Multiple sequence alignment - TraesCS6D01G269200

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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 TraesCS6D01G269200 chr6D 100.000 5004 0 0 1 5004 379521133 379516130 0.000000e+00 9241.0
1 TraesCS6D01G269200 chr6D 100.000 491 0 0 5368 5858 379515766 379515276 0.000000e+00 907.0
2 TraesCS6D01G269200 chr6D 94.118 459 24 2 5400 5858 175502757 175503212 0.000000e+00 695.0
3 TraesCS6D01G269200 chr6D 90.476 210 18 2 2235 2442 379518706 379518497 5.780000e-70 276.0
4 TraesCS6D01G269200 chr6D 90.476 210 18 2 2428 2637 379518899 379518692 5.780000e-70 276.0
5 TraesCS6D01G269200 chr6D 95.758 165 7 0 4120 4284 204160179 204160015 3.480000e-67 267.0
6 TraesCS6D01G269200 chr6D 94.286 35 1 1 4971 5004 175502556 175502590 1.100000e-02 52.8
7 TraesCS6D01G269200 chr6B 92.839 4441 217 47 394 4797 567472803 567477179 0.000000e+00 6346.0
8 TraesCS6D01G269200 chr6B 94.989 459 22 1 5400 5858 679617412 679617869 0.000000e+00 719.0
9 TraesCS6D01G269200 chr6B 94.397 464 25 1 5395 5858 679601413 679601875 0.000000e+00 712.0
10 TraesCS6D01G269200 chr6B 94.181 464 26 1 5395 5858 679585834 679586296 0.000000e+00 706.0
11 TraesCS6D01G269200 chr6B 91.429 210 16 2 2428 2637 567474629 567474836 2.670000e-73 287.0
12 TraesCS6D01G269200 chr6B 90.952 210 17 2 2235 2442 567474822 567475031 1.240000e-71 281.0
13 TraesCS6D01G269200 chr6B 90.860 186 14 3 4796 4979 16455289 16455105 4.530000e-61 246.0
14 TraesCS6D01G269200 chr6B 91.720 157 12 1 4797 4953 679616811 679616966 3.550000e-52 217.0
15 TraesCS6D01G269200 chr6B 91.304 161 9 3 4797 4955 679585414 679585571 1.280000e-51 215.0
16 TraesCS6D01G269200 chr6B 91.216 148 8 3 4797 4942 679600820 679600964 4.630000e-46 196.0
17 TraesCS6D01G269200 chr6B 100.000 35 0 0 4945 4979 679616974 679617008 1.360000e-06 65.8
18 TraesCS6D01G269200 chr6B 100.000 34 0 0 4946 4979 679585578 679585611 4.900000e-06 63.9
19 TraesCS6D01G269200 chr6B 94.286 35 1 1 4971 5004 679585635 679585669 1.100000e-02 52.8
20 TraesCS6D01G269200 chr6B 94.286 35 1 1 4971 5004 679601041 679601075 1.100000e-02 52.8
21 TraesCS6D01G269200 chr6B 94.286 35 1 1 4971 5004 679617032 679617066 1.100000e-02 52.8
22 TraesCS6D01G269200 chr6A 93.787 3348 156 31 114 3442 521479949 521483263 0.000000e+00 4983.0
23 TraesCS6D01G269200 chr6A 95.279 466 18 3 5393 5858 187078846 187078385 0.000000e+00 736.0
24 TraesCS6D01G269200 chr6A 95.395 456 21 0 3471 3926 521483252 521483707 0.000000e+00 726.0
25 TraesCS6D01G269200 chr6A 93.920 477 26 3 4322 4797 521483713 521484187 0.000000e+00 717.0
26 TraesCS6D01G269200 chr6A 91.038 212 15 4 2428 2637 521482060 521482269 3.460000e-72 283.0
27 TraesCS6D01G269200 chr6A 90.476 210 18 2 2235 2442 521482255 521482464 5.780000e-70 276.0
28 TraesCS6D01G269200 chr6A 92.547 161 11 1 4795 4955 187079264 187079105 4.570000e-56 230.0
29 TraesCS6D01G269200 chr6A 91.304 161 11 2 4796 4955 170745024 170745182 3.550000e-52 217.0
30 TraesCS6D01G269200 chr6A 100.000 35 0 0 4945 4979 187079099 187079065 1.360000e-06 65.8
31 TraesCS6D01G269200 chr7D 96.574 467 15 1 5392 5858 54775300 54775765 0.000000e+00 773.0
32 TraesCS6D01G269200 chr7D 97.516 161 4 0 4795 4955 54774664 54774824 5.780000e-70 276.0
33 TraesCS6D01G269200 chr3D 96.078 459 16 2 5400 5858 100212933 100212477 0.000000e+00 747.0
34 TraesCS6D01G269200 chr3D 93.976 166 10 0 4116 4281 2148560 2148725 9.740000e-63 252.0
35 TraesCS6D01G269200 chr4A 94.444 468 22 3 5392 5858 443479244 443478780 0.000000e+00 717.0
36 TraesCS6D01G269200 chr4A 94.771 459 19 4 5398 5856 75914938 75914485 0.000000e+00 710.0
37 TraesCS6D01G269200 chr4A 93.711 159 8 1 4797 4955 316953928 316953772 2.730000e-58 237.0
38 TraesCS6D01G269200 chr4A 91.824 159 13 0 4797 4955 75915357 75915199 7.640000e-54 222.0
39 TraesCS6D01G269200 chr4A 89.941 169 13 4 4796 4963 443479670 443479505 1.280000e-51 215.0
40 TraesCS6D01G269200 chr4A 100.000 35 0 0 4945 4979 75915193 75915159 1.360000e-06 65.8
41 TraesCS6D01G269200 chr4A 100.000 35 0 0 4945 4979 316953766 316953732 1.360000e-06 65.8
42 TraesCS6D01G269200 chr4A 100.000 33 0 0 4945 4977 443479507 443479475 1.760000e-05 62.1
43 TraesCS6D01G269200 chr5D 98.148 162 3 0 4120 4281 117355991 117356152 3.460000e-72 283.0
44 TraesCS6D01G269200 chr5D 95.238 168 7 1 4119 4285 151671547 151671714 1.250000e-66 265.0
45 TraesCS6D01G269200 chr5D 91.781 73 4 1 308 380 435886184 435886114 3.740000e-17 100.0
46 TraesCS6D01G269200 chr2D 96.933 163 2 1 4119 4281 295282082 295281923 2.690000e-68 270.0
47 TraesCS6D01G269200 chr2B 94.643 168 9 0 4119 4286 134256689 134256856 1.620000e-65 261.0
48 TraesCS6D01G269200 chr4D 93.182 176 11 1 4116 4291 416432038 416431864 2.090000e-64 257.0
49 TraesCS6D01G269200 chr7A 89.340 197 17 4 4120 4312 105168357 105168161 1.630000e-60 244.0
