Multiple sequence alignment - TraesCS1A01G107100

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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 TraesCS1A01G107100 chr1A 100.000 4157 0 0 1 4157 104923246 104919090 0.000000e+00 7677.0
1 TraesCS1A01G107100 chr1D 93.189 3010 120 35 235 3211 100660217 100663174 0.000000e+00 4344.0
2 TraesCS1A01G107100 chr1D 82.068 619 83 18 3321 3932 452249687 452250284 1.720000e-138 503.0
3 TraesCS1A01G107100 chr1B 89.043 3094 177 63 235 3236 151072428 151069405 0.000000e+00 3687.0
4 TraesCS1A01G107100 chr2D 85.238 1260 174 11 1933 3186 602451724 602450471 0.000000e+00 1286.0
5 TraesCS1A01G107100 chr2D 78.322 1144 232 13 1934 3072 651648800 651649932 0.000000e+00 725.0
6 TraesCS1A01G107100 chr2D 81.516 752 89 25 3321 4028 26926950 26927695 1.300000e-159 573.0
7 TraesCS1A01G107100 chr2D 84.643 560 65 16 3538 4087 298845828 298845280 4.730000e-149 538.0
8 TraesCS1A01G107100 chr2D 77.460 559 93 26 1315 1852 602452284 602451738 1.880000e-78 303.0
9 TraesCS1A01G107100 chr2D 84.181 177 15 7 532 696 118467159 118467334 4.300000e-35 159.0
10 TraesCS1A01G107100 chr2D 84.181 177 13 12 532 696 118519794 118519967 1.550000e-34 158.0
11 TraesCS1A01G107100 chr2D 94.845 97 4 1 1 97 640986121 640986216 2.590000e-32 150.0
12 TraesCS1A01G107100 chr2D 82.759 116 16 4 1162 1276 602453300 602453188 2.640000e-17 100.0
13 TraesCS1A01G107100 chr2B 84.897 1258 182 8 1933 3186 732568654 732567401 0.000000e+00 1264.0
14 TraesCS1A01G107100 chr2B 78.676 544 79 24 1315 1852 732569180 732568668 1.110000e-85 327.0
15 TraesCS1A01G107100 chr2A 78.117 1147 235 13 1934 3075 776022994 776021859 0.000000e+00 713.0
16 TraesCS1A01G107100 chr2A 84.946 93 12 2 1170 1262 734925509 734925419 4.420000e-15 93.5
17 TraesCS1A01G107100 chrUn 77.787 1148 237 15 1934 3075 23653088 23651953 0.000000e+00 691.0
18 TraesCS1A01G107100 chr3D 82.138 795 99 24 3321 4087 441369421 441370200 3.500000e-180 641.0
19 TraesCS1A01G107100 chr3D 81.416 791 103 24 3321 4092 352104130 352103365 1.280000e-169 606.0
20 TraesCS1A01G107100 chr3D 81.745 745 107 20 3321 4042 514004999 514004261 2.770000e-166 595.0
21 TraesCS1A01G107100 chr3D 84.810 553 65 15 3550 4094 32504780 32504239 4.730000e-149 538.0
22 TraesCS1A01G107100 chr6D 86.194 536 53 16 3538 4061 457327400 457326874 1.010000e-155 560.0
23 TraesCS1A01G107100 chr5A 82.242 687 80 13 3321 3977 282537004 282537678 4.700000e-154 555.0
24 TraesCS1A01G107100 chr7D 84.875 562 70 12 3534 4087 593672403 593672957 1.690000e-153 553.0
25 TraesCS1A01G107100 chr7D 77.083 288 27 20 445 696 613229030 613229314 3.370000e-26 130.0
26 TraesCS1A01G107100 chr4D 81.041 749 88 29 3321 4028 488605234 488604499 7.860000e-152 547.0
27 TraesCS1A01G107100 chr4D 76.860 847 161 29 2159 2986 428717520 428718350 2.950000e-121 446.0
28 TraesCS1A01G107100 chr4D 73.179 865 197 28 2138 2986 428941608 428940763 3.160000e-71 279.0
29 TraesCS1A01G107100 chr4D 85.238 210 30 1 3321 3529 434096855 434096646 9.050000e-52 215.0
30 TraesCS1A01G107100 chr4A 85.036 548 68 11 3550 4087 12455753 12456296 2.830000e-151 545.0
31 TraesCS1A01G107100 chr4A 78.255 745 91 39 3321 4028 29182434 29181724 2.990000e-111 412.0
32 TraesCS1A01G107100 chr4A 75.398 943 185 38 2159 3076 37785009 37784089 2.990000e-111 412.0
33 TraesCS1A01G107100 chr5D 83.854 576 69 17 3537 4092 498929887 498930458 1.020000e-145 527.0
34 TraesCS1A01G107100 chr5D 81.548 336 43 12 3321 3639 429981862 429981529 4.120000e-65 259.0
35 TraesCS1A01G107100 chr4B 76.505 847 164 30 2159 2986 526736897 526736067 2.970000e-116 429.0
36 TraesCS1A01G107100 chr4B 72.931 894 207 29 2109 2986 526274995 526275869 1.140000e-70 278.0
37 TraesCS1A01G107100 chr7B 89.655 145 12 2 1 143 716258766 716258623 9.180000e-42 182.0


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 TraesCS1A01G107100 chr1A 104919090 104923246 4156 True 7677.0 7677 100.0000 1 4157 1 chr1A.!!$R1 4156
1 TraesCS1A01G107100 chr1D 100660217 100663174 2957 False 4344.0 4344 93.1890 235 3211 1 chr1D.!!$F1 2976
2 TraesCS1A01G107100 chr1D 452249687 452250284 597 False 503.0 503 82.0680 3321 3932 1 chr1D.!!$F2 611
3 TraesCS1A01G107100 chr1B 151069405 151072428 3023 True 3687.0 3687 89.0430 235 3236 1 chr1B.!!$R1 3001
4 TraesCS1A01G107100 chr2D 651648800 651649932 1132 False 725.0 725 78.3220 1934 3072 1 chr2D.!!$F5 1138
5 TraesCS1A01G107100 chr2D 26926950 26927695 745 False 573.0 573 81.5160 3321 4028 1 chr2D.!!$F1 707
6 TraesCS1A01G107100 chr2D 602450471 602453300 2829 True 563.0 1286 81.8190 1162 3186 3 chr2D.!!$R2 2024
7 TraesCS1A01G107100 chr2D 298845280 298845828 548 True 538.0 538 84.6430 3538 4087 1 chr2D.!!$R1 549
8 TraesCS1A01G107100 chr2B 732567401 732569180 1779 True 795.5 1264 81.7865 1315 3186 2 chr2B.!!$R1 1871
9 TraesCS1A01G107100 chr2A 776021859 776022994 1135 True 713.0 713 78.1170 1934 3075 1 chr2A.!!$R2 1141
