Multiple sequence alignment - TraesCS1D01G074600

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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 TraesCS1D01G074600 chr1D 100.000 4213 0 0 1 4213 56424505 56428717 0.000000e+00 7781
1 TraesCS1D01G074600 chr1D 92.819 1323 56 12 2845 4130 56528262 56529582 0.000000e+00 1881
2 TraesCS1D01G074600 chr1D 94.168 1046 54 4 3169 4213 56872915 56873954 0.000000e+00 1587
3 TraesCS1D01G074600 chr1D 91.700 1012 50 5 3203 4213 56608161 56609139 0.000000e+00 1373
4 TraesCS1D01G074600 chr1D 86.892 946 100 19 1 929 56289725 56290663 0.000000e+00 1038
5 TraesCS1D01G074600 chr1D 85.897 936 114 14 1 924 56092169 56093098 0.000000e+00 981
6 TraesCS1D01G074600 chr1D 85.654 941 104 17 1 929 56101996 56102917 0.000000e+00 961
7 TraesCS1D01G074600 chr1D 85.426 940 112 18 1 925 56103625 56104554 0.000000e+00 953
8 TraesCS1D01G074600 chr1D 85.064 944 121 12 1 929 56099074 56100012 0.000000e+00 944
9 TraesCS1D01G074600 chr1D 85.714 665 85 8 18 680 56088190 56088846 0.000000e+00 693
10 TraesCS1D01G074600 chr1D 94.647 411 20 2 2513 2922 56868618 56869027 1.650000e-178 636
11 TraesCS1D01G074600 chr1D 94.636 261 14 0 2884 3144 56607891 56608151 5.070000e-109 405
12 TraesCS1D01G074600 chr1D 96.835 158 5 0 3011 3168 56869385 56869542 8.980000e-67 265
13 TraesCS1D01G074600 chr1D 84.906 212 21 8 2201 2405 56868359 56868566 1.990000e-48 204
14 TraesCS1D01G074600 chr1A 96.434 1823 62 2 2392 4213 54462010 54460190 0.000000e+00 3003
15 TraesCS1D01G074600 chr1A 93.618 1708 65 21 712 2404 54463723 54462045 0.000000e+00 2510
16 TraesCS1D01G074600 chr1A 92.767 1341 56 10 2884 4213 56371944 56370634 0.000000e+00 1901
17 TraesCS1D01G074600 chr1A 94.633 913 40 4 3308 4213 56339597 56338687 0.000000e+00 1406
18 TraesCS1D01G074600 chr1A 93.266 787 53 0 2523 3309 56341094 56340308 0.000000e+00 1160
19 TraesCS1D01G074600 chr1A 87.196 945 96 19 1 928 54684136 54683200 0.000000e+00 1051
20 TraesCS1D01G074600 chr1A 92.987 713 45 4 4 714 54486457 54485748 0.000000e+00 1035
21 TraesCS1D01G074600 chr1A 86.349 945 103 16 1 928 56480672 56481607 0.000000e+00 1007
22 TraesCS1D01G074600 chr1A 85.836 939 114 16 2 929 56451820 56452750 0.000000e+00 979
23 TraesCS1D01G074600 chr1A 85.068 951 107 22 1 929 54672612 54671675 0.000000e+00 937
24 TraesCS1D01G074600 chr1A 84.648 938 127 13 2 929 54688248 54687318 0.000000e+00 918
25 TraesCS1D01G074600 chr1A 85.350 471 44 10 443 897 54704009 54703548 8.250000e-127 464
26 TraesCS1D01G074600 chr1B 95.604 1706 60 4 2523 4213 91879200 91880905 0.000000e+00 2721
27 TraesCS1D01G074600 chr1B 93.263 1336 52 13 951 2279 91877553 91878857 0.000000e+00 1934


