Multiple sequence alignment - TraesCS7B01G111500

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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 TraesCS7B01G111500 chr7B 100.000 3434 0 0 1 3434 128072040 128068607 0.000000e+00 6342.0
1 TraesCS7B01G111500 chr7B 97.356 3442 77 8 1 3434 127775802 127772367 0.000000e+00 5840.0
2 TraesCS7B01G111500 chr7B 97.615 2683 58 2 1 2678 127654281 127651600 0.000000e+00 4595.0
3 TraesCS7B01G111500 chr7B 95.172 1947 61 10 761 2678 128436445 128438387 0.000000e+00 3044.0
4 TraesCS7B01G111500 chr7B 85.456 942 77 20 1762 2678 135035722 135034816 0.000000e+00 926.0
5 TraesCS7B01G111500 chr7B 85.391 486 34 16 2228 2678 134493384 134493867 1.440000e-128 470.0
6 TraesCS7B01G111500 chr7B 77.163 289 49 13 411 698 651193647 651193375 5.940000e-33 152.0
7 TraesCS7B01G111500 chr7D 90.189 1957 133 32 760 2678 164752991 164751056 0.000000e+00 2495.0
8 TraesCS7B01G111500 chr7D 89.446 1535 106 23 1191 2678 165118317 165119842 0.000000e+00 1886.0
9 TraesCS7B01G111500 chr7D 86.957 943 81 23 1762 2678 169421831 169420905 0.000000e+00 1022.0
10 TraesCS7B01G111500 chr7D 83.737 744 101 15 950 1680 169440989 169440253 0.000000e+00 686.0
11 TraesCS7B01G111500 chr7D 88.608 79 9 0 587 665 260698117 260698039 2.820000e-16 97.1
12 TraesCS7B01G111500 chr7A 90.159 1951 136 26 771 2678 166869089 166871026 0.000000e+00 2488.0
13 TraesCS7B01G111500 chr7A 90.430 1860 132 24 774 2599 166491748 166489901 0.000000e+00 2407.0
14 TraesCS7B01G111500 chr7A 87.082 898 64 18 1802 2678 166595046 166594180 0.000000e+00 968.0
15 TraesCS7B01G111500 chr7A 82.994 835 115 18 911 1728 171439523 171438699 0.000000e+00 730.0
16 TraesCS7B01G111500 chr7A 89.753 527 47 7 2726 3248 527158635 527158112 0.000000e+00 667.0
17 TraesCS7B01G111500 chr7A 87.121 396 30 12 1 376 166492580 166492186 2.450000e-116 429.0
18 TraesCS7B01G111500 chr7A 87.121 396 30 12 1 376 166868260 166868654 2.450000e-116 429.0
19 TraesCS7B01G111500 chr7A 76.817 289 50 13 411 698 726503833 726504105 2.760000e-31 147.0
20 TraesCS7B01G111500 chrUn 88.340 789 58 14 1916 2678 218480268 218481048 0.000000e+00 917.0
21 TraesCS7B01G111500 chrUn 93.478 46 3 0 1762 1807 244607775 244607820 6.150000e-08 69.4
22 TraesCS7B01G111500 chrUn 100.000 29 0 0 2735 2763 311079739 311079711 2.000000e-03 54.7
23 TraesCS7B01G111500 chr6A 83.745 769 101 14 972 1722 124423003 124423765 0.000000e+00 706.0
24 TraesCS7B01G111500 chr6A 83.484 775 104 14 972 1728 124916868 124916100 0.000000e+00 701.0
25 TraesCS7B01G111500 chr5A 87.339 545 61 8 2725 3265 44406444 44406984 4.870000e-173 617.0
