Multiple sequence alignment - TraesCS7B01G238000

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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 TraesCS7B01G238000 chr7B 100.000 4140 0 0 1 4140 443346706 443342567 0.000000e+00 7646
1 TraesCS7B01G238000 chr7D 93.245 3790 153 47 346 4083 426155292 426151554 0.000000e+00 5485
2 TraesCS7B01G238000 chr7A 88.899 3432 223 65 136 3482 507170763 507174121 0.000000e+00 4082
3 TraesCS7B01G238000 chr7A 87.952 166 15 4 3563 3726 113028379 113028217 1.520000e-44 191
4 TraesCS7B01G238000 chr5D 86.694 248 28 3 136 383 248588782 248589024 1.900000e-68 270
5 TraesCS7B01G238000 chr1A 82.667 300 51 1 142 441 19416798 19417096 8.820000e-67 265
6 TraesCS7B01G238000 chr1A 82.333 300 52 1 142 441 19306168 19306466 4.110000e-65 259
7 TraesCS7B01G238000 chr1D 82.119 302 48 3 142 440 15052316 15052018 1.910000e-63 254
8 TraesCS7B01G238000 chr3B 81.940 299 52 2 142 439 727007839 727008136 6.870000e-63 252
9 TraesCS7B01G238000 chr3B 81.940 299 47 4 142 440 23016172 23016463 3.200000e-61 246
10 TraesCS7B01G238000 chr3B 89.610 154 13 2 3561 3714 383704331 383704481 4.220000e-45 193
11 TraesCS7B01G238000 chr2A 81.107 307 50 8 142 444 4999636 4999938 5.350000e-59 239
12 TraesCS7B01G238000 chr2A 90.323 155 12 3 3563 3716 79316154 79316002 2.520000e-47 200
13 TraesCS7B01G238000 chr5B 80.602 299 57 1 142 440 14700331 14700628 3.220000e-56 230
14 TraesCS7B01G238000 chr5B 89.677 155 13 2 3563 3716 299602226 299602378 1.170000e-45 195
15 TraesCS7B01G238000 chr1B 80.731 301 52 6 142 440 133412498 133412794 3.220000e-56 230
16 TraesCS7B01G238000 chr4B 89.937 159 13 2 3563 3720 106227558 106227402 7.020000e-48 202
17 TraesCS7B01G238000 chr4B 90.850 153 11 2 3563 3714 146469365 146469215 7.020000e-48 202
18 TraesCS7B01G238000 chr2B 90.728 151 11 2 3564 3713 545266851 545266703 9.080000e-47 198
19 TraesCS7B01G238000 chr6B 86.782 174 16 6 3564 3734 209587536 209587367 1.970000e-43 187
20 TraesCS7B01G238000 chr6B 86.614 127 14 3 3073 3197 135709813 135709938 2.010000e-28 137
21 TraesCS7B01G238000 chr6D 86.567 134 16 2 3073 3204 61793420 61793553 3.340000e-31 147
22 TraesCS7B01G238000 chr6A 84.768 151 18 3 3073 3221 79088896 79089043 3.340000e-31 147


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 TraesCS7B01G238000 chr7B 443342567 443346706 4139 True 7646 7646 100.000 1 4140 1 chr7B.!!$R1 4139
1 TraesCS7B01G238000 chr7D 426151554 426155292 3738 True 5485 5485 93.245 346 4083 1 chr7D.!!$R1 3737
2 TraesCS7B01G238000 chr7A 507170763 507174121 3358 False 4082 4082 88.899 136 3482 1 chr7A.!!$F1 3346

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
618 657 0.033796 ACCCAGTCATGAGCCAATGG 60.034 55.0 0.0 0.0 0.00 3.16 F
1808 1878 0.182061 ATCACGCTGGATGCTGGATT 59.818 50.0 0.0 0.0 40.11 3.01 F
2386 2471 0.097325 GTCGCCGTCAACAACAACAA 59.903 50.0 0.0 0.0 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2151 2235 0.109153 TTCGGCATGATCATCCCCAG 59.891 55.000 10.20 8.25 0.00 4.45 R
2750 2840 1.281960 GCTTCGGCAGCTGCATATG 59.718 57.895 37.63 25.58 46.27 1.78 R
4027 4155 0.961857 ATTTGAGCATGCGCACCAGA 60.962 50.000 24.39 6.52 42.27 3.86 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 0.313672 TTGCTTGAACAATCACCGGC 59.686 50.000 0.00 0.00 34.61 6.13
20 21 0.537143 TGCTTGAACAATCACCGGCT 60.537 50.000 0.00 0.00 34.61 5.52
21 22 0.109597 GCTTGAACAATCACCGGCTG 60.110 55.000 0.00 0.00 34.61 4.85
22 23 0.523072 CTTGAACAATCACCGGCTGG 59.477 55.000 11.02 11.02 42.84 4.85
48 49 4.995058 GGGGGAGGGGGTGTCACA 62.995 72.222 5.12 0.00 0.00 3.58
49 50 2.856988 GGGGAGGGGGTGTCACAA 60.857 66.667 5.12 0.00 0.00 3.33
50 51 2.434774 GGGAGGGGGTGTCACAAC 59.565 66.667 5.12 0.00 0.00 3.32
51 52 2.154074 GGGAGGGGGTGTCACAACT 61.154 63.158 5.12 0.00 0.00 3.16
52 53 0.838987 GGGAGGGGGTGTCACAACTA 60.839 60.000 5.12 0.00 0.00 2.24
53 54 0.323957 GGAGGGGGTGTCACAACTAC 59.676 60.000 5.12 0.00 0.00 2.73
54 55 1.053424 GAGGGGGTGTCACAACTACA 58.947 55.000 5.12 0.00 0.00 2.74
55 56 1.418637 GAGGGGGTGTCACAACTACAA 59.581 52.381 5.12 0.00 0.00 2.41
56 57 1.847737 AGGGGGTGTCACAACTACAAA 59.152 47.619 5.12 0.00 0.00 2.83
57 58 2.445525 AGGGGGTGTCACAACTACAAAT 59.554 45.455 5.12 0.00 0.00 2.32
58 59 2.556622 GGGGGTGTCACAACTACAAATG 59.443 50.000 5.12 0.00 0.00 2.32
59 60 2.556622 GGGGTGTCACAACTACAAATGG 59.443 50.000 5.12 0.00 0.00 3.16
60 61 2.030274 GGGTGTCACAACTACAAATGGC 60.030 50.000 5.12 0.00 0.00 4.40
61 62 2.350388 GGTGTCACAACTACAAATGGCG 60.350 50.000 5.12 0.00 0.00 5.69
62 63 1.876799 TGTCACAACTACAAATGGCGG 59.123 47.619 0.00 0.00 0.00 6.13
63 64 1.199097 GTCACAACTACAAATGGCGGG 59.801 52.381 0.00 0.00 0.00 6.13
64 65 1.072489 TCACAACTACAAATGGCGGGA 59.928 47.619 0.00 0.00 0.00 5.14
65 66 1.468520 CACAACTACAAATGGCGGGAG 59.531 52.381 0.00 0.00 0.00 4.30
66 67 1.094785 CAACTACAAATGGCGGGAGG 58.905 55.000 0.00 0.00 0.00 4.30
