Multiple sequence alignment - TraesCS7B01G161600

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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 TraesCS7B01G161600 chr7B 100.000 3618 0 0 1 3618 221893529 221889912 0.000000e+00 6682.0
1 TraesCS7B01G161600 chr7B 95.884 996 36 4 2626 3618 312432235 312431242 0.000000e+00 1607.0
2 TraesCS7B01G161600 chr7B 87.342 395 40 9 44 438 29705458 29705074 9.220000e-121 444.0
3 TraesCS7B01G161600 chr2B 98.993 2581 23 2 45 2625 113193071 113195648 0.000000e+00 4619.0
4 TraesCS7B01G161600 chr2B 96.781 994 29 2 2626 3618 390918830 390917839 0.000000e+00 1655.0
5 TraesCS7B01G161600 chr2B 92.083 240 15 2 45 284 113195975 113195740 5.790000e-88 335.0
6 TraesCS7B01G161600 chr2B 89.286 168 15 2 2626 2792 390916746 390916911 1.320000e-49 207.0
7 TraesCS7B01G161600 chr3B 97.958 2596 38 4 43 2625 492742132 492744725 0.000000e+00 4486.0
8 TraesCS7B01G161600 chr3B 96.203 1343 48 3 48 1389 622479002 622480342 0.000000e+00 2194.0
9 TraesCS7B01G161600 chr3B 96.285 996 32 3 2626 3618 432692504 432691511 0.000000e+00 1629.0
10 TraesCS7B01G161600 chr3B 84.483 580 62 21 71 649 245923848 245923296 6.830000e-152 547.0
11 TraesCS7B01G161600 chr3B 92.083 240 17 2 45 284 492745054 492744817 1.610000e-88 337.0
12 TraesCS7B01G161600 chr3B 87.356 174 20 1 2605 2778 432690405 432690576 7.920000e-47 198.0
13 TraesCS7B01G161600 chr3B 87.342 158 12 6 2623 2777 249751399 249751551 1.340000e-39 174.0
14 TraesCS7B01G161600 chr3B 86.275 102 14 0 2751 2852 583061091 583060990 1.060000e-20 111.0
15 TraesCS7B01G161600 chr3B 97.500 40 1 0 2586 2625 622480338 622480377 6.480000e-08 69.4
16 TraesCS7B01G161600 chr5B 94.815 1813 72 12 827 2625 577345620 577347424 0.000000e+00 2808.0
17 TraesCS7B01G161600 chr5B 82.692 156 5 4 672 827 577334564 577334697 6.350000e-23 119.0
18 TraesCS7B01G161600 chr5A 93.111 1800 77 21 836 2625 590667761 590669523 0.000000e+00 2593.0
19 TraesCS7B01G161600 chr5D 92.607 1826 77 27 827 2625 469718839 469720633 0.000000e+00 2571.0
20 TraesCS7B01G161600 chr5D 88.759 1023 76 15 2620 3617 478688455 478687447 0.000000e+00 1216.0
21 TraesCS7B01G161600 chr7D 89.168 997 72 21 2626 3617 64465206 64464241 0.000000e+00 1210.0
22 TraesCS7B01G161600 chr6B 94.938 731 31 3 2624 3354 515764844 515764120 0.000000e+00 1140.0
23 TraesCS7B01G161600 chr1D 87.500 1000 84 22 2626 3617 481216650 481215684 0.000000e+00 1116.0
24 TraesCS7B01G161600 chr1D 87.937 630 58 13 2702 3328 291326234 291326848 0.000000e+00 726.0
25 TraesCS7B01G161600 chr1D 93.889 360 12 2 296 646 344590628 344590986 5.320000e-148 534.0
