Multiple sequence alignment - TraesCS1B01G162200

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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 TraesCS1B01G162200 chr1B 100.000 2840 0 0 1 2840 280160577 280157738 0.000000e+00 5245.0
1 TraesCS1B01G162200 chr1B 90.141 497 44 4 2208 2702 572258514 572259007 2.920000e-180 641.0
2 TraesCS1B01G162200 chr1B 83.516 637 75 22 2208 2838 577914982 577915594 5.020000e-158 568.0
3 TraesCS1B01G162200 chr1B 98.545 275 4 0 10 284 17679509 17679783 1.450000e-133 486.0
4 TraesCS1B01G162200 chr1B 100.000 138 0 0 3332 3469 280157246 280157109 4.440000e-64 255.0
5 TraesCS1B01G162200 chr1D 92.370 1848 82 21 285 2095 199593303 199591478 0.000000e+00 2577.0
6 TraesCS1B01G162200 chr1D 98.319 119 2 0 2090 2208 199578018 199577900 3.510000e-50 209.0
7 TraesCS1B01G162200 chr1A 93.974 1643 62 7 570 2208 251221537 251219928 0.000000e+00 2451.0
8 TraesCS1B01G162200 chr1A 88.696 230 17 6 285 507 251221764 251221537 4.410000e-69 272.0
9 TraesCS1B01G162200 chr6B 95.283 636 30 0 2205 2840 154369333 154369968 0.000000e+00 1009.0
10 TraesCS1B01G162200 chr6B 97.849 279 6 0 8 286 523063981 523064259 1.870000e-132 483.0
11 TraesCS1B01G162200 chr6B 97.015 134 4 0 3332 3465 154369979 154370112 3.480000e-55 226.0
12 TraesCS1B01G162200 chr6B 79.167 120 23 2 681 798 549621278 549621397 7.980000e-12 82.4
13 TraesCS1B01G162200 chr5B 97.857 280 6 0 8 287 605818577 605818856 5.210000e-133 484.0
14 TraesCS1B01G162200 chr5B 97.491 279 7 0 8 286 323882340 323882618 8.710000e-131 477.0
15 TraesCS1B01G162200 chr5B 83.080 461 48 18 2208 2651 467183275 467183722 3.250000e-105 392.0
16 TraesCS1B01G162200 chr5B 79.699 133 23 3 675 805 391299952 391300082 3.690000e-15 93.5
17 TraesCS1B01G162200 chr7B 97.491 279 7 0 8 286 619611420 619611142 8.710000e-131 477.0
18 TraesCS1B01G162200 chr7B 96.809 282 9 0 3 284 210789991 210789710 4.050000e-129 472.0
19 TraesCS1B01G162200 chr7B 80.707 311 41 15 2539 2840 673137665 673137365 1.250000e-54 224.0
20 TraesCS1B01G162200 chr7B 82.031 128 13 9 681 803 91780500 91780378 2.200000e-17 100.0
21 TraesCS1B01G162200 chr7A 97.163 282 8 0 6 287 14291851 14291570 8.710000e-131 477.0
22 TraesCS1B01G162200 chr7A 97.143 280 8 0 7 286 78662667 78662946 1.130000e-129 473.0
23 TraesCS1B01G162200 chr2B 96.831 284 9 0 10 293 778840608 778840325 3.130000e-130 475.0
24 TraesCS1B01G162200 chr2B 78.740 127 22 4 681 804 568278394 568278270 2.870000e-11 80.5
25 TraesCS1B01G162200 chr2D 85.268 448 55 9 2208 2648 585950981 585951424 5.280000e-123 451.0
26 TraesCS1B01G162200 chrUn 84.855 449 59 6 2208 2651 85060185 85060629 8.830000e-121 444.0
27 TraesCS1B01G162200 chrUn 84.396 455 52 13 2211 2651 50780246 50780695 2.470000e-116 429.0
28 TraesCS1B01G162200 chr4A 83.983 462 43 17 2208 2651 718048682 718048234 6.930000e-112 414.0
29 TraesCS1B01G162200 chr4A 83.333 462 46 20 2208 2651 718151929 718151481 6.980000e-107 398.0
30 TraesCS1B01G162200 chr3A 81.798 456 56 14 2208 2650 24971750 24972191 1.180000e-94 357.0
31 TraesCS1B01G162200 chr3A 81.250 112 17 3 681 790 535822056 535822165 1.720000e-13 87.9
32 TraesCS1B01G162200 chr6A 78.443 167 30 4 681 845 574263792 574263630 1.700000e-18 104.0
33 TraesCS1B01G162200 chr4B 83.962 106 12 3 681 784 501250731 501250833 2.850000e-16 97.1


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 TraesCS1B01G162200 chr1B 280157109 280160577 3468 True 2750.0 5245 100.000 1 3469 2 chr1B.!!$R1 3468
1 TraesCS1B01G162200 chr1B 577914982 577915594 612 False 568.0 568 83.516 2208 2838 1 chr1B.!!$F3 630
2 TraesCS1B01G162200 chr1D 199591478 199593303 1825 True 2577.0 2577 92.370 285 2095 1 chr1D.!!$R2 1810
3 TraesCS1B01G162200 chr1A 251219928 251221764 1836 True 1361.5 2451 91.335 285 2208 2 chr1A.!!$R1 1923
4 TraesCS1B01G162200 chr6B 154369333 154370112 779 False 617.5 1009 96.149 2205 3465 2 chr6B.!!$F3 1260

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
944 956 0.181350 CCACCTTGCCTACATCTCCC 59.819 60.0 0.00 0.0 0.00 4.30 F
1424 1463 0.250209 CTTCAGCAGGTGCACAGAGT 60.250 55.0 20.43 0.0 45.16 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1896 1935 0.457035 ATGTTATACGTGTCCGCCGT 59.543 50.000 0.0 0.0 42.06 5.68 R
2486 2525 2.283676 GTCCTCGTCCTCCACCCA 60.284 66.667 0.0 0.0 0.00 4.51 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
23 24 5.824429 CAACATATAAGGCTGGTCACAATG 58.176 41.667 0.00 0.00 0.00 2.82
24 25 4.464008 ACATATAAGGCTGGTCACAATGG 58.536 43.478 0.00 0.00 0.00 3.16
25 26 2.442236 ATAAGGCTGGTCACAATGGG 57.558 50.000 0.00 0.00 0.00 4.00
