Multiple sequence alignment - TraesCS2B01G457400

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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 TraesCS2B01G457400 chr2B 100.000 4127 0 0 1 4127 651935730 651931604 0.000000e+00 7622
1 TraesCS2B01G457400 chr2D 93.481 1764 74 15 519 2250 545043322 545041568 0.000000e+00 2582
2 TraesCS2B01G457400 chr2D 92.940 1034 62 8 2618 3643 545040794 545039764 0.000000e+00 1495
3 TraesCS2B01G457400 chr2D 91.139 474 29 7 3666 4127 545039771 545039299 7.530000e-177 630
4 TraesCS2B01G457400 chr2A 94.977 1533 57 12 938 2457 688230935 688232460 0.000000e+00 2386
5 TraesCS2B01G457400 chr2A 89.082 1557 104 37 2580 4127 688232599 688234098 0.000000e+00 1873
6 TraesCS2B01G457400 chr2A 96.154 754 28 1 937 1689 688220252 688221005 0.000000e+00 1230
7 TraesCS2B01G457400 chr2A 94.814 752 39 0 938 1689 688209510 688210261 0.000000e+00 1173
8 TraesCS2B01G457400 chr2A 94.762 420 22 0 329 748 688229747 688230166 0.000000e+00 654
9 TraesCS2B01G457400 chr2A 94.286 420 24 0 329 748 688219060 688219479 0.000000e+00 643
10 TraesCS2B01G457400 chr2A 93.095 420 29 0 329 748 688208320 688208739 2.110000e-172 616
11 TraesCS2B01G457400 chr2A 94.792 192 9 1 755 945 688230224 688230415 8.670000e-77 298
12 TraesCS2B01G457400 chr2A 94.565 184 8 2 761 943 688208802 688208984 2.430000e-72 283
13 TraesCS2B01G457400 chr2A 92.063 189 13 2 755 943 688219542 688219728 8.800000e-67 265
14 TraesCS2B01G457400 chr5B 93.636 330 18 2 1 328 511014474 511014802 1.330000e-134 490
15 TraesCS2B01G457400 chr5B 92.284 324 21 2 1 322 511013527 511013848 1.350000e-124 457
16 TraesCS2B01G457400 chr5B 91.071 336 23 4 1 333 648266525 648266194 8.140000e-122 448
17 TraesCS2B01G457400 chr4B 93.333 330 20 1 1 328 175852084 175852413 1.720000e-133 486
18 TraesCS2B01G457400 chr4D 91.489 329 19 6 1 328 388825978 388825658 1.050000e-120 444
19 TraesCS2B01G457400 chr7A 89.394 330 31 2 1 329 26440889 26440563 2.970000e-111 412
20 TraesCS2B01G457400 chr1A 88.855 332 34 2 1 329 467224934 467225265 4.970000e-109 405
21 TraesCS2B01G457400 chr6A 88.554 332 29 5 1 328 515664822 515665148 1.080000e-105 394
22 TraesCS2B01G457400 chr6A 87.952 332 33 4 1 328 93273089 93272761 6.470000e-103 385


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 TraesCS2B01G457400 chr2B 651931604 651935730 4126 True 7622.000000 7622 100.000000 1 4127 1 chr2B.!!$R1 4126
1 TraesCS2B01G457400 chr2D 545039299 545043322 4023 True 1569.000000 2582 92.520000 519 4127 3 chr2D.!!$R1 3608
2 TraesCS2B01G457400 chr2A 688229747 688234098 4351 False 1302.750000 2386 93.403250 329 4127 4 chr2A.!!$F3 3798
3 TraesCS2B01G457400 chr2A 688219060 688221005 1945 False 712.666667 1230 94.167667 329 1689 3 chr2A.!!$F2 1360
4 TraesCS2B01G457400 chr2A 688208320 688210261 1941 False 690.666667 1173 94.158000 329 1689 3 chr2A.!!$F1 1360
5 TraesCS2B01G457400 chr5B 511013527 511014802 1275 False 473.500000 490 92.960000 1 328 2 chr5B.!!$F1 327

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
314 317 0.030235 GTTTTGCAACCGGTCTCCAC 59.970 55.0 8.04 0.00 0.00 4.02 F
451 454 0.037326 GGAGGTGATGACGTTGAGCA 60.037 55.0 0.00 0.00 0.00 4.26 F
454 457 0.602638 GGTGATGACGTTGAGCACCA 60.603 55.0 23.61 2.56 46.27 4.17 F
457 460 0.647410 GATGACGTTGAGCACCATCG 59.353 55.0 0.00 7.68 42.11 3.84 F
805 864 0.892755 GGTGGACACCGTCATGTCTA 59.107 55.0 5.63 3.39 46.85 2.59 F
2492 3798 0.179089 CTTCAGAGCGACATGGGAGG 60.179 60.0 0.00 0.00 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2034 2885 0.106335 ATGGATCGCCTGAGCAAGAG 59.894 55.000 0.00 0.00 39.83 2.85 R
2035 2886 0.179065 CATGGATCGCCTGAGCAAGA 60.179 55.000 0.00 0.00 39.83 3.02 R
2036 2887 0.463295 ACATGGATCGCCTGAGCAAG 60.463 55.000 0.00 0.00 39.83 4.01 R
2258 3157 1.339055 TGTATGTCTCCAGCACAAGCC 60.339 52.381 0.00 0.00 43.56 4.35 R
2519 3825 0.245539 TTTTCTAGGAGGACGGCGTG 59.754 55.000 21.19 0.00 0.00 5.34 R
3475 4901 0.523072 TCGATTTCTGCCTGCAAAGC 59.477 50.000 1.42 1.42 0.00 3.51 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
30 31 2.304056 CCATGGTGCCTCCTGGTCT 61.304 63.158 2.57 0.00 37.07 3.85
32 33 1.539869 ATGGTGCCTCCTGGTCTGT 60.540 57.895 0.00 0.00 37.07 3.41
102 103 3.710722 CTCGGCCTTGGCTGTCCT 61.711 66.667 18.73 0.00 0.00 3.85
103 104 3.965539 CTCGGCCTTGGCTGTCCTG 62.966 68.421 18.73 5.93 0.00 3.86
154 157 4.319177 GGTTTCTTGAGCCGATATAGCAT 58.681 43.478 0.46 0.00 0.00 3.79
202 205 2.876645 GAGCGACAGAACGAGCCG 60.877 66.667 0.00 0.00 35.09 5.52
210 213 0.440371 CAGAACGAGCCGAAGAAAGC 59.560 55.000 1.50 0.00 0.00 3.51
232 235 4.554363 CTACACGGGCGCGAGAGG 62.554 72.222 30.98 17.12 0.00 3.69
253 256 1.453015 GCCGTGGGATGCATTGGTA 60.453 57.895 0.00 0.00 0.00 3.25
