAGCAAAGTCATATAAGAC 58.609 37.037 0.00 0.00 37.50 3.01
3115 4313 9.278978 TGTCAACAACTAGCAAAGTCATATAAA 57.721 29.630 0.00 0.00 37.50 1.40
3202 4401 4.454678 ACTGCAACAATGATCATATCCGT 58.545 39.130 9.04 1.52 0.00 4.69
3222 4421 4.383948 CCGTATCAATCATCTCATGACACG 59.616 45.833 0.00 0.00 43.01 4.49
3228 4427 3.658757 TCATCTCATGACACGACACAA 57.341 42.857 0.00 0.00 33.59 3.33
3231 4430 2.124122 TCTCATGACACGACACAAACG 58.876 47.619 0.00 0.00 0.00 3.60
3253 4452 6.435428 ACGACAAGATTATTGAACAACAACC 58.565 36.000 0.00 0.00 41.52 3.77
3261 4460 4.574599 ATTGAACAACAACCTCTTCAGC 57.425 40.909 0.00 0.00 41.52 4.26
3322 4521 2.947652 CCACAAGGCATGAATCTAGGTG 59.052 50.000 0.00 3.45 0.00 4.00
3329 4528 3.370953 GGCATGAATCTAGGTGTTCACCT 60.371 47.826 24.80 24.80 43.62 4.00
3369 4568 4.731773 GCATATCCAAGCAAAACCTTCGAG 60.732 45.833 0.00 0.00 0.00 4.04
3390 4589 2.818130 AGGTAACGGCGTAAAGAACA 57.182 45.000 15.20 0.00 46.39 3.18
3419 4618 3.011821 TGCCAGGTATAACCAATTTGGGA 59.988 43.478 19.39 7.50 43.37 4.37
3440 4639 1.003051 GACCTAGGCTTCCTCCCCA 59.997 63.158 9.30 0.00 34.61 4.96
3468 4667 2.257409 GACCGGGTCCATGACAGCAT 62.257 60.000 16.55 0.00 33.68 3.79
3479 4678 2.470983 TGACAGCATCACCATCGAAA 57.529 45.000 0.00 0.00 29.99 3.46
3486 4685 2.938451 GCATCACCATCGAAATCACTCA 59.062 45.455 0.00 0.00 0.00 3.41
3575 4774 1.037579 ACCATCCTCATGCGTCGAGA 61.038 55.000 0.00 0.00 31.84 4.04
3576 4775 0.316522 CCATCCTCATGCGTCGAGAT 59.683 55.000 0.00 0.00 31.84 2.75
3586 4785 2.204237 TGCGTCGAGATTTCATCCATG 58.796 47.619 0.00 0.00 0.00 3.66
3636 4835 8.299990 TCTAGAGAGATAAACCTTCTTGAAGG 57.700 38.462 23.44 23.44 45.46 3.46
3651 4850 1.281867 TGAAGGCCTTTCGGTGATCAT 59.718 47.619 21.54 0.00 38.71 2.45
3707 4906 1.145738 AGTTTGAAGCCACCACCATCT 59.854 47.619 0.00 0.00 0.00 2.90
3708 4907 2.375174 AGTTTGAAGCCACCACCATCTA 59.625 45.455 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
136 139 7.715657 ACATATCACAACACACATTTGAGTTT 58.284 30.769 0.00 0.00 34.66 2.66
145 148 9.007901 TCAATAATCAACATATCACAACACACA 57.992 29.630 0.00 0.00 0.00 3.72
187 191 7.933215 AAAGCCCGTGTTAAGTATCTAAAAT 57.067 32.000 0.00 0.00 0.00 1.82
191 195 5.450412 CCGTAAAGCCCGTGTTAAGTATCTA 60.450 44.000 0.00 0.00 0.00 1.98
207 211 2.202566 GTCCTCATGTAGCCGTAAAGC 58.797 52.381 0.00 0.00 0.00 3.51
295 299 9.588774 CATTATCTTTGATTGCAACTTTGTTTG 57.411 29.630 0.00 0.00 32.79 2.93
316 325 1.771255 GAGGCCTCTCACACCCATTAT 59.229 52.381 26.25 0.00 39.74 1.28
