Multiple sequence alignment - TraesCS5D01G344300

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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 TraesCS5D01G344300 chr5D 100.000 3204 0 0 1 3204 431825939 431829142 0.000000e+00 5917.0
1 TraesCS5D01G344300 chr5D 98.198 2442 43 1 764 3204 513381752 513384193 0.000000e+00 4265.0
2 TraesCS5D01G344300 chr5D 97.954 782 15 1 1 782 513362385 513363165 0.000000e+00 1354.0
3 TraesCS5D01G344300 chr5D 84.063 891 75 29 987 1853 558584945 558584098 0.000000e+00 797.0
4 TraesCS5D01G344300 chr5D 87.025 632 57 18 1894 2508 558584267 558583644 0.000000e+00 689.0
5 TraesCS5D01G344300 chr5D 78.018 1019 127 52 732 1711 558614559 558615519 4.670000e-153 551.0
6 TraesCS5D01G344300 chr5D 87.008 254 19 7 1790 2032 431827647 431827897 1.130000e-69 274.0
7 TraesCS5D01G344300 chr5D 87.008 254 19 7 1709 1959 431827728 431827970 1.130000e-69 274.0
8 TraesCS5D01G344300 chr5D 87.008 254 19 7 1709 1959 513382778 513383020 1.130000e-69 274.0
9 TraesCS5D01G344300 chr5D 87.654 243 15 8 1802 2032 513382708 513382947 5.270000e-68 268.0
10 TraesCS5D01G344300 chr5D 80.827 266 28 11 2961 3204 431779732 431779468 1.520000e-43 187.0
11 TraesCS5D01G344300 chr5D 80.827 266 28 11 2961 3204 433685838 433686102 1.520000e-43 187.0
12 TraesCS5D01G344300 chr5D 79.562 274 25 11 2961 3204 513307021 513306749 1.980000e-37 167.0
13 TraesCS5D01G344300 chr5D 86.232 138 17 2 1860 1995 558584235 558584098 7.160000e-32 148.0
14 TraesCS5D01G344300 chr5D 100.000 30 0 0 2604 2633 464690698 464690727 4.470000e-04 56.5
15 TraesCS5D01G344300 chr5B 95.086 1811 64 10 756 2558 524452438 524450645 0.000000e+00 2828.0
16 TraesCS5D01G344300 chr5B 97.043 575 14 1 2607 3181 524450637 524450066 0.000000e+00 965.0
17 TraesCS5D01G344300 chr5B 81.653 992 96 40 756 1711 524554303 524553362 0.000000e+00 745.0
18 TraesCS5D01G344300 chr5B 93.654 457 20 7 162 618 524576389 524575942 0.000000e+00 675.0
19 TraesCS5D01G344300 chr5B 88.327 257 18 6 1790 2035 524451496 524451241 6.720000e-77 298.0
20 TraesCS5D01G344300 chr5B 86.770 257 22 6 1709 1962 524451415 524451168 3.150000e-70 276.0
21 TraesCS5D01G344300 chr5B 94.318 176 10 0 1 176 524588349 524588174 1.460000e-68 270.0
22 TraesCS5D01G344300 chr5B 93.464 153 8 2 384 536 524619335 524619185 3.220000e-55 226.0
23 TraesCS5D01G344300 chr5B 79.927 274 24 13 2961 3204 522862890 522863162 4.250000e-39 172.0
24 TraesCS5D01G344300 chr5B 100.000 30 0 0 2603 2632 206474748 206474719 4.470000e-04 56.5
25 TraesCS5D01G344300 chr5B 94.444 36 2 0 2604 2639 571616755 571616720 4.470000e-04 56.5
26 TraesCS5D01G344300 chr7A 93.701 381 22 2 1 379 690950174 690950554 1.290000e-158 569.0
27 TraesCS5D01G344300 chr7A 85.714 49 7 0 2908 2956 3977916 3977964 6.000000e-03 52.8
28 TraesCS5D01G344300 chr4D 93.717 382 20 4 1 379 21732144 21731764 1.290000e-158 569.0
29 TraesCS5D01G344300 chr4D 97.143 35 0 1 2531 2565 435145571 435145604 1.240000e-04 58.4
30 TraesCS5D01G344300 chr3D 92.913 381 25 1 1 379 450996269 450996649 1.300000e-153 553.0
31 TraesCS5D01G344300 chr3D 100.000 30 0 0 2603 2632 49216570 49216599 4.470000e-04 56.5
32 TraesCS5D01G344300 chr3D 100.000 30 0 0 2603 2632 101660533 101660504 4.470000e-04 56.5
