Multiple sequence alignment - TraesCS4B01G188100

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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 TraesCS4B01G188100 chr4B 100.000 3356 0 0 1 3356 408974754 408978109 0.000000e+00 6198.0
1 TraesCS4B01G188100 chr4B 95.098 204 9 1 1 203 592204432 592204229 1.500000e-83 320.0
2 TraesCS4B01G188100 chr4D 90.764 3205 157 58 207 3356 329132788 329135908 0.000000e+00 4150.0
3 TraesCS4B01G188100 chr4A 89.957 3246 156 78 207 3356 140984278 140981107 0.000000e+00 4032.0
4 TraesCS4B01G188100 chr1B 94.364 1863 59 17 518 2352 135827583 135825739 0.000000e+00 2817.0
5 TraesCS4B01G188100 chr1B 93.758 737 33 5 2630 3356 135819466 135818733 0.000000e+00 1094.0
6 TraesCS4B01G188100 chr1B 94.928 276 12 1 2350 2623 135825578 135825303 6.650000e-117 431.0
7 TraesCS4B01G188100 chr1B 97.030 202 5 1 1 201 21522395 21522194 4.150000e-89 339.0
8 TraesCS4B01G188100 chr1B 95.536 112 5 0 294 405 135827754 135827643 2.660000e-41 180.0
9 TraesCS4B01G188100 chr1A 83.838 693 55 29 2681 3356 586341733 586342385 1.030000e-169 606.0
10 TraesCS4B01G188100 chr1A 77.364 698 79 43 2676 3356 587486339 587486974 1.150000e-89 340.0
11 TraesCS4B01G188100 chr5A 78.448 696 68 45 2679 3356 637292720 637292089 2.440000e-101 379.0
12 TraesCS4B01G188100 chr3A 78.236 703 66 37 2676 3356 55174353 55173716 1.470000e-98 370.0
13 TraesCS4B01G188100 chr7A 77.922 693 62 42 2685 3356 168660408 168659786 6.890000e-92 348.0
14 TraesCS4B01G188100 chr2B 97.030 202 6 0 1 202 436266281 436266080 1.150000e-89 340.0
15 TraesCS4B01G188100 chr2B 96.098 205 8 0 1 205 453016350 453016554 5.370000e-88 335.0
16 TraesCS4B01G188100 chr2B 96.970 198 6 0 1 198 47253233 47253036 1.930000e-87 333.0
17 TraesCS4B01G188100 chr6B 97.436 195 4 1 1 195 41766397 41766590 6.940000e-87 331.0
18 TraesCS4B01G188100 chr6B 93.088 217 13 2 1 217 513140643 513140429 1.940000e-82 316.0
19 TraesCS4B01G188100 chr5B 96.923 195 6 0 1 195 530709458 530709264 8.980000e-86 327.0
20 TraesCS4B01G188100 chr3B 94.286 210 8 4 1 206 685611803 685612012 5.400000e-83 318.0
21 TraesCS4B01G188100 chr6A 77.033 701 68 42 2676 3356 265618507 265617880 1.940000e-82 316.0
22 TraesCS4B01G188100 chr2D 87.975 158 15 2 207 360 407119888 407119731 2.060000e-42 183.0
23 TraesCS4B01G188100 chr5D 86.709 158 18 3 2475 2631 69952041 69952196 4.450000e-39 172.0
24 TraesCS4B01G188100 chr5D 100.000 31 0 0 1095 1125 218261284 218261254 1.300000e-04 58.4


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 TraesCS4B01G188100 chr4B 408974754 408978109 3355 False 6198.000000 6198 100.000000 1 3356 1 chr4B.!!$F1 3355
1 TraesCS4B01G188100 chr4D 329132788 329135908 3120 False 4150.000000 4150 90.764000 207 3356 1 chr4D.!!$F1 3149
2 TraesCS4B01G188100 chr4A 140981107 140984278 3171 True 4032.000000 4032 89.957000 207 3356 1 chr4A.!!$R1 3149
3 TraesCS4B01G188100 chr1B 135825303 135827754 2451 True 1142.666667 2817 94.942667 294 2623 3 chr1B.!!$R3 2329
4 TraesCS4B01G188100 chr1B 135818733 135819466 733 True 1094.000000 1094 93.758000 2630 3356 1 chr1B.!!$R2 726
5 TraesCS4B01G188100 chr1A 586341733 586342385 652 False 606.000000 606 83.838000 2681 3356 1 chr1A.!!$F1 675
6 TraesCS4B01G188100 chr1A 587486339 587486974 635 False 340.000000 340 77.364000 2676 3356 1 chr1A.!!$F2 680
7 TraesCS4B01G188100 chr5A 637292089 637292720 631 True 379.000000 379 78.448000 2679 3356 1 chr5A.!!$R1 677
8 TraesCS4B01G188100 chr3A 55173716 55174353 637 True 370.000000 370 78.236000 2676 3356 1 chr3A.!!$R1 680
9 TraesCS4B01G188100 chr7A 168659786 168660408 622 True 348.000000 348 77.922000 2685 3356 1 chr7A.!!$R1 671
10 TraesCS4B01G188100 chr6A 265617880 265618507 627 True 316.000000 316 77.033000 2676 3356 1 chr6A.!!$R1 680

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
971 1057 0.09473 GTTTCCGTTCGAATCGGCTG 59.905 55.0 24.92 9.91 46.49 4.85 F
1824 1913 1.16527 GTAACTGCCAATGGTCGCTT 58.835 50.0 0.00 0.00 0.00 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2013 2102 0.029163 TCCCCCAATAGCCATGGAGA 60.029 55.0 18.40 1.34 40.56 3.71 R
3044 3380 0.315568 ACAAGAAGAAGAGACGCGCT 59.684 50.0 5.73 3.91 0.00 5.92 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
26 27 3.888221 CAACAAGTTGTGCGCGAC 58.112 55.556 12.10 9.78 35.92 5.19
27 28 1.351707 CAACAAGTTGTGCGCGACT 59.648 52.632 14.63 14.63 40.95 4.18
