Multiple sequence alignment - TraesCS2D01G200000

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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 TraesCS2D01G200000 chr2D 100.000 2738 0 0 1 2738 151436716 151439453 0.000000e+00 5057.0
1 TraesCS2D01G200000 chr2B 93.325 2532 124 20 2 2527 210013524 210016016 0.000000e+00 3698.0
2 TraesCS2D01G200000 chr2B 92.694 219 14 2 2521 2738 210016416 210016633 5.690000e-82 315.0
3 TraesCS2D01G200000 chr2A 92.378 1863 111 11 2 1852 149653569 149651726 0.000000e+00 2625.0
4 TraesCS2D01G200000 chr2A 93.509 570 26 6 1906 2468 149651524 149650959 0.000000e+00 837.0
5 TraesCS2D01G200000 chr2A 91.981 212 16 1 2482 2692 149646119 149645908 2.060000e-76 296.0
6 TraesCS2D01G200000 chr2A 94.118 51 3 0 2688 2738 149637225 149637175 8.130000e-11 78.7
7 TraesCS2D01G200000 chr7B 79.781 183 23 9 2556 2738 45842236 45842068 1.330000e-23 121.0
8 TraesCS2D01G200000 chr7D 79.503 161 32 1 125 285 400152084 400152243 2.230000e-21 113.0
9 TraesCS2D01G200000 chr3A 76.995 213 38 8 2527 2738 735591557 735591759 8.010000e-21 111.0
10 TraesCS2D01G200000 chr7A 77.841 176 37 2 125 299 457849109 457849283 1.040000e-19 108.0
11 TraesCS2D01G200000 chr7A 92.958 71 3 1 2668 2738 95259156 95259224 4.820000e-18 102.0
12 TraesCS2D01G200000 chr1D 78.488 172 30 5 132 299 199327620 199327452 3.730000e-19 106.0
13 TraesCS2D01G200000 chr1A 85.366 82 10 2 125 205 250484236 250484156 1.750000e-12 84.2
14 TraesCS2D01G200000 chr6B 92.727 55 3 1 2374 2427 38218268 38218322 8.130000e-11 78.7
15 TraesCS2D01G200000 chr6D 100.000 29 0 0 423 451 57513291 57513263 1.000000e-03 54.7
16 TraesCS2D01G200000 chr4B 100.000 28 0 0 425 452 179315855 179315882 5.000000e-03 52.8


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 TraesCS2D01G200000 chr2D 151436716 151439453 2737 False 5057.0 5057 100.0000 1 2738 1 chr2D.!!$F1 2737
1 TraesCS2D01G200000 chr2B 210013524 210016633 3109 False 2006.5 3698 93.0095 2 2738 2 chr2B.!!$F1 2736
2 TraesCS2D01G200000 chr2A 149650959 149653569 2610 True 1731.0 2625 92.9435 2 2468 2 chr2A.!!$R3 2466