26 27 0.323360 TAAGGCTGGTCACAATGGGC 60.323 55.000 0.00 0.00 0.00 5.36
27 28 2.283101 GGCTGGTCACAATGGGCA 60.283 61.111 0.00 0.00 0.00 5.36
28 29 1.907807 GGCTGGTCACAATGGGCAA 60.908 57.895 0.00 0.00 0.00 4.52
29 30 1.588082 GCTGGTCACAATGGGCAAG 59.412 57.895 0.00 0.00 0.00 4.01
30 31 0.895100 GCTGGTCACAATGGGCAAGA 60.895 55.000 0.00 0.00 0.00 3.02
31 32 1.619654 CTGGTCACAATGGGCAAGAA 58.380 50.000 0.00 0.00 0.00 2.52
32 33 1.270550 CTGGTCACAATGGGCAAGAAC 59.729 52.381 0.00 0.00 0.00 3.01
33 34 1.327303 GGTCACAATGGGCAAGAACA 58.673 50.000 0.00 0.00 0.00 3.18
34 35 1.895131 GGTCACAATGGGCAAGAACAT 59.105 47.619 0.00 0.00 0.00 2.71
35 36 3.088532 GGTCACAATGGGCAAGAACATA 58.911 45.455 0.00 0.00 0.00 2.29
36 37 3.129287 GGTCACAATGGGCAAGAACATAG 59.871 47.826 0.00 0.00 0.00 2.23
37 38 3.758554 GTCACAATGGGCAAGAACATAGT 59.241 43.478 0.00 0.00 0.00 2.12
38 39 4.009675 TCACAATGGGCAAGAACATAGTC 58.990 43.478 0.00 0.00 0.00 2.59
39 40 4.012374 CACAATGGGCAAGAACATAGTCT 58.988 43.478 0.00 0.00 0.00 3.24
40 41 5.045942 TCACAATGGGCAAGAACATAGTCTA 60.046 40.000 0.00 0.00 0.00 2.59
41 42 5.647658 CACAATGGGCAAGAACATAGTCTAA 59.352 40.000 0.00 0.00 0.00 2.10
42 43 6.319658 CACAATGGGCAAGAACATAGTCTAAT 59.680 38.462 0.00 0.00 0.00 1.73
43 44 7.498900 CACAATGGGCAAGAACATAGTCTAATA 59.501 37.037 0.00 0.00 0.00 0.98
44 45 8.052748 ACAATGGGCAAGAACATAGTCTAATAA 58.947 33.333 0.00 0.00 0.00 1.40
45 46 8.345565 CAATGGGCAAGAACATAGTCTAATAAC 58.654 37.037 0.00 0.00 0.00 1.89
46 47 7.195374 TGGGCAAGAACATAGTCTAATAACT 57.805 36.000 0.00 0.00 0.00 2.24
47 48 7.630082 TGGGCAAGAACATAGTCTAATAACTT 58.370 34.615 0.00 0.00 0.00 2.66
48 49 8.764558 TGGGCAAGAACATAGTCTAATAACTTA 58.235 33.333 0.00 0.00 0.00 2.24
49 50 9.043079 GGGCAAGAACATAGTCTAATAACTTAC 57.957 37.037 0.00 0.00 0.00 2.34
50 51 9.595823 GGCAAGAACATAGTCTAATAACTTACA 57.404 33.333 0.00 0.00 0.00 2.41
75 76 9.570488 CACACTTTTCTAGACTATGTTACTACC 57.430 37.037 0.00 0.00 0.00 3.18
76 77 9.531158 ACACTTTTCTAGACTATGTTACTACCT 57.469 33.333 0.00 0.00 0.00 3.08
78 79 9.187996 ACTTTTCTAGACTATGTTACTACCTCC 57.812 37.037 0.00 0.00 0.00 4.30
79 80 9.186837 CTTTTCTAGACTATGTTACTACCTCCA 57.813 37.037 0.00 0.00 0.00 3.86
80 81 8.517062 TTTCTAGACTATGTTACTACCTCCAC 57.483 38.462 0.00 0.00 0.00 4.02
81 82 7.204243 TCTAGACTATGTTACTACCTCCACA 57.796 40.000 0.00 0.00 0.00 4.17
82 83 7.281098 TCTAGACTATGTTACTACCTCCACAG 58.719 42.308 0.00 0.00 0.00 3.66
83 84 5.828871 AGACTATGTTACTACCTCCACAGT 58.171 41.667 0.00 0.00 0.00 3.55
84 85 5.652891 AGACTATGTTACTACCTCCACAGTG 59.347 44.000 0.00 0.00 0.00 3.66
85 86 4.710375 ACTATGTTACTACCTCCACAGTGG 59.290 45.833 14.19 14.19 39.43 4.00
86 87 2.253610 TGTTACTACCTCCACAGTGGG 58.746 52.381 20.14 10.16 38.32 4.61
87 88 2.254508 GTTACTACCTCCACAGTGGGT 58.745 52.381 20.14 12.79 38.32 4.51
88 89 3.181419 TGTTACTACCTCCACAGTGGGTA 60.181 47.826 20.14 13.24 38.32 3.69
90 91 1.486211 CTACCTCCACAGTGGGTAGG 58.514 60.000 21.22 21.22 45.09 3.18
91 92 1.006758 CTACCTCCACAGTGGGTAGGA 59.993 57.143 27.21 13.73 45.09 2.94
92 93 0.192566 ACCTCCACAGTGGGTAGGAA 59.807 55.000 27.21 5.42 38.32 3.36
93 94 0.613777 CCTCCACAGTGGGTAGGAAC 59.386 60.000 20.14 0.00 38.32 3.62
94 95 1.348064 CTCCACAGTGGGTAGGAACA 58.652 55.000 20.14 0.00 38.32 3.18
95 96 1.909302 CTCCACAGTGGGTAGGAACAT 59.091 52.381 20.14 0.00 38.32 2.71
96 97 1.906574 TCCACAGTGGGTAGGAACATC 59.093 52.381 20.14 0.00 38.32 3.06
97 98 1.909302 CCACAGTGGGTAGGAACATCT 59.091 52.381 12.40 0.00 32.67 2.90
98 99 3.104512 CCACAGTGGGTAGGAACATCTA 58.895 50.000 12.40 0.00 32.67 1.98
99 100 3.711704 CCACAGTGGGTAGGAACATCTAT 59.288 47.826 12.40 0.00 32.67 1.98
100 101 4.443457 CCACAGTGGGTAGGAACATCTATG 60.443 50.000 12.40 0.00 32.67 2.23
101 102 4.162320 CACAGTGGGTAGGAACATCTATGT 59.838 45.833 0.00 0.00 44.20 2.29
102 103 5.362717 CACAGTGGGTAGGAACATCTATGTA 59.637 44.000 0.00 0.00 40.80 2.29
103 104 5.598830 ACAGTGGGTAGGAACATCTATGTAG 59.401 44.000 0.00 0.00 40.80 2.74
104 105 5.598830 CAGTGGGTAGGAACATCTATGTAGT 59.401 44.000 0.00 0.00 40.80 2.73
105 106 5.598830 AGTGGGTAGGAACATCTATGTAGTG 59.401 44.000 0.00 0.00 40.80 2.74
106 107 5.363005 GTGGGTAGGAACATCTATGTAGTGT 59.637 44.000 0.00 0.00 40.80 3.55
107 108 5.597182 TGGGTAGGAACATCTATGTAGTGTC 59.403 44.000 0.00 0.00 40.80 3.67
108 109 5.597182 GGGTAGGAACATCTATGTAGTGTCA 59.403 44.000 0.00 0.00 40.80 3.58
109 110 6.267928 GGGTAGGAACATCTATGTAGTGTCAT 59.732 42.308 0.00 0.00 40.80 3.06
110 111 7.148641 GGTAGGAACATCTATGTAGTGTCATG 58.851 42.308 0.00 0.00 40.80 3.07
111 112 5.605534 AGGAACATCTATGTAGTGTCATGC 58.394 41.667 0.00 0.00 40.80 4.06
112 113 5.129320 AGGAACATCTATGTAGTGTCATGCA 59.871 40.000 0.00 0.00 40.80 3.96
