Multiple sequence alignment - TraesCS5D01G325700

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 TraesCS5D01G325700 chr5D 100.000 4235 0 0 1 4235 417826104 417830338 0.000000e+00 7821
1 TraesCS5D01G325700 chr5D 87.825 1347 139 18 1912 3246 406416237 406417570 0.000000e+00 1555
2 TraesCS5D01G325700 chr5D 92.857 854 22 7 1 815 26893037 26892184 0.000000e+00 1203
3 TraesCS5D01G325700 chr5D 88.449 632 65 5 999 1623 406415458 406416088 0.000000e+00 756
4 TraesCS5D01G325700 chr5D 93.362 467 13 1 1 449 417857168 417856702 0.000000e+00 675
5 TraesCS5D01G325700 chr5B 90.645 2651 165 52 811 3423 505378145 505380750 0.000000e+00 3445
6 TraesCS5D01G325700 chr5B 93.277 2142 96 14 1658 3760 505275989 505278121 0.000000e+00 3114
7 TraesCS5D01G325700 chr5B 87.426 1344 150 14 1912 3246 487438449 487439782 0.000000e+00 1528
8 TraesCS5D01G325700 chr5B 90.629 843 47 15 811 1639 505275116 505275940 0.000000e+00 1090
9 TraesCS5D01G325700 chr5B 97.059 272 6 2 3423 3693 505381413 505381683 1.390000e-124 457
10 TraesCS5D01G325700 chr5B 96.053 76 3 0 3685 3760 505383201 505383276 1.600000e-24 124
11 TraesCS5D01G325700 chr5A 95.756 1555 50 11 1767 3308 532740494 532742045 0.000000e+00 2492
12 TraesCS5D01G325700 chr5A 88.136 1298 138 12 1960 3246 512060385 512061677 0.000000e+00 1530
13 TraesCS5D01G325700 chr5A 92.683 943 41 16 811 1735 531238419 531239351 0.000000e+00 1334
14 TraesCS5D01G325700 chr5A 87.717 635 67 8 999 1623 512059559 512060192 0.000000e+00 730
15 TraesCS5D01G325700 chr5A 93.122 378 26 0 1544 1921 328953201 328952824 4.780000e-154 555
16 TraesCS5D01G325700 chr1D 86.973 1351 147 18 1913 3238 440719202 440720548 0.000000e+00 1493
17 TraesCS5D01G325700 chr1D 93.389 832 21 7 1 812 468113444 468112627 0.000000e+00 1201
18 TraesCS5D01G325700 chr1D 90.046 864 28 11 1 817 31297845 31298697 0.000000e+00 1066
19 TraesCS5D01G325700 chr1D 91.634 765 19 2 92 811 35899180 35899944 0.000000e+00 1016
20 TraesCS5D01G325700 chr1D 87.650 583 61 8 999 1571 440718429 440719010 0.000000e+00 667
21 TraesCS5D01G325700 chr1A 86.944 1348 146 18 1921 3241 537347040 537345696 0.000000e+00 1487
22 TraesCS5D01G325700 chr1A 85.155 613 65 18 999 1598 537347812 537347213 4.680000e-169 604
23 TraesCS5D01G325700 chr1A 81.429 350 37 14 6 331 590854162 590854507 1.170000e-65 261
24 TraesCS5D01G325700 chr6D 86.735 1357 145 21 1913 3238 36253454 36254806 0.000000e+00 1476
25 TraesCS5D01G325700 chr6D 91.754 861 21 4 1 813 19559551 19560409 0.000000e+00 1151
26 TraesCS5D01G325700 chr6D 91.871 529 39 3 1098 1624 36252792 36253318 0.000000e+00 736
27 TraesCS5D01G325700 chr6D 80.072 833 88 41 1 811 31969849 31969073 8.010000e-152 547
28 TraesCS5D01G325700 chr6B 86.820 1305 141 15 1963 3238 75942378 75943680 0.000000e+00 1428
29 TraesCS5D01G325700 chr6B 90.548 529 46 3 1098 1624 75941666 75942192 0.000000e+00 697
30 TraesCS5D01G325700 chr7D 95.086 814 34 5 1 811 60245912 60246722 0.000000e+00 1277
31 TraesCS5D01G325700 chr7D 94.465 831 24 3 1 811 49038890 49039718 0.000000e+00 1260
