Multiple sequence alignment - TraesCS3D01G502000

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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 TraesCS3D01G502000 chr3D 100.000 3551 0 0 1 3551 590679062 590675512 0.000000e+00 6558
1 TraesCS3D01G502000 chr3D 87.478 1741 148 28 958 2675 590525870 590524177 0.000000e+00 1943
2 TraesCS3D01G502000 chr3D 92.833 293 21 0 2163 2455 360589894 360590186 3.280000e-115 425
3 TraesCS3D01G502000 chr3D 76.994 326 41 8 2825 3116 188352460 188352785 4.750000e-34 156
4 TraesCS3D01G502000 chr3B 90.929 2337 142 32 315 2618 790543396 790541097 0.000000e+00 3077
5 TraesCS3D01G502000 chr3B 87.790 1810 150 34 907 2672 790521199 790522981 0.000000e+00 2052
6 TraesCS3D01G502000 chr3B 93.860 228 14 0 1 228 686019333 686019560 9.440000e-91 344
7 TraesCS3D01G502000 chr3B 86.316 190 13 7 2640 2827 790541104 790540926 1.010000e-45 195
8 TraesCS3D01G502000 chr3A 92.058 2065 122 18 553 2607 721223907 721221875 0.000000e+00 2867
9 TraesCS3D01G502000 chr3A 88.889 1746 151 21 958 2675 721085819 721087549 0.000000e+00 2109
10 TraesCS3D01G502000 chr3A 77.373 769 95 30 2824 3544 127968903 127968166 2.000000e-102 383
11 TraesCS3D01G502000 chr3A 93.033 244 12 3 322 564 721224178 721223939 5.640000e-93 351
12 TraesCS3D01G502000 chr3A 93.421 228 15 0 1 228 19604794 19605021 4.390000e-89 339
13 TraesCS3D01G502000 chr3A 90.206 194 16 3 2636 2827 721221874 721221682 2.120000e-62 250
14 TraesCS3D01G502000 chr1B 80.261 765 90 25 2827 3551 498039500 498038757 1.460000e-143 520
15 TraesCS3D01G502000 chr1B 79.800 599 74 26 2977 3551 654914662 654914087 3.320000e-105 392
16 TraesCS3D01G502000 chr7D 78.320 738 101 29 2826 3532 511666468 511665759 4.240000e-114 422
17 TraesCS3D01G502000 chr7D 83.848 421 56 9 3140 3551 384950284 384949867 1.200000e-104 390
18 TraesCS3D01G502000 chr7D 76.285 759 101 38 2827 3544 535734000 535734720 7.350000e-87 331
19 TraesCS3D01G502000 chr7D 75.563 311 50 15 2825 3116 602026551 602026854 2.880000e-26 130
20 TraesCS3D01G502000 chr5A 77.454 754 102 24 2827 3544 290469081 290468360 4.300000e-104 388
21 TraesCS3D01G502000 chr5A 80.672 476 54 25 3069 3531 479653997 479654447 5.680000e-88 335
22 TraesCS3D01G502000 chr4B 92.683 246 16 2 1 244 125423278 125423523 1.570000e-93 353
23 TraesCS3D01G502000 chr4B 93.506 231 15 0 1 231 125384408 125384178 9.440000e-91 344
24 TraesCS3D01G502000 chr4B 93.886 229 13 1 4 231 147353517 147353289 9.440000e-91 344
25 TraesCS3D01G502000 chr4B 75.668 711 97 34 2815 3476 89054598 89053915 5.800000e-73 285
26 TraesCS3D01G502000 chr4B 87.591 137 17 0 2825 2961 500076730 500076866 3.670000e-35 159
27 TraesCS3D01G502000 chr4B 80.628 191 32 4 2830 3018 444097779 444097966 3.700000e-30 143
28 TraesCS3D01G502000 chr2B 93.562 233 15 0 1 233 652842757 652842525 7.300000e-92 348
29 TraesCS3D01G502000 chrUn 93.860 228 14 0 1 228 309589536 309589309 9.440000e-91 344
30 TraesCS3D01G502000 chrUn 93.860 228 14 0 1 228 361598812 361599039 9.440000e-91 344
31 TraesCS3D01G502000 chr4D 93.074 231 16 0 1 231 201441915 201441685 4.390000e-89 339
32 TraesCS3D01G502000 chr7B 81.633 392 55 15 3167 3544 105833223 105832835 3.440000e-80 309
33 TraesCS3D01G502000 chr6D 81.519 395 54 13 3165 3544 423800863 423800473 1.240000e-79 307
34 TraesCS3D01G502000 chr2A 80.317 315 40 7 2824 3116 598978685 598978371 5.970000e-53 219
35 TraesCS3D01G502000 chr6B 82.143 224 36 4 2825 3047 707801119 707801339 4.680000e-44 189
36 TraesCS3D01G502000 chr6B 78.481 316 46 10 2824 3117 153549343 153549028 1.680000e-43 187
37 TraesCS3D01G502000 chr2D 82.500 240 18 7 2832 3047 192725784 192726023 4.680000e-44 189
38 TraesCS3D01G502000 chr2D 77.607 326 36 10 2827 3116 615992121 615991797 2.840000e-36 163
39 TraesCS3D01G502000 chr5D 87.591 137 17 0 2825 2961 473443909 473444045 3.670000e-35 159


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 TraesCS3D01G502000 chr3D 590675512 590679062 3550 True 6558 6558 100.000000 1 3551 1 chr3D.!!$R2 3550
1 TraesCS3D01G502000 chr3D 590524177 590525870 1693 True 1943 1943 87.478000 958 2675 1 chr3D.!!$R1 1717
2 TraesCS3D01G502000 chr3B 790521199 790522981 1782 False 2052 2052 87.790000 907 2672 1 chr3B.!!$F2 1765
3 TraesCS3D01G502000 chr3B 790540926 790543396 2470 True 1636 3077 88.622500 315 2827 2 chr3B.!!$R1 2512
4 TraesCS3D01G502000 chr3A 721085819 721087549 1730 False 2109 2109 88.889000 958 2675 1 chr3A.!!$F2 1717
5 TraesCS3D01G502000 chr3A 721221682 721224178 2496 True 1156 2867 91.765667 322 2827 3 chr3A.!!$R2 2505
6 TraesCS3D01G502000 chr3A 127968166 127968903 737 True 383 383 77.373000 2824 3544 1 chr3A.!!$R1 720
7 TraesCS3D01G502000 chr1B 498038757 498039500 743 True 520 520 80.261000 2827 3551 1 chr1B.!!$R1 724
8 TraesCS3D01G502000 chr1B 654914087 654914662 575 True 392 392 79.800000 2977 3551 1 chr1B.!!$R2 574
9 TraesCS3D01G502000 chr7D 511665759 511666468 709 True 422 422 78.320000 2826 3532 1 chr7D.!!$R2 706
10 TraesCS3D01G502000 chr7D 535734000 535734720 720 False 331 331 76.285000 2827 3544 1 chr7D.!!$F1 717
11 TraesCS3D01G502000 chr5A 290468360 290469081 721 True 388 388 77.454000 2827 3544 1 chr5A.!!$R1 717
