Multiple sequence alignment - TraesCS2D01G223800

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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 TraesCS2D01G223800 chr2D 100.000 3320 0 0 1 3320 190436080 190439399 0.000000e+00 6131.0
1 TraesCS2D01G223800 chr2D 88.442 199 23 0 129 327 378038443 378038245 1.190000e-59 241.0
2 TraesCS2D01G223800 chr2D 93.798 129 8 0 2365 2493 214287890 214287762 9.400000e-46 195.0
3 TraesCS2D01G223800 chr2D 80.000 120 16 6 1284 1399 190369917 190370032 7.630000e-12 82.4
4 TraesCS2D01G223800 chr2A 91.582 1960 96 30 423 2362 204992550 204994460 0.000000e+00 2641.0
5 TraesCS2D01G223800 chr2A 79.167 120 17 6 1284 1399 204930132 204930247 3.550000e-10 76.8
6 TraesCS2D01G223800 chr2B 96.891 1544 47 1 793 2335 247559730 247561273 0.000000e+00 2584.0
7 TraesCS2D01G223800 chr2B 86.792 212 27 1 117 327 606148321 606148532 5.540000e-58 235.0
8 TraesCS2D01G223800 chr2B 86.705 173 22 1 463 635 247559284 247559455 1.220000e-44 191.0
9 TraesCS2D01G223800 chr2B 79.167 120 17 6 1284 1399 247517958 247518073 3.550000e-10 76.8
10 TraesCS2D01G223800 chr6D 94.585 831 45 0 2490 3320 348100832 348101662 0.000000e+00 1286.0
11 TraesCS2D01G223800 chr6D 85.165 182 24 3 327 506 106031269 106031089 2.030000e-42 183.0
12 TraesCS2D01G223800 chr6D 82.114 123 21 1 531 652 411505662 411505540 1.630000e-18 104.0
13 TraesCS2D01G223800 chr7A 93.234 872 59 0 2377 3248 462316927 462317798 0.000000e+00 1284.0
14 TraesCS2D01G223800 chr7A 94.574 129 6 1 2365 2493 166837615 166837488 7.260000e-47 198.0
15 TraesCS2D01G223800 chr7A 94.531 128 6 1 2366 2493 174843539 174843413 2.610000e-46 196.0
16 TraesCS2D01G223800 chr7A 83.243 185 27 4 325 506 654776824 654777007 2.050000e-37 167.0
17 TraesCS2D01G223800 chr7D 94.082 828 49 0 2490 3317 392750237 392751064 0.000000e+00 1258.0
18 TraesCS2D01G223800 chr7D 93.863 831 50 1 2490 3320 378894887 378894058 0.000000e+00 1251.0
19 TraesCS2D01G223800 chr7D 93.020 831 58 0 2490 3320 98632628 98631798 0.000000e+00 1214.0
20 TraesCS2D01G223800 chr7D 96.124 129 5 0 2365 2493 191502141 191502013 9.330000e-51 211.0
21 TraesCS2D01G223800 chr7D 86.111 180 23 2 328 506 585373162 585372984 3.380000e-45 193.0
22 TraesCS2D01G223800 chr7D 84.971 173 24 2 336 506 61033006 61033178 1.220000e-39 174.0
23 TraesCS2D01G223800 chr5D 93.855 830 46 4 2493 3320 119000549 118999723 0.000000e+00 1245.0
24 TraesCS2D01G223800 chr5D 93.261 831 54 2 2490 3320 45127315 45126487 0.000000e+00 1223.0
25 TraesCS2D01G223800 chr5D 86.250 80 7 4 1285 1362 505818469 505818392 2.120000e-12 84.2
26 TraesCS2D01G223800 chr1B 93.637 833 50 3 2490 3320 40948388 40949219 0.000000e+00 1242.0
27 TraesCS2D01G223800 chr1B 85.106 188 25 3 321 506 546674560 546674374 4.370000e-44 189.0
28 TraesCS2D01G223800 chr6A 92.900 831 59 0 2490 3320 518825728 518824898 0.000000e+00 1208.0
29 TraesCS2D01G223800 chr6A 94.574 129 7 0 2365 2493 140138306 140138434 2.020000e-47 200.0
30 TraesCS2D01G223800 chr6A 82.609 184 30 2 325 506 227115435 227115618 9.530000e-36 161.0
31 TraesCS2D01G223800 chr6A 82.703 185 28 4 325 506 427198749 427198932 9.530000e-36 161.0
32 TraesCS2D01G223800 chr4B 92.900 831 58 1 2490 3320 60324153 60323324 0.000000e+00 1206.0
33 TraesCS2D01G223800 chr5B 87.124 233 27 3 94 324 663968570 663968801 9.140000e-66 261.0
34 TraesCS2D01G223800 chr5B 83.246 191 29 3 319 506 663969096 663969286 4.400000e-39 172.0
35 TraesCS2D01G223800 chr5B 86.250 80 7 4 1285 1362 635808601 635808524 2.120000e-12 84.2
36 TraesCS2D01G223800 chr3D 86.920 237 26 4 95 327 348133035 348132800 9.140000e-66 261.0
37 TraesCS2D01G223800 chr3D 87.736 212 25 1 117 327 433420396 433420185 2.560000e-61 246.0
38 TraesCS2D01G223800 chr3D 95.312 128 5 1 2366 2493 380838011 380838137 5.620000e-48 202.0
39 TraesCS2D01G223800 chr7B 82.900 269 42 4 129 393 530707438 530707170 4.280000e-59 239.0
40 TraesCS2D01G223800 chr7B 84.746 236 34 2 94 327 446139700 446139465 5.540000e-58 235.0
41 TraesCS2D01G223800 chr5A 88.500 200 20 2 129 327 161912358 161912555 4.280000e-59 239.0
42 TraesCS2D01G223800 chr5A 85.714 70 8 2 1285 1353 633268513 633268581 4.590000e-09 73.1
43 TraesCS2D01G223800 chr5A 97.297 37 1 0 1320 1356 576265062 576265026 2.770000e-06 63.9
44 TraesCS2D01G223800 chr5A 97.222 36 1 0 1319 1354 670401138 670401173 9.950000e-06 62.1
45 TraesCS2D01G223800 chr1A 85.153 229 30 4 101 327 566589235 566589009 7.160000e-57 231.0
46 TraesCS2D01G223800 chr1A 83.243 185 27 4 325 506 516763271 516763454 2.050000e-37 167.0
47 TraesCS2D01G223800 chr3B 94.574 129 7 0 2365 2493 384313009 384313137 2.020000e-47 200.0