26 TraesCS7B01G161600 chr1D 76.087 368 79 8 2122 2484 415286272 415286635 2.220000e-42 183.0
27 TraesCS7B01G161600 chr4D 92.878 674 35 7 2948 3618 437734130 437733467 0.000000e+00 966.0
28 TraesCS7B01G161600 chr2A 88.545 550 43 10 46 580 476214501 476213957 0.000000e+00 649.0
29 TraesCS7B01G161600 chr2A 87.500 256 28 3 45 300 476211797 476212048 3.530000e-75 292.0
30 TraesCS7B01G161600 chr3D 89.339 469 29 8 191 649 284207026 284206569 1.460000e-158 569.0
31 TraesCS7B01G161600 chr3D 89.223 399 22 8 46 438 284204043 284204426 2.530000e-131 479.0
32 TraesCS7B01G161600 chr3D 74.457 368 87 7 2123 2486 428762577 428762213 6.260000e-33 152.0
33 TraesCS7B01G161600 chr1A 94.167 360 11 2 296 646 444122390 444122748 1.140000e-149 540.0
34 TraesCS7B01G161600 chr1A 88.980 245 26 1 46 290 445886783 445887026 5.870000e-78 302.0
35 TraesCS7B01G161600 chr1A 75.272 368 82 8 2122 2484 512650960 512651323 2.230000e-37 167.0
36 TraesCS7B01G161600 chr1B 93.664 363 13 2 296 649 466094267 466093906 5.320000e-148 534.0
37 TraesCS7B01G161600 chr1B 90.833 360 23 2 296 646 682437264 682437622 1.180000e-129 473.0
38 TraesCS7B01G161600 chr1B 75.543 368 81 8 2122 2484 561499183 561499546 4.800000e-39 172.0
39 TraesCS7B01G161600 chr6A 82.112 464 60 13 2626 3086 605672443 605672886 3.410000e-100 375.0
40 TraesCS7B01G161600 chr6D 88.961 308 25 5 3318 3618 463528705 463528400 4.410000e-99 372.0
41 TraesCS7B01G161600 chrUn 85.205 365 35 10 3262 3618 92820535 92820182 1.240000e-94 357.0
42 TraesCS7B01G161600 chr3A 75.815 368 82 7 2123 2486 557006340 557006704 2.870000e-41 180.0


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 TraesCS7B01G161600 chr7B 221889912 221893529 3617 True 6682.0 6682 100.0000 1 3618 1 chr7B.!!$R2 3617
1 TraesCS7B01G161600 chr7B 312431242 312432235 993 True 1607.0 1607 95.8840 2626 3618 1 chr7B.!!$R3 992
2 TraesCS7B01G161600 chr2B 113193071 113195648 2577 False 4619.0 4619 98.9930 45 2625 1 chr2B.!!$F1 2580
3 TraesCS7B01G161600 chr2B 390917839 390918830 991 True 1655.0 1655 96.7810 2626 3618 1 chr2B.!!$R2 992
4 TraesCS7B01G161600 chr3B 492742132 492744725 2593 False 4486.0 4486 97.9580 43 2625 1 chr3B.!!$F3 2582
5 TraesCS7B01G161600 chr3B 432691511 432692504 993 True 1629.0 1629 96.2850 2626 3618 1 chr3B.!!$R2 992
6 TraesCS7B01G161600 chr3B 622479002 622480377 1375 False 1131.7 2194 96.8515 48 2625 2 chr3B.!!$F4 2577
7 TraesCS7B01G161600 chr3B 245923296 245923848 552 True 547.0 547 84.4830 71 649 1 chr3B.!!$R1 578
8 TraesCS7B01G161600 chr5B 577345620 577347424 1804 False 2808.0 2808 94.8150 827 2625 1 chr5B.!!$F2 1798
9 TraesCS7B01G161600 chr5A 590667761 590669523 1762 False 2593.0 2593 93.1110 836 2625 1 chr5A.!!$F1 1789
