Multiple sequence alignment - TraesCS3D01G498100

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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 TraesCS3D01G498100 chr3D 100.000 3155 0 0 1 3155 589152805 589155959 0.000000e+00 5827.0
1 TraesCS3D01G498100 chr3D 82.609 207 19 7 393 583 589319054 589318849 1.950000e-37 167.0
2 TraesCS3D01G498100 chr3D 84.615 156 15 2 406 553 589402105 589402259 2.540000e-31 147.0
3 TraesCS3D01G498100 chr3D 83.099 142 22 2 1190 1330 32624531 32624391 9.190000e-26 128.0
4 TraesCS3D01G498100 chr3A 93.076 1993 65 27 411 2396 719195778 719193852 0.000000e+00 2848.0
5 TraesCS3D01G498100 chr3A 81.973 821 88 31 2385 3155 719193813 719193003 2.650000e-180 641.0
6 TraesCS3D01G498100 chr3A 84.211 152 17 7 406 553 719285104 719284956 1.180000e-29 141.0
7 TraesCS3D01G498100 chr3A 84.211 152 17 7 406 553 719327104 719327252 1.180000e-29 141.0
8 TraesCS3D01G498100 chr3B 88.945 1773 79 59 591 2291 787655659 787653932 0.000000e+00 2080.0
9 TraesCS3D01G498100 chr3B 82.471 348 24 12 407 731 787656179 787655846 1.440000e-68 270.0
10 TraesCS3D01G498100 chr3B 84.507 142 20 2 1190 1330 55133658 55133518 4.240000e-29 139.0
11 TraesCS3D01G498100 chr3B 82.911 158 12 12 406 553 787839745 787839593 9.190000e-26 128.0
12 TraesCS3D01G498100 chr3B 90.385 52 5 0 331 382 734169818 734169767 5.650000e-08 69.4
13 TraesCS3D01G498100 chr3B 88.333 60 3 1 498 553 787503442 787503501 5.650000e-08 69.4
14 TraesCS3D01G498100 chr5D 79.331 329 56 12 1181 1503 301995357 301995679 1.470000e-53 220.0
15 TraesCS3D01G498100 chr5D 78.313 166 20 6 106 261 6538104 6538263 3.350000e-15 93.5
16 TraesCS3D01G498100 chr5A 79.268 328 58 10 1181 1503 395852639 395852317 1.470000e-53 220.0
17 TraesCS3D01G498100 chr5B 79.027 329 57 11 1181 1503 344944036 344944358 6.850000e-52 215.0
18 TraesCS3D01G498100 chr5B 84.804 204 18 7 106 298 702261791 702261992 3.210000e-45 193.0
19 TraesCS3D01G498100 chr5B 100.000 28 0 0 355 382 14729696 14729723 6.000000e-03 52.8
20 TraesCS3D01G498100 chr6B 78.916 166 27 7 138 296 31691866 31691702 4.300000e-19 106.0
21 TraesCS3D01G498100 chr1A 92.500 40 3 0 343 382 373778429 373778468 1.220000e-04 58.4


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 TraesCS3D01G498100 chr3D 589152805 589155959 3154 False 5827.0 5827 100.0000 1 3155 1 chr3D.!!$F1 3154
1 TraesCS3D01G498100 chr3A 719193003 719195778 2775 True 1744.5 2848 87.5245 411 3155 2 chr3A.!!$R2 2744
2 TraesCS3D01G498100 chr3B 787653932 787656179 2247 True 1175.0 2080 85.7080 407 2291 2 chr3B.!!$R4 1884

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
64 65 0.322366 AGCTCCTTTCAGCCTTCTGC 60.322 55.000 0.0 0.0 40.65 4.26 F
281 282 0.958822 AATCGGGGCTTTGAACACAC 59.041 50.000 0.0 0.0 0.00 3.82 F
282 283 1.234615 ATCGGGGCTTTGAACACACG 61.235 55.000 0.0 0.0 0.00 4.49 F
286 287 1.467342 GGGGCTTTGAACACACGATAC 59.533 52.381 0.0 0.0 0.00 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1633 2051 0.460311 CCTTCTTGGGCGACGTAGAT 59.540 55.000 0.00 0.0 0.00 1.98 R
2082 2500 0.654160 TACGTAGTGCGATGTCCTCG 59.346 55.000 7.88 0.0 46.71 4.63 R
2085 2503 1.587034 GCTTTACGTAGTGCGATGTCC 59.413 52.381 7.88 0.0 45.73 4.02 R
2160 2581 1.869767 GTTGATGCCGCATTAGAGAGG 59.130 52.381 7.43 0.0 0.00 3.69 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
21 22 4.525912 ACAATGGTTTTGAGGATTGAGC 57.474 40.909 0.00 0.00 31.53 4.26
22 23 3.896888 ACAATGGTTTTGAGGATTGAGCA 59.103 39.130 0.00 0.00 31.53 4.26
23 24 4.344679 ACAATGGTTTTGAGGATTGAGCAA 59.655 37.500 0.00 0.00 31.53 3.91
24 25 4.796038 ATGGTTTTGAGGATTGAGCAAG 57.204 40.909 0.00 0.00 0.00 4.01
25 26 3.831323 TGGTTTTGAGGATTGAGCAAGA 58.169 40.909 0.00 0.00 0.00 3.02
26 27 4.214310 TGGTTTTGAGGATTGAGCAAGAA 58.786 39.130 0.00 0.00 0.00 2.52
27 28 4.279169 TGGTTTTGAGGATTGAGCAAGAAG 59.721 41.667 0.00 0.00 0.00 2.85
28 29 4.233005 GTTTTGAGGATTGAGCAAGAAGC 58.767 43.478 0.00 0.00 46.19 3.86
58 59 8.482128 AGATAATATGTATAGCTCCTTTCAGCC 58.518 37.037 0.00 0.00 40.65 4.85
59 60 6.694445 AATATGTATAGCTCCTTTCAGCCT 57.306 37.500 0.00 0.00 40.65 4.58
60 61 6.694445 ATATGTATAGCTCCTTTCAGCCTT 57.306 37.500 0.00 0.00 40.65 4.35
61 62 4.408182 TGTATAGCTCCTTTCAGCCTTC 57.592 45.455 0.00 0.00 40.65 3.46
62 63 4.033709 TGTATAGCTCCTTTCAGCCTTCT 58.966 43.478 0.00 0.00 40.65 2.85
63 64 3.557228 ATAGCTCCTTTCAGCCTTCTG 57.443 47.619 0.00 0.00 40.65 3.02
64 65 0.322366 AGCTCCTTTCAGCCTTCTGC 60.322 55.000 0.00 0.00 40.65 4.26
79 80 6.927294 GCCTTCTGCTATTGTTGTATAGTT 57.073 37.500 0.00 0.00 36.87 2.24
80 81 6.719365 GCCTTCTGCTATTGTTGTATAGTTG 58.281 40.000 0.00 0.00 36.87 3.16
81 82 6.316390 GCCTTCTGCTATTGTTGTATAGTTGT 59.684 38.462 0.00 0.00 36.87 3.32
82 83 7.148239 GCCTTCTGCTATTGTTGTATAGTTGTT 60.148 37.037 0.00 0.00 36.87 2.83
83 84 9.378551 CCTTCTGCTATTGTTGTATAGTTGTTA 57.621 33.333 0.00 0.00 31.96 2.41
109 110 9.710900 ATCTTTTCGAAAATTATTTTTGGAGCT 57.289 25.926 22.73 0.00 39.63 4.09
110 111 9.191995 TCTTTTCGAAAATTATTTTTGGAGCTC 57.808 29.630 22.73 4.71 39.63 4.09
111 112 7.883229 TTTCGAAAATTATTTTTGGAGCTCC 57.117 32.000 26.78 26.78 39.63 4.70
112 113 6.582677 TCGAAAATTATTTTTGGAGCTCCA 57.417 33.333 32.00 32.00 45.94 3.86