28 29 0.654472 CAACAAGTTGTGCGCGACTC 60.654 55.000 20.32 2.66 38.35 3.36
29 30 1.772063 AACAAGTTGTGCGCGACTCC 61.772 55.000 20.32 0.00 38.35 3.85
30 31 3.036084 AAGTTGTGCGCGACTCCG 61.036 61.111 20.32 0.00 38.35 4.63
49 50 3.917760 CGATGGAGGGGCGAGGAC 61.918 72.222 0.00 0.00 0.00 3.85
50 51 3.917760 GATGGAGGGGCGAGGACG 61.918 72.222 0.00 0.00 42.93 4.79
75 76 3.191539 GCCTTCGGCTCGCTTCAG 61.192 66.667 0.00 0.00 46.69 3.02
76 77 2.262915 CCTTCGGCTCGCTTCAGT 59.737 61.111 0.00 0.00 0.00 3.41
77 78 2.097038 CCTTCGGCTCGCTTCAGTG 61.097 63.158 0.00 0.00 0.00 3.66
78 79 2.734673 CTTCGGCTCGCTTCAGTGC 61.735 63.158 0.00 0.00 0.00 4.40
79 80 3.226429 TTCGGCTCGCTTCAGTGCT 62.226 57.895 0.00 0.00 0.00 4.40
80 81 3.485431 CGGCTCGCTTCAGTGCTG 61.485 66.667 0.00 0.00 0.00 4.41
81 82 3.123620 GGCTCGCTTCAGTGCTGG 61.124 66.667 0.00 0.00 0.00 4.85
82 83 2.358003 GCTCGCTTCAGTGCTGGT 60.358 61.111 0.00 0.00 0.00 4.00
83 84 1.079819 GCTCGCTTCAGTGCTGGTA 60.080 57.895 0.00 0.00 0.00 3.25
84 85 1.080995 GCTCGCTTCAGTGCTGGTAG 61.081 60.000 0.00 0.00 0.00 3.18
85 86 0.244994 CTCGCTTCAGTGCTGGTAGT 59.755 55.000 0.00 0.00 0.00 2.73
86 87 0.679505 TCGCTTCAGTGCTGGTAGTT 59.320 50.000 0.00 0.00 0.00 2.24
87 88 0.792640 CGCTTCAGTGCTGGTAGTTG 59.207 55.000 0.00 0.00 0.00 3.16
88 89 1.873903 CGCTTCAGTGCTGGTAGTTGT 60.874 52.381 0.00 0.00 0.00 3.32
89 90 1.801178 GCTTCAGTGCTGGTAGTTGTC 59.199 52.381 0.00 0.00 0.00 3.18
90 91 2.061773 CTTCAGTGCTGGTAGTTGTCG 58.938 52.381 0.00 0.00 0.00 4.35
91 92 0.319555 TCAGTGCTGGTAGTTGTCGC 60.320 55.000 0.00 0.00 0.00 5.19
92 93 0.319900 CAGTGCTGGTAGTTGTCGCT 60.320 55.000 0.00 0.00 0.00 4.93
93 94 1.067846 CAGTGCTGGTAGTTGTCGCTA 60.068 52.381 0.00 0.00 0.00 4.26
94 95 1.202582 AGTGCTGGTAGTTGTCGCTAG 59.797 52.381 0.00 0.00 0.00 3.42
95 96 0.530744 TGCTGGTAGTTGTCGCTAGG 59.469 55.000 0.00 0.00 0.00 3.02
96 97 0.531200 GCTGGTAGTTGTCGCTAGGT 59.469 55.000 0.00 0.00 0.00 3.08
97 98 1.747355 GCTGGTAGTTGTCGCTAGGTA 59.253 52.381 0.00 0.00 0.00 3.08
98 99 2.223525 GCTGGTAGTTGTCGCTAGGTAG 60.224 54.545 0.00 0.00 0.00 3.18
99 100 3.015327 CTGGTAGTTGTCGCTAGGTAGT 58.985 50.000 0.00 0.00 0.00 2.73
100 101 3.012518 TGGTAGTTGTCGCTAGGTAGTC 58.987 50.000 0.00 0.00 0.00 2.59
101 102 3.277715 GGTAGTTGTCGCTAGGTAGTCT 58.722 50.000 0.00 0.00 0.00 3.24
102 103 4.080919 TGGTAGTTGTCGCTAGGTAGTCTA 60.081 45.833 0.00 0.00 0.00 2.59
103 104 4.272261 GGTAGTTGTCGCTAGGTAGTCTAC 59.728 50.000 0.95 0.95 0.00 2.59
104 105 2.935201 AGTTGTCGCTAGGTAGTCTACG 59.065 50.000 3.92 0.00 0.00 3.51
105 106 1.945387 TGTCGCTAGGTAGTCTACGG 58.055 55.000 3.92 0.00 0.00 4.02
106 107 1.482182 TGTCGCTAGGTAGTCTACGGA 59.518 52.381 3.92 0.00 0.00 4.69
107 108 2.103771 TGTCGCTAGGTAGTCTACGGAT 59.896 50.000 3.92 0.00 0.00 4.18
108 109 2.736192 GTCGCTAGGTAGTCTACGGATC 59.264 54.545 3.92 0.00 0.00 3.36
109 110 2.632028 TCGCTAGGTAGTCTACGGATCT 59.368 50.000 3.92 0.00 0.00 2.75
110 111 2.737783 CGCTAGGTAGTCTACGGATCTG 59.262 54.545 0.00 0.00 0.00 2.90
111 112 3.075884 GCTAGGTAGTCTACGGATCTGG 58.924 54.545 6.47 0.00 0.00 3.86
112 113 3.244491 GCTAGGTAGTCTACGGATCTGGA 60.244 52.174 6.47 0.00 0.00 3.86
113 114 4.566070 GCTAGGTAGTCTACGGATCTGGAT 60.566 50.000 6.47 0.00 0.00 3.41
114 115 3.757270 AGGTAGTCTACGGATCTGGATG 58.243 50.000 6.47 0.00 0.00 3.51
115 116 3.138653 AGGTAGTCTACGGATCTGGATGT 59.861 47.826 6.47 0.00 0.00 3.06
116 117 4.350225 AGGTAGTCTACGGATCTGGATGTA 59.650 45.833 6.47 0.00 0.00 2.29
117 118 5.068636 GGTAGTCTACGGATCTGGATGTAA 58.931 45.833 6.47 0.00 0.00 2.41
118 119 5.711036 GGTAGTCTACGGATCTGGATGTAAT 59.289 44.000 6.47 0.00 0.00 1.89
119 120 6.208994 GGTAGTCTACGGATCTGGATGTAATT 59.791 42.308 6.47 0.00 0.00 1.40
120 121 6.732896 AGTCTACGGATCTGGATGTAATTT 57.267 37.500 6.47 0.00 0.00 1.82
121 122 6.750148 AGTCTACGGATCTGGATGTAATTTC 58.250 40.000 6.47 0.00 0.00 2.17
122 123 6.551601 AGTCTACGGATCTGGATGTAATTTCT 59.448 38.462 6.47 0.00 0.00 2.52
123 124 7.724506 AGTCTACGGATCTGGATGTAATTTCTA 59.275 37.037 6.47 0.00 0.00 2.10
124 125 8.524487 GTCTACGGATCTGGATGTAATTTCTAT 58.476 37.037 6.47 0.00 0.00 1.98
125 126 9.090103 TCTACGGATCTGGATGTAATTTCTATT 57.910 33.333 6.47 0.00 0.00 1.73
149 150 6.963049 ATTTCTGGTATTCGTTGTACTGTC 57.037 37.500 0.00 0.00 0.00 3.51
150 151 5.456548 TTCTGGTATTCGTTGTACTGTCA 57.543 39.130 0.00 0.00 0.00 3.58
