Multiple sequence alignment - TraesCS1B01G206600

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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 TraesCS1B01G206600 chr1B 100.000 2642 0 0 1 2642 373627377 373630018 0.000000e+00 4879
1 TraesCS1B01G206600 chr1D 91.250 2663 141 43 1 2633 274253635 274256235 0.000000e+00 3542
2 TraesCS1B01G206600 chr1A 92.832 2009 58 26 665 2633 346681261 346683223 0.000000e+00 2833
3 TraesCS1B01G206600 chr1A 88.759 685 66 9 2 683 346680573 346681249 0.000000e+00 828
4 TraesCS1B01G206600 chr1A 81.250 128 23 1 208 335 551906932 551906806 4.650000e-18 102
5 TraesCS1B01G206600 chr3D 80.745 322 48 12 1268 1582 132275352 132275666 3.400000e-59 239
6 TraesCS1B01G206600 chr3B 80.186 323 48 12 1268 1582 188877448 188877762 7.360000e-56 228
7 TraesCS1B01G206600 chr3A 80.186 323 48 12 1268 1582 145667466 145667780 7.360000e-56 228
8 TraesCS1B01G206600 chr3A 83.007 153 25 1 97 249 695743138 695742987 1.280000e-28 137
9 TraesCS1B01G206600 chr7A 76.398 322 56 10 2 319 673012899 673013204 3.520000e-34 156
10 TraesCS1B01G206600 chr5A 85.981 107 14 1 213 319 287149499 287149394 2.150000e-21 113


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 TraesCS1B01G206600 chr1B 373627377 373630018 2641 False 4879.0 4879 100.0000 1 2642 1 chr1B.!!$F1 2641
1 TraesCS1B01G206600 chr1D 274253635 274256235 2600 False 3542.0 3542 91.2500 1 2633 1 chr1D.!!$F1 2632
2 TraesCS1B01G206600 chr1A 346680573 346683223 2650 False 1830.5 2833 90.7955 2 2633 2 chr1A.!!$F1 2631

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
94 95 0.591488 TCGCGCCGCATATCGATATC 60.591 55.0 15.08 9.31 41.67 1.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1664 1723 1.068264 CCTCCCGAGAAAAAGCAAAGC 60.068 52.381 0.0 0.0 0.0 3.51 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
42 43 2.954318 CGCCTTTCTTCATGGATTGGAT 59.046 45.455 0.00 0.00 0.00 3.41
90 91 2.729491 CTTCGCGCCGCATATCGA 60.729 61.111 10.75 0.00 41.67 3.59
94 95 0.591488 TCGCGCCGCATATCGATATC 60.591 55.000 15.08 9.31 41.67 1.63
95 96 0.592500 CGCGCCGCATATCGATATCT 60.593 55.000 15.08 0.00 41.67 1.98
140 141 3.680786 CTCGTCGACTGGCCACCA 61.681 66.667 14.70 0.00 0.00 4.17
156 157 4.758251 CATCACAGCCACGCCCGA 62.758 66.667 0.00 0.00 0.00 5.14
304 305 3.053991 TGGGTGTTCTTCAGGAGTGAAAA 60.054 43.478 0.00 0.00 42.27 2.29
374 375 7.333528 TGTGATGGGATTTCTATTAAAGTGC 57.666 36.000 0.00 0.00 0.00 4.40
438 440 7.492669 CGAAGAATTGGTGAATCATGTACTACT 59.507 37.037 0.00 0.00 0.00 2.57
