Multiple sequence alignment - TraesCS1D01G267100

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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 TraesCS1D01G267100 chr1D 100.000 3396 0 0 1 3396 363107124 363110519 0.000000e+00 6272.0
1 TraesCS1D01G267100 chr1B 94.046 2452 78 16 1 2409 486344566 486346992 0.000000e+00 3657.0
2 TraesCS1D01G267100 chr1B 86.957 460 19 14 2405 2847 486347029 486347464 2.370000e-131 479.0
3 TraesCS1D01G267100 chr1B 94.755 286 14 1 2845 3130 486348232 486348516 8.650000e-121 444.0
4 TraesCS1D01G267100 chr1B 93.307 254 13 4 3143 3393 486348500 486348752 4.140000e-99 372.0
5 TraesCS1D01G267100 chr1A 94.657 1591 45 14 822 2406 462334856 462336412 0.000000e+00 2431.0
6 TraesCS1D01G267100 chr1A 91.069 851 36 17 1 812 462333966 462334815 0.000000e+00 1114.0
7 TraesCS1D01G267100 chr1A 93.103 551 37 1 2845 3395 462337768 462338317 0.000000e+00 806.0
8 TraesCS1D01G267100 chr1A 89.399 283 7 9 2405 2683 462336448 462336711 5.430000e-88 335.0
9 TraesCS1D01G267100 chr1A 81.176 340 36 13 1088 1423 558125547 558125862 7.280000e-62 248.0
10 TraesCS1D01G267100 chr2D 85.845 219 13 4 1270 1487 643265506 643265305 2.050000e-52 217.0
11 TraesCS1D01G267100 chr4D 90.411 73 7 0 1455 1527 12718765 12718693 2.790000e-16 97.1
12 TraesCS1D01G267100 chr4D 89.041 73 8 0 1455 1527 12697141 12697213 1.300000e-14 91.6
13 TraesCS1D01G267100 chr4B 89.041 73 8 0 1455 1527 23401751 23401823 1.300000e-14 91.6
14 TraesCS1D01G267100 chr4B 89.041 73 8 0 1455 1527 23417957 23417885 1.300000e-14 91.6
15 TraesCS1D01G267100 chr4A 89.041 73 8 0 1455 1527 589600638 589600710 1.300000e-14 91.6
16 TraesCS1D01G267100 chr4A 87.671 73 9 0 1455 1527 589595950 589596022 6.040000e-13 86.1
17 TraesCS1D01G267100 chr6B 76.613 124 29 0 3262 3385 45910899 45910776 6.080000e-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 TraesCS1D01G267100 chr1D 363107124 363110519 3395 False 6272.0 6272 100.00000 1 3396 1 chr1D.!!$F1 3395
1 TraesCS1D01G267100 chr1B 486344566 486348752 4186 False 1238.0 3657 92.26625 1 3393 4 chr1B.!!$F1 3392
2 TraesCS1D01G267100 chr1A 462333966 462338317 4351 False 1171.5 2431 92.05700 1 3395 4 chr1A.!!$F2 3394

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
921 997 0.027979 AATTCGATGCGCATTGACCG 59.972 50.0 34.67 26.96 31.23 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2509 2639 0.249489 GGCGATCGAACTGCTATGGT 60.249 55.0 21.57 0.0 0.0 3.55 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
50 51 1.153349 GAATGGGAGGCTGGTCGAC 60.153 63.158 7.13 7.13 0.00 4.20
455 478 6.014669 CCCCATTTGATTTCACTTAGGTTTGA 60.015 38.462 0.00 0.00 0.00 2.69
510 544 7.834068 TTGCTCTAGAGTAGTAATTTGCAAG 57.166 36.000 20.75 0.00 33.64 4.01
