Multiple sequence alignment - TraesCS3B01G042000

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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 TraesCS3B01G042000 chr3B 100.000 2579 0 0 1 2579 21004706 21002128 0.000000e+00 4763.0
1 TraesCS3B01G042000 chr3B 88.873 701 54 11 996 1696 21161541 21162217 0.000000e+00 841.0
2 TraesCS3B01G042000 chr3B 81.679 524 53 21 1702 2196 21162858 21163367 1.860000e-106 396.0
3 TraesCS3B01G042000 chr3B 93.478 46 2 1 2530 2574 21163641 21163686 1.660000e-07 67.6
4 TraesCS3B01G042000 chr3D 87.393 2110 120 58 234 2269 14230733 14228696 0.000000e+00 2289.0
5 TraesCS3B01G042000 chr3D 88.559 708 55 8 964 1669 14278315 14278998 0.000000e+00 835.0
6 TraesCS3B01G042000 chr3D 77.434 226 23 10 2363 2577 14228669 14228461 2.710000e-20 110.0
7 TraesCS3B01G042000 chr3A 86.843 1923 125 67 430 2296 22474520 22476370 0.000000e+00 2032.0
8 TraesCS3B01G042000 chr3A 84.861 1222 105 43 996 2190 22429857 22428689 0.000000e+00 1158.0
9 TraesCS3B01G042000 chr3A 84.888 1072 106 27 996 2048 22422661 22421627 0.000000e+00 1031.0
10 TraesCS3B01G042000 chr3A 95.161 62 3 0 270 331 22474374 22474435 5.870000e-17 99.0
11 TraesCS3B01G042000 chr3A 96.970 33 0 1 1416 1447 658864927 658864895 1.000000e-03 54.7
12 TraesCS3B01G042000 chr4A 90.000 120 8 3 1233 1352 153776722 153776837 4.440000e-33 152.0
13 TraesCS3B01G042000 chr2D 90.000 120 8 3 1233 1352 499309577 499309462 4.440000e-33 152.0


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 TraesCS3B01G042000 chr3B 21002128 21004706 2578 True 4763.000000 4763 100.0000 1 2579 1 chr3B.!!$R1 2578
1 TraesCS3B01G042000 chr3B 21161541 21163686 2145 False 434.866667 841 88.0100 996 2574 3 chr3B.!!$F1 1578
2 TraesCS3B01G042000 chr3D 14228461 14230733 2272 True 1199.500000 2289 82.4135 234 2577 2 chr3D.!!$R1 2343
3 TraesCS3B01G042000 chr3D 14278315 14278998 683 False 835.000000 835 88.5590 964 1669 1 chr3D.!!$F1 705
4 TraesCS3B01G042000 chr3A 22428689 22429857 1168 True 1158.000000 1158 84.8610 996 2190 1 chr3A.!!$R2 1194
5 TraesCS3B01G042000 chr3A 22474374 22476370 1996 False 1065.500000 2032 91.0020 270 2296 2 chr3A.!!$F1 2026
6 TraesCS3B01G042000 chr3A 22421627 22422661 1034 True 1031.000000 1031 84.8880 996 2048 1 chr3A.!!$R1 1052

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
200 201 0.30776 GCCACCACTCACGTTCAAAG 59.692 55.0 0.0 0.0 0.0 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1963 2708 1.176527 ACATTTCCATCAACGGCCAG 58.823 50.0 2.24 0.0 0.0 4.85 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
22 23 5.874895 GTCGCCTTACAATTCTTTAACCT 57.125 39.130 0.00 0.00 0.00 3.50
23 24 6.250344 GTCGCCTTACAATTCTTTAACCTT 57.750 37.500 0.00 0.00 0.00 3.50
24 25 6.312487 GTCGCCTTACAATTCTTTAACCTTC 58.688 40.000 0.00 0.00 0.00 3.46
25 26 5.998981 TCGCCTTACAATTCTTTAACCTTCA 59.001 36.000 0.00 0.00 0.00 3.02
26 27 6.148811 TCGCCTTACAATTCTTTAACCTTCAG 59.851 38.462 0.00 0.00 0.00 3.02
27 28 6.072673 CGCCTTACAATTCTTTAACCTTCAGT 60.073 38.462 0.00 0.00 0.00 3.41
28 29 7.521585 CGCCTTACAATTCTTTAACCTTCAGTT 60.522 37.037 0.00 0.00 42.83 3.16
29 30 8.141909 GCCTTACAATTCTTTAACCTTCAGTTT 58.858 33.333 0.00 0.00 40.05 2.66
56 57 2.323939 TTTTTGGCAACGTATCTGCG 57.676 45.000 0.00 0.00 40.88 5.18
57 58 1.514003 TTTTGGCAACGTATCTGCGA 58.486 45.000 0.00 0.00 40.88 5.10
58 59 1.514003 TTTGGCAACGTATCTGCGAA 58.486 45.000 0.00 4.32 40.88 4.70
59 60 1.514003 TTGGCAACGTATCTGCGAAA 58.486 45.000 5.78 0.61 40.88 3.46
60 61 1.514003 TGGCAACGTATCTGCGAAAA 58.486 45.000 4.72 0.00 40.88 2.29
61 62 1.874231 TGGCAACGTATCTGCGAAAAA 59.126 42.857 4.72 0.00 40.88 1.94
80 81 5.549742 AAAAATGATTGTGCCCTCTTGAA 57.450 34.783 0.00 0.00 0.00 2.69
81 82 5.549742 AAAATGATTGTGCCCTCTTGAAA 57.450 34.783 0.00 0.00 0.00 2.69
82 83 5.750352 AAATGATTGTGCCCTCTTGAAAT 57.250 34.783 0.00 0.00 0.00 2.17
83 84 6.855763 AAATGATTGTGCCCTCTTGAAATA 57.144 33.333 0.00 0.00 0.00 1.40
84 85 7.427989 AAATGATTGTGCCCTCTTGAAATAT 57.572 32.000 0.00 0.00 0.00 1.28
85 86 7.427989 AATGATTGTGCCCTCTTGAAATATT 57.572 32.000 0.00 0.00 0.00 1.28
86 87 8.537728 AATGATTGTGCCCTCTTGAAATATTA 57.462 30.769 0.00 0.00 0.00 0.98
87 88 8.716674 ATGATTGTGCCCTCTTGAAATATTAT 57.283 30.769 0.00 0.00 0.00 1.28
88 89 9.812347 ATGATTGTGCCCTCTTGAAATATTATA 57.188 29.630 0.00 0.00 0.00 0.98
89 90 9.066892 TGATTGTGCCCTCTTGAAATATTATAC 57.933 33.333 0.00 0.00 0.00 1.47
