Multiple sequence alignment - TraesCS3D01G028000

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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 TraesCS3D01G028000 chr3D 100.000 3561 0 0 1 3561 9633160 9636720 0.000000e+00 6577
1 TraesCS3D01G028000 chr3D 92.512 2564 189 3 2 2564 4959556 4956995 0.000000e+00 3668
2 TraesCS3D01G028000 chr3D 90.769 130 10 2 2620 2747 4956624 4956495 4.730000e-39 172
3 TraesCS3D01G028000 chr3B 93.417 3357 207 7 1 3354 13814917 13818262 0.000000e+00 4963
4 TraesCS3D01G028000 chr3B 96.175 183 6 1 3379 3561 13818260 13818441 7.470000e-77 298
5 TraesCS3D01G028000 chr3A 91.495 3598 260 18 1 3561 10884768 10881180 0.000000e+00 4907
6 TraesCS3D01G028000 chr3A 91.658 2985 230 10 1 2983 10688892 10685925 0.000000e+00 4115
7 TraesCS3D01G028000 chr3A 97.516 161 4 0 3401 3561 10684309 10684149 3.500000e-70 276
8 TraesCS3D01G028000 chr3A 93.443 183 10 1 3220 3400 10685830 10685648 1.630000e-68 270
9 TraesCS3D01G028000 chrUn 91.392 2916 232 13 1 2908 35294948 35297852 0.000000e+00 3976
10 TraesCS3D01G028000 chrUn 91.392 2916 232 13 1 2908 229344788 229347692 0.000000e+00 3976
11 TraesCS3D01G028000 chrUn 93.459 2385 155 1 7 2391 257887412 257885029 0.000000e+00 3539
12 TraesCS3D01G028000 chrUn 92.726 2392 171 3 1 2391 284402973 284400584 0.000000e+00 3450
13 TraesCS3D01G028000 chrUn 92.726 2392 171 3 1 2391 302993132 302990743 0.000000e+00 3450
14 TraesCS3D01G028000 chrUn 87.518 689 54 9 2902 3558 208765844 208766532 0.000000e+00 767


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 TraesCS3D01G028000 chr3D 9633160 9636720 3560 False 6577.000000 6577 100.000000 1 3561 1 chr3D.!!$F1 3560
1 TraesCS3D01G028000 chr3D 4956495 4959556 3061 True 1920.000000 3668 91.640500 2 2747 2 chr3D.!!$R1 2745
2 TraesCS3D01G028000 chr3B 13814917 13818441 3524 False 2630.500000 4963 94.796000 1 3561 2 chr3B.!!$F1 3560
3 TraesCS3D01G028000 chr3A 10881180 10884768 3588 True 4907.000000 4907 91.495000 1 3561 1 chr3A.!!$R1 3560
4 TraesCS3D01G028000 chr3A 10684149 10688892 4743 True 1553.666667 4115 94.205667 1 3561 3 chr3A.!!$R2 3560
5 TraesCS3D01G028000 chrUn 35294948 35297852 2904 False 3976.000000 3976 91.392000 1 2908 1 chrUn.!!$F1 2907
6 TraesCS3D01G028000 chrUn 229344788 229347692 2904 False 3976.000000 3976 91.392000 1 2908 1 chrUn.!!$F3 2907
