Multiple sequence alignment - TraesCS7A01G224900

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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 TraesCS7A01G224900 chr7A 100.000 3028 0 0 1 3028 194290210 194287183 0.000000e+00 5592
1 TraesCS7A01G224900 chr7D 91.508 2202 148 17 606 2775 189912405 189914599 0.000000e+00 2994
2 TraesCS7A01G224900 chr7D 94.561 239 12 1 1 238 189911001 189911239 4.770000e-98 368
3 TraesCS7A01G224900 chr7D 87.879 330 18 8 285 595 189911231 189911557 4.770000e-98 368
4 TraesCS7A01G224900 chr7B 88.719 2287 156 43 279 2516 334454608 334456841 0.000000e+00 2700
5 TraesCS7A01G224900 chr7B 92.727 220 9 4 1 218 334454397 334454611 8.150000e-81 311
6 TraesCS7A01G224900 chr7B 89.344 244 25 1 2533 2776 334458579 334458821 3.790000e-79 305
7 TraesCS7A01G224900 chr4B 90.367 218 16 4 1 218 624107655 624107443 6.390000e-72 281
8 TraesCS7A01G224900 chr4B 82.407 216 17 9 288 499 624107437 624107239 5.190000e-38 169
9 TraesCS7A01G224900 chr2B 88.017 242 20 3 2790 3028 733193041 733192806 8.270000e-71 278


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 TraesCS7A01G224900 chr7A 194287183 194290210 3027 True 5592.000000 5592 100.000000 1 3028 1 chr7A.!!$R1 3027
1 TraesCS7A01G224900 chr7D 189911001 189914599 3598 False 1243.333333 2994 91.316000 1 2775 3 chr7D.!!$F1 2774
2 TraesCS7A01G224900 chr7B 334454397 334458821 4424 False 1105.333333 2700 90.263333 1 2776 3 chr7B.!!$F1 2775

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
55 58 0.391228 TTGTTAGTCTGCTCGTGCCA 59.609 50.000 7.05 0.0 38.71 4.92 F
57 60 1.001974 TGTTAGTCTGCTCGTGCCATT 59.998 47.619 7.05 0.0 38.71 3.16 F
1118 2022 0.039437 TCACAGCCGTCGAGTTTCTC 60.039 55.000 0.00 0.0 0.00 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1068 1972 0.179051 GAGGAGAAGATGCCTGCAGG 60.179 60.0 29.34 29.34 33.84 4.85 R
1422 2326 0.250901 AACGCCACCAAGCTCTTCAT 60.251 50.0 0.00 0.00 0.00 2.57 R
2819 5466 0.036010 AACCCTCACAATCGCCTCAG 60.036 55.0 0.00 0.00 0.00 3.35 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 30 1.266842 CGTGTTTGTCCATGATACGCG 60.267 52.381 3.53 3.53 36.57 6.01
55 58 0.391228 TTGTTAGTCTGCTCGTGCCA 59.609 50.000 7.05 0.00 38.71 4.92
57 60 1.001974 TGTTAGTCTGCTCGTGCCATT 59.998 47.619 7.05 0.00 38.71 3.16
226 230 8.976353 GGTAGATGGACAGATCATACTGATTAT 58.024 37.037 0.00 0.00 37.20 1.28
232 236 7.933577 TGGACAGATCATACTGATTATTGTTCC 59.066 37.037 0.00 0.00 37.20 3.62
233 237 7.933577 GGACAGATCATACTGATTATTGTTCCA 59.066 37.037 0.00 0.00 37.20 3.53
234 238 8.899427 ACAGATCATACTGATTATTGTTCCAG 57.101 34.615 0.00 0.00 37.20 3.86
235 239 7.935755 ACAGATCATACTGATTATTGTTCCAGG 59.064 37.037 0.00 0.00 37.20 4.45
236 240 8.152898 CAGATCATACTGATTATTGTTCCAGGA 58.847 37.037 0.00 0.00 37.20 3.86
237 241 8.717717 AGATCATACTGATTATTGTTCCAGGAA 58.282 33.333 0.00 0.00 37.20 3.36
238 242 9.512588 GATCATACTGATTATTGTTCCAGGAAT 57.487 33.333 4.80 0.00 37.20 3.01
239 243 9.872684 ATCATACTGATTATTGTTCCAGGAATT 57.127 29.630 4.80 0.00 32.13 2.17
240 244 9.699410 TCATACTGATTATTGTTCCAGGAATTT 57.301 29.630 4.80 0.00 0.00 1.82
241 245 9.740239 CATACTGATTATTGTTCCAGGAATTTG 57.260 33.333 4.80 0.00 0.00 2.32
242 246 7.781324 ACTGATTATTGTTCCAGGAATTTGT 57.219 32.000 4.80 0.00 0.00 2.83
243 247 7.830739 ACTGATTATTGTTCCAGGAATTTGTC 58.169 34.615 4.80 0.83 0.00 3.18
244 248 7.451255 ACTGATTATTGTTCCAGGAATTTGTCA 59.549 33.333 4.80 5.21 0.00 3.58
245 249 7.829725 TGATTATTGTTCCAGGAATTTGTCAG 58.170 34.615 4.80 0.00 0.00 3.51
246 250 7.669304 TGATTATTGTTCCAGGAATTTGTCAGA 59.331 33.333 4.80 0.00 0.00 3.27
247 251 5.972107 ATTGTTCCAGGAATTTGTCAGAG 57.028 39.130 4.80 0.00 0.00 3.35
248 252 4.705110 TGTTCCAGGAATTTGTCAGAGA 57.295 40.909 4.80 0.00 0.00 3.10
249 253 5.047566 TGTTCCAGGAATTTGTCAGAGAA 57.952 39.130 4.80 0.00 0.00 2.87
250 254 5.445069 TGTTCCAGGAATTTGTCAGAGAAA 58.555 37.500 4.80 0.00 0.00 2.52
251 255 5.890985 TGTTCCAGGAATTTGTCAGAGAAAA 59.109 36.000 4.80 0.00 0.00 2.29
252 256 6.039717 TGTTCCAGGAATTTGTCAGAGAAAAG 59.960 38.462 4.80 0.00 0.00 2.27
253 257 5.072741 TCCAGGAATTTGTCAGAGAAAAGG 58.927 41.667 0.00 0.00 0.00 3.11
254 258 5.072741 CCAGGAATTTGTCAGAGAAAAGGA 58.927 41.667 0.00 0.00 0.00 3.36
255 259 5.536161 CCAGGAATTTGTCAGAGAAAAGGAA 59.464 40.000 0.00 0.00 0.00 3.36
