Multiple sequence alignment - TraesCS2D01G408300

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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 TraesCS2D01G408300 chr2D 100.000 4147 0 0 1 4147 523159871 523164017 0.000000e+00 7659.0
1 TraesCS2D01G408300 chr2D 82.044 1331 188 32 1886 3179 523359100 523357784 0.000000e+00 1086.0
2 TraesCS2D01G408300 chr2D 79.942 688 117 18 42 716 399395059 399394380 1.730000e-133 486.0
3 TraesCS2D01G408300 chr2D 77.647 340 64 11 2083 2418 523309904 523309573 3.270000e-46 196.0
4 TraesCS2D01G408300 chr2A 96.046 2858 54 22 878 3714 668532112 668529293 0.000000e+00 4597.0
5 TraesCS2D01G408300 chr2A 90.000 850 50 15 3 840 416909672 416910498 0.000000e+00 1066.0
6 TraesCS2D01G408300 chr2A 81.306 1332 197 32 1886 3179 668922504 668923821 0.000000e+00 1033.0
7 TraesCS2D01G408300 chr2A 81.278 1330 201 30 1886 3179 669109986 669108669 0.000000e+00 1033.0
8 TraesCS2D01G408300 chr2A 93.317 419 7 4 3730 4147 668529311 668528913 2.130000e-167 599.0
9 TraesCS2D01G408300 chr2A 87.124 466 45 10 42 503 164607598 164607144 7.950000e-142 514.0
10 TraesCS2D01G408300 chr2A 83.883 273 31 5 612 873 164607099 164606829 8.900000e-62 248.0
11 TraesCS2D01G408300 chr2A 77.581 339 66 9 2083 2418 668926840 668927171 3.270000e-46 196.0
12 TraesCS2D01G408300 chr2A 77.246 334 66 9 2088 2418 669105585 669105259 1.970000e-43 187.0
13 TraesCS2D01G408300 chr2A 78.986 138 23 4 2470 2603 767788998 767788863 5.710000e-14 89.8
14 TraesCS2D01G408300 chr2B 94.203 2812 113 19 918 3714 617140753 617143529 0.000000e+00 4244.0
15 TraesCS2D01G408300 chr2B 94.272 419 13 4 3730 4147 617143511 617143919 7.570000e-177 630.0
16 TraesCS2D01G408300 chr2B 87.020 547 59 8 42 581 195596998 195596457 1.270000e-169 606.0
17 TraesCS2D01G408300 chr2B 81.590 478 73 10 42 510 682260652 682261123 8.410000e-102 381.0
18 TraesCS2D01G408300 chr2B 80.859 512 69 17 74 580 473357768 473357281 3.910000e-100 375.0
19 TraesCS2D01G408300 chr2B 77.286 339 67 9 2083 2418 617528170 617527839 1.520000e-44 191.0
20 TraesCS2D01G408300 chr2B 78.986 138 23 4 2470 2603 799251511 799251376 5.710000e-14 89.8
21 TraesCS2D01G408300 chr2B 93.878 49 2 1 873 920 617140686 617140734 5.750000e-09 73.1
22 TraesCS2D01G408300 chr5D 96.571 875 13 2 1 874 20981130 20981988 0.000000e+00 1434.0
23 TraesCS2D01G408300 chr3D 95.086 875 15 12 1 874 380976770 380977617 0.000000e+00 1352.0
24 TraesCS2D01G408300 chr3D 83.761 234 25 4 612 835 23743402 23743632 4.200000e-50 209.0
25 TraesCS2D01G408300 chr3A 92.177 882 53 9 1 878 747038045 747038914 0.000000e+00 1232.0
26 TraesCS2D01G408300 chr3A 82.627 236 22 12 612 835 32998891 32999119 1.520000e-44 191.0
