Multiple sequence alignment - TraesCS6D01G282900

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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 TraesCS6D01G282900 chr6D 100.000 3855 0 0 1 3855 389988048 389984194 0.000000e+00 7119
1 TraesCS6D01G282900 chr6D 82.566 717 84 25 2588 3294 23746873 23746188 9.220000e-166 593
2 TraesCS6D01G282900 chr6D 87.598 508 45 8 1487 1978 23747391 23746886 1.200000e-159 573
3 TraesCS6D01G282900 chr6D 94.444 126 5 2 653 778 390232666 390232543 3.930000e-45 193
4 TraesCS6D01G282900 chr6B 94.652 3478 135 23 414 3855 584219684 584223146 0.000000e+00 5345
5 TraesCS6D01G282900 chr6B 85.202 446 42 18 2855 3293 38623486 38623058 1.640000e-118 436
6 TraesCS6D01G282900 chr6B 87.117 326 39 2 1 326 584219278 584219600 2.190000e-97 366
7 TraesCS6D01G282900 chr6B 78.284 373 41 18 2955 3293 46621469 46621835 1.820000e-48 204
8 TraesCS6D01G282900 chr6B 93.284 134 9 0 645 778 584035632 584035765 8.450000e-47 198
9 TraesCS6D01G282900 chr6A 95.814 1481 58 3 1451 2927 536439577 536438097 0.000000e+00 2388
10 TraesCS6D01G282900 chr6A 91.148 1220 82 15 232 1430 536440850 536439636 0.000000e+00 1631
11 TraesCS6D01G282900 chr6A 93.324 734 29 7 3141 3855 536437742 536437010 0.000000e+00 1066
12 TraesCS6D01G282900 chr6A 82.564 866 102 28 2439 3293 22274852 22274025 0.000000e+00 717
13 TraesCS6D01G282900 chr6A 95.299 234 11 0 2911 3144 536438078 536437845 4.700000e-99 372
14 TraesCS6D01G282900 chr6A 84.127 378 44 7 1490 1851 22275541 22275164 6.130000e-93 351
15 TraesCS6D01G282900 chr6A 90.417 240 17 6 670 906 536769473 536769237 1.040000e-80 311
16 TraesCS6D01G282900 chr6A 88.021 192 21 2 2100 2291 22275097 22274908 3.880000e-55 226
17 TraesCS6D01G282900 chr6A 90.000 170 14 2 1 170 536441039 536440873 2.330000e-52 217
18 TraesCS6D01G282900 chr6A 98.246 114 1 1 667 779 536458372 536458259 8.450000e-47 198
19 TraesCS6D01G282900 chr6A 92.481 133 9 1 648 779 603342229 603342361 5.080000e-44 189
20 TraesCS6D01G282900 chr7A 85.417 192 21 4 667 853 700821376 700821565 3.930000e-45 193
21 TraesCS6D01G282900 chr7D 87.500 152 18 1 1142 1293 610920231 610920381 1.420000e-39 174
22 TraesCS6D01G282900 chr7B 83.957 187 24 6 668 853 699932937 699933118 1.420000e-39 174


