Multiple sequence alignment - TraesCS4B01G152000

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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 TraesCS4B01G152000 chr4B 100.000 3164 0 0 1 3164 248906369 248903206 0.000000e+00 5843
1 TraesCS4B01G152000 chr4B 87.068 3186 361 31 17 3164 429443176 429446348 0.000000e+00 3554
2 TraesCS4B01G152000 chr5A 89.994 3178 280 24 1 3164 608618955 608615802 0.000000e+00 4072
3 TraesCS4B01G152000 chr5B 87.531 3184 350 29 17 3164 10167430 10164258 0.000000e+00 3637
4 TraesCS4B01G152000 chr5B 87.324 3187 352 34 17 3164 100041584 100044757 0.000000e+00 3600
5 TraesCS4B01G152000 chr3B 87.135 3187 355 34 17 3164 169649362 169652532 0.000000e+00 3563
6 TraesCS4B01G152000 chr3D 85.050 3184 410 33 26 3164 15042149 15038987 0.000000e+00 3182
7 TraesCS4B01G152000 chr4D 84.956 3184 415 36 26 3164 32029565 32026401 0.000000e+00 3168
8 TraesCS4B01G152000 chrUn 83.934 3193 464 29 9 3164 6067788 6064608 0.000000e+00 3009
9 TraesCS4B01G152000 chrUn 84.223 2884 384 38 1 2846 308998320 309001170 0.000000e+00 2739
10 TraesCS4B01G152000 chrUn 80.293 614 77 26 1 587 377637521 377636925 1.050000e-114 424
11 TraesCS4B01G152000 chr6B 83.818 3195 464 33 9 3164 266752453 266755633 0.000000e+00 2987
12 TraesCS4B01G152000 chr6B 83.683 3193 471 28 9 3164 558839897 558836718 0.000000e+00 2964
13 TraesCS4B01G152000 chr7B 82.924 3174 462 36 32 3164 60076891 60073757 0.000000e+00 2785


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 TraesCS4B01G152000 chr4B 248903206 248906369 3163 True 5843 5843 100.000 1 3164 1 chr4B.!!$R1 3163
1 TraesCS4B01G152000 chr4B 429443176 429446348 3172 False 3554 3554 87.068 17 3164 1 chr4B.!!$F1 3147
2 TraesCS4B01G152000 chr5A 608615802 608618955 3153 True 4072 4072 89.994 1 3164 1 chr5A.!!$R1 3163
3 TraesCS4B01G152000 chr5B 10164258 10167430 3172 True 3637 3637 87.531 17 3164 1 chr5B.!!$R1 3147
4 TraesCS4B01G152000 chr5B 100041584 100044757 3173 False 3600 3600 87.324 17 3164 1 chr5B.!!$F1 3147
5 TraesCS4B01G152000 chr3B 169649362 169652532 3170 False 3563 3563 87.135 17 3164 1 chr3B.!!$F1 3147
6 TraesCS4B01G152000 chr3D 15038987 15042149 3162 True 3182 3182 85.050 26 3164 1 chr3D.!!$R1 3138
7 TraesCS4B01G152000 chr4D 32026401 32029565 3164 True 3168 3168 84.956 26 3164 1 chr4D.!!$R1 3138