26 TraesCS7B01G111500 chr5A 76.825 315 56 13 411 724 570379416 570379118 9.860000e-36 161.0
27 TraesCS7B01G111500 chr1B 90.108 465 41 4 2743 3205 175675004 175674543 1.760000e-167 599.0
28 TraesCS7B01G111500 chr1B 80.515 272 36 10 3148 3413 679718695 679718955 3.500000e-45 193.0
29 TraesCS7B01G111500 chr2B 89.269 438 41 6 2830 3265 739539883 739539450 8.380000e-151 544.0
30 TraesCS7B01G111500 chr2B 84.416 154 21 2 559 712 131882990 131883140 7.680000e-32 148.0
31 TraesCS7B01G111500 chr1A 88.813 438 44 5 2830 3265 97869246 97869680 1.810000e-147 532.0
32 TraesCS7B01G111500 chr1A 88.636 440 43 7 2830 3265 491373689 491373253 2.350000e-146 529.0
33 TraesCS7B01G111500 chr1A 90.291 206 18 2 2726 2929 588379120 588379325 5.650000e-68 268.0
34 TraesCS7B01G111500 chr4A 88.662 441 41 9 2830 3265 651203267 651203703 2.350000e-146 529.0
35 TraesCS7B01G111500 chr4A 94.444 126 7 0 3291 3416 648656227 648656352 9.720000e-46 195.0
36 TraesCS7B01G111500 chr5B 84.837 521 68 10 2734 3248 636335207 636334692 6.570000e-142 514.0
37 TraesCS7B01G111500 chr1D 75.873 315 59 14 411 724 67973430 67973132 9.930000e-31 145.0
38 TraesCS7B01G111500 chr6B 75.210 238 42 11 429 665 399048849 399049070 2.820000e-16 97.1
39 TraesCS7B01G111500 chr6D 95.652 46 2 0 1762 1807 103052603 103052648 1.320000e-09 75.0


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 TraesCS7B01G111500 chr7B 128068607 128072040 3433 True 6342.0 6342 100.0000 1 3434 1 chr7B.!!$R3 3433
1 TraesCS7B01G111500 chr7B 127772367 127775802 3435 True 5840.0 5840 97.3560 1 3434 1 chr7B.!!$R2 3433
2 TraesCS7B01G111500 chr7B 127651600 127654281 2681 True 4595.0 4595 97.6150 1 2678 1 chr7B.!!$R1 2677
3 TraesCS7B01G111500 chr7B 128436445 128438387 1942 False 3044.0 3044 95.1720 761 2678 1 chr7B.!!$F1 1917
4 TraesCS7B01G111500 chr7B 135034816 135035722 906 True 926.0 926 85.4560 1762 2678 1 chr7B.!!$R4 916
5 TraesCS7B01G111500 chr7D 164751056 164752991 1935 True 2495.0 2495 90.1890 760 2678 1 chr7D.!!$R1 1918
6 TraesCS7B01G111500 chr7D 165118317 165119842 1525 False 1886.0 1886 89.4460 1191 2678 1 chr7D.!!$F1 1487
7 TraesCS7B01G111500 chr7D 169420905 169421831 926 True 1022.0 1022 86.9570 1762 2678 1 chr7D.!!$R2 916
8 TraesCS7B01G111500 chr7D 169440253 169440989 736 True 686.0 686 83.7370 950 1680 1 chr7D.!!$R3 730
9 TraesCS7B01G111500 chr7A 166868260 166871026 2766 False 1458.5 2488 88.6400 1 2678 2 chr7A.!!$F2 2677
10 TraesCS7B01G111500 chr7A 166489901 166492580 2679 True 1418.0 2407 88.7755 1 2599 2 chr7A.!!$R4 2598
11 TraesCS7B01G111500 chr7A 166594180 166595046 866 True 968.0 968 87.0820 1802 2678 1 chr7A.!!$R1 876