50 TraesCS6D01G269200 chr7A 94.231 52 2 1 330 380 107815986 107815935 1.750000e-10 78.7
51 TraesCS6D01G269200 chr7B 90.588 85 4 3 298 380 7562418 7562500 6.210000e-20 110.0
52 TraesCS6D01G269200 chrUn 88.764 89 5 4 301 387 320256179 320256094 2.890000e-18 104.0
53 TraesCS6D01G269200 chrUn 88.764 89 5 4 301 387 357700829 357700744 2.890000e-18 104.0
54 TraesCS6D01G269200 chr3B 86.139 101 9 4 289 387 755174787 755174884 2.890000e-18 104.0
55 TraesCS6D01G269200 chr3B 88.764 89 5 4 301 387 756117573 756117488 2.890000e-18 104.0
56 TraesCS6D01G269200 chr1A 93.023 43 2 1 338 380 33858001 33858042 1.760000e-05 62.1


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 TraesCS6D01G269200 chr6D 379515276 379521133 5857 True 2675.000000 9241 95.238000 1 5858 4 chr6D.!!$R2 5857
1 TraesCS6D01G269200 chr6D 175502556 175503212 656 False 373.900000 695 94.202000 4971 5858 2 chr6D.!!$F1 887
2 TraesCS6D01G269200 chr6B 567472803 567477179 4376 False 2304.666667 6346 91.740000 394 4797 3 chr6B.!!$F1 4403
3 TraesCS6D01G269200 chr6B 679600820 679601875 1055 False 320.266667 712 93.299667 4797 5858 3 chr6B.!!$F3 1061
4 TraesCS6D01G269200 chr6B 679616811 679617869 1058 False 263.650000 719 95.248750 4797 5858 4 chr6B.!!$F4 1061
5 TraesCS6D01G269200 chr6B 679585414 679586296 882 False 259.425000 706 94.942750 4797 5858 4 chr6B.!!$F2 1061
6 TraesCS6D01G269200 chr6A 521479949 521484187 4238 False 1397.000000 4983 92.923200 114 4797 5 chr6A.!!$F2 4683
7 TraesCS6D01G269200 chr6A 187078385 187079264 879 True 343.933333 736 95.942000 4795 5858 3 chr6A.!!$R1 1063
8 TraesCS6D01G269200 chr7D 54774664 54775765 1101 False 524.500000 773 97.045000 4795 5858 2 chr7D.!!$F1 1063
9 TraesCS6D01G269200 chr4A 75914485 75915357 872 True 332.600000 710 95.531667 4797 5856 3 chr4A.!!$R1 1059
10 TraesCS6D01G269200 chr4A 443478780 443479670 890 True 331.366667 717 94.795000 4796 5858 3 chr4A.!!$R3 1062

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
26 27 0.036952 CACGCAGTCCCTGACTTCAT 60.037 55.000 0.0 0.0 41.37 2.57 F
593 604 0.040646 AAGGGGAACGGGGAAAATCC 59.959 55.000 0.0 0.0 35.23 3.01 F
1327 1349 0.373716 GAGTTTTAGATGCCGCCGTG 59.626 55.000 0.0 0.0 0.00 4.94 F
2699 2727 0.546747 TCTGGGGAAGTCAACGGGAT 60.547 55.000 0.0 0.0 0.00 3.85 F
3326 3361 1.443702 GCGGGTGCGTTTTTCCATC 60.444 57.895 0.0 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1046 1064 0.108615 CACGAAGAGAATCGGTGGCT 60.109 55.000 1.59 0.0 46.82 4.75 R
1557 1580 2.350522 GCATGAGACACCGATGAGTTT 58.649 47.619 0.00 0.0 0.00 2.66 R
3242 3276 1.322442 GCAAGACTTTCAAGCCTGGT 58.678 50.000 0.00 0.0 0.00 4.00 R
4552 4593 0.038744 ACATAGCAACCAAGCCAGCT 59.961 50.000 0.00 0.0 40.92 4.24 R
4868 4911 0.965363 AATGGCGGGCACGAGATTTT 60.965 50.000 15.48 0.0 44.60 1.82 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
20 21 2.734591 GACACACGCAGTCCCTGA 59.265 61.111 0.00 0.00 41.61 3.86
21 22 1.664965 GACACACGCAGTCCCTGAC 60.665 63.158 0.00 0.00 41.61 3.51
22 23 2.088674 GACACACGCAGTCCCTGACT 62.089 60.000 0.00 0.00 44.44 3.41
23 24 1.069765 CACACGCAGTCCCTGACTT 59.930 57.895 0.00 0.00 41.37 3.01
24 25 0.946221 CACACGCAGTCCCTGACTTC 60.946 60.000 0.00 0.00 41.37 3.01
25 26 1.367471 CACGCAGTCCCTGACTTCA 59.633 57.895 0.00 0.00 41.37 3.02
26 27 0.036952 CACGCAGTCCCTGACTTCAT 60.037 55.000 0.00 0.00 41.37 2.57
27 28 1.204704 CACGCAGTCCCTGACTTCATA 59.795 52.381 0.00 0.00 41.37 2.15
28 29 2.111384 ACGCAGTCCCTGACTTCATAT 58.889 47.619 0.00 0.00 41.37 1.78
29 30 3.068165 CACGCAGTCCCTGACTTCATATA 59.932 47.826 0.00 0.00 41.37 0.86
30 31 3.319405 ACGCAGTCCCTGACTTCATATAG 59.681 47.826 0.00 0.00 41.37 1.31
31 32 3.319405 CGCAGTCCCTGACTTCATATAGT 59.681 47.826 0.00 0.00 41.37 2.12
32 33 4.626042 GCAGTCCCTGACTTCATATAGTG 58.374 47.826 0.00 0.00 41.37 2.74
33 34 4.502259 GCAGTCCCTGACTTCATATAGTGG 60.502 50.000 0.00 0.00 41.37 4.00
34 35 3.643792 AGTCCCTGACTTCATATAGTGGC 59.356 47.826 0.00 0.00 40.28 5.01
35 36 3.388024 GTCCCTGACTTCATATAGTGGCA 59.612 47.826 0.00 0.00 0.00 4.92
36 37 4.037222 TCCCTGACTTCATATAGTGGCAA 58.963 43.478 0.00 0.00 0.00 4.52
37 38 4.101585 TCCCTGACTTCATATAGTGGCAAG 59.898 45.833 0.00 0.00 0.00 4.01
38 39 4.141620 CCCTGACTTCATATAGTGGCAAGT 60.142 45.833 0.00 0.00 30.13 3.16
39 40 4.813161 CCTGACTTCATATAGTGGCAAGTG 59.187 45.833 0.00 0.00 28.27 3.16
40 41 4.769688 TGACTTCATATAGTGGCAAGTGG 58.230 43.478 0.00 0.00 28.27 4.00
41 42 4.469586 TGACTTCATATAGTGGCAAGTGGA 59.530 41.667 0.00 0.00 28.27 4.02
42 43 4.770795 ACTTCATATAGTGGCAAGTGGAC 58.229 43.478 0.00 0.00 0.00 4.02
43 44 4.225042 ACTTCATATAGTGGCAAGTGGACA 59.775 41.667 0.00 0.00 0.00 4.02
44 45 4.835284 TCATATAGTGGCAAGTGGACAA 57.165 40.909 0.00 0.00 35.15 3.18
45 46 5.372343 TCATATAGTGGCAAGTGGACAAT 57.628 39.130 0.00 0.00 35.15 2.71
46 47 5.368145 TCATATAGTGGCAAGTGGACAATC 58.632 41.667 0.00 0.00 35.15 2.67
