Multiple sequence alignment - TraesCS2B01G433100

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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 TraesCS2B01G433100 chr2B 100.000 3761 0 0 1 3761 622642346 622638586 0.000000e+00 6946
1 TraesCS2B01G433100 chr2B 95.541 471 19 2 163 632 679154988 679155457 0.000000e+00 752
2 TraesCS2B01G433100 chr2B 95.484 465 19 2 168 631 466215867 466216330 0.000000e+00 741
3 TraesCS2B01G433100 chr2B 94.091 220 9 1 2828 3043 622639414 622639195 7.790000e-87 331
4 TraesCS2B01G433100 chr2B 94.091 220 9 1 2933 3152 622639519 622639304 7.790000e-87 331
5 TraesCS2B01G433100 chr2B 93.694 111 3 1 2828 2934 622639305 622639195 3.010000e-36 163
6 TraesCS2B01G433100 chr2B 93.694 111 3 1 3042 3152 622639519 622639413 3.010000e-36 163
7 TraesCS2B01G433100 chr2D 94.755 3165 104 22 633 3761 525289120 525292258 0.000000e+00 4868
8 TraesCS2B01G433100 chr2D 97.273 220 6 0 2933 3152 525291318 525291537 1.280000e-99 374
9 TraesCS2B01G433100 chr2D 94.545 220 8 1 2828 3043 525291427 525291646 1.670000e-88 337
10 TraesCS2B01G433100 chr2D 97.297 111 3 0 3042 3152 525291318 525291428 4.960000e-44 189
11 TraesCS2B01G433100 chr2D 93.694 111 3 1 2828 2934 525291536 525291646 3.010000e-36 163
12 TraesCS2B01G433100 chr3A 96.178 471 17 1 164 633 209407676 209408146 0.000000e+00 769
13 TraesCS2B01G433100 chr2A 93.861 505 25 5 3263 3761 671279900 671279396 0.000000e+00 756
14 TraesCS2B01G433100 chr7D 95.349 473 18 3 168 637 219836551 219837022 0.000000e+00 749
15 TraesCS2B01G433100 chr3B 95.513 468 19 2 165 631 690854219 690854685 0.000000e+00 747
16 TraesCS2B01G433100 chr7A 95.699 465 17 3 168 631 301639173 301639635 0.000000e+00 745
17 TraesCS2B01G433100 chr6A 95.484 465 20 1 168 631 105536744 105536280 0.000000e+00 741
18 TraesCS2B01G433100 chr6A 93.996 483 27 2 164 645 237919285 237919766 0.000000e+00 730
19 TraesCS2B01G433100 chr7B 95.096 469 20 3 168 635 516134930 516135396 0.000000e+00 736


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 TraesCS2B01G433100 chr2B 622638586 622642346 3760 True 1586.8 6946 95.1140 1 3761 5 chr2B.!!$R1 3760
1 TraesCS2B01G433100 chr2D 525289120 525292258 3138 False 1186.2 4868 95.5128 633 3761 5 chr2D.!!$F1 3128
2 TraesCS2B01G433100 chr2A 671279396 671279900 504 True 756.0 756 93.8610 3263 3761 1 chr2A.!!$R1 498

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
149 150 0.035458 TGTGTGTGTGTGTGTGTGGA 59.965 50.0 0.00 0.0 0.00 4.02 F
720 722 0.036952 CTCGCCATTCACACAGTCCT 60.037 55.0 0.00 0.0 0.00 3.85 F
721 723 0.396435 TCGCCATTCACACAGTCCTT 59.604 50.0 0.00 0.0 0.00 3.36 F
1430 1444 0.685785 CTCACTGGGCTAGAGCTCCA 60.686 60.0 10.93 0.0 41.95 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1417 1431 0.110104 ATGCAATGGAGCTCTAGCCC 59.890 55.000 14.64 0.0 43.38 5.19 R
2390 2413 0.030638 GCATGCAAACACCAGTCGTT 59.969 50.000 14.21 0.0 0.00 3.85 R
2516 2539 3.057596 ACAGCCATGTGACGTAATTTTGG 60.058 43.478 0.00 0.0 38.57 3.28 R
3426 3458 1.348064 ACACAATCAACTCGGGAGGA 58.652 50.000 0.00 0.0 0.00 3.71 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 8.255394 ACATTCAATTTGCTATGCTTAAAACC 57.745 30.769 9.75 0.00 0.00 3.27
33 34 8.096414 ACATTCAATTTGCTATGCTTAAAACCT 58.904 29.630 9.75 0.00 0.00 3.50
34 35 7.887996 TTCAATTTGCTATGCTTAAAACCTG 57.112 32.000 0.00 0.00 0.00 4.00
35 36 6.397272 TCAATTTGCTATGCTTAAAACCTGG 58.603 36.000 0.00 0.00 0.00 4.45
36 37 3.866883 TTGCTATGCTTAAAACCTGGC 57.133 42.857 0.00 0.00 0.00 4.85
37 38 2.801483 TGCTATGCTTAAAACCTGGCA 58.199 42.857 0.00 0.00 39.06 4.92
38 39 3.364549 TGCTATGCTTAAAACCTGGCAT 58.635 40.909 0.00 0.00 45.57 4.40
39 40 3.381272 TGCTATGCTTAAAACCTGGCATC 59.619 43.478 2.52 0.00 43.17 3.91
40 41 3.381272 GCTATGCTTAAAACCTGGCATCA 59.619 43.478 2.52 0.00 43.17 3.07
41 42 3.874392 ATGCTTAAAACCTGGCATCAC 57.126 42.857 0.00 0.00 40.79 3.06
42 43 2.591923 TGCTTAAAACCTGGCATCACA 58.408 42.857 0.00 0.00 0.00 3.58
43 44 3.164268 TGCTTAAAACCTGGCATCACAT 58.836 40.909 0.00 0.00 0.00 3.21
44 45 3.577848 TGCTTAAAACCTGGCATCACATT 59.422 39.130 0.00 0.00 0.00 2.71
45 46 4.040217 TGCTTAAAACCTGGCATCACATTT 59.960 37.500 0.00 0.00 0.00 2.32
46 47 4.996758 GCTTAAAACCTGGCATCACATTTT 59.003 37.500 0.00 0.00 0.00 1.82
47 48 5.469760 GCTTAAAACCTGGCATCACATTTTT 59.530 36.000 0.00 0.00 0.00 1.94
48 49 6.648725 GCTTAAAACCTGGCATCACATTTTTA 59.351 34.615 0.00 0.00 0.00 1.52
49 50 7.148590 GCTTAAAACCTGGCATCACATTTTTAG 60.149 37.037 0.00 0.00 0.00 1.85
50 51 6.418057 AAAACCTGGCATCACATTTTTAGA 57.582 33.333 0.00 0.00 0.00 2.10
51 52 6.418057 AAACCTGGCATCACATTTTTAGAA 57.582 33.333 0.00 0.00 0.00 2.10
52 53 6.418057 AACCTGGCATCACATTTTTAGAAA 57.582 33.333 0.00 0.00 0.00 2.52
53 54 6.418057 ACCTGGCATCACATTTTTAGAAAA 57.582 33.333 0.00 0.00 0.00 2.29
54 55 6.825610 ACCTGGCATCACATTTTTAGAAAAA 58.174 32.000 2.82 2.82 41.59 1.94
129 130 9.706691 TTTAGAAGAACTACCTCTTTGTATGTG 57.293 33.333 0.00 0.00 35.76 3.21
130 131 7.304497 AGAAGAACTACCTCTTTGTATGTGT 57.696 36.000 0.00 0.00 35.76 3.72
131 132 7.155328 AGAAGAACTACCTCTTTGTATGTGTG 58.845 38.462 0.00 0.00 35.76 3.82
132 133 6.420913 AGAACTACCTCTTTGTATGTGTGT 57.579 37.500 0.00 0.00 0.00 3.72
133 134 6.223852 AGAACTACCTCTTTGTATGTGTGTG 58.776 40.000 0.00 0.00 0.00 3.82
