Multiple sequence alignment - TraesCS7A01G023200

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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 TraesCS7A01G023200 chr7A 100.000 2858 0 0 1 2858 9264515 9261658 0.000000e+00 5278
1 TraesCS7A01G023200 chr7D 90.043 1627 116 26 236 1851 9051322 9052913 0.000000e+00 2065
2 TraesCS7A01G023200 chr7D 93.676 1012 61 2 910 1920 9864192 9863183 0.000000e+00 1511
3 TraesCS7A01G023200 chr7D 91.659 1043 78 2 1082 2115 9390926 9389884 0.000000e+00 1435
4 TraesCS7A01G023200 chr7D 89.530 936 53 20 174 1084 9393975 9393060 0.000000e+00 1144
5 TraesCS7A01G023200 chr7D 85.501 738 48 27 179 873 9864910 9864189 0.000000e+00 715
6 TraesCS7A01G023200 chr7D 88.104 269 23 2 1856 2115 9053715 9053983 7.690000e-81 311
7 TraesCS7A01G023200 chr7D 90.728 151 13 1 1 150 9045212 9045362 1.740000e-47 200
8 TraesCS7A01G023200 chr7D 75.150 334 56 20 2356 2687 575576533 575576225 6.430000e-27 132
9 TraesCS7A01G023200 chr1A 80.167 958 167 14 916 1854 76538564 76537611 0.000000e+00 695
10 TraesCS7A01G023200 chr1A 79.634 383 72 6 424 803 76728793 76729172 1.300000e-68 270
11 TraesCS7A01G023200 chr1D 79.620 947 173 15 927 1854 75767164 75766219 0.000000e+00 662
12 TraesCS7A01G023200 chr1D 80.952 378 66 6 430 803 75841439 75841064 7.740000e-76 294
13 TraesCS7A01G023200 chr1D 80.585 376 69 4 430 803 75767657 75767284 1.300000e-73 287
14 TraesCS7A01G023200 chr1D 79.634 383 72 6 424 803 75915241 75915620 1.300000e-68 270
15 TraesCS7A01G023200 chr1B 79.514 947 174 12 927 1854 119493984 119493039 0.000000e+00 656
16 TraesCS7A01G023200 chr1B 79.343 944 175 15 927 1851 119579529 119580471 0.000000e+00 645
17 TraesCS7A01G023200 chr1B 78.564 947 183 14 927 1854 119219507 119218562 8.760000e-170 606
18 TraesCS7A01G023200 chr1B 82.440 672 116 2 929 1599 119249380 119248710 1.140000e-163 586
19 TraesCS7A01G023200 chr1B 79.634 383 72 6 424 803 119579007 119579386 1.300000e-68 270
20 TraesCS7A01G023200 chr3B 75.393 764 108 42 2114 2858 787575022 787575724 2.150000e-76 296
21 TraesCS7A01G023200 chr3B 80.690 290 46 9 2570 2858 829559384 829559104 1.720000e-52 217
22 TraesCS7A01G023200 chr5D 76.908 524 78 31 2326 2832 2327705 2328202 1.020000e-64 257
23 TraesCS7A01G023200 chr5A 74.586 665 113 27 2195 2849 1331997 1332615 1.020000e-59 241
24 TraesCS7A01G023200 chr5A 76.549 452 73 24 2117 2553 684515420 684514987 1.720000e-52 217
25 TraesCS7A01G023200 chr7B 76.854 445 60 26 2117 2543 20044897 20044478 8.020000e-51 211
26 TraesCS7A01G023200 chr7B 77.114 402 61 16 2166 2543 632264000 632264394 1.340000e-48 204
27 TraesCS7A01G023200 chr7B 84.409 186 23 6 2371 2552 371450247 371450430 8.140000e-41 178
28 TraesCS7A01G023200 chr7B 82.796 186 29 3 2371 2553 357968058 357968243 2.280000e-36 163
29 TraesCS7A01G023200 chr7B 82.486 177 26 4 2371 2545 25583211 25583038 1.770000e-32 150
30 TraesCS7A01G023200 chr2A 79.452 219 29 12 2371 2581 90034912 90035122 1.070000e-29 141
31 TraesCS7A01G023200 chr3A 81.657 169 24 6 2390 2553 698278916 698278750 1.790000e-27 134


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 TraesCS7A01G023200 chr7A 9261658 9264515 2857 True 5278.0 5278 100.0000 1 2858 1 chr7A.!!$R1 2857
1 TraesCS7A01G023200 chr7D 9389884 9393975 4091 True 1289.5 1435 90.5945 174 2115 2 chr7D.!!$R2 1941
2 TraesCS7A01G023200 chr7D 9051322 9053983 2661 False 1188.0 2065 89.0735 236 2115 2 chr7D.!!$F2 1879
3 TraesCS7A01G023200 chr7D 9863183 9864910 1727 True 1113.0 1511 89.5885 179 1920 2 chr7D.!!$R3 1741
4 TraesCS7A01G023200 chr1A 76537611 76538564 953 True 695.0 695 80.1670 916 1854 1 chr1A.!!$R1 938
5 TraesCS7A01G023200 chr1D 75766219 75767657 1438 True 474.5 662 80.1025 430 1854 2 chr1D.!!$R2 1424
6 TraesCS7A01G023200 chr1B 119493039 119493984 945 True 656.0 656 79.5140 927 1854 1 chr1B.!!$R3 927
7 TraesCS7A01G023200 chr1B 119218562 119219507 945 True 606.0 606 78.5640 927 1854 1 chr1B.!!$R1 927
8 TraesCS7A01G023200 chr1B 119248710 119249380 670 True 586.0 586 82.4400 929 1599 1 chr1B.!!$R2 670
9 TraesCS7A01G023200 chr1B 119579007 119580471 1464 False 457.5 645 79.4885 424 1851 2 chr1B.!!$F1 1427
10 TraesCS7A01G023200 chr3B 787575022 787575724 702 False 296.0 296 75.3930 2114 2858 1 chr3B.!!$F1 744
11 TraesCS7A01G023200 chr5A 1331997 1332615 618 False 241.0 241 74.5860 2195 2849 1 chr5A.!!$F1 654

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
35 36 0.102844 GCCGCACATGCAATATTGGT 59.897 50.0 17.02 3.96 42.21 3.67 F
