Multiple sequence alignment - TraesCS4A01G153500

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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 TraesCS4A01G153500 chr4A 100.000 2216 0 0 1 2216 309514944 309512729 0.000000e+00 4093.0
1 TraesCS4A01G153500 chr4A 95.021 2169 92 12 52 2216 310738341 310736185 0.000000e+00 3393.0
2 TraesCS4A01G153500 chr4A 93.182 1584 81 13 1 1578 599587782 599589344 0.000000e+00 2302.0
3 TraesCS4A01G153500 chr4A 98.182 55 1 0 1263 1317 599589096 599589042 1.810000e-16 97.1
4 TraesCS4A01G153500 chr1D 96.799 2218 60 7 1 2216 254398296 254400504 0.000000e+00 3692.0
5 TraesCS4A01G153500 chr3D 96.662 2217 62 8 1 2216 589279729 589281934 0.000000e+00 3674.0
6 TraesCS4A01G153500 chr5D 96.528 2218 65 8 1 2216 6188753 6186546 0.000000e+00 3659.0
7 TraesCS4A01G153500 chr5D 96.527 2217 66 8 1 2216 503278413 503280619 0.000000e+00 3657.0
8 TraesCS4A01G153500 chr5D 95.964 2205 73 12 1 2202 432403684 432405875 0.000000e+00 3565.0
9 TraesCS4A01G153500 chr5D 97.154 1265 33 2 1 1265 503218031 503216770 0.000000e+00 2134.0
10 TraesCS4A01G153500 chr5A 95.489 2217 90 7 1 2216 607274213 607272006 0.000000e+00 3531.0
11 TraesCS4A01G153500 chr2A 95.444 2217 71 9 1 2216 335838441 335836254 0.000000e+00 3507.0
12 TraesCS4A01G153500 chr4B 94.459 2220 95 17 1 2216 308696283 308694088 0.000000e+00 3393.0
13 TraesCS4A01G153500 chr6D 95.991 1871 60 10 351 2216 45519037 45517177 0.000000e+00 3025.0
14 TraesCS4A01G153500 chr2B 96.501 1286 38 5 1 1286 474908266 474906988 0.000000e+00 2119.0
15 TraesCS4A01G153500 chr7B 87.477 1094 109 18 896 1982 719442377 719441305 0.000000e+00 1236.0


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 TraesCS4A01G153500 chr4A 309512729 309514944 2215 True 4093 4093 100.000 1 2216 1 chr4A.!!$R1 2215
1 TraesCS4A01G153500 chr4A 310736185 310738341 2156 True 3393 3393 95.021 52 2216 1 chr4A.!!$R2 2164
2 TraesCS4A01G153500 chr4A 599587782 599589344 1562 False 2302 2302 93.182 1 1578 1 chr4A.!!$F1 1577
3 TraesCS4A01G153500 chr1D 254398296 254400504 2208 False 3692 3692 96.799 1 2216 1 chr1D.!!$F1 2215
4 TraesCS4A01G153500 chr3D 589279729 589281934 2205 False 3674 3674 96.662 1 2216 1 chr3D.!!$F1 2215
5 TraesCS4A01G153500 chr5D 6186546 6188753 2207 True 3659 3659 96.528 1 2216 1 chr5D.!!$R1 2215
6 TraesCS4A01G153500 chr5D 503278413 503280619 2206 False 3657 3657 96.527 1 2216 1 chr5D.!!$F2 2215
7 TraesCS4A01G153500 chr5D 432403684 432405875 2191 False 3565 3565 95.964 1 2202 1 chr5D.!!$F1 2201
8 TraesCS4A01G153500 chr5D 503216770 503218031 1261 True 2134 2134 97.154 1 1265 1 chr5D.!!$R2 1264
9 TraesCS4A01G153500 chr5A 607272006 607274213 2207 True 3531 3531 95.489 1 2216 1 chr5A.!!$R1 2215
10 TraesCS4A01G153500 chr2A 335836254 335838441 2187 True 3507 3507 95.444 1 2216 1 chr2A.!!$R1 2215
11 TraesCS4A01G153500 chr4B 308694088 308696283 2195 True 3393 3393 94.459 1 2216 1 chr4B.!!$R1 2215