10 TraesCS1A01G107100 chrUn 23651953 23653088 1135 True 691.0 691 77.7870 1934 3075 1 chrUn.!!$R1 1141
11 TraesCS1A01G107100 chr3D 441369421 441370200 779 False 641.0 641 82.1380 3321 4087 1 chr3D.!!$F1 766
12 TraesCS1A01G107100 chr3D 352103365 352104130 765 True 606.0 606 81.4160 3321 4092 1 chr3D.!!$R2 771
13 TraesCS1A01G107100 chr3D 514004261 514004999 738 True 595.0 595 81.7450 3321 4042 1 chr3D.!!$R3 721
14 TraesCS1A01G107100 chr3D 32504239 32504780 541 True 538.0 538 84.8100 3550 4094 1 chr3D.!!$R1 544
15 TraesCS1A01G107100 chr6D 457326874 457327400 526 True 560.0 560 86.1940 3538 4061 1 chr6D.!!$R1 523
16 TraesCS1A01G107100 chr5A 282537004 282537678 674 False 555.0 555 82.2420 3321 3977 1 chr5A.!!$F1 656
17 TraesCS1A01G107100 chr7D 593672403 593672957 554 False 553.0 553 84.8750 3534 4087 1 chr7D.!!$F1 553
18 TraesCS1A01G107100 chr4D 488604499 488605234 735 True 547.0 547 81.0410 3321 4028 1 chr4D.!!$R3 707
19 TraesCS1A01G107100 chr4D 428717520 428718350 830 False 446.0 446 76.8600 2159 2986 1 chr4D.!!$F1 827
20 TraesCS1A01G107100 chr4D 428940763 428941608 845 True 279.0 279 73.1790 2138 2986 1 chr4D.!!$R1 848
21 TraesCS1A01G107100 chr4A 12455753 12456296 543 False 545.0 545 85.0360 3550 4087 1 chr4A.!!$F1 537
22 TraesCS1A01G107100 chr4A 29181724 29182434 710 True 412.0 412 78.2550 3321 4028 1 chr4A.!!$R1 707
23 TraesCS1A01G107100 chr4A 37784089 37785009 920 True 412.0 412 75.3980 2159 3076 1 chr4A.!!$R2 917
24 TraesCS1A01G107100 chr5D 498929887 498930458 571 False 527.0 527 83.8540 3537 4092 1 chr5D.!!$F1 555
25 TraesCS1A01G107100 chr4B 526736067 526736897 830 True 429.0 429 76.5050 2159 2986 1 chr4B.!!$R1 827
26 TraesCS1A01G107100 chr4B 526274995 526275869 874 False 278.0 278 72.9310 2109 2986 1 chr4B.!!$F1 877

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
225 226 0.104304 GCATCCGTCGGGTGTAAGAT 59.896 55.0 24.98 0.00 33.83 2.40 F
518 539 0.248289 GGCACTTAGTTGTAGCCGGA 59.752 55.0 5.05 0.00 35.42 5.14 F
610 636 0.819259 GCTGTGTGGCTTGGTCAAGA 60.819 55.0 14.20 0.00 40.79 3.02 F
848 888 0.823356 AATCAGCAACACACCGCCTT 60.823 50.0 0.00 0.00 0.00 4.35 F
2786 3795 0.591659 CTCACTGAGGTCGACGTCAA 59.408 55.0 33.06 21.64 39.81 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1347 2296 0.320421 TGCCGCCTTTGTACAGAGAC 60.320 55.000 14.73 2.18 0.00 3.36 R
1913 2910 0.828022 CCTACCATCGGCCTGTACAA 59.172 55.000 0.00 0.00 0.00 2.41 R
2772 3781 2.640989 CGGTTGACGTCGACCTCA 59.359 61.111 39.29 12.44 46.16 3.86 R
2789 3798 4.929707 CGTAGGGGCCGGCATTCC 62.930 72.222 30.85 24.93 0.00 3.01 R
3647 4721 0.540365 ACCCGTACCTCTCGTGGAAA 60.540 55.000 0.00 0.00 0.00 3.13 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 6.817765 TTCTAAAATTAGACCCTGTTGCTG 57.182 37.500 2.42 0.00 39.36 4.41
24 25 6.121776 TCTAAAATTAGACCCTGTTGCTGA 57.878 37.500 0.00 0.00 34.99 4.26
25 26 6.539173 TCTAAAATTAGACCCTGTTGCTGAA 58.461 36.000 0.00 0.00 34.99 3.02
26 27 7.001674 TCTAAAATTAGACCCTGTTGCTGAAA 58.998 34.615 0.00 0.00 34.99 2.69
27 28 6.478512 AAAATTAGACCCTGTTGCTGAAAA 57.521 33.333 0.00 0.00 0.00 2.29
28 29 6.478512 AAATTAGACCCTGTTGCTGAAAAA 57.521 33.333 0.00 0.00 0.00 1.94
48 49 5.592104 AAAAACTTCACCACCGAATCTTT 57.408 34.783 0.00 0.00 0.00 2.52
49 50 6.702716 AAAAACTTCACCACCGAATCTTTA 57.297 33.333 0.00 0.00 0.00 1.85
50 51 6.894339 AAAACTTCACCACCGAATCTTTAT 57.106 33.333 0.00 0.00 0.00 1.40
51 52 6.894339 AAACTTCACCACCGAATCTTTATT 57.106 33.333 0.00 0.00 0.00 1.40
52 53 6.894339 AACTTCACCACCGAATCTTTATTT 57.106 33.333 0.00 0.00 0.00 1.40
53 54 7.989416 AACTTCACCACCGAATCTTTATTTA 57.011 32.000 0.00 0.00 0.00 1.40
54 55 8.575649 AACTTCACCACCGAATCTTTATTTAT 57.424 30.769 0.00 0.00 0.00 1.40
55 56 8.575649 ACTTCACCACCGAATCTTTATTTATT 57.424 30.769 0.00 0.00 0.00 1.40
56 57 9.020731 ACTTCACCACCGAATCTTTATTTATTT 57.979 29.630 0.00 0.00 0.00 1.40
81 82 7.814264 ATTTCTGAAACAAGATCTCTGTTGT 57.186 32.000 18.05 7.73 40.33 3.32
82 83 8.908786 ATTTCTGAAACAAGATCTCTGTTGTA 57.091 30.769 18.05 11.94 37.86 2.41
83 84 7.953158 TTCTGAAACAAGATCTCTGTTGTAG 57.047 36.000 18.05 17.52 37.86 2.74
84 85 7.290110 TCTGAAACAAGATCTCTGTTGTAGA 57.710 36.000 18.05 18.76 37.86 2.59
85 86 7.726216 TCTGAAACAAGATCTCTGTTGTAGAA 58.274 34.615 18.05 10.21 37.86 2.10
86 87 8.204160 TCTGAAACAAGATCTCTGTTGTAGAAA 58.796 33.333 18.05 7.38 37.86 2.52
87 88 8.142994 TGAAACAAGATCTCTGTTGTAGAAAC 57.857 34.615 18.05 8.94 37.86 2.78
88 89 7.226720 TGAAACAAGATCTCTGTTGTAGAAACC 59.773 37.037 18.05 6.77 37.86 3.27
89 90 6.426646 ACAAGATCTCTGTTGTAGAAACCT 57.573 37.500 0.00 0.00 37.12 3.50
90 91 6.831976 ACAAGATCTCTGTTGTAGAAACCTT 58.168 36.000 0.00 0.00 37.12 3.50
91 92 6.931840 ACAAGATCTCTGTTGTAGAAACCTTC 59.068 38.462 0.00 0.00 37.12 3.46
92 93 6.926630 AGATCTCTGTTGTAGAAACCTTCT 57.073 37.500 0.00 0.00 43.72 2.85
93 94 8.307483 CAAGATCTCTGTTGTAGAAACCTTCTA 58.693 37.037 0.00 0.00 41.14 2.10
