Multiple sequence alignment - TraesCS7B01G318900

Loading Multiple Alignment...

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 TraesCS7B01G318900 chr7B 100.000 2465 0 0 1 2465 568667215 568664751 0.000000e+00 4553.0
1 TraesCS7B01G318900 chr3B 97.732 2469 41 6 1 2465 460381849 460379392 0.000000e+00 4235.0
2 TraesCS7B01G318900 chr7A 94.495 2416 82 18 95 2463 708789159 708791570 0.000000e+00 3677.0
3 TraesCS7B01G318900 chr7A 93.220 354 24 0 1279 1632 122055 122408 2.810000e-144 521.0
4 TraesCS7B01G318900 chr7A 82.316 475 63 13 1512 1974 679164709 679164244 2.300000e-105 392.0
5 TraesCS7B01G318900 chr7A 92.237 219 12 4 2248 2465 122407 122621 3.080000e-79 305.0
6 TraesCS7B01G318900 chr2D 96.291 1348 43 4 48 1393 35056959 35055617 0.000000e+00 2206.0
7 TraesCS7B01G318900 chr2D 97.428 1011 22 3 1456 2465 35055618 35054611 0.000000e+00 1720.0
8 TraesCS7B01G318900 chr6D 95.542 1346 44 5 48 1393 364892187 364893516 0.000000e+00 2139.0
9 TraesCS7B01G318900 chr6D 97.428 1011 22 3 1456 2465 364893515 364894522 0.000000e+00 1720.0
10 TraesCS7B01G318900 chr6B 96.383 1106 33 6 1363 2465 651217517 651216416 0.000000e+00 1814.0
11 TraesCS7B01G318900 chr6B 91.353 1168 68 15 1 1138 651229707 651228543 0.000000e+00 1567.0
12 TraesCS7B01G318900 chr2B 94.281 1189 59 6 1278 2465 282993759 282992579 0.000000e+00 1810.0
13 TraesCS7B01G318900 chr1D 96.571 525 18 0 479 1003 332594028 332594552 0.000000e+00 870.0
14 TraesCS7B01G318900 chr1D 86.052 466 30 18 48 483 332581231 332581691 3.710000e-128 468.0
15 TraesCS7B01G318900 chr1D 80.412 97 8 6 109 195 400152514 400152419 2.050000e-06 63.9
16 TraesCS7B01G318900 chr4A 84.195 677 86 11 1512 2178 546002245 546001580 2.670000e-179 638.0
17 TraesCS7B01G318900 chrUn 97.460 315 4 3 2152 2465 479143922 479143611 3.610000e-148 534.0
18 TraesCS7B01G318900 chr5D 84.746 472 55 9 1512 1974 199427722 199427259 8.030000e-125 457.0
19 TraesCS7B01G318900 chr5D 91.983 237 17 2 1280 1515 324970540 324970305 5.080000e-87 331.0
20 TraesCS7B01G318900 chr7D 83.368 475 55 14 1512 1974 587258027 587257565 3.790000e-113 418.0
21 TraesCS7B01G318900 chr5B 90.678 236 22 0 1280 1515 377389075 377388840 5.120000e-82 315.0
22 TraesCS7B01G318900 chr5B 86.441 118 13 3 2062 2178 453266291 453266406 2.570000e-25 126.0
23 TraesCS7B01G318900 chr5B 79.870 154 31 0 555 708 348581493 348581646 2.000000e-21 113.0
24 TraesCS7B01G318900 chr5B 83.761 117 18 1 2062 2178 453295443 453295558 2.590000e-20 110.0
25 TraesCS7B01G318900 chr5B 100.000 28 0 0 168 195 703106087 703106060 4.000000e-03 52.8
26 TraesCS7B01G318900 chr5A 89.496 238 24 1 1278 1515 423056748 423056512 1.430000e-77 300.0
27 TraesCS7B01G318900 chr3D 86.121 281 33 5 1512 1791 164938523 164938248 5.150000e-77 298.0
28 TraesCS7B01G318900 chr1A 83.000 100 11 6 26 122 544363935 544363839 4.370000e-13 86.1
29 TraesCS7B01G318900 chr1A 100.000 28 0 0 168 195 292910545 292910518 4.000000e-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 TraesCS7B01G318900 chr7B 568664751 568667215 2464 True 4553.0 4553 100.0000 1 2465 1 chr7B.!!$R1 2464
1 TraesCS7B01G318900 chr3B 460379392 460381849 2457 True 4235.0 4235 97.7320 1 2465 1 chr3B.!!$R1 2464
2 TraesCS7B01G318900 chr7A 708789159 708791570 2411 False 3677.0 3677 94.4950 95 2463 1 chr7A.!!$F1 2368
3 TraesCS7B01G318900 chr7A 122055 122621 566 False 413.0 521 92.7285 1279 2465 2 chr7A.!!$F2 1186
4 TraesCS7B01G318900 chr2D 35054611 35056959 2348 True 1963.0 2206 96.8595 48 2465 2 chr2D.!!$R1 2417
5 TraesCS7B01G318900 chr6D 364892187 364894522 2335 False 1929.5 2139 96.4850 48 2465 2 chr6D.!!$F1 2417
6 TraesCS7B01G318900 chr6B 651216416 651217517 1101 True 1814.0 1814 96.3830 1363 2465 1 chr6B.!!$R1 1102
7 TraesCS7B01G318900 chr6B 651228543 651229707 1164 True 1567.0 1567 91.3530 1 1138 1 chr6B.!!$R2 1137
8 TraesCS7B01G318900 chr2B 282992579 282993759 1180 True 1810.0 1810 94.2810 1278 2465 1 chr2B.!!$R1 1187
9 TraesCS7B01G318900 chr1D 332594028 332594552 524 False 870.0 870 96.5710 479 1003 1 chr1D.!!$F2 524
10 TraesCS7B01G318900 chr4A 546001580 546002245 665 True 638.0 638 84.1950 1512 2178 1 chr4A.!!$R1 666