113 114 7.169158 TCGAAAATTATTTTTGGAGCTCCAT 57.831 32.000 35.42 22.84 46.97 3.41
114 115 7.035004 TCGAAAATTATTTTTGGAGCTCCATG 58.965 34.615 35.42 11.40 46.97 3.66
115 116 6.256321 CGAAAATTATTTTTGGAGCTCCATGG 59.744 38.462 35.42 14.13 46.97 3.66
116 117 6.872585 AAATTATTTTTGGAGCTCCATGGA 57.127 33.333 35.42 22.89 46.97 3.41
117 118 6.475596 AATTATTTTTGGAGCTCCATGGAG 57.524 37.500 35.42 33.73 46.97 3.86
118 119 2.220653 TTTTTGGAGCTCCATGGAGG 57.779 50.000 36.92 21.77 46.97 4.30
136 137 5.798015 GGAGGTCTCCTTTCGTAAAATTC 57.202 43.478 9.64 0.00 46.16 2.17
137 138 5.243207 GGAGGTCTCCTTTCGTAAAATTCA 58.757 41.667 9.64 0.00 46.16 2.57
138 139 5.704053 GGAGGTCTCCTTTCGTAAAATTCAA 59.296 40.000 9.64 0.00 46.16 2.69
139 140 6.206048 GGAGGTCTCCTTTCGTAAAATTCAAA 59.794 38.462 9.64 0.00 46.16 2.69
140 141 7.255346 GGAGGTCTCCTTTCGTAAAATTCAAAA 60.255 37.037 9.64 0.00 46.16 2.44
141 142 8.178313 AGGTCTCCTTTCGTAAAATTCAAAAT 57.822 30.769 0.00 0.00 0.00 1.82
142 143 8.638873 AGGTCTCCTTTCGTAAAATTCAAAATT 58.361 29.630 0.00 0.00 0.00 1.82
143 144 8.912658 GGTCTCCTTTCGTAAAATTCAAAATTC 58.087 33.333 0.00 0.00 0.00 2.17
144 145 9.458374 GTCTCCTTTCGTAAAATTCAAAATTCA 57.542 29.630 0.00 0.00 0.00 2.57
147 148 9.973450 TCCTTTCGTAAAATTCAAAATTCATCA 57.027 25.926 0.00 0.00 0.00 3.07
206 207 8.995027 AAAAATTACAGATATACATGGAGGCA 57.005 30.769 0.00 0.00 0.00 4.75
207 208 9.592196 AAAAATTACAGATATACATGGAGGCAT 57.408 29.630 0.00 0.00 0.00 4.40
211 212 9.842775 ATTACAGATATACATGGAGGCATAATG 57.157 33.333 0.00 0.00 0.00 1.90
212 213 7.262990 ACAGATATACATGGAGGCATAATGT 57.737 36.000 0.00 4.77 38.13 2.71
213 214 8.379428 ACAGATATACATGGAGGCATAATGTA 57.621 34.615 8.34 8.34 40.16 2.29
214 215 8.825774 ACAGATATACATGGAGGCATAATGTAA 58.174 33.333 9.59 2.53 39.51 2.41
215 216 9.671279 CAGATATACATGGAGGCATAATGTAAA 57.329 33.333 9.59 0.00 39.51 2.01
218 219 9.979897 ATATACATGGAGGCATAATGTAAATGT 57.020 29.630 9.59 0.00 39.51 2.71
219 220 6.395426 ACATGGAGGCATAATGTAAATGTG 57.605 37.500 0.00 0.00 32.86 3.21
220 221 5.893255 ACATGGAGGCATAATGTAAATGTGT 59.107 36.000 0.00 0.00 32.86 3.72
221 222 5.833406 TGGAGGCATAATGTAAATGTGTG 57.167 39.130 0.00 0.00 0.00 3.82
222 223 5.260424 TGGAGGCATAATGTAAATGTGTGT 58.740 37.500 0.00 0.00 0.00 3.72
223 224 6.418946 TGGAGGCATAATGTAAATGTGTGTA 58.581 36.000 0.00 0.00 0.00 2.90
224 225 6.887002 TGGAGGCATAATGTAAATGTGTGTAA 59.113 34.615 0.00 0.00 0.00 2.41
225 226 7.394641 TGGAGGCATAATGTAAATGTGTGTAAA 59.605 33.333 0.00 0.00 0.00 2.01
226 227 8.413229 GGAGGCATAATGTAAATGTGTGTAAAT 58.587 33.333 0.00 0.00 0.00 1.40
227 228 9.801873 GAGGCATAATGTAAATGTGTGTAAATT 57.198 29.630 0.00 0.00 0.00 1.82
228 229 9.801873 AGGCATAATGTAAATGTGTGTAAATTC 57.198 29.630 0.00 0.00 0.00 2.17
229 230 9.801873 GGCATAATGTAAATGTGTGTAAATTCT 57.198 29.630 0.00 0.00 0.00 2.40
254 255 9.241317 CTAAATACATTGAAATGAGGATTGTGC 57.759 33.333 9.94 0.00 39.67 4.57
255 256 6.778834 ATACATTGAAATGAGGATTGTGCA 57.221 33.333 9.94 0.00 39.67 4.57
256 257 5.471556 ACATTGAAATGAGGATTGTGCAA 57.528 34.783 9.94 0.00 39.67 4.08
257 258 5.856156 ACATTGAAATGAGGATTGTGCAAA 58.144 33.333 9.94 0.00 39.67 3.68
258 259 6.289834 ACATTGAAATGAGGATTGTGCAAAA 58.710 32.000 9.94 0.00 39.67 2.44
259 260 6.766944 ACATTGAAATGAGGATTGTGCAAAAA 59.233 30.769 9.94 0.00 39.67 1.94
278 279 5.476091 AAAAATAATCGGGGCTTTGAACA 57.524 34.783 0.00 0.00 0.00 3.18
279 280 4.450082 AAATAATCGGGGCTTTGAACAC 57.550 40.909 0.00 0.00 0.00 3.32
280 281 2.570415 TAATCGGGGCTTTGAACACA 57.430 45.000 0.00 0.00 0.00 3.72
281 282 0.958822 AATCGGGGCTTTGAACACAC 59.041 50.000 0.00 0.00 0.00 3.82
282 283 1.234615 ATCGGGGCTTTGAACACACG 61.235 55.000 0.00 0.00 0.00 4.49
283 284 1.890041 CGGGGCTTTGAACACACGA 60.890 57.895 0.00 0.00 0.00 4.35
284 285 1.234615 CGGGGCTTTGAACACACGAT 61.235 55.000 0.00 0.00 0.00 3.73
285 286 1.816074 GGGGCTTTGAACACACGATA 58.184 50.000 0.00 0.00 0.00 2.92
286 287 1.467342 GGGGCTTTGAACACACGATAC 59.533 52.381 0.00 0.00 0.00 2.24
287 288 2.423577 GGGCTTTGAACACACGATACT 58.576 47.619 0.00 0.00 0.00 2.12
288 289 3.592059 GGGCTTTGAACACACGATACTA 58.408 45.455 0.00 0.00 0.00 1.82
289 290 4.189231 GGGCTTTGAACACACGATACTAT 58.811 43.478 0.00 0.00 0.00 2.12
290 291 4.634443 GGGCTTTGAACACACGATACTATT 59.366 41.667 0.00 0.00 0.00 1.73
291 292 5.220605 GGGCTTTGAACACACGATACTATTC 60.221 44.000 0.00 0.00 0.00 1.75
292 293 5.350365 GGCTTTGAACACACGATACTATTCA 59.650 40.000 0.00 0.00 0.00 2.57
293 294 6.037172 GGCTTTGAACACACGATACTATTCAT 59.963 38.462 0.00 0.00 0.00 2.57
294 295 7.119997 GCTTTGAACACACGATACTATTCATC 58.880 38.462 0.00 0.00 0.00 2.92
295 296 7.534085 TTTGAACACACGATACTATTCATCC 57.466 36.000 0.00 0.00 0.00 3.51
296 297 6.465439 TGAACACACGATACTATTCATCCT 57.535 37.500 0.00 0.00 0.00 3.24
297 298 6.504398 TGAACACACGATACTATTCATCCTC 58.496 40.000 0.00 0.00 0.00 3.71
298 299 6.321435 TGAACACACGATACTATTCATCCTCT 59.679 38.462 0.00 0.00 0.00 3.69
299 300 6.078202 ACACACGATACTATTCATCCTCTG 57.922 41.667 0.00 0.00 0.00 3.35
300 301 5.594725 ACACACGATACTATTCATCCTCTGT 59.405 40.000 0.00 0.00 0.00 3.41
301 302 6.771267 ACACACGATACTATTCATCCTCTGTA 59.229 38.462 0.00 0.00 0.00 2.74
