Multiple sequence alignment - TraesCS2D01G536700

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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 TraesCS2D01G536700 chr2D 100.000 2681 0 0 1 2681 619047691 619045011 0.000000e+00 4951.0
1 TraesCS2D01G536700 chr2D 80.691 1419 145 73 832 2196 619058628 619057285 0.000000e+00 983.0
2 TraesCS2D01G536700 chr2D 77.357 976 112 65 882 1783 592410841 592411781 6.720000e-131 477.0
3 TraesCS2D01G536700 chr2D 94.191 241 12 2 1140 1380 619052960 619052722 1.520000e-97 366.0
4 TraesCS2D01G536700 chr2D 78.302 106 9 11 197 298 45551847 45551752 3.730000e-04 56.5
5 TraesCS2D01G536700 chr2A 89.910 2210 65 45 95 2205 749905381 749903231 0.000000e+00 2700.0
6 TraesCS2D01G536700 chr2A 92.788 416 22 3 965 1380 749910518 749910111 1.780000e-166 595.0
7 TraesCS2D01G536700 chr2A 76.670 1003 122 62 880 1806 726985955 726986921 1.130000e-123 453.0
8 TraesCS2D01G536700 chr2A 92.245 245 19 0 1228 1472 749915112 749914868 5.490000e-92 348.0
9 TraesCS2D01G536700 chr2A 84.735 321 13 10 2276 2585 749902711 749902416 3.380000e-74 289.0
10 TraesCS2D01G536700 chr2A 91.304 184 16 0 991 1174 749915310 749915127 4.430000e-63 252.0
11 TraesCS2D01G536700 chr2A 81.250 240 21 15 1967 2196 749914349 749914124 3.550000e-39 172.0
12 TraesCS2D01G536700 chr2A 92.632 95 2 1 2587 2681 749897419 749897330 6.020000e-27 132.0
13 TraesCS2D01G536700 chr2A 78.977 176 23 9 2094 2268 749912140 749911978 1.010000e-19 108.0
14 TraesCS2D01G536700 chr2B 95.080 752 29 3 725 1472 756553679 756552932 0.000000e+00 1177.0
15 TraesCS2D01G536700 chr2B 83.352 871 68 35 832 1639 756571426 756570570 0.000000e+00 734.0
16 TraesCS2D01G536700 chr2B 94.260 331 13 2 1513 1843 756552746 756552422 3.980000e-138 501.0
17 TraesCS2D01G536700 chr2B 96.825 252 6 1 1834 2085 756552298 756552049 1.150000e-113 420.0
18 TraesCS2D01G536700 chr2B 79.938 648 61 33 122 731 756554318 756553702 1.920000e-111 412.0
19 TraesCS2D01G536700 chr2B 88.667 300 5 5 2284 2581 756550799 756550527 3.310000e-89 339.0
20 TraesCS2D01G536700 chr2B 77.579 504 60 36 1300 1767 718396620 718397106 3.430000e-64 255.0
21 TraesCS2D01G536700 chr2B 91.667 168 7 2 2081 2241 756550962 756550795 2.690000e-55 226.0
22 TraesCS2D01G536700 chr2B 77.843 343 43 20 882 1197 718396231 718396567 5.900000e-42 182.0
23 TraesCS2D01G536700 chr2B 78.390 236 22 9 2211 2432 756567030 756566810 2.800000e-25 126.0
24 TraesCS2D01G536700 chr2B 95.833 48 2 0 2486 2533 756565707 756565660 7.960000e-11 78.7
25 TraesCS2D01G536700 chr2B 83.544 79 5 4 228 305 471572422 471572351 1.720000e-07 67.6
26 TraesCS2D01G536700 chr2B 100.000 33 0 0 2034 2066 756569092 756569060 8.010000e-06 62.1
27 TraesCS2D01G536700 chr4B 89.634 164 16 1 1310 1472 631608693 631608530 9.730000e-50 207.0
28 TraesCS2D01G536700 chr4B 97.297 37 1 0 1645 1681 631608341 631608305 2.230000e-06 63.9
29 TraesCS2D01G536700 chr5A 85.714 105 11 3 95 196 54829746 54829643 1.010000e-19 108.0
30 TraesCS2D01G536700 chr5A 97.297 37 1 0 1645 1681 673089386 673089350 2.230000e-06 63.9
