Multiple sequence alignment - TraesCS6A01G109200

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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 TraesCS6A01G109200 chr6A 100.000 3698 0 0 1 3698 77888712 77892409 0.000000e+00 6830.0
1 TraesCS6A01G109200 chr6A 97.184 3125 80 7 3 3120 78018227 78021350 0.000000e+00 5276.0
2 TraesCS6A01G109200 chr6A 94.933 1421 62 5 2283 3698 80491070 80492485 0.000000e+00 2217.0
3 TraesCS6A01G109200 chr6A 94.283 892 41 5 1402 2291 80477878 80478761 0.000000e+00 1356.0
4 TraesCS6A01G109200 chr6A 86.630 1092 98 14 2284 3366 5224065 5225117 0.000000e+00 1164.0
5 TraesCS6A01G109200 chr6A 97.297 592 16 0 3107 3698 78026224 78026815 0.000000e+00 1005.0
6 TraesCS6A01G109200 chr6A 97.180 461 10 3 3 461 77988141 77988600 0.000000e+00 776.0
7 TraesCS6A01G109200 chr6A 97.867 422 7 2 41 461 78136805 78137225 0.000000e+00 728.0
8 TraesCS6A01G109200 chr4A 96.886 3243 80 5 460 3698 94762238 94765463 0.000000e+00 5409.0
9 TraesCS6A01G109200 chr6D 94.301 3246 151 16 460 3698 161148020 161151238 0.000000e+00 4939.0
10 TraesCS6A01G109200 chr6D 87.363 1092 111 12 2284 3366 5854601 5855674 0.000000e+00 1227.0
11 TraesCS6A01G109200 chr6D 82.766 441 36 19 24 430 61346326 61346760 1.260000e-94 357.0
12 TraesCS6A01G109200 chr5D 95.159 1508 63 5 1373 2878 435124743 435126242 0.000000e+00 2372.0
13 TraesCS6A01G109200 chr5D 87.279 849 76 9 460 1308 435120707 435121523 0.000000e+00 941.0
14 TraesCS6A01G109200 chr5D 94.611 501 20 3 3204 3698 435151565 435152064 0.000000e+00 769.0
15 TraesCS6A01G109200 chr5D 95.897 195 8 0 3010 3204 435148640 435148834 2.140000e-82 316.0
16 TraesCS6A01G109200 chr5D 94.286 140 8 0 2876 3015 435148454 435148593 8.040000e-52 215.0
17 TraesCS6A01G109200 chr5D 86.275 204 20 6 746 943 505888578 505888779 8.040000e-52 215.0
18 TraesCS6A01G109200 chr5A 92.157 1479 94 9 1205 2674 154618525 154617060 0.000000e+00 2069.0
19 TraesCS6A01G109200 chr5A 92.919 1031 68 2 2672 3698 154493316 154492287 0.000000e+00 1495.0
20 TraesCS6A01G109200 chr3A 84.540 718 56 32 460 1148 712620343 712621034 0.000000e+00 660.0
21 TraesCS6A01G109200 chr3A 100.000 32 0 0 1173 1204 712621039 712621070 3.990000e-05 60.2
22 TraesCS6A01G109200 chr7A 81.842 749 99 15 2501 3225 342917133 342916398 2.460000e-166 595.0
23 TraesCS6A01G109200 chr7A 94.375 320 14 1 3383 3698 8738799 8739118 4.290000e-134 488.0
24 TraesCS6A01G109200 chr7A 88.136 177 15 6 975 1148 134549268 134549441 4.840000e-49 206.0
25 TraesCS6A01G109200 chr7A 100.000 32 0 0 1173 1204 134549446 134549477 3.990000e-05 60.2
