Multiple sequence alignment - TraesCS1B01G118100

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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 TraesCS1B01G118100 chr1B 100.000 2526 0 0 1 2526 137870258 137872783 0.000000e+00 4665.0
1 TraesCS1B01G118100 chr3D 95.575 2531 97 7 1 2526 10934144 10931624 0.000000e+00 4039.0
2 TraesCS1B01G118100 chr3D 95.791 2043 75 5 1 2039 588695429 588697464 0.000000e+00 3286.0
3 TraesCS1B01G118100 chr2D 95.629 2471 95 7 60 2526 586830299 586832760 0.000000e+00 3952.0
4 TraesCS1B01G118100 chr6D 94.822 2530 104 10 1 2526 372614448 372611942 0.000000e+00 3921.0
5 TraesCS1B01G118100 chr5D 95.307 2472 101 9 60 2526 556579374 556576913 0.000000e+00 3908.0
6 TraesCS1B01G118100 chr5A 94.574 1843 79 12 1 1834 155590956 155592786 0.000000e+00 2830.0
7 TraesCS1B01G118100 chr1A 94.233 1734 92 6 795 2523 379647386 379649116 0.000000e+00 2641.0
8 TraesCS1B01G118100 chr7B 93.866 1239 70 4 357 1592 97120866 97119631 0.000000e+00 1862.0
9 TraesCS1B01G118100 chr7B 92.748 1241 75 8 357 1594 89870745 89869517 0.000000e+00 1779.0
10 TraesCS1B01G118100 chr7B 96.034 933 34 3 1596 2526 97118341 97117410 0.000000e+00 1515.0
11 TraesCS1B01G118100 chr7B 94.638 746 36 4 1783 2526 89869033 89868290 0.000000e+00 1153.0
12 TraesCS1B01G118100 chr5B 96.067 712 26 2 1816 2526 528386157 528385447 0.000000e+00 1158.0
13 TraesCS1B01G118100 chr5B 94.156 462 20 1 1 462 652146250 652145796 0.000000e+00 697.0
14 TraesCS1B01G118100 chr5B 93.939 462 21 1 1 462 651941017 651940563 0.000000e+00 691.0
15 TraesCS1B01G118100 chr7D 95.518 357 9 1 1 357 473980856 473981205 4.720000e-157 564.0
16 TraesCS1B01G118100 chr3A 94.398 357 13 1 1 357 401134191 401134540 2.210000e-150 542.0
17 TraesCS1B01G118100 chr2B 95.066 304 13 2 1596 1899 559330516 559330215 6.320000e-131 477.0
18 TraesCS1B01G118100 chr2B 93.863 277 16 1 2250 2526 535697209 535697484 1.400000e-112 416.0
19 TraesCS1B01G118100 chr2B 93.137 204 14 0 370 573 43958051 43958254 1.470000e-77 300.0
20 TraesCS1B01G118100 chr6B 91.429 350 21 5 9 357 552842693 552842352 2.940000e-129 472.0
21 TraesCS1B01G118100 chr6B 95.745 47 2 0 2205 2251 149653420 149653374 2.690000e-10 76.8
22 TraesCS1B01G118100 chr2A 85.507 276 30 5 1935 2200 772518659 772518384 1.910000e-71 279.0


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 TraesCS1B01G118100 chr1B 137870258 137872783 2525 False 4665.0 4665 100.000 1 2526 1 chr1B.!!$F1 2525