27 TraesCS2D01G408300 chr6B 80.604 861 94 37 2 842 644773597 644774404 7.670000e-167 597.0
28 TraesCS2D01G408300 chr6B 87.912 91 10 1 782 872 189215281 189215192 5.670000e-19 106.0
29 TraesCS2D01G408300 chr7B 93.220 177 11 1 698 874 123655138 123655313 4.110000e-65 259.0
30 TraesCS2D01G408300 chr7B 91.057 123 6 4 443 560 123654731 123654853 1.190000e-35 161.0
31 TraesCS2D01G408300 chrUn 88.750 80 7 2 2465 2544 31552466 31552543 3.410000e-16 97.1
32 TraesCS2D01G408300 chrUn 78.986 138 23 4 2470 2603 31527550 31527415 5.710000e-14 89.8


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 TraesCS2D01G408300 chr2D 523159871 523164017 4146 False 7659.000000 7659 100.000000 1 4147 1 chr2D.!!$F1 4146
1 TraesCS2D01G408300 chr2D 523357784 523359100 1316 True 1086.000000 1086 82.044000 1886 3179 1 chr2D.!!$R3 1293
2 TraesCS2D01G408300 chr2D 399394380 399395059 679 True 486.000000 486 79.942000 42 716 1 chr2D.!!$R1 674
3 TraesCS2D01G408300 chr2A 668528913 668532112 3199 True 2598.000000 4597 94.681500 878 4147 2 chr2A.!!$R3 3269
4 TraesCS2D01G408300 chr2A 416909672 416910498 826 False 1066.000000 1066 90.000000 3 840 1 chr2A.!!$F1 837
5 TraesCS2D01G408300 chr2A 668922504 668927171 4667 False 614.500000 1033 79.443500 1886 3179 2 chr2A.!!$F2 1293
6 TraesCS2D01G408300 chr2A 669105259 669109986 4727 True 610.000000 1033 79.262000 1886 3179 2 chr2A.!!$R4 1293
7 TraesCS2D01G408300 chr2A 164606829 164607598 769 True 381.000000 514 85.503500 42 873 2 chr2A.!!$R2 831
8 TraesCS2D01G408300 chr2B 617140686 617143919 3233 False 1649.033333 4244 94.117667 873 4147 3 chr2B.!!$F2 3274
9 TraesCS2D01G408300 chr2B 195596457 195596998 541 True 606.000000 606 87.020000 42 581 1 chr2B.!!$R1 539
10 TraesCS2D01G408300 chr5D 20981130 20981988 858 False 1434.000000 1434 96.571000 1 874 1 chr5D.!!$F1 873
11 TraesCS2D01G408300 chr3D 380976770 380977617 847 False 1352.000000 1352 95.086000 1 874 1 chr3D.!!$F2 873
12 TraesCS2D01G408300 chr3A 747038045 747038914 869 False 1232.000000 1232 92.177000 1 878 1 chr3A.!!$F2 877
13 TraesCS2D01G408300 chr6B 644773597 644774404 807 False 597.000000 597 80.604000 2 842 1 chr6B.!!$F1 840
14 TraesCS2D01G408300 chr7B 123654731 123655313 582 False 210.000000 259 92.138500 443 874 2 chr7B.!!$F1 431

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
971 1189 1.497722 GCGGCGGAAAGACAAAGAG 59.502 57.895 9.78 0.0 0.00 2.85 F
1149 1367 0.734889 CGGCATTGATTTCCGCTTCT 59.265 50.000 0.00 0.0 36.53 2.85 F
1214 1432 0.904649 AACATGCTGTCGGAGATCCA 59.095 50.000 0.00 0.0 40.67 3.41 F
1235 1462 1.024579 CACGAGGGGACAAAATCGGG 61.025 60.000 0.00 0.0 39.42 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2227 2480 0.535335 ATCACGCCGTACACTTCCAT 59.465 50.000 0.0 0.0 0.00 3.41 R
