Multiple sequence alignment - TraesCS5B01G251900

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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 TraesCS5B01G251900 chr5B 100.000 6912 0 0 1 6912 434421458 434414547 0.000000e+00 12765.0
1 TraesCS5B01G251900 chr5B 95.474 2519 85 13 2389 4900 434675362 434672866 0.000000e+00 3993.0
2 TraesCS5B01G251900 chr5B 92.198 1615 79 15 684 2279 434677206 434675620 0.000000e+00 2241.0
3 TraesCS5B01G251900 chr5B 82.994 1623 248 16 4318 5929 434700174 434698569 0.000000e+00 1443.0
4 TraesCS5B01G251900 chr5B 83.091 1579 236 18 4361 5929 434425195 434423638 0.000000e+00 1408.0
5 TraesCS5B01G251900 chr5B 90.327 796 41 17 3287 4080 434568719 434567958 0.000000e+00 1011.0
6 TraesCS5B01G251900 chr5B 81.818 1100 150 32 2867 3945 434702147 434701077 0.000000e+00 878.0
7 TraesCS5B01G251900 chr5B 85.476 778 80 14 684 1439 434617121 434616355 0.000000e+00 780.0
8 TraesCS5B01G251900 chr5B 89.362 517 51 4 2752 3267 434615425 434614912 0.000000e+00 647.0
9 TraesCS5B01G251900 chr5B 82.074 675 96 16 2867 3536 434427364 434426710 2.820000e-153 553.0
10 TraesCS5B01G251900 chr5B 95.018 281 14 0 999 1279 434429077 434428797 6.360000e-120 442.0
11 TraesCS5B01G251900 chr5B 84.346 428 39 15 265 669 277030073 277029651 1.810000e-105 394.0
12 TraesCS5B01G251900 chr5B 90.672 268 24 1 1 268 434617382 434617116 8.530000e-94 355.0
13 TraesCS5B01G251900 chr5B 91.573 178 15 0 4088 4265 434567431 434567254 5.350000e-61 246.0
14 TraesCS5B01G251900 chr5B 79.427 384 47 21 2117 2486 434615899 434615534 6.930000e-60 243.0
15 TraesCS5B01G251900 chr5B 93.827 81 5 0 2536 2616 434675133 434675053 9.410000e-24 122.0
16 TraesCS5B01G251900 chr5B 92.593 81 6 0 2536 2616 434418821 434418741 4.380000e-22 117.0
17 TraesCS5B01G251900 chr5B 92.593 81 6 0 2638 2718 434418923 434418843 4.380000e-22 117.0
18 TraesCS5B01G251900 chr5D 95.632 3915 137 18 2751 6649 367242785 367238889 0.000000e+00 6252.0
19 TraesCS5B01G251900 chr5D 87.991 1782 119 35 318 2062 367245604 367243881 0.000000e+00 2017.0
20 TraesCS5B01G251900 chr5D 89.872 1333 97 21 2752 4080 367344688 367343390 0.000000e+00 1679.0
21 TraesCS5B01G251900 chr5D 82.984 1622 249 16 4318 5929 367415111 367413507 0.000000e+00 1441.0
22 TraesCS5B01G251900 chr5D 83.154 1579 235 18 4361 5929 367251670 367250113 0.000000e+00 1413.0
23 TraesCS5B01G251900 chr5D 81.860 1097 161 23 2867 3946 367253710 367252635 0.000000e+00 889.0
24 TraesCS5B01G251900 chr5D 81.296 1096 168 22 2867 3946 367384223 367383149 0.000000e+00 854.0
25 TraesCS5B01G251900 chr5D 87.467 758 62 23 713 1462 367409695 367408963 0.000000e+00 843.0
26 TraesCS5B01G251900 chr5D 96.491 456 15 1 2165 2619 367243551 367243096 0.000000e+00 752.0
27 TraesCS5B01G251900 chr5D 92.903 310 22 0 999 1308 367419544 367419235 1.060000e-122 451.0
28 TraesCS5B01G251900 chr5D 92.557 309 17 5 975 1279 367254814 367254508 8.230000e-119 438.0
29 TraesCS5B01G251900 chr5D 92.557 309 18 4 975 1279 367385851 367385544 8.230000e-119 438.0
30 TraesCS5B01G251900 chr5D 91.791 268 22 0 1 268 367365868 367365601 2.350000e-99 374.0
31 TraesCS5B01G251900 chr5D 94.561 239 13 0 1 239 367246109 367245871 3.050000e-98 370.0
32 TraesCS5B01G251900 chr5D 77.724 615 98 31 1882 2479 367345399 367344807 2.390000e-89 340.0
33 TraesCS5B01G251900 chr5D 93.011 186 13 0 4077 4262 367312739 367312554 8.830000e-69 272.0