254 257 1.447317 GCCGTGGGATGCATTGGTAG 61.447 60.000 0.00 0.00 0.00 3.18
255 258 0.819259 CCGTGGGATGCATTGGTAGG 60.819 60.000 0.00 0.00 0.00 3.18
256 259 0.180171 CGTGGGATGCATTGGTAGGA 59.820 55.000 0.00 0.00 0.00 2.94
257 260 1.680338 GTGGGATGCATTGGTAGGAC 58.320 55.000 0.00 0.00 0.00 3.85
258 261 1.064758 GTGGGATGCATTGGTAGGACA 60.065 52.381 0.00 0.00 0.00 4.02
259 262 1.212688 TGGGATGCATTGGTAGGACAG 59.787 52.381 0.00 0.00 0.00 3.51
260 263 1.477558 GGGATGCATTGGTAGGACAGG 60.478 57.143 0.00 0.00 0.00 4.00
261 264 1.212935 GGATGCATTGGTAGGACAGGT 59.787 52.381 0.00 0.00 0.00 4.00
262 265 2.292267 GATGCATTGGTAGGACAGGTG 58.708 52.381 0.00 0.00 0.00 4.00
263 266 0.327924 TGCATTGGTAGGACAGGTGG 59.672 55.000 0.00 0.00 0.00 4.61
264 267 1.032114 GCATTGGTAGGACAGGTGGC 61.032 60.000 0.00 0.00 0.00 5.01
265 268 0.744414 CATTGGTAGGACAGGTGGCG 60.744 60.000 0.00 0.00 0.00 5.69
266 269 1.910580 ATTGGTAGGACAGGTGGCGG 61.911 60.000 0.00 0.00 0.00 6.13
267 270 4.468689 GGTAGGACAGGTGGCGGC 62.469 72.222 0.00 0.00 0.00 6.53
268 271 3.702048 GTAGGACAGGTGGCGGCA 61.702 66.667 7.97 7.97 0.00 5.69
269 272 3.390521 TAGGACAGGTGGCGGCAG 61.391 66.667 13.91 2.93 0.00 4.85
270 273 3.897681 TAGGACAGGTGGCGGCAGA 62.898 63.158 13.91 0.00 0.00 4.26
271 274 4.101448 GGACAGGTGGCGGCAGAT 62.101 66.667 13.91 0.00 0.00 2.90
272 275 2.512515 GACAGGTGGCGGCAGATC 60.513 66.667 13.91 5.25 0.00 2.75
273 276 4.457496 ACAGGTGGCGGCAGATCG 62.457 66.667 13.91 3.77 0.00 3.69
276 279 4.241555 GGTGGCGGCAGATCGGAT 62.242 66.667 13.91 0.00 0.00 4.18
277 280 2.663188 GTGGCGGCAGATCGGATC 60.663 66.667 13.91 10.02 0.00 3.36
278 281 4.284860 TGGCGGCAGATCGGATCG 62.285 66.667 7.97 8.53 0.00 3.69
281 284 3.606662 CGGCAGATCGGATCGGGT 61.607 66.667 17.74 0.00 0.00 5.28
282 285 2.265904 CGGCAGATCGGATCGGGTA 61.266 63.158 17.74 0.00 0.00 3.69
283 286 1.595993 CGGCAGATCGGATCGGGTAT 61.596 60.000 17.74 0.00 0.00 2.73
284 287 0.108615 GGCAGATCGGATCGGGTATG 60.109 60.000 17.74 3.93 0.00 2.39
285 288 0.737715 GCAGATCGGATCGGGTATGC 60.738 60.000 16.04 16.04 0.00 3.14
286 289 0.603065 CAGATCGGATCGGGTATGCA 59.397 55.000 12.08 0.00 0.00 3.96
287 290 0.891373 AGATCGGATCGGGTATGCAG 59.109 55.000 12.08 0.00 0.00 4.41
288 291 0.108615 GATCGGATCGGGTATGCAGG 60.109 60.000 1.62 0.00 0.00 4.85
289 292 1.544825 ATCGGATCGGGTATGCAGGG 61.545 60.000 0.00 0.00 0.00 4.45
290 293 2.750350 GGATCGGGTATGCAGGGG 59.250 66.667 0.00 0.00 0.00 4.79
291 294 1.841556 GGATCGGGTATGCAGGGGA 60.842 63.158 0.00 0.00 0.00 4.81
292 295 1.674057 GATCGGGTATGCAGGGGAG 59.326 63.158 0.00 0.00 0.00 4.30
293 296 1.831652 GATCGGGTATGCAGGGGAGG 61.832 65.000 0.00 0.00 0.00 4.30
294 297 2.326529 ATCGGGTATGCAGGGGAGGA 62.327 60.000 0.00 0.00 0.00 3.71
295 298 2.511452 CGGGTATGCAGGGGAGGAG 61.511 68.421 0.00 0.00 0.00 3.69
296 299 1.384643 GGGTATGCAGGGGAGGAGT 60.385 63.158 0.00 0.00 0.00 3.85
297 300 0.988678 GGGTATGCAGGGGAGGAGTT 60.989 60.000 0.00 0.00 0.00 3.01
298 301 0.919710 GGTATGCAGGGGAGGAGTTT 59.080 55.000 0.00 0.00 0.00 2.66
299 302 1.285078 GGTATGCAGGGGAGGAGTTTT 59.715 52.381 0.00 0.00 0.00 2.43
300 303 2.369394 GTATGCAGGGGAGGAGTTTTG 58.631 52.381 0.00 0.00 0.00 2.44
301 304 0.613012 ATGCAGGGGAGGAGTTTTGC 60.613 55.000 0.00 0.00 0.00 3.68
302 305 1.228552 GCAGGGGAGGAGTTTTGCA 60.229 57.895 0.00 0.00 0.00 4.08
303 306 0.827507 GCAGGGGAGGAGTTTTGCAA 60.828 55.000 0.00 0.00 0.00 4.08
304 307 0.961753 CAGGGGAGGAGTTTTGCAAC 59.038 55.000 0.00 0.00 0.00 4.17
305 308 0.178961 AGGGGAGGAGTTTTGCAACC 60.179 55.000 0.00 0.00 32.70 3.77
306 309 1.524008 GGGGAGGAGTTTTGCAACCG 61.524 60.000 0.00 0.00 32.70 4.44
307 310 1.524008 GGGAGGAGTTTTGCAACCGG 61.524 60.000 0.00 0.00 32.70 5.28
308 311 0.822121 GGAGGAGTTTTGCAACCGGT 60.822 55.000 0.00 0.00 32.70 5.28
309 312 0.591659 GAGGAGTTTTGCAACCGGTC 59.408 55.000 8.04 0.00 32.70 4.79
310 313 0.182775 AGGAGTTTTGCAACCGGTCT 59.817 50.000 8.04 0.00 32.70 3.85
311 314 0.591659 GGAGTTTTGCAACCGGTCTC 59.408 55.000 8.04 8.23 32.70 3.36
312 315 0.591659 GAGTTTTGCAACCGGTCTCC 59.408 55.000 8.04 0.00 32.70 3.71
313 316 0.106918 AGTTTTGCAACCGGTCTCCA 60.107 50.000 8.04 2.04 32.70 3.86
314 317 0.030235 GTTTTGCAACCGGTCTCCAC 59.970 55.000 8.04 0.00 0.00 4.02
315 318 1.104577 TTTTGCAACCGGTCTCCACC 61.105 55.000 8.04 0.00 39.69 4.61
316 319 2.969300 TTTGCAACCGGTCTCCACCC 62.969 60.000 8.04 0.00 40.01 4.61
317 320 3.948719 GCAACCGGTCTCCACCCA 61.949 66.667 8.04 0.00 40.01 4.51
318 321 2.833227 CAACCGGTCTCCACCCAA 59.167 61.111 8.04 0.00 40.01 4.12
319 322 1.378762 CAACCGGTCTCCACCCAAT 59.621 57.895 8.04 0.00 40.01 3.16
320 323 0.251165 CAACCGGTCTCCACCCAATT 60.251 55.000 8.04 0.00 40.01 2.32
321 324 0.481128 AACCGGTCTCCACCCAATTT 59.519 50.000 8.04 0.00 40.01 1.82
