Multiple sequence alignment - TraesCS5B01G323800

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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 TraesCS5B01G323800 chr5B 100.000 2337 0 0 1 2337 508068061 508065725 0.000000e+00 4316
1 TraesCS5B01G323800 chr5B 88.670 1368 145 5 1 1358 521394987 521396354 0.000000e+00 1659
2 TraesCS5B01G323800 chr4B 93.826 1312 69 7 1 1303 86653138 86651830 0.000000e+00 1964
3 TraesCS5B01G323800 chr4D 91.927 1375 98 7 1 1365 349920260 349921631 0.000000e+00 1912
4 TraesCS5B01G323800 chr7A 90.584 1370 111 12 1 1361 241745524 241744164 0.000000e+00 1799
5 TraesCS5B01G323800 chr6A 90.742 1361 109 11 3 1350 101365541 101364185 0.000000e+00 1799
6 TraesCS5B01G323800 chr6D 90.015 1372 115 13 1 1362 356158116 356156757 0.000000e+00 1755
7 TraesCS5B01G323800 chr4A 91.406 1280 98 7 89 1357 621856356 621857634 0.000000e+00 1744
8 TraesCS5B01G323800 chr1D 88.596 1368 146 6 1 1358 360147464 360146097 0.000000e+00 1653
9 TraesCS5B01G323800 chr2D 88.676 1360 144 5 1 1350 126957123 126958482 0.000000e+00 1650
10 TraesCS5B01G323800 chr5A 91.230 878 49 19 1484 2337 535241470 535240597 0.000000e+00 1170
11 TraesCS5B01G323800 chr5D 93.429 624 28 5 1724 2337 421662975 421662355 0.000000e+00 913
12 TraesCS5B01G323800 chr5D 92.500 240 11 5 1484 1719 421663251 421663015 1.030000e-88 337


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 TraesCS5B01G323800 chr5B 508065725 508068061 2336 True 4316 4316 100.0000 1 2337 1 chr5B.!!$R1 2336
1 TraesCS5B01G323800 chr5B 521394987 521396354 1367 False 1659 1659 88.6700 1 1358 1 chr5B.!!$F1 1357
2 TraesCS5B01G323800 chr4B 86651830 86653138 1308 True 1964 1964 93.8260 1 1303 1 chr4B.!!$R1 1302
3 TraesCS5B01G323800 chr4D 349920260 349921631 1371 False 1912 1912 91.9270 1 1365 1 chr4D.!!$F1 1364
4 TraesCS5B01G323800 chr7A 241744164 241745524 1360 True 1799 1799 90.5840 1 1361 1 chr7A.!!$R1 1360
5 TraesCS5B01G323800 chr6A 101364185 101365541 1356 True 1799 1799 90.7420 3 1350 1 chr6A.!!$R1 1347
6 TraesCS5B01G323800 chr6D 356156757 356158116 1359 True 1755 1755 90.0150 1 1362 1 chr6D.!!$R1 1361
7 TraesCS5B01G323800 chr4A 621856356 621857634 1278 False 1744 1744 91.4060 89 1357 1 chr4A.!!$F1 1268
8 TraesCS5B01G323800 chr1D 360146097 360147464 1367 True 1653 1653 88.5960 1 1358 1 chr1D.!!$R1 1357