32 TraesCS5D01G325700 chr7D 92.541 858 13 6 1 811 8283311 8282458 0.000000e+00 1182
33 TraesCS5D01G325700 chr7D 92.606 825 33 12 1 811 596569236 596570046 0.000000e+00 1160
34 TraesCS5D01G325700 chr7D 87.179 1014 126 4 1935 2946 509631743 509630732 0.000000e+00 1149
35 TraesCS5D01G325700 chr7D 90.409 855 12 5 1 811 575598998 575598170 0.000000e+00 1061
36 TraesCS5D01G325700 chr7D 89.850 798 45 10 1 772 101563607 101562820 0.000000e+00 992
37 TraesCS5D01G325700 chr7D 85.624 633 76 12 997 1623 603583311 603583934 0.000000e+00 651
38 TraesCS5D01G325700 chrUn 93.435 853 13 7 1 810 10752041 10751189 0.000000e+00 1225
39 TraesCS5D01G325700 chrUn 91.704 446 19 2 3808 4235 82683795 82683350 1.680000e-168 603
40 TraesCS5D01G325700 chrUn 91.704 446 19 2 3808 4235 390432673 390433118 1.680000e-168 603
41 TraesCS5D01G325700 chrUn 91.704 446 19 2 3808 4235 390434318 390434763 1.680000e-168 603
42 TraesCS5D01G325700 chrUn 84.122 296 35 11 1 292 153522482 153522195 4.170000e-70 276
43 TraesCS5D01G325700 chr4D 92.462 849 25 16 1 812 60164699 60163853 0.000000e+00 1177
44 TraesCS5D01G325700 chr4D 90.572 297 21 5 1 294 493311421 493311713 1.850000e-103 387
45 TraesCS5D01G325700 chr2D 92.557 833 30 4 1 812 58695089 58695910 0.000000e+00 1166
46 TraesCS5D01G325700 chr2D 94.885 567 19 1 246 812 646509380 646508824 0.000000e+00 878
47 TraesCS5D01G325700 chr2D 92.593 432 21 8 3808 4235 521534824 521535248 1.010000e-170 610
48 TraesCS5D01G325700 chr2D 83.557 298 31 11 6 289 647384953 647385246 3.250000e-66 263
49 TraesCS5D01G325700 chr3D 91.837 833 25 10 1 812 568520483 568521293 0.000000e+00 1122
50 TraesCS5D01G325700 chr3D 92.544 684 14 6 82 739 24655580 24656252 0.000000e+00 946
51 TraesCS5D01G325700 chr7B 88.533 593 54 10 1000 1585 538053825 538053240 0.000000e+00 706
52 TraesCS5D01G325700 chr7B 85.550 609 75 10 1020 1623 685361108 685360508 3.600000e-175 625
53 TraesCS5D01G325700 chr7B 88.688 442 21 7 3813 4235 645246757 645246326 2.920000e-141 512
54 TraesCS5D01G325700 chr6A 90.548 529 45 4 1098 1624 40298097 40298622 0.000000e+00 695
55 TraesCS5D01G325700 chr6A 92.620 271 20 0 2968 3238 40299840 40300110 1.430000e-104 390
56 TraesCS5D01G325700 chr7A 91.704 446 19 2 3808 4235 95223372 95223817 1.680000e-168 603
57 TraesCS5D01G325700 chr7A 91.495 388 15 2 3866 4235 95230639 95231026 6.280000e-143 518
58 TraesCS5D01G325700 chr4A 90.000 450 24 5 3806 4235 35792363 35792811 2.860000e-156 562
59 TraesCS5D01G325700 chr4A 81.948 349 36 14 6 331 600369401 600369057 1.940000e-68 270
60 TraesCS5D01G325700 chr2A 95.671 231 10 0 3812 4042 777817146 777817376 5.170000e-99 372
61 TraesCS5D01G325700 chr2A 90.722 194 17 1 4043 4235 777817419 777817612 1.510000e-64 257
62 TraesCS5D01G325700 chr3B 86.379 301 27 7 1 292 811411270 811411565 2.460000e-82 316
63 TraesCS5D01G325700 chr3A 81.714 350 36 16 6 331 26155155 26154810 2.510000e-67 267
64 TraesCS5D01G325700 chr3A 81.714 350 35 15 6 331 7346859 7347203 9.030000e-67 265


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 TraesCS5D01G325700 chr5D 417826104 417830338 4234 False 7821.0 7821 100.000000 1 4235 1 chr5D.!!$F1 4234
