Multiple sequence alignment - TraesCS1B01G316300

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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 TraesCS1B01G316300 chr1B 100.000 3090 0 0 1 3090 540731106 540728017 0 5707
1 TraesCS1B01G316300 chr1A 94.480 3134 115 22 2 3090 498066000 498062880 0 4776
2 TraesCS1B01G316300 chr1D 96.286 2127 63 6 1 2124 402835507 402833394 0 3476
3 TraesCS1B01G316300 chr1D 92.849 881 47 5 2223 3090 402833400 402832523 0 1264


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 TraesCS1B01G316300 chr1B 540728017 540731106 3089 True 5707 5707 100.0000 1 3090 1 chr1B.!!$R1 3089
1 TraesCS1B01G316300 chr1A 498062880 498066000 3120 True 4776 4776 94.4800 2 3090 1 chr1A.!!$R1 3088
2 TraesCS1B01G316300 chr1D 402832523 402835507 2984 True 2370 3476 94.5675 1 3090 2 chr1D.!!$R1 3089

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
114 115 0.250295 TGCAACTCCCTTCCTGTTCG 60.250 55.0 0.0 0.0 0.00 3.95 F
157 161 0.396417 GAGGACTAGGAGCAGGAGCA 60.396 60.0 0.0 0.0 45.49 4.26 F
158 162 0.396974 AGGACTAGGAGCAGGAGCAG 60.397 60.0 0.0 0.0 45.49 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1868 1900 0.035725 CAGGACCATCAGCTCTTGCA 60.036 55.000 0.0 0.0 42.74 4.08 R
1883 1915 2.061848 TCCTCACCATTGTTTCCAGGA 58.938 47.619 0.0 0.0 0.00 3.86 R
2102 2134 5.316167 TGACAAAGTTGCATCACTATCCTT 58.684 37.500 0.0 0.0 0.00 3.36 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
55 56 1.147399 AGGGACGATAACCTCTAGGGG 59.853 57.143 7.26 7.26 40.27 4.79
58 59 0.826672 ACGATAACCTCTAGGGGCCG 60.827 60.000 9.18 10.06 40.27 6.13
114 115 0.250295 TGCAACTCCCTTCCTGTTCG 60.250 55.000 0.00 0.00 0.00 3.95
134 138 1.450312 CTTTGGCCTACCTCCAGCG 60.450 63.158 3.32 0.00 34.66 5.18
145 149 3.423380 TCCAGCGAGGGAGGACTA 58.577 61.111 0.00 0.00 38.24 2.59
153 157 0.469144 GAGGGAGGACTAGGAGCAGG 60.469 65.000 0.00 0.00 0.00 4.85
154 158 0.926720 AGGGAGGACTAGGAGCAGGA 60.927 60.000 0.00 0.00 0.00 3.86
155 159 0.469144 GGGAGGACTAGGAGCAGGAG 60.469 65.000 0.00 0.00 0.00 3.69
156 160 1.112916 GGAGGACTAGGAGCAGGAGC 61.113 65.000 0.00 0.00 42.56 4.70
157 161 0.396417 GAGGACTAGGAGCAGGAGCA 60.396 60.000 0.00 0.00 45.49 4.26
158 162 0.396974 AGGACTAGGAGCAGGAGCAG 60.397 60.000 0.00 0.00 45.49 4.24
