Multiple sequence alignment - TraesCS6B01G167600

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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 TraesCS6B01G167600 chr6B 100.000 2792 0 0 1 2792 176250862 176248071 0.000000e+00 5156.0
1 TraesCS6B01G167600 chr6B 94.351 2248 91 23 567 2792 176164310 176162077 0.000000e+00 3415.0
2 TraesCS6B01G167600 chr6B 94.343 2245 91 23 568 2790 176188186 176185956 0.000000e+00 3410.0
3 TraesCS6B01G167600 chr6B 92.359 1793 100 25 567 2338 176140099 176138323 0.000000e+00 2518.0
4 TraesCS6B01G167600 chr6B 96.450 676 24 0 986 1661 176132691 176132016 0.000000e+00 1116.0
5 TraesCS6B01G167600 chr6B 82.667 300 45 7 246 540 42350091 42350388 2.760000e-65 259.0
6 TraesCS6B01G167600 chr6B 81.387 274 36 13 2528 2792 139423192 139422925 2.820000e-50 209.0
7 TraesCS6B01G167600 chrUn 94.617 2248 85 23 567 2792 78307152 78309385 0.000000e+00 3448.0
8 TraesCS6B01G167600 chrUn 94.440 2248 88 25 567 2792 78290334 78292566 0.000000e+00 3424.0
9 TraesCS6B01G167600 chrUn 83.452 701 78 26 567 1244 356274778 356274093 3.950000e-173 617.0
10 TraesCS6B01G167600 chrUn 83.286 700 79 26 568 1244 379822007 379822691 6.610000e-171 610.0
11 TraesCS6B01G167600 chrUn 83.797 395 57 7 2402 2792 87856613 87856222 4.390000e-98 368.0
12 TraesCS6B01G167600 chr6A 90.523 1836 117 17 544 2326 111531921 111530090 0.000000e+00 2374.0
13 TraesCS6B01G167600 chr6A 88.175 1167 107 21 713 1868 111449872 111448726 0.000000e+00 1362.0
14 TraesCS6B01G167600 chr6A 82.450 302 45 8 243 539 29213055 29213353 9.920000e-65 257.0
15 TraesCS6B01G167600 chr6A 89.116 147 16 0 1866 2012 111448568 111448422 1.710000e-42 183.0
16 TraesCS6B01G167600 chr6A 82.682 179 17 5 2147 2311 111447249 111447071 2.240000e-31 147.0
17 TraesCS6B01G167600 chr6A 81.657 169 13 6 104 255 111532068 111531901 1.050000e-24 124.0
18 TraesCS6B01G167600 chr6A 80.488 123 20 4 2332 2453 575245587 575245706 1.060000e-14 91.6
19 TraesCS6B01G167600 chr6D 88.995 1463 123 27 568 2012 91821179 91819737 0.000000e+00 1775.0
20 TraesCS6B01G167600 chr6D 92.263 853 40 12 551 1382 91831232 91830385 0.000000e+00 1186.0
21 TraesCS6B01G167600 chr6D 93.469 735 38 4 1421 2153 91830126 91829400 0.000000e+00 1083.0
22 TraesCS6B01G167600 chr6D 84.239 184 15 10 2139 2308 91816667 91816484 1.720000e-37 167.0
23 TraesCS6B01G167600 chr6D 91.525 118 10 0 2209 2326 91823097 91822980 2.230000e-36 163.0
24 TraesCS6B01G167600 chr5B 89.462 465 44 5 2331 2792 678447357 678447819 1.440000e-162 582.0
25 TraesCS6B01G167600 chr5B 83.278 299 44 6 246 539 44041098 44041395 1.270000e-68 270.0
26 TraesCS6B01G167600 chr5B 83.278 299 44 6 246 539 482295337 482295634 1.270000e-68 270.0
27 TraesCS6B01G167600 chr7B 84.281 299 41 6 246 539 431386016 431385719 1.270000e-73 287.0
28 TraesCS6B01G167600 chr7B 82.609 299 47 5 245 539 617830041 617829744 2.760000e-65 259.0
29 TraesCS6B01G167600 chr4A 82.838 303 44 8 243 539 719076176 719076476 5.930000e-67 265.0
30 TraesCS6B01G167600 chr1B 82.828 297 47 4 246 539 371439993 371440288 2.130000e-66 263.0
31 TraesCS6B01G167600 chr1B 84.774 243 32 5 2332 2572 92539670 92539431 3.590000e-59 239.0
32 TraesCS6B01G167600 chr7A 82.609 299 45 7 246 539 732945997 732945701 9.920000e-65 257.0
33 TraesCS6B01G167600 chr7A 80.952 126 20 4 2332 2456 158297972 158297850 2.290000e-16 97.1
34 TraesCS6B01G167600 chr3B 75.636 472 93 19 2334 2792 741395598 741395136 6.060000e-52 215.0
35 TraesCS6B01G167600 chr2B 81.362 279 36 13 2523 2792 652611998 652611727 2.180000e-51 213.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G167600 chr6B 176248071 176250862 2791 True 5156.000000 5156 100.000000 1 2792 1 chr6B.!!$R6 2791
1 TraesCS6B01G167600 chr6B 176162077 176164310 2233 True 3415.000000 3415 94.351000 567 2792 1 chr6B.!!$R4 2225
2 TraesCS6B01G167600 chr6B 176185956 176188186 2230 True 3410.000000 3410 94.343000 568 2790 1 chr6B.!!$R5 2222
3 TraesCS6B01G167600 chr6B 176138323 176140099 1776 True 2518.000000 2518 92.359000 567 2338 1 chr6B.!!$R3 1771
4 TraesCS6B01G167600 chr6B 176132016 176132691 675 True 1116.000000 1116 96.450000 986 1661 1 chr6B.!!$R2 675
5 TraesCS6B01G167600 chrUn 78307152 78309385 2233 False 3448.000000 3448 94.617000 567 2792 1 chrUn.!!$F2 2225
6 TraesCS6B01G167600 chrUn 78290334 78292566 2232 False 3424.000000 3424 94.440000 567 2792 1 chrUn.!!$F1 2225
7 TraesCS6B01G167600 chrUn 356274093 356274778 685 True 617.000000 617 83.452000 567 1244 1 chrUn.!!$R2 677
8 TraesCS6B01G167600 chrUn 379822007 379822691 684 False 610.000000 610 83.286000 568 1244 1 chrUn.!!$F3 676
9 TraesCS6B01G167600 chr6A 111530090 111532068 1978 True 1249.000000 2374 86.090000 104 2326 2 chr6A.!!$R2 2222