326 335 1.967535 CGTGAACAGAGGCCTCTCA 59.032 57.895 33.06 24.19 42.34 3.27
327 336 1.446966 GCGTGAACAGAGGCCTCTC 60.447 63.158 33.06 21.79 37.98 3.20
340 349 9.419297 GGTTTTATAGATATGTCTATTGCGTGA 57.581 33.333 16.14 0.00 43.53 4.35
369 378 2.096565 CGTGTGCATGAGTTGAAGACTG 60.097 50.000 0.00 0.00 39.19 3.51
406 415 5.888691 ATACGTTGTTTGCCATGTATCAA 57.111 34.783 0.00 0.00 0.00 2.57
573 582 9.918630 AAGAAATTGAGTGAAATCCAATTGTAG 57.081 29.630 4.43 0.00 39.56 2.74
773 783 7.964545 GTCTCGTTGACAACAAAAGTTTATT 57.035 32.000 18.09 0.00 44.73 1.40
936 2026 6.266080 TGGATACCTAGGAAACCACTAAGAA 58.734 40.000 17.98 0.00 0.00 2.52
954 2044 4.143179 GCACAGTTTGAGTACGTTGGATAC 60.143 45.833 0.00 0.00 0.00 2.24
959 2049 2.210116 AGGCACAGTTTGAGTACGTTG 58.790 47.619 0.00 0.00 0.00 4.10
963 2053 3.728845 TGAAGAGGCACAGTTTGAGTAC 58.271 45.455 0.00 0.00 0.00 2.73
1269 2359 4.377021 TCTGTATATTGCCGCGAAAAGAT 58.623 39.130 8.23 6.89 0.00 2.40
1343 2433 2.988010 TCACCTGTCAGCCATATCAC 57.012 50.000 0.00 0.00 0.00 3.06
2080 3181 9.113838 CTTGAACACATTTATATTCTGCTACCT 57.886 33.333 0.00 0.00 0.00 3.08
2141 3242 4.092816 CAAAAACGTCGCTACAAAGTGTT 58.907 39.130 0.00 0.00 34.68 3.32
2191 3292 3.678289 TGCTTCTTCTGCTGCTTGAATA 58.322 40.909 0.00 0.00 0.00 1.75
2367 3562 8.838452 ACAATTGCAAAATGTAAACATGTTTG 57.162 26.923 29.72 15.41 37.38 2.93
2461 3656 5.745227 TGGTTCCTTGGAAGATTCAGATAC 58.255 41.667 1.83 0.00 0.00 2.24
2472 3667 3.221771 CTTGTCACATGGTTCCTTGGAA 58.778 45.455 0.00 0.00 0.00 3.53
2605 3801 2.113860 TCTGTTAATCCAGCCACAGC 57.886 50.000 0.00 0.00 37.22 4.40
2677 3873 5.085636 TGTTGTGTTGCGTATGTTTCTAC 57.914 39.130 0.00 0.00 0.00 2.59
2689 3885 2.222007 TCCTTTGCATGTTGTGTTGC 57.778 45.000 0.00 0.00 39.33 4.17
2723 3919 6.417258 TGTGATAGTTGACATCATGTTGGAT 58.583 36.000 8.58 0.00 35.02 3.41
2947 4145 7.634671 TCGTACTTGTATCCTCTTGATAACA 57.365 36.000 0.00 0.00 37.69 2.41
2966 4164 2.254459 CTGAGTGTGTGCTCATCGTAC 58.746 52.381 0.00 0.00 43.61 3.67
2967 4165 1.402852 GCTGAGTGTGTGCTCATCGTA 60.403 52.381 0.00 0.00 43.61 3.43
2985 4183 3.147629 GCATTCTAATCATGCAGAGGCT 58.852 45.455 0.00 0.00 45.50 4.58
2997 4195 4.261994 GGTGTTGGTTGTGTGCATTCTAAT 60.262 41.667 0.00 0.00 0.00 1.73
3023 4221 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3024 4222 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3025 4223 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3026 4224 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3027 4225 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3028 4226 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3029 4227 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3030 4228 1.598882 TTGTGTGTGTGTGTGTGTGT 58.401 45.000 0.00 0.00 0.00 3.72
