Multiple sequence alignment - TraesCS6D01G270600

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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 TraesCS6D01G270600 chr6D 100.000 3023 0 0 1 3023 380253875 380256897 0.000000e+00 5583.0
1 TraesCS6D01G270600 chr6D 92.707 2276 102 18 697 2925 380366256 380368514 0.000000e+00 3225.0
2 TraesCS6D01G270600 chr6D 90.917 1123 90 8 942 2055 380177548 380178667 0.000000e+00 1498.0
3 TraesCS6D01G270600 chr6D 96.262 107 4 0 2916 3022 380395485 380395591 3.100000e-40 176.0
4 TraesCS6D01G270600 chr6B 94.493 2306 109 12 1 2299 566039978 566037684 0.000000e+00 3539.0
5 TraesCS6D01G270600 chr6B 94.455 1010 54 2 1203 2211 566027192 566026184 0.000000e+00 1554.0
6 TraesCS6D01G270600 chr6B 91.339 1120 85 6 945 2055 566122444 566121328 0.000000e+00 1520.0
7 TraesCS6D01G270600 chr6B 95.467 728 32 1 2296 3023 566034288 566033562 0.000000e+00 1160.0
8 TraesCS6D01G270600 chr6B 95.408 392 17 1 817 1208 566028065 566027675 9.200000e-175 623.0
9 TraesCS6D01G270600 chr6B 92.412 369 28 0 2654 3022 565708220 565707852 7.420000e-146 527.0
10 TraesCS6D01G270600 chr6B 86.093 453 40 9 2207 2650 565708720 565708282 1.640000e-127 466.0
11 TraesCS6D01G270600 chr6B 91.270 126 7 3 711 833 566028204 566028080 5.180000e-38 169.0
12 TraesCS6D01G270600 chr6A 95.199 1354 64 1 766 2118 520650593 520649240 0.000000e+00 2139.0
13 TraesCS6D01G270600 chr6A 90.426 1128 91 11 946 2061 520670613 520669491 0.000000e+00 1469.0
14 TraesCS6D01G270600 chr6A 90.057 352 27 4 2299 2650 520622191 520621848 1.650000e-122 449.0
15 TraesCS6D01G270600 chr6A 91.489 188 15 1 2654 2841 520621728 520621542 1.080000e-64 257.0
16 TraesCS6D01G270600 chr2D 80.912 592 90 15 14 589 47429057 47429641 2.140000e-121 446.0
17 TraesCS6D01G270600 chr2D 81.584 543 88 9 83 620 116553174 116552639 3.580000e-119 438.0
18 TraesCS6D01G270600 chr2D 81.410 468 80 6 67 531 634115168 634115631 2.850000e-100 375.0
19 TraesCS6D01G270600 chr2A 82.252 524 77 11 101 617 374445149 374444635 3.580000e-119 438.0
20 TraesCS6D01G270600 chr2A 90.361 83 8 0 3 85 46321245 46321163 3.190000e-20 110.0
21 TraesCS6D01G270600 chr7D 80.570 597 88 13 76 668 64492110 64491538 4.630000e-118 435.0
22 TraesCS6D01G270600 chr7D 81.855 496 77 10 97 588 39221490 39221976 3.630000e-109 405.0
23 TraesCS6D01G270600 chr7D 75.277 542 70 25 1 511 53528228 53527720 1.840000e-47 200.0
24 TraesCS6D01G270600 chr7D 91.026 78 7 0 5 82 448342388 448342311 4.120000e-19 106.0
