Multiple sequence alignment - TraesCS5B01G461800

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 TraesCS5B01G461800 chr5B 100.000 2530 0 0 1 2530 637216476 637213947 0.000000e+00 4673
1 TraesCS5B01G461800 chr5B 87.515 2571 232 52 1 2530 637805153 637802631 0.000000e+00 2887
2 TraesCS5B01G461800 chr5B 87.350 2577 231 50 1 2530 637783987 637781459 0.000000e+00 2865
3 TraesCS5B01G461800 chr5B 87.431 2180 202 31 26 2172 637729951 637727811 0.000000e+00 2442
4 TraesCS5B01G461800 chr5D 93.040 2543 143 14 1 2530 506740234 506737713 0.000000e+00 3685
5 TraesCS5B01G461800 chr5D 90.113 2569 211 23 1 2530 507519226 507516662 0.000000e+00 3297
6 TraesCS5B01G461800 chr5D 94.588 1312 61 3 1229 2530 506703338 506702027 0.000000e+00 2021
7 TraesCS5B01G461800 chr5D 91.596 940 62 10 1 925 506704274 506703337 0.000000e+00 1282
8 TraesCS5B01G461800 chr5A 92.134 2568 162 14 1 2530 634358851 634356286 0.000000e+00 3587
9 TraesCS5B01G461800 chr5A 88.042 2584 237 36 1 2530 635244657 635247222 0.000000e+00 2994
10 TraesCS5B01G461800 chr5A 87.660 2585 236 37 1 2530 634990947 634988391 0.000000e+00 2929
11 TraesCS5B01G461800 chr5A 87.564 1745 182 27 30 1746 638380823 638382560 0.000000e+00 1988
12 TraesCS5B01G461800 chr5A 85.740 547 68 9 1993 2530 638334274 638333729 1.020000e-158 569
13 TraesCS5B01G461800 chr5A 90.333 300 28 1 30 328 638364948 638364649 2.360000e-105 392


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 TraesCS5B01G461800 chr5B 637213947 637216476 2529 True 4673.0 4673 100.000 1 2530 1 chr5B.!!$R1 2529
1 TraesCS5B01G461800 chr5B 637802631 637805153 2522 True 2887.0 2887 87.515 1 2530 1 chr5B.!!$R4 2529
2 TraesCS5B01G461800 chr5B 637781459 637783987 2528 True 2865.0 2865 87.350 1 2530 1 chr5B.!!$R3 2529
3 TraesCS5B01G461800 chr5B 637727811 637729951 2140 True 2442.0 2442 87.431 26 2172 1 chr5B.!!$R2 2146
4 TraesCS5B01G461800 chr5D 506737713 506740234 2521 True 3685.0 3685 93.040 1 2530 1 chr5D.!!$R1 2529
5 TraesCS5B01G461800 chr5D 507516662 507519226 2564 True 3297.0 3297 90.113 1 2530 1 chr5D.!!$R2 2529
6 TraesCS5B01G461800 chr5D 506702027 506704274 2247 True 1651.5 2021 93.092 1 2530 2 chr5D.!!$R3 2529
7 TraesCS5B01G461800 chr5A 634356286 634358851 2565 True 3587.0 3587 92.134 1 2530 1 chr5A.!!$R1 2529
8 TraesCS5B01G461800 chr5A 635244657 635247222 2565 False 2994.0 2994 88.042 1 2530 1 chr5A.!!$F1 2529
9 TraesCS5B01G461800 chr5A 634988391 634990947 2556 True 2929.0 2929 87.660 1 2530 1 chr5A.!!$R2 2529
10 TraesCS5B01G461800 chr5A 638380823 638382560 1737 False 1988.0 1988 87.564 30 1746 1 chr5A.!!$F2 1716
11 TraesCS5B01G461800 chr5A 638333729 638334274 545 True 569.0 569 85.740 1993 2530 1 chr5A.!!$R3 537

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
453 458 0.041833 CTTCCTCCTGGACCTCCTCA 59.958 60.0 0.0 0.0 43.06 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2115 2193 0.107643 TGTGACGACAAAGGGATGCA 59.892 50.0 0.0 0.0 0.0 3.96 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
