Multiple sequence alignment - TraesCS2B01G234400

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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 TraesCS2B01G234400 chr2B 100.000 3445 0 0 1 3445 233264761 233268205 0.000000e+00 6362.0
1 TraesCS2B01G234400 chr2D 95.736 2017 32 15 704 2714 176160567 176162535 0.000000e+00 3199.0
2 TraesCS2B01G234400 chr2D 94.573 737 26 8 2712 3445 176162597 176163322 0.000000e+00 1127.0
3 TraesCS2B01G234400 chr2D 92.331 665 22 17 2 647 176159797 176160451 0.000000e+00 918.0
4 TraesCS2B01G234400 chr2D 87.500 72 4 3 640 706 176160478 176160549 1.030000e-10 78.7
5 TraesCS2B01G234400 chr2A 93.759 2019 62 23 704 2714 187949885 187951847 0.000000e+00 2972.0
6 TraesCS2B01G234400 chr2A 89.417 737 33 20 2720 3445 187951918 187952620 0.000000e+00 887.0
7 TraesCS2B01G234400 chr2A 86.709 158 7 4 381 534 187948204 187948351 2.750000e-36 163.0
8 TraesCS2B01G234400 chr2A 91.176 102 4 1 525 626 187949595 187949691 2.160000e-27 134.0
9 TraesCS2B01G234400 chr2A 83.444 151 8 4 245 381 187939473 187939620 1.300000e-24 124.0
10 TraesCS2B01G234400 chr7D 87.000 600 49 15 2846 3439 581036187 581035611 0.000000e+00 649.0
11 TraesCS2B01G234400 chr3D 85.216 487 32 18 2846 3315 604597854 604598317 6.730000e-127 464.0
12 TraesCS2B01G234400 chr1B 75.988 329 51 16 1356 1663 183876875 183876554 9.960000e-31 145.0
13 TraesCS2B01G234400 chr4B 75.460 326 52 17 1356 1660 474483022 474483340 2.160000e-27 134.0
14 TraesCS2B01G234400 chr3B 76.562 128 17 8 1546 1660 416130270 416130397 1.340000e-04 58.4


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 TraesCS2B01G234400 chr2B 233264761 233268205 3444 False 6362.000 6362 100.00000 1 3445 1 chr2B.!!$F1 3444
1 TraesCS2B01G234400 chr2D 176159797 176163322 3525 False 1330.675 3199 92.53500 2 3445 4 chr2D.!!$F1 3443
2 TraesCS2B01G234400 chr2A 187948204 187952620 4416 False 1039.000 2972 90.26525 381 3445 4 chr2A.!!$F2 3064
3 TraesCS2B01G234400 chr7D 581035611 581036187 576 True 649.000 649 87.00000 2846 3439 1 chr7D.!!$R1 593

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
940 2343 0.334676 CCACCCACCTCTCTCTCTCT 59.665 60.0 0.00 0.00 0.0 3.10 F
2239 3647 0.324368 AGAGTCATGGCCGTGGTAGA 60.324 55.0 24.78 2.16 0.0 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2243 3651 0.107066 AACAGCCCATGCGATCATCA 60.107 50.0 0.0 0.0 44.33 3.07 R
