Multiple sequence alignment - TraesCS5B01G197200

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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 TraesCS5B01G197200 chr5B 100.000 3089 0 0 1 3089 355233800 355236888 0.000000e+00 5705.0
1 TraesCS5B01G197200 chr5D 93.556 3088 123 31 1 3053 309693580 309696626 0.000000e+00 4530.0
2 TraesCS5B01G197200 chr5A 90.316 2375 108 45 759 3089 403028158 403030454 0.000000e+00 3000.0
3 TraesCS5B01G197200 chr5A 83.805 778 48 35 1 734 403027417 403028160 0.000000e+00 667.0
4 TraesCS5B01G197200 chr7A 79.585 289 36 14 1263 1550 83636049 83635783 5.260000e-43 185.0
5 TraesCS5B01G197200 chr7A 84.416 77 9 3 1905 1978 83635422 83635346 4.270000e-09 73.1
6 TraesCS5B01G197200 chr7D 79.381 291 37 14 1263 1546 80979980 80979706 1.890000e-42 183.0
7 TraesCS5B01G197200 chr7D 85.714 77 8 3 1905 1978 80979335 80979259 9.180000e-11 78.7
8 TraesCS5B01G197200 chr7D 85.526 76 10 1 2289 2364 149082870 149082796 9.180000e-11 78.7
9 TraesCS5B01G197200 chr2A 85.185 81 9 3 2255 2333 674506782 674506703 2.550000e-11 80.5
10 TraesCS5B01G197200 chr7B 84.416 77 9 3 1905 1978 28505762 28505686 4.270000e-09 73.1
11 TraesCS5B01G197200 chr7B 96.875 32 1 0 2390 2421 298747914 298747883 2.000000e-03 54.7
12 TraesCS5B01G197200 chr6D 100.000 28 0 0 2291 2318 259232286 259232313 6.000000e-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 TraesCS5B01G197200 chr5B 355233800 355236888 3088 False 5705.0 5705 100.0000 1 3089 1 chr5B.!!$F1 3088
1 TraesCS5B01G197200 chr5D 309693580 309696626 3046 False 4530.0 4530 93.5560 1 3053 1 chr5D.!!$F1 3052
2 TraesCS5B01G197200 chr5A 403027417 403030454 3037 False 1833.5 3000 87.0605 1 3089 2 chr5A.!!$F1 3088

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
79 84 0.456221 CACGGGAGAAGCATACGTCT 59.544 55.0 0.0 0.0 37.34 4.18 F
1432 1501 0.109272 CGTCTGCCTCAGCGAGTTTA 60.109 55.0 0.0 0.0 44.31 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1637 1706 1.006102 ACGACCTCCTTTGACGCTG 60.006 57.895 0.0 0.0 0.00 5.18 R
2786 2886 0.325296 ACGGCCCAGATCCTGAGTTA 60.325 55.000 0.0 0.0 32.44 2.24 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
59 60 2.164338 GAACAGTCTCTCCGGAGTTCT 58.836 52.381 30.17 21.83 40.29 3.01
67 68 2.885861 CCGGAGTTCTCACGGGAG 59.114 66.667 8.88 8.88 43.69 4.30
79 84 0.456221 CACGGGAGAAGCATACGTCT 59.544 55.000 0.00 0.00 37.34 4.18
81 86 1.549170 ACGGGAGAAGCATACGTCTTT 59.451 47.619 0.00 0.00 34.53 2.52
108 113 2.444895 TTGGTTGGTTGGCACCCC 60.445 61.111 0.00 0.00 43.49 4.95
141 153 4.988598 AACACTGCCGCGGTCCAG 62.989 66.667 28.70 26.81 35.26 3.86
158 182 2.043939 TCCAGGTCCATGTACAGGTAGT 59.956 50.000 6.79 0.00 0.00 2.73