12 TraesCS7B01G111500 chr7A 171438699 171439523 824 True 730.0 730 82.9940 911 1728 1 chr7A.!!$R2 817
13 TraesCS7B01G111500 chr7A 527158112 527158635 523 True 667.0 667 89.7530 2726 3248 1 chr7A.!!$R3 522
14 TraesCS7B01G111500 chrUn 218480268 218481048 780 False 917.0 917 88.3400 1916 2678 1 chrUn.!!$F1 762
15 TraesCS7B01G111500 chr6A 124423003 124423765 762 False 706.0 706 83.7450 972 1722 1 chr6A.!!$F1 750
16 TraesCS7B01G111500 chr6A 124916100 124916868 768 True 701.0 701 83.4840 972 1728 1 chr6A.!!$R1 756
17 TraesCS7B01G111500 chr5A 44406444 44406984 540 False 617.0 617 87.3390 2725 3265 1 chr5A.!!$F1 540
18 TraesCS7B01G111500 chr5B 636334692 636335207 515 True 514.0 514 84.8370 2734 3248 1 chr5B.!!$R1 514

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
223 247 1.270732 GCACCTCCAGGATGAGCTATG 60.271 57.143 6.87 0.0 39.69 2.23 F
1968 2292 1.801178 GAAGAGGTTGTCTTTGAGCCG 59.199 52.381 0.00 0.0 46.21 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2149 2473 0.806868 CAATCGGACTGCAGCATGTT 59.193 50.0 15.27 0.0 39.31 2.71 R
2834 3211 5.948758 TGCAAATGACCCACATGTATTTCTA 59.051 36.0 0.00 0.0 39.39 2.10 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 5.153950 AGTCACCAGGAATTCTGTAAGTC 57.846 43.478 5.23 0.00 41.83 3.01
103 109 2.076863 GTTACAGGCCTAGCAACACAG 58.923 52.381 3.98 0.00 0.00 3.66
125 136 2.562738 GGCTCCACAAAAGTGGCTTTAT 59.437 45.455 9.72 0.00 43.90 1.40
223 247 1.270732 GCACCTCCAGGATGAGCTATG 60.271 57.143 6.87 0.00 39.69 2.23
237 261 6.939163 GGATGAGCTATGATTTGTTCCAGTAT 59.061 38.462 0.00 0.00 0.00 2.12
627 722 2.253603 GTTGAATTTGTCTGATGCGCC 58.746 47.619 4.18 0.00 0.00 6.53
702 797 4.336993 AGATTTTTGCGTGTTTCCTGTGTA 59.663 37.500 0.00 0.00 0.00 2.90
886 1094 2.124736 GCCTGCAAGCCCATCGTA 60.125 61.111 0.00 0.00 0.00 3.43
930 1156 2.281070 CCCAGATCCCAATCGCCG 60.281 66.667 0.00 0.00 36.97 6.46
1829 2129 5.876651 TCTTCCTCAGATAATAAGCAGCA 57.123 39.130 0.00 0.00 0.00 4.41
1860 2160 3.454858 AGCTACTGAGATTTCCTCCCAA 58.545 45.455 0.00 0.00 41.25 4.12
1864 2164 4.227864 ACTGAGATTTCCTCCCAATCAC 57.772 45.455 0.00 0.00 41.25 3.06
1968 2292 1.801178 GAAGAGGTTGTCTTTGAGCCG 59.199 52.381 0.00 0.00 46.21 5.52
2061 2385 2.742589 GGAAGACGACCCAATTGAAGTC 59.257 50.000 7.12 12.17 0.00 3.01
2095 2419 2.111043 CCAACACTGGCGTGGAGT 59.889 61.111 12.66 0.00 45.50 3.85
2128 2452 3.371965 GAACCTCTGTACCTGGATACCA 58.628 50.000 0.00 0.00 0.00 3.25
2149 2473 1.300963 GACCAAGGCATGCTGGAGA 59.699 57.895 27.64 0.00 36.49 3.71
2195 2522 0.107456 CCAATGTCGGGATCAGAGGG 59.893 60.000 0.00 0.00 0.00 4.30
2232 2559 1.683938 CCTGCCTTCCATGATGCTGAA 60.684 52.381 0.00 0.00 0.00 3.02
