Multiple sequence alignment - TraesCS4A01G456500

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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 TraesCS4A01G456500 chr4A 100.000 2447 0 0 1 2447 721639035 721641481 0 4519
1 TraesCS4A01G456500 chr1B 93.151 2453 122 30 1 2447 346594895 346597307 0 3557
2 TraesCS4A01G456500 chr1B 91.941 2457 175 14 2 2447 524764776 524767220 0 3419
3 TraesCS4A01G456500 chr1B 91.819 2469 160 33 2 2447 106887646 106890095 0 3402
4 TraesCS4A01G456500 chr4B 91.779 2457 183 12 2 2447 443186668 443184220 0 3400
5 TraesCS4A01G456500 chr6B 91.619 2458 183 16 2 2447 440007970 440010416 0 3376
6 TraesCS4A01G456500 chr6B 91.149 2463 190 20 2 2447 459691962 459694413 0 3315
7 TraesCS4A01G456500 chr3B 92.601 2311 147 20 2 2297 682015431 682013130 0 3299
8 TraesCS4A01G456500 chr5B 90.273 2457 212 21 2 2447 547746193 547748633 0 3188
9 TraesCS4A01G456500 chr5B 90.273 2457 212 21 2 2447 547767244 547769684 0 3188


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 TraesCS4A01G456500 chr4A 721639035 721641481 2446 False 4519 4519 100.000 1 2447 1 chr4A.!!$F1 2446
1 TraesCS4A01G456500 chr1B 346594895 346597307 2412 False 3557 3557 93.151 1 2447 1 chr1B.!!$F2 2446
2 TraesCS4A01G456500 chr1B 524764776 524767220 2444 False 3419 3419 91.941 2 2447 1 chr1B.!!$F3 2445
3 TraesCS4A01G456500 chr1B 106887646 106890095 2449 False 3402 3402 91.819 2 2447 1 chr1B.!!$F1 2445
4 TraesCS4A01G456500 chr4B 443184220 443186668 2448 True 3400 3400 91.779 2 2447 1 chr4B.!!$R1 2445
5 TraesCS4A01G456500 chr6B 440007970 440010416 2446 False 3376 3376 91.619 2 2447 1 chr6B.!!$F1 2445
6 TraesCS4A01G456500 chr6B 459691962 459694413 2451 False 3315 3315 91.149 2 2447 1 chr6B.!!$F2 2445
7 TraesCS4A01G456500 chr3B 682013130 682015431 2301 True 3299 3299 92.601 2 2297 1 chr3B.!!$R1 2295
8 TraesCS4A01G456500 chr5B 547746193 547748633 2440 False 3188 3188 90.273 2 2447 1 chr5B.!!$F1 2445
9 TraesCS4A01G456500 chr5B 547767244 547769684 2440 False 3188 3188 90.273 2 2447 1 chr5B.!!$F2 2445