1183 3435 0.036732 AAGCATCGAGTTCAAGGGCA 59.963 50.0 0.00 0.00 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1293 3545 0.534877 ACTGGAACGTGCTGCATGAA 60.535 50.0 27.26 9.42 0.00 2.57 R
2007 5085 0.735978 CAGACGTACTTGCGCCATCA 60.736 55.0 4.18 0.00 34.88 3.07 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
17 18 2.337532 CAAAGTGGCCAGCACAGC 59.662 61.111 5.11 0.00 0.00 4.40
25 26 4.111016 CCAGCACAGCCGCACATG 62.111 66.667 0.00 0.00 0.00 3.21
26 27 4.771356 CAGCACAGCCGCACATGC 62.771 66.667 5.61 5.61 38.39 4.06
28 29 4.345962 GCACAGCCGCACATGCAA 62.346 61.111 4.49 0.00 42.21 4.08
29 30 2.569657 CACAGCCGCACATGCAAT 59.430 55.556 4.49 0.00 42.21 3.56
30 31 1.801983 CACAGCCGCACATGCAATA 59.198 52.632 4.49 0.00 42.21 1.90
31 32 0.382873 CACAGCCGCACATGCAATAT 59.617 50.000 4.49 0.00 42.21 1.28
32 33 1.105457 ACAGCCGCACATGCAATATT 58.895 45.000 4.49 0.00 42.21 1.28
33 34 1.202325 ACAGCCGCACATGCAATATTG 60.202 47.619 11.27 11.27 42.21 1.90
34 35 0.386476 AGCCGCACATGCAATATTGG 59.614 50.000 17.02 3.33 42.21 3.16
35 36 0.102844 GCCGCACATGCAATATTGGT 59.897 50.000 17.02 3.96 42.21 3.67
36 37 1.336440 GCCGCACATGCAATATTGGTA 59.664 47.619 17.02 0.00 42.21 3.25
37 38 2.223688 GCCGCACATGCAATATTGGTAA 60.224 45.455 17.02 0.00 42.21 2.85
38 39 3.552684 GCCGCACATGCAATATTGGTAAT 60.553 43.478 17.02 0.00 42.21 1.89
39 40 4.619973 CCGCACATGCAATATTGGTAATT 58.380 39.130 17.02 0.00 42.21 1.40
40 41 5.049167 CCGCACATGCAATATTGGTAATTT 58.951 37.500 17.02 0.00 42.21 1.82
41 42 5.175491 CCGCACATGCAATATTGGTAATTTC 59.825 40.000 17.02 0.00 42.21 2.17
42 43 5.747675 CGCACATGCAATATTGGTAATTTCA 59.252 36.000 17.02 5.02 42.21 2.69
43 44 6.421501 CGCACATGCAATATTGGTAATTTCAT 59.578 34.615 17.02 7.04 42.21 2.57
44 45 7.567952 CGCACATGCAATATTGGTAATTTCATG 60.568 37.037 17.02 18.66 41.09 3.07
45 46 7.438757 GCACATGCAATATTGGTAATTTCATGA 59.561 33.333 24.47 0.00 39.08 3.07
46 47 8.974408 CACATGCAATATTGGTAATTTCATGAG 58.026 33.333 24.47 17.59 39.08 2.90
47 48 8.145767 ACATGCAATATTGGTAATTTCATGAGG 58.854 33.333 24.47 9.10 39.08 3.86
48 49 7.894753 TGCAATATTGGTAATTTCATGAGGA 57.105 32.000 17.02 0.00 0.00 3.71
49 50 8.303780 TGCAATATTGGTAATTTCATGAGGAA 57.696 30.769 17.02 0.00 0.00 3.36
67 68 9.398170 CATGAGGAAATAAAATATTTGCTACCG 57.602 33.333 14.29 5.10 39.28 4.02
68 69 8.514330 TGAGGAAATAAAATATTTGCTACCGT 57.486 30.769 14.29 0.00 39.28 4.83
69 70 9.616156 TGAGGAAATAAAATATTTGCTACCGTA 57.384 29.630 14.29 0.00 39.28 4.02
70 71 9.874215 GAGGAAATAAAATATTTGCTACCGTAC 57.126 33.333 14.29 1.60 39.28 3.67
71 72 9.623000 AGGAAATAAAATATTTGCTACCGTACT 57.377 29.630 13.13 0.00 37.80 2.73
77 78 7.724305 AAATATTTGCTACCGTACTACATGG 57.276 36.000 0.00 0.00 39.49 3.66
78 79 6.659745 ATATTTGCTACCGTACTACATGGA 57.340 37.500 0.00 0.00 36.71 3.41
79 80 4.804868 TTTGCTACCGTACTACATGGAA 57.195 40.909 0.00 0.00 36.71 3.53
80 81 5.347620 TTTGCTACCGTACTACATGGAAT 57.652 39.130 0.00 0.00 36.71 3.01
81 82 6.468333 TTTGCTACCGTACTACATGGAATA 57.532 37.500 0.00 0.00 36.71 1.75
82 83 6.468333 TTGCTACCGTACTACATGGAATAA 57.532 37.500 0.00 0.00 36.71 1.40
83 84 6.659745 TGCTACCGTACTACATGGAATAAT 57.340 37.500 0.00 0.00 36.71 1.28
84 85 7.764141 TGCTACCGTACTACATGGAATAATA 57.236 36.000 0.00 0.00 36.71 0.98
85 86 8.357290 TGCTACCGTACTACATGGAATAATAT 57.643 34.615 0.00 0.00 36.71 1.28
86 87 8.248253 TGCTACCGTACTACATGGAATAATATG 58.752 37.037 0.00 0.00 36.71 1.78
87 88 7.705325 GCTACCGTACTACATGGAATAATATGG 59.295 40.741 0.00 0.00 36.71 2.74
88 89 7.549147 ACCGTACTACATGGAATAATATGGT 57.451 36.000 0.00 0.00 36.71 3.55
89 90 8.654485 ACCGTACTACATGGAATAATATGGTA 57.346 34.615 0.00 0.00 36.71 3.25
90 91 8.526147 ACCGTACTACATGGAATAATATGGTAC 58.474 37.037 0.00 0.00 36.71 3.34
91 92 8.746530 CCGTACTACATGGAATAATATGGTACT 58.253 37.037 0.00 0.00 34.93 2.73
106 107 4.665833 TGGTACTTTATCTGGATGGTCG 57.334 45.455 0.00 0.00 0.00 4.79
107 108 3.386726 TGGTACTTTATCTGGATGGTCGG 59.613 47.826 0.00 0.00 0.00 4.79
108 109 3.387050 GGTACTTTATCTGGATGGTCGGT 59.613 47.826 0.00 0.00 0.00 4.69
109 110 4.586001 GGTACTTTATCTGGATGGTCGGTA 59.414 45.833 0.00 0.00 0.00 4.02
110 111 5.245526 GGTACTTTATCTGGATGGTCGGTAT 59.754 44.000 0.00 0.00 0.00 2.73
111 112 5.888982 ACTTTATCTGGATGGTCGGTATT 57.111 39.130 0.00 0.00 0.00 1.89
112 113 6.248569 ACTTTATCTGGATGGTCGGTATTT 57.751 37.500 0.00 0.00 0.00 1.40
113 114 6.659824 ACTTTATCTGGATGGTCGGTATTTT 58.340 36.000 0.00 0.00 0.00 1.82
114 115 6.766467 ACTTTATCTGGATGGTCGGTATTTTC 59.234 38.462 0.00 0.00 0.00 2.29