31 TraesCS2D01G536700 chr5D 85.882 85 4 6 225 305 22867764 22867684 1.710000e-12 84.2
32 TraesCS2D01G536700 chr3B 82.609 92 9 7 104 189 646339222 646339312 1.030000e-09 75.0
33 TraesCS2D01G536700 chr6B 85.135 74 3 6 238 308 653008232 653008164 4.790000e-08 69.4
34 TraesCS2D01G536700 chr3D 83.750 80 5 6 233 309 613075171 613075097 4.790000e-08 69.4
35 TraesCS2D01G536700 chr7D 82.558 86 5 7 226 305 464363083 464363002 1.720000e-07 67.6
36 TraesCS2D01G536700 chr7A 82.143 84 6 7 226 305 535271100 535271178 2.230000e-06 63.9
37 TraesCS2D01G536700 chr4D 97.297 37 1 0 1645 1681 493017346 493017382 2.230000e-06 63.9


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 TraesCS2D01G536700 chr2D 619045011 619047691 2680 True 4951.0 4951 100.000000 1 2681 1 chr2D.!!$R2 2680
1 TraesCS2D01G536700 chr2D 619057285 619058628 1343 True 983.0 983 80.691000 832 2196 1 chr2D.!!$R4 1364
2 TraesCS2D01G536700 chr2D 592410841 592411781 940 False 477.0 477 77.357000 882 1783 1 chr2D.!!$F1 901
3 TraesCS2D01G536700 chr2A 749902416 749905381 2965 True 1494.5 2700 87.322500 95 2585 2 chr2A.!!$R2 2490
4 TraesCS2D01G536700 chr2A 726985955 726986921 966 False 453.0 453 76.670000 880 1806 1 chr2A.!!$F1 926
5 TraesCS2D01G536700 chr2A 749910111 749915310 5199 True 295.0 595 87.312800 965 2268 5 chr2A.!!$R3 1303
6 TraesCS2D01G536700 chr2B 756550527 756554318 3791 True 512.5 1177 91.072833 122 2581 6 chr2B.!!$R2 2459
7 TraesCS2D01G536700 chr2B 756565660 756571426 5766 True 250.2 734 89.393750 832 2533 4 chr2B.!!$R3 1701
8 TraesCS2D01G536700 chr2B 718396231 718397106 875 False 218.5 255 77.711000 882 1767 2 chr2B.!!$F1 885

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
47 48 0.105039 GTGGGGTATCTGCTTCCGAG 59.895 60.0 0.0 0.0 0.0 4.63 F
976 1076 0.114560 TCCTCGATCCCTCCCATACC 59.885 60.0 0.0 0.0 0.0 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1535 1830 1.201181 GCATGCCAACATACAAACGGA 59.799 47.619 6.36 0.0 33.67 4.69 R
2602 9413 0.112412 GGGAGGAACAAGGAAAGGCA 59.888 55.000 0.00 0.0 0.00 4.75 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
18 19 2.193248 GCCTTTGATAGCGGCCCT 59.807 61.111 0.00 0.00 37.86 5.19
19 20 1.894282 GCCTTTGATAGCGGCCCTC 60.894 63.158 0.00 0.00 37.86 4.30
20 21 1.526887 CCTTTGATAGCGGCCCTCA 59.473 57.895 0.00 0.00 0.00 3.86
21 22 0.109342 CCTTTGATAGCGGCCCTCAT 59.891 55.000 0.00 0.00 0.00 2.90
22 23 1.477558 CCTTTGATAGCGGCCCTCATT 60.478 52.381 0.00 0.00 0.00 2.57
23 24 1.876156 CTTTGATAGCGGCCCTCATTC 59.124 52.381 0.00 0.00 0.00 2.67
24 25 0.836606 TTGATAGCGGCCCTCATTCA 59.163 50.000 0.00 0.00 0.00 2.57
25 26 0.394192 TGATAGCGGCCCTCATTCAG 59.606 55.000 0.00 0.00 0.00 3.02
26 27 0.321122 GATAGCGGCCCTCATTCAGG 60.321 60.000 0.00 0.00 43.01 3.86
31 32 2.825836 GCCCTCATTCAGGCGTGG 60.826 66.667 6.56 0.00 41.80 4.94
32 33 2.124570 CCCTCATTCAGGCGTGGG 60.125 66.667 6.56 0.00 41.80 4.61
33 34 2.124570 CCTCATTCAGGCGTGGGG 60.125 66.667 6.56 0.00 34.56 4.96
34 35 2.671070 CTCATTCAGGCGTGGGGT 59.329 61.111 6.56 0.00 0.00 4.95