34 TraesCS5B01G251900 chr5D 79.710 414 52 21 265 650 493899852 493900261 3.180000e-68 270.0
35 TraesCS5B01G251900 chr5D 91.667 168 8 2 6609 6770 367238899 367238732 1.940000e-55 228.0
36 TraesCS5B01G251900 chr5D 94.167 120 6 1 2062 2181 367243838 367243720 1.530000e-41 182.0
37 TraesCS5B01G251900 chr5D 93.243 74 1 4 1370 1439 367345591 367345518 9.480000e-19 106.0
38 TraesCS5B01G251900 chr5D 96.970 33 0 1 2062 2094 275415506 275415475 3.000000e-03 54.7
39 TraesCS5B01G251900 chr5A 96.045 3312 114 7 3600 6902 469056944 469053641 0.000000e+00 5374.0
40 TraesCS5B01G251900 chr5A 94.234 1561 62 11 2062 3601 469058578 469057025 0.000000e+00 2359.0
41 TraesCS5B01G251900 chr5A 88.051 1406 114 35 687 2062 469060002 469058621 0.000000e+00 1616.0
42 TraesCS5B01G251900 chr5A 82.933 1623 249 16 4318 5929 469063900 469062295 0.000000e+00 1437.0
43 TraesCS5B01G251900 chr5A 93.836 292 12 5 990 1279 469068131 469067844 1.060000e-117 435.0
44 TraesCS5B01G251900 chr5A 93.827 81 5 0 2536 2616 469057985 469057905 9.410000e-24 122.0
45 TraesCS5B01G251900 chr6D 82.999 1694 246 22 4320 6001 78352942 78354605 0.000000e+00 1495.0
46 TraesCS5B01G251900 chr6D 80.245 653 102 19 3383 4023 78352011 78352648 3.780000e-127 466.0
47 TraesCS5B01G251900 chr6D 87.059 85 10 1 549 632 468063276 468063192 2.050000e-15 95.3
48 TraesCS5B01G251900 chr3A 83.444 302 31 8 381 664 535730483 535730783 5.320000e-66 263.0
49 TraesCS5B01G251900 chr3A 100.000 29 0 0 2064 2092 209651453 209651481 3.000000e-03 54.7
50 TraesCS5B01G251900 chr3A 100.000 28 0 0 2062 2089 417926908 417926935 1.300000e-02 52.8
51 TraesCS5B01G251900 chr3A 100.000 28 0 0 2065 2092 595067761 595067788 1.300000e-02 52.8
52 TraesCS5B01G251900 chr7D 91.053 190 15 2 263 451 44659721 44659533 8.900000e-64 255.0
53 TraesCS5B01G251900 chr1A 95.385 65 3 0 370 434 505512518 505512454 3.410000e-18 104.0
54 TraesCS5B01G251900 chr6B 92.754 69 3 2 364 430 707109418 707109350 1.590000e-16 99.0
55 TraesCS5B01G251900 chr6B 94.595 37 2 0 2484 2520 262272465 262272501 2.690000e-04 58.4
56 TraesCS5B01G251900 chr2B 100.000 29 0 0 2064 2092 790686314 790686342 3.000000e-03 54.7
57 TraesCS5B01G251900 chr3D 100.000 28 0 0 2062 2089 314619719 314619746 1.300000e-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 TraesCS5B01G251900 chr5B 434414547 434421458 6911 True 4333.000000 12765 95.062000 1 6912 3 chr5B.!!$R2 6911
1 TraesCS5B01G251900 chr5B 434672866 434677206 4340 True 2118.666667 3993 93.833000 684 4900 3 chr5B.!!$R6 4216
2 TraesCS5B01G251900 chr5B 434698569 434702147 3578 True 1160.500000 1443 82.406000 2867 5929 2 chr5B.!!$R7 3062
3 TraesCS5B01G251900 chr5B 434423638 434429077 5439 True 801.000000 1408 86.727667 999 5929 3 chr5B.!!$R3 4930
4 TraesCS5B01G251900 chr5B 434567254 434568719 1465 True 628.500000 1011 90.950000 3287 4265 2 chr5B.!!$R4 978
5 TraesCS5B01G251900 chr5B 434614912 434617382 2470 True 506.250000 780 86.234250 1 3267 4 chr5B.!!$R5 3266
6 TraesCS5B01G251900 chr5D 367238732 367246109 7377 True 1633.500000 6252 93.418167 1 6770 6 chr5D.!!$R5 6769
7 TraesCS5B01G251900 chr5D 367408963 367415111 6148 True 1142.000000 1441 85.225500 713 5929 2 chr5D.!!$R9 5216
8 TraesCS5B01G251900 chr5D 367250113 367254814 4701 True 913.333333 1413 85.857000 975 5929 3 chr5D.!!$R6 4954
