Multiple sequence alignment - TraesCS1A01G012300

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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 TraesCS1A01G012300 chr1A 100.000 2431 0 0 1 2431 7110053 7107623 0.000000e+00 4490
1 TraesCS1A01G012300 chr1A 87.156 109 8 4 649 756 533694073 533693970 4.250000e-23 119
2 TraesCS1A01G012300 chrUn 96.248 1306 37 5 1118 2422 248894592 248893298 0.000000e+00 2130
3 TraesCS1A01G012300 chrUn 96.137 932 28 2 1500 2431 248892783 248891860 0.000000e+00 1515
4 TraesCS1A01G012300 chrUn 96.137 932 28 2 1500 2431 269802554 269801631 0.000000e+00 1515
5 TraesCS1A01G012300 chrUn 95.955 890 35 1 612 1501 90492751 90491863 0.000000e+00 1443
6 TraesCS1A01G012300 chrUn 96.220 582 18 2 1500 2081 90491680 90491103 0.000000e+00 950
7 TraesCS1A01G012300 chrUn 86.439 789 94 9 716 1501 297891233 297892011 0.000000e+00 852
8 TraesCS1A01G012300 chrUn 96.211 475 18 0 612 1086 248895062 248894588 0.000000e+00 778
9 TraesCS1A01G012300 chrUn 97.511 442 9 2 1982 2422 269803509 269803069 0.000000e+00 754
10 TraesCS1A01G012300 chrUn 93.968 315 16 1 297 611 248895296 248894985 7.870000e-130 473
11 TraesCS1A01G012300 chr6A 95.949 938 31 4 1497 2431 612594359 612593426 0.000000e+00 1515
12 TraesCS1A01G012300 chr6A 86.189 782 97 8 722 1501 558613458 558612686 0.000000e+00 835
13 TraesCS1A01G012300 chr6B 95.740 939 32 4 1497 2431 92402776 92403710 0.000000e+00 1506
14 TraesCS1A01G012300 chr6B 97.283 552 15 0 1871 2422 92401716 92402267 0.000000e+00 937
15 TraesCS1A01G012300 chr7D 96.309 894 29 1 612 1501 195367230 195366337 0.000000e+00 1465
16 TraesCS1A01G012300 chr7D 97.240 797 22 0 705 1501 446941251 446940455 0.000000e+00 1351
17 TraesCS1A01G012300 chr7D 96.226 583 16 4 1500 2081 195366154 195365577 0.000000e+00 950
18 TraesCS1A01G012300 chr7D 93.396 318 15 3 298 611 195367464 195367149 1.320000e-127 466
19 TraesCS1A01G012300 chr7D 93.770 305 15 3 309 611 446941608 446941306 2.850000e-124 455
20 TraesCS1A01G012300 chr7D 94.245 139 5 2 612 748 446941385 446941248 2.450000e-50 209
21 TraesCS1A01G012300 chr5D 96.111 900 25 2 612 1501 552052063 552052962 0.000000e+00 1459
22 TraesCS1A01G012300 chr5D 96.416 586 15 4 1497 2081 552053142 552053722 0.000000e+00 961
23 TraesCS1A01G012300 chr5D 93.949 314 17 2 298 611 552051829 552052140 7.870000e-130 473
24 TraesCS1A01G012300 chr1D 95.973 894 32 3 612 1501 462977513 462978406 0.000000e+00 1448
25 TraesCS1A01G012300 chr1D 96.758 586 14 3 1497 2081 462978586 462979167 0.000000e+00 972
26 TraesCS1A01G012300 chr1D 93.082 318 16 4 298 611 462977279 462977594 6.120000e-126 460
27 TraesCS1A01G012300 chr5A 95.964 892 34 1 612 1501 540850019 540850910 0.000000e+00 1447
28 TraesCS1A01G012300 chr5A 93.478 322 18 2 291 610 540849777 540850097 2.190000e-130 475
29 TraesCS1A01G012300 chr5A 96.610 118 4 0 2314 2431 618879906 618879789 1.910000e-46 196
30 TraesCS1A01G012300 chr5A 93.600 125 7 1 2079 2203 618881310 618881187 4.130000e-43 185
31 TraesCS1A01G012300 chr5A 89.655 116 7 4 2211 2322 618881088 618880974 2.520000e-30 143
32 TraesCS1A01G012300 chr7B 87.619 315 31 3 298 611 738089840 738090147 2.300000e-95 359
33 TraesCS1A01G012300 chr7B 87.580 314 32 2 298 611 737316436 737316742 8.270000e-95 357
34 TraesCS1A01G012300 chr7B 87.580 314 32 2 298 611 737610931 737611237 8.270000e-95 357
35 TraesCS1A01G012300 chr4A 89.474 95 6 2 657 751 9380762 9380672 1.530000e-22 117


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 TraesCS1A01G012300 chr1A 7107623 7110053 2430 True 4490.000000 4490 100.000000 1 2431 1 chr1A.!!$R1 2430
1 TraesCS1A01G012300 chrUn 248891860 248895296 3436 True 1224.000000 2130 95.641000 297 2431 4 chrUn.!!$R2 2134
2 TraesCS1A01G012300 chrUn 90491103 90492751 1648 True 1196.500000 1443 96.087500 612 2081 2 chrUn.!!$R1 1469
3 TraesCS1A01G012300 chrUn 269801631 269803509 1878 True 1134.500000 1515 96.824000 1500 2431 2 chrUn.!!$R3 931
4 TraesCS1A01G012300 chrUn 297891233 297892011 778 False 852.000000 852 86.439000 716 1501 1 chrUn.!!$F1 785