48 TraesCS2D01G223800 chr4D 93.023 129 9 0 2365 2493 381394324 381394196 4.370000e-44 189.0
49 TraesCS2D01G223800 chr3A 90.816 98 9 0 2008 2105 661841806 661841709 7.470000e-27 132.0
50 TraesCS2D01G223800 chr6B 84.483 116 18 0 531 646 672261731 672261616 7.530000e-22 115.0


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 TraesCS2D01G223800 chr2D 190436080 190439399 3319 False 6131.0 6131 100.000 1 3320 1 chr2D.!!$F2 3319
1 TraesCS2D01G223800 chr2A 204992550 204994460 1910 False 2641.0 2641 91.582 423 2362 1 chr2A.!!$F2 1939
2 TraesCS2D01G223800 chr2B 247559284 247561273 1989 False 1387.5 2584 91.798 463 2335 2 chr2B.!!$F3 1872
3 TraesCS2D01G223800 chr6D 348100832 348101662 830 False 1286.0 1286 94.585 2490 3320 1 chr6D.!!$F1 830
4 TraesCS2D01G223800 chr7A 462316927 462317798 871 False 1284.0 1284 93.234 2377 3248 1 chr7A.!!$F1 871
5 TraesCS2D01G223800 chr7D 392750237 392751064 827 False 1258.0 1258 94.082 2490 3317 1 chr7D.!!$F2 827
6 TraesCS2D01G223800 chr7D 378894058 378894887 829 True 1251.0 1251 93.863 2490 3320 1 chr7D.!!$R3 830
7 TraesCS2D01G223800 chr7D 98631798 98632628 830 True 1214.0 1214 93.020 2490 3320 1 chr7D.!!$R1 830
8 TraesCS2D01G223800 chr5D 118999723 119000549 826 True 1245.0 1245 93.855 2493 3320 1 chr5D.!!$R2 827
9 TraesCS2D01G223800 chr5D 45126487 45127315 828 True 1223.0 1223 93.261 2490 3320 1 chr5D.!!$R1 830
10 TraesCS2D01G223800 chr1B 40948388 40949219 831 False 1242.0 1242 93.637 2490 3320 1 chr1B.!!$F1 830
11 TraesCS2D01G223800 chr6A 518824898 518825728 830 True 1208.0 1208 92.900 2490 3320 1 chr6A.!!$R1 830
12 TraesCS2D01G223800 chr4B 60323324 60324153 829 True 1206.0 1206 92.900 2490 3320 1 chr4B.!!$R1 830
13 TraesCS2D01G223800 chr5B 663968570 663969286 716 False 216.5 261 85.185 94 506 2 chr5B.!!$F1 412

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
385 386 0.031917 TTCCCGGCTAGTCACCCATA 60.032 55.0 0.0 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2369 2561 0.105964 CCATTGGCGTATCCTCGGAA 59.894 55.0 0.0 0.0 35.26 4.3 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
19 20 2.301577 GGTCATCAGGCGGCTATATC 57.698 55.000 12.74 1.40 0.00 1.63
20 21 1.134670 GGTCATCAGGCGGCTATATCC 60.135 57.143 12.74 7.39 0.00 2.59
21 22 1.827969 GTCATCAGGCGGCTATATCCT 59.172 52.381 12.74 0.00 0.00 3.24
22 23 2.234908 GTCATCAGGCGGCTATATCCTT 59.765 50.000 12.74 0.00 0.00 3.36
23 24 2.234661 TCATCAGGCGGCTATATCCTTG 59.765 50.000 12.74 0.00 0.00 3.61
24 25 1.717032 TCAGGCGGCTATATCCTTGT 58.283 50.000 12.74 0.00 0.00 3.16
25 26 2.047061 TCAGGCGGCTATATCCTTGTT 58.953 47.619 12.74 0.00 0.00 2.83
26 27 2.146342 CAGGCGGCTATATCCTTGTTG 58.854 52.381 12.74 0.00 0.00 3.33
27 28 1.072331 AGGCGGCTATATCCTTGTTGG 59.928 52.381 11.03 0.00 37.10 3.77
28 29 1.523758 GCGGCTATATCCTTGTTGGG 58.476 55.000 0.00 0.00 36.20 4.12
29 30 1.071699 GCGGCTATATCCTTGTTGGGA 59.928 52.381 0.00 0.00 39.95 4.37
30 31 2.767505 CGGCTATATCCTTGTTGGGAC 58.232 52.381 0.00 0.00 38.30 4.46
31 32 2.368875 CGGCTATATCCTTGTTGGGACT 59.631 50.000 0.00 0.00 38.30 3.85
32 33 3.555168 CGGCTATATCCTTGTTGGGACTC 60.555 52.174 0.00 0.00 38.30 3.36
33 34 3.244596 GGCTATATCCTTGTTGGGACTCC 60.245 52.174 0.00 0.00 38.30 3.85
34 35 3.244596 GCTATATCCTTGTTGGGACTCCC 60.245 52.174 7.25 7.25 45.71 4.30
35 36 2.661176 TATCCTTGTTGGGACTCCCT 57.339 50.000 15.64 0.00 45.70 4.20
36 37 1.290134 ATCCTTGTTGGGACTCCCTC 58.710 55.000 15.64 8.95 45.70 4.30
37 38 0.840722 TCCTTGTTGGGACTCCCTCC 60.841 60.000 15.64 6.20 45.70 4.30
44 45 3.139469 GGACTCCCTCCCGACGTC 61.139 72.222 5.18 5.18 31.83 4.34
45 46 3.507009 GACTCCCTCCCGACGTCG 61.507 72.222 30.33 30.33 39.44 5.12
65 66 2.601367 CCTTGTGGGCCCCTTGTG 60.601 66.667 22.27 5.57 0.00 3.33
66 67 2.520458 CTTGTGGGCCCCTTGTGA 59.480 61.111 22.27 0.00 0.00 3.58
67 68 1.604593 CTTGTGGGCCCCTTGTGAG 60.605 63.158 22.27 4.76 0.00 3.51
68 69 3.808218 TTGTGGGCCCCTTGTGAGC 62.808 63.158 22.27 0.00 0.00 4.26
71 72 4.432741 GGGCCCCTTGTGAGCCTC 62.433 72.222 12.23 0.00 46.31 4.70
72 73 3.334054 GGCCCCTTGTGAGCCTCT 61.334 66.667 0.00 0.00 43.62 3.69
73 74 2.270527 GCCCCTTGTGAGCCTCTC 59.729 66.667 0.00 0.00 0.00 3.20
74 75 2.581354 CCCCTTGTGAGCCTCTCG 59.419 66.667 0.00 0.00 32.35 4.04
75 76 2.125350 CCCTTGTGAGCCTCTCGC 60.125 66.667 0.00 0.78 40.91 5.03
76 77 2.125350 CCTTGTGAGCCTCTCGCC 60.125 66.667 5.11 0.00 39.93 5.54
77 78 2.507992 CTTGTGAGCCTCTCGCCG 60.508 66.667 5.11 0.00 39.93 6.46
78 79 3.997064 CTTGTGAGCCTCTCGCCGG 62.997 68.421 0.00 0.00 39.93 6.13
105 106 2.203070 GGTGAGCCATAGCCACCG 60.203 66.667 7.72 0.00 44.78 4.94