322 325 0.481128 ACCGGTCTCCACCCAATTTT 59.519 50.000 0.00 0.00 40.01 1.82
323 326 1.133294 ACCGGTCTCCACCCAATTTTT 60.133 47.619 0.00 0.00 40.01 1.94
352 355 4.041723 GTCACCACTGGAAATGAAAAACG 58.958 43.478 0.71 0.00 0.00 3.60
354 357 2.223947 ACCACTGGAAATGAAAAACGCC 60.224 45.455 0.71 0.00 0.00 5.68
451 454 0.037326 GGAGGTGATGACGTTGAGCA 60.037 55.000 0.00 0.00 0.00 4.26
452 455 1.071605 GAGGTGATGACGTTGAGCAC 58.928 55.000 8.05 8.05 0.00 4.40
454 457 0.602638 GGTGATGACGTTGAGCACCA 60.603 55.000 23.61 2.56 46.27 4.17
457 460 0.647410 GATGACGTTGAGCACCATCG 59.353 55.000 0.00 7.68 42.11 3.84
482 485 3.308473 GCCTAGTTCCAGATTGAGGGTTT 60.308 47.826 0.00 0.00 0.00 3.27
528 531 3.051341 AGGGGGATACTACCTTGACATCA 60.051 47.826 0.00 0.00 40.28 3.07
633 636 2.292323 CCCTATTCCCCTAGCTATCCGT 60.292 54.545 0.00 0.00 0.00 4.69
659 662 3.948719 GCCAAGTCCGGTGGGTGA 61.949 66.667 11.30 0.00 36.58 4.02
805 864 0.892755 GGTGGACACCGTCATGTCTA 59.107 55.000 5.63 3.39 46.85 2.59
1464 2315 2.446994 ACCACCCACGGACAGGAA 60.447 61.111 0.00 0.00 0.00 3.36
1664 2515 4.680237 CCTCACCCTGCGCGTCAA 62.680 66.667 8.43 0.00 0.00 3.18
1701 2552 3.532155 GTCTCCATCCGCTCCGCT 61.532 66.667 0.00 0.00 0.00 5.52
1704 2555 3.798954 CTCCATCCGCTCCGCTTCC 62.799 68.421 0.00 0.00 0.00 3.46
1719 2570 1.305802 TTCCCTCAGGCGCCTAGAA 60.306 57.895 32.30 24.81 0.00 2.10
1915 2766 1.135083 ACATCACGCAGCTGTACCTAC 60.135 52.381 16.64 0.00 0.00 3.18
2028 2879 5.307976 TCTCTCCGTATGAATCCATGGATTT 59.692 40.000 34.93 24.56 43.98 2.17
2030 2881 5.764686 TCTCCGTATGAATCCATGGATTTTG 59.235 40.000 34.93 22.92 43.98 2.44
2031 2882 5.445069 TCCGTATGAATCCATGGATTTTGT 58.555 37.500 34.93 25.56 43.98 2.83
2032 2883 5.890985 TCCGTATGAATCCATGGATTTTGTT 59.109 36.000 34.93 22.83 43.98 2.83
2033 2884 5.978919 CCGTATGAATCCATGGATTTTGTTG 59.021 40.000 34.93 24.64 43.98 3.33
2034 2885 5.459762 CGTATGAATCCATGGATTTTGTTGC 59.540 40.000 34.93 23.13 43.98 4.17
2035 2886 5.687166 ATGAATCCATGGATTTTGTTGCT 57.313 34.783 34.93 15.38 43.98 3.91
2036 2887 5.075858 TGAATCCATGGATTTTGTTGCTC 57.924 39.130 34.93 22.34 43.98 4.26
2044 2895 3.005050 TGGATTTTGTTGCTCTTGCTCAG 59.995 43.478 0.00 0.00 40.48 3.35
2052 2903 1.519246 CTCTTGCTCAGGCGATCCA 59.481 57.895 0.00 0.00 42.25 3.41
2069 2923 5.298276 GCGATCCATGTTAATTGGTCCTTTA 59.702 40.000 7.15 0.00 35.64 1.85
2104 2958 6.483385 TCGTTTTTGTGCTTCCGATTATTA 57.517 33.333 0.00 0.00 0.00 0.98
2255 3154 4.046938 TCAGGAGAAGCAACGCTATAAG 57.953 45.455 0.00 0.00 38.25 1.73
2258 3157 3.068873 AGGAGAAGCAACGCTATAAGGAG 59.931 47.826 0.00 0.00 38.25 3.69
2312 3211 7.121020 GGTACGTAATTTCTGGGGTTCATTTTA 59.879 37.037 0.00 0.00 0.00 1.52
2325 3224 7.399765 TGGGGTTCATTTTATCAGTTCATTCAT 59.600 33.333 0.00 0.00 0.00 2.57
2336 3235 5.907207 TCAGTTCATTCATAGACTGTAGCC 58.093 41.667 0.00 0.00 0.00 3.93
2359 3258 7.823799 AGCCCAAATATTCACGATTTTGAAATT 59.176 29.630 0.00 0.00 38.95 1.82
2385 3284 6.641474 AGGAAACATGTTTAGGAGTAGTAGC 58.359 40.000 23.33 6.73 32.11 3.58
2398 3297 7.296628 AGGAGTAGTAGCTTATGATTTGGAG 57.703 40.000 0.00 0.00 0.00 3.86
2421 3621 4.443315 GGCCCATTGAAAAATCATCGGAAT 60.443 41.667 0.00 0.00 0.00 3.01
2422 3622 4.746611 GCCCATTGAAAAATCATCGGAATC 59.253 41.667 0.00 0.00 0.00 2.52
2425 3625 7.684187 GCCCATTGAAAAATCATCGGAATCTTA 60.684 37.037 0.00 0.00 0.00 2.10
2441 3645 5.357878 GGAATCTTATGTGGCTGATGTTCAA 59.642 40.000 0.00 0.00 0.00 2.69
2457 3732 1.380380 CAAGGGGAGGGTGGCATTC 60.380 63.158 0.00 0.00 0.00 2.67
2460 3735 3.728373 GGGAGGGTGGCATTCCGT 61.728 66.667 8.82 0.02 34.14 4.69
2461 3736 2.438434 GGAGGGTGGCATTCCGTG 60.438 66.667 0.00 0.00 34.14 4.94
2478 3784 1.226746 GTGGGTGACGGTTTCTTCAG 58.773 55.000 0.00 0.00 0.00 3.02
2482 3788 0.784778 GTGACGGTTTCTTCAGAGCG 59.215 55.000 0.00 0.00 41.99 5.03
2484 3790 1.061485 GACGGTTTCTTCAGAGCGAC 58.939 55.000 1.82 0.00 39.78 5.19
2489 3795 1.734465 GTTTCTTCAGAGCGACATGGG 59.266 52.381 0.00 0.00 0.00 4.00
2491 3797 0.820226 TCTTCAGAGCGACATGGGAG 59.180 55.000 0.00 0.00 0.00 4.30
2492 3798 0.179089 CTTCAGAGCGACATGGGAGG 60.179 60.000 0.00 0.00 0.00 4.30
2493 3799 0.614697 TTCAGAGCGACATGGGAGGA 60.615 55.000 0.00 0.00 0.00 3.71
2495 3801 0.249784 CAGAGCGACATGGGAGGATG 60.250 60.000 0.00 0.00 0.00 3.51
2496 3802 1.070445 GAGCGACATGGGAGGATGG 59.930 63.158 0.00 0.00 0.00 3.51
2497 3803 1.690219 GAGCGACATGGGAGGATGGT 61.690 60.000 0.00 0.00 0.00 3.55
2499 3805 1.524621 CGACATGGGAGGATGGTGC 60.525 63.158 0.00 0.00 0.00 5.01
2500 3806 1.524621 GACATGGGAGGATGGTGCG 60.525 63.158 0.00 0.00 0.00 5.34
2501 3807 1.971505 GACATGGGAGGATGGTGCGA 61.972 60.000 0.00 0.00 0.00 5.10
2502 3808 1.524621 CATGGGAGGATGGTGCGAC 60.525 63.158 0.00 0.00 0.00 5.19
2503 3809 2.746375 ATGGGAGGATGGTGCGACC 61.746 63.158 0.00 0.00 39.22 4.79