90 91 9.289782 GATTGTGCCCTCTTGAAATATTATACT 57.710 33.333 0.00 0.00 0.00 2.12
91 92 8.677148 TTGTGCCCTCTTGAAATATTATACTC 57.323 34.615 0.00 0.00 0.00 2.59
92 93 7.224297 TGTGCCCTCTTGAAATATTATACTCC 58.776 38.462 0.00 0.00 0.00 3.85
93 94 7.147391 TGTGCCCTCTTGAAATATTATACTCCA 60.147 37.037 0.00 0.00 0.00 3.86
94 95 7.719633 GTGCCCTCTTGAAATATTATACTCCAA 59.280 37.037 0.00 0.00 0.00 3.53
95 96 8.278639 TGCCCTCTTGAAATATTATACTCCAAA 58.721 33.333 0.00 0.00 0.00 3.28
96 97 9.131791 GCCCTCTTGAAATATTATACTCCAAAA 57.868 33.333 0.00 0.00 0.00 2.44
122 123 9.823098 AAAAGTAGTATATACTTCGCATCGTAG 57.177 33.333 20.21 0.00 36.82 3.51
123 124 7.002816 AGTAGTATATACTTCGCATCGTAGC 57.997 40.000 20.21 0.00 37.73 3.58
124 125 5.895348 GTAGTATATACTTCGCATCGTAGCG 59.105 44.000 20.21 15.94 46.65 4.26
125 126 5.578336 TAGTATATACTTCGCATCGTAGCGT 59.422 40.000 20.21 7.38 46.06 5.07
126 127 6.454715 TAGTATATACTTCGCATCGTAGCGTG 60.455 42.308 20.21 16.37 46.06 5.34
127 128 9.704138 TAGTATATACTTCGCATCGTAGCGTGC 62.704 44.444 20.21 6.74 46.06 5.34
131 132 3.704843 GCATCGTAGCGTGCATGA 58.295 55.556 10.93 0.00 40.94 3.07
132 133 2.005995 GCATCGTAGCGTGCATGAA 58.994 52.632 10.93 0.00 40.94 2.57
133 134 0.315382 GCATCGTAGCGTGCATGAAC 60.315 55.000 10.93 5.94 40.94 3.18
134 135 1.280982 CATCGTAGCGTGCATGAACT 58.719 50.000 10.93 0.20 0.00 3.01
135 136 2.459934 CATCGTAGCGTGCATGAACTA 58.540 47.619 10.93 0.00 0.00 2.24
136 137 2.640346 TCGTAGCGTGCATGAACTAA 57.360 45.000 10.93 0.00 0.00 2.24
137 138 3.159353 TCGTAGCGTGCATGAACTAAT 57.841 42.857 10.93 0.00 0.00 1.73
138 139 4.295857 TCGTAGCGTGCATGAACTAATA 57.704 40.909 10.93 0.00 0.00 0.98
139 140 4.674475 TCGTAGCGTGCATGAACTAATAA 58.326 39.130 10.93 0.00 0.00 1.40
140 141 5.103687 TCGTAGCGTGCATGAACTAATAAA 58.896 37.500 10.93 0.00 0.00 1.40
141 142 5.577554 TCGTAGCGTGCATGAACTAATAAAA 59.422 36.000 10.93 0.00 0.00 1.52
142 143 5.896432 CGTAGCGTGCATGAACTAATAAAAG 59.104 40.000 10.93 0.00 0.00 2.27
143 144 5.880054 AGCGTGCATGAACTAATAAAAGT 57.120 34.783 10.93 0.00 0.00 2.66
144 145 5.631026 AGCGTGCATGAACTAATAAAAGTG 58.369 37.500 10.93 0.00 0.00 3.16
145 146 5.411361 AGCGTGCATGAACTAATAAAAGTGA 59.589 36.000 10.93 0.00 0.00 3.41
146 147 6.072728 AGCGTGCATGAACTAATAAAAGTGAA 60.073 34.615 10.93 0.00 0.00 3.18
147 148 6.249260 GCGTGCATGAACTAATAAAAGTGAAG 59.751 38.462 10.93 0.00 0.00 3.02
148 149 6.249260 CGTGCATGAACTAATAAAAGTGAAGC 59.751 38.462 0.00 0.00 0.00 3.86
149 150 6.249260 GTGCATGAACTAATAAAAGTGAAGCG 59.751 38.462 0.00 0.00 0.00 4.68
150 151 5.228012 GCATGAACTAATAAAAGTGAAGCGC 59.772 40.000 0.00 0.00 0.00 5.92
151 152 6.546395 CATGAACTAATAAAAGTGAAGCGCT 58.454 36.000 2.64 2.64 0.00 5.92
152 153 5.927030 TGAACTAATAAAAGTGAAGCGCTG 58.073 37.500 12.58 0.00 0.00 5.18
153 154 4.946784 ACTAATAAAAGTGAAGCGCTGG 57.053 40.909 12.58 0.00 0.00 4.85
154 155 2.636768 AATAAAAGTGAAGCGCTGGC 57.363 45.000 12.58 7.21 40.37 4.85
164 165 3.341835 GCGCTGGCTAATCCGAGC 61.342 66.667 0.00 0.00 42.05 5.03
170 171 4.515404 GCTAATCCGAGCCACGTT 57.485 55.556 0.00 0.00 40.78 3.99
171 172 2.006772 GCTAATCCGAGCCACGTTG 58.993 57.895 0.00 0.00 40.78 4.10
172 173 0.459585 GCTAATCCGAGCCACGTTGA 60.460 55.000 0.00 0.00 40.78 3.18
173 174 2.004583 CTAATCCGAGCCACGTTGAA 57.995 50.000 0.00 0.00 40.78 2.69
174 175 2.343101 CTAATCCGAGCCACGTTGAAA 58.657 47.619 0.00 0.00 40.78 2.69
175 176 1.156736 AATCCGAGCCACGTTGAAAG 58.843 50.000 0.00 0.00 40.78 2.62
176 177 0.673644 ATCCGAGCCACGTTGAAAGG 60.674 55.000 0.00 0.00 40.78 3.11
180 181 2.644992 GCCACGTTGAAAGGCCAG 59.355 61.111 5.01 0.00 42.58 4.85
181 182 2.919494 GCCACGTTGAAAGGCCAGG 61.919 63.158 5.01 0.00 42.58 4.45
182 183 2.644992 CACGTTGAAAGGCCAGGC 59.355 61.111 5.01 1.26 0.00 4.85
194 195 3.941188 CCAGGCCACCACTCACGT 61.941 66.667 5.01 0.00 0.00 4.49
195 196 2.111043 CAGGCCACCACTCACGTT 59.889 61.111 5.01 0.00 0.00 3.99
196 197 1.961277 CAGGCCACCACTCACGTTC 60.961 63.158 5.01 0.00 0.00 3.95
197 198 2.110213 GGCCACCACTCACGTTCA 59.890 61.111 0.00 0.00 0.00 3.18
198 199 1.525077 GGCCACCACTCACGTTCAA 60.525 57.895 0.00 0.00 0.00 2.69
199 200 1.098712 GGCCACCACTCACGTTCAAA 61.099 55.000 0.00 0.00 0.00 2.69
200 201 0.307760 GCCACCACTCACGTTCAAAG 59.692 55.000 0.00 0.00 0.00 2.77
201 202 0.944386 CCACCACTCACGTTCAAAGG 59.056 55.000 0.00 0.00 0.00 3.11
202 203 0.307760 CACCACTCACGTTCAAAGGC 59.692 55.000 0.00 0.00 0.00 4.35
