Multiple sequence alignment - TraesCS5B01G116800

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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 TraesCS5B01G116800 chr5B 100.000 3544 0 0 1 3544 202893750 202890207 0.000000e+00 6545.0
1 TraesCS5B01G116800 chr5B 92.917 2386 127 9 602 2950 693958453 693956073 0.000000e+00 3432.0
2 TraesCS5B01G116800 chr5B 91.919 2376 129 16 602 2948 369340493 369338152 0.000000e+00 3265.0
3 TraesCS5B01G116800 chr5B 88.569 2397 219 23 602 2948 503241161 503238770 0.000000e+00 2857.0
4 TraesCS5B01G116800 chr5B 89.881 168 10 3 1 161 32128853 32129020 3.590000e-50 209.0
5 TraesCS5B01G116800 chr1D 95.735 3447 111 12 1 3415 209754587 209758029 0.000000e+00 5518.0
6 TraesCS5B01G116800 chr1D 94.495 218 11 1 1 218 374378751 374378535 5.670000e-88 335.0
7 TraesCS5B01G116800 chr1D 94.828 116 4 1 3429 3544 209758011 209758124 2.810000e-41 180.0
8 TraesCS5B01G116800 chr1D 88.525 122 14 0 3423 3544 20713692 20713813 7.930000e-32 148.0
9 TraesCS5B01G116800 chr1D 78.000 150 24 7 3182 3324 365974909 365974762 6.300000e-13 86.1
10 TraesCS5B01G116800 chr6B 93.128 2372 133 12 602 2948 643647842 643650208 0.000000e+00 3450.0
11 TraesCS5B01G116800 chr6B 92.596 2377 134 16 602 2950 643872921 643870559 0.000000e+00 3376.0
12 TraesCS5B01G116800 chr6B 92.275 2356 149 12 602 2928 664684777 664687128 0.000000e+00 3312.0
13 TraesCS5B01G116800 chr6B 91.702 2386 131 24 601 2953 711403937 711406288 0.000000e+00 3247.0
14 TraesCS5B01G116800 chr6B 97.391 115 3 0 3329 3443 133327624 133327738 2.790000e-46 196.0
15 TraesCS5B01G116800 chr6B 84.615 169 24 2 3160 3326 48433734 48433902 2.190000e-37 167.0
16 TraesCS5B01G116800 chr1B 91.592 2355 121 28 601 2925 566609126 566611433 0.000000e+00 3181.0
17 TraesCS5B01G116800 chr1B 92.591 2173 121 9 803 2948 311136412 311134253 0.000000e+00 3085.0
18 TraesCS5B01G116800 chr1B 90.614 863 70 6 602 1453 619144422 619143560 0.000000e+00 1134.0
19 TraesCS5B01G116800 chr1B 89.815 216 18 3 3329 3544 616814817 616814606 1.250000e-69 274.0
20 TraesCS5B01G116800 chr3B 89.933 2394 188 20 602 2948 200854333 200856720 0.000000e+00 3037.0
21 TraesCS5B01G116800 chr3B 89.850 2394 190 20 602 2948 200829424 200831811 0.000000e+00 3025.0
22 TraesCS5B01G116800 chr3B 91.008 2202 127 22 602 2776 771414590 771412433 0.000000e+00 2904.0
23 TraesCS5B01G116800 chr3B 87.435 191 18 2 3329 3519 574290742 574290926 7.710000e-52 215.0
