Multiple sequence alignment - TraesCS1A01G369000

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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 TraesCS1A01G369000 chr1A 100.000 3662 0 0 1 3662 546526287 546522626 0.000000e+00 6763.0
1 TraesCS1A01G369000 chr1A 78.578 1083 202 23 193 1261 10588701 10587635 0.000000e+00 688.0
2 TraesCS1A01G369000 chr2A 98.072 3164 56 3 1 3160 32135383 32132221 0.000000e+00 5500.0
3 TraesCS1A01G369000 chr2A 97.800 500 11 0 3161 3660 32117505 32117006 0.000000e+00 863.0
4 TraesCS1A01G369000 chr7D 94.058 3164 179 7 1 3160 127416964 127413806 0.000000e+00 4793.0
5 TraesCS1A01G369000 chr7D 93.517 3162 195 8 1 3157 58108629 58111785 0.000000e+00 4695.0
6 TraesCS1A01G369000 chr7D 95.418 502 22 1 3161 3662 127379952 127379452 0.000000e+00 798.0
7 TraesCS1A01G369000 chr7D 94.821 502 26 0 3161 3662 58127800 58128301 0.000000e+00 784.0
8 TraesCS1A01G369000 chr1D 93.586 3165 193 8 1 3160 71308016 71304857 0.000000e+00 4711.0
9 TraesCS1A01G369000 chr1D 95.020 502 25 0 3161 3662 71291322 71290821 0.000000e+00 789.0
10 TraesCS1A01G369000 chr1D 94.821 502 26 0 3161 3662 182584884 182584383 0.000000e+00 784.0
11 TraesCS1A01G369000 chr2D 93.081 3165 204 11 1 3160 345274982 345271828 0.000000e+00 4617.0
12 TraesCS1A01G369000 chr2D 93.074 3162 199 11 1 3157 639464302 639467448 0.000000e+00 4608.0
13 TraesCS1A01G369000 chr2D 95.020 502 25 0 3161 3662 639480867 639481368 0.000000e+00 789.0
14 TraesCS1A01G369000 chr2D 94.821 502 26 0 3161 3662 345255597 345255096 0.000000e+00 784.0
15 TraesCS1A01G369000 chr5D 95.863 2079 78 6 1 2075 42224958 42222884 0.000000e+00 3356.0
16 TraesCS1A01G369000 chr5D 89.738 955 95 3 2207 3160 42222895 42221943 0.000000e+00 1218.0
17 TraesCS1A01G369000 chr5D 96.016 502 20 0 3161 3662 42210626 42210125 0.000000e+00 817.0
18 TraesCS1A01G369000 chr3A 80.087 693 118 16 1 676 541220747 541221436 7.060000e-137 497.0
19 TraesCS1A01G369000 chr6B 81.300 631 93 17 1 613 669533015 669533638 4.250000e-134 488.0
20 TraesCS1A01G369000 chr5A 80.282 639 93 20 1 613 611016246 611015615 5.580000e-123 451.0
21 TraesCS1A01G369000 chr5A 74.302 179 36 7 1235 1408 461062160 461061987 2.360000e-07 67.6
22 TraesCS1A01G369000 chr2B 73.810 210 51 4 3447 3655 795802319 795802113 3.030000e-11 80.5
23 TraesCS1A01G369000 chr4A 77.099 131 28 2 1279 1408 117097621 117097492 1.410000e-09 75.0


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 TraesCS1A01G369000 chr1A 546522626 546526287 3661 True 6763 6763 100.0000 1 3662 1 chr1A.!!$R2 3661
