Multiple sequence alignment - TraesCS1D01G138700

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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 TraesCS1D01G138700 chr1D 100.000 3295 0 0 1 3295 190481708 190478414 0.000000e+00 6085.0
1 TraesCS1D01G138700 chr1B 94.280 2640 94 16 671 3285 263948818 263946211 0.000000e+00 3986.0
2 TraesCS1D01G138700 chr1B 91.441 666 48 4 21 683 263979916 263979257 0.000000e+00 905.0
3 TraesCS1D01G138700 chr1A 91.087 2401 144 45 1 2356 212017502 212019877 0.000000e+00 3184.0
4 TraesCS1D01G138700 chr1A 95.193 957 43 2 2339 3295 212021720 212022673 0.000000e+00 1509.0
5 TraesCS1D01G138700 chr2B 74.667 225 42 14 1738 1953 695859716 695859498 5.860000e-13 86.1
6 TraesCS1D01G138700 chr2A 73.384 263 51 15 1738 1989 716488109 716487855 2.730000e-11 80.5
7 TraesCS1D01G138700 chr2D 73.894 226 42 13 1738 1953 578937062 578936844 1.270000e-09 75.0
8 TraesCS1D01G138700 chr5B 90.385 52 5 0 1261 1312 136018626 136018677 5.900000e-08 69.4
9 TraesCS1D01G138700 chr5A 90.385 52 5 0 1261 1312 135154552 135154603 5.900000e-08 69.4


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 TraesCS1D01G138700 chr1D 190478414 190481708 3294 True 6085.0 6085 100.000 1 3295 1 chr1D.!!$R1 3294
1 TraesCS1D01G138700 chr1B 263946211 263948818 2607 True 3986.0 3986 94.280 671 3285 1 chr1B.!!$R1 2614
2 TraesCS1D01G138700 chr1B 263979257 263979916 659 True 905.0 905 91.441 21 683 1 chr1B.!!$R2 662
3 TraesCS1D01G138700 chr1A 212017502 212022673 5171 False 2346.5 3184 93.140 1 3295 2 chr1A.!!$F1 3294

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
635 643 0.103937 TTTTGAAAGCCCAACCTGCG 59.896 50.0 0.0 0.0 0.0 5.18 F
715 723 0.389817 GGCAGGCACGAAAATTTCCC 60.390 55.0 0.0 0.0 0.0 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2276 2377 0.961857 TCTACCACAAGCCGTAGCGA 60.962 55.000 0.0 0.0 46.67 4.93 R
2543 4505 2.146342 CACCTGTGTGTCATCTTGGAC 58.854 52.381 0.0 0.0 37.72 4.02 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
24 27 4.694339 ACTTTGGTAATACGAGCATCTCC 58.306 43.478 0.00 0.00 0.00 3.71
53 56 8.397906 TGTTCTAAAACTTCATCTCAAACAGTG 58.602 33.333 0.00 0.00 36.30 3.66
70 73 7.390440 TCAAACAGTGAAATTCTCGATAACCAT 59.610 33.333 0.00 0.00 31.51 3.55
72 75 8.425577 AACAGTGAAATTCTCGATAACCATAG 57.574 34.615 0.00 0.00 0.00 2.23
76 79 8.356657 AGTGAAATTCTCGATAACCATAGAGAG 58.643 37.037 0.00 0.00 41.92 3.20
84 87 5.182190 TCGATAACCATAGAGAGATGCTGTC 59.818 44.000 0.00 0.00 0.00 3.51
102 105 5.105716 TGCTGTCTGAAGACTAGTTATCACC 60.106 44.000 11.55 0.00 44.99 4.02
127 130 5.483583 AGCTACTTCCTGAATTGAGTCTCTT 59.516 40.000 0.65 0.00 0.00 2.85