10 TraesCS6B01G167600 chr6A 111447071 111449872 2801 True 564.000000 1362 86.657667 713 2311 3 chr6A.!!$R1 1598
11 TraesCS6B01G167600 chr6D 91829400 91831232 1832 True 1134.500000 1186 92.866000 551 2153 2 chr6D.!!$R2 1602
12 TraesCS6B01G167600 chr6D 91816484 91823097 6613 True 701.666667 1775 88.253000 568 2326 3 chr6D.!!$R1 1758

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
356 371 0.098025 CTTCGAGAGAGTGAGTCGGC 59.902 60.0 0.0 0.0 43.69 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2493 7344 0.966875 GTTGGCCCATGCATCAGTCA 60.967 55.0 0.0 0.0 40.13 3.41 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
33 34 2.044946 CGGCCAAGGGGAAAGGAG 60.045 66.667 2.24 0.00 35.59 3.69
34 35 2.907179 CGGCCAAGGGGAAAGGAGT 61.907 63.158 2.24 0.00 35.59 3.85
35 36 1.304464 GGCCAAGGGGAAAGGAGTG 60.304 63.158 0.00 0.00 35.59 3.51
36 37 1.304464 GCCAAGGGGAAAGGAGTGG 60.304 63.158 0.00 0.00 35.59 4.00
37 38 1.384191 CCAAGGGGAAAGGAGTGGG 59.616 63.158 0.00 0.00 35.59 4.61
39 40 2.907179 AAGGGGAAAGGAGTGGGCG 61.907 63.158 0.00 0.00 0.00 6.13
40 41 4.426313 GGGGAAAGGAGTGGGCGG 62.426 72.222 0.00 0.00 0.00 6.13
41 42 3.647771 GGGAAAGGAGTGGGCGGT 61.648 66.667 0.00 0.00 0.00 5.68
42 43 2.434774 GGAAAGGAGTGGGCGGTT 59.565 61.111 0.00 0.00 0.00 4.44
43 44 1.971695 GGAAAGGAGTGGGCGGTTG 60.972 63.158 0.00 0.00 0.00 3.77
44 45 1.971695 GAAAGGAGTGGGCGGTTGG 60.972 63.158 0.00 0.00 0.00 3.77
45 46 3.507377 AAAGGAGTGGGCGGTTGGG 62.507 63.158 0.00 0.00 0.00 4.12
55 56 2.744709 CGGTTGGGCGGGTGTTAG 60.745 66.667 0.00 0.00 0.00 2.34
56 57 2.433004 GGTTGGGCGGGTGTTAGT 59.567 61.111 0.00 0.00 0.00 2.24
57 58 1.969589 GGTTGGGCGGGTGTTAGTG 60.970 63.158 0.00 0.00 0.00 2.74
58 59 1.969589 GTTGGGCGGGTGTTAGTGG 60.970 63.158 0.00 0.00 0.00 4.00
63 64 4.011517 CGGGTGTTAGTGGGCGGT 62.012 66.667 0.00 0.00 0.00 5.68
64 65 2.433004 GGGTGTTAGTGGGCGGTT 59.567 61.111 0.00 0.00 0.00 4.44
65 66 1.673337 GGGTGTTAGTGGGCGGTTC 60.673 63.158 0.00 0.00 0.00 3.62
67 68 0.609662 GGTGTTAGTGGGCGGTTCTA 59.390 55.000 0.00 0.00 0.00 2.10
68 69 1.405121 GGTGTTAGTGGGCGGTTCTAG 60.405 57.143 0.00 0.00 0.00 2.43
69 70 0.899720 TGTTAGTGGGCGGTTCTAGG 59.100 55.000 0.00 0.00 0.00 3.02
70 71 1.188863 GTTAGTGGGCGGTTCTAGGA 58.811 55.000 0.00 0.00 0.00 2.94
71 72 1.551883 GTTAGTGGGCGGTTCTAGGAA 59.448 52.381 0.00 0.00 0.00 3.36
72 73 1.481871 TAGTGGGCGGTTCTAGGAAG 58.518 55.000 0.00 0.00 0.00 3.46
73 74 0.252103 AGTGGGCGGTTCTAGGAAGA 60.252 55.000 0.00 0.00 0.00 2.87
74 75 0.611714 GTGGGCGGTTCTAGGAAGAA 59.388 55.000 0.00 0.00 39.47 2.52
77 78 1.763545 GGGCGGTTCTAGGAAGAAGAT 59.236 52.381 0.00 0.00 42.40 2.40
78 79 2.483889 GGGCGGTTCTAGGAAGAAGATG 60.484 54.545 0.00 0.00 42.40 2.90
79 80 2.431057 GGCGGTTCTAGGAAGAAGATGA 59.569 50.000 0.00 0.00 42.40 2.92
82 83 4.620803 GCGGTTCTAGGAAGAAGATGAACA 60.621 45.833 0.00 0.00 42.40 3.18
83 84 4.865365 CGGTTCTAGGAAGAAGATGAACAC 59.135 45.833 0.00 0.00 42.40 3.32
84 85 5.336849 CGGTTCTAGGAAGAAGATGAACACT 60.337 44.000 0.00 0.00 42.40 3.55
85 86 6.127703 CGGTTCTAGGAAGAAGATGAACACTA 60.128 42.308 0.00 0.00 42.40 2.74
88 89 7.962995 TCTAGGAAGAAGATGAACACTACAT 57.037 36.000 0.00 0.00 0.00 2.29
89 90 8.001881 TCTAGGAAGAAGATGAACACTACATC 57.998 38.462 0.00 0.00 42.81 3.06
98 99 5.837437 GATGAACACTACATCTAGTCAGGG 58.163 45.833 0.00 0.00 40.36 4.45
99 100 4.023980 TGAACACTACATCTAGTCAGGGG 58.976 47.826 0.00 0.00 30.03 4.79
100 101 2.389715 ACACTACATCTAGTCAGGGGC 58.610 52.381 0.00 0.00 30.03 5.80
102 103 1.214673 ACTACATCTAGTCAGGGGCGA 59.785 52.381 0.00 0.00 0.00 5.54
142 143 5.362556 ACATGAGTTGGATTGAACGAAAG 57.637 39.130 0.00 0.00 0.00 2.62
154 155 1.838568 AACGAAAGCGACGGAAAGCC 61.839 55.000 0.00 0.00 41.64 4.35
157 158 0.521735 GAAAGCGACGGAAAGCCAAT 59.478 50.000 0.00 0.00 0.00 3.16
159 160 1.369625 AAGCGACGGAAAGCCAATAG 58.630 50.000 0.00 0.00 0.00 1.73
160 161 0.462047 AGCGACGGAAAGCCAATAGG 60.462 55.000 0.00 0.00 38.23 2.57
163 164 1.933853 CGACGGAAAGCCAATAGGAAG 59.066 52.381 0.00 0.00 36.89 3.46
164 165 1.671328 GACGGAAAGCCAATAGGAAGC 59.329 52.381 0.00 0.00 36.89 3.86
167 168 2.159379 CGGAAAGCCAATAGGAAGCAAC 60.159 50.000 0.00 0.00 36.89 4.17
170 171 0.618458 AGCCAATAGGAAGCAACCGA 59.382 50.000 0.00 0.00 36.89 4.69
171 172 1.212935 AGCCAATAGGAAGCAACCGAT 59.787 47.619 0.00 0.00 36.89 4.18
172 173 2.024414 GCCAATAGGAAGCAACCGATT 58.976 47.619 2.75 2.75 36.09 3.34
174 175 3.630312 GCCAATAGGAAGCAACCGATTTA 59.370 43.478 5.19 0.00 34.09 1.40
175 176 4.097286 GCCAATAGGAAGCAACCGATTTAA 59.903 41.667 5.19 0.00 34.09 1.52
185 191 4.080526 AGCAACCGATTTAATAGGTGGTCT 60.081 41.667 10.36 6.62 38.35 3.85
246 261 2.154462 CAGTGACAAAAGAGGCGGATT 58.846 47.619 0.00 0.00 0.00 3.01
248 263 3.004734 CAGTGACAAAAGAGGCGGATTTT 59.995 43.478 0.00 0.00 0.00 1.82
