Multiple sequence alignment - TraesCS6B01G351500

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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 TraesCS6B01G351500 chr6B 100.000 2900 0 0 1 2900 617030092 617032991 0.000000e+00 5356
1 TraesCS6B01G351500 chr6B 95.290 913 40 3 1361 2271 676683754 676684665 0.000000e+00 1445
2 TraesCS6B01G351500 chr6B 97.772 718 13 3 7 723 399207006 399206291 0.000000e+00 1234
3 TraesCS6B01G351500 chr6B 94.868 643 21 4 720 1361 676682720 676683351 0.000000e+00 994
4 TraesCS6B01G351500 chr6B 94.340 636 34 1 2265 2900 676703236 676703869 0.000000e+00 974
5 TraesCS6B01G351500 chr7B 96.106 1541 57 2 1361 2900 73168064 73169602 0.000000e+00 2510
6 TraesCS6B01G351500 chr7B 95.198 1541 54 4 1361 2900 517902621 517904142 0.000000e+00 2418
7 TraesCS6B01G351500 chr7B 97.790 724 15 1 1 723 709655569 709656292 0.000000e+00 1247
8 TraesCS6B01G351500 chr7B 95.046 646 28 4 720 1363 517901581 517902224 0.000000e+00 1013
9 TraesCS6B01G351500 chr7B 97.040 473 13 1 892 1363 73167193 73167665 0.000000e+00 795
10 TraesCS6B01G351500 chr3B 95.717 1541 63 2 1361 2900 766342030 766343568 0.000000e+00 2477
11 TraesCS6B01G351500 chr3B 97.040 473 13 1 892 1363 766341160 766341632 0.000000e+00 795
12 TraesCS6B01G351500 chr3B 83.992 506 51 18 233 726 3200415 3199928 2.630000e-125 459
13 TraesCS6B01G351500 chr3B 94.083 169 9 1 720 887 766340949 766341117 3.710000e-64 255
14 TraesCS6B01G351500 chr3B 86.321 212 29 0 2689 2900 512390230 512390441 6.250000e-57 231
15 TraesCS6B01G351500 chr2B 95.396 1542 66 3 1361 2900 419938652 419940190 0.000000e+00 2449
16 TraesCS6B01G351500 chr2B 93.815 1536 86 5 1371 2900 528809399 528807867 0.000000e+00 2302
17 TraesCS6B01G351500 chr2B 97.658 726 15 2 1 724 435351796 435351071 0.000000e+00 1245
18 TraesCS6B01G351500 chr2B 95.511 646 24 5 720 1363 419937609 419938251 0.000000e+00 1027
19 TraesCS6B01G351500 chr2B 92.097 620 38 10 112 725 760346331 760345717 0.000000e+00 863
20 TraesCS6B01G351500 chr2B 89.474 627 49 9 112 725 622029102 622028480 0.000000e+00 776
21 TraesCS6B01G351500 chr2B 93.939 165 10 0 723 887 528810488 528810324 1.730000e-62 250
22 TraesCS6B01G351500 chr1B 93.591 1529 77 5 1375 2900 344040425 344041935 0.000000e+00 2261
23 TraesCS6B01G351500 chr1B 97.379 725 18 1 1 725 41213472 41214195 0.000000e+00 1232
24 TraesCS6B01G351500 chr1B 97.379 725 15 3 1 722 672837376 672836653 0.000000e+00 1230
25 TraesCS6B01G351500 chr1B 97.107 726 19 2 1 725 41175460 41176184 0.000000e+00 1223
26 TraesCS6B01G351500 chr1B 96.406 473 14 3 892 1363 344012792 344013262 0.000000e+00 776
27 TraesCS6B01G351500 chr1B 93.939 165 10 0 723 887 344012585 344012749 1.730000e-62 250
28 TraesCS6B01G351500 chr7D 96.794 1123 35 1 1361 2482 83759062 83760184 0.000000e+00 1873
