Multiple sequence alignment - TraesCS2B01G251200

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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 TraesCS2B01G251200 chr2B 100.000 3020 0 0 1 3020 262805710 262808729 0.000000e+00 5578.0
1 TraesCS2B01G251200 chr2B 86.199 855 106 7 2173 3020 262638589 262639438 0.000000e+00 915.0
2 TraesCS2B01G251200 chr2B 92.308 130 10 0 2042 2171 262638047 262638176 5.140000e-43 185.0
3 TraesCS2B01G251200 chr2D 94.474 2226 86 9 811 3020 207906414 207908618 0.000000e+00 3395.0
4 TraesCS2B01G251200 chr2D 88.263 835 62 21 1 817 207905288 207906104 0.000000e+00 966.0
5 TraesCS2B01G251200 chr2A 93.887 1325 70 8 1365 2678 260548483 260549807 0.000000e+00 1988.0
6 TraesCS2B01G251200 chr2A 91.499 1341 77 21 1 1327 260547164 260548481 0.000000e+00 1810.0
7 TraesCS2B01G251200 chr2A 76.364 385 50 25 1 374 649565748 649565394 5.180000e-38 169.0
8 TraesCS2B01G251200 chr5A 79.439 321 50 10 37 342 438360802 438360483 2.360000e-51 213.0
9 TraesCS2B01G251200 chr3D 76.674 433 71 25 21 434 296035016 296034595 2.360000e-51 213.0
10 TraesCS2B01G251200 chr7A 79.710 207 24 12 12 216 79336308 79336498 1.890000e-27 134.0
11 TraesCS2B01G251200 chr4D 81.579 152 24 4 21 171 107745378 107745526 4.090000e-24 122.0
12 TraesCS2B01G251200 chr5B 84.252 127 16 4 5 130 293150224 293150347 1.470000e-23 121.0
13 TraesCS2B01G251200 chr4A 77.604 192 37 6 310 500 173405879 173406065 8.850000e-21 111.0
14 TraesCS2B01G251200 chr3B 76.344 186 33 9 36 216 603845836 603846015 4.150000e-14 89.8
15 TraesCS2B01G251200 chr7B 80.180 111 16 5 339 447 706002759 706002653 8.980000e-11 78.7
16 TraesCS2B01G251200 chr6B 96.970 33 1 0 2768 2800 130340451 130340483 4.210000e-04 56.5


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 TraesCS2B01G251200 chr2B 262805710 262808729 3019 False 5578.0 5578 100.0000 1 3020 1 chr2B.!!$F1 3019
1 TraesCS2B01G251200 chr2B 262638047 262639438 1391 False 550.0 915 89.2535 2042 3020 2 chr2B.!!$F2 978
2 TraesCS2B01G251200 chr2D 207905288 207908618 3330 False 2180.5 3395 91.3685 1 3020 2 chr2D.!!$F1 3019
3 TraesCS2B01G251200 chr2A 260547164 260549807 2643 False 1899.0 1988 92.6930 1 2678 2 chr2A.!!$F1 2677

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
809 1146 1.47432 CGTTGTCAACCCAACCTCTCA 60.474 52.381 10.12 0.0 41.3 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2442 3222 0.250338 GGTTGGAGTTCAGGCTTCGT 60.25 55.0 0.0 0.0 0.0 3.85 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
