Multiple sequence alignment - TraesCS3B01G384300

Loading Multiple Alignment...

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 TraesCS3B01G384300 chr3B 100.000 3965 0 0 1 3965 604268098 604272062 0.000000e+00 7323
1 TraesCS3B01G384300 chr3A 94.594 3163 121 20 824 3965 600021723 600024856 0.000000e+00 4848
2 TraesCS3B01G384300 chr3D 95.595 2111 67 6 865 2966 457229892 457231985 0.000000e+00 3360
3 TraesCS3B01G384300 chr3D 90.980 1031 44 25 2938 3965 457232062 457233046 0.000000e+00 1343
4 TraesCS3B01G384300 chr5D 93.100 1000 42 6 1516 2497 524597968 524596978 0.000000e+00 1439
5 TraesCS3B01G384300 chr6B 96.485 825 23 4 1 823 26499692 26500512 0.000000e+00 1358
6 TraesCS3B01G384300 chr6B 93.450 855 26 6 1 829 599875111 599874261 0.000000e+00 1242
7 TraesCS3B01G384300 chr6B 94.261 819 28 9 2 818 181113621 181114422 0.000000e+00 1234
8 TraesCS3B01G384300 chr6B 96.147 571 21 1 1517 2087 257597156 257597725 0.000000e+00 931
9 TraesCS3B01G384300 chr6B 89.614 414 32 7 2093 2497 257599019 257599430 2.110000e-142 516
10 TraesCS3B01G384300 chr4B 94.471 832 28 5 1 818 396488420 396487593 0.000000e+00 1266
11 TraesCS3B01G384300 chr4B 93.972 846 22 5 3 823 310255778 310254937 0.000000e+00 1253
12 TraesCS3B01G384300 chr5B 93.900 836 34 4 1 823 64273747 64272916 0.000000e+00 1245
13 TraesCS3B01G384300 chr5B 93.468 842 32 5 1 823 535134896 535134059 0.000000e+00 1229
14 TraesCS3B01G384300 chr5B 92.683 861 33 11 3 837 709188118 709188974 0.000000e+00 1214
15 TraesCS3B01G384300 chr5B 95.498 422 7 1 1 410 506963485 506963064 0.000000e+00 664
16 TraesCS3B01G384300 chr2B 93.750 848 24 5 1 823 549351161 549350318 0.000000e+00 1245
17 TraesCS3B01G384300 chr1B 93.483 844 22 7 1 816 571424458 571425296 0.000000e+00 1223
18 TraesCS3B01G384300 chrUn 93.413 835 29 10 2 823 86407390 86406569 0.000000e+00 1214
19 TraesCS3B01G384300 chrUn 94.831 503 25 1 1516 2018 31913106 31912605 0.000000e+00 784
20 TraesCS3B01G384300 chrUn 94.681 94 5 0 1402 1495 31913190 31913097 3.190000e-31 147
21 TraesCS3B01G384300 chr6A 91.976 835 50 5 1 823 7014732 7013903 0.000000e+00 1155
22 TraesCS3B01G384300 chr6A 91.294 827 58 7 1 825 23002604 23001790 0.000000e+00 1116


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 TraesCS3B01G384300 chr3B 604268098 604272062 3964 False 7323.0 7323 100.0000 1 3965 1 chr3B.!!$F1 3964
1 TraesCS3B01G384300 chr3A 600021723 600024856 3133 False 4848.0 4848 94.5940 824 3965 1 chr3A.!!$F1 3141
2 TraesCS3B01G384300 chr3D 457229892 457233046 3154 False 2351.5 3360 93.2875 865 3965 2 chr3D.!!$F1 3100
3 TraesCS3B01G384300 chr5D 524596978 524597968 990 True 1439.0 1439 93.1000 1516 2497 1 chr5D.!!$R1 981
4 TraesCS3B01G384300 chr6B 26499692 26500512 820 False 1358.0 1358 96.4850 1 823 1 chr6B.!!$F1 822