243 247 3.033368 AGGTCAGCGACTTCTTTCTTC 57.967 47.619 8.26 0.00 32.47 2.87
247 251 3.917985 GTCAGCGACTTCTTTCTTCTCTC 59.082 47.826 0.00 0.00 0.00 3.20
297 306 0.892063 TTTGGGGGTTGCTAATTCGC 59.108 50.000 0.00 0.00 0.00 4.70
303 312 1.747745 GTTGCTAATTCGCCCCGGT 60.748 57.895 0.00 0.00 0.00 5.28
426 437 0.460722 TCGTTCGGGGATTTATGCGA 59.539 50.000 0.00 0.00 0.00 5.10
452 463 1.894466 TGTTTAGGTTGGGATCGACGA 59.106 47.619 0.00 0.00 0.00 4.20
469 480 3.135056 GACGGGTCTCGCCGCTAAT 62.135 63.158 0.00 0.00 43.89 1.73
481 492 1.734377 GCCGCTAATTTTGTTTCCGGG 60.734 52.381 0.00 0.00 35.12 5.73
550 563 5.008712 CCTTGTTTTCGCTCTTCTTTTAGGT 59.991 40.000 0.00 0.00 0.00 3.08
561 578 6.762187 GCTCTTCTTTTAGGTGGGAATAGTAC 59.238 42.308 0.00 0.00 0.00 2.73
579 596 2.555732 ACCCTGTTCCCCGTAGAATA 57.444 50.000 0.00 0.00 0.00 1.75
696 716 9.961264 GGGTATTCTCTTTAGGAATTATTAGGG 57.039 37.037 0.00 0.00 35.40 3.53
731 751 7.609532 CACTCCTGTTCCTAAAGAATCAGAAAT 59.390 37.037 0.00 0.00 36.51 2.17
791 811 6.436843 TTTGTTCTTCTCCTTGTTCTTGTC 57.563 37.500 0.00 0.00 0.00 3.18
935 955 4.760715 GCTGCACTTATTCTCATGGATGAT 59.239 41.667 0.00 0.00 36.02 2.45
995 1015 6.949352 ATGCAGATTATTACCCTTCAACTG 57.051 37.500 0.00 0.00 0.00 3.16
1023 1043 1.333619 GTGCACGGTTCACAGATTTGT 59.666 47.619 0.00 0.00 38.31 2.83
1033 1053 4.341366 TCACAGATTTGTCTTCTGCTCA 57.659 40.909 0.78 0.00 43.57 4.26
1091 1111 2.097038 AGAAGCTGACATCACGCGC 61.097 57.895 5.73 0.00 0.00 6.86
1118 1138 1.035932 GCCATGAATGTCAGCAGGCT 61.036 55.000 0.00 0.00 38.73 4.58
1292 1324 1.539929 GGGGACAGCGATGATGAAGAG 60.540 57.143 8.12 0.00 0.00 2.85
1370 1402 3.425713 CTGCGCCGTGTGCTTGAT 61.426 61.111 4.18 0.00 40.03 2.57
1658 1690 2.412089 CACGGTCAAAATCGAAGAGGTC 59.588 50.000 0.00 0.00 43.63 3.85
1793 1825 2.909965 TGCCCAGTTTGCCGGTTC 60.910 61.111 1.90 0.00 0.00 3.62
1847 1879 0.460284 AGCCTAGCAACGTTGATCGG 60.460 55.000 31.62 29.27 44.69 4.18
1868 1900 2.395336 TAGAGAGCAGCCATGAGGAT 57.605 50.000 0.00 0.00 36.89 3.24
1883 1915 0.917533 AGGATGCAAGAGCTGATGGT 59.082 50.000 0.00 0.00 42.74 3.55
2076 2108 4.999950 CAGGGCATAGTTGATCTTATCCAC 59.000 45.833 0.00 0.00 0.00 4.02
2148 2180 8.524487 GTCAGTAGAACTCTTCTTTCCATCTTA 58.476 37.037 0.00 0.00 41.14 2.10
2152 2184 7.411486 AGAACTCTTCTTTCCATCTTATCGA 57.589 36.000 0.00 0.00 36.36 3.59