203 204 0.818040 ACCACTCACGTTCAAAGGCC 60.818 55.000 0.00 0.00 0.00 5.19
204 205 0.817634 CCACTCACGTTCAAAGGCCA 60.818 55.000 5.01 0.00 0.00 5.36
205 206 0.307760 CACTCACGTTCAAAGGCCAC 59.692 55.000 5.01 0.00 0.00 5.01
206 207 1.157870 ACTCACGTTCAAAGGCCACG 61.158 55.000 5.01 8.50 39.86 4.94
207 208 0.878523 CTCACGTTCAAAGGCCACGA 60.879 55.000 18.34 2.03 37.37 4.35
208 209 1.155424 TCACGTTCAAAGGCCACGAC 61.155 55.000 18.34 2.50 37.37 4.34
209 210 1.890510 ACGTTCAAAGGCCACGACC 60.891 57.895 18.34 0.00 37.37 4.79
210 211 2.613506 CGTTCAAAGGCCACGACCC 61.614 63.158 5.01 0.00 35.93 4.46
211 212 2.281208 TTCAAAGGCCACGACCCG 60.281 61.111 5.01 0.00 0.00 5.28
212 213 3.109592 TTCAAAGGCCACGACCCGT 62.110 57.895 5.01 0.00 42.36 5.28
213 214 2.999739 TTCAAAGGCCACGACCCGTC 63.000 60.000 5.01 0.00 38.32 4.79
214 215 3.239253 AAAGGCCACGACCCGTCT 61.239 61.111 5.01 0.00 38.32 4.18
215 216 3.530910 AAAGGCCACGACCCGTCTG 62.531 63.158 5.01 0.00 38.32 3.51
223 224 4.754667 GACCCGTCTGCCCGTTCC 62.755 72.222 0.00 0.00 0.00 3.62
228 229 3.948719 GTCTGCCCGTTCCACCCA 61.949 66.667 0.00 0.00 0.00 4.51
229 230 3.636231 TCTGCCCGTTCCACCCAG 61.636 66.667 0.00 0.00 0.00 4.45
230 231 3.636231 CTGCCCGTTCCACCCAGA 61.636 66.667 0.00 0.00 0.00 3.86
231 232 2.933287 TGCCCGTTCCACCCAGAT 60.933 61.111 0.00 0.00 0.00 2.90
232 233 1.613928 TGCCCGTTCCACCCAGATA 60.614 57.895 0.00 0.00 0.00 1.98
251 252 4.941873 AGATAGACCGCCTTTTTAGTTTGG 59.058 41.667 0.00 0.00 0.00 3.28
252 253 2.235891 AGACCGCCTTTTTAGTTTGGG 58.764 47.619 0.00 0.00 0.00 4.12
253 254 2.158579 AGACCGCCTTTTTAGTTTGGGA 60.159 45.455 0.00 0.00 0.00 4.37
254 255 2.624364 GACCGCCTTTTTAGTTTGGGAA 59.376 45.455 0.00 0.00 0.00 3.97
255 256 3.032459 ACCGCCTTTTTAGTTTGGGAAA 58.968 40.909 0.00 0.00 0.00 3.13
256 257 3.069016 ACCGCCTTTTTAGTTTGGGAAAG 59.931 43.478 0.00 0.00 0.00 2.62
257 258 3.319689 CCGCCTTTTTAGTTTGGGAAAGA 59.680 43.478 0.00 0.00 32.29 2.52
258 259 4.202172 CCGCCTTTTTAGTTTGGGAAAGAA 60.202 41.667 0.00 0.00 32.29 2.52
259 260 4.982295 CGCCTTTTTAGTTTGGGAAAGAAG 59.018 41.667 0.00 0.00 32.29 2.85
260 261 5.297547 GCCTTTTTAGTTTGGGAAAGAAGG 58.702 41.667 0.00 0.00 35.42 3.46
261 262 5.069914 GCCTTTTTAGTTTGGGAAAGAAGGA 59.930 40.000 7.55 0.00 34.49 3.36
267 268 9.967451 TTTTAGTTTGGGAAAGAAGGAAAAATT 57.033 25.926 0.00 0.00 0.00 1.82
290 291 3.853355 AATCTAATCTGGTGGCAGGAG 57.147 47.619 0.00 0.00 0.00 3.69
361 364 2.710902 CCTCACCTCACGCGATCCA 61.711 63.158 15.93 0.00 0.00 3.41
456 494 1.898154 CGACGAAATCACCTCCCCT 59.102 57.895 0.00 0.00 0.00 4.79
507 545 4.498894 TCTCGCCCCGAATAGATAGATA 57.501 45.455 0.00 0.00 34.74 1.98
508 546 4.452825 TCTCGCCCCGAATAGATAGATAG 58.547 47.826 0.00 0.00 34.74 2.08
509 547 4.163649 TCTCGCCCCGAATAGATAGATAGA 59.836 45.833 0.00 0.00 34.74 1.98
552 590 2.642311 ACAGTCACAGGAGAGAGAGAGA 59.358 50.000 0.00 0.00 0.00 3.10
554 592 2.239654 AGTCACAGGAGAGAGAGAGAGG 59.760 54.545 0.00 0.00 0.00 3.69
555 593 2.238646 GTCACAGGAGAGAGAGAGAGGA 59.761 54.545 0.00 0.00 0.00 3.71
556 594 2.505407 TCACAGGAGAGAGAGAGAGGAG 59.495 54.545 0.00 0.00 0.00 3.69
558 596 2.774234 ACAGGAGAGAGAGAGAGGAGAG 59.226 54.545 0.00 0.00 0.00 3.20
559 597 3.041211 CAGGAGAGAGAGAGAGGAGAGA 58.959 54.545 0.00 0.00 0.00 3.10
560 598 3.070734 CAGGAGAGAGAGAGAGGAGAGAG 59.929 56.522 0.00 0.00 0.00 3.20
561 599 3.051803 AGGAGAGAGAGAGAGGAGAGAGA 60.052 52.174 0.00 0.00 0.00 3.10
562 600 3.711704 GGAGAGAGAGAGAGGAGAGAGAA 59.288 52.174 0.00 0.00 0.00 2.87
563 601 4.443598 GGAGAGAGAGAGAGGAGAGAGAAC 60.444 54.167 0.00 0.00 0.00 3.01
564 602 3.133003 AGAGAGAGAGAGGAGAGAGAACG 59.867 52.174 0.00 0.00 0.00 3.95
565 603 2.838202 AGAGAGAGAGGAGAGAGAACGT 59.162 50.000 0.00 0.00 0.00 3.99
566 604 2.936498 GAGAGAGAGGAGAGAGAACGTG 59.064 54.545 0.00 0.00 0.00 4.49
567 605 2.569853 AGAGAGAGGAGAGAGAACGTGA 59.430 50.000 0.00 0.00 0.00 4.35
568 606 3.008594 AGAGAGAGGAGAGAGAACGTGAA 59.991 47.826 0.00 0.00 0.00 3.18
676 726 1.449778 GCTCCTACCAAGCCGTTCC 60.450 63.158 0.00 0.00 33.53 3.62
677 727 1.153628 CTCCTACCAAGCCGTTCCG 60.154 63.158 0.00 0.00 0.00 4.30
678 728 2.818274 CCTACCAAGCCGTTCCGC 60.818 66.667 0.00 0.00 0.00 5.54
679 729 2.047655 CTACCAAGCCGTTCCGCA 60.048 61.111 0.00 0.00 0.00 5.69
680 730 2.357760 TACCAAGCCGTTCCGCAC 60.358 61.111 0.00 0.00 0.00 5.34
681 731 3.887335 TACCAAGCCGTTCCGCACC 62.887 63.158 0.00 0.00 0.00 5.01