302 303 7.078851 CACACGATACTATTCATCCTCTGTAC 58.921 42.308 0.00 0.00 0.00 2.90
303 304 6.999272 ACACGATACTATTCATCCTCTGTACT 59.001 38.462 0.00 0.00 0.00 2.73
304 305 8.155510 ACACGATACTATTCATCCTCTGTACTA 58.844 37.037 0.00 0.00 0.00 1.82
305 306 8.444715 CACGATACTATTCATCCTCTGTACTAC 58.555 40.741 0.00 0.00 0.00 2.73
306 307 8.377034 ACGATACTATTCATCCTCTGTACTACT 58.623 37.037 0.00 0.00 0.00 2.57
307 308 9.872721 CGATACTATTCATCCTCTGTACTACTA 57.127 37.037 0.00 0.00 0.00 1.82
345 346 9.862149 TGTTTCTTTAAAGGAGTAGGATTTTCT 57.138 29.630 15.13 0.00 0.00 2.52
359 360 9.866655 AGTAGGATTTTCTATCATAATTTGCCA 57.133 29.630 0.00 0.00 0.00 4.92
360 361 9.899226 GTAGGATTTTCTATCATAATTTGCCAC 57.101 33.333 0.00 0.00 0.00 5.01
361 362 8.537728 AGGATTTTCTATCATAATTTGCCACA 57.462 30.769 0.00 0.00 0.00 4.17
362 363 9.151177 AGGATTTTCTATCATAATTTGCCACAT 57.849 29.630 0.00 0.00 0.00 3.21
374 375 9.950680 CATAATTTGCCACATAACTAGTTAAGG 57.049 33.333 18.88 19.46 0.00 2.69
375 376 9.695155 ATAATTTGCCACATAACTAGTTAAGGT 57.305 29.630 18.88 16.24 0.00 3.50
376 377 8.417273 AATTTGCCACATAACTAGTTAAGGTT 57.583 30.769 18.88 8.87 0.00 3.50
377 378 7.826918 TTTGCCACATAACTAGTTAAGGTTT 57.173 32.000 18.88 0.00 0.00 3.27
378 379 7.826918 TTGCCACATAACTAGTTAAGGTTTT 57.173 32.000 18.88 0.00 0.00 2.43
379 380 7.443259 TGCCACATAACTAGTTAAGGTTTTC 57.557 36.000 18.88 11.11 0.00 2.29
380 381 6.999272 TGCCACATAACTAGTTAAGGTTTTCA 59.001 34.615 18.88 12.98 0.00 2.69
381 382 7.502895 TGCCACATAACTAGTTAAGGTTTTCAA 59.497 33.333 18.88 0.00 0.00 2.69
382 383 8.354426 GCCACATAACTAGTTAAGGTTTTCAAA 58.646 33.333 18.88 0.00 0.00 2.69
445 446 2.997315 TGGCTGACCAGACCGAGG 60.997 66.667 0.00 0.00 42.67 4.63
585 614 2.264794 GCACGTCCACCTACTGGG 59.735 66.667 0.00 0.00 41.06 4.45
586 615 2.264794 CACGTCCACCTACTGGGC 59.735 66.667 0.00 0.00 41.93 5.36
588 617 2.264794 CGTCCACCTACTGGGCAC 59.735 66.667 0.00 0.00 46.35 5.01
680 709 3.804325 ACAAATTGCTACCAGATCGATCG 59.196 43.478 19.33 9.36 0.00 3.69
681 710 4.051237 CAAATTGCTACCAGATCGATCGA 58.949 43.478 21.86 21.86 0.00 3.59
745 1096 7.500992 TGCTGGAATCCTCTAATACTTAACAG 58.499 38.462 0.00 0.00 0.00 3.16
766 1117 2.047655 CTTAGCACCCCGCAACGA 60.048 61.111 0.00 0.00 46.13 3.85
819 1180 2.683968 GATCTTGTGCCACAACGTCTA 58.316 47.619 6.08 0.00 33.96 2.59
820 1181 1.860676 TCTTGTGCCACAACGTCTAC 58.139 50.000 6.08 0.00 33.96 2.59
822 1183 2.624364 TCTTGTGCCACAACGTCTACTA 59.376 45.455 6.08 0.00 33.96 1.82
823 1184 2.427232 TGTGCCACAACGTCTACTAC 57.573 50.000 0.00 0.00 0.00 2.73
1122 1519 4.662961 TCGCAGCACCACCACTCG 62.663 66.667 0.00 0.00 0.00 4.18
1633 2051 3.122971 ATCAGGTCGTCGACGCGA 61.123 61.111 32.19 23.50 39.60 5.87
2085 2503 3.068307 AGGATCCCAAGAATAACGACGAG 59.932 47.826 8.55 0.00 0.00 4.18
2160 2581 5.583854 GCTAGGGTTAGGCTTTTAAGTACAC 59.416 44.000 0.00 0.00 0.00 2.90
2191 2620 1.202325 CGGCATCAACCCATTCATGTG 60.202 52.381 0.00 0.00 0.00 3.21
2192 2621 1.472026 GGCATCAACCCATTCATGTGC 60.472 52.381 0.00 0.00 0.00 4.57
2193 2622 1.472026 GCATCAACCCATTCATGTGCC 60.472 52.381 0.00 0.00 0.00 5.01
2194 2623 2.104967 CATCAACCCATTCATGTGCCT 58.895 47.619 0.00 0.00 0.00 4.75
2195 2624 3.289836 CATCAACCCATTCATGTGCCTA 58.710 45.455 0.00 0.00 0.00 3.93
2196 2625 2.722094 TCAACCCATTCATGTGCCTAC 58.278 47.619 0.00 0.00 0.00 3.18
2197 2626 1.401552 CAACCCATTCATGTGCCTACG 59.598 52.381 0.00 0.00 0.00 3.51
2198 2627 0.618458 ACCCATTCATGTGCCTACGT 59.382 50.000 0.00 0.00 0.00 3.57
2210 2639 3.628487 TGTGCCTACGTTTGCTTAACTTT 59.372 39.130 0.00 0.00 34.46 2.66
2238 2667 8.956446 TTGATATAGAGAGAGAGAGAGAGAGA 57.044 38.462 0.00 0.00 0.00 3.10
2239 2668 8.956446 TGATATAGAGAGAGAGAGAGAGAGAA 57.044 38.462 0.00 0.00 0.00 2.87
2345 2778 7.822822 ACAGTAACACCAGTATTACAGGAAATC 59.177 37.037 11.83 0.10 34.36 2.17
2347 2780 4.189231 ACACCAGTATTACAGGAAATCGC 58.811 43.478 11.83 0.00 0.00 4.58
2392 2825 4.689062 TCCACTCCTTAGAGAATTGTCCT 58.311 43.478 0.00 0.00 43.39 3.85
2408 2891 1.341531 GTCCTCTCCATCCCGTACATG 59.658 57.143 0.00 0.00 0.00 3.21
2410 2893 0.034059 CTCTCCATCCCGTACATGCC 59.966 60.000 0.00 0.00 0.00 4.40
2446 2929 3.059982 CTCCGCTGGAGTTCCACA 58.940 61.111 14.22 0.00 44.25 4.17
2452 2935 1.372997 CTGGAGTTCCACACCGTCG 60.373 63.158 0.00 0.00 42.01 5.12
2483 2966 6.493458 ACAATAAAGTTCTACCAATGCAGGTT 59.507 34.615 2.55 0.00 43.08 3.50
2487 2970 2.093306 TCTACCAATGCAGGTTGTCG 57.907 50.000 2.55 0.00 43.08 4.35
2488 2971 1.621317 TCTACCAATGCAGGTTGTCGA 59.379 47.619 2.55 0.00 43.08 4.20
2504 2987 4.778534 TGTCGAGAAATTACCGTTCTCT 57.221 40.909 11.28 0.00 45.87 3.10
2507 2990 3.057104 TCGAGAAATTACCGTTCTCTGCA 60.057 43.478 11.28 0.00 45.87 4.41
2512 2995 6.640518 AGAAATTACCGTTCTCTGCAGATAA 58.359 36.000 18.63 14.03 29.04 1.75
2517 3000 3.006967 ACCGTTCTCTGCAGATAAGTGTT 59.993 43.478 18.63 0.00 0.00 3.32
2518 3001 3.369147 CCGTTCTCTGCAGATAAGTGTTG 59.631 47.826 18.63 2.66 0.00 3.33
2524 3007 0.370273 GCAGATAAGTGTTGGCGACG 59.630 55.000 0.00 0.00 0.00 5.12
2535 3018 1.314534 TTGGCGACGTCGATCCCTAA 61.315 55.000 39.74 22.60 43.02 2.69
2543 3026 2.623889 ACGTCGATCCCTAAGAATCCAG 59.376 50.000 0.00 0.00 0.00 3.86
2546 3029 3.006003 GTCGATCCCTAAGAATCCAGGAC 59.994 52.174 0.00 0.00 33.42 3.85