3126 4615 2.472695 TCACATTTTGAGGACTCGGG 57.527 50.0 0.0 0.0 0.00 5.14 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
53 54 5.124457 AGTTGAATCGGTCATGGAAAATGAG 59.876 40.000 0.00 0.00 35.70 2.90
62 63 0.602562 TGGAAAATGAGCCAAAGCCG 59.397 50.000 0.00 0.00 41.25 5.52
76 77 1.082117 AAGCCGTACGCGAATTGGAG 61.082 55.000 15.93 0.00 44.76 3.86
218 229 6.127758 CCACATCGTTTCTGATTCCCAATAAA 60.128 38.462 0.00 0.00 0.00 1.40
261 272 2.508526 GCAGAAGGCAGAAGGAAAGAA 58.491 47.619 0.00 0.00 43.97 2.52
346 359 2.356793 GCTGTCTGTGCTCGTGCT 60.357 61.111 11.19 0.00 40.48 4.40
410 423 2.203365 ATCGAGCGACGGGATCCT 60.203 61.111 12.58 0.00 42.82 3.24
476 489 1.843368 ACTACTAGTACTGCCGGCAA 58.157 50.000 32.09 14.75 0.00 4.52
541 1816 1.076923 GGAGTCCTAGGCCTGTCGA 60.077 63.158 17.99 4.65 0.00 4.20
598 1873 7.010160 GGAATGTCCCTGGGATCAATAATTTA 58.990 38.462 20.40 0.00 32.73 1.40
599 1874 7.508977 GGAATGTCCCTGGGATCAATAATTTAA 59.491 37.037 20.40 0.00 32.73 1.52
600 1875 9.093458 GAATGTCCCTGGGATCAATAATTTAAT 57.907 33.333 20.40 0.00 32.73 1.40
601 1876 9.451206 AATGTCCCTGGGATCAATAATTTAATT 57.549 29.630 20.40 4.37 32.73 1.40
602 1877 8.852671 TGTCCCTGGGATCAATAATTTAATTT 57.147 30.769 20.40 0.00 32.73 1.82
628 1915 3.650298 TACCGGGTCTGGGTCTCCG 62.650 68.421 6.32 0.00 38.99 4.63
647 1934 2.167281 CCGCTCTTGGATCATCCGATAT 59.833 50.000 0.00 0.00 40.17 1.63
651 1938 5.347342 GCTCTTGGATCATCCGATATACAG 58.653 45.833 0.00 0.00 40.17 2.74
653 1940 5.019470 TCTTGGATCATCCGATATACAGCT 58.981 41.667 0.00 0.00 40.17 4.24
654 1941 4.991153 TGGATCATCCGATATACAGCTC 57.009 45.455 0.00 0.00 40.17 4.09
696 2021 6.874664 ACGATAGAGGAGTTTCTTTCCTTTTC 59.125 38.462 0.00 0.00 45.00 2.29
697 2022 7.100409 CGATAGAGGAGTTTCTTTCCTTTTCT 58.900 38.462 0.00 0.00 45.00 2.52
698 2023 7.276878 CGATAGAGGAGTTTCTTTCCTTTTCTC 59.723 40.741 0.00 0.00 45.00 2.87
701 2026 3.502595 GGAGTTTCTTTCCTTTTCTCCCG 59.497 47.826 0.00 0.00 35.39 5.14
702 2027 2.885266 AGTTTCTTTCCTTTTCTCCCGC 59.115 45.455 0.00 0.00 0.00 6.13
937 2340 2.363172 GCCCACCCACCTCTCTCTC 61.363 68.421 0.00 0.00 0.00 3.20
938 2341 1.390125 CCCACCCACCTCTCTCTCT 59.610 63.158 0.00 0.00 0.00 3.10
939 2342 0.686112 CCCACCCACCTCTCTCTCTC 60.686 65.000 0.00 0.00 0.00 3.20