10 TraesCS7B01G161600 chr5D 469718839 469720633 1794 False 2571.0 2571 92.6070 827 2625 1 chr5D.!!$F1 1798
11 TraesCS7B01G161600 chr5D 478687447 478688455 1008 True 1216.0 1216 88.7590 2620 3617 1 chr5D.!!$R1 997
12 TraesCS7B01G161600 chr7D 64464241 64465206 965 True 1210.0 1210 89.1680 2626 3617 1 chr7D.!!$R1 991
13 TraesCS7B01G161600 chr6B 515764120 515764844 724 True 1140.0 1140 94.9380 2624 3354 1 chr6B.!!$R1 730
14 TraesCS7B01G161600 chr1D 481215684 481216650 966 True 1116.0 1116 87.5000 2626 3617 1 chr1D.!!$R1 991
15 TraesCS7B01G161600 chr1D 291326234 291326848 614 False 726.0 726 87.9370 2702 3328 1 chr1D.!!$F1 626
16 TraesCS7B01G161600 chr4D 437733467 437734130 663 True 966.0 966 92.8780 2948 3618 1 chr4D.!!$R1 670
17 TraesCS7B01G161600 chr2A 476213957 476214501 544 True 649.0 649 88.5450 46 580 1 chr2A.!!$R1 534

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
30 31 0.038526 CAGGAAGAAGGTGCGTACGT 60.039 55.0 17.9 0.0 0.0 3.57 F
976 1018 0.947244 CTGCCTACAATCGGAATGCC 59.053 55.0 0.0 0.0 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1141 1190 1.072965 GGCTCCCTTGTAGATCCCATG 59.927 57.143 0.00 0.00 0.0 3.66 R
2637 2717 0.317479 GAGCAAGTGTGGTACCGACT 59.683 55.000 7.57 8.99 35.0 4.18 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
21 22 4.773323 GGTGAACATTTCAGGAAGAAGG 57.227 45.455 0.00 0.00 41.01 3.46
22 23 4.145052 GGTGAACATTTCAGGAAGAAGGT 58.855 43.478 0.00 0.00 41.01 3.50
23 24 4.022849 GGTGAACATTTCAGGAAGAAGGTG 60.023 45.833 0.00 0.00 41.01 4.00
24 25 3.569701 TGAACATTTCAGGAAGAAGGTGC 59.430 43.478 0.00 0.00 37.57 5.01
25 26 2.154462 ACATTTCAGGAAGAAGGTGCG 58.846 47.619 0.00 0.00 37.57 5.34
26 27 2.154462 CATTTCAGGAAGAAGGTGCGT 58.846 47.619 0.00 0.00 37.57 5.24
27 28 3.244422 ACATTTCAGGAAGAAGGTGCGTA 60.244 43.478 0.00 0.00 37.57 4.42
28 29 2.450609 TTCAGGAAGAAGGTGCGTAC 57.549 50.000 0.00 0.00 0.00 3.67
29 30 0.242825 TCAGGAAGAAGGTGCGTACG 59.757 55.000 11.84 11.84 0.00 3.67
30 31 0.038526 CAGGAAGAAGGTGCGTACGT 60.039 55.000 17.90 0.00 0.00 3.57
31 32 1.200716 CAGGAAGAAGGTGCGTACGTA 59.799 52.381 17.90 10.06 0.00 3.57
32 33 1.888512 AGGAAGAAGGTGCGTACGTAA 59.111 47.619 17.90 2.64 0.00 3.18
33 34 1.988467 GGAAGAAGGTGCGTACGTAAC 59.012 52.381 13.96 13.96 0.00 2.50
34 35 2.352127 GGAAGAAGGTGCGTACGTAACT 60.352 50.000 18.70 18.70 0.00 2.24
35 36 3.119849 GGAAGAAGGTGCGTACGTAACTA 60.120 47.826 24.29 0.00 0.00 2.24
36 37 3.477899 AGAAGGTGCGTACGTAACTAC 57.522 47.619 24.29 11.37 0.00 2.73
37 38 3.077359 AGAAGGTGCGTACGTAACTACT 58.923 45.455 24.29 9.93 0.00 2.57