67 68 0.988832 AACTACAAATGGCGGGAGGA 59.011 50.000 0.00 0.00 0.00 3.71
68 69 0.252197 ACTACAAATGGCGGGAGGAC 59.748 55.000 0.00 0.00 0.00 3.85
69 70 0.251916 CTACAAATGGCGGGAGGACA 59.748 55.000 0.00 0.00 38.71 4.02
70 71 0.251916 TACAAATGGCGGGAGGACAG 59.748 55.000 0.00 0.00 36.82 3.51
71 72 1.750399 CAAATGGCGGGAGGACAGG 60.750 63.158 0.00 0.00 36.82 4.00
72 73 2.231380 AAATGGCGGGAGGACAGGT 61.231 57.895 0.00 0.00 36.82 4.00
73 74 0.912487 AAATGGCGGGAGGACAGGTA 60.912 55.000 0.00 0.00 36.82 3.08
74 75 0.912487 AATGGCGGGAGGACAGGTAA 60.912 55.000 0.00 0.00 36.82 2.85
75 76 0.694444 ATGGCGGGAGGACAGGTAAT 60.694 55.000 0.00 0.00 36.82 1.89
76 77 1.146263 GGCGGGAGGACAGGTAATG 59.854 63.158 0.00 0.00 0.00 1.90
90 91 5.362556 CAGGTAATGTCCTGTGAAGTTTG 57.637 43.478 7.92 0.00 46.92 2.93
91 92 4.821805 CAGGTAATGTCCTGTGAAGTTTGT 59.178 41.667 7.92 0.00 46.92 2.83
92 93 5.995282 CAGGTAATGTCCTGTGAAGTTTGTA 59.005 40.000 7.92 0.00 46.92 2.41
93 94 5.995897 AGGTAATGTCCTGTGAAGTTTGTAC 59.004 40.000 0.00 0.00 36.35 2.90
94 95 5.995897 GGTAATGTCCTGTGAAGTTTGTACT 59.004 40.000 0.00 0.00 35.68 2.73
95 96 6.147328 GGTAATGTCCTGTGAAGTTTGTACTC 59.853 42.308 0.00 0.00 31.99 2.59
96 97 5.552870 ATGTCCTGTGAAGTTTGTACTCT 57.447 39.130 0.00 0.00 31.99 3.24
97 98 5.353394 TGTCCTGTGAAGTTTGTACTCTT 57.647 39.130 0.00 0.00 31.99 2.85
98 99 5.357257 TGTCCTGTGAAGTTTGTACTCTTC 58.643 41.667 14.42 14.42 40.02 2.87
99 100 5.105106 TGTCCTGTGAAGTTTGTACTCTTCA 60.105 40.000 17.73 17.73 44.80 3.02
118 119 9.099454 ACTCTTCAAAATAACTCATTATCGTCC 57.901 33.333 0.00 0.00 30.27 4.79
119 120 9.319143 CTCTTCAAAATAACTCATTATCGTCCT 57.681 33.333 0.00 0.00 30.27 3.85
120 121 9.314321 TCTTCAAAATAACTCATTATCGTCCTC 57.686 33.333 0.00 0.00 30.27 3.71
121 122 9.098355 CTTCAAAATAACTCATTATCGTCCTCA 57.902 33.333 0.00 0.00 30.27 3.86
122 123 9.443323 TTCAAAATAACTCATTATCGTCCTCAA 57.557 29.630 0.00 0.00 30.27 3.02
123 124 8.879759 TCAAAATAACTCATTATCGTCCTCAAC 58.120 33.333 0.00 0.00 30.27 3.18
140 141 6.641314 GTCCTCAACGAGTATATGTATTGTGG 59.359 42.308 0.00 0.00 33.87 4.17
149 150 6.591935 AGTATATGTATTGTGGACCAACCTG 58.408 40.000 0.00 0.00 39.86 4.00
152 153 2.439880 TGTATTGTGGACCAACCTGTGA 59.560 45.455 0.00 0.00 39.86 3.58
165 166 5.314923 CAACCTGTGATTGGATTGTTAGG 57.685 43.478 0.00 0.00 0.00 2.69
166 167 4.657814 ACCTGTGATTGGATTGTTAGGT 57.342 40.909 0.00 0.00 32.74 3.08
171 172 4.202514 TGTGATTGGATTGTTAGGTGGACA 60.203 41.667 0.00 0.00 0.00 4.02
172 173 4.764823 GTGATTGGATTGTTAGGTGGACAA 59.235 41.667 0.00 0.00 40.86 3.18
179 180 5.891551 GGATTGTTAGGTGGACAATGGTATT 59.108 40.000 7.15 0.00 45.11 1.89
205 206 1.897560 CCACCAGGGTTCAAGTCTTC 58.102 55.000 0.00 0.00 0.00 2.87
209 210 1.512926 CAGGGTTCAAGTCTTCGTGG 58.487 55.000 0.00 0.00 0.00 4.94
216 217 0.716108 CAAGTCTTCGTGGTCGCATC 59.284 55.000 0.00 0.00 36.96 3.91
222 223 2.128035 CTTCGTGGTCGCATCTATTCC 58.872 52.381 0.00 0.00 36.96 3.01
225 226 1.067060 CGTGGTCGCATCTATTCCTGA 59.933 52.381 0.00 0.00 0.00 3.86
234 235 8.352942 GGTCGCATCTATTCCTGAATTTATTTT 58.647 33.333 0.00 0.00 32.50 1.82
254 255 1.544686 AAAATTTTCGGCTATGCGCG 58.455 45.000 0.00 0.00 40.44 6.86
259 260 1.292571 TTTCGGCTATGCGCGTTCAA 61.293 50.000 7.78 0.00 40.44 2.69
274 275 2.779506 GTTCAATGGGAGGAGACGTTT 58.220 47.619 0.00 0.00 0.00 3.60
277 278 1.003118 CAATGGGAGGAGACGTTTCCA 59.997 52.381 25.51 7.71 39.84 3.53
283 284 1.473278 GAGGAGACGTTTCCATCGACT 59.527 52.381 25.51 4.98 39.84 4.18
296 298 2.181021 CGACTACGAGGCGCCTTT 59.819 61.111 33.34 23.04 41.27 3.11
302 304 2.501223 TACGAGGCGCCTTTGGTGAG 62.501 60.000 33.34 17.39 34.74 3.51
308 310 1.860078 CGCCTTTGGTGAGTTCGTC 59.140 57.895 0.00 0.00 34.74 4.20
312 314 2.095718 GCCTTTGGTGAGTTCGTCAATC 60.096 50.000 0.00 0.00 36.74 2.67
314 316 3.433615 CCTTTGGTGAGTTCGTCAATCTC 59.566 47.826 0.00 0.00 36.74 2.75
329 332 4.391216 GTCAATCTCAAGATGATATGCCGG 59.609 45.833 0.00 0.00 34.49 6.13
330 333 4.040829 TCAATCTCAAGATGATATGCCGGT 59.959 41.667 1.90 0.00 34.49 5.28
331 334 3.667497 TCTCAAGATGATATGCCGGTC 57.333 47.619 1.90 0.00 0.00 4.79
334 348 2.037641 TCAAGATGATATGCCGGTCCAG 59.962 50.000 1.90 0.00 0.00 3.86
338 352 1.040646 TGATATGCCGGTCCAGTCTC 58.959 55.000 1.90 0.00 0.00 3.36
340 354 1.689273 GATATGCCGGTCCAGTCTCTT 59.311 52.381 1.90 0.00 0.00 2.85
354 368 4.383444 CCAGTCTCTTGGATGTGCTCATAA 60.383 45.833 0.32 0.00 40.87 1.90
356 370 4.469227 AGTCTCTTGGATGTGCTCATAAGT 59.531 41.667 0.32 0.00 34.06 2.24
385 399 4.387559 GTGTGCGTATGTGTGTTCATAAGA 59.612 41.667 0.00 0.00 33.77 2.10
399 413 6.036083 GTGTTCATAAGAATGAGTGTATGCGT 59.964 38.462 0.00 0.00 42.97 5.24
406 421 9.929180 ATAAGAATGAGTGTATGCGTGTATATT 57.071 29.630 0.00 0.00 0.00 1.28
415 430 1.329292 TGCGTGTATATTTTGAGCGCC 59.671 47.619 2.29 0.00 42.25 6.53
418 433 2.607635 CGTGTATATTTTGAGCGCCTGT 59.392 45.455 2.29 0.00 0.00 4.00
