Multiple sequence alignment - TraesCS5D01G415600

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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 TraesCS5D01G415600 chr5D 100.000 3150 0 0 1 3150 478002061 477998912 0.000000e+00 5818.0
1 TraesCS5D01G415600 chr5A 88.298 2521 219 39 555 3031 597280552 597278064 0.000000e+00 2952.0
2 TraesCS5D01G415600 chr5A 94.404 1108 44 9 791 1887 597265858 597264758 0.000000e+00 1687.0
3 TraesCS5D01G415600 chr5A 82.857 840 105 21 2314 3149 597264498 597263694 0.000000e+00 717.0
4 TraesCS5D01G415600 chr5A 87.140 521 62 4 15 532 597266954 597266436 1.260000e-163 586.0
5 TraesCS5D01G415600 chr5A 85.047 535 68 8 1 527 597282135 597281605 4.620000e-148 534.0
6 TraesCS5D01G415600 chr5B 93.955 1522 57 14 674 2165 585496280 585494764 0.000000e+00 2268.0
7 TraesCS5D01G415600 chr5B 92.133 966 61 8 2197 3150 585494765 585493803 0.000000e+00 1349.0
8 TraesCS5D01G415600 chr5B 92.641 693 23 11 1 680 585505970 585505293 0.000000e+00 972.0
9 TraesCS5D01G415600 chr1D 85.571 998 125 10 1019 2008 342170241 342171227 0.000000e+00 1027.0
10 TraesCS5D01G415600 chr1A 83.898 1093 144 17 922 2008 441841900 441842966 0.000000e+00 1014.0
11 TraesCS5D01G415600 chr1B 84.761 1004 128 12 1019 2008 458263003 458263995 0.000000e+00 983.0
12 TraesCS5D01G415600 chr1B 84.539 1009 130 13 1019 2008 458081466 458082467 0.000000e+00 976.0
13 TraesCS5D01G415600 chr1B 84.562 1004 130 12 1019 2008 458129635 458130627 0.000000e+00 972.0
14 TraesCS5D01G415600 chr2D 79.292 961 170 16 1058 2002 637802131 637803078 0.000000e+00 645.0
15 TraesCS5D01G415600 chr2D 82.745 510 66 14 1129 1633 12875812 12876304 4.820000e-118 435.0
16 TraesCS5D01G415600 chr2B 79.008 948 170 15 1071 2002 796341291 796342225 3.450000e-174 621.0
17 TraesCS5D01G415600 chr2B 82.908 509 67 12 1129 1633 23576332 23576824 1.040000e-119 440.0
18 TraesCS5D01G415600 chr2A 80.182 661 120 7 1346 2002 761541929 761541276 4.720000e-133 484.0
19 TraesCS5D01G415600 chr2A 83.505 194 26 2 1071 1261 761542662 761542472 3.230000e-40 176.0
20 TraesCS5D01G415600 chr7A 74.829 878 188 26 1137 2001 722777930 722778787 1.790000e-97 366.0
21 TraesCS5D01G415600 chr7B 73.613 883 206 19 1129 2001 727863355 727864220 6.560000e-82 315.0
22 TraesCS5D01G415600 chr7D 73.964 845 188 24 1157 1988 627219476 627220301 2.360000e-81 313.0
23 TraesCS5D01G415600 chr7D 80.488 123 20 3 2735 2856 68776408 68776527 1.200000e-14 91.6


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 TraesCS5D01G415600 chr5D 477998912 478002061 3149 True 5818.000000 5818 100.000000 1 3150 1 chr5D.!!$R1 3149
1 TraesCS5D01G415600 chr5A 597278064 597282135 4071 True 1743.000000 2952 86.672500 1 3031 2 chr5A.!!$R2 3030
2 TraesCS5D01G415600 chr5A 597263694 597266954 3260 True 996.666667 1687 88.133667 15 3149 3 chr5A.!!$R1 3134
3 TraesCS5D01G415600 chr5B 585493803 585496280 2477 True 1808.500000 2268 93.044000 674 3150 2 chr5B.!!$R2 2476