12 TraesCS4A01G153500 chr6D 45517177 45519037 1860 True 3025 3025 95.991 351 2216 1 chr6D.!!$R1 1865
13 TraesCS4A01G153500 chr2B 474906988 474908266 1278 True 2119 2119 96.501 1 1286 1 chr2B.!!$R1 1285
14 TraesCS4A01G153500 chr7B 719441305 719442377 1072 True 1236 1236 87.477 896 1982 1 chr7B.!!$R1 1086

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
477 480 1.000052 GGTAGAGCCGGATCTAAGTGC 60.0 57.143 29.95 17.47 33.66 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1990 2028 0.304705 GTATGCGTCCTTGGATTGCG 59.695 55.0 10.68 3.83 0.0 4.85 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
49 50 6.442952 CAGAAACCTAGGATGTAGAAGATCG 58.557 44.000 17.98 0.00 0.00 3.69
64 65 5.352284 AGAAGATCGTAACATGAGCGATTT 58.648 37.500 18.67 13.35 44.06 2.17
86 87 2.432146 GGCAGATTTGGATTCCTTTCCC 59.568 50.000 3.95 0.00 34.67 3.97
251 254 2.622064 ACTTCAACCGATATGCCCTC 57.378 50.000 0.00 0.00 0.00 4.30
291 294 5.147330 ACATAGAAATCACACGTGGAAGA 57.853 39.130 21.57 14.78 0.00 2.87
409 412 6.149807 CCGTTTAGTATCCCAAAACTGCTTAA 59.850 38.462 0.00 0.00 32.25 1.85
477 480 1.000052 GGTAGAGCCGGATCTAAGTGC 60.000 57.143 29.95 17.47 33.66 4.40
675 686 7.781548 ATTCTTCGTTGCCGTAAGTAAATAT 57.218 32.000 0.00 0.00 35.01 1.28
795 807 1.656652 CCTTGATCCACTTGGCTACG 58.343 55.000 0.00 0.00 34.44 3.51
1037 1067 4.040706 AGAAACAATAGTAACGTGGTCCCA 59.959 41.667 0.00 0.00 0.00 4.37
1174 1204 2.677971 CCTACTCGGCATTTCACGG 58.322 57.895 0.00 0.00 0.00 4.94
1325 1358 8.533569 TGGGTATTTCTGTCTTTTCTTTCTTT 57.466 30.769 0.00 0.00 0.00 2.52
1463 1497 4.997395 GGTTAGCACGGTTGATGATATCAT 59.003 41.667 18.21 18.21 39.39 2.45
1501 1537 4.096311 CGTGACCTTGACTATCAACTACG 58.904 47.826 0.00 0.00 32.21 3.51
1502 1538 4.379186 CGTGACCTTGACTATCAACTACGT 60.379 45.833 0.00 0.00 32.21 3.57
1505 1541 7.256286 GTGACCTTGACTATCAACTACGTATT 58.744 38.462 0.00 0.00 32.21 1.89
1506 1542 7.220300 GTGACCTTGACTATCAACTACGTATTG 59.780 40.741 0.00 3.74 32.21 1.90
1507 1543 6.570692 ACCTTGACTATCAACTACGTATTGG 58.429 40.000 13.93 0.46 32.21 3.16
1508 1544 6.154021 ACCTTGACTATCAACTACGTATTGGT 59.846 38.462 13.93 11.09 32.21 3.67
1509 1545 7.039882 CCTTGACTATCAACTACGTATTGGTT 58.960 38.462 13.93 5.66 32.21 3.67
1510 1546 7.010183 CCTTGACTATCAACTACGTATTGGTTG 59.990 40.741 16.14 16.14 40.87 3.77
1582 1618 2.237392 AGCAGTGAACCAGATTCCTACC 59.763 50.000 0.00 0.00 36.36 3.18
1753 1790 8.655935 ATTCATTTTCAGTAGTTTCCCTGATT 57.344 30.769 0.00 0.00 37.54 2.57
1768 1805 8.319881 GTTTCCCTGATTAAACTAGAGGTTACT 58.680 37.037 0.00 0.00 37.12 2.24
1837 1874 3.085952 ACACCTAACATGTGGAATGGG 57.914 47.619 9.12 2.82 38.05 4.00
1860 1897 3.012518 GCATAAGGATGTTGTGCTCTGT 58.987 45.455 0.00 0.00 35.30 3.41
1916 1953 6.101734 AGAGATTCCTAAAGGCATACCATCAA 59.898 38.462 0.00 0.00 39.06 2.57
1990 2028 2.648059 ACAGGAGCTGAATATGCAACC 58.352 47.619 0.00 0.00 35.18 3.77
