Multiple sequence alignment - TraesCS7D01G452600

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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 TraesCS7D01G452600 chr7D 100.000 3689 0 0 1 3689 572041222 572037534 0.000000e+00 6813.0
1 TraesCS7D01G452600 chr7D 100.000 68 0 0 3995 4062 572037228 572037161 4.260000e-25 126.0
2 TraesCS7D01G452600 chr7D 83.846 130 20 1 3559 3687 34486030 34485901 5.510000e-24 122.0
3 TraesCS7D01G452600 chr7B 91.882 2094 88 27 265 2341 629049303 629047275 0.000000e+00 2850.0
4 TraesCS7D01G452600 chr7B 93.491 845 50 4 2345 3187 629047146 629046305 0.000000e+00 1251.0
5 TraesCS7D01G452600 chr7B 89.718 496 41 3 3204 3689 629046009 629045514 3.450000e-175 625.0
6 TraesCS7D01G452600 chr7A 91.103 1922 81 30 265 2159 661301066 661299208 0.000000e+00 2519.0
7 TraesCS7D01G452600 chr7A 92.821 989 57 7 2221 3205 661299092 661298114 0.000000e+00 1421.0
8 TraesCS7D01G452600 chr7A 92.025 326 20 3 3241 3560 661298105 661297780 1.720000e-123 453.0
9 TraesCS7D01G452600 chr7A 100.000 38 0 0 2157 2194 661299127 661299090 2.030000e-08 71.3
10 TraesCS7D01G452600 chr4A 90.345 1015 70 20 970 1973 621773542 621772545 0.000000e+00 1306.0
11 TraesCS7D01G452600 chr4A 87.165 857 101 7 2346 3196 621771973 621771120 0.000000e+00 965.0
12 TraesCS7D01G452600 chr5D 91.766 923 53 15 1057 1973 547065605 547066510 0.000000e+00 1262.0
13 TraesCS7D01G452600 chr5D 86.231 857 109 9 2346 3196 547067143 547067996 0.000000e+00 920.0
14 TraesCS7D01G452600 chr5D 76.804 776 142 34 1142 1895 413283957 413284716 6.320000e-108 401.0
15 TraesCS7D01G452600 chr5D 93.227 251 16 1 4 253 451067393 451067143 6.410000e-98 368.0
16 TraesCS7D01G452600 chr5D 92.063 252 19 1 4 254 132472883 132472632 1.800000e-93 353.0
17 TraesCS7D01G452600 chr5B 91.304 920 61 13 1057 1973 690238499 690239402 0.000000e+00 1238.0
18 TraesCS7D01G452600 chr5B 86.874 838 106 3 2346 3180 690257920 690258756 0.000000e+00 935.0
19 TraesCS7D01G452600 chr5B 85.932 853 115 4 2346 3194 690239951 690240802 0.000000e+00 905.0
20 TraesCS7D01G452600 chr5B 92.371 367 27 1 1532 1897 690240981 690241347 4.650000e-144 521.0
21 TraesCS7D01G452600 chr5A 76.645 775 145 34 1142 1895 525599735 525600494 2.940000e-106 396.0
22 TraesCS7D01G452600 chr3B 93.307 254 15 2 1 253 377115153 377115405 1.380000e-99 374.0
23 TraesCS7D01G452600 chr3B 83.333 132 21 1 3559 3689 773142238 773142107 1.980000e-23 121.0
24 TraesCS7D01G452600 chr3D 92.913 254 17 1 1 253 255424425 255424678 6.410000e-98 368.0
25 TraesCS7D01G452600 chr3D 84.211 133 16 4 3559 3688 120324671 120324541 1.530000e-24 124.0
26 TraesCS7D01G452600 chr3D 83.206 131 21 1 3559 3688 579104009 579103879 7.130000e-23 119.0
27 TraesCS7D01G452600 chr4B 93.117 247 16 1 9 254 187736960 187737206 1.070000e-95 361.0
28 TraesCS7D01G452600 chr3A 92.157 255 18 1 1 253 319962345 319962599 3.860000e-95 359.0
29 TraesCS7D01G452600 chr3A 92.126 254 19 1 1 253 590715542 590715795 1.390000e-94 357.0
30 TraesCS7D01G452600 chr1A 92.157 255 19 1 1 254 478205883 478205629 3.860000e-95 359.0
31 TraesCS7D01G452600 chr4D 92.063 252 19 1 4 254 313032354 313032103 1.800000e-93 353.0
32 TraesCS7D01G452600 chr4D 84.733 131 19 1 3559 3688 130457525 130457395 3.290000e-26 130.0
33 TraesCS7D01G452600 chr4D 83.846 130 20 1 3559 3687 51919872 51920001 5.510000e-24 122.0
34 TraesCS7D01G452600 chr6A 80.591 237 36 10 1664 1895 76434205 76434436 1.500000e-39 174.0
35 TraesCS7D01G452600 chr2D 86.923 130 16 1 3560 3688 50949072 50948943 1.180000e-30 145.0
36 TraesCS7D01G452600 chr1D 86.364 132 17 1 3559 3689 221022047 221022178 4.230000e-30 143.0


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 TraesCS7D01G452600 chr7D 572037161 572041222 4061 True 3469.500000 6813 100.00000 1 4062 2 chr7D.!!$R2 4061
1 TraesCS7D01G452600 chr7B 629045514 629049303 3789 True 1575.333333 2850 91.69700 265 3689 3 chr7B.!!$R1 3424
2 TraesCS7D01G452600 chr7A 661297780 661301066 3286 True 1116.075000 2519 93.98725 265 3560 4 chr7A.!!$R1 3295
3 TraesCS7D01G452600 chr4A 621771120 621773542 2422 True 1135.500000 1306 88.75500 970 3196 2 chr4A.!!$R1 2226
4 TraesCS7D01G452600 chr5D 547065605 547067996 2391 False 1091.000000 1262 88.99850 1057 3196 2 chr5D.!!$F2 2139
5 TraesCS7D01G452600 chr5D 413283957 413284716 759 False 401.000000 401 76.80400 1142 1895 1 chr5D.!!$F1 753