5 TraesCS1A01G012300 chr6A 612593426 612594359 933 True 1515.000000 1515 95.949000 1497 2431 1 chr6A.!!$R2 934
6 TraesCS1A01G012300 chr6A 558612686 558613458 772 True 835.000000 835 86.189000 722 1501 1 chr6A.!!$R1 779
7 TraesCS1A01G012300 chr6B 92401716 92403710 1994 False 1221.500000 1506 96.511500 1497 2431 2 chr6B.!!$F1 934
8 TraesCS1A01G012300 chr7D 195365577 195367464 1887 True 960.333333 1465 95.310333 298 2081 3 chr7D.!!$R1 1783
9 TraesCS1A01G012300 chr7D 446940455 446941608 1153 True 671.666667 1351 95.085000 309 1501 3 chr7D.!!$R2 1192
10 TraesCS1A01G012300 chr5D 552051829 552053722 1893 False 964.333333 1459 95.492000 298 2081 3 chr5D.!!$F1 1783
11 TraesCS1A01G012300 chr1D 462977279 462979167 1888 False 960.000000 1448 95.271000 298 2081 3 chr1D.!!$F1 1783
12 TraesCS1A01G012300 chr5A 540849777 540850910 1133 False 961.000000 1447 94.721000 291 1501 2 chr5A.!!$F1 1210

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
197 198 0.034767 CCAGCCATCTCTGCCTTGAA 60.035 55.000 0.0 0.0 32.87 2.69 F
200 201 0.813821 GCCATCTCTGCCTTGAAACC 59.186 55.000 0.0 0.0 0.00 3.27 F
202 203 1.005215 CCATCTCTGCCTTGAAACCCT 59.995 52.381 0.0 0.0 0.00 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1078 1137 0.738975 CATGAAGACCTCGACGCCTA 59.261 55.000 0.00 0.00 0.00 3.93 R
1098 1157 1.743252 GAAAGGAGAGCGGTGGCAG 60.743 63.158 0.00 0.00 43.41 4.85 R
2125 3626 2.108168 CCCTAGCTGCACTTACAGGTA 58.892 52.381 1.02 3.71 46.10 3.08 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
24 25 3.189910 TCATTTCAGCTGACATCTGTTGC 59.810 43.478 18.03 2.41 33.48 4.17
26 27 2.556144 TCAGCTGACATCTGTTGCTT 57.444 45.000 13.74 0.00 36.51 3.91
27 28 2.420642 TCAGCTGACATCTGTTGCTTC 58.579 47.619 13.74 0.00 36.51 3.86
28 29 2.148768 CAGCTGACATCTGTTGCTTCA 58.851 47.619 8.42 0.00 36.51 3.02
29 30 2.747989 CAGCTGACATCTGTTGCTTCAT 59.252 45.455 8.42 0.00 36.51 2.57
30 31 2.747989 AGCTGACATCTGTTGCTTCATG 59.252 45.455 6.12 0.00 35.66 3.07
31 32 2.486982 GCTGACATCTGTTGCTTCATGT 59.513 45.455 0.00 0.00 0.00 3.21
33 34 4.154737 GCTGACATCTGTTGCTTCATGTAA 59.845 41.667 0.00 0.00 0.00 2.41
36 37 5.048782 TGACATCTGTTGCTTCATGTAAACC 60.049 40.000 0.00 0.00 0.00 3.27
38 39 4.829064 TCTGTTGCTTCATGTAAACCAC 57.171 40.909 0.00 0.00 0.00 4.16
39 40 4.460263 TCTGTTGCTTCATGTAAACCACT 58.540 39.130 0.00 0.00 0.00 4.00
40 41 4.275689 TCTGTTGCTTCATGTAAACCACTG 59.724 41.667 0.00 0.00 0.00 3.66
41 42 3.951037 TGTTGCTTCATGTAAACCACTGT 59.049 39.130 0.00 0.00 0.00 3.55
42 43 4.400884 TGTTGCTTCATGTAAACCACTGTT 59.599 37.500 0.00 0.00 35.82 3.16
43 44 4.829064 TGCTTCATGTAAACCACTGTTC 57.171 40.909 0.00 0.00 32.15 3.18
45 46 4.275689 TGCTTCATGTAAACCACTGTTCAG 59.724 41.667 0.00 0.00 32.15 3.02
47 48 5.221048 GCTTCATGTAAACCACTGTTCAGTT 60.221 40.000 2.47 0.00 32.15 3.16
48 49 6.017440 GCTTCATGTAAACCACTGTTCAGTTA 60.017 38.462 2.47 0.00 32.15 2.24
49 50 7.308589 GCTTCATGTAAACCACTGTTCAGTTAT 60.309 37.037 2.47 0.00 32.15 1.89
50 51 7.667043 TCATGTAAACCACTGTTCAGTTATC 57.333 36.000 2.47 0.00 32.15 1.75
51 52 7.450074 TCATGTAAACCACTGTTCAGTTATCT 58.550 34.615 2.47 0.00 32.15 1.98
52 53 7.936847 TCATGTAAACCACTGTTCAGTTATCTT 59.063 33.333 2.47 0.00 32.15 2.40
53 54 7.490962 TGTAAACCACTGTTCAGTTATCTTG 57.509 36.000 2.47 0.00 32.15 3.02
57 58 3.411446 CACTGTTCAGTTATCTTGGCCA 58.589 45.455 0.00 0.00 0.00 5.36
58 59 3.820467 CACTGTTCAGTTATCTTGGCCAA 59.180 43.478 19.25 19.25 0.00 4.52
59 60 4.278170 CACTGTTCAGTTATCTTGGCCAAA 59.722 41.667 20.91 11.07 0.00 3.28
61 62 3.252215 TGTTCAGTTATCTTGGCCAAACG 59.748 43.478 20.91 9.17 0.00 3.60
63 64 3.745799 TCAGTTATCTTGGCCAAACGAA 58.254 40.909 20.91 10.39 0.00 3.85
66 67 4.079253 AGTTATCTTGGCCAAACGAACAT 58.921 39.130 25.98 14.94 0.00 2.71
67 68 4.156008 AGTTATCTTGGCCAAACGAACATC 59.844 41.667 25.98 12.31 0.00 3.06
68 69 1.974265 TCTTGGCCAAACGAACATCA 58.026 45.000 20.91 0.00 0.00 3.07
69 70 2.513753 TCTTGGCCAAACGAACATCAT 58.486 42.857 20.91 0.00 0.00 2.45