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 TraesCS1D01G074600 chr1D 56424505 56428717 4212 False 7781.000000 7781 100.000000 1 4213 1 chr1D.!!$F2 4212
1 TraesCS1D01G074600 chr1D 56528262 56529582 1320 False 1881.000000 1881 92.819000 2845 4130 1 chr1D.!!$F3 1285
2 TraesCS1D01G074600 chr1D 56289725 56290663 938 False 1038.000000 1038 86.892000 1 929 1 chr1D.!!$F1 928
3 TraesCS1D01G074600 chr1D 56099074 56104554 5480 False 952.666667 961 85.381333 1 929 3 chr1D.!!$F5 928
4 TraesCS1D01G074600 chr1D 56607891 56609139 1248 False 889.000000 1373 93.168000 2884 4213 2 chr1D.!!$F6 1329
5 TraesCS1D01G074600 chr1D 56088190 56093098 4908 False 837.000000 981 85.805500 1 924 2 chr1D.!!$F4 923
6 TraesCS1D01G074600 chr1D 56868359 56873954 5595 False 673.000000 1587 92.639000 2201 4213 4 chr1D.!!$F7 2012
7 TraesCS1D01G074600 chr1A 54460190 54463723 3533 True 2756.500000 3003 95.026000 712 4213 2 chr1A.!!$R5 3501
8 TraesCS1D01G074600 chr1A 56370634 56371944 1310 True 1901.000000 1901 92.767000 2884 4213 1 chr1A.!!$R4 1329
9 TraesCS1D01G074600 chr1A 56338687 56341094 2407 True 1283.000000 1406 93.949500 2523 4213 2 chr1A.!!$R7 1690
10 TraesCS1D01G074600 chr1A 54485748 54486457 709 True 1035.000000 1035 92.987000 4 714 1 chr1A.!!$R1 710
11 TraesCS1D01G074600 chr1A 56480672 56481607 935 False 1007.000000 1007 86.349000 1 928 1 chr1A.!!$F2 927
12 TraesCS1D01G074600 chr1A 54683200 54688248 5048 True 984.500000 1051 85.922000 1 929 2 chr1A.!!$R6 928
13 TraesCS1D01G074600 chr1A 56451820 56452750 930 False 979.000000 979 85.836000 2 929 1 chr1A.!!$F1 927
14 TraesCS1D01G074600 chr1A 54671675 54672612 937 True 937.000000 937 85.068000 1 929 1 chr1A.!!$R2 928
15 TraesCS1D01G074600 chr1B 91877553 91880905 3352 False 2327.500000 2721 94.433500 951 4213 2 chr1B.!!$F1 3262

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
625 13271 1.068748 AGCGCTGCTGTGAAGAAATTG 60.069 47.619 10.39 0.0 37.57 2.32 F
1461 14148 0.172803 ACGAGGCCAAGTACATCGTC 59.827 55.000 5.01 0.0 42.48 4.20 F
2243 14930 0.251634 CAGGGGCTCTCTTGGTCTTC 59.748 60.000 0.00 0.0 0.00 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1701 14388 0.029577 AATGGGTTTGGGTTGGGGTT 60.030 50.000 0.00 0.00 0.00 4.11 R
2765 15652 0.776810 ATGTGGTTCCATGGTCACCA 59.223 50.000 25.96 25.96 38.30 4.17 R
3342 20602 1.931841 CAGTCGAGAGATGTGCAATGG 59.068 52.381 0.00 0.00 45.19 3.16 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
68 4048 7.879677 AGCATGCTAATAGTGTGCTATATTTGA 59.120 33.333 21.21 0.00 43.69 2.69
169 11172 5.221130 GGAGGAAATAGAATAAGACCGACG 58.779 45.833 0.00 0.00 0.00 5.12
204 11207 4.968080 AGATAGGATGAAGAGAGGTTGCTT 59.032 41.667 0.00 0.00 0.00 3.91
213 11216 3.084786 AGAGAGGTTGCTTTAATGTGGC 58.915 45.455 0.00 0.00 0.00 5.01
317 11320 4.018597 GGATATGGGATGAAGAGAAGCCAT 60.019 45.833 0.00 0.00 0.00 4.40
