Multiple sequence alignment - TraesCS5B01G487300

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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 TraesCS5B01G487300 chr5B 100.000 2396 0 0 1 2396 658444840 658447235 0.000000e+00 4425.0
1 TraesCS5B01G487300 chr6B 92.039 1520 98 4 1 1498 671145292 671146810 0.000000e+00 2115.0
2 TraesCS5B01G487300 chr6B 96.489 940 32 1 510 1449 684766094 684765156 0.000000e+00 1552.0
3 TraesCS5B01G487300 chr6B 90.167 539 28 8 1 514 684775258 684774720 0.000000e+00 678.0
4 TraesCS5B01G487300 chr1B 93.521 1389 89 1 118 1505 637980633 637979245 0.000000e+00 2065.0
5 TraesCS5B01G487300 chr1B 78.125 224 31 12 1756 1970 98903304 98903090 2.500000e-25 126.0
6 TraesCS5B01G487300 chr1B 81.208 149 18 9 1734 1874 469530780 469530634 7.000000e-21 111.0
7 TraesCS5B01G487300 chr2B 88.510 1497 150 6 2 1479 546866716 546868209 0.000000e+00 1792.0
8 TraesCS5B01G487300 chr5D 86.917 1521 176 8 1 1501 271850588 271849071 0.000000e+00 1685.0
9 TraesCS5B01G487300 chr5D 86.644 1475 172 10 1 1452 535873521 535874993 0.000000e+00 1609.0
10 TraesCS5B01G487300 chr5D 91.422 921 48 14 1498 2396 522113025 522113936 0.000000e+00 1234.0
11 TraesCS5B01G487300 chr2D 83.421 1514 232 8 2 1497 10068148 10069660 0.000000e+00 1387.0
12 TraesCS5B01G487300 chr6D 82.058 1516 242 15 4 1498 153176531 153175025 0.000000e+00 1266.0
13 TraesCS5B01G487300 chr1D 81.980 1515 248 10 4 1499 452581306 452579798 0.000000e+00 1262.0
14 TraesCS5B01G487300 chr1D 75.987 304 54 12 1723 2013 488548137 488547840 3.210000e-29 139.0
15 TraesCS5B01G487300 chr1D 81.169 154 20 5 1736 1881 62112463 62112311 5.410000e-22 115.0
16 TraesCS5B01G487300 chr5A 87.704 919 78 18 1498 2396 650247515 650248418 0.000000e+00 1038.0
17 TraesCS5B01G487300 chr5A 80.172 116 20 3 2078 2192 68623094 68623207 1.530000e-12 84.2
18 TraesCS5B01G487300 chr3D 84.746 118 11 3 1724 1835 401895935 401895819 7.000000e-21 111.0
19 TraesCS5B01G487300 chr3B 83.471 121 18 2 1759 1878 5076869 5076988 7.000000e-21 111.0
20 TraesCS5B01G487300 chr4B 83.621 116 13 5 2098 2211 122846394 122846283 1.170000e-18 104.0
21 TraesCS5B01G487300 chr7D 75.000 212 40 10 1773 1978 161930708 161930504 4.240000e-13 86.1


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 TraesCS5B01G487300 chr5B 658444840 658447235 2395 False 4425 4425 100.000 1 2396 1 chr5B.!!$F1 2395
1 TraesCS5B01G487300 chr6B 671145292 671146810 1518 False 2115 2115 92.039 1 1498 1 chr6B.!!$F1 1497
2 TraesCS5B01G487300 chr6B 684765156 684766094 938 True 1552 1552 96.489 510 1449 1 chr6B.!!$R1 939