43 45 8.801715 TCTTTCAAATGCTTGAGTAACATTTC 57.198 30.769 0.00 0.00 42.48 2.17
502 518 7.304735 TCACACACATTGTATATTTTCTGCAC 58.695 34.615 0.00 0.00 35.67 4.57
519 535 7.922505 TTCTGCACACAATTTTTATACACAC 57.077 32.000 0.00 0.00 0.00 3.82
730 751 4.373116 GCCTTCCACCTCGCGTCA 62.373 66.667 5.77 0.00 0.00 4.35
756 777 3.817709 TGCCCTCACAAAAGAAAAAGG 57.182 42.857 0.00 0.00 0.00 3.11
809 1146 1.474320 CGTTGTCAACCCAACCTCTCA 60.474 52.381 10.12 0.00 41.30 3.27
984 1322 3.551496 CTTCTCCACGCCCTTGCCA 62.551 63.158 0.00 0.00 0.00 4.92
1129 1467 0.754217 CATCCCCTCCGTCTCCGTTA 60.754 60.000 0.00 0.00 0.00 3.18
1142 1480 1.114722 TCCGTTAACGACCACCACCT 61.115 55.000 28.79 0.00 43.02 4.00
1259 1597 3.660111 GGACGCGCACCTTGCTTT 61.660 61.111 5.73 0.00 42.25 3.51
1260 1598 2.427410 GACGCGCACCTTGCTTTG 60.427 61.111 5.73 0.00 42.25 2.77
1261 1599 3.879351 GACGCGCACCTTGCTTTGG 62.879 63.158 5.73 0.00 42.25 3.28
1308 1661 0.547712 ACACCACATGCCCCTCTAGT 60.548 55.000 0.00 0.00 0.00 2.57
1309 1662 1.273609 ACACCACATGCCCCTCTAGTA 60.274 52.381 0.00 0.00 0.00 1.82
1310 1663 1.414181 CACCACATGCCCCTCTAGTAG 59.586 57.143 0.00 0.00 0.00 2.57
1320 1673 0.671251 CCTCTAGTAGGGCTGCTTCG 59.329 60.000 0.00 0.00 42.32 3.79
1362 1715 2.515071 GGAGATGGAGCTGGCCGAT 61.515 63.158 0.00 0.00 0.00 4.18
1496 1849 2.970974 GAAGGCACGGCACTGAAGC 61.971 63.158 0.00 0.00 0.00 3.86
1557 1910 1.301716 GAGGAACAAGCTGCCGTCA 60.302 57.895 0.00 0.00 0.00 4.35
1596 1949 2.388232 GCGCTCGTCATCGGGTTTT 61.388 57.895 0.00 0.00 40.06 2.43
1690 2043 4.107051 GCACCATGTCGCTGGCAC 62.107 66.667 0.00 0.00 40.15 5.01
1794 2147 0.899720 ATTTCGACCTACCGCTGGAA 59.100 50.000 1.50 0.00 0.00 3.53
2004 2357 1.521450 GGTTCTCAGTGACGTCGGGA 61.521 60.000 11.62 7.23 0.00 5.14
2099 2464 2.907696 TCTGGTTTCCCGAATCTGGTAA 59.092 45.455 0.00 0.00 0.00 2.85
2346 3125 8.521176 AGATTGCATATCTTTTCATCAATAGGC 58.479 33.333 5.80 0.00 33.33 3.93
2347 3126 7.828508 TTGCATATCTTTTCATCAATAGGCT 57.171 32.000 0.00 0.00 33.74 4.58
2365 3144 9.330063 CAATAGGCTGAAGAAAATAGTACATGA 57.670 33.333 0.00 0.00 0.00 3.07
2431 3210 3.447944 GTGGGTAAAGGGAAACAACACAA 59.552 43.478 0.00 0.00 0.00 3.33
2441 3221 8.831715 AAGGGAAACAACACAATCAAATATTC 57.168 30.769 0.00 0.00 0.00 1.75
2442 3222 7.961351 AGGGAAACAACACAATCAAATATTCA 58.039 30.769 0.00 0.00 0.00 2.57
2498 3278 0.687354 GAGACACATGACACCCAGGT 59.313 55.000 0.00 0.00 40.92 4.00