439 441 9.817809 GAAGAATTGGTGAATCATGTACTACTA 57.182 33.333 0.00 0.00 0.00 1.82
457 459 7.916914 ACTACTATGTTTTAAGATGGCGTTT 57.083 32.000 0.00 0.00 0.00 3.60
496 499 2.161609 GTGAAGTTATTTCGGTGGCCAG 59.838 50.000 5.11 0.00 38.71 4.85
609 616 7.936301 GTCCATTAATCTTTTAGGAGATGCTCT 59.064 37.037 0.00 0.00 36.53 4.09
708 744 6.861065 TCCTGTAGTTTTAAGCAAAGACAG 57.139 37.500 0.00 0.00 38.34 3.51
711 747 7.988599 TCCTGTAGTTTTAAGCAAAGACAGTTA 59.011 33.333 0.00 0.00 37.60 2.24
712 748 8.617809 CCTGTAGTTTTAAGCAAAGACAGTTAA 58.382 33.333 0.00 0.00 37.60 2.01
799 855 4.142026 CGTAGACCAAGAGAGAGAGAGAGA 60.142 50.000 0.00 0.00 0.00 3.10
800 856 4.494091 AGACCAAGAGAGAGAGAGAGAG 57.506 50.000 0.00 0.00 0.00 3.20
814 870 6.670027 AGAGAGAGAGAGTAGAGAGAGAAAGT 59.330 42.308 0.00 0.00 0.00 2.66
948 1004 1.299014 CCTCTCTCTCGCACGCATC 60.299 63.158 0.00 0.00 0.00 3.91
949 1005 1.299014 CTCTCTCTCGCACGCATCC 60.299 63.158 0.00 0.00 0.00 3.51
950 1006 2.279120 CTCTCTCGCACGCATCCC 60.279 66.667 0.00 0.00 0.00 3.85
951 1007 3.068064 TCTCTCGCACGCATCCCA 61.068 61.111 0.00 0.00 0.00 4.37
952 1008 2.107750 CTCTCGCACGCATCCCAT 59.892 61.111 0.00 0.00 0.00 4.00
953 1009 1.953138 CTCTCGCACGCATCCCATC 60.953 63.158 0.00 0.00 0.00 3.51
954 1010 2.969238 CTCGCACGCATCCCATCC 60.969 66.667 0.00 0.00 0.00 3.51
955 1011 4.545706 TCGCACGCATCCCATCCC 62.546 66.667 0.00 0.00 0.00 3.85
956 1012 4.854924 CGCACGCATCCCATCCCA 62.855 66.667 0.00 0.00 0.00 4.37
957 1013 3.211963 GCACGCATCCCATCCCAC 61.212 66.667 0.00 0.00 0.00 4.61
1146 1202 2.123982 CCAGGCCAATGCTCCTCC 60.124 66.667 5.01 0.00 37.74 4.30
1152 1208 1.144936 CCAATGCTCCTCCCTCGTC 59.855 63.158 0.00 0.00 0.00 4.20
1227 1283 1.357272 ACTGCCCCCAGGTGTACAAA 61.357 55.000 0.00 0.00 43.53 2.83
1446 1502 2.911484 CGTCACCACCGTCTCCGAA 61.911 63.158 0.00 0.00 35.63 4.30
1494 1550 2.031616 ACCGTCGTCCTCGAGTCA 59.968 61.111 12.31 0.00 46.96 3.41
1590 1646 0.318441 TCCAGAAGCTCAAGTCCGTG 59.682 55.000 0.00 0.00 0.00 4.94
1664 1723 1.956170 GGCCGGATGCTGTGATACG 60.956 63.158 5.05 0.00 40.92 3.06
1993 2058 7.337436 TGATGATGAATTAGCACTTGTTGATCA 59.663 33.333 0.00 0.00 30.86 2.92
2101 2182 2.497675 TGCTCTAAACTGTAGAGGCTGG 59.502 50.000 11.36 0.00 40.92 4.85
2102 2183 2.761208 GCTCTAAACTGTAGAGGCTGGA 59.239 50.000 11.36 0.00 40.92 3.86
2151 2232 3.149196 AGATGCTTGTTTAGTGGGTGTG 58.851 45.455 0.00 0.00 0.00 3.82
2244 2325 0.031994 AACCGGCATGAAAACACAGC 59.968 50.000 0.00 0.00 0.00 4.40
2317 2398 1.272425 CCATTTTCCCAGGCCACACTA 60.272 52.381 5.01 0.00 0.00 2.74
