Multiple sequence alignment - TraesCS3D01G121500

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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 TraesCS3D01G121500 chr3D 100.000 3363 0 0 1 3363 78946322 78942960 0.000000e+00 6211
1 TraesCS3D01G121500 chr3D 93.540 2322 122 10 1057 3363 79246875 79244567 0.000000e+00 3432
2 TraesCS3D01G121500 chr3D 95.343 1589 73 1 1057 2644 79300154 79298566 0.000000e+00 2523
3 TraesCS3D01G121500 chr3D 94.855 1069 49 5 1 1064 79247978 79246911 0.000000e+00 1664
4 TraesCS3D01G121500 chr3D 94.804 866 41 4 1 864 79301135 79300272 0.000000e+00 1347
5 TraesCS3D01G121500 chr3D 92.000 400 13 7 2642 3029 79296270 79295878 8.210000e-151 544
6 TraesCS3D01G121500 chr3D 85.886 333 33 9 2789 3114 79290919 79290594 3.210000e-90 342
7 TraesCS3D01G121500 chr3D 97.842 139 3 0 3225 3363 79295808 79295670 1.210000e-59 241
8 TraesCS3D01G121500 chr3D 97.619 84 2 0 981 1064 79300273 79300190 9.730000e-31 145
9 TraesCS3D01G121500 chr3B 92.429 2338 118 21 1057 3363 124551503 124549194 0.000000e+00 3282
10 TraesCS3D01G121500 chr3B 92.169 2337 120 24 1057 3362 124492708 124490404 0.000000e+00 3243
11 TraesCS3D01G121500 chr3B 92.038 1595 90 19 1057 2632 124356751 124355175 0.000000e+00 2207
12 TraesCS3D01G121500 chr3B 94.653 1066 52 5 1 1064 124552613 124551551 0.000000e+00 1648
13 TraesCS3D01G121500 chr3B 94.559 1066 53 5 1 1064 124493818 124492756 0.000000e+00 1642
14 TraesCS3D01G121500 chr3B 83.945 1744 244 21 1060 2777 124407946 124406213 0.000000e+00 1637
15 TraesCS3D01G121500 chr3B 92.978 1068 62 12 1 1059 124822903 124821840 0.000000e+00 1544
16 TraesCS3D01G121500 chr3B 94.369 888 44 6 179 1064 124357670 124356787 0.000000e+00 1358
17 TraesCS3D01G121500 chr3B 91.254 949 60 10 1057 1989 124821799 124820858 0.000000e+00 1271
18 TraesCS3D01G121500 chr3B 90.710 915 78 5 2042 2955 124820863 124819955 0.000000e+00 1212
19 TraesCS3D01G121500 chr3B 87.560 418 21 15 2953 3363 124817410 124817017 3.960000e-124 455
20 TraesCS3D01G121500 chr3B 92.963 270 16 1 3094 3363 124355172 124354906 1.130000e-104 390
21 TraesCS3D01G121500 chr3B 83.390 295 36 9 2825 3112 124578214 124577926 9.260000e-66 261
22 TraesCS3D01G121500 chr3B 92.899 169 11 1 795 962 124580715 124580547 9.320000e-61 244
23 TraesCS3D01G121500 chr3B 83.230 161 18 5 3212 3363 124405739 124405579 4.520000e-29 139
24 TraesCS3D01G121500 chr3A 95.720 1986 64 10 1057 3029 92540167 92538190 0.000000e+00 3177
25 TraesCS3D01G121500 chr3A 95.466 1985 68 10 1057 3029 92569292 92567318 0.000000e+00 3147