134 135 5.546621 ACTACCTCTTTGTATGTGTGTGT 57.453 39.130 0.00 0.00 0.00 3.72
135 136 5.297547 ACTACCTCTTTGTATGTGTGTGTG 58.702 41.667 0.00 0.00 0.00 3.82
136 137 4.150897 ACCTCTTTGTATGTGTGTGTGT 57.849 40.909 0.00 0.00 0.00 3.72
137 138 3.876914 ACCTCTTTGTATGTGTGTGTGTG 59.123 43.478 0.00 0.00 0.00 3.82
138 139 3.876914 CCTCTTTGTATGTGTGTGTGTGT 59.123 43.478 0.00 0.00 0.00 3.72
139 140 4.260743 CCTCTTTGTATGTGTGTGTGTGTG 60.261 45.833 0.00 0.00 0.00 3.82
140 141 4.257731 TCTTTGTATGTGTGTGTGTGTGT 58.742 39.130 0.00 0.00 0.00 3.72
141 142 4.094146 TCTTTGTATGTGTGTGTGTGTGTG 59.906 41.667 0.00 0.00 0.00 3.82
142 143 2.979240 TGTATGTGTGTGTGTGTGTGT 58.021 42.857 0.00 0.00 0.00 3.72
143 144 2.675348 TGTATGTGTGTGTGTGTGTGTG 59.325 45.455 0.00 0.00 0.00 3.82
144 145 1.819928 ATGTGTGTGTGTGTGTGTGT 58.180 45.000 0.00 0.00 0.00 3.72
145 146 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
146 147 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
147 148 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
148 149 0.167908 GTGTGTGTGTGTGTGTGTGG 59.832 55.000 0.00 0.00 0.00 4.17
149 150 0.035458 TGTGTGTGTGTGTGTGTGGA 59.965 50.000 0.00 0.00 0.00 4.02
150 151 0.726827 GTGTGTGTGTGTGTGTGGAG 59.273 55.000 0.00 0.00 0.00 3.86
151 152 0.610687 TGTGTGTGTGTGTGTGGAGA 59.389 50.000 0.00 0.00 0.00 3.71
152 153 1.002544 TGTGTGTGTGTGTGTGGAGAA 59.997 47.619 0.00 0.00 0.00 2.87
153 154 2.080693 GTGTGTGTGTGTGTGGAGAAA 58.919 47.619 0.00 0.00 0.00 2.52
154 155 2.486203 GTGTGTGTGTGTGTGGAGAAAA 59.514 45.455 0.00 0.00 0.00 2.29
155 156 2.486203 TGTGTGTGTGTGTGGAGAAAAC 59.514 45.455 0.00 0.00 0.00 2.43
156 157 2.486203 GTGTGTGTGTGTGGAGAAAACA 59.514 45.455 0.00 0.00 0.00 2.83
157 158 2.746904 TGTGTGTGTGTGGAGAAAACAG 59.253 45.455 0.00 0.00 0.00 3.16
158 159 1.742831 TGTGTGTGTGGAGAAAACAGC 59.257 47.619 0.00 0.00 0.00 4.40
159 160 1.065551 GTGTGTGTGGAGAAAACAGCC 59.934 52.381 0.00 0.00 0.00 4.85
160 161 1.064758 TGTGTGTGGAGAAAACAGCCT 60.065 47.619 0.00 0.00 0.00 4.58
161 162 1.604278 GTGTGTGGAGAAAACAGCCTC 59.396 52.381 0.00 0.00 0.00 4.70
162 163 1.211703 TGTGTGGAGAAAACAGCCTCA 59.788 47.619 0.00 0.00 0.00 3.86
163 164 1.876156 GTGTGGAGAAAACAGCCTCAG 59.124 52.381 0.00 0.00 0.00 3.35
164 165 1.768275 TGTGGAGAAAACAGCCTCAGA 59.232 47.619 0.00 0.00 0.00 3.27
165 166 2.172505 TGTGGAGAAAACAGCCTCAGAA 59.827 45.455 0.00 0.00 0.00 3.02
166 167 3.181440 TGTGGAGAAAACAGCCTCAGAAT 60.181 43.478 0.00 0.00 0.00 2.40
167 168 3.823304 GTGGAGAAAACAGCCTCAGAATT 59.177 43.478 0.00 0.00 0.00 2.17
168 169 5.003804 GTGGAGAAAACAGCCTCAGAATTA 58.996 41.667 0.00 0.00 0.00 1.40
169 170 5.649831 GTGGAGAAAACAGCCTCAGAATTAT 59.350 40.000 0.00 0.00 0.00 1.28
170 171 6.823689 GTGGAGAAAACAGCCTCAGAATTATA 59.176 38.462 0.00 0.00 0.00 0.98
171 172 7.011857 GTGGAGAAAACAGCCTCAGAATTATAG 59.988 40.741 0.00 0.00 0.00 1.31
172 173 6.017523 GGAGAAAACAGCCTCAGAATTATAGC 60.018 42.308 0.00 0.00 0.00 2.97
173 174 6.657875 AGAAAACAGCCTCAGAATTATAGCT 58.342 36.000 0.00 0.00 0.00 3.32
176 177 3.072944 CAGCCTCAGAATTATAGCTGGC 58.927 50.000 0.00 0.00 43.05 4.85
177 178 2.039613 AGCCTCAGAATTATAGCTGGCC 59.960 50.000 0.00 0.00 39.90 5.36
178 179 2.224621 GCCTCAGAATTATAGCTGGCCA 60.225 50.000 4.71 4.71 33.66 5.36
179 180 3.748668 GCCTCAGAATTATAGCTGGCCAA 60.749 47.826 7.01 0.00 33.66 4.52
180 181 4.464008 CCTCAGAATTATAGCTGGCCAAA 58.536 43.478 7.01 0.00 33.05 3.28
181 182 5.075493 CCTCAGAATTATAGCTGGCCAAAT 58.925 41.667 7.01 0.00 33.05 2.32
182 183 5.048224 CCTCAGAATTATAGCTGGCCAAATG 60.048 44.000 7.01 0.00 33.05 2.32
183 184 4.828939 TCAGAATTATAGCTGGCCAAATGG 59.171 41.667 7.01 0.00 38.53 3.16
184 185 4.021719 CAGAATTATAGCTGGCCAAATGGG 60.022 45.833 7.01 0.00 40.85 4.00
244 245 4.329545 GTCTTGGGCCAGGCACGA 62.330 66.667 15.19 9.06 32.76 4.35
245 246 4.329545 TCTTGGGCCAGGCACGAC 62.330 66.667 15.19 0.34 32.76 4.34
246 247 4.641645 CTTGGGCCAGGCACGACA 62.642 66.667 15.19 3.34 32.76 4.35
247 248 4.947147 TTGGGCCAGGCACGACAC 62.947 66.667 15.19 0.00 32.76 3.67
257 258 3.152703 CACGACACGGGCTAAACG 58.847 61.111 0.00 0.00 37.36 3.60
258 259 2.048877 ACGACACGGGCTAAACGG 60.049 61.111 0.00 0.00 35.23 4.44
259 260 2.812178 CGACACGGGCTAAACGGG 60.812 66.667 0.00 0.00 41.32 5.28
260 261 3.122971 GACACGGGCTAAACGGGC 61.123 66.667 0.00 0.00 38.56 6.13
344 345 4.848685 GGCACGACCCGATTATGT 57.151 55.556 0.00 0.00 0.00 2.29
345 346 3.074594 GGCACGACCCGATTATGTT 57.925 52.632 0.00 0.00 0.00 2.71
346 347 1.375551 GGCACGACCCGATTATGTTT 58.624 50.000 0.00 0.00 0.00 2.83
347 348 1.741145 GGCACGACCCGATTATGTTTT 59.259 47.619 0.00 0.00 0.00 2.43
348 349 2.162809 GGCACGACCCGATTATGTTTTT 59.837 45.455 0.00 0.00 0.00 1.94
399 400 9.830186 TGGCCCAATATATAAAAATAGGCTAAA 57.170 29.630 0.00 0.00 37.98 1.85
418 419 3.840890 AAAAACACTCAGTGCGTCAAA 57.159 38.095 4.13 0.00 36.98 2.69
419 420 4.370364 AAAAACACTCAGTGCGTCAAAT 57.630 36.364 4.13 0.00 36.98 2.32
420 421 5.493133 AAAAACACTCAGTGCGTCAAATA 57.507 34.783 4.13 0.00 36.98 1.40
421 422 5.493133 AAAACACTCAGTGCGTCAAATAA 57.507 34.783 4.13 0.00 36.98 1.40
422 423 4.468095 AACACTCAGTGCGTCAAATAAC 57.532 40.909 4.13 0.00 36.98 1.89
423 424 3.462982 ACACTCAGTGCGTCAAATAACA 58.537 40.909 4.13 0.00 36.98 2.41
424 425 3.494626 ACACTCAGTGCGTCAAATAACAG 59.505 43.478 4.13 0.00 36.98 3.16