24 TraesCS5B01G116800 chr3B 95.122 82 4 0 3463 3544 596828883 596828802 2.870000e-26 130.0
25 TraesCS5B01G116800 chr2A 88.959 2391 196 31 602 2948 768287679 768285313 0.000000e+00 2891.0
26 TraesCS5B01G116800 chr7B 91.708 2014 120 17 950 2948 639855661 639857642 0.000000e+00 2750.0
27 TraesCS5B01G116800 chr7B 84.375 224 28 4 1 221 606727842 606727623 2.770000e-51 213.0
28 TraesCS5B01G116800 chr7B 96.522 115 3 1 3329 3442 379427145 379427259 4.670000e-44 189.0
29 TraesCS5B01G116800 chr7B 83.333 210 27 3 1 209 328084384 328084182 1.680000e-43 187.0
30 TraesCS5B01G116800 chr7B 93.519 108 7 0 3329 3436 511353956 511353849 1.020000e-35 161.0
31 TraesCS5B01G116800 chr4B 90.583 1338 78 21 602 1908 429036069 429037389 0.000000e+00 1729.0
32 TraesCS5B01G116800 chr4B 90.323 124 12 0 3421 3544 52592656 52592779 2.830000e-36 163.0
33 TraesCS5B01G116800 chr4B 96.703 91 2 1 3327 3416 522341640 522341550 2.200000e-32 150.0
34 TraesCS5B01G116800 chr6A 94.884 215 11 0 1 215 20234564 20234350 1.580000e-88 337.0
35 TraesCS5B01G116800 chr3A 84.454 238 32 5 3089 3323 428461631 428461396 2.750000e-56 230.0
36 TraesCS5B01G116800 chr2B 85.965 228 11 2 1 228 28241849 28241643 1.280000e-54 224.0
37 TraesCS5B01G116800 chr2B 97.531 81 2 0 3329 3409 699278428 699278348 4.770000e-29 139.0
38 TraesCS5B01G116800 chr4A 95.652 115 5 0 3329 3443 675639153 675639267 6.040000e-43 185.0
39 TraesCS5B01G116800 chr4A 94.068 118 7 0 3427 3544 675654582 675654699 2.810000e-41 180.0
40 TraesCS5B01G116800 chr7D 88.889 108 12 0 3437 3544 638588837 638588944 2.220000e-27 134.0
41 TraesCS5B01G116800 chr2D 96.296 81 3 0 3464 3544 637337252 637337172 2.220000e-27 134.0
42 TraesCS5B01G116800 chr6D 88.889 99 6 3 1 96 99213223 99213127 2.240000e-22 117.0
43 TraesCS5B01G116800 chr5D 77.852 149 25 6 3182 3324 33670391 33670537 6.300000e-13 86.1


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 TraesCS5B01G116800 chr5B 202890207 202893750 3543 True 6545 6545 100.0000 1 3544 1 chr5B.!!$R1 3543
1 TraesCS5B01G116800 chr5B 693956073 693958453 2380 True 3432 3432 92.9170 602 2950 1 chr5B.!!$R4 2348
2 TraesCS5B01G116800 chr5B 369338152 369340493 2341 True 3265 3265 91.9190 602 2948 1 chr5B.!!$R2 2346
3 TraesCS5B01G116800 chr5B 503238770 503241161 2391 True 2857 2857 88.5690 602 2948 1 chr5B.!!$R3 2346
4 TraesCS5B01G116800 chr1D 209754587 209758124 3537 False 2849 5518 95.2815 1 3544 2 chr1D.!!$F2 3543