256 260 6.442112 CAGGAATTTGTCAGAGAAAAGGAAC 58.558 40.000 0.00 0.00 0.00 3.62
257 261 5.536538 AGGAATTTGTCAGAGAAAAGGAACC 59.463 40.000 0.00 0.00 0.00 3.62
258 262 5.536538 GGAATTTGTCAGAGAAAAGGAACCT 59.463 40.000 0.00 0.00 0.00 3.50
259 263 6.294231 GGAATTTGTCAGAGAAAAGGAACCTC 60.294 42.308 0.00 0.00 0.00 3.85
260 264 3.771577 TGTCAGAGAAAAGGAACCTCC 57.228 47.619 0.00 0.00 36.58 4.30
261 265 3.045634 TGTCAGAGAAAAGGAACCTCCA 58.954 45.455 0.00 0.00 39.61 3.86
262 266 3.458118 TGTCAGAGAAAAGGAACCTCCAA 59.542 43.478 0.00 0.00 39.61 3.53
263 267 4.104738 TGTCAGAGAAAAGGAACCTCCAAT 59.895 41.667 0.00 0.00 39.61 3.16
264 268 5.309543 TGTCAGAGAAAAGGAACCTCCAATA 59.690 40.000 0.00 0.00 39.61 1.90
265 269 5.644206 GTCAGAGAAAAGGAACCTCCAATAC 59.356 44.000 0.00 0.00 39.61 1.89
266 270 5.309543 TCAGAGAAAAGGAACCTCCAATACA 59.690 40.000 0.00 0.00 39.61 2.29
267 271 6.012508 TCAGAGAAAAGGAACCTCCAATACAT 60.013 38.462 0.00 0.00 39.61 2.29
268 272 7.182026 TCAGAGAAAAGGAACCTCCAATACATA 59.818 37.037 0.00 0.00 39.61 2.29
269 273 7.281100 CAGAGAAAAGGAACCTCCAATACATAC 59.719 40.741 0.00 0.00 39.61 2.39
270 274 7.027874 AGAAAAGGAACCTCCAATACATACA 57.972 36.000 0.00 0.00 39.61 2.29
271 275 7.643123 AGAAAAGGAACCTCCAATACATACAT 58.357 34.615 0.00 0.00 39.61 2.29
272 276 8.778059 AGAAAAGGAACCTCCAATACATACATA 58.222 33.333 0.00 0.00 39.61 2.29
273 277 8.980481 AAAAGGAACCTCCAATACATACATAG 57.020 34.615 0.00 0.00 39.61 2.23
274 278 6.115448 AGGAACCTCCAATACATACATAGC 57.885 41.667 0.00 0.00 39.61 2.97
275 279 5.846714 AGGAACCTCCAATACATACATAGCT 59.153 40.000 0.00 0.00 39.61 3.32
276 280 6.330250 AGGAACCTCCAATACATACATAGCTT 59.670 38.462 0.00 0.00 39.61 3.74
277 281 6.998673 GGAACCTCCAATACATACATAGCTTT 59.001 38.462 0.00 0.00 36.28 3.51
278 282 7.502561 GGAACCTCCAATACATACATAGCTTTT 59.497 37.037 0.00 0.00 36.28 2.27
279 283 8.451908 AACCTCCAATACATACATAGCTTTTC 57.548 34.615 0.00 0.00 0.00 2.29
280 284 7.573710 ACCTCCAATACATACATAGCTTTTCA 58.426 34.615 0.00 0.00 0.00 2.69
281 285 8.220559 ACCTCCAATACATACATAGCTTTTCAT 58.779 33.333 0.00 0.00 0.00 2.57
282 286 8.509690 CCTCCAATACATACATAGCTTTTCATG 58.490 37.037 0.00 0.00 0.00 3.07
283 287 7.874940 TCCAATACATACATAGCTTTTCATGC 58.125 34.615 0.00 0.00 0.00 4.06
284 288 7.720957 TCCAATACATACATAGCTTTTCATGCT 59.279 33.333 0.00 0.00 43.79 3.79
285 289 8.355169 CCAATACATACATAGCTTTTCATGCTT 58.645 33.333 0.00 0.00 41.46 3.91
354 358 5.235305 ACCTTCAAAATACATAGCTTGCG 57.765 39.130 0.00 0.00 0.00 4.85
368 386 4.392921 AGCTTGCGAGATAGTATGTGTT 57.607 40.909 4.70 0.00 0.00 3.32
390 408 8.743714 GTGTTTTTCTTGGGATAAGAAGATGAT 58.256 33.333 0.00 0.00 37.54 2.45
413 431 3.366679 CCTGAGTAAATTGTGCCAAGCTG 60.367 47.826 0.00 0.00 0.00 4.24
499 526 6.004574 ACAAGGAAAAGGATACAGAAAGACC 58.995 40.000 0.00 0.00 41.41 3.85
507 551 6.821616 AGGATACAGAAAGACCTCATCATT 57.178 37.500 0.00 0.00 41.41 2.57
557 601 9.631452 AAACACTCACATATACAGATATCATCG 57.369 33.333 5.32 0.00 0.00 3.84
686 1575 5.799936 CACTGTTTCGTCAACTGAAAACAAT 59.200 36.000 9.72 0.23 37.10 2.71
687 1576 6.307800 CACTGTTTCGTCAACTGAAAACAATT 59.692 34.615 9.72 0.83 37.10 2.32
755 1644 7.778470 ATCTTGATTTGACTCGACCTTTATC 57.222 36.000 0.00 0.00 0.00 1.75
784 1673 3.906720 TTGGCTGGTCCTAATAGTGAC 57.093 47.619 0.00 1.80 35.26 3.67
888 1783 5.638657 GCCAGAATAGCTATCTTCATGTGAG 59.361 44.000 6.72 0.00 0.00 3.51
891 1786 7.208777 CAGAATAGCTATCTTCATGTGAGTGT 58.791 38.462 6.72 0.00 0.00 3.55
896 1791 7.117285 AGCTATCTTCATGTGAGTGTCATAA 57.883 36.000 0.00 0.00 0.00 1.90
897 1792 7.733969 AGCTATCTTCATGTGAGTGTCATAAT 58.266 34.615 0.00 0.00 0.00 1.28
939 1834 1.348036 GCACCCAGAGACTTTACCAGT 59.652 52.381 0.00 0.00 39.07 4.00
940 1835 2.224548 GCACCCAGAGACTTTACCAGTT 60.225 50.000 0.00 0.00 35.01 3.16
964 1868 2.158711 CCTAATCTGGATCTTGCAGGCA 60.159 50.000 0.00 0.00 36.40 4.75
1068 1972 2.124736 TATGCCCGCAACTCCAGC 60.125 61.111 0.00 0.00 0.00 4.85
1097 2001 2.758736 TCTTCTCCTCTCTTGCTTGC 57.241 50.000 0.00 0.00 0.00 4.01
1109 2013 1.785041 TTGCTTGCTTCACAGCCGTC 61.785 55.000 0.00 0.00 46.74 4.79
1111 2015 1.664649 CTTGCTTCACAGCCGTCGA 60.665 57.895 0.00 0.00 46.74 4.20
1118 2022 0.039437 TCACAGCCGTCGAGTTTCTC 60.039 55.000 0.00 0.00 0.00 2.87
1131 2035 3.121944 CGAGTTTCTCATGTCTTGTTCCG 59.878 47.826 0.00 0.00 0.00 4.30