249 264 3.636764 AGTGACAAAAGAGGCGGATTTTT 59.363 39.130 0.00 0.00 0.00 1.94
272 287 8.938047 TTTTTAACATAGTACAAAGTAAGCGC 57.062 30.769 0.00 0.00 0.00 5.92
273 288 7.894376 TTTAACATAGTACAAAGTAAGCGCT 57.106 32.000 2.64 2.64 0.00 5.92
274 289 7.515957 TTAACATAGTACAAAGTAAGCGCTC 57.484 36.000 12.06 0.00 0.00 5.03
275 290 5.068234 ACATAGTACAAAGTAAGCGCTCA 57.932 39.130 12.06 0.00 0.00 4.26
276 291 5.661458 ACATAGTACAAAGTAAGCGCTCAT 58.339 37.500 12.06 0.00 0.00 2.90
277 292 6.802608 ACATAGTACAAAGTAAGCGCTCATA 58.197 36.000 12.06 0.00 0.00 2.15
278 293 7.434492 ACATAGTACAAAGTAAGCGCTCATAT 58.566 34.615 12.06 0.00 0.00 1.78
280 295 8.851416 CATAGTACAAAGTAAGCGCTCATATAC 58.149 37.037 12.06 9.92 0.00 1.47
281 296 6.802608 AGTACAAAGTAAGCGCTCATATACA 58.197 36.000 12.06 0.00 0.00 2.29
282 297 7.434492 AGTACAAAGTAAGCGCTCATATACAT 58.566 34.615 12.06 0.00 0.00 2.29
283 298 6.530913 ACAAAGTAAGCGCTCATATACATG 57.469 37.500 12.06 14.47 0.00 3.21
290 305 3.559530 CGCTCATATACATGCGCATAC 57.440 47.619 24.84 3.31 41.94 2.39
291 306 2.923020 CGCTCATATACATGCGCATACA 59.077 45.455 24.84 14.18 41.94 2.29
292 307 3.241773 CGCTCATATACATGCGCATACAC 60.242 47.826 24.84 4.36 41.94 2.90
293 308 3.928992 GCTCATATACATGCGCATACACT 59.071 43.478 24.84 10.63 41.55 3.55
294 309 4.032217 GCTCATATACATGCGCATACACTC 59.968 45.833 24.84 2.68 41.55 3.51
296 311 4.923281 TCATATACATGCGCATACACTCAC 59.077 41.667 24.84 0.00 31.73 3.51
297 312 1.934589 TACATGCGCATACACTCACC 58.065 50.000 24.84 0.00 0.00 4.02
299 314 0.462581 CATGCGCATACACTCACCCT 60.463 55.000 24.84 0.00 0.00 4.34
302 317 1.202521 TGCGCATACACTCACCCTATG 60.203 52.381 5.66 0.00 0.00 2.23
303 318 1.068588 GCGCATACACTCACCCTATGA 59.931 52.381 0.30 0.00 35.45 2.15
305 320 3.123804 CGCATACACTCACCCTATGAAC 58.876 50.000 0.00 0.00 36.69 3.18
306 321 3.123804 GCATACACTCACCCTATGAACG 58.876 50.000 0.00 0.00 36.69 3.95
307 322 2.953466 TACACTCACCCTATGAACGC 57.047 50.000 0.00 0.00 36.69 4.84
308 323 0.973632 ACACTCACCCTATGAACGCA 59.026 50.000 0.00 0.00 36.69 5.24
309 324 1.337823 ACACTCACCCTATGAACGCAC 60.338 52.381 0.00 0.00 36.69 5.34
310 325 0.108804 ACTCACCCTATGAACGCACG 60.109 55.000 0.00 0.00 36.69 5.34
311 326 1.421410 CTCACCCTATGAACGCACGC 61.421 60.000 0.00 0.00 36.69 5.34
314 329 1.739929 CCCTATGAACGCACGCACA 60.740 57.895 0.00 0.00 0.00 4.57
315 330 1.419922 CCTATGAACGCACGCACAC 59.580 57.895 0.00 0.00 0.00 3.82
316 331 1.288419 CCTATGAACGCACGCACACA 61.288 55.000 0.00 0.00 0.00 3.72
317 332 0.179250 CTATGAACGCACGCACACAC 60.179 55.000 0.00 0.00 0.00 3.82
318 333 0.876342 TATGAACGCACGCACACACA 60.876 50.000 0.00 0.00 0.00 3.72
319 334 2.350760 GAACGCACGCACACACAC 60.351 61.111 0.00 0.00 0.00 3.82
320 335 3.783588 GAACGCACGCACACACACC 62.784 63.158 0.00 0.00 0.00 4.16
323 338 2.280524 GCACGCACACACACCCTA 60.281 61.111 0.00 0.00 0.00 3.53
324 339 2.604174 GCACGCACACACACCCTAC 61.604 63.158 0.00 0.00 0.00 3.18
325 340 1.959226 CACGCACACACACCCTACC 60.959 63.158 0.00 0.00 0.00 3.18
326 341 2.358247 CGCACACACACCCTACCC 60.358 66.667 0.00 0.00 0.00 3.69
328 343 1.454539 GCACACACACCCTACCCTT 59.545 57.895 0.00 0.00 0.00 3.95
331 346 2.939640 GCACACACACCCTACCCTTATG 60.940 54.545 0.00 0.00 0.00 1.90
332 347 2.569853 CACACACACCCTACCCTTATGA 59.430 50.000 0.00 0.00 0.00 2.15
333 348 3.008594 CACACACACCCTACCCTTATGAA 59.991 47.826 0.00 0.00 0.00 2.57
334 349 3.008704 ACACACACCCTACCCTTATGAAC 59.991 47.826 0.00 0.00 0.00 3.18
335 350 3.008594 CACACACCCTACCCTTATGAACA 59.991 47.826 0.00 0.00 0.00 3.18
337 352 2.574824 ACACCCTACCCTTATGAACACC 59.425 50.000 0.00 0.00 0.00 4.16
338 353 2.844348 CACCCTACCCTTATGAACACCT 59.156 50.000 0.00 0.00 0.00 4.00
339 354 3.265995 CACCCTACCCTTATGAACACCTT 59.734 47.826 0.00 0.00 0.00 3.50
340 355 3.522343 ACCCTACCCTTATGAACACCTTC 59.478 47.826 0.00 0.00 0.00 3.46
341 356 3.431766 CCCTACCCTTATGAACACCTTCG 60.432 52.174 0.00 0.00 0.00 3.79
342 357 3.449737 CCTACCCTTATGAACACCTTCGA 59.550 47.826 0.00 0.00 0.00 3.71
344 359 3.170717 ACCCTTATGAACACCTTCGAGA 58.829 45.455 0.00 0.00 0.00 4.04
346 361 3.447586 CCCTTATGAACACCTTCGAGAGA 59.552 47.826 0.00 0.00 39.20 3.10
348 363 4.158764 CCTTATGAACACCTTCGAGAGAGT 59.841 45.833 0.00 0.00 43.69 3.24
349 364 3.584406 ATGAACACCTTCGAGAGAGTG 57.416 47.619 5.10 5.10 43.69 3.51
353 368 2.156098 ACACCTTCGAGAGAGTGAGTC 58.844 52.381 11.58 0.00 43.69 3.36
354 369 1.129624 CACCTTCGAGAGAGTGAGTCG 59.870 57.143 1.32 0.00 43.69 4.18
355 370 0.730265 CCTTCGAGAGAGTGAGTCGG 59.270 60.000 0.00 0.00 43.69 4.79
356 371 0.098025 CTTCGAGAGAGTGAGTCGGC 59.902 60.000 0.00 0.00 43.69 5.54
359 374 1.134491 TCGAGAGAGTGAGTCGGCATA 60.134 52.381 0.00 0.00 34.43 3.14
362 377 2.881513 GAGAGAGTGAGTCGGCATATCA 59.118 50.000 0.00 0.00 0.00 2.15
364 379 3.505680 AGAGAGTGAGTCGGCATATCATC 59.494 47.826 0.00 0.00 0.00 2.92