430 11433 1.750682 GCTGGTGGAAAACTGGTGAGT 60.751 52.381 0.00 0.00 0.00 3.41
439 13081 4.695928 GGAAAACTGGTGAGTAGTTGGATC 59.304 45.833 0.00 0.00 38.32 3.36
464 13106 5.353956 TGTTAGGCTGTATGCATTGTTGTAG 59.646 40.000 3.54 0.00 45.15 2.74
563 13208 7.851387 TGTGATACACAGAAAACACTACAAA 57.149 32.000 0.25 0.00 39.62 2.83
570 13215 7.404203 ACACAGAAAACACTACAAACGTTATC 58.596 34.615 0.00 0.00 0.00 1.75
625 13271 1.068748 AGCGCTGCTGTGAAGAAATTG 60.069 47.619 10.39 0.00 37.57 2.32
710 13371 6.188400 TCATTTCGTGTAATTGCAATGCTA 57.812 33.333 13.82 0.00 0.00 3.49
728 13390 4.906618 TGCTAGTAGTAAGCTGCCTTTTT 58.093 39.130 0.00 0.00 40.73 1.94
744 13408 7.391148 TGCCTTTTTCAATCTCTGGTATAAC 57.609 36.000 0.00 0.00 0.00 1.89
803 13468 9.649167 AATGAATGAATCAAGATCCAAAACTTC 57.351 29.630 0.00 0.00 42.54 3.01
811 13481 5.660864 TCAAGATCCAAAACTTCCAGGTTTT 59.339 36.000 0.00 0.00 46.28 2.43
895 13566 7.811282 TCCATGATAGGGTTGTACAATTATGT 58.189 34.615 12.26 0.00 43.74 2.29
896 13567 8.939932 TCCATGATAGGGTTGTACAATTATGTA 58.060 33.333 12.26 0.61 41.05 2.29
966 13637 8.940397 TCTTTGTCCTTTCTTTTTCAGGATAT 57.060 30.769 0.00 0.00 38.99 1.63
1021 13700 1.869767 CATCGTGGAATTCAGCTAGGC 59.130 52.381 7.93 0.00 0.00 3.93
1022 13701 0.901827 TCGTGGAATTCAGCTAGGCA 59.098 50.000 7.93 0.00 0.00 4.75
1023 13702 1.009829 CGTGGAATTCAGCTAGGCAC 58.990 55.000 7.93 3.45 0.00 5.01
1027 13706 1.303309 GAATTCAGCTAGGCACGCAT 58.697 50.000 0.00 0.00 0.00 4.73
1033 13714 4.371855 TCAGCTAGGCACGCATATATAC 57.628 45.455 0.00 0.00 0.00 1.47
1114 13798 2.798501 CGCACGCGGTAGTTGATGG 61.799 63.158 12.47 0.00 35.56 3.51
1461 14148 0.172803 ACGAGGCCAAGTACATCGTC 59.827 55.000 5.01 0.00 42.48 4.20
1684 14371 4.075793 TACGCCTCCCCTGCTCCT 62.076 66.667 0.00 0.00 0.00 3.69
1700 14387 2.117423 CTCACCAACCCCAACCCC 59.883 66.667 0.00 0.00 0.00 4.95
1701 14388 2.700322 TCACCAACCCCAACCCCA 60.700 61.111 0.00 0.00 0.00 4.96
1702 14389 2.283809 CACCAACCCCAACCCCAA 59.716 61.111 0.00 0.00 0.00 4.12
1703 14390 2.137528 CACCAACCCCAACCCCAAC 61.138 63.158 0.00 0.00 0.00 3.77
1704 14391 2.525629 CCAACCCCAACCCCAACC 60.526 66.667 0.00 0.00 0.00 3.77
1705 14392 2.525629 CAACCCCAACCCCAACCC 60.526 66.667 0.00 0.00 0.00 4.11
1706 14393 3.852421 AACCCCAACCCCAACCCC 61.852 66.667 0.00 0.00 0.00 4.95
1708 14395 3.851184 CCCCAACCCCAACCCCAA 61.851 66.667 0.00 0.00 0.00 4.12
1709 14396 2.525629 CCCAACCCCAACCCCAAC 60.526 66.667 0.00 0.00 0.00 3.77
1710 14397 2.525629 CCAACCCCAACCCCAACC 60.526 66.667 0.00 0.00 0.00 3.77
1711 14398 2.525629 CAACCCCAACCCCAACCC 60.526 66.667 0.00 0.00 0.00 4.11
1768 14455 2.514824 GCTTGCCCGGTCCATCTC 60.515 66.667 0.00 0.00 0.00 2.75
1791 14478 1.068194 CACACGGTCTCTCCTTCTCAC 60.068 57.143 0.00 0.00 0.00 3.51
