Multiple sequence alignment - TraesCS4D01G202700

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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 TraesCS4D01G202700 chr4D 100.000 3800 0 0 1 3800 349449557 349445758 0.000000e+00 7018.0
1 TraesCS4D01G202700 chr3A 97.414 2591 61 3 1216 3800 382440464 382437874 0.000000e+00 4409.0
2 TraesCS4D01G202700 chr3A 90.079 2268 125 36 1572 3800 216716395 216714189 0.000000e+00 2850.0
3 TraesCS4D01G202700 chr3A 96.897 709 22 0 510 1218 382441264 382440556 0.000000e+00 1188.0
4 TraesCS4D01G202700 chr3A 84.706 255 25 10 3024 3278 369298896 369299136 3.790000e-60 243.0
5 TraesCS4D01G202700 chr3A 94.393 107 5 1 1 106 110684704 110684598 3.040000e-36 163.0
6 TraesCS4D01G202700 chr3A 86.014 143 15 4 3366 3506 413684507 413684646 8.500000e-32 148.0
7 TraesCS4D01G202700 chr3A 97.059 68 2 0 106 173 110684559 110684492 8.630000e-22 115.0
8 TraesCS4D01G202700 chr1A 97.263 2594 57 9 1216 3800 255203740 255206328 0.000000e+00 4385.0
9 TraesCS4D01G202700 chr1A 97.643 2079 42 4 1727 3800 272648540 272650616 0.000000e+00 3561.0
10 TraesCS4D01G202700 chr1A 96.779 2080 58 6 1727 3800 179451962 179454038 0.000000e+00 3461.0
11 TraesCS4D01G202700 chr1A 96.327 1933 65 4 1216 3143 423169899 423167968 0.000000e+00 3171.0
12 TraesCS4D01G202700 chr1A 97.129 1219 33 2 1 1218 255202431 255203648 0.000000e+00 2056.0
13 TraesCS4D01G202700 chr1A 94.922 709 36 0 510 1218 423107280 423106572 0.000000e+00 1110.0
14 TraesCS4D01G202700 chr1A 94.781 709 37 0 510 1218 423234394 423233686 0.000000e+00 1105.0
15 TraesCS4D01G202700 chr1A 94.774 708 37 0 510 1217 423296283 423295576 0.000000e+00 1103.0
16 TraesCS4D01G202700 chr1A 94.640 709 38 0 510 1218 423170699 423169991 0.000000e+00 1099.0
17 TraesCS4D01G202700 chr1A 97.143 35 0 1 1211 1245 435569071 435569038 1.470000e-04 58.4
18 TraesCS4D01G202700 chr4A 96.602 2590 70 10 1216 3800 138466563 138463987 0.000000e+00 4279.0
19 TraesCS4D01G202700 chr4A 96.394 2080 69 2 1727 3800 481731591 481729512 0.000000e+00 3421.0
20 TraesCS4D01G202700 chr4A 91.239 993 75 7 230 1218 146401359 146402343 0.000000e+00 1341.0
21 TraesCS4D01G202700 chr4A 86.071 560 42 5 230 781 337462697 337463228 1.530000e-158 569.0
22 TraesCS4D01G202700 chr7A 97.114 2079 51 5 1727 3800 269297622 269299696 0.000000e+00 3498.0
23 TraesCS4D01G202700 chr7A 88.732 284 31 1 3367 3649 17691692 17691409 2.810000e-91 346.0
24 TraesCS4D01G202700 chr5A 93.569 2239 121 17 1572 3800 178779000 178781225 0.000000e+00 3315.0
25 TraesCS4D01G202700 chr5A 90.411 146 13 1 1568 1713 425253889 425254033 1.390000e-44 191.0