1155 2059 4.180057 CAGAACTGATTCACCTAGCTGTC 58.820 47.826 0.00 0.00 37.29 3.51
1235 2139 0.955178 CCATCGCCGATCTACTCAGT 59.045 55.000 0.00 0.00 0.00 3.41
1320 2224 1.297967 CTCGCTCTGGTGTCGATCG 60.298 63.158 9.36 9.36 0.00 3.69
1347 2251 4.457496 CCATCCGCGGTCAGTGCT 62.457 66.667 27.15 0.00 0.00 4.40
1422 2326 2.869801 GACAACGACTTCAACATGGTGA 59.130 45.455 10.05 10.05 0.00 4.02
1510 2414 1.255667 TACGGGAGGCTCTTCACCAC 61.256 60.000 15.23 0.00 0.00 4.16
1570 2477 1.757118 CTGGCTCTCCGAGGTATGAAA 59.243 52.381 0.00 0.00 34.14 2.69
1599 2522 3.486875 CGGCTCGACTTGTTTCTTTTTGT 60.487 43.478 0.00 0.00 0.00 2.83
1684 2607 1.453524 GCATACGACATCGATGAGCAC 59.546 52.381 31.33 16.79 43.02 4.40
1792 2715 1.928868 AAGAATTGGTTGCAGGAGGG 58.071 50.000 0.00 0.00 0.00 4.30
1813 2736 1.336795 CGATTGGTTGTTTCCCTTGCC 60.337 52.381 0.00 0.00 0.00 4.52
1869 2792 0.107508 CATGCCTGGGAATCAGTCGT 60.108 55.000 0.00 0.00 41.83 4.34
2082 3007 2.964464 TGAAGAGCTGAGGGAGATCATC 59.036 50.000 0.00 0.00 39.79 2.92
2165 3090 2.892640 CACGCTGATCTCCCCGAA 59.107 61.111 0.00 0.00 0.00 4.30
2297 3222 2.034687 GCAGGGCAGCTTGGAAGA 59.965 61.111 0.00 0.00 0.00 2.87
2307 3232 1.077858 CTTGGAAGAGGAGCTGGCC 60.078 63.158 0.00 0.00 0.00 5.36
2308 3233 2.866085 CTTGGAAGAGGAGCTGGCCG 62.866 65.000 0.00 0.00 0.00 6.13
2414 3339 6.423604 CGGCAGTAAAGGACAATTTGAAATTT 59.576 34.615 2.79 0.00 0.00 1.82
2442 3367 0.526954 GTCCGATCCATAACGCGTGT 60.527 55.000 14.98 5.77 0.00 4.49
2443 3368 0.173935 TCCGATCCATAACGCGTGTT 59.826 50.000 14.98 19.53 42.19 3.32
2449 3374 0.300491 CCATAACGCGTGTTGGATCG 59.700 55.000 27.89 7.56 39.12 3.69
2487 3412 4.853196 CACATGTCCGATCACATCAAAAAC 59.147 41.667 0.00 0.00 34.60 2.43
2490 3415 4.384940 TGTCCGATCACATCAAAAACAGA 58.615 39.130 0.00 0.00 0.00 3.41
2540 5186 6.584942 CCGATGATAAAAGAATATTCGTCCGA 59.415 38.462 9.78 0.00 0.00 4.55
2623 5269 3.334751 CGAAGTGTCGTTGCGCCA 61.335 61.111 4.18 0.00 42.53 5.69
2625 5271 3.558282 GAAGTGTCGTTGCGCCACG 62.558 63.158 26.31 26.31 41.78 4.94
2630 5276 4.578898 TCGTTGCGCCACGTGTCT 62.579 61.111 29.74 0.00 41.16 3.41
2654 5300 3.508840 CATTTCCGCCACCGCCTC 61.509 66.667 0.00 0.00 0.00 4.70
2706 5352 4.711892 TGCCGCTGCAACATCTTA 57.288 50.000 0.00 0.00 46.66 2.10
2736 5382 2.162208 GGCTTGCACGATCATTCTTTCA 59.838 45.455 0.00 0.00 0.00 2.69
2784 5431 6.481954 AAGAACAACATCTTGACGGATAAC 57.518 37.500 0.00 0.00 38.22 1.89
2785 5432 4.935808 AGAACAACATCTTGACGGATAACC 59.064 41.667 0.00 0.00 0.00 2.85
2796 5443 1.738432 GGATAACCGAGGTCCGTCC 59.262 63.158 0.00 0.30 36.31 4.79
2797 5444 1.738432 GATAACCGAGGTCCGTCCC 59.262 63.158 0.00 0.00 36.75 4.46
2798 5445 1.000739 ATAACCGAGGTCCGTCCCA 59.999 57.895 0.00 0.00 36.75 4.37
2799 5446 1.041447 ATAACCGAGGTCCGTCCCAG 61.041 60.000 0.00 0.00 36.75 4.45
2802 5449 3.760035 CGAGGTCCGTCCCAGGTG 61.760 72.222 0.00 0.00 36.75 4.00
2803 5450 2.603776 GAGGTCCGTCCCAGGTGT 60.604 66.667 0.00 0.00 36.75 4.16
2804 5451 2.923035 AGGTCCGTCCCAGGTGTG 60.923 66.667 0.00 0.00 36.75 3.82
2805 5452 2.920912 GGTCCGTCCCAGGTGTGA 60.921 66.667 0.00 0.00 0.00 3.58
2806 5453 2.342648 GTCCGTCCCAGGTGTGAC 59.657 66.667 0.00 0.00 0.00 3.67
2810 5457 2.826702 GTCCCAGGTGTGACGGTT 59.173 61.111 0.00 0.00 0.00 4.44
2811 5458 2.051941 GTCCCAGGTGTGACGGTTA 58.948 57.895 0.00 0.00 0.00 2.85
2812 5459 0.037605 GTCCCAGGTGTGACGGTTAG 60.038 60.000 0.00 0.00 0.00 2.34
2813 5460 1.189524 TCCCAGGTGTGACGGTTAGG 61.190 60.000 0.00 0.00 0.00 2.69
2814 5461 1.477685 CCCAGGTGTGACGGTTAGGT 61.478 60.000 0.00 0.00 0.00 3.08
2815 5462 0.037605 CCAGGTGTGACGGTTAGGTC 60.038 60.000 0.00 0.00 37.45 3.85
2816 5463 0.966920 CAGGTGTGACGGTTAGGTCT 59.033 55.000 0.00 0.00 37.81 3.85
2817 5464 1.067776 CAGGTGTGACGGTTAGGTCTC 60.068 57.143 0.00 0.00 37.81 3.36
2818 5465 0.109412 GGTGTGACGGTTAGGTCTCG 60.109 60.000 0.00 0.00 37.81 4.04
2819 5466 0.731855 GTGTGACGGTTAGGTCTCGC 60.732 60.000 0.00 0.00 37.81 5.03
2820 5467 0.892358 TGTGACGGTTAGGTCTCGCT 60.892 55.000 0.00 0.00 37.81 4.93
2821 5468 0.456312 GTGACGGTTAGGTCTCGCTG 60.456 60.000 0.00 0.00 37.81 5.18
2822 5469 0.607217 TGACGGTTAGGTCTCGCTGA 60.607 55.000 0.00 0.00 37.81 4.26
2823 5470 0.099082 GACGGTTAGGTCTCGCTGAG 59.901 60.000 0.00 0.00 34.09 3.35
2824 5471 1.313812 ACGGTTAGGTCTCGCTGAGG 61.314 60.000 5.87 0.00 0.00 3.86