2655 2916 0.727398 GTGCATAAGCCTCCGACAAC 59.273 55.000 0.0 0.0 41.13 3.32 R
3026 3287 6.359804 ACACACATCCTGAGTTATATTGCAT 58.640 36.000 0.0 0.0 0.00 3.96 R
3205 3467 9.180678 CAACACTGGAAATACAAAATACACTTC 57.819 33.333 0.0 0.0 0.00 3.01 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
98 99 1.795889 GCTTACCGCTCTCTCGTTGAG 60.796 57.143 2.61 2.61 43.96 3.02
143 144 3.589988 CTTTCTCATAGTCGGTTGCAGT 58.410 45.455 0.00 0.00 0.00 4.40
734 919 4.464597 GGAGGAGAGAGCTACAGAGAAAAA 59.535 45.833 0.00 0.00 0.00 1.94
914 1110 6.195600 AGACCGTCTCTTCCTCTATCTAAT 57.804 41.667 0.00 0.00 0.00 1.73
915 1111 6.235664 AGACCGTCTCTTCCTCTATCTAATC 58.764 44.000 0.00 0.00 0.00 1.75
916 1112 6.043938 AGACCGTCTCTTCCTCTATCTAATCT 59.956 42.308 0.00 0.00 0.00 2.40
971 1189 1.497722 GCGGCGGAAAGACAAAGAG 59.502 57.895 9.78 0.00 0.00 2.85
972 1190 1.497722 CGGCGGAAAGACAAAGAGC 59.502 57.895 0.00 0.00 0.00 4.09
973 1191 1.497722 GGCGGAAAGACAAAGAGCG 59.502 57.895 0.00 0.00 0.00 5.03
1149 1367 0.734889 CGGCATTGATTTCCGCTTCT 59.265 50.000 0.00 0.00 36.53 2.85
1214 1432 0.904649 AACATGCTGTCGGAGATCCA 59.095 50.000 0.00 0.00 40.67 3.41
1235 1462 1.024579 CACGAGGGGACAAAATCGGG 61.025 60.000 0.00 0.00 39.42 5.14
1260 1487 3.458163 TCGGCCACGGAGATGGTC 61.458 66.667 2.24 0.00 42.28 4.02
1302 1529 4.974368 ACTCAGTCGTATCTCCAAGAAG 57.026 45.455 0.00 0.00 0.00 2.85
1480 1707 1.606994 CGGAGAACATCGGTGTGGAAA 60.607 52.381 0.00 0.00 38.92 3.13
1526 1753 1.547675 GGGTGGATCAGCAACCAAGAA 60.548 52.381 1.46 0.00 37.94 2.52
1555 1782 5.337652 GGGCTGACCTACTATGAATATGGAC 60.338 48.000 0.00 0.00 35.85 4.02
1720 1950 1.341976 TGGATGAGGTGGATGAGACGA 60.342 52.381 0.00 0.00 0.00 4.20
1735 1965 3.930229 TGAGACGACACCAATAATTTCCG 59.070 43.478 0.00 0.00 0.00 4.30
1944 2174 7.182026 TGGGTATCGAATTGGTCCAGATTATAT 59.818 37.037 0.00 0.00 0.00 0.86
2039 2269 6.489700 TCTTCTTTCCAACTGCATGTATCAAA 59.510 34.615 0.00 0.00 0.00 2.69
2154 2407 1.978617 CACCCCATCTGCGGCTTTT 60.979 57.895 0.00 0.00 0.00 2.27
2261 2514 1.202188 CGTGATAGCTGCAAGAGACGA 60.202 52.381 1.02 0.00 34.07 4.20
2343 2596 7.391620 TCAATCAAGAGGTCCGTTTAGTATTT 58.608 34.615 0.00 0.00 0.00 1.40
2424 2679 9.382244 GAAATACACATCTTGTTAAGAACACAC 57.618 33.333 0.00 0.00 41.97 3.82
2572 2827 3.930634 AATCAAGCTCAAAGTGAAGGC 57.069 42.857 0.00 0.00 0.00 4.35
2655 2916 6.948886 AGTGTCATGTACTCTATATACCCCTG 59.051 42.308 0.00 0.00 30.19 4.45
3026 3287 2.852449 AGTATCCATCAAGGCCCAGAAA 59.148 45.455 0.00 0.00 37.29 2.52
3440 3735 3.393426 ACGGAGTTCCACCCTATTAGA 57.607 47.619 0.00 0.00 37.78 2.10
3456 3774 8.915036 ACCCTATTAGACTTGTAATGTACTCTG 58.085 37.037 0.00 0.00 0.00 3.35
3555 4380 3.370840 TTGTTCTGGGGAGGATGATTG 57.629 47.619 0.00 0.00 0.00 2.67
3590 4415 6.073276 TGTTATTGGCATATGCGATTACTCAC 60.073 38.462 21.04 12.76 43.26 3.51