2548 3031 2.191981 TCCCTAAGAATCCAGGACCC 57.808 55.000 0.00 0.00 33.42 4.46
2567 3055 0.366871 CGAAAGACGATGCCGAGTTG 59.633 55.000 0.00 0.00 45.77 3.16
2573 3061 0.391661 ACGATGCCGAGTTGCTCATT 60.392 50.000 0.00 0.00 39.50 2.57
2574 3062 0.302890 CGATGCCGAGTTGCTCATTC 59.697 55.000 0.00 0.00 38.22 2.67
2578 3066 1.291132 GCCGAGTTGCTCATTCCTAC 58.709 55.000 0.00 0.00 0.00 3.18
2585 3073 3.762288 AGTTGCTCATTCCTACACGTCTA 59.238 43.478 0.00 0.00 0.00 2.59
2598 3093 4.226427 ACACGTCTACCTATGTCTACCA 57.774 45.455 0.00 0.00 0.00 3.25
2603 3098 7.039882 CACGTCTACCTATGTCTACCAAAATT 58.960 38.462 0.00 0.00 0.00 1.82
2628 3129 4.680237 CCGAAGCACCACTGGCGA 62.680 66.667 0.00 0.00 36.08 5.54
2629 3130 2.434884 CGAAGCACCACTGGCGAT 60.435 61.111 0.00 0.00 36.08 4.58
2630 3131 2.743752 CGAAGCACCACTGGCGATG 61.744 63.158 0.00 0.00 36.08 3.84
2631 3132 1.375908 GAAGCACCACTGGCGATGA 60.376 57.895 0.00 0.00 36.08 2.92
2633 3134 1.237285 AAGCACCACTGGCGATGAAC 61.237 55.000 0.00 0.00 36.08 3.18
2646 3148 2.854424 GCGATGAACACACAACCAACTG 60.854 50.000 0.00 0.00 0.00 3.16
2673 3175 0.833287 GTTGAGCATAGAGGGAGGCA 59.167 55.000 0.00 0.00 0.00 4.75
2676 3178 1.915489 TGAGCATAGAGGGAGGCAAAA 59.085 47.619 0.00 0.00 0.00 2.44
2681 3183 3.448660 GCATAGAGGGAGGCAAAATTGTT 59.551 43.478 0.00 0.00 0.00 2.83
2682 3184 4.440663 GCATAGAGGGAGGCAAAATTGTTC 60.441 45.833 0.00 0.00 0.00 3.18
2684 3186 2.893489 AGAGGGAGGCAAAATTGTTCAC 59.107 45.455 0.00 0.00 0.00 3.18
2686 3188 1.691434 GGGAGGCAAAATTGTTCACCA 59.309 47.619 0.00 0.00 0.00 4.17
2687 3189 2.289010 GGGAGGCAAAATTGTTCACCAG 60.289 50.000 0.00 0.00 0.00 4.00
2688 3190 2.365293 GGAGGCAAAATTGTTCACCAGT 59.635 45.455 0.00 0.00 0.00 4.00
2689 3191 3.552890 GGAGGCAAAATTGTTCACCAGTC 60.553 47.826 0.00 0.00 0.00 3.51
2699 3211 5.808366 TTGTTCACCAGTCTTGTCTCTAT 57.192 39.130 0.00 0.00 0.00 1.98
2703 3215 7.907389 TGTTCACCAGTCTTGTCTCTATATTT 58.093 34.615 0.00 0.00 0.00 1.40
2707 3219 6.473778 CACCAGTCTTGTCTCTATATTTGACG 59.526 42.308 0.00 0.00 33.81 4.35
2708 3220 5.980116 CCAGTCTTGTCTCTATATTTGACGG 59.020 44.000 0.00 0.00 33.81 4.79
2719 3231 0.108329 ATTTGACGGCTCGGGTAGTG 60.108 55.000 0.00 0.00 0.00 2.74
2720 3232 1.466025 TTTGACGGCTCGGGTAGTGT 61.466 55.000 0.00 0.00 0.00 3.55
2729 3241 3.181469 GGCTCGGGTAGTGTTATCAATGA 60.181 47.826 0.00 0.00 0.00 2.57
2730 3242 4.439057 GCTCGGGTAGTGTTATCAATGAA 58.561 43.478 0.00 0.00 0.00 2.57
2731 3243 4.873827 GCTCGGGTAGTGTTATCAATGAAA 59.126 41.667 0.00 0.00 0.00 2.69
2732 3244 5.220605 GCTCGGGTAGTGTTATCAATGAAAC 60.221 44.000 0.00 0.00 0.00 2.78
2733 3245 5.795972 TCGGGTAGTGTTATCAATGAAACA 58.204 37.500 6.82 6.82 33.35 2.83
2734 3246 6.411376 TCGGGTAGTGTTATCAATGAAACAT 58.589 36.000 11.83 0.00 37.87 2.71
2735 3247 7.557724 TCGGGTAGTGTTATCAATGAAACATA 58.442 34.615 11.83 5.83 37.87 2.29
2736 3248 8.041919 TCGGGTAGTGTTATCAATGAAACATAA 58.958 33.333 11.83 4.19 37.87 1.90
2737 3249 8.670135 CGGGTAGTGTTATCAATGAAACATAAA 58.330 33.333 11.83 2.48 37.87 1.40
2746 3258 6.587206 TCAATGAAACATAAATGTCCAGCA 57.413 33.333 0.00 0.00 40.80 4.41
2750 3262 5.712004 TGAAACATAAATGTCCAGCACATG 58.288 37.500 0.00 0.00 45.77 3.21
2751 3263 3.788333 ACATAAATGTCCAGCACATGC 57.212 42.857 0.00 0.00 45.77 4.06
2752 3264 3.090790 ACATAAATGTCCAGCACATGCA 58.909 40.909 6.64 0.00 45.77 3.96
2753 3265 3.119388 ACATAAATGTCCAGCACATGCAC 60.119 43.478 6.64 0.00 45.77 4.57
2754 3266 0.241749 AAATGTCCAGCACATGCACG 59.758 50.000 6.64 0.00 45.77 5.34
2763 3275 0.378257 GCACATGCACGTTGATAGGG 59.622 55.000 0.00 0.00 41.59 3.53
2769 3281 0.532196 GCACGTTGATAGGGCTACCC 60.532 60.000 0.00 0.00 45.90 3.69
2793 3305 0.396811 AAGGGTGTGGTACTGCACTC 59.603 55.000 15.88 13.45 36.14 3.51
2794 3306 0.762842 AGGGTGTGGTACTGCACTCA 60.763 55.000 17.77 0.00 37.73 3.41
2795 3307 0.320771 GGGTGTGGTACTGCACTCAG 60.321 60.000 15.88 0.00 45.71 3.35
2804 3316 1.792301 CTGCACTCAGTTGCCGATG 59.208 57.895 0.00 0.00 42.25 3.84
2825 3337 5.147330 TGGTACAACAAGATCTTCATCGT 57.853 39.130 4.57 3.49 31.22 3.73
2826 3338 4.929211 TGGTACAACAAGATCTTCATCGTG 59.071 41.667 4.57 0.00 42.47 4.35
2838 3356 3.994392 TCTTCATCGTGTAACAAGGAAGC 59.006 43.478 0.00 0.00 35.74 3.86
2859 3377 3.668447 CAGTGGTAGCTCACTTCACAAT 58.332 45.455 5.36 0.00 44.74 2.71
2866 3384 3.672808 AGCTCACTTCACAATCCTCTTG 58.327 45.455 0.00 0.00 0.00 3.02
2868 3386 3.817647 GCTCACTTCACAATCCTCTTGTT 59.182 43.478 0.00 0.00 0.00 2.83
2874 3392 7.939039 TCACTTCACAATCCTCTTGTTTTAGAT 59.061 33.333 0.00 0.00 0.00 1.98
2890 3408 7.254852 TGTTTTAGATCAAAGTGTGTCCAAAC 58.745 34.615 0.00 0.00 0.00 2.93
2891 3409 7.094162 TGTTTTAGATCAAAGTGTGTCCAAACA 60.094 33.333 0.00 0.00 29.89 2.83
2901 3419 1.333619 GTGTCCAAACATGCAACGTCT 59.666 47.619 0.00 0.00 37.81 4.18
2925 3445 8.198109 TCTAAGGTTCTCACAATAGACTTATGC 58.802 37.037 0.00 0.00 0.00 3.14
2949 3469 5.220931 CGGCTTTTCAAATCTCTGGGATTAG 60.221 44.000 2.64 0.00 43.17 1.73
2966 3486 6.084326 GGATTAGTCCAGCTCAAACAAAAA 57.916 37.500 0.00 0.00 44.42 1.94
2969 3489 8.303876 GGATTAGTCCAGCTCAAACAAAAATTA 58.696 33.333 0.00 0.00 44.42 1.40
3060 3580 2.038426 CCATTACCACACACCTCAGACA 59.962 50.000 0.00 0.00 0.00 3.41
