Multiple sequence alignment - TraesCS1B01G083200

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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 TraesCS1B01G083200 chr1B 100.000 3212 0 0 1 3212 67057729 67054518 0.000000e+00 5932.0
1 TraesCS1B01G083200 chr1B 87.798 336 38 3 2440 2775 511445462 511445794 1.080000e-104 390.0
2 TraesCS1B01G083200 chr1D 95.219 3242 99 28 1 3212 47333531 47330316 0.000000e+00 5077.0
3 TraesCS1B01G083200 chr1D 86.391 338 39 5 2442 2775 381308237 381308571 2.360000e-96 363.0
4 TraesCS1B01G083200 chr1A 94.712 3139 98 24 116 3212 47215366 47212254 0.000000e+00 4815.0
5 TraesCS1B01G083200 chr1A 86.639 479 56 6 957 1434 45799771 45799300 1.020000e-144 523.0
6 TraesCS1B01G083200 chr7D 85.515 359 43 6 2438 2792 469841315 469840962 1.820000e-97 366.0
7 TraesCS1B01G083200 chr7D 84.848 363 47 4 2440 2797 483478680 483478321 3.050000e-95 359.0
8 TraesCS1B01G083200 chr7B 85.515 359 43 9 2438 2792 493524768 493524415 1.820000e-97 366.0
9 TraesCS1B01G083200 chr3A 85.070 355 48 5 2439 2793 40524 40175 1.100000e-94 357.0
10 TraesCS1B01G083200 chr3A 84.789 355 49 5 2439 2793 63441 63092 5.100000e-93 351.0
11 TraesCS1B01G083200 chr3A 100.000 28 0 0 139 166 579338092 579338065 6.000000e-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 TraesCS1B01G083200 chr1B 67054518 67057729 3211 True 5932 5932 100.000 1 3212 1 chr1B.!!$R1 3211
1 TraesCS1B01G083200 chr1D 47330316 47333531 3215 True 5077 5077 95.219 1 3212 1 chr1D.!!$R1 3211
2 TraesCS1B01G083200 chr1A 47212254 47215366 3112 True 4815 4815 94.712 116 3212 1 chr1A.!!$R2 3096

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
383 420 0.179108 CTGCTGGTAGTACGAAGGCC 60.179 60.000 0.0 0.0 0.00 5.19 F
775 813 0.867746 GTTGCGACTTCTGTCATGCA 59.132 50.000 0.0 0.0 43.06 3.96 F
970 1012 2.159226 CCTGGAGTACTTAGTCTTGGCG 60.159 54.545 0.0 0.0 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1451 1494 0.459934 TGTGTGCAAAACAAGGCTGC 60.460 50.000 1.09 0.0 41.57 5.25 R
1908 1951 1.078918 TTGCGGTGGCTGATGAGAG 60.079 57.895 0.00 0.0 40.82 3.20 R
2460 2504 2.031012 CCGACTCCTGCAGCAACA 59.969 61.111 8.66 0.0 0.00 3.33 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
86 90 1.698506 AGAATAGAGGGCGTGGAGAG 58.301 55.000 0.00 0.00 0.00 3.20
87 91 1.215673 AGAATAGAGGGCGTGGAGAGA 59.784 52.381 0.00 0.00 0.00 3.10
88 92 2.032620 GAATAGAGGGCGTGGAGAGAA 58.967 52.381 0.00 0.00 0.00 2.87
123 127 1.767681 AGGATCTGGAGGAGTTGATGC 59.232 52.381 0.00 0.00 0.00 3.91
