Multiple sequence alignment - TraesCS1A01G401700

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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 TraesCS1A01G401700 chr1A 100.000 1854 0 0 1 1854 565084818 565086671 0.000000e+00 3424
1 TraesCS1A01G401700 chr1A 99.462 1860 4 2 1 1854 565020638 565022497 0.000000e+00 3374
2 TraesCS1A01G401700 chr1A 86.459 1189 137 14 651 1821 565009390 565010572 0.000000e+00 1282
3 TraesCS1A01G401700 chr1A 100.000 667 0 0 2069 2735 565086886 565087552 0.000000e+00 1232
4 TraesCS1A01G401700 chr1A 93.253 667 44 1 2069 2735 565022758 565023423 0.000000e+00 981
5 TraesCS1A01G401700 chr1A 91.941 273 20 2 2464 2735 237132567 237132296 5.530000e-102 381
6 TraesCS1A01G401700 chr1A 90.406 271 26 0 2465 2735 227764386 227764116 9.310000e-95 357
7 TraesCS1A01G401700 chr1A 87.568 185 21 2 2079 2262 349363216 349363033 2.130000e-51 213
8 TraesCS1A01G401700 chrUn 100.000 386 0 0 1244 1629 480646711 480647096 0.000000e+00 713
9 TraesCS1A01G401700 chr2A 91.176 272 24 0 2464 2735 430567975 430568246 1.200000e-98 370
10 TraesCS1A01G401700 chr2A 90.441 272 26 0 2464 2735 456707199 456706928 2.590000e-95 359
11 TraesCS1A01G401700 chr2A 90.441 272 26 0 2464 2735 511792451 511792722 2.590000e-95 359
12 TraesCS1A01G401700 chr7A 90.809 272 25 0 2464 2735 318355117 318355388 5.570000e-97 364
13 TraesCS1A01G401700 chr7A 90.074 272 27 0 2464 2735 428247989 428247718 1.200000e-93 353
14 TraesCS1A01G401700 chr6A 90.441 272 26 0 2464 2735 436785758 436786029 2.590000e-95 359
15 TraesCS1A01G401700 chr6A 82.895 228 35 4 2069 2294 426644332 426644107 4.620000e-48 202
16 TraesCS1A01G401700 chr6A 79.401 267 43 11 2082 2339 73295069 73294806 7.780000e-41 178
17 TraesCS1A01G401700 chr5B 79.185 466 80 13 1 462 692390914 692390462 9.510000e-80 307
18 TraesCS1A01G401700 chr6B 81.618 272 39 11 2079 2344 716581679 716581945 5.930000e-52 215
19 TraesCS1A01G401700 chr5A 88.344 163 18 1 2081 2242 675534495 675534657 7.730000e-46 195
20 TraesCS1A01G401700 chr7D 82.432 222 34 5 2069 2288 35091213 35091431 3.600000e-44 189
21 TraesCS1A01G401700 chr3B 84.103 195 29 2 2069 2262 482407446 482407639 1.290000e-43 187
22 TraesCS1A01G401700 chr2B 81.567 217 39 1 2079 2294 99495523 99495307 7.780000e-41 178


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 TraesCS1A01G401700 chr1A 565084818 565087552 2734 False 2328.0 3424 100.0000 1 2735 2 chr1A.!!$F3 2734
1 TraesCS1A01G401700 chr1A 565020638 565023423 2785 False 2177.5 3374 96.3575 1 2735 2 chr1A.!!$F2 2734
2 TraesCS1A01G401700 chr1A 565009390 565010572 1182 False 1282.0 1282 86.4590 651 1821 1 chr1A.!!$F1 1170

