Multiple sequence alignment - TraesCS4A01G130000

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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 TraesCS4A01G130000 chr4A 100.000 4899 0 0 1 4899 170624085 170628983 0.000000e+00 9047.0
1 TraesCS4A01G130000 chr4A 100.000 426 0 0 5225 5650 170629309 170629734 0.000000e+00 787.0
2 TraesCS4A01G130000 chr4B 96.932 4466 111 15 443 4899 382826018 382821570 0.000000e+00 7465.0
3 TraesCS4A01G130000 chr4B 96.507 458 12 4 1 457 382826558 382826104 0.000000e+00 754.0
4 TraesCS4A01G130000 chr4B 96.930 228 7 0 5302 5529 382820928 382820701 3.190000e-102 383.0
5 TraesCS4A01G130000 chr4D 96.616 3989 99 19 919 4899 306858617 306854657 0.000000e+00 6586.0
6 TraesCS4A01G130000 chr4D 97.689 476 10 1 443 918 306859256 306858782 0.000000e+00 817.0
7 TraesCS4A01G130000 chr4D 97.380 458 9 3 1 457 306859797 306859342 0.000000e+00 776.0
8 TraesCS4A01G130000 chr4D 96.721 305 7 1 5228 5529 306854599 306854295 6.530000e-139 505.0
9 TraesCS4A01G130000 chr2B 98.592 71 1 0 747 817 204770974 204771044 5.940000e-25 126.0
10 TraesCS4A01G130000 chr5D 97.183 71 2 0 747 817 170274633 170274563 2.760000e-23 121.0
11 TraesCS4A01G130000 chr1B 97.183 71 2 0 747 817 568636509 568636579 2.760000e-23 121.0
12 TraesCS4A01G130000 chr7B 97.917 48 0 1 747 793 202117566 202117613 1.300000e-11 82.4
13 TraesCS4A01G130000 chr3B 100.000 44 0 0 747 790 648718538 648718581 1.300000e-11 82.4


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 TraesCS4A01G130000 chr4A 170624085 170629734 5649 False 4917.000000 9047 100.000000 1 5650 2 chr4A.!!$F1 5649
1 TraesCS4A01G130000 chr4B 382820701 382826558 5857 True 2867.333333 7465 96.789667 1 5529 3 chr4B.!!$R1 5528
2 TraesCS4A01G130000 chr4D 306854295 306859797 5502 True 2171.000000 6586 97.101500 1 5529 4 chr4D.!!$R1 5528

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
187 189 0.387929 CATCATTGCTCACCATGCCC 59.612 55.000 0.0 0.0 0.00 5.36 F
360 362 2.092429 TGGTAAGCACATGGATTCCCTC 60.092 50.000 0.0 0.0 0.00 4.30 F
939 1204 2.808543 GCAATCAAACTCAGAAGACCGT 59.191 45.455 0.0 0.0 0.00 4.83 F
2122 2390 3.008485 CCCTTCAGAGAGGCACTTACTTT 59.992 47.826 0.0 0.0 41.55 2.66 F
2658 2929 0.109132 CTTTTCCATTCACCAGCCGC 60.109 55.000 0.0 0.0 0.00 6.53 F
4273 4554 0.671781 GTCAGCCATCGCAGTTCACT 60.672 55.000 0.0 0.0 37.52 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1399 1664 0.040425 GCGGTGGCTGTAGTTTTGTG 60.040 55.000 0.00 0.0 35.83 3.33 R
1482 1748 0.501468 AAGGGGAGGAAACTAGGGGT 59.499 55.000 0.00 0.0 44.43 4.95 R
2639 2910 0.109132 GCGGCTGGTGAATGGAAAAG 60.109 55.000 0.00 0.0 0.00 2.27 R
3785 4066 2.546795 CCTTCGTAGCATCTGTGATCCC 60.547 54.545 0.00 0.0 0.00 3.85 R
