Multiple sequence alignment - TraesCS3B01G361900

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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 TraesCS3B01G361900 chr3B 100.000 3661 0 0 1 3661 573496579 573500239 0.000000e+00 6761.0
1 TraesCS3B01G361900 chr3A 91.286 2410 116 48 413 2757 576280790 576283170 0.000000e+00 3201.0
2 TraesCS3B01G361900 chr3A 84.478 335 21 9 115 421 576280310 576280641 5.940000e-78 302.0
3 TraesCS3B01G361900 chr3A 93.567 171 8 2 2795 2965 576283176 576283343 6.070000e-63 252.0
4 TraesCS3B01G361900 chr3D 94.609 1354 44 9 564 1913 438060341 438061669 0.000000e+00 2069.0
5 TraesCS3B01G361900 chr3D 94.082 828 30 7 1950 2761 438061668 438062492 0.000000e+00 1240.0
6 TraesCS3B01G361900 chr3D 95.092 652 31 1 3010 3661 1829399 1828749 0.000000e+00 1026.0
7 TraesCS3B01G361900 chr3D 94.615 650 35 0 3012 3661 395406074 395405425 0.000000e+00 1007.0
8 TraesCS3B01G361900 chr3D 85.312 320 18 9 117 409 438054750 438055067 1.650000e-78 303.0
9 TraesCS3B01G361900 chr3D 87.500 56 5 2 511 564 438056838 438056893 3.050000e-06 63.9
10 TraesCS3B01G361900 chr4D 94.777 651 34 0 3010 3660 433253656 433253006 0.000000e+00 1014.0
11 TraesCS3B01G361900 chr5D 94.640 653 34 1 3010 3661 373713509 373712857 0.000000e+00 1011.0
12 TraesCS3B01G361900 chr5D 94.632 652 35 0 3010 3661 465420805 465420154 0.000000e+00 1011.0
13 TraesCS3B01G361900 chr5D 94.325 652 37 0 3010 3661 344655062 344655713 0.000000e+00 1000.0
14 TraesCS3B01G361900 chr5D 90.909 110 9 1 1 110 118825724 118825616 2.950000e-31 147.0
15 TraesCS3B01G361900 chr6D 94.479 652 35 1 3011 3661 10974392 10975043 0.000000e+00 1003.0
16 TraesCS3B01G361900 chr6D 90.351 114 9 2 1 114 55901946 55901835 8.190000e-32 148.0
17 TraesCS3B01G361900 chr6D 87.805 123 12 3 1 123 5180679 5180560 1.370000e-29 141.0
18 TraesCS3B01G361900 chr1B 94.479 652 33 1 3010 3661 652000556 652001204 0.000000e+00 1002.0
19 TraesCS3B01G361900 chr1B 84.909 656 95 4 2011 2664 546149796 546150449 0.000000e+00 660.0
20 TraesCS3B01G361900 chr1B 84.541 414 64 0 1071 1484 546146388 546146801 9.460000e-111 411.0
21 TraesCS3B01G361900 chr1B 91.736 121 8 2 1 121 563215211 563215093 2.260000e-37 167.0
22 TraesCS3B01G361900 chr7D 94.316 651 37 0 3011 3661 452675017 452675667 0.000000e+00 998.0
23 TraesCS3B01G361900 chr1D 85.168 654 95 2 2011 2663 405807099 405807751 0.000000e+00 669.0
24 TraesCS3B01G361900 chr1D 83.816 414 67 0 1071 1484 405803405 405803818 9.530000e-106 394.0
25 TraesCS3B01G361900 chr1D 91.228 114 9 1 1 114 415524261 415524149 1.760000e-33 154.0
26 TraesCS3B01G361900 chr1A 84.604 656 97 4 2011 2664 501030470 501031123 0.000000e+00 649.0
27 TraesCS3B01G361900 chr1A 84.337 415 63 2 1071 1484 501026545 501026958 4.400000e-109 405.0
28 TraesCS3B01G361900 chr5A 83.465 381 62 1 1094 1473 706217426 706217806 1.620000e-93 353.0
29 TraesCS3B01G361900 chr4B 82.532 395 68 1 1094 1487 667903412 667903018 2.710000e-91 346.0
30 TraesCS3B01G361900 chr4B 90.323 124 9 2 1 124 603024856 603024736 3.780000e-35 159.0
31 TraesCS3B01G361900 chrUn 81.980 394 71 0 1091 1484 29730518 29730911 5.860000e-88 335.0
32 TraesCS3B01G361900 chrUn 81.633 392 71 1 1094 1484 29746525 29746916 1.270000e-84 324.0
33 TraesCS3B01G361900 chr5B 91.743 109 7 2 1 108 595626790 595626897 2.280000e-32 150.0
34 TraesCS3B01G361900 chr5B 90.991 111 8 2 1 110 479023369 479023260 8.190000e-32 148.0
35 TraesCS3B01G361900 chr7B 89.256 121 10 2 1 121 327278489 327278606 8.190000e-32 148.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G361900 chr3B 573496579 573500239 3660 False 6761.000000 6761 100.00000 1 3661 1 chr3B.!!$F1 3660
1 TraesCS3B01G361900 chr3A 576280310 576283343 3033 False 1251.666667 3201 89.77700 115 2965 3 chr3A.!!$F1 2850
2 TraesCS3B01G361900 chr3D 1828749 1829399 650 True 1026.000000 1026 95.09200 3010 3661 1 chr3D.!!$R1 651
3 TraesCS3B01G361900 chr3D 395405425 395406074 649 True 1007.000000 1007 94.61500 3012 3661 1 chr3D.!!$R2 649