365 380 3.495331 AGAGTGAGTCGGCATATCATCT 58.505 45.455 0.00 0.00 0.00 2.90
366 381 3.894427 AGAGTGAGTCGGCATATCATCTT 59.106 43.478 0.00 0.00 0.00 2.40
368 383 3.638627 AGTGAGTCGGCATATCATCTTGA 59.361 43.478 0.00 0.00 0.00 3.02
369 384 4.282957 AGTGAGTCGGCATATCATCTTGAT 59.717 41.667 0.00 0.00 40.72 2.57
373 388 7.332926 GTGAGTCGGCATATCATCTTGATATTT 59.667 37.037 7.17 0.00 45.10 1.40
374 389 7.879677 TGAGTCGGCATATCATCTTGATATTTT 59.120 33.333 7.17 0.00 45.10 1.82
376 391 9.896645 AGTCGGCATATCATCTTGATATTTTAT 57.103 29.630 7.17 0.00 45.10 1.40
377 392 9.926751 GTCGGCATATCATCTTGATATTTTATG 57.073 33.333 7.17 1.41 45.10 1.90
378 393 9.889128 TCGGCATATCATCTTGATATTTTATGA 57.111 29.630 7.17 0.00 45.10 2.15
391 406 8.534333 TGATATTTTATGAAGTCATCGTAGGC 57.466 34.615 0.00 0.00 37.76 3.93
393 408 4.380841 TTTATGAAGTCATCGTAGGCGT 57.619 40.909 0.00 0.00 37.76 5.68
394 409 2.493713 ATGAAGTCATCGTAGGCGTC 57.506 50.000 0.00 0.00 39.49 5.19
395 410 1.460504 TGAAGTCATCGTAGGCGTCT 58.539 50.000 0.00 0.00 39.49 4.18
397 412 0.377554 AAGTCATCGTAGGCGTCTCG 59.622 55.000 0.00 0.00 39.49 4.04
398 413 0.743701 AGTCATCGTAGGCGTCTCGT 60.744 55.000 0.00 0.00 39.49 4.18
399 414 0.933097 GTCATCGTAGGCGTCTCGTA 59.067 55.000 0.00 0.00 39.49 3.43
400 415 1.070710 GTCATCGTAGGCGTCTCGTAG 60.071 57.143 0.00 0.00 39.49 3.51
401 416 0.935898 CATCGTAGGCGTCTCGTAGT 59.064 55.000 0.00 0.00 39.49 2.73
403 418 1.142185 TCGTAGGCGTCTCGTAGTCG 61.142 60.000 0.00 0.00 39.49 4.18
404 419 1.142185 CGTAGGCGTCTCGTAGTCGA 61.142 60.000 0.00 0.00 44.12 4.20
405 420 1.216122 GTAGGCGTCTCGTAGTCGAT 58.784 55.000 0.00 0.00 45.21 3.59
406 421 1.070710 GTAGGCGTCTCGTAGTCGATG 60.071 57.143 0.00 0.00 45.21 3.84
407 422 0.461516 AGGCGTCTCGTAGTCGATGA 60.462 55.000 0.00 0.00 45.21 2.92
408 423 0.376152 GGCGTCTCGTAGTCGATGAA 59.624 55.000 0.00 0.00 45.21 2.57
409 424 1.202110 GGCGTCTCGTAGTCGATGAAA 60.202 52.381 0.00 0.00 45.21 2.69
410 425 2.512885 GCGTCTCGTAGTCGATGAAAA 58.487 47.619 0.00 0.00 45.21 2.29
411 426 2.912967 GCGTCTCGTAGTCGATGAAAAA 59.087 45.455 0.00 0.00 45.21 1.94
430 445 3.771577 AAATCTTCTCCCACTGAACGT 57.228 42.857 0.00 0.00 0.00 3.99
431 446 2.751166 ATCTTCTCCCACTGAACGTG 57.249 50.000 0.00 0.00 43.41 4.49
435 450 2.743636 TCTCCCACTGAACGTGAATC 57.256 50.000 0.00 0.00 46.81 2.52
436 451 1.067846 TCTCCCACTGAACGTGAATCG 60.068 52.381 0.00 0.00 46.81 3.34
438 453 1.635663 CCCACTGAACGTGAATCGCC 61.636 60.000 0.00 0.00 46.81 5.54
439 454 1.416049 CACTGAACGTGAATCGCCG 59.584 57.895 0.00 0.00 46.81 6.46
440 455 1.736645 ACTGAACGTGAATCGCCGG 60.737 57.895 0.00 0.00 44.19 6.13
441 456 1.445410 CTGAACGTGAATCGCCGGA 60.445 57.895 5.05 0.00 44.19 5.14
442 457 1.005984 TGAACGTGAATCGCCGGAA 60.006 52.632 5.05 0.00 44.19 4.30
444 459 0.725117 GAACGTGAATCGCCGGAAAT 59.275 50.000 5.05 0.00 44.19 2.17
446 461 1.297598 CGTGAATCGCCGGAAATGC 60.298 57.895 5.05 0.00 0.00 3.56
447 462 1.705337 CGTGAATCGCCGGAAATGCT 61.705 55.000 5.05 0.00 0.00 3.79
448 463 0.248215 GTGAATCGCCGGAAATGCTG 60.248 55.000 5.05 0.00 0.00 4.41
449 464 0.392327 TGAATCGCCGGAAATGCTGA 60.392 50.000 5.05 0.00 0.00 4.26
450 465 0.732571 GAATCGCCGGAAATGCTGAA 59.267 50.000 5.05 0.00 0.00 3.02
453 468 2.031258 TCGCCGGAAATGCTGAAATA 57.969 45.000 5.05 0.00 0.00 1.40
454 469 2.360844 TCGCCGGAAATGCTGAAATAA 58.639 42.857 5.05 0.00 0.00 1.40
455 470 2.750166 TCGCCGGAAATGCTGAAATAAA 59.250 40.909 5.05 0.00 0.00 1.40
456 471 3.380004 TCGCCGGAAATGCTGAAATAAAT 59.620 39.130 5.05 0.00 0.00 1.40
457 472 3.730715 CGCCGGAAATGCTGAAATAAATC 59.269 43.478 5.05 0.00 0.00 2.17
458 473 4.051237 GCCGGAAATGCTGAAATAAATCC 58.949 43.478 5.05 0.00 0.00 3.01
459 474 4.441356 GCCGGAAATGCTGAAATAAATCCA 60.441 41.667 5.05 0.00 0.00 3.41
460 475 5.284079 CCGGAAATGCTGAAATAAATCCAG 58.716 41.667 0.00 0.00 0.00 3.86
461 476 5.067674 CCGGAAATGCTGAAATAAATCCAGA 59.932 40.000 0.00 0.00 0.00 3.86
462 477 6.405731 CCGGAAATGCTGAAATAAATCCAGAA 60.406 38.462 0.00 0.00 0.00 3.02
478 493 7.553881 AATCCAGAATAAATACGAACACCAG 57.446 36.000 0.00 0.00 0.00 4.00
480 495 5.188163 TCCAGAATAAATACGAACACCAGGA 59.812 40.000 0.00 0.00 0.00 3.86
482 497 6.542370 CCAGAATAAATACGAACACCAGGATT 59.458 38.462 0.00 0.00 0.00 3.01
483 498 7.067008 CCAGAATAAATACGAACACCAGGATTT 59.933 37.037 0.00 0.00 0.00 2.17
484 499 8.458843 CAGAATAAATACGAACACCAGGATTTT 58.541 33.333 0.00 0.00 0.00 1.82
491 506 6.254281 ACGAACACCAGGATTTTAATTCTG 57.746 37.500 4.10 4.10 40.95 3.02
492 507 6.001460 ACGAACACCAGGATTTTAATTCTGA 58.999 36.000 11.54 0.00 43.42 3.27
493 508 6.659242 ACGAACACCAGGATTTTAATTCTGAT 59.341 34.615 11.54 0.00 43.42 2.90
494 509 6.968904 CGAACACCAGGATTTTAATTCTGATG 59.031 38.462 11.54 7.78 43.42 3.07
495 510 7.148255 CGAACACCAGGATTTTAATTCTGATGA 60.148 37.037 11.37 0.00 43.42 2.92