6 TraesCS7D01G452600 chr5B 690257920 690258756 836 False 935.000000 935 86.87400 2346 3180 1 chr5B.!!$F1 834
7 TraesCS7D01G452600 chr5B 690238499 690241347 2848 False 888.000000 1238 89.86900 1057 3194 3 chr5B.!!$F2 2137
8 TraesCS7D01G452600 chr5A 525599735 525600494 759 False 396.000000 396 76.64500 1142 1895 1 chr5A.!!$F1 753

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 0.036164 CACCATCCCTTCGTCCAACA 59.964 55.0 0.00 0.0 0.00 3.33 F
1022 1048 0.039180 ACCGGGGAAATCAAGAACCC 59.961 55.0 6.32 0.0 41.41 4.11 F
2776 3351 0.179067 TCGAGTTTGCCACCTTCGTT 60.179 50.0 0.00 0.0 33.35 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1079 1105 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.0 0.0 0.0 0.0 3.71 R
3001 3576 0.109532 TCAAACCCTCGCCATCAACA 59.890 50.0 0.0 0.0 0.0 3.33 R
3658 4528 0.519961 AAAAGTACGTCCGGCAATGC 59.480 50.0 0.0 0.0 0.0 3.56 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
20 21 1.814429 TCTCACCTTTCTTCCCACCA 58.186 50.000 0.00 0.00 0.00 4.17
21 22 2.348472 TCTCACCTTTCTTCCCACCAT 58.652 47.619 0.00 0.00 0.00 3.55
22 23 2.305927 TCTCACCTTTCTTCCCACCATC 59.694 50.000 0.00 0.00 0.00 3.51
23 24 1.354368 TCACCTTTCTTCCCACCATCC 59.646 52.381 0.00 0.00 0.00 3.51
24 25 0.704664 ACCTTTCTTCCCACCATCCC 59.295 55.000 0.00 0.00 0.00 3.85
25 26 1.002857 CCTTTCTTCCCACCATCCCT 58.997 55.000 0.00 0.00 0.00 4.20
26 27 1.359130 CCTTTCTTCCCACCATCCCTT 59.641 52.381 0.00 0.00 0.00 3.95
27 28 2.621668 CCTTTCTTCCCACCATCCCTTC 60.622 54.545 0.00 0.00 0.00 3.46
28 29 0.618458 TTCTTCCCACCATCCCTTCG 59.382 55.000 0.00 0.00 0.00 3.79
29 30 0.546747 TCTTCCCACCATCCCTTCGT 60.547 55.000 0.00 0.00 0.00 3.85
30 31 0.107654 CTTCCCACCATCCCTTCGTC 60.108 60.000 0.00 0.00 0.00 4.20
31 32 1.559065 TTCCCACCATCCCTTCGTCC 61.559 60.000 0.00 0.00 0.00 4.79
32 33 2.297895 CCCACCATCCCTTCGTCCA 61.298 63.158 0.00 0.00 0.00 4.02
33 34 1.682849 CCACCATCCCTTCGTCCAA 59.317 57.895 0.00 0.00 0.00 3.53
34 35 0.676782 CCACCATCCCTTCGTCCAAC 60.677 60.000 0.00 0.00 0.00 3.77
35 36 0.036164 CACCATCCCTTCGTCCAACA 59.964 55.000 0.00 0.00 0.00 3.33
36 37 0.991920 ACCATCCCTTCGTCCAACAT 59.008 50.000 0.00 0.00 0.00 2.71
37 38 1.354368 ACCATCCCTTCGTCCAACATT 59.646 47.619 0.00 0.00 0.00 2.71
38 39 2.225017 ACCATCCCTTCGTCCAACATTT 60.225 45.455 0.00 0.00 0.00 2.32
39 40 2.423538 CCATCCCTTCGTCCAACATTTC 59.576 50.000 0.00 0.00 0.00 2.17
40 41 2.940994 TCCCTTCGTCCAACATTTCA 57.059 45.000 0.00 0.00 0.00 2.69
41 42 3.433306 TCCCTTCGTCCAACATTTCAT 57.567 42.857 0.00 0.00 0.00 2.57
42 43 3.081061 TCCCTTCGTCCAACATTTCATG 58.919 45.455 0.00 0.00 0.00 3.07
44 45 4.006989 CCCTTCGTCCAACATTTCATGTA 58.993 43.478 0.00 0.00 44.07 2.29
45 46 4.640201 CCCTTCGTCCAACATTTCATGTAT 59.360 41.667 0.00 0.00 44.07 2.29
46 47 5.820423 CCCTTCGTCCAACATTTCATGTATA 59.180 40.000 0.00 0.00 44.07 1.47
47 48 6.486657 CCCTTCGTCCAACATTTCATGTATAT 59.513 38.462 0.00 0.00 44.07 0.86
48 49 7.355017 CCTTCGTCCAACATTTCATGTATATG 58.645 38.462 0.00 0.00 44.07 1.78
49 50 7.226523 CCTTCGTCCAACATTTCATGTATATGA 59.773 37.037 0.00 0.00 44.07 2.15
50 51 8.675705 TTCGTCCAACATTTCATGTATATGAT 57.324 30.769 2.71 0.00 44.07 2.45
51 52 8.086851 TCGTCCAACATTTCATGTATATGATG 57.913 34.615 2.71 2.59 44.07 3.07
52 53 7.930865 TCGTCCAACATTTCATGTATATGATGA 59.069 33.333 9.32 0.64 44.07 2.92
53 54 8.011673 CGTCCAACATTTCATGTATATGATGAC 58.988 37.037 9.32 11.65 44.07 3.06
54 55 8.292448 GTCCAACATTTCATGTATATGATGACC 58.708 37.037 9.32 0.00 44.07 4.02
55 56 7.997803 TCCAACATTTCATGTATATGATGACCA 59.002 33.333 9.32 0.00 44.07 4.02
56 57 8.631797 CCAACATTTCATGTATATGATGACCAA 58.368 33.333 9.32 0.00 44.07 3.67
59 60 9.577222 ACATTTCATGTATATGATGACCAATCA 57.423 29.630 9.32 0.00 44.95 2.57
72 73 8.877864 TGATGACCAATCACCTTAATTTACTT 57.122 30.769 0.00 0.00 40.50 2.24
73 74 9.967451 TGATGACCAATCACCTTAATTTACTTA 57.033 29.630 0.00 0.00 40.50 2.24
75 76 8.570068 TGACCAATCACCTTAATTTACTTACC 57.430 34.615 0.00 0.00 0.00 2.85
76 77 8.387813 TGACCAATCACCTTAATTTACTTACCT 58.612 33.333 0.00 0.00 0.00 3.08
77 78 9.239551 GACCAATCACCTTAATTTACTTACCTT 57.760 33.333 0.00 0.00 0.00 3.50
78 79 9.239551 ACCAATCACCTTAATTTACTTACCTTC 57.760 33.333 0.00 0.00 0.00 3.46
79 80 9.462606 CCAATCACCTTAATTTACTTACCTTCT 57.537 33.333 0.00 0.00 0.00 2.85
83 84 9.498176 TCACCTTAATTTACTTACCTTCTGAAC 57.502 33.333 0.00 0.00 0.00 3.18
84 85 8.727910 CACCTTAATTTACTTACCTTCTGAACC 58.272 37.037 0.00 0.00 0.00 3.62
85 86 8.442374 ACCTTAATTTACTTACCTTCTGAACCA 58.558 33.333 0.00 0.00 0.00 3.67