26 TraesCS4D01G202700 chr3B 93.044 992 63 4 230 1218 309750068 309751056 0.000000e+00 1445.0
27 TraesCS4D01G202700 chr6A 91.304 989 75 6 234 1218 279746795 279747776 0.000000e+00 1339.0
28 TraesCS4D01G202700 chr1B 91.908 173 5 4 1 171 116770953 116770788 2.280000e-57 233.0
29 TraesCS4D01G202700 chr1B 89.017 173 10 4 1 171 398647985 398648150 4.980000e-49 206.0
30 TraesCS4D01G202700 chr1B 88.571 140 12 4 3369 3506 170566783 170566646 2.350000e-37 167.0
31 TraesCS4D01G202700 chr1B 98.305 59 1 0 173 231 398648204 398648262 1.870000e-18 104.0
32 TraesCS4D01G202700 chr4B 91.329 173 9 5 1 171 178350862 178351030 8.210000e-57 231.0
33 TraesCS4D01G202700 chr4B 93.220 59 2 1 173 231 178351084 178351140 6.760000e-13 86.1
34 TraesCS4D01G202700 chrUn 94.483 145 7 1 1211 1355 300810237 300810380 4.940000e-54 222.0
35 TraesCS4D01G202700 chrUn 93.077 130 8 1 1444 1573 300810380 300810508 5.010000e-44 189.0
36 TraesCS4D01G202700 chr7B 93.458 107 6 1 1 106 392310750 392310856 1.410000e-34 158.0
37 TraesCS4D01G202700 chr7B 92.523 107 7 1 1 106 283700855 283700961 6.570000e-33 152.0
38 TraesCS4D01G202700 chr7B 98.529 68 1 0 106 173 283701000 283701067 1.850000e-23 121.0
39 TraesCS4D01G202700 chr7B 98.529 68 1 0 106 173 392310895 392310962 1.850000e-23 121.0
40 TraesCS4D01G202700 chr7B 95.385 65 3 0 109 173 74389909 74389973 1.870000e-18 104.0
41 TraesCS4D01G202700 chr7B 98.305 59 1 0 173 231 283701103 283701161 1.870000e-18 104.0
42 TraesCS4D01G202700 chr7B 97.500 40 1 0 1 40 283700804 283700843 6.810000e-08 69.4
43 TraesCS4D01G202700 chr7B 97.368 38 1 0 1 38 392310699 392310736 8.810000e-07 65.8
44 TraesCS4D01G202700 chr6B 85.263 95 13 1 3558 3652 94002011 94001918 3.120000e-16 97.1


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 TraesCS4D01G202700 chr4D 349445758 349449557 3799 True 7018.0 7018 100.0000 1 3800 1 chr4D.!!$R1 3799
1 TraesCS4D01G202700 chr3A 216714189 216716395 2206 True 2850.0 2850 90.0790 1572 3800 1 chr3A.!!$R1 2228
2 TraesCS4D01G202700 chr3A 382437874 382441264 3390 True 2798.5 4409 97.1555 510 3800 2 chr3A.!!$R3 3290
3 TraesCS4D01G202700 chr1A 272648540 272650616 2076 False 3561.0 3561 97.6430 1727 3800 1 chr1A.!!$F2 2073
4 TraesCS4D01G202700 chr1A 179451962 179454038 2076 False 3461.0 3461 96.7790 1727 3800 1 chr1A.!!$F1 2073
5 TraesCS4D01G202700 chr1A 255202431 255206328 3897 False 3220.5 4385 97.1960 1 3800 2 chr1A.!!$F3 3799
6 TraesCS4D01G202700 chr1A 423167968 423170699 2731 True 2135.0 3171 95.4835 510 3143 2 chr1A.!!$R5 2633