26 TraesCS6A01G109200 chr2A 89.549 421 34 4 529 946 579837249 579836836 3.270000e-145 525.0
27 TraesCS6A01G109200 chr2D 87.708 301 20 7 1695 1979 29648765 29649064 5.920000e-88 335.0
28 TraesCS6A01G109200 chr2D 89.831 177 10 2 1603 1771 29648585 29648761 1.730000e-53 220.0
29 TraesCS6A01G109200 chr1A 90.204 245 23 1 961 1204 485565873 485565629 5.960000e-83 318.0
30 TraesCS6A01G109200 chr1B 89.796 245 24 1 961 1204 518266326 518266082 2.770000e-81 313.0
31 TraesCS6A01G109200 chr1D 90.638 235 21 1 971 1204 386127330 386127096 9.970000e-81 311.0
32 TraesCS6A01G109200 chrUn 91.441 222 19 0 2284 2505 75991172 75990951 4.640000e-79 305.0
33 TraesCS6A01G109200 chrUn 91.441 222 19 0 2284 2505 231194857 231194636 4.640000e-79 305.0
34 TraesCS6A01G109200 chr5B 86.076 237 28 2 710 943 154016668 154016434 2.200000e-62 250.0
35 TraesCS6A01G109200 chr5B 90.395 177 9 2 1603 1771 321544110 321544286 3.720000e-55 226.0
36 TraesCS6A01G109200 chr3D 90.000 50 4 1 156 204 409024066 409024017 3.080000e-06 63.9


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 TraesCS6A01G109200 chr6A 77888712 77892409 3697 False 6830.000000 6830 100.000000 1 3698 1 chr6A.!!$F2 3697
1 TraesCS6A01G109200 chr6A 78018227 78021350 3123 False 5276.000000 5276 97.184000 3 3120 1 chr6A.!!$F4 3117
2 TraesCS6A01G109200 chr6A 80491070 80492485 1415 False 2217.000000 2217 94.933000 2283 3698 1 chr6A.!!$F8 1415
3 TraesCS6A01G109200 chr6A 80477878 80478761 883 False 1356.000000 1356 94.283000 1402 2291 1 chr6A.!!$F7 889
4 TraesCS6A01G109200 chr6A 5224065 5225117 1052 False 1164.000000 1164 86.630000 2284 3366 1 chr6A.!!$F1 1082
5 TraesCS6A01G109200 chr6A 78026224 78026815 591 False 1005.000000 1005 97.297000 3107 3698 1 chr6A.!!$F5 591
6 TraesCS6A01G109200 chr4A 94762238 94765463 3225 False 5409.000000 5409 96.886000 460 3698 1 chr4A.!!$F1 3238
7 TraesCS6A01G109200 chr6D 161148020 161151238 3218 False 4939.000000 4939 94.301000 460 3698 1 chr6D.!!$F3 3238
8 TraesCS6A01G109200 chr6D 5854601 5855674 1073 False 1227.000000 1227 87.363000 2284 3366 1 chr6D.!!$F1 1082
9 TraesCS6A01G109200 chr5D 435120707 435126242 5535 False 1656.500000 2372 91.219000 460 2878 2 chr5D.!!$F2 2418
10 TraesCS6A01G109200 chr5D 435148454 435152064 3610 False 433.333333 769 94.931333 2876 3698 3 chr5D.!!$F3 822
11 TraesCS6A01G109200 chr5A 154617060 154618525 1465 True 2069.000000 2069 92.157000 1205 2674 1 chr5A.!!$R2 1469
12 TraesCS6A01G109200 chr5A 154492287 154493316 1029 True 1495.000000 1495 92.919000 2672 3698 1 chr5A.!!$R1 1026