4506 4788 0.937304 GCATGACGTATTGCCGATGT 59.063 50.000 10.32 0.0 0.00 3.06 R
5562 6140 0.250338 AAAACGAGTCTGTGGCCTCC 60.250 55.000 3.32 0.0 0.00 4.30 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
90 91 1.522668 CTTTCACCGGATTCAGCACA 58.477 50.000 9.46 0.00 0.00 4.57
165 166 5.692115 TTAGTTTATGCTCCTCATGACCA 57.308 39.130 0.00 0.00 36.63 4.02
187 189 0.387929 CATCATTGCTCACCATGCCC 59.612 55.000 0.00 0.00 0.00 5.36
288 290 7.584122 AGGTACATATATCATATCGTGGGTC 57.416 40.000 0.00 0.00 0.00 4.46
360 362 2.092429 TGGTAAGCACATGGATTCCCTC 60.092 50.000 0.00 0.00 0.00 4.30
403 405 4.265073 GTTGATCCAGATAACAGCAACCT 58.735 43.478 0.00 0.00 0.00 3.50
513 614 7.463544 GTCAATTTTTCCACCAAAAACAAGAG 58.536 34.615 0.00 0.00 44.89 2.85
673 774 5.121811 TGTACCGACTACTCTCTCCATAAC 58.878 45.833 0.00 0.00 0.00 1.89
730 831 4.541779 TGCACAACTTTTACTTTATGCCG 58.458 39.130 0.00 0.00 0.00 5.69
806 907 6.611613 AGACAAATGATGGAAGTGAGACTA 57.388 37.500 0.00 0.00 0.00 2.59
864 965 3.519510 AGGAAAGGCAACATAGAGCACTA 59.480 43.478 0.00 0.00 41.41 2.74
883 984 8.340618 AGCACTAAAATCAAGAAGCTAAATCA 57.659 30.769 0.00 0.00 30.90 2.57
927 1192 3.608073 GTGCCTTATGAACGCAATCAAAC 59.392 43.478 0.00 0.00 33.57 2.93
939 1204 2.808543 GCAATCAAACTCAGAAGACCGT 59.191 45.455 0.00 0.00 0.00 4.83
1081 1346 3.678529 GCTTTTGTGCAGTCCCAAGAAAA 60.679 43.478 0.00 0.00 0.00 2.29
1482 1748 9.725019 CTATAAGGCTGATAAATAACATGACCA 57.275 33.333 0.00 0.00 0.00 4.02
1485 1751 4.278419 GGCTGATAAATAACATGACCACCC 59.722 45.833 0.00 0.00 0.00 4.61
1527 1793 3.243367 TGTGTGCCAAGTGAAAGCAATAC 60.243 43.478 0.00 0.00 38.45 1.89
1709 1975 4.842139 ACGATTCGAAATTCTTTCCTCG 57.158 40.909 13.95 6.19 37.97 4.63
1963 2231 6.191315 AGGTACAAGTCTATGAGATGTGTCT 58.809 40.000 0.00 0.00 37.42 3.41
2122 2390 3.008485 CCCTTCAGAGAGGCACTTACTTT 59.992 47.826 0.00 0.00 41.55 2.66
2178 2446 6.986817 GGCTTATACTCTCAACTGATGCTAAA 59.013 38.462 0.00 0.00 0.00 1.85
2639 2910 7.851822 TTAAGATTGATGTTGAGCGTTTTTC 57.148 32.000 0.00 0.00 0.00 2.29
2658 2929 0.109132 CTTTTCCATTCACCAGCCGC 60.109 55.000 0.00 0.00 0.00 6.53
2728 2999 1.065998 GTCGGCCACCACCTTAATACA 60.066 52.381 2.24 0.00 0.00 2.29
2748 3019 7.715265 ATACACAGACAAACAAGTAAGACAG 57.285 36.000 0.00 0.00 0.00 3.51
2769 3040 7.609146 AGACAGAAATGAATCTATTCTTGTGCA 59.391 33.333 4.45 0.00 37.67 4.57
2786 3057 6.714810 TCTTGTGCATGTTTACAGAAGGTAAT 59.285 34.615 7.69 0.00 41.43 1.89
2932 3210 5.941788 ACAAGAGTCACTTTTACATCCCTT 58.058 37.500 0.00 0.00 36.61 3.95
2939 3217 6.375455 AGTCACTTTTACATCCCTTTGCATAG 59.625 38.462 0.00 0.00 0.00 2.23
2968 3246 6.931281 TGAGCTATACCTGACTAATGCATTTC 59.069 38.462 18.75 10.69 0.00 2.17