12 TraesCS3D01G502000 chr4B 89053915 89054598 683 True 285 285 75.668000 2815 3476 1 chr4B.!!$R1 661

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
88 89 0.031585 GCCCAACCGGTCAGTTTTTC 59.968 55.0 8.04 0.0 0.00 2.29 F
301 302 0.036577 CCCAGCCAAGAGACTCTGTG 60.037 60.0 5.55 6.7 0.00 3.66 F
442 443 0.392461 CTGCCAGCTTTAGCCCGTAA 60.392 55.0 0.00 0.0 43.38 3.18 F
942 995 0.396435 AGCCGATCTGACCAAACACA 59.604 50.0 0.00 0.0 0.00 3.72 F
948 1001 0.464036 TCTGACCAAACACAGAGCGT 59.536 50.0 0.00 0.0 38.08 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1128 1198 0.943835 CGCACATGACAACGGTGAGA 60.944 55.000 7.88 0.0 34.81 3.27 R
1970 2052 1.227556 GTGGTGTGCACTTCCGAGT 60.228 57.895 19.41 0.0 36.25 4.18 R
2113 2222 2.126031 GTTCGCCGTCTCCAGGAC 60.126 66.667 0.00 0.0 41.28 3.85 R
2540 2649 1.218316 CCAACCAGCTACGGACCTC 59.782 63.158 0.00 0.0 0.00 3.85 R
2859 3003 1.595929 GACCCAAACGGACGCAGAA 60.596 57.895 0.00 0.0 34.64 3.02 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 4.175489 TCGTCCTAGTCAGCGCGC 62.175 66.667 26.66 26.66 0.00 6.86
18 19 4.476410 CGTCCTAGTCAGCGCGCA 62.476 66.667 35.10 11.24 0.00 6.09
19 20 2.580867 GTCCTAGTCAGCGCGCAG 60.581 66.667 35.10 26.96 0.00 5.18
20 21 3.062466 TCCTAGTCAGCGCGCAGT 61.062 61.111 35.10 18.98 0.00 4.40
21 22 2.580867 CCTAGTCAGCGCGCAGTC 60.581 66.667 35.10 23.26 0.00 3.51
22 23 2.179267 CTAGTCAGCGCGCAGTCA 59.821 61.111 35.10 12.97 0.00 3.41
23 24 1.871345 CTAGTCAGCGCGCAGTCAG 60.871 63.158 35.10 18.64 0.00 3.51
24 25 3.971453 TAGTCAGCGCGCAGTCAGC 62.971 63.158 35.10 16.15 40.87 4.26
84 85 4.280019 GGGCCCAACCGGTCAGTT 62.280 66.667 19.95 0.00 38.37 3.16
85 86 2.203437 GGCCCAACCGGTCAGTTT 60.203 61.111 8.04 0.00 35.67 2.66
86 87 1.830847 GGCCCAACCGGTCAGTTTT 60.831 57.895 8.04 0.00 35.67 2.43
87 88 1.396607 GGCCCAACCGGTCAGTTTTT 61.397 55.000 8.04 0.00 35.67 1.94
88 89 0.031585 GCCCAACCGGTCAGTTTTTC 59.968 55.000 8.04 0.00 0.00 2.29
89 90 1.687563 CCCAACCGGTCAGTTTTTCT 58.312 50.000 8.04 0.00 0.00 2.52
90 91 1.336755 CCCAACCGGTCAGTTTTTCTG 59.663 52.381 8.04 0.00 44.85 3.02
91 92 2.021457 CCAACCGGTCAGTTTTTCTGT 58.979 47.619 8.04 0.00 43.97 3.41
92 93 2.032924 CCAACCGGTCAGTTTTTCTGTC 59.967 50.000 8.04 0.00 43.97 3.51
93 94 1.963172 ACCGGTCAGTTTTTCTGTCC 58.037 50.000 0.00 0.00 44.76 4.02
97 98 3.288809 GGTCAGTTTTTCTGTCCATGC 57.711 47.619 6.33 0.00 46.48 4.06
98 99 2.350772 GGTCAGTTTTTCTGTCCATGCG 60.351 50.000 6.33 0.00 46.48 4.73
99 100 2.290641 GTCAGTTTTTCTGTCCATGCGT 59.709 45.455 0.00 0.00 43.97 5.24
100 101 3.496884 GTCAGTTTTTCTGTCCATGCGTA 59.503 43.478 0.00 0.00 43.97 4.42
101 102 4.154195 GTCAGTTTTTCTGTCCATGCGTAT 59.846 41.667 0.00 0.00 43.97 3.06
102 103 5.350365 GTCAGTTTTTCTGTCCATGCGTATA 59.650 40.000 0.00 0.00 43.97 1.47
103 104 5.935206 TCAGTTTTTCTGTCCATGCGTATAA 59.065 36.000 0.00 0.00 43.97 0.98
104 105 6.428465 TCAGTTTTTCTGTCCATGCGTATAAA 59.572 34.615 0.00 0.00 43.97 1.40
105 106 7.041030 TCAGTTTTTCTGTCCATGCGTATAAAA 60.041 33.333 0.00 0.00 43.97 1.52
106 107 7.060633 CAGTTTTTCTGTCCATGCGTATAAAAC 59.939 37.037 9.23 9.23 39.17 2.43
122 123 8.703823 CGTATAAAACGCACTTTTAGTCTTTT 57.296 30.769 3.47 0.00 46.10 2.27
123 124 9.161684 CGTATAAAACGCACTTTTAGTCTTTTT 57.838 29.630 3.47 0.00 46.10 1.94
137 138 2.026879 TTTTTGCAACGGCTCGCC 59.973 55.556 0.00 0.00 41.91 5.54
138 139 3.492311 TTTTTGCAACGGCTCGCCC 62.492 57.895 0.00 0.00 41.91 6.13
139 140 4.947147 TTTGCAACGGCTCGCCCT 62.947 61.111 0.00 0.00 41.91 5.19
140 141 3.538785 TTTGCAACGGCTCGCCCTA 62.539 57.895 0.00 0.00 41.91 3.53
141 142 3.538785 TTGCAACGGCTCGCCCTAA 62.539 57.895 0.00 0.00 41.91 2.69
142 143 2.513897 GCAACGGCTCGCCCTAAT 60.514 61.111 1.72 0.00 36.96 1.73
143 144 2.534903 GCAACGGCTCGCCCTAATC 61.535 63.158 1.72 0.00 36.96 1.75
144 145 1.144057 CAACGGCTCGCCCTAATCT 59.856 57.895 1.72 0.00 0.00 2.40
145 146 0.462047 CAACGGCTCGCCCTAATCTT 60.462 55.000 1.72 0.00 0.00 2.40
146 147 0.462047 AACGGCTCGCCCTAATCTTG 60.462 55.000 1.72 0.00 0.00 3.02
147 148 1.595382 CGGCTCGCCCTAATCTTGG 60.595 63.158 1.72 0.00 0.00 3.61
148 149 1.527370 GGCTCGCCCTAATCTTGGT 59.473 57.895 0.00 0.00 0.00 3.67
149 150 0.756903 GGCTCGCCCTAATCTTGGTA 59.243 55.000 0.00 0.00 0.00 3.25
150 151 1.540580 GGCTCGCCCTAATCTTGGTAC 60.541 57.143 0.00 0.00 0.00 3.34
151 152 1.413077 GCTCGCCCTAATCTTGGTACT 59.587 52.381 0.00 0.00 0.00 2.73
152 153 2.803492 GCTCGCCCTAATCTTGGTACTG 60.803 54.545 0.00 0.00 0.00 2.74
153 154 2.693591 CTCGCCCTAATCTTGGTACTGA 59.306 50.000 0.00 0.00 0.00 3.41
154 155 2.429610 TCGCCCTAATCTTGGTACTGAC 59.570 50.000 0.00 0.00 0.00 3.51
155 156 2.167693 CGCCCTAATCTTGGTACTGACA 59.832 50.000 0.00 0.00 0.00 3.58
156 157 3.532542 GCCCTAATCTTGGTACTGACAC 58.467 50.000 0.00 0.00 0.00 3.67
157 158 3.782046 CCCTAATCTTGGTACTGACACG 58.218 50.000 0.00 0.00 0.00 4.49
158 159 3.194968 CCCTAATCTTGGTACTGACACGT 59.805 47.826 0.00 0.00 0.00 4.49
159 160 4.400251 CCCTAATCTTGGTACTGACACGTA 59.600 45.833 0.00 0.00 0.00 3.57
160 161 5.105635 CCCTAATCTTGGTACTGACACGTAA 60.106 44.000 0.00 0.00 0.00 3.18
161 162 6.392354 CCTAATCTTGGTACTGACACGTAAA 58.608 40.000 0.00 0.00 0.00 2.01
162 163 6.869913 CCTAATCTTGGTACTGACACGTAAAA 59.130 38.462 0.00 0.00 0.00 1.52