115 116 6.494666 TTATCTGGATGGTCGGTATTTTCT 57.505 37.500 0.00 0.00 0.00 2.52
116 117 4.137116 TCTGGATGGTCGGTATTTTCTG 57.863 45.455 0.00 0.00 0.00 3.02
117 118 3.772572 TCTGGATGGTCGGTATTTTCTGA 59.227 43.478 0.00 0.00 0.00 3.27
118 119 4.408921 TCTGGATGGTCGGTATTTTCTGAT 59.591 41.667 0.00 0.00 0.00 2.90
119 120 5.104527 TCTGGATGGTCGGTATTTTCTGATT 60.105 40.000 0.00 0.00 0.00 2.57
120 121 6.099125 TCTGGATGGTCGGTATTTTCTGATTA 59.901 38.462 0.00 0.00 0.00 1.75
121 122 6.837312 TGGATGGTCGGTATTTTCTGATTAT 58.163 36.000 0.00 0.00 0.00 1.28
122 123 7.287061 TGGATGGTCGGTATTTTCTGATTATT 58.713 34.615 0.00 0.00 0.00 1.40
123 124 7.228507 TGGATGGTCGGTATTTTCTGATTATTG 59.771 37.037 0.00 0.00 0.00 1.90
124 125 7.228706 GGATGGTCGGTATTTTCTGATTATTGT 59.771 37.037 0.00 0.00 0.00 2.71
125 126 7.315247 TGGTCGGTATTTTCTGATTATTGTG 57.685 36.000 0.00 0.00 0.00 3.33
126 127 6.317642 TGGTCGGTATTTTCTGATTATTGTGG 59.682 38.462 0.00 0.00 0.00 4.17
127 128 6.540914 GGTCGGTATTTTCTGATTATTGTGGA 59.459 38.462 0.00 0.00 0.00 4.02
128 129 7.066525 GGTCGGTATTTTCTGATTATTGTGGAA 59.933 37.037 0.00 0.00 0.00 3.53
129 130 8.621286 GTCGGTATTTTCTGATTATTGTGGAAT 58.379 33.333 0.00 0.00 0.00 3.01
130 131 9.184523 TCGGTATTTTCTGATTATTGTGGAATT 57.815 29.630 0.00 0.00 0.00 2.17
131 132 9.801873 CGGTATTTTCTGATTATTGTGGAATTT 57.198 29.630 0.00 0.00 0.00 1.82
139 140 9.295825 TCTGATTATTGTGGAATTTTGTAGTGT 57.704 29.630 0.00 0.00 0.00 3.55
147 148 9.877178 TTGTGGAATTTTGTAGTGTATTTGTTT 57.123 25.926 0.00 0.00 0.00 2.83
148 149 9.307121 TGTGGAATTTTGTAGTGTATTTGTTTG 57.693 29.630 0.00 0.00 0.00 2.93
149 150 8.760569 GTGGAATTTTGTAGTGTATTTGTTTGG 58.239 33.333 0.00 0.00 0.00 3.28
150 151 8.696374 TGGAATTTTGTAGTGTATTTGTTTGGA 58.304 29.630 0.00 0.00 0.00 3.53
151 152 8.974408 GGAATTTTGTAGTGTATTTGTTTGGAC 58.026 33.333 0.00 0.00 0.00 4.02
152 153 8.880878 AATTTTGTAGTGTATTTGTTTGGACC 57.119 30.769 0.00 0.00 0.00 4.46
153 154 7.648039 TTTTGTAGTGTATTTGTTTGGACCT 57.352 32.000 0.00 0.00 0.00 3.85
154 155 7.648039 TTTGTAGTGTATTTGTTTGGACCTT 57.352 32.000 0.00 0.00 0.00 3.50
155 156 6.627395 TGTAGTGTATTTGTTTGGACCTTG 57.373 37.500 0.00 0.00 0.00 3.61
156 157 6.358178 TGTAGTGTATTTGTTTGGACCTTGA 58.642 36.000 0.00 0.00 0.00 3.02
157 158 7.001674 TGTAGTGTATTTGTTTGGACCTTGAT 58.998 34.615 0.00 0.00 0.00 2.57
158 159 6.976934 AGTGTATTTGTTTGGACCTTGATT 57.023 33.333 0.00 0.00 0.00 2.57
159 160 6.748132 AGTGTATTTGTTTGGACCTTGATTG 58.252 36.000 0.00 0.00 0.00 2.67
160 161 6.323739 AGTGTATTTGTTTGGACCTTGATTGT 59.676 34.615 0.00 0.00 0.00 2.71
161 162 7.504238 AGTGTATTTGTTTGGACCTTGATTGTA 59.496 33.333 0.00 0.00 0.00 2.41
162 163 7.807907 GTGTATTTGTTTGGACCTTGATTGTAG 59.192 37.037 0.00 0.00 0.00 2.74
163 164 6.976934 ATTTGTTTGGACCTTGATTGTAGT 57.023 33.333 0.00 0.00 0.00 2.73
164 165 6.385649 TTTGTTTGGACCTTGATTGTAGTC 57.614 37.500 0.00 0.00 0.00 2.59
165 166 5.304686 TGTTTGGACCTTGATTGTAGTCT 57.695 39.130 0.00 0.00 0.00 3.24
166 167 5.305585 TGTTTGGACCTTGATTGTAGTCTC 58.694 41.667 0.00 0.00 0.00 3.36
167 168 5.071788 TGTTTGGACCTTGATTGTAGTCTCT 59.928 40.000 0.00 0.00 0.00 3.10
168 169 5.407407 TTGGACCTTGATTGTAGTCTCTC 57.593 43.478 0.00 0.00 0.00 3.20
169 170 4.678256 TGGACCTTGATTGTAGTCTCTCT 58.322 43.478 0.00 0.00 0.00 3.10
170 171 4.707448 TGGACCTTGATTGTAGTCTCTCTC 59.293 45.833 0.00 0.00 0.00 3.20
171 172 4.098807 GGACCTTGATTGTAGTCTCTCTCC 59.901 50.000 0.00 0.00 0.00 3.71
172 173 4.027437 ACCTTGATTGTAGTCTCTCTCCC 58.973 47.826 0.00 0.00 0.00 4.30
200 201 3.577389 GCAGGTAGGCCACTGAAAT 57.423 52.632 21.77 0.00 36.86 2.17
207 208 4.280929 AGGTAGGCCACTGAAATGAAAAAC 59.719 41.667 5.01 0.00 37.19 2.43
210 211 5.096443 AGGCCACTGAAATGAAAAACAAA 57.904 34.783 5.01 0.00 0.00 2.83
211 212 5.495640 AGGCCACTGAAATGAAAAACAAAA 58.504 33.333 5.01 0.00 0.00 2.44
212 213 5.353956 AGGCCACTGAAATGAAAAACAAAAC 59.646 36.000 5.01 0.00 0.00 2.43
213 214 5.123027 GGCCACTGAAATGAAAAACAAAACA 59.877 36.000 0.00 0.00 0.00 2.83
214 215 6.183360 GGCCACTGAAATGAAAAACAAAACAT 60.183 34.615 0.00 0.00 0.00 2.71
274 277 8.974060 AGACTACAAGATAAACTTTGGTTTCA 57.026 30.769 0.00 0.00 43.62 2.69
333 340 4.337145 ACGATGTACACTTCTCTCCTCTT 58.663 43.478 0.00 0.00 0.00 2.85
335 342 4.638421 CGATGTACACTTCTCTCCTCTTCT 59.362 45.833 0.00 0.00 0.00 2.85
336 343 5.818336 CGATGTACACTTCTCTCCTCTTCTA 59.182 44.000 0.00 0.00 0.00 2.10
361 390 0.104120 TATGGACCGGCAATCTCACG 59.896 55.000 0.00 0.00 0.00 4.35
362 391 3.195698 GGACCGGCAATCTCACGC 61.196 66.667 0.00 0.00 0.00 5.34
374 403 4.323477 TCACGCAAGGAACGGGGG 62.323 66.667 0.00 0.00 46.39 5.40