151 152 5.654603 TCTGGTATTCGTTGTACTGTCAT 57.345 39.130 0.00 0.00 0.00 3.06
152 153 5.407502 TCTGGTATTCGTTGTACTGTCATG 58.592 41.667 0.00 0.00 0.00 3.07
153 154 5.184287 TCTGGTATTCGTTGTACTGTCATGA 59.816 40.000 0.00 0.00 0.00 3.07
154 155 5.972935 TGGTATTCGTTGTACTGTCATGAT 58.027 37.500 0.00 0.00 0.00 2.45
155 156 6.403049 TGGTATTCGTTGTACTGTCATGATT 58.597 36.000 0.00 0.00 0.00 2.57
156 157 6.312672 TGGTATTCGTTGTACTGTCATGATTG 59.687 38.462 0.00 0.00 0.00 2.67
157 158 6.533723 GGTATTCGTTGTACTGTCATGATTGA 59.466 38.462 0.00 0.00 0.00 2.57
158 159 7.064134 GGTATTCGTTGTACTGTCATGATTGAA 59.936 37.037 0.00 0.00 32.48 2.69
159 160 6.466308 TTCGTTGTACTGTCATGATTGAAG 57.534 37.500 0.00 0.00 32.48 3.02
160 161 5.778862 TCGTTGTACTGTCATGATTGAAGA 58.221 37.500 0.00 0.00 32.48 2.87
161 162 6.398095 TCGTTGTACTGTCATGATTGAAGAT 58.602 36.000 0.00 0.00 32.48 2.40
162 163 6.311200 TCGTTGTACTGTCATGATTGAAGATG 59.689 38.462 0.00 0.00 32.48 2.90
163 164 6.311200 CGTTGTACTGTCATGATTGAAGATGA 59.689 38.462 0.00 0.00 32.48 2.92
164 165 7.148590 CGTTGTACTGTCATGATTGAAGATGAA 60.149 37.037 0.00 0.00 32.48 2.57
165 166 8.671921 GTTGTACTGTCATGATTGAAGATGAAT 58.328 33.333 0.00 0.00 32.48 2.57
166 167 9.889128 TTGTACTGTCATGATTGAAGATGAATA 57.111 29.630 0.00 0.00 32.48 1.75
167 168 9.538508 TGTACTGTCATGATTGAAGATGAATAG 57.461 33.333 0.00 0.00 32.48 1.73
168 169 9.755804 GTACTGTCATGATTGAAGATGAATAGA 57.244 33.333 0.00 0.00 32.48 1.98
170 171 9.491675 ACTGTCATGATTGAAGATGAATAGATC 57.508 33.333 0.00 0.00 32.48 2.75
171 172 8.530269 TGTCATGATTGAAGATGAATAGATCG 57.470 34.615 0.00 0.00 32.48 3.69
172 173 8.362639 TGTCATGATTGAAGATGAATAGATCGA 58.637 33.333 0.00 0.00 32.48 3.59
173 174 9.201127 GTCATGATTGAAGATGAATAGATCGAA 57.799 33.333 0.00 0.00 32.48 3.71
174 175 9.768662 TCATGATTGAAGATGAATAGATCGAAA 57.231 29.630 0.00 0.00 0.00 3.46
184 185 8.279103 AGATGAATAGATCGAAAATTTTCTCGC 58.721 33.333 24.53 14.67 35.07 5.03
185 186 7.302350 TGAATAGATCGAAAATTTTCTCGCA 57.698 32.000 24.53 12.33 35.07 5.10
186 187 7.747888 TGAATAGATCGAAAATTTTCTCGCAA 58.252 30.769 24.53 10.74 35.07 4.85
187 188 8.233868 TGAATAGATCGAAAATTTTCTCGCAAA 58.766 29.630 24.53 9.42 35.07 3.68
188 189 8.964420 AATAGATCGAAAATTTTCTCGCAAAA 57.036 26.923 24.53 8.08 35.07 2.44
189 190 8.964420 ATAGATCGAAAATTTTCTCGCAAAAA 57.036 26.923 24.53 6.85 35.07 1.94
232 234 5.863397 ACGTTGCAGTCAATATGGATTTTTG 59.137 36.000 0.00 0.00 34.29 2.44
396 414 4.589374 AGGACAGAAACTTGTACTGCTAGT 59.411 41.667 0.00 0.00 40.73 2.57
405 424 5.804173 ACTTGTACTGCTAGTATACGAACG 58.196 41.667 0.00 0.00 32.65 3.95
406 425 5.582269 ACTTGTACTGCTAGTATACGAACGA 59.418 40.000 0.14 0.00 32.65 3.85
407 426 6.259608 ACTTGTACTGCTAGTATACGAACGAT 59.740 38.462 0.14 0.00 32.65 3.73
408 427 6.609237 TGTACTGCTAGTATACGAACGATT 57.391 37.500 0.14 0.00 32.65 3.34
409 428 7.713764 TGTACTGCTAGTATACGAACGATTA 57.286 36.000 0.14 0.00 32.65 1.75
410 429 8.141835 TGTACTGCTAGTATACGAACGATTAA 57.858 34.615 0.14 0.00 32.65 1.40
411 430 8.064222 TGTACTGCTAGTATACGAACGATTAAC 58.936 37.037 0.14 0.00 32.65 2.01
412 431 6.433766 ACTGCTAGTATACGAACGATTAACC 58.566 40.000 0.14 0.00 0.00 2.85
413 432 5.443261 TGCTAGTATACGAACGATTAACCG 58.557 41.667 0.14 0.00 0.00 4.44
414 433 5.007626 TGCTAGTATACGAACGATTAACCGT 59.992 40.000 0.00 0.00 45.64 4.83
415 434 5.338035 GCTAGTATACGAACGATTAACCGTG 59.662 44.000 0.00 0.00 42.54 4.94
416 435 4.037690 AGTATACGAACGATTAACCGTGC 58.962 43.478 0.00 0.00 42.54 5.34
419 438 2.740668 GAACGATTAACCGTGCGGA 58.259 52.632 18.16 0.00 42.54 5.54
420 439 1.070038 GAACGATTAACCGTGCGGAA 58.930 50.000 18.16 2.33 42.54 4.30
421 440 0.792031 AACGATTAACCGTGCGGAAC 59.208 50.000 18.16 3.07 42.54 3.62
422 441 0.319727 ACGATTAACCGTGCGGAACA 60.320 50.000 18.16 0.43 41.70 3.18
423 442 0.368907 CGATTAACCGTGCGGAACAG 59.631 55.000 18.16 0.09 38.96 3.16
424 443 0.096454 GATTAACCGTGCGGAACAGC 59.904 55.000 18.16 0.00 38.96 4.40
425 444 1.303091 ATTAACCGTGCGGAACAGCC 61.303 55.000 18.16 0.00 38.96 4.85
426 445 3.887335 TAACCGTGCGGAACAGCCC 62.887 63.158 18.16 0.00 38.96 5.19
429 448 4.988598 CGTGCGGAACAGCCCACT 62.989 66.667 0.00 0.00 36.36 4.00
489 508 0.253044 ACCCATCCGTCATTGACCTG 59.747 55.000 11.12 6.48 0.00 4.00
490 509 0.253044 CCCATCCGTCATTGACCTGT 59.747 55.000 11.12 0.00 0.00 4.00
491 510 1.656652 CCATCCGTCATTGACCTGTC 58.343 55.000 11.12 0.00 0.00 3.51
492 511 1.208052 CCATCCGTCATTGACCTGTCT 59.792 52.381 11.12 0.00 0.00 3.41
