Multiple sequence alignment - TraesCS1D01G145600

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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 TraesCS1D01G145600 chr1D 100.000 4055 0 0 1 4055 201052865 201056919 0.000000e+00 7489.0
1 TraesCS1D01G145600 chr1D 90.141 71 6 1 675 744 201053475 201053545 1.550000e-14 91.6
2 TraesCS1D01G145600 chr1D 84.211 57 6 3 3298 3352 318133110 318133165 7.000000e-03 52.8
3 TraesCS1D01G145600 chr1A 98.060 2165 27 6 1897 4055 254994151 254996306 0.000000e+00 3751.0
4 TraesCS1D01G145600 chr1A 96.466 1132 36 3 758 1889 254992960 254994087 0.000000e+00 1866.0
5 TraesCS1D01G145600 chr1A 100.000 32 0 0 675 706 254988509 254988540 4.380000e-05 60.2
6 TraesCS1D01G145600 chr1B 94.145 1742 75 15 1 1722 288950426 288952160 0.000000e+00 2627.0
7 TraesCS1D01G145600 chr1B 90.222 1350 93 20 1897 3240 288952974 288954290 0.000000e+00 1725.0
8 TraesCS1D01G145600 chr1B 91.772 316 20 4 3547 3858 288959437 288959750 6.220000e-118 435.0
9 TraesCS1D01G145600 chr1B 94.382 178 9 1 1720 1897 288952748 288952924 5.160000e-69 272.0
10 TraesCS1D01G145600 chr1B 93.258 178 12 0 3878 4055 288959741 288959918 3.110000e-66 263.0
11 TraesCS1D01G145600 chr1B 82.639 144 13 4 3362 3493 288958438 288958581 2.560000e-22 117.0
12 TraesCS1D01G145600 chr1B 89.855 69 5 2 677 744 288951037 288951104 2.010000e-13 87.9
13 TraesCS1D01G145600 chr4B 89.157 83 7 2 3280 3360 139763254 139763336 7.170000e-18 102.0
14 TraesCS1D01G145600 chr2D 88.372 86 8 2 3280 3363 615126609 615126524 7.170000e-18 102.0
15 TraesCS1D01G145600 chr7A 84.043 94 10 4 3280 3370 97912754 97912663 7.220000e-13 86.1
16 TraesCS1D01G145600 chr7D 93.333 45 2 1 3317 3360 447070878 447070922 9.410000e-07 65.8
17 TraesCS1D01G145600 chr6B 93.333 45 2 1 3321 3364 667156445 667156401 9.410000e-07 65.8
18 TraesCS1D01G145600 chr2A 91.111 45 3 1 3325 3368 74165929 74165885 4.380000e-05 60.2
19 TraesCS1D01G145600 chr5D 88.000 50 3 3 3311 3358 491432608 491432656 5.660000e-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 TraesCS1D01G145600 chr1D 201052865 201056919 4054 False 3790.300000 7489 95.0705 1 4055 2 chr1D.!!$F2 4054
1 TraesCS1D01G145600 chr1A 254992960 254996306 3346 False 2808.500000 3751 97.2630 758 4055 2 chr1A.!!$F2 3297
2 TraesCS1D01G145600 chr1B 288950426 288954290 3864 False 1177.975000 2627 92.1510 1 3240 4 chr1B.!!$F1 3239
3 TraesCS1D01G145600 chr1B 288958438 288959918 1480 False 271.666667 435 89.2230 3362 4055 3 chr1B.!!$F2 693

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
250 251 0.108585 GCTTCACTGGTGGTCTTCCA 59.891 55.000 0.70 0.0 42.05 3.53 F
323 324 0.109365 TTGGGCGCATCAAAATGACG 60.109 50.000 10.83 0.0 34.61 4.35 F
578 581 0.824182 AAAAATGGTGTTCCGGGCGA 60.824 50.000 0.00 0.0 36.30 5.54 F