70 71 2.890311 TCTTGGCCAAACGAACATCATT 59.110 40.909 20.91 0.00 0.00 2.57
71 72 3.057596 TCTTGGCCAAACGAACATCATTC 60.058 43.478 20.91 0.00 0.00 2.67
72 73 2.513753 TGGCCAAACGAACATCATTCT 58.486 42.857 0.61 0.00 0.00 2.40
74 75 3.320541 TGGCCAAACGAACATCATTCTTT 59.679 39.130 0.61 0.00 0.00 2.52
75 76 4.202202 TGGCCAAACGAACATCATTCTTTT 60.202 37.500 0.61 0.00 0.00 2.27
76 77 4.385748 GGCCAAACGAACATCATTCTTTTC 59.614 41.667 0.00 0.00 0.00 2.29
77 78 5.222631 GCCAAACGAACATCATTCTTTTCT 58.777 37.500 0.00 0.00 0.00 2.52
79 80 6.200854 GCCAAACGAACATCATTCTTTTCTTT 59.799 34.615 0.00 0.00 0.00 2.52
80 81 7.254421 GCCAAACGAACATCATTCTTTTCTTTT 60.254 33.333 0.00 0.00 0.00 2.27
81 82 9.243637 CCAAACGAACATCATTCTTTTCTTTTA 57.756 29.630 0.00 0.00 0.00 1.52
85 86 9.831737 ACGAACATCATTCTTTTCTTTTATCTG 57.168 29.630 0.00 0.00 0.00 2.90
86 87 9.282247 CGAACATCATTCTTTTCTTTTATCTGG 57.718 33.333 0.00 0.00 0.00 3.86
87 88 8.992835 AACATCATTCTTTTCTTTTATCTGGC 57.007 30.769 0.00 0.00 0.00 4.85
88 89 8.358582 ACATCATTCTTTTCTTTTATCTGGCT 57.641 30.769 0.00 0.00 0.00 4.75
89 90 8.248945 ACATCATTCTTTTCTTTTATCTGGCTG 58.751 33.333 0.00 0.00 0.00 4.85
90 91 8.464404 CATCATTCTTTTCTTTTATCTGGCTGA 58.536 33.333 0.00 0.00 0.00 4.26
93 94 9.136952 CATTCTTTTCTTTTATCTGGCTGAAAG 57.863 33.333 0.00 0.00 0.00 2.62
94 95 8.463930 TTCTTTTCTTTTATCTGGCTGAAAGA 57.536 30.769 0.00 0.72 36.61 2.52
97 98 7.581213 TTTCTTTTATCTGGCTGAAAGAACA 57.419 32.000 15.17 7.79 43.69 3.18
98 99 6.808008 TCTTTTATCTGGCTGAAAGAACAG 57.192 37.500 0.00 0.00 40.45 3.16
105 106 6.748333 TCTGGCTGAAAGAACAGAATTATG 57.252 37.500 0.00 0.00 43.36 1.90
106 107 6.475504 TCTGGCTGAAAGAACAGAATTATGA 58.524 36.000 7.16 0.00 43.36 2.15
107 108 6.372659 TCTGGCTGAAAGAACAGAATTATGAC 59.627 38.462 7.16 0.79 43.36 3.06
109 110 6.489700 TGGCTGAAAGAACAGAATTATGACAA 59.510 34.615 7.16 0.00 39.94 3.18
110 111 7.177216 TGGCTGAAAGAACAGAATTATGACAAT 59.823 33.333 7.16 0.00 39.94 2.71
111 112 7.699812 GGCTGAAAGAACAGAATTATGACAATC 59.300 37.037 7.16 0.12 39.94 2.67
112 113 7.699812 GCTGAAAGAACAGAATTATGACAATCC 59.300 37.037 7.16 0.00 39.94 3.01
113 114 8.634335 TGAAAGAACAGAATTATGACAATCCA 57.366 30.769 7.16 0.00 0.00 3.41
115 116 7.396540 AAGAACAGAATTATGACAATCCACC 57.603 36.000 7.16 0.00 0.00 4.61
116 117 6.484288 AGAACAGAATTATGACAATCCACCA 58.516 36.000 7.16 0.00 0.00 4.17
117 118 7.121382 AGAACAGAATTATGACAATCCACCAT 58.879 34.615 7.16 0.00 0.00 3.55
118 119 7.616935 AGAACAGAATTATGACAATCCACCATT 59.383 33.333 7.16 0.00 0.00 3.16
119 120 8.821686 AACAGAATTATGACAATCCACCATTA 57.178 30.769 7.16 0.00 0.00 1.90
121 122 7.285401 ACAGAATTATGACAATCCACCATTACC 59.715 37.037 7.16 0.00 0.00 2.85
122 123 6.486657 AGAATTATGACAATCCACCATTACCG 59.513 38.462 0.00 0.00 0.00 4.02
123 124 3.924114 ATGACAATCCACCATTACCGA 57.076 42.857 0.00 0.00 0.00 4.69
124 125 2.980568 TGACAATCCACCATTACCGAC 58.019 47.619 0.00 0.00 0.00 4.79
125 126 2.569853 TGACAATCCACCATTACCGACT 59.430 45.455 0.00 0.00 0.00 4.18
126 127 3.008594 TGACAATCCACCATTACCGACTT 59.991 43.478 0.00 0.00 0.00 3.01
127 128 4.007659 GACAATCCACCATTACCGACTTT 58.992 43.478 0.00 0.00 0.00 2.66
129 130 2.773993 TCCACCATTACCGACTTTCC 57.226 50.000 0.00 0.00 0.00 3.13
131 132 2.372504 TCCACCATTACCGACTTTCCAA 59.627 45.455 0.00 0.00 0.00 3.53
132 133 3.150767 CCACCATTACCGACTTTCCAAA 58.849 45.455 0.00 0.00 0.00 3.28
135 136 5.279256 CCACCATTACCGACTTTCCAAAAAT 60.279 40.000 0.00 0.00 0.00 1.82
137 138 6.704050 CACCATTACCGACTTTCCAAAAATTT 59.296 34.615 0.00 0.00 0.00 1.82
139 140 6.926272 CCATTACCGACTTTCCAAAAATTTCA 59.074 34.615 0.00 0.00 0.00 2.69
140 141 7.602265 CCATTACCGACTTTCCAAAAATTTCAT 59.398 33.333 0.00 0.00 0.00 2.57
141 142 9.632807 CATTACCGACTTTCCAAAAATTTCATA 57.367 29.630 0.00 0.00 0.00 2.15
173 174 9.992910 AGCTCAAAAGAAAAACAATTCAAATTC 57.007 25.926 0.00 0.00 0.00 2.17
174 175 9.992910 GCTCAAAAGAAAAACAATTCAAATTCT 57.007 25.926 0.00 0.00 0.00 2.40
179 180 8.893219 AAGAAAAACAATTCAAATTCTCCTCC 57.107 30.769 0.00 0.00 0.00 4.30
180 181 8.021898 AGAAAAACAATTCAAATTCTCCTCCA 57.978 30.769 0.00 0.00 0.00 3.86