1 TraesCS5D01G325700 chr5D 26892184 26893037 853 True 1203.0 1203 92.857000 1 815 1 chr5D.!!$R1 814
2 TraesCS5D01G325700 chr5D 406415458 406417570 2112 False 1155.5 1555 88.137000 999 3246 2 chr5D.!!$F2 2247
3 TraesCS5D01G325700 chr5B 505275116 505278121 3005 False 2102.0 3114 91.953000 811 3760 2 chr5B.!!$F2 2949
4 TraesCS5D01G325700 chr5B 487438449 487439782 1333 False 1528.0 1528 87.426000 1912 3246 1 chr5B.!!$F1 1334
5 TraesCS5D01G325700 chr5B 505378145 505383276 5131 False 1342.0 3445 94.585667 811 3760 3 chr5B.!!$F3 2949
6 TraesCS5D01G325700 chr5A 532740494 532742045 1551 False 2492.0 2492 95.756000 1767 3308 1 chr5A.!!$F2 1541
7 TraesCS5D01G325700 chr5A 531238419 531239351 932 False 1334.0 1334 92.683000 811 1735 1 chr5A.!!$F1 924
8 TraesCS5D01G325700 chr5A 512059559 512061677 2118 False 1130.0 1530 87.926500 999 3246 2 chr5A.!!$F3 2247
9 TraesCS5D01G325700 chr1D 468112627 468113444 817 True 1201.0 1201 93.389000 1 812 1 chr1D.!!$R1 811
10 TraesCS5D01G325700 chr1D 440718429 440720548 2119 False 1080.0 1493 87.311500 999 3238 2 chr1D.!!$F3 2239
11 TraesCS5D01G325700 chr1D 31297845 31298697 852 False 1066.0 1066 90.046000 1 817 1 chr1D.!!$F1 816
12 TraesCS5D01G325700 chr1D 35899180 35899944 764 False 1016.0 1016 91.634000 92 811 1 chr1D.!!$F2 719
13 TraesCS5D01G325700 chr1A 537345696 537347812 2116 True 1045.5 1487 86.049500 999 3241 2 chr1A.!!$R1 2242
14 TraesCS5D01G325700 chr6D 19559551 19560409 858 False 1151.0 1151 91.754000 1 813 1 chr6D.!!$F1 812
15 TraesCS5D01G325700 chr6D 36252792 36254806 2014 False 1106.0 1476 89.303000 1098 3238 2 chr6D.!!$F2 2140
16 TraesCS5D01G325700 chr6D 31969073 31969849 776 True 547.0 547 80.072000 1 811 1 chr6D.!!$R1 810
17 TraesCS5D01G325700 chr6B 75941666 75943680 2014 False 1062.5 1428 88.684000 1098 3238 2 chr6B.!!$F1 2140
18 TraesCS5D01G325700 chr7D 60245912 60246722 810 False 1277.0 1277 95.086000 1 811 1 chr7D.!!$F2 810
19 TraesCS5D01G325700 chr7D 49038890 49039718 828 False 1260.0 1260 94.465000 1 811 1 chr7D.!!$F1 810
20 TraesCS5D01G325700 chr7D 8282458 8283311 853 True 1182.0 1182 92.541000 1 811 1 chr7D.!!$R1 810
21 TraesCS5D01G325700 chr7D 596569236 596570046 810 False 1160.0 1160 92.606000 1 811 1 chr7D.!!$F3 810
22 TraesCS5D01G325700 chr7D 509630732 509631743 1011 True 1149.0 1149 87.179000 1935 2946 1 chr7D.!!$R3 1011
23 TraesCS5D01G325700 chr7D 575598170 575598998 828 True 1061.0 1061 90.409000 1 811 1 chr7D.!!$R4 810
24 TraesCS5D01G325700 chr7D 101562820 101563607 787 True 992.0 992 89.850000 1 772 1 chr7D.!!$R2 771
25 TraesCS5D01G325700 chr7D 603583311 603583934 623 False 651.0 651 85.624000 997 1623 1 chr7D.!!$F4 626
26 TraesCS5D01G325700 chrUn 10751189 10752041 852 True 1225.0 1225 93.435000 1 810 1 chrUn.!!$R1 809
27 TraesCS5D01G325700 chrUn 390432673 390434763 2090 False 603.0 603 91.704000 3808 4235 2 chrUn.!!$F1 427
28 TraesCS5D01G325700 chr4D 60163853 60164699 846 True 1177.0 1177 92.462000 1 812 1 chr4D.!!$R1 811