1262 1267 0.756442 TTGTGGCCTTTCTTGCTGCT 60.756 50.000 3.32 0.0 0.00 4.24 F
1263 1268 1.288127 GTGGCCTTTCTTGCTGCTG 59.712 57.895 3.32 0.0 0.00 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1262 1267 0.034337 GGTCTTCCCGCTGTTACACA 59.966 55.000 0.00 0.0 0.00 3.72 R
1263 1268 0.320697 AGGTCTTCCCGCTGTTACAC 59.679 55.000 0.00 0.0 38.74 2.90 R
2350 3022 4.679197 TGCGAAATAGCATTTTGACACAAC 59.321 37.500 11.02 0.0 42.92 3.32 R
2741 3415 1.204941 CCTGGGTACTCTCGACAAAGG 59.795 57.143 0.00 0.0 0.00 3.11 R
3072 3746 7.448748 ACCTAAAATCTCGCACAGTAAATTT 57.551 32.000 0.00 0.0 0.00 1.82 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
21 22 2.558359 ACCTACAAGATGTTTGCTTGGC 59.442 45.455 0.00 0.00 45.31 4.52
24 25 4.095483 CCTACAAGATGTTTGCTTGGCTAG 59.905 45.833 0.00 0.00 45.31 3.42
65 66 2.336554 CTGCTAACAAATTGCAGCGT 57.663 45.000 13.24 0.00 45.76 5.07
68 69 2.033927 TGCTAACAAATTGCAGCGTCAA 59.966 40.909 13.24 0.00 33.07 3.18
120 121 0.968393 GTTGAGGAGCCCGAGTCTCT 60.968 60.000 0.00 0.00 0.00 3.10
169 170 0.739462 CTCGGTAGATTTGGCACGCA 60.739 55.000 0.00 0.00 0.00 5.24
209 210 4.473520 CCGGCTTGGGCACTCGAT 62.474 66.667 0.00 0.00 40.87 3.59
223 224 0.390492 CTCGATGCCTGCACCTGATA 59.610 55.000 0.00 0.00 0.00 2.15
237 238 3.686726 CACCTGATAAGGAGTTGCTTCAC 59.313 47.826 1.89 0.00 0.00 3.18
250 251 0.108585 GCTTCACTGGTGGTCTTCCA 59.891 55.000 0.70 0.00 42.05 3.53
308 309 1.005805 TGATCACCTGGACCATTTGGG 59.994 52.381 0.00 0.00 44.81 4.12
323 324 0.109365 TTGGGCGCATCAAAATGACG 60.109 50.000 10.83 0.00 34.61 4.35
333 334 4.466828 CATCAAAATGACGTGGTCTTCAC 58.533 43.478 0.00 0.00 37.78 3.18
379 380 1.268285 TGTTGCAACGAATCCACAACG 60.268 47.619 23.79 0.00 42.68 4.10
468 471 4.443784 GTCGAGCGACAGTGAGTC 57.556 61.111 17.21 0.00 44.02 3.36
485 488 1.274167 AGTCGTCCAGATGCCGTTTTA 59.726 47.619 0.00 0.00 0.00 1.52
527 530 6.319658 ACACCGTTCTCGTATTTCCTTCTATA 59.680 38.462 0.00 0.00 35.01 1.31
578 581 0.824182 AAAAATGGTGTTCCGGGCGA 60.824 50.000 0.00 0.00 36.30 5.54
730 733 4.076394 TCTTTTACCTGAAATCAACGGGG 58.924 43.478 0.00 0.00 38.04 5.73
1101 1106 4.175337 TGCTGGTATGCCGCCTCC 62.175 66.667 12.44 0.00 37.67 4.30
1262 1267 0.756442 TTGTGGCCTTTCTTGCTGCT 60.756 50.000 3.32 0.00 0.00 4.24
1263 1268 1.288127 GTGGCCTTTCTTGCTGCTG 59.712 57.895 3.32 0.00 0.00 4.41
1302 1307 1.876664 GCTCCTTTTCCAGTTCGCC 59.123 57.895 0.00 0.00 0.00 5.54
1892 2503 5.178096 TCCTTTCTGCTGACCATTAATGA 57.822 39.130 17.23 0.00 0.00 2.57
2708 3382 3.766691 GGCATGCCAGCTGGTTGG 61.767 66.667 32.81 22.10 41.35 3.77
3045 3719 7.074653 ACAGTACCTTGTTCTTGAGGAAATA 57.925 36.000 0.00 0.00 36.84 1.40
3335 4011 7.846644 TTCAGTTAAGTTCGAACTAAAACCA 57.153 32.000 32.20 23.76 38.57 3.67