430 445 1.069513 AGCGCCTGTGTTTGTACTGTA 59.930 47.619 2.29 0.00 0.00 2.74
502 536 4.798907 CGATGTACTAGGCACACAACTAAG 59.201 45.833 1.91 0.00 0.00 2.18
503 537 5.392703 CGATGTACTAGGCACACAACTAAGA 60.393 44.000 1.91 0.00 0.00 2.10
504 538 5.794726 TGTACTAGGCACACAACTAAGAA 57.205 39.130 0.00 0.00 0.00 2.52
552 591 2.808543 CAGTTGTTGTCCCTACAAGAGC 59.191 50.000 0.00 0.00 46.06 4.09
618 657 0.033796 ACCCAGTCATGAGCCAATGG 60.034 55.000 0.00 0.00 0.00 3.16
630 669 6.951778 TCATGAGCCAATGGATTGATAATCAT 59.048 34.615 2.05 0.00 40.14 2.45
632 671 6.308566 TGAGCCAATGGATTGATAATCATCA 58.691 36.000 2.05 0.00 40.14 3.07
633 672 6.433093 TGAGCCAATGGATTGATAATCATCAG 59.567 38.462 2.05 0.00 42.11 2.90
634 673 6.312529 AGCCAATGGATTGATAATCATCAGT 58.687 36.000 2.05 0.00 42.11 3.41
817 870 7.395617 CCTCCCCTATTTTAATTCCTAGCTAC 58.604 42.308 0.00 0.00 0.00 3.58
827 882 9.817809 TTTTAATTCCTAGCTACTACATCACTG 57.182 33.333 0.00 0.00 0.00 3.66
861 916 1.835693 CTGCTTCCTCCCATCTCCC 59.164 63.158 0.00 0.00 0.00 4.30
887 942 6.831664 ACTAATTATTCCCATCACAGTCCT 57.168 37.500 0.00 0.00 0.00 3.85
1143 1204 4.176851 GACGGGAGAGACGGCGAC 62.177 72.222 16.62 7.87 35.23 5.19
1219 1280 1.469595 GCTCAAGCAACAACAACAGCA 60.470 47.619 0.00 0.00 41.59 4.41
1551 1613 1.002069 ATGAATGTGAGGGGGCTCAA 58.998 50.000 0.00 0.00 34.88 3.02
1663 1732 1.593196 TGCTTCTTTCCTTCACACGG 58.407 50.000 0.00 0.00 0.00 4.94
1797 1867 7.600375 AGGTTATTGATCTATACAATCACGCTG 59.400 37.037 0.00 0.00 38.61 5.18
1808 1878 0.182061 ATCACGCTGGATGCTGGATT 59.818 50.000 0.00 0.00 40.11 3.01
1821 1891 6.664816 TGGATGCTGGATTTCTCACTATTTTT 59.335 34.615 0.00 0.00 0.00 1.94
1822 1892 6.976925 GGATGCTGGATTTCTCACTATTTTTG 59.023 38.462 0.00 0.00 0.00 2.44
1933 2005 2.489971 GTTCCACGACATGTTCTTCCA 58.510 47.619 0.00 0.00 0.00 3.53
1934 2006 2.455674 TCCACGACATGTTCTTCCAG 57.544 50.000 0.00 0.00 0.00 3.86
1935 2007 0.798776 CCACGACATGTTCTTCCAGC 59.201 55.000 0.00 0.00 0.00 4.85
1989 2067 2.135581 AACGACGGTGGGGTCTTCA 61.136 57.895 0.00 0.00 34.75 3.02
1997 2075 4.452733 GGGGTCTTCACGCCGAGG 62.453 72.222 0.00 0.00 45.12 4.63
2009 2087 2.897350 CCGAGGAATGCCGGCTTC 60.897 66.667 29.70 25.45 39.22 3.86
2043 2121 1.143073 GGATTTACGGGCTCCTCCAAT 59.857 52.381 0.00 0.00 36.21 3.16
2120 2204 1.538687 AAAAGCAGGCCACAGCATCC 61.539 55.000 5.01 0.00 42.56 3.51
2135 2219 3.249320 CAGCATCCTACATGCATGTGTAC 59.751 47.826 36.72 21.11 46.77 2.90
2136 2220 3.135348 AGCATCCTACATGCATGTGTACT 59.865 43.478 36.72 22.68 46.77 2.73
2138 2222 4.696455 CATCCTACATGCATGTGTACTGA 58.304 43.478 36.72 24.87 41.89 3.41
2139 2223 5.303165 CATCCTACATGCATGTGTACTGAT 58.697 41.667 36.72 25.72 41.89 2.90
2140 2224 6.458210 CATCCTACATGCATGTGTACTGATA 58.542 40.000 36.72 17.01 41.89 2.15
2141 2225 6.478512 TCCTACATGCATGTGTACTGATAA 57.521 37.500 36.72 16.32 41.89 1.75
2142 2226 6.883744 TCCTACATGCATGTGTACTGATAAA 58.116 36.000 36.72 15.63 41.89 1.40
2143 2227 6.761242 TCCTACATGCATGTGTACTGATAAAC 59.239 38.462 36.72 0.00 41.89 2.01
2144 2228 5.469373 ACATGCATGTGTACTGATAAACG 57.531 39.130 30.92 0.00 40.03 3.60
2145 2229 4.332543 ACATGCATGTGTACTGATAAACGG 59.667 41.667 30.92 0.00 40.03 4.44
2146 2230 3.932822 TGCATGTGTACTGATAAACGGT 58.067 40.909 0.00 0.00 41.44 4.83
2148 2232 3.308866 GCATGTGTACTGATAAACGGTCC 59.691 47.826 0.00 0.00 39.10 4.46
2149 2233 4.755411 CATGTGTACTGATAAACGGTCCT 58.245 43.478 0.00 0.00 39.10 3.85
2150 2234 4.182693 TGTGTACTGATAAACGGTCCTG 57.817 45.455 0.00 0.00 39.10 3.86
2151 2235 2.928116 GTGTACTGATAAACGGTCCTGC 59.072 50.000 0.00 0.00 39.10 4.85
2152 2236 2.829720 TGTACTGATAAACGGTCCTGCT 59.170 45.455 0.00 0.00 39.10 4.24
2153 2237 2.386661 ACTGATAAACGGTCCTGCTG 57.613 50.000 0.00 0.00 31.75 4.41
2154 2238 1.066143 ACTGATAAACGGTCCTGCTGG 60.066 52.381 2.58 2.58 31.75 4.85
2155 2239 0.251916 TGATAAACGGTCCTGCTGGG 59.748 55.000 10.07 0.00 0.00 4.45
2158 2243 0.912487 TAAACGGTCCTGCTGGGGAT 60.912 55.000 10.07 0.00 37.73 3.85
2181 2266 1.483004 TCATGCCGAAACCCTAATCGA 59.517 47.619 0.00 0.00 41.43 3.59
2382 2467 2.202770 ACGTCGCCGTCAACAACA 60.203 55.556 0.00 0.00 46.28 3.33
2383 2468 1.810441 ACGTCGCCGTCAACAACAA 60.810 52.632 0.00 0.00 46.28 2.83
2384 2469 1.367195 CGTCGCCGTCAACAACAAC 60.367 57.895 0.00 0.00 0.00 3.32
2385 2470 1.716760 GTCGCCGTCAACAACAACA 59.283 52.632 0.00 0.00 0.00 3.33
2386 2471 0.097325 GTCGCCGTCAACAACAACAA 59.903 50.000 0.00 0.00 0.00 2.83
2387 2472 0.097325 TCGCCGTCAACAACAACAAC 59.903 50.000 0.00 0.00 0.00 3.32
2400 2485 0.453793 CAACAACAACCACGAGCCAA 59.546 50.000 0.00 0.00 0.00 4.52
2707 2797 8.600625 CACTTGTAAATAAGTCGCAGCTTAATA 58.399 33.333 1.80 0.00 38.78 0.98
2712 2802 8.979574 GTAAATAAGTCGCAGCTTAATATGTCT 58.020 33.333 1.80 0.00 34.98 3.41
2721 2811 9.056005 TCGCAGCTTAATATGTCTCAAAATATT 57.944 29.630 0.00 0.00 34.27 1.28
2747 2837 7.807977 ACAACTAATATAATGGTTGCCTCTG 57.192 36.000 14.87 0.00 41.60 3.35