133 136 2.341257 TGAATTGAGTCTCTTCTGCGC 58.659 47.619 0.00 0.00 0.00 6.09
138 141 2.771089 TGAGTCTCTTCTGCGCATTTT 58.229 42.857 12.24 0.00 0.00 1.82
142 145 4.256920 AGTCTCTTCTGCGCATTTTATGT 58.743 39.130 12.24 0.00 0.00 2.29
144 147 5.182001 AGTCTCTTCTGCGCATTTTATGTTT 59.818 36.000 12.24 0.00 0.00 2.83
145 148 5.858581 GTCTCTTCTGCGCATTTTATGTTTT 59.141 36.000 12.24 0.00 0.00 2.43
150 153 6.392353 TCTGCGCATTTTATGTTTTCATTG 57.608 33.333 12.24 0.00 41.25 2.82
151 154 4.955617 TGCGCATTTTATGTTTTCATTGC 58.044 34.783 5.66 0.00 41.25 3.56
152 155 4.450080 TGCGCATTTTATGTTTTCATTGCA 59.550 33.333 5.66 0.00 39.11 4.08
155 158 7.148523 TGCGCATTTTATGTTTTCATTGCATAA 60.149 29.630 5.66 0.00 39.11 1.90
156 159 7.691463 GCGCATTTTATGTTTTCATTGCATAAA 59.309 29.630 0.30 0.00 39.11 1.40
158 161 9.493206 GCATTTTATGTTTTCATTGCATAAAGG 57.507 29.630 0.00 0.00 42.36 3.11
187 191 2.203470 ATCGCCCCCTTTTCGTTTTA 57.797 45.000 0.00 0.00 0.00 1.52
190 194 1.542472 CGCCCCCTTTTCGTTTTACAT 59.458 47.619 0.00 0.00 0.00 2.29
191 195 2.414957 CGCCCCCTTTTCGTTTTACATC 60.415 50.000 0.00 0.00 0.00 3.06
194 198 3.824443 CCCCCTTTTCGTTTTACATCTGT 59.176 43.478 0.00 0.00 0.00 3.41
201 205 7.114811 CCTTTTCGTTTTACATCTGTTGAATGG 59.885 37.037 0.00 0.00 0.00 3.16
437 445 5.600484 AGAGACGAGATCAATCAAAGGGTAT 59.400 40.000 0.00 0.00 0.00 2.73
587 595 3.838271 TCCGCCTCATCGTCCTGC 61.838 66.667 0.00 0.00 0.00 4.85
590 598 2.268920 GCCTCATCGTCCTGCCAA 59.731 61.111 0.00 0.00 0.00 4.52
592 600 1.900351 CCTCATCGTCCTGCCAAGA 59.100 57.895 0.00 0.00 0.00 3.02
593 601 0.250234 CCTCATCGTCCTGCCAAGAA 59.750 55.000 0.00 0.00 0.00 2.52
596 604 3.012518 CTCATCGTCCTGCCAAGAATTT 58.987 45.455 0.00 0.00 0.00 1.82
611 619 0.256464 AATTTTGGATCGGGCCGGTA 59.744 50.000 27.98 8.20 0.00 4.02
614 622 0.393267 TTTGGATCGGGCCGGTAAAG 60.393 55.000 27.98 0.00 0.00 1.85
615 623 1.555477 TTGGATCGGGCCGGTAAAGT 61.555 55.000 27.98 5.32 0.00 2.66
616 624 1.222661 GGATCGGGCCGGTAAAGTT 59.777 57.895 27.98 2.13 0.00 2.66
635 643 0.103937 TTTTGAAAGCCCAACCTGCG 59.896 50.000 0.00 0.00 0.00 5.18
636 644 1.743321 TTTGAAAGCCCAACCTGCGG 61.743 55.000 0.00 0.00 0.00 5.69
642 650 4.738998 CCCAACCTGCGGCATCCA 62.739 66.667 1.75 0.00 0.00 3.41
652 660 2.537560 CGGCATCCATTCGGCTCAC 61.538 63.158 0.00 0.00 0.00 3.51
653 661 1.451927 GGCATCCATTCGGCTCACA 60.452 57.895 0.00 0.00 0.00 3.58
654 662 1.718757 GGCATCCATTCGGCTCACAC 61.719 60.000 0.00 0.00 0.00 3.82
655 663 1.026182 GCATCCATTCGGCTCACACA 61.026 55.000 0.00 0.00 0.00 3.72
656 664 1.452110 CATCCATTCGGCTCACACAA 58.548 50.000 0.00 0.00 0.00 3.33
657 665 2.019249 CATCCATTCGGCTCACACAAT 58.981 47.619 0.00 0.00 0.00 2.71
715 723 0.389817 GGCAGGCACGAAAATTTCCC 60.390 55.000 0.00 0.00 0.00 3.97