104 107 3.147595 CCGATCGCACTCTCCCCA 61.148 66.667 10.32 0.00 0.00 4.96
114 117 2.875296 CACTCTCCCCAGATCCTCTAG 58.125 57.143 0.00 0.00 0.00 2.43
148 151 0.914417 TCTTCCCATCCACCCTCCAC 60.914 60.000 0.00 0.00 0.00 4.02
162 165 1.620798 CCTCCACCACCTCTCTCATGA 60.621 57.143 0.00 0.00 0.00 3.07
293 298 1.351017 TGGAGAGAGGTGCGGATTTTT 59.649 47.619 0.00 0.00 0.00 1.94
401 406 1.462731 GGCACACCATCACCAAGCAA 61.463 55.000 0.00 0.00 35.26 3.91
453 458 0.041833 CTTCCTCCTGGACCTCCTCA 59.958 60.000 0.00 0.00 43.06 3.86
483 488 6.325028 CCATCTCCTCCATTGTAAGTTCTAGA 59.675 42.308 0.00 0.00 0.00 2.43
514 522 7.311929 GCCTTCATATCCCTATTCCATCCTTTA 60.312 40.741 0.00 0.00 0.00 1.85
555 563 4.383173 TCGTCCACCCTTTCTAGTTTTTC 58.617 43.478 0.00 0.00 0.00 2.29
565 573 8.170730 ACCCTTTCTAGTTTTTCTATCCATGTT 58.829 33.333 0.00 0.00 0.00 2.71
734 758 7.847096 TGTCTGTGTCTATATTTTGGAGCTAA 58.153 34.615 0.00 0.00 0.00 3.09
760 786 7.846644 TGATTTCATAAATGGAAAACATGCC 57.153 32.000 0.00 0.00 40.44 4.40
809 836 8.180165 TCATCAATCTATAGGATGGAAGGTACT 58.820 37.037 14.04 0.00 37.86 2.73
844 873 9.443323 TCTATTACTTTTTGATCATGTTTCGGA 57.557 29.630 0.00 0.00 0.00 4.55
952 982 6.681120 GCATGTATTTGGCATGAGTGTGTAAT 60.681 38.462 9.17 0.00 44.60 1.89
1084 1141 2.107953 GGATGGTCCTCTCGCAGC 59.892 66.667 0.00 0.00 32.53 5.25
1176 1233 7.265599 TGAGGGGAAGAAGTTTGACATTATA 57.734 36.000 0.00 0.00 0.00 0.98
1366 1425 4.161565 AGTTGTAAAGATCCGTGCTATGGA 59.838 41.667 0.00 0.42 37.75 3.41
1475 1534 3.308402 CCAAGCCTATCAAGGTTCAGGAA 60.308 47.826 0.00 0.00 45.64 3.36
1618 1677 6.092092 TGTATGCATTGTCATGTTGTTTAGC 58.908 36.000 3.54 0.00 32.28 3.09
1627 1686 6.437928 TGTCATGTTGTTTAGCTTCATTGTC 58.562 36.000 0.00 0.00 0.00 3.18
1684 1750 2.693069 AGCAAGAAGAACATGAGACGG 58.307 47.619 0.00 0.00 0.00 4.79
1689 1755 5.410924 CAAGAAGAACATGAGACGGTATCA 58.589 41.667 8.03 8.03 0.00 2.15
1693 1759 4.697514 AGAACATGAGACGGTATCATTGG 58.302 43.478 15.13 8.27 35.20 3.16
1705 1771 3.006110 GGTATCATTGGTTCCATGGCATG 59.994 47.826 20.56 20.56 0.00 4.06
1746 1812 4.858692 GCACCAATATAAATATGGCGCAAG 59.141 41.667 10.83 0.00 43.44 4.01
1863 1940 3.134458 GCATAATTTGTCGGAGAGAGGG 58.866 50.000 0.00 0.00 36.95 4.30
2115 2193 3.266772 TCCATTCTCTTGTGCTACCCAAT 59.733 43.478 0.00 0.00 0.00 3.16
2151 2229 5.128008 TCGTCACATAAGTCACCAATATGGA 59.872 40.000 2.85 0.00 40.96 3.41
2172 2250 3.829886 TTTTCCGAAGATGTGCATCAC 57.170 42.857 13.79 7.01 40.22 3.06
2238 2326 2.563179 GTGAGCAGAGAGTGGAGGTTTA 59.437 50.000 0.00 0.00 0.00 2.01
2331 2420 1.475213 GCATACTCAGGGTACAAGGCC 60.475 57.143 0.00 0.00 32.72 5.19
2374 2464 4.452455 AGCGGCAAAATAGGAAAGATATCG 59.548 41.667 1.45 0.00 0.00 2.92
2390 2480 8.429237 AAAGATATCGATTCTACTCCTCCAAT 57.571 34.615 1.71 0.00 0.00 3.16
2405 2495 7.694093 ACTCCTCCAATTCCATTATAAGATCC 58.306 38.462 0.00 0.00 0.00 3.36
2407 2497 7.922382 TCCTCCAATTCCATTATAAGATCCTC 58.078 38.462 0.00 0.00 0.00 3.71
2453 2543 6.155475 TCATCCTTTGTTTTTGTACCTTGG 57.845 37.500 0.00 0.00 0.00 3.61