5 TraesCS3B01G384300 chr6B 599874261 599875111 850 True 1242.0 1242 93.4500 1 829 1 chr6B.!!$R1 828
6 TraesCS3B01G384300 chr6B 181113621 181114422 801 False 1234.0 1234 94.2610 2 818 1 chr6B.!!$F2 816
7 TraesCS3B01G384300 chr6B 257597156 257599430 2274 False 723.5 931 92.8805 1517 2497 2 chr6B.!!$F3 980
8 TraesCS3B01G384300 chr4B 396487593 396488420 827 True 1266.0 1266 94.4710 1 818 1 chr4B.!!$R2 817
9 TraesCS3B01G384300 chr4B 310254937 310255778 841 True 1253.0 1253 93.9720 3 823 1 chr4B.!!$R1 820
10 TraesCS3B01G384300 chr5B 64272916 64273747 831 True 1245.0 1245 93.9000 1 823 1 chr5B.!!$R1 822
11 TraesCS3B01G384300 chr5B 535134059 535134896 837 True 1229.0 1229 93.4680 1 823 1 chr5B.!!$R3 822
12 TraesCS3B01G384300 chr5B 709188118 709188974 856 False 1214.0 1214 92.6830 3 837 1 chr5B.!!$F1 834
13 TraesCS3B01G384300 chr2B 549350318 549351161 843 True 1245.0 1245 93.7500 1 823 1 chr2B.!!$R1 822
14 TraesCS3B01G384300 chr1B 571424458 571425296 838 False 1223.0 1223 93.4830 1 816 1 chr1B.!!$F1 815
15 TraesCS3B01G384300 chrUn 86406569 86407390 821 True 1214.0 1214 93.4130 2 823 1 chrUn.!!$R1 821
16 TraesCS3B01G384300 chrUn 31912605 31913190 585 True 465.5 784 94.7560 1402 2018 2 chrUn.!!$R2 616
17 TraesCS3B01G384300 chr6A 7013903 7014732 829 True 1155.0 1155 91.9760 1 823 1 chr6A.!!$R1 822
18 TraesCS3B01G384300 chr6A 23001790 23002604 814 True 1116.0 1116 91.2940 1 825 1 chr6A.!!$R2 824

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
413 462 0.618981 GGTCCACCGAAGAAATCCCT 59.381 55.000 0.0 0.0 0.0 4.20 F
745 807 0.676782 CGGTAGGCAAAAGGGTCAGG 60.677 60.000 0.0 0.0 0.0 3.86 F
1479 1553 1.610886 GGCTTTTCCTACTCCACGCTT 60.611 52.381 0.0 0.0 0.0 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1464 1538 0.809385 CGAGAAGCGTGGAGTAGGAA 59.191 55.0 0.00 0.00 34.64 3.36 R
2050 2128 1.274703 ATGAGCCCGAACAGGTGGAT 61.275 55.0 0.00 0.00 38.74 3.41 R
2993 4473 0.034767 TCTGCAGCCTGAATTCTGGG 60.035 55.0 27.06 19.35 35.73 4.45 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
146 148 6.855667 ACCTAACAATTAACCACTAACCCTT 58.144 36.000 0.00 0.00 0.00 3.95
183 185 7.513560 AACATAACCACTATAACCCTAACCA 57.486 36.000 0.00 0.00 0.00 3.67
395 444 0.740737 GGTGATGAAAATGCTCCGGG 59.259 55.000 0.00 0.00 0.00 5.73
413 462 0.618981 GGTCCACCGAAGAAATCCCT 59.381 55.000 0.00 0.00 0.00 4.20
516 577 0.697854 AAGAAGAGTGGTGGTGGGGT 60.698 55.000 0.00 0.00 0.00 4.95
675 737 4.637771 GCCGTCAAATGGCCTACT 57.362 55.556 3.32 0.00 44.49 2.57
745 807 0.676782 CGGTAGGCAAAAGGGTCAGG 60.677 60.000 0.00 0.00 0.00 3.86
769 831 3.572255 CCCGAAATTTTTCTGAACTGGGA 59.428 43.478 5.85 0.00 34.33 4.37
791 853 4.844349 TCAGATCCCGATTTTCTTTCCT 57.156 40.909 0.00 0.00 0.00 3.36
792 854 5.950544 TCAGATCCCGATTTTCTTTCCTA 57.049 39.130 0.00 0.00 0.00 2.94