603 628 2.654877 GAGGCGACACGGGAGAAA 59.345 61.111 0.00 0.00 0.00 2.52
604 629 1.005394 GAGGCGACACGGGAGAAAA 60.005 57.895 0.00 0.00 0.00 2.29
605 630 0.601841 GAGGCGACACGGGAGAAAAA 60.602 55.000 0.00 0.00 0.00 1.94
632 657 0.466124 AAGGAGTAGAAGCATCGGGC 59.534 55.000 0.00 0.00 45.30 6.13
671 701 1.286257 GCCATTCCTTCCTTCCTTCCT 59.714 52.381 0.00 0.00 0.00 3.36
672 702 2.291865 GCCATTCCTTCCTTCCTTCCTT 60.292 50.000 0.00 0.00 0.00 3.36
673 703 3.625853 CCATTCCTTCCTTCCTTCCTTC 58.374 50.000 0.00 0.00 0.00 3.46
674 704 3.625853 CATTCCTTCCTTCCTTCCTTCC 58.374 50.000 0.00 0.00 0.00 3.46
699 736 1.209261 CTCTTGGCCTTCTTCCTCCTC 59.791 57.143 3.32 0.00 0.00 3.71
936 1014 2.070783 CGTCGATCTAGACTCTAGGGC 58.929 57.143 12.37 5.06 38.90 5.19
956 1035 2.918131 GCCGTCTGCATTTCTGTGTTTC 60.918 50.000 0.00 0.00 40.77 2.78
964 1050 3.547214 GCATTTCTGTGTTTCCGTTCGAA 60.547 43.478 0.00 0.00 0.00 3.71
971 1057 0.094730 GTTTCCGTTCGAATCGGCTG 59.905 55.000 24.92 9.91 46.49 4.85
1078 1164 2.281484 GGAACGCCAAGCTCACCA 60.281 61.111 0.00 0.00 0.00 4.17
1455 1544 2.675423 CTCGTCACGGGGTCCTCA 60.675 66.667 0.00 0.00 0.00 3.86
1824 1913 1.165270 GTAACTGCCAATGGTCGCTT 58.835 50.000 0.00 0.00 0.00 4.68
1836 1925 1.754803 TGGTCGCTTGATTACCTCGAT 59.245 47.619 0.00 0.00 34.23 3.59
1845 1934 2.249139 GATTACCTCGATACCTGGGCT 58.751 52.381 0.00 0.00 0.00 5.19
1992 2081 4.149598 GTGAGAAATGGGGTAACAAGGTT 58.850 43.478 0.00 0.00 39.74 3.50
2013 2102 6.722129 AGGTTTATCTCGAGAATGGCTACTAT 59.278 38.462 20.91 0.76 0.00 2.12
2226 2315 2.161855 CAGGTGTTGCACATGTATGGT 58.838 47.619 0.00 0.00 40.60 3.55
2478 2730 6.989759 ACAAGGAAATTTGGTTTTGGTATCAC 59.010 34.615 0.00 0.00 32.32 3.06
2567 2821 9.545105 AATCTATGTCTTCTGCTTCTAGAAATG 57.455 33.333 6.63 0.00 36.34 2.32
2568 2822 7.495901 TCTATGTCTTCTGCTTCTAGAAATGG 58.504 38.462 6.63 0.00 36.34 3.16
2569 2823 5.745312 TGTCTTCTGCTTCTAGAAATGGA 57.255 39.130 6.63 2.17 36.34 3.41
2570 2824 5.728471 TGTCTTCTGCTTCTAGAAATGGAG 58.272 41.667 6.63 6.76 36.34 3.86
2571 2825 5.247110 TGTCTTCTGCTTCTAGAAATGGAGT 59.753 40.000 6.63 0.00 36.34 3.85
2572 2826 6.169800 GTCTTCTGCTTCTAGAAATGGAGTT 58.830 40.000 6.63 0.00 36.34 3.01
2573 2827 7.039011 TGTCTTCTGCTTCTAGAAATGGAGTTA 60.039 37.037 6.63 0.16 36.34 2.24
2574 2828 7.491048 GTCTTCTGCTTCTAGAAATGGAGTTAG 59.509 40.741 6.63 8.54 36.34 2.34
2575 2829 7.397476 TCTTCTGCTTCTAGAAATGGAGTTAGA 59.603 37.037 6.63 10.32 36.34 2.10
2576 2830 7.106439 TCTGCTTCTAGAAATGGAGTTAGAG 57.894 40.000 6.63 0.00 0.00 2.43
2577 2831 6.892456 TCTGCTTCTAGAAATGGAGTTAGAGA 59.108 38.462 6.63 0.00 0.00 3.10
2578 2832 7.563188 TCTGCTTCTAGAAATGGAGTTAGAGAT 59.437 37.037 6.63 0.00 0.00 2.75
2579 2833 7.495901 TGCTTCTAGAAATGGAGTTAGAGATG 58.504 38.462 6.63 0.00 0.00 2.90
2580 2834 6.928492 GCTTCTAGAAATGGAGTTAGAGATGG 59.072 42.308 6.63 0.00 0.00 3.51
2581 2835 6.985653 TCTAGAAATGGAGTTAGAGATGGG 57.014 41.667 0.00 0.00 0.00 4.00
2582 2836 6.444704 TCTAGAAATGGAGTTAGAGATGGGT 58.555 40.000 0.00 0.00 0.00 4.51
2583 2837 7.592736 TCTAGAAATGGAGTTAGAGATGGGTA 58.407 38.462 0.00 0.00 0.00 3.69
2584 2838 6.487299 AGAAATGGAGTTAGAGATGGGTAC 57.513 41.667 0.00 0.00 0.00 3.34
2585 2839 6.206042 AGAAATGGAGTTAGAGATGGGTACT 58.794 40.000 0.00 0.00 0.00 2.73
2586 2840 6.325286 AGAAATGGAGTTAGAGATGGGTACTC 59.675 42.308 0.00 0.00 35.61 2.59
2587 2841 4.603094 TGGAGTTAGAGATGGGTACTCA 57.397 45.455 0.00 0.00 37.54 3.41
2619 2893 5.782047 CTCACTTCTGAATAGCTCTATGGG 58.218 45.833 0.00 0.00 0.00 4.00
2654 2950 4.606673 GCATTTTCATTTGTCGCAAGTGTG 60.607 41.667 12.27 6.87 39.48 3.82
2679 2975 9.034800 TGCATTTCACTTCCCTAAAAGATATTT 57.965 29.630 0.00 0.00 0.00 1.40
2742 3041 5.337813 CCCTCTGAGCCAATTATTTTGCTTT 60.338 40.000 0.00 0.00 34.21 3.51
2817 3127 6.191657 TGTCATATATGAGTTGGCTGGAAT 57.808 37.500 15.83 0.00 37.51 3.01
2819 3129 7.062322 TGTCATATATGAGTTGGCTGGAATTT 58.938 34.615 15.83 0.00 37.51 1.82
2885 3203 9.897744 TCATCAATTTAGTTTTGAAGCACTTAG 57.102 29.630 0.00 0.00 36.72 2.18
2892 3210 5.316987 AGTTTTGAAGCACTTAGTATGGCT 58.683 37.500 0.00 0.00 38.45 4.75
2893 3211 5.182001 AGTTTTGAAGCACTTAGTATGGCTG 59.818 40.000 0.00 0.00 36.58 4.85
2894 3212 3.266510 TGAAGCACTTAGTATGGCTGG 57.733 47.619 0.00 0.00 36.58 4.85
2895 3213 2.571653 TGAAGCACTTAGTATGGCTGGT 59.428 45.455 0.00 0.00 36.58 4.00
2896 3214 3.772572 TGAAGCACTTAGTATGGCTGGTA 59.227 43.478 0.00 0.00 36.58 3.25