2194 2226 3.117813 ACAGGGTACAAAGTTTGTGGCTA 60.118 43.478 27.65 8.07 45.03 3.93
2228 2260 1.769733 TTGCGCTCATTTCACTTTGC 58.230 45.000 9.73 0.00 0.00 3.68
2254 2286 3.014623 GTGTTATGGCTAAGTCAACCCC 58.985 50.000 0.00 0.00 0.00 4.95
2388 2420 6.233905 ACCAGAAAGCAACCTTGTTAAAAT 57.766 33.333 0.00 0.00 0.00 1.82
2424 2460 7.546667 CGCTTTATGTAGTGGTTTTCTTACCTA 59.453 37.037 0.00 0.00 39.04 3.08
2425 2461 9.392259 GCTTTATGTAGTGGTTTTCTTACCTAT 57.608 33.333 0.00 0.00 39.04 2.57
2447 2483 4.281657 TCATGCCTCTAGAAGCTTCTACA 58.718 43.478 28.47 24.05 38.70 2.74
2490 2526 4.410400 GCCAAGCCGCCTGTAGGT 62.410 66.667 0.00 0.00 37.57 3.08
2526 2562 9.927081 AAGGATGGTCAAAAAGATTATGAGTAT 57.073 29.630 0.00 0.00 0.00 2.12
2570 2606 3.367992 TGCTTGTGCATAAAGTTGGTG 57.632 42.857 12.19 0.00 45.31 4.17
2609 2645 8.960591 CCCAAAAGTATACATCTGTTTGAAGAT 58.039 33.333 5.50 0.00 37.39 2.40
2624 2660 7.530010 TGTTTGAAGATAACTCAAGCTAATGC 58.470 34.615 0.00 0.00 40.05 3.56
2672 2708 5.362430 GCCCAAAATTATACATCTGGTTGGA 59.638 40.000 0.00 0.00 37.11 3.53
2711 2747 0.439985 CAGTGTCGTCGCTTTGATGG 59.560 55.000 0.00 0.00 34.17 3.51
2728 2773 7.467947 GCTTTGATGGAATTCCTTAGCTACTTC 60.468 40.741 24.73 5.44 36.82 3.01
2749 2794 3.333680 TCCTATCATGCCTAAATTCCCCC 59.666 47.826 0.00 0.00 0.00 5.40
2770 2815 4.536765 CCCTCCTGCTATTACCAAAATGT 58.463 43.478 0.00 0.00 0.00 2.71
2787 2832 6.203338 CCAAAATGTTTTGCTATGGATATGCC 59.797 38.462 11.70 0.00 44.62 4.40
2797 2842 2.138535 TGGATATGCCATCCCCTTCT 57.861 50.000 10.98 0.00 43.33 2.85
2803 2848 5.191722 GGATATGCCATCCCCTTCTGTATAA 59.808 44.000 3.52 0.00 36.34 0.98
2836 2881 6.153067 ACAGTTCACGTTTCATTTGTTTTCA 58.847 32.000 0.00 0.00 0.00 2.69
2951 2997 3.706594 TCCTATTCCTCTGCTTACCTGTG 59.293 47.826 0.00 0.00 0.00 3.66
2996 3042 1.002624 TGCCCCTTGTCTTAAGCCG 60.003 57.895 0.00 0.00 0.00 5.52
3019 3065 5.231991 CGACATTATTGCCCATTTGTTTAGC 59.768 40.000 0.00 0.00 0.00 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 1.125633 TGGATACTTTACTCCCCGGC 58.874 55.000 0.00 0.00 37.61 6.13
58 59 3.113043 ACTGGTGGATACTTTACTCCCC 58.887 50.000 0.00 0.00 37.61 4.81
114 115 0.393132 GCTGGAGGTAGGCCAAAGAC 60.393 60.000 5.01 0.00 34.44 3.01
134 138 0.469144 CCTGCTCCTAGTCCTCCCTC 60.469 65.000 0.00 0.00 0.00 4.30