86 87 9.292195 CCTTAATTTACTTACCTTCTGAACCAA 57.708 33.333 0.00 0.00 0.00 3.67
90 91 7.754851 TTTACTTACCTTCTGAACCAATTCC 57.245 36.000 0.00 0.00 33.49 3.01
91 92 5.319043 ACTTACCTTCTGAACCAATTCCA 57.681 39.130 0.00 0.00 33.49 3.53
92 93 5.070685 ACTTACCTTCTGAACCAATTCCAC 58.929 41.667 0.00 0.00 33.49 4.02
93 94 3.884037 ACCTTCTGAACCAATTCCACT 57.116 42.857 0.00 0.00 33.49 4.00
94 95 4.184649 ACCTTCTGAACCAATTCCACTT 57.815 40.909 0.00 0.00 33.49 3.16
95 96 4.546674 ACCTTCTGAACCAATTCCACTTT 58.453 39.130 0.00 0.00 33.49 2.66
96 97 5.701224 ACCTTCTGAACCAATTCCACTTTA 58.299 37.500 0.00 0.00 33.49 1.85
97 98 6.133356 ACCTTCTGAACCAATTCCACTTTAA 58.867 36.000 0.00 0.00 33.49 1.52
98 99 6.782494 ACCTTCTGAACCAATTCCACTTTAAT 59.218 34.615 0.00 0.00 33.49 1.40
99 100 7.290014 ACCTTCTGAACCAATTCCACTTTAATT 59.710 33.333 0.00 0.00 33.49 1.40
100 101 8.150296 CCTTCTGAACCAATTCCACTTTAATTT 58.850 33.333 0.00 0.00 33.49 1.82
102 103 9.974980 TTCTGAACCAATTCCACTTTAATTTAC 57.025 29.630 0.00 0.00 33.49 2.01
103 104 9.362151 TCTGAACCAATTCCACTTTAATTTACT 57.638 29.630 0.00 0.00 33.49 2.24
104 105 9.981114 CTGAACCAATTCCACTTTAATTTACTT 57.019 29.630 0.00 0.00 33.49 2.24
108 109 9.369672 ACCAATTCCACTTTAATTTACTTACCA 57.630 29.630 0.00 0.00 0.00 3.25
154 155 9.739276 AGGTAATTTACAGTCAGAATTTGATGA 57.261 29.630 8.73 0.00 38.29 2.92
174 175 8.613613 TGATGAACATTTATTTACACAATCGC 57.386 30.769 0.00 0.00 0.00 4.58
175 176 8.239998 TGATGAACATTTATTTACACAATCGCA 58.760 29.630 0.00 0.00 0.00 5.10
176 177 9.236691 GATGAACATTTATTTACACAATCGCAT 57.763 29.630 0.00 0.00 0.00 4.73
177 178 8.978564 TGAACATTTATTTACACAATCGCATT 57.021 26.923 0.00 0.00 0.00 3.56
189 190 9.662545 TTACACAATCGCATTATAATTGACATG 57.337 29.630 0.00 0.00 35.03 3.21
190 191 7.706159 ACACAATCGCATTATAATTGACATGT 58.294 30.769 0.00 0.00 35.03 3.21
191 192 8.835439 ACACAATCGCATTATAATTGACATGTA 58.165 29.630 0.00 0.00 35.03 2.29
192 193 9.662545 CACAATCGCATTATAATTGACATGTAA 57.337 29.630 0.00 0.00 35.03 2.41
197 198 9.877137 TCGCATTATAATTGACATGTAAATCAC 57.123 29.630 8.97 0.00 0.00 3.06
198 199 9.662545 CGCATTATAATTGACATGTAAATCACA 57.337 29.630 8.97 0.00 42.69 3.58
206 207 9.577110 AATTGACATGTAAATCACAAGCTAATG 57.423 29.630 8.97 0.00 41.55 1.90
207 208 7.686438 TGACATGTAAATCACAAGCTAATGT 57.314 32.000 0.00 0.00 41.55 2.71
208 209 8.785329 TGACATGTAAATCACAAGCTAATGTA 57.215 30.769 0.00 0.00 41.55 2.29
209 210 8.882736 TGACATGTAAATCACAAGCTAATGTAG 58.117 33.333 0.00 0.00 41.55 2.74
210 211 8.792830 ACATGTAAATCACAAGCTAATGTAGT 57.207 30.769 0.00 0.00 41.55 2.73
211 212 9.884636 ACATGTAAATCACAAGCTAATGTAGTA 57.115 29.630 0.00 0.00 41.55 1.82
242 243 3.339464 CGTTGTAACGCACGGGCA 61.339 61.111 11.77 0.00 46.06 5.36
243 244 2.673114 CGTTGTAACGCACGGGCAT 61.673 57.895 11.77 0.00 46.06 4.40
244 245 1.577421 GTTGTAACGCACGGGCATT 59.423 52.632 11.77 1.95 41.24 3.56
245 246 0.727793 GTTGTAACGCACGGGCATTG 60.728 55.000 11.77 0.00 41.24 2.82
246 247 1.167155 TTGTAACGCACGGGCATTGT 61.167 50.000 11.77 0.00 41.24 2.71
247 248 1.167155 TGTAACGCACGGGCATTGTT 61.167 50.000 11.77 8.72 41.24 2.83
248 249 0.453782 GTAACGCACGGGCATTGTTC 60.454 55.000 11.77 0.00 41.24 3.18
249 250 0.604243 TAACGCACGGGCATTGTTCT 60.604 50.000 11.77 0.00 41.24 3.01
250 251 0.604243 AACGCACGGGCATTGTTCTA 60.604 50.000 11.77 0.00 41.24 2.10
251 252 1.019278 ACGCACGGGCATTGTTCTAG 61.019 55.000 11.77 0.00 41.24 2.43
252 253 1.019278 CGCACGGGCATTGTTCTAGT 61.019 55.000 11.77 0.00 41.24 2.57
253 254 1.737696 CGCACGGGCATTGTTCTAGTA 60.738 52.381 11.77 0.00 41.24 1.82
254 255 1.664151 GCACGGGCATTGTTCTAGTAC 59.336 52.381 3.77 0.00 40.72 2.73
255 256 2.277084 CACGGGCATTGTTCTAGTACC 58.723 52.381 0.00 0.00 0.00 3.34
256 257 2.093658 CACGGGCATTGTTCTAGTACCT 60.094 50.000 0.00 0.00 0.00 3.08
257 258 2.570302 ACGGGCATTGTTCTAGTACCTT 59.430 45.455 0.00 0.00 0.00 3.50
258 259 3.008704 ACGGGCATTGTTCTAGTACCTTT 59.991 43.478 0.00 0.00 0.00 3.11
259 260 4.223477 ACGGGCATTGTTCTAGTACCTTTA 59.777 41.667 0.00 0.00 0.00 1.85
260 261 4.809426 CGGGCATTGTTCTAGTACCTTTAG 59.191 45.833 0.00 0.00 0.00 1.85
261 262 5.394883 CGGGCATTGTTCTAGTACCTTTAGA 60.395 44.000 0.00 0.00 0.00 2.10
262 263 6.049790 GGGCATTGTTCTAGTACCTTTAGAG 58.950 44.000 0.00 0.00 0.00 2.43
263 264 6.127140 GGGCATTGTTCTAGTACCTTTAGAGA 60.127 42.308 0.00 0.00 0.00 3.10
299 304 6.403878 TCATTTTAGGGGTTAGAACTCTTCG 58.596 40.000 0.00 0.00 34.02 3.79
