Multiple sequence alignment - TraesCS3B01G453600

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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 TraesCS3B01G453600 chr3B 100.000 3248 0 0 1 3248 694323532 694326779 0.000000e+00 5999
1 TraesCS3B01G453600 chr3B 80.106 377 50 16 2330 2696 140589901 140590262 1.160000e-64 257
2 TraesCS3B01G453600 chr3A 94.700 3151 124 18 126 3248 660235966 660239101 0.000000e+00 4854
3 TraesCS3B01G453600 chr3A 84.762 105 10 5 1 101 660235875 660235977 2.060000e-17 100
4 TraesCS3B01G453600 chr3D 93.626 2965 137 24 1 2938 526047687 526050626 0.000000e+00 4381
5 TraesCS3B01G453600 chr3D 96.474 312 9 2 2937 3248 526050791 526051100 6.210000e-142 514
6 TraesCS3B01G453600 chr5A 81.183 372 48 15 2330 2694 580593646 580593290 2.470000e-71 279
7 TraesCS3B01G453600 chr7D 80.533 375 44 16 2330 2696 162017692 162017339 8.940000e-66 261


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 TraesCS3B01G453600 chr3B 694323532 694326779 3247 False 5999.0 5999 100.000 1 3248 1 chr3B.!!$F2 3247
1 TraesCS3B01G453600 chr3A 660235875 660239101 3226 False 2477.0 4854 89.731 1 3248 2 chr3A.!!$F1 3247
2 TraesCS3B01G453600 chr3D 526047687 526051100 3413 False 2447.5 4381 95.050 1 3248 2 chr3D.!!$F1 3247

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
118 123 0.029567 CTGCTCGACCTATCCGTGAC 59.970 60.0 0.00 0.00 0.00 3.67 F
511 524 0.524816 CGCTGCATCATGAAAGTGCC 60.525 55.0 15.37 2.55 38.06 5.01 F
1050 1068 0.514691 CAGAGAAAACACCGCTCTGC 59.485 55.0 0.00 0.00 46.12 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1032 1050 0.106708 TGCAGAGCGGTGTTTTCTCT 59.893 50.000 0.0 0.0 37.66 3.10 R
1461 1479 0.171231 GGGCTGAAACGGAGAAATGC 59.829 55.000 0.0 0.0 0.00 3.56 R
2982 3190 1.681666 CAGAGGGAGCAAGGCAAGA 59.318 57.895 0.0 0.0 0.00 3.02 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
26 27 2.252260 CGGCCGAGCAAACACTTG 59.748 61.111 24.07 0.00 35.49 3.16
28 29 1.896660 GGCCGAGCAAACACTTGGA 60.897 57.895 1.86 0.00 43.13 3.53
30 31 0.040067 GCCGAGCAAACACTTGGAAG 60.040 55.000 1.86 0.00 43.13 3.46
34 35 2.097466 CGAGCAAACACTTGGAAGTTGT 59.903 45.455 0.00 0.00 37.08 3.32
35 36 3.438360 GAGCAAACACTTGGAAGTTGTG 58.562 45.455 0.00 0.00 37.08 3.33
37 38 2.094234 GCAAACACTTGGAAGTTGTGGT 60.094 45.455 0.00 0.00 37.08 4.16
38 39 3.769536 CAAACACTTGGAAGTTGTGGTC 58.230 45.455 0.00 0.00 37.08 4.02
104 109 4.099170 CAGTTGCTGCCGCTGCTC 62.099 66.667 21.13 14.39 38.71 4.26
113 118 2.336809 CCGCTGCTCGACCTATCC 59.663 66.667 0.00 0.00 41.67 2.59
118 123 0.029567 CTGCTCGACCTATCCGTGAC 59.970 60.000 0.00 0.00 0.00 3.67
119 124 0.678684 TGCTCGACCTATCCGTGACA 60.679 55.000 0.00 0.00 0.00 3.58