113 114 5.817296 GGAACATCTATGTAGTGTCATGCAA 59.183 40.000 0.00 0.00 40.80 4.08
114 115 6.484643 GGAACATCTATGTAGTGTCATGCAAT 59.515 38.462 0.00 0.00 40.80 3.56
115 116 7.657354 GGAACATCTATGTAGTGTCATGCAATA 59.343 37.037 0.00 0.00 40.80 1.90
116 117 8.962884 AACATCTATGTAGTGTCATGCAATAA 57.037 30.769 0.00 0.00 40.80 1.40
117 118 9.565090 AACATCTATGTAGTGTCATGCAATAAT 57.435 29.630 0.00 0.00 40.80 1.28
118 119 8.996271 ACATCTATGTAGTGTCATGCAATAATG 58.004 33.333 0.00 0.00 39.68 1.90
119 120 8.996271 CATCTATGTAGTGTCATGCAATAATGT 58.004 33.333 0.00 0.00 28.84 2.71
153 154 9.401058 AGGTTATAGATTCATTGTTTCTTGGAG 57.599 33.333 0.00 0.00 0.00 3.86
154 155 9.178758 GGTTATAGATTCATTGTTTCTTGGAGT 57.821 33.333 0.00 0.00 0.00 3.85
155 156 9.994432 GTTATAGATTCATTGTTTCTTGGAGTG 57.006 33.333 0.00 0.00 0.00 3.51
156 157 9.739276 TTATAGATTCATTGTTTCTTGGAGTGT 57.261 29.630 0.00 0.00 0.00 3.55
157 158 6.323203 AGATTCATTGTTTCTTGGAGTGTG 57.677 37.500 0.00 0.00 0.00 3.82
158 159 5.829924 AGATTCATTGTTTCTTGGAGTGTGT 59.170 36.000 0.00 0.00 0.00 3.72
159 160 4.898829 TCATTGTTTCTTGGAGTGTGTG 57.101 40.909 0.00 0.00 0.00 3.82
160 161 4.522114 TCATTGTTTCTTGGAGTGTGTGA 58.478 39.130 0.00 0.00 0.00 3.58
161 162 5.132502 TCATTGTTTCTTGGAGTGTGTGAT 58.867 37.500 0.00 0.00 0.00 3.06
162 163 4.898829 TTGTTTCTTGGAGTGTGTGATG 57.101 40.909 0.00 0.00 0.00 3.07
163 164 3.884895 TGTTTCTTGGAGTGTGTGATGT 58.115 40.909 0.00 0.00 0.00 3.06
164 165 4.269183 TGTTTCTTGGAGTGTGTGATGTT 58.731 39.130 0.00 0.00 0.00 2.71
165 166 4.335315 TGTTTCTTGGAGTGTGTGATGTTC 59.665 41.667 0.00 0.00 0.00 3.18
166 167 3.126001 TCTTGGAGTGTGTGATGTTCC 57.874 47.619 0.00 0.00 0.00 3.62
167 168 1.800586 CTTGGAGTGTGTGATGTTCCG 59.199 52.381 0.00 0.00 0.00 4.30
168 169 1.044611 TGGAGTGTGTGATGTTCCGA 58.955 50.000 0.00 0.00 0.00 4.55
169 170 1.623311 TGGAGTGTGTGATGTTCCGAT 59.377 47.619 0.00 0.00 0.00 4.18
170 171 2.829120 TGGAGTGTGTGATGTTCCGATA 59.171 45.455 0.00 0.00 0.00 2.92
171 172 3.259625 TGGAGTGTGTGATGTTCCGATAA 59.740 43.478 0.00 0.00 0.00 1.75
172 173 3.617263 GGAGTGTGTGATGTTCCGATAAC 59.383 47.826 0.00 0.00 0.00 1.89
173 174 4.495422 GAGTGTGTGATGTTCCGATAACT 58.505 43.478 2.91 0.00 0.00 2.24
174 175 4.894784 AGTGTGTGATGTTCCGATAACTT 58.105 39.130 2.91 0.00 0.00 2.66
175 176 6.032956 AGTGTGTGATGTTCCGATAACTTA 57.967 37.500 2.91 0.00 0.00 2.24
176 177 6.100004 AGTGTGTGATGTTCCGATAACTTAG 58.900 40.000 2.91 0.00 0.00 2.18
177 178 4.868171 TGTGTGATGTTCCGATAACTTAGC 59.132 41.667 2.91 0.00 0.00 3.09
178 179 5.109903 GTGTGATGTTCCGATAACTTAGCT 58.890 41.667 0.00 0.00 0.00 3.32
179 180 6.127563 TGTGTGATGTTCCGATAACTTAGCTA 60.128 38.462 0.00 0.00 0.00 3.32
180 181 6.418226 GTGTGATGTTCCGATAACTTAGCTAG 59.582 42.308 0.00 0.00 0.00 3.42
181 182 6.096423 TGTGATGTTCCGATAACTTAGCTAGT 59.904 38.462 0.00 0.00 39.32 2.57
192 193 4.884668 ACTTAGCTAGTTACCACAAGCA 57.115 40.909 0.00 0.00 37.44 3.91
193 194 4.566987 ACTTAGCTAGTTACCACAAGCAC 58.433 43.478 0.00 0.00 37.44 4.40
194 195 2.474410 AGCTAGTTACCACAAGCACC 57.526 50.000 0.00 0.00 37.44 5.01
195 196 1.978580 AGCTAGTTACCACAAGCACCT 59.021 47.619 0.00 0.00 37.44 4.00
196 197 2.028020 AGCTAGTTACCACAAGCACCTC 60.028 50.000 0.00 0.00 37.44 3.85
197 198 2.028020 GCTAGTTACCACAAGCACCTCT 60.028 50.000 0.00 0.00 35.05 3.69
198 199 2.841442 AGTTACCACAAGCACCTCTC 57.159 50.000 0.00 0.00 0.00 3.20
199 200 2.330216 AGTTACCACAAGCACCTCTCT 58.670 47.619 0.00 0.00 0.00 3.10
200 201 2.300437 AGTTACCACAAGCACCTCTCTC 59.700 50.000 0.00 0.00 0.00 3.20
201 202 2.300437 GTTACCACAAGCACCTCTCTCT 59.700 50.000 0.00 0.00 0.00 3.10
202 203 1.428869 ACCACAAGCACCTCTCTCTT 58.571 50.000 0.00 0.00 0.00 2.85
203 204 1.346068 ACCACAAGCACCTCTCTCTTC 59.654 52.381 0.00 0.00 0.00 2.87
204 205 1.345741 CCACAAGCACCTCTCTCTTCA 59.654 52.381 0.00 0.00 0.00 3.02
205 206 2.027377 CCACAAGCACCTCTCTCTTCAT 60.027 50.000 0.00 0.00 0.00 2.57
206 207 3.558746 CCACAAGCACCTCTCTCTTCATT 60.559 47.826 0.00 0.00 0.00 2.57
207 208 4.323028 CCACAAGCACCTCTCTCTTCATTA 60.323 45.833 0.00 0.00 0.00 1.90
208 209 5.240891 CACAAGCACCTCTCTCTTCATTAA 58.759 41.667 0.00 0.00 0.00 1.40
209 210 5.702670 CACAAGCACCTCTCTCTTCATTAAA 59.297 40.000 0.00 0.00 0.00 1.52
210 211 6.373774 CACAAGCACCTCTCTCTTCATTAAAT 59.626 38.462 0.00 0.00 0.00 1.40
211 212 7.550551 CACAAGCACCTCTCTCTTCATTAAATA 59.449 37.037 0.00 0.00 0.00 1.40
212 213 8.270744 ACAAGCACCTCTCTCTTCATTAAATAT 58.729 33.333 0.00 0.00 0.00 1.28
213 214 9.770097 CAAGCACCTCTCTCTTCATTAAATATA 57.230 33.333 0.00 0.00 0.00 0.86
215 216 9.941325 AGCACCTCTCTCTTCATTAAATATATG 57.059 33.333 0.00 0.00 0.00 1.78