821 832 1.439679 GAGGTAGCCGAAACTTGTGG 58.560 55.000 0.00 0.00 0.00 4.17
833 844 4.319766 CGAAACTTGTGGATTTGGAGTCTG 60.320 45.833 0.00 0.00 0.00 3.51
887 898 7.173907 ACACAAGTTAAGATGAGATTGAAGGTG 59.826 37.037 0.00 0.00 0.00 4.00
895 906 8.774546 AAGATGAGATTGAAGGTGTCTCTATA 57.225 34.615 0.00 0.00 39.24 1.31
896 907 8.774546 AGATGAGATTGAAGGTGTCTCTATAA 57.225 34.615 0.00 0.00 39.24 0.98
897 908 8.637986 AGATGAGATTGAAGGTGTCTCTATAAC 58.362 37.037 0.00 0.00 39.24 1.89
900 911 9.647918 TGAGATTGAAGGTGTCTCTATAACTAT 57.352 33.333 0.00 0.00 39.24 2.12
911 926 6.870439 TGTCTCTATAACTATTACGCGCTCTA 59.130 38.462 5.73 0.00 0.00 2.43
916 931 4.407496 AACTATTACGCGCTCTAGCTAG 57.593 45.455 15.01 15.01 39.32 3.42
947 974 1.882167 GATCGGACAGAGCAGCAGC 60.882 63.158 0.00 0.00 42.56 5.25
1065 1095 1.337167 CGCCGCCTCATTCTCATCATA 60.337 52.381 0.00 0.00 0.00 2.15
1323 1353 4.942944 ACATCCTCGGTATGGGTATATCA 58.057 43.478 0.00 0.00 0.00 2.15
1395 1465 1.731700 CATTTGATCCTGCCAGCCG 59.268 57.895 0.00 0.00 0.00 5.52
1531 1601 2.485582 CGAGATCGTGGTGAGCGT 59.514 61.111 0.00 0.00 38.28 5.07
1532 1602 1.583967 CGAGATCGTGGTGAGCGTC 60.584 63.158 0.00 0.00 38.28 5.19
1559 1629 1.991230 CCCAGGGAAGGAACATCGT 59.009 57.895 0.00 0.00 0.00 3.73
1671 1772 4.401519 TCAAGGAGTACAAGGGTAAGATCG 59.598 45.833 0.00 0.00 0.00 3.69
2276 2377 2.152016 CTCATGGCGCAGATCATCAAT 58.848 47.619 10.83 0.00 0.00 2.57
2286 2387 1.615883 AGATCATCAATCGCTACGGCT 59.384 47.619 0.00 0.00 39.55 5.52
2299 2400 2.822764 CTACGGCTTGTGGTAGATTCC 58.177 52.381 0.00 0.00 38.69 3.01
2359 4320 5.470437 TGTATGGACAAGTACGAATTTGCAA 59.530 36.000 0.00 0.00 30.68 4.08
2543 4505 4.458397 ACAGCCTAATCTGACCATGATTG 58.542 43.478 0.00 0.00 37.51 2.67
2586 4548 4.441773 GCCACCGGGTAAAAAGAAGAAAAA 60.442 41.667 6.32 0.00 36.17 1.94
2619 4582 6.060136 ACCCAGAGACATGACATAAATGATG 58.940 40.000 0.00 0.00 41.79 3.07
2878 4841 4.571250 GTGATCGGCTTCACGTCA 57.429 55.556 2.32 0.00 36.93 4.35
2917 4880 2.350458 CCGAGGGCCATGTTTTGGG 61.350 63.158 6.18 0.00 46.55 4.12
2932 4895 1.967343 TTGGGGCCTTTGGGGTTCTT 61.967 55.000 0.84 0.00 37.43 2.52
2959 4922 1.450312 GACCCTCACATCCTTGCCG 60.450 63.158 0.00 0.00 0.00 5.69
2975 4938 2.621338 TGCCGTCTATTCTGCTGAAAG 58.379 47.619 10.27 9.06 35.63 2.62
3208 5172 3.224269 GAGTACCAGACTGAGGGGATAC 58.776 54.545 3.32 0.00 39.06 2.24
3264 5228 3.887621 AGAAATGACTAGGCACGCTAA 57.112 42.857 0.00 0.00 0.00 3.09
3271 5235 2.930682 GACTAGGCACGCTAAAGAAAGG 59.069 50.000 0.00 0.00 0.00 3.11
3282 5246 4.671766 CGCTAAAGAAAGGTTTGGAATCCG 60.672 45.833 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.006967 ACATGGGAGATGCTCGTATTACC 59.993 47.826 0.00 0.00 0.00 2.85