94 95 8.423906 AGATCTCTGTTGTAGAAACCTTCTAA 57.576 34.615 0.00 0.00 43.40 2.10
95 96 8.871125 AGATCTCTGTTGTAGAAACCTTCTAAA 58.129 33.333 0.00 0.00 43.40 1.85
96 97 9.490379 GATCTCTGTTGTAGAAACCTTCTAAAA 57.510 33.333 0.00 0.00 43.40 1.52
97 98 9.847224 ATCTCTGTTGTAGAAACCTTCTAAAAA 57.153 29.630 1.46 0.00 43.40 1.94
98 99 9.106070 TCTCTGTTGTAGAAACCTTCTAAAAAC 57.894 33.333 12.23 12.23 43.40 2.43
99 100 8.795842 TCTGTTGTAGAAACCTTCTAAAAACA 57.204 30.769 16.92 16.92 43.40 2.83
100 101 9.233649 TCTGTTGTAGAAACCTTCTAAAAACAA 57.766 29.630 17.74 10.51 43.30 2.83
105 106 9.545105 TGTAGAAACCTTCTAAAAACAATACGA 57.455 29.630 0.00 0.00 43.40 3.43
108 109 9.893305 AGAAACCTTCTAAAAACAATACGATTG 57.107 29.630 0.00 0.00 38.49 2.67
109 110 9.673454 GAAACCTTCTAAAAACAATACGATTGT 57.327 29.630 7.22 7.22 0.00 2.71
111 112 9.458374 AACCTTCTAAAAACAATACGATTGTTG 57.542 29.630 19.60 11.46 41.30 3.33
112 113 7.593644 ACCTTCTAAAAACAATACGATTGTTGC 59.406 33.333 19.60 0.00 41.30 4.17
113 114 7.593273 CCTTCTAAAAACAATACGATTGTTGCA 59.407 33.333 19.60 11.12 41.30 4.08
114 115 8.858003 TTCTAAAAACAATACGATTGTTGCAA 57.142 26.923 19.60 0.00 41.30 4.08
115 116 8.858003 TCTAAAAACAATACGATTGTTGCAAA 57.142 26.923 19.60 9.96 41.30 3.68
116 117 9.302345 TCTAAAAACAATACGATTGTTGCAAAA 57.698 25.926 19.60 0.00 41.30 2.44
117 118 9.907576 CTAAAAACAATACGATTGTTGCAAAAA 57.092 25.926 19.60 4.10 41.30 1.94
135 136 3.518634 AAAAATTGGTTGCACACGACT 57.481 38.095 0.00 0.00 0.00 4.18
136 137 3.518634 AAAATTGGTTGCACACGACTT 57.481 38.095 0.00 0.00 0.00 3.01
137 138 2.490328 AATTGGTTGCACACGACTTG 57.510 45.000 0.00 0.00 0.00 3.16
138 139 1.388547 ATTGGTTGCACACGACTTGT 58.611 45.000 0.00 0.00 39.97 3.16
146 147 3.041940 CACGACTTGTGGCCGTCC 61.042 66.667 0.00 0.00 45.21 4.79
147 148 3.542676 ACGACTTGTGGCCGTCCA 61.543 61.111 0.00 0.00 40.85 4.02
148 149 2.280524 CGACTTGTGGCCGTCCAA 60.281 61.111 0.00 0.00 45.53 3.53
149 150 2.604174 CGACTTGTGGCCGTCCAAC 61.604 63.158 0.00 0.00 45.53 3.77
150 151 2.590575 ACTTGTGGCCGTCCAACG 60.591 61.111 0.00 0.00 45.53 4.10
151 152 2.590575 CTTGTGGCCGTCCAACGT 60.591 61.111 0.00 0.00 45.53 3.99
152 153 1.301087 CTTGTGGCCGTCCAACGTA 60.301 57.895 0.00 0.00 45.53 3.57
153 154 0.881159 CTTGTGGCCGTCCAACGTAA 60.881 55.000 0.00 0.00 45.53 3.18
154 155 0.881159 TTGTGGCCGTCCAACGTAAG 60.881 55.000 0.00 0.00 45.53 2.34
155 156 2.357760 TGGCCGTCCAACGTAAGC 60.358 61.111 0.00 0.00 40.58 3.09
156 157 3.484547 GGCCGTCCAACGTAAGCG 61.485 66.667 0.00 0.00 40.58 4.68
157 158 4.143363 GCCGTCCAACGTAAGCGC 62.143 66.667 0.00 0.00 40.58 5.92
158 159 2.431942 CCGTCCAACGTAAGCGCT 60.432 61.111 2.64 2.64 40.58 5.92
159 160 2.442188 CCGTCCAACGTAAGCGCTC 61.442 63.158 12.06 0.00 40.58 5.03
160 161 2.774951 CGTCCAACGTAAGCGCTCG 61.775 63.158 12.06 14.49 42.83 5.03
161 162 1.443194 GTCCAACGTAAGCGCTCGA 60.443 57.895 23.31 6.69 42.83 4.04
162 163 0.801067 GTCCAACGTAAGCGCTCGAT 60.801 55.000 23.31 10.30 42.83 3.59
163 164 0.524816 TCCAACGTAAGCGCTCGATC 60.525 55.000 23.31 8.05 42.83 3.69
164 165 0.800683 CCAACGTAAGCGCTCGATCA 60.801 55.000 23.31 0.00 42.83 2.92
165 166 0.989164 CAACGTAAGCGCTCGATCAA 59.011 50.000 23.31 0.00 42.83 2.57
166 167 1.007011 CAACGTAAGCGCTCGATCAAG 60.007 52.381 23.31 8.21 42.83 3.02
167 168 0.450583 ACGTAAGCGCTCGATCAAGA 59.549 50.000 23.31 0.00 42.83 3.02
168 169 1.065701 ACGTAAGCGCTCGATCAAGAT 59.934 47.619 23.31 1.43 42.83 2.40
169 170 2.120232 CGTAAGCGCTCGATCAAGATT 58.880 47.619 12.06 0.00 0.00 2.40
170 171 2.097685 CGTAAGCGCTCGATCAAGATTG 60.098 50.000 12.06 0.00 0.00 2.67
171 172 2.299993 AAGCGCTCGATCAAGATTGA 57.700 45.000 12.06 0.00 42.14 2.57
172 173 7.943387 ACGTAAGCGCTCGATCAAGATTGAT 62.943 44.000 23.31 7.77 45.38 2.57
181 182 3.784511 ATCAAGATTGATCCGATGGCT 57.215 42.857 2.17 0.00 44.17 4.75
182 183 4.897509 ATCAAGATTGATCCGATGGCTA 57.102 40.909 2.17 0.00 44.17 3.93
183 184 3.995199 TCAAGATTGATCCGATGGCTAC 58.005 45.455 0.00 0.00 31.01 3.58
184 185 2.732412 AGATTGATCCGATGGCTACG 57.268 50.000 0.00 0.00 0.00 3.51
185 186 1.071605 GATTGATCCGATGGCTACGC 58.928 55.000 0.00 0.00 0.00 4.42
186 187 0.392706 ATTGATCCGATGGCTACGCA 59.607 50.000 0.00 0.00 0.00 5.24
187 188 0.392706 TTGATCCGATGGCTACGCAT 59.607 50.000 0.00 0.00 0.00 4.73
188 189 0.319813 TGATCCGATGGCTACGCATG 60.320 55.000 0.00 0.00 0.00 4.06
189 190 1.630244 GATCCGATGGCTACGCATGC 61.630 60.000 7.91 7.91 0.00 4.06
190 191 3.705638 CCGATGGCTACGCATGCG 61.706 66.667 36.79 36.79 46.03 4.73
191 192 3.705638 CGATGGCTACGCATGCGG 61.706 66.667 39.95 25.91 44.69 5.69
192 193 4.017877 GATGGCTACGCATGCGGC 62.018 66.667 39.95 32.92 44.69 6.53
220 221 4.735132 CGTGCATCCGTCGGGTGT 62.735 66.667 24.98 2.69 33.83 4.16
221 222 2.574929 GTGCATCCGTCGGGTGTA 59.425 61.111 24.98 18.87 33.83 2.90
222 223 1.079681 GTGCATCCGTCGGGTGTAA 60.080 57.895 24.98 11.78 33.83 2.41
223 224 1.082117 GTGCATCCGTCGGGTGTAAG 61.082 60.000 24.98 0.44 33.83 2.34
