Multiple sequence alignment - TraesCS3D01G243900

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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 TraesCS3D01G243900 chr3D 100.000 3418 0 0 1 3418 339254349 339250932 0.000000e+00 6312.0
1 TraesCS3D01G243900 chr3D 89.779 861 53 13 2565 3418 36173362 36172530 0.000000e+00 1070.0
2 TraesCS3D01G243900 chr3D 93.089 492 25 6 2929 3418 94715390 94714906 0.000000e+00 712.0
3 TraesCS3D01G243900 chr3D 90.164 549 38 13 2567 3101 107064027 107064573 0.000000e+00 701.0
4 TraesCS3D01G243900 chr3D 87.755 196 16 8 2562 2755 154427798 154427987 4.440000e-54 222.0
5 TraesCS3D01G243900 chr3D 76.226 265 49 13 1138 1392 374206907 374207167 9.960000e-26 128.0
6 TraesCS3D01G243900 chr3B 92.920 2288 78 28 332 2568 437805803 437803549 0.000000e+00 3251.0
7 TraesCS3D01G243900 chr3B 75.472 265 51 13 1138 1392 487907003 487907263 2.160000e-22 117.0
8 TraesCS3D01G243900 chr3B 84.211 76 12 0 2404 2479 16613430 16613505 1.320000e-09 75.0
9 TraesCS3D01G243900 chr3A 92.269 1979 73 34 652 2569 465542497 465544456 0.000000e+00 2734.0
10 TraesCS3D01G243900 chr3A 93.612 407 20 5 266 669 465542080 465542483 1.360000e-168 603.0
11 TraesCS3D01G243900 chr3A 75.472 265 51 13 1138 1392 496703375 496703635 2.160000e-22 117.0
12 TraesCS3D01G243900 chr5D 96.820 849 26 1 2570 3418 124349542 124348695 0.000000e+00 1417.0
13 TraesCS3D01G243900 chr5D 82.171 129 14 6 2358 2484 251956834 251956955 6.030000e-18 102.0
14 TraesCS3D01G243900 chr5D 84.058 69 8 3 2504 2570 448131637 448131704 2.850000e-06 63.9
15 TraesCS3D01G243900 chr4D 92.689 848 53 8 2575 3418 323758490 323759332 0.000000e+00 1214.0
16 TraesCS3D01G243900 chr2D 91.882 850 55 13 2575 3418 2910634 2911475 0.000000e+00 1175.0
17 TraesCS3D01G243900 chr2D 89.399 849 57 19 2575 3418 643441106 643440286 0.000000e+00 1038.0
18 TraesCS3D01G243900 chr2D 95.833 48 2 0 2432 2479 7659398 7659445 1.020000e-10 78.7
19 TraesCS3D01G243900 chr1D 89.635 849 55 12 2575 3418 200462694 200463514 0.000000e+00 1050.0
20 TraesCS3D01G243900 chr1D 85.787 394 41 10 2576 2965 297388900 297388518 1.480000e-108 403.0
21 TraesCS3D01G243900 chr1D 82.892 415 45 13 2562 2952 62224663 62224251 1.950000e-92 350.0
22 TraesCS3D01G243900 chr1D 81.879 447 49 14 2562 2990 62234578 62234146 7.020000e-92 348.0
23 TraesCS3D01G243900 chr1D 76.613 124 18 5 2349 2464 408767975 408767855 1.320000e-04 58.4
24 TraesCS3D01G243900 chr7D 95.853 434 15 3 2987 3418 614073676 614073244 0.000000e+00 699.0
25 TraesCS3D01G243900 chr7D 90.551 508 33 14 2918 3418 89869134 89869633 0.000000e+00 658.0
26 TraesCS3D01G243900 chr7D 95.500 400 17 1 2567 2965 614073960 614073561 3.720000e-179 638.0
27 TraesCS3D01G243900 chr7D 88.565 481 42 12 2561 3034 89868844 89869318 3.830000e-159 571.0
28 TraesCS3D01G243900 chr7D 87.817 197 17 4 2560 2755 535925717 535925527 1.230000e-54 224.0
29 TraesCS3D01G243900 chr7D 77.863 131 26 2 2349 2479 39960748 39960621 1.020000e-10 78.7
30 TraesCS3D01G243900 chr4B 88.205 195 16 4 2562 2755 427717956 427718144 3.430000e-55 226.0
31 TraesCS3D01G243900 chr6B 85.185 189 27 1 2568 2755 689401380 689401192 3.480000e-45 193.0
32 TraesCS3D01G243900 chr6B 84.772 197 22 4 2561 2755 583682493 583682683 1.250000e-44 191.0
33 TraesCS3D01G243900 chr5A 81.452 124 10 10 2356 2479 450883874 450883764 4.700000e-14 89.8
34 TraesCS3D01G243900 chr5A 82.278 79 10 2 2400 2478 29779700 29779626 7.920000e-07 65.8
35 TraesCS3D01G243900 chr1A 86.250 80 9 1 2400 2479 566595932 566595855 6.080000e-13 86.1
36 TraesCS3D01G243900 chr5B 84.706 85 11 1 2395 2479 284002419 284002501 2.190000e-12 84.2
37 TraesCS3D01G243900 chr5B 89.062 64 7 0 2416 2479 411094461 411094398 2.830000e-11 80.5
38 TraesCS3D01G243900 chr7B 77.863 131 27 2 2351 2479 593072034 593072164 2.830000e-11 80.5
39 TraesCS3D01G243900 chr1B 86.154 65 8 1 2416 2479 45818444 45818508 6.120000e-08 69.4


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 TraesCS3D01G243900 chr3D 339250932 339254349 3417 True 6312.0 6312 100.0000 1 3418 1 chr3D.!!$R3 3417
1 TraesCS3D01G243900 chr3D 36172530 36173362 832 True 1070.0 1070 89.7790 2565 3418 1 chr3D.!!$R1 853
2 TraesCS3D01G243900 chr3D 107064027 107064573 546 False 701.0 701 90.1640 2567 3101 1 chr3D.!!$F1 534
3 TraesCS3D01G243900 chr3B 437803549 437805803 2254 True 3251.0 3251 92.9200 332 2568 1 chr3B.!!$R1 2236
4 TraesCS3D01G243900 chr3A 465542080 465544456 2376 False 1668.5 2734 92.9405 266 2569 2 chr3A.!!$F2 2303
5 TraesCS3D01G243900 chr5D 124348695 124349542 847 True 1417.0 1417 96.8200 2570 3418 1 chr5D.!!$R1 848
6 TraesCS3D01G243900 chr4D 323758490 323759332 842 False 1214.0 1214 92.6890 2575 3418 1 chr4D.!!$F1 843
7 TraesCS3D01G243900 chr2D 2910634 2911475 841 False 1175.0 1175 91.8820 2575 3418 1 chr2D.!!$F1 843
8 TraesCS3D01G243900 chr2D 643440286 643441106 820 True 1038.0 1038 89.3990 2575 3418 1 chr2D.!!$R1 843
9 TraesCS3D01G243900 chr1D 200462694 200463514 820 False 1050.0 1050 89.6350 2575 3418 1 chr1D.!!$F1 843