3061 3581 2.902705 TTACCACACACCTCAGACAC 57.097 50.000 0.00 0.00 0.00 3.67
3063 3583 0.908910 ACCACACACCTCAGACACAA 59.091 50.000 0.00 0.00 0.00 3.33
3064 3584 1.299541 CCACACACCTCAGACACAAC 58.700 55.000 0.00 0.00 0.00 3.32
3065 3585 1.406751 CCACACACCTCAGACACAACA 60.407 52.381 0.00 0.00 0.00 3.33
3066 3586 1.665679 CACACACCTCAGACACAACAC 59.334 52.381 0.00 0.00 0.00 3.32
3067 3587 1.277842 ACACACCTCAGACACAACACA 59.722 47.619 0.00 0.00 0.00 3.72
3068 3588 2.290008 ACACACCTCAGACACAACACAA 60.290 45.455 0.00 0.00 0.00 3.33
3069 3589 2.095853 CACACCTCAGACACAACACAAC 59.904 50.000 0.00 0.00 0.00 3.32
3070 3590 2.290008 ACACCTCAGACACAACACAACA 60.290 45.455 0.00 0.00 0.00 3.33
3071 3591 2.746904 CACCTCAGACACAACACAACAA 59.253 45.455 0.00 0.00 0.00 2.83
3072 3592 3.378112 CACCTCAGACACAACACAACAAT 59.622 43.478 0.00 0.00 0.00 2.71
3074 3594 3.627123 CCTCAGACACAACACAACAATCA 59.373 43.478 0.00 0.00 0.00 2.57
3075 3595 4.260907 CCTCAGACACAACACAACAATCAG 60.261 45.833 0.00 0.00 0.00 2.90
3076 3596 4.260985 TCAGACACAACACAACAATCAGT 58.739 39.130 0.00 0.00 0.00 3.41
3077 3597 4.094739 TCAGACACAACACAACAATCAGTG 59.905 41.667 0.00 0.00 41.40 3.66
3078 3598 4.094739 CAGACACAACACAACAATCAGTGA 59.905 41.667 0.00 0.00 39.03 3.41
3079 3599 4.333649 AGACACAACACAACAATCAGTGAG 59.666 41.667 0.00 0.00 39.03 3.51
3082 3602 4.794762 CACAACACAACAATCAGTGAGTTG 59.205 41.667 18.73 18.73 45.97 3.16
3110 3640 6.038356 GTGGAATATCAAGATGCAAAAGGTG 58.962 40.000 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.896888 TGCTCAATCCTCAAAACCATTGT 59.103 39.130 0.00 0.00 0.00 2.71
1 2 4.524316 TGCTCAATCCTCAAAACCATTG 57.476 40.909 0.00 0.00 0.00 2.82
2 3 4.834496 TCTTGCTCAATCCTCAAAACCATT 59.166 37.500 0.00 0.00 0.00 3.16
3 4 4.410099 TCTTGCTCAATCCTCAAAACCAT 58.590 39.130 0.00 0.00 0.00 3.55
4 5 3.831323 TCTTGCTCAATCCTCAAAACCA 58.169 40.909 0.00 0.00 0.00 3.67
5 6 4.802999 CTTCTTGCTCAATCCTCAAAACC 58.197 43.478 0.00 0.00 0.00 3.27
6 7 4.233005 GCTTCTTGCTCAATCCTCAAAAC 58.767 43.478 0.00 0.00 38.95 2.43
7 8 4.510038 GCTTCTTGCTCAATCCTCAAAA 57.490 40.909 0.00 0.00 38.95 2.44
32 33 8.482128 GGCTGAAAGGAGCTATACATATTATCT 58.518 37.037 0.00 0.00 39.11 1.98
33 34 8.482128 AGGCTGAAAGGAGCTATACATATTATC 58.518 37.037 0.00 0.00 39.11 1.75
34 35 8.386012 AGGCTGAAAGGAGCTATACATATTAT 57.614 34.615 0.00 0.00 39.11 1.28
35 36 7.798710 AGGCTGAAAGGAGCTATACATATTA 57.201 36.000 0.00 0.00 39.11 0.98
36 37 6.694445 AGGCTGAAAGGAGCTATACATATT 57.306 37.500 0.00 0.00 39.11 1.28
37 38 6.500049 AGAAGGCTGAAAGGAGCTATACATAT 59.500 38.462 0.00 0.00 39.11 1.78
38 39 5.841237 AGAAGGCTGAAAGGAGCTATACATA 59.159 40.000 0.00 0.00 39.11 2.29
39 40 4.657969 AGAAGGCTGAAAGGAGCTATACAT 59.342 41.667 0.00 0.00 39.11 2.29
40 41 4.033709 AGAAGGCTGAAAGGAGCTATACA 58.966 43.478 0.00 0.00 39.11 2.29
41 42 4.376146 CAGAAGGCTGAAAGGAGCTATAC 58.624 47.826 0.00 0.00 45.17 1.47
42 43 3.181461 GCAGAAGGCTGAAAGGAGCTATA 60.181 47.826 0.00 0.00 45.17 1.31
43 44 2.421248 GCAGAAGGCTGAAAGGAGCTAT 60.421 50.000 0.00 0.00 45.17 2.97
44 45 1.065854 GCAGAAGGCTGAAAGGAGCTA 60.066 52.381 0.00 0.00 45.17 3.32
45 46 0.322366 GCAGAAGGCTGAAAGGAGCT 60.322 55.000 0.00 0.00 45.17 4.09
46 47 2.178856 GCAGAAGGCTGAAAGGAGC 58.821 57.895 0.00 0.00 45.17 4.70
56 57 6.316390 ACAACTATACAACAATAGCAGAAGGC 59.684 38.462 0.00 0.00 45.30 4.35
57 58 7.849804 ACAACTATACAACAATAGCAGAAGG 57.150 36.000 0.00 0.00 33.49 3.46
83 84 9.710900 AGCTCCAAAAATAATTTTCGAAAAGAT 57.289 25.926 25.87 18.77 36.62 2.40
84 85 9.191995 GAGCTCCAAAAATAATTTTCGAAAAGA 57.808 29.630 25.87 17.50 36.62 2.52
85 86 8.435430 GGAGCTCCAAAAATAATTTTCGAAAAG 58.565 33.333 28.43 11.37 36.62 2.27
86 87 7.928706 TGGAGCTCCAAAAATAATTTTCGAAAA 59.071 29.630 33.41 24.43 44.35 2.29
87 88 7.437748 TGGAGCTCCAAAAATAATTTTCGAAA 58.562 30.769 33.41 6.47 44.35 3.46
88 89 6.987386 TGGAGCTCCAAAAATAATTTTCGAA 58.013 32.000 33.41 2.89 44.35 3.71
89 90 6.582677 TGGAGCTCCAAAAATAATTTTCGA 57.417 33.333 33.41 3.32 44.35 3.71
104 105 2.132300 GAGACCTCCATGGAGCTCC 58.868 63.158 32.97 26.78 40.69 4.70
115 116 6.796705 TTGAATTTTACGAAAGGAGACCTC 57.203 37.500 0.00 0.00 30.89 3.85
116 117 7.576861 TTTTGAATTTTACGAAAGGAGACCT 57.423 32.000 0.00 0.00 33.87 3.85
117 118 8.812147 AATTTTGAATTTTACGAAAGGAGACC 57.188 30.769 0.00 0.00 0.00 3.85
118 119 9.458374 TGAATTTTGAATTTTACGAAAGGAGAC 57.542 29.630 0.00 0.00 0.00 3.36
121 122 9.973450 TGATGAATTTTGAATTTTACGAAAGGA 57.027 25.926 0.00 0.00 0.00 3.36
181 182 8.995027 TGCCTCCATGTATATCTGTAATTTTT 57.005 30.769 0.00 0.00 0.00 1.94
185 186 9.842775 CATTATGCCTCCATGTATATCTGTAAT 57.157 33.333 0.00 0.00 32.85 1.89
186 187 8.825774 ACATTATGCCTCCATGTATATCTGTAA 58.174 33.333 0.00 0.00 32.85 2.41
187 188 8.379428 ACATTATGCCTCCATGTATATCTGTA 57.621 34.615 0.00 0.00 32.85 2.74
188 189 7.262990 ACATTATGCCTCCATGTATATCTGT 57.737 36.000 0.00 0.00 32.85 3.41
189 190 9.671279 TTTACATTATGCCTCCATGTATATCTG 57.329 33.333 0.00 0.00 34.21 2.90
192 193 9.979897 ACATTTACATTATGCCTCCATGTATAT 57.020 29.630 0.00 0.00 34.21 0.86
193 194 9.230122 CACATTTACATTATGCCTCCATGTATA 57.770 33.333 0.00 0.00 34.21 1.47
194 195 7.725397 ACACATTTACATTATGCCTCCATGTAT 59.275 33.333 0.00 0.00 34.21 2.29