498 513 6.320672 CACCAGGATTTTAATTCTGATGAGCT 59.679 38.462 11.54 0.00 43.42 4.09
500 515 7.718753 ACCAGGATTTTAATTCTGATGAGCTAG 59.281 37.037 11.54 0.00 43.42 3.42
501 516 7.935755 CCAGGATTTTAATTCTGATGAGCTAGA 59.064 37.037 11.54 0.00 43.42 2.43
502 517 8.991026 CAGGATTTTAATTCTGATGAGCTAGAG 58.009 37.037 5.00 0.00 43.42 2.43
503 518 8.932610 AGGATTTTAATTCTGATGAGCTAGAGA 58.067 33.333 0.00 0.00 0.00 3.10
504 519 9.723601 GGATTTTAATTCTGATGAGCTAGAGAT 57.276 33.333 0.00 0.00 0.00 2.75
511 526 9.878667 AATTCTGATGAGCTAGAGATATCATTG 57.121 33.333 5.32 0.00 32.68 2.82
512 527 8.419922 TTCTGATGAGCTAGAGATATCATTGT 57.580 34.615 5.32 0.00 32.68 2.71
513 528 8.054152 TCTGATGAGCTAGAGATATCATTGTC 57.946 38.462 5.32 0.00 32.68 3.18
514 529 7.889600 TCTGATGAGCTAGAGATATCATTGTCT 59.110 37.037 5.32 1.55 32.68 3.41
515 530 8.419922 TGATGAGCTAGAGATATCATTGTCTT 57.580 34.615 5.32 0.00 32.68 3.01
516 531 8.868103 TGATGAGCTAGAGATATCATTGTCTTT 58.132 33.333 5.32 0.00 32.68 2.52
517 532 9.709495 GATGAGCTAGAGATATCATTGTCTTTT 57.291 33.333 5.32 0.00 32.68 2.27
527 542 9.699410 AGATATCATTGTCTTTTTAACCATCCA 57.301 29.630 5.32 0.00 0.00 3.41
530 545 6.754193 TCATTGTCTTTTTAACCATCCAACC 58.246 36.000 0.00 0.00 0.00 3.77
531 546 6.325028 TCATTGTCTTTTTAACCATCCAACCA 59.675 34.615 0.00 0.00 0.00 3.67
532 547 5.523438 TGTCTTTTTAACCATCCAACCAC 57.477 39.130 0.00 0.00 0.00 4.16
533 548 4.956700 TGTCTTTTTAACCATCCAACCACA 59.043 37.500 0.00 0.00 0.00 4.17
534 549 5.600484 TGTCTTTTTAACCATCCAACCACAT 59.400 36.000 0.00 0.00 0.00 3.21
535 550 5.925969 GTCTTTTTAACCATCCAACCACATG 59.074 40.000 0.00 0.00 0.00 3.21
536 551 5.600484 TCTTTTTAACCATCCAACCACATGT 59.400 36.000 0.00 0.00 0.00 3.21
537 552 5.878406 TTTTAACCATCCAACCACATGTT 57.122 34.783 0.00 0.00 37.80 2.71
549 564 1.596603 CACATGTTGTGGCAGAGACA 58.403 50.000 0.00 0.00 44.27 3.41
598 1951 5.237344 GGTATTTTAATCATCTGCTCGCAGT 59.763 40.000 17.53 3.87 43.96 4.40
963 2361 2.072298 GATCTCAGCCTTCACACACAC 58.928 52.381 0.00 0.00 0.00 3.82
964 2362 0.249447 TCTCAGCCTTCACACACACG 60.249 55.000 0.00 0.00 0.00 4.49
1068 2466 2.561478 TTGTTACCAGGGTGAAGCTC 57.439 50.000 0.06 0.00 0.00 4.09
1282 2680 2.754658 CAGCGGACCCCTACGAGT 60.755 66.667 0.00 0.00 0.00 4.18
2493 7344 1.736586 CGCAGAATCGGGCTAGAGT 59.263 57.895 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 3.645268 CTCCTTTCCCCTTGGCCGG 62.645 68.421 0.00 0.00 0.00 6.13
16 17 2.044946 CTCCTTTCCCCTTGGCCG 60.045 66.667 0.00 0.00 0.00 6.13
17 18 1.304464 CACTCCTTTCCCCTTGGCC 60.304 63.158 0.00 0.00 0.00 5.36
18 19 1.304464 CCACTCCTTTCCCCTTGGC 60.304 63.158 0.00 0.00 0.00 4.52
19 20 1.384191 CCCACTCCTTTCCCCTTGG 59.616 63.158 0.00 0.00 0.00 3.61
20 21 1.304464 GCCCACTCCTTTCCCCTTG 60.304 63.158 0.00 0.00 0.00 3.61
24 25 3.205851 AACCGCCCACTCCTTTCCC 62.206 63.158 0.00 0.00 0.00 3.97
27 28 2.115266 CCAACCGCCCACTCCTTT 59.885 61.111 0.00 0.00 0.00 3.11
28 29 3.966543 CCCAACCGCCCACTCCTT 61.967 66.667 0.00 0.00 0.00 3.36
39 40 1.969589 CACTAACACCCGCCCAACC 60.970 63.158 0.00 0.00 0.00 3.77
40 41 1.969589 CCACTAACACCCGCCCAAC 60.970 63.158 0.00 0.00 0.00 3.77
41 42 2.432563 CCACTAACACCCGCCCAA 59.567 61.111 0.00 0.00 0.00 4.12
42 43 3.642503 CCCACTAACACCCGCCCA 61.643 66.667 0.00 0.00 0.00 5.36
46 47 3.540367 AACCGCCCACTAACACCCG 62.540 63.158 0.00 0.00 0.00 5.28
47 48 1.673337 GAACCGCCCACTAACACCC 60.673 63.158 0.00 0.00 0.00 4.61
49 50 1.405121 CCTAGAACCGCCCACTAACAC 60.405 57.143 0.00 0.00 0.00 3.32
50 51 0.899720 CCTAGAACCGCCCACTAACA 59.100 55.000 0.00 0.00 0.00 2.41
51 52 1.188863 TCCTAGAACCGCCCACTAAC 58.811 55.000 0.00 0.00 0.00 2.34
52 53 1.829222 CTTCCTAGAACCGCCCACTAA 59.171 52.381 0.00 0.00 0.00 2.24
53 54 1.006281 TCTTCCTAGAACCGCCCACTA 59.994 52.381 0.00 0.00 0.00 2.74
55 56 0.611714 TTCTTCCTAGAACCGCCCAC 59.388 55.000 0.00 0.00 35.49 4.61
56 57 0.902531 CTTCTTCCTAGAACCGCCCA 59.097 55.000 0.00 0.00 35.49 5.36
57 58 1.192428 TCTTCTTCCTAGAACCGCCC 58.808 55.000 0.00 0.00 35.49 6.13
58 59 2.431057 TCATCTTCTTCCTAGAACCGCC 59.569 50.000 0.00 0.00 35.49 6.13
61 62 6.043854 AGTGTTCATCTTCTTCCTAGAACC 57.956 41.667 0.00 0.00 35.49 3.62
62 63 7.603651 TGTAGTGTTCATCTTCTTCCTAGAAC 58.396 38.462 0.00 0.00 35.49 3.01
63 64 7.776618 TGTAGTGTTCATCTTCTTCCTAGAA 57.223 36.000 0.00 0.00 38.06 2.10
64 65 7.836685 AGATGTAGTGTTCATCTTCTTCCTAGA 59.163 37.037 3.06 0.00 46.39 2.43
65 66 8.006298 AGATGTAGTGTTCATCTTCTTCCTAG 57.994 38.462 3.06 0.00 46.39 3.02
67 68 6.865834 AGATGTAGTGTTCATCTTCTTCCT 57.134 37.500 3.06 0.00 46.39 3.36
68 69 7.777095 ACTAGATGTAGTGTTCATCTTCTTCC 58.223 38.462 12.50 0.00 46.39 3.46
69 70 8.462811 TGACTAGATGTAGTGTTCATCTTCTTC 58.537 37.037 7.36 8.21 46.39 2.87
70 71 8.354711 TGACTAGATGTAGTGTTCATCTTCTT 57.645 34.615 7.36 0.31 46.39 2.52