10 TraesCS3D01G243900 chr7D 614073244 614073960 716 True 668.5 699 95.6765 2567 3418 2 chr7D.!!$R3 851
11 TraesCS3D01G243900 chr7D 89868844 89869633 789 False 614.5 658 89.5580 2561 3418 2 chr7D.!!$F1 857

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
762 812 0.452784 CGCAAGCGCAGTAAGGAAAC 60.453 55.0 11.47 0.0 38.40 2.78 F
2229 2304 0.179124 TTTGGCGCAACACCTGTTTC 60.179 50.0 10.83 0.0 35.83 2.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2346 2451 1.339929 GCACCCGGAGTTGAAAAACAT 59.660 47.619 0.73 0.0 0.0 2.71 R
3353 3644 0.328258 CCCGTTTCCTCTCCCACAAT 59.672 55.000 0.00 0.0 0.0 2.71 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
27 28 9.045223 GGGAAATCCAAATCAAATACTAAATGC 57.955 33.333 1.22 0.00 37.91 3.56
28 29 9.598517 GGAAATCCAAATCAAATACTAAATGCA 57.401 29.630 0.00 0.00 35.64 3.96
30 31 8.652810 AATCCAAATCAAATACTAAATGCAGC 57.347 30.769 0.00 0.00 0.00 5.25
31 32 7.408756 TCCAAATCAAATACTAAATGCAGCT 57.591 32.000 0.00 0.00 0.00 4.24
32 33 8.518430 TCCAAATCAAATACTAAATGCAGCTA 57.482 30.769 0.00 0.00 0.00 3.32
33 34 9.135189 TCCAAATCAAATACTAAATGCAGCTAT 57.865 29.630 0.00 0.00 0.00 2.97
34 35 9.188588 CCAAATCAAATACTAAATGCAGCTATG 57.811 33.333 0.00 0.00 0.00 2.23
35 36 9.740239 CAAATCAAATACTAAATGCAGCTATGT 57.260 29.630 0.00 0.00 0.00 2.29
38 39 9.784531 ATCAAATACTAAATGCAGCTATGTAGT 57.215 29.630 4.98 4.98 35.70 2.73
39 40 9.613428 TCAAATACTAAATGCAGCTATGTAGTT 57.387 29.630 4.92 0.00 33.98 2.24
42 43 9.838339 AATACTAAATGCAGCTATGTAGTTTCT 57.162 29.630 4.92 0.00 33.98 2.52
43 44 7.545362 ACTAAATGCAGCTATGTAGTTTCTG 57.455 36.000 0.00 0.00 28.80 3.02
44 45 5.824904 AAATGCAGCTATGTAGTTTCTGG 57.175 39.130 0.00 0.00 0.00 3.86
45 46 3.981071 TGCAGCTATGTAGTTTCTGGT 57.019 42.857 0.00 0.00 0.00 4.00
46 47 4.286297 TGCAGCTATGTAGTTTCTGGTT 57.714 40.909 0.00 0.00 0.00 3.67
47 48 4.651778 TGCAGCTATGTAGTTTCTGGTTT 58.348 39.130 0.00 0.00 0.00 3.27
48 49 5.070001 TGCAGCTATGTAGTTTCTGGTTTT 58.930 37.500 0.00 0.00 0.00 2.43
49 50 5.534654 TGCAGCTATGTAGTTTCTGGTTTTT 59.465 36.000 0.00 0.00 0.00 1.94
50 51 6.086871 GCAGCTATGTAGTTTCTGGTTTTTC 58.913 40.000 0.00 0.00 0.00 2.29
51 52 6.293955 GCAGCTATGTAGTTTCTGGTTTTTCA 60.294 38.462 0.00 0.00 0.00 2.69
52 53 7.648142 CAGCTATGTAGTTTCTGGTTTTTCAA 58.352 34.615 0.00 0.00 0.00 2.69
53 54 8.299570 CAGCTATGTAGTTTCTGGTTTTTCAAT 58.700 33.333 0.00 0.00 0.00 2.57
54 55 9.515226 AGCTATGTAGTTTCTGGTTTTTCAATA 57.485 29.630 0.00 0.00 0.00 1.90
55 56 9.774742 GCTATGTAGTTTCTGGTTTTTCAATAG 57.225 33.333 0.00 0.00 0.00 1.73
58 59 8.740123 TGTAGTTTCTGGTTTTTCAATAGTGA 57.260 30.769 0.00 0.00 0.00 3.41
59 60 9.179909 TGTAGTTTCTGGTTTTTCAATAGTGAA 57.820 29.630 0.56 0.56 42.12 3.18
71 72 6.494893 TTCAATAGTGAAATTTCCCGAGTG 57.505 37.500 15.48 9.89 40.87 3.51
72 73 5.800296 TCAATAGTGAAATTTCCCGAGTGA 58.200 37.500 15.48 11.98 0.00 3.41
73 74 6.234920 TCAATAGTGAAATTTCCCGAGTGAA 58.765 36.000 15.48 0.00 0.00 3.18
74 75 6.712998 TCAATAGTGAAATTTCCCGAGTGAAA 59.287 34.615 15.48 0.00 38.51 2.69
75 76 6.743575 ATAGTGAAATTTCCCGAGTGAAAG 57.256 37.500 15.48 0.00 37.63 2.62
76 77 4.714632 AGTGAAATTTCCCGAGTGAAAGA 58.285 39.130 15.48 0.00 37.63 2.52
77 78 5.130350 AGTGAAATTTCCCGAGTGAAAGAA 58.870 37.500 15.48 0.00 37.63 2.52
78 79 5.239525 AGTGAAATTTCCCGAGTGAAAGAAG 59.760 40.000 15.48 0.00 37.63 2.85
79 80 4.518970 TGAAATTTCCCGAGTGAAAGAAGG 59.481 41.667 15.48 0.00 37.63 3.46
80 81 4.367039 AATTTCCCGAGTGAAAGAAGGA 57.633 40.909 0.00 0.00 37.63 3.36
81 82 4.576330 ATTTCCCGAGTGAAAGAAGGAT 57.424 40.909 0.00 0.00 37.63 3.24
82 83 4.367039 TTTCCCGAGTGAAAGAAGGATT 57.633 40.909 0.00 0.00 30.97 3.01
83 84 4.367039 TTCCCGAGTGAAAGAAGGATTT 57.633 40.909 0.00 0.00 0.00 2.17
84 85 4.367039 TCCCGAGTGAAAGAAGGATTTT 57.633 40.909 0.00 0.00 0.00 1.82
85 86 4.725490 TCCCGAGTGAAAGAAGGATTTTT 58.275 39.130 0.00 0.00 0.00 1.94
86 87 5.871834 TCCCGAGTGAAAGAAGGATTTTTA 58.128 37.500 0.00 0.00 0.00 1.52
87 88 5.704053 TCCCGAGTGAAAGAAGGATTTTTAC 59.296 40.000 0.00 0.00 0.00 2.01
88 89 5.472137 CCCGAGTGAAAGAAGGATTTTTACA 59.528 40.000 0.00 0.00 0.00 2.41
89 90 6.151144 CCCGAGTGAAAGAAGGATTTTTACAT 59.849 38.462 0.00 0.00 0.00 2.29
90 91 7.309194 CCCGAGTGAAAGAAGGATTTTTACATT 60.309 37.037 0.00 0.00 0.00 2.71
91 92 7.538678 CCGAGTGAAAGAAGGATTTTTACATTG 59.461 37.037 0.00 0.00 0.00 2.82
92 93 8.289618 CGAGTGAAAGAAGGATTTTTACATTGA 58.710 33.333 0.00 0.00 0.00 2.57
103 104 9.855021 AGGATTTTTACATTGATTTTAGTTCGG 57.145 29.630 0.00 0.00 0.00 4.30
104 105 8.592155 GGATTTTTACATTGATTTTAGTTCGGC 58.408 33.333 0.00 0.00 0.00 5.54
105 106 9.134734 GATTTTTACATTGATTTTAGTTCGGCA 57.865 29.630 0.00 0.00 0.00 5.69
106 107 8.514136 TTTTTACATTGATTTTAGTTCGGCAG 57.486 30.769 0.00 0.00 0.00 4.85
107 108 4.096732 ACATTGATTTTAGTTCGGCAGC 57.903 40.909 0.00 0.00 0.00 5.25
108 109 3.758554 ACATTGATTTTAGTTCGGCAGCT 59.241 39.130 0.00 0.00 0.00 4.24
109 110 4.941263 ACATTGATTTTAGTTCGGCAGCTA 59.059 37.500 0.00 0.00 0.00 3.32
110 111 4.939509 TTGATTTTAGTTCGGCAGCTAC 57.060 40.909 0.00 0.00 0.00 3.58