195 196 7.013178 CACACATTTACATTATGCCTCCATGTA 59.987 37.037 0.00 0.00 33.19 2.29
196 197 5.893255 ACACATTTACATTATGCCTCCATGT 59.107 36.000 0.00 0.00 35.33 3.21
197 198 6.183360 ACACACATTTACATTATGCCTCCATG 60.183 38.462 0.00 0.00 32.85 3.66
198 199 5.893255 ACACACATTTACATTATGCCTCCAT 59.107 36.000 0.00 0.00 35.44 3.41
199 200 5.260424 ACACACATTTACATTATGCCTCCA 58.740 37.500 0.00 0.00 0.00 3.86
200 201 5.835113 ACACACATTTACATTATGCCTCC 57.165 39.130 0.00 0.00 0.00 4.30
201 202 9.801873 AATTTACACACATTTACATTATGCCTC 57.198 29.630 0.00 0.00 0.00 4.70
202 203 9.801873 GAATTTACACACATTTACATTATGCCT 57.198 29.630 0.00 0.00 0.00 4.75
203 204 9.801873 AGAATTTACACACATTTACATTATGCC 57.198 29.630 0.00 0.00 0.00 4.40
228 229 9.241317 GCACAATCCTCATTTCAATGTATTTAG 57.759 33.333 0.00 0.00 37.65 1.85
229 230 8.747471 TGCACAATCCTCATTTCAATGTATTTA 58.253 29.630 0.00 0.00 37.65 1.40
230 231 7.613585 TGCACAATCCTCATTTCAATGTATTT 58.386 30.769 0.00 0.00 37.65 1.40
231 232 7.172868 TGCACAATCCTCATTTCAATGTATT 57.827 32.000 0.00 0.00 37.65 1.89
232 233 6.778834 TGCACAATCCTCATTTCAATGTAT 57.221 33.333 0.00 0.00 37.65 2.29
233 234 6.587206 TTGCACAATCCTCATTTCAATGTA 57.413 33.333 0.00 0.00 37.65 2.29
234 235 5.471556 TTGCACAATCCTCATTTCAATGT 57.528 34.783 0.00 0.00 37.65 2.71
235 236 6.788684 TTTTGCACAATCCTCATTTCAATG 57.211 33.333 0.00 0.00 37.75 2.82
256 257 5.221541 TGTGTTCAAAGCCCCGATTATTTTT 60.222 36.000 0.00 0.00 0.00 1.94
257 258 4.282195 TGTGTTCAAAGCCCCGATTATTTT 59.718 37.500 0.00 0.00 0.00 1.82
258 259 3.829601 TGTGTTCAAAGCCCCGATTATTT 59.170 39.130 0.00 0.00 0.00 1.40
259 260 3.192633 GTGTGTTCAAAGCCCCGATTATT 59.807 43.478 0.00 0.00 0.00 1.40
260 261 2.752903 GTGTGTTCAAAGCCCCGATTAT 59.247 45.455 0.00 0.00 0.00 1.28
261 262 2.156098 GTGTGTTCAAAGCCCCGATTA 58.844 47.619 0.00 0.00 0.00 1.75
262 263 0.958822 GTGTGTTCAAAGCCCCGATT 59.041 50.000 0.00 0.00 0.00 3.34
263 264 1.234615 CGTGTGTTCAAAGCCCCGAT 61.235 55.000 0.00 0.00 0.00 4.18
264 265 1.890041 CGTGTGTTCAAAGCCCCGA 60.890 57.895 0.00 0.00 0.00 5.14
265 266 1.234615 ATCGTGTGTTCAAAGCCCCG 61.235 55.000 0.00 0.00 0.00 5.73
266 267 1.467342 GTATCGTGTGTTCAAAGCCCC 59.533 52.381 0.00 0.00 0.00 5.80
267 268 2.423577 AGTATCGTGTGTTCAAAGCCC 58.576 47.619 0.00 0.00 0.00 5.19
268 269 5.350365 TGAATAGTATCGTGTGTTCAAAGCC 59.650 40.000 0.00 0.00 0.00 4.35
269 270 6.403333 TGAATAGTATCGTGTGTTCAAAGC 57.597 37.500 0.00 0.00 0.00 3.51
270 271 7.492669 AGGATGAATAGTATCGTGTGTTCAAAG 59.507 37.037 0.00 0.00 0.00 2.77
271 272 7.327975 AGGATGAATAGTATCGTGTGTTCAAA 58.672 34.615 0.00 0.00 0.00 2.69
272 273 6.873997 AGGATGAATAGTATCGTGTGTTCAA 58.126 36.000 0.00 0.00 0.00 2.69
273 274 6.321435 AGAGGATGAATAGTATCGTGTGTTCA 59.679 38.462 0.00 0.00 0.00 3.18
274 275 6.638873 CAGAGGATGAATAGTATCGTGTGTTC 59.361 42.308 0.00 0.00 32.42 3.18
275 276 6.096987 ACAGAGGATGAATAGTATCGTGTGTT 59.903 38.462 0.00 0.00 41.25 3.32
276 277 5.594725 ACAGAGGATGAATAGTATCGTGTGT 59.405 40.000 0.00 0.00 40.10 3.72
277 278 6.078202 ACAGAGGATGAATAGTATCGTGTG 57.922 41.667 0.00 0.00 38.72 3.82
278 279 6.999272 AGTACAGAGGATGAATAGTATCGTGT 59.001 38.462 0.00 0.00 0.00 4.49
279 280 7.441890 AGTACAGAGGATGAATAGTATCGTG 57.558 40.000 0.00 0.00 0.00 4.35
280 281 8.377034 AGTAGTACAGAGGATGAATAGTATCGT 58.623 37.037 2.52 0.00 0.00 3.73
281 282 8.780846 AGTAGTACAGAGGATGAATAGTATCG 57.219 38.462 2.52 0.00 0.00 2.92
319 320 9.862149 AGAAAATCCTACTCCTTTAAAGAAACA 57.138 29.630 16.98 0.00 0.00 2.83
333 334 9.866655 TGGCAAATTATGATAGAAAATCCTACT 57.133 29.630 0.00 0.00 0.00 2.57
334 335 9.899226 GTGGCAAATTATGATAGAAAATCCTAC 57.101 33.333 0.00 0.00 0.00 3.18
335 336 9.639563 TGTGGCAAATTATGATAGAAAATCCTA 57.360 29.630 0.00 0.00 0.00 2.94
336 337 8.537728 TGTGGCAAATTATGATAGAAAATCCT 57.462 30.769 0.00 0.00 0.00 3.24
348 349 9.950680 CCTTAACTAGTTATGTGGCAAATTATG 57.049 33.333 15.92 0.00 0.00 1.90
349 350 9.695155 ACCTTAACTAGTTATGTGGCAAATTAT 57.305 29.630 15.92 0.30 0.00 1.28
350 351 9.523168 AACCTTAACTAGTTATGTGGCAAATTA 57.477 29.630 15.92 0.00 0.00 1.40
351 352 8.417273 AACCTTAACTAGTTATGTGGCAAATT 57.583 30.769 15.92 6.81 0.00 1.82
352 353 8.417273 AAACCTTAACTAGTTATGTGGCAAAT 57.583 30.769 15.92 0.00 0.00 2.32
353 354 7.826918 AAACCTTAACTAGTTATGTGGCAAA 57.173 32.000 15.92 0.00 0.00 3.68
354 355 7.502895 TGAAAACCTTAACTAGTTATGTGGCAA 59.497 33.333 15.92 0.67 0.00 4.52
355 356 6.999272 TGAAAACCTTAACTAGTTATGTGGCA 59.001 34.615 15.92 11.60 0.00 4.92
356 357 7.443259 TGAAAACCTTAACTAGTTATGTGGC 57.557 36.000 15.92 9.70 0.00 5.01
381 382 8.987890 CGGTTGGTATCTTCAATTTTGATTTTT 58.012 29.630 0.00 0.00 37.00 1.94
382 383 8.364142 TCGGTTGGTATCTTCAATTTTGATTTT 58.636 29.630 0.00 0.00 37.00 1.82
383 384 7.891561 TCGGTTGGTATCTTCAATTTTGATTT 58.108 30.769 0.00 0.00 37.00 2.17
384 385 7.461182 TCGGTTGGTATCTTCAATTTTGATT 57.539 32.000 0.00 0.00 37.00 2.57
385 386 7.416664 CCATCGGTTGGTATCTTCAATTTTGAT 60.417 37.037 0.00 0.00 40.99 2.57
386 387 6.127758 CCATCGGTTGGTATCTTCAATTTTGA 60.128 38.462 0.00 0.00 40.99 2.69
387 388 6.035843 CCATCGGTTGGTATCTTCAATTTTG 58.964 40.000 0.00 0.00 40.99 2.44
388 389 6.207691 CCATCGGTTGGTATCTTCAATTTT 57.792 37.500 0.00 0.00 40.99 1.82
