Multiple sequence alignment - TraesCS6A01G069900

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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 TraesCS6A01G069900 chr6A 100.000 4128 0 0 3528 7655 38102563 38098436 0.000000e+00 7624.0
1 TraesCS6A01G069900 chr6A 100.000 3180 0 0 1 3180 38106090 38102911 0.000000e+00 5873.0
2 TraesCS6A01G069900 chr6A 82.975 1768 237 46 847 2589 37845760 37844032 0.000000e+00 1539.0
3 TraesCS6A01G069900 chr6A 95.222 900 37 6 3528 4424 584126659 584127555 0.000000e+00 1419.0
4 TraesCS6A01G069900 chr6A 94.656 917 28 7 3528 4424 28958992 28958077 0.000000e+00 1402.0
5 TraesCS6A01G069900 chr6A 92.117 926 33 11 3528 4424 5870738 5871652 0.000000e+00 1269.0
6 TraesCS6A01G069900 chr6A 77.347 1523 272 52 1091 2581 38461591 38460110 0.000000e+00 833.0
7 TraesCS6A01G069900 chr6A 81.437 501 50 23 6549 7037 37843061 37842592 3.370000e-98 370.0
8 TraesCS6A01G069900 chr6A 98.857 175 2 0 3006 3180 584126284 584126458 5.770000e-81 313.0
9 TraesCS6A01G069900 chr6A 96.757 185 4 2 2997 3180 607592347 607592164 2.680000e-79 307.0
10 TraesCS6A01G069900 chr6A 73.423 888 171 36 1045 1910 38403328 38402484 9.790000e-69 272.0
11 TraesCS6A01G069900 chr6A 87.500 208 24 2 5883 6089 37843996 37843790 9.930000e-59 239.0
12 TraesCS6A01G069900 chr6A 82.692 208 32 4 1050 1255 38454141 38453936 1.700000e-41 182.0
13 TraesCS6A01G069900 chr6A 97.059 102 3 0 3528 3629 28930909 28930808 1.020000e-38 172.0
14 TraesCS6A01G069900 chr6A 86.765 68 5 3 6816 6883 38401184 38401121 1.070000e-08 73.1
15 TraesCS6A01G069900 chr6A 100.000 33 0 0 4444 4476 5871749 5871781 2.310000e-05 62.1
16 TraesCS6A01G069900 chr6D 93.598 3046 144 34 1 3006 33306624 33303590 0.000000e+00 4497.0
17 TraesCS6A01G069900 chr6D 93.240 1642 79 21 4472 6096 33303590 33301964 0.000000e+00 2388.0
18 TraesCS6A01G069900 chr6D 82.301 1808 253 46 847 2619 33253500 33251725 0.000000e+00 1504.0
19 TraesCS6A01G069900 chr6D 93.451 962 48 10 6082 7037 33301941 33300989 0.000000e+00 1413.0
20 TraesCS6A01G069900 chr6D 93.398 621 29 7 7040 7655 33300951 33300338 0.000000e+00 909.0
21 TraesCS6A01G069900 chr6D 77.677 1541 286 47 1057 2572 33312452 33310945 0.000000e+00 887.0
22 TraesCS6A01G069900 chr6D 76.333 1538 291 51 1050 2540 34305931 34304420 0.000000e+00 756.0
23 TraesCS6A01G069900 chr6D 85.370 540 66 11 2046 2581 34322715 34322185 1.450000e-151 547.0
24 TraesCS6A01G069900 chr6D 82.329 498 76 12 2032 2523 33148046 33147555 9.180000e-114 422.0
25 TraesCS6A01G069900 chr6D 85.915 355 31 9 6549 6894 33250258 33249914 2.030000e-95 361.0
26 TraesCS6A01G069900 chr6D 91.209 91 8 0 7296 7386 33249654 33249564 2.900000e-24 124.0
27 TraesCS6A01G069900 chr6B 92.716 1826 100 22 1 1809 70565629 70563820 0.000000e+00 2604.0
28 TraesCS6A01G069900 chr6B 93.674 1644 72 18 4472 6096 70562548 70560918 0.000000e+00 2431.0
29 TraesCS6A01G069900 chr6B 81.236 1764 237 57 870 2588 70053658 70051944 0.000000e+00 1338.0
30 TraesCS6A01G069900 chr6B 92.952 908 37 10 1836 2718 70563823 70562918 0.000000e+00 1297.0
31 TraesCS6A01G069900 chr6B 93.881 621 26 7 7040 7655 70559788 70559175 0.000000e+00 926.0
32 TraesCS6A01G069900 chr6B 77.728 1549 289 48 1046 2572 70571558 70570044 0.000000e+00 898.0
33 TraesCS6A01G069900 chr6B 93.870 571 24 7 6472 7037 70560389 70559825 0.000000e+00 850.0
34 TraesCS6A01G069900 chr6B 94.118 391 22 1 6082 6471 70560895 70560505 1.840000e-165 593.0
35 TraesCS6A01G069900 chr6B 85.042 361 30 13 6549 6894 70050725 70050374 5.690000e-91 346.0
36 TraesCS6A01G069900 chr6B 90.272 257 12 2 2717 2970 70562795 70562549 2.660000e-84 324.0