29 TraesCS6B01G351500 chr7D 96.361 632 20 3 733 1363 83758032 83758661 0.000000e+00 1037
30 TraesCS6B01G351500 chr7D 96.203 632 21 3 733 1363 366438186 366437557 0.000000e+00 1031
31 TraesCS6B01G351500 chr7D 96.044 632 22 3 733 1363 126714583 126715212 0.000000e+00 1026
32 TraesCS6B01G351500 chr4B 93.812 905 54 2 1361 2264 43573696 43572793 0.000000e+00 1360
33 TraesCS6B01G351500 chr4B 93.812 905 54 2 1361 2264 43587562 43586659 0.000000e+00 1360
34 TraesCS6B01G351500 chr4B 95.483 642 26 2 2259 2900 43564379 43563741 0.000000e+00 1022
35 TraesCS6B01G351500 chr4B 95.565 496 18 2 2258 2753 43578259 43577768 0.000000e+00 791
36 TraesCS6B01G351500 chr4B 91.716 169 13 1 720 887 43592594 43592426 1.740000e-57 233
37 TraesCS6B01G351500 chr5A 97.649 723 15 2 1 722 693958927 693959648 0.000000e+00 1240
38 TraesCS6B01G351500 chr5A 97.645 722 14 3 1 722 692980730 692981448 0.000000e+00 1236
39 TraesCS6B01G351500 chr5A 94.327 617 28 7 112 725 629867215 629867827 0.000000e+00 939
40 TraesCS6B01G351500 chr5B 97.514 724 16 2 1 722 576502957 576503680 0.000000e+00 1236
41 TraesCS6B01G351500 chr4A 97.510 723 14 4 1 722 602463631 602462912 0.000000e+00 1232
42 TraesCS6B01G351500 chr2D 96.361 632 20 3 733 1363 238092418 238091789 0.000000e+00 1037
43 TraesCS6B01G351500 chr6A 88.336 763 41 7 1 732 394644083 394644828 0.000000e+00 872
44 TraesCS6B01G351500 chr3A 83.391 578 61 21 168 732 632897993 632897438 1.200000e-138 503
45 TraesCS6B01G351500 chrUn 98.462 260 4 0 466 725 476656405 476656664 2.630000e-125 459


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 TraesCS6B01G351500 chr6B 617030092 617032991 2899 False 5356.000000 5356 100.000000 1 2900 1 chr6B.!!$F1 2899
1 TraesCS6B01G351500 chr6B 399206291 399207006 715 True 1234.000000 1234 97.772000 7 723 1 chr6B.!!$R1 716
2 TraesCS6B01G351500 chr6B 676682720 676684665 1945 False 1219.500000 1445 95.079000 720 2271 2 chr6B.!!$F3 1551
3 TraesCS6B01G351500 chr6B 676703236 676703869 633 False 974.000000 974 94.340000 2265 2900 1 chr6B.!!$F2 635
4 TraesCS6B01G351500 chr7B 517901581 517904142 2561 False 1715.500000 2418 95.122000 720 2900 2 chr7B.!!$F3 2180
5 TraesCS6B01G351500 chr7B 73167193 73169602 2409 False 1652.500000 2510 96.573000 892 2900 2 chr7B.!!$F2 2008
6 TraesCS6B01G351500 chr7B 709655569 709656292 723 False 1247.000000 1247 97.790000 1 723 1 chr7B.!!$F1 722
7 TraesCS6B01G351500 chr3B 766340949 766343568 2619 False 1175.666667 2477 95.613333 720 2900 3 chr3B.!!$F2 2180
8 TraesCS6B01G351500 chr2B 419937609 419940190 2581 False 1738.000000 2449 95.453500 720 2900 2 chr2B.!!$F1 2180
9 TraesCS6B01G351500 chr2B 528807867 528810488 2621 True 1276.000000 2302 93.877000 723 2900 2 chr2B.!!$R4 2177
10 TraesCS6B01G351500 chr2B 435351071 435351796 725 True 1245.000000 1245 97.658000 1 724 1 chr2B.!!$R1 723