726 778 1.835121 AAGAAAAAGAAACCGCACGC 58.165 45.000 0.00 0.00 0.00 5.34
727 779 0.736053 AGAAAAAGAAACCGCACGCA 59.264 45.000 0.00 0.00 0.00 5.24
728 780 0.843872 GAAAAAGAAACCGCACGCAC 59.156 50.000 0.00 0.00 0.00 5.34
729 781 0.863957 AAAAAGAAACCGCACGCACG 60.864 50.000 0.00 0.00 0.00 5.34
742 794 1.328069 CACGCACGAGTGGTTGTTTTA 59.672 47.619 5.32 0.00 38.40 1.52
745 797 2.598907 CGCACGAGTGGTTGTTTTACAG 60.599 50.000 5.32 0.00 0.00 2.74
746 798 2.610374 GCACGAGTGGTTGTTTTACAGA 59.390 45.455 5.32 0.00 0.00 3.41
749 801 5.389516 GCACGAGTGGTTGTTTTACAGATAG 60.390 44.000 5.32 0.00 0.00 2.08
758 810 2.508300 GTTTTACAGATAGCCCCCTGGA 59.492 50.000 0.00 0.00 34.85 3.86
769 821 2.770048 CCCTGGAAGATCCCGCCT 60.770 66.667 0.00 0.00 35.03 5.52
858 911 0.865769 CGCACCGCTTTTTGTACTCT 59.134 50.000 0.00 0.00 0.00 3.24
859 912 1.398451 CGCACCGCTTTTTGTACTCTG 60.398 52.381 0.00 0.00 0.00 3.35
860 913 1.871039 GCACCGCTTTTTGTACTCTGA 59.129 47.619 0.00 0.00 0.00 3.27
865 918 4.021016 ACCGCTTTTTGTACTCTGATCTCT 60.021 41.667 0.00 0.00 0.00 3.10
869 922 5.569630 GCTTTTTGTACTCTGATCTCTCCCA 60.570 44.000 0.00 0.00 0.00 4.37
872 925 2.583101 TGTACTCTGATCTCTCCCACCT 59.417 50.000 0.00 0.00 0.00 4.00
911 967 2.684843 CGCCCAGAGTGCTCTTTGC 61.685 63.158 0.00 4.61 37.98 3.68
913 969 0.892814 GCCCAGAGTGCTCTTTGCTT 60.893 55.000 0.00 0.00 43.37 3.91
1024 1097 1.724582 GAGCTCCTCCTCGTCTCTGC 61.725 65.000 0.87 0.00 0.00 4.26
1404 1480 1.064296 CGAGGACGAGATTGACGGG 59.936 63.158 0.00 0.00 42.66 5.28
1586 1662 2.452813 CGGCCGTTTGATCAGTCGG 61.453 63.158 25.82 25.82 44.86 4.79
1622 1698 2.026915 CGGATGGATGGATGGATTAGCA 60.027 50.000 0.00 0.00 0.00 3.49
1665 1742 5.391310 GCTAACCTTAGCGTTACCCTTTTTC 60.391 44.000 1.35 0.00 45.65 2.29
1732 2446 2.908688 AACCTGGAAAATGTGTTGCC 57.091 45.000 0.00 0.00 0.00 4.52
1735 2449 1.273327 CCTGGAAAATGTGTTGCCTCC 59.727 52.381 0.00 0.00 0.00 4.30
1808 2524 5.078949 TCAAGGATTCCAGAAGAAATTGCA 58.921 37.500 5.29 0.00 38.21 4.08
1812 2528 5.718130 AGGATTCCAGAAGAAATTGCATCAA 59.282 36.000 5.29 0.00 38.21 2.57
1944 2689 4.783764 ATGTGAATGAGTGTACGAGTCA 57.216 40.909 0.00 5.63 38.44 3.41
2043 2792 6.659242 CCTAACCTAATGACATGACAAACCTT 59.341 38.462 0.00 0.00 0.00 3.50
2048 2797 9.747898 ACCTAATGACATGACAAACCTTAATAA 57.252 29.630 0.00 0.00 0.00 1.40
2067 2834 9.875691 CTTAATAATGGGGAAAAAGGAAAAGAG 57.124 33.333 0.00 0.00 0.00 2.85
2121 2888 4.463891 TGGATTGGAAAATCAGAAGCTTCC 59.536 41.667 22.81 6.35 38.26 3.46
2133 2900 2.439507 AGAAGCTTCCAGTGTTCCTCAA 59.560 45.455 22.81 0.00 0.00 3.02
2143 2910 6.601332 TCCAGTGTTCCTCAAGTTTCTTTAT 58.399 36.000 0.00 0.00 0.00 1.40
2144 2911 7.741785 TCCAGTGTTCCTCAAGTTTCTTTATA 58.258 34.615 0.00 0.00 0.00 0.98
2145 2912 7.660208 TCCAGTGTTCCTCAAGTTTCTTTATAC 59.340 37.037 0.00 0.00 0.00 1.47
2178 2949 1.974236 AGATAGGCTGGGAATTCTCCG 59.026 52.381 2.04 0.00 43.51 4.63
2214 3018 0.555769 GGGGTGGATAATTCTGGCCA 59.444 55.000 4.71 4.71 0.00 5.36
2237 3041 4.701171 AGAACGGTTGACCTGTAAAACAAA 59.299 37.500 0.00 0.00 0.00 2.83
2246 3050 5.301551 TGACCTGTAAAACAAATGCATCTGT 59.698 36.000 0.00 0.00 0.00 3.41
2254 3058 9.793252 GTAAAACAAATGCATCTGTCAAGATAT 57.207 29.630 6.03 0.00 41.43 1.63
2258 3062 9.961265 AACAAATGCATCTGTCAAGATATATTG 57.039 29.630 6.03 3.60 41.43 1.90
2259 3063 9.128404 ACAAATGCATCTGTCAAGATATATTGT 57.872 29.630 9.77 0.00 41.43 2.71
2260 3064 9.961265 CAAATGCATCTGTCAAGATATATTGTT 57.039 29.630 9.77 0.00 41.43 2.83
2261 3065 9.961265 AAATGCATCTGTCAAGATATATTGTTG 57.039 29.630 9.77 2.60 41.43 3.33
2262 3066 8.687292 ATGCATCTGTCAAGATATATTGTTGT 57.313 30.769 9.77 0.00 41.43 3.32
2263 3067 7.922837 TGCATCTGTCAAGATATATTGTTGTG 58.077 34.615 9.77 5.13 41.43 3.33
2264 3068 6.854892 GCATCTGTCAAGATATATTGTTGTGC 59.145 38.462 9.77 10.14 41.43 4.57
2265 3069 7.255035 GCATCTGTCAAGATATATTGTTGTGCT 60.255 37.037 9.77 0.00 41.43 4.40
2266 3070 8.618677 CATCTGTCAAGATATATTGTTGTGCTT 58.381 33.333 9.77 0.00 41.43 3.91
2267 3071 8.565896 TCTGTCAAGATATATTGTTGTGCTTT 57.434 30.769 9.77 0.00 0.00 3.51
2268 3072 9.013229 TCTGTCAAGATATATTGTTGTGCTTTT 57.987 29.630 9.77 0.00 0.00 2.27
2269 3073 9.630098 CTGTCAAGATATATTGTTGTGCTTTTT 57.370 29.630 9.77 0.00 0.00 1.94
2341 3145 9.865321 AACAATACATACTTCTATACGTTGTGT 57.135 29.630 0.00 0.00 0.00 3.72
2342 3146 9.865321 ACAATACATACTTCTATACGTTGTGTT 57.135 29.630 0.00 0.00 0.00 3.32
2347 3151 8.430063 ACATACTTCTATACGTTGTGTTTTTCG 58.570 33.333 0.00 0.00 0.00 3.46
