Multiple sequence alignment - TraesCS6D01G087800

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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 TraesCS6D01G087800 chr6D 100.000 3458 0 0 1 3458 53176711 53173254 0.000000e+00 6386
1 TraesCS6D01G087800 chr6D 95.260 2890 101 14 1 2875 50955661 50958529 0.000000e+00 4545
2 TraesCS6D01G087800 chr6D 89.288 2838 216 42 212 2993 51342430 51345235 0.000000e+00 3476
3 TraesCS6D01G087800 chr6D 90.298 2649 202 23 388 2993 51067875 51070511 0.000000e+00 3417
4 TraesCS6D01G087800 chr6D 86.380 2467 229 45 230 2648 51348362 51350769 0.000000e+00 2595
5 TraesCS6D01G087800 chr6D 86.235 2470 231 42 230 2648 51073579 51075990 0.000000e+00 2577
6 TraesCS6D01G087800 chr6D 87.744 359 25 10 2876 3218 50958572 50958927 5.380000e-108 401
7 TraesCS6D01G087800 chr6D 84.478 335 21 13 3001 3316 51345352 51345674 5.610000e-78 302
8 TraesCS6D01G087800 chr6D 83.582 335 24 13 3001 3316 51070628 51070950 5.650000e-73 285
9 TraesCS6D01G087800 chr6D 91.743 109 8 1 85 193 51067575 51067682 2.150000e-32 150
10 TraesCS6D01G087800 chr6D 83.846 130 4 6 49 176 51348157 51348271 1.310000e-19 108
11 TraesCS6D01G087800 chr6D 83.077 130 5 6 49 176 51073374 51073488 6.110000e-18 102
12 TraesCS6D01G087800 chr6A 92.589 2982 175 26 362 3315 64168198 64165235 0.000000e+00 4241
13 TraesCS6D01G087800 chr6A 81.267 742 66 33 212 918 64175607 64174904 1.830000e-147 532
14 TraesCS6D01G087800 chr6A 86.750 400 13 10 1 369 64168755 64168365 3.210000e-110 409
15 TraesCS6D01G087800 chr6A 84.615 169 15 5 18 186 64175833 64175676 1.280000e-34 158
16 TraesCS6D01G087800 chr6B 92.862 2802 138 10 683 3458 120317471 120314706 0.000000e+00 4010
17 TraesCS6D01G087800 chr6B 90.053 2634 204 21 397 2993 120355401 120352789 0.000000e+00 3360
18 TraesCS6D01G087800 chr6B 88.392 2481 220 29 212 2648 120595922 120593466 0.000000e+00 2924
19 TraesCS6D01G087800 chr6B 85.953 2513 249 54 603 3043 120132997 120130517 0.000000e+00 2590
20 TraesCS6D01G087800 chr6B 96.373 193 7 0 212 404 120355694 120355502 5.570000e-83 318
21 TraesCS6D01G087800 chr6B 83.750 320 23 11 3013 3316 120352693 120352387 3.400000e-70 276
22 TraesCS6D01G087800 chr6B 93.048 187 6 6 1 186 120355936 120355756 2.050000e-67 267
23 TraesCS6D01G087800 chr6B 90.217 92 8 1 356 447 120317951 120317861 6.060000e-23 119
24 TraesCS6D01G087800 chr6B 88.172 93 4 4 53 143 120318233 120318146 1.700000e-18 104
25 TraesCS6D01G087800 chr1B 87.327 2675 241 53 708 3314 70232791 70235435 0.000000e+00 2972
26 TraesCS6D01G087800 chr1B 87.082 2423 220 37 334 2684 4109787 4112188 0.000000e+00 2654
27 TraesCS6D01G087800 chr1B 87.070 2413 229 36 332 2684 4519389 4517000 0.000000e+00 2651
28 TraesCS6D01G087800 chr1B 76.080 301 28 23 273 533 70232394 70232690 2.180000e-22 117
29 TraesCS6D01G087800 chr3D 87.691 2421 209 35 333 2684 560025277 560022877 0.000000e+00 2737
30 TraesCS6D01G087800 chr7A 85.714 2632 218 56 85 2608 631983741 631986322 0.000000e+00 2632
31 TraesCS6D01G087800 chr5D 88.936 2106 173 21 595 2655 57819423 57821513 0.000000e+00 2543
32 TraesCS6D01G087800 chr5D 83.879 763 86 16 2578 3314 535495205 535494454 0.000000e+00 693
33 TraesCS6D01G087800 chr5B 88.884 2105 179 17 595 2655 60826101 60824008 0.000000e+00 2540