11 TraesCS6B01G351500 chr2B 760345717 760346331 614 True 863.000000 863 92.097000 112 725 1 chr2B.!!$R3 613
12 TraesCS6B01G351500 chr2B 622028480 622029102 622 True 776.000000 776 89.474000 112 725 1 chr2B.!!$R2 613
13 TraesCS6B01G351500 chr1B 344040425 344041935 1510 False 2261.000000 2261 93.591000 1375 2900 1 chr1B.!!$F3 1525
14 TraesCS6B01G351500 chr1B 41213472 41214195 723 False 1232.000000 1232 97.379000 1 725 1 chr1B.!!$F2 724
15 TraesCS6B01G351500 chr1B 672836653 672837376 723 True 1230.000000 1230 97.379000 1 722 1 chr1B.!!$R1 721
16 TraesCS6B01G351500 chr1B 41175460 41176184 724 False 1223.000000 1223 97.107000 1 725 1 chr1B.!!$F1 724
17 TraesCS6B01G351500 chr1B 344012585 344013262 677 False 513.000000 776 95.172500 723 1363 2 chr1B.!!$F4 640
18 TraesCS6B01G351500 chr7D 83758032 83760184 2152 False 1455.000000 1873 96.577500 733 2482 2 chr7D.!!$F2 1749
19 TraesCS6B01G351500 chr7D 366437557 366438186 629 True 1031.000000 1031 96.203000 733 1363 1 chr7D.!!$R1 630
20 TraesCS6B01G351500 chr7D 126714583 126715212 629 False 1026.000000 1026 96.044000 733 1363 1 chr7D.!!$F1 630
21 TraesCS6B01G351500 chr4B 43572793 43573696 903 True 1360.000000 1360 93.812000 1361 2264 1 chr4B.!!$R2 903
22 TraesCS6B01G351500 chr4B 43586659 43587562 903 True 1360.000000 1360 93.812000 1361 2264 1 chr4B.!!$R4 903
23 TraesCS6B01G351500 chr4B 43563741 43564379 638 True 1022.000000 1022 95.483000 2259 2900 1 chr4B.!!$R1 641
24 TraesCS6B01G351500 chr5A 693958927 693959648 721 False 1240.000000 1240 97.649000 1 722 1 chr5A.!!$F3 721
25 TraesCS6B01G351500 chr5A 692980730 692981448 718 False 1236.000000 1236 97.645000 1 722 1 chr5A.!!$F2 721
26 TraesCS6B01G351500 chr5A 629867215 629867827 612 False 939.000000 939 94.327000 112 725 1 chr5A.!!$F1 613
27 TraesCS6B01G351500 chr5B 576502957 576503680 723 False 1236.000000 1236 97.514000 1 722 1 chr5B.!!$F1 721
28 TraesCS6B01G351500 chr4A 602462912 602463631 719 True 1232.000000 1232 97.510000 1 722 1 chr4A.!!$R1 721
29 TraesCS6B01G351500 chr2D 238091789 238092418 629 True 1037.000000 1037 96.361000 733 1363 1 chr2D.!!$R1 630
30 TraesCS6B01G351500 chr6A 394644083 394644828 745 False 872.000000 872 88.336000 1 732 1 chr6A.!!$F1 731
31 TraesCS6B01G351500 chr3A 632897438 632897993 555 True 503.000000 503 83.391000 168 732 1 chr3A.!!$R1 564

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
767 830 2.288273 ACTGGTTGACTGTTCTCGTAGC 60.288 50.0 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2072 2591 0.317436 GACGTGCTCGAGCTATCCAG 60.317 60.0 35.27 21.42 42.66 3.86 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
26 27 6.605995 ACATGGTGTACTGATACTAAGCTACA 59.394 38.462 0.00 0.00 32.00 2.74
348 397 7.255801 CCTGAGCCCAAGAACTAACATTAAAAA 60.256 37.037 0.00 0.00 0.00 1.94