2348 3152 6.833342 ACTTCTATACGTTGTGTTTTTCGT 57.167 33.333 0.00 0.00 39.74 3.85
2349 3153 6.870517 ACTTCTATACGTTGTGTTTTTCGTC 58.129 36.000 0.00 0.00 37.66 4.20
2350 3154 5.827568 TCTATACGTTGTGTTTTTCGTCC 57.172 39.130 0.00 0.00 37.66 4.79
2351 3155 5.288015 TCTATACGTTGTGTTTTTCGTCCA 58.712 37.500 0.00 0.00 37.66 4.02
2352 3156 2.530832 ACGTTGTGTTTTTCGTCCAC 57.469 45.000 0.00 0.00 30.71 4.02
2353 3157 1.805345 ACGTTGTGTTTTTCGTCCACA 59.195 42.857 0.00 0.00 37.32 4.17
2354 3158 2.170770 CGTTGTGTTTTTCGTCCACAC 58.829 47.619 0.00 0.00 38.71 3.82
2356 3160 1.440708 TGTGTTTTTCGTCCACACGT 58.559 45.000 0.00 0.00 46.76 4.49
2357 3161 2.614779 TGTGTTTTTCGTCCACACGTA 58.385 42.857 0.00 0.00 46.76 3.57
2358 3162 3.196463 TGTGTTTTTCGTCCACACGTAT 58.804 40.909 0.00 0.00 46.76 3.06
2359 3163 3.001431 TGTGTTTTTCGTCCACACGTATG 59.999 43.478 0.00 0.00 46.76 2.39
2360 3164 3.001533 GTGTTTTTCGTCCACACGTATGT 59.998 43.478 0.00 0.00 46.76 2.29
2390 3194 5.729510 AGAATCTTCAAGGTTAGCTGTCTC 58.270 41.667 0.00 0.00 0.00 3.36
2405 3212 0.103208 GTCTCCGTGTAGCCATCCAG 59.897 60.000 0.00 0.00 0.00 3.86
2407 3214 0.387202 CTCCGTGTAGCCATCCAGAG 59.613 60.000 0.00 0.00 0.00 3.35
2465 3272 6.755542 TTTTGAAAACCCCTCCAATACATT 57.244 33.333 0.00 0.00 0.00 2.71
2466 3273 7.857404 TTTTGAAAACCCCTCCAATACATTA 57.143 32.000 0.00 0.00 0.00 1.90
2467 3274 7.857404 TTTGAAAACCCCTCCAATACATTAA 57.143 32.000 0.00 0.00 0.00 1.40
2505 3312 9.807649 AGAAAAATCATACAGCCATTTCATTAC 57.192 29.630 0.00 0.00 0.00 1.89
2514 3321 6.949715 ACAGCCATTTCATTACATTTGGATT 58.050 32.000 0.00 0.00 0.00 3.01
2524 3331 3.575965 ACATTTGGATTTGCCGTCTTC 57.424 42.857 0.00 0.00 40.66 2.87
2526 3333 0.239879 TTTGGATTTGCCGTCTTCGC 59.760 50.000 0.00 0.00 40.66 4.70
2577 3394 3.359654 GTGGAAACATGTCGTGTCAAAC 58.640 45.455 0.00 0.00 46.14 2.93
2578 3395 3.064820 GTGGAAACATGTCGTGTCAAACT 59.935 43.478 0.00 0.00 46.14 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.874895 AGGTTAAAGAATTGTAAGGCGAC 57.125 39.130 0.00 0.00 0.00 5.19
1 2 5.998981 TGAAGGTTAAAGAATTGTAAGGCGA 59.001 36.000 0.00 0.00 0.00 5.54
2 3 6.072673 ACTGAAGGTTAAAGAATTGTAAGGCG 60.073 38.462 0.00 0.00 0.00 5.52
3 4 7.215719 ACTGAAGGTTAAAGAATTGTAAGGC 57.784 36.000 0.00 0.00 0.00 4.35
37 38 1.874231 TCGCAGATACGTTGCCAAAAA 59.126 42.857 5.18 0.00 38.31 1.94
38 39 1.514003 TCGCAGATACGTTGCCAAAA 58.486 45.000 5.18 0.00 38.31 2.44
39 40 1.514003 TTCGCAGATACGTTGCCAAA 58.486 45.000 5.18 0.00 38.31 3.28
40 41 1.514003 TTTCGCAGATACGTTGCCAA 58.486 45.000 5.18 0.00 38.31 4.52
41 42 1.514003 TTTTCGCAGATACGTTGCCA 58.486 45.000 5.18 0.00 38.31 4.92
42 43 2.604969 TTTTTCGCAGATACGTTGCC 57.395 45.000 5.18 0.00 38.31 4.52
58 59 5.549742 TTCAAGAGGGCACAATCATTTTT 57.450 34.783 0.00 0.00 0.00 1.94
59 60 5.549742 TTTCAAGAGGGCACAATCATTTT 57.450 34.783 0.00 0.00 0.00 1.82
60 61 5.750352 ATTTCAAGAGGGCACAATCATTT 57.250 34.783 0.00 0.00 0.00 2.32
61 62 7.427989 AATATTTCAAGAGGGCACAATCATT 57.572 32.000 0.00 0.00 0.00 2.57
62 63 8.716674 ATAATATTTCAAGAGGGCACAATCAT 57.283 30.769 0.00 0.00 0.00 2.45
63 64 9.066892 GTATAATATTTCAAGAGGGCACAATCA 57.933 33.333 0.00 0.00 0.00 2.57
64 65 9.289782 AGTATAATATTTCAAGAGGGCACAATC 57.710 33.333 0.00 0.00 0.00 2.67
65 66 9.289782 GAGTATAATATTTCAAGAGGGCACAAT 57.710 33.333 0.00 0.00 0.00 2.71
66 67 7.719633 GGAGTATAATATTTCAAGAGGGCACAA 59.280 37.037 0.00 0.00 0.00 3.33
67 68 7.147391 TGGAGTATAATATTTCAAGAGGGCACA 60.147 37.037 0.00 0.00 0.00 4.57
68 69 7.224297 TGGAGTATAATATTTCAAGAGGGCAC 58.776 38.462 0.00 0.00 0.00 5.01
69 70 7.387265 TGGAGTATAATATTTCAAGAGGGCA 57.613 36.000 0.00 0.00 0.00 5.36
70 71 8.691661 TTTGGAGTATAATATTTCAAGAGGGC 57.308 34.615 0.00 0.00 0.00 5.19
96 97 9.823098 CTACGATGCGAAGTATATACTACTTTT 57.177 33.333 15.74 0.00 37.83 2.27
97 98 7.961827 GCTACGATGCGAAGTATATACTACTTT 59.038 37.037 15.74 0.02 37.83 2.66
98 99 7.462731 GCTACGATGCGAAGTATATACTACTT 58.537 38.462 15.74 2.36 40.15 2.24
99 100 7.002816 GCTACGATGCGAAGTATATACTACT 57.997 40.000 15.74 1.16 34.99 2.57
114 115 0.315382 GTTCATGCACGCTACGATGC 60.315 55.000 0.00 1.03 42.40 3.91
115 116 1.280982 AGTTCATGCACGCTACGATG 58.719 50.000 0.00 0.00 0.00 3.84
116 117 2.863401 TAGTTCATGCACGCTACGAT 57.137 45.000 0.00 0.00 0.00 3.73
117 118 2.640346 TTAGTTCATGCACGCTACGA 57.360 45.000 0.00 0.00 0.00 3.43
118 119 5.383984 TTTATTAGTTCATGCACGCTACG 57.616 39.130 0.00 0.00 0.00 3.51