1 TraesCS1A01G369000 chr1A 10587635 10588701 1066 True 688 688 78.5780 193 1261 1 chr1A.!!$R1 1068
2 TraesCS1A01G369000 chr2A 32132221 32135383 3162 True 5500 5500 98.0720 1 3160 1 chr2A.!!$R2 3159
3 TraesCS1A01G369000 chr7D 127413806 127416964 3158 True 4793 4793 94.0580 1 3160 1 chr7D.!!$R2 3159
4 TraesCS1A01G369000 chr7D 58108629 58111785 3156 False 4695 4695 93.5170 1 3157 1 chr7D.!!$F1 3156
5 TraesCS1A01G369000 chr7D 127379452 127379952 500 True 798 798 95.4180 3161 3662 1 chr7D.!!$R1 501
6 TraesCS1A01G369000 chr7D 58127800 58128301 501 False 784 784 94.8210 3161 3662 1 chr7D.!!$F2 501
7 TraesCS1A01G369000 chr1D 71304857 71308016 3159 True 4711 4711 93.5860 1 3160 1 chr1D.!!$R2 3159
8 TraesCS1A01G369000 chr1D 71290821 71291322 501 True 789 789 95.0200 3161 3662 1 chr1D.!!$R1 501
9 TraesCS1A01G369000 chr1D 182584383 182584884 501 True 784 784 94.8210 3161 3662 1 chr1D.!!$R3 501
10 TraesCS1A01G369000 chr2D 345271828 345274982 3154 True 4617 4617 93.0810 1 3160 1 chr2D.!!$R2 3159
11 TraesCS1A01G369000 chr2D 639464302 639467448 3146 False 4608 4608 93.0740 1 3157 1 chr2D.!!$F1 3156
12 TraesCS1A01G369000 chr2D 639480867 639481368 501 False 789 789 95.0200 3161 3662 1 chr2D.!!$F2 501
13 TraesCS1A01G369000 chr2D 345255096 345255597 501 True 784 784 94.8210 3161 3662 1 chr2D.!!$R1 501
14 TraesCS1A01G369000 chr5D 42221943 42224958 3015 True 2287 3356 92.8005 1 3160 2 chr5D.!!$R2 3159
15 TraesCS1A01G369000 chr5D 42210125 42210626 501 True 817 817 96.0160 3161 3662 1 chr5D.!!$R1 501
16 TraesCS1A01G369000 chr3A 541220747 541221436 689 False 497 497 80.0870 1 676 1 chr3A.!!$F1 675
17 TraesCS1A01G369000 chr6B 669533015 669533638 623 False 488 488 81.3000 1 613 1 chr6B.!!$F1 612
18 TraesCS1A01G369000 chr5A 611015615 611016246 631 True 451 451 80.2820 1 613 1 chr5A.!!$R2 612

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
729 765 2.225491 ACCGCACAAACATGTATGACAC 59.775 45.455 0.00 0.0 0.0 3.67 F
2193 2249 1.076677 GATGGCATGGGATTGGAGGAT 59.923 52.381 3.81 0.0 0.0 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2318 2374 0.110486 TCGCCCAGCTTTCCTTTTCT 59.890 50.0 0.00 0.0 0.0 2.52 R
3408 3466 0.804989 ATTTGCGCCAGACTTGCTAC 59.195 50.0 4.18 0.0 0.0 3.58 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
294 322 8.397906 CAATAATGGCGGGTATATAAATGAGTG 58.602 37.037 0.00 0.00 0.00 3.51
598 634 6.485171 AGCAAAAGATTCTGGGTTGTACTAT 58.515 36.000 0.00 0.00 0.00 2.12
729 765 2.225491 ACCGCACAAACATGTATGACAC 59.775 45.455 0.00 0.00 0.00 3.67
1027 1075 9.905713 TGGAATTAGCTATTGAGAAAGTTATGT 57.094 29.630 0.00 0.00 0.00 2.29