25 TraesCS6D01G270600 chr7D 87.500 80 10 0 3 82 546232419 546232498 3.210000e-15 93.5
26 TraesCS6D01G270600 chr5D 81.568 472 77 10 96 560 255977776 255977308 6.120000e-102 381.0
27 TraesCS6D01G270600 chr5D 94.872 78 4 0 5 82 539655134 539655211 4.090000e-24 122.0
28 TraesCS6D01G270600 chr5D 86.747 83 11 0 3 85 234033160 234033078 3.210000e-15 93.5
29 TraesCS6D01G270600 chr1D 80.268 522 87 12 102 617 78114527 78115038 2.200000e-101 379.0
30 TraesCS6D01G270600 chr1D 97.059 34 1 0 1184 1217 72498134 72498167 1.170000e-04 58.4
31 TraesCS6D01G270600 chr3B 76.027 584 107 19 81 656 17573442 17572884 3.840000e-69 272.0
32 TraesCS6D01G270600 chr2B 76.325 566 89 26 98 656 651366994 651366467 8.310000e-66 261.0
33 TraesCS6D01G270600 chr7A 74.865 557 96 23 80 631 256069563 256070080 2.360000e-51 213.0
34 TraesCS6D01G270600 chr7B 91.892 74 6 0 1 74 219677414 219677487 1.480000e-18 104.0
35 TraesCS6D01G270600 chr4A 90.000 80 8 0 1 80 668291736 668291657 1.480000e-18 104.0
36 TraesCS6D01G270600 chr3A 76.923 156 28 6 510 658 547325972 547325818 6.950000e-12 82.4
37 TraesCS6D01G270600 chrUn 84.375 64 9 1 1175 1237 24657914 24657851 9.050000e-06 62.1


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 TraesCS6D01G270600 chr6D 380253875 380256897 3022 False 5583.0 5583 100.0000 1 3023 1 chr6D.!!$F2 3022
1 TraesCS6D01G270600 chr6D 380366256 380368514 2258 False 3225.0 3225 92.7070 697 2925 1 chr6D.!!$F3 2228
2 TraesCS6D01G270600 chr6D 380177548 380178667 1119 False 1498.0 1498 90.9170 942 2055 1 chr6D.!!$F1 1113
3 TraesCS6D01G270600 chr6B 566033562 566039978 6416 True 2349.5 3539 94.9800 1 3023 2 chr6B.!!$R4 3022
4 TraesCS6D01G270600 chr6B 566121328 566122444 1116 True 1520.0 1520 91.3390 945 2055 1 chr6B.!!$R1 1110
5 TraesCS6D01G270600 chr6B 566026184 566028204 2020 True 782.0 1554 93.7110 711 2211 3 chr6B.!!$R3 1500
6 TraesCS6D01G270600 chr6B 565707852 565708720 868 True 496.5 527 89.2525 2207 3022 2 chr6B.!!$R2 815
7 TraesCS6D01G270600 chr6A 520649240 520650593 1353 True 2139.0 2139 95.1990 766 2118 1 chr6A.!!$R1 1352
8 TraesCS6D01G270600 chr6A 520669491 520670613 1122 True 1469.0 1469 90.4260 946 2061 1 chr6A.!!$R2 1115
9 TraesCS6D01G270600 chr6A 520621542 520622191 649 True 353.0 449 90.7730 2299 2841 2 chr6A.!!$R3 542
10 TraesCS6D01G270600 chr2D 47429057 47429641 584 False 446.0 446 80.9120 14 589 1 chr2D.!!$F1 575
11 TraesCS6D01G270600 chr2D 116552639 116553174 535 True 438.0 438 81.5840 83 620 1 chr2D.!!$R1 537