119 120 6.682863 CACTTTTATTAGTTCATGCACGCTAC 59.317 38.462 0.00 0.00 0.00 3.58
120 121 6.592220 TCACTTTTATTAGTTCATGCACGCTA 59.408 34.615 0.00 0.00 0.00 4.26
121 122 5.411361 TCACTTTTATTAGTTCATGCACGCT 59.589 36.000 0.00 0.00 0.00 5.07
122 123 5.627172 TCACTTTTATTAGTTCATGCACGC 58.373 37.500 0.00 0.00 0.00 5.34
123 124 6.249260 GCTTCACTTTTATTAGTTCATGCACG 59.751 38.462 0.00 0.00 0.00 5.34
124 125 6.249260 CGCTTCACTTTTATTAGTTCATGCAC 59.751 38.462 0.00 0.00 0.00 4.57
125 126 6.314018 CGCTTCACTTTTATTAGTTCATGCA 58.686 36.000 0.00 0.00 0.00 3.96
126 127 5.228012 GCGCTTCACTTTTATTAGTTCATGC 59.772 40.000 0.00 0.00 0.00 4.06
127 128 6.467047 CAGCGCTTCACTTTTATTAGTTCATG 59.533 38.462 7.50 0.00 0.00 3.07
128 129 6.403636 CCAGCGCTTCACTTTTATTAGTTCAT 60.404 38.462 7.50 0.00 0.00 2.57
129 130 5.106712 CCAGCGCTTCACTTTTATTAGTTCA 60.107 40.000 7.50 0.00 0.00 3.18
130 131 5.324697 CCAGCGCTTCACTTTTATTAGTTC 58.675 41.667 7.50 0.00 0.00 3.01
131 132 4.379499 GCCAGCGCTTCACTTTTATTAGTT 60.379 41.667 7.50 0.00 0.00 2.24
132 133 3.127030 GCCAGCGCTTCACTTTTATTAGT 59.873 43.478 7.50 0.00 0.00 2.24
133 134 3.375299 AGCCAGCGCTTCACTTTTATTAG 59.625 43.478 7.50 0.00 45.55 1.73
134 135 3.343617 AGCCAGCGCTTCACTTTTATTA 58.656 40.909 7.50 0.00 45.55 0.98
135 136 2.162681 AGCCAGCGCTTCACTTTTATT 58.837 42.857 7.50 0.00 45.55 1.40
136 137 1.826385 AGCCAGCGCTTCACTTTTAT 58.174 45.000 7.50 0.00 45.55 1.40
137 138 2.465860 TAGCCAGCGCTTCACTTTTA 57.534 45.000 7.50 0.00 45.55 1.52
138 139 1.604604 TTAGCCAGCGCTTCACTTTT 58.395 45.000 7.50 0.00 45.55 2.27
139 140 1.740025 GATTAGCCAGCGCTTCACTTT 59.260 47.619 7.50 0.00 45.55 2.66
140 141 1.373570 GATTAGCCAGCGCTTCACTT 58.626 50.000 7.50 0.00 45.55 3.16
141 142 0.462759 GGATTAGCCAGCGCTTCACT 60.463 55.000 7.50 8.14 45.55 3.41
142 143 1.766143 CGGATTAGCCAGCGCTTCAC 61.766 60.000 7.50 0.00 45.55 3.18
143 144 1.521457 CGGATTAGCCAGCGCTTCA 60.521 57.895 7.50 0.00 45.55 3.02
144 145 1.218230 CTCGGATTAGCCAGCGCTTC 61.218 60.000 7.50 0.34 45.55 3.86
145 146 1.227380 CTCGGATTAGCCAGCGCTT 60.227 57.895 7.50 0.00 45.55 4.68
147 148 3.341835 GCTCGGATTAGCCAGCGC 61.342 66.667 0.00 0.00 36.45 5.92
153 154 0.459585 TCAACGTGGCTCGGATTAGC 60.460 55.000 13.91 0.00 44.69 3.09
154 155 2.004583 TTCAACGTGGCTCGGATTAG 57.995 50.000 13.91 0.00 44.69 1.73
155 156 2.343101 CTTTCAACGTGGCTCGGATTA 58.657 47.619 13.91 0.00 44.69 1.75
156 157 1.156736 CTTTCAACGTGGCTCGGATT 58.843 50.000 13.91 0.00 44.69 3.01
157 158 0.673644 CCTTTCAACGTGGCTCGGAT 60.674 55.000 13.91 0.00 44.69 4.18
158 159 1.301401 CCTTTCAACGTGGCTCGGA 60.301 57.895 13.91 0.00 44.69 4.55
159 160 2.966309 GCCTTTCAACGTGGCTCGG 61.966 63.158 13.91 0.00 44.69 4.63
160 161 2.556287 GCCTTTCAACGTGGCTCG 59.444 61.111 7.50 7.50 43.05 5.03
161 162 1.856265 CTGGCCTTTCAACGTGGCTC 61.856 60.000 12.96 4.97 45.45 4.70
162 163 1.898574 CTGGCCTTTCAACGTGGCT 60.899 57.895 12.96 0.00 45.45 4.75
163 164 2.644992 CTGGCCTTTCAACGTGGC 59.355 61.111 3.32 5.31 45.42 5.01
164 165 2.919494 GCCTGGCCTTTCAACGTGG 61.919 63.158 7.66 0.00 0.00 4.94
165 166 2.644992 GCCTGGCCTTTCAACGTG 59.355 61.111 7.66 0.00 0.00 4.49
166 167 2.597510 GGCCTGGCCTTTCAACGT 60.598 61.111 30.42 0.00 46.69 3.99
177 178 3.941188 ACGTGAGTGGTGGCCTGG 61.941 66.667 3.32 0.00 46.97 4.45
188 189 0.878523 TCGTGGCCTTTGAACGTGAG 60.879 55.000 11.78 0.00 38.43 3.51
189 190 1.144276 TCGTGGCCTTTGAACGTGA 59.856 52.632 11.78 0.00 38.43 4.35
190 191 1.278637 GTCGTGGCCTTTGAACGTG 59.721 57.895 11.78 0.00 38.43 4.49
191 192 1.890510 GGTCGTGGCCTTTGAACGT 60.891 57.895 11.78 0.00 38.43 3.99
192 193 2.613506 GGGTCGTGGCCTTTGAACG 61.614 63.158 3.32 5.04 38.64 3.95
193 194 2.613506 CGGGTCGTGGCCTTTGAAC 61.614 63.158 3.32 1.03 0.00 3.18
194 195 2.281208 CGGGTCGTGGCCTTTGAA 60.281 61.111 3.32 0.00 0.00 2.69
195 196 3.524648 GACGGGTCGTGGCCTTTGA 62.525 63.158 3.32 0.00 41.37 2.69
196 197 3.047877 GACGGGTCGTGGCCTTTG 61.048 66.667 3.32 0.00 41.37 2.77
197 198 3.239253 AGACGGGTCGTGGCCTTT 61.239 61.111 3.32 0.00 41.37 3.11
198 199 4.003788 CAGACGGGTCGTGGCCTT 62.004 66.667 3.32 0.00 41.37 4.35
206 207 4.754667 GGAACGGGCAGACGGGTC 62.755 72.222 0.00 0.00 38.39 4.46
211 212 3.901797 CTGGGTGGAACGGGCAGAC 62.902 68.421 0.00 0.00 38.12 3.51
212 213 3.636231 CTGGGTGGAACGGGCAGA 61.636 66.667 0.00 0.00 38.12 4.26
213 214 1.622607 TATCTGGGTGGAACGGGCAG 61.623 60.000 0.00 0.00 38.12 4.85