1804 14491 3.008375 TCCTTCTCACCTGACTTCCATTG 59.992 47.826 0.00 0.00 0.00 2.82
2054 14741 1.304464 CAGGGAGCCCTTTGAACCC 60.304 63.158 5.03 0.00 45.70 4.11
2243 14930 0.251634 CAGGGGCTCTCTTGGTCTTC 59.748 60.000 0.00 0.00 0.00 2.87
2246 14933 0.827368 GGGCTCTCTTGGTCTTCGAT 59.173 55.000 0.00 0.00 0.00 3.59
2310 15134 8.185003 TGTTGTCGATCACATAGAAGTAATTG 57.815 34.615 0.00 0.00 33.90 2.32
2431 15312 3.454858 TGCTTCCTAATTCTGGGAGACT 58.545 45.455 9.28 0.00 33.01 3.24
2765 15652 2.689983 GGTTGCTGCAGCCATAAACTAT 59.310 45.455 34.64 0.00 41.18 2.12
3230 19777 8.352942 GGGAATAAAATGTCATGTTGGACTATC 58.647 37.037 0.00 0.00 38.61 2.08
3342 20602 2.939460 AATTACAAGGACGGCATTGC 57.061 45.000 16.97 0.00 39.28 3.56
3525 20792 2.927477 GCCGTCGATCACATTCAAGTTA 59.073 45.455 0.00 0.00 0.00 2.24
3548 20815 1.670087 CGCAGACCTGTGGAAGTACTG 60.670 57.143 0.00 0.00 37.43 2.74
3705 20979 1.080025 GTAGTCCACCTGTGACCGC 60.080 63.158 0.00 0.00 0.00 5.68
3807 21081 1.007336 GCGTGACGAGGACGAACATT 61.007 55.000 10.10 0.00 42.66 2.71
4017 21291 5.299531 CGGTATAGTCATCAGTTCCTGAAGA 59.700 44.000 0.00 0.00 44.04 2.87
4027 21301 8.156820 TCATCAGTTCCTGAAGATAAAAGTTGA 58.843 33.333 0.00 0.00 44.04 3.18
4032 21306 8.160106 AGTTCCTGAAGATAAAAGTTGATGTCT 58.840 33.333 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
169 11172 3.576118 TCATCCTATCTCCAAGTAGCAGC 59.424 47.826 0.00 0.00 0.00 5.25
204 11207 1.434555 CAAGTCGACCGCCACATTAA 58.565 50.000 13.01 0.00 0.00 1.40
213 11216 3.414700 GTGCCAGCAAGTCGACCG 61.415 66.667 13.01 4.94 0.00 4.79
249 11252 6.819146 CCTCCAACTCTAACAATTAAGAGTCC 59.181 42.308 14.34 0.00 40.31 3.85
317 11320 1.971167 GGCGGTTCATGAGTGGCAA 60.971 57.895 13.60 0.00 0.00 4.52
430 11433 5.453339 GCATACAGCCTAACAGATCCAACTA 60.453 44.000 0.00 0.00 37.23 2.24
439 13081 4.156556 ACAACAATGCATACAGCCTAACAG 59.843 41.667 0.00 0.00 44.83 3.16
464 13106 1.342819 TGCAACACATACAAAAGCCCC 59.657 47.619 0.00 0.00 0.00 5.80
625 13271 6.122964 AGAAGGTCCAGATTACATTTTAGCC 58.877 40.000 0.00 0.00 0.00 3.93
710 13371 6.241645 AGATTGAAAAAGGCAGCTTACTACT 58.758 36.000 0.00 0.00 0.00 2.57
728 13390 6.484364 TCATGCAGTTATACCAGAGATTGA 57.516 37.500 0.00 0.00 0.00 2.57
811 13481 8.459911 TCTCGGAGTGATACATTTCTTATACA 57.540 34.615 4.69 0.00 0.00 2.29
946 13617 9.574458 GCTTTTATATCCTGAAAAAGAAAGGAC 57.426 33.333 10.50 0.00 42.78 3.85
991 13670 1.557099 TTCCACGATGTGTCTAGCCT 58.443 50.000 0.00 0.00 0.00 4.58
1021 13700 6.899114 TCTGTCACTGTAGTATATATGCGTG 58.101 40.000 0.00 0.00 0.00 5.34
1022 13701 7.506328 TTCTGTCACTGTAGTATATATGCGT 57.494 36.000 0.00 0.00 0.00 5.24
1023 13702 7.061210 GCTTTCTGTCACTGTAGTATATATGCG 59.939 40.741 0.00 0.00 0.00 4.73
1033 13714 5.991328 TCTTTTGCTTTCTGTCACTGTAG 57.009 39.130 0.00 0.00 0.00 2.74