29 TraesCS5D01G325700 chr2D 58695089 58695910 821 False 1166.0 1166 92.557000 1 812 1 chr2D.!!$F1 811
30 TraesCS5D01G325700 chr2D 646508824 646509380 556 True 878.0 878 94.885000 246 812 1 chr2D.!!$R1 566
31 TraesCS5D01G325700 chr3D 568520483 568521293 810 False 1122.0 1122 91.837000 1 812 1 chr3D.!!$F2 811
32 TraesCS5D01G325700 chr3D 24655580 24656252 672 False 946.0 946 92.544000 82 739 1 chr3D.!!$F1 657
33 TraesCS5D01G325700 chr7B 538053240 538053825 585 True 706.0 706 88.533000 1000 1585 1 chr7B.!!$R1 585
34 TraesCS5D01G325700 chr7B 685360508 685361108 600 True 625.0 625 85.550000 1020 1623 1 chr7B.!!$R3 603
35 TraesCS5D01G325700 chr6A 40298097 40300110 2013 False 542.5 695 91.584000 1098 3238 2 chr6A.!!$F1 2140

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
836 1026 1.069906 CGGCTTGAAAGTTGAACTCCG 60.070 52.381 0.00 2.18 0.00 4.63 F
950 1140 1.131826 CAATCGCGACGAAACCCAC 59.868 57.895 12.93 0.00 39.99 4.61 F
1650 1892 0.812549 GGAGGAGGTTCGTCTGTCTC 59.187 60.000 0.00 0.00 32.33 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1650 1892 0.237761 AGTCCAGTTCGTCTTCGTCG 59.762 55.0 0.0 0.0 38.33 5.12 R
2896 3208 0.311790 TACACGAACACGGTCCTGAC 59.688 55.0 0.0 0.0 0.00 3.51 R
3343 3697 0.250467 GCTTGTGCAACTCTCAGGGA 60.250 55.0 0.0 0.0 38.04 4.20 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
283 312 1.076533 GCACACGGATCGATGACGTT 61.077 55.000 18.71 10.09 39.02 3.99
434 524 2.125106 GTGCAGTCCCACGGATCC 60.125 66.667 0.00 0.00 32.73 3.36
836 1026 1.069906 CGGCTTGAAAGTTGAACTCCG 60.070 52.381 0.00 2.18 0.00 4.63
842 1032 1.732809 GAAAGTTGAACTCCGCTAGCC 59.267 52.381 9.66 0.00 0.00 3.93
950 1140 1.131826 CAATCGCGACGAAACCCAC 59.868 57.895 12.93 0.00 39.99 4.61
972 1166 1.134371 CAAATCTTCTCCTCCCCCGAC 60.134 57.143 0.00 0.00 0.00 4.79
1096 1309 2.203728 ACTACACCACCGAGCCCA 60.204 61.111 0.00 0.00 0.00 5.36
1168 1387 4.207281 CGGAGATCAAGGCGGCGA 62.207 66.667 12.98 0.00 0.00 5.54
1348 1579 4.749310 AGCTCGCCTGCAACCTCG 62.749 66.667 0.00 0.00 34.99 4.63
1647 1889 1.203075 AGAAGGAGGAGGTTCGTCTGT 60.203 52.381 0.00 0.00 32.33 3.41
1648 1890 1.202817 GAAGGAGGAGGTTCGTCTGTC 59.797 57.143 0.00 0.00 32.33 3.51
1650 1892 0.812549 GGAGGAGGTTCGTCTGTCTC 59.187 60.000 0.00 0.00 32.33 3.36
1788 2064 3.371063 GTCCCTGTCTCCGTCGCA 61.371 66.667 0.00 0.00 0.00 5.10
1811 2087 3.859414 GGAGGCAGCCGAGCAGAT 61.859 66.667 5.55 0.00 35.83 2.90
1840 2116 1.542375 ATGGAGGCCACCCTTGTCT 60.542 57.895 17.45 0.00 43.12 3.41
1847 2123 2.571216 CCACCCTTGTCTCCGTCGT 61.571 63.158 0.00 0.00 0.00 4.34
1850 2126 2.432628 CCTTGTCTCCGTCGTGGC 60.433 66.667 0.00 0.00 37.80 5.01
1958 2267 0.834687 AAGACCTCCCCACGTAAGCA 60.835 55.000 0.00 0.00 45.62 3.91
2050 2359 1.543871 GGGCCTACCGTTTCTTGTTCA 60.544 52.381 0.84 0.00 36.48 3.18
2051 2360 1.534163 GGCCTACCGTTTCTTGTTCAC 59.466 52.381 0.00 0.00 0.00 3.18
2052 2361 2.490991 GCCTACCGTTTCTTGTTCACT 58.509 47.619 0.00 0.00 0.00 3.41
2356 2665 2.094659 GTGTACATGAGCGCGCAGT 61.095 57.895 35.10 25.77 0.00 4.40
2455 2764 3.997397 TGCGCTTCGGCAGGTACA 61.997 61.111 9.73 0.00 41.88 2.90