2564 3354 3.481453 TCCACAACCGATTGAATCAACA 58.519 40.909 0.00 0.00 39.30 3.33
2610 3401 1.686355 AACGAATCAACAAGTGGGCA 58.314 45.000 0.00 0.00 0.00 5.36
2694 3485 4.864334 CCAGATGCCCACGCCCTC 62.864 72.222 0.00 0.00 0.00 4.30
2745 3536 2.094258 CGTCACCCAACATCTCGAAATG 59.906 50.000 0.00 0.00 0.00 2.32
2851 3642 2.197465 ACTGGATCTAGTGTTTCCCCC 58.803 52.381 11.42 0.00 0.00 5.40
2853 3644 1.201424 GGATCTAGTGTTTCCCCCGT 58.799 55.000 0.00 0.00 0.00 5.28
2870 3661 2.281484 TTGCTCGTTGAGGGGCAC 60.281 61.111 0.00 0.00 34.30 5.01
2910 3701 1.626825 CCTCCAAAAAGGGGACGACTA 59.373 52.381 0.00 0.00 42.25 2.59
2922 3715 0.882474 GACGACTAGCAGGTGTCACT 59.118 55.000 2.35 0.00 33.18 3.41
2943 3736 3.066190 GCCAGCATGAGCAAGCCA 61.066 61.111 0.00 0.00 45.49 4.75
2992 3785 0.323725 AGCAATCCCAAAGCCATCGT 60.324 50.000 0.00 0.00 0.00 3.73
3010 3803 3.293337 TCGTTTTAGGATCCGGAGATGA 58.707 45.455 11.34 2.65 30.90 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 8.807667 AGAAATGTTACTCAAGCATTTGAAAG 57.192 30.769 6.48 0.00 42.48 2.62
102 105 9.995003 AATGTTAACCAAGCATTTGAAAAGATA 57.005 25.926 2.48 0.00 36.36 1.98
201 205 7.555087 TGACCATTCAGAAAATGTTGAACTTT 58.445 30.769 0.00 0.00 36.26 2.66
466 480 8.801715 ATACAATGTGTGTGAGAAAATTTGAC 57.198 30.769 0.00 0.00 41.89 3.18
476 490 7.482743 GTGCAGAAAATATACAATGTGTGTGAG 59.517 37.037 0.00 0.00 41.89 3.51
497 511 5.341993 CCGTGTGTATAAAAATTGTGTGCAG 59.658 40.000 0.00 0.00 0.00 4.41
502 518 6.913132 TGTTGACCGTGTGTATAAAAATTGTG 59.087 34.615 0.00 0.00 0.00 3.33
512 528 5.759506 TGAAAAATGTTGACCGTGTGTAT 57.240 34.783 0.00 0.00 0.00 2.29
519 535 6.197468 ACGTAATGTTTGAAAAATGTTGACCG 59.803 34.615 0.00 0.00 0.00 4.79
730 751 3.627395 TCTTTTGTGAGGGCATCGTAT 57.373 42.857 0.00 0.00 0.00 3.06
791 812 2.441375 TCATGAGAGGTTGGGTTGACAA 59.559 45.455 0.00 0.00 0.00 3.18
809 1146 1.228644 TGGCTGGCTTTGCTGTCAT 60.229 52.632 2.00 0.00 0.00 3.06
841 1178 2.431942 CAGTACCGTGGTCGTGCC 60.432 66.667 0.00 0.00 35.01 5.01
984 1322 0.108329 CCATGGTACCTCGCGTCTTT 60.108 55.000 14.36 0.00 0.00 2.52
1129 1467 3.168528 AGGCAGGTGGTGGTCGTT 61.169 61.111 0.00 0.00 0.00 3.85
1142 1480 3.094062 GCGGGAGAGTATGCAGGCA 62.094 63.158 0.00 0.00 0.00 4.75
1255 1593 1.143620 TTGCCAAGTGTGCCAAAGC 59.856 52.632 0.00 0.00 40.48 3.51
1256 1594 0.530431 GGTTGCCAAGTGTGCCAAAG 60.530 55.000 0.00 0.00 0.00 2.77
1257 1595 0.975040 AGGTTGCCAAGTGTGCCAAA 60.975 50.000 0.00 0.00 0.00 3.28
