Multiple sequence alignment - TraesCS1B01G070800

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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 TraesCS1B01G070800 chr1B 100.000 2802 0 0 1 2802 55976191 55978992 0.000000e+00 5175.0
1 TraesCS1B01G070800 chr1B 98.236 1984 25 3 820 2802 55998277 56000251 0.000000e+00 3461.0
2 TraesCS1B01G070800 chr1B 91.642 1699 125 8 859 2552 56140945 56139259 0.000000e+00 2335.0
3 TraesCS1B01G070800 chr1B 97.059 1224 24 4 846 2066 56016955 56018169 0.000000e+00 2050.0
4 TraesCS1B01G070800 chr1B 96.348 712 19 5 1 707 56015945 56016654 0.000000e+00 1164.0
5 TraesCS1B01G070800 chr1B 87.305 898 99 12 830 1724 55964135 55965020 0.000000e+00 1013.0
6 TraesCS1B01G070800 chr1B 97.549 408 7 2 317 722 55997571 55997977 0.000000e+00 695.0
7 TraesCS1B01G070800 chr1B 84.146 492 59 11 231 708 56141746 56141260 2.540000e-125 459.0
8 TraesCS1B01G070800 chr1B 93.927 247 15 0 2556 2802 56138633 56138387 9.480000e-100 374.0
9 TraesCS1B01G070800 chr1B 90.283 247 22 2 2556 2802 56019015 56019259 3.480000e-84 322.0
10 TraesCS1B01G070800 chr1B 90.222 225 20 1 1 225 55943795 55944017 2.730000e-75 292.0
11 TraesCS1B01G070800 chr1B 90.222 225 20 1 1 225 55955048 55955270 2.730000e-75 292.0
12 TraesCS1B01G070800 chr1B 92.347 196 12 3 438 630 55944841 55945036 2.750000e-70 276.0
13 TraesCS1B01G070800 chr1B 91.837 196 13 3 438 630 55956094 55956289 1.280000e-68 270.0
14 TraesCS1B01G070800 chr1B 92.614 176 11 2 230 404 55944667 55944841 4.630000e-63 252.0
15 TraesCS1B01G070800 chr1B 92.614 176 11 2 230 404 55955920 55956094 4.630000e-63 252.0
16 TraesCS1B01G070800 chr1D 90.567 1993 133 13 849 2802 36315606 36317582 0.000000e+00 2588.0
17 TraesCS1B01G070800 chr1D 86.929 1423 154 17 231 1644 36363757 36362358 0.000000e+00 1568.0
18 TraesCS1B01G070800 chr1D 88.950 905 61 18 1684 2552 36362365 36361464 0.000000e+00 1081.0
19 TraesCS1B01G070800 chr1D 88.276 290 25 7 326 607 36314955 36315243 3.460000e-89 339.0
20 TraesCS1B01G070800 chr1D 91.736 121 10 0 102 222 36314452 36314572 4.800000e-38 169.0
21 TraesCS1B01G070800 chr1A 90.016 1833 142 19 999 2802 35525792 35527612 0.000000e+00 2333.0
22 TraesCS1B01G070800 chr1A 86.907 1856 186 28 231 2068 35579252 35577436 0.000000e+00 2028.0
23 TraesCS1B01G070800 chr1A 91.294 1206 93 3 866 2068 35536206 35537402 0.000000e+00 1635.0
24 TraesCS1B01G070800 chr1A 87.469 1229 129 11 844 2068 35485993 35487200 0.000000e+00 1393.0
25 TraesCS1B01G070800 chr1A 94.038 738 42 2 2065 2802 35487228 35487963 0.000000e+00 1118.0
26 TraesCS1B01G070800 chr1A 92.008 488 37 2 2065 2552 35577409 35576924 0.000000e+00 684.0