26 TraesCS3D01G121500 chr3A 95.216 1066 49 2 1 1064 92541268 92540203 0.000000e+00 1685
27 TraesCS3D01G121500 chr3A 95.794 214 9 0 851 1064 92569541 92569328 2.480000e-91 346
28 TraesCS3D01G121500 chr3A 98.561 139 2 0 3225 3363 92538120 92537982 2.590000e-61 246
29 TraesCS3D01G121500 chr3A 97.842 139 2 1 3225 3363 92567248 92567111 4.340000e-59 239
30 TraesCS3D01G121500 chr1D 76.662 677 117 25 3 643 17263876 17264547 1.490000e-88 337
31 TraesCS3D01G121500 chrUn 77.869 488 89 14 149 619 307553859 307554344 5.490000e-73 285


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 TraesCS3D01G121500 chr3D 78942960 78946322 3362 True 6211.000000 6211 100.000000 1 3363 1 chr3D.!!$R1 3362
1 TraesCS3D01G121500 chr3D 79244567 79247978 3411 True 2548.000000 3432 94.197500 1 3363 2 chr3D.!!$R3 3362
2 TraesCS3D01G121500 chr3D 79295670 79301135 5465 True 960.000000 2523 95.521600 1 3363 5 chr3D.!!$R4 3362
3 TraesCS3D01G121500 chr3B 124549194 124552613 3419 True 2465.000000 3282 93.541000 1 3363 2 chr3B.!!$R4 3362
4 TraesCS3D01G121500 chr3B 124490404 124493818 3414 True 2442.500000 3243 93.364000 1 3362 2 chr3B.!!$R3 3361
5 TraesCS3D01G121500 chr3B 124354906 124357670 2764 True 1318.333333 2207 93.123333 179 3363 3 chr3B.!!$R1 3184
6 TraesCS3D01G121500 chr3B 124817017 124822903 5886 True 1120.500000 1544 90.625500 1 3363 4 chr3B.!!$R6 3362
7 TraesCS3D01G121500 chr3B 124405579 124407946 2367 True 888.000000 1637 83.587500 1060 3363 2 chr3B.!!$R2 2303
8 TraesCS3D01G121500 chr3B 124577926 124580715 2789 True 252.500000 261 88.144500 795 3112 2 chr3B.!!$R5 2317
9 TraesCS3D01G121500 chr3A 92537982 92541268 3286 True 1702.666667 3177 96.499000 1 3363 3 chr3A.!!$R1 3362
10 TraesCS3D01G121500 chr3A 92567111 92569541 2430 True 1244.000000 3147 96.367333 851 3363 3 chr3A.!!$R2 2512
11 TraesCS3D01G121500 chr1D 17263876 17264547 671 False 337.000000 337 76.662000 3 643 1 chr1D.!!$F1 640

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
574 616 2.297698 TCTAAGGAGGACGACAACCA 57.702 50.000 0.0 0.0 0.0 3.67 F
1175 1618 4.543689 ACTTGATTACATCCCGGTCTAGA 58.456 43.478 0.0 0.0 0.0 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1487 1947 0.178998 GGCCATGCATCTCATCACCT 60.179 55.0 0.0 0.0 31.79 4.00 R
2867 5767 0.531532 GATCCGGGCATGACTCTGTG 60.532 60.0 0.0 0.0 0.00 3.66 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
431 466 2.894763 TGCTTGCATTAATCATGGGC 57.105 45.000 0.00 0.00 32.81 5.36
501 540 5.007136 GTCATAGCTACTTTGGTGAATGAGC 59.993 44.000 0.00 0.00 0.00 4.26
