Multiple sequence alignment - TraesCS5D01G200900

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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 TraesCS5D01G200900 chr5D 100.000 2855 0 0 1 2855 304164495 304161641 0.000000e+00 5273
1 TraesCS5D01G200900 chr5B 94.962 2620 97 21 1 2592 348572728 348570116 0.000000e+00 4074
2 TraesCS5D01G200900 chr5B 93.522 247 5 4 2620 2855 348570119 348569873 9.730000e-95 357
3 TraesCS5D01G200900 chr5A 95.263 1752 62 14 1117 2855 393917776 393919519 0.000000e+00 2756
4 TraesCS5D01G200900 chr5A 95.455 902 32 3 1 902 393916582 393917474 0.000000e+00 1430
5 TraesCS5D01G200900 chr7B 81.121 339 42 14 1252 1576 99089435 99089105 4.720000e-63 252
6 TraesCS5D01G200900 chr7D 82.474 291 42 7 1300 1581 582458630 582458920 2.200000e-61 246
7 TraesCS5D01G200900 chr7D 82.927 287 31 12 1305 1576 136204698 136204415 2.840000e-60 243
8 TraesCS5D01G200900 chr7A 84.074 270 27 10 1318 1573 135689647 135689380 2.200000e-61 246
9 TraesCS5D01G200900 chr4D 85.437 206 27 3 1295 1497 438153326 438153531 8.010000e-51 211
10 TraesCS5D01G200900 chr4A 83.262 233 33 5 1268 1497 27589576 27589805 2.880000e-50 209
11 TraesCS5D01G200900 chr4B 82.479 234 33 7 1268 1497 541910774 541911003 6.240000e-47 198


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 TraesCS5D01G200900 chr5D 304161641 304164495 2854 True 5273.0 5273 100.000 1 2855 1 chr5D.!!$R1 2854
1 TraesCS5D01G200900 chr5B 348569873 348572728 2855 True 2215.5 4074 94.242 1 2855 2 chr5B.!!$R1 2854
2 TraesCS5D01G200900 chr5A 393916582 393919519 2937 False 2093.0 2756 95.359 1 2855 2 chr5A.!!$F1 2854

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
134 135 0.471617 AGCAGCAGACACCAGAAAGT 59.528 50.000 0.0 0.0 0.0 2.66 F
717 720 1.787155 CTGTTCGTCTCCTTGTTCACG 59.213 52.381 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1008 1019 0.811915 CCCCGGACAGATCTATAGCG 59.188 60.000 0.73 0.0 0.0 4.26 R
2032 2128 1.065926 CGGACTAACCAAACCCTACCC 60.066 57.143 0.00 0.0 38.9 3.69 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
134 135 0.471617 AGCAGCAGACACCAGAAAGT 59.528 50.000 0.00 0.00 0.00 2.66
185 186 3.692406 GCGACACCCGGTTCCTCT 61.692 66.667 0.00 0.00 39.04 3.69
441 442 4.040584 GGAGAGGATAAACTATGGGTCACC 59.959 50.000 0.00 0.00 37.24 4.02
563 564 2.034687 CCTTCCACCAGCCACCAG 59.965 66.667 0.00 0.00 0.00 4.00
717 720 1.787155 CTGTTCGTCTCCTTGTTCACG 59.213 52.381 0.00 0.00 0.00 4.35
956 965 7.328005 GCAGATTTCTTTCTTGTTCATCTTTCC 59.672 37.037 0.00 0.00 0.00 3.13
1008 1019 2.224402 CCTAGTTCCTTAGATGGCTGCC 60.224 54.545 12.87 12.87 0.00 4.85
1095 1106 2.294078 CCCTCCACTCCACTCCCAC 61.294 68.421 0.00 0.00 0.00 4.61