120 125 0.029567 GCTCGACCTATCCGTGACAG 59.970 60.000 0.00 0.00 0.00 3.51
121 126 1.380524 CTCGACCTATCCGTGACAGT 58.619 55.000 0.00 0.00 0.00 3.55
123 128 1.092348 CGACCTATCCGTGACAGTGA 58.908 55.000 0.00 0.00 0.00 3.41
124 129 1.064208 CGACCTATCCGTGACAGTGAG 59.936 57.143 0.00 0.00 0.00 3.51
126 131 1.272536 ACCTATCCGTGACAGTGAGGT 60.273 52.381 0.00 0.00 0.00 3.85
130 135 1.069765 CCGTGACAGTGAGGTTGCT 59.930 57.895 0.00 0.00 0.00 3.91
131 136 1.224069 CCGTGACAGTGAGGTTGCTG 61.224 60.000 0.00 0.00 38.58 4.41
132 137 1.835483 CGTGACAGTGAGGTTGCTGC 61.835 60.000 0.00 0.00 36.26 5.25
133 138 1.227943 TGACAGTGAGGTTGCTGCC 60.228 57.895 0.00 0.00 36.26 4.85
134 139 2.281070 ACAGTGAGGTTGCTGCCG 60.281 61.111 0.00 0.00 36.26 5.69
135 140 3.730761 CAGTGAGGTTGCTGCCGC 61.731 66.667 0.00 0.00 0.00 6.53
136 141 3.946201 AGTGAGGTTGCTGCCGCT 61.946 61.111 0.70 0.00 36.97 5.52
152 157 4.554363 CTCCGCTACCGTCCGCAG 62.554 72.222 0.00 0.00 0.00 5.18
160 165 4.063967 CCGTCCGCAGTGGCTACA 62.064 66.667 2.02 0.00 38.10 2.74
317 323 4.946157 AGCTAGATTTTGTGCAAGCTGTAT 59.054 37.500 4.53 0.00 38.79 2.29
324 330 4.764679 TTGTGCAAGCTGTATAGGTTTG 57.235 40.909 0.65 0.00 42.41 2.93
330 336 0.657840 GCTGTATAGGTTTGCTGGCG 59.342 55.000 0.00 0.00 0.00 5.69
338 344 1.598130 GTTTGCTGGCGAGACAGGT 60.598 57.895 8.17 0.00 38.90 4.00
404 410 7.489435 CGATCTATACTTCTGCTAGAGAGAGAG 59.511 44.444 0.00 0.00 30.18 3.20
412 418 1.684869 GCTAGAGAGAGAGGCCAGTGT 60.685 57.143 5.01 0.00 0.00 3.55
416 422 2.708325 AGAGAGAGAGGCCAGTGTTTTT 59.292 45.455 5.01 0.00 0.00 1.94
417 423 3.070748 GAGAGAGAGGCCAGTGTTTTTC 58.929 50.000 5.01 0.00 0.00 2.29
423 429 1.141053 AGGCCAGTGTTTTTCTCTCGT 59.859 47.619 5.01 0.00 0.00 4.18
426 432 2.221981 GCCAGTGTTTTTCTCTCGTCTG 59.778 50.000 0.00 0.00 0.00 3.51
427 433 3.717707 CCAGTGTTTTTCTCTCGTCTGA 58.282 45.455 0.00 0.00 0.00 3.27
428 434 4.310769 CCAGTGTTTTTCTCTCGTCTGAT 58.689 43.478 0.00 0.00 0.00 2.90
429 435 5.470368 CCAGTGTTTTTCTCTCGTCTGATA 58.530 41.667 0.00 0.00 0.00 2.15
437 450 7.397892 TTTTCTCTCGTCTGATACTGATTCT 57.602 36.000 0.00 0.00 0.00 2.40
468 481 2.293399 GCTGGTTACTTTGTTCACTGGG 59.707 50.000 0.00 0.00 0.00 4.45
509 522 3.745332 TTACGCTGCATCATGAAAGTG 57.255 42.857 0.00 7.42 0.00 3.16
511 524 0.524816 CGCTGCATCATGAAAGTGCC 60.525 55.000 15.37 2.55 38.06 5.01
578 596 1.160137 GATGAAGACAAAGCAGGCGT 58.840 50.000 0.00 0.00 0.00 5.68
579 597 1.129437 GATGAAGACAAAGCAGGCGTC 59.871 52.381 0.00 0.00 0.00 5.19
813 831 2.549992 CGTGGAACAGATGGAACAAGGA 60.550 50.000 0.00 0.00 41.73 3.36
852 870 3.066900 ACACGATCAGATCTTCCGGTTAG 59.933 47.826 8.82 0.00 0.00 2.34
957 975 3.837146 TCTCAGAAGAAACCATCTCTGCT 59.163 43.478 0.00 0.00 37.42 4.24