761 824 6.919775 AACTAGATACTGGTTGACTGTTCT 57.080 37.500 0.00 0.00 34.03 3.01
762 825 6.518208 ACTAGATACTGGTTGACTGTTCTC 57.482 41.667 0.00 0.00 33.02 2.87
767 830 2.288273 ACTGGTTGACTGTTCTCGTAGC 60.288 50.000 0.00 0.00 0.00 3.58
1150 1253 7.301868 TGTTGGCAAATAGAAAGGAGAATTT 57.698 32.000 0.00 0.00 0.00 1.82
1151 1254 7.734942 TGTTGGCAAATAGAAAGGAGAATTTT 58.265 30.769 0.00 0.00 0.00 1.82
1281 1384 1.728323 TGGTGAGAGATGTTGGTGGA 58.272 50.000 0.00 0.00 0.00 4.02
1299 1402 4.202493 GGTGGACTAAAGGGTACAAGGAAA 60.202 45.833 0.00 0.00 31.19 3.13
1319 1422 7.449247 AGGAAAACATCATTAGAGGAGATAGC 58.551 38.462 0.00 0.00 0.00 2.97
1456 1967 5.934043 CCAATATTATCTTGTCGATGCTGGA 59.066 40.000 0.00 0.00 33.48 3.86
1501 2012 6.560003 TTAGCTCCATATCAAGGTCAAAGA 57.440 37.500 0.00 0.00 0.00 2.52
1538 2050 2.316108 GGACACCACAAAATCCACCTT 58.684 47.619 0.00 0.00 0.00 3.50
1571 2083 2.330440 ATATCTCAACATGCGCCACA 57.670 45.000 4.18 0.00 0.00 4.17
1612 2124 2.108250 AGAAAGGTGCTTTGGAAGGCTA 59.892 45.455 0.00 0.00 33.49 3.93
1615 2127 3.175438 AGGTGCTTTGGAAGGCTAAAT 57.825 42.857 0.00 0.00 0.00 1.40
1688 2203 1.605232 GTCGAATCATCATGGCATGCA 59.395 47.619 22.56 11.82 0.00 3.96
1809 2326 2.441375 TGGACCAACCAGAATTCTCACA 59.559 45.455 4.57 0.00 44.64 3.58
1843 2360 6.805713 ACTTCGAATGAGTGGACAAATTTTT 58.194 32.000 0.00 0.00 0.00 1.94
2048 2567 8.995027 ATTTGCTATCTCATTTGTACCCATTA 57.005 30.769 0.00 0.00 0.00 1.90
2072 2591 2.205074 CTTGTGCAGATATGGACCGTC 58.795 52.381 9.62 0.00 0.00 4.79
2140 2659 1.819288 TGGTCTTCTGATGAGGACGAC 59.181 52.381 0.00 0.00 46.35 4.34
2504 3023 7.933215 ATTGTACCTTGGTTACCTGTTATTC 57.067 36.000 2.07 0.00 0.00 1.75
2551 3070 4.209538 TGTATTTGGATCATCCCTTGCTG 58.790 43.478 0.00 0.00 35.03 4.41
2552 3071 1.477553 TTTGGATCATCCCTTGCTGC 58.522 50.000 0.00 0.00 35.03 5.25
2553 3072 0.396139 TTGGATCATCCCTTGCTGCC 60.396 55.000 0.00 0.00 35.03 4.85
2554 3073 1.284111 TGGATCATCCCTTGCTGCCT 61.284 55.000 0.00 0.00 35.03 4.75
2555 3074 0.106318 GGATCATCCCTTGCTGCCTT 60.106 55.000 0.00 0.00 0.00 4.35
2611 3137 4.907879 AAGTAGTACCGTTTCTATCCCG 57.092 45.455 0.00 0.00 0.00 5.14
2703 3230 4.348168 AGGCTAAGGGATTGTATGGTGTAG 59.652 45.833 0.00 0.00 0.00 2.74
2740 3267 5.683681 TGAACAATTGGCTGCTATCTATGA 58.316 37.500 10.83 0.00 0.00 2.15
2764 3291 5.105392 ACAAAGACATTGCAACAGGAGAAAA 60.105 36.000 0.00 0.00 43.13 2.29
2784 3311 1.296715 GCGGAAGGCTTTGGAGAGA 59.703 57.895 0.00 0.00 39.11 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 4.081697 GCACCAACCAAAATAACATAGCCT 60.082 41.667 0.00 0.00 0.00 4.58
348 397 1.343069 TTTATTTTTGGGCCACGGCT 58.657 45.000 5.23 0.00 41.60 5.52
473 534 1.911357 AGGATCTGATGTGGCTGAACA 59.089 47.619 0.00 0.00 0.00 3.18
761 824 6.925610 AAATTGCATATCAGAAAGCTACGA 57.074 33.333 0.00 0.00 0.00 3.43
762 825 6.634436 GGAAAATTGCATATCAGAAAGCTACG 59.366 38.462 0.00 0.00 0.00 3.51