111 112 4.202245 TGATTTTAGTTCGGCAGCTACT 57.798 40.909 0.00 0.00 0.00 2.57
112 113 4.575885 TGATTTTAGTTCGGCAGCTACTT 58.424 39.130 0.00 0.00 0.00 2.24
113 114 5.726397 TGATTTTAGTTCGGCAGCTACTTA 58.274 37.500 0.00 0.00 0.00 2.24
114 115 6.167685 TGATTTTAGTTCGGCAGCTACTTAA 58.832 36.000 0.00 0.00 0.00 1.85
115 116 6.821665 TGATTTTAGTTCGGCAGCTACTTAAT 59.178 34.615 0.00 0.00 0.00 1.40
116 117 6.417191 TTTTAGTTCGGCAGCTACTTAATG 57.583 37.500 0.00 0.00 0.00 1.90
117 118 3.887621 AGTTCGGCAGCTACTTAATGA 57.112 42.857 0.00 0.00 0.00 2.57
118 119 4.408182 AGTTCGGCAGCTACTTAATGAT 57.592 40.909 0.00 0.00 0.00 2.45
119 120 5.531122 AGTTCGGCAGCTACTTAATGATA 57.469 39.130 0.00 0.00 0.00 2.15
120 121 5.533482 AGTTCGGCAGCTACTTAATGATAG 58.467 41.667 0.00 0.00 0.00 2.08
121 122 4.521130 TCGGCAGCTACTTAATGATAGG 57.479 45.455 0.00 0.00 0.00 2.57
122 123 2.996621 CGGCAGCTACTTAATGATAGGC 59.003 50.000 0.00 0.00 0.00 3.93
123 124 3.306364 CGGCAGCTACTTAATGATAGGCT 60.306 47.826 0.00 0.00 0.00 4.58
124 125 4.646572 GGCAGCTACTTAATGATAGGCTT 58.353 43.478 0.00 0.00 0.00 4.35
125 126 5.066593 GGCAGCTACTTAATGATAGGCTTT 58.933 41.667 0.00 0.00 0.00 3.51
126 127 5.532779 GGCAGCTACTTAATGATAGGCTTTT 59.467 40.000 0.00 0.00 0.00 2.27
127 128 6.710744 GGCAGCTACTTAATGATAGGCTTTTA 59.289 38.462 0.00 0.00 0.00 1.52
128 129 7.228706 GGCAGCTACTTAATGATAGGCTTTTAA 59.771 37.037 0.00 0.00 0.00 1.52
129 130 8.621286 GCAGCTACTTAATGATAGGCTTTTAAA 58.379 33.333 0.00 0.00 0.00 1.52
154 155 8.776376 AAAAATCGAACCAAATTCATATTGCT 57.224 26.923 0.00 0.00 37.12 3.91
155 156 7.760131 AAATCGAACCAAATTCATATTGCTG 57.240 32.000 0.00 0.00 37.12 4.41
156 157 4.671377 TCGAACCAAATTCATATTGCTGC 58.329 39.130 0.00 0.00 37.12 5.25
157 158 4.398988 TCGAACCAAATTCATATTGCTGCT 59.601 37.500 0.00 0.00 37.12 4.24
158 159 4.736793 CGAACCAAATTCATATTGCTGCTC 59.263 41.667 0.00 0.00 37.12 4.26
159 160 4.297299 ACCAAATTCATATTGCTGCTCG 57.703 40.909 0.00 0.00 0.00 5.03
160 161 3.947196 ACCAAATTCATATTGCTGCTCGA 59.053 39.130 0.00 0.00 0.00 4.04
161 162 4.201950 ACCAAATTCATATTGCTGCTCGAC 60.202 41.667 0.00 0.00 0.00 4.20
162 163 4.036027 CCAAATTCATATTGCTGCTCGACT 59.964 41.667 0.00 0.00 0.00 4.18
163 164 5.237127 CCAAATTCATATTGCTGCTCGACTA 59.763 40.000 0.00 0.00 0.00 2.59
164 165 6.238456 CCAAATTCATATTGCTGCTCGACTAA 60.238 38.462 0.00 0.00 0.00 2.24
165 166 5.914085 ATTCATATTGCTGCTCGACTAAC 57.086 39.130 0.00 0.00 0.00 2.34
166 167 4.385358 TCATATTGCTGCTCGACTAACA 57.615 40.909 0.00 0.00 0.00 2.41
167 168 4.363138 TCATATTGCTGCTCGACTAACAG 58.637 43.478 0.00 0.00 34.48 3.16
168 169 2.751166 ATTGCTGCTCGACTAACAGT 57.249 45.000 0.00 0.00 33.87 3.55
169 170 2.526304 TTGCTGCTCGACTAACAGTT 57.474 45.000 0.00 0.00 33.87 3.16
170 171 1.783284 TGCTGCTCGACTAACAGTTG 58.217 50.000 0.00 0.00 33.87 3.16
171 172 1.068588 TGCTGCTCGACTAACAGTTGT 59.931 47.619 0.00 0.00 33.87 3.32
172 173 2.295070 TGCTGCTCGACTAACAGTTGTA 59.705 45.455 0.00 0.00 33.87 2.41
173 174 2.662156 GCTGCTCGACTAACAGTTGTAC 59.338 50.000 0.00 0.00 33.87 2.90
174 175 3.855895 GCTGCTCGACTAACAGTTGTACA 60.856 47.826 0.00 0.00 33.87 2.90
175 176 4.295870 CTGCTCGACTAACAGTTGTACAA 58.704 43.478 3.59 3.59 31.48 2.41
176 177 4.684877 TGCTCGACTAACAGTTGTACAAA 58.315 39.130 10.51 0.00 31.48 2.83
177 178 4.505191 TGCTCGACTAACAGTTGTACAAAC 59.495 41.667 10.51 5.04 31.48 2.93
178 179 4.374707 GCTCGACTAACAGTTGTACAAACG 60.375 45.833 10.51 6.91 31.48 3.60
179 180 4.671377 TCGACTAACAGTTGTACAAACGT 58.329 39.130 10.51 7.59 31.48 3.99
180 181 5.101628 TCGACTAACAGTTGTACAAACGTT 58.898 37.500 21.15 21.15 31.48 3.99
181 182 5.229887 TCGACTAACAGTTGTACAAACGTTC 59.770 40.000 21.06 10.94 31.48 3.95
182 183 5.004630 CGACTAACAGTTGTACAAACGTTCA 59.995 40.000 21.06 11.08 0.00 3.18
183 184 6.291955 CGACTAACAGTTGTACAAACGTTCAT 60.292 38.462 21.06 13.59 0.00 2.57
184 185 6.711579 ACTAACAGTTGTACAAACGTTCATG 58.288 36.000 21.06 16.05 0.00 3.07
185 186 3.947626 ACAGTTGTACAAACGTTCATGC 58.052 40.909 10.51 0.00 0.00 4.06
186 187 3.375610 ACAGTTGTACAAACGTTCATGCA 59.624 39.130 10.51 0.00 0.00 3.96
187 188 3.723764 CAGTTGTACAAACGTTCATGCAC 59.276 43.478 10.51 0.00 0.00 4.57
188 189 3.375610 AGTTGTACAAACGTTCATGCACA 59.624 39.130 10.51 1.16 0.00 4.57
189 190 4.036262 AGTTGTACAAACGTTCATGCACAT 59.964 37.500 10.51 0.00 0.00 3.21
190 191 5.237561 AGTTGTACAAACGTTCATGCACATA 59.762 36.000 10.51 0.00 0.00 2.29
191 192 5.871465 TGTACAAACGTTCATGCACATAT 57.129 34.783 0.00 0.00 0.00 1.78
192 193 6.247727 TGTACAAACGTTCATGCACATATT 57.752 33.333 0.00 0.00 0.00 1.28
193 194 6.673106 TGTACAAACGTTCATGCACATATTT 58.327 32.000 0.00 0.00 0.00 1.40
194 195 7.807680 TGTACAAACGTTCATGCACATATTTA 58.192 30.769 0.00 0.00 0.00 1.40
195 196 7.960195 TGTACAAACGTTCATGCACATATTTAG 59.040 33.333 0.00 0.00 0.00 1.85
196 197 5.799936 ACAAACGTTCATGCACATATTTAGC 59.200 36.000 0.00 0.00 0.00 3.09
197 198 5.818136 AACGTTCATGCACATATTTAGCT 57.182 34.783 0.00 0.00 0.00 3.32
198 199 6.918892 AACGTTCATGCACATATTTAGCTA 57.081 33.333 0.00 0.00 0.00 3.32