4 TraesCS5D01G415600 chr5B 585505293 585505970 677 True 972.000000 972 92.641000 1 680 1 chr5B.!!$R1 679
5 TraesCS5D01G415600 chr1D 342170241 342171227 986 False 1027.000000 1027 85.571000 1019 2008 1 chr1D.!!$F1 989
6 TraesCS5D01G415600 chr1A 441841900 441842966 1066 False 1014.000000 1014 83.898000 922 2008 1 chr1A.!!$F1 1086
7 TraesCS5D01G415600 chr1B 458263003 458263995 992 False 983.000000 983 84.761000 1019 2008 1 chr1B.!!$F3 989
8 TraesCS5D01G415600 chr1B 458081466 458082467 1001 False 976.000000 976 84.539000 1019 2008 1 chr1B.!!$F1 989
9 TraesCS5D01G415600 chr1B 458129635 458130627 992 False 972.000000 972 84.562000 1019 2008 1 chr1B.!!$F2 989
10 TraesCS5D01G415600 chr2D 637802131 637803078 947 False 645.000000 645 79.292000 1058 2002 1 chr2D.!!$F2 944
11 TraesCS5D01G415600 chr2B 796341291 796342225 934 False 621.000000 621 79.008000 1071 2002 1 chr2B.!!$F2 931
12 TraesCS5D01G415600 chr2A 761541276 761542662 1386 True 330.000000 484 81.843500 1071 2002 2 chr2A.!!$R1 931
13 TraesCS5D01G415600 chr7A 722777930 722778787 857 False 366.000000 366 74.829000 1137 2001 1 chr7A.!!$F1 864
14 TraesCS5D01G415600 chr7B 727863355 727864220 865 False 315.000000 315 73.613000 1129 2001 1 chr7B.!!$F1 872
15 TraesCS5D01G415600 chr7D 627219476 627220301 825 False 313.000000 313 73.964000 1157 1988 1 chr7D.!!$F2 831

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
574 2035 0.937304 CACGATAATCAACGGGGCTG 59.063 55.0 0.0 0.0 0.00 4.85 F
1012 2491 0.672342 CATATCCAGCAGCAAAGGCC 59.328 55.0 0.0 0.0 42.56 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1947 3911 0.240145 CGTAGCTGACACCGAGAACA 59.760 55.0 0.00 0.0 0.0 3.18 R
2528 4559 0.249447 CCTCGAATACAGCGGCATCA 60.249 55.0 1.45 0.0 0.0 3.07 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 4.180946 CGTGTCGAGGAGGAGCGG 62.181 72.222 0.00 0.00 0.00 5.52
99 100 1.378531 GATGTGGCGCCTGTCATTTA 58.621 50.000 29.70 0.07 28.63 1.40
387 409 5.055812 GGAGTTTGAATGAAATTTGCACCA 58.944 37.500 0.00 0.00 36.07 4.17
516 944 7.014422 CCTCTAAATTGTAGGAGATCGGTTAGT 59.986 40.741 0.00 0.00 31.64 2.24
557 2018 2.711542 ACTTGGGGATCACGAATTCAC 58.288 47.619 6.22 0.00 0.00 3.18
574 2035 0.937304 CACGATAATCAACGGGGCTG 59.063 55.000 0.00 0.00 0.00 4.85
592 2053 2.820197 GCTGGAAAAGTAAAGAGGTGGG 59.180 50.000 0.00 0.00 0.00 4.61
726 2188 1.234821 TTCGTCCATGTCAAACAGGC 58.765 50.000 0.00 0.00 0.00 4.85
836 2304 8.090831 TGCTAATGCTCTGACTTCGAATTATAT 58.909 33.333 0.00 0.00 40.48 0.86
837 2305 9.574458 GCTAATGCTCTGACTTCGAATTATATA 57.426 33.333 0.00 0.00 36.03 0.86
840 2308 9.988815 AATGCTCTGACTTCGAATTATATAAGT 57.011 29.630 0.00 0.00 34.96 2.24
986 2465 6.126997 TGGTCTATAAAAGGGCGACATTTAGA 60.127 38.462 0.00 0.00 44.79 2.10
1012 2491 0.672342 CATATCCAGCAGCAAAGGCC 59.328 55.000 0.00 0.00 42.56 5.19
1329 3287 1.522569 GCTCCTCCTACACCGCAAT 59.477 57.895 0.00 0.00 0.00 3.56
1569 3533 1.373748 GCCGTCCAACTACTGCGAA 60.374 57.895 0.00 0.00 0.00 4.70