145 149 3.082701 GCTCCTGCTCCTGCTCCT 61.083 66.667 0.00 0.00 40.48 3.69
297 306 2.035626 ATTTGGAGCACACCGGGG 59.964 61.111 0.00 0.00 0.00 5.73
303 312 2.290367 CGTGTTCTTGATTTGGAGCACA 59.710 45.455 9.68 0.00 41.48 4.57
426 437 4.018779 TCGATCCCAACCTAAACAAATCCT 60.019 41.667 0.00 0.00 0.00 3.24
469 480 2.503382 GGCTGCCCCGGAAACAAAA 61.503 57.895 7.66 0.00 0.00 2.44
481 492 2.672996 ACACAACATCGGGCTGCC 60.673 61.111 11.05 11.05 0.00 4.85
561 578 2.674420 TCTATTCTACGGGGAACAGGG 58.326 52.381 0.00 0.00 0.00 4.45
579 596 2.636830 CAAGAATGAGGTGCCGATTCT 58.363 47.619 10.72 10.72 37.92 2.40
658 675 0.733150 GAATACCCAACTGAAGCCGC 59.267 55.000 0.00 0.00 0.00 6.53
696 716 0.952984 GAACAGGAGTGGCAGACAGC 60.953 60.000 0.00 0.00 44.65 4.40
791 811 1.597302 CAGGAGATCAGCATGGCGG 60.597 63.158 0.00 0.00 36.16 6.13
935 955 9.906660 GAAAACAACCACACATGAGATAATTTA 57.093 29.630 0.00 0.00 0.00 1.40
943 963 4.362279 CCAAGAAAACAACCACACATGAG 58.638 43.478 0.00 0.00 0.00 2.90
995 1015 1.069906 GTGAACCGTGCACAATGAGTC 60.070 52.381 18.64 5.42 36.31 3.36
1023 1043 2.284263 CGTAGCACATGAGCAGAAGA 57.716 50.000 17.61 0.00 36.85 2.87
1091 1111 2.941064 CTGACATTCATGGCACCAGTAG 59.059 50.000 0.00 0.00 41.84 2.57
1118 1138 2.284625 ACCATGGCCTCCTCGACA 60.285 61.111 13.04 0.00 0.00 4.35
1292 1324 5.646577 ACTCACGGCCTATATCACTATTC 57.353 43.478 0.00 0.00 0.00 1.75
1370 1402 5.397360 TCTCTAAGGTCATCATGGATGCTA 58.603 41.667 1.37 0.00 39.63 3.49
1658 1690 1.000827 AGACAGACTGAACAGCTGACG 60.001 52.381 23.35 12.04 36.64 4.35
1793 1825 0.388294 TCTCATCAGATGGCAGCTCG 59.612 55.000 0.27 0.00 0.00 5.03
1847 1879 2.246469 TCCTCATGGCTGCTCTCTATC 58.754 52.381 0.00 0.00 0.00 2.08
1868 1900 0.035725 CAGGACCATCAGCTCTTGCA 60.036 55.000 0.00 0.00 42.74 4.08
1883 1915 2.061848 TCCTCACCATTGTTTCCAGGA 58.938 47.619 0.00 0.00 0.00 3.86
2071 2103 9.060347 GTATGATCATTATTCACAACAGTGGAT 57.940 33.333 14.65 0.00 35.64 3.41
2102 2134 5.316167 TGACAAAGTTGCATCACTATCCTT 58.684 37.500 0.00 0.00 0.00 3.36
2168 2200 4.081917 CCACAAACTTTGTACCCTGTTGTT 60.082 41.667 6.84 0.00 43.23 2.83
2169 2201 3.445805 CCACAAACTTTGTACCCTGTTGT 59.554 43.478 6.84 0.00 43.23 3.32
2170 2202 3.736740 GCCACAAACTTTGTACCCTGTTG 60.737 47.826 6.84 0.00 43.23 3.33
2194 2226 4.395854 TGAGCGCAAATCATATGTCAAAGT 59.604 37.500 11.47 0.00 0.00 2.66