4 TraesCS3B01G361900 chr3D 438054750 438062492 7742 False 918.975000 2069 90.37575 117 2761 4 chr3D.!!$F1 2644
5 TraesCS3B01G361900 chr4D 433253006 433253656 650 True 1014.000000 1014 94.77700 3010 3660 1 chr4D.!!$R1 650
6 TraesCS3B01G361900 chr5D 373712857 373713509 652 True 1011.000000 1011 94.64000 3010 3661 1 chr5D.!!$R2 651
7 TraesCS3B01G361900 chr5D 465420154 465420805 651 True 1011.000000 1011 94.63200 3010 3661 1 chr5D.!!$R3 651
8 TraesCS3B01G361900 chr5D 344655062 344655713 651 False 1000.000000 1000 94.32500 3010 3661 1 chr5D.!!$F1 651
9 TraesCS3B01G361900 chr6D 10974392 10975043 651 False 1003.000000 1003 94.47900 3011 3661 1 chr6D.!!$F1 650
10 TraesCS3B01G361900 chr1B 652000556 652001204 648 False 1002.000000 1002 94.47900 3010 3661 1 chr1B.!!$F1 651
11 TraesCS3B01G361900 chr1B 546146388 546150449 4061 False 535.500000 660 84.72500 1071 2664 2 chr1B.!!$F2 1593
12 TraesCS3B01G361900 chr7D 452675017 452675667 650 False 998.000000 998 94.31600 3011 3661 1 chr7D.!!$F1 650
13 TraesCS3B01G361900 chr1D 405803405 405807751 4346 False 531.500000 669 84.49200 1071 2663 2 chr1D.!!$F1 1592
14 TraesCS3B01G361900 chr1A 501026545 501031123 4578 False 527.000000 649 84.47050 1071 2664 2 chr1A.!!$F1 1593

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
28 29 0.109319 GTTTTGCCCATGCGTAGGTG 60.109 55.000 0.0 0.00 41.78 4.00 F
768 6156 0.172803 AGGACCACGCTCGACATTAC 59.827 55.000 0.0 0.00 0.00 1.89 F
1384 6784 1.270839 ACTACATCAAGGTGCGCAAGT 60.271 47.619 14.0 5.57 41.68 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1526 9459 0.240945 GATGTTGTTGAAGCCCACCG 59.759 55.0 0.0 0.0 0.00 4.94 R
1916 9866 0.593128 GCTTGTGGTGCAGTGGTTAG 59.407 55.0 0.0 0.0 0.00 2.34 R
3005 11507 0.042448 GTTTTGACACCGACAGACGC 60.042 55.0 0.0 0.0 41.07 5.19 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
21 22 2.416202 GCATTACTTGTTTTGCCCATGC 59.584 45.455 0.00 0.00 38.26 4.06
22 23 2.430546 TTACTTGTTTTGCCCATGCG 57.569 45.000 0.00 0.00 41.78 4.73
23 24 1.323412 TACTTGTTTTGCCCATGCGT 58.677 45.000 0.00 0.00 41.78 5.24
24 25 1.323412 ACTTGTTTTGCCCATGCGTA 58.677 45.000 0.00 0.00 41.78 4.42
25 26 1.269448 ACTTGTTTTGCCCATGCGTAG 59.731 47.619 0.00 0.00 41.78 3.51
26 27 0.600557 TTGTTTTGCCCATGCGTAGG 59.399 50.000 0.00 0.00 41.78 3.18
27 28 0.538516 TGTTTTGCCCATGCGTAGGT 60.539 50.000 0.00 0.00 41.78 3.08
28 29 0.109319 GTTTTGCCCATGCGTAGGTG 60.109 55.000 0.00 0.00 41.78 4.00
29 30 0.538516 TTTTGCCCATGCGTAGGTGT 60.539 50.000 0.00 0.00 41.78 4.16
30 31 1.240641 TTTGCCCATGCGTAGGTGTG 61.241 55.000 0.00 0.00 41.78 3.82
31 32 2.046314 GCCCATGCGTAGGTGTGT 60.046 61.111 0.00 0.00 0.00 3.72
32 33 2.398554 GCCCATGCGTAGGTGTGTG 61.399 63.158 0.00 0.00 0.00 3.82
33 34 1.745115 CCCATGCGTAGGTGTGTGG 60.745 63.158 0.00 0.00 0.00 4.17
34 35 1.745115 CCATGCGTAGGTGTGTGGG 60.745 63.158 0.00 0.00 0.00 4.61
35 36 2.046314 ATGCGTAGGTGTGTGGGC 60.046 61.111 0.00 0.00 0.00 5.36
36 37 2.592993 ATGCGTAGGTGTGTGGGCT 61.593 57.895 0.00 0.00 0.00 5.19
37 38 2.742372 GCGTAGGTGTGTGGGCTG 60.742 66.667 0.00 0.00 0.00 4.85
38 39 2.741092 CGTAGGTGTGTGGGCTGT 59.259 61.111 0.00 0.00 0.00 4.40
39 40 1.070786 CGTAGGTGTGTGGGCTGTT 59.929 57.895 0.00 0.00 0.00 3.16
40 41 0.534203 CGTAGGTGTGTGGGCTGTTT 60.534 55.000 0.00 0.00 0.00 2.83
41 42 1.235724 GTAGGTGTGTGGGCTGTTTC 58.764 55.000 0.00 0.00 0.00 2.78
42 43 1.136828 TAGGTGTGTGGGCTGTTTCT 58.863 50.000 0.00 0.00 0.00 2.52
43 44 0.179018 AGGTGTGTGGGCTGTTTCTC 60.179 55.000 0.00 0.00 0.00 2.87
44 45 0.179018 GGTGTGTGGGCTGTTTCTCT 60.179 55.000 0.00 0.00 0.00 3.10
45 46 1.680338 GTGTGTGGGCTGTTTCTCTT 58.320 50.000 0.00 0.00 0.00 2.85
46 47 2.024414 GTGTGTGGGCTGTTTCTCTTT 58.976 47.619 0.00 0.00 0.00 2.52
47 48 3.211045 GTGTGTGGGCTGTTTCTCTTTA 58.789 45.455 0.00 0.00 0.00 1.85
48 49 3.821033 GTGTGTGGGCTGTTTCTCTTTAT 59.179 43.478 0.00 0.00 0.00 1.40
49 50 5.001232 GTGTGTGGGCTGTTTCTCTTTATA 58.999 41.667 0.00 0.00 0.00 0.98
50 51 5.001232 TGTGTGGGCTGTTTCTCTTTATAC 58.999 41.667 0.00 0.00 0.00 1.47
51 52 5.001232 GTGTGGGCTGTTTCTCTTTATACA 58.999 41.667 0.00 0.00 0.00 2.29
