Multiple sequence alignment - TraesCS1A01G274200

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 TraesCS1A01G274200 chr1A 100.000 3785 0 0 1 3785 468463379 468459595 0.000000e+00 6990.0
1 TraesCS1A01G274200 chr1A 98.996 3785 35 1 1 3785 468412205 468408424 0.000000e+00 6776.0
2 TraesCS1A01G274200 chr1A 94.173 738 43 0 1 738 276261847 276261110 0.000000e+00 1125.0
3 TraesCS1A01G274200 chr1A 96.273 644 20 3 3143 3785 23414976 23414336 0.000000e+00 1053.0
4 TraesCS1A01G274200 chr1A 81.818 451 46 21 1096 1516 588664111 588664555 2.800000e-91 346.0
5 TraesCS1A01G274200 chr1A 88.186 237 27 1 1105 1340 587846020 587846256 8.000000e-72 281.0
6 TraesCS1A01G274200 chr1A 84.270 89 14 0 1827 1915 588664354 588664442 1.870000e-13 87.9
7 TraesCS1A01G274200 chr1A 94.000 50 2 1 858 906 587663666 587663617 1.460000e-09 75.0
8 TraesCS1A01G274200 chr1D 94.906 1433 39 13 753 2155 368676061 368674633 0.000000e+00 2211.0
9 TraesCS1A01G274200 chr1D 97.232 542 12 3 2595 3134 368674293 368673753 0.000000e+00 915.0
10 TraesCS1A01G274200 chr1D 92.975 484 28 2 3308 3785 450583917 450584400 0.000000e+00 701.0
11 TraesCS1A01G274200 chr1D 95.963 322 13 0 2266 2587 368674648 368674327 1.200000e-144 523.0
12 TraesCS1A01G274200 chr1D 82.672 479 47 21 997 1451 489301825 489301359 3.540000e-105 392.0
13 TraesCS1A01G274200 chr1D 81.876 469 51 12 1011 1451 489755856 489756318 7.730000e-97 364.0
14 TraesCS1A01G274200 chr1D 82.785 395 48 14 963 1351 488589351 488589731 6.060000e-88 335.0
15 TraesCS1A01G274200 chr1D 85.616 292 26 11 1097 1376 488505201 488504914 3.700000e-75 292.0
16 TraesCS1A01G274200 chr1D 89.130 92 8 2 2095 2185 407673101 407673011 3.090000e-21 113.0
17 TraesCS1A01G274200 chr1D 84.298 121 12 5 2747 2860 488513036 488512916 1.110000e-20 111.0
18 TraesCS1A01G274200 chr1D 96.429 56 2 0 846 901 488544153 488544098 4.030000e-15 93.5
19 TraesCS1A01G274200 chrUn 93.089 738 50 1 1 738 385763872 385764608 0.000000e+00 1079.0
20 TraesCS1A01G274200 chrUn 92.954 738 51 1 1 738 385776869 385776133 0.000000e+00 1074.0
21 TraesCS1A01G274200 chrUn 78.720 625 49 42 838 1401 205602900 205602299 1.300000e-89 340.0
22 TraesCS1A01G274200 chrUn 75.000 256 43 14 2607 2844 8748857 8748605 8.650000e-17 99.0
23 TraesCS1A01G274200 chrUn 84.091 88 7 4 1672 1759 111025288 111025368 1.130000e-10 78.7
24 TraesCS1A01G274200 chr3B 93.484 706 41 3 14 718 25915416 25914715 0.000000e+00 1044.0
25 TraesCS1A01G274200 chr3B 93.484 706 41 3 14 718 26051525 26050824 0.000000e+00 1044.0
26 TraesCS1A01G274200 chr3B 93.466 704 41 3 14 716 26393750 26393051 0.000000e+00 1040.0
27 TraesCS1A01G274200 chr3B 92.918 706 45 3 14 718 26240527 26239826 0.000000e+00 1022.0
28 TraesCS1A01G274200 chr6B 91.217 649 53 3 95 739 711318152 711317504 0.000000e+00 880.0
29 TraesCS1A01G274200 chr6B 86.985 461 25 12 3337 3785 715685812 715686249 1.580000e-133 486.0
30 TraesCS1A01G274200 chr5B 93.018 487 25 1 3308 3785 37035276 37034790 0.000000e+00 702.0
31 TraesCS1A01G274200 chr5B 94.286 35 1 1 1677 1710 12295635 12295601 7.000000e-03 52.8
32 TraesCS1A01G274200 chr5A 95.778 379 13 3 3129 3505 540383482 540383859 3.230000e-170 608.0
33 TraesCS1A01G274200 chr5A 89.604 202 5 3 3396 3597 540383852 540384037 3.780000e-60 243.0
34 TraesCS1A01G274200 chr5A 88.660 97 11 0 2096 2192 407937800 407937704 6.640000e-23 119.0
35 TraesCS1A01G274200 chr7B 87.302 504 38 15 3308 3785 585868245 585867742 1.540000e-153 553.0
36 TraesCS1A01G274200 chr7B 83.505 485 63 8 3308 3776 90516783 90517266 1.610000e-118 436.0
37 TraesCS1A01G274200 chr7B 91.765 170 9 4 3143 3309 585871763 585871596 8.180000e-57 231.0
38 TraesCS1A01G274200 chr7B 90.110 91 7 2 2096 2185 605072494 605072405 2.390000e-22 117.0
39 TraesCS1A01G274200 chr1B 78.720 625 49 42 838 1401 682488128 682487527 1.300000e-89 340.0
40 TraesCS1A01G274200 chr1B 80.800 500 36 30 950 1401 680744540 680744053 1.680000e-88 337.0
41 TraesCS1A01G274200 chr1B 84.397 141 22 0 2421 2561 681076275 681076135 5.100000e-29 139.0
42 TraesCS1A01G274200 chr1B 88.764 89 10 0 2097 2185 507850378 507850466 4.000000e-20 110.0
43 TraesCS1A01G274200 chr1B 97.826 46 1 0 858 903 681802533 681802578 3.130000e-11 80.5
44 TraesCS1A01G274200 chr1B 89.796 49 3 2 841 887 682003088 682003136 1.140000e-05 62.1
45 TraesCS1A01G274200 chr2A 91.667 168 12 2 3142 3309 724411504 724411339 8.180000e-57 231.0
46 TraesCS1A01G274200 chr2A 88.690 168 15 4 3143 3309 724404702 724404866 6.410000e-48 202.0
47 TraesCS1A01G274200 chr3A 89.773 176 15 3 3135 3309 487445504 487445677 4.920000e-54 222.0
48 TraesCS1A01G274200 chr7D 88.398 181 12 5 3135 3309 254897349 254897172 3.830000e-50 209.0
49 TraesCS1A01G274200 chr4D 87.709 179 16 5 3135 3309 240931028 240931204 1.780000e-48 204.0
50 TraesCS1A01G274200 chr4D 82.353 85 8 5 1676 1760 307492699 307492622 2.440000e-07 67.6
51 TraesCS1A01G274200 chr4B 93.333 90 6 0 2096 2185 19086548 19086459 2.370000e-27 134.0
52 TraesCS1A01G274200 chr4B 94.286 35 1 1 1677 1710 639455500 639455534 7.000000e-03 52.8
53 TraesCS1A01G274200 chr3D 88.889 90 10 0 2096 2185 23667592 23667503 1.110000e-20 111.0
54 TraesCS1A01G274200 chr3D 82.927 82 7 5 1677 1758 499945097 499945171 2.440000e-07 67.6
55 TraesCS1A01G274200 chr2D 87.629 97 4 7 2095 2187 192181496 192181588 5.170000e-19 106.0
56 TraesCS1A01G274200 chr2D 83.529 85 7 5 1676 1760 534121428 534121351 5.240000e-09 73.1
57 TraesCS1A01G274200 chr5D 82.353 85 8 4 1676 1760 41816896 41816819 2.440000e-07 67.6