2750 2840 5.765182 ACTAATATAATGGTTGCCTCTGTGC 59.235 40.000 0.00 0.00 0.00 4.57
2751 2841 2.512692 ATAATGGTTGCCTCTGTGCA 57.487 45.000 0.00 0.00 40.07 4.57
2752 2842 2.512692 TAATGGTTGCCTCTGTGCAT 57.487 45.000 0.00 0.00 41.70 3.96
2833 2923 2.261671 GGAGCAGACGCGAGGAAA 59.738 61.111 15.93 0.00 45.49 3.13
2840 2930 0.666577 AGACGCGAGGAAAACGAAGG 60.667 55.000 15.93 0.00 0.00 3.46
3128 3218 3.068732 GGATCTGACCATGTCGATCAAGA 59.931 47.826 20.08 7.24 40.56 3.02
3302 3396 6.039941 ACATGTAGTAGCTAGGATGACTGTTC 59.960 42.308 0.00 0.00 0.00 3.18
3341 3451 6.148150 GGTCACATGCATGATCAAAACAAAAT 59.852 34.615 32.75 2.54 29.46 1.82
3490 3609 5.279859 GGGTACATTAGGGCAGTCTTATACC 60.280 48.000 0.00 0.00 0.00 2.73
3495 3614 8.041143 ACATTAGGGCAGTCTTATACCAAATA 57.959 34.615 0.00 0.00 0.00 1.40
3514 3633 7.148306 ACCAAATACACACTTATCGATCAAACC 60.148 37.037 0.00 0.00 0.00 3.27
3515 3634 6.583912 AATACACACTTATCGATCAAACCG 57.416 37.500 0.00 0.00 0.00 4.44
3553 3672 8.777865 TGCACTATATCTAATTACTGGCATTC 57.222 34.615 0.00 0.00 0.00 2.67
3565 3684 6.463995 TTACTGGCATTCATAAACATTCCC 57.536 37.500 0.00 0.00 0.00 3.97
3568 3687 3.960102 TGGCATTCATAAACATTCCCTCC 59.040 43.478 0.00 0.00 0.00 4.30
3583 3702 7.060421 ACATTCCCTCCGTTCACAAATATAAT 58.940 34.615 0.00 0.00 0.00 1.28
3651 3770 3.120269 TGAACAAACGCACTAAAACGTGT 60.120 39.130 0.00 0.00 42.68 4.49
3659 3778 8.537223 CAAACGCACTAAAACGTGTCTATATAT 58.463 33.333 0.00 0.00 42.68 0.86
3661 3780 8.719478 ACGCACTAAAACGTGTCTATATATAC 57.281 34.615 0.00 0.00 41.76 1.47
3663 3782 8.624877 CGCACTAAAACGTGTCTATATATACAC 58.375 37.037 17.30 17.30 42.04 2.90
3670 3789 9.909644 AAACGTGTCTATATATACACCTGATTC 57.090 33.333 19.95 1.10 42.39 2.52
3672 3791 8.731605 ACGTGTCTATATATACACCTGATTCAG 58.268 37.037 19.95 6.70 42.39 3.02
3684 3803 9.793259 ATACACCTGATTCAGAAAAAGTTAGAA 57.207 29.630 15.36 0.00 32.44 2.10
3708 3836 6.884832 ACATCTTATATTTGTGAACGGAGGA 58.115 36.000 0.00 0.00 0.00 3.71
3760 3888 9.166173 TGCACCATATATAATGACATTAAGCTC 57.834 33.333 11.80 0.00 0.00 4.09
3780 3908 4.216687 GCTCTCCTAGTGCACTATATCGTT 59.783 45.833 26.22 1.31 35.03 3.85
3836 3964 9.698309 CTTATCTAGTGTCTTTTGTGAGAGAAA 57.302 33.333 0.00 0.00 0.00 2.52
3879 4007 4.944619 TGGTGCTAAGATCTACATCTGG 57.055 45.455 0.00 0.00 38.55 3.86
3885 4013 6.364706 GTGCTAAGATCTACATCTGGAATTCG 59.635 42.308 0.00 0.00 38.55 3.34
3893 4021 6.759272 TCTACATCTGGAATTCGGGATTAAG 58.241 40.000 8.45 8.88 0.00 1.85
3894 4022 5.630415 ACATCTGGAATTCGGGATTAAGA 57.370 39.130 8.45 0.00 0.00 2.10
3895 4023 6.192970 ACATCTGGAATTCGGGATTAAGAT 57.807 37.500 8.45 2.29 34.17 2.40
3896 4024 7.316393 ACATCTGGAATTCGGGATTAAGATA 57.684 36.000 8.45 0.00 33.05 1.98
3897 4025 7.922382 ACATCTGGAATTCGGGATTAAGATAT 58.078 34.615 8.45 0.00 33.05 1.63
3898 4026 7.826252 ACATCTGGAATTCGGGATTAAGATATG 59.174 37.037 8.45 1.92 33.05 1.78
3900 4028 6.272324 TCTGGAATTCGGGATTAAGATATGGT 59.728 38.462 0.00 0.00 0.00 3.55
3904 4032 6.575162 ATTCGGGATTAAGATATGGTTTGC 57.425 37.500 0.00 0.00 0.00 3.68
3918 4046 3.897239 TGGTTTGCTTTCTCTTTCCTCA 58.103 40.909 0.00 0.00 0.00 3.86
3932 4060 1.851304 TCCTCATGAAATTGGGTGCC 58.149 50.000 0.00 0.00 0.00 5.01
3940 4068 3.706183 TGAAATTGGGTGCCACATCATA 58.294 40.909 0.00 0.00 30.78 2.15
3944 4072 5.697082 AATTGGGTGCCACATCATATTTT 57.303 34.783 0.00 0.00 30.78 1.82
3973 4101 8.713271 GTTATGAACCTATGCTAAGATACAAGC 58.287 37.037 0.00 0.00 39.25 4.01
3984 4112 7.906327 TGCTAAGATACAAGCATACATATCCA 58.094 34.615 0.00 0.00 43.56 3.41
4034 4162 4.944048 ACTGGTTTAATTTGTTCTGGTGC 58.056 39.130 0.00 0.00 0.00 5.01
4037 4165 3.376540 GTTTAATTTGTTCTGGTGCGCA 58.623 40.909 5.66 5.66 0.00 6.09
4051 4181 2.354510 GGTGCGCATGCTCAAATACTTA 59.645 45.455 15.91 0.00 43.34 2.24
4083 4213 9.451002 TCTATACTAGATTAGGATGTGCAGTAC 57.549 37.037 0.00 0.00 30.32 2.73
4084 4214 9.456147 CTATACTAGATTAGGATGTGCAGTACT 57.544 37.037 0.00 0.00 30.32 2.73
4085 4215 8.713708 ATACTAGATTAGGATGTGCAGTACTT 57.286 34.615 0.00 0.00 0.00 2.24
4086 4216 6.810911 ACTAGATTAGGATGTGCAGTACTTG 58.189 40.000 0.00 0.00 0.00 3.16
4087 4217 5.683876 AGATTAGGATGTGCAGTACTTGT 57.316 39.130 0.00 0.00 0.00 3.16
4088 4218 6.054860 AGATTAGGATGTGCAGTACTTGTT 57.945 37.500 0.00 0.00 0.00 2.83
4089 4219 7.182817 AGATTAGGATGTGCAGTACTTGTTA 57.817 36.000 0.00 0.00 0.00 2.41
4090 4220 7.042335 AGATTAGGATGTGCAGTACTTGTTAC 58.958 38.462 0.00 0.00 0.00 2.50
4091 4221 4.617253 AGGATGTGCAGTACTTGTTACA 57.383 40.909 0.00 0.00 32.41 2.41
4092 4222 4.315803 AGGATGTGCAGTACTTGTTACAC 58.684 43.478 0.00 0.00 31.88 2.90
4093 4223 3.122948 GGATGTGCAGTACTTGTTACACG 59.877 47.826 0.00 0.00 31.88 4.49
4094 4224 2.475818 TGTGCAGTACTTGTTACACGG 58.524 47.619 0.00 0.00 32.41 4.94
4095 4225 1.193874 GTGCAGTACTTGTTACACGGC 59.806 52.381 0.00 0.00 32.41 5.68
4096 4226 0.794473 GCAGTACTTGTTACACGGCC 59.206 55.000 0.00 0.00 32.41 6.13