12 TraesCS6D01G270600 chr2A 374444635 374445149 514 True 438.0 438 82.2520 101 617 1 chr2A.!!$R2 516
13 TraesCS6D01G270600 chr7D 64491538 64492110 572 True 435.0 435 80.5700 76 668 1 chr7D.!!$R2 592
14 TraesCS6D01G270600 chr1D 78114527 78115038 511 False 379.0 379 80.2680 102 617 1 chr1D.!!$F2 515
15 TraesCS6D01G270600 chr3B 17572884 17573442 558 True 272.0 272 76.0270 81 656 1 chr3B.!!$R1 575
16 TraesCS6D01G270600 chr2B 651366467 651366994 527 True 261.0 261 76.3250 98 656 1 chr2B.!!$R1 558
17 TraesCS6D01G270600 chr7A 256069563 256070080 517 False 213.0 213 74.8650 80 631 1 chr7A.!!$F1 551

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
322 333 0.684535 TGTTGGATGAAGCTCACGGA 59.315 50.0 0.0 0.0 0.0 4.69 F
647 669 0.878523 TTGCGAGTGACCGTTTGAGG 60.879 55.0 0.0 0.0 37.3 3.86 F
1285 1847 0.105593 GCCAGCGGATGAGAAGATGA 59.894 55.0 0.0 0.0 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1286 1848 0.723981 GCCGTCGTTCGAGTAGTACT 59.276 55.000 1.37 1.37 42.86 2.73 R
1753 2321 2.165030 CCATCTGATGCCCAAAGTTGAC 59.835 50.000 12.17 0.00 0.00 3.18 R
2211 2783 2.212652 CCTTGCAGCGCTGATAATGTA 58.787 47.619 40.21 10.45 0.00 2.29 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
31 32 1.649348 CGCGTGCATGATTCGCTTC 60.649 57.895 10.93 0.00 46.31 3.86
90 92 1.911057 TCCGTGATCGCCATCTAGAT 58.089 50.000 0.00 0.00 35.54 1.98
91 93 1.541588 TCCGTGATCGCCATCTAGATG 59.458 52.381 23.53 23.53 38.51 2.90
94 96 2.227626 CGTGATCGCCATCTAGATGACT 59.772 50.000 30.40 13.57 41.20 3.41
184 187 6.892691 AGAGATCGTAAGTTTTGCTTCTTTG 58.107 36.000 0.00 0.00 38.57 2.77
269 276 0.744414 GTGCTGCCGTGATGTACCAT 60.744 55.000 0.00 0.00 0.00 3.55
322 333 0.684535 TGTTGGATGAAGCTCACGGA 59.315 50.000 0.00 0.00 0.00 4.69
527 549 6.885952 TTGATGATTTTCTCCGGTTTGTTA 57.114 33.333 0.00 0.00 0.00 2.41
600 622 3.069586 TCCGTGTCCACATAATGATCTCC 59.930 47.826 0.00 0.00 0.00 3.71
607 629 3.062763 CACATAATGATCTCCTGTCCGC 58.937 50.000 0.00 0.00 0.00 5.54
633 655 3.016736 GGATGAGGAAGGAAATTTGCGA 58.983 45.455 3.87 0.00 0.00 5.10
640 662 1.156736 AGGAAATTTGCGAGTGACCG 58.843 50.000 3.87 0.00 0.00 4.79
647 669 0.878523 TTGCGAGTGACCGTTTGAGG 60.879 55.000 0.00 0.00 37.30 3.86
652 674 2.112297 TGACCGTTTGAGGTGCCC 59.888 61.111 0.00 0.00 46.09 5.36
691 717 5.402270 GCTTAAACAATCACAACATGTCACC 59.598 40.000 0.00 0.00 0.00 4.02
704 730 6.605594 ACAACATGTCACCCTCTAAAAGAAAA 59.394 34.615 0.00 0.00 0.00 2.29
723 749 4.699522 ACCCGCCACGAAGAAGGC 62.700 66.667 0.00 0.00 45.51 4.35