37 TraesCS6A01G069900 chr6B 73.563 957 201 26 978 1908 69720105 69719175 1.240000e-82 318.0
38 TraesCS6A01G069900 chr6B 72.727 1001 204 41 948 1891 69959307 69958319 9.790000e-69 272.0
39 TraesCS6A01G069900 chr2A 96.882 898 26 2 3528 4424 489058431 489059327 0.000000e+00 1502.0
40 TraesCS6A01G069900 chr2A 96.774 899 25 4 3528 4424 751528037 751528933 0.000000e+00 1496.0
41 TraesCS6A01G069900 chr2A 96.567 903 23 5 3528 4424 71905672 71904772 0.000000e+00 1489.0
42 TraesCS6A01G069900 chr2A 96.214 898 26 6 3528 4424 770627524 770628414 0.000000e+00 1463.0
43 TraesCS6A01G069900 chr2A 96.571 875 23 7 3528 4396 775407029 775406156 0.000000e+00 1443.0
44 TraesCS6A01G069900 chr2A 87.704 675 45 14 3837 4476 264614866 264614195 0.000000e+00 752.0
45 TraesCS6A01G069900 chr2A 75.448 892 194 17 1042 1911 766994792 766993904 1.990000e-110 411.0
46 TraesCS6A01G069900 chr4A 96.329 899 25 6 3528 4424 685609079 685609971 0.000000e+00 1471.0
47 TraesCS6A01G069900 chr4A 93.643 818 39 11 3528 4341 635671982 635672790 0.000000e+00 1210.0
48 TraesCS6A01G069900 chr4A 98.315 178 3 0 3003 3180 614834870 614835047 5.770000e-81 313.0
49 TraesCS6A01G069900 chr5A 95.991 898 33 3 3528 4424 94098928 94099823 0.000000e+00 1456.0
50 TraesCS6A01G069900 chr5A 98.864 176 2 0 3005 3180 508022738 508022913 1.600000e-81 315.0
51 TraesCS6A01G069900 chr5A 98.295 176 3 0 3005 3180 637721472 637721297 7.460000e-80 309.0
52 TraesCS6A01G069900 chr5A 100.000 29 0 0 4444 4472 446616968 446616940 4.000000e-03 54.7
53 TraesCS6A01G069900 chr7A 95.333 900 38 4 3528 4424 51587169 51586271 0.000000e+00 1426.0
54 TraesCS6A01G069900 chr7A 97.790 181 3 1 3001 3180 115645468 115645648 2.070000e-80 311.0
55 TraesCS6A01G069900 chr7A 100.000 29 0 0 4444 4472 89513868 89513896 4.000000e-03 54.7
56 TraesCS6A01G069900 chr7A 100.000 29 0 0 4444 4472 696290214 696290242 4.000000e-03 54.7
57 TraesCS6A01G069900 chr1A 97.326 187 5 0 2994 3180 41908040 41908226 1.240000e-82 318.0
58 TraesCS6A01G069900 chr1A 100.000 29 0 0 4444 4472 510675695 510675667 4.000000e-03 54.7
59 TraesCS6A01G069900 chr3A 98.870 177 2 0 3004 3180 696395198 696395374 4.460000e-82 316.0
60 TraesCS6A01G069900 chr3A 96.277 188 4 3 2994 3180 15978179 15977994 9.650000e-79 305.0
61 TraesCS6A01G069900 chr3A 100.000 29 0 0 4444 4472 687642215 687642243 4.000000e-03 54.7
62 TraesCS6A01G069900 chr4B 93.434 198 6 2 3533 3729 550468871 550469062 3.500000e-73 287.0
63 TraesCS6A01G069900 chr4B 86.634 202 17 7 3528 3729 401314988 401315179 1.670000e-51 215.0
64 TraesCS6A01G069900 chr4B 95.588 68 3 0 3528 3595 646111709 646111642 8.120000e-20 110.0
65 TraesCS6A01G069900 chr4B 95.455 66 3 0 3529 3594 472426328 472426263 1.050000e-18 106.0
66 TraesCS6A01G069900 chr1D 89.109 202 7 8 3528 3729 443275389 443275203 3.570000e-58 237.0
67 TraesCS6A01G069900 chr1D 96.939 98 3 0 3528 3625 30563741 30563838 1.710000e-36 165.0
68 TraesCS6A01G069900 chr1D 96.809 94 3 0 3528 3621 457782880 457782787 2.860000e-34 158.0
69 TraesCS6A01G069900 chr5D 97.059 102 3 0 3528 3629 523041584 523041483 1.020000e-38 172.0
70 TraesCS6A01G069900 chr5D 96.078 102 4 0 3528 3629 392244618 392244719 4.750000e-37 167.0
71 TraesCS6A01G069900 chr5D 96.809 94 3 0 3528 3621 41582475 41582568 2.860000e-34 158.0
72 TraesCS6A01G069900 chr5D 94.845 97 4 1 3528 3624 427624515 427624610 4.790000e-32 150.0
73 TraesCS6A01G069900 chr5D 97.531 81 2 0 3528 3608 132864910 132864830 1.040000e-28 139.0
74 TraesCS6A01G069900 chr5D 95.349 86 4 0 3528 3613 23731363 23731278 3.730000e-28 137.0
75 TraesCS6A01G069900 chr5D 91.089 101 4 2 3528 3628 422037391 422037486 1.730000e-26 132.0