47 48 2.489938 TAGTGGCAAGTGGACAATCC 57.510 50.000 0.00 0.00 35.15 3.01
48 49 0.251341 AGTGGCAAGTGGACAATCCC 60.251 55.000 0.00 0.00 35.15 3.85
49 50 0.539438 GTGGCAAGTGGACAATCCCA 60.539 55.000 0.00 0.00 35.15 4.37
50 51 0.409092 TGGCAAGTGGACAATCCCAT 59.591 50.000 0.00 0.00 38.66 4.00
51 52 1.106285 GGCAAGTGGACAATCCCATC 58.894 55.000 0.00 0.00 38.66 3.51
52 53 1.616725 GGCAAGTGGACAATCCCATCA 60.617 52.381 0.00 0.00 38.66 3.07
53 54 2.381911 GCAAGTGGACAATCCCATCAT 58.618 47.619 0.00 0.00 38.66 2.45
54 55 2.360165 GCAAGTGGACAATCCCATCATC 59.640 50.000 0.00 0.00 38.66 2.92
55 56 3.623703 CAAGTGGACAATCCCATCATCA 58.376 45.455 0.00 0.00 38.66 3.07
56 57 4.018490 CAAGTGGACAATCCCATCATCAA 58.982 43.478 0.00 0.00 38.66 2.57
57 58 3.624777 AGTGGACAATCCCATCATCAAC 58.375 45.455 0.00 0.00 38.66 3.18
58 59 3.010472 AGTGGACAATCCCATCATCAACA 59.990 43.478 0.00 0.00 38.66 3.33
59 60 3.763360 GTGGACAATCCCATCATCAACAA 59.237 43.478 0.00 0.00 38.66 2.83
60 61 4.018490 TGGACAATCCCATCATCAACAAG 58.982 43.478 0.00 0.00 35.03 3.16
61 62 4.263860 TGGACAATCCCATCATCAACAAGA 60.264 41.667 0.00 0.00 35.03 3.02
62 63 4.337555 GGACAATCCCATCATCAACAAGAG 59.662 45.833 0.00 0.00 0.00 2.85
63 64 3.698040 ACAATCCCATCATCAACAAGAGC 59.302 43.478 0.00 0.00 0.00 4.09
64 65 2.028420 TCCCATCATCAACAAGAGCG 57.972 50.000 0.00 0.00 0.00 5.03
65 66 1.019673 CCCATCATCAACAAGAGCGG 58.980 55.000 0.00 0.00 0.00 5.52
66 67 0.379669 CCATCATCAACAAGAGCGGC 59.620 55.000 0.00 0.00 0.00 6.53
67 68 1.089112 CATCATCAACAAGAGCGGCA 58.911 50.000 1.45 0.00 0.00 5.69
68 69 1.089920 ATCATCAACAAGAGCGGCAC 58.910 50.000 1.45 0.00 0.00 5.01
69 70 0.250252 TCATCAACAAGAGCGGCACA 60.250 50.000 1.45 0.00 0.00 4.57
70 71 0.110056 CATCAACAAGAGCGGCACAC 60.110 55.000 1.45 0.00 0.00 3.82
71 72 0.250467 ATCAACAAGAGCGGCACACT 60.250 50.000 1.45 0.00 0.00 3.55
72 73 0.391228 TCAACAAGAGCGGCACACTA 59.609 50.000 1.45 0.00 0.00 2.74
73 74 1.202592 TCAACAAGAGCGGCACACTAA 60.203 47.619 1.45 0.00 0.00 2.24
74 75 1.601903 CAACAAGAGCGGCACACTAAA 59.398 47.619 1.45 0.00 0.00 1.85
75 76 2.185004 ACAAGAGCGGCACACTAAAT 57.815 45.000 1.45 0.00 0.00 1.40
76 77 2.076863 ACAAGAGCGGCACACTAAATC 58.923 47.619 1.45 0.00 0.00 2.17
77 78 2.076100 CAAGAGCGGCACACTAAATCA 58.924 47.619 1.45 0.00 0.00 2.57
78 79 2.679837 CAAGAGCGGCACACTAAATCAT 59.320 45.455 1.45 0.00 0.00 2.45
79 80 2.991250 AGAGCGGCACACTAAATCATT 58.009 42.857 1.45 0.00 0.00 2.57
80 81 2.939103 AGAGCGGCACACTAAATCATTC 59.061 45.455 1.45 0.00 0.00 2.67
81 82 2.677836 GAGCGGCACACTAAATCATTCA 59.322 45.455 1.45 0.00 0.00 2.57
82 83 2.679837 AGCGGCACACTAAATCATTCAG 59.320 45.455 1.45 0.00 0.00 3.02
83 84 2.420022 GCGGCACACTAAATCATTCAGT 59.580 45.455 0.00 0.00 0.00 3.41
84 85 3.621268 GCGGCACACTAAATCATTCAGTA 59.379 43.478 0.00 0.00 0.00 2.74
85 86 4.273480 GCGGCACACTAAATCATTCAGTAT 59.727 41.667 0.00 0.00 0.00 2.12
86 87 5.741425 CGGCACACTAAATCATTCAGTATG 58.259 41.667 0.00 0.00 35.45 2.39
87 88 5.294306 CGGCACACTAAATCATTCAGTATGT 59.706 40.000 0.00 0.00 37.40 2.29
88 89 6.478673 CGGCACACTAAATCATTCAGTATGTA 59.521 38.462 0.00 0.00 37.40 2.29
89 90 7.171508 CGGCACACTAAATCATTCAGTATGTAT 59.828 37.037 0.00 0.00 37.40 2.29
90 91 8.285394 GGCACACTAAATCATTCAGTATGTATG 58.715 37.037 0.00 0.00 44.13 2.39
91 92 8.830580 GCACACTAAATCATTCAGTATGTATGT 58.169 33.333 0.00 0.00 43.37 2.29
162 163 3.995705 TGCAAGCAAGTCAAATAAATGCC 59.004 39.130 0.00 0.00 37.73 4.40
170 171 3.381272 AGTCAAATAAATGCCCGACATGG 59.619 43.478 0.00 0.00 39.60 3.66
175 176 0.887933 AAATGCCCGACATGGTTCAC 59.112 50.000 0.00 0.00 39.60 3.18
210 211 4.348486 TGCCCTTGGTTGATTGCTATTAA 58.652 39.130 0.00 0.00 0.00 1.40
245 246 3.428862 GCACCACACTTAGCAACAAGTTT 60.429 43.478 0.00 0.00 36.61 2.66
246 247 4.351192 CACCACACTTAGCAACAAGTTTC 58.649 43.478 0.00 0.00 36.61 2.78
247 248 4.096382 CACCACACTTAGCAACAAGTTTCT 59.904 41.667 0.00 0.00 36.61 2.52
248 249 4.705023 ACCACACTTAGCAACAAGTTTCTT 59.295 37.500 0.00 0.00 36.61 2.52
293 294 7.242359 AGCTCTGTAGGACAATACCATACTAT 58.758 38.462 0.00 0.00 0.00 2.12
302 303 9.517868 AGGACAATACCATACTATAGTGTACTC 57.482 37.037 15.90 5.45 36.10 2.59
304 305 8.647256 ACAATACCATACTATAGTGTACTCCC 57.353 38.462 15.90 0.00 28.41 4.30
370 371 7.705325 GTGACCTGAACGCTCTTATATTTCTTA 59.295 37.037 0.00 0.00 0.00 2.10
371 372 7.705325 TGACCTGAACGCTCTTATATTTCTTAC 59.295 37.037 0.00 0.00 0.00 2.34
372 373 7.553334 ACCTGAACGCTCTTATATTTCTTACA 58.447 34.615 0.00 0.00 0.00 2.41
373 374 7.707035 ACCTGAACGCTCTTATATTTCTTACAG 59.293 37.037 0.00 0.00 0.00 2.74
374 375 7.921214 CCTGAACGCTCTTATATTTCTTACAGA 59.079 37.037 0.00 0.00 0.00 3.41
375 376 8.858003 TGAACGCTCTTATATTTCTTACAGAG 57.142 34.615 0.00 0.00 0.00 3.35
380 381 6.871492 GCTCTTATATTTCTTACAGAGGGAGC 59.129 42.308 0.00 0.00 34.36 4.70
455 461 2.115266 AACCCTTTGCTCCCACGG 59.885 61.111 0.00 0.00 0.00 4.94