9 TraesCS5B01G323800 chr2D 126957123 126958482 1359 False 1650 1650 88.6760 1 1350 1 chr2D.!!$F1 1349
10 TraesCS5B01G323800 chr5A 535240597 535241470 873 True 1170 1170 91.2300 1484 2337 1 chr5A.!!$R1 853
11 TraesCS5B01G323800 chr5D 421662355 421663251 896 True 625 913 92.9645 1484 2337 2 chr5D.!!$R1 853

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
286 288 1.404391 TCGATTCGGTCTGCTTACTCC 59.596 52.381 6.18 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1606 1626 1.146041 TATCTGGTGATGTGCGGCC 59.854 57.895 0.0 0.0 34.32 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
56 57 2.425392 GGAAGATGCCTGGATCCCAAAT 60.425 50.000 9.90 0.00 30.80 2.32
71 72 3.572255 TCCCAAATTGTGCCACTAGAAAC 59.428 43.478 0.00 0.00 0.00 2.78
214 215 3.140325 TCTTTCAATCCCACTTTCGCT 57.860 42.857 0.00 0.00 0.00 4.93
286 288 1.404391 TCGATTCGGTCTGCTTACTCC 59.596 52.381 6.18 0.00 0.00 3.85
306 308 3.118775 TCCGTGGAGTGGAATTATCAGTG 60.119 47.826 0.00 0.00 30.98 3.66
335 342 7.783119 GGAGTAAACTAAAATATTGGGATGGGT 59.217 37.037 0.00 0.00 0.00 4.51
359 366 7.093902 GGTCGAATCACACCTAATCCTATATGA 60.094 40.741 0.00 0.00 0.00 2.15
432 440 4.384056 GCATACATTACATGGCACTCTCT 58.616 43.478 0.00 0.00 33.60 3.10
456 464 1.468736 GCCGGGTAACACTCTCTAACG 60.469 57.143 2.18 0.00 39.74 3.18
702 711 9.935241 ATGTACGAGAAATGATAGCTATTTCAT 57.065 29.630 18.26 12.09 43.56 2.57
765 775 9.768662 ACAAAGAATTAACTCAGAATGCAAATT 57.231 25.926 0.00 0.00 34.76 1.82
876 888 3.154710 CCCTAGGGGTTTTGTGAAACTC 58.845 50.000 21.44 0.00 44.00 3.01
959 971 5.861727 AGACGACAAAGGTAGGTTTATTGT 58.138 37.500 0.00 0.00 36.96 2.71
1004 1016 0.324614 TGTGCGGATGTTCTGATGGT 59.675 50.000 0.00 0.00 0.00 3.55
1161 1175 4.992951 GCAATTTTTGAGGACTGCTTTCAT 59.007 37.500 0.00 0.00 0.00 2.57
1217 1231 7.653713 CGAACACTGTAATAGAGAGGCAAATAT 59.346 37.037 0.00 0.00 0.00 1.28
1273 1289 3.812156 TCGACTTCAGACTGGTTTGAA 57.188 42.857 1.81 6.54 33.46 2.69
1305 1321 9.177608 CCTAAATGAAATTGTACTGATCCTCAA 57.822 33.333 0.00 0.00 36.10 3.02
1424 1440 8.512138 ACACGAATCTCCTTGTAAAATTAAAGG 58.488 33.333 0.00 0.00 41.60 3.11
1425 1441 8.726988 CACGAATCTCCTTGTAAAATTAAAGGA 58.273 33.333 3.53 3.53 45.63 3.36
1426 1442 9.292195 ACGAATCTCCTTGTAAAATTAAAGGAA 57.708 29.630 5.02 0.00 46.70 3.36
1427 1443 9.774742 CGAATCTCCTTGTAAAATTAAAGGAAG 57.225 33.333 5.02 0.90 46.70 3.46