76 TraesCS6A01G069900 chr1B 96.907 97 3 0 3528 3624 565338955 565338859 6.150000e-36 163.0
77 TraesCS6A01G069900 chrUn 100.000 28 0 0 4444 4471 63419758 63419785 1.400000e-02 52.8


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 TraesCS6A01G069900 chr6A 38098436 38106090 7654 True 6748.500000 7624 100.000000 1 7655 2 chr6A.!!$R7 7654
1 TraesCS6A01G069900 chr6A 28958077 28958992 915 True 1402.000000 1402 94.656000 3528 4424 1 chr6A.!!$R2 896
2 TraesCS6A01G069900 chr6A 584126284 584127555 1271 False 866.000000 1419 97.039500 3006 4424 2 chr6A.!!$F2 1418
3 TraesCS6A01G069900 chr6A 38460110 38461591 1481 True 833.000000 833 77.347000 1091 2581 1 chr6A.!!$R4 1490
4 TraesCS6A01G069900 chr6A 37842592 37845760 3168 True 716.000000 1539 83.970667 847 7037 3 chr6A.!!$R6 6190
5 TraesCS6A01G069900 chr6A 5870738 5871781 1043 False 665.550000 1269 96.058500 3528 4476 2 chr6A.!!$F1 948
6 TraesCS6A01G069900 chr6D 33300338 33306624 6286 True 2301.750000 4497 93.421750 1 7655 4 chr6D.!!$R6 7654
7 TraesCS6A01G069900 chr6D 33310945 33312452 1507 True 887.000000 887 77.677000 1057 2572 1 chr6D.!!$R2 1515
8 TraesCS6A01G069900 chr6D 34304420 34305931 1511 True 756.000000 756 76.333000 1050 2540 1 chr6D.!!$R3 1490
9 TraesCS6A01G069900 chr6D 33249564 33253500 3936 True 663.000000 1504 86.475000 847 7386 3 chr6D.!!$R5 6539
10 TraesCS6A01G069900 chr6D 34322185 34322715 530 True 547.000000 547 85.370000 2046 2581 1 chr6D.!!$R4 535
11 TraesCS6A01G069900 chr6B 70559175 70565629 6454 True 1289.285714 2604 93.069000 1 7655 7 chr6B.!!$R5 7654
12 TraesCS6A01G069900 chr6B 70570044 70571558 1514 True 898.000000 898 77.728000 1046 2572 1 chr6B.!!$R3 1526
13 TraesCS6A01G069900 chr6B 70050374 70053658 3284 True 842.000000 1338 83.139000 870 6894 2 chr6B.!!$R4 6024
14 TraesCS6A01G069900 chr6B 69719175 69720105 930 True 318.000000 318 73.563000 978 1908 1 chr6B.!!$R1 930
15 TraesCS6A01G069900 chr6B 69958319 69959307 988 True 272.000000 272 72.727000 948 1891 1 chr6B.!!$R2 943
16 TraesCS6A01G069900 chr2A 489058431 489059327 896 False 1502.000000 1502 96.882000 3528 4424 1 chr2A.!!$F1 896
17 TraesCS6A01G069900 chr2A 751528037 751528933 896 False 1496.000000 1496 96.774000 3528 4424 1 chr2A.!!$F2 896
18 TraesCS6A01G069900 chr2A 71904772 71905672 900 True 1489.000000 1489 96.567000 3528 4424 1 chr2A.!!$R1 896
19 TraesCS6A01G069900 chr2A 770627524 770628414 890 False 1463.000000 1463 96.214000 3528 4424 1 chr2A.!!$F3 896
20 TraesCS6A01G069900 chr2A 775406156 775407029 873 True 1443.000000 1443 96.571000 3528 4396 1 chr2A.!!$R4 868
21 TraesCS6A01G069900 chr2A 264614195 264614866 671 True 752.000000 752 87.704000 3837 4476 1 chr2A.!!$R2 639
22 TraesCS6A01G069900 chr2A 766993904 766994792 888 True 411.000000 411 75.448000 1042 1911 1 chr2A.!!$R3 869
23 TraesCS6A01G069900 chr4A 685609079 685609971 892 False 1471.000000 1471 96.329000 3528 4424 1 chr4A.!!$F3 896
24 TraesCS6A01G069900 chr4A 635671982 635672790 808 False 1210.000000 1210 93.643000 3528 4341 1 chr4A.!!$F2 813
25 TraesCS6A01G069900 chr5A 94098928 94099823 895 False 1456.000000 1456 95.991000 3528 4424 1 chr5A.!!$F1 896
26 TraesCS6A01G069900 chr7A 51586271 51587169 898 True 1426.000000 1426 95.333000 3528 4424 1 chr7A.!!$R1 896

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
987 1021 0.615331 ATCCTTTCTTGCCTCGCAGA 59.385 50.000 0.00 0.0 40.61 4.26 F
1404 1486 1.134401 TCCCTCGAAATCTCACATGCC 60.134 52.381 0.00 0.0 0.00 4.40 F
1653 1741 2.041115 GCCGGGCCTTGTCTCTTTC 61.041 63.158 8.12 0.0 0.00 2.62 F
3083 3378 0.838554 TCCAGAACCGGGACCAATGA 60.839 55.000 6.32 0.0 0.00 2.57 F