375 404 4.323477 CACGCAAGGAACGGGGGA 62.323 66.667 0.00 0.00 46.39 4.81
385 419 3.697439 AACGGGGGATCACATGCCG 62.697 63.158 9.31 9.31 42.46 5.69
413 447 7.598278 CCAGTATAATTCTTCGTCATCTAGCT 58.402 38.462 0.00 0.00 0.00 3.32
418 452 6.885952 AATTCTTCGTCATCTAGCTAGCTA 57.114 37.500 22.85 22.85 0.00 3.32
419 453 5.933187 TTCTTCGTCATCTAGCTAGCTAG 57.067 43.478 36.20 36.20 45.38 3.42
485 519 1.985116 GAGGCCTTCACCGGAGTCT 60.985 63.158 9.46 0.00 33.69 3.24
611 662 4.379243 ACGCTCAAGGACGGCCTG 62.379 66.667 12.91 5.28 46.28 4.85
692 743 0.329596 GGAAGTGCCTCCACCTCAAT 59.670 55.000 0.00 0.00 43.09 2.57
834 888 1.740585 CTAGCTATCGTCGATGGAGGG 59.259 57.143 21.32 6.73 0.00 4.30
858 917 1.134128 ACATGCACAGAGTGTTCACCA 60.134 47.619 0.00 0.00 35.75 4.17
899 958 0.581529 CATGTTGACACGAACGCTGT 59.418 50.000 0.00 0.00 0.00 4.40
900 959 0.859232 ATGTTGACACGAACGCTGTC 59.141 50.000 16.44 16.44 38.86 3.51
901 960 1.198397 GTTGACACGAACGCTGTCG 59.802 57.895 17.35 4.54 46.54 4.35
902 961 2.582265 TTGACACGAACGCTGTCGC 61.582 57.895 17.35 0.00 45.00 5.19
903 962 3.764049 GACACGAACGCTGTCGCC 61.764 66.667 5.88 0.00 45.00 5.54
993 1110 3.931247 ACGTGCGGTGGGCTTGTA 61.931 61.111 0.00 0.00 44.05 2.41
1087 3339 1.516603 GTCCGCACTAACTCCGCTC 60.517 63.158 0.00 0.00 0.00 5.03
1107 3359 4.065281 CTCCCGTCGCCGTTCCTT 62.065 66.667 0.00 0.00 0.00 3.36
1128 3380 4.939368 CGTGGGGCCACCGACAAA 62.939 66.667 0.20 0.00 44.90 2.83
1183 3435 0.036732 AAGCATCGAGTTCAAGGGCA 59.963 50.000 0.00 0.00 0.00 5.36
1404 3656 3.484547 GTCGCCGTAAACTGCCGG 61.485 66.667 0.00 0.00 46.90 6.13
1457 3709 2.233922 TCTTCGGAAACATGGTCCTCTC 59.766 50.000 13.96 0.00 32.53 3.20
1506 3758 0.112606 TCCTATCCTCCAGCTACCCG 59.887 60.000 0.00 0.00 0.00 5.28
1797 4067 2.676471 GGTGGCGCCCATCTGTTT 60.676 61.111 26.77 0.00 35.28 2.83
1834 4104 1.618837 AGCACGTAGAAGCCTTCAAGA 59.381 47.619 7.29 0.00 33.18 3.02
1851 4121 7.632245 GCCTTCAAGAAGATTTGCTATTCCATT 60.632 37.037 11.25 0.00 40.79 3.16
1862 4931 4.132336 TGCTATTCCATTGAGTGATGAGC 58.868 43.478 0.00 0.00 0.00 4.26
1863 4932 3.186001 GCTATTCCATTGAGTGATGAGCG 59.814 47.826 0.00 0.00 0.00 5.03
1869 4938 3.455327 CATTGAGTGATGAGCGATGACT 58.545 45.455 0.00 0.00 29.99 3.41
1882 4951 3.499918 AGCGATGACTGCAAATTATAGCC 59.500 43.478 0.00 0.00 33.85 3.93
1977 5053 7.921041 ATCATTCATGGTCCTCTCTAAAGTA 57.079 36.000 0.00 0.00 0.00 2.24
2022 5100 1.290203 AGAATGATGGCGCAAGTACG 58.710 50.000 10.83 0.00 41.68 3.67
2052 5130 8.798153 GGCTTTCAATTAATAAAGTCATCAACG 58.202 33.333 9.46 0.00 37.29 4.10
2056 5134 8.343168 TCAATTAATAAAGTCATCAACGGGTT 57.657 30.769 0.00 0.00 0.00 4.11
2068 5146 8.262227 AGTCATCAACGGGTTAGAATTACATTA 58.738 33.333 0.00 0.00 0.00 1.90
2088 5166 3.369546 ACAGCATACAAACCAGCAAAC 57.630 42.857 0.00 0.00 0.00 2.93
2108 5186 2.929398 ACAGAAAAACAAAGCGGCAAAG 59.071 40.909 1.45 0.00 0.00 2.77
2115 5193 2.446435 ACAAAGCGGCAAAGGATACAT 58.554 42.857 1.45 0.00 41.41 2.29
2116 5194 2.164219 ACAAAGCGGCAAAGGATACATG 59.836 45.455 1.45 0.00 41.41 3.21
2117 5195 2.128771 AAGCGGCAAAGGATACATGT 57.871 45.000 2.69 2.69 41.41 3.21
2127 5205 7.807907 CGGCAAAGGATACATGTTATTTTATCC 59.192 37.037 13.16 13.16 40.22 2.59
2157 5235 8.997621 TTAAGCTAAGTACATGATCGAAAGTT 57.002 30.769 0.00 0.00 0.00 2.66
2165 5243 8.827177 AGTACATGATCGAAAGTTGTTCTTAA 57.173 30.769 0.00 0.00 35.02 1.85
2201 5279 9.468532 AGATGTTCTTGCTTTTAGAAAATGTTC 57.531 29.630 0.00 0.00 31.29 3.18
2228 5306 9.974750 GAAATTTCAAAACAAATGGTCGTTTTA 57.025 25.926 13.40 0.00 42.00 1.52
2233 5311 9.595357 TTCAAAACAAATGGTCGTTTTAAAAAC 57.405 25.926 1.31 0.00 42.00 2.43
2234 5312 8.770828 TCAAAACAAATGGTCGTTTTAAAAACA 58.229 25.926 1.31 0.74 42.00 2.83
2238 5316 9.762062 AACAAATGGTCGTTTTAAAAACAATTC 57.238 25.926 1.31 0.00 0.00 2.17
2239 5317 8.936864 ACAAATGGTCGTTTTAAAAACAATTCA 58.063 25.926 1.31 0.00 0.00 2.57
2267 5345 8.922931 AAATAGGGATTTTCAAACAATGCTTT 57.077 26.923 0.00 0.00 30.77 3.51
2268 5346 8.922931 AATAGGGATTTTCAAACAATGCTTTT 57.077 26.923 0.00 0.00 0.00 2.27
2290 5388 9.956797 CTTTTATTTTCCAAAATATGTTGCGAG 57.043 29.630 0.00 0.00 39.73 5.03
2294 5392 7.013787 ATTTTCCAAAATATGTTGCGAGTGCA 61.014 34.615 0.00 0.00 42.17 4.57
2315 5413 7.066043 AGTGCATTTGTTCAACATTTTCACAAT 59.934 29.630 12.83 0.00 0.00 2.71
2318 5416 8.525071 GCATTTGTTCAACATTTTCACAATTTG 58.475 29.630 0.00 0.00 0.00 2.32
2350 5467 8.527567 AATGTTCGGGTGTTAAAAATATTGTG 57.472 30.769 0.00 0.00 0.00 3.33
2352 5469 5.061920 TCGGGTGTTAAAAATATTGTGCC 57.938 39.130 0.00 0.00 0.00 5.01