52 53 5.001232 TGTGGGCTGTTTCTCTTTATACAC 58.999 41.667 0.00 0.00 0.00 2.90
53 54 4.395231 GTGGGCTGTTTCTCTTTATACACC 59.605 45.833 0.00 0.00 0.00 4.16
54 55 4.042311 TGGGCTGTTTCTCTTTATACACCA 59.958 41.667 0.00 0.00 0.00 4.17
55 56 4.395231 GGGCTGTTTCTCTTTATACACCAC 59.605 45.833 0.00 0.00 0.00 4.16
56 57 5.001232 GGCTGTTTCTCTTTATACACCACA 58.999 41.667 0.00 0.00 0.00 4.17
57 58 5.106673 GGCTGTTTCTCTTTATACACCACAC 60.107 44.000 0.00 0.00 0.00 3.82
58 59 5.468746 GCTGTTTCTCTTTATACACCACACA 59.531 40.000 0.00 0.00 0.00 3.72
59 60 6.017440 GCTGTTTCTCTTTATACACCACACAA 60.017 38.462 0.00 0.00 0.00 3.33
60 61 7.468084 GCTGTTTCTCTTTATACACCACACAAA 60.468 37.037 0.00 0.00 0.00 2.83
61 62 8.282455 TGTTTCTCTTTATACACCACACAAAA 57.718 30.769 0.00 0.00 0.00 2.44
62 63 8.908903 TGTTTCTCTTTATACACCACACAAAAT 58.091 29.630 0.00 0.00 0.00 1.82
66 67 9.733556 TCTCTTTATACACCACACAAAATATGT 57.266 29.630 0.00 0.00 45.34 2.29
78 79 3.763897 ACAAAATATGTGGGCAGACTTCC 59.236 43.478 0.00 0.00 41.93 3.46
79 80 4.019174 CAAAATATGTGGGCAGACTTCCT 58.981 43.478 0.00 0.00 0.00 3.36
80 81 5.192927 CAAAATATGTGGGCAGACTTCCTA 58.807 41.667 0.00 0.00 0.00 2.94
81 82 5.450818 AAATATGTGGGCAGACTTCCTAA 57.549 39.130 0.00 0.00 0.00 2.69
82 83 5.653255 AATATGTGGGCAGACTTCCTAAT 57.347 39.130 0.00 0.00 0.00 1.73
83 84 2.787473 TGTGGGCAGACTTCCTAATG 57.213 50.000 0.00 0.00 0.00 1.90
84 85 1.340017 TGTGGGCAGACTTCCTAATGC 60.340 52.381 0.00 0.00 37.95 3.56
87 88 3.882131 GCAGACTTCCTAATGCCCA 57.118 52.632 0.00 0.00 32.49 5.36
88 89 1.383523 GCAGACTTCCTAATGCCCAC 58.616 55.000 0.00 0.00 32.49 4.61
89 90 1.340017 GCAGACTTCCTAATGCCCACA 60.340 52.381 0.00 0.00 32.49 4.17
90 91 2.359900 CAGACTTCCTAATGCCCACAC 58.640 52.381 0.00 0.00 0.00 3.82
91 92 1.066143 AGACTTCCTAATGCCCACACG 60.066 52.381 0.00 0.00 0.00 4.49
92 93 0.676782 ACTTCCTAATGCCCACACGC 60.677 55.000 0.00 0.00 0.00 5.34
93 94 1.705337 CTTCCTAATGCCCACACGCG 61.705 60.000 3.53 3.53 0.00 6.01
94 95 2.435938 CCTAATGCCCACACGCGT 60.436 61.111 5.58 5.58 0.00 6.01
95 96 2.749865 CCTAATGCCCACACGCGTG 61.750 63.158 35.99 35.99 43.21 5.34
103 104 3.561429 CACACGCGTGGCACTTAT 58.439 55.556 39.21 17.03 39.64 1.73
104 105 1.419922 CACACGCGTGGCACTTATC 59.580 57.895 39.21 1.26 39.64 1.75
105 106 2.092291 ACACGCGTGGCACTTATCG 61.092 57.895 39.21 13.98 34.19 2.92
106 107 2.508439 ACGCGTGGCACTTATCGG 60.508 61.111 12.93 0.00 0.00 4.18
107 108 3.925238 CGCGTGGCACTTATCGGC 61.925 66.667 16.72 9.39 0.00 5.54
108 109 3.925238 GCGTGGCACTTATCGGCG 61.925 66.667 16.72 0.00 0.00 6.46
109 110 2.508439 CGTGGCACTTATCGGCGT 60.508 61.111 16.72 0.00 0.00 5.68
110 111 2.798501 CGTGGCACTTATCGGCGTG 61.799 63.158 16.72 0.00 0.00 5.34
153 154 2.221169 TGCAGCCTGTCAACAGTTTAG 58.779 47.619 9.19 0.00 42.27 1.85
214 217 3.818961 ATGACAATGAACAAGAGCACG 57.181 42.857 0.00 0.00 0.00 5.34
247 267 1.808411 TTCCATCTGAACTCCAACGC 58.192 50.000 0.00 0.00 0.00 4.84
312 334 5.643777 AGAAGAAATCTGTTAACATGGTCCG 59.356 40.000 9.13 0.00 36.88 4.79
328 350 4.515361 TGGTCCGTGAAAACAGTTTCTTA 58.485 39.130 0.00 0.00 43.13 2.10
394 427 5.049405 CCTGAATCTCGTAAAATATGTGCCC 60.049 44.000 0.00 0.00 0.00 5.36
417 450 2.025969 CACAGGTCAGACGCTGCAG 61.026 63.158 10.11 10.11 0.00 4.41
421 454 0.898320 AGGTCAGACGCTGCAGTAAT 59.102 50.000 16.64 0.29 0.00 1.89
429 621 2.484264 GACGCTGCAGTAATTCCACTTT 59.516 45.455 16.64 0.00 0.00 2.66
436 628 7.570140 CGCTGCAGTAATTCCACTTTAGATATG 60.570 40.741 16.64 0.00 0.00 1.78
564 2504 1.299014 GCGATCGACTGCAGAGGAG 60.299 63.158 23.35 8.38 0.00 3.69
615 6003 1.529010 CGACGCATCAACCGATTTTCC 60.529 52.381 0.00 0.00 0.00 3.13
617 6005 1.468520 ACGCATCAACCGATTTTCCAG 59.531 47.619 0.00 0.00 0.00 3.86
636 6024 1.372087 GCCCCTCTCGATGCAAACAG 61.372 60.000 0.00 0.00 0.00 3.16
741 6129 5.152097 CGTGAGTGAGTAACATTACGACTT 58.848 41.667 9.51 0.00 38.65 3.01
742 6130 6.073058 ACGTGAGTGAGTAACATTACGACTTA 60.073 38.462 0.00 4.96 46.97 2.24
743 6131 6.248001 CGTGAGTGAGTAACATTACGACTTAC 59.752 42.308 14.92 14.92 38.65 2.34
766 6154 0.389948 GAAGGACCACGCTCGACATT 60.390 55.000 0.00 0.00 0.00 2.71