162 186 5.141182 CAGGTCCATGTACAGGTAGTAGAT 58.859 45.833 6.79 0.00 37.18 1.98
237 261 1.009449 GCTACGATCGAGCTCGCTT 60.009 57.895 30.97 20.26 42.35 4.68
240 264 2.663630 TACGATCGAGCTCGCTTGCC 62.664 60.000 30.97 15.37 42.35 4.52
241 265 2.105930 GATCGAGCTCGCTTGCCT 59.894 61.111 30.97 10.64 39.60 4.75
242 266 1.948635 GATCGAGCTCGCTTGCCTC 60.949 63.158 30.97 15.17 39.60 4.70
243 267 3.764810 ATCGAGCTCGCTTGCCTCG 62.765 63.158 30.97 5.49 39.60 4.63
755 817 2.433664 CCCTGCCCAACGTACGTC 60.434 66.667 23.05 9.71 0.00 4.34
806 872 1.590147 CGTAGCTTCCCGGTTGACT 59.410 57.895 0.00 0.00 0.00 3.41
913 979 2.091541 GAGAGAGCTATCTGGGATCGG 58.908 57.143 17.19 0.00 35.30 4.18
917 983 1.080434 GCTATCTGGGATCGGTCGC 60.080 63.158 5.66 5.66 37.78 5.19
919 985 1.152631 TATCTGGGATCGGTCGCCA 60.153 57.895 10.57 7.93 36.53 5.69
1074 1140 1.284982 CCGGCGATGATGGATTCGTC 61.285 60.000 9.30 0.00 37.66 4.20
1431 1500 1.373497 CGTCTGCCTCAGCGAGTTT 60.373 57.895 0.00 0.00 44.31 2.66
1432 1501 0.109272 CGTCTGCCTCAGCGAGTTTA 60.109 55.000 0.00 0.00 44.31 2.01
1433 1502 1.634702 GTCTGCCTCAGCGAGTTTAG 58.365 55.000 0.00 1.66 44.31 1.85
1435 1504 1.079127 TGCCTCAGCGAGTTTAGCC 60.079 57.895 0.00 0.00 44.31 3.93
1521 1590 4.504916 CTCCGCTCCAGCTCCACG 62.505 72.222 0.00 0.00 39.32 4.94
1632 1701 0.326427 AGAAGCAGGAGCAGGAGGAT 60.326 55.000 0.00 0.00 45.49 3.24
1633 1702 0.179051 GAAGCAGGAGCAGGAGGATG 60.179 60.000 0.00 0.00 45.49 3.51
1634 1703 2.203181 GCAGGAGCAGGAGGATGC 60.203 66.667 0.00 0.00 46.88 3.91
1659 1728 0.318445 CGTCAAAGGAGGTCGTCGTT 60.318 55.000 0.00 0.00 34.66 3.85
1667 1736 1.891060 GAGGTCGTCGTTGCAAGCAG 61.891 60.000 0.00 0.00 0.00 4.24
1812 1881 1.654954 CCTACCAGTACGTGCTCGCT 61.655 60.000 2.06 0.00 41.18 4.93
2276 2350 1.755179 CTCGGAAGTGGATGGCAAAT 58.245 50.000 0.00 0.00 0.00 2.32
2311 2385 1.259507 TGACAGTTTTAGTTGCGACGC 59.740 47.619 14.19 14.19 0.00 5.19
2334 2408 3.139077 AGATCAAACGGTGACAGTTTCC 58.861 45.455 10.80 4.31 39.72 3.13
2349 2423 2.357952 AGTTTCCGTCTGTTTTTGCCTC 59.642 45.455 0.00 0.00 0.00 4.70
2383 2457 6.544928 TCTTCTCAGAAGTTACCATGCATA 57.455 37.500 14.32 0.00 0.00 3.14
2384 2458 7.129457 TCTTCTCAGAAGTTACCATGCATAT 57.871 36.000 14.32 0.00 0.00 1.78
2385 2459 8.250143 TCTTCTCAGAAGTTACCATGCATATA 57.750 34.615 14.32 0.00 0.00 0.86
2386 2460 8.704668 TCTTCTCAGAAGTTACCATGCATATAA 58.295 33.333 14.32 0.00 0.00 0.98
2388 2462 8.023021 TCTCAGAAGTTACCATGCATATAAGT 57.977 34.615 0.00 1.60 0.00 2.24
2413 2496 0.383949 ATGCCAGCAAAAACGTTCGT 59.616 45.000 0.00 0.00 0.00 3.85
2425 2508 2.385013 ACGTTCGTAAATACCACCCC 57.615 50.000 0.00 0.00 0.00 4.95
2446 2529 1.853319 CAGTGAACGTTCGTCAGCC 59.147 57.895 22.48 6.77 0.00 4.85