163 164 7.385752 CCTAATCTTGGTACTGACACGTAAAAA 59.614 37.037 0.00 0.00 0.00 1.94
164 165 7.739498 AATCTTGGTACTGACACGTAAAAAT 57.261 32.000 0.00 0.00 0.00 1.82
165 166 7.739498 ATCTTGGTACTGACACGTAAAAATT 57.261 32.000 0.00 0.00 0.00 1.82
166 167 8.836268 ATCTTGGTACTGACACGTAAAAATTA 57.164 30.769 0.00 0.00 0.00 1.40
167 168 8.836268 TCTTGGTACTGACACGTAAAAATTAT 57.164 30.769 0.00 0.00 0.00 1.28
168 169 8.928733 TCTTGGTACTGACACGTAAAAATTATC 58.071 33.333 0.00 0.00 0.00 1.75
169 170 8.604640 TTGGTACTGACACGTAAAAATTATCA 57.395 30.769 0.00 0.00 0.00 2.15
170 171 8.604640 TGGTACTGACACGTAAAAATTATCAA 57.395 30.769 0.00 0.00 0.00 2.57
171 172 9.221933 TGGTACTGACACGTAAAAATTATCAAT 57.778 29.630 0.00 0.00 0.00 2.57
172 173 9.698617 GGTACTGACACGTAAAAATTATCAATC 57.301 33.333 0.00 0.00 0.00 2.67
175 176 9.825972 ACTGACACGTAAAAATTATCAATCTTG 57.174 29.630 0.00 0.00 0.00 3.02
176 177 9.277565 CTGACACGTAAAAATTATCAATCTTGG 57.722 33.333 0.00 0.00 0.00 3.61
177 178 8.788806 TGACACGTAAAAATTATCAATCTTGGT 58.211 29.630 0.00 0.00 0.00 3.67
180 181 9.498307 CACGTAAAAATTATCAATCTTGGTACC 57.502 33.333 4.43 4.43 0.00 3.34
181 182 9.233649 ACGTAAAAATTATCAATCTTGGTACCA 57.766 29.630 11.60 11.60 0.00 3.25
187 188 9.479549 AAATTATCAATCTTGGTACCAATCTGT 57.520 29.630 27.24 13.60 35.20 3.41
188 189 8.682936 ATTATCAATCTTGGTACCAATCTGTC 57.317 34.615 27.24 0.00 35.20 3.51
189 190 5.762179 TCAATCTTGGTACCAATCTGTCT 57.238 39.130 27.24 6.85 35.20 3.41
190 191 5.734720 TCAATCTTGGTACCAATCTGTCTC 58.265 41.667 27.24 0.00 35.20 3.36
191 192 4.762289 ATCTTGGTACCAATCTGTCTCC 57.238 45.455 27.24 0.00 35.20 3.71
192 193 3.516586 TCTTGGTACCAATCTGTCTCCA 58.483 45.455 27.24 1.40 35.20 3.86
193 194 3.907474 TCTTGGTACCAATCTGTCTCCAA 59.093 43.478 27.24 0.85 35.20 3.53
194 195 4.536090 TCTTGGTACCAATCTGTCTCCAAT 59.464 41.667 27.24 0.00 34.35 3.16
195 196 4.220693 TGGTACCAATCTGTCTCCAATG 57.779 45.455 13.60 0.00 0.00 2.82
196 197 2.945668 GGTACCAATCTGTCTCCAATGC 59.054 50.000 7.15 0.00 0.00 3.56
197 198 2.134789 ACCAATCTGTCTCCAATGCC 57.865 50.000 0.00 0.00 0.00 4.40
198 199 1.637553 ACCAATCTGTCTCCAATGCCT 59.362 47.619 0.00 0.00 0.00 4.75
199 200 2.295885 CCAATCTGTCTCCAATGCCTC 58.704 52.381 0.00 0.00 0.00 4.70
200 201 2.356432 CCAATCTGTCTCCAATGCCTCA 60.356 50.000 0.00 0.00 0.00 3.86
201 202 3.349927 CAATCTGTCTCCAATGCCTCAA 58.650 45.455 0.00 0.00 0.00 3.02
202 203 3.947612 ATCTGTCTCCAATGCCTCAAT 57.052 42.857 0.00 0.00 0.00 2.57
203 204 3.726557 TCTGTCTCCAATGCCTCAATT 57.273 42.857 0.00 0.00 0.00 2.32
204 205 4.842531 TCTGTCTCCAATGCCTCAATTA 57.157 40.909 0.00 0.00 0.00 1.40
205 206 5.378230 TCTGTCTCCAATGCCTCAATTAT 57.622 39.130 0.00 0.00 0.00 1.28
206 207 5.128205 TCTGTCTCCAATGCCTCAATTATG 58.872 41.667 0.00 0.00 0.00 1.90
207 208 5.104402 TCTGTCTCCAATGCCTCAATTATGA 60.104 40.000 0.00 0.00 0.00 2.15
208 209 5.698104 TGTCTCCAATGCCTCAATTATGAT 58.302 37.500 0.00 0.00 34.37 2.45
209 210 6.840527 TGTCTCCAATGCCTCAATTATGATA 58.159 36.000 0.00 0.00 34.37 2.15
210 211 6.712095 TGTCTCCAATGCCTCAATTATGATAC 59.288 38.462 0.00 0.00 34.37 2.24
211 212 6.939163 GTCTCCAATGCCTCAATTATGATACT 59.061 38.462 0.00 0.00 34.37 2.12
212 213 7.446625 GTCTCCAATGCCTCAATTATGATACTT 59.553 37.037 0.00 0.00 34.37 2.24
213 214 7.663081 TCTCCAATGCCTCAATTATGATACTTC 59.337 37.037 0.00 0.00 34.37 3.01
214 215 7.520798 TCCAATGCCTCAATTATGATACTTCT 58.479 34.615 0.00 0.00 34.37 2.85
215 216 7.446319 TCCAATGCCTCAATTATGATACTTCTG 59.554 37.037 0.00 0.00 34.37 3.02
216 217 7.230108 CCAATGCCTCAATTATGATACTTCTGT 59.770 37.037 0.00 0.00 34.37 3.41
217 218 7.741027 ATGCCTCAATTATGATACTTCTGTG 57.259 36.000 0.00 0.00 34.37 3.66
218 219 5.528690 TGCCTCAATTATGATACTTCTGTGC 59.471 40.000 0.00 0.00 34.37 4.57
219 220 5.528690 GCCTCAATTATGATACTTCTGTGCA 59.471 40.000 0.00 0.00 34.37 4.57
220 221 6.038603 GCCTCAATTATGATACTTCTGTGCAA 59.961 38.462 0.00 0.00 34.37 4.08
221 222 7.255381 GCCTCAATTATGATACTTCTGTGCAAT 60.255 37.037 0.00 0.00 34.37 3.56
222 223 8.627403 CCTCAATTATGATACTTCTGTGCAATT 58.373 33.333 0.00 0.00 34.37 2.32
228 229 6.985188 TGATACTTCTGTGCAATTTACTCC 57.015 37.500 0.00 0.00 0.00 3.85
229 230 6.711277 TGATACTTCTGTGCAATTTACTCCT 58.289 36.000 0.00 0.00 0.00 3.69
230 231 6.818644 TGATACTTCTGTGCAATTTACTCCTC 59.181 38.462 0.00 0.00 0.00 3.71
231 232 3.997021 ACTTCTGTGCAATTTACTCCTCG 59.003 43.478 0.00 0.00 0.00 4.63
232 233 3.678056 TCTGTGCAATTTACTCCTCGT 57.322 42.857 0.00 0.00 0.00 4.18
233 234 3.325870 TCTGTGCAATTTACTCCTCGTG 58.674 45.455 0.00 0.00 0.00 4.35
234 235 3.006430 TCTGTGCAATTTACTCCTCGTGA 59.994 43.478 0.00 0.00 0.00 4.35
235 236 3.935203 CTGTGCAATTTACTCCTCGTGAT 59.065 43.478 0.00 0.00 0.00 3.06
236 237 3.932710 TGTGCAATTTACTCCTCGTGATC 59.067 43.478 0.00 0.00 0.00 2.92
237 238 3.309954 GTGCAATTTACTCCTCGTGATCC 59.690 47.826 0.00 0.00 0.00 3.36
238 239 3.197766 TGCAATTTACTCCTCGTGATCCT 59.802 43.478 0.00 0.00 0.00 3.24
239 240 4.192317 GCAATTTACTCCTCGTGATCCTT 58.808 43.478 0.00 0.00 0.00 3.36
240 241 4.271291 GCAATTTACTCCTCGTGATCCTTC 59.729 45.833 0.00 0.00 0.00 3.46
241 242 5.665459 CAATTTACTCCTCGTGATCCTTCT 58.335 41.667 0.00 0.00 0.00 2.85
242 243 5.941555 ATTTACTCCTCGTGATCCTTCTT 57.058 39.130 0.00 0.00 0.00 2.52