768 6156 0.172803 AGGACCACGCTCGACATTAC 59.827 55.000 0.00 0.00 0.00 1.89
771 6159 1.918609 GACCACGCTCGACATTACTTC 59.081 52.381 0.00 0.00 0.00 3.01
774 6162 2.092211 CCACGCTCGACATTACTTCAAC 59.908 50.000 0.00 0.00 0.00 3.18
775 6163 2.729360 CACGCTCGACATTACTTCAACA 59.271 45.455 0.00 0.00 0.00 3.33
776 6164 3.367932 CACGCTCGACATTACTTCAACAT 59.632 43.478 0.00 0.00 0.00 2.71
777 6165 3.367932 ACGCTCGACATTACTTCAACATG 59.632 43.478 0.00 0.00 0.00 3.21
778 6166 3.612423 CGCTCGACATTACTTCAACATGA 59.388 43.478 0.00 0.00 0.00 3.07
779 6167 4.091365 CGCTCGACATTACTTCAACATGAA 59.909 41.667 0.00 0.00 34.79 2.57
780 6168 5.316770 GCTCGACATTACTTCAACATGAAC 58.683 41.667 0.00 0.00 32.21 3.18
782 6170 6.466308 TCGACATTACTTCAACATGAACTG 57.534 37.500 0.00 0.00 32.21 3.16
783 6171 5.082059 CGACATTACTTCAACATGAACTGC 58.918 41.667 0.00 0.00 32.21 4.40
784 6172 5.334028 CGACATTACTTCAACATGAACTGCA 60.334 40.000 0.00 0.00 32.21 4.41
931 6328 2.306847 GACCAAGCTGAACCAGGAAAA 58.693 47.619 0.00 0.00 31.21 2.29
1384 6784 1.270839 ACTACATCAAGGTGCGCAAGT 60.271 47.619 14.00 5.57 41.68 3.16
1477 6877 2.570284 ATGGTCGAGTCCGTGCACA 61.570 57.895 18.64 0.00 37.05 4.57
1554 9487 1.440850 CAACAACATCACGCGCCTG 60.441 57.895 5.73 0.00 0.00 4.85
1913 9863 3.758023 TGAATTAATGCCGCCATCCATAG 59.242 43.478 0.00 0.00 0.00 2.23
1916 9866 2.185004 AATGCCGCCATCCATAGTAC 57.815 50.000 0.00 0.00 0.00 2.73
1925 9899 4.632153 GCCATCCATAGTACTAACCACTG 58.368 47.826 6.70 0.00 0.00 3.66
1931 9905 2.833631 AGTACTAACCACTGCACCAC 57.166 50.000 0.00 0.00 0.00 4.16
1933 9907 2.436542 AGTACTAACCACTGCACCACAA 59.563 45.455 0.00 0.00 0.00 3.33
1935 9909 0.593128 CTAACCACTGCACCACAAGC 59.407 55.000 0.00 0.00 0.00 4.01
1939 9913 1.386525 CCACTGCACCACAAGCAACT 61.387 55.000 0.00 0.00 42.17 3.16
1940 9914 0.248743 CACTGCACCACAAGCAACTG 60.249 55.000 0.00 0.00 42.17 3.16
1944 9918 1.274728 TGCACCACAAGCAACTGTTTT 59.725 42.857 0.00 0.00 39.39 2.43
1945 9919 2.493675 TGCACCACAAGCAACTGTTTTA 59.506 40.909 0.00 0.00 39.39 1.52
1946 9920 3.131933 TGCACCACAAGCAACTGTTTTAT 59.868 39.130 0.00 0.00 39.39 1.40
1947 9921 4.339530 TGCACCACAAGCAACTGTTTTATA 59.660 37.500 0.00 0.00 39.39 0.98
1949 9923 5.925969 GCACCACAAGCAACTGTTTTATATT 59.074 36.000 0.00 0.00 0.00 1.28
1977 10007 6.430451 AGTAATCGCGATTTGATTTGATTCC 58.570 36.000 36.42 7.89 37.28 3.01
1995 10221 5.724370 TGATTCCCTCACCTAATTAGTCACA 59.276 40.000 11.50 0.00 0.00 3.58
2667 11161 1.520342 GCTGAGATGTGAGCGACCC 60.520 63.158 0.00 0.00 0.00 4.46
2730 11232 5.448438 TCAAATTATGAAGTGTTGACGTGC 58.552 37.500 0.00 0.00 34.30 5.34
2761 11263 4.512571 CGAGTTCTTAGTAGCTACTCCCTC 59.487 50.000 29.28 22.51 37.73 4.30
2762 11264 5.685599 CGAGTTCTTAGTAGCTACTCCCTCT 60.686 48.000 29.28 20.11 37.73 3.69
2763 11265 6.082228 AGTTCTTAGTAGCTACTCCCTCTT 57.918 41.667 29.28 10.34 37.73 2.85
2764 11266 6.495847 AGTTCTTAGTAGCTACTCCCTCTTT 58.504 40.000 29.28 6.46 37.73 2.52
2765 11267 6.604396 AGTTCTTAGTAGCTACTCCCTCTTTC 59.396 42.308 29.28 13.12 37.73 2.62
2766 11268 5.447757 TCTTAGTAGCTACTCCCTCTTTCC 58.552 45.833 29.28 0.00 37.73 3.13
2767 11269 3.035055 AGTAGCTACTCCCTCTTTCCC 57.965 52.381 20.95 0.00 0.00 3.97
2768 11270 2.315155 AGTAGCTACTCCCTCTTTCCCA 59.685 50.000 20.95 0.00 0.00 4.37
2769 11271 1.574263 AGCTACTCCCTCTTTCCCAC 58.426 55.000 0.00 0.00 0.00 4.61
2770 11272 1.203313 AGCTACTCCCTCTTTCCCACA 60.203 52.381 0.00 0.00 0.00 4.17
2771 11273 1.628846 GCTACTCCCTCTTTCCCACAA 59.371 52.381 0.00 0.00 0.00 3.33
2772 11274 2.239907 GCTACTCCCTCTTTCCCACAAT 59.760 50.000 0.00 0.00 0.00 2.71
2773 11275 3.454812 GCTACTCCCTCTTTCCCACAATA 59.545 47.826 0.00 0.00 0.00 1.90
2774 11276 4.103311 GCTACTCCCTCTTTCCCACAATAT 59.897 45.833 0.00 0.00 0.00 1.28
2775 11277 5.307196 GCTACTCCCTCTTTCCCACAATATA 59.693 44.000 0.00 0.00 0.00 0.86
2776 11278 6.183361 GCTACTCCCTCTTTCCCACAATATAA 60.183 42.308 0.00 0.00 0.00 0.98
2777 11279 6.253946 ACTCCCTCTTTCCCACAATATAAG 57.746 41.667 0.00 0.00 0.00 1.73
2778 11280 5.970640 ACTCCCTCTTTCCCACAATATAAGA 59.029 40.000 0.00 0.00 0.00 2.10