2825 5472 1.142097 GGTTAGGTCTCGCTGAGGC 59.858 63.158 5.87 4.07 32.92 4.70
2835 5482 3.805267 GCTGAGGCGATTGTGAGG 58.195 61.111 0.00 0.00 0.00 3.86
2836 5483 1.817099 GCTGAGGCGATTGTGAGGG 60.817 63.158 0.00 0.00 0.00 4.30
2837 5484 1.599047 CTGAGGCGATTGTGAGGGT 59.401 57.895 0.00 0.00 0.00 4.34
2838 5485 0.036010 CTGAGGCGATTGTGAGGGTT 60.036 55.000 0.00 0.00 0.00 4.11
2839 5486 0.036388 TGAGGCGATTGTGAGGGTTC 60.036 55.000 0.00 0.00 0.00 3.62
2840 5487 1.079127 AGGCGATTGTGAGGGTTCG 60.079 57.895 0.00 0.00 34.83 3.95
2842 5489 3.486263 CGATTGTGAGGGTTCGCC 58.514 61.111 0.00 0.00 32.76 5.54
2843 5490 2.452813 CGATTGTGAGGGTTCGCCG 61.453 63.158 0.00 0.00 38.45 6.46
2844 5491 2.746277 ATTGTGAGGGTTCGCCGC 60.746 61.111 0.00 0.00 38.45 6.53
2959 5606 4.016706 CCCCTCACCCACGTCCAC 62.017 72.222 0.00 0.00 0.00 4.02
2960 5607 4.016706 CCCTCACCCACGTCCACC 62.017 72.222 0.00 0.00 0.00 4.61
2961 5608 4.016706 CCTCACCCACGTCCACCC 62.017 72.222 0.00 0.00 0.00 4.61
2962 5609 4.016706 CTCACCCACGTCCACCCC 62.017 72.222 0.00 0.00 0.00 4.95
2965 5612 4.912299 ACCCACGTCCACCCCCTT 62.912 66.667 0.00 0.00 0.00 3.95
2966 5613 4.029809 CCCACGTCCACCCCCTTC 62.030 72.222 0.00 0.00 0.00 3.46
2967 5614 4.029809 CCACGTCCACCCCCTTCC 62.030 72.222 0.00 0.00 0.00 3.46
2968 5615 3.246112 CACGTCCACCCCCTTCCA 61.246 66.667 0.00 0.00 0.00 3.53
2969 5616 2.928396 ACGTCCACCCCCTTCCAG 60.928 66.667 0.00 0.00 0.00 3.86
2970 5617 2.928396 CGTCCACCCCCTTCCAGT 60.928 66.667 0.00 0.00 0.00 4.00
2971 5618 2.526046 CGTCCACCCCCTTCCAGTT 61.526 63.158 0.00 0.00 0.00 3.16
2972 5619 1.851267 GTCCACCCCCTTCCAGTTT 59.149 57.895 0.00 0.00 0.00 2.66
2973 5620 0.187606 GTCCACCCCCTTCCAGTTTT 59.812 55.000 0.00 0.00 0.00 2.43
2974 5621 0.481128 TCCACCCCCTTCCAGTTTTC 59.519 55.000 0.00 0.00 0.00 2.29
2975 5622 0.187361 CCACCCCCTTCCAGTTTTCA 59.813 55.000 0.00 0.00 0.00 2.69
2976 5623 1.620822 CACCCCCTTCCAGTTTTCAG 58.379 55.000 0.00 0.00 0.00 3.02
2977 5624 0.482887 ACCCCCTTCCAGTTTTCAGG 59.517 55.000 0.00 0.00 0.00 3.86
2978 5625 0.482887 CCCCCTTCCAGTTTTCAGGT 59.517 55.000 0.00 0.00 0.00 4.00
2979 5626 1.547901 CCCCCTTCCAGTTTTCAGGTC 60.548 57.143 0.00 0.00 0.00 3.85
2980 5627 1.425448 CCCCTTCCAGTTTTCAGGTCT 59.575 52.381 0.00 0.00 0.00 3.85
2981 5628 2.508526 CCCTTCCAGTTTTCAGGTCTG 58.491 52.381 0.00 0.00 0.00 3.51
2982 5629 1.882623 CCTTCCAGTTTTCAGGTCTGC 59.117 52.381 0.00 0.00 0.00 4.26
2983 5630 2.487986 CCTTCCAGTTTTCAGGTCTGCT 60.488 50.000 0.00 0.00 0.00 4.24
2984 5631 2.260844 TCCAGTTTTCAGGTCTGCTG 57.739 50.000 0.00 0.00 0.00 4.41
2985 5632 0.595095 CCAGTTTTCAGGTCTGCTGC 59.405 55.000 0.00 0.00 0.00 5.25
2986 5633 1.602311 CAGTTTTCAGGTCTGCTGCT 58.398 50.000 0.00 0.00 0.00 4.24
2987 5634 2.550855 CCAGTTTTCAGGTCTGCTGCTA 60.551 50.000 0.00 0.00 0.00 3.49
2988 5635 2.740981 CAGTTTTCAGGTCTGCTGCTAG 59.259 50.000 0.00 0.00 0.00 3.42
2989 5636 2.079925 GTTTTCAGGTCTGCTGCTAGG 58.920 52.381 0.00 0.00 0.00 3.02
2990 5637 1.352083 TTTCAGGTCTGCTGCTAGGT 58.648 50.000 0.00 0.00 0.00 3.08
2991 5638 0.610174 TTCAGGTCTGCTGCTAGGTG 59.390 55.000 0.00 0.00 0.00 4.00
2992 5639 1.449246 CAGGTCTGCTGCTAGGTGC 60.449 63.158 0.00 0.00 43.25 5.01
2993 5640 2.510238 GGTCTGCTGCTAGGTGCG 60.510 66.667 0.00 0.00 46.63 5.34
2994 5641 3.191539 GTCTGCTGCTAGGTGCGC 61.192 66.667 0.00 0.00 46.63 6.09
2995 5642 4.457496 TCTGCTGCTAGGTGCGCC 62.457 66.667 8.71 8.71 46.63 6.53
3002 5649 4.111016 CTAGGTGCGCCGTCGTGA 62.111 66.667 11.42 0.00 40.50 4.35
3003 5650 4.111016 TAGGTGCGCCGTCGTGAG 62.111 66.667 11.42 0.00 40.50 3.51
3017 5664 2.661594 TCGTGAGACATCGAGTTGTTG 58.338 47.619 0.00 0.00 33.31 3.33
3018 5665 2.034179 TCGTGAGACATCGAGTTGTTGT 59.966 45.455 0.00 0.00 33.21 3.32
3019 5666 2.794910 CGTGAGACATCGAGTTGTTGTT 59.205 45.455 0.00 0.00 30.68 2.83
3020 5667 3.121328 CGTGAGACATCGAGTTGTTGTTC 60.121 47.826 0.00 0.00 30.68 3.18
3021 5668 3.184581 GTGAGACATCGAGTTGTTGTTCC 59.815 47.826 0.00 0.00 30.68 3.62
3022 5669 2.737252 GAGACATCGAGTTGTTGTTCCC 59.263 50.000 0.00 0.00 30.68 3.97
3023 5670 1.804748 GACATCGAGTTGTTGTTCCCC 59.195 52.381 0.00 0.00 30.68 4.81
3024 5671 1.420138 ACATCGAGTTGTTGTTCCCCT 59.580 47.619 0.00 0.00 0.00 4.79
3025 5672 2.076863 CATCGAGTTGTTGTTCCCCTC 58.923 52.381 0.00 0.00 0.00 4.30