1536 1632 1.153086 GCTCCATGCCTCCGTTGAT 60.153 57.895 0.00 0.00 35.15 2.57
1882 1978 4.148348 CAGTTTGTGTTCGTCAGCTACTAC 59.852 45.833 0.00 0.00 0.00 2.73
1901 1997 4.938226 ACTACTACTACCGTCTTTAGCGTT 59.062 41.667 0.00 0.00 0.00 4.84
2137 2233 3.358076 CTCCGGCCGGTGAAGTCTC 62.358 68.421 41.57 0.00 36.47 3.36
2224 2321 7.544622 AGTCTGTCATGTAAAATTAGCTCGTA 58.455 34.615 0.00 0.00 0.00 3.43
2290 2387 8.781067 TCGTTTTGTCTTGTAAATTCATGAAG 57.219 30.769 14.54 0.00 0.00 3.02
2292 2389 7.358352 CGTTTTGTCTTGTAAATTCATGAAGGC 60.358 37.037 14.54 0.00 0.00 4.35
2293 2390 6.647334 TTGTCTTGTAAATTCATGAAGGCA 57.353 33.333 14.54 2.83 0.00 4.75
2294 2391 6.839124 TGTCTTGTAAATTCATGAAGGCAT 57.161 33.333 14.54 2.67 34.29 4.40
2304 2405 3.799137 CATGAAGGCATGTTTTTGTGC 57.201 42.857 0.00 0.00 45.41 4.57
2311 2412 4.959723 AGGCATGTTTTTGTGCTGTAAAT 58.040 34.783 0.00 0.00 41.04 1.40
2358 2459 4.397420 TGGAACTAGTGGTAGTGAACGTA 58.603 43.478 0.00 0.00 39.60 3.57
2362 2463 6.149474 GGAACTAGTGGTAGTGAACGTAACTA 59.851 42.308 0.00 6.88 39.60 2.24
2363 2464 6.734104 ACTAGTGGTAGTGAACGTAACTAG 57.266 41.667 10.44 9.40 38.14 2.57
2364 2465 6.234177 ACTAGTGGTAGTGAACGTAACTAGT 58.766 40.000 10.44 6.74 41.21 2.57
2365 2466 5.368256 AGTGGTAGTGAACGTAACTAGTG 57.632 43.478 10.44 0.00 30.90 2.74
2366 2467 4.217118 AGTGGTAGTGAACGTAACTAGTGG 59.783 45.833 10.44 0.00 30.90 4.00
2368 2469 5.181245 GTGGTAGTGAACGTAACTAGTGGTA 59.819 44.000 10.44 0.00 30.90 3.25
2369 2470 5.412594 TGGTAGTGAACGTAACTAGTGGTAG 59.587 44.000 10.44 0.00 30.90 3.18
2392 2506 2.813754 ACATGCGCAGATACTGTGTTTT 59.186 40.909 18.32 0.00 43.09 2.43
2396 2510 2.726066 GCGCAGATACTGTGTTTTCAGC 60.726 50.000 0.30 0.00 43.09 4.26
2405 2519 3.636300 ACTGTGTTTTCAGCCTTGCAATA 59.364 39.130 0.00 0.00 38.84 1.90
2409 2523 4.860907 GTGTTTTCAGCCTTGCAATAGATG 59.139 41.667 0.00 3.89 0.00 2.90
2413 2527 3.282021 TCAGCCTTGCAATAGATGGTTC 58.718 45.455 13.09 0.00 0.00 3.62
2471 2588 1.607148 GCCTGGTGACCAAACTTGTAC 59.393 52.381 5.53 0.00 30.80 2.90
2564 2681 6.201044 GGTAGAAGAAGCAAAAAGGAAAAAGC 59.799 38.462 0.00 0.00 0.00 3.51
2570 2687 3.118775 AGCAAAAAGGAAAAAGCGGAACT 60.119 39.130 0.00 0.00 0.00 3.01
2588 2705 0.528924 CTCATCCACGTCGTGGGTTA 59.471 55.000 37.16 24.94 45.95 2.85
2589 2706 1.136305 CTCATCCACGTCGTGGGTTAT 59.864 52.381 37.16 24.01 45.95 1.89
2590 2707 1.551430 TCATCCACGTCGTGGGTTATT 59.449 47.619 37.16 18.30 45.95 1.40
2591 2708 2.759535 TCATCCACGTCGTGGGTTATTA 59.240 45.455 37.16 21.54 45.95 0.98
2592 2709 3.385433 TCATCCACGTCGTGGGTTATTAT 59.615 43.478 37.16 22.69 45.95 1.28
2593 2710 4.124238 CATCCACGTCGTGGGTTATTATT 58.876 43.478 37.16 14.06 45.95 1.40