2355 5472 5.625656 CGGGTGTTAAAAATATTGTGCCCAT 60.626 40.000 0.00 0.00 32.98 4.00
2356 5473 6.176896 GGGTGTTAAAAATATTGTGCCCATT 58.823 36.000 0.00 0.00 32.98 3.16
2359 5476 8.233868 GGTGTTAAAAATATTGTGCCCATTTTC 58.766 33.333 0.00 0.00 32.22 2.29
2360 5477 8.778358 GTGTTAAAAATATTGTGCCCATTTTCA 58.222 29.630 0.00 0.00 32.22 2.69
2368 5485 9.694137 AATATTGTGCCCATTTTCAAAAATTTG 57.306 25.926 0.00 0.00 36.52 2.32
2433 5551 7.537596 TGTCCCAGTTTCAAATATTGTTCAT 57.462 32.000 0.00 0.00 0.00 2.57
2505 5623 5.695851 ATATGTCCGCATCTCCAAATTTC 57.304 39.130 0.00 0.00 36.58 2.17
2506 5624 2.789213 TGTCCGCATCTCCAAATTTCA 58.211 42.857 0.00 0.00 0.00 2.69
2509 5627 4.946772 TGTCCGCATCTCCAAATTTCATTA 59.053 37.500 0.00 0.00 0.00 1.90
2511 5629 6.770303 TGTCCGCATCTCCAAATTTCATTATA 59.230 34.615 0.00 0.00 0.00 0.98
2546 5665 8.989653 AAACGTTCCTGTTTTAAAGAAAATCA 57.010 26.923 0.00 0.00 38.89 2.57
2547 5666 9.594478 AAACGTTCCTGTTTTAAAGAAAATCAT 57.406 25.926 0.00 0.00 38.89 2.45
2548 5667 8.574196 ACGTTCCTGTTTTAAAGAAAATCATG 57.426 30.769 0.00 0.00 36.92 3.07
2549 5668 8.410141 ACGTTCCTGTTTTAAAGAAAATCATGA 58.590 29.630 0.00 0.00 36.92 3.07
2550 5669 9.410556 CGTTCCTGTTTTAAAGAAAATCATGAT 57.589 29.630 1.18 1.18 36.92 2.45
2588 5707 9.774413 AAAATCATGATTTTCAAAAGAAGCTCT 57.226 25.926 31.60 12.03 44.98 4.09
2592 5711 7.864379 TCATGATTTTCAAAAGAAGCTCTTGTC 59.136 33.333 0.00 0.00 36.71 3.18
2597 5716 6.757897 TTCAAAAGAAGCTCTTGTCTTTCA 57.242 33.333 10.73 0.48 41.98 2.69
2638 5758 6.935771 TGGAAATCATTGTTCAGAAATTTGGG 59.064 34.615 0.00 0.00 0.00 4.12
2653 5773 6.593770 AGAAATTTGGGAAGTGTTTGTGTTTC 59.406 34.615 0.00 0.00 0.00 2.78
2654 5774 5.675684 ATTTGGGAAGTGTTTGTGTTTCT 57.324 34.783 0.00 0.00 0.00 2.52
2658 5778 4.642885 TGGGAAGTGTTTGTGTTTCTTAGG 59.357 41.667 0.00 0.00 0.00 2.69
2837 5960 4.481930 ACATCTTCGCAAATTTCGTTCA 57.518 36.364 8.98 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.111016 CATGTGCGGCTGTGCTGG 62.111 66.667 0.00 0.00 35.15 4.85
9 10 4.771356 GCATGTGCGGCTGTGCTG 62.771 66.667 14.40 0.00 38.08 4.41
11 12 2.268988 TATTGCATGTGCGGCTGTGC 62.269 55.000 14.67 14.67 45.83 4.57
12 13 0.382873 ATATTGCATGTGCGGCTGTG 59.617 50.000 0.00 0.00 45.83 3.66
13 14 1.105457 AATATTGCATGTGCGGCTGT 58.895 45.000 0.00 0.00 45.83 4.40
14 15 1.483316 CAATATTGCATGTGCGGCTG 58.517 50.000 1.74 0.00 45.83 4.85
15 16 0.386476 CCAATATTGCATGTGCGGCT 59.614 50.000 10.11 0.00 45.83 5.52
16 17 0.102844 ACCAATATTGCATGTGCGGC 59.897 50.000 10.11 0.00 45.83 6.53
17 18 3.706802 TTACCAATATTGCATGTGCGG 57.293 42.857 10.11 0.00 45.83 5.69
18 19 5.747675 TGAAATTACCAATATTGCATGTGCG 59.252 36.000 10.11 0.00 45.83 5.34
19 20 7.438757 TCATGAAATTACCAATATTGCATGTGC 59.561 33.333 20.08 0.00 44.29 4.57
20 21 8.874744 TCATGAAATTACCAATATTGCATGTG 57.125 30.769 20.08 7.94 44.29 3.21
21 22 8.145767 CCTCATGAAATTACCAATATTGCATGT 58.854 33.333 20.08 12.58 44.29 3.21
22 23 8.361889 TCCTCATGAAATTACCAATATTGCATG 58.638 33.333 17.15 17.15 44.88 4.06
23 24 8.481492 TCCTCATGAAATTACCAATATTGCAT 57.519 30.769 10.11 3.61 32.57 3.96
24 25 7.894753 TCCTCATGAAATTACCAATATTGCA 57.105 32.000 10.11 1.29 0.00 4.08
41 42 9.398170 CGGTAGCAAATATTTTATTTCCTCATG 57.602 33.333 0.00 0.00 0.00 3.07
42 43 9.131791 ACGGTAGCAAATATTTTATTTCCTCAT 57.868 29.630 0.00 0.00 0.00 2.90
43 44 8.514330 ACGGTAGCAAATATTTTATTTCCTCA 57.486 30.769 0.00 0.00 0.00 3.86
44 45 9.874215 GTACGGTAGCAAATATTTTATTTCCTC 57.126 33.333 0.00 0.00 0.00 3.71
45 46 9.623000 AGTACGGTAGCAAATATTTTATTTCCT 57.377 29.630 0.00 0.00 0.00 3.36
51 52 9.263538 CCATGTAGTACGGTAGCAAATATTTTA 57.736 33.333 0.00 0.00 0.00 1.52
52 53 7.988599 TCCATGTAGTACGGTAGCAAATATTTT 59.011 33.333 0.00 0.00 0.00 1.82
53 54 7.502696 TCCATGTAGTACGGTAGCAAATATTT 58.497 34.615 0.00 0.00 0.00 1.40
54 55 7.058023 TCCATGTAGTACGGTAGCAAATATT 57.942 36.000 0.00 0.00 0.00 1.28
55 56 6.659745 TCCATGTAGTACGGTAGCAAATAT 57.340 37.500 0.00 0.00 0.00 1.28
56 57 6.468333 TTCCATGTAGTACGGTAGCAAATA 57.532 37.500 0.00 0.00 0.00 1.40
57 58 5.347620 TTCCATGTAGTACGGTAGCAAAT 57.652 39.130 0.00 0.00 0.00 2.32
58 59 4.804868 TTCCATGTAGTACGGTAGCAAA 57.195 40.909 0.00 0.00 0.00 3.68
59 60 6.468333 TTATTCCATGTAGTACGGTAGCAA 57.532 37.500 0.00 0.00 0.00 3.91
60 61 6.659745 ATTATTCCATGTAGTACGGTAGCA 57.340 37.500 0.00 0.00 0.00 3.49
61 62 7.705325 CCATATTATTCCATGTAGTACGGTAGC 59.295 40.741 0.00 0.00 0.00 3.58
62 63 8.746530 ACCATATTATTCCATGTAGTACGGTAG 58.253 37.037 0.00 0.00 0.00 3.18
63 64 8.654485 ACCATATTATTCCATGTAGTACGGTA 57.346 34.615 0.00 0.00 0.00 4.02