2955 3279 5.954296 AACCAATTGAGAGTTGATGTGAG 57.046 39.130 7.12 0.00 0.00 3.51
2960 3286 3.309961 TGAGAGTTGATGTGAGCTGTC 57.690 47.619 0.00 0.00 0.00 3.51
3037 3373 1.883209 GCCAATGCAAATGCCCTGTTT 60.883 47.619 2.46 0.00 41.18 2.83
3038 3374 2.614987 GCCAATGCAAATGCCCTGTTTA 60.615 45.455 2.46 0.00 41.18 2.01
3039 3375 3.876341 CCAATGCAAATGCCCTGTTTAT 58.124 40.909 2.46 0.00 41.18 1.40
3040 3376 3.623960 CCAATGCAAATGCCCTGTTTATG 59.376 43.478 2.46 0.00 41.18 1.90
3041 3377 4.255301 CAATGCAAATGCCCTGTTTATGT 58.745 39.130 2.46 0.00 41.18 2.29
3042 3378 5.417811 CAATGCAAATGCCCTGTTTATGTA 58.582 37.500 2.46 0.00 41.18 2.29
3043 3379 5.674052 ATGCAAATGCCCTGTTTATGTAA 57.326 34.783 2.46 0.00 41.18 2.41
3044 3380 5.474578 TGCAAATGCCCTGTTTATGTAAA 57.525 34.783 2.46 0.00 41.18 2.01
3045 3381 5.477510 TGCAAATGCCCTGTTTATGTAAAG 58.522 37.500 2.46 0.00 41.18 1.85
3046 3382 4.329801 GCAAATGCCCTGTTTATGTAAAGC 59.670 41.667 0.00 0.00 34.31 3.51
3047 3383 4.370364 AATGCCCTGTTTATGTAAAGCG 57.630 40.909 0.00 0.00 0.00 4.68
3048 3384 1.470890 TGCCCTGTTTATGTAAAGCGC 59.529 47.619 0.00 0.00 0.00 5.92
3051 3387 2.222953 CCCTGTTTATGTAAAGCGCGTC 60.223 50.000 8.43 0.00 0.00 5.19
3061 3406 2.156343 AAAGCGCGTCTCTTCTTCTT 57.844 45.000 8.43 0.00 0.00 2.52
3066 3411 2.128035 CGCGTCTCTTCTTCTTGTTGT 58.872 47.619 0.00 0.00 0.00 3.32
3123 3470 1.002134 CGCCAAGGGGATTGTCAGT 60.002 57.895 0.00 0.00 37.17 3.41
3143 3490 5.009610 TCAGTTTTTGACTATGCTTTGGACC 59.990 40.000 0.00 0.00 36.65 4.46
3154 3501 2.370519 TGCTTTGGACCTAGTGTAGCAA 59.629 45.455 0.00 0.00 34.55 3.91
3231 3589 5.070580 AGGGTAATTCGGTTATCTTCTCCTG 59.929 44.000 0.00 0.00 0.00 3.86
3238 3596 5.128919 TCGGTTATCTTCTCCTGGTAGTAC 58.871 45.833 0.00 0.00 0.00 2.73
3239 3597 4.277921 CGGTTATCTTCTCCTGGTAGTACC 59.722 50.000 12.80 12.80 39.22 3.34
3255 3613 3.707316 AGTACCAGAGTTCTGCATCTCT 58.293 45.455 3.58 9.44 42.47 3.10
3317 3682 1.106351 TCCATGTGTTGTGTGGTGCC 61.106 55.000 0.00 0.00 34.61 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.362693 GCGCACAACTTGTTGTAGTAGAC 60.363 47.826 17.26 4.55 33.17 2.59
3 4 2.409752 CGCGCACAACTTGTTGTAGTAG 60.410 50.000 17.26 7.80 33.17 2.57
4 5 1.523515 CGCGCACAACTTGTTGTAGTA 59.476 47.619 17.26 0.00 33.17 1.82
5 6 0.303493 CGCGCACAACTTGTTGTAGT 59.697 50.000 17.26 0.00 33.17 2.73
6 7 0.579630 TCGCGCACAACTTGTTGTAG 59.420 50.000 17.26 14.94 33.17 2.74
7 8 0.302288 GTCGCGCACAACTTGTTGTA 59.698 50.000 17.26 1.01 33.17 2.41
8 9 1.061887 GTCGCGCACAACTTGTTGT 59.938 52.632 8.75 12.73 35.14 3.32
9 10 0.654472 GAGTCGCGCACAACTTGTTG 60.654 55.000 8.75 11.44 0.00 3.33
10 11 1.641677 GAGTCGCGCACAACTTGTT 59.358 52.632 8.75 0.00 0.00 2.83
11 12 2.244651 GGAGTCGCGCACAACTTGT 61.245 57.895 8.75 0.00 0.00 3.16
12 13 2.551270 GGAGTCGCGCACAACTTG 59.449 61.111 8.75 0.00 0.00 3.16
13 14 3.036084 CGGAGTCGCGCACAACTT 61.036 61.111 8.75 0.00 0.00 2.66
22 23 4.933064 CTCCATCGCCGGAGTCGC 62.933 72.222 5.05 0.00 46.48 5.19
32 33 3.917760 GTCCTCGCCCCTCCATCG 61.918 72.222 0.00 0.00 0.00 3.84
33 34 3.917760 CGTCCTCGCCCCTCCATC 61.918 72.222 0.00 0.00 0.00 3.51
60 61 2.734673 GCACTGAAGCGAGCCGAAG 61.735 63.158 0.00 0.00 0.00 3.79
61 62 2.738521 GCACTGAAGCGAGCCGAA 60.739 61.111 0.00 0.00 0.00 4.30
62 63 3.684990 AGCACTGAAGCGAGCCGA 61.685 61.111 0.00 0.00 40.15 5.54
63 64 3.485431 CAGCACTGAAGCGAGCCG 61.485 66.667 0.00 0.00 40.15 5.52
64 65 2.507110 TACCAGCACTGAAGCGAGCC 62.507 60.000 0.00 0.00 40.15 4.70
65 66 1.079819 TACCAGCACTGAAGCGAGC 60.080 57.895 0.00 0.00 40.15 5.03
66 67 0.244994 ACTACCAGCACTGAAGCGAG 59.755 55.000 0.00 0.00 40.15 5.03
67 68 0.679505 AACTACCAGCACTGAAGCGA 59.320 50.000 0.00 0.00 40.15 4.93
68 69 0.792640 CAACTACCAGCACTGAAGCG 59.207 55.000 0.00 0.00 40.15 4.68
69 70 1.801178 GACAACTACCAGCACTGAAGC 59.199 52.381 0.00 0.00 0.00 3.86
70 71 2.061773 CGACAACTACCAGCACTGAAG 58.938 52.381 0.00 0.00 0.00 3.02
71 72 1.872237 GCGACAACTACCAGCACTGAA 60.872 52.381 0.00 0.00 0.00 3.02
72 73 0.319555 GCGACAACTACCAGCACTGA 60.320 55.000 0.00 0.00 0.00 3.41
73 74 0.319900 AGCGACAACTACCAGCACTG 60.320 55.000 0.00 0.00 0.00 3.66
74 75 1.202582 CTAGCGACAACTACCAGCACT 59.797 52.381 0.00 0.00 0.00 4.40
75 76 1.630148 CTAGCGACAACTACCAGCAC 58.370 55.000 0.00 0.00 0.00 4.40
76 77 0.530744 CCTAGCGACAACTACCAGCA 59.469 55.000 0.00 0.00 0.00 4.41