310 315 4.402056 AGAACTCTTCGGTCAAAGTCAA 57.598 40.909 0.00 0.00 34.02 3.18
358 364 7.457380 AAAATCCCTCTATGATGGAAAGAGA 57.543 36.000 0.24 0.00 39.29 3.10
359 365 7.645132 AAATCCCTCTATGATGGAAAGAGAT 57.355 36.000 0.24 0.00 39.29 2.75
360 366 7.645132 AATCCCTCTATGATGGAAAGAGATT 57.355 36.000 0.24 0.00 39.29 2.40
361 367 8.748179 AATCCCTCTATGATGGAAAGAGATTA 57.252 34.615 0.24 0.00 39.29 1.75
363 369 7.967908 TCCCTCTATGATGGAAAGAGATTAAC 58.032 38.462 0.24 0.00 39.29 2.01
364 370 7.568738 TCCCTCTATGATGGAAAGAGATTAACA 59.431 37.037 0.24 0.00 39.29 2.41
365 371 8.381636 CCCTCTATGATGGAAAGAGATTAACAT 58.618 37.037 0.24 0.00 39.29 2.71
366 372 9.217278 CCTCTATGATGGAAAGAGATTAACATG 57.783 37.037 0.24 0.00 39.29 3.21
367 373 9.993454 CTCTATGATGGAAAGAGATTAACATGA 57.007 33.333 0.00 0.00 39.29 3.07
371 377 8.899427 TGATGGAAAGAGATTAACATGATCTC 57.101 34.615 12.75 12.75 46.32 2.75
393 399 8.155821 TCTCATTTTGTTCGTTTGTGGTATTA 57.844 30.769 0.00 0.00 0.00 0.98
395 401 8.958175 TCATTTTGTTCGTTTGTGGTATTATC 57.042 30.769 0.00 0.00 0.00 1.75
397 403 6.542574 TTTGTTCGTTTGTGGTATTATCGT 57.457 33.333 0.00 0.00 0.00 3.73
430 436 3.801050 CGATCAGACTCTTTACCATGCTG 59.199 47.826 0.00 0.00 0.00 4.41
458 464 0.515564 ACACGCTACAAAATCGCACC 59.484 50.000 0.00 0.00 0.00 5.01
464 470 3.303132 CGCTACAAAATCGCACCCTAATC 60.303 47.826 0.00 0.00 0.00 1.75
483 489 2.816689 TCGAGAACGTTTCTTTCTGCA 58.183 42.857 0.46 0.00 40.87 4.41
527 541 0.835971 TGAAGCTAGCCAGGTCACCA 60.836 55.000 12.13 0.00 0.00 4.17
597 612 2.993853 GAGAGAGTGGGGCCCAAG 59.006 66.667 30.70 0.00 34.18 3.61
602 617 3.267233 AGTGGGGCCCAAGATGCA 61.267 61.111 30.70 8.31 34.18 3.96
604 619 3.267233 TGGGGCCCAAGATGCACT 61.267 61.111 26.55 0.00 31.13 4.40
673 689 0.965439 GGCAGAGCAGAGTATCGGAT 59.035 55.000 0.00 0.00 42.67 4.18
685 701 5.048154 CAGAGTATCGGATCACATCACATCT 60.048 44.000 0.00 0.00 42.67 2.90
723 740 3.050275 GTGCTGCCCGTCTCCAAC 61.050 66.667 0.00 0.00 0.00 3.77
724 741 4.329545 TGCTGCCCGTCTCCAACC 62.330 66.667 0.00 0.00 0.00 3.77
725 742 4.329545 GCTGCCCGTCTCCAACCA 62.330 66.667 0.00 0.00 0.00 3.67
726 743 2.429930 CTGCCCGTCTCCAACCAA 59.570 61.111 0.00 0.00 0.00 3.67
727 744 1.228124 CTGCCCGTCTCCAACCAAA 60.228 57.895 0.00 0.00 0.00 3.28
728 745 0.609131 CTGCCCGTCTCCAACCAAAT 60.609 55.000 0.00 0.00 0.00 2.32
729 746 0.608035 TGCCCGTCTCCAACCAAATC 60.608 55.000 0.00 0.00 0.00 2.17
730 747 1.644786 GCCCGTCTCCAACCAAATCG 61.645 60.000 0.00 0.00 0.00 3.34
731 748 1.644786 CCCGTCTCCAACCAAATCGC 61.645 60.000 0.00 0.00 0.00 4.58
743 760 3.270027 ACCAAATCGCATCGAATTCTCA 58.730 40.909 3.52 0.00 39.99 3.27
804 825 2.094659 CGCGTGTGTGATCAGTCCC 61.095 63.158 0.00 0.00 0.00 4.46
805 826 1.005037 GCGTGTGTGATCAGTCCCA 60.005 57.895 0.00 0.00 0.00 4.37
925 946 4.695791 AGACCAACCCCCTCCCCC 62.696 72.222 0.00 0.00 0.00 5.40
1022 1048 0.039180 ACCGGGGAAATCAAGAACCC 59.961 55.000 6.32 0.00 41.41 4.11
1089 1115 4.144727 GGAGCGGGAGGAGGAGGA 62.145 72.222 0.00 0.00 0.00 3.71
1090 1116 2.520741 GAGCGGGAGGAGGAGGAG 60.521 72.222 0.00 0.00 0.00 3.69
1091 1117 4.150454 AGCGGGAGGAGGAGGAGG 62.150 72.222 0.00 0.00 0.00 4.30
1092 1118 4.144727 GCGGGAGGAGGAGGAGGA 62.145 72.222 0.00 0.00 0.00 3.71
1093 1119 2.197324 CGGGAGGAGGAGGAGGAG 59.803 72.222 0.00 0.00 0.00 3.69
1094 1120 2.612251 GGGAGGAGGAGGAGGAGG 59.388 72.222 0.00 0.00 0.00 4.30
1097 1123 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
1914 1970 7.040617 GCAGGTAATCATCAATTCACTCATCAT 60.041 37.037 0.00 0.00 0.00 2.45
1917 1973 9.674824 GGTAATCATCAATTCACTCATCATTTC 57.325 33.333 0.00 0.00 0.00 2.17
1935 1992 9.168353 CATCATTTCGATTATTAAATCAACGCA 57.832 29.630 0.00 0.00 41.44 5.24
1956 2013 2.044888 AACGCATTGCTTTACAACCG 57.955 45.000 7.12 0.00 42.27 4.44
1996 2053 0.392461 ATCACGTTGGCAGCCGTTAT 60.392 50.000 7.03 7.01 34.59 1.89
2027 2088 5.403766 GTCGATCCACTACAGCTATTGATTG 59.596 44.000 0.00 0.00 0.00 2.67
2040 2104 8.486210 ACAGCTATTGATTGGTATTGTTCTCTA 58.514 33.333 0.00 0.00 0.00 2.43
2217 2391 1.651240 CCACGAGTCCACGACCGTAT 61.651 60.000 0.00 0.00 37.36 3.06
2239 2413 3.130869 TGAGCAACTTGCAAGTTCATGTT 59.869 39.130 35.97 25.72 45.65 2.71
2427 3002 6.405397 GGTTTTCTTCACAAAAGGCAAGAGTA 60.405 38.462 0.00 0.00 0.00 2.59
2455 3030 1.001378 GCCACAAACCATCTGTGACAC 60.001 52.381 4.57 0.00 45.80 3.67
2457 3032 1.264020 CACAAACCATCTGTGACACGG 59.736 52.381 8.20 8.20 45.80 4.94
2458 3033 1.134220 ACAAACCATCTGTGACACGGT 60.134 47.619 14.06 5.73 0.00 4.83