199 200 6.530913 ACGTTCATGCACATATTTAGCTAG 57.469 37.500 0.00 0.00 0.00 3.42
200 201 6.049149 ACGTTCATGCACATATTTAGCTAGT 58.951 36.000 0.00 0.00 0.00 2.57
201 202 6.201044 ACGTTCATGCACATATTTAGCTAGTC 59.799 38.462 0.00 0.00 0.00 2.59
202 203 6.584954 GTTCATGCACATATTTAGCTAGTCG 58.415 40.000 0.00 0.00 0.00 4.18
203 204 4.686091 TCATGCACATATTTAGCTAGTCGC 59.314 41.667 0.00 0.00 39.57 5.19
215 216 1.912110 GCTAGTCGCTACACAGAAACG 59.088 52.381 0.00 0.00 35.14 3.60
216 217 2.413765 GCTAGTCGCTACACAGAAACGA 60.414 50.000 0.00 0.00 35.14 3.85
217 218 3.731264 GCTAGTCGCTACACAGAAACGAT 60.731 47.826 0.00 0.00 34.96 3.73
218 219 4.495349 GCTAGTCGCTACACAGAAACGATA 60.495 45.833 0.00 0.00 34.96 2.92
219 220 4.430137 AGTCGCTACACAGAAACGATAA 57.570 40.909 0.00 0.00 34.96 1.75
220 221 4.801891 AGTCGCTACACAGAAACGATAAA 58.198 39.130 0.00 0.00 34.96 1.40
221 222 4.857588 AGTCGCTACACAGAAACGATAAAG 59.142 41.667 0.00 0.00 34.96 1.85
222 223 4.031426 GTCGCTACACAGAAACGATAAAGG 59.969 45.833 0.00 0.00 34.96 3.11
223 224 4.082625 TCGCTACACAGAAACGATAAAGGA 60.083 41.667 0.00 0.00 0.00 3.36
224 225 4.624024 CGCTACACAGAAACGATAAAGGAA 59.376 41.667 0.00 0.00 0.00 3.36
225 226 5.291128 CGCTACACAGAAACGATAAAGGAAT 59.709 40.000 0.00 0.00 0.00 3.01
226 227 6.474427 CGCTACACAGAAACGATAAAGGAATA 59.526 38.462 0.00 0.00 0.00 1.75
227 228 7.306051 CGCTACACAGAAACGATAAAGGAATAG 60.306 40.741 0.00 0.00 0.00 1.73
228 229 7.491696 GCTACACAGAAACGATAAAGGAATAGT 59.508 37.037 0.00 0.00 0.00 2.12
229 230 9.367444 CTACACAGAAACGATAAAGGAATAGTT 57.633 33.333 0.00 0.00 0.00 2.24
230 231 8.029642 ACACAGAAACGATAAAGGAATAGTTG 57.970 34.615 0.00 0.00 0.00 3.16
231 232 7.876068 ACACAGAAACGATAAAGGAATAGTTGA 59.124 33.333 0.00 0.00 0.00 3.18
232 233 8.883731 CACAGAAACGATAAAGGAATAGTTGAT 58.116 33.333 0.00 0.00 0.00 2.57
233 234 9.099454 ACAGAAACGATAAAGGAATAGTTGATC 57.901 33.333 0.00 0.00 0.00 2.92
234 235 8.552034 CAGAAACGATAAAGGAATAGTTGATCC 58.448 37.037 0.00 0.00 35.88 3.36
236 237 8.438676 AAACGATAAAGGAATAGTTGATCCTG 57.561 34.615 0.00 0.00 45.33 3.86
237 238 5.992217 ACGATAAAGGAATAGTTGATCCTGC 59.008 40.000 0.00 0.00 45.33 4.85
238 239 5.991606 CGATAAAGGAATAGTTGATCCTGCA 59.008 40.000 0.00 0.00 45.33 4.41
239 240 6.483307 CGATAAAGGAATAGTTGATCCTGCAA 59.517 38.462 0.00 0.00 45.33 4.08
240 241 7.012327 CGATAAAGGAATAGTTGATCCTGCAAA 59.988 37.037 0.00 0.00 45.33 3.68
241 242 6.916360 AAAGGAATAGTTGATCCTGCAAAA 57.084 33.333 0.00 0.00 45.33 2.44
242 243 7.486407 AAAGGAATAGTTGATCCTGCAAAAT 57.514 32.000 0.00 0.00 45.33 1.82
243 244 8.593945 AAAGGAATAGTTGATCCTGCAAAATA 57.406 30.769 0.00 0.00 45.33 1.40
244 245 7.573968 AGGAATAGTTGATCCTGCAAAATAC 57.426 36.000 0.00 0.00 44.38 1.89
245 246 7.118723 AGGAATAGTTGATCCTGCAAAATACA 58.881 34.615 0.00 0.00 44.38 2.29
246 247 7.781693 AGGAATAGTTGATCCTGCAAAATACAT 59.218 33.333 0.00 0.00 44.38 2.29
247 248 7.864379 GGAATAGTTGATCCTGCAAAATACATG 59.136 37.037 0.00 0.00 32.75 3.21
248 249 7.886629 ATAGTTGATCCTGCAAAATACATGT 57.113 32.000 2.69 2.69 0.00 3.21
249 250 8.978874 ATAGTTGATCCTGCAAAATACATGTA 57.021 30.769 8.27 8.27 0.00 2.29
250 251 7.886629 AGTTGATCCTGCAAAATACATGTAT 57.113 32.000 12.75 12.75 0.00 2.29
251 252 8.297470 AGTTGATCCTGCAAAATACATGTATT 57.703 30.769 22.70 22.70 37.36 1.89
252 253 8.752187 AGTTGATCCTGCAAAATACATGTATTT 58.248 29.630 29.81 29.81 44.89 1.40
318 319 5.939883 TGAAGGAATTGTTGATCCTGTACAG 59.060 40.000 16.34 16.34 45.33 2.74
334 335 6.069331 CCTGTACAGTATAGTAGTCATGGGT 58.931 44.000 21.18 0.00 0.00 4.51
458 459 2.547211 GTGAGCTGGATTTGATCATCGG 59.453 50.000 0.00 0.00 32.37 4.18
475 476 5.242434 TCATCGGCGGTTTGCTTATAATAT 58.758 37.500 7.21 0.00 45.43 1.28
476 477 6.399743 TCATCGGCGGTTTGCTTATAATATA 58.600 36.000 7.21 0.00 45.43 0.86
621 624 7.361457 AGAATGATAGTATTTGTCTTCCGGA 57.639 36.000 0.00 0.00 0.00 5.14
677 711 8.419076 AGTATTGTGTTGATTTTGGTTGTTTC 57.581 30.769 0.00 0.00 0.00 2.78
724 765 2.228343 GGCCGTCGCTAGTTGAGTATAT 59.772 50.000 0.00 0.00 34.44 0.86
730 771 3.895656 TCGCTAGTTGAGTATATTGGGCT 59.104 43.478 0.00 0.00 0.00 5.19
750 796 2.823196 TTCCATATTGTTCGCAAGCG 57.177 45.000 8.36 8.36 40.85 4.68
762 812 0.452784 CGCAAGCGCAGTAAGGAAAC 60.453 55.000 11.47 0.00 38.40 2.78
798 848 1.230635 GCGTGCTGTTGACATGGACT 61.231 55.000 0.00 0.00 0.00 3.85
846 908 2.035783 GGAAGGACCTTGTGGGGC 59.964 66.667 12.68 0.00 44.23 5.80
855 920 2.204291 TTGTGGGGCCTGGGATCT 60.204 61.111 0.84 0.00 0.00 2.75
856 921 1.856873 TTGTGGGGCCTGGGATCTT 60.857 57.895 0.84 0.00 0.00 2.40
993 1059 4.849329 GGCGAGCGATCGTCCGTT 62.849 66.667 25.15 5.76 35.26 4.44
1421 1493 4.980805 GTCTCGGCGCACCACCAA 62.981 66.667 10.83 0.00 34.57 3.67
1595 1667 1.600413 GCCGCCAAGAACAACAAGAAG 60.600 52.381 0.00 0.00 0.00 2.85
1945 2017 4.760047 CAGCCCCGTCGTTCCCAG 62.760 72.222 0.00 0.00 0.00 4.45
2054 2126 2.580962 CTGGAGGAGATGAGATCGTCA 58.419 52.381 4.93 0.00 40.38 4.35
2091 2166 7.603963 GAGTAGATCGATTGATGACTAGCTA 57.396 40.000 0.00 0.00 34.09 3.32
2125 2200 4.468095 TTTCGCTTACTCTTTGACTTGC 57.532 40.909 0.00 0.00 0.00 4.01