5 TraesCS5B01G116800 chr6B 643647842 643650208 2366 False 3450 3450 93.1280 602 2948 1 chr6B.!!$F3 2346
6 TraesCS5B01G116800 chr6B 643870559 643872921 2362 True 3376 3376 92.5960 602 2950 1 chr6B.!!$R1 2348
7 TraesCS5B01G116800 chr6B 664684777 664687128 2351 False 3312 3312 92.2750 602 2928 1 chr6B.!!$F4 2326
8 TraesCS5B01G116800 chr6B 711403937 711406288 2351 False 3247 3247 91.7020 601 2953 1 chr6B.!!$F5 2352
9 TraesCS5B01G116800 chr1B 566609126 566611433 2307 False 3181 3181 91.5920 601 2925 1 chr1B.!!$F1 2324
10 TraesCS5B01G116800 chr1B 311134253 311136412 2159 True 3085 3085 92.5910 803 2948 1 chr1B.!!$R1 2145
11 TraesCS5B01G116800 chr1B 619143560 619144422 862 True 1134 1134 90.6140 602 1453 1 chr1B.!!$R3 851
12 TraesCS5B01G116800 chr3B 200854333 200856720 2387 False 3037 3037 89.9330 602 2948 1 chr3B.!!$F2 2346
13 TraesCS5B01G116800 chr3B 200829424 200831811 2387 False 3025 3025 89.8500 602 2948 1 chr3B.!!$F1 2346
14 TraesCS5B01G116800 chr3B 771412433 771414590 2157 True 2904 2904 91.0080 602 2776 1 chr3B.!!$R2 2174
15 TraesCS5B01G116800 chr2A 768285313 768287679 2366 True 2891 2891 88.9590 602 2948 1 chr2A.!!$R1 2346
16 TraesCS5B01G116800 chr7B 639855661 639857642 1981 False 2750 2750 91.7080 950 2948 1 chr7B.!!$F2 1998
17 TraesCS5B01G116800 chr4B 429036069 429037389 1320 False 1729 1729 90.5830 602 1908 1 chr4B.!!$F2 1306

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
599 602 1.021390 CAACCATGGACGGAGAGCAC 61.021 60.000 21.47 0.0 0.00 4.40 F
1217 1306 0.430196 AGGGGAATAGGGGGAAAGGT 59.570 55.000 0.00 0.0 0.00 3.50 F
1661 1770 1.468520 CACGGCATTGGATTCGTTCTT 59.531 47.619 0.00 0.0 33.31 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1961 2103 0.178995 TGGAGTCAGGCATTGCACAA 60.179 50.0 11.39 0.0 0.0 3.33 R
2480 2627 0.612744 TGACGACCTCAATGCCATCA 59.387 50.0 0.00 0.0 0.0 3.07 R
3462 3639 0.031917 TTACGGGGTGGCCTATCTCA 60.032 55.0 3.32 0.0 0.0 3.27 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
171 172 1.349688 TCGGATGGCCACAAACTAGTT 59.650 47.619 8.16 1.12 0.00 2.24
303 304 2.436115 GGCCGGTCCTGCACTAAC 60.436 66.667 1.90 0.00 0.00 2.34
380 381 7.121272 GCGCTTTTATACTTATCGCTTTTGTA 58.879 34.615 0.00 0.00 38.29 2.41
410 411 2.833631 TGTCGTCTTTTCTCTTCCCC 57.166 50.000 0.00 0.00 0.00 4.81
417 418 4.244066 GTCTTTTCTCTTCCCCGTTCTAC 58.756 47.826 0.00 0.00 0.00 2.59
510 513 2.338785 GCTTTGAGCTGACAGCCCC 61.339 63.158 23.74 16.00 43.77 5.80