2776 3351 0.179067 TCGAGTTTGCCACCTTCGTT 60.179 50.000 0.00 0.00 33.35 3.85
2791 3366 1.885560 TCGTTTGGCTTCGGATCAAA 58.114 45.000 0.00 0.00 0.00 2.69
2827 3402 1.453745 CCCCTACCGTGTACCGCTA 60.454 63.158 0.00 0.00 34.38 4.26
2833 3408 0.391130 ACCGTGTACCGCTACGACTA 60.391 55.000 5.14 0.00 42.54 2.59
2973 3548 8.665685 GGTGTATTACCTCATGAAGTTTTGTAG 58.334 37.037 1.50 0.00 46.51 2.74
3001 3576 1.692411 GGTTCCTCAAGTTTGGCACT 58.308 50.000 0.00 0.00 37.30 4.40
3004 3579 2.427095 GTTCCTCAAGTTTGGCACTGTT 59.573 45.455 0.00 0.00 35.12 3.16
3035 3610 3.002656 GGGTTTGATGTATGAGCGTCATG 59.997 47.826 9.77 0.00 37.70 3.07
3043 3618 1.039068 ATGAGCGTCATGAGGAGAGG 58.961 55.000 19.26 0.00 35.43 3.69
3199 3774 7.162062 CAGCGAAATAGCGTTTTTCATAGTTAC 59.838 37.037 8.91 0.00 43.00 2.50
3201 3776 8.323140 GCGAAATAGCGTTTTTCATAGTTACTA 58.677 33.333 0.00 0.00 33.61 1.82
3341 4197 1.336887 GCTAGGTTGTTGAGTCGAGCA 60.337 52.381 0.00 0.00 0.00 4.26
3354 4210 0.392706 TCGAGCACTCTCCTTTTGCA 59.607 50.000 0.00 0.00 38.81 4.08
3356 4212 1.606480 CGAGCACTCTCCTTTTGCAGA 60.606 52.381 0.00 0.00 38.81 4.26
3526 4396 9.911788 ACAATTCATAAATCTTCTATGACACCT 57.088 29.630 0.00 0.00 35.90 4.00
3549 4419 4.265073 AGTTAGATCATGGCTTGGTGAAC 58.735 43.478 0.00 1.05 0.00 3.18
3563 4433 4.164843 TGGTGAACCATATAGAAAGGGC 57.835 45.455 0.00 0.00 42.01 5.19
3572 4442 5.006386 CCATATAGAAAGGGCATCTCCAAC 58.994 45.833 0.00 0.00 36.21 3.77
3574 4444 0.678048 AGAAAGGGCATCTCCAACGC 60.678 55.000 0.00 0.00 36.21 4.84
3585 4455 2.281208 CCAACGCCGACCCTCAAA 60.281 61.111 0.00 0.00 0.00 2.69
3642 4512 2.282180 AAGCCATCCAACGCGGTT 60.282 55.556 12.47 0.00 35.57 4.44
3643 4513 2.253414 GAAGCCATCCAACGCGGTTC 62.253 60.000 12.47 0.00 35.57 3.62
3651 4521 1.418342 CCAACGCGGTTCTGTATCGG 61.418 60.000 12.47 0.00 0.00 4.18
3655 4525 1.514087 GCGGTTCTGTATCGGTCCA 59.486 57.895 0.00 0.00 0.00 4.02
3658 4528 1.538204 CGGTTCTGTATCGGTCCATGG 60.538 57.143 4.97 4.97 0.00 3.66
3660 4530 1.134521 GTTCTGTATCGGTCCATGGCA 60.135 52.381 6.96 0.00 0.00 4.92
3661 4531 1.423584 TCTGTATCGGTCCATGGCAT 58.576 50.000 6.96 0.00 0.00 4.40
3677 4547 0.519961 GCATTGCCGGACGTACTTTT 59.480 50.000 5.05 0.00 0.00 2.27
3679 4549 2.846693 CATTGCCGGACGTACTTTTTC 58.153 47.619 5.05 0.00 0.00 2.29
3680 4550 1.228533 TTGCCGGACGTACTTTTTCC 58.771 50.000 5.05 0.00 0.00 3.13
4023 4893 4.382320 GCTTACCACCCGGCGTCA 62.382 66.667 6.01 0.00 34.57 4.35
4037 4907 1.293963 GCGTCAGCTGTCTGCATTCA 61.294 55.000 14.67 0.00 45.94 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.348472 TGGTGGGAAGAAAGGTGAGAT 58.652 47.619 0.00 0.00 0.00 2.75
1 2 1.814429 TGGTGGGAAGAAAGGTGAGA 58.186 50.000 0.00 0.00 0.00 3.27
4 5 1.616994 GGGATGGTGGGAAGAAAGGTG 60.617 57.143 0.00 0.00 0.00 4.00
5 6 0.704664 GGGATGGTGGGAAGAAAGGT 59.295 55.000 0.00 0.00 0.00 3.50
6 7 1.002857 AGGGATGGTGGGAAGAAAGG 58.997 55.000 0.00 0.00 0.00 3.11
7 8 2.728007 GAAGGGATGGTGGGAAGAAAG 58.272 52.381 0.00 0.00 0.00 2.62
8 9 1.004277 CGAAGGGATGGTGGGAAGAAA 59.996 52.381 0.00 0.00 0.00 2.52
9 10 0.618458 CGAAGGGATGGTGGGAAGAA 59.382 55.000 0.00 0.00 0.00 2.52
10 11 0.546747 ACGAAGGGATGGTGGGAAGA 60.547 55.000 0.00 0.00 0.00 2.87
11 12 0.107654 GACGAAGGGATGGTGGGAAG 60.108 60.000 0.00 0.00 0.00 3.46
12 13 1.559065 GGACGAAGGGATGGTGGGAA 61.559 60.000 0.00 0.00 0.00 3.97
13 14 1.993391 GGACGAAGGGATGGTGGGA 60.993 63.158 0.00 0.00 0.00 4.37
14 15 1.847798 TTGGACGAAGGGATGGTGGG 61.848 60.000 0.00 0.00 0.00 4.61
15 16 0.676782 GTTGGACGAAGGGATGGTGG 60.677 60.000 0.00 0.00 0.00 4.61
16 17 0.036164 TGTTGGACGAAGGGATGGTG 59.964 55.000 0.00 0.00 0.00 4.17
17 18 0.991920 ATGTTGGACGAAGGGATGGT 59.008 50.000 0.00 0.00 0.00 3.55
18 19 2.128771 AATGTTGGACGAAGGGATGG 57.871 50.000 0.00 0.00 0.00 3.51
19 20 3.081061 TGAAATGTTGGACGAAGGGATG 58.919 45.455 0.00 0.00 0.00 3.51
20 21 3.433306 TGAAATGTTGGACGAAGGGAT 57.567 42.857 0.00 0.00 0.00 3.85
21 22 2.940994 TGAAATGTTGGACGAAGGGA 57.059 45.000 0.00 0.00 0.00 4.20
22 23 3.492421 CATGAAATGTTGGACGAAGGG 57.508 47.619 0.00 0.00 40.20 3.95
34 35 9.836076 GTGATTGGTCATCATATACATGAAATG 57.164 33.333 0.00 0.00 46.75 2.32
35 36 9.017509 GGTGATTGGTCATCATATACATGAAAT 57.982 33.333 0.00 0.00 44.11 2.17
36 37 8.219868 AGGTGATTGGTCATCATATACATGAAA 58.780 33.333 0.00 0.00 44.11 2.69
37 38 7.748677 AGGTGATTGGTCATCATATACATGAA 58.251 34.615 0.00 0.00 44.11 2.57
38 39 7.320384 AGGTGATTGGTCATCATATACATGA 57.680 36.000 0.00 0.00 44.11 3.07