1444 1460 9.798994 TTAAAGGAAGATACTATCGACTGAAAC 57.201 33.333 0.00 0.00 0.00 2.78
1445 1461 7.406031 AAGGAAGATACTATCGACTGAAACA 57.594 36.000 0.00 0.00 0.00 2.83
1446 1462 7.589958 AGGAAGATACTATCGACTGAAACAT 57.410 36.000 0.00 0.00 0.00 2.71
1447 1463 8.693120 AGGAAGATACTATCGACTGAAACATA 57.307 34.615 0.00 0.00 0.00 2.29
1448 1464 9.132923 AGGAAGATACTATCGACTGAAACATAA 57.867 33.333 0.00 0.00 0.00 1.90
1449 1465 9.182933 GGAAGATACTATCGACTGAAACATAAC 57.817 37.037 0.00 0.00 0.00 1.89
1450 1466 9.731819 GAAGATACTATCGACTGAAACATAACA 57.268 33.333 0.00 0.00 0.00 2.41
1454 1470 9.871238 ATACTATCGACTGAAACATAACAAAGT 57.129 29.630 0.00 0.00 0.00 2.66
1455 1471 8.240883 ACTATCGACTGAAACATAACAAAGTC 57.759 34.615 0.00 0.00 0.00 3.01
1456 1472 8.088981 ACTATCGACTGAAACATAACAAAGTCT 58.911 33.333 0.00 0.00 33.49 3.24
1457 1473 6.764877 TCGACTGAAACATAACAAAGTCTC 57.235 37.500 0.00 0.00 33.49 3.36
1458 1474 6.277605 TCGACTGAAACATAACAAAGTCTCA 58.722 36.000 0.00 0.00 33.49 3.27
1459 1475 6.759356 TCGACTGAAACATAACAAAGTCTCAA 59.241 34.615 0.00 0.00 33.49 3.02
1460 1476 7.279090 TCGACTGAAACATAACAAAGTCTCAAA 59.721 33.333 0.00 0.00 33.49 2.69
1461 1477 8.070171 CGACTGAAACATAACAAAGTCTCAAAT 58.930 33.333 0.00 0.00 33.49 2.32
1462 1478 9.173939 GACTGAAACATAACAAAGTCTCAAATG 57.826 33.333 0.00 0.00 33.02 2.32
1463 1479 8.902806 ACTGAAACATAACAAAGTCTCAAATGA 58.097 29.630 0.00 0.00 0.00 2.57
1464 1480 9.173939 CTGAAACATAACAAAGTCTCAAATGAC 57.826 33.333 0.00 0.00 37.23 3.06
1465 1481 8.681806 TGAAACATAACAAAGTCTCAAATGACA 58.318 29.630 0.00 0.00 39.27 3.58
1466 1482 9.173939 GAAACATAACAAAGTCTCAAATGACAG 57.826 33.333 0.00 0.00 39.27 3.51
1467 1483 8.450578 AACATAACAAAGTCTCAAATGACAGA 57.549 30.769 0.00 0.00 39.27 3.41
1468 1484 8.092521 ACATAACAAAGTCTCAAATGACAGAG 57.907 34.615 0.00 0.00 39.27 3.35
1469 1485 7.933577 ACATAACAAAGTCTCAAATGACAGAGA 59.066 33.333 0.00 0.00 39.27 3.10
1476 1492 5.665916 TCTCAAATGACAGAGACATAGCA 57.334 39.130 0.00 0.00 36.05 3.49
1477 1493 6.041423 TCTCAAATGACAGAGACATAGCAA 57.959 37.500 0.00 0.00 36.05 3.91
1478 1494 6.466812 TCTCAAATGACAGAGACATAGCAAA 58.533 36.000 0.00 0.00 36.05 3.68
1479 1495 6.936335 TCTCAAATGACAGAGACATAGCAAAA 59.064 34.615 0.00 0.00 36.05 2.44
1480 1496 6.902341 TCAAATGACAGAGACATAGCAAAAC 58.098 36.000 0.00 0.00 0.00 2.43