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
353 354 0.106521 GCACCAATTGCCCACACTTT 59.893 50.0 0.0 0.0 46.63 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2236 2263 0.178068 CCACCGATCCCGAGAACATT 59.822 55.0 0.0 0.0 38.22 2.71 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
188 189 3.319405 ACAGTAGCAGATCCAATACCTCG 59.681 47.826 0.00 0.00 0.00 4.63
196 197 5.482006 CAGATCCAATACCTCGATGCAATA 58.518 41.667 0.00 0.00 0.00 1.90
202 203 7.276658 TCCAATACCTCGATGCAATAAAACTA 58.723 34.615 0.00 0.00 0.00 2.24
203 204 7.771361 TCCAATACCTCGATGCAATAAAACTAA 59.229 33.333 0.00 0.00 0.00 2.24
262 263 4.100808 AGGAACCTACTCTGATTGATGCTC 59.899 45.833 0.00 0.00 0.00 4.26
353 354 0.106521 GCACCAATTGCCCACACTTT 59.893 50.000 0.00 0.00 46.63 2.66
496 497 4.831107 TGCACATACATCTAAGCAAGTCA 58.169 39.130 0.00 0.00 0.00 3.41
658 659 6.996879 CAGTGATGGTGATGAGGAGAATATTT 59.003 38.462 0.00 0.00 0.00 1.40
807 808 6.669154 AGGAAGAGAGATCTCAACTTGAAGAT 59.331 38.462 27.65 12.07 45.21 2.40
822 823 8.877779 CAACTTGAAGATGAAATACTCGAAGAT 58.122 33.333 0.00 0.00 33.89 2.40
904 905 9.160496 CATCTACTACTCTTGAAGAAGCAAAAT 57.840 33.333 0.00 0.00 0.00 1.82
1034 1035 4.391830 TGACTTATTTGCTTCTACCTTGCG 59.608 41.667 0.00 0.00 0.00 4.85
1093 1094 9.976511 AAAAGTATTTGCTTGGATATGATCATG 57.023 29.630 18.72 1.21 39.02 3.07
1102 1103 7.623278 TGCTTGGATATGATCATGTATACCCTA 59.377 37.037 18.72 5.36 0.00 3.53
1491 1493 2.288518 ACGAAGAAGAGTGAAGCTGGAC 60.289 50.000 0.00 0.00 0.00 4.02
1519 1528 2.304180 TGAGGAAGCAAAGGAGAAGAGG 59.696 50.000 0.00 0.00 0.00 3.69
1520 1529 2.569404 GAGGAAGCAAAGGAGAAGAGGA 59.431 50.000 0.00 0.00 0.00 3.71
1532 1542 3.287222 GAGAAGAGGAGCAGCTTAGAGA 58.713 50.000 0.00 0.00 0.00 3.10
1584 1596 1.168714 GTGAGCTGTTTCATGACCCC 58.831 55.000 0.00 0.00 0.00 4.95
1599 1611 4.437682 TGACCCCAATCTGAATACCATC 57.562 45.455 0.00 0.00 0.00 3.51
1600 1612 3.785325 TGACCCCAATCTGAATACCATCA 59.215 43.478 0.00 0.00 0.00 3.07
1601 1613 4.416513 TGACCCCAATCTGAATACCATCAT 59.583 41.667 0.00 0.00 0.00 2.45
1602 1614 5.610557 TGACCCCAATCTGAATACCATCATA 59.389 40.000 0.00 0.00 0.00 2.15
1603 1615 5.880901 ACCCCAATCTGAATACCATCATAC 58.119 41.667 0.00 0.00 0.00 2.39
1604 1616 5.372363 ACCCCAATCTGAATACCATCATACA 59.628 40.000 0.00 0.00 0.00 2.29
1606 1618 6.950041 CCCCAATCTGAATACCATCATACATT 59.050 38.462 0.00 0.00 0.00 2.71
1645 1657 4.215109 ACTGTTATTTGGGTTGCTTGAGT 58.785 39.130 0.00 0.00 0.00 3.41
1659 1671 7.755373 GGGTTGCTTGAGTCATTTCTTAAATAC 59.245 37.037 0.00 0.00 0.00 1.89
1691 1703 4.879545 TGAATTTTACCTTCGACATAGGGC 59.120 41.667 6.59 0.00 37.09 5.19
1746 1759 8.486210 TGAATGCCTTGTAAACTAGTGATCTAT 58.514 33.333 0.00 0.00 0.00 1.98
1774 1787 3.854784 GCTTGCTTTGCTGAAAGTAGTGG 60.855 47.826 0.00 0.00 40.77 4.00
1875 1890 2.831685 TCACCACGTTTAGATGCTGT 57.168 45.000 0.00 0.00 0.00 4.40
2002 2017 9.023962 AGTGATGATTCCTATTTTTGTGCTTAA 57.976 29.630 0.00 0.00 0.00 1.85
2076 2092 0.908910 TAGCATGTCATGTTCCCGGT 59.091 50.000 14.26 0.00 0.00 5.28
2079 2095 1.603802 GCATGTCATGTTCCCGGTATG 59.396 52.381 14.26 0.00 0.00 2.39