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 TraesCS1A01G274200 chr1A 468459595 468463379 3784 True 6990.000000 6990 100.000000 1 3785 1 chr1A.!!$R4 3784
1 TraesCS1A01G274200 chr1A 468408424 468412205 3781 True 6776.000000 6776 98.996000 1 3785 1 chr1A.!!$R3 3784
2 TraesCS1A01G274200 chr1A 276261110 276261847 737 True 1125.000000 1125 94.173000 1 738 1 chr1A.!!$R2 737
3 TraesCS1A01G274200 chr1A 23414336 23414976 640 True 1053.000000 1053 96.273000 3143 3785 1 chr1A.!!$R1 642
4 TraesCS1A01G274200 chr1D 368673753 368676061 2308 True 1216.333333 2211 96.033667 753 3134 3 chr1D.!!$R6 2381
5 TraesCS1A01G274200 chrUn 385763872 385764608 736 False 1079.000000 1079 93.089000 1 738 1 chrUn.!!$F2 737
6 TraesCS1A01G274200 chrUn 385776133 385776869 736 True 1074.000000 1074 92.954000 1 738 1 chrUn.!!$R3 737
7 TraesCS1A01G274200 chrUn 205602299 205602900 601 True 340.000000 340 78.720000 838 1401 1 chrUn.!!$R2 563
8 TraesCS1A01G274200 chr3B 25914715 25915416 701 True 1044.000000 1044 93.484000 14 718 1 chr3B.!!$R1 704
9 TraesCS1A01G274200 chr3B 26050824 26051525 701 True 1044.000000 1044 93.484000 14 718 1 chr3B.!!$R2 704
10 TraesCS1A01G274200 chr3B 26393051 26393750 699 True 1040.000000 1040 93.466000 14 716 1 chr3B.!!$R4 702
11 TraesCS1A01G274200 chr3B 26239826 26240527 701 True 1022.000000 1022 92.918000 14 718 1 chr3B.!!$R3 704
12 TraesCS1A01G274200 chr6B 711317504 711318152 648 True 880.000000 880 91.217000 95 739 1 chr6B.!!$R1 644
13 TraesCS1A01G274200 chr5A 540383482 540384037 555 False 425.500000 608 92.691000 3129 3597 2 chr5A.!!$F1 468
14 TraesCS1A01G274200 chr7B 585867742 585871763 4021 True 392.000000 553 89.533500 3143 3785 2 chr7B.!!$R2 642
15 TraesCS1A01G274200 chr1B 682487527 682488128 601 True 340.000000 340 78.720000 838 1401 1 chr1B.!!$R3 563