2343 2425 8.210265 ACAAAATTTGGTGAATTTATGTCCAGT 58.790 29.630 10.71 0.00 44.98 4.00
2411 2493 3.088532 TGTGATCCATTTGTGTTAGCCC 58.911 45.455 0.00 0.00 0.00 5.19
2500 2584 8.706492 TTTTTCATGATCAAATCCATTGCTAC 57.294 30.769 0.00 0.00 38.98 3.58
2508 2592 4.276678 TCAAATCCATTGCTACTGCTATGC 59.723 41.667 6.87 0.00 46.08 3.14
2536 2620 5.649395 TGCTTAAAGATTCAGACATGGAAGG 59.351 40.000 0.00 0.00 0.00 3.46
2538 2622 6.375455 GCTTAAAGATTCAGACATGGAAGGAA 59.625 38.462 0.00 0.00 0.00 3.36
2581 2673 3.952931 AGAATGCAAGATGCTCAAGAGT 58.047 40.909 3.78 0.00 45.31 3.24
2603 2695 2.354259 CCAGCGAGCATCTTCTTTTCT 58.646 47.619 0.00 0.00 0.00 2.52
2604 2696 2.746362 CCAGCGAGCATCTTCTTTTCTT 59.254 45.455 0.00 0.00 0.00 2.52
2605 2697 3.190118 CCAGCGAGCATCTTCTTTTCTTT 59.810 43.478 0.00 0.00 0.00 2.52
2606 2698 4.320788 CCAGCGAGCATCTTCTTTTCTTTT 60.321 41.667 0.00 0.00 0.00 2.27
2607 2699 4.850470 CAGCGAGCATCTTCTTTTCTTTTC 59.150 41.667 0.00 0.00 0.00 2.29
2608 2700 4.759183 AGCGAGCATCTTCTTTTCTTTTCT 59.241 37.500 0.00 0.00 0.00 2.52
2634 2726 7.928908 TTTTTCTTTTCAATCAATCTGTCCG 57.071 32.000 0.00 0.00 0.00 4.79
2635 2727 4.685169 TCTTTTCAATCAATCTGTCCGC 57.315 40.909 0.00 0.00 0.00 5.54
2636 2728 3.440173 TCTTTTCAATCAATCTGTCCGCC 59.560 43.478 0.00 0.00 0.00 6.13
2637 2729 2.787473 TTCAATCAATCTGTCCGCCT 57.213 45.000 0.00 0.00 0.00 5.52
2638 2730 2.315925 TCAATCAATCTGTCCGCCTC 57.684 50.000 0.00 0.00 0.00 4.70
2639 2731 1.134401 TCAATCAATCTGTCCGCCTCC 60.134 52.381 0.00 0.00 0.00 4.30
2640 2732 1.134280 CAATCAATCTGTCCGCCTCCT 60.134 52.381 0.00 0.00 0.00 3.69
2641 2733 0.755686 ATCAATCTGTCCGCCTCCTC 59.244 55.000 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 4.005650 CGATACCCATCCAATCCATGAAG 58.994 47.826 0.00 0.00 0.00 3.02
42 43 0.032952 GCTATGCGGTTCGATACCCA 59.967 55.000 10.07 9.43 44.70 4.51
75 76 0.591488 GATATCGATATGCGGCGCGA 60.591 55.000 28.09 18.35 41.33 5.87
76 77 0.592500 AGATATCGATATGCGGCGCG 60.593 55.000 28.09 12.63 41.33 6.86
90 91 7.256619 CCAAGCAATTAGAGAAGGAGGAGATAT 60.257 40.741 0.00 0.00 0.00 1.63
94 95 4.163078 TCCAAGCAATTAGAGAAGGAGGAG 59.837 45.833 0.00 0.00 0.00 3.69
95 96 4.104086 TCCAAGCAATTAGAGAAGGAGGA 58.896 43.478 0.00 0.00 0.00 3.71
110 111 0.171231 CGACGAGTGAGATCCAAGCA 59.829 55.000 0.00 0.00 0.00 3.91
140 141 4.760047 GTCGGGCGTGGCTGTGAT 62.760 66.667 1.93 0.00 0.00 3.06
164 165 4.077184 TAGTGCCAAGCCCGTCCG 62.077 66.667 0.00 0.00 0.00 4.79
250 251 1.498865 CTGCGTGCTCGAAACTTGGT 61.499 55.000 13.13 0.00 39.71 3.67