1481 1497 6.712095 TCAAATGACAGAGACATAGCAAAACT 59.288 34.615 0.00 0.00 0.00 2.66
1482 1498 6.734104 AATGACAGAGACATAGCAAAACTC 57.266 37.500 0.00 0.00 0.00 3.01
1525 1541 2.687370 TCATCATGACACTCACCAACG 58.313 47.619 0.00 0.00 0.00 4.10
1575 1591 0.944386 CAACCGAACACCTCCAACAG 59.056 55.000 0.00 0.00 0.00 3.16
1632 1652 4.645535 GCACATCACCAGATACACCATAT 58.354 43.478 0.00 0.00 31.88 1.78
1720 1757 1.865865 ACTGAAAGCCACTACACACG 58.134 50.000 0.00 0.00 37.60 4.49
1721 1758 1.148310 CTGAAAGCCACTACACACGG 58.852 55.000 0.00 0.00 0.00 4.94
1722 1759 0.753867 TGAAAGCCACTACACACGGA 59.246 50.000 0.00 0.00 0.00 4.69
1753 1814 2.932614 CTGCTTAATCGACCTGACCTTG 59.067 50.000 0.00 0.00 0.00 3.61
1783 1848 0.032952 TAGTTCACCACACGGCAGTC 59.967 55.000 0.00 0.00 34.57 3.51
2156 2221 3.712881 GTCGTGCACCGTGCCTTC 61.713 66.667 20.67 10.11 44.23 3.46
2193 2258 1.070471 TGTGATCGTCATCGTGCACG 61.070 55.000 32.76 32.76 41.18 5.34
2200 2265 1.459624 CGTCATCGTGCACGTTACAAC 60.460 52.381 35.74 24.58 40.80 3.32
2211 2276 6.406896 CGTGCACGTTACAACAATATACAATC 59.593 38.462 30.50 0.00 34.11 2.67
2226 2295 3.340814 ACAATCGTGCTTTCTCTCCAT 57.659 42.857 0.00 0.00 0.00 3.41
2227 2296 3.005554 ACAATCGTGCTTTCTCTCCATG 58.994 45.455 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 4.036262 GTCACAATGTTTCTAGTGGCACAA 59.964 41.667 21.41 2.16 44.16 3.33
214 215 6.707608 GGCAATGAAGTCTGTCATATCATGTA 59.292 38.462 0.00 0.00 37.25 2.29
269 271 1.135083 CACGGAGTAAGCAGACCGAAT 60.135 52.381 11.27 0.00 46.94 3.34
286 288 3.618594 CACACTGATAATTCCACTCCACG 59.381 47.826 0.00 0.00 0.00 4.94
306 308 8.630037 CATCCCAATATTTTAGTTTACTCCCAC 58.370 37.037 0.00 0.00 0.00 4.61
335 342 8.470002 CATCATATAGGATTAGGTGTGATTCGA 58.530 37.037 0.00 0.00 0.00 3.71
359 366 9.125026 GGACAAGATAACTTCCATATTTGACAT 57.875 33.333 0.00 0.00 33.70 3.06
412 420 5.876651 TGAGAGAGTGCCATGTAATGTAT 57.123 39.130 0.00 0.00 44.81 2.29
432 440 0.535335 GAGAGTGTTACCCGGCATGA 59.465 55.000 0.00 0.00 0.00 3.07
456 464 1.208293 GGGAGAGACCTTCATGTGTCC 59.792 57.143 8.48 0.00 38.98 4.02
702 711 5.659971 GTCTTTCCCACTATAGGTACCAAGA 59.340 44.000 15.94 7.26 0.00 3.02
715 725 5.362430 TGCACTAATTTTTGTCTTTCCCACT 59.638 36.000 0.00 0.00 0.00 4.00
765 775 6.097412 AGTGCTATGATCGCCATTGATATCTA 59.903 38.462 3.98 0.00 36.71 1.98
876 888 4.158949 TGATCAAAGGAGGCATCAACATTG 59.841 41.667 0.00 0.00 0.00 2.82