958 976 4.081752 TCTCAGAAGAAACCATCTCTGCTC 60.082 45.833 0.00 0.00 37.42 4.26
1021 1039 0.743701 GCTCACCCACTCATCTGCTG 60.744 60.000 0.00 0.00 0.00 4.41
1023 1041 1.748122 CACCCACTCATCTGCTGCC 60.748 63.158 0.00 0.00 0.00 4.85
1025 1043 3.200593 CCACTCATCTGCTGCCGC 61.201 66.667 0.00 0.00 0.00 6.53
1026 1044 2.125229 CACTCATCTGCTGCCGCT 60.125 61.111 0.70 0.00 36.97 5.52
1027 1045 2.125229 ACTCATCTGCTGCCGCTG 60.125 61.111 0.70 0.54 36.97 5.18
1028 1046 3.574445 CTCATCTGCTGCCGCTGC 61.574 66.667 14.83 14.83 36.97 5.25
1029 1047 4.091939 TCATCTGCTGCCGCTGCT 62.092 61.111 21.13 0.52 38.71 4.24
1030 1048 3.132139 CATCTGCTGCCGCTGCTT 61.132 61.111 21.13 5.63 38.71 3.91
1031 1049 2.823147 ATCTGCTGCCGCTGCTTC 60.823 61.111 21.13 0.00 38.71 3.86
1032 1050 3.617143 ATCTGCTGCCGCTGCTTCA 62.617 57.895 21.13 7.19 38.71 3.02
1033 1051 3.800863 CTGCTGCCGCTGCTTCAG 61.801 66.667 21.13 8.43 38.71 3.02
1034 1052 4.318949 TGCTGCCGCTGCTTCAGA 62.319 61.111 21.13 0.00 38.71 3.27
1044 1062 1.069636 GCTGCTTCAGAGAAAACACCG 60.070 52.381 0.00 0.00 32.44 4.94
1050 1068 0.514691 CAGAGAAAACACCGCTCTGC 59.485 55.000 0.00 0.00 46.12 4.26
1061 1079 1.968017 CGCTCTGCACACCACCAAT 60.968 57.895 0.00 0.00 0.00 3.16
1104 1122 1.986882 ACCTTCCAAAACTCCTGCAG 58.013 50.000 6.78 6.78 0.00 4.41
1247 1265 2.821366 CCTGATGGCGGTGTCTGC 60.821 66.667 0.00 0.00 0.00 4.26
1254 1272 2.581354 GCGGTGTCTGCCTCTGAT 59.419 61.111 0.00 0.00 0.00 2.90
1278 1296 2.747686 GGAGTGGCTCCGGTGAAA 59.252 61.111 7.92 0.00 41.08 2.69
1281 1299 0.744771 GAGTGGCTCCGGTGAAATCC 60.745 60.000 7.92 0.00 0.00 3.01
1461 1479 1.315257 GGTACTGTGCAAGCCCCATG 61.315 60.000 0.00 0.00 0.00 3.66
1479 1497 0.881118 TGCATTTCTCCGTTTCAGCC 59.119 50.000 0.00 0.00 0.00 4.85
1702 1720 0.104304 ACGTCGTGTTCCTCAAGCTT 59.896 50.000 0.00 0.00 0.00 3.74
2152 2175 9.937175 GGAGTTTATGCTGTAAATAGTCATTTC 57.063 33.333 0.00 0.00 35.88 2.17
2222 2245 6.825946 GGCATACCAAGCATGTTTTGCAAAT 61.826 40.000 13.65 0.00 44.87 2.32
2362 2388 9.109393 GTGTCTCATAACTTCAAATATTAGCCA 57.891 33.333 0.00 0.00 0.00 4.75
2506 2534 7.329471 TCTGATGTGTTCTAGAAACATCTTTCG 59.671 37.037 32.48 24.88 46.69 3.46
2680 2708 4.978083 ATCTAAATGGAGTGCAAAGCAG 57.022 40.909 0.00 0.00 40.08 4.24
2686 2714 1.073763 TGGAGTGCAAAGCAGGTACAT 59.926 47.619 0.00 0.00 40.08 2.29
2702 2730 9.563748 AGCAGGTACATTTTACTAGTTTTGTTA 57.436 29.630 0.00 0.00 0.00 2.41
2747 2786 2.485814 GAGCTTAAACTGCTTGTGGAGG 59.514 50.000 0.00 0.00 41.30 4.30
2763 2802 9.169592 GCTTGTGGAGGTTACAAACTTATTATA 57.830 33.333 0.00 0.00 37.56 0.98
2880 2919 2.440409 AGCATCCCAACTTAGTTGCAG 58.560 47.619 18.72 12.26 41.62 4.41
2982 3190 4.022503 GCTTTTCAGCTCCTCAAAAGACAT 60.023 41.667 15.86 0.00 43.51 3.06