4097 4227 1.435577 CAGTACTTGTTACACGGCCC 58.564 55.000 0.00 0.00 32.41 5.80
4098 4228 0.322648 AGTACTTGTTACACGGCCCC 59.677 55.000 0.00 0.00 32.41 5.80
4099 4229 1.015607 GTACTTGTTACACGGCCCCG 61.016 60.000 4.96 4.96 46.03 5.73
4100 4230 2.784889 TACTTGTTACACGGCCCCGC 62.785 60.000 6.63 0.00 44.19 6.13
4101 4231 3.894547 CTTGTTACACGGCCCCGCT 62.895 63.158 6.63 0.00 44.19 5.52
4102 4232 3.887335 TTGTTACACGGCCCCGCTC 62.887 63.158 6.63 0.00 44.19 5.03
4103 4233 4.382320 GTTACACGGCCCCGCTCA 62.382 66.667 6.63 0.00 44.19 4.26
4104 4234 3.627952 TTACACGGCCCCGCTCAA 61.628 61.111 6.63 0.00 44.19 3.02
4105 4235 3.179888 TTACACGGCCCCGCTCAAA 62.180 57.895 6.63 0.00 44.19 2.69
4106 4236 2.677765 TTACACGGCCCCGCTCAAAA 62.678 55.000 6.63 0.00 44.19 2.44
4107 4237 2.677765 TACACGGCCCCGCTCAAAAA 62.678 55.000 6.63 0.00 44.19 1.94
4129 4259 3.658757 GGTACGTGTTACCCAGTGTAA 57.341 47.619 0.00 0.00 44.41 2.41
4130 4260 4.192429 GGTACGTGTTACCCAGTGTAAT 57.808 45.455 0.00 0.00 44.41 1.89
4131 4261 4.568956 GGTACGTGTTACCCAGTGTAATT 58.431 43.478 0.00 0.00 44.41 1.40
4132 4262 4.996758 GGTACGTGTTACCCAGTGTAATTT 59.003 41.667 0.00 0.00 44.41 1.82
4133 4263 6.162777 GGTACGTGTTACCCAGTGTAATTTA 58.837 40.000 0.00 0.00 44.41 1.40
4134 4264 6.648725 GGTACGTGTTACCCAGTGTAATTTAA 59.351 38.462 0.00 0.00 44.41 1.52
4135 4265 6.790285 ACGTGTTACCCAGTGTAATTTAAG 57.210 37.500 0.00 0.00 41.33 1.85
4136 4266 5.179929 ACGTGTTACCCAGTGTAATTTAAGC 59.820 40.000 0.00 0.00 41.33 3.09
4137 4267 5.624292 GTGTTACCCAGTGTAATTTAAGCG 58.376 41.667 0.00 0.00 41.33 4.68
4138 4268 4.154556 TGTTACCCAGTGTAATTTAAGCGC 59.845 41.667 0.00 0.00 41.33 5.92
4139 4269 2.785562 ACCCAGTGTAATTTAAGCGCA 58.214 42.857 11.47 0.00 0.00 6.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.313672 GCCGGTGATTGTTCAAGCAA 59.686 50.000 1.90 0.00 32.48 3.91
3 4 0.523072 CCAGCCGGTGATTGTTCAAG 59.477 55.000 1.90 0.00 32.48 3.02
5 6 1.454104 ACCAGCCGGTGATTGTTCA 59.546 52.632 1.90 0.00 46.79 3.18
6 7 4.397348 ACCAGCCGGTGATTGTTC 57.603 55.556 1.90 0.00 46.79 3.18
31 32 4.995058 TGTGACACCCCCTCCCCC 62.995 72.222 2.45 0.00 0.00 5.40
32 33 2.856988 TTGTGACACCCCCTCCCC 60.857 66.667 2.45 0.00 0.00 4.81
33 34 0.838987 TAGTTGTGACACCCCCTCCC 60.839 60.000 2.45 0.00 0.00 4.30
34 35 0.323957 GTAGTTGTGACACCCCCTCC 59.676 60.000 2.45 0.00 0.00 4.30
35 36 1.053424 TGTAGTTGTGACACCCCCTC 58.947 55.000 2.45 0.00 0.00 4.30
36 37 1.513858 TTGTAGTTGTGACACCCCCT 58.486 50.000 2.45 0.00 0.00 4.79
37 38 2.351706 TTTGTAGTTGTGACACCCCC 57.648 50.000 2.45 0.00 0.00 5.40
38 39 2.556622 CCATTTGTAGTTGTGACACCCC 59.443 50.000 2.45 0.00 0.00 4.95
39 40 2.030274 GCCATTTGTAGTTGTGACACCC 60.030 50.000 2.45 0.00 0.00 4.61
40 41 2.350388 CGCCATTTGTAGTTGTGACACC 60.350 50.000 2.45 0.00 0.00 4.16
41 42 2.350388 CCGCCATTTGTAGTTGTGACAC 60.350 50.000 0.00 0.00 0.00 3.67
42 43 1.876799 CCGCCATTTGTAGTTGTGACA 59.123 47.619 0.00 0.00 0.00 3.58
43 44 1.199097 CCCGCCATTTGTAGTTGTGAC 59.801 52.381 0.00 0.00 0.00 3.67
44 45 1.072489 TCCCGCCATTTGTAGTTGTGA 59.928 47.619 0.00 0.00 0.00 3.58
45 46 1.468520 CTCCCGCCATTTGTAGTTGTG 59.531 52.381 0.00 0.00 0.00 3.33
46 47 1.613255 CCTCCCGCCATTTGTAGTTGT 60.613 52.381 0.00 0.00 0.00 3.32
47 48 1.094785 CCTCCCGCCATTTGTAGTTG 58.905 55.000 0.00 0.00 0.00 3.16
48 49 0.988832 TCCTCCCGCCATTTGTAGTT 59.011 50.000 0.00 0.00 0.00 2.24
49 50 0.252197 GTCCTCCCGCCATTTGTAGT 59.748 55.000 0.00 0.00 0.00 2.73
50 51 0.251916 TGTCCTCCCGCCATTTGTAG 59.748 55.000 0.00 0.00 0.00 2.74
51 52 0.251916 CTGTCCTCCCGCCATTTGTA 59.748 55.000 0.00 0.00 0.00 2.41
52 53 1.002134 CTGTCCTCCCGCCATTTGT 60.002 57.895 0.00 0.00 0.00 2.83
53 54 1.750399 CCTGTCCTCCCGCCATTTG 60.750 63.158 0.00 0.00 0.00 2.32
54 55 0.912487 TACCTGTCCTCCCGCCATTT 60.912 55.000 0.00 0.00 0.00 2.32
55 56 0.912487 TTACCTGTCCTCCCGCCATT 60.912 55.000 0.00 0.00 0.00 3.16
56 57 0.694444 ATTACCTGTCCTCCCGCCAT 60.694 55.000 0.00 0.00 0.00 4.40
57 58 1.306654 ATTACCTGTCCTCCCGCCA 60.307 57.895 0.00 0.00 0.00 5.69
58 59 1.146263 CATTACCTGTCCTCCCGCC 59.854 63.158 0.00 0.00 0.00 6.13
59 60 1.905512 ACATTACCTGTCCTCCCGC 59.094 57.895 0.00 0.00 29.94 6.13
68 69 8.169460 AGTACAAACTTCACAGGACATTACCTG 61.169 40.741 12.37 12.37 46.90 4.00
69 70 5.048846 ACAAACTTCACAGGACATTACCT 57.951 39.130 0.00 0.00 41.43 3.08
70 71 5.995897 AGTACAAACTTCACAGGACATTACC 59.004 40.000 0.00 0.00 29.00 2.85
71 72 6.929606 AGAGTACAAACTTCACAGGACATTAC 59.070 38.462 0.00 0.00 35.56 1.89
72 73 7.062749 AGAGTACAAACTTCACAGGACATTA 57.937 36.000 0.00 0.00 35.56 1.90
73 74 5.930135 AGAGTACAAACTTCACAGGACATT 58.070 37.500 0.00 0.00 35.56 2.71
74 75 5.552870 AGAGTACAAACTTCACAGGACAT 57.447 39.130 0.00 0.00 35.56 3.06
75 76 5.105106 TGAAGAGTACAAACTTCACAGGACA 60.105 40.000 18.94 3.80 44.59 4.02
76 77 5.357257 TGAAGAGTACAAACTTCACAGGAC 58.643 41.667 18.94 0.00 44.59 3.85
77 78 5.607939 TGAAGAGTACAAACTTCACAGGA 57.392 39.130 18.94 4.34 44.59 3.86