33 TraesCS5D01G344300 chr2A 90.551 381 34 1 1 379 124665191 124664811 1.330000e-138 503.0
34 TraesCS5D01G344300 chr4A 82.004 489 57 20 868 1341 611918543 611919015 1.390000e-103 387.0
35 TraesCS5D01G344300 chr4A 78.689 305 33 16 1419 1711 611920399 611920683 1.180000e-39 174.0
36 TraesCS5D01G344300 chrUn 90.244 246 16 1 756 1001 478696079 478695842 6.670000e-82 315.0
37 TraesCS5D01G344300 chr6B 92.857 196 12 2 1 195 140338409 140338215 1.880000e-72 283.0
38 TraesCS5D01G344300 chr6B 92.670 191 12 2 191 379 140336021 140335831 1.130000e-69 274.0
39 TraesCS5D01G344300 chr6B 94.444 54 3 0 1009 1062 577474914 577474967 2.050000e-12 84.2
40 TraesCS5D01G344300 chr1B 84.375 224 17 9 915 1124 683240360 683240579 1.510000e-48 204.0
41 TraesCS5D01G344300 chr1B 81.538 260 33 4 874 1125 683236066 683236318 1.950000e-47 200.0
42 TraesCS5D01G344300 chr1B 78.039 255 27 12 824 1065 683310727 683310965 2.010000e-27 134.0
43 TraesCS5D01G344300 chr1B 90.566 53 5 0 1527 1579 683236954 683237006 1.590000e-08 71.3
44 TraesCS5D01G344300 chr5A 92.308 52 3 1 3092 3143 546772223 546772273 4.430000e-09 73.1
45 TraesCS5D01G344300 chr7D 100.000 30 0 0 2603 2632 528895834 528895805 4.470000e-04 56.5
46 TraesCS5D01G344300 chr6A 100.000 28 0 0 2929 2956 11843799 11843826 6.000000e-03 52.8
47 TraesCS5D01G344300 chr6A 100.000 28 0 0 2929 2956 174191240 174191267 6.000000e-03 52.8
48 TraesCS5D01G344300 chr6A 100.000 28 0 0 2929 2956 425592458 425592431 6.000000e-03 52.8
49 TraesCS5D01G344300 chr6A 91.892 37 3 0 2920 2956 502952085 502952121 6.000000e-03 52.8
50 TraesCS5D01G344300 chr3A 100.000 28 0 0 2929 2956 468527808 468527781 6.000000e-03 52.8
51 TraesCS5D01G344300 chr1A 100.000 28 0 0 2929 2956 118558438 118558411 6.000000e-03 52.8
52 TraesCS5D01G344300 chr1A 90.244 41 3 1 2592 2631 484329350 484329390 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 TraesCS5D01G344300 chr5D 431825939 431829142 3203 False 2155.000000 5917 91.338667 1 3204 3 chr5D.!!$F5 3203
1 TraesCS5D01G344300 chr5D 513381752 513384193 2441 False 1602.333333 4265 90.953333 764 3204 3 chr5D.!!$F6 2440
2 TraesCS5D01G344300 chr5D 513362385 513363165 780 False 1354.000000 1354 97.954000 1 782 1 chr5D.!!$F3 781
3 TraesCS5D01G344300 chr5D 558614559 558615519 960 False 551.000000 551 78.018000 732 1711 1 chr5D.!!$F4 979
4 TraesCS5D01G344300 chr5D 558583644 558584945 1301 True 544.666667 797 85.773333 987 2508 3 chr5D.!!$R3 1521
5 TraesCS5D01G344300 chr5B 524450066 524452438 2372 True 1091.750000 2828 91.806500 756 3181 4 chr5B.!!$R7 2425
6 TraesCS5D01G344300 chr5B 524553362 524554303 941 True 745.000000 745 81.653000 756 1711 1 chr5B.!!$R2 955
7 TraesCS5D01G344300 chr4A 611918543 611920683 2140 False 280.500000 387 80.346500 868 1711 2 chr4A.!!$F1 843
8 TraesCS5D01G344300 chr6B 140335831 140338409 2578 True 278.500000 283 92.763500 1 379 2 chr6B.!!$R1 378

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
866 3067 0.175989 GAACAGCGAGGGACCCTAAG 59.824 60.0 14.87 12.18 31.76 2.18 F
1528 5112 0.842467 CACCCCTTCCTTGGAGGACT 60.842 60.0 0.00 0.00 45.78 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1798 5386 3.118956 ACTCCTGTAGCAGAGGAAAATCG 60.119 47.826 4.14 0.0 39.2 3.34 R