214 215 1.613928 TATCTGGGTGGAACGGGCA 60.614 57.895 0.00 0.00 38.12 5.36
215 216 1.146263 CTATCTGGGTGGAACGGGC 59.854 63.158 0.00 0.00 38.12 6.13
216 217 0.464452 GTCTATCTGGGTGGAACGGG 59.536 60.000 0.00 0.00 38.12 5.28
217 218 0.464452 GGTCTATCTGGGTGGAACGG 59.536 60.000 0.00 0.00 38.12 4.44
218 219 0.102481 CGGTCTATCTGGGTGGAACG 59.898 60.000 0.00 0.00 38.12 3.95
219 220 0.179081 GCGGTCTATCTGGGTGGAAC 60.179 60.000 0.00 0.00 0.00 3.62
220 221 1.335132 GGCGGTCTATCTGGGTGGAA 61.335 60.000 0.00 0.00 0.00 3.53
221 222 1.760875 GGCGGTCTATCTGGGTGGA 60.761 63.158 0.00 0.00 0.00 4.02
222 223 1.338136 AAGGCGGTCTATCTGGGTGG 61.338 60.000 0.00 0.00 0.00 4.61
223 224 0.541863 AAAGGCGGTCTATCTGGGTG 59.458 55.000 0.00 0.00 0.00 4.61
224 225 1.286248 AAAAGGCGGTCTATCTGGGT 58.714 50.000 0.00 0.00 0.00 4.51
225 226 2.420058 AAAAAGGCGGTCTATCTGGG 57.580 50.000 0.00 0.00 0.00 4.45
226 227 4.138487 ACTAAAAAGGCGGTCTATCTGG 57.862 45.455 0.00 0.00 0.00 3.86
227 228 5.163754 CCAAACTAAAAAGGCGGTCTATCTG 60.164 44.000 0.00 0.00 0.00 2.90
228 229 4.941873 CCAAACTAAAAAGGCGGTCTATCT 59.058 41.667 0.00 0.00 0.00 1.98
229 230 4.095932 CCCAAACTAAAAAGGCGGTCTATC 59.904 45.833 0.00 0.00 0.00 2.08
230 231 4.014406 CCCAAACTAAAAAGGCGGTCTAT 58.986 43.478 0.00 0.00 0.00 1.98
231 232 3.072768 TCCCAAACTAAAAAGGCGGTCTA 59.927 43.478 0.00 0.00 0.00 2.59
232 233 2.158579 TCCCAAACTAAAAAGGCGGTCT 60.159 45.455 0.00 0.00 0.00 3.85
259 260 9.098355 GCCACCAGATTAGATTTAAATTTTTCC 57.902 33.333 1.43 0.00 0.00 3.13
260 261 9.651913 TGCCACCAGATTAGATTTAAATTTTTC 57.348 29.630 1.43 0.00 0.00 2.29
261 262 9.657419 CTGCCACCAGATTAGATTTAAATTTTT 57.343 29.630 1.43 0.00 41.77 1.94
267 268 5.428457 TCTCCTGCCACCAGATTAGATTTAA 59.572 40.000 0.00 0.00 41.77 1.52
290 291 7.491696 ACGGCTACTAAACTTGACTTGATATTC 59.508 37.037 0.00 0.00 0.00 1.75
342 345 2.583593 GATCGCGTGAGGTGAGGC 60.584 66.667 5.77 0.00 38.83 4.70
376 399 0.110373 GATTTGTCGTGGTCCGTTGC 60.110 55.000 0.00 0.00 37.94 4.17
382 415 1.359459 GGGCGAGATTTGTCGTGGTC 61.359 60.000 0.00 0.00 42.17 4.02
385 418 1.787847 GTGGGCGAGATTTGTCGTG 59.212 57.895 0.00 0.00 42.17 4.35
462 500 2.898472 ATCTGGAAGGAGGACCGGGG 62.898 65.000 6.32 0.00 41.83 5.73
507 545 4.944930 GTGTGTGTCTGACCTACTCTATCT 59.055 45.833 5.17 0.00 0.00 1.98
508 546 4.700692 TGTGTGTGTCTGACCTACTCTATC 59.299 45.833 5.17 0.00 0.00 2.08
509 547 4.459685 GTGTGTGTGTCTGACCTACTCTAT 59.540 45.833 5.17 0.00 0.00 1.98
552 590 4.873746 TTTCATTCACGTTCTCTCTCCT 57.126 40.909 0.00 0.00 0.00 3.69
554 592 6.532365 AGTTTTTCATTCACGTTCTCTCTC 57.468 37.500 0.00 0.00 0.00 3.20
555 593 6.927294 AAGTTTTTCATTCACGTTCTCTCT 57.073 33.333 0.00 0.00 0.00 3.10
556 594 9.498307 TTTTAAGTTTTTCATTCACGTTCTCTC 57.502 29.630 0.00 0.00 0.00 3.20
592 630 3.523087 ATGTGGGTGTGCGTGCGTA 62.523 57.895 0.00 0.00 0.00 4.42
654 698 2.782222 CGGCTTGGTAGGAGCGCTA 61.782 63.158 11.50 0.00 41.03 4.26
657 701 1.810030 GAACGGCTTGGTAGGAGCG 60.810 63.158 0.00 0.00 41.03 5.03
658 702 1.449778 GGAACGGCTTGGTAGGAGC 60.450 63.158 0.00 0.00 39.41 4.70
726 778 5.389516 GCTATCTGTAAAACAACCACTCGTG 60.390 44.000 0.00 0.00 0.00 4.35
727 779 4.689345 GCTATCTGTAAAACAACCACTCGT 59.311 41.667 0.00 0.00 0.00 4.18
728 780 4.092968 GGCTATCTGTAAAACAACCACTCG 59.907 45.833 0.00 0.00 0.00 4.18
729 781 4.395231 GGGCTATCTGTAAAACAACCACTC 59.605 45.833 0.00 0.00 0.00 3.51
742 794 0.343372 TCTTCCAGGGGGCTATCTGT 59.657 55.000 0.00 0.00 0.00 3.41
745 797 0.988063 GGATCTTCCAGGGGGCTATC 59.012 60.000 0.00 0.00 36.28 2.08
746 798 0.476611 GGGATCTTCCAGGGGGCTAT 60.477 60.000 0.00 0.00 38.64 2.97
749 801 3.878667 CGGGATCTTCCAGGGGGC 61.879 72.222 0.00 0.00 38.64 5.80
788 840 0.460284 CTTATATAGCGCCGGGCCAG 60.460 60.000 14.55 0.00 45.17 4.85
789 841 1.594833 CTTATATAGCGCCGGGCCA 59.405 57.895 14.55 0.00 45.17 5.36
858 911 0.615331 GCACAAGGTGGGAGAGATCA 59.385 55.000 0.00 0.00 33.64 2.92
859 912 3.467776 GCACAAGGTGGGAGAGATC 57.532 57.895 0.00 0.00 33.64 2.75
1134 1210 2.667199 TCGTCGTCGAGCAGGTCA 60.667 61.111 0.00 0.00 41.35 4.02
1509 1585 1.800713 GAAGGACTCGTCGCCGAAC 60.801 63.158 0.00 0.00 43.69 3.95
1665 1742 6.719829 AGAAACTTTACATCCCCAAAGGTTAG 59.280 38.462 0.00 0.00 40.76 2.34
1732 2446 8.728337 TTTTCTCTCTACATCATTCATTGGAG 57.272 34.615 0.00 0.00 0.00 3.86
1855 2572 8.129211 AGCGGATTAATTTATTCTTTTCTTCCG 58.871 33.333 0.00 0.00 42.95 4.30