224 225 1.252215 TGCATCCGTCGGGTGTAAGA 61.252 55.000 24.98 5.12 33.83 2.10
225 226 0.104304 GCATCCGTCGGGTGTAAGAT 59.896 55.000 24.98 0.00 33.83 2.40
226 227 1.338973 GCATCCGTCGGGTGTAAGATA 59.661 52.381 24.98 0.00 33.83 1.98
227 228 2.607282 GCATCCGTCGGGTGTAAGATAG 60.607 54.545 24.98 0.00 33.83 2.08
228 229 1.027357 TCCGTCGGGTGTAAGATAGC 58.973 55.000 12.29 0.00 33.83 2.97
229 230 0.317603 CCGTCGGGTGTAAGATAGCG 60.318 60.000 2.34 0.00 0.00 4.26
230 231 0.379669 CGTCGGGTGTAAGATAGCGT 59.620 55.000 0.00 0.00 0.00 5.07
231 232 1.202222 CGTCGGGTGTAAGATAGCGTT 60.202 52.381 0.00 0.00 0.00 4.84
232 233 2.733227 CGTCGGGTGTAAGATAGCGTTT 60.733 50.000 0.00 0.00 0.00 3.60
233 234 3.256558 GTCGGGTGTAAGATAGCGTTTT 58.743 45.455 0.00 0.00 0.00 2.43
451 472 7.118971 ACAAAAGATACTGACTTGATCTTCTGC 59.881 37.037 0.00 0.00 38.64 4.26
456 477 2.415857 CTGACTTGATCTTCTGCAGCAC 59.584 50.000 9.47 0.00 0.00 4.40
511 532 1.677820 GGCGTATGGGCACTTAGTTGT 60.678 52.381 0.00 0.00 41.77 3.32
514 535 2.864343 CGTATGGGCACTTAGTTGTAGC 59.136 50.000 0.00 0.00 0.00 3.58
518 539 0.248289 GGCACTTAGTTGTAGCCGGA 59.752 55.000 5.05 0.00 35.42 5.14
524 545 3.322828 ACTTAGTTGTAGCCGGAAGTTCA 59.677 43.478 5.05 0.00 0.00 3.18
528 549 3.008049 AGTTGTAGCCGGAAGTTCATTCT 59.992 43.478 5.05 0.65 38.07 2.40
539 560 6.405953 CCGGAAGTTCATTCTCTAGAAGCTTA 60.406 42.308 0.00 0.00 37.48 3.09
540 561 6.474102 CGGAAGTTCATTCTCTAGAAGCTTAC 59.526 42.308 0.00 0.00 37.48 2.34
543 564 6.791303 AGTTCATTCTCTAGAAGCTTACGAG 58.209 40.000 0.00 5.88 37.48 4.18
553 576 3.991121 AGAAGCTTACGAGAGAGCAAAAC 59.009 43.478 0.00 0.00 41.31 2.43
584 607 7.833786 AGCAGATTGTTGGGCATTATATTATG 58.166 34.615 0.00 0.00 0.00 1.90
589 612 9.793252 GATTGTTGGGCATTATATTATGATGAC 57.207 33.333 11.50 8.76 33.78 3.06
592 615 5.424121 GGGCATTATATTATGATGACCGC 57.576 43.478 15.45 3.50 43.52 5.68
610 636 0.819259 GCTGTGTGGCTTGGTCAAGA 60.819 55.000 14.20 0.00 40.79 3.02
611 637 1.901591 CTGTGTGGCTTGGTCAAGAT 58.098 50.000 14.20 0.00 40.79 2.40
623 649 4.760530 TGGTCAAGATCCTCCTTGTATG 57.239 45.455 0.00 0.00 42.95 2.39
767 799 1.439644 CTCCTGCCTAGTCTTCCGC 59.560 63.158 0.00 0.00 0.00 5.54
783 815 1.812571 TCCGCTTGAGCCAAAGATTTC 59.187 47.619 0.27 0.00 37.91 2.17
784 816 1.135286 CCGCTTGAGCCAAAGATTTCC 60.135 52.381 0.27 0.00 37.91 3.13
785 817 1.135286 CGCTTGAGCCAAAGATTTCCC 60.135 52.381 0.27 0.00 37.91 3.97
786 818 1.205655 GCTTGAGCCAAAGATTTCCCC 59.794 52.381 0.27 0.00 34.31 4.81
787 819 1.827344 CTTGAGCCAAAGATTTCCCCC 59.173 52.381 0.00 0.00 0.00 5.40
811 851 2.143008 TTTGCGTTCGAGCTGACTTA 57.857 45.000 0.00 0.00 38.13 2.24
832 872 9.818796 GACTTAGAGTCAAAGATTGAAACAATC 57.181 33.333 14.24 14.24 44.45 2.67
848 888 0.823356 AATCAGCAACACACCGCCTT 60.823 50.000 0.00 0.00 0.00 4.35
1015 1068 2.051334 TACCATGGGGAAATTGCTCG 57.949 50.000 18.09 0.00 38.05 5.03
1066 1119 7.291566 TGAAGGTTAGTTTTCCCAAGTTCATA 58.708 34.615 0.00 0.00 0.00 2.15
1095 1148 4.953579 ACAGTTTGTATTTCCAACACCAGT 59.046 37.500 0.00 0.00 0.00 4.00
1117 1170 1.661509 GTTCCTTGCGGTTTGCTGC 60.662 57.895 0.00 0.00 46.63 5.25
1156 1214 6.138088 CACCGATTGCACATTGTAAGATATG 58.862 40.000 0.00 0.00 0.00 1.78
1292 1987 7.230747 TGGATTTGTGTTCCTTCTTATCTTGA 58.769 34.615 0.00 0.00 34.17 3.02
1312 2007 8.925161 TCTTGAAACTAAAGGATGTTGTTTTG 57.075 30.769 0.00 0.00 32.01 2.44
1347 2296 1.523258 CTTGAGCAGCCCGATGAGG 60.523 63.158 0.00 0.00 40.63 3.86
1604 2586 3.262420 ACTGCACCATCGTCATTTACTC 58.738 45.455 0.00 0.00 0.00 2.59
1620 2602 8.483218 GTCATTTACTCGTGATCTTGTGATATG 58.517 37.037 0.00 0.00 32.19 1.78
1641 2627 5.710513 TGCTGTATTTTCTTGTTGCTCAT 57.289 34.783 0.00 0.00 0.00 2.90
1642 2628 5.463286 TGCTGTATTTTCTTGTTGCTCATG 58.537 37.500 0.00 0.00 0.00 3.07
1722 2708 4.760047 GCACGGCGGTGGTGAGAT 62.760 66.667 23.86 0.00 44.54 2.75
1904 2890 3.288964 TCAACGCCAAAAAGGGAAACTA 58.711 40.909 0.00 0.00 38.09 2.24
1910 2907 4.743151 CGCCAAAAAGGGAAACTAAAGTTC 59.257 41.667 0.00 0.00 35.93 3.01
1913 2910 5.451381 CCAAAAAGGGAAACTAAAGTTCGCT 60.451 40.000 0.00 0.00 37.25 4.93
2017 3014 3.379445 GTCTGTCGGCCGGGAAGA 61.379 66.667 27.83 21.75 0.00 2.87
2523 3520 1.651240 CGTCGTCCGAGGTGTACCAT 61.651 60.000 3.56 0.00 39.56 3.55
2772 3781 1.997874 GGTCCCCATCTGGCTCACT 60.998 63.158 0.00 0.00 0.00 3.41
2785 3794 1.853114 GCTCACTGAGGTCGACGTCA 61.853 60.000 32.04 32.04 38.29 4.35
2786 3795 0.591659 CTCACTGAGGTCGACGTCAA 59.408 55.000 33.06 21.64 39.81 3.18
2789 3798 1.442184 CTGAGGTCGACGTCAACCG 60.442 63.158 33.06 21.84 39.81 4.44
2793 3802 1.080298 GGTCGACGTCAACCGGAAT 60.080 57.895 10.47 0.00 42.24 3.01
2940 3949 4.881850 ACGGACAACAACTTCAAGAATCTT 59.118 37.500 0.00 0.00 0.00 2.40
3170 4180 1.618487 GTGTAGGGACTAGGGATCGG 58.382 60.000 0.00 0.00 44.14 4.18
3176 4186 1.481871 GGACTAGGGATCGGACACAA 58.518 55.000 0.00 0.00 0.00 3.33
3247 4257 9.813826 TTCTTGAGAAGAAATTTCTTTCCCTAT 57.186 29.630 29.24 10.06 46.84 2.57