216 217 9.935241 GCACCTCTCTCTTCATTAAATATATGA 57.065 33.333 0.00 0.00 0.00 2.15
238 239 6.676950 TGACACATAAGCAAAGTTGTATTGG 58.323 36.000 0.00 0.00 0.00 3.16
239 240 6.488344 TGACACATAAGCAAAGTTGTATTGGA 59.512 34.615 0.00 0.00 0.00 3.53
240 241 6.913170 ACACATAAGCAAAGTTGTATTGGAG 58.087 36.000 0.00 0.00 0.00 3.86
241 242 6.490040 ACACATAAGCAAAGTTGTATTGGAGT 59.510 34.615 0.00 0.00 0.00 3.85
242 243 6.803320 CACATAAGCAAAGTTGTATTGGAGTG 59.197 38.462 0.00 0.00 0.00 3.51
243 244 6.490040 ACATAAGCAAAGTTGTATTGGAGTGT 59.510 34.615 0.00 0.00 0.00 3.55
244 245 4.836125 AGCAAAGTTGTATTGGAGTGTG 57.164 40.909 0.00 0.00 0.00 3.82
245 246 4.207165 AGCAAAGTTGTATTGGAGTGTGT 58.793 39.130 0.00 0.00 0.00 3.72
246 247 4.036734 AGCAAAGTTGTATTGGAGTGTGTG 59.963 41.667 0.00 0.00 0.00 3.82
247 248 4.036262 GCAAAGTTGTATTGGAGTGTGTGA 59.964 41.667 0.00 0.00 0.00 3.58
248 249 5.278463 GCAAAGTTGTATTGGAGTGTGTGAT 60.278 40.000 0.00 0.00 0.00 3.06
249 250 5.947228 AAGTTGTATTGGAGTGTGTGATG 57.053 39.130 0.00 0.00 0.00 3.07
250 251 4.973168 AGTTGTATTGGAGTGTGTGATGT 58.027 39.130 0.00 0.00 0.00 3.06
251 252 5.376625 AGTTGTATTGGAGTGTGTGATGTT 58.623 37.500 0.00 0.00 0.00 2.71
252 253 6.530120 AGTTGTATTGGAGTGTGTGATGTTA 58.470 36.000 0.00 0.00 0.00 2.41
253 254 6.426937 AGTTGTATTGGAGTGTGTGATGTTAC 59.573 38.462 0.00 0.00 0.00 2.50
254 255 6.109156 TGTATTGGAGTGTGTGATGTTACT 57.891 37.500 0.00 0.00 0.00 2.24
255 256 6.163476 TGTATTGGAGTGTGTGATGTTACTC 58.837 40.000 0.00 0.00 38.98 2.59
261 262 6.026947 GAGTGTGTGATGTTACTCCTAAGT 57.973 41.667 0.00 0.00 39.66 2.24
262 263 6.420913 AGTGTGTGATGTTACTCCTAAGTT 57.579 37.500 0.00 0.00 36.92 2.66
263 264 6.456501 AGTGTGTGATGTTACTCCTAAGTTC 58.543 40.000 0.00 0.00 36.92 3.01
264 265 5.638234 GTGTGTGATGTTACTCCTAAGTTCC 59.362 44.000 0.00 0.00 36.92 3.62
265 266 5.542635 TGTGTGATGTTACTCCTAAGTTCCT 59.457 40.000 0.00 0.00 36.92 3.36
266 267 6.100668 GTGTGATGTTACTCCTAAGTTCCTC 58.899 44.000 0.00 0.00 36.92 3.71
267 268 5.187186 TGTGATGTTACTCCTAAGTTCCTCC 59.813 44.000 0.00 0.00 36.92 4.30
268 269 4.715297 TGATGTTACTCCTAAGTTCCTCCC 59.285 45.833 0.00 0.00 36.92 4.30
269 270 3.447950 TGTTACTCCTAAGTTCCTCCCC 58.552 50.000 0.00 0.00 36.92 4.81
270 271 3.181404 TGTTACTCCTAAGTTCCTCCCCA 60.181 47.826 0.00 0.00 36.92 4.96
271 272 2.972153 ACTCCTAAGTTCCTCCCCAT 57.028 50.000 0.00 0.00 28.74 4.00
272 273 3.222394 ACTCCTAAGTTCCTCCCCATT 57.778 47.619 0.00 0.00 28.74 3.16
273 274 2.846827 ACTCCTAAGTTCCTCCCCATTG 59.153 50.000 0.00 0.00 28.74 2.82
274 275 2.846827 CTCCTAAGTTCCTCCCCATTGT 59.153 50.000 0.00 0.00 0.00 2.71
275 276 2.576191 TCCTAAGTTCCTCCCCATTGTG 59.424 50.000 0.00 0.00 0.00 3.33
276 277 2.576191 CCTAAGTTCCTCCCCATTGTGA 59.424 50.000 0.00 0.00 0.00 3.58
277 278 2.586648 AAGTTCCTCCCCATTGTGAC 57.413 50.000 0.00 0.00 0.00 3.67
278 279 0.698818 AGTTCCTCCCCATTGTGACC 59.301 55.000 0.00 0.00 0.00 4.02
279 280 0.404040 GTTCCTCCCCATTGTGACCA 59.596 55.000 0.00 0.00 0.00 4.02
280 281 0.698238 TTCCTCCCCATTGTGACCAG 59.302 55.000 0.00 0.00 0.00 4.00
281 282 1.379044 CCTCCCCATTGTGACCAGC 60.379 63.158 0.00 0.00 0.00 4.85
282 283 1.379044 CTCCCCATTGTGACCAGCC 60.379 63.158 0.00 0.00 0.00 4.85
283 284 1.852157 TCCCCATTGTGACCAGCCT 60.852 57.895 0.00 0.00 0.00 4.58
302 303 5.471456 CAGCCTAAGAACTGAAGTTGTCATT 59.529 40.000 0.00 0.00 38.56 2.57
304 305 5.335191 GCCTAAGAACTGAAGTTGTCATTGG 60.335 44.000 0.00 0.00 38.56 3.16
305 306 5.182001 CCTAAGAACTGAAGTTGTCATTGGG 59.818 44.000 0.00 0.00 38.56 4.12
328 329 2.361771 CCAATGGAAGCTGGGCCT 59.638 61.111 4.53 0.00 0.00 5.19
345 346 2.422803 GGCCTAGGCACATCCACATTAA 60.423 50.000 34.09 0.00 44.11 1.40
450 458 5.911752 AGACTTATATGGTCTTCTGTGCAG 58.088 41.667 7.18 0.00 40.65 4.41
542 550 1.804151 CGCGAAAGTGATTTCTTCCCA 59.196 47.619 0.00 0.00 46.66 4.37
552 560 4.917415 GTGATTTCTTCCCAACGATGTTTG 59.083 41.667 0.00 0.00 0.00 2.93
554 562 1.243902 TCTTCCCAACGATGTTTGCC 58.756 50.000 0.00 0.00 0.00 4.52
555 563 0.958091 CTTCCCAACGATGTTTGCCA 59.042 50.000 0.00 0.00 0.00 4.92
556 564 1.545582 CTTCCCAACGATGTTTGCCAT 59.454 47.619 0.00 0.00 36.13 4.40
557 565 2.498644 TCCCAACGATGTTTGCCATA 57.501 45.000 0.00 0.00 32.56 2.74
558 566 2.088423 TCCCAACGATGTTTGCCATAC 58.912 47.619 0.00 0.00 32.56 2.39
559 567 1.815613 CCCAACGATGTTTGCCATACA 59.184 47.619 0.00 0.00 32.56 2.29
560 568 2.426738 CCCAACGATGTTTGCCATACAT 59.573 45.455 0.09 0.09 38.86 2.29
650 658 3.057315 AGAACCATGTCAAAAATCTGCGG 60.057 43.478 0.00 0.00 0.00 5.69
743 754 9.961265 TTTTATAATGTCGACTAGATACAGTGG 57.039 33.333 17.92 0.00 0.00 4.00
878 890 3.575687 CCAGAAGAAAAATCTGCCAAGGT 59.424 43.478 0.00 0.00 42.36 3.50