599 602 1.021390 CAACCATGGACGGAGAGCAC 61.021 60.000 21.47 0.00 0.00 4.40
840 845 2.548295 GCCACGTTGCTTCCCGAAA 61.548 57.895 4.03 0.00 0.00 3.46
953 968 1.229209 ACCACCGGACTCCATCACT 60.229 57.895 9.46 0.00 0.00 3.41
1044 1061 5.906073 TCTTCGACATGAATGCTAGATTCA 58.094 37.500 15.42 15.42 41.59 2.57
1217 1306 0.430196 AGGGGAATAGGGGGAAAGGT 59.570 55.000 0.00 0.00 0.00 3.50
1244 1333 4.082523 CGGACACCGGCTGACCAT 62.083 66.667 19.27 0.00 44.15 3.55
1279 1368 2.842462 TGTGGAGTGGCTGGTCGT 60.842 61.111 0.00 0.00 0.00 4.34
1517 1609 6.127140 GGTCATTAGGAGCAAAGTAGGTCTTA 60.127 42.308 0.00 0.00 43.54 2.10
1661 1770 1.468520 CACGGCATTGGATTCGTTCTT 59.531 47.619 0.00 0.00 33.31 2.52
1668 1794 2.787473 TGGATTCGTTCTTCATGGCT 57.213 45.000 0.00 0.00 0.00 4.75
1669 1795 3.904800 TGGATTCGTTCTTCATGGCTA 57.095 42.857 0.00 0.00 0.00 3.93
1670 1796 4.214986 TGGATTCGTTCTTCATGGCTAA 57.785 40.909 0.00 0.00 0.00 3.09
1871 1999 1.637035 GGTGGGTAAATAGTGGTGGGT 59.363 52.381 0.00 0.00 0.00 4.51
1961 2103 5.259632 AGCTCTTGAATTAGCCATGAACTT 58.740 37.500 0.00 0.00 39.64 2.66
2321 2467 2.682856 GTTCAAGCTCAGGAACAACACA 59.317 45.455 16.52 0.00 42.23 3.72
2322 2468 3.213206 TCAAGCTCAGGAACAACACAT 57.787 42.857 0.00 0.00 0.00 3.21
2480 2627 5.089970 TCAAGGTCATCATCTTCGACAAT 57.910 39.130 0.00 0.00 0.00 2.71
2688 2857 3.282885 TGATGTGTGTTGCCAAAGTGTA 58.717 40.909 0.00 0.00 0.00 2.90
2841 3016 0.039472 TAAGAGGGCATGCAGGCAAA 59.961 50.000 26.25 0.00 46.44 3.68
2932 3107 1.582968 CGGGTACTGTAGCACACGT 59.417 57.895 17.71 0.00 36.82 4.49
2953 3128 1.460273 AACCAAACACGCCCATGGTC 61.460 55.000 11.73 0.00 45.15 4.02
2957 3132 2.632602 AAACACGCCCATGGTCACCA 62.633 55.000 11.73 0.00 38.19 4.17
3000 3175 2.281208 CGCTCCGGGAAACAACCA 60.281 61.111 0.00 0.00 0.00 3.67
3016 3191 2.712539 CAGCGTCACCGTTTTGCA 59.287 55.556 0.00 0.00 36.15 4.08
3066 3242 1.066573 ACCAGCATCACACTCTGCTAC 60.067 52.381 0.00 0.00 46.62 3.58
3075 3251 2.166050 CACACTCTGCTACAGCTCAGAT 59.834 50.000 3.53 0.00 42.66 2.90
3106 3282 2.291465 CCAAGCATCACCATGGAATACG 59.709 50.000 21.47 3.60 34.82 3.06
3157 3333 2.825836 CGAACCTGCATCCCTGGC 60.826 66.667 0.00 0.00 36.07 4.85
3239 3415 3.466836 GGATTTGCTACATCCATCACGA 58.533 45.455 0.00 0.00 40.21 4.35
3259 3435 1.355916 GGAGCTGCGACCTACTACG 59.644 63.158 0.00 0.00 0.00 3.51
3303 3480 4.369182 CGTCCTCGGATTTTGCTAATACT 58.631 43.478 0.00 0.00 0.00 2.12
3306 3483 5.234543 GTCCTCGGATTTTGCTAATACTGAC 59.765 44.000 0.00 0.00 0.00 3.51