522 528 1.153066 TCCGAGGCTGCAAAACACA 60.153 52.632 0.50 0.00 0.00 3.72
523 529 0.749818 TCCGAGGCTGCAAAACACAA 60.750 50.000 0.50 0.00 0.00 3.33
526 532 1.856802 GAGGCTGCAAAACACAAAGG 58.143 50.000 0.50 0.00 0.00 3.11
537 543 0.172352 ACACAAAGGCAACAACCACG 59.828 50.000 0.00 0.00 41.41 4.94
572 580 3.181456 CCAGGAAAACTTGATTTTGGCCA 60.181 43.478 0.00 0.00 40.73 5.36
573 581 4.060205 CAGGAAAACTTGATTTTGGCCAG 58.940 43.478 5.11 0.00 40.73 4.85
576 587 4.751600 GGAAAACTTGATTTTGGCCAGAAG 59.248 41.667 14.78 10.96 40.73 2.85
593 604 0.040646 AAGGGGAACGGGGAAAATCC 59.959 55.000 0.00 0.00 35.23 3.01
868 883 3.719121 CTCCACTGGTCCCTGGAG 58.281 66.667 15.28 15.28 45.97 3.86
1046 1064 0.940126 GACGCCGACGAGGACTTATA 59.060 55.000 0.00 0.00 45.00 0.98
1084 1103 0.733223 GTTCTTCCTCGTGGACGCTC 60.733 60.000 5.53 0.00 43.06 5.03
1130 1150 1.270041 GCAAATCCAAAGGTGCGGAAA 60.270 47.619 0.00 0.00 34.22 3.13
1138 1158 0.902984 AAGGTGCGGAAATTTCCCCC 60.903 55.000 27.72 23.50 44.67 5.40
1141 1161 0.530744 GTGCGGAAATTTCCCCCTTC 59.469 55.000 27.72 14.01 44.67 3.46
1146 1166 1.827344 GGAAATTTCCCCCTTCTGCAG 59.173 52.381 24.44 7.63 41.62 4.41
1197 1217 1.130561 CGAATTTGGGAGGCGAAAGTC 59.869 52.381 0.00 0.00 0.00 3.01
1200 1222 2.286365 TTTGGGAGGCGAAAGTCAAT 57.714 45.000 0.00 0.00 38.99 2.57
1204 1226 3.963129 TGGGAGGCGAAAGTCAATAATT 58.037 40.909 0.00 0.00 38.99 1.40
1237 1259 1.450312 CAAGAAGGCTTCGCGGGAT 60.450 57.895 20.78 0.00 30.14 3.85
1238 1260 1.026718 CAAGAAGGCTTCGCGGGATT 61.027 55.000 20.78 6.48 30.14 3.01
1291 1313 1.405391 GGAGTGAAGAGGAAGCAGCTC 60.405 57.143 0.00 0.00 0.00 4.09
1306 1328 2.741517 GCAGCTCAAGAAGAAGAAGGAC 59.258 50.000 0.00 0.00 0.00 3.85
1321 1343 4.837972 AGAAGGACAGAGTTTTAGATGCC 58.162 43.478 0.00 0.00 0.00 4.40
1327 1349 0.373716 GAGTTTTAGATGCCGCCGTG 59.626 55.000 0.00 0.00 0.00 4.94
1403 1425 8.450180 CCTGCCATTTTGTTTTGGATAATTAAC 58.550 33.333 0.00 0.00 34.81 2.01
1404 1426 8.908786 TGCCATTTTGTTTTGGATAATTAACA 57.091 26.923 0.00 0.00 34.81 2.41
1405 1427 9.342308 TGCCATTTTGTTTTGGATAATTAACAA 57.658 25.926 0.00 0.00 38.35 2.83
1448 1471 8.298030 AGTGAAGTTTGTATGCTTAAAAATGC 57.702 30.769 0.00 0.00 0.00 3.56
1539 1562 7.972832 AACGTAGAATGGTATGACAGAAAAA 57.027 32.000 0.00 0.00 0.00 1.94
1577 1600 2.015736 AACTCATCGGTGTCTCATGC 57.984 50.000 0.00 0.00 0.00 4.06
1584 1607 2.432456 GTGTCTCATGCGCACGGA 60.432 61.111 14.90 13.35 0.00 4.69
1627 1650 3.436704 TCATTTCCTGAGCGCTTGTTAAG 59.563 43.478 13.26 4.69 0.00 1.85
1651 1674 2.550830 TGGTTCCAGCTCTTTGAGTC 57.449 50.000 0.00 0.00 31.39 3.36
1652 1675 1.768275 TGGTTCCAGCTCTTTGAGTCA 59.232 47.619 0.00 0.00 31.39 3.41
1673 1696 7.612677 AGTCATTTATTAGGCCCTACTTATCG 58.387 38.462 0.00 0.00 0.00 2.92
1684 1707 4.608951 CCCTACTTATCGCTGACAACTAC 58.391 47.826 0.00 0.00 0.00 2.73
1688 1711 5.892160 ACTTATCGCTGACAACTACTGTA 57.108 39.130 0.00 0.00 38.84 2.74
1890 1913 7.041712 GGAACACCTAAACTCAAGAAGAAGAAG 60.042 40.741 0.00 0.00 0.00 2.85
1892 1915 7.213678 ACACCTAAACTCAAGAAGAAGAAGAG 58.786 38.462 0.00 0.00 0.00 2.85
1893 1916 6.147000 CACCTAAACTCAAGAAGAAGAAGAGC 59.853 42.308 0.00 0.00 0.00 4.09
1895 1918 6.708054 CCTAAACTCAAGAAGAAGAAGAGCAA 59.292 38.462 0.00 0.00 0.00 3.91
1896 1919 6.616774 AAACTCAAGAAGAAGAAGAGCAAG 57.383 37.500 0.00 0.00 0.00 4.01
1899 1922 5.990996 ACTCAAGAAGAAGAAGAGCAAGAAG 59.009 40.000 0.00 0.00 0.00 2.85
1935 1961 3.251004 GCAAAAGTCCTGTTGAGGTACAG 59.749 47.826 1.31 0.00 44.07 2.74
2043 2069 5.262009 CCCAATGATGCAGATGATATCCTT 58.738 41.667 0.00 0.00 0.00 3.36
2205 2231 2.562298 CAAGCAACTATGGCCTTTTCCA 59.438 45.455 3.32 0.00 40.97 3.53
2297 2325 3.144506 CAGCTGATGTCAACCAACTTCT 58.855 45.455 8.42 0.00 0.00 2.85
2642 2670 7.112122 TGCATAGATATTTGTGTTTCCTGACT 58.888 34.615 0.00 0.00 0.00 3.41
2695 2723 0.804989 GCAATCTGGGGAAGTCAACG 59.195 55.000 0.00 0.00 0.00 4.10
2699 2727 0.546747 TCTGGGGAAGTCAACGGGAT 60.547 55.000 0.00 0.00 0.00 3.85
2704 2732 2.037381 GGGGAAGTCAACGGGATAGATC 59.963 54.545 0.00 0.00 0.00 2.75
2833 2861 9.841295 AAAGTAATGTCTACACTTCTGGTTTTA 57.159 29.630 0.00 0.00 31.43 1.52
2840 2869 8.100791 TGTCTACACTTCTGGTTTTATATTGCT 58.899 33.333 0.00 0.00 0.00 3.91
2905 2936 4.552166 AGTGTCCACAATGAAAAAGACG 57.448 40.909 0.00 0.00 0.00 4.18
2910 2941 5.765677 TGTCCACAATGAAAAAGACGGAATA 59.234 36.000 0.00 0.00 0.00 1.75
3019 3050 8.191446 TGAAACTGACAGATATACAAGTCTAGC 58.809 37.037 10.08 0.00 32.41 3.42
3020 3051 7.889873 AACTGACAGATATACAAGTCTAGCT 57.110 36.000 10.08 0.00 32.41 3.32
3021 3052 7.889873 ACTGACAGATATACAAGTCTAGCTT 57.110 36.000 10.08 0.00 38.08 3.74
3041 3072 4.214119 GCTTGTCTGCTTGTTACAATCAGA 59.786 41.667 22.60 22.60 33.01 3.27
3104 3135 9.071276 CCCTTATTAGTTGATATTGTGCTCAAT 57.929 33.333 17.35 17.35 45.00 2.57
3119 3150 2.351157 GCTCAATTGAGTTCCACAGTGC 60.351 50.000 30.88 13.85 43.85 4.40