4143 4474 0.532862 ACAACGAGTGCAGACTTGGG 60.533 55.000 0.00 0.0 37.87 4.12 F
5414 5884 0.303493 TTTGTCGAACTCACTTGCGC 59.697 50.000 0.00 0.0 0.00 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1840 1946 0.842635 GAGATCCCACCCAGAAGCAT 59.157 55.000 0.00 0.0 0.00 3.79 R
3083 3378 1.065709 ACGAACCGGGATAAATGCACT 60.066 47.619 6.32 0.0 0.00 4.40 R
4037 4368 7.120579 AGTCACACATTTCACTGTTTGAGTTTA 59.879 33.333 0.00 0.0 36.54 2.01 R
5237 5702 0.107312 AATGCTTCTCGCTGAGCCAT 60.107 50.000 0.00 0.0 40.11 4.40 R
6193 7891 0.035056 TAAGGGCAAGAAGCTGCTCC 60.035 55.000 1.00 0.0 44.44 4.70 R
6655 8470 1.065126 CAACCCAGATCTTCTCACCCC 60.065 57.143 0.00 0.0 0.00 4.95 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
96 98 2.566952 AAAATCAGCCAATACGCAGC 57.433 45.000 0.00 0.00 0.00 5.25
103 105 1.714899 GCCAATACGCAGCGTTCCAT 61.715 55.000 28.31 11.19 41.54 3.41
106 108 0.744414 AATACGCAGCGTTCCATGCT 60.744 50.000 28.31 0.00 42.06 3.79
340 348 6.253298 CGTCCAAATTCAAAATATTCGTGCAT 59.747 34.615 0.00 0.00 0.00 3.96
455 470 9.020731 GGGAACAATTTTAAGTAATCCTCAGAA 57.979 33.333 0.00 0.00 0.00 3.02
540 555 8.553459 AGAAACGTCTCATGAACATCTATTTT 57.447 30.769 0.00 0.00 0.00 1.82
559 574 4.927978 TTTGGCCCGTGGAAAATATATG 57.072 40.909 0.00 0.00 0.00 1.78
611 626 6.403866 AGTTGAACAATTATTGCAACCAGA 57.596 33.333 18.11 0.00 39.57 3.86
614 629 8.752187 AGTTGAACAATTATTGCAACCAGATAT 58.248 29.630 18.11 3.74 39.57 1.63
630 645 9.950680 CAACCAGATATGGACAATATGTTTTAC 57.049 33.333 14.70 0.00 31.22 2.01
681 697 9.899226 AAAAATTGAACGAGAAAGAAATAGGAG 57.101 29.630 0.00 0.00 0.00 3.69
689 705 6.819146 ACGAGAAAGAAATAGGAGAATGAACC 59.181 38.462 0.00 0.00 0.00 3.62
953 986 4.417854 TCCATCTCATCCCATTTTCTCCAT 59.582 41.667 0.00 0.00 0.00 3.41
955 988 5.382616 CATCTCATCCCATTTTCTCCATCA 58.617 41.667 0.00 0.00 0.00 3.07
987 1021 0.615331 ATCCTTTCTTGCCTCGCAGA 59.385 50.000 0.00 0.00 40.61 4.26
1383 1451 2.031314 TGCAAAGTTCGGGCGCTA 59.969 55.556 7.64 0.00 0.00 4.26
1384 1452 1.376683 TGCAAAGTTCGGGCGCTAT 60.377 52.632 7.64 0.00 0.00 2.97
1404 1486 1.134401 TCCCTCGAAATCTCACATGCC 60.134 52.381 0.00 0.00 0.00 4.40
1415 1497 5.894298 ATCTCACATGCCTATTTCTACCA 57.106 39.130 0.00 0.00 0.00 3.25
1635 1723 2.237751 CCGGCTCCGCATTTCTACG 61.238 63.158 2.18 0.00 38.24 3.51
1653 1741 2.041115 GCCGGGCCTTGTCTCTTTC 61.041 63.158 8.12 0.00 0.00 2.62
1810 1913 7.915293 AATAAGAACGGATGTGTCAATTGTA 57.085 32.000 5.13 0.00 0.00 2.41
1883 1989 5.931441 AGTGCTAAACATCTTGAACTGAC 57.069 39.130 0.00 0.00 0.00 3.51
2000 2109 7.553881 AAACCGGAGATAAACAGATTACATG 57.446 36.000 9.46 0.00 0.00 3.21
2001 2110 6.479972 ACCGGAGATAAACAGATTACATGA 57.520 37.500 9.46 0.00 0.00 3.07
2002 2111 7.067496 ACCGGAGATAAACAGATTACATGAT 57.933 36.000 9.46 0.00 0.00 2.45
2004 2113 7.442364 ACCGGAGATAAACAGATTACATGATTG 59.558 37.037 9.46 0.00 0.00 2.67
2006 2115 8.278408 CGGAGATAAACAGATTACATGATTGTG 58.722 37.037 0.00 0.00 36.53 3.33
2026 2170 8.782339 ATTGTGAATATGATCATCTCGCATTA 57.218 30.769 23.98 15.82 0.00 1.90
2236 2384 6.412362 AGAGAAGCTCACTCTTCAACTTTA 57.588 37.500 14.91 0.00 43.64 1.85
2239 2387 7.936301 AGAGAAGCTCACTCTTCAACTTTATTT 59.064 33.333 14.91 0.00 43.64 1.40
2358 2516 6.011981 AGGGACCAACTCATAAAGTGGAAATA 60.012 38.462 0.00 0.00 38.58 1.40
2564 2732 8.428186 TCATACGTGGGAATGAAACTAATAAC 57.572 34.615 0.00 0.00 0.00 1.89
2665 2833 3.630769 AGACAGATAGAATACGAACGGCA 59.369 43.478 0.00 0.00 0.00 5.69
2710 2878 5.466819 CCGATATTGTACGGCTGAGATTTA 58.533 41.667 0.00 0.00 42.55 1.40
2912 3204 7.148239 CCAATTCAATTAGTACTCGGCTTCTTT 60.148 37.037 0.00 0.00 0.00 2.52
3083 3378 0.838554 TCCAGAACCGGGACCAATGA 60.839 55.000 6.32 0.00 0.00 2.57