3026 5673 0.395312 TCGAGTTGTTGTTCCCCTCC 59.605 55.000 0.00 0.00 0.00 4.30
3027 5674 0.605589 CGAGTTGTTGTTCCCCTCCC 60.606 60.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 15 0.809636 CTGCCGCGTATCATGGACAA 60.810 55.000 4.92 0.00 0.00 3.18
55 58 0.627986 AGCAGCAGGGAAAGGCTAAT 59.372 50.000 0.00 0.00 38.56 1.73
57 60 0.911525 AGAGCAGCAGGGAAAGGCTA 60.912 55.000 0.00 0.00 38.56 3.93
194 198 5.411831 TGATCTGTCCATCTACCATATGC 57.588 43.478 0.00 0.00 0.00 3.14
226 230 5.047566 TCTCTGACAAATTCCTGGAACAA 57.952 39.130 12.11 0.00 38.70 2.83
232 236 6.442112 GTTCCTTTTCTCTGACAAATTCCTG 58.558 40.000 0.00 0.00 0.00 3.86
233 237 5.536538 GGTTCCTTTTCTCTGACAAATTCCT 59.463 40.000 0.00 0.00 0.00 3.36
234 238 5.536538 AGGTTCCTTTTCTCTGACAAATTCC 59.463 40.000 0.00 0.00 0.00 3.01
235 239 6.294231 GGAGGTTCCTTTTCTCTGACAAATTC 60.294 42.308 0.00 0.00 32.53 2.17
236 240 5.536538 GGAGGTTCCTTTTCTCTGACAAATT 59.463 40.000 0.00 0.00 32.53 1.82
237 241 5.073428 GGAGGTTCCTTTTCTCTGACAAAT 58.927 41.667 0.00 0.00 32.53 2.32
238 242 4.080015 TGGAGGTTCCTTTTCTCTGACAAA 60.080 41.667 0.00 0.00 37.46 2.83
239 243 3.458118 TGGAGGTTCCTTTTCTCTGACAA 59.542 43.478 0.00 0.00 37.46 3.18
240 244 3.045634 TGGAGGTTCCTTTTCTCTGACA 58.954 45.455 0.00 0.00 37.46 3.58
241 245 3.771577 TGGAGGTTCCTTTTCTCTGAC 57.228 47.619 0.00 0.00 37.46 3.51
242 246 5.309543 TGTATTGGAGGTTCCTTTTCTCTGA 59.690 40.000 0.00 0.00 37.46 3.27
243 247 5.560724 TGTATTGGAGGTTCCTTTTCTCTG 58.439 41.667 0.00 0.00 37.46 3.35
244 248 5.843019 TGTATTGGAGGTTCCTTTTCTCT 57.157 39.130 0.00 0.00 37.46 3.10
245 249 7.110155 TGTATGTATTGGAGGTTCCTTTTCTC 58.890 38.462 0.00 0.00 37.46 2.87
246 250 7.027874 TGTATGTATTGGAGGTTCCTTTTCT 57.972 36.000 0.00 0.00 37.46 2.52
247 251 7.881775 ATGTATGTATTGGAGGTTCCTTTTC 57.118 36.000 0.00 0.00 37.46 2.29
248 252 7.502561 GCTATGTATGTATTGGAGGTTCCTTTT 59.497 37.037 0.00 0.00 37.46 2.27
249 253 6.998673 GCTATGTATGTATTGGAGGTTCCTTT 59.001 38.462 0.00 0.00 37.46 3.11
250 254 6.330250 AGCTATGTATGTATTGGAGGTTCCTT 59.670 38.462 0.00 0.00 37.46 3.36
251 255 5.846714 AGCTATGTATGTATTGGAGGTTCCT 59.153 40.000 0.00 0.00 37.46 3.36
252 256 6.115448 AGCTATGTATGTATTGGAGGTTCC 57.885 41.667 0.00 0.00 36.96 3.62
253 257 8.451908 AAAAGCTATGTATGTATTGGAGGTTC 57.548 34.615 0.00 0.00 0.00 3.62
254 258 8.052748 TGAAAAGCTATGTATGTATTGGAGGTT 58.947 33.333 0.00 0.00 0.00 3.50
255 259 7.573710 TGAAAAGCTATGTATGTATTGGAGGT 58.426 34.615 0.00 0.00 0.00 3.85
256 260 8.509690 CATGAAAAGCTATGTATGTATTGGAGG 58.490 37.037 0.00 0.00 0.00 4.30
257 261 8.019669 GCATGAAAAGCTATGTATGTATTGGAG 58.980 37.037 0.00 0.00 0.00 3.86
258 262 7.720957 AGCATGAAAAGCTATGTATGTATTGGA 59.279 33.333 0.00 0.00 41.32 3.53
259 263 7.879070 AGCATGAAAAGCTATGTATGTATTGG 58.121 34.615 0.00 0.00 41.32 3.16
262 266 9.559732 TGTAAGCATGAAAAGCTATGTATGTAT 57.440 29.630 0.00 0.00 42.53 2.29
263 267 8.956533 TGTAAGCATGAAAAGCTATGTATGTA 57.043 30.769 0.00 0.00 42.53 2.29
264 268 7.012704 CCTGTAAGCATGAAAAGCTATGTATGT 59.987 37.037 0.00 0.00 42.53 2.29
265 269 7.227314 TCCTGTAAGCATGAAAAGCTATGTATG 59.773 37.037 0.00 0.00 42.53 2.39
266 270 7.282585 TCCTGTAAGCATGAAAAGCTATGTAT 58.717 34.615 0.00 0.00 42.53 2.29
267 271 6.649155 TCCTGTAAGCATGAAAAGCTATGTA 58.351 36.000 0.00 0.00 42.53 2.29
268 272 5.500234 TCCTGTAAGCATGAAAAGCTATGT 58.500 37.500 0.00 0.00 42.53 2.29
269 273 6.261118 GTTCCTGTAAGCATGAAAAGCTATG 58.739 40.000 0.00 0.00 42.53 2.23
270 274 5.358160 GGTTCCTGTAAGCATGAAAAGCTAT 59.642 40.000 0.00 0.00 42.53 2.97
271 275 4.700213 GGTTCCTGTAAGCATGAAAAGCTA 59.300 41.667 0.00 0.00 42.53 3.32
272 276 3.507622 GGTTCCTGTAAGCATGAAAAGCT 59.492 43.478 0.00 0.00 45.97 3.74
273 277 3.507622 AGGTTCCTGTAAGCATGAAAAGC 59.492 43.478 0.00 0.00 38.08 3.51
274 278 5.241506 TGAAGGTTCCTGTAAGCATGAAAAG 59.758 40.000 0.00 0.00 38.08 2.27
275 279 5.136828 TGAAGGTTCCTGTAAGCATGAAAA 58.863 37.500 0.00 0.00 38.08 2.29
276 280 4.724399 TGAAGGTTCCTGTAAGCATGAAA 58.276 39.130 0.00 0.00 38.08 2.69
277 281 4.365514 TGAAGGTTCCTGTAAGCATGAA 57.634 40.909 0.00 0.00 38.08 2.57
278 282 4.365514 TTGAAGGTTCCTGTAAGCATGA 57.634 40.909 0.00 0.00 38.08 3.07
279 283 5.647658 TGTATTGAAGGTTCCTGTAAGCATG 59.352 40.000 0.00 0.00 38.08 4.06
280 284 5.815581 TGTATTGAAGGTTCCTGTAAGCAT 58.184 37.500 0.00 0.00 38.08 3.79