9 TraesCS5B01G251900 chr5D 367343390 367345591 2201 True 708.333333 1679 86.946333 1370 4080 3 chr5D.!!$R7 2710
10 TraesCS5B01G251900 chr5D 367383149 367385851 2702 True 646.000000 854 86.926500 975 3946 2 chr5D.!!$R8 2971
11 TraesCS5B01G251900 chr5A 469053641 469068131 14490 True 1890.500000 5374 91.487667 687 6902 6 chr5A.!!$R1 6215
12 TraesCS5B01G251900 chr6D 78352011 78354605 2594 False 980.500000 1495 81.622000 3383 6001 2 chr6D.!!$F1 2618

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
707 918 0.031585 GGTTTGAAAGTGCCCGAACC 59.968 55.000 0.00 0.00 39.02 3.62 F
889 8341 0.389948 GGTCGGCTGTCCACTACAAG 60.390 60.000 3.70 0.00 37.74 3.16 F
1482 9855 0.467844 GACCATACATGCCATGGCCA 60.468 55.000 33.44 21.36 45.85 5.36 F
1483 9856 0.756442 ACCATACATGCCATGGCCAC 60.756 55.000 33.44 7.65 45.85 5.01 F
1486 9859 0.756442 ATACATGCCATGGCCACCAC 60.756 55.000 33.44 6.02 41.09 4.16 F
2737 12074 1.472480 CCCTTAAACGCTCAACCCATG 59.528 52.381 0.00 0.00 0.00 3.66 F
3432 12784 1.935873 TGAGCGAATTGATACAGCTGC 59.064 47.619 15.27 0.00 38.39 5.25 F
3726 13286 3.390521 ATGGCACGGGAGAAGCGA 61.391 61.111 0.00 0.00 35.80 4.93 F
5389 16265 2.677914 ACGAGTCCATGGATATCACCA 58.322 47.619 19.62 0.00 44.41 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1948 10570 0.759346 GGGTTGTGACACTGGTCTCT 59.241 55.000 7.20 0.00 44.61 3.10 R
2012 10748 1.323412 ATTGCCCGCTGTGTTTTGTA 58.677 45.000 0.00 0.00 0.00 2.41 R
3186 12525 0.540365 CACTCCTTTGGGGTGCACAT 60.540 55.000 20.43 0.00 36.25 3.21 R
3203 12542 3.055385 TGCTTACCCTGATAAGTGACCAC 60.055 47.826 0.00 0.00 35.05 4.16 R
3373 12720 4.959723 TCTCCTGCCCAAAAATGAAAAAG 58.040 39.130 0.00 0.00 0.00 2.27 R
3726 13286 3.245229 TGAAATTATGGTGGTGCTGAGGT 60.245 43.478 0.00 0.00 0.00 3.85 R
5383 16259 8.314021 ACACATACGACATATATGAATGGTGAT 58.686 33.333 19.63 7.56 34.65 3.06 R
5698 16574 1.640917 TTTGACTAAGCCCTCCGACT 58.359 50.000 0.00 0.00 0.00 4.18 R
6886 21415 1.308998 CTTTGCTGTCGTTCCCACTT 58.691 50.000 0.00 0.00 0.00 3.16 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
150 151 1.450312 GACATGGGAAGGGTGAGCG 60.450 63.158 0.00 0.00 0.00 5.03
152 153 3.329889 ATGGGAAGGGTGAGCGCA 61.330 61.111 11.47 0.00 0.00 6.09
223 225 2.057408 GGCCGGCATTGGGATTTCA 61.057 57.895 30.85 0.00 0.00 2.69
236 238 2.823154 GGGATTTCAAATGTCCGAACCA 59.177 45.455 0.00 0.00 32.71 3.67
253 255 5.279256 CCGAACCAATCCAACCTAAAATGTT 60.279 40.000 0.00 0.00 0.00 2.71
265 267 5.949735 ACCTAAAATGTTTGTCCGCATTAG 58.050 37.500 0.00 0.00 34.61 1.73
283 285 2.378028 GAGCATCTCCACTCGTTGC 58.622 57.895 0.00 0.00 0.00 4.17
286 288 1.450312 CATCTCCACTCGTTGCCCC 60.450 63.158 0.00 0.00 0.00 5.80
287 289 2.670148 ATCTCCACTCGTTGCCCCC 61.670 63.158 0.00 0.00 0.00 5.40
288 290 3.322466 CTCCACTCGTTGCCCCCT 61.322 66.667 0.00 0.00 0.00 4.79
289 291 3.316573 CTCCACTCGTTGCCCCCTC 62.317 68.421 0.00 0.00 0.00 4.30
290 292 4.410400 CCACTCGTTGCCCCCTCC 62.410 72.222 0.00 0.00 0.00 4.30
308 310 2.854076 CCCCCAGGAGCCACTTTT 59.146 61.111 0.00 0.00 33.47 2.27
309 311 1.156095 CCCCCAGGAGCCACTTTTT 59.844 57.895 0.00 0.00 33.47 1.94
311 313 0.178964 CCCCAGGAGCCACTTTTTCA 60.179 55.000 0.00 0.00 0.00 2.69
312 314 1.703411 CCCAGGAGCCACTTTTTCAA 58.297 50.000 0.00 0.00 0.00 2.69
316 318 1.133915 AGGAGCCACTTTTTCAACCGA 60.134 47.619 0.00 0.00 0.00 4.69
332 522 3.219198 GATTGGGGTCATGCCGGC 61.219 66.667 22.73 22.73 38.44 6.13