1 TraesCS1B01G118100 chr3D 10931624 10934144 2520 True 4039.0 4039 95.575 1 2526 1 chr3D.!!$R1 2525
2 TraesCS1B01G118100 chr3D 588695429 588697464 2035 False 3286.0 3286 95.791 1 2039 1 chr3D.!!$F1 2038
3 TraesCS1B01G118100 chr2D 586830299 586832760 2461 False 3952.0 3952 95.629 60 2526 1 chr2D.!!$F1 2466
4 TraesCS1B01G118100 chr6D 372611942 372614448 2506 True 3921.0 3921 94.822 1 2526 1 chr6D.!!$R1 2525
5 TraesCS1B01G118100 chr5D 556576913 556579374 2461 True 3908.0 3908 95.307 60 2526 1 chr5D.!!$R1 2466
6 TraesCS1B01G118100 chr5A 155590956 155592786 1830 False 2830.0 2830 94.574 1 1834 1 chr5A.!!$F1 1833
7 TraesCS1B01G118100 chr1A 379647386 379649116 1730 False 2641.0 2641 94.233 795 2523 1 chr1A.!!$F1 1728
8 TraesCS1B01G118100 chr7B 97117410 97120866 3456 True 1688.5 1862 94.950 357 2526 2 chr7B.!!$R2 2169
9 TraesCS1B01G118100 chr7B 89868290 89870745 2455 True 1466.0 1779 93.693 357 2526 2 chr7B.!!$R1 2169
10 TraesCS1B01G118100 chr5B 528385447 528386157 710 True 1158.0 1158 96.067 1816 2526 1 chr5B.!!$R1 710

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
950 958 0.976641 TCTGGATCAAGCAGTTCGGT 59.023 50.0 0.0 0.0 0.0 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2137 3739 0.883153 GTGGTGTGCTTGATGATGCA 59.117 50.0 0.0 0.0 36.79 3.96 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
67 68 7.265599 TGTGTATTTCCTTTGATTCCCTAGA 57.734 36.000 0.00 0.00 0.00 2.43
187 188 6.312180 GCGTGGTACTTAGCTATTTAAGTTGT 59.688 38.462 4.99 0.00 40.11 3.32
188 189 7.148523 GCGTGGTACTTAGCTATTTAAGTTGTT 60.149 37.037 4.99 0.00 40.11 2.83
189 190 8.166706 CGTGGTACTTAGCTATTTAAGTTGTTG 58.833 37.037 4.99 0.00 40.11 3.33
190 191 8.448615 GTGGTACTTAGCTATTTAAGTTGTTGG 58.551 37.037 4.99 0.00 40.11 3.77
191 192 8.158789 TGGTACTTAGCTATTTAAGTTGTTGGT 58.841 33.333 4.99 0.00 40.11 3.67
192 193 9.657419 GGTACTTAGCTATTTAAGTTGTTGGTA 57.343 33.333 4.99 0.00 40.11 3.25
395 402 6.593382 TGCCCTGTTTATATGAATTGTTTTGC 59.407 34.615 0.00 0.00 0.00 3.68
453 460 1.992667 CGCAACGAGCAACTAATCAGA 59.007 47.619 0.00 0.00 46.13 3.27
583 590 4.679373 ATTTGTGTGCCCATGTAAAACA 57.321 36.364 0.00 0.00 0.00 2.83
593 600 5.046735 TGCCCATGTAAAACATATGCAGTTT 60.047 36.000 1.58 3.95 38.51 2.66
618 625 2.742116 GGCTAGATCCCAACCCGCA 61.742 63.158 0.00 0.00 0.00 5.69
789 796 7.571059 GCATCAAATGGTTAAATGTTTCCACAC 60.571 37.037 0.00 0.00 35.03 3.82
793 800 8.356657 CAAATGGTTAAATGTTTCCACACTCTA 58.643 33.333 0.00 0.00 35.03 2.43