793 855 6.500589 TCAGATCCCGATTTTCTTTCCTAT 57.499 37.500 0.00 0.00 0.00 2.57
794 856 7.612065 TCAGATCCCGATTTTCTTTCCTATA 57.388 36.000 0.00 0.00 0.00 1.31
795 857 8.207350 TCAGATCCCGATTTTCTTTCCTATAT 57.793 34.615 0.00 0.00 0.00 0.86
826 888 1.908066 AACACGAAATTCGGCCTCGC 61.908 55.000 19.95 0.00 45.59 5.03
863 925 4.334552 TGAAATCTGAATGCTGCCACTTA 58.665 39.130 0.00 0.00 0.00 2.24
877 948 1.812571 CCACTTACGCCATTTTGCTCT 59.187 47.619 0.00 0.00 0.00 4.09
888 959 2.890808 TTTTGCTCTGACGAGTGTCT 57.109 45.000 0.00 0.00 45.70 3.41
928 999 2.281761 CAAACGTCCCTGCCAGCT 60.282 61.111 0.00 0.00 0.00 4.24
980 1051 4.475135 GCCACTCCCGCTCCCTTC 62.475 72.222 0.00 0.00 0.00 3.46
981 1052 3.787001 CCACTCCCGCTCCCTTCC 61.787 72.222 0.00 0.00 0.00 3.46
982 1053 4.148825 CACTCCCGCTCCCTTCCG 62.149 72.222 0.00 0.00 0.00 4.30
1007 1078 4.133796 GCCAAGACCAATGCCGCC 62.134 66.667 0.00 0.00 0.00 6.13
1008 1079 3.814268 CCAAGACCAATGCCGCCG 61.814 66.667 0.00 0.00 0.00 6.46
1009 1080 2.745884 CAAGACCAATGCCGCCGA 60.746 61.111 0.00 0.00 0.00 5.54
1479 1553 1.610886 GGCTTTTCCTACTCCACGCTT 60.611 52.381 0.00 0.00 0.00 4.68
1530 1604 3.114616 CACGCGCTCACCTTCCTG 61.115 66.667 5.73 0.00 0.00 3.86
1752 1830 2.356313 CTGCTGCTCCACGACGTT 60.356 61.111 0.00 0.00 0.00 3.99
1755 1833 2.805353 CTGCTCCACGACGTTCCG 60.805 66.667 0.00 0.00 0.00 4.30
2064 2142 2.511600 GCGATCCACCTGTTCGGG 60.512 66.667 0.00 0.00 36.97 5.14
2262 3632 0.984230 TCCTGTCCATCTGGGTGAAC 59.016 55.000 0.00 0.00 38.11 3.18
2298 3670 2.512515 GCCGCCAAGCTCTTCGAT 60.513 61.111 0.00 0.00 0.00 3.59
2300 3672 0.601311 GCCGCCAAGCTCTTCGATAT 60.601 55.000 0.00 0.00 0.00 1.63
2392 3771 1.876664 CTCGTCTCGCAGTCCAAGA 59.123 57.895 0.00 0.00 0.00 3.02
2670 4049 0.176219 TTACCATGAACGCCTACGGG 59.824 55.000 0.00 0.00 46.04 5.28
2775 4154 1.153489 GATGCTCAGCTTGCTCGGA 60.153 57.895 0.00 0.00 0.00 4.55
2793 4172 0.457681 GAGCTCAGCAGGACTTCGAC 60.458 60.000 9.40 0.00 0.00 4.20
2883 4262 4.253257 GCCGGCGTCTACGAGAGG 62.253 72.222 12.58 6.81 43.02 3.69
2968 4448 4.425520 CGTCCAGAAACTCAGATAAGGAC 58.574 47.826 0.00 0.00 40.57 3.85
2989 4469 1.827969 GAAGCTTCAGTGCCTCCTCTA 59.172 52.381 21.67 0.00 0.00 2.43
2993 4473 2.559440 CTTCAGTGCCTCCTCTAATGC 58.441 52.381 0.00 0.00 0.00 3.56
2999 4479 0.839946 GCCTCCTCTAATGCCCAGAA 59.160 55.000 0.00 0.00 0.00 3.02
3045 4525 6.316890 ACAAAATTTGAATGTCAGCAAGCTTT 59.683 30.769 13.19 0.00 0.00 3.51
3046 4526 6.930667 AAATTTGAATGTCAGCAAGCTTTT 57.069 29.167 0.00 0.00 0.00 2.27
3081 4561 8.443937 GTCTTGTGTCATTCCTTAGTGATTTAC 58.556 37.037 0.00 0.00 0.00 2.01
3166 4648 4.241681 TCGGCAAAAATGCTGGTAAAATC 58.758 39.130 9.55 0.00 41.28 2.17
3237 4722 8.463930 TCTGACTGAAACCTTGATTAAATGTT 57.536 30.769 0.00 0.00 0.00 2.71