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
72 74 0.107017 CCTCCAATCGCACCCAAGAT 60.107 55.000 0.0 0.0 0.0 2.40 F
227 259 1.886585 CCCTAGATCAGATCCCGCG 59.113 63.158 6.8 0.0 0.0 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1291 1362 0.973632 ACTCCAGCACCGAACATGTA 59.026 50.000 0.0 0.0 0.00 2.29 R
1592 1665 1.272092 TGCATCACCAGAAAAGGGGAG 60.272 52.381 0.0 0.0 46.06 4.30 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
72 74 0.107017 CCTCCAATCGCACCCAAGAT 60.107 55.000 0.00 0.00 0.00 2.40
74 76 2.487934 CTCCAATCGCACCCAAGATAG 58.512 52.381 0.00 0.00 0.00 2.08
227 259 1.886585 CCCTAGATCAGATCCCGCG 59.113 63.158 6.80 0.00 0.00 6.46
541 601 2.115910 CCAAGCCTTGCCACTCCA 59.884 61.111 0.00 0.00 0.00 3.86
687 750 2.224159 ACCTCATTCCCTGCCGTGT 61.224 57.895 0.00 0.00 0.00 4.49
900 965 3.245797 TCTGCAATTTCTCGAGAGAACG 58.754 45.455 15.94 7.82 46.13 3.95
926 991 3.118261 TGGAGAACCTAACTCATGGATGC 60.118 47.826 0.00 0.00 36.26 3.91
1141 1206 3.013921 GTTATCAATTCACTTGGCCGGA 58.986 45.455 5.05 0.00 35.43 5.14
1173 1238 5.009410 CCATGCAAGATTATCACTTTCCCTC 59.991 44.000 0.00 0.00 0.00 4.30
1291 1362 3.878103 GCTTCTGCATGATCACATCTTCT 59.122 43.478 0.00 0.00 39.41 2.85
1400 1471 6.152932 TCGGATAATGGTTCTGGTAGTTAC 57.847 41.667 0.00 0.00 0.00 2.50
1592 1665 5.668558 ACAAGTGAACTCATTTAACGGTC 57.331 39.130 0.00 0.00 0.00 4.79
1830 1911 7.517614 TTTTTATCAGTGCACATACCTTCAA 57.482 32.000 21.04 0.00 0.00 2.69
1919 2000 7.979115 TTGTTAGTTCTGTTGTGCAAATAAC 57.021 32.000 0.00 0.00 0.00 1.89
2335 2452 7.648112 GCCTTCTGTTTTCGAATTCTTAGTTTT 59.352 33.333 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 48 1.095807 GTGCGATTGGAGGTTAGGCC 61.096 60.000 0.00 0.00 37.58 5.19
89 91 8.428186 TTTTTCGCTGGTTAATATTCGTAGAT 57.572 30.769 0.00 0.00 35.04 1.98
227 259 3.462678 GAGGAGGGGCAGTCGTCC 61.463 72.222 5.03 5.03 40.81 4.79
451 511 2.537714 GAAGGAGGGAGAGGAGGGCA 62.538 65.000 0.00 0.00 0.00 5.36
541 601 1.963515 GATTTGGCCAAAGTGACCACT 59.036 47.619 32.85 16.01 44.94 4.00
687 750 1.611977 CCACAGTAGTTGACGGAGACA 59.388 52.381 0.00 0.00 0.00 3.41
900 965 4.003648 CCATGAGTTAGGTTCTCCACAAC 58.996 47.826 0.00 0.00 35.89 3.32
926 991 4.935352 TCATCCCAAAAACTGAACCAAG 57.065 40.909 0.00 0.00 0.00 3.61
1096 1161 8.340618 ACAAGTAGTAAGAGTATAAACCACGA 57.659 34.615 0.00 0.00 0.00 4.35
1141 1206 5.069516 GTGATAATCTTGCATGGGGTTTCAT 59.930 40.000 0.00 0.00 0.00 2.57
1173 1238 8.883731 AGTGACTAATCCAGAAATTATTGAACG 58.116 33.333 0.00 0.00 0.00 3.95
1291 1362 0.973632 ACTCCAGCACCGAACATGTA 59.026 50.000 0.00 0.00 0.00 2.29
1400 1471 7.446319 TGAGGATGCCAAAGAATATGAATGTAG 59.554 37.037 0.00 0.00 0.00 2.74
1592 1665 1.272092 TGCATCACCAGAAAAGGGGAG 60.272 52.381 0.00 0.00 46.06 4.30
1757 1830 5.981088 TGTTTACCATTCCACGTAGAGTA 57.019 39.130 0.00 0.00 0.00 2.59
1830 1911 7.037658 ACAAGATAGCCCCATTGGTTTATTTTT 60.038 33.333 1.20 0.00 36.04 1.94
1919 2000 4.778534 AGCTCATCAACACAAAGAATGG 57.221 40.909 0.00 0.00 0.00 3.16
2268 2381 9.983024 CCTCCGATCCTGGAAGTATATATATAT 57.017 37.037 10.10 10.10 37.64 0.86
2269 2382 9.179104 TCCTCCGATCCTGGAAGTATATATATA 57.821 37.037 0.00 0.00 37.64 0.86
2335 2452 6.646653 CAGCTTCAACAAGTACAGAGATGTTA 59.353 38.462 0.00 0.00 34.45 2.41


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

AutoCloner maintained by Alex Coulton.