181 182 8.146412 AGAAAAACAATTCAAATTCTCCTCCAG 58.854 33.333 0.00 0.00 0.00 3.86
183 184 3.766051 ACAATTCAAATTCTCCTCCAGCC 59.234 43.478 0.00 0.00 0.00 4.85
184 185 3.744940 ATTCAAATTCTCCTCCAGCCA 57.255 42.857 0.00 0.00 0.00 4.75
186 187 3.287867 TCAAATTCTCCTCCAGCCATC 57.712 47.619 0.00 0.00 0.00 3.51
187 188 2.848694 TCAAATTCTCCTCCAGCCATCT 59.151 45.455 0.00 0.00 0.00 2.90
188 189 3.118112 TCAAATTCTCCTCCAGCCATCTC 60.118 47.826 0.00 0.00 0.00 2.75
192 193 2.042404 CTCCTCCAGCCATCTCTGCC 62.042 65.000 0.00 0.00 32.87 4.85
193 194 2.071262 CCTCCAGCCATCTCTGCCT 61.071 63.158 0.00 0.00 32.87 4.75
194 195 1.633915 CCTCCAGCCATCTCTGCCTT 61.634 60.000 0.00 0.00 32.87 4.35
195 196 0.464013 CTCCAGCCATCTCTGCCTTG 60.464 60.000 0.00 0.00 32.87 3.61
197 198 0.034767 CCAGCCATCTCTGCCTTGAA 60.035 55.000 0.00 0.00 32.87 2.69
200 201 0.813821 GCCATCTCTGCCTTGAAACC 59.186 55.000 0.00 0.00 0.00 3.27
201 202 1.467920 CCATCTCTGCCTTGAAACCC 58.532 55.000 0.00 0.00 0.00 4.11
202 203 1.005215 CCATCTCTGCCTTGAAACCCT 59.995 52.381 0.00 0.00 0.00 4.34
203 204 2.239654 CCATCTCTGCCTTGAAACCCTA 59.760 50.000 0.00 0.00 0.00 3.53
204 205 3.539604 CATCTCTGCCTTGAAACCCTAG 58.460 50.000 0.00 0.00 0.00 3.02
207 208 4.164981 TCTCTGCCTTGAAACCCTAGTTA 58.835 43.478 0.00 0.00 34.19 2.24
209 210 4.843728 TCTGCCTTGAAACCCTAGTTATG 58.156 43.478 0.00 0.00 34.19 1.90
210 211 3.352648 TGCCTTGAAACCCTAGTTATGC 58.647 45.455 0.00 0.00 34.19 3.14
214 215 5.501156 CCTTGAAACCCTAGTTATGCTCTT 58.499 41.667 0.00 0.00 34.19 2.85
216 217 5.499004 TGAAACCCTAGTTATGCTCTTGT 57.501 39.130 0.00 0.00 34.19 3.16
218 219 5.705441 TGAAACCCTAGTTATGCTCTTGTTG 59.295 40.000 0.00 0.00 34.19 3.33
220 221 5.242795 ACCCTAGTTATGCTCTTGTTGTT 57.757 39.130 0.00 0.00 0.00 2.83
221 222 6.368779 ACCCTAGTTATGCTCTTGTTGTTA 57.631 37.500 0.00 0.00 0.00 2.41
222 223 6.775708 ACCCTAGTTATGCTCTTGTTGTTAA 58.224 36.000 0.00 0.00 0.00 2.01
223 224 7.402862 ACCCTAGTTATGCTCTTGTTGTTAAT 58.597 34.615 0.00 0.00 0.00 1.40
225 226 7.336931 CCCTAGTTATGCTCTTGTTGTTAATGT 59.663 37.037 0.00 0.00 0.00 2.71
227 228 9.760660 CTAGTTATGCTCTTGTTGTTAATGTTC 57.239 33.333 0.00 0.00 0.00 3.18
228 229 8.165239 AGTTATGCTCTTGTTGTTAATGTTCA 57.835 30.769 0.00 0.00 0.00 3.18
229 230 8.796475 AGTTATGCTCTTGTTGTTAATGTTCAT 58.204 29.630 0.00 0.00 0.00 2.57
230 231 8.853345 GTTATGCTCTTGTTGTTAATGTTCATG 58.147 33.333 0.00 0.00 0.00 3.07
231 232 6.389830 TGCTCTTGTTGTTAATGTTCATGT 57.610 33.333 0.00 0.00 0.00 3.21
232 233 6.804677 TGCTCTTGTTGTTAATGTTCATGTT 58.195 32.000 0.00 0.00 0.00 2.71
234 235 8.575589 TGCTCTTGTTGTTAATGTTCATGTTAT 58.424 29.630 0.00 0.00 0.00 1.89
260 261 9.814899 TTTTTCATATGAGAAACTGCAAAAAGA 57.185 25.926 15.44 0.00 37.24 2.52
261 262 9.814899 TTTTCATATGAGAAACTGCAAAAAGAA 57.185 25.926 6.23 0.00 37.24 2.52
262 263 8.801715 TTCATATGAGAAACTGCAAAAAGAAC 57.198 30.769 5.39 0.00 0.00 3.01
371 372 8.647226 GCATTGCCACGGAATAATAAAAATATC 58.353 33.333 0.00 0.00 0.00 1.63
428 429 6.709018 AATATGGGTTAAGCATGGTTACAC 57.291 37.500 16.65 15.98 0.00 2.90
450 451 6.317140 ACACTTAGATTTCATCATGCAACGAT 59.683 34.615 0.00 0.00 0.00 3.73
523 525 4.809426 CCTTAACTAACCAAATCGATCGCT 59.191 41.667 11.09 0.00 0.00 4.93
524 526 5.981315 CCTTAACTAACCAAATCGATCGCTA 59.019 40.000 11.09 0.00 0.00 4.26
525 527 6.074463 CCTTAACTAACCAAATCGATCGCTAC 60.074 42.308 11.09 0.00 0.00 3.58
596 601 9.841295 AGTAGTATTAGTACTCTCTCTGGAAAG 57.159 37.037 0.00 0.00 41.35 2.62
597 602 9.835389 GTAGTATTAGTACTCTCTCTGGAAAGA 57.165 37.037 0.00 0.00 41.35 2.52
599 604 9.403583 AGTATTAGTACTCTCTCTGGAAAGAAG 57.596 37.037 0.00 0.00 36.41 2.85
600 605 9.398538 GTATTAGTACTCTCTCTGGAAAGAAGA 57.601 37.037 0.00 0.00 0.00 2.87
601 606 8.887264 ATTAGTACTCTCTCTGGAAAGAAGAA 57.113 34.615 0.00 0.00 0.00 2.52
602 607 8.707796 TTAGTACTCTCTCTGGAAAGAAGAAA 57.292 34.615 0.00 0.00 0.00 2.52
603 608 7.790782 AGTACTCTCTCTGGAAAGAAGAAAT 57.209 36.000 0.00 0.00 0.00 2.17
604 609 8.887264 AGTACTCTCTCTGGAAAGAAGAAATA 57.113 34.615 0.00 0.00 0.00 1.40