8 TraesCS4B01G152000 chrUn 6064608 6067788 3180 True 3009 3009 83.934 9 3164 1 chrUn.!!$R1 3155
9 TraesCS4B01G152000 chrUn 308998320 309001170 2850 False 2739 2739 84.223 1 2846 1 chrUn.!!$F1 2845
10 TraesCS4B01G152000 chrUn 377636925 377637521 596 True 424 424 80.293 1 587 1 chrUn.!!$R2 586
11 TraesCS4B01G152000 chr6B 266752453 266755633 3180 False 2987 2987 83.818 9 3164 1 chr6B.!!$F1 3155
12 TraesCS4B01G152000 chr6B 558836718 558839897 3179 True 2964 2964 83.683 9 3164 1 chr6B.!!$R1 3155
13 TraesCS4B01G152000 chr7B 60073757 60076891 3134 True 2785 2785 82.924 32 3164 1 chr7B.!!$R1 3132

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
224 255 0.187361 CACCCAACCCTCCCTTTCAA 59.813 55.0 0.00 0.0 0.00 2.69 F
399 433 0.326264 AAGACATGGCAGGTGAGACC 59.674 55.0 10.56 0.0 38.99 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2150 2191 1.134159 CAAGCTCTCATCCAGGAAGGG 60.134 57.143 0.0 0.0 38.24 3.95 R
2266 2310 3.057969 TGCACAGAGTCATTTAGGGTG 57.942 47.619 0.0 0.0 0.00 4.61 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
98 100 1.826385 AGTCCTTGGAGGCGAATTTG 58.174 50.000 0.00 0.00 34.61 2.32
99 101 1.351017 AGTCCTTGGAGGCGAATTTGA 59.649 47.619 0.00 0.00 34.61 2.69
100 102 1.740025 GTCCTTGGAGGCGAATTTGAG 59.260 52.381 0.00 0.00 34.61 3.02
101 103 1.628340 TCCTTGGAGGCGAATTTGAGA 59.372 47.619 0.00 0.00 34.61 3.27
132 138 1.903877 CTGGGCTCCGATCTGGTGTT 61.904 60.000 3.97 0.00 39.52 3.32
133 139 1.153349 GGGCTCCGATCTGGTGTTC 60.153 63.158 3.97 0.57 39.52 3.18
134 140 1.519455 GGCTCCGATCTGGTGTTCG 60.519 63.158 3.97 0.00 39.52 3.95
140 146 4.778143 ATCTGGTGTTCGGGCGGC 62.778 66.667 0.00 0.00 0.00 6.53
224 255 0.187361 CACCCAACCCTCCCTTTCAA 59.813 55.000 0.00 0.00 0.00 2.69
235 266 3.553508 CCTCCCTTTCAATGCTGTTTGTG 60.554 47.826 0.00 0.00 0.00 3.33
247 279 4.893601 TTTGTGTGGCGACGCGGA 62.894 61.111 14.61 0.00 46.31 5.54
264 296 2.990066 GGATTTCCACCGATCTGAGT 57.010 50.000 0.00 0.00 35.64 3.41
301 333 0.538746 GTGGTTGGTTTCCGGGTGAT 60.539 55.000 0.00 0.00 0.00 3.06
341 374 2.669240 CCCCCTCAAACTCGTCCC 59.331 66.667 0.00 0.00 0.00 4.46
343 376 1.489560 CCCCCTCAAACTCGTCCCTT 61.490 60.000 0.00 0.00 0.00 3.95
360 394 1.081892 CTTGACCGGATCTGCAAGTG 58.918 55.000 9.46 0.00 34.54 3.16
365 399 1.487976 ACCGGATCTGCAAGTGATGAT 59.512 47.619 9.46 0.00 33.76 2.45