809 816 5.239744 CACACTCTATAGGATTAGTGCGTCT 59.760 44.000 15.66 0.00 42.44 4.18
836 843 3.679917 GCTTGTTGCTAGCTGTAGGATCA 60.680 47.826 17.23 0.00 38.95 2.92
839 846 3.769300 TGTTGCTAGCTGTAGGATCAGAA 59.231 43.478 17.23 0.00 37.61 3.02
921 929 1.209019 TCTGGGAGCTCATGAAGAAGC 59.791 52.381 17.19 0.00 0.00 3.86
950 958 0.976641 TCTGGATCAAGCAGTTCGGT 59.023 50.000 0.00 0.00 0.00 4.69
951 959 1.081892 CTGGATCAAGCAGTTCGGTG 58.918 55.000 0.00 0.00 0.00 4.94
1054 1067 5.257082 TCTTTGCACTGTTTTAACCCTTC 57.743 39.130 0.00 0.00 0.00 3.46
1072 1085 3.629398 CCTTCTGTTTGCAAGTGTCTCTT 59.371 43.478 0.00 0.00 36.75 2.85
1088 1101 4.345257 TGTCTCTTCAAGGAGCTAACTTGT 59.655 41.667 22.73 0.00 44.29 3.16
1231 1245 1.930251 AGCTCCAGCACAAGACTCTA 58.070 50.000 0.48 0.00 45.16 2.43
1247 1261 2.234908 ACTCTAATGCGCAAGGAGTTCT 59.765 45.455 26.28 12.55 45.13 3.01
1308 1322 6.828785 ACTCCAGAGTTTTGTACTTGAATTGT 59.171 34.615 0.00 0.00 38.83 2.71
1347 1361 6.916440 TCTAAGCTACAATTGTAAGTCACGA 58.084 36.000 18.55 8.81 0.00 4.35
1481 1496 4.215349 CTGCTCCAGCTTGCTACC 57.785 61.111 0.00 0.00 42.66 3.18
1505 1520 1.880796 GCCGCCGCTTGTTGTTTTT 60.881 52.632 0.00 0.00 0.00 1.94
1594 2895 3.616956 CTGTTGATTCCTCCTACAGCA 57.383 47.619 0.00 0.00 30.88 4.41
1669 3213 7.362142 GGTCCTGCTTATTGTCTTTAAAGAAGG 60.362 40.741 19.30 17.93 43.60 3.46
2132 3734 2.429610 GCAATGGCAAGAAGATCATGGT 59.570 45.455 0.00 0.00 40.72 3.55
2137 3739 2.821969 GGCAAGAAGATCATGGTTGTGT 59.178 45.455 0.00 0.00 0.00 3.72
2252 3854 7.582667 TGTTAGTATGCTTCTGCTGACTATA 57.417 36.000 0.00 0.00 37.13 1.31
2265 3867 8.011844 TCTGCTGACTATACAATGTGACTTAT 57.988 34.615 0.00 0.00 0.00 1.73
2304 3906 6.447162 CATGTTGTAGACTGTTGACTGTAGA 58.553 40.000 0.00 0.00 0.00 2.59
2369 3971 5.732528 GCAATTGCATGAAGATAGTCCACAG 60.733 44.000 25.36 0.00 41.59 3.66
2397 3999 8.686334 ACAAAAACTATGTGTAATGGATCCATC 58.314 33.333 27.45 16.29 35.31 3.51
2414 4016 5.654603 TCCATCACTTACAATCTGTACGT 57.345 39.130 0.00 0.00 36.00 3.57
2507 4111 4.408270 ACTCATGATTGATCTACTGCCAGT 59.592 41.667 1.54 1.54 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
419 426 2.417239 TCGTTGCGCGGAGATTTTAATT 59.583 40.909 8.83 0.00 41.72 1.40
445 452 1.134699 TGCTTCACGGCCTCTGATTAG 60.135 52.381 0.00 0.00 0.00 1.73
453 460 0.533308 TAAACGTTGCTTCACGGCCT 60.533 50.000 0.00 0.00 44.82 5.19
583 590 4.901849 TCTAGCCTAGGACAAACTGCATAT 59.098 41.667 14.75 0.00 0.00 1.78