605 610 9.487442 AGTACTCTCTCTGGAAAGAAGAAATAT 57.513 33.333 0.00 0.00 0.00 1.28
615 620 7.989826 TGGAAAGAAGAAATATAAGAGCAAGC 58.010 34.615 0.00 0.00 0.00 4.01
627 632 2.983229 AGAGCAAGCACTCATAACTGG 58.017 47.619 4.51 0.00 39.26 4.00
636 643 9.388506 GCAAGCACTCATAACTGGATATATATT 57.611 33.333 0.00 0.00 0.00 1.28
702 711 9.307121 AGAAATATAAGAGTGTTTCGATCACTG 57.693 33.333 22.39 0.00 44.68 3.66
759 807 2.638363 GGAGGGAGTACCACTCAACTTT 59.362 50.000 13.49 0.00 46.79 2.66
795 853 7.769507 TGTGTCACTATTACAAGGTACACAAAA 59.230 33.333 4.27 0.00 40.37 2.44
796 854 8.280497 GTGTCACTATTACAAGGTACACAAAAG 58.720 37.037 0.00 0.00 36.76 2.27
824 882 8.318412 TGACAGTCAATATTACAAGGTACACAT 58.682 33.333 0.00 0.00 0.00 3.21
860 918 8.997621 TCACTATTACAAGGTACACAAAGATC 57.002 34.615 0.00 0.00 0.00 2.75
1078 1137 2.369257 CTGGTCGTGGTCACAGCAGT 62.369 60.000 16.72 0.00 35.40 4.40
1098 1157 2.167861 GGCGTCGAGGTCTTCATGC 61.168 63.158 7.01 0.00 0.00 4.06
1182 1241 1.190178 ACCGGCCTTTAAGTCCGTCT 61.190 55.000 13.39 0.00 41.46 4.18
1341 1401 1.675310 CGCAAGCATCACCTTCCCA 60.675 57.895 0.00 0.00 0.00 4.37
1422 1482 5.465390 CCTGCTTCCATGAAAATGCAATATG 59.535 40.000 0.00 0.00 0.00 1.78
1494 1554 8.217111 TCCTAGTATGATGAAACATTTATGCCA 58.783 33.333 0.00 0.00 0.00 4.92
1633 3127 8.757982 AATTATCTCACTGCTCCAAACATATT 57.242 30.769 0.00 0.00 0.00 1.28
1774 3270 7.202526 ACATATACATCGGGAATTTGCAAAAG 58.797 34.615 17.19 5.87 0.00 2.27
1834 3334 7.993183 TCCAGAGAACTAACTGAACAAAGAAAT 59.007 33.333 0.00 0.00 36.38 2.17
2117 3618 4.515191 GCTGTGAAAACTGAAGTATGTGGA 59.485 41.667 0.00 0.00 0.00 4.02
2277 3779 1.202698 GGAGGTTGCGATGGCTAAGAT 60.203 52.381 0.15 0.00 40.82 2.40
2361 3863 2.613133 TGCATCCAAAACTTTTTGCTGC 59.387 40.909 21.47 21.47 45.38 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.152097 CAACAGATGTCAGCTGAAATGAAC 58.848 41.667 24.38 9.87 36.86 3.18
3 4 3.190744 AGCAACAGATGTCAGCTGAAATG 59.809 43.478 24.38 18.23 37.73 2.32
4 5 3.418995 AGCAACAGATGTCAGCTGAAAT 58.581 40.909 24.35 19.68 37.73 2.17
5 6 2.854963 AGCAACAGATGTCAGCTGAAA 58.145 42.857 24.35 14.91 37.73 2.69
6 7 2.556144 AGCAACAGATGTCAGCTGAA 57.444 45.000 24.35 9.51 37.73 3.02
7 8 2.224354 TGAAGCAACAGATGTCAGCTGA 60.224 45.455 24.35 13.74 38.65 4.26
11 12 5.868043 TTACATGAAGCAACAGATGTCAG 57.132 39.130 0.00 0.00 0.00 3.51
12 13 5.048782 GGTTTACATGAAGCAACAGATGTCA 60.049 40.000 0.00 0.00 0.00 3.58
13 14 5.048782 TGGTTTACATGAAGCAACAGATGTC 60.049 40.000 0.00 0.00 34.41 3.06
15 16 5.048504 AGTGGTTTACATGAAGCAACAGATG 60.049 40.000 0.00 0.00 38.58 2.90
16 17 5.048504 CAGTGGTTTACATGAAGCAACAGAT 60.049 40.000 0.00 0.00 38.58 2.90
19 20 3.951037 ACAGTGGTTTACATGAAGCAACA 59.049 39.130 0.00 0.00 38.58 3.33
21 22 4.642437 TGAACAGTGGTTTACATGAAGCAA 59.358 37.500 0.00 0.00 38.58 3.91
24 25 6.377327 AACTGAACAGTGGTTTACATGAAG 57.623 37.500 8.25 0.00 41.58 3.02
26 27 7.450074 AGATAACTGAACAGTGGTTTACATGA 58.550 34.615 8.25 0.00 41.58 3.07
27 28 7.672983 AGATAACTGAACAGTGGTTTACATG 57.327 36.000 8.25 0.00 41.58 3.21
28 29 7.174946 CCAAGATAACTGAACAGTGGTTTACAT 59.825 37.037 8.25 0.00 41.58 2.29
29 30 6.485313 CCAAGATAACTGAACAGTGGTTTACA 59.515 38.462 8.25 0.00 41.58 2.41
30 31 6.567891 GCCAAGATAACTGAACAGTGGTTTAC 60.568 42.308 8.25 0.00 41.58 2.01
31 32 5.472137 GCCAAGATAACTGAACAGTGGTTTA 59.528 40.000 8.25 0.00 41.58 2.01
33 34 3.821033 GCCAAGATAACTGAACAGTGGTT 59.179 43.478 8.25 0.00 41.58 3.67
36 37 3.411446 TGGCCAAGATAACTGAACAGTG 58.589 45.455 0.61 0.00 41.58 3.66
38 39 4.613622 CGTTTGGCCAAGATAACTGAACAG 60.614 45.833 19.48 3.85 0.00 3.16
39 40 3.252215 CGTTTGGCCAAGATAACTGAACA 59.748 43.478 19.48 0.00 0.00 3.18
40 41 3.500680 TCGTTTGGCCAAGATAACTGAAC 59.499 43.478 19.48 9.60 0.00 3.18
41 42 3.745799 TCGTTTGGCCAAGATAACTGAA 58.254 40.909 19.48 0.00 0.00 3.02
42 43 3.410631 TCGTTTGGCCAAGATAACTGA 57.589 42.857 19.48 12.23 0.00 3.41
43 44 3.252215 TGTTCGTTTGGCCAAGATAACTG 59.748 43.478 26.11 16.24 0.00 3.16
45 46 3.907894 TGTTCGTTTGGCCAAGATAAC 57.092 42.857 19.48 21.33 0.00 1.89
47 48 3.680490 TGATGTTCGTTTGGCCAAGATA 58.320 40.909 19.48 0.21 0.00 1.98