1258 1596 1.381056 AGGTTGCCAAGTGTGCCAA 60.381 52.632 0.00 0.00 0.00 4.52
1259 1597 1.827789 GAGGTTGCCAAGTGTGCCA 60.828 57.895 0.00 0.00 0.00 4.92
1260 1598 2.564721 GGAGGTTGCCAAGTGTGCC 61.565 63.158 0.00 0.00 0.00 5.01
1261 1599 1.518903 GAGGAGGTTGCCAAGTGTGC 61.519 60.000 0.00 0.00 0.00 4.57
1262 1600 1.230635 CGAGGAGGTTGCCAAGTGTG 61.231 60.000 0.00 0.00 0.00 3.82
1263 1601 1.071471 CGAGGAGGTTGCCAAGTGT 59.929 57.895 0.00 0.00 0.00 3.55
1264 1602 1.672356 CCGAGGAGGTTGCCAAGTG 60.672 63.158 0.00 0.00 34.51 3.16
1265 1603 2.750350 CCGAGGAGGTTGCCAAGT 59.250 61.111 0.00 0.00 34.51 3.16
1308 1661 2.427245 GCTCCTCGAAGCAGCCCTA 61.427 63.158 4.21 0.00 42.05 3.53
1309 1662 3.780173 GCTCCTCGAAGCAGCCCT 61.780 66.667 4.21 0.00 42.05 5.19
1310 1663 4.087892 TGCTCCTCGAAGCAGCCC 62.088 66.667 7.71 0.00 47.00 5.19
1362 1715 2.079158 AGGATGACGTCGAACTCGTTA 58.921 47.619 11.62 0.00 41.64 3.18
1794 2147 2.103373 TCTTCGCAGCCTAGAATGAGT 58.897 47.619 0.00 0.00 0.00 3.41
2004 2357 3.521995 CGCCTATGAATCTGCGGAT 57.478 52.632 0.90 0.90 43.08 4.18
2099 2464 5.751243 ACAAGAAACTGCGAGTACATTTT 57.249 34.783 0.00 0.00 0.00 1.82
2347 3126 9.554395 TGTTCACTTCATGTACTATTTTCTTCA 57.446 29.630 0.00 0.00 30.23 3.02
2365 3144 8.474025 CCTCTCTTCTCTATGTAATGTTCACTT 58.526 37.037 0.00 0.00 0.00 3.16
2431 3210 5.882557 AGTTCAGGCTTCGTGAATATTTGAT 59.117 36.000 5.43 0.00 39.75 2.57
2441 3221 0.868406 GTTGGAGTTCAGGCTTCGTG 59.132 55.000 0.00 0.00 0.00 4.35
2442 3222 0.250338 GGTTGGAGTTCAGGCTTCGT 60.250 55.000 0.00 0.00 0.00 3.85
2533 3316 2.436115 GTTGTGGAGCCGTAGCCC 60.436 66.667 0.00 0.00 41.25 5.19
2564 3354 1.270835 TAAGGTGGGGGAGGGGATAT 58.729 55.000 0.00 0.00 0.00 1.63
2596 3387 0.896940 CCTGCTGCCCACTTGTTGAT 60.897 55.000 0.00 0.00 0.00 2.57
2610 3401 1.826024 GACCGGATCATGTCCTGCT 59.174 57.895 9.46 0.00 45.46 4.24
2694 3485 2.095364 GTGGATTGCTTCAGTGCTTCTG 60.095 50.000 3.68 3.68 44.85 3.02
2745 3536 3.645975 CGGTGTCCGTGGTGTTGC 61.646 66.667 0.00 0.00 42.73 4.17
2797 3588 2.126071 CGGCGGAGTCACGATGTT 60.126 61.111 0.00 0.00 35.47 2.71
2853 3644 2.281484 GTGCCCCTCAACGAGCAA 60.281 61.111 0.00 0.00 36.91 3.91
2943 3736 1.553706 CTGAGGCAAAATCCCTGCTT 58.446 50.000 0.00 0.00 39.82 3.91
2970 3763 0.034186 ATGGCTTTGGGATTGCTCGA 60.034 50.000 0.00 0.00 0.00 4.04
2992 3785 5.630415 AACATCATCTCCGGATCCTAAAA 57.370 39.130 3.57 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.