2498 2807 4.207281 CAAGATCTCGGCGGGCGA 62.207 66.667 25.27 25.27 0.00 5.54
2770 3081 3.483954 ATCCACCTGATCAAAGGCG 57.516 52.632 0.00 0.00 41.46 5.52
2896 3208 4.207281 TCGCGCCGGAGAAGATGG 62.207 66.667 10.31 0.00 0.00 3.51
3083 3428 2.107750 CAGCTCGATGCCGGTGAT 59.892 61.111 1.90 0.00 44.23 3.06
3308 3662 1.300620 TCTTTGCACGGTCACGGAG 60.301 57.895 0.00 0.00 46.48 4.63
3315 3669 0.389296 CACGGTCACGGAGCATTGTA 60.389 55.000 0.00 0.00 46.48 2.41
3317 3671 0.108804 CGGTCACGGAGCATTGTACT 60.109 55.000 0.00 0.00 36.18 2.73
3318 3672 1.133598 CGGTCACGGAGCATTGTACTA 59.866 52.381 0.00 0.00 36.18 1.82
3319 3673 2.537401 GGTCACGGAGCATTGTACTAC 58.463 52.381 0.00 0.00 0.00 2.73
3323 3677 1.134788 ACGGAGCATTGTACTACTGGC 60.135 52.381 0.00 0.00 0.00 4.85
3330 3684 3.470709 CATTGTACTACTGGCCCATGAG 58.529 50.000 0.00 0.00 0.00 2.90
3360 3714 2.957402 AATCCCTGAGAGTTGCACAA 57.043 45.000 0.00 0.00 0.00 3.33
3361 3715 2.486472 ATCCCTGAGAGTTGCACAAG 57.514 50.000 0.00 0.00 0.00 3.16
3362 3716 0.250467 TCCCTGAGAGTTGCACAAGC 60.250 55.000 0.00 0.00 42.57 4.01
3385 3739 7.826690 AGCTATTTAAAAGAAGAAATTGGCGA 58.173 30.769 0.00 0.00 32.65 5.54
3395 3749 9.657419 AAAGAAGAAATTGGCGATTCATAAATT 57.343 25.926 0.00 0.00 0.00 1.82
3434 4452 7.251994 TGCGATTTTATTTATACAACCCACAC 58.748 34.615 0.00 0.00 0.00 3.82
3460 4478 2.615747 GGCTTTCTGACCCACCTTACTC 60.616 54.545 0.00 0.00 0.00 2.59
3748 6297 2.434884 CCTGCACGCGGATCAGTT 60.435 61.111 12.47 0.00 0.00 3.16
3767 6316 4.719369 GCTCGACAGCGGTTCGGT 62.719 66.667 15.49 0.00 35.39 4.69
3768 6317 2.504244 CTCGACAGCGGTTCGGTC 60.504 66.667 15.49 6.46 34.62 4.79
3776 6325 2.127383 CGGTTCGGTCGCTTTTGC 60.127 61.111 0.00 0.00 43.23 3.68
3786 6335 4.633980 GCTTTTGCGTTGTCCCAG 57.366 55.556 0.00 0.00 34.86 4.45
3787 6336 1.661509 GCTTTTGCGTTGTCCCAGC 60.662 57.895 0.00 0.00 34.86 4.85
3788 6337 2.032981 CTTTTGCGTTGTCCCAGCT 58.967 52.632 0.00 0.00 0.00 4.24
3789 6338 1.234821 CTTTTGCGTTGTCCCAGCTA 58.765 50.000 0.00 0.00 0.00 3.32
3790 6339 1.606668 CTTTTGCGTTGTCCCAGCTAA 59.393 47.619 0.00 0.00 0.00 3.09
3791 6340 1.681538 TTTGCGTTGTCCCAGCTAAA 58.318 45.000 0.00 0.00 0.00 1.85
3792 6341 1.904287 TTGCGTTGTCCCAGCTAAAT 58.096 45.000 0.00 0.00 0.00 1.40
3793 6342 2.772077 TGCGTTGTCCCAGCTAAATA 57.228 45.000 0.00 0.00 0.00 1.40
3794 6343 2.627945 TGCGTTGTCCCAGCTAAATAG 58.372 47.619 0.00 0.00 0.00 1.73
3795 6344 1.940613 GCGTTGTCCCAGCTAAATAGG 59.059 52.381 0.00 0.00 0.00 2.57
3796 6345 1.940613 CGTTGTCCCAGCTAAATAGGC 59.059 52.381 0.00 0.00 0.00 3.93
3797 6346 2.298610 GTTGTCCCAGCTAAATAGGCC 58.701 52.381 0.00 0.00 0.00 5.19
3798 6347 1.590591 TGTCCCAGCTAAATAGGCCA 58.409 50.000 5.01 0.00 0.00 5.36
3799 6348 1.490490 TGTCCCAGCTAAATAGGCCAG 59.510 52.381 5.01 0.00 0.00 4.85
3800 6349 0.474184 TCCCAGCTAAATAGGCCAGC 59.526 55.000 5.01 4.32 35.49 4.85
3801 6350 0.475906 CCCAGCTAAATAGGCCAGCT 59.524 55.000 8.68 8.68 46.36 4.24
3802 6351 1.699634 CCCAGCTAAATAGGCCAGCTA 59.300 52.381 13.74 0.00 43.66 3.32
3803 6352 2.551071 CCCAGCTAAATAGGCCAGCTAC 60.551 54.545 13.74 0.00 43.66 3.58