92 93 9.099454 GGACGATAATGAGTTATTTTGAAGAGT 57.901 33.333 0.00 0.00 30.75 3.24
93 94 9.319143 AGGACGATAATGAGTTATTTTGAAGAG 57.681 33.333 0.00 0.00 30.75 2.85
94 95 9.314321 GAGGACGATAATGAGTTATTTTGAAGA 57.686 33.333 0.00 0.00 30.75 2.87
95 96 9.098355 TGAGGACGATAATGAGTTATTTTGAAG 57.902 33.333 0.00 0.00 30.75 3.02
96 97 9.443323 TTGAGGACGATAATGAGTTATTTTGAA 57.557 29.630 0.00 0.00 30.75 2.69
97 98 8.879759 GTTGAGGACGATAATGAGTTATTTTGA 58.120 33.333 0.00 0.00 30.75 2.69
115 116 6.641314 CCACAATACATATACTCGTTGAGGAC 59.359 42.308 0.00 0.00 33.35 3.85
116 117 6.548251 TCCACAATACATATACTCGTTGAGGA 59.452 38.462 0.00 0.00 35.15 3.71
117 118 6.641314 GTCCACAATACATATACTCGTTGAGG 59.359 42.308 0.00 0.00 33.35 3.86
118 119 6.641314 GGTCCACAATACATATACTCGTTGAG 59.359 42.308 0.00 0.00 35.52 3.02
119 120 6.097129 TGGTCCACAATACATATACTCGTTGA 59.903 38.462 0.00 0.00 0.00 3.18
120 121 6.277605 TGGTCCACAATACATATACTCGTTG 58.722 40.000 0.00 0.00 0.00 4.10
121 122 6.474140 TGGTCCACAATACATATACTCGTT 57.526 37.500 0.00 0.00 0.00 3.85
122 123 6.278363 GTTGGTCCACAATACATATACTCGT 58.722 40.000 0.00 0.00 41.95 4.18
123 124 5.694910 GGTTGGTCCACAATACATATACTCG 59.305 44.000 0.00 0.00 41.95 4.18
124 125 6.706270 CAGGTTGGTCCACAATACATATACTC 59.294 42.308 0.00 0.00 41.95 2.59
125 126 6.157994 ACAGGTTGGTCCACAATACATATACT 59.842 38.462 0.00 0.00 41.95 2.12
126 127 6.260050 CACAGGTTGGTCCACAATACATATAC 59.740 42.308 0.00 0.00 41.95 1.47
127 128 6.157123 TCACAGGTTGGTCCACAATACATATA 59.843 38.462 0.00 0.00 41.95 0.86
128 129 5.045213 TCACAGGTTGGTCCACAATACATAT 60.045 40.000 0.00 0.00 41.95 1.78
129 130 4.287326 TCACAGGTTGGTCCACAATACATA 59.713 41.667 0.00 0.00 41.95 2.29
130 131 3.073798 TCACAGGTTGGTCCACAATACAT 59.926 43.478 0.00 0.00 41.95 2.29
131 132 2.439880 TCACAGGTTGGTCCACAATACA 59.560 45.455 0.00 0.00 41.95 2.29
132 133 3.134574 TCACAGGTTGGTCCACAATAC 57.865 47.619 0.00 0.00 41.95 1.89
133 134 4.078537 CAATCACAGGTTGGTCCACAATA 58.921 43.478 0.00 0.00 41.95 1.90
134 135 2.892852 CAATCACAGGTTGGTCCACAAT 59.107 45.455 0.00 0.00 41.95 2.71
138 139 1.144691 TCCAATCACAGGTTGGTCCA 58.855 50.000 8.75 0.00 45.05 4.02
140 141 3.157087 ACAATCCAATCACAGGTTGGTC 58.843 45.455 8.75 0.00 45.05 4.02
149 150 4.331968 TGTCCACCTAACAATCCAATCAC 58.668 43.478 0.00 0.00 0.00 3.06
152 153 4.711355 CCATTGTCCACCTAACAATCCAAT 59.289 41.667 0.00 0.00 43.62 3.16
156 157 6.039382 GGAATACCATTGTCCACCTAACAATC 59.961 42.308 0.00 0.00 43.62 2.67
159 160 4.324719 GGGAATACCATTGTCCACCTAACA 60.325 45.833 0.00 0.00 39.85 2.41
200 201 2.493713 ATAGATGCGACCACGAAGAC 57.506 50.000 0.00 0.00 42.66 3.01
203 204 1.754803 AGGAATAGATGCGACCACGAA 59.245 47.619 0.00 0.00 42.66 3.85
205 206 1.067060 TCAGGAATAGATGCGACCACG 59.933 52.381 0.00 0.00 42.93 4.94
234 235 2.096174 ACGCGCATAGCCGAAAATTTTA 59.904 40.909 5.73 0.00 44.76 1.52
236 237 0.450184 ACGCGCATAGCCGAAAATTT 59.550 45.000 5.73 0.00 44.76 1.82
237 238 0.450184 AACGCGCATAGCCGAAAATT 59.550 45.000 5.73 0.00 44.76 1.82
242 243 1.520564 ATTGAACGCGCATAGCCGA 60.521 52.632 5.73 0.00 44.76 5.54
247 248 0.813610 CCTCCCATTGAACGCGCATA 60.814 55.000 5.73 0.00 0.00 3.14
252 253 1.084370 CGTCTCCTCCCATTGAACGC 61.084 60.000 0.00 0.00 0.00 4.84
254 255 2.474410 AACGTCTCCTCCCATTGAAC 57.526 50.000 0.00 0.00 0.00 3.18
259 260 1.486726 GATGGAAACGTCTCCTCCCAT 59.513 52.381 9.80 6.29 43.31 4.00
274 275 2.831366 GCGCCTCGTAGTCGATGGA 61.831 63.158 0.00 0.00 45.21 3.41
277 278 1.664321 AAAGGCGCCTCGTAGTCGAT 61.664 55.000 32.93 7.72 45.21 3.59
283 284 2.047655 CACCAAAGGCGCCTCGTA 60.048 61.111 32.93 0.00 0.00 3.43
290 292 0.878523 TGACGAACTCACCAAAGGCG 60.879 55.000 0.00 0.00 0.00 5.52
295 297 3.744238 TGAGATTGACGAACTCACCAA 57.256 42.857 0.00 0.00 36.04 3.67
296 298 3.320826 TCTTGAGATTGACGAACTCACCA 59.679 43.478 2.24 0.00 39.80 4.17
302 304 6.347240 GGCATATCATCTTGAGATTGACGAAC 60.347 42.308 0.00 0.00 31.21 3.95
308 310 4.321718 ACCGGCATATCATCTTGAGATTG 58.678 43.478 0.00 0.00 31.21 2.67
312 314 2.037641 TGGACCGGCATATCATCTTGAG 59.962 50.000 0.00 0.00 0.00 3.02
314 316 2.224378 ACTGGACCGGCATATCATCTTG 60.224 50.000 0.00 0.00 0.00 3.02
331 334 1.277273 TGAGCACATCCAAGAGACTGG 59.723 52.381 0.00 0.00 37.87 4.00
334 348 4.569966 CACTTATGAGCACATCCAAGAGAC 59.430 45.833 11.99 0.00 37.87 3.36
338 352 4.813161 CCTACACTTATGAGCACATCCAAG 59.187 45.833 0.00 2.59 37.87 3.61
340 354 3.134623 CCCTACACTTATGAGCACATCCA 59.865 47.826 0.00 0.00 37.87 3.41
344 358 2.903784 ACACCCTACACTTATGAGCACA 59.096 45.455 0.00 0.00 0.00 4.57
354 368 1.067142 CACATACGCACACCCTACACT 60.067 52.381 0.00 0.00 0.00 3.55
356 370 0.970640 ACACATACGCACACCCTACA 59.029 50.000 0.00 0.00 0.00 2.74
385 399 8.432110 TCAAAATATACACGCATACACTCATT 57.568 30.769 0.00 0.00 0.00 2.57
399 413 3.605634 ACACAGGCGCTCAAAATATACA 58.394 40.909 7.64 0.00 0.00 2.29
406 421 1.332375 GTACAAACACAGGCGCTCAAA 59.668 47.619 7.64 0.00 0.00 2.69