376 566 2.284552 TTTTCCAGCCATGCCCCC 60.285 61.111 0.00 0.00 0.00 5.40
478 668 3.243301 GCATGCAAGAGAGAGAGAGAGAG 60.243 52.174 14.21 0.00 0.00 3.20
479 669 3.003394 TGCAAGAGAGAGAGAGAGAGG 57.997 52.381 0.00 0.00 0.00 3.69
480 670 2.575735 TGCAAGAGAGAGAGAGAGAGGA 59.424 50.000 0.00 0.00 0.00 3.71
481 671 3.209410 GCAAGAGAGAGAGAGAGAGGAG 58.791 54.545 0.00 0.00 0.00 3.69
482 672 3.118261 GCAAGAGAGAGAGAGAGAGGAGA 60.118 52.174 0.00 0.00 0.00 3.71
483 673 4.701765 CAAGAGAGAGAGAGAGAGGAGAG 58.298 52.174 0.00 0.00 0.00 3.20
484 674 4.271807 AGAGAGAGAGAGAGAGGAGAGA 57.728 50.000 0.00 0.00 0.00 3.10
485 675 4.222336 AGAGAGAGAGAGAGAGGAGAGAG 58.778 52.174 0.00 0.00 0.00 3.20
499 689 0.324275 AGAGAGGGAGTGTGAGGCTC 60.324 60.000 7.79 7.79 0.00 4.70
582 784 1.670083 GTCGCCGGCCTAGTTTTGT 60.670 57.895 23.46 0.00 0.00 2.83
583 785 1.071814 TCGCCGGCCTAGTTTTGTT 59.928 52.632 23.46 0.00 0.00 2.83
590 792 3.366985 CCGGCCTAGTTTTGTTCAAATCC 60.367 47.826 0.00 0.00 0.00 3.01
650 852 3.907894 TTTTACTGCCGGTGCTAAAAG 57.092 42.857 1.90 0.00 38.71 2.27
660 862 3.057596 CCGGTGCTAAAAGAATTGCTTGA 60.058 43.478 0.00 0.00 36.80 3.02
663 865 4.488879 GTGCTAAAAGAATTGCTTGAGGG 58.511 43.478 0.00 0.00 36.80 4.30
668 879 3.515602 AAGAATTGCTTGAGGGTGTCT 57.484 42.857 0.00 0.00 34.93 3.41
682 893 0.671781 GTGTCTGCGTGGAGATGCTT 60.672 55.000 0.00 0.00 34.90 3.91
697 908 6.207417 TGGAGATGCTTTTAGAGGTTTGAAAG 59.793 38.462 0.00 0.00 33.41 2.62
698 909 6.207614 GGAGATGCTTTTAGAGGTTTGAAAGT 59.792 38.462 0.00 0.00 32.97 2.66
699 910 6.974965 AGATGCTTTTAGAGGTTTGAAAGTG 58.025 36.000 0.00 0.00 32.97 3.16
700 911 4.932146 TGCTTTTAGAGGTTTGAAAGTGC 58.068 39.130 0.00 0.00 32.97 4.40
701 912 4.202111 TGCTTTTAGAGGTTTGAAAGTGCC 60.202 41.667 0.00 0.00 32.97 5.01
703 914 2.178912 TAGAGGTTTGAAAGTGCCCG 57.821 50.000 0.00 0.00 0.00 6.13
704 915 0.472471 AGAGGTTTGAAAGTGCCCGA 59.528 50.000 0.00 0.00 0.00 5.14
705 916 1.133915 AGAGGTTTGAAAGTGCCCGAA 60.134 47.619 0.00 0.00 0.00 4.30
706 917 1.001706 GAGGTTTGAAAGTGCCCGAAC 60.002 52.381 0.00 0.00 0.00 3.95
707 918 0.031585 GGTTTGAAAGTGCCCGAACC 59.968 55.000 0.00 0.00 39.02 3.62
708 919 0.741915 GTTTGAAAGTGCCCGAACCA 59.258 50.000 0.00 0.00 0.00 3.67
709 920 1.339929 GTTTGAAAGTGCCCGAACCAT 59.660 47.619 0.00 0.00 0.00 3.55
710 921 1.243902 TTGAAAGTGCCCGAACCATC 58.756 50.000 0.00 0.00 0.00 3.51
711 922 0.608035 TGAAAGTGCCCGAACCATCC 60.608 55.000 0.00 0.00 0.00 3.51
712 923 1.644786 GAAAGTGCCCGAACCATCCG 61.645 60.000 0.00 0.00 0.00 4.18
713 924 2.119484 AAAGTGCCCGAACCATCCGA 62.119 55.000 0.00 0.00 0.00 4.55
714 925 1.910580 AAGTGCCCGAACCATCCGAT 61.911 55.000 0.00 0.00 0.00 4.18
715 926 1.887707 GTGCCCGAACCATCCGATC 60.888 63.158 0.00 0.00 0.00 3.69
716 927 2.661866 GCCCGAACCATCCGATCG 60.662 66.667 8.51 8.51 36.39 3.69
779 8224 2.117206 GGTGTTGCCATGTGGGGA 59.883 61.111 0.54 0.00 37.04 4.81
789 8234 0.894642 CATGTGGGGATGTGTGTGCA 60.895 55.000 0.00 0.00 0.00 4.57
889 8341 0.389948 GGTCGGCTGTCCACTACAAG 60.390 60.000 3.70 0.00 37.74 3.16
1302 8791 1.079197 TGTATGCTCCGGCTGTGTG 60.079 57.895 0.00 0.00 39.59 3.82
1466 9835 1.217882 CGGACTGTGAGTTTGTGACC 58.782 55.000 0.00 0.00 0.00 4.02
1477 9850 3.696051 GAGTTTGTGACCATACATGCCAT 59.304 43.478 0.00 0.00 0.00 4.40
1478 9851 3.444742 AGTTTGTGACCATACATGCCATG 59.555 43.478 2.40 2.40 0.00 3.66