130 134 1.734465 GGAGGAGTTGATGCGAACAAG 59.266 52.381 0.00 0.00 0.00 3.16
134 138 2.158449 GGAGTTGATGCGAACAAGTCTG 59.842 50.000 17.86 0.00 43.22 3.51
136 140 0.874390 TTGATGCGAACAAGTCTGCC 59.126 50.000 0.00 0.00 0.00 4.85
156 160 2.613474 CCCGACACTTATTTTGGGACGA 60.613 50.000 0.00 0.00 38.64 4.20
239 253 3.522731 CCGCCTCCTCTCCGAGTG 61.523 72.222 0.00 0.00 0.00 3.51
370 407 0.615331 TCTCAAACCCTAGCTGCTGG 59.385 55.000 13.43 9.59 0.00 4.85
383 420 0.179108 CTGCTGGTAGTACGAAGGCC 60.179 60.000 0.00 0.00 0.00 5.19
402 439 1.591863 GCGGCTTCATACCCTCGTC 60.592 63.158 0.00 0.00 0.00 4.20
491 528 2.965831 GCCCCCTTCTCCATATTTTTCC 59.034 50.000 0.00 0.00 0.00 3.13
500 537 4.814234 TCTCCATATTTTTCCGTTCCATCG 59.186 41.667 0.00 0.00 0.00 3.84
591 629 6.081693 GCATTTGTTCTTGATTGGAAATTGC 58.918 36.000 0.00 0.00 0.00 3.56
646 684 9.267084 GGTTTAATAAAAGTTGAAATCCAAGCA 57.733 29.630 0.00 0.00 35.03 3.91
656 694 7.049754 AGTTGAAATCCAAGCAAAATTTCTGT 58.950 30.769 12.20 0.00 39.20 3.41
774 812 1.136141 CAGTTGCGACTTCTGTCATGC 60.136 52.381 3.02 0.00 43.06 4.06
775 813 0.867746 GTTGCGACTTCTGTCATGCA 59.132 50.000 0.00 0.00 43.06 3.96
901 943 6.515272 AATGCTGAATTCGTAAGGACAAAT 57.485 33.333 0.04 0.00 38.47 2.32
918 960 5.355350 GGACAAATTACTGTGCAATAGCTCT 59.645 40.000 0.00 0.00 42.74 4.09
970 1012 2.159226 CCTGGAGTACTTAGTCTTGGCG 60.159 54.545 0.00 0.00 0.00 5.69
1086 1129 2.770164 AGAGGCAGAAGCAACGTAAT 57.230 45.000 0.00 0.00 44.61 1.89
1209 1252 2.609459 GCATAGATTTGTGGAGTGGTCG 59.391 50.000 0.00 0.00 0.00 4.79
1294 1337 4.518970 TCAAAGGTCTAACCAGCAACAATC 59.481 41.667 0.00 0.00 41.95 2.67
1317 1360 4.082026 CCATCTTGGGTTTGGAATGAAGAC 60.082 45.833 0.00 0.00 32.67 3.01
1350 1393 4.712122 ATTTTATGGCACCCTTTACGTG 57.288 40.909 0.00 0.00 0.00 4.49
1434 1477 2.824341 AGATCTTGAAAAGGCCTTGCTG 59.176 45.455 21.33 11.39 46.24 4.41
1531 1574 3.821421 ATCCCGACATTGGTCTAGTTC 57.179 47.619 0.00 0.00 42.05 3.01
1908 1951 1.153086 CCAGCAGCCCATGTCCTAC 60.153 63.158 0.00 0.00 0.00 3.18
1975 2018 3.069872 TGATTCAACAGTTGCCAGCAATT 59.930 39.130 8.52 0.88 38.28 2.32
2028 2071 5.733373 GCACGAGAAAGTTGTGAAAGGATTT 60.733 40.000 0.00 0.00 42.69 2.17
2040 2083 5.070180 TGTGAAAGGATTTGAGGCAATTGAA 59.930 36.000 10.34 0.00 39.27 2.69
2184 2227 0.392193 AAGCTCATCAAGGTGGCGAG 60.392 55.000 0.00 0.00 35.40 5.03
2204 2247 2.039405 GTCCTTCTGCAGCAGCTGG 61.039 63.158 24.13 19.94 42.74 4.85
2420 2464 1.003718 GTGACAGGGGCGCTACTTT 60.004 57.895 7.64 0.00 0.00 2.66