35 36 1.622607 CCTCATTCAGGCGTGGGGTA 61.623 60.000 6.56 0.00 34.56 3.69
36 37 0.469917 CTCATTCAGGCGTGGGGTAT 59.530 55.000 6.56 0.00 0.00 2.73
37 38 0.468226 TCATTCAGGCGTGGGGTATC 59.532 55.000 6.56 0.00 0.00 2.24
38 39 0.469917 CATTCAGGCGTGGGGTATCT 59.530 55.000 6.56 0.00 0.00 1.98
39 40 0.469917 ATTCAGGCGTGGGGTATCTG 59.530 55.000 6.56 0.00 0.00 2.90
40 41 2.203070 CAGGCGTGGGGTATCTGC 60.203 66.667 0.00 0.00 0.00 4.26
41 42 2.365635 AGGCGTGGGGTATCTGCT 60.366 61.111 0.00 0.00 0.00 4.24
42 43 1.995626 AGGCGTGGGGTATCTGCTT 60.996 57.895 0.00 0.00 0.00 3.91
43 44 1.523938 GGCGTGGGGTATCTGCTTC 60.524 63.158 0.00 0.00 0.00 3.86
44 45 1.523938 GCGTGGGGTATCTGCTTCC 60.524 63.158 0.00 0.00 0.00 3.46
45 46 1.227263 CGTGGGGTATCTGCTTCCG 60.227 63.158 0.00 0.00 0.00 4.30
46 47 1.672854 CGTGGGGTATCTGCTTCCGA 61.673 60.000 0.00 0.00 0.00 4.55
47 48 0.105039 GTGGGGTATCTGCTTCCGAG 59.895 60.000 0.00 0.00 0.00 4.63
60 61 4.686839 GCTTCCGAGCTAAAATGTTCTT 57.313 40.909 0.00 0.00 45.65 2.52
61 62 5.048153 GCTTCCGAGCTAAAATGTTCTTT 57.952 39.130 0.00 0.00 45.65 2.52
62 63 4.853743 GCTTCCGAGCTAAAATGTTCTTTG 59.146 41.667 0.00 0.00 45.65 2.77
63 64 5.334879 GCTTCCGAGCTAAAATGTTCTTTGA 60.335 40.000 0.00 0.00 45.65 2.69
64 65 6.623767 GCTTCCGAGCTAAAATGTTCTTTGAT 60.624 38.462 0.00 0.00 45.65 2.57
65 66 6.182039 TCCGAGCTAAAATGTTCTTTGATG 57.818 37.500 0.00 0.00 0.00 3.07
66 67 5.937540 TCCGAGCTAAAATGTTCTTTGATGA 59.062 36.000 0.00 0.00 0.00 2.92
67 68 6.024049 CCGAGCTAAAATGTTCTTTGATGAC 58.976 40.000 0.00 0.00 0.00 3.06
68 69 6.348458 CCGAGCTAAAATGTTCTTTGATGACA 60.348 38.462 0.00 0.00 0.00 3.58
69 70 6.740002 CGAGCTAAAATGTTCTTTGATGACAG 59.260 38.462 0.00 0.00 0.00 3.51
70 71 7.360353 CGAGCTAAAATGTTCTTTGATGACAGA 60.360 37.037 0.00 0.00 0.00 3.41
71 72 8.169977 AGCTAAAATGTTCTTTGATGACAGAA 57.830 30.769 0.00 0.00 0.00 3.02
72 73 8.632679 AGCTAAAATGTTCTTTGATGACAGAAA 58.367 29.630 0.00 0.00 0.00 2.52
73 74 9.248291 GCTAAAATGTTCTTTGATGACAGAAAA 57.752 29.630 0.00 0.00 0.00 2.29
155 156 2.029649 GCATTTTGGAGTGCTGATGTGT 60.030 45.455 0.00 0.00 38.30 3.72
182 183 2.079158 CCATGACTTGCACGAATGTCT 58.921 47.619 0.00 0.00 0.00 3.41
215 232 8.715191 ATGAAAAACATTTGTCTAAGTTTGCA 57.285 26.923 0.00 0.00 35.45 4.08
443 487 7.996098 TTTTTACTCCTAGAACCAAATCCAG 57.004 36.000 0.00 0.00 0.00 3.86
444 488 5.693769 TTACTCCTAGAACCAAATCCAGG 57.306 43.478 0.00 0.00 0.00 4.45
445 489 3.532102 ACTCCTAGAACCAAATCCAGGT 58.468 45.455 0.00 0.00 42.34 4.00
452 496 2.765689 ACCAAATCCAGGTTGACCAA 57.234 45.000 2.56 0.00 35.33 3.67
453 497 3.039252 ACCAAATCCAGGTTGACCAAA 57.961 42.857 2.56 0.00 35.33 3.28
454 498 3.586429 ACCAAATCCAGGTTGACCAAAT 58.414 40.909 2.56 0.00 35.33 2.32
455 499 3.578282 ACCAAATCCAGGTTGACCAAATC 59.422 43.478 2.56 0.00 35.33 2.17
456 500 3.055891 CCAAATCCAGGTTGACCAAATCC 60.056 47.826 2.56 0.00 38.89 3.01
457 501 3.541242 AATCCAGGTTGACCAAATCCA 57.459 42.857 2.56 0.00 38.89 3.41
534 582 1.599518 GTGTTCCATGTCACCGCCA 60.600 57.895 0.00 0.00 0.00 5.69
613 661 0.297820 GATAGGCGAGCGTTTTGTCG 59.702 55.000 0.00 0.00 39.25 4.35