425 426 3.067106 ACTCAGTGCGTCAAATAACAGG 58.933 45.455 0.00 0.00 0.00 4.00
426 427 1.804151 TCAGTGCGTCAAATAACAGGC 59.196 47.619 0.00 0.00 0.00 4.85
427 428 1.806542 CAGTGCGTCAAATAACAGGCT 59.193 47.619 0.00 0.00 0.00 4.58
428 429 1.806542 AGTGCGTCAAATAACAGGCTG 59.193 47.619 14.16 14.16 0.00 4.85
429 430 1.804151 GTGCGTCAAATAACAGGCTGA 59.196 47.619 23.66 0.00 0.00 4.26
430 431 2.225491 GTGCGTCAAATAACAGGCTGAA 59.775 45.455 23.66 9.24 0.00 3.02
431 432 2.881513 TGCGTCAAATAACAGGCTGAAA 59.118 40.909 23.66 8.84 0.00 2.69
432 433 3.316588 TGCGTCAAATAACAGGCTGAAAA 59.683 39.130 23.66 6.07 0.00 2.29
433 434 4.022416 TGCGTCAAATAACAGGCTGAAAAT 60.022 37.500 23.66 8.29 0.00 1.82
434 435 5.182190 TGCGTCAAATAACAGGCTGAAAATA 59.818 36.000 23.66 8.85 0.00 1.40
435 436 6.127758 TGCGTCAAATAACAGGCTGAAAATAT 60.128 34.615 23.66 10.72 0.00 1.28
436 437 6.197096 GCGTCAAATAACAGGCTGAAAATATG 59.803 38.462 23.66 12.30 0.00 1.78
437 438 6.197096 CGTCAAATAACAGGCTGAAAATATGC 59.803 38.462 23.66 4.75 0.00 3.14
438 439 6.197096 GTCAAATAACAGGCTGAAAATATGCG 59.803 38.462 23.66 8.60 0.00 4.73
439 440 4.836125 ATAACAGGCTGAAAATATGCGG 57.164 40.909 23.66 0.00 0.00 5.69
440 441 0.740737 ACAGGCTGAAAATATGCGGC 59.259 50.000 23.66 0.00 35.68 6.53
443 444 2.114638 GCTGAAAATATGCGGCCCA 58.885 52.632 0.00 0.00 0.00 5.36
444 445 0.249031 GCTGAAAATATGCGGCCCAC 60.249 55.000 0.00 0.00 0.00 4.61
445 446 0.385390 CTGAAAATATGCGGCCCACC 59.615 55.000 0.00 0.00 0.00 4.61
463 464 2.559330 GTGCTAAACGGGCCAACG 59.441 61.111 4.39 1.48 40.31 4.10
477 478 4.622650 AACGTGCCGGCCCGTTTA 62.623 61.111 38.23 11.19 44.16 2.01
480 481 2.265424 GTGCCGGCCCGTTTACTA 59.735 61.111 26.77 0.00 0.00 1.82
481 482 1.375780 GTGCCGGCCCGTTTACTAA 60.376 57.895 26.77 0.00 0.00 2.24
482 483 1.375780 TGCCGGCCCGTTTACTAAC 60.376 57.895 26.77 0.00 0.00 2.34
483 484 1.078918 GCCGGCCCGTTTACTAACT 60.079 57.895 18.11 0.00 31.89 2.24
484 485 1.363885 GCCGGCCCGTTTACTAACTG 61.364 60.000 18.11 0.00 31.89 3.16
485 486 0.741927 CCGGCCCGTTTACTAACTGG 60.742 60.000 0.85 0.00 40.48 4.00
486 487 0.741927 CGGCCCGTTTACTAACTGGG 60.742 60.000 0.00 11.19 44.21 4.45
488 489 3.164026 CCCGTTTACTAACTGGGCC 57.836 57.895 0.00 0.00 39.48 5.80
489 490 0.741927 CCCGTTTACTAACTGGGCCG 60.742 60.000 0.00 0.00 39.48 6.13
490 491 0.741927 CCGTTTACTAACTGGGCCGG 60.742 60.000 11.83 11.83 31.89 6.13
491 492 0.741927 CGTTTACTAACTGGGCCGGG 60.742 60.000 18.49 6.00 31.89 5.73
492 493 1.028330 GTTTACTAACTGGGCCGGGC 61.028 60.000 22.00 22.00 0.00 6.13
544 545 3.610637 GGCACGGCCCGTATAATAA 57.389 52.632 9.25 0.00 44.06 1.40
545 546 2.103537 GGCACGGCCCGTATAATAAT 57.896 50.000 9.25 0.00 44.06 1.28
546 547 2.004733 GGCACGGCCCGTATAATAATC 58.995 52.381 9.25 0.00 44.06 1.75
547 548 1.657094 GCACGGCCCGTATAATAATCG 59.343 52.381 9.25 0.00 38.32 3.34
548 549 2.927871 GCACGGCCCGTATAATAATCGT 60.928 50.000 9.25 0.00 38.32 3.73
549 550 2.664568 CACGGCCCGTATAATAATCGTG 59.335 50.000 9.25 0.00 38.32 4.35
550 551 1.657094 CGGCCCGTATAATAATCGTGC 59.343 52.381 0.00 0.00 0.00 5.34
551 552 2.004733 GGCCCGTATAATAATCGTGCC 58.995 52.381 0.00 0.00 40.23 5.01
552 553 2.004733 GCCCGTATAATAATCGTGCCC 58.995 52.381 0.00 0.00 0.00 5.36
553 554 2.354403 GCCCGTATAATAATCGTGCCCT 60.354 50.000 0.00 0.00 0.00 5.19
554 555 3.259064 CCCGTATAATAATCGTGCCCTG 58.741 50.000 0.00 0.00 0.00 4.45
555 556 3.259064 CCGTATAATAATCGTGCCCTGG 58.741 50.000 0.00 0.00 0.00 4.45
556 557 2.671396 CGTATAATAATCGTGCCCTGGC 59.329 50.000 0.00 0.00 42.35 4.85
557 558 1.808411 ATAATAATCGTGCCCTGGCG 58.192 50.000 3.32 0.00 45.51 5.69
558 559 0.250124 TAATAATCGTGCCCTGGCGG 60.250 55.000 3.32 0.00 45.51 6.13
584 585 2.895372 GGGCCAGGCACGATTACG 60.895 66.667 15.19 0.00 45.75 3.18
585 586 2.185867 GGCCAGGCACGATTACGA 59.814 61.111 15.19 0.00 42.66 3.43
586 587 1.227556 GGCCAGGCACGATTACGAT 60.228 57.895 15.19 0.00 42.66 3.73
587 588 1.498865 GGCCAGGCACGATTACGATG 61.499 60.000 15.19 0.00 42.66 3.84
588 589 1.498865 GCCAGGCACGATTACGATGG 61.499 60.000 6.55 0.00 42.66 3.51
589 590 0.880278 CCAGGCACGATTACGATGGG 60.880 60.000 0.00 0.00 42.66 4.00
590 591 1.227556 AGGCACGATTACGATGGGC 60.228 57.895 0.00 0.00 42.66 5.36
591 592 2.251642 GGCACGATTACGATGGGCC 61.252 63.158 0.00 0.00 42.66 5.80
592 593 2.594962 GCACGATTACGATGGGCCG 61.595 63.158 0.00 0.00 42.66 6.13
593 594 1.954146 CACGATTACGATGGGCCGG 60.954 63.158 0.00 0.00 42.66 6.13
594 595 2.357034 CGATTACGATGGGCCGGG 60.357 66.667 2.18 0.00 42.66 5.73
595 596 2.668550 GATTACGATGGGCCGGGC 60.669 66.667 22.00 22.00 0.00 6.13
651 652 1.340405 ACTCAGAATGCCGGCAAATCT 60.340 47.619 36.33 33.37 34.76 2.40
671 672 2.512515 GGCTAGCCCAACGCAGAG 60.513 66.667 24.19 0.00 41.38 3.35
705 707 2.974698 CCCATCCATTCGCCTCGC 60.975 66.667 0.00 0.00 0.00 5.03
714 716 1.369091 ATTCGCCTCGCCATTCACAC 61.369 55.000 0.00 0.00 0.00 3.82
715 717 2.723586 TTCGCCTCGCCATTCACACA 62.724 55.000 0.00 0.00 0.00 3.72
716 718 2.743752 CGCCTCGCCATTCACACAG 61.744 63.158 0.00 0.00 0.00 3.66
717 719 1.672356 GCCTCGCCATTCACACAGT 60.672 57.895 0.00 0.00 0.00 3.55
719 721 1.021390 CCTCGCCATTCACACAGTCC 61.021 60.000 0.00 0.00 0.00 3.85
720 722 0.036952 CTCGCCATTCACACAGTCCT 60.037 55.000 0.00 0.00 0.00 3.85
721 723 0.396435 TCGCCATTCACACAGTCCTT 59.604 50.000 0.00 0.00 0.00 3.36