2594 2711 4.210537 CATCCACGTCGTGGGTTATTATTC 59.789 45.833 37.16 0.00 45.95 1.75
2595 2712 4.741536 ATCCACGTCGTGGGTTATTATTCC 60.742 45.833 37.16 0.00 45.95 3.01
2596 2713 2.536803 CACGTCGTGGGTTATTATTCCG 59.463 50.000 17.75 0.00 0.00 4.30
2597 2714 2.426738 ACGTCGTGGGTTATTATTCCGA 59.573 45.455 0.00 0.00 0.00 4.55
2598 2715 3.068590 ACGTCGTGGGTTATTATTCCGAT 59.931 43.478 0.00 0.00 0.00 4.18
2599 2716 4.278170 ACGTCGTGGGTTATTATTCCGATA 59.722 41.667 0.00 0.00 0.00 2.92
2600 2717 4.618489 CGTCGTGGGTTATTATTCCGATAC 59.382 45.833 0.00 0.00 0.00 2.24
2601 2718 4.618489 GTCGTGGGTTATTATTCCGATACG 59.382 45.833 0.00 0.00 0.00 3.06
2602 2719 4.278170 TCGTGGGTTATTATTCCGATACGT 59.722 41.667 0.00 0.00 32.49 3.57
2603 2720 5.471797 TCGTGGGTTATTATTCCGATACGTA 59.528 40.000 0.00 0.00 32.49 3.57
2604 2721 6.150976 TCGTGGGTTATTATTCCGATACGTAT 59.849 38.462 8.05 8.05 32.49 3.06
2605 2722 6.808212 CGTGGGTTATTATTCCGATACGTATT 59.192 38.462 9.92 0.00 0.00 1.89
2606 2723 7.329226 CGTGGGTTATTATTCCGATACGTATTT 59.671 37.037 9.92 0.00 0.00 1.40
2607 2724 8.650714 GTGGGTTATTATTCCGATACGTATTTC 58.349 37.037 9.92 0.00 0.00 2.17
2608 2725 7.818930 TGGGTTATTATTCCGATACGTATTTCC 59.181 37.037 9.92 0.00 0.00 3.13
2609 2726 8.037166 GGGTTATTATTCCGATACGTATTTCCT 58.963 37.037 9.92 0.00 0.00 3.36
2614 2731 9.985730 ATTATTCCGATACGTATTTCCTAACAA 57.014 29.630 9.92 0.00 0.00 2.83
2615 2732 9.814899 TTATTCCGATACGTATTTCCTAACAAA 57.185 29.630 9.92 0.00 0.00 2.83
2616 2733 8.897872 ATTCCGATACGTATTTCCTAACAAAT 57.102 30.769 9.92 0.00 0.00 2.32
2617 2734 7.703298 TCCGATACGTATTTCCTAACAAATG 57.297 36.000 9.92 0.00 0.00 2.32
2618 2735 6.702723 TCCGATACGTATTTCCTAACAAATGG 59.297 38.462 9.92 0.00 0.00 3.16
2674 2825 3.491652 GGCAGGAAGCTTCGCGAC 61.492 66.667 19.91 11.82 44.79 5.19
2808 2960 2.008543 GCTGAACTGATGATGCGTCCA 61.009 52.381 2.83 0.00 0.00 4.02
2829 2987 1.131826 CCATCGTTTTCGTGGCGAC 59.868 57.895 0.00 0.00 44.46 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
134 135 3.706373 GCGAGGCCTTGGTGGAGA 61.706 66.667 22.06 0.00 38.35 3.71
222 223 4.459089 GAGCTCCGCCAGTGGGAC 62.459 72.222 12.15 0.00 35.59 4.46
563 564 1.826340 ATTGGGGCTTTTTCGGTGGC 61.826 55.000 0.00 0.00 0.00 5.01
566 567 0.902984 GGGATTGGGGCTTTTTCGGT 60.903 55.000 0.00 0.00 0.00 4.69
614 615 2.029828 CGGATCTATGCTTACCTCGCTT 60.030 50.000 0.00 0.00 0.00 4.68
732 735 3.197116 GGGATCTAAAACGTCCTGGAGAA 59.803 47.826 0.00 0.00 32.55 2.87
791 794 0.597637 CGCCTGGCCGATTACTACAG 60.598 60.000 14.12 0.00 0.00 2.74
985 996 3.134804 GCAGCCATCTAAGGAACTAGGAA 59.865 47.826 0.00 0.00 38.49 3.36
1008 1019 0.811915 CCCCGGACAGATCTATAGCG 59.188 60.000 0.73 0.00 0.00 4.26
1079 1090 0.838122 AAGGTGGGAGTGGAGTGGAG 60.838 60.000 0.00 0.00 0.00 3.86