636 676 4.982999 TGTCTCTAACTAATGACTGCGAC 58.017 43.478 0.00 0.00 0.00 5.19
714 757 2.423185 TGCCCGCTAGTTTGATTTGATG 59.577 45.455 0.00 0.00 0.00 3.07
715 758 2.682856 GCCCGCTAGTTTGATTTGATGA 59.317 45.455 0.00 0.00 0.00 2.92
716 759 3.242870 GCCCGCTAGTTTGATTTGATGAG 60.243 47.826 0.00 0.00 0.00 2.90
717 760 3.941483 CCCGCTAGTTTGATTTGATGAGT 59.059 43.478 0.00 0.00 0.00 3.41
748 793 3.505293 GCCAGTTGCTTTCAGAATCTTCT 59.495 43.478 0.00 0.00 35.80 2.85
749 794 4.022503 GCCAGTTGCTTTCAGAATCTTCTT 60.023 41.667 0.00 0.00 34.07 2.52
808 853 2.372690 CGTCGTTCTTGTCCGGCTG 61.373 63.158 0.00 0.00 0.00 4.85
892 968 5.303589 GGATAATTCGGGATGGGTCGATATA 59.696 44.000 0.00 0.00 35.25 0.86
893 969 4.737855 AATTCGGGATGGGTCGATATAG 57.262 45.455 0.00 0.00 35.25 1.31
894 970 2.893215 TCGGGATGGGTCGATATAGT 57.107 50.000 0.00 0.00 0.00 2.12
921 997 0.027979 AATTCGATGCGCATTGACCG 59.972 50.000 34.67 26.96 31.23 4.79
993 1070 1.869767 CTCAGCATATCCGTTTGCCTC 59.130 52.381 0.00 0.00 39.72 4.70
1141 1218 4.087892 CAGCGGTGGTGGAGGAGG 62.088 72.222 6.74 0.00 0.00 4.30
1142 1219 4.316823 AGCGGTGGTGGAGGAGGA 62.317 66.667 0.00 0.00 0.00 3.71
1143 1220 3.775654 GCGGTGGTGGAGGAGGAG 61.776 72.222 0.00 0.00 0.00 3.69
1308 1385 2.202222 CGTACGTCGTGTCCGGTC 60.202 66.667 8.47 0.00 34.52 4.79
1309 1386 2.176792 GTACGTCGTGTCCGGTCC 59.823 66.667 8.47 0.00 33.95 4.46
1316 1393 2.436646 GTGTCCGGTCCATGCCTG 60.437 66.667 0.00 0.00 0.00 4.85
1322 1399 1.746615 CGGTCCATGCCTGGTTGAG 60.747 63.158 7.98 0.00 43.61 3.02
1350 1427 4.209080 GCGTTTCTTGCTGCTTTTAATGTT 59.791 37.500 0.00 0.00 0.00 2.71
2094 2172 4.549516 GGGAGGTACGACTCGCGC 62.550 72.222 0.00 0.00 46.04 6.86
2168 2246 4.436998 GTCTGGTCGGCCGGTCAG 62.437 72.222 29.78 29.78 41.89 3.51
2266 2347 4.323477 CGGTTCGGTTCAGGGCCA 62.323 66.667 6.18 0.00 0.00 5.36
2282 2363 1.751927 CCATGGAGTTGGAGGCAGC 60.752 63.158 5.56 0.00 39.25 5.25
2352 2433 3.181476 CCTTGTTAGCAGGCTGTTTTGTT 60.181 43.478 17.16 0.00 0.00 2.83
2385 2466 6.945435 TGTTATCCAGGCTGAGAATTAACAAA 59.055 34.615 17.94 1.96 0.00 2.83
2509 2639 2.103094 AGCAACAACTGTAGCAGAGTCA 59.897 45.455 2.91 0.00 35.18 3.41
2580 2710 6.215477 TCGAAAATGCTTATGCTATCTTCG 57.785 37.500 15.05 15.05 40.48 3.79
2600 2733 2.736721 CGCTTAAGCAACAACTCTAGCA 59.263 45.455 26.29 0.00 42.21 3.49
2603 2736 4.452455 GCTTAAGCAACAACTCTAGCAGAA 59.548 41.667 22.59 0.00 41.59 3.02
2620 2753 3.798889 GCAGAATCGTCATATCAACCCGA 60.799 47.826 0.00 0.00 0.00 5.14
2704 2837 2.222027 CCCTCGATGGCCATAGTTTTC 58.778 52.381 20.84 4.73 0.00 2.29
2728 2861 2.038837 GTGCTCCAAACCTACCCGC 61.039 63.158 0.00 0.00 0.00 6.13
2738 2871 4.208686 CTACCCGCGAGCCTCCAC 62.209 72.222 8.23 0.00 0.00 4.02
2771 2914 0.955428 TTGGAGCGCGCTTCATTCTT 60.955 50.000 40.46 14.67 30.62 2.52