48 49 2.513753 TGATGTTCGTTTGGCCAAGAT 58.486 42.857 19.48 0.12 0.00 2.40
49 50 1.974265 TGATGTTCGTTTGGCCAAGA 58.026 45.000 19.48 10.98 0.00 3.02
50 51 3.057315 AGAATGATGTTCGTTTGGCCAAG 60.057 43.478 19.48 8.45 0.00 3.61
51 52 2.890311 AGAATGATGTTCGTTTGGCCAA 59.110 40.909 16.05 16.05 0.00 4.52
52 53 2.513753 AGAATGATGTTCGTTTGGCCA 58.486 42.857 0.00 0.00 0.00 5.36
53 54 3.575965 AAGAATGATGTTCGTTTGGCC 57.424 42.857 0.00 0.00 0.00 5.36
59 60 9.831737 CAGATAAAAGAAAAGAATGATGTTCGT 57.168 29.630 0.00 0.00 0.00 3.85
61 62 9.080915 GCCAGATAAAAGAAAAGAATGATGTTC 57.919 33.333 0.00 0.00 0.00 3.18
63 64 8.248945 CAGCCAGATAAAAGAAAAGAATGATGT 58.751 33.333 0.00 0.00 0.00 3.06
66 67 8.408043 TTCAGCCAGATAAAAGAAAAGAATGA 57.592 30.769 0.00 0.00 0.00 2.57
67 68 9.136952 CTTTCAGCCAGATAAAAGAAAAGAATG 57.863 33.333 0.00 0.00 31.81 2.67
68 69 9.082313 TCTTTCAGCCAGATAAAAGAAAAGAAT 57.918 29.630 0.00 0.00 35.43 2.40
69 70 8.463930 TCTTTCAGCCAGATAAAAGAAAAGAA 57.536 30.769 0.00 0.00 35.43 2.52
70 71 8.352942 GTTCTTTCAGCCAGATAAAAGAAAAGA 58.647 33.333 9.86 0.00 44.69 2.52
71 72 8.137437 TGTTCTTTCAGCCAGATAAAAGAAAAG 58.863 33.333 9.86 0.00 44.69 2.27
72 73 8.006298 TGTTCTTTCAGCCAGATAAAAGAAAA 57.994 30.769 9.86 3.61 44.69 2.29
74 75 6.998074 TCTGTTCTTTCAGCCAGATAAAAGAA 59.002 34.615 5.32 5.32 42.41 2.52
75 76 6.533730 TCTGTTCTTTCAGCCAGATAAAAGA 58.466 36.000 0.00 0.00 36.29 2.52
76 77 6.808008 TCTGTTCTTTCAGCCAGATAAAAG 57.192 37.500 0.00 0.00 35.63 2.27
77 78 7.765695 ATTCTGTTCTTTCAGCCAGATAAAA 57.234 32.000 0.00 0.00 34.19 1.52
79 80 8.896744 CATAATTCTGTTCTTTCAGCCAGATAA 58.103 33.333 0.00 0.00 34.19 1.75
80 81 8.267183 TCATAATTCTGTTCTTTCAGCCAGATA 58.733 33.333 0.00 0.00 34.19 1.98
81 82 7.066766 GTCATAATTCTGTTCTTTCAGCCAGAT 59.933 37.037 0.00 0.00 34.19 2.90
83 84 6.149973 TGTCATAATTCTGTTCTTTCAGCCAG 59.850 38.462 0.00 0.00 35.63 4.85
85 86 6.500684 TGTCATAATTCTGTTCTTTCAGCC 57.499 37.500 0.00 0.00 35.63 4.85
86 87 7.699812 GGATTGTCATAATTCTGTTCTTTCAGC 59.300 37.037 0.00 0.00 35.63 4.26
87 88 8.733458 TGGATTGTCATAATTCTGTTCTTTCAG 58.267 33.333 0.00 0.00 36.85 3.02
88 89 8.514594 GTGGATTGTCATAATTCTGTTCTTTCA 58.485 33.333 0.00 0.00 0.00 2.69
89 90 7.970614 GGTGGATTGTCATAATTCTGTTCTTTC 59.029 37.037 0.00 0.00 0.00 2.62
90 91 7.451255 TGGTGGATTGTCATAATTCTGTTCTTT 59.549 33.333 0.00 0.00 0.00 2.52
93 94 6.757897 TGGTGGATTGTCATAATTCTGTTC 57.242 37.500 0.00 0.00 0.00 3.18
94 95 7.722949 AATGGTGGATTGTCATAATTCTGTT 57.277 32.000 0.00 0.00 0.00 3.16
97 98 6.486657 CGGTAATGGTGGATTGTCATAATTCT 59.513 38.462 0.00 0.00 0.00 2.40
98 99 6.485313 TCGGTAATGGTGGATTGTCATAATTC 59.515 38.462 0.00 0.00 0.00 2.17
99 100 6.262273 GTCGGTAATGGTGGATTGTCATAATT 59.738 38.462 0.00 0.00 0.00 1.40
100 101 5.763204 GTCGGTAATGGTGGATTGTCATAAT 59.237 40.000 0.00 0.00 0.00 1.28
102 103 4.407621 AGTCGGTAATGGTGGATTGTCATA 59.592 41.667 0.00 0.00 0.00 2.15
104 105 2.569853 AGTCGGTAATGGTGGATTGTCA 59.430 45.455 0.00 0.00 0.00 3.58
105 106 3.261981 AGTCGGTAATGGTGGATTGTC 57.738 47.619 0.00 0.00 0.00 3.18
106 107 3.713826 AAGTCGGTAATGGTGGATTGT 57.286 42.857 0.00 0.00 0.00 2.71
107 108 3.377172 GGAAAGTCGGTAATGGTGGATTG 59.623 47.826 0.00 0.00 0.00 2.67
109 110 2.574369 TGGAAAGTCGGTAATGGTGGAT 59.426 45.455 0.00 0.00 0.00 3.41
110 111 1.979308 TGGAAAGTCGGTAATGGTGGA 59.021 47.619 0.00 0.00 0.00 4.02
111 112 2.483014 TGGAAAGTCGGTAATGGTGG 57.517 50.000 0.00 0.00 0.00 4.61
112 113 4.839668 TTTTGGAAAGTCGGTAATGGTG 57.160 40.909 0.00 0.00 0.00 4.17
113 114 6.413783 AATTTTTGGAAAGTCGGTAATGGT 57.586 33.333 0.00 0.00 0.00 3.55
115 116 7.938563 TGAAATTTTTGGAAAGTCGGTAATG 57.061 32.000 0.00 0.00 0.00 1.90
147 148 9.992910 GAATTTGAATTGTTTTTCTTTTGAGCT 57.007 25.926 0.00 0.00 0.00 4.09
148 149 9.992910 AGAATTTGAATTGTTTTTCTTTTGAGC 57.007 25.926 0.00 0.00 0.00 4.26
155 156 8.021898 TGGAGGAGAATTTGAATTGTTTTTCT 57.978 30.769 0.00 0.00 0.00 2.52
156 157 7.095481 GCTGGAGGAGAATTTGAATTGTTTTTC 60.095 37.037 0.00 0.00 0.00 2.29
157 158 6.707608 GCTGGAGGAGAATTTGAATTGTTTTT 59.292 34.615 0.00 0.00 0.00 1.94