2516 3822 4.100084 CGACCAGCTGCCATCCCA 62.100 66.667 8.66 0.00 0.00 4.37
2518 3824 3.259314 ACCAGCTGCCATCCCACA 61.259 61.111 8.66 0.00 0.00 4.17
2519 3825 2.753043 CCAGCTGCCATCCCACAC 60.753 66.667 8.66 0.00 0.00 3.82
2520 3826 2.034532 CAGCTGCCATCCCACACA 59.965 61.111 0.00 0.00 0.00 3.72
2521 3827 2.034687 AGCTGCCATCCCACACAC 59.965 61.111 0.00 0.00 0.00 3.82
2522 3828 3.434319 GCTGCCATCCCACACACG 61.434 66.667 0.00 0.00 0.00 4.49
2523 3829 3.434319 CTGCCATCCCACACACGC 61.434 66.667 0.00 0.00 0.00 5.34
2526 3832 4.697756 CCATCCCACACACGCCGT 62.698 66.667 0.00 0.00 0.00 5.68
2527 3833 3.118454 CATCCCACACACGCCGTC 61.118 66.667 0.00 0.00 0.00 4.79
2528 3834 4.388499 ATCCCACACACGCCGTCC 62.388 66.667 0.00 0.00 0.00 4.79
2532 3838 3.991051 CACACACGCCGTCCTCCT 61.991 66.667 0.00 0.00 0.00 3.69
2545 3851 4.122776 CCGTCCTCCTAGAAAATGTCATG 58.877 47.826 0.00 0.00 0.00 3.07
2553 3859 5.645067 TCCTAGAAAATGTCATGTTGCTCTG 59.355 40.000 0.00 0.00 0.00 3.35
2554 3860 5.413833 CCTAGAAAATGTCATGTTGCTCTGT 59.586 40.000 0.00 0.00 0.00 3.41
2559 3865 6.492007 AAATGTCATGTTGCTCTGTAGAAG 57.508 37.500 0.00 0.00 0.00 2.85
2566 3872 0.907486 TGCTCTGTAGAAGCTGCCAT 59.093 50.000 0.00 0.00 0.00 4.40
2568 3874 1.809651 GCTCTGTAGAAGCTGCCATCC 60.810 57.143 0.00 0.00 0.00 3.51
2580 3886 1.078497 GCCATCCCACACACATCGA 60.078 57.895 0.00 0.00 0.00 3.59
2581 3887 0.676466 GCCATCCCACACACATCGAA 60.676 55.000 0.00 0.00 0.00 3.71
2582 3888 1.819928 CCATCCCACACACATCGAAA 58.180 50.000 0.00 0.00 0.00 3.46
2583 3889 2.158559 CCATCCCACACACATCGAAAA 58.841 47.619 0.00 0.00 0.00 2.29
2596 3902 0.726827 TCGAAAATGCCATGTCGCTC 59.273 50.000 6.24 0.00 33.58 5.03
2598 3904 1.933181 CGAAAATGCCATGTCGCTCTA 59.067 47.619 0.00 0.00 0.00 2.43
2613 3919 4.923871 GTCGCTCTAAAGAAACTGTCATCA 59.076 41.667 0.00 0.00 0.00 3.07
2616 4030 6.481976 TCGCTCTAAAGAAACTGTCATCAAAA 59.518 34.615 0.00 0.00 0.00 2.44
2625 4039 1.262950 CTGTCATCAAAACGTTCGCCA 59.737 47.619 0.00 0.00 0.00 5.69
2646 4060 2.100197 GCTAAGGGGGTCCAAAATCAC 58.900 52.381 0.00 0.00 34.83 3.06
2648 4062 2.009681 AAGGGGGTCCAAAATCACAC 57.990 50.000 0.00 0.00 34.83 3.82
2653 4067 2.817844 GGGGTCCAAAATCACACAGTAC 59.182 50.000 0.00 0.00 0.00 2.73
2685 4099 5.250235 TGCACTATGTACTGTAGCTCTTC 57.750 43.478 0.00 0.00 0.00 2.87
2700 4114 3.639094 AGCTCTTCGCCTAATGTAGTCAT 59.361 43.478 0.00 0.00 40.39 3.06
2701 4115 4.827835 AGCTCTTCGCCTAATGTAGTCATA 59.172 41.667 0.00 0.00 40.39 2.15
2702 4116 5.478679 AGCTCTTCGCCTAATGTAGTCATAT 59.521 40.000 0.00 0.00 40.39 1.78
2872 4287 3.733337 AGATCAATACGTTCATGGGAGC 58.267 45.455 0.00 0.00 0.00 4.70
2891 4306 2.042162 AGCAGATGACCAGGTGGAATTT 59.958 45.455 0.00 0.00 38.94 1.82
2892 4307 2.424956 GCAGATGACCAGGTGGAATTTC 59.575 50.000 0.00 0.00 38.94 2.17
2898 4313 4.168101 TGACCAGGTGGAATTTCTAGAGT 58.832 43.478 0.00 0.00 38.94 3.24
3062 4477 5.135508 TCTCCAACGAGAGGTTTTTAGAG 57.864 43.478 0.00 0.00 40.34 2.43
3094 4512 5.366477 TGTAAGAAGTGGATCCTATGCATGA 59.634 40.000 14.23 0.00 31.75 3.07
3125 4551 2.224113 TGGTTTGTTAGTGGTCGTCTCC 60.224 50.000 0.00 0.00 0.00 3.71
3161 4587 4.857037 TGACTGATAAACTTCGTGTCGATG 59.143 41.667 0.00 4.07 35.23 3.84
3191 4617 5.962423 GTGCTCTAAAATCTCGATTTCAAGC 59.038 40.000 17.54 17.54 39.88 4.01
3211 4637 2.610727 GCCTAGCACGGTTGATATCCTC 60.611 54.545 0.00 0.00 0.00 3.71
3226 4652 1.302033 CCTCTGCAGCACGTTTCCT 60.302 57.895 9.47 0.00 0.00 3.36
3238 4664 1.597461 GTTTCCTAGCAGACCGCCT 59.403 57.895 0.00 0.00 44.04 5.52
3283 4709 0.105142 ACCACTGGTAGTCACCCACT 60.105 55.000 0.00 0.00 45.11 4.00
3303 4729 3.008049 ACTGCTTTGTCCGATAGAGGTTT 59.992 43.478 0.00 0.00 39.76 3.27
3339 4765 1.228510 CCAGGATTTCAGGGGGAGC 59.771 63.158 0.00 0.00 0.00 4.70
3359 4785 1.279271 CCACTCCCCTGACAAGGTTAG 59.721 57.143 0.00 0.00 42.74 2.34
3403 4829 2.386661 TTCGATCTTGCAGAACCTCC 57.613 50.000 0.00 0.00 0.00 4.30
3456 4882 2.175499 CTCCTGGGATAATTTCCTGGCA 59.825 50.000 10.94 0.00 44.75 4.92
3463 4889 3.774766 GGATAATTTCCTGGCAAAAGGGT 59.225 43.478 0.00 0.00 41.78 4.34
3490 4916 2.336088 GCGCTTTGCAGGCAGAAA 59.664 55.556 0.00 0.00 45.45 2.52
3520 4946 1.273781 TGGTGGATGAGTGGAGATGGA 60.274 52.381 0.00 0.00 0.00 3.41
3635 5061 2.686915 AGGCTCACTATTGCAATGAAGC 59.313 45.455 22.27 20.92 0.00 3.86
3636 5062 2.424601 GGCTCACTATTGCAATGAAGCA 59.575 45.455 22.27 0.04 43.99 3.91
3637 5063 3.488721 GGCTCACTATTGCAATGAAGCAG 60.489 47.826 22.27 12.91 46.54 4.24
3638 5064 3.692576 CTCACTATTGCAATGAAGCAGC 58.307 45.455 22.27 0.00 46.54 5.25
3639 5065 3.083293 TCACTATTGCAATGAAGCAGCA 58.917 40.909 22.27 0.00 46.54 4.41
3643 5069 2.598686 TTGCAATGAAGCAGCAACAA 57.401 40.000 0.00 0.00 46.54 2.83
3644 5070 1.855513 TGCAATGAAGCAGCAACAAC 58.144 45.000 0.00 0.00 40.11 3.32