3317 3494 7.525688 TTGCTAATACTGACGAGAGATTTTG 57.474 36.000 0.00 0.00 0.00 2.44
3365 3542 9.860650 ATTGTAGCCTTATTGTGTAATCCATAA 57.139 29.630 0.00 0.00 0.00 1.90
3459 3636 9.696917 ATATATATATCTGTGTGTGTGTGTGTG 57.303 33.333 0.00 0.00 0.00 3.82
3460 3637 2.401583 ATCTGTGTGTGTGTGTGTGT 57.598 45.000 0.00 0.00 0.00 3.72
3461 3638 1.437625 TCTGTGTGTGTGTGTGTGTG 58.562 50.000 0.00 0.00 0.00 3.82
3462 3639 1.155889 CTGTGTGTGTGTGTGTGTGT 58.844 50.000 0.00 0.00 0.00 3.72
3463 3640 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3464 3641 1.152510 GTGTGTGTGTGTGTGTGTGA 58.847 50.000 0.00 0.00 0.00 3.58
3478 3655 2.063979 TGTGAGATAGGCCACCCCG 61.064 63.158 5.01 0.00 39.21 5.73
3511 3688 1.146152 CCAGTTCCCCCAAAACCTACA 59.854 52.381 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
171 172 9.368416 AGACTACTGATATTTGCTACCTATCAA 57.632 33.333 0.00 0.00 32.93 2.57
380 381 6.369065 AGAGAAAAGACGACAAAAGCGATAAT 59.631 34.615 0.00 0.00 0.00 1.28
410 411 1.274447 AGAGGGGAAAACGGTAGAACG 59.726 52.381 0.00 0.00 40.31 3.95
417 418 1.478916 GAGAGAGAGAGGGGAAAACGG 59.521 57.143 0.00 0.00 0.00 4.44
501 504 2.605607 CCTCCATGTGGGGCTGTCA 61.606 63.158 0.00 0.00 37.22 3.58
510 513 2.821366 GCTCGCCACCTCCATGTG 60.821 66.667 0.00 0.00 35.98 3.21
536 539 0.036765 TACCCTAACACCGCTTGCAG 60.037 55.000 0.00 0.00 0.00 4.41
599 602 4.639171 GCAACCAAACACGCCCCG 62.639 66.667 0.00 0.00 0.00 5.73
643 646 1.497309 AACAGGCCGAATCCTTCCCA 61.497 55.000 0.00 0.00 33.25 4.37
825 830 1.441732 GGTGTTTCGGGAAGCAACGT 61.442 55.000 0.00 0.00 33.43 3.99
840 845 2.829720 TGAGGCTAATAACTGTCGGTGT 59.170 45.455 0.00 0.00 0.00 4.16
925 940 0.685660 GTCCGGTGGTCTTCTTCCTT 59.314 55.000 0.00 0.00 0.00 3.36
1044 1061 2.065993 CGAATCTATCGCCGTGGATT 57.934 50.000 0.00 0.00 45.89 3.01
1069 1086 3.334891 CCCCATTCCCGTCCACCA 61.335 66.667 0.00 0.00 0.00 4.17
1217 1306 1.661480 CGGTGTCCGTTCTGTACCA 59.339 57.895 0.00 0.00 42.73 3.25
1336 1428 2.033602 TCGACTCTGCCGAGGACA 59.966 61.111 10.11 0.00 41.71 4.02
1517 1609 4.373156 AAGGAAGAAGTGGCACAAGTAT 57.627 40.909 21.41 1.26 44.16 2.12
1668 1794 3.849911 CTCGAACTTCAGCTCCATGTTA 58.150 45.455 0.00 0.00 0.00 2.41
1669 1795 2.693069 CTCGAACTTCAGCTCCATGTT 58.307 47.619 0.00 0.00 0.00 2.71
1670 1796 1.674221 GCTCGAACTTCAGCTCCATGT 60.674 52.381 0.00 0.00 32.48 3.21
1961 2103 0.178995 TGGAGTCAGGCATTGCACAA 60.179 50.000 11.39 0.00 0.00 3.33
2159 2303 2.975248 TTGCGGCGCTTGTTGCTA 60.975 55.556 33.26 6.83 40.11 3.49