3129 3160 5.046663 TGAGTTCCACAGTGCTTATGTATCA 60.047 40.000 0.00 0.00 0.00 2.15
3132 3163 6.886459 AGTTCCACAGTGCTTATGTATCATTT 59.114 34.615 0.00 0.00 0.00 2.32
3162 3194 1.818060 TGGAACCTGCAAATTGATCCG 59.182 47.619 0.00 0.00 0.00 4.18
3168 3200 2.419021 CCTGCAAATTGATCCGCCAAAT 60.419 45.455 0.00 0.00 0.00 2.32
3242 3276 1.905637 TGGAGTACAGACAGAAGCGA 58.094 50.000 0.00 0.00 0.00 4.93
3326 3361 1.443702 GCGGGTGCGTTTTTCCATC 60.444 57.895 0.00 0.00 0.00 3.51
3347 3382 9.919416 TCCATCCATTAAACATTCAAGAATCTA 57.081 29.630 0.00 0.00 0.00 1.98
3471 3506 2.708386 CGAAGTCGTCTCCTTTCTGT 57.292 50.000 0.00 0.00 34.11 3.41
3479 3514 6.102663 AGTCGTCTCCTTTCTGTCATTTATG 58.897 40.000 0.00 0.00 0.00 1.90
3481 3516 6.254589 GTCGTCTCCTTTCTGTCATTTATGAG 59.745 42.308 0.00 0.00 37.51 2.90
3482 3517 5.521735 CGTCTCCTTTCTGTCATTTATGAGG 59.478 44.000 0.00 0.00 37.51 3.86
3519 3554 7.039504 CCCTTATGTCTATTTTGGCATAGCAAT 60.040 37.037 0.00 0.00 0.00 3.56
3526 3561 2.495409 TTGGCATAGCAATTGCATCG 57.505 45.000 30.89 18.78 45.16 3.84
3783 3818 5.564550 AGAAGCTCAAATGAGTGGTATGTT 58.435 37.500 11.77 0.00 43.85 2.71
3784 3819 5.413833 AGAAGCTCAAATGAGTGGTATGTTG 59.586 40.000 11.77 0.00 43.85 3.33
3789 3824 6.922957 GCTCAAATGAGTGGTATGTTGAAAAA 59.077 34.615 11.77 0.00 43.85 1.94
3891 3927 7.067129 TGCATTAGAATCTAGACTACGTTCAGT 59.933 37.037 0.00 0.00 0.00 3.41
3893 3929 7.918536 TTAGAATCTAGACTACGTTCAGTGT 57.081 36.000 0.00 0.00 0.00 3.55
3916 3952 1.708341 AGTTTGCCATGCCAGTCTTT 58.292 45.000 0.00 0.00 0.00 2.52
3918 3954 2.036346 AGTTTGCCATGCCAGTCTTTTC 59.964 45.455 0.00 0.00 0.00 2.29
3926 3962 4.761739 CCATGCCAGTCTTTTCACTTTCTA 59.238 41.667 0.00 0.00 0.00 2.10
3931 3967 6.545666 TGCCAGTCTTTTCACTTTCTATTTGA 59.454 34.615 0.00 0.00 0.00 2.69
3962 4000 7.857885 GTCTGTTCTGGTTTTGAGAAAATACAG 59.142 37.037 0.00 0.00 38.48 2.74
3976 4014 6.245408 AGAAAATACAGTGCCCAAGTCATTA 58.755 36.000 0.00 0.00 0.00 1.90
3992 4030 7.775093 CCAAGTCATTATCCCTTGATCTTGTAA 59.225 37.037 0.00 0.00 38.23 2.41
4001 4039 4.568359 CCCTTGATCTTGTAATCAGTGTCG 59.432 45.833 0.00 0.00 37.01 4.35
4012 4050 3.942130 ATCAGTGTCGTGTGAATCTCA 57.058 42.857 0.00 0.00 0.00 3.27
4043 4081 8.287503 CACCAGAGGTTATTTTGTGTAGTAAAC 58.712 37.037 0.00 0.00 31.02 2.01
4141 4180 7.472741 TCATACTCCCTCCGTTCCTAAATATA 58.527 38.462 0.00 0.00 0.00 0.86
4142 4181 7.951806 TCATACTCCCTCCGTTCCTAAATATAA 59.048 37.037 0.00 0.00 0.00 0.98
4149 4188 8.645110 CCCTCCGTTCCTAAATATAAGTCTTTA 58.355 37.037 0.00 0.00 0.00 1.85
4150 4189 9.694137 CCTCCGTTCCTAAATATAAGTCTTTAG 57.306 37.037 0.00 0.00 35.60 1.85
4167 4206 8.789767 AGTCTTTAGAGAGATTCCATTATGGA 57.210 34.615 10.29 10.29 37.39 3.41
4168 4207 8.646900 AGTCTTTAGAGAGATTCCATTATGGAC 58.353 37.037 14.25 3.50 38.34 4.02
4177 4217 3.762407 TCCATTATGGACCACATACGG 57.238 47.619 10.29 0.00 42.67 4.02
4197 4237 5.431765 ACGGAGCAAAATGAGTGAATCTAT 58.568 37.500 0.00 0.00 0.00 1.98
4233 4273 9.474313 TGCATCTATATACATCTGTATGTGGTA 57.526 33.333 12.10 1.05 45.99 3.25
4317 4358 2.821378 TCTGCTACAAGTTGCATGCAAT 59.179 40.909 33.94 21.16 40.23 3.56
4383 4424 2.042569 TGGGAGAGCTACTGACCTGTAA 59.957 50.000 0.00 0.00 0.00 2.41
4530 4571 1.531149 CAGTGTTCGTTCCACATCACC 59.469 52.381 0.00 0.00 35.24 4.02
4712 4753 6.515512 AGTGTATTATTGGTTATCTGGCCT 57.484 37.500 3.32 0.00 0.00 5.19
4724 4765 7.004086 TGGTTATCTGGCCTATTTTATTGGAG 58.996 38.462 3.32 0.00 0.00 3.86
4760 4802 1.534235 AGGAGCTGAAGGTGGTCGT 60.534 57.895 0.00 0.00 33.26 4.34
4761 4803 1.079750 GGAGCTGAAGGTGGTCGTC 60.080 63.158 0.00 0.00 33.26 4.20
4766 4809 2.432628 GAAGGTGGTCGTCAGGCG 60.433 66.667 0.00 0.00 43.01 5.52
4770 4813 4.736896 GTGGTCGTCAGGCGGTCC 62.737 72.222 0.00 0.00 41.72 4.46
4781 4824 2.588439 GCGGTCCCTTAGGTTCCC 59.412 66.667 0.00 0.00 0.00 3.97
4886 4930 0.965363 AAAAATCTCGTGCCCGCCAT 60.965 50.000 0.00 0.00 0.00 4.40
5409 5581 4.384647 GGCTCTAGGGTTGTGAGATTTCAT 60.385 45.833 0.00 0.00 35.39 2.57
5633 5806 9.840427 AAAGGAAGTGATTGTACAAATTTATCG 57.160 29.630 13.23 0.00 0.00 2.92
5683 5856 3.916359 TGTCACCAGACTACACCAAAA 57.084 42.857 0.00 0.00 45.20 2.44
5749 5922 4.003648 ACCATCTTCCTCGACAACAATTC 58.996 43.478 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.643792 GCCACTATATGAAGTCAGGGACT 59.356 47.826 0.00 0.00 45.64 3.85
13 14 3.388024 TGCCACTATATGAAGTCAGGGAC 59.612 47.826 0.00 0.00 0.00 4.46
14 15 3.653164 TGCCACTATATGAAGTCAGGGA 58.347 45.455 0.00 0.00 0.00 4.20
15 16 4.141620 ACTTGCCACTATATGAAGTCAGGG 60.142 45.833 0.00 0.00 0.00 4.45
16 17 4.813161 CACTTGCCACTATATGAAGTCAGG 59.187 45.833 0.00 0.00 0.00 3.86
17 18 4.813161 CCACTTGCCACTATATGAAGTCAG 59.187 45.833 0.00 0.00 0.00 3.51
18 19 4.469586 TCCACTTGCCACTATATGAAGTCA 59.530 41.667 0.00 0.00 0.00 3.41
19 20 4.811557 GTCCACTTGCCACTATATGAAGTC 59.188 45.833 0.00 0.00 0.00 3.01
20 21 4.225042 TGTCCACTTGCCACTATATGAAGT 59.775 41.667 0.00 0.00 0.00 3.01