3 TraesCS5B01G487300 chr6B 684774720 684775258 538 True 678 678 90.167 1 514 1 chr6B.!!$R2 513
4 TraesCS5B01G487300 chr1B 637979245 637980633 1388 True 2065 2065 93.521 118 1505 1 chr1B.!!$R3 1387
5 TraesCS5B01G487300 chr2B 546866716 546868209 1493 False 1792 1792 88.510 2 1479 1 chr2B.!!$F1 1477
6 TraesCS5B01G487300 chr5D 271849071 271850588 1517 True 1685 1685 86.917 1 1501 1 chr5D.!!$R1 1500
7 TraesCS5B01G487300 chr5D 535873521 535874993 1472 False 1609 1609 86.644 1 1452 1 chr5D.!!$F2 1451
8 TraesCS5B01G487300 chr5D 522113025 522113936 911 False 1234 1234 91.422 1498 2396 1 chr5D.!!$F1 898
9 TraesCS5B01G487300 chr2D 10068148 10069660 1512 False 1387 1387 83.421 2 1497 1 chr2D.!!$F1 1495
10 TraesCS5B01G487300 chr6D 153175025 153176531 1506 True 1266 1266 82.058 4 1498 1 chr6D.!!$R1 1494
11 TraesCS5B01G487300 chr1D 452579798 452581306 1508 True 1262 1262 81.980 4 1499 1 chr1D.!!$R2 1495
12 TraesCS5B01G487300 chr5A 650247515 650248418 903 False 1038 1038 87.704 1498 2396 1 chr5A.!!$F2 898

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
310 335 1.072331 GAGCCTTCTTCTGGTCCAACA 59.928 52.381 0.0 0.0 0.0 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1683 1722 0.039074 CTCGATCACGACCATAGGCC 60.039 60.0 0.0 0.0 43.81 5.19 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
19 20 1.760192 GCTCTTCTCACCATTGCCAT 58.240 50.000 0.00 0.00 0.00 4.40
48 49 2.425312 ACCACTCAAAACAACATCGCAA 59.575 40.909 0.00 0.00 0.00 4.85
116 117 2.610873 CTCCCTCTATCCCCTACCAAC 58.389 57.143 0.00 0.00 0.00 3.77
243 268 6.147821 CCCTAGCCGTTTATTTCATGTCTATG 59.852 42.308 0.00 0.00 35.57 2.23
270 295 3.349022 CCTCCCTAAGTCTATCCTAGCG 58.651 54.545 0.00 0.00 0.00 4.26
310 335 1.072331 GAGCCTTCTTCTGGTCCAACA 59.928 52.381 0.00 0.00 0.00 3.33
327 352 1.178534 ACAAGGAAACATGCACGGGG 61.179 55.000 0.00 0.00 30.52 5.73
355 380 2.828520 TGTCTGGTTGCTTGGAAAAACA 59.171 40.909 0.00 0.00 0.00 2.83
417 442 3.476552 TCTTGAAATTCAGAACCGCTGT 58.523 40.909 0.00 0.00 45.14 4.40
459 485 4.346418 TCCAAAATACTGCAACACCCAAAT 59.654 37.500 0.00 0.00 0.00 2.32
549 575 6.353429 CCTCCTTCCTCTGGAAAATAGTGAAT 60.353 42.308 0.53 0.00 41.54 2.57
710 737 5.544650 TGACAAGGTTTTAGTGGCTACTAC 58.455 41.667 9.78 0.98 39.06 2.73
732 759 9.073475 ACTACTTGGCAAAACAACTTATTATCA 57.927 29.630 0.00 0.00 0.00 2.15
760 787 4.297299 CGGAACCGTCTTACTAATGCTA 57.703 45.455 4.99 0.00 34.35 3.49
792 819 4.805219 AGTTGGACTGTGTTTTGTTGTTC 58.195 39.130 0.00 0.00 0.00 3.18
880 907 5.104360 TCAGCTAAAAATGCCTACAGATCCT 60.104 40.000 0.00 0.00 0.00 3.24
