Multiple sequence alignment - TraesCS5B01G072700

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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 TraesCS5B01G072700 chr5B 100.000 3454 0 0 1 3454 85116401 85119854 0.000000e+00 6379.0
1 TraesCS5B01G072700 chr5B 96.548 3273 85 10 202 3454 85178696 85181960 0.000000e+00 5393.0
2 TraesCS5B01G072700 chr5B 86.286 700 68 9 3 677 85285425 85286121 0.000000e+00 736.0
3 TraesCS5B01G072700 chr5B 94.975 199 10 0 1 199 85147848 85148046 2.590000e-81 313.0
4 TraesCS5B01G072700 chr5B 83.974 312 45 3 406 715 563936085 563936393 9.370000e-76 294.0
5 TraesCS5B01G072700 chr5B 77.564 468 88 10 2123 2579 88781313 88781774 2.040000e-67 267.0
6 TraesCS5B01G072700 chr5B 85.714 217 22 5 410 617 563864275 563864491 1.610000e-53 220.0
7 TraesCS5B01G072700 chr5D 96.797 3465 90 10 1 3454 76756456 76753002 0.000000e+00 5764.0
8 TraesCS5B01G072700 chr5D 95.412 3487 108 21 3 3454 76692229 76688760 0.000000e+00 5505.0
9 TraesCS5B01G072700 chr5D 82.866 321 41 11 406 715 459690010 459690327 3.400000e-70 276.0
10 TraesCS5B01G072700 chr5D 76.253 459 86 18 2123 2570 79106214 79106660 4.490000e-54 222.0
11 TraesCS5B01G072700 chr5D 85.922 206 20 4 421 617 459577466 459577671 9.710000e-51 211.0
12 TraesCS5B01G072700 chr5D 85.315 143 12 5 760 899 459581952 459582088 4.650000e-29 139.0
13 TraesCS5B01G072700 chr5D 96.226 53 2 0 1 53 76674780 76674728 1.710000e-13 87.9
14 TraesCS5B01G072700 chr5A 92.037 3328 177 33 174 3454 72230536 72227250 0.000000e+00 4597.0
15 TraesCS5B01G072700 chr5A 94.513 1877 83 9 1587 3454 72388938 72387073 0.000000e+00 2878.0
16 TraesCS5B01G072700 chr5A 93.110 1553 88 9 1911 3454 72330698 72329156 0.000000e+00 2257.0
17 TraesCS5B01G072700 chr5A 94.286 1120 48 4 783 1890 72331807 72330692 0.000000e+00 1700.0
18 TraesCS5B01G072700 chr5A 87.745 1428 102 30 174 1558 72390333 72388936 0.000000e+00 1600.0
19 TraesCS5B01G072700 chr5A 86.119 353 25 7 783 1115 72260105 72259757 3.280000e-95 359.0
20 TraesCS5B01G072700 chr5A 76.793 474 87 15 2123 2579 75050051 75050518 9.580000e-61 244.0
21 TraesCS5B01G072700 chr7D 94.828 58 3 0 2933 2990 60673904 60673847 1.320000e-14 91.6
22 TraesCS5B01G072700 chr7D 94.828 58 3 0 2933 2990 576283706 576283649 1.320000e-14 91.6
23 TraesCS5B01G072700 chr2B 85.000 80 7 4 2933 3012 416830043 416829969 3.700000e-10 76.8
24 TraesCS5B01G072700 chr2B 100.000 30 0 0 717 746 21856951 21856922 4.820000e-04 56.5
25 TraesCS5B01G072700 chr2A 100.000 30 0 0 717 746 13878746 13878775 4.820000e-04 56.5


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 TraesCS5B01G072700 chr5B 85116401 85119854 3453 False 6379.0 6379 100.000 1 3454 1 chr5B.!!$F1 3453
1 TraesCS5B01G072700 chr5B 85178696 85181960 3264 False 5393.0 5393 96.548 202 3454 1 chr5B.!!$F3 3252
2 TraesCS5B01G072700 chr5B 85285425 85286121 696 False 736.0 736 86.286 3 677 1 chr5B.!!$F4 674
3 TraesCS5B01G072700 chr5D 76753002 76756456 3454 True 5764.0 5764 96.797 1 3454 1 chr5D.!!$R3 3453
4 TraesCS5B01G072700 chr5D 76688760 76692229 3469 True 5505.0 5505 95.412 3 3454 1 chr5D.!!$R2 3451
5 TraesCS5B01G072700 chr5A 72227250 72230536 3286 True 4597.0 4597 92.037 174 3454 1 chr5A.!!$R1 3280
6 TraesCS5B01G072700 chr5A 72387073 72390333 3260 True 2239.0 2878 91.129 174 3454 2 chr5A.!!$R4 3280
7 TraesCS5B01G072700 chr5A 72329156 72331807 2651 True 1978.5 2257 93.698 783 3454 2 chr5A.!!$R3 2671