3303 4313 3.637714 GCTTTTGCTCGTCCGTCA 58.362 55.556 0.00 0.00 43.35 4.35
3304 4314 2.162716 GCTTTTGCTCGTCCGTCAT 58.837 52.632 0.00 0.00 43.35 3.06
3305 4315 1.355971 GCTTTTGCTCGTCCGTCATA 58.644 50.000 0.00 0.00 43.35 2.15
3306 4316 1.730064 GCTTTTGCTCGTCCGTCATAA 59.270 47.619 0.00 0.00 43.35 1.90
3307 4317 2.222819 GCTTTTGCTCGTCCGTCATAAG 60.223 50.000 0.00 8.88 43.35 1.73
3308 4318 3.250744 CTTTTGCTCGTCCGTCATAAGA 58.749 45.455 8.10 0.00 0.00 2.10
3309 4319 3.520290 TTTGCTCGTCCGTCATAAGAT 57.480 42.857 0.00 0.00 0.00 2.40
3310 4320 3.520290 TTGCTCGTCCGTCATAAGATT 57.480 42.857 0.00 0.00 0.00 2.40
3311 4321 4.642445 TTGCTCGTCCGTCATAAGATTA 57.358 40.909 0.00 0.00 0.00 1.75
3312 4322 3.961182 TGCTCGTCCGTCATAAGATTAC 58.039 45.455 0.00 0.00 0.00 1.89
3313 4323 3.243301 TGCTCGTCCGTCATAAGATTACC 60.243 47.826 0.00 0.00 0.00 2.85
3314 4324 3.856267 GCTCGTCCGTCATAAGATTACCC 60.856 52.174 0.00 0.00 0.00 3.69
3315 4325 3.289836 TCGTCCGTCATAAGATTACCCA 58.710 45.455 0.00 0.00 0.00 4.51
3316 4326 3.893200 TCGTCCGTCATAAGATTACCCAT 59.107 43.478 0.00 0.00 0.00 4.00
3317 4327 3.987868 CGTCCGTCATAAGATTACCCATG 59.012 47.826 0.00 0.00 0.00 3.66
3318 4328 4.261867 CGTCCGTCATAAGATTACCCATGA 60.262 45.833 0.00 0.00 0.00 3.07
3319 4329 5.230942 GTCCGTCATAAGATTACCCATGAG 58.769 45.833 0.00 0.00 0.00 2.90
3352 4362 3.589654 CTTCGGGAGCCTCGCAACA 62.590 63.158 9.61 0.00 0.00 3.33
3367 4377 1.669502 GCAACAATCAGCGCCATTTGA 60.670 47.619 17.45 9.77 0.00 2.69
3402 4412 4.719616 GCCACGTGTCGCGCTTTC 62.720 66.667 15.65 0.00 46.11 2.62
3422 4436 1.514873 GCGCTTGCTCCGGATTTTG 60.515 57.895 3.57 0.00 35.07 2.44
3427 4447 3.610585 CGCTTGCTCCGGATTTTGTTTTA 60.611 43.478 3.57 0.00 0.00 1.52
3432 4452 6.339587 TGCTCCGGATTTTGTTTTATTTCT 57.660 33.333 3.57 0.00 0.00 2.52
3439 4459 5.389411 GGATTTTGTTTTATTTCTGCACGCC 60.389 40.000 0.00 0.00 0.00 5.68
3483 4513 3.781341 TTTCGACGTCCTGATTTTTCG 57.219 42.857 10.58 0.00 0.00 3.46
3493 4523 3.077359 CCTGATTTTTCGCTGGTCTTCT 58.923 45.455 0.00 0.00 0.00 2.85
3498 4528 5.995282 TGATTTTTCGCTGGTCTTCTTTAGA 59.005 36.000 0.00 0.00 0.00 2.10
3508 4539 7.809806 CGCTGGTCTTCTTTAGATTTTTGATTT 59.190 33.333 0.00 0.00 34.79 2.17
3561 4626 0.111266 CTTTCGCGAGTCACGGTTTG 60.111 55.000 9.59 0.00 42.83 2.93
3792 5075 0.038251 TGTGCTTTCGCGAGAGTCAT 60.038 50.000 25.34 0.00 43.69 3.06
3811 5094 1.737008 GGTCGTGCCTCTCGGAAAC 60.737 63.158 0.00 0.00 0.00 2.78
3848 5134 8.100164 ACATTTTCTGTTTTTCCTTTCCTTTCA 58.900 29.630 0.00 0.00 32.90 2.69
3867 5153 0.878961 ACGAGAGTCACGGTTTTGCC 60.879 55.000 14.49 0.00 44.19 4.52
3884 5170 4.598894 CTCCGCGAGAGGCATGGG 62.599 72.222 8.23 0.00 43.84 4.00
3886 5172 3.536917 CCGCGAGAGGCATGGGTA 61.537 66.667 8.23 0.00 43.84 3.69
3913 5199 2.887568 GAGAGTCATGGCCGTGCG 60.888 66.667 20.86 0.00 0.00 5.34
3977 5266 1.213094 CGCGAGAGTCACGGTTTTGT 61.213 55.000 11.95 0.00 0.00 2.83
3999 5288 2.260434 GCGAGAGGCACGGTTGTA 59.740 61.111 0.00 0.00 42.87 2.41
4004 5293 2.352030 CGAGAGGCACGGTTGTACTTTA 60.352 50.000 0.00 0.00 0.00 1.85
4007 5296 1.071071 AGGCACGGTTGTACTTTAGCA 59.929 47.619 0.00 0.00 0.00 3.49
4092 5394 3.115554 AGACACAATTTTGCTTTCACGC 58.884 40.909 0.00 0.00 0.00 5.34
4094 5396 0.852136 ACAATTTTGCTTTCACGCGC 59.148 45.000 5.73 0.00 0.00 6.86
4095 5397 0.851495 CAATTTTGCTTTCACGCGCA 59.149 45.000 5.73 0.00 0.00 6.09
4096 5398 1.257415 CAATTTTGCTTTCACGCGCAA 59.743 42.857 5.73 0.00 43.68 4.85
4098 5400 1.142778 TTTTGCTTTCACGCGCAACC 61.143 50.000 5.73 0.00 44.88 3.77
4100 5402 4.700365 GCTTTCACGCGCAACCCC 62.700 66.667 5.73 0.00 0.00 4.95
4101 5403 2.978010 CTTTCACGCGCAACCCCT 60.978 61.111 5.73 0.00 0.00 4.79
4103 5405 2.458006 CTTTCACGCGCAACCCCTTC 62.458 60.000 5.73 0.00 0.00 3.46
4106 5408 4.922026 ACGCGCAACCCCTTCGTT 62.922 61.111 5.73 0.00 0.00 3.85
4107 5409 4.383602 CGCGCAACCCCTTCGTTG 62.384 66.667 8.75 0.00 44.87 4.10
4108 5410 4.038080 GCGCAACCCCTTCGTTGG 62.038 66.667 0.30 0.00 42.78 3.77
4109 5411 4.038080 CGCAACCCCTTCGTTGGC 62.038 66.667 3.85 0.00 42.78 4.52
4110 5412 4.038080 GCAACCCCTTCGTTGGCG 62.038 66.667 3.85 0.00 42.78 5.69
4111 5413 2.593436 CAACCCCTTCGTTGGCGT 60.593 61.111 0.00 0.00 39.58 5.68
4126 5441 2.476051 CGTGCCGTGCATCAGAAC 59.524 61.111 1.90 0.00 41.91 3.01
4131 5446 1.868997 CCGTGCATCAGAACACACC 59.131 57.895 0.00 0.00 36.57 4.16
4133 5448 1.159285 CGTGCATCAGAACACACCAT 58.841 50.000 0.00 0.00 36.57 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 6.817765 TTCAGCAACAGGGTCTAATTTTAG 57.182 37.500 0.00 0.00 0.00 1.85
4 5 6.478512 TTTTCAGCAACAGGGTCTAATTTT 57.521 33.333 0.00 0.00 0.00 1.82
5 6 6.478512 TTTTTCAGCAACAGGGTCTAATTT 57.521 33.333 0.00 0.00 0.00 1.82
26 27 5.592104 AAAGATTCGGTGGTGAAGTTTTT 57.408 34.783 0.00 0.00 0.00 1.94
27 28 6.894339 ATAAAGATTCGGTGGTGAAGTTTT 57.106 33.333 0.00 0.00 0.00 2.43
28 29 6.894339 AATAAAGATTCGGTGGTGAAGTTT 57.106 33.333 0.00 0.00 0.00 2.66