1482 9855 0.467844 GACCATACATGCCATGGCCA 60.468 55.000 33.44 21.36 45.85 5.36
1483 9856 0.756442 ACCATACATGCCATGGCCAC 60.756 55.000 33.44 7.65 45.85 5.01
1486 9859 0.756442 ATACATGCCATGGCCACCAC 60.756 55.000 33.44 6.02 41.09 4.16
1506 9881 5.441700 CACTCAATAGTGTAAACAGCGAG 57.558 43.478 0.00 0.00 46.76 5.03
1672 10261 4.266714 TCCCAAATTGTTCGGTCTAATCC 58.733 43.478 0.00 0.00 0.00 3.01
1674 10263 4.644685 CCCAAATTGTTCGGTCTAATCCAT 59.355 41.667 0.00 0.00 0.00 3.41
1715 10304 6.150140 GGAGTTGGTCTAATCCATATGATTGC 59.850 42.308 3.65 0.00 43.57 3.56
1717 10306 5.581350 TGGTCTAATCCATATGATTGCCA 57.419 39.130 3.65 9.36 43.57 4.92
1920 10526 6.647334 TTTCAGTATGTTGGCTGATTTTCA 57.353 33.333 0.00 0.00 40.83 2.69
1948 10570 4.021368 GCTCTTGGACTCAGTTAGGTACAA 60.021 45.833 0.00 0.00 35.33 2.41
1955 10577 4.737578 ACTCAGTTAGGTACAAGAGACCA 58.262 43.478 0.00 0.00 39.65 4.02
1956 10578 4.767928 ACTCAGTTAGGTACAAGAGACCAG 59.232 45.833 0.00 0.00 39.65 4.00
1957 10579 4.737578 TCAGTTAGGTACAAGAGACCAGT 58.262 43.478 0.00 0.00 39.65 4.00
1958 10580 4.523173 TCAGTTAGGTACAAGAGACCAGTG 59.477 45.833 0.00 0.00 39.65 3.66
2049 10785 4.364860 GCAATTTCTAACGGGTGTTTTGT 58.635 39.130 0.00 0.00 39.54 2.83
2154 10944 3.639094 ACTTCAACGAGATAGCAGCCTAT 59.361 43.478 0.00 0.00 36.98 2.57
2164 10954 5.994250 AGATAGCAGCCTATTGAGTTTCAA 58.006 37.500 0.00 0.00 41.09 2.69
2508 11645 2.981081 TCCCTCCTTTCCGGTTTAAAGA 59.019 45.455 14.10 1.47 36.27 2.52
2737 12074 1.472480 CCCTTAAACGCTCAACCCATG 59.528 52.381 0.00 0.00 0.00 3.66
3153 12492 3.177884 AGCCAAGGTCACCAGCCA 61.178 61.111 0.00 0.00 0.00 4.75
3186 12525 4.040095 CAGAGTCAGATGGGCATCAAGATA 59.960 45.833 0.00 0.00 40.22 1.98
3203 12542 2.092212 AGATATGTGCACCCCAAAGGAG 60.092 50.000 15.69 0.00 39.89 3.69
3373 12720 3.988379 TTTGGCATGACAACTGACTTC 57.012 42.857 15.21 0.00 0.00 3.01
3432 12784 1.935873 TGAGCGAATTGATACAGCTGC 59.064 47.619 15.27 0.00 38.39 5.25
3465 12817 6.206048 GGTAAAATTTCGGAGGAAGTCAAAGA 59.794 38.462 0.00 0.00 32.80 2.52
3691 13251 5.702865 CAAATGATGACGAAGGAAATGTGT 58.297 37.500 0.00 0.00 0.00 3.72
3726 13286 3.390521 ATGGCACGGGAGAAGCGA 61.391 61.111 0.00 0.00 35.80 4.93
3809 13373 4.991789 TGCCCCATCATACTAAGCATAA 57.008 40.909 0.00 0.00 0.00 1.90
4196 14681 3.556543 AAGCGCACCCAATTGCACG 62.557 57.895 11.47 1.77 43.15 5.34
5383 16259 3.895041 TGCAGATTACGAGTCCATGGATA 59.105 43.478 19.62 2.81 0.00 2.59
5389 16265 2.677914 ACGAGTCCATGGATATCACCA 58.322 47.619 19.62 0.00 44.41 4.17
5402 16278 8.985805 CATGGATATCACCATTCATATATGTCG 58.014 37.037 12.42 2.82 47.00 4.35
5515 16391 7.730084 TGGTCAGAAGAATAACCTCATATCTG 58.270 38.462 0.00 0.00 35.53 2.90
5638 16514 3.118542 GCAAGAAATCATGGAATTCGGC 58.881 45.455 0.00 2.21 0.00 5.54
5698 16574 7.277098 GTCGCATTACTCAACCTTATTTGTCTA 59.723 37.037 0.00 0.00 0.00 2.59
5845 16724 2.751806 GAGGAAGGACAAAGGCAGAATG 59.248 50.000 0.00 0.00 40.87 2.67
6126 19872 3.403038 GGCCTACCTAATACACATGCTG 58.597 50.000 0.00 0.00 0.00 4.41
6128 19874 4.058817 GCCTACCTAATACACATGCTGAC 58.941 47.826 0.00 0.00 0.00 3.51
6290 20036 1.356124 AGCAAGATGGACCACAGAGT 58.644 50.000 0.00 0.00 0.00 3.24
6321 20067 6.209788 AGACTACCCTCTTCTAAGAAACTGTG 59.790 42.308 0.00 0.00 34.03 3.66
6372 20724 4.884164 GTCAGATAAACATCTTGAAGGGGG 59.116 45.833 0.00 0.00 0.00 5.40
6807 21335 8.126700 AGTTACACATAAAACAAGTGTTACAGC 58.873 33.333 13.97 0.00 43.97 4.40