3031 3309 7.168219 GCTGACCATCCAATAAATGTAGGATA 58.832 38.462 0.00 0.00 38.77 2.59
3118 3398 6.910972 CGCGGATATATACAACTACATACAGG 59.089 42.308 0.00 0.00 0.00 4.00
3500 3781 3.686016 TCACCACAGCTTTAATTCTCCC 58.314 45.455 0.00 0.00 0.00 4.30
3501 3782 3.073798 TCACCACAGCTTTAATTCTCCCA 59.926 43.478 0.00 0.00 0.00 4.37
3520 3801 6.530019 TCCCAAAGAGAAGAAATAAATGGC 57.470 37.500 0.00 0.00 0.00 4.40
3521 3802 6.015918 TCCCAAAGAGAAGAAATAAATGGCA 58.984 36.000 0.00 0.00 0.00 4.92
3522 3803 6.071391 TCCCAAAGAGAAGAAATAAATGGCAC 60.071 38.462 0.00 0.00 0.00 5.01
3785 4066 6.808008 TTTACAAGCTTTGAGGAGATTGAG 57.192 37.500 9.53 0.00 43.75 3.02
3968 4249 5.505654 GCAAATGAAAGAAAGAGGACACGAA 60.506 40.000 0.00 0.00 0.00 3.85
4245 4526 2.424234 CCCACTGGAAGACCTGGAAAAA 60.424 50.000 0.00 0.00 39.06 1.94
4273 4554 0.671781 GTCAGCCATCGCAGTTCACT 60.672 55.000 0.00 0.00 37.52 3.41
4366 4647 7.433719 CCAGAGAAAGTATTCGAGAACTATGTG 59.566 40.741 2.55 2.34 40.63 3.21
4447 4728 2.362889 CAACCCCATGCCCAGGAC 60.363 66.667 0.00 0.00 0.00 3.85
4586 4868 8.173542 GAGAAATCCTCTCCTACTTTACCTAG 57.826 42.308 0.00 0.00 44.39 3.02
4592 4874 7.827787 TCCTCTCCTACTTTACCTAGAATGAT 58.172 38.462 0.00 0.00 0.00 2.45
4593 4875 8.956860 TCCTCTCCTACTTTACCTAGAATGATA 58.043 37.037 0.00 0.00 0.00 2.15
4771 5055 5.371526 GAGGGACTTGATCATCTATTTGCA 58.628 41.667 0.00 0.00 41.55 4.08
4776 5060 7.201848 GGGACTTGATCATCTATTTGCAATCAA 60.202 37.037 0.00 3.79 33.46 2.57
4791 5075 5.707931 TGCAATCAAGAATAATCGTTTGCA 58.292 33.333 3.14 3.14 44.02 4.08
4792 5076 5.572511 TGCAATCAAGAATAATCGTTTGCAC 59.427 36.000 3.14 0.00 42.11 4.57
4835 5119 1.868997 CGACGCACAAATCCAAGCT 59.131 52.632 0.00 0.00 0.00 3.74
4840 5124 0.599558 GCACAAATCCAAGCTGCAGA 59.400 50.000 20.43 0.00 0.00 4.26
5484 6059 2.029623 CATCTCTTTCCCCTGGCAATG 58.970 52.381 0.00 0.00 0.00 2.82
5539 6117 4.077184 CTGTAAGGCACGGGGCGA 62.077 66.667 5.22 0.00 46.16 5.54
5540 6118 4.077184 TGTAAGGCACGGGGCGAG 62.077 66.667 5.22 0.00 46.16 5.03
5541 6119 3.766691 GTAAGGCACGGGGCGAGA 61.767 66.667 5.22 0.00 46.16 4.04
5542 6120 2.762459 TAAGGCACGGGGCGAGAT 60.762 61.111 5.22 0.00 46.16 2.75
5543 6121 3.088941 TAAGGCACGGGGCGAGATG 62.089 63.158 5.22 0.00 46.16 2.90
5575 6153 3.699894 CGCTGGAGGCCACAGACT 61.700 66.667 26.18 0.00 38.20 3.24
5576 6154 2.267324 GCTGGAGGCCACAGACTC 59.733 66.667 26.18 5.31 38.20 3.36
5577 6155 2.575993 CTGGAGGCCACAGACTCG 59.424 66.667 19.54 0.00 38.20 4.18
5578 6156 2.203640 TGGAGGCCACAGACTCGT 60.204 61.111 5.01 0.00 34.58 4.18
5579 6157 1.821061 CTGGAGGCCACAGACTCGTT 61.821 60.000 19.54 0.00 38.20 3.85
5580 6158 1.371558 GGAGGCCACAGACTCGTTT 59.628 57.895 5.01 0.00 34.58 3.60
5581 6159 0.250338 GGAGGCCACAGACTCGTTTT 60.250 55.000 5.01 0.00 34.58 2.43