27 TraesCS1B01G070800 chr1A 87.660 470 45 7 231 688 35514565 35515033 4.110000e-148 534.0
28 TraesCS1B01G070800 chr1A 88.657 432 39 6 231 653 35535471 35535901 4.140000e-143 518.0
29 TraesCS1B01G070800 chr1A 83.942 548 50 22 238 762 35485052 35485584 9.020000e-135 490.0
30 TraesCS1B01G070800 chr1A 92.713 247 18 0 2556 2802 35576297 35576051 9.540000e-95 357.0
31 TraesCS1B01G070800 chr1A 88.202 178 17 4 2571 2746 31030194 31030019 2.830000e-50 209.0
32 TraesCS1B01G070800 chr1A 90.756 119 8 3 2680 2797 25302862 25302746 3.740000e-34 156.0
33 TraesCS1B01G070800 chr1A 94.340 53 3 0 102 154 35513786 35513838 6.430000e-12 82.4
34 TraesCS1B01G070800 chrUn 90.541 222 19 1 4 225 480727034 480726815 2.730000e-75 292.0
35 TraesCS1B01G070800 chr4D 96.226 53 2 0 102 154 336663895 336663947 1.380000e-13 87.9
36 TraesCS1B01G070800 chr3B 81.553 103 18 1 2611 2713 369044897 369044998 1.790000e-12 84.2
37 TraesCS1B01G070800 chr4B 95.652 46 2 0 102 147 414865548 414865593 1.080000e-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 TraesCS1B01G070800 chr1B 55976191 55978992 2801 False 5175.000000 5175 100.000000 1 2802 1 chr1B.!!$F2 2801
1 TraesCS1B01G070800 chr1B 55997571 56000251 2680 False 2078.000000 3461 97.892500 317 2802 2 chr1B.!!$F5 2485
2 TraesCS1B01G070800 chr1B 56015945 56019259 3314 False 1178.666667 2050 94.563333 1 2802 3 chr1B.!!$F6 2801
3 TraesCS1B01G070800 chr1B 56138387 56141746 3359 True 1056.000000 2335 89.905000 231 2802 3 chr1B.!!$R1 2571
4 TraesCS1B01G070800 chr1B 55964135 55965020 885 False 1013.000000 1013 87.305000 830 1724 1 chr1B.!!$F1 894
5 TraesCS1B01G070800 chr1B 55943795 55945036 1241 False 273.333333 292 91.727667 1 630 3 chr1B.!!$F3 629
6 TraesCS1B01G070800 chr1B 55955048 55956289 1241 False 271.333333 292 91.557667 1 630 3 chr1B.!!$F4 629
7 TraesCS1B01G070800 chr1D 36361464 36363757 2293 True 1324.500000 1568 87.939500 231 2552 2 chr1D.!!$R1 2321
8 TraesCS1B01G070800 chr1D 36314452 36317582 3130 False 1032.000000 2588 90.193000 102 2802 3 chr1D.!!$F1 2700
9 TraesCS1B01G070800 chr1A 35525792 35527612 1820 False 2333.000000 2333 90.016000 999 2802 1 chr1A.!!$F1 1803
10 TraesCS1B01G070800 chr1A 35535471 35537402 1931 False 1076.500000 1635 89.975500 231 2068 2 chr1A.!!$F4 1837
11 TraesCS1B01G070800 chr1A 35576051 35579252 3201 True 1023.000000 2028 90.542667 231 2802 3 chr1A.!!$R3 2571
12 TraesCS1B01G070800 chr1A 35485052 35487963 2911 False 1000.333333 1393 88.483000 238 2802 3 chr1A.!!$F2 2564
13 TraesCS1B01G070800 chr1A 35513786 35515033 1247 False 308.200000 534 91.000000 102 688 2 chr1A.!!$F3 586

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