12 15 2.388735 AGAACATGGGAGATGCTCGTA 58.611 47.619 0.00 0.00 0.00 3.43
14 17 3.459232 TTAGAACATGGGAGATGCTCG 57.541 47.619 0.00 0.00 0.00 5.03
17 20 5.415701 TGAAGTTTTAGAACATGGGAGATGC 59.584 40.000 0.00 0.00 38.26 3.91
19 22 7.637511 AGATGAAGTTTTAGAACATGGGAGAT 58.362 34.615 0.00 0.00 38.26 2.75
24 27 8.352201 TGTTTGAGATGAAGTTTTAGAACATGG 58.648 33.333 0.00 0.00 38.26 3.66
53 56 9.352784 CATCTCTCTATGGTTATCGAGAATTTC 57.647 37.037 0.00 0.00 35.47 2.17
84 87 5.590530 AGCTGGTGATAACTAGTCTTCAG 57.409 43.478 7.71 6.24 0.00 3.02
102 105 5.083533 AGACTCAATTCAGGAAGTAGCTG 57.916 43.478 0.00 0.00 0.00 4.24
127 130 5.163972 GCAATGAAAACATAAAATGCGCAGA 60.164 36.000 18.32 0.69 0.00 4.26
142 145 8.871629 TTCCTAGTACCTTTATGCAATGAAAA 57.128 30.769 0.00 0.00 0.00 2.29
144 147 9.120538 GATTTCCTAGTACCTTTATGCAATGAA 57.879 33.333 0.00 0.00 0.00 2.57
145 148 7.441157 CGATTTCCTAGTACCTTTATGCAATGA 59.559 37.037 0.00 0.00 0.00 2.57
150 153 4.451435 GGCGATTTCCTAGTACCTTTATGC 59.549 45.833 0.00 0.00 0.00 3.14
151 154 4.995487 GGGCGATTTCCTAGTACCTTTATG 59.005 45.833 0.00 0.00 0.00 1.90
152 155 4.041321 GGGGCGATTTCCTAGTACCTTTAT 59.959 45.833 0.00 0.00 0.00 1.40
155 158 1.767088 GGGGCGATTTCCTAGTACCTT 59.233 52.381 0.00 0.00 0.00 3.50
156 159 1.421480 GGGGCGATTTCCTAGTACCT 58.579 55.000 0.00 0.00 0.00 3.08
158 161 1.421480 AGGGGGCGATTTCCTAGTAC 58.579 55.000 0.00 0.00 0.00 2.73
187 191 3.843422 TGGAAACCCATTCAACAGATGT 58.157 40.909 0.00 0.00 39.98 3.06
201 205 0.170339 CCTCCGCGAAAATGGAAACC 59.830 55.000 8.23 0.00 32.89 3.27
216 220 1.474077 CCTGTTTGCTGTATTGCCTCC 59.526 52.381 0.00 0.00 0.00 4.30
393 399 2.068831 TTCCTTTCCCCACCAGGTAT 57.931 50.000 0.00 0.00 0.00 2.73
437 445 1.205460 GGCCCCTCCTACTTCCACAA 61.205 60.000 0.00 0.00 0.00 3.33
469 477 0.252467 AGCCTCTCAGGTAGCCAAGT 60.252 55.000 0.00 0.00 37.80 3.16
587 595 1.136891 GGCCCGATCCAAAATTCTTGG 59.863 52.381 11.15 11.15 40.87 3.61
590 598 0.751643 CCGGCCCGATCCAAAATTCT 60.752 55.000 3.71 0.00 0.00 2.40
592 600 0.256464 TACCGGCCCGATCCAAAATT 59.744 50.000 3.71 0.00 0.00 1.82
593 601 0.256464 TTACCGGCCCGATCCAAAAT 59.744 50.000 3.71 0.00 0.00 1.82
596 604 1.222387 CTTTACCGGCCCGATCCAA 59.778 57.895 3.71 0.00 0.00 3.53
611 619 4.260985 CAGGTTGGGCTTTCAAAAACTTT 58.739 39.130 0.00 0.00 0.00 2.66
614 622 1.939934 GCAGGTTGGGCTTTCAAAAAC 59.060 47.619 0.00 0.00 0.00 2.43
615 623 1.472376 CGCAGGTTGGGCTTTCAAAAA 60.472 47.619 0.00 0.00 0.00 1.94
616 624 0.103937 CGCAGGTTGGGCTTTCAAAA 59.896 50.000 0.00 0.00 0.00 2.44
635 643 1.451927 TGTGAGCCGAATGGATGCC 60.452 57.895 0.00 0.00 37.49 4.40
636 644 1.026182 TGTGTGAGCCGAATGGATGC 61.026 55.000 0.00 0.00 37.49 3.91