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 TraesCS6D01G282900 chr6D 389984194 389988048 3854 True 7119.000000 7119 100.0000 1 3855 1 chr6D.!!$R1 3854
1 TraesCS6D01G282900 chr6D 23746188 23747391 1203 True 583.000000 593 85.0820 1487 3294 2 chr6D.!!$R3 1807
2 TraesCS6D01G282900 chr6B 584219278 584223146 3868 False 2855.500000 5345 90.8845 1 3855 2 chr6B.!!$F3 3854
3 TraesCS6D01G282900 chr6A 536437010 536441039 4029 True 1134.800000 2388 93.1170 1 3855 5 chr6A.!!$R4 3854
4 TraesCS6D01G282900 chr6A 22274025 22275541 1516 True 431.333333 717 84.9040 1490 3293 3 chr6A.!!$R3 1803

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
982 1020 0.107017 AAGCCCATCCTCCATTGACG 60.107 55.0 0.00 0.00 0.00 4.35 F
1480 1562 0.320374 TTCAGACGTCCATGTGGGTC 59.680 55.0 13.01 0.12 38.11 4.46 F
1852 1962 0.329596 ACAACATCCTCTTGAGGGCC 59.670 55.0 15.81 0.00 0.00 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2722 2838 0.263172 TGGGGGTTTTCTTGGAAGCA 59.737 50.00 0.00 0.0 0.00 3.91 R
2752 2868 3.805971 GCTTGCTTGCAGAGTTTGAATTT 59.194 39.13 0.00 0.0 0.00 1.82 R
3550 3835 0.179116 CATCTCAGAGGTGGTGAGCG 60.179 60.00 2.24 0.0 41.16 5.03 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
61 62 8.097038 TCCCATAAATCCTTTCTGATCTATTCG 58.903 37.037 0.00 0.00 0.00 3.34
63 64 9.149225 CCATAAATCCTTTCTGATCTATTCGAG 57.851 37.037 0.00 0.00 0.00 4.04
102 103 2.275134 TGTCTGATTGGCTGCAAAGA 57.725 45.000 0.50 0.00 0.00 2.52
126 127 5.578005 AGAAAATGGATGTCTGCAATCTG 57.422 39.130 0.00 0.00 0.00 2.90
145 146 8.268738 GCAATCTGTTTAGTTTTGTTGATGTTC 58.731 33.333 0.00 0.00 0.00 3.18
146 147 8.471457 CAATCTGTTTAGTTTTGTTGATGTTCG 58.529 33.333 0.00 0.00 0.00 3.95
178 179 6.541278 ACGAAATAGACTATTTTTACAGGCCC 59.459 38.462 19.11 5.10 38.42 5.80
186 187 0.249676 TTTTACAGGCCCGCGTATGA 59.750 50.000 4.92 0.00 0.00 2.15
195 196 2.059541 GCCCGCGTATGAAGAAGTATC 58.940 52.381 4.92 0.00 0.00 2.24
219 220 4.019411 TCATGTGTCATTGGGAAGCTAAGA 60.019 41.667 0.00 0.00 0.00 2.10
226 227 0.324943 TGGGAAGCTAAGAGTGCACC 59.675 55.000 14.63 5.12 0.00 5.01
228 229 1.677217 GGGAAGCTAAGAGTGCACCTG 60.677 57.143 14.63 0.41 32.75 4.00
229 230 1.082690 GAAGCTAAGAGTGCACCTGC 58.917 55.000 14.63 10.81 42.50 4.85
269 270 0.955428 TGAAGATGCTCAACCGGCAC 60.955 55.000 0.00 0.00 42.69 5.01
280 281 1.169661 AACCGGCACTGATTTTGCGA 61.170 50.000 0.00 0.00 41.18 5.10