2523 2606 9.528018 CAACATCATCATCATCATCATCAAAAA 57.472 29.630 0.00 0.00 0.00 1.94
2524 2607 9.529325 AACATCATCATCATCATCATCAAAAAC 57.471 29.630 0.00 0.00 0.00 2.43
2525 2608 7.860872 ACATCATCATCATCATCATCAAAAACG 59.139 33.333 0.00 0.00 0.00 3.60
2526 2609 6.203647 TCATCATCATCATCATCAAAAACGC 58.796 36.000 0.00 0.00 0.00 4.84
2527 2610 4.923893 TCATCATCATCATCAAAAACGCC 58.076 39.130 0.00 0.00 0.00 5.68
2528 2611 3.403613 TCATCATCATCAAAAACGCCG 57.596 42.857 0.00 0.00 0.00 6.46
2529 2612 2.746904 TCATCATCATCAAAAACGCCGT 59.253 40.909 0.00 0.00 0.00 5.68
2530 2613 3.190327 TCATCATCATCAAAAACGCCGTT 59.810 39.130 0.00 0.00 0.00 4.44
2531 2614 3.634568 TCATCATCAAAAACGCCGTTT 57.365 38.095 9.83 9.83 37.34 3.60
2532 2615 3.304257 TCATCATCAAAAACGCCGTTTG 58.696 40.909 16.86 5.61 35.80 2.93
2533 2616 3.003793 TCATCATCAAAAACGCCGTTTGA 59.996 39.130 16.86 11.38 46.12 2.69
2534 2617 3.422417 TCATCAAAAACGCCGTTTGAA 57.578 38.095 16.86 5.24 45.43 2.69
2535 2618 3.770666 TCATCAAAAACGCCGTTTGAAA 58.229 36.364 16.86 4.88 45.43 2.69
2536 2619 4.363999 TCATCAAAAACGCCGTTTGAAAT 58.636 34.783 16.86 7.03 45.43 2.17
2537 2620 4.442733 TCATCAAAAACGCCGTTTGAAATC 59.557 37.500 16.86 0.00 45.43 2.17
2538 2621 2.784380 TCAAAAACGCCGTTTGAAATCG 59.216 40.909 16.86 1.93 40.96 3.34
2539 2622 1.125270 AAAACGCCGTTTGAAATCGC 58.875 45.000 16.86 0.00 35.80 4.58
2540 2623 0.029567 AAACGCCGTTTGAAATCGCA 59.970 45.000 15.33 0.00 34.23 5.10
2541 2624 0.385473 AACGCCGTTTGAAATCGCAG 60.385 50.000 0.00 0.00 0.00 5.18
2566 2651 6.686630 CATATGGCTACTCATATAGCTAGCC 58.313 44.000 12.13 12.12 45.81 3.93
2603 2688 4.716784 TGTACTGCTCCACTGGAATATTCT 59.283 41.667 14.95 0.00 0.00 2.40
2706 2796 1.000163 CCGAATCTGAGGTCCCATACG 60.000 57.143 0.00 0.00 0.00 3.06
2773 2870 1.069823 CTCACTCACCTGTGCTCTTGT 59.930 52.381 0.00 0.00 37.81 3.16
2786 2886 4.202419 TGTGCTCTTGTAGTACCACCATTT 60.202 41.667 0.00 0.00 39.88 2.32
2854 2954 0.329931 TTGGCTTCTGGCGGGATTAA 59.670 50.000 0.00 0.00 42.94 1.40
2861 2961 2.696775 TCTGGCGGGATTAATTAGGGA 58.303 47.619 0.00 0.00 0.00 4.20
2921 3021 1.134098 ACCCATCTACCGCCATTCTTG 60.134 52.381 0.00 0.00 0.00 3.02
2922 3022 1.134098 CCCATCTACCGCCATTCTTGT 60.134 52.381 0.00 0.00 0.00 3.16
3014 3120 5.123979 CACAGTATAGTACAGTCTGCAGTGA 59.876 44.000 14.67 0.00 0.00 3.41
3069 3179 1.503542 GAGCGTTGTTGGGCATGAG 59.496 57.895 0.00 0.00 0.00 2.90
3070 3180 0.955428 GAGCGTTGTTGGGCATGAGA 60.955 55.000 0.00 0.00 0.00 3.27
3071 3181 0.322816 AGCGTTGTTGGGCATGAGAT 60.323 50.000 0.00 0.00 0.00 2.75
3072 3182 0.179156 GCGTTGTTGGGCATGAGATG 60.179 55.000 0.00 0.00 0.00 2.90
3073 3183 1.452110 CGTTGTTGGGCATGAGATGA 58.548 50.000 0.00 0.00 0.00 2.92
3074 3184 2.019249 CGTTGTTGGGCATGAGATGAT 58.981 47.619 0.00 0.00 0.00 2.45