619 667 1.397945 GCGAGCGTTTTGTCGAAATCA 60.398 47.619 0.00 0.00 38.50 2.57
791 869 4.600062 ACTTGTCTTGTCCACCTTTCTTT 58.400 39.130 0.00 0.00 0.00 2.52
861 941 7.035004 GCTATAAAGAGAGAGCACCATCTATG 58.965 42.308 0.00 0.00 34.96 2.23
924 1024 5.335897 GCTACATTTGACTTGCTTCCATTCA 60.336 40.000 0.00 0.00 0.00 2.57
925 1025 5.733620 ACATTTGACTTGCTTCCATTCAT 57.266 34.783 0.00 0.00 0.00 2.57
926 1026 6.105397 ACATTTGACTTGCTTCCATTCATT 57.895 33.333 0.00 0.00 0.00 2.57
927 1027 6.161381 ACATTTGACTTGCTTCCATTCATTC 58.839 36.000 0.00 0.00 0.00 2.67
937 1037 3.582998 TCCATTCATTCCATCCACTCC 57.417 47.619 0.00 0.00 0.00 3.85
953 1053 3.558746 CCACTCCACTCAAGCAAGATCTT 60.559 47.826 0.88 0.88 0.00 2.40
958 1058 3.683822 CCACTCAAGCAAGATCTTCTGTC 59.316 47.826 4.57 0.00 0.00 3.51
962 1062 2.928757 CAAGCAAGATCTTCTGTCCTCG 59.071 50.000 4.57 0.00 0.00 4.63
964 1064 3.030291 AGCAAGATCTTCTGTCCTCGAT 58.970 45.455 4.57 0.00 0.00 3.59
965 1065 3.068024 AGCAAGATCTTCTGTCCTCGATC 59.932 47.826 4.57 0.00 34.05 3.69
976 1076 0.114560 TCCTCGATCCCTCCCATACC 59.885 60.000 0.00 0.00 0.00 2.73
1495 1663 1.646189 GGCTACTTCTCTCTTTGCCG 58.354 55.000 0.00 0.00 0.00 5.69
1560 1863 1.462616 TGTATGTTGGCATGCAGGAC 58.537 50.000 21.36 14.47 41.59 3.85
2092 5170 5.495926 CCTGGTCTGGCAAGAAGATATAT 57.504 43.478 0.00 0.00 33.05 0.86
2118 5196 6.745116 AGATGAATGACAAATACATGCATGG 58.255 36.000 29.41 14.24 42.13 3.66
2169 5258 2.895372 CATACCGTGGGCGCCTTC 60.895 66.667 28.56 18.14 36.67 3.46
2347 8096 2.431057 ACATGTTCTCGATACTCACCCC 59.569 50.000 0.00 0.00 0.00 4.95
2437 8193 3.419915 GACAAACATGCGTGCTATCAAG 58.580 45.455 5.64 0.00 0.00 3.02
2585 9396 2.848678 TACATAGCCTGTCCTGTCCT 57.151 50.000 0.00 0.00 39.39 3.85
2586 9397 1.198713 ACATAGCCTGTCCTGTCCTG 58.801 55.000 0.00 0.00 29.94 3.86
2587 9398 1.198713 CATAGCCTGTCCTGTCCTGT 58.801 55.000 0.00 0.00 0.00 4.00
2588 9399 1.137872 CATAGCCTGTCCTGTCCTGTC 59.862 57.143 0.00 0.00 0.00 3.51
2590 9401 2.217038 GCCTGTCCTGTCCTGTCCA 61.217 63.158 0.00 0.00 0.00 4.02
2591 9402 1.674057 CCTGTCCTGTCCTGTCCAC 59.326 63.158 0.00 0.00 0.00 4.02
2592 9403 1.121407 CCTGTCCTGTCCTGTCCACA 61.121 60.000 0.00 0.00 0.00 4.17
2593 9404 0.034059 CTGTCCTGTCCTGTCCACAC 59.966 60.000 0.00 0.00 0.00 3.82
2594 9405 1.006102 GTCCTGTCCTGTCCACACG 60.006 63.158 0.00 0.00 0.00 4.49
2595 9406 2.357517 CCTGTCCTGTCCACACGC 60.358 66.667 0.00 0.00 0.00 5.34
2596 9407 2.421314 CTGTCCTGTCCACACGCA 59.579 61.111 0.00 0.00 0.00 5.24
2597 9408 1.227527 CTGTCCTGTCCACACGCAA 60.228 57.895 0.00 0.00 0.00 4.85
2598 9409 1.498865 CTGTCCTGTCCACACGCAAC 61.499 60.000 0.00 0.00 0.00 4.17
2599 9410 2.279851 TCCTGTCCACACGCAACG 60.280 61.111 0.00 0.00 0.00 4.10
2600 9411 4.012895 CCTGTCCACACGCAACGC 62.013 66.667 0.00 0.00 0.00 4.84
2601 9412 4.012895 CTGTCCACACGCAACGCC 62.013 66.667 0.00 0.00 0.00 5.68
2602 9413 4.539083 TGTCCACACGCAACGCCT 62.539 61.111 0.00 0.00 0.00 5.52
2603 9414 4.012895 GTCCACACGCAACGCCTG 62.013 66.667 0.00 0.00 0.00 4.85
2611 9422 2.985847 GCAACGCCTGCCTTTCCT 60.986 61.111 0.00 0.00 46.13 3.36