64 65 7.549147 ACCATATTATTCCATGTAGTACGGT 57.451 36.000 0.00 0.00 0.00 4.83
65 66 8.746530 AGTACCATATTATTCCATGTAGTACGG 58.253 37.037 0.00 0.00 31.02 4.02
80 81 8.528643 CGACCATCCAGATAAAGTACCATATTA 58.471 37.037 0.00 0.00 0.00 0.98
81 82 7.386851 CGACCATCCAGATAAAGTACCATATT 58.613 38.462 0.00 0.00 0.00 1.28
82 83 6.070767 CCGACCATCCAGATAAAGTACCATAT 60.071 42.308 0.00 0.00 0.00 1.78
83 84 5.245301 CCGACCATCCAGATAAAGTACCATA 59.755 44.000 0.00 0.00 0.00 2.74
84 85 4.040461 CCGACCATCCAGATAAAGTACCAT 59.960 45.833 0.00 0.00 0.00 3.55
85 86 3.386726 CCGACCATCCAGATAAAGTACCA 59.613 47.826 0.00 0.00 0.00 3.25
86 87 3.387050 ACCGACCATCCAGATAAAGTACC 59.613 47.826 0.00 0.00 0.00 3.34
87 88 4.667519 ACCGACCATCCAGATAAAGTAC 57.332 45.455 0.00 0.00 0.00 2.73
88 89 6.989155 AATACCGACCATCCAGATAAAGTA 57.011 37.500 0.00 0.00 0.00 2.24
89 90 5.888982 AATACCGACCATCCAGATAAAGT 57.111 39.130 0.00 0.00 0.00 2.66
90 91 6.992715 AGAAAATACCGACCATCCAGATAAAG 59.007 38.462 0.00 0.00 0.00 1.85
91 92 6.765989 CAGAAAATACCGACCATCCAGATAAA 59.234 38.462 0.00 0.00 0.00 1.40
92 93 6.099125 TCAGAAAATACCGACCATCCAGATAA 59.901 38.462 0.00 0.00 0.00 1.75
93 94 5.600898 TCAGAAAATACCGACCATCCAGATA 59.399 40.000 0.00 0.00 0.00 1.98
94 95 4.408921 TCAGAAAATACCGACCATCCAGAT 59.591 41.667 0.00 0.00 0.00 2.90
95 96 3.772572 TCAGAAAATACCGACCATCCAGA 59.227 43.478 0.00 0.00 0.00 3.86
96 97 4.137116 TCAGAAAATACCGACCATCCAG 57.863 45.455 0.00 0.00 0.00 3.86
97 98 4.771114 ATCAGAAAATACCGACCATCCA 57.229 40.909 0.00 0.00 0.00 3.41
98 99 7.228706 ACAATAATCAGAAAATACCGACCATCC 59.771 37.037 0.00 0.00 0.00 3.51
99 100 8.070171 CACAATAATCAGAAAATACCGACCATC 58.930 37.037 0.00 0.00 0.00 3.51
100 101 7.013274 CCACAATAATCAGAAAATACCGACCAT 59.987 37.037 0.00 0.00 0.00 3.55
101 102 6.317642 CCACAATAATCAGAAAATACCGACCA 59.682 38.462 0.00 0.00 0.00 4.02
102 103 6.540914 TCCACAATAATCAGAAAATACCGACC 59.459 38.462 0.00 0.00 0.00 4.79
103 104 7.548196 TCCACAATAATCAGAAAATACCGAC 57.452 36.000 0.00 0.00 0.00 4.79
104 105 8.746052 ATTCCACAATAATCAGAAAATACCGA 57.254 30.769 0.00 0.00 0.00 4.69
105 106 9.801873 AAATTCCACAATAATCAGAAAATACCG 57.198 29.630 0.00 0.00 0.00 4.02
113 114 9.295825 ACACTACAAAATTCCACAATAATCAGA 57.704 29.630 0.00 0.00 0.00 3.27
121 122 9.877178 AAACAAATACACTACAAAATTCCACAA 57.123 25.926 0.00 0.00 0.00 3.33
122 123 9.307121 CAAACAAATACACTACAAAATTCCACA 57.693 29.630 0.00 0.00 0.00 4.17
123 124 8.760569 CCAAACAAATACACTACAAAATTCCAC 58.239 33.333 0.00 0.00 0.00 4.02
124 125 8.696374 TCCAAACAAATACACTACAAAATTCCA 58.304 29.630 0.00 0.00 0.00 3.53
125 126 8.974408 GTCCAAACAAATACACTACAAAATTCC 58.026 33.333 0.00 0.00 0.00 3.01
126 127 8.974408 GGTCCAAACAAATACACTACAAAATTC 58.026 33.333 0.00 0.00 0.00 2.17
127 128 8.700973 AGGTCCAAACAAATACACTACAAAATT 58.299 29.630 0.00 0.00 0.00 1.82
128 129 8.245195 AGGTCCAAACAAATACACTACAAAAT 57.755 30.769 0.00 0.00 0.00 1.82
129 130 7.648039 AGGTCCAAACAAATACACTACAAAA 57.352 32.000 0.00 0.00 0.00 2.44
130 131 7.339721 TCAAGGTCCAAACAAATACACTACAAA 59.660 33.333 0.00 0.00 0.00 2.83
131 132 6.829298 TCAAGGTCCAAACAAATACACTACAA 59.171 34.615 0.00 0.00 0.00 2.41
132 133 6.358178 TCAAGGTCCAAACAAATACACTACA 58.642 36.000 0.00 0.00 0.00 2.74
133 134 6.870971 TCAAGGTCCAAACAAATACACTAC 57.129 37.500 0.00 0.00 0.00 2.73
134 135 7.504238 ACAATCAAGGTCCAAACAAATACACTA 59.496 33.333 0.00 0.00 0.00 2.74
135 136 6.323739 ACAATCAAGGTCCAAACAAATACACT 59.676 34.615 0.00 0.00 0.00 3.55
136 137 6.512297 ACAATCAAGGTCCAAACAAATACAC 58.488 36.000 0.00 0.00 0.00 2.90
137 138 6.723298 ACAATCAAGGTCCAAACAAATACA 57.277 33.333 0.00 0.00 0.00 2.29
138 139 7.882179 ACTACAATCAAGGTCCAAACAAATAC 58.118 34.615 0.00 0.00 0.00 1.89
139 140 7.942341 AGACTACAATCAAGGTCCAAACAAATA 59.058 33.333 0.00 0.00 0.00 1.40
140 141 6.777580 AGACTACAATCAAGGTCCAAACAAAT 59.222 34.615 0.00 0.00 0.00 2.32
141 142 6.126409 AGACTACAATCAAGGTCCAAACAAA 58.874 36.000 0.00 0.00 0.00 2.83
142 143 5.690865 AGACTACAATCAAGGTCCAAACAA 58.309 37.500 0.00 0.00 0.00 2.83
143 144 5.071788 AGAGACTACAATCAAGGTCCAAACA 59.928 40.000 0.00 0.00 0.00 2.83
144 145 5.552178 AGAGACTACAATCAAGGTCCAAAC 58.448 41.667 0.00 0.00 0.00 2.93
145 146 5.544176 AGAGAGACTACAATCAAGGTCCAAA 59.456 40.000 0.00 0.00 0.00 3.28
146 147 5.087323 AGAGAGACTACAATCAAGGTCCAA 58.913 41.667 0.00 0.00 0.00 3.53
147 148 4.678256 AGAGAGACTACAATCAAGGTCCA 58.322 43.478 0.00 0.00 0.00 4.02
148 149 4.098807 GGAGAGAGACTACAATCAAGGTCC 59.901 50.000 0.00 0.00 0.00 4.46
149 150 4.098807 GGGAGAGAGACTACAATCAAGGTC 59.901 50.000 0.00 0.00 0.00 3.85