399 433 0.326264 AAGACATGGCAGGTGAGACC 59.674 55.000 10.56 0.00 38.99 3.85
408 442 1.555075 GCAGGTGAGACCCAAGATACA 59.445 52.381 0.00 0.00 39.75 2.29
410 444 2.169352 CAGGTGAGACCCAAGATACAGG 59.831 54.545 0.00 0.00 39.75 4.00
428 462 3.181434 ACAGGGTGTTTGGAGCTTGAATA 60.181 43.478 0.00 0.00 0.00 1.75
531 565 2.472695 AGAACTTCGCCAGCATACAA 57.527 45.000 0.00 0.00 0.00 2.41
533 567 2.484264 AGAACTTCGCCAGCATACAAAC 59.516 45.455 0.00 0.00 0.00 2.93
534 568 1.890876 ACTTCGCCAGCATACAAACA 58.109 45.000 0.00 0.00 0.00 2.83
600 634 2.238395 GCAGTCAGGGGAAGAAGAAGAT 59.762 50.000 0.00 0.00 0.00 2.40
616 650 6.673537 AGAAGAAGATGAGGAGGAAGAAAGAT 59.326 38.462 0.00 0.00 0.00 2.40
689 723 1.930371 GCAACTGCCGAACAACCAATC 60.930 52.381 0.00 0.00 34.31 2.67
715 750 6.101150 TCCTACTATAAACATGACCCTGCAAT 59.899 38.462 0.00 0.00 0.00 3.56
734 769 4.264253 CAATTGTGGGATCTGCTGTTCTA 58.736 43.478 0.00 0.00 0.00 2.10
793 828 2.913617 GCACTCCTAAGGGCCCTTATAT 59.086 50.000 38.61 23.30 46.90 0.86
834 869 2.949447 ACAAGCAGGAATTCCACACTT 58.051 42.857 26.22 20.71 38.89 3.16
851 886 0.879765 CTTCTCAACAGCAGCAAGGG 59.120 55.000 0.00 0.00 0.00 3.95
866 901 3.256631 AGCAAGGGCAAGTCATAAAACAG 59.743 43.478 0.00 0.00 44.61 3.16
868 903 4.549458 CAAGGGCAAGTCATAAAACAGTG 58.451 43.478 0.00 0.00 0.00 3.66
921 956 5.965486 AGGGTAGAAGGGAAAGAAACAAAT 58.035 37.500 0.00 0.00 0.00 2.32
1066 1106 4.825085 GGACACCAATTGAACAAAGGACTA 59.175 41.667 7.12 0.00 0.00 2.59
1164 1204 1.578423 GCACAAGTTCTGCTCTGCC 59.422 57.895 0.00 0.00 0.00 4.85
1165 1205 1.864862 CACAAGTTCTGCTCTGCCG 59.135 57.895 0.00 0.00 0.00 5.69
1196 1236 7.176515 ACAAAGATTTGCCATAACATCTGTGTA 59.823 33.333 5.23 0.00 40.83 2.90
1243 1283 7.335924 ACAAGTTAACTCAGCAAACTTCAGTTA 59.664 33.333 8.95 0.00 40.52 2.24
1251 1291 7.171678 ACTCAGCAAACTTCAGTTACTCAATAC 59.828 37.037 0.00 0.00 37.25 1.89
1418 1459 8.727890 ACCAAAGCTATGTGGTTAGCCAGAAT 62.728 42.308 10.16 0.00 46.17 2.40
1441 1482 3.356529 TTGAGAAATCTTGCCCTCCTC 57.643 47.619 0.00 0.00 0.00 3.71
1473 1514 4.040755 AGAAGTCCTATGTGCCCAACTAT 58.959 43.478 0.00 0.00 0.00 2.12
1510 1551 5.705905 CCAAGGGAAGTTTCTAAACCTGTAG 59.294 44.000 2.02 0.00 39.71 2.74
1635 1676 3.732721 GCAAGATGTCACAAAAAGCTCAC 59.267 43.478 0.00 0.00 0.00 3.51
1683 1724 7.284034 GTGGAAAATCCTGACATCATCTACATT 59.716 37.037 0.00 0.00 37.46 2.71