110 111 2.516225 GCCATAGCCACCGGTTCC 60.516 66.667 2.97 0.00 0.00 3.62
111 112 3.043999 GCCATAGCCACCGGTTCCT 62.044 63.158 2.97 6.69 0.00 3.36
113 114 1.622607 CCATAGCCACCGGTTCCTGA 61.623 60.000 2.97 0.00 0.00 3.86
114 115 0.469917 CATAGCCACCGGTTCCTGAT 59.530 55.000 2.97 0.00 0.00 2.90
115 116 0.759346 ATAGCCACCGGTTCCTGATC 59.241 55.000 2.97 0.00 0.00 2.92
121 122 1.067425 CACCGGTTCCTGATCGTTACA 60.067 52.381 2.97 0.00 0.00 2.41
126 127 2.232941 GGTTCCTGATCGTTACACCTGA 59.767 50.000 0.00 0.00 0.00 3.86
168 169 3.967987 ACAGACCAACACTAGTCTTTCCT 59.032 43.478 0.00 0.00 41.38 3.36
171 172 5.010719 CAGACCAACACTAGTCTTTCCTACA 59.989 44.000 0.00 0.00 41.38 2.74
172 173 5.780793 AGACCAACACTAGTCTTTCCTACAT 59.219 40.000 0.00 0.00 40.43 2.29
174 175 6.932947 ACCAACACTAGTCTTTCCTACATAC 58.067 40.000 0.00 0.00 0.00 2.39
181 182 9.968870 CACTAGTCTTTCCTACATACTTTATCC 57.031 37.037 0.00 0.00 0.00 2.59
184 185 7.942990 AGTCTTTCCTACATACTTTATCCTCG 58.057 38.462 0.00 0.00 0.00 4.63
188 189 4.454847 TCCTACATACTTTATCCTCGCTCG 59.545 45.833 0.00 0.00 0.00 5.03
209 210 1.298859 GCGCATCCGAGACCAACTTT 61.299 55.000 0.30 0.00 36.29 2.66
210 211 1.156736 CGCATCCGAGACCAACTTTT 58.843 50.000 0.00 0.00 36.29 2.27
234 235 3.056465 GGTCGATCACCCATCCTAGAATC 60.056 52.174 0.00 0.00 39.69 2.52
235 236 2.820197 TCGATCACCCATCCTAGAATCG 59.180 50.000 0.00 0.00 0.00 3.34
247 248 2.632377 CTAGAATCGCTCCAAGCCAAA 58.368 47.619 0.00 0.00 38.18 3.28
264 265 3.735514 GCCAAACACGCTTAACTTTGGAA 60.736 43.478 11.36 0.00 43.68 3.53
272 273 7.039270 ACACGCTTAACTTTGGAATTCTTTTT 58.961 30.769 5.23 0.00 0.00 1.94
285 286 5.047092 GGAATTCTTTTTGAATGAGCTCCCA 60.047 40.000 12.15 3.79 43.99 4.37
291 292 5.867903 TTTTGAATGAGCTCCCAGAAAAA 57.132 34.783 12.15 8.96 0.00 1.94
317 318 9.965902 AAAGAATTCCTTGTTGATATGAGTAGT 57.034 29.630 0.65 0.00 34.79 2.73
318 319 9.606631 AAGAATTCCTTGTTGATATGAGTAGTC 57.393 33.333 0.65 0.00 32.92 2.59
319 320 8.986991 AGAATTCCTTGTTGATATGAGTAGTCT 58.013 33.333 0.65 0.00 0.00 3.24
323 324 8.996651 TCCTTGTTGATATGAGTAGTCTATCA 57.003 34.615 12.17 12.17 31.71 2.15
324 325 9.593565 TCCTTGTTGATATGAGTAGTCTATCAT 57.406 33.333 14.93 8.76 39.44 2.45
329 330 9.352784 GTTGATATGAGTAGTCTATCATTCTGC 57.647 37.037 14.93 0.00 37.36 4.26
330 331 8.641498 TGATATGAGTAGTCTATCATTCTGCA 57.359 34.615 12.17 0.00 37.36 4.41
331 332 9.252635 TGATATGAGTAGTCTATCATTCTGCAT 57.747 33.333 12.17 0.00 37.36 3.96
334 335 8.648698 ATGAGTAGTCTATCATTCTGCATACT 57.351 34.615 0.00 0.00 32.20 2.12
335 336 8.470657 TGAGTAGTCTATCATTCTGCATACTT 57.529 34.615 0.00 0.00 0.00 2.24
336 337 8.918116 TGAGTAGTCTATCATTCTGCATACTTT 58.082 33.333 0.00 0.00 0.00 2.66
337 338 9.190858 GAGTAGTCTATCATTCTGCATACTTTG 57.809 37.037 0.00 0.00 0.00 2.77
347 348 1.009829 GCATACTTTGCCCTCAGTCG 58.990 55.000 0.00 0.00 46.15 4.18
348 349 1.676014 GCATACTTTGCCCTCAGTCGT 60.676 52.381 0.00 0.00 46.15 4.34
349 350 2.002586 CATACTTTGCCCTCAGTCGTG 58.997 52.381 0.00 0.00 0.00 4.35
350 351 0.320421 TACTTTGCCCTCAGTCGTGC 60.320 55.000 0.00 0.00 0.00 5.34
351 352 2.664851 TTTGCCCTCAGTCGTGCG 60.665 61.111 0.00 0.00 0.00 5.34
364 365 4.980805 GTGCGCACCCGAGACCAA 62.981 66.667 30.12 0.00 36.29 3.67
365 366 4.980805 TGCGCACCCGAGACCAAC 62.981 66.667 5.66 0.00 36.29 3.77
366 367 4.681978 GCGCACCCGAGACCAACT 62.682 66.667 0.30 0.00 36.29 3.16
367 368 2.030562 CGCACCCGAGACCAACTT 59.969 61.111 0.00 0.00 36.29 2.66
368 369 2.027625 CGCACCCGAGACCAACTTC 61.028 63.158 0.00 0.00 36.29 3.01
369 370 1.671379 GCACCCGAGACCAACTTCC 60.671 63.158 0.00 0.00 0.00 3.46
370 371 1.003718 CACCCGAGACCAACTTCCC 60.004 63.158 0.00 0.00 0.00 3.97
371 372 2.264794 CCCGAGACCAACTTCCCG 59.735 66.667 0.00 0.00 0.00 5.14
372 373 2.264794 CCGAGACCAACTTCCCGG 59.735 66.667 0.00 0.00 0.00 5.73
373 374 2.434359 CGAGACCAACTTCCCGGC 60.434 66.667 0.00 0.00 0.00 6.13
374 375 2.943978 CGAGACCAACTTCCCGGCT 61.944 63.158 0.00 0.00 0.00 5.52
375 376 1.601419 CGAGACCAACTTCCCGGCTA 61.601 60.000 0.00 0.00 0.00 3.93
376 377 0.175989 GAGACCAACTTCCCGGCTAG 59.824 60.000 0.00 0.00 0.00 3.42
377 378 0.544595 AGACCAACTTCCCGGCTAGT 60.545 55.000 0.00 0.00 0.00 2.57
378 379 0.108281 GACCAACTTCCCGGCTAGTC 60.108 60.000 7.10 0.00 0.00 2.59
379 380 0.834687 ACCAACTTCCCGGCTAGTCA 60.835 55.000 7.10 0.00 0.00 3.41
380 381 0.391263 CCAACTTCCCGGCTAGTCAC 60.391 60.000 7.10 0.00 0.00 3.67
381 382 0.391263 CAACTTCCCGGCTAGTCACC 60.391 60.000 7.10 0.00 0.00 4.02
382 383 1.551019 AACTTCCCGGCTAGTCACCC 61.551 60.000 7.10 0.00 0.00 4.61
383 384 1.987855 CTTCCCGGCTAGTCACCCA 60.988 63.158 0.00 0.00 0.00 4.51