2433 2477 4.234574 GCGCTACTTTTGCTGGTAAATTT 58.765 39.130 0.00 0.00 0.00 1.82
2434 2478 5.395642 GCGCTACTTTTGCTGGTAAATTTA 58.604 37.500 0.00 0.00 0.00 1.40
2435 2479 5.859648 GCGCTACTTTTGCTGGTAAATTTAA 59.140 36.000 0.00 0.00 0.00 1.52
2460 2504 1.700955 AACTAGATGATACCCCGCGT 58.299 50.000 4.92 0.00 0.00 6.01
3096 3144 4.942761 AGGAATGTTGCTTGATGTTTGT 57.057 36.364 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 69 2.432510 CTCTCCACGCCCTCTATTCTTT 59.567 50.000 0.00 0.00 0.00 2.52
68 72 1.693627 TCTCTCCACGCCCTCTATTC 58.306 55.000 0.00 0.00 0.00 1.75
71 75 1.933021 TTTTCTCTCCACGCCCTCTA 58.067 50.000 0.00 0.00 0.00 2.43
105 109 1.410517 TCGCATCAACTCCTCCAGATC 59.589 52.381 0.00 0.00 0.00 2.75
107 111 1.066858 GTTCGCATCAACTCCTCCAGA 60.067 52.381 0.00 0.00 0.00 3.86
111 115 2.413453 GACTTGTTCGCATCAACTCCTC 59.587 50.000 0.00 0.00 0.00 3.71
114 118 2.412065 GCAGACTTGTTCGCATCAACTC 60.412 50.000 0.00 0.00 0.00 3.01
123 127 3.550656 GTCGGGCAGACTTGTTCG 58.449 61.111 10.66 0.00 46.13 3.95
134 138 1.471287 GTCCCAAAATAAGTGTCGGGC 59.529 52.381 0.00 0.00 33.43 6.13
136 140 2.690786 TCGTCCCAAAATAAGTGTCGG 58.309 47.619 0.00 0.00 0.00 4.79
175 179 1.649664 CAGCAGATCTCCTTTGTCCG 58.350 55.000 0.00 0.00 0.00 4.79
176 180 1.556911 TCCAGCAGATCTCCTTTGTCC 59.443 52.381 0.00 0.00 0.00 4.02
177 181 3.340814 TTCCAGCAGATCTCCTTTGTC 57.659 47.619 0.00 0.00 0.00 3.18
178 182 3.073650 AGTTTCCAGCAGATCTCCTTTGT 59.926 43.478 0.00 0.00 0.00 2.83
179 183 3.439476 CAGTTTCCAGCAGATCTCCTTTG 59.561 47.826 0.00 0.00 0.00 2.77
180 184 3.560882 CCAGTTTCCAGCAGATCTCCTTT 60.561 47.826 0.00 0.00 0.00 3.11
181 185 2.026449 CCAGTTTCCAGCAGATCTCCTT 60.026 50.000 0.00 0.00 0.00 3.36
183 187 1.556911 TCCAGTTTCCAGCAGATCTCC 59.443 52.381 0.00 0.00 0.00 3.71
239 253 2.830370 GCAGCATAGGTGGCCCAC 60.830 66.667 4.93 4.93 0.00 4.61
370 407 2.278401 CCGCGGCCTTCGTACTAC 60.278 66.667 14.67 0.00 41.72 2.73
402 439 0.250295 TGGCGACCAGAAACTCCAAG 60.250 55.000 0.00 0.00 0.00 3.61
451 488 2.092429 GGCAGGGATGTACCAATCAGAA 60.092 50.000 0.00 0.00 41.20 3.02
491 528 2.180204 GCCATGGTCCGATGGAACG 61.180 63.158 14.67 0.00 43.50 3.95
500 537 1.143073 CCTAAACCTAGGCCATGGTCC 59.857 57.143 14.18 14.80 38.50 4.46
544 582 2.548480 GACTGGAAAACCCTTGTCTTCG 59.452 50.000 0.00 0.00 36.71 3.79
591 629 5.102953 TCATACATTGTTCTTCAGGGGAG 57.897 43.478 0.00 0.00 0.00 4.30
673 711 7.834068 GTGTCAGCACAAGAAAATAGAGATA 57.166 36.000 0.00 0.00 44.64 1.98
699 737 6.436261 GCATCGATGTAAGCTACTGTAGTTA 58.564 40.000 25.47 10.15 0.00 2.24