944 956 0.181350 CCACCTTGCCTACATCTCCC 59.819 60.000 0.00 0.00 0.00 4.30
949 988 2.487986 CCTTGCCTACATCTCCCCATTC 60.488 54.545 0.00 0.00 0.00 2.67
950 989 2.196742 TGCCTACATCTCCCCATTCT 57.803 50.000 0.00 0.00 0.00 2.40
951 990 2.050144 TGCCTACATCTCCCCATTCTC 58.950 52.381 0.00 0.00 0.00 2.87
974 1013 3.113477 TTTCCCCAACTGGCCCCA 61.113 61.111 0.00 0.00 0.00 4.96
1030 1069 3.439129 GCACTAAAAACCCTACTTGCGAT 59.561 43.478 0.00 0.00 0.00 4.58
1154 1193 0.836400 ACCACCACCTCAAGATCCGT 60.836 55.000 0.00 0.00 0.00 4.69
1257 1296 0.974010 CCTCTACTACCCCAACGGCA 60.974 60.000 0.00 0.00 33.26 5.69
1261 1300 1.126329 TACTACCCCAACGGCAACCA 61.126 55.000 0.00 0.00 33.26 3.67
1297 1336 1.676916 CCACGTGTCCGTCTACCTCTA 60.677 57.143 15.65 0.00 46.28 2.43
1414 1453 2.743928 GGCGGTGACTTCAGCAGG 60.744 66.667 9.01 0.00 44.00 4.85
1421 1460 0.533531 TGACTTCAGCAGGTGCACAG 60.534 55.000 20.43 11.73 45.16 3.66
1424 1463 0.250209 CTTCAGCAGGTGCACAGAGT 60.250 55.000 20.43 0.00 45.16 3.24
1502 1541 3.054802 AGAAATCGAAGCATCTCAAGGGT 60.055 43.478 0.00 0.00 0.00 4.34
1686 1725 2.109126 GCTGGTGGCGAGACATTCC 61.109 63.158 0.00 0.00 0.00 3.01
1690 1729 3.000819 TGGCGAGACATTCCCGGT 61.001 61.111 0.00 0.00 0.00 5.28
1762 1801 0.676736 GGCTCGATGAAGGAGGGTAG 59.323 60.000 0.00 0.00 32.10 3.18
2303 2342 3.590824 CCAAATGAGTGGTCGGCC 58.409 61.111 0.00 0.00 33.63 6.13
2310 2349 1.375523 GAGTGGTCGGCCGTTTCAT 60.376 57.895 27.15 9.98 37.67 2.57
2395 2434 0.651551 CGAACCGTTTGTTTGACCGA 59.348 50.000 0.00 0.00 40.30 4.69
2420 2459 9.745880 GATTATTTGACCGTTAACTGAGATCTA 57.254 33.333 3.84 0.00 0.00 1.98
2510 2549 0.395862 GGAGGACGAGGACCAGATCA 60.396 60.000 0.00 0.00 0.00 2.92
2617 2656 2.423660 CCTTCTCACCCGACCTCTCTAT 60.424 54.545 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.221106 CCATTGTGACCAGCCTTATATGTTG 60.221 44.000 0.00 0.00 0.00 3.33
1 2 4.889409 CCATTGTGACCAGCCTTATATGTT 59.111 41.667 0.00 0.00 0.00 2.71
2 3 4.464008 CCATTGTGACCAGCCTTATATGT 58.536 43.478 0.00 0.00 0.00 2.29
3 4 3.822735 CCCATTGTGACCAGCCTTATATG 59.177 47.826 0.00 0.00 0.00 1.78
4 5 3.751893 GCCCATTGTGACCAGCCTTATAT 60.752 47.826 0.00 0.00 0.00 0.86
5 6 2.422803 GCCCATTGTGACCAGCCTTATA 60.423 50.000 0.00 0.00 0.00 0.98
6 7 1.686115 GCCCATTGTGACCAGCCTTAT 60.686 52.381 0.00 0.00 0.00 1.73
7 8 0.323360 GCCCATTGTGACCAGCCTTA 60.323 55.000 0.00 0.00 0.00 2.69
8 9 1.607467 GCCCATTGTGACCAGCCTT 60.607 57.895 0.00 0.00 0.00 4.35
9 10 2.036256 GCCCATTGTGACCAGCCT 59.964 61.111 0.00 0.00 0.00 4.58
10 11 1.880819 CTTGCCCATTGTGACCAGCC 61.881 60.000 0.00 0.00 0.00 4.85
11 12 0.895100 TCTTGCCCATTGTGACCAGC 60.895 55.000 0.00 0.00 0.00 4.85
12 13 1.270550 GTTCTTGCCCATTGTGACCAG 59.729 52.381 0.00 0.00 0.00 4.00
13 14 1.327303 GTTCTTGCCCATTGTGACCA 58.673 50.000 0.00 0.00 0.00 4.02
14 15 1.327303 TGTTCTTGCCCATTGTGACC 58.673 50.000 0.00 0.00 0.00 4.02
15 16 3.758554 ACTATGTTCTTGCCCATTGTGAC 59.241 43.478 0.00 0.00 0.00 3.67
16 17 4.009675 GACTATGTTCTTGCCCATTGTGA 58.990 43.478 0.00 0.00 29.34 3.58
17 18 4.012374 AGACTATGTTCTTGCCCATTGTG 58.988 43.478 0.00 0.00 29.34 3.33
18 19 4.307032 AGACTATGTTCTTGCCCATTGT 57.693 40.909 0.00 0.00 31.33 2.71
19 20 6.949352 ATTAGACTATGTTCTTGCCCATTG 57.051 37.500 0.00 0.00 0.00 2.82
20 21 8.275040 AGTTATTAGACTATGTTCTTGCCCATT 58.725 33.333 0.00 0.00 0.00 3.16
21 22 7.806180 AGTTATTAGACTATGTTCTTGCCCAT 58.194 34.615 0.00 0.00 0.00 4.00
22 23 7.195374 AGTTATTAGACTATGTTCTTGCCCA 57.805 36.000 0.00 0.00 0.00 5.36
23 24 9.043079 GTAAGTTATTAGACTATGTTCTTGCCC 57.957 37.037 0.00 0.00 0.00 5.36
24 25 9.595823 TGTAAGTTATTAGACTATGTTCTTGCC 57.404 33.333 0.00 0.00 0.00 4.52
49 50 9.570488 GGTAGTAACATAGTCTAGAAAAGTGTG 57.430 37.037 0.00 0.00 0.00 3.82
50 51 9.531158 AGGTAGTAACATAGTCTAGAAAAGTGT 57.469 33.333 0.00 0.00 0.00 3.55
52 53 9.187996 GGAGGTAGTAACATAGTCTAGAAAAGT 57.812 37.037 0.00 0.00 0.00 2.66
53 54 9.186837 TGGAGGTAGTAACATAGTCTAGAAAAG 57.813 37.037 0.00 0.00 0.00 2.27
54 55 8.964772 GTGGAGGTAGTAACATAGTCTAGAAAA 58.035 37.037 0.00 0.00 0.00 2.29
55 56 8.111545 TGTGGAGGTAGTAACATAGTCTAGAAA 58.888 37.037 0.00 0.00 0.00 2.52
56 57 7.636579 TGTGGAGGTAGTAACATAGTCTAGAA 58.363 38.462 0.00 0.00 0.00 2.10
57 58 7.092533 ACTGTGGAGGTAGTAACATAGTCTAGA 60.093 40.741 0.00 0.00 30.96 2.43
58 59 7.012515 CACTGTGGAGGTAGTAACATAGTCTAG 59.987 44.444 0.00 0.00 33.84 2.43
59 60 6.827251 CACTGTGGAGGTAGTAACATAGTCTA 59.173 42.308 0.00 0.00 33.84 2.59
60 61 5.652891 CACTGTGGAGGTAGTAACATAGTCT 59.347 44.000 0.00 0.00 33.84 3.24
61 62 5.163540 CCACTGTGGAGGTAGTAACATAGTC 60.164 48.000 22.33 0.00 40.96 2.59
62 63 4.710375 CCACTGTGGAGGTAGTAACATAGT 59.290 45.833 22.33 0.00 40.96 2.12