1893 2632 6.746745 AGCATATTTTTCTTGGCCAAAATG 57.253 33.333 20.91 8.35 34.94 2.32
1944 2689 3.367703 CCAGAAATCCGCATCTGCTTTTT 60.368 43.478 0.09 0.00 41.36 1.94
1963 2708 1.176527 ACATTTCCATCAACGGCCAG 58.823 50.000 2.24 0.00 0.00 4.85
2008 2754 4.081807 GTCATTAGGTTAGGTCAACGTCCT 60.082 45.833 0.00 0.00 38.09 3.85
2043 2792 9.608718 TTCTCTTTTCCTTTTTCCCCATTATTA 57.391 29.630 0.00 0.00 0.00 0.98
2048 2797 4.284490 GCTTCTCTTTTCCTTTTTCCCCAT 59.716 41.667 0.00 0.00 0.00 4.00
2051 2800 4.937201 TGCTTCTCTTTTCCTTTTTCCC 57.063 40.909 0.00 0.00 0.00 3.97
2067 2834 4.498682 GGGCAGTTGAATCACATATGCTTC 60.499 45.833 1.58 4.65 39.05 3.86
2121 2888 8.608844 AGTATAAAGAAACTTGAGGAACACTG 57.391 34.615 0.00 0.00 0.00 3.66
2168 2939 3.203716 AGAATAAACGCCGGAGAATTCC 58.796 45.455 13.83 3.80 40.33 3.01
2169 2940 4.495844 CCAAGAATAAACGCCGGAGAATTC 60.496 45.833 13.83 16.49 0.00 2.17
2178 2949 1.681264 CCCCATCCAAGAATAAACGCC 59.319 52.381 0.00 0.00 0.00 5.68
2214 3018 3.876341 TGTTTTACAGGTCAACCGTTCT 58.124 40.909 2.82 0.00 42.08 3.01
2237 3041 8.565416 CACAACAATATATCTTGACAGATGCAT 58.435 33.333 0.00 0.00 40.28 3.96
2284 3088 8.849168 TGATGAAAAATCAAGACACAACATAGT 58.151 29.630 0.00 0.00 0.00 2.12
2285 3089 9.681692 TTGATGAAAAATCAAGACACAACATAG 57.318 29.630 0.00 0.00 33.55 2.23
2287 3091 8.945481 TTTGATGAAAAATCAAGACACAACAT 57.055 26.923 1.46 0.00 38.98 2.71
2288 3092 8.945481 ATTTGATGAAAAATCAAGACACAACA 57.055 26.923 1.46 0.00 38.98 3.33
2315 3119 9.865321 ACACAACGTATAGAAGTATGTATTGTT 57.135 29.630 0.00 0.00 0.00 2.83
2316 3120 9.865321 AACACAACGTATAGAAGTATGTATTGT 57.135 29.630 0.00 0.00 0.00 2.71
2321 3125 8.430063 CGAAAAACACAACGTATAGAAGTATGT 58.570 33.333 0.00 0.00 0.00 2.29
2323 3127 8.524870 ACGAAAAACACAACGTATAGAAGTAT 57.475 30.769 0.00 0.00 37.22 2.12
2324 3128 7.114811 GGACGAAAAACACAACGTATAGAAGTA 59.885 37.037 0.00 0.00 39.04 2.24
2325 3129 6.074142 GGACGAAAAACACAACGTATAGAAGT 60.074 38.462 0.00 0.00 39.04 3.01
2326 3130 6.074195 TGGACGAAAAACACAACGTATAGAAG 60.074 38.462 0.00 0.00 39.04 2.85
2328 3132 5.175491 GTGGACGAAAAACACAACGTATAGA 59.825 40.000 0.00 0.00 39.04 1.98
2329 3133 5.050904 TGTGGACGAAAAACACAACGTATAG 60.051 40.000 0.00 0.00 41.65 1.31
2330 3134 4.807834 TGTGGACGAAAAACACAACGTATA 59.192 37.500 0.00 0.00 41.65 1.47
2331 3135 3.622163 TGTGGACGAAAAACACAACGTAT 59.378 39.130 0.00 0.00 41.65 3.06
2332 3136 2.998670 TGTGGACGAAAAACACAACGTA 59.001 40.909 0.00 0.00 41.65 3.57
2333 3137 1.805345 TGTGGACGAAAAACACAACGT 59.195 42.857 0.00 0.00 41.65 3.99
2334 3138 2.170770 GTGTGGACGAAAAACACAACG 58.829 47.619 0.00 0.00 45.53 4.10
2347 3151 5.746307 TCTCTGTATACATACGTGTGGAC 57.254 43.478 17.05 11.40 39.39 4.02
2348 3152 6.771267 AGATTCTCTGTATACATACGTGTGGA 59.229 38.462 17.05 8.70 39.39 4.02
2349 3153 6.971602 AGATTCTCTGTATACATACGTGTGG 58.028 40.000 17.05 0.00 39.39 4.17
2350 3154 8.129211 TGAAGATTCTCTGTATACATACGTGTG 58.871 37.037 11.09 11.09 39.39 3.82
2351 3155 8.221965 TGAAGATTCTCTGTATACATACGTGT 57.778 34.615 5.91 0.00 42.39 4.49
2352 3156 9.175060 CTTGAAGATTCTCTGTATACATACGTG 57.825 37.037 5.91 0.00 36.06 4.49
2353 3157 8.353684 CCTTGAAGATTCTCTGTATACATACGT 58.646 37.037 5.91 0.00 36.06 3.57
2354 3158 8.353684 ACCTTGAAGATTCTCTGTATACATACG 58.646 37.037 5.91 0.00 36.06 3.06
2358 3162 8.198109 GCTAACCTTGAAGATTCTCTGTATACA 58.802 37.037 5.25 5.25 0.00 2.29
2359 3163 8.417884 AGCTAACCTTGAAGATTCTCTGTATAC 58.582 37.037 0.00 0.00 0.00 1.47
2360 3164 8.417106 CAGCTAACCTTGAAGATTCTCTGTATA 58.583 37.037 0.00 0.00 0.00 1.47
2390 3194 0.824109 TTCTCTGGATGGCTACACGG 59.176 55.000 0.00 0.00 0.00 4.94
2442 3249 6.755542 AATGTATTGGAGGGGTTTTCAAAA 57.244 33.333 0.00 0.00 0.00 2.44
2443 3250 7.857404 TTAATGTATTGGAGGGGTTTTCAAA 57.143 32.000 0.00 0.00 0.00 2.69
2444 3251 8.442660 AATTAATGTATTGGAGGGGTTTTCAA 57.557 30.769 0.00 0.00 0.00 2.69
2445 3252 9.548631 TTAATTAATGTATTGGAGGGGTTTTCA 57.451 29.630 0.00 0.00 0.00 2.69
2494 3301 6.238157 CGGCAAATCCAAATGTAATGAAATGG 60.238 38.462 0.00 0.00 34.01 3.16
2505 3312 2.518949 CGAAGACGGCAAATCCAAATG 58.481 47.619 0.00 0.00 35.72 2.32
2514 3321 1.353804 GTGTTTGCGAAGACGGCAA 59.646 52.632 0.00 0.00 40.15 4.52
2524 3331 3.117832 GTGACAAAATCGATGTGTTTGCG 59.882 43.478 17.07 0.61 36.01 4.85
2526 3333 4.522877 TCGTGACAAAATCGATGTGTTTG 58.477 39.130 16.01 16.01 38.06 2.93


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

AutoCloner maintained by Alex Coulton.