2149 2224 4.567747 GGTGGATGTCCTTGTTATTGTCCT 60.568 45.833 0.09 0.00 36.82 3.85
2150 2225 5.338871 GGTGGATGTCCTTGTTATTGTCCTA 60.339 44.000 0.09 0.00 36.82 2.94
2151 2226 6.357367 GTGGATGTCCTTGTTATTGTCCTAT 58.643 40.000 0.09 0.00 36.82 2.57
2152 2227 7.419750 GGTGGATGTCCTTGTTATTGTCCTATA 60.420 40.741 0.09 0.00 36.82 1.31
2153 2228 7.657761 GTGGATGTCCTTGTTATTGTCCTATAG 59.342 40.741 0.09 0.00 36.82 1.31
2181 2256 6.432607 TCAGTTGACGTATACTTAGAGTGG 57.567 41.667 0.56 0.00 0.00 4.00
2229 2304 0.179124 TTTGGCGCAACACCTGTTTC 60.179 50.000 10.83 0.00 35.83 2.78
2276 2352 9.779237 CGTTATATCTTGCATTTTAAGTACGAG 57.221 33.333 0.00 0.00 0.00 4.18
2320 2397 4.379339 TTTCTCCAAACAAACTTTCCCG 57.621 40.909 0.00 0.00 0.00 5.14
2322 2399 1.681264 CTCCAAACAAACTTTCCCGCT 59.319 47.619 0.00 0.00 0.00 5.52
2323 2400 2.100749 CTCCAAACAAACTTTCCCGCTT 59.899 45.455 0.00 0.00 0.00 4.68
2324 2401 2.498078 TCCAAACAAACTTTCCCGCTTT 59.502 40.909 0.00 0.00 0.00 3.51
2346 2451 8.784043 GCTTTATAAGAGGTGTTCAAAGAAGAA 58.216 33.333 0.00 0.00 0.00 2.52
2366 2473 0.741915 TGTTTTTCAACTCCGGGTGC 59.258 50.000 0.00 0.00 33.58 5.01
2464 2572 1.953686 TGCTCAAACTTTGTAGGTGCC 59.046 47.619 1.44 0.00 0.00 5.01
2479 2587 1.134907 GGTGCCTGCAAGATTTCATGG 60.135 52.381 0.00 0.00 34.07 3.66
2489 2597 5.179742 TGCAAGATTTCATGGCAAATTTCAC 59.820 36.000 0.00 0.00 0.00 3.18
2490 2598 5.179742 GCAAGATTTCATGGCAAATTTCACA 59.820 36.000 0.00 0.00 0.00 3.58
2491 2599 6.595794 CAAGATTTCATGGCAAATTTCACAC 58.404 36.000 0.00 0.00 0.00 3.82
2492 2600 5.856156 AGATTTCATGGCAAATTTCACACA 58.144 33.333 0.00 0.00 0.00 3.72
2493 2601 5.697633 AGATTTCATGGCAAATTTCACACAC 59.302 36.000 0.00 0.00 0.00 3.82
2494 2602 4.397481 TTCATGGCAAATTTCACACACA 57.603 36.364 0.00 0.00 0.00 3.72
2584 2692 4.618920 AAGTTTGGGTCTCGATAACTGT 57.381 40.909 0.00 0.00 0.00 3.55
2866 2977 4.174009 CCTCTTCCATGTACGTGTAACTG 58.826 47.826 13.91 0.00 31.75 3.16
2932 3043 0.110056 GTTGCCATGTCGCTGAACTG 60.110 55.000 0.00 0.00 0.00 3.16
2935 3046 1.855213 GCCATGTCGCTGAACTGCAA 61.855 55.000 4.76 0.00 0.00 4.08
2946 3192 1.962100 TGAACTGCAATTGCCATGTCA 59.038 42.857 26.94 20.15 41.18 3.58
2948 3194 1.624336 ACTGCAATTGCCATGTCAGT 58.376 45.000 26.94 18.77 41.18 3.41
2954 3200 3.571571 CAATTGCCATGTCAGTCAACTG 58.428 45.455 3.69 3.69 45.08 3.16
3002 3292 1.855213 TTGCCATGTCGCTGAACTGC 61.855 55.000 0.00 0.00 0.00 4.40
3003 3293 2.327343 GCCATGTCGCTGAACTGCA 61.327 57.895 4.76 0.00 0.00 4.41
3005 3295 0.952497 CCATGTCGCTGAACTGCAGT 60.952 55.000 15.25 15.25 46.62 4.40
3006 3296 0.870393 CATGTCGCTGAACTGCAGTT 59.130 50.000 31.57 31.57 46.62 3.16
3007 3297 0.870393 ATGTCGCTGAACTGCAGTTG 59.130 50.000 35.67 22.76 46.62 3.16
3008 3298 1.082496 GTCGCTGAACTGCAGTTGC 60.082 57.895 35.67 29.39 46.62 4.17
3009 3299 2.253452 CGCTGAACTGCAGTTGCC 59.747 61.111 35.67 22.23 46.62 4.52
3045 3335 0.110056 GTTGCCATGTCGCTGAACTG 60.110 55.000 0.00 0.00 0.00 3.16
3046 3336 0.534877 TTGCCATGTCGCTGAACTGT 60.535 50.000 0.00 0.00 0.00 3.55
3058 3348 2.554032 GCTGAACTGTAGTTGCCATGTT 59.446 45.455 1.35 0.00 38.56 2.71
3062 3352 2.504367 ACTGTAGTTGCCATGTTGGAC 58.496 47.619 0.00 0.00 40.96 4.02
3286 3576 4.406003 GGGTAAAGAGAGAGTTGCCATCTA 59.594 45.833 0.00 0.00 31.65 1.98
3297 3587 4.848357 AGTTGCCATCTACTTACAAGCAT 58.152 39.130 0.00 0.00 0.00 3.79
3353 3644 4.081406 ACATGGCAACTGATAGCTTTTGA 58.919 39.130 0.00 0.00 37.61 2.69
3367 3659 3.157087 GCTTTTGATTGTGGGAGAGGAA 58.843 45.455 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.598517 TGCATTTAGTATTTGATTTGGATTTCC 57.401 29.630 0.00 0.00 0.00 3.13
7 8 7.408756 AGCTGCATTTAGTATTTGATTTGGA 57.591 32.000 1.02 0.00 0.00 3.53
8 9 9.188588 CATAGCTGCATTTAGTATTTGATTTGG 57.811 33.333 1.02 0.00 0.00 3.28
9 10 9.740239 ACATAGCTGCATTTAGTATTTGATTTG 57.260 29.630 1.02 0.00 0.00 2.32
13 14 9.613428 AACTACATAGCTGCATTTAGTATTTGA 57.387 29.630 1.02 0.00 0.00 2.69
16 17 9.838339 AGAAACTACATAGCTGCATTTAGTATT 57.162 29.630 1.02 4.71 0.00 1.89
17 18 9.265901 CAGAAACTACATAGCTGCATTTAGTAT 57.734 33.333 1.02 0.00 0.00 2.12
18 19 7.710907 CCAGAAACTACATAGCTGCATTTAGTA 59.289 37.037 1.02 0.00 0.00 1.82
19 20 6.540189 CCAGAAACTACATAGCTGCATTTAGT 59.460 38.462 1.02 4.08 0.00 2.24
20 21 6.540189 ACCAGAAACTACATAGCTGCATTTAG 59.460 38.462 1.02 3.49 0.00 1.85
21 22 6.414732 ACCAGAAACTACATAGCTGCATTTA 58.585 36.000 1.02 0.00 0.00 1.40
22 23 5.256474 ACCAGAAACTACATAGCTGCATTT 58.744 37.500 1.02 0.00 0.00 2.32
23 24 4.848357 ACCAGAAACTACATAGCTGCATT 58.152 39.130 1.02 0.00 0.00 3.56
24 25 4.494091 ACCAGAAACTACATAGCTGCAT 57.506 40.909 1.02 0.00 0.00 3.96
25 26 3.981071 ACCAGAAACTACATAGCTGCA 57.019 42.857 1.02 0.00 0.00 4.41
26 27 5.629079 AAAACCAGAAACTACATAGCTGC 57.371 39.130 0.00 0.00 0.00 5.25
27 28 7.202016 TGAAAAACCAGAAACTACATAGCTG 57.798 36.000 0.00 0.00 0.00 4.24
28 29 7.817418 TTGAAAAACCAGAAACTACATAGCT 57.183 32.000 0.00 0.00 0.00 3.32
29 30 9.774742 CTATTGAAAAACCAGAAACTACATAGC 57.225 33.333 0.00 0.00 0.00 2.97