63 64 4.099573 CCCACTGTGGAGGTAGTAACATAG 59.900 50.000 27.94 2.06 40.96 2.23
64 65 4.028131 CCCACTGTGGAGGTAGTAACATA 58.972 47.826 27.94 0.00 40.96 2.29
65 66 2.838202 CCCACTGTGGAGGTAGTAACAT 59.162 50.000 27.94 0.00 40.96 2.71
66 67 2.253610 CCCACTGTGGAGGTAGTAACA 58.746 52.381 27.94 0.00 40.96 2.41
67 68 2.254508 ACCCACTGTGGAGGTAGTAAC 58.745 52.381 27.94 0.00 40.96 2.50
68 69 2.708037 ACCCACTGTGGAGGTAGTAA 57.292 50.000 27.94 0.00 40.96 2.24
69 70 3.377253 CTACCCACTGTGGAGGTAGTA 57.623 52.381 27.94 18.08 45.39 1.82
70 71 2.233305 CTACCCACTGTGGAGGTAGT 57.767 55.000 27.94 17.93 45.39 2.73
72 73 1.086565 TCCTACCCACTGTGGAGGTA 58.913 55.000 27.94 19.39 40.96 3.08
73 74 0.192566 TTCCTACCCACTGTGGAGGT 59.807 55.000 27.94 19.31 40.96 3.85
74 75 0.613777 GTTCCTACCCACTGTGGAGG 59.386 60.000 27.94 24.85 40.96 4.30
75 76 1.348064 TGTTCCTACCCACTGTGGAG 58.652 55.000 27.94 19.03 40.96 3.86
76 77 1.906574 GATGTTCCTACCCACTGTGGA 59.093 52.381 27.94 8.24 40.96 4.02
77 78 1.909302 AGATGTTCCTACCCACTGTGG 59.091 52.381 20.01 20.01 37.25 4.17
78 79 4.162320 ACATAGATGTTCCTACCCACTGTG 59.838 45.833 0.00 0.00 37.90 3.66
79 80 4.362677 ACATAGATGTTCCTACCCACTGT 58.637 43.478 0.00 0.00 37.90 3.55
80 81 5.598830 ACTACATAGATGTTCCTACCCACTG 59.401 44.000 0.00 0.00 41.97 3.66
81 82 5.598830 CACTACATAGATGTTCCTACCCACT 59.401 44.000 0.00 0.00 41.97 4.00
82 83 5.363005 ACACTACATAGATGTTCCTACCCAC 59.637 44.000 0.00 0.00 41.97 4.61
83 84 5.525484 ACACTACATAGATGTTCCTACCCA 58.475 41.667 0.00 0.00 41.97 4.51
84 85 5.597182 TGACACTACATAGATGTTCCTACCC 59.403 44.000 0.00 0.00 41.97 3.69
85 86 6.710597 TGACACTACATAGATGTTCCTACC 57.289 41.667 0.00 0.00 41.97 3.18
86 87 6.642950 GCATGACACTACATAGATGTTCCTAC 59.357 42.308 0.00 0.00 41.97 3.18
87 88 6.323739 TGCATGACACTACATAGATGTTCCTA 59.676 38.462 0.00 0.00 41.97 2.94
88 89 5.129320 TGCATGACACTACATAGATGTTCCT 59.871 40.000 0.00 0.00 41.97 3.36
89 90 5.359756 TGCATGACACTACATAGATGTTCC 58.640 41.667 0.00 0.00 41.97 3.62
90 91 6.908870 TTGCATGACACTACATAGATGTTC 57.091 37.500 0.00 0.00 41.97 3.18
91 92 8.962884 TTATTGCATGACACTACATAGATGTT 57.037 30.769 0.00 0.00 41.97 2.71
92 93 8.996271 CATTATTGCATGACACTACATAGATGT 58.004 33.333 0.00 0.08 44.48 3.06
93 94 8.996271 ACATTATTGCATGACACTACATAGATG 58.004 33.333 0.00 0.00 0.00 2.90
127 128 9.401058 CTCCAAGAAACAATGAATCTATAACCT 57.599 33.333 0.00 0.00 0.00 3.50
128 129 9.178758 ACTCCAAGAAACAATGAATCTATAACC 57.821 33.333 0.00 0.00 0.00 2.85
129 130 9.994432 CACTCCAAGAAACAATGAATCTATAAC 57.006 33.333 0.00 0.00 0.00 1.89
130 131 9.739276 ACACTCCAAGAAACAATGAATCTATAA 57.261 29.630 0.00 0.00 0.00 0.98
131 132 9.166173 CACACTCCAAGAAACAATGAATCTATA 57.834 33.333 0.00 0.00 0.00 1.31
132 133 7.667219 ACACACTCCAAGAAACAATGAATCTAT 59.333 33.333 0.00 0.00 0.00 1.98
133 134 6.998074 ACACACTCCAAGAAACAATGAATCTA 59.002 34.615 0.00 0.00 0.00 1.98
134 135 5.829924 ACACACTCCAAGAAACAATGAATCT 59.170 36.000 0.00 0.00 0.00 2.40
135 136 5.916883 CACACACTCCAAGAAACAATGAATC 59.083 40.000 0.00 0.00 0.00 2.52
136 137 5.593909 TCACACACTCCAAGAAACAATGAAT 59.406 36.000 0.00 0.00 0.00 2.57
137 138 4.946772 TCACACACTCCAAGAAACAATGAA 59.053 37.500 0.00 0.00 0.00 2.57
138 139 4.522114 TCACACACTCCAAGAAACAATGA 58.478 39.130 0.00 0.00 0.00 2.57
139 140 4.898829 TCACACACTCCAAGAAACAATG 57.101 40.909 0.00 0.00 0.00 2.82
140 141 4.889409 ACATCACACACTCCAAGAAACAAT 59.111 37.500 0.00 0.00 0.00 2.71
141 142 4.269183 ACATCACACACTCCAAGAAACAA 58.731 39.130 0.00 0.00 0.00 2.83
142 143 3.884895 ACATCACACACTCCAAGAAACA 58.115 40.909 0.00 0.00 0.00 2.83
143 144 4.261197 GGAACATCACACACTCCAAGAAAC 60.261 45.833 0.00 0.00 0.00 2.78
144 145 3.882888 GGAACATCACACACTCCAAGAAA 59.117 43.478 0.00 0.00 0.00 2.52
145 146 3.476552 GGAACATCACACACTCCAAGAA 58.523 45.455 0.00 0.00 0.00 2.52
146 147 2.547855 CGGAACATCACACACTCCAAGA 60.548 50.000 0.00 0.00 0.00 3.02
147 148 1.800586 CGGAACATCACACACTCCAAG 59.199 52.381 0.00 0.00 0.00 3.61
148 149 1.414550 TCGGAACATCACACACTCCAA 59.585 47.619 0.00 0.00 0.00 3.53
149 150 1.044611 TCGGAACATCACACACTCCA 58.955 50.000 0.00 0.00 0.00 3.86
150 151 2.386661 ATCGGAACATCACACACTCC 57.613 50.000 0.00 0.00 0.00 3.85
151 152 4.495422 AGTTATCGGAACATCACACACTC 58.505 43.478 4.31 0.00 0.00 3.51
152 153 4.537135 AGTTATCGGAACATCACACACT 57.463 40.909 4.31 0.00 0.00 3.55
153 154 5.220416 GCTAAGTTATCGGAACATCACACAC 60.220 44.000 4.31 0.00 0.00 3.82
154 155 4.868171 GCTAAGTTATCGGAACATCACACA 59.132 41.667 4.31 0.00 0.00 3.72
155 156 5.109903 AGCTAAGTTATCGGAACATCACAC 58.890 41.667 0.00 0.00 0.00 3.82