6828 21357 6.017770 ACAGCACGCTTAATGTGTAAACTTTA 60.018 34.615 9.07 0.00 39.53 1.85
6830 21359 7.216317 CAGCACGCTTAATGTGTAAACTTTATC 59.784 37.037 9.07 0.00 39.53 1.75
6867 21396 8.681486 TGTGCAGCTATATCATTGTTAAATCT 57.319 30.769 0.00 0.00 0.00 2.40
6886 21415 5.957771 ATCTGAACTGAGGGCTAACATAA 57.042 39.130 0.00 0.00 0.00 1.90
6895 21424 3.945921 GAGGGCTAACATAAAGTGGGAAC 59.054 47.826 0.00 0.00 0.00 3.62
6897 21426 3.602483 GGCTAACATAAAGTGGGAACGA 58.398 45.455 0.00 0.00 0.00 3.85
6902 21431 2.224426 ACATAAAGTGGGAACGACAGCA 60.224 45.455 0.00 0.00 0.00 4.41
6903 21432 2.623878 TAAAGTGGGAACGACAGCAA 57.376 45.000 0.00 0.00 0.00 3.91
6904 21433 1.757682 AAAGTGGGAACGACAGCAAA 58.242 45.000 0.00 0.00 0.00 3.68
6905 21434 1.308998 AAGTGGGAACGACAGCAAAG 58.691 50.000 0.00 0.00 0.00 2.77
6906 21435 0.180406 AGTGGGAACGACAGCAAAGT 59.820 50.000 0.00 0.00 0.00 2.66
6907 21436 1.021968 GTGGGAACGACAGCAAAGTT 58.978 50.000 0.00 0.00 0.00 2.66
6908 21437 1.021202 TGGGAACGACAGCAAAGTTG 58.979 50.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 71 0.037590 TACCTGCATTCAAGCCCGTT 59.962 50.000 0.00 0.00 0.00 4.44
71 72 0.392998 CTACCTGCATTCAAGCCCGT 60.393 55.000 0.00 0.00 0.00 5.28
223 225 2.560981 GGTTGGATTGGTTCGGACATTT 59.439 45.455 0.00 0.00 0.00 2.32
236 238 5.778862 CGGACAAACATTTTAGGTTGGATT 58.221 37.500 0.00 0.00 0.00 3.01
253 255 2.483714 GGAGATGCTCTAATGCGGACAA 60.484 50.000 0.00 0.00 35.36 3.18
265 267 1.086634 GGCAACGAGTGGAGATGCTC 61.087 60.000 0.00 0.00 37.20 4.26
273 275 4.410400 GGAGGGGGCAACGAGTGG 62.410 72.222 0.00 0.00 37.60 4.00
293 295 1.341209 GTTGAAAAAGTGGCTCCTGGG 59.659 52.381 0.00 0.00 0.00 4.45
294 296 1.341209 GGTTGAAAAAGTGGCTCCTGG 59.659 52.381 0.00 0.00 0.00 4.45
296 298 1.133915 TCGGTTGAAAAAGTGGCTCCT 60.134 47.619 0.00 0.00 0.00 3.69
298 300 3.308530 CAATCGGTTGAAAAAGTGGCTC 58.691 45.455 0.90 0.00 37.53 4.70
299 301 2.035832 CCAATCGGTTGAAAAAGTGGCT 59.964 45.455 10.75 0.00 37.53 4.75
300 302 2.403259 CCAATCGGTTGAAAAAGTGGC 58.597 47.619 10.75 0.00 37.53 5.01
301 303 2.288763 CCCCAATCGGTTGAAAAAGTGG 60.289 50.000 10.75 0.00 37.53 4.00
302 304 2.364002 ACCCCAATCGGTTGAAAAAGTG 59.636 45.455 10.75 0.00 37.53 3.16
303 305 2.626266 GACCCCAATCGGTTGAAAAAGT 59.374 45.455 10.75 0.00 37.53 2.66
304 306 2.625790 TGACCCCAATCGGTTGAAAAAG 59.374 45.455 10.75 0.00 37.53 2.27
305 307 2.667470 TGACCCCAATCGGTTGAAAAA 58.333 42.857 10.75 0.00 37.53 1.94
306 308 2.366640 TGACCCCAATCGGTTGAAAA 57.633 45.000 10.75 0.00 37.53 2.29
307 309 2.166829 CATGACCCCAATCGGTTGAAA 58.833 47.619 10.75 0.00 37.53 2.69
308 310 1.832883 CATGACCCCAATCGGTTGAA 58.167 50.000 10.75 0.00 37.53 2.69
309 311 0.679640 GCATGACCCCAATCGGTTGA 60.680 55.000 10.75 0.00 37.53 3.18
311 313 1.379843 GGCATGACCCCAATCGGTT 60.380 57.895 0.00 0.00 35.79 4.44
312 314 2.275418 GGCATGACCCCAATCGGT 59.725 61.111 0.00 0.00 39.49 4.69
332 522 0.107752 CCCCCATGCCAAAATTTCCG 60.108 55.000 0.00 0.00 0.00 4.30
376 566 4.039245 TCTCTTGTCTTCTAGTGTTGGGTG 59.961 45.833 0.00 0.00 0.00 4.61
451 641 3.055312 TCTCTCTCTCTTGCATGCAACAT 60.055 43.478 28.80 0.00 0.00 2.71
478 668 1.326951 GCCTCACACTCCCTCTCTCC 61.327 65.000 0.00 0.00 0.00 3.71
479 669 0.324275 AGCCTCACACTCCCTCTCTC 60.324 60.000 0.00 0.00 0.00 3.20
480 670 0.324275 GAGCCTCACACTCCCTCTCT 60.324 60.000 0.00 0.00 0.00 3.10
481 671 0.613292 TGAGCCTCACACTCCCTCTC 60.613 60.000 0.00 0.00 32.98 3.20