3645 5071 1.136500 TGCAATGAAGCAGCAACAACA 59.864 42.857 0.00 0.00 40.11 3.33
3646 5072 2.203401 GCAATGAAGCAGCAACAACAA 58.797 42.857 0.00 0.00 0.00 2.83
3647 5073 2.033492 GCAATGAAGCAGCAACAACAAC 60.033 45.455 0.00 0.00 0.00 3.32
3648 5074 3.188492 CAATGAAGCAGCAACAACAACA 58.812 40.909 0.00 0.00 0.00 3.33
3649 5075 3.523606 ATGAAGCAGCAACAACAACAA 57.476 38.095 0.00 0.00 0.00 2.83
3650 5076 2.605030 TGAAGCAGCAACAACAACAAC 58.395 42.857 0.00 0.00 0.00 3.32
3651 5077 2.029560 TGAAGCAGCAACAACAACAACA 60.030 40.909 0.00 0.00 0.00 3.33
3652 5078 2.739885 AGCAGCAACAACAACAACAA 57.260 40.000 0.00 0.00 0.00 2.83
3653 5079 2.336667 AGCAGCAACAACAACAACAAC 58.663 42.857 0.00 0.00 0.00 3.32
3654 5080 2.064762 GCAGCAACAACAACAACAACA 58.935 42.857 0.00 0.00 0.00 3.33
3656 5082 3.664014 GCAGCAACAACAACAACAACAAC 60.664 43.478 0.00 0.00 0.00 3.32
3657 5083 3.492383 CAGCAACAACAACAACAACAACA 59.508 39.130 0.00 0.00 0.00 3.33
3658 5084 4.025396 CAGCAACAACAACAACAACAACAA 60.025 37.500 0.00 0.00 0.00 2.83
3659 5085 4.025313 AGCAACAACAACAACAACAACAAC 60.025 37.500 0.00 0.00 0.00 3.32
3661 5087 5.727791 GCAACAACAACAACAACAACAACAA 60.728 36.000 0.00 0.00 0.00 2.83
3662 5088 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
3663 5089 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
3680 5106 3.178267 CAACAACAACAACAACAGCGAT 58.822 40.909 0.00 0.00 0.00 4.58
3685 5111 5.468746 ACAACAACAACAACAGCGATATACT 59.531 36.000 0.00 0.00 0.00 2.12
3720 5149 8.791675 TGACAATCACAGTAATGAAATTAAGCA 58.208 29.630 0.00 0.00 41.12 3.91
3726 5155 7.395772 TCACAGTAATGAAATTAAGCATGGGAA 59.604 33.333 0.00 0.00 41.12 3.97
3936 5367 6.475402 GGATACCAAAATTAAATCCAACGCAG 59.525 38.462 0.00 0.00 36.83 5.18
3943 5374 0.168788 AAATCCAACGCAGCACATCG 59.831 50.000 0.00 0.00 0.00 3.84
3954 5385 3.674423 GCAGCACATCGTAATTCAAGAC 58.326 45.455 0.00 0.00 0.00 3.01
3981 5419 7.852971 TGTTAATTGTTCCTATAAAGGGTCG 57.147 36.000 0.00 0.00 43.84 4.79
3987 5425 4.456566 TGTTCCTATAAAGGGTCGTTTTGC 59.543 41.667 0.00 0.00 43.84 3.68
3988 5426 4.289238 TCCTATAAAGGGTCGTTTTGCA 57.711 40.909 0.00 0.00 43.84 4.08
3993 5431 6.310224 CCTATAAAGGGTCGTTTTGCATTTTG 59.690 38.462 0.00 0.00 39.48 2.44
4025 5463 7.595819 TTATTTTGGACCATCACTTCACTTT 57.404 32.000 0.00 0.00 0.00 2.66
4039 5477 2.672714 TCACTTTCCAGATCGAACACG 58.327 47.619 0.00 0.00 0.00 4.49
4040 5478 2.295070 TCACTTTCCAGATCGAACACGA 59.705 45.455 0.00 0.00 40.29 4.35
4078 5521 6.587273 AGAAACATAGAGAAGATGGGTTAGC 58.413 40.000 0.00 0.00 0.00 3.09
4084 5527 3.964031 AGAGAAGATGGGTTAGCTGGTAG 59.036 47.826 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 103 0.324552 CCCATCTTGTTCCATGCCCA 60.325 55.000 0.00 0.00 0.00 5.36
103 104 1.044790 CCCCATCTTGTTCCATGCCC 61.045 60.000 0.00 0.00 0.00 5.36
104 105 0.033208 TCCCCATCTTGTTCCATGCC 60.033 55.000 0.00 0.00 0.00 4.40
106 107 3.131577 CACAATCCCCATCTTGTTCCATG 59.868 47.826 0.00 0.00 33.45 3.66
184 187 2.569134 GGCTCGTTCTGTCGCTCT 59.431 61.111 0.00 0.00 0.00 4.09
189 192 1.721926 CTTTCTTCGGCTCGTTCTGTC 59.278 52.381 0.00 0.00 0.00 3.51
192 195 0.033504 TGCTTTCTTCGGCTCGTTCT 59.966 50.000 0.00 0.00 0.00 3.01
202 205 0.093705 CGTGTAGCGCTGCTTTCTTC 59.906 55.000 25.90 8.69 40.44 2.87
225 228 4.899239 CCCACGGCATCCTCTCGC 62.899 72.222 0.00 0.00 0.00 5.03
230 233 3.410628 TGCATCCCACGGCATCCT 61.411 61.111 0.00 0.00 34.58 3.24
236 239 0.819259 CCTACCAATGCATCCCACGG 60.819 60.000 0.00 0.00 0.00 4.94
240 243 1.477558 CCTGTCCTACCAATGCATCCC 60.478 57.143 0.00 0.00 0.00 3.85
241 244 1.212935 ACCTGTCCTACCAATGCATCC 59.787 52.381 0.00 0.00 0.00 3.51
254 257 4.101448 ATCTGCCGCCACCTGTCC 62.101 66.667 0.00 0.00 0.00 4.02
255 258 2.512515 GATCTGCCGCCACCTGTC 60.513 66.667 0.00 0.00 0.00 3.51
256 259 4.457496 CGATCTGCCGCCACCTGT 62.457 66.667 0.00 0.00 0.00 4.00
259 262 4.241555 ATCCGATCTGCCGCCACC 62.242 66.667 0.00 0.00 0.00 4.61
260 263 2.663188 GATCCGATCTGCCGCCAC 60.663 66.667 0.75 0.00 0.00 5.01
261 264 4.284860 CGATCCGATCTGCCGCCA 62.285 66.667 6.81 0.00 0.00 5.69
264 267 1.595993 ATACCCGATCCGATCTGCCG 61.596 60.000 6.81 0.00 0.00 5.69
265 268 0.108615 CATACCCGATCCGATCTGCC 60.109 60.000 6.81 0.00 0.00 4.85
266 269 0.737715 GCATACCCGATCCGATCTGC 60.738 60.000 6.81 5.47 0.00 4.26
267 270 0.603065 TGCATACCCGATCCGATCTG 59.397 55.000 6.81 0.00 0.00 2.90
268 271 0.891373 CTGCATACCCGATCCGATCT 59.109 55.000 6.81 0.00 0.00 2.75
269 272 0.108615 CCTGCATACCCGATCCGATC 60.109 60.000 0.00 0.00 0.00 3.69
270 273 1.544825 CCCTGCATACCCGATCCGAT 61.545 60.000 0.00 0.00 0.00 4.18
271 274 2.207229 CCCTGCATACCCGATCCGA 61.207 63.158 0.00 0.00 0.00 4.55
272 275 2.343758 CCCTGCATACCCGATCCG 59.656 66.667 0.00 0.00 0.00 4.18
273 276 1.831652 CTCCCCTGCATACCCGATCC 61.832 65.000 0.00 0.00 0.00 3.36