1950 1991 1.004277 GTGACTGTAGCAAATGGGGGA 59.996 52.381 0.00 0.00 0.00 4.81
2069 2110 6.338214 TGATATCATACTTGGAGCTGACTC 57.662 41.667 0.00 0.00 42.66 3.36
2084 2125 4.112634 GCTGACTCGATGTATAAGCACAA 58.887 43.478 0.00 0.00 32.91 3.33
2087 2128 6.149129 TGACTCGATGTATAAGCACAATCT 57.851 37.500 0.00 0.00 30.84 2.40
2150 2191 9.662545 CAAACATTCCAATGGAAAACAAATAAC 57.337 29.630 19.57 0.00 45.41 1.89
2384 2429 3.827876 AGAATGTGACCATGCAATCAACA 59.172 39.130 0.00 0.00 0.00 3.33
2455 2501 7.318141 CACATCACCAGAAAAATGCTTTAGAT 58.682 34.615 0.00 0.00 0.00 1.98
2677 2723 8.250332 GCAAAAATATTCACCAAACTGGATCTA 58.750 33.333 0.00 0.00 40.96 1.98
2692 2738 5.364157 ACTGGATCTAAGGAGTGGTTATCAC 59.636 44.000 0.00 0.00 46.39 3.06
2785 2834 3.806949 AGTAATGCCCTTTGGAGTGAA 57.193 42.857 0.00 0.00 0.00 3.18
2792 2841 2.368548 GCCCTTTGGAGTGAAAAATGGT 59.631 45.455 0.00 0.00 0.00 3.55
2806 2855 8.116026 AGTGAAAAATGGTCCTCCTACATTTAT 58.884 33.333 0.00 0.00 42.21 1.40
2809 2858 8.996651 AAAAATGGTCCTCCTACATTTATAGG 57.003 34.615 0.00 0.00 42.21 2.57
2936 2985 0.111253 CCCTGGTTCTGGAAGCACTT 59.889 55.000 10.59 0.00 43.00 3.16
3011 3060 7.122715 ACAAAGTGGAATATTTGGGCTATGTA 58.877 34.615 3.08 0.00 40.05 2.29
3122 3171 4.478686 AGTTTCTTGGGATTAGCTGGGTAT 59.521 41.667 0.00 0.00 0.00 2.73
3136 3185 3.886123 CTGGGTATTACAGGAGGTTTGG 58.114 50.000 0.00 0.00 32.38 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.069586 TGAATTCTCACACGAACAGAGGT 59.930 43.478 7.05 0.00 0.00 3.85
49 51 3.257375 ACGCTCTGTATACCACTTGACAA 59.743 43.478 0.00 0.00 0.00 3.18
140 146 1.298157 TTTCTGCTGCCGATCAACCG 61.298 55.000 0.00 0.00 0.00 4.44
142 148 0.449388 CCTTTCTGCTGCCGATCAAC 59.551 55.000 0.00 0.00 0.00 3.18
224 255 1.654220 GTCGCCACACAAACAGCAT 59.346 52.632 0.00 0.00 0.00 3.79
235 266 3.861263 GGAAATCCGCGTCGCCAC 61.861 66.667 12.44 0.00 0.00 5.01
263 295 1.741770 ACCAGCTCGATTTCGCCAC 60.742 57.895 0.00 0.00 39.60 5.01
264 296 1.741401 CACCAGCTCGATTTCGCCA 60.741 57.895 0.00 0.00 39.60 5.69
301 333 3.405823 ACGGAAGGAATTTTACACCGA 57.594 42.857 14.75 0.00 41.09 4.69
329 362 0.032952 CGGTCAAGGGACGAGTTTGA 59.967 55.000 0.00 0.00 45.28 2.69
331 364 1.117142 TCCGGTCAAGGGACGAGTTT 61.117 55.000 0.00 0.00 45.28 2.66
334 367 1.038130 AGATCCGGTCAAGGGACGAG 61.038 60.000 0.00 0.00 45.28 4.18
341 374 1.081892 CACTTGCAGATCCGGTCAAG 58.918 55.000 0.00 10.82 41.07 3.02