2826 2969 0.331954 TCTACTCTTCCTGCCCTCGT 59.668 55.000 0.00 0.00 0.00 4.18
2827 2970 1.187087 CTACTCTTCCTGCCCTCGTT 58.813 55.000 0.00 0.00 0.00 3.85
2829 2972 1.122019 ACTCTTCCTGCCCTCGTTGT 61.122 55.000 0.00 0.00 0.00 3.32
2843 2986 1.375326 GTTGTCGCCTTCCTTCCCT 59.625 57.895 0.00 0.00 0.00 4.20
2930 4254 0.647925 GGCTCGTCGATGAAGAAAGC 59.352 55.000 8.98 7.95 33.16 3.51
2954 4278 4.023963 AGTTCGAGGAAGCAAACTTTAAGC 60.024 41.667 0.00 0.00 35.82 3.09
2958 4282 1.611977 GGAAGCAAACTTTAAGCCCGT 59.388 47.619 0.00 0.00 35.82 5.28
3021 4345 3.518068 GCAATCGCCGGGAAAGGG 61.518 66.667 2.18 0.00 0.00 3.95
3146 4470 3.935203 AGAGTTCAAGATATGTGCAACCG 59.065 43.478 0.00 0.00 34.36 4.44
3279 4604 3.190535 GCATTACCGACAAATGACCAAGT 59.809 43.478 8.07 0.00 36.61 3.16
3359 4684 7.869800 AGAAGTTGAAGACAAGAAATGATGAC 58.130 34.615 0.00 0.00 36.64 3.06
3362 4687 4.893608 TGAAGACAAGAAATGATGACGGA 58.106 39.130 0.00 0.00 0.00 4.69
3369 4694 4.286297 AGAAATGATGACGGAGGTTCAA 57.714 40.909 0.00 0.00 0.00 2.69
3386 4711 3.243359 TCAAAAACTGGGAGGAGCAAT 57.757 42.857 0.00 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 3.585990 CTGCTTATTGGCGCGGGG 61.586 66.667 8.83 0.00 34.52 5.73
301 304 1.448717 GGGAGAGAAGCAACCGAGC 60.449 63.158 0.00 0.00 0.00 5.03
302 305 1.219393 GGGGAGAGAAGCAACCGAG 59.781 63.158 0.00 0.00 0.00 4.63
455 478 4.946157 AGAAGAGGCGTCATCAAATCAAAT 59.054 37.500 13.47 0.00 0.00 2.32
520 555 3.726782 GCGCGACCACGAAATAATCTTTT 60.727 43.478 12.10 0.00 42.66 2.27
521 556 2.222953 GCGCGACCACGAAATAATCTTT 60.223 45.455 12.10 0.00 42.66 2.52
522 557 1.326548 GCGCGACCACGAAATAATCTT 59.673 47.619 12.10 0.00 42.66 2.40
524 559 0.928229 AGCGCGACCACGAAATAATC 59.072 50.000 12.10 0.00 42.66 1.75
525 560 0.650512 CAGCGCGACCACGAAATAAT 59.349 50.000 12.10 0.00 42.66 1.28
526 561 0.388778 TCAGCGCGACCACGAAATAA 60.389 50.000 12.10 0.00 42.66 1.40
527 562 0.800683 CTCAGCGCGACCACGAAATA 60.801 55.000 12.10 0.00 42.66 1.40
528 563 2.048597 TCAGCGCGACCACGAAAT 60.049 55.556 12.10 0.00 42.66 2.17
636 676 1.822990 AGCCTGGCAAATCACAATCAG 59.177 47.619 22.65 0.00 0.00 2.90
714 757 1.941668 GCAACTGGCACTCTGGTACTC 60.942 57.143 0.00 0.00 43.97 2.59
715 758 0.035458 GCAACTGGCACTCTGGTACT 59.965 55.000 0.00 0.00 43.97 2.73
716 759 2.544726 GCAACTGGCACTCTGGTAC 58.455 57.895 0.00 0.00 43.97 3.34
760 805 6.750501 ACTAAAACGGTCAAAAGAAGAAAAGC 59.249 34.615 0.00 0.00 0.00 3.51
808 853 4.244066 CCATCTATCTGCAGTGTATGAGC 58.756 47.826 14.67 0.00 0.00 4.26
892 968 3.255888 TGCGCATCGAATTATCTCCTACT 59.744 43.478 5.66 0.00 0.00 2.57
893 969 3.575630 TGCGCATCGAATTATCTCCTAC 58.424 45.455 5.66 0.00 0.00 3.18
894 970 3.934457 TGCGCATCGAATTATCTCCTA 57.066 42.857 5.66 0.00 0.00 2.94
921 997 3.561725 GTGCTTTAGTAGATGCCACATCC 59.438 47.826 4.00 0.00 0.00 3.51