384 385 1.306654 TTCCCGGCTAGTCACCCAT 60.307 57.895 0.00 0.00 0.00 4.00
385 386 0.031917 TTCCCGGCTAGTCACCCATA 60.032 55.000 0.00 0.00 0.00 2.74
386 387 0.757935 TCCCGGCTAGTCACCCATAC 60.758 60.000 0.00 0.00 0.00 2.39
387 388 0.759436 CCCGGCTAGTCACCCATACT 60.759 60.000 0.00 0.00 0.00 2.12
388 389 1.479942 CCCGGCTAGTCACCCATACTA 60.480 57.143 0.00 0.00 0.00 1.82
389 390 1.887198 CCGGCTAGTCACCCATACTAG 59.113 57.143 6.01 6.01 46.09 2.57
390 391 2.488528 CCGGCTAGTCACCCATACTAGA 60.489 54.545 13.10 0.00 46.20 2.43
391 392 3.220110 CGGCTAGTCACCCATACTAGAA 58.780 50.000 13.10 0.00 46.20 2.10
392 393 3.827302 CGGCTAGTCACCCATACTAGAAT 59.173 47.826 13.10 0.00 46.20 2.40
393 394 4.082679 CGGCTAGTCACCCATACTAGAATC 60.083 50.000 13.10 2.87 46.20 2.52
394 395 4.082679 GGCTAGTCACCCATACTAGAATCG 60.083 50.000 13.10 0.00 46.20 3.34
395 396 4.616373 GCTAGTCACCCATACTAGAATCGC 60.616 50.000 13.10 0.00 46.20 4.58
396 397 3.567397 AGTCACCCATACTAGAATCGCT 58.433 45.455 0.00 0.00 0.00 4.93
397 398 3.570550 AGTCACCCATACTAGAATCGCTC 59.429 47.826 0.00 0.00 0.00 5.03
398 399 2.891580 TCACCCATACTAGAATCGCTCC 59.108 50.000 0.00 0.00 0.00 4.70
399 400 2.628178 CACCCATACTAGAATCGCTCCA 59.372 50.000 0.00 0.00 0.00 3.86
400 401 3.069586 CACCCATACTAGAATCGCTCCAA 59.930 47.826 0.00 0.00 0.00 3.53
401 402 3.069729 ACCCATACTAGAATCGCTCCAAC 59.930 47.826 0.00 0.00 0.00 3.77
402 403 3.555168 CCCATACTAGAATCGCTCCAACC 60.555 52.174 0.00 0.00 0.00 3.77
403 404 3.555168 CCATACTAGAATCGCTCCAACCC 60.555 52.174 0.00 0.00 0.00 4.11
404 405 1.568504 ACTAGAATCGCTCCAACCCA 58.431 50.000 0.00 0.00 0.00 4.51
405 406 1.906574 ACTAGAATCGCTCCAACCCAA 59.093 47.619 0.00 0.00 0.00 4.12
406 407 2.093447 ACTAGAATCGCTCCAACCCAAG 60.093 50.000 0.00 0.00 0.00 3.61
407 408 0.678048 AGAATCGCTCCAACCCAAGC 60.678 55.000 0.00 0.00 35.13 4.01
408 409 0.960364 GAATCGCTCCAACCCAAGCA 60.960 55.000 0.00 0.00 38.45 3.91
409 410 0.323725 AATCGCTCCAACCCAAGCAT 60.324 50.000 0.00 0.00 38.45 3.79
410 411 0.546122 ATCGCTCCAACCCAAGCATA 59.454 50.000 0.00 0.00 38.45 3.14
411 412 0.392461 TCGCTCCAACCCAAGCATAC 60.392 55.000 0.00 0.00 38.45 2.39
412 413 0.392998 CGCTCCAACCCAAGCATACT 60.393 55.000 0.00 0.00 38.45 2.12
413 414 1.839424 GCTCCAACCCAAGCATACTT 58.161 50.000 0.00 0.00 38.42 2.24
414 415 2.679639 CGCTCCAACCCAAGCATACTTA 60.680 50.000 0.00 0.00 38.45 2.24
415 416 3.352648 GCTCCAACCCAAGCATACTTAA 58.647 45.455 0.00 0.00 38.42 1.85
416 417 3.128764 GCTCCAACCCAAGCATACTTAAC 59.871 47.826 0.00 0.00 38.42 2.01
417 418 4.589908 CTCCAACCCAAGCATACTTAACT 58.410 43.478 0.00 0.00 33.74 2.24
418 419 4.993028 TCCAACCCAAGCATACTTAACTT 58.007 39.130 0.00 0.00 33.74 2.66
419 420 5.390387 TCCAACCCAAGCATACTTAACTTT 58.610 37.500 0.00 0.00 33.74 2.66
420 421 5.242838 TCCAACCCAAGCATACTTAACTTTG 59.757 40.000 0.00 0.00 33.74 2.77
421 422 5.469479 CAACCCAAGCATACTTAACTTTGG 58.531 41.667 0.00 0.00 33.74 3.28
432 433 8.968242 GCATACTTAACTTTGGAGTTCTTTTTG 58.032 33.333 0.00 0.00 44.75 2.44
438 439 5.359756 ACTTTGGAGTTCTTTTTGAATGGC 58.640 37.500 0.00 0.00 36.99 4.40
439 440 5.129320 ACTTTGGAGTTCTTTTTGAATGGCT 59.871 36.000 0.00 0.00 36.99 4.75
440 441 4.853924 TGGAGTTCTTTTTGAATGGCTC 57.146 40.909 0.00 0.00 36.99 4.70
441 442 3.573967 TGGAGTTCTTTTTGAATGGCTCC 59.426 43.478 0.00 0.00 41.81 4.70
443 444 2.558359 AGTTCTTTTTGAATGGCTCCCG 59.442 45.455 0.00 0.00 36.99 5.14
444 445 2.556622 GTTCTTTTTGAATGGCTCCCGA 59.443 45.455 0.00 0.00 36.99 5.14
448 449 3.658757 TTTTGAATGGCTCCCGAAAAG 57.341 42.857 0.00 0.00 0.00 2.27
451 452 2.436417 TGAATGGCTCCCGAAAAGAAG 58.564 47.619 0.00 0.00 0.00 2.85
508 511 7.661536 TCTATTAAGTTAGGCTCTCACACAT 57.338 36.000 0.00 0.00 0.00 3.21
544 547 1.078143 ATCAAAGAGGCAGCCCGAC 60.078 57.895 8.22 0.00 35.76 4.79
565 568 1.969923 CCCATGCTTTTGAGAAACCCA 59.030 47.619 0.00 0.00 0.00 4.51
586 589 0.324943 AGAACAAGTCCACATCCCGG 59.675 55.000 0.00 0.00 0.00 5.73
594 597 1.123077 TCCACATCCCGGATCAAGAG 58.877 55.000 0.73 0.00 0.00 2.85
598 601 0.181114 CATCCCGGATCAAGAGGCAA 59.819 55.000 0.73 0.00 0.00 4.52
640 643 1.202348 ACATGCACGAGAATCTCCGAG 60.202 52.381 4.47 0.61 0.00 4.63
641 644 0.387202 ATGCACGAGAATCTCCGAGG 59.613 55.000 4.47 0.00 0.00 4.63
642 645 0.965866 TGCACGAGAATCTCCGAGGT 60.966 55.000 4.47 0.00 0.00 3.85
643 646 0.526524 GCACGAGAATCTCCGAGGTG 60.527 60.000 4.47 8.00 0.00 4.00
644 647 1.095600 CACGAGAATCTCCGAGGTGA 58.904 55.000 4.47 0.00 0.00 4.02
645 648 1.472878 CACGAGAATCTCCGAGGTGAA 59.527 52.381 4.47 0.00 0.00 3.18
646 649 1.473278 ACGAGAATCTCCGAGGTGAAC 59.527 52.381 4.47 0.00 0.00 3.18
647 650 1.472878 CGAGAATCTCCGAGGTGAACA 59.527 52.381 4.47 0.00 0.00 3.18