156 157 5.339008 AGCTAAGTTATCGGAACATCACA 57.661 39.130 0.00 0.00 0.00 3.58
157 158 6.505272 ACTAGCTAAGTTATCGGAACATCAC 58.495 40.000 0.00 0.00 33.35 3.06
158 159 6.710597 ACTAGCTAAGTTATCGGAACATCA 57.289 37.500 0.00 0.00 33.35 3.07
177 178 3.511934 AGAGAGGTGCTTGTGGTAACTAG 59.488 47.826 0.00 0.00 37.61 2.57
178 179 3.507411 AGAGAGGTGCTTGTGGTAACTA 58.493 45.455 0.00 0.00 37.61 2.24
179 180 2.300437 GAGAGAGGTGCTTGTGGTAACT 59.700 50.000 0.00 0.00 37.61 2.24
180 181 2.300437 AGAGAGAGGTGCTTGTGGTAAC 59.700 50.000 0.00 0.00 0.00 2.50
181 182 2.609747 AGAGAGAGGTGCTTGTGGTAA 58.390 47.619 0.00 0.00 0.00 2.85
182 183 2.310779 AGAGAGAGGTGCTTGTGGTA 57.689 50.000 0.00 0.00 0.00 3.25
183 184 1.346068 GAAGAGAGAGGTGCTTGTGGT 59.654 52.381 0.00 0.00 0.00 4.16
184 185 1.345741 TGAAGAGAGAGGTGCTTGTGG 59.654 52.381 0.00 0.00 0.00 4.17
185 186 2.827800 TGAAGAGAGAGGTGCTTGTG 57.172 50.000 0.00 0.00 0.00 3.33
186 187 5.489792 TTAATGAAGAGAGAGGTGCTTGT 57.510 39.130 0.00 0.00 0.00 3.16
187 188 6.998968 ATTTAATGAAGAGAGAGGTGCTTG 57.001 37.500 0.00 0.00 0.00 4.01
189 190 9.941325 CATATATTTAATGAAGAGAGAGGTGCT 57.059 33.333 0.00 0.00 0.00 4.40
190 191 9.935241 TCATATATTTAATGAAGAGAGAGGTGC 57.065 33.333 0.00 0.00 30.52 5.01
212 213 8.458052 CCAATACAACTTTGCTTATGTGTCATA 58.542 33.333 0.00 0.00 0.00 2.15
213 214 7.176515 TCCAATACAACTTTGCTTATGTGTCAT 59.823 33.333 0.00 0.00 0.00 3.06
214 215 6.488344 TCCAATACAACTTTGCTTATGTGTCA 59.512 34.615 0.00 0.00 0.00 3.58
215 216 6.908825 TCCAATACAACTTTGCTTATGTGTC 58.091 36.000 0.00 0.00 0.00 3.67
216 217 6.490040 ACTCCAATACAACTTTGCTTATGTGT 59.510 34.615 0.00 0.00 0.00 3.72
217 218 6.803320 CACTCCAATACAACTTTGCTTATGTG 59.197 38.462 0.00 0.00 0.00 3.21
218 219 6.490040 ACACTCCAATACAACTTTGCTTATGT 59.510 34.615 0.00 0.00 0.00 2.29
219 220 6.803320 CACACTCCAATACAACTTTGCTTATG 59.197 38.462 0.00 0.00 0.00 1.90
220 221 6.490040 ACACACTCCAATACAACTTTGCTTAT 59.510 34.615 0.00 0.00 0.00 1.73
221 222 5.825679 ACACACTCCAATACAACTTTGCTTA 59.174 36.000 0.00 0.00 0.00 3.09
222 223 4.644685 ACACACTCCAATACAACTTTGCTT 59.355 37.500 0.00 0.00 0.00 3.91
223 224 4.036734 CACACACTCCAATACAACTTTGCT 59.963 41.667 0.00 0.00 0.00 3.91
224 225 4.036262 TCACACACTCCAATACAACTTTGC 59.964 41.667 0.00 0.00 0.00 3.68
225 226 5.749596 TCACACACTCCAATACAACTTTG 57.250 39.130 0.00 0.00 0.00 2.77
226 227 5.827797 ACATCACACACTCCAATACAACTTT 59.172 36.000 0.00 0.00 0.00 2.66
227 228 5.376625 ACATCACACACTCCAATACAACTT 58.623 37.500 0.00 0.00 0.00 2.66
228 229 4.973168 ACATCACACACTCCAATACAACT 58.027 39.130 0.00 0.00 0.00 3.16
229 230 5.689383 AACATCACACACTCCAATACAAC 57.311 39.130 0.00 0.00 0.00 3.32
230 231 6.530120 AGTAACATCACACACTCCAATACAA 58.470 36.000 0.00 0.00 0.00 2.41
231 232 6.109156 AGTAACATCACACACTCCAATACA 57.891 37.500 0.00 0.00 0.00 2.29
232 233 6.648725 GAGTAACATCACACACTCCAATAC 57.351 41.667 0.00 0.00 32.93 1.89
238 239 6.026947 ACTTAGGAGTAACATCACACACTC 57.973 41.667 0.00 0.00 37.32 3.51
239 240 6.420913 AACTTAGGAGTAACATCACACACT 57.579 37.500 0.00 0.00 34.21 3.55
240 241 5.638234 GGAACTTAGGAGTAACATCACACAC 59.362 44.000 0.00 0.00 34.21 3.82
241 242 5.542635 AGGAACTTAGGAGTAACATCACACA 59.457 40.000 0.00 0.00 34.21 3.72
242 243 6.038997 AGGAACTTAGGAGTAACATCACAC 57.961 41.667 0.00 0.00 34.21 3.82
243 244 5.187186 GGAGGAACTTAGGAGTAACATCACA 59.813 44.000 0.00 0.00 41.55 3.58
244 245 5.395435 GGGAGGAACTTAGGAGTAACATCAC 60.395 48.000 0.00 0.00 41.55 3.06
245 246 4.715297 GGGAGGAACTTAGGAGTAACATCA 59.285 45.833 0.00 0.00 41.55 3.07
246 247 4.101274 GGGGAGGAACTTAGGAGTAACATC 59.899 50.000 0.00 0.00 41.55 3.06
247 248 4.038633 GGGGAGGAACTTAGGAGTAACAT 58.961 47.826 0.00 0.00 41.55 2.71
248 249 3.181404 TGGGGAGGAACTTAGGAGTAACA 60.181 47.826 0.00 0.00 41.55 2.41
249 250 3.447950 TGGGGAGGAACTTAGGAGTAAC 58.552 50.000 0.00 0.00 41.55 2.50
250 251 3.858696 TGGGGAGGAACTTAGGAGTAA 57.141 47.619 0.00 0.00 41.55 2.24
251 252 4.037927 CAATGGGGAGGAACTTAGGAGTA 58.962 47.826 0.00 0.00 41.55 2.59
252 253 2.846827 CAATGGGGAGGAACTTAGGAGT 59.153 50.000 0.00 0.00 41.55 3.85
253 254 2.846827 ACAATGGGGAGGAACTTAGGAG 59.153 50.000 0.00 0.00 41.55 3.69
254 255 2.576191 CACAATGGGGAGGAACTTAGGA 59.424 50.000 0.00 0.00 41.55 2.94
255 256 2.576191 TCACAATGGGGAGGAACTTAGG 59.424 50.000 0.00 0.00 41.55 2.69
256 257 3.610911 GTCACAATGGGGAGGAACTTAG 58.389 50.000 0.00 0.00 41.55 2.18
257 258 2.307686 GGTCACAATGGGGAGGAACTTA 59.692 50.000 0.00 0.00 41.55 2.24
258 259 1.075536 GGTCACAATGGGGAGGAACTT 59.924 52.381 0.00 0.00 41.55 2.66
260 261 0.404040 TGGTCACAATGGGGAGGAAC 59.596 55.000 0.00 0.00 0.00 3.62
261 262 0.698238 CTGGTCACAATGGGGAGGAA 59.302 55.000 0.00 0.00 0.00 3.36