7 TraesCS3D01G028000 chrUn 257885029 257887412 2383 True 3539.000000 3539 93.459000 7 2391 1 chrUn.!!$R1 2384
8 TraesCS3D01G028000 chrUn 284400584 284402973 2389 True 3450.000000 3450 92.726000 1 2391 1 chrUn.!!$R2 2390
9 TraesCS3D01G028000 chrUn 302990743 302993132 2389 True 3450.000000 3450 92.726000 1 2391 1 chrUn.!!$R3 2390
10 TraesCS3D01G028000 chrUn 208765844 208766532 688 False 767.000000 767 87.518000 2902 3558 1 chrUn.!!$F2 656

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
68 69 0.178891 TTGGGGCTCTCCTCTTGTCT 60.179 55.0 0.00 0.00 32.58 3.41 F
789 790 0.466922 CCATCCCACCTCAGATTGCC 60.467 60.0 0.00 0.00 0.00 4.52 F
2016 2018 0.037160 TGACAGCACATGTGGCAGAT 59.963 50.0 26.55 8.81 44.17 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1944 1946 0.541392 AGTCACAGTGCAAGACCACA 59.459 50.0 0.00 0.0 38.18 4.17 R
2083 2085 0.396139 CCTGGTGCCATGTAGCCAAT 60.396 55.0 0.00 0.0 0.00 3.16 R
3065 3420 0.249155 TTGTGACACCGTCTTCGACC 60.249 55.0 2.45 0.0 39.71 4.79 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 69 0.178891 TTGGGGCTCTCCTCTTGTCT 60.179 55.000 0.00 0.00 32.58 3.41
91 92 2.389715 ACCTCCAAACTATCTCCCTCG 58.610 52.381 0.00 0.00 0.00 4.63
280 281 1.821216 TCCGGAAGAATTTGGACAGC 58.179 50.000 0.00 0.00 29.43 4.40
310 311 3.326006 ACTCACTGTGTTGGATGTCTCAT 59.674 43.478 7.79 0.00 0.00 2.90
316 317 6.818142 CACTGTGTTGGATGTCTCATACAATA 59.182 38.462 10.04 5.55 42.70 1.90
354 355 2.567615 TCCTGCTTCTCTTGGTAACCTC 59.432 50.000 0.00 0.00 0.00 3.85
372 373 5.799827 ACCTCTCTGAATTAGCATACCTC 57.200 43.478 0.00 0.00 0.00 3.85
400 401 9.974980 TCTTAAACAAAAATATGTTCCTTGGAC 57.025 29.630 0.00 0.00 42.49 4.02
447 448 9.703892 AGTATCAACTCTATGCTTCATATTGAC 57.296 33.333 4.46 0.00 30.70 3.18
500 501 9.877178 TCTTAGCTTCTTATCCAGTTTTTCTAG 57.123 33.333 0.00 0.00 0.00 2.43
501 502 9.103861 CTTAGCTTCTTATCCAGTTTTTCTAGG 57.896 37.037 0.00 0.00 0.00 3.02
599 600 1.515736 GCCAGCTGCAGATTTTCGC 60.516 57.895 20.43 6.10 40.77 4.70
714 715 6.008960 GGATAGCAAGATTCCAGAATCCATT 58.991 40.000 15.16 3.51 46.28 3.16
743 744 1.377536 GAGAATCTCCAGTGGCTTGC 58.622 55.000 3.51 0.00 0.00 4.01
789 790 0.466922 CCATCCCACCTCAGATTGCC 60.467 60.000 0.00 0.00 0.00 4.52
811 812 6.432162 TGCCATGCTCAAGAATATAGGAAATC 59.568 38.462 0.00 0.00 0.00 2.17
928 929 9.512588 AGTTATCATCAATTATCCCATCAAGTC 57.487 33.333 0.00 0.00 0.00 3.01