3130 3425 1.213296 AGGCATTAGTCCCGGTTCAT 58.787 50.000 0.00 0.00 0.00 2.57
4143 4474 0.532862 ACAACGAGTGCAGACTTGGG 60.533 55.000 0.00 0.00 37.87 4.12
4274 4612 9.671279 TTAGAGATTAAATTGAGCAGTGATGAA 57.329 29.630 0.00 0.00 0.00 2.57
4424 4802 4.055178 GGGCCTTTAGTCCCGGTA 57.945 61.111 0.84 0.00 32.00 4.02
4561 5017 8.779096 TTAGTTTTATGGGGAAAAACCTACAA 57.221 30.769 7.59 0.00 44.29 2.41
4563 5019 6.612049 AGTTTTATGGGGAAAAACCTACAACA 59.388 34.615 7.59 0.00 44.29 3.33
4648 5104 4.489679 AAAAGATCAACGTGGCTTCTTC 57.510 40.909 8.01 0.00 0.00 2.87
4782 5238 9.638239 AGAAAATAATTTCAACATAACATGCGT 57.362 25.926 6.07 0.00 46.03 5.24
4857 5313 8.524870 AGATGAATGTGTTTGAAACAATAAGC 57.475 30.769 12.89 0.47 44.16 3.09
4881 5337 6.203723 GCAAAGAGTTCAGTACAATGAAGACT 59.796 38.462 0.00 0.00 39.78 3.24
4927 5383 1.681793 GCTAATAGAGTCCACGGAGCA 59.318 52.381 0.00 0.00 0.00 4.26
4972 5428 7.812690 ATAATGCATGAGATAGCACAAGAAA 57.187 32.000 0.00 0.00 44.49 2.52
5004 5460 4.414852 GTTCATGCCAATGTCATGTGTAC 58.585 43.478 4.12 0.00 41.40 2.90
5138 5594 7.871973 TGCTGAACAATACAACATAGCAAAAAT 59.128 29.630 0.00 0.00 37.03 1.82
5139 5595 8.164153 GCTGAACAATACAACATAGCAAAAATG 58.836 33.333 0.00 0.00 0.00 2.32
5203 5668 7.568366 TCCATAATTTCCCAAAAGGATAATGCT 59.432 33.333 0.00 0.00 46.94 3.79
5237 5702 2.969950 AGCGGGCTATACCATTTAGTGA 59.030 45.455 0.00 0.00 42.05 3.41
5269 5734 3.762779 AGAAGCATTGCAAAACTATCGC 58.237 40.909 11.91 0.00 0.00 4.58
5300 5767 6.650120 ACAGCAAAGCTAAGCCTATTTAGTA 58.350 36.000 6.68 0.00 36.40 1.82
5414 5884 0.303493 TTTGTCGAACTCACTTGCGC 59.697 50.000 0.00 0.00 0.00 6.09
5518 5988 5.700846 TCTCGTCATTCTCAGTTTAGTGTC 58.299 41.667 0.00 0.00 0.00 3.67
5537 6007 3.869832 TGTCAAATGTGCATTGTTTGGTG 59.130 39.130 16.35 0.00 34.48 4.17
5543 6013 4.603989 TGTGCATTGTTTGGTGATCAAT 57.396 36.364 0.00 0.00 34.98 2.57
5588 6058 2.158827 GGCTGACAAAATTTTGGTGGGT 60.159 45.455 29.37 12.35 42.34 4.51
5617 6087 2.824936 TGGCACCAATCAAACATACCAG 59.175 45.455 0.00 0.00 0.00 4.00
5628 6099 9.426837 CAATCAAACATACCAGAAAAATCATGT 57.573 29.630 0.00 0.00 0.00 3.21
5822 6293 7.945033 TGCAGAGACCATTTCAAAATTAAAC 57.055 32.000 0.00 0.00 0.00 2.01
5825 6296 7.653311 GCAGAGACCATTTCAAAATTAAACTGT 59.347 33.333 0.00 0.00 0.00 3.55
5864 6335 2.710377 TGAATCTAGCCACGCAAATGT 58.290 42.857 0.00 0.00 0.00 2.71
5953 6424 7.040409 GGCTCGGAAATGAAACCAATATAATCT 60.040 37.037 0.00 0.00 0.00 2.40
5964 6435 8.877864 AAACCAATATAATCTGTTCTGTTGGA 57.122 30.769 7.71 0.00 35.84 3.53
6002 6473 2.253758 TGTTGCCAGAACAGCGAGC 61.254 57.895 0.00 0.00 0.00 5.03
6026 6497 8.530311 AGCATAACACAATATGGATTTGTTGAA 58.470 29.630 0.00 0.00 35.18 2.69
6054 6525 3.278574 TGCTTTTATTCGGCACTAGCAT 58.721 40.909 0.00 0.00 44.61 3.79
6111 7808 6.954944 TGAACAGTAACTTAAATGTCTGCAC 58.045 36.000 0.00 0.00 0.00 4.57
6147 7845 4.604843 TGACTCATTGCATTGTCGAATC 57.395 40.909 8.36 2.27 32.64 2.52
6160 7858 3.331150 TGTCGAATCGTTGGTGCTAATT 58.669 40.909 1.52 0.00 0.00 1.40
6193 7891 1.737838 TATTTTGGCTCACTGGCTCG 58.262 50.000 0.00 0.00 42.34 5.03
6244 7942 1.452145 TTCGGCACCCAGTTTGCTTC 61.452 55.000 0.00 0.00 40.07 3.86
6391 8089 6.705302 TGCATATTTAACATTTCCTTTGCCA 58.295 32.000 0.00 0.00 0.00 4.92
6446 8144 7.455058 TCATTTGGGAGTAGTTTAGCTAAACA 58.545 34.615 37.77 25.72 45.97 2.83
6556 8369 1.929836 CATAACGAGCTCTGTTCCAGC 59.070 52.381 21.54 0.00 37.12 4.85
6591 8406 0.447801 GTCAAGTAGCCGTGCATTGG 59.552 55.000 3.67 3.67 0.00 3.16
6623 8438 5.871524 TGCAGACACATCAGACTTATCTTTC 59.128 40.000 0.00 0.00 30.42 2.62
6633 8448 7.369803 TCAGACTTATCTTTCTCATTTGTGC 57.630 36.000 0.00 0.00 30.42 4.57