648 651 2.099921 CGAGAATCTCCGAGGTGAACAT 59.900 50.000 4.47 0.00 0.00 2.71
649 652 3.452474 GAGAATCTCCGAGGTGAACATG 58.548 50.000 0.00 0.00 0.00 3.21
650 653 2.834549 AGAATCTCCGAGGTGAACATGT 59.165 45.455 0.00 0.00 0.00 3.21
651 654 2.680312 ATCTCCGAGGTGAACATGTG 57.320 50.000 0.00 0.00 0.00 3.21
652 655 1.338107 TCTCCGAGGTGAACATGTGT 58.662 50.000 0.00 0.00 0.00 3.72
653 656 2.521126 TCTCCGAGGTGAACATGTGTA 58.479 47.619 0.00 0.00 0.00 2.90
654 657 2.230508 TCTCCGAGGTGAACATGTGTAC 59.769 50.000 0.00 1.22 0.00 2.90
655 658 2.231478 CTCCGAGGTGAACATGTGTACT 59.769 50.000 0.00 0.00 0.00 2.73
656 659 2.631062 TCCGAGGTGAACATGTGTACTT 59.369 45.455 0.00 0.00 0.00 2.24
661 664 5.227569 AGGTGAACATGTGTACTTGATGA 57.772 39.130 0.00 0.00 0.00 2.92
669 672 6.233434 ACATGTGTACTTGATGATCTTGTGT 58.767 36.000 0.00 0.00 0.00 3.72
672 675 6.993079 TGTGTACTTGATGATCTTGTGTAGT 58.007 36.000 0.00 0.00 0.00 2.73
675 678 9.587772 GTGTACTTGATGATCTTGTGTAGTATT 57.412 33.333 0.00 0.00 0.00 1.89
695 698 7.836842 AGTATTTGTGGACCCATAATGAAAAC 58.163 34.615 0.00 0.00 0.00 2.43
720 726 7.754924 ACCGAGTTTAATATTTGAATTGTGCAG 59.245 33.333 0.00 0.00 0.00 4.41
736 742 1.539388 TGCAGTTTAAATGTCGCCTGG 59.461 47.619 0.00 0.00 0.00 4.45
737 743 1.135402 GCAGTTTAAATGTCGCCTGGG 60.135 52.381 0.00 0.00 0.00 4.45
745 751 4.451150 GTCGCCTGGGCATGACGA 62.451 66.667 12.34 0.00 42.06 4.20
779 793 2.978000 GGATTTGCCGGGTTTGGG 59.022 61.111 2.18 0.00 0.00 4.12
805 973 2.581354 CTTAGCAGAGCTGGCGGT 59.419 61.111 0.00 0.00 40.10 5.68
806 974 1.812922 CTTAGCAGAGCTGGCGGTG 60.813 63.158 0.00 0.00 40.10 4.94
917 1086 8.470805 AGAACAGTTCTCATTCGTCAAGTATAT 58.529 33.333 10.27 0.00 34.07 0.86
918 1087 9.088512 GAACAGTTCTCATTCGTCAAGTATATT 57.911 33.333 6.00 0.00 0.00 1.28
931 1100 6.701841 CGTCAAGTATATTTGTATCCAGCACT 59.298 38.462 7.73 0.00 0.00 4.40
1086 1255 3.774959 ATCGAGTCGTGGCATCCGC 62.775 63.158 13.12 0.00 37.44 5.54
1098 1267 1.440145 GCATCCGCCTTGAGCTAACC 61.440 60.000 0.00 0.00 40.39 2.85
1349 1519 3.201494 CGACCTCATCTGGACGCT 58.799 61.111 0.00 0.00 38.25 5.07
1950 2139 1.581934 GCGGGTTCATCATCGATTCA 58.418 50.000 0.00 0.00 0.00 2.57
2335 2524 7.577616 GCAAGCTATAGGATTGGTGAAAGTTTT 60.578 37.037 1.04 0.00 41.16 2.43
2458 2650 1.669604 TCGCTAGCTAGGAGTCACAG 58.330 55.000 22.10 0.00 0.00 3.66
2462 2654 1.944024 CTAGCTAGGAGTCACAGACCG 59.056 57.143 13.32 0.00 32.18 4.79
2477 2669 1.538135 ACCGACCCTAACCAAGCCT 60.538 57.895 0.00 0.00 0.00 4.58
2478 2670 1.221021 CCGACCCTAACCAAGCCTC 59.779 63.158 0.00 0.00 0.00 4.70
2483 2675 0.322546 CCCTAACCAAGCCTCCACAC 60.323 60.000 0.00 0.00 0.00 3.82
2649 2842 0.034670 GAGGAGTGCATCAAAGGGCT 60.035 55.000 0.00 0.00 0.00 5.19
2756 2949 2.114670 CGAGGACAATTGCCGCCAT 61.115 57.895 5.05 0.00 0.00 4.40
2989 3182 2.975489 AGAATCACTCCAACCTCACTGT 59.025 45.455 0.00 0.00 0.00 3.55
3075 3268 0.467290 GCAAGGACCAGAACCACCAA 60.467 55.000 0.00 0.00 0.00 3.67
3160 3353 4.657824 CGGCACCAACTCCGTCGT 62.658 66.667 0.00 0.00 40.72 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.134670 GGATATAGCCGCCTGATGACC 60.135 57.143 0.00 0.00 0.00 4.02
1 2 1.827969 AGGATATAGCCGCCTGATGAC 59.172 52.381 0.33 0.00 0.00 3.06
2 3 2.234661 CAAGGATATAGCCGCCTGATGA 59.765 50.000 0.33 0.00 31.06 2.92
3 4 2.027745 ACAAGGATATAGCCGCCTGATG 60.028 50.000 12.06 4.76 31.06 3.07
4 5 2.260822 ACAAGGATATAGCCGCCTGAT 58.739 47.619 12.06 0.00 31.06 2.90
5 6 1.717032 ACAAGGATATAGCCGCCTGA 58.283 50.000 12.06 0.00 31.06 3.86
6 7 2.146342 CAACAAGGATATAGCCGCCTG 58.854 52.381 0.33 3.51 31.06 4.85
7 8 1.072331 CCAACAAGGATATAGCCGCCT 59.928 52.381 0.33 0.00 41.22 5.52
8 9 1.523758 CCAACAAGGATATAGCCGCC 58.476 55.000 0.33 0.00 41.22 6.13
9 10 1.071699 TCCCAACAAGGATATAGCCGC 59.928 52.381 0.33 0.00 41.22 6.53
10 11 2.368875 AGTCCCAACAAGGATATAGCCG 59.631 50.000 0.33 0.00 41.22 5.52
11 12 3.244596 GGAGTCCCAACAAGGATATAGCC 60.245 52.174 0.00 0.00 41.22 3.93
12 13 3.244596 GGGAGTCCCAACAAGGATATAGC 60.245 52.174 24.35 0.00 44.65 2.97
13 14 4.625607 GGGAGTCCCAACAAGGATATAG 57.374 50.000 24.35 0.00 44.65 1.31
27 28 3.139469 GACGTCGGGAGGGAGTCC 61.139 72.222 0.00 0.00 46.10 3.85
28 29 3.507009 CGACGTCGGGAGGGAGTC 61.507 72.222 29.70 0.00 35.37 3.36
48 49 2.601367 CACAAGGGGCCCACAAGG 60.601 66.667 27.72 11.32 39.47 3.61
49 50 1.604593 CTCACAAGGGGCCCACAAG 60.605 63.158 27.72 13.62 0.00 3.16
50 51 2.520458 CTCACAAGGGGCCCACAA 59.480 61.111 27.72 4.03 0.00 3.33
51 52 4.284550 GCTCACAAGGGGCCCACA 62.285 66.667 27.72 1.71 0.00 4.17
54 55 4.432741 GAGGCTCACAAGGGGCCC 62.433 72.222 17.12 17.12 46.31 5.80
55 56 3.334054 AGAGGCTCACAAGGGGCC 61.334 66.667 18.26 0.00 45.57 5.80