71 72 7.068103 CCTGACTAGATGTAGTGTTCATCTTCT 59.932 40.741 7.36 0.80 46.39 2.85
72 73 7.199766 CCTGACTAGATGTAGTGTTCATCTTC 58.800 42.308 7.36 7.05 46.39 2.87
73 74 6.097554 CCCTGACTAGATGTAGTGTTCATCTT 59.902 42.308 7.36 0.00 46.39 2.40
77 78 4.023980 CCCCTGACTAGATGTAGTGTTCA 58.976 47.826 7.36 0.00 39.78 3.18
78 79 3.181474 GCCCCTGACTAGATGTAGTGTTC 60.181 52.174 7.36 0.00 39.78 3.18
79 80 2.766828 GCCCCTGACTAGATGTAGTGTT 59.233 50.000 7.36 0.00 39.78 3.32
82 83 1.214673 TCGCCCCTGACTAGATGTAGT 59.785 52.381 1.42 1.42 42.59 2.73
83 84 1.883275 CTCGCCCCTGACTAGATGTAG 59.117 57.143 0.00 0.00 0.00 2.74
84 85 1.478837 CCTCGCCCCTGACTAGATGTA 60.479 57.143 0.00 0.00 0.00 2.29
85 86 0.757188 CCTCGCCCCTGACTAGATGT 60.757 60.000 0.00 0.00 0.00 3.06
88 89 2.279073 CCCTCGCCCCTGACTAGA 59.721 66.667 0.00 0.00 0.00 2.43
89 90 2.840102 CCCCTCGCCCCTGACTAG 60.840 72.222 0.00 0.00 0.00 2.57
90 91 3.352748 TCCCCTCGCCCCTGACTA 61.353 66.667 0.00 0.00 0.00 2.59
95 96 4.806339 CTTCCTCCCCTCGCCCCT 62.806 72.222 0.00 0.00 0.00 4.79
96 97 4.798682 TCTTCCTCCCCTCGCCCC 62.799 72.222 0.00 0.00 0.00 5.80
97 98 2.446802 ATCTTCCTCCCCTCGCCC 60.447 66.667 0.00 0.00 0.00 6.13
98 99 2.812619 CCATCTTCCTCCCCTCGCC 61.813 68.421 0.00 0.00 0.00 5.54
99 100 2.825264 CCATCTTCCTCCCCTCGC 59.175 66.667 0.00 0.00 0.00 5.03
100 101 2.812619 GGCCATCTTCCTCCCCTCG 61.813 68.421 0.00 0.00 0.00 4.63
102 103 1.230281 TTGGCCATCTTCCTCCCCT 60.230 57.895 6.09 0.00 0.00 4.79
142 143 0.461339 TCCTATTGGCTTTCCGTCGC 60.461 55.000 0.00 0.00 34.14 5.19
154 155 7.228706 ACCTATTAAATCGGTTGCTTCCTATTG 59.771 37.037 0.00 0.00 0.00 1.90
157 158 6.053005 CACCTATTAAATCGGTTGCTTCCTA 58.947 40.000 0.00 0.00 0.00 2.94
159 160 4.036380 CCACCTATTAAATCGGTTGCTTCC 59.964 45.833 0.00 0.00 0.00 3.46
160 161 4.638865 ACCACCTATTAAATCGGTTGCTTC 59.361 41.667 0.00 0.00 0.00 3.86
163 164 4.196971 AGACCACCTATTAAATCGGTTGC 58.803 43.478 0.00 0.00 0.00 4.17
164 165 6.753107 AAAGACCACCTATTAAATCGGTTG 57.247 37.500 0.00 0.00 0.00 3.77
174 175 9.884636 GGCATAATTTTAAAAAGACCACCTATT 57.115 29.630 4.44 0.00 0.00 1.73
175 176 9.041354 TGGCATAATTTTAAAAAGACCACCTAT 57.959 29.630 4.44 0.00 0.00 2.57
248 263 8.314143 AGCGCTTACTTTGTACTATGTTAAAA 57.686 30.769 2.64 0.00 0.00 1.52
249 264 7.599621 TGAGCGCTTACTTTGTACTATGTTAAA 59.400 33.333 13.26 0.00 0.00 1.52
250 265 7.092079 TGAGCGCTTACTTTGTACTATGTTAA 58.908 34.615 13.26 0.00 0.00 2.01
251 266 6.623486 TGAGCGCTTACTTTGTACTATGTTA 58.377 36.000 13.26 0.00 0.00 2.41
253 268 5.068234 TGAGCGCTTACTTTGTACTATGT 57.932 39.130 13.26 0.00 0.00 2.29
254 269 7.875316 ATATGAGCGCTTACTTTGTACTATG 57.125 36.000 13.26 0.00 0.00 2.23
255 270 8.573885 TGTATATGAGCGCTTACTTTGTACTAT 58.426 33.333 13.26 2.01 0.00 2.12
256 271 7.933396 TGTATATGAGCGCTTACTTTGTACTA 58.067 34.615 13.26 0.00 0.00 1.82
257 272 6.802608 TGTATATGAGCGCTTACTTTGTACT 58.197 36.000 13.26 0.00 0.00 2.73
258 273 7.502339 CATGTATATGAGCGCTTACTTTGTAC 58.498 38.462 13.26 6.31 36.36 2.90
259 274 6.145534 GCATGTATATGAGCGCTTACTTTGTA 59.854 38.462 13.26 0.00 36.36 2.41
262 277 4.150627 CGCATGTATATGAGCGCTTACTTT 59.849 41.667 13.26 0.00 43.80 2.66
264 279 3.245797 CGCATGTATATGAGCGCTTACT 58.754 45.455 13.26 0.67 43.80 2.24
265 280 3.624726 CGCATGTATATGAGCGCTTAC 57.375 47.619 13.26 10.96 43.80 2.34
272 287 5.061435 GTGAGTGTATGCGCATGTATATGAG 59.939 44.000 32.48 0.87 36.36 2.90
273 288 4.923281 GTGAGTGTATGCGCATGTATATGA 59.077 41.667 32.48 8.02 36.36 2.15
274 289 4.091945 GGTGAGTGTATGCGCATGTATATG 59.908 45.833 32.48 0.00 37.36 1.78
275 290 4.245660 GGTGAGTGTATGCGCATGTATAT 58.754 43.478 32.48 14.31 0.00 0.86
276 291 3.554129 GGGTGAGTGTATGCGCATGTATA 60.554 47.826 32.48 10.12 0.00 1.47
277 292 2.483876 GGTGAGTGTATGCGCATGTAT 58.516 47.619 32.48 15.41 0.00 2.29
278 293 1.472552 GGGTGAGTGTATGCGCATGTA 60.473 52.381 32.48 17.97 0.00 2.29
280 295 0.462581 AGGGTGAGTGTATGCGCATG 60.463 55.000 32.48 0.00 0.00 4.06
281 296 1.119684 TAGGGTGAGTGTATGCGCAT 58.880 50.000 28.23 28.23 0.00 4.73
282 297 1.119684 ATAGGGTGAGTGTATGCGCA 58.880 50.000 14.96 14.96 0.00 6.09
283 298 1.068588 TCATAGGGTGAGTGTATGCGC 59.931 52.381 0.00 0.00 31.80 6.09
286 301 3.123804 GCGTTCATAGGGTGAGTGTATG 58.876 50.000 0.00 0.00 38.29 2.39
287 302 2.764010 TGCGTTCATAGGGTGAGTGTAT 59.236 45.455 0.00 0.00 38.29 2.29
288 303 2.094390 GTGCGTTCATAGGGTGAGTGTA 60.094 50.000 0.00 0.00 38.29 2.90
289 304 0.973632 TGCGTTCATAGGGTGAGTGT 59.026 50.000 0.00 0.00 38.29 3.55
290 305 1.359848 GTGCGTTCATAGGGTGAGTG 58.640 55.000 0.00 0.00 38.29 3.51
291 306 0.108804 CGTGCGTTCATAGGGTGAGT 60.109 55.000 0.00 0.00 38.29 3.41
292 307 1.421410 GCGTGCGTTCATAGGGTGAG 61.421 60.000 0.00 0.00 38.29 3.51
293 308 1.447140 GCGTGCGTTCATAGGGTGA 60.447 57.895 0.00 0.00 34.25 4.02
294 309 1.739929 TGCGTGCGTTCATAGGGTG 60.740 57.895 0.00 0.00 0.00 4.61