1114 13798 2.381589 GCGGCTACTGTTTTTGTTGTC 58.618 47.619 0.00 0.00 0.00 3.18
1168 13852 4.013728 TCGGGGTTGGATGAAGTTTTATG 58.986 43.478 0.00 0.00 0.00 1.90
1169 13853 4.014406 GTCGGGGTTGGATGAAGTTTTAT 58.986 43.478 0.00 0.00 0.00 1.40
1170 13854 3.414269 GTCGGGGTTGGATGAAGTTTTA 58.586 45.455 0.00 0.00 0.00 1.52
1684 14371 2.325364 TTGGGGTTGGGGTTGGTGA 61.325 57.895 0.00 0.00 0.00 4.02
1700 14387 0.766288 ATGGGTTTGGGTTGGGGTTG 60.766 55.000 0.00 0.00 0.00 3.77
1701 14388 0.029577 AATGGGTTTGGGTTGGGGTT 60.030 50.000 0.00 0.00 0.00 4.11
1702 14389 0.472925 GAATGGGTTTGGGTTGGGGT 60.473 55.000 0.00 0.00 0.00 4.95
1703 14390 1.198094 GGAATGGGTTTGGGTTGGGG 61.198 60.000 0.00 0.00 0.00 4.96
1704 14391 0.472734 TGGAATGGGTTTGGGTTGGG 60.473 55.000 0.00 0.00 0.00 4.12
1705 14392 0.684535 GTGGAATGGGTTTGGGTTGG 59.315 55.000 0.00 0.00 0.00 3.77
1706 14393 1.418334 TGTGGAATGGGTTTGGGTTG 58.582 50.000 0.00 0.00 0.00 3.77
1707 14394 2.182516 TTGTGGAATGGGTTTGGGTT 57.817 45.000 0.00 0.00 0.00 4.11
1708 14395 1.977129 CATTGTGGAATGGGTTTGGGT 59.023 47.619 0.00 0.00 36.12 4.51
1709 14396 1.977129 ACATTGTGGAATGGGTTTGGG 59.023 47.619 0.00 0.00 43.00 4.12
1710 14397 2.352617 CGACATTGTGGAATGGGTTTGG 60.353 50.000 0.00 0.00 43.00 3.28
1711 14398 2.352617 CCGACATTGTGGAATGGGTTTG 60.353 50.000 0.00 0.00 43.00 2.93
1768 14455 1.889530 GAAGGAGAGACCGTGTGGGG 61.890 65.000 0.00 0.00 44.74 4.96
1791 14478 1.734465 GTTCGAGCAATGGAAGTCAGG 59.266 52.381 0.00 0.00 0.00 3.86
2054 14741 3.499737 GTTGAGCCGGGCATGACG 61.500 66.667 23.09 0.00 0.00 4.35
2243 14930 3.186001 GCAAGCTGAATCATACCTCATCG 59.814 47.826 0.00 0.00 0.00 3.84
2246 14933 2.507058 AGGCAAGCTGAATCATACCTCA 59.493 45.455 0.00 0.00 0.00 3.86
2310 15134 3.568007 TCAGAAATTGTGTAGTTGCCACC 59.432 43.478 0.00 0.00 31.71 4.61
2356 15180 7.495901 TGATGAATCTCCAGAACAGAGAATAC 58.504 38.462 0.00 0.00 43.35 1.89
2431 15312 4.728772 ACAATGATCAGAAAGTTGTCCCA 58.271 39.130 0.09 0.00 0.00 4.37
2705 15592 2.299975 GCCAATGGGAAGGCCATTT 58.700 52.632 5.01 0.00 45.18 2.32
2765 15652 0.776810 ATGTGGTTCCATGGTCACCA 59.223 50.000 25.96 25.96 38.30 4.17
3230 19777 6.747280 ACTTTGAAAAGAACTTCAACATCACG 59.253 34.615 9.71 0.00 43.29 4.35
3342 20602 1.931841 CAGTCGAGAGATGTGCAATGG 59.068 52.381 0.00 0.00 45.19 3.16
3357 20617 3.809832 ACTGATGTTCCTGTTTTCAGTCG 59.190 43.478 0.00 0.00 42.40 4.18
3525 20792 3.241530 TTCCACAGGTCTGCGCCT 61.242 61.111 4.18 0.00 39.99 5.52
3705 20979 3.234041 CAGCTCGTCTCGTTCGCG 61.234 66.667 0.00 0.00 42.98 5.87
4027 21301 6.805016 AGTATTGGTCTGATGAAGAGACAT 57.195 37.500 0.00 0.00 41.50 3.06
4032 21306 7.069344 TGATCCTAGTATTGGTCTGATGAAGA 58.931 38.462 0.00 0.00 0.00 2.87
4159 21434 2.119495 CACCAGGAGTACAAGGCCTAT 58.881 52.381 5.16 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.