944 945 7.337689 CCCATCAAGTCTATTTGATCTTGACAA 59.662 37.037 8.29 0.00 43.93 3.18
952 953 8.203485 GTCTATTTGATCTTGACAATCTCCTCT 58.797 37.037 0.00 0.00 0.00 3.69
992 993 4.357918 ACTTCTTGACTGGCACATTACT 57.642 40.909 0.00 0.00 38.20 2.24
1007 1008 4.516698 CACATTACTGGTTGATATGGGCTC 59.483 45.833 0.00 0.00 0.00 4.70
1153 1154 4.518211 CACTTCCAGAATCTTTCAGCAAGT 59.482 41.667 0.00 0.00 33.66 3.16
1334 1335 4.017222 ACAATCCTTGATGGGGAATTCTGA 60.017 41.667 5.23 0.00 36.37 3.27
1474 1476 8.956533 TGTAGCTTTCTGCATATATGTAACAA 57.043 30.769 14.14 3.17 45.94 2.83
1570 1572 4.106029 GTCTCGTACCATGAGCTTGTTA 57.894 45.455 0.00 0.00 31.39 2.41
1582 1584 3.999001 TGAGCTTGTTAGAGCAACTGATG 59.001 43.478 0.00 0.00 45.12 3.07
1602 1604 6.946340 TGATGATTTTAGTGAGAGCAACCTA 58.054 36.000 0.00 0.00 0.00 3.08
1668 1670 5.549347 AGCAATGGTTTGATTGTTGCAATA 58.451 33.333 0.59 0.00 45.54 1.90
1798 1800 1.886542 CCAACTTGGAGTTTAGGGCAC 59.113 52.381 0.92 0.00 40.96 5.01
1944 1946 4.801330 TCTTCACCATGAACACTACGAT 57.199 40.909 0.00 0.00 32.21 3.73
1992 1994 4.154015 CCTAGCAATGTGTTGTTCGATGAA 59.846 41.667 0.00 0.00 37.65 2.57
2016 2018 0.037160 TGACAGCACATGTGGCAGAT 59.963 50.000 26.55 8.81 44.17 2.90
2083 2085 1.153369 GCGAGCATGCCTGGAACTA 60.153 57.895 15.66 0.00 0.00 2.24
2107 2109 1.473434 GCTACATGGCACCAGGTACTC 60.473 57.143 10.00 2.38 41.39 2.59
2108 2110 2.111384 CTACATGGCACCAGGTACTCT 58.889 52.381 10.00 0.00 41.39 3.24
2145 2147 7.596494 CAATTTTCTTGCTCAATCTACTTCCA 58.404 34.615 0.00 0.00 0.00 3.53
2438 2440 3.192633 GCCGATATTTGAGTTGGGTTTGT 59.807 43.478 0.00 0.00 0.00 2.83
2617 2938 0.318120 AAAGGGCGAAAACCATGCAG 59.682 50.000 0.00 0.00 0.00 4.41
2748 3075 5.396436 CCTTAACCGTCTTCCATGTAATCCT 60.396 44.000 0.00 0.00 0.00 3.24
2797 3124 4.494091 AGTCCAATAACCTCTGGATGTG 57.506 45.455 0.00 0.00 43.52 3.21
2827 3155 6.294361 TGCTTGTATGCTATTACGGGATAT 57.706 37.500 0.00 0.00 0.00 1.63
2950 3278 1.319541 CGATCACTACCCCGATCTGT 58.680 55.000 0.00 0.00 36.66 3.41
3026 3369 3.641434 AGGAAATCACCTCATGTGGAG 57.359 47.619 20.43 12.58 45.48 3.86
3099 3458 5.387279 GTGTCACAAACAAAAGAAGACGAA 58.613 37.500 0.00 0.00 40.31 3.85
3306 3771 2.205074 GAGTCACCATCGCCAATACAG 58.795 52.381 0.00 0.00 0.00 2.74
3318 3783 2.354821 GCCAATACAGAAAAGGGTAGCG 59.645 50.000 0.00 0.00 0.00 4.26
3514 5317 3.496331 TCATCGTATGGGTGAGCTCATA 58.504 45.455 21.47 10.16 37.03 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 0.605319 TCACCGGTGAATCTGTTGCC 60.605 55.000 34.60 0.00 36.53 4.52