296 311 1.739929 TGTGCGTGCGTTCATAGGG 60.740 57.895 0.00 0.00 0.00 3.53
297 312 1.288419 TGTGTGCGTGCGTTCATAGG 61.288 55.000 0.00 0.00 0.00 2.57
299 314 0.876342 TGTGTGTGCGTGCGTTCATA 60.876 50.000 0.00 0.00 0.00 2.15
302 317 2.350760 GTGTGTGTGCGTGCGTTC 60.351 61.111 0.00 0.00 0.00 3.95
303 318 3.871574 GGTGTGTGTGCGTGCGTT 61.872 61.111 0.00 0.00 0.00 4.84
306 321 2.280524 TAGGGTGTGTGTGCGTGC 60.281 61.111 0.00 0.00 0.00 5.34
307 322 1.959226 GGTAGGGTGTGTGTGCGTG 60.959 63.158 0.00 0.00 0.00 5.34
308 323 2.424302 GGTAGGGTGTGTGTGCGT 59.576 61.111 0.00 0.00 0.00 5.24
309 324 2.358247 GGGTAGGGTGTGTGTGCG 60.358 66.667 0.00 0.00 0.00 5.34
310 325 0.688487 TAAGGGTAGGGTGTGTGTGC 59.312 55.000 0.00 0.00 0.00 4.57
311 326 2.569853 TCATAAGGGTAGGGTGTGTGTG 59.430 50.000 0.00 0.00 0.00 3.82
314 329 3.008704 GTGTTCATAAGGGTAGGGTGTGT 59.991 47.826 0.00 0.00 0.00 3.72
315 330 3.606687 GTGTTCATAAGGGTAGGGTGTG 58.393 50.000 0.00 0.00 0.00 3.82
316 331 2.574824 GGTGTTCATAAGGGTAGGGTGT 59.425 50.000 0.00 0.00 0.00 4.16
317 332 2.844348 AGGTGTTCATAAGGGTAGGGTG 59.156 50.000 0.00 0.00 0.00 4.61
318 333 3.216230 AGGTGTTCATAAGGGTAGGGT 57.784 47.619 0.00 0.00 0.00 4.34
319 334 3.431766 CGAAGGTGTTCATAAGGGTAGGG 60.432 52.174 0.00 0.00 32.36 3.53
320 335 3.449737 TCGAAGGTGTTCATAAGGGTAGG 59.550 47.826 0.00 0.00 32.36 3.18
321 336 4.401519 TCTCGAAGGTGTTCATAAGGGTAG 59.598 45.833 0.00 0.00 32.36 3.18
322 337 4.346730 TCTCGAAGGTGTTCATAAGGGTA 58.653 43.478 0.00 0.00 32.36 3.69
323 338 3.170717 TCTCGAAGGTGTTCATAAGGGT 58.829 45.455 0.00 0.00 32.36 4.34
324 339 3.447586 TCTCTCGAAGGTGTTCATAAGGG 59.552 47.826 0.00 0.00 32.36 3.95
325 340 4.158764 ACTCTCTCGAAGGTGTTCATAAGG 59.841 45.833 0.00 0.00 32.36 2.69
326 341 5.098893 CACTCTCTCGAAGGTGTTCATAAG 58.901 45.833 0.00 0.00 32.36 1.73
328 343 4.332828 TCACTCTCTCGAAGGTGTTCATA 58.667 43.478 0.00 0.00 32.36 2.15
331 346 2.554893 ACTCACTCTCTCGAAGGTGTTC 59.445 50.000 0.00 0.00 31.71 3.18
332 347 2.554893 GACTCACTCTCTCGAAGGTGTT 59.445 50.000 0.00 0.00 31.71 3.32
333 348 2.156098 GACTCACTCTCTCGAAGGTGT 58.844 52.381 0.00 0.00 31.71 4.16
334 349 1.129624 CGACTCACTCTCTCGAAGGTG 59.870 57.143 0.00 0.00 0.00 4.00
335 350 1.444836 CGACTCACTCTCTCGAAGGT 58.555 55.000 0.00 0.00 0.00 3.50
337 352 0.098025 GCCGACTCACTCTCTCGAAG 59.902 60.000 0.00 0.00 0.00 3.79
338 353 0.605589 TGCCGACTCACTCTCTCGAA 60.606 55.000 0.00 0.00 0.00 3.71
339 354 0.393132 ATGCCGACTCACTCTCTCGA 60.393 55.000 0.00 0.00 0.00 4.04
340 355 1.300481 TATGCCGACTCACTCTCTCG 58.700 55.000 0.00 0.00 0.00 4.04
341 356 2.881513 TGATATGCCGACTCACTCTCTC 59.118 50.000 0.00 0.00 0.00 3.20
342 357 2.937519 TGATATGCCGACTCACTCTCT 58.062 47.619 0.00 0.00 0.00 3.10
344 359 3.495331 AGATGATATGCCGACTCACTCT 58.505 45.455 0.00 0.00 0.00 3.24
346 361 3.638627 TCAAGATGATATGCCGACTCACT 59.361 43.478 0.00 0.00 0.00 3.41
348 363 4.879197 ATCAAGATGATATGCCGACTCA 57.121 40.909 0.00 0.00 34.88 3.41
349 364 7.840342 AAATATCAAGATGATATGCCGACTC 57.160 36.000 12.30 0.00 46.26 3.36
365 380 8.988934 GCCTACGATGACTTCATAAAATATCAA 58.011 33.333 0.00 0.00 36.57 2.57
366 381 7.328493 CGCCTACGATGACTTCATAAAATATCA 59.672 37.037 0.00 0.00 43.93 2.15
368 383 7.152645 ACGCCTACGATGACTTCATAAAATAT 58.847 34.615 0.00 0.00 43.93 1.28
369 384 6.509656 ACGCCTACGATGACTTCATAAAATA 58.490 36.000 0.00 0.00 43.93 1.40
371 386 4.751060 ACGCCTACGATGACTTCATAAAA 58.249 39.130 0.00 0.00 43.93 1.52
373 388 3.630769 AGACGCCTACGATGACTTCATAA 59.369 43.478 0.00 0.00 43.93 1.90
374 389 3.211865 AGACGCCTACGATGACTTCATA 58.788 45.455 0.00 0.00 43.93 2.15
376 391 1.400846 GAGACGCCTACGATGACTTCA 59.599 52.381 0.00 0.00 43.93 3.02
377 392 1.595003 CGAGACGCCTACGATGACTTC 60.595 57.143 0.00 0.00 43.93 3.01
378 393 0.377554 CGAGACGCCTACGATGACTT 59.622 55.000 0.00 0.00 43.93 3.01
379 394 0.743701 ACGAGACGCCTACGATGACT 60.744 55.000 0.00 0.00 43.93 3.41
381 396 1.215244 CTACGAGACGCCTACGATGA 58.785 55.000 0.00 0.00 43.93 2.92
382 397 0.935898 ACTACGAGACGCCTACGATG 59.064 55.000 0.00 0.00 43.93 3.84
383 398 1.216122 GACTACGAGACGCCTACGAT 58.784 55.000 0.00 0.00 43.93 3.73
384 399 1.142185 CGACTACGAGACGCCTACGA 61.142 60.000 0.00 0.00 41.40 3.43
386 401 2.670635 TCGACTACGAGACGCCTAC 58.329 57.895 0.00 0.00 43.81 3.18
408 423 4.275936 CACGTTCAGTGGGAGAAGATTTTT 59.724 41.667 0.00 0.00 46.77 1.94
409 424 3.815401 CACGTTCAGTGGGAGAAGATTTT 59.185 43.478 0.00 0.00 46.77 1.82
410 425 3.403038 CACGTTCAGTGGGAGAAGATTT 58.597 45.455 0.00 0.00 46.77 2.17
411 426 3.045601 CACGTTCAGTGGGAGAAGATT 57.954 47.619 0.00 0.00 46.77 2.40
412 427 2.751166 CACGTTCAGTGGGAGAAGAT 57.249 50.000 0.00 0.00 46.77 2.40
422 437 1.736645 CCGGCGATTCACGTTCAGT 60.737 57.895 9.30 0.00 44.60 3.41