2984 3192 4.630644 TTCAGCTCCTCAAAAGACATCT 57.369 40.909 0.00 0.00 0.00 2.90
3037 3245 2.039084 ACTAGACCCTGGCTGTTTGAAG 59.961 50.000 0.00 0.00 0.00 3.02
3196 3404 1.792993 GCAATCTCAGCATTGTCGTGC 60.793 52.381 0.00 0.00 45.38 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.452145 TTCCAAGTGTTTGCTCGGCC 61.452 55.000 0.00 0.00 32.79 6.13
26 27 1.155424 TCGTTGCGACCACAACTTCC 61.155 55.000 0.00 0.00 46.21 3.46
28 29 0.655733 CTTCGTTGCGACCACAACTT 59.344 50.000 0.00 0.00 46.21 2.66
30 31 1.155424 TCCTTCGTTGCGACCACAAC 61.155 55.000 0.00 0.00 45.19 3.32
34 35 2.357034 GCTCCTTCGTTGCGACCA 60.357 61.111 0.00 0.00 34.89 4.02
35 36 1.696832 GATGCTCCTTCGTTGCGACC 61.697 60.000 0.00 0.00 34.89 4.79
37 38 0.737367 CTGATGCTCCTTCGTTGCGA 60.737 55.000 0.00 0.00 0.00 5.10
38 39 1.712081 CTGATGCTCCTTCGTTGCG 59.288 57.895 0.00 0.00 0.00 4.85
103 108 1.092348 CACTGTCACGGATAGGTCGA 58.908 55.000 0.00 0.00 0.00 4.20
104 109 1.064208 CTCACTGTCACGGATAGGTCG 59.936 57.143 0.00 0.00 0.00 4.79
113 118 1.835483 GCAGCAACCTCACTGTCACG 61.835 60.000 0.00 0.00 36.26 4.35
118 123 3.730761 GCGGCAGCAACCTCACTG 61.731 66.667 3.18 0.00 44.35 3.66
135 140 4.554363 CTGCGGACGGTAGCGGAG 62.554 72.222 19.72 10.14 42.01 4.63
151 156 5.242795 AGGTAGAAAAACATGTAGCCACT 57.757 39.130 0.00 0.00 0.00 4.00
152 157 5.699839 CAAGGTAGAAAAACATGTAGCCAC 58.300 41.667 0.00 0.00 0.00 5.01
156 161 5.607119 ACGCAAGGTAGAAAAACATGTAG 57.393 39.130 0.00 0.00 46.39 2.74
160 165 2.095919 GCGACGCAAGGTAGAAAAACAT 60.096 45.455 16.42 0.00 46.39 2.71
317 323 0.037326 CTGTCTCGCCAGCAAACCTA 60.037 55.000 0.00 0.00 0.00 3.08
324 330 0.461961 ATTCTACCTGTCTCGCCAGC 59.538 55.000 0.00 0.00 0.00 4.85
330 336 3.232213 TGTGCGAATTCTACCTGTCTC 57.768 47.619 3.52 0.00 0.00 3.36
338 344 0.793861 GCCACGTTGTGCGAATTCTA 59.206 50.000 3.52 0.00 44.77 2.10
404 410 1.531578 GACGAGAGAAAAACACTGGCC 59.468 52.381 0.00 0.00 0.00 5.36
412 418 7.831753 AGAATCAGTATCAGACGAGAGAAAAA 58.168 34.615 0.00 0.00 0.00 1.94
416 422 7.254137 CAAAAGAATCAGTATCAGACGAGAGA 58.746 38.462 0.00 0.00 0.00 3.10
417 423 6.475076 CCAAAAGAATCAGTATCAGACGAGAG 59.525 42.308 0.00 0.00 0.00 3.20
423 429 6.765036 GCATCTCCAAAAGAATCAGTATCAGA 59.235 38.462 0.00 0.00 37.61 3.27
426 432 6.017275 CCAGCATCTCCAAAAGAATCAGTATC 60.017 42.308 0.00 0.00 37.61 2.24
427 433 5.826737 CCAGCATCTCCAAAAGAATCAGTAT 59.173 40.000 0.00 0.00 37.61 2.12
428 434 5.188434 CCAGCATCTCCAAAAGAATCAGTA 58.812 41.667 0.00 0.00 37.61 2.74
429 435 4.015084 CCAGCATCTCCAAAAGAATCAGT 58.985 43.478 0.00 0.00 37.61 3.41
437 450 4.892934 ACAAAGTAACCAGCATCTCCAAAA 59.107 37.500 0.00 0.00 0.00 2.44
578 596 5.820131 TGACTGAAACGAGTAAAGTTACGA 58.180 37.500 0.00 0.00 38.65 3.43