2103 2119 2.026729 TGGCATGTGAAATCGGGTTAGA 60.027 45.455 0.00 0.00 0.00 2.10
2236 2263 1.386525 GGTCGAGCCGGGTGTATACA 61.387 60.000 12.94 0.08 0.00 2.29
2392 2424 1.043816 TTCTCGGGATCATGCTCTCC 58.956 55.000 0.00 0.00 0.00 3.71
2405 2437 3.914426 TGCTCTCCTTAGGAACCATTC 57.086 47.619 1.41 0.00 0.00 2.67
2421 2453 1.866601 CATTCGGCGCAGTCATCATTA 59.133 47.619 10.83 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
188 189 7.119846 ACTCAGTCTGGTTAGTTTTATTGCATC 59.880 37.037 0.00 0.00 0.00 3.91
196 197 6.415573 ACTTTGACTCAGTCTGGTTAGTTTT 58.584 36.000 6.33 0.00 33.15 2.43
202 203 2.945668 GCAACTTTGACTCAGTCTGGTT 59.054 45.455 6.33 5.69 33.15 3.67
203 204 2.092968 TGCAACTTTGACTCAGTCTGGT 60.093 45.455 6.33 0.00 33.15 4.00
262 263 6.401394 TCTCCATATCTTGTTGTCTCAACTG 58.599 40.000 12.66 6.91 0.00 3.16
353 354 8.356657 CAAATTTCCCAGATACAGTTGTAACAA 58.643 33.333 0.00 0.00 33.76 2.83
496 497 4.329638 TCTCTCTCCTTGGAATGTCTCT 57.670 45.455 0.00 0.00 0.00 3.10
658 659 1.621992 ACCTCGCTGTCTTTCTGAGA 58.378 50.000 0.00 0.00 0.00 3.27
807 808 6.280855 TGTTCCTCATCTTCGAGTATTTCA 57.719 37.500 0.00 0.00 0.00 2.69
822 823 3.118482 GCTCTGGATCATCTTGTTCCTCA 60.118 47.826 0.00 0.00 37.20 3.86
904 905 7.441836 TCTTCAAGTTCATCTACAGCAACTTA 58.558 34.615 0.00 0.00 37.04 2.24
1093 1094 8.033626 GTGAGTAATGCCACTAATAGGGTATAC 58.966 40.741 0.00 0.00 0.00 1.47
1102 1103 7.792374 CACTAATGTGAGTAATGCCACTAAT 57.208 36.000 0.00 0.00 46.55 1.73
1183 1185 9.618890 TTTATCATTAAGCTCAAGACTAGCATT 57.381 29.630 0.22 0.00 42.62 3.56
1302 1304 3.679824 GGGATAATACCCTCCAAGTCG 57.320 52.381 0.00 0.00 45.90 4.18
1491 1493 2.029623 CCTTTGCTTCCTCATGGATGG 58.970 52.381 0.00 0.00 42.81 3.51
1506 1508 1.278699 AGCTGCTCCTCTTCTCCTTTG 59.721 52.381 0.00 0.00 0.00 2.77
1519 1528 3.825308 CTCGATCATCTCTAAGCTGCTC 58.175 50.000 1.00 0.00 0.00 4.26
1520 1529 2.030007 GCTCGATCATCTCTAAGCTGCT 60.030 50.000 0.00 0.00 31.24 4.24
1552 1562 0.609131 AGCTCACCGGGTTTTGATGG 60.609 55.000 6.32 0.00 0.00 3.51
1614 1626 7.039082 AGCAACCCAAATAACAGTTGATTACAT 60.039 33.333 5.95 0.00 41.65 2.29
1645 1657 5.878116 CAGTGGGACGGTATTTAAGAAATGA 59.122 40.000 0.00 0.00 32.38 2.57
1659 1671 3.067684 AGGTAAAATTCAGTGGGACGG 57.932 47.619 0.00 0.00 0.00 4.79
1691 1703 7.010830 ACTCAGTTCACATATTCACATCAATCG 59.989 37.037 0.00 0.00 0.00 3.34
1832 1846 3.160777 AGGTGTATCGAGGTAAAAGCG 57.839 47.619 0.00 0.00 0.00 4.68
2053 2069 1.672881 GGGAACATGACATGCTACTGC 59.327 52.381 15.49 3.29 40.20 4.40
2076 2092 2.296792 CGATTTCACATGCCACCCATA 58.703 47.619 0.00 0.00 31.47 2.74
2079 2095 1.666209 CCCGATTTCACATGCCACCC 61.666 60.000 0.00 0.00 0.00 4.61
2213 2240 0.683828 TACACCCGGCTCGACCAATA 60.684 55.000 0.00 0.00 39.03 1.90
2236 2263 0.178068 CCACCGATCCCGAGAACATT 59.822 55.000 0.00 0.00 38.22 2.71
2367 2399 3.420893 AGCATGATCCCGAGAACAAAAA 58.579 40.909 0.00 0.00 0.00 1.94
2392 2424 0.742990 TGCGCCGAATGGTTCCTAAG 60.743 55.000 4.18 0.00 37.67 2.18
2405 2437 2.095853 AGTTTTAATGATGACTGCGCCG 59.904 45.455 4.18 0.00 0.00 6.46


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

AutoCloner maintained by Alex Coulton.