423 438 1.011968 TTCCGGCGATTCACGTTCAG 61.012 55.000 9.30 0.00 44.60 3.02
424 439 0.600518 TTTCCGGCGATTCACGTTCA 60.601 50.000 9.30 0.00 44.60 3.18
425 440 0.725117 ATTTCCGGCGATTCACGTTC 59.275 50.000 9.30 0.00 44.60 3.95
427 442 1.977594 GCATTTCCGGCGATTCACGT 61.978 55.000 9.30 0.00 44.60 4.49
428 443 1.297598 GCATTTCCGGCGATTCACG 60.298 57.895 9.30 0.00 45.66 4.35
429 444 0.248215 CAGCATTTCCGGCGATTCAC 60.248 55.000 9.30 0.00 36.08 3.18
430 445 0.392327 TCAGCATTTCCGGCGATTCA 60.392 50.000 9.30 0.00 36.08 2.57
431 446 0.732571 TTCAGCATTTCCGGCGATTC 59.267 50.000 9.30 0.00 36.08 2.52
435 450 2.842208 TTATTTCAGCATTTCCGGCG 57.158 45.000 0.00 0.00 36.08 6.46
436 451 4.051237 GGATTTATTTCAGCATTTCCGGC 58.949 43.478 0.00 0.00 0.00 6.13
438 453 6.135290 TCTGGATTTATTTCAGCATTTCCG 57.865 37.500 0.00 0.00 0.00 4.30
453 468 7.067008 CCTGGTGTTCGTATTTATTCTGGATTT 59.933 37.037 0.00 0.00 0.00 2.17
454 469 6.542370 CCTGGTGTTCGTATTTATTCTGGATT 59.458 38.462 0.00 0.00 0.00 3.01
455 470 6.055588 CCTGGTGTTCGTATTTATTCTGGAT 58.944 40.000 0.00 0.00 0.00 3.41
456 471 5.188163 TCCTGGTGTTCGTATTTATTCTGGA 59.812 40.000 0.00 0.00 0.00 3.86
457 472 5.424757 TCCTGGTGTTCGTATTTATTCTGG 58.575 41.667 0.00 0.00 0.00 3.86
458 473 7.553881 AATCCTGGTGTTCGTATTTATTCTG 57.446 36.000 0.00 0.00 0.00 3.02
459 474 8.575649 AAAATCCTGGTGTTCGTATTTATTCT 57.424 30.769 0.00 0.00 0.00 2.40
465 480 8.458843 CAGAATTAAAATCCTGGTGTTCGTATT 58.541 33.333 0.00 0.00 0.00 1.89
466 481 7.827236 TCAGAATTAAAATCCTGGTGTTCGTAT 59.173 33.333 0.00 0.00 0.00 3.06
467 482 7.162761 TCAGAATTAAAATCCTGGTGTTCGTA 58.837 34.615 0.00 0.00 0.00 3.43
468 483 6.001460 TCAGAATTAAAATCCTGGTGTTCGT 58.999 36.000 0.00 0.00 0.00 3.85
469 484 6.494893 TCAGAATTAAAATCCTGGTGTTCG 57.505 37.500 0.00 0.00 0.00 3.95
470 485 8.055279 TCATCAGAATTAAAATCCTGGTGTTC 57.945 34.615 2.64 0.00 38.51 3.18
471 486 7.363268 GCTCATCAGAATTAAAATCCTGGTGTT 60.363 37.037 2.64 0.00 38.51 3.32
472 487 6.096001 GCTCATCAGAATTAAAATCCTGGTGT 59.904 38.462 2.64 0.00 38.51 4.16
473 488 6.320672 AGCTCATCAGAATTAAAATCCTGGTG 59.679 38.462 0.00 0.00 38.68 4.17
474 489 6.430007 AGCTCATCAGAATTAAAATCCTGGT 58.570 36.000 0.00 0.00 0.00 4.00
475 490 6.956202 AGCTCATCAGAATTAAAATCCTGG 57.044 37.500 0.00 0.00 0.00 4.45
476 491 8.899427 TCTAGCTCATCAGAATTAAAATCCTG 57.101 34.615 0.00 0.00 0.00 3.86
478 493 9.723601 ATCTCTAGCTCATCAGAATTAAAATCC 57.276 33.333 0.00 0.00 0.00 3.01
486 501 9.038072 ACAATGATATCTCTAGCTCATCAGAAT 57.962 33.333 3.98 0.00 0.00 2.40
487 502 8.419922 ACAATGATATCTCTAGCTCATCAGAA 57.580 34.615 3.98 0.00 0.00 3.02
488 503 7.889600 AGACAATGATATCTCTAGCTCATCAGA 59.110 37.037 3.98 0.00 0.00 3.27
489 504 8.058667 AGACAATGATATCTCTAGCTCATCAG 57.941 38.462 3.98 0.00 0.00 2.90
491 506 9.709495 AAAAGACAATGATATCTCTAGCTCATC 57.291 33.333 3.98 0.00 0.00 2.92
501 516 9.699410 TGGATGGTTAAAAAGACAATGATATCT 57.301 29.630 3.98 0.00 0.00 1.98
504 519 8.527810 GGTTGGATGGTTAAAAAGACAATGATA 58.472 33.333 0.00 0.00 0.00 2.15
505 520 7.016072 TGGTTGGATGGTTAAAAAGACAATGAT 59.984 33.333 0.00 0.00 0.00 2.45
506 521 6.325028 TGGTTGGATGGTTAAAAAGACAATGA 59.675 34.615 0.00 0.00 0.00 2.57
507 522 6.423604 GTGGTTGGATGGTTAAAAAGACAATG 59.576 38.462 0.00 0.00 0.00 2.82
508 523 6.098982 TGTGGTTGGATGGTTAAAAAGACAAT 59.901 34.615 0.00 0.00 0.00 2.71
509 524 5.422331 TGTGGTTGGATGGTTAAAAAGACAA 59.578 36.000 0.00 0.00 0.00 3.18
510 525 4.956700 TGTGGTTGGATGGTTAAAAAGACA 59.043 37.500 0.00 0.00 0.00 3.41
511 526 5.523438 TGTGGTTGGATGGTTAAAAAGAC 57.477 39.130 0.00 0.00 0.00 3.01
512 527 5.600484 ACATGTGGTTGGATGGTTAAAAAGA 59.400 36.000 0.00 0.00 0.00 2.52
513 528 5.852827 ACATGTGGTTGGATGGTTAAAAAG 58.147 37.500 0.00 0.00 0.00 2.27
514 529 5.878406 ACATGTGGTTGGATGGTTAAAAA 57.122 34.783 0.00 0.00 0.00 1.94
515 530 5.878406 AACATGTGGTTGGATGGTTAAAA 57.122 34.783 0.00 0.00 38.60 1.52
531 546 1.417517 TCTGTCTCTGCCACAACATGT 59.582 47.619 0.00 0.00 0.00 3.21
532 547 2.174363 TCTGTCTCTGCCACAACATG 57.826 50.000 0.00 0.00 0.00 3.21
533 548 3.430042 AATCTGTCTCTGCCACAACAT 57.570 42.857 0.00 0.00 0.00 2.71
534 549 2.936919 AATCTGTCTCTGCCACAACA 57.063 45.000 0.00 0.00 0.00 3.33
535 550 4.574599 AAAAATCTGTCTCTGCCACAAC 57.425 40.909 0.00 0.00 0.00 3.32
560 575 9.090692 TGATTAAAATACCGTAGCTACAAGTTC 57.909 33.333 23.21 11.98 0.00 3.01
598 1951 5.067674 CCAGGTGTCAATTTTTCTGACTTGA 59.932 40.000 4.74 0.00 43.03 3.02
963 2361 1.491670 CCTAGAACGATGGATGTGCG 58.508 55.000 0.00 0.00 0.00 5.34
964 2362 1.202580 AGCCTAGAACGATGGATGTGC 60.203 52.381 0.00 0.00 0.00 4.57
1085 2483 3.906718 CGTCCTCGTAGCTCAGGT 58.093 61.111 0.00 0.00 0.00 4.00
2493 7344 0.966875 GTTGGCCCATGCATCAGTCA 60.967 55.000 0.00 0.00 40.13 3.41
2749 7600 2.618709 CCTTTTCTTTTGTCTCGTGCCT 59.381 45.455 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.