29 30 6.894339 AAATAAAGATTCGGTGGTGAAGTT 57.106 33.333 0.00 0.00 0.00 2.66
30 31 8.575649 AATAAATAAAGATTCGGTGGTGAAGT 57.424 30.769 0.00 0.00 0.00 3.01
55 56 9.342308 ACAACAGAGATCTTGTTTCAGAAATAA 57.658 29.630 15.99 1.76 0.00 1.40
56 57 8.908786 ACAACAGAGATCTTGTTTCAGAAATA 57.091 30.769 15.99 0.00 0.00 1.40
57 58 7.814264 ACAACAGAGATCTTGTTTCAGAAAT 57.186 32.000 15.99 0.00 0.00 2.17
58 59 8.204160 TCTACAACAGAGATCTTGTTTCAGAAA 58.796 33.333 15.99 0.00 32.77 2.52
59 60 7.726216 TCTACAACAGAGATCTTGTTTCAGAA 58.274 34.615 15.99 7.65 32.77 3.02
60 61 7.290110 TCTACAACAGAGATCTTGTTTCAGA 57.710 36.000 15.99 16.41 32.77 3.27
61 62 7.953158 TTCTACAACAGAGATCTTGTTTCAG 57.047 36.000 15.99 15.10 33.83 3.02
62 63 7.226720 GGTTTCTACAACAGAGATCTTGTTTCA 59.773 37.037 15.99 9.15 33.83 2.69
63 64 7.442666 AGGTTTCTACAACAGAGATCTTGTTTC 59.557 37.037 15.99 0.00 33.83 2.78
64 65 7.283329 AGGTTTCTACAACAGAGATCTTGTTT 58.717 34.615 15.99 11.86 33.83 2.83
65 66 6.831976 AGGTTTCTACAACAGAGATCTTGTT 58.168 36.000 13.96 13.96 33.83 2.83
66 67 6.426646 AGGTTTCTACAACAGAGATCTTGT 57.573 37.500 0.00 0.00 33.83 3.16
67 68 7.158021 AGAAGGTTTCTACAACAGAGATCTTG 58.842 38.462 0.00 0.00 38.59 3.02
68 69 7.309770 AGAAGGTTTCTACAACAGAGATCTT 57.690 36.000 0.00 0.00 40.60 2.40
69 70 6.926630 AGAAGGTTTCTACAACAGAGATCT 57.073 37.500 0.00 0.00 38.49 2.75
70 71 9.490379 TTTTAGAAGGTTTCTACAACAGAGATC 57.510 33.333 0.00 0.00 41.70 2.75
71 72 9.847224 TTTTTAGAAGGTTTCTACAACAGAGAT 57.153 29.630 0.00 0.00 41.70 2.75
72 73 9.106070 GTTTTTAGAAGGTTTCTACAACAGAGA 57.894 33.333 11.60 0.00 41.70 3.10
73 74 8.889717 TGTTTTTAGAAGGTTTCTACAACAGAG 58.110 33.333 13.61 0.00 41.70 3.35
74 75 8.795842 TGTTTTTAGAAGGTTTCTACAACAGA 57.204 30.769 13.61 0.00 41.70 3.41
79 80 9.545105 TCGTATTGTTTTTAGAAGGTTTCTACA 57.455 29.630 0.00 0.00 41.70 2.74
82 83 9.893305 CAATCGTATTGTTTTTAGAAGGTTTCT 57.107 29.630 0.00 0.00 43.72 2.52
83 84 9.673454 ACAATCGTATTGTTTTTAGAAGGTTTC 57.327 29.630 7.22 0.00 0.00 2.78
85 86 9.458374 CAACAATCGTATTGTTTTTAGAAGGTT 57.542 29.630 17.62 0.00 40.30 3.50
86 87 7.593644 GCAACAATCGTATTGTTTTTAGAAGGT 59.406 33.333 17.62 0.00 40.30 3.50
87 88 7.593273 TGCAACAATCGTATTGTTTTTAGAAGG 59.407 33.333 17.62 9.33 40.30 3.46
88 89 8.500837 TGCAACAATCGTATTGTTTTTAGAAG 57.499 30.769 17.62 9.81 40.30 2.85
89 90 8.858003 TTGCAACAATCGTATTGTTTTTAGAA 57.142 26.923 17.62 4.98 40.30 2.10
90 91 8.858003 TTTGCAACAATCGTATTGTTTTTAGA 57.142 26.923 17.62 6.37 40.30 2.10
91 92 9.907576 TTTTTGCAACAATCGTATTGTTTTTAG 57.092 25.926 17.62 11.01 40.30 1.85
115 116 3.518634 AGTCGTGTGCAACCAATTTTT 57.481 38.095 0.00 0.00 34.36 1.94
116 117 3.186119 CAAGTCGTGTGCAACCAATTTT 58.814 40.909 0.00 0.00 34.36 1.82
117 118 2.165437 ACAAGTCGTGTGCAACCAATTT 59.835 40.909 0.00 0.00 39.72 1.82
118 119 1.748493 ACAAGTCGTGTGCAACCAATT 59.252 42.857 0.00 0.00 39.72 2.32
119 120 1.388547 ACAAGTCGTGTGCAACCAAT 58.611 45.000 0.00 0.00 39.72 3.16
120 121 2.861364 ACAAGTCGTGTGCAACCAA 58.139 47.368 0.00 0.00 39.72 3.67
121 122 4.627788 ACAAGTCGTGTGCAACCA 57.372 50.000 0.00 0.00 39.72 3.67
128 129 2.279918 GACGGCCACAAGTCGTGT 60.280 61.111 2.24 0.00 44.78 4.49
129 130 3.041940 GGACGGCCACAAGTCGTG 61.042 66.667 0.00 0.00 45.92 4.35
130 131 3.096633 TTGGACGGCCACAAGTCGT 62.097 57.895 11.33 0.00 45.94 4.34
131 132 2.280524 TTGGACGGCCACAAGTCG 60.281 61.111 11.33 0.00 45.94 4.18
132 133 2.604174 CGTTGGACGGCCACAAGTC 61.604 63.158 11.33 1.00 45.94 3.01
133 134 2.590575 CGTTGGACGGCCACAAGT 60.591 61.111 11.33 0.00 45.94 3.16
143 144 0.801067 ATCGAGCGCTTACGTTGGAC 60.801 55.000 13.26 0.00 39.76 4.02
144 145 0.524816 GATCGAGCGCTTACGTTGGA 60.525 55.000 13.26 0.00 41.03 3.53
145 146 0.800683 TGATCGAGCGCTTACGTTGG 60.801 55.000 13.26 0.00 42.83 3.77
146 147 0.989164 TTGATCGAGCGCTTACGTTG 59.011 50.000 13.26 0.00 42.83 4.10
147 148 1.135489 TCTTGATCGAGCGCTTACGTT 60.135 47.619 13.26 6.57 42.83 3.99
148 149 0.450583 TCTTGATCGAGCGCTTACGT 59.549 50.000 13.26 2.18 42.83 3.57
149 150 1.759994 ATCTTGATCGAGCGCTTACG 58.240 50.000 13.26 12.47 44.07 3.18
150 151 3.116300 TCAATCTTGATCGAGCGCTTAC 58.884 45.455 13.26 0.00 31.01 2.34
151 152 3.436700 TCAATCTTGATCGAGCGCTTA 57.563 42.857 13.26 2.98 31.01 3.09
152 153 2.299993 TCAATCTTGATCGAGCGCTT 57.700 45.000 13.26 0.00 31.01 4.68
153 154 2.522836 ATCAATCTTGATCGAGCGCT 57.477 45.000 11.27 11.27 44.17 5.92
162 163 3.552890 CGTAGCCATCGGATCAATCTTGA 60.553 47.826 0.00 0.00 42.14 3.02
163 164 2.733552 CGTAGCCATCGGATCAATCTTG 59.266 50.000 0.00 0.00 0.00 3.02
164 165 3.032017 CGTAGCCATCGGATCAATCTT 57.968 47.619 0.00 0.00 0.00 2.40
165 166 2.732412 CGTAGCCATCGGATCAATCT 57.268 50.000 0.00 0.00 0.00 2.40
203 204 2.822418 TTACACCCGACGGATGCACG 62.822 60.000 17.49 0.00 40.31 5.34
204 205 1.079681 TTACACCCGACGGATGCAC 60.080 57.895 17.49 0.00 0.00 4.57
205 206 1.216977 CTTACACCCGACGGATGCA 59.783 57.895 17.49 0.00 0.00 3.96