593 600 2.679082 GTTGGGATCTAGCCTAGGACA 58.321 52.381 14.75 0.00 0.00 4.02
618 625 5.762218 GGAAATCATAGTGTGCAGCTCTAAT 59.238 40.000 0.00 0.00 0.00 1.73
789 796 6.320494 ACAAGACGCACTAATCCTATAGAG 57.680 41.667 0.00 0.00 0.00 2.43
793 800 3.871594 GCAACAAGACGCACTAATCCTAT 59.128 43.478 0.00 0.00 0.00 2.57
836 843 6.234177 TCACCAAAACAACAACCAAAATTCT 58.766 32.000 0.00 0.00 0.00 2.40
839 846 5.942826 ACATCACCAAAACAACAACCAAAAT 59.057 32.000 0.00 0.00 0.00 1.82
921 929 4.318332 TGCTTGATCCAGAAGTAGTTGTG 58.682 43.478 0.00 0.41 0.00 3.33
934 942 1.079503 GTCACCGAACTGCTTGATCC 58.920 55.000 0.00 0.00 0.00 3.36
950 958 1.383456 GCACCTTGGTGTTGCTGTCA 61.383 55.000 19.47 0.00 0.00 3.58
951 959 1.360192 GCACCTTGGTGTTGCTGTC 59.640 57.895 19.47 0.00 0.00 3.51
974 985 0.251165 GGTTGTTGGGCTCCTTGCTA 60.251 55.000 0.00 0.00 42.39 3.49
1054 1067 4.497006 CCTTGAAGAGACACTTGCAAACAG 60.497 45.833 0.00 0.00 39.13 3.16
1072 1085 3.476552 CCACAACAAGTTAGCTCCTTGA 58.523 45.455 24.96 0.00 41.44 3.02
1088 1101 0.105760 AAACCACATCAGCCCCACAA 60.106 50.000 0.00 0.00 0.00 3.33
1147 1160 0.252103 AACCTTGTCCTCTCCCGCTA 60.252 55.000 0.00 0.00 0.00 4.26
1231 1245 0.890542 TGCAGAACTCCTTGCGCATT 60.891 50.000 12.75 0.49 0.00 3.56
1247 1261 0.111061 ACAGACTTGGCCATCTTGCA 59.889 50.000 6.09 0.00 0.00 4.08
1308 1322 3.545703 GCTTAGAAGCCAAGCATAAGGA 58.454 45.455 2.68 0.00 46.17 3.36
1347 1361 2.022718 AGGAGGAAGCAGAGACAAGT 57.977 50.000 0.00 0.00 0.00 3.16
1471 1486 4.785453 GCAGCGGGGTAGCAAGCT 62.785 66.667 7.43 7.43 41.07 3.74
1505 1520 6.556974 TGACTAACTAGTAGGAGCAGTAGA 57.443 41.667 0.00 0.00 36.50 2.59
1669 3213 6.033966 GCACAAAATAAGGTAGGTACATTGC 58.966 40.000 0.00 0.00 32.05 3.56
1850 3450 8.596380 GCTGTTTTAGTAGTAGCAAATACTCTG 58.404 37.037 0.00 0.00 43.90 3.35
2046 3647 6.269769 AGAACAAAATCACCACATTAACCCAT 59.730 34.615 0.00 0.00 0.00 4.00
2137 3739 0.883153 GTGGTGTGCTTGATGATGCA 59.117 50.000 0.00 0.00 36.79 3.96
2252 3854 9.672673 ACAGCTAGAAATTATAAGTCACATTGT 57.327 29.630 0.00 0.00 0.00 2.71
2265 3867 7.064609 GTCTACAACATGCACAGCTAGAAATTA 59.935 37.037 0.00 0.00 0.00 1.40
2270 3872 3.511540 AGTCTACAACATGCACAGCTAGA 59.488 43.478 0.00 0.00 0.00 2.43
2369 3971 6.751888 GGATCCATTACACATAGTTTTTGTGC 59.248 38.462 6.95 0.00 46.65 4.57
2414 4016 9.679661 AATAACAGTCATTACACATGGTATTCA 57.320 29.630 0.00 0.00 29.95 2.57


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

AutoCloner maintained by Alex Coulton.