482 672 0.902516 GTGAGCCTCACACTCCCTCT 60.903 60.000 19.77 0.00 46.22 3.69
483 673 1.594310 GTGAGCCTCACACTCCCTC 59.406 63.158 19.77 0.00 46.22 4.30
484 674 3.798758 GTGAGCCTCACACTCCCT 58.201 61.111 19.77 0.00 46.22 4.20
572 773 3.669557 CGCCGGATTTGAACAAAACTAGG 60.670 47.826 5.05 9.87 33.56 3.02
575 777 1.601914 GCGCCGGATTTGAACAAAACT 60.602 47.619 5.05 0.00 33.56 2.66
582 784 0.661780 CGTTTTGCGCCGGATTTGAA 60.662 50.000 5.05 0.00 0.00 2.69
583 785 1.081774 CGTTTTGCGCCGGATTTGA 60.082 52.632 5.05 0.00 0.00 2.69
604 806 4.767255 CAGCCACGCCCTCAGGAC 62.767 72.222 0.00 0.00 33.47 3.85
650 852 1.200948 GCAGACACCCTCAAGCAATTC 59.799 52.381 0.00 0.00 0.00 2.17
660 862 1.610673 ATCTCCACGCAGACACCCT 60.611 57.895 0.00 0.00 0.00 4.34
663 865 0.671781 AAGCATCTCCACGCAGACAC 60.672 55.000 0.00 0.00 0.00 3.67
668 879 2.621338 CTCTAAAAGCATCTCCACGCA 58.379 47.619 0.00 0.00 0.00 5.24
682 893 2.882137 CGGGCACTTTCAAACCTCTAAA 59.118 45.455 0.00 0.00 0.00 1.85
697 908 1.887707 GATCGGATGGTTCGGGCAC 60.888 63.158 0.00 0.00 0.00 5.01
698 909 2.504032 GATCGGATGGTTCGGGCA 59.496 61.111 0.00 0.00 0.00 5.36
699 910 2.661866 CGATCGGATGGTTCGGGC 60.662 66.667 7.38 0.00 34.88 6.13
700 911 1.007271 CTCGATCGGATGGTTCGGG 60.007 63.158 16.41 0.00 38.19 5.14
701 912 1.007271 CCTCGATCGGATGGTTCGG 60.007 63.158 16.41 0.00 38.19 4.30
703 914 1.661821 CGCCTCGATCGGATGGTTC 60.662 63.158 16.41 3.33 0.00 3.62
704 915 1.464376 ATCGCCTCGATCGGATGGTT 61.464 55.000 16.41 2.95 43.45 3.67
705 916 1.464376 AATCGCCTCGATCGGATGGT 61.464 55.000 16.41 0.00 46.30 3.55
706 917 0.319900 AAATCGCCTCGATCGGATGG 60.320 55.000 16.41 15.60 46.30 3.51
707 918 0.786581 CAAATCGCCTCGATCGGATG 59.213 55.000 16.41 5.19 46.30 3.51
708 919 0.673985 TCAAATCGCCTCGATCGGAT 59.326 50.000 16.41 7.02 46.30 4.18
709 920 0.673985 ATCAAATCGCCTCGATCGGA 59.326 50.000 16.41 4.64 46.30 4.55
710 921 0.786581 CATCAAATCGCCTCGATCGG 59.213 55.000 16.41 5.93 46.30 4.18
711 922 1.718178 CTCATCAAATCGCCTCGATCG 59.282 52.381 9.36 9.36 46.30 3.69
712 923 2.728839 GACTCATCAAATCGCCTCGATC 59.271 50.000 2.01 0.00 46.30 3.69
714 925 1.533965 CGACTCATCAAATCGCCTCGA 60.534 52.381 0.00 0.00 41.13 4.04
715 926 0.848942 CGACTCATCAAATCGCCTCG 59.151 55.000 0.00 0.00 0.00 4.63
716 927 1.590238 CACGACTCATCAAATCGCCTC 59.410 52.381 0.00 0.00 39.47 4.70
767 8212 1.304299 CACACATCCCCACATGGCA 60.304 57.895 0.00 0.00 0.00 4.92
789 8234 3.941188 CACTGCCCCACTCCACGT 61.941 66.667 0.00 0.00 0.00 4.49
1179 8661 2.681064 ACCCAGTAGGCGGCGTAA 60.681 61.111 9.37 0.00 40.58 3.18
1466 9835 0.756070 TGGTGGCCATGGCATGTATG 60.756 55.000 36.56 11.77 44.11 2.39
1486 9859 4.177026 AGCTCGCTGTTTACACTATTGAG 58.823 43.478 0.00 0.00 0.00 3.02
1591 10180 1.542492 AACACGTCCGGACACTATCT 58.458 50.000 32.80 10.00 0.00 1.98
1672 10261 3.074985 ACTCCATCCCCACCAATCATATG 59.925 47.826 0.00 0.00 0.00 1.78
1674 10263 2.787956 ACTCCATCCCCACCAATCATA 58.212 47.619 0.00 0.00 0.00 2.15
1715 10304 1.066573 CCAGTTGTCTAGGCAGTCTGG 60.067 57.143 25.32 25.32 36.66 3.86
1717 10306 1.896465 GTCCAGTTGTCTAGGCAGTCT 59.104 52.381 0.00 0.00 0.00 3.24
1920 10526 4.081198 CCTAACTGAGTCCAAGAGCTTCAT 60.081 45.833 0.00 0.00 0.00 2.57
1948 10570 0.759346 GGGTTGTGACACTGGTCTCT 59.241 55.000 7.20 0.00 44.61 3.10
1955 10577 4.724399 TCATTATTGTGGGTTGTGACACT 58.276 39.130 7.20 0.00 38.39 3.55