159 160 5.279657 GGCTGGAGGAGAATTTGAATTGTTT 60.280 40.000 0.00 0.00 0.00 2.83
160 161 4.221482 GGCTGGAGGAGAATTTGAATTGTT 59.779 41.667 0.00 0.00 0.00 2.83
161 162 3.766051 GGCTGGAGGAGAATTTGAATTGT 59.234 43.478 0.00 0.00 0.00 2.71
163 164 4.051661 TGGCTGGAGGAGAATTTGAATT 57.948 40.909 0.00 0.00 0.00 2.17
164 165 3.744940 TGGCTGGAGGAGAATTTGAAT 57.255 42.857 0.00 0.00 0.00 2.57
166 167 2.848694 AGATGGCTGGAGGAGAATTTGA 59.151 45.455 0.00 0.00 0.00 2.69
167 168 3.117963 AGAGATGGCTGGAGGAGAATTTG 60.118 47.826 0.00 0.00 0.00 2.32
168 169 3.117963 CAGAGATGGCTGGAGGAGAATTT 60.118 47.826 0.00 0.00 32.26 1.82
169 170 2.438763 CAGAGATGGCTGGAGGAGAATT 59.561 50.000 0.00 0.00 32.26 2.17
170 171 2.048601 CAGAGATGGCTGGAGGAGAAT 58.951 52.381 0.00 0.00 32.26 2.40
171 172 1.493861 CAGAGATGGCTGGAGGAGAA 58.506 55.000 0.00 0.00 32.26 2.87
172 173 1.047596 GCAGAGATGGCTGGAGGAGA 61.048 60.000 0.00 0.00 36.41 3.71
173 174 1.446791 GCAGAGATGGCTGGAGGAG 59.553 63.158 0.00 0.00 36.41 3.69
174 175 2.068821 GGCAGAGATGGCTGGAGGA 61.069 63.158 0.00 0.00 36.41 3.71
175 176 1.633915 AAGGCAGAGATGGCTGGAGG 61.634 60.000 4.99 0.00 44.26 4.30
176 177 0.464013 CAAGGCAGAGATGGCTGGAG 60.464 60.000 4.99 0.00 44.26 3.86
178 179 0.034767 TTCAAGGCAGAGATGGCTGG 60.035 55.000 4.99 2.36 44.26 4.85
179 180 1.471684 GTTTCAAGGCAGAGATGGCTG 59.528 52.381 4.99 0.00 44.26 4.85
181 182 0.813821 GGTTTCAAGGCAGAGATGGC 59.186 55.000 0.00 0.00 0.00 4.40
183 184 2.503895 AGGGTTTCAAGGCAGAGATG 57.496 50.000 0.00 0.00 0.00 2.90
184 185 3.185455 ACTAGGGTTTCAAGGCAGAGAT 58.815 45.455 0.00 0.00 0.00 2.75
186 187 3.425162 AACTAGGGTTTCAAGGCAGAG 57.575 47.619 0.00 0.00 30.55 3.35
187 188 4.843728 CATAACTAGGGTTTCAAGGCAGA 58.156 43.478 0.00 0.00 36.92 4.26
188 189 3.378427 GCATAACTAGGGTTTCAAGGCAG 59.622 47.826 0.00 0.00 36.92 4.85
192 193 5.940470 ACAAGAGCATAACTAGGGTTTCAAG 59.060 40.000 0.00 0.00 36.92 3.02
193 194 5.876357 ACAAGAGCATAACTAGGGTTTCAA 58.124 37.500 0.00 0.00 36.92 2.69
194 195 5.499004 ACAAGAGCATAACTAGGGTTTCA 57.501 39.130 0.00 0.00 36.92 2.69
195 196 5.705905 ACAACAAGAGCATAACTAGGGTTTC 59.294 40.000 0.00 0.00 36.92 2.78
197 198 5.242795 ACAACAAGAGCATAACTAGGGTT 57.757 39.130 0.00 0.00 39.26 4.11
200 201 8.268850 ACATTAACAACAAGAGCATAACTAGG 57.731 34.615 0.00 0.00 0.00 3.02
201 202 9.760660 GAACATTAACAACAAGAGCATAACTAG 57.239 33.333 0.00 0.00 0.00 2.57
202 203 9.278978 TGAACATTAACAACAAGAGCATAACTA 57.721 29.630 0.00 0.00 0.00 2.24
203 204 8.165239 TGAACATTAACAACAAGAGCATAACT 57.835 30.769 0.00 0.00 0.00 2.24
204 205 8.853345 CATGAACATTAACAACAAGAGCATAAC 58.147 33.333 0.00 0.00 0.00 1.89
207 208 6.985117 ACATGAACATTAACAACAAGAGCAT 58.015 32.000 0.00 0.00 0.00 3.79
209 210 8.970691 ATAACATGAACATTAACAACAAGAGC 57.029 30.769 0.00 0.00 0.00 4.09
234 235 9.814899 TCTTTTTGCAGTTTCTCATATGAAAAA 57.185 25.926 6.90 3.27 37.63 1.94
236 237 9.248291 GTTCTTTTTGCAGTTTCTCATATGAAA 57.752 29.630 6.90 1.97 34.05 2.69
237 238 8.412456 TGTTCTTTTTGCAGTTTCTCATATGAA 58.588 29.630 6.90 0.00 0.00 2.57
238 239 7.939782 TGTTCTTTTTGCAGTTTCTCATATGA 58.060 30.769 5.07 5.07 0.00 2.15
239 240 7.864379 ACTGTTCTTTTTGCAGTTTCTCATATG 59.136 33.333 0.00 0.00 40.13 1.78
240 241 7.945134 ACTGTTCTTTTTGCAGTTTCTCATAT 58.055 30.769 0.00 0.00 40.13 1.78
241 242 7.333528 ACTGTTCTTTTTGCAGTTTCTCATA 57.666 32.000 0.00 0.00 40.13 2.15
242 243 6.212888 ACTGTTCTTTTTGCAGTTTCTCAT 57.787 33.333 0.00 0.00 40.13 2.90
243 244 5.643379 ACTGTTCTTTTTGCAGTTTCTCA 57.357 34.783 0.00 0.00 40.13 3.27
268 269 9.809096 TGTTAAAAACTGAGTATGATGCAAAAA 57.191 25.926 0.00 0.00 0.00 1.94
269 270 9.979578 ATGTTAAAAACTGAGTATGATGCAAAA 57.020 25.926 0.00 0.00 0.00 2.44
270 271 9.409312 CATGTTAAAAACTGAGTATGATGCAAA 57.591 29.630 0.00 0.00 0.00 3.68
272 273 8.236586 GTCATGTTAAAAACTGAGTATGATGCA 58.763 33.333 0.00 0.00 0.00 3.96
282 283 9.706691 CCTTCTACTAGTCATGTTAAAAACTGA 57.293 33.333 0.00 0.00 0.00 3.41
283 284 8.443937 GCCTTCTACTAGTCATGTTAAAAACTG 58.556 37.037 0.00 0.00 0.00 3.16