2321 2467 1.203441 TCACCTTCCAGGAGCAGCAT 61.203 55.000 0.00 0.00 37.67 3.79
2322 2468 1.842920 TCACCTTCCAGGAGCAGCA 60.843 57.895 0.00 0.00 37.67 4.41
2342 2488 2.093973 CCTACCGTTCATCAGCTTGACT 60.094 50.000 0.00 0.00 0.00 3.41
2372 2519 2.616458 GGTGGCCCAACCCTGATCT 61.616 63.158 0.00 0.00 37.83 2.75
2480 2627 0.612744 TGACGACCTCAATGCCATCA 59.387 50.000 0.00 0.00 0.00 3.07
2638 2804 6.674037 GCACAACAGAGTATAAACAGAGCATG 60.674 42.308 0.00 0.00 0.00 4.06
2932 3107 1.459455 CCATGGGCGTGTTTGGTTGA 61.459 55.000 2.85 0.00 0.00 3.18
3016 3191 2.667318 CGACGCGGTGAAGCATGTT 61.667 57.895 12.47 0.00 36.85 2.71
3066 3242 3.200593 GGGCGTGCATCTGAGCTG 61.201 66.667 0.00 0.00 34.99 4.24
3106 3282 1.907936 AGCTAGATGGATGGATGGAGC 59.092 52.381 0.00 0.00 0.00 4.70
3141 3317 2.825836 CGCCAGGGATGCAGGTTC 60.826 66.667 0.00 0.00 0.00 3.62
3160 3336 1.457823 TTTGGCTCAGCTGGTTGCAG 61.458 55.000 15.13 4.27 45.94 4.41
3239 3415 1.033574 GTAGTAGGTCGCAGCTCCAT 58.966 55.000 6.32 0.00 0.00 3.41
3285 3462 5.041287 TCGTCAGTATTAGCAAAATCCGAG 58.959 41.667 0.00 0.00 0.00 4.63
3299 3476 6.208988 TGTAGCAAAATCTCTCGTCAGTAT 57.791 37.500 0.00 0.00 0.00 2.12
3303 3480 5.724328 AGAATGTAGCAAAATCTCTCGTCA 58.276 37.500 0.00 0.00 0.00 4.35
3306 3483 9.684448 TCTAATAGAATGTAGCAAAATCTCTCG 57.316 33.333 0.00 0.00 0.00 4.04
3333 3510 8.951787 TTACACAATAAGGCTACAATACGAAT 57.048 30.769 0.00 0.00 0.00 3.34
3336 3513 7.439955 TGGATTACACAATAAGGCTACAATACG 59.560 37.037 0.00 0.00 0.00 3.06
3365 3542 9.154632 TGTCATACAAGTCCTATACCAATATGT 57.845 33.333 0.00 0.00 0.00 2.29
3433 3610 9.696917 CACACACACACACACAGATATATATAT 57.303 33.333 4.86 4.86 0.00 0.86
3443 3620 1.136000 CACACACACACACACACACAG 60.136 52.381 0.00 0.00 0.00 3.66
3459 3636 1.527370 GGGGTGGCCTATCTCACAC 59.473 63.158 3.32 0.00 36.63 3.82
3460 3637 2.063979 CGGGGTGGCCTATCTCACA 61.064 63.158 3.32 0.00 35.74 3.58
3461 3638 0.757935 TACGGGGTGGCCTATCTCAC 60.758 60.000 3.32 0.00 0.00 3.51
3462 3639 0.031917 TTACGGGGTGGCCTATCTCA 60.032 55.000 3.32 0.00 0.00 3.27
3463 3640 1.070289 CTTTACGGGGTGGCCTATCTC 59.930 57.143 3.32 0.00 0.00 2.75
3464 3641 1.129058 CTTTACGGGGTGGCCTATCT 58.871 55.000 3.32 0.00 0.00 1.98
3478 3655 2.160205 GGAACTGGCTCAACCCTTTAC 58.840 52.381 0.00 0.00 37.83 2.01
3511 3688 8.019656 AGGTTAGACTCGATACCATGTAAAAT 57.980 34.615 0.00 0.00 33.02 1.82


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

AutoCloner maintained by Alex Coulton.