3649 4976 3.242549 TGCAGTCAAGCTAGACATGAG 57.757 47.619 0.00 0.00 40.98 2.90
3703 5197 3.505836 GGAAAGAGTCCGTTAAGTACCG 58.494 50.000 0.00 0.00 36.40 4.02
3704 5198 3.191371 GGAAAGAGTCCGTTAAGTACCGA 59.809 47.826 0.00 0.00 36.40 4.69
3706 5200 3.064900 AGAGTCCGTTAAGTACCGAGT 57.935 47.619 0.00 0.00 0.00 4.18
3707 5201 3.416156 AGAGTCCGTTAAGTACCGAGTT 58.584 45.455 0.00 0.00 0.00 3.01
3708 5202 4.579869 AGAGTCCGTTAAGTACCGAGTTA 58.420 43.478 0.00 0.00 0.00 2.24
3710 5204 5.473504 AGAGTCCGTTAAGTACCGAGTTAAA 59.526 40.000 0.00 0.00 33.27 1.52
3713 5207 7.154656 AGTCCGTTAAGTACCGAGTTAAAATT 58.845 34.615 0.00 0.00 33.27 1.82
3714 5208 7.329471 AGTCCGTTAAGTACCGAGTTAAAATTC 59.671 37.037 0.00 0.00 33.27 2.17
3715 5209 6.589907 TCCGTTAAGTACCGAGTTAAAATTCC 59.410 38.462 0.00 0.00 33.27 3.01
3716 5210 6.183360 CCGTTAAGTACCGAGTTAAAATTCCC 60.183 42.308 0.00 0.00 33.27 3.97
3717 5211 6.183360 CGTTAAGTACCGAGTTAAAATTCCCC 60.183 42.308 0.00 0.00 33.27 4.81
3718 5212 4.226427 AGTACCGAGTTAAAATTCCCCC 57.774 45.455 0.00 0.00 0.00 5.40
3719 5213 2.118313 ACCGAGTTAAAATTCCCCCG 57.882 50.000 0.00 0.00 0.00 5.73
3720 5214 0.736636 CCGAGTTAAAATTCCCCCGC 59.263 55.000 0.00 0.00 0.00 6.13
3722 5216 1.813786 CGAGTTAAAATTCCCCCGCAA 59.186 47.619 0.00 0.00 0.00 4.85
3723 5217 2.229302 CGAGTTAAAATTCCCCCGCAAA 59.771 45.455 0.00 0.00 0.00 3.68
3725 5219 4.633175 GAGTTAAAATTCCCCCGCAAAAA 58.367 39.130 0.00 0.00 0.00 1.94
3809 5303 0.531200 CCGACAACAGGACCCTCTAC 59.469 60.000 0.00 0.00 0.00 2.59
3832 5326 5.840149 ACCCCGTACCTATTCATTATGTGTA 59.160 40.000 0.00 0.00 0.00 2.90
3946 5720 6.002704 ACTTGTTCTTTGCAGATGATTCTCT 58.997 36.000 0.00 0.00 0.00 3.10
3947 5721 6.489361 ACTTGTTCTTTGCAGATGATTCTCTT 59.511 34.615 0.00 0.00 0.00 2.85
3948 5722 7.663081 ACTTGTTCTTTGCAGATGATTCTCTTA 59.337 33.333 0.00 0.00 0.00 2.10
3949 5723 8.571461 TTGTTCTTTGCAGATGATTCTCTTAT 57.429 30.769 0.00 0.00 0.00 1.73
3950 5724 9.671279 TTGTTCTTTGCAGATGATTCTCTTATA 57.329 29.630 0.00 0.00 0.00 0.98
3951 5725 9.322773 TGTTCTTTGCAGATGATTCTCTTATAG 57.677 33.333 0.00 0.00 0.00 1.31
4093 6138 4.277593 TGCGGCAACAAAAGCGGG 62.278 61.111 0.00 0.00 33.50 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 0.530650 CGTGCGGCAATGATAGGAGT 60.531 55.000 3.23 0.00 0.00 3.85
143 144 4.320202 CCGGCGAAGAAAATCAGAGAAAAA 60.320 41.667 9.30 0.00 0.00 1.94
245 251 4.673298 ACATGCGACGGCGGTGAA 62.673 61.111 15.06 0.00 44.10 3.18
734 919 4.876107 CCCACGCACTGTATTTCTCTTATT 59.124 41.667 0.00 0.00 0.00 1.40
874 1070 0.690762 TCTTTGCTAGGGTTTCGGCT 59.309 50.000 0.00 0.00 0.00 5.52
916 1112 8.803235 GCCCTTCTTTCTTTTCCTTTAGATTTA 58.197 33.333 0.00 0.00 0.00 1.40
1149 1367 4.039004 CCCATCTCCAATTTTGTGTCAACA 59.961 41.667 0.00 0.00 0.00 3.33