285 286 7.148289 GGGCCTTCTACTAGTCATGTTAAAAAC 60.148 40.741 0.84 0.00 0.00 2.43
288 289 5.394883 CGGGCCTTCTACTAGTCATGTTAAA 60.395 44.000 0.84 0.00 0.00 1.52
289 290 4.098960 CGGGCCTTCTACTAGTCATGTTAA 59.901 45.833 0.84 0.00 0.00 2.01
290 291 3.635373 CGGGCCTTCTACTAGTCATGTTA 59.365 47.826 0.84 0.00 0.00 2.41
371 372 7.576236 AGAAGAATAGTTTGATCAACGTGTTG 58.424 34.615 7.89 6.39 40.75 3.33
409 410 3.799432 AGTGTAACCATGCTTAACCCA 57.201 42.857 0.00 0.00 37.80 4.51
428 429 6.951643 TCATCGTTGCATGATGAAATCTAAG 58.048 36.000 22.76 2.02 44.92 2.18
523 525 1.809133 TGAGTTCTTGGGTGGTGGTA 58.191 50.000 0.00 0.00 0.00 3.25
524 526 1.149101 ATGAGTTCTTGGGTGGTGGT 58.851 50.000 0.00 0.00 0.00 4.16
525 527 3.081804 GTTATGAGTTCTTGGGTGGTGG 58.918 50.000 0.00 0.00 0.00 4.61
590 595 7.611467 TGCTTGCTCTTATATTTCTTCTTTCCA 59.389 33.333 0.00 0.00 0.00 3.53
591 596 7.912773 GTGCTTGCTCTTATATTTCTTCTTTCC 59.087 37.037 0.00 0.00 0.00 3.13
592 597 8.672815 AGTGCTTGCTCTTATATTTCTTCTTTC 58.327 33.333 0.00 0.00 0.00 2.62
593 598 8.572855 AGTGCTTGCTCTTATATTTCTTCTTT 57.427 30.769 0.00 0.00 0.00 2.52
594 599 7.826252 TGAGTGCTTGCTCTTATATTTCTTCTT 59.174 33.333 0.00 0.00 36.51 2.52
595 600 7.334090 TGAGTGCTTGCTCTTATATTTCTTCT 58.666 34.615 0.00 0.00 36.51 2.85
596 601 7.545362 TGAGTGCTTGCTCTTATATTTCTTC 57.455 36.000 0.00 0.00 36.51 2.87
597 602 9.618890 TTATGAGTGCTTGCTCTTATATTTCTT 57.381 29.630 9.02 0.00 36.51 2.52
598 603 9.050601 GTTATGAGTGCTTGCTCTTATATTTCT 57.949 33.333 9.02 0.00 36.51 2.52
599 604 9.050601 AGTTATGAGTGCTTGCTCTTATATTTC 57.949 33.333 9.02 5.22 36.51 2.17
600 605 8.834465 CAGTTATGAGTGCTTGCTCTTATATTT 58.166 33.333 9.02 1.32 36.51 1.40
601 606 7.443575 CCAGTTATGAGTGCTTGCTCTTATATT 59.556 37.037 9.02 1.57 36.51 1.28
602 607 6.933521 CCAGTTATGAGTGCTTGCTCTTATAT 59.066 38.462 9.02 3.93 36.51 0.86
603 608 6.098266 TCCAGTTATGAGTGCTTGCTCTTATA 59.902 38.462 5.47 5.47 36.51 0.98
604 609 5.104776 TCCAGTTATGAGTGCTTGCTCTTAT 60.105 40.000 7.04 7.04 36.51 1.73
605 610 4.222810 TCCAGTTATGAGTGCTTGCTCTTA 59.777 41.667 0.00 0.00 36.51 2.10
606 611 3.008375 TCCAGTTATGAGTGCTTGCTCTT 59.992 43.478 0.00 2.54 36.51 2.85
607 612 2.568956 TCCAGTTATGAGTGCTTGCTCT 59.431 45.455 0.00 0.00 36.51 4.09
608 613 2.977914 TCCAGTTATGAGTGCTTGCTC 58.022 47.619 0.00 0.00 36.12 4.26
609 614 3.641434 ATCCAGTTATGAGTGCTTGCT 57.359 42.857 0.00 0.00 0.00 3.91
610 615 8.954950 ATATATATCCAGTTATGAGTGCTTGC 57.045 34.615 0.00 0.00 0.00 4.01
702 711 8.859517 ATAAGAGCGTTTAGATTCACTACTTC 57.140 34.615 0.00 0.00 0.00 3.01
759 807 4.400529 AATAGTGACACATGGATGCGTA 57.599 40.909 8.59 0.00 0.00 4.42
795 853 8.372459 TGTACCTTGTAATATTGACTGTCAACT 58.628 33.333 24.17 15.53 39.45 3.16
796 854 8.440833 GTGTACCTTGTAATATTGACTGTCAAC 58.559 37.037 24.17 13.14 39.45 3.18
860 918 5.551760 AAGAGGCTTATGTGAATTTGTCG 57.448 39.130 0.00 0.00 0.00 4.35
1078 1137 0.738975 CATGAAGACCTCGACGCCTA 59.261 55.000 0.00 0.00 0.00 3.93
1098 1157 1.743252 GAAAGGAGAGCGGTGGCAG 60.743 63.158 0.00 0.00 43.41 4.85
1422 1482 4.846779 TGCCTTTTGGTGACTATGAAAC 57.153 40.909 0.00 0.00 42.99 2.78
1494 1554 8.037166 GCTTGATTTGGAGACATTTCCTATTTT 58.963 33.333 0.00 0.00 42.32 1.82
1633 3127 6.859112 AAGGAGATTTCTTAGCAGTACTGA 57.141 37.500 27.08 3.31 0.00 3.41
1668 3162 9.547279 TCTCATCAGTGGGCTAATTCTATAATA 57.453 33.333 0.00 0.00 0.00 0.98
1669 3163 8.441311 TCTCATCAGTGGGCTAATTCTATAAT 57.559 34.615 0.00 0.00 0.00 1.28
1670 3164 7.855784 TCTCATCAGTGGGCTAATTCTATAA 57.144 36.000 0.00 0.00 0.00 0.98
1767 3262 4.578516 CCCGATGTATATGTTCCTTTTGCA 59.421 41.667 0.00 0.00 0.00 4.08
1774 3270 5.723672 TCTTCTCCCGATGTATATGTTCC 57.276 43.478 0.00 0.00 0.00 3.62
2125 3626 2.108168 CCCTAGCTGCACTTACAGGTA 58.892 52.381 1.02 3.71 46.10 3.08
2242 3744 2.085176 ACCTCCTGAACAAGGTTTGCG 61.085 52.381 0.00 0.00 43.45 4.85
2317 3819 2.644798 AGCTGGGTGGTTTCTTCATAGT 59.355 45.455 0.00 0.00 0.00 2.12
2361 3863 8.369218 ACAAAACTATTGATTCTTTTTGGCTG 57.631 30.769 9.26 0.00 40.10 4.85


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

AutoCloner maintained by Alex Coulton.