3268 4753 4.305769 CAGCCTCTTGACATCATAGCTAC 58.694 47.826 0.00 0.00 0.00 3.58
3298 4783 7.703621 CCTTGAACTGTGCATTAGATTAAATGG 59.296 37.037 7.80 0.00 37.34 3.16
3496 4982 0.178903 TGTACAAGTGCTCTCCCCCT 60.179 55.000 0.00 0.00 0.00 4.79
3497 4983 1.078159 TGTACAAGTGCTCTCCCCCTA 59.922 52.381 0.00 0.00 0.00 3.53
3498 4984 2.185387 GTACAAGTGCTCTCCCCCTAA 58.815 52.381 0.00 0.00 0.00 2.69
3538 5027 2.617532 GCAGGCACTTGATTCTTCTCCT 60.618 50.000 0.00 0.00 34.60 3.69
3539 5028 3.269178 CAGGCACTTGATTCTTCTCCTC 58.731 50.000 0.00 0.00 34.60 3.71
3540 5029 2.238395 AGGCACTTGATTCTTCTCCTCC 59.762 50.000 0.00 0.00 27.25 4.30
3559 5048 5.788533 TCCTCCACCTAAACAATTCTTAGGA 59.211 40.000 21.89 3.27 45.74 2.94
3560 5049 6.070194 TCCTCCACCTAAACAATTCTTAGGAG 60.070 42.308 21.89 16.29 45.74 3.69
3641 5130 3.415087 AGGGCTGGCCTCACATCC 61.415 66.667 18.27 0.00 36.10 3.51
3751 5240 3.560636 AATTAGAGGACCGGAACCATG 57.439 47.619 9.46 0.00 0.00 3.66
3752 5241 2.241281 TTAGAGGACCGGAACCATGA 57.759 50.000 9.46 0.00 0.00 3.07
3797 5286 5.009710 AGTTACTTGATCGTCTGAGTGTTGA 59.990 40.000 0.00 0.00 0.00 3.18
3940 5429 7.119407 CACATGCTCTCTATATTCCCTGAAATG 59.881 40.741 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
146 148 5.971881 AGTGGTTATGTTAGGGGTTATGGTA 59.028 40.000 0.00 0.00 0.00 3.25
183 185 2.757894 TGTTGGGTGGTTATGTTGGT 57.242 45.000 0.00 0.00 0.00 3.67
395 444 2.742204 GCTAGGGATTTCTTCGGTGGAC 60.742 54.545 0.00 0.00 0.00 4.02
404 453 4.530875 CACTCCATTTGCTAGGGATTTCT 58.469 43.478 0.00 0.00 0.00 2.52
413 462 3.648067 CCCTAGATCCACTCCATTTGCTA 59.352 47.826 0.00 0.00 0.00 3.49
516 577 2.840753 GGGAGGGCTGGTTTGTGGA 61.841 63.158 0.00 0.00 0.00 4.02
745 807 4.546570 CCAGTTCAGAAAAATTTCGGGAC 58.453 43.478 8.79 8.79 40.00 4.46
769 831 5.379706 AGGAAAGAAAATCGGGATCTGAT 57.620 39.130 0.00 0.00 0.00 2.90
792 854 9.634163 GAATTTCGTGTTTTGACCCTTTTATAT 57.366 29.630 0.00 0.00 0.00 0.86
793 855 7.804129 CGAATTTCGTGTTTTGACCCTTTTATA 59.196 33.333 10.61 0.00 34.72 0.98
794 856 6.639279 CGAATTTCGTGTTTTGACCCTTTTAT 59.361 34.615 10.61 0.00 34.72 1.40
795 857 5.972382 CGAATTTCGTGTTTTGACCCTTTTA 59.028 36.000 10.61 0.00 34.72 1.52
826 888 2.656947 TTTCAGAACTTGGGACTGGG 57.343 50.000 0.00 0.00 33.19 4.45
829 891 4.982241 TCAGATTTCAGAACTTGGGACT 57.018 40.909 0.00 0.00 0.00 3.85
833 895 5.399858 CAGCATTCAGATTTCAGAACTTGG 58.600 41.667 0.00 0.00 0.00 3.61
863 925 0.602638 TCGTCAGAGCAAAATGGCGT 60.603 50.000 0.00 0.00 44.50 5.68
877 948 1.067565 GCTGGATTGAGACACTCGTCA 60.068 52.381 0.00 0.00 45.23 4.35
888 959 0.387929 GACGTATCGGGCTGGATTGA 59.612 55.000 0.00 0.00 0.00 2.57
983 1054 3.583882 ATTGGTCTTGGCCGGGGTG 62.584 63.158 2.18 0.00 0.00 4.61
984 1055 3.264845 ATTGGTCTTGGCCGGGGT 61.265 61.111 2.18 0.00 0.00 4.95