190 208 1.344763 GTTAGCGGCCATCTCCATAGT 59.655 52.381 2.24 0.0 0.0 2.12 F
1011 2117 0.251297 CCTTGGCCATGGTGAACTCA 60.251 55.000 26.14 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1629 2737 0.901124 GAGCAGAGGAAGCAGAGGAA 59.099 55.0 0.00 0.0 0.00 3.36 R
2384 3593 0.324943 CACTCGGGTTTCCCAGACAT 59.675 55.0 5.64 0.0 45.83 3.06 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
190 208 1.344763 GTTAGCGGCCATCTCCATAGT 59.655 52.381 2.24 0.00 0.00 2.12
267 974 2.880963 ACGTTTTTGACCATGTTGGG 57.119 45.000 0.00 0.00 43.37 4.12
485 1199 7.750903 GCTGTCGAATGAAGCTTTAAAGTATTT 59.249 33.333 16.38 8.83 36.68 1.40
691 1450 5.059955 CGGCAAAACACCGTTTCATAAATAC 59.940 40.000 0.00 0.00 45.70 1.89
734 1493 5.665916 ATCCCCAAAAAGACATAAAGCAG 57.334 39.130 0.00 0.00 0.00 4.24
783 1542 2.147958 GGGTAGTGTTGAATTCACGCA 58.852 47.619 7.89 7.69 40.28 5.24
828 1809 2.559698 TCACCAACGACACATCCATT 57.440 45.000 0.00 0.00 0.00 3.16
1011 2117 0.251297 CCTTGGCCATGGTGAACTCA 60.251 55.000 26.14 0.00 0.00 3.41
1049 2155 1.542108 GGCTTTCCCATCGGATCTCAG 60.542 57.143 0.00 0.00 38.24 3.35
1555 2663 0.324368 AGACATCTACGGCCTCACCA 60.324 55.000 0.00 0.00 39.03 4.17
1629 2737 1.079819 CGATGTGAGTTCCCGTGCT 60.080 57.895 0.00 0.00 0.00 4.40
1630 2738 0.670546 CGATGTGAGTTCCCGTGCTT 60.671 55.000 0.00 0.00 0.00 3.91
1631 2739 1.079503 GATGTGAGTTCCCGTGCTTC 58.920 55.000 0.00 0.00 0.00 3.86
1632 2740 0.321653 ATGTGAGTTCCCGTGCTTCC 60.322 55.000 0.00 0.00 0.00 3.46
1633 2741 1.371558 GTGAGTTCCCGTGCTTCCT 59.628 57.895 0.00 0.00 0.00 3.36
1634 2742 0.670854 GTGAGTTCCCGTGCTTCCTC 60.671 60.000 0.00 0.00 0.00 3.71
1635 2743 0.832135 TGAGTTCCCGTGCTTCCTCT 60.832 55.000 0.00 0.00 0.00 3.69
1636 2744 0.390472 GAGTTCCCGTGCTTCCTCTG 60.390 60.000 0.00 0.00 0.00 3.35
1637 2745 2.035442 GTTCCCGTGCTTCCTCTGC 61.035 63.158 0.00 0.00 0.00 4.26
1638 2746 2.217038 TTCCCGTGCTTCCTCTGCT 61.217 57.895 0.00 0.00 0.00 4.24
1732 2844 1.858739 ATAAACGCTCCTGCCCCCAA 61.859 55.000 0.00 0.00 35.36 4.12
2376 3585 1.266178 TGCTTCCTGATTCCTCGTGA 58.734 50.000 0.00 0.00 0.00 4.35
2611 4452 5.411781 CAGAGCGACTATTCCTACAGTTTT 58.588 41.667 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 8.783660 AGTTACTTATCCTCAATGTATCTGGA 57.216 34.615 0.00 0.00 0.00 3.86
64 65 3.031736 GTTAGGTGGAGAGGAGCATACA 58.968 50.000 0.00 0.00 0.00 2.29
190 208 1.740585 CGGAAGGACACACACAAAACA 59.259 47.619 0.00 0.00 0.00 2.83
267 974 1.899142 TCCAATAGCTGCCCAAAAACC 59.101 47.619 0.00 0.00 0.00 3.27
575 1297 8.414778 TGGATCACCGTTTTTAACTAATGTTTT 58.585 29.630 0.00 0.00 39.42 2.43
707 1466 8.601546 TGCTTTATGTCTTTTTGGGGATTATTT 58.398 29.630 0.00 0.00 0.00 1.40
708 1467 8.144862 TGCTTTATGTCTTTTTGGGGATTATT 57.855 30.769 0.00 0.00 0.00 1.40