1653 3617 4.910195 TCTCCTACAACTACAACTACGGA 58.090 43.478 0.00 0.00 0.00 4.69
1911 3875 2.682494 GGGCAGGACTCACGGGTA 60.682 66.667 0.00 0.00 0.00 3.69
1944 3908 1.067071 GGGTTCTACAAGCGCTACTGT 60.067 52.381 18.09 18.09 0.00 3.55
1947 3911 4.430908 GGTTCTACAAGCGCTACTGTAAT 58.569 43.478 19.53 0.00 0.00 1.89
2015 3979 3.201708 AGGCCATTCACTAGCTGAGAAAT 59.798 43.478 5.01 0.00 0.00 2.17
2036 4000 1.004440 GCTTCTCAGTTGGGCTCGT 60.004 57.895 0.00 0.00 0.00 4.18
2041 4006 2.669569 CAGTTGGGCTCGTGGGTG 60.670 66.667 0.00 0.00 0.00 4.61
2046 4011 2.668550 GGGCTCGTGGGTGACAAC 60.669 66.667 0.00 0.00 0.00 3.32
2050 4015 1.445942 CTCGTGGGTGACAACTGGT 59.554 57.895 0.00 0.00 0.00 4.00
2103 4084 6.543831 GCTGGCTTCCTTAATTTCTCTCATTA 59.456 38.462 0.00 0.00 0.00 1.90
2205 4195 0.918983 GGATCCACCATCTCCAACCA 59.081 55.000 6.95 0.00 38.79 3.67
2282 4272 2.880268 TCTGCACCATCTTCACAAACAG 59.120 45.455 0.00 0.00 0.00 3.16
2298 4288 3.402628 AACAGCACCGTCTACATCTTT 57.597 42.857 0.00 0.00 0.00 2.52
2410 4427 2.165167 CTCAAATGCTCCCACACATGT 58.835 47.619 0.00 0.00 0.00 3.21
2434 4451 4.983671 ATGATGTGACTTGCGAGTAGTA 57.016 40.909 6.58 0.00 35.88 1.82
2443 4460 6.530534 GTGACTTGCGAGTAGTACATTACATT 59.469 38.462 6.58 0.00 35.88 2.71
2444 4461 6.750501 TGACTTGCGAGTAGTACATTACATTC 59.249 38.462 6.58 0.00 35.88 2.67
2445 4462 6.864342 ACTTGCGAGTAGTACATTACATTCT 58.136 36.000 4.25 0.00 33.32 2.40
2446 4463 7.321153 ACTTGCGAGTAGTACATTACATTCTT 58.679 34.615 4.25 0.00 33.32 2.52
2447 4464 8.464404 ACTTGCGAGTAGTACATTACATTCTTA 58.536 33.333 4.25 0.00 33.32 2.10
2448 4465 9.297586 CTTGCGAGTAGTACATTACATTCTTAA 57.702 33.333 2.52 0.00 0.00 1.85
2449 4466 9.642327 TTGCGAGTAGTACATTACATTCTTAAA 57.358 29.630 2.52 0.00 0.00 1.52
2528 4559 4.019174 CCTTGAAACTCATGCCAACCTAT 58.981 43.478 0.00 0.00 0.00 2.57
2597 4628 8.335532 TGTGGATTTAAAAGTATCTGAACTGG 57.664 34.615 0.00 0.00 0.00 4.00
2599 4630 8.451748 GTGGATTTAAAAGTATCTGAACTGGTC 58.548 37.037 0.00 0.00 0.00 4.02
2640 4672 4.626287 GCTCCATAGGAATGTTGGTTCTCA 60.626 45.833 0.00 0.00 0.00 3.27
2707 4739 5.336372 GCTGGTATTTTGCATGTTTAGGTCA 60.336 40.000 0.00 0.00 0.00 4.02
2834 4866 0.786074 GCTCGTTCGCTCGAAAAAGC 60.786 55.000 17.82 17.82 39.34 3.51
2856 4888 4.801891 CAAACACCTAACTGTCGCTACTA 58.198 43.478 0.00 0.00 0.00 1.82
2912 4944 5.637387 TCAACAAAGTCCAAAAGAAAGCAAC 59.363 36.000 0.00 0.00 0.00 4.17
3001 5035 5.722021 AATAGGTTTCACAAACATGGGAC 57.278 39.130 0.00 0.00 43.15 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.895238 GGTCTAGGTACAAGCGGCA 59.105 57.895 1.45 0.00 0.00 5.69
55 56 3.744426 ACTTGTACAACTCATACAACCGC 59.256 43.478 3.59 0.00 37.56 5.68
99 100 1.137086 AGTCGTCGCTGGAGCAAATAT 59.863 47.619 0.00 0.00 42.21 1.28
206 215 4.154347 CTCCTCGCCCACTCTGCC 62.154 72.222 0.00 0.00 0.00 4.85
207 216 3.071206 TCTCCTCGCCCACTCTGC 61.071 66.667 0.00 0.00 0.00 4.26
247 256 6.252869 TCGTTATCGCTCTTGTTTATCAACTC 59.747 38.462 0.00 0.00 36.96 3.01