206 207 0.104304 ATCTTACACCCGACGGATGC 59.896 55.000 17.49 0.00 0.00 3.91
207 208 2.607282 GCTATCTTACACCCGACGGATG 60.607 54.545 17.49 12.23 0.00 3.51
208 209 1.612463 GCTATCTTACACCCGACGGAT 59.388 52.381 17.49 0.00 0.00 4.18
209 210 1.027357 GCTATCTTACACCCGACGGA 58.973 55.000 17.49 0.00 0.00 4.69
210 211 0.317603 CGCTATCTTACACCCGACGG 60.318 60.000 6.99 6.99 0.00 4.79
211 212 0.379669 ACGCTATCTTACACCCGACG 59.620 55.000 0.00 0.00 0.00 5.12
212 213 2.573941 AACGCTATCTTACACCCGAC 57.426 50.000 0.00 0.00 0.00 4.79
213 214 3.514645 GAAAACGCTATCTTACACCCGA 58.485 45.455 0.00 0.00 0.00 5.14
214 215 2.606272 GGAAAACGCTATCTTACACCCG 59.394 50.000 0.00 0.00 0.00 5.28
215 216 3.870274 AGGAAAACGCTATCTTACACCC 58.130 45.455 0.00 0.00 0.00 4.61
216 217 6.335777 TCTTAGGAAAACGCTATCTTACACC 58.664 40.000 0.00 0.00 0.00 4.16
217 218 7.823149 TTCTTAGGAAAACGCTATCTTACAC 57.177 36.000 0.00 0.00 0.00 2.90
221 222 9.057089 CCAATATTCTTAGGAAAACGCTATCTT 57.943 33.333 0.00 0.00 34.90 2.40
222 223 8.429641 TCCAATATTCTTAGGAAAACGCTATCT 58.570 33.333 0.00 0.00 34.90 1.98
223 224 8.603242 TCCAATATTCTTAGGAAAACGCTATC 57.397 34.615 0.00 0.00 34.90 2.08
224 225 8.974060 TTCCAATATTCTTAGGAAAACGCTAT 57.026 30.769 3.17 0.00 37.22 2.97
225 226 8.836413 CATTCCAATATTCTTAGGAAAACGCTA 58.164 33.333 8.57 0.00 42.83 4.26
226 227 7.682021 GCATTCCAATATTCTTAGGAAAACGCT 60.682 37.037 8.57 0.00 42.83 5.07
227 228 6.417930 GCATTCCAATATTCTTAGGAAAACGC 59.582 38.462 8.57 8.24 42.83 4.84
228 229 7.479980 TGCATTCCAATATTCTTAGGAAAACG 58.520 34.615 8.57 3.52 42.83 3.60
229 230 9.651913 TTTGCATTCCAATATTCTTAGGAAAAC 57.348 29.630 8.57 5.49 42.83 2.43
288 289 6.265422 GCTTGGTAGCTAATCAACCCAATATT 59.735 38.462 10.66 0.00 44.27 1.28
291 292 3.954258 GCTTGGTAGCTAATCAACCCAAT 59.046 43.478 10.66 0.00 44.27 3.16
293 294 2.999331 GCTTGGTAGCTAATCAACCCA 58.001 47.619 0.00 0.00 44.27 4.51
339 340 9.006839 AGTCAATACGAATAGATACCGTGAATA 57.993 33.333 0.00 0.00 37.69 1.75
435 456 2.415857 GTGCTGCAGAAGATCAAGTCAG 59.584 50.000 20.43 0.00 0.00 3.51
436 457 2.038164 AGTGCTGCAGAAGATCAAGTCA 59.962 45.455 20.43 0.00 0.00 3.41
451 472 1.528586 CGGAAAGACTTGACAGTGCTG 59.471 52.381 0.00 0.00 31.22 4.41
456 477 5.802956 GTCTAGAATCGGAAAGACTTGACAG 59.197 44.000 0.00 0.00 36.32 3.51
511 532 4.533815 TCTAGAGAATGAACTTCCGGCTA 58.466 43.478 0.00 0.00 34.11 3.93
514 535 4.116238 GCTTCTAGAGAATGAACTTCCGG 58.884 47.826 0.00 0.00 34.11 5.14
518 539 7.121463 TCTCGTAAGCTTCTAGAGAATGAACTT 59.879 37.037 19.60 0.00 35.34 2.66
524 545 5.238650 GCTCTCTCGTAAGCTTCTAGAGAAT 59.761 44.000 24.30 0.00 41.46 2.40
528 549 3.875125 TGCTCTCTCGTAAGCTTCTAGA 58.125 45.455 0.00 3.64 39.31 2.43
539 560 0.759346 ACCCTGTTTTGCTCTCTCGT 59.241 50.000 0.00 0.00 0.00 4.18
540 561 2.611518 CTACCCTGTTTTGCTCTCTCG 58.388 52.381 0.00 0.00 0.00 4.04
543 564 2.079925 CTGCTACCCTGTTTTGCTCTC 58.920 52.381 0.00 0.00 0.00 3.20
553 576 1.755179 CCCAACAATCTGCTACCCTG 58.245 55.000 0.00 0.00 0.00 4.45
584 607 1.672356 AAGCCACACAGCGGTCATC 60.672 57.895 0.00 0.00 38.01 2.92
589 612 3.357079 GACCAAGCCACACAGCGG 61.357 66.667 0.00 0.00 38.01 5.52
591 614 0.819259 TCTTGACCAAGCCACACAGC 60.819 55.000 4.94 0.00 38.28 4.40
592 615 1.808945 GATCTTGACCAAGCCACACAG 59.191 52.381 4.94 0.00 38.28 3.66
623 649 6.529220 ACAATCCAGAGATAGTAATTGCTCC 58.471 40.000 0.00 0.00 30.42 4.70
635 661 7.639062 ATTGATAGGGTTACAATCCAGAGAT 57.361 36.000 0.00 0.00 29.89 2.75
636 662 8.742125 ATATTGATAGGGTTACAATCCAGAGA 57.258 34.615 0.00 0.00 36.06 3.10
767 799 1.827344 GGGGGAAATCTTTGGCTCAAG 59.173 52.381 0.00 0.00 0.00 3.02
785 817 1.579429 CTCGAACGCAAAAAGGGGG 59.421 57.895 0.00 0.00 33.80 5.40
786 818 1.081442 GCTCGAACGCAAAAAGGGG 60.081 57.895 0.00 0.00 33.80 4.79
787 819 0.385974 CAGCTCGAACGCAAAAAGGG 60.386 55.000 0.00 0.00 0.00 3.95
811 851 6.263842 TGCTGATTGTTTCAATCTTTGACTCT 59.736 34.615 18.81 0.00 39.87 3.24
832 872 1.299316 CAAAGGCGGTGTGTTGCTG 60.299 57.895 0.00 0.00 0.00 4.41
848 888 2.121291 TCCGTGCTTGATAATGCCAA 57.879 45.000 0.00 0.00 0.00 4.52
895 935 6.161381 GGTATGTTTTAGTTGACGGAGAGAA 58.839 40.000 0.00 0.00 0.00 2.87
1066 1119 7.430441 GTGTTGGAAATACAAACTGTGGTAAT 58.570 34.615 0.00 0.00 37.91 1.89
1117 1170 1.666700 TCGGTGGAAACTTGAAACACG 59.333 47.619 0.00 0.00 33.07 4.49
1156 1214 9.534565 CACCCTACATACATATACATCATTAGC 57.465 37.037 0.00 0.00 0.00 3.09
1292 1987 9.533253 CAAGATCAAAACAACATCCTTTAGTTT 57.467 29.630 0.00 0.00 34.19 2.66
1312 2007 4.034975 GCTCAAGCACTGGATAACAAGATC 59.965 45.833 0.00 0.00 41.59 2.75
1347 2296 0.320421 TGCCGCCTTTGTACAGAGAC 60.320 55.000 14.73 2.18 0.00 3.36
1604 2586 6.775939 AATACAGCATATCACAAGATCACG 57.224 37.500 0.00 0.00 35.67 4.35
1620 2602 5.344128 CACATGAGCAACAAGAAAATACAGC 59.656 40.000 0.00 0.00 0.00 4.40
1641 2627 3.772572 AGCCATATATATACGGGCACACA 59.227 43.478 26.95 0.00 46.96 3.72
1642 2628 4.369182 GAGCCATATATATACGGGCACAC 58.631 47.826 26.95 18.21 46.96 3.82