21 22 4.769688 TGTCCACTTGCCACTATATGAAG 58.230 43.478 0.00 0.00 0.00 3.02
22 23 4.835284 TGTCCACTTGCCACTATATGAA 57.165 40.909 0.00 0.00 0.00 2.57
23 24 4.835284 TTGTCCACTTGCCACTATATGA 57.165 40.909 0.00 0.00 0.00 2.15
24 25 4.516698 GGATTGTCCACTTGCCACTATATG 59.483 45.833 0.00 0.00 36.28 1.78
25 26 4.446311 GGGATTGTCCACTTGCCACTATAT 60.446 45.833 0.00 0.00 38.64 0.86
26 27 3.118038 GGGATTGTCCACTTGCCACTATA 60.118 47.826 0.00 0.00 38.64 1.31
27 28 2.357154 GGGATTGTCCACTTGCCACTAT 60.357 50.000 0.00 0.00 38.64 2.12
28 29 1.004277 GGGATTGTCCACTTGCCACTA 59.996 52.381 0.00 0.00 38.64 2.74
29 30 0.251341 GGGATTGTCCACTTGCCACT 60.251 55.000 0.00 0.00 38.64 4.00
30 31 0.539438 TGGGATTGTCCACTTGCCAC 60.539 55.000 0.00 0.00 38.64 5.01
31 32 0.409092 ATGGGATTGTCCACTTGCCA 59.591 50.000 0.00 0.00 39.97 4.92
32 33 1.106285 GATGGGATTGTCCACTTGCC 58.894 55.000 0.00 0.00 39.97 4.52
33 34 1.838112 TGATGGGATTGTCCACTTGC 58.162 50.000 0.00 0.00 39.97 4.01
34 35 3.623703 TGATGATGGGATTGTCCACTTG 58.376 45.455 0.00 0.00 39.97 3.16
35 36 4.019174 GTTGATGATGGGATTGTCCACTT 58.981 43.478 0.00 0.00 39.97 3.16
36 37 3.010472 TGTTGATGATGGGATTGTCCACT 59.990 43.478 0.00 0.00 39.97 4.00
37 38 3.355378 TGTTGATGATGGGATTGTCCAC 58.645 45.455 0.00 0.00 39.97 4.02
38 39 3.735720 TGTTGATGATGGGATTGTCCA 57.264 42.857 0.00 0.00 38.64 4.02
39 40 4.272489 TCTTGTTGATGATGGGATTGTCC 58.728 43.478 0.00 0.00 35.23 4.02
40 41 4.201990 GCTCTTGTTGATGATGGGATTGTC 60.202 45.833 0.00 0.00 0.00 3.18
41 42 3.698040 GCTCTTGTTGATGATGGGATTGT 59.302 43.478 0.00 0.00 0.00 2.71
42 43 3.242969 CGCTCTTGTTGATGATGGGATTG 60.243 47.826 0.00 0.00 0.00 2.67
43 44 2.947652 CGCTCTTGTTGATGATGGGATT 59.052 45.455 0.00 0.00 0.00 3.01
44 45 2.569059 CGCTCTTGTTGATGATGGGAT 58.431 47.619 0.00 0.00 0.00 3.85
45 46 1.407299 CCGCTCTTGTTGATGATGGGA 60.407 52.381 0.00 0.00 0.00 4.37
46 47 1.019673 CCGCTCTTGTTGATGATGGG 58.980 55.000 0.00 0.00 0.00 4.00
47 48 0.379669 GCCGCTCTTGTTGATGATGG 59.620 55.000 0.00 0.00 0.00 3.51
48 49 1.089112 TGCCGCTCTTGTTGATGATG 58.911 50.000 0.00 0.00 0.00 3.07
49 50 1.089920 GTGCCGCTCTTGTTGATGAT 58.910 50.000 0.00 0.00 0.00 2.45
50 51 0.250252 TGTGCCGCTCTTGTTGATGA 60.250 50.000 0.00 0.00 0.00 2.92
51 52 0.110056 GTGTGCCGCTCTTGTTGATG 60.110 55.000 0.00 0.00 0.00 3.07
52 53 0.250467 AGTGTGCCGCTCTTGTTGAT 60.250 50.000 0.00 0.00 0.00 2.57
53 54 0.391228 TAGTGTGCCGCTCTTGTTGA 59.609 50.000 0.00 0.00 0.00 3.18
54 55 1.225855 TTAGTGTGCCGCTCTTGTTG 58.774 50.000 0.00 0.00 0.00 3.33
55 56 1.961793 TTTAGTGTGCCGCTCTTGTT 58.038 45.000 0.00 0.00 0.00 2.83
56 57 2.076863 GATTTAGTGTGCCGCTCTTGT 58.923 47.619 0.00 0.00 0.00 3.16
57 58 2.076100 TGATTTAGTGTGCCGCTCTTG 58.924 47.619 0.00 0.00 0.00 3.02
58 59 2.472695 TGATTTAGTGTGCCGCTCTT 57.527 45.000 0.00 0.00 0.00 2.85
59 60 2.698855 ATGATTTAGTGTGCCGCTCT 57.301 45.000 0.00 0.00 0.00 4.09
60 61 2.677836 TGAATGATTTAGTGTGCCGCTC 59.322 45.455 0.00 0.00 0.00 5.03
61 62 2.679837 CTGAATGATTTAGTGTGCCGCT 59.320 45.455 0.00 0.00 0.00 5.52
62 63 2.420022 ACTGAATGATTTAGTGTGCCGC 59.580 45.455 1.49 0.00 0.00 6.53
63 64 5.294306 ACATACTGAATGATTTAGTGTGCCG 59.706 40.000 21.00 4.58 37.14 5.69
64 65 6.683974 ACATACTGAATGATTTAGTGTGCC 57.316 37.500 21.00 0.00 37.14 5.01
65 66 8.830580 ACATACATACTGAATGATTTAGTGTGC 58.169 33.333 21.00 0.00 37.14 4.57
110 111 9.910267 TGTGTCCTAGTAGTGTAGTCATATAAA 57.090 33.333 0.00 0.00 0.00 1.40
111 112 9.910267 TTGTGTCCTAGTAGTGTAGTCATATAA 57.090 33.333 0.00 0.00 0.00 0.98
112 113 9.334947 GTTGTGTCCTAGTAGTGTAGTCATATA 57.665 37.037 0.00 0.00 0.00 0.86
113 114 8.053963 AGTTGTGTCCTAGTAGTGTAGTCATAT 58.946 37.037 0.00 0.00 0.00 1.78
114 115 7.400439 AGTTGTGTCCTAGTAGTGTAGTCATA 58.600 38.462 0.00 0.00 0.00 2.15
115 116 6.246919 AGTTGTGTCCTAGTAGTGTAGTCAT 58.753 40.000 0.00 0.00 0.00 3.06
116 117 5.628130 AGTTGTGTCCTAGTAGTGTAGTCA 58.372 41.667 0.00 0.00 0.00 3.41
117 118 6.380190 CAAGTTGTGTCCTAGTAGTGTAGTC 58.620 44.000 0.00 0.00 0.00 2.59
130 131 1.134946 ACTTGCTTGCAAGTTGTGTCC 59.865 47.619 28.63 9.43 42.16 4.02
162 163 0.037697 TCTTCCGTGAACCATGTCGG 60.038 55.000 0.00 0.00 43.65 4.79
170 171 2.930682 GGCAGATAACTCTTCCGTGAAC 59.069 50.000 0.00 0.00 0.00 3.18
175 176 2.555199 CAAGGGCAGATAACTCTTCCG 58.445 52.381 0.00 0.00 35.81 4.30
210 211 0.321298 GTGGTGCGGGTGATACTTGT 60.321 55.000 0.00 0.00 0.00 3.16
245 246 5.030147 TCTGGGCTTAATTCCTCTGTAAGA 58.970 41.667 0.00 0.00 43.69 2.10
246 247 5.359194 TCTGGGCTTAATTCCTCTGTAAG 57.641 43.478 0.00 0.00 0.00 2.34
247 248 4.384208 GCTCTGGGCTTAATTCCTCTGTAA 60.384 45.833 0.00 0.00 38.06 2.41
248 249 3.134804 GCTCTGGGCTTAATTCCTCTGTA 59.865 47.826 0.00 0.00 38.06 2.74
351 352 7.382759 CCCTCTGTAAGAAATATAAGAGCGTTC 59.617 40.741 0.00 0.00 46.34 3.95
380 381 5.128827 TCCTGCTTGGTAGGAGTAATTAGTG 59.871 44.000 0.00 0.00 39.41 2.74