32 33 9.349713 TCACTATTGAAAAACCAGAAACTACAT 57.650 29.630 0.00 0.00 0.00 2.29
33 34 8.740123 TCACTATTGAAAAACCAGAAACTACA 57.260 30.769 0.00 0.00 0.00 2.74
48 49 6.234920 TCACTCGGGAAATTTCACTATTGAA 58.765 36.000 18.03 0.94 40.14 2.69
49 50 5.800296 TCACTCGGGAAATTTCACTATTGA 58.200 37.500 18.03 13.62 0.00 2.57
50 51 6.494893 TTCACTCGGGAAATTTCACTATTG 57.505 37.500 18.03 11.62 0.00 1.90
51 52 6.940298 TCTTTCACTCGGGAAATTTCACTATT 59.060 34.615 18.03 0.00 36.29 1.73
52 53 6.472887 TCTTTCACTCGGGAAATTTCACTAT 58.527 36.000 18.03 0.81 36.29 2.12
53 54 5.860611 TCTTTCACTCGGGAAATTTCACTA 58.139 37.500 18.03 6.68 36.29 2.74
54 55 4.714632 TCTTTCACTCGGGAAATTTCACT 58.285 39.130 18.03 0.00 36.29 3.41
55 56 5.432885 TTCTTTCACTCGGGAAATTTCAC 57.567 39.130 19.49 15.33 36.29 3.18
56 57 4.518970 CCTTCTTTCACTCGGGAAATTTCA 59.481 41.667 19.49 0.00 36.29 2.69
57 58 4.760204 TCCTTCTTTCACTCGGGAAATTTC 59.240 41.667 9.83 9.83 36.29 2.17
58 59 4.725490 TCCTTCTTTCACTCGGGAAATTT 58.275 39.130 0.00 0.00 36.29 1.82
59 60 4.367039 TCCTTCTTTCACTCGGGAAATT 57.633 40.909 0.00 0.00 36.29 1.82
60 61 4.576330 ATCCTTCTTTCACTCGGGAAAT 57.424 40.909 0.00 0.00 36.29 2.17
61 62 4.367039 AATCCTTCTTTCACTCGGGAAA 57.633 40.909 0.00 0.00 35.59 3.13
62 63 4.367039 AAATCCTTCTTTCACTCGGGAA 57.633 40.909 0.00 0.00 0.00 3.97
63 64 4.367039 AAAATCCTTCTTTCACTCGGGA 57.633 40.909 0.00 0.00 0.00 5.14
64 65 5.472137 TGTAAAAATCCTTCTTTCACTCGGG 59.528 40.000 0.00 0.00 0.00 5.14
65 66 6.554334 TGTAAAAATCCTTCTTTCACTCGG 57.446 37.500 0.00 0.00 0.00 4.63
66 67 8.289618 TCAATGTAAAAATCCTTCTTTCACTCG 58.710 33.333 0.00 0.00 0.00 4.18
77 78 9.855021 CCGAACTAAAATCAATGTAAAAATCCT 57.145 29.630 0.00 0.00 0.00 3.24
78 79 8.592155 GCCGAACTAAAATCAATGTAAAAATCC 58.408 33.333 0.00 0.00 0.00 3.01
79 80 9.134734 TGCCGAACTAAAATCAATGTAAAAATC 57.865 29.630 0.00 0.00 0.00 2.17
80 81 9.139174 CTGCCGAACTAAAATCAATGTAAAAAT 57.861 29.630 0.00 0.00 0.00 1.82
81 82 7.115663 GCTGCCGAACTAAAATCAATGTAAAAA 59.884 33.333 0.00 0.00 0.00 1.94
82 83 6.584563 GCTGCCGAACTAAAATCAATGTAAAA 59.415 34.615 0.00 0.00 0.00 1.52
83 84 6.072175 AGCTGCCGAACTAAAATCAATGTAAA 60.072 34.615 0.00 0.00 0.00 2.01
84 85 5.414454 AGCTGCCGAACTAAAATCAATGTAA 59.586 36.000 0.00 0.00 0.00 2.41
85 86 4.941263 AGCTGCCGAACTAAAATCAATGTA 59.059 37.500 0.00 0.00 0.00 2.29
86 87 3.758554 AGCTGCCGAACTAAAATCAATGT 59.241 39.130 0.00 0.00 0.00 2.71
87 88 4.361451 AGCTGCCGAACTAAAATCAATG 57.639 40.909 0.00 0.00 0.00 2.82
88 89 5.186198 AGTAGCTGCCGAACTAAAATCAAT 58.814 37.500 0.00 0.00 0.00 2.57
89 90 4.575885 AGTAGCTGCCGAACTAAAATCAA 58.424 39.130 0.00 0.00 0.00 2.57
90 91 4.202245 AGTAGCTGCCGAACTAAAATCA 57.798 40.909 0.00 0.00 0.00 2.57
91 92 6.657836 TTAAGTAGCTGCCGAACTAAAATC 57.342 37.500 0.00 0.00 0.00 2.17
92 93 6.821665 TCATTAAGTAGCTGCCGAACTAAAAT 59.178 34.615 0.00 0.11 0.00 1.82
93 94 6.167685 TCATTAAGTAGCTGCCGAACTAAAA 58.832 36.000 0.00 0.00 0.00 1.52
94 95 5.726397 TCATTAAGTAGCTGCCGAACTAAA 58.274 37.500 0.00 0.00 0.00 1.85
95 96 5.333299 TCATTAAGTAGCTGCCGAACTAA 57.667 39.130 0.00 0.00 0.00 2.24
96 97 4.994907 TCATTAAGTAGCTGCCGAACTA 57.005 40.909 0.00 0.00 0.00 2.24
97 98 3.887621 TCATTAAGTAGCTGCCGAACT 57.112 42.857 0.00 0.00 0.00 3.01
98 99 4.686554 CCTATCATTAAGTAGCTGCCGAAC 59.313 45.833 0.00 0.00 0.00 3.95
99 100 4.799586 GCCTATCATTAAGTAGCTGCCGAA 60.800 45.833 0.00 0.00 0.00 4.30
100 101 3.306088 GCCTATCATTAAGTAGCTGCCGA 60.306 47.826 0.00 0.00 0.00 5.54
101 102 2.996621 GCCTATCATTAAGTAGCTGCCG 59.003 50.000 0.00 0.00 0.00 5.69
102 103 4.278975 AGCCTATCATTAAGTAGCTGCC 57.721 45.455 0.00 0.00 0.00 4.85
103 104 6.625873 AAAAGCCTATCATTAAGTAGCTGC 57.374 37.500 0.00 0.00 0.00 5.25
129 130 8.658609 CAGCAATATGAATTTGGTTCGATTTTT 58.341 29.630 0.00 0.00 39.80 1.94
130 131 7.201548 GCAGCAATATGAATTTGGTTCGATTTT 60.202 33.333 0.00 0.00 39.80 1.82
131 132 6.256321 GCAGCAATATGAATTTGGTTCGATTT 59.744 34.615 0.00 0.00 39.80 2.17
132 133 5.750067 GCAGCAATATGAATTTGGTTCGATT 59.250 36.000 0.00 0.00 39.80 3.34
133 134 5.068198 AGCAGCAATATGAATTTGGTTCGAT 59.932 36.000 0.00 0.00 39.80 3.59
134 135 4.398988 AGCAGCAATATGAATTTGGTTCGA 59.601 37.500 0.00 0.00 39.80 3.71
135 136 4.675510 AGCAGCAATATGAATTTGGTTCG 58.324 39.130 0.00 0.00 39.80 3.95
136 137 4.736793 CGAGCAGCAATATGAATTTGGTTC 59.263 41.667 0.00 0.00 32.81 3.62
137 138 4.398988 TCGAGCAGCAATATGAATTTGGTT 59.601 37.500 0.00 0.00 32.81 3.67
138 139 3.947196 TCGAGCAGCAATATGAATTTGGT 59.053 39.130 0.00 0.00 35.31 3.67
139 140 4.036027 AGTCGAGCAGCAATATGAATTTGG 59.964 41.667 0.00 0.00 0.00 3.28
140 141 5.165911 AGTCGAGCAGCAATATGAATTTG 57.834 39.130 0.00 0.00 0.00 2.32
141 142 6.316140 TGTTAGTCGAGCAGCAATATGAATTT 59.684 34.615 0.00 0.00 0.00 1.82
142 143 5.817296 TGTTAGTCGAGCAGCAATATGAATT 59.183 36.000 0.00 0.00 0.00 2.17
143 144 5.359756 TGTTAGTCGAGCAGCAATATGAAT 58.640 37.500 0.00 0.00 0.00 2.57
144 145 4.754322 TGTTAGTCGAGCAGCAATATGAA 58.246 39.130 0.00 0.00 0.00 2.57
145 146 4.142160 ACTGTTAGTCGAGCAGCAATATGA 60.142 41.667 0.00 0.00 33.87 2.15