150 151 4.027437 GGGAGAGAGACTACAATCAAGGT 58.973 47.826 0.00 0.00 0.00 3.50
151 152 4.285863 AGGGAGAGAGACTACAATCAAGG 58.714 47.826 0.00 0.00 0.00 3.61
152 153 7.432869 CATTAGGGAGAGAGACTACAATCAAG 58.567 42.308 0.00 0.00 0.00 3.02
153 154 6.325028 CCATTAGGGAGAGAGACTACAATCAA 59.675 42.308 0.00 0.00 40.01 2.57
154 155 5.835819 CCATTAGGGAGAGAGACTACAATCA 59.164 44.000 0.00 0.00 40.01 2.57
155 156 6.071984 TCCATTAGGGAGAGAGACTACAATC 58.928 44.000 0.00 0.00 42.15 2.67
156 157 6.031964 TCCATTAGGGAGAGAGACTACAAT 57.968 41.667 0.00 0.00 42.15 2.71
157 158 5.467668 TCCATTAGGGAGAGAGACTACAA 57.532 43.478 0.00 0.00 42.15 2.41
169 170 2.408565 CTACCTGCCTTCCATTAGGGA 58.591 52.381 0.00 0.00 46.61 4.20
170 171 1.421646 CCTACCTGCCTTCCATTAGGG 59.578 57.143 0.00 0.00 35.74 3.53
171 172 1.202818 GCCTACCTGCCTTCCATTAGG 60.203 57.143 0.00 0.00 38.40 2.69
172 173 2.262423 GCCTACCTGCCTTCCATTAG 57.738 55.000 0.00 0.00 0.00 1.73
274 277 7.964604 ACTTTAATTAGCGACTCTCAACTTT 57.035 32.000 0.00 0.00 0.00 2.66
333 340 5.483937 AGATTGCCGGTCCATATATTGTAGA 59.516 40.000 1.90 0.00 0.00 2.59
335 342 5.247337 TGAGATTGCCGGTCCATATATTGTA 59.753 40.000 1.90 0.00 0.00 2.41
336 343 4.041567 TGAGATTGCCGGTCCATATATTGT 59.958 41.667 1.90 0.00 0.00 2.71
361 390 1.749258 GTGATCCCCCGTTCCTTGC 60.749 63.158 0.00 0.00 0.00 4.01
362 391 0.255890 ATGTGATCCCCCGTTCCTTG 59.744 55.000 0.00 0.00 0.00 3.61
385 419 5.986135 AGATGACGAAGAATTATACTGGCAC 59.014 40.000 0.00 0.00 0.00 5.01
413 447 0.546122 CCATGGTTGGTGGCTAGCTA 59.454 55.000 15.72 5.44 38.30 3.32
421 455 1.067425 CATTCACTGCCATGGTTGGTG 60.067 52.381 14.67 18.19 45.57 4.17
591 642 2.665185 GCCGTCCTTGAGCGTGTT 60.665 61.111 0.00 0.00 0.00 3.32
629 680 2.034687 CCTGCCAGGTGTGGGAAG 59.965 66.667 1.39 0.00 44.94 3.46
657 708 1.246056 TTCCTTCCGTGGTCGTCGAT 61.246 55.000 0.00 0.00 35.01 3.59
692 743 2.681064 ACTAGCACCCCGGCGTTA 60.681 61.111 6.01 0.00 39.27 3.18
808 859 5.167121 TCCATCGACGATAGCTAGTACTAC 58.833 45.833 10.57 0.00 42.67 2.73
809 860 5.397142 TCCATCGACGATAGCTAGTACTA 57.603 43.478 10.57 1.89 42.67 1.82
810 861 4.247258 CTCCATCGACGATAGCTAGTACT 58.753 47.826 10.57 0.00 42.67 2.73
811 862 3.371591 CCTCCATCGACGATAGCTAGTAC 59.628 52.174 10.57 0.00 42.67 2.73
812 863 3.597255 CCTCCATCGACGATAGCTAGTA 58.403 50.000 10.57 0.00 42.67 1.82
813 864 2.428491 CCTCCATCGACGATAGCTAGT 58.572 52.381 10.57 0.00 42.67 2.57
814 865 1.740585 CCCTCCATCGACGATAGCTAG 59.259 57.143 10.57 5.62 42.67 3.42
815 866 1.613520 CCCCTCCATCGACGATAGCTA 60.614 57.143 10.57 0.00 42.67 3.32
816 867 0.896019 CCCCTCCATCGACGATAGCT 60.896 60.000 10.57 0.00 42.67 3.32
817 868 0.894184 TCCCCTCCATCGACGATAGC 60.894 60.000 10.57 0.00 42.67 2.97
818 869 1.169577 CTCCCCTCCATCGACGATAG 58.830 60.000 10.57 3.08 46.19 2.08
819 870 0.769247 TCTCCCCTCCATCGACGATA 59.231 55.000 10.57 0.00 0.00 2.92
820 871 0.824182 GTCTCCCCTCCATCGACGAT 60.824 60.000 4.05 4.05 0.00 3.73
821 872 1.453379 GTCTCCCCTCCATCGACGA 60.453 63.158 0.00 0.00 0.00 4.20
822 873 1.109920 ATGTCTCCCCTCCATCGACG 61.110 60.000 0.00 0.00 0.00 5.12
825 876 1.070445 GCATGTCTCCCCTCCATCG 59.930 63.158 0.00 0.00 0.00 3.84
834 888 2.072298 GAACACTCTGTGCATGTCTCC 58.928 52.381 0.00 0.00 36.98 3.71
858 917 3.196254 GGATCATGTGCACCTTTGGAAAT 59.804 43.478 15.69 0.00 0.00 2.17
899 958 2.786539 AAGAACTGCATGCTCGGCGA 62.787 55.000 20.33 10.14 0.00 5.54
900 959 2.393768 AAGAACTGCATGCTCGGCG 61.394 57.895 20.33 0.00 0.00 6.46
901 960 1.136147 CAAGAACTGCATGCTCGGC 59.864 57.895 20.33 6.18 0.00 5.54
902 961 0.957395 ACCAAGAACTGCATGCTCGG 60.957 55.000 20.33 11.40 0.00 4.63
903 962 0.445436 GACCAAGAACTGCATGCTCG 59.555 55.000 20.33 12.41 0.00 5.03
904 963 0.445436 CGACCAAGAACTGCATGCTC 59.555 55.000 20.33 8.36 0.00 4.26
984 1101 0.751277 CCATGCCGATTACAAGCCCA 60.751 55.000 0.00 0.00 0.00 5.36
1139 3391 3.283684 CGAACACCGGCAAAGGCA 61.284 61.111 0.00 0.00 43.71 4.75
1151 3403 1.640428 GATGCTTCCGTGATCGAACA 58.360 50.000 0.00 0.00 39.71 3.18
1291 3543 1.001487 CTGGAACGTGCTGCATGAAAA 60.001 47.619 27.26 9.41 0.00 2.29
1292 3544 0.592637 CTGGAACGTGCTGCATGAAA 59.407 50.000 27.26 9.10 0.00 2.69
1293 3545 0.534877 ACTGGAACGTGCTGCATGAA 60.535 50.000 27.26 9.42 0.00 2.57
1294 3546 1.071299 ACTGGAACGTGCTGCATGA 59.929 52.632 27.26 4.88 0.00 3.07
1457 3709 2.974698 GCATCCTCGGGAATGCCG 60.975 66.667 6.93 6.93 34.34 5.69
1566 3818 1.614241 CCTCCCCGAAGTCCACGAAT 61.614 60.000 0.00 0.00 0.00 3.34
1647 3917 1.050988 GCCAGCTATCCACCTCCAGA 61.051 60.000 0.00 0.00 0.00 3.86