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
255 256 0.526211 CGCCTGCTATAGTATCCGCA 59.474 55.0 0.84 6.8 0.0 5.69 F
1335 1352 0.464452 GGAGGGGTACGTCTTCATGG 59.536 60.0 0.00 0.0 0.0 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1684 1701 1.135199 TGGATCGTTGAAGTAGACGGC 60.135 52.381 0.00 0.00 39.59 5.68 R
2664 3259 0.600557 CCAAAAACGCTGCCATGGTA 59.399 50.000 14.67 8.24 0.00 3.25 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
76 77 9.492730 AATATGGATCAACCTAATTCCACTTTT 57.507 29.630 0.00 0.00 40.87 2.27
118 119 5.844301 CACCTAAAAATTTGATGGTGTGC 57.156 39.130 19.91 0.00 39.80 4.57
161 162 3.691118 CCAACACACACCATCTAATCTGG 59.309 47.826 0.00 0.00 39.80 3.86
255 256 0.526211 CGCCTGCTATAGTATCCGCA 59.474 55.000 0.84 6.80 0.00 5.69
270 271 1.091771 CCGCAGTCGCCATCTTTCAT 61.092 55.000 0.00 0.00 33.11 2.57
286 289 6.317663 TCTTTCATCATCCCATCTTCAGAA 57.682 37.500 0.00 0.00 0.00 3.02
287 290 6.724351 TCTTTCATCATCCCATCTTCAGAAA 58.276 36.000 0.00 0.00 0.00 2.52
451 458 1.450360 AACTCTCCCCTCCAAGCTTT 58.550 50.000 0.00 0.00 0.00 3.51
655 666 7.492344 GCAAAAACAGGAAAGAAGAGAATTCAA 59.508 33.333 8.44 0.00 0.00 2.69
819 836 2.113910 ACAAAACGTGCAAATCGTCC 57.886 45.000 1.00 0.00 40.69 4.79
829 846 0.645355 CAAATCGTCCCGTGTCGATG 59.355 55.000 0.63 0.00 44.29 3.84
876 893 1.679898 CACCCCCTGTCCAGACTTC 59.320 63.158 0.00 0.00 0.00 3.01
971 988 2.472909 CCAAGCGAGCCCCGAAATC 61.473 63.158 0.00 0.00 41.76 2.17
984 1001 2.357154 CCCGAAATCTCCATCAAACCCT 60.357 50.000 0.00 0.00 0.00 4.34
1047 1064 2.317609 CGACGTGGCCCAGAACAAG 61.318 63.158 0.00 0.00 0.00 3.16
1098 1115 2.747460 ACACGCCTGCGCATCAAT 60.747 55.556 12.24 0.00 44.19 2.57
1281 1298 2.949678 CACCGCGACGAGGAATCG 60.950 66.667 25.04 3.87 42.55 3.34
1335 1352 0.464452 GGAGGGGTACGTCTTCATGG 59.536 60.000 0.00 0.00 0.00 3.66
1464 1481 2.671682 GAGACCACCAGGGGAAGC 59.328 66.667 0.00 0.00 42.91 3.86
1466 1483 2.190488 GAGACCACCAGGGGAAGCAG 62.190 65.000 0.00 0.00 42.91 4.24
1468 1485 3.970410 CCACCAGGGGAAGCAGCA 61.970 66.667 0.00 0.00 0.00 4.41
1684 1701 0.962356 GATGGACAAGGTGGTGCAGG 60.962 60.000 0.00 0.00 42.49 4.85
2122 2308 5.668471 TGCTTTTCATGTGTTTCATTTCCA 58.332 33.333 0.00 0.00 34.09 3.53
2247 2433 1.200760 TATCCATAGCCATGCCCGCT 61.201 55.000 0.56 0.56 40.45 5.52
2279 2465 2.154462 GCACACCTGCATACTCTGTTT 58.846 47.619 0.00 0.00 43.62 2.83
2292 2478 4.222124 ACTCTGTTTGTATCCATGTCCC 57.778 45.455 0.00 0.00 0.00 4.46
2322 2508 8.127954 GGTACCAAACGAACAACTAATTAAACA 58.872 33.333 7.15 0.00 0.00 2.83
2369 2556 3.990959 AGGACCTTTTGGCAAAACAAA 57.009 38.095 20.81 1.51 45.59 2.83
2509 2697 8.480133 AACTATAGGAAACTCTTCGATATGGT 57.520 34.615 4.43 0.00 43.67 3.55
2522 2710 0.319900 ATATGGTCGGCTGATCACGC 60.320 55.000 11.59 8.20 38.26 5.34
2527 2715 3.554692 CGGCTGATCACGCGTTCC 61.555 66.667 10.22 1.54 0.00 3.62
2529 2717 2.740714 GGCTGATCACGCGTTCCAC 61.741 63.158 10.22 1.90 0.00 4.02
2531 2719 1.959899 GCTGATCACGCGTTCCACTG 61.960 60.000 10.22 6.99 0.00 3.66
2532 2720 1.354337 CTGATCACGCGTTCCACTGG 61.354 60.000 10.22 0.00 0.00 4.00
2552 3147 0.179062 CTCCTGCCACTGCTATCACC 60.179 60.000 0.00 0.00 38.71 4.02
2554 3149 1.219124 CTGCCACTGCTATCACCGT 59.781 57.895 0.00 0.00 38.71 4.83
2604 3199 4.411869 TGATCATATCCTTTACCTGTGGCA 59.588 41.667 0.00 0.00 0.00 4.92
2617 3212 3.169378 TGGCAGGCATCCACTTGA 58.831 55.556 0.00 0.00 0.00 3.02
2622 3217 2.356278 GGCATCCACTTGAGCCCA 59.644 61.111 0.00 0.00 41.25 5.36
2627 3222 2.469465 ATCCACTTGAGCCCACCACG 62.469 60.000 0.00 0.00 0.00 4.94
2633 3228 1.208535 CTTGAGCCCACCACGGTTATA 59.791 52.381 0.00 0.00 0.00 0.98