262 263 1.852157 GCTGGTCACAATGGGGAGGA 61.852 60.000 0.00 0.00 0.00 3.71
263 264 1.379044 GCTGGTCACAATGGGGAGG 60.379 63.158 0.00 0.00 0.00 4.30
264 265 1.379044 GGCTGGTCACAATGGGGAG 60.379 63.158 0.00 0.00 0.00 4.30
265 266 0.548926 TAGGCTGGTCACAATGGGGA 60.549 55.000 0.00 0.00 0.00 4.81
266 267 0.331278 TTAGGCTGGTCACAATGGGG 59.669 55.000 0.00 0.00 0.00 4.96
267 268 1.281867 TCTTAGGCTGGTCACAATGGG 59.718 52.381 0.00 0.00 0.00 4.00
268 269 2.749621 GTTCTTAGGCTGGTCACAATGG 59.250 50.000 0.00 0.00 0.00 3.16
269 270 3.438087 CAGTTCTTAGGCTGGTCACAATG 59.562 47.826 0.00 0.00 0.00 2.82
270 271 3.327757 TCAGTTCTTAGGCTGGTCACAAT 59.672 43.478 0.00 0.00 33.81 2.71
271 272 2.703536 TCAGTTCTTAGGCTGGTCACAA 59.296 45.455 0.00 0.00 33.81 3.33
272 273 2.325484 TCAGTTCTTAGGCTGGTCACA 58.675 47.619 0.00 0.00 33.81 3.58
273 274 3.244249 ACTTCAGTTCTTAGGCTGGTCAC 60.244 47.826 0.00 0.00 33.81 3.67
274 275 2.972713 ACTTCAGTTCTTAGGCTGGTCA 59.027 45.455 0.00 0.00 33.81 4.02
275 276 3.686916 ACTTCAGTTCTTAGGCTGGTC 57.313 47.619 0.00 0.00 33.81 4.02
276 277 3.136626 ACAACTTCAGTTCTTAGGCTGGT 59.863 43.478 0.00 0.00 35.83 4.00
277 278 3.744660 ACAACTTCAGTTCTTAGGCTGG 58.255 45.455 0.00 0.00 35.83 4.85
278 279 4.380531 TGACAACTTCAGTTCTTAGGCTG 58.619 43.478 0.00 0.00 35.83 4.85
279 280 4.689612 TGACAACTTCAGTTCTTAGGCT 57.310 40.909 0.00 0.00 35.83 4.58
280 281 5.335191 CCAATGACAACTTCAGTTCTTAGGC 60.335 44.000 0.00 0.00 37.77 3.93
281 282 5.182001 CCCAATGACAACTTCAGTTCTTAGG 59.818 44.000 0.00 0.00 37.77 2.69
282 283 5.997746 TCCCAATGACAACTTCAGTTCTTAG 59.002 40.000 0.00 0.00 37.77 2.18
283 284 5.935945 TCCCAATGACAACTTCAGTTCTTA 58.064 37.500 0.00 0.00 37.77 2.10
304 305 1.000396 AGCTTCCATTGGGCACTCC 60.000 57.895 2.09 0.00 0.00 3.85
305 306 1.318158 CCAGCTTCCATTGGGCACTC 61.318 60.000 2.09 0.00 0.00 3.51
328 329 9.868277 CTTTAAAAATTAATGTGGATGTGCCTA 57.132 29.630 0.00 0.00 37.63 3.93
401 402 2.748461 TGCGAAACTTTACACAGTGC 57.252 45.000 0.00 0.00 0.00 4.40
402 403 4.904116 TCTTTGCGAAACTTTACACAGTG 58.096 39.130 0.00 0.00 0.00 3.66
403 404 5.554822 TTCTTTGCGAAACTTTACACAGT 57.445 34.783 0.00 0.00 0.00 3.55
404 405 6.745450 TCTTTTCTTTGCGAAACTTTACACAG 59.255 34.615 0.00 0.00 41.13 3.66
513 521 1.497991 TCACTTTCGCGTTCTTCTGG 58.502 50.000 5.77 0.00 0.00 3.86
523 531 3.565516 GTTGGGAAGAAATCACTTTCGC 58.434 45.455 0.00 0.00 44.52 4.70
531 539 3.920412 GCAAACATCGTTGGGAAGAAATC 59.080 43.478 0.00 0.00 0.00 2.17
659 667 6.634805 AGTACATGACAACTAGATTCAGGTG 58.365 40.000 15.58 6.41 39.27 4.00
661 669 6.276847 GGAGTACATGACAACTAGATTCAGG 58.723 44.000 0.00 0.00 0.00 3.86
663 671 5.958380 AGGGAGTACATGACAACTAGATTCA 59.042 40.000 0.00 0.00 0.00 2.57
664 672 6.461788 GGAGGGAGTACATGACAACTAGATTC 60.462 46.154 0.00 0.00 0.00 2.52
944 956 1.453928 GGGAAAGCCGGGAGAATGG 60.454 63.158 2.18 0.00 33.83 3.16
949 988 2.361230 GTTGGGGAAAGCCGGGAG 60.361 66.667 2.18 0.00 33.83 4.30
950 989 2.856988 AGTTGGGGAAAGCCGGGA 60.857 61.111 2.18 0.00 33.83 5.14
951 990 2.676471 CAGTTGGGGAAAGCCGGG 60.676 66.667 2.18 0.00 33.83 5.73
974 1013 2.131023 GAGGTGGGGATTGAGGAAGAT 58.869 52.381 0.00 0.00 0.00 2.40
1257 1296 4.379243 CACGCTCTCCGCCTGGTT 62.379 66.667 0.00 0.00 41.76 3.67
1297 1336 0.526662 GTCCACATTCTCGTCGAGGT 59.473 55.000 21.63 9.41 0.00 3.85
1402 1441 0.533531 CTGTGCACCTGCTGAAGTCA 60.534 55.000 15.69 0.00 42.66 3.41
1411 1450 1.571460 GCGAAACTCTGTGCACCTG 59.429 57.895 15.69 7.53 0.00 4.00
1414 1453 1.571460 CTGGCGAAACTCTGTGCAC 59.429 57.895 10.75 10.75 0.00 4.57
1421 1460 2.747855 CCCTGGCTGGCGAAACTC 60.748 66.667 4.64 0.00 0.00 3.01
1452 1491 2.791383 TTCCATTGCACGAACTTTGG 57.209 45.000 0.00 0.00 0.00 3.28
1568 1607 1.202698 ACGAACTTTGGAGCTGCTTCT 60.203 47.619 9.76 0.00 0.00 2.85
1712 1751 4.657824 CTGAACACCGGCGACCGT 62.658 66.667 9.30 0.00 46.80 4.83
1762 1801 3.195698 GGACCAGATCGTTGGCGC 61.196 66.667 0.00 0.00 42.18 6.53
1835 1874 1.958205 CATCTCCGGCAGCGAATCC 60.958 63.158 0.00 0.00 0.00 3.01
1896 1935 0.457035 ATGTTATACGTGTCCGCCGT 59.543 50.000 0.00 0.00 42.06 5.68
2303 2342 6.563222 TGGTCTTTAGGGTTTTATGAAACG 57.437 37.500 6.98 0.00 44.83 3.60
2310 2349 9.238368 CTAAATCACATGGTCTTTAGGGTTTTA 57.762 33.333 0.00 0.00 30.89 1.52
2395 2434 9.751542 CTAGATCTCAGTTAACGGTCAAATAAT 57.248 33.333 0.00 0.00 0.00 1.28
2420 2459 4.052518 GGCTGACATGTGGGCCCT 62.053 66.667 25.70 0.15 38.77 5.19
2486 2525 2.283676 GTCCTCGTCCTCCACCCA 60.284 66.667 0.00 0.00 0.00 4.51
2660 2699 3.267860 CTGCCTCGCATCTTCGGC 61.268 66.667 0.00 0.00 38.13 5.54


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

AutoCloner maintained by Alex Coulton.