345 369 6.652205 TGATTACTTGGGGTTTATCTTCCT 57.348 37.500 0.00 0.00 0.00 3.36
373 397 3.124560 TGCAACTGACGAATAACGACAA 58.875 40.909 0.00 0.00 44.34 3.18
397 421 1.757682 TGTCCTTGGTCCACACAAAC 58.242 50.000 0.00 0.00 0.00 2.93
407 431 2.693074 GTCCACACAAACTGGTTCCAAT 59.307 45.455 0.00 0.00 0.00 3.16
408 432 2.692557 TCCACACAAACTGGTTCCAATG 59.307 45.455 0.00 0.00 0.00 2.82
409 433 2.472816 CACACAAACTGGTTCCAATGC 58.527 47.619 0.00 0.00 0.00 3.56
411 435 1.066908 CACAAACTGGTTCCAATGCGT 59.933 47.619 0.00 0.00 0.00 5.24
412 436 1.066908 ACAAACTGGTTCCAATGCGTG 59.933 47.619 0.00 0.00 0.00 5.34
476 502 0.239879 TGTCGCCTTTTCAATTCGGC 59.760 50.000 0.00 0.00 39.14 5.54
484 517 4.672409 CCTTTTCAATTCGGCTGGTAATC 58.328 43.478 0.00 0.00 0.00 1.75
572 605 3.782656 ATGTAACGAGGGAAACACCTT 57.217 42.857 0.00 0.00 42.10 3.50
629 665 5.163447 TGAGTCAAGGGTAATACTGATTCGG 60.163 44.000 0.00 0.00 0.00 4.30
804 842 0.179056 ACGCCTCCATTAATCCCACG 60.179 55.000 0.00 0.00 0.00 4.94
830 868 1.075836 CACCGTCCATCCCCCAAAA 59.924 57.895 0.00 0.00 0.00 2.44
832 870 1.680989 CCGTCCATCCCCCAAAACC 60.681 63.158 0.00 0.00 0.00 3.27
853 891 2.046285 CCATCCCAGCCGTCCAAAC 61.046 63.158 0.00 0.00 0.00 2.93
958 996 4.481112 CCGCGCTCCAATGCAACC 62.481 66.667 5.56 0.00 0.00 3.77
961 999 3.451894 CGCTCCAATGCAACCCCC 61.452 66.667 0.00 0.00 0.00 5.40
965 1003 1.304052 TCCAATGCAACCCCCGAAG 60.304 57.895 0.00 0.00 0.00 3.79
980 1018 0.181114 CGAAGCCCATCCTCCATTGA 59.819 55.000 0.00 0.00 0.00 2.57
981 1019 1.685148 GAAGCCCATCCTCCATTGAC 58.315 55.000 0.00 0.00 0.00 3.18
982 1020 0.107017 AAGCCCATCCTCCATTGACG 60.107 55.000 0.00 0.00 0.00 4.35
986 1024 2.039418 CCCATCCTCCATTGACGACTA 58.961 52.381 0.00 0.00 0.00 2.59
1348 1386 1.754234 CACCATGCCCTACCCTTGC 60.754 63.158 0.00 0.00 0.00 4.01
1365 1403 2.409870 GCGCCCAACTCAATCAGGG 61.410 63.158 0.00 0.00 44.37 4.45
1403 1444 1.755959 CATGAGCTAGAGCCAGTGTCT 59.244 52.381 0.00 0.00 43.38 3.41
1431 1475 8.827677 GCTTAACTTACATAAGGTACCTTGATG 58.172 37.037 33.19 28.91 35.37 3.07
1445 1489 5.543507 ACCTTGATGTAGGATTGCTCTAG 57.456 43.478 0.00 0.00 38.73 2.43
1448 1492 5.988561 CCTTGATGTAGGATTGCTCTAGAAC 59.011 44.000 0.00 0.00 37.50 3.01
1472 1554 6.829298 ACTCTAGATAAGATTTCAGACGTCCA 59.171 38.462 13.01 0.00 32.41 4.02
1480 1562 0.320374 TTCAGACGTCCATGTGGGTC 59.680 55.000 13.01 0.12 38.11 4.46