1797 4067 3.289128 CTCGTTGTCAAGAGCCACA 57.711 52.632 0.00 0.00 0.00 4.17
1834 4104 7.558807 TCATCACTCAATGGAATAGCAAATCTT 59.441 33.333 0.00 0.00 0.00 2.40
1851 4121 1.470458 GCAGTCATCGCTCATCACTCA 60.470 52.381 0.00 0.00 0.00 3.41
1862 4931 4.153117 GGAGGCTATAATTTGCAGTCATCG 59.847 45.833 0.00 0.00 0.00 3.84
1863 4932 4.153117 CGGAGGCTATAATTTGCAGTCATC 59.847 45.833 0.00 0.00 0.00 2.92
1869 4938 4.947388 AGAAAACGGAGGCTATAATTTGCA 59.053 37.500 0.00 0.00 0.00 4.08
1882 4951 2.064762 CAGTCAGCTGAGAAAACGGAG 58.935 52.381 18.89 0.00 45.28 4.63
1930 5006 8.757877 TGATATTAAAGGGCTTGCTAAACATTT 58.242 29.630 0.00 0.00 0.00 2.32
2007 5085 0.735978 CAGACGTACTTGCGCCATCA 60.736 55.000 4.18 0.00 34.88 3.07
2010 5088 2.048597 CCAGACGTACTTGCGCCA 60.049 61.111 4.18 0.00 34.88 5.69
2014 5092 1.508632 TGAAAGCCAGACGTACTTGC 58.491 50.000 0.00 0.00 37.51 4.01
2016 5094 8.556213 TTATTAATTGAAAGCCAGACGTACTT 57.444 30.769 0.00 0.00 0.00 2.24
2022 5100 9.508567 GATGACTTTATTAATTGAAAGCCAGAC 57.491 33.333 9.63 2.78 36.34 3.51
2052 5130 8.671384 TGTATGCTGTAATGTAATTCTAACCC 57.329 34.615 0.00 0.00 37.87 4.11
2056 5134 9.674068 TGGTTTGTATGCTGTAATGTAATTCTA 57.326 29.630 0.00 0.00 37.87 2.10
2068 5146 2.692557 TGTTTGCTGGTTTGTATGCTGT 59.307 40.909 0.00 0.00 0.00 4.40
2081 5159 3.242059 CCGCTTTGTTTTTCTGTTTGCTG 60.242 43.478 0.00 0.00 0.00 4.41
2088 5166 2.284952 CCTTTGCCGCTTTGTTTTTCTG 59.715 45.455 0.00 0.00 0.00 3.02
2136 5214 6.648725 ACAACTTTCGATCATGTACTTAGC 57.351 37.500 0.00 0.00 0.00 3.09
2143 5221 9.965824 AAAATTAAGAACAACTTTCGATCATGT 57.034 25.926 0.00 0.00 39.72 3.21
2173 5251 9.822185 ACATTTTCTAAAAGCAAGAACATCTTT 57.178 25.926 0.00 0.00 33.78 2.52
2175 5253 9.468532 GAACATTTTCTAAAAGCAAGAACATCT 57.531 29.630 0.00 0.00 32.81 2.90
2176 5254 8.420189 CGAACATTTTCTAAAAGCAAGAACATC 58.580 33.333 0.00 0.00 32.81 3.06
2201 5279 6.267500 ACGACCATTTGTTTTGAAATTTCG 57.733 33.333 13.34 0.00 35.86 3.46
2214 5292 9.760660 TTGAATTGTTTTTAAAACGACCATTTG 57.239 25.926 12.14 0.00 0.00 2.32
2241 5319 8.922931 AAGCATTGTTTGAAAATCCCTATTTT 57.077 26.923 0.00 0.00 45.78 1.82
2246 5324 8.922931 AATAAAAGCATTGTTTGAAAATCCCT 57.077 26.923 0.00 0.00 0.00 4.20
2247 5325 9.964303 AAAATAAAAGCATTGTTTGAAAATCCC 57.036 25.926 0.00 0.00 0.00 3.85
2264 5342 9.956797 CTCGCAACATATTTTGGAAAATAAAAG 57.043 29.630 8.29 5.27 42.29 2.27
2267 5345 7.062839 GCACTCGCAACATATTTTGGAAAATAA 59.937 33.333 8.29 0.00 39.76 1.40
2268 5346 6.529829 GCACTCGCAACATATTTTGGAAAATA 59.470 34.615 6.95 6.95 40.17 1.40
2290 5388 6.104439 TGTGAAAATGTTGAACAAATGCAC 57.896 33.333 14.47 14.47 0.00 4.57
2323 5421 9.549078 ACAATATTTTTAACACCCGAACATTTT 57.451 25.926 0.00 0.00 0.00 1.82
2344 5461 8.230472 ACAAATTTTTGAAAATGGGCACAATA 57.770 26.923 9.88 0.00 40.55 1.90
2350 5467 9.526713 ACATTTTACAAATTTTTGAAAATGGGC 57.473 25.926 28.55 0.00 45.20 5.36
2408 5526 7.537596 TGAACAATATTTGAAACTGGGACAT 57.462 32.000 0.00 0.00 38.20 3.06
2506 5624 9.990360 ACAGGAACGTTTTTCCAAATTTATAAT 57.010 25.926 0.46 0.00 41.00 1.28
2509 5627 8.725405 AAACAGGAACGTTTTTCCAAATTTAT 57.275 26.923 0.46 0.00 41.00 1.40
2511 5629 7.441890 AAAACAGGAACGTTTTTCCAAATTT 57.558 28.000 0.46 0.00 44.61 1.82
2524 5643 8.795786 TCATGATTTTCTTTAAAACAGGAACG 57.204 30.769 0.00 0.00 37.41 3.95
2563 5682 9.774413 AAGAGCTTCTTTTGAAAATCATGATTT 57.226 25.926 24.83 24.83 36.63 2.17
2564 5683 9.204570 CAAGAGCTTCTTTTGAAAATCATGATT 57.795 29.630 15.36 15.36 33.78 2.57
2565 5684 8.365647 ACAAGAGCTTCTTTTGAAAATCATGAT 58.634 29.630 1.18 1.18 33.78 2.45
2614 5734 7.160726 TCCCAAATTTCTGAACAATGATTTCC 58.839 34.615 0.00 0.00 0.00 3.13
2619 5739 6.098124 ACACTTCCCAAATTTCTGAACAATGA 59.902 34.615 0.00 0.00 0.00 2.57
2620 5740 6.282930 ACACTTCCCAAATTTCTGAACAATG 58.717 36.000 0.00 0.00 0.00 2.82
2638 5758 6.431198 TGTCCTAAGAAACACAAACACTTC 57.569 37.500 0.00 0.00 0.00 3.01
2722 5843 8.900762 CAAAAATGAATAAATTTTGAAACCCGC 58.099 29.630 0.00 0.00 43.36 6.13
2812 5935 6.913132 TGAACGAAATTTGCGAAGATGTTTTA 59.087 30.769 3.21 0.00 0.00 1.52
2815 5938 4.854399 TGAACGAAATTTGCGAAGATGTT 58.146 34.783 3.21 0.00 0.00 2.71
2816 5939 4.481930 TGAACGAAATTTGCGAAGATGT 57.518 36.364 3.21 0.00 0.00 3.06
2818 5941 5.046910 ACATGAACGAAATTTGCGAAGAT 57.953 34.783 3.21 0.00 0.00 2.40
2819 5942 4.481930 ACATGAACGAAATTTGCGAAGA 57.518 36.364 3.21 0.00 0.00 2.87
2824 5947 9.643652 TTTTCAAAATACATGAACGAAATTTGC 57.356 25.926 0.00 0.00 36.57 3.68


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

AutoCloner maintained by Alex Coulton.