5582 6160 1.594331 GAGGCCACAGACTCGTTTTT 58.406 50.000 5.01 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 91 3.088532 TGTGGCCATCGCTTTATCTTTT 58.911 40.909 9.72 0.00 34.44 2.27
165 166 1.399714 CATGGTGAGCAATGATGGCT 58.600 50.000 0.00 0.00 46.07 4.75
288 290 1.339631 TGAGGGAAGCAAATGGTACCG 60.340 52.381 7.57 0.00 0.00 4.02
360 362 3.829601 ACCAGTCTTCTCCAGAGTAGTTG 59.170 47.826 1.83 2.78 32.84 3.16
609 710 8.603242 TTTAAGTTCACTCTAATTGGTGAGAC 57.397 34.615 10.51 10.76 42.31 3.36
653 754 3.118482 TCGTTATGGAGAGAGTAGTCGGT 60.118 47.826 0.00 0.00 0.00 4.69
730 831 9.099454 CAAGTTCAGTTATAGATAGGTTCAACC 57.901 37.037 0.00 0.00 38.99 3.77
883 984 9.586435 GGCACATAAAGTAAGCTTGAAATTTAT 57.414 29.630 9.86 8.84 34.71 1.40
939 1204 1.069091 CAGATGTGCATGCGTGTGAAA 60.069 47.619 14.09 0.00 0.00 2.69
947 1212 3.364068 CGAATCTGATCAGATGTGCATGC 60.364 47.826 33.48 11.82 46.75 4.06
1081 1346 7.372260 AGGAACTCATTCTATTACAGATGCT 57.628 36.000 0.00 0.00 34.98 3.79
1137 1402 9.539825 GACTGAATGCATCTAGAAGAAGAATTA 57.460 33.333 14.89 0.00 0.00 1.40
1399 1664 0.040425 GCGGTGGCTGTAGTTTTGTG 60.040 55.000 0.00 0.00 35.83 3.33
1482 1748 0.501468 AAGGGGAGGAAACTAGGGGT 59.499 55.000 0.00 0.00 44.43 4.95
1485 1751 3.267031 ACATGAAAGGGGAGGAAACTAGG 59.733 47.826 0.00 0.00 44.43 3.02
1527 1793 8.407832 TCATTCTGCACTATCAAATATGGTTTG 58.592 33.333 0.00 0.00 0.00 2.93
1709 1975 2.945668 CAGTCTTATAAGGCAGGCAACC 59.054 50.000 18.91 0.00 31.65 3.77
1963 2231 6.230472 ACTAAACTTCACATGCATGACACTA 58.770 36.000 32.75 11.70 0.00 2.74
2178 2446 1.078159 GGGGTCCATTTTAACCTGGGT 59.922 52.381 0.00 0.00 35.78 4.51
2400 2671 4.647564 AAATGCTATGGATACCTGGAGG 57.352 45.455 0.00 0.00 42.17 4.30
2620 2891 6.200854 GGAAAAGAAAAACGCTCAACATCAAT 59.799 34.615 0.00 0.00 0.00 2.57
2639 2910 0.109132 GCGGCTGGTGAATGGAAAAG 60.109 55.000 0.00 0.00 0.00 2.27
2658 2929 1.674441 CTGTTGCTATGGTGCATCCTG 59.326 52.381 0.00 0.00 42.96 3.86
2728 2999 7.552687 TCATTTCTGTCTTACTTGTTTGTCTGT 59.447 33.333 0.00 0.00 0.00 3.41
2748 3019 8.922058 AACATGCACAAGAATAGATTCATTTC 57.078 30.769 5.11 0.00 39.23 2.17
2769 3040 8.863872 AGCAAGTTATTACCTTCTGTAAACAT 57.136 30.769 0.00 0.00 42.51 2.71
2786 3057 9.212641 GCATTGATCTGATAAGATAGCAAGTTA 57.787 33.333 0.00 0.00 0.00 2.24
2922 3200 6.881065 GCTCATATCTATGCAAAGGGATGTAA 59.119 38.462 0.00 0.00 33.76 2.41
2923 3201 6.214208 AGCTCATATCTATGCAAAGGGATGTA 59.786 38.462 0.00 0.00 33.76 2.29
2924 3202 5.013913 AGCTCATATCTATGCAAAGGGATGT 59.986 40.000 0.00 0.00 33.76 3.06
2925 3203 5.498393 AGCTCATATCTATGCAAAGGGATG 58.502 41.667 0.00 0.00 33.76 3.51
2926 3204 5.775813 AGCTCATATCTATGCAAAGGGAT 57.224 39.130 0.00 0.00 33.76 3.85