574 616 2.297698 TCTAAGGAGGACGACAACCA 57.702 50.000 0.00 0.00 0.00 3.67
1175 1618 4.543689 ACTTGATTACATCCCGGTCTAGA 58.456 43.478 0.00 0.00 0.00 2.43
1187 1630 4.960469 TCCCGGTCTAGAAAACTCATACAT 59.040 41.667 0.00 0.00 0.00 2.29
1364 1821 9.877178 ACCTTTAAGTCTACACATGAGAATAAG 57.123 33.333 0.00 0.00 0.00 1.73
1487 1947 1.272490 CACCTACTCCAGCACGAGAAA 59.728 52.381 7.03 0.00 33.83 2.52
1611 2077 4.223700 AGACCAATAGTGTGCAGAGAATGA 59.776 41.667 0.00 0.00 0.00 2.57
1621 2087 2.290450 TGCAGAGAATGATGACAAGGCA 60.290 45.455 0.00 0.00 0.00 4.75
1670 2136 4.734398 ACAAATCCAACAACTTGAAGCA 57.266 36.364 0.00 0.00 0.00 3.91
2056 2553 5.066375 TGAACATGGTAGCATGCATACTTTC 59.934 40.000 29.91 23.73 36.08 2.62
2071 2569 8.276252 TGCATACTTTCCTAACCACTAAAATC 57.724 34.615 0.00 0.00 0.00 2.17
2072 2570 7.065324 TGCATACTTTCCTAACCACTAAAATCG 59.935 37.037 0.00 0.00 0.00 3.34
2080 2578 1.591158 ACCACTAAAATCGCGCATACG 59.409 47.619 8.75 0.00 44.07 3.06
2140 2638 3.848975 ACACCAAGAATCTTCAGGGAGAT 59.151 43.478 5.04 0.00 37.99 2.75
2146 2644 6.418101 CAAGAATCTTCAGGGAGATAACCAA 58.582 40.000 0.00 0.00 35.37 3.67
2156 2654 6.377146 TCAGGGAGATAACCAAATGCTAAAAC 59.623 38.462 0.00 0.00 0.00 2.43
2317 2817 2.210961 GCCACCGCCTATCTTAAAGAC 58.789 52.381 0.00 0.00 0.00 3.01
2356 2856 0.178987 TGTGGCACCAATTTACCCGT 60.179 50.000 16.26 0.00 0.00 5.28
2493 3001 8.624776 GCTGCTGGTTTATTTCTTTATGTAGAT 58.375 33.333 0.00 0.00 0.00 1.98
2581 3089 1.304713 AGTGGCTTTGGGATGGCAG 60.305 57.895 0.00 0.00 39.38 4.85
2622 3131 2.573915 ACTCATGTCTTTCTCCCTTCCC 59.426 50.000 0.00 0.00 0.00 3.97
2637 3146 3.499563 CCCTTCCCATTTGTACCTGAACA 60.500 47.826 0.00 0.00 0.00 3.18
2673 5481 6.922957 TGGTCAAATGAATAGACAAGCAAAAC 59.077 34.615 0.00 0.00 34.04 2.43
2679 5488 7.951530 ATGAATAGACAAGCAAAACCAAAAG 57.048 32.000 0.00 0.00 0.00 2.27
2712 5522 1.431496 ATGCCGCACAAGAATTTTGC 58.569 45.000 0.00 0.00 0.00 3.68
2732 5542 5.431420 TGCGTGTCTTGTAACATTTGATT 57.569 34.783 0.00 0.00 0.00 2.57
2787 5602 1.734465 GTTGATCCTTCTCGGCAACAG 59.266 52.381 0.00 0.00 36.40 3.16
2812 5627 6.505048 AAGTGGTATGAGATCATTGATCCA 57.495 37.500 20.49 17.73 39.66 3.41
2823 5714 2.842496 TCATTGATCCAGTTCTGGAGCT 59.158 45.455 28.93 14.60 44.15 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
431 466 6.055231 CAGCATGCAAATTTTATTCCATGG 57.945 37.500 21.98 4.97 32.79 3.66
462 499 8.157476 AGTAGCTATGACCATCCGAATTTAAAT 58.843 33.333 0.00 0.00 0.00 1.40
574 616 4.338400 GCTTAAGGAAATACCGATGGCTTT 59.662 41.667 4.29 0.00 44.74 3.51