722 724 0.798776 CGCCATTCACACAGTCCTTC 59.201 55.000 0.00 0.00 0.00 3.46
728 730 2.685106 TCACACAGTCCTTCCTCTCT 57.315 50.000 0.00 0.00 0.00 3.10
769 771 1.080093 CGCGGTTCTAGTCTGCCAA 60.080 57.895 0.00 0.00 34.10 4.52
796 798 3.628280 GAGCGAACCGGCGAAGACT 62.628 63.158 9.30 0.00 38.18 3.24
813 815 2.126618 TAACGCGACGCAGGTGAG 60.127 61.111 21.35 4.53 0.00 3.51
859 861 3.127352 CTACCTCGCTCTCCGGCAC 62.127 68.421 0.00 0.00 37.59 5.01
896 898 5.106118 GCCTTCCACTTATCTCAACCTTTTC 60.106 44.000 0.00 0.00 0.00 2.29
916 918 2.031012 TTGGCTGTCCGTGCTCTG 59.969 61.111 0.00 0.00 34.14 3.35
956 958 2.107141 CTCGACGGAATGCTCCCC 59.893 66.667 0.00 0.00 38.71 4.81
1011 1025 2.278013 GCGGAGATGGACGACGTC 60.278 66.667 19.70 19.70 35.24 4.34
1146 1160 4.208686 GACTTCGGGAGCGCCGAT 62.209 66.667 2.29 0.00 39.46 4.18
1195 1209 2.549611 CTTCCTCCGTCGCCACTCAG 62.550 65.000 0.00 0.00 0.00 3.35
1244 1258 2.214181 CTGGACGACAGGGAGTTCGG 62.214 65.000 0.00 0.00 43.70 4.30
1281 1295 2.030946 GTCCTTTCAGCATGTGTATCGC 59.969 50.000 0.00 0.00 37.40 4.58
1363 1377 2.275380 AACCCCAACTTCCGCATGC 61.275 57.895 7.91 7.91 0.00 4.06
1417 1431 1.190833 ACTCTCCCAGCACCTCACTG 61.191 60.000 0.00 0.00 34.82 3.66
1430 1444 0.685785 CTCACTGGGCTAGAGCTCCA 60.686 60.000 10.93 0.00 41.95 3.86
1435 1449 1.273986 TGGGCTAGAGCTCCATTGCA 61.274 55.000 10.93 0.00 41.95 4.08
1455 1469 1.061570 CCGCTGCGCTCTTGATTTC 59.938 57.895 18.00 0.00 0.00 2.17
1500 1514 1.929836 CTTAAGATGGAGCAGTGCGTC 59.070 52.381 10.00 7.69 0.00 5.19
1547 1561 1.186200 TCCTTGCGACAGCTGAGTAT 58.814 50.000 23.35 0.00 45.42 2.12
1570 1584 1.973515 TCTGCTGTGAACTCTCCATGT 59.026 47.619 0.00 0.00 0.00 3.21
1573 1587 1.446907 CTGTGAACTCTCCATGTGGC 58.553 55.000 0.00 0.00 34.44 5.01
1585 1599 1.935873 CCATGTGGCATCGTACTCAAG 59.064 52.381 0.00 0.00 0.00 3.02
1636 1650 8.682710 TGGAATTAATTAATTGTGCTGGTAGAC 58.317 33.333 24.60 8.26 36.13 2.59
1734 1748 2.303890 TGTGTCAGGCTGTCTTGATGAT 59.696 45.455 15.27 0.00 0.00 2.45
1754 1768 2.874014 TGATCCATGCTTTGGTTGTCA 58.126 42.857 6.22 6.82 46.52 3.58
1825 1839 1.002792 GTTTGTCTCGAGCCAAACACC 60.003 52.381 34.82 16.81 46.06 4.16
1870 1884 1.743996 TGCGGTATGTATGCTTGCAA 58.256 45.000 0.00 0.00 0.00 4.08
1890 1904 5.365314 TGCAACCCCTTTATTTTGTCTTCTT 59.635 36.000 0.00 0.00 0.00 2.52
1923 1937 5.872617 TCAAGAACCATACCATCAACTAACG 59.127 40.000 0.00 0.00 0.00 3.18
2006 2020 8.352137 TCAACCAACATCATAATTCAGTCAAT 57.648 30.769 0.00 0.00 0.00 2.57
2007 2021 8.805175 TCAACCAACATCATAATTCAGTCAATT 58.195 29.630 0.00 0.00 38.35 2.32
2083 2106 3.587951 CAGGAATCCCCTCATGATCTGAT 59.412 47.826 0.00 0.00 45.60 2.90
2092 2115 6.158520 TCCCCTCATGATCTGATCTTTTTGTA 59.841 38.462 17.82 0.00 32.10 2.41
2150 2173 8.798402 CCAAAATGGTACCTTTACTATGACAAA 58.202 33.333 14.36 0.00 30.21 2.83
2211 2234 8.477984 TGCTACAAATCTTTTCCATTATTTGC 57.522 30.769 0.00 0.00 41.06 3.68
2272 2295 4.637534 ACCGAAATGATTGGTCTCATTCTG 59.362 41.667 0.21 0.00 43.37 3.02
2281 2304 8.722480 TGATTGGTCTCATTCTGTACATAAAG 57.278 34.615 0.00 0.00 0.00 1.85
2284 2307 7.252612 TGGTCTCATTCTGTACATAAAGGAA 57.747 36.000 0.00 0.00 0.00 3.36
2286 2309 6.539103 GGTCTCATTCTGTACATAAAGGAACC 59.461 42.308 0.00 8.19 0.00 3.62
2290 2313 4.216411 TCTGTACATAAAGGAACCAGCC 57.784 45.455 0.00 0.00 0.00 4.85
2300 2323 1.810030 GAACCAGCCGGCTTACTCG 60.810 63.158 30.60 15.77 34.57 4.18
2390 2413 7.685481 TCCCATGTTAAAGACTTTGATACTCA 58.315 34.615 10.80 0.00 0.00 3.41
2472 2495 7.390718 GCCAAATCTTGAGAAGGTTACTCTTAA 59.609 37.037 0.00 0.00 35.66 1.85
2478 2501 8.784043 TCTTGAGAAGGTTACTCTTAAATTTGC 58.216 33.333 0.00 0.00 35.66 3.68
2516 2539 3.871594 GTGGATGGATAGCTGTGTGTTAC 59.128 47.826 0.00 0.00 0.00 2.50
2603 2627 4.808414 TGGTGACAGAAGGAGATAACAG 57.192 45.455 0.00 0.00 35.01 3.16
2728 2752 5.389859 TTGTGGCATATCACTGGAAAAAG 57.610 39.130 0.00 0.00 38.40 2.27
2787 2811 7.201530 CCTGGATGTGAGTTAAAAGTATCGAAC 60.202 40.741 0.00 0.00 0.00 3.95
2821 2845 6.963049 TCTTCTGTTTACGCTATTTTCCTC 57.037 37.500 0.00 0.00 0.00 3.71
2950 2978 5.999600 AGTGTAGTTTTGCTTATAAACGGGT 59.000 36.000 0.00 0.00 39.77 5.28
2971 2999 5.826208 GGGTCAAAAGAGAACCTCAAACTTA 59.174 40.000 0.00 0.00 42.30 2.24
3011 3039 9.619316 TTTATTTGAATGTATGTGGAAGAAACG 57.381 29.630 0.00 0.00 0.00 3.60
3074 3102 1.298859 CGGGGCAAAAGAGAACCTCG 61.299 60.000 0.00 0.00 40.26 4.63
3076 3104 1.544759 GGGGCAAAAGAGAACCTCGAA 60.545 52.381 0.00 0.00 35.36 3.71
3139 3167 8.467402 AGAAACATAGAAACTACATTCGTGAG 57.533 34.615 0.00 0.00 34.46 3.51
3187 3215 7.849322 ACTGGTAAAACCTGTCCAAAATTAT 57.151 32.000 3.06 0.00 45.70 1.28
3255 3285 2.877043 ATTTGCTGCCATTCGGATTC 57.123 45.000 0.00 0.00 0.00 2.52
3279 3309 6.866770 TCCACTTATGAAAACTAACGTCTGAG 59.133 38.462 0.00 0.00 0.00 3.35
3361 3392 8.229811 GTCCATGAAAACTTTCCATTTTTATGC 58.770 33.333 0.00 0.00 39.70 3.14
3459 3493 8.633075 AGTTGATTGTGTTGTTTGAATACTTG 57.367 30.769 0.00 0.00 0.00 3.16
3516 3551 4.813697 CCTCAGCTAAAGGTAAGAAGATGC 59.186 45.833 6.22 0.00 0.00 3.91
3609 3645 2.202566 GTAGCTGTCTGCCGTAAATCC 58.797 52.381 0.00 0.00 44.23 3.01
3736 3774 5.957798 AGATAATCATGTTTGCTTGTGGTG 58.042 37.500 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 8.720562 GGTTTTAAGCATAGCAAATTGAATGTT 58.279 29.630 0.00 0.00 0.00 2.71