6642 8457 5.302568 TCTTTCTCATTTGTGCACAGGATTT 59.697 36.000 20.59 1.53 0.00 2.17
6706 8528 0.252197 ACCGGCCCTTGACTATTCAC 59.748 55.000 0.00 0.00 0.00 3.18
6886 8715 6.304356 TCTTGTAATCTCTGTTGCACTTTG 57.696 37.500 0.00 0.00 0.00 2.77
6906 8736 8.385111 CACTTTGGTTCATGATGAATTTATTGC 58.615 33.333 11.46 0.00 38.79 3.56
6999 8829 9.693739 TGTTATGAATTTATTCCCTGCTTTCTA 57.306 29.630 0.32 0.00 35.97 2.10
7037 8867 3.456280 TGATTTCCACAAACTTTGCTGC 58.544 40.909 1.14 0.00 0.00 5.25
7058 8923 1.686800 GGGGAGTGCCATGCCATTT 60.687 57.895 1.97 0.00 35.15 2.32
7146 9017 0.745486 CAAGCACATCCTCGATGCCA 60.745 55.000 4.38 0.00 43.15 4.92
7210 9081 5.816258 CAGCAGACACATATGATGTTCTCTT 59.184 40.000 10.38 0.00 42.70 2.85
7277 9148 0.172578 CTCGCACGGTATCTTCCACA 59.827 55.000 0.00 0.00 0.00 4.17
7291 9162 3.578282 TCTTCCACAGTGTAGAAGCATCA 59.422 43.478 22.18 6.54 37.51 3.07
7325 9196 5.279657 GGCCATTTTCCCCAATGAATATCTC 60.280 44.000 0.00 0.00 36.39 2.75
7476 9347 5.014123 AGGGAACAAGATCAACCATTGTCTA 59.986 40.000 0.00 0.00 36.18 2.59
7486 9357 8.207545 AGATCAACCATTGTCTATCTCTTAACC 58.792 37.037 0.00 0.00 0.00 2.85
7524 9395 5.187186 AGAGCTTATTTTACCCTCTCAACGA 59.813 40.000 0.00 0.00 0.00 3.85
7595 9469 3.022406 TCTCTAGCCCGTTCCTTTCTAC 58.978 50.000 0.00 0.00 0.00 2.59
7597 9471 2.758979 TCTAGCCCGTTCCTTTCTACAG 59.241 50.000 0.00 0.00 0.00 2.74
7598 9472 1.349067 AGCCCGTTCCTTTCTACAGT 58.651 50.000 0.00 0.00 0.00 3.55
7599 9473 2.532843 AGCCCGTTCCTTTCTACAGTA 58.467 47.619 0.00 0.00 0.00 2.74
7600 9474 3.105283 AGCCCGTTCCTTTCTACAGTAT 58.895 45.455 0.00 0.00 0.00 2.12
7601 9475 3.118738 AGCCCGTTCCTTTCTACAGTATG 60.119 47.826 0.00 0.00 46.00 2.39
7603 9477 4.430908 CCCGTTCCTTTCTACAGTATGAC 58.569 47.826 0.00 0.00 39.69 3.06
7606 9480 6.040616 CCCGTTCCTTTCTACAGTATGACTAT 59.959 42.308 0.00 0.00 39.69 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 42 3.895704 ACAACCCACCTTTAGTCCATT 57.104 42.857 0.00 0.00 0.00 3.16
41 43 3.895704 AACAACCCACCTTTAGTCCAT 57.104 42.857 0.00 0.00 0.00 3.41
44 46 5.766174 TGTGATAAACAACCCACCTTTAGTC 59.234 40.000 0.00 0.00 35.24 2.59
80 82 0.744414 AACGCTGCGTATTGGCTGAT 60.744 50.000 29.18 6.23 39.99 2.90
92 94 1.063649 CATGAGCATGGAACGCTGC 59.936 57.895 2.54 0.00 40.63 5.25
106 108 3.472283 ACAAATTGCCAAGTTGCATGA 57.528 38.095 16.73 0.00 41.70 3.07
116 118 7.222872 AGTTTGGAATTATGAACAAATTGCCA 58.777 30.769 0.00 0.00 34.75 4.92
484 499 8.993121 TCATCACAACTATTCTTCTTTCTGAAC 58.007 33.333 0.00 0.00 0.00 3.18
540 555 3.586470 ACATATATTTTCCACGGGCCA 57.414 42.857 4.39 0.00 0.00 5.36
614 629 6.663093 AGCCATCTTGTAAAACATATTGTCCA 59.337 34.615 0.00 0.00 0.00 4.02
681 697 7.206981 TCTTTCTGTCTTCATTGGTTCATTC 57.793 36.000 0.00 0.00 0.00 2.67
779 799 9.176751 AGAAAGGCTATATAGGAAGGAAAATCT 57.823 33.333 11.72 0.00 0.00 2.40
781 801 8.387039 GGAGAAAGGCTATATAGGAAGGAAAAT 58.613 37.037 11.72 0.00 0.00 1.82
921 954 2.492012 GGATGAGATGGACAGATGCAC 58.508 52.381 0.00 0.00 0.00 4.57
953 986 2.171079 GGATCAAACGGCGCGATGA 61.171 57.895 12.10 9.73 33.15 2.92
955 988 1.024579 AAAGGATCAAACGGCGCGAT 61.025 50.000 12.10 6.81 0.00 4.58
987 1021 2.809601 GTCATTGCGTCGTCGGCT 60.810 61.111 3.90 0.00 37.56 5.52
1074 1127 2.363147 AGGAGACTGTCGGGGAGC 60.363 66.667 1.52 0.00 41.13 4.70
1383 1451 2.486191 GGCATGTGAGATTTCGAGGGAT 60.486 50.000 0.00 0.00 0.00 3.85
1384 1452 1.134401 GGCATGTGAGATTTCGAGGGA 60.134 52.381 0.00 0.00 0.00 4.20
1415 1497 2.948720 GCAAGAGGCAGGTCGTCCT 61.949 63.158 0.00 0.00 46.37 3.85
1635 1723 2.034221 AAAGAGACAAGGCCCGGC 59.966 61.111 0.00 0.00 0.00 6.13
1653 1741 6.721571 TTACCGAAAAAGTCATCTAGCTTG 57.278 37.500 0.00 0.00 0.00 4.01
1810 1913 3.016031 TGCTGCCATCGTTATGTGAAAT 58.984 40.909 0.00 0.00 0.00 2.17