3135 6732 2.297701 GTGTCTGCTGGGAAAACTTGA 58.702 47.619 0.00 0.0 0.0 3.02 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
58 59 4.250464 CATGCATCCAAAGAAAGCACATT 58.750 39.130 0.00 0.00 39.13 2.71
229 2428 0.742505 AGTTCGTCCTCGTCACACAA 59.257 50.000 0.00 0.00 38.33 3.33
360 2561 0.598562 TTCAGCGACACAGAGAGACC 59.401 55.000 0.00 0.00 0.00 3.85
388 2589 1.202065 CGCACGTGCTTGCTTAATGAT 60.202 47.619 35.27 0.00 40.62 2.45
456 2657 1.710816 TGCCTCCGGTGGAAAATTTT 58.289 45.000 26.61 2.28 0.00 1.82
522 2723 8.519526 AGTTAGATTCATCCGAGTCATTAGATC 58.480 37.037 0.00 0.00 30.49 2.75
713 2914 2.106477 TTATCACTTGCCATGTCGCA 57.894 45.000 0.00 0.00 36.85 5.10
714 2915 1.655484 TATCACTTGCCATGTCGCAG 58.345 50.000 0.00 0.00 40.53 5.18
814 3015 1.281867 ACTTCCCGATCCATCAAAGCA 59.718 47.619 0.00 0.00 0.00 3.91
866 3067 0.175989 GAACAGCGAGGGACCCTAAG 59.824 60.000 14.87 12.18 31.76 2.18
943 3144 1.067635 GTAGTTCCGACCCGCAAGTTA 60.068 52.381 0.00 0.00 0.00 2.24
1001 3206 2.161855 TCGATTCCTGCTTGTTTGCAT 58.838 42.857 0.00 0.00 42.48 3.96
1004 3209 1.042229 TTCCTGCTTGTTTGCATGCT 58.958 45.000 20.33 0.00 43.58 3.79
1528 5112 0.842467 CACCCCTTCCTTGGAGGACT 60.842 60.000 0.00 0.00 45.78 3.85
2560 6157 5.807520 AGTGCTAGATACATCTGTTTGAACG 59.192 40.000 1.88 0.00 37.76 3.95
2576 6173 6.183360 TGTTTGAACGACAAGCTTTTTAGGAT 60.183 34.615 0.00 0.00 39.76 3.24
2586 6183 8.738645 ACAAGCTTTTTAGGATGGAGTATTAG 57.261 34.615 0.00 0.00 0.00 1.73
2990 6587 2.551287 CGGGTCATCCTTGTTGGTGTTA 60.551 50.000 0.00 0.00 37.07 2.41
3055 6652 3.561725 ACAAGGCTTTCTCGTTTTCTCAG 59.438 43.478 0.00 0.00 0.00 3.35
3135 6732 4.220602 AGCAAACTCAAACAAACTTGACCT 59.779 37.500 0.00 0.00 32.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 6.636454 AGATGGTTTTAACTGGAGGTATCA 57.364 37.500 0.00 0.00 0.00 2.15
229 2428 1.081892 CAGCGAACATACTGCAAGCT 58.918 50.000 0.00 0.00 37.60 3.74
388 2589 7.227156 GCCCTCATCTCCTTCATAATTTTCTA 58.773 38.462 0.00 0.00 0.00 2.10
456 2657 1.599518 CAGTTACCTTGGGCACGCA 60.600 57.895 0.00 0.00 0.00 5.24
568 2769 4.252971 TCTTTTCTAAGACCACCGTCAG 57.747 45.455 0.00 0.00 41.87 3.51
629 2830 1.766496 TGGTTTCTCTGTCCGGTTTCT 59.234 47.619 0.00 0.00 0.00 2.52
643 2844 1.077716 CCCTGGTCCGGATGGTTTC 60.078 63.158 7.81 0.00 36.30 2.78
797 2998 1.212688 ACATGCTTTGATGGATCGGGA 59.787 47.619 0.00 0.00 0.00 5.14
814 3015 2.383855 CGAGGAGGAGAAGAAGGACAT 58.616 52.381 0.00 0.00 0.00 3.06
858 3059 2.305052 ACTGGTTGTTAGGCTTAGGGTC 59.695 50.000 0.00 0.00 0.00 4.46
866 3067 2.429610 TCGGATCTACTGGTTGTTAGGC 59.570 50.000 0.00 0.00 0.00 3.93
1110 3321 2.186903 GCGAGCCGGAGATGGAAA 59.813 61.111 5.05 0.00 0.00 3.13
1528 5112 2.956194 CTGGATTTGCGCTGCACA 59.044 55.556 9.73 0.25 38.71 4.57
1798 5386 3.118956 ACTCCTGTAGCAGAGGAAAATCG 60.119 47.826 4.14 0.00 39.20 3.34
2532 6129 7.836842 TCAAACAGATGTATCTAGCACTAACA 58.163 34.615 0.00 0.00 34.85 2.41
2560 6157 7.631717 AATACTCCATCCTAAAAAGCTTGTC 57.368 36.000 0.00 0.00 0.00 3.18
2576 6173 5.738619 TTGAGCACAAGTCTAATACTCCA 57.261 39.130 0.00 0.00 37.50 3.86
2586 6183 8.709386 TTTATAAGAGAGATTGAGCACAAGTC 57.291 34.615 2.37 2.18 39.46 3.01
3055 6652 8.841300 ACAAGGTGTTTTCTCTTCTATCTTTTC 58.159 33.333 0.00 0.00 0.00 2.29
3135 6732 2.297701 GTGTCTGCTGGGAAAACTTGA 58.702 47.619 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.