68 69 4.689150 CGAGGGAGATAGTTTGGAGGTAGA 60.689 50.000 0.00 0.00 0.00 2.59
91 92 3.084786 CACCCTCAAAGAAACTCCCATC 58.915 50.000 0.00 0.00 0.00 3.51
98 99 2.481276 GGCACAACACCCTCAAAGAAAC 60.481 50.000 0.00 0.00 0.00 2.78
129 130 5.753721 AACTGAGATGAGAAAGCTTACCT 57.246 39.130 0.00 0.00 0.00 3.08
132 133 6.365970 AGGAAACTGAGATGAGAAAGCTTA 57.634 37.500 0.00 0.00 41.13 3.09
280 281 1.942657 CAACACAGTGAGTTGGTCCAG 59.057 52.381 21.57 0.00 41.92 3.86
310 311 8.026396 GGAATGGGTCCTACTAGTTTATTGTA 57.974 38.462 0.00 0.00 43.98 2.41
354 355 6.418057 AAGAGGAGGTATGCTAATTCAGAG 57.582 41.667 0.00 0.00 0.00 3.35
372 373 9.423061 CCAAGGAACATATTTTTGTTTAAGAGG 57.577 33.333 0.00 0.00 39.85 3.69
400 401 1.271707 ACCAATTGTTCCTGGTACCGG 60.272 52.381 14.38 14.38 44.28 5.28
447 448 2.932614 CACTAGGCGGTTCTCTGAAATG 59.067 50.000 0.00 0.00 0.00 2.32
473 474 8.554835 AGAAAAACTGGATAAGAAGCTAAGAC 57.445 34.615 0.00 0.00 0.00 3.01
500 501 7.448748 TGAATAAACTGGAGCTTTCTAAACC 57.551 36.000 0.00 0.00 0.00 3.27
501 502 9.914131 ATTTGAATAAACTGGAGCTTTCTAAAC 57.086 29.630 0.00 0.00 0.00 2.01
743 744 0.101759 CAAGCGATTTCCATGCAGGG 59.898 55.000 12.23 12.23 38.24 4.45
789 790 8.618702 ACAGATTTCCTATATTCTTGAGCATG 57.381 34.615 0.00 0.00 0.00 4.06
928 929 9.695526 CTAGAGGAGATTGTCAAGATCAAATAG 57.304 37.037 0.00 0.00 0.00 1.73
934 935 5.789643 AGCTAGAGGAGATTGTCAAGATC 57.210 43.478 0.00 0.00 0.00 2.75
944 945 5.073008 TGAGACACATCTAGCTAGAGGAGAT 59.927 44.000 35.18 22.70 37.53 2.75
952 953 7.233389 AGAAGTTTTGAGACACATCTAGCTA 57.767 36.000 0.00 0.00 34.34 3.32
992 993 4.272489 CTTCAAAGAGCCCATATCAACCA 58.728 43.478 0.00 0.00 0.00 3.67
1007 1008 7.223387 GGTCCATGCTATAAATTTGCTTCAAAG 59.777 37.037 0.00 0.00 36.76 2.77
1153 1154 3.449018 TCCAAACTTTGCAAGCTGGTTAA 59.551 39.130 14.25 0.00 36.60 2.01
1220 1221 3.367703 GCTGGTCAGGATGGTGAAATTTG 60.368 47.826 0.00 0.00 36.16 2.32
1334 1335 0.748005 ACGTGAAGCACCACAAAGCT 60.748 50.000 8.80 0.00 44.31 3.74
1474 1476 5.414144 GCTGCTTCTTAATCTTCTTTCTGGT 59.586 40.000 0.00 0.00 0.00 4.00
1570 1572 6.705302 TCTCACTAAAATCATCAGTTGCTCT 58.295 36.000 0.00 0.00 0.00 4.09
1582 1584 6.981559 CCTAGTAGGTTGCTCTCACTAAAATC 59.018 42.308 8.17 0.00 0.00 2.17
1602 1604 3.323775 TCCAAAACTTCCAGACCCTAGT 58.676 45.455 0.00 0.00 0.00 2.57