1722 2708 1.278127 GTTGGGATCCTTGAAGACGGA 59.722 52.381 12.58 0.00 0.00 4.69
1868 2854 4.624882 TGGCGTTGAACAATTAATTCATGC 59.375 37.500 14.65 14.65 36.02 4.06
1904 2890 1.235724 GGCCTGTACAAGCGAACTTT 58.764 50.000 10.27 0.00 32.29 2.66
1910 2907 2.173669 CCATCGGCCTGTACAAGCG 61.174 63.158 10.27 6.23 0.00 4.68
1913 2910 0.828022 CCTACCATCGGCCTGTACAA 59.172 55.000 0.00 0.00 0.00 2.41
2772 3781 2.640989 CGGTTGACGTCGACCTCA 59.359 61.111 39.29 12.44 46.16 3.86
2789 3798 4.929707 CGTAGGGGCCGGCATTCC 62.930 72.222 30.85 24.93 0.00 3.01
3121 4130 2.859273 ATAGTGTGCTCCACCGCAGC 62.859 60.000 3.84 0.00 45.74 5.25
3170 4180 4.282068 CTGCTGTGTATTGTGTTTGTGTC 58.718 43.478 0.00 0.00 0.00 3.67
3176 4186 4.389374 ACTAAGCTGCTGTGTATTGTGTT 58.611 39.130 1.35 0.00 0.00 3.32
3278 4288 3.429085 GGACGAGCAAAAGCAATACATG 58.571 45.455 0.00 0.00 0.00 3.21
3279 4289 2.095853 CGGACGAGCAAAAGCAATACAT 59.904 45.455 0.00 0.00 0.00 2.29
3280 4290 1.463056 CGGACGAGCAAAAGCAATACA 59.537 47.619 0.00 0.00 0.00 2.29
3281 4291 1.463444 ACGGACGAGCAAAAGCAATAC 59.537 47.619 0.00 0.00 0.00 1.89
3282 4292 1.730064 GACGGACGAGCAAAAGCAATA 59.270 47.619 0.00 0.00 0.00 1.90
3283 4293 0.517316 GACGGACGAGCAAAAGCAAT 59.483 50.000 0.00 0.00 0.00 3.56
3284 4294 0.812014 TGACGGACGAGCAAAAGCAA 60.812 50.000 0.00 0.00 0.00 3.91
3285 4295 0.602638 ATGACGGACGAGCAAAAGCA 60.603 50.000 0.00 0.00 0.00 3.91
3286 4296 1.355971 TATGACGGACGAGCAAAAGC 58.644 50.000 0.00 0.00 0.00 3.51
3287 4297 3.250744 TCTTATGACGGACGAGCAAAAG 58.749 45.455 0.00 0.00 0.00 2.27
3288 4298 3.306917 TCTTATGACGGACGAGCAAAA 57.693 42.857 0.00 0.00 0.00 2.44
3289 4299 3.520290 ATCTTATGACGGACGAGCAAA 57.480 42.857 0.00 0.00 0.00 3.68
3290 4300 3.520290 AATCTTATGACGGACGAGCAA 57.480 42.857 0.00 0.00 0.00 3.91
3291 4301 3.243301 GGTAATCTTATGACGGACGAGCA 60.243 47.826 0.00 0.00 0.00 4.26
3292 4302 3.306818 GGTAATCTTATGACGGACGAGC 58.693 50.000 0.00 0.00 0.00 5.03
3293 4303 3.317149 TGGGTAATCTTATGACGGACGAG 59.683 47.826 0.00 0.00 0.00 4.18
3294 4304 3.289836 TGGGTAATCTTATGACGGACGA 58.710 45.455 0.00 0.00 0.00 4.20
3295 4305 3.720949 TGGGTAATCTTATGACGGACG 57.279 47.619 0.00 0.00 0.00 4.79
3296 4306 5.209818 TCATGGGTAATCTTATGACGGAC 57.790 43.478 0.00 0.00 0.00 4.79
3297 4307 4.283467 CCTCATGGGTAATCTTATGACGGA 59.717 45.833 0.00 0.00 0.00 4.69
3298 4308 4.569943 CCTCATGGGTAATCTTATGACGG 58.430 47.826 0.00 0.00 0.00 4.79
3312 4322 1.066143 AGTGCTCGTTAACCTCATGGG 60.066 52.381 0.00 0.00 41.89 4.00
3313 4323 2.271800 GAGTGCTCGTTAACCTCATGG 58.728 52.381 0.00 0.00 39.83 3.66
3314 4324 2.093973 AGGAGTGCTCGTTAACCTCATG 60.094 50.000 0.00 0.00 0.00 3.07
3315 4325 2.180276 AGGAGTGCTCGTTAACCTCAT 58.820 47.619 0.00 0.00 0.00 2.90
3316 4326 1.629043 AGGAGTGCTCGTTAACCTCA 58.371 50.000 0.00 0.00 0.00 3.86
3317 4327 2.608268 GAAGGAGTGCTCGTTAACCTC 58.392 52.381 7.06 0.30 37.75 3.85
3318 4328 1.067776 CGAAGGAGTGCTCGTTAACCT 60.068 52.381 7.06 0.00 37.75 3.50
3319 4329 1.347320 CGAAGGAGTGCTCGTTAACC 58.653 55.000 7.06 0.00 37.75 2.85
3363 4373 2.738521 GGCTGAGAGCGCGTCAAA 60.739 61.111 15.16 0.00 43.62 2.69
3367 4377 2.510238 GAATGGCTGAGAGCGCGT 60.510 61.111 8.43 0.00 43.62 6.01
3410 4420 5.062183 GCAGAAATAAAACAAAATCCGGAGC 59.938 40.000 11.34 0.00 0.00 4.70
3422 4436 4.143618 CGAAAAGGCGTGCAGAAATAAAAC 60.144 41.667 0.00 0.00 0.00 2.43
3427 4447 0.240945 CCGAAAAGGCGTGCAGAAAT 59.759 50.000 0.00 0.00 0.00 2.17
3439 4459 3.708890 ACCCGTTTAAAAAGCCGAAAAG 58.291 40.909 0.00 0.00 0.00 2.27
3472 4502 3.077359 AGAAGACCAGCGAAAAATCAGG 58.923 45.455 0.00 0.00 0.00 3.86
3476 4506 7.454260 AATCTAAAGAAGACCAGCGAAAAAT 57.546 32.000 0.00 0.00 36.93 1.82
3548 4613 0.234884 GAAAGCCAAACCGTGACTCG 59.765 55.000 0.00 0.00 39.52 4.18
3647 4721 0.540365 ACCCGTACCTCTCGTGGAAA 60.540 55.000 0.00 0.00 0.00 3.13
3824 5110 7.277760 CGTGAAAGGAAAGGAAAAACAGAAAAT 59.722 33.333 0.00 0.00 0.00 1.82
3837 5123 3.060602 GTGACTCTCGTGAAAGGAAAGG 58.939 50.000 0.00 0.00 0.00 3.11
3838 5124 2.726760 CGTGACTCTCGTGAAAGGAAAG 59.273 50.000 0.00 0.00 0.00 2.62
3848 5134 0.878961 GGCAAAACCGTGACTCTCGT 60.879 55.000 0.24 0.00 0.00 4.18
3867 5153 4.598894 CCCATGCCTCTCGCGGAG 62.599 72.222 6.13 11.96 42.08 4.63
3999 5288 1.608283 GGCCGTGACTCTTGCTAAAGT 60.608 52.381 0.00 0.00 34.78 2.66
4004 5293 3.616721 ACGGCCGTGACTCTTGCT 61.617 61.111 33.75 0.00 0.00 3.91
4042 5336 6.915843 GCGAAAGGAAAGAAACAGAAAACATA 59.084 34.615 0.00 0.00 0.00 2.29
4056 5355 2.872245 TGTGTCTCTTGCGAAAGGAAAG 59.128 45.455 2.54 0.00 42.23 2.62
4073 5375 1.851666 CGCGTGAAAGCAAAATTGTGT 59.148 42.857 0.00 0.00 36.85 3.72
4092 5394 4.038080 GCCAACGAAGGGGTTGCG 62.038 66.667 0.00 0.00 44.58 4.85
4110 5412 1.207593 GTGTTCTGATGCACGGCAC 59.792 57.895 0.50 0.00 43.04 5.01
4111 5413 1.227793 TGTGTTCTGATGCACGGCA 60.228 52.632 0.00 1.01 44.86 5.69


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

AutoCloner maintained by Alex Coulton.