3804 6353 2.104792 CCAGCTAAATAGGCCAGCTACA 59.895 50.000 13.74 0.00 43.66 2.74
3805 6354 3.397482 CAGCTAAATAGGCCAGCTACAG 58.603 50.000 13.74 0.00 43.66 2.74
3806 6355 2.370189 AGCTAAATAGGCCAGCTACAGG 59.630 50.000 12.61 0.00 43.67 4.00
3827 6376 3.362706 GGGGAGTGGATTTTTCCTAACC 58.637 50.000 0.00 0.00 0.00 2.85
3830 6379 4.524053 GGAGTGGATTTTTCCTAACCGAT 58.476 43.478 0.00 0.00 0.00 4.18
3883 8077 2.700773 GGGCGCTGTCCAATCAACC 61.701 63.158 7.64 0.00 0.00 3.77
3898 8092 1.533753 AACCTGCCCCACCATGTTG 60.534 57.895 0.00 0.00 0.00 3.33
3900 8094 1.978617 CCTGCCCCACCATGTTGTC 60.979 63.158 0.00 0.00 0.00 3.18
3923 8117 1.064463 CCATGCAGTGTATTCCCAGGT 60.064 52.381 0.00 0.00 0.00 4.00
3934 8128 6.101734 AGTGTATTCCCAGGTCATGTGATATT 59.898 38.462 0.00 0.00 0.00 1.28
3982 8176 2.585698 CAAATGTGGGGCCATGGC 59.414 61.111 29.47 29.47 41.06 4.40
3998 8192 3.370315 CCATGGCCTATAGATTCTCCTGC 60.370 52.174 3.32 0.00 0.00 4.85
4082 8276 9.717942 ATCTATGCAAGTCTAGATACAAATTCC 57.282 33.333 5.88 0.00 33.87 3.01
4091 8285 9.530633 AGTCTAGATACAAATTCCGTAACATTC 57.469 33.333 0.00 0.00 0.00 2.67
4092 8286 9.530633 GTCTAGATACAAATTCCGTAACATTCT 57.469 33.333 0.00 0.00 0.00 2.40
4093 8287 9.529325 TCTAGATACAAATTCCGTAACATTCTG 57.471 33.333 0.00 0.00 0.00 3.02
4095 8289 8.786826 AGATACAAATTCCGTAACATTCTGAA 57.213 30.769 0.00 0.00 0.00 3.02
4097 8291 9.274065 GATACAAATTCCGTAACATTCTGAAAC 57.726 33.333 0.00 0.00 0.00 2.78
4173 8385 4.760530 ATGCCACTTTCTAGCATAGTCA 57.239 40.909 0.00 0.00 45.10 3.41
4227 8439 7.907214 ACTGAACTTGTGATAAAGTCCATAC 57.093 36.000 0.00 0.00 39.48 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
434 524 1.613317 TACCCCTCTGCCACGTCATG 61.613 60.000 0.00 0.00 0.00 3.07
842 1032 2.658593 GACATGGCGGATCGACGG 60.659 66.667 0.00 0.00 37.93 4.79
950 1140 0.553333 GGGGGAGGAGAAGATTTGGG 59.447 60.000 0.00 0.00 0.00 4.12
1096 1309 2.606826 GAGGAAGGGGTGGGACGT 60.607 66.667 0.00 0.00 0.00 4.34
1101 1314 2.284699 AGGTCGAGGAAGGGGTGG 60.285 66.667 0.00 0.00 0.00 4.61
1227 1458 0.543174 AGAAGAAGTCGAGGCAGGGT 60.543 55.000 0.00 0.00 0.00 4.34
1635 1877 3.679831 GTCGAGACAGACGAACCTC 57.320 57.895 0.00 0.00 41.31 3.85
1647 1889 0.516001 CCAGTTCGTCTTCGTCGAGA 59.484 55.000 0.00 0.00 38.52 4.04
1648 1890 0.516001 TCCAGTTCGTCTTCGTCGAG 59.484 55.000 0.00 0.00 38.52 4.04
1650 1892 0.237761 AGTCCAGTTCGTCTTCGTCG 59.762 55.000 0.00 0.00 38.33 5.12
1831 2107 2.571216 CCACGACGGAGACAAGGGT 61.571 63.158 0.00 0.00 36.56 4.34
1876 2152 2.105128 GACGACCTCCATCGCCTG 59.895 66.667 0.00 0.00 46.22 4.85
1958 2267 2.027377 CAGACCTTCTTGGACATCTGCT 60.027 50.000 0.00 0.00 39.71 4.24
2455 2764 1.153369 CGGCCTTCACGTCATCCAT 60.153 57.895 0.00 0.00 0.00 3.41
2498 2807 1.954362 GATCTCGTGTGGCAGGAGCT 61.954 60.000 12.34 4.80 43.42 4.09
2534 2843 3.461773 CGTCGTCCTCCTGGCCAT 61.462 66.667 5.51 0.00 0.00 4.40
2896 3208 0.311790 TACACGAACACGGTCCTGAC 59.688 55.000 0.00 0.00 0.00 3.51
3308 3662 1.949525 CATGGGCCAGTAGTACAATGC 59.050 52.381 13.78 1.84 0.00 3.56
3310 3664 2.158755 GCTCATGGGCCAGTAGTACAAT 60.159 50.000 13.78 0.00 0.00 2.71