39 40 7.991084 AAGGTGATTGGTCATCATATACATG 57.009 36.000 0.00 0.00 44.11 3.21
46 47 9.479549 AAGTAAATTAAGGTGATTGGTCATCAT 57.520 29.630 0.00 0.00 44.11 2.45
47 48 8.877864 AAGTAAATTAAGGTGATTGGTCATCA 57.122 30.769 0.00 0.00 37.97 3.07
49 50 9.185680 GGTAAGTAAATTAAGGTGATTGGTCAT 57.814 33.333 0.00 0.00 36.60 3.06
50 51 8.387813 AGGTAAGTAAATTAAGGTGATTGGTCA 58.612 33.333 0.00 0.00 0.00 4.02
51 52 8.803397 AGGTAAGTAAATTAAGGTGATTGGTC 57.197 34.615 0.00 0.00 0.00 4.02
52 53 9.239551 GAAGGTAAGTAAATTAAGGTGATTGGT 57.760 33.333 0.00 0.00 0.00 3.67
53 54 9.462606 AGAAGGTAAGTAAATTAAGGTGATTGG 57.537 33.333 0.00 0.00 0.00 3.16
57 58 9.498176 GTTCAGAAGGTAAGTAAATTAAGGTGA 57.502 33.333 0.00 0.00 0.00 4.02
58 59 8.727910 GGTTCAGAAGGTAAGTAAATTAAGGTG 58.272 37.037 0.00 0.00 0.00 4.00
59 60 8.442374 TGGTTCAGAAGGTAAGTAAATTAAGGT 58.558 33.333 0.00 0.00 0.00 3.50
60 61 8.857694 TGGTTCAGAAGGTAAGTAAATTAAGG 57.142 34.615 0.00 0.00 0.00 2.69
64 65 8.803235 GGAATTGGTTCAGAAGGTAAGTAAATT 58.197 33.333 0.00 0.00 36.01 1.82
65 66 7.947890 TGGAATTGGTTCAGAAGGTAAGTAAAT 59.052 33.333 0.00 0.00 36.01 1.40
66 67 7.229907 GTGGAATTGGTTCAGAAGGTAAGTAAA 59.770 37.037 0.00 0.00 36.01 2.01
67 68 6.713450 GTGGAATTGGTTCAGAAGGTAAGTAA 59.287 38.462 0.00 0.00 36.01 2.24
68 69 6.043938 AGTGGAATTGGTTCAGAAGGTAAGTA 59.956 38.462 0.00 0.00 36.01 2.24
69 70 5.070685 GTGGAATTGGTTCAGAAGGTAAGT 58.929 41.667 0.00 0.00 36.01 2.24
70 71 5.316987 AGTGGAATTGGTTCAGAAGGTAAG 58.683 41.667 0.00 0.00 36.01 2.34
71 72 5.319043 AGTGGAATTGGTTCAGAAGGTAA 57.681 39.130 0.00 0.00 36.01 2.85
72 73 4.993705 AGTGGAATTGGTTCAGAAGGTA 57.006 40.909 0.00 0.00 36.01 3.08
73 74 3.884037 AGTGGAATTGGTTCAGAAGGT 57.116 42.857 0.00 0.00 36.01 3.50
74 75 6.648879 TTAAAGTGGAATTGGTTCAGAAGG 57.351 37.500 0.00 0.00 36.01 3.46
76 77 9.974980 GTAAATTAAAGTGGAATTGGTTCAGAA 57.025 29.630 0.00 0.00 36.01 3.02
77 78 9.362151 AGTAAATTAAAGTGGAATTGGTTCAGA 57.638 29.630 0.00 0.00 36.01 3.27
78 79 9.981114 AAGTAAATTAAAGTGGAATTGGTTCAG 57.019 29.630 0.00 0.00 36.01 3.02
82 83 9.369672 TGGTAAGTAAATTAAAGTGGAATTGGT 57.630 29.630 0.00 0.00 0.00 3.67
128 129 9.739276 TCATCAAATTCTGACTGTAAATTACCT 57.261 29.630 0.18 0.00 36.69 3.08
148 149 9.071221 GCGATTGTGTAAATAAATGTTCATCAA 57.929 29.630 0.00 0.00 0.00 2.57
149 150 8.239998 TGCGATTGTGTAAATAAATGTTCATCA 58.760 29.630 0.00 0.00 0.00 3.07
150 151 8.613613 TGCGATTGTGTAAATAAATGTTCATC 57.386 30.769 0.00 0.00 0.00 2.92
151 152 9.585099 AATGCGATTGTGTAAATAAATGTTCAT 57.415 25.926 0.00 0.00 0.00 2.57
152 153 8.978564 AATGCGATTGTGTAAATAAATGTTCA 57.021 26.923 0.00 0.00 0.00 3.18
163 164 9.662545 CATGTCAATTATAATGCGATTGTGTAA 57.337 29.630 0.00 0.00 33.60 2.41
164 165 8.835439 ACATGTCAATTATAATGCGATTGTGTA 58.165 29.630 0.00 0.00 33.60 2.90
165 166 7.706159 ACATGTCAATTATAATGCGATTGTGT 58.294 30.769 0.00 3.86 33.60 3.72
166 167 9.662545 TTACATGTCAATTATAATGCGATTGTG 57.337 29.630 0.00 11.71 33.60 3.33
171 172 9.877137 GTGATTTACATGTCAATTATAATGCGA 57.123 29.630 0.00 0.00 0.00 5.10
172 173 9.662545 TGTGATTTACATGTCAATTATAATGCG 57.337 29.630 0.00 0.00 33.42 4.73
180 181 9.577110 CATTAGCTTGTGATTTACATGTCAATT 57.423 29.630 0.00 0.00 39.48 2.32
181 182 8.742777 ACATTAGCTTGTGATTTACATGTCAAT 58.257 29.630 0.00 2.53 39.48 2.57
182 183 8.109705 ACATTAGCTTGTGATTTACATGTCAA 57.890 30.769 0.00 0.00 39.48 3.18
183 184 7.686438 ACATTAGCTTGTGATTTACATGTCA 57.314 32.000 0.00 0.00 39.48 3.58
184 185 8.883731 ACTACATTAGCTTGTGATTTACATGTC 58.116 33.333 0.00 0.00 39.48 3.06
185 186 8.792830 ACTACATTAGCTTGTGATTTACATGT 57.207 30.769 2.69 2.69 39.48 3.21
226 227 0.727793 CAATGCCCGTGCGTTACAAC 60.728 55.000 0.00 0.00 44.83 3.32
227 228 1.167155 ACAATGCCCGTGCGTTACAA 61.167 50.000 0.00 0.00 44.83 2.41
228 229 1.167155 AACAATGCCCGTGCGTTACA 61.167 50.000 0.00 0.00 44.83 2.41
229 230 0.453782 GAACAATGCCCGTGCGTTAC 60.454 55.000 0.00 0.00 44.83 2.50
230 231 0.604243 AGAACAATGCCCGTGCGTTA 60.604 50.000 0.00 0.00 44.83 3.18
232 233 1.004320 TAGAACAATGCCCGTGCGT 60.004 52.632 0.00 0.00 41.78 5.24
233 234 1.019278 ACTAGAACAATGCCCGTGCG 61.019 55.000 0.00 0.00 41.78 5.34
234 235 1.664151 GTACTAGAACAATGCCCGTGC 59.336 52.381 0.00 0.00 38.26 5.34
235 236 2.093658 AGGTACTAGAACAATGCCCGTG 60.094 50.000 0.00 0.00 36.02 4.94
236 237 2.185387 AGGTACTAGAACAATGCCCGT 58.815 47.619 0.00 0.00 36.02 5.28
237 238 2.981859 AGGTACTAGAACAATGCCCG 57.018 50.000 0.00 0.00 36.02 6.13
238 239 5.985911 TCTAAAGGTACTAGAACAATGCCC 58.014 41.667 0.00 0.00 38.49 5.36