756 789 4.935352 ACTTTTGCCTACAAAGCATCAA 57.065 36.364 0.00 0.00 46.08 2.57
757 790 4.874970 ACTTTTGCCTACAAAGCATCAAG 58.125 39.130 0.00 0.00 46.08 3.02
758 791 3.302365 TTTGCCTACAAAGCATCAAGC 57.698 42.857 0.00 0.00 40.84 4.01
833 896 4.453478 AGTCAACATTGTCAGTGCACTATG 59.547 41.667 21.20 20.91 36.10 2.23
875 938 2.051334 TATTCCCCGGTTGCAATCAG 57.949 50.000 10.93 0.00 0.00 2.90
1102 1167 2.154462 CTTCTTCCGTGAATGGCAAGT 58.846 47.619 0.00 0.00 0.00 3.16
1285 1847 0.105593 GCCAGCGGATGAGAAGATGA 59.894 55.000 0.00 0.00 0.00 2.92
1286 1848 1.473965 GCCAGCGGATGAGAAGATGAA 60.474 52.381 0.00 0.00 0.00 2.57
1397 1959 4.400961 GAAGCTCGGCTGCCACCT 62.401 66.667 20.29 8.18 39.62 4.00
1461 2023 2.890474 CCATACACGGCCGCAGTC 60.890 66.667 28.58 0.00 0.00 3.51
1599 2161 2.361357 CCGGACCCGAGACTCACT 60.361 66.667 10.42 0.00 42.83 3.41
2211 2783 7.360946 GCAAGTATGTTCGTTTAGTGGAGAATT 60.361 37.037 0.00 0.00 0.00 2.17
2228 2800 4.129380 AGAATTACATTATCAGCGCTGCA 58.871 39.130 32.44 20.83 0.00 4.41
2266 2838 4.082787 TCAATTTCAAGATTTGTCGGCTCC 60.083 41.667 0.00 0.00 0.00 4.70
2269 2841 1.546923 TCAAGATTTGTCGGCTCCGTA 59.453 47.619 8.28 0.00 40.74 4.02
2450 6430 2.061773 CATCTCTACAATTAGGGCGCG 58.938 52.381 0.00 0.00 0.00 6.86
2454 6434 2.089433 CTACAATTAGGGCGCGCACG 62.089 60.000 34.42 18.93 44.07 5.34
2493 6473 9.260002 ACAAGCAAAATTATAACAGACCAAAAG 57.740 29.630 0.00 0.00 0.00 2.27
2545 6544 3.548770 TCCGAAGACTACGTCCATATGT 58.451 45.455 1.24 0.00 32.18 2.29
2621 6620 3.871775 GACACTCCGGTCGTTGTAA 57.128 52.632 0.00 0.00 0.00 2.41
2783 6898 6.653320 AGCAAAACTTATACGAAACTCCATCA 59.347 34.615 0.00 0.00 0.00 3.07
2849 6964 2.325583 TGGATGCGACTTGGATAACC 57.674 50.000 0.00 0.00 0.00 2.85
2970 7085 2.027192 GCTTGTCCAAGGATCACACCTA 60.027 50.000 8.97 0.00 39.62 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.183686 AATCATGCACGCGCTGCC 62.184 61.111 24.00 11.53 46.51 4.85
31 32 0.931662 GCAATATGCTTTCGCGCCTG 60.932 55.000 0.00 0.00 40.96 4.85
37 38 1.069906 GTAGGGCGCAATATGCTTTCG 60.070 52.381 10.83 0.00 42.25 3.46
45 47 0.878523 GCATGTCGTAGGGCGCAATA 60.879 55.000 10.83 0.00 41.07 1.90
51 53 0.461870 TGATGTGCATGTCGTAGGGC 60.462 55.000 0.00 0.00 0.00 5.19
90 92 2.752354 CCACAAAACTTGGTGACAGTCA 59.248 45.455 0.00 0.00 44.54 3.41
91 93 2.752903 ACCACAAAACTTGGTGACAGTC 59.247 45.455 0.00 0.00 46.09 3.51
151 154 4.273148 ACTTACGATCTCTTTGGCTGTT 57.727 40.909 0.00 0.00 0.00 3.16