1956 10578 5.219633 GTTCATTATTGTGGGTTGTGACAC 58.780 41.667 0.00 0.00 38.08 3.67
1957 10579 4.279671 GGTTCATTATTGTGGGTTGTGACA 59.720 41.667 0.00 0.00 0.00 3.58
1958 10580 4.279671 TGGTTCATTATTGTGGGTTGTGAC 59.720 41.667 0.00 0.00 0.00 3.67
2012 10748 1.323412 ATTGCCCGCTGTGTTTTGTA 58.677 45.000 0.00 0.00 0.00 2.41
2154 10944 4.279671 AGTGTTGTGTGGTTTGAAACTCAA 59.720 37.500 8.09 6.30 34.03 3.02
2164 10954 2.422127 GTGCACTTAGTGTTGTGTGGTT 59.578 45.455 14.23 0.00 35.75 3.67
2403 11532 9.462174 CTAAGTTAGTGATCTCTGATCATCAAC 57.538 37.037 12.53 16.34 30.76 3.18
2508 11645 7.503902 ACCACTTTTCTTTTCTTGAGATAAGCT 59.496 33.333 6.39 0.00 36.36 3.74
2683 11820 6.416631 TCTAAACAGATGATGGAGATGGAG 57.583 41.667 0.00 0.00 0.00 3.86
2737 12074 2.897969 TGAAGTACTCACTCCCTGGTTC 59.102 50.000 0.00 0.00 32.29 3.62
3153 12492 4.709397 CCCATCTGACTCTGAGAAGTAAGT 59.291 45.833 12.44 0.00 30.69 2.24
3186 12525 0.540365 CACTCCTTTGGGGTGCACAT 60.540 55.000 20.43 0.00 36.25 3.21
3203 12542 3.055385 TGCTTACCCTGATAAGTGACCAC 60.055 47.826 0.00 0.00 35.05 4.16
3373 12720 4.959723 TCTCCTGCCCAAAAATGAAAAAG 58.040 39.130 0.00 0.00 0.00 2.27
3432 12784 5.472137 TCCTCCGAAATTTTACCTGACAAAG 59.528 40.000 0.00 0.00 0.00 2.77
3465 12817 9.841295 CCCATTCATGAAATCCTTTATGATTTT 57.159 29.630 13.09 0.00 43.23 1.82
3691 13251 3.566322 GCCATGTACACAAGTGTTGGTAA 59.434 43.478 18.60 0.00 41.83 2.85
3726 13286 3.245229 TGAAATTATGGTGGTGCTGAGGT 60.245 43.478 0.00 0.00 0.00 3.85
3844 13413 8.883731 TGCTGCTAAGAATCAGTATAAGAAAAC 58.116 33.333 0.00 0.00 33.09 2.43
4196 14681 5.982516 TGGCAATTCTTGTAACACAAATGAC 59.017 36.000 0.00 0.00 37.69 3.06
4228 14713 3.675698 GCTTGTTTTTGTTGTTGGACGAA 59.324 39.130 0.00 0.00 0.00 3.85
5383 16259 8.314021 ACACATACGACATATATGAATGGTGAT 58.686 33.333 19.63 7.56 34.65 3.06
5389 16265 9.981114 TTCTTCACACATACGACATATATGAAT 57.019 29.630 19.63 6.55 34.65 2.57
5402 16278 9.144747 CAGGCTATACATATTCTTCACACATAC 57.855 37.037 0.00 0.00 0.00 2.39
5515 16391 2.996621 GACAGTGTCAGTCAAGCCATAC 59.003 50.000 18.54 0.00 36.06 2.39
5638 16514 5.211174 TCACATATTCTGGAGCTGATGAG 57.789 43.478 0.00 0.00 0.00 2.90
5698 16574 1.640917 TTTGACTAAGCCCTCCGACT 58.359 50.000 0.00 0.00 0.00 4.18
5845 16724 3.522553 AGCTAATGTAACTGAGAACGGC 58.477 45.455 0.00 0.00 0.00 5.68
6038 16917 3.187227 GTCTTGTGCAGTACCAAGTGATG 59.813 47.826 12.84 0.00 0.00 3.07
6093 19263 3.933861 AGGTAGGCCCTAGTGAAATTG 57.066 47.619 0.00 0.00 43.87 2.32
6126 19872 2.165845 AGTTGTACCTGCTGGATACGTC 59.834 50.000 17.64 10.91 42.51 4.34
6128 19874 2.481449 GGAGTTGTACCTGCTGGATACG 60.481 54.545 17.64 0.00 42.51 3.06
6321 20067 7.440523 TGCTGTAAAAATTCTCTTTCCTCTC 57.559 36.000 0.00 0.00 0.00 3.20
6612 20969 8.571461 ACATTCACTGACATCTAATCATGTTT 57.429 30.769 0.00 0.00 37.11 2.83
6775 21303 8.516234 ACACTTGTTTTATGTGTAACTGAACAA 58.484 29.630 0.00 0.00 43.48 2.83
6788 21316 4.378616 GCGTGCTGTAACACTTGTTTTATG 59.621 41.667 0.00 0.00 39.31 1.90
6807 21335 6.681178 CCGATAAAGTTTACACATTAAGCGTG 59.319 38.462 0.00 6.32 40.32 5.34
6828 21357 2.939103 GCTGCACATTTAACTCTCCGAT 59.061 45.455 0.00 0.00 0.00 4.18
6830 21359 2.350522 AGCTGCACATTTAACTCTCCG 58.649 47.619 1.02 0.00 0.00 4.63
6867 21396 5.245531 CACTTTATGTTAGCCCTCAGTTCA 58.754 41.667 0.00 0.00 0.00 3.18
6886 21415 1.308998 CTTTGCTGTCGTTCCCACTT 58.691 50.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.