77 78 0.531200 ACCTAGCGACAACTACCAGC 59.469 55.000 0.00 0.00 0.00 4.85
78 79 3.015327 ACTACCTAGCGACAACTACCAG 58.985 50.000 0.00 0.00 0.00 4.00
79 80 3.012518 GACTACCTAGCGACAACTACCA 58.987 50.000 0.00 0.00 0.00 3.25
80 81 3.277715 AGACTACCTAGCGACAACTACC 58.722 50.000 0.00 0.00 0.00 3.18
81 82 4.026145 CGTAGACTACCTAGCGACAACTAC 60.026 50.000 7.05 0.00 0.00 2.73
82 83 4.115516 CGTAGACTACCTAGCGACAACTA 58.884 47.826 7.05 0.00 0.00 2.24
83 84 2.935201 CGTAGACTACCTAGCGACAACT 59.065 50.000 7.05 0.00 0.00 3.16
84 85 2.031437 CCGTAGACTACCTAGCGACAAC 59.969 54.545 7.05 0.00 0.00 3.32
85 86 2.093500 TCCGTAGACTACCTAGCGACAA 60.093 50.000 7.05 0.00 0.00 3.18
86 87 1.482182 TCCGTAGACTACCTAGCGACA 59.518 52.381 7.05 0.00 0.00 4.35
87 88 2.231215 TCCGTAGACTACCTAGCGAC 57.769 55.000 7.05 0.00 0.00 5.19
88 89 2.632028 AGATCCGTAGACTACCTAGCGA 59.368 50.000 7.05 0.00 0.00 4.93
89 90 2.737783 CAGATCCGTAGACTACCTAGCG 59.262 54.545 7.05 0.00 0.00 4.26
90 91 3.075884 CCAGATCCGTAGACTACCTAGC 58.924 54.545 7.05 0.00 0.00 3.42
91 92 4.620589 TCCAGATCCGTAGACTACCTAG 57.379 50.000 7.05 0.00 0.00 3.02
92 93 4.350225 ACATCCAGATCCGTAGACTACCTA 59.650 45.833 7.05 0.00 0.00 3.08
93 94 3.138653 ACATCCAGATCCGTAGACTACCT 59.861 47.826 7.05 0.00 0.00 3.08
94 95 3.488363 ACATCCAGATCCGTAGACTACC 58.512 50.000 7.05 0.00 0.00 3.18
95 96 6.821031 ATTACATCCAGATCCGTAGACTAC 57.179 41.667 2.24 2.24 0.00 2.73
96 97 7.724506 AGAAATTACATCCAGATCCGTAGACTA 59.275 37.037 0.00 0.00 0.00 2.59
97 98 6.551601 AGAAATTACATCCAGATCCGTAGACT 59.448 38.462 0.00 0.00 0.00 3.24
98 99 6.750148 AGAAATTACATCCAGATCCGTAGAC 58.250 40.000 0.00 0.00 0.00 2.59
99 100 6.978674 AGAAATTACATCCAGATCCGTAGA 57.021 37.500 0.00 0.00 0.00 2.59
123 124 9.095065 GACAGTACAACGAATACCAGAAATAAT 57.905 33.333 0.00 0.00 0.00 1.28
124 125 8.089597 TGACAGTACAACGAATACCAGAAATAA 58.910 33.333 0.00 0.00 0.00 1.40
125 126 7.604549 TGACAGTACAACGAATACCAGAAATA 58.395 34.615 0.00 0.00 0.00 1.40
126 127 6.460781 TGACAGTACAACGAATACCAGAAAT 58.539 36.000 0.00 0.00 0.00 2.17
127 128 5.845103 TGACAGTACAACGAATACCAGAAA 58.155 37.500 0.00 0.00 0.00 2.52
128 129 5.456548 TGACAGTACAACGAATACCAGAA 57.543 39.130 0.00 0.00 0.00 3.02
129 130 5.184287 TCATGACAGTACAACGAATACCAGA 59.816 40.000 0.00 0.00 0.00 3.86
130 131 5.407502 TCATGACAGTACAACGAATACCAG 58.592 41.667 0.00 0.00 0.00 4.00
131 132 5.394224 TCATGACAGTACAACGAATACCA 57.606 39.130 0.00 0.00 0.00 3.25
132 133 6.533723 TCAATCATGACAGTACAACGAATACC 59.466 38.462 0.00 0.00 0.00 2.73
133 134 7.520119 TCAATCATGACAGTACAACGAATAC 57.480 36.000 0.00 0.00 0.00 1.89
134 135 8.032451 TCTTCAATCATGACAGTACAACGAATA 58.968 33.333 0.00 0.00 34.61 1.75
135 136 6.873605 TCTTCAATCATGACAGTACAACGAAT 59.126 34.615 0.00 0.00 34.61 3.34
136 137 6.220201 TCTTCAATCATGACAGTACAACGAA 58.780 36.000 0.00 0.00 34.61 3.85
137 138 5.778862 TCTTCAATCATGACAGTACAACGA 58.221 37.500 0.00 0.00 34.61 3.85
138 139 6.311200 TCATCTTCAATCATGACAGTACAACG 59.689 38.462 0.00 0.00 34.61 4.10
139 140 7.601073 TCATCTTCAATCATGACAGTACAAC 57.399 36.000 0.00 0.00 34.61 3.32
140 141 8.797350 ATTCATCTTCAATCATGACAGTACAA 57.203 30.769 0.00 0.00 34.61 2.41
141 142 9.538508 CTATTCATCTTCAATCATGACAGTACA 57.461 33.333 0.00 0.00 34.61 2.90
142 143 9.755804 TCTATTCATCTTCAATCATGACAGTAC 57.244 33.333 0.00 0.00 34.61 2.73
144 145 9.491675 GATCTATTCATCTTCAATCATGACAGT 57.508 33.333 0.00 0.00 34.61 3.55
145 146 8.648968 CGATCTATTCATCTTCAATCATGACAG 58.351 37.037 0.00 0.00 34.61 3.51
146 147 8.362639 TCGATCTATTCATCTTCAATCATGACA 58.637 33.333 0.00 0.00 34.61 3.58
147 148 8.754230 TCGATCTATTCATCTTCAATCATGAC 57.246 34.615 0.00 0.00 34.61 3.06
148 149 9.768662 TTTCGATCTATTCATCTTCAATCATGA 57.231 29.630 0.00 0.00 0.00 3.07
158 159 8.279103 GCGAGAAAATTTTCGATCTATTCATCT 58.721 33.333 21.98 2.97 41.92 2.90
159 160 8.064222 TGCGAGAAAATTTTCGATCTATTCATC 58.936 33.333 21.98 11.00 41.92 2.92
160 161 7.919690 TGCGAGAAAATTTTCGATCTATTCAT 58.080 30.769 21.98 3.86 41.92 2.57
161 162 7.302350 TGCGAGAAAATTTTCGATCTATTCA 57.698 32.000 21.98 11.42 41.92 2.57
162 163 8.601243 TTTGCGAGAAAATTTTCGATCTATTC 57.399 30.769 21.98 12.79 41.92 1.75
163 164 8.964420 TTTTGCGAGAAAATTTTCGATCTATT 57.036 26.923 21.98 5.88 41.92 1.73
164 165 8.964420 TTTTTGCGAGAAAATTTTCGATCTAT 57.036 26.923 21.98 6.55 41.92 1.98
201 202 7.598278 TCCATATTGACTGCAACGTTATTTTT 58.402 30.769 0.00 0.00 36.72 1.94