146 147 4.115516 ACTGTTAGTCGAGCAGCAATATG 58.884 43.478 0.00 0.00 33.87 1.78
147 148 4.392921 ACTGTTAGTCGAGCAGCAATAT 57.607 40.909 0.00 0.00 33.87 1.28
148 149 3.868757 ACTGTTAGTCGAGCAGCAATA 57.131 42.857 0.00 0.00 33.87 1.90
149 150 2.738846 CAACTGTTAGTCGAGCAGCAAT 59.261 45.455 0.00 0.00 33.87 3.56
150 151 2.135139 CAACTGTTAGTCGAGCAGCAA 58.865 47.619 0.00 0.00 33.87 3.91
151 152 1.068588 ACAACTGTTAGTCGAGCAGCA 59.931 47.619 0.00 0.00 33.87 4.41
152 153 1.784525 ACAACTGTTAGTCGAGCAGC 58.215 50.000 0.00 0.00 33.87 5.25
153 154 3.897325 TGTACAACTGTTAGTCGAGCAG 58.103 45.455 0.00 0.00 36.41 4.24
154 155 3.994204 TGTACAACTGTTAGTCGAGCA 57.006 42.857 0.00 0.00 0.00 4.26
155 156 4.374707 CGTTTGTACAACTGTTAGTCGAGC 60.375 45.833 8.07 0.00 0.00 5.03
156 157 4.736793 ACGTTTGTACAACTGTTAGTCGAG 59.263 41.667 8.07 0.00 0.00 4.04
157 158 4.671377 ACGTTTGTACAACTGTTAGTCGA 58.329 39.130 8.07 0.00 0.00 4.20
158 159 5.004630 TGAACGTTTGTACAACTGTTAGTCG 59.995 40.000 19.27 11.68 0.00 4.18
159 160 6.335176 TGAACGTTTGTACAACTGTTAGTC 57.665 37.500 19.27 11.36 0.00 2.59
160 161 6.711579 CATGAACGTTTGTACAACTGTTAGT 58.288 36.000 19.27 11.34 0.00 2.24
161 162 5.619607 GCATGAACGTTTGTACAACTGTTAG 59.380 40.000 19.27 14.57 0.00 2.34
162 163 5.064834 TGCATGAACGTTTGTACAACTGTTA 59.935 36.000 19.27 11.40 0.00 2.41
163 164 4.142578 TGCATGAACGTTTGTACAACTGTT 60.143 37.500 19.31 19.31 0.00 3.16
164 165 3.375610 TGCATGAACGTTTGTACAACTGT 59.624 39.130 8.07 6.94 0.00 3.55
165 166 3.723764 GTGCATGAACGTTTGTACAACTG 59.276 43.478 8.07 6.26 0.00 3.16
166 167 3.375610 TGTGCATGAACGTTTGTACAACT 59.624 39.130 17.84 0.00 35.87 3.16
167 168 3.686128 TGTGCATGAACGTTTGTACAAC 58.314 40.909 17.84 7.46 35.87 3.32
168 169 4.560136 ATGTGCATGAACGTTTGTACAA 57.440 36.364 22.06 3.59 40.88 2.41
169 170 5.871465 ATATGTGCATGAACGTTTGTACA 57.129 34.783 20.98 20.98 41.56 2.90
170 171 7.044966 GCTAAATATGTGCATGAACGTTTGTAC 60.045 37.037 3.21 12.55 0.00 2.90
171 172 6.964370 GCTAAATATGTGCATGAACGTTTGTA 59.036 34.615 3.21 0.00 0.00 2.41
172 173 5.799936 GCTAAATATGTGCATGAACGTTTGT 59.200 36.000 3.21 0.00 0.00 2.83
173 174 6.029607 AGCTAAATATGTGCATGAACGTTTG 58.970 36.000 3.21 0.00 0.00 2.93
174 175 6.194796 AGCTAAATATGTGCATGAACGTTT 57.805 33.333 3.21 5.49 0.00 3.60
175 176 5.818136 AGCTAAATATGTGCATGAACGTT 57.182 34.783 3.21 0.00 0.00 3.99
176 177 6.049149 ACTAGCTAAATATGTGCATGAACGT 58.951 36.000 3.46 3.46 0.00 3.99
177 178 6.530913 ACTAGCTAAATATGTGCATGAACG 57.469 37.500 0.00 0.00 0.00 3.95
178 179 6.584954 CGACTAGCTAAATATGTGCATGAAC 58.415 40.000 0.00 0.00 0.00 3.18
179 180 5.177511 GCGACTAGCTAAATATGTGCATGAA 59.822 40.000 0.00 0.00 44.04 2.57
180 181 4.686091 GCGACTAGCTAAATATGTGCATGA 59.314 41.667 0.00 0.00 44.04 3.07
181 182 4.950926 GCGACTAGCTAAATATGTGCATG 58.049 43.478 0.00 0.00 44.04 4.06
196 197 3.466712 TCGTTTCTGTGTAGCGACTAG 57.533 47.619 0.00 0.00 0.00 2.57
197 198 5.550232 TTATCGTTTCTGTGTAGCGACTA 57.450 39.130 0.00 0.00 34.36 2.59
198 199 4.430137 TTATCGTTTCTGTGTAGCGACT 57.570 40.909 0.00 0.00 34.36 4.18
199 200 4.031426 CCTTTATCGTTTCTGTGTAGCGAC 59.969 45.833 0.00 0.00 34.36 5.19
200 201 4.082625 TCCTTTATCGTTTCTGTGTAGCGA 60.083 41.667 0.00 0.00 36.02 4.93
201 202 4.171005 TCCTTTATCGTTTCTGTGTAGCG 58.829 43.478 0.00 0.00 0.00 4.26
202 203 6.663944 ATTCCTTTATCGTTTCTGTGTAGC 57.336 37.500 0.00 0.00 0.00 3.58
203 204 8.928270 ACTATTCCTTTATCGTTTCTGTGTAG 57.072 34.615 0.00 0.00 0.00 2.74
204 205 9.146984 CAACTATTCCTTTATCGTTTCTGTGTA 57.853 33.333 0.00 0.00 0.00 2.90
205 206 7.876068 TCAACTATTCCTTTATCGTTTCTGTGT 59.124 33.333 0.00 0.00 0.00 3.72
206 207 8.251750 TCAACTATTCCTTTATCGTTTCTGTG 57.748 34.615 0.00 0.00 0.00 3.66
207 208 9.099454 GATCAACTATTCCTTTATCGTTTCTGT 57.901 33.333 0.00 0.00 0.00 3.41
208 209 8.552034 GGATCAACTATTCCTTTATCGTTTCTG 58.448 37.037 0.00 0.00 0.00 3.02
209 210 8.487028 AGGATCAACTATTCCTTTATCGTTTCT 58.513 33.333 0.00 0.00 39.36 2.52
210 211 8.552034 CAGGATCAACTATTCCTTTATCGTTTC 58.448 37.037 0.00 0.00 40.44 2.78
211 212 7.012421 GCAGGATCAACTATTCCTTTATCGTTT 59.988 37.037 0.00 0.00 40.44 3.60
212 213 6.483640 GCAGGATCAACTATTCCTTTATCGTT 59.516 38.462 0.00 0.00 40.44 3.85
213 214 5.992217 GCAGGATCAACTATTCCTTTATCGT 59.008 40.000 0.00 0.00 40.44 3.73
214 215 5.991606 TGCAGGATCAACTATTCCTTTATCG 59.008 40.000 0.00 0.00 40.44 2.92
215 216 7.807977 TTGCAGGATCAACTATTCCTTTATC 57.192 36.000 0.00 0.00 40.44 1.75
216 217 8.593945 TTTTGCAGGATCAACTATTCCTTTAT 57.406 30.769 0.00 0.00 40.44 1.40
217 218 8.593945 ATTTTGCAGGATCAACTATTCCTTTA 57.406 30.769 0.00 0.00 40.44 1.85
218 219 6.916360 TTTTGCAGGATCAACTATTCCTTT 57.084 33.333 0.00 0.00 40.44 3.11
219 220 7.615365 TGTATTTTGCAGGATCAACTATTCCTT 59.385 33.333 0.00 0.00 40.44 3.36
220 221 7.118723 TGTATTTTGCAGGATCAACTATTCCT 58.881 34.615 0.00 0.00 43.24 3.36
221 222 7.333528 TGTATTTTGCAGGATCAACTATTCC 57.666 36.000 0.00 0.00 0.00 3.01
222 223 8.408601 ACATGTATTTTGCAGGATCAACTATTC 58.591 33.333 0.00 0.00 0.00 1.75
223 224 8.297470 ACATGTATTTTGCAGGATCAACTATT 57.703 30.769 0.00 0.00 0.00 1.73