2024 2062 2.547826 GCATACCCAGACGGAAACTAC 58.452 52.381 0.00 0.00 34.64 2.73
2040 2078 0.594602 CTACGTTCCCACTCACGACA 59.405 55.000 0.00 0.00 39.76 4.35
2044 2082 1.148310 GTTCCCACTCACGACACATG 58.852 55.000 0.00 0.00 0.00 3.21
2140 2178 1.826720 GATGCAGCTTCCCAAATTGGA 59.173 47.619 14.62 0.00 40.96 3.53
2163 2202 2.852495 AAGTGCAATCCGATCGCCGT 62.852 55.000 10.32 0.00 36.31 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 0.165944 GGTTTCTGCGTTCCGTCATG 59.834 55.000 0.00 0.00 0.00 3.07
29 30 6.832384 TGTTACGATCTTCTACATCCTAGGTT 59.168 38.462 9.08 0.00 0.00 3.50
49 50 2.677836 TCTGCCAAATCGCTCATGTTAC 59.322 45.455 0.00 0.00 0.00 2.50
64 65 3.099141 GGAAAGGAATCCAAATCTGCCA 58.901 45.455 0.61 0.00 39.42 4.92
291 294 1.141858 GCTCTAGCTAATTGCCCACCT 59.858 52.381 0.00 0.00 44.23 4.00
409 412 1.005450 ACCCACTTGTCCAACTGTTGT 59.995 47.619 18.38 0.00 0.00 3.32
417 420 2.489985 CCCAACATTACCCACTTGTCCA 60.490 50.000 0.00 0.00 0.00 4.02
675 686 8.815565 TGCAATTTTCCATATTCCTAGTTACA 57.184 30.769 0.00 0.00 0.00 2.41
795 807 1.119574 TAGCTGGATAAGGGGCGGAC 61.120 60.000 0.00 0.00 0.00 4.79
1006 1036 8.943002 CCACGTTACTATTGTTTCTTTATCCTT 58.057 33.333 0.00 0.00 0.00 3.36
1011 1041 6.650390 GGGACCACGTTACTATTGTTTCTTTA 59.350 38.462 0.00 0.00 0.00 1.85
1037 1067 2.370189 GTGGGTAGAATGCTAGATGCCT 59.630 50.000 0.00 0.00 42.00 4.75
1109 1139 8.652810 ACGTACCATAGGATTTGTTATGTAAC 57.347 34.615 0.00 0.00 36.74 2.50
1132 1162 0.530288 AATTCCCCCAATTTGCGACG 59.470 50.000 0.00 0.00 29.60 5.12
1174 1204 8.470002 AGTATCCTTTCTTGCATTTTCATAACC 58.530 33.333 0.00 0.00 0.00 2.85
1463 1497 6.549433 AGGTCACGTTATTAATACTTGGGA 57.451 37.500 0.00 0.00 0.00 4.37
1481 1515 7.255569 CAATACGTAGTTGATAGTCAAGGTCA 58.744 38.462 0.08 0.00 37.78 4.02
1501 1537 7.254624 GGTTTCAATTTCAACCACAACCAATAC 60.255 37.037 9.76 0.00 41.97 1.89
1502 1538 6.763610 GGTTTCAATTTCAACCACAACCAATA 59.236 34.615 9.76 0.00 41.97 1.90
1505 1541 4.020218 TGGTTTCAATTTCAACCACAACCA 60.020 37.500 12.46 0.00 46.16 3.67
1506 1542 4.508662 TGGTTTCAATTTCAACCACAACC 58.491 39.130 12.46 0.00 46.16 3.77
1753 1790 8.755977 CATGGTTCCTTAGTAACCTCTAGTTTA 58.244 37.037 8.17 0.00 45.53 2.01
1768 1805 3.199727 TCAGTGCTATGCATGGTTCCTTA 59.800 43.478 10.16 0.00 41.91 2.69
1837 1874 3.012518 AGAGCACAACATCCTTATGCAC 58.987 45.455 0.00 0.00 38.79 4.57
1916 1953 4.528206 CCCTATTGGTCAAGGAAGCTTTTT 59.472 41.667 0.00 0.00 34.58 1.94
1990 2028 0.304705 GTATGCGTCCTTGGATTGCG 59.695 55.000 10.68 3.83 0.00 4.85
2024 2062 0.319555 ATGTGTCGTGAGTGGGAACG 60.320 55.000 0.00 0.00 41.11 3.95
2040 2078 4.714632 ACTTGGTGTAGCTTGTTACATGT 58.285 39.130 2.69 2.69 36.08 3.21
2044 2082 6.704937 ACTTCTTACTTGGTGTAGCTTGTTAC 59.295 38.462 0.00 0.00 32.08 2.50
2140 2178 2.290641 GGCGATCGGATTGCACTTTTAT 59.709 45.455 26.93 0.00 41.59 1.40
2163 2202 6.860034 TCTGGTGCTATTATCCCTACTTCTA 58.140 40.000 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.