343 376 0.904649 ATCACTTGCAGATCCGGTCA 59.095 50.000 0.00 0.00 0.00 4.02
360 394 6.152379 GTCTTCAGGGTTTTTGTTGATCATC 58.848 40.000 0.00 0.00 0.00 2.92
365 399 4.099266 CCATGTCTTCAGGGTTTTTGTTGA 59.901 41.667 0.00 0.00 40.22 3.18
399 433 3.347216 CTCCAAACACCCTGTATCTTGG 58.653 50.000 0.00 0.00 37.20 3.61
408 442 2.683211 ATTCAAGCTCCAAACACCCT 57.317 45.000 0.00 0.00 0.00 4.34
410 444 4.439289 GCAGATATTCAAGCTCCAAACACC 60.439 45.833 0.00 0.00 0.00 4.16
428 462 5.068198 AGTGTTTTGATGTCAAGTTGCAGAT 59.932 36.000 0.00 0.00 37.15 2.90
533 567 9.667989 GGATGGTTTGAATTTTCTTGAAATTTG 57.332 29.630 0.00 0.00 45.54 2.32
534 568 9.631257 AGGATGGTTTGAATTTTCTTGAAATTT 57.369 25.926 0.00 0.00 45.54 1.82
557 591 2.771089 CTGCAGTTAACTTCAGCAGGA 58.229 47.619 27.02 9.56 46.55 3.86
600 634 4.653341 GGATCAGATCTTTCTTCCTCCTCA 59.347 45.833 10.36 0.00 29.52 3.86
634 668 3.454812 GGAGGAACAACTATGCTTCCCTA 59.545 47.826 0.00 0.00 37.40 3.53
689 723 5.070446 TGCAGGGTCATGTTTATAGTAGGAG 59.930 44.000 0.00 0.00 0.00 3.69
715 750 2.906389 ACTAGAACAGCAGATCCCACAA 59.094 45.455 0.00 0.00 0.00 3.33
734 769 1.338973 CTGCATGTTGCTTTGTCCACT 59.661 47.619 0.75 0.00 45.31 4.00
834 869 1.601759 GCCCTTGCTGCTGTTGAGA 60.602 57.895 0.00 0.00 33.53 3.27
866 901 5.104900 AGGTAATTCCTCCACTGTCATACAC 60.105 44.000 0.00 0.00 44.42 2.90
868 903 5.128827 TCAGGTAATTCCTCCACTGTCATAC 59.871 44.000 0.00 0.00 46.24 2.39
986 1021 3.875727 CCACTGCATCTACTCCATCAAAG 59.124 47.826 0.00 0.00 0.00 2.77
1066 1106 9.847224 TCCTTTCAAGTAAGAAACTGTTATCTT 57.153 29.630 16.44 16.44 38.88 2.40
1164 1204 6.146216 TGTTATGGCAAATCTTTGTGTAACG 58.854 36.000 0.00 0.00 42.39 3.18
1165 1205 8.028938 AGATGTTATGGCAAATCTTTGTGTAAC 58.971 33.333 0.00 10.39 40.24 2.50
1196 1236 4.344679 TGTGGAAGGCTTTCACATTTTCAT 59.655 37.500 32.44 0.00 34.90 2.57
1251 1291 7.977904 TCATATGTTGTTCAAACTCAGCTATG 58.022 34.615 1.90 0.00 0.00 2.23
1418 1459 5.440610 GAGGAGGGCAAGATTTCTCAATTA 58.559 41.667 0.00 0.00 0.00 1.40
1441 1482 5.009210 GCACATAGGACTTCTGAGTAGTAGG 59.991 48.000 0.00 0.00 35.88 3.18
1473 1514 3.847042 TCCCTTGGAGTTCCTCTTCTA 57.153 47.619 0.00 0.00 36.82 2.10
1489 1530 6.465464 GGAACTACAGGTTTAGAAACTTCCCT 60.465 42.308 5.20 0.00 38.41 4.20
1495 1536 5.061179 TGCAGGAACTACAGGTTTAGAAAC 58.939 41.667 0.00 0.00 38.41 2.78