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
414 454 1.296056 GAAAACTGGCGCCGCTTCTA 61.296 55.0 23.90 0.87 0.00 2.10 F
1400 1485 0.817634 CCACTCTTGGCCACGAACAA 60.818 55.0 13.63 0.00 35.56 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2071 2196 1.021968 GCGCGGTCCCTTCATAAAAT 58.978 50.0 8.83 0.0 0.0 1.82 R
3095 3232 0.465642 GATTTCTTACCCAGGGCCGG 60.466 60.0 4.91 0.0 0.0 6.13 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
63 64 8.863872 AAGCCTATTTAACATGTGTTCTAGTT 57.136 30.769 0.00 0.00 39.31 2.24
81 82 2.771372 AGTTTTGGCCCATTCACAACTT 59.229 40.909 0.00 0.00 33.07 2.66
123 124 4.214119 TGTTGCTCAAAGATCTGCTGTTAC 59.786 41.667 0.00 0.00 0.00 2.50
267 279 2.620251 CCGGATTCTTGGCTATGTGA 57.380 50.000 0.00 0.00 0.00 3.58
336 348 2.846827 AGAACTAGATTGTTGGGGAGGG 59.153 50.000 0.00 0.00 0.00 4.30
356 368 4.471747 AGGGGATGAAAAGTAGAGAGGAAC 59.528 45.833 0.00 0.00 0.00 3.62
385 402 7.556275 GGAGGAACCAAGTTGACATGAAATATA 59.444 37.037 3.87 0.00 38.79 0.86
414 454 1.296056 GAAAACTGGCGCCGCTTCTA 61.296 55.000 23.90 0.87 0.00 2.10
532 580 9.333497 CATAAAATGTCAGAACACTGTAACATG 57.667 33.333 0.00 0.00 38.48 3.21
644 702 7.600752 ACAAACTAAAACAAACTAAAGCTGCAA 59.399 29.630 1.02 0.00 0.00 4.08
647 705 7.992008 ACTAAAACAAACTAAAGCTGCAACTA 58.008 30.769 1.02 0.00 0.00 2.24
778 839 2.830475 GGGGGACGCTATTGACCTA 58.170 57.895 0.00 0.00 38.67 3.08
1023 1084 2.517875 GCCGGCGGTAGTAGGAGA 60.518 66.667 28.82 0.00 0.00 3.71
1285 1370 1.550327 TCCTCTCAACATCGACTGCT 58.450 50.000 0.00 0.00 0.00 4.24
1350 1435 3.016736 ACAACGCATAATTTCCTCCCAG 58.983 45.455 0.00 0.00 0.00 4.45
1400 1485 0.817634 CCACTCTTGGCCACGAACAA 60.818 55.000 13.63 0.00 35.56 2.83
1748 1864 3.472652 TCCGGATCAATTCATTTACCCG 58.527 45.455 0.00 0.00 35.88 5.28
1787 1903 2.287427 GCAATTCTTCGCCAGATCCATG 60.287 50.000 0.00 0.00 0.00 3.66
2071 2196 8.554835 TTATTGTCTAACGTTGGATTTCATGA 57.445 30.769 17.77 0.00 0.00 3.07
2144 2269 5.122869 GTGCAGAATCAAGTCTTTGCATCTA 59.877 40.000 11.10 0.00 31.51 1.98
2342 2467 0.976641 AGTGCGAGAAATCTGGGACA 59.023 50.000 16.75 0.00 43.39 4.02
2394 2519 6.371595 ACCTTCTCAGATCTTTTGACATCT 57.628 37.500 0.00 0.00 0.00 2.90
2831 2961 3.392285 AGTTAACCGTACCCTCAAAAGGT 59.608 43.478 0.88 0.00 41.59 3.50
2914 3044 8.882736 CAGCGAATTCATATAGCCATAATGTAA 58.117 33.333 6.22 0.00 0.00 2.41
3092 3229 8.620416 GGAACATAAATAGTCATGTAATGCACA 58.380 33.333 0.00 0.00 46.21 4.57
3095 3232 9.787532 ACATAAATAGTCATGTAATGCACAAAC 57.212 29.630 0.00 0.00 46.21 2.93
3101 3238 1.214325 GTAATGCACAAACCGGCCC 59.786 57.895 0.00 0.00 0.00 5.80
3198 3337 7.839680 AAAAGATAAAGTGGTTGTCTTCCAT 57.160 32.000 0.00 0.00 44.36 3.41
3328 3468 6.712114 TTCCTAGCTAGATGAGGTCTATCT 57.288 41.667 22.70 0.00 38.71 1.98