2664 3259 8.279800 GCTTGCCGAAAATAAAATAAAAACACT 58.720 29.630 0.00 0.00 0.00 3.55
2689 3284 4.324424 CAGCGTTTTTGGGTGCAG 57.676 55.556 0.00 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 6.437928 TCTTTTTGTCAGATTCGGTTGAATG 58.562 36.000 0.00 0.00 44.79 2.67
76 77 4.202223 GGTGTAGTGACAGAGGTTTTCAGA 60.202 45.833 0.00 0.00 35.82 3.27
118 119 1.078848 CGAGGTCAAGGGCTCAAGG 60.079 63.158 0.00 0.00 0.00 3.61
161 162 1.600916 GGTGGCTTGGTGAGGTCAC 60.601 63.158 1.17 1.17 45.72 3.67
164 165 4.643387 GCGGTGGCTTGGTGAGGT 62.643 66.667 0.00 0.00 35.83 3.85
255 256 2.486191 GGGATGATGAAAGATGGCGACT 60.486 50.000 0.00 0.00 0.00 4.18
286 289 6.741992 TTTGAACTATGATGCGTTCATCTT 57.258 33.333 11.19 2.38 46.06 2.40
287 290 6.595326 TCTTTTGAACTATGATGCGTTCATCT 59.405 34.615 11.19 0.00 46.06 2.90
356 359 4.395625 CTCTGATGATGGTTGGTGCATAT 58.604 43.478 0.00 0.00 0.00 1.78
655 666 3.067106 CGGTTTCAGCTATGTGTCTGTT 58.933 45.455 0.00 0.00 0.00 3.16
746 761 1.945354 GATTGCGAGTGGAGTCCGGA 61.945 60.000 0.00 0.00 0.00 5.14
819 836 2.403259 TGCTTATATGCATCGACACGG 58.597 47.619 0.19 0.00 38.12 4.94
829 846 0.436531 GACGAGCGCTGCTTATATGC 59.563 55.000 18.48 3.70 39.88 3.14
842 859 1.153349 GTGGATTGGGGAGACGAGC 60.153 63.158 0.00 0.00 0.00 5.03
876 893 2.760385 GGGAGGACGAGGGACTGG 60.760 72.222 0.00 0.00 41.55 4.00
984 1001 1.406887 GCCATGCTCGTCCTTCCTTAA 60.407 52.381 0.00 0.00 0.00 1.85
1043 1060 2.746277 GGATCGGGTTGCGCTTGT 60.746 61.111 9.73 0.00 0.00 3.16
1047 1064 2.791927 GAAAGGATCGGGTTGCGC 59.208 61.111 0.00 0.00 0.00 6.09
1083 1100 3.204827 GGATTGATGCGCAGGCGT 61.205 61.111 18.32 0.00 44.10 5.68
1281 1298 3.880846 CGGCGCTTGGATTCTGGC 61.881 66.667 7.64 0.00 0.00 4.85
1282 1299 2.125147 TCGGCGCTTGGATTCTGG 60.125 61.111 7.64 0.00 0.00 3.86
1335 1352 3.843240 CCGAAAGAGCTGCGCGAC 61.843 66.667 12.10 0.88 0.00 5.19
1464 1481 3.020026 CTCAAACCGCGAGCTGCTG 62.020 63.158 8.23 0.28 43.27 4.41
1684 1701 1.135199 TGGATCGTTGAAGTAGACGGC 60.135 52.381 0.00 0.00 39.59 5.68
1947 2127 3.000476 CGACACCGTATTGTAACCAATCG 60.000 47.826 0.00 0.00 41.50 3.34
2028 2214 6.332976 AGACATACAGATTTGATTTCCCCT 57.667 37.500 0.00 0.00 0.00 4.79
2230 2416 3.170672 AGCGGGCATGGCTATGGA 61.171 61.111 19.78 0.00 39.39 3.41
2292 2478 1.605232 GTTGTTCGTTTGGTACCCCTG 59.395 52.381 10.07 0.00 0.00 4.45
2334 2521 5.505181 AAGGTCCTTTCAGTGACATACAT 57.495 39.130 0.00 0.00 33.09 2.29
2335 2522 4.974645 AAGGTCCTTTCAGTGACATACA 57.025 40.909 0.00 0.00 33.09 2.29
2336 2523 5.048713 CCAAAAGGTCCTTTCAGTGACATAC 60.049 44.000 17.35 0.00 31.99 2.39
2341 2528 2.306847 GCCAAAAGGTCCTTTCAGTGA 58.693 47.619 17.35 0.00 31.99 3.41
2353 2540 7.778470 TTGTAGTATTTGTTTTGCCAAAAGG 57.222 32.000 2.15 0.00 37.81 3.11
2507 2695 4.796231 ACGCGTGATCAGCCGACC 62.796 66.667 12.93 0.00 0.00 4.79
2509 2697 2.506217 GAACGCGTGATCAGCCGA 60.506 61.111 14.98 0.00 0.00 5.54
2522 2710 2.743928 GCAGGAGCCAGTGGAACG 60.744 66.667 15.20 0.00 36.87 3.95
2532 2720 0.813210 GTGATAGCAGTGGCAGGAGC 60.813 60.000 0.00 0.00 44.61 4.70
2552 3147 3.960998 GCGCACGCGACTGATACG 61.961 66.667 15.93 6.44 42.83 3.06
2604 3199 2.233566 TGGGCTCAAGTGGATGCCT 61.234 57.895 7.63 0.00 44.36 4.75
2617 3212 3.809324 GCATAATATAACCGTGGTGGGCT 60.809 47.826 0.00 0.00 44.64 5.19
2622 3217 3.818773 GGCAAGCATAATATAACCGTGGT 59.181 43.478 0.00 0.00 0.00 4.16
2627 3222 9.685828 TTTATTTTCGGCAAGCATAATATAACC 57.314 29.630 0.00 0.00 0.00 2.85
2664 3259 0.600557 CCAAAAACGCTGCCATGGTA 59.399 50.000 14.67 8.24 0.00 3.25


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

AutoCloner maintained by Alex Coulton.