940 2343 0.334676 CCACCCACCTCTCTCTCTCT 59.665 60.000 0.00 0.00 0.00 3.10
941 2344 1.684869 CCACCCACCTCTCTCTCTCTC 60.685 61.905 0.00 0.00 0.00 3.20
942 2345 1.284785 CACCCACCTCTCTCTCTCTCT 59.715 57.143 0.00 0.00 0.00 3.10
943 2346 1.564348 ACCCACCTCTCTCTCTCTCTC 59.436 57.143 0.00 0.00 0.00 3.20
944 2347 1.846439 CCCACCTCTCTCTCTCTCTCT 59.154 57.143 0.00 0.00 0.00 3.10
945 2348 2.158755 CCCACCTCTCTCTCTCTCTCTC 60.159 59.091 0.00 0.00 0.00 3.20
946 2349 2.774234 CCACCTCTCTCTCTCTCTCTCT 59.226 54.545 0.00 0.00 0.00 3.10
1956 3364 2.433664 CCGGTGTTCTACGTGCCC 60.434 66.667 0.00 0.00 0.00 5.36
1989 3397 1.895020 ATTACCTCAACGCGGCTGGA 61.895 55.000 12.47 0.61 0.00 3.86
2072 3480 2.224090 CGGGAGATCTCTACTCGTCTGA 60.224 54.545 21.81 0.00 35.49 3.27
2224 3632 2.960688 GCGCAAGGGGAGGAAGAGT 61.961 63.158 0.30 0.00 38.28 3.24
2233 3641 1.617947 GGAGGAAGAGTCATGGCCGT 61.618 60.000 0.00 0.00 0.00 5.68
2234 3642 0.460987 GAGGAAGAGTCATGGCCGTG 60.461 60.000 19.62 19.62 0.00 4.94
2235 3643 1.450312 GGAAGAGTCATGGCCGTGG 60.450 63.158 24.78 6.59 0.00 4.94
2236 3644 1.296715 GAAGAGTCATGGCCGTGGT 59.703 57.895 24.78 12.61 0.00 4.16
2237 3645 0.535335 GAAGAGTCATGGCCGTGGTA 59.465 55.000 24.78 3.39 0.00 3.25
2238 3646 0.537188 AAGAGTCATGGCCGTGGTAG 59.463 55.000 24.78 0.00 0.00 3.18
2239 3647 0.324368 AGAGTCATGGCCGTGGTAGA 60.324 55.000 24.78 2.16 0.00 2.59
2240 3648 0.753262 GAGTCATGGCCGTGGTAGAT 59.247 55.000 24.78 6.56 0.00 1.98
2241 3649 1.139058 GAGTCATGGCCGTGGTAGATT 59.861 52.381 24.78 1.88 0.00 2.40
2242 3650 1.139058 AGTCATGGCCGTGGTAGATTC 59.861 52.381 24.78 7.08 0.00 2.52
2243 3651 1.139058 GTCATGGCCGTGGTAGATTCT 59.861 52.381 24.78 0.00 0.00 2.40
2244 3652 1.138859 TCATGGCCGTGGTAGATTCTG 59.861 52.381 24.78 0.00 0.00 3.02
2245 3653 1.138859 CATGGCCGTGGTAGATTCTGA 59.861 52.381 17.90 0.00 0.00 3.27
2246 3654 1.496060 TGGCCGTGGTAGATTCTGAT 58.504 50.000 0.00 0.00 0.00 2.90
2247 3655 1.138859 TGGCCGTGGTAGATTCTGATG 59.861 52.381 0.00 0.00 0.00 3.07
2248 3656 1.412710 GGCCGTGGTAGATTCTGATGA 59.587 52.381 0.00 0.00 0.00 2.92
2249 3657 2.037772 GGCCGTGGTAGATTCTGATGAT 59.962 50.000 0.00 0.00 0.00 2.45
2250 3658 3.321497 GCCGTGGTAGATTCTGATGATC 58.679 50.000 0.00 0.00 0.00 2.92
2251 3659 3.569548 CCGTGGTAGATTCTGATGATCG 58.430 50.000 0.00 0.00 0.00 3.69