1214 1432 0.673644 CGATTTTGTCCCCTCGTGCT 60.674 55.000 0.00 0.00 0.00 4.40
1235 1462 4.436998 CCGTGGCCGACTGAGTCC 62.437 72.222 7.07 0.00 35.63 3.85
1260 1487 1.049855 AGGAGCAGATCTCAGCCCTG 61.050 60.000 11.73 0.00 43.70 4.45
1302 1529 2.035442 GGCTTTCAGCTCCGTGACC 61.035 63.158 0.00 0.00 41.99 4.02
1480 1707 5.960811 TGTCTTCAGTCCTAATCTGAATCCT 59.039 40.000 8.46 0.00 46.30 3.24
1555 1782 2.489329 ACCCGTTGAAGATTGCATTCAG 59.511 45.455 10.98 0.00 37.91 3.02
1720 1950 7.442364 CAGAGTATCATCGGAAATTATTGGTGT 59.558 37.037 0.00 0.00 37.82 4.16
1735 1965 1.001860 GGCTGCCTCCAGAGTATCATC 59.998 57.143 12.43 0.00 41.77 2.92
1944 2174 2.160205 CTCGTCTCTGTGAAGGTACCA 58.840 52.381 15.94 0.00 0.00 3.25
2154 2407 0.681175 TCTGCAGAGTGCTAGCAACA 59.319 50.000 21.29 11.69 45.31 3.33
2227 2480 0.535335 ATCACGCCGTACACTTCCAT 59.465 50.000 0.00 0.00 0.00 3.41
2261 2514 2.435422 TGTTGCGATTGTGATCCACAT 58.565 42.857 0.27 0.00 44.16 3.21
2343 2596 9.462606 GACCAGGAAAGATAAAATAGGAAGAAA 57.537 33.333 0.00 0.00 0.00 2.52
2424 2679 1.667236 TAGTGGGCAATCGCTTGATG 58.333 50.000 2.58 0.00 38.60 3.07
2572 2827 5.523188 GCAATATCTTCAGACTCTGTTCCAG 59.477 44.000 5.94 0.00 32.61 3.86
2655 2916 0.727398 GTGCATAAGCCTCCGACAAC 59.273 55.000 0.00 0.00 41.13 3.32
3026 3287 6.359804 ACACACATCCTGAGTTATATTGCAT 58.640 36.000 0.00 0.00 0.00 3.96
3205 3467 9.180678 CAACACTGGAAATACAAAATACACTTC 57.819 33.333 0.00 0.00 0.00 3.01
3440 3735 8.848474 ATAAGTTTGCAGAGTACATTACAAGT 57.152 30.769 0.00 0.00 0.00 3.16
3456 3774 6.558909 CAAGAATCTTGGGAGATAAGTTTGC 58.441 40.000 14.85 0.00 41.78 3.68
3555 4380 3.574284 TGCCAATAACACATTGTCTGC 57.426 42.857 0.00 0.00 0.00 4.26
3590 4415 2.441001 ACCCTTTCTCCTATGCATCAGG 59.559 50.000 0.19 9.11 34.20 3.86
3649 4976 2.594592 ACCCGTCACAAGCCTTGC 60.595 61.111 3.88 0.00 0.00 4.01
3703 5197 3.945981 TTTGCGGGGGAATTTTAACTC 57.054 42.857 0.00 0.00 0.00 3.01
3704 5198 4.691326 TTTTTGCGGGGGAATTTTAACT 57.309 36.364 0.00 0.00 0.00 2.24
3729 5223 7.710475 CCCCGATTAATTTTAACTCGGTACTTA 59.290 37.037 20.11 0.00 39.45 2.24
3730 5224 6.539826 CCCCGATTAATTTTAACTCGGTACTT 59.460 38.462 20.11 0.00 39.45 2.24
3733 5227 4.815846 GCCCCGATTAATTTTAACTCGGTA 59.184 41.667 20.11 0.00 39.45 4.02
3735 5229 3.881089 AGCCCCGATTAATTTTAACTCGG 59.119 43.478 17.57 17.57 40.02 4.63
3736 5230 5.494632 AAGCCCCGATTAATTTTAACTCG 57.505 39.130 0.00 0.00 0.00 4.18
3809 5303 5.223449 ACACATAATGAATAGGTACGGGG 57.777 43.478 0.00 0.00 0.00 5.73
3832 5326 2.218603 ACATTCGGAAAACGCTTCAGT 58.781 42.857 0.00 0.00 43.86 3.41
4058 5838 3.000727 CGCACTTGTCCCCTTACTAAAG 58.999 50.000 0.00 0.00 0.00 1.85
4093 6138 5.918576 GCAATACCCAAACTAACAAGAACAC 59.081 40.000 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.