455 489 6.238103 CGTATAAGCGTGACAATTCTTTCCAT 60.238 38.462 0.00 0.00 0.00 3.41
532 571 2.224548 GGCTCTTGTAGGGACAACAACT 60.225 50.000 0.00 0.00 40.72 3.16
552 591 1.148310 CGTTGACACTTGCCACTAGG 58.852 55.000 0.00 0.00 38.23 3.02
618 657 5.495640 GAGGGGGACTGATGATTATCAATC 58.504 45.833 0.00 0.57 42.48 2.67
630 669 3.208592 AGTGGGGAGGGGGACTGA 61.209 66.667 0.00 0.00 0.00 3.41
632 671 4.026357 GGAGTGGGGAGGGGGACT 62.026 72.222 0.00 0.00 0.00 3.85
633 672 3.883822 TTGGAGTGGGGAGGGGGAC 62.884 68.421 0.00 0.00 0.00 4.46
634 673 2.446337 AATTGGAGTGGGGAGGGGGA 62.446 60.000 0.00 0.00 0.00 4.81
817 870 3.003068 GCATAAGCAAGCCAGTGATGTAG 59.997 47.826 0.00 0.00 41.58 2.74
827 882 0.310232 GCAGCTAGCATAAGCAAGCC 59.690 55.000 18.83 0.00 45.30 4.35
861 916 7.016661 AGGACTGTGATGGGAATAATTAGTAGG 59.983 40.741 0.00 0.00 0.00 3.18
887 942 0.253347 ATGGGGGCAGGAAGAAGAGA 60.253 55.000 0.00 0.00 0.00 3.10
1132 1193 0.390866 TAGTTCTCGTCGCCGTCTCT 60.391 55.000 0.00 0.00 35.01 3.10
1143 1204 1.591632 CCATCGTCGTCGTAGTTCTCG 60.592 57.143 1.33 0.00 38.33 4.04
1219 1280 3.499338 TGCTTTCTGATTCATGGTTGGT 58.501 40.909 0.00 0.00 0.00 3.67
1434 1496 3.456280 CGGGGGAATTAATTACGACGAA 58.544 45.455 16.11 0.00 0.00 3.85
1663 1732 1.583495 GGGTTAGGTCCAACGCTTGC 61.583 60.000 11.48 0.00 38.10 4.01
1759 1829 2.092429 TCAATAACCTGAGGACATGGCC 60.092 50.000 10.65 10.65 0.00 5.36
1797 1867 6.705863 AAAATAGTGAGAAATCCAGCATCC 57.294 37.500 0.00 0.00 0.00 3.51
1808 1878 8.635765 AATTCCTAGTGCAAAAATAGTGAGAA 57.364 30.769 0.00 0.00 0.00 2.87
1821 1891 6.127647 GGTCATGAAAATGAATTCCTAGTGCA 60.128 38.462 2.27 0.00 31.60 4.57
1822 1892 6.096001 AGGTCATGAAAATGAATTCCTAGTGC 59.904 38.462 2.27 0.00 31.60 4.40
1864 1936 0.804989 CATGGGCGAAAAGACTGTCC 59.195 55.000 3.76 0.00 0.00 4.02
1865 1937 1.808411 TCATGGGCGAAAAGACTGTC 58.192 50.000 0.00 0.00 0.00 3.51
2043 2121 3.407083 TAATGGAGGCTGCCGGCA 61.407 61.111 30.59 30.59 44.01 5.69
2120 2204 6.292328 CCGTTTATCAGTACACATGCATGTAG 60.292 42.308 30.92 24.85 39.39 2.74
2135 2219 1.656652 CCAGCAGGACCGTTTATCAG 58.343 55.000 0.00 0.00 36.89 2.90
2136 2220 0.251916 CCCAGCAGGACCGTTTATCA 59.748 55.000 0.00 0.00 38.24 2.15
2138 2222 0.912487 TCCCCAGCAGGACCGTTTAT 60.912 55.000 0.00 0.00 38.24 1.40
2139 2223 0.912487 ATCCCCAGCAGGACCGTTTA 60.912 55.000 0.00 0.00 39.24 2.01
2140 2224 2.231380 ATCCCCAGCAGGACCGTTT 61.231 57.895 0.00 0.00 39.24 3.60
2141 2225 2.610859 ATCCCCAGCAGGACCGTT 60.611 61.111 0.00 0.00 39.24 4.44
2142 2226 3.402681 CATCCCCAGCAGGACCGT 61.403 66.667 0.00 0.00 39.24 4.83
2143 2227 2.388890 GATCATCCCCAGCAGGACCG 62.389 65.000 0.00 0.00 39.24 4.79
2144 2228 1.348008 TGATCATCCCCAGCAGGACC 61.348 60.000 0.00 0.00 39.24 4.46
2145 2229 0.769873 ATGATCATCCCCAGCAGGAC 59.230 55.000 1.18 0.00 39.24 3.85
2146 2230 0.769247 CATGATCATCCCCAGCAGGA 59.231 55.000 4.86 0.00 41.18 3.86
2148 2232 0.894184 GGCATGATCATCCCCAGCAG 60.894 60.000 4.05 0.00 0.00 4.24
2149 2233 1.152138 GGCATGATCATCCCCAGCA 59.848 57.895 4.05 0.00 0.00 4.41
2150 2234 1.970114 CGGCATGATCATCCCCAGC 60.970 63.158 10.20 8.13 0.00 4.85
2151 2235 0.109153 TTCGGCATGATCATCCCCAG 59.891 55.000 10.20 8.25 0.00 4.45
2152 2236 0.550432 TTTCGGCATGATCATCCCCA 59.450 50.000 10.20 0.00 0.00 4.96
2153 2237 0.954452 GTTTCGGCATGATCATCCCC 59.046 55.000 10.20 10.43 0.00 4.81
2154 2238 0.954452 GGTTTCGGCATGATCATCCC 59.046 55.000 5.48 5.48 0.00 3.85
2155 2239 0.954452 GGGTTTCGGCATGATCATCC 59.046 55.000 4.86 9.39 0.00 3.51
2158 2243 3.476552 GATTAGGGTTTCGGCATGATCA 58.523 45.455 0.00 0.00 0.00 2.92
2181 2266 3.819564 TTCCTAGACGCAAGCATGTAT 57.180 42.857 0.00 0.00 45.62 2.29
2382 2467 0.738389 CTTGGCTCGTGGTTGTTGTT 59.262 50.000 0.00 0.00 0.00 2.83
2383 2468 1.724582 GCTTGGCTCGTGGTTGTTGT 61.725 55.000 0.00 0.00 0.00 3.32
2384 2469 1.008538 GCTTGGCTCGTGGTTGTTG 60.009 57.895 0.00 0.00 0.00 3.33
2385 2470 2.193536 GGCTTGGCTCGTGGTTGTT 61.194 57.895 0.00 0.00 0.00 2.83
2386 2471 2.594592 GGCTTGGCTCGTGGTTGT 60.595 61.111 0.00 0.00 0.00 3.32
2387 2472 3.726517 CGGCTTGGCTCGTGGTTG 61.727 66.667 0.00 0.00 0.00 3.77
2400 2485 4.753662 TCTGGCCTACGGTCGGCT 62.754 66.667 21.25 0.00 46.73 5.52
2694 2779 5.718649 TTTGAGACATATTAAGCTGCGAC 57.281 39.130 0.00 0.00 0.00 5.19
2721 2811 9.337396 CAGAGGCAACCATTATATTAGTTGTTA 57.663 33.333 7.45 0.00 41.27 2.41
2727 2817 5.764686 TGCACAGAGGCAACCATTATATTAG 59.235 40.000 0.00 0.00 41.65 1.73
2750 2840 1.281960 GCTTCGGCAGCTGCATATG 59.718 57.895 37.63 25.58 46.27 1.78
2751 2841 3.741860 GCTTCGGCAGCTGCATAT 58.258 55.556 37.63 0.00 46.27 1.78
2824 2914 1.635663 ATGCCTTCGTTTTCCTCGCG 61.636 55.000 0.00 0.00 0.00 5.87
3128 3218 5.874093 ACTTGAAAGATCTCACTCCAATGT 58.126 37.500 0.00 0.00 0.00 2.71
3302 3396 4.320714 GCATGTGACCATATAATGTGGCAG 60.321 45.833 0.00 0.00 40.49 4.85
3341 3451 4.160065 CCAATGATACCATGCCTGACAAAA 59.840 41.667 0.00 0.00 32.36 2.44