202 203 7.151999 TCCATATTGACTGCAACGTTATTTT 57.848 32.000 0.00 0.00 36.72 1.82
203 204 6.751514 TCCATATTGACTGCAACGTTATTT 57.248 33.333 0.00 0.00 36.72 1.40
204 205 6.942532 ATCCATATTGACTGCAACGTTATT 57.057 33.333 0.00 0.00 36.72 1.40
205 206 6.942532 AATCCATATTGACTGCAACGTTAT 57.057 33.333 0.00 0.00 36.72 1.89
219 220 7.848223 GCTTTTGTAGCCAAAAATCCATATT 57.152 32.000 3.07 0.00 46.80 1.28
245 247 3.181476 ACGGATAAAAGCCATGGAAATGC 60.181 43.478 18.40 0.00 0.00 3.56
255 257 2.273557 TGCTCGTTACGGATAAAAGCC 58.726 47.619 4.53 0.00 33.40 4.35
396 414 3.035251 CGCACGGTTAATCGTTCGTATA 58.965 45.455 22.26 0.00 42.68 1.47
405 424 0.096454 GCTGTTCCGCACGGTTAATC 59.904 55.000 9.23 0.00 33.70 1.75
406 425 1.303091 GGCTGTTCCGCACGGTTAAT 61.303 55.000 9.23 0.00 33.70 1.40
407 426 1.962306 GGCTGTTCCGCACGGTTAA 60.962 57.895 9.23 0.00 33.70 2.01
408 427 2.357760 GGCTGTTCCGCACGGTTA 60.358 61.111 9.23 0.00 33.70 2.85
412 431 4.988598 AGTGGGCTGTTCCGCACG 62.989 66.667 4.15 0.00 39.50 5.34
413 432 3.357079 CAGTGGGCTGTTCCGCAC 61.357 66.667 1.68 1.68 39.64 5.34
414 433 2.616797 TTTCAGTGGGCTGTTCCGCA 62.617 55.000 0.00 0.00 43.05 5.69
415 434 1.896660 TTTCAGTGGGCTGTTCCGC 60.897 57.895 0.00 0.00 43.05 5.54
416 435 0.817634 TGTTTCAGTGGGCTGTTCCG 60.818 55.000 0.00 0.00 43.05 4.30
417 436 1.067060 GTTGTTTCAGTGGGCTGTTCC 59.933 52.381 0.00 0.00 43.05 3.62
418 437 1.268539 CGTTGTTTCAGTGGGCTGTTC 60.269 52.381 0.00 0.00 43.05 3.18
419 438 0.738389 CGTTGTTTCAGTGGGCTGTT 59.262 50.000 0.00 0.00 43.05 3.16
420 439 1.101049 CCGTTGTTTCAGTGGGCTGT 61.101 55.000 0.00 0.00 43.05 4.40
421 440 1.654220 CCGTTGTTTCAGTGGGCTG 59.346 57.895 0.00 0.00 43.87 4.85
422 441 2.193536 GCCGTTGTTTCAGTGGGCT 61.194 57.895 0.00 0.00 37.57 5.19
423 442 2.335011 GCCGTTGTTTCAGTGGGC 59.665 61.111 0.00 0.00 0.00 5.36
424 443 1.826054 TGGCCGTTGTTTCAGTGGG 60.826 57.895 0.00 0.00 0.00 4.61
425 444 1.358759 GTGGCCGTTGTTTCAGTGG 59.641 57.895 0.00 0.00 0.00 4.00
426 445 1.358759 GGTGGCCGTTGTTTCAGTG 59.641 57.895 0.00 0.00 0.00 3.66
427 446 1.826487 GGGTGGCCGTTGTTTCAGT 60.826 57.895 0.00 0.00 0.00 3.41
428 447 1.106944 AAGGGTGGCCGTTGTTTCAG 61.107 55.000 0.00 0.00 29.93 3.02
429 448 1.076632 AAGGGTGGCCGTTGTTTCA 60.077 52.632 0.00 0.00 29.93 2.69
430 449 1.658114 GAAGGGTGGCCGTTGTTTC 59.342 57.895 0.00 0.00 31.35 2.78
431 450 1.830847 GGAAGGGTGGCCGTTGTTT 60.831 57.895 0.00 0.00 31.35 2.83
432 451 2.203437 GGAAGGGTGGCCGTTGTT 60.203 61.111 0.00 0.00 31.35 2.83
433 452 4.636435 CGGAAGGGTGGCCGTTGT 62.636 66.667 0.00 0.00 42.49 3.32
489 508 1.654743 GCGTCGCGAGGTGATAGAC 60.655 63.158 27.37 7.54 0.00 2.59
490 509 2.713770 GCGTCGCGAGGTGATAGA 59.286 61.111 27.37 0.00 0.00 1.98
491 510 2.353607 GGCGTCGCGAGGTGATAG 60.354 66.667 27.37 7.00 0.00 2.08
492 511 3.896133 GGGCGTCGCGAGGTGATA 61.896 66.667 27.37 0.00 0.00 2.15
511 530 5.276773 CGTTGGTTGGTTTGATTTGTTGATG 60.277 40.000 0.00 0.00 0.00 3.07
512 531 4.808364 CGTTGGTTGGTTTGATTTGTTGAT 59.192 37.500 0.00 0.00 0.00 2.57
513 532 4.082190 TCGTTGGTTGGTTTGATTTGTTGA 60.082 37.500 0.00 0.00 0.00 3.18
516 535 3.697045 TCTCGTTGGTTGGTTTGATTTGT 59.303 39.130 0.00 0.00 0.00 2.83
604 629 7.363431 CGATGCTTCTACTCCTTTTTCTTTTT 58.637 34.615 0.00 0.00 0.00 1.94
605 630 6.072452 CCGATGCTTCTACTCCTTTTTCTTTT 60.072 38.462 0.00 0.00 0.00 2.27
609 634 3.623510 CCCGATGCTTCTACTCCTTTTTC 59.376 47.826 0.00 0.00 0.00 2.29
610 635 3.610911 CCCGATGCTTCTACTCCTTTTT 58.389 45.455 0.00 0.00 0.00 1.94
611 636 2.681097 GCCCGATGCTTCTACTCCTTTT 60.681 50.000 0.00 0.00 36.87 2.27
612 637 1.134371 GCCCGATGCTTCTACTCCTTT 60.134 52.381 0.00 0.00 36.87 3.11
613 638 0.466124 GCCCGATGCTTCTACTCCTT 59.534 55.000 0.00 0.00 36.87 3.36
647 677 0.323725 GGAAGGAAGGAATGGCAGCA 60.324 55.000 0.00 0.00 0.00 4.41
671 701 0.326264 GAAGGCCAAGAGCAGAGGAA 59.674 55.000 5.01 0.00 46.50 3.36
672 702 0.546267 AGAAGGCCAAGAGCAGAGGA 60.546 55.000 5.01 0.00 46.50 3.71
673 703 0.327591 AAGAAGGCCAAGAGCAGAGG 59.672 55.000 5.01 0.00 46.50 3.69
674 704 1.678425 GGAAGAAGGCCAAGAGCAGAG 60.678 57.143 5.01 0.00 46.50 3.35
699 736 2.193248 GGATTCTCGCCTTGGGGG 59.807 66.667 3.89 0.00 36.96 5.40
936 1014 2.350772 GGAAACACAGAAATGCAGACGG 60.351 50.000 0.00 0.00 0.00 4.79
1455 1544 3.249189 TTCTCGCAGGGCTTGGGT 61.249 61.111 13.23 0.00 40.42 4.51
1806 1895 1.164411 CAAGCGACCATTGGCAGTTA 58.836 50.000 1.54 0.00 0.00 2.24