274 277 1.674057 CTCCCCTGCATACCCGATC 59.326 63.158 0.00 0.00 0.00 3.69
275 278 1.843376 CCTCCCCTGCATACCCGAT 60.843 63.158 0.00 0.00 0.00 4.18
276 279 2.445845 CCTCCCCTGCATACCCGA 60.446 66.667 0.00 0.00 0.00 5.14
277 280 2.445845 TCCTCCCCTGCATACCCG 60.446 66.667 0.00 0.00 0.00 5.28
278 281 0.988678 AACTCCTCCCCTGCATACCC 60.989 60.000 0.00 0.00 0.00 3.69
279 282 0.919710 AAACTCCTCCCCTGCATACC 59.080 55.000 0.00 0.00 0.00 2.73
280 283 2.369394 CAAAACTCCTCCCCTGCATAC 58.631 52.381 0.00 0.00 0.00 2.39
281 284 1.340991 GCAAAACTCCTCCCCTGCATA 60.341 52.381 0.00 0.00 0.00 3.14
282 285 0.613012 GCAAAACTCCTCCCCTGCAT 60.613 55.000 0.00 0.00 0.00 3.96
283 286 1.228552 GCAAAACTCCTCCCCTGCA 60.229 57.895 0.00 0.00 0.00 4.41
284 287 0.827507 TTGCAAAACTCCTCCCCTGC 60.828 55.000 0.00 0.00 0.00 4.85
285 288 0.961753 GTTGCAAAACTCCTCCCCTG 59.038 55.000 0.00 0.00 0.00 4.45
286 289 0.178961 GGTTGCAAAACTCCTCCCCT 60.179 55.000 0.00 0.00 0.00 4.79
287 290 1.524008 CGGTTGCAAAACTCCTCCCC 61.524 60.000 0.00 0.00 0.00 4.81
288 291 1.524008 CCGGTTGCAAAACTCCTCCC 61.524 60.000 0.00 0.00 0.00 4.30
289 292 0.822121 ACCGGTTGCAAAACTCCTCC 60.822 55.000 0.00 0.00 0.00 4.30
290 293 0.591659 GACCGGTTGCAAAACTCCTC 59.408 55.000 9.42 0.00 0.00 3.71
291 294 0.182775 AGACCGGTTGCAAAACTCCT 59.817 50.000 9.42 0.00 0.00 3.69
292 295 0.591659 GAGACCGGTTGCAAAACTCC 59.408 55.000 9.42 0.00 0.00 3.85
293 296 0.591659 GGAGACCGGTTGCAAAACTC 59.408 55.000 9.42 8.74 0.00 3.01
294 297 0.106918 TGGAGACCGGTTGCAAAACT 60.107 50.000 9.42 0.00 0.00 2.66
295 298 0.030235 GTGGAGACCGGTTGCAAAAC 59.970 55.000 9.42 0.00 0.00 2.43
296 299 1.104577 GGTGGAGACCGGTTGCAAAA 61.105 55.000 9.42 0.00 30.61 2.44
297 300 1.527380 GGTGGAGACCGGTTGCAAA 60.527 57.895 9.42 0.00 30.61 3.68
298 301 2.112297 GGTGGAGACCGGTTGCAA 59.888 61.111 9.42 0.00 30.61 4.08
299 302 3.948719 GGGTGGAGACCGGTTGCA 61.949 66.667 9.42 7.77 44.23 4.08
300 303 2.764637 ATTGGGTGGAGACCGGTTGC 62.765 60.000 9.42 3.38 44.23 4.17
301 304 0.251165 AATTGGGTGGAGACCGGTTG 60.251 55.000 9.42 0.00 44.23 3.77
302 305 0.481128 AAATTGGGTGGAGACCGGTT 59.519 50.000 9.42 0.00 44.23 4.44
303 306 0.481128 AAAATTGGGTGGAGACCGGT 59.519 50.000 6.92 6.92 44.23 5.28
304 307 1.627864 AAAAATTGGGTGGAGACCGG 58.372 50.000 0.00 0.00 44.23 5.28
322 325 3.779846 TTCCAGTGGTGACGCGGAAAA 62.780 52.381 12.47 0.00 44.48 2.29
323 326 2.313051 TTCCAGTGGTGACGCGGAAA 62.313 55.000 12.47 0.00 44.48 3.13
352 355 1.968540 GTGTGCTCTTGGTGGAGGC 60.969 63.158 0.00 0.00 34.21 4.70
354 357 1.669115 CGGTGTGCTCTTGGTGGAG 60.669 63.158 0.00 0.00 36.50 3.86
451 454 2.499685 GAACTAGGCGGCGATGGT 59.500 61.111 12.98 2.89 0.00 3.55
452 455 2.280186 GGAACTAGGCGGCGATGG 60.280 66.667 12.98 2.11 0.00 3.51
454 457 1.115930 ATCTGGAACTAGGCGGCGAT 61.116 55.000 12.98 0.00 0.00 4.58
457 460 0.178068 TCAATCTGGAACTAGGCGGC 59.822 55.000 0.00 0.00 0.00 6.53
538 541 1.676968 GGTTTGGGCACATTTCCCC 59.323 57.895 0.00 0.00 43.24 4.81
602 605 2.157989 AGGGGAATAGGGAGGTATGGAC 60.158 54.545 0.00 0.00 0.00 4.02
633 636 2.674754 GGACTTGGCCGGATCCAA 59.325 61.111 13.41 9.84 43.36 3.53
648 651 2.283529 GCTCTCTTCACCCACCGGA 61.284 63.158 9.46 0.00 0.00 5.14
652 655 0.952984 GTGCTGCTCTCTTCACCCAC 60.953 60.000 0.00 0.00 0.00 4.61
659 662 1.808799 CGATGCGTGCTGCTCTCTT 60.809 57.895 0.00 0.00 46.63 2.85
732 735 2.104967 CACCCCGATGAGTGTAGGTTA 58.895 52.381 0.00 0.00 0.00 2.85
864 923 1.529244 GGTGAAGGTGGCAGCAAGT 60.529 57.895 20.04 3.17 34.13 3.16
894 953 8.589335 TTTTTGACATCTTCTGTAGTAGACAC 57.411 34.615 0.00 0.00 38.54 3.67
1448 2281 0.676782 GATTTCCTGTCCGTGGGTGG 60.677 60.000 0.00 0.00 0.00 4.61
1464 2315 2.273449 CAAGGGGGCAGCTCGATT 59.727 61.111 0.00 0.00 0.00 3.34
1557 2408 4.357947 GTCAGGACGGTGAGCGCA 62.358 66.667 11.47 0.00 0.00 6.09
1701 2552 0.691078 ATTCTAGGCGCCTGAGGGAA 60.691 55.000 38.98 30.90 33.58 3.97
1704 2555 0.598680 CGAATTCTAGGCGCCTGAGG 60.599 60.000 38.98 26.14 0.00 3.86
2028 2879 1.509644 CGCCTGAGCAAGAGCAACAA 61.510 55.000 0.00 0.00 45.49 2.83
2030 2881 1.023513 ATCGCCTGAGCAAGAGCAAC 61.024 55.000 0.00 0.00 45.49 4.17
2031 2882 0.742281 GATCGCCTGAGCAAGAGCAA 60.742 55.000 0.00 0.00 45.49 3.91
2032 2883 1.153489 GATCGCCTGAGCAAGAGCA 60.153 57.895 0.00 0.00 45.49 4.26
2033 2884 1.886777 GGATCGCCTGAGCAAGAGC 60.887 63.158 0.00 0.00 39.83 4.09
2034 2885 0.106335 ATGGATCGCCTGAGCAAGAG 59.894 55.000 0.00 0.00 39.83 2.85
2035 2886 0.179065 CATGGATCGCCTGAGCAAGA 60.179 55.000 0.00 0.00 39.83 3.02
2036 2887 0.463295 ACATGGATCGCCTGAGCAAG 60.463 55.000 0.00 0.00 39.83 4.01
2044 2895 2.293399 GGACCAATTAACATGGATCGCC 59.707 50.000 14.45 7.40 40.56 5.54
2069 2923 7.481275 AGCACAAAAACGAATCATCAAAATT 57.519 28.000 0.00 0.00 0.00 1.82
2104 2958 4.632105 ATCCCTCCATTCCCTGAAAAAT 57.368 40.909 0.00 0.00 0.00 1.82