7 TraesCS4D01G202700 chr1A 423106572 423107280 708 True 1110.0 1110 94.9220 510 1218 1 chr1A.!!$R1 708
8 TraesCS4D01G202700 chr1A 423233686 423234394 708 True 1105.0 1105 94.7810 510 1218 1 chr1A.!!$R2 708
9 TraesCS4D01G202700 chr1A 423295576 423296283 707 True 1103.0 1103 94.7740 510 1217 1 chr1A.!!$R3 707
10 TraesCS4D01G202700 chr4A 138463987 138466563 2576 True 4279.0 4279 96.6020 1216 3800 1 chr4A.!!$R1 2584
11 TraesCS4D01G202700 chr4A 481729512 481731591 2079 True 3421.0 3421 96.3940 1727 3800 1 chr4A.!!$R2 2073
12 TraesCS4D01G202700 chr4A 146401359 146402343 984 False 1341.0 1341 91.2390 230 1218 1 chr4A.!!$F1 988
13 TraesCS4D01G202700 chr4A 337462697 337463228 531 False 569.0 569 86.0710 230 781 1 chr4A.!!$F2 551
14 TraesCS4D01G202700 chr7A 269297622 269299696 2074 False 3498.0 3498 97.1140 1727 3800 1 chr7A.!!$F1 2073
15 TraesCS4D01G202700 chr5A 178779000 178781225 2225 False 3315.0 3315 93.5690 1572 3800 1 chr5A.!!$F1 2228
16 TraesCS4D01G202700 chr3B 309750068 309751056 988 False 1445.0 1445 93.0440 230 1218 1 chr3B.!!$F1 988
17 TraesCS4D01G202700 chr6A 279746795 279747776 981 False 1339.0 1339 91.3040 234 1218 1 chr6A.!!$F1 984

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
123 124 1.078918 CATCAGGGTCGAAGCTGCA 60.079 57.895 1.02 0.00 0.00 4.41 F
194 195 1.376037 CACGGAGGCAAGGTTCTCC 60.376 63.158 0.00 0.00 44.50 3.71 F
1019 1034 1.814292 ATGGGTGTGGCTTGGGGATT 61.814 55.000 0.00 0.00 0.00 3.01 F
1128 1143 2.125512 CTAGCGAACCGGCAAGCT 60.126 61.111 19.57 19.57 43.07 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1128 1143 4.038642 GGGAAAGGAACAAACAACTGCATA 59.961 41.667 0.0 0.0 0.00 3.14 R
1663 1775 4.541250 AGCAAATGAAGGAATATCCCCA 57.459 40.909 0.0 0.0 37.19 4.96 R
2580 2729 4.218417 GCTGCCTTTTTCTCCAATGTTCTA 59.782 41.667 0.0 0.0 0.00 2.10 R
2879 3029 6.248569 ACTGTAATAGGATCGTGGGAATTT 57.751 37.500 0.0 0.0 0.00 1.82 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
40 41 2.023771 CGGTGGATGGATCGATGCG 61.024 63.158 12.54 0.00 0.00 4.73
92 93 4.292178 GCGAGGCCGGAGATCCAG 62.292 72.222 5.05 0.00 36.06 3.86
123 124 1.078918 CATCAGGGTCGAAGCTGCA 60.079 57.895 1.02 0.00 0.00 4.41
150 151 3.333219 TCCCCAAGCTGCCTCCAG 61.333 66.667 0.00 0.00 42.13 3.86
194 195 1.376037 CACGGAGGCAAGGTTCTCC 60.376 63.158 0.00 0.00 44.50 3.71
699 707 5.632034 ATGGAGTTCTATTGGTCCTAACC 57.368 43.478 0.00 0.00 46.66 2.85
1018 1033 2.248374 ATGGGTGTGGCTTGGGGAT 61.248 57.895 0.00 0.00 0.00 3.85
1019 1034 1.814292 ATGGGTGTGGCTTGGGGATT 61.814 55.000 0.00 0.00 0.00 3.01
1128 1143 2.125512 CTAGCGAACCGGCAAGCT 60.126 61.111 19.57 19.57 43.07 3.74