7 8 8.096414 AGGTTTTAAGCATAGCAAATTGAATGT 58.904 29.630 0.00 0.00 0.00 2.71
8 9 8.385111 CAGGTTTTAAGCATAGCAAATTGAATG 58.615 33.333 0.00 0.81 0.00 2.67
9 10 7.550196 CCAGGTTTTAAGCATAGCAAATTGAAT 59.450 33.333 0.00 0.00 0.00 2.57
10 11 6.873076 CCAGGTTTTAAGCATAGCAAATTGAA 59.127 34.615 0.00 0.00 0.00 2.69
11 12 6.397272 CCAGGTTTTAAGCATAGCAAATTGA 58.603 36.000 0.00 0.00 0.00 2.57
12 13 5.063817 GCCAGGTTTTAAGCATAGCAAATTG 59.936 40.000 0.00 0.00 0.00 2.32
13 14 5.178061 GCCAGGTTTTAAGCATAGCAAATT 58.822 37.500 0.00 0.00 0.00 1.82
14 15 4.222588 TGCCAGGTTTTAAGCATAGCAAAT 59.777 37.500 0.00 0.00 0.00 2.32
15 16 3.576118 TGCCAGGTTTTAAGCATAGCAAA 59.424 39.130 0.00 0.00 0.00 3.68
16 17 3.161067 TGCCAGGTTTTAAGCATAGCAA 58.839 40.909 0.00 0.00 0.00 3.91
17 18 2.801483 TGCCAGGTTTTAAGCATAGCA 58.199 42.857 0.00 0.00 0.00 3.49
18 19 3.381272 TGATGCCAGGTTTTAAGCATAGC 59.619 43.478 0.00 0.00 45.57 2.97
19 20 4.398988 TGTGATGCCAGGTTTTAAGCATAG 59.601 41.667 0.00 0.00 45.57 2.23
20 21 4.339748 TGTGATGCCAGGTTTTAAGCATA 58.660 39.130 0.00 0.00 45.57 3.14
22 23 2.591923 TGTGATGCCAGGTTTTAAGCA 58.408 42.857 0.00 0.00 40.00 3.91
23 24 3.874392 ATGTGATGCCAGGTTTTAAGC 57.126 42.857 0.00 0.00 0.00 3.09
24 25 8.087750 TCTAAAAATGTGATGCCAGGTTTTAAG 58.912 33.333 0.00 0.00 0.00 1.85
25 26 7.957002 TCTAAAAATGTGATGCCAGGTTTTAA 58.043 30.769 0.00 0.00 0.00 1.52
26 27 7.531857 TCTAAAAATGTGATGCCAGGTTTTA 57.468 32.000 0.00 0.00 0.00 1.52
27 28 6.418057 TCTAAAAATGTGATGCCAGGTTTT 57.582 33.333 0.00 0.00 0.00 2.43
28 29 6.418057 TTCTAAAAATGTGATGCCAGGTTT 57.582 33.333 0.00 0.00 0.00 3.27
29 30 6.418057 TTTCTAAAAATGTGATGCCAGGTT 57.582 33.333 0.00 0.00 0.00 3.50
30 31 6.418057 TTTTCTAAAAATGTGATGCCAGGT 57.582 33.333 0.00 0.00 0.00 4.00
103 104 9.706691 CACATACAAAGAGGTAGTTCTTCTAAA 57.293 33.333 0.00 0.00 36.42 1.85
104 105 8.867097 ACACATACAAAGAGGTAGTTCTTCTAA 58.133 33.333 0.00 0.00 36.42 2.10
105 106 8.304596 CACACATACAAAGAGGTAGTTCTTCTA 58.695 37.037 0.00 0.00 36.42 2.10
106 107 7.155328 CACACATACAAAGAGGTAGTTCTTCT 58.845 38.462 0.00 0.00 36.42 2.85
107 108 6.929606 ACACACATACAAAGAGGTAGTTCTTC 59.070 38.462 0.00 0.00 36.42 2.87
108 109 6.706270 CACACACATACAAAGAGGTAGTTCTT 59.294 38.462 0.00 0.00 39.03 2.52
109 110 6.183360 ACACACACATACAAAGAGGTAGTTCT 60.183 38.462 0.00 0.00 0.00 3.01
110 111 5.989777 ACACACACATACAAAGAGGTAGTTC 59.010 40.000 0.00 0.00 0.00 3.01
111 112 5.758296 CACACACACATACAAAGAGGTAGTT 59.242 40.000 0.00 0.00 0.00 2.24
112 113 5.163343 ACACACACACATACAAAGAGGTAGT 60.163 40.000 0.00 0.00 0.00 2.73
113 114 5.177511 CACACACACACATACAAAGAGGTAG 59.822 44.000 0.00 0.00 0.00 3.18
114 115 5.053811 CACACACACACATACAAAGAGGTA 58.946 41.667 0.00 0.00 0.00 3.08
115 116 3.876914 CACACACACACATACAAAGAGGT 59.123 43.478 0.00 0.00 0.00 3.85
116 117 3.876914 ACACACACACACATACAAAGAGG 59.123 43.478 0.00 0.00 0.00 3.69
117 118 4.332543 ACACACACACACACATACAAAGAG 59.667 41.667 0.00 0.00 0.00 2.85
118 119 4.094146 CACACACACACACACATACAAAGA 59.906 41.667 0.00 0.00 0.00 2.52
119 120 4.142708 ACACACACACACACACATACAAAG 60.143 41.667 0.00 0.00 0.00 2.77
120 121 3.753797 ACACACACACACACACATACAAA 59.246 39.130 0.00 0.00 0.00 2.83
121 122 3.126000 CACACACACACACACACATACAA 59.874 43.478 0.00 0.00 0.00 2.41
122 123 2.675348 CACACACACACACACACATACA 59.325 45.455 0.00 0.00 0.00 2.29
123 124 2.675844 ACACACACACACACACACATAC 59.324 45.455 0.00 0.00 0.00 2.39
124 125 2.675348 CACACACACACACACACACATA 59.325 45.455 0.00 0.00 0.00 2.29
125 126 1.468127 CACACACACACACACACACAT 59.532 47.619 0.00 0.00 0.00 3.21
126 127 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
127 128 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
128 129 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
129 130 0.167908 CCACACACACACACACACAC 59.832 55.000 0.00 0.00 0.00 3.82
130 131 0.035458 TCCACACACACACACACACA 59.965 50.000 0.00 0.00 0.00 3.72
131 132 0.726827 CTCCACACACACACACACAC 59.273 55.000 0.00 0.00 0.00 3.82
132 133 0.610687 TCTCCACACACACACACACA 59.389 50.000 0.00 0.00 0.00 3.72
133 134 1.732941 TTCTCCACACACACACACAC 58.267 50.000 0.00 0.00 0.00 3.82
134 135 2.481289 TTTCTCCACACACACACACA 57.519 45.000 0.00 0.00 0.00 3.72
135 136 2.486203 TGTTTTCTCCACACACACACAC 59.514 45.455 0.00 0.00 0.00 3.82
136 137 2.746904 CTGTTTTCTCCACACACACACA 59.253 45.455 0.00 0.00 0.00 3.72
137 138 2.477863 GCTGTTTTCTCCACACACACAC 60.478 50.000 0.00 0.00 0.00 3.82
138 139 1.742831 GCTGTTTTCTCCACACACACA 59.257 47.619 0.00 0.00 0.00 3.72
139 140 1.065551 GGCTGTTTTCTCCACACACAC 59.934 52.381 0.00 0.00 0.00 3.82
140 141 1.064758 AGGCTGTTTTCTCCACACACA 60.065 47.619 0.00 0.00 0.00 3.72
141 142 1.604278 GAGGCTGTTTTCTCCACACAC 59.396 52.381 0.00 0.00 0.00 3.82
142 143 1.211703 TGAGGCTGTTTTCTCCACACA 59.788 47.619 0.00 0.00 0.00 3.72
143 144 1.876156 CTGAGGCTGTTTTCTCCACAC 59.124 52.381 0.00 0.00 0.00 3.82
144 145 1.768275 TCTGAGGCTGTTTTCTCCACA 59.232 47.619 0.00 0.00 0.00 4.17
145 146 2.550830 TCTGAGGCTGTTTTCTCCAC 57.449 50.000 0.00 0.00 0.00 4.02
146 147 3.795688 ATTCTGAGGCTGTTTTCTCCA 57.204 42.857 0.00 0.00 0.00 3.86
147 148 6.017523 GCTATAATTCTGAGGCTGTTTTCTCC 60.018 42.308 0.00 0.00 0.00 3.71
148 149 6.765512 AGCTATAATTCTGAGGCTGTTTTCTC 59.234 38.462 0.00 0.00 0.00 2.87