2612 9423 2.564721 GCAACGCCTGCCTTTCCTT 61.565 57.895 0.00 0.00 46.13 3.36
2613 9424 1.286880 CAACGCCTGCCTTTCCTTG 59.713 57.895 0.00 0.00 0.00 3.61
2614 9425 1.152756 AACGCCTGCCTTTCCTTGT 60.153 52.632 0.00 0.00 0.00 3.16
2615 9426 0.755327 AACGCCTGCCTTTCCTTGTT 60.755 50.000 0.00 0.00 0.00 2.83
2616 9427 1.172812 ACGCCTGCCTTTCCTTGTTC 61.173 55.000 0.00 0.00 0.00 3.18
2617 9428 1.866853 CGCCTGCCTTTCCTTGTTCC 61.867 60.000 0.00 0.00 0.00 3.62
2618 9429 0.540597 GCCTGCCTTTCCTTGTTCCT 60.541 55.000 0.00 0.00 0.00 3.36
2619 9430 1.539157 CCTGCCTTTCCTTGTTCCTC 58.461 55.000 0.00 0.00 0.00 3.71
2620 9431 1.539157 CTGCCTTTCCTTGTTCCTCC 58.461 55.000 0.00 0.00 0.00 4.30
2621 9432 0.112412 TGCCTTTCCTTGTTCCTCCC 59.888 55.000 0.00 0.00 0.00 4.30
2622 9433 0.405973 GCCTTTCCTTGTTCCTCCCT 59.594 55.000 0.00 0.00 0.00 4.20
2623 9434 1.203063 GCCTTTCCTTGTTCCTCCCTT 60.203 52.381 0.00 0.00 0.00 3.95
2624 9435 2.756576 GCCTTTCCTTGTTCCTCCCTTT 60.757 50.000 0.00 0.00 0.00 3.11
2625 9436 3.157881 CCTTTCCTTGTTCCTCCCTTTC 58.842 50.000 0.00 0.00 0.00 2.62
2626 9437 3.436470 CCTTTCCTTGTTCCTCCCTTTCA 60.436 47.826 0.00 0.00 0.00 2.69
2627 9438 2.951229 TCCTTGTTCCTCCCTTTCAC 57.049 50.000 0.00 0.00 0.00 3.18
2628 9439 2.131854 TCCTTGTTCCTCCCTTTCACA 58.868 47.619 0.00 0.00 0.00 3.58
2629 9440 2.716424 TCCTTGTTCCTCCCTTTCACAT 59.284 45.455 0.00 0.00 0.00 3.21
2630 9441 3.084786 CCTTGTTCCTCCCTTTCACATC 58.915 50.000 0.00 0.00 0.00 3.06
2631 9442 2.879103 TGTTCCTCCCTTTCACATCC 57.121 50.000 0.00 0.00 0.00 3.51
2632 9443 2.061848 TGTTCCTCCCTTTCACATCCA 58.938 47.619 0.00 0.00 0.00 3.41
2633 9444 2.649312 TGTTCCTCCCTTTCACATCCAT 59.351 45.455 0.00 0.00 0.00 3.41
2634 9445 3.282885 GTTCCTCCCTTTCACATCCATC 58.717 50.000 0.00 0.00 0.00 3.51
2635 9446 2.561187 TCCTCCCTTTCACATCCATCA 58.439 47.619 0.00 0.00 0.00 3.07
2639 9450 3.184628 TCCCTTTCACATCCATCACTCT 58.815 45.455 0.00 0.00 0.00 3.24
2640 9451 4.361783 TCCCTTTCACATCCATCACTCTA 58.638 43.478 0.00 0.00 0.00 2.43
2642 9453 5.070981 TCCCTTTCACATCCATCACTCTATC 59.929 44.000 0.00 0.00 0.00 2.08
2644 9455 6.268617 CCCTTTCACATCCATCACTCTATCTA 59.731 42.308 0.00 0.00 0.00 1.98
2645 9456 7.038445 CCCTTTCACATCCATCACTCTATCTAT 60.038 40.741 0.00 0.00 0.00 1.98
2655 9466 8.811017 TCCATCACTCTATCTATCCATCTTTTC 58.189 37.037 0.00 0.00 0.00 2.29
2666 9477 8.581253 TCTATCCATCTTTTCTTTTCTTTCCC 57.419 34.615 0.00 0.00 0.00 3.97
2667 9478 8.394040 TCTATCCATCTTTTCTTTTCTTTCCCT 58.606 33.333 0.00 0.00 0.00 4.20
2668 9479 7.862274 ATCCATCTTTTCTTTTCTTTCCCTT 57.138 32.000 0.00 0.00 0.00 3.95
2671 9482 8.204160 TCCATCTTTTCTTTTCTTTCCCTTTTC 58.796 33.333 0.00 0.00 0.00 2.29
2672 9483 7.442364 CCATCTTTTCTTTTCTTTCCCTTTTCC 59.558 37.037 0.00 0.00 0.00 3.13
2675 9486 4.937201 TCTTTTCTTTCCCTTTTCCTGC 57.063 40.909 0.00 0.00 0.00 4.85
2676 9487 4.546674 TCTTTTCTTTCCCTTTTCCTGCT 58.453 39.130 0.00 0.00 0.00 4.24
2678 9489 4.670896 TTTCTTTCCCTTTTCCTGCTTG 57.329 40.909 0.00 0.00 0.00 4.01