2779 11281 6.126739 ACTCCCTCTTTCCCACAATATAAGAC 60.127 42.308 0.00 0.00 0.00 3.01
2780 11282 5.057149 CCCTCTTTCCCACAATATAAGACG 58.943 45.833 0.00 0.00 0.00 4.18
2781 11283 5.396436 CCCTCTTTCCCACAATATAAGACGT 60.396 44.000 0.00 0.00 0.00 4.34
2782 11284 6.113411 CCTCTTTCCCACAATATAAGACGTT 58.887 40.000 0.00 0.00 0.00 3.99
2783 11285 6.598064 CCTCTTTCCCACAATATAAGACGTTT 59.402 38.462 0.00 0.00 0.00 3.60
2784 11286 7.120726 CCTCTTTCCCACAATATAAGACGTTTT 59.879 37.037 0.00 0.00 0.00 2.43
2785 11287 8.398878 TCTTTCCCACAATATAAGACGTTTTT 57.601 30.769 0.00 0.00 0.00 1.94
2855 11357 7.100458 ACTTGTGCTACATTATGAATTTCCC 57.900 36.000 0.00 0.00 0.00 3.97
2856 11358 6.096846 ACTTGTGCTACATTATGAATTTCCCC 59.903 38.462 0.00 0.00 0.00 4.81
2880 11382 8.621286 CCCTTTTTGCGATAGAACTTGTATTAT 58.379 33.333 0.00 0.00 39.76 1.28
2929 11431 1.787155 CACAAGTTCTCAACGTCCTCG 59.213 52.381 0.00 0.00 43.34 4.63
2965 11467 1.202359 GCCAAACAACACCACGATTGT 60.202 47.619 0.00 0.00 40.76 2.71
2969 11471 2.782171 CAACACCACGATTGTTGCG 58.218 52.632 12.99 0.00 45.36 4.85
2970 11472 1.008995 AACACCACGATTGTTGCGC 60.009 52.632 0.00 0.00 35.82 6.09
2971 11473 2.126888 CACCACGATTGTTGCGCC 60.127 61.111 4.18 0.00 0.00 6.53
2972 11474 2.281484 ACCACGATTGTTGCGCCT 60.281 55.556 4.18 0.00 0.00 5.52
2973 11475 1.004320 ACCACGATTGTTGCGCCTA 60.004 52.632 4.18 0.00 0.00 3.93
2974 11476 1.019278 ACCACGATTGTTGCGCCTAG 61.019 55.000 4.18 0.00 0.00 3.02
2992 11494 6.853720 CGCCTAGCATAATAACTAGCTAAGA 58.146 40.000 0.00 0.00 38.92 2.10
2993 11495 7.313646 CGCCTAGCATAATAACTAGCTAAGAA 58.686 38.462 0.00 0.00 38.92 2.52
2994 11496 7.273815 CGCCTAGCATAATAACTAGCTAAGAAC 59.726 40.741 0.00 0.00 38.92 3.01
2995 11497 8.088981 GCCTAGCATAATAACTAGCTAAGAACA 58.911 37.037 0.00 0.00 38.92 3.18
3004 11506 5.523438 ACTAGCTAAGAACATCTACAGCC 57.477 43.478 0.00 0.00 36.11 4.85
3005 11507 3.444703 AGCTAAGAACATCTACAGCCG 57.555 47.619 9.17 0.00 36.11 5.52
3006 11508 1.861575 GCTAAGAACATCTACAGCCGC 59.138 52.381 3.65 0.00 31.92 6.53
3007 11509 2.120232 CTAAGAACATCTACAGCCGCG 58.880 52.381 0.00 0.00 0.00 6.46
3008 11510 0.246635 AAGAACATCTACAGCCGCGT 59.753 50.000 4.92 0.00 0.00 6.01
3025 11527 1.567504 CGTCTGTCGGTGTCAAAACT 58.432 50.000 0.00 0.00 35.71 2.66
3027 11529 2.546778 GTCTGTCGGTGTCAAAACTGA 58.453 47.619 0.00 0.00 32.97 3.41
3030 11532 1.563111 GTCGGTGTCAAAACTGACGA 58.437 50.000 0.87 0.00 44.29 4.20
3038 11540 4.272504 GTGTCAAAACTGACGAATCTTGGA 59.727 41.667 0.00 0.00 41.43 3.53
3045 11547 2.965831 CTGACGAATCTTGGATAGGGGA 59.034 50.000 0.00 0.00 0.00 4.81
3047 11549 3.973973 TGACGAATCTTGGATAGGGGATT 59.026 43.478 0.00 0.00 0.00 3.01
3062 11564 1.359459 GGATTCCGAACTGTGCGTCC 61.359 60.000 7.51 4.01 0.00 4.79
3069 11571 1.845809 GAACTGTGCGTCCAAGGCTG 61.846 60.000 0.00 0.00 0.00 4.85
3086 11588 1.069204 GCTGATGATAACAGGAGGCGA 59.931 52.381 0.00 0.00 36.09 5.54
3154 11656 2.025887 ACCCTACTTCCTGCTTGATTGG 60.026 50.000 0.00 0.00 0.00 3.16
3367 11876 1.181098 AGCTTGCCTTCCACGCAAAT 61.181 50.000 0.00 0.00 45.11 2.32
3454 11963 4.307432 CCAAAGTATATAGTCCGGCTGTG 58.693 47.826 0.00 0.00 0.00 3.66
3498 12007 1.517832 CTCAGTAGCCCCTGAACCG 59.482 63.158 4.66 0.00 40.78 4.44
3574 12083 3.430513 GGTTCCTTCTCCGAATACTCCAC 60.431 52.174 0.00 0.00 0.00 4.02
3630 12139 5.477510 TCTGCAAAACAAATTTCACACACT 58.522 33.333 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.416202 GCATGGGCAAAACAAGTAATGC 59.584 45.455 0.00 0.00 40.72 3.56
1 2 2.667481 CGCATGGGCAAAACAAGTAATG 59.333 45.455 0.00 0.00 41.24 1.90
2 3 2.298729 ACGCATGGGCAAAACAAGTAAT 59.701 40.909 10.10 0.00 41.24 1.89
3 4 1.683917 ACGCATGGGCAAAACAAGTAA 59.316 42.857 10.10 0.00 41.24 2.24
4 5 1.323412 ACGCATGGGCAAAACAAGTA 58.677 45.000 10.10 0.00 41.24 2.24
5 6 1.269448 CTACGCATGGGCAAAACAAGT 59.731 47.619 10.10 0.00 41.24 3.16
6 7 1.402720 CCTACGCATGGGCAAAACAAG 60.403 52.381 10.10 0.00 41.24 3.16
7 8 0.600557 CCTACGCATGGGCAAAACAA 59.399 50.000 10.10 0.00 41.24 2.83
8 9 0.538516 ACCTACGCATGGGCAAAACA 60.539 50.000 10.10 0.00 41.24 2.83
9 10 0.109319 CACCTACGCATGGGCAAAAC 60.109 55.000 10.10 0.00 41.24 2.43