3031 4229 2.695613 TTTGTGTGTGTGTGTGTGTG 57.304 45.000 0.00 0.00 0.00 3.82
3032 4230 3.181515 CGTATTTGTGTGTGTGTGTGTGT 60.182 43.478 0.00 0.00 0.00 3.72
3033 4231 3.350043 CGTATTTGTGTGTGTGTGTGTG 58.650 45.455 0.00 0.00 0.00 3.82
3034 4232 2.223157 GCGTATTTGTGTGTGTGTGTGT 60.223 45.455 0.00 0.00 0.00 3.72
3035 4233 2.371432 GCGTATTTGTGTGTGTGTGTG 58.629 47.619 0.00 0.00 0.00 3.82
3076 4274 8.770828 GCTAGTTGTTGACATAACTTTGTCTTA 58.229 33.333 9.93 0.00 45.07 2.10
3081 4279 7.915397 ACTTTGCTAGTTGTTGACATAACTTTG 59.085 33.333 9.93 6.33 38.11 2.77
3115 4313 8.428186 TTTTCTCGTCTACACATAACTTTGTT 57.572 30.769 0.00 0.00 0.00 2.83
3143 4341 6.834168 TCTGATCACTTTGGGTATTTTTCC 57.166 37.500 0.00 0.00 0.00 3.13
3150 4349 3.118775 CGTGGATCTGATCACTTTGGGTA 60.119 47.826 18.64 0.00 0.00 3.69
3152 4351 2.093500 TCGTGGATCTGATCACTTTGGG 60.093 50.000 18.64 1.86 0.00 4.12
3159 4358 2.985957 TGCAATCGTGGATCTGATCA 57.014 45.000 18.64 0.00 0.00 2.92
3202 4401 5.979517 GTGTCGTGTCATGAGATGATTGATA 59.020 40.000 16.97 1.18 42.04 2.15
3222 4421 7.129622 TGTTCAATAATCTTGTCGTTTGTGTC 58.870 34.615 0.00 0.00 0.00 3.67
3228 4427 6.915843 GGTTGTTGTTCAATAATCTTGTCGTT 59.084 34.615 0.00 0.00 38.38 3.85
3231 4430 7.875971 AGAGGTTGTTGTTCAATAATCTTGTC 58.124 34.615 8.67 0.00 38.38 3.18
3253 4452 2.291741 GTGTTGTTCCCTTGCTGAAGAG 59.708 50.000 0.00 0.00 0.00 2.85
3261 4460 3.065371 GTCACTTGAGTGTTGTTCCCTTG 59.935 47.826 10.66 0.00 45.76 3.61
3322 4521 5.216614 AGGACTAACTCTTCAAGGTGAAC 57.783 43.478 0.00 0.00 32.21 3.18
3329 4528 6.839134 TGGATATGCTAGGACTAACTCTTCAA 59.161 38.462 0.00 0.00 0.00 2.69
3369 4568 3.059166 TGTTCTTTACGCCGTTACCTTC 58.941 45.455 0.00 0.00 0.00 3.46
3390 4589 4.339747 TGGTTATACCTGGCAATGCCGT 62.340 50.000 20.39 14.52 43.86 5.68
3419 4618 0.325765 GGGAGGAAGCCTAGGTCTGT 60.326 60.000 11.31 0.00 31.76 3.41
3440 4639 2.438795 GACCCGGTCTCGAGCTCT 60.439 66.667 12.85 0.00 39.00 4.09
3468 4667 4.206477 ACATGAGTGATTTCGATGGTGA 57.794 40.909 0.00 0.00 0.00 4.02
3551 4750 0.036732 ACGCATGAGGATGGTTGTGT 59.963 50.000 0.00 0.00 0.00 3.72
3586 4785 2.293399 GGTGGTTGACTTTGATGGTGAC 59.707 50.000 0.00 0.00 0.00 3.67
3676 4875 4.573201 GTGGCTTCAAACTGTACTGTAACA 59.427 41.667 5.76 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.