1510 1551 3.265791 CAGGAGATGTACTTGCAGGAAC 58.734 50.000 1.40 0.00 0.00 3.62
1581 1622 1.750399 CCCTGGAAACCATGGCTCG 60.750 63.158 13.04 0.00 32.89 5.03
1635 1676 3.358707 TGTTCTTGCAGTGCTTGAATG 57.641 42.857 17.60 0.00 0.00 2.67
1683 1724 3.291584 CTGTACCTCCTCTGCATCTACA 58.708 50.000 0.00 0.00 0.00 2.74
2069 2110 6.588348 TGACAAGATTGTGCTTATACATCG 57.412 37.500 2.31 0.00 42.43 3.84
2098 2139 4.473196 TCCCAACTTCATGTTAGGCAGATA 59.527 41.667 0.00 0.00 37.36 1.98
2150 2191 1.134159 CAAGCTCTCATCCAGGAAGGG 60.134 57.143 0.00 0.00 38.24 3.95
2266 2310 3.057969 TGCACAGAGTCATTTAGGGTG 57.942 47.619 0.00 0.00 0.00 4.61
2270 2314 5.916883 CAGGTTTTTGCACAGAGTCATTTAG 59.083 40.000 0.00 0.00 0.00 1.85
2455 2501 7.572523 ATGGCGAAGATCTTTAATGATTTCA 57.427 32.000 9.87 0.00 0.00 2.69
2542 2588 9.676861 TCAATTCATAATCTTCAAGTCATGTCT 57.323 29.630 0.00 0.00 0.00 3.41
2563 2609 8.367911 TGTGTATTCAGTCTTCTGTAGTCAATT 58.632 33.333 0.00 0.00 41.91 2.32
2577 2623 6.785488 TCTTGATTGTGTGTGTATTCAGTC 57.215 37.500 0.00 0.00 0.00 3.51
2677 2723 5.014123 TCTGATTTGGTGATAACCACTCCTT 59.986 40.000 0.00 0.00 45.03 3.36
2692 2738 6.432162 TGTCTCCTTCTTTCATTCTGATTTGG 59.568 38.462 0.00 0.00 0.00 3.28
2744 2793 6.240549 ACTAGGAACTCAAATAGACCCATG 57.759 41.667 0.00 0.00 41.75 3.66
2747 2796 6.706716 GCATTACTAGGAACTCAAATAGACCC 59.293 42.308 0.00 0.00 41.75 4.46
2785 2834 8.344939 TCCTATAAATGTAGGAGGACCATTTT 57.655 34.615 2.13 0.00 44.07 1.82
2806 2855 4.306600 CAATACAGTATGCATGCGTCCTA 58.693 43.478 17.45 0.00 42.53 2.94
2809 2858 2.224079 CCCAATACAGTATGCATGCGTC 59.776 50.000 17.45 8.39 42.53 5.19
2812 2861 1.270550 GCCCCAATACAGTATGCATGC 59.729 52.381 11.82 11.82 42.53 4.06
2879 2928 8.095937 AGTGCTCCTTGTATGTTTTACTAAAC 57.904 34.615 0.00 0.00 43.17 2.01
2936 2985 9.135189 AGCTTTGCATATAATTGATGTTTCCTA 57.865 29.630 0.00 0.00 0.00 2.94
3011 3060 4.104086 TGGATACTCCCTTGTCAGTGATT 58.896 43.478 0.00 0.00 35.03 2.57
3034 3083 5.995565 TGCTTCTACTTTAGCAGGTTCTA 57.004 39.130 0.00 0.00 42.12 2.10
3038 3087 5.165961 TGATTGCTTCTACTTTAGCAGGT 57.834 39.130 0.00 0.00 46.95 4.00
3122 3171 4.993705 ATTCTGACCAAACCTCCTGTAA 57.006 40.909 0.00 0.00 0.00 2.41
3136 3185 6.441093 TGCAAATCAGTCCATAATTCTGAC 57.559 37.500 0.00 0.00 40.29 3.51


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

AutoCloner maintained by Alex Coulton.