10 11 0.538516 ACACCTACGCATGGGCAAAA 60.539 50.000 10.10 0.00 41.24 2.44
11 12 1.074072 ACACCTACGCATGGGCAAA 59.926 52.632 10.10 0.00 41.24 3.68
12 13 1.673993 CACACCTACGCATGGGCAA 60.674 57.895 10.10 0.00 41.24 4.52
13 14 2.046411 CACACCTACGCATGGGCA 60.046 61.111 10.10 0.00 41.24 5.36
14 15 2.046314 ACACACCTACGCATGGGC 60.046 61.111 10.10 0.00 0.00 5.36
15 16 1.745115 CCACACACCTACGCATGGG 60.745 63.158 8.44 8.44 0.00 4.00
16 17 1.745115 CCCACACACCTACGCATGG 60.745 63.158 0.00 0.00 0.00 3.66
17 18 2.398554 GCCCACACACCTACGCATG 61.399 63.158 0.00 0.00 0.00 4.06
18 19 2.046314 GCCCACACACCTACGCAT 60.046 61.111 0.00 0.00 0.00 4.73
19 20 3.238497 AGCCCACACACCTACGCA 61.238 61.111 0.00 0.00 0.00 5.24
20 21 2.742372 CAGCCCACACACCTACGC 60.742 66.667 0.00 0.00 0.00 4.42
21 22 0.534203 AAACAGCCCACACACCTACG 60.534 55.000 0.00 0.00 0.00 3.51
22 23 1.202770 AGAAACAGCCCACACACCTAC 60.203 52.381 0.00 0.00 0.00 3.18
23 24 1.071699 GAGAAACAGCCCACACACCTA 59.928 52.381 0.00 0.00 0.00 3.08
24 25 0.179018 GAGAAACAGCCCACACACCT 60.179 55.000 0.00 0.00 0.00 4.00
25 26 0.179018 AGAGAAACAGCCCACACACC 60.179 55.000 0.00 0.00 0.00 4.16
26 27 1.680338 AAGAGAAACAGCCCACACAC 58.320 50.000 0.00 0.00 0.00 3.82
27 28 2.435372 AAAGAGAAACAGCCCACACA 57.565 45.000 0.00 0.00 0.00 3.72
28 29 5.001232 TGTATAAAGAGAAACAGCCCACAC 58.999 41.667 0.00 0.00 0.00 3.82
29 30 5.001232 GTGTATAAAGAGAAACAGCCCACA 58.999 41.667 0.00 0.00 0.00 4.17
30 31 4.395231 GGTGTATAAAGAGAAACAGCCCAC 59.605 45.833 0.00 0.00 34.99 4.61
31 32 4.042311 TGGTGTATAAAGAGAAACAGCCCA 59.958 41.667 0.00 0.00 39.08 5.36
32 33 4.395231 GTGGTGTATAAAGAGAAACAGCCC 59.605 45.833 0.00 0.00 39.08 5.19
33 34 5.001232 TGTGGTGTATAAAGAGAAACAGCC 58.999 41.667 0.00 0.00 39.08 4.85
34 35 5.468746 TGTGTGGTGTATAAAGAGAAACAGC 59.531 40.000 0.00 0.00 39.99 4.40
35 36 7.490962 TTGTGTGGTGTATAAAGAGAAACAG 57.509 36.000 0.00 0.00 0.00 3.16
36 37 7.867305 TTTGTGTGGTGTATAAAGAGAAACA 57.133 32.000 0.00 0.00 0.00 2.83
40 41 9.733556 ACATATTTTGTGTGGTGTATAAAGAGA 57.266 29.630 0.00 0.00 37.11 3.10
56 57 3.763897 GGAAGTCTGCCCACATATTTTGT 59.236 43.478 0.00 0.00 39.91 2.83
57 58 4.019174 AGGAAGTCTGCCCACATATTTTG 58.981 43.478 0.00 0.00 0.00 2.44
58 59 4.322057 AGGAAGTCTGCCCACATATTTT 57.678 40.909 0.00 0.00 0.00 1.82
59 60 5.450818 TTAGGAAGTCTGCCCACATATTT 57.549 39.130 0.00 0.00 0.00 1.40
60 61 5.380043 CATTAGGAAGTCTGCCCACATATT 58.620 41.667 0.00 0.00 0.00 1.28
61 62 4.747931 GCATTAGGAAGTCTGCCCACATAT 60.748 45.833 0.00 0.00 0.00 1.78
62 63 3.433598 GCATTAGGAAGTCTGCCCACATA 60.434 47.826 0.00 0.00 0.00 2.29
63 64 2.684927 GCATTAGGAAGTCTGCCCACAT 60.685 50.000 0.00 0.00 0.00 3.21
64 65 1.340017 GCATTAGGAAGTCTGCCCACA 60.340 52.381 0.00 0.00 0.00 4.17
65 66 1.383523 GCATTAGGAAGTCTGCCCAC 58.616 55.000 0.00 0.00 0.00 4.61
66 67 0.255890 GGCATTAGGAAGTCTGCCCA 59.744 55.000 0.93 0.00 46.76 5.36
67 68 3.102090 GGCATTAGGAAGTCTGCCC 57.898 57.895 0.93 0.00 46.76 5.36
69 70 1.340017 TGTGGGCATTAGGAAGTCTGC 60.340 52.381 0.00 0.00 0.00 4.26
70 71 2.359900 GTGTGGGCATTAGGAAGTCTG 58.640 52.381 0.00 0.00 0.00 3.51
71 72 1.066143 CGTGTGGGCATTAGGAAGTCT 60.066 52.381 0.00 0.00 0.00 3.24
72 73 1.369625 CGTGTGGGCATTAGGAAGTC 58.630 55.000 0.00 0.00 0.00 3.01
73 74 0.676782 GCGTGTGGGCATTAGGAAGT 60.677 55.000 0.00 0.00 0.00 3.01
74 75 1.705337 CGCGTGTGGGCATTAGGAAG 61.705 60.000 0.00 0.00 0.00 3.46
75 76 1.743623 CGCGTGTGGGCATTAGGAA 60.744 57.895 0.00 0.00 0.00 3.36
76 77 2.125310 CGCGTGTGGGCATTAGGA 60.125 61.111 0.00 0.00 0.00 2.94
77 78 2.435938 ACGCGTGTGGGCATTAGG 60.436 61.111 12.93 0.00 0.00 2.69
78 79 2.784596 CACGCGTGTGGGCATTAG 59.215 61.111 30.50 0.71 42.59 1.73
86 87 1.419922 GATAAGTGCCACGCGTGTG 59.580 57.895 34.81 26.49 46.00 3.82
87 88 2.092291 CGATAAGTGCCACGCGTGT 61.092 57.895 34.81 20.21 0.00 4.49
88 89 2.695055 CGATAAGTGCCACGCGTG 59.305 61.111 31.77 31.77 0.00 5.34
89 90 2.508439 CCGATAAGTGCCACGCGT 60.508 61.111 5.58 5.58 0.00 6.01
90 91 3.925238 GCCGATAAGTGCCACGCG 61.925 66.667 3.53 3.53 0.00 6.01
91 92 3.925238 CGCCGATAAGTGCCACGC 61.925 66.667 0.00 0.00 0.00 5.34