1840 1946 0.842635 GAGATCCCACCCAGAAGCAT 59.157 55.000 0.00 0.00 0.00 3.79
1883 1989 4.447054 GTCATACCTTGCTCGATTCAGATG 59.553 45.833 0.00 0.00 0.00 2.90
1970 2079 4.941263 TCTGTTTATCTCCGGTTTTCCATG 59.059 41.667 0.00 0.00 40.70 3.66
1979 2088 7.442364 ACAATCATGTAATCTGTTTATCTCCGG 59.558 37.037 0.00 0.00 38.24 5.14
2000 2109 6.716898 TGCGAGATGATCATATTCACAATC 57.283 37.500 8.54 0.00 0.00 2.67
2001 2110 7.683437 AATGCGAGATGATCATATTCACAAT 57.317 32.000 8.54 0.85 0.00 2.71
2002 2111 8.782339 ATAATGCGAGATGATCATATTCACAA 57.218 30.769 8.54 1.14 0.00 3.33
2004 2113 8.326713 GTGATAATGCGAGATGATCATATTCAC 58.673 37.037 8.54 10.28 31.43 3.18
2006 2115 8.645730 AGTGATAATGCGAGATGATCATATTC 57.354 34.615 8.54 8.73 0.00 1.75
2008 2117 9.096160 GAAAGTGATAATGCGAGATGATCATAT 57.904 33.333 8.54 5.08 0.00 1.78
2009 2118 8.309656 AGAAAGTGATAATGCGAGATGATCATA 58.690 33.333 8.54 0.00 0.00 2.15
2026 2170 8.816894 TCAAGTAATCCTTACTGAGAAAGTGAT 58.183 33.333 0.57 0.00 45.33 3.06
2082 2227 8.433126 GCATTTCAAATCTCTTGTGAAAATGAG 58.567 33.333 8.27 0.00 42.70 2.90
2168 2316 2.093235 GCAAGCTAGTGGATCCAAGTCT 60.093 50.000 18.20 12.39 0.00 3.24
2202 2350 3.257127 GTGAGCTTCTCTAGAACTGGTGT 59.743 47.826 0.00 0.00 0.00 4.16
2358 2516 4.082125 CCATTGGACTGTAGCTTCCTTTT 58.918 43.478 0.00 0.00 32.55 2.27
2392 2550 7.796054 ACTATGTTAAGGTGCTCTGATATTGT 58.204 34.615 0.00 0.00 0.00 2.71
2544 2712 6.526674 GCTTTGTTATTAGTTTCATTCCCACG 59.473 38.462 0.00 0.00 0.00 4.94
2592 2760 6.072175 TCCCTACAAACTGTTTTCATGCATAC 60.072 38.462 0.00 0.00 0.00 2.39
2647 2815 4.135306 TCTCTGCCGTTCGTATTCTATCT 58.865 43.478 0.00 0.00 0.00 1.98
2710 2878 9.445878 CATGCTGTGAGTTCCTATATATTTGAT 57.554 33.333 0.00 0.00 0.00 2.57
2752 3044 4.918810 ATTGGCCGACTGAATTATTTCC 57.081 40.909 0.00 0.00 0.00 3.13
2977 3272 7.117236 AGTGCATTCATCAAAAATAACAAGCTG 59.883 33.333 0.00 0.00 0.00 4.24
2978 3273 7.156673 AGTGCATTCATCAAAAATAACAAGCT 58.843 30.769 0.00 0.00 0.00 3.74
2979 3274 7.355332 AGTGCATTCATCAAAAATAACAAGC 57.645 32.000 0.00 0.00 0.00 4.01
2992 3287 9.534565 TTTTCTACTAGTGATAGTGCATTCATC 57.465 33.333 5.39 0.00 0.00 2.92
3083 3378 1.065709 ACGAACCGGGATAAATGCACT 60.066 47.619 6.32 0.00 0.00 4.40
4037 4368 7.120579 AGTCACACATTTCACTGTTTGAGTTTA 59.879 33.333 0.00 0.00 36.54 2.01
4143 4474 3.244249 CCGGGTTCTATTCTCCCTCATTC 60.244 52.174 0.00 0.00 39.10 2.67
4274 4612 8.855804 TTTAACCTCTAATCTCTAATCACCCT 57.144 34.615 0.00 0.00 0.00 4.34
4424 4802 0.981943 CTGAACCGGGACTAAAGGGT 59.018 55.000 6.32 0.00 0.00 4.34
4561 5017 2.577700 TGTACCCGCAACTTTTGATGT 58.422 42.857 0.00 0.00 0.00 3.06
4563 5019 4.947388 ACATATGTACCCGCAACTTTTGAT 59.053 37.500 6.56 0.00 0.00 2.57
4616 5072 8.609176 GCCACGTTGATCTTTTTGTTCTATATA 58.391 33.333 0.00 0.00 0.00 0.86
4617 5073 7.336931 AGCCACGTTGATCTTTTTGTTCTATAT 59.663 33.333 0.00 0.00 0.00 0.86
4627 5083 3.882888 TGAAGAAGCCACGTTGATCTTTT 59.117 39.130 8.75 0.00 30.89 2.27
4638 5094 0.383949 TTGCCGTTTGAAGAAGCCAC 59.616 50.000 0.00 0.00 0.00 5.01
4648 5104 6.755461 TGTAATTTACATTGTTGCCGTTTG 57.245 33.333 5.14 0.00 32.89 2.93
4730 5186 5.567423 CGCCACCACATATCTCATCTTATCA 60.567 44.000 0.00 0.00 0.00 2.15
4779 5235 3.831715 ATTAGCAGAAGGAACAAACGC 57.168 42.857 0.00 0.00 0.00 4.84
4857 5313 7.721286 AGTCTTCATTGTACTGAACTCTTTG 57.279 36.000 0.00 0.00 31.98 2.77
4881 5337 9.381033 CAACCAAATCCATGAATTTTTATGCTA 57.619 29.630 0.00 0.00 0.00 3.49
4972 5428 4.964262 ACATTGGCATGAACCCATAGATTT 59.036 37.500 0.00 0.00 34.11 2.17
5108 5564 6.597280 TGCTATGTTGTATTGTTCAGCATACA 59.403 34.615 0.00 0.00 37.73 2.29
5109 5565 7.015226 TGCTATGTTGTATTGTTCAGCATAC 57.985 36.000 0.00 0.00 37.73 2.39