281 282 2.338809 TCACTCCTGAAGAACACCCAT 58.661 47.619 0.00 0.00 0.00 4.00
295 296 2.171003 CACCCCATCCTTTTTCACTCC 58.829 52.381 0.00 0.00 0.00 3.85
304 305 2.065799 ACAAGAACTCACCCCATCCTT 58.934 47.619 0.00 0.00 0.00 3.36
351 352 7.333528 TGCACTTTAATAGAAATCCCATCAC 57.666 36.000 0.00 0.00 0.00 3.06
368 369 7.524717 AACTAGAACCACAATTATGCACTTT 57.475 32.000 0.00 0.00 0.00 2.66
670 677 5.437060 ACTACAGGAACAACACTTTGATGT 58.563 37.500 0.00 0.00 34.74 3.06
711 747 7.500992 TGCATATTCTCTCTTCGGATTTACTT 58.499 34.615 0.00 0.00 0.00 2.24
712 748 7.055667 TGCATATTCTCTCTTCGGATTTACT 57.944 36.000 0.00 0.00 0.00 2.24
799 855 4.569015 GGACCAGGACTTTCTCTCTCTACT 60.569 50.000 0.00 0.00 0.00 2.57
800 856 3.697542 GGACCAGGACTTTCTCTCTCTAC 59.302 52.174 0.00 0.00 0.00 2.59
814 870 0.554865 ATGGGGAATTGGGACCAGGA 60.555 55.000 0.00 0.00 36.27 3.86
917 973 1.992277 GAGAGGCTTGGAGCAGGGA 60.992 63.158 2.04 0.00 44.75 4.20
950 1006 4.060667 GTGGGGTGGGGTGGGATG 62.061 72.222 0.00 0.00 0.00 3.51
1227 1283 2.037136 GCAGCTGCGGATGAAGTGT 61.037 57.895 25.23 0.00 0.00 3.55
1467 1523 1.506718 GACGACGGTGCAGATCTCA 59.493 57.895 0.00 0.00 0.00 3.27
1664 1723 1.068264 CCTCCCGAGAAAAAGCAAAGC 60.068 52.381 0.00 0.00 0.00 3.51
2018 2083 4.398319 TCATCATCGATCAGCAGGTAGTA 58.602 43.478 0.00 0.00 0.00 1.82
2019 2084 3.225940 TCATCATCGATCAGCAGGTAGT 58.774 45.455 0.00 0.00 0.00 2.73
2020 2085 3.930634 TCATCATCGATCAGCAGGTAG 57.069 47.619 0.00 0.00 0.00 3.18
2101 2182 6.831769 ACAATCAATCACAGTAACATCGTTC 58.168 36.000 0.00 0.00 0.00 3.95
2102 2183 6.650807 AGACAATCAATCACAGTAACATCGTT 59.349 34.615 0.00 0.00 0.00 3.85
2151 2232 6.564328 ACATGACAAGAAAGAGACAAAAACC 58.436 36.000 0.00 0.00 0.00 3.27
2244 2325 1.416049 CAACAAGTGTCGATCGCCG 59.584 57.895 11.09 0.00 40.25 6.46
2317 2398 8.210265 ACTGGACATAAATTCACCAAATTTTGT 58.790 29.630 8.26 6.11 43.51 2.83
2488 2572 3.819337 CAGCATAGCAGTAGCAATGGATT 59.181 43.478 0.00 0.00 45.49 3.01
2500 2584 3.273434 TCTTTAAGCACCAGCATAGCAG 58.727 45.455 0.00 0.00 45.49 4.24
2508 2592 5.163683 CCATGTCTGAATCTTTAAGCACCAG 60.164 44.000 0.00 0.00 0.00 4.00
2536 2620 3.120165 GCTGCTACTGTACTGGCTTTTTC 60.120 47.826 4.66 0.00 0.00 2.29
2538 2622 2.224523 TGCTGCTACTGTACTGGCTTTT 60.225 45.455 0.00 0.00 0.00 2.27
2577 2669 0.975040 AAGATGCTCGCTGGGACTCT 60.975 55.000 0.00 0.00 0.00 3.24
2581 2673 0.615331 AAAGAAGATGCTCGCTGGGA 59.385 50.000 0.00 0.00 0.00 4.37


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

AutoCloner maintained by Alex Coulton.