2927 3205 6.881067 ATAGCTCATATCTATGCAAAGGGA 57.119 37.500 0.00 0.00 33.76 4.20
2932 3210 7.617329 AGTCAGGTATAGCTCATATCTATGCAA 59.383 37.037 0.26 0.00 32.88 4.08
2939 3217 7.776107 TGCATTAGTCAGGTATAGCTCATATC 58.224 38.462 0.26 0.00 0.00 1.63
3047 3325 8.508883 TTCCTGTCTCTAGTGTATAGTTTCTC 57.491 38.462 0.00 0.00 0.00 2.87
3094 3374 7.993101 TCCTGTATGTAGTTGTATATATCCGC 58.007 38.462 0.00 0.00 0.00 5.54
3500 3781 6.381801 ACGTGCCATTTATTTCTTCTCTTTG 58.618 36.000 0.00 0.00 0.00 2.77
3501 3782 6.575162 ACGTGCCATTTATTTCTTCTCTTT 57.425 33.333 0.00 0.00 0.00 2.52
3520 3801 5.351465 AGACCATCACTATTTTAGCAACGTG 59.649 40.000 0.00 0.00 0.00 4.49
3521 3802 5.351465 CAGACCATCACTATTTTAGCAACGT 59.649 40.000 0.00 0.00 0.00 3.99
3522 3803 5.220662 CCAGACCATCACTATTTTAGCAACG 60.221 44.000 0.00 0.00 0.00 4.10
3785 4066 2.546795 CCTTCGTAGCATCTGTGATCCC 60.547 54.545 0.00 0.00 0.00 3.85
3968 4249 6.039717 TGCTTAGCTTGTTGAGAAACAAATCT 59.960 34.615 5.60 7.79 41.55 2.40
4245 4526 1.376543 CGATGGCTGACAGCAAAGAT 58.623 50.000 27.87 13.82 44.75 2.40
4366 4647 6.578919 GCAAAGCATATAATAAAGGAGAACGC 59.421 38.462 0.00 0.00 0.00 4.84
4447 4728 5.893512 CATTACCAATCCAATGCAAATCG 57.106 39.130 0.00 0.00 0.00 3.34
4506 4788 0.937304 GCATGACGTATTGCCGATGT 59.063 50.000 10.32 0.00 0.00 3.06
4611 4893 1.380785 CAGGGTCAGGCAATGGCAT 60.381 57.895 10.05 0.00 43.71 4.40
4771 5055 5.331902 CGGTGCAAACGATTATTCTTGATT 58.668 37.500 6.21 0.00 0.00 2.57
4776 5060 1.400494 GCCGGTGCAAACGATTATTCT 59.600 47.619 13.03 0.00 37.47 2.40
4791 5075 2.119655 CCACTAGCTCGTAGCCGGT 61.120 63.158 1.90 0.00 43.77 5.28
4792 5076 2.722487 CCACTAGCTCGTAGCCGG 59.278 66.667 0.00 0.00 43.77 6.13
4835 5119 1.641140 CGTTGTTTCAGCGTCTGCA 59.359 52.632 2.45 0.00 46.23 4.41
4840 5124 2.251642 GGAGCCGTTGTTTCAGCGT 61.252 57.895 5.45 0.00 36.40 5.07
5224 5508 2.358247 GGGAAGAAGCGGCGTTCA 60.358 61.111 19.14 0.00 0.00 3.18
5225 5509 3.125573 GGGGAAGAAGCGGCGTTC 61.126 66.667 9.37 11.19 0.00 3.95
5226 5510 3.607370 GAGGGGAAGAAGCGGCGTT 62.607 63.158 9.37 0.00 0.00 4.84
5484 6059 1.488393 AGGAGAAGCTATTGTGGGCTC 59.512 52.381 0.00 0.00 37.87 4.70
5558 6136 3.655810 GAGTCTGTGGCCTCCAGCG 62.656 68.421 15.72 0.00 45.17 5.18
5559 6137 2.267324 GAGTCTGTGGCCTCCAGC 59.733 66.667 15.72 11.65 42.60 4.85
5560 6138 1.821061 AACGAGTCTGTGGCCTCCAG 61.821 60.000 14.70 14.70 32.34 3.86
5561 6139 1.407656 AAACGAGTCTGTGGCCTCCA 61.408 55.000 3.32 0.00 0.00 3.86
5562 6140 0.250338 AAAACGAGTCTGTGGCCTCC 60.250 55.000 3.32 0.00 0.00 4.30
5563 6141 1.594331 AAAAACGAGTCTGTGGCCTC 58.406 50.000 3.32 0.00 0.00 4.70
5564 6142 3.800826 AAAAACGAGTCTGTGGCCT 57.199 47.368 3.32 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.