2463 2553 7.364200 TGTTTTTGTACCTTGGTTTATCATCG 58.636 34.615 0.00 0.00 0.00 3.84
2486 2576 7.891782 TCGAGCTTGTAATAGTTTTTGTATCG 58.108 34.615 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 0.837272 CGGTGGGTGGGATAAGATGT 59.163 55.000 0.00 0.00 0.00 3.06
114 117 1.468914 GGAAGAAGAACATTGGCGACC 59.531 52.381 0.00 0.00 0.00 4.79
148 151 2.682594 TGGGTATCATGAGAGAGGTGG 58.317 52.381 0.09 0.00 0.00 4.61
162 165 2.653543 TAGAGGGGTGTGTTGGGTAT 57.346 50.000 0.00 0.00 0.00 2.73
259 262 8.150945 GCACCTCTCTCCACTCAAATAAATATA 58.849 37.037 0.00 0.00 0.00 0.86
280 283 0.171007 CGATGCAAAAATCCGCACCT 59.829 50.000 0.00 0.00 41.79 4.00
401 406 0.321919 TTCCGCTCTTGCTGCTTGAT 60.322 50.000 0.00 0.00 36.97 2.57
453 458 3.071967 ACAATGGAGGAGATGGAGGAT 57.928 47.619 0.00 0.00 0.00 3.24
483 488 7.588866 TGGAATAGGGATATGAAGGCTAATT 57.411 36.000 0.00 0.00 0.00 1.40
535 543 6.598457 GGATAGAAAAACTAGAAAGGGTGGAC 59.402 42.308 0.00 0.00 34.35 4.02
643 652 5.394443 GGCATAAACATGGATGTCAACACAT 60.394 40.000 0.00 0.00 46.64 3.21
711 735 9.330063 CATTTAGCTCCAAAATATAGACACAGA 57.670 33.333 0.00 0.00 0.00 3.41
734 758 8.895737 GGCATGTTTTCCATTTATGAAATCATT 58.104 29.630 0.55 0.00 37.76 2.57
929 959 6.183360 CCATTACACACTCATGCCAAATACAT 60.183 38.462 0.00 0.00 0.00 2.29
1028 1085 4.989168 CCTCAACAACTAGTACCTTCACAC 59.011 45.833 0.00 0.00 0.00 3.82
1084 1141 6.142139 TCTCACATTGAAAATTGCGTAACAG 58.858 36.000 0.00 0.00 0.00 3.16
1117 1174 2.554032 CTGCTTCTTTTCCATTCACGGT 59.446 45.455 0.00 0.00 0.00 4.83
1176 1233 1.067635 GGCATGTCCTTGTCGCAAAAT 60.068 47.619 0.00 0.00 0.00 1.82
1260 1319 9.651718 GACTTATGTTCGAATCAATACATTTCC 57.348 33.333 0.00 0.00 33.58 3.13
1275 1334 8.953990 CAAACTTAAAACAAGGACTTATGTTCG 58.046 33.333 0.00 0.00 38.75 3.95
1316 1375 6.260870 TGTTAAGCAACACAACAAGAGAAA 57.739 33.333 0.00 0.00 39.75 2.52
1366 1425 5.242393 CCAACAATCTTCACATCAGTTTCCT 59.758 40.000 0.00 0.00 0.00 3.36
1407 1466 2.537633 ATGAACACCTCCATGGCATT 57.462 45.000 6.96 0.00 40.22 3.56
1475 1534 4.704057 ACTTCCTTAATTACGGACTCGAGT 59.296 41.667 20.18 20.18 40.11 4.18
1684 1750 4.247267 CATGCCATGGAACCAATGATAC 57.753 45.455 18.40 0.00 0.00 2.24
1714 1780 5.964958 ATTTATATTGGTGCCGATCAAGG 57.035 39.130 0.00 0.00 0.00 3.61
1746 1812 4.940463 ACAATGGACAAATATGCATGCTC 58.060 39.130 20.33 5.75 0.00 4.26
1863 1940 3.512033 ACAATCTCAAGTAGCTCCGAC 57.488 47.619 0.00 0.00 0.00 4.79
2115 2193 0.107643 TGTGACGACAAAGGGATGCA 59.892 50.000 0.00 0.00 0.00 3.96
2151 2229 4.012374 AGTGATGCACATCTTCGGAAAAT 58.988 39.130 11.66 0.00 38.60 1.82
2238 2326 2.799017 TGCACTTCCTTCAAGATGCAT 58.201 42.857 0.00 0.00 40.85 3.96
2331 2420 3.689649 GCTTCACTATTTGGTGGTAGTGG 59.310 47.826 11.34 0.39 44.91 4.00
2390 2480 6.240002 GGCTGAAGGAGGATCTTATAATGGAA 60.240 42.308 0.00 0.00 33.73 3.53
2405 2495 1.072965 GGGATATGTGGGCTGAAGGAG 59.927 57.143 0.00 0.00 0.00 3.69
2407 2497 1.143813 AGGGATATGTGGGCTGAAGG 58.856 55.000 0.00 0.00 0.00 3.46
2463 2553 9.638300 CATCGATACAAAAACTATTACAAGCTC 57.362 33.333 0.00 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.