767 830 8.853126 TGGATAGGAAAATTGCATATCAGAAAG 58.147 33.333 7.79 0.00 0.00 2.62
1003 1105 1.736032 CGCACTTAAGGGAAGACGAGG 60.736 57.143 9.50 0.00 39.21 4.63
1150 1253 8.979534 GTTCTCTCCCCTTAACTCTCTAATTAA 58.020 37.037 0.00 0.00 0.00 1.40
1151 1254 8.345306 AGTTCTCTCCCCTTAACTCTCTAATTA 58.655 37.037 0.00 0.00 0.00 1.40
1281 1384 6.607019 TGATGTTTTCCTTGTACCCTTTAGT 58.393 36.000 0.00 0.00 0.00 2.24
1299 1402 4.322349 GCCGCTATCTCCTCTAATGATGTT 60.322 45.833 0.00 0.00 0.00 2.71
1319 1422 8.171196 GTGATAATACATACAAGAATGATGCCG 58.829 37.037 0.00 0.00 0.00 5.69
1348 1451 9.739276 TCATGTGTAGAACCTATTTTTGAGATT 57.261 29.630 0.00 0.00 0.00 2.40
1456 1967 7.095816 GCTAAAAATCCTTTTGCGTTTGTGTAT 60.096 33.333 0.00 0.00 35.50 2.29
1538 2050 6.935167 TGTTGAGATATTCTTCTGTGCTACA 58.065 36.000 0.00 0.00 0.00 2.74
1571 2083 7.177041 CCTTTCTACTATATTTCGGGCTCTAGT 59.823 40.741 0.00 0.00 0.00 2.57
1612 2124 2.469563 AAATCCCCCACCGGCCATTT 62.470 55.000 0.00 0.00 0.00 2.32
1615 2127 3.595758 AAAATCCCCCACCGGCCA 61.596 61.111 0.00 0.00 0.00 5.36
1775 2291 0.991920 TGGTCCAATTCTCCCTCCAC 59.008 55.000 0.00 0.00 0.00 4.02
1809 2326 6.322456 TCCACTCATTCGAAGTTGAGATAGAT 59.678 38.462 27.38 8.74 39.76 1.98
1843 2360 1.887956 GCCCTGAGCAAGTTCATTCCA 60.888 52.381 0.00 0.00 42.97 3.53
1994 2513 5.034152 TGAAAGAGAACAAATGCAAACGAC 58.966 37.500 0.00 0.00 0.00 4.34
2029 2548 8.849168 CAAGCAATAATGGGTACAAATGAGATA 58.151 33.333 0.00 0.00 0.00 1.98
2072 2591 0.317436 GACGTGCTCGAGCTATCCAG 60.317 60.000 35.27 21.42 42.66 3.86
2350 2869 2.505407 TCGACTTCCATCCCATGTGAAT 59.495 45.455 0.00 0.00 0.00 2.57
2528 3047 4.277672 CAGCAAGGGATGATCCAAATACAG 59.722 45.833 14.36 0.00 38.64 2.74
2551 3070 5.024785 AGGAATAGTAGCACTAACAAGGC 57.975 43.478 1.06 0.00 33.89 4.35
2552 3071 8.008513 TCTTAGGAATAGTAGCACTAACAAGG 57.991 38.462 1.06 0.00 33.89 3.61
2553 3072 9.469807 CATCTTAGGAATAGTAGCACTAACAAG 57.530 37.037 1.06 0.00 33.89 3.16
2554 3073 8.978472 ACATCTTAGGAATAGTAGCACTAACAA 58.022 33.333 1.06 0.00 33.89 2.83
2555 3074 8.534954 ACATCTTAGGAATAGTAGCACTAACA 57.465 34.615 1.06 0.00 33.89 2.41
2611 3137 7.328493 GGTTTTCAATAGCAAGGACAATAACAC 59.672 37.037 0.00 0.00 0.00 3.32
2659 3186 5.183904 GCCTCCTTGTGAATCTACATGTTTT 59.816 40.000 2.30 0.00 0.00 2.43
2660 3187 4.702131 GCCTCCTTGTGAATCTACATGTTT 59.298 41.667 2.30 0.00 0.00 2.83
2661 3188 4.018960 AGCCTCCTTGTGAATCTACATGTT 60.019 41.667 2.30 0.00 0.00 2.71
2703 3230 6.402442 GCCAATTGTTCAAAGTATGGAAATGC 60.402 38.462 4.43 0.00 0.00 3.56
2740 3267 3.554934 TCTCCTGTTGCAATGTCTTTGT 58.445 40.909 0.59 0.00 37.65 2.83
2764 3291 0.393537 CTCTCCAAAGCCTTCCGCAT 60.394 55.000 0.00 0.00 41.38 4.73
2784 3311 2.158608 CCTTCTCCAAGTTTCCCACTGT 60.159 50.000 0.00 0.00 35.12 3.55


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

AutoCloner maintained by Alex Coulton.