455 461 2.109126 GGTGGTCAAGAGCATCCGC 61.109 63.158 5.17 0.00 41.20 5.54
522 528 0.454196 GTGACGTGGTTGTTGCCTTT 59.546 50.000 0.00 0.00 0.00 3.11
523 529 1.711060 CGTGACGTGGTTGTTGCCTT 61.711 55.000 0.00 0.00 0.00 4.35
526 532 1.011574 GTCGTGACGTGGTTGTTGC 60.012 57.895 4.40 0.00 0.00 4.17
537 543 0.391597 TTCCTGGGTTCAGTCGTGAC 59.608 55.000 0.00 0.00 39.31 3.67
572 580 1.005569 GATTTTCCCCGTTCCCCTTCT 59.994 52.381 0.00 0.00 0.00 2.85
573 581 1.471119 GATTTTCCCCGTTCCCCTTC 58.529 55.000 0.00 0.00 0.00 3.46
576 587 4.349682 GGATTTTCCCCGTTCCCC 57.650 61.111 0.00 0.00 0.00 4.81
593 604 3.110178 GTTCGCCGAGGTTCGTGG 61.110 66.667 0.00 0.00 38.40 4.94
855 870 3.314331 CGCACTCCAGGGACCAGT 61.314 66.667 0.00 0.00 0.00 4.00
868 883 0.603975 GATTCTATCCAGGCCCGCAC 60.604 60.000 0.00 0.00 0.00 5.34
877 892 1.140312 GGTGGGCCTGATTCTATCCA 58.860 55.000 4.53 0.00 0.00 3.41
1040 1058 4.261656 CGAAGAGAATCGGTGGCTATAAGT 60.262 45.833 0.00 0.00 42.67 2.24
1046 1064 0.108615 CACGAAGAGAATCGGTGGCT 60.109 55.000 1.59 0.00 46.82 4.75
1084 1103 1.135972 CCGAGAACAAATCAGCAACGG 60.136 52.381 0.00 0.00 0.00 4.44
1138 1158 0.309922 CAACAGTGTGCCTGCAGAAG 59.690 55.000 17.39 0.00 45.68 2.85
1141 1161 1.731433 AAGCAACAGTGTGCCTGCAG 61.731 55.000 18.16 6.78 46.14 4.41
1146 1166 0.880278 TCGAGAAGCAACAGTGTGCC 60.880 55.000 12.26 0.60 46.14 5.01
1197 1217 7.809331 TCTTGTCTACAAAGCAGCAAATTATTG 59.191 33.333 0.00 0.00 36.14 1.90
1200 1222 6.875948 TCTTGTCTACAAAGCAGCAAATTA 57.124 33.333 0.00 0.00 35.15 1.40
1204 1226 3.565482 CCTTCTTGTCTACAAAGCAGCAA 59.435 43.478 0.00 0.00 35.15 3.91
1237 1259 4.335416 CCAGCTTCTTATCAACCTTGGAA 58.665 43.478 0.00 0.00 0.00 3.53
1238 1260 3.873801 GCCAGCTTCTTATCAACCTTGGA 60.874 47.826 0.00 0.00 0.00 3.53
1291 1313 6.934048 AAAACTCTGTCCTTCTTCTTCTTG 57.066 37.500 0.00 0.00 0.00 3.02
1306 1328 0.652592 CGGCGGCATCTAAAACTCTG 59.347 55.000 10.53 0.00 0.00 3.35
1403 1425 6.115446 TCACTTAGGATGAGCTTAACCATTG 58.885 40.000 7.56 0.00 0.00 2.82
1404 1426 6.313519 TCACTTAGGATGAGCTTAACCATT 57.686 37.500 7.56 0.00 0.00 3.16
1405 1427 5.957771 TCACTTAGGATGAGCTTAACCAT 57.042 39.130 7.56 0.00 0.00 3.55
1406 1428 5.248477 ACTTCACTTAGGATGAGCTTAACCA 59.752 40.000 7.56 0.00 0.00 3.67
1549 1572 3.551846 ACACCGATGAGTTTGAAGGTTT 58.448 40.909 0.00 0.00 0.00 3.27
1557 1580 2.350522 GCATGAGACACCGATGAGTTT 58.649 47.619 0.00 0.00 0.00 2.66
1577 1600 2.539547 CCTCATGCTATTTTTCCGTGCG 60.540 50.000 0.00 0.00 0.00 5.34
1584 1607 4.192317 GAGACGGTCCTCATGCTATTTTT 58.808 43.478 4.14 0.00 33.50 1.94
1627 1650 4.142160 ACTCAAAGAGCTGGAACCAAAAAC 60.142 41.667 0.00 0.00 32.04 2.43
1651 1674 6.313905 CAGCGATAAGTAGGGCCTAATAAATG 59.686 42.308 16.44 6.84 0.00 2.32
1652 1675 6.212791 TCAGCGATAAGTAGGGCCTAATAAAT 59.787 38.462 16.44 11.46 0.00 1.40
1673 1696 3.493503 ACGCTTTTACAGTAGTTGTCAGC 59.506 43.478 0.00 0.00 41.29 4.26
1684 1707 5.108385 AGTTCCATTTCACGCTTTTACAG 57.892 39.130 0.00 0.00 0.00 2.74
1688 1711 7.865706 AGATATAGTTCCATTTCACGCTTTT 57.134 32.000 0.00 0.00 0.00 2.27
1865 1888 7.711339 TCTTCTTCTTCTTGAGTTTAGGTGTTC 59.289 37.037 0.00 0.00 0.00 3.18
1875 1898 5.543507 TCTTGCTCTTCTTCTTCTTGAGT 57.456 39.130 0.00 0.00 0.00 3.41
1878 1901 4.514441 TGCTTCTTGCTCTTCTTCTTCTTG 59.486 41.667 0.00 0.00 43.37 3.02
1890 1913 2.704572 TCCTTTAGCTGCTTCTTGCTC 58.295 47.619 7.79 0.00 43.37 4.26
1892 1915 3.831112 CTTTCCTTTAGCTGCTTCTTGC 58.169 45.455 7.79 0.00 43.25 4.01
1893 1916 3.254166 TGCTTTCCTTTAGCTGCTTCTTG 59.746 43.478 7.79 0.00 39.38 3.02
1895 1918 3.146104 TGCTTTCCTTTAGCTGCTTCT 57.854 42.857 7.79 0.00 39.38 2.85
1896 1919 3.923017 TTGCTTTCCTTTAGCTGCTTC 57.077 42.857 7.79 0.00 39.38 3.86
1899 1922 3.982475 ACTTTTGCTTTCCTTTAGCTGC 58.018 40.909 0.00 0.00 39.38 5.25
2043 2069 7.821359 AGAGTTTCTTCATCGAGATTTTCATGA 59.179 33.333 0.00 0.00 0.00 3.07
2297 2325 8.363390 CAATATCCATAACTTCACTCTCTGCTA 58.637 37.037 0.00 0.00 0.00 3.49
2595 2623 8.999220 TGCAATAGATAGCTGATAATTGAGAG 57.001 34.615 14.28 0.00 0.00 3.20
2623 2651 6.012658 TGCAAGTCAGGAAACACAAATATC 57.987 37.500 0.00 0.00 0.00 1.63
2642 2670 3.243670 TGCGTCCAATGAAAAGAATGCAA 60.244 39.130 0.00 0.00 0.00 4.08
2695 2723 4.093011 ACTGATACCTGCAGATCTATCCC 58.907 47.826 17.39 0.00 36.86 3.85
2699 2727 6.842676 TCTCTAACTGATACCTGCAGATCTA 58.157 40.000 17.39 1.49 36.86 1.98
2704 2732 4.037446 GTCCTCTCTAACTGATACCTGCAG 59.963 50.000 6.78 6.78 39.26 4.41
3018 3049 4.214119 TCTGATTGTAACAAGCAGACAAGC 59.786 41.667 16.69 7.37 37.71 4.01
3019 3050 5.929697 TCTGATTGTAACAAGCAGACAAG 57.070 39.130 16.69 0.00 37.71 3.16
3023 3054 7.661437 ACATTTAGTCTGATTGTAACAAGCAGA 59.339 33.333 16.69 16.69 39.98 4.26
3024 3055 7.810658 ACATTTAGTCTGATTGTAACAAGCAG 58.189 34.615 0.00 0.00 35.18 4.24
3025 3056 7.744087 ACATTTAGTCTGATTGTAACAAGCA 57.256 32.000 0.00 0.00 0.00 3.91
3041 3072 8.279970 TGCACTGCATAAGATTAACATTTAGT 57.720 30.769 0.00 0.00 31.71 2.24