243 244 5.740290 TTTACTCCTCGTGATCCTTCTTT 57.260 39.130 0.00 0.00 0.00 2.52
244 245 5.740290 TTACTCCTCGTGATCCTTCTTTT 57.260 39.130 0.00 0.00 0.00 2.27
245 246 4.625607 ACTCCTCGTGATCCTTCTTTTT 57.374 40.909 0.00 0.00 0.00 1.94
246 247 4.570930 ACTCCTCGTGATCCTTCTTTTTC 58.429 43.478 0.00 0.00 0.00 2.29
247 248 4.284746 ACTCCTCGTGATCCTTCTTTTTCT 59.715 41.667 0.00 0.00 0.00 2.52
248 249 4.822026 TCCTCGTGATCCTTCTTTTTCTC 58.178 43.478 0.00 0.00 0.00 2.87
249 250 4.528596 TCCTCGTGATCCTTCTTTTTCTCT 59.471 41.667 0.00 0.00 0.00 3.10
250 251 5.012148 TCCTCGTGATCCTTCTTTTTCTCTT 59.988 40.000 0.00 0.00 0.00 2.85
251 252 5.703130 CCTCGTGATCCTTCTTTTTCTCTTT 59.297 40.000 0.00 0.00 0.00 2.52
252 253 6.128418 CCTCGTGATCCTTCTTTTTCTCTTTC 60.128 42.308 0.00 0.00 0.00 2.62
253 254 6.525629 TCGTGATCCTTCTTTTTCTCTTTCT 58.474 36.000 0.00 0.00 0.00 2.52
254 255 6.647067 TCGTGATCCTTCTTTTTCTCTTTCTC 59.353 38.462 0.00 0.00 0.00 2.87
255 256 6.425114 CGTGATCCTTCTTTTTCTCTTTCTCA 59.575 38.462 0.00 0.00 0.00 3.27
256 257 7.570324 CGTGATCCTTCTTTTTCTCTTTCTCAC 60.570 40.741 0.00 0.00 0.00 3.51
257 258 6.425114 TGATCCTTCTTTTTCTCTTTCTCACG 59.575 38.462 0.00 0.00 0.00 4.35
258 259 5.914033 TCCTTCTTTTTCTCTTTCTCACGA 58.086 37.500 0.00 0.00 0.00 4.35
259 260 6.525629 TCCTTCTTTTTCTCTTTCTCACGAT 58.474 36.000 0.00 0.00 0.00 3.73
260 261 6.647067 TCCTTCTTTTTCTCTTTCTCACGATC 59.353 38.462 0.00 0.00 0.00 3.69
261 262 6.128418 CCTTCTTTTTCTCTTTCTCACGATCC 60.128 42.308 0.00 0.00 0.00 3.36
262 263 4.923871 TCTTTTTCTCTTTCTCACGATCCG 59.076 41.667 0.00 0.00 0.00 4.18
263 264 4.514781 TTTTCTCTTTCTCACGATCCGA 57.485 40.909 0.00 0.00 0.00 4.55
264 265 4.514781 TTTCTCTTTCTCACGATCCGAA 57.485 40.909 0.00 0.00 0.00 4.30
265 266 4.720649 TTCTCTTTCTCACGATCCGAAT 57.279 40.909 0.00 0.00 0.00 3.34
266 267 4.720649 TCTCTTTCTCACGATCCGAATT 57.279 40.909 0.00 0.00 0.00 2.17
267 268 4.424626 TCTCTTTCTCACGATCCGAATTG 58.575 43.478 0.00 0.00 0.00 2.32
268 269 4.082190 TCTCTTTCTCACGATCCGAATTGT 60.082 41.667 0.00 0.00 0.00 2.71
269 270 4.174009 TCTTTCTCACGATCCGAATTGTC 58.826 43.478 0.00 0.00 0.00 3.18
270 271 2.579207 TCTCACGATCCGAATTGTCC 57.421 50.000 0.00 0.00 0.00 4.02
271 272 1.200483 CTCACGATCCGAATTGTCCG 58.800 55.000 0.00 0.00 0.00 4.79
272 273 0.804544 TCACGATCCGAATTGTCCGC 60.805 55.000 0.00 0.00 0.00 5.54
273 274 1.520787 ACGATCCGAATTGTCCGCC 60.521 57.895 0.00 0.00 0.00 6.13
274 275 1.520564 CGATCCGAATTGTCCGCCA 60.521 57.895 0.00 0.00 0.00 5.69
275 276 0.880278 CGATCCGAATTGTCCGCCAT 60.880 55.000 0.00 0.00 0.00 4.40
276 277 1.604438 CGATCCGAATTGTCCGCCATA 60.604 52.381 0.00 0.00 0.00 2.74
277 278 2.069273 GATCCGAATTGTCCGCCATAG 58.931 52.381 0.00 0.00 0.00 2.23
278 279 0.531974 TCCGAATTGTCCGCCATAGC 60.532 55.000 0.00 0.00 0.00 2.97
279 280 1.507141 CCGAATTGTCCGCCATAGCC 61.507 60.000 0.00 0.00 34.57 3.93
280 281 1.831389 CGAATTGTCCGCCATAGCCG 61.831 60.000 0.00 0.00 34.57 5.52
281 282 2.117941 GAATTGTCCGCCATAGCCGC 62.118 60.000 0.00 0.00 34.57 6.53
282 283 4.849310 TTGTCCGCCATAGCCGCC 62.849 66.667 0.00 0.00 34.57 6.13
290 291 4.504596 CATAGCCGCCCCAGCCAA 62.505 66.667 0.00 0.00 34.57 4.52
291 292 4.195334 ATAGCCGCCCCAGCCAAG 62.195 66.667 0.00 0.00 34.57 3.61
295 296 4.785453 CCGCCCCAGCCAAGAGAC 62.785 72.222 0.00 0.00 34.57 3.36
296 297 3.710722 CGCCCCAGCCAAGAGACT 61.711 66.667 0.00 0.00 34.57 3.24
297 298 2.270527 GCCCCAGCCAAGAGACTC 59.729 66.667 0.00 0.00 0.00 3.36
298 299 2.297129 GCCCCAGCCAAGAGACTCT 61.297 63.158 0.00 0.00 0.00 3.24
299 300 1.601171 CCCCAGCCAAGAGACTCTG 59.399 63.158 5.55 0.50 0.00 3.35
300 301 1.197430 CCCCAGCCAAGAGACTCTGT 61.197 60.000 5.55 0.00 0.00 3.41
301 302 0.036577 CCCAGCCAAGAGACTCTGTG 60.037 60.000 5.55 6.70 0.00 3.66
302 303 0.683973 CCAGCCAAGAGACTCTGTGT 59.316 55.000 5.55 0.00 0.00 3.72
303 304 1.607509 CCAGCCAAGAGACTCTGTGTG 60.608 57.143 5.55 0.45 0.00 3.82
304 305 1.342496 CAGCCAAGAGACTCTGTGTGA 59.658 52.381 5.55 0.00 0.00 3.58
306 307 1.615883 GCCAAGAGACTCTGTGTGAGA 59.384 52.381 5.55 0.00 45.39 3.27
319 320 0.894141 TGTGAGAGAGAGAGCCAAGC 59.106 55.000 0.00 0.00 0.00 4.01
438 439 1.325476 ATTGCTGCCAGCTTTAGCCC 61.325 55.000 18.96 0.00 42.97 5.19
441 442 1.220749 CTGCCAGCTTTAGCCCGTA 59.779 57.895 0.00 0.00 43.38 4.02
442 443 0.392461 CTGCCAGCTTTAGCCCGTAA 60.392 55.000 0.00 0.00 43.38 3.18
473 474 0.779997 AACTCCCCAATTGGACAGCT 59.220 50.000 26.60 9.18 37.39 4.24
581 625 4.023707 CACACAGGAAGAAGATTTGACCAC 60.024 45.833 0.00 0.00 0.00 4.16
591 635 2.206182 ATTTGACCACCGGCTACCCC 62.206 60.000 0.00 0.00 0.00 4.95
592 636 3.857521 TTGACCACCGGCTACCCCT 62.858 63.158 0.00 0.00 0.00 4.79
634 682 4.877282 AGCTTCCAATCTTCTCTATACGC 58.123 43.478 0.00 0.00 0.00 4.42
635 683 4.342378 AGCTTCCAATCTTCTCTATACGCA 59.658 41.667 0.00 0.00 0.00 5.24
636 684 4.683781 GCTTCCAATCTTCTCTATACGCAG 59.316 45.833 0.00 0.00 0.00 5.18
652 703 3.898529 ACGCAGTATATCCTTTAGCGAC 58.101 45.455 10.98 0.00 45.78 5.19
660 713 2.902705 TCCTTTAGCGACACACAAGT 57.097 45.000 0.00 0.00 0.00 3.16
746 799 9.104965 TGGGACAATTAATACTTGTATTTCTCG 57.895 33.333 10.72 2.60 36.98 4.04
800 853 1.819903 GAGAGTGAGTAGGTGGGTGAC 59.180 57.143 0.00 0.00 0.00 3.67
854 907 6.321321 TCTGAAGATGAGATGGATAGGTCAT 58.679 40.000 0.00 0.00 32.24 3.06