2680 9491 2.958355 TCTTTCCCTTTTCCTGCTTGTG 59.042 45.455 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.876156 GAATGAGGGCCGCTATCAAAG 59.124 52.381 9.19 0.00 0.00 2.77
4 5 1.211703 TGAATGAGGGCCGCTATCAAA 59.788 47.619 9.19 0.00 0.00 2.69
6 7 0.394192 CTGAATGAGGGCCGCTATCA 59.606 55.000 9.19 11.55 0.00 2.15
7 8 0.321122 CCTGAATGAGGGCCGCTATC 60.321 60.000 9.19 7.34 38.36 2.08
9 10 3.106986 GCCTGAATGAGGGCCGCTA 62.107 63.158 9.19 0.00 43.07 4.26
12 13 4.473520 ACGCCTGAATGAGGGCCG 62.474 66.667 0.00 0.00 45.01 6.13
14 15 2.825836 CCACGCCTGAATGAGGGC 60.826 66.667 0.00 0.00 43.07 5.19
15 16 2.124570 CCCACGCCTGAATGAGGG 60.125 66.667 0.00 0.00 43.07 4.30
16 17 1.622607 TACCCCACGCCTGAATGAGG 61.623 60.000 0.00 0.00 46.13 3.86
17 18 0.469917 ATACCCCACGCCTGAATGAG 59.530 55.000 0.00 0.00 0.00 2.90
18 19 0.468226 GATACCCCACGCCTGAATGA 59.532 55.000 0.00 0.00 0.00 2.57
19 20 0.469917 AGATACCCCACGCCTGAATG 59.530 55.000 0.00 0.00 0.00 2.67
20 21 0.469917 CAGATACCCCACGCCTGAAT 59.530 55.000 0.00 0.00 0.00 2.57
21 22 1.904771 CAGATACCCCACGCCTGAA 59.095 57.895 0.00 0.00 0.00 3.02
22 23 2.731571 GCAGATACCCCACGCCTGA 61.732 63.158 0.00 0.00 0.00 3.86
23 24 2.203070 GCAGATACCCCACGCCTG 60.203 66.667 0.00 0.00 0.00 4.85
24 25 1.972660 GAAGCAGATACCCCACGCCT 61.973 60.000 0.00 0.00 0.00 5.52
25 26 1.523938 GAAGCAGATACCCCACGCC 60.524 63.158 0.00 0.00 0.00 5.68
26 27 1.523938 GGAAGCAGATACCCCACGC 60.524 63.158 0.00 0.00 0.00 5.34
27 28 1.227263 CGGAAGCAGATACCCCACG 60.227 63.158 0.00 0.00 0.00 4.94
28 29 0.105039 CTCGGAAGCAGATACCCCAC 59.895 60.000 0.00 0.00 0.00 4.61
29 30 2.516448 CTCGGAAGCAGATACCCCA 58.484 57.895 0.00 0.00 0.00 4.96
40 41 6.241207 TCAAAGAACATTTTAGCTCGGAAG 57.759 37.500 0.00 0.00 0.00 3.46
41 42 6.429692 TCATCAAAGAACATTTTAGCTCGGAA 59.570 34.615 0.00 0.00 0.00 4.30
42 43 5.937540 TCATCAAAGAACATTTTAGCTCGGA 59.062 36.000 0.00 0.00 0.00 4.55
43 44 6.024049 GTCATCAAAGAACATTTTAGCTCGG 58.976 40.000 0.00 0.00 0.00 4.63
44 45 6.602179 TGTCATCAAAGAACATTTTAGCTCG 58.398 36.000 0.00 0.00 0.00 5.03
45 46 7.810658 TCTGTCATCAAAGAACATTTTAGCTC 58.189 34.615 0.00 0.00 0.00 4.09
46 47 7.750229 TCTGTCATCAAAGAACATTTTAGCT 57.250 32.000 0.00 0.00 0.00 3.32
47 48 8.801715 TTTCTGTCATCAAAGAACATTTTAGC 57.198 30.769 0.00 0.00 32.26 3.09
98 99 9.895138 AGCATTTTTGGAGCATTAATTTAGATT 57.105 25.926 0.00 0.00 0.00 2.40
423 467 4.695606 ACCTGGATTTGGTTCTAGGAGTA 58.304 43.478 10.40 0.00 44.82 2.59
443 487 2.028203 CCCAACATGGATTTGGTCAACC 60.028 50.000 11.46 0.00 40.96 3.77
444 488 2.896685 TCCCAACATGGATTTGGTCAAC 59.103 45.455 11.46 0.00 40.96 3.18
445 489 3.251016 TCCCAACATGGATTTGGTCAA 57.749 42.857 11.46 0.00 40.96 3.18
446 490 2.988636 TCCCAACATGGATTTGGTCA 57.011 45.000 11.46 0.00 40.96 4.02
447 491 3.364549 TCATCCCAACATGGATTTGGTC 58.635 45.455 11.46 0.00 42.62 4.02
448 492 3.471430 TCATCCCAACATGGATTTGGT 57.529 42.857 11.46 0.00 42.62 3.67
449 493 4.162698 ACAATCATCCCAACATGGATTTGG 59.837 41.667 6.60 6.60 42.62 3.28
450 494 5.113383 CACAATCATCCCAACATGGATTTG 58.887 41.667 0.00 0.00 42.62 2.32
451 495 4.162698 CCACAATCATCCCAACATGGATTT 59.837 41.667 0.00 0.00 42.62 2.17