5138 5594 3.020984 GTTCCAACTTGTCTTGGGTTCA 58.979 45.455 0.00 0.00 41.15 3.18
5139 5595 2.361119 GGTTCCAACTTGTCTTGGGTTC 59.639 50.000 0.00 0.00 41.15 3.62
5203 5668 7.992033 TGGTATAGCCCGCTATTTAAAACTTTA 59.008 33.333 14.11 0.00 39.65 1.85
5237 5702 0.107312 AATGCTTCTCGCTGAGCCAT 60.107 50.000 0.00 0.00 40.11 4.40
5255 5720 0.446222 GCTCCGCGATAGTTTTGCAA 59.554 50.000 8.23 0.00 33.97 4.08
5269 5734 1.929836 CTTAGCTTTGCTGTAGCTCCG 59.070 52.381 10.36 1.76 45.52 4.63
5277 5742 7.736447 ATACTAAATAGGCTTAGCTTTGCTG 57.264 36.000 3.59 0.00 40.10 4.41
5388 5858 4.002906 AGTGAGTTCGACAAAGCCATTA 57.997 40.909 0.00 0.00 0.00 1.90
5414 5884 1.175983 CGCTACAGCTAGAGGAGGGG 61.176 65.000 0.00 0.00 39.32 4.79
5518 5988 4.750598 TGATCACCAAACAATGCACATTTG 59.249 37.500 10.70 10.70 33.90 2.32
5537 6007 4.970662 TTTGGCTGCTACTTGATTGATC 57.029 40.909 0.00 0.00 0.00 2.92
5543 6013 6.127647 CCTTTGATATTTTGGCTGCTACTTGA 60.128 38.462 0.00 0.00 0.00 3.02
5588 6058 9.593134 GTATGTTTGATTGGTGCCAAAATATAA 57.407 29.630 7.81 0.00 39.55 0.98
5864 6335 1.618837 GAACTAGCAGACTGACCCACA 59.381 52.381 6.65 0.00 0.00 4.17
5953 6424 4.952957 TGAACATCCTTTTCCAACAGAACA 59.047 37.500 0.00 0.00 32.95 3.18
5964 6435 7.981225 GGCAACACATATATTGAACATCCTTTT 59.019 33.333 0.00 0.00 0.00 2.27
6026 6497 5.186198 AGTGCCGAATAAAAGCAGAACTAT 58.814 37.500 0.00 0.00 37.15 2.12
6142 7840 4.536364 ATCAATTAGCACCAACGATTCG 57.464 40.909 4.14 4.14 0.00 3.34
6147 7845 5.938322 ACTTGTTATCAATTAGCACCAACG 58.062 37.500 0.00 0.00 32.82 4.10
6160 7858 9.255304 GTGAGCCAAAATAAAAACTTGTTATCA 57.745 29.630 0.00 0.00 0.00 2.15
6175 7873 0.962356 CCGAGCCAGTGAGCCAAAAT 60.962 55.000 0.00 0.00 0.00 1.82
6193 7891 0.035056 TAAGGGCAAGAAGCTGCTCC 60.035 55.000 1.00 0.00 44.44 4.70
6244 7942 3.962481 GCGAATAATTTAGCGCTTGACAG 59.038 43.478 18.68 0.00 45.41 3.51
6272 7970 5.142061 TGAATTCGTAGGCAAGTCTACAA 57.858 39.130 11.88 6.07 39.51 2.41
6376 8074 5.048573 GCAATTTCATGGCAAAGGAAATGTT 60.049 36.000 19.22 8.40 40.17 2.71
6391 8089 6.473455 GCAGAAAACGCTATAAGCAATTTCAT 59.527 34.615 19.76 9.08 42.76 2.57
6470 8283 5.591472 TGAATCTAGGCATGAACTTCCATTG 59.409 40.000 0.00 0.00 0.00 2.82
6556 8369 7.487189 GGCTACTTGACAATGAAAATGAAGATG 59.513 37.037 0.00 0.00 0.00 2.90
6591 8406 4.065088 TCTGATGTGTCTGCAAAAGTACC 58.935 43.478 0.00 0.00 0.00 3.34
6623 8438 3.006110 ACCAAATCCTGTGCACAAATGAG 59.994 43.478 21.98 8.57 0.00 2.90
6655 8470 1.065126 CAACCCAGATCTTCTCACCCC 60.065 57.143 0.00 0.00 0.00 4.95
6706 8528 3.627577 AGCATACTTACGCCTTCCATTTG 59.372 43.478 0.00 0.00 0.00 2.32
6778 8605 8.538409 TTCTAAATTACTCCTTTGTTCGGTAC 57.462 34.615 0.00 0.00 0.00 3.34
6872 8701 3.316029 TCATGAACCAAAGTGCAACAGAG 59.684 43.478 0.00 0.00 41.43 3.35
6886 8715 7.010738 CCAACAGCAATAAATTCATCATGAACC 59.989 37.037 0.98 0.00 39.45 3.62
7002 8832 9.713684 TTTGTGGAAATCAAATAGGGAGAATAT 57.286 29.630 0.00 0.00 31.17 1.28
7037 8867 4.828296 GGCATGGCACTCCCCAGG 62.828 72.222 15.47 0.00 38.50 4.45
7058 8923 1.699634 CCACTGAAGAAAGGGACTCCA 59.300 52.381 0.00 0.00 38.49 3.86
7146 9017 2.594592 GGGGCAGCAACACTTCGT 60.595 61.111 0.00 0.00 0.00 3.85
7210 9081 3.146066 GGAGACCATTAATAATGCCGCA 58.854 45.455 7.45 0.00 37.57 5.69
7277 9148 4.338118 GCTAGAGTCTGATGCTTCTACACT 59.662 45.833 1.86 6.14 0.00 3.55
7291 9162 1.134371 GGAAAATGGCCGCTAGAGTCT 60.134 52.381 0.00 0.00 0.00 3.24
7433 9304 3.244911 CCCTTGGTACCATATCCCATGTC 60.245 52.174 17.17 0.00 0.00 3.06
7524 9395 4.706842 TCAGCTTGAAGTAGAAAAGGGT 57.293 40.909 0.00 0.00 0.00 4.34
7609 9483 9.650714 ATTAGGAGTTAAGTTTTAGGGTGTTTT 57.349 29.630 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.