1668 1670 6.042638 TCTAGCTGCATGTCTAGAACTTTT 57.957 37.500 14.39 0.00 38.55 2.27
1798 1800 3.489355 TGGGCATATATTGAAGCACCAG 58.511 45.455 0.00 0.00 0.00 4.00
1839 1841 5.361571 TGTTGTACCTTGAGAGTTGTGTAGA 59.638 40.000 0.00 0.00 0.00 2.59
1944 1946 0.541392 AGTCACAGTGCAAGACCACA 59.459 50.000 0.00 0.00 38.18 4.17
2016 2018 2.706339 ACAACCTTGCAATGCCAAAA 57.294 40.000 1.53 0.00 0.00 2.44
2083 2085 0.396139 CCTGGTGCCATGTAGCCAAT 60.396 55.000 0.00 0.00 0.00 3.16
2438 2440 1.032657 GGAGAGTCGCTAGTGCAGGA 61.033 60.000 0.00 0.00 39.64 3.86
2548 2550 1.167851 ATGTTGGTCAATGACTGGCG 58.832 50.000 13.53 0.00 32.47 5.69
2617 2938 4.090498 GCTTTTTGACATCTTGAATTCGGC 59.910 41.667 0.04 0.00 0.00 5.54
2771 3098 5.779241 TCCAGAGGTTATTGGACTTGAAT 57.221 39.130 0.00 0.00 38.53 2.57
2772 3099 5.014123 ACATCCAGAGGTTATTGGACTTGAA 59.986 40.000 0.00 0.00 45.66 2.69
2773 3100 4.536090 ACATCCAGAGGTTATTGGACTTGA 59.464 41.667 0.00 0.00 45.66 3.02
2774 3101 4.637534 CACATCCAGAGGTTATTGGACTTG 59.362 45.833 0.00 0.00 45.66 3.16
2775 3102 4.536090 TCACATCCAGAGGTTATTGGACTT 59.464 41.667 0.00 0.00 45.66 3.01
2776 3103 4.104086 TCACATCCAGAGGTTATTGGACT 58.896 43.478 0.00 0.00 45.66 3.85
2777 3104 4.487714 TCACATCCAGAGGTTATTGGAC 57.512 45.455 0.00 0.00 45.66 4.02
2778 3105 5.715439 AATCACATCCAGAGGTTATTGGA 57.285 39.130 0.00 0.00 46.79 3.53
2797 3124 6.347725 CCGTAATAGCATACAAGCAGGAAATC 60.348 42.308 0.00 0.00 36.85 2.17
2827 3155 6.384258 ACAATGTATTTATATTGCGGTGCA 57.616 33.333 6.89 0.00 38.04 4.57
2950 3278 2.931105 ATGTGGTGGCCGTGGGTA 60.931 61.111 0.00 0.00 0.00 3.69
3026 3369 3.244249 GGTTAGTGGCATGATCTAGTCCC 60.244 52.174 0.00 0.00 0.00 4.46
3065 3420 0.249155 TTGTGACACCGTCTTCGACC 60.249 55.000 2.45 0.00 39.71 4.79
3069 3424 3.750639 TTTGTTTGTGACACCGTCTTC 57.249 42.857 2.45 0.00 38.18 2.87
3162 3521 2.284995 AGAGGGAGGTCAGCACCC 60.285 66.667 0.07 0.07 45.12 4.61
3164 3523 1.194781 TTGGAGAGGGAGGTCAGCAC 61.195 60.000 0.00 0.00 0.00 4.40
3227 3690 1.541588 GGTTTTGATCACAGTCCAGGC 59.458 52.381 0.00 0.00 0.00 4.85
3306 3771 2.180432 AAGGACACGCTACCCTTTTC 57.820 50.000 0.00 0.00 36.98 2.29
3318 3783 9.628500 ATGGGTTCTAATCTTATTAAAGGACAC 57.372 33.333 0.00 0.00 33.22 3.67
3514 5317 7.725251 TGAAATTGCTAGTTTTCACAGGAAAT 58.275 30.769 11.27 0.00 42.31 2.17


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

AutoCloner maintained by Alex Coulton.