1095 1106 1.338136 ATGGCGAGGTGGGACTAAGG 61.338 60.000 0.00 0.00 0.00 2.69
1482 1578 1.566018 CGTTGTCGGGGAAGTTGAGC 61.566 60.000 0.00 0.00 0.00 4.26
1536 1632 2.530151 AGGGTCTGGAGCTTGGCA 60.530 61.111 0.00 0.00 0.00 4.92
1583 1679 2.815647 CGGAGGCGGACTTCTTGC 60.816 66.667 0.00 0.00 0.00 4.01
1717 1813 4.320456 CTCTGCTGCGGTGGTGGT 62.320 66.667 8.55 0.00 0.00 4.16
1882 1978 4.726416 TGAAACGCTAAAGACGGTAGTAG 58.274 43.478 0.00 0.00 34.00 2.57
1901 1997 5.376625 GACCCATTAACCTAGCATCATGAA 58.623 41.667 0.00 0.00 0.00 2.57
2029 2125 2.372837 GACTAACCAAACCCTACCCACA 59.627 50.000 0.00 0.00 0.00 4.17
2030 2126 2.290514 GGACTAACCAAACCCTACCCAC 60.291 54.545 0.00 0.00 38.79 4.61
2031 2127 1.987368 GGACTAACCAAACCCTACCCA 59.013 52.381 0.00 0.00 38.79 4.51
2032 2128 1.065926 CGGACTAACCAAACCCTACCC 60.066 57.143 0.00 0.00 38.90 3.69
2137 2233 3.181471 CCTAGCTAGAACCATGGACACAG 60.181 52.174 22.70 10.99 0.00 3.66
2290 2387 5.671742 AATTTACAGCACAAAAACATGCC 57.328 34.783 0.00 0.00 43.12 4.40
2292 2389 8.602328 TCAAGAAATTTACAGCACAAAAACATG 58.398 29.630 0.00 0.00 0.00 3.21
2293 2390 8.715191 TCAAGAAATTTACAGCACAAAAACAT 57.285 26.923 0.00 0.00 0.00 2.71
2294 2391 8.539770 TTCAAGAAATTTACAGCACAAAAACA 57.460 26.923 0.00 0.00 0.00 2.83
2295 2392 9.986833 ATTTCAAGAAATTTACAGCACAAAAAC 57.013 25.926 2.31 0.00 37.74 2.43
2303 2404 8.579682 AACTGACATTTCAAGAAATTTACAGC 57.420 30.769 20.42 3.83 38.84 4.40
2311 2412 5.242069 TCGCAAACTGACATTTCAAGAAA 57.758 34.783 0.00 0.00 34.46 2.52
2358 2459 2.494471 TGCGCATGTACTACCACTAGTT 59.506 45.455 5.66 0.00 34.79 2.24
2362 2463 1.182667 TCTGCGCATGTACTACCACT 58.817 50.000 12.24 0.00 0.00 4.00
2363 2464 2.225068 ATCTGCGCATGTACTACCAC 57.775 50.000 12.24 0.00 0.00 4.16
2364 2465 2.956333 AGTATCTGCGCATGTACTACCA 59.044 45.455 24.77 0.00 0.00 3.25
2365 2466 3.243434 ACAGTATCTGCGCATGTACTACC 60.243 47.826 25.23 6.87 34.37 3.18
2366 2467 3.731216 CACAGTATCTGCGCATGTACTAC 59.269 47.826 25.23 16.21 34.37 2.73
2368 2469 2.166459 ACACAGTATCTGCGCATGTACT 59.834 45.455 22.07 22.07 34.37 2.73
2369 2470 2.540515 ACACAGTATCTGCGCATGTAC 58.459 47.619 12.24 16.82 34.37 2.90
2392 2506 3.282021 GAACCATCTATTGCAAGGCTGA 58.718 45.455 4.94 0.61 0.00 4.26
2396 2510 6.949352 AACTATGAACCATCTATTGCAAGG 57.051 37.500 4.94 2.33 0.00 3.61
2405 2519 5.556915 TCGACCAAAAACTATGAACCATCT 58.443 37.500 0.00 0.00 0.00 2.90
2409 2523 5.934935 TTCTCGACCAAAAACTATGAACC 57.065 39.130 0.00 0.00 0.00 3.62
2413 2527 5.698832 TGCATTTCTCGACCAAAAACTATG 58.301 37.500 0.00 0.00 0.00 2.23
2486 2603 1.078709 CAACCGTGATCGAGCACAAT 58.921 50.000 30.82 16.78 38.69 2.71
2527 2644 4.083961 GCTTCTTCTACCTTGACCGAAAAC 60.084 45.833 0.00 0.00 0.00 2.43