452 496 3.707611 CCACAATCATCCCAACATGGATT 59.292 43.478 0.00 0.00 42.62 3.01
453 497 3.302161 CCACAATCATCCCAACATGGAT 58.698 45.455 0.00 0.00 46.22 3.41
454 498 2.042842 ACCACAATCATCCCAACATGGA 59.957 45.455 0.00 0.00 40.96 3.41
455 499 2.428171 GACCACAATCATCCCAACATGG 59.572 50.000 0.00 0.00 37.25 3.66
456 500 2.428171 GGACCACAATCATCCCAACATG 59.572 50.000 0.00 0.00 0.00 3.21
457 501 2.738743 GGACCACAATCATCCCAACAT 58.261 47.619 0.00 0.00 0.00 2.71
619 667 8.041323 ACCGACTAAGTTTCACTCATATTTGAT 58.959 33.333 0.00 0.00 0.00 2.57
791 869 1.350319 GCACGTGAAGTTTGCGACA 59.650 52.632 22.23 0.00 0.00 4.35
861 941 3.437049 GCAGAGAGTTATTTGGTCCACAC 59.563 47.826 0.00 0.00 0.00 3.82
924 1024 2.356535 GCTTGAGTGGAGTGGATGGAAT 60.357 50.000 0.00 0.00 0.00 3.01
925 1025 1.003580 GCTTGAGTGGAGTGGATGGAA 59.996 52.381 0.00 0.00 0.00 3.53
926 1026 0.615331 GCTTGAGTGGAGTGGATGGA 59.385 55.000 0.00 0.00 0.00 3.41
927 1027 0.325933 TGCTTGAGTGGAGTGGATGG 59.674 55.000 0.00 0.00 0.00 3.51
937 1037 3.683822 GGACAGAAGATCTTGCTTGAGTG 59.316 47.826 14.00 1.52 0.00 3.51
953 1053 1.230497 GGGAGGGATCGAGGACAGA 59.770 63.158 0.00 0.00 0.00 3.41
958 1058 0.178932 TGGTATGGGAGGGATCGAGG 60.179 60.000 0.00 0.00 0.00 4.63
962 1062 2.541466 CTACCTGGTATGGGAGGGATC 58.459 57.143 7.07 0.00 34.40 3.36
964 1064 0.105142 GCTACCTGGTATGGGAGGGA 60.105 60.000 7.07 0.00 38.49 4.20
965 1065 0.104934 AGCTACCTGGTATGGGAGGG 60.105 60.000 7.07 0.00 38.49 4.30
976 1076 5.047731 TCGATGATCTTATCCAAGCTACCTG 60.048 44.000 0.00 0.00 0.00 4.00
1533 1828 2.487762 CATGCCAACATACAAACGGAGT 59.512 45.455 0.00 0.00 37.15 3.85
1534 1829 2.731968 GCATGCCAACATACAAACGGAG 60.732 50.000 6.36 0.00 33.67 4.63
1535 1830 1.201181 GCATGCCAACATACAAACGGA 59.799 47.619 6.36 0.00 33.67 4.69
1610 1934 2.308690 GCTGGAGGGTACTACTAGTGG 58.691 57.143 5.39 4.89 0.00 4.00
2092 5170 8.354426 CCATGCATGTATTTGTCATTCATCTAA 58.646 33.333 24.58 0.00 29.72 2.10
2109 5187 7.891712 TCCATTTTATCATAGATCCATGCATGT 59.108 33.333 24.58 7.78 0.00 3.21
2169 5258 1.784283 GGCACGAAACAAAACCGAATG 59.216 47.619 0.00 0.00 0.00 2.67
2347 8096 5.615581 CGTTGACGACATTAACAGTGAAAAG 59.384 40.000 0.00 0.00 43.02 2.27
2373 8126 6.312426 GGCACATATATGTTGCATAGAGACTC 59.688 42.308 26.88 12.73 39.39 3.36
2437 8193 9.238368 AGCTAGATAGATAACTCCAGTTGATAC 57.762 37.037 2.01 0.00 38.90 2.24
2457 8627 1.133761 ACTCCGCCTCATGTAGCTAGA 60.134 52.381 0.00 0.00 0.00 2.43
2550 9356 1.222936 GTATGACTGCTGCAGCCCT 59.777 57.895 34.64 20.14 41.18 5.19
2585 9396 4.539083 AGGCGTTGCGTGTGGACA 62.539 61.111 0.00 0.00 0.00 4.02
2586 9397 4.012895 CAGGCGTTGCGTGTGGAC 62.013 66.667 3.49 0.00 39.23 4.02
2595 9406 1.286880 CAAGGAAAGGCAGGCGTTG 59.713 57.895 0.00 0.00 0.00 4.10
2596 9407 0.755327 AACAAGGAAAGGCAGGCGTT 60.755 50.000 0.00 0.00 0.00 4.84
2597 9408 1.152756 AACAAGGAAAGGCAGGCGT 60.153 52.632 0.00 0.00 0.00 5.68
2598 9409 1.581447 GAACAAGGAAAGGCAGGCG 59.419 57.895 0.00 0.00 0.00 5.52
2599 9410 0.540597 AGGAACAAGGAAAGGCAGGC 60.541 55.000 0.00 0.00 0.00 4.85
2600 9411 1.539157 GAGGAACAAGGAAAGGCAGG 58.461 55.000 0.00 0.00 0.00 4.85