281 285 5.235850 TGTATTGAAGGTTCCTGTAAGCA 57.764 39.130 0.00 0.00 38.08 3.91
282 286 6.017852 GCTATGTATTGAAGGTTCCTGTAAGC 60.018 42.308 0.00 0.00 35.75 3.09
283 287 7.275920 AGCTATGTATTGAAGGTTCCTGTAAG 58.724 38.462 0.00 0.00 0.00 2.34
284 288 7.195374 AGCTATGTATTGAAGGTTCCTGTAA 57.805 36.000 0.00 0.00 0.00 2.41
285 289 6.808321 AGCTATGTATTGAAGGTTCCTGTA 57.192 37.500 0.00 0.00 0.00 2.74
286 290 5.700402 AGCTATGTATTGAAGGTTCCTGT 57.300 39.130 0.00 0.00 0.00 4.00
324 328 8.107095 AGCTATGTATTTTGAAGGTTCCTGTAA 58.893 33.333 0.00 0.00 0.00 2.41
325 329 7.630082 AGCTATGTATTTTGAAGGTTCCTGTA 58.370 34.615 0.00 0.00 0.00 2.74
326 330 6.485171 AGCTATGTATTTTGAAGGTTCCTGT 58.515 36.000 0.00 0.00 0.00 4.00
354 358 8.738645 ATCCCAAGAAAAACACATACTATCTC 57.261 34.615 0.00 0.00 0.00 2.75
368 386 7.776969 CAGGATCATCTTCTTATCCCAAGAAAA 59.223 37.037 0.00 0.00 40.11 2.29
543 587 8.535335 AGTCCATTTTAGCGATGATATCTGTAT 58.465 33.333 3.98 0.00 0.00 2.29
557 601 6.228616 ACTTCTCCTCTAGTCCATTTTAGC 57.771 41.667 0.00 0.00 0.00 3.09
565 609 2.423446 ACCGACTTCTCCTCTAGTCC 57.577 55.000 0.00 0.00 37.98 3.85
566 610 4.753107 CAGATACCGACTTCTCCTCTAGTC 59.247 50.000 0.00 0.00 37.90 2.59
686 1575 1.206849 TGTCAGCACATGAGCCGATAA 59.793 47.619 11.77 0.00 39.07 1.75
687 1576 0.823460 TGTCAGCACATGAGCCGATA 59.177 50.000 11.77 2.51 39.07 2.92
820 1715 4.837972 AGGCCACTGTTCTATCTCTTTTC 58.162 43.478 5.01 0.00 0.00 2.29
822 1717 6.567602 ATTAGGCCACTGTTCTATCTCTTT 57.432 37.500 5.01 0.00 0.00 2.52
825 1720 7.389053 CCAATAATTAGGCCACTGTTCTATCTC 59.611 40.741 5.01 0.00 0.00 2.75
829 1724 6.119536 CACCAATAATTAGGCCACTGTTCTA 58.880 40.000 5.01 0.00 0.00 2.10
903 1798 4.985538 TGGGTGCTCAGAACTTAGATTTT 58.014 39.130 0.00 0.00 0.00 1.82
904 1799 4.287067 TCTGGGTGCTCAGAACTTAGATTT 59.713 41.667 0.00 0.00 40.43 2.17
905 1800 3.840666 TCTGGGTGCTCAGAACTTAGATT 59.159 43.478 0.00 0.00 40.43 2.40
906 1801 3.445008 TCTGGGTGCTCAGAACTTAGAT 58.555 45.455 0.00 0.00 40.43 1.98
907 1802 2.828520 CTCTGGGTGCTCAGAACTTAGA 59.171 50.000 3.18 0.00 42.46 2.10
908 1803 2.828520 TCTCTGGGTGCTCAGAACTTAG 59.171 50.000 3.18 0.00 42.46 2.18
939 1834 5.195940 CCTGCAAGATCCAGATTAGGAAAA 58.804 41.667 0.00 0.00 41.92 2.29
940 1835 4.785301 CCTGCAAGATCCAGATTAGGAAA 58.215 43.478 0.00 0.00 41.92 3.13
964 1868 1.435515 GCTGAGCTTCCGATCTCGT 59.564 57.895 0.00 0.00 37.74 4.18
984 1888 1.030457 CCATGGATCTTGCTCAAGCC 58.970 55.000 5.56 2.68 41.18 4.35
1068 1972 0.179051 GAGGAGAAGATGCCTGCAGG 60.179 60.000 29.34 29.34 33.84 4.85
1076 1980 2.937799 GCAAGCAAGAGAGGAGAAGATG 59.062 50.000 0.00 0.00 0.00 2.90
1097 2001 0.784778 GAAACTCGACGGCTGTGAAG 59.215 55.000 0.80 2.20 0.00 3.02
1109 2013 3.121944 CGGAACAAGACATGAGAAACTCG 59.878 47.826 0.00 0.00 32.35 4.18
1111 2015 2.808543 GCGGAACAAGACATGAGAAACT 59.191 45.455 0.00 0.00 0.00 2.66
1118 2022 1.522668 TTCTGGCGGAACAAGACATG 58.477 50.000 4.22 0.00 0.00 3.21
1131 2035 2.093235 AGCTAGGTGAATCAGTTCTGGC 60.093 50.000 0.00 7.90 35.33 4.85
1155 2059 0.592637 TGCAAGCGAGTTTCATGGTG 59.407 50.000 0.00 0.00 0.00 4.17
1253 2157 2.743752 CGCGACCACCATGCTTCTG 61.744 63.158 0.00 0.00 0.00 3.02
1301 2205 2.099143 GATCGACACCAGAGCGAGA 58.901 57.895 0.00 0.00 37.48 4.04
1305 2209 2.583593 GGCGATCGACACCAGAGC 60.584 66.667 21.57 0.00 0.00 4.09
1422 2326 0.250901 AACGCCACCAAGCTCTTCAT 60.251 50.000 0.00 0.00 0.00 2.57
1449 2353 4.736896 GACGACCGACCTGTGGCC 62.737 72.222 0.00 0.00 0.00 5.36
1487 2391 1.135053 GTGAAGAGCCTCCCGTAGAAC 60.135 57.143 0.00 0.00 0.00 3.01
1510 2414 2.178890 GCGAGATGCAAGGAGCCAG 61.179 63.158 0.00 0.00 45.45 4.85
1570 2477 2.450609 ACAAGTCGAGCCGTGTAAAT 57.549 45.000 0.00 0.00 0.00 1.40
1599 2522 5.298276 CACCTCCAAAGTTAAACTTACTGCA 59.702 40.000 0.00 0.00 37.47 4.41
1684 2607 2.202492 CGTCTTCCTCGCCTCACG 60.202 66.667 0.00 0.00 45.62 4.35
1783 2706 2.905996 AACCAATCGCCCTCCTGCA 61.906 57.895 0.00 0.00 0.00 4.41
1792 2715 1.934849 GCAAGGGAAACAACCAATCGC 60.935 52.381 0.00 0.00 0.00 4.58
1813 2736 3.006756 TTCTTCAGAGCGCCTCCCG 62.007 63.158 2.29 0.00 40.75 5.14
1869 2792 6.787458 TGAGGCCATCTCACTTAATATAAGGA 59.213 38.462 5.01 0.00 46.71 3.36
1954 2877 3.007979 TGTCACAGTCACATACACGAC 57.992 47.619 0.00 0.00 0.00 4.34
2058 2983 2.539432 TCTCCCTCAGCTCTTCATCA 57.461 50.000 0.00 0.00 0.00 3.07