3379 3519 6.959639 ATTCAACAATTGAGTGGTAACTGT 57.040 33.333 13.59 0.00 41.38 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 3.571590 AGTAAGTTGTGAATGGGCCAAA 58.428 40.909 11.89 0.00 0.00 3.28
81 82 9.587772 GAGCAACATTATTCTAGAAAGTGAGTA 57.412 33.333 9.71 0.00 0.00 2.59
123 124 4.695455 CAGTGGTTGTAGACATTAAGTGGG 59.305 45.833 0.00 0.00 0.00 4.61
267 279 4.042187 AGACCATCAACCTAAGTGAAGCTT 59.958 41.667 0.00 0.00 41.05 3.74
336 348 4.865365 CACGTTCCTCTCTACTTTTCATCC 59.135 45.833 0.00 0.00 0.00 3.51
385 402 3.057526 GGCGCCAGTTTTCTATTTCAGTT 60.058 43.478 24.80 0.00 0.00 3.16
414 454 5.012458 TGGCGATTCTATGAGAAGGATCATT 59.988 40.000 0.00 0.00 40.40 2.57
532 580 1.630878 AGTCAGGAATGAGGGACCAAC 59.369 52.381 0.00 0.00 0.00 3.77
623 681 8.342634 TCTAGTTGCAGCTTTAGTTTGTTTTAG 58.657 33.333 8.85 0.00 0.00 1.85
647 705 7.615365 TGCTTCCAACAAAAAGGATATACATCT 59.385 33.333 0.00 0.00 33.10 2.90
1023 1084 1.546476 CTCTTCCTGGTAGTCGCACTT 59.454 52.381 0.00 0.00 0.00 3.16
1285 1370 2.459060 TTAGAACGGGCGATTTCACA 57.541 45.000 0.00 0.00 0.00 3.58
1400 1485 2.185350 CGGCAGCATCGTTCTCCT 59.815 61.111 0.00 0.00 0.00 3.69
1748 1864 2.346803 TGCCGACTTCAATGCTTCTAC 58.653 47.619 0.00 0.00 0.00 2.59
1787 1903 1.810959 GATGATGAGCTCCTCCATGC 58.189 55.000 12.15 3.32 0.00 4.06
1886 2002 1.359168 ACAACCTAGGGACTCCAACC 58.641 55.000 14.81 0.00 41.75 3.77
2057 2182 7.436080 CCCTTCATAAAATCATGAAATCCAACG 59.564 37.037 0.00 0.00 42.73 4.10
2071 2196 1.021968 GCGCGGTCCCTTCATAAAAT 58.978 50.000 8.83 0.00 0.00 1.82
2144 2269 5.983720 GTCCAAACATAGAGTACGCATACAT 59.016 40.000 0.00 0.00 33.30 2.29
2342 2467 4.201930 TGTTTACGACGCCACAAATTCTTT 60.202 37.500 0.00 0.00 0.00 2.52
2814 2944 1.426751 TCACCTTTTGAGGGTACGGT 58.573 50.000 0.00 0.00 35.00 4.83
2815 2945 2.554370 TTCACCTTTTGAGGGTACGG 57.446 50.000 0.00 0.00 34.94 4.02
2816 2946 4.069304 TGATTTCACCTTTTGAGGGTACG 58.931 43.478 0.00 0.00 34.94 3.67
2817 2947 6.183360 TGTTTGATTTCACCTTTTGAGGGTAC 60.183 38.462 0.00 0.00 34.94 3.34
2818 2948 5.894393 TGTTTGATTTCACCTTTTGAGGGTA 59.106 36.000 0.00 0.00 34.94 3.69
2831 2961 7.993821 TTTGCGTATCTTTTGTTTGATTTCA 57.006 28.000 0.00 0.00 0.00 2.69
2991 3124 6.237901 AGGAAAACAAGTGAAAAGGCTTTTT 58.762 32.000 24.79 6.20 39.16 1.94
2992 3125 5.804639 AGGAAAACAAGTGAAAAGGCTTTT 58.195 33.333 24.33 24.33 35.12 2.27
3092 3229 1.428718 TTCTTACCCAGGGCCGGTTT 61.429 55.000 4.91 0.53 34.66 3.27
3093 3230 1.428718 TTTCTTACCCAGGGCCGGTT 61.429 55.000 4.91 0.00 34.66 4.44
3094 3231 1.212250 ATTTCTTACCCAGGGCCGGT 61.212 55.000 4.91 8.25 37.40 5.28
3095 3232 0.465642 GATTTCTTACCCAGGGCCGG 60.466 60.000 4.91 0.00 0.00 6.13
3101 3238 5.587388 ATGTGCAATGATTTCTTACCCAG 57.413 39.130 0.00 0.00 0.00 4.45
3424 3564 5.559035 CGTTCAGCAACCTTTAGCTATATGC 60.559 44.000 0.00 1.63 39.50 3.14


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

AutoCloner maintained by Alex Coulton.