38 39 3.126000 AGAAGGTGCGTACGTAACTACTC 59.874 47.826 24.29 18.18 0.00 2.59
39 40 2.704572 AGGTGCGTACGTAACTACTCT 58.295 47.619 22.84 7.80 0.00 3.24
40 41 3.861840 AGGTGCGTACGTAACTACTCTA 58.138 45.455 22.84 0.00 0.00 2.43
41 42 3.619038 AGGTGCGTACGTAACTACTCTAC 59.381 47.826 22.84 0.00 0.00 2.59
976 1018 0.947244 CTGCCTACAATCGGAATGCC 59.053 55.000 0.00 0.00 0.00 4.40
1141 1190 2.507769 GCAATGGCGCCTTTGCTC 60.508 61.111 46.86 31.82 46.67 4.26
1350 1400 1.741770 GTCGGCTCGGCTGTCATTT 60.742 57.895 4.89 0.00 36.18 2.32
1461 1527 3.579335 TGTTGTATGCACGTGTAGCTA 57.421 42.857 18.38 0.00 0.00 3.32
2637 2717 1.555967 GCTGGGGGAGTTAATTGCAA 58.444 50.000 0.00 0.00 0.00 4.08
2640 2720 2.755103 CTGGGGGAGTTAATTGCAAGTC 59.245 50.000 1.02 0.00 0.00 3.01
2664 2744 1.768870 ACCACACTTGCTCACCTACTT 59.231 47.619 0.00 0.00 0.00 2.24
2694 2775 1.257743 ACCACTACTCGTGCATGTCT 58.742 50.000 5.68 0.00 42.42 3.41
2695 2776 1.202582 ACCACTACTCGTGCATGTCTC 59.797 52.381 5.68 0.00 42.42 3.36
2778 2859 4.282950 GTATTGACGACGTATCTGACCA 57.717 45.455 0.00 0.00 0.00 4.02
2779 2860 4.856664 GTATTGACGACGTATCTGACCAT 58.143 43.478 0.00 0.00 0.00 3.55
3160 3278 4.660938 GTCAAACCCCGCTGCCCT 62.661 66.667 0.00 0.00 0.00 5.19
3346 3471 3.580904 GTGACGAGCACCACACTAA 57.419 52.632 0.00 0.00 41.78 2.24
3561 3688 7.919091 CCAACTCAGAGTTACTGCGTATATTTA 59.081 37.037 15.73 0.00 42.69 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.022849 CACCTTCTTCCTGAAATGTTCACC 60.023 45.833 0.00 0.00 35.46 4.02
1 2 4.557496 GCACCTTCTTCCTGAAATGTTCAC 60.557 45.833 0.00 0.00 35.46 3.18
2 3 3.569701 GCACCTTCTTCCTGAAATGTTCA 59.430 43.478 0.00 0.00 38.17 3.18
3 4 3.365364 CGCACCTTCTTCCTGAAATGTTC 60.365 47.826 0.00 0.00 33.79 3.18
4 5 2.554032 CGCACCTTCTTCCTGAAATGTT 59.446 45.455 0.00 0.00 33.79 2.71
5 6 2.154462 CGCACCTTCTTCCTGAAATGT 58.846 47.619 0.00 0.00 33.79 2.71
6 7 2.154462 ACGCACCTTCTTCCTGAAATG 58.846 47.619 0.00 0.00 33.79 2.32
7 8 2.568623 ACGCACCTTCTTCCTGAAAT 57.431 45.000 0.00 0.00 33.79 2.17
8 9 2.762745 GTACGCACCTTCTTCCTGAAA 58.237 47.619 0.00 0.00 33.79 2.69
9 10 1.336517 CGTACGCACCTTCTTCCTGAA 60.337 52.381 0.52 0.00 0.00 3.02
10 11 0.242825 CGTACGCACCTTCTTCCTGA 59.757 55.000 0.52 0.00 0.00 3.86
11 12 0.038526 ACGTACGCACCTTCTTCCTG 60.039 55.000 16.72 0.00 0.00 3.86
12 13 1.538047 TACGTACGCACCTTCTTCCT 58.462 50.000 16.72 0.00 0.00 3.36
13 14 1.988467 GTTACGTACGCACCTTCTTCC 59.012 52.381 16.72 0.00 0.00 3.46
14 15 2.938869 AGTTACGTACGCACCTTCTTC 58.061 47.619 16.72 0.00 0.00 2.87
15 16 3.503748 AGTAGTTACGTACGCACCTTCTT 59.496 43.478 16.72 0.00 0.00 2.52
16 17 3.077359 AGTAGTTACGTACGCACCTTCT 58.923 45.455 16.72 8.40 0.00 2.85