709 1468 7.619302 TCTGCTTTATGTCTTTTTGGGGATTAT 59.381 33.333 0.00 0.00 0.00 1.28
710 1469 6.951198 TCTGCTTTATGTCTTTTTGGGGATTA 59.049 34.615 0.00 0.00 0.00 1.75
762 1521 1.467342 GCGTGAATTCAACACTACCCC 59.533 52.381 10.35 0.00 36.29 4.95
763 1522 2.147958 TGCGTGAATTCAACACTACCC 58.852 47.619 10.35 0.00 36.29 3.69
764 1523 4.390603 TGTATGCGTGAATTCAACACTACC 59.609 41.667 10.35 0.00 36.29 3.18
765 1524 5.107259 TGTGTATGCGTGAATTCAACACTAC 60.107 40.000 27.82 21.22 37.30 2.73
766 1525 4.991687 TGTGTATGCGTGAATTCAACACTA 59.008 37.500 27.82 17.73 37.30 2.74
767 1526 3.812609 TGTGTATGCGTGAATTCAACACT 59.187 39.130 27.82 15.24 37.30 3.55
768 1527 3.906008 GTGTGTATGCGTGAATTCAACAC 59.094 43.478 24.04 24.04 37.00 3.32
769 1528 3.363477 CGTGTGTATGCGTGAATTCAACA 60.363 43.478 10.35 12.06 0.00 3.33
770 1529 3.152983 CGTGTGTATGCGTGAATTCAAC 58.847 45.455 10.35 6.25 0.00 3.18
771 1530 2.412195 GCGTGTGTATGCGTGAATTCAA 60.412 45.455 10.35 0.00 0.00 2.69
800 1559 6.315393 GGATGTGTCGTTGGTGAATAAGTAAT 59.685 38.462 0.00 0.00 0.00 1.89
816 1583 4.207165 AGGGGAAATAAATGGATGTGTCG 58.793 43.478 0.00 0.00 0.00 4.35
828 1809 2.946791 GCGTGGGCTAAAGGGGAAATAA 60.947 50.000 0.00 0.00 35.83 1.40
1049 2155 1.433471 GTAATGCCGCCTTCCTTGC 59.567 57.895 0.00 0.00 0.00 4.01
1629 2737 0.901124 GAGCAGAGGAAGCAGAGGAA 59.099 55.000 0.00 0.00 0.00 3.36
1630 2738 0.975040 GGAGCAGAGGAAGCAGAGGA 60.975 60.000 0.00 0.00 0.00 3.71
1631 2739 1.521616 GGAGCAGAGGAAGCAGAGG 59.478 63.158 0.00 0.00 0.00 3.69
1632 2740 0.977108 AGGGAGCAGAGGAAGCAGAG 60.977 60.000 0.00 0.00 0.00 3.35
1633 2741 0.975040 GAGGGAGCAGAGGAAGCAGA 60.975 60.000 0.00 0.00 0.00 4.26
1634 2742 1.521616 GAGGGAGCAGAGGAAGCAG 59.478 63.158 0.00 0.00 0.00 4.24
1635 2743 1.992277 GGAGGGAGCAGAGGAAGCA 60.992 63.158 0.00 0.00 0.00 3.91
1636 2744 2.741055 GGGAGGGAGCAGAGGAAGC 61.741 68.421 0.00 0.00 0.00 3.86
1637 2745 2.069430 GGGGAGGGAGCAGAGGAAG 61.069 68.421 0.00 0.00 0.00 3.46
1638 2746 2.041265 GGGGAGGGAGCAGAGGAA 59.959 66.667 0.00 0.00 0.00 3.36
1732 2844 2.513897 GCGCCGGGAAATAGCAGT 60.514 61.111 2.18 0.00 0.00 4.40
2215 3424 3.433615 CCACAACAGTTAGCTAGCAGAAC 59.566 47.826 18.83 19.29 0.00 3.01
2218 3427 1.734465 GCCACAACAGTTAGCTAGCAG 59.266 52.381 18.83 4.35 0.00 4.24
2376 3585 0.482446 TTTCCCAGACATGCCAACCT 59.518 50.000 0.00 0.00 0.00 3.50
2384 3593 0.324943 CACTCGGGTTTCCCAGACAT 59.675 55.000 5.64 0.00 45.83 3.06
2611 4452 8.846943 ACATAGTATTGTCACAAAAGACATGA 57.153 30.769 0.00 0.00 46.90 3.07
2630 4471 4.649218 AGGTTTGGAAGTGCAAAACATAGT 59.351 37.500 14.63 0.00 35.88 2.12


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

AutoCloner maintained by Alex Coulton.