2588 2705 9.985730 TTGTTAGGAAATACGTATCGGAATAAT 57.014 29.630 8.86 0.00 0.00 1.28
2589 2706 9.814899 TTTGTTAGGAAATACGTATCGGAATAA 57.185 29.630 8.86 2.86 0.00 1.40
2590 2707 9.985730 ATTTGTTAGGAAATACGTATCGGAATA 57.014 29.630 8.86 0.00 0.00 1.75
2591 2708 8.770828 CATTTGTTAGGAAATACGTATCGGAAT 58.229 33.333 8.86 0.00 0.00 3.01
2592 2709 7.225145 CCATTTGTTAGGAAATACGTATCGGAA 59.775 37.037 8.86 0.00 0.00 4.30
2593 2710 6.702723 CCATTTGTTAGGAAATACGTATCGGA 59.297 38.462 8.86 0.00 0.00 4.55
2594 2711 6.702723 TCCATTTGTTAGGAAATACGTATCGG 59.297 38.462 8.86 0.00 0.00 4.18
2595 2712 7.437267 ACTCCATTTGTTAGGAAATACGTATCG 59.563 37.037 8.86 0.00 32.57 2.92
2596 2713 8.658499 ACTCCATTTGTTAGGAAATACGTATC 57.342 34.615 8.86 0.00 32.57 2.24
2597 2714 9.760077 CTACTCCATTTGTTAGGAAATACGTAT 57.240 33.333 1.14 1.14 32.57 3.06
2598 2715 8.199449 CCTACTCCATTTGTTAGGAAATACGTA 58.801 37.037 0.00 0.00 32.57 3.57
2599 2716 7.046033 CCTACTCCATTTGTTAGGAAATACGT 58.954 38.462 0.00 0.00 32.57 3.57
2600 2717 7.046033 ACCTACTCCATTTGTTAGGAAATACG 58.954 38.462 0.49 0.00 32.57 3.06
2601 2718 7.224167 CGACCTACTCCATTTGTTAGGAAATAC 59.776 40.741 0.49 0.00 32.57 1.89
2602 2719 7.124599 TCGACCTACTCCATTTGTTAGGAAATA 59.875 37.037 0.49 0.00 32.57 1.40
2603 2720 6.070424 TCGACCTACTCCATTTGTTAGGAAAT 60.070 38.462 0.49 0.00 32.57 2.17
2604 2721 5.246656 TCGACCTACTCCATTTGTTAGGAAA 59.753 40.000 0.49 0.00 32.57 3.13
2605 2722 4.773674 TCGACCTACTCCATTTGTTAGGAA 59.226 41.667 0.49 0.00 32.57 3.36
2606 2723 4.346730 TCGACCTACTCCATTTGTTAGGA 58.653 43.478 0.49 0.00 0.00 2.94
2607 2724 4.730949 TCGACCTACTCCATTTGTTAGG 57.269 45.455 0.00 0.00 0.00 2.69
2608 2725 4.561606 CGTTCGACCTACTCCATTTGTTAG 59.438 45.833 0.00 0.00 0.00 2.34
2609 2726 4.487948 CGTTCGACCTACTCCATTTGTTA 58.512 43.478 0.00 0.00 0.00 2.41
2610 2727 3.323243 CGTTCGACCTACTCCATTTGTT 58.677 45.455 0.00 0.00 0.00 2.83
2611 2728 2.353406 CCGTTCGACCTACTCCATTTGT 60.353 50.000 0.00 0.00 0.00 2.83
2612 2729 2.094390 TCCGTTCGACCTACTCCATTTG 60.094 50.000 0.00 0.00 0.00 2.32
2613 2730 2.173519 TCCGTTCGACCTACTCCATTT 58.826 47.619 0.00 0.00 0.00 2.32
2614 2731 1.843368 TCCGTTCGACCTACTCCATT 58.157 50.000 0.00 0.00 0.00 3.16
2615 2732 1.955080 GATCCGTTCGACCTACTCCAT 59.045 52.381 0.00 0.00 0.00 3.41
2616 2733 1.386533 GATCCGTTCGACCTACTCCA 58.613 55.000 0.00 0.00 0.00 3.86
2674 2825 8.433126 CCTACAAATACTCCTAAAAATATCGCG 58.567 37.037 0.00 0.00 0.00 5.87
2808 2960 1.366111 CGCCACGAAAACGATGGGAT 61.366 55.000 0.00 0.00 33.81 3.85
2833 2991 2.098298 CATTTCTGGAACGCGCGG 59.902 61.111 35.22 16.11 0.00 6.46


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

AutoCloner maintained by Alex Coulton.