34 TraesCS6D01G087800 chr7B 84.828 725 66 16 2650 3342 591463530 591464242 0.000000e+00 689
35 TraesCS6D01G087800 chr7D 83.531 759 73 23 2650 3374 548235179 548235919 0.000000e+00 662


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 TraesCS6D01G087800 chr6D 53173254 53176711 3457 True 6386.00 6386 100.0000 1 3458 1 chr6D.!!$R1 3457
1 TraesCS6D01G087800 chr6D 50955661 50958927 3266 False 2473.00 4545 91.5020 1 3218 2 chr6D.!!$F1 3217
2 TraesCS6D01G087800 chr6D 51342430 51350769 8339 False 1620.25 3476 85.9980 49 3316 4 chr6D.!!$F3 3267
3 TraesCS6D01G087800 chr6D 51067575 51075990 8415 False 1306.20 3417 86.9870 49 3316 5 chr6D.!!$F2 3267
4 TraesCS6D01G087800 chr6A 64165235 64168755 3520 True 2325.00 4241 89.6695 1 3315 2 chr6A.!!$R1 3314
5 TraesCS6D01G087800 chr6A 64174904 64175833 929 True 345.00 532 82.9410 18 918 2 chr6A.!!$R2 900
6 TraesCS6D01G087800 chr6B 120593466 120595922 2456 True 2924.00 2924 88.3920 212 2648 1 chr6B.!!$R2 2436
7 TraesCS6D01G087800 chr6B 120130517 120132997 2480 True 2590.00 2590 85.9530 603 3043 1 chr6B.!!$R1 2440
8 TraesCS6D01G087800 chr6B 120314706 120318233 3527 True 1411.00 4010 90.4170 53 3458 3 chr6B.!!$R3 3405
9 TraesCS6D01G087800 chr6B 120352387 120355936 3549 True 1055.25 3360 90.8060 1 3316 4 chr6B.!!$R4 3315
10 TraesCS6D01G087800 chr1B 4109787 4112188 2401 False 2654.00 2654 87.0820 334 2684 1 chr1B.!!$F1 2350
11 TraesCS6D01G087800 chr1B 4517000 4519389 2389 True 2651.00 2651 87.0700 332 2684 1 chr1B.!!$R1 2352
12 TraesCS6D01G087800 chr1B 70232394 70235435 3041 False 1544.50 2972 81.7035 273 3314 2 chr1B.!!$F2 3041
13 TraesCS6D01G087800 chr3D 560022877 560025277 2400 True 2737.00 2737 87.6910 333 2684 1 chr3D.!!$R1 2351
14 TraesCS6D01G087800 chr7A 631983741 631986322 2581 False 2632.00 2632 85.7140 85 2608 1 chr7A.!!$F1 2523
15 TraesCS6D01G087800 chr5D 57819423 57821513 2090 False 2543.00 2543 88.9360 595 2655 1 chr5D.!!$F1 2060
16 TraesCS6D01G087800 chr5D 535494454 535495205 751 True 693.00 693 83.8790 2578 3314 1 chr5D.!!$R1 736
17 TraesCS6D01G087800 chr5B 60824008 60826101 2093 True 2540.00 2540 88.8840 595 2655 1 chr5B.!!$R1 2060
18 TraesCS6D01G087800 chr7B 591463530 591464242 712 False 689.00 689 84.8280 2650 3342 1 chr7B.!!$F1 692
19 TraesCS6D01G087800 chr7D 548235179 548235919 740 False 662.00 662 83.5310 2650 3374 1 chr7D.!!$F1 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
50 51 1.265454 TTCCTTCCTCTTCCTCCGCC 61.265 60.0 0.00 0.0 0.0 6.13 F
627 1198 1.334160 TCAGCACGTGGGTCTTCTTA 58.666 50.0 18.88 0.0 0.0 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2264 3015 2.158813 ACCTCATGACACAACCGAAGTT 60.159 45.455 0.0 0.0 36.33 2.66 R
2731 3523 0.693622 TCTTGGGGGCGATTTGTACA 59.306 50.000 0.0 0.0 0.00 2.90 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
50 51 1.265454 TTCCTTCCTCTTCCTCCGCC 61.265 60.000 0.00 0.00 0.00 6.13
209 259 2.509336 CGGCCGTGCTCAAGGTAG 60.509 66.667 19.50 0.00 32.29 3.18
210 260 2.978824 GGCCGTGCTCAAGGTAGA 59.021 61.111 3.93 0.00 32.29 2.59
550 1084 7.119262 GCAAGAGCTACAAGTACTAATTTCCAA 59.881 37.037 0.00 0.00 37.91 3.53
627 1198 1.334160 TCAGCACGTGGGTCTTCTTA 58.666 50.000 18.88 0.00 0.00 2.10