2255 3154 1.376553 GTCTCCAGCACAAGCCTCC 60.377 63.158 0.00 0.00 43.56 4.30
2258 3157 1.339055 TGTATGTCTCCAGCACAAGCC 60.339 52.381 0.00 0.00 43.56 4.35
2300 3199 7.169158 TGAATGAACTGATAAAATGAACCCC 57.831 36.000 0.00 0.00 0.00 4.95
2312 3211 6.463614 GGGCTACAGTCTATGAATGAACTGAT 60.464 42.308 8.24 0.00 31.74 2.90
2325 3224 5.361571 TCGTGAATATTTGGGCTACAGTCTA 59.638 40.000 0.00 0.00 0.00 2.59
2359 3258 8.255905 GCTACTACTCCTAAACATGTTTCCTTA 58.744 37.037 26.46 9.09 34.23 2.69
2384 3283 2.071778 TGGGCCTCCAAATCATAAGC 57.928 50.000 4.53 0.00 40.73 3.09
2398 3297 2.430332 TCCGATGATTTTTCAATGGGCC 59.570 45.455 0.00 0.00 0.00 5.80
2421 3621 4.264253 CCTTGAACATCAGCCACATAAGA 58.736 43.478 0.00 0.00 0.00 2.10
2422 3622 3.379372 CCCTTGAACATCAGCCACATAAG 59.621 47.826 0.00 0.00 0.00 1.73
2425 3625 1.617804 CCCCTTGAACATCAGCCACAT 60.618 52.381 0.00 0.00 0.00 3.21
2441 3645 3.023735 GGAATGCCACCCTCCCCT 61.024 66.667 0.00 0.00 0.00 4.79
2460 3735 1.070134 CTCTGAAGAAACCGTCACCCA 59.930 52.381 0.00 0.00 0.00 4.51
2461 3736 1.797025 CTCTGAAGAAACCGTCACCC 58.203 55.000 0.00 0.00 0.00 4.61
2478 3784 1.070445 CCATCCTCCCATGTCGCTC 59.930 63.158 0.00 0.00 0.00 5.03
2482 3788 1.524621 CGCACCATCCTCCCATGTC 60.525 63.158 0.00 0.00 0.00 3.06
2484 3790 1.524621 GTCGCACCATCCTCCCATG 60.525 63.158 0.00 0.00 0.00 3.66
2496 3802 3.503363 GATGGCAGCTGGTCGCAC 61.503 66.667 17.12 0.00 42.61 5.34
2497 3803 4.783621 GGATGGCAGCTGGTCGCA 62.784 66.667 17.12 0.75 42.61 5.10
2499 3805 4.100084 TGGGATGGCAGCTGGTCG 62.100 66.667 17.12 0.00 0.00 4.79
2500 3806 2.439156 GTGGGATGGCAGCTGGTC 60.439 66.667 17.12 0.00 0.00 4.02
2501 3807 3.259314 TGTGGGATGGCAGCTGGT 61.259 61.111 17.12 0.00 0.00 4.00
2502 3808 2.753043 GTGTGGGATGGCAGCTGG 60.753 66.667 17.12 0.00 0.00 4.85
2503 3809 2.034532 TGTGTGGGATGGCAGCTG 59.965 61.111 10.11 10.11 0.00 4.24
2504 3810 2.034687 GTGTGTGGGATGGCAGCT 59.965 61.111 1.50 0.00 0.00 4.24
2506 3812 3.434319 GCGTGTGTGGGATGGCAG 61.434 66.667 0.00 0.00 0.00 4.85
2509 3815 4.697756 ACGGCGTGTGTGGGATGG 62.698 66.667 13.76 0.00 0.00 3.51
2510 3816 3.118454 GACGGCGTGTGTGGGATG 61.118 66.667 21.19 0.00 0.00 3.51
2511 3817 4.388499 GGACGGCGTGTGTGGGAT 62.388 66.667 21.19 0.00 0.00 3.85
2515 3821 2.543687 CTAGGAGGACGGCGTGTGTG 62.544 65.000 21.19 0.00 0.00 3.82
2516 3822 2.282674 TAGGAGGACGGCGTGTGT 60.283 61.111 21.19 0.00 0.00 3.72
2518 3824 0.896940 TTTCTAGGAGGACGGCGTGT 60.897 55.000 21.19 3.59 0.00 4.49
2519 3825 0.245539 TTTTCTAGGAGGACGGCGTG 59.754 55.000 21.19 0.00 0.00 5.34
2520 3826 1.134788 CATTTTCTAGGAGGACGGCGT 60.135 52.381 14.65 14.65 0.00 5.68
2521 3827 1.134788 ACATTTTCTAGGAGGACGGCG 60.135 52.381 4.80 4.80 0.00 6.46
2522 3828 2.093658 TGACATTTTCTAGGAGGACGGC 60.094 50.000 0.00 0.00 0.00 5.68
2523 3829 3.887621 TGACATTTTCTAGGAGGACGG 57.112 47.619 0.00 0.00 0.00 4.79
2524 3830 4.759782 ACATGACATTTTCTAGGAGGACG 58.240 43.478 0.00 0.00 0.00 4.79
2525 3831 5.163713 GCAACATGACATTTTCTAGGAGGAC 60.164 44.000 0.00 0.00 0.00 3.85
2526 3832 4.943705 GCAACATGACATTTTCTAGGAGGA 59.056 41.667 0.00 0.00 0.00 3.71
2527 3833 4.946157 AGCAACATGACATTTTCTAGGAGG 59.054 41.667 0.00 0.00 0.00 4.30
2528 3834 5.879223 AGAGCAACATGACATTTTCTAGGAG 59.121 40.000 0.00 0.00 0.00 3.69
2529 3835 5.645067 CAGAGCAACATGACATTTTCTAGGA 59.355 40.000 0.00 0.00 0.00 2.94
2530 3836 5.413833 ACAGAGCAACATGACATTTTCTAGG 59.586 40.000 0.00 0.00 0.00 3.02
2531 3837 6.492007 ACAGAGCAACATGACATTTTCTAG 57.508 37.500 0.00 0.00 0.00 2.43
2532 3838 7.386059 TCTACAGAGCAACATGACATTTTCTA 58.614 34.615 0.00 0.00 0.00 2.10
2545 3851 1.082690 GGCAGCTTCTACAGAGCAAC 58.917 55.000 0.00 0.00 0.00 4.17
2553 3859 0.253044 TGTGGGATGGCAGCTTCTAC 59.747 55.000 1.50 0.00 0.00 2.59
2554 3860 0.253044 GTGTGGGATGGCAGCTTCTA 59.747 55.000 1.50 0.00 0.00 2.10
2559 3865 1.660560 GATGTGTGTGGGATGGCAGC 61.661 60.000 0.00 0.00 0.00 5.25
2566 3872 1.539388 GCATTTTCGATGTGTGTGGGA 59.461 47.619 0.00 0.00 0.00 4.37
2568 3874 1.269174 TGGCATTTTCGATGTGTGTGG 59.731 47.619 0.00 0.00 0.00 4.17
2580 3886 4.009675 TCTTTAGAGCGACATGGCATTTT 58.990 39.130 0.00 0.00 34.64 1.82
2581 3887 3.609853 TCTTTAGAGCGACATGGCATTT 58.390 40.909 0.00 0.00 34.64 2.32
2582 3888 3.266510 TCTTTAGAGCGACATGGCATT 57.733 42.857 0.00 0.00 34.64 3.56
2583 3889 2.988010 TCTTTAGAGCGACATGGCAT 57.012 45.000 0.00 0.00 34.64 4.40
2596 3902 7.110216 CGAACGTTTTGATGACAGTTTCTTTAG 59.890 37.037 0.46 0.00 0.00 1.85
2598 3904 5.737290 CGAACGTTTTGATGACAGTTTCTTT 59.263 36.000 0.46 0.00 0.00 2.52
2613 3919 0.872388 CCTTAGCTGGCGAACGTTTT 59.128 50.000 0.46 0.00 0.00 2.43
2616 4030 2.264794 CCCTTAGCTGGCGAACGT 59.735 61.111 0.00 0.00 0.00 3.99
2625 4039 2.000048 TGATTTTGGACCCCCTTAGCT 59.000 47.619 0.00 0.00 0.00 3.32