3075 3185 2.032550 CGTTGTTGGGCATGAGATGATC 59.967 50.000 0.00 0.00 0.00 2.92
3076 3186 1.957668 TGTTGGGCATGAGATGATCG 58.042 50.000 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 2.297597 CTCCGGAGAGACTGTTCAAACT 59.702 50.000 28.21 0.00 43.39 2.66
59 60 0.454600 GACGTATGCTTCTCCCGTGA 59.545 55.000 0.00 0.00 0.00 4.35
67 68 2.096013 GCCAAGGAAAGACGTATGCTTC 59.904 50.000 0.00 0.00 0.00 3.86
79 84 1.118838 CCAACCAACTGCCAAGGAAA 58.881 50.000 0.00 0.00 0.00 3.13
81 86 0.032615 AACCAACCAACTGCCAAGGA 60.033 50.000 0.00 0.00 0.00 3.36
108 113 3.074412 AGTGTTTTCTGCAGGATTACGG 58.926 45.455 15.13 0.00 0.00 4.02
141 153 5.138276 TCATCTACTACCTGTACATGGACC 58.862 45.833 5.38 0.00 31.29 4.46
158 182 1.119684 CACGGGTGGACCATCATCTA 58.880 55.000 7.16 0.00 40.22 1.98
162 186 4.028490 GGCACGGGTGGACCATCA 62.028 66.667 7.16 0.00 40.22 3.07
326 361 4.525949 GCGAGCCGGGGTACTTCC 62.526 72.222 2.18 0.00 0.00 3.46
454 497 0.817654 ACGTTGGATCGATCAGCTCA 59.182 50.000 25.93 12.33 34.70 4.26
481 531 2.617274 GCACCACGTGAAGCTTCCC 61.617 63.158 23.42 11.63 35.23 3.97
482 532 2.617274 GGCACCACGTGAAGCTTCC 61.617 63.158 23.42 13.49 35.23 3.46
550 604 1.252904 TTAGCGGGGCGTTGTCTAGT 61.253 55.000 0.00 0.00 0.00 2.57
551 605 0.804933 GTTAGCGGGGCGTTGTCTAG 60.805 60.000 0.00 0.00 0.00 2.43
577 631 3.524606 GGGTCGCCGTGCTAGCTA 61.525 66.667 17.23 0.00 0.00 3.32
750 812 2.799488 TTCCGCGATGCAACGACGTA 62.799 55.000 21.39 7.42 33.69 3.57
751 813 4.710695 TCCGCGATGCAACGACGT 62.711 61.111 21.39 0.00 33.69 4.34
752 814 2.487443 TTTTCCGCGATGCAACGACG 62.487 55.000 21.39 20.59 35.09 5.12
753 815 0.384974 TTTTTCCGCGATGCAACGAC 60.385 50.000 21.39 10.35 35.09 4.34
755 817 1.065031 CCTTTTTCCGCGATGCAACG 61.065 55.000 12.54 12.54 0.00 4.10
806 872 3.502123 AACAAAAGATCCCTCGGTGAA 57.498 42.857 0.00 0.00 0.00 3.18
892 958 2.290896 CCGATCCCAGATAGCTCTCTCT 60.291 54.545 0.00 0.00 0.00 3.10
893 959 2.091541 CCGATCCCAGATAGCTCTCTC 58.908 57.143 0.00 0.00 0.00 3.20
913 979 4.641094 AGCTATATATCCACTACTGGCGAC 59.359 45.833 0.00 0.00 37.49 5.19
917 983 4.100189 GCCCAGCTATATATCCACTACTGG 59.900 50.000 0.00 0.00 42.47 4.00
919 985 3.954904 CGCCCAGCTATATATCCACTACT 59.045 47.826 0.00 0.00 0.00 2.57
1345 1414 2.094539 CTCGACGTACGCGAACGA 59.905 61.111 26.18 22.90 45.68 3.85
1609 1678 1.745864 CCTGCTCCTGCTTCTGCTG 60.746 63.158 0.00 0.00 40.48 4.41
1632 1701 1.664649 CTCCTTTGACGCTGACGCA 60.665 57.895 0.00 0.00 45.53 5.24
1633 1702 2.383527 CCTCCTTTGACGCTGACGC 61.384 63.158 0.00 0.00 45.53 5.19
1635 1704 1.009389 CGACCTCCTTTGACGCTGAC 61.009 60.000 0.00 0.00 0.00 3.51
1636 1705 1.289066 CGACCTCCTTTGACGCTGA 59.711 57.895 0.00 0.00 0.00 4.26