149 150 6.541641 CAGCTATAATTCTGAGGCTGTTTTCT 59.458 38.462 0.00 0.00 41.21 2.52
150 151 6.238593 CCAGCTATAATTCTGAGGCTGTTTTC 60.239 42.308 10.97 0.00 43.57 2.29
151 152 5.591877 CCAGCTATAATTCTGAGGCTGTTTT 59.408 40.000 10.97 0.00 43.57 2.43
152 153 5.128919 CCAGCTATAATTCTGAGGCTGTTT 58.871 41.667 10.97 0.00 43.57 2.83
153 154 4.712476 CCAGCTATAATTCTGAGGCTGTT 58.288 43.478 10.97 0.00 43.57 3.16
154 155 3.495806 GCCAGCTATAATTCTGAGGCTGT 60.496 47.826 10.97 0.00 43.57 4.40
155 156 3.072944 GCCAGCTATAATTCTGAGGCTG 58.927 50.000 0.00 0.00 44.35 4.85
156 157 2.039613 GGCCAGCTATAATTCTGAGGCT 59.960 50.000 0.00 0.00 32.26 4.58
157 158 2.224621 TGGCCAGCTATAATTCTGAGGC 60.225 50.000 0.00 0.00 32.26 4.70
158 159 3.777106 TGGCCAGCTATAATTCTGAGG 57.223 47.619 0.00 0.00 32.26 3.86
159 160 5.048224 CCATTTGGCCAGCTATAATTCTGAG 60.048 44.000 5.11 0.00 32.26 3.35
160 161 4.828939 CCATTTGGCCAGCTATAATTCTGA 59.171 41.667 5.11 0.00 32.26 3.27
161 162 4.021719 CCCATTTGGCCAGCTATAATTCTG 60.022 45.833 5.11 0.00 0.00 3.02
162 163 4.154942 CCCATTTGGCCAGCTATAATTCT 58.845 43.478 5.11 0.00 0.00 2.40
163 164 4.525912 CCCATTTGGCCAGCTATAATTC 57.474 45.455 5.11 0.00 0.00 2.17
227 228 4.329545 TCGTGCCTGGCCCAAGAC 62.330 66.667 17.53 6.10 0.00 3.01
228 229 4.329545 GTCGTGCCTGGCCCAAGA 62.330 66.667 17.53 7.29 0.00 3.02
229 230 4.641645 TGTCGTGCCTGGCCCAAG 62.642 66.667 17.53 4.85 0.00 3.61
230 231 4.947147 GTGTCGTGCCTGGCCCAA 62.947 66.667 17.53 0.00 0.00 4.12
236 237 3.583276 TTAGCCCGTGTCGTGCCTG 62.583 63.158 0.00 0.00 29.06 4.85
237 238 2.874664 TTTAGCCCGTGTCGTGCCT 61.875 57.895 0.00 0.00 29.06 4.75
238 239 2.357760 TTTAGCCCGTGTCGTGCC 60.358 61.111 0.00 0.00 29.06 5.01
239 240 2.858158 GTTTAGCCCGTGTCGTGC 59.142 61.111 0.00 0.00 0.00 5.34
240 241 2.377310 CCGTTTAGCCCGTGTCGTG 61.377 63.158 0.00 0.00 0.00 4.35
241 242 2.048877 CCGTTTAGCCCGTGTCGT 60.049 61.111 0.00 0.00 0.00 4.34
242 243 2.812178 CCCGTTTAGCCCGTGTCG 60.812 66.667 0.00 0.00 0.00 4.35
243 244 3.122971 GCCCGTTTAGCCCGTGTC 61.123 66.667 0.00 0.00 0.00 3.67
244 245 4.710167 GGCCCGTTTAGCCCGTGT 62.710 66.667 0.00 0.00 45.16 4.49
322 323 2.546645 TAATCGGGTCGTGCCGTGTC 62.547 60.000 0.00 0.00 38.44 3.67
323 324 1.952102 ATAATCGGGTCGTGCCGTGT 61.952 55.000 0.00 0.00 38.44 4.49
324 325 1.227147 ATAATCGGGTCGTGCCGTG 60.227 57.895 0.00 0.00 38.44 4.94
325 326 1.227147 CATAATCGGGTCGTGCCGT 60.227 57.895 0.00 0.00 38.44 5.68
326 327 0.808453 AACATAATCGGGTCGTGCCG 60.808 55.000 0.00 0.00 38.44 5.69
327 328 1.375551 AAACATAATCGGGTCGTGCC 58.624 50.000 0.00 0.00 0.00 5.01
328 329 3.481112 AAAAACATAATCGGGTCGTGC 57.519 42.857 0.00 0.00 0.00 5.34
373 374 9.830186 TTTAGCCTATTTTTATATATTGGGCCA 57.170 29.630 0.00 0.00 37.98 5.36
398 399 3.840890 TTTGACGCACTGAGTGTTTTT 57.159 38.095 14.82 0.00 42.04 1.94
399 400 5.163703 TGTTATTTGACGCACTGAGTGTTTT 60.164 36.000 14.82 0.00 42.04 2.43
400 401 4.334203 TGTTATTTGACGCACTGAGTGTTT 59.666 37.500 14.82 0.81 42.04 2.83
401 402 3.874543 TGTTATTTGACGCACTGAGTGTT 59.125 39.130 14.82 1.21 42.04 3.32
402 403 3.462982 TGTTATTTGACGCACTGAGTGT 58.537 40.909 14.82 0.00 45.36 3.55
403 404 3.120546 CCTGTTATTTGACGCACTGAGTG 60.121 47.826 8.52 8.52 36.51 3.51
404 405 3.067106 CCTGTTATTTGACGCACTGAGT 58.933 45.455 0.00 0.00 0.00 3.41
405 406 2.159653 GCCTGTTATTTGACGCACTGAG 60.160 50.000 0.00 0.00 0.00 3.35
406 407 1.804151 GCCTGTTATTTGACGCACTGA 59.196 47.619 0.00 0.00 0.00 3.41
407 408 1.806542 AGCCTGTTATTTGACGCACTG 59.193 47.619 0.00 0.00 0.00 3.66
408 409 1.806542 CAGCCTGTTATTTGACGCACT 59.193 47.619 0.00 0.00 0.00 4.40
409 410 1.804151 TCAGCCTGTTATTTGACGCAC 59.196 47.619 0.00 0.00 0.00 5.34
410 411 2.177394 TCAGCCTGTTATTTGACGCA 57.823 45.000 0.00 0.00 0.00 5.24
411 412 3.552604 TTTCAGCCTGTTATTTGACGC 57.447 42.857 0.00 0.00 0.00 5.19
412 413 6.197096 GCATATTTTCAGCCTGTTATTTGACG 59.803 38.462 0.00 0.00 0.00 4.35
413 414 6.197096 CGCATATTTTCAGCCTGTTATTTGAC 59.803 38.462 0.00 0.00 0.00 3.18
414 415 6.264832 CGCATATTTTCAGCCTGTTATTTGA 58.735 36.000 0.00 0.00 0.00 2.69
415 416 5.459762 CCGCATATTTTCAGCCTGTTATTTG 59.540 40.000 0.00 0.00 0.00 2.32
416 417 5.591099 CCGCATATTTTCAGCCTGTTATTT 58.409 37.500 0.00 0.00 0.00 1.40
417 418 4.499696 GCCGCATATTTTCAGCCTGTTATT 60.500 41.667 0.00 0.00 0.00 1.40
418 419 3.004734 GCCGCATATTTTCAGCCTGTTAT 59.995 43.478 0.00 0.00 0.00 1.89
419 420 2.357637 GCCGCATATTTTCAGCCTGTTA 59.642 45.455 0.00 0.00 0.00 2.41
420 421 1.134946 GCCGCATATTTTCAGCCTGTT 59.865 47.619 0.00 0.00 0.00 3.16
421 422 0.740737 GCCGCATATTTTCAGCCTGT 59.259 50.000 0.00 0.00 0.00 4.00
422 423 0.031178 GGCCGCATATTTTCAGCCTG 59.969 55.000 0.00 0.00 37.42 4.85
423 424 1.109323 GGGCCGCATATTTTCAGCCT 61.109 55.000 0.00 0.00 40.32 4.58
424 425 1.363807 GGGCCGCATATTTTCAGCC 59.636 57.895 0.00 0.00 39.73 4.85
425 426 0.249031 GTGGGCCGCATATTTTCAGC 60.249 55.000 13.30 0.00 0.00 4.26
426 427 0.385390 GGTGGGCCGCATATTTTCAG 59.615 55.000 20.39 0.00 0.00 3.02
427 428 2.499214 GGTGGGCCGCATATTTTCA 58.501 52.632 20.39 0.00 0.00 2.69
438 439 3.428282 CGTTTAGCACGGTGGGCC 61.428 66.667 10.60 0.00 45.89 5.80
446 447 2.255881 ACGTTGGCCCGTTTAGCAC 61.256 57.895 0.00 0.00 37.96 4.40
447 448 2.111460 ACGTTGGCCCGTTTAGCA 59.889 55.556 0.00 0.00 37.96 3.49
448 449 2.559330 CACGTTGGCCCGTTTAGC 59.441 61.111 4.13 0.00 39.45 3.09