239 240 6.875076 TCTCTAAAGGTACTAGAACAATGCC 58.125 40.000 0.00 0.00 38.49 4.40
240 241 8.950208 AATCTCTAAAGGTACTAGAACAATGC 57.050 34.615 0.00 0.00 38.49 3.56
259 260 9.790344 CCCTAAAATGAGATCATGTTAATCTCT 57.210 33.333 18.58 6.20 46.14 3.10
260 261 9.007901 CCCCTAAAATGAGATCATGTTAATCTC 57.992 37.037 13.46 13.46 46.16 2.75
261 262 8.506083 ACCCCTAAAATGAGATCATGTTAATCT 58.494 33.333 6.85 0.00 36.07 2.40
262 263 8.697507 ACCCCTAAAATGAGATCATGTTAATC 57.302 34.615 6.85 0.00 36.07 1.75
271 272 7.797062 AGAGTTCTAACCCCTAAAATGAGATC 58.203 38.462 0.00 0.00 0.00 2.75
277 278 5.250082 ACCGAAGAGTTCTAACCCCTAAAAT 59.750 40.000 0.00 0.00 0.00 1.82
289 290 4.120589 GTTGACTTTGACCGAAGAGTTCT 58.879 43.478 4.13 0.00 0.00 3.01
299 304 5.532779 AGATTCCTCTTTGTTGACTTTGACC 59.467 40.000 0.00 0.00 0.00 4.02
310 315 2.026449 CAGGCTCCAGATTCCTCTTTGT 60.026 50.000 0.00 0.00 0.00 2.83
345 351 9.504708 GAGATCATGTTAATCTCTTTCCATCAT 57.495 33.333 13.19 0.00 43.78 2.45
347 353 8.899427 TGAGATCATGTTAATCTCTTTCCATC 57.101 34.615 18.58 0.32 46.14 3.51
355 361 9.430838 CGAACAAAATGAGATCATGTTAATCTC 57.569 33.333 13.46 13.46 46.16 2.75
356 362 8.950210 ACGAACAAAATGAGATCATGTTAATCT 58.050 29.630 0.00 0.00 36.56 2.40
357 363 9.559958 AACGAACAAAATGAGATCATGTTAATC 57.440 29.630 0.00 0.48 36.56 1.75
358 364 9.912634 AAACGAACAAAATGAGATCATGTTAAT 57.087 25.926 0.00 0.00 36.56 1.40
359 365 9.179552 CAAACGAACAAAATGAGATCATGTTAA 57.820 29.630 0.00 0.00 36.56 2.01
360 366 8.349245 ACAAACGAACAAAATGAGATCATGTTA 58.651 29.630 0.00 0.00 36.56 2.41
361 367 7.167968 CACAAACGAACAAAATGAGATCATGTT 59.832 33.333 0.00 0.00 36.56 2.71
363 369 6.088483 CCACAAACGAACAAAATGAGATCATG 59.912 38.462 0.00 0.00 36.56 3.07
364 370 6.151691 CCACAAACGAACAAAATGAGATCAT 58.848 36.000 0.00 0.00 38.41 2.45
365 371 5.067153 ACCACAAACGAACAAAATGAGATCA 59.933 36.000 0.00 0.00 0.00 2.92
366 372 5.519722 ACCACAAACGAACAAAATGAGATC 58.480 37.500 0.00 0.00 0.00 2.75
367 373 5.514274 ACCACAAACGAACAAAATGAGAT 57.486 34.783 0.00 0.00 0.00 2.75
368 374 4.974368 ACCACAAACGAACAAAATGAGA 57.026 36.364 0.00 0.00 0.00 3.27
369 375 8.964420 ATAATACCACAAACGAACAAAATGAG 57.036 30.769 0.00 0.00 0.00 2.90
370 376 7.746916 CGATAATACCACAAACGAACAAAATGA 59.253 33.333 0.00 0.00 0.00 2.57
371 377 7.535940 ACGATAATACCACAAACGAACAAAATG 59.464 33.333 0.00 0.00 0.00 2.32
372 378 7.586747 ACGATAATACCACAAACGAACAAAAT 58.413 30.769 0.00 0.00 0.00 1.82
373 379 6.957150 ACGATAATACCACAAACGAACAAAA 58.043 32.000 0.00 0.00 0.00 2.44
380 386 4.567558 TGCCTTACGATAATACCACAAACG 59.432 41.667 0.00 0.00 0.00 3.60
393 399 2.694829 GATCGCCGGTGCCTTACGAT 62.695 60.000 11.05 10.49 45.37 3.73
395 401 2.960129 GATCGCCGGTGCCTTACG 60.960 66.667 11.05 0.00 0.00 3.18
397 403 2.055633 TCTGATCGCCGGTGCCTTA 61.056 57.895 11.05 0.00 0.00 2.69
430 436 1.762419 TTGTAGCGTGTCACTCGTTC 58.238 50.000 0.60 0.00 0.00 3.95
458 464 5.444745 GCAGAAAGAAACGTTCTCGATTAGG 60.445 44.000 0.00 1.47 39.61 2.69
464 470 3.242284 TGTTGCAGAAAGAAACGTTCTCG 60.242 43.478 0.00 0.00 38.74 4.04
483 489 1.406069 GGCTCATGACATCTCCGTGTT 60.406 52.381 0.00 0.00 31.16 3.32
579 594 3.003173 TTGGGCCCCACTCTCTCG 61.003 66.667 22.27 0.00 30.78 4.04
597 612 2.983229 ACTGATTCAGGTGAGTGCATC 58.017 47.619 17.66 0.00 35.51 3.91
602 617 1.338200 GCGGAACTGATTCAGGTGAGT 60.338 52.381 17.66 0.00 36.46 3.41
604 619 0.684535 TGCGGAACTGATTCAGGTGA 59.315 50.000 17.66 0.00 36.46 4.02
673 689 2.094078 TGCGTGATGAGATGTGATGTGA 60.094 45.455 0.00 0.00 0.00 3.58
685 701 4.032786 CACAACGAATTCTATGCGTGATGA 59.967 41.667 3.52 0.00 38.39 2.92
723 740 3.950087 TGAGAATTCGATGCGATTTGG 57.050 42.857 0.00 0.00 35.23 3.28
724 741 5.086888 TGATGAGAATTCGATGCGATTTG 57.913 39.130 0.00 0.00 35.23 2.32
725 742 5.334646 CCATGATGAGAATTCGATGCGATTT 60.335 40.000 0.00 0.00 35.23 2.17
726 743 4.153655 CCATGATGAGAATTCGATGCGATT 59.846 41.667 0.00 0.00 35.23 3.34
727 744 3.683340 CCATGATGAGAATTCGATGCGAT 59.317 43.478 0.00 0.00 35.23 4.58
728 745 3.062042 CCATGATGAGAATTCGATGCGA 58.938 45.455 0.00 0.00 0.00 5.10
729 746 3.062042 TCCATGATGAGAATTCGATGCG 58.938 45.455 0.00 0.00 0.00 4.73
730 747 5.391736 GGATTCCATGATGAGAATTCGATGC 60.392 44.000 9.46 0.00 32.91 3.91
731 748 6.179504 GGATTCCATGATGAGAATTCGATG 57.820 41.667 9.46 0.00 32.91 3.84
743 760 2.028658 CGAGATCCACGGATTCCATGAT 60.029 50.000 0.00 0.00 34.60 2.45
1079 1105 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