1637 1706 1.006102 ACGACCTCCTTTGACGCTG 60.006 57.895 0.00 0.00 0.00 5.18
1638 1707 1.289380 GACGACCTCCTTTGACGCT 59.711 57.895 0.00 0.00 0.00 5.07
1892 1961 2.401699 CTTGCCCTGCTGGTCACTGA 62.402 60.000 9.00 0.00 36.04 3.41
2058 2127 3.807631 TTCTTGCCTCGTGCTGCGT 62.808 57.895 0.00 0.00 42.00 5.24
2311 2385 2.065993 ACTGTCACCGTTTGATCTCG 57.934 50.000 0.00 0.00 36.32 4.04
2334 2408 5.717038 AAAATTTGAGGCAAAAACAGACG 57.283 34.783 0.00 0.00 36.90 4.18
2338 2412 7.920160 AGAAGAAAAATTTGAGGCAAAAACA 57.080 28.000 0.00 0.00 36.90 2.83
2383 2457 6.586082 CGTTTTTGCTGGCATTTTCTACTTAT 59.414 34.615 0.00 0.00 0.00 1.73
2384 2458 5.918011 CGTTTTTGCTGGCATTTTCTACTTA 59.082 36.000 0.00 0.00 0.00 2.24
2385 2459 4.744631 CGTTTTTGCTGGCATTTTCTACTT 59.255 37.500 0.00 0.00 0.00 2.24
2386 2460 4.202111 ACGTTTTTGCTGGCATTTTCTACT 60.202 37.500 0.00 0.00 0.00 2.57
2388 2462 4.314740 ACGTTTTTGCTGGCATTTTCTA 57.685 36.364 0.00 0.00 0.00 2.10
2413 2496 2.270858 TCACTGCAGGGGTGGTATTTA 58.729 47.619 17.80 0.00 35.61 1.40
2425 2508 0.504384 CTGACGAACGTTCACTGCAG 59.496 55.000 26.71 20.94 0.00 4.41
2523 2606 1.206578 CTGCGATTTCAAACGGCGT 59.793 52.632 6.77 6.77 0.00 5.68
2524 2607 2.145905 GCTGCGATTTCAAACGGCG 61.146 57.895 4.80 4.80 0.00 6.46
2525 2608 0.456653 ATGCTGCGATTTCAAACGGC 60.457 50.000 0.00 0.00 0.00 5.68
2526 2609 2.823196 TATGCTGCGATTTCAAACGG 57.177 45.000 0.00 0.00 0.00 4.44
2527 2610 3.038017 CCATATGCTGCGATTTCAAACG 58.962 45.455 0.00 0.00 0.00 3.60
2528 2611 2.791004 GCCATATGCTGCGATTTCAAAC 59.209 45.455 0.00 0.00 36.87 2.93
2529 2612 3.082698 GCCATATGCTGCGATTTCAAA 57.917 42.857 0.00 0.00 36.87 2.69
2530 2613 2.780065 GCCATATGCTGCGATTTCAA 57.220 45.000 0.00 0.00 36.87 2.69
2541 2624 6.155827 GCTAGCTATATGAGTAGCCATATGC 58.844 44.000 7.70 0.00 46.48 3.14
2566 2651 5.314923 AGCAGTACAAAATGTAGCAATGG 57.685 39.130 0.00 0.00 32.84 3.16
2603 2688 2.575735 TCCAGGCAGATGATAAACACCA 59.424 45.455 0.00 0.00 0.00 4.17
2688 2778 1.412710 TGCGTATGGGACCTCAGATTC 59.587 52.381 0.00 0.00 0.00 2.52
2773 2870 6.901300 AGATCCTGAGTTAAATGGTGGTACTA 59.099 38.462 0.00 0.00 0.00 1.82
2786 2886 0.325296 ACGGCCCAGATCCTGAGTTA 60.325 55.000 0.00 0.00 32.44 2.24
2854 2954 4.660168 CATCAGCCATTAAGCTCCCTAAT 58.340 43.478 0.00 0.00 42.61 1.73
2861 2961 1.019673 CACGCATCAGCCATTAAGCT 58.980 50.000 0.00 0.00 46.45 3.74
2922 3022 4.343323 TTGCCCTTGCTGCGGCTA 62.343 61.111 20.27 10.73 45.90 3.93
2938 3038 2.980233 GTCTGCGGTTGCTGGCTT 60.980 61.111 0.00 0.00 41.00 4.35
3014 3120 1.115326 TGATCCCAGTGCCGATCGAT 61.115 55.000 18.66 0.00 38.17 3.59
3059 3169 0.839277 ACCGATCATCTCATGCCCAA 59.161 50.000 0.00 0.00 0.00 4.12


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

AutoCloner maintained by Alex Coulton.