978 990 4.323417 TCAGAACATCCGCACAATAGTTT 58.677 39.130 0.00 0.00 0.00 2.66
979 991 3.937814 TCAGAACATCCGCACAATAGTT 58.062 40.909 0.00 0.00 0.00 2.24
1004 1016 5.048504 CCAAATTTGAGTGCTAGAGCTTCAA 60.049 40.000 19.86 14.11 40.62 2.69
1161 1175 5.711506 AGTCATGACAAAATCACAGGCATAA 59.288 36.000 27.02 0.00 41.24 1.90
1251 1267 4.131649 TCAAACCAGTCTGAAGTCGAAA 57.868 40.909 0.00 0.00 0.00 3.46
1273 1289 5.888161 CAGTACAATTTCATTTAGGGGCTCT 59.112 40.000 0.00 0.00 0.00 4.09
1398 1414 8.512138 CCTTTAATTTTACAAGGAGATTCGTGT 58.488 33.333 0.00 0.00 39.73 4.49
1399 1415 8.726988 TCCTTTAATTTTACAAGGAGATTCGTG 58.273 33.333 0.00 0.00 41.02 4.35
1400 1416 8.857694 TCCTTTAATTTTACAAGGAGATTCGT 57.142 30.769 0.00 0.00 41.02 3.85
1401 1417 9.774742 CTTCCTTTAATTTTACAAGGAGATTCG 57.225 33.333 0.42 0.00 45.45 3.34
1418 1434 9.798994 GTTTCAGTCGATAGTATCTTCCTTTAA 57.201 33.333 8.49 0.00 37.40 1.52
1419 1435 8.963725 TGTTTCAGTCGATAGTATCTTCCTTTA 58.036 33.333 8.49 0.00 37.40 1.85
1420 1436 7.837863 TGTTTCAGTCGATAGTATCTTCCTTT 58.162 34.615 8.49 0.00 37.40 3.11
1421 1437 7.406031 TGTTTCAGTCGATAGTATCTTCCTT 57.594 36.000 8.49 0.00 37.40 3.36
1422 1438 7.589958 ATGTTTCAGTCGATAGTATCTTCCT 57.410 36.000 8.49 0.00 37.40 3.36
1423 1439 9.182933 GTTATGTTTCAGTCGATAGTATCTTCC 57.817 37.037 8.49 0.00 37.40 3.46
1424 1440 9.731819 TGTTATGTTTCAGTCGATAGTATCTTC 57.268 33.333 8.49 1.74 37.40 2.87
1428 1444 9.871238 ACTTTGTTATGTTTCAGTCGATAGTAT 57.129 29.630 0.00 0.00 37.40 2.12
1429 1445 9.350357 GACTTTGTTATGTTTCAGTCGATAGTA 57.650 33.333 0.00 0.00 37.40 1.82
1430 1446 8.088981 AGACTTTGTTATGTTTCAGTCGATAGT 58.911 33.333 0.00 0.00 37.40 2.12
1431 1447 8.467402 AGACTTTGTTATGTTTCAGTCGATAG 57.533 34.615 0.00 0.00 0.00 2.08
1432 1448 8.085909 TGAGACTTTGTTATGTTTCAGTCGATA 58.914 33.333 0.00 0.00 0.00 2.92
1433 1449 6.929049 TGAGACTTTGTTATGTTTCAGTCGAT 59.071 34.615 0.00 0.00 0.00 3.59
1434 1450 6.277605 TGAGACTTTGTTATGTTTCAGTCGA 58.722 36.000 0.00 0.00 0.00 4.20
1435 1451 6.525121 TGAGACTTTGTTATGTTTCAGTCG 57.475 37.500 0.00 0.00 0.00 4.18
1436 1452 9.173939 CATTTGAGACTTTGTTATGTTTCAGTC 57.826 33.333 0.00 0.00 30.81 3.51
1437 1453 8.902806 TCATTTGAGACTTTGTTATGTTTCAGT 58.097 29.630 0.00 0.00 30.81 3.41
1438 1454 9.173939 GTCATTTGAGACTTTGTTATGTTTCAG 57.826 33.333 0.00 0.00 35.65 3.02
1439 1455 8.681806 TGTCATTTGAGACTTTGTTATGTTTCA 58.318 29.630 0.00 0.00 39.27 2.69