1824 1913 1.968493 GCCCAGGTATCGAGGTAATCA 59.032 52.381 0.00 0.00 0.00 2.57
1869 1958 1.065418 ACCTTTCCAGCCTCAATACGG 60.065 52.381 0.00 0.00 0.00 4.02
1992 2081 6.600032 GGAGATAGTAGCCATTCTCGAGATAA 59.400 42.308 17.44 1.92 36.34 1.75
2013 2102 0.029163 TCCCCCAATAGCCATGGAGA 60.029 55.000 18.40 1.34 40.56 3.71
2226 2315 2.032054 CGCAAGAGACTTGTGCTCAAAA 59.968 45.455 11.14 0.00 43.02 2.44
2478 2730 3.936372 ACAACATAGATATCCGTCCCG 57.064 47.619 0.00 0.00 0.00 5.14
2567 2821 3.319689 GCTGAGTACCCATCTCTAACTCC 59.680 52.174 0.00 0.00 36.56 3.85
2568 2822 4.211920 AGCTGAGTACCCATCTCTAACTC 58.788 47.826 0.00 0.00 37.64 3.01
2569 2823 4.258457 AGCTGAGTACCCATCTCTAACT 57.742 45.455 0.00 0.00 33.59 2.24
2570 2824 5.595133 AGTTAGCTGAGTACCCATCTCTAAC 59.405 44.000 0.00 12.31 35.77 2.34
2571 2825 5.594725 CAGTTAGCTGAGTACCCATCTCTAA 59.405 44.000 0.00 0.00 45.28 2.10
2572 2826 5.133941 CAGTTAGCTGAGTACCCATCTCTA 58.866 45.833 0.00 0.00 45.28 2.43
2573 2827 3.957497 CAGTTAGCTGAGTACCCATCTCT 59.043 47.826 0.00 0.00 45.28 3.10
2574 2828 3.491792 GCAGTTAGCTGAGTACCCATCTC 60.492 52.174 11.20 0.00 45.28 2.75
2575 2829 2.432510 GCAGTTAGCTGAGTACCCATCT 59.567 50.000 11.20 0.00 45.28 2.90
2576 2830 2.827652 GCAGTTAGCTGAGTACCCATC 58.172 52.381 11.20 0.00 45.28 3.51
2577 2831 2.990066 GCAGTTAGCTGAGTACCCAT 57.010 50.000 11.20 0.00 45.28 4.00
2605 2879 9.660180 CTAAATAGGAAACCCATAGAGCTATTC 57.340 37.037 0.00 0.00 0.00 1.75
2654 2950 9.305925 CAAATATCTTTTAGGGAAGTGAAATGC 57.694 33.333 0.00 0.00 0.00 3.56
2679 2975 5.069318 TGAAGAACCAATAAGCACATGACA 58.931 37.500 0.00 0.00 0.00 3.58
2742 3041 3.106054 ACCAATGGCAATGCAAATAGGA 58.894 40.909 7.79 0.00 0.00 2.94
2807 3117 3.253188 CAGTTTCGAGAAATTCCAGCCAA 59.747 43.478 1.35 0.00 32.36 4.52
2809 3119 2.814336 ACAGTTTCGAGAAATTCCAGCC 59.186 45.455 1.35 0.00 32.36 4.85
2817 3127 2.367567 AGGCAGGTACAGTTTCGAGAAA 59.632 45.455 0.00 0.00 0.00 2.52
2819 3129 1.272490 CAGGCAGGTACAGTTTCGAGA 59.728 52.381 0.00 0.00 0.00 4.04
2885 3203 5.003160 TGATGTATTGCATACCAGCCATAC 58.997 41.667 0.00 0.00 41.16 2.39
2892 3210 6.098679 GCAAAAACTGATGTATTGCATACCA 58.901 36.000 4.10 0.00 43.05 3.25
2893 3211 5.229887 CGCAAAAACTGATGTATTGCATACC 59.770 40.000 9.16 0.00 43.38 2.73
2894 3212 5.799936 ACGCAAAAACTGATGTATTGCATAC 59.200 36.000 9.16 0.00 43.38 2.39
2895 3213 5.948588 ACGCAAAAACTGATGTATTGCATA 58.051 33.333 9.16 0.00 43.38 3.14
2896 3214 4.808558 ACGCAAAAACTGATGTATTGCAT 58.191 34.783 9.16 0.00 43.38 3.96
2916 3240 8.339714 TCAATTGGTTTAGAACTTCAAAGTACG 58.660 33.333 5.42 0.00 38.57 3.67
2955 3279 7.041372 TGACTAAATTTGGTTAGAACTGACAGC 60.041 37.037 8.72 0.00 35.45 4.40
3037 3373 3.777465 AGAAGAGACGCGCTTTACATA 57.223 42.857 5.73 0.00 0.00 2.29
3038 3374 2.656560 AGAAGAGACGCGCTTTACAT 57.343 45.000 5.73 0.00 0.00 2.29
3039 3375 2.030185 AGAAGAAGAGACGCGCTTTACA 60.030 45.455 5.73 0.00 0.00 2.41
3040 3376 2.597520 AGAAGAAGAGACGCGCTTTAC 58.402 47.619 5.73 0.00 0.00 2.01
3041 3377 2.987149 CAAGAAGAAGAGACGCGCTTTA 59.013 45.455 5.73 0.00 0.00 1.85
3042 3378 1.795286 CAAGAAGAAGAGACGCGCTTT 59.205 47.619 5.73 0.00 0.00 3.51
3043 3379 1.269831 ACAAGAAGAAGAGACGCGCTT 60.270 47.619 5.73 0.37 0.00 4.68
3044 3380 0.315568 ACAAGAAGAAGAGACGCGCT 59.684 50.000 5.73 3.91 0.00 5.92
3045 3381 1.136502 CAACAAGAAGAAGAGACGCGC 60.137 52.381 5.73 0.00 0.00 6.86
3046 3382 2.128035 ACAACAAGAAGAAGAGACGCG 58.872 47.619 3.53 3.53 0.00 6.01
3047 3383 4.149046 CAGTACAACAAGAAGAAGAGACGC 59.851 45.833 0.00 0.00 0.00 5.19
3048 3384 5.282510 ACAGTACAACAAGAAGAAGAGACG 58.717 41.667 0.00 0.00 0.00 4.18
3051 3387 6.696148 ACGTAACAGTACAACAAGAAGAAGAG 59.304 38.462 0.00 0.00 0.00 2.85
3061 3406 6.724694 ACTGAAAAACGTAACAGTACAACA 57.275 33.333 12.64 0.00 40.96 3.33
3066 3411 8.931385 ACTAGAAACTGAAAAACGTAACAGTA 57.069 30.769 13.97 2.66 41.73 2.74
3123 3470 6.206634 CACTAGGTCCAAAGCATAGTCAAAAA 59.793 38.462 0.00 0.00 0.00 1.94
3154 3501 7.118390 GTGATTGTAGCATAGTCAAGACAAACT 59.882 37.037 2.72 0.00 31.19 2.66
3231 3589 3.702045 AGATGCAGAACTCTGGTACTACC 59.298 47.826 8.74 0.00 43.94 3.18
3238 3596 3.118847 TGCTAAGAGATGCAGAACTCTGG 60.119 47.826 17.38 14.56 43.94 3.86
3239 3597 4.120792 TGCTAAGAGATGCAGAACTCTG 57.879 45.455 17.38 2.17 46.40 3.35
3317 3682 2.280389 CCGACCAGATCCATGGCG 60.280 66.667 6.96 2.45 44.80 5.69


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

AutoCloner maintained by Alex Coulton.