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
455 459 0.109226 CGTCGTCCAAGTCCTCCTTC 60.109 60.0 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3052 3156 3.733443 AAAAACAGGGCAGTCATGAAC 57.267 42.857 0.0 0.0 0.0 3.18 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
67 68 4.044825 AGAGAAGAGAACCTCTCCCACTTA 59.955 45.833 0.00 0.00 44.42 2.24
68 69 4.753186 AGAAGAGAACCTCTCCCACTTAA 58.247 43.478 0.00 0.00 44.42 1.85
77 78 1.168714 CTCCCACTTAAGCTGCCAAC 58.831 55.000 1.29 0.00 0.00 3.77
165 166 2.301870 AGTTTCATAGTGGACGGCTTCA 59.698 45.455 0.00 0.00 0.00 3.02
201 202 1.376543 CAGCAGAATCACCGCATCTT 58.623 50.000 0.00 0.00 0.00 2.40
370 371 1.541588 CTGGCTGTAGGTTTTGAAGGC 59.458 52.381 0.00 0.00 0.00 4.35
455 459 0.109226 CGTCGTCCAAGTCCTCCTTC 60.109 60.000 0.00 0.00 0.00 3.46
456 460 1.258676 GTCGTCCAAGTCCTCCTTCT 58.741 55.000 0.00 0.00 0.00 2.85
457 461 1.619332 GTCGTCCAAGTCCTCCTTCTT 59.381 52.381 0.00 0.00 0.00 2.52
653 661 2.733218 CTTGCCGCGTCGAGAACA 60.733 61.111 4.92 0.00 0.00 3.18
793 803 2.270923 CGTGCAGAGATGGATTTTCGA 58.729 47.619 0.00 0.00 0.00 3.71
3052 3156 6.305877 GTGACGTCTTGTACAGATACTTTCAG 59.694 42.308 17.92 0.00 32.60 3.02
3117 3222 3.265791 GGCTTGTCTTGACCTAGTCATG 58.734 50.000 0.00 1.47 42.40 3.07
3205 3310 7.472543 GGCAATTTCTAGAAACATCAATACGT 58.527 34.615 19.94 0.00 32.51 3.57
3750 7321 3.424565 CCGTATCAGGCGTATCGAAGTAG 60.425 52.174 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.325583 TGACTTTGTCGGCAACTTCT 57.674 45.000 0.00 0.00 34.95 2.85
67 68 4.269523 TGGCTCCGTTGGCAGCTT 62.270 61.111 0.00 0.00 37.59 3.74
201 202 0.032217 GGCCCATGGAATTTCAGGGA 60.032 55.000 19.26 0.00 40.70 4.20
414 415 1.338200 GGTCTTCGATGAGCAACCTGT 60.338 52.381 21.54 0.00 34.88 4.00
455 459 4.592942 TGATGAAGGAGTTGGGATTGAAG 58.407 43.478 0.00 0.00 0.00 3.02
456 460 4.656100 TGATGAAGGAGTTGGGATTGAA 57.344 40.909 0.00 0.00 0.00 2.69
457 461 4.043310 AGTTGATGAAGGAGTTGGGATTGA 59.957 41.667 0.00 0.00 0.00 2.57
612 619 4.858680 GCGGCCTCCTAGGGTTGC 62.859 72.222 9.46 9.15 35.37 4.17
653 661 0.909623 CCTACCACCGATCAAACCCT 59.090 55.000 0.00 0.00 0.00 4.34
3052 3156 3.733443 AAAAACAGGGCAGTCATGAAC 57.267 42.857 0.00 0.00 0.00 3.18
3165 3270 1.457823 TTGCCGTATCCCGTATCGCT 61.458 55.000 0.00 0.00 33.66 4.93
3394 6853 2.282958 AGTCTTCCCTGTCGCCGA 60.283 61.111 0.00 0.00 0.00 5.54
3404 6863 3.594134 CATGGAGTGACTTGAGTCTTCC 58.406 50.000 19.47 19.47 44.99 3.46
3555 7126 5.413309 AACCTAACATCAGTTCTCTCCTG 57.587 43.478 0.00 0.00 39.15 3.86
3564 7135 4.565652 CCACAAGCCTAACCTAACATCAGT 60.566 45.833 0.00 0.00 0.00 3.41
3750 7321 2.877582 CGTACTGTACGTGGCCGC 60.878 66.667 27.27 6.11 46.41 6.53


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

AutoCloner maintained by Alex Coulton.