56 57 2.270527 GAGAGGCTCACAAGGGGC 59.729 66.667 18.26 0.00 0.00 5.80
57 58 2.581354 CGAGAGGCTCACAAGGGG 59.419 66.667 18.26 0.00 0.00 4.79
58 59 2.125350 GCGAGAGGCTCACAAGGG 60.125 66.667 18.26 0.00 39.11 3.95
80 81 1.457643 TATGGCTCACCGAGGGGAG 60.458 63.158 16.74 16.74 39.70 4.30
81 82 1.457643 CTATGGCTCACCGAGGGGA 60.458 63.158 0.00 0.00 39.70 4.81
82 83 3.142393 CTATGGCTCACCGAGGGG 58.858 66.667 0.00 0.00 39.70 4.79
83 84 2.423446 GCTATGGCTCACCGAGGG 59.577 66.667 0.00 0.00 39.70 4.30
84 85 2.423446 GGCTATGGCTCACCGAGG 59.577 66.667 0.00 0.00 39.70 4.63
85 86 1.227380 GTGGCTATGGCTCACCGAG 60.227 63.158 0.00 0.00 39.70 4.63
86 87 2.731571 GGTGGCTATGGCTCACCGA 61.732 63.158 20.25 0.00 43.90 4.69
87 88 2.203070 GGTGGCTATGGCTCACCG 60.203 66.667 20.25 0.00 43.90 4.94
88 89 2.203070 CGGTGGCTATGGCTCACC 60.203 66.667 23.09 23.09 46.52 4.02
89 90 2.203070 CCGGTGGCTATGGCTCAC 60.203 66.667 12.23 12.23 38.22 3.51
90 91 2.252072 GAACCGGTGGCTATGGCTCA 62.252 60.000 8.52 0.00 38.73 4.26
91 92 1.523938 GAACCGGTGGCTATGGCTC 60.524 63.158 8.52 0.00 38.73 4.70
92 93 2.590092 GAACCGGTGGCTATGGCT 59.410 61.111 8.52 0.00 38.73 4.75
105 106 2.232941 TCAGGTGTAACGATCAGGAACC 59.767 50.000 0.00 0.00 38.12 3.62
110 111 2.496070 TCCCTTCAGGTGTAACGATCAG 59.504 50.000 0.00 0.00 38.12 2.90
111 112 2.531771 TCCCTTCAGGTGTAACGATCA 58.468 47.619 0.00 0.00 38.12 2.92
113 114 3.375699 AGATCCCTTCAGGTGTAACGAT 58.624 45.455 0.00 0.00 38.12 3.73
114 115 2.816411 AGATCCCTTCAGGTGTAACGA 58.184 47.619 0.00 0.00 38.12 3.85
115 116 3.952323 TCTAGATCCCTTCAGGTGTAACG 59.048 47.826 0.00 0.00 38.12 3.18
121 122 3.437344 GGCTAGTCTAGATCCCTTCAGGT 60.437 52.174 11.27 0.00 36.75 4.00
126 127 1.866943 TGGGGCTAGTCTAGATCCCTT 59.133 52.381 26.11 0.00 39.79 3.95
168 169 4.556104 GCACGAGCGAGGATAAAGTATGTA 60.556 45.833 0.00 0.00 0.00 2.29
171 172 3.014604 GCACGAGCGAGGATAAAGTAT 57.985 47.619 0.00 0.00 0.00 2.12
172 173 2.486951 GCACGAGCGAGGATAAAGTA 57.513 50.000 0.00 0.00 0.00 2.24
188 189 2.434185 TTGGTCTCGGATGCGCAC 60.434 61.111 14.90 6.86 0.00 5.34
216 217 2.564947 AGCGATTCTAGGATGGGTGATC 59.435 50.000 0.00 0.00 0.00 2.92
234 235 2.252260 CGTGTTTGGCTTGGAGCG 59.748 61.111 0.00 0.00 43.62 5.03
235 236 2.050077 GCGTGTTTGGCTTGGAGC 60.050 61.111 0.00 0.00 41.46 4.70
247 248 5.767816 AAGAATTCCAAAGTTAAGCGTGT 57.232 34.783 0.65 0.00 0.00 4.49
291 292 9.965902 ACTACTCATATCAACAAGGAATTCTTT 57.034 29.630 5.23 0.35 32.41 2.52
292 293 9.606631 GACTACTCATATCAACAAGGAATTCTT 57.393 33.333 5.23 0.00 35.79 2.52
293 294 8.986991 AGACTACTCATATCAACAAGGAATTCT 58.013 33.333 5.23 0.00 0.00 2.40
297 298 9.421399 TGATAGACTACTCATATCAACAAGGAA 57.579 33.333 0.00 0.00 33.99 3.36
298 299 8.996651 TGATAGACTACTCATATCAACAAGGA 57.003 34.615 0.00 0.00 33.99 3.36
303 304 9.352784 GCAGAATGATAGACTACTCATATCAAC 57.647 37.037 7.44 0.00 38.89 3.18
304 305 9.082313 TGCAGAATGATAGACTACTCATATCAA 57.918 33.333 7.44 0.00 38.89 2.57
305 306 8.641498 TGCAGAATGATAGACTACTCATATCA 57.359 34.615 7.44 0.00 39.69 2.15
308 309 9.746457 AGTATGCAGAATGATAGACTACTCATA 57.254 33.333 0.00 0.00 39.69 2.15
309 310 8.648698 AGTATGCAGAATGATAGACTACTCAT 57.351 34.615 0.00 0.00 39.69 2.90
310 311 8.470657 AAGTATGCAGAATGATAGACTACTCA 57.529 34.615 0.00 0.00 39.69 3.41
311 312 9.190858 CAAAGTATGCAGAATGATAGACTACTC 57.809 37.037 0.00 0.00 39.69 2.59
329 330 2.002586 CACGACTGAGGGCAAAGTATG 58.997 52.381 0.00 0.00 0.00 2.39
330 331 1.676014 GCACGACTGAGGGCAAAGTAT 60.676 52.381 0.00 0.00 0.00 2.12
331 332 0.320421 GCACGACTGAGGGCAAAGTA 60.320 55.000 0.00 0.00 0.00 2.24
332 333 1.598130 GCACGACTGAGGGCAAAGT 60.598 57.895 0.00 0.00 0.00 2.66
333 334 2.671177 CGCACGACTGAGGGCAAAG 61.671 63.158 0.00 0.00 0.00 2.77
334 335 2.664851 CGCACGACTGAGGGCAAA 60.665 61.111 0.00 0.00 0.00 3.68
347 348 4.980805 TTGGTCTCGGGTGCGCAC 62.981 66.667 32.15 32.15 0.00 5.34
348 349 4.980805 GTTGGTCTCGGGTGCGCA 62.981 66.667 5.66 5.66 0.00 6.09
349 350 4.681978 AGTTGGTCTCGGGTGCGC 62.682 66.667 0.00 0.00 0.00 6.09
350 351 2.027625 GAAGTTGGTCTCGGGTGCG 61.028 63.158 0.00 0.00 0.00 5.34
351 352 1.671379 GGAAGTTGGTCTCGGGTGC 60.671 63.158 0.00 0.00 0.00 5.01
352 353 1.003718 GGGAAGTTGGTCTCGGGTG 60.004 63.158 0.00 0.00 0.00 4.61
353 354 2.580601 CGGGAAGTTGGTCTCGGGT 61.581 63.158 0.00 0.00 37.87 5.28
354 355 2.264794 CGGGAAGTTGGTCTCGGG 59.735 66.667 0.00 0.00 37.87 5.14
356 357 1.601419 TAGCCGGGAAGTTGGTCTCG 61.601 60.000 2.18 0.00 41.34 4.04
357 358 0.175989 CTAGCCGGGAAGTTGGTCTC 59.824 60.000 2.18 0.00 0.00 3.36
358 359 0.544595 ACTAGCCGGGAAGTTGGTCT 60.545 55.000 2.18 0.00 0.00 3.85