889 916 2.170607 GCCTACAGATCCTTTGTGGCTA 59.829 50.000 14.33 0.00 38.52 3.93
1094 1121 4.220382 CCTCATCTCTAACTGCTCCTATGG 59.780 50.000 0.00 0.00 0.00 2.74
1312 1341 3.914426 TTGTAGCAGATTTCTCCCTCC 57.086 47.619 0.00 0.00 0.00 4.30
1369 1398 1.443828 GCTAGGCTCTGGCTACACC 59.556 63.158 0.00 0.00 39.70 4.16
1393 1422 1.904440 ATCCTCTGCAATCCCCTCTT 58.096 50.000 0.00 0.00 0.00 2.85
1395 1424 2.845659 TCCTCTGCAATCCCCTCTTAA 58.154 47.619 0.00 0.00 0.00 1.85
1524 1562 9.683069 GATCTTTGAAAGTTTCTTTATTGCTCA 57.317 29.630 16.33 0.00 0.00 4.26
1532 1570 7.472334 AGTTTCTTTATTGCTCATCCACATT 57.528 32.000 0.00 0.00 0.00 2.71
1569 1608 0.829333 CAGTGGAGAGTGCTATGGCT 59.171 55.000 1.68 0.00 39.59 4.75
1571 1610 0.539051 GTGGAGAGTGCTATGGCTGT 59.461 55.000 1.68 0.00 39.59 4.40
1572 1611 0.538584 TGGAGAGTGCTATGGCTGTG 59.461 55.000 1.68 0.00 39.59 3.66
1598 1637 4.754114 GGACACATGAGCTATTTGATCTCC 59.246 45.833 0.00 0.00 31.32 3.71
1604 1643 6.837568 ACATGAGCTATTTGATCTCCCAATTT 59.162 34.615 0.00 0.00 31.32 1.82
1614 1653 9.650714 ATTTGATCTCCCAATTTGAGATTATCA 57.349 29.630 15.16 9.31 46.80 2.15
1674 1713 8.690203 TGTCAAACTTTTGGAGAATTCTGATA 57.310 30.769 14.00 0.00 38.66 2.15
1683 1722 9.787532 TTTTGGAGAATTCTGATATTTTTAGCG 57.212 29.630 14.00 0.00 0.00 4.26
1796 1844 6.683974 ATGTTAGCATGTGATTTACCTGTC 57.316 37.500 0.00 0.00 33.37 3.51
1955 2003 8.053355 AGGTCAATAAAACATAGGGAGTTAAGG 58.947 37.037 0.00 0.00 0.00 2.69
1956 2004 7.201794 GGTCAATAAAACATAGGGAGTTAAGGC 60.202 40.741 0.00 0.00 0.00 4.35
2058 2110 2.028112 TGGTTCGAAGGATGAAGTGGAG 60.028 50.000 0.00 0.00 0.00 3.86
2059 2111 2.233922 GGTTCGAAGGATGAAGTGGAGA 59.766 50.000 0.00 0.00 0.00 3.71
2109 2161 4.083164 TGTTATCTAGCGAACGTCAGTTGA 60.083 41.667 0.00 0.00 41.34 3.18
2112 2164 2.747989 TCTAGCGAACGTCAGTTGAGAT 59.252 45.455 0.00 0.00 41.34 2.75
2131 2183 2.380410 GGCGATGACAAGCGAACGT 61.380 57.895 5.39 0.00 37.39 3.99
2258 2321 0.035317 TCGCAAATGTCACCTCTGCT 59.965 50.000 0.00 0.00 0.00 4.24
2266 2329 1.961394 TGTCACCTCTGCTAACGAACT 59.039 47.619 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 3.866703 TGTTTTGAGTGGTGGTATCCA 57.133 42.857 0.00 0.00 34.85 3.41
116 117 0.039074 GCTGTCTATGATCGGGTCGG 60.039 60.000 0.00 0.00 0.00 4.79
243 268 1.772836 TAGACTTAGGGAGGCGGAAC 58.227 55.000 0.00 0.00 38.95 3.62
270 295 4.612943 CTCTCCTAATGGCGTCTAGTTTC 58.387 47.826 0.00 0.00 0.00 2.78
310 335 1.606313 CCCCCGTGCATGTTTCCTT 60.606 57.895 4.96 0.00 0.00 3.36
327 352 1.166531 AAGCAACCAGACAACTCGCC 61.167 55.000 0.00 0.00 0.00 5.54
355 380 6.048509 CACCAAGTTCTTTAGGTTTGCAAAT 58.951 36.000 16.21 2.51 30.44 2.32