3104 3135 4.085357 ACATAAGCACTGTGGAACTCAA 57.915 40.909 10.21 0.00 38.04 3.02
3168 3200 6.040729 CCACATATCAGTATTTGCCATTGGAA 59.959 38.462 6.95 0.00 0.00 3.53
3242 3276 1.322442 GCAAGACTTTCAAGCCTGGT 58.678 50.000 0.00 0.00 0.00 4.00
3347 3382 7.398024 AGCTATAAATCAGGACAGTTCACTTT 58.602 34.615 0.00 0.00 0.00 2.66
3352 3387 6.754193 AGCTAGCTATAAATCAGGACAGTTC 58.246 40.000 17.69 0.00 0.00 3.01
3404 3439 9.841295 ACTTGTCTTAACTTCCACAATAACTTA 57.159 29.630 0.00 0.00 0.00 2.24
3462 3497 4.788075 TCCCCTCATAAATGACAGAAAGGA 59.212 41.667 0.00 0.00 32.50 3.36
3496 3531 7.652909 GCAATTGCTATGCCAAAATAGACATAA 59.347 33.333 23.21 0.00 37.85 1.90
3502 3537 5.118050 CGATGCAATTGCTATGCCAAAATAG 59.882 40.000 29.37 9.22 43.16 1.73
3504 3539 3.805422 CGATGCAATTGCTATGCCAAAAT 59.195 39.130 29.37 12.38 43.16 1.82
3519 3554 2.164422 TGACAAACCAACAACGATGCAA 59.836 40.909 0.00 0.00 0.00 4.08
3526 3561 3.518634 ACCACATGACAAACCAACAAC 57.481 42.857 0.00 0.00 0.00 3.32
3852 3888 8.471361 AGATTCTAATGCATCATACATGTACG 57.529 34.615 7.96 0.00 0.00 3.67
3884 3920 2.353269 TGGCAAACTACAACACTGAACG 59.647 45.455 0.00 0.00 0.00 3.95
3891 3927 1.612950 CTGGCATGGCAAACTACAACA 59.387 47.619 23.47 0.00 0.00 3.33
3893 3929 1.885887 GACTGGCATGGCAAACTACAA 59.114 47.619 23.47 0.00 0.00 2.41
3916 3952 9.778741 AACAGACTACATCAAATAGAAAGTGAA 57.221 29.630 0.00 0.00 0.00 3.18
3918 3954 9.429359 AGAACAGACTACATCAAATAGAAAGTG 57.571 33.333 0.00 0.00 0.00 3.16
3926 3962 7.502226 TCAAAACCAGAACAGACTACATCAAAT 59.498 33.333 0.00 0.00 0.00 2.32
3931 3967 6.174720 TCTCAAAACCAGAACAGACTACAT 57.825 37.500 0.00 0.00 0.00 2.29
3962 4000 2.689983 CAAGGGATAATGACTTGGGCAC 59.310 50.000 0.00 0.00 38.29 5.01
3976 4014 6.319048 ACACTGATTACAAGATCAAGGGAT 57.681 37.500 0.00 0.00 35.74 3.85
3992 4030 3.579709 GTGAGATTCACACGACACTGAT 58.420 45.455 4.42 0.00 46.22 2.90
4001 4039 8.468756 ACCTCTGGTGTATGTGAGATTCACAC 62.469 46.154 13.54 7.22 46.92 3.82
4012 4050 6.303839 ACACAAAATAACCTCTGGTGTATGT 58.696 36.000 0.00 0.00 36.36 2.29
4021 4059 9.269453 GTCTGTTTACTACACAAAATAACCTCT 57.731 33.333 0.00 0.00 32.10 3.69
4024 4062 8.833493 ACAGTCTGTTTACTACACAAAATAACC 58.167 33.333 0.00 0.00 32.10 2.85
4109 4148 1.620819 CGGAGGGAGTATGATGGAAGG 59.379 57.143 0.00 0.00 0.00 3.46
4141 4180 9.218525 TCCATAATGGAATCTCTCTAAAGACTT 57.781 33.333 0.00 0.00 45.00 3.01
4142 4181 8.789767 TCCATAATGGAATCTCTCTAAAGACT 57.210 34.615 0.00 0.00 45.00 3.24
4157 4196 3.310193 TCCGTATGTGGTCCATAATGGA 58.690 45.455 0.00 1.41 45.98 3.41
4158 4197 3.664107 CTCCGTATGTGGTCCATAATGG 58.336 50.000 0.00 0.00 37.77 3.16
4161 4200 2.112190 TGCTCCGTATGTGGTCCATAA 58.888 47.619 0.00 0.00 37.77 1.90
4162 4201 1.783071 TGCTCCGTATGTGGTCCATA 58.217 50.000 0.00 0.00 34.86 2.74
4164 4203 0.687920 TTTGCTCCGTATGTGGTCCA 59.312 50.000 0.00 0.00 0.00 4.02
4166 4205 3.006940 TCATTTTGCTCCGTATGTGGTC 58.993 45.455 0.00 0.00 0.00 4.02
4167 4206 3.009723 CTCATTTTGCTCCGTATGTGGT 58.990 45.455 0.00 0.00 0.00 4.16
4168 4207 3.009723 ACTCATTTTGCTCCGTATGTGG 58.990 45.455 0.00 0.00 0.00 4.17
4177 4217 8.885494 AGAGTATAGATTCACTCATTTTGCTC 57.115 34.615 4.70 0.00 42.99 4.26
4250 4291 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
4257 4298 8.731591 AATACTCCCTCCGTTCCTAAATATAA 57.268 34.615 0.00 0.00 0.00 0.98
4258 4299 8.731591 AAATACTCCCTCCGTTCCTAAATATA 57.268 34.615 0.00 0.00 0.00 0.86
4317 4358 2.123342 GTTGCATAAAAACGCACTGCA 58.877 42.857 1.11 0.00 40.79 4.41
4325 4366 4.209080 GCCACACTCAAGTTGCATAAAAAC 59.791 41.667 0.00 0.00 0.00 2.43
4383 4424 0.316204 GCCAGCTCTGCACAACAAAT 59.684 50.000 0.00 0.00 0.00 2.32
4547 4588 1.286880 CAACCAAGCCAGCTTTCCG 59.713 57.895 1.19 0.00 33.42 4.30
4551 4592 1.180029 CATAGCAACCAAGCCAGCTT 58.820 50.000 0.00 0.00 38.47 3.74
4552 4593 0.038744 ACATAGCAACCAAGCCAGCT 59.961 50.000 0.00 0.00 40.92 4.24
4605 4646 4.217334 ACATTTGTCCAACGATGCAACATA 59.783 37.500 0.00 0.00 0.00 2.29
4760 4802 1.229400 AACCTAAGGGACCGCCTGA 60.229 57.895 0.00 0.00 36.25 3.86
4761 4803 1.221021 GAACCTAAGGGACCGCCTG 59.779 63.158 0.00 0.00 36.25 4.85
4823 4866 8.977505 CCTTAATTTATTTACCATCATTTGCCG 58.022 33.333 0.00 0.00 0.00 5.69
4868 4911 0.965363 AATGGCGGGCACGAGATTTT 60.965 50.000 15.48 0.00 44.60 1.82
5504 5677 8.246180 GTGAAGGACAAATTACATCATTGTGAT 58.754 33.333 0.00 0.00 37.41 3.06
5609 5782 7.610305 ACCGATAAATTTGTACAATCACTTCCT 59.390 33.333 9.56 0.00 0.00 3.36
5633 5806 1.817447 AGCCACTAGACACGAGTAACC 59.183 52.381 0.00 0.00 0.00 2.85
5683 5856 4.415596 TGGGGTTATTGTGAAGCTCAATT 58.584 39.130 4.62 0.00 34.44 2.32
5749 5922 0.313043 CAACTTTGGCAGCTCCACAG 59.687 55.000 13.56 13.56 46.55 3.66
5784 5958 7.393841 TCATCAATGCTCATGTTCATTGTAA 57.606 32.000 26.22 16.87 45.76 2.41
5808 5982 1.404035 GTGTTGCGACTGTTCCCTTTT 59.596 47.619 5.50 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.