722 1395 8.920174 TCTGCTACTTATGGTGCTAGTTTAATA 58.080 33.333 0.00 0.00 0.00 0.98
921 1650 8.780249 TCTTCACATGCATTATTCTGATATGTG 58.220 33.333 0.00 0.00 40.63 3.21
2552 3307 2.173669 GGGTGTGCATCATCCGACG 61.174 63.158 3.31 0.00 37.60 5.12
2752 3544 1.947456 GTACAAATCGCCCCCAAGATC 59.053 52.381 0.00 0.00 0.00 2.75
2754 3546 0.395586 CAAATCGCCCCCAAGATCCA 60.396 55.000 0.00 0.00 0.00 3.41
2780 3600 6.317857 TGTTTTTGCTGTTTGGTTTTATTGC 58.682 32.000 0.00 0.00 0.00 3.56
2788 3610 6.363357 GCTGTTTGGTTTTATTGCTTCTACTG 59.637 38.462 0.00 0.00 0.00 2.74
2866 3702 0.096976 CCTGCTATTTTCGTGTGGCG 59.903 55.000 0.00 0.00 43.01 5.69
2883 3761 2.948979 TGGCGATTTTGGTATGGATCAC 59.051 45.455 0.00 0.00 0.00 3.06
2930 3819 0.843984 ACCTGTACTGCAAAGGTGGT 59.156 50.000 8.76 2.57 42.78 4.16
2975 3864 5.843019 TTCTACTTGGGGATGTCTTTTCT 57.157 39.130 0.00 0.00 0.00 2.52
3278 4331 4.373717 CGTGATTATCGCGTACTAAGTTGC 60.374 45.833 18.55 0.00 44.47 4.17
3375 6646 7.201504 GGCTAAAGGTCGTACTTTGAGAATAAC 60.202 40.741 14.35 0.00 40.64 1.89
3433 6706 0.905357 TCACCTTCTTAGCCTGAGCC 59.095 55.000 0.00 0.00 41.25 4.70
3446 6719 1.615116 CCTGAGCCCAAATGAGCTTGA 60.615 52.381 0.00 0.00 40.11 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 4.424711 GAAGATGTGGGGCCGGCA 62.425 66.667 30.85 7.48 0.00 5.69
50 51 1.009829 CGCATTTCCTCTCCTTTCCG 58.990 55.000 0.00 0.00 0.00 4.30
209 259 0.744771 GGGGTCAGGTGAAGCGAATC 60.745 60.000 0.00 0.00 0.00 2.52
210 260 1.201429 AGGGGTCAGGTGAAGCGAAT 61.201 55.000 0.00 0.00 0.00 3.34
466 984 0.741221 GCCGATGAGTTCACAGGGTC 60.741 60.000 6.78 0.00 0.00 4.46
627 1198 1.019278 ATCGACGCAAGCAATTCCGT 61.019 50.000 0.00 0.00 45.62 4.69
681 1338 5.609423 AGTAGCAGAGCCTGAATAATGAAG 58.391 41.667 6.40 0.00 32.44 3.02
722 1395 8.413309 AATGAAGCTACATGCCACATTATTAT 57.587 30.769 0.00 0.00 41.92 1.28
727 1400 5.410355 AAAATGAAGCTACATGCCACATT 57.590 34.783 0.00 0.00 43.82 2.71
921 1650 5.005875 GCGAAGAGCTGGAGTAAAACTTATC 59.994 44.000 0.00 0.00 44.04 1.75
2264 3015 2.158813 ACCTCATGACACAACCGAAGTT 60.159 45.455 0.00 0.00 36.33 2.66
2536 3291 1.200483 CTACGTCGGATGATGCACAC 58.800 55.000 3.82 0.00 34.28 3.82
2731 3523 0.693622 TCTTGGGGGCGATTTGTACA 59.306 50.000 0.00 0.00 0.00 2.90
2752 3544 2.971307 ACCAAACAGCAAAAACAGTGG 58.029 42.857 0.00 0.00 0.00 4.00
2754 3546 7.525759 CAATAAAACCAAACAGCAAAAACAGT 58.474 30.769 0.00 0.00 0.00 3.55
2780 3600 7.148787 GGTTCACGACATTTCTTACAGTAGAAG 60.149 40.741 0.00 0.00 35.69 2.85
2788 3610 5.469084 AGAAAGGGTTCACGACATTTCTTAC 59.531 40.000 0.00 0.00 40.24 2.34
2866 3702 8.958119 TTACTACAGTGATCCATACCAAAATC 57.042 34.615 0.00 0.00 0.00 2.17
2883 3761 7.433708 TGTGAAACATTGACCATTACTACAG 57.566 36.000 0.00 0.00 45.67 2.74
3187 4238 7.423844 TCTCATATGGTGTACTGAATTCTGT 57.576 36.000 20.07 20.07 0.00 3.41
3195 4246 8.818141 ATACGATTTTCTCATATGGTGTACTG 57.182 34.615 2.13 0.00 0.00 2.74
3206 4259 9.667107 TCCAACTTTTAGATACGATTTTCTCAT 57.333 29.630 0.00 0.00 0.00 2.90
3262 4315 3.551890 CAGATTGCAACTTAGTACGCGAT 59.448 43.478 15.93 8.60 0.00 4.58
3397 6669 0.750546 TGACTATCCAGGCGTACGCT 60.751 55.000 36.24 20.80 41.60 5.07
3433 6706 3.567164 ACTGTTCACTCAAGCTCATTTGG 59.433 43.478 0.00 0.00 0.00 3.28


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

AutoCloner maintained by Alex Coulton.