417 442 4.717877 TGGAAGAAAACTTCATGAGCAGA 58.282 39.130 11.21 0.00 35.19 4.26
459 485 2.642171 ACCACTGAGTCCAAGGGATA 57.358 50.000 0.00 0.00 32.73 2.59
549 575 6.134535 TCAATAAGGAGAGGCAGGTTTTTA 57.865 37.500 0.00 0.00 0.00 1.52
710 737 8.495148 GGTTTGATAATAAGTTGTTTTGCCAAG 58.505 33.333 0.00 0.00 0.00 3.61
760 787 1.696336 ACAGTCCAACTCATGAGCAGT 59.304 47.619 22.83 6.10 0.00 4.40
792 819 1.180029 CCTGTTGGAAATCCTGCAGG 58.820 55.000 27.87 27.87 44.92 4.85
880 907 5.475564 GGTCAAAATAGTCCTTAGCCACAAA 59.524 40.000 0.00 0.00 0.00 2.83
889 916 2.433436 GTGCGGGTCAAAATAGTCCTT 58.567 47.619 0.00 0.00 0.00 3.36
1094 1121 0.317020 GCGAGACCAAACTTGTGCAC 60.317 55.000 10.75 10.75 0.00 4.57
1369 1398 4.140536 GAGGGGATTGCAGAGGATAAAAG 58.859 47.826 0.00 0.00 0.00 2.27
1393 1422 9.860650 AGCAGTATTATGGGTACAAATTCATTA 57.139 29.630 0.00 0.00 0.00 1.90
1395 1424 7.779798 ACAGCAGTATTATGGGTACAAATTCAT 59.220 33.333 0.00 0.00 0.00 2.57
1508 1546 7.472334 AATGTGGATGAGCAATAAAGAAACT 57.528 32.000 0.00 0.00 0.00 2.66
1558 1597 0.618680 TCCTCCACAGCCATAGCACT 60.619 55.000 0.00 0.00 43.56 4.40
1571 1610 3.519107 TCAAATAGCTCATGTGTCCTCCA 59.481 43.478 0.00 0.00 0.00 3.86
1572 1611 4.142609 TCAAATAGCTCATGTGTCCTCC 57.857 45.455 0.00 0.00 0.00 4.30
1598 1637 9.512435 GAAGACAACATGATAATCTCAAATTGG 57.488 33.333 0.00 0.00 37.22 3.16
1674 1713 2.218603 CGACCATAGGCCGCTAAAAAT 58.781 47.619 0.00 0.00 0.00 1.82
1683 1722 0.039074 CTCGATCACGACCATAGGCC 60.039 60.000 0.00 0.00 43.81 5.19
1771 1819 7.041780 GGACAGGTAAATCACATGCTAACATAG 60.042 40.741 0.00 0.00 42.76 2.23
1868 1916 8.856153 AAGTTCTTACCAAACCAAACAAAATT 57.144 26.923 0.00 0.00 0.00 1.82
1942 1990 3.264964 TGAAAACCGCCTTAACTCCCTAT 59.735 43.478 0.00 0.00 0.00 2.57
1943 1991 2.638855 TGAAAACCGCCTTAACTCCCTA 59.361 45.455 0.00 0.00 0.00 3.53
1954 2002 3.378911 TGATTTTCCTTGAAAACCGCC 57.621 42.857 4.28 0.00 42.98 6.13
1955 2003 3.181575 CGTTGATTTTCCTTGAAAACCGC 59.818 43.478 4.28 0.00 42.98 5.68
1956 2004 3.733727 CCGTTGATTTTCCTTGAAAACCG 59.266 43.478 4.28 5.31 42.98 4.44
2058 2110 8.705048 ACCGAAAAGAGTGTAAGATTCTATTC 57.295 34.615 0.00 0.00 0.00 1.75
2109 2161 0.108186 TTCGCTTGTCATCGCCATCT 60.108 50.000 0.00 0.00 0.00 2.90
2112 2164 2.379634 CGTTCGCTTGTCATCGCCA 61.380 57.895 0.00 0.00 0.00 5.69
2204 2257 6.370453 AGTTGTATGGGTAGGTTGTTTCTTT 58.630 36.000 0.00 0.00 0.00 2.52
2266 2329 3.610040 TTTATCTCTCAGCTGGCGAAA 57.390 42.857 15.13 3.72 0.00 3.46


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

AutoCloner maintained by Alex Coulton.