2082 3007 2.224621 TGAGAAAGAACCCTCTGCTTGG 60.225 50.000 0.00 0.00 30.03 3.61
2165 3090 0.322277 CAGCAGACTGGCCATCTTGT 60.322 55.000 5.51 0.00 40.48 3.16
2297 3222 4.035102 GGTTTCCGGCCAGCTCCT 62.035 66.667 2.24 0.00 0.00 3.69
2319 3244 8.785468 TTTTTAGCGACACAACTAAAATAACC 57.215 30.769 8.32 0.00 43.90 2.85
2361 3286 2.892425 GCGGGTCGAGATGCCTTG 60.892 66.667 0.00 0.00 0.00 3.61
2363 3288 2.257409 ATTTGCGGGTCGAGATGCCT 62.257 55.000 0.00 0.00 0.00 4.75
2414 3339 6.074195 CGCGTTATGGATCGGACTTTTATTTA 60.074 38.462 0.00 0.00 0.00 1.40
2487 3412 9.546909 CATGTAAAACTTAAGCATACTTGTCTG 57.453 33.333 1.29 0.00 36.57 3.51
2490 3415 8.512138 GGACATGTAAAACTTAAGCATACTTGT 58.488 33.333 21.43 21.43 37.48 3.16
2527 3452 2.223433 ACGGACTGTCGGACGAATATTC 60.223 50.000 20.36 5.30 0.00 1.75
2540 5186 3.380004 TCTCAAAATTTTGCACGGACTGT 59.620 39.130 23.36 0.00 38.05 3.55
2617 5263 4.735132 GGCTAGACACGTGGCGCA 62.735 66.667 21.57 9.63 0.00 6.09
2623 5269 1.207329 GGAAATGGAGGCTAGACACGT 59.793 52.381 0.00 0.00 0.00 4.49
2625 5271 1.941325 CGGAAATGGAGGCTAGACAC 58.059 55.000 0.00 0.00 0.00 3.67
2630 5276 1.223487 GTGGCGGAAATGGAGGCTA 59.777 57.895 0.00 0.00 0.00 3.93
2653 5299 1.975327 CAGCGGACAAAGAGGAGGA 59.025 57.895 0.00 0.00 0.00 3.71
2654 5300 1.743252 GCAGCGGACAAAGAGGAGG 60.743 63.158 0.00 0.00 0.00 4.30
2661 5307 1.896660 GTTGGAGGCAGCGGACAAA 60.897 57.895 0.00 0.00 0.00 2.83
2736 5382 0.911769 TGGAGTCTTTGGATGCCGAT 59.088 50.000 0.00 0.00 0.00 4.18
2778 5425 1.738432 GGACGGACCTCGGTTATCC 59.262 63.158 0.00 0.00 44.45 2.59
2779 5426 1.039233 TGGGACGGACCTCGGTTATC 61.039 60.000 0.00 0.00 44.45 1.75
2780 5427 1.000739 TGGGACGGACCTCGGTTAT 59.999 57.895 0.00 0.00 44.45 1.89
2781 5428 1.679977 CTGGGACGGACCTCGGTTA 60.680 63.158 0.00 0.00 44.45 2.85
2782 5429 2.995574 CTGGGACGGACCTCGGTT 60.996 66.667 0.00 0.00 44.45 4.44
2785 5432 3.760035 CACCTGGGACGGACCTCG 61.760 72.222 0.00 0.00 45.88 4.63
2786 5433 2.603776 ACACCTGGGACGGACCTC 60.604 66.667 0.00 0.00 36.31 3.85
2787 5434 2.923035 CACACCTGGGACGGACCT 60.923 66.667 0.00 0.00 36.31 3.85
2788 5435 2.920912 TCACACCTGGGACGGACC 60.921 66.667 0.00 0.00 36.31 4.46
2789 5436 2.342648 GTCACACCTGGGACGGAC 59.657 66.667 0.00 0.00 38.85 4.79
2793 5440 0.037605 CTAACCGTCACACCTGGGAC 60.038 60.000 0.00 0.00 44.72 4.46
2794 5441 1.189524 CCTAACCGTCACACCTGGGA 61.190 60.000 0.00 0.00 0.00 4.37
2795 5442 1.295423 CCTAACCGTCACACCTGGG 59.705 63.158 0.00 0.00 0.00 4.45
2796 5443 0.037605 GACCTAACCGTCACACCTGG 60.038 60.000 0.00 0.00 32.74 4.45
2797 5444 0.966920 AGACCTAACCGTCACACCTG 59.033 55.000 0.00 0.00 35.07 4.00
2798 5445 1.254954 GAGACCTAACCGTCACACCT 58.745 55.000 0.00 0.00 35.07 4.00
2799 5446 0.109412 CGAGACCTAACCGTCACACC 60.109 60.000 0.00 0.00 35.07 4.16
2800 5447 0.731855 GCGAGACCTAACCGTCACAC 60.732 60.000 0.00 0.00 35.07 3.82
2801 5448 0.892358 AGCGAGACCTAACCGTCACA 60.892 55.000 0.00 0.00 35.07 3.58
2802 5449 0.456312 CAGCGAGACCTAACCGTCAC 60.456 60.000 0.00 0.00 35.07 3.67
2803 5450 0.607217 TCAGCGAGACCTAACCGTCA 60.607 55.000 0.00 0.00 35.07 4.35
2804 5451 0.099082 CTCAGCGAGACCTAACCGTC 59.901 60.000 0.00 0.00 0.00 4.79
2805 5452 1.313812 CCTCAGCGAGACCTAACCGT 61.314 60.000 7.07 0.00 0.00 4.83
2806 5453 1.433879 CCTCAGCGAGACCTAACCG 59.566 63.158 7.07 0.00 0.00 4.44
2807 5454 1.142097 GCCTCAGCGAGACCTAACC 59.858 63.158 7.07 0.00 0.00 2.85
2808 5455 4.816990 GCCTCAGCGAGACCTAAC 57.183 61.111 7.07 0.00 0.00 2.34
2818 5465 1.817099 CCCTCACAATCGCCTCAGC 60.817 63.158 0.00 0.00 0.00 4.26
2819 5466 0.036010 AACCCTCACAATCGCCTCAG 60.036 55.000 0.00 0.00 0.00 3.35
2820 5467 0.036388 GAACCCTCACAATCGCCTCA 60.036 55.000 0.00 0.00 0.00 3.86
2821 5468 1.084370 CGAACCCTCACAATCGCCTC 61.084 60.000 0.00 0.00 0.00 4.70
2822 5469 1.079127 CGAACCCTCACAATCGCCT 60.079 57.895 0.00 0.00 0.00 5.52
2823 5470 3.486263 CGAACCCTCACAATCGCC 58.514 61.111 0.00 0.00 0.00 5.54
2825 5472 2.452813 CGGCGAACCCTCACAATCG 61.453 63.158 0.00 0.00 38.28 3.34
2826 5473 2.750888 GCGGCGAACCCTCACAATC 61.751 63.158 12.98 0.00 0.00 2.67
2827 5474 2.746277 GCGGCGAACCCTCACAAT 60.746 61.111 12.98 0.00 0.00 2.71
2942 5589 4.016706 GTGGACGTGGGTGAGGGG 62.017 72.222 0.00 0.00 0.00 4.79
2943 5590 4.016706 GGTGGACGTGGGTGAGGG 62.017 72.222 0.00 0.00 0.00 4.30
2944 5591 4.016706 GGGTGGACGTGGGTGAGG 62.017 72.222 0.00 0.00 0.00 3.86