17 18 3.126000 AGAGTAGTTACGTACGCACCTTC 59.874 47.826 16.72 9.90 0.00 3.46
18 19 3.077359 AGAGTAGTTACGTACGCACCTT 58.923 45.455 16.72 0.00 0.00 3.50
19 20 2.704572 AGAGTAGTTACGTACGCACCT 58.295 47.619 16.72 10.60 0.00 4.00
20 21 3.542291 CGTAGAGTAGTTACGTACGCACC 60.542 52.174 16.72 2.64 39.13 5.01
21 22 3.588318 CGTAGAGTAGTTACGTACGCAC 58.412 50.000 16.72 12.63 39.13 5.34
22 23 3.907178 CGTAGAGTAGTTACGTACGCA 57.093 47.619 16.72 0.00 39.13 5.24
37 38 5.706916 ACAGCGAATTTTTCTCTACGTAGA 58.293 37.500 23.34 23.34 0.00 2.59
38 39 6.196724 CCTACAGCGAATTTTTCTCTACGTAG 59.803 42.308 16.73 16.73 0.00 3.51
39 40 6.032094 CCTACAGCGAATTTTTCTCTACGTA 58.968 40.000 0.00 0.00 0.00 3.57
40 41 4.863131 CCTACAGCGAATTTTTCTCTACGT 59.137 41.667 0.00 0.00 0.00 3.57
41 42 4.863131 ACCTACAGCGAATTTTTCTCTACG 59.137 41.667 0.00 0.00 0.00 3.51
173 175 2.351726 GCCAAGTCAGCAAATACGTAGG 59.648 50.000 0.08 0.00 0.00 3.18
276 281 3.372954 CATTGTTCCGGCGTTTTTACAA 58.627 40.909 6.01 8.83 0.00 2.41
277 282 2.859032 GCATTGTTCCGGCGTTTTTACA 60.859 45.455 6.01 0.00 0.00 2.41
976 1018 7.697352 TCAAATTGCAGTTGTTGTTTATCTG 57.303 32.000 10.87 0.00 0.00 2.90
1141 1190 1.072965 GGCTCCCTTGTAGATCCCATG 59.927 57.143 0.00 0.00 0.00 3.66
1350 1400 7.774625 TGTCAGGAATGTGCATATTTCAGATAA 59.225 33.333 16.01 4.65 0.00 1.75
2042 2121 1.144716 GATCAGCTCGTCCATGCCA 59.855 57.895 0.00 0.00 0.00 4.92
2244 2323 2.974698 GCACCACGACAGCAGCTT 60.975 61.111 0.00 0.00 0.00 3.74
2637 2717 0.317479 GAGCAAGTGTGGTACCGACT 59.683 55.000 7.57 8.99 35.00 4.18
2640 2720 0.949105 GGTGAGCAAGTGTGGTACCG 60.949 60.000 7.57 0.00 35.00 4.02
2664 2744 4.330894 CACGAGTAGTGGTACTGATTCGTA 59.669 45.833 13.01 0.00 46.77 3.43
2694 2775 1.684450 TGAGTTGGTACTGAACTGCGA 59.316 47.619 13.45 0.00 33.71 5.10
2695 2776 2.061773 CTGAGTTGGTACTGAACTGCG 58.938 52.381 13.45 3.58 33.71 5.18
2778 2859 3.567579 CTGGCACACGGGTCCCAAT 62.568 63.158 0.03 0.00 0.00 3.16
2779 2860 4.263572 CTGGCACACGGGTCCCAA 62.264 66.667 0.03 0.00 0.00 4.12
2882 2971 2.440247 GCAAGCCCGGCAAGGTAT 60.440 61.111 13.15 0.00 38.74 2.73
2932 3030 3.506096 CCGACGAGCCAGCGACTA 61.506 66.667 0.00 0.00 34.83 2.59
3181 3299 3.560481 GCTCGATCGGAATATCGGATCTA 59.440 47.826 16.41 11.65 45.45 1.98
3333 3458 1.607148 GTGGGTTTTAGTGTGGTGCTC 59.393 52.381 0.00 0.00 0.00 4.26
3346 3471 0.963355 ATATTGCCGTGCGTGGGTTT 60.963 50.000 0.00 0.00 0.00 3.27
3450 3577 2.088104 TGTGGTCCTGAGTGAAGTCT 57.912 50.000 0.00 0.00 0.00 3.24
3452 3579 1.271054 GCATGTGGTCCTGAGTGAAGT 60.271 52.381 0.00 0.00 0.00 3.01
3561 3688 9.988350 CGAGTAACTCTGCATTAAAAATACAAT 57.012 29.630 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.