2228 2260 5.122396 GGTTGACTTAGCCATAACACTGAAG 59.878 44.000 0.00 0.00 0.00 3.02
2346 2378 5.235616 TCTGGTCGATGTTTACAAGTGAAAC 59.764 40.000 0.00 0.00 37.32 2.78
2388 2420 3.770933 ACTACATAAAGCGTAAGGGGACA 59.229 43.478 0.00 0.00 38.28 4.02
2424 2460 4.898265 TGTAGAAGCTTCTAGAGGCATGAT 59.102 41.667 31.81 12.89 40.23 2.45
2425 2461 4.281657 TGTAGAAGCTTCTAGAGGCATGA 58.718 43.478 31.81 10.72 40.23 3.07
2428 2464 4.621747 GCTTTGTAGAAGCTTCTAGAGGCA 60.622 45.833 31.64 25.34 40.23 4.75
2453 2489 1.674322 GGCAAGCTACCGGAAGCAA 60.674 57.895 9.46 0.00 45.30 3.91
2481 2517 2.436115 GGCCGTTCACCTACAGGC 60.436 66.667 0.00 0.00 46.51 4.85
2485 2521 1.447314 CCTTCGGCCGTTCACCTAC 60.447 63.158 27.15 0.00 0.00 3.18
2490 2526 2.267642 CCATCCTTCGGCCGTTCA 59.732 61.111 27.15 9.72 0.00 3.18
2526 2562 4.048970 AGCTTGACTTCCCTACAGACTA 57.951 45.455 0.00 0.00 0.00 2.59
2570 2606 2.897326 ACTTTTGGGCAACAATACCTCC 59.103 45.455 0.00 0.00 39.21 4.30
2624 2660 6.747280 GCAACAATACCTAACTTTATGCACAG 59.253 38.462 0.00 0.00 0.00 3.66
2681 2717 4.093850 AGCGACGACACTGTTAAAAGTTTT 59.906 37.500 6.06 6.06 0.00 2.43
2682 2718 3.619929 AGCGACGACACTGTTAAAAGTTT 59.380 39.130 0.00 0.00 0.00 2.66
2683 2719 3.192466 AGCGACGACACTGTTAAAAGTT 58.808 40.909 0.00 0.00 0.00 2.66
2697 2733 2.006888 GGAATTCCATCAAAGCGACGA 58.993 47.619 20.04 0.00 35.64 4.20
2711 2747 7.333174 GCATGATAGGAAGTAGCTAAGGAATTC 59.667 40.741 0.00 0.00 0.00 2.17
2728 2773 3.701664 GGGGGAATTTAGGCATGATAGG 58.298 50.000 0.00 0.00 0.00 2.57
2749 2794 6.530019 AAACATTTTGGTAATAGCAGGAGG 57.470 37.500 0.00 0.00 0.00 4.30
2787 2832 6.841601 TCAAAGGATTATACAGAAGGGGATG 58.158 40.000 0.00 0.00 0.00 3.51
2791 2836 7.112779 ACTGTTCAAAGGATTATACAGAAGGG 58.887 38.462 0.00 0.00 34.87 3.95
2797 2842 6.932400 ACGTGAACTGTTCAAAGGATTATACA 59.068 34.615 23.55 0.00 42.15 2.29
2803 2848 4.638421 TGAAACGTGAACTGTTCAAAGGAT 59.362 37.500 23.55 13.51 42.15 3.24
2836 2881 8.612145 AGGTTGATAGGACCATTTAGTTAAACT 58.388 33.333 0.00 0.00 39.71 2.66
2951 2997 3.128589 TCAACTTGGAGCAAACAACTGTC 59.871 43.478 0.00 0.00 0.00 3.51
2996 3042 5.231991 CGCTAAACAAATGGGCAATAATGTC 59.768 40.000 0.00 0.00 0.00 3.06
3019 3065 1.401761 TTTCAATCCCATGGCATCCG 58.598 50.000 6.09 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.