3315 3669 0.254178 CTTGCTCATGGGCCAGTAGT 59.746 55.000 16.70 0.00 0.00 2.73
3317 3671 1.609239 CCTTGCTCATGGGCCAGTA 59.391 57.895 16.70 0.65 0.00 2.74
3318 3672 2.357836 CCTTGCTCATGGGCCAGT 59.642 61.111 16.70 0.00 0.00 4.00
3319 3673 2.441532 CCCTTGCTCATGGGCCAG 60.442 66.667 16.70 14.01 38.71 4.85
3323 3677 2.806945 TTACTTCCCTTGCTCATGGG 57.193 50.000 13.11 13.11 44.74 4.00
3343 3697 0.250467 GCTTGTGCAACTCTCAGGGA 60.250 55.000 0.00 0.00 38.04 4.20
3345 3699 2.462456 TAGCTTGTGCAACTCTCAGG 57.538 50.000 0.00 0.00 42.74 3.86
3346 3700 6.486253 TTAAATAGCTTGTGCAACTCTCAG 57.514 37.500 0.00 0.00 42.74 3.35
3360 3714 7.826690 TCGCCAATTTCTTCTTTTAAATAGCT 58.173 30.769 0.00 0.00 0.00 3.32
3361 3715 8.634475 ATCGCCAATTTCTTCTTTTAAATAGC 57.366 30.769 0.00 0.00 0.00 2.97
3434 4452 1.340114 GGTGGGTCAGAAAGCCCTAAG 60.340 57.143 0.00 0.00 45.54 2.18
3437 4455 1.068352 AAGGTGGGTCAGAAAGCCCT 61.068 55.000 0.00 0.00 45.54 5.19
3453 4471 6.700520 GGTTAAGGATTACATCACGAGTAAGG 59.299 42.308 0.00 0.00 35.18 2.69
3460 4478 6.204108 GGGTAATGGTTAAGGATTACATCACG 59.796 42.308 14.30 0.00 36.95 4.35
3736 6285 2.125512 GAGCCAACTGATCCGCGT 60.126 61.111 4.92 0.00 0.00 6.01
3748 6297 4.717629 CGAACCGCTGTCGAGCCA 62.718 66.667 0.00 0.00 42.91 4.75
3760 6309 2.127383 CGCAAAAGCGACCGAACC 60.127 61.111 3.45 0.00 34.88 3.62
3761 6310 1.010462 AACGCAAAAGCGACCGAAC 60.010 52.632 17.27 0.00 36.94 3.95
3762 6311 1.010574 CAACGCAAAAGCGACCGAA 60.011 52.632 17.27 0.00 36.94 4.30
3763 6312 2.096481 GACAACGCAAAAGCGACCGA 62.096 55.000 17.27 0.00 36.94 4.69
3764 6313 1.721133 GACAACGCAAAAGCGACCG 60.721 57.895 17.27 6.63 36.94 4.79
3765 6314 1.370051 GGACAACGCAAAAGCGACC 60.370 57.895 17.27 9.90 36.94 4.79
3766 6315 1.370051 GGGACAACGCAAAAGCGAC 60.370 57.895 17.27 5.01 36.94 5.19
3767 6316 1.781025 CTGGGACAACGCAAAAGCGA 61.781 55.000 17.27 0.00 38.70 4.93
3768 6317 1.370414 CTGGGACAACGCAAAAGCG 60.370 57.895 8.45 8.45 38.70 4.68
3769 6318 1.661509 GCTGGGACAACGCAAAAGC 60.662 57.895 0.00 0.00 38.70 3.51
3770 6319 1.234821 TAGCTGGGACAACGCAAAAG 58.765 50.000 0.00 0.00 38.70 2.27
3771 6320 1.681538 TTAGCTGGGACAACGCAAAA 58.318 45.000 0.00 0.00 38.70 2.44
3772 6321 1.681538 TTTAGCTGGGACAACGCAAA 58.318 45.000 0.00 0.00 38.70 3.68
3773 6322 1.904287 ATTTAGCTGGGACAACGCAA 58.096 45.000 0.00 0.00 38.70 4.85
3774 6323 2.627945 CTATTTAGCTGGGACAACGCA 58.372 47.619 0.00 0.00 38.70 5.24
3775 6324 1.940613 CCTATTTAGCTGGGACAACGC 59.059 52.381 0.00 0.00 38.70 4.84
3776 6325 1.940613 GCCTATTTAGCTGGGACAACG 59.059 52.381 0.00 0.00 38.70 4.10
3777 6326 2.298610 GGCCTATTTAGCTGGGACAAC 58.701 52.381 0.00 0.00 38.70 3.32
3778 6327 1.919654 TGGCCTATTTAGCTGGGACAA 59.080 47.619 3.32 0.00 38.70 3.18
3779 6328 1.490490 CTGGCCTATTTAGCTGGGACA 59.510 52.381 3.32 0.00 33.10 4.02
3780 6329 1.815795 GCTGGCCTATTTAGCTGGGAC 60.816 57.143 3.32 0.00 34.70 4.46
3781 6330 0.474184 GCTGGCCTATTTAGCTGGGA 59.526 55.000 3.32 0.00 34.70 4.37
3782 6331 0.475906 AGCTGGCCTATTTAGCTGGG 59.524 55.000 13.41 0.00 45.40 4.45
3783 6332 2.104792 TGTAGCTGGCCTATTTAGCTGG 59.895 50.000 21.56 0.00 46.45 4.85