855 908 7.473593 TCTGAAGATGAGATGGATAGGTCATA 58.526 38.462 0.00 0.00 29.66 2.15
856 909 7.614974 TCTGAAGATGAGATGGATAGGTCATAG 59.385 40.741 0.00 0.00 29.66 2.23
857 910 6.666980 TGAAGATGAGATGGATAGGTCATAGG 59.333 42.308 0.00 0.00 29.66 2.57
858 911 6.164425 AGATGAGATGGATAGGTCATAGGT 57.836 41.667 0.00 0.00 29.66 3.08
859 912 5.957168 AGATGAGATGGATAGGTCATAGGTG 59.043 44.000 0.00 0.00 29.66 4.00
860 913 3.834813 TGAGATGGATAGGTCATAGGTGC 59.165 47.826 0.00 0.00 0.00 5.01
861 914 3.177228 AGATGGATAGGTCATAGGTGCC 58.823 50.000 0.00 0.00 0.00 5.01
862 915 1.338107 TGGATAGGTCATAGGTGCCG 58.662 55.000 0.00 0.00 0.00 5.69
887 940 0.545548 AGGCCGGAGACTTCCTCTTT 60.546 55.000 5.05 0.00 41.67 2.52
942 995 0.396435 AGCCGATCTGACCAAACACA 59.604 50.000 0.00 0.00 0.00 3.72
943 996 0.798776 GCCGATCTGACCAAACACAG 59.201 55.000 0.00 0.00 35.72 3.66
944 997 1.608025 GCCGATCTGACCAAACACAGA 60.608 52.381 0.00 0.00 45.19 3.41
946 999 1.728971 CGATCTGACCAAACACAGAGC 59.271 52.381 0.00 0.00 44.50 4.09
947 1000 1.728971 GATCTGACCAAACACAGAGCG 59.271 52.381 0.00 0.00 44.50 5.03
948 1001 0.464036 TCTGACCAAACACAGAGCGT 59.536 50.000 0.00 0.00 38.08 5.07
1128 1198 3.186613 GCTTCGTCCATTTCTTCTTCGTT 59.813 43.478 0.00 0.00 0.00 3.85
1137 1207 3.447918 TTCTTCTTCGTTCTCACCGTT 57.552 42.857 0.00 0.00 0.00 4.44
1386 1459 2.234613 CACCGACGTGTGCTTCATT 58.765 52.632 0.00 0.00 35.10 2.57
1530 1609 2.045926 CGCAAGTGGGAGAAGGGG 60.046 66.667 0.00 0.00 0.00 4.79
1680 1762 3.324671 CACGCGTTCAACGACGGT 61.325 61.111 23.76 12.23 46.05 4.83
1813 1895 2.048597 GCCACCACGTGATCGACA 60.049 61.111 19.30 0.00 40.62 4.35
1941 2023 1.325355 TCGACTTCCACGACTTCCTT 58.675 50.000 0.00 0.00 34.85 3.36
1970 2052 4.764336 CAAGGACGACGGCGCGTA 62.764 66.667 24.31 0.00 45.72 4.42
1971 2053 4.766088 AAGGACGACGGCGCGTAC 62.766 66.667 24.52 24.52 45.72 3.67
2113 2222 3.980989 TGGGGTTCGACGTGTCCG 61.981 66.667 0.00 0.00 40.83 4.79
2315 2424 3.272334 GGCGACGACCATGATGGC 61.272 66.667 12.25 3.56 42.67 4.40
2471 2580 3.414700 CAGCGGCCAGAACGTGAC 61.415 66.667 2.24 0.00 0.00 3.67
2481 2590 1.212229 GAACGTGACCCTCGACCTC 59.788 63.158 0.00 0.00 0.00 3.85
2559 2684 1.229082 AGGTCCGTAGCTGGTTGGA 60.229 57.895 0.00 0.00 30.51 3.53
2616 2757 1.107538 TAATCGAGAGCAGGTCCGGG 61.108 60.000 0.00 0.00 0.00 5.73
2617 2758 2.856039 AATCGAGAGCAGGTCCGGGA 62.856 60.000 0.00 0.00 0.00 5.14
2702 2844 5.029807 AGGGGTACAACCATTTTGTTTTG 57.970 39.130 8.36 0.00 41.02 2.44
2731 2874 2.407090 CTGTTCGACAGCACAGATCAA 58.593 47.619 8.96 0.00 42.89 2.57
2780 2924 9.535878 TTCAATTTAGATTGGGTTTGTTTGTAC 57.464 29.630 6.17 0.00 42.36 2.90
2785 2929 6.144078 AGATTGGGTTTGTTTGTACTTGTC 57.856 37.500 0.00 0.00 0.00 3.18
2786 2930 5.891551 AGATTGGGTTTGTTTGTACTTGTCT 59.108 36.000 0.00 0.00 0.00 3.41
2792 2936 6.293790 GGGTTTGTTTGTACTTGTCTATGTCC 60.294 42.308 0.00 0.00 0.00 4.02
2793 2937 6.360329 GTTTGTTTGTACTTGTCTATGTCCG 58.640 40.000 0.00 0.00 0.00 4.79
2859 3003 0.893727 GCAACGACCCAAATCACCCT 60.894 55.000 0.00 0.00 0.00 4.34
2897 3041 1.959226 GCGCGGACAAAAGTGGAGA 60.959 57.895 8.83 0.00 0.00 3.71
2927 3082 1.817209 GACCCAAACCCAAAACGCA 59.183 52.632 0.00 0.00 0.00 5.24
2962 3117 2.278336 CCGATGCATTTGCGGCAG 60.278 61.111 11.84 0.00 45.68 4.85
3067 3265 5.105106 TCAGCTTAATTTATGACCTCGGACA 60.105 40.000 0.00 0.00 0.00 4.02
3071 3269 4.553330 AATTTATGACCTCGGACACACT 57.447 40.909 0.00 0.00 0.00 3.55
3073 3271 2.509166 TATGACCTCGGACACACTCT 57.491 50.000 0.00 0.00 0.00 3.24
3112 3316 0.937231 TTTTTAAGCCAAGCGTGCGC 60.937 50.000 8.67 8.67 42.33 6.09
3219 3435 4.957164 GCAACCCTAGCCACCTAC 57.043 61.111 0.00 0.00 0.00 3.18
3250 3473 1.852157 ATGGGCTTCTTCTCCGGCAA 61.852 55.000 0.00 0.00 0.00 4.52
3295 3518 2.283966 CACCCCTCTCCACCGTCT 60.284 66.667 0.00 0.00 0.00 4.18
3296 3519 2.037527 ACCCCTCTCCACCGTCTC 59.962 66.667 0.00 0.00 0.00 3.36
3477 3718 1.915078 AAGGGAACATGCGGAGGAGG 61.915 60.000 0.00 0.00 34.40 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.175489 GCGCGCTGACTAGGACGA 62.175 66.667 26.67 0.00 0.00 4.20
1 2 4.476410 TGCGCGCTGACTAGGACG 62.476 66.667 33.29 0.00 0.00 4.79
3 4 3.052620 GACTGCGCGCTGACTAGGA 62.053 63.158 39.03 14.07 0.00 2.94
4 5 2.580867 GACTGCGCGCTGACTAGG 60.581 66.667 39.03 18.84 0.00 3.02
5 6 1.871345 CTGACTGCGCGCTGACTAG 60.871 63.158 39.03 26.60 0.00 2.57
6 7 2.179267 CTGACTGCGCGCTGACTA 59.821 61.111 39.03 23.70 0.00 2.59
67 68 3.802852 AAACTGACCGGTTGGGCCC 62.803 63.158 17.59 17.59 46.01 5.80
68 69 1.396607 AAAAACTGACCGGTTGGGCC 61.397 55.000 9.42 0.00 46.01 5.80
70 71 1.687563 AGAAAAACTGACCGGTTGGG 58.312 50.000 9.42 4.56 40.75 4.12
81 82 6.811253 TTTATACGCATGGACAGAAAAACT 57.189 33.333 0.00 0.00 0.00 2.66
82 83 6.032042 CGTTTTATACGCATGGACAGAAAAAC 59.968 38.462 0.00 0.00 44.26 2.43
83 84 6.081049 CGTTTTATACGCATGGACAGAAAAA 58.919 36.000 0.00 0.00 44.26 1.94
84 85 5.623335 CGTTTTATACGCATGGACAGAAAA 58.377 37.500 0.00 0.00 44.26 2.29
85 86 5.211266 CGTTTTATACGCATGGACAGAAA 57.789 39.130 0.00 0.00 44.26 2.52
86 87 4.850859 CGTTTTATACGCATGGACAGAA 57.149 40.909 0.00 0.00 44.26 3.02
120 121 2.026879 GGCGAGCCGTTGCAAAAA 59.973 55.556 0.00 0.00 41.13 1.94
121 122 3.972276 GGGCGAGCCGTTGCAAAA 61.972 61.111 0.00 0.00 41.13 2.44