3360 4036 5.468746 CGACAAGTATTTTGAACAGAGGGAA 59.531 40.000 0.00 0.00 0.00 3.97
3448 4150 5.049818 GGCAATATCTGTTGAGTATGACTGC 60.050 44.000 0.00 0.00 0.00 4.40
3451 4153 7.518052 GCAATATCTGTTGAGTATGACTGCTTC 60.518 40.741 0.00 0.00 0.00 3.86
3452 4154 5.674052 ATCTGTTGAGTATGACTGCTTCT 57.326 39.130 0.00 0.00 0.00 2.85
3453 4155 5.065704 TCTGTTGAGTATGACTGCTTCTC 57.934 43.478 0.00 0.00 0.00 2.87
3454 4156 4.769488 TCTGTTGAGTATGACTGCTTCTCT 59.231 41.667 0.00 0.00 0.00 3.10
3455 4157 5.244851 TCTGTTGAGTATGACTGCTTCTCTT 59.755 40.000 0.00 0.00 0.00 2.85
3456 4158 5.858381 TGTTGAGTATGACTGCTTCTCTTT 58.142 37.500 0.00 0.00 0.00 2.52
3457 4159 5.928839 TGTTGAGTATGACTGCTTCTCTTTC 59.071 40.000 0.00 0.00 0.00 2.62
3458 4160 5.728637 TGAGTATGACTGCTTCTCTTTCA 57.271 39.130 0.00 0.00 0.00 2.69
3459 4161 6.101650 TGAGTATGACTGCTTCTCTTTCAA 57.898 37.500 0.00 0.00 0.00 2.69
3460 4162 6.705302 TGAGTATGACTGCTTCTCTTTCAAT 58.295 36.000 0.00 0.00 0.00 2.57
3461 4163 6.592994 TGAGTATGACTGCTTCTCTTTCAATG 59.407 38.462 0.00 0.00 0.00 2.82
3475 4177 4.571984 TCTTTCAATGATATCGTGTGCTGG 59.428 41.667 0.00 0.00 0.00 4.85
3742 5249 8.514594 CAAGCTCAGAAGTAACATTATTTTCCA 58.485 33.333 0.00 0.00 0.00 3.53
3852 5360 5.012046 TGAAGAGCTCAGTAAGGATCAACAA 59.988 40.000 17.77 0.00 0.00 2.83
3858 5366 6.373774 AGCTCAGTAAGGATCAACAATTGAAG 59.626 38.462 13.59 3.96 43.95 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 0.969894 CACCTATCCTTCGGGGCTAG 59.030 60.000 0.00 0.00 35.37 3.42
24 25 0.463833 CAACACCTATCCTTCGGGGC 60.464 60.000 0.00 0.00 35.37 5.80
27 28 3.782046 CAGTACAACACCTATCCTTCGG 58.218 50.000 0.00 0.00 0.00 4.30
65 66 0.983467 TGCTGATGTGGTAGGCTTGA 59.017 50.000 0.00 0.00 0.00 3.02
68 69 1.910722 CCTGCTGATGTGGTAGGCT 59.089 57.895 0.00 0.00 30.54 4.58
74 75 2.882876 GCAAGCCTGCTGATGTGG 59.117 61.111 0.00 0.00 45.74 4.17
98 99 1.816863 GACTCGGGCTCCTCAACACA 61.817 60.000 0.00 0.00 0.00 3.72
136 137 0.889186 ACCGAGCAAACACACATCCC 60.889 55.000 0.00 0.00 0.00 3.85
169 170 1.461461 CCCCCATGACCCCGATACT 60.461 63.158 0.00 0.00 0.00 2.12
193 194 3.197790 CATCGAGTGCCCAAGCCG 61.198 66.667 0.00 0.00 38.69 5.52
209 210 0.543277 CTCCTTATCAGGTGCAGGCA 59.457 55.000 0.00 0.00 41.69 4.75
213 214 1.630369 AGCAACTCCTTATCAGGTGCA 59.370 47.619 12.05 0.00 40.63 4.57
223 224 1.477558 CCACCAGTGAAGCAACTCCTT 60.478 52.381 0.00 0.00 0.00 3.36
237 238 0.397941 TGCTCTTGGAAGACCACCAG 59.602 55.000 0.00 0.00 46.80 4.00
250 251 6.609212 TCAAAGTATCTCTATCCACTGCTCTT 59.391 38.462 0.00 0.00 0.00 2.85
308 309 0.109781 ACCACGTCATTTTGATGCGC 60.110 50.000 0.00 0.00 36.89 6.09
323 324 0.603975 GTGGCTCCAGTGAAGACCAC 60.604 60.000 7.10 7.10 46.03 4.16
361 362 1.262950 CTCGTTGTGGATTCGTTGCAA 59.737 47.619 0.00 0.00 0.00 4.08