359 360 0.108281 GACTAGCCGGGAAGTTGGTC 60.108 60.000 2.18 0.00 0.00 4.02
360 361 0.834687 TGACTAGCCGGGAAGTTGGT 60.835 55.000 2.18 0.00 0.00 3.67
361 362 0.391263 GTGACTAGCCGGGAAGTTGG 60.391 60.000 2.18 0.00 0.00 3.77
362 363 0.391263 GGTGACTAGCCGGGAAGTTG 60.391 60.000 2.18 0.00 0.00 3.16
363 364 1.551019 GGGTGACTAGCCGGGAAGTT 61.551 60.000 2.18 0.00 34.27 2.66
364 365 1.988406 GGGTGACTAGCCGGGAAGT 60.988 63.158 2.18 0.00 34.27 3.01
365 366 2.901042 GGGTGACTAGCCGGGAAG 59.099 66.667 2.18 0.00 34.27 3.46
371 372 4.082679 CGATTCTAGTATGGGTGACTAGCC 60.083 50.000 5.17 0.00 44.08 3.93
372 373 4.616373 GCGATTCTAGTATGGGTGACTAGC 60.616 50.000 5.17 0.00 44.08 3.42
373 374 4.762765 AGCGATTCTAGTATGGGTGACTAG 59.237 45.833 3.86 3.86 45.24 2.57
374 375 4.726583 AGCGATTCTAGTATGGGTGACTA 58.273 43.478 0.00 0.00 0.00 2.59
375 376 3.567397 AGCGATTCTAGTATGGGTGACT 58.433 45.455 0.00 0.00 0.00 3.41
376 377 3.305471 GGAGCGATTCTAGTATGGGTGAC 60.305 52.174 0.98 0.00 0.00 3.67
377 378 2.891580 GGAGCGATTCTAGTATGGGTGA 59.108 50.000 0.98 0.00 0.00 4.02
378 379 2.628178 TGGAGCGATTCTAGTATGGGTG 59.372 50.000 0.98 0.00 0.00 4.61
379 380 2.958818 TGGAGCGATTCTAGTATGGGT 58.041 47.619 0.00 0.00 0.00 4.51
380 381 3.555168 GGTTGGAGCGATTCTAGTATGGG 60.555 52.174 0.00 0.00 0.00 4.00
381 382 3.555168 GGGTTGGAGCGATTCTAGTATGG 60.555 52.174 0.00 0.00 0.00 2.74
382 383 3.069586 TGGGTTGGAGCGATTCTAGTATG 59.930 47.826 0.00 0.00 0.00 2.39
383 384 3.305720 TGGGTTGGAGCGATTCTAGTAT 58.694 45.455 0.00 0.00 0.00 2.12
384 385 2.742348 TGGGTTGGAGCGATTCTAGTA 58.258 47.619 0.00 0.00 0.00 1.82
385 386 1.568504 TGGGTTGGAGCGATTCTAGT 58.431 50.000 0.00 0.00 0.00 2.57
386 387 2.555199 CTTGGGTTGGAGCGATTCTAG 58.445 52.381 0.00 0.00 0.00 2.43
387 388 1.406887 GCTTGGGTTGGAGCGATTCTA 60.407 52.381 0.00 0.00 0.00 2.10
388 389 0.678048 GCTTGGGTTGGAGCGATTCT 60.678 55.000 0.00 0.00 0.00 2.40
389 390 0.960364 TGCTTGGGTTGGAGCGATTC 60.960 55.000 0.00 0.00 41.75 2.52
390 391 0.323725 ATGCTTGGGTTGGAGCGATT 60.324 50.000 0.00 0.00 41.75 3.34
391 392 0.546122 TATGCTTGGGTTGGAGCGAT 59.454 50.000 0.00 0.00 41.75 4.58
392 393 0.392461 GTATGCTTGGGTTGGAGCGA 60.392 55.000 0.00 0.00 41.75 4.93
393 394 0.392998 AGTATGCTTGGGTTGGAGCG 60.393 55.000 0.00 0.00 41.75 5.03
394 395 1.839424 AAGTATGCTTGGGTTGGAGC 58.161 50.000 0.00 0.00 39.33 4.70
395 396 4.589908 AGTTAAGTATGCTTGGGTTGGAG 58.410 43.478 6.28 0.00 36.22 3.86
396 397 4.650972 AGTTAAGTATGCTTGGGTTGGA 57.349 40.909 6.28 0.00 36.22 3.53
397 398 5.469479 CAAAGTTAAGTATGCTTGGGTTGG 58.531 41.667 6.28 0.00 36.22 3.77
398 399 5.242838 TCCAAAGTTAAGTATGCTTGGGTTG 59.757 40.000 6.28 5.46 35.40 3.77
399 400 5.390387 TCCAAAGTTAAGTATGCTTGGGTT 58.610 37.500 6.28 0.00 35.40 4.11
400 401 4.993028 TCCAAAGTTAAGTATGCTTGGGT 58.007 39.130 6.28 0.00 35.40 4.51
401 402 5.010282 ACTCCAAAGTTAAGTATGCTTGGG 58.990 41.667 6.28 1.86 35.23 4.12
402 403 6.431234 AGAACTCCAAAGTTAAGTATGCTTGG 59.569 38.462 6.28 5.45 45.80 3.61
403 404 7.440523 AGAACTCCAAAGTTAAGTATGCTTG 57.559 36.000 6.28 0.00 45.80 4.01
404 405 8.465273 AAAGAACTCCAAAGTTAAGTATGCTT 57.535 30.769 0.56 0.56 45.80 3.91
405 406 8.465273 AAAAGAACTCCAAAGTTAAGTATGCT 57.535 30.769 0.00 0.00 45.80 3.79
406 407 8.968242 CAAAAAGAACTCCAAAGTTAAGTATGC 58.032 33.333 0.00 0.00 45.80 3.14
410 411 9.586435 CATTCAAAAAGAACTCCAAAGTTAAGT 57.414 29.630 0.00 0.00 45.80 2.24
411 412 9.034544 CCATTCAAAAAGAACTCCAAAGTTAAG 57.965 33.333 0.00 0.00 45.80 1.85
412 413 7.494298 GCCATTCAAAAAGAACTCCAAAGTTAA 59.506 33.333 0.00 0.00 45.80 2.01
413 414 6.983890 GCCATTCAAAAAGAACTCCAAAGTTA 59.016 34.615 0.00 0.00 45.80 2.24
415 416 5.129320 AGCCATTCAAAAAGAACTCCAAAGT 59.871 36.000 0.00 0.00 39.49 2.66
416 417 5.604565 AGCCATTCAAAAAGAACTCCAAAG 58.395 37.500 0.00 0.00 39.49 2.77
417 418 5.453198 GGAGCCATTCAAAAAGAACTCCAAA 60.453 40.000 0.00 0.00 42.42 3.28
418 419 4.039124 GGAGCCATTCAAAAAGAACTCCAA 59.961 41.667 0.00 0.00 42.42 3.53
419 420 3.573967 GGAGCCATTCAAAAAGAACTCCA 59.426 43.478 0.00 0.00 42.42 3.86
420 421 3.056536 GGGAGCCATTCAAAAAGAACTCC 60.057 47.826 0.00 0.00 42.26 3.85
421 422 3.366374 CGGGAGCCATTCAAAAAGAACTC 60.366 47.826 0.00 0.00 39.49 3.01
432 433 2.711542 TCTTCTTTTCGGGAGCCATTC 58.288 47.619 0.00 0.00 0.00 2.67
438 439 5.966742 AAGGAATTTCTTCTTTTCGGGAG 57.033 39.130 0.00 0.00 26.94 4.30
439 440 7.668052 TCAATAAGGAATTTCTTCTTTTCGGGA 59.332 33.333 1.07 0.00 33.27 5.14
440 441 7.826690 TCAATAAGGAATTTCTTCTTTTCGGG 58.173 34.615 1.07 0.00 33.27 5.14
484 487 7.201920 GGATGTGTGAGAGCCTAACTTAATAGA 60.202 40.741 0.00 0.00 0.00 1.98
494 497 0.339859 AGGGGATGTGTGAGAGCCTA 59.660 55.000 0.00 0.00 0.00 3.93