92 93 2.508439 ACGCCGATAAGTGCCACG 60.508 61.111 0.00 0.00 0.00 4.94
93 94 3.089784 CACGCCGATAAGTGCCAC 58.910 61.111 0.00 0.00 0.00 5.01
97 98 3.733024 TTTTAAGCACGCCGATAAGTG 57.267 42.857 0.00 0.00 41.01 3.16
121 122 3.028850 ACAGGCTGCATGATGCTAAATT 58.971 40.909 22.12 0.00 45.31 1.82
153 154 9.346725 CAGCTAATCAAAAAGTGTCTAAAATCC 57.653 33.333 0.00 0.00 0.00 3.01
247 267 3.736530 AGCGTAGACGTACAGTTACTG 57.263 47.619 11.21 11.21 42.22 2.74
289 309 5.411669 ACGGACCATGTTAACAGATTTCTTC 59.588 40.000 14.65 3.56 0.00 2.87
297 317 4.035792 TGTTTTCACGGACCATGTTAACAG 59.964 41.667 14.65 3.88 0.00 3.16
394 427 2.801162 CGTCTGACCTGTGACGCG 60.801 66.667 3.53 3.53 46.94 6.01
417 450 7.520614 GCTGTGCCATATCTAAAGTGGAATTAC 60.521 40.741 0.00 0.00 34.94 1.89
421 454 4.199310 GCTGTGCCATATCTAAAGTGGAA 58.801 43.478 0.00 0.00 34.94 3.53
429 621 3.977427 CACTTACGCTGTGCCATATCTA 58.023 45.455 0.00 0.00 0.00 1.98
472 666 3.562343 GGGGTGATCCTCCTAGTTTTC 57.438 52.381 4.44 0.00 35.33 2.29
502 696 1.153309 TGGCATCTCCATCTGCACG 60.153 57.895 0.00 0.00 40.72 5.34
556 2496 0.107945 ATTCTGTTCCGCTCCTCTGC 60.108 55.000 0.00 0.00 0.00 4.26
615 6003 1.078214 TTTGCATCGAGAGGGGCTG 60.078 57.895 0.00 0.00 0.00 4.85
617 6005 1.372087 CTGTTTGCATCGAGAGGGGC 61.372 60.000 0.00 0.00 0.00 5.80
636 6024 0.931005 GATGATCGTCTCCGGTTTGC 59.069 55.000 7.73 0.00 33.95 3.68
741 6129 1.674441 CGAGCGTGGTCCTTCATAGTA 59.326 52.381 0.00 0.00 0.00 1.82
742 6130 0.456221 CGAGCGTGGTCCTTCATAGT 59.544 55.000 0.00 0.00 0.00 2.12
743 6131 0.738975 TCGAGCGTGGTCCTTCATAG 59.261 55.000 0.00 0.00 0.00 2.23
766 6154 3.740832 CGACTGCAGTTCATGTTGAAGTA 59.259 43.478 22.65 0.00 37.91 2.24
768 6156 2.802247 TCGACTGCAGTTCATGTTGAAG 59.198 45.455 22.65 3.12 37.00 3.02
771 6159 3.187022 TGAATCGACTGCAGTTCATGTTG 59.813 43.478 22.65 1.20 0.00 3.33
774 6162 3.936661 CATGAATCGACTGCAGTTCATG 58.063 45.455 30.44 30.44 46.34 3.07
775 6163 2.941064 CCATGAATCGACTGCAGTTCAT 59.059 45.455 22.65 21.62 40.78 2.57
776 6164 2.349590 CCATGAATCGACTGCAGTTCA 58.650 47.619 22.65 20.30 35.33 3.18
777 6165 1.667724 CCCATGAATCGACTGCAGTTC 59.332 52.381 22.65 14.93 0.00 3.01
778 6166 1.679944 CCCCATGAATCGACTGCAGTT 60.680 52.381 22.65 4.27 0.00 3.16
779 6167 0.107508 CCCCATGAATCGACTGCAGT 60.108 55.000 21.88 21.88 0.00 4.40
780 6168 1.442526 GCCCCATGAATCGACTGCAG 61.443 60.000 13.48 13.48 0.00 4.41
782 6170 2.189499 GGCCCCATGAATCGACTGC 61.189 63.158 0.00 0.00 0.00 4.40
783 6171 0.758734 TAGGCCCCATGAATCGACTG 59.241 55.000 0.00 0.00 0.00 3.51
784 6172 0.759346 GTAGGCCCCATGAATCGACT 59.241 55.000 0.00 0.00 0.00 4.18
931 6328 1.194781 AGCTCCGGTGGACTGTGAAT 61.195 55.000 0.00 0.00 0.00 2.57
984 6381 0.809241 CCATGGCTGACTCTTCTCGC 60.809 60.000 0.00 0.00 0.00 5.03
985 6382 0.820226 TCCATGGCTGACTCTTCTCG 59.180 55.000 6.96 0.00 0.00 4.04
1384 6784 0.681733 AAGAGCTCGAGGTTGCAGAA 59.318 50.000 19.66 0.00 0.00 3.02
1526 9459 0.240945 GATGTTGTTGAAGCCCACCG 59.759 55.000 0.00 0.00 0.00 4.94
1795 9728 1.174712 ACGAAATGCTGCTTGCTGGT 61.175 50.000 0.00 0.00 43.37 4.00
1913 9863 2.536761 TGTGGTGCAGTGGTTAGTAC 57.463 50.000 0.00 0.00 0.00 2.73
1916 9866 0.593128 GCTTGTGGTGCAGTGGTTAG 59.407 55.000 0.00 0.00 0.00 2.34
1925 9899 2.008752 AAAACAGTTGCTTGTGGTGC 57.991 45.000 0.00 0.00 0.00 5.01
1954 9928 5.625311 GGGAATCAAATCAAATCGCGATTAC 59.375 40.000 32.67 10.00 32.79 1.89
1977 10007 6.316390 GGACAAATGTGACTAATTAGGTGAGG 59.684 42.308 16.73 1.72 0.00 3.86
1995 10221 3.490759 CTGCTCGCGCGGACAAAT 61.491 61.111 31.69 0.00 45.62 2.32
2546 11040 1.337384 CGGGGGACTCCATCATGTCA 61.337 60.000 0.00 0.00 37.22 3.58
2614 11108 2.252714 AGAGCTCTTCCTTTTCGAGGT 58.747 47.619 11.45 0.00 46.39 3.85
2715 11217 1.745232 AAAGGCACGTCAACACTTCA 58.255 45.000 0.00 0.00 0.00 3.02
2716 11218 2.844122 AAAAGGCACGTCAACACTTC 57.156 45.000 0.00 0.00 0.00 3.01
2747 11249 2.315155 TGGGAAAGAGGGAGTAGCTACT 59.685 50.000 26.35 26.35 39.71 2.57
2757 11259 5.057149 CGTCTTATATTGTGGGAAAGAGGG 58.943 45.833 0.00 0.00 31.66 4.30