449 450 2.559330 GCACGTTGGCCCGTTTAG 59.441 61.111 4.13 0.00 39.45 1.85
463 464 1.375780 TTAGTAAACGGGCCGGCAC 60.376 57.895 31.78 26.77 0.00 5.01
464 465 1.375780 GTTAGTAAACGGGCCGGCA 60.376 57.895 31.78 11.85 0.00 5.69
465 466 1.078918 AGTTAGTAAACGGGCCGGC 60.079 57.895 31.78 21.18 40.73 6.13
466 467 0.741927 CCAGTTAGTAAACGGGCCGG 60.742 60.000 31.78 12.53 42.77 6.13
467 468 0.741927 CCCAGTTAGTAAACGGGCCG 60.742 60.000 27.06 27.06 46.22 6.13
468 469 3.164026 CCCAGTTAGTAAACGGGCC 57.836 57.895 0.00 0.00 46.22 5.80
470 471 0.741927 CGGCCCAGTTAGTAAACGGG 60.742 60.000 11.93 11.93 46.88 5.28
471 472 0.741927 CCGGCCCAGTTAGTAAACGG 60.742 60.000 0.00 0.00 40.73 4.44
472 473 0.741927 CCCGGCCCAGTTAGTAAACG 60.742 60.000 0.00 0.00 40.73 3.60
473 474 1.028330 GCCCGGCCCAGTTAGTAAAC 61.028 60.000 0.00 0.00 35.72 2.01
474 475 1.300634 GCCCGGCCCAGTTAGTAAA 59.699 57.895 0.00 0.00 0.00 2.01
475 476 2.672181 GGCCCGGCCCAGTTAGTAA 61.672 63.158 18.83 0.00 44.06 2.24
476 477 3.085296 GGCCCGGCCCAGTTAGTA 61.085 66.667 18.83 0.00 44.06 1.82
527 528 1.657094 CGATTATTATACGGGCCGTGC 59.343 52.381 39.80 16.99 41.39 5.34
528 529 2.664568 CACGATTATTATACGGGCCGTG 59.335 50.000 39.80 22.32 41.39 4.94
529 530 2.950433 CACGATTATTATACGGGCCGT 58.050 47.619 35.91 35.91 44.35 5.68
533 534 3.259064 CAGGGCACGATTATTATACGGG 58.741 50.000 0.00 0.00 0.00 5.28
534 535 3.259064 CCAGGGCACGATTATTATACGG 58.741 50.000 0.00 0.00 0.00 4.02
535 536 2.671396 GCCAGGGCACGATTATTATACG 59.329 50.000 5.20 0.00 41.49 3.06
536 537 2.671396 CGCCAGGGCACGATTATTATAC 59.329 50.000 11.42 0.00 42.06 1.47
537 538 2.354303 CCGCCAGGGCACGATTATTATA 60.354 50.000 11.42 0.00 42.06 0.98
538 539 1.610624 CCGCCAGGGCACGATTATTAT 60.611 52.381 11.42 0.00 42.06 1.28
539 540 0.250124 CCGCCAGGGCACGATTATTA 60.250 55.000 11.42 0.00 42.06 0.98
540 541 1.525995 CCGCCAGGGCACGATTATT 60.526 57.895 11.42 0.00 42.06 1.40
541 542 2.111043 CCGCCAGGGCACGATTAT 59.889 61.111 11.42 0.00 42.06 1.28
565 566 4.169696 TAATCGTGCCTGGCCCGG 62.170 66.667 22.84 9.24 0.00 5.73
566 567 2.895372 GTAATCGTGCCTGGCCCG 60.895 66.667 17.67 17.67 0.00 6.13
567 568 2.660258 ATCGTAATCGTGCCTGGCCC 62.660 60.000 17.53 2.94 38.33 5.80
568 569 1.227556 ATCGTAATCGTGCCTGGCC 60.228 57.895 17.53 6.66 38.33 5.36
569 570 1.498865 CCATCGTAATCGTGCCTGGC 61.499 60.000 12.87 12.87 38.33 4.85
570 571 0.880278 CCCATCGTAATCGTGCCTGG 60.880 60.000 0.00 0.00 38.33 4.45
571 572 1.498865 GCCCATCGTAATCGTGCCTG 61.499 60.000 0.00 0.00 38.33 4.85
572 573 1.227556 GCCCATCGTAATCGTGCCT 60.228 57.895 0.00 0.00 38.33 4.75
573 574 2.251642 GGCCCATCGTAATCGTGCC 61.252 63.158 0.00 0.00 38.33 5.01
574 575 2.594962 CGGCCCATCGTAATCGTGC 61.595 63.158 0.00 0.00 38.33 5.34
575 576 1.954146 CCGGCCCATCGTAATCGTG 60.954 63.158 0.00 0.00 38.33 4.35
576 577 2.420043 CCGGCCCATCGTAATCGT 59.580 61.111 0.00 0.00 38.33 3.73
577 578 2.357034 CCCGGCCCATCGTAATCG 60.357 66.667 0.00 0.00 38.55 3.34
578 579 2.668550 GCCCGGCCCATCGTAATC 60.669 66.667 0.00 0.00 0.00 1.75
579 580 4.265056 GGCCCGGCCCATCGTAAT 62.265 66.667 18.83 0.00 44.06 1.89
614 615 0.544697 AGTATACCTGGCCAAACGGG 59.455 55.000 7.01 7.12 42.81 5.28
615 616 1.208535 TGAGTATACCTGGCCAAACGG 59.791 52.381 7.01 7.56 0.00 4.44
616 617 2.167693 TCTGAGTATACCTGGCCAAACG 59.832 50.000 7.01 0.00 0.00 3.60
617 618 3.906720 TCTGAGTATACCTGGCCAAAC 57.093 47.619 7.01 0.00 0.00 2.93
618 619 4.780815 CATTCTGAGTATACCTGGCCAAA 58.219 43.478 7.01 0.00 0.00 3.28
619 620 3.433598 GCATTCTGAGTATACCTGGCCAA 60.434 47.826 7.01 0.00 0.00 4.52
620 621 2.104792 GCATTCTGAGTATACCTGGCCA 59.895 50.000 4.71 4.71 0.00 5.36
621 622 2.551071 GGCATTCTGAGTATACCTGGCC 60.551 54.545 0.00 0.00 0.00 5.36
622 623 2.772287 GGCATTCTGAGTATACCTGGC 58.228 52.381 0.00 0.00 0.00 4.85
623 624 2.289072 CCGGCATTCTGAGTATACCTGG 60.289 54.545 0.00 0.00 0.00 4.45
624 625 2.868044 GCCGGCATTCTGAGTATACCTG 60.868 54.545 24.80 0.00 0.00 4.00
625 626 1.344763 GCCGGCATTCTGAGTATACCT 59.655 52.381 24.80 0.00 0.00 3.08
626 627 1.070134 TGCCGGCATTCTGAGTATACC 59.930 52.381 29.03 0.00 0.00 2.73
627 628 2.526304 TGCCGGCATTCTGAGTATAC 57.474 50.000 29.03 0.00 0.00 1.47
628 629 3.552132 TTTGCCGGCATTCTGAGTATA 57.448 42.857 33.25 8.24 0.00 1.47
629 630 2.418368 TTTGCCGGCATTCTGAGTAT 57.582 45.000 33.25 0.00 0.00 2.12
630 631 2.092968 AGATTTGCCGGCATTCTGAGTA 60.093 45.455 33.25 10.05 0.00 2.59
631 632 1.098050 GATTTGCCGGCATTCTGAGT 58.902 50.000 33.25 12.02 0.00 3.41
651 652 1.971167 CTGCGTTGGGCTAGCCAAA 60.971 57.895 34.09 27.67 44.05 3.28
705 707 2.304180 AGAGGAAGGACTGTGTGAATGG 59.696 50.000 0.00 0.00 0.00 3.16
714 716 1.099689 GTCGGAGAGAGGAAGGACTG 58.900 60.000 0.00 0.00 36.95 3.51
715 717 0.393267 CGTCGGAGAGAGGAAGGACT 60.393 60.000 0.00 0.00 36.95 3.85
716 718 1.378124 CCGTCGGAGAGAGGAAGGAC 61.378 65.000 4.91 0.00 37.67 3.85
717 719 1.077644 CCGTCGGAGAGAGGAAGGA 60.078 63.158 4.91 0.00 37.67 3.36
719 721 1.378124 GGTCCGTCGGAGAGAGGAAG 61.378 65.000 15.95 0.00 44.19 3.46
720 722 1.378250 GGTCCGTCGGAGAGAGGAA 60.378 63.158 15.95 0.00 44.19 3.36
721 723 2.271497 GGTCCGTCGGAGAGAGGA 59.729 66.667 15.95 0.00 41.25 3.71
722 724 2.829458 GGGTCCGTCGGAGAGAGG 60.829 72.222 15.95 0.00 36.95 3.69
755 757 1.404315 CGGAGGTTGGCAGACTAGAAC 60.404 57.143 0.00 0.00 0.00 3.01