2267 3675 1.913951 ATCGCATGGGCTGTTCCTGA 61.914 55.000 4.59 0.00 38.10 3.86
2276 3684 0.321298 GCTGTTCCTGAAGCCGGTTA 60.321 55.000 1.90 0.00 33.12 2.85
2297 3705 8.873830 CGGTTAATTCTGATGATCGCTTATATT 58.126 33.333 0.00 0.00 0.00 1.28
2714 4132 7.495901 TGTTCTTGTATGCCAGAAATTTTGAA 58.504 30.769 0.00 0.00 0.00 2.69
2715 4133 7.437862 TGTTCTTGTATGCCAGAAATTTTGAAC 59.562 33.333 0.00 0.00 0.00 3.18
2716 4134 7.048629 TCTTGTATGCCAGAAATTTTGAACA 57.951 32.000 0.00 0.00 0.00 3.18
2717 4135 7.147312 TCTTGTATGCCAGAAATTTTGAACAG 58.853 34.615 0.00 0.00 0.00 3.16
2718 4136 5.782047 TGTATGCCAGAAATTTTGAACAGG 58.218 37.500 0.00 0.00 0.00 4.00
2889 4373 6.484643 TCAAGAGGAAAGTGTCATTTCTGAAG 59.515 38.462 0.00 0.00 38.86 3.02
2901 4385 7.222611 GTGTCATTTCTGAAGAGAGAAGCTATC 59.777 40.741 0.00 0.00 33.50 2.08
2925 4409 8.497910 TCCCAAATATACTTGAGAGAATAGCT 57.502 34.615 0.00 0.00 0.00 3.32
2981 4465 0.391661 TCGACTCTGCATTGCCCTTC 60.392 55.000 6.12 0.00 0.00 3.46
2990 4474 2.433604 TGCATTGCCCTTCTGAAACAAA 59.566 40.909 6.12 0.00 0.00 2.83
2991 4475 3.071312 TGCATTGCCCTTCTGAAACAAAT 59.929 39.130 6.12 0.00 0.00 2.32
2992 4476 3.434299 GCATTGCCCTTCTGAAACAAATG 59.566 43.478 0.00 7.10 0.00 2.32
2993 4477 2.818130 TGCCCTTCTGAAACAAATGC 57.182 45.000 0.00 0.00 0.00 3.56
2994 4478 2.318908 TGCCCTTCTGAAACAAATGCT 58.681 42.857 0.00 0.00 0.00 3.79
2995 4479 2.036217 TGCCCTTCTGAAACAAATGCTG 59.964 45.455 0.00 0.00 0.00 4.41
2996 4480 2.680577 CCCTTCTGAAACAAATGCTGC 58.319 47.619 0.00 0.00 0.00 5.25
2997 4481 2.036217 CCCTTCTGAAACAAATGCTGCA 59.964 45.455 4.13 4.13 0.00 4.41
2998 4482 3.314553 CCTTCTGAAACAAATGCTGCAG 58.685 45.455 10.11 10.11 0.00 4.41
2999 4483 2.427232 TCTGAAACAAATGCTGCAGC 57.573 45.000 31.89 31.89 42.50 5.25
3019 4503 2.680221 GCCTGCAGATATGCCATCCTAG 60.680 54.545 17.39 0.00 0.00 3.02
3020 4504 2.836372 CCTGCAGATATGCCATCCTAGA 59.164 50.000 17.39 0.00 0.00 2.43
3126 4615 4.987285 TCGTCTACATCGTAGTACCAGATC 59.013 45.833 1.36 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.114627 ACAGATCCATCGCAGCTACA 58.885 50.000 0.00 0.00 0.00 2.74
53 54 2.248274 AATTCGCGTACGGCTTTGGC 62.248 55.000 18.39 0.00 40.44 4.52
94 95 2.046411 ATTGCGCATCCACGTCCA 60.046 55.556 12.75 0.00 34.88 4.02
137 148 3.485431 CAACTGCTGCGCTCGGAG 61.485 66.667 9.73 13.00 36.62 4.63