184 187 5.830912 TCAATCAATCAACAAGTTGGACAC 58.169 37.500 12.54 0.00 40.78 3.67
269 276 1.893315 ATGGTTTGCCCTCTAGCCTA 58.107 50.000 0.00 0.00 0.00 3.93
322 333 5.007034 TCATGTCGTCCCACACATAATTTT 58.993 37.500 0.00 0.00 31.78 1.82
402 415 8.895845 CAACAATAGTTCAAATTCAACGAGAAG 58.104 33.333 0.00 0.00 36.22 2.85
483 502 5.048364 TCAAACCCGACGAAATTCATCAAAT 60.048 36.000 0.00 0.00 0.00 2.32
527 549 5.344884 CGCATATATTTCAAACCGGGTTTT 58.655 37.500 22.13 10.75 33.10 2.43
563 585 4.217112 GGATATGGGAGCCGGTCT 57.783 61.111 1.90 0.00 0.00 3.85
607 629 0.535335 TTTCCTTCCTCATCCGTCCG 59.465 55.000 0.00 0.00 0.00 4.79
613 635 3.691609 ACTCGCAAATTTCCTTCCTCATC 59.308 43.478 0.00 0.00 0.00 2.92
633 655 1.227853 GGCACCTCAAACGGTCACT 60.228 57.895 0.00 0.00 34.29 3.41
647 669 5.582689 AGCAAATTAGACAATTAGGGCAC 57.417 39.130 0.00 0.00 33.09 5.01
677 699 4.698201 TTTAGAGGGTGACATGTTGTGA 57.302 40.909 0.00 0.00 0.00 3.58
679 701 5.304686 TCTTTTAGAGGGTGACATGTTGT 57.695 39.130 0.00 0.00 0.00 3.32
704 730 1.599797 CCTTCTTCGTGGCGGGTTT 60.600 57.895 0.00 0.00 0.00 3.27
723 749 3.165071 AGGCAAAAGTATTGAAGGGTGG 58.835 45.455 0.00 0.00 0.00 4.61
875 938 3.119352 GGATTCAGACAGCATTTGGGTTC 60.119 47.826 0.00 0.00 0.00 3.62
1152 1226 2.343163 CTGCACGGACGATCTCCTCC 62.343 65.000 0.00 1.51 36.80 4.30
1285 1847 1.129437 GCCGTCGTTCGAGTAGTACTT 59.871 52.381 0.00 0.00 42.86 2.24
1286 1848 0.723981 GCCGTCGTTCGAGTAGTACT 59.276 55.000 1.37 1.37 42.86 2.73
1644 2209 2.582498 CCGCCGACGTTCTCCATC 60.582 66.667 0.00 0.00 37.70 3.51
1753 2321 2.165030 CCATCTGATGCCCAAAGTTGAC 59.835 50.000 12.17 0.00 0.00 3.18
2211 2783 2.212652 CCTTGCAGCGCTGATAATGTA 58.787 47.619 40.21 10.45 0.00 2.29
2228 2800 8.792633 TCTTGAAATTGACGAAATAATCACCTT 58.207 29.630 0.00 0.00 28.94 3.50
2266 2838 5.215903 ACTACGAATGCATGAGAAGATACG 58.784 41.667 0.00 0.00 0.00 3.06
2269 2841 5.911752 AGAACTACGAATGCATGAGAAGAT 58.088 37.500 0.00 0.00 0.00 2.40
2450 6430 4.624024 TGCTTGTGACTTATTAGTACGTGC 59.376 41.667 0.00 0.00 33.84 5.34
2493 6473 3.087781 ACCCTCTTCGTTGTAGGTCTAC 58.912 50.000 1.43 1.43 36.63 2.59
2621 6620 8.397148 CACATTGGTTTTGCTTTTAGTCATTTT 58.603 29.630 0.00 0.00 0.00 1.82
2783 6898 3.494749 CCAGCATGTTTGGTCATTGGTTT 60.495 43.478 9.48 0.00 0.00 3.27
2849 6964 8.440059 TCCATTATATTTTGCGCTATAAAGTCG 58.560 33.333 9.73 0.36 0.00 4.18
2888 7003 7.351414 TGTTTTCGTCATGAAGAGACTATTG 57.649 36.000 19.76 0.00 37.99 1.90
2970 7085 4.307032 AGAACATGTGATACCTTTGCCT 57.693 40.909 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.