709 747 0.833287 ACAGGGCATCGATGTAAGCT 59.167 50.000 25.47 4.44 0.00 3.74
710 748 1.668419 AACAGGGCATCGATGTAAGC 58.332 50.000 25.47 11.82 0.00 3.09
774 812 6.573664 TGGTTGACAAGAGGTTAATCATTG 57.426 37.500 2.98 2.98 31.80 2.82
775 813 7.177878 AGATGGTTGACAAGAGGTTAATCATT 58.822 34.615 0.26 0.00 44.24 2.57
780 818 5.012664 TGCTAGATGGTTGACAAGAGGTTAA 59.987 40.000 0.00 0.00 0.00 2.01
901 943 9.098355 CATAACTTTAGAGCTATTGCACAGTAA 57.902 33.333 1.12 0.00 42.74 2.24
918 960 7.179694 AGTTACTCACTAGGTGGCATAACTTTA 59.820 37.037 0.00 0.00 35.02 1.85
978 1021 3.764885 GCTTTATGCCTGTAAGTGTGG 57.235 47.619 0.00 0.00 35.15 4.17
1086 1129 5.011125 GGTAGATCTAGCAGCAACATAAGGA 59.989 44.000 23.80 0.00 34.00 3.36
1230 1273 3.037549 AGTGGACAAATCAAAAGGGCAA 58.962 40.909 0.00 0.00 0.00 4.52
1294 1337 4.082026 GTCTTCATTCCAAACCCAAGATGG 60.082 45.833 0.00 0.00 37.25 3.51
1317 1360 3.124466 TGCCATAAAATTGTCTCACGACG 59.876 43.478 0.00 0.00 43.21 5.12
1329 1372 3.445805 CCACGTAAAGGGTGCCATAAAAT 59.554 43.478 0.00 0.00 34.08 1.82
1451 1494 0.459934 TGTGTGCAAAACAAGGCTGC 60.460 50.000 1.09 0.00 41.57 5.25
1531 1574 8.472683 AGATCAACTTCAGTTTTAAGATCTCG 57.527 34.615 11.70 0.00 38.55 4.04
1908 1951 1.078918 TTGCGGTGGCTGATGAGAG 60.079 57.895 0.00 0.00 40.82 3.20
1975 2018 6.936900 CCCTCTATCAGTTTTGAAAGTTGAGA 59.063 38.462 0.00 0.00 36.78 3.27
2028 2071 2.229792 AGTCGCTTTTCAATTGCCTCA 58.770 42.857 0.00 0.00 0.00 3.86
2040 2083 3.502211 CCTCCATTGTGTAAAGTCGCTTT 59.498 43.478 9.27 9.27 37.46 3.51
2184 2227 2.749441 GCTGCTGCAGAAGGACCC 60.749 66.667 32.30 9.52 39.41 4.46
2204 2247 2.365941 GACAGGTAGGGAAGCTATGGAC 59.634 54.545 0.00 0.00 33.59 4.02
2433 2477 8.192774 CGCGGGGTATCATCTAGTTTATTATTA 58.807 37.037 0.00 0.00 0.00 0.98
2434 2478 7.039882 CGCGGGGTATCATCTAGTTTATTATT 58.960 38.462 0.00 0.00 0.00 1.40
2435 2479 6.154021 ACGCGGGGTATCATCTAGTTTATTAT 59.846 38.462 12.47 0.00 0.00 1.28
2460 2504 2.031012 CCGACTCCTGCAGCAACA 59.969 61.111 8.66 0.00 0.00 3.33
2469 2513 5.680619 TGAAATATATTGCAACCGACTCCT 58.319 37.500 0.00 0.00 0.00 3.69
2639 2683 5.840149 ACCACATTATACAATGCATGGGAAT 59.160 36.000 5.94 1.29 44.62 3.01
2641 2685 4.583907 CACCACATTATACAATGCATGGGA 59.416 41.667 5.94 0.00 44.62 4.37
2863 2911 4.041691 AGGTTGTGGAAGTGCTACTTGTAT 59.958 41.667 6.31 0.00 38.80 2.29
3096 3144 6.575267 TCAGTAGTTGTAGTAACTGTGCAAA 58.425 36.000 2.75 0.00 40.18 3.68


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

AutoCloner maintained by Alex Coulton.