224 225 7.886629 ACATGTATTTTGCAGGATCAACTAT 57.113 32.000 0.00 0.00 0.00 2.12
225 226 8.978874 ATACATGTATTTTGCAGGATCAACTA 57.021 30.769 12.75 0.00 0.00 2.24
226 227 7.886629 ATACATGTATTTTGCAGGATCAACT 57.113 32.000 12.75 0.00 0.00 3.16
227 228 8.931385 AAATACATGTATTTTGCAGGATCAAC 57.069 30.769 29.81 0.00 41.49 3.18
276 277 9.857656 ATTCCTTCATCATTTATGTGTAGTGAT 57.142 29.630 0.00 0.00 36.89 3.06
277 278 9.685276 AATTCCTTCATCATTTATGTGTAGTGA 57.315 29.630 0.00 0.00 36.89 3.41
290 291 6.192773 ACAGGATCAACAATTCCTTCATCAT 58.807 36.000 0.00 0.00 40.44 2.45
291 292 5.573219 ACAGGATCAACAATTCCTTCATCA 58.427 37.500 0.00 0.00 40.44 3.07
301 302 9.422681 ACTACTATACTGTACAGGATCAACAAT 57.577 33.333 24.16 1.88 33.19 2.71
318 319 6.281405 CAAGTTCCACCCATGACTACTATAC 58.719 44.000 0.00 0.00 0.00 1.47
334 335 4.974645 ATCACAGTAAGTCCAAGTTCCA 57.025 40.909 0.00 0.00 0.00 3.53
476 477 8.964533 AGTAGAGGGAGAATGAACATATGTAT 57.035 34.615 9.21 0.00 0.00 2.29
724 765 7.571511 CTTGCGAACAATATGGAAAGCCCAA 62.572 44.000 0.00 0.00 41.15 4.12
730 771 2.730715 GCGCTTGCGAACAATATGGAAA 60.731 45.455 19.55 0.00 34.61 3.13
750 796 4.035909 TCCGTTTTTCAGTTTCCTTACTGC 59.964 41.667 0.00 0.00 44.10 4.40
798 848 0.539518 TTTGGGCTACGCAGATGCTA 59.460 50.000 2.95 0.00 39.32 3.49
833 895 4.366684 CCAGGCCCCACAAGGTCC 62.367 72.222 0.00 0.00 28.80 4.46
834 896 4.366684 CCCAGGCCCCACAAGGTC 62.367 72.222 0.00 0.00 0.00 3.85
835 897 4.938756 TCCCAGGCCCCACAAGGT 62.939 66.667 0.00 0.00 0.00 3.50
836 898 3.350163 ATCCCAGGCCCCACAAGG 61.350 66.667 0.00 0.00 0.00 3.61
837 899 1.867595 AAGATCCCAGGCCCCACAAG 61.868 60.000 0.00 0.00 0.00 3.16
838 900 1.856873 AAGATCCCAGGCCCCACAA 60.857 57.895 0.00 0.00 0.00 3.33
839 901 2.204291 AAGATCCCAGGCCCCACA 60.204 61.111 0.00 0.00 0.00 4.17
840 902 2.276740 CAAGATCCCAGGCCCCAC 59.723 66.667 0.00 0.00 0.00 4.61
841 903 2.500381 TACCAAGATCCCAGGCCCCA 62.500 60.000 0.00 0.00 0.00 4.96
846 908 1.139853 GTCTGCTACCAAGATCCCAGG 59.860 57.143 0.00 0.00 0.00 4.45
855 920 1.335597 CGAGTTCGTGTCTGCTACCAA 60.336 52.381 0.00 0.00 34.11 3.67
856 921 0.240145 CGAGTTCGTGTCTGCTACCA 59.760 55.000 0.00 0.00 34.11 3.25
947 1012 0.822164 ACTGTGTATCCACCTACGGC 59.178 55.000 0.00 0.00 41.09 5.68
993 1059 2.046700 GCGGACGGGTTGGAATCA 60.047 61.111 0.00 0.00 0.00 2.57
1684 1756 2.029666 CCGGATGATCGTCCTGGC 59.970 66.667 27.55 5.73 36.07 4.85
1771 1843 2.711542 AGTCATTCGGATTCACAACCC 58.288 47.619 0.00 0.00 0.00 4.11
1779 1851 4.218417 CCACCAAAAGAAGTCATTCGGATT 59.782 41.667 0.00 0.00 40.58 3.01
1945 2017 3.365265 CCACGGGCTTGTCCTTGC 61.365 66.667 0.00 0.00 34.39 4.01
1947 2019 1.779061 ATGACCACGGGCTTGTCCTT 61.779 55.000 0.00 0.00 34.39 3.36
2054 2126 3.670895 CGATCTACTCGTGTTGCTTGACT 60.671 47.826 0.00 0.00 42.56 3.41
2091 2166 7.379750 AGAGTAAGCGAAAACATCTTTCTAGT 58.620 34.615 0.00 0.00 0.00 2.57
2125 2200 3.343617 ACAATAACAAGGACATCCACCG 58.656 45.455 0.00 0.00 38.89 4.94
2181 2256 4.560513 GCTTAGATACAGGGATCTGAGTGC 60.561 50.000 13.10 5.17 43.49 4.40
2305 2382 7.142680 TCTTATAAAGCGGGAAAGTTTGTTTG 58.857 34.615 0.00 0.00 0.00 2.93
2318 2395 5.642063 TCTTTGAACACCTCTTATAAAGCGG 59.358 40.000 0.00 0.00 39.31 5.52
2320 2397 8.324163 TCTTCTTTGAACACCTCTTATAAAGC 57.676 34.615 0.00 0.00 0.00 3.51
2323 2400 9.793259 ACATTCTTCTTTGAACACCTCTTATAA 57.207 29.630 0.00 0.00 0.00 0.98
2324 2401 9.793259 AACATTCTTCTTTGAACACCTCTTATA 57.207 29.630 0.00 0.00 0.00 0.98
2346 2451 1.339929 GCACCCGGAGTTGAAAAACAT 59.660 47.619 0.73 0.00 0.00 2.71
2366 2473 2.626743 CTGTTCGTATAGGGTGTAGGGG 59.373 54.545 0.00 0.00 0.00 4.79
2464 2572 5.410132 TGAAATTTGCCATGAAATCTTGCAG 59.590 36.000 0.00 0.00 0.00 4.41
2479 2587 4.917887 TTTGTGTGTGTGTGAAATTTGC 57.082 36.364 0.00 0.00 0.00 3.68
2866 2977 1.855213 TTCAGCGACATGGCAACTGC 61.855 55.000 12.73 0.88 41.14 4.40
2932 3043 2.029649 AGTTGACTGACATGGCAATTGC 60.030 45.455 22.47 22.47 41.14 3.56
2935 3046 1.542915 GCAGTTGACTGACATGGCAAT 59.457 47.619 14.98 0.00 46.59 3.56
2954 3200 1.080298 GAGCAACCATGGCAACTGC 60.080 57.895 13.04 15.46 41.14 4.40
3002 3292 0.238289 GTTGTCCGACATGGCAACTG 59.762 55.000 1.09 0.00 44.47 3.16
3003 3293 2.629002 GTTGTCCGACATGGCAACT 58.371 52.632 1.09 0.00 44.47 3.16
3004 3294 0.238289 CAGTTGTCCGACATGGCAAC 59.762 55.000 1.09 5.44 46.38 4.17
3005 3295 1.514678 GCAGTTGTCCGACATGGCAA 61.515 55.000 1.09 0.00 37.80 4.52
3006 3296 1.965930 GCAGTTGTCCGACATGGCA 60.966 57.895 1.09 0.00 37.80 4.92
3007 3297 1.915614 CTGCAGTTGTCCGACATGGC 61.916 60.000 5.25 7.26 37.80 4.40
3008 3298 0.603707 ACTGCAGTTGTCCGACATGG 60.604 55.000 15.25 0.00 40.09 3.66
3009 3299 1.229428 AACTGCAGTTGTCCGACATG 58.771 50.000 30.66 0.00 36.80 3.21
3045 3335 3.282831 GTTGTCCAACATGGCAACTAC 57.717 47.619 19.92 7.71 44.03 2.73
3286 3576 2.911484 GCCTCTAGCATGCTTGTAAGT 58.089 47.619 28.02 1.31 42.97 2.24
3353 3644 0.328258 CCCGTTTCCTCTCCCACAAT 59.672 55.000 0.00 0.00 0.00 2.71
3367 3659 4.424711 ATCGCCCACATGCCCGTT 62.425 61.111 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.