2834 11336 5.765510 AGGGGAAATTCATAATGTAGCACA 58.234 37.500 0.00 0.00 0.00 4.57
2838 11340 7.222611 CGCAAAAAGGGGAAATTCATAATGTAG 59.777 37.037 0.00 0.00 0.00 2.74
2843 11345 5.730296 TCGCAAAAAGGGGAAATTCATAA 57.270 34.783 0.00 0.00 0.00 1.90
2849 11351 5.016831 AGTTCTATCGCAAAAAGGGGAAAT 58.983 37.500 0.00 0.00 33.18 2.17
2852 11354 3.713826 AGTTCTATCGCAAAAAGGGGA 57.286 42.857 0.00 0.00 0.00 4.81
2853 11355 3.506067 ACAAGTTCTATCGCAAAAAGGGG 59.494 43.478 0.00 0.00 0.00 4.79
2854 11356 4.766404 ACAAGTTCTATCGCAAAAAGGG 57.234 40.909 0.00 0.00 0.00 3.95
2880 11382 5.887598 CCTGATTGTAATCCTGGTGATTGAA 59.112 40.000 2.41 0.00 43.57 2.69
2929 11431 1.352083 TGGCTATATGCTCTGGTCCC 58.648 55.000 0.00 0.00 42.39 4.46
2957 11459 1.060937 GCTAGGCGCAACAATCGTG 59.939 57.895 10.83 0.00 38.92 4.35
2967 11469 3.851098 AGCTAGTTATTATGCTAGGCGC 58.149 45.455 0.00 0.00 36.21 6.53
2968 11470 6.853720 TCTTAGCTAGTTATTATGCTAGGCG 58.146 40.000 0.00 0.00 38.90 5.52
2969 11471 8.088981 TGTTCTTAGCTAGTTATTATGCTAGGC 58.911 37.037 0.00 0.00 38.90 3.93
2978 11480 8.145122 GGCTGTAGATGTTCTTAGCTAGTTATT 58.855 37.037 0.00 0.00 36.42 1.40
2979 11481 7.522399 CGGCTGTAGATGTTCTTAGCTAGTTAT 60.522 40.741 0.00 0.00 36.42 1.89
2980 11482 6.238676 CGGCTGTAGATGTTCTTAGCTAGTTA 60.239 42.308 0.00 0.00 36.42 2.24
2981 11483 5.450688 CGGCTGTAGATGTTCTTAGCTAGTT 60.451 44.000 0.00 0.00 36.42 2.24
2982 11484 4.036971 CGGCTGTAGATGTTCTTAGCTAGT 59.963 45.833 0.00 0.00 36.42 2.57
2983 11485 4.541779 CGGCTGTAGATGTTCTTAGCTAG 58.458 47.826 0.00 0.00 36.42 3.42
2984 11486 3.243434 GCGGCTGTAGATGTTCTTAGCTA 60.243 47.826 0.00 0.00 36.42 3.32
2985 11487 2.482142 GCGGCTGTAGATGTTCTTAGCT 60.482 50.000 0.00 0.00 36.42 3.32
2986 11488 1.861575 GCGGCTGTAGATGTTCTTAGC 59.138 52.381 0.00 0.00 35.84 3.09
2987 11489 2.120232 CGCGGCTGTAGATGTTCTTAG 58.880 52.381 0.00 0.00 0.00 2.18
2988 11490 1.475280 ACGCGGCTGTAGATGTTCTTA 59.525 47.619 12.47 0.00 0.00 2.10
2989 11491 0.246635 ACGCGGCTGTAGATGTTCTT 59.753 50.000 12.47 0.00 0.00 2.52
2990 11492 0.179134 GACGCGGCTGTAGATGTTCT 60.179 55.000 12.47 0.00 0.00 3.01
2991 11493 0.179134 AGACGCGGCTGTAGATGTTC 60.179 55.000 17.28 0.00 0.00 3.18
2992 11494 0.458543 CAGACGCGGCTGTAGATGTT 60.459 55.000 33.82 0.00 0.00 2.71
2993 11495 1.139734 CAGACGCGGCTGTAGATGT 59.860 57.895 33.82 0.00 0.00 3.06
2994 11496 1.139734 ACAGACGCGGCTGTAGATG 59.860 57.895 44.60 21.00 46.67 2.90
2995 11497 3.604629 ACAGACGCGGCTGTAGAT 58.395 55.556 44.60 22.21 46.67 1.98
3004 11506 1.484227 TTTTGACACCGACAGACGCG 61.484 55.000 3.53 3.53 41.07 6.01
3005 11507 0.042448 GTTTTGACACCGACAGACGC 60.042 55.000 0.00 0.00 41.07 5.19
3006 11508 1.257936 CAGTTTTGACACCGACAGACG 59.742 52.381 0.00 0.00 42.18 4.18
3007 11509 2.546778 TCAGTTTTGACACCGACAGAC 58.453 47.619 0.00 0.00 0.00 3.51
3008 11510 2.971660 TCAGTTTTGACACCGACAGA 57.028 45.000 0.00 0.00 0.00 3.41
3025 11527 3.040655 TCCCCTATCCAAGATTCGTCA 57.959 47.619 0.00 0.00 0.00 4.35
3027 11529 3.328050 GGAATCCCCTATCCAAGATTCGT 59.672 47.826 0.00 0.00 43.54 3.85
3030 11532 3.598264 TCGGAATCCCCTATCCAAGATT 58.402 45.455 0.00 0.00 35.34 2.40
3038 11540 1.141053 GCACAGTTCGGAATCCCCTAT 59.859 52.381 0.00 0.00 0.00 2.57
3045 11547 0.250124 TTGGACGCACAGTTCGGAAT 60.250 50.000 0.00 0.00 0.00 3.01
3047 11549 1.300620 CTTGGACGCACAGTTCGGA 60.301 57.895 0.00 0.00 0.00 4.55
3062 11564 3.474600 CCTCCTGTTATCATCAGCCTTG 58.525 50.000 0.00 0.00 0.00 3.61
3069 11571 1.001406 CCCTCGCCTCCTGTTATCATC 59.999 57.143 0.00 0.00 0.00 2.92
3086 11588 2.225017 CCTGGGTAAACATTGTGTCCCT 60.225 50.000 18.51 0.00 36.23 4.20
3297 11806 4.139786 TCTGTAACCGACTCTGTGTAACT 58.860 43.478 0.00 0.00 38.04 2.24
3454 11963 1.759459 CTGGATTAGGGGGTCCTCGC 61.759 65.000 0.00 0.00 43.66 5.03
3498 12007 3.134458 GGACTCATCGTCATTGAATCCC 58.866 50.000 0.00 0.00 44.68 3.85
3501 12010 2.826428 CCGGACTCATCGTCATTGAAT 58.174 47.619 0.00 0.00 44.68 2.57
3574 12083 6.082338 CGATCCTTGTGTTCAAAATCTTCTG 58.918 40.000 0.00 0.00 32.87 3.02
3630 12139 6.717997 TGTGGAATATTATGCTCTCTACGGTA 59.282 38.462 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.