1484 1566 1.289109 GACGTCCATGTGGGTCAACG 61.289 60.000 3.51 8.81 37.60 4.10
1618 1712 2.246719 ACGGCATCTATTCCAAGCTC 57.753 50.000 0.00 0.00 0.00 4.09
1645 1739 1.145900 TGATGGGAAGGAAGGGGCAA 61.146 55.000 0.00 0.00 0.00 4.52
1852 1962 0.329596 ACAACATCCTCTTGAGGGCC 59.670 55.000 15.81 0.00 0.00 5.80
1979 2094 5.105473 GGATATGGGAAGAATGGCATGATTG 60.105 44.000 0.00 0.00 0.00 2.67
2269 2384 2.408050 ACGCAAGAGTGTCTCATCAAC 58.592 47.619 0.00 0.00 43.62 3.18
2275 2390 5.583854 GCAAGAGTGTCTCATCAACATGTAT 59.416 40.000 0.00 0.00 32.06 2.29
2356 2471 5.109903 CAAAGTACTGTTCCCCTATCTTCG 58.890 45.833 0.00 0.00 0.00 3.79
2670 2786 6.432162 TCAAGTAGAGATTCTGCAAGCAATTT 59.568 34.615 0.00 0.00 31.12 1.82
2722 2838 3.577805 AGTACTTTGGAAGCAGTTGGT 57.422 42.857 0.00 0.00 0.00 3.67
2752 2868 4.123745 AGAAAACCCCCAGGATATTACCA 58.876 43.478 0.00 0.00 36.73 3.25
2925 3043 5.304614 GCTTGTACCAAGTGATATCCTAGGA 59.695 44.000 15.46 15.46 0.00 2.94
2987 3142 7.557719 ACCATCCTAGATGTCAGGTTAAAATTG 59.442 37.037 4.04 0.00 34.56 2.32
3111 3267 2.806745 GCTTTGGCAAGGGTTTTCTTCC 60.807 50.000 11.55 0.00 38.54 3.46
3219 3486 3.182967 GTGCTTCAGAGGAACAGTATCG 58.817 50.000 0.00 0.00 0.00 2.92
3341 3625 9.863845 GGTGCTTTAGGTAAATTTAATGCTTTA 57.136 29.630 0.00 0.00 33.53 1.85
3535 3820 4.339247 ACCTCAACACTGGATTTCAAACAG 59.661 41.667 0.00 0.00 38.19 3.16
3550 3835 1.755179 AACAGTATGGAGCCATGTGC 58.245 50.000 12.18 2.94 43.62 4.57
3645 3930 2.837591 AGGTGTTTCCTTGCCAACTTTT 59.162 40.909 0.00 0.00 45.67 2.27
3646 3931 2.935849 GGTGTTTCCTTGCCAACTTTTG 59.064 45.455 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 5.299531 GAAAGGATTTATGGGACAGCCTTAC 59.700 44.000 0.00 0.00 40.29 2.34
31 32 4.526970 TCAGAAAGGATTTATGGGACAGC 58.473 43.478 0.00 0.00 46.57 4.40
102 103 6.014840 ACAGATTGCAGACATCCATTTTCTTT 60.015 34.615 0.00 0.00 0.00 2.52
126 127 5.684184 GGTCCGAACATCAACAAAACTAAAC 59.316 40.000 0.00 0.00 0.00 2.01
145 146 7.998753 AAAATAGTCTATTTCGTAAGGTCCG 57.001 36.000 16.45 0.00 37.39 4.79
165 166 1.673920 CATACGCGGGCCTGTAAAAAT 59.326 47.619 14.55 0.00 0.00 1.82
178 179 5.116225 CACATGAGATACTTCTTCATACGCG 59.884 44.000 3.53 3.53 30.30 6.01
186 187 6.070021 TCCCAATGACACATGAGATACTTCTT 60.070 38.462 0.00 0.00 30.30 2.52
195 196 2.719739 AGCTTCCCAATGACACATGAG 58.280 47.619 0.00 0.00 0.00 2.90