652 694 6.823689 GGAGTATTCCTGCTCAACATTAGAAA 59.176 38.462 0.00 0.00 40.58 2.52
724 766 5.719563 TCTTTGTGTATCCACTCACTCCATA 59.280 40.000 0.00 0.00 42.34 2.74
841 883 8.003044 AGCCATAAATAATAGCATCATAGGCAT 58.997 33.333 0.00 0.00 38.31 4.40
1166 1609 7.658261 TCATATGTATGAGTTTTCTAGACCGG 58.342 38.462 0.00 0.00 37.76 5.28
1261 1704 5.148651 AGTAGACTTTAGTTGCCAACGAT 57.851 39.130 1.20 0.00 36.23 3.73
1487 1947 0.178998 GGCCATGCATCTCATCACCT 60.179 55.000 0.00 0.00 31.79 4.00
1566 2026 3.938963 TCTCCATCGTTATTGTTGCCTTC 59.061 43.478 0.00 0.00 0.00 3.46
1611 2077 6.282930 GGTTATAATTTGCATGCCTTGTCAT 58.717 36.000 16.68 4.24 0.00 3.06
1740 2207 6.346096 GCTTTCCTGGAACACACTACATATA 58.654 40.000 9.04 0.00 0.00 0.86
1822 2289 2.167487 GGAACCAAAACTTGACCTGCAA 59.833 45.455 0.00 0.00 34.73 4.08
2056 2553 2.004017 TGCGCGATTTTAGTGGTTAGG 58.996 47.619 12.10 0.00 0.00 2.69
2071 2569 6.661828 GCATTTATTAATTTCACGTATGCGCG 60.662 38.462 0.00 0.00 42.83 6.86
2072 2570 6.141527 TGCATTTATTAATTTCACGTATGCGC 59.858 34.615 0.00 0.00 42.83 6.09
2080 2578 7.041107 TCTTGCCCTGCATTTATTAATTTCAC 58.959 34.615 0.00 0.00 38.76 3.18
2140 2638 7.987458 TGGTTTTCATGTTTTAGCATTTGGTTA 59.013 29.630 0.00 0.00 0.00 2.85
2146 2644 5.469760 GGCTTGGTTTTCATGTTTTAGCATT 59.530 36.000 0.00 0.00 0.00 3.56
2156 2654 3.991773 CACTTGATGGCTTGGTTTTCATG 59.008 43.478 0.00 0.00 0.00 3.07
2343 2843 3.244630 TGCTTAGTCACGGGTAAATTGGT 60.245 43.478 0.00 0.00 0.00 3.67
2356 2856 1.613925 AGAAGACGCTGTGCTTAGTCA 59.386 47.619 0.00 0.00 36.18 3.41
2493 3001 4.308526 TCCCATATAGCAACCACAACAA 57.691 40.909 0.00 0.00 0.00 2.83
2581 3089 2.109126 GGACCGAGCTTCATGGCAC 61.109 63.158 0.00 0.00 34.17 5.01
2622 3131 4.516698 ACTTGAGCTGTTCAGGTACAAATG 59.483 41.667 7.47 4.23 43.56 2.32
2637 3146 4.623932 TCATTTGACCACTACTTGAGCT 57.376 40.909 0.00 0.00 0.00 4.09
2673 5481 4.919754 GCATTCAACTAGCAGAACTTTTGG 59.080 41.667 0.06 0.00 0.00 3.28
2679 5488 1.202076 GCGGCATTCAACTAGCAGAAC 60.202 52.381 0.00 0.00 0.00 3.01
2712 5522 6.140580 CACACAATCAAATGTTACAAGACACG 59.859 38.462 0.00 0.00 31.30 4.49
2732 5542 3.796764 TGAATGGCACACTCACACA 57.203 47.368 0.00 0.00 40.69 3.72
2787 5602 6.994496 TGGATCAATGATCTCATACCACTTTC 59.006 38.462 21.04 2.44 38.91 2.62
2812 5627 1.339291 GCAAGCAAAAGCTCCAGAACT 59.661 47.619 0.00 0.00 0.00 3.01
2823 5714 1.117994 TGTGTGGATGGCAAGCAAAA 58.882 45.000 0.00 0.00 0.00 2.44
2837 5728 0.930310 CCGAGAAGTGTGTGTGTGTG 59.070 55.000 0.00 0.00 0.00 3.82
2867 5767 0.531532 GATCCGGGCATGACTCTGTG 60.532 60.000 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.