2945 5592 4.016706 GGGGTGGACGTGGGTGAG 62.017 72.222 0.00 0.00 0.00 3.51
2948 5595 4.912299 AAGGGGGTGGACGTGGGT 62.912 66.667 0.00 0.00 0.00 4.51
2949 5596 4.029809 GAAGGGGGTGGACGTGGG 62.030 72.222 0.00 0.00 0.00 4.61
2950 5597 4.029809 GGAAGGGGGTGGACGTGG 62.030 72.222 0.00 0.00 0.00 4.94
2951 5598 3.246112 TGGAAGGGGGTGGACGTG 61.246 66.667 0.00 0.00 0.00 4.49
2952 5599 2.928396 CTGGAAGGGGGTGGACGT 60.928 66.667 0.00 0.00 0.00 4.34
2953 5600 2.064242 AAACTGGAAGGGGGTGGACG 62.064 60.000 0.00 0.00 39.30 4.79
2954 5601 0.187606 AAAACTGGAAGGGGGTGGAC 59.812 55.000 0.00 0.00 39.30 4.02
2955 5602 0.481128 GAAAACTGGAAGGGGGTGGA 59.519 55.000 0.00 0.00 39.30 4.02
2956 5603 0.187361 TGAAAACTGGAAGGGGGTGG 59.813 55.000 0.00 0.00 39.30 4.61
2957 5604 1.620822 CTGAAAACTGGAAGGGGGTG 58.379 55.000 0.00 0.00 39.30 4.61
2958 5605 0.482887 CCTGAAAACTGGAAGGGGGT 59.517 55.000 0.00 0.00 39.30 4.95
2959 5606 0.482887 ACCTGAAAACTGGAAGGGGG 59.517 55.000 0.00 0.00 39.30 5.40
2960 5607 1.425448 AGACCTGAAAACTGGAAGGGG 59.575 52.381 0.00 0.00 39.30 4.79
2961 5608 2.508526 CAGACCTGAAAACTGGAAGGG 58.491 52.381 0.00 0.00 39.30 3.95
2962 5609 1.882623 GCAGACCTGAAAACTGGAAGG 59.117 52.381 0.47 0.00 39.30 3.46
2963 5610 2.551459 CAGCAGACCTGAAAACTGGAAG 59.449 50.000 0.47 0.00 44.64 3.46
2964 5611 2.575532 CAGCAGACCTGAAAACTGGAA 58.424 47.619 0.47 0.00 44.64 3.53
2965 5612 1.815408 GCAGCAGACCTGAAAACTGGA 60.815 52.381 0.47 0.00 44.64 3.86
2966 5613 0.595095 GCAGCAGACCTGAAAACTGG 59.405 55.000 0.47 0.00 44.64 4.00
2967 5614 1.602311 AGCAGCAGACCTGAAAACTG 58.398 50.000 0.47 0.00 44.64 3.16
2968 5615 2.289945 CCTAGCAGCAGACCTGAAAACT 60.290 50.000 0.47 0.00 44.64 2.66
2969 5616 2.079925 CCTAGCAGCAGACCTGAAAAC 58.920 52.381 0.47 0.00 44.64 2.43
2970 5617 1.699634 ACCTAGCAGCAGACCTGAAAA 59.300 47.619 0.47 0.00 44.64 2.29
2971 5618 1.002430 CACCTAGCAGCAGACCTGAAA 59.998 52.381 0.47 0.00 44.64 2.69
2972 5619 0.610174 CACCTAGCAGCAGACCTGAA 59.390 55.000 0.47 0.00 44.64 3.02
2973 5620 1.892819 GCACCTAGCAGCAGACCTGA 61.893 60.000 0.47 0.00 44.64 3.86
2974 5621 1.449246 GCACCTAGCAGCAGACCTG 60.449 63.158 0.00 0.00 44.79 4.00
2975 5622 2.985456 GCACCTAGCAGCAGACCT 59.015 61.111 0.00 0.00 44.79 3.85
2976 5623 2.510238 CGCACCTAGCAGCAGACC 60.510 66.667 0.00 0.00 46.13 3.85
2977 5624 3.191539 GCGCACCTAGCAGCAGAC 61.192 66.667 0.30 0.00 46.13 3.51
2978 5625 4.457496 GGCGCACCTAGCAGCAGA 62.457 66.667 10.83 0.00 46.13 4.26
2985 5632 4.111016 TCACGACGGCGCACCTAG 62.111 66.667 12.58 0.00 42.48 3.02
2986 5633 4.111016 CTCACGACGGCGCACCTA 62.111 66.667 12.58 0.00 42.48 3.08
2989 5636 4.994201 TGTCTCACGACGGCGCAC 62.994 66.667 12.58 2.54 43.21 5.34
2990 5637 3.964221 GATGTCTCACGACGGCGCA 62.964 63.158 12.58 0.00 43.21 6.09
2991 5638 3.248171 GATGTCTCACGACGGCGC 61.248 66.667 12.58 0.00 43.21 6.53
2992 5639 2.944557 CGATGTCTCACGACGGCG 60.945 66.667 10.39 10.39 43.21 6.46
2993 5640 1.583967 CTCGATGTCTCACGACGGC 60.584 63.158 0.00 0.00 43.21 5.68
2994 5641 0.168348 AACTCGATGTCTCACGACGG 59.832 55.000 0.00 0.00 43.21 4.79
2995 5642 1.251355 CAACTCGATGTCTCACGACG 58.749 55.000 0.00 0.00 43.21 5.12
2996 5643 2.333389 ACAACTCGATGTCTCACGAC 57.667 50.000 0.00 0.00 40.64 4.34
2997 5644 2.034179 ACAACAACTCGATGTCTCACGA 59.966 45.455 0.00 0.00 37.03 4.35
2998 5645 2.394708 ACAACAACTCGATGTCTCACG 58.605 47.619 0.00 0.00 31.81 4.35
2999 5646 3.184581 GGAACAACAACTCGATGTCTCAC 59.815 47.826 0.00 0.00 31.81 3.51
3000 5647 3.390135 GGAACAACAACTCGATGTCTCA 58.610 45.455 0.00 0.00 31.81 3.27
3001 5648 2.737252 GGGAACAACAACTCGATGTCTC 59.263 50.000 0.00 0.00 31.81 3.36
3002 5649 2.550208 GGGGAACAACAACTCGATGTCT 60.550 50.000 0.00 0.00 31.81 3.41
3003 5650 1.804748 GGGGAACAACAACTCGATGTC 59.195 52.381 0.00 0.00 31.81 3.06
3004 5651 1.420138 AGGGGAACAACAACTCGATGT 59.580 47.619 0.00 0.00 34.24 3.06
3005 5652 2.076863 GAGGGGAACAACAACTCGATG 58.923 52.381 0.00 0.00 0.00 3.84
3006 5653 1.003233 GGAGGGGAACAACAACTCGAT 59.997 52.381 0.00 0.00 0.00 3.59
3007 5654 0.395312 GGAGGGGAACAACAACTCGA 59.605 55.000 0.00 0.00 0.00 4.04
3008 5655 0.605589 GGGAGGGGAACAACAACTCG 60.606 60.000 0.00 0.00 0.00 4.18
3009 5656 3.341263 GGGAGGGGAACAACAACTC 57.659 57.895 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.