1131 1179 6.395629 CAGCAAATTCAAGTCAGATTTCCAT 58.604 36.000 0.00 0.00 0.00 3.41
1376 1424 6.209192 AGTTGTCCAATGCATCTATTTGTTCA 59.791 34.615 0.00 0.00 0.00 3.18
1387 1435 7.553760 TGCATCTATTTGTTCATCAGTACATGT 59.446 33.333 2.69 2.69 0.00 3.21
1534 1582 1.494721 TCTGCTTTTTCAGGTGTCCCT 59.505 47.619 0.00 0.00 44.02 4.20
1760 1808 3.831323 TGATGATGGACCACAAGTGTTT 58.169 40.909 0.00 0.00 0.00 2.83
1999 2055 1.748122 CTGCCAGCCCATCTGTCAC 60.748 63.158 0.00 0.00 41.25 3.67
2149 2205 8.757982 AATGCTCAAGATAACAATGGATAAGT 57.242 30.769 0.00 0.00 0.00 2.24
2193 2249 1.076677 GATGGCATGGGATTGGAGGAT 59.923 52.381 3.81 0.00 0.00 3.24
2319 2375 3.571119 CTGAAAGCACCGGAGCAG 58.429 61.111 26.04 10.49 36.85 4.24
2374 2430 7.382110 CAGAGATAAACCTCCATACGATGATT 58.618 38.462 0.00 0.00 33.76 2.57
2585 2641 2.504175 GTGGCCATAGGAGAAACACCTA 59.496 50.000 9.72 0.00 42.99 3.08
2674 2730 6.088824 GCTTTGGTTTGAACTCATGTGATAG 58.911 40.000 0.94 0.00 0.00 2.08
2977 3034 5.086058 CCGTTTGAATTTTGTACTGATCGG 58.914 41.667 0.00 0.00 0.00 4.18
3027 3084 2.447408 TACCGATACCTTGCCTCTCA 57.553 50.000 0.00 0.00 0.00 3.27
3167 3224 6.371809 ACCACATACAAGTTTACACAAGTG 57.628 37.500 0.00 0.00 0.00 3.16
3223 3280 0.533755 GCATCCTACTCCGCAGCAAT 60.534 55.000 0.00 0.00 0.00 3.56
3293 3350 1.065564 GCTCTTCAAGGACCTGCAGAT 60.066 52.381 17.39 0.00 0.00 2.90
3314 3371 6.421501 CAGATTGCACAATGCTTGTCTTAAAA 59.578 34.615 0.00 0.00 45.31 1.52
3330 3387 7.981142 TGTCTTAAAAACCGATATCCATCAAC 58.019 34.615 0.00 0.00 0.00 3.18
3367 3424 1.750778 GTCATTGCATTACCCACCCAG 59.249 52.381 0.00 0.00 0.00 4.45
3370 3427 1.917872 TTGCATTACCCACCCAGAAC 58.082 50.000 0.00 0.00 0.00 3.01
3405 3463 5.556915 AGATGAACAAAACTTACCGGATCA 58.443 37.500 9.46 0.00 0.00 2.92
3459 3517 2.657297 GCTTGGCCCAAGTGAATGA 58.343 52.632 23.90 0.00 42.77 2.57
3484 3542 1.340017 CCGACCTCACATCACCCAAAT 60.340 52.381 0.00 0.00 0.00 2.32
3490 3548 4.228210 ACCTCACATCACCCAAATAGTCAT 59.772 41.667 0.00 0.00 0.00 3.06
3567 3625 0.244721 GCACCCTTGGAACTGATTGC 59.755 55.000 0.00 0.00 0.00 3.56
3586 3644 4.824479 TGCTTCACTGAACCTGATGATA 57.176 40.909 0.00 0.00 0.00 2.15
3592 3650 4.471025 TCACTGAACCTGATGATACATGGT 59.529 41.667 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
269 297 7.067008 GCACTCATTTATATACCCGCCATTATT 59.933 37.037 0.00 0.00 0.00 1.40
278 306 5.865085 TGTCCTGCACTCATTTATATACCC 58.135 41.667 0.00 0.00 0.00 3.69
294 322 1.741706 CATGGTTGTGATCTGTCCTGC 59.258 52.381 0.00 0.00 0.00 4.85
598 634 3.345508 TCTTCGTCAGGCTGTACTCTA 57.654 47.619 15.27 0.00 0.00 2.43