379 380 2.033372 GGTAGTCTAGTTGCTCCCCTC 58.967 57.143 0.00 0.00 0.00 4.30
386 387 2.159226 AGTGATGCGGTAGTCTAGTTGC 60.159 50.000 0.00 0.00 0.00 4.17
462 465 4.504132 GGCATCTGGACGACTCAC 57.496 61.111 0.00 0.00 0.00 3.51
527 530 0.036952 CCTGGAGACGTGTCATGCTT 60.037 55.000 15.28 0.00 0.00 3.91
610 613 7.174946 AGGACCAAAAGTATGAACAGTTATGTG 59.825 37.037 0.00 0.00 40.39 3.21
611 614 7.174946 CAGGACCAAAAGTATGAACAGTTATGT 59.825 37.037 0.00 0.00 43.15 2.29
665 668 9.730420 AGTATGAACAGTAATGTGAAAACAAAC 57.270 29.630 0.00 0.00 0.00 2.93
695 698 8.575649 TTCAGGTAAAAGAAATAATCAGGACC 57.424 34.615 0.00 0.00 0.00 4.46
834 837 4.142093 GCACCAGCACCTCATATGAAAAAT 60.142 41.667 6.90 0.00 41.58 1.82
851 854 2.202987 GGCTCTCGGATGCACCAG 60.203 66.667 0.00 0.00 38.90 4.00
1101 1106 1.866853 GCAAGCCGAGGGAAGTTTGG 61.867 60.000 0.00 0.00 0.00 3.28
1262 1267 0.034337 GGTCTTCCCGCTGTTACACA 59.966 55.000 0.00 0.00 0.00 3.72
1263 1268 0.320697 AGGTCTTCCCGCTGTTACAC 59.679 55.000 0.00 0.00 38.74 2.90
1326 1331 0.816018 AAATGAACACCACGTGCCGA 60.816 50.000 10.91 0.00 36.98 5.54
1892 2503 6.745159 TGTGTAACACATTGTTGTAAGTGT 57.255 33.333 1.73 0.00 45.67 3.55
2350 3022 4.679197 TGCGAAATAGCATTTTGACACAAC 59.321 37.500 11.02 0.00 42.92 3.32
2741 3415 1.204941 CCTGGGTACTCTCGACAAAGG 59.795 57.143 0.00 0.00 0.00 3.11
2882 3556 9.453572 AAATCATGAAAACATACTAGCTCAAGA 57.546 29.630 0.00 0.00 0.00 3.02
3072 3746 7.448748 ACCTAAAATCTCGCACAGTAAATTT 57.551 32.000 0.00 0.00 0.00 1.82
3335 4011 4.755123 CCCTCTGTTCAAAATACTTGTCGT 59.245 41.667 0.00 0.00 0.00 4.34
3448 4150 6.257411 AGCACACGATATCATTGAAAGAGAAG 59.743 38.462 3.12 0.00 0.00 2.85
3451 4153 5.277202 CCAGCACACGATATCATTGAAAGAG 60.277 44.000 3.12 0.00 0.00 2.85
3452 4154 4.571984 CCAGCACACGATATCATTGAAAGA 59.428 41.667 3.12 0.00 0.00 2.52
3453 4155 4.333649 ACCAGCACACGATATCATTGAAAG 59.666 41.667 3.12 0.00 0.00 2.62
3454 4156 4.094739 CACCAGCACACGATATCATTGAAA 59.905 41.667 3.12 0.00 0.00 2.69
3455 4157 3.622612 CACCAGCACACGATATCATTGAA 59.377 43.478 3.12 0.00 0.00 2.69
3456 4158 3.197265 CACCAGCACACGATATCATTGA 58.803 45.455 3.12 0.00 0.00 2.57
3457 4159 2.938451 ACACCAGCACACGATATCATTG 59.062 45.455 3.12 1.74 0.00 2.82
3458 4160 3.266510 ACACCAGCACACGATATCATT 57.733 42.857 3.12 0.00 0.00 2.57
3459 4161 2.988010 ACACCAGCACACGATATCAT 57.012 45.000 3.12 0.00 0.00 2.45
3460 4162 2.028567 TGAACACCAGCACACGATATCA 60.029 45.455 3.12 0.00 0.00 2.15
3461 4163 2.616960 TGAACACCAGCACACGATATC 58.383 47.619 0.00 0.00 0.00 1.63
3475 4177 9.455847 GCTAATTCTATTTGATGGAATGAACAC 57.544 33.333 1.09 0.00 39.21 3.32
3742 5249 7.239143 TGATCTCTTCCATGGGAGATATTTCAT 59.761 37.037 23.65 8.52 45.72 2.57
3858 5366 1.909302 TGTGGGAGAAGATGGGAGTTC 59.091 52.381 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.