2613 2970 4.138290 TGGATTTTCTGAACCTTGCGTTA 58.862 39.130 0.00 0.00 33.74 3.18
2689 3063 2.555670 CCTTTTTGTACCCCGGGAATGA 60.556 50.000 26.32 0.00 0.00 2.57
2696 3070 0.999712 ACCCCGGGAATGAAGAATGT 59.000 50.000 26.32 3.48 0.00 2.71
2697 3071 2.201830 ACCCCGGGAATGAAGAATGTA 58.798 47.619 26.32 0.00 0.00 2.29
2912 3292 5.012328 AGAATGTTCATAGAAGACCGGTC 57.988 43.478 27.67 27.67 0.00 4.79
3234 3617 8.099364 ACGAACTCACTCATTTCAATTAACAT 57.901 30.769 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
125 136 2.957680 TGCAAGTCATGGCTGAAGAAAA 59.042 40.909 0.00 0.00 31.85 2.29
223 247 7.872113 AGAATCCTTCATACTGGAACAAATC 57.128 36.000 0.00 0.00 38.70 2.17
237 261 9.748708 CAGAAATTGTACAAAAAGAATCCTTCA 57.251 29.630 13.23 0.00 0.00 3.02
627 722 2.363683 GGAACAAGATCCTTGGCAGAG 58.636 52.381 10.91 0.00 36.50 3.35
672 767 1.336755 ACACGCAAAAATCTCACCACC 59.663 47.619 0.00 0.00 0.00 4.61
827 1035 2.761767 TCCAAATAGAATCACGGACGGA 59.238 45.455 0.00 0.00 0.00 4.69
837 1045 5.949735 ACGCGTCAAATTTCCAAATAGAAT 58.050 33.333 5.58 0.00 0.00 2.40
878 1086 4.921515 CCGGCGATATTTATATACGATGGG 59.078 45.833 9.30 0.00 0.00 4.00
886 1094 2.504175 AGGTGGCCGGCGATATTTATAT 59.496 45.455 22.54 0.00 0.00 0.86
947 1178 2.225066 GCTAGCTAGCTAGGAAGGGGTA 60.225 54.545 39.60 13.88 45.62 3.69
1860 2160 1.696336 ACAGACTCCAGCACAAGTGAT 59.304 47.619 4.04 0.00 0.00 3.06
1864 2164 2.141517 CTTGACAGACTCCAGCACAAG 58.858 52.381 0.00 0.00 0.00 3.16
1947 2271 2.548920 CGGCTCAAAGACAACCTCTTCT 60.549 50.000 0.00 0.00 38.37 2.85
1968 2292 3.489229 GCAAATCGGAAATAGGCTCCAAC 60.489 47.826 0.00 0.00 32.77 3.77
1997 2321 1.234821 GTCAAAACCATCTGCGTCCA 58.765 50.000 0.00 0.00 0.00 4.02
2061 2385 4.803426 GCTCCAGTGACCGGCTCG 62.803 72.222 0.00 0.00 0.00 5.03
2095 2419 1.152830 GAGGTTCCTGTTGGCCCAA 59.847 57.895 0.00 0.00 0.00 4.12
2128 2452 1.380785 CCAGCATGCCTTGGTCCAT 60.381 57.895 15.66 0.00 32.51 3.41
2149 2473 0.806868 CAATCGGACTGCAGCATGTT 59.193 50.000 15.27 0.00 39.31 2.71
2195 2522 3.747976 GGTTGTGCATGGCCCGAC 61.748 66.667 0.00 0.00 0.00 4.79
2232 2559 3.619979 CGGCATTGTACCTCTTCTCCTTT 60.620 47.826 0.00 0.00 0.00 3.11
2262 2589 1.424493 GAAGCGATGGAGCGTCAAGG 61.424 60.000 0.00 0.00 43.40 3.61
2511 2859 1.374252 CAGAGGTACACGTGTGGCC 60.374 63.158 30.83 28.35 34.19 5.36
2613 2970 3.430453 ACAGAGCAGAAGAAGTAGAGCT 58.570 45.455 0.00 0.00 34.61 4.09
2834 3211 5.948758 TGCAAATGACCCACATGTATTTCTA 59.051 36.000 0.00 0.00 39.39 2.10
2912 3292 7.358066 AGAGAGAATATTTTAACATGCATGCG 58.642 34.615 26.53 4.36 0.00 4.73


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

AutoCloner maintained by Alex Coulton.