3784 6333 3.397482 CTGTAGCTGGCCTATTTAGCTG 58.603 50.000 21.56 4.47 46.45 4.24
3786 6335 2.551071 CCCTGTAGCTGGCCTATTTAGC 60.551 54.545 3.32 3.62 37.71 3.09
3787 6336 2.039084 CCCCTGTAGCTGGCCTATTTAG 59.961 54.545 3.32 0.00 0.00 1.85
3788 6337 2.054799 CCCCTGTAGCTGGCCTATTTA 58.945 52.381 3.32 0.00 0.00 1.40
3789 6338 0.846693 CCCCTGTAGCTGGCCTATTT 59.153 55.000 3.32 0.00 0.00 1.40
3790 6339 1.062488 CCCCCTGTAGCTGGCCTATT 61.062 60.000 3.32 0.00 0.00 1.73
3791 6340 1.462238 CCCCCTGTAGCTGGCCTAT 60.462 63.158 3.32 0.00 0.00 2.57
3792 6341 2.040884 CCCCCTGTAGCTGGCCTA 60.041 66.667 3.32 0.00 0.00 3.93
3793 6342 4.024984 TCCCCCTGTAGCTGGCCT 62.025 66.667 3.32 0.00 0.00 5.19
3794 6343 3.483869 CTCCCCCTGTAGCTGGCC 61.484 72.222 0.00 0.00 0.00 5.36
3795 6344 2.689034 ACTCCCCCTGTAGCTGGC 60.689 66.667 0.00 0.00 0.00 4.85
3796 6345 2.370445 CCACTCCCCCTGTAGCTGG 61.370 68.421 0.00 0.00 0.00 4.85
3797 6346 0.692419 ATCCACTCCCCCTGTAGCTG 60.692 60.000 0.00 0.00 0.00 4.24
3798 6347 0.044855 AATCCACTCCCCCTGTAGCT 59.955 55.000 0.00 0.00 0.00 3.32
3799 6348 0.919710 AAATCCACTCCCCCTGTAGC 59.080 55.000 0.00 0.00 0.00 3.58
3800 6349 3.621558 GAAAAATCCACTCCCCCTGTAG 58.378 50.000 0.00 0.00 0.00 2.74
3801 6350 2.310647 GGAAAAATCCACTCCCCCTGTA 59.689 50.000 0.00 0.00 0.00 2.74
3802 6351 1.077169 GGAAAAATCCACTCCCCCTGT 59.923 52.381 0.00 0.00 0.00 4.00
3803 6352 1.359130 AGGAAAAATCCACTCCCCCTG 59.641 52.381 0.00 0.00 0.00 4.45
3804 6353 1.773541 AGGAAAAATCCACTCCCCCT 58.226 50.000 0.00 0.00 0.00 4.79
3805 6354 3.362706 GTTAGGAAAAATCCACTCCCCC 58.637 50.000 0.00 0.00 0.00 5.40
3806 6355 3.362706 GGTTAGGAAAAATCCACTCCCC 58.637 50.000 0.00 0.00 0.00 4.81
3827 6376 4.088762 AGGTTGTGCGCGCAATCG 62.089 61.111 38.24 0.00 34.85 3.34
3830 6379 1.906994 GATACAGGTTGTGCGCGCAA 61.907 55.000 38.24 31.06 0.00 4.85
3843 6392 1.541233 GGATGGACGGCAAGGATACAG 60.541 57.143 0.00 0.00 41.41 2.74
3870 8064 0.967380 GGGGCAGGTTGATTGGACAG 60.967 60.000 0.00 0.00 0.00 3.51
3883 8077 1.228521 TGACAACATGGTGGGGCAG 60.229 57.895 16.70 0.00 0.00 4.85
3898 8092 1.672881 GGAATACACTGCATGGCTGAC 59.327 52.381 0.00 0.00 0.00 3.51
3900 8094 1.027357 GGGAATACACTGCATGGCTG 58.973 55.000 0.00 0.00 0.00 4.85
3934 8128 4.180817 CGGCTTCATATACACACAACAGA 58.819 43.478 0.00 0.00 0.00 3.41
3982 8176 3.648067 TGGTTGGCAGGAGAATCTATAGG 59.352 47.826 0.00 0.00 33.73 2.57
3984 8178 4.345257 GTCTGGTTGGCAGGAGAATCTATA 59.655 45.833 0.00 0.00 33.73 1.31
3998 8192 2.362889 GGCCATGGGTCTGGTTGG 60.363 66.667 15.13 0.00 38.63 3.77
4082 8276 5.444613 CGACCAGATGTTTCAGAATGTTACG 60.445 44.000 0.00 0.00 37.40 3.18
4091 8285 4.935205 TGAATTACCGACCAGATGTTTCAG 59.065 41.667 0.00 0.00 0.00 3.02
4092 8286 4.900684 TGAATTACCGACCAGATGTTTCA 58.099 39.130 0.00 0.00 0.00 2.69
4093 8287 7.280205 ACTTATGAATTACCGACCAGATGTTTC 59.720 37.037 0.00 0.00 0.00 2.78
4095 8289 6.650120 ACTTATGAATTACCGACCAGATGTT 58.350 36.000 0.00 0.00 0.00 2.71
4097 8291 6.201044 GTGACTTATGAATTACCGACCAGATG 59.799 42.308 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.