122 123 3.538785 TAGGGCGAGCCGTTGCAAA 62.539 57.895 14.75 0.00 41.13 3.68
123 124 2.813226 ATTAGGGCGAGCCGTTGCAA 62.813 55.000 14.75 0.00 41.13 4.08
124 125 3.323758 ATTAGGGCGAGCCGTTGCA 62.324 57.895 14.75 0.55 41.13 4.08
125 126 2.513897 ATTAGGGCGAGCCGTTGC 60.514 61.111 14.75 0.00 36.85 4.17
126 127 0.462047 AAGATTAGGGCGAGCCGTTG 60.462 55.000 14.75 0.00 36.85 4.10
127 128 0.462047 CAAGATTAGGGCGAGCCGTT 60.462 55.000 14.75 4.90 36.85 4.44
128 129 1.144057 CAAGATTAGGGCGAGCCGT 59.856 57.895 14.00 14.00 36.85 5.68
129 130 1.595382 CCAAGATTAGGGCGAGCCG 60.595 63.158 8.14 0.00 36.85 5.52
130 131 0.756903 TACCAAGATTAGGGCGAGCC 59.243 55.000 5.37 5.37 0.00 4.70
131 132 1.413077 AGTACCAAGATTAGGGCGAGC 59.587 52.381 0.00 0.00 0.00 5.03
132 133 2.693591 TCAGTACCAAGATTAGGGCGAG 59.306 50.000 0.00 0.00 0.00 5.03
133 134 2.429610 GTCAGTACCAAGATTAGGGCGA 59.570 50.000 0.00 0.00 0.00 5.54
134 135 2.167693 TGTCAGTACCAAGATTAGGGCG 59.832 50.000 0.00 0.00 0.00 6.13
135 136 3.532542 GTGTCAGTACCAAGATTAGGGC 58.467 50.000 0.00 0.00 0.00 5.19
136 137 3.194968 ACGTGTCAGTACCAAGATTAGGG 59.805 47.826 0.00 0.00 0.00 3.53
137 138 4.451629 ACGTGTCAGTACCAAGATTAGG 57.548 45.455 0.00 0.00 0.00 2.69
138 139 7.878477 TTTTACGTGTCAGTACCAAGATTAG 57.122 36.000 0.00 0.00 0.00 1.73
139 140 8.836268 ATTTTTACGTGTCAGTACCAAGATTA 57.164 30.769 0.00 0.00 0.00 1.75
140 141 7.739498 ATTTTTACGTGTCAGTACCAAGATT 57.261 32.000 0.00 0.00 0.00 2.40
141 142 7.739498 AATTTTTACGTGTCAGTACCAAGAT 57.261 32.000 0.00 0.00 0.00 2.40
142 143 8.836268 ATAATTTTTACGTGTCAGTACCAAGA 57.164 30.769 0.00 0.00 0.00 3.02
143 144 8.714179 TGATAATTTTTACGTGTCAGTACCAAG 58.286 33.333 0.00 0.00 0.00 3.61
144 145 8.604640 TGATAATTTTTACGTGTCAGTACCAA 57.395 30.769 0.00 0.00 0.00 3.67
145 146 8.604640 TTGATAATTTTTACGTGTCAGTACCA 57.395 30.769 0.00 0.00 0.00 3.25
146 147 9.698617 GATTGATAATTTTTACGTGTCAGTACC 57.301 33.333 0.00 0.00 0.00 3.34
149 150 9.825972 CAAGATTGATAATTTTTACGTGTCAGT 57.174 29.630 0.00 0.00 0.00 3.41
150 151 9.277565 CCAAGATTGATAATTTTTACGTGTCAG 57.722 33.333 0.00 0.00 0.00 3.51
151 152 8.788806 ACCAAGATTGATAATTTTTACGTGTCA 58.211 29.630 0.00 0.00 0.00 3.58
154 155 9.498307 GGTACCAAGATTGATAATTTTTACGTG 57.502 33.333 7.15 0.00 0.00 4.49
155 156 9.233649 TGGTACCAAGATTGATAATTTTTACGT 57.766 29.630 13.60 0.00 0.00 3.57
161 162 9.479549 ACAGATTGGTACCAAGATTGATAATTT 57.520 29.630 30.00 10.77 39.47 1.82
162 163 9.125026 GACAGATTGGTACCAAGATTGATAATT 57.875 33.333 30.00 11.29 39.47 1.40
163 164 8.497745 AGACAGATTGGTACCAAGATTGATAAT 58.502 33.333 30.00 12.02 39.47 1.28
164 165 7.861629 AGACAGATTGGTACCAAGATTGATAA 58.138 34.615 30.00 6.54 39.47 1.75
165 166 7.419057 GGAGACAGATTGGTACCAAGATTGATA 60.419 40.741 30.00 7.30 39.47 2.15
166 167 6.319048 AGACAGATTGGTACCAAGATTGAT 57.681 37.500 30.00 14.22 39.47 2.57
167 168 5.338381 GGAGACAGATTGGTACCAAGATTGA 60.338 44.000 30.00 8.85 39.47 2.57
168 169 4.878397 GGAGACAGATTGGTACCAAGATTG 59.122 45.833 30.00 26.29 39.47 2.67
169 170 4.536090 TGGAGACAGATTGGTACCAAGATT 59.464 41.667 30.00 15.71 36.04 2.40
170 171 4.104086 TGGAGACAGATTGGTACCAAGAT 58.896 43.478 30.00 19.00 36.04 2.40
171 172 3.516586 TGGAGACAGATTGGTACCAAGA 58.483 45.455 30.00 11.20 36.04 3.02
172 173 3.981071 TGGAGACAGATTGGTACCAAG 57.019 47.619 30.00 19.80 36.04 3.61
173 174 4.588899 CATTGGAGACAGATTGGTACCAA 58.411 43.478 28.95 28.95 44.54 3.67
174 175 3.622206 GCATTGGAGACAGATTGGTACCA 60.622 47.826 11.60 11.60 44.54 3.25
175 176 2.945668 GCATTGGAGACAGATTGGTACC 59.054 50.000 4.43 4.43 44.54 3.34
176 177 2.945668 GGCATTGGAGACAGATTGGTAC 59.054 50.000 0.00 0.00 44.54 3.34
177 178 2.846206 AGGCATTGGAGACAGATTGGTA 59.154 45.455 0.00 0.00 44.54 3.25
178 179 1.637553 AGGCATTGGAGACAGATTGGT 59.362 47.619 0.00 0.00 44.54 3.67
179 180 2.295885 GAGGCATTGGAGACAGATTGG 58.704 52.381 0.00 0.00 44.54 3.16
180 181 2.995283 TGAGGCATTGGAGACAGATTG 58.005 47.619 0.00 0.00 44.54 2.67
181 182 3.726557 TTGAGGCATTGGAGACAGATT 57.273 42.857 0.00 0.00 44.54 2.40
182 183 3.947612 ATTGAGGCATTGGAGACAGAT 57.052 42.857 0.00 0.00 44.54 2.90
183 184 3.726557 AATTGAGGCATTGGAGACAGA 57.273 42.857 0.00 0.00 44.54 3.41
184 185 5.128205 TCATAATTGAGGCATTGGAGACAG 58.872 41.667 0.00 0.00 44.54 3.51
185 186 5.114764 TCATAATTGAGGCATTGGAGACA 57.885 39.130 0.00 0.00 39.83 3.41
186 187 6.939163 AGTATCATAATTGAGGCATTGGAGAC 59.061 38.462 0.00 0.00 34.73 3.36
187 188 7.083062 AGTATCATAATTGAGGCATTGGAGA 57.917 36.000 0.00 0.00 34.73 3.71
188 189 7.664731 AGAAGTATCATAATTGAGGCATTGGAG 59.335 37.037 0.00 0.00 34.73 3.86
189 190 7.446319 CAGAAGTATCATAATTGAGGCATTGGA 59.554 37.037 0.00 0.00 34.73 3.53
190 191 7.230108 ACAGAAGTATCATAATTGAGGCATTGG 59.770 37.037 0.00 0.00 34.73 3.16
191 192 8.074370 CACAGAAGTATCATAATTGAGGCATTG 58.926 37.037 0.00 0.00 34.73 2.82
192 193 7.255381 GCACAGAAGTATCATAATTGAGGCATT 60.255 37.037 0.00 0.00 34.73 3.56
193 194 6.206243 GCACAGAAGTATCATAATTGAGGCAT 59.794 38.462 0.00 0.00 34.73 4.40
194 195 5.528690 GCACAGAAGTATCATAATTGAGGCA 59.471 40.000 0.00 0.00 34.73 4.75
195 196 5.528690 TGCACAGAAGTATCATAATTGAGGC 59.471 40.000 0.00 0.00 34.73 4.70
196 197 7.558161 TTGCACAGAAGTATCATAATTGAGG 57.442 36.000 0.00 0.00 34.73 3.86