985 1056 2.755469 CATTGGTCTTGGCCGGGG 60.755 66.667 2.18 0.00 0.00 5.73
986 1057 3.451894 GCATTGGTCTTGGCCGGG 61.452 66.667 2.18 0.00 0.00 5.73
987 1058 3.451894 GGCATTGGTCTTGGCCGG 61.452 66.667 0.00 0.00 36.58 6.13
989 1060 4.133796 GCGGCATTGGTCTTGGCC 62.134 66.667 0.00 0.00 42.98 5.36
990 1061 4.133796 GGCGGCATTGGTCTTGGC 62.134 66.667 3.07 0.00 36.38 4.52
1131 1205 1.450312 CTGGAGCTCCGCGGATTTT 60.450 57.895 31.19 17.23 39.43 1.82
1464 1538 0.809385 CGAGAAGCGTGGAGTAGGAA 59.191 55.000 0.00 0.00 34.64 3.36
2050 2128 1.274703 ATGAGCCCGAACAGGTGGAT 61.275 55.000 0.00 0.00 38.74 3.41
2064 2142 4.471726 GCGGTGCTGCACATGAGC 62.472 66.667 31.35 24.78 35.86 4.26
2565 3944 3.423154 CGGTGCCGCCTGTTCTTC 61.423 66.667 0.00 0.00 34.25 2.87
2670 4049 2.440539 TGTCGAACTCCTTGAGCTTC 57.559 50.000 0.00 0.00 32.04 3.86
2720 4099 2.357517 AGAACACGCAGCCTTCCG 60.358 61.111 0.00 0.00 0.00 4.30
2775 4154 1.589113 GTCGAAGTCCTGCTGAGCT 59.411 57.895 5.83 0.00 0.00 4.09
2883 4262 1.369625 CCTCGTCAAACCTGTATGCC 58.630 55.000 0.00 0.00 0.00 4.40
2968 4448 0.739112 GAGGAGGCACTGAAGCTTCG 60.739 60.000 21.11 17.22 41.55 3.79
2993 4473 0.034767 TCTGCAGCCTGAATTCTGGG 60.035 55.000 27.06 19.35 35.73 4.45
2999 4479 2.504585 TCAGAATCTCTGCAGCCTGAAT 59.495 45.455 9.47 0.00 43.95 2.57
3045 4525 7.004086 AGGAATGACACAAGACTGGATTTTAA 58.996 34.615 0.00 0.00 0.00 1.52
3046 4526 6.542821 AGGAATGACACAAGACTGGATTTTA 58.457 36.000 0.00 0.00 0.00 1.52
3095 4575 9.896645 CCATCTGATATTTACATGCCTAATACT 57.103 33.333 0.00 0.00 0.00 2.12
3145 4627 3.370672 GGATTTTACCAGCATTTTTGCCG 59.629 43.478 0.00 0.00 34.90 5.69
3237 4722 4.551702 TGTCAAGAGGCTGCATTAACTA 57.448 40.909 0.50 0.00 0.00 2.24
3268 4753 4.318332 TCTAATGCACAGTTCAAGGTCTG 58.682 43.478 0.00 0.00 37.65 3.51
3298 4783 8.359060 TGTTGTAAATTTGTTTGTTGATAGCC 57.641 30.769 0.00 0.00 0.00 3.93
3496 4982 3.558321 GCCACGCCATATGTCCCTTATTA 60.558 47.826 1.24 0.00 0.00 0.98
3497 4983 2.814097 GCCACGCCATATGTCCCTTATT 60.814 50.000 1.24 0.00 0.00 1.40
3498 4984 1.271379 GCCACGCCATATGTCCCTTAT 60.271 52.381 1.24 0.00 0.00 1.73
3540 5029 4.640647 GGCCTCCTAAGAATTGTTTAGGTG 59.359 45.833 18.26 16.41 44.85 4.00
3558 5047 0.103937 CCTCGAACTGATCAGGCCTC 59.896 60.000 26.08 17.18 0.00 4.70
3559 5048 1.333636 CCCTCGAACTGATCAGGCCT 61.334 60.000 26.08 0.00 0.00 5.19
3560 5049 1.144936 CCCTCGAACTGATCAGGCC 59.855 63.158 26.08 15.58 0.00 5.19
3766 5255 8.470805 ACTCAGACGATCAAGTAACTGATAATT 58.529 33.333 0.00 0.00 36.15 1.40
3797 5286 2.665165 TGTGTTCCATTTTCAGCTGGT 58.335 42.857 15.13 0.00 34.03 4.00
3926 5415 4.141018 GGGGTGTACCATTTCAGGGAATAT 60.141 45.833 3.11 0.00 42.91 1.28
3940 5429 0.320697 GATATCAGCGGGGGTGTACC 59.679 60.000 0.00 0.00 39.11 3.34


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

AutoCloner maintained by Alex Coulton.