389 390 5.835113 CCATCGGTTGGTATCTTCAATTT 57.165 39.130 0.00 0.00 40.99 1.82
402 403 1.364626 GAGCAGCTGACCATCGGTTG 61.365 60.000 20.43 0.00 35.25 3.77
403 404 1.078848 GAGCAGCTGACCATCGGTT 60.079 57.895 20.43 0.00 35.25 4.44
404 405 2.581354 GAGCAGCTGACCATCGGT 59.419 61.111 20.43 0.00 39.44 4.69
405 406 2.360949 ATCGAGCAGCTGACCATCGG 62.361 60.000 20.43 6.13 34.29 4.18
445 446 4.309950 ACCGGTCGAACAGCACCC 62.310 66.667 0.00 0.00 0.00 4.61
471 474 1.000955 ACTCACGCGAAAAGGAGTGAT 59.999 47.619 15.93 0.00 43.97 3.06
575 604 2.045926 GCCAGTGCCCAGTAGGTG 60.046 66.667 0.00 0.00 38.26 4.00
585 614 1.200948 GATTTGGAAGTGAGCCAGTGC 59.799 52.381 0.00 0.00 36.64 4.40
586 615 1.815003 GGATTTGGAAGTGAGCCAGTG 59.185 52.381 0.00 0.00 36.64 3.66
588 617 2.205022 TGGATTTGGAAGTGAGCCAG 57.795 50.000 0.00 0.00 36.64 4.85
687 716 3.496130 ACTTTTCAGTCAACATCGAGCAG 59.504 43.478 0.00 0.00 0.00 4.24
690 719 5.119279 CCACTACTTTTCAGTCAACATCGAG 59.881 44.000 0.00 0.00 34.06 4.04
745 1096 1.019805 GTTGCGGGGTGCTAAGAGTC 61.020 60.000 0.00 0.00 46.63 3.36
751 1102 2.185867 GATCGTTGCGGGGTGCTA 59.814 61.111 0.00 0.00 46.63 3.49
819 1180 7.015877 TGCCTATTAAAAGGGATCGTATGTAGT 59.984 37.037 0.00 0.00 37.11 2.73
820 1181 7.383687 TGCCTATTAAAAGGGATCGTATGTAG 58.616 38.462 0.00 0.00 37.11 2.74
822 1183 6.182507 TGCCTATTAAAAGGGATCGTATGT 57.817 37.500 0.00 0.00 37.11 2.29
1633 2051 0.460311 CCTTCTTGGGCGACGTAGAT 59.540 55.000 0.00 0.00 0.00 1.98
2082 2500 0.654160 TACGTAGTGCGATGTCCTCG 59.346 55.000 7.88 0.00 46.71 4.63
2085 2503 1.587034 GCTTTACGTAGTGCGATGTCC 59.413 52.381 7.88 0.00 45.73 4.02
2160 2581 1.869767 GTTGATGCCGCATTAGAGAGG 59.130 52.381 7.43 0.00 0.00 3.69
2219 2648 5.069648 CAGCTTCTCTCTCTCTCTCTCTCTA 59.930 48.000 0.00 0.00 0.00 2.43
2322 2755 6.238022 GCGATTTCCTGTAATACTGGTGTTAC 60.238 42.308 14.63 11.60 38.25 2.50
2323 2756 5.813672 GCGATTTCCTGTAATACTGGTGTTA 59.186 40.000 14.63 1.95 38.25 2.41
2324 2757 4.634443 GCGATTTCCTGTAATACTGGTGTT 59.366 41.667 14.63 2.77 38.25 3.32
2325 2758 4.189231 GCGATTTCCTGTAATACTGGTGT 58.811 43.478 14.63 4.07 38.25 4.16
2326 2759 3.560068 GGCGATTTCCTGTAATACTGGTG 59.440 47.826 14.63 4.38 38.25 4.17
2327 2760 3.199071 TGGCGATTTCCTGTAATACTGGT 59.801 43.478 14.63 0.00 38.25 4.00
2328 2761 3.804036 TGGCGATTTCCTGTAATACTGG 58.196 45.455 9.72 9.72 38.41 4.00
2331 2764 5.945155 TGTTTTGGCGATTTCCTGTAATAC 58.055 37.500 0.00 0.00 0.00 1.89
2367 2800 6.052360 GGACAATTCTCTAAGGAGTGGATTC 58.948 44.000 0.00 0.00 40.29 2.52
2392 2825 1.407656 GGGCATGTACGGGATGGAGA 61.408 60.000 0.00 0.00 0.00 3.71
2410 2893 2.742372 CAACTCCGGCCGTCTTGG 60.742 66.667 26.12 8.39 42.50 3.61
2446 2929 4.184079 ACTTTATTGTTCTAGCGACGGT 57.816 40.909 4.41 4.41 0.00 4.83
2487 2970 4.495422 TCTGCAGAGAACGGTAATTTCTC 58.505 43.478 13.74 4.92 46.43 2.87
2488 2971 4.537135 TCTGCAGAGAACGGTAATTTCT 57.463 40.909 13.74 0.00 35.96 2.52
2504 2987 1.438651 GTCGCCAACACTTATCTGCA 58.561 50.000 0.00 0.00 0.00 4.41
2507 2990 1.731424 CGACGTCGCCAACACTTATCT 60.731 52.381 26.59 0.00 0.00 1.98
2512 2995 1.443872 GATCGACGTCGCCAACACT 60.444 57.895 32.19 10.47 39.60 3.55
2517 3000 1.721664 CTTAGGGATCGACGTCGCCA 61.722 60.000 32.19 17.51 39.60 5.69
2518 3001 1.008767 CTTAGGGATCGACGTCGCC 60.009 63.158 32.19 26.52 39.60 5.54
2524 3007 3.006003 GTCCTGGATTCTTAGGGATCGAC 59.994 52.174 0.00 0.00 34.76 4.20
2535 3018 1.555533 GTCTTTCGGGTCCTGGATTCT 59.444 52.381 0.00 0.00 0.00 2.40
2543 3026 1.814169 GGCATCGTCTTTCGGGTCC 60.814 63.158 0.00 0.00 40.32 4.46
2546 3029 1.878522 CTCGGCATCGTCTTTCGGG 60.879 63.158 0.00 0.00 40.32 5.14
2548 3031 0.366871 CAACTCGGCATCGTCTTTCG 59.633 55.000 0.00 0.00 41.41 3.46
2567 3055 2.688958 AGGTAGACGTGTAGGAATGAGC 59.311 50.000 0.00 0.00 0.00 4.26
2573 3061 4.767578 AGACATAGGTAGACGTGTAGGA 57.232 45.455 0.00 0.00 0.00 2.94
2574 3062 4.754114 GGTAGACATAGGTAGACGTGTAGG 59.246 50.000 0.00 0.00 0.00 3.18
2578 3066 5.571784 TTTGGTAGACATAGGTAGACGTG 57.428 43.478 0.00 0.00 0.00 4.49
2616 3117 1.965930 TGTTCATCGCCAGTGGTGC 60.966 57.895 18.36 4.10 32.51 5.01
2627 3128 2.543653 GGCAGTTGGTTGTGTGTTCATC 60.544 50.000 0.00 0.00 0.00 2.92
2628 3129 1.408702 GGCAGTTGGTTGTGTGTTCAT 59.591 47.619 0.00 0.00 0.00 2.57
2629 3130 0.814457 GGCAGTTGGTTGTGTGTTCA 59.186 50.000 0.00 0.00 0.00 3.18
2630 3131 0.102300 GGGCAGTTGGTTGTGTGTTC 59.898 55.000 0.00 0.00 0.00 3.18
2631 3132 1.326951 GGGGCAGTTGGTTGTGTGTT 61.327 55.000 0.00 0.00 0.00 3.32
2633 3134 0.179004 TAGGGGCAGTTGGTTGTGTG 60.179 55.000 0.00 0.00 0.00 3.82
2646 3148 0.750850 TCTATGCTCAACGTAGGGGC 59.249 55.000 5.12 5.12 38.27 5.80
2673 3175 5.888161 AGAGACAAGACTGGTGAACAATTTT 59.112 36.000 0.00 0.00 0.00 1.82
2676 3178 4.696479 AGAGACAAGACTGGTGAACAAT 57.304 40.909 0.00 0.00 0.00 2.71
2681 3183 7.548097 GTCAAATATAGAGACAAGACTGGTGA 58.452 38.462 0.00 0.00 32.68 4.02
2682 3184 6.473778 CGTCAAATATAGAGACAAGACTGGTG 59.526 42.308 0.00 0.00 32.68 4.17
2684 3186 5.980116 CCGTCAAATATAGAGACAAGACTGG 59.020 44.000 0.00 0.00 32.68 4.00
2686 3188 5.361285 AGCCGTCAAATATAGAGACAAGACT 59.639 40.000 0.00 0.00 32.68 3.24
2687 3189 5.593010 AGCCGTCAAATATAGAGACAAGAC 58.407 41.667 0.00 0.00 32.68 3.01
2688 3190 5.505819 CGAGCCGTCAAATATAGAGACAAGA 60.506 44.000 0.00 0.00 32.68 3.02