642 650 2.747446 GGTTGTATTGTGTGAGCCGAAT 59.253 45.455 0.00 0.00 0.00 3.34
652 660 1.750778 GATGGGCTGGGTTGTATTGTG 59.249 52.381 0.00 0.00 0.00 3.33
653 661 1.640670 AGATGGGCTGGGTTGTATTGT 59.359 47.619 0.00 0.00 0.00 2.71
654 662 2.092212 AGAGATGGGCTGGGTTGTATTG 60.092 50.000 0.00 0.00 0.00 1.90
655 663 2.208872 AGAGATGGGCTGGGTTGTATT 58.791 47.619 0.00 0.00 0.00 1.89
656 664 1.898863 AGAGATGGGCTGGGTTGTAT 58.101 50.000 0.00 0.00 0.00 2.29
657 665 2.023404 TCTAGAGATGGGCTGGGTTGTA 60.023 50.000 0.00 0.00 0.00 2.41
698 706 2.352715 GGAAGGGAAATTTTCGTGCCTG 60.353 50.000 8.75 0.00 0.00 4.85
737 748 1.853319 GTGTGAGCGTTGTCTTCGG 59.147 57.895 0.00 0.00 0.00 4.30
821 832 5.413833 TCTTGCAAGATTCAGACTCCAAATC 59.586 40.000 25.16 0.00 0.00 2.17
833 844 3.131755 CCTCCCCATTTCTTGCAAGATTC 59.868 47.826 28.89 0.00 34.49 2.52
887 898 6.168164 AGAGCGCGTAATAGTTATAGAGAC 57.832 41.667 8.43 0.00 0.00 3.36
911 926 3.058293 CGATCGATGCTTCTCTTCTAGCT 60.058 47.826 10.26 0.00 38.22 3.32
916 931 2.223595 TGTCCGATCGATGCTTCTCTTC 60.224 50.000 18.66 0.00 0.00 2.87
947 974 2.047844 CTCACACCACGCCTCCTG 60.048 66.667 0.00 0.00 0.00 3.86
985 1015 2.821366 CATGCCTGCTCCGGTGTC 60.821 66.667 0.00 0.00 0.00 3.67
1065 1095 0.534877 TCAATGCCACGAGTGCTGTT 60.535 50.000 0.00 0.00 0.00 3.16
1323 1353 2.101917 GCCATGCATGCTTGAACCTTAT 59.898 45.455 29.52 5.41 0.00 1.73
1559 1629 8.884124 ATTTCATCTTGGAAGTGGAGATAAAA 57.116 30.769 0.00 0.00 0.00 1.52
2276 2377 0.961857 TCTACCACAAGCCGTAGCGA 60.962 55.000 0.00 0.00 46.67 4.93
2286 2387 3.118445 TGATGATGCGGAATCTACCACAA 60.118 43.478 0.00 0.00 36.15 3.33
2299 2400 6.779117 AGAGATTGTAAAGTTTGATGATGCG 58.221 36.000 0.00 0.00 0.00 4.73
2331 2432 7.334749 CAAATTCGTACTTGTCCATACATACG 58.665 38.462 5.69 5.69 42.14 3.06
2359 4320 4.657504 TGCTTATCAGGATTCTGGAGACAT 59.342 41.667 0.00 0.00 41.51 3.06
2453 4415 4.407365 CAAAGTCTGGTTTATTCCCTGGT 58.593 43.478 0.00 0.00 0.00 4.00
2543 4505 2.146342 CACCTGTGTGTCATCTTGGAC 58.854 52.381 0.00 0.00 37.72 4.02
2586 4548 4.702131 GTCATGTCTCTGGGTATGCTTTTT 59.298 41.667 0.00 0.00 0.00 1.94
2587 4549 4.263462 TGTCATGTCTCTGGGTATGCTTTT 60.263 41.667 0.00 0.00 0.00 2.27
2878 4841 1.334869 CCTTCACGTTTCAAGCTGCTT 59.665 47.619 9.53 9.53 0.00 3.91
2908 4871 1.133181 CCCCAAAGGCCCCAAAACAT 61.133 55.000 0.00 0.00 0.00 2.71
2917 4880 1.913262 CCCAAGAACCCCAAAGGCC 60.913 63.158 0.00 0.00 40.58 5.19
2941 4904 1.450312 CGGCAAGGATGTGAGGGTC 60.450 63.158 0.00 0.00 0.00 4.46
2975 4938 7.703328 TCTAATCTGTTTGAAAACCACTGAAC 58.297 34.615 3.59 0.00 38.11 3.18
3264 5228 4.407365 ACATCGGATTCCAAACCTTTCTT 58.593 39.130 3.09 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.