292 302 9.993881 CTTAGACAAAATTTAAACAAGATTGCG 57.006 29.630 0.00 0.00 0.00 4.85
516 944 5.150715 AGTATCCCAAGTATGAGAGCATCA 58.849 41.667 0.00 0.00 43.70 3.07
557 2018 0.105964 TCCAGCCCCGTTGATTATCG 59.894 55.000 0.00 0.00 0.00 2.92
574 2035 4.700692 GTCATCCCACCTCTTTACTTTTCC 59.299 45.833 0.00 0.00 0.00 3.13
592 2053 6.313905 ACACGGAACTAAGAATTCATGTCATC 59.686 38.462 8.44 0.00 0.00 2.92
836 2304 7.822334 TCCTAGATCGCATCTTTGAAAAACTTA 59.178 33.333 4.35 0.00 40.76 2.24
837 2305 6.655003 TCCTAGATCGCATCTTTGAAAAACTT 59.345 34.615 4.35 0.00 40.76 2.66
839 2307 6.128282 TGTCCTAGATCGCATCTTTGAAAAAC 60.128 38.462 4.35 0.00 40.76 2.43
840 2308 5.937540 TGTCCTAGATCGCATCTTTGAAAAA 59.062 36.000 4.35 0.00 40.76 1.94
845 2313 4.437239 ACTTGTCCTAGATCGCATCTTTG 58.563 43.478 4.35 0.27 40.76 2.77
917 2385 2.087009 GGAAAGTCGTCGGCTCGTG 61.087 63.158 0.00 0.00 0.00 4.35
986 2465 0.894184 GCTGCTGGATATGCATGGCT 60.894 55.000 10.16 0.00 39.86 4.75
1012 2491 1.739466 CGACATGGTCTGATGGGTTTG 59.261 52.381 0.00 0.00 0.00 2.93
1944 3908 3.427098 CGTAGCTGACACCGAGAACATTA 60.427 47.826 0.00 0.00 0.00 1.90
1947 3911 0.240145 CGTAGCTGACACCGAGAACA 59.760 55.000 0.00 0.00 0.00 3.18
2015 3979 0.322975 GAGCCCAACTGAGAAGCTGA 59.677 55.000 0.00 0.00 32.97 4.26
2019 3983 0.671781 CCACGAGCCCAACTGAGAAG 60.672 60.000 0.00 0.00 0.00 2.85
2027 3991 2.747443 TTGTCACCCACGAGCCCAA 61.747 57.895 0.00 0.00 0.00 4.12
2041 4006 1.007734 TCGCGAGTGACCAGTTGTC 60.008 57.895 3.71 0.00 44.72 3.18
2046 4011 4.778415 CCCGTCGCGAGTGACCAG 62.778 72.222 10.24 3.46 35.40 4.00
2057 4022 2.108362 GCCCTTATGGACCCGTCG 59.892 66.667 0.00 0.00 35.39 5.12
2103 4084 7.610580 TGGAAAACATTTAGGTCTCCAAAAT 57.389 32.000 0.00 0.00 0.00 1.82
2168 4157 5.163269 TGGATCCAACATGATAAGTCCTCAG 60.163 44.000 13.46 0.00 0.00 3.35
2169 4158 4.721274 TGGATCCAACATGATAAGTCCTCA 59.279 41.667 13.46 0.00 0.00 3.86
2170 4159 5.059833 GTGGATCCAACATGATAAGTCCTC 58.940 45.833 18.20 0.00 0.00 3.71
2205 4195 6.141844 GTGACGACGATAACGATGATTTGTAT 59.858 38.462 0.00 0.00 42.66 2.29
2282 4272 3.684788 ACATTGAAAGATGTAGACGGTGC 59.315 43.478 0.00 0.00 38.43 5.01
2298 4288 0.776810 ACACATGGGGGTGACATTGA 59.223 50.000 0.00 0.00 41.32 2.57
2390 4407 2.165167 ACATGTGTGGGAGCATTTGAG 58.835 47.619 0.00 0.00 0.00 3.02
2394 4411 4.343231 TCATAAACATGTGTGGGAGCATT 58.657 39.130 0.00 0.00 0.00 3.56
2410 4427 5.720202 ACTACTCGCAAGTCACATCATAAA 58.280 37.500 0.00 0.00 36.92 1.40
2528 4559 0.249447 CCTCGAATACAGCGGCATCA 60.249 55.000 1.45 0.00 0.00 3.07
2597 4628 9.807649 ATGGAGCATAGAATTTTAAACAATGAC 57.192 29.630 0.00 0.00 0.00 3.06
2640 4672 1.914764 CCCAAAGCCCCAATGCACT 60.915 57.895 0.00 0.00 0.00 4.40
2670 4702 1.559368 TACCAGCGTAAAGGTAGGCA 58.441 50.000 1.78 0.00 42.39 4.75
2707 4739 1.086696 CCATGACGAACAGCCGAAAT 58.913 50.000 0.00 0.00 0.00 2.17
2834 4866 3.650139 AGTAGCGACAGTTAGGTGTTTG 58.350 45.455 0.00 0.00 0.00 2.93


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

AutoCloner maintained by Alex Coulton.