1080 1106 0.998945 CTCCTCCTCCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
1081 1107 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
1082 1108 1.541672 CCTCCTCCTCCTCCTCCTC 59.458 68.421 0.00 0.00 0.00 3.71
1083 1109 2.018086 CCCTCCTCCTCCTCCTCCT 61.018 68.421 0.00 0.00 0.00 3.69
1084 1110 2.612251 CCCTCCTCCTCCTCCTCC 59.388 72.222 0.00 0.00 0.00 4.30
1085 1111 2.612251 CCCCTCCTCCTCCTCCTC 59.388 72.222 0.00 0.00 0.00 3.71
1086 1112 3.773154 GCCCCTCCTCCTCCTCCT 61.773 72.222 0.00 0.00 0.00 3.69
1087 1113 4.890306 GGCCCCTCCTCCTCCTCC 62.890 77.778 0.00 0.00 0.00 4.30
1094 1120 3.866582 CATGTCCGGCCCCTCCTC 61.867 72.222 0.00 0.00 0.00 3.71
1914 1970 8.359409 CGTTTTGCGTTGATTTAATAATCGAAA 58.641 29.630 0.00 0.00 38.38 3.46
1917 1973 6.104622 GCGTTTTGCGTTGATTTAATAATCG 58.895 36.000 0.00 0.00 41.76 3.34
1935 1992 2.792116 CGGTTGTAAAGCAATGCGTTTT 59.208 40.909 12.10 4.73 46.59 2.43
1986 2043 3.120792 TCGACAGAAATATAACGGCTGC 58.879 45.455 0.00 0.00 0.00 5.25
2027 2088 9.204570 ACGCATTAATATGTAGAGAACAATACC 57.795 33.333 0.00 0.00 42.70 2.73
2040 2104 9.230122 TGATCATGGAAATACGCATTAATATGT 57.770 29.630 0.00 0.00 34.12 2.29
2068 2132 4.265856 TCCATCCATCTGGTGTACTAGT 57.734 45.455 0.00 0.00 37.57 2.57
2069 2133 5.815233 AATCCATCCATCTGGTGTACTAG 57.185 43.478 0.00 0.00 37.57 2.57
2239 2413 7.759489 AAAAACTTGGCTGAACATATCTGTA 57.241 32.000 0.00 0.00 33.36 2.74
2427 3002 1.347378 GATGGTTTGTGGCCAAATGGT 59.653 47.619 7.24 0.00 42.26 3.55
2455 3030 4.406069 CTGCATTTCAGTGACATTAACCG 58.594 43.478 0.00 0.00 38.02 4.44
2457 3032 4.168760 GCCTGCATTTCAGTGACATTAAC 58.831 43.478 0.00 0.00 41.25 2.01
2458 3033 3.825585 TGCCTGCATTTCAGTGACATTAA 59.174 39.130 0.00 0.00 41.25 1.40
2470 3045 1.746615 AGCGATCGTGCCTGCATTT 60.747 52.632 17.81 0.00 34.65 2.32
2626 3201 0.817634 TATTGAAGATTGGGGCGCGG 60.818 55.000 8.83 0.00 0.00 6.46
2776 3351 1.582610 GCCGTTTGATCCGAAGCCAA 61.583 55.000 0.00 0.00 0.00 4.52
2827 3402 4.013702 ACGATGCCTGGTAGTCGT 57.986 55.556 14.30 14.30 41.90 4.34
2833 3408 1.194781 AGAGGACAACGATGCCTGGT 61.195 55.000 12.11 0.00 34.52 4.00
3001 3576 0.109532 TCAAACCCTCGCCATCAACA 59.890 50.000 0.00 0.00 0.00 3.33
3004 3579 0.327924 ACATCAAACCCTCGCCATCA 59.672 50.000 0.00 0.00 0.00 3.07
3035 3610 0.466124 CCGACATTTCCCCTCTCCTC 59.534 60.000 0.00 0.00 0.00 3.71
3043 3618 1.539827 CCTCAAACACCGACATTTCCC 59.460 52.381 0.00 0.00 0.00 3.97
3214 4068 2.278142 GCCATAAAAGCGGCGCAG 60.278 61.111 35.02 15.17 38.82 5.18
3236 4090 8.136057 AGAGAAAAGCAATGATATGTACGAAG 57.864 34.615 0.00 0.00 0.00 3.79
3341 4197 7.530426 AAAACATAATCTGCAAAAGGAGAGT 57.470 32.000 0.00 0.00 0.00 3.24
3379 4235 3.683847 GCAATGCTTCTCTCCTACCACAT 60.684 47.826 0.00 0.00 0.00 3.21
3526 4396 5.428253 GTTCACCAAGCCATGATCTAACTA 58.572 41.667 0.00 0.00 0.00 2.24
3549 4419 4.916041 TGGAGATGCCCTTTCTATATGG 57.084 45.455 0.00 0.00 34.97 2.74
3563 4433 2.511600 GGGTCGGCGTTGGAGATG 60.512 66.667 6.85 0.00 0.00 2.90
3572 4442 2.434359 GAGGTTTGAGGGTCGGCG 60.434 66.667 0.00 0.00 0.00 6.46
3574 4444 2.669240 GGGAGGTTTGAGGGTCGG 59.331 66.667 0.00 0.00 0.00 4.79
3639 4509 1.810412 GCCATGGACCGATACAGAACC 60.810 57.143 18.40 0.00 0.00 3.62
3642 4512 1.423584 ATGCCATGGACCGATACAGA 58.576 50.000 18.40 0.00 0.00 3.41
3643 4513 1.875514 CAATGCCATGGACCGATACAG 59.124 52.381 18.40 0.00 0.00 2.74
3658 4528 0.519961 AAAAGTACGTCCGGCAATGC 59.480 50.000 0.00 0.00 0.00 3.56
3660 4530 1.808343 GGAAAAAGTACGTCCGGCAAT 59.192 47.619 0.00 0.00 0.00 3.56
3661 4531 1.228533 GGAAAAAGTACGTCCGGCAA 58.771 50.000 0.00 0.00 0.00 4.52
3666 4536 1.228533 TTGCGGGAAAAAGTACGTCC 58.771 50.000 0.00 0.00 0.00 4.79
3668 4538 1.334556 GGTTTGCGGGAAAAAGTACGT 59.665 47.619 0.00 0.00 0.00 3.57
4006 4876 4.382320 TGACGCCGGGTGGTAAGC 62.382 66.667 12.97 0.00 37.67 3.09
4007 4877 2.125673 CTGACGCCGGGTGGTAAG 60.126 66.667 12.97 1.57 37.67 2.34
4008 4878 4.382320 GCTGACGCCGGGTGGTAA 62.382 66.667 12.97 0.00 37.67 2.85
4017 4887 1.975363 GAATGCAGACAGCTGACGCC 61.975 60.000 23.35 11.17 45.17 5.68
4018 4888 1.293963 TGAATGCAGACAGCTGACGC 61.294 55.000 23.35 20.86 45.17 5.19
4019 4889 1.062148 CATGAATGCAGACAGCTGACG 59.938 52.381 23.35 11.82 45.17 4.35
4020 4890 2.826979 CATGAATGCAGACAGCTGAC 57.173 50.000 23.35 15.44 45.17 3.51
4031 4901 1.002684 GCTCTACAGCAGCATGAATGC 60.003 52.381 13.76 13.76 46.06 3.56


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

AutoCloner maintained by Alex Coulton.