226 227 2.995283 TGAGATCTTCCATTGGTGCAG 58.005 47.619 1.86 0.00 0.00 4.41
228 229 3.698040 ACATTGAGATCTTCCATTGGTGC 59.302 43.478 1.86 0.00 0.00 5.01
229 230 4.945543 TCACATTGAGATCTTCCATTGGTG 59.054 41.667 1.86 0.46 0.00 4.17
280 281 9.193133 CGACGATTATTTAGGAGATGTAAACAT 57.807 33.333 0.00 0.00 39.70 2.71
326 327 3.053917 GGCAGGAAGATAAACCCCAAGTA 60.054 47.826 0.00 0.00 0.00 2.24
373 397 2.306847 GTGTGGACCAAGGACAAATGT 58.693 47.619 0.00 0.00 0.00 2.71
380 404 1.409521 CCAGTTTGTGTGGACCAAGGA 60.410 52.381 0.00 0.00 37.23 3.36
397 421 2.228582 TCAATTCACGCATTGGAACCAG 59.771 45.455 3.49 0.00 35.22 4.00
407 431 3.867493 CAGAAGCTAGATCAATTCACGCA 59.133 43.478 0.00 0.00 0.00 5.24
408 432 4.026145 GTCAGAAGCTAGATCAATTCACGC 60.026 45.833 0.00 0.00 0.00 5.34
409 433 4.505922 GGTCAGAAGCTAGATCAATTCACG 59.494 45.833 0.00 0.00 0.00 4.35
411 435 5.946942 AGGTCAGAAGCTAGATCAATTCA 57.053 39.130 0.00 0.00 0.00 2.57
476 502 5.884792 AGAAAGGATTCTTGCTGATTACCAG 59.115 40.000 0.00 0.00 43.43 4.00
558 591 5.959618 AGAAAATAAAGGTGTTTCCCTCG 57.040 39.130 0.00 0.00 36.75 4.63
629 665 6.388435 AAGTTATATCACAGTACGGACCTC 57.612 41.667 0.00 0.00 0.00 3.85
649 685 6.534079 GGTGTGCTACTGATCGTTAATTAAGT 59.466 38.462 0.00 0.00 0.00 2.24
658 694 0.963856 TCCGGTGTGCTACTGATCGT 60.964 55.000 0.00 0.00 37.93 3.73
659 695 0.385751 ATCCGGTGTGCTACTGATCG 59.614 55.000 0.00 0.00 37.93 3.69
662 698 1.663379 CGGATCCGGTGTGCTACTGA 61.663 60.000 26.95 0.00 37.93 3.41
663 699 1.226974 CGGATCCGGTGTGCTACTG 60.227 63.158 26.95 0.00 35.56 2.74
665 701 1.518572 CACGGATCCGGTGTGCTAC 60.519 63.158 35.87 0.00 44.69 3.58
666 702 2.717044 CCACGGATCCGGTGTGCTA 61.717 63.158 35.87 0.00 44.69 3.49
778 815 3.882888 GGATTAATGGAGGCGTGAATTGA 59.117 43.478 0.00 0.00 0.00 2.57
779 816 3.004734 GGGATTAATGGAGGCGTGAATTG 59.995 47.826 0.00 0.00 0.00 2.32
804 842 0.455815 GGATGGACGGTGGATTTTGC 59.544 55.000 0.00 0.00 0.00 3.68
830 868 3.256960 ACGGCTGGGATGGTTGGT 61.257 61.111 0.00 0.00 0.00 3.67
832 870 2.438434 GGACGGCTGGGATGGTTG 60.438 66.667 0.00 0.00 0.00 3.77
958 996 3.878667 GGAGGATGGGCTTCGGGG 61.879 72.222 0.00 0.00 0.00 5.73
961 999 0.181114 TCAATGGAGGATGGGCTTCG 59.819 55.000 0.00 0.00 0.00 3.79
965 1003 0.815615 GTCGTCAATGGAGGATGGGC 60.816 60.000 0.00 0.00 39.82 5.36
982 1020 4.814294 CTGGGCCGTGCGGTAGTC 62.814 72.222 12.46 0.00 37.65 2.59