202 203 9.109393 GGAGTAAATTGCACAGAAGTATCATAA 57.891 33.333 0.00 0.00 0.00 1.90
203 204 8.486210 AGGAGTAAATTGCACAGAAGTATCATA 58.514 33.333 0.00 0.00 0.00 2.15
204 205 7.341805 AGGAGTAAATTGCACAGAAGTATCAT 58.658 34.615 0.00 0.00 0.00 2.45
205 206 6.711277 AGGAGTAAATTGCACAGAAGTATCA 58.289 36.000 0.00 0.00 0.00 2.15
206 207 6.019479 CGAGGAGTAAATTGCACAGAAGTATC 60.019 42.308 0.00 0.00 0.00 2.24
207 208 5.812642 CGAGGAGTAAATTGCACAGAAGTAT 59.187 40.000 0.00 0.00 0.00 2.12
208 209 5.168569 CGAGGAGTAAATTGCACAGAAGTA 58.831 41.667 0.00 0.00 0.00 2.24
209 210 3.997021 CGAGGAGTAAATTGCACAGAAGT 59.003 43.478 0.00 0.00 0.00 3.01
210 211 3.997021 ACGAGGAGTAAATTGCACAGAAG 59.003 43.478 0.00 0.00 0.00 2.85
211 212 3.745975 CACGAGGAGTAAATTGCACAGAA 59.254 43.478 0.00 0.00 0.00 3.02
212 213 3.006430 TCACGAGGAGTAAATTGCACAGA 59.994 43.478 0.00 0.00 0.00 3.41
213 214 3.325870 TCACGAGGAGTAAATTGCACAG 58.674 45.455 0.00 0.00 0.00 3.66
214 215 3.394674 TCACGAGGAGTAAATTGCACA 57.605 42.857 0.00 0.00 0.00 4.57
215 216 3.309954 GGATCACGAGGAGTAAATTGCAC 59.690 47.826 0.00 0.00 0.00 4.57
216 217 3.197766 AGGATCACGAGGAGTAAATTGCA 59.802 43.478 0.00 0.00 0.00 4.08
217 218 3.798202 AGGATCACGAGGAGTAAATTGC 58.202 45.455 0.00 0.00 0.00 3.56
218 219 5.665459 AGAAGGATCACGAGGAGTAAATTG 58.335 41.667 0.00 0.00 0.00 2.32
219 220 5.941555 AGAAGGATCACGAGGAGTAAATT 57.058 39.130 0.00 0.00 0.00 1.82
220 221 5.941555 AAGAAGGATCACGAGGAGTAAAT 57.058 39.130 0.00 0.00 0.00 1.40
221 222 5.740290 AAAGAAGGATCACGAGGAGTAAA 57.260 39.130 0.00 0.00 0.00 2.01
222 223 5.740290 AAAAGAAGGATCACGAGGAGTAA 57.260 39.130 0.00 0.00 0.00 2.24
223 224 5.480772 AGAAAAAGAAGGATCACGAGGAGTA 59.519 40.000 0.00 0.00 0.00 2.59
224 225 4.284746 AGAAAAAGAAGGATCACGAGGAGT 59.715 41.667 0.00 0.00 0.00 3.85
225 226 4.826556 AGAAAAAGAAGGATCACGAGGAG 58.173 43.478 0.00 0.00 0.00 3.69
226 227 4.528596 AGAGAAAAAGAAGGATCACGAGGA 59.471 41.667 0.00 0.00 0.00 3.71
227 228 4.826556 AGAGAAAAAGAAGGATCACGAGG 58.173 43.478 0.00 0.00 0.00 4.63
228 229 6.648725 AGAAAGAGAAAAAGAAGGATCACGAG 59.351 38.462 0.00 0.00 0.00 4.18
229 230 6.525629 AGAAAGAGAAAAAGAAGGATCACGA 58.474 36.000 0.00 0.00 0.00 4.35
230 231 6.425114 TGAGAAAGAGAAAAAGAAGGATCACG 59.575 38.462 0.00 0.00 0.00 4.35
231 232 7.570324 CGTGAGAAAGAGAAAAAGAAGGATCAC 60.570 40.741 0.00 0.00 0.00 3.06
232 233 6.425114 CGTGAGAAAGAGAAAAAGAAGGATCA 59.575 38.462 0.00 0.00 0.00 2.92
233 234 6.647067 TCGTGAGAAAGAGAAAAAGAAGGATC 59.353 38.462 0.00 0.00 37.03 3.36
234 235 6.525629 TCGTGAGAAAGAGAAAAAGAAGGAT 58.474 36.000 0.00 0.00 37.03 3.24
235 236 5.914033 TCGTGAGAAAGAGAAAAAGAAGGA 58.086 37.500 0.00 0.00 37.03 3.36
252 253 1.200483 CGGACAATTCGGATCGTGAG 58.800 55.000 0.00 0.00 0.00 3.51
253 254 0.804544 GCGGACAATTCGGATCGTGA 60.805 55.000 0.00 0.00 0.00 4.35
254 255 1.636340 GCGGACAATTCGGATCGTG 59.364 57.895 0.00 0.00 0.00 4.35
255 256 1.520787 GGCGGACAATTCGGATCGT 60.521 57.895 0.00 0.00 0.00 3.73
256 257 0.880278 ATGGCGGACAATTCGGATCG 60.880 55.000 0.00 0.00 0.00 3.69
257 258 2.069273 CTATGGCGGACAATTCGGATC 58.931 52.381 0.00 0.00 0.00 3.36
258 259 1.878102 GCTATGGCGGACAATTCGGAT 60.878 52.381 0.00 0.00 0.00 4.18
259 260 0.531974 GCTATGGCGGACAATTCGGA 60.532 55.000 0.00 0.00 0.00 4.55
260 261 1.507141 GGCTATGGCGGACAATTCGG 61.507 60.000 0.00 0.00 39.81 4.30
261 262 1.941812 GGCTATGGCGGACAATTCG 59.058 57.895 0.00 0.00 39.81 3.34
273 274 4.504596 TTGGCTGGGGCGGCTATG 62.505 66.667 9.56 0.00 39.81 2.23
274 275 4.195334 CTTGGCTGGGGCGGCTAT 62.195 66.667 9.56 0.00 39.81 2.97
278 279 4.785453 GTCTCTTGGCTGGGGCGG 62.785 72.222 0.00 0.00 39.81 6.13
279 280 3.672295 GAGTCTCTTGGCTGGGGCG 62.672 68.421 0.00 0.00 39.81 6.13
280 281 2.270527 GAGTCTCTTGGCTGGGGC 59.729 66.667 0.00 0.00 37.82 5.80
281 282 1.197430 ACAGAGTCTCTTGGCTGGGG 61.197 60.000 0.00 0.00 32.82 4.96
282 283 0.036577 CACAGAGTCTCTTGGCTGGG 60.037 60.000 0.00 0.00 32.82 4.45
283 284 0.683973 ACACAGAGTCTCTTGGCTGG 59.316 55.000 0.00 0.00 32.82 4.85
284 285 1.342496 TCACACAGAGTCTCTTGGCTG 59.658 52.381 0.00 0.00 34.65 4.85
285 286 1.617850 CTCACACAGAGTCTCTTGGCT 59.382 52.381 0.00 0.00 39.62 4.75
286 287 1.615883 TCTCACACAGAGTCTCTTGGC 59.384 52.381 0.00 0.00 44.98 4.52
287 288 3.574284 CTCTCACACAGAGTCTCTTGG 57.426 52.381 0.00 0.00 43.61 3.61
296 297 1.074566 TGGCTCTCTCTCTCACACAGA 59.925 52.381 0.00 0.00 0.00 3.41
297 298 1.543607 TGGCTCTCTCTCTCACACAG 58.456 55.000 0.00 0.00 0.00 3.66
298 299 1.891811 CTTGGCTCTCTCTCTCACACA 59.108 52.381 0.00 0.00 0.00 3.72
299 300 1.404047 GCTTGGCTCTCTCTCTCACAC 60.404 57.143 0.00 0.00 0.00 3.82
300 301 0.894141 GCTTGGCTCTCTCTCTCACA 59.106 55.000 0.00 0.00 0.00 3.58
301 302 0.894141 TGCTTGGCTCTCTCTCTCAC 59.106 55.000 0.00 0.00 0.00 3.51
302 303 1.755959 GATGCTTGGCTCTCTCTCTCA 59.244 52.381 0.00 0.00 0.00 3.27
303 304 1.755959 TGATGCTTGGCTCTCTCTCTC 59.244 52.381 0.00 0.00 0.00 3.20
304 305 1.863325 TGATGCTTGGCTCTCTCTCT 58.137 50.000 0.00 0.00 0.00 3.10
305 306 2.687700 TTGATGCTTGGCTCTCTCTC 57.312 50.000 0.00 0.00 0.00 3.20
306 307 3.648507 ATTTGATGCTTGGCTCTCTCT 57.351 42.857 0.00 0.00 0.00 3.10
307 308 5.824904 TTAATTTGATGCTTGGCTCTCTC 57.175 39.130 0.00 0.00 0.00 3.20
308 309 5.655532 ACATTAATTTGATGCTTGGCTCTCT 59.344 36.000 1.35 0.00 0.00 3.10