1440 1456 9.173939 CTGTCATTTGAGACTTTGTTATGTTTC 57.826 33.333 0.00 0.00 39.27 2.78
1441 1457 8.902806 TCTGTCATTTGAGACTTTGTTATGTTT 58.097 29.630 0.00 0.00 39.27 2.83
1442 1458 8.450578 TCTGTCATTTGAGACTTTGTTATGTT 57.549 30.769 0.00 0.00 39.27 2.71
1443 1459 7.933577 TCTCTGTCATTTGAGACTTTGTTATGT 59.066 33.333 0.00 0.00 39.27 2.29
1444 1460 8.315391 TCTCTGTCATTTGAGACTTTGTTATG 57.685 34.615 0.00 0.00 39.27 1.90
1454 1470 5.665916 TGCTATGTCTCTGTCATTTGAGA 57.334 39.130 0.00 0.00 37.03 3.27
1455 1471 6.732531 TTTGCTATGTCTCTGTCATTTGAG 57.267 37.500 0.00 0.00 0.00 3.02
1456 1472 6.712095 AGTTTTGCTATGTCTCTGTCATTTGA 59.288 34.615 0.00 0.00 0.00 2.69
1457 1473 6.906659 AGTTTTGCTATGTCTCTGTCATTTG 58.093 36.000 0.00 0.00 0.00 2.32
1458 1474 6.939163 AGAGTTTTGCTATGTCTCTGTCATTT 59.061 34.615 0.00 0.00 34.74 2.32
1459 1475 6.471146 AGAGTTTTGCTATGTCTCTGTCATT 58.529 36.000 0.00 0.00 34.74 2.57
1460 1476 6.047511 AGAGTTTTGCTATGTCTCTGTCAT 57.952 37.500 0.00 0.00 34.74 3.06
1461 1477 5.474578 AGAGTTTTGCTATGTCTCTGTCA 57.525 39.130 0.00 0.00 34.74 3.58
1462 1478 6.793492 AAAGAGTTTTGCTATGTCTCTGTC 57.207 37.500 0.00 0.00 35.94 3.51
1463 1479 7.420800 CAAAAAGAGTTTTGCTATGTCTCTGT 58.579 34.615 0.00 0.00 45.20 3.41
1464 1480 7.848716 CAAAAAGAGTTTTGCTATGTCTCTG 57.151 36.000 0.00 0.00 45.20 3.35
1500 1516 5.169992 TGGTGAGTGTCATGATGATTTCT 57.830 39.130 0.00 0.00 0.00 2.52
1505 1521 2.037121 ACGTTGGTGAGTGTCATGATGA 59.963 45.455 0.00 0.00 0.00 2.92
1525 1541 3.496884 TGTGCTTTTCTCCGTGTATTCAC 59.503 43.478 0.00 0.00 40.79 3.18
1575 1591 9.213799 TGGCTTGTCAAAATAATTAATTTCACC 57.786 29.630 5.91 0.00 36.76 4.02
1606 1626 1.146041 TATCTGGTGATGTGCGGCC 59.854 57.895 0.00 0.00 34.32 6.13
1648 1671 9.418045 GAAATAAGCTGCTAGATTCTAACTAGG 57.582 37.037 0.90 0.00 38.11 3.02
1976 2041 2.949451 ACTACATCAACCTGCTCTCG 57.051 50.000 0.00 0.00 0.00 4.04
2193 2258 8.889849 AAAGCACGATTGTATATTGTTGTAAC 57.110 30.769 0.00 0.00 0.00 2.50
2200 2265 6.479990 TGGAGAGAAAGCACGATTGTATATTG 59.520 38.462 0.00 0.00 0.00 1.90
2211 2276 4.083110 ACATTTTCATGGAGAGAAAGCACG 60.083 41.667 0.00 0.00 36.45 5.34
2226 2295 5.401972 GTCGTTGAATCATTGCACATTTTCA 59.598 36.000 0.00 0.00 0.00 2.69
2227 2296 5.441872 CGTCGTTGAATCATTGCACATTTTC 60.442 40.000 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.