2689 3191 4.677378 CGAGCCGTCAAATATAGAGACAAG 59.323 45.833 0.00 0.00 32.68 3.16
2699 3211 1.135527 CACTACCCGAGCCGTCAAATA 59.864 52.381 0.00 0.00 0.00 1.40
2703 3215 0.608856 TAACACTACCCGAGCCGTCA 60.609 55.000 0.00 0.00 0.00 4.35
2707 3219 2.973694 TTGATAACACTACCCGAGCC 57.026 50.000 0.00 0.00 0.00 4.70
2708 3220 4.054780 TCATTGATAACACTACCCGAGC 57.945 45.455 0.00 0.00 0.00 5.03
2719 3231 9.023967 GCTGGACATTTATGTTTCATTGATAAC 57.976 33.333 0.00 0.00 41.95 1.89
2720 3232 8.747471 TGCTGGACATTTATGTTTCATTGATAA 58.253 29.630 0.00 0.00 41.95 1.75
2729 3241 4.021280 TGCATGTGCTGGACATTTATGTTT 60.021 37.500 12.37 0.00 43.20 2.83
2730 3242 3.510753 TGCATGTGCTGGACATTTATGTT 59.489 39.130 12.37 0.00 43.20 2.71
2731 3243 3.090790 TGCATGTGCTGGACATTTATGT 58.909 40.909 12.37 0.00 43.20 2.29
2732 3244 3.441163 GTGCATGTGCTGGACATTTATG 58.559 45.455 12.37 4.23 43.20 1.90
2733 3245 2.097954 CGTGCATGTGCTGGACATTTAT 59.902 45.455 12.37 0.00 45.83 1.40
2734 3246 1.468127 CGTGCATGTGCTGGACATTTA 59.532 47.619 12.37 1.81 45.83 1.40
2735 3247 0.241749 CGTGCATGTGCTGGACATTT 59.758 50.000 12.37 0.00 45.83 2.32
2736 3248 0.890542 ACGTGCATGTGCTGGACATT 60.891 50.000 11.65 0.00 45.83 2.71
2737 3249 0.890542 AACGTGCATGTGCTGGACAT 60.891 50.000 13.39 9.14 45.83 3.06
2740 3252 0.606130 ATCAACGTGCATGTGCTGGA 60.606 50.000 13.39 8.71 42.66 3.86
2741 3253 1.063027 CTATCAACGTGCATGTGCTGG 59.937 52.381 13.39 3.23 42.66 4.85
2744 3256 0.378257 CCCTATCAACGTGCATGTGC 59.622 55.000 13.39 0.00 42.50 4.57
2746 3258 0.253044 AGCCCTATCAACGTGCATGT 59.747 50.000 5.51 5.51 0.00 3.21
2749 3261 0.177141 GGTAGCCCTATCAACGTGCA 59.823 55.000 0.00 0.00 0.00 4.57
2750 3262 0.532196 GGGTAGCCCTATCAACGTGC 60.532 60.000 0.00 0.00 41.34 5.34
2751 3263 0.249322 CGGGTAGCCCTATCAACGTG 60.249 60.000 5.12 0.00 42.67 4.49
2752 3264 0.396139 TCGGGTAGCCCTATCAACGT 60.396 55.000 5.12 0.00 42.67 3.99
2753 3265 0.314302 CTCGGGTAGCCCTATCAACG 59.686 60.000 5.12 0.00 42.67 4.10
2754 3266 0.033642 GCTCGGGTAGCCCTATCAAC 59.966 60.000 5.12 0.00 46.25 3.18
2769 3281 0.670546 CAGTACCACACCCTTGCTCG 60.671 60.000 0.00 0.00 0.00 5.03
2772 3284 1.228124 TGCAGTACCACACCCTTGC 60.228 57.895 0.00 0.00 0.00 4.01
2793 3305 1.518325 TGTTGTACCATCGGCAACTG 58.482 50.000 7.91 0.00 41.93 3.16
2794 3306 2.151202 CTTGTTGTACCATCGGCAACT 58.849 47.619 7.91 0.00 41.93 3.16
2795 3307 2.147958 TCTTGTTGTACCATCGGCAAC 58.852 47.619 0.00 0.00 41.81 4.17
2801 3313 5.812642 ACGATGAAGATCTTGTTGTACCATC 59.187 40.000 14.00 15.20 0.00 3.51
2804 3316 4.929808 ACACGATGAAGATCTTGTTGTACC 59.070 41.667 14.00 0.00 37.72 3.34
2823 3335 1.531149 CCACTGCTTCCTTGTTACACG 59.469 52.381 0.00 0.00 0.00 4.49
2825 3337 3.805807 GCTACCACTGCTTCCTTGTTACA 60.806 47.826 0.00 0.00 0.00 2.41
2826 3338 2.742589 GCTACCACTGCTTCCTTGTTAC 59.257 50.000 0.00 0.00 0.00 2.50
2827 3339 2.637872 AGCTACCACTGCTTCCTTGTTA 59.362 45.455 0.00 0.00 37.52 2.41
2838 3356 2.820059 TGTGAAGTGAGCTACCACTG 57.180 50.000 8.70 0.00 45.82 3.66
2852 3370 8.690203 TTGATCTAAAACAAGAGGATTGTGAA 57.310 30.769 0.00 0.00 32.22 3.18
2859 3377 7.054124 ACACACTTTGATCTAAAACAAGAGGA 58.946 34.615 0.00 0.00 0.00 3.71
2866 3384 7.254852 TGTTTGGACACACTTTGATCTAAAAC 58.745 34.615 0.00 0.00 0.00 2.43
2868 3386 7.424803 CATGTTTGGACACACTTTGATCTAAA 58.575 34.615 0.00 0.00 38.91 1.85
2874 3392 2.757314 TGCATGTTTGGACACACTTTGA 59.243 40.909 0.00 0.00 38.91 2.69
2890 3408 3.123621 GTGAGAACCTTAGACGTTGCATG 59.876 47.826 0.00 0.00 0.00 4.06
2891 3409 3.244078 TGTGAGAACCTTAGACGTTGCAT 60.244 43.478 0.00 0.00 0.00 3.96
2901 3419 6.978659 CGCATAAGTCTATTGTGAGAACCTTA 59.021 38.462 0.00 0.00 0.00 2.69
2925 3445 2.436417 TCCCAGAGATTTGAAAAGCCG 58.564 47.619 0.00 0.00 0.00 5.52
2949 3469 8.925700 CCTAAATAATTTTTGTTTGAGCTGGAC 58.074 33.333 0.00 0.00 0.00 4.02
3036 3556 3.904965 TCTGAGGTGTGTGGTAATGGTTA 59.095 43.478 0.00 0.00 0.00 2.85
3060 3580 4.985413 CAACTCACTGATTGTTGTGTTGT 58.015 39.130 7.88 0.00 37.05 3.32
3066 3586 2.951642 ACCCACAACTCACTGATTGTTG 59.048 45.455 8.81 8.81 44.44 3.33
3067 3587 2.951642 CACCCACAACTCACTGATTGTT 59.048 45.455 4.87 0.00 36.92 2.83
3068 3588 2.575532 CACCCACAACTCACTGATTGT 58.424 47.619 0.00 0.00 39.63 2.71
3069 3589 1.881973 CCACCCACAACTCACTGATTG 59.118 52.381 0.00 0.00 0.00 2.67
3070 3590 1.774254 TCCACCCACAACTCACTGATT 59.226 47.619 0.00 0.00 0.00 2.57
3071 3591 1.434188 TCCACCCACAACTCACTGAT 58.566 50.000 0.00 0.00 0.00 2.90
3072 3592 1.208706 TTCCACCCACAACTCACTGA 58.791 50.000 0.00 0.00 0.00 3.41
3074 3594 3.587061 TGATATTCCACCCACAACTCACT 59.413 43.478 0.00 0.00 0.00 3.41
3075 3595 3.950397 TGATATTCCACCCACAACTCAC 58.050 45.455 0.00 0.00 0.00 3.51
3076 3596 4.288366 TCTTGATATTCCACCCACAACTCA 59.712 41.667 0.00 0.00 0.00 3.41
3077 3597 4.843728 TCTTGATATTCCACCCACAACTC 58.156 43.478 0.00 0.00 0.00 3.01
3078 3598 4.927267 TCTTGATATTCCACCCACAACT 57.073 40.909 0.00 0.00 0.00 3.16
3079 3599 4.202050 GCATCTTGATATTCCACCCACAAC 60.202 45.833 0.00 0.00 0.00 3.32
3082 3602 3.554934 TGCATCTTGATATTCCACCCAC 58.445 45.455 0.00 0.00 0.00 4.61
3084 3604 5.452356 CCTTTTGCATCTTGATATTCCACCC 60.452 44.000 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.