526 529 1.078143 GTCGGGCTGCCTCTTTGAT 60.078 57.895 19.68 0.00 0.00 2.57
544 547 1.276138 GGGTTTCTCAAAAGCATGGGG 59.724 52.381 0.00 0.00 43.19 4.96
565 568 1.276421 CGGGATGTGGACTTGTTCTCT 59.724 52.381 0.00 0.00 0.00 3.10
594 597 9.316730 TGCAGAAAATTCATAATCTTATTTGCC 57.683 29.630 0.00 0.00 0.00 4.52
627 630 1.472878 TGTTCACCTCGGAGATTCTCG 59.527 52.381 6.58 3.81 33.89 4.04
635 638 2.244695 AGTACACATGTTCACCTCGGA 58.755 47.619 0.00 0.00 0.00 4.55
640 643 5.877012 AGATCATCAAGTACACATGTTCACC 59.123 40.000 0.00 0.00 0.00 4.02
641 644 6.974932 AGATCATCAAGTACACATGTTCAC 57.025 37.500 0.00 0.00 0.00 3.18
642 645 6.936335 ACAAGATCATCAAGTACACATGTTCA 59.064 34.615 0.00 0.00 0.00 3.18
643 646 7.095060 ACACAAGATCATCAAGTACACATGTTC 60.095 37.037 0.00 0.00 0.00 3.18
644 647 6.712095 ACACAAGATCATCAAGTACACATGTT 59.288 34.615 0.00 0.00 0.00 2.71
645 648 6.233434 ACACAAGATCATCAAGTACACATGT 58.767 36.000 0.00 0.00 0.00 3.21
646 649 6.732531 ACACAAGATCATCAAGTACACATG 57.267 37.500 0.00 0.00 0.00 3.21
647 650 7.615403 ACTACACAAGATCATCAAGTACACAT 58.385 34.615 0.00 0.00 0.00 3.21
648 651 6.993079 ACTACACAAGATCATCAAGTACACA 58.007 36.000 0.00 0.00 0.00 3.72
649 652 9.587772 AATACTACACAAGATCATCAAGTACAC 57.412 33.333 0.00 0.00 0.00 2.90
653 656 8.939929 CACAAATACTACACAAGATCATCAAGT 58.060 33.333 0.00 0.00 0.00 3.16
654 657 8.393366 CCACAAATACTACACAAGATCATCAAG 58.607 37.037 0.00 0.00 0.00 3.02
655 658 8.100164 TCCACAAATACTACACAAGATCATCAA 58.900 33.333 0.00 0.00 0.00 2.57
656 659 7.549134 GTCCACAAATACTACACAAGATCATCA 59.451 37.037 0.00 0.00 0.00 3.07
661 664 5.013704 TGGGTCCACAAATACTACACAAGAT 59.986 40.000 0.00 0.00 0.00 2.40
669 672 8.962679 GTTTTCATTATGGGTCCACAAATACTA 58.037 33.333 0.00 0.00 0.00 1.82
672 675 6.127591 CGGTTTTCATTATGGGTCCACAAATA 60.128 38.462 0.00 0.00 0.00 1.40
675 678 3.508012 CGGTTTTCATTATGGGTCCACAA 59.492 43.478 0.00 0.00 0.00 3.33
677 680 3.349022 TCGGTTTTCATTATGGGTCCAC 58.651 45.455 0.00 0.00 0.00 4.02
695 698 7.754924 ACTGCACAATTCAAATATTAAACTCGG 59.245 33.333 0.00 0.00 0.00 4.63
720 726 0.885196 TGCCCAGGCGACATTTAAAC 59.115 50.000 3.83 0.00 45.51 2.01
772 779 2.683362 GCTAAGCATCTACACCCAAACC 59.317 50.000 0.00 0.00 0.00 3.27
775 782 2.837591 TCTGCTAAGCATCTACACCCAA 59.162 45.455 0.00 0.00 38.13 4.12
776 783 2.432146 CTCTGCTAAGCATCTACACCCA 59.568 50.000 0.00 0.00 38.13 4.51
779 793 3.122297 CAGCTCTGCTAAGCATCTACAC 58.878 50.000 12.44 0.00 45.00 2.90
805 973 1.876416 GCTACAACCTTTGGCGTCTCA 60.876 52.381 0.00 0.00 34.12 3.27
806 974 0.796927 GCTACAACCTTTGGCGTCTC 59.203 55.000 0.00 0.00 34.12 3.36
1086 1255 1.003839 TGCGTGGGTTAGCTCAAGG 60.004 57.895 0.00 0.00 0.00 3.61
1464 1647 0.252197 AGCAATGGTACCTCGGGTTC 59.748 55.000 14.36 0.00 37.09 3.62
1465 1648 0.252197 GAGCAATGGTACCTCGGGTT 59.748 55.000 14.36 0.00 37.09 4.11
2311 2500 8.422577 AAAAACTTTCACCAATCCTATAGCTT 57.577 30.769 0.00 0.00 0.00 3.74
2366 2558 2.476126 TTGGCGTATCCTCGGAAAAA 57.524 45.000 0.00 0.00 35.26 1.94
2367 2559 2.285083 CATTGGCGTATCCTCGGAAAA 58.715 47.619 0.00 0.00 35.26 2.29
2368 2560 1.474320 CCATTGGCGTATCCTCGGAAA 60.474 52.381 0.00 0.00 35.26 3.13
2369 2561 0.105964 CCATTGGCGTATCCTCGGAA 59.894 55.000 0.00 0.00 35.26 4.30
2370 2562 1.745890 CCATTGGCGTATCCTCGGA 59.254 57.895 0.00 0.00 35.26 4.55
2371 2563 1.961277 GCCATTGGCGTATCCTCGG 60.961 63.158 12.82 0.00 39.62 4.63
2372 2564 3.642755 GCCATTGGCGTATCCTCG 58.357 61.111 12.82 0.00 39.62 4.63
2428 2620 5.914033 TCCTAGCTAGCGATGTGTAATTTT 58.086 37.500 15.74 0.00 0.00 1.82
2430 2622 4.585162 ACTCCTAGCTAGCGATGTGTAATT 59.415 41.667 15.74 0.00 0.00 1.40
2449 2641 0.323178 TAGGGTCGGTCTGTGACTCC 60.323 60.000 0.00 0.00 37.56 3.85
2458 2650 1.078637 GGCTTGGTTAGGGTCGGTC 60.079 63.158 0.00 0.00 0.00 4.79
2462 2654 0.035343 GTGGAGGCTTGGTTAGGGTC 60.035 60.000 0.00 0.00 0.00 4.46
2477 2669 1.229400 GGGTAGGGAGTGGTGTGGA 60.229 63.158 0.00 0.00 0.00 4.02
2478 2670 1.131303 TTGGGTAGGGAGTGGTGTGG 61.131 60.000 0.00 0.00 0.00 4.17
2483 2675 0.322187 CGGTTTTGGGTAGGGAGTGG 60.322 60.000 0.00 0.00 0.00 4.00
2649 2842 0.976641 ATTGTGCTGGGAGACGAGAA 59.023 50.000 0.00 0.00 38.67 2.87
2676 2869 1.951602 TCTTTGACGTCGTTCCTCTGA 59.048 47.619 11.62 0.00 0.00 3.27
2740 2933 2.114670 CGATGGCGGCAATTGTCCT 61.115 57.895 18.31 0.00 0.00 3.85
2741 2934 2.408835 CGATGGCGGCAATTGTCC 59.591 61.111 18.31 6.65 0.00 4.02
2756 2949 2.033448 ATTTGCCTCGTTGCCCGA 59.967 55.556 0.00 0.00 45.00 5.14
2796 2989 4.335416 GTGGATGTCATTTTCCTTCCTGA 58.665 43.478 0.00 0.00 32.95 3.86


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

AutoCloner maintained by Alex Coulton.