1348 1386 0.609131 AACCCTGATTGAGTTGGGCG 60.609 55.000 0.00 0.00 43.25 6.13
1365 1403 8.830201 AGCTCATGAATGAATGATCTAGTAAC 57.170 34.615 0.00 0.00 36.03 2.50
1403 1444 8.377034 TCAAGGTACCTTATGTAAGTTAAGCAA 58.623 33.333 26.66 0.00 34.50 3.91
1448 1492 7.265647 TGGACGTCTGAAATCTTATCTAGAG 57.734 40.000 16.46 0.00 36.02 2.43
1467 1549 2.032634 CCGTTGACCCACATGGACG 61.033 63.158 0.00 1.14 37.39 4.79
1472 1554 3.426787 TCATAAACCGTTGACCCACAT 57.573 42.857 0.00 0.00 0.00 3.21
1480 1562 5.371115 ACTCCACAAATCATAAACCGTTG 57.629 39.130 0.00 0.00 0.00 4.10
1484 1566 6.924111 ACATCAACTCCACAAATCATAAACC 58.076 36.000 0.00 0.00 0.00 3.27
1618 1712 4.506271 CCCTTCCTTCCCATCACAGATATG 60.506 50.000 0.00 0.00 0.00 1.78
1645 1739 3.419793 CCACATGGCCATCCGTATT 57.580 52.632 17.61 0.00 34.14 1.89
1852 1962 3.826754 TCGCTAGCCCGAGCACAG 61.827 66.667 9.66 0.00 42.99 3.66
1979 2094 3.133721 ACCAATACAGACTCCATCTCTGC 59.866 47.826 0.00 0.00 39.08 4.26
2269 2384 5.454520 ACGCAATCACAATATGCATACATG 58.545 37.500 8.99 13.46 40.04 3.21
2275 2390 3.269178 TGAGACGCAATCACAATATGCA 58.731 40.909 0.00 0.00 40.04 3.96
2684 2800 1.956477 ACTTAACACTGGCTTGCTTGG 59.044 47.619 0.00 0.00 0.00 3.61
2722 2838 0.263172 TGGGGGTTTTCTTGGAAGCA 59.737 50.000 0.00 0.00 0.00 3.91
2752 2868 3.805971 GCTTGCTTGCAGAGTTTGAATTT 59.194 39.130 0.00 0.00 0.00 1.82
3046 3201 5.183530 TGAAGTTGAATGGGATGAGATGT 57.816 39.130 0.00 0.00 0.00 3.06
3219 3486 7.067008 AGTCCATAACCAACTGTTATAACATGC 59.933 37.037 18.35 1.12 46.14 4.06
3341 3625 8.076178 GCATGTGTTGACAAAAGTAGACTAATT 58.924 33.333 0.00 0.00 35.11 1.40
3418 3703 6.595326 TGCTGTCAATCCTTTGTAGAACATAG 59.405 38.462 0.00 0.00 34.32 2.23
3496 3781 1.757699 GAGGTCTCCCTAATGTTCGCT 59.242 52.381 0.00 0.00 42.86 4.93
3535 3820 1.524621 AGCGCACATGGCTCCATAC 60.525 57.895 11.47 0.00 41.67 2.39
3550 3835 0.179116 CATCTCAGAGGTGGTGAGCG 60.179 60.000 2.24 0.00 41.16 5.03
3625 3910 2.935849 CAAAAGTTGGCAAGGAAACACC 59.064 45.455 0.00 0.00 39.35 4.16
3645 3930 0.615331 CTAGAGAAGGTTGCAGGGCA 59.385 55.000 0.00 0.00 36.47 5.36
3646 3931 0.905357 TCTAGAGAAGGTTGCAGGGC 59.095 55.000 0.00 0.00 0.00 5.19
3695 3980 1.581934 TCTTCAACCTTGACACTGCG 58.418 50.000 0.00 0.00 36.83 5.18
3745 4030 2.226437 TCTTTGCGCTGATTCTTTGTCC 59.774 45.455 9.73 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.