3490 3609 6.899771 CGGTTTGATCGATAAGTGTGTATTTG 59.100 38.462 0.00 0.00 0.00 2.32
3495 3614 3.921677 ACGGTTTGATCGATAAGTGTGT 58.078 40.909 0.00 0.00 0.00 3.72
3505 3624 6.792250 GCATCTTATGATTAACGGTTTGATCG 59.208 38.462 0.00 0.00 31.69 3.69
3545 3664 4.038402 GGAGGGAATGTTTATGAATGCCAG 59.962 45.833 0.00 0.00 0.00 4.85
3553 3672 4.006989 TGTGAACGGAGGGAATGTTTATG 58.993 43.478 0.00 0.00 0.00 1.90
3561 3680 8.215050 ACATATTATATTTGTGAACGGAGGGAA 58.785 33.333 0.00 0.00 0.00 3.97
3608 3727 9.419297 TGTTCACTCATTTTAGTCTGTATGTAC 57.581 33.333 0.00 0.00 0.00 2.90
3616 3735 5.295787 TGCGTTTGTTCACTCATTTTAGTCT 59.704 36.000 0.00 0.00 0.00 3.24
3621 3740 4.370364 AGTGCGTTTGTTCACTCATTTT 57.630 36.364 0.00 0.00 39.11 1.82
3659 3778 9.052759 GTTCTAACTTTTTCTGAATCAGGTGTA 57.947 33.333 10.71 0.00 31.51 2.90
3661 3780 7.930217 TGTTCTAACTTTTTCTGAATCAGGTG 58.070 34.615 10.71 0.00 31.51 4.00
3663 3782 9.007901 AGATGTTCTAACTTTTTCTGAATCAGG 57.992 33.333 10.71 0.00 31.51 3.86
3678 3797 9.916397 CCGTTCACAAATATAAGATGTTCTAAC 57.084 33.333 0.00 0.00 0.00 2.34
3680 3799 9.529325 CTCCGTTCACAAATATAAGATGTTCTA 57.471 33.333 0.00 0.00 0.00 2.10
3681 3800 7.495934 CCTCCGTTCACAAATATAAGATGTTCT 59.504 37.037 0.00 0.00 0.00 3.01
3682 3801 7.494625 TCCTCCGTTCACAAATATAAGATGTTC 59.505 37.037 0.00 0.00 0.00 3.18
3684 3803 6.884832 TCCTCCGTTCACAAATATAAGATGT 58.115 36.000 0.00 0.00 0.00 3.06
3695 3823 3.576982 ACATCTACTTCCTCCGTTCACAA 59.423 43.478 0.00 0.00 0.00 3.33
3757 3885 3.754323 ACGATATAGTGCACTAGGAGAGC 59.246 47.826 29.05 16.54 32.26 4.09
3760 3888 7.591795 CACTAAAACGATATAGTGCACTAGGAG 59.408 40.741 29.05 21.33 41.63 3.69
3805 3933 6.042781 TCACAAAAGACACTAGATAAGGGTGT 59.957 38.462 0.00 0.00 43.93 4.16
3806 3934 6.464222 TCACAAAAGACACTAGATAAGGGTG 58.536 40.000 0.00 0.00 43.93 4.61
3854 3982 6.769822 CCAGATGTAGATCTTAGCACCAAATT 59.230 38.462 0.00 0.00 36.75 1.82
3860 3988 6.364706 CGAATTCCAGATGTAGATCTTAGCAC 59.635 42.308 0.00 0.00 36.75 4.40
3873 4001 7.281774 CCATATCTTAATCCCGAATTCCAGATG 59.718 40.741 0.00 0.00 33.03 2.90
3879 4007 7.040409 AGCAAACCATATCTTAATCCCGAATTC 60.040 37.037 0.00 0.00 0.00 2.17
3885 4013 7.503902 AGAGAAAGCAAACCATATCTTAATCCC 59.496 37.037 0.00 0.00 0.00 3.85
3893 4021 6.375455 TGAGGAAAGAGAAAGCAAACCATATC 59.625 38.462 0.00 0.00 0.00 1.63
3894 4022 6.248433 TGAGGAAAGAGAAAGCAAACCATAT 58.752 36.000 0.00 0.00 0.00 1.78
3895 4023 5.630121 TGAGGAAAGAGAAAGCAAACCATA 58.370 37.500 0.00 0.00 0.00 2.74
3896 4024 4.473444 TGAGGAAAGAGAAAGCAAACCAT 58.527 39.130 0.00 0.00 0.00 3.55
3897 4025 3.897239 TGAGGAAAGAGAAAGCAAACCA 58.103 40.909 0.00 0.00 0.00 3.67
3898 4026 4.520492 TCATGAGGAAAGAGAAAGCAAACC 59.480 41.667 0.00 0.00 0.00 3.27
3900 4028 6.713762 TTTCATGAGGAAAGAGAAAGCAAA 57.286 33.333 0.00 0.00 40.51 3.68
3918 4046 2.538222 TGATGTGGCACCCAATTTCAT 58.462 42.857 16.26 0.00 34.18 2.57
3966 4094 9.371136 CGAGTTTATGGATATGTATGCTTGTAT 57.629 33.333 0.00 0.00 0.00 2.29
4027 4155 0.961857 ATTTGAGCATGCGCACCAGA 60.962 50.000 24.39 6.52 42.27 3.86
4031 4159 2.549633 AAGTATTTGAGCATGCGCAC 57.450 45.000 24.39 12.41 42.27 5.34
4032 4160 4.693538 TTTAAGTATTTGAGCATGCGCA 57.306 36.364 20.84 20.84 42.27 6.09
4034 4162 8.398491 AGAAAATTTAAGTATTTGAGCATGCG 57.602 30.769 13.01 0.00 0.00 4.73
4076 4206 1.504359 GCCGTGTAACAAGTACTGCA 58.496 50.000 0.00 0.00 35.74 4.41
4083 4213 3.428282 GCGGGGCCGTGTAACAAG 61.428 66.667 0.00 0.00 42.09 3.16
4084 4214 3.887335 GAGCGGGGCCGTGTAACAA 62.887 63.158 0.00 0.00 42.09 2.83
4085 4215 4.382320 GAGCGGGGCCGTGTAACA 62.382 66.667 0.00 0.00 42.09 2.41
4086 4216 3.887335 TTGAGCGGGGCCGTGTAAC 62.887 63.158 0.00 0.00 42.09 2.50
4087 4217 2.677765 TTTTGAGCGGGGCCGTGTAA 62.678 55.000 0.00 0.00 42.09 2.41
4088 4218 2.677765 TTTTTGAGCGGGGCCGTGTA 62.678 55.000 0.00 0.00 42.09 2.90
4089 4219 4.572571 TTTTGAGCGGGGCCGTGT 62.573 61.111 0.00 0.00 42.09 4.49
4090 4220 3.291383 TTTTTGAGCGGGGCCGTG 61.291 61.111 0.00 0.00 42.09 4.94
4110 4240 7.622048 GCTTAAATTACACTGGGTAACACGTAC 60.622 40.741 4.34 0.00 44.36 3.67
4111 4241 6.368516 GCTTAAATTACACTGGGTAACACGTA 59.631 38.462 4.34 0.00 44.36 3.57
4112 4242 5.179929 GCTTAAATTACACTGGGTAACACGT 59.820 40.000 4.34 0.00 44.36 4.49
4113 4243 5.624292 GCTTAAATTACACTGGGTAACACG 58.376 41.667 4.34 0.00 44.36 4.49
4114 4244 5.624292 CGCTTAAATTACACTGGGTAACAC 58.376 41.667 4.34 0.00 44.36 3.32
4115 4245 4.154556 GCGCTTAAATTACACTGGGTAACA 59.845 41.667 4.34 0.00 44.36 2.41
4116 4246 4.154556 TGCGCTTAAATTACACTGGGTAAC 59.845 41.667 9.73 0.00 44.36 2.50
4117 4247 4.325119 TGCGCTTAAATTACACTGGGTAA 58.675 39.130 9.73 4.77 45.55 2.85
4118 4248 3.940319 TGCGCTTAAATTACACTGGGTA 58.060 40.909 9.73 0.00 0.00 3.69
4119 4249 2.785562 TGCGCTTAAATTACACTGGGT 58.214 42.857 9.73 0.00 0.00 4.51


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

AutoCloner maintained by Alex Coulton.