579 597 5.911280 TCTGACTGAAACGAGTAAAGTTACG 59.089 40.000 0.00 0.00 38.65 3.18
607 625 4.701765 GCATCTTAGATGCTTCTCCTTCA 58.298 43.478 32.53 0.00 41.52 3.02
813 831 3.884774 TGGTGCCCTGCTCGGTTT 61.885 61.111 0.00 0.00 0.00 3.27
958 976 5.509716 TTGGTGGTATATATCGGCTATCG 57.490 43.478 0.00 0.00 40.90 2.92
1021 1039 0.110010 GTTTTCTCTGAAGCAGCGGC 60.110 55.000 0.00 0.00 41.61 6.53
1023 1041 1.069636 GGTGTTTTCTCTGAAGCAGCG 60.070 52.381 0.00 0.00 30.72 5.18
1025 1043 1.069636 GCGGTGTTTTCTCTGAAGCAG 60.070 52.381 0.00 0.00 0.00 4.24
1026 1044 0.944386 GCGGTGTTTTCTCTGAAGCA 59.056 50.000 0.00 0.00 0.00 3.91
1027 1045 1.195674 GAGCGGTGTTTTCTCTGAAGC 59.804 52.381 0.00 0.00 0.00 3.86
1028 1046 2.760374 AGAGCGGTGTTTTCTCTGAAG 58.240 47.619 0.00 0.00 35.99 3.02
1029 1047 2.910688 AGAGCGGTGTTTTCTCTGAA 57.089 45.000 0.00 0.00 35.99 3.02
1032 1050 0.106708 TGCAGAGCGGTGTTTTCTCT 59.893 50.000 0.00 0.00 37.66 3.10
1033 1051 0.235926 GTGCAGAGCGGTGTTTTCTC 59.764 55.000 0.00 0.00 0.00 2.87
1034 1052 0.463654 TGTGCAGAGCGGTGTTTTCT 60.464 50.000 0.00 0.00 0.00 2.52
1044 1062 0.242017 GAATTGGTGGTGTGCAGAGC 59.758 55.000 6.03 6.03 0.00 4.09
1050 1068 1.066908 GTGGTGTGAATTGGTGGTGTG 59.933 52.381 0.00 0.00 0.00 3.82
1238 1256 1.153489 CCATCAGAGGCAGACACCG 60.153 63.158 0.00 0.00 33.69 4.94
1254 1272 2.039624 GGAGCCACTCCTCTCCCA 59.960 66.667 6.38 0.00 46.41 4.37
1278 1296 4.162690 GTCTCCAAGCCGCCGGAT 62.163 66.667 7.68 0.00 0.00 4.18
1461 1479 0.171231 GGGCTGAAACGGAGAAATGC 59.829 55.000 0.00 0.00 0.00 3.56
1479 1497 5.788450 ACAGTAGTTCATCAGTGAAGAAGG 58.212 41.667 10.93 2.57 44.58 3.46
1690 1708 3.648339 TTGCAATCAAGCTTGAGGAAC 57.352 42.857 31.14 20.78 41.08 3.62
1702 1720 3.256383 CCCTGTTGTCTTGATTGCAATCA 59.744 43.478 33.08 33.08 43.28 2.57
2152 2175 6.381801 AGCAACCGTATTTTCAGAAAGATTG 58.618 36.000 0.00 0.00 0.00 2.67
2362 2388 5.869579 ACCGTTTGATAGAGCATATCCAAT 58.130 37.500 6.52 0.00 0.00 3.16
2506 2534 8.783833 TTATTAGAGAATCAGATAAGCATGGC 57.216 34.615 0.00 0.00 37.82 4.40
2543 2571 5.131809 CCCCTCTAGAATCCAGATTGTTCTT 59.868 44.000 0.00 0.00 34.33 2.52
2629 2657 5.182001 ACAGCATGGAAAAATACACTCTGAC 59.818 40.000 0.00 0.00 43.62 3.51
2712 2740 8.830201 CAGTTTAAGCTCTGCATCTTAGATAT 57.170 34.615 0.00 0.00 0.00 1.63
2763 2802 7.034397 GCGTAGGTATTCAGAGTTACTTTTCT 58.966 38.462 0.00 0.00 0.00 2.52
2982 3190 1.681666 CAGAGGGAGCAAGGCAAGA 59.318 57.895 0.00 0.00 0.00 3.02
2984 3192 2.034687 GCAGAGGGAGCAAGGCAA 59.965 61.111 0.00 0.00 0.00 4.52
3037 3245 5.344933 GTCGCTGATGAAAACAAAATTACCC 59.655 40.000 0.00 0.00 0.00 3.69
3211 3419 2.282745 GCTCTTGGTGCCCTGCTT 60.283 61.111 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.