1433 1545 4.058124 TCATGTTGTATGCGCTTAGGATC 58.942 43.478 9.73 0.00 31.61 3.36
1663 1775 7.088272 GCTAATTTACCGTTCTTGATTTTGGT 58.912 34.615 0.00 0.00 0.00 3.67
2126 2263 4.660771 AGAGTTCCTTTCTCTCCTTCCAAA 59.339 41.667 0.00 0.00 37.70 3.28
2248 2385 7.087007 GGTCCAGTTTCTCATTTTTCAGAATC 58.913 38.462 0.00 0.00 0.00 2.52
2580 2729 7.734942 TCATTTTTGCAGGTAAAAGAAGGAAT 58.265 30.769 1.68 0.00 31.80 3.01
2742 2892 5.221362 CCCCGTTCAAGGTTTACAGAATTTT 60.221 40.000 0.00 0.00 0.00 1.82
3200 3352 0.460311 ATCCTCGGCGTTTCGATTCT 59.540 50.000 6.85 0.00 38.55 2.40
3446 3599 3.576550 GCCTGGTTAATTGAGGAAAACCA 59.423 43.478 7.78 7.78 46.88 3.67
3461 3614 6.022958 AGGAAAACCAGGCTAAAACCAATAT 58.977 36.000 0.00 0.00 0.00 1.28
3513 3666 1.477553 CAACCTGGCCACATGCTAAT 58.522 50.000 0.00 0.00 40.92 1.73
3605 3758 2.203112 GCGCTGATCATGCCCTCA 60.203 61.111 0.00 0.00 0.00 3.86
3675 3828 2.734948 AATCAACGCCCCCGAAACGA 62.735 55.000 0.00 0.00 38.29 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 3.358932 ATCCATCCACCGTTGGGGC 62.359 63.158 0.00 0.00 44.11 5.80
31 32 0.930742 GTCGTCACCTCGCATCGATC 60.931 60.000 0.00 0.00 34.61 3.69
40 41 1.984321 GAGGAGCTCGTCGTCACCTC 61.984 65.000 19.74 9.19 39.48 3.85
72 73 4.959596 GATCTCCGGCCTCGCTGC 62.960 72.222 0.00 0.00 32.89 5.25
108 109 3.123620 GCTGCAGCTTCGACCCTG 61.124 66.667 31.33 7.05 38.21 4.45
150 151 2.376228 GATGGAGGAGGAAGCGAGCC 62.376 65.000 0.00 0.00 0.00 4.70
699 707 6.668323 TCTTTTTGAAGGATTTAGAACAGCG 58.332 36.000 0.00 0.00 0.00 5.18
1128 1143 4.038642 GGGAAAGGAACAAACAACTGCATA 59.961 41.667 0.00 0.00 0.00 3.14
1433 1545 9.618890 TTGAATCTAATGAATAAAGACAGGAGG 57.381 33.333 0.00 0.00 0.00 4.30
1663 1775 4.541250 AGCAAATGAAGGAATATCCCCA 57.459 40.909 0.00 0.00 37.19 4.96
2248 2385 6.650427 TTATACACATCCCTGCTACTACAG 57.350 41.667 0.00 0.00 37.42 2.74
2537 2681 4.942761 ATGAAGCATGTTCCACAAACTT 57.057 36.364 0.00 0.00 38.76 2.66
2580 2729 4.218417 GCTGCCTTTTTCTCCAATGTTCTA 59.782 41.667 0.00 0.00 0.00 2.10
2742 2892 6.878923 CAGAACAAACTGTAATAGGATGGTGA 59.121 38.462 0.00 0.00 33.73 4.02
2879 3029 6.248569 ACTGTAATAGGATCGTGGGAATTT 57.751 37.500 0.00 0.00 0.00 1.82
3200 3352 4.522789 GCCAAACAAAGGAGAGATTGGTAA 59.477 41.667 0.00 0.00 39.53 2.85
3446 3599 6.605995 GGGTTGAGTTATATTGGTTTTAGCCT 59.394 38.462 0.00 0.00 0.00 4.58
3461 3614 3.218453 CCATGTTGTGTGGGTTGAGTTA 58.782 45.455 0.00 0.00 32.98 2.24
3513 3666 0.812549 TTCGCGTGTGTAGCCATCTA 59.187 50.000 5.77 0.00 0.00 1.98
3605 3758 0.108585 ACACTCGGTGGTCATTTGCT 59.891 50.000 8.57 0.00 37.94 3.91


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

AutoCloner maintained by Alex Coulton.