309 310 5.899299 ACATTAATTTGATGCTTGGCTCTC 58.101 37.500 1.35 0.00 0.00 3.20
310 311 5.927281 ACATTAATTTGATGCTTGGCTCT 57.073 34.783 1.35 0.00 0.00 4.09
311 312 5.220529 GCAACATTAATTTGATGCTTGGCTC 60.221 40.000 11.94 0.00 40.89 4.70
312 313 4.632688 GCAACATTAATTTGATGCTTGGCT 59.367 37.500 11.94 0.00 40.89 4.75
313 314 4.201841 GGCAACATTAATTTGATGCTTGGC 60.202 41.667 17.62 17.62 42.90 4.52
364 365 7.000472 CCTCAAATGGTAGTATGTCATTGGAT 59.000 38.462 0.00 0.00 32.40 3.41
378 379 2.939640 GCGCCTTCTTCCTCAAATGGTA 60.940 50.000 0.00 0.00 0.00 3.25
379 380 1.826385 CGCCTTCTTCCTCAAATGGT 58.174 50.000 0.00 0.00 0.00 3.55
380 381 0.453390 GCGCCTTCTTCCTCAAATGG 59.547 55.000 0.00 0.00 0.00 3.16
438 439 7.795482 TGGGGAGTTTTATTATGACATTACG 57.205 36.000 0.00 0.00 0.00 3.18
441 442 8.485392 CCAATTGGGGAGTTTTATTATGACATT 58.515 33.333 17.36 0.00 0.00 2.71
442 443 7.843760 TCCAATTGGGGAGTTTTATTATGACAT 59.156 33.333 24.29 0.00 37.22 3.06
473 474 5.993441 GGTAGTAAGTGAGTGCCAAACTAAA 59.007 40.000 0.00 0.00 40.07 1.85
581 625 3.155167 GTGGAGAGGGGTAGCCGG 61.155 72.222 4.56 0.00 0.00 6.13
591 635 3.685139 TGCTAACTTTGGAGTGGAGAG 57.315 47.619 0.00 0.00 35.91 3.20
592 636 3.807209 GCTTGCTAACTTTGGAGTGGAGA 60.807 47.826 0.00 0.00 35.91 3.71
634 682 5.588240 TGTGTGTCGCTAAAGGATATACTG 58.412 41.667 0.00 0.00 0.00 2.74
635 683 5.847111 TGTGTGTCGCTAAAGGATATACT 57.153 39.130 0.00 0.00 0.00 2.12
636 684 6.040878 ACTTGTGTGTCGCTAAAGGATATAC 58.959 40.000 4.41 0.00 0.00 1.47
690 743 9.586435 GTCCCCTAAATAAAATTGTCTCAAATG 57.414 33.333 0.00 0.00 0.00 2.32
696 749 8.539544 CCAAATGTCCCCTAAATAAAATTGTCT 58.460 33.333 0.00 0.00 0.00 3.41
698 751 7.459444 TCCCAAATGTCCCCTAAATAAAATTGT 59.541 33.333 0.00 0.00 0.00 2.71
800 853 0.249447 TTCTGCGTCACACACTCCAG 60.249 55.000 0.00 0.00 0.00 3.86
854 907 4.954933 GCCTTGATTCGGCACCTA 57.045 55.556 0.00 0.00 46.77 3.08
859 912 2.897350 CTCCGGCCTTGATTCGGC 60.897 66.667 0.00 0.00 46.83 5.54
860 913 1.521681 GTCTCCGGCCTTGATTCGG 60.522 63.158 0.00 0.00 44.59 4.30
861 914 0.108138 AAGTCTCCGGCCTTGATTCG 60.108 55.000 0.00 0.00 0.00 3.34
862 915 1.657822 GAAGTCTCCGGCCTTGATTC 58.342 55.000 0.00 0.00 0.00 2.52
887 940 1.885388 CACCGGCGTCAGTTCACAA 60.885 57.895 6.01 0.00 0.00 3.33
929 982 0.464036 ACGCTCTGTGTTTGGTCAGA 59.536 50.000 0.00 0.00 38.20 3.27
966 1022 3.449746 TGGAGAAATGGAAACGGGATT 57.550 42.857 0.00 0.00 0.00 3.01
1128 1198 0.943835 CGCACATGACAACGGTGAGA 60.944 55.000 7.88 0.00 34.81 3.27
1219 1289 4.208686 GGCTGCTCTACCGGACGG 62.209 72.222 9.46 9.56 42.03 4.79
1220 1290 4.554363 CGGCTGCTCTACCGGACG 62.554 72.222 9.46 0.00 45.74 4.79
1777 1859 4.477975 CGAGAGCCCCGACACGAC 62.478 72.222 0.00 0.00 0.00 4.34
1970 2052 1.227556 GTGGTGTGCACTTCCGAGT 60.228 57.895 19.41 0.00 36.25 4.18
1971 2053 2.310233 CGTGGTGTGCACTTCCGAG 61.310 63.158 19.41 13.37 0.00 4.63
1972 2054 2.279851 CGTGGTGTGCACTTCCGA 60.280 61.111 19.41 8.60 0.00 4.55
1973 2055 3.345808 CCGTGGTGTGCACTTCCG 61.346 66.667 19.41 14.02 0.00 4.30
1974 2056 3.660111 GCCGTGGTGTGCACTTCC 61.660 66.667 19.41 19.53 0.00 3.46
2087 2196 4.078516 CGAACCCCACCGACTCCC 62.079 72.222 0.00 0.00 0.00 4.30
2113 2222 2.126031 GTTCGCCGTCTCCAGGAC 60.126 66.667 0.00 0.00 41.28 3.85
2540 2649 1.218316 CCAACCAGCTACGGACCTC 59.782 63.158 0.00 0.00 0.00 3.85
2634 2775 1.740296 GCCCTGTCACGTACGCAAT 60.740 57.895 16.72 0.00 0.00 3.56
2702 2844 2.067013 GCTGTCGAACAGGAACCTAAC 58.933 52.381 14.19 0.00 46.01 2.34
2764 2907 7.286775 ACATAGACAAGTACAAACAAACCCAAT 59.713 33.333 0.00 0.00 0.00 3.16
2780 2924 5.753921 GTCCTTATTTCCGGACATAGACAAG 59.246 44.000 18.32 12.08 46.98 3.16
2792 2936 6.458751 CCATCACAAGATTGTCCTTATTTCCG 60.459 42.308 0.00 0.00 39.91 4.30
2793 2937 6.681368 GCCATCACAAGATTGTCCTTATTTCC 60.681 42.308 0.00 0.00 39.91 3.13
2859 3003 1.595929 GACCCAAACGGACGCAGAA 60.596 57.895 0.00 0.00 34.64 3.02
2983 3162 4.796231 AACGAGAAGGCGCGCGAT 62.796 61.111 37.18 19.15 41.21 4.58
3041 3220 5.128827 TCCGAGGTCATAAATTAAGCTGACT 59.871 40.000 5.54 0.00 38.41 3.41
3067 3265 2.049063 GCCGTCGCTGAAGAGTGT 60.049 61.111 0.00 0.00 0.00 3.55
3071 3269 4.415332 GACCGCCGTCGCTGAAGA 62.415 66.667 0.00 0.00 0.00 2.87
3131 3335 2.706071 GGATGAGGACCCTCCCCT 59.294 66.667 13.10 0.00 42.09 4.79
3132 3336 2.844839 CGGATGAGGACCCTCCCC 60.845 72.222 13.10 12.49 42.09 4.81
3133 3337 3.551407 GCGGATGAGGACCCTCCC 61.551 72.222 13.10 7.33 42.09 4.30
3134 3338 2.034048 GAAGCGGATGAGGACCCTCC 62.034 65.000 13.10 4.83 42.09 4.30
3135 3339 1.443828 GAAGCGGATGAGGACCCTC 59.556 63.158 9.08 9.08 43.01 4.30
3136 3340 2.066999 GGAAGCGGATGAGGACCCT 61.067 63.158 0.00 0.00 0.00 4.34
3137 3341 2.317149 CTGGAAGCGGATGAGGACCC 62.317 65.000 0.00 0.00 0.00 4.46
3138 3342 1.144936 CTGGAAGCGGATGAGGACC 59.855 63.158 0.00 0.00 0.00 4.46
3170 3382 4.899239 CGGAGGGTGGCGAGATGC 62.899 72.222 0.00 0.00 45.38 3.91
3289 3512 4.755507 GGAGACGGGGGAGACGGT 62.756 72.222 0.00 0.00 35.23 4.83
3409 3650 1.227089 CTCTCCGGATCCAAGTGCG 60.227 63.158 13.41 0.00 0.00 5.34
3463 3704 2.045926 GCACCTCCTCCGCATGTT 60.046 61.111 0.00 0.00 0.00 2.71
3464 3705 4.457496 CGCACCTCCTCCGCATGT 62.457 66.667 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.