163 174 2.124942 TCTTGGCACACACGCACA 60.125 55.556 0.00 0.00 39.29 4.57
346 359 2.314647 CGGCGAAAAAGCTGGACGA 61.315 57.895 0.00 0.00 39.71 4.20
410 423 8.740123 TGCTAAAATATTCCCGAATAAAGTCA 57.260 30.769 1.44 0.00 36.90 3.41
476 489 0.465705 ATCTCGACATGGACGCCAAT 59.534 50.000 9.17 0.00 36.95 3.16
541 1816 0.621571 TGCACAGAGCCCTAGGGAAT 60.622 55.000 33.21 19.10 44.83 3.01
628 1915 5.330455 TGTATATCGGATGATCCAAGAGC 57.670 43.478 12.67 0.00 35.91 4.09
647 1934 3.117963 GGAGACCAGTAGTAGGAGCTGTA 60.118 52.174 0.00 0.00 0.00 2.74
651 1938 2.427812 GTTGGAGACCAGTAGTAGGAGC 59.572 54.545 0.00 0.00 33.81 4.70
653 1940 2.306805 TCGTTGGAGACCAGTAGTAGGA 59.693 50.000 0.00 0.00 33.81 2.94
654 1941 2.719739 TCGTTGGAGACCAGTAGTAGG 58.280 52.381 0.00 0.00 33.81 3.18
718 2109 9.628500 AAATCTCTACTTACAACTTTCCTTTGT 57.372 29.630 0.00 0.00 40.34 2.83
937 2340 1.942657 CTTGCGAGGAGAGAGAGAGAG 59.057 57.143 0.00 0.00 0.00 3.20
938 2341 1.280710 ACTTGCGAGGAGAGAGAGAGA 59.719 52.381 5.79 0.00 0.00 3.10
939 2342 1.750193 ACTTGCGAGGAGAGAGAGAG 58.250 55.000 5.79 0.00 0.00 3.20
940 2343 1.815613 CAACTTGCGAGGAGAGAGAGA 59.184 52.381 5.79 0.00 0.00 3.10
941 2344 1.735369 GCAACTTGCGAGGAGAGAGAG 60.735 57.143 5.79 0.00 31.71 3.20
942 2345 0.244994 GCAACTTGCGAGGAGAGAGA 59.755 55.000 5.79 0.00 31.71 3.10
943 2346 2.748268 GCAACTTGCGAGGAGAGAG 58.252 57.895 5.79 0.00 31.71 3.20
944 2347 4.996976 GCAACTTGCGAGGAGAGA 57.003 55.556 5.79 0.00 31.71 3.10
1190 2598 4.468689 GAGGCGGGTGGTGGTAGC 62.469 72.222 0.00 0.00 0.00 3.58
1191 2599 3.782443 GGAGGCGGGTGGTGGTAG 61.782 72.222 0.00 0.00 0.00 3.18
1192 2600 4.326227 AGGAGGCGGGTGGTGGTA 62.326 66.667 0.00 0.00 0.00 3.25
1956 3364 4.823419 TAATGGACCGGGCGCACG 62.823 66.667 28.36 28.36 0.00 5.34
1971 3379 2.047655 CCAGCCGCGTTGAGGTAA 60.048 61.111 4.92 0.00 0.00 2.85
2224 3632 1.138859 CAGAATCTACCACGGCCATGA 59.861 52.381 0.00 0.00 0.00 3.07
2233 3641 4.562143 CCATGCGATCATCAGAATCTACCA 60.562 45.833 0.00 0.00 0.00 3.25
2234 3642 3.931468 CCATGCGATCATCAGAATCTACC 59.069 47.826 0.00 0.00 0.00 3.18
2235 3643 3.931468 CCCATGCGATCATCAGAATCTAC 59.069 47.826 0.00 0.00 0.00 2.59
2236 3644 3.618263 GCCCATGCGATCATCAGAATCTA 60.618 47.826 0.00 0.00 0.00 1.98
2237 3645 2.874861 GCCCATGCGATCATCAGAATCT 60.875 50.000 0.00 0.00 0.00 2.40