796 798 2.126618 CTCACCTGCGTCGCGTTA 60.127 61.111 13.38 0.00 0.00 3.18
813 815 3.855853 GAGGAAGGGAGGAGCCGC 61.856 72.222 0.00 0.00 37.63 6.53
864 866 0.611714 TAAGTGGAAGGCCGGAAGAC 59.388 55.000 5.05 0.00 36.79 3.01
896 898 4.335647 AGCACGGACAGCCAAGGG 62.336 66.667 0.00 0.00 0.00 3.95
956 958 3.260740 CTGTTCTTGAGCTGCTTCCTAG 58.739 50.000 2.53 0.00 0.00 3.02
1011 1025 0.747255 ACGAGATGACGATGGGAAGG 59.253 55.000 0.00 0.00 37.03 3.46
1123 1137 4.144703 GCTCCCGAAGTCCCCGAC 62.145 72.222 0.00 0.00 0.00 4.79
1195 1209 0.392193 CATGACTCCAGTGGGCAGTC 60.392 60.000 19.55 19.55 37.63 3.51
1242 1256 1.993370 GACGAGATGGAGTTGAAACCG 59.007 52.381 0.00 0.00 0.00 4.44
1244 1258 3.320673 AGGACGAGATGGAGTTGAAAC 57.679 47.619 0.00 0.00 0.00 2.78
1281 1295 2.436292 GCAGACTGCAGGCTCCAG 60.436 66.667 22.46 10.51 44.26 3.86
1363 1377 3.526931 TTCAGATAGTTGCTCGGGAAG 57.473 47.619 0.00 0.00 0.00 3.46
1417 1431 0.110104 ATGCAATGGAGCTCTAGCCC 59.890 55.000 14.64 0.00 43.38 5.19
1455 1469 2.290122 CTAGCACTGGACAGCCCGAG 62.290 65.000 0.00 0.00 37.93 4.63
1500 1514 2.717580 ACATTTCAGCAGCATGTGTG 57.282 45.000 0.00 0.00 39.31 3.82
1547 1561 0.681733 GGAGAGTTCACAGCAGACCA 59.318 55.000 0.00 0.00 0.00 4.02
1570 1584 2.829720 AGGTTACTTGAGTACGATGCCA 59.170 45.455 0.00 0.00 0.00 4.92
1573 1587 5.032863 CGGTAAGGTTACTTGAGTACGATG 58.967 45.833 0.00 0.00 37.53 3.84
1585 1599 4.201656 GCGAACAAGATTCGGTAAGGTTAC 60.202 45.833 10.71 0.00 41.76 2.50
1636 1650 4.022068 TGGCAAGCTTTCAAGTAATGGAAG 60.022 41.667 0.00 0.00 46.05 3.46
1715 1729 2.568509 TCATCATCAAGACAGCCTGACA 59.431 45.455 0.00 0.00 0.00 3.58
1870 1884 8.721133 AACATAAGAAGACAAAATAAAGGGGT 57.279 30.769 0.00 0.00 0.00 4.95
1907 1921 4.332543 ACATGCACGTTAGTTGATGGTATG 59.667 41.667 0.00 0.00 0.00 2.39
1917 1931 1.621814 ACTGGGTACATGCACGTTAGT 59.378 47.619 0.00 0.00 0.00 2.24
1923 1937 3.016736 AGCATAAACTGGGTACATGCAC 58.983 45.455 12.82 0.00 43.46 4.57
2006 2020 6.262944 AGACAATGAATGTGACTGCACTAAAA 59.737 34.615 0.00 0.00 44.12 1.52
2007 2021 5.764686 AGACAATGAATGTGACTGCACTAAA 59.235 36.000 0.00 0.00 44.12 1.85
2010 2024 3.748083 AGACAATGAATGTGACTGCACT 58.252 40.909 0.00 0.00 44.12 4.40
2011 2025 4.023792 TGAAGACAATGAATGTGACTGCAC 60.024 41.667 0.00 0.00 44.12 4.57
2012 2026 4.136051 TGAAGACAATGAATGTGACTGCA 58.864 39.130 0.00 0.00 44.12 4.41
2013 2027 4.754372 TGAAGACAATGAATGTGACTGC 57.246 40.909 0.00 0.00 44.12 4.40
2272 2295 2.285977 CCGGCTGGTTCCTTTATGTAC 58.714 52.381 2.29 0.00 0.00 2.90
2281 2304 1.449778 GAGTAAGCCGGCTGGTTCC 60.450 63.158 33.60 15.98 37.67 3.62
2284 2307 2.017559 GATCGAGTAAGCCGGCTGGT 62.018 60.000 33.60 19.03 37.67 4.00
2286 2309 0.318275 GAGATCGAGTAAGCCGGCTG 60.318 60.000 33.60 17.89 0.00 4.85
2300 2323 6.489675 ACACAACATGCAAATAATCGAGATC 58.510 36.000 0.00 0.00 0.00 2.75
2353 2376 2.124320 ATGGGAAATGTCGGGCGG 60.124 61.111 0.00 0.00 0.00 6.13
2390 2413 0.030638 GCATGCAAACACCAGTCGTT 59.969 50.000 14.21 0.00 0.00 3.85
2472 2495 7.615365 TCCACAAAAGATATACCTCAGCAAATT 59.385 33.333 0.00 0.00 0.00 1.82
2477 2500 5.471456 CCATCCACAAAAGATATACCTCAGC 59.529 44.000 0.00 0.00 0.00 4.26
2478 2501 6.830912 TCCATCCACAAAAGATATACCTCAG 58.169 40.000 0.00 0.00 0.00 3.35
2516 2539 3.057596 ACAGCCATGTGACGTAATTTTGG 60.058 43.478 0.00 0.00 38.57 3.28
2603 2627 6.986231 AGATGAAAATGTTCCTTCCAACAAAC 59.014 34.615 0.00 0.00 39.69 2.93
2657 2681 9.974980 TGTTAATTCTTCCATCAACCTTTAAAC 57.025 29.630 0.00 0.00 0.00 2.01
2728 2752 4.814234 TGTATTGGCTTGTCGGATATTGAC 59.186 41.667 2.90 2.90 36.88 3.18
2787 2811 5.668866 GCGTAAACAGAAGAAGCATACACAG 60.669 44.000 0.00 0.00 0.00 3.66
2821 2845 6.262601 CCCCGTTTATAAGTAAAACATGCAG 58.737 40.000 0.00 0.00 36.78 4.41
2937 2965 6.312487 GTTCTCTTTTGACCCGTTTATAAGC 58.688 40.000 0.00 0.00 0.00 3.09
2943 2971 3.211865 GAGGTTCTCTTTTGACCCGTTT 58.788 45.455 0.00 0.00 0.00 3.60
3011 3039 8.333186 ACTGTTTTTCACGAATGTAGTTTCTAC 58.667 33.333 0.00 0.59 0.00 2.59
3176 3204 9.965824 CCAAACTGATATGGTATAATTTTGGAC 57.034 33.333 9.14 0.00 41.94 4.02
3187 3215 9.976776 TGTAAATTAACCCAAACTGATATGGTA 57.023 29.630 0.00 0.00 34.79 3.25
3230 3260 3.698539 TCCGAATGGCAGCAAATTCAATA 59.301 39.130 16.33 2.95 33.27 1.90
3255 3285 6.645415 ACTCAGACGTTAGTTTTCATAAGTGG 59.355 38.462 0.00 0.00 0.00 4.00
3279 3309 9.202273 CCATAGCTCAAGTGAAGAATAAGATAC 57.798 37.037 0.00 0.00 0.00 2.24
3361 3392 2.416747 TCGACCATCAGACAGCTTTTG 58.583 47.619 0.00 0.00 0.00 2.44
3420 3452 4.408921 ACAATCAACTCGGGAGGATTATCA 59.591 41.667 6.00 0.00 0.00 2.15
3426 3458 1.348064 ACACAATCAACTCGGGAGGA 58.652 50.000 0.00 0.00 0.00 3.71
3427 3459 1.806542 CAACACAATCAACTCGGGAGG 59.193 52.381 0.00 0.00 0.00 4.30
3428 3460 2.494059 ACAACACAATCAACTCGGGAG 58.506 47.619 0.00 0.00 0.00 4.30
3459 3493 6.970043 TGTGCACACAAAATTAGAACTTGTAC 59.030 34.615 17.42 0.00 38.56 2.90
3516 3551 1.371183 TGGAAAGACCAGCAGACCG 59.629 57.895 0.00 0.00 44.64 4.79
3561 3597 4.887071 TGCCCATAATAAAGCTTTGATCGT 59.113 37.500 22.02 4.78 0.00 3.73
3609 3645 5.460646 AGTTATCTTGCAAAACCATTCACG 58.539 37.500 0.00 0.00 0.00 4.35
3736 3774 5.533903 ACATCTTTATGACCTCATTCATGGC 59.466 40.000 0.00 0.00 36.84 4.40


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

AutoCloner maintained by Alex Coulton.