2646 4060 9.056005 ACATAGTGCATTAATTATGGTACTGTG 57.944 33.333 19.62 19.62 34.66 3.66
2676 4090 5.278561 ATGACTACATTAGGCGAAGAGCTAC 60.279 44.000 0.00 0.00 38.68 3.58
2872 4287 3.960571 AGAAATTCCACCTGGTCATCTG 58.039 45.455 0.00 0.00 36.34 2.90
2891 4306 5.475220 GCATCTGGATACTAGCAACTCTAGA 59.525 44.000 6.02 0.00 46.12 2.43
2898 4313 3.742327 GCACTGCATCTGGATACTAGCAA 60.742 47.826 0.00 0.00 37.61 3.91
3062 4477 4.382793 GGATCCACTTCTTACAGTACCACC 60.383 50.000 6.95 0.00 0.00 4.61
3094 4512 7.548075 CGACCACTAACAAACCAATAGTTAGAT 59.452 37.037 15.90 3.93 44.56 1.98
3161 4587 2.673368 CGAGATTTTAGAGCACACACCC 59.327 50.000 0.00 0.00 0.00 4.61
3191 4617 2.894126 AGAGGATATCAACCGTGCTAGG 59.106 50.000 4.83 0.00 37.30 3.02
3211 4637 0.950555 TGCTAGGAAACGTGCTGCAG 60.951 55.000 10.11 10.11 35.14 4.41
3226 4652 3.449227 CCACGAGGCGGTCTGCTA 61.449 66.667 3.10 0.00 45.43 3.49
3238 4664 1.578206 CGAGAGTGCAGAGACCACGA 61.578 60.000 0.00 0.00 38.22 4.35
3283 4709 3.695830 AAACCTCTATCGGACAAAGCA 57.304 42.857 0.00 0.00 0.00 3.91
3303 4729 8.477419 AATCCTGGAAAAATGTGAGTTCTTAA 57.523 30.769 0.00 0.00 0.00 1.85
3339 4765 1.279271 CTAACCTTGTCAGGGGAGTGG 59.721 57.143 5.89 0.00 46.01 4.00
3403 4829 1.078848 CCTTGAGAACCCAGCTCCG 60.079 63.158 0.00 0.00 0.00 4.63
3430 4856 4.104383 GGAAATTATCCCAGGAGCATCA 57.896 45.455 0.00 0.00 43.00 3.07
3456 4882 1.534729 CGCCAGAAGCTTACCCTTTT 58.465 50.000 0.00 0.00 40.39 2.27
3475 4901 0.523072 TCGATTTCTGCCTGCAAAGC 59.477 50.000 1.42 1.42 0.00 3.51
3478 4904 0.881118 GGTTCGATTTCTGCCTGCAA 59.119 50.000 0.00 0.00 0.00 4.08
3484 4910 1.197721 CACCAGTGGTTCGATTTCTGC 59.802 52.381 13.62 0.00 31.02 4.26
3520 4946 1.686110 CGGGGGCAGAACTAGAGGT 60.686 63.158 0.00 0.00 0.00 3.85
3635 5061 3.492383 TGTTGTTGTTGTTGTTGTTGCTG 59.508 39.130 0.00 0.00 0.00 4.41
3636 5062 3.722147 TGTTGTTGTTGTTGTTGTTGCT 58.278 36.364 0.00 0.00 0.00 3.91
3637 5063 4.207599 GTTGTTGTTGTTGTTGTTGTTGC 58.792 39.130 0.00 0.00 0.00 4.17
3638 5064 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
3639 5065 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
3640 5066 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
3641 5067 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
3642 5068 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
3643 5069 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
3644 5070 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
3645 5071 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
3646 5072 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
3647 5073 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
3648 5074 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
3649 5075 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
3650 5076 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
3651 5077 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
3652 5078 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
3653 5079 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
3654 5080 4.025313 GCTGTTGTTGTTGTTGTTGTTGTT 60.025 37.500 0.00 0.00 0.00 2.83
3656 5082 3.421569 CGCTGTTGTTGTTGTTGTTGTTG 60.422 43.478 0.00 0.00 0.00 3.33
3657 5083 2.728839 CGCTGTTGTTGTTGTTGTTGTT 59.271 40.909 0.00 0.00 0.00 2.83
3658 5084 2.030717 TCGCTGTTGTTGTTGTTGTTGT 60.031 40.909 0.00 0.00 0.00 3.32
3659 5085 2.590073 TCGCTGTTGTTGTTGTTGTTG 58.410 42.857 0.00 0.00 0.00 3.33
3661 5087 4.829064 ATATCGCTGTTGTTGTTGTTGT 57.171 36.364 0.00 0.00 0.00 3.32
3662 5088 5.927030 AGTATATCGCTGTTGTTGTTGTTG 58.073 37.500 0.00 0.00 0.00 3.33
3663 5089 5.121768 GGAGTATATCGCTGTTGTTGTTGTT 59.878 40.000 0.00 0.00 0.00 2.83
3680 5106 7.135591 TGTGATTGTCAATCCATGGAGTATA 57.864 36.000 21.33 6.45 37.09 1.47
3685 5111 4.305539 ACTGTGATTGTCAATCCATGGA 57.694 40.909 18.88 18.88 37.09 3.41
3936 5367 5.689819 ACAAAGTCTTGAATTACGATGTGC 58.310 37.500 0.00 0.00 36.33 4.57
3966 5397 4.653868 TGCAAAACGACCCTTTATAGGAA 58.346 39.130 0.00 0.00 45.05 3.36
3968 5399 5.576447 AATGCAAAACGACCCTTTATAGG 57.424 39.130 0.00 0.00 41.60 2.57
3969 5400 6.183360 GCAAAATGCAAAACGACCCTTTATAG 60.183 38.462 0.00 0.00 44.26 1.31
3971 5402 4.450757 GCAAAATGCAAAACGACCCTTTAT 59.549 37.500 0.00 0.00 44.26 1.40
3987 5425 7.014702 GGTCCAAAATAATTTCGTGCAAAATG 58.985 34.615 0.00 0.00 0.00 2.32
3988 5426 6.708054 TGGTCCAAAATAATTTCGTGCAAAAT 59.292 30.769 0.00 0.00 0.00 1.82
3993 5431 5.288472 GTGATGGTCCAAAATAATTTCGTGC 59.712 40.000 0.00 0.00 0.00 5.34
3997 5435 8.306761 AGTGAAGTGATGGTCCAAAATAATTTC 58.693 33.333 0.00 0.00 0.00 2.17
4039 5477 8.668510 TCTATGTTTCTTGCTTTCCATCTATC 57.331 34.615 0.00 0.00 0.00 2.08
4040 5478 8.489489 TCTCTATGTTTCTTGCTTTCCATCTAT 58.511 33.333 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.