13 TraesCS6A01G109200 chr3A 712620343 712621070 727 False 360.100000 660 92.270000 460 1204 2 chr3A.!!$F1 744
14 TraesCS6A01G109200 chr7A 342916398 342917133 735 True 595.000000 595 81.842000 2501 3225 1 chr7A.!!$R1 724

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
676 684 0.460311 CCCTTCTATCGAGCGGTGTT 59.540 55.000 0.0 0.0 0.0 3.32 F
742 762 1.146152 CCTCCTCCTCCTATCTTCCGT 59.854 57.143 0.0 0.0 0.0 4.69 F
743 763 2.425102 CCTCCTCCTCCTATCTTCCGTT 60.425 54.545 0.0 0.0 0.0 4.44 F
849 871 2.737830 GTCTCCTATGCCCCGCTC 59.262 66.667 0.0 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1626 4884 3.385193 AAAGGGAAAAGAAATGCCACG 57.615 42.857 0.0 0.0 0.00 4.94 R
1897 5156 4.077982 AGGATGGAAGATTGGACCTACCTA 60.078 45.833 0.0 0.0 39.86 3.08 R
2678 5961 5.937540 TCAAATCATCGTGACACCTTGTATT 59.062 36.000 0.0 0.0 0.00 1.89 R
2795 6085 7.431249 TGTCTACAGTTCTCAAATAAGACGTT 58.569 34.615 0.0 0.0 35.90 3.99 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
61 63 9.189156 TGCTTAGATAATTGTTTTTATGGCTCT 57.811 29.630 0.00 0.0 0.00 4.09
79 81 6.426587 TGGCTCTAATTTTATCTTCTTGCCT 58.573 36.000 0.00 0.0 36.73 4.75
122 124 0.655733 CGTGAAACTTTGCACCTCGT 59.344 50.000 0.00 0.0 31.75 4.18
132 134 4.518970 ACTTTGCACCTCGTTCATGTTTAT 59.481 37.500 0.00 0.0 0.00 1.40
227 231 6.092092 CGCCATGTTTGAAAAATCTACATCA 58.908 36.000 0.00 0.0 0.00 3.07
320 324 1.278985 TGGATCTGCAAGGATTCGTGT 59.721 47.619 0.00 0.0 0.00 4.49
443 448 1.494766 CGTTGCACGTCCACATGTCA 61.495 55.000 0.00 0.0 36.74 3.58
667 675 1.696097 CCACCCCACCCCTTCTATCG 61.696 65.000 0.00 0.0 0.00 2.92
676 684 0.460311 CCCTTCTATCGAGCGGTGTT 59.540 55.000 0.00 0.0 0.00 3.32
742 762 1.146152 CCTCCTCCTCCTATCTTCCGT 59.854 57.143 0.00 0.0 0.00 4.69
743 763 2.425102 CCTCCTCCTCCTATCTTCCGTT 60.425 54.545 0.00 0.0 0.00 4.44
849 871 2.737830 GTCTCCTATGCCCCGCTC 59.262 66.667 0.00 0.0 0.00 5.03
1255 1307 3.405831 CCTTCTCTCTTGTGTGATGCAA 58.594 45.455 0.00 0.0 0.00 4.08
1510 4767 6.582636 TCGTTTCATCTGTTAAGATAGCCAT 58.417 36.000 0.00 0.0 41.43 4.40
1514 4771 9.331282 GTTTCATCTGTTAAGATAGCCATAACT 57.669 33.333 6.03 0.0 41.43 2.24
1626 4884 7.386851 TCTATATATTTGGCTCTGGCTTACAC 58.613 38.462 0.00 0.0 38.73 2.90
1677 4935 8.135382 AGGATAGAACTTTTCACTGTAAGCTA 57.865 34.615 0.00 0.0 37.60 3.32
1897 5156 5.435686 TGTATCCTGTGGCATTCTTAGTT 57.564 39.130 0.00 0.0 0.00 2.24
2678 5961 3.056107 GGTGTACTACTTGACCATGCAGA 60.056 47.826 0.00 0.0 0.00 4.26
2795 6085 3.872696 ACAAGTCGGTGATGATATTGCA 58.127 40.909 0.00 0.0 0.00 4.08
2935 6232 7.973048 TCTGTTCTCAAGGGTATAGTAATGT 57.027 36.000 0.00 0.0 0.00 2.71