729 765 0.591170 AACGAACAGTCCAAATGGCG 59.409 50.000 0.00 0.00 34.44 5.69
1027 1075 2.037121 ACCATCGATGTGTTGTGTCAGA 59.963 45.455 23.27 0.00 0.00 3.27
1131 1179 7.659799 ACTGTCAACATGTGCTGTACTATTTTA 59.340 33.333 0.00 0.00 36.98 1.52
1376 1424 5.769662 TCAAAAAGAAGCCACATGTACTGAT 59.230 36.000 0.00 0.00 0.00 2.90
1387 1435 4.263462 TGCCTCTCTATCAAAAAGAAGCCA 60.263 41.667 0.00 0.00 0.00 4.75
1534 1582 5.630121 AGGGTGTGTTCATTCTCATTACAA 58.370 37.500 0.00 0.00 0.00 2.41
1760 1808 3.856638 GCTCGAAATTGCCACATTCACAA 60.857 43.478 0.00 0.00 0.00 3.33
1871 1927 6.543465 CACATAGGTGGTGTTTCATCATACAT 59.457 38.462 0.00 0.00 41.45 2.29
2149 2205 2.158813 GGGCAGCAGCTACAGGTATTAA 60.159 50.000 0.00 0.00 41.70 1.40
2153 2209 2.721167 CGGGCAGCAGCTACAGGTA 61.721 63.158 0.00 0.00 41.70 3.08
2193 2249 4.471904 AAGTTGCATCCGATGAGTTCTA 57.528 40.909 12.79 0.00 0.00 2.10
2313 2369 1.543358 CCAGCTTTCCTTTTCTGCTCC 59.457 52.381 0.00 0.00 0.00 4.70
2318 2374 0.110486 TCGCCCAGCTTTCCTTTTCT 59.890 50.000 0.00 0.00 0.00 2.52
2319 2375 0.241213 GTCGCCCAGCTTTCCTTTTC 59.759 55.000 0.00 0.00 0.00 2.29
2674 2730 0.169009 GCAAAGCCCTCAACATCGTC 59.831 55.000 0.00 0.00 0.00 4.20
2746 2802 7.145323 ACCACAATAAGTTACAAGATTTGTGC 58.855 34.615 14.95 0.00 45.03 4.57
2832 2889 6.312529 AGAAGTGAATATATACACTCGGGGA 58.687 40.000 6.49 0.00 44.94 4.81
3027 3084 0.980231 GAGAGTCAGGGGTGCTGGAT 60.980 60.000 0.00 0.00 0.00 3.41
3167 3224 8.014517 GCTTAGCTTTGCTGATAGAATTGTATC 58.985 37.037 14.21 14.21 40.10 2.24
3314 3371 6.376864 TGTTGAAATGTTGATGGATATCGGTT 59.623 34.615 0.00 0.00 36.04 4.44
3367 3424 5.751586 TGTTCATCTAATTAGGTGGGGTTC 58.248 41.667 22.64 10.98 35.17 3.62
3370 3427 6.663523 AGTTTTGTTCATCTAATTAGGTGGGG 59.336 38.462 22.64 0.97 35.17 4.96
3405 3463 2.261671 CGCCAGACTTGCTACGGT 59.738 61.111 0.00 0.00 0.00 4.83
3408 3466 0.804989 ATTTGCGCCAGACTTGCTAC 59.195 50.000 4.18 0.00 0.00 3.58
3441 3499 1.188863 ATCATTCACTTGGGCCAAGC 58.811 50.000 39.34 0.00 44.43 4.01
3459 3517 1.070758 GGTGATGTGAGGTCGGCATAT 59.929 52.381 0.00 0.00 0.00 1.78
3484 3542 0.963856 ACGACGGCACCAGATGACTA 60.964 55.000 0.00 0.00 31.94 2.59
3490 3548 3.529341 ATGCAACGACGGCACCAGA 62.529 57.895 0.00 0.00 45.23 3.86
3567 3625 5.526479 CCATGTATCATCAGGTTCAGTGAAG 59.474 44.000 5.62 0.00 0.00 3.02
3586 3644 3.939740 AGGATGCATTGACTACCATGT 57.060 42.857 0.00 0.00 0.00 3.21
3592 3650 1.667236 CGCCAAGGATGCATTGACTA 58.333 50.000 0.00 0.00 0.00 2.59
3616 3674 3.110178 GTACACGCGGCCAGACAC 61.110 66.667 12.47 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.