2601 9412 1.539157 GGAGGAACAAGGAAAGGCAG 58.461 55.000 0.00 0.00 0.00 4.85
2602 9413 0.112412 GGGAGGAACAAGGAAAGGCA 59.888 55.000 0.00 0.00 0.00 4.75
2603 9414 0.405973 AGGGAGGAACAAGGAAAGGC 59.594 55.000 0.00 0.00 0.00 4.35
2604 9415 2.980246 AAGGGAGGAACAAGGAAAGG 57.020 50.000 0.00 0.00 0.00 3.11
2605 9416 3.570125 GTGAAAGGGAGGAACAAGGAAAG 59.430 47.826 0.00 0.00 0.00 2.62
2606 9417 3.053245 TGTGAAAGGGAGGAACAAGGAAA 60.053 43.478 0.00 0.00 0.00 3.13
2607 9418 2.512056 TGTGAAAGGGAGGAACAAGGAA 59.488 45.455 0.00 0.00 0.00 3.36
2608 9419 2.131854 TGTGAAAGGGAGGAACAAGGA 58.868 47.619 0.00 0.00 0.00 3.36
2609 9420 2.656947 TGTGAAAGGGAGGAACAAGG 57.343 50.000 0.00 0.00 0.00 3.61
2610 9421 3.084786 GGATGTGAAAGGGAGGAACAAG 58.915 50.000 0.00 0.00 0.00 3.16
2611 9422 2.445145 TGGATGTGAAAGGGAGGAACAA 59.555 45.455 0.00 0.00 0.00 2.83
2612 9423 2.061848 TGGATGTGAAAGGGAGGAACA 58.938 47.619 0.00 0.00 0.00 3.18
2613 9424 2.879103 TGGATGTGAAAGGGAGGAAC 57.121 50.000 0.00 0.00 0.00 3.62
2614 9425 2.918934 TGATGGATGTGAAAGGGAGGAA 59.081 45.455 0.00 0.00 0.00 3.36
2615 9426 2.239654 GTGATGGATGTGAAAGGGAGGA 59.760 50.000 0.00 0.00 0.00 3.71
2616 9427 2.240667 AGTGATGGATGTGAAAGGGAGG 59.759 50.000 0.00 0.00 0.00 4.30
2617 9428 3.199508 AGAGTGATGGATGTGAAAGGGAG 59.800 47.826 0.00 0.00 0.00 4.30
2618 9429 3.184628 AGAGTGATGGATGTGAAAGGGA 58.815 45.455 0.00 0.00 0.00 4.20
2619 9430 3.641434 AGAGTGATGGATGTGAAAGGG 57.359 47.619 0.00 0.00 0.00 3.95
2620 9431 6.172136 AGATAGAGTGATGGATGTGAAAGG 57.828 41.667 0.00 0.00 0.00 3.11
2621 9432 8.034215 GGATAGATAGAGTGATGGATGTGAAAG 58.966 40.741 0.00 0.00 0.00 2.62
2622 9433 7.510343 TGGATAGATAGAGTGATGGATGTGAAA 59.490 37.037 0.00 0.00 0.00 2.69
2623 9434 7.012607 TGGATAGATAGAGTGATGGATGTGAA 58.987 38.462 0.00 0.00 0.00 3.18
2624 9435 6.555711 TGGATAGATAGAGTGATGGATGTGA 58.444 40.000 0.00 0.00 0.00 3.58
2625 9436 6.847421 TGGATAGATAGAGTGATGGATGTG 57.153 41.667 0.00 0.00 0.00 3.21
2626 9437 7.420856 AGATGGATAGATAGAGTGATGGATGT 58.579 38.462 0.00 0.00 0.00 3.06
2627 9438 7.901283 AGATGGATAGATAGAGTGATGGATG 57.099 40.000 0.00 0.00 0.00 3.51
2628 9439 8.914213 AAAGATGGATAGATAGAGTGATGGAT 57.086 34.615 0.00 0.00 0.00 3.41
2629 9440 8.733092 AAAAGATGGATAGATAGAGTGATGGA 57.267 34.615 0.00 0.00 0.00 3.41
2630 9441 8.814931 AGAAAAGATGGATAGATAGAGTGATGG 58.185 37.037 0.00 0.00 0.00 3.51
2640 9451 9.194972 GGGAAAGAAAAGAAAAGATGGATAGAT 57.805 33.333 0.00 0.00 0.00 1.98
2642 9453 8.586879 AGGGAAAGAAAAGAAAAGATGGATAG 57.413 34.615 0.00 0.00 0.00 2.08
2644 9455 7.862274 AAGGGAAAGAAAAGAAAAGATGGAT 57.138 32.000 0.00 0.00 0.00 3.41
2645 9456 7.675161 AAAGGGAAAGAAAAGAAAAGATGGA 57.325 32.000 0.00 0.00 0.00 3.41
2655 9466 4.944619 AGCAGGAAAAGGGAAAGAAAAG 57.055 40.909 0.00 0.00 0.00 2.27
2657 9468 4.030216 ACAAGCAGGAAAAGGGAAAGAAA 58.970 39.130 0.00 0.00 0.00 2.52
2658 9469 3.384467 CACAAGCAGGAAAAGGGAAAGAA 59.616 43.478 0.00 0.00 0.00 2.52
2659 9470 2.958355 CACAAGCAGGAAAAGGGAAAGA 59.042 45.455 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.