3102 6460 3.305335 GGCAGTGAACATTTGTTTCCGAT 60.305 43.478 0.00 0.0 38.56 4.18
3157 6515 9.612620 CTCTAAAAATGAACTATTGTGGTGTTC 57.387 33.333 0.00 0.0 40.09 3.18
3507 9604 6.490040 TGCCTTAAATCCCTTATGATAAGCAC 59.510 38.462 6.69 0.0 0.00 4.40
3643 9740 2.124983 CCACGTCATCCCTGCCAG 60.125 66.667 0.00 0.0 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 9.889128 TGGATGTTCATTTTTCTTTTCTTTCTT 57.111 25.926 0.00 0.00 0.00 2.52
11 12 9.977762 GCAATATGGATGTTCATTTTTCTTTTC 57.022 29.630 0.00 0.00 0.00 2.29
184 188 0.171903 GCACATGCACCCAGATGAAC 59.828 55.000 0.00 0.00 41.59 3.18
227 231 5.246883 AGGGCTTTGTATGAAAAAGAGCAAT 59.753 36.000 0.25 0.00 36.88 3.56
320 324 7.070571 AGTGATACACCAAAAAGGAAAAATCCA 59.929 33.333 0.00 0.00 41.22 3.41
582 590 3.104512 TGAAGGCGATTTTCTCCTCCTA 58.895 45.455 0.00 0.00 28.59 2.94
629 637 3.541713 GGCGCCGGAGAAGAGGAT 61.542 66.667 12.58 0.00 0.00 3.24
676 684 1.684734 GTACCGGGAAGGAGAGGCA 60.685 63.158 6.32 0.00 45.00 4.75
742 762 4.299547 ACTGCAGCGGCGAGACAA 62.300 61.111 15.27 0.00 45.35 3.18
743 763 4.724602 GACTGCAGCGGCGAGACA 62.725 66.667 15.27 3.16 45.35 3.41
849 871 1.075896 AGAGGAAGAGTAGGCGGGG 60.076 63.158 0.00 0.00 0.00 5.73
1064 1115 0.681733 AGAACAAGAGCGCCTCTCAA 59.318 50.000 2.29 0.00 44.35 3.02
1067 1118 1.375268 GCAGAACAAGAGCGCCTCT 60.375 57.895 2.29 3.29 43.37 3.69
1255 1307 6.431234 ACTCAGTGAAACAAAGAACTCAAAGT 59.569 34.615 0.00 0.00 41.43 2.66
1626 4884 3.385193 AAAGGGAAAAGAAATGCCACG 57.615 42.857 0.00 0.00 0.00 4.94
1677 4935 9.471702 TGAATAGTAGGTTACTGCTAAGTTAGT 57.528 33.333 11.51 0.00 43.63 2.24
1874 5133 5.435686 ACTAAGAATGCCACAGGATACAA 57.564 39.130 0.00 0.00 41.41 2.41
1897 5156 4.077982 AGGATGGAAGATTGGACCTACCTA 60.078 45.833 0.00 0.00 39.86 3.08
2129 5392 9.672086 CGATTTACCTTCAAACTAAATTGACAA 57.328 29.630 0.00 0.00 38.95 3.18
2632 5907 6.976925 CCTTCTGATGGCAATAACAAATTCTC 59.023 38.462 0.00 0.00 0.00 2.87
2678 5961 5.937540 TCAAATCATCGTGACACCTTGTATT 59.062 36.000 0.00 0.00 0.00 1.89
2795 6085 7.431249 TGTCTACAGTTCTCAAATAAGACGTT 58.569 34.615 0.00 0.00 35.90 3.99
3057 6414 6.128145 GCCATTGTCTTAAAGAGAAGTTCTCC 60.128 42.308 25.93 11.63 44.42 3.71
3157 6515 2.768253 TGGCACACTGATAGGTGAAG 57.232 50.000 1.52 0.00 40.13 3.02
3169 6527 7.377766 TTCTTAGATAGAAAACATGGCACAC 57.622 36.000 0.00 0.00 40.04 3.82
3311 9402 4.407365 CCAGGAAGTTACCCAGATGTTTT 58.593 43.478 0.00 0.00 0.00 2.43
3507 9604 3.499737 GCACCCAGATCAACCGCG 61.500 66.667 0.00 0.00 0.00 6.46


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

AutoCloner maintained by Alex Coulton.