2238 3646 1.467734 GCCCATGCGATCATCAGAATC 59.532 52.381 0.00 0.00 0.00 2.52
2239 3647 1.073444 AGCCCATGCGATCATCAGAAT 59.927 47.619 0.00 0.00 44.33 2.40
2240 3648 0.471191 AGCCCATGCGATCATCAGAA 59.529 50.000 0.00 0.00 44.33 3.02
2241 3649 0.250166 CAGCCCATGCGATCATCAGA 60.250 55.000 0.00 0.00 44.33 3.27
2242 3650 0.534427 ACAGCCCATGCGATCATCAG 60.534 55.000 0.00 0.00 44.33 2.90
2243 3651 0.107066 AACAGCCCATGCGATCATCA 60.107 50.000 0.00 0.00 44.33 3.07
2244 3652 0.590195 GAACAGCCCATGCGATCATC 59.410 55.000 0.00 0.00 44.33 2.92
2245 3653 0.820891 GGAACAGCCCATGCGATCAT 60.821 55.000 0.00 0.00 44.33 2.45
2246 3654 1.451927 GGAACAGCCCATGCGATCA 60.452 57.895 0.00 0.00 44.33 2.92
2247 3655 1.153086 AGGAACAGCCCATGCGATC 60.153 57.895 0.00 0.00 44.33 3.69
2248 3656 1.452651 CAGGAACAGCCCATGCGAT 60.453 57.895 0.00 0.00 44.33 4.58
2249 3657 2.046023 CAGGAACAGCCCATGCGA 60.046 61.111 0.00 0.00 44.33 5.10
2250 3658 1.651240 CTTCAGGAACAGCCCATGCG 61.651 60.000 0.00 0.00 44.33 4.73
2251 3659 1.941999 GCTTCAGGAACAGCCCATGC 61.942 60.000 0.00 0.00 37.37 4.06
2267 3675 3.809832 CGATCATCAGAATTAACCGGCTT 59.190 43.478 0.00 0.00 0.00 4.35
2271 3679 6.712241 ATAAGCGATCATCAGAATTAACCG 57.288 37.500 0.00 0.00 0.00 4.44
2276 3684 8.449397 GCTCAAATATAAGCGATCATCAGAATT 58.551 33.333 0.00 0.00 0.00 2.17
2297 3705 4.931002 GGCAATGCAAAAATCTTAGCTCAA 59.069 37.500 7.79 0.00 0.00 3.02
2715 4133 7.970671 ACATGTTAATGCCAGGAAAAGACCTG 61.971 42.308 7.65 7.65 44.75 4.00
2716 4134 4.112634 TGTTAATGCCAGGAAAAGACCT 57.887 40.909 0.00 0.00 41.43 3.85
2717 4135 4.220602 ACATGTTAATGCCAGGAAAAGACC 59.779 41.667 0.00 0.00 37.29 3.85
2718 4136 5.391312 ACATGTTAATGCCAGGAAAAGAC 57.609 39.130 0.00 0.00 37.29 3.01
2765 4248 9.480861 AATAAGTAGAGAATCATCCGGATATGA 57.519 33.333 18.63 13.93 40.07 2.15
2798 4281 2.002586 CGAAGATCGAAGCCAACATGT 58.997 47.619 0.00 0.00 43.74 3.21
2889 4373 8.589338 TCAAGTATATTTGGGATAGCTTCTCTC 58.411 37.037 7.99 0.00 0.00 3.20
2901 4385 9.213799 GAAGCTATTCTCTCAAGTATATTTGGG 57.786 37.037 7.99 4.90 32.33 4.12
2925 4409 5.016831 TGATACAAGCCACTGTCTCTAGAA 58.983 41.667 0.00 0.00 0.00 2.10
2981 4465 1.000506 AGGCTGCAGCATTTGTTTCAG 59.999 47.619 37.63 0.00 44.36 3.02
3126 4615 2.472695 TCACATTTTGAGGACTCGGG 57.527 50.000 0.00 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.