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
1752 1774 9.442047 GATAATAAAGATACTATTGCAGCAGGT 57.558 33.333 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2594 2662 0.670162 GAGGCAGCAACAGCTTCAAA 59.33 50.0 0.0 0.0 37.93 2.69 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
1752 1774 9.442047 GATAATAAAGATACTATTGCAGCAGGT 57.558 33.333 0.00 0.00 0.00 4.00
1775 1797 6.882678 GGTAGTACACCTGACATAATTTTGGT 59.117 38.462 2.06 0.00 44.79 3.67
2109 2177 1.073284 TGGTGCTTCCTTTGGTAGGTC 59.927 52.381 0.00 0.00 45.03 3.85
2183 2251 5.684704 CACCATATATGTGAGGTCACCTTT 58.315 41.667 11.73 0.00 45.88 3.11
2264 2332 9.733556 TTCCTTAGTAACAAATTGCTAATCTCA 57.266 29.630 0.00 0.00 40.75 3.27
2422 2490 1.750022 TAAAGGGGTGTTGGTAGGCT 58.250 50.000 0.00 0.00 0.00 4.58
2424 2492 2.361230 GGGGTGTTGGTAGGCTGC 60.361 66.667 0.00 0.00 0.00 5.25
2437 2505 4.564116 GCTGCATGCGCACATCCC 62.564 66.667 14.90 0.00 45.36 3.85
2439 2507 1.524393 CTGCATGCGCACATCCCTA 60.524 57.895 14.90 0.00 45.36 3.53
2441 2509 2.885676 GCATGCGCACATCCCTACG 61.886 63.158 14.90 0.00 38.36 3.51
2449 2517 0.172578 CACATCCCTACGAAGCGACA 59.827 55.000 0.00 0.00 0.00 4.35
2496 2564 2.479560 GGCCTCATCGTTAAATTGTGGC 60.480 50.000 13.93 13.93 45.00 5.01
2507 2575 1.619654 AATTGTGGCAGTAGCTTGCA 58.380 45.000 12.28 0.00 45.86 4.08
2512 2580 0.950555 TGGCAGTAGCTTGCACTTCG 60.951 55.000 12.28 0.00 45.86 3.79
2531 2599 0.393132 GAGTAGCTCTTTGGGGGTGC 60.393 60.000 0.00 0.00 0.00 5.01
2544 2612 2.960129 GGTGCGAGGCCGTATTCG 60.960 66.667 7.71 7.71 39.69 3.34
2556 2624 0.098200 CGTATTCGTCGGCTGTCAGA 59.902 55.000 3.32 0.00 0.00 3.27
2559 2627 0.732880 ATTCGTCGGCTGTCAGAACG 60.733 55.000 3.32 9.92 0.00 3.95
2589 2657 2.037121 TCTGTCGTTGAGCAAATCCTGA 59.963 45.455 0.00 0.00 0.00 3.86
2619 2687 1.775869 GCTGTTGCTGCCTCTTTTTC 58.224 50.000 0.00 0.00 36.03 2.29
2643 2711 1.366111 TTCTTGCCGTGGCGATTAGC 61.366 55.000 6.37 0.00 45.51 3.09
2659 2727 2.515996 TAGCCGGCACTTAAAGCGCT 62.516 55.000 31.54 2.64 34.06 5.92
2686 2754 3.229659 AGGGGTTCCTCCGGTACGT 62.230 63.158 0.00 0.00 44.19 3.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1752 1774 7.915293 CACCAAAATTATGTCAGGTGTACTA 57.085 36.000 0.00 0.00 41.11 1.82
1775 1797 8.267183 AGATATGAACATATGAAGTGTTGGACA 58.733 33.333 10.38 0.00 39.72 4.02
2075 2143 2.565841 AGCACCAAATAAGATCTCGCC 58.434 47.619 0.00 0.00 0.00 5.54
2077 2145 4.446371 AGGAAGCACCAAATAAGATCTCG 58.554 43.478 0.00 0.00 42.04 4.04
2153 2221 6.605594 TGACCTCACATATATGGTGCGATATA 59.394 38.462 16.96 0.00 36.22 0.86
2175 2243 9.535878 CCTATGTCTATCTTTTAGAAAGGTGAC 57.464 37.037 1.04 7.23 0.00 3.67
2210 2278 8.243961 TCTGATTTTGTTTTGGAAGGTTATCA 57.756 30.769 0.00 0.00 0.00 2.15
2216 2284 8.534496 AGGAATATCTGATTTTGTTTTGGAAGG 58.466 33.333 0.00 0.00 0.00 3.46
2239 2307 9.162764 GTGAGATTAGCAATTTGTTACTAAGGA 57.837 33.333 0.00 0.00 0.00 3.36
2389 2457 7.750947 ACACCCCTTTAATAGTAGAGATGTT 57.249 36.000 0.00 0.00 0.00 2.71
2424 2492 0.809636 TTCGTAGGGATGTGCGCATG 60.810 55.000 19.33 1.73 35.07 4.06
2431 2499 0.172803 GTGTCGCTTCGTAGGGATGT 59.827 55.000 11.81 0.00 44.10 3.06
2437 2505 1.665544 CGCACAGTGTCGCTTCGTAG 61.666 60.000 13.40 0.00 0.00 3.51
2439 2507 3.030308 CGCACAGTGTCGCTTCGT 61.030 61.111 13.40 0.00 0.00 3.85
2481 2549 4.261801 AGCTACTGCCACAATTTAACGAT 58.738 39.130 0.00 0.00 40.80 3.73
2496 2564 2.071688 ACTCGAAGTGCAAGCTACTG 57.928 50.000 0.00 0.00 0.00 2.74
2507 2575 1.550976 CCCCAAAGAGCTACTCGAAGT 59.449 52.381 0.00 0.00 35.36 3.01
2512 2580 0.393132 GCACCCCCAAAGAGCTACTC 60.393 60.000 0.00 0.00 0.00 2.59
2531 2599 2.353145 CCGACGAATACGGCCTCG 60.353 66.667 10.33 10.33 45.81 4.63
2544 2612 1.004277 CTGACGTTCTGACAGCCGAC 61.004 60.000 17.61 13.06 33.78 4.79
2574 2642 5.048504 TCAAACTGATCAGGATTTGCTCAAC 60.049 40.000 26.08 0.00 31.98 3.18
2589 2657 2.288030 GCAGCAACAGCTTCAAACTGAT 60.288 45.455 0.00 0.00 38.55 2.90
2594 2662 0.670162 GAGGCAGCAACAGCTTCAAA 59.330 50.000 0.00 0.00 37.93 2.69
2648 2716 2.731976 CTCGAACAAGAGCGCTTTAAGT 59.268 45.455 13.26 5.67 30.14 2.24
2659 2727 3.159141 AGGAACCCCTCGAACAAGA 57.841 52.632 0.00 0.00 38.86 3.02
2686 2754 2.279741 CCTCGGCGATGAAGATTTCAA 58.720 47.619 11.27 0.00 43.95 2.69


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

AutoCloner maintained by Alex Coulton.