993 1070 4.438145 GCGTATATATTCTTGCTCGATCGG 59.562 45.833 16.41 7.26 0.00 4.18
1141 1218 4.890306 GGGGGCCTCCTCCTCCTC 62.890 77.778 17.08 0.00 43.73 3.71
1316 1393 1.782028 AAGAAACGCACGCCTCAACC 61.782 55.000 0.00 0.00 0.00 3.77
1322 1399 2.427410 CAGCAAGAAACGCACGCC 60.427 61.111 0.00 0.00 0.00 5.68
1328 1405 5.659426 CAACATTAAAAGCAGCAAGAAACG 58.341 37.500 0.00 0.00 0.00 3.60
1364 1441 3.082579 GCACGCGGGGAGAAGAGAT 62.083 63.158 11.92 0.00 0.00 2.75
2208 2286 2.509336 ATCGTCGCCGCCTTCTTG 60.509 61.111 0.00 0.00 0.00 3.02
2226 2304 0.322975 CAGAACCACCTCAGTCCCAG 59.677 60.000 0.00 0.00 0.00 4.45
2266 2347 0.610232 GTTGCTGCCTCCAACTCCAT 60.610 55.000 0.00 0.00 39.47 3.41
2352 2433 4.661222 TCAGCCTGGATAACATTTCAACA 58.339 39.130 0.00 0.00 0.00 3.33
2385 2466 3.256631 GTGCCCTGACATGTGAAGAAAAT 59.743 43.478 1.15 0.00 0.00 1.82
2398 2479 1.507141 CGACAGTTTGGTGCCCTGAC 61.507 60.000 0.00 0.00 0.00 3.51
2509 2639 0.249489 GGCGATCGAACTGCTATGGT 60.249 55.000 21.57 0.00 0.00 3.55
2580 2710 3.997021 TCTGCTAGAGTTGTTGCTTAAGC 59.003 43.478 20.84 20.84 42.50 3.09
2600 2733 4.280929 TGATCGGGTTGATATGACGATTCT 59.719 41.667 0.00 0.00 43.42 2.40
2603 2736 3.615110 GCTGATCGGGTTGATATGACGAT 60.615 47.826 3.14 0.00 45.70 3.73
2738 2871 1.270785 GCTCCAAACAACCCCCAAATG 60.271 52.381 0.00 0.00 0.00 2.32
2771 2914 1.666054 ACTCACGCCAAACCGTTTTA 58.334 45.000 0.00 0.00 39.83 1.52
2826 2969 1.677552 GAGGGAAGGAAGGCGACAA 59.322 57.895 0.00 0.00 0.00 3.18
2827 2970 2.646175 CGAGGGAAGGAAGGCGACA 61.646 63.158 0.00 0.00 0.00 4.35
2829 2972 3.771160 GCGAGGGAAGGAAGGCGA 61.771 66.667 0.00 0.00 0.00 5.54
2921 4245 3.393800 CTTCCTCGAACTGCTTTCTTCA 58.606 45.455 0.00 0.00 31.20 3.02
2930 4254 3.971032 AAAGTTTGCTTCCTCGAACTG 57.029 42.857 0.00 0.00 39.82 3.16
2954 4278 3.879295 ACAAGAGCAATATCATCAACGGG 59.121 43.478 0.00 0.00 0.00 5.28
2958 4282 8.735692 TGTCATAACAAGAGCAATATCATCAA 57.264 30.769 0.00 0.00 30.70 2.57
3000 4324 3.885538 TTTCCCGGCGATTGCGTCA 62.886 57.895 9.30 0.00 43.65 4.35
3021 4345 5.718649 TCTAATACTTTGCACTCGATTGC 57.281 39.130 19.84 19.84 43.31 3.56
3146 4470 2.630580 TGCTCCAAATAACCCAACCAAC 59.369 45.455 0.00 0.00 0.00 3.77
3199 4523 7.112122 ACAAGATTGCTTACATATTGGTCAGA 58.888 34.615 0.00 0.00 31.81 3.27
3200 4524 7.325660 ACAAGATTGCTTACATATTGGTCAG 57.674 36.000 0.00 0.00 31.81 3.51
3279 4604 3.323403 AGGCCAAACAAATTTCCATTCGA 59.677 39.130 5.01 0.00 0.00 3.71
3284 4609 2.402564 TGGAGGCCAAACAAATTTCCA 58.597 42.857 5.01 2.38 0.00 3.53
3359 4684 1.880027 CTCCCAGTTTTTGAACCTCCG 59.120 52.381 0.00 0.00 0.00 4.63
3362 4687 2.753168 GCTCCTCCCAGTTTTTGAACCT 60.753 50.000 0.00 0.00 0.00 3.50
3369 4694 4.336280 GAACTATTGCTCCTCCCAGTTTT 58.664 43.478 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.